@article {pmid38637082, year = {2024}, author = {Sonets, IV and Solovyev, MA and Ivanova, VA and Vasiluev, PA and Kachalkin, AV and Ochkalova, SD and Korobeynikov, AI and Razin, SV and Ulianov, SV and Tyakht, AV}, title = {Hi-C metagenomics facilitate comparative genome analysis of bacteria and yeast from spontaneous beer and cider.}, journal = {Food microbiology}, volume = {121}, number = {}, pages = {104520}, doi = {10.1016/j.fm.2024.104520}, pmid = {38637082}, issn = {1095-9998}, abstract = {Sequence-based analysis of fermented foods and beverages' microbiomes offers insights into their impact on taste and consumer health. High-throughput metagenomics provide detailed taxonomic and functional community profiling, but bacterial and yeast genome reconstruction and mobile genetic elements tracking are to be improved. We established a pipeline for exploring fermented foods microbiomes using metagenomics coupled with chromosome conformation capture (Hi-C metagenomics). The approach was applied to analyze a collection of spontaneously fermented beers and ciders (n = 12). The Hi-C reads were used to reconstruct the metagenome-assembled genomes (MAGs) of bacteria and yeasts facilitating subsequent comparative genomic analysis, assembly scaffolding and exploration of "plasmid-bacteria" links. For a subset of beverages, yeasts were isolated and characterized phenotypically. The reconstructed Hi-C MAGs primarily belonged to the Lactobacillaceae family in beers, along with Acetobacteraceae and Enterobacteriaceae in ciders, exhibiting improved quality compared to conventional metagenomic MAGs. Comparative genomic analysis of Lactobacillaceae Hi-C MAGs revealed clustering by niche and suggested genetic determinants of survival and probiotic potential. For Pediococcus damnosus, Hi-C-based networks of contigs enabled linking bacteria with plasmids. Analyzing phylogeny and accessory genes in the context of known reference genomes offered insights into the niche specialization of beer lactobacilli. The subspecies-level diversity of cider Tatumella spp. was disentangled using a Hi-C-based graph. We obtained highly complete yeast Hi-C MAGs primarily represented by Brettanomyces and Saccharomyces, with Hi-C-facilitated chromosome-level genome assembly for the former. Utilizing Hi-C metagenomics to unravel the genomic content of individual species can provide a deeper understanding of the ecological interactions within the food microbiome, aid in bioprospecting beneficial microorganisms, improving quality control and improving innovative fermented products.}, } @article {pmid38637066, year = {2024}, author = {Lee, AW and Ng, IC and Wong, EY and Wong, IT and Sze, RP and Chan, KY and So, TY and Zhang, Z and Ka-Yee Fung, S and Choi-Ying Wong, S and Tam, WY and Lao, HY and Lee, LK and Leung, JS and Chan, CT and Ng, TT and Zhang, J and Chow, FW and Leung, PH and Siu, GK}, title = {Comprehensive identification of pathogenic microbes and antimicrobial resistance genes in food products using nanopore sequencing-based metagenomics.}, journal = {Food microbiology}, volume = {121}, number = {}, pages = {104493}, doi = {10.1016/j.fm.2024.104493}, pmid = {38637066}, issn = {1095-9998}, abstract = {Foodborne pathogens, particularly antimicrobial-resistant (AMR) bacteria, remain a significant threat to global health. Given the limitations of conventional culture-based approaches, which are limited in scope and time-consuming, metagenomic sequencing of food products emerges as a promising solution. This method provides a fast and comprehensive way to detect the presence of pathogenic microbes and antimicrobial resistance genes (ARGs). Notably, nanopore long-read sequencing provides more accurate bacterial taxonomic classification in comparison to short-read sequencing. Here, we revealed the impact of food types and attributes (origin, retail place, and food processing methods) on microbial communities and the AMR profile using nanopore metagenomic sequencing. We analyzed a total of 260 food products, including raw meat, sashimi, and ready-to-eat (RTE) vegetables. Clostridium botulinum, Acinetobacter baumannii, and Vibrio parahaemolyticus were identified as the top three foodborne pathogens in raw meat and sashimi. Importantly, even with low pathogen abundance, higher percentages of samples containing carbapenem and cephalosporin resistance genes were identified in chicken and RTE vegetables, respectively. In parallel, our results demonstrated that fresh, peeled, and minced foods exhibited higher levels of pathogenic bacteria. In conclusion, this comprehensive study offers invaluable data that can contribute to food safety assessments and serve as a basis for quality indicators.}, } @article {pmid38636877, year = {2024}, author = {Lv, L and Chen, J and Wei, Z and Hao, P and Wang, P and Liu, X and Gao, W and Sun, L and Liang, J and Ren, Z and Zhang, G and Li, W}, title = {A new strategy for accelerating recovery of anaerobic granular sludge after low-temperature shock: In situ regulation of quorum sensing microorganisms embedded in polyvinyl alcohol sodium alginate.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {130709}, doi = {10.1016/j.biortech.2024.130709}, pmid = {38636877}, issn = {1873-2976}, abstract = {Low-temperature could inhibit the performance of anaerobic granular sludge (AnGS). Quorum sensing (QS), as a communication mode between microorganisms, can effectively regulate AnGS. In this study, a kind of embedded particles (PVA/SA@Serratia) based on signal molecule secreting bacteria was prepared by microbial immobilization technology based on polyvinyl alcohol and sodium alginate to accelerate the recovery of AnGS system after low temperature. Low-temperature shock experiment verified the positive effect of PVA/SA@Serratia on restoring the COD removal rate and methanogenesis capacity of AnGS. Further analysis by metagenomics analysis showed that PVA/SA@Serratia stimulated higher QS activity and promoted the secretion of extracellular polymeric substance (EPS) in AnGS. The rapid construction of EPS protective layer effectively accelerated the establishment of a robust microbial community structure. PVA/SA@Serratia also enhanced multiple methanogenic pathways, including direct interspecies electron transfer. In conclusion, this study demonstrated that PVA/SA@Serratia could effectively strengthen AnGS after low-temperature shock.}, } @article {pmid38636860, year = {2024}, author = {Zhou, ZZ and Zhu, J and Yin, Y and Ding, LJ}, title = {Seasonal variations of profiles of antibiotic resistance genes and virulence factor genes in household dust from Beijing, China revealed by the metagenomics.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {172542}, doi = {10.1016/j.scitotenv.2024.172542}, pmid = {38636860}, issn = {1879-1026}, abstract = {Household-related microbiome is closely related with human health. However, the knowledge about profiles of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs) which are carried by microbes inside homes and their temporal dynamics are rather limited. Here we monitored the seasonal changes of bacterial community (especially pathogenic bacteria), ARGs, and VFGs in household dust samples during two years. Based on metagenomic sequencing, the dust-related bacterial pathogenic community, ARGs, and VFGs all harbored the lowest richness in spring among four seasons. Their structure (except that of VFGs) also exhibited remarkable differences among the seasons. The structural variations of ARGs and VFGs were almost explained by mobile genetic elements (MGEs), bacterial pathogens, and particulate matter-related factors, with MGEs explaining the most. Moreover, the total normalized abundance of ARGs or VFGs showed no significant change across the seasons. Results of metagenomic binning and microbial network both showed that several pathogenic taxa (e.g., Ralstonia pickettii) were strongly linked with numerous ARGs (mainly resistant to multidrug) and VFGs (mainly encoding motility) simultaneously. Overall, these findings underline the significance of MGEs in structuring ARGs and VFGs inside homes along with seasonal variations, suggesting that household dust is a neglected reservoir for ARGs and VFGs.}, } @article {pmid38636642, year = {2024}, author = {Wen, X and Cui, L and Lin, H and Zhu, W and Shao, Z and Wang, Y}, title = {Comparison of nitrification performance in SBR and SBBR with response to NaCl salinity shock: microbial structure and functional genes.}, journal = {Environmental research}, volume = {}, number = {}, pages = {118917}, doi = {10.1016/j.envres.2024.118917}, pmid = {38636642}, issn = {1096-0953}, abstract = {Ammonia removal by nitrifiers at the extremely high salinity poses a great challenge for saline wastewater treatment. Sequencing batch reactor (SBR) was conducted with a stepwise increase of salinity from 10 to 40 g-NaCl·L[-1], while sequencing batch biofilm reactor (SBBR) with one-step salinity enhancement, their nitrification performance, microbial structure and interaction were evaluated. Both SBR and SBBR can achieve high-efficiency nitrification (98% ammonia removal) at 40 g-NaCl·L[-1]. However, SBBR showed more stable nitrification performance than SBR at 40 g-NaCl·L[-1] after a shorter adaptation period of 4-15 d compared to previous studies. High-throughput sequencing and metagenomic analysis demonstrated that the abundance and capability of conventional ammonia-oxidizing bacteria (Nitrosomonas) were suppressed in SBBR relative to SBR. Gelidibacter, Anaerolineales were the predominant genus in SBBR, which were not found in SBR. NorB and nosZ responsible for reducing NO to N2O and reducing N2O to N2 respectively had s strong synergistic effect in SBBR. This study will provide a valuable reference for the startup of nitrification process within a short period of time under the extremely high NaCl salinity.}, } @article {pmid38636618, year = {2024}, author = {Ergunay, K and Bourke, BP and Reinbold-Wasson, DD and Caicedo-Quiroga, L and Vaydayko, N and Kirkitadze, G and Chunashvili, T and Tucker, CL and Linton, YM}, title = {Novel clades of tick-borne pathogenic nairoviruses in Europe.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105593}, doi = {10.1016/j.meegid.2024.105593}, pmid = {38636618}, issn = {1567-7257}, abstract = {Members of the Orthonairovirus genus (family Nairoviridae) include many tick-borne viruses of significant human and animal health impact, with several recently-documented pathogenic viruses lacking sufficient epidemiological information. We screened 215 adult ticks of seven species collected in Bulgaria, Georgia, Latvia and Poland for orthonairoviruses, followed by nanopore sequencing (NS) for genome characterization. Initial generic amplification revealed Sulina virus (SULV, Orthonairovirus sulinaense), for which an updated amplification assay was used, revealing an overall prevalence of 2.7% in Ixodes ricinus ticks from Latvia. Three complete and additional partial SULV genomes were generated, that consistently formed a separate, distinct clade with further intragroup divergence in the maximum likelihood analyses. Comparisons with previously described viruses from Romania exhibited similar genome topologies, albeit with divergent motifs and cleavage sites on the glycoprotein precursor. Preliminary evidence of recombination involving the S segment was documented, in addition to variations in predicted viral glycoproteins. Generic screening further identified Tacheng tick virus 1 (TCTV1, Orthonairovirus tachengense), with documented human infections, in Dermacentor reticulatus ticks from Poland, with a prevalence of 0.9%. Subsequent NS and assembly provided the first complete TCTV1 genome outside of China, where it was originally described. Phylogenetic analysis of virus genome segments revealed TCTV1-Poland as a discrete taxon within the TCTV1 cluster in the Orthonairovirus genus, representing a geographically segregated clade. Comparable genome topology with TCTV1 from China was observed, aside from minor variations in the M segment. Similar to SULV, TCTV1 exhibited several mismatches on previously described screening primer binding sites, likely to prevent amplification. These findings indicate presence of novel TCTV1 and SULV clades in Eastern Europe, confirming the expansion of orthonairoviruses with pathogenic potential.}, } @article {pmid38636385, year = {2024}, author = {Xu, L and Mao, T and Xia, M and Wu, W and Chen, J and Jiang, C and Zeng, T and Tian, Y and Lu, L and Cai, Z}, title = {New evidence for gut-muscle axis: Lactic acid bacteria-induced gut microbiota regulates duck meat flavor.}, journal = {Food chemistry}, volume = {450}, number = {}, pages = {139354}, doi = {10.1016/j.foodchem.2024.139354}, pmid = {38636385}, issn = {1873-7072}, abstract = {The interaction between gut microbiota and muscles through the gut-muscle axis has received increasing attention. This study attempted to address existing research gaps by investigating the effects of gut microbiota on meat flavor. Specifically, lactic acid bacteria were administered to ducks, and the results of e-nose and e-tongue showed significantly enhanced meat flavor in the treatment group. Further analyses using GC-MS revealed an increase in 6 characteristic volatile flavor compounds, including pentanal, hexanal, heptanal, 1-octen-3-ol, 2,3-octanedione, and 2-pentylfuran. Linoleic acid was identified as the key fatty acid that influences meat flavor. Metagenomic and transcriptomic results further confirmed that cecal microbiota affects the duck meat flavor by regulating the metabolic pathways of fatty acids and amino acids, especially ACACB was related to fatty acid biosynthesis and ACAT2, ALDH1A1 with fatty acid degradation. This study sheds light on a novel approach to improving the flavor of animal-derived food.}, } @article {pmid38635882, year = {2024}, author = {Al Radi, ZMA and Prins, FM and Collij, V and Vich Vila, A and Festen, EAM and Dijkstra, G and Weersma, RK and Klaassen, MAY and Gacesa, R}, title = {Exploring the Predictive Value of Gut Microbiome Signatures for Therapy Intensification in Patients With Inflammatory Bowel Disease: A 10-Year Follow-up Study.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izae064}, pmid = {38635882}, issn = {1536-4844}, support = {//Netherlands Organization for Scientific Research/ ; MLDS D16-14//Dutch Digestive Foundation/ ; }, abstract = {BACKGROUND: Inflammatory bowel diseases (IBDs) pose a significant challenge due to their diverse, often debilitating, and unpredictable clinical manifestations. The absence of prognostic tools to anticipate the future complications that require therapy intensification presents a substantial burden to patient private life and health. We aimed to explore whether the gut microbiome is a potential biomarker for future therapy intensification in a cohort of 90 IBD patients.

METHODS: We conducted whole-genome metagenomics sequencing on fecal samples from these patients, allowing us to profile the taxonomic and functional composition of their gut microbiomes. Additionally, we conducted a retrospective analysis of patients' electronic records over a period of 10 years following the sample collection and classified patients into (1) those requiring and (2) not requiring therapy intensification. Therapy intensification included medication escalation, intestinal resections, or a loss of response to a biological treatment. We applied gut microbiome diversity analysis, dissimilarity assessment, differential abundance analysis, and random forest modeling to establish associations between baseline microbiome profiles and future therapy intensification.

RESULTS: We identified 12 microbial species (eg, Roseburia hominis and Dialister invisus) and 16 functional pathways (eg, biosynthesis of L-citrulline and L-threonine) with significant correlations to future therapy intensifications. Random forest models using microbial species and pathways achieved areas under the curve of 0.75 and 0.72 for predicting therapy intensification.

CONCLUSIONS: The gut microbiome is a potential biomarker for therapy intensification in IBD patients and personalized management strategies. Further research should validate our findings in other cohorts to enhance the generalizability of these results.}, } @article {pmid38635629, year = {2024}, author = {Wang, T and Weiss, A and You, L}, title = {A generic approach to infer community-level fitness of microbial genes.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {17}, pages = {e2318380121}, doi = {10.1073/pnas.2318380121}, pmid = {38635629}, issn = {1091-6490}, support = {R01AI125604//HHS | National Institutes of Health (NIH)/ ; R01GM098642//HHS | National Institutes of Health (NIH)/ ; R01EB031869//HHS | National Institutes of Health (NIH)/ ; MCB-1937259//National Science Foundation (NSF)/ ; }, abstract = {The gene content in a metagenomic pool defines the function potential of a microbial community. Natural selection, operating on the level of genomes or genes, shapes the evolution of community functions by enriching some genes while depriving the others. Despite the importance of microbiomes in the environment and health, a general metric to evaluate the community-wide fitness of microbial genes remains lacking. In this work, we adapt the classic neutral model of species and use it to predict how the abundances of different genes will be shaped by selection, regardless of at which level the selection acts. We establish a simple metric that quantitatively infers the average survival capability of each gene in a microbiome. We then experimentally validate the predictions using synthetic communities of barcoded Escherichia coli strains undergoing neutral assembly and competition. We further show that this approach can be applied to publicly available metagenomic datasets to gain insights into the environment-function interplay of natural microbiomes.}, } @article {pmid38635609, year = {2024}, author = {Xu, R and Zhang, J and Zheng, J and Wu, Q}, title = {Allergic bronchopulmonary mycosis due to Schizophyllum commune in a patient with chronic hepatitis B.}, journal = {Journal of infection in developing countries}, volume = {18}, number = {3}, pages = {488-494}, doi = {10.3855/jidc.18024}, pmid = {38635609}, issn = {1972-2680}, abstract = {INTRODUCTION: Schizophyllum commune (S. commune) is an opportunistic pathogenic fungus and can cause infection of the respiratory system in immunocompromised hosts. Allergic bronchopulmonary mycosis (ABPM) is the major disease caused by S. commune. However, identification of S. commune using routine mycological diagnostic methods is difficult. It is easy to make mistakes in diagnosis and treatment, resulting in deterioration of the disease. We report the first case of ABPM due to S. commune in a Chinese patient with chronic hepatitis B.

CASE PRESENTATION: The patient presented cough, sputum and dyspnea for six months. The pathogen was missed during routine laboratory workup. We performed bronchoscopy examination and bronchoalveolar lavage. S. commune was identified by metagenomic next-generation sequencing (mNGS) of bronchial alveolar lavage fluid (BALF). Hence, the patient was immediately treated with 200 mg voriconazole twice daily (intravenous infusion) and 20 mg prednisone once a day (oral therapy), along with oral entecavir for hepatitis B. There was no recurrence of infection after the medication was discontinued.

CONCLUSIONS: S. commune infection should be considered in the diagnosis of patients with refractory cough, sputum and dyspnea, especially in immunocompromised individuals. The mNGS technique is an effective supplementary technique for the diagnosis of S. commune infection, enabling precise clinical decision-making and appropriate treatment. Most patients have good prognosis with a combination of proper antifungal therapy and hormonal therapy.}, } @article {pmid38635587, year = {2024}, author = {Ohdera, AH and Mansbridge, M and Wang, M and Naydenkov, P and Kamel, B and Goentoro, L}, title = {The microbiome of a Pacific moon jellyfish Aurelia coerulea.}, journal = {PloS one}, volume = {19}, number = {4}, pages = {e0298002}, doi = {10.1371/journal.pone.0298002}, pmid = {38635587}, issn = {1932-6203}, abstract = {The impact of microbiome in animal physiology is well appreciated, but characterization of animal-microbe symbiosis in marine environments remains a growing need. This study characterizes the microbial communities associated with the moon jellyfish Aurelia coerulea, first isolated from the East Pacific Ocean and has since been utilized as an experimental system. We find that the microbiome of this Pacific Aurelia culture is dominated by two taxa, a Mollicutes and Rickettsiales. The microbiome is stable across life stages, although composition varies. Mining the host sequencing data, we assembled the bacterial metagenome-assembled genomes (MAGs). The bacterial MAGs are highly reduced, and predict a high metabolic dependence on the host. Analysis using multiple metrics suggest that both bacteria are likely new species. We therefore propose the names Ca. Mariplasma lunae (Mollicutes) and Ca. Marinirickettsia aquamalans (Rickettsiales). Finally, comparison with studies of Aurelia from other geographical populations suggests the association with Ca. Mariplasma lunae occurs in Aurelia from multiple geographical locations. The low-diversity microbiome of Aurelia provides a relatively simple system to study host-microbe interactions.}, } @article {pmid38635326, year = {2024}, author = {Wang, M and Rieber, L and van Baaren, J and Morgan, M and Merrett, S and McDowell, I and Bowen, T}, title = {Diverse Class 2 CRISPR Effectors as Active Nucleases with Expanded Targeting Capabilities.}, journal = {The CRISPR journal}, volume = {7}, number = {2}, pages = {120-130}, doi = {10.1089/crispr.2023.0058}, pmid = {38635326}, issn = {2573-1602}, abstract = {CRISPR-Cas systems have proven effective in a variety of applications due to their ease of use and relatively high editing efficiency. Yet, any individual CRISPR-Cas system has inherent limitations, necessitating a diversity of RNA-guided nucleases to suit applications with distinct needs. We searched through metagenomic sequences to identify RNA-guided nucleases and found enzymes from diverse CRISPR-Cas types and subtypes, the most promising of which we developed into gene-editing platforms. Based on prior annotations of the metagenomic sequences, we establish the likely taxa and sampling locations where Class 2 CRISPR-Cas systems active in eukaryotes may be found. The newly discovered systems show robust capabilities as gene editors and base editors.}, } @article {pmid38635321, year = {2024}, author = {Wang, M and Lkhagva, E and Kim, S and Zhai, C and Islam, MM and Kim, HJ and Hong, ST}, title = {The gut microbe pair of Oribacterium sp. GMB0313 and Ruminococcus sp. GMB0270 confers complete protection against SARS-CoV-2 infection by activating CD8+ T cell-mediated immunity.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2342497}, doi = {10.1080/19490976.2024.2342497}, pmid = {38635321}, issn = {1949-0984}, abstract = {Despite the potential protective role of the gut microbiome against COVID-19, specific microbes conferring resistance to COVID-19 have not yet been identified. In this work, we aimed to identify and validate gut microbes at the species level that provide protection against SARS-CoV-2 infection. To identify gut microbes conferring protection against COVID-19, we conducted a fecal microbiota transplantation (FMT) from an individual with no history of COVID-19 infection or immunization into a lethal COVID-19 hamster model. FMT from this COVID-19-resistant donor resulted in significant phenotypic changes related to COVID-19 sensitivity in the hamsters. Metagenomic analysis revealed distinct differences in the gut microbiome composition among the hamster groups, leading to the identification of two previously unknown bacterial species: Oribacterium sp. GMB0313 and Ruminococcus sp. GMB0270, both associated with COVID-19 resistance. Subsequently, we conducted a proof-of-concept confirmation animal experiment adhering to Koch's postulates. Oral administration of this gut microbe pair, Oribacterium sp. GMB0313 and Ruminococcus sp. GMB0270, to the hamsters provided complete protection against SARS-CoV-2 infection through the activation of CD8+ T cell mediated immunity. The prophylactic efficacy of the gut microbe pair against SARS-CoV-2 infection was comparable to, or even superior to, current mRNA vaccines. This strong prophylactic efficacy suggests that the gut microbe pair could be developed as a host-directed universal vaccine for all betacoronaviruses, including potential future emerging viruses.}, } @article {pmid38634770, year = {2024}, author = {Lee, I and Jo, JW and Woo, HJ and Suk, KT and Lee, SS and Kim, BS}, title = {Proton pump inhibitors increase the risk of carbapenem-resistant Enterobacteriaceae colonization by facilitating the transfer of antibiotic resistance genes among bacteria in the gut microbiome.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2341635}, doi = {10.1080/19490976.2024.2341635}, pmid = {38634770}, issn = {1949-0984}, abstract = {Carbapenem-resistant Enterobacteriaceae (CRE) pose a global health threat; however, there is still limited understanding of the risk factors and underlying mechanisms of CRE colonization in the gut microbiome. We conducted a matched case-control study involving 282 intensive care unit patients to analyze influencing covariates on CRE colonization. Subsequently, their effects on the gut microbiome were analyzed in a subset of 98 patients (47 CRE carriers and 51 non-CRE carriers) using whole metagenome sequences. The concomitant use of proton pump inhibitors (PPIs) and antibiotics was a significant risk factor for CRE colonization. The gut microbiome differed according to PPI administration, even within the CRE and non-CRE groups. Moreover, the transfer of mobile genetic elements (MGEs) harboring carbapenem resistance genes (CRGs) between bacteria was higher in the PPI-treated group than in the PPI-not-treated group among CRE carriers. The concomitant use of PPIs and antibiotics significantly alters the gut microbiome and increases the risk of CRE colonization by facilitating the transfer of CRGs among bacteria of the gut microbiome. Based on these findings, improved stewardship of PPIs as well as antibiotics can provide strategies to reduce the risk of CRE colonization, thereby potentially improving patient prognosis.}, } @article {pmid38633703, year = {2024}, author = {Arisan, D and Moya-Beltrán, A and Rojas-Villalobos, C and Issotta, F and Castro, M and Ulloa, R and Chiacchiarini, PA and Díez, B and Martín, AJM and Ñancucheo, I and Giaveno, A and Johnson, DB and Quatrini, R}, title = {Acidithiobacillia class members originating at sites within the Pacific Ring of Fire and other tectonically active locations and description of the novel genus 'Igneacidithiobacillus'.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1360268}, pmid = {38633703}, issn = {1664-302X}, abstract = {Recent studies have expanded the genomic contours of the Acidithiobacillia, highlighting important lacunae in our comprehension of the phylogenetic space occupied by certain lineages of the class. One such lineage is 'Igneacidithiobacillus', a novel genus-level taxon, represented by 'Igneacidithiobacillus copahuensis' VAN18-1[T] as its type species, along with two other uncultivated metagenome-assembled genomes (MAGs) originating from geothermally active sites across the Pacific Ring of Fire. In this study, we investigate the genetic and genomic diversity, and the distribution patterns of several uncharacterized Acidithiobacillia class strains and sequence clones, which are ascribed to the same 16S rRNA gene sequence clade. By digging deeper into this data and contributing to novel MAGs emerging from environmental studies in tectonically active locations, the description of this novel genus has been consolidated. Using state-of-the-art genomic taxonomy methods, we added to already recognized taxa, an additional four novel Candidate (Ca.) species, including 'Ca. Igneacidithiobacillus chanchocoensis' (mCHCt20-1[TS]), 'Igneacidithiobacillus siniensis' (S30A2[T]), 'Ca. Igneacidithiobacillus taupoensis' (TVZ-G3 [TS]), and 'Ca. Igneacidithiobacillus waiarikiensis' (TVZ-G4 [TS]). Analysis of published data on the isolation, enrichment, cultivation, and preliminary microbiological characterization of several of these unassigned or misassigned strains, along with the type species of the genus, plus the recoverable environmental data from metagenomic studies, allowed us to identify habitat preferences of these taxa. Commonalities and lineage-specific adaptations of the seven species of the genus were derived from pangenome analysis and comparative genomic metabolic reconstruction. The findings emerging from this study lay the groundwork for further research on the ecology, evolution, and biotechnological potential of the novel genus 'Igneacidithiobacillus'.}, } @article {pmid38633701, year = {2024}, author = {Jia, Y and He, C and Lahm, M and Chen, Q and Powers, L and Gonsior, M and Chen, F}, title = {A pilot study suggests the correspondence between SAR202 bacteria and dissolved organic matter in the late stage of a year-long microcosm incubation.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1357822}, pmid = {38633701}, issn = {1664-302X}, abstract = {SAR202 bacteria are abundant in the marine environment and they have been suggested to contribute to the utilization of recalcitrant organic matter (RDOM) within the ocean's biogeochemical cycle. However, this functional role has only been postulated by metagenomic studies. During a one-year microcosm incubation of an open ocean microbial community with lysed Synechococcus and its released DOM, SAR202 became relatively more abundant in the later stage (after day 30) of the incubation. Network analysis illustrated a high degree of negative associations between SAR202 and a unique group of molecular formulae (MFs) in phase 2 (day 30 to 364) of the incubation, which is empirical evidence that SAR202 bacteria are major consumers of the more oxygenated, unsaturated, and higher-molecular-weight MFs. Further investigation of the SAR202-associated MFs suggested that they were potentially secondary products arising from initial heterotrophic activities following the amendment of labile Synechococcus-derived DOM. This pilot study provided a preliminary observation on the correspondence between SAR202 bacteria and more resistant DOM, further supporting the hypothesis that SAR202 bacteria play important roles in the degradation of RDOM and thus the ocean's biogeochemical cycle.}, } @article {pmid38633306, year = {2024}, author = {Zhang, L and Liu, X and Fan, B and Chen, J and Chen, J and Li, Q and Wu, X}, title = {Microbiome features in bronchoalveolar lavage fluid of patients with idiopathic inflammatory myopathy-related interstitial lung disease.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1338947}, pmid = {38633306}, issn = {2296-858X}, abstract = {BACKGROUND: Interstitial lung disease (ILD) is a common complication of idiopathic inflammatory myopathy (IIM), which is one of the connective tissue diseases (CTD). It can lead to poor prognosis and increased mortality. However, the distribution and role of the lower respiratory tract (LRT) microbiome in patients with IIM-ILD remains unclear. This study aimed to investigate the microbial diversity and community differences in bronchoalveolar lavage fluid (BALF) in patients with IIM-ILD.

METHODS: From 28 June 2021 to 26 December 2023, 51 individual BALF samples were enrolled, consisting of 20 patients with IIM-ILD, 16 patients with other CTD-ILD (including 8 patients with SLE and 8 with RA) and 15 patients with CAP. The structure and function of microbiota in BALF were identified by metagenomic next-generation sequencing (mNGS).

RESULTS: The community evenness of LRT microbiota within the IIM-ILD group was marginally lower compared to the other CTD-ILD and CAP groups. Nonetheless, there were no noticeable differences. The species community structure was similar among the three groups, based on the Bray-Curtis distance between the samples. At the level of genus, the IIM-ILD group displayed a considerably higher abundance of Pseudomonas and Corynebacterium in comparison to the CAP group (p < 0.01, p < 0.05). At the species level, we found that the relative abundance of Pseudomonas aeruginosa increased significantly in the IIM-ILD group compared to the CAP group (p < 0.05). Additionally, the relative abundance of Prevotella pallens was significantly higher in other CTD-ILD groups compared to that in the IIM-ILD group (p < 0.05). Of all the clinical indicators examined in the correlation analysis, ferritin level demonstrated the strongest association with LRT flora, followed by Serum interleukin-6 level (p < 0.05).

CONCLUSION: Our research has identified particular LRT microorganisms that were found to be altered in the IIM-ILD group and were significantly associated with immune function and inflammatory markers in patients. The lower respiratory tract microbiota has potential in the diagnosis and treatment of IIM-ILD.}, } @article {pmid38632606, year = {2024}, author = {Liu, X and Zeng, X and Li, X and Xin, S and Zhang, F and Liu, F and Zeng, Y and Wu, J and Zou, Y and Xiong, X}, title = {Landscapes of gut bacterial and fecal metabolic signatures and their relationship in severe preeclampsia.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {360}, pmid = {38632606}, issn = {1479-5876}, support = {82160298//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Preeclampsia is a pregnancy-specific disease leading to maternal and perinatal morbidity. Hypertension and inflammation are the main characteristics of preeclampsia. Many factors can lead to hypertension and inflammation, including gut microbiota which plays an important role in hypertension and inflammation in humans. However, alterations to the gut microbiome and fecal metabolome, and their relationships in severe preeclampsia are not well known. This study aims to identify biomarkers significantly associated with severe preeclampsia and provide a knowledge base for treatments regulating the gut microbiome.

METHODS: In this study, fecal samples were collected from individuals with severe preeclampsia and healthy controls for shotgun metagenomic sequencing to evaluate changes in gut microbiota composition. Quantitative polymerase chain reaction analysis was used to validate the reliability of our shotgun metagenomic sequencing results. Additionally, untargeted metabolomics analysis was performed to measure fecal metabolome concentrations.

RESULTS: We identified several Lactobacillaceae that were significantly enriched in the gut of healthy controls, including Limosilactobacillus fermentum, the key biomarker distinguishing severe preeclampsia from healthy controls. Limosilactobacillus fermentum was significantly associated with shifts in KEGG Orthology (KO) genes and KEGG pathways of the gut microbiome in severe preeclampsia, such as flagellar assembly. Untargeted fecal metabolome analysis found that severe preeclampsia had higher concentrations of Phenylpropanoate and Agmatine. Increased concentrations of Phenylpropanoate and Agmatine were associated with the abundance of Limosilactobacillus fermentum. Furthermore, all metabolites with higher abundances in healthy controls were enriched in the arginine and proline metabolism pathway.

CONCLUSION: Our research indicates that changes in metabolites, possibly due to the gut microbe Limosilactobacillus fermentum, can contribute to the development of severe preeclampsia. This study provides insights into the interaction between gut microbiome and fecal metabolites and offers a basis for improving severe preeclampsia by modulating the gut microbiome.}, } @article {pmid38632536, year = {2024}, author = {Mao, JY and Li, DK and Zhang, D and Yang, QW and Long, Y and Cui, N}, title = {Utility of paired plasma and drainage fluid mNGS in diagnosing acute intra-abdominal infections with sepsis.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {409}, pmid = {38632536}, issn = {1471-2334}, support = {No. 2022-PUMCH-A-219//National High Level Hospital Clinical Research Funding/ ; No. 2022-PUMCH-B-126//National High Level Hospital Clinical Research Funding/ ; 2022YFC2009803//National Key R&D Program of China/ ; No. 82072226//National Natural Science Foundation of China/ ; (CIFMS) 2021-I2M-1-062//CAMS Innovation Fund for Medical Sciences/ ; No. Z201100005520049//Beijing Municipal Science and Technology Commission/ ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has been increasingly applied in sepsis. We aimed to evaluate the diagnostic and therapeutic utility of mNGS of paired plasma and peritoneal drainage (PD) fluid samples in comparison to culture-based microbiological tests (CMTs) among critically ill patients with suspected acute intra-abdominal infections (IAIs).

METHODS: We conducted a prospective study from October 2021 to December 2022 enrolling septic patients with suspected IAIs (n = 111). Pairwise CMTs and mNGS of plasma and PD fluid were sent for pathogen detection. The mNGS group underwent therapeutic regimen adjustment based on mNGS results for better treatment. The microbial community structure, clinical features, antibiotic use and prognoses of the patients were analyzed.

RESULTS: Higher positivity rates were observed with mNGS versus CMTs for both PD fluid (90.0% vs. 48.3%, p < 0.005) and plasma (76.7% vs. 1.6%, p < 0.005). 90% of enrolled patients had clues of suspected pathogens combining mNGS and CMT methods. Gram-negative pathogens consist of most intra-abdominal pathogens, including a great variety of anaerobes represented by Bacteroides and Clostridium. Patients with matched plasma- and PD-mNGS results had higher mortality and sepsis severity. Reduced usage of carbapenem (30.0% vs. 49.4%, p < 0.05) and duration of anti-MRSA treatment (5.1 ± 3.3 vs. 7.0 ± 8.4 days, p < 0.05) was shown in the mNGS group in our study.

CONCLUSIONS: Pairwise plasma and PD fluid mNGS improves microbiological diagnosis compared to CMTs for acute IAI. Combining plasma and PD mNGS could predict poor prognosis. mNGS may enable optimize empirical antibiotic use.}, } @article {pmid38629078, year = {2024}, author = {Lancaster, AK and Single, RM and Mack, SJ and Sochat, V and Mariani, MP and Webster, GD}, title = {PyPop: a mature open-source software pipeline for population genomics.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1378512}, pmid = {38629078}, issn = {1664-3224}, mesh = {*Metagenomics ; *Software ; Genetics, Population ; Haplotypes ; Genotype ; }, abstract = {Python for Population Genomics (PyPop) is a software package that processes genotype and allele data and performs large-scale population genetic analyses on highly polymorphic multi-locus genotype data. In particular, PyPop tests data conformity to Hardy-Weinberg equilibrium expectations, performs Ewens-Watterson tests for selection, estimates haplotype frequencies, measures linkage disequilibrium, and tests significance. Standardized means of performing these tests is key for contemporary studies of evolutionary biology and population genetics, and these tests are central to genetic studies of disease association as well. Here, we present PyPop 1.0.0, a new major release of the package, which implements new features using the more robust infrastructure of GitHub, and is distributed via the industry-standard Python Package Index. New features include implementation of the asymmetric linkage disequilibrium measures and, of particular interest to the immunogenetics research communities, support for modern nomenclature, including colon-delimited allele names, and improvements to meta-analysis features for aggregating outputs for multiple populations. Code available at: https://zenodo.org/records/10080668 and https://github.com/alexlancaster/pypop.}, } @article {pmid38631646, year = {2024}, author = {Muscarella, SM and Alduina, R and Badalucco, L and Capri, FC and Di Leto, Y and Gallo, G and Laudicina, VA and Paliaga, S and Mannina, G}, title = {Water reuse of treated domestic wastewater in agriculture: Effects on tomato plants, soil nutrient availability and microbial community structure.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {172259}, doi = {10.1016/j.scitotenv.2024.172259}, pmid = {38631646}, issn = {1879-1026}, abstract = {The reuse of treated wastewater (TWW) in agriculture for crop irrigation is desirable. Crop responses to irrigation with TWW depend on the characteristics of TWW and on intrinsic and extrinsic soil properties. The aim of this study was to assess the response of tomato (Solanum lycopersicum L.) cultivated in five different soils to irrigation with TWW, compared to tap water (TAP) and an inorganic NPK solution (IFW). In addition, since soil microbiota play many important roles in plant growth, a metataxonomic analysis was performed to reveal the prokaryotic community structures of TAP, TWW and IFW treated soil, respectively. A 56-days pot experiment was carried out. Plant biometric parameters, and chemical, biochemical and microbiological properties of different soils were investigated. Shoot and root dry and fresh weights, as well as plant height, were the highest in plants irrigated with IFW followed by those irrigated with TWW, and finally with TAP water. Plant biometric parameters were positively affected by soil total organic carbon (TOC) and nitrogen (TN). Electrical conductivity was increased by TWW and IFW, being such an increase proportional to clay and TOC. Soil available P was not affected by TWW, whereas mineral N increased following their application. Total microbial biomass, as well as, main microbial groups were positively affected by TOC and TN, and increased according to the following order: IFW > TWW > TAP. However, the fungi-to-bacteria ratio was lowered in soil irrigated with TWW because of its adverse effect on fungi. The germicidal effect of sodium hypochlorite on soil microorganisms was affected by soil pH. Nutrients supplied by TWW are not sufficient to meet the whole nutrients requirement of tomato, thus integration by fertilization is required. Bacteria were more stimulated than fungi by TWW, thus leading to a lower fungi-to-bacteria ratio. Interestingly, IFW and TWW treatment led to an increased abundance of Proteobacteria and Acidobacteria phyla and Balneimonas, Rubrobacter, and Steroidobacter genera. This soil microbiota structure modulation paralleled a general decrement of fungi versus bacteria abundance ratio, the increment of electrical conductivity and nitrogen content of soil and an improvement of tomato growth. Finally, the potential adverse effect of TWW added with sodium chloride on soil microorganisms depends on soil pH.}, } @article {pmid38631637, year = {2024}, author = {Zhang, D and Liu, F and Al, MA and Yang, Y and Yu, H and Li, M and Wu, K and Niu, M and Wang, C and He, Z and Yan, Q}, title = {Nitrogen and sulfur cycling and their coupling mechanisms in eutrophic lake sediment microbiomes.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {172518}, doi = {10.1016/j.scitotenv.2024.172518}, pmid = {38631637}, issn = {1879-1026}, abstract = {Microorganisms play important roles in the biogeochemical cycles of lake sediment. However, the integrated metabolic mechanisms governing nitrogen (N) and sulfur (S) cycling in eutrophic lakes remain poorly understood. Here, metagenomic analysis of field and bioreactor enriched sediment samples from a typical eutrophic lake were applied to elucidate the metabolic coupling of N and S cycling. Our results showed significant diverse genes involved in the pathways of dissimilatory sulfur metabolism, denitrification and dissimilatory nitrate reduction to ammonium (DNRA). The N and S associated functional genes and microbial groups generally showed significant correlation with the concentrations of NH4[+], NO2[-] and SO4[2], while with relatively low effects from other environmental factors. The gene-based co-occurrence network indicated clear cooperative interactions between N and S cycling in the sediment. Additionally, our analysis identified key metabolic processes, including the coupled dissimilatory sulfur oxidation (DSO) and DNRA as well as the association of thiosulfate oxidation complex (SOX systems) with denitrification pathway. However, the enriched N removal microorganisms in the bioreactor ecosystem demonstrated an additional electron donor, incorporating both the SOX systems and DSO processes. Metagenome-assembled genomes-based ecological model indicated that carbohydrate metabolism is the key linking factor for the coupling of N and S cycling. Our findings uncover the coupling mechanisms of microbial N and S metabolism, involving both inorganic and organic respiration pathways in lake sediment. This study will enhance our understanding of coupled biogeochemical cycles in lake ecosystems.}, } @article {pmid38631472, year = {2024}, author = {Wong, MH and Minkina, T and Vasilchenko, N and Sushkova, S and Delegan, Y and Ranjan, A and Saxena, P and Tarigholizadeh, S and Dudnikova, T and Barbashev, A and Maksimov, A and Faenson, A and Kızılkaya, R}, title = {Assessment of Antibiotic Resistance Genes in Soils Polluted by Chemical and Technogenic Ways with Poly-Aromatic Hydrocarbons and Heavy Metals.}, journal = {Environmental research}, volume = {}, number = {}, pages = {118949}, doi = {10.1016/j.envres.2024.118949}, pmid = {38631472}, issn = {1096-0953}, abstract = {Anthropogenic activities are leaving lots of chemical footprints on the soil. It alters the physiochemical characteristics of the soil thereby modifying the natural soil microbiome. The prevalence of antimicrobial-resistance microbes in polluted soil has gained attention due to its obvious public health risks. This study focused on assessing the prevalence and distribution of antibiotic-resistance genes in polluted soil ecosystems impacted by industrial enterprises in southern Russia. Metagenomic analysis was conducted on soil samples collected from polluted sites using various approaches, and the prevalence of antibiotic-resistance genes was investigated. The results revealed that efflux-encoding pump sequences were the most widely represented group of genes, while genes whose products replaced antibiotic targets were less represented. The level of soil contamination increased, and there was an increase in the total number of antibiotic-resistance genes in proteobacteria, but a decrease in actinobacteria. The study proposed an optimal mechanism for processing metagenomic data in polluted soil ecosystems, which involves mapping raw reads by the KMA method, followed by a detailed study of specific genes. The study's conclusions provide valuable insights into the prevalence and distribution of antibiotic-resistance genes in polluted soils and have been illustrated in heat maps.}, } @article {pmid38631413, year = {2024}, author = {Ravichandran, A and Sivapackiyam, J and Periasamy, S}, title = {Oral bacterial insights from a comparative study between healthy and comorbid diseased human individuals.}, journal = {Microbial pathogenesis}, volume = {}, number = {}, pages = {106643}, doi = {10.1016/j.micpath.2024.106643}, pmid = {38631413}, issn = {1096-1208}, abstract = {The human oral cavity is colonized by a diverse microbial community, which includes both native and transient colonizers. The microbial composition is crucial for maintaining oral homeostasis, but due to overgrowth or imbalances of these microbial communities, dysbiosis can occur. There is a lack of understanding of the research of native and transient colonizers in the oral cavity of the Indian subpopulation Therefore, in our present study, we explored the role and prevalence of transient and native colonizers between healthy and comorbid oral diseased human individuals. Culture-dependent techniques and culture-independent 16Sr DNA metagenomic analyses were employed to isolate and study the interactions of native and transient colonizers from human oral samples. Among the 66 human individuals of both healthy and comorbid individuals, the most abundant isolate was found to be Bacillus amyloliquefaciens MCC 4424. In addition, the more prevalent culturable isolate from the healthy samples was Streptococcus salivarius MTCC 13009, whereas in comorbid samples Staphylococcus pasteuri MTCC 13076, Rothia dentocariosa MTCC 13010 and Pseudomonas aeruginosa MTCC 13077 were prevalent to a greater extent. 16S rDNA metagenomic analyses revealed the prevalence and abundance of genera such as Bacteroidetes and Proteobacteria in healthy individuals; consequently, Fusobacteria and Firmicutes were observed mostly in comorbid individuals. The significant differences in bacterial population density were observed in terms of Shannon index (p = 0.5145) and Simpson index (p = 0.9061) between the healthy and comorbid groups. B. amyloliquefaciens MCC 4424 exhibits antagonistic behavior when grown as a dual species with native and transient colonizers. This result is very consistent with the findings of antibiofilm studies using confocal laser scanning microscopy, which revealed a significant reduction in biofilm biovolume (73%) and maximum thickness (80%) and an increase in the rough coefficient of biofilms (30%). Our data suggested that B. amyloliquefaciens MCC 4424 can be a native colonizer of Indian sub-populations. It may act as a novel candidate for oral healthcare applications and greatly aids in the regulation of transient species in the oral cavity.}, } @article {pmid38631239, year = {2024}, author = {Yu, Y and Trottmann, NF and Schärer, MR and Fenner, K and Robinson, SL}, title = {Substrate promiscuity of xenobiotic-transforming hydrolases from stream biofilms impacted by treated wastewater.}, journal = {Water research}, volume = {256}, number = {}, pages = {121593}, doi = {10.1016/j.watres.2024.121593}, pmid = {38631239}, issn = {1879-2448}, abstract = {Organic contaminants enter aquatic ecosystems from various sources, including wastewater treatment plant effluent. Freshwater biofilms play a major role in the removal of organic contaminants from receiving water bodies, but knowledge of the molecular mechanisms driving contaminant biotransformations in complex stream biofilm (periphyton) communities remains limited. Previously, we demonstrated that biofilms in experimental flume systems grown at higher ratios of treated wastewater (WW) to stream water displayed an increased biotransformation potential for a number of organic contaminants. We identified a positive correlation between WW percentage and biofilm biotransformation rates for the widely-used insect repellent, N,N-diethyl-meta-toluamide (DEET) and a number of other wastewater-borne contaminants with hydrolyzable moieties. Here, we conducted deep shotgun sequencing of flume biofilms and identified a positive correlation between WW percentage and metagenomic read abundances of DEET hydrolase (DH) homologs. To test the causality of this association, we constructed a targeted metagenomic library of DH homologs from flume biofilms. We screened our complete metagenomic library for activity with four different substrates, including DEET, and a subset thereof with 183 WW-related organic compounds. The majority of active hydrolases in the metagenomic library preferred aliphatic and aromatic ester substrates while, remarkably, only a single reference enzyme was capable of DEET hydrolysis. Of the 626 total enzyme-substrate combinations tested, approximately 5% were active enzyme-substrate pairs. Metagenomic DH family homologs revealed a broad substrate promiscuity spanning 22 different compounds when summed across all enzymes tested. We biochemically characterized the most promiscuous and active enzymes identified based on metagenomic analysis from uncultivated Rhodospirillaceae and Planctomycetaceae. In addition to characterizing new DH family enzymes, we exemplified a framework for linking metagenome-guided hypothesis generation with experimental validation. Overall, this study expands the scope of known enzymatic contaminant biotransformations for metagenomic hydrolases from WW-receiving stream biofilm communities.}, } @article {pmid38631236, year = {2024}, author = {Wu, H and Nie, WB and Tan, X and Xie, GJ and Qu, H and Zhang, X and Xian, Z and Dai, J and Yang, C and Chen, Y}, title = {Different oxygen affinities of methanotrophs and Comammox Nitrospira inform an electrically induced symbiosis for nitrogen loss.}, journal = {Water research}, volume = {256}, number = {}, pages = {121606}, doi = {10.1016/j.watres.2024.121606}, pmid = {38631236}, issn = {1879-2448}, abstract = {Aerobic methanotrophs establish a symbiotic association with denitrifiers to facilitate the process of aerobic methane oxidation coupled with denitrification (AME-D). However, the symbiosis has been frequently observed in hypoxic conditions continuing to pose an enigma. The present study has firstly characterized an electrically induced symbiosis primarily governed by Methylosarcina and Hyphomicrobium for the AME-D process in a hypoxic niche caused by Comammox Nitrospira. The kinetic analysis revealed that Comammox Nitrospira exhibited a higher apparent oxygen affinity compared to Methylosarcina. While the coexistence of comammox and AME-D resulted in an increase in methane oxidation and nitrogen loss rates, from 0.82 ± 0.10 to 1.72 ± 0.09 mmol CH4 d[-1] and from 0.59 ± 0.04 to 1.30 ± 0.15 mmol N2 d[-1], respectively. Furthermore, the constructed microbial fuel cells demonstrated a pronounced dependence of the biocurrents on AME-D due to oxygen competition, suggesting the involvement of direct interspecies electron transfer in the AME-D process under hypoxic conditions. Metagenomic and metatranscriptomic analysis revealed that Methylosarcina efficiently oxidized methane to formaldehyde, subsequently generating abundant NAD(P)H for nitrate reduction by Hyphomicrobium through the dissimilatory RuMP pathway, leading to CO2 production. This study challenges the conventional understanding of survival mechanism employed by AME-D symbionts, thereby contributing to the characterization responsible for limiting methane emissions and promoting nitrogen removal in hypoxic regions.}, } @article {pmid38631226, year = {2024}, author = {Rubin-Blum, M and Makovsky, Y and Rahav, E and Belkin, N and Antler, G and Sisma-Ventura, G and Herut, B}, title = {Active microbial communities facilitate carbon turnover in brine pools found in the deep Southeastern Mediterranean Sea.}, journal = {Marine environmental research}, volume = {198}, number = {}, pages = {106497}, doi = {10.1016/j.marenvres.2024.106497}, pmid = {38631226}, issn = {1879-0291}, abstract = {Discharge of gas-rich brines fuels productive chemosynthetic ecosystems in the deep sea. In these salty, methanic and sulfidic brines, microbial communities adapt to specific niches along the physicochemical gradients. However, the molecular mechanisms that underpin these adaptations are not fully known. Using metagenomics, we investigated the dense (∼10[6] cell ml[-1]) microbial communities that occupy small deep-sea brine pools found in the Southeastern Mediterranean Sea (1150 m water depth, ∼22 °C, ∼60 PSU salinity, sulfide, methane, ammonia reaching millimolar levels, and oxygen usually depleted), reaching high productivity rates of 685 μg C L[-1] d[-1] ex-situ. We curated 266 metagenome-assembled genomes of bacteria and archaea from the several pools and adjacent sediment-water interface, highlighting the dominance of a single Sulfurimonas, which likely fuels its autotrophy using sulfide oxidation or inorganic sulfur disproportionation. This lineage may be dominant in its niche due to genome streamlining, limiting its metabolic repertoire, particularly by using a single variant of sulfide: quinone oxidoreductase. These primary producers co-exist with ANME-2c archaea that catalyze the anaerobic oxidation of methane. Other lineages can degrade the necromass aerobically (Halomonas and Alcanivorax), or anaerobically through fermentation of macromolecules (e.g., Caldatribacteriota, Bipolaricaulia, Chloroflexota, etc). These low-abundance organisms likely support the autotrophs, providing energy-rich H2, and vital organics such as vitamin B12.}, } @article {pmid38632506, year = {2024}, author = {Alkathiry, HA and Alghamdi, SQ and Sinha, A and Margos, G and Stekolnikov, AA and Alagaili, AN and Darby, AC and Makepeace, BL and Khoo, JJ}, title = {Microbiome and mitogenomics of the chigger mite Pentidionis agamae: potential role as an Orientia vector and associations with divergent clades of Wolbachia and Borrelia.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {380}, pmid = {38632506}, issn = {1471-2164}, abstract = {BACKGROUND: Trombiculid mites are globally distributed, highly diverse arachnids that largely lack molecular resources such as whole mitogenomes for the elucidation of taxonomic relationships. Trombiculid larvae (chiggers) parasitise vertebrates and can transmit bacteria (Orientia spp.) responsible for scrub typhus, a zoonotic febrile illness. Orientia tsutsugamushi causes most cases of scrub typhus and is endemic to the Asia-Pacific Region, where it is transmitted by Leptotrombidium spp. chiggers. However, in Dubai, Candidatus Orientia chuto was isolated from a case of scrub typhus and is also known to circulate among rodents in Saudi Arabia and Kenya, although its vectors remain poorly defined. In addition to Orientia, chiggers are often infected with other potential pathogens or arthropod-specific endosymbionts, but their significance for trombiculid biology and public health is unclear.

RESULTS: Ten chigger species were collected from rodents in southwestern Saudi Arabia. Chiggers were pooled according to species and screened for Orientia DNA by PCR. Two species (Microtrombicula muhaylensis and Pentidionis agamae) produced positive results for the htrA gene, although Ca. Orientia chuto DNA was confirmed by Sanger sequencing only in P. agamae. Metagenomic sequencing of three pools of P. agamae provided evidence for two other bacterial associates: a spirochaete and a Wolbachia symbiont. Phylogenetic analysis of 16S rRNA and multi-locus sequence typing genes placed the spirochaete in a clade of micromammal-associated Borrelia spp. that are widely-distributed globally with no known vector. For the Wolbachia symbiont, a genome assembly was obtained that allowed phylogenetic localisation in a novel, divergent clade. Cytochrome c oxidase I (COI) barcodes for Saudi Arabian chiggers enabled comparisons with global chigger diversity, revealing several cases of discordance with classical taxonomy. Complete mitogenome assemblies were obtained for the three P. agamae pools and almost 50 SNPs were identified, despite a common geographic origin.

CONCLUSIONS: P. agamae was identified as a potential vector of Ca. Orientia chuto on the Arabian Peninsula. The detection of an unusual Borrelia sp. and a divergent Wolbachia symbiont in P. agamae indicated links with chigger microbiomes in other parts of the world, while COI barcoding and mitogenomic analyses greatly extended our understanding of inter- and intraspecific relationships in trombiculid mites.}, } @article {pmid38632404, year = {2024}, author = {Hossain, AA and Pigli, YZ and Baca, CF and Heissel, S and Thomas, A and Libis, VK and Burian, J and Chappie, JS and Brady, SF and Rice, PA and Marraffini, LA}, title = {DNA glycosylases provide antiviral defence in prokaryotes.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {38632404}, issn = {1476-4687}, abstract = {Bacteria have adapted to phage predation by evolving a vast assortment of defence systems[1]. Although anti-phage immunity genes can be identified using bioinformatic tools, the discovery of novel systems is restricted to the available prokaryotic sequence data[2]. Here, to overcome this limitation, we infected Escherichia coli carrying a soil metagenomic DNA library[3] with the lytic coliphage T4 to isolate clones carrying protective genes. Following this approach, we identified Brig1, a DNA glycosylase that excises α-glucosyl-hydroxymethylcytosine nucleobases from the bacteriophage T4 genome to generate abasic sites and inhibit viral replication. Brig1 homologues that provide immunity against T-even phages are present in multiple phage defence loci across distinct clades of bacteria. Our study highlights the benefits of screening unsequenced DNA and reveals prokaryotic DNA glycosylases as important players in the bacteria-phage arms race.}, } @article {pmid38632370, year = {2024}, author = {Sterzi, L and Nodari, R and Di Marco, F and Ferrando, ML and Saluzzo, F and Spitaleri, A and Allahverdi, H and Papaleo, S and Panelli, S and Rimoldi, SG and Batisti Biffignandi, G and Corbella, M and Cavallero, A and Prati, P and Farina, C and Cirillo, DM and Zuccotti, G and Bandi, C and Comandatore, F}, title = {Genetic barriers more than environmental associations explain Serratia marcescens population structure.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {468}, pmid = {38632370}, issn = {2399-3642}, abstract = {Bacterial species often comprise well-separated lineages, likely emerged and maintained by genetic isolation and/or ecological divergence. How these two evolutionary actors interact in the shaping of bacterial population structure is currently not fully understood. In this study, we investigate the genetic and ecological drivers underlying the evolution of Serratia marcescens, an opportunistic pathogen with high genomic flexibility and able to colonise diverse environments. Comparative genomic analyses reveal a population structure composed of five deeply-demarcated genetic clusters with open pan-genome but limited inter-cluster gene flow, partially explained by Restriction-Modification (R-M) systems incompatibility. Furthermore, a large-scale research on hundred-thousands metagenomic datasets reveals only a partial habitat separation of the clusters. Globally, two clusters only show a separate gene composition coherent with ecological adaptations. These results suggest that genetic isolation has preceded ecological adaptations in the shaping of the species diversity, an evolutionary scenario coherent with the Evolutionary Extended Synthesis.}, } @article {pmid38632042, year = {2024}, author = {Coskun, ÖK and Gomez-Saez, GV and Beren, M and Özcan, D and Günay, SD and Elkin, V and Hoşgörmez, H and Einsiedl, F and Eisenreich, W and Orsi, WD}, title = {Quantifying genome specific carbon fixation in a 750 meter deep subsurface hydrothermal microbial community.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiae062}, pmid = {38632042}, issn = {1574-6941}, abstract = {Dissolved inorganic carbon has been hypothesized to stimulate microbial chemoautotrophic activity as a biological sink in the carbon cycle of deep subsurface environments. Here, we tested this hypothesis using quantitative DNA stable isotope probing of metagenome assembled genomes (MAGs) at multiple 13C-labeled bicarbonate concentrations in hydrothermal fluids from a 750 meter deep subsurface aquifer in the Biga Peninsula (Turkey). The diversity of microbial populations assimilating 13C-labeled bicarbonate was significantly different at higher bicarbonate concentrations, and could be linked to four separate carbon fixation pathways encoded within 13C-labeled MAGs. Microbial populations encoding the Calvin-Benson-Bassham cycle had the highest contribution to carbon fixation across all bicarbonate concentrations tested, spanning 1-10 mM. However, out of all the active carbon fixation pathways detected, MAGs affiliated with the phylum Aquificae encoding the reverse tricarboxylic acid (rTCA) pathway were the only microbial populations that exhibited an increased 13C-bicarbonate assimilation under increasing bicarbonate concentrations. Our study provides the first experimental data supporting predictions that increased bicarbonate concentrations may promote chemoautotrophy via the rTCA cycle and its biological sink for deep subsurface inorganic carbon.}, } @article {pmid38630611, year = {2024}, author = {Roy, G and Prifti, E and Belda, E and Zucker, JD}, title = {Deep learning methods in metagenomics: a review.}, journal = {Microbial genomics}, volume = {10}, number = {4}, pages = {}, doi = {10.1099/mgen.0.001231}, pmid = {38630611}, issn = {2057-5858}, abstract = {The ever-decreasing cost of sequencing and the growing potential applications of metagenomics have led to an unprecedented surge in data generation. One of the most prevalent applications of metagenomics is the study of microbial environments, such as the human gut. The gut microbiome plays a crucial role in human health, providing vital information for patient diagnosis and prognosis. However, analysing metagenomic data remains challenging due to several factors, including reference catalogues, sparsity and compositionality. Deep learning (DL) enables novel and promising approaches that complement state-of-the-art microbiome pipelines. DL-based methods can address almost all aspects of microbiome analysis, including novel pathogen detection, sequence classification, patient stratification and disease prediction. Beyond generating predictive models, a key aspect of these methods is also their interpretability. This article reviews DL approaches in metagenomics, including convolutional networks, autoencoders and attention-based models. These methods aggregate contextualized data and pave the way for improved patient care and a better understanding of the microbiome's key role in our health.}, } @article {pmid38630394, year = {2024}, author = {Balázs, B and Boros, Á and Pankovics, P and Nagy, G and Szekeres, S and Urbán, P and Reuter, G}, title = {Detection and complete genome characterization of a genogroup X (GX) sapovirus (family Caliciviridae) from a golden jackal (Canis aureus) in Hungary.}, journal = {Archives of virology}, volume = {169}, number = {5}, pages = {100}, pmid = {38630394}, issn = {1432-8798}, abstract = {In this study, a novel genotype of genogroup X (GX) sapovirus (family Caliciviridae) was detected in the small intestinal contents of a golden jackal (Canis aureus) in Hungary and characterised by viral metagenomics and next-generation sequencing techniques. The complete genome of the detected strain, GX/Dömsöd/DOCA-11/2020/HUN (PP105600), is 7,128 nt in length. The ORF1- and ORF2-encoded viral proteins (NSP, VP1, and VP2) have 98%, 95%, and 88% amino acid sequence identity to the corresponding proteins of genogroup GX sapoviruses from domestic pigs, but the nucleic acid sequence identity values for their genes are significantly lower (83%, 77%, and 68%). During an RT-PCR-based epidemiological investigation of additional jackal and swine samples, no other GX strains were detected, but a GXI sapovirus strain, GXI/Tótfalu/WBTF-10/2012/HUN (PP105601), was identified in a faecal sample from a wild boar (Sus scrofa). We report the detection of members of two likely underdiagnosed groups of sapoviruses (GX and GXI) in a golden jackal and, serendipitously, in a wild boar in Europe.}, } @article {pmid38630379, year = {2024}, author = {Sharafi, R and Salehi Jouzani, G and Karimi, E and Ghanavati, H and Kowsari, M}, title = {Integrating bioprocess and metagenomics studies to enhance humic acid production from rice straw.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {6}, pages = {173}, pmid = {38630379}, issn = {1573-0972}, support = {2-05-05-017-960740//Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)/ ; 2-05-05-017-960740//Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)/ ; 2-05-05-017-960740//Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)/ ; 2-05-05-017-960740//Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)/ ; 2-05-05-017-960740//Agricultural Biotechnology Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO)/ ; }, abstract = {Rice straw burning annually (millions of tons) leads to greenhouse gas emissions, and an alternative solution is producing humic acid with high added-value. This study aimed to examine the influence of a microbial consortium and other additives (chicken manure, urea, olive mill waste, zeolite, and biochar) on the composting process of rice straw and the subsequent production of humic acid. Results showed that among the fungal species, Thermoascus aurantiacus exhibited the most prominent impact in expediting maturation and improving compost quality, and Bacillus subtilis was the most abundant bacterial species based on metagenomics analysis. The highest temperature, C/N ratio reduction, and amount of humic acid production (Respectively in lab 61 °C, 54.67%, 298 g kg[-1] and in pilot level 65 °C, 72.11%, 310 g kg[-1]) were related to treatments containing these microorganisms and other additives except urea. Consequently, T. aurantiacus and B. subtilis can be employed on an industrial scale as compost additives to further elevate quality. Functional analysis showed that the bacterial enzymes in the treatments had the highest metabolic activities, including carbohydrate and amino acid metabolism compared to the control. The maximum enzymatic activities were in the thermophilic phase in treatments which were significantly higher than that in the control. The research emphasizes the importance of identifying and incorporating enzymatically active strains that are suitable for temperature conditions, alongside the native strains in decomposing materials. This strategy significantly improves the composting process and yields high-quality humic acid during the thermophilic phase.}, } @article {pmid38630153, year = {2024}, author = {Salam, LB}, title = {Metagenomic investigations into the microbial consortia, degradation pathways, and enzyme systems involved in the biodegradation of plastics in a tropical lentic pond sediment.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {6}, pages = {172}, pmid = {38630153}, issn = {1573-0972}, abstract = {The exploitation of exciting features of plastics for diverse applications has resulted in significant plastic waste generation, which negatively impacts environmental compartments, metabolic processes, and the well-being of aquatic ecosystems biota. A shotgun metagenomic approach was deployed to investigate the microbial consortia, degradation pathways, and enzyme systems involved in the degradation of plastics in a tropical lentic pond sediment (APS). Functional annotation of the APS proteome (ORFs) using the PlasticDB database revealed annotation of 1015 proteins of enzymes such as depolymerase, esterase, lipase, hydrolase, nitrobenzylesterase, chitinase, carboxylesterase, polyesterase, oxidoreductase, polyamidase, PETase, MHETase, laccase, alkane monooxygenase, among others involved in the depolymerization of the plastic polymers. It also revealed that polyethylene glycol (PEG), polyhydroxyalkanoates (PHA), polyhydroxybutyrate (PHB), polylactic acid (PLA), polybutylene adipate terephthalate (PBAT), polyethylene terephthalate (PET), and nylon have the highest number of annotated enzymes. Further annotation using the KEGG GhostKOALA revealed that except for terephthalate, all the other degradation products of the plastic polymers depolymerization such as glyoxylate, adipate, succinate, 1,4-butanediol, ethylene glycol, lactate, and acetaldehyde were further metabolized to intermediates of the tricarboxylic acid cycle. Taxonomic characterization of the annotated proteins using the AAI Profiler and BLASTP revealed that Pseudomonadota members dominate most plastic types, followed by Actinomycetota and Acidobacteriota. The study reveals novel plastic degraders from diverse phyla hitherto not reported to be involved in plastic degradation. This suggests that plastic pollution in aquatic environments is prevalent with well-adapted degrading communities and could be the silver lining in mitigating the impacts of plastic pollution in aquatic environments.}, } @article {pmid38629898, year = {2024}, author = {Li, W and He, Y and Li, Y and Li, X and Bian, T and Liu, T and Liu, X and Jiang, W}, title = {Metagenomic next-generation sequencing for the diagnosis of neurobrucellosis.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {}, doi = {10.2217/fmb-2023-0177}, pmid = {38629898}, issn = {1746-0921}, support = {XJZT19MJ21//Discipline Promotion Project of Xijing Hospital/ ; }, abstract = {Objective: This study investigates the application of metagenomic next-generation sequencing (mNGS) in the diagnosis of neurobrucellosis (NB). Methods: We retrospectively analyzed patients diagnosed with NB who underwent cerebrospinal fluid (CSF) mNGS testing in Xijing Hospital from 2015 to 2021. Results: Among the 20 individuals included in the study, the serum rose bengal test was positive in 11 out of 16 cases, serum agglutination test was positive in 13 out of 16 cases, CSF culture was positive in 6 out of 11 cases, and CSF mNGS tests were positive in 18 out of 20 cases. Conclusion: CSF mNGS demonstrates superior sensitivity; therefore, it is recommended to collect CSF for mNGS testing prior to antibiotic therapy when NB is suspected.}, } @article {pmid38629830, year = {2024}, author = {Castro, AE and Montecillo, AD and Villanueva, RMD and Obusan, MCM}, title = {Bacterial community profiles of select tributaries of Laguna Lake in the Philippines.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0116123}, doi = {10.1128/mra.01161-23}, pmid = {38629830}, issn = {2576-098X}, abstract = {Laguna Lake is known for its ecological, economic, and cultural importance. Effects of urbanization and accumulation of emerging pollutants have been associated with its water quality; however, the microbial ecology of its tributaries remains to be explored. We report bacterial community profiles from shotgun metagenomes of its select tributary waters.}, } @article {pmid38629119, year = {2024}, author = {Mason, B and Cervena, B and Frias, L and Goossens, B and Hasegawa, H and Keuk, K and Langgeng, A and Majewski, K and Matsumoto, T and Matsuura, K and Mendonça, R and Okamoto, M and Peter, S and Petrzelkova, KJ and Sipangkui, S and Xu, Z and Pafco, B and MacIntosh, AJJ}, title = {Novel insight into the genetic diversity of strongylid nematodes infecting South-East and East Asian primates.}, journal = {Parasitology}, volume = {}, number = {}, pages = {1-9}, doi = {10.1017/S0031182024000386}, pmid = {38629119}, issn = {1469-8161}, support = {15H04283//Japan Society for the Promotion of Science/ ; 16H06181//Japan Society for the Promotion of Science/ ; 20H03333//Japan Society for the Promotion of Science/ ; 24770232//Japan Society for the Promotion of Science/ ; 446//Japan Society for the Promotion of Science/ ; 22-16475S//Grantová Agentura České Republiky/ ; }, abstract = {With many non-human primates (NHPs) showing continued population decline, there is an ongoing need to better understand their ecology and conservation threats. One such threat is the risk of disease, with various bacterial, viral and parasitic infections previously reported to have damaging consequences for NHP hosts. Strongylid nematodes are one of the most commonly reported parasitic infections in NHPs. Current knowledge of NHP strongylid infections is restricted by their typical occurrence as mixed infections of multiple genera, which are indistinguishable through traditional microscopic approaches. Here, modern metagenomics approaches were applied for insight into the genetic diversity of strongylid infections in South-East and East Asian NHPs. We hypothesized that strongylid nematodes occur in mixed communities of multiple taxa, dominated by Oesophagostomum, matching previous findings using single-specimen genetics. Utilizing the Illumina MiSeq platform, ITS-2 strongylid metabarcoding was applied to 90 samples from various wild NHPs occurring in Malaysian Borneo and Japan. A clear dominance of Oesophagostomum aculeatum was found, with almost all sequences assigned to this species. This study suggests that strongylid communities of Asian NHPs may be less species-rich than those in African NHPs, where multi-genera communities are reported. Such knowledge contributes baseline data, assisting with ongoing monitoring of health threats to NHPs.}, } @article {pmid38628865, year = {2024}, author = {Zhu, Q and Cui, J and Liu, S and Wei, S and Wu, Q and You, Y}, title = {Synbiotic regulates gut microbiota in patients with lupus nephritis: an analysis using metagenomic and metabolome sequencing.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1295378}, pmid = {38628865}, issn = {1664-302X}, abstract = {OBJECTIVE: To investigate the changes in gut microbes and their metabolites after administering synbiotics to patients with new-onset lupus nephritis (LN) treated using a conventional method and provide a theoretical basis for finding new targets for the diagnosis and treatment of LN.

METHODS: In this study, a total of 12 participants were divided into the lupus and synbiotic groups. Stool samples and clinical data were collected before and after treatment for metagenomic, nontargeted metabolomic, and statistical analyses.

RESULTS: The relative abundances of the pathogenic bacteria Prevotella, Bacteroides, and Enterobacteriaceae_unclassified decreased after synbiotic treatment, whereas the abundances of Actinobacteria and Firmicutes increased. Further, the Firmicutes to Bacteroidetes ratio increased; however, the difference was not statistically significant (p > 0.05). α diversity analysis showed no significant differences in the intestinal microbial richness and diversity index of patients with LN between the groups before and after treatment (p > 0.05). β analysis showed the differences in the community structure between the samples of the two groups before and after treatment. Linear discriminant analysis effect size and receiver operating characteristic curve analyses revealed that Negativicutes (AUC = 0.9722) and Enterobacteriaceae_unclassified (AUC = 0.9722) were the best predictors of the lupus and synbiotic groups, respectively, before and after treatment. Joint analyses revealed that amino acid biosynthesis, aminoacyl-tRNA biosynthesis, purine metabolism, and other metabolic pathways may be involved in the changes in the metabolic function of patients with LN after the addition of synbiotics. Spearman's correlation analysis revealed the interaction between clinical features and flora, and flora exhibited a complex biological network regulatory relationship.

CONCLUSION: Synbiotics regulate the metabolic functions of intestinal microorganisms in patients with LN and play a role in various biological functions. Synbiotic supplements may be safe and promising candidates for patients with LN.}, } @article {pmid38628241, year = {2024}, author = {Yuan, L and Lai, LM and Zhu, X and Rui, Z and Liu, Y and Chen, Q}, title = {Haemophilus aphrophilus and Eikenella corrodens Coinfection of Brain: An Unusual Case from China.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {1439-1445}, pmid = {38628241}, issn = {1178-6973}, abstract = {BACKGROUND: The HACEK group comprises Haemophilus spp., Aggregatibacter actinomycetemcomitans, Cardiobacterium hominis, Eikenella corrodens, and Kingella kingae, are Gram-negative bacteria that are slow-growing and fastidious. These organisms are common causes of culture-negative endocarditis. However, brain abscesses caused by Haemophilus aphrophilus and E. corrodens have been rarely reported. The case we describe, which was promptly identified and successfully treated, will be meaningful for the diagnosis and treatment of such infectious diseases.

CASE PRESENTATION: Herein, we report a case of brain abscess in a young man who was infected with Haemophilus aphrophilus and E. corrodens. The patient was admitted to the hospital with sudden onset of vomiting, coma, and fever. Magnetic resonance imaging (MRI) of the brain and cerebrospinal fluid cell counts suggested cerebral abscess, he underwent drainage of the abscess and empirical antimicrobial therapy of meropenem (2 g every 8 hours) and linezolid (0.6 g every 12 hours) for more than 10 days without significant improvement. Metagenomic next-generation sequencing (mNGS) of drainage fluid and matrix-assisted laser desorption ionization-time-of-flight mass spectrometry (MALDI-TOF MS) detection for isolated bacteria from samples suggested the presence of H. aphrophilus and E. corrodens. After 7 weeks of ceftriaxone (2 g every 12 hours) and meropenem (2 g every 8 hours) intravenously, the patient was discharged with a normal temperature and brain MRI showed improvement of the lesion.

CONCLUSION: Similar cases reported in previous studies were always associated with bacterial blood dissemination after dental surgery or myocarditis; however, the patient in our case had no any associated risk factors. As far as we know, this is the only case of central nervous system infection caused by H. aphrophilus and E. corrodens that has utilized combined mNGS and MALDI-TOF MS in the diagnosis.}, } @article {pmid38628239, year = {2024}, author = {Li, S and Han, X and Ma, J and Huang, GH and Yang, ST and Wang, CM}, title = {Study on mNGS Technique in Diagnosing Pneumocystis jirovecii Pneumonia in Non-HIV-Infected Patients.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {1397-1405}, pmid = {38628239}, issn = {1178-6973}, abstract = {OBJECTIVE: To investigate the value of metagenomic Next-Generation Sequencing (mNGS) in diagnosing Pneumocystis jirovecii pneumonia (PJP) in non-human immunodeficiency virus (HIV)-infected patients.

METHODS: In this retrospective study, non-HIV-infected patients with PJP and those diagnosed with non-PJP from August 2022 to December 2024 were selected as subjects. The presence of Pneumocystis jirovecii (PJ) and other co-pathogens in bronchoalveolar lavage fluid (BALF) was analyzed, and the diagnostic efficacy of NGS, polymerase chain reaction (PCR) and serum 1,3-β-D-glucan (BDG) in PJP was compared with the reference standard of clinical compound diagnosis.

RESULTS: Eighty-nine non-HIV-infected patients were recruited, with dyspnea as the primary symptom (69.66%) and solid malignant tumor as the most common underlying disease (20.22%). Taking clinical compound diagnosis as the reference standard, the sensitivity, specificity, negative predictive value and positive predictive value of mNGS were higher than those detected by PCR and serum BDG. Among 42 non-HIV-infected patients with PJP who underwent mNGS and conventional pathogen detection of BALF, 6 had simple PJ infection and 36 had combined PJ infection. The detection rate of mNGS in mixed infections was significantly higher than that of conventional pathogen detection (85.71 vs 61.70%, P = 0.012). A total of 127 pathogens were detected in BALF using mNGS, among which fungi had the highest detection rate (46.46%). The fungi, viruses and bacteria detected were mainly Pneumocystis jirovecii, human gammaherpesvirus 4 and Acinetobacter baumannii.

CONCLUSION: mNGS is highly effective in diagnosing non-HIV-infected patients with PJP and exhibits ideal performance in the detection of co-pathogens. In addition, it has certain value for clinical diagnosis and guidance of targeted anti-infective drug treatment.}, } @article {pmid38627869, year = {2024}, author = {Ortiz Sanjuán, JM and Argüello, H and Cabrera-Rubio, R and Crispie, F and Cotter, PD and Garrido, JJ and Ekhlas, D and Burgess, CM and Manzanilla, EG}, title = {Effects of removing in-feed antibiotics and zinc oxide on the taxonomy and functionality of the microbiota in post weaning pigs.}, journal = {Animal microbiome}, volume = {6}, number = {1}, pages = {18}, pmid = {38627869}, issn = {2524-4671}, support = {0376//Teagasc Walsh Scholarship Programme/ ; 0376//Teagasc Walsh Scholarship Programme/ ; BEAGAL-18-106//Spanish Government (Ministerio de Educación y Formación Profesional)/ ; }, abstract = {BACKGROUND: Post weaning diarrhoea (PWD) causes piglet morbidity and mortality at weaning and is a major driver for antimicrobial use worldwide. New regulations in the EU limit the use of in-feed antibiotics (Ab) and therapeutic zinc oxide (ZnO) to prevent PWD. New approaches to control PWD are needed, and understanding the role of the microbiota in this context is key. In this study, shotgun metagenome sequencing was used to describe the taxonomic and functional evolution of the faecal microbiota of the piglet during the first two weeks post weaning within three experimental groups, Ab, ZnO and no medication, on commercial farms using antimicrobials regularly in the post weaning period.

RESULTS: Diversity was affected by day post weaning (dpw), treatment used and diarrhoea but not by the farm. Microbiota composition evolved towards the dominance of groups of species such as Prevotella spp. at day 14dpw. ZnO inhibited E. coli overgrowth, promoted higher abundance of the family Bacteroidaceae and decreased Megasphaera spp. Animals treated with Ab exhibited inconsistent taxonomic changes across time points, with an overall increase of Limosilactobacillus reuteri and Megasphaera elsdenii. Samples from non-medicated pigs showed virulence-related functions at 7dpw, and specific ETEC-related virulence factors were detected in all samples presenting diarrhoea. Differential microbiota functions of pigs treated with ZnO were related to sulphur and DNA metabolism, as well as mechanisms of antimicrobial and heavy metal resistance, whereas Ab treated animals exhibited functions related to antimicrobial resistance and virulence.

CONCLUSION: Ab and particularly ZnO maintained a stable microbiota composition and functionality during the two weeks post weaning, by limiting E. coli overgrowth, and ultimately preventing microbiota dysbiosis. Future approaches to support piglet health should be able to reproduce this stable gut microbiota transition during the post weaning period, in order to maintain optimal gut physiological and productive conditions.}, } @article {pmid38627868, year = {2024}, author = {Ho, M and Nguyen, HN and Van Hoang, M and Bui, TTT and Vu, BQ and Dinh, THT and Vo, HTM and Blaydon, DC and Eldirany, SA and Bunick, CG and Bui, CB}, title = {Altered skin microbiome, inflammation, and JAK/STAT signaling in Southeast Asian ichthyosis patients.}, journal = {Human genomics}, volume = {18}, number = {1}, pages = {38}, pmid = {38627868}, issn = {1479-7364}, support = {K08AR070290/AR/NIAMS NIH HHS/United States ; }, abstract = {BACKGROUND: Congenital ichthyosis (CI) is a collective group of rare hereditary skin disorders. Patients present with epidermal scaling, fissuring, chronic inflammation, and increased susceptibility to infections. Recently, there is increased interest in the skin microbiome; therefore, we hypothesized that CI patients likely exhibit an abnormal profile of epidermal microbes because of their various underlying skin barrier defects. Among recruited individuals of Southeast Asian ethnicity, we performed skin meta-genomics (i.e., whole-exome sequencing to capture the entire multi-kingdom profile, including fungi, protists, archaea, bacteria, and viruses), comparing 36 CI patients (representing seven subtypes) with that of 15 CI age-and gender-matched controls who had no family history of CI.

RESULTS: This case-control study revealed 20 novel and 31 recurrent pathogenic variants. Microbiome meta-analysis showed distinct microbial populations, decreases in commensal microbiota, and higher colonization by pathogenic species associated with CI; these were correlated with increased production of inflammatory cytokines and Th17- and JAK/STAT-signaling pathways in peripheral blood mononuclear cells. In the wounds of CI patients, we identified specific changes in microbiota and alterations in inflammatory pathways, which are likely responsible for impaired wound healing.

CONCLUSIONS: Together, this research enhances our understanding of the microbiological, immunological, and molecular properties of CI and should provide critical information for improving therapeutic management of CI patients.}, } @article {pmid38622339, year = {2024}, author = {Salojärvi, J and Rambani, A and Yu, Z and Guyot, R and Strickler, S and Lepelley, M and Wang, C and Rajaraman, S and Rastas, P and Zheng, C and Muñoz, DS and Meidanis, J and Paschoal, AR and Bawin, Y and Krabbenhoft, TJ and Wang, ZQ and Fleck, SJ and Aussel, R and Bellanger, L and Charpagne, A and Fournier, C and Kassam, M and Lefebvre, G and Métairon, S and Moine, D and Rigoreau, M and Stolte, J and Hamon, P and Couturon, E and Tranchant-Dubreuil, C and Mukherjee, M and Lan, T and Engelhardt, J and Stadler, P and Correia De Lemos, SM and Suzuki, SI and Sumirat, U and Wai, CM and Dauchot, N and Orozco-Arias, S and Garavito, A and Kiwuka, C and Musoli, P and Nalukenge, A and Guichoux, E and Reinout, H and Smit, M and Carretero-Paulet, L and Filho, OG and Braghini, MT and Padilha, L and Sera, GH and Ruttink, T and Henry, R and Marraccini, P and Van de Peer, Y and Andrade, A and Domingues, D and Giuliano, G and Mueller, L and Pereira, LF and Plaisance, S and Poncet, V and Rombauts, S and Sankoff, D and Albert, VA and Crouzillat, D and de Kochko, A and Descombes, P}, title = {The genome and population genomics of allopolyploid Coffea arabica reveal the diversification history of modern coffee cultivars.}, journal = {Nature genetics}, volume = {56}, number = {4}, pages = {721-731}, pmid = {38622339}, issn = {1546-1718}, support = {1442190//NSF | Directorate for Biological Sciences (BIO)/ ; 2030871//NSF | Directorate for Biological Sciences (BIO)/ ; 343656//Academy of Finland (Suomen Akatemia)/ ; G056517N//Fonds Wetenschappelijk Onderzoek (Research Foundation Flanders)/ ; BOF.MET.2021.0005.01//Universitair Ziekenhuis Gent (Ghent University Hospital)/ ; }, mesh = {*Coffea/genetics ; Coffee ; Genome, Plant/genetics ; Metagenomics ; Plant Breeding ; }, abstract = {Coffea arabica, an allotetraploid hybrid of Coffea eugenioides and Coffea canephora, is the source of approximately 60% of coffee products worldwide, and its cultivated accessions have undergone several population bottlenecks. We present chromosome-level assemblies of a di-haploid C. arabica accession and modern representatives of its diploid progenitors, C. eugenioides and C. canephora. The three species exhibit largely conserved genome structures between diploid parents and descendant subgenomes, with no obvious global subgenome dominance. We find evidence for a founding polyploidy event 350,000-610,000 years ago, followed by several pre-domestication bottlenecks, resulting in narrow genetic variation. A split between wild accessions and cultivar progenitors occurred ~30.5 thousand years ago, followed by a period of migration between the two populations. Analysis of modern varieties, including lines historically introgressed with C. canephora, highlights their breeding histories and loci that may contribute to pathogen resistance, laying the groundwork for future genomics-based breeding of C. arabica.}, } @article {pmid38489588, year = {2024}, author = {David, G and Bertolotti, A and Layer, R and Scofield, D and Hayward, A and Baril, T and Burnett, HA and Gudmunds, E and Jensen, H and Husby, A}, title = {Calling Structural Variants with Confidence from Short-Read Data in Wild Bird Populations.}, journal = {Genome biology and evolution}, volume = {16}, number = {4}, pages = {}, pmid = {38489588}, issn = {1759-6653}, support = {/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Genomics ; *Genome ; Metagenomics ; Polymorphism, Single Nucleotide ; }, abstract = {Comprehensive characterization of structural variation in natural populations has only become feasible in the last decade. To investigate the population genomic nature of structural variation, reproducible and high-confidence structural variation callsets are first required. We created a population-scale reference of the genome-wide landscape of structural variation across 33 Nordic house sparrows (Passer domesticus). To produce a consensus callset across all samples using short-read data, we compare heuristic-based quality filtering and visual curation (Samplot/PlotCritic and Samplot-ML) approaches. We demonstrate that curation of structural variants is important for reducing putative false positives and that the time invested in this step outweighs the potential costs of analyzing short-read-discovered structural variation data sets that include many potential false positives. We find that even a lenient manual curation strategy (e.g. applied by a single curator) can reduce the proportion of putative false positives by up to 80%, thus enriching the proportion of high-confidence variants. Crucially, in applying a lenient manual curation strategy with a single curator, nearly all (>99%) variants rejected as putative false positives were also classified as such by a more stringent curation strategy using three additional curators. Furthermore, variants rejected by manual curation failed to reflect the expected population structure from SNPs, whereas variants passing curation did. Combining heuristic-based quality filtering with rapid manual curation of structural variants in short-read data can therefore become a time- and cost-effective first step for functional and population genomic studies requiring high-confidence structural variation callsets.}, } @article {pmid38627038, year = {2024}, author = {Girão, M and Alexandrino, DAM and Cao, W and Costa, I and Jia, Z and Carvalho, MF}, title = {Unveiling the culturable and non-culturable actinobacterial diversity in two macroalgae species from the northern Portuguese coast.}, journal = {Environmental microbiology}, volume = {26}, number = {4}, pages = {e16620}, doi = {10.1111/1462-2920.16620}, pmid = {38627038}, issn = {1462-2920}, support = {SFRH/BD/145646/2019//Fundação para a Ciência e a Tecnologia/ ; UIDB/04423/2020//European Regional Development Fund/ ; UIDP/04423/2020//European Regional Development Fund/ ; CEECIND/02968/2017//Fundação para a Ciência e Tecnologia/ ; //Fundo Social Europeu and Programa Operacional Potencial Humano/ ; C644915664-00000026//WP9 - Portuguese Blue Biobank under the Blue Economy Pact/ ; }, abstract = {Actinomycetota, associated with macroalgae, remains one of the least explored marine niches. The secondary metabolism of Actinomycetota, the primary microbial source of compounds relevant to biotechnology, continues to drive research into the distribution, dynamics, and metabolome of these microorganisms. In this study, we employed a combination of traditional cultivation and metagenomic analysis to investigate the diversity of Actinomycetota in two native macroalgae species from the Portuguese coast. We obtained and taxonomically identified a collection of 380 strains, which were distributed across 12 orders, 15 families, and 25 genera affiliated with the Actinomycetia class, with Streptomyces making up approximately 60% of the composition. Metagenomic results revealed the presence of Actinomycetota in both Chondrus crispus and Codium tomentosum datasets, with relative abundances of 11% and 2%, respectively. This approach identified 12 orders, 16 families, and 17 genera affiliated with Actinomycetota, with minimal overlap with the cultivation results. Acidimicrobiales emerged as the dominant actinobacterial order in both macroalgae, although no strain affiliated with this taxonomic group was successfully isolated. Our findings suggest that macroalgae represent a hotspot for Actinomycetota. The synergistic use of both culture-dependent and independent approaches proved beneficial, enabling the identification and recovery of not only abundant but also rare taxonomic members.}, } @article {pmid38627797, year = {2024}, author = {Lv, Y and Liu, X}, title = {Hemorrhagic cystitis induced by JC polyomavirus infection following COVID-19: a case report.}, journal = {BMC urology}, volume = {24}, number = {1}, pages = {87}, pmid = {38627797}, issn = {1471-2490}, abstract = {JC polyomavirus (JCPyV) is a human polyomavirus that can establish lifelong persistent infection in the majority of adults. It is typically asymptomatic in immunocompetent individuals. However, there is a risk of developing progressive multifocal leukoencephalopathy (PML) in immunocompromised or immunosuppressed patients. Though JCPyV commonly resides in the kidney-urinary tract, its involvement in urinary system diseases is extremely rare. Here, we reported a case of a 60-year-old male patient with coronavirus disease 2019 (COVID-19) infection who developed hemorrhagic cystitis after receiving treatment with nirmatrelvir 300 mg/ritonavir 100 mg quaque die (QD). Subsequent metagenomic next-generation sequencing (mNGS) confirmed the infection to be caused by JCPyV type 2. Then, human immunoglobulin (PH4) for intravenous injection at a dose of 25 g QD was administered to the patient. Three days later, the hematuria resolved. This case illustrates that in the setting of compromised host immune function, JCPyV is not limited to causing central nervous system diseases but can also exhibit pathogenicity in the urinary system. Moreover, mNGS technology facilitates rapid diagnosis of infectious etiology by clinical practitioners, contributing to precise treatment for patients.}, } @article {pmid38627687, year = {2024}, author = {Zhang, K and Paul, K and Jacobs, JP and Cockburn, MG and Bronstein, JM and Del Rosario, I and Ritz, B}, title = {Ambient long-term exposure to organophosphorus pesticides and the human gut microbiome: an observational study.}, journal = {Environmental health : a global access science source}, volume = {23}, number = {1}, pages = {41}, pmid = {38627687}, issn = {1476-069X}, support = {K01AG07204401/AG/NIA NIH HHS/United States ; R01ES031106/ES/NIEHS NIH HHS/United States ; }, abstract = {BACKGROUND: Organophosphorus pesticides (OP) have been associated with various human health conditions. Animal experiments and in-vitro models suggested that OP may also affect the gut microbiota. We examined associations between ambient chronic exposure to OP and gut microbial changes in humans.

METHODS: We recruited 190 participants from a community-based epidemiologic study of Parkinson's disease living in a region known for heavy agricultural pesticide use in California. Of these, 61% of participants had Parkinson's disease and their mean age was 72 years. Microbiome and predicted metagenome data were generated by 16S rRNA gene sequencing of fecal samples. Ambient long-term OP exposures were assessed using pesticide application records combined with residential addresses in a geographic information system. We examined gut microbiome differences due to OP exposures, specifically differences in microbial diversity based on the Shannon index and Bray-Curtis dissimilarities, and differential taxa abundance and predicted Metacyc pathway expression relying on regression models and adjusting for potential confounders.

RESULTS: OP exposure was not associated with alpha or beta diversity of the gut microbiome. However, the predicted metagenome was sparser and less evenly expressed among those highly exposed to OP (p = 0.04). Additionally, we found that the abundance of two bacterial families, 22 genera, and the predicted expression of 34 Metacyc pathways were associated with long-term OP exposure. These pathways included perturbed processes related to cellular respiration, increased biosynthesis and degradation of compounds related to bacterial wall structure, increased biosynthesis of RNA/DNA precursors, and decreased synthesis of Vitamin B1 and B6.

CONCLUSION: In support of previous animal studies and in-vitro findings, our results suggest that ambient chronic OP pesticide exposure alters gut microbiome composition and its predicted metabolism in humans.}, } @article {pmid38627615, year = {2024}, author = {Peres da Silva, R and Suphavilai, C and Nagarajan, N}, title = {MetageNN: a memory-efficient neural network taxonomic classifier robust to sequencing errors and missing genomes.}, journal = {BMC bioinformatics}, volume = {25}, number = {Suppl 1}, pages = {153}, pmid = {38627615}, issn = {1471-2105}, abstract = {BACKGROUND: With the rapid increase in throughput of long-read sequencing technologies, recent studies have explored their potential for taxonomic classification by using alignment-based approaches to reduce the impact of higher sequencing error rates. While alignment-based methods are generally slower, k-mer-based taxonomic classifiers can overcome this limitation, potentially at the expense of lower sensitivity for strains and species that are not in the database.

RESULTS: We present MetageNN, a memory-efficient long-read taxonomic classifier that is robust to sequencing errors and missing genomes. MetageNN is a neural network model that uses short k-mer profiles of sequences to reduce the impact of distribution shifts on error-prone long reads. Benchmarking MetageNN against other machine learning approaches for taxonomic classification (GeNet) showed substantial improvements with long-read data (20% improvement in F1 score). By utilizing nanopore sequencing data, MetageNN exhibits improved sensitivity in situations where the reference database is incomplete. It surpasses the alignment-based MetaMaps and MEGAN-LR, as well as the k-mer-based Kraken2 tools, with improvements of 100%, 36%, and 23% respectively at the read-level analysis. Notably, at the community level, MetageNN consistently demonstrated higher sensitivities than the previously mentioned tools. Furthermore, MetageNN requires < 1/4th of the database storage used by Kraken2, MEGAN-LR and MMseqs2 and is > 7× faster than MetaMaps and GeNet and > 2× faster than MEGAN-LR and MMseqs2.

CONCLUSION: This proof of concept work demonstrates the utility of machine-learning-based methods for taxonomic classification using long reads. MetageNN can be used on sequences not classified by conventional methods and offers an alternative approach for memory-efficient classifiers that can be optimized further.}, } @article {pmid38627246, year = {2024}, author = {Siqueira, JAM and Teixeira, DM and da Piedade, GJL and de Oliveira Souza, C and Moura, TCF and de Nazaré Miranda Bahia, M and Brasiliense, DM and de Sousa Santos, DSA and de Sa Morais, LLC and de Fátima Lobato da Silva, D and Carneiro, BS and da Costa Pinheiro, K and Sousa Junior, EC and Catete, CP and de Paula Souza E Guimarães, RJ and Ferreira, JL and Dias das Chagas Junior, W and Machado, RS and Tavares, FN and Resque, HR and Dos Santos Lobo, P and de Fátima Dos Santos Guerra, S and Soares, LS and da Silva, LD and Gabbay, YB}, title = {Environmental Health of Water Bodies From a Brazilian Amazon Metropolis Based On a Conventional and Metagenomic Approach.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxae101}, pmid = {38627246}, issn = {1365-2672}, abstract = {AIMS: The present study aimed to use a conventional and metagenomic approach to investigate the microbiological diversity of water bodies in a network of drainage channels and rivers located in the central area of the city of Belém, Northern Brazil, which is considered one of the largest cities in the Brazilian Amazon.

METHODS AND RESULTS: In eight of the analyzed points, both bacterial and viral microbiological indicators of environmental contamination, the physical-chemical and metals were assessed. The bacterial resistance genes, drug resistance mechanisms, and viral viability in the environment were also assessed. A total of 473 families of bacteria and 83 families of viruses were identified. Based on the analysis of metals, the levels of three metals (Cd, Fe, and Mn) were found to be above the recommended acceptable level by local legislation. The levels of the following three physicochemical parameters were also higher than recommended: Biochemical Oxygen Demand, dissolved oxygen, and turbidity. Sixty-three bacterial resistance genes that conferred resistance to 13 different classes of antimicrobials were identified. Further, five mechanisms of antimicrobial resistance were identified and viral viability in the environment was confirmed.

CONCLUSIONS: Intense human actions combined with a lack of public policies and poor environmental education of the population cause environmental degradation, especially in water bodies. Thus, urgent interventions are warranted to restore the quality of this precious and scarce asset worldwide.}, } @article {pmid38626494, year = {2024}, author = {Zhu, Y and Ke, M and Yu, Z and Lei, C and Liu, M and Yang, Y and Lu, T and Zhou, NY and Peijnenburg, WJGM and Tang, T and Qian, H}, title = {Combined effects of azoxystrobin and oxytetracycline on rhizosphere microbiota of Arabidopsis thaliana.}, journal = {Environment international}, volume = {186}, number = {}, pages = {108655}, doi = {10.1016/j.envint.2024.108655}, pmid = {38626494}, issn = {1873-6750}, abstract = {The rhizosphere is one of the key determinants of plant health and productivity. Mixtures of pesticides are commonly used in intensified agriculture. However, the combined mechanisms underlying their impacts on soil microbiota remain unknown. The present study revealed that the rhizosphere microbiota was more sensitive to azoxystrobin and oxytetracycline, two commonly used pesticides, than was the microbiota present in bulk soil. Moreover, the rhizosphere microbiota enhanced network complexity and stability and increased carbohydrate metabolism and xenobiotic biodegradation as well as the expression of metabolic genes involved in defence against pesticide stress. Co-exposure to azoxystrobin and oxytetracycline had antagonistic effects on Arabidopsis thaliana growth and soil microbial variation by recruiting organic-degrading bacteria and regulating ABC transporters to reduce pesticide uptake. Our study explored the composition and function of soil microorganisms through amplicon sequencing and metagenomic approaches, providing comprehensive insights into the synergistic effect of plants and rhizosphere microbiota on pesticides and contributing to our understanding of the ecological risks associated with pesticide use.}, } @article {pmid38626487, year = {2024}, author = {Zhou, Z and Shi, X and Bhople, P and Jiang, J and Chater, CCC and Yang, S and Perez-Moreno, J and Yu, F and Liu, D}, title = {Enhancing C and N turnover, functional bacteria abundance, and the efficiency of biowaste conversion using Streptomyces-Bacillus inoculation.}, journal = {Journal of environmental management}, volume = {358}, number = {}, pages = {120895}, doi = {10.1016/j.jenvman.2024.120895}, pmid = {38626487}, issn = {1095-8630}, abstract = {Microbial inoculation plays a significant role in promoting the efficiency of biowaste conversion. This study investigates the function of Streptomyces-Bacillus Inoculants (SBI) on carbon (C) and nitrogen (N) conversion, and microbial dynamics, during cow manure (10% and 20% addition) and corn straw co-composting. Compared to inoculant-free controls, inoculant application accelerated the compost's thermophilic stage (8 vs 15 days), and significantly increased compost total N contents (+47%) and N-reductase activities (nitrate reductase: +60%; nitrite reductase: +219%). Both bacterial and fungal community succession were significantly affected by DOC, urease, and NH4[+]-N, while the fungal community was also significantly affected by cellulase. The contribution rate of Cupriavidus to the physicochemical factors of compost was as high as 83.40%, but by contrast there were no significantly different contributions (∼60%) among the top 20 fungal genera. Application of SBI induced significant correlations between bacteria, compost C/N ratio, and catalase enzymes, indicative of compost maturation. We recommend SBI as a promising bio-composting additive to accelerate C and N turnover and high-quality biowaste maturation. SBI boosts organic cycling by transforming biowastes into bio-fertilizers efficiently. This highlights the potential for SBI application to improve plant growth and soil quality in multiple contexts.}, } @article {pmid38626484, year = {2024}, author = {Su, X and Zhang, L and Meng, H and Wang, H and Zhao, J and Sun, X and Song, X and Zhang, X and Mao, L}, title = {Long-term conservation tillage increase cotton rhizosphere sequestration of soil organic carbon by changing specific microbial CO2 fixation pathways in coastal saline soil.}, journal = {Journal of environmental management}, volume = {358}, number = {}, pages = {120743}, doi = {10.1016/j.jenvman.2024.120743}, pmid = {38626484}, issn = {1095-8630}, abstract = {Coastal saline soil is an important reserve resource for arable land globally. Data from 10 years of continuous stubble return and subsoiling experiments have revealed that these two conservation tillage measures significantly improve cotton rhizosphere soil organic carbon sequestration in coastal saline soil. However, the contribution of microbial fixation of atmospheric carbon dioxide (CO2) has remained unclear. Here, metagenomics and metabolomics analyses were used to deeply explore the microbial CO2 fixation process in rhizosphere soil of coastal saline cotton fields under long-term stubble return and subsoiling. Metagenomics analysis showed that stubble return and subsoiling mainly optimized CO2 fixing microorganism (CFM) communities by increasing the abundance of Acidobacteria, Gemmatimonadetes, and Chloroflexi, and improving composition diversity. Conjoint metagenomics and metabolomics analyses investigated the effects of stubble return and subsoiling on the reverse tricarboxylic acid (rTCA) cycle. The conversion of citrate to oxaloacetate was inhibited in the citrate cleavage reaction of the rTCA cycle. More citrate was converted to acetyl-CoA, which enhanced the subsequent CO2 fixation process of acetyl-CoA conversion to pyruvate. In the rTCA cycle reductive carboxylation reaction from 2-oxoglutarate to isocitrate, synthesis of the oxalosuccinate intermediate product was inhibited, with strengthened CO2 fixation involving the direct conversion of 2-oxoglutarate to isocitrate. The collective results demonstrate that stubble return and subsoiling optimizes rhizosphere CFM communities by increasing microbial diversity, in turn increasing CO2 fixation by enhancing the utilization of rTCA and 3-hydroxypropionate/4-hydroxybutyrate cycles by CFMs. These events increase the microbial CO2 fixation in the cotton rhizosphere, thereby promoting the accumulation of microbial biomass, and ultimately improving rhizosphere soil organic carbon. This study clarifies the impact of conservation tillage measures on microbial CO2 fixation in cotton rhizosphere of coastal saline soil, and provides fundamental data for the improvement of carbon sequestration in saline soil in agricultural ecosystems.}, } @article {pmid38626236, year = {2024}, author = {Remenyik, J and Csige, L and Dávid, P and Fauszt, P and Szilágyi-Rácz, AA and Szőllősi, E and Bacsó, ZR and Szepsy Jnr, I and Molnár, K and Rácz, C and Fidler, G and Kállai, Z and Stündl, L and Dobos, AC and Paholcsek, M}, title = {Exploring the interplay between the core microbiota, physicochemical factors, agrobiochemical cycles in the soil of the historic tokaj mád wine region.}, journal = {PloS one}, volume = {19}, number = {4}, pages = {e0300563}, doi = {10.1371/journal.pone.0300563}, pmid = {38626236}, issn = {1932-6203}, abstract = {A Hungarian survey of Tokaj-Mád vineyards was conducted. Shotgun metabarcoding was applied to decipher the microbial-terroir. The results of 60 soil samples showed that there were three dominant fungal phyla, Ascomycota 66.36% ± 15.26%, Basidiomycota 18.78% ± 14.90%, Mucoromycota 11.89% ± 8.99%, representing 97% of operational taxonomic units (OTUs). Mutual interactions between microbiota diversity and soil physicochemical parameters were revealed. Principal component analysis showed descriptive clustering patterns of microbial taxonomy and resistance gene profiles in the case of the four historic vineyards (Szent Tamás, Király, Betsek, Nyúlászó). Linear discriminant analysis effect size was performed, revealing pronounced shifts in community taxonomy based on soil physicochemical properties. Twelve clades exhibited the most significant shifts (LDA > 4.0), including the phyla Verrucomicrobia, Bacteroidetes, Chloroflexi, and Rokubacteria, the classes Acidobacteria, Deltaproteobacteria, Gemmatimonadetes, and Betaproteobacteria, the order Sphingomonadales, Hypomicrobiales, as well as the family Sphingomonadaceae and the genus Sphingomonas. Three out of the four historic vineyards exhibited the highest occurrences of the bacterial genus Bradyrhizobium, known for its positive influence on plant development and physiology through the secretion of steroid phytohormones. During ripening, the taxonomical composition of the soil fungal microbiota clustered into distinct groups depending on altitude, differences that were not reflected in bacteriomes. Network analyses were performed to unravel changes in fungal interactiomes when comparing postveraison and preharvest samples. In addition to the arbuscular mycorrhiza Glomeraceae, the families Mycosphaerellacae and Rhyzopodaceae and the class Agaricomycetes were found to have important roles in maintaining soil microbial community resilience. Functional metagenomics showed that the soil Na content stimulated several of the microbiota-related agrobiogeochemical cycles, such as nitrogen and sulphur metabolism; steroid, bisphenol, toluene, dioxin and atrazine degradation and the synthesis of folate.}, } @article {pmid38625103, year = {2024}, author = {Zhao, Z and Li, C and Huang, J and Yuan, X and Cui, Y and Liu, Y and Zhou, Y and Zhu, Z and Zhang, Z}, title = {Phlorizin Limits Bovine Viral Diarrhea Virus Infection in Mice via Regulating Gut Microbiota Composition.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.4c01228}, pmid = {38625103}, issn = {1520-5118}, abstract = {Phlorizin (PHZ) is one of the main pharmacologically active ingredients in Lithocarpus polystachyus. We have previously shown that PHZ inhibits the replication of bovine viral diarrhea virus (BVDV), but the exact antiviral mechanism, especially in vivo, is still unknown. Here, we further confirm that PHZ has good protective effects in BVDV-infected mice. We analyzed BVDV-induced CD3[+], CD4[+], and CD8[+] T cells among peripheral blood lymphocytes and found that PHZ significantly restored their percentage. Metagenomic analyses revealed that PHZ markedly improved the richness and diversity of intestinal microbiota and increased the abundance of potentially health-related microbes (families Lachnosipiraceae, Ruminococcaceae, and Oscillospiraceae). Specifically, the relative abundance of short chain fatty acid (SCFA)-producing bacteria, including Lachnospiraceae_UCG-006, unclassified_f_Ruminococcaceae, Oscillibacter, Intestinimonas, Blautia, and Lachnoclostridium increased significantly after PHZ treatment. Interestingly, BVDV-infected mice that received fecal microbiota from PHZ-treated mice (PHZ-FMT) had a significantly lower viral load in the duodenum and jejunum than untreated mice. Pathological lesions of duodenum and jejunum were also greatly reduced in the PHZ-FMT group, confirming a significant antiviral effect. These findings show that gut microbiota play an important role in PHZ's antiviral activity and suggest that their targeted intervention might be a promising endogenous strategy to prevent and control BVDV.}, } @article {pmid38625060, year = {2024}, author = {Garvin, ZK and Abades, SR and Trefault, N and Alfaro, FD and Sipes, K and Lloyd, KG and Onstott, TC}, title = {Prevalence of trace gas-oxidizing soil bacteria increases with radial distance from Polloquere hot spring within a high-elevation Andean cold desert.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae062}, pmid = {38625060}, issn = {1751-7370}, abstract = {High-elevation arid regions harbor microbial communities reliant on metabolic niches and flexibility to survive under biologically stressful conditions, including nutrient limitation that necessitates the utilization of atmospheric trace gases as electron donors. Geothermal springs present "oases" of microbial activity, diversity, and abundance by delivering water and substrates, including reduced gases. However, it is unknown whether these springs exhibit a gradient of effects, increasing the spatial reach of their impact on trace gas-oxidizing microbes in the surrounding soils. This study assessed whether proximity to Polloquere, a high-altitude geothermal spring in an Andean salt flat, alters the diversity and metabolic structure of nearby soil bacterial populations compared to the surrounding cold desert. Recovered DNA quantities and metagenomic analyses indicate that the spring represents an oasis for microbes in this challenging environment, supporting greater biomass with more diverse metabolic functions in proximal soils that declines sharply with radial distance from the spring. Despite the sharp decrease in biomass, potential rates of atmospheric hydrogen (H2) and carbon monoxide (CO) uptake increase away from the spring. Kinetic estimates suggest that this activity is due to high-affinity trace gas consumption, likely as a survival strategy for energy and/or carbon acquisition. These results demonstrate that Polloquere regulates a gradient of diverse microbial communities and metabolisms, culminating in increased activity of trace gas-oxidizers as the influence of the spring yields to that of the regional salt flat environment. This suggests that the spring holds local importance within the context of the broader salt flat and potentially represents a model ecosystem for other geothermal systems in high-altitude desert environments.}, } @article {pmid38625036, year = {2024}, author = {Srikrishna, D}, title = {Pentagon Found Daily, Metagenomic Detection of Novel Bioaerosol Threats to Be Cost-Prohibitive: Can Virtualization and AI Make It Cost-Effective?.}, journal = {Health security}, volume = {22}, number = {2}, pages = {108-129}, doi = {10.1089/hs.2023.0048}, pmid = {38625036}, issn = {2326-5108}, abstract = {In 2022, the Pentagon Force Protection Agency found threat agnostic detection of novel bioaerosol threats to be "not feasible for daily operations" due to the cost of reagents used for metagenomics, cost of sequencing instruments, and cost of labor for subject matter experts to analyze bioinformatics. Similar operational difficulties might extend to many of the 280,000 buildings (totaling 2.3 billion square feet) at 5,000 secure US Department of Defense military sites, 250 Navy ships, as well as many civilian buildings. These economic barriers can still be addressed in a threat agnostic manner by dynamically pooling samples from dry filter units, called spike-triggered virtualization, whereby pooling and sequencing depth are automatically modulated based on novel biothreats in the sequencing output. By running at a high average pooling factor, the daily and annual cost per dry filter unit can be reduced by 10 to 100 times depending on the chosen trigger thresholds. Artificial intelligence can further enhance the sensitivity of spike-triggered virtualization. The risk of infection during the 12- to 24-hour window between a bioaerosol incident and its detection remains, but in some cases it can be reduced by 80% or more with high-speed indoor air cleaning exceeding 12 air changes per hour, which is similar to the rate of air cleaning in passenger airplanes in flight. That level of air changes per hour or higher is likely to be cost-prohibitive using central heating ventilation and air conditioning systems, but it can be achieved economically by using portable air filtration in rooms with typical ceiling heights (less than 10 feet) for a cost of approximately $0.50 to $1 per square foot for do-it-yourself units and $2 to $5 per square foot for high-efficiency particulate air filters.}, } @article {pmid38624235, year = {2024}, author = {Osborn, LJ and Fissel, J and Gomez, S and Mestas, J and Flores-Vazquez, J and Lee, J and Hakimjavadi, H and Costales, C and Dien Bard, J}, title = {Development of an automated amplicon-based next-generation sequencing pipeline for rapid detection of bacteria and fungi directly from clinical specimens.}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {e0174923}, doi = {10.1128/jcm.01749-23}, pmid = {38624235}, issn = {1098-660X}, abstract = {UNLABELLED: The timely identification of microbial pathogens is essential to guide targeted antimicrobial therapy and ultimately, successful treatment of an infection. However, the yield of standard microbiology testing (SMT) is directly related to the duration of antecedent antimicrobial therapy as SMT culture methods are dependent on the recovery of viable organisms, the fastidious nature of certain pathogens, and other pre-analytic factors. In the last decade, metagenomic next-generation sequencing (mNGS) has been successfully utilized as a diagnostic tool for various applications within the clinical laboratory. However, mNGS is resource, time, and labor-intensive-requiring extensive laborious preliminary benchwork, followed by complex bioinformatic analysis. We aimed to address these shortcomings by developing a largely Automated targeted Metagenomic next-generation sequencing (tmNGS) PipeLine for rapId inFectIous disEase Diagnosis (AMPLIFIED) to detect bacteria and fungi directly from clinical specimens. Therefore, AMPLIFIED may serve as an adjunctive approach to complement SMT. This tmNGS pipeline requires less than 1 hour of hands-on time before sequencing and less than 2 hours of total processing time, including bioinformatic analysis. We performed tmNGS on 50 clinical specimens with concomitant cultures to assess feasibility and performance in the hospital laboratory. Of the 50 specimens, 34 (68%) were from true clinical infections. Specimens from cases of true infection were more often tmNGS positive compared to those from the non-infected group (82.4% vs 43.8%, respectively, P = 0.0087). Overall, the clinical sensitivity of AMPLIFIED was 54.6% with 85.7% specificity, equating to 70.6% and 75% negative and positive predictive values, respectively. AMPLIFIED represents a rapid supplementary approach to SMT; the typical time from specimen receipt to identification of potential pathogens by AMPLIFIED is roughly 24 hours which is markedly faster than the days, weeks, and months required to recover bacterial, fungal, and mycobacterial pathogens by culture, respectively.

IMPORTANCE: To our knowledge, this represents the first application of an automated sequencing and bioinformatics pipeline in an exclusively pediatric population. Next-generation sequencing is time-consuming, labor-intensive, and requires experienced personnel; perhaps contributing to hesitancy among clinical laboratories to adopt such a test. Here, we report a strong case for use by removing these barriers through near-total automation of our sequencing pipeline.}, } @article {pmid38624222, year = {2024}, author = {Ali, R and Chaluvadi, SR and Wang, X and Hazzouri, KM and Sudalaimuthuasari, N and Rafi, M and Al-Nuaimi, M and Sasi, S and Antepenko, E and Bennetzen, JL and Amiri, KMA}, title = {Microbiome properties in the root nodules of Prosopis cineraria, a leguminous desert tree.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0361723}, doi = {10.1128/spectrum.03617-23}, pmid = {38624222}, issn = {2165-0497}, abstract = {We conducted a comprehensive analysis of the total microbiome and transcriptionally active microbiome communities in the roots and root nodules of Prosopis cineraria, an important leguminous tree in arid regions of many Asian countries. Mature P. cineraria trees growing in the desert did not exhibit any detected root nodules. However, we observed root nodules on the roots of P. cineraria growing on a desert farm and on young plants growing in a growth chamber, when inoculated with rhizosphere soil, including with rhizosphere soil from near desert tree roots that had no nodules. Compared to nearby soil, non-nodulated roots were enriched with Actinobacteria (e.g., Actinophytocola sp.), whereas root nodules sampled from the desert farm and growth chamber had abundant Alphaproteobacteria (e.g., Ensifer sp.). These nodules yielded many microbes in addition to such nitrogen-fixing bacteria as Ensifer and Sinorhizobium species. Significant differences exist in the composition and abundance of microbial isolates between the nodule surface and the nodule endosphere. Shotgun metagenome analysis of nodule endospheres revealed that the root nodules comprised over 90% bacterial DNA, whereas metatranscriptome analysis showed that the plant produces vastly more transcripts than the microbes in these nodules. Control inoculations demonstrated that four out of six Rhizobium, Agrobacterium, or Ensifer isolates purified from P. cineraria nodules produced nodules in the roots of P. cineraria seedlings under greenhouse conditions. The best nodulation was achieved when seedlings were inoculated with a mixture of those bacterial strains. Though root nodulation could be achieved under water stress conditions, nodule number and nodule biomass increased with copious water availability. .IMPORTANCEMicrobial communities were investigated in roots and root nodules of Prosopis cineraria, a leguminous tree species in arid Asian regions that is responsible for exceptionally important contributions to soil fertility in these dramatically dry locations. Soil removed from regions near nodule-free roots on these mature plants contained an abundance of bacteria with the genetic ability to generate nodules and fix nitrogen but did not normally nodulate in their native rhizosphere environment, suggesting a very different co-evolved relationship than that observed for herbaceous legumes. The relative over-expression of the low-gene-density plant DNA compared to the bacterial DNA in the nodules was also unexpected, indicating a very powerful induction of host genetic contributions within the nodule. Finally, the water dependence of nodulation in inoculated seedlings suggested a possible link between early seedling growth (before a deep root system can be developed) and the early development of nitrogen-fixing capability.}, } @article {pmid38623900, year = {2024}, author = {Zhang, Y and Lo, KL and Liman, AN and Feng, XP and Ye, W}, title = {Tongue-Coating Microbial and Metabolic Characteristics in Halitosis.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345241230067}, doi = {10.1177/00220345241230067}, pmid = {38623900}, issn = {1544-0591}, abstract = {Halitosis is a common oral condition, which leads to social embarrassment and affects quality of life. Cumulative evidence has suggested the association of tongue-coating microbiome with the development of intraoral halitosis. The dynamic variations of tongue-coating microbiota and metabolites in halitosis have not been fully elucidated. Therefore, the present study aimed to determine the tongue-coating microbial and metabolic characteristics in halitosis subjects without other oral diseases using metagenomics and metabolomics analysis. The participants underwent oral examination, halitosis assessment, and tongue-coating sample collection for the microbiome and metabolome analysis. It was found that the microbiota richness and diversity were significantly elevated in the halitosis group. Furthermore, species from Actinomyces, Prevotella, Veillonella, and Solobacterium were significantly more abundant in the halitosis group. However, the Rothia and Streptococcus species exhibited opposite tendencies. Eleven Kyoto Encyclopedia of Genes and Genomes pathways were significantly enriched in the halitosis tongue coatings, including cysteine and methionine metabolism. Functional genes related to sulfur, indole, skatole, and cadaverine metabolic processes (such as serA, metH, metK and dsrAB) were identified to be more abundant in the halitosis samples. The metabolome analysis revealed that indole-3-acetic, ornithine, and L-tryptophan were significantly elevated in the halitosis samples. Furthermore, it was observed that the values of volatile sulfur compounds and indole-3-acetic abundances were positively correlated. The multiomics analysis identified the metagenomic and metabolomic characteristics to differentiate halitosis from healthy individuals using the least absolute shrinkage and selection operator logistic regression and random forest classifier. A total of 19 species and 39 metabolites were identified as features in halitosis patients, which included indole-3-acetic acid, Bacillus altitudinis, Candidatus Saccharibacteria, and Actinomyces species. In conclusion, an evident shift in microbiome and metabolome characteristics was observed in the halitosis tongue coating, which may have a potential etiological significance and provide novel insights into the mechanism for halitosis.}, } @article {pmid38623014, year = {2024}, author = {Wang, Q and Yang, JH and Chen, X and Zhang, YJ and Zhu, XY and Li, XF and Su, J and Sa, CRG and Yang, B and Lu, GP and Xu, Y}, title = {[Metagenomic next-generation sequencing-based retrospective investigation of the drug resistance sites of mycoplasma pneumoniae in children].}, journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics}, volume = {62}, number = {5}, pages = {457-461}, doi = {10.3760/cma.j.cn112140-20240105-00019}, pmid = {38623014}, issn = {0578-1310}, support = {2021YFC2701800, 2021YFC2701801//National Strategic Plan for Research and Development/ ; }, abstract = {Objective: To analyze the drug-resistant gene loci of Mycoplasma pneumoniae (MP) using metagenomic next-generation sequencing (mNGS). Methods: From November 2022 to October 2023, 697 clinical samples (including sputum, alveolar lavage fluid and blood) of 686 children with Mycoplasma pneumoniae positive detected by mNGS were retrospectively analyzed. Samples were divided into intensive care unit (ICU) group and non-ICU group, Chi-square test was used to compare groups, and Mann-Kendall trend test was used to analyze the change trend of the detection rate of drug resistance gene loci over time. Results: Of the 697 samples, 164 were from the ICU group and 533 were from the non-ICU group. The detection rate of Mycoplasma pneumoniae resistance gene was 44.3% (309/697), and all detected drug-resistant gene loci of MP were A2063G. The detection rate of Mycoplasma pneumoniae in ICU group was 50.0% (82/164), and the detection rates of Mycoplasma pneumoniae resistance gene loci in sputum, alveolus lavage fluid and blood samples were 75.0% (18/24) and 48.4% (62/128), respectively. The detection rate in sputum was higher than alveolus lavage fluid samples (χ[2]=5.72,P=0.017). The detection rate of Mycoplasma pneumoniae in non-ICU group was 42.6% (227/533), the detection rate of Mycoplasma pneumoniae resistance gene loci in sputum and alveolar lavage fluid was 40.0% (16/40), 44.3% (201/454), and no detection rate in blood samples (0/12). There was no significant difference in the detection rate of alveolar lavage fluid and sputum (χ[2]=0.27, P=0.602). From November 2022 to October 2023, the detection rate of submitted samples showed an increasing trend month by month (overall: Z=3.99, ICU inspection group: Z=2.93, non-ICU group: Z=3.01, all P<0.01). Among the bacteria commonly detected with Mycoplasma pneumoniae, Streptococcus pneumoniae accounted for the highest proportion, the detection rate was 15.5% (108/697), and Epstein-Barr virus accounted for the highest proportion of 17.6% (123/697). Conclusions: From November 2022 to October 2023, the detection rate of Mycoplasma pneumoniae drug resistance gene loci showed an increasing trend. The detection rate of drug resistance gene loci in sputum samples of ICU group was higher than alveolus lavage fluid. No new drug resistance site were detected.}, } @article {pmid38622738, year = {2024}, author = {Wu, LY and Wijesekara, Y and Piedade, GJ and Pappas, N and Brussaard, CPD and Dutilh, BE}, title = {Benchmarking bioinformatic virus identification tools using real-world metagenomic data across biomes.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {97}, pmid = {38622738}, issn = {1474-760X}, support = {Consolidator grant 865694//H2020 European Research Council/ ; Consolidator grant 865694//H2020 European Research Council/ ; 955974//H2020 Marie Skłodowska-Curie Actions/ ; grant ALWPP.2016.019//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; grant ALWPP.2016.019//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; EXC 2051 - Project-ID 390713860//Deutsche Forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: As most viruses remain uncultivated, metagenomics is currently the main method for virus discovery. Detecting viruses in metagenomic data is not trivial. In the past few years, many bioinformatic virus identification tools have been developed for this task, making it challenging to choose the right tools, parameters, and cutoffs. As all these tools measure different biological signals, and use different algorithms and training and reference databases, it is imperative to conduct an independent benchmarking to give users objective guidance.

RESULTS: We compare the performance of nine state-of-the-art virus identification tools in thirteen modes on eight paired viral and microbial datasets from three distinct biomes, including a new complex dataset from Antarctic coastal waters. The tools have highly variable true positive rates (0-97%) and false positive rates (0-30%). PPR-Meta best distinguishes viral from microbial contigs, followed by DeepVirFinder, VirSorter2, and VIBRANT. Different tools identify different subsets of the benchmarking data and all tools, except for Sourmash, find unique viral contigs. Performance of tools improved with adjusted parameter cutoffs, indicating that adjustment of parameter cutoffs before usage should be considered.

CONCLUSIONS: Together, our independent benchmarking facilitates selecting choices of bioinformatic virus identification tools and gives suggestions for parameter adjustments to viromics researchers.}, } @article {pmid38622723, year = {2024}, author = {Gan, M and Zhang, Y and Yan, G and Wang, Y and Lu, G and Wu, B and Chen, W and Zhou, W}, title = {Antimicrobial resistance prediction by clinical metagenomics in pediatric severe pneumonia patients.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {23}, number = {1}, pages = {33}, pmid = {38622723}, issn = {1476-0711}, support = {2021YFC2701800 and 2021YFC2701805//National Key Research and Development Program of China/ ; 2022YFC2703603//National Key Research and Development Program of China/ ; 22Y11902700//the Science and Technology Commission of Shanghai Municipality/ ; MTP2022A014//the China Primary Health Care Foundation/ ; 2023ZDFC0103//the Shanghai Municipal Health System key supports discipline projects/ ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a major threat to children's health, particularly in respiratory infections. Accurate identification of pathogens and AMR is crucial for targeted antibiotic treatment. Metagenomic next-generation sequencing (mNGS) shows promise in directly detecting microorganisms and resistance genes in clinical samples. However, the accuracy of AMR prediction through mNGS testing needs further investigation for practical clinical decision-making.

METHODS: We aimed to evaluate the performance of mNGS in predicting AMR for severe pneumonia in pediatric patients. We conducted a retrospective analysis at a tertiary hospital from May 2022 to May 2023. Simultaneous mNGS and culture were performed on bronchoalveolar lavage fluid samples obtained from pediatric patients with severe pneumonia. By comparing the results of mNGS detection of microorganisms and antibiotic resistance genes with those of culture, sensitivity, specificity, positive predictive value, and negative predictive value were calculated.

RESULTS: mNGS detected bacterial in 71.7% cases (86/120), significantly higher than culture (58/120, 48.3%). Compared to culture, mNGS demonstrated a sensitivity of 96.6% and a specificity of 51.6% in detecting pathogenic microorganisms. Phenotypic susceptibility testing (PST) of 19 antibiotics revealed significant variations in antibiotics resistance rates among different bacteria. Sensitivity prediction of mNGS for carbapenem resistance was higher than penicillins and cephalosporin (67.74% vs. 28.57%, 46.15%), while specificity showed no significant difference (85.71%, 75.00%, 75.00%). mNGS also showed a high sensitivity of 94.74% in predicting carbapenem resistance in Acinetobacter baumannii.

CONCLUSIONS: mNGS exhibits variable predictive performance among different pathogens and antibiotics, indicating its potential as a supplementary tool to conventional PST. However, mNGS currently cannot replace conventional PST.}, } @article {pmid38621967, year = {2024}, author = {Wang, ZH and Liu, S and Yang, G and Lu, ZY and Zhu, RQ and Li, Y and Shen, Y and Kang, LP and Chen, ML}, title = {[Effects of organic fertilizer from traditional Chinese medicine residues on growth and soil microbial community of Salvia miltiorrhiza by metagenomic technique].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {49}, number = {5}, pages = {1206-1216}, doi = {10.19540/j.cnki.cjcmm.20231213.101}, pmid = {38621967}, issn = {1001-5302}, abstract = {Soil microbiome is a key evaluation index of soil health. Previous studies have shown that organic fertilizer from traditional Chinese medicine(TCM)residues can improve the yield and quality of cultivated traditional Chinese medicinal materials. However, there are few reports on the effects of organic fertilizer from TCM residues on soil microbiome. Therefore, on the basis of evaluating the effects of organic fertilizer from TCM residues on the yield and quality of cultivated Salvia miltiorrhiza, the metagenomic sequencing technique was used to study the effects of organic fertilizer from TCM residues on rhizosphere microbiome community and function of cultivated S. miltiorrhiza. The results showed that:(1) the application of organic fertilizer from TCM residues promoted the growth of S. miltiorrhiza and the accumulation of active components, and the above-ground and underground dry weight and fresh weight of S. miltiorrhiza increased by 371.4%, 288.3%, 313.4%, and 151.9%. The increases of rosmarinic acid and salvianolic acid B were 887.0% and 183.0%.(2)The application of organic fertilizer from TCM residues significantly changed the rhizosphere bacterial and fungal community structures, and the microbial community composition was significantly different.(3)The relative abundance of soil-beneficial bacteria, such as Nitrosospira multiformis, Bacillus subtilis, Lysobacter enzymogenes, and Trichoderma was significantly increased by the application of organic fertilizer from TCM residues.(4)KEGG function prediction analysis showed that metabolism-related microorganisms were more easily enriched in the soil environment after organic fertilizer application. The abundance of functional genes related to nitrification and denitrification could also be increased after the application of organic fertilizer from TCM residues. The results of this study provide guidance for the future application of organic fertilizer from TCM residues in the cultivation of traditio-nal Chinese medicinal materials and enrich the content of green cultivation technology of traditional Chinese medicinal materials.}, } @article {pmid38621394, year = {2024}, author = {Paull, JS and Petros, BA and Brock-Fisher, TM and Jalbert, SA and Selser, VM and Messer, KS and Dobbins, ST and DeRuff, KC and Deng, D and Springer, M and Sabeti, PC}, title = {Optimisation and evaluation of viral genomic sequencing of SARS-CoV-2 rapid diagnostic tests: a laboratory and cohort-based study.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2666-5247(23)00399-3}, pmid = {38621394}, issn = {2666-5247}, abstract = {BACKGROUND: Sequencing of SARS-CoV-2 from rapid diagnostic tests (RDTs) can bolster viral genomic surveillance efforts; however, approaches to maximise and standardise pathogen genome recovery from RDTs remain underdeveloped. We aimed to systematically optimise the elution of genetic material from RDT components and to evaluate the efficacy of RDT sequencing for outbreak investigation.

METHODS: In this laboratory and cohort-based study we seeded RDTs with inactivated SARS-CoV-2 to optimise the elution of genomic material from RDT lateral flow strips. We measured the effect of changes in buffer type, time in buffer, and rotation on PCR cycle threshold (Ct) value. We recruited individuals older than 18 years residing in the greater Boston area, MA, USA, from July 18 to Nov 5, 2022, via email advertising to students and staff at Harvard University, MA, USA, and via broad social media advertising. All individuals recruited were within 5 days of a positive diagnostic test for SARS-CoV-2; no other relevant exclusion criteria were applied. Each individual completed two RDTs and one PCR swab. On Dec 29, 2022, we also collected RDTs from a convenience sample of individuals who were positive for SARS-CoV-2 and associated with an outbreak at a senior housing facility in MA, USA. We extracted all returned PCR swabs and RDT components (ie, swab, strip, or buffer); samples with a Ct of less than 40 were subject to amplicon sequencing. We compared the efficacy of elution and sequencing across RDT brands and components and used RDT-derived sequences to infer transmission links within the outbreak at the senior housing facility. We conducted metagenomic sequencing of negative RDTs from symptomatic individuals living in the senior housing facility.

FINDINGS: Neither elution duration of greater than 10 min nor rotation during elution impacted viral titres. Elution in Buffer AVL (Ct=31·4) and Tris-EDTA Buffer (Ct=30·8) were equivalent (p=0·34); AVL outperformed elution in lysis buffer and 50% lysis buffer (Ct=40·0, p=0·0029 for both) as well as Universal Viral Transport Medium (Ct=36·7, p=0·079). Performance of RDT strips was poorer than that of matched PCR swabs (mean Ct difference 10·2 [SD 4·3], p<0·0001); however, RDT swabs performed similarly to PCR swabs (mean Ct difference 4·1 [5·2], p=0·055). No RDT brand significantly outperformed another. Across sample types, viral load predicted the viral genome assembly length. We assembled greater than 80% complete genomes from 12 of 17 RDT-derived swabs, three of 18 strips, and four of 11 residual buffers. We generated outbreak-associated SARS-CoV-2 genomes using both amplicon and metagenomic sequencing and identified multiple introductions of the virus that resulted in downstream transmission.

INTERPRETATION: RDT-derived swabs are a reasonable alternative to PCR swabs for viral genomic surveillance and outbreak investigation. RDT-derived lateral flow strips yield accurate, but significantly fewer, viral reads than matched PCR swabs. Metagenomic sequencing of negative RDTs can identify viruses that might underlie patient symptoms.

FUNDING: The National Science Foundation, the Hertz Foundation, the National Institute of General Medical Sciences, Harvard Medical School, the Howard Hughes Medical Institute, the US Centers for Disease Control and Prevention, the Broad Institute and the National Institute of Allergy and Infectious Diseases.}, } @article {pmid38622589, year = {2024}, author = {Gao, J and Yang, Y and Xiang, X and Zheng, H and Yi, X and Wang, F and Liang, Z and Chen, D and Shi, W and Wang, L and Wu, D and Feng, S and Huang, Q and Li, X and Shu, W and Chen, R and Zhong, N and Wang, Z}, title = {Human genetic associations of the airway microbiome in chronic obstructive pulmonary disease.}, journal = {Respiratory research}, volume = {25}, number = {1}, pages = {165}, pmid = {38622589}, issn = {1465-993X}, abstract = {Little is known about the relationships between human genetics and the airway microbiome. Deeply sequenced airway metagenomics, by simultaneously characterizing the microbiome and host genetics, provide a unique opportunity to assess the microbiome-host genetic associations. Here we performed a co-profiling of microbiome and host genetics with the identification of over 5 million single nucleotide polymorphisms (SNPs) through deep metagenomic sequencing in sputum of 99 chronic obstructive pulmonary disease (COPD) and 36 healthy individuals. Host genetic variation was the most significant factor associated with the microbiome except for geography and disease status, with its top 5 principal components accounting for 12.11% of the microbiome variability. Within COPD individuals, 113 SNPs mapped to candidate genes reported as genetically associated with COPD exhibited associations with 29 microbial species and 48 functional modules (P < 1 × 10[-5]), where Streptococcus salivarius exhibits the strongest association to SNP rs6917641 in TBC1D32 (P = 9.54 × 10[-8]). Integration of concurrent host transcriptomic data identified correlations between the expression of host genes and their genetically-linked microbiome features, including NUDT1, MAD1L1 and Veillonella parvula, TTLL9 and Stenotrophomonas maltophilia, and LTA4H and Haemophilus influenzae. Mendelian randomization analyses revealed a potential causal link between PARK7 expression and microbial type III secretion system, and a genetically-mediated association between COPD and increased relative abundance of airway Streptococcus intermedius. These results suggest a previously underappreciated role of host genetics in shaping the airway microbiome and provide fresh hypotheses for genetic-based host-microbiome interactions in COPD.}, } @article {pmid38622147, year = {2024}, author = {Yu, M and Zhang, M and Zeng, R and Cheng, R and Zhang, R and Hou, Y and Kuang, F and Feng, X and Dong, X and Li, Y and Shao, Z and Jin, M}, title = {Diversity and potential host-interactions of viruses inhabiting deep-sea seamount sediments.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3228}, pmid = {38622147}, issn = {2041-1723}, support = {41976084//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Seamounts are globally distributed across the oceans and form one of the major oceanic biomes. Here, we utilized combined analyses of bulk metagenome and virome to study viral communities in seamount sediments in the western Pacific Ocean. Phylogenetic analyses and the protein-sharing network demonstrate extensive diversity and previously unknown viral clades. Inference of virus-host linkages uncovers extensive interactions between viruses and dominant prokaryote lineages, and suggests that viruses play significant roles in carbon, sulfur, and nitrogen cycling by compensating or augmenting host metabolisms. Moreover, temperate viruses are predicted to be prevalent in seamount sediments, which tend to carry auxiliary metabolic genes for host survivability. Intriguingly, the geographical features of seamounts likely compromise the connectivity of viral communities and thus contribute to the high divergence of viral genetic spaces and populations across seamounts. Altogether, these findings provides knowledge essential for understanding the biogeography and ecological roles of viruses in globally widespread seamounts.}, } @article {pmid38621316, year = {2024}, author = {Wang, S and Nie, W and Gu, Q and Wang, X and Yang, D and Li, H and Wang, P and Liao, W and Huang, J and Yuan, Q and Zhou, S and Ahmad, I and Kotaro, K and Chen, G and Zhu, B}, title = {Spread of antibiotic resistance genes in drinking water reservoirs: Insights from a deep metagenomic study using a curated database.}, journal = {Water research}, volume = {256}, number = {}, pages = {121572}, doi = {10.1016/j.watres.2024.121572}, pmid = {38621316}, issn = {1879-2448}, abstract = {The exploration of antibiotic resistance genes (ARGs) in drinking water reservoirs is an emerging field. Using a curated database, we enhanced the ARG detection and conducted a comprehensive analysis using 2.2 Tb of deep metagenomic sequencing data to determine the distribution of ARGs across 16 drinking water reservoirs and associated environments. Our findings reveal a greater diversity of ARGs in sediments than in water, underscoring the importance of extensive background surveys. Crucial ARG carriers-specifically Acinetobacter, Pseudomonas, and Mycobacterium were identified in drinking water reservoirs. Extensive analysis of the data uncovered a considerable concern for drinking water safety, particularly in regions reliant on river sources. Mobile genetic elements have been found to contribute markedly to the propagation of ARGs. The results of this research suggest that the establishment of drinking water reservoirs for supplying raw water may be an effective strategy for alleviating the spread of water-mediated ARGs.}, } @article {pmid38620144, year = {2024}, author = {Eme, L and Tamarit, D}, title = {Microbial Diversity and Open Questions about the Deep Tree of Life.}, journal = {Genome biology and evolution}, volume = {16}, number = {4}, pages = {}, doi = {10.1093/gbe/evae053}, pmid = {38620144}, issn = {1759-6653}, support = {803151/ERC_/European Research Council/International ; }, abstract = {In this perspective, we explore the transformative impact and inherent limitations of metagenomics and single-cell genomics on our understanding of microbial diversity and their integration into the Tree of Life. We delve into the key challenges associated with incorporating new microbial lineages into the Tree of Life through advanced phylogenomic approaches. Additionally, we shed light on enduring debates surrounding various aspects of the microbial Tree of Life, focusing on recent advances in some of its deepest nodes, such as the roots of bacteria, archaea, and eukaryotes. We also bring forth current limitations in genome recovery and phylogenomic methodology, as well as new avenues of research to uncover additional key microbial lineages and resolve the shape of the Tree of Life.}, } @article {pmid38619550, year = {2024}, author = {Wang, X and Guo, H and Wang, J and He, P and Kuzyakov, Y and Ma, M and Ling, N}, title = {Microbial phosphorus-cycling genes in soil under global change.}, journal = {Global change biology}, volume = {30}, number = {4}, pages = {e17281}, doi = {10.1111/gcb.17281}, pmid = {38619550}, issn = {1365-2486}, support = {lzujbky-2022-ct04//Fundamental Research Funds for the Central Universities/ ; 42277100//National Natural Science Foundation of China/ ; }, abstract = {The ongoing climate change on the Tibetan Plateau, leading to warming and precipitation anomalies, modifies phosphorus (P) cycling in alpine meadow soils. However, the interactions and cascading effects of warming and precipitation changes on the key "extracellular" and "intracellular" P cycling genes (PCGs) of bacteria are largely unknown for these P-limited ecosystems. We used metagenomics to analyze the individual and combined effects of warming and altered precipitation on soil PCGs and P transformation in a manipulation experiment. Warming and increased precipitation raised Olsen-P (bioavailable P, AP) by 13% and 20%, respectively, mainly caused by augmented hydrolysis of organic P compounds (NaOH-Po). The decreased precipitation reduced soil AP by 5.3%. The richness and abundance of the PCGs' community in soils on the cold Tibetan plateau were more sensitive to warming than altered precipitation. The abundance of PCGs and P cycling processes decreased under the influence of individual climate change factors (i.e., warming and altered precipitation alone), except for the warming combined with increased precipitation. Pyruvate metabolism, phosphotransferase system, oxidative phosphorylation, and purine metabolism (all "intracellular" PCG) were closely correlated with P pools under climate change conditions. Specifically, warming recruited bacteria with the phoD and phoX genes, which encode enzymes responsible for phosphoester hydrolysis (extracellular P cycling), strongly accelerated organic P mineralization and so, directly impacted P bioavailability in alpine soil. The interactions between warming and altered precipitation profoundly influenced the PCGs' community and facilitated microbial adaptation to these environmental changes. Warming combined with increased precipitation compensated for the detrimental impacts of the individual climate change factors on PCGs. In conclusion, warming combined with rising precipitation has boosting effect on most P-related functions, leading to the acceleration of P cycling within microbial cells and extracellularly, including mineralization and more available P release for microorganisms and plants in alpine soils.}, } @article {pmid38618705, year = {2024}, author = {Sarkar, S and Anyaso-Samuel, S and Qiu, P and Datta, S}, title = {Multiblock partial least squares and rank aggregation: Applications to detection of bacteriophages associated with antimicrobial resistance in the presence of potential confounding factors.}, journal = {Statistics in medicine}, volume = {}, number = {}, pages = {}, doi = {10.1002/sim.10058}, pmid = {38618705}, issn = {1097-0258}, abstract = {Urban environments, characterized by bustling mass transit systems and high population density, host a complex web of microorganisms that impact microbial interactions. These urban microbiomes, influenced by diverse demographics and constant human movement, are vital for understanding microbial dynamics. We explore urban metagenomics, utilizing an extensive dataset from the Metagenomics & Metadesign of Subways & Urban Biomes (MetaSUB) consortium, and investigate antimicrobial resistance (AMR) patterns. In this pioneering research, we delve into the role of bacteriophages, or "phages"-viruses that prey on bacteria and can facilitate the exchange of antibiotic resistance genes (ARGs) through mechanisms like horizontal gene transfer (HGT). Despite their potential significance, existing literature lacks a consensus on their significance in ARG dissemination. We argue that they are an important consideration. We uncover that environmental variables, such as those on climate, demographics, and landscape, can obscure phage-resistome relationships. We adjust for these potential confounders and clarify these relationships across specific and overall antibiotic classes with precision, identifying several key phages. Leveraging machine learning tools and validating findings through clinical literature, we uncover novel associations, adding valuable insights to our comprehension of AMR development.}, } @article {pmid38618581, year = {2024}, author = {Cheng, X and Li, T and Wu, F and Liu, D}, title = {Clinical Manifestation, mNGS Based Diagnosis and Treatment of Pulmonary Mucormycosis with Rhizopus delemar in a Diabetic Patient.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {1379-1384}, pmid = {38618581}, issn = {1178-6973}, abstract = {Pulmonary mucormycosis is a severe and often fatal disease that commonly affects patients with underlying conditions, such as diabetes. Early diagnosis and appropriate treatment are crucial for improving survival rates. However, clinical diagnosis remains challenging due to difficulty in obtaining etiological evidence. In this particular case, the patient presented with a cough-producing bloody sputum, and a chest CT revealed lesions in the right upper lobe of the lung. The patient was ultimately diagnosed with pulmonary mucormycosis caused by Rhizopus delemar through clinical bronchoscopy biopsy and metagenomic next-generation sequencing (mNGS) analysis of bronchoalveolar lavage fluid sample. Subsequently, antifungal therapy using the less toxic Amphotericin B cholesterol Organosulfate complex was initiated, improving the patient's condition. In conclusion, our findings underscore the potential of mNGS to provide an accurate and rapid etiological diagnosis of pulmonary mucormycosis, offering a foundation for treatment.}, } @article {pmid38617453, year = {2024}, author = {Chen, SJ and Zhang, DY and Wu, X and Zhang, FM and Cui, BT and Huang, YH and Zhang, ZL and Wang, R and Bai, FH}, title = {Washed microbiota transplantation for Crohn's disease: A metagenomic, metatranscriptomic, and metabolomic-based study.}, journal = {World journal of gastroenterology}, volume = {30}, number = {11}, pages = {1572-1587}, pmid = {38617453}, issn = {2219-2840}, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is a promising therapeutic approach for treating Crohn's disease (CD). The new method of FMT, based on the automatic washing process, was named as washed microbiota transplantation (WMT). Most existing studies have focused on observing the clinical phenomena. However, the mechanism of action of FMT for the effective management of CD-particularly in-depth multi-omics analysis involving the metagenome, metatranscriptome, and metabolome-has not yet been reported.

AIM: To assess the efficacy of WMT for CD and explore alterations in the microbiome and metabolome in response to WMT.

METHODS: We conducted a prospective, open-label, single-center clinical study. Eleven CD patients underwent WMT. Their clinical responses (defined as a decrease in their CD Activity Index score of > 100 points) and their microbiome (metagenome, metatranscriptome) and metabolome profiles were evaluated three months after the procedure.

RESULTS: Seven of the 11 patients (63.6%) showed an optimal clinical response three months post-WMT. Gut microbiome diversity significantly increased after WMT, consistent with improved clinical symptoms. Comparison of the metagenome and metatranscriptome analyses revealed consistent alterations in certain strains, such as Faecalibacterium prausnitzii, Roseburia intestinalis, and Escherichia coli. In addition, metabolomics analyses demonstrated that CD patients had elevated levels of various amino acids before treatment compared to the donors. However, levels of vital amino acids that may be associated with disease progression (e.g., L-glutamic acid, gamma-glutamyl-leucine, and prolyl-glutamine) were reduced after WMT.

CONCLUSION: WMT demonstrated therapeutic efficacy in CD treatment, likely due to the effective reconstruction of the patient's microbiome. Multi-omics techniques can effectively help decipher the potential mechanisms of WMT in treating CD.}, } @article {pmid38617439, year = {2024}, author = {Ogaya, Y and Kadota, T and Hamada, M and Nomura, R and Nakano, K}, title = {Characterization of the unique oral microbiome of children harboring Helicobacter pylori in the oral cavity.}, journal = {Journal of oral microbiology}, volume = {16}, number = {1}, pages = {2339158}, pmid = {38617439}, issn = {2000-2297}, abstract = {OBJECTIVE: Helicobacter pylori infection is acquired in childhood via the oral cavity, although its relationship with the characteristics of the oral microbiome has not been elucidated. In this study, we performed comprehensive analysis of the oral microbiome in children and adults with or without H. pylori in the oral cavity.

METHODS: Bacterial DNA was extracted from 41 adult and 21 child saliva specimens, and H. pylori was detected using PCR. 16S rRNA gene amplification was performed for next-generation sequencing. Bioinformatic analyses were conducted using Quantitative Insights into Microbial Ecology 2 (QIIME 2).

RESULTS: Faith's phylogenetic diversity analysis showed a significant difference between H. pylori-negative adult and child specimens in terms of α-diversity (p < 0.05), while no significant difference was observed between H. pylori-positive adult and child specimens. There was also a significant difference in β-diversity between H. pylori-positive and negative child specimens (p < 0.05). Taxonomic analysis at the genus level revealed that Porphyromonas was the only bacterium that was significantly more abundant in both H. pylori-positive adults and children than in corresponding negative specimens (p < 0.01 and p < 0.05, respectively).

CONCLUSION: These results suggest unique oral microbiome characteristics in children with H. pylori infection in the oral cavity.}, } @article {pmid38617292, year = {2024}, author = {Blakeley-Ruiz, JA and Bartlett, A and McMillan, AS and Awan, A and Vanhoy Walsh, M and Meyerhoffer, AK and Vintila, S and Maier, J and Richie, T and Theriot, CM and Kleiner, M}, title = {Dietary protein source strongly alters gut microbiota composition and function.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.04.04.588169}, pmid = {38617292}, abstract = {The source of protein in a persons diet affects their total life expectancy. However, the mechanisms by which dietary protein sources differentially impact human health and life expectancy are poorly understood. Dietary choices have major impacts on the composition and function of the intestinal microbiota that ultimately mediate host health. This raises the possibility that health outcomes based on dietary protein sources might be driven by interactions between dietary protein and the gut microbiota. In this study, we determine the effects of seven different sources of dietary protein on the gut microbiota in mice. We apply an integrated metagenomics-metaproteomics approach to simultaneously investigate the effects of these dietary protein sources on the gut microbiotas composition and function. The protein abundances measured by metaproteomics can provide microbial species abundances, and evidence for the phenotype of microbiota members on the molecular level because measured proteins allow us to infer the metabolic and physiological processes used by a microbial community. We showed that dietary protein source significantly altered the species composition and overall function of the gut microbiota. Different dietary protein sources led to changes in the abundance of microbial amino acid degrading proteins and proteins involved in the degradation of glycosylations on dietary protein. In particular, brown rice and egg white protein increased the abundance of amino acid degrading enzymes and egg white protein increased the abundance of bacteria and proteins usually associated with the degradation of the intestinal mucus barrier. These results show that dietary protein source can change the gut microbiotas metabolism, which could have major implications in the context of gut microbiota mediated diseases.}, } @article {pmid38616262, year = {2024}, author = {Yao, Y and Xu, Q and Liang, W and Ji, S and Kosari, M and Xu, S and Zhu, Z and Mao, Z}, title = {Multi-organ involvement caused by Scedosporium apiospermum infection after near drowning: a case report and literature review.}, journal = {BMC neurology}, volume = {24}, number = {1}, pages = {124}, pmid = {38616262}, issn = {1471-2377}, support = {82171465//National Natural Science Fundation of China/ ; 81901303//National Natural Science Fundation of China/ ; }, abstract = {BACKGROUND: Scedosporium apiospermum (S. apiospermum) is a rare fungal pathogen that causes disseminated infections. It rarely affects immunocompetent individuals and has a poor prognosis.

CASE PRESENTATION: A 37-year-old woman presented with multiple lesions in the lungs, brain, and eyes, shortly after near drowning in a car accident. The primary symptoms were chest tightness, limb weakness, headache, and poor vision in the left eye. S. apiospermum infection was confirmed by metagenomic next-generation sequencing (mNGS) of intracranial abscess drainage fluid, although intracranial metastases were initially considered. After systemic treatment with voriconazole, her symptoms improved significantly; however, she lost vision in her left eye due to delayed diagnosis.

CONCLUSION: While S. apiospermum infection is rare, it should be considered even in immunocompetent patients. Prompt diagnosis and treatment are essential. Voriconazole may be an effective treatment option.}, } @article {pmid38615602, year = {2024}, author = {Huang, P and Chen, Y and Li, Z and Zhang, B and Yu, S and Zhou, Y}, title = {Ammonia-dependent reducing power redistribution for purple phototrophic bacteria culture-based biohydrogen production.}, journal = {Water research}, volume = {256}, number = {}, pages = {121599}, doi = {10.1016/j.watres.2024.121599}, pmid = {38615602}, issn = {1879-2448}, abstract = {The global energy crisis has intensified the search for sustainable and clean alternatives, with biohydrogen emerging as a promising solution to address environmental challenges. Leveraging photo fermentation (PF) process, purple phototrophic bacteria (PPB) can harness reducing power derived from organic substrates to facilitate hydrogen production. However, existing studies report much lower H2 yields than theoretical value when using acetate as carbon source and ammonia as nitrogen source, primarily attributed to the widely employed pulse-feeding mode which suffers from ammonia inhibition effect on nitrogenase. To address this issue, a continuous feeding mode was applied to avoid ammonia accumulation in this study. On the other hand, other pathways like carbon fixation and polyhydroxyalkanoate (PHA) formation could compete reducing power with H2 production. However, the reducing power allocation under continuous feeding mode is not yet clear. In this study, the reducing power allocation and hydrogen production performance were evaluated under various ammonia loading, using acetate as carbon source and infrared LED at around 50 W·m[-2] as light source. The results show that (a) The absence of ammonia resulted in the best performance for hydrogen production, with 44 % of the reducing power distributed to H2 and the highest H2 volumetric productivity, while the allocation of reducing power to hydrogen production stopped when ammonia loading was above 7.6 mg NH4-N·L[-1]·d[-1]; (b) when PPB required to eliminate reducing power under ammonia limited conditions, PHA production was the preferred pathway followed by the hydrogen production pathway, but once PHA accumulation reached saturation, hydrogen generation pathway dominated; (c) under ammonia limited conditions, the TCA cycle was more activated rendering higher NADH (i.e. reducing power) production compared with that under ammonia sufficient conditions which was verified by metagenomics analysis, and all the hydrogen production, PHA accumulation and carbon fixation pathways were highly active to dissipate reducing power. This work provides the insight of reducing power distribution and PPB biohydrogen production variated by ammonia loading under continuous feeding mode.}, } @article {pmid38585881, year = {2024}, author = {Knuth, MM and Campos, CV and Smith, K and Hutchins, EK and Lewis, S and York, M and Coghill, LM and Franklin, C and MacFarlane, A and Ericsson, AC and Magnuson, T and Ideraabdullah, F}, title = {Timing of standard chow exposure determines the variability of mouse phenotypic outcomes and gut microbiota profile.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38585881}, support = {R21 DK122242/DK/NIDDK NIH HHS/United States ; R25 GM089569/GM/NIGMS NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; T32 CA217824/CA/NCI NIH HHS/United States ; U42 OD010924/OD/NIH HHS/United States ; }, abstract = {Standard chow diet contributes to reproducibility in animal model experiments since chows differ in nutrient composition, which can independently influence phenotypes. However, there is little evidence of the role of timing in the extent of variability caused by chow exposure. Here, we measured the impact of diet (5V5M, 5V0G, 2920X, and 5058) and timing of exposure (adult exposure (AE), lifetime exposure (LE), and developmental exposure (DE)) on growth & development, metabolic health indicators, and gut bacterial microbiota profiles across genetically identical C57BL6/J mice. Diet drove differences in macro- and micronutrient intake for all exposure models. AE had no effect on measured outcomes. However, LE mice exhibited significant sex-dependent diet effects on growth, body weight, and body composition. LE effects were mostly absent in the DE model, where mice were exposed to chow differences from conception to weaning. Both AE and LE models exhibited similar diet-driven beta diversity profiles for the gut bacterial microbiota, with 5058 diet driving the most distinct profile. Diet-induced beta diversity profiles were sex-dependent for LE mice. Compared to AE, LE drove 9X more diet-driven differentially abundant genera, majority of which were the result of inverse effects of 2920X and 5058. Our findings demonstrate that lifetime exposure to different chow diets has the greatest impact on reproducibility of experimental measures that are common components of preclinical mouse model studies. Importantly, weaning DE mice onto a uniform diet is likely an effective way to reduce unwanted phenotypic variability among experimental models.}, } @article {pmid38615598, year = {2024}, author = {Li, W and Wang, S and Zheng, D}, title = {Metagenomic next-generation sequencing for diagnosing severe leptospirosis in a patient suspected COVID-19: A case report.}, journal = {Diagnostic microbiology and infectious disease}, volume = {109}, number = {3}, pages = {116288}, doi = {10.1016/j.diagmicrobio.2024.116288}, pmid = {38615598}, issn = {1879-0070}, abstract = {Leptospirosis is a zoonotic and neglected waterborne disease caused by the pathogenic helical spirochetes. Early diagnosis of leptospirosis remains challenging due to non-specific symptoms and the limited availability of rapid point-of-care diagnostic tests. Herein, we present a case where a patient suspected of having COVID-19 was diagnosed with leptospirosis using metagenomic next-generation sequencing (mNGS). This case highlights the potential of mNGS to diagnose leptospirosis in the context of the COVID-19 pandemic.}, } @article {pmid38614455, year = {2024}, author = {Li, X and Kurahara, LH and Zhao, Z and Zhao, F and Ishikawa, R and Ohmichi, K and Li, G and Yamashita, T and Hashimoto, T and Hirano, M and Sun, Z and Hirano, K}, title = {The therapeutic effect of proteinase-activated receptor-1 antagonist on colitis-associated carcinogenesis.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcmgh.2024.04.001}, pmid = {38614455}, issn = {2352-345X}, abstract = {BACKGROUND & AIMS: Inflammatory bowel disease is associated with carcinogenesis, which limits the prognosis of the patients. The local expression of proteinases and proteinase-activated receptor 1 (PAR1) increases in the inflammatory bowel disease. The present study investigated the therapeutic effects of PAR1 antagonism on colitis-associated carcinogenesis.

METHODS: A colitis-associated carcinogenesis model was prepared in mice by treatment with azoxymethane (AOM) and dextran sulfate sodium (DSS). PAR1 antagonist, E5555, was administered in long- and short-term protocol, starting on the day of AOM injection and 1 week after completing AOM/DSS treatment, respectively. The fecal samples were collected for metagenome analysis of gut microbiota. The intestinal myofibroblast of the Crohn's disease patients were used to elucidate underlying cellular mechanisms. Caco-2 cells were used to investigate a possible source of PAR1 agonist proteinases.

RESULTS: AOM/DSS model showed weight loss, diarrhea, tumor development, inflammation, fibrosis, and increased production of inflammatory cytokines. The β-diversity, but not α-diversity, of microbiota significantly differed between AOM/DSS and control mice. E5555 alleviated these pathological changes and altered the microbiota β-diversity in AOM/DSS mice. The thrombin expression was upregulated in tumor and non-tumor areas, while PAR1 mRNA expression was higher in tumor areas compared to non-tumor areas. E5555 inhibited thrombin-triggered elevation of cytosolic Ca[2+] concentration and ERK1/2 phosphorylation, as well as IL6-induced STAT3 phosphorylation in intestinal myofibroblasts. Caco-2 cell-conditioned media contained immunoreactive thrombin, which cleaved the recombinant protein containing the extracellular domain of PAR1 at the thrombin cleavage site.

CONCLUSIONS: PAR1 antagonism is proposed to be a novel therapeutic strategy for treatment of inflammatory bowel disease and it associated carcinogenesis.}, } @article {pmid38614184, year = {2024}, author = {Sharma, N and Patel, SN and Rai, AK and Singh, SP}, title = {Biochemical characterization of a novel acid-active endopolygalacturonase for pectin depolymerization, pectic-oligomer production, and fruit juice clarification.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {131565}, doi = {10.1016/j.ijbiomac.2024.131565}, pmid = {38614184}, issn = {1879-0003}, abstract = {Endopolygalacturonases are crucial pectinases known for their efficient and sustainable pectin depolymerization activities. The present study identified a novel gene encoding endopolygalacturonase from an acidic mine tailing metagenome. The putative gene showed a maximum identity of 67.55 % with an uncharacterized peptide sequence from Flavobacterium fluvii. The gene was cloned and expressed in a heterologous host, E. coli. Biochemical characterization of the novel endopolygalacturonase enzyme variant (EPHM) showed maximum activity at 60 °C and at 5.0 pH, while retaining 50 % activity under the temperature and pH range of 20 °C to 70 °C for 6 h, and 3.0 to 10.0 for 3 h, respectively. The enzyme exhibited tolerance to different metal ions. EPHM was characterized for the depolymerization of methylated pectin into pectic oligosaccharides. Further, its utility was established for fruit juice clarification, as endorsed by high transmittance, significant viscosity reduction, and release of reducing sugars in the treated fruit juice samples.}, } @article {pmid38614128, year = {2024}, author = {Li, C and Guo, X and He, Y and Wang, J and Hao, J and Liu, X}, title = {Cohabiting with ulcerative colitis patients decreases differences of gut microbiome between healthy individuals and the patients.}, journal = {Annals of medicine}, volume = {56}, number = {1}, pages = {2337712}, doi = {10.1080/07853890.2024.2337712}, pmid = {38614128}, issn = {1365-2060}, abstract = {Background: Ulcerative colitis (UC), which is characterized by chronic relapsing inflammation of the colon, results from a complex interaction of factors involving the host, environment, and microbiome. The present study aimed to investigate the gut microbial composition and metabolic variations in patients with UC and their spouses. Materials and Methods: Fecal samples were collected from 13 healthy spouses and couples with UC. 16S rRNA gene amplicon sequencing and metagenomics sequencing were used to analyze gut microbiota composition, pathways, gene expression, and enzyme activity, followed by the Kyoto Encyclopedia of Genes and Genomes. Results: We found that the microbiome diversity of couples with UC decreased, especially that of UC patients. Bacterial composition, such as Firmicutes, was altered between UC patients and healthy controls, but was not significantly different between UC patients and their spouses. This has also been observed in pathways, such as metabolism, genetic information processing, organismal systems, and human diseases. However, the genes and enzymes of spouses with UC were not significantly different from those of healthy individuals. Furthermore, the presence of Faecalibacterium correlated with oxidative phosphorylation, starch and sucrose metabolism, amino sugar and nucleotide sugar metabolism, and the bacterial secretion system, showed a marked decline in the UC group compared with their spouses, but did not vary between healthy couples. Conclusion: Our study revealed that cohabitation with UC patients decreased differences in the gut microbiome between healthy individuals and patients. Not only was the composition and diversity of the microbiota diminished, but active pathways also showed some decline. Furthermore, Firmicutes, Faecalibacterium, and the four related pathways may be associated with the pathological state of the host rather than with human behavior.}, } @article {pmid38614031, year = {2024}, author = {Wang, C and Mao, Y and Zhang, L and Wei, H and Wang, Z}, title = {Insight into environmental adaptability of antibiotic resistome from surface water to deep sediments in anthropogenic lakes by metagenomics.}, journal = {Water research}, volume = {256}, number = {}, pages = {121583}, doi = {10.1016/j.watres.2024.121583}, pmid = {38614031}, issn = {1879-2448}, abstract = {The escalating antibiotic resistance threatens the long-term global health. Lake sediment is a vital hotpot in transmitting antibiotic resistance genes (ARGs); however, their vertical distribution pattern and driving mechanisms in sediment cores remain unclear. This study first utilized metagenomics to reveal how resistome is distributed from surface water to 45 cm sediments in four representative lakes, central China. Significant vertical variations in ARG profiles were observed (R[2] = 0.421, p < 0.001), with significant reductions in numbers, abundance, and Shannon index from the surface water to deep sediment (all p-values < 0.05). ARGs also has interconnections within the vertical profile of the lakes: twelve ARGs persistently exist all sites and depths, and shared ARGs (e.g., vanS and mexF) were assembled by diverse hosts at varying depths. The 0-18 cm sediment had the highest mobility and health risk of ARGs, followed by the 18-45 cm sediment and water. The drivers of ARGs transformed along the profile of lakes: microbial communities and mobile genetic elements (MGEs) dominated in water, whereas environmental variables gradually become the primary through regulating microbial communities and MGEs with increasing sediment depth. Interestingly, the stochastic process governed ARG assembly, while the stochasticity diminished under the mediation of Chloroflexi, Candidatus Bathyarcaeota and oxidation-reduction potential with increasing depth. Overall, we formulated a conceptual framework to elucidate the vertical environmental adaptability of resistome in anthropogenic lakes. This study shed on the resistance risks and their environmental adaptability from sediment cores, which could reinforce the governance of public health issues.}, } @article {pmid38613799, year = {2024}, author = {Zhanbo, Q and Jing, Z and Shugao, H and Yinhang, W and Jian, C and Xiang, Y and Feimin, Z and Jian, L and Xinyue, W and Wei, W and Shuwen, H}, title = {Age and aging process alter the gut microbes.}, journal = {Aging}, volume = {16}, number = {}, pages = {}, doi = {10.18632/aging.205728}, pmid = {38613799}, issn = {1945-4589}, abstract = {BACKGROUND: Gut microbes and age are both factors that influence the development of disease. The community structure of gut microbes is affected by age.

OBJECTIVE: To plot time-dependent gut microbe profiles in individuals over 45 years old and explore the correlation between age and gut microbes.

METHODS: Fecal samples were collected from 510 healthy individuals over 45 years old. Shannon index, Simpson index, Ace index, etc. were used to analyze the diversity of gut microbes. The beta diversity analysis, including non-metric multidimensional scaling (NMDS), was used to analyze community distribution. Linear discriminant analysis (LDA) and random forest (RF) algorithm were used to analyze the differences of gut microbes. Trend analysis was used to plot the abundances of characteristic gut microbes in different ages.

RESULTS: The individuals aged 45-49 had the highest richness of gut bacteria. Fifteen characteristic gut microbes, including Siphoviridae and Bifidobacterium breve, were screened by RF algorithm. The abundance of Ligiactobacillus and Microviridae were higher in individuals older than 65 years. Moreover, the abundance of Blautia_A massiliensis, Lubbockvirus and Enterocloster clostridioformis decreased with age and the abundance of Klebsiella variicola and Prevotella increased with age. The functional genes, such as human diseases and aging, were significantly different among different aged individuals.

CONCLUSIONS: The individuals in different ages have characteristic gut microbes. The changes in community structure of gut microbes may be related to age-induced diseases.}, } @article {pmid38613781, year = {2024}, author = {Gheorghe, CE and Leigh, SJ and Tofani, GSS and Bastiaanssen, TFS and Lyte, JM and Gardellin, E and Govindan, A and Strain, C and Martinez-Herrero, S and Goodson, MS and Kelley-Loughnane, N and Cryan, JF and Clarke, G}, title = {The microbiota drives diurnal rhythms in tryptophan metabolism in the stressed gut.}, journal = {Cell reports}, volume = {43}, number = {4}, pages = {114079}, doi = {10.1016/j.celrep.2024.114079}, pmid = {38613781}, issn = {2211-1247}, abstract = {Chronic stress disrupts microbiota-gut-brain axis function and is associated with altered tryptophan metabolism, impaired gut barrier function, and disrupted diurnal rhythms. However, little is known about the effects of acute stress on the gut and how it is influenced by diurnal physiology. Here, we used germ-free and antibiotic-depleted mice to understand how microbiota-dependent oscillations in tryptophan metabolism would alter gut barrier function at baseline and in response to an acute stressor. Cecal metabolomics identified tryptophan metabolism as most responsive to a 15-min acute stressor, while shotgun metagenomics revealed that most bacterial species exhibiting rhythmicity metabolize tryptophan. Our findings highlight that the gastrointestinal response to acute stress is dependent on the time of day and the microbiome, with a signature of stress-induced functional alterations in the ileum and altered tryptophan metabolism in the colon.}, } @article {pmid38613509, year = {2024}, author = {Uçak, S}, title = {Determination of Bacterial Community Structure of Table Olive via Metagenomic Approach in Şarköy.}, journal = {Chemistry & biodiversity}, volume = {}, number = {}, pages = {e202302120}, doi = {10.1002/cbdv.202302120}, pmid = {38613509}, issn = {1612-1880}, abstract = {One of the most popular pickled foods created worldwide is table olives. The aim was to identify the bacterial microbiota of table olive samples collected from Şarköy, Tekirdağ-Türkiye using next generation sequencing and 16S metagenomic analysis. Samples were studied as non-pre-enriched (n:10) and after pre-enrichment (n:10) to compare the effects of the enrichment process on the bacterial diversity. In non-pre-enriched, the most common genus found was Sphingomonas, followed by Altererythrobacter and Lysobacter. The most common phylum found was Proteobacteria, followed by Bacteroidota and Actinobacteria. In pre-enriched, Bacillus was the most commonly detected genus, followed by Pantoea and Staphylococcus. The most frequently found phylum was Firmicutes, followed by Proteobacteria and Cyanobacteria. This study is the first study for Şarköy, which is the only table olive production place in the Tekirdağ region due to its microclimate feature. Further studies are needed in more table olive samples from different geographical areas to confirm and develop current findings.}, } @article {pmid38613119, year = {2024}, author = {Zhou, Y and Zeng, Y and Wang, R and Pang, J and Wang, X and Pan, Z and Jin, Y and Chen, Y and Yang, Y and Ling, W}, title = {Resveratrol Improves Hyperuricemia and Ameliorates Renal Injury by Modulating the Gut Microbiota.}, journal = {Nutrients}, volume = {16}, number = {7}, pages = {}, doi = {10.3390/nu16071086}, pmid = {38613119}, issn = {2072-6643}, support = {81730090//National Natural Science Foundation of China/ ; 81973022//National Natural Science Foundation of China/ ; }, abstract = {Resveratrol (RES) has been reported to prevent hyperuricemia (HUA); however, its effect on intestinal uric acid metabolism remains unclear. This study evaluated the impact of RES on intestinal uric acid metabolism in mice with HUA induced by a high-fat diet (HFD). Moreover, we revealed the underlying mechanism through metagenomics, fecal microbiota transplantation (FMT), and 16S ribosomal RNA analysis. We demonstrated that RES reduced the serum uric acid, creatinine, urea nitrogen, and urinary protein levels, and improved the glomerular atrophy, unclear renal tubule structure, fibrosis, and renal inflammation. The results also showed that RES increased intestinal uric acid degradation. RES significantly changed the intestinal flora composition of HFD-fed mice by enriching the beneficial bacteria that degrade uric acid, reducing harmful bacteria that promote inflammation, and improving microbial function via the upregulation of purine metabolism. The FMT results further showed that the intestinal microbiota is essential for the effect of RES on HUA, and that Lactobacillus may play a key role in this process. The present study demonstrated that RES alleviates HFD-induced HUA and renal injury by regulating the gut microbiota composition and the metabolism of uric acid.}, } @article {pmid38613058, year = {2024}, author = {Lombardi, M and Troisi, J and Motta, BM and Torre, P and Masarone, M and Persico, M}, title = {Gut-Liver Axis Dysregulation in Portal Hypertension: Emerging Frontiers.}, journal = {Nutrients}, volume = {16}, number = {7}, pages = {}, doi = {10.3390/nu16071025}, pmid = {38613058}, issn = {2072-6643}, abstract = {Portal hypertension (PH) is a complex clinical challenge with severe complications, including variceal bleeding, ascites, hepatic encephalopathy, and hepatorenal syndrome. The gut microbiota (GM) and its interconnectedness with human health have emerged as a captivating field of research. This review explores the intricate connections between the gut and the liver, aiming to elucidate how alterations in GM, intestinal barrier function, and gut-derived molecules impact the development and progression of PH. A systematic literature search, following PRISMA guidelines, identified 12 original articles that suggest a relationship between GM, the gut-liver axis, and PH. Mechanisms such as dysbiosis, bacterial translocation, altered microbial structure, and inflammation appear to orchestrate this relationship. One notable study highlights the pivotal role of the farnesoid X receptor axis in regulating the interplay between the gut and liver and proposes it as a promising therapeutic target. Fecal transplantation experiments further emphasize the pathogenic significance of the GM in modulating liver maladies, including PH. Recent advancements in metagenomics and metabolomics have expanded our understanding of the GM's role in human ailments. The review suggests that addressing the unmet need of identifying gut-liver axis-related metabolic and molecular pathways holds potential for elucidating pathogenesis and directing novel therapeutic interventions.}, } @article {pmid38612976, year = {2024}, author = {Fagunwa, O and Davies, K and Bradbury, J}, title = {The Human Gut and Dietary Salt: The Bacteroides/Prevotella Ratio as a Potential Marker of Sodium Intake and Beyond.}, journal = {Nutrients}, volume = {16}, number = {7}, pages = {}, doi = {10.3390/nu16070942}, pmid = {38612976}, issn = {2072-6643}, support = {FMoH/PTDF//Federal Government of Nigeria/ ; NA//University of Huddersfield/ ; publishing//Queen's University Belfast/ ; }, abstract = {The gut microbiota is a dynamic ecosystem that plays a pivotal role in maintaining host health. The perturbation of these microbes has been linked to several health conditions. Hence, they have emerged as promising targets for understanding and promoting good health. Despite the growing body of research on the role of sodium in health, its effects on the human gut microbiome remain under-explored. Here, using nutrition and metagenomics methods, we investigate the influence of dietary sodium intake and alterations of the human gut microbiota. We found that a high-sodium diet (HSD) altered the gut microbiota composition with a significant reduction in Bacteroides and inverse increase in Prevotella compared to a low-sodium diet (LSD). However, there is no clear distinction in the Firmicutes/Bacteroidetes (F/B) ratio between the two diet types. Metabolic pathway reconstruction revealed the presence of sodium reabsorption genes in the HSD, but not LSD. Since it is currently difficult in microbiome studies to confidently associate the F/B ratio with what is considered healthy (e.g., low sodium) or unhealthy (e.g., high sodium), we suggest that the use of a genus-based ratio such as the Bacteroides/Prevotella (B/P) ratio may be more beneficial for the application of microbiome studies in health.}, } @article {pmid38612922, year = {2024}, author = {Neagu, AN and Bruno, P and Johnson, KR and Ballestas, G and Darie, CC}, title = {Biological Basis of Breast Cancer-Related Disparities in Precision Oncology Era.}, journal = {International journal of molecular sciences}, volume = {25}, number = {7}, pages = {}, doi = {10.3390/ijms25074113}, pmid = {38612922}, issn = {1422-0067}, support = {R15CA260126/CA/NCI NIH HHS/United States ; }, abstract = {Precision oncology is based on deep knowledge of the molecular profile of tumors, allowing for more accurate and personalized therapy for specific groups of patients who are different in disease susceptibility as well as treatment response. Thus, onco-breastomics is able to discover novel biomarkers that have been found to have racial and ethnic differences, among other types of disparities such as chronological or biological age-, sex/gender- or environmental-related ones. Usually, evidence suggests that breast cancer (BC) disparities are due to ethnicity, aging rate, socioeconomic position, environmental or chemical exposures, psycho-social stressors, comorbidities, Western lifestyle, poverty and rurality, or organizational and health care system factors or access. The aim of this review was to deepen the understanding of BC-related disparities, mainly from a biomedical perspective, which includes genomic-based differences, disparities in breast tumor biology and developmental biology, differences in breast tumors' immune and metabolic landscapes, ecological factors involved in these disparities as well as microbiomics- and metagenomics-based disparities in BC. We can conclude that onco-breastomics, in principle, based on genomics, proteomics, epigenomics, hormonomics, metabolomics and exposomics data, is able to characterize the multiple biological processes and molecular pathways involved in BC disparities, clarifying the differences in incidence, mortality and treatment response for different groups of BC patients.}, } @article {pmid38612702, year = {2024}, author = {McDermott, G and Walsh, A and Crispie, F and Frost, S and Greally, P and Cotter, PD and O'Sullivan, O and Renwick, J}, title = {Insights into the Adolescent Cystic Fibrosis Airway Microbiome Using Shotgun Metagenomics.}, journal = {International journal of molecular sciences}, volume = {25}, number = {7}, pages = {}, doi = {10.3390/ijms25073893}, pmid = {38612702}, issn = {1422-0067}, support = {204814/Z/16/A/WT_/Wellcome Trust/United Kingdom ; }, abstract = {Cystic fibrosis (CF) is an inherited genetic disorder which manifests primarily in airway disease. Recent advances in molecular technologies have unearthed the diverse polymicrobial nature of the CF airway. Numerous studies have characterised the genus-level composition of this airway community using targeted 16S rDNA sequencing. Here, we employed whole-genome shotgun metagenomics to provide a more comprehensive understanding of the early CF airway microbiome. We collected 48 sputum samples from 11 adolescents and children with CF over a 12-month period and performed shotgun metagenomics on the Illumina NextSeq platform. We carried out functional and taxonomic analysis of the lung microbiome at the species and strain levels. Correlations between microbial diversity measures and independent demographic and clinical variables were performed. Shotgun metagenomics detected a greater diversity of bacteria than culture-based methods. A large proportion of the top 25 most-dominant species were anaerobes. Samples dominated by Staphylococcus aureus and Prevotella melaninogenica had significantly higher microbiome diversity, while no CF pathogen was associated with reduced microbial diversity. There was a diverse resistome present in all samples in this study, with 57.8% agreement between shotgun metagenomics and culture-based methods for detection of resistance. Pathogenic sequence types (STs) of S. aureus, Pseudomonas aeruginosa, Haemophilus influenzae and Stenotrophomonas maltophilia were observed to persist in young CF patients, while STs of S. aureus were both persistent and shared between patients. This study provides new insight into the temporal changes in strain level composition of the microbiome and the landscape of the resistome in young people with CF. Shotgun metagenomics could provide a very useful one-stop assay for detecting pathogens, emergence of resistance and conversion to persistent colonisation in early CF disease.}, } @article {pmid38612577, year = {2024}, author = {Feng, C and Li, N and Gao, G and He, Q and Kwok, LY and Zhang, H}, title = {Dynamic Changes of the Gut Microbiota and Its Functional Metagenomic Potential during the Development of Non-Small Cell Lung Cancer.}, journal = {International journal of molecular sciences}, volume = {25}, number = {7}, pages = {}, doi = {10.3390/ijms25073768}, pmid = {38612577}, issn = {1422-0067}, support = {NDYB2022-41//Research Initiation Project for Introducing Excellent Doctoral Talents from Inner Mongolia Agricultural University/ ; 2022YFD2100700//Research Fund for the National Key R&D Program of China/ ; U22A20540//National Natural Science Foundation of China/ ; 2021ZD0014//Inner Mongolia Science and Technology Major Projects/ ; CARS36//earmarked fund/ ; }, abstract = {The gut microbiota plays a significant role in tumor pathogenesis by regulating the host metabolism and immune response, and there are few studies focused on tracking changes in the gut microbiota from the onset of lung cancer. Therefore, the aim of our study is combining preclinical and clinical research to thoroughly analyze the signatures of fecal microbiota in lung cancer, which will be useful for early diagnosis and predicting the therapeutic efficacy of lung cancer. The first part of this study analyzed the fecal metagenomic differences between patients with non-small cell lung cancer and healthy subjects, and the second part of this work constructed a murine lung cancer model to monitor changes in mouse fecal metagenomics and T cell immunology during lung cancer progression. We found that the fecal microbiota was altered in both humans and mice with lung cancer, characterized by a significantly reduced microbial diversity and number of beneficial microbes, with increases in potential pathogens. The fecal level of Akkermansia muciniphila and the gut metabolic module of the secondary bile acid metabolism were diminished in both humans and mice with lung cancer compared with healthy subjects. Splenomegaly was observed in the lung cancer mice. Flow cytometer analysis of the splenocytes revealed substantial alterations in the proportions of T cell subsets in the lung cancer mice, characterized by significant increases in CD4[+]Foxp3[+]CD25[+] T regulatory cells (p < 0.05) while significant decreases in CD3[+] T cells (p < 0.001), CD4[+] T cells (p < 0.001), and the CD4[+]/CD8[+] ratio (p < 0.01). Vertical and longitudinal analyses of the fecal microbiota of the two mouse groups identified some lung cancer biomarkers (including Acutalibacter timonensis, Lachnospiraceae bacterium NSJ-38 sp014337195, etc.). The fecal microbiota of the lung cancer mice had a reduced metagenomic potential for neurotransmitters (melatonin, γ-aminobutyric acid, and histamine) compared with healthy mice. In summary, this study found that the diversity, structure, and composition of gut microbiota vary between cancer and healthy conditions, ultimately leading to changes in the potential for functional metagenomics.}, } @article {pmid38612511, year = {2024}, author = {Parra, M and Aldabaldetrecu, M and Arce, P and Soto-Aguilera, S and Vargas, R and Guerrero, J and Tello, M and Modak, B}, title = {[Cu(NN1)2]ClO4, a Copper (I) Complex as an Antimicrobial Agent for the Treatment of Piscirickettsiosis in Atlantic Salmon.}, journal = {International journal of molecular sciences}, volume = {25}, number = {7}, pages = {}, doi = {10.3390/ijms25073700}, pmid = {38612511}, issn = {1422-0067}, support = {VIU 21P0017//Agencia Nacional de Investigación y Desarrollo/ ; DICYT022341MC//University of Santiago Chile/ ; DICYT 022343TR//University of Santiago Chile/ ; }, abstract = {Piscirickettsia salmonis is the pathogen that most affects the salmon industry in Chile. Large quantities of antibiotics have been used to control it. In search of alternatives, we have developed [Cu(NN1)2]ClO4 where NN1 = 6-((quinolin-2-ylmethylene)amino)-2H-chromen-2-one. The antibacterial capacity of [Cu(NN1)2]ClO4 was determined. Subsequently, the effect of the administration of [Cu(NN1)2]ClO4 on the growth of S. salar, modulation of the immune system and the intestinal microbiota was studied. Finally, the ability to protect against a challenge with P. salmonis was evaluated. The results obtained showed that the compound has an MIC between 15 and 33.9 μg/mL in four isolates. On the other hand, the compound did not affect the growth of the fish; however, an increase in the transcript levels of IFN-γ, IL-12, IL-1β, CD4, lysozyme and perforin was observed in fish treated with 40 μg/g of fish. Furthermore, modulation of the intestinal microbiota was observed, increasing the genera of beneficial bacteria such as Lactobacillus and Bacillus as well as potential pathogens such as Vibrio and Piscirickettsia. Finally, the treatment increased survival in fish challenged with P. salmonis by more than 60%. These results demonstrate that the compound is capable of protecting fish against P. salmonis, probably by modulating the immune system and the composition of the intestinal microbiota.}, } @article {pmid38611776, year = {2024}, author = {Szulc, J and Okrasa, M and Nowak, A and Ryngajłło, M and Nizioł, J and Kuźniar, A and Ruman, T and Gutarowska, B}, title = {Uncontrolled Post-Industrial Landfill-Source of Metals, Potential Toxic Compounds, Dust, and Pathogens in Environment-A Case Study.}, journal = {Molecules (Basel, Switzerland)}, volume = {29}, number = {7}, pages = {}, doi = {10.3390/molecules29071496}, pmid = {38611776}, issn = {1420-3049}, support = {Phase IV of the National Program "Safety and working conditions improvement"//Ministry of Science and Higher Education and the National Centre for Research and Development/ ; 726/BN/D/2019-2021//Regional Found for Environmental Protection and Water Management in Lodz/ ; }, abstract = {The aim of this case study was the evaluation of the selected metals' concentration, potential toxic compound identification, cytotoxicity analysis, estimation of the airborne dust concentration, biodiversity, and number of microorganisms in the environment (leachate, soil, air) of the biggest uncontrolled post-industrial landfills in Poland. Based on the results obtained, preliminary solutions for the future management of post-industrial objects that have become an uncontrolled landfill were indicated. In the air, the PM1 fraction dominated, constituting 78.1-98.2% of the particulate matter. Bacterial counts were in the ranges of 9.33 × 10[1]-3.21 × 10[3] CFU m[-3] (air), 1.87 × 10[5]-2.30 × 10[6] CFU mL[-1] (leachates), and 8.33 × 10[4]-2.69 × 10[6] CFU g[-1] (soil). In the air, the predominant bacteria were Cellulosimicrobium and Stenotrophomonas. The predominant fungi were Mycosphaerella, Cladosporium, and Chalastospora. The main bacteria in the leachates and soils were Acinetobacter, Mortierella, Proteiniclasticum, Caloramator, and Shewanella. The main fungi in the leachates and soils were Lindtneria. Elevated concentrations of Pb, Zn, and Hg were detected. The soil showed the most pronounced cytotoxic potential, with rates of 36.55%, 63.08%, and 100% for the A-549, Caco-2, and A-549 cell lines. Nine compounds were identified which may be responsible for this cytotoxic effect, including 2,4,8-trimethylquinoline, benzo(f)quinoline, and 1-(m-tolyl)isoquinoline. The microbiome included bacteria and fungi potentially metabolizing toxic compounds and pathogenic species.}, } @article {pmid38611599, year = {2024}, author = {Tsang, HF and Cheung, YS and Yu, CA and Chan, CS and Wong, CT and Yim, KA and Pei, X and Wong, SC}, title = {Menstrual Blood as a Diagnostic Specimen for Human Papillomavirus Genotyping and Genital Tract Infection Using Next-Generation Sequencing as a Novel Diagnostic Tool.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {14}, number = {7}, pages = {}, doi = {10.3390/diagnostics14070686}, pmid = {38611599}, issn = {2075-4418}, support = {RGCQ71P//Research Grants Council HK/ ; UIM/354//HK Innovation and Technology Fund University-Industry Collaborative Programme/ ; }, abstract = {BACKGROUND: Menstrual blood (MB) is a convenient specimen type that can be self-collected easily and non-invasively by women. This study assessed the potential application of MB as a diagnostic specimen to detect genital tract infections (GTIs) and human papillomavirus (HPV) infections in women.

METHOD: Genomic DNA was extracted from MB samples. Pacific Bioscience (Pacbio) 16S ribosomal DNA (rDNA) high-fidelity (HiFi) long-read sequencing and HPV PCR were performed.

RESULTS: MB samples were collected from women with a pathological diagnosis of CIN1, CIN2, CIN3 or HPV infection. The sensitivity and positive predictive value (PPV) of high-risk HPV detection using MB were found to be 66.7%. A shift in vaginal flora and a significant depletion in Lactobacillus spp. in the vaginal microbiota communities were observed in the MB samples using 16S rDNA sequencing.

CONCLUSIONS: In this study, we demonstrated that MB is a proper diagnostic specimen of consideration for non-invasive detection of HPV DNA and genotyping using PCR and the diagnosis of GTIs using metagenomic next-generation sequencing (mNGS). MB testing is suitable for all women who menstruate and this study has opened up the possibility of the use of MB as a diagnostic specimen to maintain women's health.}, } @article {pmid38611483, year = {2024}, author = {Rojas-Sánchez, B and Castelán-Sánchez, H and Garfias-Zamora, EY and Santoyo, G}, title = {Diversity of the Maize Root Endosphere and Rhizosphere Microbiomes Modulated by the Inoculation with Pseudomonas fluorescens UM270 in a Milpa System.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, doi = {10.3390/plants13070954}, pmid = {38611483}, issn = {2223-7747}, abstract = {Milpa is an agroecological production system based on the polyculture of plant species, with corn featuring as a central component. Traditionally, the milpa system does not require the application of chemicals, and so pest attacks and poor growth in poor soils can have adverse effects on its production. Therefore, the application of bioinoculants could be a strategy for improving crop growth and health; however, the effect of external inoculant agents on the endemic microbiota associated with corn has not been extensively studied. Here, the objective of this work was to fertilize a maize crop under a milpa agrosystem with the PGPR Pseudomonas fluorescens UM270, evaluating its impact on the diversity of the rhizosphere (rhizobiome) and root endophytic (root endobiome) microbiomes of maize plants. The endobiome of maize roots was evaluated by 16S rRNA and internal transcribed spacer region (ITS) sequencing, and the rhizobiome was assessed by metagenomic sequencing upon inoculation with the strain UM270. The results showed that UM270 inoculation of the rhizosphere of P. fluorescens UM270 did not increase alpha diversity in either the monoculture or milpa, but it did alter the endophytic microbiome of maize plant roots by stimulating the presence of bacterial operational taxonomic units (OTUs) of the genera Burkholderia and Pseudomonas (in a monoculture), whereas, in the milpa system, the PGPR stimulated greater endophytic diversity and the presence of genera such as Burkholderia, Variovorax, and N-fixing rhizobia genera, including Rhizobium, Mesorhizobium, and Bradyrhizobium. No clear association was found between fungal diversity and the presence of strain UM270, but beneficial fungi, such as Rizophagus irregularis and Exophiala pisciphila, were detected in the Milpa system. In addition, network analysis revealed unique interactions with species such as Stenotrophomonas sp., Burkholderia xenovorans, and Sphingobium yanoikuyae, which could potentially play beneficial roles in the plant. Finally, the UM270 strain does not seem to have a strong impact on the microbial diversity of the rhizosphere, but it does have a strong impact on some functions, such as trehalose synthesis, ammonium assimilation, and polyamine metabolism. The inoculation of UM270 biofertilizer in maize plants modifies the rhizo- and endophytic microbiomes with a high potential for stimulating plant growth and health in agroecological crop models.}, } @article {pmid38611432, year = {2024}, author = {Papadimitriou, K and Georgalaki, M and Anastasiou, R and Alexandropoulou, AM and Manolopoulou, E and Zoumpopoulou, G and Tsakalidou, E}, title = {Study of the Microbiome of the Cretan Sour Cream Staka Using Amplicon Sequencing and Shotgun Metagenomics and Isolation of Novel Strains with an Important Antimicrobial Potential.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, doi = {10.3390/foods13071129}, pmid = {38611432}, issn = {2304-8158}, abstract = {Staka is a traditional Greek sour cream made mostly from spontaneously fermented sheep milk or a mixture of sheep and goat milk. At the industrial scale, cream separators and starter cultures may also be used. Staka is sometimes cooked with flour to absorb most of the fat. In this study, we employed culture-based techniques, amplicon sequencing, and shotgun metagenomics to analyze the Staka microbiome for the first time. The samples were dominated by Lactococcus or Leuconostoc spp. Most other bacteria were lactic acid bacteria (LAB) from the Streptococcus and Enterococcus genera or Gram-negative bacteria from the Buttiauxella, Pseudomonas, Enterobacter, Escherichia-Shigella, and Hafnia genera. Debaryomyces, Kluyveromyces, or Alternaria were the most prevalent genera in the samples, followed by other yeasts and molds like Saccharomyces, Penicillium, Aspergillus, Stemphylium, Coniospotium, or Cladosporium spp. Shotgun metagenomics allowed the species-level identification of Lactococcus lactis, Lactococcus raffinolactis, Streptococcus thermophilus, Streptococcus gallolyticus, Escherichia coli, Hafnia alvei, Streptococcus parauberis, and Enterococcus durans. Binning of assembled shotgun reads followed by recruitment plot analysis of single reads could determine near-complete metagenome assembled genomes (MAGs). Culture-dependent and culture-independent analyses were in overall agreement with some distinct differences. For example, lactococci could not be isolated, presumably because they had entered a viable but not culturable (VBNC) state or because they were dead. Finally, several LAB, Hafnia paralvei, and Pseudomonas spp. isolates exhibited antimicrobial activities against oral or other pathogenic streptococci, and certain spoilage and pathogenic bacteria establishing their potential role in food bio-protection or new biomedical applications. Our study may pave the way for additional studies concerning artisanal sour creams to better understand the factors affecting their production and the quality.}, } @article {pmid38611328, year = {2024}, author = {Tsouggou, N and Slavko, A and Tsipidou, O and Georgoulis, A and Dimov, SG and Yin, J and Vorgias, CE and Kapolos, J and Papadelli, M and Papadimitriou, K}, title = {Investigation of the Microbiome of Industrial PDO Sfela Cheese and Its Artisanal Variants Using 16S rDNA Amplicon Sequencing and Shotgun Metagenomics.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {7}, pages = {}, doi = {10.3390/foods13071023}, pmid = {38611328}, issn = {2304-8158}, support = {MIS 5047289//European Union and Greek national funds/ ; }, abstract = {Sfela is a white brined Greek cheese of protected designation of origin (PDO) produced in the Peloponnese region from ovine, caprine milk, or a mixture of the two. Despite the PDO status of Sfela, very few studies have addressed its properties, including its microbiology. For this reason, we decided to investigate the microbiome of two PDO industrial Sfela cheese samples along with two non-PDO variants, namely Sfela touloumotiri and Xerosfeli. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), 16S rDNA amplicon sequencing and shotgun metagenomics analysis were used to identify the microbiome of these traditional cheeses. Cultured-based analysis showed that the most frequent species that could be isolated from Sfela cheese were Enterococcus faecium, Lactiplantibacillus plantarum, Levilactobacillus brevis, Pediococcus pentosaceus and Streptococcus thermophilus. Shotgun analysis suggested that in industrial Sfela 1, Str. thermophilus dominated, while industrial Sfela 2 contained high levels of Lactococcus lactis. The two artisanal samples, Sfela touloumotiri and Xerosfeli, were dominated by Tetragenococcus halophilus and Str. thermophilus, respectively. Debaryomyces hansenii was the only yeast species with abundance > 1% present exclusively in the Sfela touloumotiri sample. Identifying additional yeast species in the shotgun data was challenging, possibly due to their low abundance. Sfela cheese appears to contain a rather complex microbial ecosystem and thus needs to be further studied and understood. This might be crucial for improving and standardizing both its production and safety measures.}, } @article {pmid38610059, year = {2024}, author = {Liu, Y and Lin, J}, title = {Periprosthetic bacterial and fugal infection after total knee arthroplasty with one-stage debridement: a case report.}, journal = {Journal of medical case reports}, volume = {18}, number = {1}, pages = {177}, pmid = {38610059}, issn = {1752-1947}, abstract = {BACKGROUND: Periprosthetic infection is a serious complication after arthroplasty and is characterized by a long duration, recurrence, and a low cure rate. Although fungal infections are infrequent, they are often catastrophic, with an insidious onset, a long duration, atypical clinical symptoms, and imaging features in the early stage. They are easily misdiagnosed, or the diagnosis is missed, resulting in wrong treatment approaches.

CASE PRESENTATION: This paper reports a case involving a 62-year-old female patient of Korean ethnicity with a periprosthetic infection after knee arthroplasty who underwent joint debridement. A preoperative metagenomic next-generation sequencing of joint aspirate revealed Staphylococcus epidermidis. However, postsurgical tissue cultures confirmed the fungal infection. The patient received oral voriconazole and intra-articular injection of voriconazole for antifungal treatment. Since bacterial infection could not be ruled out, we also prescribed levofloxacin. No infection recurrence was observed after more than 22 months of follow-up. In the treatment of this patient, successful short-term follow-up was achieved, but long-term efficacy still cannot be determined.

CONCLUSIONS: In addition to the case study, we provide an analysis of the diagnosis and treatment of fungal infection after arthroplasty, especially the efficacy of debridement, antibiotics, and implant retention for a short-term outcome.}, } @article {pmid38609443, year = {2024}, author = {Kholousi Adab, F and Mehdi Yaghoobi, M and Gharechahi, J}, title = {Enhanced crystalline cellulose degradation by a novel metagenome-derived cellulase enzyme.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {8560}, pmid = {38609443}, issn = {2045-2322}, abstract = {Metagenomics has revolutionized access to genomic information of microorganisms inhabiting the gut of herbivorous animals, circumventing the need for their isolation and cultivation. Exploring these microorganisms for novel hydrolytic enzymes becomes unattainable without utilizing metagenome sequencing. In this study, we harnessed a suite of bioinformatic analyses to discover a novel cellulase-degrading enzyme from the camel rumen metagenome. Among the protein-coding sequences containing cellulase-encoding domains, we identified and subsequently cloned and purified a promising candidate cellulase enzyme, Celcm05-2, to a state of homogeneity. The enzyme belonged to GH5 subfamily 4 and exhibited robust enzymatic activity under acidic pH conditions. It maintained hydrolytic activity under various environmental conditions, including the presence of metal ions, non-ionic surfactant Triton X-100, organic solvents, and varying temperatures. With an optimal temperature of 40 °C, Celcm05-2 showcased remarkable efficiency when deployed on crystalline cellulose (> 3.6 IU/mL), specifically Avicel, thereby positioning it as an attractive candidate for a myriad of biotechnological applications spanning biofuel production, paper and pulp processing, and textile manufacturing. Efficient biodegradation of waste paper pulp residues and the evidence of biopolishing suggested that Celcm05-2 can be used in the bioprocessing of cellulosic craft fabrics in the textile industry. Our findings suggest that the camel rumen microbiome can be mined for novel cellulase enzymes that can find potential applications across diverse biotechnological processes.}, } @article {pmid38609404, year = {2024}, author = {Lim, FS and González-Cabrera, J and Keilwagen, J and Kleespies, RG and Jehle, JA and Wennmann, JT}, title = {Advancing pathogen surveillance by nanopore sequencing and genotype characterization of Acheta domesticus densovirus in mass-reared house crickets.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {8525}, pmid = {38609404}, issn = {2045-2322}, abstract = {Rapid and reliable detection of pathogens is crucial to complement the growing industry of mass-reared insects, in order to safeguard the insect colonies from outbreak of diseases, which may cause significant economic loss. Current diagnostic methods are mainly based on conventional PCR and microscopic examination, requiring prior knowledge of disease symptoms and are limited to identifying known pathogens. Here, we present a rapid nanopore-based metagenomics approach for detecting entomopathogens from the European house cricket (Acheta domesticus). In this study, the Acheta domesticus densovirus (AdDV) was detected from diseased individuals using solely Nanopore sequencing. Virus reads and genome assemblies were obtained within twenty-four hours after sequencing. Subsequently, due to the length of the Nanopore reads, it was possible to reconstruct significantly large parts or even the entire AdDV genome to conduct studies for genotype identification. Variant analysis indicated the presence of three AdDV genotypes within the same house cricket population, with association to the vital status of the diseased crickets. This contrast provided compelling evidence for the existence of non-lethal AdDV genotypes. These findings demonstrated nanopore-based metagenomics sequencing as a powerful addition to the diagnostic tool kit for routine pathogen surveillance and diagnosis in the insect rearing industry.}, } @article {pmid38609359, year = {2024}, author = {Han, P and Tang, X and Koch, H and Dong, X and Hou, L and Wang, D and Zhao, Q and Li, Z and Liu, M and Lücker, S and Shi, G}, title = {Unveiling unique microbial nitrogen cycling and nitrification driver in coastal Antarctica.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3143}, pmid = {38609359}, issn = {2041-1723}, support = {42276243//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42371064//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42230505//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Largely removed from anthropogenic delivery of nitrogen (N), Antarctica has notably low levels of nitrogen. Though our understanding of biological sources of ammonia have been elucidated, the microbial drivers of nitrate (NO3[-]) cycling in coastal Antarctica remains poorly understood. Here, we explore microbial N cycling in coastal Antarctica, unraveling the biological origin of NO3[-] via oxygen isotopes in soil and lake sediment, and through the reconstruction of 1968 metagenome-assembled genomes from 29 microbial phyla. Our analysis reveals the metabolic potential for microbial N2 fixation, nitrification, and denitrification, but not for anaerobic ammonium oxidation, signifying a unique microbial N-cycling dynamic. We identify the predominance of complete ammonia oxidizing (comammox) Nitrospira, capable of performing the entire nitrification process. Their adaptive strategies to the Antarctic environment likely include synthesis of trehalose for cold stress, high substrate affinity for resource utilization, and alternate metabolic pathways for nutrient-scarce conditions. We confirm the significant role of comammox Nitrospira in the autotrophic, nitrification process via [13]C-DNA-based stable isotope probing. This research highlights the crucial contribution of nitrification to the N budget in coastal Antarctica, identifying comammox Nitrospira clade B as a nitrification driver.}, } @article {pmid38609235, year = {2024}, author = {Hou, Q and Wang, Y and Qu, D and Zhao, H and Tian, L and Zhou, J and Liu, J and Guo, Z}, title = {Microbial communities, functional, and flavor differences among three different-colored high-temperature Daqu: A comprehensive metagenomic, physicochemical, and electronic sensory analysis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {184}, number = {}, pages = {114257}, doi = {10.1016/j.foodres.2024.114257}, pmid = {38609235}, issn = {1873-7145}, abstract = {High-temperature Daqu (HTD) is the starter for producing sauce-flavor Baijiu, with different-colored Daqu (white, yellow, and black) reflecting variations in fermentation chamber conditions, chemical reactions, and associated microbiota. Understanding the relationship between Daqu characteristics and flavor/taste is challenging yet vital for improving Baijiu fermentation. This study utilized metagenomic sequencing, physicochemical analysis, and electronic sensory evaluation to compare three different-colored HTD and their roles in fermentation. Fungi and bacteria dominated the HTD-associated microbiota, with fungi increasing as the fermentation temperature rose. The major fungal genera were Aspergillus (40.17%) and Kroppenstedtia (21.16%), with Aspergillus chevalieri (25.65%) and Kroppenstedtia eburnean (21.07%) as prevalent species. Microbial communities, functionality, and physicochemical properties, particularly taste and flavor, were color-specific in HTD. Interestingly, the microbial communities in different-colored HTDs demonstrated robust functional complementarity. White Daqu exhibited non-significantly higher α-diversity compared to the other two Daqu. It played a crucial role in breaking down substrates such as starch, proteins, hyaluronic acid, and glucan, contributing to flavor precursor synthesis. Yellow Daqu, which experienced intermediate temperature and humidity, demonstrated good esterification capacity and a milder taste profile. Black Daqu efficiently broke down raw materials, especially complex polysaccharides, but had inferior flavor and taste. Notably, large within-group variations in physicochemical quality and microbial composition were observed, highlighting limitations in color-based HTD quality assessment. Water content in HTD was associated with Daqu flavor, implicating its crucial role. This study revealed the complementary roles of the three HTD types in sauce-flavor Baijiu fermentation, providing valuable insights for product enhancement.}, } @article {pmid38609223, year = {2024}, author = {Ma, J and Qian, C and Hu, Q and Zhang, J and Gu, G and Liang, X and Zhang, L}, title = {The bacteriome-coupled phage communities continuously contract and shift to orchestrate the traditional rice vinegar fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {184}, number = {}, pages = {114244}, doi = {10.1016/j.foodres.2024.114244}, pmid = {38609223}, issn = {1873-7145}, abstract = {Amounts of microbiome studies have uncovered the microbial communities of traditional food fermentations, while in which the phageome development with time is poorly understood. Here, we conducted a study to decipher both phageome and bacteriome of the traditional rice vinegar fermentation. The vinegar phageomes showed significant differences in the alpha diversity, network density and clustering coefficient over time. Peduoviridae had the highest relative abundance. Moreover, the phageome negatively correlated to the cognate bacteriome in alpha diversity, and undergone constantly contracting and shifting across the temporal scale. Nevertheless, 257 core virial clusters (VCs) persistently occurred with time whatever the significant impacts imposed by the varied physiochemical properties. Glycoside hydrolase (GH) and glycosyltransferase (GT) families genes displayed the higher abundances across all samples. Intriguingly, diversely structuring of toxin-antitoxin systems (TAs) and CRISPR-Cas arrays were frequently harbored by phage genomes. Their divergent organization and encoding attributes underlie the multiple biological roles in modulation of network and/or contest of phage community as well as bacterial host community. This phageome-wide mapping will fuel the current insights of phage community ecology in other traditional fermented ecosystems that are challenging to decipher.}, } @article {pmid38608888, year = {2024}, author = {Feng, K and Lu, Y and Zhou, W and Xu, Z and Ye, J and Zhang, S and Chen, J and Zhao, J}, title = {Metagenomics revealing biomolecular insights into the enhanced toluene removal and electricity generation in PANI@CNT bioanode.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {172402}, doi = {10.1016/j.scitotenv.2024.172402}, pmid = {38608888}, issn = {1879-1026}, abstract = {Microbial fuel cells (MFCs) have significant potential for environmental remediation and energy recycling directly from refractory aromatic hydrocarbons. To boost the capacities of toluene removal and the electricity production in MFCs, this study constructed a polyaniline@carbon nanotube (PANI@CNT) bioanode with a three-dimensional framework structure. Compared with the control bioanode based on graphite sheet, the PANI@CNT bioanode increased the output voltage and toluene degradation kinetics by 2.27-fold and 1.40-fold to 0.399 V and 0.60 h[-1], respectively. Metagenomic analysis revealed that the PANI@CNT bioanode promoted the selective enrichment of Pseudomonas, with the dual functions of degrading toluene and generating exogenous electrons. Additionally, compelling genomic evidence elucidating the relationship between functional genes and microorganisms was found. It was interesting that the genes derived from Pseudomonas related to extracellular electron transfer, tricarboxylic acid cycle, and toluene degradation were upregulated due to the existence of PANI@CNT. This study provided biomolecular insights into key genes and related microorganisms that effectively facilitated the organic pollutant degradation and energy recovery in MFCs, offering a novel alternative for high-performance bioanode.}, } @article {pmid38608842, year = {2024}, author = {Sun, Z and Ning, Z and Figeys, D}, title = {The Landscape and Perspectives of the Human Gut Metaproteomics.}, journal = {Molecular & cellular proteomics : MCP}, volume = {}, number = {}, pages = {100763}, doi = {10.1016/j.mcpro.2024.100763}, pmid = {38608842}, issn = {1535-9484}, abstract = {The human gut microbiome is closely associated with human health and diseases. Metaproteomics has emerged as a valuable tool for studying the functionality of the gut microbiome by analyzing the entire proteins present in microbial communities. Recent advancements in liquid chromatography and tandem mass spectrometry (LC-MS/MS) techniques have expanded the detection range of metaproteomics. However, the overall coverage of the proteome in metaproteomics is still limited. While metagenomics studies have revealed substantial microbial diversity and functional potential of the human gut microbiome, few studies have summarized and studied the human gut microbiome landscape revealed with metaproteomics. In this paper, we present the current landscape of human gut metaproteomics studies by re-analyzing the identification results from fifteen published studies. We quantified the limited proteome coverage in metaproteomics and revealed a high proportion of annotation coverage of metaproteomics-identified proteins. We conducted a preliminary comparison between the metaproteomics view and the metagenomics view of the human gut microbiome, identifying key areas of consistency and divergence. Based on the current landscape of human gut metaproteomics, we discuss the feasibility of using metaproteomics to study functionally unknown proteins and propose a whole workflow peptide-centric analysis. Additionally, we suggest enhancing metaproteomics analysis by refining taxonomic classification and calculating confidence scores, as well as developing tools for analyzing the interaction between taxonomy and function.}, } @article {pmid38608741, year = {2024}, author = {Kebede, V and Ravizza, T and Balosso, S and Di Sapia, R and Canali, L and Soldi, S and Galletti, S and Papazlatani, C and Karas, PA and Vasileiadis, S and Sforzini, A and Pasetto, L and Bonetto, V and Vezzani, A and Vesci, L}, title = {Early treatment with rifaximin during epileptogenesis reverses gut alterations and reduces seizure duration in a mouse model of acquired epilepsy.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bbi.2024.04.007}, pmid = {38608741}, issn = {1090-2139}, abstract = {The gut microbiota is altered in epilepsy and is emerging as a potential target for new therapies. We studied the effects of rifaximin, a gastrointestinal tract-specific antibiotic, on seizures and neuropathology and on alterations in the gut and its microbiota in a mouse model of temporal lobe epilepsy (TLE). Epilepsy was induced by intra-amygdala kainate injection causing status epilepticus (SE) in C57Bl6 adult male mice. Sham mice were injected with vehicle. Two cohorts of SE mice were fed a rifaximin-supplemented diet for 21 days, starting either at 24 h post-SE (early disease stage) or at day 51 post-SE (chronic disease stage). Corresponding groups of SE mice (one each disease stage) were fed a standard (control) diet. Cortical ECoG recording was done at each disease stage (24/7) for 21 days in all SE mice to measure the number and duration of spontaneous seizures during either rifaximin treatment or control diet. Then, epileptic mice ± rifaximin and respective sham mice were sacrificed and brain, gut and feces collected. Biospecimens were used for: (i) quantitative histological analysis of the gut structural and cellular components; (ii) markers of gut inflammation and intestinal barrier integrity by RTqPCR; (iii) 16S rRNA metagenomics analysis in feces. Hippocampal neuronal cell loss was assessed in epileptic mice killed in the early disease phase. Rifaximin administered for 21 days post-SE (early disease stage) reduced seizure duration (p < 0.01) and prevented hilar mossy cells loss in the hippocampus compared to epileptic mice fed a control diet. Epileptic mice fed a control diet showed a reduction of both villus height and villus/crypt depth ratio (p < 0.01) and a decreased number of goblet cells (p < 0.01) in the duodenum, as well as increased macrophage (Iba1)-immunostaining in the jejunum (p < 0.05), compared to respective sham mice. Rifaximin's effect on seizures was associated with a reversal of gut structural and cellular changes, except for goblet cells which remained reduced. Seizure duration in epileptic mice was negatively correlated with the number of mossy cells (p < 0.01) and with villus height/crypt depth ratio (p < 0.05). Rifaximin-treated epileptic mice also showed increased tight junctions (occludin and ZO-1, p < 0.01) and decreased TNF mRNA expression (p < 0.01) in the duodenum compared to epileptic mice fed a control diet. Rifaximin administered for 21 days in chronic epileptic mice (chronic disease stage) did not change the number or duration of seizures compared to epileptic mice fed a control diet. Chronic epileptic mice fed a control diet showed an increased crypt depth (p < 0.05) and reduced villus height/crypt depth ratio (p < 0.01) compared to respective sham mice. Rifaximin treatment did not affect these intestinal changes. At both disease stages, rifaximin modified α- and β-diversity in epileptic and sham mice compared to respective mice fed a control diet. The microbiota composition in epileptic mice, as well as the effects of rifaximin at the phylum, family and genus levels, depended on the stage of the disease. During the early disease phase, the abundance of specific taxa was positively correlated with seizure duration in epileptic mice. In conclusion, gut-related alterations reflecting a dysfunctional state, occur during epilepsy development in a TLE mouse model. A short-term treatment with rifaximin during the early phase of the disease, reduced seizure duration and neuropathology, and reversed some intestinal changes, strengthening the therapeutic effects of gut-based therapies in epilepsy.}, } @article {pmid38608237, year = {2024}, author = {Downie, DL and Rao, P and David-Ferdon, C and Courtney, S and Lee, JS and Kugley, S and MacDonald, PDM and Barnes, K and Fisher, S and Andreadis, JL and Chaitram, J and Mauldin, MR and Salerno, RM and Schiffer, J and Gundlapalli, AV}, title = {Literature Review of Pathogen Agnostic Molecular Testing of Clinical Specimens From Difficult-to-Diagnose Patients: Implications for Public Health.}, journal = {Health security}, volume = {}, number = {}, pages = {}, doi = {10.1089/hs.2023.0100}, pmid = {38608237}, issn = {2326-5108}, abstract = {To better identify emerging or reemerging pathogens in patients with difficult-to-diagnose infections, it is important to improve access to advanced molecular testing methods. This is particularly relevant for cases where conventional microbiologic testing has been unable to detect the pathogen and the patient's specimens test negative. To assess the availability and utility of such testing for human clinical specimens, a literature review of published biomedical literature was conducted. From a corpus of more than 4,000 articles, a set of 34 reports was reviewed in detail for data on where the testing was being performed, types of clinical specimens tested, pathogen agnostic techniques and methods used, and results in terms of potential pathogens identified. This review assessed the frequency of advanced molecular testing, such as metagenomic next generation sequencing that has been applied to clinical specimens for supporting clinicians in caring for difficult-to-diagnose patients. Specimen types tested were from cerebrospinal fluid, respiratory secretions, and other body tissues and fluids. Publications included case reports and series, and there were several that involved clinical trials, surveillance studies, research programs, or outbreak situations. Testing identified both known human pathogens (sometimes in new sites) and previously unknown human pathogens. During this review, there were no apparent coordinated efforts identified to develop regional or national reports on emerging or reemerging pathogens. Therefore, development of a coordinated sentinel surveillance system that applies advanced molecular methods to clinical specimens which are negative by conventional microbiological diagnostic testing would provide a foundation for systematic characterization of emerging and underdiagnosed pathogens and contribute to national biodefense strategy goals.}, } @article {pmid38608141, year = {2024}, author = {Hunt, KA and Carr, AV and Otwell, AE and Valenzuela, JJ and Walker, KS and Dixon, ER and Lui, LM and Nielsen, TN and Bowman, S and von Netzer, F and Moon, JW and Schadt, CW and Rodriguez, M and Lowe, K and Joyner, D and Davis, KJ and Wu, X and Chakraborty, R and Fields, MW and Zhou, J and Hazen, TC and Arkin, AP and Wankel, SD and Baliga, NS and Stahl, DA}, title = {Contribution of Microorganisms with the Clade II Nitrous Oxide Reductase to Suppression of Surface Emissions of Nitrous Oxide.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c07972}, pmid = {38608141}, issn = {1520-5851}, abstract = {The sources and sinks of nitrous oxide, as control emissions to the atmosphere, are generally poorly constrained for most environmental systems. Initial depth-resolved analysis of nitrous oxide flux from observation wells and the proximal surface within a nitrate contaminated aquifer system revealed high subsurface production but little escape from the surface. To better understand the environmental controls of production and emission at this site, we used a combination of isotopic, geochemical, and molecular analyses to show that chemodenitrification and bacterial denitrification are major sources of nitrous oxide in this subsurface, where low DO, low pH, and high nitrate are correlated with significant nitrous oxide production. Depth-resolved metagenomes showed that consumption of nitrous oxide near the surface was correlated with an enrichment of Clade II nitrous oxide reducers, consistent with a growing appreciation of their importance in controlling release of nitrous oxide to the atmosphere. Our work also provides evidence for the reduction of nitrous oxide at a pH of 4, well below the generally accepted limit of pH 5.}, } @article {pmid38606356, year = {2024}, author = {Monger, XC and Saucier, L and Guay, F and Turcotte, A and Lemieux, J and Pouliot, E and Fournaise, S and Vincent, AT}, title = {Effect of a probiotic and an antibiotic on the mobilome of the porcine microbiota.}, journal = {Frontiers in genetics}, volume = {15}, number = {}, pages = {1355134}, pmid = {38606356}, issn = {1664-8021}, abstract = {Introduction: To consider the growing health issues caused by antibiotic resistance from a "one health" perspective, the contribution of meat production needs to be addressed. While antibiotic resistance is naturally present in microbial communities, the treatment of farm animals with antibiotics causes an increase in antibiotic resistance genes (ARG) in the gut microbiome. Pigs are among the most prevalent animals in agriculture; therefore, reducing the prevalence of antibiotic-resistant bacteria in the pig gut microbiome could reduce the spread of antibiotic resistance. Probiotics are often studied as a way to modulate the microbiome and are, therefore, an interesting way to potentially decrease antibiotic resistance. Methods: To assess the efficacy of a probiotic to reduce the prevalence of ARGs in the pig microbiome, six pigs received either treatment with antibiotics (tylvalosin), probiotics (Pediococcus acidilactici MA18/5M; Biopower[®] PA), or a combination of both. Their faeces and ileal digesta were collected and DNA was extracted for whole genome shotgun sequencing. The reads were compared with taxonomy and ARG databases to identify the taxa and resistance genes in the samples. Results: The results showed that the ARG profiles in the faeces of the antibiotic and combination treatments were similar, and both were different from the profiles of the probiotic treatment (p < 0.05). The effects of the treatments were different in the digesta and faeces. Many macrolide resistance genes were detected in a higher proportion in the microbiome of the pigs treated with antibiotics or the combination of probiotics and antibiotics. Resistance-carrying conjugative plasmids and horizontal transfer genes were also amplified in faeces samples for the antibiotic and combined treatments. There was no effect of treatment on the short chain fatty acid content in the digesta or the faeces. Conclusion: There is no positive effect of adding probiotics to an antibiotic treatment when these treatments are administered simultaneously.}, } @article {pmid38606341, year = {2024}, author = {Eitel, M and Osigus, HJ and Brenzinger, B and Wörheide, G}, title = {Beauty in the beast - Placozoan biodiversity explored through molluscan predator genomics.}, journal = {Ecology and evolution}, volume = {14}, number = {4}, pages = {e11220}, pmid = {38606341}, issn = {2045-7758}, abstract = {The marine animal phylum Placozoa is characterized by a poorly explored cryptic biodiversity combined with very limited knowledge of their ecology. While placozoans are typically found as part of the epibenthos of coastal waters, known placozoan predators, namely small, shell-less sea slugs belonging to the family Rhodopidae (Mollusca: Gastropoda: Heterobranchia), inhabit the interstitium of seafloor sediment. In order to gain further insights into this predator-prey relationship and to expand our understanding of placozoan ecological niches, we screened publicly available whole-body metagenomic data from two rhodopid specimens collected from coastal sediments. Our analysis not only revealed the signatures of three previously unknown placozoan lineages in these sea slug samples but also enabled the assembly of three complete and two partial mitochondrial chromosomes belonging to four previously described placozoan genera, substantially extending the picture of placozoan biodiversity. Our findings further refine the molecular phylogeny of the Placozoa, corroborate the recently established taxonomic ranks in this phylum, and provide molecular support that known placozoan clades should be referred to as genera. We finally discuss the main finding of our study - the presence of placozoans in the sea floor sediment interstitium - in the context of their ecological, biological, and natural history implications.}, } @article {pmid38606292, year = {2024}, author = {Jiang, Z and Gai, W and Zhang, X and Zheng, Y and Jin, X and Han, Z and Ao, G and He, J and Shu, D and Liu, X and Zhou, Y and Hua, Z}, title = {Clinical performance of metagenomic next-generation sequencing for diagnosis of pulmonary Aspergillus infection and colonization.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1345706}, pmid = {38606292}, issn = {2235-2988}, abstract = {BACKGROUND: Investigations assessing the value of metagenomic next-generation sequencing (mNGS) for distinguish Aspergillus infection from colonization are currently insufficient.

METHODS: The performance of mNGS in distinguishing Aspergillus infection from colonization, along with the differences in patients' characteristics, antibiotic adjustment, and lung microbiota, were analyzed.

RESULTS: The abundance of Aspergillus significantly differed between patients with Aspergillus infection (n=36) and colonization (n=32) (P < 0.0001). Receiver operating characteristic (ROC) curve result for bronchoalveolar lavage fluid (BALF) mNGS indicated an area under the curve of 0.894 (95%CI: 0.811-0.976), with an optimal threshold value of 23 for discriminating between Aspergillus infection and colonization. The infection group exhibited a higher proportion of antibiotic adjustments in comparison to the colonization group (50% vs. 12.5%, P = 0.001), with antibiotic escalation being more dominant. Age, length of hospital stay, hemoglobin, cough and chest distress were significantly positively correlated with Aspergillus infection. The abundance of A. fumigatus and Epstein-Barr virus (EBV) significantly increased in the infection group, whereas the colonization group exhibited higher abundance of A. niger.

CONCLUSION: BALF mNGS is a valuable tool for differentiating between colonization and infection of Aspergillus. Variations in patients' age, length of hospital stay, hemoglobin, cough and chest distress are observable between patients with Aspergillus infection and colonization.}, } @article {pmid38605646, year = {2024}, author = {Heston, SM and Hurst, JH and Kelly, MS}, title = {Understanding the influence of the microbiome on childhood infections.}, journal = {Expert review of anti-infective therapy}, volume = {}, number = {}, pages = {1-17}, doi = {10.1080/14787210.2024.2340664}, pmid = {38605646}, issn = {1744-8336}, abstract = {INTRODUCTION: The microbiome is known to have a substantial impact on human health and disease. However, the impacts of the microbiome on immune system development, susceptibility to infectious diseases, and vaccine-elicited immune responses are emerging areas of interest.

AREAS COVERED: In this review, we provide an overview of development of the microbiome during childhood. We highlight available data suggesting that the microbiome is critical to maturation of the immune system and modifies susceptibility to a variety of infections during childhood and adolescence, including respiratory tract infections, Clostridioides difficile infection, and sexually transmitted infections. We discuss currently available and investigational therapeutics that have the potential to modify the microbiome to prevent or treat infections among children. Finally, we review the accumulating evidence that the gut microbiome influences vaccine-elicited immune responses among children.

EXPERT OPINION: Recent advances in sequencing technologies have led to an explosion of studies associating the human microbiome with the risk and severity of infectious diseases. As our knowledge of the extent to which the microbiome influences childhood infections continues to grow, microbiome-based diagnostics and therapeutics will increasingly be incorporated into clinical practice to improve the prevention, diagnosis, and treatment of infectious diseases among children.}, } @article {pmid38605401, year = {2024}, author = {Feng, X and Li, H}, title = {Evaluating and improving the representation of bacterial contents in long-read metagenome assemblies.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {92}, pmid = {38605401}, issn = {1474-760X}, support = {R01HG010040/HG/NHGRI NIH HHS/United States ; U01HG010961/HG/NHGRI NIH HHS/United States ; }, abstract = {BACKGROUND: In the metagenomic assembly of a microbial community, abundant species are often thought to assemble well given their deeper sequencing coverage. This conjuncture is rarely tested or evaluated in practice. We often do not know how many abundant species are missing and do not have an approach to recover them.

RESULTS: Here, we propose k-mer based and 16S RNA based methods to measure the completeness of metagenome assembly. We show that even with PacBio high-fidelity (HiFi) reads, abundant species are often not assembled, as high strain diversity may lead to fragmented contigs. We develop a novel reference-free algorithm to recover abundant metagenome-assembled genomes (MAGs) by identifying circular assembly subgraphs. Complemented with a reference-free genome binning heuristics based on dimension reduction, the proposed method rescues many abundant species that would be missing with existing methods and produces competitive results compared to those state-of-the-art binners in terms of total number of near-complete genome bins.

CONCLUSIONS: Our work emphasizes the importance of metagenome completeness, which has often been overlooked. Our algorithm generates more circular MAGs and moves a step closer to the complete representation of microbial communities.}, } @article {pmid38604482, year = {2024}, author = {Chang, H and Du, B and He, K and Yin, Q and Wu, G}, title = {Mechanistic understanding of acclimation and energy metabolism of acetoclastic methanogens under different substrate to microorganism ratios.}, journal = {Environmental research}, volume = {}, number = {}, pages = {118911}, doi = {10.1016/j.envres.2024.118911}, pmid = {38604482}, issn = {1096-0953}, abstract = {Mechanistic understanding of acetoclastic methanogenesis is pivotal for optimizing anaerobic digestion for efficient methane production. In this study, two different operational modes, continuous flow reactor (CFR) and sequencing batch reactor (SBR), accompanied with solids retention times (SRT) of 10 days (SBR10d and CFR10d) and 25 days (SBR25d and CFR25d) were implemented to elucidate their impacts on microbial communities and energy metabolism of methanogens in acetate-fed systems. Microbial community analysis revealed that the relative abundance of Methanosarcina (16.0% ∼ 46.0%) surpassed Methanothrix (3.7% ∼ 22.9%) in each reactor. SBRs had the potential to enrich both Methanothrix and Methanosarcina. Compared to SBRs, CFRs had lower total relative abundance of methanogens. Methanosarcina exhibited a superior enrichment in reactors with 10-day SRT, while Methanothrix preferred to be acclimated in reactors with 25-day SRT. The operational mode and SRT were also observed to affect the distribution of acetate-utilizing bacteria, including Pseudomonas, Desulfocurvus, Mesotoga, and Thauera. Regarding enzymes involved in energy metabolism, Ech and Vho/Vht demonstrated higher relative abundances at 10-day SRT compared to 25-day SRT, whereas Fpo and MtrA-H showed higher relative abundances in SBRs than those in CFRs. The relative abundance of genes encoding ATPase harbored by Methanothrix was higher than Methanosarcina at 25-day SRT. Additionally, the relative abundance of V/A-type ATPase (typically for methanogens) was observed higher in SBRs compared to CFRs, while the F-type ATPase (typically for bacteria) exhibited higher relative abundance in CFRs than that in SBRs.}, } @article {pmid38604355, year = {2024}, author = {Yin, Z and Liang, J and Zhang, M and Chen, B and Yu, Z and Tian, X and Deng, X and Peng, L}, title = {Pan-genome insights into adaptive evolution of bacterial symbionts in mixed host-microbe symbioses represented by human gut microbiota Bacteroides cellulosilyticus.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {172251}, doi = {10.1016/j.scitotenv.2024.172251}, pmid = {38604355}, issn = {1879-1026}, abstract = {Animal hosts harbor diverse assemblages of microbial symbionts that play crucial roles in the host's lifestyle. The link between microbial symbiosis and host development remains poorly understood. In particular, little is known about the adaptive evolution of gut bacteria in host-microbe symbioses. Recently, symbiotic relationships have been categorized as open, closed, or mixed, reflecting their modes of inter-host transmission and resulting in distinct genomic features. Members of the genus Bacteroides are the most abundant human gut microbiota and possess both probiotic and pathogenic potential, providing an excellent model for studying pan-genome evolution in symbiotic systems. Here, we determined the complete genome of an novel clinical strain PL2022, which was isolated from a blood sample and performed pan-genome analyses on a representative set of Bacteroides cellulosilyticus strains to quantify the influence of the symbiotic relationship on the evolutionary dynamics. B. cellulosilyticus exhibited correlated genomic features with both open and closed symbioses, suggesting a mixed symbiosis. An open pan-genome is characterized by abundant accessory gene families, potential horizontal gene transfer (HGT), and diverse mobile genetic elements (MGEs), indicating an innovative gene pool, mainly associated with genomic islands and plasmids. However, massive parallel gene loss, weak purifying selection, and accumulation of positively selected mutations were the main drivers of genome reduction in B. cellulosilyticus. Metagenomic read recruitment analyses showed that B. cellulosilyticus members are globally distributed and active in human gut habitats, in line with predominant vertical transmission in the human gut. However, existence and/or high abundance were also detected in non-intestinal tissues, other animal hosts, and non-host environments, indicating occasional horizontal transmission to new niches, thereby creating arenas for the acquisition of novel genes. This case study of adaptive evolution under a mixed host-microbe symbiosis advances our understanding of symbiotic pan-genome evolution. Our results highlight the complexity of genetic evolution in this unusual intestinal symbiont.}, } @article {pmid38603815, year = {2024}, author = {Bai, H and He, LY and Gao, FZ and Yao, KS and Zhang, M and Qiao, LK and Chen, ZY and He, LX and Liu, YS and Zhao, JL and Ying, GG}, title = {Airborne antibiotic resistome and microbiome in pharmaceutical factories.}, journal = {Environment international}, volume = {186}, number = {}, pages = {108639}, doi = {10.1016/j.envint.2024.108639}, pmid = {38603815}, issn = {1873-6750}, abstract = {Antimicrobial resistance is considered to be one of the biggest public health problems, and airborne transmission is an important but under-appreciated pathway for the spread of antibiotic resistance genes (ARGs) in the environment. Previous research has shown pharmaceutical factories to be a major source of ARGs and antibiotic resistant bacteria (ARB) in the surrounding receiving water and soil environments. Pharmaceutical factories are hotspots of antibiotic resistance, but the atmospheric transmission and its environmental risk remain more concerns. Here, we conducted a metagenomic investigation into the airborne microbiome and resistome in three pharmaceutical factories in China. Soil (average: 38.45%) and wastewater (average: 28.53%) were major contributors of airborne resistome. ARGs (vanR/vanS, blaOXA, and CfxA) conferring resistance to critically important clinically used antibiotics were identified in the air samples. The wastewater treatment area had significantly higher relative abundances of ARGs (average: 0.64 copies/16S rRNA). Approximately 28.2% of the detected airborne ARGs were found to be associated with plasmids, and this increased to about 50% in the wastewater treatment area. We have compiled a list of high-risk airborne ARGs found in pharmaceutical factories. Moreover, A total of 1,043 viral operational taxonomic units were identified and linked to 47 family-group taxa. Different CRISPR-Cas immune systems have been identified in bacterial hosts in response to phage infection. Similarly, higher phage abundance (average: 2451.70 PPM) was found in the air of the wastewater treatment area. Our data provide insights into the antibiotic resistance gene profiles and microbiome (bacterial and non-bacterial) in pharmaceutical factories and reveal the potential role of horizontal transfer in the spread of airborne ARGs, with implications for human and animal health.}, } @article {pmid38602400, year = {2024}, author = {Shcherbakova, VA and Rechkina, VI and Trubitsyn, VE}, title = {Metagenome-assembled genomes of the methanogenic enrichment obtained from drilling fluid wastes stored in permafrost.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0115923}, doi = {10.1128/mra.01159-23}, pmid = {38602400}, issn = {2576-098X}, abstract = {We studied methanogenic enrichment (Kha) from spent drilling fluid stored in permafrost, Kharasavey (71°10'50″N 66°51'50″E) gas field located in the western part of the Yamal Peninsula. The metagenome-assembled genomes showed that Kha consists of representatives of Methanosarcina, Methanobacterium, Proteinifillum, and Synergistetes genera.}, } @article {pmid38601940, year = {2024}, author = {Sohaib, H and Fays, M and Khatib, A and Rivière, J and El Aouad, N and Desoignies, N}, title = {Contribution to the characterization of the seed endophyte microbiome of Argania spinosa across geographical locations in Central Morocco using metagenomic approaches.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1310395}, pmid = {38601940}, issn = {1664-302X}, abstract = {Microbial endophytes are microorganisms that live inside plants, and some of them play important yet understudied roles in plant health, growth, and adaptation to environmental conditions. Their diversity within plants has traditionally been underestimated due to the limitations of culture-dependent techniques. Metagenomic profiling provides a culture-independent approach to characterize entire microbial communities. The argan tree (Argania spinosa) is ecologically and economically important in Morocco, yet its seed endophyte microbiome remains unexplored. This study aimed to compare the bacterial and fungal endophyte communities associated with argan seeds collected from six sites across Morocco using Illumina MiSeq sequencing of the 16S rRNA gene and ITS regions, respectively. Bacterial DNA was extracted from surface-sterilized seeds and amplified using universal primers, while fungal DNA was isolated directly from seeds. Bioinformatics analysis of sequencing data identified taxonomic profiles at the phylum to genus levels. The results indicated that bacterial communities were dominated by the genus Rhodoligotrophos, while fungal communities exhibited varying degrees of dominance between Ascomycota and Basidiomycota depending on site, with Penicillium being the most abundant overall. Distinct site-specific profiles were observed, with Pseudomonas, Bacillus, and Aspergillus present across multiple locations. Alpha diversity indices revealed variation in endophyte richness between seed sources. In conclusion, this first exploration of the argan seed endophyte microbiome demonstrated environmental influence on community structure. While facing limitations due to small sample sizes and lack of ecological metadata, it provides a foundation for future mechanistic investigations into how specific endophyte-host interactions shape argan adaptation across Morocco's diverse landscapes.}, } @article {pmid38601936, year = {2024}, author = {Ortañez, J and Degnan, PH}, title = {Tracking and characterization of a novel conjugative transposon identified by shotgun transposon mutagenesis.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1241582}, pmid = {38601936}, issn = {1664-302X}, abstract = {The horizontal transfer of mobile genetic elements (MGEs) is an essential process determining the functional and genomic diversity of bacterial populations. MGEs facilitate the exchange of fitness determinant genes like antibiotic resistance and virulence factors. Various computational methods exist to identify potential MGEs, but confirming their ability to transfer requires additional experimental approaches. Here, we apply a transposon (Tn) mutagenesis technique for confirming mobilization without the need for targeted mutations. Using this method, we identified two MGEs, including a previously known conjugative transposon (CTn) called BoCTn found in Bacteroides ovatus and a novel CTn, PvCTn, identified in Phocaeicola vulgatus. In addition, Tn mutagenesis and subsequent genetic deletion enabled our characterization of a helix-turn-helix motif gene, BVU3433 which negatively regulates the conjugation efficiency of PvCTn in vitro. Furthermore, our transcriptomics data revealed that BVU3433 plays a crucial role in the repression of PvCTn genes, including genes involved in forming complete conjugation machinery [Type IV Secretion System (T4SS)]. Finally, analysis of individual strain genomes and community metagenomes identified the widespread prevalence of PvCTn-like elements with putative BVU3433 homologs among human gut-associated bacteria. In summary, this Tn mutagenesis mobilization method (TMMM) enables observation of transfer events in vitro and can ultimately be applied in vivo to identify a broader diversity of functional MGEs that may underly the transfer of important fitness determinants.}, } @article {pmid38600953, year = {2024}, author = {Shen, Y and Cao, J and Hu, T and Yang, X and Zhao, Y and Shen, Y and Ye, B and Yu, Y and Wu, D}, title = {Successful Treatment of an AML Patient Infected with Hypervirulent ST463 Pseudomonas Aeruginosa Harboring Rare Carbapenem-Resistant Genes blaAFM-1 and blaKPC-2 Following Allogeneic Hematopoietic Stem Cell Transplantation.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {1357-1365}, pmid = {38600953}, issn = {1178-6973}, abstract = {BACKGROUND: Carbapenem-resistant P. aeruginosa (CRPA) is a common hospital-acquired bacterium. It exhibits high resistance to many antibiotics, including ceftazidime/avibactam and cefteolozane/tazobactam. The presence of carbapenem-resistant genes and co-existence Klebsiella pneumoniae carbapenemase (KPC) and metallo-β-lactamases (MBLs) further inactivated all β-lactams. Understanding the resistance genes of CRPA can help in uncovering the resistance mechanism and guiding anti-infective treatment. Herein, we reported a case of perianal infection with hypervirulent ST463 Pseudomonas aeruginosa.

CASE PRESENTATION: The case is a 32-year-old acute myeloid leukemia (AML) patient with fever and septic shock during hematopoietic stem cell transplantation (HSCT), and the pathogen was finally identified as a highly virulent sequence type 463 (ST463) P. aeruginosa harboring carbapenem-resistant genes blaAFM-1 and blaKPC-2, which was detected in the bloodstream and originated from a perianal infection. The strain was resistant to ceftazidime/avibactam but successfully treated with polymyxin B, surgical debridement, and granulocyte engraftment after HSCT. The AML was cured during the 19-month follow-up.

CONCLUSION: This case emphasizes the importance of metagenomic next-generation sequencing (mNGS) and whole-genome sequencing (WGS) in identifying microbes with rare resistant genes, and managing CRPA, especially in immunocompromised patients. Polymyxin B may be the least resistant option.}, } @article {pmid38600293, year = {2024}, author = {Jiang, MZ and Liu, C and Xu, C and Jiang, H and Wang, Y and Liu, SJ}, title = {Gut microbial interactions based on network construction and bacterial pairwise cultivation.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {38600293}, issn = {1869-1889}, abstract = {Association networks are widely applied for the prediction of bacterial interactions in studies of human gut microbiomes. However, the experimental validation of the predicted interactions is challenging due to the complexity of gut microbiomes and the limited number of cultivated bacteria. In this study, we addressed this challenge by integrating in vitro time series network (TSN) associations and co-cultivation of TSN taxon pairs. Fecal samples were collected and used for cultivation and enrichment of gut microbiome on YCFA agar plates for 13 days. Enriched cells were harvested for DNA extraction and metagenomic sequencing. A total of 198 metagenome-assembled genomes (MAGs) were recovered. Temporal dynamics of bacteria growing on the YCFA agar were used to infer microbial association networks. To experimentally validate the interactions of taxon pairs in networks, we selected 24 and 19 bacterial strains from this study and from the previously established human gut microbial biobank, respectively, for pairwise co-cultures. The co-culture experiments revealed that most of the interactions between taxa in networks were identified as neutralism (51.67%), followed by commensalism (21.67%), amensalism (18.33%), competition (5%) and exploitation (3.33%). Genome-centric analysis further revealed that the commensal gut bacteria (helpers and beneficiaries) might interact with each other via the exchanges of amino acids with high biosynthetic costs, short-chain fatty acids, and/or vitamins. We also validated 12 beneficiaries by adding 16 additives into the basic YCFA medium and found that the growth of 66.7% of these strains was significantly promoted. This approach provides new insights into the gut microbiome complexity and microbial interactions in association networks. Our work highlights that the positive relationships in gut microbial communities tend to be overestimated, and that amino acids, short-chain fatty acids, and vitamins are contributed to the positive relationships.}, } @article {pmid38600101, year = {2024}, author = {Ma, X and Wen, G and Zhao, Z and Lu, L and Li, T and Gao, N and Han, G}, title = {Alternations in the human skin, gut and vaginal microbiomes in perimenopausal or postmenopausal Vulvar lichen sclerosus.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {8429}, pmid = {38600101}, issn = {2045-2322}, support = {YN2021QX02//Peking University International Hospital/ ; }, abstract = {Vulvar lichen sclerosus (VLS) is a chronic and progressive dermatologic condition that can cause physical dysfunction, disfigurement, and impaired quality of life. However, the etiology of VLS remains unknown. The vulvar skin, intestinal and vaginal microbiomes have been postulated to play important roles in the pathogenesis of this disease. The aim of this study was to compare the compositional characteristics of the vulvar skin, vagina, and gut microbiota between perimenopausal or postmenopausal VLS patients and healthy controls. The study involved six perimenopausal or postmenopausal VLS patients which were based on characteristic clinical manifestations and histologic confirmation and five healthy controls. The pruritus severity of each patient was evaluated using the NRS scale, and the dermatology-specific health-related quality of life was assessed using the Skindex-16. Metagenomic sequencing was performed, and the results were analyzed for alpha and beta diversity. LEfSe analysis were used to investigate the microbial alterations in vulvar skin, gut and vagina. KEGG databases were used to analyze differences in functional abundance. The study found significant differences in alpha diversity between the two groups in stool and vaginal samples (P < 0.05). Patients with VLS had a higher abundance of Enterobacter cloacae, Flavobacterium_branchiophilum, Mediterranea_sp._An20, Parabacteroides_johnsoniiand Streptococcus_bovimastitidis on the vulvar skin, while Corynebacterium_sp._zg-913 was less abundant compared to the control group. The relative abundance of Sphingomonas_sp._SCN_67_18, Sphingobium_sp._Ant17, and Pontibacter_sp_BT213 was significantly higher in the gut samples of patients with VLS.Paenibacillus_popilliae,Gemella_asaccharolytica, and Coriobacteriales_bacterium_DNF00809 compared to the control group. Additionally, the vaginal samples of patients with VLS exhibited a significantly lower relative abundance of Bacteroidales_bacterium_43_8, Bacteroides_sp._CAG:20, Blautia_sp._AM28-10, Fibrobacter_sp._UWB16, Lachnospiraceae_bacterium_AM25-39, Holdemania_filiformis, Lachnospiraceae_bacterium_GAM79, and Tolumonas_sp. Additionally, the butyrate-producing bacterium SS3/4 showed a significant difference compared to the controls. The study found a negative relationship between Sphingobium_sp._Ant17 in stool and Skindex-16 (P < 0.05), while Mediterranea_sp._An20 had a positive correlation with Skindex-16 (P < 0.05) in the skin. Additionally, our functional analysis revealed alterations in Aminoacyl_tRNA_biosynthesis, Glutathione_metabolism, the pentose phosphate pathway, and Alanine__aspartate_and_glutamate_metabolism in the VLS patient group. The study suggests that perimenopausal or postmenopausal patients with VLS have a modified microbiome in the vulvar skin, gut, and vagina. This modification is linked to abnormal energy metabolism, increased oxidative stress, and abnormal amino acid metabolism.}, } @article {pmid38183619, year = {2024}, author = {Almeida, TE and Santos Leal, BS}, title = {Recurrent allopolyploidy and its implications for conservation in vascular plants: a commentary on 'Population genomics of the Isoetes appalachiana (Isoetaceae) complex supports a "diploids-first" approach to conservation'.}, journal = {Annals of botany}, volume = {133}, number = {2}, pages = {i-ii}, pmid = {38183619}, issn = {1095-8290}, mesh = {*Metagenomics ; Diploidy ; *Tracheophyta ; Phylogeny ; }, abstract = {This article comments on: David Wickell, Jacob Landis, Elizabeth Zimmer and Fay-Wei Li, Population genomics of the Isoetes appalachiana (Isoetaceae) complex supports a ‘diploids-first’ approach to conservation, Annals of Botany, Volume 133, Issue 2, 01 February 2024, Pages 261–272, https://doi.org/10.1093/aob/mcad180}, } @article {pmid37967308, year = {2024}, author = {Wickell, D and Landis, J and Zimmer, E and Li, FW}, title = {Population genomics of the Isoetes appalachiana (Isoetaceae) complex supports a 'diploids-first' approach to conservation.}, journal = {Annals of botany}, volume = {133}, number = {2}, pages = {261-272}, pmid = {37967308}, issn = {1095-8290}, mesh = {Phylogeny ; *Diploidy ; Metagenomics ; Biological Evolution ; *Tracheophyta ; Polyploidy ; }, abstract = {BACKGROUND AND AIMS: Allopolyploidy is an important driver of diversification and a key contributor to genetic novelty across the tree of life. However, many studies have questioned the importance of extant polyploid lineages, suggesting that the vast majority may constitute evolutionary 'dead ends'. This has important implications for conservation efforts where polyploids and diploid progenitors often compete for wildlife management resources. Isoetes appalachiana is an allotetraploid that is broadly distributed throughout the eastern USA alongside its diploid progenitors, I. valida and I. engelmannii. As such, this species complex provides an excellent opportunity to investigate the processes that underpin the formation and survival of allopolyploid lineages.

METHODS: Here we utilized RADseq and whole-chloroplast sequencing to unravel the demographic and evolutionary history of hybridization in this widespread species complex. We developed a modified protocol for phasing RADseq loci from an allopolyploid in order to examine each progenitor's genetic contribution independently in a phylogenetic context. Additionally, we conducted population-level analyses to examine genetic diversity and evidence of gene flow within species.

KEY RESULTS: Isoetes appalachiana is the product of multiple phylogenetic origins, suggesting that formation and establishment of allopolyploids are common in this group. Hybridization appears to be unidirectional, with I. engelmannii consistently being the maternal progenitor. Additionally, we find that polyploid lineages are genetically isolated, rarely if ever experiencing gene flow between geographically distinct populations.

CONCLUSIONS: Allopolyploid lineages of I. appalachiana appear to form frequently and experience a high degree of genetic isolation following formation. Thus, our results appear to corroborate the hypothesis that the vast majority of recently formed polyploids may represent evolutionary dead ends. However, this does not necessarily lessen the evolutionary importance or ecological impact of polyploidy per se. Accordingly, we propose a conservation strategy that prioritizes diploid taxa, thus preserving downstream processes that recurrently generate allopolyploid diversity.}, } @article {pmid38599786, year = {2024}, author = {Su, ACY and Ding, X and Lau, HCH and Kang, X and Li, Q and Wang, X and Liu, Y and Jiang, L and Lu, Y and Liu, W and Ding, Y and Cheung, AH and To, KF and Yu, J}, title = {Lactococcus lactis HkyuLL 10 suppresses colorectal tumourigenesis and restores gut microbiota through its generated alpha-mannosidase.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2023-330835}, pmid = {38599786}, issn = {1468-3288}, abstract = {OBJECTIVE: Probiotic Lactococcus lactis is known to confer health benefits to humans. Here, we aimed to investigate the role of L. lactis in colorectal cancer (CRC).

DESIGN: L. lactis abundance was evaluated in patients with CRC (n=489) and healthy individuals (n=536). L. lactis was isolated from healthy human stools with verification by whole genome sequencing. The effect of L. lactis on CRC tumourigenesis was assessed in transgenic Apc [Min/+] mice and carcinogen-induced CRC mice. Faecal microbiota was profiled by metagenomic sequencing. Candidate proteins were characterised by nano liquid chromatography-mass spectrometry. Biological function of L. lactis conditioned medium (HkyuLL 10-CM) and functional protein was studied in human CRC cells, patient-derived organoids and xenograft mice.

RESULTS: Faecal L. lactis was depleted in patients with CRC. A new L. lactis strain was isolated from human stools and nomenclated as HkyuLL 10. HkyuLL 10 supplementation suppressed CRC tumourigenesis in Apc [Min/+] mice, and this tumour-suppressing effect was confirmed in mice with carcinogen-induced CRC. Microbiota profiling revealed probiotic enrichment including Lactobacillus johnsonii in HkyuLL 10-treated mice. HkyuLL 10-CM significantly abrogated the growth of human CRC cells and patient-derived organoids. Such protective effect was attributed to HkyuLL 10-secreted proteins, and we identified that α-mannosidase was the functional protein. The antitumourigenic effect of α-mannosidase was demonstrated in human CRC cells and organoids, and its supplementation significantly reduced tumour growth in xenograft mice.

CONCLUSION: HkyuLL 10 suppresses CRC tumourigenesis in mice through restoring gut microbiota and secreting functional protein α-mannosidase. HkyuLL 10 administration may serve as a prophylactic measure against CRC.}, } @article {pmid38599353, year = {2024}, author = {Liu, Y and Song, X and Xu, Z and Wang, Y and Hou, X and Wang, Y and Cao, X and Wang, W}, title = {Biomineralized manganese oxide mediated nitrogen-contained wastewater treatment.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {130689}, doi = {10.1016/j.biortech.2024.130689}, pmid = {38599353}, issn = {1873-2976}, abstract = {In recent years, manganese (Mn) has emerged as an accelerator for nitrogen metabolism. However, the bioactivity of manganese is limited by the restricted contact between microbes and manganese minerals in the solid phase and by the toxicity of manganese to microbes. To enhance the bioactivity of solid-phase manganese, biomineralized manganese oxide (MnOx) modified by Lactobacillus was introduced. Nitrogen removal performance have confirmed the effective role of biomineralized MnOx in accelerating the removal of total inorganic nitrogen (TIN). Metagenomic analysis has confirmed the enhancement of the nitrogen metabolic pathway and microbial extracellular electron transfer (MEET) in biomineralized MnOx treatment group (BIOA group). Additionally, the enrichment of manganese oxidation and denitrification genus indicates a coupling between nitrogen metabolism and manganese metabolism. One point of views is that biomineralized MnOx-mediated nitrogen transformation processes could serve as a substitute for traditional nitrogen removal processes.}, } @article {pmid38599211, year = {2024}, author = {Battaglia, TW and Mimpen, IL and Traets, JJH and van Hoeck, A and Zeverijn, LJ and Geurts, BS and de Wit, GF and Noë, M and Hofland, I and Vos, JL and Cornelissen, S and Alkemade, M and Broeks, A and Zuur, CL and Cuppen, E and Wessels, L and van de Haar, J and Voest, E}, title = {A pan-cancer analysis of the microbiome in metastatic cancer.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2024.03.021}, pmid = {38599211}, issn = {1097-4172}, abstract = {Microbial communities are resident to multiple niches of the human body and are important modulators of the host immune system and responses to anticancer therapies. Recent studies have shown that complex microbial communities are present within primary tumors. To investigate the presence and relevance of the microbiome in metastases, we integrated mapping and assembly-based metagenomics, genomics, transcriptomics, and clinical data of 4,160 metastatic tumor biopsies. We identified organ-specific tropisms of microbes, enrichments of anaerobic bacteria in hypoxic tumors, associations between microbial diversity and tumor-infiltrating neutrophils, and the association of Fusobacterium with resistance to immune checkpoint blockade (ICB) in lung cancer. Furthermore, longitudinal tumor sampling revealed temporal evolution of the microbial communities and identified bacteria depleted upon ICB. Together, we generated a pan-cancer resource of the metastatic tumor microbiome that may contribute to advancing treatment strategies.}, } @article {pmid38599113, year = {2024}, author = {Pilkington, LI and Kerner, W and Bertoldi, D and Larcher, R and Lee, SA and Goddard, MR and Albanese, D and Franceschi, P and Fedrizzi, B}, title = {Integration and holistic analysis of multiple multidimensional soil data sets.}, journal = {Talanta}, volume = {274}, number = {}, pages = {125954}, doi = {10.1016/j.talanta.2024.125954}, pmid = {38599113}, issn = {1873-3573}, abstract = {Complex matrices such as soil have a range of measurable characteristics, and thus data to describe them can be considered multidimensional. These characteristics can be strongly influenced by factors that introduce confounding effects that hinder analyses. Traditional statistical approaches lack the flexibility and granularity required to adequately evaluate such matrices, particularly those with large dataset of varying data types (i.e. quantitative non-compositional, quantitative compositional). We present a statistical workflow designed to effectively analyse complex, multidimensional systems, even in the presence of confounding variables. The developed methodology involves exploratory analysis to identify the presence of confounding variables, followed by data decomposition (including strategies for both compositional and non-compositional quantitative data) to minimise the influence of these confounding factors such as sampling site/location. These data processing methods then allow for common patterns to be highlighted in the data, including the identification of biomarkers and determination of non-trivial associations between variables. We demonstrate the utility of this statistical workflow by jointly analysing the chemical composition and fungal biodiversity of New Zealand vineyard soils that have been managed with either organic low-input or conventional input approaches. By applying this pipeline, we were able to identify biomarkers that distinguish viticultural soil from both approaches and also unearth links and associations between the chemical and metagenomic profiles. While soil is an example of a system that can require this type of statistical methodology, there are a range of biological and ecological systems that are challenging to analyse due to the complex interplay of global and local effects. Utilising our developed pipeline will greatly enhance the way that these systems can be studied and the quality and impact of insight gained from their analysis.}, } @article {pmid38598950, year = {2024}, author = {Lei, L and Chen, N and Chen, Z and Zhao, Y and Lin, H and Li, X and Hu, W and Zhang, H and Shi, J and Luo, Y}, title = {Dissemination of antibiotic resistance genes from aboveground sources to groundwater in livestock farms.}, journal = {Water research}, volume = {256}, number = {}, pages = {121584}, doi = {10.1016/j.watres.2024.121584}, pmid = {38598950}, issn = {1879-2448}, abstract = {Antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) are prevalent in various environments on livestock farms, including livestock waste, soil, and groundwater. Contamination of groundwater by ARB and ARGs in livestock farms is a growing concern as it may have potentially huge risks to human health. However, the source of groundwater-borne ARB and ARGs in animal farms remains largely unknown. In this study, different types of samples including groundwater and its potential contamination sources from aboveground (pig feces, wastewater, and soil) from both working and abandoned swine feedlots in southern China were collected and subjected to metagenomic sequencing and ARB isolation. The source tracking based on metagenomic analysis revealed that 56-95 % of ARGs in groundwater was attributable to aboveground sources. Using metagenomic assembly, we found that 45 ARGs predominantly conferring resistance to aminoglycosides, sulfonamides, and tetracyclines could be transferred from the aboveground sources to groundwater, mostly through plasmid-mediated horizontal gene transfer. Furthermore, the full-length nucleotide sequences of sul1, tetA, and TEM-1 detected in ARB isolates exhibited the close evolutionary relationships between aboveground sources and groundwater. Some isolated strains of antibiotic-resistant Pseudomonas spp. from aboveground sources and groundwater had the high similarity (average nucleotide identity > 99 %). Notably, the groundwater-borne ARGs were identified as mainly carried by bacterial pathogens, potentially posing risks to human and animal health. Overall, this study underscores the dissemination of ARGs from aboveground sources to groundwater in animal farms and associated risks.}, } @article {pmid38599814, year = {2024}, author = {Yang, S and Guo, JQ and Li, TX and Tang, SJ}, title = {[Annual progress of interventional diagnosis and treatment of tuberculosis in 2023].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {47}, number = {4}, pages = {363-370}, doi = {10.360/cma.j.cn112147-20231114-00308}, pmid = {38599814}, issn = {1001-0939}, support = {2022MSXM149, 2024MSXM061//Medical Research Project of Chongqing Science and Technology Commission and Health Commission/ ; 20201214//Beijing Key Clinical Specialty Project and Tongzhou District Development Support Plan for High-Level Talent/ ; }, abstract = {A series of studies on the interventional diagnosis and treatment of tuberculosis(TB)were carried out by domestic and foreign researchers in 2023. The combination of minimally invasive interventional procedures with endoscopes, guidance, material acquisition techniques by multiple ways and multichannel and highly accurate laboratory testing techniques is becoming more and more widely practiced clinically, which has played an important role in the accurate diagnosis of problematic TB. Diagnostic procedures for pulmonary TB, tracheobronchial TB, mediastinal lymphatic TB and extrapulmonary TB included conventional flexible bronchoscopy and specific types of bronchoscopy(ultrathin bronchoscopy and endobronchial ultrasound), transbronchial needle aspiration biopsy, endobronchial ultrasound and virtual bronchoscopic navigation system-guided forceps biopsy, thoracoscopic cryobiopsy of pleura, percutaneous biopsy, and so on. The time to diagnosis has been significantly reduced and the diagnostic efficacy has been improved by the clinical specimen detection using either Gene Xpert MTB/RIF, Ultra, loop-mediated isothermal amplification, metagenomic next-generation sequencing, or nanopore sequencing, etc. Interventional therapy was focused on the following diseases: pulmonary TB with massive hemoptysis, tracheobronchial TB, pleural TB and TB-related fistulas. Interventional treatment of tracheobronchial TB mainly included the application of rigid bronchoscopy, bronchoscopic cold and thermal ablation treatment, endoscopic clamp, dilatations of narrow airway with balloon and stent placement, etc. The interventional treatment of pulmonary TB complicated by massive hemoptysis included endovascular embolization, coated stent placement, etc. Interventional treatment of pleural TB involved the application of thoracoscopy, endoscopic forceps, the implantation of stent and other occlusive devices and the closure of fistulas with autologous fat transplantation. In this article, we reviewed the progress of interventional diagnosis and treatment of TB by the search of published literatures from October 2022 to September 2023.}, } @article {pmid38598617, year = {2024}, author = {Gilbert, JA and Alverdy, J}, title = {Where do the pathogens that cause surgical site infections come from?.}, journal = {Science translational medicine}, volume = {16}, number = {742}, pages = {eado1449}, doi = {10.1126/scitranslmed.ado1449}, pmid = {38598617}, issn = {1946-6242}, abstract = {A study from Long et al. shows that many pathogens that cause surgical site infections during spine surgery come from the patient's own microbiome, suggesting a paradigm shift in the understanding of surgical site infections that questions the effectiveness of current enhanced sterility and antibiotic protocols.}, } @article {pmid38597887, year = {2024}, author = {Liu, G and Chen, X and Luan, Y and Li, D}, title = {VirusPredictor: XGBoost-based software to predict virus-related sequences in human data.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btae192}, pmid = {38597887}, issn = {1367-4811}, abstract = {MOTIVATION: Discovering disease causative pathogens, particularly viruses without reference genomes, poses a technical challenge as they are often unidentifiable through sequence alignment. Machine learning prediction of patient high-throughput sequences unmappable to human and pathogen genomes may reveal sequences originating from uncharacterized viruses. Currently, there is a lack of software specifically designed for accurately predicting such viral sequences in human data.

RESULTS: We developed a fast XGBoost method and software VirusPredictor leveraging an in-house viral genome database. Our two-step XGBoost models first classify each query sequence into one of three groups: infectious virus, endogenous retrovirus (ERV) or non-ERV human. The prediction accuracies increased as the sequences became longer, ie, 0.76, 0.93, and 0.98 for 150-350 (Illumina short reads), 850-950 (Sanger sequencing data), and 2,000-5,000 bp sequences, respectively. Then, sequences predicted to be from infectious viruses are further classified into one of six virus taxonomic subgroups, and the accuracies increased from 0.92 to > 0.98 when query sequences increased from 150-350 to > 850 bp. The results suggest that Illumina short reads should be de novo assembled into contigs (e.g., ∼1,000 bp or longer) before prediction whenever possible. We applied VirusPredictor to multiple real genomic and metagenomic datasets and obtained high accuracies. VirusPredictor, a user-friendly open-source Python software, is useful for predicting the origins of patients' unmappable sequences. This study is the first to classify ERVs in infectious viral sequence prediction. This is also the first study combining virus sub-group predictions.

AVAILABILITY: www.dllab.org/software/VirusPredictor.html.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid38597375, year = {2024}, author = {Arunan, B and Talukdar, D and Swain, S and Varadarajan, A and Sarda, R and Singh, G and Nischal, N and Soneja, M and Bakshi, S and Jana, P and Tanwar, S and Sikka, K and Verma, H and Subramanian, A and Xess, I and Wig, N and Das, B and Ray, A}, title = {Metagenomic insights into fungal community composition of the nasopharyngeal region of COVID-19 associated mucormycosis patients from India.}, journal = {Journal of medical virology}, volume = {96}, number = {4}, pages = {e29601}, doi = {10.1002/jmv.29601}, pmid = {38597375}, issn = {1096-9071}, support = {//All-India Institute of Medical Sciences Intramural Grant/ ; RAD-22017/19/2022-KGD-DBT//Department of Biotechnology (DBT), Govt. of India/ ; }, abstract = {Coronavirus disease 2019 (COVID-19) associated mucormycosis (CAM) was reported predominantly from India during the second wave of COVID-19 and has a high mortality rate. The present study aims to understand the fungal community composition of the nasopharyngeal region of CAM-infected individuals and compare it with severe COVID-19 patients and healthy controls. The fungal community composition was decoded by analyzing the sequence homology of the internal transcribed spacer-2-(ITS-2) region of metagenomic DNA extracted from the upper respiratory samples. The alpha-diversity indices were found to be significantly altered in CAM patients (p < 0.05). Interestingly, a higher abundance of Candida africana, Candida haemuloni, Starmerella floris, and Starmerella lactiscondensi was observed exclusively in CAM patients. The interindividual changes in mycobiome composition were well supported by beta-diversity analysis (p < 0.05). The current study provides insights into the dysbiosis of the nasal mycobiome during CAM infection. In conclusion, our study shows that severe COVID-19 and CAM are associated with alteration in mycobiome as compared to healthy controls. However, the sequential alteration in the fungal flora which ultimately leads to the development of CAM needs to be addressed by future studies.}, } @article {pmid38596883, year = {2024}, author = {Feng, C and Peng, C and Zhang, W and Zhang, T and He, Q and Kwok, LY and Zhang, H}, title = {Postbiotic Administration Ameliorates Colitis and Inflammation in Rats Possibly through Gut Microbiota Modulation.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.3c03901}, pmid = {38596883}, issn = {1520-5118}, abstract = {Postbiotics are preparations of inanimate microorganisms and/or their components that are beneficial to host health. Compared with probiotics, the postbiotic dose required for exerting obvious protective effects is unknown. Thus, we conducted a dose-dependent postbiotic intervention study in dextran sulfate sodium (DSS)-induced colitis rats. The trial included five rat groups, including: control without DSS/postbiotic treatment, group C; 7-day DSS treatment, group D; 14-day low, medium, and high probiotic doses (0.1, 0.2, 0.4 g/kg; groups L, M, H, respectively) after DSS induction. We found that postbiotic intervention effectively mitigated the symptoms and inflammation in colitis rats, evidenced by the improved spleen index, less severe colon tissue damage, and changes in serum cytokine levels (decreases in tumor necrosis factor-α and interleukin-1β; increase in interleukin-10) in postbiotic groups compared with group D. Moreover, the therapeutic effect was dose-dependent. Fecal metabolomics analysis revealed that the postbiotic recipients had more anti-inflammatory metabolites, namely, salicyloyl phytophingosine, podophylloxin, securinine, baicalein, and diosmetin. Fecal metagenomics analysis revealed that the postbiotic recipients had more beneficial microbes and less pro-inflammatory bacteria. This study confirmed that postbiotics are effective in alleviating colitis in a dose-dependent manner. Our findings are of interest to food scientists, clinicians, and the health food industry.}, } @article {pmid38596448, year = {2024}, author = {El Mouzan, M and Al Sarkhy, A and Assiri, A}, title = {Gut microbiota predicts the diagnosis of ulcerative colitis in Saudi children.}, journal = {World journal of clinical pediatrics}, volume = {13}, number = {1}, pages = {90755}, pmid = {38596448}, issn = {2219-2808}, abstract = {BACKGROUND: Ulcerative colitis (UC) is an immune-mediated chronic inflammatory condition with a worldwide distribution. Although the etiology of this disease is still unknown, the understanding of the role of the microbiota is becoming increasingly strong.

AIM: To investigate the predictive power of the gut microbiota for the diagnosis of UC in a cohort of newly diagnosed treatment-naïve Saudi children with UC.

METHODS: The study population included 20 children with a confirmed diagnosis of UC and 20 healthy controls. Microbial DNA was extracted and sequenced, and shotgun metagenomic analysis was performed for bacteria and bacteriophages. Biostatistics and bioinformatics demonstrated significant dysbiosis in the form of reduced alpha diversity, beta diversity, and significant difference of abundance of taxa between children with UC and control groups. The receiver operating characteristic curve, a probability curve, was used to determine the difference between the UC and control groups. The area under the curve (AUC) represents the degree of separability between the UC group and the control group. The AUC was calculated for all identified bacterial species and for bacterial species identified by the random forest classification algorithm as important potential biomarkers of UC. A similar method of AUC calculation for all bacteriophages and important species was used.

RESULTS: The median age and range were 14 (0.5-21) and 12.9 (6.8-16.3) years for children with UC and controls, respectively, and 40% and 35% were male for children with UC and controls, respectively. The AUC for all identified bacterial species was 89.5%. However, when using the bacterial species identified as important by random forest classification algorithm analysis, the accuracy increased to 97.6%. Similarly, the AUC for all the identified bacteriophages was 87.4%, but this value increased to 94.5% when the important bacteriophage biomarkers were used.

CONCLUSION: The very high to excellent AUCs of fecal bacterial and viral species suggest the potential use of noninvasive microbiota-based tests for the diagnosis of unusual cases of UC in children. In addition, the identification of important bacteria and bacteriophages whose abundance is reduced in children with UC suggests the potential of preventive and adjuvant microbial therapy for UC.}, } @article {pmid38596372, year = {2024}, author = {Ye, H and Zhao, Y and He, S and Wu, Z and Yue, M and Hong, M}, title = {Metagenomics reveals the response of desert steppe microbial communities and carbon-nitrogen cycling functional genes to nitrogen deposition.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1369196}, pmid = {38596372}, issn = {1664-302X}, abstract = {INTRODUCTION: Nitrogen (N) deposition seriously affects the function of carbon (C) and N cycling in terrestrial ecosystems by altering soil microbial communities, especially in desert steppe ecosystems. However, there is a need for a comprehensive understanding of how microorganisms involved in each C and N cycle process respond to N deposition.

METHODS: In this study, shotgun metagenome sequencing was used to investigate variations in soil C and N cycling-related genes in the desert steppe in northern China after 6 years of the following N deposition: N0 (control); N30 (N addition 30 kg ha[-1] year[-1]): N50 (N addition 50 kg ha[-1] year[-1]).

RESULTS: N deposition significantly increased the relative abundance of Actinobacteria (P < 0.05) while significantly decreased the relative abundances of Proteobacteria and Acidobacteria (P < 0.05). This significantly impacted the microbial community composition in desert steppe soils. The annual addition or deposition of 50 kg ha[-1] year[-1] for up to 6 years did not affect the C cycle gene abundance but changed the C cycle-related microorganism community structure. The process of the N cycle in the desert steppe was affected by N deposition (50 kg ha[-1] year[-1]), which increased the abundance of the pmoA-amoA gene related to nitrification and the nirB gene associated with assimilation nitrite reductase. There may be a niche overlap between microorganisms involved in the same C and N cycling processes.

DISCUSSION: This study provides new insights into the effects of N deposition on soil microbial communities and functions in desert steppe and a better understanding of the ecological consequences of anthropogenic N addition.}, } @article {pmid38596092, year = {2024}, author = {Wang, C and Pan, M and Lin, Q and Mofatteh, M and Chen, Y and Baizabal-Carvallo, JF and Su, F and Wang, Z}, title = {Metagenomic next-generation sequencing assistance in identifying Mycobacterium avium meningoencephalitis: A case report and literature review.}, journal = {Heliyon}, volume = {10}, number = {7}, pages = {e28630}, pmid = {38596092}, issn = {2405-8440}, abstract = {Nontuberculous mycobacteria associated intracranial infection is a rare disease that mainly occurs in HIV-infected patients. The disease has a poor prognosis. The authors report a case of non-tuberculous mycobacterial meningoencephalitis in a non-AIDS patient, but long history of poorly controlled type 2 diabetes mellitus. A 55-year-old, right-handed, male patient presented with an 8-day history of fever, episodes of severe headache with signs of meningeal irritation. MRI showed hyperintensities/contrast enhancement in the visual pathways, basal ganglia sellar region and leptomeninges. No etiological diagnosis was reached until metagenomic next-generation sequencing (mNGS) was used, showing the presence of Mycobacterium avium. The patient was cured with aggressive antimycobacterial therapy. The authors discuss the clinical manifestations and drug therapy of nontuberculous mycobacteria-related intracranial infections by reviewing relevant literature. As meningoencephalitis by Mycobacterium avium has a high mortality an early diagnosis and appropriate therapeutic interventions are warranted. For this reason, the use of mNGS can be helpful to avoid therapeutic delay.}, } @article {pmid38595798, year = {2024}, author = {Hassani, Y and Aboudharam, G and Drancourt, M and Grine, G}, title = {The discovery of Candidatus Nanopusillus phoceensis sheds light on the diversity of the microbiota nanoarchaea.}, journal = {iScience}, volume = {27}, number = {4}, pages = {109488}, pmid = {38595798}, issn = {2589-0042}, abstract = {To further assess the spectrum of nanoarchaea in human microbiota, we prospectively searched for nanoarchaea in 110 leftover stool specimens, using the complementary approaches of PCR-sequencing screening, fluorescent in situ hybridization, scanning electron microscopy and metagenomics. These investigations yielded a nanoarchaea, Candidatus Nanopusillus phoceensis sp. nov., detected in stool samples by specific PCR-based assays. Microscopic observations indicated its close contact with the archaea Methanobrevibacter smithii. Genomic sequencing revealed 607,775-bp contig with 24.5% G + C content encoding 30 tRNAs, 3 rRNA genes, and 1,403 coding DNA sequences, of which 719 were assigned to clusters of orthologous groups. Ca. Nanopusillus phoceensis is only the second nanoarchaea to be detected in humans, expanding our knowledge of the repertoire of nanoarchaea associated with the human microbiota and encouraging further research to explore the repertoire of this emerging group of nanomicrobes in clinical samples.}, } @article {pmid38594499, year = {2024}, author = {Franceschetti, L and Lodetti, G and Blandino, A and Amadasi, A and Bugelli, V}, title = {Exploring the role of the human microbiome in forensic identification: opportunities and challenges.}, journal = {International journal of legal medicine}, volume = {}, number = {}, pages = {}, pmid = {38594499}, issn = {1437-1596}, abstract = {Forensic microbiology is rapidly emerging as a novel tool for human identification. The human microbiome, comprising diverse microbial communities including fungi, bacteria, protozoa, and viruses, is unique to each individual, offering a new dimension to forensic investigations. While traditional identification methods primarily rely on DNA profiling and fingerprint analysis, they face limitations when complete DNA or fingerprints profiles are unattainable or degraded. In this context, the microbial signatures of the human skin microbiome present a promising alternative due to their resilience to environmental stresses and individual-specific composition. This review explores the potential of microbiome analysis in forensic human identification, evaluating its applications, advantages, limitations, and future prospects. The uniqueness of an individual's microbial community, particularly the skin microbiota, can provide distinctive biological markers for identification purposes, while technological advancements like 16 S rRNA sequencing and metagenomic shotgun sequencing are enhancing the specificity of microbial identification, enabling detailed analysis of these complex ecological communities. Despite these promising findings, current research has not yet achieved a level of identification probability that could establish microbial analysis as a stand-alone evidence tool. Therefore, it is presently considered ancillary to traditional methods, contributing to a more comprehensive biological profile of individuals.}, } @article {pmid38594478, year = {2024}, author = {Felipe Benites, L and Stephens, TG and Van Etten, J and James, T and Christian, WC and Barry, K and Grigoriev, IV and McDermott, TR and Bhattacharya, D}, title = {Hot springs viruses at Yellowstone National Park have ancient origins and are adapted to thermophilic hosts.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {312}, pmid = {38594478}, issn = {2399-3642}, support = {NA//National Aeronautics and Space Administration (NASA)/ ; 80NSSC19K0462//National Aeronautics and Space Administration (NASA)/ ; NA//National Aeronautics and Space Administration (NASA)/ ; }, abstract = {Geothermal springs house unicellular red algae in the class Cyanidiophyceae that dominate the microbial biomass at these sites. Little is known about host-virus interactions in these environments. We analyzed the virus community associated with red algal mats in three neighboring habitats (creek, endolithic, soil) at Lemonade Creek, Yellowstone National Park (YNP), USA. We find that despite proximity, each habitat houses a unique collection of viruses, with the giant viruses, Megaviricetes, dominant in all three. The early branching phylogenetic position of genes encoded on metagenome assembled virus genomes (vMAGs) suggests that the YNP lineages are of ancient origin and not due to multiple invasions from mesophilic habitats. The existence of genomic footprints of adaptation to thermophily in the vMAGs is consistent with this idea. The Cyanidiophyceae at geothermal sites originated ca. 1.5 Bya and are therefore relevant to understanding biotic interactions on the early Earth.}, } @article {pmid38593965, year = {2024}, author = {Bounaga, A and Alsanea, A and Danouche, M and Rittmann, BE and Zhou, C and Boulif, R and Zeroual, Y and Benhida, R and Lyamlouli, K}, title = {Elemental sulfur biorecovery from phosphogypsum using oxygen-membrane biofilm reactor: Bioreactor parameters optimization, metagenomic analysis and metabolic prediction of the biofilm activity.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {130680}, doi = {10.1016/j.biortech.2024.130680}, pmid = {38593965}, issn = {1873-2976}, abstract = {This work investigated elemental sulfur (S[0]) biorecovery from Phosphogypsum (PG) using sulfur-oxidizing bacteria in an O2-based membrane biofilm reactor (MBfR). The system was first optimized using synthetic sulfide medium (SSM) as influent, then switched to biogenic sulfide medium (BSM) generated by biological reduction of PG alkaline leachate. The results using SSM had high sulfide-oxidation efficiency (98 %), sulfide to S[0] conversion (∼90 %), and S0 production rate up to 2.7 g S[0]/(m[2].d), when the O2/S ratio was ∼0.5 g O2/g S. With the BSM influent, the system maintained high sulfide-to-S[0] conversion rate (97 %), and S[0]-production rate of 1.6 g S[0]/(m[2].d). Metagenomic analysis revealed that Thauera was the dominant genus in SSM and BSM biofilms. Furthermore, influent composition affected the bacterial community structure and abundances of functional microbial sulfur genes, modifying the sulfur-transformation pathways in the biofilms. Overall, this work shows promise for O2-MBfR usage in S[0] biorecovery from PG leachate and sulfidogenic effluents.}, } @article {pmid38593737, year = {2024}, author = {Wang, Y and Gao, Y and Wang, X and Lin, Y and Xu, G and Yang, F and Ni, K}, title = {Insights into the phage community structure and potential function in silage fermentation.}, journal = {Journal of environmental management}, volume = {358}, number = {}, pages = {120837}, doi = {10.1016/j.jenvman.2024.120837}, pmid = {38593737}, issn = {1095-8630}, abstract = {The virus that infects bacteria known as phage, plays a crucial role in the biogeochemical cycling of nutrients. However, the community structure and potential functions of phages in silage fermentation remain largely unexplored. In this study, we utilized viral metagenomics (viromics) to investigate the types, lifestyles, functions, and nutrient utilization patterns of phages in silage. Our findings indicated a high prevalence of annotated phages belonging to Caudovirales and Geplafuvirales, as well as unclassified phages in silage. The predominant host types for these phages were Campylobacterales and Enterobacterales. Virulent phages dominated the silage environment due to their broader range of hosts and enhanced survival capabilities. All identified phages present in silage were found to be non-pathogenic. Although temperate and virulent phages carried distinct genes associated with nutrient cycling processes, the shared genes (prsA) involved in carbon metabolism underscore the potential significance of phages in regulating carbon metabolism in silage. Overall, our findings provide a valuable foundation for further exploring the complex interactions between phages and microorganisms in regulating silage fermentation quality.}, } @article {pmid38593604, year = {2024}, author = {Ferrinho, S and Connaris, H and Mouncey, NJ and Goss, RJM}, title = {Compendium of Metabolomic and Genomic Datasets for Cyanobacteria: Mined the Gap.}, journal = {Water research}, volume = {256}, number = {}, pages = {121492}, doi = {10.1016/j.watres.2024.121492}, pmid = {38593604}, issn = {1879-2448}, abstract = {Cyanobacterial blooms, producing toxic secondary metabolites, are becoming increasingly common phenomena in the face of rising global temperatures. They are the world's most abundant photosynthetic organisms, largely owing their success to a range of highly diverse and complex natural products possessing a broad spectrum of different bioactivities. Over 2600 compounds have been isolated from cyanobacteria thus far, and their characterisation has revealed unusual and useful chemistries and motifs including alkynes, halogens, and non-canonical amino acids. Genome sequencing of cyanobacteria lags behind natural product isolation, with only 19% of cyanobacterial natural products associated with a sequenced organism. Recent advances in meta(genomics) provide promise to narrow this gap and has also facilitated the uprise of combined genomic and metabolomic approaches, heralding a new era of discovery of novel compounds. Analyses of the datasets described within this manuscript reveal the asynchrony of current genomic and metabolomic data, highlight the chemical diversity of cyanobacterial natural products. Linked to this manuscript, we make these manually curated datasets freely accessible for the public to facilitate further research in this important area.}, } @article {pmid38593566, year = {2024}, author = {Pelpolage, SW and Kobayashi, H and Fukuma, N and Hoshizawa, M and Hamamoto, T and Han, KH and Fukushima, M}, title = {Temporal changes in the fermentation characteristics, bacterial community structure and the functionality of the predicted metagenome of a batch fermenter medium containing the upper gastrointestinal enzyme resistant fraction of white sorghum (Sorghum bicolor L. Moench).}, journal = {Food chemistry}, volume = {448}, number = {}, pages = {139102}, doi = {10.1016/j.foodchem.2024.139102}, pmid = {38593566}, issn = {1873-7072}, abstract = {Sorghum is a potential prebiotic ascribed to the high native resistant starch (RS) content. Our previous studies on raw sorghum have revealed prominent amino acid fermentation despite the high RS content. Interestingly, autoclaved-freeze-dried sorghum fed rats exhibited beneficial microbial and biochemical profiles. Having a keen interest to reciprocally scrutinize the underlying mechanisms behind these contrasting outcomes, we used an in vitro porcine batch fermentation model. The fermentable substrates in raw and autoclaved-freeze-dried (three cycles) sorghum (AC) after in vitro gastrointestinal digestion fostered similar bacterial community structures, yet with significant differences in the characteristic amylolytic microbial taxa abundance and their temporal variation. Further, significant differences in the concentration of organic acids in raw and AC manifested the differences in the predicted abundance of the underlying pathways of carbohydrate and organic acid metabolism. Thus, this study highlights the propensity of the heat-moisture treatment of sorghum in modifying the fermentability of its RS.}, } @article {pmid38594375, year = {2024}, author = {Poulsen, CS and Hesse, D and Fernandes, GR and Hansen, TH and Kern, T and Linneberg, A and Van Espen, L and Jørgensen, T and Nielsen, T and Alibegovic, AC and Matthijnssens, J and Pedersen, O and Vestergaard, H and Hansen, T and Andersen, MK}, title = {Characterization of the gut bacterial and viral microbiota in latent autoimmune diabetes in adults.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {8315}, pmid = {38594375}, issn = {2045-2322}, support = {1S25720N//Fonds voor Wetenschappelijk Onderzoek/ ; po0115//The Danish Diabetes Academy/ ; DFF-5053-00159//Danish Council for Independent Research/ ; }, abstract = {Latent autoimmune diabetes in adults (LADA) is a heterogeneous disease characterized by autoantibodies against insulin producing pancreatic beta cells and initial lack of need for insulin treatment. The aim of the present study was to investigate if individuals with LADA have an altered gut microbiota relative to non-diabetic control subjects, individuals with type 1 diabetes (T1D), and individuals with type 2 diabetes (T2D). Bacterial community profiling was performed with primers targeting the variable region 4 of the 16S rRNA gene and sequenced. Amplicon sequence variants (ASVs) were generated with DADA2 and annotated to the SILVA database. The gut virome was sequenced, using a viral particle enrichment and metagenomics approach, assembled, and quantified to describe the composition of the viral community. Comparison of the bacterial alpha- and beta-diversity measures revealed that the gut bacteriome of individuals with LADA resembled that of individuals with T2D. Yet, specific genera were found to differ in abundance in individuals with LADA compared with T1D and T2D, indicating that LADA has unique taxonomical features. The virome composition reflected the stability of the most dominant order Caudovirales and the families Siphoviridae, Podoviridae, and Inoviridae, and the dominant family Microviridae. Further studies are needed to confirm these findings.}, } @article {pmid38594362, year = {2024}, author = {Lateef, AA and Azeez, AA and Ren, W and Hamisu, HS and Oke, OA and Asiegbu, FO}, title = {Bacterial biota associated with the invasive insect pest Tuta absoluta (Meyrick).}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {8268}, pmid = {38594362}, issn = {2045-2322}, support = {Grant number 4400T-2002//Maa- ja MetsätalousministeriÖ/ ; }, abstract = {Tuta absoluta (the tomato pinworm) is an invasive insect pest with a highly damaging effect on tomatoes causing between 80 and 100% yield losses if left uncontrolled. Resistance to chemical pesticides have been reported in some T. absoluta populations. Insect microbiome plays an important role in the behavior, physiology, and survivability of their host. In a bid to explore and develop an alternative control method, the associated microbiome of this insect was studied. In this study, we unraveled the bacterial biota of T. absoluta larvae and adults by sequencing and analyzing the 16S rRNA V3-V4 gene regions using Illumina NovaSeq PE250. Out of 2,092,015 amplicon sequence variants (ASVs) recovered from 30 samples (15 larvae and 15 adults), 1,268,810 and 823,205 ASVs were obtained from the larvae and adults, respectively. A total of 433 bacterial genera were shared between the adults and larval samples while 264 and 139 genera were unique to the larvae and adults, respectively. Amplicon metagenomic analyses of the sequences showed the dominance of the phylum Proteobacteria in the adult samples while Firmicutes and Proteobacteria dominated in the larval samples. Linear discriminant analysis effect size (LEfSe) comparison revealed the genera Pseudomonas, Delftia and Ralstonia to be differentially enriched in the adult samples while Enterococcus, Enterobacter, Lactococcus, Klebsiella and Wiessella were differentially abundant in the larvae. The diversity indices showed that the bacterial communities were not different between the insect samples collected from different geographical regions. However, the bacterial communities significantly differed based on the sample type between larvae and adults. A co-occurrence network of significantly correlated taxa revealed a strong interaction between the microbial communities. The functional analysis of the microbiome using FAPROTAX showed that denitrification, arsenite oxidation, methylotrophy and methanotrophy as the active functional groups of the adult and larvae microbiomes. Our results have revealed the core taxonomic, functional, and interacting microbiota of T. absoluta and these indicate that the larvae and adults harbor a similar but transitory set of bacteria. The results provide a novel insight and a basis for exploring microbiome-based biocontrol strategy for this invasive insect pest as well as the ecological significance of some of the identified microbiota is discussed.}, } @article {pmid38594229, year = {2024}, author = {Yang, C and Hu, J and Su, Q and Zhang, Z and Du, Y and Wang, J and Sun, H and Han, B and Tang, J and Guo, L and Li, H and Cai, W and Zheng, H and Zhou, X and Zhang, X}, title = {A review on recent taxonomic updates of gut bacteria associated with social bees, with a curated genomic reference database.}, journal = {Insect science}, volume = {}, number = {}, pages = {}, doi = {10.1111/1744-7917.13365}, pmid = {38594229}, issn = {1744-7917}, support = {//2115 Talent Development Program of China Agricultural University grants/ ; 32000346//National Natural Science Foundation of China/ ; 32370550//National Natural Science Foundation of China/ ; SYND-2021-30//Sanya Institute of China Agricultural University/ ; }, abstract = {Honeybees and bumblebees play a crucial role as essential pollinators. The special gut microbiome of social bees is a key factor in determining the overall fitness and health of the host. Although bees harbor relatively simple microbial communities at the genus level, recent studies have unveiled significant genetic divergence and variations in gene content within each bacterial genus. However, a comprehensive and refined genomics-based taxonomic database specific to social bee gut microbiomes remains lacking. Here, we first provided an overview of the current knowledge on the distribution and function of social bee gut bacteria, as well as the factors that influence the gut population dynamics. We then consolidated all available genomes of the gut bacteria of social bees and refined the species-level taxonomy, by constructing a maximum-likelihood core genome phylogeny and calculating genome-wide pairwise average nucleotide identity. On the basis of the refined species taxonomy, we constructed a curated genomic reference database, named the bee gut microbe genome sequence database (BGM-GDb). To evaluate the species-profiling performance of the curated BGM-GDb, we retrieved a series of bee gut metagenomic data and inferred the species-level composition using metagenomic intra-species diversity analysis system (MIDAS), and then compared the results with those obtained from a prebuilt MIDAS database. We found that compared with the default database, the BGM-GDb excelled in aligned read counts and bacterial richness. Overall, this high-resolution and precise genomic reference database will facilitate research in understanding the gut community structure of social bees.}, } @article {pmid38593340, year = {2024}, author = {Suárez-Moo, P and Prieto-Davó, A}, title = {Biosynthetic potential of the sediment microbial subcommunities of an unexplored karst ecosystem and its ecological implications.}, journal = {MicrobiologyOpen}, volume = {13}, number = {2}, pages = {e1407}, doi = {10.1002/mbo3.1407}, pmid = {38593340}, issn = {2045-8827}, support = {//Consejo Nacional de Humanidades Ciencias y Tecnologías (CONAHCYT), México project A1-S-10785 (APD) and postdoctoral fellowship (362331) (PSM)/ ; }, abstract = {Microbial communities from various environments have been studied in the quest for new natural products with a broad range of applications in medicine and biotechnology. We employed an enrichment method and genome mining tools to examine the biosynthetic potential of microbial communities in the sediments of a coastal sinkhole within the karst ecosystem of the Yucatán Peninsula, Mexico. Our investigation led to the detection of 203 biosynthetic gene clusters (BGCs) and 55 secondary metabolites (SMs) within 35 high-quality metagenome-assembled genomes (MAGs) derived from these subcommunities. The most abundant types of BGCs were Terpene, Nonribosomal peptide-synthetase, and Type III polyketide synthase. Some of the in silico identified BGCs and SMs have been previously reported to exhibit biological activities against pathogenic bacteria and fungi. Others could play significant roles in the sinkhole ecosystem, such as iron solubilization and osmotic stress protection. Interestingly, 75% of the BGCs showed no sequence homology with bacterial BGCs previously reported in the MiBIG database. This suggests that the microbial communities in this environment could be an untapped source of genes encoding novel specialized compounds. The majority of the BGCs were identified in pathways found in the genus Virgibacillus, followed by Sporosarcina, Siminovitchia, Rhodococcus, and Halomonas. The latter, along with Paraclostridium and Lysinibacillus, had the highest number of identified BGC types. This study offers fresh insights into the potential ecological role of SMs from sediment microbial communities in an unexplored environment, underscoring their value as a source of novel natural products.}, } @article {pmid38591882, year = {2024}, author = {Xing, Y and Clark, JR and Chang, JD and Zulk, JJ and Chirman, DM and Piedra, F-A and Vaughan, EE and Hernandez Santos, HJ and Patras, KA and Maresso, AW}, title = {Progress toward a vaccine for extraintestinal pathogenic E. coli (ExPEC) II: efficacy of a toxin-autotransporter dual antigen approach.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {e0044023}, doi = {10.1128/iai.00440-23}, pmid = {38591882}, issn = {1098-5522}, abstract = {Extraintestinal pathogenic Escherichia coli (ExPEC) is a leading cause of worldwide morbidity and mortality, the top cause of antimicrobial-resistant (AMR) infections, and the most frequent cause of life-threatening sepsis and urinary tract infections (UTI) in adults. The development of an effective and universal vaccine is complicated by this pathogen's pan-genome, its ability to mix and match virulence factors and AMR genes via horizontal gene transfer, an inability to decipher commensal from pathogens, and its intimate association and co-evolution with mammals. Using a pan virulome analysis of >20,000 sequenced E. coli strains, we identified the secreted cytolysin α-hemolysin (HlyA) as a high priority target for vaccine exploration studies. We demonstrate that a catalytically inactive pure form of HlyA, expressed in an autologous host using its own secretion system, is highly immunogenic in a murine host, protects against several forms of ExPEC infection (including lethal bacteremia), and significantly lowers bacterial burdens in multiple organ systems. Interestingly, the combination of a previously reported autotransporter (SinH) with HlyA was notably effective, inducing near complete protection against lethal challenge, including commonly used infection strains ST73 (CFT073) and ST95 (UTI89), as well as a mixture of 10 of the most highly virulent sequence types and strains from our clinical collection. Both HlyA and HlyA-SinH combinations also afforded some protection against UTI89 colonization in a murine UTI model. These findings suggest recombinant, inactive hemolysin and/or its combination with SinH warrant investigation in the development of an E. coli vaccine against invasive disease.}, } @article {pmid38591043, year = {2024}, author = {Qian, L and Wang, Y and Deng, P and Zhang, J and Qin, Y and Li, Z and Liao, H and Chen, F}, title = {Enterococcus casseliflavus regulates amino acid metabolism in edible insect Clanis bilineata tsingtauica: a functional metagenomics study.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1343265}, pmid = {38591043}, issn = {1664-302X}, abstract = {INTRODUCTION: The soybean hawkmoth, Clanis bilineata tsingtauica, is an edible insect that possesses high nutritional, medicinal and economic value. It has developed into a characteristic agricultural industry in China.

METHODS: The dominant gut bacterium in diapause larvae of soybean hawkmoths was identified by metagenomics, and the effect of diapause time on gut microbiome composition, diversity and function was investigated.

RESULTS: Enterococcus and Enterobacter were measured to be the dominant genera, with Enterococcus casseliflavus and Enterococcus pernyi being the dominant species. Compared to the controls, the relative abundance of E. casseliflavus and E. pernyi on day 14 was lower by 54.51 and 42.45%, respectively. However, the species richness (including the index of Chao and ACE) of gut microbiota increased on day 28 compared to controls. The gene function was mainly focused on carbohydrate and amino acid metabolism. Metabolic pathways annotated for amino acids on day 14 increased by 9.83% compared to controls. It is speculated that diapause soybean hawkmoths may up-regulate amino acid metabolism by reducing E. casseliflavus abundance to maintain their nutritional balance. Additionally, tetracycline, chloromycetin and ampicillin were screened as the top three antibiotics against E. casseliflavus.

DISCUSSION: This study not only extends our knowledge of gut microbiome in soybean hawkmoths at the species level, but also provides an initial investigation of gene functionality in interaction with insect hosts.}, } @article {pmid38591039, year = {2024}, author = {Wang, H and Wang, Y and Yang, L and Feng, J and Tian, S and Chen, L and Huang, W and Liu, J and Wang, X}, title = {Integrated 16S rRNA sequencing and metagenomics insights into microbial dysbiosis and distinct virulence factors in inflammatory bowel disease.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1375804}, pmid = {38591039}, issn = {1664-302X}, abstract = {INTRODUCTION: The escalation of urbanization correlates with rising rates of inflammatory bowel disease (IBD), necessitating research into new etiological factors. This study aims to elucidate the gut microbiota profiles in IBD patients and compare them with healthy controls in a western city of China.

METHODS: We conducted a multicenter case-control study from the end of 2020, using 16S rRNA gene sequencing (n = 36) and metagenomic sequencing (n = 12) to analyze the gut microbiota of newly diagnosed IBD patients, including those with Crohn's disease (CD) and ulcerative colitis (UC).

RESULTS: Our results demonstrated a significant enrichment of the phylum Proteobacteria, particularly the genus Escherichia-Shigella, in CD patients. Conversely, the genus Enterococcus was markedly increased in UC patients. The core gut microbiota, such as the Christensenellaceae R-7 group, Fusicatenibacter, and Holdemanella, were primarily identified in healthy subjects. Additionally, significant interactions between the microbiome and virulence factors were observed.

DISCUSSION: The findings suggest that oxidative stress may play a pivotal role in the pathology of IBD. This study contributes to the growing dialogue about the impact of gut microbiota on the development of IBD and its variations across different geographies, highlighting potential avenues for further research.}, } @article {pmid38591036, year = {2024}, author = {Zhao, C and Yan, S and Luo, Y and Song, Y and Xia, X}, title = {Analyzing resistome in soil and Human gut: a study on the characterization and risk evaluation of antimicrobial peptide resistance.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1352531}, pmid = {38591036}, issn = {1664-302X}, abstract = {OBJECTIVE: The limited existing knowledge regarding resistance to antimicrobial peptides (AMPs) is hindering their broad utilization. The aim of this study is to enhance the understanding of AMP resistance, a pivotal factor in the exploration of alternative drug development in response to the escalating challenge of antibiotic resistance.

METHODS: We utilized metagenomic functional selection to analyze genes resistant to AMPs, with a specific focus on the microbiota in soil and the human gut. Through a combination of experimental methods and bioinformatics analyses, our investigation delved into the possibilities of the evolution of resistance to AMPs, as well as the transfer or interchange of resistance genes among the environment, the human body, and pathogens. Additionally, we examined the cross-resistance between AMPs and evaluated interactions among AMPs and conventional antibiotics.

RESULTS: The presence of AMP resistance, including various resistance mechanisms, was observed in both soil and the human gut microbiota, as indicated by our findings. Significantly, the study underscored the facile evolution of AMP resistance and the potential for gene sharing or exchange among different environments. Notably, cross-resistance among AMPs was identified as a phenomenon, while cross-resistance between AMPs and antibiotics was found to be relatively infrequent.

CONCLUSION: The results of our study highlight the significance of taking a cautious stance when considering the extensive application of AMPs. It is imperative to thoroughly assess potential resistance risks, with a particular focus on the development of resistance to AMPs across diverse domains. A comprehensive grasp of these aspects is essential for making well-informed decisions and ensuring the responsible utilization of AMPs in the ongoing fight against antibiotic resistance.}, } @article {pmid38590894, year = {2024}, author = {Gu, Y and Wang, Z and Xia, X and Zhao, G}, title = {Nocardia farcinica brain abscess with torque teno virus co-infection: A case report.}, journal = {Heliyon}, volume = {10}, number = {7}, pages = {e28632}, pmid = {38590894}, issn = {2405-8440}, abstract = {BACKGROUND: Brain abscesses caused by Nocardia are rare and difficult to diagnose. Nocardia farcinica is among the most common species; however, the conventional diagnosis of N. farcinica infection consists of cerebrospinal fluid (CSF) and blood culture and Gram staining. These procedures prolong the time to diagnosis and initiating treatment.

CASE PRESENTATION: A 69-year-old woman with diabetes mellitus presented with headaches and dizziness persisting for 2 weeks, which was initially diagnosed as a brain abscess. Due to the unusual presentation and rapid progression of symptoms, she underwent surgical resection of the brain abscess. No pathogens were detected in blood or CSF cultures. However, metagenomic next-generation sequencing (mNGS) identified N. farcinica and Torque teno virus in pus extracted from the abscesses. The patient received appropriate antibiotic therapy and recovered fully without any residual neurological deficits.

CONCLUSION: mNGS useful for prompt diagnosis and selection of antibiotic therapy for brain abscesses caused by Nocardia. Surgical intervention is necessary in some cases.}, } @article {pmid38590553, year = {2024}, author = {Wang, J and Jia, P and Zhang, D and Zhao, Y and Sui, X and Jin, Z and Song, W}, title = {Diagnosis of a Familial Psittacosis Outbreak with Clinical Analysis and Metagenomic Next-Generation Sequencing Under COVID-19: A Case Series.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {1099-1105}, pmid = {38590553}, issn = {1178-6973}, abstract = {PURPOSE: To explore the clinical characteristics, diagnosis, and treatment of family outbreak of psittacosis and to improve the success rate of treatment.

PATIENTS AND METHODS: The clinical characteristics, diagnosis, treatment, and outcome of family outbreak of psittacosis, which consists three patients, diagnosed by clinical analysis and metagenomic next-generation sequencing (mNGS) in our hospital were analyzed retrospectively.

RESULTS: We report on three instances of clustered atypical pneumonia, which were caused by Chlamydia psittaci during the COVID-19 pandemic. All patients exhibited symptoms of fever and cough, while one patient also experienced gastrointestinal symptoms such as nausea, vomiting, and diarrhea. Laboratory tests indicated no significant increase in leukocytes and neutrophils, but a mild increase in C-reactive protein was observed in all three patients. Chest computed tomography (CT) scans revealed a consolidation shadow in a unilateral lung lobe in all three patients. Both patients were treated with empirical moxifloxacin, yielding unsatisfactory outcomes. mNGS was conducted on sputum samples from one adult patient, revealing the presence of Chlamydia psittaci. Additional doxycycline was prescribed immediately, and then the patients' temperatures were stabilized, and the lesion in chest CT was absorbed. The pediatric patient exhibited less severe symptoms compared to the adult patients and exhibited a favorable response to azithromycin administration.

CONCLUSION: This study reports a cluster of a family outbreak of atypical pneumonia caused by C. psittaci in China. The occurrence of a family outbreak during the COVID-19 pandemic may be attributed to familial aggregation resulting from the epidemic. The three cases reported in this study did not experience severe complications, which can be attributed to the prompt medical intervention and swift diagnosis. This finding implies the need to enhance patients' awareness and vigilance towards their health. Additionally, mNGS emerges as a valuable technique for accurately identifying pathogens causing pulmonary infections.}, } @article {pmid38590441, year = {2024}, author = {Zhang, X and Zhang, L and Li, Y and Wang, N and Zhang, Y}, title = {Clinical performance of metagenomic next-generation sequencing for diagnosis of invasive fungal disease after hematopoietic cell transplant.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1210857}, pmid = {38590441}, issn = {2235-2988}, abstract = {BACKGROUND: Timely diagnosis and appropriate antifungal therapy are critical for improving the prognosis of patients with invasive fungal disease (IFD) after hematopoietic stem cell transplantation (HSCT). We evaluated the performance of metagenomic next-generation sequencing (mNGS) and conventional microbiological testing (CMT), as well as the diagnosis, therapeutic management, and outcomes of IFD after HSCT.

METHODS: We retrospectively studied 189 patients who underwent HSCT and were considered at risk for IFD. In total, 46 patients with IFD were enrolled in this study. The IFD consensus was followed for classifying IFD incidents.

RESULTS: Forty-six patients were diagnosed with proven/probable (n = 12), possible (n = 27), and undefined (n = 7) IFD. Aspergillus was the most commonly detected fungal genus. Mucormycosis was found in 15 patients; two had Aspergillus, and one had Candida infections. Compared to CMT, mNGS significantly reduced the time required to identify pathogens (P = 0.0016). mNGS had a much higher sensitivity than CMT (84.78% vs. 36.96%; P < 0.0001). A total of 76.09% of patients received antifungal prophylaxis during fungal infections. All Pneumocystis infections occurred later than 100 days after transplantation. Among patients with Pneumocystis infection, 71.43% occurred following sulfonamide withdrawal, and subsequent treatment with sulfonamide alone or in combination with other drugs was effective. Based on the empirical antifungal treatment, the dosages, modes of administration, frequency of administration, or antifungal of 55.26% of the patients were changed according to the mNGS results. The 4-year overall survival rate of patients diagnosed with IFD after transplantation was 71.55% (95% CI, 55.18%-85.82%). Hypoproteinemia and corticosteroid use are independent risk factors for IFD.

CONCLUSION: mNGS, which has a high sensitivity and a short detection time, aids in the diagnosis and prognosis of pathogenic fungi. As a powerful technology, mNGS can influence treatment decisions in patients with IFD following HSCT.}, } @article {pmid38590185, year = {2024}, author = {Gao, Q and Liu, Q and Zhang, G and Lu, Y and Li, Y and Tang, M and Liu, S and Zhang, H and Hu, X}, title = {Identification of pathogen composition in a Chinese population with iatrogenic and native vertebral osteomyelitis by using mNGS.}, journal = {Annals of medicine}, volume = {56}, number = {1}, pages = {2337738}, doi = {10.1080/07853890.2024.2337738}, pmid = {38590185}, issn = {1365-2060}, abstract = {BACKGROUND: Early antimicrobial therapy is crucial regarding the prognosis of vertebral osteomyelitis, but early pathogen diagnosis remains challenging.

OBJECTIVE: In this study, we aimed to differentiate the types of pathogens in iatrogenic vertebral osteomyelitis (IVO) and native vertebral osteomyelitis (NVO) to guide early antibiotic treatment.

METHODS: A total of 145 patients, who had confirmed spinal infection and underwent metagenomic next-generation sequencing (mNGS) testing, were included, with 114 in the NVO group and 31 in the IVO group. Using mNGS, we detected and classified 53 pathogens in the 31 patients in the IVO group and 169 pathogens in the 114 patients in the NVO group. To further distinguish IVO from NVO, we employed machine learning algorithms to select serum biomarkers and developed a nomogram model.

RESULTS: The results revealed that the proportion of the Actinobacteria phylum in the NVO group was approximately 28.40%, which was significantly higher than the 15.09% in the IVO group. Conversely, the proportion of the Firmicutes phylum (39.62%) in the IVO group was markedly increased compared to the 21.30% in the NVO group. Further genus-level classification demonstrated that Staphylococcus was the most common pathogen in the IVO group, whereas Mycobacterium was predominant in the NVO group. Through LASSO regression and random forest algorithms, we identified 5 serum biomarkers including percentage of basophils (BASO%), percentage of monocytes (Mono%), platelet volume (PCT), globulin (G), activated partial thromboplastin time (APTT) for distinguishing IVO from NVO. Based on these biomarkers, we established a nomogram model capable of accurately discriminating between the two conditions.

CONCLUSION: The results of this study hold promise in providing valuable guidance to clinical practitioners for the differential diagnosis and early antimicrobial treatment of vertebral osteomyelitis.}, } @article {pmid38589778, year = {2024}, author = {Wang, D and Hu, MT and Liu, WJ and Zhao, Y and Xu, YC}, title = {Bacteremia caused by Nocardia farcinica: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {381}, pmid = {38589778}, issn = {1471-2334}, support = {2022-PUMCH-C-052//National High Level Hospital Clinical Research Funding/ ; }, abstract = {BACKGROUND: Nocardia farcinica is one of the most common Nocardia species causing human infections. It is an opportunistic pathogen that often infects people with compromised immune systems. It could invade human body through respiratory tract or skin wounds, cause local infection, and affect other organs via hematogenous dissemination. However, N. farcinica-caused bacteremia is uncommon. In this study, we report a case of bacteremia caused by N. farcinica in China.

CASE PRESENTATION: An 80-year-old woman was admitted to Peking Union Medical College Hospital with recurrent fever, right abdominal pain for one and a half month, and right adrenal gland occupation. N. farcinica was identified as the causative pathogen using blood culture and plasma metagenomics next-generation sequencing (mNGS). The clinical considerations included bacteremia and adrenal gland abscess caused by Nocardia infection. As the patient was allergic to sulfanilamide, imipenem/cilastatin and linezolid were empirically administered. Unfortunately, the patient eventually died less than a month after the initiation of anti-infection treatment.

CONCLUSION: N. farcinica bacteremia is rare and its clinical manifestations are not specific. Its diagnosis depends on etiological examination, which can be confirmed using techniques such as Sanger sequencing and mNGS. In this report, we have reviewed cases of Nocardia bloodstream infection reported in the past decade, hoping to improve clinicians' understanding of Nocardia bloodstream infection and help in its early diagnosis and timely treatment.}, } @article {pmid38589361, year = {2024}, author = {Barker-Tejeda, TC and Zubeldia-Varela, E and Macías-Camero, A and Alonso, L and Martín-Antoniano, IA and Rey-Stolle, MF and Mera-Berriatua, L and Bazire, R and Cabrera-Freitag, P and Shanmuganathan, M and Britz-McKibbin, P and Ubeda, C and Francino, MP and Barber, D and Ibáñez-Sandín, MD and Barbas, C and Pérez-Gordo, M and Villaseñor, A}, title = {Comparative characterization of the infant gut microbiome and their maternal lineage by a multi-omics approach.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {3004}, pmid = {38589361}, issn = {2041-1723}, support = {PI17/01087//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PI19/00044//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PI20/01366//Ministry of Economy and Competitiveness | Instituto de Salud Carlos III (Institute of Health Carlos III)/ ; PCI2018-092930//Ministry of Economy and Competitiveness | Agencia Estatal de Investigación (Spanish Agencia Estatal de Investigación)/ ; }, abstract = {The human gut microbiome establishes and matures during infancy, and dysregulation at this stage may lead to pathologies later in life. We conducted a multi-omics study comprising three generations of family members to investigate the early development of the gut microbiota. Fecal samples from 200 individuals, including infants (0-12 months old; 55% females, 45% males) and their respective mothers and grandmothers, were analyzed using two independent metabolomics platforms and metagenomics. For metabolomics, gas chromatography and capillary electrophoresis coupled to mass spectrometry were applied. For metagenomics, both 16S rRNA gene and shotgun sequencing were performed. Here we show that infants greatly vary from their elders in fecal microbiota populations, function, and metabolome. Infants have a less diverse microbiota than adults and present differences in several metabolite classes, such as short- and branched-chain fatty acids, which are associated with shifts in bacterial populations. These findings provide innovative biochemical insights into the shaping of the gut microbiome within the same generational line that could be beneficial in improving childhood health outcomes.}, } @article {pmid38588959, year = {2024}, author = {Namuwulya, P and Ashraf, S and Niebel, M and Ssekagiri, A and Tushabe, P and Kakooza, P and Tong, L and Bukenya, H and Jerome, H and Davis, C and Birungi, M and Turyahabwe, I and Mugaga, A and Eliku, JP and Francis, A and Nakabazzi, L and Nsubuga, F and Katushabe, E and Kisakye, A and Ampeire, I and Nanteza, A and Kaleebu, P and Bakamutumaho, B and Nsamba, P and Kazibwe, A and da Silva Filipe, A and Tweyongyere, R and Bwogi, J and Thomson, EC}, title = {Viruses associated with measles-like illnesses in Uganda.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {106148}, doi = {10.1016/j.jinf.2024.106148}, pmid = {38588959}, issn = {1532-2742}, abstract = {OBJECTIVES: In this study, we investigated the causes of measles-like illnesses (MLI) in the Uganda national surveillance programme in order to inform diagnostic assay selection and vaccination strategies.

METHODS: We used metagenomic next-generation sequencing (M-NGS) on the Illumina platform to identify viruses associated with MLI (defined as fever and rash in the presence of either cough, coryza or conjunctivitis) in patient samples that had tested IgM negative for measles between 2010 and 2019.

RESULTS: Viral genomes were identified in 87/271 (32%) of samples, of which 44/271 (16%) contained 12 known viral pathogens. Expected viruses included rubella, human parvovirus B19, Epstein Barr virus, human herpesvirus 6B, human cytomegalovirus, varicella zoster virus and measles virus (detected within the seronegative window-period of infection) and the blood-borne hepatitis B virus. We also detected Saffold virus, human parvovirus type 4, the human adenovirus C2 and vaccine-associated poliovirus type 1.

CONCLUSIONS: The study highlights the presence of undiagnosed viruses causing MLI in Uganda, including vaccine-preventable illnesses. NGS can be used to monitor common viral infections at a population level, especially in regions where such infections are prevalent, including low and middle income countries to guide vaccination policy and optimize diagnostic assays.}, } @article {pmid38588591, year = {2024}, author = {Lubkowicz, D and Hava, DL and Lewis, K and Isabella, VM}, title = {Rational Engineering of Escherichia coli Nissle 1917 as Live Biotherapeutic to Degrade Uremic Toxin Precursors.}, journal = {ACS synthetic biology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acssynbio.3c00686}, pmid = {38588591}, issn = {2161-5063}, abstract = {Uremic toxins (UTs) are microbiota-derived metabolites that accelerate the progression of kidney damage in patients with chronic kidney disease (CKD). One of the major UTs involved in CKD progression is p-cresol-sulfate (PCS), derived from dietary l-tyrosine (l-Tyr). Here, we engineered a probiotic strain of Escherichia coli Nissle 1917, to convert l-Tyr to the nontoxic compound p-coumaric acid via tyrosine ammonia lyase (TAL). First, a small metagenomic library was assessed to identify the TAL with the greatest whole-cell activity. Second, accessory genes implicated in the import of l-Tyr and export of PCA were overexpressed to enhance l-Tyr degradation by 106% and 56%, respectively. Last, random mutagenesis coupled to a novel selection and screening strategy was developed that identified a TAL variant with a 25% increase in whole-cell activity. Taken together, the final strain exhibits a 183% improvement over initial whole-cell activity and provides a promising candidate to degrade l-Tyr mediated PCS accumulation.}, } @article {pmid38588312, year = {2024}, author = {Recio, MI and de la Torre, J and Daddaoua, A and Udaondo, Z and Duque, E and Gavira, JA and López-Sánchez, C and Ramos, JL}, title = {Characterization of an extremophile bacterial acid phosphatase derived from metagenomics analysis.}, journal = {Microbial biotechnology}, volume = {17}, number = {4}, pages = {e14404}, doi = {10.1111/1751-7915.14404}, pmid = {38588312}, issn = {1751-7915}, support = {EJPSOIL862695//Ministerio de Ciencia e Innovación/ ; PID2021123469OBI00//Ministerio de Ciencia e Innovación/ ; PREPSOIL (HE/CL5SOILM/0102)//Ministerio de Ciencia e Innovación/ ; TED2021129632BI00//Ministerio de Ciencia e Innovación/ ; }, abstract = {Acid phosphatases are enzymes that play a crucial role in the hydrolysis of various organophosphorous molecules. A putative acid phosphatase called FS6 was identified using genetic profiles and sequences from different environments. FS6 showed high sequence similarity to type C acid phosphatases and retained more than 30% of consensus residues in its protein sequence. A histidine-tagged recombinant FS6 produced in Escherichia coli exhibited extremophile properties, functioning effectively in a broad pH range between 3.5 and 8.5. The enzyme demonstrated optimal activity at temperatures between 25 and 50°C, with a melting temperature of 51.6°C. Kinetic parameters were determined using various substrates, and the reaction catalysed by FS6 with physiological substrates was at least 100-fold more efficient than with p-nitrophenyl phosphate. Furthermore, FS6 was found to be a decamer in solution, unlike the dimeric forms of crystallized proteins in its family.}, } @article {pmid38587784, year = {2024}, author = {Kufner, V and Frey, AC and Burkhard, SH and Schmutz, S and Ziltener, G and Zaheri, M and Wiedmer, CV and Plate, A and Trkola, A and Huber, M and Mueller, NJ}, title = {Exploring viral aetiology in upper respiratory tract infections: insights from metagenomic next-generation sequencing in Swiss outpatients before and during the SARS-CoV-2 pandemic.}, journal = {Swiss medical weekly}, volume = {154}, number = {}, pages = {3797}, doi = {10.57187/s.3797}, pmid = {38587784}, issn = {1424-3997}, abstract = {AIMS OF THE STUDY: Upper respiratory tract infections are among the most common reasons for primary care consultations. They are diagnosed predominantly based on clinical assessment. Here, we investigated the benefit of viral metagenomic next-generation sequencing (mNGS) in an outpatient setting.

METHODS: This prospective cross-sectional study included immunocompetent patients with acute upper respiratory tract infections. General practitioners collected pharyngeal swabs and demographic and clinical data. Specimens were analysed using viral mNGS and conventional tests.

RESULTS: Two hundred seventy-seven patients were recruited by 21 general practitioners between 10/2019 and 12/2020, of which 91% had a suspected viral aetiology. For 138 patients (49.8%), mNGS identified one or more respiratory viruses. The mNGS showed a high overall agreement with conventional routine diagnostic tests. Rhinoviruses were the most frequently detected respiratory viruses (20.2% of patients). Viral mNGS reflected the influenza wave in early 2020 and the SARS-CoV-2 pandemic outbreak in Switzerland in March 2020. Notably, rhinoviruses continued to circulate despite non-pharmaceutical hygiene measures.

CONCLUSIONS: Viral mNGS allowed the initial diagnosis to be retrospectively re-evaluated. Assuming reduced turnaround times, mNGS has the potential to directly guide the treatment of upper respiratory tract infections. On an epidemiological level, our study highlights the utility of mNGS in respiratory infection surveillance, allowing early detection of epidemics and providing information crucial for prevention.}, } @article {pmid38587642, year = {2024}, author = {Srinivasan, S and Jnana, A and Murali, TS}, title = {Modeling Microbial Community Networks: Methods and Tools for Studying Microbial Interactions.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {56}, pmid = {38587642}, issn = {1432-184X}, support = {CRG/2022/003227//Science and Engineering Research Board/ ; }, abstract = {Microbial interactions function as a fundamental unit in complex ecosystems. By characterizing the type of interaction (positive, negative, neutral) occurring in these dynamic systems, one can begin to unravel the role played by the microbial species. Towards this, various methods have been developed to decipher the function of the microbial communities. The current review focuses on the various qualitative and quantitative methods that currently exist to study microbial interactions. Qualitative methods such as co-culturing experiments are visualized using microscopy-based techniques and are combined with data obtained from multi-omics technologies (metagenomics, metabolomics, metatranscriptomics). Quantitative methods include the construction of networks and network inference, computational models, and development of synthetic microbial consortia. These methods provide a valuable clue on various roles played by interacting partners, as well as possible solutions to overcome pathogenic microbes that can cause life-threatening infections in susceptible hosts. Studying the microbial interactions will further our understanding of complex less-studied ecosystems and enable design of effective frameworks for treatment of infectious diseases.}, } @article {pmid38587419, year = {2024}, author = {Powell, T and Sumner, DY and Jungblut, AD and Hawes, I and Mackey, T and Grettenberger, C}, title = {Metagenome-assembled bacterial genomes from benthic microbial mats in ice-covered Lake Vanda, Antarctica.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0125023}, doi = {10.1128/mra.01250-23}, pmid = {38587419}, issn = {2576-098X}, abstract = {We recovered 57 bacterial metagenome-assembled genomes (MAGs) from benthic microbial mat pinnacles from Lake Vanda, Antarctica. These MAGs provide access to genomes from polar environments and can assist in culturing and utilizing these Antarctic bacteria.}, } @article {pmid38586336, year = {2024}, author = {Zhu, H and Zhu, J and Wang, Y and Xi, X and Wang, K and Wang, Y and Ding, R and Li, H}, title = {Osteomyelitis of the femur caused by Metamycoplasma orale in an immunocompromised patient using metagenomic next-generation sequencing: A case report.}, journal = {Heliyon}, volume = {10}, number = {7}, pages = {e28730}, pmid = {38586336}, issn = {2405-8440}, abstract = {BACKGROUND: Metamycoplasma orale (M.orale), a symbiotic bacterium observed in the human oral cavity, is generally regarded as non-pathogenic to humans. Although infrequent, symptomatic infections caused by M.orale may occur in individuals with compromised humoral immunity. Accurate identification and early diagnosis of M.orale still present significant challenges due the limitations associated with conventional detection methods. Although metagenomic next-generation sequencing (mNGS) is currently widely utilized in clinical practices and exhibits a remarkable specificity and sensitivity for detecting various pathogens, its application in the diagnosis of M.orale-induced osteomyelitis remains largely unexplored.

CASE DESCRIPTION: In this report, we present a case study of osteonecrosis caused by M.orale in a 20-year-old female patient with nephrotic syndrome and other comorbidities. She was administered long-term hormone therapy and immunosuppressants, leading to her admission to the hospital due to recurrent fever, hip abscess and left thigh pain. Imaging examination revealed bilateral mid-femoral lesions, with the extensive nature of the left femoral lesion suggesting a potential secondary infection. Although no pathogen was detected in pus culture, mNGS analysis identified M.orale in the sample. Following treatment with doxycycline and levofloxacin, the patient's symotoms improved and she was discharged with favorable outcomes.

CONCLUSION: mNGS enables rapid identification of etiology in patients with osteomyelitis caused by the rare pathogen M.orale. This case accentuate the strength of mNGS for early detection and targeted clinical treatment of infectious diseases caused by uncommon pathogens.}, } @article {pmid38586148, year = {2024}, author = {Kawooya, A and Emmanuel, E and Nakavuma, J and Kumar, S and Kafeero, HM and Mwambi, DB and Adeyemo, RO and Adebayo, IA and Akinola, SA}, title = {16S-Metagenomic data profiling of the bacterial community in ready-to-eat vegetable salads sold in Kampala, Uganda.}, journal = {Data in brief}, volume = {54}, number = {}, pages = {110350}, pmid = {38586148}, issn = {2352-3409}, abstract = {This article presents a dataset on bacterial community structure associated with Ready-to-eat (RTE) vegetable salads sold in Kampala City, Uganda. The Illumina Miseq sequencing of 16S rRNA gene amplicon unveiled the bacterial communities and generated a metagenomic library from RTE vegetable salads to understand the diversities and distribution. The metagenome contained a total of 23,805 sequences with 35,420 Taxonomic units (OTUs). Metagenome sequence information is obtainable at NCBI under the Bioproject assigned accession number PRJNA1064313. Taxonomic hits distribution from VSEARCH analysis at phylum level classification of NN-3 discovered predominantly Proteobacteria (65.34%) followed by Firmicutes (31.60%) and Bacteroidota (0.14%). Deinococcota (0.01%) and Planctomycetota (0.01%) were also detected. Also, VSEARCH-assisted analysis of NN-4 detected a higher prevalence of Firmicutes (65.68%) than Proteobacteria (33.25%), while Bacteroidota (0.04%) indicating the presence of contaminants of faecal sources.}, } @article {pmid38585727, year = {2024}, author = {Sarhan, MS and Filosi, M and Maixner, F and Fuchsberger, C}, title = {Taxonize-gb: A tool for filtering GenBank non-redundant databases based on taxonomy.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.03.22.586347}, pmid = {38585727}, abstract = {Analyzing taxonomic diversity and identification in diverse ecological samples has become a crucial routine in various research and industrial fields. While DNA barcoding marker-gene approaches were once prevalent, the decreasing costs of next-generation sequencing have made metagenomic shotgun sequencing more popular and feasible. In contrast to DNA-barcoding, metagenomic shotgun sequencing offers possibilities for in-depth characterization of structural and functional diversity. However, analysis of such data is still considered a hurdle due to absence of taxa-specific databases. Here we present taxonize-gb, a command-line software tool to extract GenBank non-redundant nucleotide and protein databases, related to one or more input taxonomy identifier. Our tool allows the creation of taxa-specific reference databases tailored to specific research questions, which reduces search times and therefore represents a practical solution for researchers analyzing large metagenomic data on regular basis. Taxonize-gb is an open-source command-line Python-based tool freely available for installation at https://pypi.org/project/taxonize-gb/ and on GitHub https://github.com/msabrysarhan/taxonize_genbank . It is released under Creative Commons Attribution-NonCommercial 4.0 International License (CC BY-NC 4.0).}, } @article {pmid38585649, year = {2024}, author = {Yang, Y and Chen, J and Gao, H and Cui, M and Zhu, M and Xiang, X and Wang, Q}, title = {Characterization of the gut microbiota and fecal and blood metabolomes under various factors in urban children from Northwest China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1374544}, pmid = {38585649}, issn = {2235-2988}, abstract = {INTRODUCTION: Children have regional dynamics in the gut microbiota development trajectory. Hitherto, the features and influencing factors of the gut microbiota and fecal and plasma metabolites in children from Northwest China remain unclear.

METHODS: Shotgun metagenomic sequencing and untargeted metabolomics were performed on 100 healthy volunteers aged 2-12 years.

RESULTS: Age, body mass index (BMI), regular physical exercise (RPE), and delivery mode (DM) significantly affect gut microbiota and metabolites. Lactobacillus, Butyricimonas, Prevotella, Alistipes, and predicted pathway propanoate production were significantly increased with age while Bifidobacterium breve, B. animalis, B. pseudocatenulatum, Streptococcus infantis, and carbohydrate degradation were decreased. Fecal metabolome revealed that the metabolism of caffeine, amino acids, and lipid significantly increased with age while galactose metabolism decreased. Noticeably, BMI was positively associated with pathogens including Erysipelatoclostridium ramosum, Parabacteroides distasonis, Ruminococcus gnavus, and amino acid metabolism but negatively associated with beneficial Akkermansia muciniphila, Alistipes finegoldii, Eubacterium ramulus, and caffeine metabolism. RPE has increased probiotic Faecalibacterium prausnitzii and Anaerostipes hadrus, acetate and lactate production, and major nutrient metabolism in gut and plasma, but decreased pathobiont Bilophila wadsworthia, taurine degradation, and pentose phosphate pathway. Interestingly, DM affects the gut microbiota and metabolites throughout the whole childhood. Bifidobacterium animalis, Lactobacillus mucosae, L. ruminis, primary bile acid, and neomycin biosynthesis were enriched in eutocia, while anti-inflammatory Anaerofustis stercorihominis, Agathobaculum butyriciproducens, Collinsella intestinalis, and pathogenic Streptococcus salivarius, Catabacter hongkongensis, and amino acid metabolism were enriched in Cesarean section children.

DISCUSSION: Our results provided theoretical and data foundation for the gut microbiota and metabolites in preadolescent children's growth and development in Northwest China.}, } @article {pmid38585427, year = {2024}, author = {Mengis, T and Zajac, N and Bernhard, L and Heggli, I and Herger, N and Devan, J and Marcus, R and Brunner, F and Laux, C and Farshad, M and Distler, O and Dudli, S}, title = {Intervertebral disc microbiome in Modic changes: Lack of result replication underscores the need for a consensus in low-biomass microbiome analysis.}, journal = {JOR spine}, volume = {7}, number = {2}, pages = {e1330}, pmid = {38585427}, issn = {2572-1143}, abstract = {INTRODUCTION: The emerging field of the disc microbiome challenges traditional views of disc sterility, which opens new avenues for novel clinical insights. However, the lack of methodological consensus in disc microbiome studies introduces discrepancies. The aims of this study were to (1) compare the disc microbiome of non-Modic (nonMC), Modic type 1 change (MC1), and MC2 discs to findings from prior disc microbiome studies, and (2) investigate if discrepancies to prior studies can be explained with bioinformatic variations.

METHODS: Sequencing of 16S rRNA in 70 discs (24 nonMC, 25 MC1, and 21 MC2) for microbiome profiling. The experimental setup included buffer contamination controls and was performed under aseptic conditions. Methodology and results were contrasted with previous disc microbiome studies. Critical bioinformatic steps that were different in our best-practice approach and previous disc microbiome studies (taxonomic lineage assignment, prevalence cut-off) were varied and their effect on results were compared.

RESULTS: There was limited overlap of results with a previous study on MC disc microbiome. No bacterial genera were shared using the same bioinformatic parameters. Taxonomic lineage assignment using "amplicon sequencing variants" was more sensitive and detected 48 genera compared to 22 with "operational taxonomic units" (previous study). Increasing filter cut-off from 4% to 50% (previous study) reduced genera from 48 to 4 genera. Despite these differences, both studies observed dysbiosis with an increased abundance of gram-negative bacteria in MC discs as well as a lower beta-diversity. Cutibacterium was persistently detected in all groups independent of the bioinformatic approach, emphasizing its prevalence.

CONCLUSION: There is dysbiosis in MC discs. Bioinformatic parameters impact results yet cannot explain the different findings from this and a previous study. Therefore, discrepancies are likely caused by different sample preparations or true biologic differences. Harmonized protocols are required to advance understanding of the disc microbiome and its clinical implications.}, } @article {pmid38585188, year = {2024}, author = {Yang, L and Su, J and Zhuo, C}, title = {A case of intracranial infection caused by Aspergillus flavus originating from chronic otitis media.}, journal = {Medical mycology case reports}, volume = {44}, number = {}, pages = {100637}, pmid = {38585188}, issn = {2211-7539}, abstract = {Central nervous system (CNS) aspergillosis is uncommon in immunocompetent patients. We present a 64-year-old man with chronic otitis media and uncontrolled diabetes. Aspergillus flavus was identified in cerebrospinal fluid via metagenomics next-generation sequencing technology. Initial voriconazole treatment offered limited relief, but personalized dosage adjustments, guided by drug concentration, led to remission. This case underscores the importance of diverse diagnostic approaches and tailored therapy for CNS Aspergillus infections.}, } @article {pmid38584937, year = {2024}, author = {Tang, H and Huang, Y and Yuan, D and Liu, J}, title = {Atherosclerosis, gut microbiome, and exercise in a meta-omics perspective: a literature review.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e17185}, pmid = {38584937}, issn = {2167-8359}, abstract = {BACKGROUND: Cardiovascular diseases are the leading cause of death worldwide, significantly impacting public health. Atherosclerotic cardiovascular diseases account for the majority of these deaths, with atherosclerosis marking the initial and most critical phase of their pathophysiological progression. There is a complex relationship between atherosclerosis, the gut microbiome's composition and function, and the potential mediating role of exercise. The adaptability of the gut microbiome and the feasibility of exercise interventions present novel opportunities for therapeutic and preventative approaches.

METHODOLOGY: We conducted a comprehensive literature review using professional databases such as PubMed and Web of Science. This review focuses on the application of meta-omics techniques, particularly metagenomics and metabolomics, in studying the effects of exercise interventions on the gut microbiome and atherosclerosis.

RESULTS: Meta-omics technologies offer unparalleled capabilities to explore the intricate connections between exercise, the microbiome, the metabolome, and cardiometabolic health. This review highlights the advancements in metagenomics and metabolomics, their applications in research, and examines how exercise influences the gut microbiome. We delve into the mechanisms connecting these elements from a metabolic perspective. Metagenomics provides insight into changes in microbial strains post-exercise, while metabolomics sheds light on the shifts in metabolites. Together, these approaches offer a comprehensive understanding of how exercise impacts atherosclerosis through specific mechanisms.

CONCLUSIONS: Exercise significantly influences atherosclerosis, with the gut microbiome serving as a critical intermediary. Meta-omics technology holds substantial promise for investigating the gut microbiome; however, its methodologies require further refinement. Additionally, there is a pressing need for more extensive cohort studies to enhance our comprehension of the connection among these element.}, } @article {pmid38584645, year = {2024}, author = {Pold, G and Bonilla-Rosso, G and Saghaï, A and Strous, M and Jones, CM and Hallin, S}, title = {Phylogenetics and environmental distribution of nitric oxide-forming nitrite reductases reveal their distinct functional and ecological roles.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae020}, pmid = {38584645}, issn = {2730-6151}, abstract = {The two evolutionarily unrelated nitric oxide-producing nitrite reductases, NirK and NirS, are best known for their redundant role in denitrification. They are also often found in organisms that do not perform denitrification. To assess the functional roles of the two enzymes and to address the sequence and structural variation within each, we reconstructed robust phylogenies of both proteins with sequences recovered from 6973 isolate and metagenome-assembled genomes and identified 32 well-supported clades of structurally distinct protein lineages. We then inferred the potential niche of each clade by considering other functional genes of the organisms carrying them as well as the relative abundances of each nir gene in 4082 environmental metagenomes across diverse aquatic, terrestrial, host-associated, and engineered biomes. We demonstrate that Nir phylogenies recapitulate ecology distinctly from the corresponding organismal phylogeny. While some clades of the nitrite reductase were equally prevalent across biomes, others had more restricted ranges. Nitrifiers make up a sizeable proportion of the nitrite-reducing community, especially for NirK in marine waters and dry soils. Furthermore, the two reductases showed distinct associations with genes involved in oxidizing and reducing other compounds, indicating that the NirS and NirK activities may be linked to different elemental cycles. Accordingly, the relative abundance and diversity of NirS versus NirK vary between biomes. Our results show the divergent ecological roles NirK and NirS-encoding organisms may play in the environment and provide a phylogenetic framework to distinguish the traits associated with organisms encoding the different lineages of nitrite reductases.}, } @article {pmid38583688, year = {2024}, author = {Thorman, AW and Morrow, AL and Groeneveld, A and Nauta, A and Newburg, DS}, title = {Validation of collection and anaerobic fermentation techniques for measuring prebiotic impact on gut microbiota.}, journal = {Pharmacological research}, volume = {}, number = {}, pages = {107169}, doi = {10.1016/j.phrs.2024.107169}, pmid = {38583688}, issn = {1096-1186}, abstract = {BACKGROUND: Defining the ability of prebiotic dietary carbohydrates to influence the composition and metabolism of the gut microbiota is central to defining their health impact in diverse individuals. Many clinical trials are using indirect methods. This study aimed to validate collection and fermentation methods enabling their use in the context of clinical studies.

METHODS AND RESULTS: Parameters tested included stool sample acquisition, storage, and growth conditions. Stool from 3 infants and 3 adults was collected and stored under varying conditions. Samples were cultured anaerobically for two days in the presence of prebiotics, whereupon optical density and pH were measured across time. Whole genome shotgun sequencing and NMR metabolomics were performed. Neither the type of collection vial (standard vial and two different BD anaerobic collection vials) nor cryopreservation (-80[o]C or 4[o]C) significantly influenced either microbial composition at 16hrs of anaerobic culture or the principal components of the metabolome at 8 or 16hrs. Metagenomic differences were driven primarily by subject, while metabolomic differences were driven by fermentation sugar (2'-fucosyllactose or dextrose).

CONCLUSIONS: These data identified a feasible and valid approach for prebiotic fermentation analysis of individual samples in large clinical studies: collection of stool microbiota using standard vials; cryopreservation prior to testing; and collecting fermentation read-out at 8 and 16hr. Thus, fermentation analysis can be a valid technique for testing the effects of prebiotics on human fecal microbiota.}, } @article {pmid38583614, year = {2024}, author = {Díaz-Torres, O and Los Cobos, EOV and Kreft, JU and Loge, FJ and Díaz-Vázquez, D and Mahlknecht, J and Gradilla-Hernández, MS and Senés-Guerrero, C}, title = {A metagenomic study of antibiotic resistance genes in a hypereutrophic subtropical lake contaminated by anthropogenic sources.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {172216}, doi = {10.1016/j.scitotenv.2024.172216}, pmid = {38583614}, issn = {1879-1026}, abstract = {Antibiotic resistance genes (ARGs) are a major threat to human and environmental health. This study investigated the occurrence and distribution of ARGs in Lake Cajititlán, a hypereutrophic subtropical lake in Mexico contaminated by anthropogenic sources (urban wastewater and runoff from crop and livestock production). ARGs (a total of 475 genes) were detected in 22 bacterial genera, with Pseudomonas (144 genes), Stenotrophomonas (88 genes), Mycobacterium (54 genes), and Rhodococcus (27 genes) displaying the highest frequencies of ARGs. Among these, Pseudomonas aeruginosa and Stenotrophomonas maltophilia showed the highest number of ARGs. The results revealed a diverse array of ARGs, including resistance to macrolides (11.55 %), aminoglycosides (8.22 %), glycopeptides (6.22 %), tetracyclines (4 %), sulfonamides (4 %), carbapenems (1.11 %), phenicols (0.88 %), fluoroquinolones (0.44 %), and lincosamides (0.22 %). The most frequently observed ARGs were associated with multidrug resistance (63.33 %), with MexF (42 genes), MexW (36 genes), smeD (31 genes), mtrA (25 genes), and KHM-1 (22 genes) being the most common. Lake Cajititlán is a recreational area for swimming, fishing, and boating, while also supporting irrigation for agriculture and potentially acting as a drinking water source for some communities. This raises concerns about the potential for exposure to antibiotic-resistant bacteria through these activities. The presence of ARGs in Lake Cajititlán poses a significant threat to both human and environmental health. Developing strategies to mitigate the risks of antibiotic resistance, including improving wastewater treatment, and promoting strategic antibiotic use and disposal, is crucial. This study represents a significant advancement in the understanding of antibiotic resistance dynamics in a hypereutrophic subtropical lake in a developing country, providing valuable insights for the scientific community and policymakers.}, } @article {pmid38507648, year = {2024}, author = {Upadhyay, M and Pogorevc, N and Medugorac, I}, title = {scalepopgen: Bioinformatic Workflow Resources Implemented in Nextflow for Comprehensive Population Genomic Analyses.}, journal = {Molecular biology and evolution}, volume = {41}, number = {4}, pages = {}, pmid = {38507648}, issn = {1537-1719}, support = {526367023//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; Workflow ; *Metagenomics ; *Software ; Genomics/methods ; Computational Biology/methods ; }, abstract = {Population genomic analyses such as inference of population structure and identifying signatures of selection usually involve the application of a plethora of tools. The installation of tools and their dependencies, data transformation, or series of data preprocessing in a particular order sometimes makes the analyses challenging. While the usage of container-based technologies has significantly resolved the problems associated with the installation of tools and their dependencies, population genomic analyses requiring multistep pipelines or complex data transformation can greatly be facilitated by the application of workflow management systems such as Nextflow and Snakemake. Here, we present scalepopgen, a collection of fully automated workflows that can carry out widely used population genomic analyses on the biallelic single nucleotide polymorphism data stored in either variant calling format files or the plink-generated binary files. scalepopgen is developed in Nextflow and can be run locally or on high-performance computing systems using either Conda, Singularity, or Docker. The automated workflow includes procedures such as (i) filtering of individuals and genotypes; (ii) principal component analysis, admixture with identifying optimal K-values; (iii) running TreeMix analysis with or without bootstrapping and migration edges, followed by identification of an optimal number of migration edges; (iv) implementing single-population and pair-wise population comparison-based procedures to identify genomic signatures of selection. The pipeline uses various open-source tools; additionally, several Python and R scripts are also provided to collect and visualize the results. The tool is freely available at https://github.com/Popgen48/scalepopgen.}, } @article {pmid38302666, year = {2024}, author = {Gose, MA and Humble, E and Brownlow, A and Wall, D and Rogan, E and Sigurðsson, GM and Kiszka, JJ and Thøstesen, CB and IJsseldijk, LL and Ten Doeschate, M and Davison, NJ and Øien, N and Deaville, R and Siebert, U and Ogden, R}, title = {Population genomics of the white-beaked dolphin (Lagenorhynchus albirostris): Implications for conservation amid climate-driven range shifts.}, journal = {Heredity}, volume = {132}, number = {4}, pages = {192-201}, pmid = {38302666}, issn = {1365-2540}, mesh = {Animals ; *Dolphins/genetics ; Metagenomics ; Climate Change ; Temperature ; }, abstract = {Climate change is rapidly affecting species distributions across the globe, particularly in the North Atlantic. For highly mobile and elusive cetaceans, the genetic data needed to understand population dynamics are often scarce. Cold-water obligate species such as the white-beaked dolphin (Lagenorhynchus albirostris) face pressures from habitat shifts due to rising sea surface temperatures in addition to other direct anthropogenic threats. Unravelling the genetic connectivity between white-beaked dolphins across their range is needed to understand the extent to which climate change and anthropogenic pressures may impact species-wide genetic diversity and identify ways to protect remaining habitat. We address this by performing a population genomic assessment of white-beaked dolphins using samples from much of their contemporary range. We show that the species displays significant population structure across the North Atlantic at multiple scales. Analysis of contemporary migration rates suggests a remarkably high connectivity between populations in the western North Atlantic, Iceland and the Barents Sea, while two regional populations in the North Sea and adjacent UK and Irish waters are highly differentiated from all other clades. Our results have important implications for the conservation of white-beaked dolphins by providing guidance for the delineation of more appropriate management units and highlighting the risk that local extirpation may have on species-wide genetic diversity. In a broader context, this study highlights the importance of understanding genetic structure of all species threatened with climate change-driven range shifts to assess the risk of loss of species-wide genetic diversity.}, } @article {pmid38583533, year = {2024}, author = {Hassan, S and Bhadwal, SS and Khan, M and Sabreena, and Nissa, KU and Shah, RA and Bhat, HM and Bhat, SA and Lone, IM and Ganai, BA}, title = {Revitalizing contaminated lands: A state-of-the-art review on the remediation of mine-tailings using phytoremediation and genomic approaches.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {141889}, doi = {10.1016/j.chemosphere.2024.141889}, pmid = {38583533}, issn = {1879-1298}, abstract = {The mining industry has historically served as a critical reservoir of essential raw materials driving global economic progress. Nevertheless, the consequential by-product known as mine tailings has consistently produced a substantial footprint of environmental contamination. With annual discharges of mine tailings surpassing 10 billion tons globally, the need for effective remediation strategies is more pressing than ever as traditional physical and chemical remediation techniques are hindered by their high costs and limited efficacy. Phytoremediation utilizing plants for remediation of polluted soil has developed as a promising and eco-friendly approach to addressing mine tailings contamination. Furthermore, sequencing of genomic DNA and transcribed RNA extracted from mine tailings presents a pivotal opportunity to provide critical supporting insights for activities directed towards the reconstruction of ecosystem functions on contaminated lands. This review explores the growing prominence of phytoremediation and metagenomics as an ecologically sustainable techniques for rehabilitating mine-tailings. The present study envisages that plant species such as Solidago chilensis, Festuca arundinacea, Lolium perenne, Polygonum capitatum, Pennisetum purpureum, Maireana brevifolia, Prosopis tamarugo etc. could be utilized for the remediation of mine-tailings. Furthermore, a critical evaluation of the organic and inorganic ammendments that optimize conditions for the remediation of mine tailings is also provided. The focus of this review extends to the exploration of environmental genomics to characterize microbial communities in mining sites. By delving into the multifaceted dimensions of phytoremediation and genomics for mine tailings, this study contributes to the ongoing efforts to revitalize contaminated lands for a sustainable and environmentally friendly future.}, } @article {pmid38583079, year = {2024}, author = {Jalandra, R and Dalal, N and Mohan, A and Solanki, PR and Kumar, A}, title = {A novel method for enrichment of Morganella morganii in fecal samples using designed culture medium.}, journal = {Cell biochemistry and function}, volume = {42}, number = {3}, pages = {e4004}, doi = {10.1002/cbf.4004}, pmid = {38583079}, issn = {1099-0844}, support = {//National Institute of Immunology/ ; }, abstract = {Morganella morganii is a gram negative, facultative anaerobic rod-shaped bacterium, commonly found in environment and in the intestine of human, mammals, and reptiles as a part of their gut microbiome. M. morganii can cause Gram-negative folliculitis, black nail infection, acute retiform purpura, fetal demise, and subdural empyema. The increasing frequency of M. morganii infections generate the need for efficient methods to enrich the presence of M. morganii in clinical samples to make its detection easier. Culturomics aims to grow and maximize the number of culturable bacteria. Different methods are followed to maximize the growth of minority population of bacteria by disrupting the growth of bacteria which are present in higher concentration. This article presents a method for selective enriching the M. morganii in human fecal samples. This method includes prior incubation of fecal microbiota in an anaerobic environment, adding supplement like fecal water to give dormant bacteria a break to become active to grow to threshold concentration, and an enrichment stage which provides the additional opportunity of growing to M. morganii on the selective medium. This method also provides an ingenuous way for augmenting the growth of fecal M. morganii species.}, } @article {pmid38582183, year = {2024}, author = {Huang, D and Sun, X and Ghani, MU and Li, B and Yang, J and Chen, Z and Kong, T and Xiao, E and Liu, H and Wang, Q and Sun, W}, title = {Bacteria associated with Comamonadaceae are key arsenite oxidizer associated with Pteris vittata root.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {123909}, doi = {10.1016/j.envpol.2024.123909}, pmid = {38582183}, issn = {1873-6424}, abstract = {Pteris vittata (P. vittata), an arsenic (As) hyperaccumulator commonly used in the phytoremediation of As-contaminated soils, contains root-associated bacteria (RAB) including those that colonize the root rhizosphere and endosphere, which can adapt to As contamination and improve plant health. As(III)-oxidizing RAB can convert the more toxic arsenite (As(III)) to less toxic arsenate (As(V)) under As-rich conditions, which may promote plant survial. Previous studies have shown that microbial As(III) oxidation occurs in the rhizospheres and endospheres of P. vittata. However, knowledge of RAB of P. vittata responsible for As(III) oxidation remained limited. In this study, members of the Comamonadaceae family were identified as putative As(III) oxidizers, and the core microbiome associated with P. vittata roots using DNA-stable isotope probing (SIP), amplicon sequencing and metagenomic analysis. Metagenomic binning revealed that metagenome assembled genomes (MAGs) associated with Comamonadaceae contained several functional genes related to carbon fixation, arsenic resistance, plant growth promotion and bacterial colonization. As(III) oxidation and plant growth promotion may be key features of RAB in promoting P. vittata growth. These results extend the current knowledge of the diversity of As(III)-oxidizing RAB and provide new insights into improving the efficacy of arsenic phytoremediation.}, } @article {pmid38582109, year = {2024}, author = {Chen, Q and Lyu, W and Pan, C and Ma, L and Sun, Y and Yang, H and Wang, W and Xiao, Y}, title = {Tracking investigation of archaeal composition and methanogenesis function from parental to offspring pigs.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {172078}, doi = {10.1016/j.scitotenv.2024.172078}, pmid = {38582109}, issn = {1879-1026}, abstract = {Archaea play a crucial role in microbial systems, including driving biochemical reactions and affecting host health by producing methane through hydrogen. The study of swine gut archaea has a positive significance in reducing methane emissions and improving feed utilization efficiency. However, the development and functional changes of archaea in the pig intestines have been overlooked for a long time. In this study, 54 fecal samples were collected from 36 parental pigs (18 boars and 18 pregnant/lactating sows), and 108 fecal samples from 18 offspring pigs during lactation, nursery, growing, and finishing stages were tracked and collected for metagenomic sequencing. We obtained 14 archaeal non-redundant metagenome-assembled genomes (MAGs). These archaea were classified as Methanobacteriota and Thermoplasmatota at the phylum level, and Methanobrevibacter, Methanosphaera, MX-02, and UBA71 at the genus level, involving hydrogenotrophic, methylotrophic, and acetoclastic pathways. The hydrogenotrophic pathway dominated the methanogenesis function, and the vast majority of archaea participated in it. Dietary changes profoundly affected the archaeal composition and methanogenesis function in pigs. The abundance of hydrogen-producing bacteria in parental pigs fed high-fiber diets was higher than that in offspring pigs fed low-fiber diets. The methanogenesis function was positively correlated with fiber decomposition functions and negatively correlated with the starch decomposition function. Increased abundance of sulfate reductase and fumarate reductase, as well as decreased acetate/propionate ratio, indicated that the upregulation of alternative hydrogen uptake pathways competing with methanogens may be the reason for the reduced methanogenesis function. These findings contribute to providing information and direction in the pig industry for the development of strategies to reduce methane emissions, improve feed efficiency, and maintain intestinal health.}, } @article {pmid38581983, year = {2024}, author = {Liang, L and Zhao, Z and Zhou, H and Zhang, Y}, title = {Insights into feasibility and microbial characterizations on simultaneous elimination of dissolved methane from anaerobic effluents and nitrate/nitrite reduction in a conventional anoxic reactor with magnetite.}, journal = {Water research}, volume = {256}, number = {}, pages = {121567}, doi = {10.1016/j.watres.2024.121567}, pmid = {38581983}, issn = {1879-2448}, abstract = {Discovery of nitrate/nitrite-dependent anaerobic methane oxidation (DAMO) challenges the conventional biological treatment processes, since it provides a possibility of simultaneously mitigating dissolved methane emissions from anaerobic effluents and reducing additional carbon sources for denitrification. Due to the slow growth of specialized DAMO microbes, this possibility has been just practiced with biofilms in membrane biofilm reactors or granular sludge in membrane bioreactors. In this study, simultaneous elimination of dissolved methane from anaerobic effluents and nitrate/nitrite reduction was achieved in a conventional anoxic reactor with magnetite. Calculations of electron flow balance showed that, with magnetite the eliminated dissolved methane was almost entirely used for nitrate/nitrite reduction, while without magnetite approximately 52 % of eliminated dissolved methane was converted to unknown organics. Metagenomic sequencing showed that, when dissolved methane served as an electron donor, the abundance of genes for reverse methanogenesis and denitrification dramatically increased, indicating that anaerobic oxidation of methane (AOM) coupled to nitrate/nitrite reduction occurred. Magnetite increased the abundance of genes encoding the key enzymes involved in whole reverse methanogenesis and Nir and Nor involved in denitrification, compared to that without magnetite. Analysis of microbial communities showed that, AOM coupled to nitrate/nitrite reduction was proceeded by syntrophic consortia comprised of methane oxidizers, Methanolinea and Methanobacterium, and nitrate/nitrite reducers, Armatimonadetes_gp5 and Thauera. With magnetite syntrophic consortia exchanged electrons more effectively than that without magnetite, further supporting the microbial growth.}, } @article {pmid38581982, year = {2024}, author = {Han, Y and Li, W and Gao, Y and Cai, T and Wang, J and Liu, Z and Yin, J and Lu, X and Zhen, G}, title = {Biogas upgrading and membrane anti-fouling mechanisms in electrochemical anaerobic membrane bioreactor (EC-AnMBR): Focusing on spatio-temporal distribution of metabolic functionality of microorganisms.}, journal = {Water research}, volume = {256}, number = {}, pages = {121557}, doi = {10.1016/j.watres.2024.121557}, pmid = {38581982}, issn = {1879-2448}, abstract = {Electrochemical anaerobic membrane bioreactor (EC-AnMBR) by integrating a composite anodic membrane (CAM), represents an effective method for promoting methanogenic performance and mitigating membrane fouling. However, the development and formation of electroactive biofilm on CAM, and the spatio-temporal distribution of key functional microorganisms, especially the degradation mechanism of organic pollutants in metabolic pathways were not well documented. In this work, two AnMBR systems (EC-AnMBR and traditional AnMBR) were constructed and operated to identify the role of CAM in metabolic pathway on biogas upgrading and mitigation of membrane fouling. The methane yield of EC-AnMBR at HRT of 20 days was 217.1 ± 25.6 mL-CH4/g COD, about 32.1 % higher compared to the traditional AnMBR. The 16S rRNA analysis revealed that the EC-AnMBR significantly promoted the growth of hydrolysis bacteria (Lactobacillus and SJA-15) and methanogenic archaea (Methanosaeta and Methanobacterium). Metagenomic analysis revealed that the EC-AnMBR promotes the upregulation of functional genes involved in carbohydrate metabolism (gap and kor) and methane metabolism (mtr, mcr, and hdr), improving the degradation of soluble microbial products (SMPs)/extracellular polymeric substances (EPS) on the CAM and enhancing the methanogens activity on the cathode. Moreover, CAM biofilm exhibits heterogeneity in the degradation of organic pollutants along its vertical depth. The bacteria with high hydrolyzing ability accumulated in the upper part, driving the feedstock degradation for higher starch, sucrose and galactose metabolism. A three-dimensional mesh-like cake structure with larger pores was formed as a biofilter in the middle and lower part of CAM, where the electroactive Geobacter sulfurreducens had high capabilities to directly store and transfer electrons for the degradation of organic pollutants. This outcome will further contribute to the comprehension of the metabolic mechanisms of CAM module on membrane fouling control and organic solid waste treatment and disposal.}, } @article {pmid38581039, year = {2024}, author = {Li, Y and Liu, Y and Cui, J and Zhu, M and Wang, W and Chen, K and Huang, L and Liu, Y}, title = {Oral-gut microbial transmission promotes diabetic coronary heart disease.}, journal = {Cardiovascular diabetology}, volume = {23}, number = {1}, pages = {123}, pmid = {38581039}, issn = {1475-2840}, support = {82022076//National Outstanding Youth Foundation of China/ ; }, abstract = {BACKGROUND: Diabetes is a predominant driver of coronary artery disease worldwide. This study aims to unravel the distinct characteristics of oral and gut microbiota in diabetic coronary heart disease (DCHD). Simultaneously, we aim to establish a causal link between the diabetes-driven oral-gut microbiota axis and increased susceptibility to diabetic myocardial ischemia-reperfusion injury (MIRI).

METHODS: We comprehensively investigated the microbial landscape in the oral and gut microbiota in DCHD using a discovery cohort (n = 183) and a validation chohort (n = 68). Systematically obtained oral (tongue-coating) and fecal specimens were subjected to metagenomic sequencing and qPCR analysis, respectively, to holistically characterize the microbial consortia. Next, we induced diabetic MIRI by administering streptozotocin to C57BL/6 mice and subsequently investigated the potential mechanisms of the oral-gut microbiota axis through antibiotic pre-treatment followed by gavage with specific bacterial strains (Fusobacterium nucleatum or fecal microbiota from DCHD patients) to C57BL/6 mice.

RESULTS: Specific microbial signatures such as oral Fusobacterium nucleatum and gut Lactobacillus, Eubacterium, and Roseburia faecis, were identified as potential microbial biomarkers in DCHD. We further validated that oral Fusobacterium nucleatum and gut Lactobacillus are increased in DCHD patients, with a positive correlation between the two. Experimental evidence revealed that in hyperglycemic mice, augmented Fusobacterium nucleatum levels in the oral cavity were accompanied by an imbalance in the oral-gut axis, characterized by an increased coexistence of Fusobacterium nucleatum and Lactobacillus, along with elevated cardiac miRNA-21 and a greater extent of myocardial damage indicated by TTC, HE, TUNEL staining, all of which contributed to exacerbated MIRI.

CONCLUSION: Our findings not only uncover dysregulation of the oral-gut microbiota axis in diabetes patients but also highlight the pivotal intermediary role of the increased abundance of oral F. nucleatum and gut Lactobacillus in exacerbating MIRI. Targeting the oral-gut microbiota axis emerges as a potent strategy for preventing and treating DCHD. Oral-gut microbial transmission constitutes an intermediate mechanism by which diabetes influences myocardial injury, offering new insights into preventing acute events in diabetic patients with coronary heart disease.}, } @article {pmid38580930, year = {2024}, author = {Hu, X and Yu, C and He, Y and Zhu, S and Wang, S and Xu, Z and You, S and Jiao, Y and Liu, SL and Bao, H}, title = {Integrative metagenomic analysis reveals distinct gut microbial signatures related to obesity.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {119}, pmid = {38580930}, issn = {1471-2180}, abstract = {Obesity is a metabolic disorder closely associated with profound alterations in gut microbial composition. However, the dynamics of species composition and functional changes in the gut microbiome in obesity remain to be comprehensively investigated. In this study, we conducted a meta-analysis of metagenomic sequencing data from both obese and non-obese individuals across multiple cohorts, totaling 1351 fecal metagenomes. Our results demonstrate a significant decrease in both the richness and diversity of the gut bacteriome and virome in obese patients. We identified 38 bacterial species including Eubacterium sp. CAG:274, Ruminococcus gnavus, Eubacterium eligens and Akkermansia muciniphila, and 1 archaeal species, Methanobrevibacter smithii, that were significantly altered in obesity. Additionally, we observed altered abundance of five viral families: Mesyanzhinovviridae, Chaseviridae, Salasmaviridae, Drexlerviridae, and Casjensviridae. Functional analysis of the gut microbiome indicated distinct signatures associated to obesity and identified Ruminococcus gnavus as the primary driver for function enrichment in obesity, and Methanobrevibacter smithii, Akkermansia muciniphila, Ruminococcus bicirculans, and Eubacterium siraeum as functional drivers in the healthy control group. Additionally, our results suggest that antibiotic resistance genes and bacterial virulence factors may influence the development of obesity. Finally, we demonstrated that gut vOTUs achieved a diagnostic accuracy with an optimal area under the curve of 0.766 for distinguishing obesity from healthy controls. Our findings offer comprehensive and generalizable insights into the gut bacteriome and virome features associated with obesity, with the potential to guide the development of microbiome-based diagnostics.}, } @article {pmid38580669, year = {2024}, author = {Schadt, C and Martin, S and Carrell, A and Fortner, A and Hopp, D and Jacobson, D and Klingeman, D and Kristy, B and Phillips, J and Piatkowski, B and Miller, MA and Smith, M and Patil, S and Flynn, M and Canon, S and Clum, A and Mungall, CJ and Pennacchio, C and Bowen, B and Louie, K and Northen, T and Eloe-Fadrosh, EA and Mayes, MA and Muchero, W and Weston, DJ and Mitchell, J and Doktycz, M}, title = {An integrated metagenomic, metabolomic and transcriptomic survey of Populus across genotypes and environments.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {339}, pmid = {38580669}, issn = {2052-4463}, abstract = {Bridging molecular information to ecosystem-level processes would provide the capacity to understand system vulnerability and, potentially, a means for assessing ecosystem health. Here, we present an integrated dataset containing environmental and metagenomic information from plant-associated microbial communities, plant transcriptomics, plant and soil metabolomics, and soil chemistry and activity characterization measurements derived from the model tree species Populus trichocarpa. Soil, rhizosphere, root endosphere, and leaf samples were collected from 27 different P. trichocarpa genotypes grown in two different environments leading to an integrated dataset of 318 metagenomes, 98 plant transcriptomes, and 314 metabolomic profiles that are supported by diverse soil measurements. This expansive dataset will provide insights into causal linkages that relate genomic features and molecular level events to system-level properties and their environmental influences.}, } @article {pmid38580608, year = {2024}, author = {Ruppé, E and Lazarevic, V and Schrenzel, J}, title = {Current state and perspective of implementation of clinical metagenomics: Geneva ICCMg meeting report.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2024.03.008}, pmid = {38580608}, issn = {1878-4380}, } @article {pmid38579997, year = {2024}, author = {Cao, Y and Li, Y and Jia, L and Wang, Q and Niu, T and Yang, Q and Wang, Q and Zeng, X and Wang, R and Yue, L}, title = {Long-term and combined heavy-metal contamination forms a unique microbiome and resistome: A case study in a Yellow River tributary sediments.}, journal = {Environmental research}, volume = {}, number = {}, pages = {118861}, doi = {10.1016/j.envres.2024.118861}, pmid = {38579997}, issn = {1096-0953}, abstract = {Microorganisms have developed mechanisms to adapt to environmental stress, but how microbial communities adapt to long-term and combined heavy-metal contamination under natural environmental conditions remains unclear. Specifically, this study analyzed the characteristics of heavy metal composition, microbial community, and heavy metal resistance genes (MRGs) in sediments along Mang River, a tributary of the Yellow River, which has been heavily polluted by industrial production for more than 40 years. The results showed that the concentrations of Cr, Zn, Pb, Cu and As in most sediments were higher than the ambient background values. Bringing the heavy metals speciation and concentration into the risk evaluation method, two-thirds of the sediment samples were at or above the moderate risk level, and the ecological risk of combined heavy metals in the sediments decreased along the river stream. The high ecological risk of heavy metals affected the microbial community structure, metabolic pathways and MRG distribution. The formation of a HM-resistant microbiome possibly occurred through the spread of insertion sequences (ISs) carrying multiple MRGs, the types of ISs carrying MRGs outnumber those of plasmids, and the quantity of MRGs on ISs is also higher than that on plasmids. These findings could improve our understanding of the adaptation mechanism of microbial communities to long-term combined heavy metal contamination.}, } @article {pmid38579995, year = {2024}, author = {Zeng, Z and Lv, B and Tang, YE and Sun, H and Li, S and He, Y and Wang, J and Wang, Z}, title = {Effects of dietary selenized glucose on intestinal microbiota and tryptophan metabolism in rats: Assessing skatole reduction potential.}, journal = {Environmental research}, volume = {}, number = {}, pages = {118874}, doi = {10.1016/j.envres.2024.118874}, pmid = {38579995}, issn = {1096-0953}, abstract = {3-Methylindole (Skatole), a degradation product of tryptophan produced by intestinal microbial activity, significantly contributes to odor nuisance. Its adverse effects on animal welfare, human health, and environmental pollution have been noted. However, it is still unclear whether the intestinal microbiota mediates the impact of selenium (Se) on skatole production and what the underlying mechanisms remain elusive. A selenized glucose (SeGlu) derivative is a novel organic selenium compound. In this study, a diverse range of dietary SeGlu-treated levels, including SeGlu-deficient (CK), SeGlu-adequate (0.15 mg Se per L), and SeGlu-supranutritional (0.4 mg Se per L) conditions, were used to investigate the complex interaction of SeGlu on intestinal microbiome and serum metabolome changes in male Sprague-Dawley (SD) rats. The study showed that SeGlu supplementation enhanced the antioxidant ability in rats, significantly manifested in the increases of the activity of catalase (CAT) and glutathione peroxidase (GSH-Px), while no change in the level of malonaldehyde (MDA). Metagenomic sequencing analysis verified that the SeGlu treatment group significantly increased the abundance of beneficial microorganisms such as Clostridium, Ruminococcus, Faecalibacterium, Lactobacillus, and Alloprevotella while reducing the abundance of opportunistic pathogens such as Bacteroides and Alistipes significantly. Further metabolomic analysis revealed phenylalanine, tyrosine, and tryptophan biosynthesis changes in the SeGlu treatment group. Notably, the biosynthesis of indole, a critical pathway, was affected by SeGlu treatment, with several crucial enzymes implicated. Correlation analysis demonstrated strong associations between specific bacterial species - Treponema, Bacteroides, and Ruminococcus, and changes in indole and derivative concentrations. Moreover, the efficacy of SeGlu-treated fecal microbiota was confirmed through fecal microbiota transplantation, leading to a decrease in the concentration of skatole in rats. Collectively, the analysis of microbiota and metabolome response to diverse SeGlu levels suggests that SeGlu is a promising dietary additive in modulating intestinal microbiota and reducing odor nuisance in the livestock and poultry industry.}, } @article {pmid38579579, year = {2024}, author = {Lavilla-Lerma, ML and Aibar-Almazán, A and Martínez-Amat, A and Jiménez-García, JD and Hita-Contreras, F}, title = {Moderate-intensity continuous training and high-intensity interval training modulate the composition of the oral microbiota of elderly adults: Randomized controlled trial.}, journal = {Maturitas}, volume = {185}, number = {}, pages = {107973}, doi = {10.1016/j.maturitas.2024.107973}, pmid = {38579579}, issn = {1873-4111}, abstract = {OBJECTIVE: We investigates the effects of 16-week high-intensity interval training and moderate-intensity continuous training on the composition of the oral microbiota. To the best of our knowledge, at the time of writing this paper no other scholars had described the oral metagenomic changes associated with prescribed exercise in older adults.

METHODS: Forty-three participants aged 60-74 years were randomized 1:1:1 to a control group, high-intensity interval training or moderate-intensity continuous training twice weekly for 16 weeks. Saliva samples were sequenced at baseline, week 8 and week 16 of intervention.

RESULTS: High-intensity interval training produced significant differences over time in Richness and a clear trend to decreased Simpson and Shannon diversity indices. In contrast, Simpson and Shannon indices showed an upward trend over time with moderate-intensity continuous training, which also decreased Firmicutes and increased Bacteroidetes levels. Significant differences in the abundance of pathogenic species were also observed after the participants completed the exercise interventions of either type.

CONCLUSIONS: Both types of exercise promoted subtle changes in the oral microbiota, confirming the modulatory effect of high-intensity interval training and moderate-intensity continuous training on the oral microbiome. Clinical trial registration NCT05220670.}, } @article {pmid38579536, year = {2024}, author = {Yang, Y and Huang, S and Liao, Y and Wu, X and Zhang, C and Wang, X and Yang, Z}, title = {Hippuric acid alleviates dextran sulfate sodium-induced colitis via suppressing inflammatory activity and modulating gut microbiota.}, journal = {Biochemical and biophysical research communications}, volume = {710}, number = {}, pages = {149879}, doi = {10.1016/j.bbrc.2024.149879}, pmid = {38579536}, issn = {1090-2104}, abstract = {Inflammatory bowel disease (IBD) is a chronic inflammatory disease associated with metabolic disorder and gut dysbiosis. Decreased abundance of hippuric acid (HA) was found in patients with IBD. HA, metabolized directly from benzoic acid in the intestine and indirectly from polyphenols, serves as a marker of polyphenol catabolism. While polyphenols and benzoic acid have been shown to alleviate intestinal inflammation, the role of HA in this context remains unknown. Herein, we investigated the effects and mechanism of HA on DSS-induced colitis mice. The results revealed that HA alleviated clinical activity and intestinal barrier damage, decreased pro-inflammatory cytokine production. Metagenomic sequencing suggested that HA treatment restored the gut microbiota, including an increase in beneficial gut bacteria such as Adlercreutzia, Eubacterium, Schaedlerella and Bifidobacterium_pseudolongum. Furthermore, we identified 113 candidate genes associated with IBD that are potentially under HA regulation through network pharmacological analyses. 10 hub genes including ALB, IL-6, HSP90AA1, and others were identified using PPI analysis and validated using molecular docking and mRNA expression analysis. Additionally, KEGG analysis suggested that the renin-angiotensin system (RAS), NF-κB signaling and Rap1 signaling pathways were important pathways in the response of HA to colitis. Thus, HA may provide novel biotherapy options for IBD.}, } @article {pmid38578803, year = {2024}, author = {Daw Elbait, G and Daou, M and Abuoudah, M and Elmekawy, A and Hasan, SW and Everett, DB and Alsafar, H and Henschel, A and Yousef, AF}, title = {Comparison of qPCR and metagenomic sequencing methods for quantifying antibiotic resistance genes in wastewater.}, journal = {PloS one}, volume = {19}, number = {4}, pages = {e0298325}, doi = {10.1371/journal.pone.0298325}, pmid = {38578803}, issn = {1932-6203}, abstract = {Surveillance methods of circulating antibiotic resistance genes (ARGs) are of utmost importance in order to tackle what has been described as one of the greatest threats to humanity in the 21st century. In order to be effective, these methods have to be accurate, quickly deployable, and scalable. In this study, we compare metagenomic shotgun sequencing (TruSeq DNA sequencing) of wastewater samples with a state-of-the-art PCR-based method (Resistomap HT-qPCR) on four wastewater samples that were taken from hospital, industrial, urban and rural areas. ARGs that confer resistance to 11 antibiotic classes have been identified in these wastewater samples using both methods, with the most abundant observed classes of ARGs conferring resistance to aminoglycoside, multidrug-resistance (MDR), macrolide-lincosamide-streptogramin B (MLSB), tetracycline and beta-lactams. In comparing the methods, we observed a strong correlation of relative abundance of ARGs obtained by the two tested methods for the majority of antibiotic classes. Finally, we investigated the source of discrepancies in the results obtained by the two methods. This analysis revealed that false negatives were more likely to occur in qPCR due to mutated primer target sites, whereas ARGs with incomplete or low coverage were not detected by the sequencing method due to the parameters set in the bioinformatics pipeline. Indeed, despite the good correlation between the methods, each has its advantages and disadvantages which are also discussed here. By using both methods together, a more robust ARG surveillance program can be established. Overall, the work described here can aid wastewater treatment plants that plan on implementing an ARG surveillance program.}, } @article {pmid38578779, year = {2024}, author = {Frey, B and Aiesi, M and Rast, BM and Rüthi, J and Julmi, J and Stierli, B and Qi, W and Brunner, I}, title = {Searching for new plastic-degrading enzymes from the plastisphere of alpine soils using a metagenomic mining approach.}, journal = {PloS one}, volume = {19}, number = {4}, pages = {e0300503}, doi = {10.1371/journal.pone.0300503}, pmid = {38578779}, issn = {1932-6203}, abstract = {Plastic materials, including microplastics, accumulate in all types of ecosystems, even in remote and cold environments such as the European Alps. This pollution poses a risk for the environment and humans and needs to be addressed. Using shotgun DNA metagenomics of soils collected in the eastern Swiss Alps at about 3,000 m a.s.l., we identified genes and their proteins that potentially can degrade plastics. We screened the metagenomes of the plastisphere and the bulk soil with a differential abundance analysis, conducted similarity-based screening with specific databases dedicated to putative plastic-degrading genes, and selected those genes with a high probability of signal peptides for extracellular export and a high confidence for functional domains. This procedure resulted in a final list of nine candidate genes. The lengths of the predicted proteins were between 425 and 845 amino acids, and the predicted genera producing these proteins belonged mainly to Caballeronia and Bradyrhizobium. We applied functional validation, using heterologous expression followed by enzymatic assays of the supernatant. Five of the nine proteins tested showed significantly increased activities when we used an esterase assay, and one of these five proteins from candidate genes, a hydrolase-type esterase, clearly had the highest activity, by more than double. We performed the fluorescence assays for plastic degradation of the plastic types BI-OPL and ecovio® only with proteins from the five candidate genes that were positively active in the esterase assay, but like the negative controls, these did not show any significantly increased activity. In contrast, the activity of the positive control, which contained a PLA-degrading gene insert known from the literature, was more than 20 times higher than that of the negative controls. These findings suggest that in silico screening followed by functional validation is suitable for finding new plastic-degrading enzymes. Although we only found one new esterase enzyme, our approach has the potential to be applied to any type of soil and to plastics in various ecosystems to search rapidly and efficiently for new plastic-degrading enzymes.}, } @article {pmid38578711, year = {2024}, author = {Kerek, Á and Szabó, Á and Bányai, K and Kaszab, E and Bali, K and Papp, M and Kovács, L and Jerzsele, Á}, title = {Resistome analysis of Escherichia coli isolates from layers in Hungary.}, journal = {Acta veterinaria Hungarica}, volume = {}, number = {}, pages = {}, doi = {10.1556/004.2024.00988}, pmid = {38578711}, issn = {0236-6290}, abstract = {The authors aimed to investigate eight strains of Escherichia coli (E. coli) strains from Hungarian layer flocks for antimicrobial resistance genes (ARG), using metagenomic methods. The strains were isolated from cloacal swabs of healthy adult layers. This study employed shotgun sequencing-based genetic and bioinformatic analysis along with determining phenotypic minimum inhibitory concentrations. A total of 59 ARGs were identified in the eight E. coli isolates, carrying ARGs against 15 groups of antibiotics. Among these, 28 ARGs were identified as transferable. Specifically, four ARGs were plasmid-derived, 18 ARGs were phage-derived and an additional six ARGs were predicted to be mobile, contributing to their mobility and potential spread between bacteria.}, } @article {pmid38577582, year = {2024}, author = {Corbera-Rubio, F and Stouten, GR and Bruins, J and Dost, SF and Merkel, AY and Müller, S and van Loosdrecht, MCM and van Halem, D and Laureni, M}, title = {"Candidatus Siderophilus nitratireducens": a putative nap-dependent nitrate-reducing iron oxidizer within the new order Siderophiliales.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae008}, pmid = {38577582}, issn = {2730-6151}, abstract = {Nitrate leaching from agricultural soils is increasingly found in groundwater, a primary source of drinking water worldwide. This nitrate influx can potentially stimulate the biological oxidation of iron in anoxic groundwater reservoirs. Nitrate-dependent iron-oxidizing (NDFO) bacteria have been extensively studied in laboratory settings, yet their ecophysiology in natural environments remains largely unknown. To this end, we established a pilot-scale filter on nitrate-rich groundwater to elucidate the structure and metabolism of nitrate-reducing iron-oxidizing microbiomes under oligotrophic conditions mimicking natural groundwaters. The enriched community stoichiometrically removed iron and nitrate consistently with the NDFO metabolism. Genome-resolved metagenomics revealed the underlying metabolic network between the dominant iron-dependent denitrifying autotrophs and the less abundant organoheterotrophs. The most abundant genome belonged to a new Candidate order, named Siderophiliales. This new species, "Candidatus Siderophilus nitratireducens," carries genes central genes to iron oxidation (cytochrome c cyc2), carbon fixation (rbc), and for the sole periplasmic nitrate reductase (nap). Using thermodynamics, we demonstrate that iron oxidation coupled to nap based dissimilatory reduction of nitrate to nitrite is energetically favorable under realistic Fe[3+]/Fe[2+] and NO3[-]/NO2[-] concentration ratios. Ultimately, by bridging the gap between laboratory investigations and nitrate real-world conditions, this study provides insights into the intricate interplay between nitrate and iron in groundwater ecosystems, and expands our understanding of NDFOs taxonomic diversity and ecological role.}, } @article {pmid38576823, year = {2024}, author = {Wu, N and Shen, X and Li, J and Chen, M and Wu, G and Niu, H and Liang, H and Yang, T}, title = {Extracorporeal Membrane Oxygenation in Septic Cardiomyopathy Caused by Aspergillus Infection: The First Case Report.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {1303-1307}, pmid = {38576823}, issn = {1178-6973}, abstract = {Septic cardiomyopathy (SCM) is often associated with bacterial infections but also occurs with infections with viruses such as influenza and spirochetes, including syphilis. However, there has been no systematic investigation into whether Aspergillus infections can cause septic cardiomyopathy. We report on such a case for the first time in a patient without immunodeficiency. Therefore, clinicians should be concerned with septic cardiomyopathy caused by some atypical or rare pathogens when admitting such patients.}, } @article {pmid38576373, year = {2024}, author = {Choi, SI and Kim, N and Choi, Y and Nam, RH and Jang, JY and Cho, SY}, title = {The Effect of Clostridium butyricum on Gut Microbial Changes and Functional Profiles of Metabolism in High-fat Diet-fed Rats Depending on Age and Sex.}, journal = {Journal of neurogastroenterology and motility}, volume = {30}, number = {2}, pages = {236-250}, doi = {10.5056/jnm23096}, pmid = {38576373}, issn = {2093-0879}, abstract = {BACKGROUND/AIMS: A high-fat diet (HFD) causes dysbiosis and promotes inflammatory responses in the colon. This study aims to evaluate the effects of Clostridium butyricum on HFD-induced gut microbial changes in rats.

METHODS: Six-week-old Fischer-344 rats with both sexes were given a control or HFD during 8 weeks, and 1-to-100-fold diluted Clostridium butyricum were administered by gavage. Fecal microbiota analyses were conducted using 16S ribosomal RNA metagenomic sequencing and predictive functional profiling of microbial communities in metabolism.

RESULTS: A significant increase in Ruminococcaceae and Lachnospiraceae, which are butyric acid-producing bacterial families, was observed in the probiotics groups depending on sex. In contrast, Akkermansia muciniphila, which increased through a HFD regardless of sex, and decreased in the probiotics groups. A. muciniphila positively correlated with Claudin-1 expression in males (P < 0.001) and negatively correlated with the expression of Claudin-2 (P = 0.042), IL-1β (P = 0.037), and IL-6 (P = 0.044) in females. In terms of functional analyses, a HFD decreased the relative abundances of M00131 (carbohydrate metabolism module), M00579, and M00608 (energy metabolism), and increased those of M00307 (carbohydrate metabolism), regardless of sex. However, these changes recovered especially in male C. butyricum groups. Furthermore, M00131, M00579, and M00608 showed a positive correlation and M00307 showed a negative correlation with the relative abundance of A. muciniphila (P < 0.001).

CONCLUSION: The beneficial effects of C. butyricum on HFD-induced gut dysbiosis in young male rats originate from the functional profiles of carbohydrate and energy metabolism.}, } @article {pmid38575906, year = {2024}, author = {Navgire, GS and Goel, N and Sawhney, G and Sharma, M and Kaushik, P and Mohanta, YK and Mohanta, TK and Al-Harrasi, A}, title = {Correction: Analysis and Interpretation of Metagenomics Data: An Approach.}, journal = {Biological procedures online}, volume = {26}, number = {1}, pages = {8}, doi = {10.1186/s12575-024-00235-4}, pmid = {38575906}, issn = {1480-9222}, } @article {pmid38575895, year = {2024}, author = {Zhang, M and Zhao, Y and Umar, A and Zhang, H and Yang, L and Huang, J and Long, Y and Yu, Z}, title = {Comparative analysis of microbial composition and functional characteristics in dental plaque and saliva of oral cancer patients.}, journal = {BMC oral health}, volume = {24}, number = {1}, pages = {411}, pmid = {38575895}, issn = {1472-6831}, support = {32170071 and 82273466//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The oral cavity is home to various ecological niches, each with its own unique microbial composition. Understanding the microbial communities and gene composition in different ecological niches within the oral cavity of oral cancer (OC) patients is crucial for determining how these microbial populations contribute to disease progression.

METHODS: In this study, saliva and dental plaque samples were collected from patients with OC. Metagenomic sequencing was employed to analyze the microbial community classification and functional composition of the different sample groups.

RESULTS: The results of the study revealed significant differences in both the function and classification of microbial communities between saliva and dental plaque samples. The diversity of microbial species in saliva was found to be higher compared to  that in plaque samples. Notably, Actinobacteria were enriched in the dental plaque of OC patients. Furthermore, the study identified several inter-group differential marker species, including Prevotella intermedia, Haemophilus parahaemolyticus, Actinomyces radius, Corynebacterium matruchitii, and Veillonella atypica. Additionally, 1,353 differential genes were annotated into 23 functional pathways. Interestingly, a significant correlation was observed between differentially labeled species and Herpes simplex virus 1 (HSV-1) infection, which may be related to the occurrence and development of cancer.

CONCLUSIONS: Significant differences in the microbial and genetic composition of saliva and dental plaque samples were observed in OC patients. Furthermore, pathogenic bacteria associated with oral diseases were predominantly enriched in saliva. The identification of inter-group differential biomarkers and pathways provide insights into the relationship between oral microbiota and the occurrence and development of OC.}, } @article {pmid38575138, year = {2024}, author = {Macey, MC}, title = {Genome-resolved metagenomics identifies novel active microbes in biogeochemical cycling within methanol-enriched soil.}, journal = {Environmental microbiology reports}, volume = {16}, number = {2}, pages = {e13246}, doi = {10.1111/1758-2229.13246}, pmid = {38575138}, issn = {1758-2229}, support = {//Earth and Life Systems Alliance, University of East Anglia/ ; //Norwich Research Park BBSRC Doctoral Training Program/ ; 124.18//Research England/ ; }, abstract = {Metagenome assembled genomes (MAGs), generated from sequenced [13]C-labelled DNA from [13]C-methanol enriched soils, were binned using an ensemble approach. This method produced a significantly larger number of higher-quality MAGs compared to direct binning approaches. These MAGs represent both the primary methanol utilizers and the secondary utilizers labelled via cross-feeding and predation on the labelled methylotrophs, including numerous uncultivated taxa. Analysis of these MAGs enabled the identification of multiple metabolic pathways within these active taxa that have climatic relevance relating to nitrogen, sulfur and trace gas metabolism. This includes denitrification, dissimilatory nitrate reduction to ammonium, ammonia oxidation and metabolism of organic sulfur species. The binning of viral sequence data also yielded extensive viral MAGs, identifying active viral replication by both lytic and lysogenic phages within the methanol-enriched soils. These MAGs represent a valuable resource for characterizing biogeochemical cycling within terrestrial environments.}, } @article {pmid38575861, year = {2024}, author = {Murtaza, N and Nawaz, M and Yaqub, T and Mehmood, AK}, title = {Impact of Limosilactobacillus fermentum probiotic treatment on gut microbiota composition in sahiwal calves with rotavirus diarrhea: A 16S metagenomic analysis study".}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {114}, pmid = {38575861}, issn = {1471-2180}, abstract = {BACKGROUND: Diarrhea poses a major threat to bovine calves leading to mortality and economic losses. Among the causes of calf diarrhea, bovine rotavirus is a major etiological agent and may result in dysbiosis of gut microbiota. The current study was designed to investigate the effect of probiotic Limosilactobacillus fermentum (Accession No.OR504458) on the microbial composition of rotavirus-infected calves using 16S metagenomic analysis technique. Screening of rotavirus infection in calves below one month of age was done through clinical signs and Reverse Transcriptase PCR. The healthy calves (n = 10) were taken as control while the infected calves (n = 10) before treatment was designated as diarrheal group were treated with Probiotic for 5 days. All the calves were screened for the presence of rotavirus infection on each day and fecal scoring was done to assess the fecal consistency. Infected calves after treatment were designated as recovered group. Fecal samples from healthy, recovered and diarrheal (infected calves before sampling) were processed for DNA extraction while four samples from each group were processed for 16S metagenomic analysis using Illumina sequencing technique and analyzed via QIIME 2.

RESULTS: The results show that Firmicutes were more abundant in the healthy and recovered group than in the diarrheal group. At the same time Proteobacteria was higher in abundance in the diarrheal group. Order Oscillospirales dominated healthy and recovered calves and Enterobacterials dominated the diarrheal group. Alpha diversity indices show that diversity indices based on richness were higher in the healthy group and lower in the diarrheal group while a mixed pattern of clustering between diarrheal and recovered groups samples in PCA plots based on beta diversity indices was observed.

CONCLUSION: It is concluded that probiotic Limosilactobacillus Fermentum N-30 ameliorate the dysbiosis caused by rotavirus diarrhea and may be used to prevent diarrhea in pre-weaned calves after further exploration.}, } @article {pmid38575625, year = {2024}, author = {Flores, VS and Amgarten, DE and Iha, BKV and Ryon, KA and Danko, D and Tierney, BT and Mason, C and da Silva, AM and Setubal, JC}, title = {Discovery and description of novel phage genomes from urban microbiomes sampled by the MetaSUB consortium.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {7913}, pmid = {38575625}, issn = {2045-2322}, abstract = {Bacteriophages are recognized as the most abundant members of microbiomes and have therefore a profound impact on microbial communities through the interactions with their bacterial hosts. The International Metagenomics and Metadesign of Subways and Urban Biomes Consortium (MetaSUB) has sampled mass-transit systems in 60 cities over 3 years using metagenomics, throwing light into these hitherto largely unexplored urban environments. MetaSUB focused primarily on the bacterial community. In this work, we explored MetaSUB metagenomic data in order to recover and analyze bacteriophage genomes. We recovered and analyzed 1714 phage genomes with size at least 40 kbp, from the class Caudoviricetes, the vast majority of which (80%) are novel. The recovered genomes were predicted to belong to temperate (69%) and lytic (31%) phages. Thirty-three of these genomes have more than 200 kbp, and one of them reaches 572 kbp, placing it among the largest phage genomes ever found. In general, the phages tended to be site-specific or nearly so, but 194 genomes could be identified in every city from which phage genomes were retrieved. We predicted hosts for 48% of the phages and observed general agreement between phage abundance and the respective bacterial host abundance, which include the most common nosocomial multidrug-resistant pathogens. A small fraction of the phage genomes are carriers of antibiotic resistance genes, and such genomes tended to be particularly abundant in the sites where they were found. We also detected CRISPR-Cas systems in five phage genomes. This study expands the previously reported MetaSUB results and is a contribution to the knowledge about phage diversity, global distribution, and phage genome content.}, } @article {pmid38575584, year = {2024}, author = {Messer, LF and Bourne, DG and Robbins, SJ and Clay, M and Bell, SC and McIlroy, SJ and Tyson, GW}, title = {A genome-centric view of the role of the Acropora kenti microbiome in coral health and resilience.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2902}, pmid = {38575584}, issn = {2041-1723}, abstract = {Microbial diversity has been extensively explored in reef-building corals. However, the functional roles of coral-associated microorganisms remain poorly elucidated. Here, we recover 191 bacterial and 10 archaeal metagenome-assembled genomes (MAGs) from the coral Acropora kenti (formerly A. tenuis) and adjacent seawater, to identify microbial functions and metabolic interactions within the holobiont. We show that 82 MAGs were specific to the A. kenti holobiont, including members of the Pseudomonadota, Bacteroidota, and Desulfobacterota. A. kenti-specific MAGs displayed significant differences in their genomic features and functional potential relative to seawater-specific MAGs, with a higher prevalence of genes involved in host immune system evasion, nitrogen and carbon fixation, and synthesis of five essential B-vitamins. We find a diversity of A. kenti-specific MAGs encode the biosynthesis of essential amino acids, such as tryptophan, histidine, and lysine, which cannot be de novo synthesised by the host or Symbiodiniaceae. Across a water quality gradient spanning 2° of latitude, A. kenti microbial community composition is correlated to increased temperature and dissolved inorganic nitrogen, with corresponding enrichment in molecular chaperones, nitrate reductases, and a heat-shock protein. We reveal mechanisms of A. kenti-microbiome-symbiosis on the Great Barrier Reef, highlighting the interactions underpinning the health of this keystone holobiont.}, } @article {pmid38575441, year = {2024}, author = {Tarzi, C and Zampieri, G and Sullivan, N and Angione, C}, title = {Emerging methods for genome-scale metabolic modeling of microbial communities.}, journal = {Trends in endocrinology and metabolism: TEM}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tem.2024.02.018}, pmid = {38575441}, issn = {1879-3061}, abstract = {Genome-scale metabolic models (GEMs) are consolidating as platforms for studying mixed microbial populations, by combining biological data and knowledge with mathematical rigor. However, deploying these models to answer research questions can be challenging due to the increasing number of available computational tools, the lack of universal standards, and their inherent limitations. Here, we present a comprehensive overview of foundational concepts for building and evaluating genome-scale models of microbial communities. We then compare tools in terms of requirements, capabilities, and applications. Next, we highlight the current pitfalls and open challenges to consider when adopting existing tools and developing new ones. Our compendium can be relevant for the expanding community of modelers, both at the entry and experienced levels.}, } @article {pmid38574329, year = {2024}, author = {Downie, DL and Rao, P and David-Ferdon, C and Courtney, S and Lee, JS and Quiner, C and MacDonald, PDM and Barnes, K and Fisher, S and Andreadis, JL and Chaitram, J and Mauldin, MR and Salerno, RM and Schiffer, J and Gundlapalli, AV}, title = {Surveillance for Emerging and Reemerging Pathogens Using Pathogen Agnostic Metagenomic Sequencing in the United States: A Critical Role for Federal Government Agencies.}, journal = {Health security}, volume = {}, number = {}, pages = {}, doi = {10.1089/hs.2023.0099}, pmid = {38574329}, issn = {2326-5108}, abstract = {The surveillance and identification of emerging, reemerging, and unknown infectious disease pathogens is essential to national public health preparedness and relies on fluidity, coordination, and interconnectivity between public and private pathogen surveillance systems and networks. Developing a national sentinel surveillance network with existing resources and infrastructure could increase efficiency, accelerate the identification of emerging public health threats, and support coordinated intervention strategies that reduce morbidity and mortality. However, implementing and sustaining programs to detect emerging and reemerging pathogens in humans using advanced molecular methods, such as metagenomic sequencing, requires making large investments in testing equipment and developing networks of clinicians, laboratory scientists, and bioinformaticians. In this study, we sought to gain an understanding of how federal government agencies currently support such pathogen agnostic testing of human specimens in the United States. We conducted a landscape analysis of federal agency websites for publicly accessible information on the availability and type of pathogen agnostic testing and details on flow of clinical specimens and data. The website analysis was supplemented by an expert review of results with representatives from the federal agencies. Operating divisions within the US Department of Health and Human Services and the US Department of Veterans Affairs have developed and sustained extensive clinical and research networks to obtain patient specimens and perform metagenomic sequencing. Metagenomic facilities supported by US agencies were not equally geographically distributed across the United States. Although many entities have work dedicated to metagenomics and/or support emerging infectious disease surveillance specimen collection, there was minimal formal collaboration across agencies.}, } @article {pmid38573983, year = {2024}, author = {Jensen, TBN and Dall, SM and Knutsson, S and Karst, SM and Albertsen, M}, title = {High-throughput DNA extraction and cost-effective miniaturized metagenome and amplicon library preparation of soil samples for DNA sequencing.}, journal = {PloS one}, volume = {19}, number = {4}, pages = {e0301446}, doi = {10.1371/journal.pone.0301446}, pmid = {38573983}, issn = {1932-6203}, abstract = {Reductions in sequencing costs have enabled widespread use of shotgun metagenomics and amplicon sequencing, which have drastically improved our understanding of the microbial world. However, large sequencing projects are now hampered by the cost of library preparation and low sample throughput, comparatively to the actual sequencing costs. Here, we benchmarked three high-throughput DNA extraction methods: ZymoBIOMICS™ 96 MagBead DNA Kit, MP BiomedicalsTM FastDNATM-96 Soil Microbe DNA Kit, and DNeasy® 96 PowerSoil® Pro QIAcube® HT Kit. The DNA extractions were evaluated based on length, quality, quantity, and the observed microbial community across five diverse soil types. DNA extraction of all soil types was successful for all kits, however DNeasy® 96 PowerSoil® Pro QIAcube® HT Kit excelled across all performance parameters. We further used the nanoliter dispensing system I.DOT One to miniaturize Illumina amplicon and metagenomic library preparation volumes by a factor of 5 and 10, respectively, with no significant impact on the observed microbial communities. With these protocols, DNA extraction, metagenomic, or amplicon library preparation for one 96-well plate are approx. 3, 5, and 6 hours, respectively. Furthermore, the miniaturization of amplicon and metagenome library preparation reduces the chemical and plastic costs from 5.0 to 3.6 and 59 to 7.3 USD pr. sample. This enhanced efficiency and cost-effectiveness will enable researchers to undertake studies with greater sample sizes and diversity, thereby providing a richer, more detailed view of microbial communities and their dynamics.}, } @article {pmid38573185, year = {2024}, author = {Hall, MB and Coin, LJM}, title = {Pangenome databases improve host removal and mycobacteria classification from clinical metagenomic data.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, doi = {10.1093/gigascience/giae010}, pmid = {38573185}, issn = {2047-217X}, support = {2020/MRF1200856//Australian Government Medical Research Future Fund/ ; //Genomics Health Futures Mission/ ; }, abstract = {BACKGROUND: Culture-free real-time sequencing of clinical metagenomic samples promises both rapid pathogen detection and antimicrobial resistance profiling. However, this approach introduces the risk of patient DNA leakage. To mitigate this risk, we need near-comprehensive removal of human DNA sequences at the point of sequencing, typically involving the use of resource-constrained devices. Existing benchmarks have largely focused on the use of standardized databases and largely ignored the computational requirements of depletion pipelines as well as the impact of human genome diversity.

RESULTS: We benchmarked host removal pipelines on simulated and artificial real Illumina and Nanopore metagenomic samples. We found that construction of a custom kraken database containing diverse human genomes results in the best balance of accuracy and computational resource usage. In addition, we benchmarked pipelines using kraken and minimap2 for taxonomic classification of Mycobacterium reads using standard and custom databases. With a database representative of the Mycobacterium genus, both tools obtained improved specificity and sensitivity, compared to the standard databases for classification of Mycobacterium tuberculosis. Computational efficiency of these custom databases was superior to most standard approaches, allowing them to be executed on a laptop device.

CONCLUSIONS: Customized pangenome databases provide the best balance of accuracy and computational efficiency when compared to standard databases for the task of human read removal and M. tuberculosis read classification from metagenomic samples. Such databases allow for execution on a laptop, without sacrificing accuracy, an especially important consideration in low-resource settings. We make all customized databases and pipelines freely available.}, } @article {pmid38572990, year = {2024}, author = {Sorouri, B and Scales, NC and Gaut, BS and Allison, SD}, title = {Sphingomonas clade and functional distribution with simulated climate change.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0023624}, doi = {10.1128/spectrum.00236-24}, pmid = {38572990}, issn = {2165-0497}, abstract = {Microbes are essential for the functioning of all ecosystems, and as global warming and anthropogenic pollution threaten ecosystems, it is critical to understand how microbes respond to these changes. We investigated the climate response of Sphingomonas, a widespread gram-negative bacterial genus, during an 18-month microbial community reciprocal transplant experiment across a Southern California climate gradient. We hypothesized that after 18 months, the transplanted Sphingomonas clade and functional composition would correspond with site conditions and reflect the Sphingomonas composition of native communities. We extracted Sphingomonas sequences from metagenomic data across the gradient and assessed their clade and functional composition. Representatives of at least 12 major Sphingomonas clades were found at varying relative abundances along the climate gradient, and transplanted Sphingomonas clade composition shifted after 18 months. Site had a significant effect (PERMANOVA; P < 0.001) on the distribution of both Sphingomonas functional (R[2] = 0.465) and clade composition (R[2] = 0.400), suggesting that Sphingomonas composition depends on climate parameters. Additionally, for both Sphingomonas clade and functional composition, ordinations revealed that the transplanted communities shifted closer to the native Sphingomonas composition of the grassland site compared with the site they were transplanted into. Overall, our results indicate that climate and substrate collectively determine Sphingomonas clade and functional composition.IMPORTANCESphingomonas is the most abundant gram-negative bacterial genus in litter-degrading microbial communities of desert, grassland, shrubland, and forest ecosystems in Southern California. We aimed to determine whether Sphingomonas responds to climate change in the same way as gram-positive bacteria and whole bacterial communities in these ecosystems. Within Sphingomonas, both clade composition and functional genes shifted in response to climate and litter chemistry, supporting the idea that bacteria respond similarly to climate at different scales of genetic variation. This understanding of how microbes respond to perturbation across scales may aid in future predictions of microbial responses to climate change.}, } @article {pmid38572865, year = {2024}, author = {Dunham, SJB and Avelar-Barragan, J and Rothman, JA and Adams, ED and Faraci, G and Forner, S and Kawauchi, S and Tenner, AJ and Green, KN and LaFerla, FM and MacGregor, GR and Mapstone, M and Whiteson, KL}, title = {Sex-specific associations between AD genotype and the microbiome of human amyloid beta knock-in (hAβ-KI) mice.}, journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association}, volume = {}, number = {}, pages = {}, doi = {10.1002/alz.13794}, pmid = {38572865}, issn = {1552-5279}, support = {U54 AG054349/AG/NIA NIH HHS/United States ; T32 AG00096-38/AG/NIA NIH HHS/United States ; }, abstract = {INTRODUCTION: Emerging evidence links changes in the gut microbiome to late-onset Alzheimer's disease (LOAD), necessitating examination of AD mouse models with consideration of the microbiome.

METHODS: We used shotgun metagenomics and untargeted metabolomics to study the human amyloid beta knock-in (hAβ-KI) murine model for LOAD compared to both wild-type (WT) mice and a model for early-onset AD (3xTg-AD).

RESULTS: Eighteen-month female (but not male) hAβ-KI microbiomes were distinct from WT microbiomes, with AD genotype accounting for 18% of the variance by permutational multivariate analysis of variance (PERMANOVA). Metabolomic diversity differences were observed in females, however no individual metabolites were differentially abundant. hAβ-KI mice microbiomes were distinguishable from 3xTg-AD animals (81% accuracy by random forest modeling), with separation primarily driven by Romboutsia ilealis and Turicibacter species. Microbiomes were highly cage specific, with cage assignment accounting for more than 40% of the PERMANOVA variance between the groups.

DISCUSSION: These findings highlight a sex-dependent variation in the microbiomes of hAβ-KI mice and underscore the importance of considering the microbiome when designing studies that use murine models for AD.

HIGHLIGHTS: Microbial diversity and the abundance of several species differed in human amyloid beta knock-in (hAβ-KI) females but not males. Correlations to Alzheimer's disease (AD) genotype were stronger for the microbiome than the metabolome. Microbiomes from hAβ-KI mice were distinct from 3xTg-AD mice. Cage effects accounted for most of the variance in the microbiome and metabolome.}, } @article {pmid38572228, year = {2024}, author = {Liao, J and Yuan, Z and Wang, X and Chen, T and Qian, K and Cui, Y and Rong, A and Zheng, C and Liu, Y and Wang, D and Pan, L}, title = {Magnesium oxide nanoparticles reduce clubroot by regulating plant defense response and rhizosphere microbial community of tumorous stem mustard (Brassica juncea var. tumida).}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1370427}, pmid = {38572228}, issn = {1664-302X}, abstract = {Clubroot, caused by Plasmodiophora brassicae, is a major disease that significantly impairs the yield of cruciferous crops and causes significant economic losses across the globe. The prevention of clubroot, especially in tumorous stem mustard (without resistant varieties), are is limited and primarily relies on fungicides. Engineered nanoparticles have opened up new avenues for the management of plant diseases, but there is no report on their application in the prevention of clubroot. The results showed that the control efficacy of 500 mg/L MgO NPs against clubroot was 54.92%. However, when the concentration was increased to 1,500 and 2,500 mg/L, there was no significant change in the control effect. Compared with CK, the average fresh and dry weight of the aerial part of plants treated with MgO NPs increased by 392.83 and 240.81%, respectively. Compared with the F1000 treatment, increases were observed in the content of soil available phosphorus (+16.72%), potassium (+9.82%), exchangeable magnesium (+24.20%), and water-soluble magnesium (+20.64%) in the 1,500 mg/L MgO NPs treatment. The enzyme-linked immune sorbent assay (ELISA) results showed that the application of MgO NPs significantly increased soil peroxidase (POD, +52.69%), alkaline protease (AP, +41.21%), alkaline phosphatase (ALP, +79.26%), urease (+52.69%), and sucrase (+56.88%) activities; And also increased plant L-phenylalanine ammonla-lyase (PAL, +70.49%), polyphenol oxidase (PPO, +36.77%), POD (+38.30%), guaiacol peroxidase (POX, +55.46%) activities and salicylic acid (SA, +59.86%) content. However, soil and plant catalase (CAT, -27.22 and - 19.89%, respectively), and plant super oxidase dismutase (SOD, -36.33%) activities were significantly decreased after the application of MgO NPs. The metagenomic sequencing analysis showed that the MgO NPs treatments significantly improved the α-diversity of the rhizosphere soil microbial community. The relative abundance of beneficial bacteria genera in the rhizosphere soil, including Pseudomonas, Sphingopyxis, Acidovorax, Variovorax, and Bosea, was significantly increased. Soil metabolic functions, such as oxidative phosphorylation (ko00190), carbon fixation pathways in prokaryotes (ko00720), indole alkaloid biosynthesis (ko00901), and biosynthesis of various antibiotics (ko00998) were significantly enriched. These results suggested that MgO NPs might control clubroot by promoting the transformation and utilization of soil nutrients, stimulating plant defense responses, and enriching soil beneficial bacteria.}, } @article {pmid38571744, year = {2024}, author = {Peng, S and Ye, L and Li, Y and Wang, F and Sun, T and Wang, L and Zhao, J and Dong, Z}, title = {Metagenomic insights into jellyfish-associated microbiome dynamics during strobilation.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae036}, pmid = {38571744}, issn = {2730-6151}, abstract = {Host-associated microbiomes can play key roles in the metamorphosis of animals. Most scyphozoan jellyfish undergo strobilation in their life cycles, similar to metamorphosis in classic bilaterians. The exploration of jellyfish microbiomes may elucidate the ancestral mechanisms and evolutionary trajectories of metazoan-microbe associations and interactions during metamorphosis. However, current knowledge of the functional features of jellyfish microbiomes remains limited. Here, we performed a genome-centric analysis of associated microbiota across four successive life stages (polyp, early strobila, advanced strobila, and ephyra) during strobilation in the common jellyfish Aurelia coerulea. We observed shifts in taxonomic and functional diversity of microbiomes across distinct stages and proposed that the low microbial diversity in ephyra stage may be correlated with the high expression of the host-derived antimicrobial peptide aurelin. Furthermore, we recovered 43 high-quality metagenome-assembled genomes and determined the nutritional potential of the dominant Vibrio members. Interestingly, we observed increased abundances of genes related to the biosynthesis of amino acids, vitamins, and cofactors, as well as carbon fixation during the loss of host feeding ability, indicating the functional potential of Aurelia-associated microbiota to support the synthesis of essential nutrients. We also identified several potential mechanisms by which jellyfish-associated microbes establish stage-specific community structures and maintain stable colonization in dynamic host environments, including eukaryotic-like protein production, bacterial secretion systems, restriction-modification systems, and clustered regularly interspaced short palindromic repeats-Cas systems. Our study characterizes unique taxonomic and functional changes in jellyfish microbiomes during strobilation and provides foundations for uncovering the ancestral mechanism of host-microbe interactions during metamorphosis.}, } @article {pmid38570877, year = {2024}, author = {Yin, X and Zhou, G and Cai, M and Richter-Heitmann, T and Zhu, QZ and Maeke, M and Kulkarni, AC and Nimzyk, R and Elvert, M and Friedrich, MW}, title = {Physiological versatility of ANME-1 and Bathyarchaeotoa-8 archaea evidenced by inverse stable isotope labeling.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {68}, pmid = {38570877}, issn = {2049-2618}, support = {49926684//Cluster of Excellence EXC 309/ ; 49926684//Cluster of Excellence EXC 309/ ; 390741601//Cluster of Excellence EXC 2077/ ; 390741601//Cluster of Excellence EXC 2077/ ; }, abstract = {BACKGROUND: The trophic strategy is one key principle to categorize microbial lifestyles, by broadly classifying microorganisms based on the combination of their preferred carbon sources, electron sources, and electron sinks. Recently, a novel trophic strategy, i.e., chemoorganoautotrophy-the utilization of organic carbon as energy source but inorganic carbon as sole carbon source-has been specifically proposed for anaerobic methane oxidizing archaea (ANME-1) and Bathyarchaeota subgroup 8 (Bathy-8).

RESULTS: To further explore chemoorganoautotrophy, we employed stable isotope probing (SIP) of nucleic acids (rRNA or DNA) using unlabeled organic carbon and [13]C-labeled dissolved inorganic carbon (DIC), i.e., inverse stable isotope labeling, in combination with metagenomics. We found that ANME-1 archaea actively incorporated [13]C-DIC into RNA in the presence of methane and lepidocrocite when sulfate was absent, but assimilated organic carbon when cellulose was added to incubations without methane additions. Bathy-8 archaea assimilated [13]C-DIC when lignin was amended; however, their DNA was derived from both inorganic and organic carbon sources rather than from inorganic carbon alone. Based on SIP results and supported by metagenomics, carbon transfer between catabolic and anabolic branches of metabolism is possible in these archaeal groups, indicating their anabolic versatility.

CONCLUSION: We provide evidence for the incorporation of the mixed organic and inorganic carbon by ANME-1 and Bathy-8 archaea in the environment. Video Abstract.}, } @article {pmid38570504, year = {2024}, author = {Hwang, Y and Cornman, AL and Kellogg, EH and Ovchinnikov, S and Girguis, PR}, title = {Genomic language model predicts protein co-regulation and function.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2880}, pmid = {38570504}, issn = {2041-1723}, support = {9208//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; OCE-1635365//National Science Foundation (NSF)/ ; 80NSSC19K1427//National Aeronautics and Space Administration (NASA)/ ; }, abstract = {Deciphering the relationship between a gene and its genomic context is fundamental to understanding and engineering biological systems. Machine learning has shown promise in learning latent relationships underlying the sequence-structure-function paradigm from massive protein sequence datasets. However, to date, limited attempts have been made in extending this continuum to include higher order genomic context information. Evolutionary processes dictate the specificity of genomic contexts in which a gene is found across phylogenetic distances, and these emergent genomic patterns can be leveraged to uncover functional relationships between gene products. Here, we train a genomic language model (gLM) on millions of metagenomic scaffolds to learn the latent functional and regulatory relationships between genes. gLM learns contextualized protein embeddings that capture the genomic context as well as the protein sequence itself, and encode biologically meaningful and functionally relevant information (e.g. enzymatic function, taxonomy). Our analysis of the attention patterns demonstrates that gLM is learning co-regulated functional modules (i.e. operons). Our findings illustrate that gLM's unsupervised deep learning of the metagenomic corpus is an effective and promising approach to encode functional semantics and regulatory syntax of genes in their genomic contexts and uncover complex relationships between genes in a genomic region.}, } @article {pmid38569972, year = {2024}, author = {Yu, Z and Liu, Z and Sun, L and Dong, C and Jin, Y and Hu, B and Cheng, D}, title = {Mobile genetic elements mediate the cross-media transmission of antibiotic resistance genes from pig farms and their risks.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {172115}, doi = {10.1016/j.scitotenv.2024.172115}, pmid = {38569972}, issn = {1879-1026}, abstract = {Manure composting in traditional small-scale pig farms leads to the migration and diffusion of antibiotics and antibiotics resistance genes (ARGs) along the chain of transmission to the surrounding environment, increasing the risk of environmental resistance. Understanding the transmission patterns, driving factors, and health risks of ARGs on small-scale pig farms is important for effective control of ARGs transmission. This study was conducted on a small pig farm and its surrounding environment. The cross-media transmission of ARGs and their risks in the farming habitat were investigated using Metagenomic annotation and qPCR quantitative detection. The results indicate that ARGs in farms spread with manure pile-soil-channel sediment-mudflat sediment. Pig farm manure contributed 22.49 % of the mudflat sediment ARGs. Mobile genetic elements mediate the spread of ARGs across different media. Among them, tnpA and IS26 have the highest degree. Transmission of high-risk ARGs sul1 and tetM resulted in a 50 % and 116 % increase in host risk for sediment, respectively. This study provides a basis for farm manure management and control of the ARGs spread.}, } @article {pmid38569543, year = {2024}, author = {Li, C and Stražar, M and Mohamed, AMT and Pacheco, JA and Walker, RL and Lebar, T and Zhao, S and Lockart, J and Dame, A and Thurimella, K and Jeanfavre, S and Brown, EM and Ang, QY and Berdy, B and Sergio, D and Invernizzi, R and Tinoco, A and Pishchany, G and Vasan, RS and Balskus, E and Huttenhower, C and Vlamakis, H and Clish, C and Shaw, SY and Plichta, DR and Xavier, RJ}, title = {Gut microbiome and metabolome profiling in Framingham heart study reveals cholesterol-metabolizing bacteria.}, journal = {Cell}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cell.2024.03.014}, pmid = {38569543}, issn = {1097-4172}, abstract = {Accumulating evidence suggests that cardiovascular disease (CVD) is associated with an altered gut microbiome. Our understanding of the underlying mechanisms has been hindered by lack of matched multi-omic data with diagnostic biomarkers. To comprehensively profile gut microbiome contributions to CVD, we generated stool metagenomics and metabolomics from 1,429 Framingham Heart Study participants. We identified blood lipids and cardiovascular health measurements associated with microbiome and metabolome composition. Integrated analysis revealed microbial pathways implicated in CVD, including flavonoid, γ-butyrobetaine, and cholesterol metabolism. Species from the Oscillibacter genus were associated with decreased fecal and plasma cholesterol levels. Using functional prediction and in vitro characterization of multiple representative human gut Oscillibacter isolates, we uncovered conserved cholesterol-metabolizing capabilities, including glycosylation and dehydrogenation. These findings suggest that cholesterol metabolism is a broad property of phylogenetically diverse Oscillibacter spp., with potential benefits for lipid homeostasis and cardiovascular health.}, } @article {pmid38569357, year = {2024}, author = {Li, C and Ma, X and Wang, Y and Sun, Q and Chen, M and Zhang, C and Ding, S and Dai, Z}, title = {Root-mediated acidification, phosphatase activity and the phosphorus-cycling microbial community enhance phosphorus mobilization in the rhizosphere of wetland plants.}, journal = {Water research}, volume = {255}, number = {}, pages = {121548}, doi = {10.1016/j.watres.2024.121548}, pmid = {38569357}, issn = {1879-2448}, abstract = {Rhizoremediation of wetland plants is an environmentally friendly strategy for sediment phosphorous (P) removal, the basic underlying principle of which is the complex interactions between roots and microorganisms. This study investigated the immobilization and mobilization mechanisms of P in the rhizosphere of wetland plants using high-resolution spatial visualization techniques and metagenomic sequencing. Two-dimensional visualization of the spatial distribution of P, iron (Fe) and manganese (Mn) indicated that the sequestration of Fe-oxides rather than Mn-oxides caused the depletion of labile P, resulting in an increase in the Fe-adsorbed P fraction. Plants altered the rhizospheric environments and P-cycling microbial community to mobilize low-availability P from sediments. Mineral P solubilization and organic P mineralization were enhanced by local acidification and increased phosphatase activity, respectively. Microbial P mobilization also increased with increasing relative abundances of P solubilization and mineralization genes (gcd and phnW) and decreasing P transportation genes (ugpA, ugpB, and pit) genes in the rhizosphere. These processes led to the remobilization of 10.04 % of inorganic P, and 15.23 % of organic P, in the rhizosphere during the incubation period. However, the resupply of P via the above processes did not compensate for the depletion of rhizospheric P via root uptake and mineral sequestration. Our results provide novel insights into the mechanisms of rhizospheric P cycling, which will help to inform future phytoremediation strategies.}, } @article {pmid38569319, year = {2024}, author = {You, X and Wang, S and Du, L and Chen, Y and Wang, T and Bo, X}, title = {Metagenomics reveals the variations in functional metabolism associated with greenhouse gas emissions during legume-vegetable rotation process.}, journal = {Ecotoxicology and environmental safety}, volume = {275}, number = {}, pages = {116268}, doi = {10.1016/j.ecoenv.2024.116268}, pmid = {38569319}, issn = {1090-2414}, abstract = {Legume-based rotation is commonly recognized for its mitigation efficiency of greenhouse gas (GHG) emissions. However, variations in GHG emission-associated metabolic functions during the legume-vegetable rotation process remain largely uncharacterized. Accordingly, a soybean-radish rotation field experiment was designed to clarify the responses of microbial communities and their GHG emission-associated functional metabolism through metagenomics. The results showed that the contents of soil organic carbon and total phosphorus significantly decreased during the soybean-radish process (P < 0.05), while soil total potassium content and bacterial richness and diversity significantly increased (P < 0.05). Moreover, the predominant bacterial phyla varied, with a decrease in the relative abundance of Proteobacteria and an increase in the relative abundance of Acidobacteria, Gemmatimonadetes, and Chloroflexi. Metagenomics clarified that bacterial carbohydrate metabolism substantially increased during the rotation process, whereas formaldehyde assimilation, methanogenesis, nitrification, and dissimilatory nitrate reduction decreased (P < 0.05). Specifically, the expression of phosphate acetyltransferase (functional methanogenesis gene, pta) and nitrate reductase gamma subunit (functional dissimilatory nitrate reduction gene, narI) was inhibited, indicating of low methane production and nitrogen metabolism. Additionally, the partial least squares path model revealed that the Shannon diversity index was negatively correlated with methane and nitrogen metabolism (P < 0.01), further demonstrating that the response of the soil bacterial microbiome responses are closely linked with GHG-associated metabolism during the soybean-radish rotation process. Collectively, our findings shed light on the responses of soil microbial communities to functional metabolism associated with GHG emissions and provide important insights to mitigate GHG emissions during the rotational cropping of legumes and vegetables.}, } @article {pmid38570378, year = {2024}, author = {Ślusarczyk, A and Ismail, H and Zapała, Ł and Piecha, T and Zapała, P and Radziszewski, P}, title = {Changes in the Urinary Microbiome After Transurethral Resection of Non-muscle-Invasive Bladder Cancer: Insights from a Prospective Observational Study.}, journal = {Annals of surgical oncology}, volume = {}, number = {}, pages = {}, pmid = {38570378}, issn = {1534-4681}, support = {M/MB/07/22//Warszawski Uniwersytet Medyczny/ ; }, abstract = {BACKGROUND: This study aimed to characterize the urinary and tumor microbiomes in patients with non-muscle-invasive bladder cancer (NMIBC) before and after transurethral resection of the bladder tumor (TURBT).

METHODS: This single-center prospective study included 26 samples from 11 patients with low-grade Ta papillary NMIBC. Urine samples were collected at the index TURBT and at a 1-year follow-up cystoscopy. The metagenomic analysis of bacterial and archaeal populations was performed based on the highly variable V3-V4 region of the 16S rRNA gene.

RESULTS: Phylogenetic alpha diversity of the bladder microbiome detected in urine was found to be lower at the 1-year follow-up cystoscopy compared to the time of the index TURBT (p < 0.01). Actinomyces, Candidatus cloacimonas, Sphingobacterium, Sellimonas, Fusobacterium, and Roseobacter were more differentially enriched taxa in urine at the follow-up cystoscopy than at the index TURBT. Beta diversity of urine microbiome significantly changed over time (p < 0.05). Phylogenetic alpha diversity of the microbiome was greater in tumor tissues than in paired urine samples (p<0.01). Sphingomonas, Acinetobacter, Candidatus, and Kocuria were more differentially overrepresented in tumor tissues than in urine. The enrichment of the abundance of Corynebacterium and Anaerococcus species in urine collected at TURBT was observed in patients who experienced recurrence within the follow-up period.

CONCLUSIONS: In patients with low-grade NMIBC, the urine microbiome undergoes changes over time after removal of the tumor. The microbiome detected in tumor tissues is more phylogenetically diverse than in paired urine samples collected at TURBT. The interplay between bladder microbiome, tumor microbiome, and their alterations requires further studies to elucidate their predictive value and perhaps therapeutic implications.}, } @article {pmid38570158, year = {2024}, author = {Xu, C and Zhang, Y and Hu, C and Shen, C and Li, F and Xu, Y and Liu, W and Shi, D}, title = {From disinfection to pathogenicity: Occurrence, resistome risks and assembly mechanism of biocide and metal resistance genes in hospital wastewaters.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {123910}, doi = {10.1016/j.envpol.2024.123910}, pmid = {38570158}, issn = {1873-6424}, abstract = {Hospital wastewaters (HWWs) represent critical reservoir for the accumulation and propagation of resistance genes. However, studies on biocide and metal resistance genes (BMRGs) and their associated resistome risks and driving mechanisms in HWWs are still in their infancy. Here, metagenomic assembly was firstly used to investigate host pathogenicity and transferability profiles of BMGRs in a typical HWWs system. As a result, genes conferring resistance to Ethidium Bromide, Benzylkonium Chloride, and Cetylpyridinium Chloride dominated biocide resistance genes (BRGs), whereas Cu resistance gene was the largest metal resistance genes (MRGs) contributor. Most BMRGs experienced significant reduction during anoxic-aerobic treatment and sedimentation stages but exhibited enrichment after chlorine disinfection. Network analysis indicated intense interactions between BMRGs and virulence factors (VFs). Polar_flagella, belonging to the adherence was identified to play important role in the network. Contig-based analysis further revealed noteworthy shifts in host associations along the treatment processes, with Pseudomonadota emerging as the primary carrier, hosting 91.1% and 85.3% of the BRGs and MRGs. A total of 199 opportunistic pathogens were identified to carry 285 BMRG subtypes, which mainly included Pseudomonas alcaligenes, Pseudomonas lundensis, and Escherichia coli. Notably, ruvB conferring resistance to Cr, Cetylpyridinium Chloride, and Dodine were characterized with the highest frequency carried by pathogens. Diverse co-occurrence patterns between BMRGs and mobile genetic elements (MGEs) were found from the raw influent to final effluent. Overall, 10.5% BRGs and 8.84% MRGs were mobile and among the 4 MGEs, transposase exhibited the greatest potential for the BMRGs dissemination. Furthermore, deterministic processes played a dominant role in bacterial communities and BMRGs assembly in HWWs. Bacterial communities contributed more than MGEs in shaping the resistome. Taken together, this work demonstrated widespread BMRGs pollution throughout the HWWs treatment system, emphasizing the potential for informing resistome risk and ecological mechanism in medical practice.}, } @article {pmid38568776, year = {2024}, author = {Hu, ZQ and Hung, YM and Chen, LH and Lai, LC and Pan, MH and Chuang, EY and Tsai, MH}, title = {NURECON: A Novel Online System for Determining Nutrition Requirements Based on Microbial Composition.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {21}, number = {2}, pages = {254-264}, doi = {10.1109/TCBB.2024.3349572}, pmid = {38568776}, issn = {1557-9964}, abstract = {Dietary habits have been proven to have an impact on the microbial composition and health of the human gut. Over the past decade, researchers have discovered that gut microbiota can use nutrients to produce metabolites that have major implications for human physiology. However, there is no comprehensive system that specifically focuses on identifying nutrient deficiencies based on gut microbiota, making it difficult to interpret and compare gut microbiome data in the literature. This study proposes an analytical platform, NURECON, that can predict nutrient deficiency information in individuals by comparing their metagenomic information to a reference baseline. NURECON integrates a next-generation bacterial 16S rRNA analytical pipeline (QIIME2), metabolic pathway prediction tools (PICRUSt2 and KEGG), and a food compound database (FooDB) to enable the identification of missing nutrients and provide personalized dietary suggestions. Metagenomic information from total number of 287 healthy subjects was used to establish baseline microbial composition and metabolic profiles. The uploaded data is analyzed and compared to the baseline for nutrient deficiency assessment. Visualization results include gut microbial composition, related enzymes, pathways, and nutrient abundance. NURECON is a user-friendly online platform that provides nutritional advice to support dietitians' research or menu design.}, } @article {pmid38568082, year = {2024}, author = {Sánchez-Porro, C and Aghdam, EM and Montazersaheb, S and Tarhriz, V and Kazemi, E and Amoozegar, MA and Ventosa, A and Hejazi, MS}, title = {Marinobacter azerbaijanicus sp. nov., a moderately halophilic bacterium from Urmia Lake, Iran.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {4}, pages = {}, doi = {10.1099/ijsem.0.006308}, pmid = {38568082}, issn = {1466-5034}, abstract = {A novel moderately halophilic, Gram-stain-negative and facultatively anaerobic bacterium, designated as strain TBZ242[T], was isolated from water of Urmia Lake in the Azerbaijan region of Iran. The cells were found to be rod-shaped and motile by a single polar flagellum, producing circular and yellowish colonies. The strain could grow in the presence of 0.5-10 % (w/v) NaCl (optimum, 2.5-5 %). The temperature and pH ranges for growth were 15-45 °C (optimum 30 °C) and pH 7.0-11.0 (optimum pH 8.0) on marine agar. The 16S rRNA gene sequence analysis revealed that strain TBZ242[T] belonged to the genus Marinobacter, showing the highest similarities to Marinobacter algicola DG893[T] (98.8 %), Marinobacter vulgaris F01[T] (98.8 %), Marinobacter salarius R9SW1[T] (98.5 %), Marinobacter panjinensis PJ-16[T] (98.4 %), Marinobacter orientalis W62[T] (98.0 %) and Marinobacter denitrificans JB2H27[T] (98.0 %). The 16S rRNA and core-genome phylogenetic trees showed that strain TBZ242[T] formed a distinct branch, closely related to a subclade accommodating M. vulgaris, M. orientalis, M. panjinensis, M. denitrificans, M. algicola, M. salarius and M. iranensis, within the genus Marinobacter. Average nucleotide identity and digital DNA-DNA hybridization values between strain TBZ242[T] and the type strains of the related species of Marinobacter were ≤85.0 and 28.6 %, respectively, confirming that strain TBZ242[T] represents a distinct species. The major cellular fatty acids of strain TBZ242[T] were C16 : 0 and C16 : 1 ω7c/C16 : 1 ω6c and the quinone was ubiquinone Q-9. The genomic DNA G+C content of strain TBZ242[T] is 57.2 mol%. Based on phenotypic, chemotaxonomic and genomic data, strain TBZ242[T] represents a novel species within the genus Marinobacter, for which the name Marinobacter azerbaijanicus sp. nov. is proposed. The type strain is TBZ242[T] (= CECT 30649[T] = IBRC-M 11466[T]). Genomic fragment recruitment analysis showed that this species prefers aquatic saline environments with intermediate salinities, being detected on metagenomic databases of Lake Meyghan (Iran) with 5 and 18 % salinity, respectively.}, } @article {pmid38567644, year = {2024}, author = {Chen, J and Lin, L and Tu, Q and Peng, Q and Wang, X and Liang, C and Zhou, J and Yu, X}, title = {Metagenomic-based discovery and comparison of the lignin degrading potential of microbiomes in aquatic and terrestrial ecosystems via the LCdb database.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e13950}, doi = {10.1111/1755-0998.13950}, pmid = {38567644}, issn = {1755-0998}, support = {2019YFA0606704//National Key Research and Development Program of China/ ; 32370115//National Natural Science Foundation of China/ ; }, abstract = {Lignin, as an abundant organic carbon, plays a vital role in the global carbon cycle. However, our understanding of the global lignin-degrading microbiome remains elusive. The greatest barrier has been absence of a comprehensive and accurate functional gene database. Here, we first developed a curated functional gene database (LCdb) for metagenomic profiling of lignin degrading microbial consortia. Via the LCdb, we draw a clear picture describing the global biogeography of communities with lignin-degrading potential. They exhibit clear niche differentiation at the levels of taxonomy and functional traits. The terrestrial microbiomes showed the highest diversity, yet the lowest correlations. In particular, there were few correlations between genes involved in aerobic and anaerobic degradation pathways, showing a clear functional redundancy property. In contrast, enhanced correlations, especially closer inter-connections between anaerobic and aerobic groups, were observed in aquatic consortia in response to the lower diversity. Specifically, dypB and dypA, are widespread on Earth, indicating their essential roles in lignin depolymerization. Estuarine and marine consortia featured the laccase and mnsod genes, respectively. Notably, the roles of archaea in lignin degradation were revealed in marine ecosystems. Environmental factors strongly influenced functional traits, but weakly shaped taxonomic groups. Null mode analysis further verified that composition of functional traits was deterministic, while taxonomic composition was highly stochastic, demonstrating that the environment selects functional genes rather than taxonomic groups. Our study not only develops a useful tool to study lignin degrading microbial communities via metagenome sequencing but also advances our understanding of ecological traits of these global microbiomes.}, } @article {pmid38567082, year = {2024}, author = {Zhang, Y and Jiang, C and Li, Y and Sun, J and Chen, Z and Zhang, Q and Sun, G}, title = {Screening, identification, and mechanism analysis of starch-degrading bacteria during curing process in tobacco leaf.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {12}, number = {}, pages = {1332113}, pmid = {38567082}, issn = {2296-4185}, abstract = {Tobacco, a vital economic crop, had its quality post-curing significantly influenced by starch content. Nonetheless, the existing process parameters during curing were inadequate to satisfy the starch degradation requirements. Microorganisms exhibit inherent advantages in starch degradation, offering significant potential in the tobacco curing process. Our study concentrated on the microbial populations on the surface of tobacco leaves and in the rhizosphere soil. A strain capable of starch degradation, designated as BS3, was successfully isolated and identified as Bacillus subtilis by phylogenetic tree analysis based on 16SrDNA sequence. The application of BS3 on tobacco significantly enhanced enzyme activity and accelerated starch degradation during the curing process. Furthermore, analyses of the metagenome, transcriptome, and metabolome indicated that the BS3 strain facilitated starch degradation by regulating surface microbiota composition and affecting genes related to starch hydrolyzed protein and key metabolites in tobacco leaves. This study offered new strategies for efficiently improving the quality of tobacco leaves.}, } @article {pmid38567077, year = {2024}, author = {Hameed, M and Wahaab, A and Shan, T and Wang, X and Khan, S and Di, D and Xiqian, L and Zhang, JJ and Anwar, MN and Nawaz, M and Li, B and Liu, K and Shao, D and Qiu, Y and Wei, J and Ma, Z}, title = {Corrigendum: A metagenomic analysis of mosquito virome collected from different animal farms at Yunnan-Myanmar border of China.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1393495}, doi = {10.3389/fmicb.2024.1393495}, pmid = {38567077}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2020.591478.].}, } @article {pmid38567023, year = {2024}, author = {Zou, H and Gao, S and Liu, X and Liu, Y and Xiao, Y and Li, A and Jiang, Y}, title = {Combination of metagenomic next-generation sequencing and conventional tests unraveled pathogen profiles in infected patients undergoing allogeneic hematopoietic stem cell transplantation in Jilin Province of China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1378112}, pmid = {38567023}, issn = {2235-2988}, abstract = {BACKGROUND: Infection is the main cause of death for patients after allogeneic hematopoietic stem cell transplantation (HSCT). However, pathogen profiles still have not been reported in detail due to their heterogeneity caused by geographic region.

OBJECTIVE: To evaluate the performance of metagenomic next-generation sequencing (mNGS) and summarize regional pathogen profiles of infected patients after HSCT.

METHODS: From February 2021 to August 2022, 64 patients, admitted to the Department of Hematology of The First Hospital of Jilin University for HSCT and diagnosed as suspected infections, were retrospectively enrolled.

RESULTS: A total of 38 patients were diagnosed as having infections, including bloodstream (n =17), pulmonary (n =16), central nervous system (CNS) (n =4), and chest (n =1) infections. Human betaherpesvirus 5 (CMV) was the most common pathogen in both bloodstream (n =10) and pulmonary (n =8) infections, while CNS (n =2) and chest (n =1) infections were mainly caused by Human gammaherpesvirus 4 (EBV). For bloodstream infection, Mycobacterium tuberculosis complex (n =3), Staphylococcus epidermidis (n =1), and Candida tropicalis (n =1) were also diagnosed as causative pathogens. Furthermore, mNGS combined with conventional tests can identify more causative pathogens with high sensitivity of 82.9% (95% CI 70.4-95.3%), and the total coincidence rate can reach up to 76.7% (95% CI 64.1-89.4%).

CONCLUSIONS: Our findings emphasized the importance of mNGS in diagnosing, managing, and ruling out infections, and an era of more rapid, independent, and impartial diagnosis of infections after HSCT can be expected.}, } @article {pmid38566975, year = {2024}, author = {Moubset, O and Filloux, D and Fontes, H and Julian, C and Fernandez, E and Galzi, S and Blondin, L and Chehida, SB and Lett, JM and Mesléard, F and Kraberger, S and Custer, JM and Salywon, A and Makings, E and Marais, A and Chiroleu, F and Lefeuvre, P and Martin, DP and Candresse, T and Varsani, A and Ravigné, V and Roumagnac, P}, title = {Virome release of an invasive exotic plant species in southern France.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {veae025}, pmid = {38566975}, issn = {2057-1577}, abstract = {The increase in human-mediated introduction of plant species to new regions has resulted in a rise of invasive exotic plant species (IEPS) that has had significant effects on biodiversity and ecosystem processes. One commonly accepted mechanism of invasions is that proposed by the enemy release hypothesis (ERH), which states that IEPS free from their native herbivores and natural enemies in new environments can outcompete indigenous species and become invasive. We here propose the virome release hypothesis (VRH) as a virus-centered variant of the conventional ERH that is only focused on enemies. The VRH predicts that vertically transmitted plant-associated viruses (PAV, encompassing phytoviruses and mycoviruses) should be co-introduced during the dissemination of the IEPS, while horizontally transmitted PAV of IEPS should be left behind or should not be locally transmitted in the introduced area due to a maladaptation of local vectors. To document the VRH, virome richness and composition as well as PAV prevalence, co-infection, host range, and transmission modes were compared between indigenous plant species and an invasive grass, cane bluestem (Bothriochloa barbinodis), in both its introduced range (southern France) and one area of its native range (Sonoran Desert, Arizona, USA). Contrary to the VRH, we show that invasive populations of B. barbinodis in France were not associated with a lower PAV prevalence or richness than native populations of B. barbinodis from the USA. However, comparison of virome compositions and network analyses further revealed more diverse and complex plant-virus interactions in the French ecosystem, with a significant richness of mycoviruses. Setting mycoviruses apart, only one putatively vertically transmitted phytovirus (belonging to the Amalgaviridae family) and one putatively horizontally transmitted phytovirus (belonging to the Geminiviridae family) were identified from B. barbinodis plants in the introduced area. Collectively, these characteristics of the B. barbinodis-associated PAV community in southern France suggest that a virome release phase may have immediately followed the introduction of B. barbinodis to France in the 1960s or 1970s, and that, since then, the invasive populations of this IEPS have already transitioned out of this virome release phase, and have started interacting with several local mycoviruses and a few local plant viruses.}, } @article {pmid38566380, year = {2024}, author = {Syafarina, I and Mazaya, M and Indrawati, A and Akbar, SZ and Sadikin, R and Sukowati, C}, title = {Skin Microbial Composition and Genetic Mutation Analysis in Precision Medicine for Epidermolysis Bullosa.}, journal = {Current drug targets}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113894501290512240327091531}, pmid = {38566380}, issn = {1873-5592}, abstract = {Epidermolysis bullosa (EB) is an inherited skin disease representing a spectrum of rare genetic disorders. These conditions share the common trait that causes fragile skin, resulting in the development of blisters and erosions. The inheritance follows an autosomal pattern, and the array of clinical presentations leads to significant physical suffering, considerable morbidity, and mortality. Despite EB having no cure, effectively managing EB remains an exceptional challenge due to its rarity and complexity, occasionally casting a profound impact on the lives of affected individuals. Considering that EB management requires a multidisciplinary approach, this sometimes worsens the condition of patients with EB due to inappropriate handling. Thus, more appropriate and precise treatment management of EB is essentially needed. Advanced technology in medicine and health comes into the bioinformatics era. Including treatment for skin diseases, omics-based approaches aim to evaluate and handle better disease management and treatment. In this work, we review several approaches regarding the implementation of omics-based technology, including genetics, pathogenic mutation, skin microbiomics, and metagenomics analysis for EB. In addition, we highlight recent updates on the potential of metagenomics analysis in precision medicine for EB.}, } @article {pmid38566102, year = {2024}, author = {Luo, WC and Mei, SQ and Huang, ZJ and Chen, ZH and Zhang, YC and Yang, MY and Liu, JQ and Xu, JY and Yang, XR and Zhong, RW and Tang, LB and Yin, LX and Deng, Y and Peng, YL and Lu, C and Chen, BL and Ke, DX and Tu, HY and Yang, JJ and Xu, CR and Wu, YL and Zhou, Q}, title = {Correlation of distribution characteristics and dynamic changes of gut microbiota with the efficacy of immunotherapy in EGFR-mutated non-small cell lung cancer.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {326}, pmid = {38566102}, issn = {1479-5876}, support = {82102808//National Natural Science Foundation of China/ ; 82373349//National Natural Science Foundation of China/ ; G623281109//The Southern Medical University's Young Talents Climbing Program for Science and Technology Development/ ; 2017B030314120//Guangdong Provincial Key Lab of Translational Medicine in Lung Cancer/ ; KY0120220136//Guangdong Provincial People's Hospital Young Talent Project/ ; }, abstract = {BACKGROUND: The effects of gut microbiota and metabolites on the responses to immune checkpoint inhibitors (ICIs) in advanced epidermal growth factor receptor (EGFR) wild-type non-small cell lung cancer (NSCLC) have been studied. However, their effects on EGFR-mutated (EGFR +) NSCLC remain unknown.

METHODS: We prospectively recorded the clinicopathological characteristics of patients with advanced EGFR + NSCLC and assessed potential associations between the use of antibiotics or probiotics and immunotherapy efficacy. Fecal samples were collected at baseline, early on-treatment, response and progression status and were subjected to metagenomic next-generation sequencing and ultra-high-performance liquid chromatography-mass spectrometry analyses to assess the effects of gut microbiota and metabolites on immunotherapy efficacy.

RESULTS: The clinical data of 74 advanced EGFR + NSCLC patients were complete and 18 patients' fecal samples were dynamically collected. Patients that used antibiotics had shorter progression-free survival (PFS) (mPFS, 4.8 vs. 6.7 months; P = 0.037); probiotics had no impact on PFS. Two dynamic types of gut microbiota during immunotherapy were identified: one type showed the lowest relative abundance at the response time point, whereas the other type showed the highest abundance at the response time point. Metabolomics revealed significant differences in metabolites distribution between responders and non-responders. Deoxycholic acid, glycerol, and quinolinic acid were enriched in responders, whereas L-citrulline was enriched in non-responders. There was a significant correlation between gut microbiota and metabolites.

CONCLUSIONS: The use of antibiotics weakens immunotherapy efficacy in patients with advanced EGFR + NSCLC. The distribution characteristics and dynamic changes of gut microbiota and metabolites may indicate the efficacy of immunotherapy in advanced EGFR + NSCLC.}, } @article {pmid38565843, year = {2024}, author = {Brar, NK and Dhariwal, A and Åmdal, HA and Junges, R and Salvadori, G and Baker, JL and Edlund, A and Petersen, FC}, title = {Exploring ex vivo biofilm dynamics: consequences of low ampicillin concentrations on the human oral microbiome.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {37}, pmid = {38565843}, issn = {2055-5008}, abstract = {Prolonged exposure to antibiotics at low concentration can promote processes associated with bacterial biofilm formation, virulence and antibiotic resistance. This can be of high relevance in microbial communities like the oral microbiome, where commensals and pathogens share a common habitat and where the total abundance of antibiotic resistance genes surpasses the abundance in the gut. Here, we used an ex vivo model of human oral biofilms to investigate the impact of ampicillin on biofilm viability. The ecological impact on the microbiome and resistome was investigated using shotgun metagenomics. The results showed that low concentrations promoted significant shifts in microbial taxonomic profile and could enhance biofilm viability by up to 1 to 2-log. For the resistome, low concentrations had no significant impact on antibiotic resistance gene (ARG) diversity, while ARG abundance decreased by up to 84%. A positive correlation was observed between reduced microbial diversity and reduced ARG abundance. The WHO priority pathogens Streptococcus pneumoniae and Staphylococcus aureus were identified in some of the samples, but their abundance was not significantly altered by ampicillin. Most of the antibiotic resistance genes that increased in abundance in the ampicillin group were associated with streptococci, including Streptococcus mitis, a well-known potential donor of ARGs to S. pneumoniae. Overall, the results highlight the potential of using the model to further our understanding of ecological and evolutionary forces driving antimicrobial resistance in oral microbiomes.}, } @article {pmid38565623, year = {2024}, author = {Hamad, I and Ranque, S and Azhar, EI and Yasir, M and Jiman-Fatani, AA and Tissot-Dupont, H and Raoult, D and Bittar, F}, title = {Retraction Note: Culturomics and Amplicon-based Metagenomic Approaches for the Study of Fungal Population in Human Gut Microbiota.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {7771}, doi = {10.1038/s41598-024-58471-3}, pmid = {38565623}, issn = {2045-2322}, } @article {pmid38565143, year = {2024}, author = {Kirsch, JM and Hryckowian, AJ and Duerkop, BA}, title = {A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2024.03.005}, pmid = {38565143}, issn = {1934-6069}, abstract = {Insertion sequence (IS) elements are mobile genetic elements in bacterial genomes that support adaptation. We developed a database of IS elements coupled to a computational pipeline that identifies IS element insertions in the microbiota. We discovered that diverse IS elements insert into the genomes of intestinal bacteria regardless of human host lifestyle. These insertions target bacterial accessory genes that aid in their adaptation to unique environmental conditions. Using IS expansion in Bacteroides, we show that IS activity leads to the insertion of "hot spots" in accessory genes. We show that IS insertions are stable and can be transferred between humans. Extreme environmental perturbations force IS elements to fall out of the microbiota, and many fail to rebound following homeostasis. Our work shows that IS elements drive bacterial genome diversification within the microbiota and establishes a framework for understanding how strain-level variation within the microbiota impacts human health.}, } @article {pmid38565017, year = {2024}, author = {Zhang, P and Lu, G and Sun, Y and Yan, Z and Zhang, L and Liu, J}, title = {Effect of microplastics on oxytetracycline trophic transfer: Immune, gut microbiota and antibiotic resistance gene responses.}, journal = {Journal of hazardous materials}, volume = {470}, number = {}, pages = {134147}, doi = {10.1016/j.jhazmat.2024.134147}, pmid = {38565017}, issn = {1873-3336}, abstract = {Microplastics and antibiotics are prevalent and emerging pollutants in aquatic ecosystems, but their interactions in aquatic food chains remain largely unexplored. This study investigated the impact of polypropylene microplastics (PP-MPs) on oxytetracycline (OTC) trophic transfer from the shrimp (Neocaridina denticulate) to crucian carp (Carassius auratus) by metagenomic sequencing. The carrier effects of PP-MPs promoted OTC bioaccumulation and trophic transfer, which exacerbated enterocyte vacuolation and hepatocyte eosinophilic necrosis. PP-MPs enhanced the inhibitory effect of OTC on intestinal lysozyme activities and complement C3 levels in shrimp and fish, and hepatic immunoglobulin M levels in fish (p < 0.05). Co-exposure of MPs and OTC markedly increased the abundance of Actinobacteria in shrimp and Firmicutes in fish, which caused disturbances in carbohydrate, amino acid, and energy metabolism. Moreover, OTC exacerbated the enrichment of antibiotic resistance genes (ARGs) in aquatic animals, and PP-MPs significantly increased the diversity and abundance of ARGs and facilitated the trophic transfer of teta and tetm. Our findings disclosed the impacts of PP-MPs on the mechanism of antibiotic toxicity in aquatic food chains and emphasized the importance of gut microbiota for ARGs trophic transfer, which contributed to a deeper understanding of potential risks posed by complex pollutants on aquatic ecosystems.}, } @article {pmid38564890, year = {2024}, author = {Xie, Y and Zhang, Q and Wu, Q and Zhang, J and Dzakpasu, M and Wang, XC}, title = {Novel adaptive activated sludge process leverages flow fluctuations for simultaneous nitrification and denitrification in rural sewage treatment.}, journal = {Water research}, volume = {255}, number = {}, pages = {121535}, doi = {10.1016/j.watres.2024.121535}, pmid = {38564890}, issn = {1879-2448}, abstract = {The fluctuating characteristics of rural sewage flow pose a significant challenge for wastewater treatment plants, leading to poor effluent quality. This study establishes a novel adaptive activated sludge (AAS) process specifically designed to address this challenge. By dynamically adjusting to fluctuating water flow in situ, the AAS maintains system stability and promotes efficient pollutant removal. The core strategy of AAS leverages the inherent dissolved oxygen (DO) variations caused by flow fluctuations to establish an alternating anoxic-aerobic environment within the system. This alternating operation mode fosters the growth of aerobic denitrifiers, enabling the simultaneous nitrification and denitrification (SND) process. Over a 284-day operational period, the AAS achieved consistently high removal efficiencies, reaching 94 % for COD and 62.8 % for TN. Metagenomics sequencing revealed HN-AD bacteria as the dominant population, with the characteristic nap gene exhibiting a high relative abundance of 0.008 %, 0.010 %, 0.014 %, and 0.015 % in the anaerobic, anoxic, dynamic, and oxic zones, respectively. Overall, the AAS process demonstrates efficient pollutant removal and low-carbon treatment of rural sewage by transforming the disadvantage of flow fluctuation into an advantage for robust DO regulation. Thus, AAS offers a promising model for SND in rural sewage treatment.}, } @article {pmid38564866, year = {2024}, author = {Liu, X and Tu, P and Zhang, Y and Xu, W and Shan, J and Gao, B}, title = {Aldicarb disturbed bile acid, steroid hormone and oxylipin homeostasis in C57BL/6 J mice.}, journal = {Ecotoxicology and environmental safety}, volume = {275}, number = {}, pages = {116285}, doi = {10.1016/j.ecoenv.2024.116285}, pmid = {38564866}, issn = {1090-2414}, abstract = {Mounting evidence has shown that the gut microbiota plays a key role in human health. The homeostasis of the gut microbiota could be affected by many factors, including environmental chemicals. Aldicarb is a carbamate insecticide used to control a variety of insects and nematode pests in agriculture. Aldicarb is highly toxic and its wide existence has become a global public health concern. In our previous study, we have demonstrated that aldicarb disturbed the gut microbial community structure and composition. However, the impacts of aldicarb on gut microbiota-derived metabolites, bile acids, remain elusive. In present study, we performed targeted metabolomics analysis to explore the effects of aldicarb exposure on bile acids, as well as steroid hormones and oxylipins in the serum, feces and liver of C57BL/6 J mice. Our results showed that aldicarb exposure disturbed the level of various bile acids, steroid hormones and oxylipins in the serum and feces of C57BL/6 J mice. In the liver, the level of cortisol was decreased, meanwhile 15,16-dihydroxyoctadeca-9,12-dienoic acid was increased in aldicarb-treated mice. Metagenomic sequencing analysis showed that the relative abundance of a bile salt hydrolase, choloylglycine hydrolase (EC:3.5.1.24) and a sulfatase enzyme involved in steroid hormone metabolism, arylsulfatase, was significantly increased by aldicarb exposure. Furthermore, correlations were found between gut microbiota and various serum metabolites. The results from this study are helpful to improve the understanding of the impact of carbamate insecticides on host and microbial metabolism.}, } @article {pmid38565528, year = {2024}, author = {Liang, JL and Feng, SW and Lu, JL and Wang, XN and Li, FL and Guo, YQ and Liu, SY and Zhuang, YY and Zhong, SJ and Zheng, J and Wen, P and Yi, X and Jia, P and Liao, B and Shu, WS and Li, JT}, title = {Hidden diversity and potential ecological function of phosphorus acquisition genes in widespread terrestrial bacteriophages.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2827}, pmid = {38565528}, issn = {2041-1723}, support = {41622106//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42177009//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Phosphorus (P) limitation of ecosystem processes is widespread in terrestrial habitats. While a few auxiliary metabolic genes (AMGs) in bacteriophages from aquatic habitats are reported to have the potential to enhance P-acquisition ability of their hosts, little is known about the diversity and potential ecological function of P-acquisition genes encoded by terrestrial bacteriophages. Here, we analyze 333 soil metagenomes from five terrestrial habitat types across China and identify 75 viral operational taxonomic units (vOTUs) that encode 105 P-acquisition AMGs. These AMGs span 17 distinct functional genes involved in four primary processes of microbial P-acquisition. Among them, over 60% (11/17) have not been reported previously. We experimentally verify in-vitro enzymatic activities of two pyrophosphatases and one alkaline phosphatase encoded by P-acquisition vOTUs. Thirty-six percent of the 75 P-acquisition vOTUs are detectable in a published global topsoil metagenome dataset. Further analyses reveal that, under certain circumstances, the identified P-acquisition AMGs have a greater influence on soil P availability and are more dominant in soil metatranscriptomes than their corresponding bacterial genes. Overall, our results reinforce the necessity of incorporating viral contributions into biogeochemical P cycling.}, } @article {pmid38565493, year = {2024}, author = {Fonnes, S and Mollerup, S and Paulsen, SJ and Holzknecht, BJ and Westh, H and Rosenberg, J}, title = {The microbiome of the appendix differs in patients with and without appendicitis: A prospective cohort study.}, journal = {Surgery}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.surg.2024.02.020}, pmid = {38565493}, issn = {1532-7361}, abstract = {BACKGROUND: Appendicitis seems to be a disease of infectious origin, but the detailed pathogenesis is unknown. We aimed to investigate the microbiome of the appendix lumen in patients with and without appendicitis, including a comparison of the subgroups of complicated versus uncomplicated appendicitis.

METHODS: This prospective observational cohort study included adult patients undergoing laparoscopic appendectomy for suspected appendicitis. According to histopathologic findings, the investigated groups consisted of patients with and without appendicitis, including subgroups of complicated versus uncomplicated appendicitis based on the surgical report. A swab of the appendix lumen was analyzed for genetic material from bacteria with shotgun metagenomics, and outcomes included analyses of microbiome diversity and differential abundance of bacteria.

RESULTS: A total of 53 swabs from patients with suspected appendicitis were analyzed: 42 with appendicitis (16 complicated) and 11 without appendicitis. When comparing patients with and without appendicitis, they were equally rich in bacteria (alpha diversity), but the microbiome composition was dissimilar between these groups (beta diversity) (P < .01). No consistent bacterial species were detected in all patients with appendicitis, but a least 3 genera (Blautia, Faecalibacterium, and Fusicatenibacter) and 2 species, Blautia faecis and Blautia wexlerae, were more abundant in patients without appendicitis. For the subgroups complicated versus uncomplicated appendicitis, both measures for microbiome diversity were similar.

CONCLUSION: The appendix microbiome composition of genetic material from bacteria in adult patients with and without appendicitis differed, but the microbiome was similar for patients with complicated versus uncomplicated appendicitis. Trial registration NCT03349814.}, } @article {pmid38565354, year = {2024}, author = {Li, X and Chen, T and Ren, Q and Lu, J and Cao, S and Liu, C and Li, Y}, title = {Phages in sludge from the A/O wastewater treatment process play an important role in the transmission of ARGs.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {172111}, doi = {10.1016/j.scitotenv.2024.172111}, pmid = {38565354}, issn = {1879-1026}, abstract = {Phages can influence the horizontal gene transfer (HGT) of antibiotic resistance genes (ARGs) through transduction, but their profiles and effects on the transmission of ARGs are unclear, especially in complex swine sludge. In this study, we investigated the characterization of phage and ARG profiles in sludge generated from anoxic/oxic (A/O) wastewater treatment processes on swine farms using metagenomes and viromes. The results demonstrated that 205-221 subtypes of ARGs could be identified in swine sludge, among which sul1, tet(M), and floR were the dominant ARGs, indicating that sludge is an important reservoir of ARGs, especially in sludge tanks. The greater abundance of mobile genetic elements (MGEs) in the sludge (S) could be a significant factor regarding the greater abundance of ARGs in the sludge than in the anoxic (A) and oxic (O) tanks (P < 0.05). However, when we compared the abundances of ARGs and MGEs in the A and O tanks, we observed opposite significant differences (P < 0.05), suggesting that MGEs are not the only factor influencing the abundance of ARGs. The high proportion of lysogenic phages in sludge from the S tank can also have a major impact on the ARG profile. Siphoviridae, Myoviridae, and Podoviridae were the dominant phage families in sludge, and a network diagram of bacteria-ARG-phages revealed that dominant phages and bacteria acted simultaneously as potential hosts for ARGs, which may have led to phage-mediated HGT of ARGs. Therefore, the risk of phage-mediated HGT of ARGs cannot be overlooked.}, } @article {pmid38564675, year = {2024}, author = {Lehman, SS and Verhoeve, VI and Driscoll, TP and Beckmann, JF and Gillespie, JJ}, title = {Metagenome diversity illuminates the origins of pathogen effectors.}, journal = {mBio}, volume = {}, number = {}, pages = {e0075923}, doi = {10.1128/mbio.00759-23}, pmid = {38564675}, issn = {2150-7511}, abstract = {Recent metagenome-assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. The discovery of basal lineages (novel families Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles exposed an evolutionary timepoint for the transition to host dependency, which seemingly occurred independent of mitochondrial evolution. Notably, these basal rickettsiae carry the Rickettsiales vir homolog (rvh) type IV secretion system and purportedly use rvh to kill congener microbes rather than parasitize host cells as described for later-evolving rickettsial pathogens. MAG analysis also substantially increased diversity for the genus Rickettsia and delineated a sister lineage (the novel genus Tisiphia) that stands to inform on the emergence of human pathogens from protist and invertebrate endosymbionts. Herein, we probed Rickettsiales MAG and genomic diversity for the distribution of Rickettsia rvh effectors to ascertain their origins. A sparse distribution of most Rickettsia rvh effectors outside of Rickettsiaceae lineages illuminates unique rvh evolution from basal extracellular species and other rickettsial families. Remarkably, nearly every effector was found in multiple divergent forms with variable architectures, indicating profound roles for gene duplication and recombination in shaping effector repertoires in Rickettsia pathogens. Lateral gene transfer plays a prominent role in shaping the rvh effector landscape, as evinced by the discovery of many effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchange between Rickettsia and Legionella species. Our study exemplifies how MAGs can yield insight into pathogen effector origins, particularly how effector architectures might become tailored to the discrete host cell functions of different eukaryotic hosts.IMPORTANCEWhile rickettsioses are deadly vector-borne human diseases, factors distinguishing Rickettsia pathogens from the innumerable bevy of environmental rickettsial endosymbionts remain lacking. Recent metagenome-assembled genome (MAG) studies revealed evolutionary timepoints for rickettsial transitions to host dependency. The rvh type IV secretion system was likely repurposed from congener killing in basal extracellular species to parasitizing host cells in later-evolving pathogens. Our analysis of MAG diversity for over two dozen rvh effectors unearthed their presence in some non-pathogens. However, most effectors were found in multiple divergent forms with variable architectures, indicating gene duplication and recombination-fashioned effector repertoires of Rickettsia pathogens. Lateral gene transfer substantially shaped pathogen effector arsenals, evinced by the discovery of effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchanges between Rickettsia and Legionella species. Our study exemplifies how MAGs yield insight into pathogen effector origins and evolutionary processes tailoring effectors to eukaryotic host cell biology.}, } @article {pmid38564031, year = {2024}, author = {Sharma, S and Patel, SN and Singh, SP}, title = {A novel thermotolerant L-rhamnose isomerase variant for biocatalytic conversion of D-allulose to D-allose.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {279}, pmid = {38564031}, issn = {1432-0614}, abstract = {A novel L-rhamnose isomerase was identified and cloned from an extreme-temperature aquatic habitat metagenome. The deduced amino acid sequence homology suggested the possible source of this metagenomic sequence to be Chloroflexus islandicus. The gene expression was performed in a heterologous host, Escherichia coli, and the recombinant protein L-rhamnose isomerase (L-RIM) was extracted and purified. The catalytic function of L-RIM was characterized for D-allulose to D-allose bioconversion. D-Allose is a sweet, rare sugar molecule with anti-tumour, anti-hypertensive, cryoprotective, and antioxidative properties. The characterization experiments showed L-RIM to be a Co[++]- or Mn[++]-dependent metalloenzyme. L-RIM was remarkably active (~ 80%) in a broad spectrum of pH (6.0 to 9.0) and temperature (70 to 80 °C) ranges. Optimal L-RIM activity with D-allulose as the substrate occurred at pH 7.0 and 75 °C. The enzyme was found to be excessively heat stable, displaying a half-life of about 12 days and 5 days at 65 °C and 70 °C, respectively. L-RIM catalysis conducted at slightly acidic pH of 6.0 and 70 °C achieved biosynthesis of about 30 g L[-1] from 100 g L[-1] D-allulose in 3 h. KEY POINTS: • The present study explored an extreme temperature metagenome to identify a novel gene that encodes a thermostable l-rhamnose isomerase (L-RIM) • L-RIM exhibits substantial (80% or more) activity in a broad spectrum of pH (6.0 to 9.0) and temperature (70 to 80 °C) ranges • L-RIM is excessively heat stable, displaying a half-life of about 12 days and 5 days at 65 °C and 70 °C, respectively.}, } @article {pmid38563656, year = {2024}, author = {Zhu, J and Yin, J and Chen, J and Hu, M and Lu, W and Wang, H and Zhang, H and Chen, W}, title = {Integrative analysis with microbial modelling and machine learning uncovers potential alleviators for ulcerative colitis.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2336877}, doi = {10.1080/19490976.2024.2336877}, pmid = {38563656}, issn = {1949-0984}, abstract = {Ulcerative colitis (UC) is a challenging form of inflammatory bowel disease, and its etiology is intricately linked to disturbances in the gut microbiome. To identify the potential alleviators of UC, we employed an integrative analysis combining microbial community modeling with advanced machine learning techniques. Using metagenomics data sourced from the Integrated Human Microbiome Project, we constructed individualized microbiome community models for each participant. Our analysis highlighted a significant decline in both α and β-diversity of strain-level microbial populations in UC subjects compared to controls. Distinct differences were also observed in the predicted fecal metabolite profiles and strain-to-metabolite contributions between the two groups. Using tree-based machine learning models, we successfully identified specific microbial strains and their associated metabolites as potential alleviators of UC. Notably, our experimental validation using a dextran sulfate sodium-induced UC mouse model demonstrated that the administration of Parabacteroides merdae ATCC 43,184 and N-acetyl-D-mannosamine provided notable relief from colitis symptoms. In summary, our study underscores the potential of an integrative approach to identify novel therapeutic avenues for UC, paving the way for future targeted interventions.}, } @article {pmid38563313, year = {2024}, author = {Zou, YS and Cao, ZL and Guo, Y and Wang, BB and Wang, JL and Cheng, R and Yang, Y and Zhou, XG}, title = {The application value of metagenomic next-generation sequencing technology in the diagnosis and treatment of neonatal infectious meningitis - a single center retrospective case-control study.}, journal = {Neurological research}, volume = {}, number = {}, pages = {1-7}, doi = {10.1080/01616412.2024.2337523}, pmid = {38563313}, issn = {1743-1328}, abstract = {OBJECTIVE: This retrospective study was conducted to investigate the application value of metagenomics next generation sequencing (mNGS) technology in the diagnosis and treatment of neonatal infectious meningitis.

METHODS: From 1 January 2020 to 31 December 2022, 73 newborns suspected of infectious meningitis were hospitalized. After screening by inclusion and exclusion criteria, 69 newborns were subsequently included in the study, containing 27 cases with positive mNGS result and 42 cases with negative mNGS result. Furthermore, according to the diagnosis of meningitis, mNGS positive group and mNGS negative group were further divided into infectious meningitis with mNGS (+) group (n = 27) and infectious meningitis with mNGS (-) group (n = 26), respectively.

RESULTS: (1) Compared with cerebrospinal fluid (CSF) culture, mNGS has better diagnostic value [positive predictive value (PPV) = 100.00% (27/27), negative predictive value (NPV) = 38.10% (16/42), agreement rate = 62.32% (43/69), area under the curve (AUC) = 0.750, 95% confidence interval (CI): 0.636-0.864]. (2) There were significant differences in the onset age, age at first CSF test, CSF leukocyte count, CSF glucose, positive rate of CSF culture, blood leukocyte count, procalcitonin (PCT), C-reaction protein (CRP), age at first mNGS test and adjusting anti-infective medication in the comparison between infectious meningitis with mNGS (+) group and infectious meningitis with mNGS (-) group (p < 0.05). (3) mNGS could help improve the cure rate [crude odds ratio (OR) = 3.393, 95%CI: 1.072-10.737; adjusted OR = 15.580, 95%CI: 2.114-114.798].

CONCLUSION: Compared with classic meningitis detection methods, mNGS has better PPV, NPV, agreement rate, and AUC. mNGS could help improve the cure rate.}, } @article {pmid38562820, year = {2024}, author = {Ammar, A and Singh, V and Ilic, S and Samiksha, F and Marsh, A and Rodriguez-Palacios, A}, title = {Rodent Gut Bacteria Coexisting with an Insect Gut Virus in Parasitic Cysts: Metagenomic Evidence of Microbial Translocation and Co-adaptation in Spatially-Confined Niches.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.03.22.585885}, pmid = {38562820}, abstract = {In medicine, parasitic cysts or cysticerci (fluid-filled cysts, larval stage of tapeworms) are believed to be sterile (no bacteria), and therein, the treatment of cysticerci infestations of deep extra-intestinal tissues (e . g ., brain) relies almost exclusively on the use of antiparasitic medications, and rarely antibiotics. To date, however, it is unclear why common post-treatment complications include abscessation. This study quantified the microbial composition of parasitic cyst contents in a higher-order rodent host, using multi-kingdom shotgun metagenomics, to improve our understanding of gut microbial translocation and adaptation strategies in wild environments. Analysis was conducted on DNA from two hepatic parasitic cysts (Hydatigera (Taeenia) taeniaeformis) in an adult vole mouse (Microtus arvalis), and from feces, liver, and peritoneal fluid of three other vole family members living in a vegetable garden in Ohio, USA. Bacterial metagenomics revealed the presence of gut commensal/opportunistic species, including Parabacteroides distasonis, Klebsiella variicola, Enterococcus faecium , and Lactobacillus acidophilus , inhabiting the cysts. Parabacteroides distasonis and other species were also present outside the cyst in the peritoneal fluid. Remarkably, viral metagenomics revealed various murine viral species, but unexpectedly, it detected an insect-origin virus from the army moth (Pseudaletia / Mythimna unipuncta) known as Mythimna unipuncta granulovirus A (MyunGV-A) in both cysts, and in one fecal and one peritoneal sample from two different voles, indicating survival of the insect virus and adaption in voles. Metagenomics also revealed a significantly lower probability of fungal detection in the cysts compared to other samples (peritoneal fluid, p<0.05; and feces p<0.05), with single taxon detection in each cyst for Malassezia and Pseudophaeomoniella oleicola . The samples with a higher probability of fungi were the peritoneal fluid. In conclusion, commensal/pathobiont bacterial species can inhabit parasitic tapeworm cysts, which needs to be considered during therapeutic decisions of cysticerci or other chronic disease scenarios where immune privileged and spatially restricted ecosystems with limited nutrients and minimal presence of immune cells could facilitate microbial adaptation, such as within gut wall cavitating micropathologies in Crohn's disease.}, } @article {pmid38562514, year = {2024}, author = {Olthoff, M and Kobayashi, T and Parsons, MG and Ford, B and Prasidthrathsint, K and Non, L and Salinas, JL and Diekema, DJ and Ince, D}, title = {Impact of metagenomic next-generation sequencing on clinical decision-making at an academic medical center, a retrospective study, Iowa, 2020-2022.}, journal = {Antimicrobial stewardship & healthcare epidemiology : ASHE}, volume = {4}, number = {1}, pages = {e39}, pmid = {38562514}, issn = {2732-494X}, abstract = {We assessed the impact of metagenomic next-generation sequencing (mNGS) on patient care using previously established criteria. Among 37 patients receiving mNGS testing, 16% showed results that had a positive clinical impact. While mNGS results may offer valuable supplementary information, results should be interpreted within the broader clinical context and evaluation.}, } @article {pmid38562473, year = {2024}, author = {Seth, N and Vats, S and Lakhanpaul, S and Arafat, Y and Mazumdar-Leighton, S and Bansal, M and Babu, CR}, title = {Microbial community diversity of an integrated constructed wetland used for treatment of sewage.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1355718}, pmid = {38562473}, issn = {1664-302X}, abstract = {The microbial community diversity in Constructed Wetland System (CWS) plays a key role in the removal of pollutants from waste water. An integrated functional CWS developed at Neela Hauz Biodiversity Park, Delhi was selected to assess the diversity in composition and structure of microbial community diversity of sludge and sediment of CWS, based on metagenomic approach using 16S rRNA genes. The sediment showed higher diversity than sludge and both formed distinct clusters. The taxonomic structure of the microbial community of CWS is represented by 6,731 OTUs distributed among 2 kingdoms, 103 phyla, 227 classes, 337 orders, 320 families, 295 identified genera, and 84 identified species. The relative abundance of top 5 dominant phyla of sludge and sediment varied from 3.77% (Acidobacteria) to 35.33% (Proteobacteria) and 4.07% (Firmicutes) to 28.20% (Proteobacteria), respectively. The range of variation in relative abundance of top 5 dominant genera of sludge and sediment was 2.58% (Hyphomicrobium) to 6.61% (Planctomyces) and 2.47% (Clostridium) to 4.22% (Syntrophobacter), respectively. The rich microbial diversity of CWS makes it perform better in pollutants removal (59.91-95.76%) than other CWs. Based on the abundance values of taxa, the taxa are grouped under four frequency distribution classes-abundant (>20), common (10-19), rare (5-9), and very rare (1-4). The unique structure of microbial communities of integrated CWS is that the number of abundant taxa decreases in descending order of taxonomic hierarchy, while the number of rare and very rare taxa increases. For example, the number of abundant phyla was 14 and 21 in sludge and sediment, respectively and both communities have only 3 abundant genera each. This is in contrast to 4 and 17 very rare phyla in sludge and sediment, respectively and both the communities have 114 and 91 very rare genera, respectively. The outcomes of the study is that the integrated CWS has much higher microbial community diversity than the diversity reported for other CWs, and the rich diversity can be used for optimizing the performance efficiency of CWS in the removal of pollutants from waste water. Such structural diversity might be an adaptation to heterogeneous environment of CWS.}, } @article {pmid38562470, year = {2024}, author = {Hsiao, YK and Lee, BH and Wu, SC}, title = {Lactiplantibacillus plantarum-encapsulated microcapsules prepared from okra polysaccharides improved intestinal microbiota in Alzheimer's disease mice.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1305617}, pmid = {38562470}, issn = {1664-302X}, abstract = {BACKGROUND: Okra contains a viscous substance rich in water-soluble material, including fibers, pectin, proteoglycans, gum, and polysaccharides. This study explored the use of okra polysaccharides by microorganisms and their potential to improve microbiota.

METHODS: The regulation of microcapsules prepared from okra polysaccharides with or without L. plantarum encapsulation on intestinal microbiota was assessed through 16S metagenomic analysis and short-chain fatty acids (SCFAs) in App[NL-G-F/NL-G-F] mice (Alzheimer's disease; AD model).

RESULTS: We found that Lactobacillaceae and Lactobacillus were majorly regulated by microcapsules prepared from okra polysaccharides in AD mice. Similarly, microcapsules prepared from okra polysaccharides with L. plantarum encapsulation markedly elevated the abundance of Lactobacillaceae and Lactobacillus and increased SCFAs in AD mice.

CONCLUSION: Our results suggest that microcapsules prepared from okra polysaccharides with or without L. plantarum encapsulation may improve intestinal microbiota by elevating Lactobacillus levels in AD mice.}, } @article {pmid38561853, year = {2024}, author = {Chen, H and Huang, Q and Wu, W and Wang, Z and Wang, W and Liu, Y and Ruan, F and He, C and Li, J and Liu, J and Wu, G}, title = {Assessment and clinical utility of metagenomic next-generation sequencing for suspected lower respiratory tract infections.}, journal = {European journal of medical research}, volume = {29}, number = {1}, pages = {213}, pmid = {38561853}, issn = {2047-783X}, abstract = {OBJECTIVES: This study aims to compare the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) to traditional diagnostic methods in patients with lower respiratory tract infections (LRTIs), elucidate the etiological spectrum of these infections, and explore the impact of mNGS on guiding antimicrobial therapy.

METHODS: We retrospectively analyzed data from 128 patients admitted to the Respiratory Department of Anqing 116 Hospital between July 2022 and July 2023. All patients had undergone both mNGS and conventional microbiological techniques (CMT) for LRTI diagnosis. We assessed the diagnostic performance of these methods and examined the influence of mNGS on antimicrobial decision-making.

RESULTS: Overall, mNGS demonstrated superior sensitivity (96.8%) and accuracy (96.8%) compared to CMT. For Mycobacterium tuberculosis detection, the accuracy and sensitivity of mNGS was 88.8% and 77.6%, which was lower than the 94.7% sensitivity of the T-spot test and the 79.6% sensitivity of CMT. In fungal pathogen detection, mNGS showed excellent sensitivity (90.5%), specificity (86.7%), and accuracy (88.0%). Bacteria were the predominant pathogens detected (75.34%), with Mycobacterium tuberculosis (41.74%), Streptococcus pneumoniae (21.74%), and Haemophilus influenzae (16.52%) being most prevalent. Bacterial infections were most common (62.10%), followed by fungal and mixed infections (17.74%). Of the 118 patients whose treatment regimens were adjusted based on mNGS results, 102 (86.5%) improved, 7 (5.9%) did not respond favorably, and follow-up was lost for 9 patients (7.6%).

CONCLUSIONS: mNGS offers rapid and precise pathogen detection for patients with suspected LRTIs and shows considerable promise in diagnosing Mycobacterium tuberculosis and fungal infections. By broadening the pathogen spectrum and identifying polymicrobial infections, mNGS can significantly inform and refine antibiotic therapy.}, } @article {pmid38561814, year = {2024}, author = {Logares, R}, title = {Decoding populations in the ocean microbiome.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {67}, pmid = {38561814}, issn = {2049-2618}, support = {PID2019-105775RB-I00//Agencia Estatal de Investigación/ ; }, abstract = {Understanding the characteristics and structure of populations is fundamental to comprehending ecosystem processes and evolutionary adaptations. While the study of animal and plant populations has spanned a few centuries, microbial populations have been under scientific scrutiny for a considerably shorter period. In the ocean, analyzing the genetic composition of microbial populations and their adaptations to multiple niches can yield important insights into ecosystem function and the microbiome's response to global change. However, microbial populations have remained elusive to the scientific community due to the challenges associated with isolating microorganisms in the laboratory. Today, advancements in large-scale metagenomics and metatranscriptomics facilitate the investigation of populations from many uncultured microbial species directly from their habitats. The knowledge acquired thus far reveals substantial genetic diversity among various microbial species, showcasing distinct patterns of population differentiation and adaptations, and highlighting the significant role of selection in structuring populations. In the coming years, population genomics is expected to significantly increase our understanding of the architecture and functioning of the ocean microbiome, providing insights into its vulnerability or resilience in the face of ongoing global change. Video Abstract.}, } @article {pmid38561516, year = {2024}, author = {Lu, G and Gao, D and Jiang, W and Yu, X and Tong, J and Liu, X and Qiao, T and Wang, R and Zhang, M and Wang, S and Yang, J and Li, D and Lv, Z}, title = {Disrupted gut microecology after high-dose [131]I therapy and radioprotective effects of arachidonic acid supplementation.}, journal = {European journal of nuclear medicine and molecular imaging}, volume = {}, number = {}, pages = {}, pmid = {38561516}, issn = {1619-7089}, support = {21ZR1449600//Natural Science Foundation of Shanghai/ ; 82071964//National Natural Science Foundation of China/ ; 22YF1433600//Science and Technology Commission of Shanghai Municipality/ ; 2019//Shanghai Leading Talent Program sponsored by Shanghai Human Resources and Social Security Bureau/ ; GWVI-11.2-YQ51//Shanghai Municipal Health Commission/ ; }, abstract = {BACKGROUND: Despite the potential radiotoxicity in differentiated thyroid cancer (DTC) patients with high-dose [131]I therapy, the alterations and regulatory mechanisms dependent on intestinal microecology remain poorly understood. We aimed to identify the characteristics of the gut microbiota and metabolites in DTC patients suffering from high-dose [131]I therapy and explore the radioprotective mechanisms underlying arachidonic acid (ARA) treatment.

METHODS: A total of 102 patients with DTC were recruited, with fecal samples collected before and after [131]I therapy for microbiome and untargeted and targeted metabolomic analyses. Mice were exposed to total body irradiation with ARA replenishment and antibiotic pretreatment and were subjected to metagenomic, metabolomic, and proteomic analyses.

RESULTS: [131]I therapy significantly changed the structure of gut microbiota and metabolite composition in patients with DTC. Lachnospiraceae were the most dominant bacteria after [131]I treatment, and metabolites with decreased levels and pathways related to ARA and linoleic acid were observed. In an irradiation mouse model, ARA supplementation not only improved quality of life and recovered hematopoietic and gastrointestinal systems but also ameliorated oxidative stress and inflammation and preserved enteric microecology composition. Additionally, antibiotic intervention eliminated the radioprotective effects of ARA. Proteomic analysis and ursolic acid pretreatment showed that ARA therapy greatly influenced intestinal lipid metabolism in mice subjected to irradiation by upregulating the expression of hydroxy-3-methylglutaryl-coenzyme A synthase 1.

CONCLUSION: These findings highlight that ARA, as a key metabolite, substantially contributes to radioprotection. Our study provides novel insights into the pivotal role that the microbiota-metabolite axis plays in radionuclide protection and offers effective biological targets for treating radiation-induced adverse effects.}, } @article {pmid38561312, year = {2024}, author = {Hong, L and Huang, Y and Han, J and Li, S and Zhang, L and Zhou, Q and Cao, X and Yu, W and Guo, X and Yang, Y and Zhou, Y and Yan, W and Hong, S and Jiang, S and Cao, Y}, title = {Pathogen-specific alterations in intestinal microbiota precede urinary tract infections in preterm infants: a longitudinal case-control study.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2333413}, doi = {10.1080/19490976.2024.2333413}, pmid = {38561312}, issn = {1949-0984}, abstract = {Urinary tract infections (UTIs) are among the most common late-onset infections in preterm infants, characterized by nonspecific symptoms and a pathogenic spectrum that diverges from that of term infants and older children, which present unique diagnostic and therapeutic challenges. Existing data on the role of gut microbiota in UTI pathogenesis in this demographic are limited. This study aims to investigate alterations in gut microbiota and fecal calprotectin levels and their association with the development of UTIs in hospitalized preterm infants. A longitudinal case-control study was conducted involving preterm infants admitted between January 2018 and October 2020. Fecal samples were collected weekly and analyzed for microbial profiles and calprotectin levels. Propensity score matching, accounting for key perinatal factors including age and antibiotic use, was utilized to match samples from UTI-diagnosed infants to those from non-UTI counterparts. Among the 151 preterm infants studied, 53 were diagnosed with a UTI, predominantly caused by Enterobacteriaceae (79.3%) and Enterococcaceae (19.0%). Infants with UTIs showed a significantly higher abundance of these families compared to non-UTI infants, for both Gram-negative and positive pathogens, respectively. Notably, there was a significant pre-UTI increase in the abundance of pathogen-specific taxa in infants later diagnosed with UTIs, offering high predictive value for early detection. Shotgun metagenomic sequencing further confirmed the dominance of specific pathogenic species pre-UTI and revealed altered virulence factor profiles associated with Klebsiella aerogenes and Escherichia coli infections. Additionally, a decline in fecal calprotectin levels was observed preceding UTI onset, particularly in cases involving Enterobacteriaceae. The observed pathogen-specific alterations in the gut microbiota preceding UTI onset offer novel insight into the UTI pathogenesis and promising early biomarkers for UTIs in preterm infants, potentially enhancing the timely management of this common infection. However, further validation in larger cohorts is essential to confirm these findings.}, } @article {pmid38561162, year = {2024}, author = {Ozsefil, IC and Miraloglu, IH and Ozbayram, EG and Ince, B and Ince, O}, title = {Bioaugmentation of anaerobic digesters with the enriched lignin-degrading microbial consortia through a metagenomic approach.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {141831}, doi = {10.1016/j.chemosphere.2024.141831}, pmid = {38561162}, issn = {1879-1298}, abstract = {The recalcitrance of lignin impedes the efficient utilization of lignocellulosic biomass, hindering the efficient production of biogas and value-added materials. Despite the emergence of anaerobic digestion as a superior alternative to the aerobic method for lignin processing, achieving its feasibility requires thorough characterization of lignin-degrading anaerobic microorganisms, assessment of their biomethane production potential, and a comprehensive understanding of the degradation pathway. This study aimed to address the aforementioned necessities by bioaugmenting seed sludge with three distinct enriched lignin-degrading microbial consortia at both 25 °C and 37 °C. Enhanced biomethane yields was detected in the bioaugmented digesters, while the highest production was observed as 188 mLN CH4 gVS[-1] in digesters operated at 37 °C. Moreover, methane yield showed a significant improvement in the samples at 37 °C ranging from 110% to 141% compared to the control, demonstrating the efficiency of the enriched lignin-degrading microbial community. Temperature and substrate were identified as key factors influencing microbial community dynamics. The observation that microbial communities tended to revert to the initial state after lignin depletion, indicating the stability of the overall microbiota composition in the digesters, is a promising finding for large-scale studies. Noteworthy candidates for lignin degradation, including Sporosarcina psychrophila, Comamonas aquatica, Shewanella baltica, Pseudomonas sp. C27, and Brevefilum fermentans were identified in the bioaugmented samples. PICRUSt2 predictions suggest that the pathway and specific proteins involved in anaerobic lignin degradation might share similarities with those engaged in the degradation of aromatic compounds.}, } @article {pmid38561127, year = {2024}, author = {Xu, D and Zhang, X and Usman, S and Bai, J and Sheoran, N and Guo, X}, title = {Reducing transmission of high-risk antibiotic resistance genes in whole-crop corn silage through lactic acid bacteria inoculation and increasing ensiling temperature.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {172114}, doi = {10.1016/j.scitotenv.2024.172114}, pmid = {38561127}, issn = {1879-1026}, abstract = {The microbial hosts of antibiotic resistance genes (ARGs) found epiphytically on plant materials could grow and flourish during silage fermentation. This study employed metagenomic analysis and elucidated the occurrence and transmission mechanisms of ARGs and their microbial hosts in whole-crop corn silage inoculated with homofermentative strain Lactiplantibacillus plantarum or heterofermentative strain Lentilactobacillus buchneri ensiled under different temperature (20 and 30 °C). The results revealed that the corn silage was dominated by Lactobacillus, Leuconostoc, Lentilactobacillus, and Latilactobacillus. Both the ensiling temperature and inoculation had greatly modified the silage microbiota. However, regardless of the ensiling temperature, L. buchneri had significantly higher ARGs, while it only exhibited significantly higher mobile genetic elements (MGEs) in low temperature treatments. The microbial community of the corn silage hosted highly diverse form of ARGs, which were primarily MacB, RanA, bcrA, msbA, TetA (58), and TetT and mainly corresponded to macrolides and tetracyclines drug classes. Plasmids were identified as the most abundant MGEs with significant correlation with some high-risk ARGs (tetM, TolC, mdtH, and NorA), and their abundances have been reduced by ensiling process. Furthermore, higher temperature and L. buchneri reduced abundances of high-risk ARGs by modifying their hosts and reduced their transmission in the silage. Therefore, ensiling, L. buchneri inoculation and higher storage temperature could improve the biosafety of corn silage.}, } @article {pmid38561038, year = {2024}, author = {Lim, TW and Huang, S and Zhang, Y and Burrow, MF and McGrath, C}, title = {A comparison of the prevalence of respiratory pathogens and opportunistic respiratory pathogenic profile of 'clean' and 'unclean' removable dental prostheses.}, journal = {Journal of dentistry}, volume = {}, number = {}, pages = {104968}, doi = {10.1016/j.jdent.2024.104968}, pmid = {38561038}, issn = {1879-176X}, abstract = {OBJECTIVES: To determine and compare the opportunistic respiratory pathogenic index (ORPI) and prevalence of respiratory pathogens between clean and unclean removable prostheses.

METHODS: A cross-sectional study was conducted among 97 removable prosthesis wearers at a teaching dental hospital. Participants' prosthesis hygiene was grouped into clean and unclean. After prosthesis plaque samples were sequenced using the Type IIB Restriction-site Associated DNA Sequencing for Microbiome method, the prevalence was assessed for the presence of respiratory pathogens on each sample. The ORPIs for clean and unclean prostheses were quantified based on the sum of the relative abundance of respiratory pathogenic bacteria in a microbiome using a reference database that contains opportunistic respiratory pathogens and disease-associated information.

RESULTS: A total of 30 opportunistic respiratory pathogens were identified on the removable prostheses. Eighty-one (83.5%) removable prostheses harboured respiratory pathogenic bacteria. Stenotrophomonas maltophilia (34.0%), Pseudomonas aeruginosa (27.8%), and Streptococcus agalactiae (27.8%) were the top three prevalent respiratory pathogens detected in plaque samples. There was a significantly higher prevalence of respiratory pathogens residing on unclean than clean prostheses (P = 0.046). However, the ORPIs in both groups showed no statistically significant difference (P = 0.516).

CONCLUSIONS: The ORPIs for both clean and unclean prostheses demonstrated a similar abundance of respiratory pathogens. However, the high prevalence of respiratory pathogens residing on unclean prostheses should not be underestimated. Therefore, maintaining good prosthesis hygiene is still important for overall oral and systemic health, even though the direct link between prosthesis cleanliness and reduced abundance of respiratory pathogens has not been established.

CLINICAL SIGNIFICANCE: The association between the prevalence of respiratory pathogens and unclean removable prostheses has been demonstrated and might increase the theoretical risk of respiratory disease development.}, } @article {pmid38560681, year = {2024}, author = {Niya, B and Yaakoubi, K and Beraich, FZ and Arouch, M and Meftah Kadmiri, I}, title = {Current status and future developments of assessing microbiome composition and dynamics in anaerobic digestion systems using metagenomic approaches.}, journal = {Heliyon}, volume = {10}, number = {6}, pages = {e28221}, doi = {10.1016/j.heliyon.2024.e28221}, pmid = {38560681}, issn = {2405-8440}, abstract = {The metagenomic approach stands as a powerful technique for examining the composition of microbial communities and their involvement in various anaerobic digestion (AD) systems. Understanding the structure, function, and dynamics of microbial communities becomes pivotal for optimizing the biogas process, enhancing its stability and improving overall performance. Currently, taxonomic profiling of biogas-producing communities relies mainly on high-throughput 16S rRNA sequencing, offering insights into the bacterial and archaeal structures of AD assemblages and their correlations with fed substrates and process parameters. To delve even deeper, shotgun and genome-centric metagenomic approaches are employed to recover individual genomes from the metagenome. This provides a nuanced understanding of collective functionalities, interspecies interactions, and microbial associations with abiotic factors. The application of OMICs in AD systems holds the potential to revolutionize the field, leading to more efficient and sustainable waste management practices particularly through the implementation of precision anaerobic digestion systems. As ongoing research in this area progresses, anticipations are high for further exciting developments in the future. This review serves to explore the current landscape of metagenomic analyses, with focus on advancing our comprehension and critically evaluating biases and recommendations in the analysis of microbial communities in anaerobic digesters. Its objective is to explore how contemporary metagenomic approaches can be effectively applied to enhance our understanding and contribute to the refinement of the AD process. This marks a substantial stride towards achieving a more comprehensive understanding of anaerobic digestion systems.}, } @article {pmid38560625, year = {2024}, author = {Balcha, ES and Macey, MC and Gemeda, MT and Cavalazzi, B and Woldesemayat, AA}, title = {Mining the microbiome of Lake Afdera to gain insights into microbial diversity and biosynthetic potential.}, journal = {FEMS microbes}, volume = {5}, number = {}, pages = {xtae008}, doi = {10.1093/femsmc/xtae008}, pmid = {38560625}, issn = {2633-6685}, abstract = {Microorganisms inhabiting hypersaline environments have received significant attention due to their ability to thrive under poly-extreme conditions, including high salinity, elevated temperatures and heavy metal stress. They are believed to possess biosynthetic gene clusters (BGCs) that encode secondary metabolites as survival strategy and offer potential biotechnological applications. In this study, we mined BGCs in shotgun metagenomic sequences generated from Lake Afdera, a hypersaline lake in the Afar Depression, Ethiopia. The microbiome of Lake Afdera is predominantly bacterial, with Acinetobacter (18.6%) and Pseudomonas (11.8%) being ubiquitously detected. A total of 94 distinct BGCs were identified in the metagenomic data. These BGCs are found to encode secondary metabolites with two main categories of functions: (i) potential pharmaceutical applications (nonribosomal peptide synthase NRPs, polyketide synthase, others) and (ii) miscellaneous roles conferring adaptation to extreme environment (bacteriocins, ectoine, others). Notably, NRPs (20.6%) and bacteriocins (10.6%) were the most abundant. Furthermore, our metagenomic analysis predicted gene clusters that enable microbes to defend against a wide range of toxic metals, oxidative stress and osmotic stress. These findings suggest that Lake Afdera is a rich biological reservoir, with the predicted BGCs playing critical role in the survival and adaptation of extremophiles.}, } @article {pmid38560624, year = {2024}, author = {Wilson, NG and Hernandez-Leyva, A and Schwartz, DJ and Bacharier, LB and Kau, AL}, title = {The gut metagenome harbors metabolic and antibiotic resistance signatures of moderate-to-severe asthma.}, journal = {FEMS microbes}, volume = {5}, number = {}, pages = {xtae010}, doi = {10.1093/femsmc/xtae010}, pmid = {38560624}, issn = {2633-6685}, abstract = {Asthma is a common allergic airway disease that has been associated with the development of the human microbiome early in life. Both the composition and function of the infant gut microbiota have been linked to asthma risk, but functional alterations in the gut microbiota of older patients with established asthma remain an important knowledge gap. Here, we performed whole metagenomic shotgun sequencing of 95 stool samples from a cross-sectional cohort of 59 healthy and 36 subjects with moderate-to-severe asthma to characterize the metagenomes of gut microbiota in adults and children 6 years and older. Mapping of functional orthologs revealed that asthma contributes to 2.9% of the variation in metagenomic content even when accounting for other important clinical demographics. Differential abundance analysis showed an enrichment of long-chain fatty acid (LCFA) metabolism pathways, which have been previously implicated in airway smooth muscle and immune responses in asthma. We also observed increased richness of antibiotic resistance genes (ARGs) in people with asthma. Several differentially abundant ARGs in the asthma cohort encode resistance to macrolide antibiotics, which are often prescribed to patients with asthma. Lastly, we found that ARG and virulence factor (VF) richness in the microbiome were correlated in both cohorts. ARG and VF pairs co-occurred in both cohorts suggesting that virulence and antibiotic resistance traits are coselected and maintained in the fecal microbiota of people with asthma. Overall, our results show functional alterations via LCFA biosynthetic genes and increases in antibiotic resistance genes in the gut microbiota of subjects with moderate-to-severe asthma and could have implications for asthma management and treatment.}, } @article {pmid38560517, year = {2024}, author = {Chorlton, SD}, title = {Ten common issues with reference sequence databases and how to mitigate them.}, journal = {Frontiers in bioinformatics}, volume = {4}, number = {}, pages = {1278228}, doi = {10.3389/fbinf.2024.1278228}, pmid = {38560517}, issn = {2673-7647}, abstract = {Metagenomic sequencing has revolutionized our understanding of microbiology. While metagenomic tools and approaches have been extensively evaluated and benchmarked, far less attention has been given to the reference sequence database used in metagenomic classification. Issues with reference sequence databases are pervasive. Database contamination is the most recognized issue in the literature; however, it remains relatively unmitigated in most analyses. Other common issues with reference sequence databases include taxonomic errors, inappropriate inclusion and exclusion criteria, and sequence content errors. This review covers ten common issues with reference sequence databases and the potential downstream consequences of these issues. Mitigation measures are discussed for each issue, including bioinformatic tools and database curation strategies. Together, these strategies present a path towards more accurate, reproducible and translatable metagenomic sequencing.}, } @article {pmid38560444, year = {2024}, author = {Li, X and Li, S and Liu, X and Fang, M and Lu, S}, title = {Commentary: Metagenomic next-generation sequencing for Mycobacterium tuberculosis complex detection: a meta-analysis.}, journal = {Frontiers in public health}, volume = {12}, number = {}, pages = {1291793}, doi = {10.3389/fpubh.2024.1291793}, pmid = {38560444}, issn = {2296-2565}, } @article {pmid38559251, year = {2024}, author = {Ma, C and Liu, S and Koslicki, D}, title = {MetagenomicKG: a knowledge graph for metagenomic applications.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.03.14.585056}, pmid = {38559251}, abstract = {MOTIVATION: The sheer volume and variety of genomic content within microbial communities makes metagenomics a field rich in biomedical knowledge. To traverse these complex communities and their vast unknowns, metagenomic studies often depend on distinct reference databases, such as the Genome Taxonomy Database (GTDB), the Kyoto Encyclopedia of Genes and Genomes (KEGG), and the Bacterial and Viral Bioinformatics Resource Center (BV-BRC), for various analytical purposes. These databases are crucial for genetic and functional annotation of microbial communities. Nevertheless, the inconsistent nomenclature or identifiers of these databases present challenges for effective integration, representation, and utilization. Knowledge graphs (KGs) offer an appropriate solution by organizing biological entities and their interrelations into a cohesive network. The graph structure not only facilitates the unveiling of hidden patterns but also enriches our biological understanding with deeper insights. Despite KGs having shown potential in various biomedical fields, their application in metagenomics remains underexplored.

RESULTS: We present MetagenomicKG , a novel knowledge graph specifically tailored for metagenomic analysis. MetagenomicKG integrates taxonomic, functional, and pathogenesis-related information from widely used databases, and further links these with established biomedical knowledge graphs to expand biological connections. Through several use cases, we demonstrate its utility in enabling hypothesis generation regarding the relationships between microbes and diseases, generating sample-specific graph embeddings, and providing robust pathogen prediction.

The source code and technical details for constructing the MetagenomicKG and reproducing all analyses are available at Github: https://github.com/KoslickiLab/MetagenomicKG . We also host a Neo4j instance: http://mkg.cse.psu.edu:7474 for accessing and querying this graph.

CONTACT: dmk333@psu.edu.

SUPPLEMENTARY INFORMATION: available at Bioinformatics online.}, } @article {pmid38559035, year = {2024}, author = {Kapur, N and Alam, MA and Hassan, SA and Patel, PH and Wempe, LA and Bhogoju, S and Goretsky, T and Kim, JH and Herzog, J and Ge, Y and Awuah, SG and Byndloss, M and Baumler, AJ and Zadeh, MM and Sartor, RB and Barrett, T}, title = {Enhanced mucosal mitochondrial function corrects dysbiosis and OXPHOS metabolism in IBD.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.03.14.584471}, pmid = {38559035}, abstract = {BACKGROUND: Mitochondrial (Mito) dysfunction in IBD reduces mucosal O2 consumption and increases O2 delivery to the microbiome. Increased enteric O2 promotes blooms of facultative anaerobes (eg. Proteobacteria) and restricts obligate anaerobes (eg. Firmicutes). Dysbiotic metabolites negatively affect host metabolism and immunity. Our novel compound (AuPhos) upregulates intestinal epithelial cell (IEC) mito function, attenuates colitis and corrects dysbiosis in humanized Il10-/- mice. We posit that AuPhos corrects IBD-associated dysbiotic metabolism.

METHODS: Primary effect of AuPhos on mucosal Mito respiration and healing process was studied in ex vivo treated human colonic biopsies and piroxicam-accelerated (Px) Il10-/- mice. Secondary effect on microbiome was tested in DSS-colitis WT B6 and germ-free 129.SvEv WT or Il10-/- mice reconstituted with human IBD stool (Hu- Il10-/-). Mice were treated orally with AuPhos (10- or 25- mg/kg; q3d) or vehicle, stool samples collected for fecal lipocalin-2 (f-LCN2) assay and microbiome analyses using 16S rRNA sequencing. AuPhos effect on microbial metabolites was determined using untargeted global metabolomics. AuPhos-induced hypoxia in IECs was assessed by Hypoxyprobe-1 staining in sections from pimonidazole HCl-infused DSS-mice. Effect of AuPhos on enteric oxygenation was assessed by E. coli Nissle 1917 WT (aerobic respiration-proficient) and cytochrome oxidase (cydA) mutant (aerobic respiration-deficient).

RESULTS: Metagenomic (16S) analysis revealed AuPhos reduced relative abundances of Proteobacteria and increased blooms of Firmicutes in uninflamed B6 WT, DSS-colitis, Hu-WT and Hu- Il10-/- mice. AuPhos also increased hypoxyprobe-1 staining in surface IECs suggesting enhanced O2 utilization. AuPhos-induced anaerobiosis was confirmed by a significant increase in cydA mutant compared to WT (O2-utlizing) E.coli . Ex vivo treatment of human biopsies with AuPhos showed significant increase in Mito mass, and complexes I and IV. Further, gene expression analysis of AuPhos-treated biopsies showed increase in stem cell markers (Lgr4, Lgr5, Lrig1), with concomitant decreases in pro-inflammatory markers (IL1β,MCP1, RankL). Histological investigation of AuPhos-fed Px- Il10-/- mice showed significantly decreased colitis score in AuPhos-treated Px- Il10-/- mice, with decrease in mRNA of pro-inflammatory cytokines and increase in Mito complexes (ND5 , ATP6). AuPhos significantly altered microbial metabolites associated with SCFA synthesis, FAO, TCA cycle, tryptophan and polyamine biosynthesis pathways. AuPhos increased pyruvate, 4-hydroxybutyrate, 2-hydroxyglutarate and succinate, suggesting an upregulation of pyruvate and glutarate pathways of butyrate production. AuPhos reduced IBD-associated primary bile acids (BA) with concomitant increase in secondary BA (SBA). AuPhos treatment significantly decreased acylcarnitines and increased L-carnitine reflective of enhanced FAO. AuPhos increases TCA cycle intermediates and creatine, energy reservoir substrates indicating enhanced OxPHOS. Besides, AuPhos also upregulates tryptophan metabolism, decreases Kynurenine and its derivatives, and increases polyamine biosynthesis pathway (Putresceine and Spermine).

CONCLUSION: These findings indicate that AuPhos-enhanced IEC mitochondrial function reduces enteric O2 delivery, which corrects disease-associated metabolomics by restoring short-chain fatty acids, SBA, AA and IEC energy metabolism.}, } @article {pmid38559026, year = {2024}, author = {Marini, S and Barquero, A and Wadhwani, AA and Bian, J and Ruiz, J and Boucher, C and Prosperi, M}, title = {OCTOPUS: Disk-based, Multiplatform, Mobile-friendly Metagenomics Classifier.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.03.15.585215}, pmid = {38559026}, abstract = {Portable genomic sequencers such as Oxford Nanopore's MinION enable real-time applications in both clinical and environmental health, e.g., detection of bacterial outbreaks. However, there is a bottleneck in the downstream analytics when bioinformatics pipelines are unavailable, e.g., when cloud processing is unreachable due to absence of Internet connection, or only low-end computing devices can be carried on site. For instance, metagenomics classifiers usually require a large amount of memory or specific operating systems/libraries. In this work, we present a platform-friendly software for portable metagenomic analysis of Nanopore data, the Oligomer-based Classifier of Taxonomic Operational and Pan-genome Units via Singletons (OCTOPUS). OCTOPUS is written in Java, reimplements several features of the popular Kraken2 and KrakenUniq software, with original components for improving metagenomics classification on incomplete/sampled reference databases (e.g., selection of bacteria of public health priority), making it ideal for running on smartphones or tablets. We indexed both OCTOPUS and Kraken2 on a bacterial database with ∼4,000 reference genomes, then simulated a positive (bacterial genomes from the same species, but different genomes) and two negative (viral, mammalian) Nanopore test sets. On the bacterial test set OCTOPUS yielded sensitivity and precision comparable to Kraken2 (94.4% and 99.8% versus 94.5% and 99.1%, respectively). On non-bacterial sequences (mammals and viral), OCTOPUS dramatically decreased (4-to 16-fold) the false positive rate when compared to Kraken2 (2.1% and 0.7% versus 8.2% and 11.2%, respectively). We also developed customized databases including viruses, and the World Health Organization's set of bacteria of concern for drug resistance, tested with real Nanopore data on an Android smartphone. OCTOPUS is publicly available at https://github.com/DataIntellSystLab/OCTOPUS and https://github.com/Ruiz-HCI-Lab/OctopusMobile .}, } @article {pmid38559015, year = {2024}, author = {Maghini, DG and Oduaran, OH and Wirbel, J and Olubayo, LAI and Smyth, N and Mathema, T and Belger, CW and Agongo, G and Boua, PR and Choma, SS and Gómez-Olivé, FX and Kisiangani, I and Mashaba, GR and Micklesfield, L and Mohamed, SF and Nonterah, EA and Norris, S and Sorgho, H and Tollman, S and Wafawanaka, F and Tluway, F and Ramsay, M and Bhatt, AS and Hazelhurst, S}, title = {Expanding the human gut microbiome atlas of Africa.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.03.13.584859}, pmid = {38559015}, abstract = {Population studies are crucial in understanding the complex interplay between the gut microbiome and geographical, lifestyle, genetic, and environmental factors. However, populations from low- and middle-income countries, which represent ∼84% of the world population, have been excluded from large-scale gut microbiome research. Here, we present the AWI-Gen 2 Microbiome Project, a cross-sectional gut microbiome study sampling 1,803 women from Burkina Faso, Ghana, Kenya, and South Africa. By intensively engaging with communities that range from rural and horticultural to urban informal settlements and post-industrial, we capture population diversity that represents a far greater breadth of the world's population. Using shotgun metagenomic sequencing, we find that study site explains substantially more microbial variation than disease status. We identify taxa with strong geographic and lifestyle associations, including loss of Treponema and Cryptobacteroides species and gain of Bifidobacterium species in urban populations. We uncover a wealth of prokaryotic and viral novelty, including 1,005 new bacterial metagenome-assembled genomes, and identify phylogeography signatures in Treponema succinifaciens . Finally, we find a microbiome signature of HIV infection that is defined by several taxa not previously associated with HIV, including Dysosmobacter welbionis and Enterocloster sp. This study represents the largest population-representative survey of gut metagenomes of African individuals to date, and paired with extensive clinical biomarkers, demographic data, and lifestyle information, provides extensive opportunity for microbiome-related discovery and research.}, } @article {pmid38558854, year = {2024}, author = {Wang, C and Xu, H and Liu, G and Liu, J and Yu, H and Chen, B and Zheng, G and Shu, M and Du, L and Xu, Z and Huang, L and Li, H and Shu, S and Chen, Y}, title = {A multicenter clinical epidemiology of pediatric pneumococcal meningitis in China: results from the Chinese Pediatric Bacterial Meningitis Surveillance (CPBMS) 2019-2020.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1353433}, doi = {10.3389/fcimb.2024.1353433}, pmid = {38558854}, issn = {2235-2988}, abstract = {OBJECTIVE: To analyze the clinical epidemiological characteristics including clinical features, disease prognosis of pneumococcal meningitis (PM), and drug sensitivity of S. pneumoniae isolates in Chinese children.

METHODS: A retrospective analysis was performed on the clinical, laboratory microbiological data of 160 hospitalized children less than 15 years of age with PM from January 2019 to December 2020 in 33 tertiary hospitals in China.

RESULTS: A total of 160 PM patients were diagnosed, including 103 males and 57 females The onset age was 15 days to 15 years old, and the median age was 1 year and 3 months. There were 137 cases (85.6%) in the 3 months to <5 years age group, especially in the 3 months to <3 years age group (109 cases, 68.2%); S. pneumoniae was isolated from cerebrospinal fluid (CSF) culture in 95(35.6%), and 57(35.6%) in blood culture. The positive rates of S. pneumoniae detection by CSF metagenomic next-generation sequencing (mNGS)and antigen detection method were 40.2% (35/87) and 26.9% (21/78). Fifty-five cases (34.4%) had one or more predisposing factors of bacterial meningitis; and 113 cases (70.6%) had one or more extracranial infection diseases Fever (147, 91.9%) was the most common clinical symptom, followed by vomiting (61, 38.1%) and altered mental status (47,29.4%). Among 160 children with PM, the main intracranial imaging complications were subdural effusion and (or) empyema in 43 cases (26.9%), hydrocephalus in 24 cases (15.0%), cerebral abscess in 23 cases (14.4%), intracranial hemorrhage in 8 cases (5.0%), and other cerebrovascular diseases in 13 cases (8.1%) including encephalomalacia, cerebral infarction, and encephalatrophy. Subdural effusion and (or) empyema and hydrocephalus mainly occurred in children < 1 years old (90.7% (39/43) and 83.3% (20/24), respectively). 17 cases with PM (39.5%) had more than one intracranial imaging abnormality. S. pneumoniae isolates were completely sensitive to vancomycin (100.0%, 75/75), linezolid (100.0%,56/56), ertapenem (6/6); highly sensitive to levofloxacin (81.5%, 22/27), moxifloxacin (14/17), rifampicin (96.2%, 25/26), and chloramphenicol (91.3%, 21/23); moderately sensitive to cefotaxime (56.1%, 23/41), meropenem (51.1%, 23/45) and ceftriaxone (63.5, 33/52); less sensitive to penicillin (19.6%, 27/138) and clindamycin (1/19); completely resistant to erythromycin (100.0%, 31/31). The cure and improvement rate were 22.5% (36/160)and 66.3% (106/160), respectively. 18 cases (11.3%) had an adverse outcome, including 6 cases withdrawing treatment therapy, 5 cases unhealed, 5 cases died, and 2 recurrences. S. pneumoniae was completely susceptible to vancomycin (100.0%, 75/75), linezolid (100.0%, 56/56), and ertapenem (6/6); susceptible to cefotaxime, meropenem, and ceftriaxone in the order of 56.1% (23/41), 51.1% (23/45), and 63.5 (33/52); completely resistant to erythromycin (100.0%, 31/31).

CONCLUSION: Pediatric PM is more common in children aged 3 months to < 3 years old. Intracranial complications mostly occur in children < 1 year of age with fever being the most common clinical manifestations and subdural effusion and (or) empyema and hydrocephalus being the most common complications, respectively. CSF non-culture methods can facilitate improving the detection rate of pathogenic bacteria. More than 10% of PM children had adverse outcomes. S. pneumoniae strains are susceptible to vancomycin, linezolid, ertapenem, levofloxacin, moxifloxacin, rifampicin, and chloramphenicol.}, } @article {pmid38558836, year = {2024}, author = {Guo, J and Tian, W and Lin, H and Hu, L and Gao, X and Xia, J and Yu, H and Chen, H and Li, W and Wu, W}, title = {Analytical and clinical validation of multiplex droplet digital PCR assay for detecting pathogenic fungal infection in lungs.}, journal = {Mycology}, volume = {15}, number = {1}, pages = {110-119}, doi = {10.1080/21501203.2023.2296941}, pmid = {38558836}, issn = {2150-1203}, abstract = {Pulmonary invasive fungal infection in immunocompromised hosts is difficult to diagnose, and current tools for diagnosis or monitoring of response to antifungal treatments have inherent limitations. Droplet digital PCR (ddPCR) has emerged as a promising tool for pulmonary pathogen detection with high sensitivity. This study presents a novel ddPCR panel for rapid and sensitive identification of pulmonary fungal pathogens. First, a ddPCR method for detecting three fungal genera, including Pneumocystis, Aspergillus, and Cryptococcus, was established and evaluated. Then, the clinical validation performance of ddPCR was compared with that of qPCR using 170 specimens, and the 6 specimens with inconsistent results were further verified by metagenomics next-generation sequencing, which yielded results consistent with the ddPCR findings. Finally, the area under the ROC curve (AUC) was used to evaluate the efficiency of ddPCR. While the qPCR identified 16 (9.41%) cases of Aspergillus and 6 (3.53%) cases of Pneumocystis, ddPCR detected 20 (11.76%) Aspergillus cases and 8 (4.71%) Pneumocystis cases. The AUC for Aspergillus, Cryptococcus, and Pneumocystis was 0.974, 0.998, and 0.975, respectively. These findings demonstrated that the ddPCR assay is a highly sensitive method for identifying pathogens responsible for invasive fungal pulmonary infections, and is a promising tool for early diagnosis. .}, } @article {pmid38558411, year = {2024}, author = {Lee, D and Braly, K and Nuding, M and Braly, I and Hopp, C and Twible, H and Pope, C and Hayden, HS and Hoffman, L and Zheng, H and Wahbeh, G and Suskind, DL}, title = {Reverse-engineered exclusive enteral nutrition in pediatric Crohn's disease: A pilot trial.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1002/jpn3.12196}, pmid = {38558411}, issn = {1536-4801}, support = {//Wendy and John Evans/ ; //Richards Family Foundation/ ; //Marco Agenti/ ; //Nanyang Li/ ; }, abstract = {BACKGROUND: In pediatric Crohn's disease (CD), commercial formulas used as exclusive enteral nutrition (EEN) are effective at inducing remission. This study aims to assess the impact of a whole-food blended smoothie as EEN on CD activity and the intestinal microbiome.

METHODS: A 4-week prospective trial assessed the impact of EEN with a whole-food smoothie on newly diagnosed mild-to-moderate active pediatric CD. The smoothie with a multivitamin were developed to meet age-appropriate nutritional requirements. Assessment over 4 weeks included Pediatric Crohn's Disease Activity Index (PCDAI), serum laboratories, fecal calprotectin (FCP), and stool collection for metagenomic shotgun sequencing and microbiota composition analysis. Clinical remission was defined as PCDAI ≤ 10 at week 4.

RESULTS: Ten participants were enrolled with median age 14.5 years, and 8 completed the trial. Baseline mean PCDAI was 26.3 ± 9.1 and mean FCP 1149 ± 718 µg/g. At week 4, 80% of participants achieved clinical remission. FCP decreased by over half in 60% of participants, with FCP below 250 µg/g in 60% and below 100 µg/g in 40%. Microbiome analysis showed a significant increase in species richness over 4 weeks (p = 0.01). Compared to baseline, the relative abundance at week 2 and at week 4 was significantly increased for Bifidobacterium and Streptococcus and decreased for Blautia (p < 0.05 for all).

CONCLUSION: A whole-food blended smoothie was effective for inducing clinical remission and decreasing FCP in pediatric CD similar to commercial EEN formulas. Further research may give insight into data-driven whole-food dietary approaches for CD management.

CLINICALTRIALS: gov NCT03508193.}, } @article {pmid38558277, year = {2024}, author = {Ye, S and Lu, Y and Li, G and Li, D and Wu, Y and Yao, Y}, title = {Stenotrophomonas maltophilia Isolated from the Gut Symbiotic Community of the Plastic-Eating Tenebrio molitor.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {38558277}, issn = {1559-0291}, support = {02020200-K02013008//Zhejiang University/ ; }, abstract = {Polyvinyl chloride (PVC) waste is a major environmental challenge. In this study, we found that a PVC-eating insect, Tenebrio molitor, could survive by consuming PVC as a dietary supplement. To understand the gut symbiotic community, metagenomic analysis was performed to reveal the biodiversity of a symbiotic community in the midgut of Tenebrio molitor. Among them, seven genera were enriched from the midgut of the insect under culture conditions with PVC as carbon source. A strain of Stenotrophomonas maltophilia was isolated from the midgut symbiotic community of the plastic-eating Tenebrio molitor. To unravel the functional gene for the biodegradation enzyme, we sequenced the whole genome of Stenotrophomonas maltophilia and found that orf00390, annotated as a hydrolase, was highly expressed in the PVC culture niche.}, } @article {pmid38558266, year = {2024}, author = {Rassner, SME and Cook, JM and Mitchell, AC and Stevens, IT and Irvine-Fynn, TDL and Hodson, AJ and Edwards, A}, title = {The distinctive weathering crust habitat of a High Arctic glacier comprises discrete microbial micro-habitats.}, journal = {Environmental microbiology}, volume = {26}, number = {4}, pages = {e16617}, doi = {10.1111/1462-2920.16617}, pmid = {38558266}, issn = {1462-2920}, support = {//The Rolex Foundation/ ; NE/S001034/1//Natural Environment Research Council/ ; NE/V012991/1//Natural Environment Research Council/ ; RF-2018-584/4//Leverhulme Trust/ ; 288402//Norges Forskningsråd/ ; }, abstract = {Sunlight penetrates the ice surfaces of glaciers and ice sheets, forming a water-bearing porous ice matrix known as the weathering crust. This crust is home to a significant microbial community. Despite the potential implications of microbial processes in the weathering crust for glacial melting, biogeochemical cycles, and downstream ecosystems, there have been few explorations of its microbial communities. In our study, we used 16S rRNA gene sequencing and shotgun metagenomics of a Svalbard glacier surface catchment to characterise the microbial communities within the weathering crust, their origins and destinies, and the functional potential of the weathering crust metagenome. Our findings reveal that the bacterial community in the weathering crust is distinct from those in upstream and downstream habitats. However, it comprises two separate micro-habitats, each with different taxa and functional categories. The interstitial porewater is dominated by Polaromonas, influenced by the transfer of snowmelt, and exported via meltwater channels. In contrast, the ice matrix is dominated by Hymenobacter, and its metagenome exhibits a diverse range of functional adaptations. Given that the global weathering crust area and the subsequent release of microbes from it are strongly responsive to climate projections for the rest of the century, our results underscore the pressing need to integrate the microbiome of the weathering crust with other communities and processes in glacial ecosystems.}, } @article {pmid38557867, year = {2024}, author = {Bar Ziv, O and Cahn, A and Jansen, T and Istomin, V and Kedem, E and Olshtain-Pops, K and Israel, S and Oster, Y and Orenbuch-Harroch, E and Korem, M and Strahilevitz, J and Levy, I and Valdés-Mas, R and Ivanova, V and Elinav, E and Shahar, E and Elinav, H}, title = {Diagnosis and Risk Factors of Prediabetes and Diabetes in People Living with HIV- Evaluation of Clinical and Microbiome Parameters.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiae167}, pmid = {38557867}, issn = {1537-6613}, abstract = {Diabetes is more common among people living with HIV (PLWH), as compared with healthy individuals. In a prospective multicenter study (N = 248), we identified normoglycemic (48.7%), prediabetic (44.4%) and diabetic (6.9%) PLWH. HbA1c and fasting blood glucose (FBG) sensitivity in defining dysglycemia was 96.8%, while addition of oral glucose tolerance test led to reclassification of only 4 patients. Inclusion of 93 additional PLWH with known DM enabled identification of multiple independent predictors of dysglycemia or diabetes: older age, higher BMI, Ethiopian origin, HIV duration, lower integrase inhibitor exposure and advanced disease at diagnosis. Shotgun metagenomic microbiome analysis revealed 4 species that were significantly expanded with hyperglycemia/hyperinsulinemia, and 2 species that were differentially more prevalent in prediabetic/diabetic PLWH. Collectively, we uncover multiple potential host and microbiome predictors of altered glycemic status in PLWH, while demonstrating that FBG and HbA1C likely suffice for diabetes screening. These potential diabetic predictors merit future prospective validation.}, } @article {pmid38557755, year = {2024}, author = {Cho, A and Lax, G and Livingston, SJ and Masukagami, Y and Naumova, M and Millar, O and Husnik, F and Keeling, PJ}, title = {Genomic analyses of Symbiomonas scintillans show no evidence for endosymbiotic bacteria but does reveal the presence of giant viruses.}, journal = {PLoS genetics}, volume = {20}, number = {4}, pages = {e1011218}, doi = {10.1371/journal.pgen.1011218}, pmid = {38557755}, issn = {1553-7404}, abstract = {Symbiomonas scintillans Guillou et Chrétiennot-Dinet, 1999 is a tiny (1.4 μm) heterotrophic microbial eukaryote. The genus was named based on the presence of endosymbiotic bacteria in its endoplasmic reticulum, however, like most such endosymbionts neither the identity nor functional association with its host were known. We generated both amplification-free shotgun metagenomics and whole genome amplification sequencing data from S. scintillans strains RCC257 and RCC24, but were unable to detect any sequences from known lineages of endosymbiotic bacteria. The absence of endobacteria was further verified with FISH analyses. Instead, numerous contigs in assemblies from both RCC24 and RCC257 were closely related to prasinoviruses infecting the green algae Ostreococcus lucimarinus, Bathycoccus prasinos, and Micromonas pusilla (OlV, BpV, and MpV, respectively). Using the BpV genome as a reference, we assembled a near-complete 190 kbp draft genome encoding all hallmark prasinovirus genes, as well as two additional incomplete assemblies of closely related but distinct viruses from RCC247, and three similar draft viral genomes from RCC24, which we collectively call SsVs. A multi-gene tree showed the three SsV genome types branched within highly supported clades with each of BpV2, OlVs, and MpVs, respectively. Interestingly, transmission electron microscopy also revealed a 190 nm virus-like particle similar the morphology and size of the endosymbiont originally reported in S. scintillans. Overall, we conclude that S. scintillans currently does not harbour an endosymbiotic bacterium, but is associated with giant viruses.}, } @article {pmid38557102, year = {2024}, author = {Aljabr, W and Dandachi, I and Abbas, B and Karkashan, A and Al-Amari, A and AlShahrani, D}, title = {Metagenomic next-generation sequencing of nasopharyngeal microbiota in COVID-19 patients with different disease severities.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0416623}, doi = {10.1128/spectrum.04166-23}, pmid = {38557102}, issn = {2165-0497}, abstract = {Throughout the COVID-19 pandemic, extensive research has been conducted on SARS-COV-2 to elucidate its genome, prognosis, and possible treatments. However, few looked at the microbial markers that could be explored in infected patients and that could predict possible disease severity. The aim of this study is to compare the nasopharyngeal microbiota of healthy subjects, moderate, under medication, and recovered SARS-COV-2 patients. In 2020, 38 nasopharyngeal swabs were collected from 6 healthy subjects, 14 moderates, 10 under medication and 8 recovered SARS-COV-2 patients at King Fahad Medical city. Metatranscriptomic sequencing was performed using Minion Oxford nanopore sequencing. No significant difference in alpha as well as beta diversity was observed among all four categories. Nevertheless, we have found that Streptococcus spp including Streptococcus pneumoniae and Streptococcus thermophilus were among the top 15 most abundant species detected in COVID-19 patients but not in healthy subjects. The genus Staphylococcus was found to be associated with COVID-19 patients compared to healthy subjects. Furthermore, the abundance of Leptotrichia was significantly higher in healthy subjects compared to recovered patients. Corynebacterium on the other hand, was associated with under-medication patients. Taken together, our study revealed no differences in the overall microbial composition between healthy subjects and COVID-19 patients. Significant differences were seen only at specific taxonomic level. Future studies should explore the nasopharyngeal microbiota between controls and COVID-19 patients while controlling for confounders including age, gender, and comorbidities; since these latter could affect the results and accordingly the interpretation.IMPORTANCEIn this work, no significant difference in the microbial diversity was seen between healthy subjects and COVID-19 patients. Changes in specific taxa including Leptotrichia, Staphylococcus, and Corynebacterium were only observed. Leptotrichia was significantly higher in healthy subjects, whereas Staphylococcus and Corynebacterium were mostly associated with COVID-19, and specifically with under-medication SARS-COV-2 patients, respectively. Although the COVID-19 pandemic has ended, the SARS-COV-2 virus is continuously evolving and the emergence of new variants causing more severe disease should be always kept in mind. Microbial markers in SARS-COV-2 infected patients can be useful in the early suspicion of the disease, predicting clinical outcomes, framing hospital and intensive care unit admission as well as, risk stratification. Data on which microbial marker to tackle is still controversial and more work is needed, hence the importance of this study.}, } @article {pmid38557040, year = {2024}, author = {Li, C and Lü, F and Peng, W and He, PJ and Zhang, H}, title = {Functional Redundant Microbiome Enhanced Anaerobic Digestion Efficiency under Ammonium Inhibition Conditions.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c01227}, pmid = {38557040}, issn = {1520-5851}, abstract = {Revealing the role of functional redundancy is of great importance considering its key role in maintaining the stability of microbial ecosystems in response to various disturbances. However, experimental evidence on this point is still lacking due to the difficulty in "manipulating" and depicting the degree of redundancy. In this study, manipulative experiments of functional redundancy were conducted by adopting the mixed inoculation strategy to evaluate its role in engineered anaerobic digestion systems under ammonium inhibition conditions. The results indicated that the functional redundancy gradient was successfully constructed and confirmed by evidence from pathway levels. All mixed inoculation groups exhibited higher methane production regardless of the ammonium level, indicating that functional redundancy is crucial in maintaining the system's efficiency. Further analysis of the metagenome-assembled genomes within different functional guilds revealed that the extent of redundancy decreased along the direction of the anaerobic digestion flow, and the role of functional redundancy appeared to be related to the stress level. The study also found that microbial diversity of key functional populations might play a more important role than their abundance on the system's performance under stress. The findings provide direct evidence and highlight the critical role of functional redundancy in enhancing the efficiency and stability of anaerobic digestion.}, } @article {pmid38556999, year = {2024}, author = {Liu, W and Xu, C and Li, T and Ren, Z and Hao, S and Chen, Z and Huang, X and Wen, X}, title = {Temporal Dynamics and Contribution of Phage Community to the Prevalence of Antibiotic Resistance Genes in a Full-Scale Sludge Anaerobic Digestion Plant.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.4c00712}, pmid = {38556999}, issn = {1520-5851}, abstract = {Anaerobic digestion (AD) is an important biological resource recovery process, where microorganisms play key roles for material transformation. There has been some knowledge about the prokaryotic community and antibiotic resistance genes (ARGs) in AD, but there has been very limited knowledge of phages. In this study, samples from a full-scale AD plant were collected over 13 months, sequenced, and analyzed for viral and prokaryotic metagenomes. Totally, 3015 viral operational taxonomic units (vOTUs) were detected, mostly assigned to Caudoviricetes. The phage community had faster temporal variation than the prokaryotic community. Warm seasons harbored a higher abundance of both temperate phages and broad host-range phages. Seven ARGs of 6 subtypes were carried by 20 vOTUs, a representative ermT gene was synthesized and expressed, and the resistance activity in the host was examined, confirming the real activity of virus-carried ARGs in the AD process. Some of the ARGs were horizontally transferred between the phage and prokaryotic genomes. However, phage infection was not found to contribute to ARG transfer. This study provided an insight into the ecological patterns of the phage community, confirmed the antibiotic resistance activity of virus-carried ARGs, evaluated the contribution of phages on the ARG prevalence, and laid the foundation for the control strategies of the community and antibiotic resistance in the AD process.}, } @article {pmid38556303, year = {2024}, author = {Tanaka, U and Mogi, K and Fujita, N and Moriwake, M and Morito, K and Takayama, K and Morimoto, H and Yasukawa, T and Uozumi, Y and Nagasawa, K}, title = {Alteration of Sweet and Bitter Taste Sensitivity with Development of Glucose Intolerance in Non-insulin-Dependent Diabetes Mellitus Model OLETF Rats.}, journal = {Biological & pharmaceutical bulletin}, volume = {47}, number = {3}, pages = {739-749}, doi = {10.1248/bpb.b23-00756}, pmid = {38556303}, issn = {1347-5215}, abstract = {Patients with diabetes exhibit altered taste sensitivity, but its details have not been clarified yet. Here, we examined alteration of sweet taste sensitivity with development of glucose intolerance in Otsuka Long-Evans Tokushima Fatty (OLETF) rats as a model of non-insulin-dependent diabetes mellitus. Compared to the cases of Long Evans Tokushima Otsuka (LETO) rats as a control, glucose tolerance of OLETF rats decreased with aging, resulting in development of diabetes at 36-weeks-old. In brief-access tests with a mixture of sucrose and quinine hydrochloride, OLETF rats at 25 or more-weeks-old seemed to exhibit lower sweet taste sensitivity than age-matched LETO ones, but the lick ratios of LETO, but not OLETF, rats for the mixture and quinine hydrochloride solutions decreased and increased, respectively, aging-dependently. Expression of sweet taste receptors, T1R2 and T1R3, in circumvallate papillae (CP) was almost the same in LETO and OLETF rats at 10- and 40-weeks-old, while expression levels of a bitter taste receptor, T2R16, were greater in 40-weeks-old rats than in 10-weeks-old ones in both strains. There was no apparent morphological alteration in taste buds in CP between 10- and 40-weeks-old LETO and OLETF rats. Metagenomic analysis of gut microbiota revealed strain- and aging-dependent alteration of mucus layer-regulatory microbiota. Collectively, we concluded that the apparent higher sweet taste sensitivity in 25 or more-weeks-old OLETF rats than in age-matched LETO rats was due to the aging-dependent increase of bitter taste sensitivity in LETO rats with alteration of the gut microbiota.}, } @article {pmid38556024, year = {2024}, author = {Chen, T and Liu, S and Zhang, S and Song, H and Zhuang, Y and Ma, J and Xiao, J and Wang, J and Ma, Y and Wang, Y and Wang, W and Li, S and Cao, Z}, title = {Initial diet shapes resistance-gene composition and fecal microbiome dynamics in young ruminants during nursing.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {172103}, doi = {10.1016/j.scitotenv.2024.172103}, pmid = {38556024}, issn = {1879-1026}, abstract = {This study was conducted to examine how colostrum pasteurization affects resistance genes and microbial communities in calf feces. Forty female Holstein calves were randomly assigned to either the control (CON) group, which received unheated colostrum, or the pasteurized colostrum (PAT) group. The calves body weight was measured weekly before morning feeding. Calf starter intake were measured and recorded daily before morning feeding. Samples of colostrum were collected before feeding. Blood was collected on d 1 and 70 before morning feeding. Ten calves were randomly selected from each group (n = 20 calves total) for fecal sampling on d 3, 28, 56 and 70 for subsequent DNA extraction and metagenomic sequencing. Total bacterial counts in the colostrum were markedly higher in the CON group than in the PAT group. Pasteurized colostrum administration substantially reduced the ARO diversity and diminishes the abundance of Enterobacteriaceae, thereby decreasing their contribution to resistance genes. Pasteurization also reduced glucoside hydrolase-66 activity in 3-day-old calves which led to an increase in the activity of aminoglycoside antibiotics, resulting in 52.63 % of PAT-enriched bacteria acquiring aminoglycoside resistance genes. However, from the perspective of overall microbial community, the proportion of aminoglycoside, beta-lactam and tetracycline resistance genes carried by microbial community in PAT group was lower than CON group (P < 0.05). Fecal samples from the PAT group contained greater abundances of Subdoligranulum (P < 0.05) and Lachnospiraceae_NK4A136_group (P < 0.05) on days 28 and 70 compared to CON. Network analysis and abundance variations of the different bacteria obtained by linear discriminant analysis effect size analysis showed that pasteurized colostrum feeding reduced the interactions among related bacteria and maintained stability of the hind-gut microbiome. In conclusion, these findings underscore the intricate interactions between early diet, calf resistance-gene transmission and microbial dynamics, which should be carefully considered in calf-rearing practices.}, } @article {pmid38555823, year = {2024}, author = {Itarte, M and Calvo, M and Martínez-Frago, L and Mejías-Molina, C and Martínez-Puchol, S and Girones, R and Medema, G and Bofill-Mas, S and Rusiñol, M}, title = {Assessing environmental exposure to viruses in wastewater treatment plant and swine farm scenarios with next-generation sequencing and occupational risk approaches.}, journal = {International journal of hygiene and environmental health}, volume = {259}, number = {}, pages = {114360}, doi = {10.1016/j.ijheh.2024.114360}, pmid = {38555823}, issn = {1618-131X}, abstract = {Occupational exposure to pathogens can pose health risks. This study investigates the viral exposure of workers in a wastewater treatment plant (WWTP) and a swine farm by analyzing aerosol and surfaces samples. Viral contamination was evaluated using quantitative polymerase chain reaction (qPCR) assays, and target enrichment sequencing (TES) was performed to identify the vertebrate viruses to which workers might be exposed. Additionally, Quantitative Microbial Risk Assessment (QMRA) was conducted to estimate the occupational risk associated with viral exposure for WWTP workers, choosing Human Adenovirus (HAdV) as the reference pathogen. In the swine farm, QMRA was performed as an extrapolation, considering a hypothetical zoonotic virus with characteristics similar to Porcine Adenovirus (PAdV). The modelled exposure routes included aerosol inhalation and oral ingestion through contaminated surfaces and hand-to-mouth contact. HAdV and PAdV were widespread viruses in the WWTP and the swine farm, respectively, by qPCR assays. TES identified human and other vertebrate viruses WWTP samples, including viruses from families such as Adenoviridae, Circoviridae, Orthoherpesviridae, Papillomaviridae, and Parvoviridae. In the swine farm, most of the identified vertebrate viruses were porcine viruses belonging to Adenoviridae, Astroviridae, Circoviridae, Herpesviridae, Papillomaviridae, Parvoviridae, Picornaviridae, and Retroviridae. QMRA analysis revealed noteworthy risks of viral infections for WWTP workers if safety measures are not taken. The probability of illness due to HAdV inhalation was higher in summer compared to winter, while the greatest risk from oral ingestion was observed in workspaces during winter. Swine farm QMRA simulation suggested a potential occupational risk in the case of exposure to a hypothetical zoonotic virus. This study provides valuable insights into WWTP and swine farm worker's occupational exposure to human and other vertebrate viruses. QMRA and NGS analyses conducted in this study will assist managers in making evidence-based decisions, facilitating the implementation of protection measures, and risk mitigation practices for workers.}, } @article {pmid38555785, year = {2024}, author = {Zhou, M and Wang, J and Wang, H and Ran, X and Xue, H and Liu, C and Wang, Y}, title = {Revealing the comprehensive impact of organic compounds on the partial nitrification-anammox system during incineration leachate treatment: metabolic hierarchy and adaptation.}, journal = {Water research}, volume = {255}, number = {}, pages = {121534}, doi = {10.1016/j.watres.2024.121534}, pmid = {38555785}, issn = {1879-2448}, abstract = {Organics, as widespread pollutants in high-strength ammonia wastewater, typically exert adverse effects on the performance of partial nitrification-anammox (PNA) systems. However, the in-depth knowledge on how microbial consortia respond to these disturbances remains limited. In this study, we unveiled the evolution of complex organic matter flow and its impact on the metabolic hierarchy and adaptation of microbial consortia, employing multi-omics approaches, i.e., 16S amplicon sequencing, metagenomics, and metabolomics. In a two-stage PNA system sequentially treating synthetic wastewater and incineration leachate over 230 days, partial nitrification stayed stable (nitrite accumulation > 97%) while anammox efficiency dropped (nitrogen removal decreased from 86% to 78%). The phenomenon was revealed to be correlated with the evolution of dissolved organic matter (DOM) and xenobiotic organic compounds (XOCs). In the PN stage, ammonia-oxidizing bacteria (AOB) exhibited excellent adaptability through active metabolic regulation after treating leachate. Numerous heterotrophs proliferated to utilize DOM and XOCs, triggering a "boom" state evident in the glycerophospholipid metabolism. However, in the anammox stage, the competition between carbon fixation and central carbon metabolism within autotrophs and heterotrophs became evident. Increased biosynthesis costs inhibited the central metabolism (specific anammox activity decreased by 66%) and the Wood-Ljungdahl pathway of anammox bacteria (AnAOB) in the presence of recalcitrant organics. Additionally, the degradation of organics was limited, exhibiting a "bust" state. This study revealed the metabolic adaption and susceptibility of AOB and AnAOB in response to organics from the leachate, demonstrating the applicability of the two-stage configuration for treating high-strength wastewater containing abundant and diverse organics.}, } @article {pmid38555499, year = {2024}, author = {Heston, SM and Young, RR and Jenkins, K and Martin, PL and Stokhuyzen, A and Ward, DV and Bhattarai, SK and Bucci, V and Arshad, M and Chao, NJ and Seed, PC and Kelly, MS}, title = {The effects of antibiotic exposures on the gut resistome during hematopoietic cell transplantation in children.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2333748}, doi = {10.1080/19490976.2024.2333748}, pmid = {38555499}, issn = {1949-0984}, abstract = {Antibiotic resistance is a global threat driven primarily by antibiotic use. We evaluated the effects of antibiotic exposures on the gut microbiomes and resistomes of children at high risk of colonization by antibiotic-resistant bacteria. We performed shotgun metagenomic sequencing of 691 serially collected fecal samples from 80 children (<18 years) undergoing hematopoietic cell transplantation. We evaluated the effects of aerobic (cefepime, vancomycin, fluoroquinolones, aminoglycosides, macrolides, and trimethoprim-sulfamethoxazole) and anaerobic (piperacillin-tazobactam, carbapenems, metronidazole, and clindamycin) antibiotic exposures on the diversity and composition of the gut microbiome and resistome. We identified 372 unique antibiotic resistance genes (ARGs); the most frequent ARGs identified encode resistance to tetracyclines (n = 88), beta-lactams (n = 84), and fluoroquinolones (n = 79). Both aerobic and anaerobic antibiotic exposures were associated with a decrease in the number of bacterial species (aerobic, β = 0.71, 95% CI: 0.64, 0.79; anaerobic, β = 0.66, 95% CI: 0.53, 0.82) and the number of unique ARGs (aerobic, β = 0.81, 95% CI: 0.74, 0.90; anaerobic, β = 0.73, 95% CI: 0.61, 0.88) within the gut metagenome. However, only antibiotic regimens that included anaerobic activity were associated with an increase in acquisition of new ARGs (anaerobic, β = 1.50; 95% CI: 1.12, 2.01) and an increase in the relative abundance of ARGs in the gut resistome (anaerobic, β = 1.62; 95% CI: 1.15, 2.27). Specific antibiotic exposures were associated with distinct changes in the number and abundance of ARGs for individual antibiotic classes. Our findings detail the impact of antibiotics on the gut microbiome and resistome and demonstrate that anaerobic antibiotics are particularly likely to promote acquisition and expansion of antibiotic-resistant bacteria.}, } @article {pmid38555472, year = {2024}, author = {Pan, J and Zhang, Z and Li, Y and Yu, J and You, Z and Li, C and Wang, S and Zhu, M and Ren, F and Zhang, X and Sun, Y and Wang, S}, title = {A microbial knowledge graph-based deep learning model for predicting candidate microbes for target hosts.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {3}, pages = {}, doi = {10.1093/bib/bbae119}, pmid = {38555472}, issn = {1477-4054}, support = {2022FY101100//Science & Technology Fundamental Resources Investigation Program/ ; 62325308//National Science Fund for Distinguished Young Scholars of China/ ; 32170114//National Natural Science Foundation of China/ ; }, abstract = {Predicting interactions between microbes and hosts plays critical roles in microbiome population genetics and microbial ecology and evolution. How to systematically characterize the sophisticated mechanisms and signal interplay between microbes and hosts is a significant challenge for global health risks. Identifying microbe-host interactions (MHIs) can not only provide helpful insights into their fundamental regulatory mechanisms, but also facilitate the development of targeted therapies for microbial infections. In recent years, computational methods have become an appealing alternative due to the high risk and cost of wet-lab experiments. Therefore, in this study, we utilized rich microbial metagenomic information to construct a novel heterogeneous microbial network (HMN)-based model named KGVHI to predict candidate microbes for target hosts. Specifically, KGVHI first built a HMN by integrating human proteins, viruses and pathogenic bacteria with their biological attributes. Then KGVHI adopted a knowledge graph embedding strategy to capture the global topological structure information of the whole network. A natural language processing algorithm is used to extract the local biological attribute information from the nodes in HMN. Finally, we combined the local and global information and fed it into a blended deep neural network (DNN) for training and prediction. Compared to state-of-the-art methods, the comprehensive experimental results show that our model can obtain excellent results on the corresponding three MHI datasets. Furthermore, we also conducted two pathogenic bacteria case studies to further indicate that KGVHI has excellent predictive capabilities for potential MHI pairs.}, } @article {pmid38555432, year = {2024}, author = {Scicchitano, D and Leuzzi, D and Babbi, G and Palladino, G and Turroni, S and Laczny, CC and Wilmes, P and Correa, F and Leekitcharoenphon, P and Savojardo, C and Luise, D and Martelli, P and Trevisi, P and Aarestrup, FM and Candela, M and Rampelli, S}, title = {Dispersion of antimicrobial resistant bacteria in pig farms and in the surrounding environment.}, journal = {Animal microbiome}, volume = {6}, number = {1}, pages = {17}, pmid = {38555432}, issn = {2524-4671}, support = {818290//Horizon 2020 Framework Programme/ ; }, abstract = {BACKGROUND: Antimicrobial resistance has been identified as a major threat to global health. The pig food chain is considered an important source of antimicrobial resistance genes (ARGs). However, there is still a lack of knowledge on the dispersion of ARGs in pig production system, including the external environment.

RESULTS: In the present study, we longitudinally followed one swine farm located in Italy from the weaning phase to the slaughterhouse to comprehensively assess the diversity of ARGs, their diffusion, and the bacteria associated with them. We obtained shotgun metagenomic sequences from 294 samples, including pig feces, farm environment, soil around the farm, wastewater, and slaughterhouse environment. We identified a total of 530 species-level genome bins (SGBs), which allowed us to assess the dispersion of microorganisms and their associated ARGs in the farm system. We identified 309 SGBs being shared between the animals gut microbiome, the internal and external farm environments. Specifically, these SGBs were characterized by a diverse and complex resistome, with ARGs active against 18 different classes of antibiotic compounds, well matching antibiotic use in the pig food chain in Europe.

CONCLUSIONS: Collectively, our results highlight the urgency to implement more effective countermeasures to limit the dispersion of ARGs in the pig food systems and the relevance of metagenomics-based approaches to monitor the spread of ARGs for the safety of the farm working environment and the surrounding ecosystems.}, } @article {pmid38555351, year = {2024}, author = {Han, CJ and Cheng, CH and Yeh, TF and Pauchet, Y and Shelomi, M}, title = {Coconut rhinoceros beetle digestive symbiosis with potential plant cell wall degrading microbes.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {34}, pmid = {38555351}, issn = {2055-5008}, support = {MOST-109-643 2311-B-002-016-MY3//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; }, abstract = {Coconut rhinoceros beetle (CRB, Oryctes rhinoceros) is an invasive palm pest whose larvae eat wood, yet lack the necessary digestive enzymes. This study confirmed endogenous CRB cellulase is inactive, suggesting microbial fermentation. The inner lining of the CRB hindgut has tree-like structures covered with a conspicuous biofilm. To identify possible symbionts, 16 S rRNA amplicon sequencing was used on individuals from across Taiwan. Several taxa of Clostridia, an anaerobic class including many cellulolytic bacteria, were highly abundant in most individuals from all locations. Whole metagenome sequencing further confirmed many lignocellulose degrading enzymes are derived from these taxa. Analyses of eggs, larvae, adults, and soil found these cellulolytic microbes are not transmitted vertically or transstadially. The core microbiomes of the larval CRB are likely acquired and enriched from the environment with each molt, and enable efficient digestion of wood.}, } @article {pmid38555322, year = {2024}, author = {Nagy, NA and Tóth, GE and Kurucz, K and Kemenesi, G and Laczkó, L}, title = {The updated genome of the Hungarian population of Aedes koreicus.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {7545}, pmid = {38555322}, issn = {2045-2322}, support = {OTKA PD142602//National Research, Development and Innovation Office/ ; FK-138563//National Research, Development and Innovation Office/ ; }, abstract = {Vector-borne diseases pose a potential risk to human and animal welfare, and understanding their spread requires genomic resources. The mosquito Aedes koreicus is an emerging vector that has been introduced into Europe more than 15 years ago but only a low quality, fragmented genome was available. In this study, we carried out additional sequencing and assembled and characterized the genome of the species to provide a background for understanding its evolution and biology. The updated genome was 1.1 Gbp long and consisted of 6099 contigs with an N50 value of 329,610 bp and a BUSCO score of 84%. We identified 22,580 genes that could be functionally annotated and paid particular attention to the identification of potential insecticide resistance genes. The assessment of the orthology of the genes indicates a high turnover at the terminal branches of the species tree of mosquitoes with complete genomes, which could contribute to the adaptation and evolutionary success of the species. These results could form the basis for numerous downstream analyzes to develop targets for the control of mosquito populations.}, } @article {pmid38554650, year = {2024}, author = {Zhao, M and Liu, H and Liu, M and Yue, Z and Li, C and Liu, L and Li, F}, title = {Metagenomics and metabolomics reveal that gut microbiome adapts to the diet transition in Hyla rabbits.}, journal = {Microbiological research}, volume = {283}, number = {}, pages = {127705}, doi = {10.1016/j.micres.2024.127705}, pmid = {38554650}, issn = {1618-0623}, abstract = {There is still a lack of longitudinal dynamic studies on the taxonomic features, functional reserves, and metabolites of the rabbit gut microbiome. An experiment was conducted to characterize the bacterial community of rabbits. By combining metagenomics and metabolomics, we have comprehensively analyzed the longitudinal dynamics of the rabbit gut microbiota and its effect on host adaptability. Our data reveal an overall increasing trend in microbial community and functional gene diversity and richness during the pre-harvest lifespan of rabbits. The introduction of solid feed is an important driving factor affecting rabbit gut microbiological compositions. Clostridium and Ruminococcus had significantly higher relative abundances in the solid feed stage. Further, the starch and fiber in solid feed promote the secretion of carbohydrate-degrading enzymes, which helps the host adapt to dietary changes. The rabbit gut microbiota can synthesize lysine, and the synthase is gradually enriched during the diet transformation. The gut microbiota of newborn rabbits has a higher abundance of lipid metabolism, which helps the host obtain more energy from breast milk lipids. The rabbit gut microbiota can also synthesize a variety of secondary bile acids after the introduction of solid feed. These findings provide a novel understanding of how the gut microbiota mediates adaptability to environment and diet in rabbits and provide multiple potential strategies for regulating intestinal health and promoting higher feed efficiency.}, } @article {pmid38554507, year = {2024}, author = {Wang, W and Fan, Q and Gong, T and Zhang, M and Li, C and Zhang, Y and Li, H}, title = {Superb green cycling strategies for microbe-Fe[0] neural network-type interaction: Harnessing eight key genes encoding enzymes and mineral transformations to efficiently treat PFOA.}, journal = {Journal of hazardous materials}, volume = {470}, number = {}, pages = {134143}, doi = {10.1016/j.jhazmat.2024.134143}, pmid = {38554507}, issn = {1873-3336}, abstract = {To address time-consuming and efficiency-limited challenges in conventional zero-valent iron (ZVI, Fe[0]) reduction or biotransformation for perfluorooctanoic acid (PFOA) treatment, two calcium alginate-embedded amendments (biochar-immobilized PFOA-degrading bacteria (CB) and ZVI (CZ)) were developed to construct microbe-Fe[0] high-rate interaction systems. Interaction mechanisms and key metabolic pathways were systematically explored using metagenomics and a multi-process coupling model for PFOA under microbe-Fe[0] interaction. Compared to Fe[0] (0.0076 day[-1]) or microbe (0.0172 day[-1]) systems, the PFOA removal rate (0.0426 day[-1]) increased by 1.5 to 4.6 folds in the batch microbe-Fe[0] interaction system. Moreover, Pseudomonas accelerated the transformation of Fe[0] into Fe[3+], which profoundly impacted PFOA transport and fate. Model results demonstrated microbe-Fe[0] interaction improved retardation effect for PFOA in columns, with decreased dispersivity a (0.48 to 0.20 cm), increased reaction rate λ (0.15 to 0.22 h[-1]), distribution coefficient Kd (0.22 to 0.46 cm[3]∙g[-1]), and fraction f´(52 % to 60 %) of first-order kinetic sorption of PFOA in microbe-Fe[0] interaction column system. Moreover, intermediates analysis showed that microbe-Fe[0] interaction diversified PFOA reaction pathways. Three key metabolic pathways (ko00362, ko00626, ko00361), eight functional genes, and corresponding enzymes for PFOA degradation were identified. These findings provide insights into microbe-Fe[0] "neural network-type" interaction by unveiling biotransformation and mineral transformation mechanisms for efficient PFOA treatment.}, } @article {pmid38553666, year = {2024}, author = {Ma, ZS}, title = {Towards a unified medical microbiome ecology of the OMU for metagenomes and the OTU for microbes.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {137}, pmid = {38553666}, issn = {1471-2105}, abstract = {BACKGROUND: Metagenomic sequencing technologies offered unprecedented opportunities and also challenges to microbiology and microbial ecology particularly. The technology has revolutionized the studies of microbes and enabled the high-profile human microbiome and earth microbiome projects. The terminology-change from microbes to microbiomes signals that our capability to count and classify microbes (microbiomes) has achieved the same or similar level as we can for the biomes (macrobiomes) of plants and animals (macrobes). While the traditional investigations of macrobiomes have usually been conducted through naturalists' (Linnaeus & Darwin) naked eyes, and aerial and satellite images (remote-sensing), the large-scale investigations of microbiomes have been made possible by DNA-sequencing-based metagenomic technologies. Two major types of metagenomic sequencing technologies-amplicon sequencing and whole-genome (shotgun sequencing)-respectively generate two contrastingly different categories of metagenomic reads (data)-OTU (operational taxonomic unit) tables representing microorganisms and OMU (operational metagenomic unit), a new term coined in this article to represent various cluster units of metagenomic genes.

RESULTS: The ecological science of microbiomes based on the OTU representing microbes has been unified with the classic ecology of macrobes (macrobiomes), but the unification based on OMU representing metagenomes has been rather limited. In a previous series of studies, we have demonstrated the applications of several classic ecological theories (diversity, composition, heterogeneity, and biogeography) to the studies of metagenomes. Here I push the envelope for the unification of OTU and OMU again by demonstrating the applications of metacommunity assembly and ecological networks to the metagenomes of human gut microbiomes. Specifically, the neutral theory of biodiversity (Sloan's near neutral model), Ning et al.stochasticity framework, core-periphery network, high-salience skeleton network, special trio-motif, and positive-to-negative ratio are applied to analyze the OMU tables from whole-genome sequencing technologies, and demonstrated with seven human gut metagenome datasets from the human microbiome project.

CONCLUSIONS: All of the ecological theories demonstrated previously and in this article, including diversity, composition, heterogeneity, stochasticity, and complex network analyses, are equally applicable to OMU metagenomic analyses, just as to OTU analyses. Consequently, I strongly advocate the unification of OTU/OMU (microbiomes) with classic ecology of plants and animals (macrobiomes) in the context of medical ecology.}, } @article {pmid38553222, year = {2024}, author = {Hafeez, R and Guo, J and Ahmed, T and Jiang, H and Raza, M and Shahid, M and Ibrahim, E and Wang, Y and Wang, J and Yan, C and An, Q and White, JC and Li, B}, title = {Bio-formulated chitosan nanoparticles enhance disease resistance against rice blast by physiomorphic, transcriptional, and microbiome modulation of rice (Oryza sativa L.).}, journal = {Carbohydrate polymers}, volume = {334}, number = {}, pages = {122023}, doi = {10.1016/j.carbpol.2024.122023}, pmid = {38553222}, issn = {1879-1344}, abstract = {Rice blast disease (RBD) caused by Magnaporthe oryzae, threaten food security by cutting agricultural output. Nano agrochemicals are now perceived as sustainable, cost-effective alternatives to traditional pesticides. This study investigated bioformulation of moringa chitosan nanoparticles (M-CsNPs) and their mechanisms for suppressing RBD while minimizing toxic effects on the microenvironment. M-CsNPs, sized 46 nm with semi-spherical morphology, significantly suppressed pathogen growth, integrity, and colonization at 200 mg L[-1]in vitro. Greenhouse tests with foliar exposure to the same concentration resulted in a substantial 77.7 % reduction in RBD, enhancing antioxidant enzyme activity and plant health. Furthermore, M-CsNPs improved photosynthesis, gas exchange, and the nutritional profile of diseased rice plants. RNA-seq analysis highlighted upregulated defense-related genes in treated rice plants. Metagenomic study showcased reshaping of the rice microbiome, reducing Magnaporthe abundance by 93.5 %. Both healthy and diseased rice plants showed increased microbial diversity, particularly favoring specific beneficial species Thiobacillus, Nitrospira, Nocardioides, and Sphingomicrobium in the rhizosphere and Azonexus, Agarivorans, and Bradyrhizobium in the phyllosphere. This comprehensive study unravels the diverse mechanisms by which M-CsNPs interact with plants and pathogens, curbing M. oryzae damage, promoting plant growth, and modulating the rice microbiome. It underscores the significant potential for effective plant disease management.}, } @article {pmid38552880, year = {2024}, author = {Thiele, M and Villesen, IF and Niu, L and Johansen, S and Sulek, K and Nishijima, S and Van Espen, L and Keller, M and Israelsen, M and Suvitaival, T and de Zawadzki, A and Juel, HB and Brol, MJ and Stinson, SE and Huang, Y and Alvarez Silva, MC and Kuhn, M and Anastasiadou, E and Leeming, DJ and Karsdal, M and Matthijnssens, J and Arumugam, M and Dalgaard, LT and Legido-Quigley, C and Mann, M and Trebicka, J and Bork, P and Jensen, LJ and Hansen, T and Krag, A and , and , and , }, title = {Review: Opportunities and barriers for omics-based biomarker discovery in steatotic liver diseases.}, journal = {Journal of hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhep.2024.03.035}, pmid = {38552880}, issn = {1600-0641}, abstract = {The rising prevalence of liver diseases related to obesity and excessive use of alcohol is fuelling an increasing demand for accurate biomarkers aimed at community screening, diagnosis of steatohepatitis and significant fibrosis, monitoring, prognosis and prediction of treatment efficacy. Breakthroughs in omics methodologies and the power of bioinformatics have created an excellent opportunity to combine clinical needs with technological advancements. Omics technologies allow for advanced investigations into biological processes from the genes to transcription and regulation, to circulating protein, metabolite and lipid levels, as well as the microbiome including bacteria, viruses and fungi. We consequently find ourselves in a period of rapid progress in technology and bioinformatics that may allow for development of precision biomarkers for personalised medicine. However, there are important barriers to consider in omics biomarker discovery and validation, including the use of semi-quantitative measurements from untargeted platforms, which may exhibit high analytical, inter- and intra-individual variance. Standardising methods and the need to validate across diverse populations, presents a challenge, partly due to disease complexity and the dynamic nature of biomarker expression in different disease stages. Lack of validity causes lost opportunities when studies fail to provide the knowledge needed for regulatory approvals, all of which contributes to a delayed translation of these discoveries into clinical practice. While no omics-based biomarkers have matured to clinical implementation, the extent of data generated through omics-technologies holds the power of hypothesis-free discovery of a plethora of candidate biomarkers to be further validated. To explore the many opportunities of omics technologies, hepatologists need detailed knowledge of commonalities and differences between the various omics layers, and both the barriers to and advantages of these approaches.}, } @article {pmid38552390, year = {2024}, author = {Yang, H and Li, Q}, title = {Modifying humus-phosphorus-arsenic interactions in sludge composting: The strengthening of phosphorus availability and arsenic efflux detoxification mechanisms.}, journal = {Journal of hazardous materials}, volume = {470}, number = {}, pages = {134131}, doi = {10.1016/j.jhazmat.2024.134131}, pmid = {38552390}, issn = {1873-3336}, abstract = {Arsenic (As) in sewage sludge poses a significant threat to environmental and human health, which has attracted widespread attention. This study investigated the value of adding sodium percarbonate (SP) on phosphorus (P) availability and As efflux detoxification through HS-P-As interactions. Due to the unique structure of humus (HS) and the similar chemical properties of P and As, the conditions for HS-P-As interaction are provided. This study discussed the content, morphology and microbial communities of HS, P and As by using metagenomic and correlation analysis. The results showed that the humification index in the experiment group (SPC) was 2.34 times higher than that in the control group (CK). The available phosphorus (AP) content of SPC increased from 71.09 mg/kg to 126.14 mg/kg, and SPC was 1.11 times that of CK. The relative abundance of ACR3/ArsB increased. Pst, Actinomyces and Bacillus commonly participated in P and As conversion. The correlation analysis revealed that the humification process was enhanced, the AP was strengthened, and the As was efflux detoxified after SP amendment. All in all, this study elucidated the key mechanism of HS-P-As interaction and put forward a new strategy for sewage sludge resource utilization and detoxification.}, } @article {pmid38551914, year = {2024}, author = {Hochroth, A and Pfister, CA}, title = {Ammonification by kelp associated microbes increases ammonium availability.}, journal = {PloS one}, volume = {19}, number = {3}, pages = {e0296622}, pmid = {38551914}, issn = {1932-6203}, abstract = {Microbes contribute biologically available nitrogen to the ocean by fixing nitrogen gas from the atmosphere and by mineralizing organic nitrogen into bioavailable dissolved inorganic nitrogen (DIN). Although the large concentration of plants and algae in marine coastal environments provides ample habitat and reliable resources for microbial communities, the role of the microbiome in host-microbe nitrogen cycling remains poorly understood. We tested whether ammonification by epiphytic microbes increased water column ammonium and improved host access to nitrogen resources by converting organic nitrogen into inorganic nitrogen that is available for assimilation by hosts. When bull kelp (Nereocystis luetkeana) in the northeast Pacific was incubated with 15N labelled amino acid tracers, there was accumulation of 15N in kelp tissue, as well as accumulation of 15NH4 in seawater, all consistent with the conversion of dissolved organic nitrogen to ammonium. Metagenomic analysis of surface microbes from two populations of Nereocystis indicated relative similarity in the percentage of genes related to ammonification between the two locations, though the stressed kelp population that had lower tissue nitrogen and a sparser microbiome had greater ammonification rates. Microbial communities on coastal macrophytes may contribute to the nitrogen requirements of their hosts through metabolisms that make ammonium available.}, } @article {pmid38551904, year = {2024}, author = {Quarton, S and McGee, K and Cumley, N and Behruznia, M and Jeff, C and Belchamber, K and Cox, M and Thickett, D and Scott, A and Parekh, D and McNally, A and Sapey, E}, title = {Towards personalised anti-microbial and immune approaches to infections in acute care. Can real-time genomic-informed diagnosis of pathogens, and immune-focused therapies improve outcomes for patients? An observational, experimental study protocol.}, journal = {PloS one}, volume = {19}, number = {3}, pages = {e0298425}, pmid = {38551904}, issn = {1932-6203}, abstract = {INTRODUCTION: Infection causes a vast burden of disease, with significant mortality, morbidity and costs to health-care systems. However, identifying the pathogen causative infection can be challenging, resulting in high use of broad-spectrum antibiotics, much of which may be inappropriate. Novel metagenomic methods have potential to rapidly identify pathogens, however their clinical utility for many infections is currently unclear. Outcome from infection is also impacted by the effectiveness of immune responses, which can be impaired by age, co-morbidity and the infection itself. The aims of this study are twofold: To compare diversity of organisms identified and time-to-result using metagenomic methods versus traditional culture -based techniques, to explore the potential clinical role of metagenomic approaches to pathogen identification in a range of infections.To characterise the ex vivo function of immune cells from patients with acute infection, exploring host and pathogen-specific factors which may affect immune function and overall outcomes.

METHODS: This is a prospective observational study of patients with acute infection. Patients with symptoms suggestive of an acute infection will be recruited, and blood and bodily fluid relevant to the site of infection collected (for example, sputum and naso-oropharyngeal swabs for respiratory tract infections, or urine for a suspected urinary tract infection). Metagenomic analysis of samples will be compared to traditional microbiology, alongside the antimicrobials received. Blood and respiratory samples such as bronchoalveolar lavage will be used to isolate immune cells and interrogate immune cell function. Where possible, similar samples will be collected from matched participants without a suspected infection to determine the impact of infection on both microbiome and immune cell function.}, } @article {pmid38551595, year = {2024}, author = {Wissink, M and Glodowska, M and van der Kolk, MR and Jetten, MSM and Welte, CU}, title = {Probing Denitrifying Anaerobic Methane Oxidation via Antimicrobial Intervention: Implications for Innovative Wastewater Management.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c07197}, pmid = {38551595}, issn = {1520-5851}, abstract = {Methane emissions present a significant environmental challenge in both natural and engineered aquatic environments. Denitrifying anaerobic methane oxidation (N-DAMO) has the potential for application in wastewater treatment plants. However, our understanding of the N-DAMO process is primarily based on studies conducted on environmental samples or enrichment cultures using metagenomic approaches. To gain deeper insights into N-DAMO, we used antimicrobial compounds to study the function and physiology of 'Candidatus Methanoperedens nitroreducens' and 'Candidatus Methylomirabilis oxyfera' in N-DAMO enrichment cultures. We explored the effects of inhibitors and antibiotics and investigated the potential application of N-DAMO in wastewater contaminated with ammonium and heavy metals. Our results showed that 'Ca. M. nitroreducens' was susceptible to puromycin and 2-bromoethanesulfonate, while the novel methanogen inhibitor 3-nitrooxypropanol had no effect on N-DAMO. Furthermore, 'Ca. M. oxyfera' was shown to be susceptible to the particulate methane monooxygenase inhibitor 1,7-octadiyne and a bacteria-suppressing antibiotic cocktail. The N-DAMO activity was not affected by ammonium concentrations below 10 mM. Finally, the N-DAMO community appeared to be remarkably resistant to lead (Pb) but susceptible to nickel (Ni) and cadmium (Cd). This study provides insights into microbial functions in N-DAMO communities, facilitating further investigation of their application in methanogenic, nitrogen-polluted water systems.}, } @article {pmid38551467, year = {2024}, author = {Li, Y and Sun, X and Yang, R and Guo, L and Li, C and Wang, X and Li, B and Liu, H and Wang, Q and Soleimani, M and Ren, Y and Sun, W}, title = {Phototrophic Nitrogen Fixation, a Neglected Biogeochemical Process in Mine Tailings?.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c09460}, pmid = {38551467}, issn = {1520-5851}, abstract = {Biological nitrogen fixation (BNF) has important ecological significance in mine tailing by contributing to the initial accumulation of nitrogen. In addition to chemolithotrophic and heterotrophic BNF, light may also fuel BNF in oligotrophic mine tailings. However, knowledge regarding the occurrence and ecological significance of this biogeochemical process in mine tailings remains ambiguous. The current study observed phototrophic BNF in enrichment cultures established from three primary successional stages (i.e., original tailings, biological crusts, and pioneer plants) of tailings. Notably, phototrophic BNF in tailings may be more active at vegetation stages (i.e., biological crusts and pioneering plants) than in bare tailings. DNA-stable isotope probing identified Roseomonas species as potential aerobic anoxygenic phototrophs responsible for phototrophic BNF. Furthermore, metagenomic binning as well as genome mining revealed that Roseomonas spp. contained essential genes involved in nitrogen fixation, anoxygenic photosynthesis, and carbon fixation, suggesting their genetic potential to mediate phototrophic BNF. A causal inference framework equipped with the structural causal model suggested that the enrichment of putative phototrophic diazotrophic Roseomonas may contribute to an elevated total nitrogen content during primary succession in these mine tailings. Collectively, our findings suggest that phototrophic diazotrophs may play important roles in nutrient accumulation and hold the potential to facilitate ecological succession in tailings.}, } @article {pmid38551370, year = {2024}, author = {Demin, KA and Prazdnova, EV and Minkina, TM and Gorovtsov, AV}, title = {Sulfate-reducing bacteria unearthed: ecological functions of the diverse prokaryotic group in terrestrial environments.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0139023}, doi = {10.1128/aem.01390-23}, pmid = {38551370}, issn = {1098-5336}, abstract = {Sulfate-reducing prokaryotes (SRPs) are essential microorganisms that play crucial roles in various ecological processes. Even though SRPs have been studied for over a century, there are still gaps in our understanding of their biology. In the past two decades, a significant amount of data on SRP ecology has been accumulated. This review aims to consolidate that information, focusing on SRPs in soils, their relation to the rare biosphere, uncultured sulfate reducers, and their interactions with other organisms in terrestrial ecosystems. SRPs in soils form part of the rare biosphere and contribute to various processes as a low-density population. The data reveal a diverse range of sulfate-reducing taxa intricately involved in terrestrial carbon and sulfur cycles. While some taxa like Desulfitobacterium and Desulfosporosinus are well studied, others are more enigmatic. For example, members of the Acidobacteriota phylum appear to hold significant importance for the terrestrial sulfur cycle. Many aspects of SRP ecology remain mysterious, including sulfate reduction in different bacterial phyla, interactions with bacteria and fungi in soils, and the existence of soil sulfate-reducing archaea. Utilizing metagenomic, metatranscriptomic, and culture-dependent approaches will help uncover the diversity, functional potential, and adaptations of SRPs in the global environment.}, } @article {pmid38550938, year = {2023}, author = {Aryal, S and Manandhar, I and Mei, X and Yeoh, BS and Tummala, R and Saha, P and Osman, I and Zubcevic, J and Durgan, DJ and Vijay-Kumar, M and Joe, B}, title = {Combating hypertension beyond genome-wide association studies: Microbiome and artificial intelligence as opportunities for precision medicine.}, journal = {Cambridge prisms. Precision medicine}, volume = {1}, number = {}, pages = {e26}, doi = {10.1017/pcm.2023.13}, pmid = {38550938}, issn = {2752-6143}, abstract = {The single largest contributor to human mortality is cardiovascular disease, the top risk factor for which is hypertension (HTN). The last two decades have placed much emphasis on the identification of genetic factors contributing to HTN. As a result, over 1,500 genetic alleles have been associated with human HTN. Mapping studies using genetic models of HTN have yielded hundreds of blood pressure (BP) loci but their individual effects on BP are minor, which limits opportunities to target them in the clinic. The value of collecting genome-wide association data is evident in ongoing research, which is beginning to utilize these data at individual-level genetic disparities combined with artificial intelligence (AI) strategies to develop a polygenic risk score (PRS) for the prediction of HTN. However, PRS alone may or may not be sufficient to account for the incidence and progression of HTN because genetics is responsible for <30% of the risk factors influencing the etiology of HTN pathogenesis. Therefore, integrating data from other nongenetic factors influencing BP regulation will be important to enhance the power of PRS. One such factor is the composition of gut microbiota, which constitute a more recently discovered important contributor to HTN. Studies to-date have clearly demonstrated that the transition from normal BP homeostasis to a state of elevated BP is linked to compositional changes in gut microbiota and its interaction with the host. Here, we first document evidence from studies on gut dysbiosis in animal models and patients with HTN followed by a discussion on the prospects of using microbiota data to develop a metagenomic risk score (MRS) for HTN to be combined with PRS and a clinical risk score (CRS). Finally, we propose that integrating AI to learn from the combined PRS, MRS and CRS may further enhance predictive power for the susceptibility and progression of HTN.}, } @article {pmid38550858, year = {2024}, author = {Zhou, S and Wang, G and Han, Q and Zhang, J and Dang, H and Ning, H and Gao, Y and Sun, J}, title = {Long-term saline water irrigation affected soil carbon and nitrogen cycling functional profiles in the cotton field.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1310387}, doi = {10.3389/fmicb.2024.1310387}, pmid = {38550858}, issn = {1664-302X}, abstract = {Saline water irrigation (SWI) plays an important role in alleviating water resource shortages. At the same time, the salt input of irrigation water affects soil microorganisms which participate in various ecological processes of terrestrial ecosystems. However, the responses of soil microbial functional potential to long-term SWI remains unclear. Therefore, Metagenomics method was utilized in cotton fields under long-term SWI to reveal the microbial functional profiles associated with soil carbon and nitrogen cycles. Results indicated that SWI impacted the microbial functional profiles of soil carbon and nitrogen cycles in the cotton fields significantly. Especially, irrigation water salinity inhibited the relative abundances of sacC and vanB, which are soil carbon degradation genes. SWI also affected the functional gene abundance of nitrogen degradation, dissimilatory nitrate reduction, and nitrification. Moreover, SWI significantly increased the abundance of Candidatus_Cloacimonetes in both carbon and nitrogen cycles. In the discussion, we used person analysis found that soil salinity, pH, and ammonium nitrogen were important factors affecting the abundance of functional genes and microbial taxa. Overall, this study indicated that long-term SWI significantly influenced specific microbial functional genes and taxa abundance, which may lead to predictable outcomes for soil carbon and nitrogen cycling, and is of great importance in exploring the impact of SWI on soil environments.}, } @article {pmid38550310, year = {2024}, author = {Ni, L and Wu, Z and Huang, J}, title = {Detection of pulmonary actinomycosis by metagenomic next-generation sequencing in a cancer patient receiving maintenance olaparib: A review and case report.}, journal = {Respiratory medicine case reports}, volume = {48}, number = {}, pages = {102007}, doi = {10.1016/j.rmcr.2024.102007}, pmid = {38550310}, issn = {2213-0071}, abstract = {A 52-year-old female patient receiving olaparib maintenance treatment was admitted to hospital with a low fever and chest tightness. A CT scan of the patient's chest showed diffuse ground glass shadow or miliary nodular shadow in the bilateral lungs. Her inflammatory biomarkers were almost normal, except the slightly elevated C-reactive protein. Moreover, lymphocytes count obviously decreased. Empirical treatment did not relieve her symptoms, while traditional testing developed negative results. The results of metagenomic next-generation sequencing (mNGS) revealed the presence of a potential pathogen, Actinomyces odontolyticus (A. odontolyticus), in bronchoalveolar lavage fluid (BLAF). Once large-dosed penicillin G was administered, the fever returned to normal and chest tightness disappeared. Reexamination of chest CT revealed that the pulmonary lesions was almost absorbed. Our case demonstrated that mNGS is a novel approach to identify pathogens sensitively and accurately, especially for uncommon and atypical infection.}, } @article {pmid38549423, year = {2024}, author = {Peng, Y and Zhao, Q and Chen, S and Li, Z and An, D and Zhang, X}, title = {Potential contributions of keystone species to intestinal ecosystem in patients with Crohn's disease.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxae086}, pmid = {38549423}, issn = {1365-2672}, abstract = {AIMS: Ravelling the central but poorly understood issue that potential contributions of keystone species to intestinal ecosystem functioning of patients with certain life-altering diseases including Crohn's disease (CD).

METHODS AND RESULTS: In this study, a combination of 16S rRNA gene amplicon sequencing and amplicon-oriented metagenomic profiling was applied to gain insights into the shifts in bacterial community composition at different stages of CD course, and explore the functional roles of identified keystone species in intestinal microecosystem. Our results showed significant alterations in structure and composition of gut microbiota between CD patients and healthy control (P < 0.05), but was no difference at active and remission stages. Whole-community-based comprehensive analyses were employed to identify the differential species such as Escherichia coli, Anaerostipes hadrus, and Eubacterium hallii in CD patients, with healthy populations as the control. Metagenome-wide functional analyses further revealed that the relative abundance of specialized metabolism-related genes such as cynS, frdB, serA and gltB from these bacterial species in CD group was significantly different (P < 0.05) from that in healthy control, and highlighted the potential roles of the keystone species in regulating the accumulation of important metabolites such as succinate, formate, ammonia, L-glutamate, and L-serine, which might have an effect on homeostasis of intestinal ecosystem.

CONCLUSIONS: The findings identify several potential keystone species that may influence the intestinal microecosystem functioning of CD patients and provide some reference for future CD treatment.}, } @article {pmid38549118, year = {2024}, author = {Rosch, MEG and Rehner, J and Schmartz, GP and Manier, SK and Becker, U and Müller, R and Meyer, MR and Keller, A and Becker, SL and Keller, V}, title = {Time series of chicken stool metagenomics and egg metabolomics in changing production systems: preliminary insights from a proof-of-concept.}, journal = {One health outlook}, volume = {6}, number = {1}, pages = {4}, pmid = {38549118}, issn = {2524-4655}, abstract = {BACKGROUND: Different production systems of livestock animals influence various factors, including the gut microbiota.

METHODS: We investigated whether changing the conditions from barns to free-range chicken farming impacts the microbiome over the course of three weeks. We compared the stool microbiota of chicken from industrial barns after introducing them either in community or separately to a free-range environment.

RESULTS: Over the six time points, 12 taxa-mostly lactobacilli-changed significantly. As expected, the former barn chicken cohort carries more resistances to common antibiotics. These, however, remained positive over the observed period. At the end of the study, we collected eggs and compared metabolomic profiles of the egg white and yolk to profiles of eggs from commercial suppliers. Here, we observed significant differences between commercial and fresh collected eggs as well as differences between the former barn chicken and free-range chicken.

CONCLUSION: Our data indicate that the gut microbiota can undergo alterations over time in response to changes in production systems. These changes subsequently exert an influence on the metabolites found in the eggs. The preliminary results of our proof-of-concept study motivate larger scale observations with more individual chicken and longer observation periods.}, } @article {pmid38549112, year = {2024}, author = {Edwin, NR and Fitzpatrick, AH and Brennan, F and Abram, F and O'Sullivan, O}, title = {An in-depth evaluation of metagenomic classifiers for soil microbiomes.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {19}, pmid = {38549112}, issn = {2524-6372}, support = {SFI/16/RC/3835//VistaMilk/ ; Ref: 2020019//Teagasc Walsh Scholarship Programme/ ; }, abstract = {BACKGROUND: Recent endeavours in metagenomics, exemplified by projects such as the human microbiome project and TARA Oceans, have illuminated the complexities of microbial biomes. A robust bioinformatic pipeline and meticulous evaluation of their methodology have contributed to the success of these projects. The soil environment, however, with its unique challenges, requires a specialized methodological exploration to maximize microbial insights. A notable limitation in soil microbiome studies is the dearth of soil-specific reference databases available to classifiers that emulate the complexity of soil communities. There is also a lack of in-vitro mock communities derived from soil strains that can be assessed for taxonomic classification accuracy.

RESULTS: In this study, we generated a custom in-silico mock community containing microbial genomes commonly observed in the soil microbiome. Using this mock community, we simulated shotgun sequencing data to evaluate the performance of three leading metagenomic classifiers: Kraken2 (supplemented with Bracken, using a custom database derived from GTDB-TK genomes along with its own default database), Kaiju, and MetaPhlAn, utilizing their respective default databases for a robust analysis. Our results highlight the importance of optimizing taxonomic classification parameters, database selection, as well as analysing trimmed reads and contigs. Our study showed that classifiers tailored to the specific taxa present in our samples led to fewer errors compared to broader databases including microbial eukaryotes, protozoa, or human genomes, highlighting the effectiveness of targeted taxonomic classification. Notably, an optimal classifier performance was achieved when applying a relative abundance threshold of 0.001% or 0.005%. The Kraken2 supplemented with bracken, with a custom database demonstrated superior precision, sensitivity, F1 score, and overall sequence classification. Using a custom database, this classifier classified 99% of in-silico reads and 58% of real-world soil shotgun reads, with the latter identifying previously overlooked phyla using a custom database.

CONCLUSION: This study underscores the potential advantages of in-silico methodological optimization in metagenomic analyses, especially when deciphering the complexities of soil microbiomes. We demonstrate that the choice of classifier and database significantly impacts microbial taxonomic profiling. Our findings suggest that employing Kraken2 with Bracken, coupled with a custom database of GTDB-TK genomes and fungal genomes at a relative abundance threshold of 0.001% provides optimal accuracy in soil shotgun metagenome analysis.}, } @article {pmid38548676, year = {2024}, author = {Jiao, B and Ouyang, Z and Liu, Q and Xu, T and Wan, M and Ma, G and Zhou, L and Guo, J and Wang, J and Tang, B and Zhao, Z and Shen, L}, title = {Integrated analysis of gut metabolome, microbiome, and brain function reveal the role of gut-brain axis in longevity.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2331434}, doi = {10.1080/19490976.2024.2331434}, pmid = {38548676}, issn = {1949-0984}, abstract = {The role of microbiota-gut-brain axis in modulating longevity remains undetermined. Here, we performed a multiomics analysis of gut metagenomics, gut metabolomics, and brain functional near-infrared spectroscopy (fNIRS) in a cohort of 164 participants, including 83 nonagenarians (NAs) and 81 non-nonagenarians (NNAs) matched with their spouses and offspring. We found that 438 metabolites were significantly different between the two groups; among them, neuroactive compounds and anti-inflammatory substances were enriched in NAs. In addition, increased levels of neuroactive metabolites in NAs were significantly associated with NA-enriched species that had three corresponding biosynthetic potentials: Enterocloster asparagiformis, Hungatella hathewayi and Oxalobacter formigenes. Further analysis showed that the altered gut microbes and metabolites were linked to the enhanced brain connectivity in NAs, including the left dorsolateral prefrontal cortex (DLPFC)-left premotor cortex (PMC), left DLPFC-right primary motor area (M1), and right inferior frontal gyrus (IFG)-right M1. Finally, we found that neuroactive metabolites, altered microbe and enhanced brain connectivity contributed to the cognitive preservation in NAs. Our findings provide a comprehensive understanding of the microbiota-gut-brain axis in a long-lived population and insights into the establishment of a microbiome and metabolite homeostasis that can benefit human longevity and cognition by enhancing functional brain connectivity.}, } @article {pmid38548661, year = {2024}, author = {Aya, JV and Vega, LC and Muñoz, E and Muñoz, M and López, DF and Guzmán, MP and Martínez, DF and Cruz-Saavedra, LB and Castillo, AK and Quintero, KJ and Gónzalez Soltero, RR and Cala, MP and Ramírez, JD}, title = {Divergent Gut Microbiota: Archaeal and Bacterial Signatures Unveil Unique Patterns in Colombian Cyclists Compared to Weightlifters and Non-Athletes.}, journal = {Advanced biology}, volume = {}, number = {}, pages = {e2400069}, doi = {10.1002/adbi.202400069}, pmid = {38548661}, issn = {2701-0198}, support = {//Research and Innovation Directorate of Universidad del Rosario/ ; //Universidad del Rosario/ ; //Universidad Europea de Madrid/ ; }, abstract = {Engagement in physical activity, across various sports, promotes a diverse microbiota in active individuals. This study examines the gut microbiota of Colombian athletes, specifically weightlifters (n = 16) and road cyclists (n = 13), compared to non-athletes (n = 15). Using Kruskal-Wallis tests, the physical activity level of a group of non-athletic individuals and the sports experience of a group of professional athletes is analyzed. The median age of participants is 24 years, comprising 25 men and 19 women. The microbiota is collected using fecal samples. Participants provided these samples during their pre-competitive stage, specifically during the concentration phase occurring two weeks prior to national competitions. This timing is chosen to capture the microbial composition during a period of heightened physical preparation. Questionnaire responses and microbial composition assessments identify disparities among groups. Microbial composition analysis explores core microbiome, abundance, and taxonomy using Pavian, MicrobiomeAnalyst 2.0, and GraPhlAn. ANCOM-BC2 reveals differentially abundant species. Road cyclists exhibit decreased Bacteria and increased Archaea abundance. Phylum-level variations included Planctomycetes, Acidobacteria, and Proteobacteria, while Bacteroidetes prevailed. Key families influencing gut microbiota are Bacteroidaceae, Muribaculaceae, and Selenomonadaceae. Weightlifters exhibit unique viral and archaeal community connections, while cyclists showed specialized microbial interplay influenced by endurance exercise. Correlation network analysis emphasizes distinctive microbial interactions within athlete groups, shedding light on the impact of physical activities on gut microbiota and athlete health.}, } @article {pmid38548397, year = {2024}, author = {Lin, WP and Mu, X and Chen, SH and He, CJ and Li, HH and Sun, CW and Bian, HN and Lai, W and Huang, ZF}, title = {[Clinical characteristics of 11 patients with Vibrio vulnificus infection and the establishment of a rapid diagnosis procedure for this disease].}, journal = {Zhonghua shao shang yu chuang mian xiu fu za zhi}, volume = {40}, number = {3}, pages = {266-272}, doi = {10.3760/cma.j.cn501225-20230803-00036}, pmid = {38548397}, issn = {2097-1109}, support = {2020B151520088//Key Project of Guangdong Province Basic and Applied Basic Research Regional Joint Fund/ ; }, abstract = {Objective: To analyze the clinical characteristics of patients with Vibrio vulnificus infection, share diagnosis and treatment experience, and establish a rapid diagnosis procedure for this disease. Methods: This study was a retrospective case series study. From January 2009 to November 2022, 11 patients with Vibrio vulnificus infection who met the inclusion criteria were admitted to the Department of Burns and Wound Repair of Guangdong Provincial People's Hospital Affiliated to Southern Medical University. The gender, age, time of onset of illness, time of admission, time of diagnosis, route of infection, underlying diseases, affected limbs, clinical manifestations and signs on admission, white blood cell count, hemoglobin, platelet count, C-reactive protein (CRP), alanine transaminase (ALT), aspartate transaminase (AST), creatinine, procalcitonin, albumin, N-terminal pro-B-type natriuretic peptide (NT-proBNP), and blood sodium levels on admission, culture results and metagenomic next-generation sequencing (mNGS) results of pathogenic bacteria and the Vibrio vulnificus drug susceptibility test results during hospitalization, treatment methods, length of hospital stay, and outcomes of all patients were recorded. Comparative analysis was conducted on the admission time and diagnosis time of patients with and without a history of exposure to seawater/marine products, as well as the fatality ratio and amputation of limbs/digits ratio of patients with and without early adequate antibiotic treatment. For the survived patients with hand involvement, the hand function was assessed using Brunnstrom staging at the last follow-up. Based on patients' clinical characteristics and treatment conditions, a rapid diagnosis procedure for Vibrio vulnificus infection was established. Results: There were 7 males and 4 females among the patients, aged (56±17) years. Most of the patients developed symptoms in summer and autumn. The admission time was 3.00 (1.00, 4.00) d after the onset of illness, and the diagnosis time was 4.00 (2.00, 8.00) d after the onset of illness. There were 7 and 4 patients with and without a history of contact with seawater/marine products, respectively, and the admission time of these two types of patients was similar (P>0.05). The diagnosis time of patients with a history of contact with seawater/marine products was 2.00 (2.00, 5.00) d after the onset of illness, which was significantly shorter than 9.00 (4.25, 13.00) d after the onset of illness for patients without a history of contact with seawater/marine products (Z=-2.01, P<0.05). Totally 10 patients had underlying diseases. The affected limbs were right-hand in 8 cases, left-hand in 1 case, and lower limb in 2 cases. On admission, a total of 9 patients had fever; 11 patients had pain at the infected site, and redness and swelling of the affected limb, and 9 patients each had ecchymosis/necrosis and blisters/blood blisters; 6 patients suffered from shock, and 2 patients developed multiple organ dysfunction syndrome. On admission, there were 8 patients with abnormal white blood cell count, hemoglobin, and albumin levels, 10 patients with abnormal CRP, procalcitonin, and NT-proBNP levels, 5 patients with abnormal creatinine and blood sodium levels, and fewer patients with abnormal platelet count, ALT, and AST levels. During hospitalization, 4 of the 11 wound tissue/exudation samples had positive pathogenic bacterial culture results, and the result reporting time was 5.00 (5.00, 5.00) d; 4 of the 9 blood specimens had positive pathogenic bacterial culture results, and the result reporting time was 3.50 (1.25, 5.00) d; the mNGS results of 7 wound tissue/exudation or blood samples were all positive, and the result reporting time was 1.00 (1.00, 2.00) d. The three strains of Vibrio vulnificus detected were sensitive to 10 commonly used clinical antibiotics, including ciprofloxacin, levofloxacin, and amikacin, etc. A total of 10 patients received surgical treatment, 4 of whom had amputation of limbs/digits; all patients received anti-infection treatment. The length of hospital stay of 11 patients was (26±11) d, of whom 9 patients were cured and 2 patients died. Compared with that of the 6 patients who did not receive early adequate antibiotic treatment, the 5 patients who received early adequate antibiotic treatment had no significant changes in the fatality ratio or amputation of limbs/digits ratio (P>0.05). In 3 months to 2 years after surgery, the hand function of 8 patients was assessed, with results showing 4 cases of disabled hands, 2 cases of incompletely disabled hands, and 2 cases of recovered hands. When a patient had clinical symptoms of limb redness and swelling and a history of contact with seawater/marine products or a pre-examination triage RiCH score of Vibrio vulnificus sepsis ≥1, the etiological testing should be initiated immediately to quickly diagnose Vibrio vulnificus infection. Conclusions: Vibrio vulnificus infection occurs most frequently in summer and autumn, with clinical manifestations and laboratory test results showing obvious infection characteristics, and may be accompanied by damage to multiple organ functions. Both the fatality and disability ratios are high and have a great impact on the function of the affected limbs. Early diagnosis is difficult and treatment is easily delayed, but mNGS could facilitate rapid detection. For patients with red and swollen limbs accompanied by a history of contact with seawater/marine products or with a pre-examination triage RiCH score of Vibrio vulnificus sepsis ≥1, the etiological testing should be initiated immediately to quickly diagnose Vibrio vulnificus infection.}, } @article {pmid38548243, year = {2024}, author = {Chen, W and Liu, G and Cui, L and Tian, F and Zhang, J and Zhao, J and Lv, Y and Du, J and Huan, X and Wu, Y and Zhang, Y}, title = {Evaluation of metagenomic and pathogen-targeted next-generation sequencing for diagnosis of meningitis and encephalitis in adults: A multicenter prospective observational cohort study in China.}, journal = {The Journal of infection}, volume = {}, number = {}, pages = {106143}, doi = {10.1016/j.jinf.2024.106143}, pmid = {38548243}, issn = {1532-2742}, abstract = {BACKGROUND: Next-generation sequencing (NGS) might aid in identification of causal pathogens. However, the optimal approaches applied to cerebrospinal fluid (CSF) for detection are unclear, and studies evaluating application of different NGS workflows for diagnosis of intracranial infections are limited.

METHODS: In this multicenter, prospective observational cohort study, we described the diagnostic efficacy of pathogen-targeted NGS (ptNGS) and metagenomic NGS (mNGS) compared to that of composite microbiologic assays, for infectious meningitis/encephalitis (M/E).

RESULTS: In total, 152 patients diagnosed with clinically suspected M/E at four tertiary hospitals were enrolled; ptNGS and mNGS were used in parallel for pathogen detection in CSF. Among the 89 patients who were diagnosed with definite infectious M/E, 57 and 39 patients had causal microbial detection via ptNGS and mNGS, respectively. The overall accuracy of ptNGS was 65.1%, with a positive percent agreement (PPA) of 64% and a negative percent agreement (NPA) of 66.7%; and the overall accuracy of mNGS was 47.4%, with a PPA of 43.8% and an NPA of 52.4% after discrepancy analysis. There was a significant difference in the detection efficiency between these two methods both for PPA (sensitivity) and overall accuracy for pathogen detection (P<0.05).

CONCLUSIONS: NGS testings have provided new information in addition to conventional microbiologic tests. ptNGS seems to have superior performance over mNGS for common causative pathogen detection in CSF for infectious M/E.}, } @article {pmid38547976, year = {2024}, author = {Jia, WL and Zhang, M and Gao, FZ and Bai, H and He, LX and He, LY and Liu, T and Han, Y and Ying, GG}, title = {Antibiotic resistome in landfill leachate and impact on groundwater.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {171991}, doi = {10.1016/j.scitotenv.2024.171991}, pmid = {38547976}, issn = {1879-1026}, abstract = {Landfill leachate is a hotspot in antibiotic resistance development. However, little is known about antibiotic resistome and host pathogens in leachate and their effects on surrounding groundwater. Here, metagenomic sequencing was used to explore profiles, host bacteria, environmental risks and influencing factors of antibiotic resistome in raw and treated leachate and surrounding groundwater of three landfills. Results showed detection of a total of 324 antibiotic resistance genes (ARGs). The ARGs conferring resistance to multidrug (8.8 %-25.7 %), aminoglycoside (13.1 %-39.2 %), sulfonamide (10.0 %-20.9 %), tetracycline (5.7 %-34.4 %) and macrolide-lincosamide-streptogramin (MLS, 5.3 %-29.5 %) were dominant in raw leachate, while multidrug resistance genes were the major ARGs in treated leachate (64.1 %-83.0 %) and groundwater (28.7 %-76.6 %). Source tracking analysis suggests non-negligible influence of leachate on the ARGs in groundwater. The pathogens including Acinetobacter pittii, Pseudomonas stutzeri and P. alcaligenes were the major ARG-carrying hosts. Variance partitioning analysis indicates that the microbial community, abiotic variables and their interaction contributed most to the antibiotic resistance development. Our results shed light on the dissemination and driving mechanisms of ARGs from leachate to the groundwater, indicating that a comprehensive risk assessment and efficient treatment approaches are needed to deal with ARGs in landfill leachate and nearby groundwater. ENVIRONMENTAL IMPLICATIONS: Antibiotic resistance genes are found abundant in the landfill sites, and these genes could be disseminated into groundwater via leaching of wastewater and infiltration of leachate. This results in deterioration of groundwater quality and human health risks posed by these ARGs and related pathogens. Thus measures should be taken to minimize potential negative impacts of landfills on the surrounding environment.}, } @article {pmid38547405, year = {2024}, author = {Li, J and Wang, Z and Fan, X and Yao, R and Zhang, G and Fan, R and Wang, Z}, title = {Rapid multiple protein sequence search by parallel and heterogeneous computation.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btae151}, pmid = {38547405}, issn = {1367-4811}, abstract = {MOTIVATION: Protein sequence database search and multiple sequence alignment (MSA) generation is a fundamental task in many bioinformatics analyses. As the data volume of sequences continues to grow rapidly, there is an increasing need for efficient and scalable multiple sequence query algorithms for super-large databases without expensive time and computational costs.

RESULTS: We introduce Chorus, a novel protein sequence query system that leverages parallel model and heterogeneous computation architecture to enable users to query thousands of protein sequences concurrently against large protein databases on a desktop workstation. Chorus achieves over 100x speedup over BLASTP without sacrificing sensitivity. We demonstrate the utility of Chorus through a case study of analyzing a ∼1.5TB large-scale metagenomic datasets for novel CRISPR-Cas protein discovery within 30 minutes.

AVAILABILITY: Chorus is open-source and its code repository is available at https://github.com/Bio-Acc/Chorus.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid38547246, year = {2024}, author = {Wang, Z and Peters, BA and Yu, B and Grove, ML and Wang, T and Xue, X and Thyagarajan, B and Daviglus, ML and Boerwinkle, E and Hu, G and Mossavar-Rahmani, Y and Isasi, CR and Knight, R and Burk, RD and Kaplan, RC and Qi, Q}, title = {Gut Microbiota and Blood Metabolites Related to Fiber Intake and Type 2 Diabetes.}, journal = {Circulation research}, volume = {134}, number = {7}, pages = {842-854}, doi = {10.1161/CIRCRESAHA.123.323634}, pmid = {38547246}, issn = {1524-4571}, abstract = {BACKGROUND: Consistent evidence suggests diabetes-protective effects of dietary fiber intake. However, the underlying mechanisms, particularly the role of gut microbiota and host circulating metabolites, are not fully understood. We aimed to investigate gut microbiota and circulating metabolites associated with dietary fiber intake and their relationships with type 2 diabetes (T2D).

METHODS: This study included up to 11 394 participants from the HCHS/SOL (Hispanic Community Health Study/Study of Latinos). Diet was assessed with two 24-hour dietary recalls at baseline. We examined associations of dietary fiber intake with gut microbiome measured by shotgun metagenomics (350 species/85 genera and 1958 enzymes; n=2992 at visit 2), serum metabolome measured by untargeted metabolomics (624 metabolites; n=6198 at baseline), and associations between fiber-related gut bacteria and metabolites (n=804 at visit 2). We examined prospective associations of serum microbial-associated metabolites (n=3579 at baseline) with incident T2D over 6 years.

RESULTS: We identified multiple bacterial genera, species, and related enzymes associated with fiber intake. Several bacteria (eg, Butyrivibrio, Faecalibacterium) and enzymes involved in fiber degradation (eg, xylanase EC3.2.1.156) were positively associated with fiber intake, inversely associated with prevalent T2D, and favorably associated with T2D-related metabolic traits. We identified 159 metabolites associated with fiber intake, 47 of which were associated with incident T2D. We identified 18 of these 47 metabolites associated with the identified fiber-related bacteria, including several microbial metabolites (eg, indolepropionate and 3-phenylpropionate) inversely associated with the risk of T2D. Both Butyrivibrio and Faecalibacterium were associated with these favorable metabolites. The associations of fiber-related bacteria, especially Faecalibacterium and Butyrivibrio, with T2D were attenuated after further adjustment for these microbial metabolites.

CONCLUSIONS: Among United States Hispanics/Latinos, dietary fiber intake was associated with favorable profiles of gut microbiota and circulating metabolites for T2D. These findings advance our understanding of the role of gut microbiota and microbial metabolites in the relationship between diet and T2D.}, } @article {pmid38546675, year = {2024}, author = {Pötgens, SA and Havelange, V and Lecop, S and Li, F and Neyrinck, AM and Bindels, F and Neveux, N and Demoulin, JB and Moors, I and Kerre, T and Maertens, J and Walter, J and Schoemans, H and Delzenne, NM and Bindels, LB}, title = {Gut microbiome alterations at acute myeloid leukemia diagnosis are associated with muscle weakness and anorexia.}, journal = {Haematologica}, volume = {}, number = {}, pages = {}, doi = {10.3324/haematol.2023.284138}, pmid = {38546675}, issn = {1592-8721}, abstract = {The gut microbiota makes critical contributions to host homeostasis, and its role in the treatment of acute myeloid leukaemia (AML) has attracted attention. We investigated whether the gut microbiome is affected by AML, and whether such changes are associated with cachectic hallmarks. Biological samples and clinical data were collected from 30 antibiotic-free AML patients at diagnosis and matched volunteers (1:1) in a multicenter cross-sectional prospective study. The composition and functional potential of the faecal microbiota were analyzed using shotgun metagenomics. Faecal, blood, and urine metabolomics analyses were performed. AML patients displayed muscle weakness, anorexia, signs of altered gut function, and glycaemic disorders. The composition of the faecal microbiota differed between patients with AML and control subjects, with an increase in oral bacteria. Alterations in bacterial functions and faecal metabolome support an altered redox status in the gut microbiota, which may contribute to the altered redox status observed in patients with AML. Eubacterium eligens, reduced 3-fold in AML patients, was strongly correlated with muscle strength and citrulline, a marker of enterocyte mass and function. Blautia and Parabacteroides, increased in patients with AML, were correlated with anorexia. Several bacterial taxa and metabolites (e.g. Blautia, Prevotella, phenylacetate, and hippurate) previously associated with glycaemic disorders were altered. Our work revealed important perturbations in the gut microbiome of AML patients at diagnosis, which are associated with muscle strength, altered redox status, and anorexia. These findings pave the way for future mechanistic work to explore the function and therapeutic potential of the bacteria identified in this study.}, } @article {pmid38546528, year = {2024}, author = {Wang, Z and Zhang, J and Yuan, J and Min, F and Gao, J and Liu, W and Huang, M and Wu, Y and Chen, H}, title = {Oral administration of egg ovalbumin allergen induces dysregulation of tryptophan metabolism in sensitized BALB/c mice.}, journal = {Food & function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d3fo05300h}, pmid = {38546528}, issn = {2042-650X}, abstract = {Food allergy (FA), triggered by specific dietary allergens, has emerged as a substantial global concern for food safety and public health. While studies have elucidated changes in immune cells and cytokines associated with allergen exposure, a comprehensive analysis of the host's metabolic features and the interaction between metabolites and the gut microbiota has not been conducted. In this study, egg allergen ovalbumin (OVA) was administered by the oral route to sensitized BALB/c mice to faithfully replicate key aspects of human FA, including severe allergic diarrhea, mast cell infiltration, and elevated levels of serum IgE, mMCPT-1, and Th2 cell hallmark cytokines (such as IL-4, IL-5, and IL-13). Furthermore, the untargeted and targeted metabolomic analyses indicated that FA in mice precipitated a substantial decrease in the tryptophan metabolites indole-3-acrylic acid (IA) and indole-3-lactic acid (ILA). The integration of shotgun metagenome and metabolome data further unveiled that the dysregulation of indole metabolism is related to a decline in the abundance of beneficial bacteria such as Lactobacillus and Bifidobacterium. Additionally, disruption of the tryptophan indole derivative pathway compromises the maintenance of intestinal mucosal function through the AHR signaling pathway, manifested by decreased expression of Reg3g and IL22. Taken together, this study demonstrated that the anaphylaxis triggered by oral ingestion of food allergens can lead to disruptions in tryptophan metabolism, consequently impairing intestinal immune homeostasis.}, } @article {pmid38545984, year = {2024}, author = {Liu, W and Liu, G and Zhang, R and Zheng, L and Lu, Z and Zhang, X and Wang, S and Shen, C and Shi, J and Xu, Z and Chai, L}, title = {[Metagenomics unveils the differences in the functions of microbial community of medium-temperature Daqu before and after maturation].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {40}, number = {3}, pages = {877-894}, doi = {10.13345/j.cjb.230340}, pmid = {38545984}, issn = {1872-2075}, abstract = {Daqu is the saccharifying, fermenting, and aroma-producing agent used in Baijiu brewing, and its maturation is crucial for obtaining high-quality Daqu. Previous studies have explored the microbial community composition and diversity before and after maturation. However, little is known about the changes in the functions of microbial community. In this study, based on the analyses of enzyme activities and volatile compounds of medium-temperature Daqu before and after maturation, metagenomics was used to analyze the differences in the composition of microbial community and the potential functions, with the aim to explore the microorganisms involved in changes in enzyme activities and important volatiles. The results showed that the moisture (P≤0.05), starch content, liquefying activity, saccharifying activity (P≤0.05), and fermentative activity decreased, while the acidity and esterifying activity (P≤0.05) increased after Daqu maturation. In the meantime, the composition of volatile compounds changed significantly (P=0.001), with significant decreases in the contents of aromatic alcohols and esters as well as significant increases in the contents of pyrazines, ketones, and higher fatty alcohols. The relative abundances of Mucorales (34.8%-23.0%) and Eurotiales (34.3%-20.1%) decreased in matured Daqu, and functional predictions showed these changes decreased the gene abundances of α-amylase, α-glucosidase, alcohol dehydrogenase, and alcohol dehydrogenase (NADP[+]) (P > 0.05), resulting in lower levels of liquefying activity (P > 0.05), saccharifying activity (P≤0.05), fermentative activity (P > 0.05), as well as aromatic alcohols such as phenylethyl alcohol (P≤0.05). In addition, higher relative abundances of Saccharomycetales (2.9%-16.6%), Lactobacillales (14.9%-23.6%), and Bacillales (0.8%-3.8%) were observed after maturation, and they were conducive to improving the gene abundances of alcohol O-acetyltransferase, carboxylesterase, acetolactate decarboxylase, (R)-acetoin dehydrogenase, and (S)-acetoin dehydrogenase (P≤0.05), resulting in significantly higher levels of esterifying activity and pyrazines (P≤0.05). The microorganisms involved in the changes in enzyme activities and important volatiles before and after Daqu maturation were studied at the gene level in this work, which may facilitate further rational regulation for Daqu production.}, } @article {pmid38545162, year = {2024}, author = {Zhong, L and Yan, Y and Chen, L and Sun, N and Li, H and Wang, Y and Liu, H and Jia, Y and Lu, Y and Liu, X and Zhang, Y and Guo, H and Wang, X}, title = {Nanopore-based metagenomics analysis reveals microbial presence in amniotic fluid: A prospective study.}, journal = {Heliyon}, volume = {10}, number = {6}, pages = {e28163}, pmid = {38545162}, issn = {2405-8440}, abstract = {BACKGROUND: Current research on amniotic fluid (AF) microbiota yields contradictory data, necessitating an accurate, comprehensive, and scientifically rigorous evaluation.

OBJECTIVE: This study aimed to characterise the microbial features of AF and explore the correlation between microbial information and clinical parameters.

METHODS: 76 AF samples were collected in this prospective cohort study. Fourteen samples were utilised to establish the nanopore metagenomic sequencing methodology, whereas the remaining 62 samples underwent a final statistical analysis along with clinical information. Negative controls included the operating room environment (OE), surgical instruments (SI), and laboratory experimental processes (EP) to elucidate the background contamination at each step. Simultaneously, levels of five cytokines (IL-1β, IL-6, IL-8, TNF-α, MMP-8) in AF were assessed.

RESULTS: Among the 62 AF samples, microbial analysis identified seven without microbes and 55 with low microbial diversity and abundance. No significant clinical differences were observed between AF samples with and without microbes. The correlation between microbes and clinical parameters in AF with normal chromosomal structure revealed noteworthy findings. In particular, the third trimester exhibited richer microbial diversity. Pseudomonas demonstrated higher detection rates and relative abundance in the second trimester and Preterm Birth (PTB) groups. S. yanoikuyae in the PTB group exhibited elevated detection frequencies and relative abundance. Notably, Pseudomonas negatively correlated with activated partial thromboplastin time (APTT) (r = -0.329, P = 0.016), while Staphylococcus showed positive correlations with APTT (r = 0.395, P = 0.003). Furthermore, Staphylococcus negatively correlated with birth weight (r = -0.297, P = 0.034).

CONCLUSION: Most AF samples exhibited low microbial diversity and abundance. Certain microbes in AF may correlate with clinical parameters such as gestational age and PTB. However, these associations require further investigation. It is essential to expand the sample size and undertake more comprehensive research to elucidate the clinical implications of microbial presence in AF.}, } @article {pmid38544983, year = {2024}, author = {Liang, D and Li, X}, title = {Application of the metagenomic next-generation sequencing in diagnosis and therapy of chronic kidney disease patients with infections.}, journal = {Pakistan journal of medical sciences}, volume = {40}, number = {4}, pages = {791-792}, pmid = {38544983}, issn = {1682-024X}, } @article {pmid38544856, year = {2024}, author = {Kokilaramani, S and Satheeshkumar, A and Nandini, MS and Narenkumar, J and AlSalhi, MS and Devanesan, S and Natarajan, PM and Rajamohan, R and Rajasekar, A and Malik, T}, title = {Application of photoelectrochemical oxidation of wastewater used in the cooling tower water and its influence on microbial corrosion.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1297721}, pmid = {38544856}, issn = {1664-302X}, abstract = {BACKGROUND: Cooling towers are specialized heat exchanger devices in which air and water interact closely to cool the water's temperature. However, the cooling water contains organic nutrients that can cause microbial corrosion (MC) on the metal surfaces of the tower. This research explores the combined wastewater treatment approach using electrochemical-oxidation (EO), photo-oxidation (PO), and photoelectrochemical oxidation (PEO) to contain pollutants and prevent MC.

METHODS: The study employed electro-oxidation, a process involving direct current (DC) power supply, to degrade wastewater. MC studies were conducted using weight loss assessments, scanning electron microscopy (SEM), and x-ray diffraction (XRD).

RESULTS: After wastewater is subjected to electro-oxidation for 4 h, a notable decrease in pollutants was observed, with degradation efficiencies of 71, 75, and 96%, respectively. In the wastewater treated by PEO, microbial growth is restricted as the chemical oxygen demand decreases.

DISCUSSION: A metagenomics study revealed that bacteria present in the cooling tower water consists of 12% of Nitrospira genus and 22% of Fusobacterium genus. Conclusively, PEO serves as an effective method for treating wastewater, inhibiting microbial growth, degrading pollutants, and protecting metal from biocorrosion.}, } @article {pmid38544523, year = {2024}, author = {Pyles, RB and Miller, AL and Urban, RJ and Sheffield-Moore, M and Wright, TJ and Maxwell, CA and Randolph, KM and Danesi, CP and McGovern, KA and Vargas, J and Armstrong, P and Kreber, L and Cumpa, G and Randall, K and Morrison, M and Masel, BE}, title = {The altered TBI fecal microbiome is stable and functionally distinct.}, journal = {Frontiers in molecular neuroscience}, volume = {17}, number = {}, pages = {1341808}, pmid = {38544523}, issn = {1662-5099}, abstract = {INTRODUCTION: Patients who suffer a traumatic brain injury (TBI) often experience chronic and sometimes debilitating sequelae. Recent reports have illustrated both acute and long-term dysbiosis of the gastrointestinal microbiome with significant alterations in composition and predicted functional consequences.

METHODS: Working with participants from past research, metagenomic stability of the TBI- associated fecal microbiome (FMB) was evaluated by custom qPCR array comparing a fecal sample from 2015 to one collected in 2020. Metatranscriptomics identified differently expressed bacterial genes and biochemical pathways in the TBI FMB. Microbiota that contributed the largest RNA amounts identified a set of core bacteria most responsible for functional consequences of the TBI FMB.

RESULTS: A remarkably stable FMB metagenome with significant similarity (two-tail Spearman nonparametric correlation p < 0.001) was observed between 2015 and 2020 fecal samples from subjects with TBI. Comparing the 2020 TBI FMB metagenome to FMBs from healthy controls confirmed and extended the dysbiotic genera and species. Abundance differences between average TBI and healthy FMBs revealed Bacteroides caccae, B. uniformis, Blautia spp., Collinsella spp., Dialister spp., and Ordoribacter spp. were significantly different. Functionally, the Parabacteroides genus contributed the highest percentage of RNA sequences in control FMBs followed by the Bacteroides genus as the second highest contributor. In the TBI FMB, the Corynebacterium genus contributed the most RNA followed by the Alistipes genus. Corynebacterium and Pseudomonas were distinct in the top 10 contributing genera in the TBI FMB while Parabacteroides and Ruminococcus were unique to the top 10 in controls. Comparing RNA profiles, TBI samples had ∼1.5 fold more expressed genes with almost 700 differently expressed genes (DEGs) mapped to over 100 bacterial species. Bioinformatic analysis associated DEGs with pathways led identifying 311 functions in the average TBI FMB profile and 264 in the controls. By average profile comparison, 30 pathways had significantly different abundance (p < 0.05, t-test) or were detected in >80% of the samples in only one of the cohorts (binary distinction).

DISCUSSION: Functional differences between TBI and healthy control FMBs included amino acid metabolism, energy and carbon source usage, fatty acid metabolism, bacterial cell wall component production and nucleic acid synthesis and processing pathways. Together these data shed light on the functional consequences of the dysbiotic TBI FMB decades after injury.}, } @article {pmid38543840, year = {2024}, author = {Popgeorgiev, N and Krupovic, M and Hiblot, J and Fancello, L and Monteil-Bouchard, S and Desnues, C}, title = {A New Inovirus from the Human Blood Encodes Proteins with Nuclear Subcellular Localization.}, journal = {Viruses}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/v16030475}, pmid = {38543840}, issn = {1999-4915}, abstract = {Viruses infecting bacteria (bacteriophages) represent the most abundant viral particles in the human body. They participate in the control of the human-associated bacterial communities and play an important role in the dissemination of virulence genes. Here, we present the identification of a new filamentous single-stranded DNA phage of the family Inoviridae, named Ralstonia Inoviridae Phage 1 (RIP1), in the human blood. Metagenomics and PCR analyses detected the RIP1 genome in blood serum, in the absence of concomitant bacterial infection or contamination, suggesting inovirus persistence in the human blood. Finally, we have experimentally demonstrated that the RIP1-encoded rolling circle replication initiation protein and serine integrase have functional nuclear localization signals and upon expression in eukaryotic cells both proteins were translocated into the nucleus. This observation adds to the growing body of data suggesting that phages could have an overlooked impact on the evolution of eukaryotic cells.}, } @article {pmid38543762, year = {2024}, author = {Liu, J and Li, X and Song, W and Zeng, X and Li, H and Yang, L and Wang, D}, title = {The Multi-Kingdom Microbiome of Wintering Migratory Birds in Poyang Lake, China.}, journal = {Viruses}, volume = {16}, number = {3}, pages = {}, doi = {10.3390/v16030396}, pmid = {38543762}, issn = {1999-4915}, support = {2022YFC2303800//National Key Research and Development Program of China/ ; 81961128002//National Nature Science Foundation of China/ ; }, abstract = {Wild birds are a natural reservoir for zoonotic viruses. To clarify the role of migratory birds in viruses spread in Poyang Lake, we investigated the microbiome of 250 wild bird samples from 19 species in seven orders. The bacterial and viral content abundance and diversity were preliminarily evaluated by Kraken2 and Bracken. After de novo assembly by Megahit and Vamb, viral contigs were identified by CheckV. The reads remapped to viral contigs were quantified using Bowtie2. The bacterial microbiome composition of the samples covers 1526 genera belonging to 175 bacterial orders, while the composition of viruses covers 214 species belonging to 22 viral families. Several taxonomic biomarkers associated with avian carnivory, oral sampling, and raptor migration were identified. Additionally, 17 complete viral genomes belonging to Astroviridae, Caliciviridae, Dicistroviridae, Picornaviridae, and Tombusviridae were characterized, and their phylogenetic relationships were analyzed. This pioneering metagenomic study of migratory birds in Poyang Lake, China illuminates the diverse microbial landscape within these birds. It identifies potential pathogens, and uncovers taxonomic biomarkers relevant to varied bird habitats, feeding habits, ecological classifications, and sample types, underscoring the public health risks associated with wintering migratory birds.}, } @article {pmid38543680, year = {2024}, author = {Mang, Q and Gao, J and Li, Q and Sun, Y and Xu, G and Xu, P}, title = {Metagenomic Insight into the Effect of Probiotics on Nitrogen Cycle in the Coilia nasus Aquaculture Pond Water.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/microorganisms12030627}, pmid = {38543680}, issn = {2076-2607}, support = {2022YFD2400904//National Key Research and development Program of China/ ; JSGS[2021]134//Jiangsu Province seed industry revitalization "revealing-list" project/ ; }, abstract = {Recently, probiotics have been widely applied for the in situ remediation of aquatic water. Numerous studies have proved that probiotics can regulate water quality by improving the microbial community. Nitrogen cycling, induced by microorganisms, is a crucial process for maintaining the balance of the aquatic ecosystem. Nevertheless, the underlying mechanisms by which probiotics enhance water quality in aquatic systems remain poorly understood. To explore the water quality indicators and their correlation with nitrogen cycling-related functional genes, metagenomic analysis of element cycling was performed to identify nitrogen cycling-related functional genes in Coilia nasus aquatic water between the control group (C) and the groups supplemented with probiotics in feed (PF) or water (PW). The results showed that adding probiotics to the aquatic water could reduce the concentrations of ammonia nitrogen (NH4[+]-N), nitrite (NO2[-]-N), and total nitrogen (TN) in the water. Community structure analysis revealed that the relative abundance of Verrucomicrobiota was increased from 30 d to 120 d (2.61% to 6.35%) in the PW group, while the relative abundance of Cyanobacteria was decreased from 30 d to 120 d (5.66% to 1.77%). We constructed a nitrogen cycling pathway diagram for C. nasus aquaculture ponds. The nitrogen cycle functional analysis showed that adding probiotics to the water could increase the relative abundance of the amoC_B and hao (Nitrification pathways) and the nirS and nosZ (Denitrification pathways). Correlation analysis revealed that NH4[+]-N was significantly negatively correlated with Limnohabitans, Sediminibacterium, and Algoriphagus, while NO2[-]-N was significantly negatively correlated with Roseomonas and Rubrivivax. Our study demonstrated that adding probiotics to the water can promote nitrogen element conversion and migration, facilitate nitrogen cycling, benefit ecological environment protection, and remove nitrogen-containing compounds in aquaculture systems by altering the relative abundance of nitrogen cycling-related functional genes and microorganisms.}, } @article {pmid38543648, year = {2024}, author = {Blanco, P and Rodríguez, I and Fernández-Fernández, V and Ramil, M and Castrillo, D and Acín-Albiac, M and Adamo, I and Fernández-Trujillo, C and García-Jiménez, B and Acedo, A and Calvo-Portela, N and Parente-Sendín, A and Acemel-Míguez, L and Alonso-Vega, F}, title = {Physicochemical Properties and Microbiome of Vineyard Soils from DOP Ribeiro (NW Spain) Are Influenced by Agricultural Management.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/microorganisms12030595}, pmid = {38543648}, issn = {2076-2607}, support = {AC2021E-02//Consellería do Medio Rural, Xunta de Galicia/ ; }, abstract = {Agricultural management influences the soil ecosystem by affecting its physicochemical properties, residues of pesticides and microbiome. As vineyards grow crops with the highest incidence of pesticides, the aim of this study was to evaluate the impact of conventional and sustainable management systems of vineyards from DOP Ribeiro on the soil's condition. Samples from soils under three different management systems were collected, and the main soil physicochemical properties were evaluated. A selection of 50 pesticides were investigated by liquid chromatography with tandem mass spectrometry. The bacterial and fungal microbiomes were characterized through amplicon sequencing. The results show that organic agriculture positively influences soil pH and the concentration of some nutrients compared to conventional management. Our microbiome analysis demonstrated that transitioning from conventional to organic management significantly improves several BeCrop[®] indexes related to key microbial metabolism and soil bio-sustainability. Such a transition does not affect soil alpha diversity, but leads to a higher interconnected microbial network structure. Moreover, differential core genera and species for each management system are observed. In addition, the correlation of the microbiome with geographical distance is evidence of the existence of different microbial terroirs within DOP Ribeiro. Indeed, sustainable management leads to higher nutrient availability and enhances soil health in the short term, while lowering pesticide usage.}, } @article {pmid38543644, year = {2024}, author = {Pinheiro, LRS and Rodrigues, ÉDL and Paiva, FADS and Cruz, ACR and Medeiros, DBA and Casseb, ADR and Silva, SPD and Casseb, LMN}, title = {Identification of Viruses in Molossus Bats from the Brazilian Amazon: A Descriptive Metagenomic Analysis.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/microorganisms12030593}, pmid = {38543644}, issn = {2076-2607}, support = {88887.636483/2021-00//Coordination of Superior Level Staff Improvement (CAPES)/ ; }, abstract = {Bats are widely distributed in Brazil, including the Amazon region, and their association with viral pathogens is well-known. This work aimed to evaluate the metavirome in samples of Molossus sp. bats captured in the Brazilian Amazon from 2019 to 2021. Lung samples from 58 bats were divided into 13 pools for RNA isolation and sequencing followed by bioinformatic analysis. The Retroviridae family showed the highest abundance of viral reads. Although no complete genome could be recovered, the Paramyxoviridae and Dicistroviridae families showed the formation of contigs with satisfactory identity and size characteristics for further analysis. One contig of the Paramyxoviridae family was characterized as belonging to the genus Morbillivirus, being grouped most closely phylogenetically to Porcine morbillivirus. The contig related to the Dicistroviridae family was identified within the Cripavirus genus, with 94%, 91%, and 42% amino acid identity with Culex dicistrovirus 2, Rhopalosiphum padi, and Aphid lethal paralysis, respectively. The presence of viruses in bats needs constant updating since the study was able to identify viral sequences related to families or genera still poorly described in the literature in association with bats.}, } @article {pmid38543628, year = {2024}, author = {Tegopoulos, K and Tsirka, T and Stekas, C and Gerasimidi, E and Skavdis, G and Kolovos, P and Grigoriou, ME}, title = {Spatiotemporal Dynamics of Assyrtiko Grape Microbiota.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/microorganisms12030577}, pmid = {38543628}, issn = {2076-2607}, support = {project code: 2018ΣΕ01300000//Public Investments Program (PIP) of General Secretariat for Research & Technology (GSRT)/ ; MIS 5046239//Operational Program Competitiveness, Entrepreneurship and Innovation (NSRF 2014-2020) and co-financed by Greece and the European Union (European Regional Development Fund)/ ; }, abstract = {Vitis vinifera, an economically significant grapevine species, is known for wine, juice, and table grape production. The berries of wine grapes host a diverse range of microorganisms influencing both grapevine health and the winemaking process. Indigenous to Greece, the emblematic variety Assyrtiko, renowned for high-quality white wines, originated from Santorini and spread to various Greek regions. Despite existing studies on the microbiota of several varieties, the carposphere microbiota of Assyrtiko grapes remains unexplored. Thus, we conducted a spatiotemporal metagenomic study to identify the epiphytic microbial community composition of Assyrtiko grapes. The study was conducted in two consecutive vintage years (2019 and 2020) across three different and distinct viticulture regions in Greece (Attica, Thessaloniki, Evros). We performed amplicon sequencing, targeting the 16S rRNA gene for bacteria and the ITS region for fungi, with subsequent comprehensive bioinformatic analysis. Our data indicate that the distribution and relative abundance of the epiphytic carposphere microbial communities of the Assyrtiko variety are shaped both by vintage and biogeography.}, } @article {pmid38543622, year = {2024}, author = {Bhandary, R and Venugopalan, G and Ramesh, A and Tartaglia, GM and Singhal, I and Khijmatgar, S}, title = {Microbial Symphony: Navigating the Intricacies of the Human Oral Microbiome and Its Impact on Health.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/microorganisms12030571}, pmid = {38543622}, issn = {2076-2607}, abstract = {This comprehensive review delves into the forefront of research on the human oral microbiome, exploring recent advancements that span microbial colonization, state-of-the-art detection methodologies, and the complex interplay involved in disease progression. Through an exhaustive analysis of the contemporary literature, we illuminate the dynamic orchestration of microbial communities within the oral cavity, underscoring their pivotal role in health and disease. Cutting-edge detection techniques, including metagenomics and high-throughput sequencing, are discussed regarding their transformative impact on understanding the intricacies of oral microbial ecosystems. As we stand on the cusp of a new decade, this review anticipates a paradigm shift in the field, emphasizing the potential for rapid identification and targeted management of detrimental oral microorganisms. Insights gained from this exploration not only contribute to our fundamental understanding of the oral microbiome but also hold promise for the development of innovative therapeutic strategies to maintain oral health. This article aims to serve as a valuable resource for researchers, clinicians, and public health professionals engaged in unraveling the mysteries of the microbial symphony within the human oral cavity.}, } @article {pmid38543620, year = {2024}, author = {Tao, J and Li, B and Shi, Y and Cheng, J and Tang, P and Jiao, J and Liu, H}, title = {Genomic Evolution and Selective Pressure Analysis of a Novel Porcine Sapovirus in Shanghai, China.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/microorganisms12030569}, pmid = {38543620}, issn = {2076-2607}, support = {2022-02-08-00-12-F01167//Shanghai Agricultural Technology Development Program/ ; 2022/012//SAAS Program for Excellent Research Team/ ; }, abstract = {Porcine sapovirus (PoSaV) is one of the most significant pathogens causing piglet diarrhea, and one with limited genetic characterization. In this study, the prevalence, infection pattern, and genetic evolution of porcine sapovirus were elucidated in detail. The positive rate of PoSaV was 10.1% (20/198), with dual, triple, and quadruple infections of 45%, 40%, and 5%, respectively. To further explore the viral composition in the PoSaV-positive diarrhea feces, metagenomic sequencing was carried out. The results confirmed that RNA viruses accounted for a higher proportion (55.47%), including the two primary viruses of PoSaV (21.78%) and porcine astrovirus (PAstV) (24.54%) in the tested diarrhea feces samples. Afterward, a full-length sequence of the PoSaV isolate was amplified and named SHCM/Mega2023, and also given the identifier of GenBank No. PP388958. Phylogenetic analysis identified the prevalent PoSaV strain SHCM/Mega2023 in the GIII genogroup, involving a recombinant event with MK962338 and KT922089, with the breakpoint at 2969-5132 nucleotides (nt). The time tree revealed that the GIII genogroup exhibits the widest divergence time span, indicating a high likelihood of viral recombination. Moreover, SHCM/Mega2023 had three nucleotide "RPL" insertions at the 151-153 nt site in the VP2 gene, compared to the other GIII strains. Further selective pressure calculations demonstrate that the whole genome of the SHCM/Mega2023 strain was under purifying selection (dN/dS < 1), with seven positively selected sites in the VP1 protein, which might be related to antigenicity. In conclusion, this study presents a novel genomic evolution of PoSaV, offering valuable insights into antigenicity and for vaccine research.}, } @article {pmid38543596, year = {2024}, author = {Ilbeigi Khamseh Nejad, M and Cappelli, A and Damiani, C and Falcinelli, M and Catapano, PL and Nanfack-Minkeu, F and Mayi, MPA and Currà, C and Ricci, I and Favia, G}, title = {Wolbachia and Asaia Distribution among Different Mosquito Vectors Is Affected by Tissue Localization and Host Species.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/microorganisms12030545}, pmid = {38543596}, issn = {2076-2607}, support = {PRIN 2022 PNRR MUR P20225TJWB//European Union - NextGenerationEU/ ; }, abstract = {Microbial communities play an important role in the fitness of mosquito hosts. However, the factors shaping microbial communities in wild populations, with regard to interactions among microbial species, are still largely unknown. Previous research has demonstrated that two of the most studied mosquito symbionts, the bacteria Wolbachia and Asaia, seem to compete or not compete, depending on the genetic background of the reference mosquito host. The large diversity of Wolbachia-Asaia strain combinations that infect natural populations of mosquitoes may offer a relevant opportunity to select suitable phenotypes for the suppression of pathogen transmission and for the manipulation of host reproduction. We surveyed Wolbachia and Asaia in 44 mosquito populations belonging to 11 different species of the genera Anopheles, Aedes, and Culex using qualitative PCR. Through quantitative PCR, the amounts of both bacteria were assessed in different mosquito organs, and through metagenomics, we determined the microbiota compositions in some selected mosquito populations. We show that variation in microbial community structure is likely associated with the species/strain of mosquito, its geographical position, and tissue localization. Together, our results shed light on the interactions among different bacterial species in the microbial communities of mosquito vectors, and this can aid the development and/or improvement of methods for symbiotic control of insect vectors.}, } @article {pmid38543590, year = {2024}, author = {Ding, JJ and Zhou, GJ and Chen, XJ and Xu, W and Gao, XM and Zhang, YZ and Jiang, B and Li, HF and Wang, KL}, title = {Analysis of Microbial Diversity and Community Structure of Rhizosphere Soil of Three Astragalus Species Grown in Special High-Cold Environment of Northwestern Yunnan, China.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/microorganisms12030539}, pmid = {38543590}, issn = {2076-2607}, support = {32060032//the National Natural Science Foundations of China/ ; 82360708//the National Natural Science Foundations of China/ ; }, abstract = {Astragalus is a medicinal plant with obvious rhizosphere effects. At present, there are many Astragalus plants with high application value but low recognition and resource reserves in the northwestern area of Yunnan province, China. In this study, metagenomics was used to analyze the microbial diversity and community structure of rhizosphere soil of A. forrestii, A. acaulis, and A. ernestii plants grown in a special high-cold environment of northwestern Yunnan, China, at different altitudes ranging from 3225 to 4353 m. These microbes were taxonomically annotated to obtain 24 phyla and 501 genera for A. forrestii, 30 phyla and 504 genera for A. acaulis, as well as 39 phyla and 533 genera for A. ernestii. Overall, the dominant bacterial phyla included Proteobacteria, Actinobacteria, and Acidobacteria, while the dominant fungal ones were Ascomycota and Basidiomycota. At the genus level, Bradyrhizobium, Afipia, and Paraburkholderia were the most prevalent bacteria, and Hyaloscypha, Pseudogymnoascus, and Russula were the dominant fungal genera. Some of them are considered biocontrol microbes that could sustain the growth and health of host Astragalus plants. Redundancy analysis revealed that pH, TN, and SOM had a significant impact on the microbial community structures (p < 0.05). Finally, triterpene, flavonoid, polysaccharide, and amino acid metabolisms accounted for a high proportion of the enriched KEGG pathways, which possibly contributed to the synthesis of bioactive constituents in the Astragalus plants.}, } @article {pmid38543584, year = {2024}, author = {He, J and Li, Y and Sun, X and Zuo, D and Wang, M and Zheng, X and Yu, P and Shi, P}, title = {Characterization of a Novel Hyperthermophilic GH1 β-Glucosidase from Acidilobus sp. and Its Application in the Hydrolysis of Soybean Isoflavone Glycosides.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/microorganisms12030533}, pmid = {38543584}, issn = {2076-2607}, abstract = {A putative β-glucosidase gene, BglAc, was amplified from Acidilobus sp. through metagenome database sampling from a hot spring in Yellowstone National Park. BglAc is composed of 485 amino acid residues and bioinformatics analysis showed that it belongs to the GH1 family of β-glucosidases. The gene was successfully expressed in Escherichia coli with a molecular weight of approximately 55.3 kDa. The purified recombinant enzyme showed the maximum activity using p-nitrophenyl-β-D-glucopyranoside (pNPG) as the substrate at optimal pH 5.0 and 100 °C. BglAc exhibited extraordinary thermostability, and its half-life at 90 °C was 6 h. The specific activity, Km, Vmax, and Kcat/Km of BglAc toward pNPG were 357.62 U mg[-1], 3.41 mM, 474.0 μmol min[-1]·mg[-1], and 122.7 s[-1]mM[-1]. BglAc exhibited the characteristic of glucose tolerance, and the inhibition constant Ki was 180.0 mM. Furthermore, a significant ethanol tolerance was observed, retaining 96% relative activity at 10% ethanol, and even 78% at 20% ethanol, suggesting BglAc as a promising enzyme for cellulose saccharification. BglAc also had a strong ability to convert the major soybean isoflavone glycosides (daidzin, genistin, and glycitin) into their corresponding aglycones. Overall, BglAc was actually a new β-glucosidase with excellent thermostability, ethanol tolerance, and glycoside hydrolysis ability, indicating its wide prospects for applications in the food industry, animal feed, and lignocellulosic biomass degradation.}, } @article {pmid38543568, year = {2024}, author = {Li, J and Cheng, H and Yin, F and Liu, J and Zhang, XH and Yu, M}, title = {Deciphering Microbial Communities and Distinct Metabolic Pathways in the Tangyin Hydrothermal Fields of Okinawa Trough through Metagenomic and Genomic Analyses.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/microorganisms12030517}, pmid = {38543568}, issn = {2076-2607}, support = {42376145 and 41976137//National Natural Science Foundation of China/ ; 202172002//Fundamental Research Funds for the Central Universities/ ; }, abstract = {Deep-sea hydrothermal vents have been extensively explored around the globe in the past decades, and the diversity of microbial communities and their ecological functions related to hydrothermal vents have become hotspots in the study of microbial biogeochemistry. However, knowledge of dominant microbial communities and their unique metabolic characteristics adapting to hydrothermal vents is still limited. In our study, the sediment sample near the Tangyin hydrothermal vent in the southern part of the Okinawa Trough was collected, and the most abundant phyla are Proteobacteria and Desulfobacterota based on the 16S rRNA genes and metagenome sequencing. Metagenomic analysis revealed that methane metabolism, sulfur reduction, and Fe[2+] uptake were abundantly distributed in hydrothermal sediment. In addition, most of the metagenomic assembly genomes (MAGs), belonging to Chloroflexota, Desulfobacterota, and Gammaproteobacteria, were found to be involved in methanogenesis, sulfur oxidation/reduction, and ferrous/ferric iron metabolisms. Among these MAGs, the two representative groups (Bathyarchaeia and Thioglobaceae) also showed distinct metabolic characteristics related to carbon, sulfur, and iron to adapt to hydrothermal environments. Our results reveal the dominant microbial populations and their metabolic features in the sediment near the Tangyin hydrothermal fields, providing a better understanding of microbial survival strategies in the extreme environment.}, } @article {pmid38543566, year = {2024}, author = {Spencer, L and Costine, B and Irwin, T and Dixit, A and Spern, C and Diaz, A and Lozzi, B and Li, W and Khodadad, C and Smith, T and Wheeler, R and O'Rourke, A}, title = {Substrate Matters: Ionic Silver Alters Lettuce Growth, Nutrient Uptake, and Root Microbiome in a Hydroponics System.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/microorganisms12030515}, pmid = {38543566}, issn = {2076-2607}, abstract = {Ionic silver (Ag[+]) is being investigated as a residual biocide for use in NASA spacecraft potable water systems on future crewed missions. This water will be used to irrigate future spaceflight crop production systems. We have evaluated the impact of three concentrations (31 ppb, 125 ppb, and 500 ppb) of ionic silver biocide solutions on lettuce in an arcillite (calcinated clay particle substrate) and hydroponic (substrate-less) growth setup after 28 days. Lettuce plant growth was reduced in the hydroponic samples treated with 31 ppb silver and severely stunted for samples treated at 125 ppb and 500 ppb silver. No growth defects were observed in arcillite-grown lettuce. Silver was detectable in the hydroponic-grown lettuce leaves at each concentration but was not detected in the arcillite-grown lettuce leaves. Specifically, when 125 ppb silver water was applied to a hydroponics tray, Ag[+] was detected at an average amount of 7 μg/g (dry weight) in lettuce leaves. The increase in Ag[+] corresponded with a decrease in several essential elements in the lettuce tissue (Ca, K, P, S). In the arcillite growth setup, silver did not impact the plant root zone microbiome in terms of alpha diversity and relative abundance between treatments and control. However, with increasing silver concentration, the alpha diversity increased in lettuce root samples and in the water from the hydroponics tray samples. The genera in the hydroponic root and water samples were similar across the silver concentrations but displayed different relative abundances. This suggests that ionic silver was acting as a selective pressure for the microbes that colonize the hydroponic water. The surviving microbes likely utilized exudates from the stunted plant roots as a carbon source. Analysis of the root-associated microbiomes in response to silver showed enrichment of metagenomic pathways associated with alternate carbon source utilization, fatty-acid synthesis, and the ppGpp (guanosine 3'-diphosphate 5'-diphosphate) stringent response global regulatory system that operates under conditions of environmental stress. Nutrient solutions containing Ag[+] in concentrations greater than 31 ppb in hydroponic systems lacking cation-exchange capacity can severely impact crop production due to stunting of plant growth.}, } @article {pmid38543562, year = {2024}, author = {Masenya, K and Manganyi, MC and Dikobe, TB}, title = {Exploring Cereal Metagenomics: Unravelling Microbial Communities for Improved Food Security.}, journal = {Microorganisms}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/microorganisms12030510}, pmid = {38543562}, issn = {2076-2607}, abstract = {Food security is an urgent global challenge, with cereals playing a crucial role in meeting the nutritional requirements of populations worldwide. In recent years, the field of metagenomics has emerged as a powerful tool for studying the microbial communities associated with cereal crops and their impact on plant health and growth. This chapter aims to provide a comprehensive overview of cereal metagenomics and its role in enhancing food security through the exploration of beneficial and pathogenic microbial interactions. Furthermore, we will examine how the integration of metagenomics with other tools can effectively address the adverse effects on food security. For this purpose, we discuss the integration of metagenomic data and machine learning in providing novel insights into the dynamic interactions shaping plant-microbe relationships. We also shed light on the potential applications of leveraging microbial diversity and epigenetic modifications in improving crop resilience and yield sustainability. Ultimately, cereal metagenomics has revolutionized the field of food security by harnessing the potential of beneficial interactions between cereals and their microbiota, paving the way for sustainable agricultural practices.}, } @article {pmid38542697, year = {2024}, author = {Shearer, J and Shah, S and MacInnis, MJ and Shen-Tu, G and Mu, C}, title = {Dose-Responsive Effects of Iron Supplementation on the Gut Microbiota in Middle-Aged Women.}, journal = {Nutrients}, volume = {16}, number = {6}, pages = {}, doi = {10.3390/nu16060786}, pmid = {38542697}, issn = {2072-6643}, support = {150364/CAPMC/CIHR/Canada ; }, abstract = {Oral iron supplementation is the first-line treatment for addressing iron deficiency, a concern particularly relevant to women who are susceptible to sub-optimal iron levels. Nevertheless, the impact of iron supplementation on the gut microbiota of middle-aged women remains unclear. To investigate the association between iron supplementation and the gut microbiota, healthy females aged 40-65 years (n = 56, BMI = 23 ± 2.6 kg/m[2]) were retrospectively analyzed from the Alberta's Tomorrow Project. Fecal samples along with various lifestyle, diet, and health questionnaires were obtained. The gut microbiota was assessed by 16S rRNA sequencing. Individuals were matched by age and BMI and classified as either taking no iron supplement, a low-dose iron supplement (6-10 mg iron/day), or high-dose iron (>100 mg/day). Compositional and functional analyses of microbiome data in relation to iron supplementation were investigated using various bioinformatics tools. Results revealed that iron supplementation had a dose-dependent effect on microbial communities. Elevated iron intake (>100 mg) was associated with an augmentation of Proteobacteria and a reduction in various taxa, including Akkermansia, Butyricicoccus, Verrucomicrobia, Ruminococcus, Alistipes, and Faecalibacterium. Metagenomic prediction further suggested the upregulation of iron acquisition and siderophore biosynthesis following high iron intake. In conclusion, adequate iron levels are essential for the overall health and wellbeing of women through their various life stages. Our findings offer insights into the complex relationships between iron supplementation and the gut microbiota in middle-aged women and underscore the significance of iron dosage in maintaining optimal gut health.}, } @article {pmid38542307, year = {2024}, author = {Kan, CM and Tsang, HF and Pei, XM and Ng, SSM and Yim, AK and Yu, AC and Wong, SCC}, title = {Enhancing Clinical Utility: Utilization of International Standards and Guidelines for Metagenomic Sequencing in Infectious Disease Diagnosis.}, journal = {International journal of molecular sciences}, volume = {25}, number = {6}, pages = {}, doi = {10.3390/ijms25063333}, pmid = {38542307}, issn = {1422-0067}, support = {P0046023//Lim Peng Suan Charitable Trust Research Grant/ ; }, abstract = {Metagenomic sequencing has emerged as a transformative tool in infectious disease diagnosis, offering a comprehensive and unbiased approach to pathogen detection. Leveraging international standards and guidelines is essential for ensuring the quality and reliability of metagenomic sequencing in clinical practice. This review explores the implications of international standards and guidelines for the application of metagenomic sequencing in infectious disease diagnosis. By adhering to established standards, such as those outlined by regulatory bodies and expert consensus, healthcare providers can enhance the accuracy and clinical utility of metagenomic sequencing. The integration of international standards and guidelines into metagenomic sequencing workflows can streamline diagnostic processes, improve pathogen identification, and optimize patient care. Strategies in implementing these standards for infectious disease diagnosis using metagenomic sequencing are discussed, highlighting the importance of standardized approaches in advancing precision infectious disease diagnosis initiatives.}, } @article {pmid38542271, year = {2024}, author = {Park, W and Park, J}, title = {A Comparative Investigation of the Bile Microbiome in Patients with Choledocholithiasis and Cholecystolithiasis through Metagenomic Analysis.}, journal = {International journal of molecular sciences}, volume = {25}, number = {6}, pages = {}, doi = {10.3390/ijms25063297}, pmid = {38542271}, issn = {1422-0067}, support = {0//Biomedical Research Institute, Jeonbuk National University Hospital./ ; }, abstract = {While the precise triggers of gallstone formation remain incompletely understood, it is believed to arise from a complex interplay of genetic and environmental factors. The bile microbiome is being increasingly recognized as a possible contributor to the onset of gallstone disease. The primary objective of this study was to investigate distinctions in the microbial communities within bile specimens from patients with choledocholithiasis (common bile duct stones) and cholecystolithiasis (gallbladder stones). We employed massively parallel sequencing of the 16S rRNA gene to examine the microbial communities within bile samples obtained from 28 patients with choledocholithiasis (group DS) and cholecystolithiasis (group GS). The taxonomic composition of the bile microbial communities displayed significant disparities between the group DS and the group GS. Within the 16 prevalent genera, only Streptococcus, Ralstonia, Lactobacillus, and Enterococcus were predominantly found in the group GS. In contrast, the group DS displayed a more diverse range of genera. The alpha diversity of bile specimens was also notably lower in the group GS compared to the group DS (p = 0.041). Principal coordinate analysis unveiled distinct clustering of bile microbial communities depending on the location of the gallstone. Linear discriminant analysis effect size analysis, with a score threshold of >3 and the Kruskall-Wallis test (α < 0.05), recognized Bacilli and Lactobacillales as potential taxonomic markers for distinguishing patients with cholecystolithiasis limited to the gallbladder. Significant variations were found in the distribution and diversity of bile microbial communities between patients with choledocholithiasis and cholecystolithiasis. This observation suggests that alterations in the bile microbiome may contribute to the development of gallstones in these patients.}, } @article {pmid38541726, year = {2024}, author = {Neagu, AN and Jayaweera, T and Corrice, L and Johnson, K and Darie, CC}, title = {Breast Cancer Exposomics.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/life14030402}, pmid = {38541726}, issn = {2075-1729}, support = {Award Number R15CA260126//the National Cancer Institute of the National Institutes of Health/ ; }, abstract = {We are exposed to a mixture of environmental man-made and natural xenobiotics. We experience a wide spectrum of environmental exposure in our lifetime, including the effects of xenobiotics on gametogenesis and gametes that undergo fertilization as the starting point of individual development and, moreover, in utero exposure, which can itself cause the first somatic or germline mutation necessary for breast cancer (BC) initiation. Most xenobiotics are metabolized or/and bioaccumulate and biomagnify in our tissues and cells, including breast tissues, so the xenobiotic metabolism plays an important role in BC initiation and progression. Many considerations necessitate a more valuable explanation regarding the molecular mechanisms of action of xenobiotics which act as genotoxic and epigenetic carcinogens. Thus, exposomics and the exposome concept are based on the diversity and range of exposures to physical factors, synthetic chemicals, dietary components, and psychosocial stressors, as well as their associated biologic processes and molecular pathways. Existing evidence for BC risk (BCR) suggests that food-borne chemical carcinogens, air pollution, ionizing radiation, and socioeconomic status are closely related to breast carcinogenesis. The aim of this review was to depict the dynamics and kinetics of several xenobiotics involved in BC development, emphasizing the role of new omics fields related to BC exposomics, such as environmental toxicogenomics, epigenomics and interactomics, metagenomics, nutrigenomics, nutriproteomics, and nutrimiRomics. We are mainly focused on food and nutrition, as well as endocrine-disrupting chemicals (EDCs), involved in BC development. Overall, cell and tissue accumulation and xenobiotic metabolism or biotransformation can lead to modifications in breast tissue composition and breast cell morphology, DNA damage and genomic instability, epimutations, RNA-mediated and extracellular vesicle effects, aberrant blood methylation, stimulation of epithelial-mesenchymal transition (EMT), disruption of cell-cell junctions, reorganization of the actin cytoskeleton, metabolic reprogramming, and overexpression of mesenchymal genes. Moreover, the metabolism of xenobiotics into BC cells impacts almost all known carcinogenic pathways. Conversely, in our food, there are many bioactive compounds with anti-cancer potential, exerting pro-apoptotic roles, inhibiting cell cycle progression and proliferation, migration, invasion, DNA damage, and cell stress conditions. We can conclude that exposomics has a high potential to demonstrate how environmental exposure to xenobiotics acts as a double-edged sword, promoting or suppressing tumorigenesis in BC.}, } @article {pmid38541662, year = {2024}, author = {Xu, Z and Zhang, M and Ning, Z and He, Z and Zhang, F}, title = {Assessing the Natural Source Zone Depletion of a Petroleum-Contaminated Clayey Soil Site in Southern China Combining Concentration Gradient Method and Metagenomics.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/life14030337}, pmid = {38541662}, issn = {2075-1729}, support = {22373901D//Hebei Provincial Department of Science and Technology/ ; D2021504025//Natural Science Foundation of Hebei Province/ ; }, abstract = {Natural source zone depletion (NSZD) is the main process of LNAPL (Light Non-Aqueous Phase Liquid) removal under natural conditions. The NSZD rates assessed ranged from 0.55 to 11.55 kg·m[-2]·a[-1] (kilograms per square meter per year) in previous studies. However, most of these data were obtained from sandy sites, with few clayey sites. To gain knowledge of NSZD in clayey soil sites, the study assessed the NSZD of a petroleum hydrocarbon-contaminated clayey soil site in China, combining the concentration gradient method with metagenomic sequencing technology. The results show that the abundance of methane-producing key enzyme mcrA gene in the source zone was more abundant than in background areas, which suggests that there was methanogenesis, the key process of NSZD. The concentration gradients of oxygen and carbon dioxide existed only in shallow soil (<0.7 m), which suggests that there was a thin methane oxidation zone in the shallow zone. The calculated NSZD rates range from 0.23 to 1.15 kg·m[-2]·a[-1], which fall within the moderate range compared to previous NSZD sites. This study expands the knowledge of NSZD in clayey soil and enriches the attenuation rate data for contaminated sites, which is of significant importance in managing petroleum contaminants.}, } @article {pmid38541334, year = {2024}, author = {Kataržytė, M and Rapolienė, L and Kalvaitienė, G and Picazo-Espinosa, R}, title = {Microbial Composition Dynamics in Peloids Used for Spa Procedures in Lithuania: Pilot Study.}, journal = {International journal of environmental research and public health}, volume = {21}, number = {3}, pages = {}, doi = {10.3390/ijerph21030335}, pmid = {38541334}, issn = {1660-4601}, support = {S-REP-22-6//Lithuanian Science Council/ ; S-A-UEI-23-9//Lithuanian Science Council (LMT) and Ministry of Education, Science and Sports of the Republic of Lithuania/ ; }, abstract = {Despite peloids' acknowledged therapeutic and cosmetic potential, there remains a limited understanding of their microbial diversity and dynamics, especially concerning beneficial and non-beneficial microorganisms under different heating conditions. Our study employs both cultivation and metagenomic methods to assess the microbiota of peloids, focusing on lake sapropel and peat under heating conditions recommended for external application and safety assurance. By applying microbial indicators specified in national regulatory documents, we found that all peloids reached thresholds for sulphite-reducing clostridia and colony-forming units. Each peloid exhibited a distinctive bacterial composition based on metagenomic analysis, and temperature-induced changes were observed in microbial diversity. We identified beneficial bacteria potentially contributing to the therapeutic properties of peloids. However, the same peloids indicated the presence of bacteria of human faecal origin, with a notably higher abundance of Escherichia coli, pointing to a potential source of contamination. Unfortunately, it remains unclear at which stage this contamination entered the peloids. The findings underscore the importance of monitoring and controlling microbial aspects in peloid applications, emphasising the need for measures to prevent and address contamination during their preparation and application processes.}, } @article {pmid38540316, year = {2024}, author = {Tesolato, S and Vicente-Valor, J and Paz-Cabezas, M and Gómez-Garre, D and Sánchez-González, S and Ortega-Hernández, A and de la Serna, S and Domínguez-Serrano, I and Dziakova, J and Rivera, D and Jarabo, JR and Gómez-Martínez, AM and Hernando, F and Torres, A and Iniesta, P}, title = {Gut Microbiota Signatures with Potential Clinical Usefulness in Colorectal and Non-Small Cell Lung Cancers.}, journal = {Biomedicines}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/biomedicines12030703}, pmid = {38540316}, issn = {2227-9059}, support = {PI19/00073//Instituto de Salud Carlos III/ ; }, abstract = {The application of bacterial metagenomic analysis as a biomarker for cancer detection is emerging. Our aim was to discover gut microbiota signatures with potential utility in the diagnosis of colorectal cancer (CRC) and non-small cell lung cancer (NSCLC). A prospective study was performed on a total of 77 fecal samples from CRC and NSCLC patients and controls. DNA from stool was analyzed for bacterial genomic sequencing using the Ion Torrent™ technology. Bioinformatic analysis was performed using the QIIME2 pipeline. We applied logistic regression to adjust for differences attributable to sex, age, and body mass index, and the diagnostic accuracy of our gut signatures was compared with other previously published results. The feces of patients affected by different tumor types, such as CRC and NSCLC, showed a differential intestinal microbiota profile. After adjusting for confounders, Parvimonas (OR = 53.3), Gemella (OR = 6.01), Eisenbergiella (OR = 5.35), Peptostreptococcus (OR = 9.42), Lactobacillus (OR = 6.72), Salmonella (OR = 5.44), and Fusobacterium (OR = 78.9) remained significantly associated with the risk of CRC. Two genera from the Ruminococcaceae family, DTU089 (OR = 20.1) and an uncharacterized genus (OR = 160.1), were associated with the risk of NSCLC. Our two panels had better diagnostic capacity for CRC (AUC = 0.840) and NSLC (AUC = 0.747) compared to the application of two other published panels to our population. Thus, we propose a gut bacteria panel for each cancer type and show its potential application in cancer diagnosis.}, } @article {pmid38540144, year = {2024}, author = {Zhao, F and Hiraishi, K and Li, X and Hu, Y and Kojima, D and Sun, Z and Zhang, H and Kurahara, LH}, title = {Long-Term Tracking of the Effects of Colostrum-Derived Lacticaseibacillus rhamnosus Probio-M9 on Gut Microbiota in Mice with Colitis-Associated Tumorigenesis.}, journal = {Biomedicines}, volume = {12}, number = {3}, pages = {}, doi = {10.3390/biomedicines12030531}, pmid = {38540144}, issn = {2227-9059}, support = {21K11699//KAKENHI/ ; 2021ZD0014//Inner Mongolia Science and Technology Major Projects/ ; 196001//Central Research Institute of Fukuoka University/ ; 2021//Takeda Science Foundation/ ; 2022//Suzuken Memorial Foundation/ ; }, abstract = {Intestinal bacteria play important roles in the progression of colitis-associated carcinogenesis. Colostrum-derived Lacticaseibacillus rhamnosus Probio-M9 (Probio-M9) has shown a protective effect in a colitis-associated cancer (CAC) model, but detailed metagenomic analysis had not been performed. Here, we investigated the preventive effects of the probiotic Probio-M9 on CAC-model mice, tracking the microbiota. Feces were obtained at four time points for evaluation of gut microbiota. The effect of Probio-M9 on tight junction protein expression was evaluated in co-cultured Caco-2 cells. Probio-M9 treatment decreased the number of tumors as well as stool consistency score, spleen weight, inflammatory score, and macrophage expression in the CAC model. Probio-M9 accelerated the recovery of the structure, composition, and function of the intestinal microbiota destroyed by azoxymethane (AOM)/dextran sulfate sodium (DSS) by regulating key bacteria (including Lactobacillus murinus, Muribaculaceae bacterium DSM 103720, Muribaculum intestinale, and Lachnospiraceae bacterium A4) and pathways from immediately after administration until the end of the experiment. Probio-M9 co-culture protected against lipopolysaccharide-induced impairment of tight junctions in Caco-2 cells. This study provides valuable insight into the role of Probio-M9 in correcting gut microbiota defects associated with inflammatory bowel disease carcinogenesis and may have clinical application in the treatment of inflammatory carcinogenesis.}, } @article {pmid38540015, year = {2024}, author = {Zuo, C and Ma, P and Ma, X and Zhu, Y and Yan, S and Zhang, Z}, title = {Integrated Metagenomic and Metabolomic Analysis on Two Competing Mussels, Mytella strigata and Perna viridis, in China.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/ani14060918}, pmid = {38540015}, issn = {2076-2615}, support = {2022YFD2401204//National Key R&D Program of China/ ; 42006080//National Natural Science Foundation of China/ ; }, abstract = {Biological invasion is a primary direct driver of biodiversity loss. Recently, owing to exploitation competition with an invasive mussel, Mytella strigata (Hanley, 1843), there has been a drastic decrease in the population of native Perna viridis (Linnaeus, 1758) in several western Pacific regions. In the present study, intestinal microbiota, metabolome, and key digestive enzyme activities were compared between the two competing mussels, M. strigata and P. viridis, to elucidate the differences in intestinal microbiota and metabolic points. We observed that Proteobacteria, Firmicutes, and Bacteroidota were the three predominant bacterial phyla in the two species. The relative abundance of Bacteroidota related to carbohydrate-degrading ability was significantly higher in M. strigata than in P. viridis. Compared to P. viridis, different metabolites including maltose and trehalose were enriched in M. strigata. Lastly, higher carbohydrases activities of alpha-amylase, cellulase, and xylanase were observed in M. strigata than in P. viridis. These differences might play an important role in the adaptation process of M. strigata to the new environment. This study provides important basic knowledge for investigating the competition between M. strigata and P. viridis in terms of food resources utilization.}, } @article {pmid38539968, year = {2024}, author = {Dias, EFF and de Carvalho, FE and Polizel, GHG and Cançado, FACQ and Furlan, É and Fernandes, AC and Schalch Júnior, FJ and Santos, GEC and Ferraz, JBS and Santana, MHA}, title = {Fetal Programming Influence on Microbiome Diversity and Ruminal and Cecal Epithelium in Beef Cattle.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {6}, pages = {}, doi = {10.3390/ani14060870}, pmid = {38539968}, issn = {2076-2615}, support = {17/12105-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 20/15192-6//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 307593/2021-5//National Council for Scientific and Technological Development/ ; }, abstract = {We explored the influence of maternal nutritional strategies on the development of the rumen and cecum in offspring. Additionally, we investigated the potential repercussions of prenatal nutrition on the rumen and fecal microbiota composition, utilizing metagenomic 16S techniques, to understand the effects of fetal programming (FP) in Nellore cattle. A total of 63 bulls submitted to different prenatal nutrition strategies, namely, non-programming (NP), partial programming (PP), and complete programming (CP), were evaluated. The rumen epithelium was methodically evaluated based on the presence of rumenitis and structural irregularities. The assessment of cecum lesions was conducted post-evisceration, whereby all thoroughly cleaned ceca were methodically evaluated. Samples from 15 animals of rumen fluid at slaughter and feces during the finishing phase were collected, respectively. All DNA extraction were carried out using the Macherey Nagel NucleoSpin Tissue[®], and 16S sequencing was conducted using the V4 primers on the MiSeq platform. Within the ruminal ecosystem, an estimated range of 90 to 130 distinct amplicon sequence variants was discerned, as distributed across 45,000 to 70,000 sequencing reads. Our metagenomic exploration unveils microbial communities that distinctly mirror gastrointestinal tract microenvironments and dietary influences. In sum, this comprehensive study advances our comprehension of FP, highlighting the interplay of maternal nutrition, gastrointestinal development, and microbial communities, contributing significantly to the fields of animal science.}, } @article {pmid38538803, year = {2024}, author = {Masuda, S and Gan, P and Kiguchi, Y and Anda, M and Sasaki, K and Shibata, A and Iwasaki, W and Suda, W and Shirasu, K}, title = {Uncovering microbiomes of the rice phyllosphere using long-read metagenomic sequencing.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {357}, pmid = {38538803}, issn = {2399-3642}, abstract = {The plant microbiome is crucial for plant growth, yet many important questions remain, such as the identification of specific bacterial species in plants, their genetic content, and location of these genes on chromosomes or plasmids. To gain insights into the genetic makeup of the rice-phyllosphere, we perform a metagenomic analysis using long-read sequences. Here, 1.8 Gb reads are assembled into 26,067 contigs including 142 circular sequences. Within these contigs, 669 complete 16S rRNA genes are clustered into 166 bacterial species, 121 of which show low identity (<97%) to defined sequences, suggesting novel species. The circular contigs contain novel chromosomes and a megaplasmid, and most of the smaller circular contigs are defined as novel plasmids or bacteriophages. One circular contig represents the complete chromosome of a difficult-to-culture bacterium Candidatus Saccharibacteria. Our findings demonstrate the efficacy of long-read-based metagenomics for profiling microbial communities and discovering novel sequences in plant-microbiome studies.}, } @article {pmid38538312, year = {2024}, author = {Oba, K and Suenaga, T and Yasuda, S and Kuroiwa, M and Hori, T and Lackner, S and Terada, A}, title = {Quest for Nitrous Oxide-reducing Bacteria Present in an Anammox Biofilm Fed with Nitrous Oxide.}, journal = {Microbes and environments}, volume = {39}, number = {1}, pages = {}, doi = {10.1264/jsme2.ME23106}, pmid = {38538312}, issn = {1347-4405}, abstract = {N2O-reducing bacteria have been examined and harnessed to develop technologies that reduce the emission of N2O, a greenhouse gas produced by biological nitrogen removal. Recent investigations using omics and physiological activity approaches have revealed the ecophysiologies of these bacteria during nitrogen removal. Nevertheless, their involvement in‍ ‍anammox processes remain unclear. Therefore, the present study investigated the identity, genetic potential, and activity‍ ‍of N2O reducers in an anammox reactor. We hypothesized that N2O is limiting for N2O-reducing bacteria‍ ‍and an‍ ‍exogeneous N2O supply enriches as-yet-uncultured N2O-reducing bacteria. We conducted a 1200-day incubation of N2O-reducing bacteria in an anammox consortium using gas-permeable membrane biofilm reactors (MBfRs), which efficiently supply N2O in a bubbleless form directly to a biofilm grown on a gas-permeable membrane. A [15]N tracer test indicated that the supply of N2O resulted in an enriched biomass with a higher N2O sink potential. Quantitative PCR and 16S rRNA amplicon sequencing revealed Clade II nosZ type-carrying N2O-reducing bacteria as protagonists of N2O sinks. Shotgun metagenomics showed the genetic potentials of the predominant Clade II nosZ-carrying bacteria, Anaerolineae and Ignavibacteria in MBfRs. Gemmatimonadota and non-anammox Planctomycetota increased their abundance in MBfRs despite their overall lower abundance. The implication of N2O as an inhibitory compound scavenging vitamin B12, which is essential for the synthesis of methionine, suggested its limited suppressive effect on the growth of B12-dependent bacteria, including N2O reducers. We identified Dehalococcoidia and Clostridia as predominant N2O sinks in an anammox consortium fed exogenous N2O because of the higher metabolic potential of vitamin B12-dependent biosynthesis.}, } @article {pmid38537467, year = {2024}, author = {Wang, X and Wang, J and Zou, Y and Bie, Y and Mahmood, A and Zhang, L and Liao, L and Song, Z and Liu, G and Zhang, C}, title = {Urea fertilization increased CO2 and CH4 emissions by enhancing C-cycling genes in semi-arid grasslands.}, journal = {Journal of environmental management}, volume = {356}, number = {}, pages = {120718}, doi = {10.1016/j.jenvman.2024.120718}, pmid = {38537467}, issn = {1095-8630}, abstract = {Global climate change is predicted to increase exogenous N input into terrestrial ecosystems, leading to significant changes in soil C-cycling. However, it remains largely unknown how these changes affect soil C-cycling, especially in semi-arid grasslands, which are one of the most vulnerable ecosystems. Here, based on a 3-year field study involving N additions (0, 25, 50, and 100 kg ha[-1] yr[-1] of urea) in a semi-arid grassland on the Loess Plateau, we investigated the impact of urea fertilization on plant characteristics, soil properties, CO2 and CH4 emissions, and microbial C cycling genes. The compositions of genes involved in C cycling, including C fixation, degradation, methanogenesis, and methane oxidation, were determined using metagenomics analysis. We found that N enrichment increased both above- and belowground biomasses and soil organic C content, but this positive effect was weakened when excessive N was input (N100). N enrichment also altered the C-cycling processes by modifying C-cycle-related genes, specifically stimulating the Calvin cycle C-fixation process, which led to an increase in the relative abundance of cbbS, prkB, and cbbL genes. However, it had no significant effect on the Reductive citrate cycle and 3-hydroxypropionate bi-cycle. N enrichment led to higher soil CO2 and CH4 emissions compared to treatments without added N. This increase showed significant correlations with C degradation genes (bglA, per, and lpo), methanogenesis genes (mch, ftr, and mcr), methane oxidation genes (pmoA, pmoB, and pmoC), and the abundance of microbial taxa harboring these genes. Microbial C-cycling genes were primarily influenced by N-induced changes in soil properties. Specifically, reduced soil pH largely explained the alterations in methane metabolism, while elevated available N levels were mainly responsible for the shift in C fixation and C degradation genes. Our results suggest that soil N enrichment enhances microbial C-cycling processes and soil CO2 and CH4 emissions in semi-arid ecosystems, which contributes to more accurate predictions of ecosystem C-cycling under future climate change.}, } @article {pmid38536208, year = {2024}, author = {Prentice, MB and Gilbertson, MLJ and Storm, DJ and Turner, WC and Walsh, DP and Pinkerton, ME and Kamath, PL}, title = {Metagenomic sequencing sheds light on microbes putatively associated with pneumonia-related fatalities of white-tailed deer (Odocoileus virginianus).}, journal = {Microbial genomics}, volume = {10}, number = {3}, pages = {}, doi = {10.1099/mgen.0.001214}, pmid = {38536208}, issn = {2057-5858}, abstract = {With emerging infectious disease outbreaks in human, domestic and wild animal populations on the rise, improvements in pathogen characterization and surveillance are paramount for the protection of human and animal health, as well as the conservation of ecologically and economically important wildlife. Genomics offers a range of suitable tools to meet these goals, with metagenomic sequencing facilitating the characterization of whole microbial communities associated with emerging and endemic disease outbreaks. Here, we use metagenomic sequencing in a case-control study to identify microbes in lung tissue associated with newly observed pneumonia-related fatalities in 34 white-tailed deer (Odocoileus virginianus) in Wisconsin, USA. We identified 20 bacterial species that occurred in more than a single individual. Of these, only Clostridium novyi was found to substantially differ (in number of detections) between case and control sample groups; however, this difference was not statistically significant. We also detected several bacterial species associated with pneumonia and/or other diseases in ruminants (Mycoplasma ovipneumoniae, Trueperella pyogenes, Pasteurella multocida, Anaplasma phagocytophilum, Fusobacterium necrophorum); however, these species did not substantially differ between case and control sample groups. On average, we detected a larger number of bacterial species in case samples than controls, supporting the potential role of polymicrobial infections in this system. Importantly, we did not detect DNA of viruses or fungi, suggesting that they are not significantly associated with pneumonia in this system. Together, these results highlight the utility of metagenomic sequencing for identifying disease-associated microbes. This preliminary list of microbes will help inform future research on pneumonia-associated fatalities of white-tailed deer.}, } @article {pmid38535607, year = {2024}, author = {George, UE and Faleye, TOC and De Coninck, L and Agbaje, ST and Ifeorah, IM and Onoja, BA and Oni, EI and Olayinka, AO and Ajileye, TG and Oragwa, AO and Akinleye, TE and Popoola, BO and Osasona, OG and Olayinka, OT and George, OA and Muhammad, AI and Komolafe, I and Adeniji, AJ and Matthijnssens, J and Adewumi, MO}, title = {Metagenomic Detection and Genetic Characterization of Human Sapoviruses among Children with Acute Flaccid Paralysis in Nigeria.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/pathogens13030264}, pmid = {38535607}, issn = {2076-0817}, abstract = {Using a metagenomic sequencing approach on stool samples from children with Acute Flaccid Paralysis (AFP), we describe the genetic diversity of Sapoviruses (SaVs) in children in Nigeria. We identified six complete genome sequences and two partial genome sequences. Several SaV genogroups and genotypes were detected, including GII (GII.4 and GII.8), GIV (GIV.1), and GI (GI.2 and GI.7). To our knowledge, this is the first description of SaV infections and complete genomes from Nigeria. Pairwise identity and phylogenetic analysis showed that the Nigerian SaVs were related to previously documented gastroenteritis outbreaks with associated strains from China and Japan. Minor variations in the functional motifs of the nonstructural proteins NS3 and NS5 were seen in the Nigerian strains. To adequately understand the effect of such amino acid changes, a better understanding of the biological function of these proteins is vital. The identification of distinct SaVs reinforces the need for robust surveillance in acute gastroenteritis (AGE) and non-AGE cohorts to better understand SaVs genotype diversity, evolution, and its role in disease burden in Nigeria. Future studies in different populations are, therefore, recommended.}, } @article {pmid38535561, year = {2024}, author = {Yang, Z and Cai, K and Liao, Y and Wu, WC and Xing, L and Hu, M and Ren, J and Zhang, J and Zhu, X and Yuan, K and Wang, S and Huang, H and Yang, C and Zhang, M and Shi, M and Lu, H}, title = {Total Infectome Characterization of Respiratory Infections during the 2022-23 COVID-19 Outbreak in China Revealed Extensive Coinfections with Links to SARS-CoV-2 Status, Age, and Disease Severity.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/pathogens13030216}, pmid = {38535561}, issn = {2076-0817}, support = {KQTD20200820145822023//Shenzhen Science and Technology Program/ ; }, abstract = {Between 7 December 2022 and 28 February 2023, China experienced a new wave of COVID-19 that swept across the entire country and resulted in an increasing amount of respiratory infections and hospitalizations. The purpose of this study is to reveal the intensity and composition of coinfecting microbial agents. In total, 196 inpatients were recruited from The Third People's Hospital of Shenzhen, and 169 respiratory and 73 blood samples were collected for metagenomic next-generation sequencing. The total "Infectome" was characterized and compared across different groups defined by the SARS-CoV-2 detection status, age groups, and severity of disease. Our results revealed a total of 22 species of pathogenic microbes (4 viruses, 13 bacteria, and 5 fungi), and more were discovered in the respiratory tract than in blood. The diversity of the total infectome was highly distinguished between respiratory and blood samples, and it was generally higher in patients that were SARS-CoV-2-positive, older in age, and with more severe disease. At the individual pathogen level, HSV-1 seemed to be the major contributor to these differences observed in the overall comparisons. Collectively, this study reveals the highly complex respiratory infectome and high-intensity coinfection in patients admitted to the hospital during the period of the 2023 COVID-19 pandemic in China.}, } @article {pmid38535319, year = {2024}, author = {Tao, P and Conarello, S and Wyche, TP and Zhang, NR and Chng, K and Kang, J and Sana, TR}, title = {Metabolomics and Lipidomics Analyses Aid Model Classification of Type 2 Diabetes in Non-Human Primates.}, journal = {Metabolites}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/metabo14030159}, pmid = {38535319}, issn = {2218-1989}, abstract = {Type 2 diabetes (T2D) is a global public health issue characterized by excess weight, abdominal obesity, dyslipidemia, hyperglycemia, and a progressive increase in insulin resistance. Human population studies of T2D development and its effects on systemic metabolism are confounded by many factors that cannot be controlled, complicating the interpretation of results and the identification of early biomarkers. Aged, sedentary, and overweight/obese non-human primates (NHPs) are one of the best animal models to mimic spontaneous T2D development in humans. We sought to identify and distinguish a set of plasma and/or fecal metabolite biomarkers, that have earlier disease onset predictability, and that could be evaluated for their predictability in subsequent T2D studies in human cohorts. In this study, a single plasma and fecal sample was collected from each animal in a colony of 57 healthy and dysmetabolic NHPs and analyzed for metabolomics and lipidomics. The samples were comprehensively analyzed using untargeted and targeted LC/MS/MS. The changes in each animal's disease phenotype were monitored using IVGTT, HbA1c, and other clinical metrics, and correlated with their metabolic profile. The plasma and fecal lipids, as well as bile acid profiles, from Healthy, Dysmetabolic (Dys), and Diabetic (Dia) animals were compared. Following univariate and multivariate analyses, including adjustments for weight, age, and sex, several plasma lipid species were identified to be significantly different between these animal groups. Medium and long-chain plasma phosphatidylcholines (PCs) ranked highest at distinguishing Healthy from Dys animals, whereas plasma triglycerides (TG) primarily distinguished Dia from Dys animals. Random Forest (RF) analysis of fecal bile acids showed a reduction in the secondary bile acid glycoconjugate, GCDCA, in diseased animals (AUC 0.76[0.64, 0.89]). Moreover, metagenomics results revealed several bacterial species, belonging to the genera Roseburia, Ruminococcus, Clostridium, and Streptococcus, to be both significantly enriched in non-healthy animals and associated with secondary bile acid levels. In summary, our results highlight the detection of several elevated circulating plasma PCs and microbial species associated with fecal secondary bile acids in NHP dysmetabolic states. The lipids and metabolites we have identified may help researchers to differentiate individual NHPs more precisely between dysmetabolic and overtly diabetic states. This could help assign animals to study groups that are more likely to respond to potential therapies where a difference in efficacy might be anticipated between early vs. advanced disease.}, } @article {pmid38535318, year = {2024}, author = {Huang, S and Zhu, L and Wang, K and Zhang, X and Mao, D and Rasool, A}, title = {Unravel the Supremacy of Klebsiella variicola over Native Microbial Strains for Aroma-Enhancing Compound Production in Reconstituted Tobacco Concentrate through Metagenomic Analysis.}, journal = {Metabolites}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/metabo14030158}, pmid = {38535318}, issn = {2218-1989}, support = {21546012//National Natural Science Foundation of China/ ; }, abstract = {Sensory attributes strongly influence consumers' preferences for products. The inoculation of the Klebsiella variicola H8 strain in a reconstituted tobacco leaf concentrate (RTLC) solution increased neutral aroma-enhancing compound (NAEC) production by 45%, decreased the nicotine level by 25%, decreased the water-soluble total sugar content by ~36%, and improved the sensory quality by 5.71%. The production of NAECs such as dihydrokiwi lactone (DHKL: 192.86%), 1,2,3,4-tetrahydro-1,1,6-trimethylnaphthalene (THTMN: 177.77%), 2,4-di-tert-butylphenol (DTBP: 25%), 4-oxoisofolkone (OIFK: 116.66%,) 1,9-heptadecadiene-4,6-diyn-3-ol (HDD: 116.67%), β-damastrone (BDS: 116.67), and megastigmatrienone A (MSTA: 116.67%) was increased. A metagenomics analysis of the microbial community in the fermented RTLC (FRTLC) was performed to elucidate the mechanism by which NAECs were produced. As a result, 24 groups of functional genes were identified, and among them, five families of carbohydrate-active enzymes, (i) glycoside hydrolase (GH), (ii) glycosyltransferase (GT), (iii) polysaccharide lyase (PL), (iv) carbohydrate esterase (CE), and (v) auxiliary active enzyme (AA), were found to be positively correlated with the production of NAECs. However, among the GHs, the GHs annotated from the H8 strain chromosome displayed the highest relative abundance and a positive correlation with the production of NAECs. Specifically, the GH13-14, GH13-20, GH13-38, GH13-25, GH13-10, GH42, and GH28 genes of the H8 strain were relatively more abundant and were key contributors to the production of NAECs. The correlation analyses revealed that the H8 strain plays a leading role among all the microorganisms in FRTLC in the production of NAECs. Our findings support the application of Klebsiella variicola in NAEC production and a reduction in nicotine content in tobacco products.}, } @article {pmid38535317, year = {2024}, author = {Dessì, A and Pintus, R and Fanos, V and Bosco, A}, title = {Integrative Multiomics Approach to Skin: The Sinergy between Individualised Medicine and Futuristic Precision Skin Care?.}, journal = {Metabolites}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/metabo14030157}, pmid = {38535317}, issn = {2218-1989}, abstract = {The skin is a complex ecosystem colonized by millions of microorganisms, the skin microbiota, which are crucial in regulating not only the physiological functions of the skin but also the metabolic changes underlying the onset of skin diseases. The high microbial colonization together with a low diversity at the phylum level and a high diversity at the species level of the skin is very similar to that of the gastrointestinal tract. Moreover, there is an important communication pathway along the gut-brain-skin axis, especially associated with the modulation of neurotransmitters by the microbiota. Therefore, it is evident that the high complexity of the skin system, due not only to the genetics of the host but also to the interaction of the host with resident microbes and between microbe and microbe, requires a multi-omics approach to be deeply understood. Therefore, an integrated analysis, with high-throughput technologies, of the consequences of microbial interaction with the host through the study of gene expression (genomics and metagenomics), transcription (transcriptomics and meta-transcriptomics), and protein production (proteomics and meta-proteomics) and metabolite formation (metabolomics and lipidomics) would be useful. Although to date very few studies have integrated skin metabolomics data with at least one other 'omics' technology, in the future, this approach will be able to provide simple and fast tests that can be routinely applied in both clinical and cosmetic settings for the identification of numerous skin diseases and conditions. It will also be possible to create large archives of multi-omics data that can predict individual responses to pharmacological treatments and the efficacy of different cosmetic products on individual subjects by means of specific allotypes, with a view to increasingly tailor-made medicine. In this review, after analyzing the complexity of the skin ecosystem, we have highlighted the usefulness of this emerging integrated omics approach for the analysis of skin problems, starting with one of the latest 'omics' sciences, metabolomics, which can photograph the expression of the genome during its interaction with the environment.}, } @article {pmid38535292, year = {2024}, author = {Bidkhori, G and Shoaie, S}, title = {MIGRENE: The Toolbox for Microbial and Individualized GEMs, Reactobiome and Community Network Modelling.}, journal = {Metabolites}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/metabo14030132}, pmid = {38535292}, issn = {2218-1989}, support = {EP/S001301/1//Engineering and Physical Sciences Research Council/ ; BB/S016899/1//Biotechnology Biological Sciences Research Council/ ; }, abstract = {Understanding microbial metabolism is crucial for evaluating shifts in human host-microbiome interactions during periods of health and disease. However, the primary hurdle in the realm of constraint-based modeling and genome-scale metabolic models (GEMs) pertaining to host-microbiome interactions lays in the efficient utilization of metagenomic data for constructing GEMs that encompass unexplored and uncharacterized genomes. Challenges persist in effectively employing metagenomic data to address individualized microbial metabolisms to investigate host-microbiome interactions. To tackle this issue, we have created a computational framework designed for personalized microbiome metabolisms. This framework takes into account factors such as microbiome composition, metagenomic species profiles and microbial gene catalogues. Subsequently, it generates GEMs at the microbial level and individualized microbiome metabolisms, including reaction richness, reaction abundance, reactobiome, individualized reaction set enrichment (iRSE), and community models. Using the toolbox, our findings revealed a significant reduction in both reaction richness and GEM richness in individuals with liver cirrhosis. The study highlighted a potential link between the gut microbiota and liver cirrhosis, i.e., increased level of LPS, ammonia production and tyrosine metabolism on liver cirrhosis, emphasizing the importance of microbiome-related factors in liver health.}, } @article {pmid38534459, year = {2024}, author = {Yaish, MW and Al-Busaidi, A and Glick, BR and Ahmed, T and Alatalo, JM}, title = {The Effects of Salinity and Genotype on the Rhizospheric Mycobiomes in Date Palm Seedlings.}, journal = {Biology}, volume = {13}, number = {3}, pages = {}, doi = {10.3390/biology13030190}, pmid = {38534459}, issn = {2079-7737}, support = {IG/SCI/BIOL/24/03//Sultan Qaboos University/ ; }, abstract = {Salinity severely affects the health and productivity of plants, with root-associated microbes, including fungi, potentially playing a crucial role in mitigating this effect and promoting plant health. This study employed metagenomics to investigate differences in the structures of the epiphyte mycobiomes in the rhizospheres of seedlings of two distinct date palm cultivars with contrasting salinity tolerances, the susceptible cultivar, 'Zabad', and the tolerant cultivar, 'Umsila'. Next-generation sequencing (NGS) of the internal transcribed spacer (ITS) rRNA was utilized as a DNA barcoding tool. The sequencing of 12 mycobiome libraries yielded 905,198 raw sequences of 268,829 high-quality reads that coded for 135 unique and annotatable operational taxonomic units (OTUs). An OTU analysis revealed differences in the rhizofungal community structures between the treatments regardless of genotype, and non-metric dimensional scaling (N-MDS) analyses demonstrated distinct separations between the cultivars under saline stress. However, these differences were not detected under the control environmental conditions, i.e., no salinity. The rhizospheric fungal community included four phyla (Ascomycota, Basidiomycota, Chytridiomycota, and Mucoromycota), with differences in the abundances of Aspergillus, Clonostachys, and Fusarium genera in response to salinity, regardless of the genotype. Differential pairwise comparisons showed that Fusarium falciforme-solani and Aspergillus sydowii-versicolor increased in abundance under saline conditions, providing potential future in vitro isolation guidelines for plant growth-promoting fungi. This study highlights the intricate dynamics of the rhizosphere microbial communities in date palms and their responses to salt stress. Additionally, we found no support for the hypothesis that indigenous epiphytic fungal communities are significantly involved in salinity tolerance in date palms.}, } @article {pmid38534158, year = {2024}, author = {Oliver, A and Podell, S and Wegley Kelly, L and Sparagon, WJ and Plominsky, AM and Nelson, RS and Laurens, LML and Augyte, S and Sims, NA and Nelson, CE and Allen, EE}, title = {Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish.}, journal = {mBio}, volume = {}, number = {}, pages = {e0049624}, doi = {10.1128/mbio.00496-24}, pmid = {38534158}, issn = {2150-7511}, abstract = {Coastal herbivorous fishes consume macroalgae, which is then degraded by microbes along their digestive tract. However, there is scarce genomic information about the microbiota that perform this degradation. This study explores the potential of Kyphosus gastrointestinal microbial symbionts to collaboratively degrade and ferment polysaccharides from red, green, and brown macroalgae through in silico study of carbohydrate-active enzyme and sulfatase sequences. Recovery of metagenome-assembled genomes (MAGs) from previously described Kyphosus gut metagenomes and newly sequenced bioreactor enrichments reveals differences in enzymatic capabilities between the major microbial taxa in Kyphosus guts. The most versatile of the recovered MAGs were from the Bacteroidota phylum, whose MAGs house enzyme collections able to decompose a variety of algal polysaccharides. Unique enzymes and predicted degradative capacities of genomes from the Bacillota (genus Vallitalea) and Verrucomicrobiota (order Kiritimatiellales) highlight the importance of metabolic contributions from multiple phyla to broaden polysaccharide degradation capabilities. Few genomes contain the required enzymes to fully degrade any complex sulfated algal polysaccharide alone. The distribution of suitable enzymes between MAGs originating from different taxa, along with the widespread detection of signal peptides in candidate enzymes, is consistent with cooperative extracellular degradation of these carbohydrates. This study leverages genomic evidence to reveal an untapped diversity at the enzyme and strain level among Kyphosus symbionts and their contributions to macroalgae decomposition. Bioreactor enrichments provide a genomic foundation for degradative and fermentative processes central to translating the knowledge gained from this system to the aquaculture and bioenergy sectors.IMPORTANCESeaweed has long been considered a promising source of sustainable biomass for bioenergy and aquaculture feed, but scalable industrial methods for decomposing terrestrial compounds can struggle to break down seaweed polysaccharides efficiently due to their unique sulfated structures. Fish of the genus Kyphosus feed on seaweed by leveraging gastrointestinal bacteria to degrade algal polysaccharides into simple sugars. This study reconstructs metagenome-assembled genomes for these gastrointestinal bacteria to enhance our understanding of herbivorous fish digestion and fermentation of algal sugars. Investigations at the gene level identify Kyphosus guts as an untapped source of seaweed-degrading enzymes ripe for further characterization. These discoveries set the stage for future work incorporating marine enzymes and microbial communities in the industrial degradation of algal polysaccharides.}, } @article {pmid38534152, year = {2024}, author = {Saini, JS and Adler, A and Cardona, L and Rodilla Ramírez, PN and Pei, R and Holliger, C}, title = {Microbial genome collection of aerobic granular sludge cultivated in sequencing batch reactors using different carbon source mixtures.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0010224}, doi = {10.1128/mra.00102-24}, pmid = {38534152}, issn = {2576-098X}, abstract = {Aerobic granular sludge (AGS) consists of a microbial consortium that has an important role in wastewater treatment. This study investigates AGS microorganisms cultivated in a laboratory-scale sequencing batch reactor. Metagenomic sequencing was conducted using PacBio and Illumina, resulting in 759 metagenome-assembled genomes, 331 of which remained after dereplication.}, } @article {pmid38533900, year = {2024}, author = {Jackson, I and Woodman, P and Dowd, M and Fibiger, L and Cassidy, LM}, title = {Ancient Genomes From Bronze Age Remains Reveal Deep Diversity and Recent Adaptive Episodes for Human Oral Pathobionts.}, journal = {Molecular biology and evolution}, volume = {41}, number = {3}, pages = {}, doi = {10.1093/molbev/msae017}, pmid = {38533900}, issn = {1537-1719}, support = {IRCLA/2022/126//Wellcome Trust Institutional Strategic Support Fund/ ; 18/CRT/6214//Science Foundation Ireland Centre for Research Training in Genomics Data Science/ ; }, abstract = {Ancient microbial genomes can illuminate pathobiont evolution across millenia, with teeth providing a rich substrate. However, the characterization of prehistoric oral pathobiont diversity is limited. In Europe, only preagricultural genomes have been subject to phylogenetic analysis, with none compared to more recent archaeological periods. Here, we report well-preserved microbiomes from two 4,000-year-old teeth from an Irish limestone cave. These contained bacteria implicated in periodontitis, as well as Streptococcus mutans, the major cause of caries and rare in the ancient genomic record. Despite deriving from the same individual, these teeth produced divergent Tannerella forsythia genomes, indicating higher levels of strain diversity in prehistoric populations. We find evidence of microbiome dysbiosis, with a disproportionate quantity of S. mutans sequences relative to other oral streptococci. This high abundance allowed for metagenomic assembly, resulting in its first reported ancient genome. Phylogenetic analysis indicates major postmedieval population expansions for both species, highlighting the inordinate impact of recent dietary changes. In T. forsythia, this expansion is associated with the replacement of older lineages, possibly reflecting a genome-wide selective sweep. Accordingly, we see dramatic changes in T. forsythia's virulence repertoire across this period. S. mutans shows a contrasting pattern, with deeply divergent lineages persisting in modern populations. This may be due to its highly recombining nature, allowing for maintenance of diversity through selective episodes. Nonetheless, an explosion in recent coalescences and significantly shorter branch lengths separating bacteriocin-carrying strains indicate major changes in S. mutans demography and function coinciding with sugar popularization during the industrial period.}, } @article {pmid38533516, year = {2024}, author = {Chen, L and Lin, X and Cai, X and Zeng, S and Yuan, Y and Huang, Z and Yan, J and Li, Y}, title = {The challenge of managing ischemic stroke in brucellosis: a case report.}, journal = {Frontiers in immunology}, volume = {15}, number = {}, pages = {1347216}, pmid = {38533516}, issn = {1664-3224}, abstract = {A 64-year-old woman was admitted to the hospital for sudden weakness in one of her left limbs. The patient was diagnosed with acute ischemic stroke (IS) of undetermined cause and received intravenous thrombolysis. Following thrombolysis, the patient's left limb weakness improved, but she subsequently developed recurrent high fever and delirium. Further diagnostic tests revealed that she had been infected with Brucella melitensis. The patient showed significant improvement during anti-infection treatment for Brucellosis and secondary prevention treatment for IS. However, her condition unexpectedly worsened on the 44th day after admission due to a hemorrhagic stroke (HS), which required an urgent craniotomy. Immunohistochemical analysis of the hematoma sample collected during the operation showed the presence of CD4[+] and CD8[+] T lymphocytes surrounding the blood vessels. This case highlights the unique challenge of managing IS in brucellosis and sheds light on the potential role of T lymphocytes in the immune response related to stroke.}, } @article {pmid38533070, year = {2024}, author = {Munyai, R and Ogola, HJO and Wambui Kimani, V and Modise, DM}, title = {Unlocking water potential in drylands: Quicklime and fly ash enhance soil microbiome structure, ecological networks and function in acid mine drainage water-irrigated agriculture.}, journal = {Heliyon}, volume = {10}, number = {6}, pages = {e27985}, pmid = {38533070}, issn = {2405-8440}, abstract = {In water-stressed regions, treated acid mine drainage (AMD) water for irrigated agriculture is a potential solution to address freshwater scarcity. However, a significant knowledge gap exists on the short and long-term effects of treated AMD water on soil health. This study used high-throughput Illumina sequencing and predictive metagenomic profiling to investigate the impact of untreated AMD (AMD), quicklime- (A1Q and A2Q) and quicklime and fly ash-treated AMD water (AFQ) irrigation on soil bacterial diversity, co-occurrence networks and function. Results showed that untreated AMD water significantly increased soil acidity, electrical conductivity (EC), sulfate (SO4[2-]), and heavy metals (HM), including reduced microbial diversity, disrupted interaction networks, and functional capacity. pH, EC, Cu, and Pb were identified as key environmental factors shaping soil microbial diversity and structure. Predominantly, Pseudomonas, Ralstonia picketti, Methylotenera KB913035, Brevundimonas vesicularis, and Methylobacteriumoryzae, known for their adaptability to acidic conditions and metal resistance, were abundant in AMD soils. However, soils irrigated with treated AMD water exhibited significantly reduced acidity (pH > 6.5), HM and SO4[2-] levels, with an enrichment of a balanced bacterial taxa associated with diverse functions related to soil health and agricultural productivity. These taxa included Sphingomonas, Pseudoxanthomonas, Achromobacter, Microbacterium, Rhodobacter, Clostridium, Massillia, Rhizobium, Paenibacillus, and Hyphomicrobium. Moreover, treated AMD water contributed to higher connectivity and balance within soil bacterial co-occurrence networks compared to untreated AMD water. These results show that quicklime/fly ash treatments can help lessen impacts of AMD water on soil microbiome and health, suggesting its potential for irrigated agriculture in water-scarce regions.}, } @article {pmid38532703, year = {2024}, author = {Sheikh, IA and Bianchi-Smak, J and Laubitz, D and Schiro, G and Midura-Kiela, MT and Besselsen, DG and Vedantam, G and Jarmakiewicz, S and Filip, R and Ghishan, FK and Gao, N and Kiela, PR}, title = {Transplant of microbiota from Crohn's disease patients to germ-free mice results in colitis.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2333483}, doi = {10.1080/19490976.2024.2333483}, pmid = {38532703}, issn = {1949-0984}, abstract = {Although the role of the intestinal microbiota in the pathogenesis of inflammatory bowel disease (IBD) is beyond debate, attempts to verify the causative role of IBD-associated dysbiosis have been limited to reports of promoting the disease in genetically susceptible mice or in chemically induced colitis. We aimed to further test the host response to fecal microbiome transplantation (FMT) from Crohn's disease patients on mucosal homeostasis in ex-germ-free (xGF) mice. We characterized and transferred fecal microbiota from healthy patients and patients with defined Crohn's ileocolitis (CD_L3) to germ-free mice and analyzed the resulting microbial and mucosal homeostasis by 16S profiling, shotgun metagenomics, histology, immunofluorescence (IF) and RNAseq analysis. We observed a markedly reduced engraftment of CD_L3 microbiome compared to healthy control microbiota. FMT from CD_L3 patients did not lead to ileitis but resulted in colitis with features consistent with CD: a discontinued pattern of colitis, more proximal colonic localization, enlarged isolated lymphoid follicles and/or tertiary lymphoid organ neogenesis, and a transcriptomic pattern consistent with epithelial reprograming and promotion of the Paneth cell-like signature in the proximal colon and immune dysregulation characteristic of CD. The observed inflammatory response was associated with persistently increased abundance of Ruminococcus gnavus, Erysipelatoclostridium ramosum, Faecalimonas umbilicate, Blautia hominis, Clostridium butyricum, and C. paraputrificum and unexpected growth of toxigenic C. difficile, which was below the detection level in the community used for inoculation. Our study provides the first evidence that the transfer of a dysbiotic community from CD patients can lead to spontaneous inflammatory changes in the colon of xGF mice and identifies a signature microbial community capable of promoting colonization of pathogenic and conditionally pathogenic bacteria.}, } @article {pmid38532461, year = {2024}, author = {Pax, K and Buduneli, N and Alan, M and Meric, P and Gurlek, O and Dabdoub, SM and Kumar, PS}, title = {Placental TLR recognition of salivary and subgingival microbiota is associated with pregnancy complications.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {64}, pmid = {38532461}, issn = {2049-2618}, support = {1F30DE029676-01A1/DE/NIDCR NIH HHS/United States ; R01DE027857/DE/NIDCR NIH HHS/United States ; R01DE027857/DE/NIDCR NIH HHS/United States ; }, abstract = {BACKGROUND: Pre-term birth, the leading cause of neonatal mortality, has been associated with maternal periodontal disease and the presence of oral pathogens in the placenta. However, the mechanisms that underpin this link are not known. This investigation aimed to identify the origins of placental microbiota and to interrogate the association between parturition complications and immune recognition of placental microbial motifs. Video Abstract METHODS: Saliva, plaque, serum, and placenta were collected during 130 full-term (FT), pre-term (PT), or pre-term complicated by pre-eclampsia (PTPE) deliveries and subjected to whole-genome shotgun sequencing. Real-time quantitative PCR was used to measure toll-like receptors (TLR) 1-10 expression in placental samples. Source tracking was employed to trace the origins of the placental microbiota.

RESULTS: We discovered 10,007 functionally annotated genes representing 420 taxa in the placenta that could not be attributed to contamination. Placental microbial composition was the biggest discriminator of pregnancy complications, outweighing hypertension, BMI, smoking, and maternal age. A machine-learning algorithm trained on this microbial dataset predicted PTPE and PT with error rates of 4.05% and 8.6% (taxonomy) and 6.21% and 7.38% (function). Logistic regression revealed 32% higher odds of parturition complication (95% CI 2.8%, 81%) for every IQR increase in the Shannon diversity index after adjusting for maternal smoking status, maternal age, and gravida. We also discovered distinct expression patterns of TLRs that detect RNA- and DNA-containing antigens in the three groups, with significant upregulation of TLR9, and concomitant downregulation of TLR7 in PTPE and PT groups, and dense correlation networks between microbial genes and these TLRs. 70-82% of placental microbiota were traced to serum and thence to the salivary and subgingival microbiomes. The oral and serum microbiomes of PTPE and PT groups displayed significant enrichment of genes encoding iron transport, exosome, adhesion, quorum sensing, lipopolysaccharide, biofilm, and steroid degradation.

CONCLUSIONS: Within the limits of cross-sectional analysis, we find evidence to suggest that oral bacteria might translocate to the placenta via serum and trigger immune signaling pathways capable of inducing placental vascular pathology. This might explain, in part, the higher incidence of obstetric syndromes in women with periodontal disease.}, } @article {pmid38532348, year = {2024}, author = {Yang, H and Xu, N and Yan, M and Yang, L and Wen, S and Wang, S and Qu, C and Xu, K and Yang, X and Wang, G}, title = {Comparison of metagenomic next-generation sequencing and conventional culture for the diagnostic performance in febrile patients with suspected infections.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {350}, pmid = {38532348}, issn = {1471-2334}, abstract = {BACKGROUND: Timely and accurate identification of pathogens is crucial for appropriate treatment and prognosis of infectious diseases. As an increasingly popular pathogen detection method, the performance of metagenomic next-generation sequencing (mNGS) in detecting pathogens in febrile patients with suspected infection requires further exploration.

METHODS: This study included 368 febrile patients with suspected infections who were admitted to the Infectious Disease Department of Qilu Hospital, Shandong University between January 5, 2021 and April 14, 2023. Both mNGS testing and conventional culture were performed in all patients. Clinical data of enrolled patients were collected, and the diagnostic performances of mNGS and culture were compared.

RESULTS: Of the 368 enrolled patients, 231 were finally diagnosed with infection and 137 were with diseases other than infection. The sensitivity (58.01% vs. 21.65%, p < 0.001) and negative predictive value (54.67% vs. 42.9%) of mNGS were superior to those of culture. In contrast, the culture exhibited higher specificity (99.27% vs. 85.40%, p < 0.001) and positive predictive value (98.84% vs. 87.01%) than mNGS. Among infected patients with positive mNGS results, 64 received adjusted antibiotic therapy including treatment transitions, antibiotic downgrading, and combination therapy. Among them, 9 had additional antifungal drugs and 21 patients had a treatment turning point based on the mNGS results and these patients recovered and discharged due to timely antibiotic adjustment. Both positive rates of puncture fluid mNGS and tissue mNGS were higher than those of culture in the patients who had prior antibiotic use, and this difference was statistically significant (p = 0.000).

CONCLUSION: mNGS is more sensitive and accurate than traditional culture, making it ideal for identifying pathogens and screening infectious diseases, especially for those with uncultivated or difficult-to-cultivate species. Early diagnosis allows for prompt treatment with targeted antibiotics, and mNGS is recommended when samples are limited.}, } @article {pmid38531781, year = {2024}, author = {Jiang, X and Li, H and Ma, J and Li, H and Ma, X and Tang, Y and Li, J and Chi, X and Deng, Y and Zeng, S and Liu, Z}, title = {Role of type VI secretion system in pathogenic remodeling of host gut microbiota during Aeromonas veronii infection.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae053}, pmid = {38531781}, issn = {1751-7370}, abstract = {Intestinal microbial disturbance is a direct cause of host disease. The bacterial Type VI Secretion System (T6SS) often plays a crucial role in the fitness of pathogenic bacteria by delivering toxic effectors into target cells. However, its impact on the gut microbiota and host pathogenesis is poorly understood. To address this question, we characterized a new T6SS in the pathogenic Aeromonas veronii C4. First, we validated the secretion function of the core machinery of A. veronii C4 T6SS. Second, we found that the pathogenesis and colonization of A. veronii C4 is largely dependent on its T6SS. The effector secretion activity of A. veronii C4 T6SS not only provides an advantage in competition among bacteria in vitro, but also contributes to occupation of an ecological niche in the nutritionally deficient and anaerobic environment of the host intestine. Metagenomic analysis showed that the T6SS directly inhibits or eliminates symbiotic strains from the intestine, resulting in dysregulated gut microbiome homeostasis. In addition, we identified three unknown effectors, Tse1, Tse2, and Tse3, in the T6SS, which contribute to T6SS-mediated bacterial competition and pathogenesis by impairing targeted cell integrity. Our findings highlight that T6SS can remodel the host gut microbiota by intricate interplay between T6SS-mediated bacterial competition and altered host immune responses, which synergistically promote pathogenesis of A. veronii C4. Therefore, this newly characterized T6SS could represent a general interaction mechanism between the host and pathogen, and may offer a potential therapeutic target for controlling bacterial pathogens.}, } @article {pmid38530113, year = {2024}, author = {Singh, S and Segal, LN}, title = {Vive la Resistome: Are We Ready for a Metagenomics Revolution in Bronchiectasis?.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1164/rccm.202402-0352ED}, pmid = {38530113}, issn = {1535-4970}, } @article {pmid38529900, year = {2024}, author = {Street, TL and Sanderson, ND and Barker, L and Kavanagh, J and Cole, K and The GonFast Investigators Group, and Llewelyn, M and Eyre, DW}, title = {Target enrichment improves culture-independent detection of Neisseria gonorrhoeae and antimicrobial resistance determinants direct from clinical samples with Nanopore sequencing.}, journal = {Microbial genomics}, volume = {10}, number = {3}, pages = {}, doi = {10.1099/mgen.0.001208}, pmid = {38529900}, issn = {2057-5858}, abstract = {Multi-drug-resistant Neisseria gonorrhoeae infection is a significant public health risk. Rapidly detecting N. gonorrhoeae and antimicrobial-resistant (AMR) determinants by metagenomic sequencing of urine is possible, although high levels of host DNA and overgrowth of contaminating species hamper sequencing and limit N. gonorrhoeae genome coverage. We performed Nanopore sequencing of nucleic acid amplification test-positive urine samples and culture-positive urethral swabs with and without probe-based target enrichment, using a custom SureSelect panel, to investigate whether selective enrichment of N. gonorrhoeae DNA improves detection of both species and AMR determinants. Probes were designed to cover the entire N. gonorrhoeae genome, with tenfold enrichment of probes covering selected AMR determinants. Multiplexing was tested in a subset of samples. The proportion of sequence bases classified as N. gonorrhoeae increased in all samples after enrichment, from a median (IQR) of 0.05 % (0.01-0.1 %) to 76 % (42-82 %), giving a corresponding median improvement in fold genome coverage of 365 times (112-720). Over 20-fold coverage, required for robust AMR determinant detection, was achieved in 13/15(87 %) samples, compared to 2/15(13 %) without enrichment. The four samples multiplexed together also achieved >20-fold genome coverage. Coverage of AMR determinants was sufficient to predict resistance conferred by changes in chromosomal genes, where present, and genome coverage also enabled phylogenetic relationships to be reconstructed. Probe-based target enrichment can improve N. gonorrhoeae genome coverage when sequencing DNA extracts directly from urine or urethral swabs, allowing for detection of AMR determinants. Additionally, multiplexing prior to enrichment provided enough genome coverage for AMR detection and reduces the costs associated with this method.}, } @article {pmid38529721, year = {2024}, author = {Pankey, MS and Gochfeld, DJ and Gastaldi, M and Macartney, KJ and Clayshulte Abraham, A and Slattery, M and Lesser, MP}, title = {Phylosymbiosis and metabolomics resolve phenotypically plastic and cryptic sponge species in the genus Agelas across the Caribbean basin.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17321}, doi = {10.1111/mec.17321}, pmid = {38529721}, issn = {1365-294X}, support = {1632333//Division of Ocean Sciences/ ; 1632348//Division of Ocean Sciences/ ; 1638289//Division of Ocean Sciences/ ; 1638296//Division of Ocean Sciences/ ; }, abstract = {Fundamental to holobiont biology is recognising how variation in microbial composition and function relates to host phenotypic variation. Sponges often exhibit considerable phenotypic plasticity and also harbour dense microbial communities that function to protect and nourish hosts. One of the most prominent sponge genera on Caribbean coral reefs is Agelas. Using a comprehensive set of morphological (growth form, spicule), chemical and molecular data on 13 recognised species of Agelas in the Caribbean basin, we were able to define only five species (=clades) and found that many morphospecies designations were incongruent with phylogenomic and population genetic analyses. Microbial communities were also strongly differentiated between phylogenetic species, showing little evidence of cryptic divergence and relatively low correlation with morphospecies assignment. Metagenomic analyses also showed strong correspondence to phylogenetic species, and to a lesser extent, geographical and morphological characters. Surprisingly, the variation in secondary metabolites produced by sponge holobionts was explained by geography and morphospecies assignment, in addition to phylogenetic species, and covaried significantly with a subset of microbial symbionts. Spicule characteristics were highly plastic, under greater impact from geographical location than phylogeny. Our results suggest that while phenotypic plasticity is rampant in Agelas, morphological differences within phylogenetic species affect functionally important ecological traits, including the composition of the symbiotic microbial communities and metabolomic profiles.}, } @article {pmid38529486, year = {2024}, author = {Yutin, N and Mutz, P and Krupovic, M and Koonin, EV}, title = {Mriyaviruses: Small Relatives of Giant Viruses.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.02.29.582850}, pmid = {38529486}, abstract = {UNLABELLED: The phylum Nucleocytoviricota consists of large and giant viruses that range in genome size from about 100 kilobases (kb) to more than 2.5 megabases. Here, using metagenome mining followed by extensive phylogenomic analysis and protein structure comparison, we delineate a distinct group of viruses with double-stranded (ds) DNA genomes in the range of 35-45 kb that appear to be related to the Nucleocytoviricota. In phylogenetic trees of the conserved double jelly-roll major capsid proteins (MCP) and DNA packaging ATPases, these viruses do not show affinity to any particular branch of the Nucleocytoviricota and accordingly would comprise a class which we propose to name " Mriyaviricetes " (after Ukrainian Mriya, dream). Structural comparison of the MCP suggests that, among the extant virus lineages, mriyaviruses are the closest one to the ancestor of the Nucleocytoviricota . In the phylogenetic trees, mriyaviruses split into two well-separated branches, the family Yaraviridae and proposed new family " Gamadviridae ". The previously characterized members of these families, Yaravirus and Pleurochrysis sp. endemic viruses, infect amoeba and haptophytes, respectively. The genomes of the rest of the mriyaviruses were assembled from metagenomes from diverse environments, suggesting that mriyaviruses infect various unicellular eukaryotes. Mriyaviruses lack DNA polymerase, which is encoded by all other members of the Nucleocytoviricota, and RNA polymerase subunits encoded by all cytoplasmic viruses among the Nucleocytoviricota , suggesting that they replicate in the host cell nuclei. All mriyaviruses encode a HUH superfamily endonuclease that is likely to be essential for the initiation of virus DNA replication via the rolling circle mechanism.

IMPORTANCE: The origin of giant viruses of eukaryotes that belong to the phylum Nucleocytoviricota is not thoroughly understood and remains a matter of major interest and debate. Here we combine metagenome database searches with extensive protein sequence and structure analysis to describe a distinct group of viruses with comparatively small genomes of 35-45 kilobases that appears to comprise a distinct class within the phylum Nucleocytoviricota that we provisionally named "Mriyaviricetes". Mriyaviruses appear to be the closest identified relatives of the ancestors of the Nucleocytoviricota. Analysis of proteins encoded in mriyavirus genomes suggest that they replicate their genome via the rolling circle mechanism that is unusual among viruses with double-stranded DNA genomes and so far not described for members of Nucleocytoviricota .}, } @article {pmid38529196, year = {2024}, author = {Ajeeb, TT and Gonzalez, E and Solomons, NW and Vossenaar, M and Koski, KG}, title = {Human milk microbiome: associations with maternal diet and infant growth.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1341777}, pmid = {38529196}, issn = {2296-861X}, abstract = {INTRODUCTION: Ingestion of human milk (HM) is identified as a significant factor associated with early infant gut microbial colonization, which has been associated with infant health and development. Maternal diet has been associated with the HM microbiome (HMM). However, a few studies have explored the associations among maternal diet, HMM, and infant growth during the first 6 months of lactation.

METHODS: For this cross-sectional study, Mam-Mayan mother-infant dyads (n = 64) were recruited from 8 rural communities in the Western Highlands of Guatemala at two stages of lactation: early (6-46 days postpartum, n = 29) or late (109-184 days postpartum, n = 35). Recruited mothers had vaginally delivered singleton births, had no subclinical mastitis or antibiotic treatments, and breastfed their infants. Data collected at both stages of lactation included two 24-h recalls, milk samples, and infant growth status indicators: head-circumference-for-age-z-score (HCAZ), length-for-age-z-score (LAZ), and weight-for-age-z-score (WAZ). Infants were divided into subgroups: normal weight (WAZ ≥ -1SD) and mildly underweight (WAZ < -1SD), non-stunted (LAZ ≥ -1.5SD) and mildly stunted (LAZ < -1.5SD), and normal head-circumference (HCAZ ≥ -1SD) and smaller head-circumference (HCAZ < -1SD). HMM was identified using 16S rRNA gene sequencing; amplicon analysis was performed with the high-resolution ANCHOR pipeline, and DESeq2 identified the differentially abundant (DA) HMM at the species-level between infant growth groups (FDR < 0.05) in both early and late lactation.

RESULTS: Using both cluster and univariate analyses, we identified (a) positive correlations between infant growth clusters and maternal dietary clusters, (b) both positive and negative associations among maternal macronutrient and micronutrient intakes with the HMM at the species level and (c) distinct correlations between HMM DA taxa with maternal nutrient intakes and infant z-scores that differed between breast-fed infants experiencing growth faltering and normal growth in early and late lactation.

CONCLUSION: Collectively, these findings provide important evidence of the potential influence of maternal diet on the early-life growth of breastfed infants via modulation of the HMM.}, } @article {pmid38529182, year = {2024}, author = {Yin, PK and Xiao, H and Yang, ZB and Yang, DS and Yang, YH}, title = {Shotgun metagenomics reveals the gut microbial diversity and functions in Vespa mandarinia (Hymenoptera: Vespidae) at multiple life stages.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1288051}, pmid = {38529182}, issn = {1664-302X}, abstract = {Wasps play important roles as predators and pollinators in the ecosystem. The Jingpo minority residing in Yunnan Province, China, has a traditional practice of using wine infused with mature wasps as a customary remedy for managing rheumatoid arthritis. The larva of the wasp is also a tasteful folk dish that has created a tremendous market. There is a paucity of survival knowledge, which has greatly restricted their potential applications in food and healthcare. Recent research has highlighted the importance of gut microbiota in insect growth. Nevertheless, there is still a lack of understanding regarding the composition, changes, and functions of the gut microbiota in Vespa mandarinia during development. In this research, the gut microbiota were investigated across three growth stages of Vespa mandarinia using a metagenomic technology. The result revealed that there are significant variations in the proportion of main gut microbes during the metamorphosis of Vespa mandarinia. Tenericutes were found to dominate during the larval stage, while Proteobacteria emerged as the dominant group post-pupation. Through a comprehensive analysis of the gut microbiota metagenome, this study revealed functional differences in the wasp gut microbiota at various growth stages. During the larval stage, the gut microbiota plays a central role in promoting metabolism. Following pupation, the gut microbiota exhibited diversified functions, likely due to the complex environments and diverse food sources encountered after metamorphosis. These functions included amino acid metabolism, compound degradation, and defense mechanisms. This research provides an extensive dataset on the gut microbiota during the metamorphosis of Vespa mandarinia, contributing to a deeper understanding of the influence of gut microbiota on wasp growth. Furthermore, this study uncovers a unique microbial treasure within insect guts, which is important for advancing the application of wasps in the fields of food and medicine.}, } @article {pmid38529181, year = {2024}, author = {Yang, Z and Chen, X and Yu, M and Jing, R and Bao, L and Zhao, X and Pan, K and Chao, B and Qu, M}, title = {Metagenomic sequencing identified microbial species in the rumen and cecum microbiome responsible for niacin treatment and related to intramuscular fat content in finishing cattle.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1334068}, pmid = {38529181}, issn = {1664-302X}, abstract = {INTRODUCTION: Niacin is one of the essential vitamins for mammals. It plays important roles in maintaining rumen microecological homeostasis. Our previous study indicated that dietary niacin significantly elevated intramuscular fat content (IMF) in castrated finishing steers. Whether niacin affects fat deposition by regulating the microbial composition and functional capacities of gastrointestinal microbiome has been unknown yet.

METHODS: In this study, 16 castrated Xiangzhong Black cattle were randomly assigned into either control group fed with a basal concentrate diet (n = 8) or niacin group fed with a basal concentrate diet added 1000 mg/kg niacin (n = 8). Seven rumen samples and five cecum content samples were randomly collected from each of control and niacin groups for metagenomic sequencing analysis.

RESULTS: A total of 2,981,786 non-redundant microbial genes were obtained from all tested samples. Based on this, the phylogenetic compositions of the rumen and cecum microbiome were characterized. We found that bacteria dominated the rumen and cecum microbiome. Prevotella ruminicola and Ruminococcus flavefaciens were the most abundant bacterial species in the rumen microbiome, while Clostridiales bacterium and Eubacterium rectale were predominant bacterial species in the cecum microbiome. Rumen microbiome had significantly higher abundances of GHs, GTs, and PLs, while cecum microbiome was enriched by CBMs and AAs. We found a significant effect of dietary niacin on rumen microbiome, but not on cecum microbiome. Dietary niacin up-regulated the abundances of bacterial species producing lactic acid and butyrate, fermenting lactic acid, and participating in lipid hydrolysis, and degradation and assimilation of nitrogen-containing compounds, but down-regulated the abundances of several pathogens and bacterial species involved in the metabolism of proteins and peptides, and methane emissions. From the correlation analysis, we suggested that niacin improved nutrient digestion and absorption, but reduced energy loss, and Valine, leucine and isoleucine degradation of rumen microbiome, which resulted in the increased host IMF.

CONCLUSION: The results suggested that dietary manipulation, such as the supplementation of niacin, should be regarded as the effective and convenient way to improve IMF of castrated finishing steers by regulating rumen microbiome.}, } @article {pmid38529176, year = {2024}, author = {Kumar, V and Ameen, F and Verma, P}, title = {Unraveling the shift in bacterial communities profile grown in sediments co-contaminated with chlorolignin waste of pulp-paper mill by metagenomics approach.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1350164}, pmid = {38529176}, issn = {1664-302X}, abstract = {Pulp-paper mills (PPMs) are known for consistently generating a wide variety of pollutants, that are often unidentified and highly resistant to environmental degradation. The current study aims to investigate the changes in the indigenous bacterial communities profile grown in the sediment co-contaminated with organic and inorganic pollutants discharged from the PPMs. The two sediment samples, designated PPS-1 and PPS-2, were collected from two different sites. Physico-chemical characterization of PPS-1 and PPS-2 revealed the presence of heavy metals (mg kg[-1]) like Cu (0.009-0.01), Ni (0.005-0.002), Mn (0.078-0.056), Cr (0.015-0.009), Pb (0.008-0.006), Zn (0.225-0.086), Fe (2.124-0.764), Al (3.477-22.277), and Ti (99.792-45.012) along with high content of chlorophenol, and lignin. The comparative analysis of organic pollutants in sediment samples using gas chromatography-mass spectrometry (GC-MS) revealed the presence of major highly refractory compounds, such as stigmasterol, β-sitosterol, hexadecanoic acid, octadecanoic acid; 2,4-di-tert-butylphenol; heptacosane; dimethyl phthalate; hexachlorobenzene; 1-decanol,2-hexyl; furane 2,5-dimethyl, etc in sediment samples which are reported as a potential toxic compounds. Simultaneously, high-throughput sequencing targeting the V3-V4 hypervariable region of the 16S rRNA genes, resulted in the identification of 1,249 and 1,345 operational taxonomic units (OTUs) derived from a total of 115,665 and 119,386 sequences read, in PPS-1 and PPS-2, respectively. Analysis of rarefaction curves indicated a diversity in OTU abundance between PPS-1 (1,249 OTUs) and PPS-2 (1,345 OTUs). Furthermore, taxonomic assignment of metagenomics sequence data showed that Proteobacteria (55.40%; 56.30%), Bacteoidetes (11.30%; 12.20%), and Planctomycetes (5.40%; 4.70%) were the most abundant phyla; Alphproteobacteria (20.50%; 23.50%), Betaproteobacteria (16.00%; 12.30%), and Gammaproteobacteria were the most recorded classes in PPS-1 and PPS-2, respectively. At the genus level, Thiobacillus (7.60%; 4.50%) was the most abundant genera grown in sediment samples. The results indicate significant differences in both the diversity and relative abundance of taxa in the bacterial communities associated with PPS-2 when compared to PPS-1. This study unveils key insights into contaminant characteristics and shifts in bacterial communities within contaminated environments. It highlights the potential for developing efficient bioremediation techniques to restore ecological balance in pulp-paper mill waste-polluted areas, stressing the importance of identifying a significant percentage of unclassified genera and species to explore novel genes.}, } @article {pmid38529114, year = {2024}, author = {Zhang, A and Liang, J and Lao, X and Xia, X and Liang, J}, title = {Pneumonia Caused by Chlamydia psittaci and SARS-CoV-2 Coinfection Diagnosed Using Metagenomic Next-Generation Sequencing: A Case Report.}, journal = {International medical case reports journal}, volume = {17}, number = {}, pages = {187-194}, pmid = {38529114}, issn = {1179-142X}, abstract = {We report a case of pneumonia caused by coinfection with Chlamydia psittaci and the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron XBB.1 variant, confirmed using metagenomic next-generation sequencing (mNGS) and quantitative polymerase chain reaction (qPCR). C. psittaci and SARS-CoV-2 were detected in bronchoalveolar lavage fluid using mNGS. Additionally, mNGS detected C. psittaci in blood and nasopharyngeal specimens and was more sensitive than qPCR. The patient recovered after treatment with moxifloxacin. This report highlights the use of coinfections of C. psittaci and SARS-CoV-2, as mNGS has already been recognized to be a diagnostic tool for identifying coinfections.}, } @article {pmid38528961, year = {2024}, author = {Manzoor, M and Leskelä, J and Pietiäinen, M and Martinez-Majander, N and Könönen, E and Niiranen, T and Lahti, L and Sinisalo, J and Putaala, J and Pussinen, PJ and Paju, S}, title = {Shotgun metagenomic analysis of the oral microbiome in gingivitis: a nested case-control study.}, journal = {Journal of oral microbiology}, volume = {16}, number = {1}, pages = {2330867}, pmid = {38528961}, issn = {2000-2297}, abstract = {BACKGROUND: Gingivitis, i.e. inflammation of the gums, is often induced by dentalplaque. However, its exact link to the oral microbiota remains unclear.

METHODS: In a case-control study involving 120 participants, comprising 60 cases and 60 controls (mean age (SD) 36.6 (7.6) years; 50% males), nested within a prospective multicentre cohort study, we examined theoral microbiome composition of gingivitis patients and their controlsusing shotgun metagenomic sequencing of saliva samples. Participants underwent clinical and radiographic oral health examinations, including bleeding on probing (BOP), at six tooth sites. BOP ≥33%was considered 'generalized gingivitis/initial periodontitis'(GG/IP), and BOP <33% as 'healthy and localized gingivitis'(H/LG). Functional potential was inferred using HUMANn3.

RESULTS: GG/IP exhibited an increase in the abundance of Actinomyces, Porphyromonas, Aggregatibacter, Corynebacterium, Olsenella, and Treponema, whereas H/LG exhibited an increased abundance of Candidatus Nanosynbacter. Nineteen bacterial species and fourmicrobial functional profiles, including L-methionine, glycogen, andinosine-5'-phosphate biosynthesis, were associated with GG/IP. Constructing models with multiple markers resulted in a strong predictive value for GG/IP, with an area under the curve (ROC) of 0.907 (95% CI: 0.848-0.966).

CONCLUSION: We observed distinct differences in the oral microbiome between the GG/IP and H/LG groups, indicating similar yet unique microbial profiles and emphasizing their potential role in progression of periodontal diseases.}, } @article {pmid38528620, year = {2024}, author = {Ruta, GV and Ciciani, M and Kheir, E and Gentile, MD and Amistadi, S and Casini, A and Cereseto, A}, title = {Eukaryotic-driven directed evolution of Cas9 nucleases.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {79}, pmid = {38528620}, issn = {1474-760X}, support = {825825//Horizon 2020/ ; 01071041//HORIZON EUROPE European Innovation Council/ ; }, abstract = {BACKGROUND: Further advancement of genome editing highly depends on the development of tools with higher compatibility with eukaryotes. A multitude of described Cas9s have great potential but require optimization for genome editing purposes. Among these, the Cas9 from Campylobacter jejuni, CjCas9, has a favorable small size, facilitating delivery in mammalian cells. Nonetheless, its full exploitation is limited by its poor editing activity.

RESULTS: Here, we develop a Eukaryotic Platform to Improve Cas Activity (EPICA) to steer weakly active Cas9 nucleases into highly active enzymes by directed evolution. The EPICA platform is obtained by coupling Cas nuclease activity with yeast auxotrophic selection followed by mammalian cell selection through a sensitive reporter system. EPICA is validated with CjCas9, generating an enhanced variant, UltraCjCas9, following directed evolution rounds. UltraCjCas9 is up to 12-fold more active in mammalian endogenous genomic loci, while preserving high genome-wide specificity.

CONCLUSIONS: We report a eukaryotic pipeline allowing enhancement of Cas9 systems, setting the ground to unlock the multitude of RNA-guided nucleases existing in nature.}, } @article {pmid38528230, year = {2024}, author = {Liu, Y and Ritchie, SC and Teo, SM and Ruuskanen, MO and Kambur, O and Zhu, Q and Sanders, J and Vázquez-Baeza, Y and Verspoor, K and Jousilahti, P and Lahti, L and Niiranen, T and Salomaa, V and Havulinna, AS and Knight, R and Méric, G and Inouye, M}, title = {Integration of polygenic and gut metagenomic risk prediction for common diseases.}, journal = {Nature aging}, volume = {}, number = {}, pages = {}, pmid = {38528230}, issn = {2662-8465}, abstract = {Multiomics has shown promise in noninvasive risk profiling and early detection of various common diseases. In the present study, in a prospective population-based cohort with ~18 years of e-health record follow-up, we investigated the incremental and combined value of genomic and gut metagenomic risk assessment compared with conventional risk factors for predicting incident coronary artery disease (CAD), type 2 diabetes (T2D), Alzheimer disease and prostate cancer. We found that polygenic risk scores (PRSs) improved prediction over conventional risk factors for all diseases. Gut microbiome scores improved predictive capacity over baseline age for CAD, T2D and prostate cancer. Integrated risk models of PRSs, gut microbiome scores and conventional risk factors achieved the highest predictive performance for all diseases studied compared with models based on conventional risk factors alone. The present study demonstrates that integrated PRSs and gut metagenomic risk models improve the predictive value over conventional risk factors for common chronic diseases.}, } @article {pmid38528097, year = {2024}, author = {Wang, B and Sun, F and Luan, Y}, title = {Comparison of the effectiveness of different normalization methods for metagenomic cross-study phenotype prediction under heterogeneity.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {7024}, pmid = {38528097}, issn = {2045-2322}, support = {2018YFA0703900//National Key Research and Development Program of China/ ; 2018YFA0703900//National Key Research and Development Program of China/ ; 11971264//National Science Foundation of China/ ; 11971264//National Science Foundation of China/ ; }, abstract = {The human microbiome, comprising microorganisms residing within and on the human body, plays a crucial role in various physiological processes and has been linked to numerous diseases. To analyze microbiome data, it is essential to account for inherent heterogeneity and variability across samples. Normalization methods have been proposed to mitigate these variations and enhance comparability. However, the performance of these methods in predicting binary phenotypes remains understudied. This study systematically evaluates different normalization methods in microbiome data analysis and their impact on disease prediction. Our findings highlight the strengths and limitations of scaling, compositional data analysis, transformation, and batch correction methods. Scaling methods like TMM show consistent performance, while compositional data analysis methods exhibit mixed results. Transformation methods, such as Blom and NPN, demonstrate promise in capturing complex associations. Batch correction methods, including BMC and Limma, consistently outperform other approaches. However, the influence of normalization methods is constrained by population effects, disease effects, and batch effects. These results provide insights for selecting appropriate normalization approaches in microbiome research, improving predictive models, and advancing personalized medicine. Future research should explore larger and more diverse datasets and develop tailored normalization strategies for microbiome data analysis.}, } @article {pmid38527840, year = {2024}, author = {Fu, R and Lin, R and Fan, ZP and Huang, F and Xu, N and Xuan, L and Huang, YF and Liu, H and Zhao, K and Wang, ZX and Jiang, L and Dai, M and Sun, J and Liu, QF}, title = {[Metagenomic next-generation sequencing for the diagnosis of Pneumocystis jirovecii pneumonia after allogeneic hematopoietic stem cell transplantation].}, journal = {Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi}, volume = {45}, number = {1}, pages = {62-67}, doi = {10.3760/cma.j.cn121090-20230928-00147}, pmid = {38527840}, issn = {0253-2727}, support = {82070190, 81970161//National Natural Science Foundation of China/ ; }, abstract = {Objectives: To investigate the value of metagenomic next-generation sequencing (mNGS) in the diagnosis of Pneumocystis jirovecii pneumonia (PJP) in patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT) . Methods: The data of 98 patients with suspected pulmonary infection after allo-HSCT who underwent pathogen detection from bronchoalveolar lavage fluid between June 2016 and August 2023 at Nanfang Hospital were analyzed. The diagnostic performance of mNGS, conventional methods, and real-time quantitative polymerase chain reaction (qPCR) for PJP were compared. Results: A total of 12 patients were diagnosed with PJP, including 11 with a proven diagnosis and 1 with a probable diagnosis. Among the patients with a proven diagnosis, 1 was positive by both conventional methods and qPCR, and 10 were positive by qPCR only. Pneumocystis jirovecii was detected by mNGS in all 12 patients. The diagnostic sensitivity of mNGS for PJP was 100%, which was greater than that of conventional methods (8.3%, P=0.001) and similar to that of qPCR (91.6%, P=1.000) . A total of 75% of the patients developed mixed pulmonary infections, and cytomegalovirus and Epstein-Barr virus were the most common pathogens. Mixed infection was detected in eight patients by mNGS and in five patients by qPCR, but not by conventional methods (P=0.008) . Conclusions: mNGS had good sensitivity for diagnosing PJP after allo-HSCT and was advantageous for detecting mixed infectious pathogens; therefore, mNGS might be an effective supplement to regular detection methods and qPCR.}, } @article {pmid38527552, year = {2024}, author = {Wei, Y and Ye, M and Chen, Y and Li, YY}, title = {Competitive bio-augmentation overcoming unusual direct inhibitor inefficacy in mainstream nitrite-oxidizing bacteria suppression: Unveiling the underpinnings in microbial and nitrogen metabolism aspects.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {171900}, doi = {10.1016/j.scitotenv.2024.171900}, pmid = {38527552}, issn = {1879-1026}, abstract = {The long-stabilized mainstream partial nitritation/Anammox (PN/A) process continues to encounter significant challenges from nitrite-oxidizing bacteria (NOB). Therefore, this study aimed to determine an efficient, rapid, and easily implementable strategy for inhibiting NOB. A laboratory-scale reactor was operated continuously for 325 days, experiencing NOB outbreak in mainstream and recovery with simulated sidestream support. The results show that direct inhibitory strategies including intermittent aeration and approximately 35 mg/L free ammonia had unusual weak inhibitory effects on NOB activity. Subsequently, the exogenous Anammox from sidestream employed as a competitive bio-augmentation approach rapidly inhibited NOB dynamics. Evidence suggests that the damaged hydroxyapatite granules under low pH conditions might have contributed to NOB dominance by diminishing Anammox bacteria activity, thereby creating a substrate-rich environment favoring NOB survival. In contrast, the introduction of exogenous Candidatus Kuenenia facilitated the nitrogen removal efficiency from 32.5 % to over 80 %. This coincided with a decrease in the relative abundance of Nitrospira from 16.5 % to 2.7 % and NOB activity from 0.34 to 0.07 g N/(g mixed liquor volatile suspended solid)/d. Metagenomic analysis reveals a decrease in the functional potential of most nitrite transport proteins, coupled with a significant increase in eukaryotic-like serine/threonine-protein kinase involved in cellular regulation, during the Anammox recovery. This study's findings reveal the feasibility of the bio-augmentation based on substrate competition, wherein sidestream processes support the mainstream PN/A integration, offering significant potential for practical applications.}, } @article {pmid38445567, year = {2024}, author = {Gottscho, AD and Mulcahy, DG and Leaché, AD and de Queiroz, K and Lovich, RE}, title = {Population genomics of flat-tailed horned lizards (Phrynosoma mcallii) informs conservation and management across a fragmented Colorado Desert landscape.}, journal = {Molecular ecology}, volume = {33}, number = {7}, pages = {e17308}, doi = {10.1111/mec.17308}, pmid = {38445567}, issn = {1365-294X}, support = {//Smithsonian Institution, L.A.B./ ; //Smithsonian Institution, Peter Buck Postdoctoral Fellowship/ ; 16-824//Department of Defense Legacy Resource Management Program/ ; }, mesh = {Animals ; Phylogeny ; *Metagenomics ; Colorado ; Ecosystem ; *Lizards/genetics ; Genetic Variation/genetics ; DNA, Mitochondrial/genetics ; Phylogeography ; }, abstract = {Phrynosoma mcallii (flat-tailed horned lizards) is a species of conservation concern in the Colorado Desert of the United States and Mexico. We analysed ddRADseq data from 45 lizards to estimate population structure, infer phylogeny, identify migration barriers, map genetic diversity hotspots, and model demography. We identified the Colorado River as the main geographic feature contributing to population structure, with the populations west of this barrier further subdivided by the Salton Sea. Phylogenetic analysis confirms that northwestern populations are nested within southeastern populations. The best-fit demographic model indicates Pleistocene divergence across the Colorado River, with significant bidirectional gene flow, and a severe Holocene population bottleneck. These patterns suggest that management strategies should focus on maintaining genetic diversity on both sides of the Colorado River and the Salton Sea. We recommend additional lands in the United States and Mexico that should be considered for similar conservation goals as those in the Rangewide Management Strategy. We also recommend periodic rangewide genomic sampling to monitor ongoing attrition of diversity, hybridization, and changing structure due to habitat fragmentation, climate change, and other long-term impacts.}, } @article {pmid38419064, year = {2024}, author = {Sutherland, BJG and Rycroft, C and Duguid, A and Beacham, TD and Tucker, S}, title = {Population genomics of harbour seal Phoca vitulina from northern British Columbia through California and comparison to the Atlantic subspecies.}, journal = {Molecular ecology}, volume = {33}, number = {7}, pages = {e17293}, doi = {10.1111/mec.17293}, pmid = {38419064}, issn = {1365-294X}, support = {//Fisheries and Oceans Canada/ ; //Pinniped Research Program/ ; //Species At Risk Program/ ; }, mesh = {Humans ; Animals ; *Phoca/genetics ; British Columbia ; Ecosystem ; Metagenomics ; California ; }, abstract = {The harbour seal Phoca vitulina is a ubiquitous pinniped species found throughout coastal waters of the Northern Hemisphere. Harbour seal impacts on ecosystem dynamics may be significant due to their high abundance and food web position. Two subspecies exist in North America, P. v. richardii in the Pacific Ocean and P. v. vitulina in the Atlantic. Strong natal philopatry of harbour seals can result in fine-scale genetic structure and isolation by distance. Management of harbour seals is expected to benefit from improved resolution of seal population structure and dynamics. Here, we use genotyping-by-sequencing to genotype 146 harbour seals from the eastern Pacific Ocean (i.e. British Columbia (BC), Oregon and California) and the western Atlantic Ocean (i.e. Québec, Newfoundland and Labrador). Using 12,742 identified variants, we confirm the recently identified elevated genetic diversity in the eastern Pacific relative to the western Atlantic and greatest differentiation between the subspecies. Further, we demonstrate that this is independent of reference genome bias or other potential technical artefacts. Coast-specific analyses with 8933 and 3828 variants in Pacific and Atlantic subspecies, respectively, identify divergence between BC and Oregon-California, and between Québec and Newfoundland-Labrador. Unexpected PCA outlier clusters were observed in two populations due to cryptic relatedness of individuals; subsequently, closely related samples were removed. Admixture analysis indicates an isolation-by-distance signature where Oregon seals contained some of the BC signature, whereas California did not. Additional sampling is needed in the central and north coast of BC to determine whether a discrete separation of populations exists within the region.}, } @article {pmid38527398, year = {2024}, author = {Xue, YX and Huang, LJ and Wang, HY and Peng, JJ and Jin, MK and Hu, SL and Li, HB and Xue, XM and Zhu, YG}, title = {Interaction of tetracycline and copper co-intake in inducing antibiotic resistance genes and potential pathogens in mouse gut.}, journal = {Environment international}, volume = {186}, number = {}, pages = {108594}, doi = {10.1016/j.envint.2024.108594}, pmid = {38527398}, issn = {1873-6750}, abstract = {The widespread use of copper and tetracycline as growth promoters in the breeding industry poses a potential threat to environmental health. Nevertheless, to the best of our knowledge, the potential adverse effects of copper and tetracycline on the gut microbiota remain unknown. Herein, mice were fed different concentrations of copper and/or tetracycline for 6 weeks to simulate real life-like exposure in the breeding industry. Following the exposure, antibiotic resistance genes (ARGs), potential pathogens, and other pathogenic factors were analyzed in mouse feces. The co-exposure of copper with tetracycline significantly increased the abundance of ARGs and enriched more potential pathogens in the gut of the co-treated mice. Copper and/or tetracycline exposure increased the abundance of bacteria carrying either ARGs, metal resistance genes, or virulence factors, contributing to the widespread dissemination of potentially harmful genes posing a severe risk to public health. Our study provides insights into the effects of copper and tetracycline exposure on the gut resistome and potential pathogens, and our findings can help reduce the risks associated with antibiotic resistance under the One Health framework.}, } @article {pmid38526092, year = {2024}, author = {Sakurai, R and Fukuda, Y and Tada, C}, title = {Circular metagenome-assembled genome of Candidatus Patescibacteria recovered from anaerobic digestion sludge.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0008324}, doi = {10.1128/mra.00083-24}, pmid = {38526092}, issn = {2576-098X}, abstract = {A single-contig, circular metagenome-assembled genome (cMAG) of Candidatus (Ca.) Patescibacteria was reconstructed from a mesophilic full-scale food waste treatment plant in Japan. The genome is of small size and lacks fundamental biosynthetic pathways. Taxonomic analysis using the Genome Taxonomy Database revealed that this cMAG belonged to the genus JAEZRQ01 (Ca. Parcubacteria).}, } @article {pmid38525689, year = {2024}, author = {Song, Y and Lei, H and Cao, Z and Zhang, C and Chen, C and Wu, M and Zhang, H and Du, R and Lijun, L and Chen, X and Zhang, L}, title = {Long-Term Triclocarban Exposure Induced Enterotoxicity by Triggering Intestinal AhR-Mediated Inflammation and Disrupting Microbial Community in Mice.}, journal = {Chemical research in toxicology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.chemrestox.4c00042}, pmid = {38525689}, issn = {1520-5010}, abstract = {Exposure to triclocarban (TCC), a commonly used antibacterial agent, has been shown to induce significant intestine injuries and colonic inflammation in mice. However, the detailed mechanisms by which TCC exposure triggered enterotoxicity remain largely unclear. Herein, intestinal toxicity effects of long-term and chronic TCC exposure were investigated using a combination of histopathological assessments, metagenomics, targeted metabolomics, and biological assays. Mechanically, TCC exposure caused induction of intestinal aryl hydrocarbon receptor (AhR) and its transcriptional target cytochrome P4501A1 (Cyp1a1) leading to dysfunction of the gut barrier and disruption of the gut microbial community. A large number of lipopolysaccharides (LPS) are released from the gut lumen into blood circulation owing to the markedly increased permeability and gut leakage. Consequently, toll-like receptor-4 (TLR4) and NF-κB signaling pathways were activated by high levels of LPS. Simultaneously, classic macrophage phenotypes were switched by TCC, shown with marked upregulation of macrophage M1 and downregulation of macrophage M2 that was accompanied by striking upregulation of proinflammatory factors such as Il-1β, Il-6, Il-17, and Tnf-α in the intestinal lamina propria. These findings provide new evidence for the TCC-induced enterotoxicity.}, } @article {pmid38525073, year = {2024}, author = {Jiang, B and Qin, C and Xu, Y and Song, X and Fu, Y and Li, R and Liu, Q and Shi, D}, title = {Multi-omics reveals the mechanism of rumen microbiome and its metabolome together with host metabolome participating in the regulation of milk production traits in dairy buffaloes.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1301292}, pmid = {38525073}, issn = {1664-302X}, abstract = {Recently, it has been discovered that certain dairy buffaloes can produce higher milk yield and milk fat yield under the same feeding management conditions, which is a potential new trait. It is unknown to what extent, the rumen microbiome and its metabolites, as well as the host metabolism, contribute to milk yield and milk fat yield. Therefore, we will analyze the rumen microbiome and host-level potential regulatory mechanisms on milk yield and milk fat yield through rumen metagenomics, rumen metabolomics, and serum metabolomics experiments. Microbial metagenomics analysis revealed a significantly higher abundance of several species in the rumen of high-yield dairy buffaloes, which mainly belonged to genera, such as Prevotella, Butyrivibrio, Barnesiella, Lachnospiraceae, Ruminococcus, and Bacteroides. These species contribute to the degradation of diets and improve functions related to fatty acid biosynthesis and lipid metabolism. Furthermore, the rumen of high-yield dairy buffaloes exhibited a lower abundance of methanogenic bacteria and functions, which may produce less methane. Rumen metabolome analysis showed that high-yield dairy buffaloes had significantly higher concentrations of metabolites, including lipids, carbohydrates, and organic acids, as well as volatile fatty acids (VFAs), such as acetic acid and butyric acid. Meanwhile, several Prevotella, Butyrivibrio, Barnesiella, and Bacteroides species were significantly positively correlated with these metabolites. Serum metabolome analysis showed that high-yield dairy buffaloes had significantly higher concentrations of metabolites, mainly lipids and organic acids. Meanwhile, several Prevotella, Bacteroides, Barnesiella, Ruminococcus, and Butyrivibrio species were significantly positively correlated with these metabolites. The combined analysis showed that several species were present, including Prevotella.sp.CAG1031, Prevotella.sp.HUN102, Prevotella.sp.KHD1, Prevotella.phocaeensis, Butyrivibrio.sp.AE3009, Barnesiella.sp.An22, Bacteroides.sp.CAG927, and Bacteroidales.bacterium.52-46, which may play a crucial role in rumen and host lipid metabolism, contributing to milk yield and milk fat yield. The "omics-explainability" analysis revealed that the rumen microbial composition, functions, metabolites, and serum metabolites contributed 34.04, 47.13, 39.09, and 50.14%, respectively, to milk yield and milk fat yield. These findings demonstrate how the rumen microbiota and host jointly affect milk production traits in dairy buffaloes. This information is essential for developing targeted feeding management strategies to improve the quality and yield of buffalo milk.}, } @article {pmid38525041, year = {2024}, author = {Abo-Hammam, RH and Salah, M and Shabayek, S and Hanora, A and Zakeer, S and Khattab, RH}, title = {Metagenomic analysis of fecal samples in colorectal cancer Egyptians patients post colectomy: A pilot study.}, journal = {AIMS microbiology}, volume = {10}, number = {1}, pages = {148-160}, pmid = {38525041}, issn = {2471-1888}, abstract = {One of the most prevalent malignancies that significantly affects world health is colorectal cancer (CRC). While genetics are involved in a portion of CRC patients, most cases are sporadic. The microbiome composition could be a new source of tumor initiation and progression. This research was conducted to investigate the microbiota composition of CRC patients post colectomy at taxonomic and functional levels. Using a next-generation sequencing approach, using an Illumina Novaseq 6000, the fecal samples of 13 patients were analyzed and the obtained data was subjected to a bioinformatics analysis. The bacterial abundance and uniqueness varied in CRC patients alongside differences in bacterial counts between patients. Bacteroides fragilis, Bacteroides vulgatus, Escherichia coli, and Fusobacterium nucleatum were among the pro-cancerous microorganisms found. Concurrently, bacteria linked to CRC progression were detected that have been previously linked to metastasis and recurrence. At the same time, probiotic bacteria such as Bifidobacterium dentium, Bifidobacterium bifidum, and Akkermansia muciniphila increased in abundance after colectomies. Additionally, numerous pathways were deferentially enriched in CRC, which emerged from functional pathways based on bacterial shotgun data. CRC-specific microbiome signatures include an altered bacterial composition. Our research showed that microbial biomarkers could be more usefully employed to explore the link between gut microbiota and CRC using metagenomic techniques in the diagnosis, prognosis, and remission of CRC, thereby opening new avenues for CRC treatment.}, } @article {pmid38524764, year = {2024}, author = {Deng, Y and Liang, C and Zhu, X and Zhu, X and Chen, L and Pan, H and Xun, F and Tao, Y and Xing, P}, title = {Methylomonadaceae was the active and dominant methanotroph in Tibet lake sediments.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae032}, pmid = {38524764}, issn = {2730-6151}, abstract = {Methane (CH4), an important greenhouse gas, significantly impacts the local and global climate. Our study focused on the composition and activity of methanotrophs residing in the lakes on the Tibetan Plateau, a hotspot for climate change research. Based on the field survey, the family Methylomonadaceae had a much higher relative abundance in freshwater lakes than in brackish and saline lakes, accounting for ~92% of total aerobic methanotrophs. Using the microcosm sediment incubation with [13]CH4 followed by high throughput sequencing and metagenomic analysis, we further demonstrated that the family Methylomonadaceae was actively oxidizing CH4. Moreover, various methylotrophs, such as the genera Methylotenera and Methylophilus, were detected in the [13]C-labeled DNAs, which suggested their participation in CH4-carbon sequential assimilation. The presence of CH4 metabolism, such as the tetrahydromethanopterin and the ribulose monophosphate pathways, was identified in the metagenome-assembled genomes of the family Methylomonadaceae. Furthermore, they had the potential to adapt to oxygen-deficient conditions and utilize multiple electron acceptors, such as metal oxides (Fe[3+]), nitrate, and nitrite, for survival in the Tibet lakes. Our findings highlighted the predominance of Methylomonadaceae and the associated microbes as active CH4 consumers, potentially regulating the CH4 emissions in the Tibet freshwater lakes. These insights contributed to understanding the plateau carbon cycle and emphasized the significance of methanotrophs in mitigating climate change.}, } @article {pmid38524763, year = {2024}, author = {Pellitier, PT and Van Nuland, M and Salamov, A and Grigoriev, IV and Peay, KG}, title = {Potential for functional divergence in ectomycorrhizal fungal communities across a precipitation gradient.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae031}, pmid = {38524763}, issn = {2730-6151}, abstract = {Functional traits influence the assembly of microbial communities, but identifying these traits in the environment has remained challenging. We studied ectomycorrhizal fungal (EMF) communities inhabiting Populus trichocarpa roots distributed across a precipitation gradient in the Pacific Northwest, USA. We profiled these communities using taxonomic (meta-barcoding) and functional (metagenomic) approaches. We hypothesized that genes involved in fungal drought-stress tolerance and fungal mediated plant water uptake would be most abundant in drier soils. We were unable to detect support for this hypothesis; instead, the abundance of genes involved in melanin synthesis, hydrophobins, aquaporins, trehalose-synthases, and other gene families exhibited no significant shifts across the gradient. Finally, we studied variation in sequence homology for certain genes, finding that fungal communities in dry soils are composed of distinct aquaporin and hydrophobin gene sequences. Altogether, our results suggest that while EMF communities exhibit significant compositional shifts across this gradient, coupled functional turnover, at least as inferred using community metagenomics is limited. Accordingly, the consequences of these distinct EMF communities on plant water uptake remain critically unknown, and future studies targeting the expression of genes involved in drought stress tolerance are required.}, } @article {pmid38524761, year = {2024}, author = {Yu, L and Jia, R and Liu, S and Li, S and Zhong, S and Liu, G and Zeng, RJ and Rensing, C and Zhou, S}, title = {Ferrihydrite-mediated methanotrophic nitrogen fixation in paddy soil under hypoxia.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae030}, pmid = {38524761}, issn = {2730-6151}, abstract = {Biological nitrogen fixation (BNF) by methanotrophic bacteria has been shown to play an important role in maintaining fertility. However, this process is still limited to aerobic methane oxidation with sufficient oxygen. It has remained unknown whether and how methanotrophic BNF proceeds in hypoxic environments. Herein, we incubated paddy soils with a ferrihydrite-containing mineral salt medium to enrich methanotrophic bacteria in the presence of methane (20%, v/v) under oxygen constraints (0.27%, v/v). The resulting microcosms showed that ferrihydrite-dependent aerobic methane oxidation significantly contributed (81%) to total BNF, increasing the [15]N fixation rate by 13-fold from 0.02 to 0.28 μmol [15]N2 (g dry weight soil) [-1] d[-1]. BNF was reduced by 97% when ferrihydrite was omitted, demonstrating the involvement of ferrihydrite in methanotrophic BNF. DNA stable-isotope probing indicated that Methylocystis, Methylophilaceae, and Methylomicrobium were the dominant methanotrophs/methylotrophs that assimilated labeled isotopes ([13]C or [15]N) into biomass. Metagenomic binning combined with electrochemical analysis suggested that Methylocystis and Methylophilaceae had the potential to perform methane-induced BNF and likely utilized riboflavin and c-type cytochromes as electron carriers for ferrihydrite reduction. It was concluded that ferrihydrite mediated methanotrophic BNF by methanotrophs/methylotrophs solely or in conjunction with iron-reducing bacteria. Overall, this study revealed a previously overlooked yet pronounced coupling of iron-dependent aerobic methane oxidation to BNF and improves our understanding of methanotrophic BNF in hypoxic zones.}, } @article {pmid38524669, year = {2024}, author = {D'Amico, F and Rinaldi, M and Pascale, R and Fabbrini, M and Morelli, MC and Siniscalchi, A and Laici, C and Coladonato, S and Ravaioli, M and Cescon, M and Ambretti, S and Viale, P and Brigidi, P and Turroni, S and Giannella, M}, title = {Gut microbiome dynamics and Enterobacterales infection in liver transplant recipients: A prospective observational study.}, journal = {JHEP reports : innovation in hepatology}, volume = {6}, number = {4}, pages = {101039}, pmid = {38524669}, issn = {2589-5559}, abstract = {BACKGROUND & AIMS: The aim of this study was to investigate gut microbiome (GM) dynamics in relation to carbapenem-resistant Enterobacterales (CRE) colonization, CRE infection, and non-CRE infection development within 2 months after liver transplant (LT).

METHODS: A single-center, prospective study was performed in patients undergoing LT from November 2018 to January 2020. The GM was profiled through 16S rRNA amplicon sequencing of a rectal swab taken on the day of transplantation, and fecal samples were collected weekly until 1 month after LT. A subset of samples was subjected to shotgun metagenomics, including resistome dynamics. The primary endpoint was to explore changes in the GM in the following groups: (1) CRE carriers developing CRE infection (CRE_I); (2) CRE carriers not developing infection (CRE_UI); (3) non-CRE carriers developing microbial infection (INF); and (4) non-CRE carriers not developing infection (NEG).

RESULTS: Overall, 97 patients were enrolled, and 91 provided fecal samples. Of these, five, nine, 22, and 55 patients were classified as CRE_I, CRE_UI, INF, and NEG, respectively. CRE_I patients showed an immediate and sustained post-LT decrease in alpha diversity, with depletion of the GM structure and gradual over-representation of Klebsiella and Enterococcus. The proportions of Klebsiella were significantly higher in CRE_I patients than in NEG patients even before LT, serving as an early marker of subsequent CRE infection. CRE_UI patients had a more stable and diverse GM, whose compositional dynamics tended to overlap with those of NEG patients.

CONCLUSIONS: GM profiling before LT could improve patient stratification and risk prediction and guide early GM-based intervention strategies to reduce infectious complications and improve overall prognosis.

IMPACT AND IMPLICATIONS: Little is known about the temporal dynamics of gut microbiome (GM) in liver transplant recipients associated with carbapenem-resistant Enterobacterales (CRE) colonization and infection. The GM structure and functionality of patients colonized with CRE and developing infection appeared to be distinct compared with CRE carriers without infection or patients with other microbial infection or no infection and CRE colonization. Higher proportions of antimicrobial-resistant pathogens and poor representation of bacteria and metabolic pathways capable of promoting overall host health were observed in CRE carriers who developed infection, even before liver transplant. Therefore, pretransplant GM profiling could improve patient stratification and risk prediction and guide early GM-based intervention strategies to reduce infectious complications and improve overall prognosis.}, } @article {pmid38524178, year = {2024}, author = {Tu, JB and Liao, WJ and Long, SP and Li, MP and Gao, XH}, title = {Construction and validation of a machine learning model for the diagnosis of juvenile idiopathic arthritis based on fecal microbiota.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1371371}, pmid = {38524178}, issn = {2235-2988}, abstract = {PURPOSE: Human gut microbiota has been shown to be significantly associated with various inflammatory diseases. Therefore, this study aimed to develop an excellent auxiliary tool for the diagnosis of juvenile idiopathic arthritis (JIA) based on fecal microbial biomarkers.

METHOD: The fecal metagenomic sequencing data associated with JIA were extracted from NCBI, and the sequencing data were transformed into the relative abundance of microorganisms by professional data cleaning (KneadData, Trimmomatic and Bowtie2) and comparison software (Kraken2 and Bracken). After that, the fecal microbes with high abundance were extracted for subsequent analysis. The extracted fecal microbes were further screened by least absolute shrinkage and selection operator (LASSO) regression, and the selected fecal microbe biomarkers were used for model training. In this study, we constructed six different machine learning (ML) models, and then selected the best model for constructing a JIA diagnostic tool by comparing the performance of the models based on a combined consideration of area under receiver operating characteristic curve (AUC), accuracy, specificity, F1 score, calibration curves and clinical decision curves. In addition, to further explain the model, Permutation Importance analysis and Shapley Additive Explanations (SHAP) were performed to understand the contribution of each biomarker in the prediction process.

RESULT: A total of 231 individuals were included in this study, including 203 JIA patients and Non-JIA individuals. In the analysis of diversity at the genus level, the alpha diversity represented by Shannon value was not significantly different between the two groups, while the belt diversity was slightly different. After selection by LASSO regression, 10 fecal microbe biomarkers were selected for model training. By comparing six different models, the XGB model showed the best performance, which average AUC, accuracy and F1 score were 0.976, 0.914 and 0.952, respectively, thus being used to construct the final JIA diagnosis model.

CONCLUSION: A JIA diagnosis model based on XGB algorithm was constructed with excellent performance, which may assist physicians in early detection of JIA patients and improve the prognosis of JIA patients.}, } @article {pmid38522607, year = {2024}, author = {Stehling, EG and Rueda Furlan, JP and Lopes, R and Chodkowski, J and Stopnisek, N and Savazzi, EA and Shade, A}, title = {The relationship between water quality and the microbial virulome and resistome in urban streams in Brazil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {123849}, doi = {10.1016/j.envpol.2024.123849}, pmid = {38522607}, issn = {1873-6424}, abstract = {Urban streams that receive untreated domestic and hospital waste can transmit infectious diseases and spread drug residues, including antimicrobials, which can then increase the selection of antimicrobial-resistant bacteria. Here, water samples were collected from three different urban streams in the state of São Paulo, Brazil, to relate their range of Water Quality Indices (WQIs) to the diversity and composition of aquatic microbial taxa, virulence genes (virulome), and antimicrobial resistance determinants (resistome), all assessed using untargeted metagenome sequencing. There was a predominance of phyla Proteobacteria, Actinobacteria, and Bacteroidetes in all samples, and Pseudomonas was the most abundant detected genus. Virulence genes associated with motility, adherence, and secretion systems were highly abundant and mainly associated with Pseudomonas aeruginosa. Furthermore, some opportunistic pathogenic genera had negative correlations with WQI. Many clinically relevant antimicrobial resistance genes (ARGs) and efflux pump-encoding genes that confer resistance to critically important antimicrobials were detected. The highest relative abundances of ARGs were β-lactams and macrolide-lincosamide-streptogramin. No statistically supported relationship was detected between the abundance of virulome/resistome and collection type/WQI. On the other hand, total solids were a weak predictor of gene abundance patterns. These results provide insights into various microbial outcomes given urban stream quality and point to its ecological complexity. In addition, this study suggests potential consequences for human health as mediated by aquatic microbial communities responding to typical urban outputs.}, } @article {pmid38522537, year = {2024}, author = {Ye, L and Zheng, Z and Wang, Y and Hu, Q and Zhong, L and Heng, H and Guo, Z and Li, R and Chan, EWC and Chen, S}, title = {Integrating metagenomic and isolation strategies revealed high contamination of pathogenies and resistome in market shrimps.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {171924}, doi = {10.1016/j.scitotenv.2024.171924}, pmid = {38522537}, issn = {1879-1026}, abstract = {This study employs a comprehensive approach combining metagenomic analysis and bacterial isolation to elucidate the microbial composition, antibiotic resistance genes (ARGs), and virulence factors (VFGs) present in shrimps from market and supermarket. Metagenomic analysis of shrimps revealed a dominance of Proteobacteria and Bacteroidetes with Firmicutes notably enriched in some samples. On the other hand, the dominant bacteria isolated included Citrobacter portucalensis, Escherichia coli, Salmonella enterica, Vibrio species and Klebsiella pneumonaie. Metagenomic analysis unveiled a diverse spectrum of 23 main types and 380 subtypes of ARGs in shrimp samples including many clinical significant ARGs such as blaKPC, blaNDM, mcr, tet(X4) etc. Genomic analysis of isolated bacterial strains identified 14 ARG types with 109 subtype genes, which complemented the metagenomic data. Genomic analysis also allowed us to identify a rich amount of MDR plasmids, which provided further insights into the dissemination of resistance genes in different species of bacteria in the same samples. Examination of VFGs and mobile genetic elements (MGEs) in both metagenomic and bacterial genomes revealed a complex landscape of factors contributing to bacterial virulence and genetic mobility. Potential co-occurrence patterns of ARGs and VFGs within human pathogenic bacteria underlined the intricate interplay between antibiotic resistance and virulence. In conclusion, this integrated analysis for the first time provides a comprehensive view and sheds new light on the potential hazards associated with shrimp products in the markets. The findings underscore the necessity of ongoing surveillance and intervention strategies to mitigate risks posed by antibiotic-resistant bacteria in the food supply chain using the novel comprehensive approaches.}, } @article {pmid38521963, year = {2024}, author = {Sengupta, P and Muthamilselvi Sivabalan, SK and Singh, NK and Raman, K and Venkateswaran, K}, title = {Genomic, functional, and metabolic enhancements in multidrug-resistant Enterobacter bugandensis facilitating its persistence and succession in the International Space Station.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {62}, pmid = {38521963}, issn = {2049-2618}, support = {19-12829-26//2012 Space Biology NNH12ZTT001N/ ; 19-12829-26//2012 Space Biology NNH12ZTT001N/ ; MTR/2020/000490//Science and Engineering Board (SERB) MATRICS/ ; }, abstract = {BACKGROUND: The International Space Station (ISS) stands as a testament to human achievement in space exploration. Despite its highly controlled environment, characterised by microgravity, increased CO 2 levels, and elevated solar radiation, microorganisms occupy a unique niche. These microbial inhabitants play a significant role in influencing the health and well-being of astronauts on board. One microorganism of particular interest in our study is Enterobacter bugandensis, primarily found in clinical specimens including the human gastrointestinal tract, and also reported to possess pathogenic traits, leading to a plethora of infections.

RESULTS: Distinct from their Earth counterparts, ISS E. bugandensis strains have exhibited resistance mechanisms that categorise them within the ESKAPE pathogen group, a collection of pathogens recognised for their formidable resistance to antimicrobial treatments. During the 2-year Microbial Tracking 1 mission, 13 strains of multidrug-resistant E. bugandensis were isolated from various locations within the ISS. We have carried out a comprehensive study to understand the genomic intricacies of ISS-derived E. bugandensis in comparison to terrestrial strains, with a keen focus on those associated with clinical infections. We unravel the evolutionary trajectories of pivotal genes, especially those contributing to functional adaptations and potential antimicrobial resistance. A hypothesis central to our study was that the singular nature of the stresses of the space environment, distinct from any on Earth, could be driving these genomic adaptations. Extending our investigation, we meticulously mapped the prevalence and distribution of E. bugandensis across the ISS over time. This temporal analysis provided insights into the persistence, succession, and potential patterns of colonisation of E. bugandensis in space. Furthermore, by leveraging advanced analytical techniques, including metabolic modelling, we delved into the coexisting microbial communities alongside E. bugandensis in the ISS across multiple missions and spatial locations. This exploration revealed intricate microbial interactions, offering a window into the microbial ecosystem dynamics within the ISS.

CONCLUSIONS: Our comprehensive analysis illuminated not only the ways these interactions sculpt microbial diversity but also the factors that might contribute to the potential dominance and succession of E. bugandensis within the ISS environment. The implications of these findings are twofold. Firstly, they shed light on microbial behaviour, adaptation, and evolution in extreme, isolated environments. Secondly, they underscore the need for robust preventive measures, ensuring the health and safety of astronauts by mitigating risks associated with potential pathogenic threats. Video Abstract.}, } @article {pmid38521945, year = {2024}, author = {Bemmelen, JV and Smyth, DS and Baaijens, JA}, title = {Amplidiff: an optimized amplicon sequencing approach to estimating lineage abundances in viral metagenomes.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {126}, pmid = {38521945}, issn = {1471-2105}, abstract = {BACKGROUND: Metagenomic profiling algorithms commonly rely on genomic differences between lineages, strains, or species to infer the relative abundances of sequences present in a sample. This observation plays an important role in the analysis of diverse microbial communities, where targeted sequencing of 16S and 18S rRNA, both well-known hypervariable genomic regions, have led to insights into microbial diversity and the discovery of novel organisms. However, the variable nature of discriminatory regions can also act as a double-edged sword, as the sought-after variability can make it difficult to design primers for their amplification through PCR. Moreover, the most variable regions are not necessarily the most informative regions for the purpose of differentiation; one should focus on regions that maximize the number of lineages that can be distinguished.

RESULTS: Here we present AmpliDiff, a computational tool that simultaneously finds highly discriminatory genomic regions in viral genomes of a single species, as well as primers allowing for the amplification of these regions. We show that regions and primers found by AmpliDiff can be used to accurately estimate relative abundances of SARS-CoV-2 lineages, for example in wastewater sequencing data. We obtain errors that are comparable with using whole genome information to estimate relative abundances. Furthermore, our results show that AmpliDiff is robust against incomplete input data and that primers designed by AmpliDiff also bind to genomes sampled months after the primers were selected.

CONCLUSIONS: With AmpliDiff we provide an effective, cost-efficient alternative to whole genome sequencing for estimating lineage abundances in viral metagenomes.}, } @article {pmid38521276, year = {2024}, author = {Liu, Q and Peng, Y and Liao, J and Liu, X and Peng, J and Wang, JH and Shao, Z}, title = {Broad-spectrum hydrocarbon-degrading microbes in the global ocean metagenomes.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {171746}, doi = {10.1016/j.scitotenv.2024.171746}, pmid = {38521276}, issn = {1879-1026}, abstract = {Understanding the diversity and functions of hydrocarbon-degrading microorganisms in marine environments is crucial for both advancing knowledge of biogeochemical processes and improving bioremediation methods. In this study, we leveraged nearly 20,000 metagenome-assembled genomes (MAGs), recovered from a wide array of marine samples across the global oceans, to map the diversity of aerobic hydrocarbon-degrading microorganisms. A broad bacterial diversity was uncovered, with a notable preference for degrading aliphatic hydrocarbons over aromatic ones, primarily within Proteobacteria and Actinobacteriota. Three types of broad-spectrum hydrocarbon-degrading bacteria were identified for their ability to degrade various hydrocarbons and possession of multiple copies of hydrocarbon biodegradation genes. These bacteria demonstrate extensive metabolic versatility, aiding their survival and adaptability in diverse environmental conditions. Evidence of gene duplication and horizontal gene transfer in these microbes suggests a potential enhancement in the diversity of hydrocarbon-degrading bacteria. Positive correlations were observed between the abundances of hydrocarbon-degrading genes and environmental parameters such as temperature (-5 to 35 °C) and salinity (20 to 42 PSU). Overall, our findings offer valuable insights into marine hydrocarbon-degrading microorganisms and suggest considerations for selecting microbial strains for oil pollution remediation.}, } @article {pmid38521099, year = {2024}, author = {Rahmati, F and Sethi, D and Shu, W and Lajayer, BA and Mosaferi, M and Thomson, A and Price, GW}, title = {Advances in microbial exoenzymes bioengineering for improvement of bioplastics degradation.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {141749}, doi = {10.1016/j.chemosphere.2024.141749}, pmid = {38521099}, issn = {1879-1298}, abstract = {Plastic pollution has become a major global concern, posing numerous challenges for the environment and wildlife. Most conventional ways of plastics degradation are inefficient and cause great damage to ecosystems. The development of biodegradable plastics offers a promising solution for waste management. These plastics are designed to break down under various conditions, opening up new possibilities to mitigate the negative impact of traditional plastics. Microbes, including bacteria and fungi, play a crucial role in the degradation of bioplastics by producing and secreting extracellular enzymes, such as cutinase, lipases, and proteases. However, these microbial enzymes are sensitive to extreme environmental conditions, such as temperature and acidity, affecting their functions and stability. To address these challenges, scientists have employed protein engineering and immobilization techniques to enhance enzyme stability and predict protein structures. Strategies such as improving enzyme and substrate interaction, increasing enzyme thermostability, reinforcing the bonding between the active site of the enzyme and substrate, and refining enzyme activity are being utilized to boost enzyme immobilization and functionality. Recently, bioengineering through gene cloning and expression in potential microorganisms, has revolutionized the biodegradation of bioplastics. This review aimed to discuss the most recent protein engineering strategies for modifying bioplastic-degrading enzymes in terms of stability and functionality, including enzyme thermostability enhancement, reinforcing the substrate binding to the enzyme active site, refining with other enzymes, and improvement of enzyme surface and substrate action. Additionally, discovered bioplastic-degrading exoenzymes by metagenomics techniques were emphasized.}, } @article {pmid38520777, year = {2024}, author = {Nguyen Quoc, B and Cavanaugh, SK and Hunt, KA and Bryson, SJ and Winkler, MKH}, title = {Impact of aerobic granular sludge sizes and dissolved oxygen concentration on greenhouse gas N2O emission.}, journal = {Water research}, volume = {255}, number = {}, pages = {121479}, doi = {10.1016/j.watres.2024.121479}, pmid = {38520777}, issn = {1879-2448}, abstract = {Aerobic granular sludge (AGS) at wastewater treatment plants (WWTPs) are known to produce nitrous oxide (N2O), a greenhouse gas which has a ∼300 times higher global warming potential than carbon dioxide. In this research, we studied N2O emissions from different sizes of AGS developed at a dissolved oxygen (DO) level of 2 mgO2/L while exposing them to disturbances at various DO concentrations ranging from 1 to 4 mgO2/L. Five different AGS size classes were studied: 212-600 µm, 600-1000 µm, 1000-1400 µm, 1400-2000 µm, and > 2000 µm. Metagenomic data showed N2O reductase genes (nosZ) were more abundant in the smaller AGS sizes which aligned with the observation of higher N2O reduction rates in small AGS under anaerobic conditions. However, when oxygen was present, the activity measurements of N2O emission showed an opposite trend compared to metagenomic data, smaller AGS (212 to 1000 µm) emitted significantly higher N2O (p < 0.05) than larger AGS (1000 µm to >2000 µm) at DO of 2, 3, and 4 mgO2/L. The N2O emission rate showed positive correlation with both oxygen levels and nitrification rate. This pattern indicates a connection between N2O emission and nitrification. In addition, the data suggested the penetration of oxygen into the anoxic zone of granules might have hindered nitrous oxide reduction, resulting in incomplete denitrification stopping at N2O and consequently contributing to an increase in N2O emissions. This work sets the stage to better understand the impacts of AGS size on N2O emissions in WWTPs under different disturbance of DO conditions, and thus ensure that wastewater treatment will comply with possible future regulations demanding lowering greenhouse gas emissions in an effort to combat climate change.}, } @article {pmid38520323, year = {2024}, author = {Cao, S and Ren, X and Zhang, G and Wang, H and Wei, B and Niu, C}, title = {Gut microbiota metagenomics and mediation of phenol degradation in Bactrocera minax (Diptera, Tephritidae).}, journal = {Pest management science}, volume = {}, number = {}, pages = {}, doi = {10.1002/ps.8096}, pmid = {38520323}, issn = {1526-4998}, abstract = {BACKGROUND: Gut microbiota mediating insect-plant interactions have many manifestations, either by provisioning missing nutrients, or overcoming plant defensive reactions. However, how gut microbiota empower insects to survive by overcoming a variety of plant secondary metabolites remains largely unknown. Bactrocera minax larvae develop in immature citrus fruits, which present numerous phenolic compounds that challenge the larvae. To explore the role of gut microbes in host use and adaptability, we uncovered the mechanisms of phenol degradation by gut microbes using metagenomic and metatranscriptomic analyses, and verified the degradation ability of isolated and cultured bacteria. Research on this subject can help develop potential strain for the environmental friendly pest management operations.

RESULTS: We demonstrated the ability of gut microbes in B. minax larvae to degrade phenols in unripe citrus. After antibiotic treatment, coniferyl alcohol and coumaric aldehyde significantly reduced the survival rate, body length and body weight of the larvae. The metagenomic and metatranscriptomic analyses in B. minax provided evidence for the presence of genes in bacteria and the related pathway involved in phenol degradation. Among them, Enterococcus faecalis and Serratia marcescens, isolated from the gut of B. minax larvae, played critical roles in phenol degradation. Furthermore, supplementation of E. faecalis and S. marcescens in artificial diets containing coniferyl alcohol and coumaric aldehyde increased the survival rate of larvae.

CONCLUSION: In summary, our results provided the first comprehensive analysis of gut bacterial communities by high-throughput sequencing and elucidated the role of bacteria in phenol degradation in B. minax, which shed light on the mechanism underlying specialist insects adapt to host secondary metabolites via gut bacteria. This article is protected by copyright. All rights reserved.}, } @article {pmid38519761, year = {2024}, author = {Bombaywala, S and Bajaj, A and Dafale, NA}, title = {Oxygen mediated mobilization and co-occurrence of antibiotic resistance in lab-scale bioreactor using metagenomic binning.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {5}, pages = {142}, pmid = {38519761}, issn = {1573-0972}, abstract = {Sub-lethal levels of antibiotic stimulate bacteria to generate reactive oxygen species (ROS) that promotes emergence and spread of antibiotic resistance mediated by mobile genetic elements (MGEs). Nevertheless, the influence of dissolved oxygen (DO) levels on mobility of antibiotic resistance genes (ARGs) in response to ROS-induced stress remains elusive. Thus, the study employs metagenomic assembly and binning approaches to decipher mobility potential and co-occurrence frequency of ARGs and MGEs under hyperoxic (5.5-7 mgL[- 1]), normoxic (2.5-4 mgL[- 1]), and hypoxic (0.5-1 mgL[- 1]) conditions in lab-scale bioreactor for 6 months. Among 163 high-quality metagenome-assembled genomes (MAGs) recovered from 13 metagenomes, 42 MAGs harboured multiple ARGs and were assigned to priority pathogen group. Total ARG count increased by 4.3 and 2.5% in hyperoxic and normoxic, but decreased by 0.53% in hypoxic conditions after 150 days. On contrary, MGE count increased by 7.3-1.3% in all the DO levels, with only two ARGs showed positive correlation with MGEs in hypoxic compared to 20 ARGs under hyperoxic conditions. Opportunistic pathogens (Escherichia, Klebsiella, Clostridium, and Proteus) were detected as potential hosts of ARGs wherein co-localisation of critical ARG gene cassette (sul1, dfr1,adeF, and qacC) were identified in class 1 integron/Tn1 family transposons. Thus, enhanced co-occurrence frequency of ARGs with MGEs in pathogens suggested promotion of ARGs mobility under oxidative stress. The study offers valuable insights into ARG dissemination and hosts dynamics that is essential for controlling oxygen-related stress for mitigating MGEs and ARGs in the environment.}, } @article {pmid38519631, year = {2024}, author = {Pan, YF and Zhao, H and Gou, QY and Shi, PB and Tian, JH and Feng, Y and Li, K and Yang, WH and Wu, D and Tang, G and Zhang, B and Ren, Z and Peng, S and Luo, GY and Le, SJ and Xin, GY and Wang, J and Hou, X and Peng, MW and Kong, JB and Chen, XX and Yang, CH and Mei, SQ and Liao, YQ and Cheng, JX and Wang, J and Chaolemen, and Wu, YH and Wang, JB and An, T and Huang, X and Eden, JS and Li, J and Guo, D and Liang, G and Jin, X and Holmes, EC and Li, B and Wang, D and Li, J and Wu, WC and Shi, M}, title = {Metagenomic analysis of individual mosquito viromes reveals the geographical patterns and drivers of viral diversity.}, journal = {Nature ecology & evolution}, volume = {}, number = {}, pages = {}, pmid = {38519631}, issn = {2397-334X}, abstract = {Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology of viruses within individual mosquito hosts. Here, using a meta-transcriptomic approach, we determined the viromes of 2,438 individual mosquitoes (81 species), spanning ~4,000 km along latitudes and longitudes in China. From these data we identified 393 viral species associated with mosquitoes, including 7 (putative) species of arthropod-borne viruses (that is, arboviruses). We identified potential mosquito species and geographic hotspots of viral diversity and arbovirus occurrence, and demonstrated that the composition of individual mosquito viromes was strongly associated with host phylogeny. Our data revealed a large number of viruses shared among mosquito species or genera, enhancing our understanding of the host specificity of insect-associated viruses. We also detected multiple virus species that were widespread throughout the country, perhaps reflecting long-distance mosquito dispersal. Together, these results greatly expand the known mosquito virome, linked viral diversity at the scale of individual insects to that at a country-wide scale, and offered unique insights into the biogeography and diversity of viruses in insect vectors.}, } @article {pmid38519592, year = {2024}, author = {Kunasegaran, T and Balasubramaniam, VRMT and Thirunavuk Arasoo, VJ and Palanisamy, UD and Tan, YK and Ramadas, A}, title = {Diet, lifestyle and gut microbiota composition among Malaysian women with gestational diabetes mellitus: a prospective cohort study.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6891}, pmid = {38519592}, issn = {2045-2322}, support = {SCH SEED/2020/005//Jeffrey Cheah School of Medicine and Health Sciences, Monash University Malaysia/ ; }, abstract = {The study addressed a significant gap in the profiling and understanding of the gut microbiota's influence on Malaysian Malay women with gestational diabetes mellitus (GDM). This prospective cohort study aimed to explore the intricate relationship between gut microbiota, dietary choices, and lifestyle factors among Malay women, both with and without GDM. The research specifically focused on participants during the second (T0) and third (T1) trimesters of pregnancy in Johor Bahru, Malaysia. In Part 1 of the study, a diverse pool of pregnant women at T0 was categorized into two groups: those diagnosed with GDM and those without GDM, with a total sample size of 105 individuals. The assessments encompassed demographic, clinical, lifestyle, and dietary factors at the T0 and T1 trimesters. Part 2 of the study delved into microbiome analysis, targeting a better understanding of the gut microbiota among the participants. Stool samples were randomly collected from 50% of the individuals in each group (GDM and non-GDM) at T0 and T1. The collected samples underwent processing, and 16s rRNA metagenomic analysis was employed to study the microbial composition. The results suggested an association between elevated body weight and glucose levels, poor sleep quality, lack of physical activity, greater intake of iron and meat, and reduced fruit consumption among women with GDM compared to non-GDM groups. The microbiome analysis revealed changes in microbial composition over time, with reduced diversity observed in the GDM group during the third trimester. The genera Lactiplantibacillus, Parvibacter, Prevotellaceae UCG001, and Vagococcus positively correlated with physical activity levels in GDM women in the second trimester. Similarly, the genus Victivallis exhibited a strong positive correlation with gravida and parity. On the contrary, the genus Bacteroides and Roseburia showed a negative correlation with omega-3 polyunsaturated fatty acids (PUFAs) in women without GDM in the third trimester. The study highlighted the multifaceted nature of GDM, involving a combination of lifestyle factors, dietary choices, and changes in gut microbiota composition. The findings emphasized the importance of considering these interconnected elements in understanding and managing gestational diabetes among Malaysian Malay women. Further exploration is essential to comprehend the mechanisms underlying this relationship and develop targeted interventions for effective GDM management.}, } @article {pmid38519541, year = {2024}, author = {Baker, BA and Gutiérrez-Preciado, A and Rodríguez Del Río, Á and McCarthy, CGP and López-García, P and Huerta-Cepas, J and Susko, E and Roger, AJ and Eme, L and Moreira, D}, title = {Expanded phylogeny of extremely halophilic archaea shows multiple independent adaptations to hypersaline environments.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {38519541}, issn = {2058-5276}, support = {787904//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; 803151//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, abstract = {Extremely halophilic archaea (Haloarchaea, Nanohaloarchaeota, Methanonatronarchaeia and Halarchaeoplasmatales) thrive in saturating salt concentrations where they must maintain osmotic equilibrium with their environment. The evolutionary history of adaptations enabling salt tolerance remains poorly understood, in particular because the phylogeny of several lineages is conflicting. Here we present a resolved phylogeny of extremely halophilic archaea obtained using improved taxon sampling and state-of-the-art phylogenetic approaches designed to cope with the strong compositional biases of their proteomes. We describe two uncultured lineages, Afararchaeaceae and Asbonarchaeaceae, which break the long branches at the base of Haloarchaea and Nanohaloarchaeota, respectively. We obtained 13 metagenome-assembled genomes (MAGs) of these archaea from metagenomes of hypersaline aquatic systems of the Danakil Depression (Ethiopia). Our phylogenomic analyses including these taxa show that at least four independent adaptations to extreme halophily occurred during archaeal evolution. Gene-tree/species-tree reconciliation suggests that gene duplication and horizontal gene transfer played an important role in this process, for example, by spreading key genes (such as those encoding potassium transporters) across extremely halophilic lineages.}, } @article {pmid38519112, year = {2024}, author = {Deng, Y and Yang, S and Zhang, L and Chen, C and Cheng, X and Hou, C}, title = {Chronic bee paralysis virus exploits host AMPs and alters gut microbiota composition to facilitate viral infection.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae051}, pmid = {38519112}, issn = {1751-7370}, abstract = {The significance of gut microbiota in regulating animal immune response to viral infection is increasingly recognized. However, how chronic bee paralysis virus (CBPV) exploits host immune to disturb microbiota for its proliferation remains elusive. Through histopathological examination, we discovered that the hindgut harbored the highest level of CBPV, and displayed visible signs of damages. The metagenomic analysis showed that a notable reduction in the levels of Snodgrassella alvi and Lactobacillus apis, and a significant increase in the abundance of the opportunistic pathogens such as Enterobacter hormaechei and Enterobacter cloacae following CBPV infection. Subsequent co-inoculation experiments showed that these opportunistic pathogens facilitated the CBPV proliferation, leading to accelerated mortality in bees and exacerbation of bloated abdomen symptoms after CBPV infection. The expression level of antimicrobial peptide (AMP) was found to be significantly up-regulated by over 1000 times in response to CBPV infection, as demonstrated by subsequent transcriptome and qPCR investigations. In particular, through correlation analysis and a bacteriostatic test revealed that the AMPs did not exhibit any inhibitory effect against the two opportunistic pathogens. However, they did demonstrate inhibitory activity against S. alvi and L. apis. Our findings provide different evidence that the virus infection may stimulate and utilize the host's AMPs to eradicate probiotic species and facilitate the proliferation of opportunistic bacteria. This process weakens the intestinal barrier and ultimately resulting in the typical bloated abdomen.}, } @article {pmid38519004, year = {2024}, author = {Sepulveda, M and Rasic, M and Lei, YM and Kwan, M and Chen, L and Chen, Y and Perkins, D and Alegre, ML}, title = {Coordinated elimination of bacterial taxa optimally attenuates alloimmunity and prolongs allograft survival.}, journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajt.2024.03.020}, pmid = {38519004}, issn = {1600-6143}, abstract = {This study aimed to dissect the relationship between specific gut commensal bacterial subgroups, their functional metabolic pathways, and their impact on skin allograft outcome and alloimmunity. We previously showed that oral broad-spectrum antibiotic pre-treatment in mice delayed skin, heart and lung allograft rejection and dampened alloimmune responses. Here, rationally designed antibiotic combinations targeting major bacterial groups were used to elucidate their individual contribution to modulating alloimmune responses. Antibiotic cocktails targeting intestinal Gram-negative, Gram-positive, or anaerobic/Gram-positive bacteria by oral gavage, all delayed skin allograft rejection and reduced alloreactive T cell priming to different extents. Notably, the most pronounced extension of skin allograft survival and attenuation of alloimmunity were achieved when all gut bacterial groups were simultaneously targeted. These results suggest a model in which the strength of the alloimmune response is additively tuned up by gut microbial diversity. Shotgun metagenomic sequencing enabled strain-level resolution and identified a shared commensal, Parabacteroides distasonis, as the most enriched following all antibiotic treatments. Oral administration of P. distasonis to mice harboring a diverse microbiota significantly prolonged skin allograft survival, identifying a probiotic with therapeutic benefit in transplantation.}, } @article {pmid38518910, year = {2024}, author = {Hou, Y and Diao, W and Jia, R and Sun, W and Feng, W and Li, B and Zhu, J}, title = {Variations in antibiotic resistomes associated with archaeal, bacterial, and viral communities affected by integrated rice-fish farming in the paddy field ecosystem.}, journal = {Environmental research}, volume = {}, number = {}, pages = {118717}, doi = {10.1016/j.envres.2024.118717}, pmid = {38518910}, issn = {1096-0953}, abstract = {Antibiotic resistance genes (ARGs) serving as a newly recognized pollutant that poses potential risks to global human health, which in the paddy soil can be potentially altered by different agricultural production patterns. To elucidate the impacts and mechanisms of the widely used and sustainable agricultural production pattern, namely integrated rice-fish farming, on the antibiotic resistomes, we applied metagenomic sequencing to assess ARGs, mobile genetic elements (MGEs), bacteria, archaea, and viruses in paddy soil. There were 20 types and 359 subtypes of ARGs identified in paddy soil. The integrated rice-fish farming reduced the ARG and MGE diversities and the abundances of dominant ARGs and MGEs. Significantly decreased ARGs were mainly antibiotic deactivation and regulator types and primarily ranked level IV based on their potential threat to human health. The integrated rice-fish farming decreased the alpha diversities and altered microbial community compositions. MGEs, bacteria, archaea, and virus exhibited significant correlations with ARGs, while integrated rice-fish farming effectively changed their interrelationships. Viruses, bacteria, and MGEs played crucial roles in affecting the ARGs by the integrated rice-fish farming. The most crucial pathway by which integrated rice-fish farming affected ARGs was through the modulation of viral communities, thereby directly or indirectly influencing ARG abundance. Our research contributed to the control and restoration of ARGs pollution from a new perspective and providing theoretical support for the development of clean and sustainable agricultural production.}, } @article {pmid38518499, year = {2024}, author = {Xie, Y and Liu, X and Liu, L and Zhou, Y and Wang, Z and Huang, C and He, H and Zhai, Y}, title = {Deep eutectic solvents pretreatment enhances methane production from anaerobic digestion of waste activated sludge: Effectiveness evaluation and mechanism elucidation.}, journal = {Journal of environmental management}, volume = {356}, number = {}, pages = {120615}, doi = {10.1016/j.jenvman.2024.120615}, pmid = {38518499}, issn = {1095-8630}, abstract = {Anaerobic digestion (AD) is a prevalent waste activated sludge (WAS) treatment, and optimizing methane production is a core focus of AD. Two DESs were developed in this study and significantly increased methane production, including choline chloride-urea (ChCl-Urea) 390% and chloride-ethylene glycol (ChCl-EG) 540%. Results showed that ChCl-Urea mainly disrupted extracellular polymeric substances (EPS) structures, aiding in initial sludge solubilization during pretreatment. ChCl-EG, instead, induced sludge self-driven organic solubilization and enhanced hydrolysis and acidification processes during AD process. Based on the extent to which the two DESs promoted AD for methane production, the AD process can be divided into stage Ⅰ and stage Ⅱ. In stage Ⅰ, ChCl-EG promoted methanogenesis more significantly, microbiological analysis showed both DESs enriched aceticlastic methanogens-Methanosarcina. Notably, ChCl-Urea particularly influenced polysaccharide-related metabolism, whereas ChCl-EG targeted protein-related metabolism. In stage Ⅱ, ChCl-Urea was more dominant than ChCl-EG, ChCl-Urea bolstered metabolism and ChCl-EG promoted genetic information processing in this stage. In essence, this study investigated the microbial mechanism of DES-enhanced sludge methanogenesis and provided a reference for future research.}, } @article {pmid38518494, year = {2024}, author = {Tian, F and Guo, G and Fu, W and Li, S and Ding, K and Yang, F and Liang, C}, title = {Decolorization and detoxification of Brilliant Crocein GR by a newly enriched thermophilic consortium.}, journal = {Journal of environmental management}, volume = {356}, number = {}, pages = {120623}, doi = {10.1016/j.jenvman.2024.120623}, pmid = {38518494}, issn = {1095-8630}, abstract = {The environmental pollution caused by azo dyes at high temperatures has become an urgent problem. However, little attention has been paid to decolorizing azo dyes by thermophilic consortiums. In this study, a thermophilic bacterial consortium (BCGR-T) mainly composed of two genera, namely, Caldibacillus (70.90%) and Aeribacillus (17.63%) was first enriched, which can decolorize Brilliant Crocein GR (BCGR) at high temperatures (50-75 °C), pH values of 6∼8, dye concentrations (100-400 mg/L) and salinities (1-5%, w/v). The enzyme activity results showed that the azoreductase activity was nearly 8.8 times that of the control (p < 0.01), and the intracellular lignin peroxidase was also highly expressed with enzyme activity of 5.64 U (min[-1] mg[-1] protein) (p < 0.05), indicated that both azoreductase and intracellular lignin peroxidase played an important part in the decolorization process. Furthermore, seven new intermediate metabolic products, including aniline, phthalic acid, 2-carboxy benzaldehyde, phenylacetic acid, benzoic acid, toluene, and 4-methyl-hexanoic acid, were identified. In addition, functional genes related with the azo dye decolorization, such as those encoding the azoreductase, laccase, FMN reductase, NADPH-/NADH-quinone oxidoreductases and NADPH-/NADH dehydrogenases, catechol dioxygenase, homogentisate 1,2-dioxygenase, protocatechuate 3,4-dioxygenase, gentisate 1,2-dioxygenase, azobenzene reductase, naphthalene 1,2-dioxygenase, benzoate/toluate 1,2-dioxygenase, and anthranilate 1,2-dioxygenase and so on were found in the metagenome of the consortium BCGR-T. Finally, a new decolorization pathway of the thermophilic consortium BCGR-T was proposed. In addition, the phototoxicity of BCGR decreased after decolorization. Overall, the thermophilic consortium BCGR-T could be a promising candidate in the treatment of high concentration azo dye wastewater at high temperatures.}, } @article {pmid38517267, year = {2024}, author = {Tian, Y and Duan, Y and Gao, R and Gao, W and Xu, S and Wang, S and Li, F and Fang, F and Su, R and Chen, Y and Xu, N and Li, W and Zhang, L and Zhou, JX}, title = {Diagnostic Performance of central nervous system infections in patients with neurosurgical intensive care using metagenomic next-generation sequencing: A Prospective Observational Study.}, journal = {Shock (Augusta, Ga.)}, volume = {}, number = {}, pages = {}, doi = {10.1097/SHK.0000000000002320}, pmid = {38517267}, issn = {1540-0514}, abstract = {BACKGROUND: Identifying the causative pathogens of central nervous system infections (CNSIs) is crucial, but the low detection rate of traditional culture methods in cerebrospinal fluid (CSF) has made the pathogenic diagnosis of CNSIs a longstanding challenge. Patients with CNSIs after neurosurgery often overlap with inflammatory and bleeding. Metagenomic next generation sequencing (mNGS) has shown some benefits in pathogen detection. This study aimed to investigate the diagnostic performance of mNGS in the etiological diagnosis of CNSIs in patients after neurosurgery.

METHODS: In this prospective observational study, we enrolled patients with suspected CNSIs after neurosurgical operations who were admitted to the intensive care unit of Beijing Tiantan Hospital. All enrolled patients' CSF was tested using mNGS and pathogen culture. According to comprehensive clinical diagnosis, the enrolled patients were divided into CNSIs group and non-CNSIs group to compare the diagnostic efficiency of mNGS and pathogen culture.

RESULTS: From December 2021 to March 2023, 139 patients were enrolled while 66 in CNSIs group and 73 in non-CNSIs. The mNGS exceeded culture in the variety and quantity of pathogens detected. The mNGS outperformed traditional pathogen culture in terms of positive percent agreement (63.63%), accuracy (82.01%), and negative predictive value (75.00%), with statistically significant differences (P < 0.05) for traditional pathogen culture. The mNGS also detected bacterial spectrum and antimicrobial resistance genes.

CONCLUSIONS: Metagenomics has the potential to assist in the diagnosis of patients with CNSIs who have a negative culture.}, } @article {pmid38517167, year = {2024}, author = {Pereira-Mora, L and Guerrero, LD and Erijman, L and Fernández-Scavino, A}, title = {Tartrate fermentation with H2 production by a new member of Sporomusaceae enriched from rice paddy soil.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0235123}, doi = {10.1128/aem.02351-23}, pmid = {38517167}, issn = {1098-5336}, abstract = {In rice paddies, soil and plant-derived organic matter are degraded anaerobically to methane (CH4), a powerful greenhouse gas. The highest rate of methane emission occurs during the reproductive stage of the plant when mostly dicarboxylic acids are exudated by the roots. The emission of methane at this stage depends largely on the cooperative interaction between dicarboxylic acid-fermenting bacteria and methanogenic archaea in the rhizosphere. The fermentation of tartrate, one of the major acids exudated, has been scarcely explored in rice paddy soils. In this work, we characterized an anaerobic consortium from rice paddy soil composed of four bacterial strains, whose principal member (LT8) can ferment tartrate, producing H2 and acetate. Tartrate fermentation was accelerated by co-inoculation with a hydrogenotrophic methanogen. The assembled genome of LT8 possesses a Na[+]-dependent oxaloacetate decarboxylase and shows that this bacterium likely invests part of the H2 produced to reduce NAD(P)[+] to assimilate C from tartrate. The phylogenetic analysis of the 16S rRNA gene, the genome-based classification as well as the average amino acid identity (AAI) indicated that LT8 belongs to a new genus within the Sporomusaceae family. LT8 shares a few common features with its closest relatives, for which tartrate degradation has not been described. LT8 is limited to a few environments but is more common in rice paddy soils, where it might contribute to methane emissions from root exudates.IMPORTANCEThis is the first report of the metabolic characterization of a new anaerobic bacterium able to degrade tartrate, a compound frequently associated with plants, but rare as a microbial metabolite. Tartrate fermentation by this bacterium can be coupled to methanogenesis in the rice rhizosphere where tartrate is mainly produced at the reproductive stage of the plant, when the maximum methane rate emission occurs. The interaction between secondary fermentative bacteria, such as LT8, and methanogens could represent a fundamental step in exploring mitigation strategies for methane emissions from rice fields. Possible strategies could include controlling the activity of these secondary fermentative bacteria or selecting plants whose exudates are more difficult to ferment.}, } @article {pmid38516656, year = {2024}, author = {Brait, N and Hackl, T and Morel, C and Exbrayat, A and Gutierrez, S and Lequime, S}, title = {A tale of caution: How endogenous viral elements affect virus discovery in transcriptomic data.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {vead088}, doi = {10.1093/ve/vead088}, pmid = {38516656}, issn = {2057-1577}, abstract = {Large-scale metagenomic and -transcriptomic studies have revolutionized our understanding of viral diversity and abundance. In contrast, endogenous viral elements (EVEs), remnants of viral sequences integrated into host genomes, have received limited attention in the context of virus discovery, especially in RNA-Seq data. EVEs resemble their original viruses, a challenge that makes distinguishing between active infections and integrated remnants difficult, affecting virus classification and biases downstream analyses. Here, we systematically assess the effects of EVEs on a prototypical virus discovery pipeline, evaluate their impact on data integrity and classification accuracy, and provide some recommendations for better practices. We examined EVEs and exogenous viral sequences linked to Orthomyxoviridae, a diverse family of negative-sense segmented RNA viruses, in 13 genomic and 538 transcriptomic datasets of Culicinae mosquitoes. Our analysis revealed a substantial number of viral sequences in transcriptomic datasets. However, a significant portion appeared not to be exogenous viruses but transcripts derived from EVEs. Distinguishing between transcribed EVEs and exogenous virus sequences was especially difficult in samples with low viral abundance. For example, three transcribed EVEs showed full-length segments, devoid of frameshift and nonsense mutations, exhibiting sufficient mean read depths that qualify them as exogenous virus hits. Mapping reads on a host genome containing EVEs before assembly somewhat alleviated the EVE burden, but it led to a drastic reduction of viral hits and reduced quality of assemblies, especially in regions of the viral genome relatively similar to EVEs. Our study highlights that our knowledge of the genetic diversity of viruses can be altered by the underestimated presence of EVEs in transcriptomic datasets, leading to false positives and altered or missing sequence information. Thus, recognizing and addressing the influence of EVEs in virus discovery pipelines will be key in enhancing our ability to capture the full spectrum of viral diversity.}, } @article {pmid38516330, year = {2023}, author = {White, MFM and Wallace, S}, title = {A New PETase from the Human Saliva Metagenome and Its Functional Modification via Genetic Code Expansion in Bacteria.}, journal = {Angewandte Chemie (Weinheim an der Bergstrasse, Germany)}, volume = {135}, number = {12}, pages = {e202216963}, doi = {10.1002/ange.202216963}, pmid = {38516330}, issn = {0044-8249}, abstract = {The discovery and engineering of new plastic degrading enzymes is an important challenge in chemical biotechnology to enable transition to a more sustainable and circular plastics economy. This field has so far yielded a range of enzymes and microbial pathways for the recycling and valorization of plastic waste. New research from Uttamapinant et al. reports the discovery of a novel polyethylene terephthalate (PET) hydrolase from the human saliva metagenome that displays improved properties and catalytic performance over previously characterized PET hydrolases (PETases). The authors also demonstrate the site-specific incorporation of a photocaged unnatural amino acid, 2,3-diaminopropionic acid (DAP), which upon photodecaging enables covalent binding of DAP to the PET surface. Thus, this work highlights metagenomic datasets as an untapped source of new PET degrading enzymes and the chemical modification of PETases via genetic code expansion, enabling new biotechnologies for the circular plastics economy.}, } @article {pmid38516019, year = {2024}, author = {Hui, X and Yang, J and Sun, J and Liu, F and Pan, W}, title = {MCSS: microbial community simulator based on structure.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1358257}, doi = {10.3389/fmicb.2024.1358257}, pmid = {38516019}, issn = {1664-302X}, abstract = {De novo assembly plays a pivotal role in metagenomic analysis, and the incorporation of third-generation sequencing technology can significantly improve the integrity and accuracy of assembly results. Recently, with advancements in sequencing technology (Hi-Fi, ultra-long), several long-read-based bioinformatic tools have been developed. However, the validation of the performance and reliability of these tools is a crucial concern. To address this gap, we present MCSS (microbial community simulator based on structure), which has the capability to generate simulated microbial community and sequencing datasets based on the structure attributes of real microbiome communities. The evaluation results indicate that it can generate simulated communities that exhibit both diversity and similarity to actual community structures. Additionally, MCSS generates synthetic PacBio Hi-Fi and Oxford Nanopore Technologies (ONT) long reads for the species within the simulated community. This innovative tool provides a valuable resource for benchmarking and refining metagenomic analysis methods. Code available at: https://github.com/panlab-bio/mcss.}, } @article {pmid38515324, year = {2024}, author = {Zou, S and Chen, Z and Tan, Y and Tan, M and Guo, W and Wu, S and Liu, J and Song, S and Peng, Y and Wang, M and Liang, K}, title = {Microbiomes detected by cerebrospinal fluid metagenomic next-generation sequencing among patients with and without HIV with suspected central nervous system infection.}, journal = {HIV medicine}, volume = {}, number = {}, pages = {}, doi = {10.1111/hiv.13634}, pmid = {38515324}, issn = {1468-1293}, support = {PTXM2020008//Medical Science Advancement Program (Basic Medical Sciences) of Wuhan University/ ; //Science and Technology Innovation Cultivation Fund of Zhongnan Hospital/ ; 2020-PT320-004//Non-profit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; //Medical Science and Technology Innovation Platform Support Project of Zhongnan Hospital, Wuhan University/ ; ZNXKPY2021027//Discipline Cultivation Funding, Zhongnan Hospital of Wuhan University/ ; }, abstract = {BACKGROUND: Opportunistic infections in the central nervous system (CNS) can be a serious threat to people living with HIV. Early aetiological diagnosis and targeted treatment are crucial but difficult. Metagenomic next-generation sequencing (mNGS) has significant advantages over traditional detection methods. However, differences in the cerebrospinal fluid (CSF) microbiome profiles of patients living with and without HIV with suspected CNS infections using mNGS and conventional testing methods have not yet been adequately evaluated.

METHODS: We conducted a retrospective cohort study in the first hospital of Changsha between January 2019 and June 2022 to investigate the microbiomes detected using mNGS of the CSF of patients living with and without HIV with suspected CNS infections. The pathogens causing CNS infections were concurrently identified using both mNGS and traditional detection methods. The spectrum of pathogens identified was compared between the two groups.

RESULTS: Overall, 173 patients (140 with and 33 without HIV) with suspected CNS infection were enrolled in our study. In total, 106 (75.7%) patients with and 16 (48.5%) patients without HIV tested positive with mNGS (p = 0.002). Among the enrolled patients, 71 (50.7%) with HIV and five (15.2%) without HIV tested positive for two or more pathogens (p < 0.001). Patients with HIV had significantly higher proportions of fungus (20.7% vs. 3.0%, p = 0.016) and DNA virus (59.3% vs. 21.2%, p < 0.001) than those without HIV. Epstein-Barr virus (33.6%) was the most commonly identified potential pathogen in the CSF of patients living with HIV using mNGS, followed by cytomegalovirus (20.7%) and torque teno virus (13.8%). The top three causative pathogens identified in patients without HIV were Streptococcus (18.2%), Epstein-Barr virus (12.1%), and Mycobacterium tuberculosis (9.1%). In total, 113 patients living with HIV were diagnosed as having CNS infections. The rate of pathogen detection in people living with HIV with a CNS infection was significantly higher with mNGS than with conventional methods (93.8% vs. 15.0%, p < 0.001).

CONCLUSION: CSF microbiome profiles differ between patients living with and without HIV with suspected CNS infection. mNGS is a powerful tool for the diagnosis of CNS infection among people living with HIV, especially in those with mixed infections.}, } @article {pmid38515075, year = {2024}, author = {Yan, P and Chen, J and Wang, H and Jia, Q and Xie, J and Mo, G}, title = {A systemic infection involved in lung, brain and spine caused by Scedosporium apiospermum species complex after near-drowning: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {342}, pmid = {38515075}, issn = {1471-2334}, abstract = {Scedosporium apiospermum species complex are widely distributed fungi that can be found in a variety of polluted environments, including soil, sewage, and decaying vegetation. Those opportunistic pathogens with strong potential of invasion commonly affect immunosuppressed populations However, few cases of scedosporiosis are reported in immunocompetent individuals, who might be misdiagnosed, leading to a high mortality rate. Here, we reported an immunocompetent case of systemtic infection involved in lung, brain and spine, caused by S. apiospermum species complex (S. apiospermum and S. boydii). The patient was an elderly male with persistent fever and systemtic infection after near-drowning. In the two tertiary hospitals he visited, definite diagnosis was extremely difficult. After being admitted to our hospital, he was misdiagnosed as tuberculosis infection, before diagnosis of S. apiospermum species complex infection by the metagenomic next-generation sequencing. His symptoms were alleviated after voriconazole treatment. In the present case, the details associated with its course were reported and published studies on Scedosporium spp. infection were also reviewed, for a better understanding of this disease and reducing the misdiagnosis rate.}, } @article {pmid38515054, year = {2024}, author = {Tang, Y and Zhu, Y and You, Z}, title = {Mycobacterium tuberculosis sepsis with multiple intermuscular abscesses and respiratory failure as the main manifestations: a case report.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {340}, pmid = {38515054}, issn = {1471-2334}, support = {2023jstg047//Chongqing Health Appropriate Technology Extension Project/ ; 2023jstg047//Chongqing Health Appropriate Technology Extension Project/ ; 2023jstg047//Chongqing Health Appropriate Technology Extension Project/ ; }, abstract = {BACKGROUND: Tuberculous sepsis is uncommon in individuals without human immunodeficiency virus (HIV) infection, and some patients may not exhibit clinical signs and symptoms of suspected sepsis upon admission, leading to delayed diagnosis and treatment.

CASE PRESENTATION: This report present the case of a 60-year-old female patient who presented with erythema, edema, and pain in her right upper limb accompanied by fever and chills. Further evaluation revealed multiple intermuscular abscesses caused by suspected gram-positive bacteria. Despite receiving anti-infection treatment, the patient rapidly progressed to septic shock and respiratory failure. Metagenomic next-generation sequencing (mNGS) analysis of blood samples detected Mycobacterium tuberculosis complex groups (11 reads). Additionally, mNGS analysis of fluid obtained from puncture of the abscess in the right upper extremity also suggested Mycobacterium tuberculosis complex groups (221 981 reads). Consequently, the patient was diagnosed with tuberculous sepsis resulting from hematogenous dissemination of Mycobacterium tuberculosis. Following the administration of anti-tuberculosis treatment, a gradual recovery was observed during the subsequent follow-up period.

CONCLUSION: It is noteworthy that atypical hematogenous disseminated tuberculosis can be prone to misdiagnosis or oversight, potentially leading to septic shock. This case illustrates the importance of early diagnosis and treatment of tuberculosis sepsis. Advanced diagnostic techniques such as mNGS can aid clinicians in the early identification of pathogens for definitive diagnosis.}, } @article {pmid38514648, year = {2024}, author = {Liu, J and Yan, Q and Li, S and Jiao, J and Hao, Y and Zhang, G and Zhang, Q and Luo, F and Zhang, Y and Lv, Q and Zhang, W and Zhang, A and Song, H and Xin, Y and Ma, Y and Owusu, L and Ma, X and Yin, P and Shang, D}, title = {Integrative metagenomic and metabolomic analyses reveal the potential of gut microbiota to exacerbate acute pancreatitis.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {29}, pmid = {38514648}, issn = {2055-5008}, support = {81873156//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82004152//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Early dysbiosis in the gut microbiota may contribute to the severity of acute pancreatitis (AP), however, a comprehensive understanding of the gut microbiome, potential pathobionts, and host metabolome in individuals with AP remains elusive. Hence, we employed fecal whole-metagenome shotgun sequencing in 82 AP patients and 115 matched healthy controls, complemented by untargeted serum metabolome and lipidome profiling in a subset of participants. Analyses of the gut microbiome in AP patients revealed reduced diversity, disrupted microbial functions, and altered abundance of 77 species, influenced by both etiology and severity. AP-enriched species, mostly potential pathobionts, correlated positively with host liver function and serum lipid indicators. Conversely, many AP-depleted species were short-chain fatty acid producers. Gut microflora changes were accompanied by shifts in the serum metabolome and lipidome. Specifically, certain gut species, like enriched Bilophila wadsworthia and depleted Bifidobacterium spp., appeared to contribute to elevated triglyceride levels in biliary or hyperlipidemic AP patients. Through culturing and whole-genome sequencing of bacterial isolates, we identified virulence factors and clinically relevant antibiotic resistance in patient-derived strains, suggesting a predisposition to opportunistic infections. Finally, our study demonstrated that gavage of specific pathobionts could exacerbate pancreatitis in a caerulein-treated mouse model. In conclusion, our comprehensive analysis sheds light on the gut microbiome and serum metabolome in AP, elucidating the role of pathobionts in disease progression. These insights offer valuable perspectives for etiologic diagnosis, prevention, and intervention in AP and related conditions.}, } @article {pmid38513871, year = {2024}, author = {Kang, Y and Wang, J and Li, Z}, title = {Profiles of phage in global hospital wastewater: Association with microbial hosts, antibiotic resistance genes, metal resistance genes, and mobile genetic elements.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {171766}, doi = {10.1016/j.scitotenv.2024.171766}, pmid = {38513871}, issn = {1879-1026}, abstract = {Hospital wastewater (HWW) is known to host taxonomically diverse microbial communities, yet limited information is available on the phages infecting these microorganisms. To fill this knowledge gap, we conducted an in-depth analysis using 377 publicly available HWW metagenomic datasets from 16 countries across 4 continents in the NCBI SRA database to elucidate phage-host dynamics and phage contributions to resistance gene transmission. We first assembled a metagenomic HWW phage catalog comprising 13,812 phage operational taxonomic units (pOTUs). The majority of these pOTUs belonged to the Caudoviricetes order, representing 75.29 % of this catalog. Based on the lifestyle of phages, we found that potentially virulent phages predominated in HWW. Specifically, 583 pOTUs have been predicted to have the capability to lyse 81 potentially pathogenic bacteria, suggesting the promising role of HWW phages as a viable alternative to antibiotics. Among all pOTUs, 1.56 % of pOTUs carry 108 subtypes of antibiotic resistance genes (ARGs), 0.96 % of pOTUs carry 76 subtypes of metal resistance genes (MRGs), and 0.96 % of pOTUs carry 22 subtypes of non-phage mobile genetic elements (MGEs). Predictions indicate that certain phages carrying ARGs, MRGs, and non-phage MGEs could infect bacteria hosts, even potential pathogens. This suggests that phages in HWW may contribute to the dissemination of resistance-associated genes in the environment. This meta-analysis provides the first global catalog of HWW phages, revealing their correlations with microbial hosts and pahge-associated ARGs, MRG, and non-phage MGEs. The insights gained from this research hold promise for advancing the applications of phages in medical and industrial contexts.}, } @article {pmid38513845, year = {2024}, author = {Wang, JF and Liu, C and Xu, ZM and Wang, FP and Sun, YY and Huang, JW and Li, QS}, title = {Microbial mechanisms in nitrogen fertilization: Modulating the re-mobilization of clay mineral-bound cadmium in agricultural soils.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {171809}, doi = {10.1016/j.scitotenv.2024.171809}, pmid = {38513845}, issn = {1879-1026}, abstract = {Soil cadmium (Cd) can affect crop growth and food safety, and through the enrichment in the food chain, it ultimately poses a risk to human health. Reducing the re-mobilization of Cd caused by the release of protons and acids by crops and microorganisms after stabilization is one of the significant technical challenges in agricultural activities. This study aimed to investigate the re-mobilization of stabilized Cd within the clay mineral-bound fraction of soil and its subsequent accumulation in crops utilizing nitrogen ammonium nitrogen (NH4[+]-N) and nitrate nitrogen (NO3[-]-N), at 60 and 120 mg kg[-1]. Furthermore, the study harvested root exudates at various growth stages to assess their direct influence on the re-mobilization of stabilized Cd and to evaluate the indirect effects mediated by soil microorganisms. The results revealed that, in contrast to the NO3[-]-N treatment, the NH4[+]-N treatment significantly enhanced the conversion of clay mineral-bound Cd in the soil to NH4NO3-extractable Cd. It also amplified the accumulation of Cd in edible amaranth, with concentrations in roots and shoots rising from 1.7-6.0 mg kg[-1] to 4.3-9.8 mg kg[-1]. The introduction of NH4[+]-N caused a decrease in the pH value of the rhizosphere soil and stimulated the production and secretion organic and amino acids, such as oxalic acid, lactic acid, stearic acid, succinic acid, and l-serine, from the crop roots. Furthermore, compared to NO3[-]-N, the combined interaction of root exudates with NH4[+]-N has a more pronounced impact on the abundance of microbial genes associated with glycolysis pathway and tricarboxylic acid cycle, such as pkfA, pfkB, sucB, sucC, and sucD. The effects of NH4[+]-N on crops and microorganisms ultimately result in a significant increase in the re-mobilization of stabilized Cd. However, the simulated experiments showed that microorganisms only contribute to 3.8-6.6 % of the re-mobilization of clay mineral-bound Cd in soil. Therefore, the fundamental strategy to inhibit the re-mobilization of stabilized Cd in vegetable cultivation involves the regulation of proton and organic acid secretion by crops.}, } @article {pmid36740755, year = {2024}, author = {Dang, Z and Li, J and Liu, Y and Song, M and Lockhart, PJ and Tian, Y and Niu, M and Wang, Q}, title = {RADseq-based population genomic analysis and environmental adaptation of rare and endangered recretohalophyte Reaumuria trigyna.}, journal = {The plant genome}, volume = {17}, number = {1}, pages = {e20303}, doi = {10.1002/tpg2.20303}, pmid = {36740755}, issn = {1940-3372}, support = {31860078//National Natural Science Foundation of China/ ; 32160088//National Natural Science Foundation of China/ ; NJYT22093//Program for Young Talents of Science and Technology in Universities of Inner Mongolia Autonomous Region of China/ ; 2020MS03005//Natural Science Foundation of Inner Mongolia Autonomous Region of China/ ; MAU1707//New Zealand Marsden Fund/ ; }, mesh = {*Metagenomics ; *Genomics ; Sequence Analysis, DNA ; China ; }, abstract = {Genetic diversity reflects the survival potential, history, and population dynamics of an organism. It underlies the adaptive potential of populations and their response to environmental change. Reaumuria trigyna is an endemic species in the Eastern Alxa and West Ordos desert regions in China. The species has been considered a good candidate to explore the unique survival strategies of plants that inhabit this area. In this study, we performed population genomic analyses based on restriction-site associated DNA sequencing to understand the genetic diversity, population genetic structure, and differentiation of the species. Analyses of 92,719 high-quality single-nucleotide polymorphisms (SNPs) indicated that overall genetic diversity of R. trigyna was low (HO = 0.249 and HE = 0.208). No significant genetic differentiation was observed among the investigated populations. However, a subtle population genetic structure was detected. We suggest that this might be explained by adaptive diversification reinforced by the geographical isolation of populations. Overall, 3513 outlier SNPs were located in 243 gene-coding sequences in the R. trigyna transcriptome. Potential sites under diversifying selection occurred in genes (e.g., AP2/EREBP, E3 ubiquitin-protein ligase, FLS, and 4CL) related to phytohormone regulation and synthesis of secondary metabolites which have roles in adaptation of species. Our genetic analyses provide scientific criteria for evaluating the evolutionary capacity of R. trigyna and the discovery of unique adaptions. Our findings extend knowledge of refugia, environmental adaption, and evolution of germplasm resources that survive in the Ordos area.}, } @article {pmid38511953, year = {2024}, author = {Zhao, Z and Baltar, F and Herndl, GJ}, title = {Decoupling between the genetic potential and the metabolic regulation and expression in microbial organic matter cleavage across microbiomes.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0303623}, doi = {10.1128/spectrum.03036-23}, pmid = {38511953}, issn = {2165-0497}, abstract = {UNLABELLED: Metagenomics, metatranscriptomics, and metaproteomics are used to explore the microbial capability of enzyme secretion, but the links between protein-encoding genes and corresponding transcripts/proteins across ecosystems are underexplored. By conducting a multi-omics comparison focusing on key enzymes (carbohydrate-active enzymes [CAZymes] and peptidases) cleaving the main biomolecules across distinct microbiomes living in the ocean, soil, and human gut, we show that the community structure, functional diversity, and secretion mechanisms of microbial secretory CAZymes and peptidases vary drastically between microbiomes at metagenomic, metatranscriptomic, and metaproteomic levels. Such variations lead to decoupled relationships between CAZymes and peptidases from genetic potentials to protein expressions due to the different responses of key players toward organic matter sources and concentrations. Our results highlight the need for systematic analysis of the factors shaping patterns of microbial cleavage on organic matter to better link omics data to ecosystem processes.

IMPORTANCE: Omics tools are used to explore adaptive mechanism of microbes in diverse systems, but the advantages and limitations of different omics tools remain skeptical. Here, we reported distinct profiles in microbial secretory enzyme composition revealed by different omics methods. In general, the predicted function from metagenomic analysis decoupled from the expression of corresponding transcripts/proteins. Linking omics results to taxonomic origin, functional capability, substrate specificity, secretion preference, and enzymatic activity measurement suggested the substrate's source, concentration and stoichiometry impose strong filtering on the expression of extracellular enzymes, which may overwrite the genetic potentials. Our results present an integrated perspective on the need for multi-dimensional characterization of microbial adaptation in a changing environment.}, } @article {pmid38511950, year = {2024}, author = {Blais, M-A and Vincent, WF and Vigneron, A and Labarre, A and Matveev, A and Coelho, LF and Lovejoy, C}, title = {Diverse winter communities and biogeochemical cycling potential in the under-ice microbial plankton of a subarctic river-to-sea continuum.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0416023}, doi = {10.1128/spectrum.04160-23}, pmid = {38511950}, issn = {2165-0497}, abstract = {UNLABELLED: Winter conditions greatly alter the limnological properties of lotic ecosystems and the availability of nutrients, carbon, and energy resources for microbial processes. However, the composition and metabolic capabilities of winter microbial communities are still largely uncharacterized. Here, we sampled the winter under-ice microbiome of the Great Whale River (Nunavik, Canada) and its discharge plume into Hudson Bay. We used a combination of 16S and 18S rRNA gene amplicon analysis and metagenomic sequencing to evaluate the size-fractionated composition and functional potential of the microbial plankton. These under-ice communities were diverse in taxonomic composition and metabolically versatile in terms of energy and carbon acquisition, including the capacity to carry out phototrophic processes and degrade aromatic organic matter. Limnological properties, community composition, and metabolic potential differed between shallow and deeper sites in the river, and between fresh and brackish water in the vertical profile of the plume. Community composition also varied by size fraction, with a greater richness of prokaryotes in the larger size fraction (>3 µm) and of microbial eukaryotes in the smaller size fraction (0.22-3 µm). The freshwater communities included cosmopolitan bacterial genera that were previously detected in the summer, indicating their persistence over time in a wide range of physico-chemical conditions. These observations imply that the microbial communities of subarctic rivers and their associated discharge plumes retain a broad taxonomic and functional diversity throughout the year and that microbial processing of complex terrestrial materials persists beneath the ice during the long winter season.

IMPORTANCE: Microbiomes vary over multiple timescales, with short- and long-term changes in the physico-chemical environment. However, there is a scarcity of data and understanding about the structure and functioning of aquatic ecosystems during winter relative to summer. This is especially the case for seasonally ice-covered rivers, limiting our understanding of these ecosystems that are common throughout the boreal, subpolar, and polar regions. Here, we examined the winter under-ice microbiome of a Canadian subarctic river and its entry to the sea to characterize the taxonomic and functional features of the microbial community. We found substantial diversity in both composition and functional capabilities, including the capacity to degrade complex terrestrial compounds, despite the constraints imposed by a prolonged seasonal ice-cover and near-freezing water temperatures. This study indicates the ecological complexity and importance of winter microbiomes in ice-covered rivers and the coastal marine environment that they discharge into.}, } @article {pmid38511460, year = {2024}, author = {Chu, PF and Xing, J and Wang, SZ and Li, T and Qiao, ZL and Yuan, BD}, title = {[Comparison on the diversity of antibiotic resistance genes of three rodent species].}, journal = {Ying yong sheng tai xue bao = The journal of applied ecology}, volume = {35}, number = {1}, pages = {229-236}, doi = {10.13287/j.1001-9332.202401.031}, pmid = {38511460}, issn = {1001-9332}, abstract = {Antibiotic resistance genes (ARGs) have attracted widespread attention as a new global pollutant, mainly due to the abuse of antibiotics. To investigate the diversity of ARGs in three rodent species, we used metagenomic sequencing analysis to analyze the diversity of antibiotic resistance genes of 17 individuals of Apodemus peninsulae and 17 individuals of Myodes rufocanus collected from Mudanfeng, and nine individuals of Apodemus agrarius collected from Sandaoguan. A total of 19 types and 248 subclasses of ARGs were detected in the three rodent species. Seven ARGs showed significant difference and five ARGs showed extremely significant difference between M. rufocanus and A. agrarius. Seven ARGs showed significant difference and four ARGs showed extremely significant difference between A. peninsulae and A. agrarius. Four ARGs showed significant difference and five ARGs showed extremely significant difference between M. rufocanus and A. peninsulae. ARGs showing high abundance in three rodents were macrolides, lincoamides, tetracyclines, and β-lactams. ARGs were widely distributed in the three rodent species. The significant differences in ARGs among different species might be due to the different distribution areas and their diet differentiation. The study could provide a basis for further studies of ARGs in mice and improve the understanding of the harm of ARGs transmission.}, } @article {pmid38510442, year = {2024}, author = {Mousa, WK and Abu-Izneid, T and Salah-Tantawy, A}, title = {High-throughput sequencing reveals the structure and metabolic resilience of desert microbiome confronting climate change.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1294173}, pmid = {38510442}, issn = {1664-462X}, abstract = {INTRODUCTION: Desert ecosystems harbor a unique microbial diversity that is crucial for ecological stability and biogeochemical cycles. An in-depth understanding of the biodiversity, compositions, and functions of these microbial communities is imperative to navigate global changes and confront potential threats and opportunities applicable to agricultural ecosystems amid climate change.

METHODS: This study explores microbial communities in the rhizosphere and endosphere of desert plants native to the Arabian Peninsula using next-generation sequencing of the 16S rRNA gene (V3-V4 hypervariable region).

RESULTS: Our results reveal that each microbial community has a diverse and unique microbial composition. Based on alpha and beta diversity indices, the rhizosphere microbiome is significantly diverse and richer in microbial taxa compared to the endosphere. The data reveals a shift towards fast-growing microbes with active metabolism, involvement in nutrient cycling, nitrogen fixation, and defense pathways. Our data reveals the presence of habitat-specific microbial communities in the desert, highlighting their remarkable resilience and adaptability to extreme environmental conditions. Notably, we observed the existence of radiation-resistant microbes such as Deinococcus radiotolerans, Kocuria sp., and Rubrobacter radiotolerans which can tolerate high levels of ionizing radiation. Additionally, examples of microbes exhibiting tolerance to challenging conditions include Nocardioides halotolerans, thriving in high-salinity environments, and hyperthermophilic microbes such as Quasibacillus thermotolerans. Moreover, functional analysis reveals enrichment in chaperon biosynthesis pathways associated with correct protein folding under heat stress conditions.

DISCUSSION: Our research sheds light on the unique diversity of desert microbes and underscores their potential applications to increase the resilience of agriculture ecosystems, offering a promising strategy to fortify crops against the challenges posed by climate change, ultimately supporting sustainable food production for our ever-expanding global population.}, } @article {pmid38509359, year = {2024}, author = {Zepeda-Rivera, M and Minot, SS and Bouzek, H and Wu, H and Blanco-Míguez, A and Manghi, P and Jones, DS and LaCourse, KD and Wu, Y and McMahon, EF and Park, SN and Lim, YK and Kempchinsky, AG and Willis, AD and Cotton, SL and Yost, SC and Sicinska, E and Kook, JK and Dewhirst, FE and Segata, N and Bullman, S and Johnston, CD}, title = {A distinct Fusobacterium nucleatum clade dominates the colorectal cancer niche.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {38509359}, issn = {1476-4687}, abstract = {Fusobacterium nucleatum (Fn), a bacterium present in the human oral cavity and rarely found in the lower gastrointestinal tract of healthy individuals[1], is enriched in human colorectal cancer (CRC) tumours[2-5]. High intratumoural Fn loads are associated with recurrence, metastases and poorer patient prognosis[5-8]. Here, to delineate Fn genetic factors facilitating tumour colonization, we generated closed genomes for 135 Fn strains; 80 oral strains from individuals without cancer and 55 unique cancer strains cultured from tumours from 51 patients with CRC. Pangenomic analyses identified 483 CRC-enriched genetic factors. Tumour-isolated strains predominantly belong to Fn subspecies animalis (Fna). However, genomic analyses reveal that Fna, considered a single subspecies, is instead composed of two distinct clades (Fna C1 and Fna C2). Of these, only Fna C2 dominates the CRC tumour niche. Inter-Fna analyses identified 195 Fna C2-associated genetic factors consistent with increased metabolic potential and colonization of the gastrointestinal tract. In support of this, Fna C2-treated mice had an increased number of intestinal adenomas and altered metabolites. Microbiome analysis of human tumour tissue from 116 patients with CRC demonstrated Fna C2 enrichment. Comparison of 62 paired specimens showed that only Fna C2 is tumour enriched compared to normal adjacent tissue. This was further supported by metagenomic analysis of stool samples from 627 patients with CRC and 619 healthy individuals. Collectively, our results identify the Fna clade bifurcation, show that specifically Fna C2 drives the reported Fn enrichment in human CRC and reveal the genetic underpinnings of pathoadaptation of Fna C2 to the CRC niche.}, } @article {pmid38509097, year = {2024}, author = {Gunter, HM and Youlten, SE and Reis, ALM and McCubbin, T and Madala, BS and Wong, T and Stevanovski, I and Cipponi, A and Deveson, IW and Santini, NS and Kummerfeld, S and Croucher, PI and Marcellin, E and Mercer, TR}, title = {A universal molecular control for DNA, mRNA and protein expression.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2480}, pmid = {38509097}, issn = {2041-1723}, abstract = {The expression of genes encompasses their transcription into mRNA followed by translation into protein. In recent years, next-generation sequencing and mass spectrometry methods have profiled DNA, RNA and protein abundance in cells. However, there are currently no reference standards that are compatible across these genomic, transcriptomic and proteomic methods, and provide an integrated measure of gene expression. Here, we use synthetic biology principles to engineer a multi-omics control, termed pREF, that can act as a universal molecular standard for next-generation sequencing and mass spectrometry methods. The pREF sequence encodes 21 synthetic genes that can be in vitro transcribed into spike-in mRNA controls, and in vitro translated to generate matched protein controls. The synthetic genes provide qualitative controls that can measure sensitivity and quantitative accuracy of DNA, RNA and peptide detection. We demonstrate the use of pREF in metagenome DNA sequencing and RNA sequencing experiments and evaluate the quantification of proteins using mass spectrometry. Unlike previous spike-in controls, pREF can be independently propagated and the synthetic mRNA and protein controls can be sustainably prepared by recipient laboratories using common molecular biology techniques. Together, this provides a universal synthetic standard able to integrate genomic, transcriptomic and proteomic methods.}, } @article {pmid38509054, year = {2024}, author = {Kittel, E and Crosby, T and Kocurek, B and Ottesen, A and Gieseker, C}, title = {Microbiota of laboratory channel catfish skin mucosa and aquaria water exposed to chloramine-T trihydrate.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0112523}, doi = {10.1128/mra.01125-23}, pmid = {38509054}, issn = {2576-098X}, abstract = {Here, we describe the skin mucosa microbiome of channel catfish (Ictalurus punctatus) before and after exposure to chloramine-T trihydrate. We also describe the aquaria water microbiome after the post-treatment period. These data provide a unique baseline description of skin mucosa and aquaria water microbiome from catfish reared in research aquaria.}, } @article {pmid38508778, year = {2024}, author = {Hatton-Jones, KM and West, NP and Thang, MWC and Chen, PY and Davoren, P and Cripps, AW and Cox, AJ}, title = {Gut Microbiome and Metabolic and Immune Indices in Males with or without Evidence of Metabolic Dysregulation.}, journal = {Journal of obesity & metabolic syndrome}, volume = {}, number = {}, pages = {}, doi = {10.7570/jomes23022}, pmid = {38508778}, issn = {2508-7576}, abstract = {BACKGROUND: The contributions of the gut microbiota to obesity and metabolic disease represent a potentially modifiable factor that may explain variation in risk between individuals. This study aimed to explore relationships among microbial composition and imputed functional attributes, a range of soluble metabolic and immune indices, and gene expression markers in males with or without evidence of metabolic dysregulation (MetDys).

METHODS: This case-control study included healthy males (n=15; 41.9±11.7 years; body mass index [BMI], 22.9±1.2 kg/m[2]) and males with evidence of MetDys (n=14; 46.6±10.0 years; BMI, 35.1±3.3 kg/m[2]) who provided blood and faecal samples for assessment of a range of metabolic and immune markers and microbial composition using 16S rRNA gene sequencing. Metagenomic functions were imputed from microbial sequence data for analysis.

RESULTS: In addition to elevated values in a range of traditional metabolic, adipokine and inflammatory indices in the MetDys group, 23 immunomodulatory genes were significantly altered in the MetDys group. Overall microbial diversity did not differ between groups; however, a trend for a higher relative abundance of the Bacteroidetes (P=0.06) and a lower relative abundance of the Verrucomicrobia (P=0.09) phyla was noted in the MetDys group. Using both family- and genera-level classifications, a partial least square discriminant analysis revealed unique microbial signatures between the groups.

CONCLUSION: These findings confirm the need for ongoing investigations in human clinical cohorts to further resolve the relationships between the gut microbiota and metabolic and immune markers and risk for metabolic disease.}, } @article {pmid38508564, year = {2024}, author = {Ariaeenejad, S and Barani, M and Sarani, M and Lohrasbi-Nejad, A and Mohammadi-Nejad, G and Salekdeh, GH}, title = {Green synthesis of NiO NPs for metagenome-derived laccase stabilization: Detoxifying pollutants and wastes.}, journal = {International journal of biological macromolecules}, volume = {}, number = {}, pages = {130986}, doi = {10.1016/j.ijbiomac.2024.130986}, pmid = {38508564}, issn = {1879-0003}, abstract = {Laccases play a crucial role in neutralizing environmental pollutants, including antibiotics and phenolic compounds, by converting them into less harmful substances via a unique oxidation process. This study introduces an environmentally sustainable remediation technique, utilizing NiO nanoparticles (NPs) synthesized through green chemistry to immobilize a metagenome-derived laccase, PersiLac1, enhancing its application in pollutant detoxification. Salvadora persica leaf extract was used for the synthesis of NiO nanoparticles, utilizing its phytochemical constituents as reducing and capping agents, followed by characterization through different analyses. Characterization of NiO nanoparticles revealed distinctive FTIR absorption peaks indicating the nanoparticulate structure, while FESEM showed structured NiO with robust interconnections and dimensionality of about 50nm, confirmed by EDX analysis to have a consistent distribution of Ni and O. The immobilized PersiLac1 demonstrated enhanced thermal stability, with 85.55 % activity at 80 °C and reduced enzyme leaching, retaining 67.93 % activity across 15 biocatalytic cycles. It efficiently reduced rice straw (RS) phenol by 67.97 % within 210 min and degraded 70-78 % of tetracycline (TC) across a wide pH range (4.0-8.0), showing superior performance over the free enzyme. Immobilized laccase achieved up to 71 % TC removal at 40-80 °C, significantly outperforming the free enzyme. Notably, 54 % efficiency was achieved at 500 mg/L TC by immobilized laccase at 120 min. This research showed the potential of green-synthesized NiO nanoparticles to effectively immobilize laccase, presenting an eco-friendly approach to purify pollutants such as phenols and antibiotics. The durability and reusability of the immobilized enzyme, coupled with its ability to reduce pollutants, indicates a viable method for cleaning the environment. Nonetheless, the production costs and scalability of NiO nanoparticles for widespread industrial applications pose significant challenges. Future studies should focus on implementation at an industrial level and examine a wider range of pollutants to fully leverage the environmental clean-up capabilities of this innovative technology.}, } @article {pmid38366032, year = {2024}, author = {Ertl, H}, title = {Single-cell sequencing of diverse microorganisms.}, journal = {Nature reviews. Genetics}, volume = {25}, number = {4}, pages = {234}, pmid = {38366032}, issn = {1471-0064}, mesh = {Sequence Analysis, DNA ; *Metagenomics ; }, } @article {pmid38508446, year = {2024}, author = {Tao, S and Fan, J and Li, J and Wu, Z and Yao, Y and Wang, Z and Wu, Y and Liu, X and Xiao, Y and Wei, H}, title = {Extracellular vesicles derived from Lactobacillus johnsonii promote gut barrier homeostasis by enhancing M2 macrophage polarization.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2024.03.011}, pmid = {38508446}, issn = {2090-1224}, abstract = {INTRODUCTION: Diarrheic disease is a common intestinal health problem worldwide, causing great suffering to humans and animals. Precise manipulation strategies based on probiotics to combat diarrheic diseases have not been fully developed.

OBJECTIVES: The aim of this study was to investigate the molecular mechanisms by which probiotics manipulate macrophage against diarrheic disease.

METHODS: Metagenome reveals gut microbiome profiles of healthy and diarrheic piglets. Fecal microbial transplantation (FMT) was employed to explore the causal relationship between gut microbes and diarrhea. The protective role of probiotics and their derived extracellular vesicles (EVs) was investigated in ETEC K88-infected mice. Macrophage depletion was performed to assess the role of macrophages in EVs against diarrhea. Execution of in vitro cell co-culture and transcriptome analyses elucidated the molecular mechanisms by which EVs modulate the macrophage and intestinal epithelial barrier.

RESULTS: Escherichia coli was enriched in weaned diarrheic piglets, while Lactobacillus johnsonii (L. john) showed a negative correlation with Escherichia coli. The transmission of diarrheic illness symptoms was achieved by transferring fecal microbiota, but not metabolites, from diarrheic pigs to germ-free (GF) mice. L. john's intervention prevented the transmission of disease phenotypes from diarrheic piglets to GF mice. L. john also reduces the gut inflammation induced by ETEC K88. The EVs secreted by L. john demonstrated enhanced efficacy in mitigating the adverse impacts induced by ETEC K88 through the modulation of macrophage phenotype. In vitro experiments have revealed that EVs activate M2 macrophages in a manner that shuts down ERK, thereby inhibiting NLRP3 activation in intestinal epithelial cells.

CONCLUSION: Our results reveal that intestinal microbiota drives the onset of diarrheic disease and that probiotic-derived EVs ameliorate diarrheic disease symptoms by modulating macrophage phenotypes. These findings can enhance the advancement of innovative therapeutic approaches for diarrheic conditions based on probiotic-derived EVs.}, } @article {pmid38508364, year = {2024}, author = {Tóth, F and Gáspár, G and Pankovics, P and Urbán, P and Herczeg, R and Albert, M and Reuter, G and Boros, Á}, title = {Co-infecting viruses of species Bovine rhinitis B virus (Picornaviridae) and Bovine nidovirus 1 (Tobaniviridae) identified for the first time from a post-mortem respiratory sample of a sheep (Ovis aries) in Hungary.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105585}, doi = {10.1016/j.meegid.2024.105585}, pmid = {38508364}, issn = {1567-7257}, abstract = {In this study, a picornavirus and a nidovirus were identified from a single available nasopharyngeal swab (NPS) sample of a freshly deceased sheep, as the only vertebrate viruses found with viral metagenomics and next-generation sequencing methods. The sample was originated from a mixed feedlot farm in Hungary where sheep and cattle were held together but in separate stalls. Most of the sheep had respiratory signs (coughing and increased respiratory effort) at the time of sampling. Other NPS were not, but additional enteric samples were collected from sheep (n = 27) and cattle (n = 11) of the same farm at that time. The complete/nearly complete genomes of the identified viruses were determined using RT-PCR and Nanopore (MinION-Flonge) / Dye-terminator sequencing techniques. The results of detailed genomic and phylogenetic analyses indicate that the identified picornavirus most likely belongs to a type 4 genotype of species Bovine rhinitis B virus (BRBV-4, OR885914) of genus Aphthovirus, family Picornaviridae while the ovine nidovirus (OvNV, OR885915) - as a novel variant - could belong to the recently created Bovine nidovirus 1 (BoNV) species of genus Bostovirus, family Tobaniviridae. None of the identified viruses were detectable in the enteric samples using RT-PCR and generic screening primer pairs. Both viruses are well-known respiratory pathogens of cattle, but their presence was not demonstrated before in other animals, like sheep. Furthermore, neither BRBV-4 nor BoNVs were investigated in European cattle and/or sheep flocks, therefore it cannot be determined whether the presence of these viruses in sheep was a result of a single host species switch/spillover event or these viruses are circulating in not just cattle but sheep populations as well. Further studies required to investigate the spread of these viruses in Hungarian and European sheep and cattle populations and to identify their pathogenic potential in sheep.}, } @article {pmid38508266, year = {2024}, author = {He, D and Li, J and Yu, W and Zhang, Y and Wang, B and Wang, T and Yang, H and Zhang, Y and Chen, W and Li, Y and Feng, F and Hou, LA}, title = {Deciphering the removal of antibiotics and the antibiotic resistome from typical hospital wastewater treatment systems.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {171806}, doi = {10.1016/j.scitotenv.2024.171806}, pmid = {38508266}, issn = {1879-1026}, abstract = {Hospital wastewater treatment systems (HWTSs) are a significant source and reservoir of antibiotic resistance genes (ARGs) and a crucial hub for transmitting ARGs from clinical to natural environments. However, there is a lack of research on the antibiotic resistome of clinical wastewater in HWTSs. In this study, we used metagenomics to analyze the prevalence and abundance of ARGs in five typical HWTSs. A total of 17 antibiotics from six categories were detected in the five HWTSs; β-lactam antibiotics were found at the highest concentrations, with up to 4074.08 ng·L[-1]. We further found a total of 21 ARG types and 1106 subtypes of ARGs with the highest percentage of multi-drug resistance genes (evgS, msbA, arlS, and baeS). The most abundant last-resort ARGs were mcr, which were detected in 100 % of the samples. HWTSs effluent is a major pathway for the transmission of last-resort ARGs into urban wastewater networks. The removal of antibiotics, antibiotic-resistant bacteria, and ARGs from HWTSs was mainly achieved by tertiary treatment, i.e., chlorine disinfection, but antibiotics and ARGs were still present in the HWTSs effluent or even increased after treatment. Moreover, antibiotics and heavy metals (especially mercury) in hospital effluents can exert selective pressure for antibiotic resistance, even at low concentrations. Qualitative analyses based on metagenome-assembled genome analysis revealed that the putative hosts of the identified ARGs are widely distributed among Pseudomonas, Acidovorax, Flavobacterium, Polaromonas, and Arcobacter. Moreover, we further assessed the clinical availability of ARGs and found that multidrug ARGs had the highest clinical relevance values. This study provides new impulses for monitoring and removing antibiotics and ARGs in the hospital sewage treatment process.}, } @article {pmid38508263, year = {2024}, author = {Sánchez-Marañón, M and Ortega, R and Pulido-Fernández, M and Barrena-González, J and Lavado-Contador, F and Miralles, I and García-Salcedo, JA and Soriano, M}, title = {Compositional and functional analysis of the bacterial community of Mediterranean Leptosols under livestock grazing.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {171811}, doi = {10.1016/j.scitotenv.2024.171811}, pmid = {38508263}, issn = {1879-1026}, abstract = {The composition and functioning of soil bacterial communities, as well as their responses to multiple perturbations, are not well understood in the terrestrial ecosystems. Our study focuses on the bacterial community of erosive and poorly developed soils (Haplic Leptosols) in Mediterranean rangelands of Extremadura (W Spain) with different grazing intensities. Leptosols from similar natural conditions were selected and sampled at two depths to determine the soil properties as well as the structure and activity of bacterial communities. As grazing intensified, the soil C and N content increased, as did the number and diversity of bacteria, mainly of fast-growing lineages. Aridibacter, Acidobacteria Gp6 and Gp10, Gemmatimonas, and Segetibacter increased their abundance along the grazing-intensity gradient. Firmicutes such as Romboutsia and Turicibacter from livestock microbiome also increased. In functional terms, the KEGG pathways enriched in the soils with moderate and high grazing intensity were ABC transporters, DNA repair and recombination proteins, the two-component system, and the degradation of xenobiotics. All of these proved to be related to stronger cell division and response mechanisms to environmental stressors such as drought, warming, toxic substances, and nutrient deprivation. Consequently, the bacterial community was affected by grazing, but appeared to adapt and counteract the effects of a high grazing intensity. Therefore, a clearly detrimental effect of grazing was not detected in the bacterial community of the soils studied.}, } @article {pmid38508004, year = {2024}, author = {Adams, M and Wang, Y and Du, B and Olbert, I and Wu, G}, title = {Operational mode and powdered activated carbon promoting syntrophic propionate oxidation during anaerobic digestion of complex organic substances.}, journal = {Journal of environmental management}, volume = {356}, number = {}, pages = {120593}, doi = {10.1016/j.jenvman.2024.120593}, pmid = {38508004}, issn = {1095-8630}, abstract = {Operational mode and powdered activated carbon (PAC) are key factors facilitating microbial syntrophy and interspecies electron transfer during anaerobic digestion, consequently benefiting process stability and efficient methanogenesis. In this study, continuous-flow reactor (CFR) and sequencing batch reactor (SBR), with and without the addition of PAC, respectively, were operated to examine their effects on system performance and methanogenic activity. Based on the cycle-test result, the PAC-amended CFR (CFRPAC) recorded both the highest methane yield (690.1 mL/L) and the maximum CH4 production rate (28.8 mL/(L·h)), while SBRs exhibited slow methanogenic rates. However, activity assays indicated that SBRs were beneficial for organics removal in batch experiments fed with peptone. Taxonomic and functional analysis confirmed that CFRs were optimal for proliferating oligotrophs (e.g., Geobacter) and SBRs were more suitable for copiotrophs (e.g., Desulfobulbus). Metagenomic analysis revealed that CFRs had efficient acetate metabolic pathways from propionate and ethanol, whereas SBRs did not, resulting in the buildup of propionate. Furthermore, Methanobacterium and Methanothrix were acclimated to the different operational conditions, while acetoclastic Methanosarcina and hydrogenotrophic Methanolinea were acclimated in SBRs (5.1-13.4%) and CFRs (0.3-1.7%), respectively. This study confirmed the enhancement of microbial syntrophy by the addition of PAC as well as the acclimation of electroactive bacteria (e.g., Geobacter) with complex organic substances.}, } @article {pmid38507933, year = {2024}, author = {Xu, J and Xu, X and Jiang, Y and Fu, Y and Shen, C}, title = {Waste to resource: Mining antimicrobial peptides in sludge from metagenomes using machine learning.}, journal = {Environment international}, volume = {186}, number = {}, pages = {108574}, doi = {10.1016/j.envint.2024.108574}, pmid = {38507933}, issn = {1873-6750}, abstract = {The emergence of antibiotic-resistant bacteria poses a huge threat to the treatment of infections. Antimicrobial peptides are a class of short peptides that widely exist in organisms and are considered as potential substitutes for traditional antibiotics. Here, we use metagenomics combined with machine learning to find antimicrobial peptides from environmental metagenomes and successfully obtained 16,044,909 predicted AMPs. We compared the abundance of potential antimicrobial peptides in natural environments and engineered environments, and found that engineered environments also have great potential. Further, we chose sludge as a typical engineered environmental sample, and tried to mine antimicrobial peptides from it. Through metaproteome analysis and correlation analysis, we mined 27 candidate AMPs from sludge. We successfully synthesized 25 peptides by chemical synthesis, and experimentally verified that 21 peptides had antibacterial activity against the 4 strains tested. Our work highlights the potential for mining new antimicrobial peptides from engineered environments and demonstrates the effectiveness of mining antimicrobial peptides from sludge.}, } @article {pmid38506717, year = {2024}, author = {Lin, BW and Hong, JC and Jiang, ZJ and Zhang, WQ and Fan, QC and Yao, XP}, title = {Performance of metagenomic next-generation sequencing in cerebrospinal fluid for diagnosis of tuberculous meningitis.}, journal = {Journal of medical microbiology}, volume = {73}, number = {3}, pages = {}, doi = {10.1099/jmm.0.001818}, pmid = {38506717}, issn = {1473-5644}, abstract = {Purpose. Metagenomic next-generation sequencing (mNGS) has been widely used in the diagnosis of infectious diseases, while its performance in diagnosis of tuberculous meningitis (TBM) is incompletely characterized. The aim of this study was to assess the performance of mNGS in the diagnosis of TBM, and illustrate the sensitivity and specificity of different methods.Methods. We retrospectively recruited TBM patients between January 2021 and March 2023 to evaluate the performance of mNGS on cerebrospinal fluid (CSF) samples, in comparison with conventional microbiological testing, including culturing of Mycobacterium tuberculosis (MTB), acid-fast bacillus (AFB) stain, reverse transcription PCR and Xpert MTB/RIF.Results. Of the 40 enrolled, 34 participants were diagnosed with TBM, including 15(44.12 %) definite and 19(55.88 %) clinical diagnosis based upon clinical manifestations, CSF parameters, brain imaging, pathogen evidence and treatment response. The mNGS method identified sequences of Mycobacterium tuberculosis complex (MTBC) in 11 CSF samples. In patients with definite TBM, the sensitivity, specificity, positive predictive value, negative predictive value and accuracy of mNGS were 78.57, 100, 100, 66.67 and 85 %, respectively. Compared to conventional diagnostic methods, the sensitivity of mNGS (78.57 %) was higher than AFB (0 %), culturing (0 %), RT-PCR (60 %) and Xpert MTB/RIF (14.29 %).Conclusions. Our study indicates that mNGS of CSF exhibited an overall improved sensitivity over conventional diagnostic methods for TBM and can be considered a front-line CSF test.}, } @article {pmid38506520, year = {2024}, author = {Lv, L-J and Wen, J-Y and Zhang, Y and Guo, R-C and Li, H and Yi, Z-T and He, T-W and Chen, M-C and Chen, Y and Wu, X-Y and Li, S-h and Kang, J and Hou, Y-P and Yan, Q-l and Yin, A-H}, title = {Deep metagenomic characterization of the gut virome in pregnant women with preeclampsia.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0067623}, doi = {10.1128/msphere.00676-23}, pmid = {38506520}, issn = {2379-5042}, abstract = {Preeclampsia (PE), a pregnancy-specific syndrome, has been associated with the gut bacteriome. Here, to investigate the impact of the gut virome on the development of PE, we identified over 8,000 nonredundant viruses from the fecal metagenomes of 40 early-onset PE and 37 healthy pregnant women and profiled their abundances. Comparison and correlation analysis showed that PE-enriched viruses frequently connected to Blautia species enriched in PE. By contrast, bacteria linked to PE-depleted viruses were often the Bacteroidaceae members such as Bacteroides spp., Phocaeicola spp., Parabacteroides spp., and Alistipes shahii. In terms of viral function, PE-depleted viruses had auxiliary metabolic genes that participated in the metabolism of simple and complex polysaccharides, sulfur metabolism, lipopolysaccharide biosynthesis, and peptidoglycan biosynthesis, while PE-enriched viruses had a gene encoding cyclic pyranopterin monophosphate synthase, which seemed to be special, that participates in the biosynthesis of the molybdenum cofactor. Furthermore, the classification model based on gut viral signatures was developed to discriminate PE patients from healthy controls and showed an area under the receiver operating characteristic curve of 0.922 that was better than that of the bacterium-based model. This study opens up new avenues for further research, providing valuable insights into the PE gut virome and offering potential directions for future mechanistic and therapeutic investigations, with the ultimate goal of improving the diagnosis and management of PE.IMPORTANCEThe importance of this study lies in its exploration of the previously overlooked but potentially critical role of the gut virome in preeclampsia (PE). While the association between PE and the gut bacteriome has been recognized, this research takes a pioneering step into understanding how the gut virome, represented by over 8,000 nonredundant viruses, contributes to this condition. The findings reveal intriguing connections between PE-enriched viruses and specific gut bacteria, such as the prevalence of Blautia species in individuals with PE, contrasting with bacteria linked to PE-depleted viruses, including members of the Bacteroidaceae family. These viral interactions and associations provide a deeper understanding of the complex dynamics at play in PE.}, } @article {pmid38506511, year = {2024}, author = {Zhi, Q and Tan, G and Wu, S and Ma, Q and Fan, J and Chen, Y and Li, J and Hu, Z and Xiao, Y and Li, L and Liu, Z and Yang, Z and Yang, Z and Meng, D and Yin, H and Tang, Q and Liu, T}, title = {What role do biocontrol agents with Mg[2+] play in the fate of antibiotic resistome and pathogenic bacteria in the phyllosphere?.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0112623}, doi = {10.1128/msystems.01126-23}, pmid = {38506511}, issn = {2379-5077}, abstract = {UNLABELLED: The contamination of the plant phyllosphere with antibiotics and antibiotic resistance genes (ARGs), caused by application of antibiotics, is a significant environmental issue in agricultural management. Alternatively, biocontrol agents are environmentally friendly and have attracted a lot of interest. However, the influence of biocontrol agents on the phyllosphere resistome remains unknown. In this study, we applied biocontrol agents to control the wildfire disease in the Solanaceae crops and investigated their effects on the resistome and the pathogen in the phyllosphere by using metagenomics. A total of 250 ARGs were detected from 15 samples, which showed a variation in distribution across treatments of biocontrol agents (BA), BA with Mg[2+] (T1), BA with Mn[2+] (T2), and kasugamycin (T3) and nontreated (CK). The results showed that the abundance of ARGs under the treatment of BA-Mg[2+] was lower than that in the CK group. The abundance of cphA3 (carbapenem resistance), PME-1 (carbapenem resistance), tcr3 (tetracycline antibiotic resistance), and AAC (3)-VIIIa (aminoglycoside antibiotic resistance) in BA-Mg[2+] was significantly higher than that in BA-Mn[2+] (P < 0.05). The abundance of cphA3, PME_1, and tcr3 was significantly negatively related to the abundance of the phyllosphere pathogen Pseudomonas syringae (P < 0.05). We also found that the upstream and downstream regions of cphA3 were relatively conserved, in which rpl, rpm, and rps gene families were identified in most sequences (92%). The Ka/Ks of cphA3 was 0 in all observed sequences, indicating that under the action of purifying selection, nonsynonymous substitutions are often gradually eliminated in the population. Overall, this study clarifies the effect of biocontrol agents with Mg[2+] on the distribution of the phyllosphere resistome and provides evolutionary insights into the biocontrol process.

IMPORTANCE: Our study applied metagenomics analysis to examine the impact of biocontrol agents (BAs) on the phyllosphere resistome and the pathogen. Irregular use of antibiotics has led to the escalating dissemination of antibiotic resistance genes (ARGs) in the environment. The majority of BA research has focused on the effect of monospecies on the plant disease control process, the role of the compound BA with nutrition elements in the phyllosphere disease, and the resistome is still unknown. We believe BAs are eco-friendly alternatives for antibiotics to combat the transfer of ARGs. Our results revealed that BA-Mg[2+] had a lower relative abundance of ARGs compared to the CK group, and the phyllosphere pathogen Pseudomonas syringae was negatively related to three specific ARGs, cphA3, PME-1, and tcr3. These three genes also present different Ka/Ks. We believe that the identification of the distribution and evolution modes of ARGs further elucidates the ecological role and facilitates the development of BAs, which will attract general interest in this field.}, } @article {pmid38505556, year = {2024}, author = {Chakraborty, N}, title = {Metabolites: a converging node of host and microbe to explain meta-organism.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1337368}, pmid = {38505556}, issn = {1664-302X}, abstract = {Meta-organisms encompassing the host and resident microbiota play a significant role in combatting diseases and responding to stress. Hence, there is growing traction to build a knowledge base about this ecosystem, particularly to characterize the bidirectional relationship between the host and microbiota. In this context, metabolomics has emerged as the major converging node of this entire ecosystem. Systematic comprehension of this resourceful omics component can elucidate the organism-specific response trajectory and the communication grid across the ecosystem embodying meta-organisms. Translating this knowledge into designing nutraceuticals and next-generation therapy are ongoing. Its major hindrance is a significant knowledge gap about the underlying mechanisms maintaining a delicate balance within this ecosystem. To bridge this knowledge gap, a holistic picture of the available information has been presented with a primary focus on the microbiota-metabolite relationship dynamics. The central theme of this article is the gut-brain axis and the participating microbial metabolites that impact cerebral functions.}, } @article {pmid38505550, year = {2024}, author = {Yang, S and Zhang, W and Yang, B and Feng, X and Li, Y and Li, X and Liu, Q}, title = {Metagenomic evidence for antibiotic-associated actinomycetes in the Karamay Gobi region.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1330880}, pmid = {38505550}, issn = {1664-302X}, abstract = {Due to the misuse of antibiotics, there is an increasing emergence and spread of multidrug-resistant (MDR) bacteria, leading to a human health crisis. To address clinical antibiotic resistance and prevent/control pathogenic microorganisms, the development of novel antibiotics is essential. This also offers a new approach to discovering valuable actinobacterial flora capable of producing natural bioactive products. In this study, we employed bioinformatics and macro-genome sequencing to collect 15 soil samples from three different locations in the Karamay Gobi region. First, we assessed the diversity of microorganisms in soil samples from different locations, analyzing the content of bacteria, archaea, actinomycetes, and fungi. The biodiversity of soil samples from outside the Gobi was found to be higher than that of soil samples from within and in the center of the Gobi. Second, through microbial interaction network analysis, we identified actinomycetes as the dominant group in the system. We have identified the top four antibiotic genes, such as Ecol_fabG_TRC, Efac_liaR_DAP, tetA (58), and macB, by CARD. These genes are associated with peptide antibiotics, disinfecting agents and antiseptics, tetracycline antibiotics, and macrolide antibiotics. In addition, we also obtained 40 other antibiotic-related genes through CARD alignment. Through in-depth analysis of desert soil samples, we identified several unstudied microbial species belonging to different families, including Erythrobacteriaceae, Solirubrobacterales, Thermoleophilaceae, Gaiellaceae, Nocardioidaceae, Actinomycetia, Egibacteraceae, and Acidimicrobiales. These species have the capability to produce peptide antibiotics, macrolide antibiotics, and tetracycline antibiotics, as well as disinfectants and preservatives. This study provides valuable theoretical support for future in-depth research.}, } @article {pmid38504332, year = {2024}, author = {Wu, E and Mallawaarachchi, V and Zhao, J and Yang, Y and Liu, H and Wang, X and Shen, C and Lin, Y and Qiao, L}, title = {Contigs directed gene annotation (ConDiGA) for accurate protein sequence database construction in metaproteomics.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {58}, pmid = {38504332}, issn = {2049-2618}, support = {22022401//National Natural Science Foundation of China/ ; M-0614//Chinesisch-Deutsche Zentrum für Wissenschaftsförderung/ ; 2020YFF0304502//Ministry of Science and Technology of the People's Republic of China/ ; }, abstract = {BACKGROUND: Microbiota are closely associated with human health and disease. Metaproteomics can provide a direct means to identify microbial proteins in microbiota for compositional and functional characterization. However, in-depth and accurate metaproteomics is still limited due to the extreme complexity and high diversity of microbiota samples. It is generally recommended to use metagenomic data from the same samples to construct the protein sequence database for metaproteomic data analysis. Although different metagenomics-based database construction strategies have been developed, an optimization of gene taxonomic annotation has not been reported, which, however, is extremely important for accurate metaproteomic analysis.

RESULTS: Herein, we proposed an accurate taxonomic annotation pipeline for genes from metagenomic data, namely contigs directed gene annotation (ConDiGA), and used the method to build a protein sequence database for metaproteomic analysis. We compared our pipeline (ConDiGA or MD3) with two other popular annotation pipelines (MD1 and MD2). In MD1, genes were directly annotated against the whole bacterial genome database; in MD2, contigs were annotated against the whole bacterial genome database and the taxonomic information of contigs was assigned to the genes; in MD3, the most confident species from the contigs annotation results were taken as reference to annotate genes. Annotation tools, including BLAST, Kaiju, and Kraken2, were compared. Based on a synthetic microbial community of 12 species, it was found that Kaiju with the MD3 pipeline outperformed the others in the construction of protein sequence database from metagenomic data. Similar performance was also observed with a fecal sample, as well as in silico mixed datasets of the simulated microbial community and the fecal sample.

CONCLUSIONS: Overall, we developed an optimized pipeline for gene taxonomic annotation to construct protein sequence databases. Our study can tackle the current taxonomic annotation reliability problem in metagenomics-derived protein sequence database and can promote the in-depth metaproteomic analysis of microbiome. The unique metagenomic and metaproteomic datasets of the 12 bacterial species are publicly available as a standard benchmarking sample for evaluating various analysis pipelines. The code of ConDiGA is open access at GitHub for the analysis of microbiota samples. Video Abstract.}, } @article {pmid38503977, year = {2024}, author = {Chang, HW and Lee, EM and Wang, Y and Zhou, C and Pruss, KM and Henrissat, S and Chen, RY and Kao, C and Hibberd, MC and Lynn, HM and Webber, DM and Crane, M and Cheng, J and Rodionov, DA and Arzamasov, AA and Castillo, JJ and Couture, G and Chen, Y and Balcazo, NP and Lebrilla, CB and Terrapon, N and Henrissat, B and Ilkayeva, O and Muehlbauer, MJ and Newgard, CB and Mostafa, I and Das, S and Mahfuz, M and Osterman, AL and Barratt, MJ and Ahmed, T and Gordon, JI}, title = {Prevotella copri and microbiota members mediate the beneficial effects of a therapeutic food for malnutrition.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {38503977}, issn = {2058-5276}, support = {T32 HG000045/HG/NHGRI NIH HHS/United States ; F30 DK131866/DK/NIDDK NIH HHS/United States ; F30 DK123838/DK/NIDDK NIH HHS/United States ; }, abstract = {Microbiota-directed complementary food (MDCF) formulations have been designed to repair the gut communities of malnourished children. A randomized controlled trial demonstrated that one formulation, MDCF-2, improved weight gain in malnourished Bangladeshi children compared to a more calorically dense standard nutritional intervention. Metagenome-assembled genomes from study participants revealed a correlation between ponderal growth and expression of MDCF-2 glycan utilization pathways by Prevotella copri strains. To test this correlation, here we use gnotobiotic mice colonized with defined consortia of age- and ponderal growth-associated gut bacterial strains, with or without P. copri isolates closely matching the metagenome-assembled genomes. Combining gut metagenomics and metatranscriptomics with host single-nucleus RNA sequencing and gut metabolomic analyses, we identify a key role of P. copri in metabolizing MDCF-2 glycans and uncover its interactions with other microbes including Bifidobacterium infantis. P. copri-containing consortia mediated weight gain and modulated energy metabolism within intestinal epithelial cells. Our results reveal structure-function relationships between MDCF-2 and members of the gut microbiota of malnourished children with potential implications for future therapies.}, } @article {pmid38503380, year = {2024}, author = {Madhukar, MK and Singh, N and Iyer, VR and Sowpati, DT and Tallapaka, KB and Mishra, RK and Moharir, SC}, title = {Antimicrobial resistance landscape in a metropolitan city context using open drain wastewater-based metagenomic analysis.}, journal = {Environmental research}, volume = {}, number = {}, pages = {118556}, doi = {10.1016/j.envres.2024.118556}, pmid = {38503380}, issn = {1096-0953}, abstract = {One Health concept recognizes the inextricable interactions of diverse ecosystems and their subsequent effect on human, animal and plant health. Antimicrobial resistance (AMR) is a major One Health concern and is predicted to cause catastrophes if appropriate measures are not implemented. To understand the AMR landscape in a south Indian metropolitan city, metagenomic analysis of open drains was performed. The data suggests that in January 2022, macrolide class of antibiotics contributed the highest resistance of 40.1% in the city, followed by aminoglycoside- 24.4%, tetracycline- 11.3% and lincosamide- 6.7%. The 'mutations in the 23S rRNA gene conferring resistance to macrolide antibiotics' were the major contributor of resistance with a prevalence of 39.7%, followed by '16s rRNA with mutation conferring resistance to aminoglycoside antibiotics'- 22.2%, '16S rRNA with mutation conferring resistance to tetracycline derivatives'- 9.2%, and '23S rRNA with mutation conferring resistance to lincosamide antibiotics'- 6.7%. The most prevalent antimicrobial resistance gene (ARG) 'mutations in the 23S rRNA gene conferring resistance to macrolide antibiotics' was present in multiple pathogens including Escherichia coli, Campylobacter jejuni, Acinetobacter baumannii, Streptococcus pneumoniae, Pseudomonas aeruginosa, Neisseria gonorrhoeae, Klebsiella pneumoniae and Helicobacter pylori. Most of the geographical locations in the city showed a similar landscape for AMR. Considering human mobility and anthropogenic activities, such an AMR landscape could be common across other regions too. The data indicates that pathogens are evolving and acquiring antibiotic resistance genes to evade antibiotics of multiple major drug classes in diverse hosts. The outcomes of the study are relevant not only in understanding the resistance landscape at a broader level but are also important for identifying the resistant drug classes, the mechanisms of gaining resistance and for developing new drugs that target specific pathways. This kind of surveillance protocol can be extended to regions in other developing countries to assess and combat the problem of antimicrobial resistance.}, } @article {pmid38502869, year = {2024}, author = {Nelson, AR and Fegel, TS and Danczak, RE and Caiafa, MV and Roth, HK and Dunn, OI and Turvold, CA and Borch, T and Glassman, SI and Barnes, RT and Rhoades, CC and Wilkins, MJ}, title = {Soil microbiome feedbacks during disturbance-driven forest ecosystem conversion.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae047}, pmid = {38502869}, issn = {1751-7370}, abstract = {Disturbances cause rapid changes to forests, with different disturbance types and severities creating unique ecosystem trajectories that can impact the underlying soil microbiome. Pile burning - the combustion of logging residue on the forest floor - is a common fuel reduction practice that can have impacts on forest soils analogous to those following high severity wildfire. Further, pile burning following clear-cut harvesting can create persistent openings dominated by non-woody plants surrounded by dense regenerating conifer forest. A paired 60-year chronosequence of burn scar openings and surrounding regenerating forest after clear-cut harvesting provides a unique opportunity to assess whether belowground microbial processes mirror aboveground vegetation during disturbance-induced ecosystem shifts. Soil ectomycorrhizal fungal diversity was reduced the first decade after pile burning, which could explain poor tree seedling establishment and subsequent persistence of herbaceous species within the openings. Fine-scale changes in the soil microbiome mirrored aboveground shifts in vegetation, with short-term changes to microbial carbon cycling functions resembling a post-fire microbiome (e.g., enrichment of aromatic degradation genes) and respiration in burn scars decoupled from substrate quantity and quality. Broadly, however, soil microbiome composition and function within burn scar soils converged with that of the surrounding regenerating forest six decades after the disturbances, indicating potential microbial resilience that was disconnected from aboveground vegetation shifts. This work begins to unravel the belowground microbial processes that underlie disturbance-induced ecosystem changes, which are increasing in frequency tied to climate change.}, } @article {pmid38502690, year = {2024}, author = {Rosay, T and Jimenez, AG and Sperandio, V}, title = {Glucuronic acid confers colonization advantage to enteric pathogens.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {13}, pages = {e2400226121}, doi = {10.1073/pnas.2400226121}, pmid = {38502690}, issn = {1091-6490}, support = {AI053067//HHS | NIH | NIAID | Division of Intramural Research (DIR, NIAID)/ ; AI154597//HHS | NIH | NIAID | Division of Intramural Research (DIR, NIAID)/ ; AI155398//HHS | NIH | NIAID | Division of Intramural Research (DIR, NIAID)/ ; }, abstract = {Glucuronidation is a detoxification process to eliminate endo- and xeno-biotics and neurotransmitters from the host circulation. Glucuronosyltransferase binds these compounds to glucuronic acid (GlcA), deactivating them and allowing their elimination through the gastrointestinal (GI) tract. However, the microbiota produces β-glucuronidases that release GlcA and reactivate these compounds. Enteric pathogens such as enterohemorrhagic Escherichia coli (EHEC) and Citrobacter rodentium sense and utilize galacturonic acid (GalA), an isomer of GlcA, to outcompete the microbiota promoting gut colonization. However, the role of GlcA in pathogen colonization has not been explored. Here, we show that treatment of mice with a microbial β-glucuronidase inhibitor (GUSi) decreased C. rodentium's colonization of the GI tract, without modulating bacterial virulence or host inflammation. Metagenomic studies indicated that GUSi did not change the composition of the intestinal microbiota in these animals. GlcA confers an advantage for pathogen expansion through its utilization as a carbon source. Congruently mutants unable to catabolize GlcA depict lower GI colonization compared to wild type and are not sensitive to GUSi. Germfree mice colonized with a commensal E. coli deficient for β-glucuronidase production led to a decrease of C. rodentium tissue colonization, compared to animals monocolonized with an E. coli proficient for production of this enzyme. GlcA is not sensed as a signal and doesn't activate virulence expression but is used as a metabolite. Because pathogens can use GlcA to promote their colonization, inhibitors of microbial β-glucuronidases could be a unique therapeutic against enteric infections without disturbing the host or microbiota physiology.}, } @article {pmid38501864, year = {2024}, author = {Xiong, C and K Singh, B and Zhu, Y-G and Hu, H-W and Li, P-P and Han, Y-L and Han, L-L and Zhang, Q-B and Wang, J-T and Liu, S-Y and Wu, C-F and Ge, A-H and Zhang, L-M and He, J-Z}, title = {Microbial species pool-mediated diazotrophic community assembly in crop microbiomes during plant development.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0105523}, doi = {10.1128/msystems.01055-23}, pmid = {38501864}, issn = {2379-5077}, abstract = {Plant-associated diazotrophs strongly relate to plant nitrogen (N) supply and growth. However, our knowledge of diazotrophic community assembly and microbial N metabolism in plant microbiomes is largely limited. Here we examined the assembly and temporal dynamics of diazotrophic communities across multiple compartments (soils, epiphytic and endophytic niches of root and leaf, and grain) of three cereal crops (maize, wheat, and barley) and identified the potential N-cycling pathways in phylloplane microbiomes. Our results demonstrated that the microbial species pool, influenced by site-specific environmental factors (e.g., edaphic factors), had a stronger effect than host selection (i.e., plant species and developmental stage) in shaping diazotrophic communities across the soil-plant continuum. Crop diazotrophic communities were dominated by a few taxa (~0.7% of diazotrophic phylotypes) which were mainly affiliated with Methylobacterium, Azospirillum, Bradyrhizobium, and Rhizobium. Furthermore, eight dominant taxa belonging to Azospirillum and Methylobacterium were identified as keystone diazotrophic taxa for three crops and were potentially associated with microbial network stability and crop yields. Metagenomic binning recovered 58 metagenome-assembled genomes (MAGs) from the phylloplane, and the majority of them were identified as novel species (37 MAGs) and harbored genes potentially related to multiple N metabolism processes (e.g., nitrate reduction). Notably, for the first time, a high-quality MAG harboring genes involved in the complete denitrification process was recovered in the phylloplane and showed high identity to Pseudomonas mendocina. Overall, these findings significantly expand our understanding of ecological drivers of crop diazotrophs and provide new insights into the potential microbial N metabolism in the phyllosphere.IMPORTANCEPlants harbor diverse nitrogen-fixing microorganisms (i.e., diazotrophic communities) in both belowground and aboveground tissues, which play a vital role in plant nitrogen supply and growth promotion. Understanding the assembly and temporal dynamics of crop diazotrophic communities is a prerequisite for harnessing them to promote plant growth. In this study, we show that the site-specific microbial species pool largely shapes the structure of diazotrophic communities in the leaves and roots of three cereal crops. We further identify keystone diazotrophic taxa in crop microbiomes and characterize potential microbial N metabolism pathways in the phyllosphere, which provides essential information for developing microbiome-based tools in future sustainable agricultural production.}, } @article {pmid38501800, year = {2024}, author = {Munk, P and Yang, D and Röder, T and Maier, L and Petersen, TN and Duarte, ASR and Clausen, PTLC and Brinch, C and Van Gompel, L and Luiken, R and Wagenaar, JA and Schmitt, H and Heederik, DJJ and Mevius, DJ and Smit, LAM and , and Bosser, A and Aarestrup, FM}, title = {The European livestock resistome.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0132823}, doi = {10.1128/msystems.01328-23}, pmid = {38501800}, issn = {2379-5077}, abstract = {Metagenomic sequencing has proven to be a powerful tool in the monitoring of antimicrobial resistance (AMR). Here, we provide a comparative analysis of the resistome from pigs, poultry, veal calves, turkey, and rainbow trout, for a total of 538 herds across nine European countries. We calculated the effects of per-farm management practices and antimicrobial usage (AMU) on the resistome in pigs, broilers, and veal calves. We also provide an in-depth study of the associations between bacterial diversity, resistome diversity, and AMR abundances as well as co-occurrence analysis of bacterial taxa and antimicrobial resistance genes (ARGs) and the universality of the latter. The resistomes of veal calves and pigs clustered together, as did those of avian origin, while the rainbow trout resistome was different. Moreover, we identified clear core resistomes for each specific food-producing animal species. We identified positive associations between bacterial alpha diversity and both resistome alpha diversity and abundance. Network analyses revealed very few taxa-ARG associations in pigs but a large number for the avian species. Using updated reference databases and optimized bioinformatics, previously reported significant associations between AMU, biosecurity, and AMR in pig and poultry farms were validated. AMU is an important driver for AMR; however, our integrated analyses suggest that factors contributing to increased bacterial diversity might also be associated with higher AMR load. We also found that dispersal limitations of ARGs are shaping livestock resistomes, and future efforts to fight AMR should continue to emphasize biosecurity measures.IMPORTANCEUnderstanding the occurrence, diversity, and drivers for antimicrobial resistance (AMR) is important to focus future control efforts. So far, almost all attempts to limit AMR in livestock have addressed antimicrobial consumption. We here performed an integrated analysis of the resistomes of five important farmed animal populations across Europe finding that the resistome and AMR levels are also shaped by factors related to bacterial diversity, as well as dispersal limitations. Thus, future studies and interventions aimed at reducing AMR should not only address antimicrobial usage but also consider other epidemiological and ecological factors.}, } @article {pmid38501431, year = {2024}, author = {Lamoth, F and Kontoyiannis, DP}, title = {PCR diagnostic platforms for non-Aspergillus mold infections: ready for routine implementation in the clinic?.}, journal = {Expert review of molecular diagnostics}, volume = {}, number = {}, pages = {1-10}, doi = {10.1080/14737159.2024.2326474}, pmid = {38501431}, issn = {1744-8352}, abstract = {INTRODUCTION: While Aspergillus spp. remain the predominant cause of invasive mold infections, non-Aspergillus molds, such as the Mucorales or Fusarium spp., account for an increasing proportion of cases. The diagnosis of non-Aspergillus invasive mold infections (NAIMI) is challenging because of the low sensitivity and delay of conventional microbiological tests. Therefore, there is a particular interest to develop molecular tools for their early detection in blood or other clinical samples.

AREAS COVERED: This extensive review of the literature discusses the performance of Mucorales-specific PCR and other genus-specific or broad-range fungal PCR that can be used for the diagnosis of NAIMI in diverse clinical samples, with a focus on novel technologies.

EXPERT OPINION: PCR currently represents the most promising approach, combining good sensitivity/specificity and ability to detect NAIMI in clinical samples before diagnosis by conventional cultures and histopathology. Several PCR assays have been designed for the detection of Mucorales in particular, but also Fusarium spp. or Scedosporium/Lomentospora spp. Some commercial Mucorales PCRs are now available. While efforts are still needed for standardized protocols and the development of more rapid and simpler techniques, PCR is on the way to becoming an essential test for the early diagnosis of mucormycosis and possibly other NAIMIs.}, } @article {pmid38501246, year = {2024}, author = {Palombo, R and Barneschi, L and Pedraza-González, L and Yang, X and Olivucci, M}, title = {Picosecond quantum-classical dynamics reveals that the coexistence of light-induced microbial and animal chromophore rotary motion modulates the isomerization quantum yield of heliorhodopsin.}, journal = {Physical chemistry chemical physics : PCCP}, volume = {}, number = {}, pages = {}, doi = {10.1039/d4cp00193a}, pmid = {38501246}, issn = {1463-9084}, abstract = {Rhodopsins are light-responsive proteins forming two vast and evolutionary distinct superfamilies whose functions are invariably triggered by the photoisomerization of a single retinal chromophore. In 2018 a third widespread superfamily of rhodopsins called heliorhodopsins was discovered using functional metagenomics. Heliorhodopsins, with their markedly different structural features with respect to the animal and microbial superfamilies, offer an opportunity to study how evolution has manipulated the chromophore photoisomerization to achieve adaptation. One question is related to the mechanism of such a reaction and how it differs from that of animal and microbial rhodopsins. To address this question, we use hundreds of quantum-classical trajectories to simulate the spectroscopically documented picosecond light-induced dynamics of a heliorhodopsin from the archaea thermoplasmatales archaeon (TaHeR). We show that, consistently with the observations, the trajectories reveal two excited state decay channels. However, inconsistently with previous hypotheses, only one channel is associated with the -C13(?)C14- rotation of microbial rhodopsins while the second channel is characterized by the -C11(?)C12- rotation typical of animal rhodopsins. The fact that such -C11(?)C12- rotation is aborted upon decay and ground state relaxation, explains why illumination of TaHeR only produces the 13-cis isomer with a low quantum efficiency. We argue that the documented lack of regioselectivity in double-bond excited state twisting motion is the result of an "adaptation" that could be completely lost via specific residue substitutions modulating the steric hindrance experienced along the isomerization motion.}, } @article {pmid38500954, year = {2024}, author = {Yang, QF and Shu, CM and Ji, QY}, title = {Diagnosis of pulmonary hemorrhagic leptospirosis complicated by invasive pulmonary aspergillosis complemented by metagenomic next-generation sequencing: a case report.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1365096}, pmid = {38500954}, issn = {2296-858X}, abstract = {BACKGROUND: Leptospirosis is a bacterial zoonosis with variable clinical manifestations. Pulmonary diffuse hemorrhagic leptospirosis often occurs rapidly and, when not promptly diagnosed and treated, it can be life-threatening. Aspergillus flavus is an opportunistic fungus that is commonly seen in immunosuppressed patients. Invasive pulmonary aspergillosis also progresses rapidly. This case study describes a patient with severe pneumonia caused by pulmonary hemorrhagic leptospirosis combined with invasive pulmonary aspergillosis. We have found almost no clinical reports to date on these two diseases occurring in the same patient.

CASE PRESENTATION: A 73-year-old male arrived at our hospital complaining of fever, general malaise, and hemoptysis that had lasted 4 days. The patient was initially diagnosed with severe pneumonia in the emergency department, but he did not respond well to empiric antibiotics. Subsequently, the patient's condition worsened and was transferred to the ICU ward after emergency tracheal intubation and invasive ventilator. In the ICU, antibacterial drugs were adjusted to treat bacteria and fungi extensively. Although the inflammatory indices decreased, the patient still had recurrent fever, and a series of etiological tests were negative. Finally, metagenomic next-generation sequencing (mNGS) of bronchial alveolar lavage fluid detected Leptospira interrogans and Aspergillus flavus. After targeted treatment with penicillin G and voriconazole, the patient's condition improved rapidly, and he was eventually transferred out of the ICU and recovered.

CONCLUSION: Early recognition and diagnosis of leptospirosis is difficult, especially when a patient is co-infected with other pathogens. The use of mNGS to detect pathogens in bronchial alveolar lavage fluid is conducive to early diagnosis and treatment of the disease, and may significantly improve the prognosis in severe cases.}, } @article {pmid38500705, year = {2024}, author = {Ospino, MC and Engel, K and Ruiz-Navas, S and Binns, WJ and Doxey, AC and Neufeld, JD}, title = {Evaluation of multiple displacement amplification for metagenomic analysis of low biomass samples.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae024}, pmid = {38500705}, issn = {2730-6151}, abstract = {Combining multiple displacement amplification (MDA) with metagenomics enables the analysis of samples with extremely low DNA concentrations, making them suitable for high-throughput sequencing. Although amplification bias and nonspecific amplification have been reported from MDA-amplified samples, the impact of MDA on metagenomic datasets is not well understood. We compared three MDA methods (i.e. bulk MDA, emulsion MDA, and primase MDA) for metagenomic analysis of two DNA template concentrations (approx. 1 and 100 pg) derived from a microbial community standard "mock community" and two low biomass environmental samples (i.e. borehole fluid and groundwater). We assessed the impact of MDA on metagenome-based community composition, assembly quality, functional profiles, and binning. We found amplification bias against high GC content genomes but relatively low nonspecific amplification such as chimeras, artifacts, or contamination for all MDA methods. We observed MDA-associated representational bias for microbial community profiles, especially for low-input DNA and with the primase MDA method. Nevertheless, similar taxa were represented in MDA-amplified libraries to those of unamplified samples. The MDA libraries were highly fragmented, but similar functional profiles to the unamplified libraries were obtained for bulk MDA and emulsion MDA at higher DNA input and across these MDA libraries for the groundwater sample. Medium to low-quality bins were possible for the high input bulk MDA metagenomes for the most simple microbial communities, borehole fluid, and mock community. Although MDA-based amplification should be avoided, it can still reveal meaningful taxonomic and functional information from samples with extremely low DNA concentration where direct metagenomics is otherwise impossible.}, } @article {pmid38500700, year = {2024}, author = {Li, S and Mosier, D and Kouris, A and Humez, P and Mayer, B and Strous, M and Diao, M}, title = {High diversity, abundance, and expression of hydrogenases in groundwater.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae023}, pmid = {38500700}, issn = {2730-6151}, abstract = {Hydrogen may be the most important electron donor available in the subsurface. Here we analyse the diversity, abundance and expression of hydrogenases in 5 proteomes, 25 metagenomes, and 265 amplicon datasets of groundwaters with diverse geochemistry. A total of 1545 new [NiFe]-hydrogenase gene sequences were recovered, which considerably increased the number of sequences (1999) in a widely used database. [NiFe]-hydrogenases were highly abundant, as abundant as the DNA-directed RNA polymerase. The abundance of hydrogenase genes increased with depth from 0 to 129 m. Hydrogenases were present in 481 out of 1245 metagenome-assembled genomes. The relative abundance of microbes with hydrogenases accounted for ~50% of the entire community. Hydrogenases were actively expressed, making up as much as 5.9% of methanogen proteomes. Most of the newly discovered diversity of hydrogenases was in "Group 3b", which has been associated with sulfur metabolism. "Group 3d", facilitating the interconversion of electrons between hydrogen and NAD, was the most abundant and mainly observed in methanotrophs and chemoautotrophs. "Group 3a", associated with methanogenesis, was the most abundant in proteomes. Two newly discovered groups of [NiFe]-hydrogenases, observed in Methanobacteriaceae and Anaerolineaceae, further expanded diversity. Our results highlight the vast diversity, abundance and expression of hydrogenases in groundwaters, suggesting a high potential for hydrogen oxidation in subsurface habitats.}, } @article {pmid38500637, year = {2024}, author = {Li, K and Han, D and Alhaskawi, A and Liu, T and Wang, X and Yang, W and Lu, H and Fang, X}, title = {Sepsis and Hepatapostema Secondary to Chromobacterium Violaceum Infection on Lower Limb Skin: A Case Report.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {1003-1010}, pmid = {38500637}, issn = {1178-6973}, abstract = {BACKGROUND: Chromobacterium violaceum (C. violaceum) is a Gram-negative bacterium capable of causing severe infections in both humans and specific animals. Despite its infrequency, C. violaceum infections exhibit a notably high mortality rate. The timely and precise detection of this pathogen stands as a critical factor in achieving effective diagnosis and treatment. Traditional diagnostic approaches possess limitations, particularly in terms of their time-consuming nature and the range of pathogens they can identify. Metagenomic next-generation sequencing (mNGS) testing has emerged as a highly promising diagnostic tool for infectious diseases.

METHODS: Within this case report, we present a patient who developed a C. violaceum infection subsequent to a lower limb infection, leading to the progression of sepsis, a liver abscess, septic shock, multi-organ dysfunction, and altered mental status. Samples of the patient's blood and tissue from the lower limb skin are collected, and the infection is swiftly diagnosed through mNGS, allowing for the immediate initiation of suitable treatment.

RESULTS: The mNGS results revealed the patient's infection with C. violaceum. Subsequent conventional bacterial culture results were concordant with the mNGS findings. Following comprehensive management measures, including prompt and effective anti-infective treatment, the patient achieved cure and was successfully discharged.

CONCLUSION: This case underscores the significance of employing advanced diagnostic methodologies like mNGS for the early detection of uncommon pathogens such as C. violaceum. The expedited diagnosis and timely intervention hold the potential to substantially enhance patient outcomes in cases of severe infections instigated by this bacterium.}, } @article {pmid38500586, year = {2024}, author = {Xiao, H and Wei, Y and Sun, X and Song, X and Liu, J and Bai, Z and Hu, G and Qin, L}, title = {Metagenomics study of soil microorganisms involved in the carbon cycle in a saline-alkaline meadow steppe in the Songnen Plain in Northeast China.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1335488}, pmid = {38500586}, issn = {1664-302X}, abstract = {Soil microorganisms play an important role in regulating and contributing to carbon cycling processes in grassland ecosystems. Soil salinization is one of the major problems causing soil degradation, and its effects on carbon cycle immobilization-related functional genes in soil microorganisms remain unknown. Therefore, we took Songnen salinization grassland as the research object, selected grasslands with different salinization levels, and explored the diversity of soil microorganisms and functional genes related to carbon cycling in Songnen grassland with different salinization levels through metagenomic technology. The results showed that with the increase of salinity, the relative abundance of Ascomycetes increased, while the relative abundance of Proteus and Firmicutes decreased. In addition, the relative abundance of functional genes related to carbon cycling fixation has also decreased. As the degree of soil salinization increases, the relative abundance of glycoside hydrolases (GH)130 family significantly increases, while the relative abundance of soil carbohydrate enzymes belonging to GH3 and GH55 families significantly decreases. Using structural equation modeling (SEM), it was found that soil pH and conductivity (EC) have a significant impact on soil microbial diversity and functional genes related to carbon cycling fixation. The increase in soil pH directly reduces the Shannon diversity of soil microbial diversity and functional genes related to carbon cycling fixation. Therefore, it can be concluded that the intensification of grassland salinization reduces the diversity of bacteria and fungi, and affects the diversity of functional genes related to carbon cycling fixation by reducing the total diversity of bacteria. The increase in salinity has a negative feedback effect on grassland soil carbon cycling. This study provides a theoretical framework for grassland soil carbon sequestration and degradation restoration.}, } @article {pmid38500507, year = {2024}, author = {Tan, J and Wu, L and Zhan, L and Sheng, M and Tang, Z and Xu, J and Ma, H}, title = {Optimal selection of specimens for metagenomic next-generation sequencing in diagnosing periprosthetic joint infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1356804}, pmid = {38500507}, issn = {2235-2988}, abstract = {OBJECTIVE: This study aimed to assess the diagnostic value of metagenomic next-generation sequencing (mNGS) across synovial fluid, prosthetic sonicate fluid, and periprosthetic tissues among patients with periprosthetic joint infection (PJI), intending to optimize specimen selection for mNGS in these patients.

METHODS: This prospective study involved 61 patients undergoing revision arthroplasty between September 2021 and September 2022 at the First Affiliated Hospital of Zhengzhou University. Among them, 43 cases were diagnosed as PJI, and 18 as aseptic loosening (AL) based on the American Musculoskeletal Infection Society (MSIS) criteria. Preoperative or intraoperative synovial fluid, periprosthetic tissues, and prosthetic sonicate fluid were collected, each divided into two portions for mNGS and culture. Comparative analyses were conducted between the microbiological results and diagnostic efficacy derived from mNGS and culture tests. Furthermore, the variability in mNGS diagnostic efficacy for PJI across different specimen types was assessed.

RESULTS: The sensitivity and specificity of mNGS diagnosis was 93% and 94.4% for all types of PJI specimens; the sensitivity and specificity of culture diagnosis was 72.1% and 100%, respectively. The diagnostic sensitivity of mNGS was significantly higher than that of culture (X[2] = 6.541, P=0.011), with no statistically significant difference in specificity (X[2] = 1.029, P=0.310). The sensitivity of the synovial fluid was 83.7% and the specificity was 94.4%; the sensitivity of the prosthetic sonicate fluid was 90.7% and the specificity was 94.4%; and the sensitivity of the periprosthetic tissue was 81.4% and the specificity was 100%. Notably, the mNGS of prosthetic sonicate fluid displayed a superior pathogen detection rate compared to other specimen types.

CONCLUSION: mNGS can function as a precise diagnostic tool for identifying pathogens in PJI patients using three types of specimens. Due to its superior ability in pathogen identification, prosthetic sonicate fluid can replace synovial fluid and periprosthetic tissue as the optimal sample choice for mNGS.}, } @article {pmid38500502, year = {2024}, author = {Chen, GJ and Chen, XB and Rao, WY and Pan, XY and Li, SY and Su, ZQ}, title = {Airway necrosis and granulation tissue formation caused by Rhizopus oryzae leading to severe upper airway obstruction: a case report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1366472}, pmid = {38500502}, issn = {2235-2988}, abstract = {Pulmonary Mucormycosis is a fatal infectious disease with high mortality rate. The occurrence of Mucormycosis is commonly related to the fungal virulence and the host's immunological defenses against pathogens. Mucormycosis infection and granulation tissue formation occurred in the upper airway was rarely reported. This patient was a 60-year-old male with diabetes mellitus, who was admitted to hospital due to progressive cough, sputum and dyspnea. High-resolution computed tomography (HRCT) and bronchoscopy revealed extensive tracheal mucosal necrosis, granulation tissue proliferation, and severe airway stenosis. The mucosal necrotic tissue was induced by the infection of Rhizopus Oryzae, confirmed by metagenomic next-generation sequencing (mNGS) in tissue biopsy. This patient was treated with the placement of a covered stent and local instillation of amphotericin B via bronchoscope. The tracheal mucosal necrosis was markedly alleviated, the symptoms of cough, shortness of breath, as well as exercise tolerance were significantly improved. The placement of airway stent and transbronchial microtube drip of amphotericin B could conduce to rapidly relieve the severe airway obstruction due to Mucormycosis infection.}, } @article {pmid38500448, year = {2024}, author = {Fan, L and Guan, G and Zhao, J and Li, D and Yu, X and Shentu, X}, title = {Comparative analysis of the diversity of symbionts in fat body of long- and short-winged brown planthoppers.}, journal = {Archives of insect biochemistry and physiology}, volume = {115}, number = {3}, pages = {e22096}, doi = {10.1002/arch.22096}, pmid = {38500448}, issn = {1520-6327}, support = {U21A20223//National Natural Science Foundation of China/ ; 2022C02047//Zhejiang Provincial Programs for Science and Technology Development/ ; 2023SNJF034//"San Nong Jiu Fang" project/ ; }, abstract = {The microbial community structure plays an important role in the internal environment of brown planthopper (BPH), Nilaparvata lugens (Hemiptera: Delphacidae), which is an indispensable part to reflect the internal environment of BPH. Wing dimorphism is a strategy for balancing flight and reproduction of insects. Here, quantitative fluorescence PCR was used to analyse the number and changes of the symbionts in the fat body of long- and short-winged BPHs at different developmental stages. A metagenomic library was constructed based on the 16 S rRNA sequence and internal transcribed spacer sequence for high-throughput sequencing, to analyze the community structure and population number of the symbionts of long- and short-winged BPHs, and to make functional prediction. This study enriches the connotation of BPH symbionts, and laid a theoretical foundation for the subsequent study of BPH-symbionts interaction and the function of symbionts in the host.}, } @article {pmid38500090, year = {2024}, author = {Wu, X and Qin, N and Yi, F and Wang, J and Yan, X and Wang, L}, title = {Cerebral malaria presenting as nonconvulsive status epilepticus: a case report.}, journal = {Malaria journal}, volume = {23}, number = {1}, pages = {84}, pmid = {38500090}, issn = {1475-2875}, abstract = {BACKGROUND: Malaria is an infectious malady caused by Plasmodium parasites, cerebral malaria standing out as one of its most severe complications. Clinical manifestation include elevated body temperature, loss of consciousness, and seizures. However, reports of cerebral malaria presenting as nonconvulsive status epilepticus are extremely rare. The case presented involves psychiatric symptoms, with the electroencephalogram indicated nonconvulsive status epilepticus associated with cerebral malaria.

CASE PRESENTATION: A 53-year-old male, was urgently admitted, due to confusion and abnormal behaviour for 10 h. The patient returned to China after developing a fever while working in Tanzania two months ago. The blood smear revealed Plasmodium vivax and Plasmodium falciparum, and he was diagnosed with malaria. He recovered following anti-malarial treatment. After admission, the patient was confused, unable to communicate normally, and unwilling to cooperate with the physical examination. Plasmodium was not found in the blood smear, but the DNA sequence of P. falciparum was discovered using metagenomic next-generation sequencing of cerebrospinal fluid. Brain MRI revealed no significant abnormalities. Continuous electroencephalogram monitoring revealed that the patient had non-convulsive status epilepticus, which was treated with diazepam and levetiracetam. The patient had normal consciousness and behaviour. He received anti-malarial treatment for two weeks and fully recovered.

CONCLUSIONS: This case demonstrates that nonconvulsive status epilepticus can be a manifestation of cerebral malaria. It is imperative for attending physicians to heighten vigilance when encountering patients with a history of travel to malaria-endemic regions or a prior malaria infection, especially in the presence of unusual clinical presentations.}, } @article {pmid38500025, year = {2024}, author = {Nose, S and Shiroma, H and Yamada, T and Uno, Y}, title = {QNetDiff: a quantitative measurement of network rewiring.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {118}, pmid = {38500025}, issn = {1471-2105}, support = {JP17K00017//JSPS KAKENHI/ ; }, abstract = {Bacteria in the human body, particularly in the large intestine, are known to be associated with various diseases. To identify disease-associated bacteria (markers), a typical method is to statistically compare the relative abundance of bacteria between healthy subjects and diseased patients. However, since bacteria do not necessarily cause diseases in isolation, it is also important to focus on the interactions and relationships among bacteria when examining their association with diseases. In fact, although there are common approaches to represent and analyze bacterial interaction relationships as networks, there are limited methods to find bacteria associated with diseases through network-driven analysis. In this paper, we focus on rewiring of the bacterial network and propose a new method for quantifying the rewiring. We then apply the proposed method to a group of colorectal cancer patients. We show that it can identify and detect bacteria that cannot be detected by conventional methods such as abundance comparison. Furthermore, the proposed method is implemented as a general-purpose tool and made available to the general public.}, } @article {pmid38499445, year = {2024}, author = {Russ, L and Andreo Jimenez, B and Nijhuis, E and Postma, J}, title = {Rhizoctonia solani disease suppression: addition of keratin-rich soil amendment leads to functional shifts in soil microbial communities.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiae024}, pmid = {38499445}, issn = {1574-6941}, abstract = {Promoting soil suppressiveness against soil borne pathogens could be a promising strategy to manage crop diseases. One way to increase the suppression potential in agricultural soils is via the addition of organic amendments. This microbe-mediated phenomenon, although not fully understood, prompted our study to explore the microbial taxa and functional properties associated with Rhizoctonia solani disease suppression in sugar beet seedlings after amending soil with a keratin-rich waste stream. Soil samples were analyzed using shotgun metagenomics sequencing. Results showed that both amended soils were enriched in bacterial families found in disease suppressive soils before, indicating that the amendment of keratin-rich material can support the transformation into a suppressive soil. On a functional level, genes encoding keratinolytic enzymes were found to be abundant in the keratin-amended samples. Proteins enriched in amended soils were those potentially involved in the production of secondary metabolites/antibiotics, motility, keratin-degradation, and contractile secretion system proteins. We hypothesize these taxa contribute to the amendment-induced suppression effect due to their genomic potential to produce antibiotics, secrete effectors via the contractile secretion system, and degrade oxalate -a potential virulence factor of R. solani- while simultaneously possessing the ability to metabolize keratin.}, } @article {pmid38499102, year = {2024}, author = {Gao, Y and Tariq, A and Zeng, F and Sardans, J and Graciano, C and Li, X and Wang, W and Peñuelas, J}, title = {Soil microbial functional profiles of P-cycling reveal drought-induced constraints on P-transformation in a hyper-arid desert ecosystem.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {171767}, doi = {10.1016/j.scitotenv.2024.171767}, pmid = {38499102}, issn = {1879-1026}, abstract = {Soil water conditions are known to influence soil nutrient availability, but the specific impact of different conditions on soil phosphorus (P) availability through the modulation of P-cycling functional microbial communities in hyper-arid desert ecosystems remains largely unexplored. To address this knowledge gap, we conducted a 3-year pot experiment using a typical desert plant species (Alhagi sparsifolia Shap.) subjected to two water supply levels (25 %-35 % and 65 %-75 % of maximum field capacity, MFC) and four P-supply levels (0, 1, 3, and 5 g P m[-2] y[-1]). Our investigation focused on the soil Hedley-P pool and the four major microbial groups involved in the critical phases of soil microbial P-cycling. The results revealed that the drought (25 %-35 % MFC) and no P-supply treatments reduced soil resin-P and NaHCO3-Pi concentrations by 87.03 % and 93.22 %, respectively, compared to the well-watered (65 %-75 % MFC) and high P-supply (5 g P m[-2] y[-1]) treatments. However, the P-supply treatment resulted in a 12 %-22 % decrease in the soil NH4[+]-N concentration preferred by microbes compared to the no P-supply treatment. Moreover, the abundance of genes engaged in microbial P-cycling (e.g. gcd and phoD) increased under the drought and no P-supply treatments (p < 0.05), suggesting that increased NH4[+]-N accumulation under these conditions may stimulate P-solubilizing microbes, thereby promoting the microbial community's investment in resources to enhance the P-cycling potential. Furthermore, the communities of Steroidobacter cummioxidans, Mesorhizobium alhagi, Devosia geojensis, and Ensifer sojae, associated with the major P-cycling genes, were enriched in drought and no or low-P soils. Overall, the drought and no or low-P treatments stimulated microbial communities and gene abundances involved in P-cycling. However, this increase was insufficient to maintain soil P-bioavailability. These findings shed light on the responses and feedback of microbial-mediated P-cycling behaviors in desert ecosystems under three-year drought and soil P-deficiency.}, } @article {pmid38417271, year = {2024}, author = {Pudelko, L and Cabianca, DS}, title = {The influencers' era: how the environment shapes chromatin in 3D.}, journal = {Current opinion in genetics & development}, volume = {85}, number = {}, pages = {102173}, doi = {10.1016/j.gde.2024.102173}, pmid = {38417271}, issn = {1879-0380}, mesh = {*Chromatin/genetics ; *Epigenome ; Metagenomics ; }, abstract = {Environment-epigenome interactions are emerging as contributors to disease risk and health outcomes. In fact, organisms outside of the laboratory are constantly exposed to environmental changes that can influence chromatin regulation at multiple levels, potentially impacting on genome function. In this review, we will summarize recent findings on how major external cues impact on 3D chromatin organization in different experimental systems. We will describe environment-induced 3D genome alterations ranging from chromatin accessibility to the spatial distribution of the genome and discuss their role in regulating gene expression.}, } @article {pmid38498215, year = {2024}, author = {Sarkar, J and Mondal, M and Bhattacharya, S and Dutta, S and Chatterjee, S and Mondal, N and N, S and Peketi, A and Mazumdar, A and Ghosh, W}, title = {Extremely oligotrophic and complex-carbon-degrading microaerobic bacteria from Arabian Sea oxygen minimum zone sediments.}, journal = {Archives of microbiology}, volume = {206}, number = {4}, pages = {179}, pmid = {38498215}, issn = {1432-072X}, support = {Ad hoc Fellowship//Council of Scientific and Industrial Research, India/ ; Ad hoc Fellowship//Department of Biotechnology, Ministry of Science and Technology, India/ ; Intramural Faculty Grants//Bose Institute/ ; GAP2303//Ministry of Earth Sciences/ ; MoES/36/00IS/Extra/19/2013//Earth System Sciences Organization, Ministry of Earth Sciences/ ; }, abstract = {Sediments underlying marine hypoxic zones are huge sinks of unreacted complex organic matter, where despite acute O2 limitation, obligately aerobic bacteria thrive, and steady depletion of organic carbon takes place within a few meters below the seafloor. However, little knowledge exists about the sustenance and complex carbon degradation potentials of aerobic chemoorganotrophs in these sulfidic ecosystems. We isolated and characterized a number of aerobic bacterial chemoorganoheterotrophs from across a ~ 3 m sediment horizon underlying the perennial hypoxic zone of the eastern Arabian Sea. High levels of sequence correspondence between the isolates' genomes and the habitat's metagenomes and metatranscriptomes illustrated that the strains were widespread and active across the sediment cores explored. The isolates catabolized several complex organic compounds of marine and terrestrial origins in the presence of high or low, but not zero, O2. Some of them could also grow anaerobically on yeast extract or acetate by reducing nitrate and/or nitrite. Fermentation did not support growth, but enabled all the strains to maintain a fraction of their cell populations over prolonged anoxia. Under extreme oligotrophy, limited growth followed by protracted stationary phase was observed for all the isolates at low cell density, amid high or low, but not zero, O2 concentration. While population control and maintenance could be particularly useful for the strains' survival in the critically carbon-depleted layers below the explored sediment depths (core-bottom organic carbon: 0.5-1.0% w/w), metagenomic data suggested that in situ anoxia could be surmounted via potential supplies of cryptic O2 from previously reported sources such as Nitrosopumilus species.}, } @article {pmid38497819, year = {2024}, author = {Sekeresova Kralova, J and Donic, C and Dassa, B and Livyatan, I and Jansen, PM and Ben-Dor, S and Fidel, L and Trzebanski, S and Narunsky-Haziza, L and Asraf, O and Brenner, O and Dafni, H and Jona, G and Boura-Halfon, S and Stettner, N and Segal, E and Brunke, S and Pilpel, Y and Straussman, R and Zeevi, D and Bacher, P and Hube, B and Shlezinger, N and Jung, S}, title = {Competitive fungal commensalism mitigates candidiasis pathology.}, journal = {The Journal of experimental medicine}, volume = {221}, number = {5}, pages = {}, doi = {10.1084/jem.20231686}, pmid = {38497819}, issn = {1540-9538}, support = {696/21//Israeli Science Foundation/ ; //Weizmann Institute/ ; //Morris Kahn Institute for Human Immunology/ ; //Henry H. Drake Professorial Chair of Immunology/ ; 390713860//Deutsche Forschungsgemeinschaft/ ; }, abstract = {The mycobiota are a critical part of the gut microbiome, but host-fungal interactions and specific functional contributions of commensal fungi to host fitness remain incompletely understood. Here, we report the identification of a new fungal commensal, Kazachstania heterogenica var. weizmannii, isolated from murine intestines. K. weizmannii exposure prevented Candida albicans colonization and significantly reduced the commensal C. albicans burden in colonized animals. Following immunosuppression of C. albicans colonized mice, competitive fungal commensalism thereby mitigated fatal candidiasis. Metagenome analysis revealed K. heterogenica or K. weizmannii presence among human commensals. Our results reveal competitive fungal commensalism within the intestinal microbiota, independent of bacteria and immune responses, that could bear potential therapeutic value for the management of C. albicans-mediated diseases.}, } @article {pmid38497641, year = {2024}, author = {Dean, CJ and Peña-Mosca, F and Ray, T and Wehri, TJ and Sharpe, K and Antunes, AM and Doster, E and Fernandes, L and Calles, VF and Bauman, C and Godden, S and Heins, B and Pinedo, P and Machado, VS and Caixeta, LS and Noyes, NR}, title = {Exploring associations between the teat apex metagenome and Staphylococcus aureus intramammary infections in primiparous cows under organic directives.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0223423}, doi = {10.1128/aem.02234-23}, pmid = {38497641}, issn = {1098-5336}, abstract = {UNLABELLED: The primary objective of this study was to identify associations between the prepartum teat apex microbiome and the presence of Staphylococcus aureus intramammary infections (IMI) in primiparous cows during the first 5 weeks after calving. We performed a case-control study using shotgun metagenomics of the teat apex and culture-based milk data collected longitudinally from 710 primiparous cows on five organic dairy farms. Cases had higher odds of having S. aureus metagenomic DNA on the teat apex prior to parturition compared to controls (OR = 38.9, 95% CI: 14.84-102.21). Differential abundance analysis confirmed this association, with cases having a 23.8 higher log fold change (LFC) in the abundance of S. aureus in their samples compared to controls. Of the most prevalent microorganisms in controls, those associated with a lower risk of post-calving S. aureus IMI included Microbacterium phage Min 1 (OR = 0.37, 95% CI: 0.25-0.53), Corynebacterium efficiens (OR = 0.53, 95% CI: 0.30-0.94), Kocuria polaris (OR = 0.54, 95% CI: 0.35-0.82), Micrococcus terreus (OR = 0.64, 95% CI: 0.44-0.93), and Dietzia alimentaria (OR = 0.45, 95% CI: 0.26-0.75). Genes encoding for Microcin B17 AMPs were the most prevalent on the teat apex of cases and controls (99.7% in both groups). The predicted abundance of genes encoding for Microcin B17 was also higher in cases compared to controls (LFC 0.26).

IMPORTANCE: Intramammary infections (IMI) caused by Staphylococcus aureus remain an important problem for the dairy industry. The microbiome on the external skin of the teat apex may play a role in mitigating S. aureus IMI risk, in particular the production of antimicrobial peptides (AMPs) by commensal microbes. However, current studies of the teat apex microbiome utilize a 16S approach, which precludes the detection of genomic features such as genes that encode for AMPs. Therefore, further research using a shotgun metagenomic approach is needed to understand what role prepartum teat apex microbiome dynamics play in IMI risk.}, } @article {pmid38497626, year = {2024}, author = {Mulay, SA and Hahn, CR and Klingeman, DM and Elshahed, MS and Youssef, NH and Podar, M}, title = {Metagenomic sequencing of a Patescibacteria-containing enrichment from Zodletone spring in Oklahoma, USA.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0011424}, doi = {10.1128/mra.00114-24}, pmid = {38497626}, issn = {2576-098X}, abstract = {An enrichment of sulfidic sediments from Zodletone spring was sequenced as a metagenome. Draft genomes representing Cloacimonadota, Deltabacterota, Firmicutes, and Patescibacteria were binned and annotated and will aid functional genomics and cultivation efforts.}, } @article {pmid38497257, year = {2024}, author = {Maritan, E and Quagliariello, A and Frago, E and Patarnello, T and Martino, ME}, title = {The role of animal hosts in shaping gut microbiome variation.}, journal = {Philosophical transactions of the Royal Society of London. Series B, Biological sciences}, volume = {379}, number = {1901}, pages = {20230071}, doi = {10.1098/rstb.2023.0071}, pmid = {38497257}, issn = {1471-2970}, abstract = {Millions of years of co-evolution between animals and their associated microbial communities have shaped and diversified the nature of their relationship. Studies continue to reveal new layers of complexity in host-microbe interactions, the fate of which depends on a variety of different factors, ranging from neutral processes and environmental factors to local dynamics. Research is increasingly integrating ecosystem-based approaches, metagenomics and mathematical modelling to disentangle the individual contribution of ecological factors to microbiome evolution. Within this framework, host factors are known to be among the dominant drivers of microbiome composition in different animal species. However, the extent to which they shape microbiome assembly and evolution remains unclear. In this review, we summarize our understanding of how host factors drive microbial communities and how these dynamics are conserved and vary across taxa. We conclude by outlining key avenues for research and highlight the need for implementation of and key modifications to existing theory to fully capture the dynamics of host-associated microbiomes. This article is part of the theme issue 'Sculpting the microbiome: how host factors determine and respond to microbial colonization'.}, } @article {pmid38496006, year = {2024}, author = {Hong, J and Fu, T and Liu, W and Du, Y and Bu, J and Wei, G and Yu, M and Lin, Y and Min, C and Lin, D}, title = {An Update on the Role and Potential Molecules in Relation to Ruminococcus gnavus in Inflammatory Bowel Disease, Obesity and Diabetes Mellitus.}, journal = {Diabetes, metabolic syndrome and obesity : targets and therapy}, volume = {17}, number = {}, pages = {1235-1248}, pmid = {38496006}, issn = {1178-7007}, abstract = {Ruminococcus gnavus (R. gnavus) is a gram-positive anaerobe commonly resides in the human gut microbiota. The advent of metagenomics has linked R. gnavus with various diseases, including inflammatory bowel disease (IBD), obesity, and diabetes mellitus (DM), which has become a growing area of investigation. The initial focus of research primarily centered on assessing the abundance of R. gnavus and its potential association with disease presentation, taking into account variations in sample size, sequencing and analysis methods. However, recent investigations have shifted towards elucidating the underlying mechanistic pathways through which R. gnavus may contribute to disease manifestation. In this comprehensive review, we aim to provide an updated synthesis of the current literature on R. gnavus in the context of IBD, obesity, and DM. We critically analyze relevant studies and summarize the potential molecular mediators implicated in the association between R. gnavus and these diseases. Across numerous studies, various molecules such as methylation-controlled J (MCJ), glucopolysaccharides, ursodeoxycholic acid (UDCA), interleukin(IL)-10, IL-17, and capric acid have been proposed as potential contributors to the link between R. gnavus and IBD. Similarly, in the realm of obesity, molecules such as hydrogen peroxide, butyrate, and UDCA have been suggested as potential mediators, while glycine ursodeoxycholic acid (GUDCA) has been implicated in the connection between R. gnavus and DM. Furthermore, it is imperative to emphasize the necessity for additional studies to evaluate the potential efficacy of targeting pathways associated with R. gnavus as a viable strategy for managing these diseases. These findings have significantly expanded our understanding of the functional role of R. gnavus in the context of IBD, obesity, and DM. This review aims to offer updated insights into the role and potential mechanisms of R. gnavus, as well as potential strategies for the treatment of these diseases.}, } @article {pmid38495624, year = {2024}, author = {Yang, Z and Shi, Z and Fang, K and Ren, D}, title = {Atypical Rickettsia japonica Infection Involving Critical Illness Diagnosed by Metagenomic Next-Generation Sequencing: A Case Report.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {963-967}, pmid = {38495624}, issn = {1178-6973}, abstract = {BACKGROUND: Rickettsia japonica infection is a rare disease, it is rare to report critical and severe case caused by this disease in Zhejiang Province, China.

PATIENT CONCERNS: We report a patient who initially sought medical attention due to fever and developed coma and convulsions during treatment. The patient did not develop typical eschar and rash. Eventually, the patient needed to be treated in the intensive care unit due to acute respiratory failure.

DIAGNOSES: The patient was diagnosed with Rickettsia japonica bloodstream infection by metagenomic next-generation sequencing (mNGS).

OUTCOMES: Due to the critical illness, the patient was transferred to the intensive care unit, received doxycycline and other treatments, and rapidly recovered and discharged.

CONCLUSION: The patient developed a critical illness after being infected with Rickettsia, when the medical history is unclear and clinical symptoms and signs are atypical, it is necessary to use mNGS examination for diagnosis.}, } @article {pmid38495515, year = {2024}, author = {Buytaers, FE and Verhaegen, B and Van Nieuwenhuysen, T and Roosens, NHC and Vanneste, K and Marchal, K and De Keersmaecker, SCJ}, title = {Strain-level characterization of foodborne pathogens without culture enrichment for outbreak investigation using shotgun metagenomics facilitated with nanopore adaptive sampling.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1330814}, pmid = {38495515}, issn = {1664-302X}, abstract = {INTRODUCTION: Shotgun metagenomics has previously proven effective in the investigation of foodborne outbreaks by providing rapid and comprehensive insights into the microbial contaminant. However, culture enrichment of the sample has remained a prerequisite, despite the potential impact on pathogen detection resulting from the growth competition. To circumvent the need for culture enrichment, we explored the use of adaptive sampling using various databases for a targeted nanopore sequencing, compared to shotgun metagenomics alone.

METHODS: The adaptive sampling method was first tested on DNA of mashed potatoes mixed with DNA of a Staphylococcus aureus strain previously associated with a foodborne outbreak. The selective sequencing was used to either deplete the potato sequencing reads or enrich for the pathogen sequencing reads, and compared to a shotgun sequencing. Then, living S. aureus were spiked at 10[5] CFU into 25 g of mashed potatoes. Three DNA extraction kits were tested, in combination with enrichment using adaptive sampling, following whole genome amplification. After data analysis, the possibility to characterize the contaminant with the different sequencing and extraction methods, without culture enrichment, was assessed.

RESULTS: Overall, the adaptive sampling outperformed the shotgun sequencing. While the use of a host removal DNA extraction kit and targeted sequencing using a database of foodborne pathogens allowed rapid detection of the pathogen, the most complete characterization was achieved when using solely a database of S. aureus combined with a conventional DNA extraction kit, enabling accurate placement of the strain on a phylogenetic tree alongside outbreak cases.

DISCUSSION: This method shows great potential for strain-level analysis of foodborne outbreaks without the need for culture enrichment, thereby enabling faster investigations and facilitating precise pathogen characterization. The integration of adaptive sampling with metagenomics presents a valuable strategy for more efficient and targeted analysis of microbial communities in foodborne outbreaks, contributing to improved food safety and public health.}, } @article {pmid38495510, year = {2024}, author = {Yang, L and Guo, Y and Yang, H and Li, S and Zhang, Y and Gao, C and Wei, T and Hao, L}, title = {Distinct microbiota assembly and functional patterns in disease-resistant and susceptible varieties of tobacco.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1361883}, pmid = {38495510}, issn = {1664-302X}, abstract = {The plant microbiota is believed to be an accessory genome that extends plant functions, forming holobionts together with the host plant. Plant disease resistance, therefore, is inextricably linked with plant microbiota, which play important roles in plant growth and health. To explore the relationship between plant microbiota and disease resistance, we investigated the tobacco microbiome of two varieties with contrasting disease-resistance levels to bacterial wilt and black shank diseases. Comparative microbiome analysis indicated that the resistant variety assembled a distinct microbiota with higher network complexity and diversity. While Pseudomonas and Ensifer, which contain biocontrol and beneficial members, were enriched in the rhizosphere of the resistant variety, Ralstonia, a genus including the known causative pathogen, was enriched in the susceptible variety. Metagenome sequencing revealed that biocontrol functions, such as hydrogen cyanide synthase, pyochelin biosynthesis, and arthrofactin-type cyclic lipopeptide synthetase, were more abundant in the resistant variety. Further analysis indicated that contigs encoding the corresponding genes were mostly assigned to Pseudomonas. Among all the metagenome-assembled genomes, positive selection was suggested in the genome assigned to Pseudomonas only in the rhizosphere of the resistant variety. The search of biosynthetic gene clusters in the Pseudomonas genome revealed a non-ribosomal peptide synthetase, the compound of which was brabantamide A, with known antimicrobial activity. Collectively, our study suggests that the plant microbiota might be involved in microbe-mediated disease resistance. Particularly, our results highlight Pseudomonas in the rhizosphere of the disease-resistant variety as a promising biocontrol candidate. Our study may facilitate further screening of bacterial isolates and the targeted design of microbial communities.}, } @article {pmid38495448, year = {2024}, author = {Hosokawa, M and Nishikawa, Y}, title = {Tools for microbial single-cell genomics for obtaining uncultured microbial genomes.}, journal = {Biophysical reviews}, volume = {16}, number = {1}, pages = {69-77}, pmid = {38495448}, issn = {1867-2450}, abstract = {The advent of next-generation sequencing technologies has facilitated the acquisition of large amounts of DNA sequence data at a relatively low cost, leading to numerous breakthroughs in decoding microbial genomes. Among the various genome sequencing activities, metagenomic analysis, which entails the direct analysis of uncultured microbial DNA, has had a profound impact on microbiome research and has emerged as an indispensable technology in this field. Despite its valuable contributions, metagenomic analysis is a "bulk analysis" technique that analyzes samples containing a wide diversity of microbes, such as bacteria, yielding information that is averaged across the entire microbial population. In order to gain a deeper understanding of the heterogeneous nature of the microbial world, there is a growing need for single-cell analysis, similar to its use in human cell biology. With this paradigm shift in mind, comprehensive single-cell genomics technology has become a much-anticipated innovation that is now poised to revolutionize microbiome research. It has the potential to enable the discovery of differences at the strain level and to facilitate a more comprehensive examination of microbial ecosystems. In this review, we summarize the current state-of-the-art in microbial single-cell genomics, highlighting the potential impact of this technology on our understanding of the microbial world. The successful implementation of this technology is expected to have a profound impact in the field, leading to new discoveries and insights into the diversity and evolution of microbes.}, } @article {pmid38495366, year = {2024}, author = {Jayasinghe, H and Chang, HX and Knobloch, S and Yang, SH and Hendalage, DPB and Ariyawansa, KGSU and Liu, PY and Stadler, M and Ariyawansa, HA}, title = {Metagenomic insight to apprehend the fungal communities associated with leaf blight of Welsh onion in Taiwan.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1352997}, pmid = {38495366}, issn = {1664-462X}, abstract = {Plants are associated with a large diversity of microbes, and these complex plant-associated microbial communities are critical for plant health. Welsh onion (Allium fistulosum L.) is one of the key and oldest vegetable crops cultivated in Taiwan. The leaf of the Welsh onion is one of the famous spices in Taiwanese cuisine, thus, it is crucial to control foliar diseases. In recent years, Welsh onion cultivation in Taiwan has been severely threatened by the occurrence of leaf blight disease, greatly affecting their yield and quality. However, the overall picture of microbiota associated with the Welsh onion plant is still not clear as most of the recent etiological investigations were heavily based on the isolation of microorganisms from diseased plants. Therefore, studying the diversity of fungal communities associated with the leaf blight symptoms of Welsh onion may provide information regarding key taxa possibly involved in the disease. Therefore, this investigation was mainly designed to understand the major fungal communities associated with leaf blight to identify key taxa potentially involved in the disease and further evaluate any shifts in both phyllosphere and rhizosphere mycobiome assembly due to foliar pathogen infection by amplicon sequencing targeting the Internal Transcribed Spacer (ITS) 1 region of the rRNA. The alpha and beta-diversity analyses were used to compare the fungal communities and significant fungal groups were recognized based on linear discriminant analyses. Based on the results of relative abundance data and co-occurrence networks in symptomatic plants we revealed that the leaf blight of Welsh onion in Sanxing, is a disease complex mainly involving Stemphylium and Colletotrichum taxa. In addition, genera such as Aspergillus, Athelia and Colletotrichum were abundantly found associated with the symptomatic rhizosphere. Alpha-diversity in some fields indicated a significant increase in species richness in the symptomatic phyllosphere compared to the asymptomatic phyllosphere. These results will broaden our knowledge of pathogens of Welsh onion associated with leaf blight symptoms and will assist in developing effective disease management strategies to control the progress of the disease.}, } @article {pmid38494442, year = {2024}, author = {Hogg, BN and Schnepel, C and Finnigan, JD and Charnock, SJ and Hayes, MA and Turner, NJ}, title = {The Impact of Metagenomics on Biocatalysis.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {}, number = {}, pages = {e202402316}, doi = {10.1002/anie.202402316}, pmid = {38494442}, issn = {1521-3773}, abstract = {In the ever-growing demand for sustainable ways to produce high-value small molecules, biocatalysis has come to the forefront of greener routes to these chemicals. As such, the need to constantly find and optimise suitable biocatalysts for specific transformations has never been greater. Metagenome mining has been shown to rapidly expand the toolkit of promiscuous enzymes needed for new transformations, without requiring protein engineering steps. If protein engineering is needed, the metagenomic candidate can often provide a better starting point for engineering than a previously discovered enzyme on the open database or from literature, for instance. In this review, we highlight where metagenomics has made substantial impact on the area of biocatalysis in recent years. We review the discovery of enzymes in previously unexplored or 'hidden' sequence space, leading to the characterisation of enzymes with enhanced properties that originate from natural selection pressures in native environments.}, } @article {pmid38494258, year = {2024}, author = {Vaish, S and Soni, SK and Singh, B and Garg, N and Zareen Ahmad, I and Manoharan, M and Trivedi, AK}, title = {Meta-analysis of biodynamic (BD) preparations reveal the bacterial population involved in improving soil health, crop yield and quality.}, journal = {Journal, genetic engineering & biotechnology}, volume = {22}, number = {1}, pages = {100345}, doi = {10.1016/j.jgeb.2023.100345}, pmid = {38494258}, issn = {2090-5920}, abstract = {BACKGROUND: Bacterial community found in biodynamic preparations (BD500-BD507) can help improve soil health, plant development, yield, and quality. The current work describes a metagenomic investigation of these preparations to identify the bacterial communities along with the functional diversity present within them.

RESULTS: Metagenome sequencing was performed using the Illumina MiSeq platform, which employs next-generation sequencing (NGS) technology, to provide an understanding of the bacterial communities and their functional diversity in BD preparations. NGS data of BD preparations revealed that maximum operational taxonomic units (OTUs) of the phylum Proteobacteria were present in BD506 (23429) followed by BD505 (22712) and BD501 (21591), respectively. Moreover, unclassified phylum (16657) and genus (16657) were also highest in BD506. Maximum alpha diversity was reported in BD501 (1095 OTU) and minimum in BD507 (257 OTU). Further, the OTUs for five major metabolic functional groups viz carbohydrate metabolism, xenobiotic degradation, membrane transport functions, energy metabolism, and enzyme activities were abundant in BD506 and BD501.

CONCLUSION: The bacterial communities in BD506 and BD501 are found to be unique and rare; they belong to functional categories that are involved in enzyme activity, membrane transport, xenobiotic degradation, and carbohydrate metabolism. These preparations might therefore be thought to be more effective. The investigation also found a highly varied population of bacteria, which could explain why BD preparations work well in the field. In view of this, the BD preparations may be utilized for unexploited bacterial communities for sustainable agriculture production.}, } @article {pmid38493845, year = {2024}, author = {Sun, J and Zhang, X and Gong, X and Sun, Y and Zhang, S and Wang, F}, title = {Metagenomic analysis reveals gene taxonomic and functional diversity response to microplastics and cadmium in an agricultural soil.}, journal = {Environmental research}, volume = {}, number = {}, pages = {118673}, doi = {10.1016/j.envres.2024.118673}, pmid = {38493845}, issn = {1096-0953}, abstract = {Both microplastics (MPs) and heavy metals are common soil pollutants and can interact to generate combined toxicity to soil ecosystems, but their impact on soil microbial communities (e.g., archaea and viruses) remains poorly studied. Here, metagenomic analysis was used to explore the response of soil microbiome in an agricultural soil exposed to MPs [i.e., polyethylene (PE), polystyrene (PS), and polylactic acid (PLA)] and/or Cd. Results showed that MPs had more profound effects on microbial community composition, diversity, and gene abundances when compared to Cd or their combination. Metagenomic analysis indicated that the gene taxonomic diversity and functional diversity of microbial communities varied with MPs type and dose. MPs affected the relative abundance of major microbial phyla and genera, while their coexistence with Cd influenced dominant fungi and viruses. Nitrogen-transforming and pathogenic genera, which were more sensitive to MPs variations, could serve as the indicative taxa for MPs contamination. High-dose PLA treatments (10%, w/w) not only elevated nitrogen metabolism and pathogenic genes, but also enriched copiotrophic microbes from the Proteobacteria phylum. Overall, MPs and Cd showed minimal interactions on soil microbial communities. This study highlights the microbial shifts due to co-occurring MPs and Cd, providing evidence for understanding their environmental risks.}, } @article {pmid38493518, year = {2024}, author = {Suárez, E and Tobajas, M and Mohedano, AF and de la Rubia, MA}, title = {Biowaste management by hydrothermal carbonization and anaerobic co-digestion: Synergistic effects and comparative metagenomic analysis.}, journal = {Waste management (New York, N.Y.)}, volume = {180}, number = {}, pages = {1-8}, doi = {10.1016/j.wasman.2024.03.019}, pmid = {38493518}, issn = {1879-2456}, abstract = {The feasibility of anaerobic co-digestion in semicontinuous mode of two major urban biowaste, food waste (FW) and garden and park waste (GPW) (75 % FW and 25 % GPW) as well as the co-digestion of FW with the process water originated from the hydrothermal carbonization of GPW (95 % FW and 5 % process water), both on a COD basis, has been assessed. The effect of varying organic loading rate (OLR) from 1.5 to 3.5 g COD/L·d on methane yield, gross energy recovery, and microbiome population was evaluated. For comparison, anaerobic digestion of FW was also conducted to determine the best strategy for sustainable biowaste management. This study showed an optimal OLR of 2.5 g COD/L·d. Acetic and propionic acid content increased as OLR raised for each condition studied, while methane yield decreased at the highest OLR tested indicating overloading of the system. The anaerobic co-digestion of FW and process water showed a 10 % increase on methane production compared to anaerobic digestion of FW (324 vs. 294 mL CH4 STP/L·d). Moreover, it enhances the process due to a greater abundance and diversity of hydrolytic and acidogenic bacteria belonging to Bacterioidota, Firmicutes, and Chloroflexi phyla, as well as promotes the hydrogenotrophic pathway under higher propionic concentrations which is not usually favoured for methane production. The integration of hydrothermal carbonization of GPW with the anaerobic co-digestion of 95 % FW and 5 % of process water results in the highest potential energy recovery and could be a good strategy for sustainable management of urban biowaste.}, } @article {pmid38493232, year = {2024}, author = {Moreno-Pino, M and Manrique-de-la-Cuba, MF and López-Rodríguez, M and Parada-Pozo, G and Rodríguez-Marconi, S and Ribeiro, CG and Flores-Herrera, P and Guajardo, M and Trefault, N}, title = {Unveiling microbial guilds and symbiotic relationships in Antarctic sponge microbiomes.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6371}, pmid = {38493232}, issn = {2045-2322}, support = {3210656//ANID FONDECYT Postdoctoral Grant/ ; 21211164//ANID Doctoral Fellowships/ ; 21192150//ANID Doctoral Fellowships/ ; 21190286//ANID Doctoral Fellowships/ ; DG_02-22//INACH Grants/ ; DG_15-20//INACH Grants/ ; DG_12-20//INACH Grants/ ; RT_34-17//INACH Grants/ ; 1230758//ANID FONDECYT Grant/ ; }, abstract = {Marine sponges host diverse microbial communities. Although we know many of its ecological patterns, a deeper understanding of the polar sponge holobiont is still needed. We combine high-throughput sequencing of ribosomal genes, including the largest taxonomic repertoire of Antarctic sponge species analyzed to date, functional metagenomics, and metagenome-assembled genomes (MAGs). Our findings show that sponges harbor more exclusive bacterial and archaeal communities than seawater, while microbial eukaryotes are mostly shared. Furthermore, bacteria in Antarctic sponge holobionts establish more cooperative interactions than in sponge holobionts from other environments. The bacterial classes that established more positive relations were Bacteroidia, Gamma- and Alphaproteobacteria. Antarctic sponge microbiomes contain microbial guilds that encompass ammonia-oxidizing archaea, ammonia-oxidizing bacteria, nitrite-oxidizing bacteria, and sulfur-oxidizing bacteria. The retrieved MAGs showed a high level of novelty and streamlining signals and belong to the most abundant members of the main microbial guilds in the Antarctic sponge holobiont. Moreover, the genomes of these symbiotic bacteria contain highly abundant functions related to their adaptation to the cold environment, vitamin production, and symbiotic lifestyle, helping the holobiont survive in this extreme environment.}, } @article {pmid38493135, year = {2024}, author = {Lin, GL and Drysdale, SB and Snape, MD and O'Connor, D and Brown, A and MacIntyre-Cockett, G and Mellado-Gomez, E and de Cesare, M and Ansari, MA and Bonsall, D and Bray, JE and Jolley, KA and Bowden, R and Aerssens, J and Bont, L and Openshaw, PJM and Martinon-Torres, F and Nair, H and Golubchik, T and Pollard, AJ and , }, title = {Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2379}, pmid = {38493135}, issn = {2041-1723}, support = {116019//Innovative Medicines Initiative (IMI)/ ; 116019//Innovative Medicines Initiative (IMI)/ ; 116019//Innovative Medicines Initiative (IMI)/ ; 116019//Innovative Medicines Initiative (IMI)/ ; 116019//Innovative Medicines Initiative (IMI)/ ; 116019//Innovative Medicines Initiative (IMI)/ ; 116019//Innovative Medicines Initiative (IMI)/ ; 116019//Innovative Medicines Initiative (IMI)/ ; 116019//Innovative Medicines Initiative (IMI)/ ; 116019//Innovative Medicines Initiative (IMI)/ ; 220171/Z/20/Z//Royal Society/ ; 220171/Z/20/Z//Wellcome Trust (Wellcome)/ ; 218205/Z/19/Z//Wellcome Trust (Wellcome)/ ; 218205/Z/19/Z//Wellcome Trust (Wellcome)/ ; }, abstract = {Respiratory syncytial virus (RSV) is the leading cause of hospitalisation for respiratory infection in young children. RSV disease severity is known to be age-dependent and highest in young infants, but other correlates of severity, particularly the presence of additional respiratory pathogens, are less well understood. In this study, nasopharyngeal swabs were collected from two cohorts of RSV-positive infants <12 months in Spain, the UK, and the Netherlands during 2017-20. We show, using targeted metagenomic sequencing of >100 pathogens, including all common respiratory viruses and bacteria, from samples collected from 433 infants, that burden of additional viruses is common (111/433, 26%) but only modestly correlates with RSV disease severity. In contrast, there is strong evidence in both cohorts and across age groups that presence of Haemophilus bacteria (194/433, 45%) is associated with higher severity, including much higher rates of hospitalisation (odds ratio 4.25, 95% CI 2.03-9.31). There is no evidence for association between higher severity and other detected bacteria, and no difference in severity between RSV genotypes. Our findings reveal the genomic diversity of additional pathogens during RSV infection in infants, and provide an evidence base for future causal investigations of the impact of co-infection on RSV disease severity.}, } @article {pmid38492594, year = {2024}, author = {Lienhart, PH and Rohra, V and Clement, C and Toppen, LC and DeCola, AC and Rizzo, DM and Scarborough, MJ}, title = {Landfill intermediate cover soil microbiomes and their potential for mitigating greenhouse gas emissions revealed through metagenomics.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {171697}, doi = {10.1016/j.scitotenv.2024.171697}, pmid = {38492594}, issn = {1879-1026}, abstract = {Landfills are a major source of anthropogenic methane emissions and have been found to produce nitrous oxide, an even more potent greenhouse gas than methane. Intermediate cover soil (ICS) plays a key role in reducing methane emissions but may also result in nitrous oxide production. To assess the potential for microbial methane oxidation and nitrous oxide production, long sequencing reads were generated from ICS microbiome DNA and reads were functionally annotated for 24 samples across ICS at a large landfill in New York. Further, incubation experiments were performed to assess methane consumption and nitrous oxide production with varying amounts of ammonia supplemented. Methane was readily consumed by microbes in the composite ICS and all incubations with methane produced small amounts of nitrous oxide even when ammonia was not supplemented. Incubations without methane produced significantly less nitrous oxide than those incubated with methane. In incubations with methane added, the observed specific rate of methane consumption was 0.776 +/- 0.055 μg CH4 g dry weight (DW) soil[-1] h[-][1] and the specific rate of nitrous oxide production was 3.64 × 10[-5] +/- 1.30 × 10[-5] μg N2O g DW soil[-1] h[-][1]. The methanotrophs Methylobacter and an unclassified genus within the family Methlyococcaceae were present in the original ICS samples and the incubation samples, and their abundance increased during incubations with methane. Genes encoding particulate methane monooxygenase/ ammonia monooxygenase (pMMO) were much more abundant than genes encoding soluble methane monooxygenase (sMMO) across the landfill ICS. Genes encoding proteins that convert hydroxylamine to nitrous oxide were not highly abundant in the ICS or incubation metagenomes. In total, these results suggest that although ammonia oxidation via methanotrophs may result in low levels of nitrous oxide production, ICS microbial communities have the potential to greatly reduce the overall global warming potential of landfill emissions.}, } @article {pmid38492564, year = {2024}, author = {Şapcı, AOB and Rachtman, E and Mirarab, S}, title = {CONSULT-II: Accurate taxonomic identification and profiling using locality-sensitive hashing.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btae150}, pmid = {38492564}, issn = {1367-4811}, abstract = {MOTIVATION: Taxonomic classification of short reads and taxonomic profiling of metagenomic samples are well-studied yet challenging problems. The presence of species belonging to ranks without close representation in a reference dataset is particularly challenging. While k-mer-based methods have performed well in terms of running time and accuracy, they tend to have reduced accuracy for such novel species. Thus, there is a growing need for methods that combine the scalability of k-merswith increased sensitivity.

RESULTS: Here, we show that using locality-sensitive hashing (LSH) can increase the sensitivity of the k-mer-based search. Our method, which combines LSH with several heuristics techniques including soft LCA labeling and voting is, more accurate than alternatives in both taxonomic classification of individual reads and abundance profiling.

CONSULT-II is implemented in C ++, and the software, together with reference libraries, is publicly available on GitHub https://github.com/bo1929/CONSULT-II.

CONTACT: Siavash Mirarab. E-mail: smirarab@ucsd.edu. Address: UC San Diego, 9500 Gilman Drive, La Jolla, CA, USA 92093-0407.

SUPPLEMENTARY INFORMATION: Supplementary information is available at Bioinformatics online.}, } @article {pmid38492480, year = {2024}, author = {Keenum, I and Calarco, J and Majeed, H and Hager-Soto, EE and Bott, C and Garner, E and Harwood, VJ and Pruden, A}, title = {To what extent do water reuse treatments reduce antibiotic resistance indicators? A comparison of two full-scale systems.}, journal = {Water research}, volume = {254}, number = {}, pages = {121425}, doi = {10.1016/j.watres.2024.121425}, pmid = {38492480}, issn = {1879-2448}, abstract = {Water reuse is an essential strategy for reducing water demand from conventional sources, alleviating water stress, and promoting sustainability, but understanding the effectiveness of associated treatment processes as barriers to the spread of antibiotic resistance is an important consideration to protecting human health. We comprehensively evaluated the reduction of antibiotic resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) in two field-operational water reuse systems with distinct treatment trains, one producing water for indirect potable reuse (ozone/biologically-active carbon/granular activated carbon) and the other for non-potable reuse (denitrification-filtration/chlorination) using metagenomic sequencing and culture. Relative abundances of total ARGs/clinically-relevant ARGs and cultured ARB were reduced by several logs during primary and secondary stages of wastewater treatment, but to a lesser extent during the tertiary water reuse treatments. In particular, ozonation tended to enrich multi-drug ARGs. The effect of chlorination was facility-dependent, increasing the relative abundance of ARGs when following biologically-active carbon filters, but generally providing a benefit in reduced bacterial numbers and ecological and human health resistome risk scores. Relative abundances of total ARGs and resistome risk scores were lowest in aquifer samples, although resistant Escherichia coli and Klebsiella pneumoniae were occasionally detected in the monitoring well 3-days downgradient from injection, but not 6-months downgradient. Resistant E. coli and Pseudomonas aeruginosa were occasionally detected in the nonpotable reuse distribution system, along with increased levels of multidrug, sulfonamide, phenicol, and aminoglycoside ARGs. This study illuminates specific vulnerabilities of water reuse systems to persistence, selection, and growth of ARGs and ARB and emphasizes the role of multiple treatment barriers, including aquifers and distribution systems.}, } @article {pmid38492367, year = {2024}, author = {Wu, Y and Mo, J and Liang, J and Pu, X and Dong, Y and Zhu, X and Zhao, H and Qiu, H and Wu, S and Lu, T}, title = {Multiomic study of the protective mechanism of Persicaria capitata (Buch.-Ham. ex D.Don) H.Gross against streptozotocin-induced diabetic nephropathy in Guizhou miniature pigs.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {128}, number = {}, pages = {155499}, doi = {10.1016/j.phymed.2024.155499}, pmid = {38492367}, issn = {1618-095X}, abstract = {BACKGROUND: Persicaria capitata (Buch.-Ham. ex D.Don) H.Gross (P. capitata, PCB), a traditional drug of the Miao people in China, is potential traditional drug used for the treatment of diabetic nephropathy (DN).

PURPOSE: The purpose of this study is to investigate the function of P. capitata and clarify its protective mechanism against DN.

METHODS: We induced DN in the Guizhou miniature pig with injections of streptozotocin, and P. capitata was added to the pigs' diet to treat DN. In week 16, all the animals were slaughtered, samples were collected, and the relative DN indices were measured. 16S rRNA sequencing, metagenomics, metabolomics, RNA sequencing, and proteomics were used to explore the protective mechanism of P. capitata against DN.

RESULTS: Dietary supplementation with P. capitata significantly reduced the extent of the disease, not only in term of the relative disease indices but also in hematoxylin-eosin-stained tissues. A multiomic analysis showed that two microbes (Clostridium baratii and Escherichia coli), five metabolites (oleic acid, linoleic acid, 4-phenylbutyric acid, 18-β-glycyrrhetinic acid, and ergosterol peroxide), four proteins (ENTPD5, EPHX1, ARVCF and TREH), four important mRNAs (encoding ENTPD5, EPHX1, ARVCF, and TREH), six lncRNAs (TCONS_00024194, TCONS_00085825, TCONS_00006937, TCONS_00070981, TCONS_00074099, and TCONS_00097913), and two circRNAs (novel_circ_0001514 and novel_circ_0017507) are all involved in the protective mechanism of P. capitata against DN.

CONCLUSIONS: Our results provide multidimensional theoretical support for the study and application of P. capitata.}, } @article {pmid38491814, year = {2024}, author = {Malakar, S and Sutaoney, P and Madhyastha, H and Shah, K and Chauhan, NS and Banerjee, P}, title = {Understanding gut microbiome-based machine learning platforms: A review on therapeutic approaches using deep learning.}, journal = {Chemical biology & drug design}, volume = {103}, number = {3}, pages = {e14505}, doi = {10.1111/cbdd.14505}, pmid = {38491814}, issn = {1747-0285}, abstract = {Human beings possess trillions of microbial cells in a symbiotic relationship. This relationship benefits both partners for a long time. The gut microbiota helps in many bodily functions from harvesting energy from digested food to strengthening biochemical barriers of the gut and intestine. But the changes in microbiota composition and bacteria that can enter the gastrointestinal tract can cause infection. Several approaches like culture-independent techniques such as high-throughput and meta-omics projects targeting 16S ribosomal RNA (rRNA) sequencing are popular methods to investigate the composition of the human gastrointestinal tract microbiota and taxonomically characterizing microbial communities. The microbiota conformation and diversity should be provided by whole-genome shotgun metagenomic sequencing of site-specific community DNA associating genome mapping, gene inventory, and metabolic remodelling and reformation, to ease the functional study of human microbiota. Preliminary examination of the therapeutic potency for dysbiosis-associated diseases permits investigation of pharmacokinetic-pharmacodynamic changes in microbial communities for escalation of treatment and dosage plan. Gut microbiome study is an integration of metagenomics which has influenced the field in the last two decades. And the incorporation of artificial intelligence and deep learning through "omics-based" methods and microfluidic evaluation enhanced the capability of identification of thousands of microbes.}, } @article {pmid38491556, year = {2024}, author = {Elradi, M and Ahmed, AI and Saleh, AM and Abdel-Raouf, KMA and Berika, L and Daoud, Y and Amleh, A}, title = {Derivation of a novel antimicrobial peptide from the Red Sea Brine Pools modified to enhance its anticancer activity against U2OS cells.}, journal = {BMC biotechnology}, volume = {24}, number = {1}, pages = {14}, pmid = {38491556}, issn = {1472-6750}, abstract = {Cancer associated drug resistance is a major cause for cancer aggravation, particularly as conventional therapies have presented limited efficiency, low specificity, resulting in long term deleterious side effects. Peptide based drugs have emerged as potential alternative cancer treatment tools due to their selectivity, ease of design and synthesis, safety profile, and low cost of manufacturing. In this study, we utilized the Red Sea metagenomics database, generated during AUC/KAUST Red Sea microbiome project, to derive a viable anticancer peptide (ACP). We generated a set of peptide hits from our library that shared similar composition to ACPs. A peptide with a homeodomain was selected, modified to improve its anticancer properties, verified to maintain high anticancer properties, and processed for further in-silico prediction of structure and function. The peptide's anticancer properties were then assessed in vitro on osteosarcoma U2OS cells, through cytotoxicity assay (MTT assay), scratch-wound healing assay, apoptosis/necrosis detection assay (Annexin/PI assay), RNA expression analysis of Caspase 3, KI67 and Survivin, and protein expression of PARP1. L929 mouse fibroblasts were also assessed for cytotoxicity treatment. In addition, the antimicrobial activity of the peptide was also examined on E coli and S. aureus, as sample representative species of the human bacterial microbiome, by examining viability, disk diffusion, morphological assessment, and hemolytic analysis. We observed a dose dependent cytotoxic response from peptide treatment of U2OS, with a higher tolerance in L929s. Wound closure was debilitated in cells exposed to the peptide, while annexin fluorescent imaging suggested peptide treatment caused apoptosis as a major mode of cell death. Caspase 3 gene expression was not altered, while KI67 and Survivin were both downregulated in peptide treated cells. Additionally, PARP-1 protein analysis showed a decrease in expression with peptide exposure. The peptide exhibited minimal antimicrobial activity on critical human microbiome species E. coli and S. aureus, with a low inhibition rate, maintenance of structural morphology and minimal hemolytic impact. These findings suggest our novel peptide displayed preliminary ACP properties against U2OS cells, through limited specificity, while triggering apoptosis as a primary mode of cell death and while having minimal impact on the microbiological species E. coli and S. aureus.}, } @article {pmid38491508, year = {2024}, author = {Maestre-Carballa, L and Navarro-López, V and Martinez-Garcia, M}, title = {City-scale monitoring of antibiotic resistance genes by digital PCR and metagenomics.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {16}, pmid = {38491508}, issn = {2524-6372}, abstract = {BACKGROUND: Anthropogenic activities significantly contribute to the dissemination of antibiotic resistance genes (ARGs), posing a substantial threat to humankind. The development of methods that allow robust ARG surveillance is a long-standing challenge. Here, we use city-scale monitoring of ARGs by using two of the most promising cutting-edge technologies, digital PCR (dPCR) and metagenomics.

METHODS: ARG hot-spots were sampled from the urban water and wastewater distribution systems. Metagenomics was used to provide a broad view of ARG relative abundance and richness in the prokaryotic and viral fractions. From the city-core ARGs in all samples, the worldwide dispersed sul2 and tetW conferring resistance to sulfonamide and tetracycline, respectively, were monitored by dPCR and metagenomics.

RESULTS: The largest relative overall ARG abundance and richness were detected in the hospital wastewater and the WWTP inlet (up to ≈6,000 ARGs/Gb metagenome) with a large fraction of unclassified resistant bacteria. The abundance of ARGs in DNA and RNA contigs classified as viruses was notably lower, demonstrating a reduction of up to three orders of magnitude compared to contigs associated to prokaryotes. By metagenomics and dPCR, a similar abundance tendency of sul2 and tetW was obtained, with higher abundances in hospital wastewater and WWTP input (≈125-225 ARGs/Gb metagenome). dPCR absolute abundances were between 6,000 and 18,600 copies per ng of sewage DNA (≈10[5-7] copies/mL) and 6.8 copies/mL in seawater near the WWTP discharging point.

CONCLUSIONS: dPCR was more sensitive and accurate, while metagenomics provided broader coverage of ARG detection. While desirable, a reliable correlation of dPCR absolute abundance units into metagenomic relative abundance units was not obtained here (r[2] < 0.4) suggesting methodological factors that introduce variability. Evolutionary pressure does not significantly select the targeted ARGs in natural aquatic environments.}, } @article {pmid38491422, year = {2024}, author = {Martínez-Álvaro, M and Mattock, J and González-Recio, Ó and Saborío-Montero, A and Weng, Z and Lima, J and Duthie, CA and Dewhurst, R and Cleveland, MA and Watson, M and Roehe, R}, title = {Including microbiome information in a multi-trait genomic evaluation: a case study on longitudinal growth performance in beef cattle.}, journal = {Genetics, selection, evolution : GSE}, volume = {56}, number = {1}, pages = {19}, pmid = {38491422}, issn = {1297-9686}, support = {BBSRC BB/N01720X/1//BBRSC/ ; BB/N016742/1//UKRI/ ; BB/S006567/1//UKRI/ ; BB/S006680/1//UKRI/ ; }, abstract = {BACKGROUND: Growth rate is an important component of feed conversion efficiency in cattle and varies across the different stages of the finishing period. The metabolic effect of the rumen microbiome is essential for cattle growth, and investigating the genomic and microbial factors that underlie this temporal variation can help maximize feed conversion efficiency at each growth stage.

RESULTS: By analysing longitudinal body weights during the finishing period and genomic and metagenomic data from 359 beef cattle, our study demonstrates that the influence of the host genome on the functional rumen microbiome contributes to the temporal variation in average daily gain (ADG) in different months (ADG1, ADG2, ADG3, ADG4). Five hundred and thirty-three additive log-ratio transformed microbial genes (alr-MG) had non-zero genomic correlations (rg) with at least one ADG-trait (ranging from |0.21| to |0.42|). Only a few alr-MG correlated with more than one ADG-trait, which suggests that a differential host-microbiome determinism underlies ADG at different stages. These alr-MG were involved in ribosomal biosynthesis, energy processes, sulphur and aminoacid metabolism and transport, or lipopolysaccharide signalling, among others. We selected two alternative subsets of 32 alr-MG that had a non-uniform or a uniform rg sign with all the ADG-traits, regardless of the rg magnitude, and used them to develop a microbiome-driven breeding strategy based on alr-MG only, or combined with ADG-traits, which was aimed at shaping the rumen microbiome towards increased ADG at all finishing stages. Combining alr-MG information with ADG records increased prediction accuracy of genomic estimated breeding values (GEBV) by 11 to 22% relative to the direct breeding strategy (using ADG-traits only), whereas using microbiome information, only, achieved lower accuracies (from 7 to 41%). Predicted selection responses varied consistently with accuracies. Restricting alr-MG based on their rg sign (uniform subset) did not yield a gain in the predicted response compared to the non-uniform subset, which is explained by the absence of alr-MG showing non-zero rg at least with more than one of the ADG-traits.

CONCLUSIONS: Our work sheds light on the role of the microbial metabolism in the growth trajectory of beef cattle at the genomic level and provides insights into the potential benefits of using microbiome information in future genomic breeding programs to accurately estimate GEBV and increase ADG at each finishing stage in beef cattle.}, } @article {pmid38491115, year = {2024}, author = {Barbosa Dos Santos, M and Koide Albuquerque, N and Patroca da Silva, S and Silva da Silva, F and Damous Dias, D and Brito Mendes, S and Fernandes Souza Barbosa Coelho, T and Barros, MC and Ribeiro Cruz, AC}, title = {A novel hantavirus identified in bats (Carollia perspicillata) in Brazil.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6346}, pmid = {38491115}, issn = {2045-2322}, support = {8887.510220/2020-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; 314522/2021-02//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Bats play an essential role in maintaining ecosystems. Their unique characteristics increase the likelihood of interactions with various species, making them a potential source for the emergence and spread of infectious diseases. Hantaviruses are continuously expanding their range of hosts. This study presents the identification of a partial genome associated with Hantavirus in samples collected from neotropical bats. We conducted a metagenomic study using samples from Carollia perspicillata in Maranhão, Brazil. Tissue fragments were used for RNA extraction and subsequent sequencing. The resulting data was subjected to bioinformatic analysis. A sequence showing an identity of 72.86% with the L gene in the reference genome was obtained. The phylogenetic analysis revealed the study sequence, denoted as Buritiense, clustering within the Mobatvirus clade. The intragroup analysis showed a broader dispersion and were markedly asymmetric. This observation suggests the possibility that Buritiense could potentially represent a new species within the bat-borne hantaviruses, but further analyses are needed to provide additional insights if bats plays a role as reservoirs and the potential for transmission to human populations.}, } @article {pmid38491069, year = {2024}, author = {Begmatov, S and Beletsky, AV and Dorofeev, AG and Pimenov, NV and Mardanov, AV and Ravin, NV}, title = {Metagenomic insights into the wastewater resistome before and after purification at large‑scale wastewater treatment plants in the Moscow city.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6349}, pmid = {38491069}, issn = {2045-2322}, support = {22-74-00022//Russian Science Foundation/ ; }, abstract = {Wastewater treatment plants (WWTPs) are considered to be hotspots for the spread of antibiotic resistance genes (ARGs). We performed a metagenomic analysis of the raw wastewater, activated sludge and treated wastewater from two large WWTPs responsible for the treatment of urban wastewater in Moscow, Russia. In untreated wastewater, several hundred ARGs that could confer resistance to most commonly used classes of antibiotics were found. WWTPs employed a nitrification/denitrification or an anaerobic/anoxic/oxic process and enabled efficient removal of organic matter, nitrogen and phosphorus, as well as fecal microbiota. The resistome constituted about 0.05% of the whole metagenome, and after water treatment its share decreased by 3-4 times. The resistomes were dominated by ARGs encoding resistance to beta-lactams, macrolides, aminoglycosides, tetracyclines, quaternary ammonium compounds, and sulfonamides. ARGs for macrolides and tetracyclines were removed more efficiently than beta-lactamases, especially ampC, the most abundant ARG in the treated effluent. The removal efficiency of particular ARGs was impacted by the treatment technology. Metagenome-assembled genomes of multidrug-resistant strains were assembled both for the influent and the treated effluent. Ccomparison of resistomes from WWTPs in Moscow and around the world suggested that the abundance and content of ARGs depend on social, economic, medical, and environmental factors.}, } @article {pmid38490631, year = {2024}, author = {Hu, M and Sardans, J and Sun, D and Yan, R and Wu, H and Ni, R and Peñuelas, J}, title = {Microbial diversity and keystone species drive soil nutrient cycling and multifunctionality following mangrove restoration.}, journal = {Environmental research}, volume = {}, number = {}, pages = {118715}, doi = {10.1016/j.envres.2024.118715}, pmid = {38490631}, issn = {1096-0953}, abstract = {Vegetation restoration exerts transformative effects on nutrient cycling, microbial communities, and ecosystem functions. While extensive research has been conducted on the significance of mangroves and their restoration efforts, the effectiveness of mangrove restoration in enhancing soil multifunctionality in degraded coastal wetlands remains unclear. Herein, we carried out a field experiment to explore the impacts of mangrove restoration and its chronosequence on soil microbial communities, keystone species, and soil multifunctionality, using unrestored aquaculture ponds as controls. The results revealed that mangrove restoration enhanced soil multifunctionality, with these positive effects progressively amplifying over the restoration chronosequence. Furthermore, mangrove restoration led to a substantial increase in microbial diversity and a reshaping of microbial community composition, increasing the relative abundance of dominant phyla such as Nitrospirae, Deferribacteres, and Fusobacteria. Soil multifunctionality exhibited positive correlations with microbial diversity, suggesting a link between variations in microbial diversity and soil multifunctionality. Metagenomic screening demonstrated that mangrove restoration resulted in a simultaneous increase in the abundance of nitrogen (N) related genes, such as N fixation (nirD/H/K), nitrification (pmoA-amoA/B/C), and denitrification (nirK, norB/C, narG/H, napA/B), as well as phosphorus (P)-related genes, including organic P mineralization (phnX/W, phoA/D/G, phnJ/N/P), inorganic P solubilization (gcd, ppx-gppA), and transporters (phnC/D/E, pstA/B/C/S)). The relationship between the abundance of keystone species (such as phnC/D/E) and restoration-induced changes in soil multifunctionality indicates that mangrove restoration enhances soil multifunctionality through an increase in the abundance of keystone species associated with N and P cycles. Additionally, it was observed that changes in microbial community and multifunctionality were largely associated with shifts in soil salinity. These findings demonstrate that mangrove restoration positively influences soil multifunctionality and shapes nutrient dynamics, microbial communities, and overall ecosystem resilience. As global efforts continue to focus on ecosystem restoration, understanding the complexity of mangrove-soil interactions is critical for effective nutrient management and mangrove conservation.}, } @article {pmid38490625, year = {2024}, author = {Hu, P and Xiao, M and Wang, N and Zhang, S and Shi, J and Shi, J and Tang, T and Liu, L}, title = {Metagenome reveals the possible mechanism that microbial strains promote methanogenesis during anaerobic digestion of food waste.}, journal = {Environmental research}, volume = {251}, number = {Pt 2}, pages = {118723}, doi = {10.1016/j.envres.2024.118723}, pmid = {38490625}, issn = {1096-0953}, abstract = {For better understanding the mechanism of microbial strains promoting methane production, four strains Hungatella xylanolytica A5, Bacillus licheniformis B1, Paraclostridium benzoelyticum C2 and Advenella faeciporci E1 were inoculated into anaerobic digestion systems. After bioaugmentation, the cumulative methane production of A5, B1, C2 and E1 groups elevated by 11.68%, 8.20%, 18.21% and 15.67% compared to CK group, respectively. The metagenomic analysis revealed that the species diversity and uniformity of the experimental groups was improved, and hydrolytic acidifying bacteria, represented by Clostridiaceae, Anaerolineaceae and Oscillospiraceae, and methanogens, such as Methanotrichaceae and Methanobacteriaceae, were enriched. Meanwhile, the abundance of key genes in carbohydrate, pyruvate and methane metabolism was increased in the inoculated groups, providing reasonable reasons for more methane production. The strengthening mechanism of microbial strains in this study offered a theoretical foundation for selecting a suitable bioaugmentation strategy to solve the problems of slow start-up and low methane production in anaerobic digestion.}, } @article {pmid38490247, year = {2024}, author = {Ahmed, S and Mahapatra, S and Mishra, R and Murmu, KC and Padhan, P and Prasad, P and Misra, R}, title = {16s RNA-based metagenomics reveal previously unreported gut microbiota associated with reactive arthritis and undifferentiated peripheral spondyloarthritis.}, journal = {Rheumatology (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/rheumatology/keae165}, pmid = {38490247}, issn = {1462-0332}, abstract = {OBJECTIVES: Reactive arthritis (ReA) provides a unique opportunity to comprehend how a mucosal infection leads to inflammatory arthritis at a distant site without the apparent invasion of the pathogen. Unfortunately, conventional stool cultures after ReA provide limited information, and there is a dearth of metagenomic studies in ReA. The objective of this study was to identify gut microbiota associated with the development of ReA.

METHODS: Patients with ReA or undifferentiated peripheral spondyloarthritis (UpSpA) were included if they presented within 4 weeks of the onset of the current episode of arthritis. Metagenomic DNA was extracted from the stools of these patients and of 36 age- and sex-similar controls. Sequencing and analysis were done using a standard 16S ribosomal pipeline.

RESULTS: Of 55 patients, there was no difference between the gut microbiota of postdiarrheal ReA(n = 20) and of upSpA (n = 35). Comparing the gut microbiota of patients vs healthy controls, the patients had significantly higher alpha and beta diversity measures. After stringency filters, Proteobacteria had high abundance while Firmicutes had lesser as compared with the controls. Six families were overexpressed in patients, while another five were overexpressed in controls. Sixteen genera and 18 species were significantly different between patients and controls. At the species level there was strong association of Staphylococcus aureus, Clostridium septicum Klebsiella pneumoniae, Escherichia coli, Empedobacter brevis, Roseburia hominis, Bacillus velezensis, and Crassaminicella with ReA.

CONCLUSION: The microbiota of classical gut-associated ReA and upSpA is similar. Patients have higher diversities in their gut microbiota compared with healthy controls. Both known and previously unreported species associated with ReA/upSpA were identified.}, } @article {pmid38490226, year = {2024}, author = {Nabirumbi, R and Onohuean, H and Drago, KC and Alagbonsi, AI and Adedeji, AA}, title = {Fluoxetine attenuates stress-induced depression-like behavior due to decrease in pro-inflammatory cytokines in male rats.}, journal = {Science progress}, volume = {107}, number = {1}, pages = {368504241234786}, doi = {10.1177/00368504241234786}, pmid = {38490226}, issn = {2047-7163}, abstract = {Background: Pro-inflammatory cytokines are implicated in depression caused by both environmental- and alcohol-induced stress. The purpose of the study was to investigate the cytokine levels in serum and hippocampus following induction of depression-like behaviors (DLB) by either forced swimming test (FST) or ethanol-induced DLB (EID). We also investigated the effect of prior administration of antidepressant drug fluoxetine on cytokines in animals exposed to both models of DLB. Methods: Animals were pretreated with fluoxetine before inducing DLB, while DLB was induced in some animals using FST and ethanol in different groups of rats without fluoxetine pretreatment. The ELISA was used to detect changes in cytokine (IL-1β, IL-6, and TNF-α) levels in serum and hippocampus. Results: The mean levels of IL-1β and IL-6 measured in serum and hippocampus were significantly higher in FST and EID models when compared to the control group. The serum concentrations of IL-1β and IL-6 were significantly reduced in animals pre-treated with 5 mg/kg and 10 mg/kg of fluoxetine in both FST and EID models when compared to the untreated FST and EID groups respectively. Conclusions: In conclusion, both environment and alcohol can induce stress and DLB in rats with similar intensity, and their mechanisms of DLB induction involve activation of pro-inflammatory cytokines. Moreover, fluoxetine can prevent stress-induced inflammation in models of DLB.}, } @article {pmid38490149, year = {2024}, author = {Lou, EG and Fu, Y and Wang, Q and Treangen, TJ and Stadler, LB}, title = {Sensitivity and consistency of long- and short-read metagenomics and epicPCR for the detection of antibiotic resistance genes and their bacterial hosts in wastewater.}, journal = {Journal of hazardous materials}, volume = {469}, number = {}, pages = {133939}, doi = {10.1016/j.jhazmat.2024.133939}, pmid = {38490149}, issn = {1873-3336}, abstract = {Wastewater surveillance is a powerful tool to assess the risks associated with antibiotic resistance in communities. One challenge is selecting which analytical tool to deploy to measure risk indicators, such as antibiotic resistance genes (ARGs) and their respective bacterial hosts. Although metagenomics is frequently used for analyzing ARGs, few studies have compared the performance of long-read and short-read metagenomics in identifying which bacteria harbor ARGs in wastewater. Furthermore, for ARG host detection, untargeted metagenomics has not been compared to targeted methods such as epicPCR. Here, we 1) evaluated long-read and short-read metagenomics as well as epicPCR for detecting ARG hosts in wastewater, and 2) investigated the host range of ARGs across the wastewater treatment plant (WWTP) to evaluate host proliferation. Results highlighted long-read revealed a wider range of ARG hosts compared to short-read metagenomics. Nonetheless, the ARG host range detected by long-read metagenomics only represented a subset of the hosts detected by epicPCR. The ARG-host linkages across the influent and effluent of the WWTP were characterized. Results showed the ARG-host phylum linkages were relatively consistent across the WWTP, whereas new ARG-host species linkages appeared in the WWTP effluent. The ARG-host linkages of several clinically relevant species found in the effluent were identified.}, } @article {pmid38489069, year = {2024}, author = {Ray, M and Manu, S and Rastogi, G and Umapathy, G}, title = {Cyanobacterial Genomes from a Brackish Coastal Lagoon Reveal Potential for Novel Biogeochemical Functions and Their Evolution.}, journal = {Journal of molecular evolution}, volume = {}, number = {}, pages = {}, pmid = {38489069}, issn = {1432-1432}, support = {BT/PR29032/FCB/125/4/2018//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, abstract = {Cyanobacteria are recognised for their pivotal roles in aquatic ecosystems, serving as primary producers and major agents in diazotrophic processes. Currently, the primary focus of cyanobacterial research lies in gaining a more detailed understanding of these well-established ecosystem functions. However, their involvement and impact on other crucial biogeochemical cycles remain understudied. This knowledge gap is partially attributed to the challenges associated with culturing cyanobacteria in controlled laboratory conditions and the limited understanding of their specific growth requirements. This can be circumvented partially by the culture-independent methods which can shed light on the genomic potential of cyanobacterial species and answer more profound questions about the evolution of other key biogeochemical functions. In this study, we assembled 83 cyanobacterial genomes from metagenomic data generated from environmental DNA extracted from a brackish water lagoon (Chilika Lake, India). We taxonomically classified these metagenome-assembled genomes (MAGs) and found that about 92.77% of them are novel genomes at the species level. We then annotated these cyanobacterial MAGs for all the encoded functions using KEGG Orthology. Interestingly, we found two previously unreported functions in Cyanobacteria, namely, DNRA (Dissimilatory Nitrate Reduction to Ammonium) and DMSP (Dimethylsulfoniopropionate) synthesis in multiple MAGs using nirBD and dsyB genes as markers. We validated their presence in several publicly available cyanobacterial isolate genomes. Further, we identified incongruities between the evolutionary patterns of species and the marker genes and elucidated the underlying reasons for these discrepancies. This study expands our overall comprehension of the contribution of cyanobacteria to the biogeochemical cycling in coastal brackish ecosystems.}, } @article {pmid38489008, year = {2024}, author = {Wu, J and Hu, Y and Perlin, MH and Danko, D and Lu, J and Oliveira, M and Werner, J and Zambrano, MM and Sierra, MA and Osuolale, OO and Łabaj, P and Rascovan, N and Hazrin-Chong, NH and Jang, S and Suzuki, H and Nieto-Caballero, M and Prithiviraj, B and Lee, PKH and Chmielarczyk, A and Różańska, A and Zhao, Y and Wang, L and Mason, CE and Shi, T}, title = {Landscape of global urban environmental resistome and its association with local socioeconomic and medical status.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {38489008}, issn = {1869-1889}, abstract = {Antimicrobial resistance (AMR) poses a critical threat to global health and development, with environmental factors-particularly in urban areas-contributing significantly to the spread of antibiotic resistance genes (ARGs). However, most research to date has been conducted at a local level, leaving significant gaps in our understanding of the global status of antibiotic resistance in urban environments. To address this issue, we thoroughly analyzed a total of 86,213 ARGs detected within 4,728 metagenome samples, which were collected by the MetaSUB International Consortium involving diverse urban environments in 60 cities of 27 countries, utilizing a deep-learning based methodology. Our findings demonstrated the strong geographical specificity of urban environmental resistome, and their correlation with various local socioeconomic and medical conditions. We also identified distinctive evolutionary patterns of ARG-related biosynthetic gene clusters (BGCs) across different countries, and discovered that the urban environment represents a rich source of novel antibiotics. Our study provides a comprehensive overview of the global urban environmental resistome, and fills a significant gap in our knowledge of large-scale urban antibiotic resistome analysis.}, } @article {pmid38488837, year = {2024}, author = {Wang, F and Liu, X and Huang, F and Zhou, Y and Wang, X and Song, Z and Wang, S and Wang, X and Shi, D and Ruan, G and Ji, X and Zhang, E and Tan, Z and Ye, Y and Wang, C and Zhu, J and Wang, W}, title = {Gut microbiota-derived gamma-aminobutyric acid from metformin treatment reduces hepatic ischemia/reperfusion injury through inhibiting ferroptosis.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, doi = {10.7554/eLife.89045}, pmid = {38488837}, issn = {2050-084X}, support = {2022R413C074//Zhejiang University Student Science and Technology Innovation Activity Plan/ ; LGF22H030011//Zhejiang Province Public Welfare Technology Application Research Project/ ; KJHX2212//Suzhou Inhale Pharma Co, Ltd/ ; KJHX2202//Zhejiang Xiaolun Intelligent Manufacturing Co, Ltd/ ; }, abstract = {Hepatic ischemia/reperfusion injury (HIRI) is a common and inevitable factor leading to poor prognosis in various liver diseases, making the outcomes of current treatments in clinic unsatisfactory. Metformin has been demonstrated to be beneficial to alleviate HIRI in recent studies, however, the underpinning mechanism remains unclear. In this study, we found metformin mitigates HIRI-induced ferroptosis through reshaped gut microbiota in mice, which was confirmed by the results of fecal microbiota transplantation treatment but showed the elimination of the beneficial effects when gut bacteria were depleted using antibiotics. Detailedly, through 16S rRNA and metagenomic sequencing, we identified that the metformin-reshaped microbiota was characterized by the increase of gamma-aminobutyric acid (GABA) producing bacteria. This increase was further confirmed by the elevation of GABA synthesis key enzymes, glutamic acid decarboxylase and putrescine aminotransferase, in gut microbes of metformin-treated mice and healthy volunteers. Furthermore, the benefit of GABA against HIRI-induced ferroptosis was demonstrated in GABA-treated mice. Collectively, our data indicate that metformin can mitigate HIRI-induced ferroptosis by reshaped gut microbiota, with GABA identified as a key metabolite.}, } @article {pmid38488359, year = {2024}, author = {Royer, C and Patin, NV and Jesser, KJ and Peña-Gonzalez, A and Hatt, JK and Trueba, G and Levy, K and Konstantinidis, KT}, title = {Comparison of metagenomic and traditional methods for diagnosis of E. coli enteric infections.}, journal = {mBio}, volume = {}, number = {}, pages = {e0342223}, doi = {10.1128/mbio.03422-23}, pmid = {38488359}, issn = {2150-7511}, abstract = {UNLABELLED: Diarrheagenic Escherichia coli, collectively known as DEC, is a leading cause of diarrhea, particularly in children in low- and middle-income countries. Diagnosing infections caused by different DEC pathotypes traditionally relies on the cultivation and identification of virulence genes, a resource-intensive and error-prone process. Here, we compared culture-based DEC identification with shotgun metagenomic sequencing of whole stool using 35 randomly drawn samples from a cohort of diarrhea-afflicted patients. Metagenomic sequencing detected the cultured isolates in 97% of samples, revealing, overall, reliable detection by this approach. Genome binning yielded high-quality E. coli metagenome-assembled genomes (MAGs) for 13 samples, and we observed that the MAG did not carry the diagnostic DEC virulence genes of the corresponding isolate in 60% of these samples. Specifically, two distinct scenarios were observed: diffusely adherent E. coli (DAEC) isolates without corresponding DAEC MAGs appeared to be relatively rare members of the microbiome, which was further corroborated by quantitative PCR (qPCR), and thus unlikely to represent the etiological agent in 3 of the 13 samples (~23%). In contrast, ETEC virulence genes were located on plasmids and largely escaped binning in associated MAGs despite being prevalent in the sample (5/13 samples or ~38%), revealing limitations of the metagenomic approach. These results provide important insights for diagnosing DEC infections and demonstrate how metagenomic methods can complement isolation efforts and PCR for pathogen identification and population abundance.

IMPORTANCE: Diagnosing enteric infections based on traditional methods involving isolation and PCR can be erroneous due to isolation and other biases, e.g., the most abundant pathogen may not be recovered on isolation media. By employing shotgun metagenomics together with traditional methods on the same stool samples, we show that mixed infections caused by multiple pathogens are much more frequent than traditional methods indicate in the case of acute diarrhea. Further, in at least 8.5% of the total samples examined, the metagenomic approach reliably identified a different pathogen than the traditional approach. Therefore, our results provide a methodology to complement existing methods for enteric infection diagnostics with cutting-edge, culture-independent metagenomic techniques, and highlight the strengths and limitations of each approach.}, } @article {pmid38488280, year = {2024}, author = {Giacomini, JJ and Torres-Morales, J and Tang, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Spatial ecology of Haemophilus and Aggregatibacter in the human oral cavity.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0401723}, doi = {10.1128/spectrum.04017-23}, pmid = {38488280}, issn = {2165-0497}, abstract = {UNLABELLED: Haemophilus and Aggregatibacter are two of the most common bacterial genera in the human oral cavity, encompassing both commensals and pathogens of substantial ecological and medical significance. In this study, we conducted a metapangenomic analysis of oral Haemophilus and Aggregatibacter species to uncover genomic diversity, phylogenetic relationships, and habitat specialization within the human oral cavity. Using three metrics-pangenomic gene content, phylogenomics, and average nucleotide identity (ANI)-we first identified distinct species and sub-species groups among these genera. Mapping of metagenomic reads then revealed clear patterns of habitat specialization, such as Aggregatibacter species predominantly in dental plaque, a distinctive Haemophilus parainfluenzae sub-species group on the tongue dorsum, and H. sp. HMT-036 predominantly in keratinized gingiva and buccal mucosa. In addition, we found that supragingival plaque samples contained predominantly only one out of the three taxa, H. parainfluenzae, Aggregatibacter aphrophilus, and A. sp. HMT-458, suggesting independent niches or a competitive relationship. Functional analyses revealed the presence of key metabolic genes, such as oxaloacetate decarboxylase, correlated with habitat specialization, suggesting metabolic versatility as a driving force. Additionally, heme synthesis distinguishes H. sp. HMT-036 from closely related Haemophilus haemolyticus, suggesting that the availability of micronutrients, particularly iron, was important in the evolutionary ecology of these species. Overall, our study exemplifies the power of metapangenomics to identify factors that may affect ecological interactions within microbial communities, including genomic diversity, habitat specialization, and metabolic versatility.

IMPORTANCE: Understanding the microbial ecology of the mouth is essential for comprehending human physiology. This study employs metapangenomics to reveal that various Haemophilus and Aggregatibacter species exhibit distinct ecological preferences within the oral cavity of healthy individuals, thereby supporting the site-specialist hypothesis. Additionally, it was observed that the gene pool of different Haemophilus species correlates with their ecological niches. These findings shed light on the significance of key metabolic functions in shaping microbial distribution patterns and interspecies interactions in the oral ecosystem.}, } @article {pmid38487846, year = {2024}, author = {Wu, S and Feng, T and Tang, W and Qi, C and Gao, J and He, X and Wang, J and Zhou, H and Fang, Z}, title = {metaProbiotics: a tool for mining probiotic from metagenomic binning data based on a language model.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {2}, pages = {}, doi = {10.1093/bib/bbae085}, pmid = {38487846}, issn = {1477-4054}, support = {2022YFA0806400//National Key Research and Development Program of China/ ; 82102508//National Natural Science Foundation of China/ ; }, abstract = {Beneficial bacteria remain largely unexplored. Lacking systematic methods, understanding probiotic community traits becomes challenging, leading to various conclusions about their probiotic effects among different publications. We developed language model-based metaProbiotics to rapidly detect probiotic bins from metagenomes, demonstrating superior performance in simulated benchmark datasets. Testing on gut metagenomes from probiotic-treated individuals, it revealed the probioticity of intervention strains-derived bins and other probiotic-associated bins beyond the training data, such as a plasmid-like bin. Analyses of these bins revealed various probiotic mechanisms and bai operon as probiotic Ruminococcaceae's potential marker. In different health-disease cohorts, these bins were more common in healthy individuals, signifying their probiotic role, but relevant health predictions based on the abundance profiles of these bins faced cross-disease challenges. To better understand the heterogeneous nature of probiotics, we used metaProbiotics to construct a comprehensive probiotic genome set from global gut metagenomic data. Module analysis of this set shows that diseased individuals often lack certain probiotic gene modules, with significant variation of the missing modules across different diseases. Additionally, different gene modules on the same probiotic have heterogeneous effects on various diseases. We thus believe that gene function integrity of the probiotic community is more crucial in maintaining gut homeostasis than merely increasing specific gene abundance, and adding probiotics indiscriminately might not boost health. We expect that the innovative language model-based metaProbiotics tool will promote novel probiotic discovery using large-scale metagenomic data and facilitate systematic research on bacterial probiotic effects. The metaProbiotics program can be freely downloaded at https://github.com/zhenchengfang/metaProbiotics.}, } @article {pmid38487325, year = {2024}, author = {Li, N and Zhang, R and Wang, J and Zhu, X and Meng, F and Cao, Y and Wang, G and Yang, Y}, title = {Case report: Acute HHV6B encephalitis/myelitis post CAR-T cell therapy in patients with relapsed/refractory aggressive B-cell lymphoma.}, journal = {Frontiers in neurology}, volume = {15}, number = {}, pages = {1334000}, doi = {10.3389/fneur.2024.1334000}, pmid = {38487325}, issn = {1664-2295}, abstract = {BACKGROUND: The development of chimeric antigen receptor (CAR)-T cell therapy has revolutionized treatment outcomes in patients with lymphoid malignancies. However, several studies have reported a relatively high rate of infection in adult patients following CD19-targeting CAR T-cell therapy, particularly in the first 28 days. Notably, acute human herpesvirus 6 B (HHV6B) reactivation occurs in up to two-thirds of allogeneic hematopoietic stem cell transplantation patients.

CASE PRESENTATIONS: Herein, we describe a report of HHV6B encephalitis/myelitis in three patients with relapsed/refractory diffuse large B-cell lymphoma post CAR T-cell therapy. All three patients received multiple lines of prior treatment (range: 2-9 lines). All patients presented with fever that persisted for at least 2 weeks after CAR-T cell infusion (CTI). Both the onset time and duration were similar to those of the cytokine release syndrome (CRS); nevertheless, the CRS grades of the patients were low (grade 1 or 2). Delirium and memory loss after CTI were the earliest notable mental presentations. Neurological manifestations progressed rapidly, with patients experiencing varying degrees of impaired consciousness, seizures, and coma. Back pain, lumbago, lower limb weakness and uroschesis were also observed in Patient 3, indicating myelitis. High HHV6B loads were detected in all Cerebral spinal fluid (CSF) samples using metagenomic next-generation sequencing (mNGS). Only one patient required high-activity antivirals and IgG intravenous pulse treatment finally recovered, whereas the other two patients died from HHV6B encephalitis.

CONCLUSION: Considering its fatal potential, HHV6B encephalitis/myelitis should be urgently diagnosed post CAR-T cell-based therapy. Furthermore, hematologists should differentially diagnose these conditions from CRS or other immunotherapy-related neurotoxicities as early as possible. The results of this study demonstrate the potential of mNGS in the early diagnosis of HHV6B infection, particularly when the organism is difficult to culture.}, } @article {pmid38486809, year = {2024}, author = {Novikova, PV and Bhanu Busi, S and Probst, AJ and May, P and Wilmes, P}, title = {Functional prediction of proteins from the human gut archaeome.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycad014}, pmid = {38486809}, issn = {2730-6151}, abstract = {The human gastrointestinal tract contains diverse microbial communities, including archaea. Among them, Methanobrevibacter smithii represents a highly active and clinically relevant methanogenic archaeon, being involved in gastrointestinal disorders, such as inflammatory bowel disease and obesity. Herein, we present an integrated approach using sequence and structure information to improve the annotation of M. smithii proteins using advanced protein structure prediction and annotation tools, such as AlphaFold2, trRosetta, ProFunc, and DeepFri. Of an initial set of 873 481 archaeal proteins, we found 707 754 proteins exclusively present in the human gut. Having analysed archaeal proteins together with 87 282 994 bacterial proteins, we identified unique archaeal proteins and archaeal-bacterial homologs. We then predicted and characterized functional domains and structures of 73 unique and homologous archaeal protein clusters linked the human gut and M. smithii. We refined annotations based on the predicted structures, extending existing sequence similarity-based annotations. We identified gut-specific archaeal proteins that may be involved in defense mechanisms, virulence, adhesion, and the degradation of toxic substances. Interestingly, we identified potential glycosyltransferases that could be associated with N-linked and O-glycosylation. Additionally, we found preliminary evidence for interdomain horizontal gene transfer between Clostridia species and M. smithii, which includes sporulation Stage V proteins AE and AD. Our study broadens the understanding of archaeal biology, particularly M. smithii, and highlights the importance of considering both sequence and structure for the prediction of protein function.}, } @article {pmid38486736, year = {2024}, author = {Castañeda-Barreto, A and Olivera-Gonzales, P and Tamariz-Angeles, C}, title = {A natural consortium of thermophilic bacteria from Huancarhuaz hot spring (Ancash-Peru) for promising lignocellulose bioconversion.}, journal = {Heliyon}, volume = {10}, number = {5}, pages = {e27272}, pmid = {38486736}, issn = {2405-8440}, abstract = {The lignocellulose bioconversion process is an eco-friendly and green-economy alternative technology that allows the reduction of pollution and global warming, so it is necessary for thermophilic and thermostable hydrolytic enzymes from natural sources. This research aimed to isolate cellulolytic and xylanolytic microbial consortia from Huancarhuaz hot spring (Peru) from sludge or in situ baiting cultured with or without sugarcane bagasse. According to the hydrolytic activities consortium T4 from in situ baiting was selected. It was cultivated in submerged fermentation at 65 °C, pH 6.5 for eight days using LB supplemented with sugar cane bagasse (SCB), pine wood sawdust (PWS), CMC, xylan of birchwood, or micro granular cellulose. Crude extract of culture supplemented with SCB (T4B) showed better endoglucanase and xylanase activities with higher activities at 75 °C and pH 6. In these conditions, cellulase activity was kept up to 57% after 1 h of incubation, while xylanase activity was up to 63% after 72 h. Furthermore, this crude extract released reduced sugars from pretreated SCB and PWS. According to metagenomic analysis of 16S rDNA, Geobacillus was the predominant genus. It was found thermostable genes: a type of endoglucanase (GH5), an endo-xylanase (GH10), and alkali xylanase (GH10) previously reported in Geobacillus sp. strains. Finally, Huancarhuaz hot spring harbors a genetic microbial diversity for lignocellulosic waste bioconversion in high temperatures, and the T4B consortium will be a promising source of novel extreme condition stable enzymes for the saccharification process.}, } @article {pmid38486699, year = {2024}, author = {Yang, R and Wang, Y and Ying, Z and Shi, Z and Song, Y and Yan, J and Hou, S and Zhao, Z and Hu, Y and Chen, Q and Peng, W and Li, X}, title = {Inspecting mother-to-infant microbiota transmission: disturbance of strain inheritance by cesarian section.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1292377}, doi = {10.3389/fmicb.2024.1292377}, pmid = {38486699}, issn = {1664-302X}, abstract = {INTRODUCTION: The initial acquisition and subsequent development of the microbiota in early life is crucial to future health. Cesarean-section (CS) birth is considered to affect early microbial transmission from mother to infant.

METHODS: In this study, we collected fecal samples from 34 CS infants and their mothers from West China Second Hospital, Sichuan University to assess the microbiota developmental trajectory of mothers and infants. We explored mother-infant gut microbiome transmission via comparison with corresponding Finnish data.

RESULTS: Metagenomic analysis of gut microbiota profiles indicated that the communities of mothers and infants were distinct. The composition of the infant gut microbiome was highly variable but also followed predictable patterns in the early stages of life. Maternal communities were stable and mainly dominated by species from Bacteroidacea spp. We used PStrain to analyze and visualize strain transmission in each mother-infant pair. Excluding missing data, we included 32 mother-infant pairs for analysis of strain transmission. Most CS deliveries (65.6%, 21/32) did not demonstrate transmission of strains from mother to infant. To further explore the mother-infant strain transmission, we analyzed metagenomics data from Finnish mother-infant pairs. A total of 32 mother-infant pairs were included in the analysis, including 28 vaginal delivery (VD) infants and four CS infants. Strain transmission was observed in 30 infants, including 28 VD infants and two CS infants. All VD infants received transmitted stains from their mothers. Finally, a total of 193 strain transmission events were observed, comprising 131 strains and 45 species.

DISCUSSION: Taken together, our data suggested that delivery mode was an important factor influencing the mother-infant strain transmission.}, } @article {pmid38486696, year = {2024}, author = {Bedoya-Urrego, K and Alzate, JF}, title = {Phylogenomic discernments into Anaerolineaceae thermal adaptations and the proposal of a candidate genus Mesolinea.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1349453}, doi = {10.3389/fmicb.2024.1349453}, pmid = {38486696}, issn = {1664-302X}, abstract = {This study delves into the evolutionary history of Anaerolineaceae, a diverse bacterial family within the Chloroflexota phylum. Employing a multi-faceted approach, including phylogenetic analyses, genomic comparisons, and exploration of adaptive features, the research unveils novel insights into the family's taxonomy and evolutionary dynamics. The investigation employs metagenome-assembled genomes (MAGs), emphasizing their prevalence in anaerobic environments. Notably, a novel mesophilic lineage, tentatively named Mesolinea, emerges within Anaerolineaceae, showcasing a distinctive genomic profile and apparent adaptation to a mesophilic lifestyle. The comprehensive genomic analyses shed light on the family's complex evolutionary patterns, including the conservation of key operons in thermophiles, providing a foundation for understanding the diverse ecological roles and adaptive strategies of Anaerolineaceae members.}, } @article {pmid38486264, year = {2024}, author = {Lian, Q and Song, X and Yang, J and Wang, L and Xu, P and Wang, X and Xu, X and Yang, B and He, J and Ju, C}, title = {Alterations of lung microbiota in lung transplant recipients with pneumocystis jirovecii pneumonia.}, journal = {Respiratory research}, volume = {25}, number = {1}, pages = {125}, pmid = {38486264}, issn = {1465-993X}, support = {ZNSA-2020013//Zhongnanshan Medical Foundation of Guangdong Province/ ; SKLRHQN20205//State Key Laboratory of Respiratory Disease/Guangzhou Institute of Respiratory Health/National Center for Respiratory Medicine/ ; 2023C-TS10//Specific Clinical Technology Project of Guangzhou City/ ; 2022A1515012216//Natural Science Foundation of Guangdong Province/ ; 202201020371//Basic Research Program of Guangzhou Institute of Respiratory Health/ ; }, abstract = {BACKGROUND: Increasing evidence revealed that lung microbiota dysbiosis was associated with pulmonary infection in lung transplant recipients (LTRs). Pneumocystis jirovecii (P. jirovecii) is an opportunistic fungal pathogen that frequently causes lethal pneumonia in LTRs. However, the lung microbiota in LTRs with P. jirovecii pneumonia (PJP) remains unknow.

METHODS: In this prospective observational study, we performed metagenomic next-generation sequencing (mNGS) on 72 bronchoalveolar lavage fluid (BALF) samples from 61 LTRs (20 with PJP, 22 with PJC, 19 time-matched stable LTRs, and 11 from LTRs after PJP recovery). We compared the lung microbiota composition of LTRs with and without P. jirovecii, and analyzed the related clinical variables.

RESULTS: BALFs collected at the episode of PJP showed a more discrete distribution with a lower species diversity, and microbiota composition differed significantly compared to P. jirovecii colonization (PJC) and control group. Human gammaherpesvirus 4, Phreatobacter oligotrophus, and Pseudomonas balearica were the differential microbiota species between the PJP and the other two groups. The network analysis revealed that most species had a positive correlation, while P. jirovecii was correlated negatively with 10 species including Acinetobacter venetianus, Pseudomonas guariconensis, Paracandidimonas soli, Acinetobacter colistiniresistens, and Castellaniella defragrans, which were enriched in the control group. The microbiota composition and diversity of BALF after PJP recovery were also different from the PJP and control groups, while the main components of the PJP recovery similar to control group. Clinical variables including age, creatinine, total protein, albumin, IgG, neutrophil, lymphocyte, CD3[+]CD45[+], CD3[+]CD4[+] and CD3[+]CD8[+] T cells were deeply implicated in the alterations of lung microbiota in LTRs.

CONCLUSIONS: This study suggests that LTRs with PJP had altered lung microbiota compared to PJC, control, and after recovery groups. Furthermore, lung microbiota is related to age, renal function, nutritional and immune status in LTRs.}, } @article {pmid38486253, year = {2024}, author = {Meriggi, N and Russo, A and Renzi, S and Cerasuolo, B and Nerini, M and Ugolini, A and Marvasi, M and Cavalieri, D}, title = {Enhancing seafood traceability: tracking the origin of seabass and seabream from the tuscan coast area by the analysis of the gill bacterial communities.}, journal = {Animal microbiome}, volume = {6}, number = {1}, pages = {13}, pmid = {38486253}, issn = {2524-4671}, support = {Project code: 2/SSL/16/TO-1/ICR/21/TO//Regione Toscana with the project PO FEAMP 2014 - 2020 - Misura 1.39 SSL FLAG Costa degli Etruschi/ ; grant n. 101060712//European Commission by FishEUTrust project Horizon-CL6-2021-FARM2FORK 01/ ; }, abstract = {BACKGROUND: The seafood consumption and trade have increased over the years, and along its expected expansion pose major challenges to the seafood industry and government institutions. In particular, the global trade in fish products and the consequent consumption are linked to reliable authentication, necessary to guarantee lawful trade and healthy consumption. Alterations or errors in this process can lead to commercial fraud and/or health threats. Consequently, the development of new investigative tools became crucial in ensuring unwanted scenarios. Here we used NGS techniques through targeted metagenomics approach on the V3-V4 region of the 16S rRNA genes to characterize the gill bacterial communities in wild-caught seabream (Sparus aurata) and seabass (Dicentrarchus labrax) within different fisheries areas of the "Costa degli Etruschi'' area in the Tuscan coast. Our challenge involved the possibility of discriminating between the microbiota of both fish species collected from three different fishing sites very close to each other (all within 100 km) in important areas from a commercial and tourist point of view.

RESULTS: Our results showed a significant difference in the assembly of gill bacterial communities in terms of diversity (alpha and beta diversity) of both seabass and seabream in accordance with the three fishing areas. These differences were represented by a unique site -related bacterial signature, more evident in seabream compared to the seabass. Accordingly, the core membership of seabream specimens within the three different sites was minimal compared to the seabass which showed a greater number of sequence variants shared among the different fishing sites. Therefore, the LRT analysis highlighted the possibility of obtaining specific fish bacterial signatures associated with each site; it is noteworthy that specific taxa showed a unique association with the fishing site regardless of the fish species. This study demonstrates the effectiveness of target-metagenomic sequencing of gills in discriminating bacterial signatures of specimens collected from fishing areas located at a limited distance to each other.

CONCLUSIONS: This study provides new information relating the structure of the gill microbiota of seabass and seabream in a fishing area with a crucial commercial and tourist interest, namely "Costa degli Etruschi". This study demonstrated that microbiome-based approaches can represent an important tool for validating the seafood origins with a central applicative perspective in the seafood traceability system.}, } @article {pmid38485793, year = {2024}, author = {Shchyogolev, SY and Dykman, LA and Sokolov, AO and Sokolov, OI and Matora, LY}, title = {Quantitative intra- and intergeneric taxonomic relationships among Micrococcaceae strains reveal contradictions in the historical assignments of the strains and indicate the need for species reclassification.}, journal = {Archives of microbiology}, volume = {206}, number = {4}, pages = {165}, pmid = {38485793}, issn = {1432-072X}, abstract = {This article reports the results of quantitative intra- and intergeneric taxonomic relationships among Micrococcaceae strains and a novel endophytic bacterium (SG) isolated from a suspension culture of Arabidopsis thaliana (L.) Heynh in our laboratory. The known strain Rothia sp. ND6WE1A was used as a reference one for SG. Whole-genome sequencing and phylogenetic analysis were based on the 16S rRNA test. Quantitative analysis for the nucleotide identity (ANI) and calculation of evolutionary distances were based on the identified amino acids (AAI) test indicating the generic assignment of the reference strain within and between the identified monophyletic groups of Micrococcaceae. The amino acid data structure of Rothia sp. ND6WE1A was compared against the UniProt database (250 million records) of close lineage of Micrococcaceae, including other Rothia spp. These data presented unique and evolutionary amino acid alignments, eventually expected in the new SG isolate as well. The metagenomic entries of the respective genome and proteome, characterized at the genus and species levels, could be considered for evolutionary taxonomic reclassification of the isolated and the reference strain (SG + Rothia sp. ND6WE1A). Therefore, our results warrant further investigations on the isolated SG strain.}, } @article {pmid38485699, year = {2024}, author = {Hauswedell, H and Hetzel, S and Gottlieb, SG and Kretzmer, H and Meissner, A and Reinert, K}, title = {Lambda3: homology search for protein, nucleotide and bisulfite-converted sequences.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btae097}, pmid = {38485699}, issn = {1367-4811}, abstract = {MOTIVATION: Local alignments of query sequences in large databases represent a core part of metagenomic studies and facilitate homology search. Following the development of NCBI Blast, many applications aimed to provide faster and equally sensitive local alignment frameworks. Most applications focus on protein alignments, while only few also facilitate DNA-based searches. None of the established programs allow searching DNA sequences from bisulfite sequencing experiments commonly used for DNA methylation profiling, for which specific alignment strategies need to be implemented.

RESULTS: Here, we introduce Lambda3, a new version of the local alignment application Lambda. Lambda3 is the first solution that enables the search of protein, nucleotide as well as bisulfite-converted nucleotide query sequences. Its protein mode achieves comparable performance to that of the highly optimised protein alignment application Diamond, while the nucleotide mode consistently outperforms established local nucleotide aligners. Combined, Lambda3 presents a universal local alignment framework that enables fast and sensitive homology searches for a wide range of use cases.

Lambda3 is free and open source software publicly available at https://github.com/seqan/lambda/.

SUPPLEMENTARY INFORMATION: Supplementary data are provided with this article.}, } @article {pmid38485151, year = {2024}, author = {Frayman, KB and Macowan, M and Caparros-Martin, J and Ranganathan, SC and Marsland, BJ and , }, title = {The Longitudinal Microbial and Metabolic Landscape of infant Cystic Fibrosis: The gut-lung axis.}, journal = {The European respiratory journal}, volume = {}, number = {}, pages = {}, doi = {10.1183/13993003.02290-2023}, pmid = {38485151}, issn = {1399-3003}, abstract = {BACKGROUND AND AIM: : In cystic fibrosis (CF), gastrointestinal dysfunction and lower airway infection occur early and are independently associated with poorer outcomes in childhood. This study aimed to define the relationship between the microbiota at each niche during the first 2-years of life, its association with growth and airway inflammation, and explanatory features in the metabolome.

MATERIALS AND METHODS: Sixty-seven bronchoalveolar lavage (BAL), 62 plasma and 105 stool samples were collected from 39 infants with CF between 0-24-months who were treated with prophylactic antibiotics. 16S rRNA amplicon and shotgun metagenomic sequencing were performed on BAL and stool respectively; metabolomic analyses were performed on all sample types. Sequencing data from healthy age-matched infants were used as controls.

RESULTS: Bacterial diversity increased over the first 2-years in both BAL and stool, and microbial maturation was delayed in comparison to healthy controls from the RESONANCE cohort. Correlations between their respective abundances in both sites suggest stool may serve as a non-invasive alternative for detecting BAL Pseudomonas and Veillonella. Multi-site metabolomic analyses revealed age- and growth-related changes, associations with neutrophilic airway inflammation, and a set of core systemic metabolites. BAL Pseudomonas abundance was correlated with altered stool microbiome composition and systemic metabolite alterations, highlighting a complex gut-plasma-lung interplay and new targets with therapeutic potential.

CONCLUSION: Exploration of the gut-lung microbiome and metabolome reveals diverse multi-site interactions in CF that emerge in early life. Gut-lung metabolomic links with airway inflammation and Pseudomonas abundance warrant further investigation for clinical utility, particularly in non-expectorating patients.}, } @article {pmid38485093, year = {2024}, author = {Riva, A and Sahin, E and Volpedo, G and Petretto, A and Lavarello, C and Di Sapia, R and Barbarossa, D and Zaniani, NR and Craparotta, I and Barbera, MC and Sezerman, U and Vezzani, A and Striano, P and Ravizza, T}, title = {Identification of an epilepsy-linked gut microbiota signature in a pediatric rat model of acquired epilepsy.}, journal = {Neurobiology of disease}, volume = {}, number = {}, pages = {106469}, doi = {10.1016/j.nbd.2024.106469}, pmid = {38485093}, issn = {1095-953X}, abstract = {A dysfunctional gut microbiota-brain axis is emerging as a potential pathogenic mechanism in epilepsy, particularly in pediatric forms of epilepsy. To add new insights into gut-related changes in acquired epilepsy that develops early in life, we used a multi-omics approach in a rat model with a 56% incidence of epilepsy. The presence of spontaneous seizures was assessed in adult rats (n = 46) 5 months after status epilepticus induced by intra-amygdala kainate at postnatal day 13, by 2 weeks (24/7) ECoG monitoring. Twenty-six rats developed epilepsy (Epi) while the remaining 20 rats (No-Epi) did not show spontaneous seizures. At the end of ECoG monitoring, all rats and their sham controls (n = 20) were sacrificed for quantitative histopathological and immunohistochemical analyses of the gut structure, glia and macrophages, as well as RTqPCR analysis of inflammation/oxidative stress markers. By comparing Epi, No-Epi rats, and sham controls, we found structural, cellular, and molecular alterations reflecting a dysfunctional gut, which were specifically associated with epilepsy. In particular, the villus height-to-crypt depth ratio and number of Goblet cells were reduced in the duodenum of Epi rats vs both No-Epi rats and sham controls (p < 0.01). Villus height and crypt depth in the duodenum and jejunum (p < 0.01) were increased in No-Epi vs both Epi and sham controls. We also detected enhanced Iba1-positive macrophages, together with increased IL1b and NFE2L2 transcripts and TNF protein, in the small intestine of Epi vs both No-Epi and sham control rats (p < 0.01), denoting the presence of inflammation and oxidative stress. Astroglial GFAP-immunostaining was similar in all experimental groups. Metagenomic analysis in the feces collected 5 months after status epilepticus showed that the ratio of two dominant phyla (Bacteroidota-to-Firmicutes) was similarly increased in Epi and No-Epi rats vs sham control rats. Notably, the relative abundance of families, genera and species associated with SCFA production differed in Epi vs No-Epi rats, describing a bacterial imprint associated with epilepsy. Furthermore, Epi rats showed a blood metabolic signature characterized by changes in lipid metabolism compared to both No-Epi and sham control rats. Our study provides new evidence of long-term gut alterations, along with microbiota-related metabolic changes, occurring specifically in rats that develop epilepsy after brain injury early in life.}, } @article {pmid38485034, year = {2024}, author = {Gong, J and Xu, F and Li, Y and He, Y and Liang, Z and Chen, X and Zhang, X and Liu, L and Zhou, L and Huang, X}, title = {Metagenomic analysis of intestinal microbial function and key genes responsive to acute high-salinity stress in Nile tilapia (Oreochromis niloticus).}, journal = {Gene}, volume = {}, number = {}, pages = {148371}, doi = {10.1016/j.gene.2024.148371}, pmid = {38485034}, issn = {1879-0038}, abstract = {The intestinal microbiota is increasingly recognized as playing an important role in aquatic animals. To investigate the functional roles and mechanisms of the intestinal microbial genes/enzymes responding to salinity stress or osmotic pressure in fish, metagenomic analysis was carried out to evaluate the response of intestinal microbiota and especially their functional genes/enzymes from freshwater (the control group) to acute high salinity stress (the treatment group) in Nile tilapia. Our results showed that at the microbial community level, the intestinal microbiota in Nile tilapia generally underwent significant changes in diversity after acute high salinity stress. Among them, the shift in the bacterial community (mainly from Actinobacteria to Proteobacteria) dominated and had a large impact, the fungal community showed a very limited response, and other microbiota, such as phages, likely had a negligible response. At the functional level, the intestinal bacteriadecreased the normal physiological demand and processes, such as those of the digestive system and nervous system, but enhanced energy metabolism. Furthermore, at the gene level, some gene biomarkers, such as glutathione S-transferase, myo-inositol-1(or 4)-monophosphatase, glycine betaine/proline transport system permease protein, and some families of carbohydrate-active enzymes (GT4, GT2), were significantly enriched. However, GH15, GH23 and so on were significantly reduced. Exploring the functional details of the intestinal microbial genes/enzymes that respond to salinity stress in Nile tilapia sheds light on the mechanism of action of the intestinal microbiota with respect to the salinity adaptation of fish.}, } @article {pmid38485002, year = {2024}, author = {Zhao, T and Huang, S and Zhang, Y and Chow, AT and Chen, P and Wang, Y and Lu, Y and Xiong, J}, title = {Removal of sulfur and nitrogen pollutants in a sediment microbial fuel cell coupled with Vallisneria natans: Efficiency, microbial community structure, and functional genes.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {141667}, doi = {10.1016/j.chemosphere.2024.141667}, pmid = {38485002}, issn = {1879-1298}, abstract = {The rapid development of the economy has led to an increase in the sulfur and nitrogen load in surface water, which has the potential to cause river eutrophication and the emission of malodorous gases. A lab-scale sediment microbial fuel cell coupled with Vallisneria natans (P-SMFC) was designed for surface water remediation. The enhancement of pollutant removal performance of P-SMFC was evaluated in contrast to the SMFC system without plants (SMFC), the open-circuit control system with plants (C-P), and the open-circuit control system without plants (C-S), while illustrating the mechanisms of the sulfur and nitrogen transformation process. The results demonstrated that the effluent and sediment of P-SMFC had lower concentrations of sulfide compared to other systems. Furthermore, P-SMFC exhibited higher removal efficiency for COD (86.7 ± 7.2%), NH4[+]-N (80.5 ± 19.8%), and NO3[-]-N (88.5 ± 11.8%) compared to other systems. The closed-circuit conditions and growth of Vallisneria natans create a favorable ecological niche for functional microorganisms involved in power generation, sulfur oxidation, and nitrogen transformation. Additionally, metagenomic analysis revealed that multifunctional bacteria possessing both denitrification and sulfur oxidation genes, such as Thiobacillus, Dechloromonas, and Bacillus, may play simultaneous roles in metabolizing sulfur and nitrogen, thus serving as integral factors in maintaining the performance of P-SMFC. In summary, these findings provide a theoretical reference for the concurrent enhancement of sulfur and nitrogen pollutants removal in P-SMFC and will facilitate its practical application in the remediation of contaminated surface water.}, } @article {pmid38484907, year = {2024}, author = {Song, P and Tian, Y and Chen, S and Zhang, S and Li, X and You, Z and Fu, J and Xu, W and Li, Z and Luan, J and Zhao, Q and Wang, C and Pang, F}, title = {A novel method for simultaneous detection of hematological tumors and infectious pathogens by metagenomic next generation sequencing of plasma.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {}, number = {}, pages = {117874}, doi = {10.1016/j.cca.2024.117874}, pmid = {38484907}, issn = {1873-3492}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is valuable for pathogen identification; however, distinguishing between infectious diseases and conditions with potentially similar clinical manifestations, including malignant tumors, is challenging. Therefore, we developed a method for simultaneous detection of infectious pathogens and cancer in blood samples.

METHODS: Plasma samples (n = 244) were collected from 150 and 94 patients with infections and hematological malignancies, respectively, and analyzed by mNGS for pathogen detection, alongside human tumor chromosomal copy number variation (CNV) analysis (≥5Mbp or 10Mbp CNV region). Further, an evaluation set, comprising 87 plasma samples, was analyzed by mNGS and human CNV analysis, to validate the feasibility of the method.

RESULTS: Among 94 patients with hematological malignancy, sensitivity values of CNV detection for tumor diagnosis were 69.15 % and 32.98 % for CNV region 5Mbp and 10Mbp, respectively, with corresponding specificities of 92.62 % and 100 % in the infection group. Area under the ROC curve (AUC) values for 5Mbp and 10Mbp region were 0.825 and 0.665, respectively, which was a significant difference of 0.160 (95 % CI: 0.110-0.210; p < 0.001), highlighting the superiority of 5Mbp output region data. Six patients with high-risk CNV results were identified in the validation study: three with history of tumor treatment, two eventually newly-diagnosed with hematological malignancies, and one with indeterminate final diagnosis.

CONCLUSIONS: Concurrent CNV analysis alongside mNGS for infection diagnosis is promising for detecting malignant tumors. We recommend adopting a CNV region of 10Mbp over 5Mbp for our model, because of the lower false-positive rate (FPR).}, } @article {pmid38484748, year = {2024}, author = {Shafer, MM and Bobholz, MJ and Vuyk, WC and Gregory, DA and Roguet, A and Haddock Soto, LA and Rushford, C and Janssen, KH and Emmen, IE and Ries, HJ and Pilch, HE and Mullen, PA and Fahney, RB and Wei, W and Lambert, M and Wenzel, J and Halfmann, P and Kawaoka, Y and Wilson, NA and Friedrich, TC and Pray, IW and Westergaard, R and O'Connor, DH and Johnson, MC}, title = {Tracing the origin of SARS-CoV-2 omicron-like spike sequences detected in an urban sewershed: a targeted, longitudinal surveillance study of a cryptic wastewater lineage.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2666-5247(23)00372-5}, pmid = {38484748}, issn = {2666-5247}, abstract = {BACKGROUND: The origin of novel SARS-CoV-2 spike sequences found in wastewater, without corresponding detection in clinical specimens, remains unclear. We sought to determine the origin of one such cryptic wastewater lineage by tracking and characterising its persistence and genomic evolution over time.

METHODS: We first detected a cryptic lineage, WI-CL-001, in municipal wastewater in Wisconsin, USA, in January, 2022. To determine the source of WI-CL-001, we systematically sampled wastewater from targeted sub-sewershed lines and maintenance holes using compositing autosamplers. Viral concentrations in wastewater samples over time were measured by RT digital PCR. In addition to using metagenomic 12s rRNA sequencing to determine the virus's host species, we also sequenced SARS-CoV-2 spike receptor binding domains, and, where possible, whole viral genomes to identify and characterise the evolution of this lineage.

FINDINGS: We traced WI-CL-001 to its source at a single commercial building. There we detected the cryptic lineage at concentrations as high as 2·7 × 10[9] genome copies per L. The majority of 12s rRNA sequences detected in wastewater leaving the identified source building were human. Additionally, we generated over 100 viral receptor binding domain and whole-genome sequences from wastewater samples containing the cryptic lineage collected over the 13 consecutive months this virus was detectable (January, 2022, to January, 2023). These sequences contained a combination of fixed nucleotide substitutions characteristic of Pango lineage B.1.234, which circulated in humans in Wisconsin at low levels from October, 2020, to February, 2021. Despite this, mutations in the spike gene and elsewhere resembled those subsequently found in omicron variants.

INTERPRETATION: We propose that prolonged detection of WI-CL-001 in wastewater indicates persistent shedding of SARS-CoV-2 from a single human initially infected by an ancestral B.1.234 virus. The accumulation of convergent omicron-like mutations in WI-CL-001's ancestral B.1.234 genome probably reflects persistent infection and extensive within-host evolution. People who shed cryptic lineages could be an important source of highly divergent viruses that sporadically emerge and spread.

FUNDING: The Rockefeller Foundation, Wisconsin Department of Health Services, Centers for Disease Control and Prevention, National Institute on Drug Abuse, and the Center for Research on Influenza Pathogenesis and Transmission.}, } @article {pmid38484575, year = {2024}, author = {Deepa, N and Chauhan, S and Singh, A}, title = {Unraveling the functional characteristics of endophytic bacterial diversity for plant growth promotion and enhanced secondary metabolite production in Pelargonium graveolens.}, journal = {Microbiological research}, volume = {283}, number = {}, pages = {127673}, doi = {10.1016/j.micres.2024.127673}, pmid = {38484575}, issn = {1618-0623}, abstract = {The rich diversity of microbial endophytic communities associated with plants, often referred to as the second genome, serves as a compelling illustration of efficient co-evolution. This noteworthy partnership plays a pivotal role in sustaining plant well-being and enhancing plant adaptability across diverse habitats. Therefore, examining the diversity of endophytic microbes associated with their particular host plant is valuable for gaining insights into the vast spectrum of plant-microbe interactions. The present experiments aimed at investigating the bacterial endophytic diversity in both root and shoot tissues of Pelargonium graveolens, employing culture dependent and culture independent high-throughput metagenomics approach. A total of 614 and 620 operational taxonomic units (OTUs), encompassing 291 and 229 genera, were identified in the shoot and root tissues of P. graveolens, respectively. Furthermore, the subsequent classification of OTUs revealed 15 highly abundant phyla, with Proteobacteria dominating both root and shoot tissues. Notably, an exceptionally high abundance of Firmicutes phyla was observed in the shoot compared to the root. Additionally, 30 bacterial endophytes from the root, stem, petiole, and leaves were isolated and molecularly characterized, unveiling a consistent pattern of diversity distribution between the root and shoot of P. graveolens. Upon screening all isolates for plant growth promoting traits, Pseudomonas oryzihabitans was found to be positive for major biochemical test like nitrogen fixation, phosphate solubilization etc. and on inoculation resulted in about two-fold increase in content of essential oil accompanied by a significant rise in the geraniol and citronellol content. Diving deep into the genetic constitution of P. oryzihabitans unveiled a substantial number of genes directly and indirectly contributing to the endophyte's capability in colonizing host plants effectively. In summary, data obtained from metagenomics and culture dependent approaches including glass house trials suggest potential bacterial endophytes suitable for field applications for yield enhancement and in planta secondary metabolite enhancement investigations.}, } @article {pmid38484351, year = {2024}, author = {Chen, Q and Guo, W and Guo, W and Mu, X and Guo, J}, title = {Pulmonary histoplasmosis on the Chinese mainland: two case reports and literature review.}, journal = {Journal of infection in developing countries}, volume = {18}, number = {2}, pages = {318-325}, doi = {10.3855/jidc.17934}, pmid = {38484351}, issn = {1972-2680}, abstract = {INTRODUCTION: Pulmonary histoplasmosis is a fungal disease that is endemic in North and Central America. It is relatively rare in China and commonly misdiagnosed as tuberculosis or cancer due to nonspecific clinical and radiographic manifestations. Rapid and accurate pathogen tests are critical for the diagnosis of pulmonary histoplasmosis.

METHODOLOGY: We report two cases of pulmonary histoplasmosis. We collected all the relevant case reports on the Chinese mainland (from 1990 to 2022) to analyze features of this disease among Chinese patients.

RESULTS: A total of 42 articles reporting 101 cases were identified, and the two cases reported in this article were also included for analysis. Sixty-three (61.2%) patients had respiratory symptoms and 35 (34.0%) patients were asymptomatic. The most common radiographic findings were pulmonary nodules or masses (81.6%). Twenty-two (21.4%) patients were misdiagnosed as tuberculosis, and 37 (35.9%) were misdiagnosed as lung tumors before pathological findings. Metagenomic next‑generation sequencing (mNGS) testing provided a rapid diagnostic and therapeutic basis for three patients.

CONCLUSIONS: Clinical features and imaging findings of pulmonary histoplasmosis are not specific. Relevant epidemiological history and timely pathogen detection are important for diagnosis. mNGS can shorten the time required for diagnosis and allow earlier initiation of targeted antibiotic therapy.}, } @article {pmid38483744, year = {2024}, author = {Bharathi Rathinam, R and Tripathi, G and Das, BK and Jain, R and Acharya, A}, title = {Comparative analysis of gut microbiome in Pangasionodon hypopthalmus and Labeo catla during health and disease.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {38483744}, issn = {1618-1905}, abstract = {The present study was conducted to study the composition of gut microbiome in the advanced fingerling and fingerling stage of striped pangasius catfish and catla during healthy and diseased conditions. Healthy pangasius and catla fishes were obtained from commercial farms and injected with the LD50 dose of A. hydrophila. The intestinal samples from the control and injected group were collected and pooled for 16 s metagenomic analysis. Community analysis was performed by targeting the 16 s rRNA gene to explore and compare the gut microbiota composition of these fishes. The operational taxonomic units (OTUs) consisted of four major phyla: Bacteroidia, Proteobacteria, Firmicutes, and Actinobacteria. Alpha and beta diversity indices were carried out to understand the diversity of microbes within and between a sample. While comparing the advanced fingerling and fingerling stage gut microbiome of Pangasius catfish, the dominance of Proteobacteria was found in fingerlings, whereas Firmicutes and Bacteroides were found in advanced fingerlings. In catla, Proteobacteria and Bacteroides were predominant. Taxonomic abundance of the microbiota in control and diseased Pangasius and catla fishes at phylum, class, order, family, genus, and species levels were also depicted. The present study is the first of its kind, and it will help to identify the diversity of novel potential bacterial species involved in disease protection of fishes. It can lead to the development of sustainable prophylactic measures against (re-)emerging bacterial diseases in aquaculture.}, } @article {pmid38483146, year = {2024}, author = {Yuanjun, Z and Yan, C and Qingyan, Z and Feng, X}, title = {Porphyromonas gingivalis-induced hematogenous disseminated severe pneumonia: a case report.}, journal = {The Journal of international medical research}, volume = {52}, number = {3}, pages = {3000605231213760}, doi = {10.1177/03000605231213760}, pmid = {38483146}, issn = {1473-2300}, abstract = {Porphyromonas gingivalis, a gram-negative oral anaerobe among more than more than 500 bacterial species that colonizing the oral cavity, is involved in the pathogenesis and prototypic polybacterial consortium of periodontitis. It is mainly found in oral infections and rarely present in other organ diseases. Here, we describe a 43-year-old man with underlying diabetes who developed hematogenous disseminated severe pneumonia after P. gingivalis had invaded the blood. Next-generation sequencing of early alveolar lavage fluid and blood samples confirmed the diagnosis. The patient's lung infection improved after targeted antimicrobial treatment. He was successfully weaned from ventilatory support and transferred to the general ward. This case illustrates bacterial entry into the bloodstream of a patient with diabetes who had periodontal disease but did not maintain oral hygiene, leading to severe pneumonia. Periodontal disease is often ignored by the public, and it is difficult for critical care physicians to link severe pneumonia with periodontal disease. Thus, this case represents an important warning to critical care clinicians.}, } @article {pmid38483068, year = {2024}, author = {Lehman, A and Goren, L and Evans, MD and Toles, O and Drozdov, D and Andrews, S and McAllister, S and Thielen, BK}, title = {Clinical Performance of Plasma Metagenomic Sequencing in Immunocompromised Pediatric Patients.}, journal = {Journal of the Pediatric Infectious Diseases Society}, volume = {}, number = {}, pages = {}, doi = {10.1093/jpids/piae024}, pmid = {38483068}, issn = {2048-7207}, } @article {pmid38482731, year = {2024}, author = {Jiang, S and Du, L and Zhao, Q and Su, S and Huang, S and Zhang, J}, title = {Tropical postbiotics alleviate the disorders in the gut microbiota and kidney damage induced by ochratoxin A exposure.}, journal = {Food & function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d3fo05213c}, pmid = {38482731}, issn = {2042-650X}, abstract = {Ochratoxin A (OTA), commonly found in various foods, significantly impacts the health of humans and animals, especially their kidneys. Our study explores OTA's effects on the gut microbiota and kidney damage while examining how postbiotics offer protection. Using metagenomic sequencing, we observed that OTA increased the potential gut pathogens such as Alistipes, elevating detrimental metabolites and inflammation. Also, OTA inhibited the Nrf2/HO-1 pathway, reducing kidney ROS elimination and leading to cellular ferroptosis and subsequent kidney damage. Postbiotics mitigate OTA's effects by downregulating the abundance of the assimilatory sulfate reduction IV pathway and virulence factors associated with iron uptake and relieving the inhibition of OTA on Nrf2/HO-1, restoring ROS-clearing capabilities and thereby alleviating chronic OTA-induced kidney damage. Understanding the OTA-gut-kidney link provides new approaches for preventing kidney damage, with postbiotics showing promise as a preventive treatment.}, } @article {pmid38482369, year = {2024}, author = {Kawato, S and Nozaki, R and Kondo, H and Hirono, I}, title = {Metagenome-assembled genomes of three Hepatoplasmataceae provide insights into isopod-mollicute symbiosis.}, journal = {Access microbiology}, volume = {6}, number = {2}, pages = {}, pmid = {38482369}, issn = {2516-8290}, abstract = {The digestive organs of terrestrial isopods harbour bacteria of the recently proposed mollicute family Hepatoplasmataceae. The only complete genome available so far for Hepatoplasmataceae is that of 'Candidatus Hepatoplasma crinochetorum'. The scarcity of genome sequences has hampered our understanding of the symbiotic relationship between isopods and mollicutes. Here, we present four complete metagenome-assembled genomes (MAGs) of uncultured Hepatoplasmataceae members identified from shotgun sequencing data of isopods. We propose genomospecies names for three MAGs that show substantial sequence divergence from any previously known Hepatoplamsataceae members: 'Candidatus Tyloplasma litorale' identified from the semiterrestrial isopod Tylos granuliferus, 'Candidatus Hepatoplasma vulgare' identified from the common pill bug Armadillidium vulgare, and 'Candidatus Hepatoplasma scabrum' identified from the common rough woodlouse Porcellio scaber. Phylogenomic analysis of 155 mollicutes confirmed that Hepatoplasmataceae is a sister clade of Metamycoplasmataceae in the order Mycoplasmoidales. The 16S ribosomal RNA gene sequences and phylogenomic analysis showed that 'Candidatus Tyloplasma litorale' and other semiterrestrial isopod-associated mollicutes represent the placeholder genus 'g_Bg2' in the r214 release of the Genome Taxonomy Database, warranting their assignment to a novel genus. Our analysis also revealed that Hepatoplasmataceae lack major metabolic pathways but has a likely intact type IIA CRISPR-Cas9 machinery. Although the localization of the Hepatoplasmatacae members have not been verified microscopically in this study, these genomic characteristics are compatible with the idea that these mollicutes have an ectosymbiotic lifestyle with high nutritional dependence on their host, as has been demonstrated for other members of the family. We could not find evidence that Hepatoplasmataceae encode polysaccharide-degrading enzymes that aid host digestion. If they are to provide nutritional benefits, it may be through extra-copy nucleases, peptidases, and a patatin-like lipase. Exploration of potential host-symbiont interaction-associated genes revealed large, repetitive open reading frames harbouring beta-sandwich domains, possibly involved with host cell adhesion. Overall, genomic analyses suggest that isopod-mollicute symbiosis is not characterized by carbohydrate degradation, and we speculate on their potential role as defensive symbionts through spatial competition with pathogens to prevent infection.}, } @article {pmid38482351, year = {2024}, author = {Kaur, R and Singh, DP and Rawal, R}, title = {Metagenomics analysis of mice gut microbiome to unravel the role of metal exposure and piperine.}, journal = {Access microbiology}, volume = {6}, number = {2}, pages = {}, pmid = {38482351}, issn = {2516-8290}, abstract = {The gut and intestinal microbiota consists of trillions of microorganisms inhabiting the human gastrointestinal tract. It plays a crucial role in human health leading to understanding the dynamic crosstalk of host-microbe interaction in the gut and has become necessary for the detection, prevention, or therapy of diseases. Gut microbiota deviations are linked with many diseases, suggesting that various pathways involved in immunity, energy, lipid, and glucose metabolism are affected. Further, it is also altered by external insults such as metal toxicity, antibiotics and pesticides. Heavy metals like arsenic, mercury, cadmium and chromium are some of the well-studied classes of environmental pollutants. Mouse models have become the model of choice for most studies in this emerging field, as they allow perturbations in the gut microbiota to be studied in a controlled experimental setup. Here, we investigate the composition and diversity of intestinal microbes utilizing cecal samples from different intervention groups: arsenic exposure (As(III)), arsenic and piperine co-administration (As +Pp), piperine per se and control group. We obtained DNA samples from these groups and performed PCR amplification and sequencing of the 16S V3-V4 region. The findings showed shift in microbial composition and abundance among different intervention groups, revealing taxa that may contribute to the microbial diversity.}, } @article {pmid38481824, year = {2024}, author = {Kirdat, K and Tiwarekar, B and Manjula, KN and Padma, S and Sathe, S and Sundararaj, R and Yadav, A}, title = {Draft genome sequence of 'Candidatus Phytoplasma asteris,' strain SW86 associated with sandal spike disease (SSD).}, journal = {3 Biotech}, volume = {14}, number = {4}, pages = {109}, pmid = {38481824}, issn = {2190-572X}, abstract = {UNLABELLED: The sandal spike disease (SSD), related to 'Ca. Phytoplasma asteris' (Aster Yellows group), poses a significant threat to Indian sandalwood (Santalum album L.), making it the second most expensive wood globally due to declining population density. The epidemiology of SSD and the nature of the pathogen remain poorly understood. The SW86 isolate, collected from the Marayoor Sandalwood Reserve, was chosen for genome sequencing subsequent to confirming its titer and enriching phytoplasma DNA. Genome sequencing, utilizing Illumina and Oxford Nanopore Technology platforms, enabled a targeted hybrid metagenomic assembly resulting in 20 scaffolds totaling 554,025 bp, housing 436 protein-coding genes, 27 tRNA, and 1 rRNA operon. The genome analysis highlighted specific gene distributions, emphasizing translation, ribosomal structure, and biogenesis, with 352 genes assigned to 18 functional categories. Additionally, 322 proteins received functional assignments in the KEGG database, emphasizing 'Genetic Information Processing' and 'Environmental Information Processing'. Key potential pathogenicity factors, including signal peptide proteins and virulence proteins, were identified. Noteworthy findings include homologs of effectors genes like SAP11 and SAP05 and pathogenesis-related proteins, such as hemolysin III and SodA genes, in the SW86 genome. The duplicated cation-transporting P-type ATPase in the SW86 genome suggests a role in enhancing adaptability and contributing to the severity of SSD symptoms. This genome analysis provides crucial insights into the genomic features and potential virulence factors of 'Ca. Phytoplasma asteris' strain SW86, advancing our understanding of pathogenicity mechanisms and offering avenues for future disease management strategies in Indian sandalwood.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-024-03952-5.}, } @article {pmid38481663, year = {2024}, author = {Aardal, AM and Soltvedt, EM and Nørstebø, SF and Haverkamp, THA and Rodriguez-Campos, S and Skancke, E and Llarena, AK}, title = {Defining a metagenomic threshold for detecting low abundances of Providencia alcalifaciens in canine faecal samples.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1305742}, pmid = {38481663}, issn = {2235-2988}, abstract = {INTRODUCTION: Acute haemorrhagic diarrhoea syndrome (AHDS) in dogs is a condition of unknown aetiology. Providencia alcalifaciens is suspected to play a role in the disease as it was commonly found in dogs suffering from AHDS during a Norwegian outbreak in 2019. The role of this bacterium as a constituent of the canine gut microbiota is unknown, hence this study set out to investigate its occurrence in healthy dogs using metagenomics.

MATERIALS AND METHODS: To decrease the likelihood of false detection, we established a metagenomic threshold for P. alcalifaciens by spiking culture-negative stool samples with a range of bacterial dilutions and analysing these by qPCR and shotgun metagenomics. The detection limit for P. alcalifaciens was determined and used to establish a metagenomic threshold. The threshold was validated on naturally contaminated faecal samples with known cultivation status for P. alcalifaciens. Finally, the metagenomic threshold was used to determine the occurrence of P. alcalifaciens in shotgun metagenomic datasets from canine faecal samples (n=362) collected in the HUNT One Health project.

RESULTS: The metagenomic assay and qPCR had a detection limit of 1.1x10[3] CFU P. alcalifaciens per faecal sample, which corresponded to a Cq value of 31.4 and 569 unique k-mer counts by shotgun metagenomics. Applying this metagenomic threshold to 362 faecal metagenomic datasets from healthy dogs, P. alcalifaciens was found in only 1.1% (95% CI [0.0, 6.8]) of the samples, and then in low relative abundances (median: 0.04%; range: 0.00 to 0.81%). The sensitivity of the qPCR and shotgun metagenomics assay was low, as only 40% of culture-positive samples were also positive by qPCR and metagenomics.

DISCUSSION: Using our detection limit, the occurrence of P. alcalifaciens in faecal samples from healthy dogs was low. Given the low sensitivity of the metagenomic assay, these results do not rule out a significantly higher occurrence of this bacterium at a lower abundance.}, } @article {pmid38481578, year = {2024}, author = {Bi, L and He, JZ and Hu, HW}, title = {Total metagenomes outperform viromes in recovering viral diversity from sulfuric soils.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae017}, pmid = {38481578}, issn = {2730-6151}, abstract = {Recent metagenomic advancements have offered unprecedented insights into soil viral ecology. However, it remains a challenge to select the suitable metagenomic method for investigating soil viruses under different environmental conditions. Here, we assessed the performance of viral size-fraction metagenomes (viromes) and total metagenomes in capturing viral diversity from hypersulfidic soils with neutral pH and sulfuric soils with pH <3.3. Viromes effectively enhanced the sequencing coverage of viral genomes in both soil types. Viomes of hypersulfidic soils outperformed total metagenomes by recovering a significantly higher number of viral operational taxonomic units (vOTUs). However, total metagenomes of sulfuric soils recovered ~4.5 times more vOTUs than viromes on average. Altogether, our findings suggest that the choice between viromes and total metagenomes for studying soil viruses should be carefully considered based on the specific environmental conditions.}, } @article {pmid38481150, year = {2024}, author = {Yuan, L and Chen, Q and Zhu, XY and Lai, LM and Zhao, R and Liu, Y}, title = {Evaluation of clinical characteristics and risk factors associated with Chlamydia psittaci infection based on metagenomic next-generation sequencing.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {86}, pmid = {38481150}, issn = {1471-2180}, support = {GJJ200220//Science and Technology Project of Jiangxi Provincial Department of Education/ ; SKJP220212485//Science and Technology Plan of Jiangxi Provincial Health Commission/ ; jsxq2019201102//Double Thousand Plan of Jiangxi Province/ ; }, abstract = {INTRODUCTION: Psittacosis is a zoonosis caused by Chlamydia psittaci, the clinical manifestations of Psittacosis range from mild illness to fulminant severe pneumonia with multiple organ failure. This study aimed to evaluate the clinical characteristics of Chlamydia psittaci infection diagnosed based on metagenomic next-generation sequencing(mNGS), as well as the risk factors affecting the progress of Chlamydia psittaci infection, in order to improve the effect of therapeutics.

METHODS: We retrospectively analyzed the clinical data of patients infected with chlamydia psittaci in the First Affiliated Hospital of Nanchang University from January 2021 to December 2021. The patient's past medical history, clinical manifestations, laboratory examinations, chest CT results, treatment status, and prognosis data were collected. we also investigated both the pathogenic profile characteristics and the lower respiratory tract microbiota of patients with Chlamydia psittaci pneumonia using mNGS.

RESULTS: All cases of Chlamydia psittaci in our research have been confirmed by mNGS. Among 46 cases of Chlamydia psittaci pneumonia, Poultry exposure was reported in 35 cases. In severe cases of Chlamydia psittaci pneumonia, Neutrophils, Procalcitonin (PCT), Lactate Dehydrogenase (LDH), Hydroxybutyrate Dehydrogenase (HBDH), Creatine Kinase Isoenzymes-B (CK-MB) and D-Dimer levels were remarkably higher than that of non-severe cases, except for lymphocytes (all P < 0.05). Chest CT scans showed Bilateral (77.8%), multiple lobar lungs (85.2%), pleural effusions (44.4%) involvement in those suffering from severe Chlamydia psittaci pneumonia, whereas its incidence was 0%, 21.1% and 10.5% in non-severe patients, respectively (P < 0.05). Multivariate analysis revealed that higher lymphocyte concentrations (OR 0.836, 95% CI 0.714-0.962, P = 0.041) were the only protective factor for survival. mNGS results indicated that 41.3% of patients (19/46) had suspected coinfections with a coinfection rate of 84.2% (16/19) in the severe group, much higher than that in the non severe group (p < 0.05). No significantly different profiles of lower respiratory tract microbiota diversity were found between non severe group and severe group.

CONCLUSION: A history of poultry exposure in patients can serve as an important basis for diagnosing Chlamydia psittaci pneumonia, and patients with severe Chlamydia psittaci pneumonia are more likely to develop elevated inflammatory biomarkers as well as elevated cardiac markers. Higher lymphocyte concentrations are protective factors associated with severe C. psittaci pneumonia. The higher proportion of patients with coinfections in our study supports the use of mNGS for comprehensive early detection of respiratory infections in patients with C. psittaci pneumonia.}, } @article {pmid38481149, year = {2024}, author = {Han, J and Liang, L and Li, Q and Deng, R and Liu, C and Wu, X and Zhang, Y and Zhang, R and Dai, H}, title = {Diagnosis of pulmonary Scedosporium apiospermum infection from bronchoalveolar lavage fluid by metagenomic next-generation sequencing in an immunocompetent female patient with normal lung structure: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {308}, pmid = {38481149}, issn = {1471-2334}, abstract = {BACKGROUND: Scedosporium apiospermum (S. apiospermum) belongs to the asexual form of Pseudallescheria boydii and is widely distributed in various environments. S. apiospermum is the most common cause of pulmonary infection; however, invasive diseases are usually limited to patients with immunodeficiency.

CASE PRESENTATION: A 54-year-old Chinese non-smoker female patient with normal lung structure and function was diagnosed with pulmonary S. apiospermum infection by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF). The patient was admitted to the hospital after experiencing intermittent right chest pain for 8 months. Chest computed tomography revealed a thick-walled cavity in the upper lobe of the right lung with mild soft tissue enhancement. S. apiospermum was detected by the mNGS of BALF, and DNA sequencing reads were 426. Following treatment with voriconazole (300 mg q12h d1; 200 mg q12h d2-d20), there was no improvement in chest imaging, and a thoracoscopic right upper lobectomy was performed. Postoperative pathological results observed silver staining and PAS-positive oval spores in the alveolar septum, bronchiolar wall, and alveolar cavity, and fungal infection was considered. The patient's symptoms improved; the patient continued voriconazole for 2 months after surgery. No signs of radiological progression or recurrence were observed at the 10-month postoperative follow-up.

CONCLUSION: This case report indicates that S. apiospermum infection can occur in immunocompetent individuals and that the mNGS of BALF can assist in its diagnosis and treatment. Additionally, the combined therapy of antifungal drugs and surgery exhibits a potent effect on the disease.}, } @article {pmid38480867, year = {2024}, author = {Fronton, F and Villemur, R and Robert, D and St-Pierre, Y}, title = {Divergent bacterial landscapes: unraveling geographically driven microbiomes in Atlantic cod.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6088}, pmid = {38480867}, issn = {2045-2322}, abstract = {Establishing microbiome signatures is now recognized as a critical step toward identifying genetic and environmental factors shaping animal-associated microbiomes and informing the health status of a given host. In the present work, we prospectively collected 63 blood samples of the Atlantic cod population of the Southern Gulf of Saint Lawrence (GSL) and characterized their 16S rRNA circulating microbiome signature. Our results revealed that the blood microbiome signature was dominated at the phylum level by Proteobacteria, Bacteroidetes, Acidobacteria and Actinobacteria, a typical signature for fish populations inhabiting the GSL and other marine ecosystems. At the genus level, however, we identified two distinct cod groups. While the microbiome signature of the first group was dominated by Pseudoalteromonas, a genus we previously found in the microbiome signature of Greenland and Atlantic halibut populations of the GSL, the second group had a microbiome signature dominated by Nitrobacter and Sediminibacterium (approximately 75% of the circulating microbiome). Cods harboring a Nitrobacter/Sediminibacterium-rich microbiome signature were localized in the most southern part of the GSL, just along the northern coast of Cape Breton Island. Atlantic cod microbiome signatures did not correlate with the weight, length, relative condition, depth, temperature, sex, and salinity, as previously observed in the halibut populations. Our study provides, for the first time, a unique snapshot of the circulating microbiome signature of Atlantic cod populations and the potential existence of dysbiotic signatures associated with the geographical distribution of the population, probably linked with the presence of nitrite in the environment.}, } @article {pmid38480864, year = {2024}, author = {Sato, Y and Sato, R and Fukui, E and Yoshizawa, F}, title = {Impact of rumen microbiome on cattle carcass traits.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {6064}, pmid = {38480864}, issn = {2045-2322}, support = {22K20608//Japan Society for the Promotion of Science/ ; }, abstract = {Rumen microbes are crucial in the anaerobic fermentation of plant polysaccharides to produce volatile fatty acids. However, limited information exists about the specific microbial species and strains in the rumen that affect carcass traits, and it is unclear whether there is a relationship between rumen metabolic functions and these traits. This study investigated the relationship between the rumen microbiome and carcass traits in beef cattle using 16S rRNA amplicon and shotgun sequencing. Metagenomic sequencing was used to compare the rumen microbiome between high-carcass weight (HW) and low-carcass weight (LW) cattle, and high-marbling (HM) and low-marbling (LM) cattle. Prokaryotic communities in the rumen of HW vs. LW and HM vs. LM were separated using 16S rRNA amplicon sequencing. Notably, shotgun metagenomic sequencing revealed that HW cattle had more methane-producing bacteria and ciliate protozoa, suggesting higher methane emissions. Additionally, variations were observed in the abundances of certain glycoside hydrolases and polysaccharide lyases involved in the ruminal degradation of plant polysaccharides between HW and LW. From our metagenome dataset, 807 non-redundant metagenome-assembled genomes (MAGs) of medium to high quality were obtained. Among these, 309 and 113 MAGs were associated with carcass weight and marbling, respectively.}, } @article {pmid38477684, year = {2024}, author = {Alicehajic, A and Duivenvoorden, AAM and Lenaerts, K}, title = {Unveiling the molecular complexity of intestinal ischemia-reperfusion injury through omics technologies.}, journal = {Proteomics}, volume = {}, number = {}, pages = {e2300160}, doi = {10.1002/pmic.202300160}, pmid = {38477684}, issn = {1615-9861}, abstract = {Intestinal ischemia-reperfusion injury (IR) is implicated in various clinical conditions and causes damage to the intestinal epithelium resulting in intestinal barrier loss. This presents a substantial clinical challenge, emphasizing the importance of gaining a comprehensive understanding of molecular events to aid in the identification of novel therapeutic targets. This review systematically explores the extent to which omics technologies-transcriptomics, proteomics, metabolomics, and metagenomics-have already contributed to deciphering the molecular mechanisms contributing to intestinal IR injury, in in vivo and in vitro animal and human models, and in clinical samples. Recent breakthroughs involve applying omics methodologies on exosomes, organoids, and single cells, shedding light on promising avenues and valuable targets to reduce intestinal IR injury. Future directions aimed at expediting clinical translation are discussed as well and include multi-omics data integration to facilitate the identification of key regulatory nodes driving intestinal IR injury and advancing human organoid models based on the novel insights by single-cell omics technologies, offering hope for clinical application of therapeutic strategies in the years to come.}, } @article {pmid38476947, year = {2024}, author = {Bandara, AY and Kang, S}, title = {Trichoderma application methods differentially affect the tomato growth, rhizomicrobiome, and rhizosphere soil suppressiveness against Fusarium oxysporum.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1366690}, pmid = {38476947}, issn = {1664-302X}, abstract = {Trichoderma spp. are widely used to enhance crop growth and suppress diverse diseases. However, inconsistent field efficacy remains a major barrier to their use as a reliable alternative to synthetic pesticides. Various strategies have been investigated to enhance the robustness of their application. Here, we evaluated how T. virens application methods (pre-, at-, and post-transplant) affect the growth of two tomato varieties and their rhizosphere fungal and bacterial communities. Although the greatest rhizosphere abundance of T. virens was observed in the post-transplant application, the at-transplant application promoted tomato growth the most, indicating that greater rhizosphere abundance does not necessarily result in better tomato growth. None of the application methods significantly altered the global rhizosphere fungal and bacterial communities of the tested varieties. Changes in specific microbial genera and guilds may underpin the enhanced tomato growth. We also investigated whether the resulting microbiome changes affect the mycelial growth and conidial germination of Fusarium oxysporum f. sp. lycopersici and F. oxysporum f. sp. radicis-lycopersici, soilborne fungal pathogens of tomato, upon exposure to volatile compounds emitted by culturable rhizosphere microbes and metabolites extracted from the rhizosphere soils after Trichoderma treatments. Volatile compounds produced by cultured rhizosphere microbes after the at-transplant application suppressed the mycelial growth of both pathogens better than those after the other treatments. Similarly, water-soluble metabolites extracted from the rhizosphere soil samples after the at-transplant application most effectively suppressed the germination rate of F. oxysporum spores. Overall, our results suggest that the at-transplant application is most advantageous for promoting the growth of the tested tomato varieties and building soil suppressiveness against the tested fusaria. However, further studies are needed before applying this method to support tomato production. We discuss critical future questions.}, } @article {pmid38062703, year = {2024}, author = {Xie, L and Wu, D and Fang, Y and Ye, C and Zhu, QH and Wei, X and Fan, L}, title = {Population genomic analysis unravels the evolutionary roadmap of pericarp color in rice.}, journal = {Plant communications}, volume = {5}, number = {3}, pages = {100778}, doi = {10.1016/j.xplc.2023.100778}, pmid = {38062703}, issn = {2590-3462}, mesh = {*Genes, Plant ; Genetic Variation ; *Oryza/genetics ; Genome-Wide Association Study ; Metagenomics ; Evolution, Molecular ; Sequence Analysis, DNA ; Genomics ; }, abstract = {Pigmented rice stands out for its nutritional value and is gaining more and more attention. Wild rice, domesticated red rice, and weedy rice all have a red pericarp and a comprehensive genetic background in terms of the red-pericarp phenotype. We performed population genetic analyses using 5104 worldwide rice accessions, including 2794 accessions with red or black pericarps, 85 of which were newly sequenced in this study. The results suggested an evolutionary trajectory of red landraces originating from wild rice, and the split times of cultivated red and white rice populations were estimated to be within the past 3500 years. Cultivated red rice was found to feralize to weedy rice, and weedy rice could be further re-domesticated to cultivated red rice. A genome-wide association study based on the 2794 accessions with pigmented pericarps revealed several new candidate genes associated with the red-pericarp trait for further functional characterization. Our results provide genomic evidence for the origin of pigmented rice and a valuable genomic resource for genetic investigation and breeding of pigmented rice.}, } @article {pmid38476940, year = {2024}, author = {Buendia, P and Fernandez, K and Raley, C and Rahnavard, A and Crandall, KA and Castro, JG}, title = {Hospital antimicrobial stewardship: profiling the oral microbiome after exposure to COVID-19 and antibiotics.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1346762}, pmid = {38476940}, issn = {1664-302X}, abstract = {INTRODUCTION: During the COVID-19 Delta variant surge, the CLAIRE cross-sectional study sampled saliva from 120 hospitalized patients, 116 of whom had a positive COVID-19 PCR test. Patients received antibiotics upon admission due to possible secondary bacterial infections, with patients at risk of sepsis receiving broad-spectrum antibiotics (BSA).

METHODS: The saliva samples were analyzed with shotgun DNA metagenomics and respiratory RNA virome sequencing. Medical records for the period of hospitalization were obtained for all patients. Once hospitalization outcomes were known, patients were classified based on their COVID-19 disease severity and the antibiotics they received.

RESULTS: Our study reveals that BSA regimens differentially impacted the human salivary microbiome and disease progression. 12 patients died and all of them received BSA. Significant associations were found between the composition of the COVID-19 saliva microbiome and BSA use, between SARS-CoV-2 genome coverage and severity of disease. We also found significant associations between the non-bacterial microbiome and severity of disease, with Candida albicans detected most frequently in critical patients. For patients who did not receive BSA before saliva sampling, our study suggests Staphylococcus aureus as a potential risk factor for sepsis.

DISCUSSION: Our results indicate that the course of the infection may be explained by both monitoring antibiotic treatment and profiling a patient's salivary microbiome, establishing a compelling link between microbiome and the specific antibiotic type and timing of treatment. This approach can aid with emergency room triage and inpatient management but also requires a better understanding of and access to narrow-spectrum agents that target pathogenic bacteria.}, } @article {pmid38476920, year = {2024}, author = {Jiang, J and Dai, J and Hu, X and Yao, X and Mo, W and Wang, H}, title = {Type B3 thymoma complicated with Chlamydia psittaci pneumonia with rare features: A case report.}, journal = {Experimental and therapeutic medicine}, volume = {27}, number = {4}, pages = {153}, pmid = {38476920}, issn = {1792-1015}, abstract = {The case of a patient with type B3 thymomacomorbid with Chlamydia psittaci (C. psittaci) pneumonia exhibiting rare features is presented in the current report. The patient was admitted at the Second Affiliated Hospital of Jiaxing University (Jiaxing, China) with a history of direct contact with poultry. Clinical manifestations included fever, shivers, cough, fatigue and poor appetite. Chest computed tomography (CT) indicated right lung pneumonia, while metagenomics next-generation sequencing using bronchoalveolar lavage fluid confirmed infection with C. psittaci. Additionally, positron emission tomography-CT suggested the presence of thymoma. After surgery and treatment with doxycycline and imipenem cilastatin, the patient was discharged showing signs of improvement.}, } @article {pmid38476447, year = {2024}, author = {Guo, Z and Zuo, A and Liu, X and Jiang, Y and Yang, S and Lu, D}, title = {Multiple pulmonary cavities in an immunocompetent patient: a case report and literature review.}, journal = {Frontiers in medicine}, volume = {11}, number = {}, pages = {1329381}, pmid = {38476447}, issn = {2296-858X}, abstract = {Legionella pneumonia (LP) is a relatively uncommon yet well-known type of atypical community-acquired pneumonia (CAP). It is characterized by a rapid progression to severe pneumonia and can be easily misdiagnosed. In most patients, chest computed tomography (CT) showed patchy infiltration, which may progress to lobar infiltration or even lobar consolidation. While pulmonary cavities are commonly observed in immunocompromised patients with LP, they are considered rare in immunocompetent individuals. Herein, we present a case of LP in an immunocompetent patient with multiple cavities in both lungs. Pathogen detection was performed using metagenomic next-generation sequencing (mNGS). This case highlights the unusual radiographic presentation of LP in an immunocompetent patient and emphasizes the importance of considering LP as a possible diagnosis in patients with pulmonary cavities, regardless of their immune status. Furthermore, the timely utilization of mNGS is crucial for early pathogen identification, as it provides multiple benefits in enhancing the diagnosis and prognosis of LP patients.}, } @article {pmid38476299, year = {2024}, author = {Xu, S and Morgan, DC and Qian, G and Huang, Y and Ho, JWK}, title = {MetaQuad: shared informative variants discovery in metagenomic samples.}, journal = {Bioinformatics advances}, volume = {4}, number = {1}, pages = {vbae030}, pmid = {38476299}, issn = {2635-0041}, abstract = {MOTIVATION: Strain-level analysis of metagenomic data has garnered significant interest in recent years. Microbial single nucleotide polymorphisms (SNPs) are genomic variants that can reflect strain-level differences within a microbial species. The diversity and emergence of SNPs in microbial genomes may reveal evolutionary history and environmental adaptation in microbial populations. However, efficient discovery of shared polymorphic variants in a large collection metagenomic samples remains a computational challenge.

RESULTS: MetaQuad utilizes a density-based clustering technique to effectively distinguish between shared variants and non-polymorphic sites using shotgun metagenomic data. Empirical comparisons with other state-of-the-art methods show that MetaQuad significantly reduces the number of false positive SNPs without greatly affecting the true positive rate. We used MetaQuad to identify antibiotic-associated variants in patients who underwent Helicobacter pylori eradication therapy. MetaQuad detected 7591 variants across 529 antibiotic resistance genes. The nucleotide diversity of some genes is increased 6 weeks after antibiotic treatment, potentially indicating the role of these genes in specific antibiotic treatments.

MetaQuad is an open-source Python package available via https://github.com/holab-hku/MetaQuad.}, } @article {pmid38476164, year = {2024}, author = {Kumar, V and Roy, S and Parida, SN and Bisai, K and Dhar, S and Jana, AK and Das, BK}, title = {Deciphering the impact of endoparasitic infection on immune response and gut microbial composition of Channa punctata.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1296769}, pmid = {38476164}, issn = {2235-2988}, abstract = {Intestinal parasitic infections caused by helminths are globally distributed and are a major cause of morbidity worldwide. Parasites may modulate the virulence, gut microbiota diversity and host responses during infection. Despite numerous works, little is known about the complex interaction between parasites and the gut microbiota. In the present study, the complex interplay between parasites and the gut microbiota was investigated. A total of 12 bacterial strains across four major families, including Enterobacteriaceae, Morganellaceae, Flavobacteriaceae, and Pseudomonadaceae, were isolated from Channa punctata, infected with the nematode species Aporcella sp., Axonchium sp., Tylencholaimus mirabilis, and Dioctophyme renale. The findings revealed that nematode infection shaped the fish gut bacterial microbiota and significantly affected their virulence levels. Nematode-infected fish bacterial isolates are more likely to be pathogenic, with elevated hemolytic activity and biofilm formation, causing high fish mortality. In contrast, isolates recovered further from non-parasitised C. punctata were observed to be non-pathogenic and had negligible hemolytic activity and biofilm formation. Antibiogram analysis of the bacterial isolates revealed a disproportionately high percentage of bacteria that were either marginally or multidrug resistant, suggesting that parasitic infection-induced stress modulates the gut microenvironment and enables colonization by antibiotic-resistant strains. This isolation-based study provides an avenue to unravel the influence of parasitic infection on gut bacterial characteristics, which is valuable for understanding the infection mechanism and designing further studies aimed at optimizing treatment strategies. In addition, the cultured isolates can supplement future gut microbiome studies by providing wet lab specimens to compare (meta)genomic information discovered within the gut microenvironment of fish.}, } @article {pmid38475926, year = {2024}, author = {Suarez, C and Rosenqvist, T and Dimitrova, I and Sedlacek, CJ and Modin, O and Paul, CJ and Hermansson, M and Persson, F}, title = {Biofilm colonization and succession in a full-scale partial nitritation-anammox moving bed biofilm reactor.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {51}, pmid = {38475926}, issn = {2049-2618}, support = {2018-01423//Svenska Forskningsrådet Formas/ ; 2019-00432//Svenska Forskningsrådet Formas/ ; 2019-00432//Svenska Forskningsrådet Formas/ ; 2018-01423//Svenska Forskningsrådet Formas/ ; 2020-01905//Svenska Forskningsrådet Formas/ ; ZK74//Austrian Science Fund/ ; }, abstract = {BACKGROUND: Partial nitritation-anammox (PNA) is a biological nitrogen removal process commonly used in wastewater treatment plants for the treatment of warm and nitrogen-rich sludge liquor from anaerobic digestion, often referred to as sidestream wastewater. In these systems, biofilms are frequently used to retain biomass with aerobic ammonia-oxidizing bacteria (AOB) and anammox bacteria, which together convert ammonium to nitrogen gas. Little is known about how these biofilm communities develop, and whether knowledge about the assembly of biofilms in natural communities can be applied to PNA biofilms.

RESULTS: We followed the start-up of a full-scale PNA moving bed biofilm reactor for 175 days using shotgun metagenomics. Environmental filtering likely restricted initial biofilm colonization, resulting in low phylogenetic diversity, with the initial microbial community comprised mainly of Proteobacteria. Facilitative priority effects allowed further biofilm colonization, with the growth of initial aerobic colonizers promoting the arrival and growth of anaerobic taxa like methanogens and anammox bacteria. Among the early colonizers were known 'oligotrophic' ammonia oxidizers including comammox Nitrospira and Nitrosomonas cluster 6a AOB. Increasing the nitrogen load in the bioreactor allowed colonization by 'copiotrophic' Nitrosomonas cluster 7 AOB and resulted in the exclusion of the initial ammonia- and nitrite oxidizers.

CONCLUSIONS: We show that complex dynamic processes occur in PNA microbial communities before a stable bioreactor process is achieved. The results of this study not only contribute to our knowledge about biofilm assembly and PNA bioreactor start-up but could also help guide strategies for the successful implementation of PNA bioreactors. Video Abstract.}, } @article {pmid38475541, year = {2024}, author = {Hathurusinghe, SHK and Azizoglu, U and Shin, JH}, title = {Holistic Approaches to Plant Stress Alleviation: A Comprehensive Review of the Role of Organic Compounds and Beneficial Bacteria in Promoting Growth and Health.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {5}, pages = {}, doi = {10.3390/plants13050695}, pmid = {38475541}, issn = {2223-7747}, support = {2021R1A6C101A416//Korea Basic Science Institute/ ; }, abstract = {Plants select microorganisms from the surrounding bulk soil, which act as a reservoir of microbial diversity and enrich a rhizosphere microbiome that helps in growth and stress alleviation. Plants use organic compounds that are released through root exudates to shape the rhizosphere microbiome. These organic compounds are of various spectrums and technically gear the interplay between plants and the microbial world. Although plants naturally produce organic compounds that influence the microbial world, numerous efforts have been made to boost the efficiency of the microbiome through the addition of organic compounds. Despite further crucial investigations, synergistic effects from organic compounds and beneficial bacteria combinations have been reported. In this review, we examine the relationship between organic compounds and beneficial bacteria in determining plant growth and biotic and abiotic stress alleviation. We investigate the molecular mechanism and biochemical responses of bacteria to organic compounds, and we discuss the plant growth modifications and stress alleviation done with the help of beneficial bacteria. We then exhibit the synergistic effects of both components to highlight future research directions to dwell on how microbial engineering and metagenomic approaches could be utilized to enhance the use of beneficial microbes and organic compounds.}, } @article {pmid38474789, year = {2024}, author = {Fernandez-Sanjurjo, M and Fernandez, J and Martinez-Camblor, P and Rodriguez-Alonso, M and Ortolano-Rios, R and Pinto-Hernandez, P and Castilla-Silgado, J and Coto-Vilcapoma, A and Ruiz, L and Villar, CJ and Tomas-Zapico, C and Margolles, A and Fernandez-Garcia, B and Iglesias-Gutierrez, E and Lombó, F}, title = {Dynamics of Gut Microbiota and Short-Chain Fatty Acids during a Cycling Grand Tour Are Related to Exercise Performance and Modulated by Dietary Intake.}, journal = {Nutrients}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/nu16050661}, pmid = {38474789}, issn = {2072-6643}, support = {AYUD/2021/51347//Foundation for the Promotion of Applied Scientific Research and Technology in Asturias/ ; PID2021-127812OB-I00//Ministerio de Ciencia e Innovación/ ; RTI2018-095021-J-I00//Agencia Estatal de Investigación/ ; }, abstract = {BACKGROUND: Regular exercise has been described to modify both the diversity and the relative abundance of certain bacterial taxa. To our knowledge, the effect of a cycling stage race, which entails extreme physiological and metabolic demands, on the gut microbiota composition and its metabolic activity has not been analysed.

OBJECTIVE: The aim of this cohort study was to analyse the dynamics of faecal microbiota composition and short-chain fatty acids (SCFAs) content of professional cyclists over a Grand Tour and their relationship with performance and dietary intake.

METHODS: 16 professional cyclists competing in La Vuelta 2019 were recruited. Faecal samples were collected at four time points: the day before the first stage (A); after 9 stages (B); after 15 stages (C); and on the last stage (D). Faecal microbiota populations and SCFA content were analysed using 16S rRNA sequencing and gas chromatography, respectively. A principal component analysis (PCA) followed by Generalised Estimating Equation (GEE) models were carried out to explore the dynamics of microbiota and SCFAs and their relationship with performance.

RESULTS: Bifidobacteriaceae, Coriobacteriaceae, Erysipelotrichaceae, and Sutterellaceae dynamics showed a strong final performance predictive value (r = 0.83, ranking, and r = 0.81, accumulated time). Positive correlations were observed between Coriobacteriaceae with acetate (r = 0.530) and isovalerate (r = 0.664) and between Bifidobacteriaceae with isobutyrate (r = 0.682). No relationship was observed between SCFAs and performance. The abundance of Erysipelotrichaceae at the beginning of La Vuelta was directly related to the previous intake of complex-carbohydrate-rich foods (r = 0.956), while during the competition, the abundance of Bifidobacteriaceae was negatively affected by the intake of simple carbohydrates from supplements (r = -0.650).

CONCLUSIONS: An ecological perspective represents more realistically the relationship between gut microbiota composition and performance compared to single-taxon approaches. The composition and periodisation of diet and supplementation during a Grand Tour, particularly carbohydrates, could be designed to modulate gut microbiota composition to allow better performance.}, } @article {pmid38474715, year = {2024}, author = {Mellai, M and Allesina, M and Edoardo, B and Cascella, F and Nobile, V and Spina, A and Amone, F and Zaccaria, V and Insolia, V and Perri, A and Lofaro, D and Puoci, F}, title = {A Randomized, Double-Blind, Placebo-Controlled Trial: Efficacy of Opuntia ficus-indica Prebiotic Supplementation in Subjects with Gut Dysbiosis.}, journal = {Nutrients}, volume = {16}, number = {5}, pages = {}, doi = {10.3390/nu16050586}, pmid = {38474715}, issn = {2072-6643}, support = {0002559/2021 Rev.02 by 08/04/2022//Bionap S.r.l./ ; }, abstract = {Gut dysbiosis refers to an imbalance in gut microbiota composition and function. Opuntia ficus-indica extract has been shown to modulate gut microbiota by improving SCFA production in vivo and gastrointestinal discomfort (GD) in humans. The aim of this study was to demonstrate the efficacy of Odilia[TM] on gastrointestinal health by changing the microbial diversity of species involved in inflammation, immunity, oxidation, and the brain-gut-muscle axis. A randomized, double-blind clinical trial was conducted in 80 adults with gut dysbiosis. The intervention consisted of a 300 mg daily intake of Odilia[TM] (n = 40) or maltodextrin as a placebo (n = 40), administered for 8 weeks. Intervention effect was evaluated using 16S metagenomics and GIQLI/GSAS scores at baseline, at 4 and 8 weeks. Eight weeks of Odilia[TM] supplementation positively modulates gut microbiota composition with a significant reduction in the Firmicutes to Bacteroidetes ratio (p = 0.0012). Relative abundances of beneficial bacteria (Bacteroides and Clostridium_XIVa) were significantly increased (p < 0.001), in contrast to a significant reduction in pro-inflammatory bacteria (p < 0.001). Accordingly, GIQLI and GSAS scores revealed successful improvement in GD. Odilia[TM] may represent an effective and well-tolerated treatment in subjects with gut dysbiosis.}, } @article {pmid38474529, year = {2024}, author = {Zhu, Q and Huang, Y and Yang, Z and Wu, X and Zhu, Q and Zheng, H and Zhu, D and Lv, Z and Yin, Y}, title = {A Recombinant Thermophilic and Glucose-Tolerant GH1 β-Glucosidase Derived from Hehua Hot Spring.}, journal = {Molecules (Basel, Switzerland)}, volume = {29}, number = {5}, pages = {}, doi = {10.3390/molecules29051017}, pmid = {38474529}, issn = {1420-3049}, support = {202101AU070138//Yunnan Applied Basic Research Project/ ; KY2126109940//Cangshan Comprehensive Scientific Investigation in Dali (Phase II)/ ; 202305AM070003//Foundation of Yunnan Province Science and Technology Department/ ; }, abstract = {As a crucial enzyme for cellulose degradation, β-glucosidase finds extensive applications in food, feed, and bioethanol production; however, its potential is often limited by inadequate thermal stability and glucose tolerance. In this study, a functional gene (lq-bg5) for a GH1 family β-glucosidase was obtained from the metagenomic DNA of a hot spring sediment sample and heterologously expressed in E. coli and the recombinant enzyme was purified and characterized. The optimal temperature and pH of LQ-BG5 were 55 °C and 4.6, respectively. The relative residual activity of LQ-BG5 exceeded 90% at 55 °C for 9 h and 60 °C for 6 h and remained above 100% after incubation at pH 5.0-10.0 for 12 h. More importantly, LQ-BG5 demonstrated exceptional glucose tolerance with more than 40% activity remaining even at high glucose concentrations of 3000 mM. Thus, LQ-BG5 represents a thermophilic β-glucosidase exhibiting excellent thermal stability and remarkable glucose tolerance, making it highly promising for lignocellulose development and utilization.}, } @article {pmid38473829, year = {2024}, author = {Ng, HY and Liao, Y and Zhang, R and Chan, KH and To, WP and Hui, CH and Seto, WK and Leung, WK and Hung, IFN and Lam, TTY and Cheung, KS}, title = {The Predictive Value of Gut Microbiota Composition for Sustained Immunogenicity following Two Doses of CoronaVac.}, journal = {International journal of molecular sciences}, volume = {25}, number = {5}, pages = {}, doi = {10.3390/ijms25052583}, pmid = {38473829}, issn = {1422-0067}, support = {COVID1903010, Project 16//Health and Medical Research Fund, Food and Health Bureau, The Government of the Hong Kong Special Administrative Region/ ; D24H, C2i//InnoHK funding from the Innovation and Technology Commission/ ; }, abstract = {CoronaVac immunogenicity decreases with time, and we aimed to investigate whether gut microbiota associate with longer-term immunogenicity of CoronaVac. This was a prospective cohort study recruiting two-dose CoronaVac recipients from three centres in Hong Kong. We collected blood samples at baseline and day 180 after the first dose and used chemiluminescence immunoassay to test for neutralizing antibodies (NAbs) against the receptor-binding domain (RBD) of wild-type SARS-CoV-2 virus. We performed shotgun metagenomic sequencing performed on baseline stool samples. The primary outcome was the NAb seroconversion rate (seropositivity defined as NAb ≥ 15AU/mL) at day 180. Linear discriminant analysis [LDA] effect size analysis was used to identify putative bacterial species and metabolic pathways. A univariate logistic regression model was used to derive the odds ratio (OR) of seropositivity with bacterial species. Of 119 CoronaVac recipients (median age: 53.4 years [IQR: 47.8-61.3]; male: 39 [32.8%]), only 8 (6.7%) remained seropositive at 6 months after vaccination. Bacteroides uniformis (log10LDA score = 4.39) and Bacteroides eggerthii (log10LDA score = 3.89) were significantly enriched in seropositive than seronegative participants. Seropositivity was associated with B. eggerthii (OR: 5.73; 95% CI: 1.32-29.55; p = 0.022) and B. uniformis with borderline significance (OR: 3.27; 95% CI: 0.73-14.72; p = 0.110). Additionally, B. uniformis was positively correlated with most enriched metabolic pathways in seropositive vaccinees, including the superpathway of adenosine nucleotide de novo biosynthesis I (log10LDA score = 2.88) and II (log10LDA score = 2.91), as well as pathways related to vitamin B biosynthesis, all of which are known to promote immune functions. In conclusion, certain gut bacterial species (B. eggerthii and B. uniformis) and metabolic pathways were associated with longer-term CoronaVac immunogenicity.}, } @article {pmid38473117, year = {2024}, author = {Tavera Gonzales, A and Bazalar Gonzales, J and Silvestre Espejo, T and Leiva Galarza, M and Rodríguez Cueva, C and Carhuaricra Huamán, D and Luna Espinoza, L and Maturrano Hernández, A}, title = {Possible Spreading of SARS-CoV-2 from Humans to Captive Non-Human Primates in the Peruvian Amazon.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {5}, pages = {}, doi = {10.3390/ani14050732}, pmid = {38473117}, issn = {2076-2615}, support = {076-2021-FONDECYT.//Consejo Nacional de Ciencia, Tecnología e Innovación Tecnológica/ ; }, abstract = {Human-to-animal transmission events of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) have been reported in both domestic and wild species worldwide. Despite the high rates of contagion and mortality during the COVID-19 (Coronavirus Diseases 2019) pandemic in Peru, no instances of natural virus infection have been documented in wild animals, particularly in the Amazonian regions where human-wildlife interactions are prevalent. In this study, we conducted a surveillance investigation using viral RNA sequencing of fecal samples collected from 76 captive and semi-captive non-human primates (NHPs) in the Loreto, Ucayali, and Madre de Dios regions between August 2022 and February 2023. We detected a segment of the RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2 by metagenomic sequencing in a pooled fecal sample from captive white-fronted capuchins (Cebus unicolor) at a rescue center in Bello Horizonte, Ucayali. Phylogenetic analysis further confirmed that the retrieved partial sequence of the RdRp gene matched the SARS-CoV-2 genome. This study represents the first documented instance of molecular SARS-CoV-2 detection in NHPs in the Peruvian Amazon, underscoring the adverse impact of anthropic activities on the human-NHP interface and emphasizing the importance of ongoing surveillance for early detection and prediction of future emergence of new SARS-CoV-2 variants in animals.}, } @article {pmid38472519, year = {2024}, author = {Aubry, A and Corvilain, E and Ghelfenstein-Ferreira, T and Camelena, F and Meignin, V and Berçot, B and Le Goff, J and Salmona, M}, title = {Unmasking Bartonella henselae infection in the shadows of long COVID thanks to clinical metagenomics.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {38472519}, issn = {1435-4373}, abstract = {The diagnosis of long COVID often relies on symptoms post-COVID-19, occasionally lacking biological evidence. This case study illustrates how investigating long COVID uncovered an underlying bartonellosis through clinical metagenomics. Following mild COVID-19, a 26-year-old woman experienced persistent symptoms during 5 months, including axillary adenopathy. Pathological examination, 16 S rRNA PCR, and clinical metagenomic analysis were done on an adenopathy biopsy. The latter revealed Bartonella henselae DNA and RNA. Treatment with clarithromycin improved symptoms. This case underscores the relevance of clinical metagenomics in diagnosing hidden infections. Post-COVID symptoms warrant thorough investigation, and bartonellosis should be considered in polyadenopathy cases, regardless of a recent history of cat or flea exposures.}, } @article {pmid38471894, year = {2024}, author = {Li, YT and Yu, H and Liu, K and Bai, HC and Wang, J and Zhu, ZJ}, title = {[Microbial Mechanisms of Removal of Phthalic Acid Esters in Purple Soils Revealed Using Metagenomic Analysis].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {45}, number = {3}, pages = {1830-1839}, doi = {10.13227/j.hjkx.202303127}, pmid = {38471894}, issn = {0250-3301}, abstract = {The removal mechanisms of phthalic acid esters (PAEs) have attracted much attention because of their endocrine-disrupting properties and persistence in environmental media. In order to reveal the removal mechanism of PAEs and involved keystone taxa and functional genes, purple soils were polluted by di-n-butyl phthalate (DBP) and di-2-ethylhexyl phthalate (DEHP), respectively, along a gradient of 0, 5, 10, and 20 mg·kg[-1] and cultured for 90 days in the dark. The results showed that the degradation dynamics of DBP and DEHP were well-fitted by the first-order kinetic model, and the half-life of DBP and DEHP ranged from 17.0 to 38.2 days. The degradation rate of DBP (5 mg·kg[-1]) was the fastest, and that of DEHP (20 mg·kg[-1]) was the slowest. The soil samples of the seventh day and the fifteenth day were analyzed using metagenomic sequencing. NMDS and cluster analysis showed that there was a significant difference between the bacterial community structure of soil samples from the seventh day and the fifteenth day. The relative abundance of Actinobacteria increased from the seventh day to the fifteenth day. The smaller the half-life of DBP or DEHP, the higher the relative abundance of Actinobacteria in the different treatments. In addition, Streptomyces was the dominant genus in all polluted soils. Co-occurrence network analysis elucidated that Pandoraea was a keystone genus of the soil bacterial communities, which could be used to indicate the pollution levels of DBP and DEHP. The results of KEGG annotation demonstrated that Pandoraea was responsible for benzoate degradation, quorum sensing, ABC transporters, and the two-component system and could promote the intercellular communications and the microbial growth and proliferation and maintain the stability of the community structure. Therefore, the degradation rate of DBP and DEHP in purple soils depended on their initial content and their own properties. Actinobacteria played an important role in the PAEs degradation, and Pandoraea played a major part in promoting PAEs degradation and regulating the stability of the structure and function of degrading bacterial communities.}, } @article {pmid38471893, year = {2024}, author = {Li, CL and Zhang, F and Wang, LD and Zhao, HR and Zhao, XC and Zhang, HP}, title = {[Soil Microbial Community Structure and Functional Diversity Character of Abandoned Farmland in Minqin Oasis].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {45}, number = {3}, pages = {1821-1829}, doi = {10.13227/j.hjkx.202305174}, pmid = {38471893}, issn = {0250-3301}, abstract = {To clarify the impact of the structure and function of soil microbial communities in the stage of abandoned farmland, three different stages of land abandoned in desert oasis areas were selected as the research objects. We used metagenomic sequencing technology to research soil microbial community structure and functional diversity characteristics of different stages of abandoned farmland. The results showed that there were significant differences in the relative abundance of the dominant phyla Actinobacteria, Proteobacteria, and Gemmatimonadetes in the soil of the three stages of returning farmland. Compared with that in the early stage of abandoned farmland, the later stage of abandoned farmland restoration increased the gene proportion involved in Quorum sensing, porphyrin and chlorophyll metabolism, pantothenate and CoA biosynthesis, and styrene degradation, and there was a significant difference in relative abundance (P<0.05), which indicated that different stages of abandoned farmland had changed the functional potential of the nutrient cycle and energy metabolism in soil microbial communities. The RDA results showed that EC, AK, and TN had a significant impact on the functional composition of soil microbes, and soil EC had the greatest impact on microbial functional composition. The results showed that different stages of abandoned farmland had a significant impact on the soil microbial community structure and functional composition. In the ecological restoration of abandoned farmland in Minqin Oasis, the sensitivity of microbial community structure and functional composition to soil restoration at different stages should be considered using comprehensive relevant indicators.}, } @article {pmid38471631, year = {2024}, author = {Yin, M and Wu, Y and Li, D and Zhang, Y and Bian, X and Li, J and Pei, Y and Cui, Y and Li, J}, title = {Non-filamentous bulking of activated sludge induced by graphene oxide: Insights from extracellular polymeric substances.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {130574}, doi = {10.1016/j.biortech.2024.130574}, pmid = {38471631}, issn = {1873-2976}, abstract = {Widespread use of nanomaterials raises concerns. The underlying mechanism by which graphene oxide (GO) nanoparticles causes poor settleability of activated sludge remains unclear. To explore this mechanism, three reactors with different GO concentrations were established. Extended Derjaguin-Landau-Verwey-Overbeek theory indicated that GO destroyed the property of extracellular polymeric substances (EPS), increasing the energy barrier between bacteria. Low levels of uronic acid and hydrogen bonding in exopolysaccharide weakened the EPS gelation increasing aggregation repulsion. Lager amounts of hydrophilic amino acid and looser structure of extracellular proteins for exposing inner hydrophilic groups significantly contributed to the hydrophilicity of EPS. Both changes implied deterioration in EPS structure under GO stress. Metagenome demonstrated a decrease in genes responsible for capsular polysaccharide colonization and genes regulated the translocation of loose proteins were increased, which increased repulsion between bacteria. This study elucidated that changes in EPS secretion under GO exposure are the underlying causes of poor settleability.}, } @article {pmid38471380, year = {2024}, author = {Meng, S and Peng, T and Liu, Y and Zhang, S and Qian, Z and Huang, T and Xie, Q and Gu, JD and Hu, Z}, title = {Novel insights into the synergetic degradation of pyrene by microbial communities from mangroves in China.}, journal = {Journal of hazardous materials}, volume = {469}, number = {}, pages = {133907}, doi = {10.1016/j.jhazmat.2024.133907}, pmid = {38471380}, issn = {1873-3336}, abstract = {Pyrene is a high molecular weight polycyclic aromatic hydrocarbon (HMW-PAHs). It is a ubiquitous, persistent, and carcinogenic environmental contaminant that has raised concern worldwide. This research explored synergistic bacterial communities for efficient pyrene degradation in seven typical Southern China mangroves. The bacterial communities of seven typical mangroves were enriched by pyrene, and enriched bacterial communities showed an excellent pyrene degradation capacity of > 95% (except for HK mangrove and ZJ mangrove). Devosia, Hyphomicrobium, Flavobacterium, Marinobacter, Algoriphahus, and Youhaiella all have significant positive correlations with pyrene (R>0, p < 0.05) by 16SrRNA gene sequencing and metagenomics analysis, indicated that these genera play a vital role in pyrene metabolism. Meanwhile, the functional genes were involved in pyrene degradation that was enriched in the bacterial communities, including the genes of nagAa, ndoR, pcaG, etc. Furthermore, the analyses of functional genes and binning genomes demonstrated that some bacterial communities as a unique teamwork to cooperatively participate in pyrene degradation. Interestingly, the genes related to biogeochemical cycles were enriched, such as narG , soxA, and cyxJ, suggested that bacterial communities were also helpful in maintaining the stability of the ecological environment. In addition, some novel species with pyrene-degradation potential were identified in the pyrene-degrading bacterial communities, which can enrich the resource pool of pyrene-degrading strains. Overall, this study will help develop further research strategies for pollutant removal.}, } @article {pmid38471376, year = {2024}, author = {Chu, G and Wang, Q and Gao, C and Zhang, Z and Jin, C and Chen, W and Lu, S and Guo, L and Gao, M}, title = {Performance evaluation and metagenomic analysis of sequencing batch reactor under transient 2,4,6-trichlorophenol shock.}, journal = {Journal of hazardous materials}, volume = {469}, number = {}, pages = {133983}, doi = {10.1016/j.jhazmat.2024.133983}, pmid = {38471376}, issn = {1873-3336}, abstract = {The transient chlorophenol shock under some emergency conditions might directly affect the pollutant removal of bioreactor. Therefore, the recovery of bioreactor performance after transient chlorophenol shock is a noteworthy issue. In the present research, the performance, antioxidant response, microbial succession and functional genes of sequencing batch reactor (SBR) were evaluated under transient 2,4,6-trichlorophenol (2,4,6-TCP) shock. The chemical oxygen demand (COD) and ammonia nitrogen (NH4[+]-N) removal efficiencies decreased sharply in the first 4 days after 60 mg/L 2,4,6-TCP shock for 24 h and gradually recovered to normal in the subsequent 8 days. The nitrogen removal rates and their corresponding enzymatic activities rapidly decreased after transient 2,4,6-TCP shock and then gradually increased to normal. The increase of antioxidant enzymatic activity, Cu-Zn SOD genes and Fe-Mn SOD genes contributed to the recovery of SBR performance. The abundance of genes encoding ammonia monooxygenase and hydroxylamine dehydrogenase decreased after transient 2,4,6-TCP shock, including amoA, amoC and nxrA. Thauera, Dechloromonas and Candidatus_Competibacter played key roles in the restorative process, which provided stable abundances of narG, norB , norC and nosZ. The results will deeply understand into the effect of transient 2,4,6-TCP shock on bioreactor performance and provide theoretical basis to build promising recoveries strategy of bioreactor performance.}, } @article {pmid38471337, year = {2024}, author = {Conco-Biyela, T and Malla, MA and Olatunji Awolusi, O and Allam, M and Ismail, A and Stenström, TA and Bux, F and Kumari, S}, title = {Metagenomics insights into microbiome and antibiotic resistance genes from free living amoeba in chlorinated wastewater effluents.}, journal = {International journal of hygiene and environmental health}, volume = {258}, number = {}, pages = {114345}, doi = {10.1016/j.ijheh.2024.114345}, pmid = {38471337}, issn = {1618-131X}, abstract = {Free living amoeba (FLA) are among the organisms commonly found in wastewater and are well-established hosts for diverse microbial communities. Despite its clinical significance, there is little knowledge on the FLA microbiome and resistome, with previous studies relying mostly on conventional approaches. In this study we comprehensively analyzed the microbiome, antibiotic resistome and virulence factors (VFs) within FLA isolated from final treated effluents of two wastewater treatment plants (WWTPs) using shotgun metagenomics. Acanthamoeba has been identified as the most common FLA, followed by Entamoeba. The bacterial diversity showed no significant difference (p > 0.05) in FLA microbiomes obtained from the two WWTPs. At phylum level, the most dominant taxa were Proteobacteria, followed by Firmicutes and Actinobacteria. The most abundant genera identified were Enterobacter followed by Citrobacter, Paenibacillus, and Cupriavidus. The latter three genera are reported here for the first time in Acanthamoeba. In total, we identified 43 types of ARG conferring resistance to cephalosporins, phenicol, streptomycin, trimethoprim, quinolones, cephalosporins, tigecycline, rifamycin, and kanamycin. Similarly, a variety of VFs in FLA metagenomes were detected which included flagellar proteins, Type IV pili twitching motility proteins (pilH and rpoN), alginate biosynthesis genes AlgI, AlgG, AlgD and AlgW and Type VI secretion system proteins and general secretion pathway proteins (tssM, tssA, tssL, tssK, tssJ, fha, tssG, tssF, tssC and tssB, gspC, gspE, gspD, gspF, gspG, gspH, gspI, gspJ, gspK, and gspM). To the best of our knowledge, this is the first study of its kind to examine both the microbiomes and resistome in FLA, as well as their potential pathogenicity in treated effluents. Additionally, this study showed that FLA can host a variety of potentially pathogenic bacteria including Paenibacillus, and Cupriavidus that had not previously been reported, indicating that their relationship may play a role in the spread and persistence of antibiotic resistant bacteria (ARBs) and antibiotic resistance genes (ARGs) as well as the evolution of novel pathogens.}, } @article {pmid38471180, year = {2024}, author = {Deng, LJ and Ye, Q and Luo, SY and Wang, QX and Fang, S}, title = {Case Report: Clinical and Pathological Findings of Tuberculous Gumma: A Case Report and Literature Review.}, journal = {The American journal of tropical medicine and hygiene}, volume = {}, number = {}, pages = {}, doi = {10.4269/ajtmh.23-0510}, pmid = {38471180}, issn = {1476-1645}, abstract = {Tuberculous gumma (TG) is a rare type of cutaneous tuberculosis thought to occur as a result of the hematogenous spread of Mycobacterium tuberculosis, which is more common in immunosuppressed individuals. An 8-year-old boy presented with a 2-month history of multiple indolent enlarging ulcerated nodules on his left upper extremity. He had a past medical history of bacille Calmette-Guerin vaccine induced lupus vulgaris. Skin biopsy of the nodules showed granulomas and neutrophil-dominated purulent inflammation. Ziehl-Neelsen staining was negative, and the cultures were positive for M. tuberculosis. Furthermore, the M. tuberculosis complex was identified using metagenomic next-generation sequencing. Standard antitubercular therapy was started at full doses, and the skin lesions had significantly improved 3 months later. Here we review the literature since 2000 and describe the clinical and pathological features of TG.}, } @article {pmid38470313, year = {2024}, author = {Yu, J and Lee, JYY and Tang, SN and Lee, PKH}, title = {Niche differentiation in microbial communities with stable genomic traits over time in engineered systems.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae042}, pmid = {38470313}, issn = {1751-7370}, abstract = {Microbial communities in full-scale engineered systems undergo dynamic compositional changes. However, mechanisms governing assembly of such microbes and succession of their functioning and genomic traits under various environmental conditions are unclear. In this study, we used the activated sludge (AS) and anaerobic treatment systems of four full-scale industrial wastewater treatment plants as models to investigate the niches of microbes in communities and the temporal succession patterns of community compositions. High-quality representative metagenome-assembled genomes revealed that taxonomic, functional, and trait-based compositions were strongly shaped by environmental selection, with replacement processes primarily driving variations in taxonomic and functional compositions. Plant-specific indicators were associated with system environmental conditions and exhibited strong determinism and trajectory directionality over time. The partitioning of microbes in a co-abundance network according to groups of plant-specific indicators, together with significant between-group differences in genomic traits, indicated the occurrence of niche differentiation. The indicators of the treatment plant with rich nutrient input and high substrate removal efficiency exhibited a faster predicted growth rate, lower guanine-cytosine content, smaller genome size, and higher codon usage bias than the indicators of the other plants. In individual plants, taxonomic composition displayed a more rapid temporal succession than functional and trait-based compositions. The succession of taxonomic, functional, and trait-based compositions were correlated with the kinetics of treatment processes in the AS systems. This study provides insights into ecological niches of microbes in engineered systems and succession patterns of their functions and traits, which will aid microbial community management to improve treatment performance.}, } @article {pmid38470142, year = {2024}, author = {Zhang, Z and Zhang, L and Zhang, L and Chu, H and Zhou, J and Ju, F}, title = {Diversity and distribution of biosynthetic gene clusters in agricultural soil microbiomes.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0126323}, doi = {10.1128/msystems.01263-23}, pmid = {38470142}, issn = {2379-5077}, abstract = {Bacterial secondary metabolites serve as an important source of molecules for drug discovery. They also play an important function in mediating the interactions of microbial producers with their living environment and surrounding organisms. However, little is known about the genetic novelty, distribution, and community-level impacts of soil bacterial biosynthetic potential on a large geographic scale. Here, we constructed the first catalog of 11,149 biosynthetic gene clusters (BGCs) from agricultural soils across China and unearthed hidden biosynthetic potential for new natural product discovery from the not-yet-cultivated soil bacteria. Notably, we revealed soil pH as the strongest environmental driver of BGC biogeography and predicted that soil acidification and global climate change could damage the biosynthetic potential of the soil microbiome. The co-occurrence network of bacterial genomes revealed two BGC-rich species, i.e., Nocardia niigatensis from Actinobacteriota and PSRF01 from Acidobacteriota, as the module hub and connector, respectively, indicating their keystone positions in the soil microbial communities. We also uncovered a dominant role of BGC-inferred biotic interactions over environmental drivers in structuring the soil microbiome. Overall, this study achieved novel insights into the BGC landscape in agricultural soils of China, substantially expanding our understanding of the diversity and novelty of bacterial secondary metabolism and the potential role of secondary metabolites in microbiota assembly.IMPORTANCEBacterial secondary metabolites not only serve as the foundation for numerous therapeutics (e.g., antibiotics and anticancer drugs), but they also play critical ecological roles in mediating microbial interactions (e.g., competition and communication). However, our knowledge of bacterial secondary metabolism is limited to only a small fraction of cultured strains, thus restricting our comprehensive understanding of their diversity, novelty, and potential ecological roles in soil ecosystems. Here, we used culture-independent metagenomics to explore biosynthetic potentials in agricultural soils of China. Our analyses revealed a high degree of genetic diversity and novelty within biosynthetic gene clusters in agricultural soil environments, offering valuable insights for biochemists seeking to synthesize novel bioactive products. Furthermore, we uncovered the pivotal role of BGC-rich species in microbial communities and the significant relationship between BGC richness and microbial phylogenetic turnover. This information emphasizes the importance of biosynthetic potential in the assembly of microbial communities.}, } @article {pmid38470044, year = {2024}, author = {Liu, D and Xie, L-S and Lian, S and Li, K and Yang, Y and Wang, W-Z and Hu, S and Liu, S-J and Liu, C and He, Z}, title = {Anaerostipes hadrus, a butyrate-producing bacterium capable of metabolizing 5-fluorouracil.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0081623}, doi = {10.1128/msphere.00816-23}, pmid = {38470044}, issn = {2379-5042}, abstract = {UNLABELLED: Anaerostipes hadrus (A. hadrus) is a dominant species in the human gut microbiota and considered a beneficial bacterium for producing probiotic butyrate. However, recent studies have suggested that A. hadrus may negatively affect the host through synthesizing fatty acid and metabolizing the anticancer drug 5-fluorouracil, indicating that the impact of A. hadrus is complex and unclear. Therefore, comprehensive genomic studies on A. hadrus need to be performed. We integrated 527 high-quality public A. hadrus genomes and five distinct metagenomic cohorts. We analyzed these data using the approaches of comparative genomics, metagenomics, and protein structure prediction. We also performed validations with culture-based in vitro assays. We constructed the first large-scale pan-genome of A. hadrus (n = 527) and identified 5-fluorouracil metabolism genes as ubiquitous in A. hadrus genomes as butyrate-producing genes. Metagenomic analysis revealed the wide and stable distribution of A. hadrus in healthy individuals, patients with inflammatory bowel disease, and patients with colorectal cancer, with healthy individuals carrying more A. hadrus. The predicted high-quality protein structure indicated that A. hadrus might metabolize 5-fluorouracil by producing bacterial dihydropyrimidine dehydrogenase (encoded by the preTA operon). Through in vitro assays, we validated the short-chain fatty acid production and 5-fluorouracil metabolism abilities of A. hadrus. We observed for the first time that A. hadrus can convert 5-fluorouracil to α-fluoro-β-ureidopropionic acid, which may result from the combined action of the preTA operon and adjacent hydA (encoding bacterial dihydropyrimidinase). Our results offer novel understandings of A. hadrus, exceptionally functional features, and potential applications.

IMPORTANCE: This work provides new insights into the evolutionary relationships, functional characteristics, prevalence, and potential applications of Anaerostipes hadrus.}, } @article {pmid38469667, year = {2024}, author = {Alemasi, A and Gu, L and Zhou, Y}, title = {Gut microbiota in the association between obesity and kidney function decline: a metagenomics-based study in a rat model.}, journal = {Renal failure}, volume = {46}, number = {1}, pages = {2328320}, doi = {10.1080/0886022X.2024.2328320}, pmid = {38469667}, issn = {1525-6049}, abstract = {OBJECTIVES: Obesity can induce dysbiosis in the gut microbiota and is considered a separate risk factor for kidney function decline. Nonetheless, the precise function of intestinal microorganisms in facilitating the connection between obesity and kidney function decline remains uncertain. Hence, the objective of this study was to investigate the alterations in the gut microbiota composition that take place during obesity and their correlations with renal function utilizing a rat model.

METHODS: For 20 weeks, 25 Sprague-Dawley rats were fed either a high-fat diet (HFD) or a normal-fat normal diet (ND). Physiological indices, peripheral plasma, kidney tissue, and colon contents were collected for comparison between groups. Metagenomic analysis of intestinal flora was performed.

RESULTS: The HFD group demonstrated significantly increased levels of creatinine and urea nitrogen in the peripheral blood. Additionally, the HFD rats exhibited a significantly larger glomerular diameter compared to the ND group, accompanied by the presence of glomerulosclerosis, tubular vacuolar transformation, and other pathological changes in certain glomeruli. Metagenomics analysis revealed a notable rise in the prevalence of the Firmicutes phylum within the HFD group, primarily comprising the Rumenococcus genus. Functional analysis indicated that the gut microbiota in the HFD group primarily correlated with infectious diseases, signal transduction, and signaling molecules and interactions.

CONCLUSIONS: This study provides evidence that the consumption of a HFD induces modifications in the composition and functionality of the gut microbiome in rats, which may serve as a potential mechanism underlying the relationship between obesity and the progression of kidney function decline.}, } @article {pmid38469364, year = {2024}, author = {Qiu, YY and Xia, J and Guo, J and Gong, X and Zhang, L and Jiang, F}, title = {Groundwater chromate removal by autotrophic sulfur disproportionation.}, journal = {Environmental science and ecotechnology}, volume = {21}, number = {}, pages = {100399}, pmid = {38469364}, issn = {2666-4984}, abstract = {Chromate [Cr(VI)] contamination in groundwater is a global environmental challenge. Traditional elemental sulfur-based biotechnologies for Cr(VI) removal depend heavily on the synthesis of dissolved organic carbon to fuel heterotrophic Cr(VI) reduction, a bottleneck in the remediation process. Here we show an alternative approach by leveraging sulfur-disproportionating bacteria (SDB) inherent to groundwater ecosystems, offering a novel and efficient Cr(VI) removal strategy. We implemented SDB within a sulfur-packed bed reactor for treating Cr(VI)-contaminated groundwater, achieving a notable removal rate of 6.19 mg L[-1] h[-1] under oligotrophic conditions. We identified the chemical reduction of Cr(VI) via sulfide, produced through sulfur disproportionation, as a key mechanism, alongside microbial Cr(VI) reduction within the sulfur-based biosystem. Genome-centric metagenomic analysis revealed a symbiotic relationship among SDB, sulfur-oxidizing, and chromate-reducing bacteria within the reactor, suggesting that Cr(VI) detoxification by these microbial communities enhances the sulfur-disproportionation process. This research highlights the significance of sulfur disproportionation in the cryptic sulfur cycle in Cr(VI)-contaminated groundwater and proposes its practical application in groundwater remediation efforts.}, } @article {pmid38468846, year = {2024}, author = {Qiang, L and Deng, X and Yang, Y and Wang, Z and Gai, W}, title = {Disseminated Histoplasmosis Infection Diagnosed by Metagenomic Next-Generation Sequencing: A Case Report.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {865-873}, pmid = {38468846}, issn = {1178-6973}, abstract = {Histoplasmosis is an endemic disease caused by Histoplasma capsulatum. This systemic disease can affect various organs beyond the lungs, such as the liver, spleen, adrenal gland, and lymph nodes. The clinical symptoms can range from asymptomatic to severe, life-threatening conditions, depending on the state of the patient's immune system. This report describes a 40-year-old male who presented with reports of weight loss, low back pain, and progressively worsening movement disorder of the bilateral lower extremities for months. Computed tomography (CT) examination showed multiple lytic lesions of vertebral bodies, bilateral ribs, and pelvic bone, histopathological examination and tumor-related serum markers exclude tumors. mNGS was employed to identify H. capsulatum var. capsulatum as the etiological agent of the lesions in the bone biopsy. Through phylogenetic tree analysis, Histoplasma capsulatum var. Capsulatum (Hcc) was the main responsible pathogen, rarely reported in bone lesions. The patient underwent spinal surgery and was successfully treated with liposomal amphotericin B and itraconazole. Based on the diagnosis and treatment of this case, we discuss the epidemiologic status, clinical presentations, diagnostic criteria, and treatment guidelines of histoplasmosis to provide additional information about this disease. mNGS is utilized in this case, and it appears to be a reliable method for early and accurate diagnosis of this disease.}, } @article {pmid38468305, year = {2024}, author = {d'Humières, C and Delavy, M and Alla, L and Ichou, F and Gauliard, E and Ghozlane, A and Levenez, F and Galleron, N and Quinquis, B and Pons, N and Mullaert, J and Bridier-Nahmias, A and Condamine, B and Touchon, M and Rainteau, D and Lamazière, A and Lesnik, P and Ponnaiah, M and Lhomme, M and Sertour, N and Devente, S and Docquier, JD and Bougnoux, ME and Tenaillon, O and Magnan, M and Ruppé, E and Grall, N and Duval, X and Ehrlich, D and Mentré, F and Denamur, E and Rocha, EPC and Le Chatelier, E and Burdet, C and , }, title = {Perturbation and resilience of the gut microbiome up to 3 months after β-lactams exposure in healthy volunteers suggest an important role of microbial β-lactamases.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {50}, pmid = {38468305}, issn = {2049-2618}, abstract = {BACKGROUND: Antibiotics notoriously perturb the gut microbiota. We treated healthy volunteers either with cefotaxime or ceftriaxone for 3 days, and collected in each subject 12 faecal samples up to day 90. Using untargeted and targeted phenotypic and genotypic approaches, we studied the changes in the bacterial, phage and fungal components of the microbiota as well as the metabolome and the β-lactamase activity of the stools. This allowed assessing their degrees of perturbation and resilience.

RESULTS: While only two subjects had detectable concentrations of antibiotics in their faeces, suggesting important antibiotic degradation in the gut, the intravenous treatment perturbed very significantly the bacterial and phage microbiota, as well as the composition of the metabolome. In contrast, treatment impact was relatively low on the fungal microbiota. At the end of the surveillance period, we found evidence of resilience across the gut system since most components returned to a state like the initial one, even if the structure of the bacterial microbiota changed and the dynamics of the different components over time were rarely correlated. The observed richness of the antibiotic resistance genes repertoire was significantly reduced up to day 30, while a significant increase in the relative abundance of β-lactamase encoding genes was observed up to day 10, consistent with a concomitant increase in the β-lactamase activity of the microbiota. The level of β-lactamase activity at baseline was positively associated with the resilience of the metabolome content of the stools.

CONCLUSIONS: In healthy adults, antibiotics perturb many components of the microbiota, which return close to the baseline state within 30 days. These data suggest an important role of endogenous β-lactamase-producing anaerobes in protecting the functions of the microbiota by de-activating the antibiotics reaching the colon. Video Abstract.}, } @article {pmid38468206, year = {2024}, author = {Watai, K and Suda, W and Kurokawa, R and Sekiya, K and Hayashi, H and Iwata, M and Nagayama, K and Nakamura, Y and Hamada, Y and Kamide, Y and Fukutomi, Y and Nakabayashi, T and Tanaka, K and Kamita, M and Taniguchi, M and Hattori, M}, title = {Metagenomic gut microbiome analysis of Japanese patients with multiple chemical sensitivity/idiopathic environmental intolerance.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {84}, pmid = {38468206}, issn = {1471-2180}, support = {2015-EBM-02//Grant-in-Aid for Evidence-Based Medicine Research from the National Hospital Organization, Japan/ ; 2015-EBM-02//Grant-in-Aid for Evidence-Based Medicine Research from the National Hospital Organization, Japan/ ; }, abstract = {BACKGROUND: Although the pathology of multiple chemical sensitivity (MCS) is unknown, the central nervous system is reportedly involved. The gut microbiota is important in modifying central nervous system diseases. However, the relationship between the gut microbiota and MCS remains unclear. This study aimed to identify gut microbiota variations associated with MCS using shotgun metagenomic sequencing of fecal samples.

METHODS: We prospectively recruited 30 consecutive Japanese female patients with MCS and analyzed their gut microbiomes using shotgun metagenomic sequencing. The data were compared with metagenomic data obtained from 24 age- and sex-matched Japanese healthy controls (HC).

RESULTS: We observed no significant difference in alpha and beta diversity of the gut microbiota between the MCS patients and HC. Focusing on the important changes in the literatures, at the genus level, Streptococcus, Veillonella, and Akkermansia were significantly more abundant in MCS patients than in HC (p < 0.01, p < 0.01, p = 0.01, respectively, fold change = 4.03, 1.53, 2.86, respectively). At the species level, Akkermansia muciniphila was significantly more abundant (p = 0.02, fold change = 3.3) and Faecalibacterium prausnitzii significantly less abundant in MCS patients than in HC (p = 0.03, fold change = 0.53). Functional analysis revealed that xylene and dioxin degradation pathways were significantly enriched (p < 0.01, p = 0.01, respectively, fold change = 1.54, 1.46, respectively), whereas pathways involved in amino acid metabolism and synthesis were significantly depleted in MCS (p < 0.01, fold change = 0.96). Pathways related to antimicrobial resistance, including the two-component system and cationic antimicrobial peptide resistance, were also significantly enriched in MCS (p < 0.01, p < 0.01, respectively, fold change = 1.1, 1.2, respectively).

CONCLUSIONS: The gut microbiota of patients with MCS shows dysbiosis and alterations in bacterial functions related to exogenous chemicals and amino acid metabolism and synthesis. These findings may contribute to the further development of treatment for MCS.

TRIAL REGISTRATION: This study was registered with the University Hospital Medical Information Clinical Trials Registry as UMIN000031031. The date of first trial registration: 28/01/2018.}, } @article {pmid38468006, year = {2024}, author = {Ma, J and Yao, Z and Zhang, M and Gao, J and Li, W and Yang, W}, title = {Microbial and environmental medium-driven responses to phosphorus fraction changes in the sediments of different lake types during the freezing period.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38468006}, issn = {1614-7499}, support = {42167018//the National Natural Science Foundation of China/ ; 2023YXXS026//the Fundamental Research Funds for Inner Mongolia University of Science & Technology/ ; }, abstract = {The comparative study of the transformation among sediment phosphorus (P) fractions in different lake types is a global issue in lake ecosystems. However, interactions between sediment P fractions, environmental factors, and microorganisms vary with the nutrient status of lakes. In this study, we combine sequential extraction and metagenomics sequencing to assess the characteristics of P fractions and transformation in sediments from different lake types in the Inner Mongolian section of the Yellow River Basin. We then further explore the response of relevant microbial and environmental drivers to P fraction transformation and bioavailability in sediments. The sediments of all three lakes exhibited strong exogenous pollution input characteristics, and higher nutritional conditions led to enhanced sediment P fraction transformation ability. The transformation capacity of the sediment P fractions also differed among the different lake types at the same latitudes, which is affected by many factors such as lake environmental factors and microorganisms. Different drivers reflected the mutual control of weakly adsorbed phosphorus (WA-P), potential active phosphorus (PA-P), Fe/Al-bound phosphorus (NaOH-P), and Ca-bound phosphorus (HCl-P) with the bio-directly available phosphorus (Bio-P). The transformation of NaOH-P in reducing environments can improve P bioavailability, while HCl-P is not easily bioavailable in weakly alkaline environments. There were significant differences in the bacterial community diversity and composition between the different lake types at the same latitude (p < 0.05), and the role of P fractions was stronger in the sediments of lakes with rich biodiversity than in poor biodiversity. Lake eutrophication recovery was somewhat hindered by the microbial interactions of P cycling and P fractions within the sediment. This study provides data and theoretical support for exploring the commonalities and differences among different lake types in the Inner Mongolian section of the Yellow River Basin. Besides, it is representative and typical for promoting the optimization of ecological security patterns in ecologically fragile watersheds.}, } @article {pmid38468001, year = {2024}, author = {Ling, Y and Li, L and Zhou, C and Li, Z and Xu, J and Shan, Q and Hei, D and Shi, C and Zhang, J and Jia, W}, title = {Mechanism of improving anaerobic fermentation performance of kitchen waste pretreated by ionizing irradiation-part 1: rice.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38468001}, issn = {1614-7499}, abstract = {Ionizing irradiation, as a new pretreatment method for the anaerobic fermentation of organic pollutants, is featured with fast reaction speed, good treatment effect, no need to add any chemical reagents, and no secondary pollution. This study explores the mechanism of improving anaerobic fermentation performance of rice samples pretreated by cobalt-60 gamma irradiation through the influence on fermentation substrate, acidogenic phase and methanogenic phase. The results reveal that the soluble chemical oxygen demand of the irradiated rice sample at an absorbed dose of 9.6 kGy increases by 12.4 times due to the dissolution of small molecules of fat-soluble organic matter. The yield of biogas in the acidogenic phase increases by 22.2% with a slight increase in hydrogen gas content. The yield of biogas and methane gas content in the methanogenic phase increases by 27.3% and 15%, respectively. Microbial genome analysis, performed with MiSeq high-throughput sequencing and metagenomic methods, suggests the microbial abundance and metabolic functions in the anaerobic fermentation process change significantly as a result of the pretreatment by gamma irradiation.}, } @article {pmid38467825, year = {2024}, author = {Li, Y and Li, S and Lu, N and Wang, W and Wang, D}, title = {Secondary hemophagocytic lymphohistiocytosis in pediatric patients with visceral leishmaniasis and Epstein-Barr virus infection.}, journal = {Annals of hematology}, volume = {}, number = {}, pages = {}, pmid = {38467825}, issn = {1432-0584}, abstract = {Visceral leishmaniasis-associated hemophagocytic lymphohistiocytosis (VL-HLH) is indistinguishable from those of HLH of other etiologies due to the overlap symptoms, posing a serious threat to life. In this study, we aimed to provide insights for early diagnosis and improve outcomes in pediatric patients with VL-HLH. We retrospectively analyzed the clinical and laboratory data of 10 pediatric patients with VL-HLH and 58 pediatric patients with Epstein-Barr virus-associated hemophagocytic lymphohistiocytosis (EBV-HLH). The median time from symptom onset to cytopenia in patients with VL-HLH and EBV-HLH was 11 days (interquartile range, 7-15 days) and five days (interquartile range, 3.75-9.25 days) (P = 0.005). Both groups showed liver injury and increased lactate dehydrogenase levels; however the levels of aspartate aminotransferase, alanine aminotransferase, direct bilirubin, and lactate dehydrogenase in patients with VL-HLH were significantly lower than those in patients with EBV-HLH (P < 0.05). The fibrinogen and triglyceride levels were almost normal in VL-HLH patients but were significantly altered in EBV-HLH cases (P < 0.05). The positive rate of first bone marrow microscopy examination, anti-rK39 IgG detection, and blood metagenomic next-generation sequencing was 50%, 100%, and 100%, respectively. After VL diagnosis, eight patients were treated with sodium stibogluconate and two were treated with liposomal amphotericin B. All the patients with VL-HLH recovered. Our study demonstrates that regular triglyceride and fibrinogen levels in pediatric patients with VL-HLH may help in differential diagnosis from EBV-HLH. VL-HLH is milder than EBV-HLH, with less severe liver injury and inflammatory responses, and timely treatment with antileishmanial agents is essential to improve the outcomes of pediatric patients with VL-HLH.}, } @article {pmid38467684, year = {2024}, author = {Qiu, Z and Yuan, L and Lian, CA and Lin, B and Chen, J and Mu, R and Qiao, X and Zhang, L and Xu, Z and Fan, L and Zhang, Y and Wang, S and Li, J and Cao, H and Li, B and Chen, B and Song, C and Liu, Y and Shi, L and Tian, Y and Ni, J and Zhang, T and Zhou, J and Zhuang, WQ and Yu, K}, title = {BASALT refines binning from metagenomic data and increases resolution of genome-resolved metagenomic analysis.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2179}, pmid = {38467684}, issn = {2041-1723}, abstract = {Metagenomic binning is an essential technique for genome-resolved characterization of uncultured microorganisms in various ecosystems but hampered by the low efficiency of binning tools in adequately recovering metagenome-assembled genomes (MAGs). Here, we introduce BASALT (Binning Across a Series of Assemblies Toolkit) for binning and refinement of short- and long-read sequencing data. BASALT employs multiple binners with multiple thresholds to produce initial bins, then utilizes neural networks to identify core sequences to remove redundant bins and refine non-redundant bins. Using the same assemblies generated from Critical Assessment of Metagenome Interpretation (CAMI) datasets, BASALT produces up to twice as many MAGs as VAMB, DASTool, or metaWRAP. Processing assemblies from a lake sediment dataset, BASALT produces ~30% more MAGs than metaWRAP, including 21 unique class-level prokaryotic lineages. Functional annotations reveal that BASALT can retrieve 47.6% more non-redundant opening-reading frames than metaWRAP. These results highlight the robust handling of metagenomic sequencing data of BASALT.}, } @article {pmid38467264, year = {2024}, author = {Zhu, Y and Chen, Y and An, G and Zhang, C and Yang, J and Yang, R and Chen, G and Yang, Y}, title = {Significance of homogeneous operation in light-assisted fixed-bed bioprocess under ammonia stress: Optimization, long-term operation and metagenomic analysis.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {130568}, doi = {10.1016/j.biortech.2024.130568}, pmid = {38467264}, issn = {1873-2976}, abstract = {Activating microbes with light is a promising strategy for addressing ammonia-stressed anaerobic digestion (AD). However, as a critical in-process parameter, homogenous operation, in light-assisted AD amended by bio-fixed bed has received limited attention. This research endeavors to establish a uniform-illuminated biosystem and assess its practical feasibility through a 90-day semi-continuous operation at pilot scale under solar light illumination. With optimal stirring mode (intermittent stirring for 3 min every 15 min), robust methane yields were achieved across various organic loads, reaching 88.7-94.3 % of theoretical yield under high ammonium stress (3500 mg/L). The metagenomic analysis unveiled that uniform illumination triggered synergistic effects in AD, fostering a diversified microbial consortium, enhancing carbohydrate and methane metabolism, and facilitating the formation of an electroactive bio-cluster. This study underscores the significance of homogenous illumination in AD systems for efficient waste-to-energy conversion, highlighting the implementation of solar light as a greener approach for scale-up application.}, } @article {pmid38467173, year = {2024}, author = {Karlsmose, AK and Ivanova, M and Kragh, ML and Kjeldgaard, JS and Otani, S and Svendsen, CA and Papić, B and Zdovc, I and Tasara, T and Stephan, R and Heir, E and Langsrud, S and Møretrø, T and Dalgaard, P and Fagerlund, A and Hansen, LT and Aarestrup, FM and Leekitcharoenphon, P}, title = {A novel metagenomic approach uncovers phage genes as markers for increased disinfectant tolerance in mixed Listeria monocytogenes communities.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105582}, doi = {10.1016/j.meegid.2024.105582}, pmid = {38467173}, issn = {1567-7257}, abstract = {Listeria monocytogenes is an important human pathogen with a high mortality rate. Consumption of contaminated ready-to-eat food is the main mode of transmission to humans. Disinfectant-tolerant L. monocytogenes have emerged, which are believed to have increased persistence potential. Elucidating the mechanisms of L. monocytogenes disinfectant tolerance has been the focus of previous studies using pure cultures. A limitation of such approach is the difficulty to identify strains with reduced susceptibility due to inter-strain variation and the need to screen large numbers of strains and genes. In this study, we applied a novel metagenomic approach to detect genes associated with disinfectant tolerance in mixed L. monocytogenes planktonic communities. Two communities, consisting of 71 and 80 isolates each, were treated with the food industry disinfectants benzalkonium chloride (BC, 1.75 mg/L) or peracetic acid (PAA, 38 mg/L). The communities were subjected to metagenomic sequencing and differences in individual gene abundances between biocide-free control communities and biocide-treated communities were determined. A significant increase in the abundance of Listeria phage-associated genes was observed in both communities after treatment, suggesting that prophage carriage could lead to an increased disinfectant tolerance in mixed L. monocytogenes planktonic communities. In contrast, a significant decrease in the abundance of a high-copy emrC-harbouring plasmid pLmN12-0935 was observed in both communities after treatment. In PAA-treated community, a putative ABC transporter previously found to be necessary for L. monocytogenes resistance to antimicrobial agents and virulence, was among the genes with the highest weight for differentiating treated from control samples. The undertaken metagenomic approach in this study can be applied to identify genes associated with increased tolerance to other antimicrobials in mixed bacterial communities.}, } @article {pmid38469477, year = {2023}, author = {Leierer, D and Olmstead, M and Oppert, B}, title = {Sequencing to identify pathogens in Tenebrio molitor: Implications in insects farmed for food and feed.}, journal = {Frontiers in insect science}, volume = {3}, number = {}, pages = {1059046}, pmid = {38469477}, issn = {2673-8600}, abstract = {INTRODUCTION: The farmed insect industry is increasing in number and size to meet the demand for sustainably-produced protein. Larger insect farms are prone to losses due to pathogens, and more information is needed regarding the health of insects reared for food and feed.

METHODS: In this study, high throughput sequencing was used to identify potential pathogens in a colony of Tenebrio molitor (yellow mealworm, Coleoptera: Tenebrionidae) that exhibited increased mortality in immature stages with eventual colony collapse. Sequences also were obtained from a healthy new colony of T. molitor, as well as a recovered individual from the collapsed colony.

RESULTS: Screening of sequences obtained from the colonies and their rearing diet indicated that the collapsed colony had low diversity in microbial taxa, with predominantly sequences from the families Staphylococcaeceae and Streptococcaceae constituting from 53 to 88% of the total microbial reads. Conversely, in the new colony and their rearing diet, microbial sequences were from more than 15 different taxa, with Lactobacilleceae the most prevalent but representing only 21% of the total microbial reads. Evidence indicates that Bacillus thuringiensis may have been involved in the collapse of the colony, leading to sepsis and microbial dysbiosis, although the source of the bacteria was not identified. Sequences from the recovered individual reflected a microbial flora profile that was intermediate between those of the diseased collapsed and new colonies.

DISCUSSION: These findings have implications for insects reared in confined environments and provide a rapid method to screen insect colonies by sequencing healthy and potentially diseased individuals.}, } @article {pmid38466915, year = {2024}, author = {Huang, Z and Peng, C and Rong, Z and Jiang, L and Li, Y and Feng, Y and Chen, S and Xie, C and Jiang, C}, title = {Longitudinal Mapping of Personal Biotic and Abiotic Exposomes and Transcriptome in Underwater Confined Space Using Wearable Passive Samplers.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c09379}, pmid = {38466915}, issn = {1520-5851}, abstract = {Silicone-based passive samplers, commonly paired with gas chromatography-mass spectrometry (GC-MS) analysis, are increasingly utilized for personal exposure assessments. However, its compatibility with the biotic exposome remains underexplored. In this study, we introduce the wearable silicone-based AirPie passive sampler, coupled with nontargeted liquid chromatography with high-resolution tandem mass spectrometry (LC-HRMS/MS), GC-HRMS, and metagenomic shotgun sequencing methods, offering a comprehensive view of personalized airborne biotic and abiotic exposomes. We applied the AirPie samplers to 19 participants in a unique deep underwater confined environment, annotating 4,390 chemical and 2,955 microbial exposures, integrated with corresponding transcriptomic data. We observed significant shifts in environmental exposure and gene expression upon entering this unique environment. We noted increased exposure to pollutants, such as benzenoids, polycyclic aromatic hydrocarbons (PAHs), opportunistic pathogens, and associated antibiotic-resistance genes (ARGs). Transcriptomic analyses revealed the activation of neurodegenerative disease-related pathways, mostly related to chemical exposure, and the repression of immune-related pathways, linked to both biological and chemical exposures. In summary, we provided a comprehensive, longitudinal exposome map of the unique environment and underscored the intricate linkages between external exposures and human health. We believe that the AirPie sampler and associated analytical methods will have broad applications in exposome and precision medicine.}, } @article {pmid38466428, year = {2024}, author = {Sonthiphand, P and Rueangmongkolrat, N and Uthaipaisanwong, P and Kusonmano, K and Mhuantong, W and Termsaithong, T and Limthamprasert, C and Chotpantarat, S and Luepromchai, E}, title = {Soil Microbiomes and their Arsenic Functional Genes in Chronically High-Arsenic Contaminated Soils.}, journal = {Bulletin of environmental contamination and toxicology}, volume = {112}, number = {3}, pages = {49}, pmid = {38466428}, issn = {1432-0800}, support = {RGNS 63- 173//Office of the Permanent Secretary, Ministry of Higher Education, Science, Research and Innovation (OPS MHESI), Thailand Science Research and Innovation (TSRI) and Mahidol University/ ; Faculty of Science, Mahidol University//Faculty of Science, Mahidol University/ ; }, abstract = {Microbial arsenic transformations play essential roles in controlling pollution and ameliorating risk. This study combined high-throughput sequencing and PCR-based approaches targeting both the 16 S rRNA and arsenic functional genes to investigate the temporal and spatial dynamics of the soil microbiomes impacted by high arsenic contamination (9.13 to 911.88 mg/kg) and to investigate the diversity and abundance of arsenic functional genes in soils influenced by an arsenic gradient. The results showed that the soil microbiomes were relatively consistent and mainly composed of Actinobacteria (uncultured Gaiellales and an unknown_67 - 14 bacterium), Proteobacteria, Firmicutes (particularly, Bacillus), Chloroflexi, and Acidobacteria (unknown_Subgroup_6). Although a range of arsenic functional genes (e.g., arsM, arsC, arrA, and aioA) were identified by shotgun metagenomics, only the arsM gene was detected by the PCR-based method. The relative abundance of the arsM gene accounted for 0.20%-1.57% of the total microbial abundance. Combining all analyses, arsenic methylation mediated by the arsM gene was proposed to be a key process involved in the arsenic biogeochemical cycle and mitigation of arsenic toxicity. This study advances our knowledge about arsenic mechanisms over the long-term in highly contaminated soils.}, } @article {pmid38466099, year = {2024}, author = {Wang, Y and Lin, X and Li, C and Liu, G and Wang, S and Chen, M and Wei, X and Wen, H and Tao, Z and Xu, Y}, title = {Metagenomic sequencing reveals viral diversity of mosquitoes from Shandong Province, China.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0393223}, doi = {10.1128/spectrum.03932-23}, pmid = {38466099}, issn = {2165-0497}, abstract = {UNLABELLED: Mosquitoes carry a large number of known and unknown viruses, some of which could cause serious diseases in humans or animals. Metagenomic sequencing for mosquito viromes is crucial for understanding the evolutionary history of viruses and preventing emerging mosquito-borne diseases. We collected 1,598 mosquitoes belonging to four species from five counties in Shandong Province, China in 2021. They were grouped by species and sampling locations and subjected to metagenomic next-generation sequencing for the analysis of the viromes. A total of 233,317,352 sequencing reads were classified into 30 viral families and an unclassified group. Comparative analysis showed that mosquitoes in Shandong Province generally possessed host-specific virome. We detected mosquito-borne viruses including Japanese encephalitis virus, Getah virus, and Kadipiro virus in Culex tritaeniorhynchus and Anopheles sinensis samples. Phylogenetic analysis showed that these pathogenic viruses may have existed in mosquitoes in Shandong Province for a long time. Meanwhile, we identified 22 novel viruses belonging to seven families and the genus Negevirus. Our study comprehensively described the viromes of several common mosquito species in Shandong Province, China, and demonstrated the major role of host species in shaping mosquito viromes. Furthermore, the metagenomic data provided valuable epidemiological information on multiple mosquito-borne viruses, highlighting the potential risk of infection transmission.

IMPORTANCE: Mosquitoes are known as the source of various pathogens for humans and animals. Culex tritaeniorhynchus, Armigeres subalbatus, and Anopheles sinensis have been found to transmit the Getah virus, which has recently caused increasing infections in China. Cx. tritaeniorhynchus and Culex pipiens are the main vectors of Japanese encephalitis virus and have caused epidemics of Japanese encephalitis in China in past decades. These mosquitoes are widely present in Shandong Province, China, leading to a great threat to public health and the breeding industry. This study provided a comprehensive insight into the viromes of several common mosquito species in Shandong Province, China. The metagenomic sequencing data revealed the risks of multiple pathogenic mosquito-borne viruses, including Japanese encephalitis virus, Getah virus, and Kadipiro virus, which are of great importance for preventing emerging viral epidemics.}, } @article {pmid38466097, year = {2024}, author = {Möller, L and Vainshtein, Y and Meyer, B and Neidhardt, J and Eren, AM and Sohn, K and Rabus, R}, title = {Rich microbial and depolymerising diversity in Antarctic krill gut.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0403523}, doi = {10.1128/spectrum.04035-23}, pmid = {38466097}, issn = {2165-0497}, abstract = {With almost a quadrillion individuals, the Antarctic krill processes five million tons of organic carbon every day during austral summer. This high carbon flux requires a broad range of hydrolytic enzymes to decompose the diverse food-derived biopolymers. While krill itself possesses numerous such enzymes, it is unclear, to what extent the endogenous microbiota contribute to the hydrolytic potential of the gut environment. Here we applied amplicon sequencing, shotgun metagenomics, cultivation, and physiological assays to characterize the krill gut microbiota. The broad bacterial diversity (273 families, 919 genera, and 2,309 species) also included a complex potentially anaerobic sub-community. Plate-based assays with 198 isolated pure cultures revealed widespread capacities to utilize lipids (e.g., tributyrin), followed by proteins (casein) and to a lesser extent by polysaccharides (e.g., alginate and chitin). While most isolates affiliated with the genera Pseudoalteromonas and Psychrobacter, also Rubritalea spp. (Verrucomicrobia) were observed. The krill gut microbiota growing on marine broth agar plates possess 13,012 predicted hydrolyses; 15-fold more than previously predicted from a transcriptome-proteome compendium of krill. Cultivation-independent and -dependent approaches indicated members of the families Flavobacteriaceae and Pseudoalteromonadaceae to dominate the capacities for lipid/protein hydrolysis and to provide a plethora of carbohydrate-active enzymes, sulfatases, and laminarin- or porphyrin-depolymerizing hydrolases. Notably, also the potential to hydrolyze plastics such as polyethylene terephthalate and polylactatide was observed, affiliating mostly with Moraxellaceae. Overall, this study shows extensive microbial diversity in the krill gut, and suggests that the microbiota likely play a significant role in the nutrient acquisition of the krill by enriching its hydrolytic enzyme repertoire.IMPORTANCEThe Antarctic krill (Euphausia superba) is a keystone species of the Antarctic marine food web, connecting the productivity of phyto- and zooplankton with the nutrition of the higher trophic levels. Accordingly, krill significantly contributes to biomass turnover, requiring the decomposition of seasonally varying plankton-derived biopolymers. This study highlights the likely role of the krill gut microbiota in this ecosystem function by revealing the great number of diverse hydrolases that microbes contribute to the krill gut environment. The here resolved repertoire of hydrolytic enzymes could contribute to the overall nutritional resilience of krill and to the general organic matter cycling under changing environmental conditions in the Antarctic sea water. Furthermore, the krill gut microbiome could serve as a valuable resource of cold-adapted hydrolytic enzymes for diverse biotechnological applications.}, } @article {pmid38465466, year = {2024}, author = {Brüssow, H}, title = {Pandemic preparedness: On the efficacy of non-pharmaceutical interventions in COVID-19 and about approaches to predict future pandemic viruses.}, journal = {Microbial biotechnology}, volume = {17}, number = {3}, pages = {e14431}, doi = {10.1111/1751-7915.14431}, pmid = {38465466}, issn = {1751-7915}, abstract = {With three major viral pandemics over the last 100 years, namely the Spanish flu, AIDS and COVID-19 each claiming many millions of lives, pandemic preparedness has become an important issue for public health. The economic, social and political consequences of the upheaval caused by such pandemics also represent a major challenge for governments with respect to sustainable development goals. The field of pandemic preparedness is vast and the current article can only address selected aspects. The article looks first backwards and addresses the question of the efficacy of non-pharmaceutical interventions (NPI) on the trajectory of the COVID-19 pandemic. The article looks then forward by asking to what extent viral candidates for future pandemics can be predicted by virome analyses from metagenome and transcriptome sequencing, by focusing on the virome from specific animal species and using ecological and epidemiological data about spillover viral infections in veterinary and human medicine. As a comprehensive overview on pandemic preparedness is beyond the capacity of a single reviewer, only selected topics will be discussed using recent key scientific publications. Since COVID-19 has not run its course, a computational program able to predict the future evolution of SARS-CoV-2 is mentioned that could assist proactive mRNA vaccine developments against possible future variants of concern. Ending the COVID-19 epidemic necessitates mucosal vaccines that can suppress the transmission of SARS-CoV-2 and therefore this article closes by discussing a promising and versatile protein nanoparticle experimental vaccine approach for inhalation that does not depend on needles nor a cold chain for distribution.}, } @article {pmid38464923, year = {2024}, author = {Wu, XX and Cui, J and Wang, SY and Zhao, TT and Yuan, YF and Yang, L and Zuo, W and Liao, WJ}, title = {Clinical evolution of antisynthetase syndrome-associated interstitial lung disease after COVID-19 in a man with Klinefelter syndrome: A case report.}, journal = {World journal of clinical cases}, volume = {12}, number = {6}, pages = {1144-1149}, pmid = {38464923}, issn = {2307-8960}, abstract = {BACKGROUND: This study presents a case of rapidly developing respiratory failure due to antisynthetase syndrome (AS) following coronavirus disease 2019 (COVID-19) in a 33-year-old man diagnosed with Klinefelter syndrome (KS).

CASE SUMMARY: A 33-year-old man with a diagnosis of KS was admitted to the Department of Pulmonary and Critical Care Medicine of a tertiary hospital in China for fever and shortness of breath 2 wk after the onset of COVID-19. Computed tomography of both lungs revealed diffuse multiple patchy heightened shadows in both lungs, accompanied by signs of partial bronchial inflation. Metagenomic next-generation sequencing of the bronchoalveolar lavage fluid suggested absence of pathogen. A biopsy specimen revealed organizing pneumonia with alveolar septal thickening. Additionally, extensive auto-antibody tests showed strong positivity for anti-SSA, anti-SSB, anti-Jo-1, and anti-Ro-52. Following multidisciplinary discussions, the patient received a final diagnosis of AS, leading to rapidly progressing respiratory failure.

CONCLUSION: This study underscores the clinical progression of AS-associated interstitial lung disease subsequent to viral infections such as COVID-19 in patients diagnosed with KS.}, } @article {pmid38464367, year = {2024}, author = {Ramos-Lopez, O}, title = {Genotype-based precision nutrition strategies for the prediction and clinical management of type 2 diabetes mellitus.}, journal = {World journal of diabetes}, volume = {15}, number = {2}, pages = {142-153}, pmid = {38464367}, issn = {1948-9358}, abstract = {Globally, type 2 diabetes mellitus (T2DM) is one of the most common metabolic disorders. T2DM physiopathology is influenced by complex interrelationships between genetic, metabolic and lifestyle factors (including diet), which differ between populations and geographic regions. In fact, excessive consumptions of high fat/high sugar foods generally increase the risk of developing T2DM, whereas habitual intakes of plant-based healthy diets usually exert a protective effect. Moreover, genomic studies have allowed the characterization of sequence DNA variants across the human genome, some of which may affect gene expression and protein functions relevant for glucose homeostasis. This comprehensive literature review covers the impact of gene-diet interactions on T2DM susceptibility and disease progression, some of which have demonstrated a value as biomarkers of personal responses to certain nutritional interventions. Also, novel genotype-based dietary strategies have been developed for improving T2DM control in comparison to general lifestyle recommendations. Furthermore, progresses in other omics areas (epigenomics, metagenomics, proteomics, and metabolomics) are improving current understanding of genetic insights in T2DM clinical outcomes. Although more investigation is still needed, the analysis of the genetic make-up may help to decipher new paradigms in the pathophysiology of T2DM as well as offer further opportunities to personalize the screening, prevention, diagnosis, management, and prognosis of T2DM through precision nutrition.}, } @article {pmid38464323, year = {2024}, author = {Jin, DM and Morton, JT and Bonneau, R}, title = {Meta-analysis of the human gut microbiome uncovers shared and distinct microbial signatures between diseases.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.02.27.582333}, pmid = {38464323}, abstract = {UNLABELLED: Microbiome studies have revealed gut microbiota's potential impact on complex diseases. However, many studies often focus on one disease per cohort. We developed a meta-analysis workflow for gut microbiome profiles and analyzed shotgun metagenomic data covering 11 diseases. Using interpretable machine learning and differential abundance analysis, our findings reinforce the generalization of binary classifiers for Crohn's disease (CD) and colorectal cancer (CRC) to hold-out cohorts and highlight the key microbes driving these classifications. We identified high microbial similarity in disease pairs like CD vs ulcerative colitis (UC), CD vs CRC, Parkinson's disease vs type 2 diabetes (T2D), and schizophrenia vs T2D. We also found strong inverse correlations in Alzheimer's disease vs CD and UC. These findings detected by our pipeline provide valuable insights into these diseases.

IMPORTANCE: Assessing disease similarity is an essential initial step preceding disease-based approach for drug repositioning. Our study provides a modest first step in underscoring the potential of integrating microbiome insights into the disease similarity assessment. Recent microbiome research has predominantly focused on analyzing individual disease to understand its unique characteristics, which by design excludes comorbidities individuals. We analyzed shotgun metagenomic data from existing studies and identified previously unknown similarities between diseases. Our research represents a pioneering effort that utilize both interpretable machine learning and differential abundance analysis to assess microbial similarity between diseases.}, } @article {pmid38464150, year = {2024}, author = {Zhang, Q and Hutchison, ER and Pan, C and Warren, MF and Keller, MP and Attie, AD and Lusis, AJ and Rey, FE}, title = {Systems genetics approach uncovers associations between host amylase locus, gut microbiome and metabolic traits in hyperlipidemic mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.02.28.582610}, pmid = {38464150}, abstract = {The molecular basis for how host genetic variation impacts gut microbial community and bacterial metabolic niches remain largely unknown. We leveraged 90 inbred hyperlipidemic mouse strains from the Hybrid Mouse Diversity Panel (HMDP), previously studied for a variety of cardio-metabolic traits. Metagenomic analysis of cecal DNA followed by genome-wide association analysis identified genomic loci that were associated with microbial enterotypes in the gut. Among these we detected a genetic locus surrounding multiple amylase genes that was associated with abundances of Firmicutes (Lachnospiraceae family) and Bacteroidetes (Muribaculaceae family) taxa encoding distinct starch and sugar metabolism functions. We also found that lower amylase gene number in the mouse genome was associated with higher gut Muribaculaceae levels. Previous work suggests that modulation of host amylase activity impacts the availability of carbohydrates to the host and potentially to gut bacteria. The genetic variants described above were associated with distinct gut microbial communities (enterotypes) with different predicted metabolic capacities for carbohydrate degradation. Mendelian randomization analysis revealed host phenotypes, including liver fibrosis and plasma HDL-cholesterol levels, that were associated with gut microbiome enterotypes. This work reveals novel relationships between host genetic variation, gut microbial enterotypes and host physiology/disease phenotypes in mice.}, } @article {pmid38464051, year = {2024}, author = {Worthan, SB and McCarthy, RDP and Delaleau, M and Stikeleather, R and Bratton, BP and Boudvillain, M and Behringer, MG}, title = {Evolution of pH-sensitive transcription termination during adaptation to repeated long-term starvation.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.03.01.582989}, pmid = {38464051}, abstract = {Fluctuating environments that consist of regular cycles of co-occurring stress are a common challenge faced by cellular populations. For a population to thrive in constantly changing conditions, an ability to coordinate a rapid cellular response is essential. Here, we identify a mutation conferring an arginine-to-histidine (Arg to His) substitution in the transcription terminator Rho. The rho R109H mutation frequently arose in E. coli populations experimentally evolved under repeated long-term starvation conditions, during which feast and famine result in drastic environmental pH fluctuations. Metagenomic sequencing revealed that populations containing the rho mutation also possess putative loss-of-function mutations in ydcI , which encodes a recently characterized transcription factor associated with pH homeostasis. Genetic reconstructions of these mutations show that the rho allele confers a plastic alkaline-induced reduction of Rho function that, when found in tandem with a Δ ydcI allele, leads to intracellular alkalinization and genetic assimilation of Rho mutant function. We further identify Arg to His substitutions at analogous sites in rho alleles from species originating from fluctuating alkaline environments. Our results suggest that Arg to His substitutions in global regulators of gene expression can serve to rapidly coordinate complex responses through pH sensing and shed light on how cellular populations across the tree of life use environmental cues to coordinate rapid responses to complex, fluctuating environments.}, } @article {pmid38464031, year = {2024}, author = {Zolfo, M and Silverj, A and Blanco-Miguez, A and Manghi, P and Rota-Stabelli, O and Heidrich, V and Jensen, J and Maharjan, S and Franzosa, E and Menni, C and Visconti, A and Pinto, F and Ciciani, M and Huttenhower, C and Cereseto, A and Asnicar, F and Kitano, H and Yamada, T and Segata, N}, title = {Discovering and exploring the hidden diversity of human gut viruses using highly enriched virome samples.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.02.19.580813}, pmid = {38464031}, abstract = {Viruses are an abundant and crucial component of the human microbiome, but accurately discovering them via metagenomics is still challenging. Currently, the available viral reference genomes poorly represent the diversity in microbiome samples, and expanding such a set of viral references is difficult. As a result, many viruses are still undetectable through metagenomics even when considering the power of de novo metagenomic assembly and binning, as viruses lack universal markers. Here, we describe a novel approach to catalog new viral members of the human gut microbiome and show how the resulting resource improves metagenomic analyses. We retrieved >3,000 viral-like particles (VLP) enriched metagenomic samples (viromes), evaluated the efficiency of the enrichment in each sample to leverage the viromes of highest purity, and applied multiple analysis steps involving assembly and comparison with hundreds of thousands of metagenome-assembled genomes to discover new viral genomes. We reported over 162,000 viral sequences passing quality control from thousands of gut metagenomes and viromes. The great majority of the retrieved viral sequences (~94.4%) were of unknown origin, most had a CRISPR spacer matching host bacteria, and four of them could be detected in >50% of a set of 18,756 gut metagenomes we surveyed. We included the obtained collection of sequences in a new MetaPhlAn 4.1 release, which can quantify reads within a metagenome matching the known and newly uncovered viral diversity. Additionally, we released the viral database for further virome and metagenomic studies of the human microbiome.}, } @article {pmid38463387, year = {2024}, author = {Zhang, A and Lao, X and Liang, J and Xia, X and Ma, L and Liang, J}, title = {Case Report: Pneumonia Caused by Chlamydia Psittaci and Cryptococcus Co-Infection.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {845-849}, pmid = {38463387}, issn = {1178-6973}, abstract = {This study presents a rare case of pneumonia caused by a co-infection of Chlamydia psittaci and Cryptococcus, confirmed by metagenomic next-generation sequencing (mNGS). The patient, who had underlying chronic hepatitis B, had adopted a stray pigeon before the onset of the disease. The primary symptoms were fever, and a productive cough. The patient recovered following treatment with moxifloxacin and itraconazole. C. psittaci and Cryptococcus infections may both have been transmitted from the stray pigeon. This report highlights the potential for infections caused by multiple zoonotic pathogens and the value of mNGS for making the diagnosis of these infections.}, } @article {pmid38463002, year = {2024}, author = {Geng, Y and Xiong, Z and Yang, L and Lian, CA and Pavlostathis, SG and Qiu, Z and Chen, H and Luo, Q and Liu, Y and Liu, Z and Shao, P and Zou, JP and Jiang, H and Luo, S and Yu, K and Luo, X}, title = {Bidirectional Enhancement of Nitrogen Removal by Indigenous Synergetic Microalgal-Bacterial Consortia in Harsh Low-C/N Wastewater.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c10322}, pmid = {38463002}, issn = {1520-5851}, abstract = {Conventional microalgal-bacterial consortia have limited capacity to treat low-C/N wastewater due to carbon limitation and single nitrogen (N) removal mode. In this work, indigenous synergetic microalgal-bacterial consortia with high N removal performance and bidirectional interaction were successful in treating rare earth tailing wastewaters with low-C/N. Ammonia removal reached 0.89 mg N L[-1] h[-1], 1.84-fold more efficient than a common microalgal-bacterial system. Metagenomics-based metabolic reconstruction revealed bidirectional microalgal-bacterial interactions. The presence of microalgae increased the abundance of bacterial N-related genes by 1.5- to 57-fold. Similarly, the presence of bacteria increased the abundance of microalgal N assimilation by 2.5- to 15.8-fold. Furthermore, nine bacterial species were isolated, and the bidirectional promotion of N removal by the microalgal-bacterial system was verified. The mechanism of microalgal N assimilation enhanced by indole-3-acetic acid was revealed. In addition, the bidirectional mode of the system ensured the scavenging of toxic byproducts from nitrate metabolism to maintain the stability of the system. Collectively, the bidirectional enhancement system of synergetic microalgae-bacteria was established as an effective N removal strategy to broaden the stable application of this system for the effective treatment of low C/N ratio wastewater.}, } @article {pmid38462942, year = {2024}, author = {Leis, E and Katona, R and Dziki, S and McCann, R and Standish, I and Opgenorth, E and Dikkeboom, A and Lim, A and Ford, CE and Goldberg, TL}, title = {Novel Aquareovirus isolated from channel catfish (Ictalurus punctatus) used in mussel restoration efforts in Wisconsin.}, journal = {Journal of fish diseases}, volume = {}, number = {}, pages = {e13938}, doi = {10.1111/jfd.13938}, pmid = {38462942}, issn = {1365-2761}, support = {(R/SFA-24)//University of Wisconsin Seagrant Institute/ ; //University of Wisconsin-Madison/ ; //U.S. Fish and Wildlife Service/ ; }, abstract = {Channel catfish (Ictalurus punctatus) are a food fish extensively reared in aquaculture facilities throughout the world and are also among the most abundant wild catfish species in North America, making them a popular target of anglers. Furthermore, channel catfish are important members of aquatic ecosystems; for example, they serve as a glochidial host for the endangered winged mapleleaf mussel (Quadrula fragosa), making them critical for conserving this species through hatchery-based restoration efforts. During a routine health inspection, a novel aquareovirus was isolated from channel catfish used in mussel propagation efforts at a fish hatchery in Wisconsin. This virus was isolated on brown bullhead cells (ATCC CCL-59) and identified through metagenomic sequencing as a novel member of the family Spinareoviridae, genus Aquareovirus. The virus genome consists of 11 segments, as is typical of the aquareoviruses, with phylogenetic relationships based on RNA-dependent RNA polymerase and major outer capsid protein amino acid sequences showing it to be most closely related to golden shiner virus (aquareovirus C) and aquareovirus C/American grass carp reovirus (aquareovirus G) respectively. The potential of the new virus, which we name genictpun virus 1 (GNIPV-1), to cause disease in channel catfish or other species remains unknown.}, } @article {pmid38462073, year = {2024}, author = {Duan, Y and Zhang, X and Deng, W and Wang, S and Hu, J and Wang, X and Li, W and Chen, B}, title = {The first reported pulmonary nocardiosis caused by Nocardia gipuzkoensis resisted to TMP-SMZ in an immunocompetent patient.}, journal = {Journal of global antimicrobial resistance}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgar.2024.02.008}, pmid = {38462073}, issn = {2213-7173}, abstract = {BACKGROUND: . Nocardia gipuzkoensis was first described as a novel and distinct species in 2020 by Imen Nouioui and pulmonary nocardiosis associated with Nocardia gipuzkoensis was once reported in two bronchiectasis patients. Noteworthy, both reported Nocardia gipuzkoensis cases showed sensitivity to Trimethoprim/Sulfamethoxazol (TMP-SMZ), which are usually recommended for empirical therapy.

METHODS: We reported the third case of Nocardia gipuzkoensis infection in a 16-year-old girl with chief complaints of cough, persistent chest and back pain. No underlying immuno-suppressive conditions and glucocorticoid use was revealed. Patchy lesions next to spine and located in the posterior basal segment of lower lobes of left lung were seen in thorax computed tomography (CT), but no pathogenic bacteria was detected according to routine laboratory testings.

RESULTS: Metagenomic next-generation sequencing (mNGS) combined with Whole Genome Sequencing (WGS) was used to classified our isolate from bronchoalveolar lavage fluid (BALF) as a Nocardia gipuzkoensis. It is worth mentioning that drug susceptibility testing of our isolate showed resistance to TMP-SMZ, which was never reported before. The patient improved remarkably both clinically and radiographically according to the treatment with Imipenem-cilastatin infusion alone.

CONCLUSION: mNGS and WGS showed excellent performance in identifying Nocardia genus to the species level and improving detection rate of Nocardia gipuzkoensis ignored by traditional culture. Different from previously reported cases, Nocardia gipuzkoensis infection case showed resistance to TMP-SMZ, which is an unprecedented finding and a crucial addition to our understanding of the antibacterial spectrum of Nocardia gipuzkoensis. The successful treatment with Imipenem-cilastatin infusion alone in this case is a testament to the importance of precise identification and tailored antibiotic therapy.}, } @article {pmid38462069, year = {2024}, author = {Rossi, A and Marroni, F and Renoldi, N and Di Filippo, G and Gover, E and Marino, M and Innocente, N}, title = {An integrated approach to explore the microbial biodiversity of natural milk cultures for cheesemaking.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2024-24463}, pmid = {38462069}, issn = {1525-3198}, abstract = {The use of natural milk culture (NMC) represents a key factor in PDO Montasio cheeses, contributing to its distinctive sensory profile. The complex microbial ecosystem of NMCs is the result of heat treatment and incubation conditions, which can vary considerably among different production plants. In this study, the microbiota of NMCs collected from 10 PDO Montasio cheese dairies was investigated employing colony counts and metagenomic analysis. Furthermore, residual sugars, organic acids, and volatile profiles were quantitatively investigated. Results showed that Streptococcus thermophilus was the dominant species in all NMCs, and a subdominant population made of other streptococci and L. salivarius was also present. The incubation temperature appeared to be the main driver of biodiversity in NMCs. Metagenomics allowed us to evidence the presence of minor species involving safety (e.g., Staph. aureus) as well as possible functional aspects (Next Generation Probiotics). Statistical analysis based on residual sugars, organic acids, and volatiles' content allowed to correlate the presence of specific microbial groups with metabolites of great technological and sensory relevance, which can contribute to giving value to the artisanal production procedures of NMCs and clarify their role in the creation of the characteristics of PDO Montasio cheese.}, } @article {pmid38459056, year = {2024}, author = {Beavogui, A and Lacroix, A and Wiart, N and Poulain, J and Delmont, TO and Paoli, L and Wincker, P and Oliveira, PH}, title = {The defensome of complex bacterial communities.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {2146}, pmid = {38459056}, issn = {2041-1723}, mesh = {Humans ; *Bacteria/genetics ; *Genome, Bacterial ; Metagenomics ; Genome Size ; CRISPR-Cas Systems ; }, abstract = {Bacteria have developed various defense mechanisms to avoid infection and killing in response to the fast evolution and turnover of viruses and other genetic parasites. Such pan-immune system (defensome) encompasses a growing number of defense lines that include well-studied innate and adaptive systems such as restriction-modification, CRISPR-Cas and abortive infection, but also newly found ones whose mechanisms are still poorly understood. While the abundance and distribution of defense systems is well-known in complete and culturable genomes, there is a void in our understanding of their diversity and richness in complex microbial communities. Here we performed a large-scale in-depth analysis of the defensomes of 7759 high-quality bacterial population genomes reconstructed from soil, marine, and human gut environments. We observed a wide variation in the frequency and nature of the defensome among large phyla, which correlated with lifestyle, genome size, habitat, and geographic background. The defensome's genetic mobility, its clustering in defense islands, and genetic variability was found to be system-specific and shaped by the bacterial environment. Hence, our results provide a detailed picture of the multiple immune barriers present in environmentally distinct bacterial communities and set the stage for subsequent identification of novel and ingenious strategies of diversification among uncultivated microbes.}, } @article {pmid38461661, year = {2024}, author = {Yan, H and Gu, Z and Zhang, Q and Wang, Y and Cui, X and Liu, Y and Yu, Z and Ruan, R}, title = {Detoxification of copper and zinc from anaerobic digestate effluent by indigenous bacteria: Mechanisms, pathways and metagenomic analysis.}, journal = {Journal of hazardous materials}, volume = {469}, number = {}, pages = {133993}, doi = {10.1016/j.jhazmat.2024.133993}, pmid = {38461661}, issn = {1873-3336}, abstract = {The presence of organic-complexed copper and zinc in anaerobic digestate effluent (ADE) poses persistent ecological toxicity. This study investigated the detoxification performance and biotic responses of indigenous bacteria against ethylene diamine tetraacetic acid (EDTA)-complexed Cu(II) and Zn(II). Heavy metals (HMs) stress induced reactive oxygen species (ROS) generation and enhanced extracellular polymeric substances (EPS) secretion. At a Cu(II) influent concentration of 20.0 mg·L[-1], indigenous bacteria removed 88.2% of Cu(II) within nine days. The majority of copper and zinc sequestered by bacteria were stored in the cell envelope, with over 50% of copper and 60% of zinc being immobilized. Transmission electron microscopy mapping (TEM-mapping) revealed significant mineralization of copper and zinc on the cell wall. Proteins abundant in EPS, alongside humic acid-like substances, effectively adsorbed HMs. Indigenous bacteria exhibited the capacity to reduce cupric to the cuprous state and cupric is preferentially reduced to cuprous before reaching reducing capacity saturation. Sulfur precipitation emerges as a crucial pathway for Zn(II) removal. Metagenomic analysis indicated that indigenous bacteria upregulated genes related to HMs homeostasis, efflux, and DNA repair, enhancing its resistance to high concentrations HMs. This study provided theoretical guidance for employing bacterial consortia to eliminate HMs in complex aquatic environments.}, } @article {pmid38461607, year = {2024}, author = {Wang, S and Zhang, C and Zhang, K and Zhang, L and Bi, R and Zhang, Y and Hu, Z}, title = {One-step bioremediation of hypersaline and nutrient-rich food industry process water with a domestic microbial community containing diatom Halamphora coffeaeformis.}, journal = {Water research}, volume = {254}, number = {}, pages = {121430}, doi = {10.1016/j.watres.2024.121430}, pmid = {38461607}, issn = {1879-2448}, abstract = {Proper treatment of hypersaline and nutrient-rich food industry process water (FIPW) is challenging in conventional wastewater plants. Insufficient treatment leads to serious environmental hazards. However, bioremediation of FIPW with an indigenous microbial community can not only recover nutrients but generate biomass of diverse applications. In this study, monoculture of Halamphora coffeaeformis, together with synthetic bacteria isolated from a local wastewater plant, successfully recovered 91% of NH4[+]-N, 78% of total nitrogen, 95% of total phosphorus as well as 82% of total organic carbon from medium enriched with 10% FIPW. All identified organic acids and amino acids, except oxalic acid, were completely removed after 14 days treatment. A significantly higher biomass concentration (1.74 g L[-1]) was achieved after 14 days treatment in the medium with 10% FIPW than that in a nutrient-replete lab medium as control. The harvested biomass could be a potential feedstock for high-value biochemicals and fertilizer production, due to fucoxanthin accumulation (3 mg g[-1]) and a fantastic performance in P assimilation. Metagenomic analysis revealed that bacteria community in the algal system, dominated by Psychrobacter and Halomonas, also contributed to the biomass accumulation and uptake of nutrients. Transcriptomic analysis further disclosed that multiple pathways, involved in translation, folding, sorting and degradation as well as transport and catabolism, were depressed in H. coffeaeformis grown in FIPW-enriched medium, as compared to the control. Collectively, the proposed one-step strategy in this work offers an opportunity to achieve sustainable wastewater management and a way towards circular economy.}, } @article {pmid38461598, year = {2024}, author = {Gou, J and Xia, J and Li, Y and Qiu, Y and Jiang, F}, title = {A novel sulfidogenic process via sulfur reduction to remove arsenate in acid mine drainage: Insights into the performance and microbial mechanisms.}, journal = {Water research}, volume = {254}, number = {}, pages = {121423}, doi = {10.1016/j.watres.2024.121423}, pmid = {38461598}, issn = {1879-2448}, abstract = {Biological sulfidogenic processes based on sulfate-reducing bacteria (SRB) are not suitable for arsenic (As)-containing acid mine drainage (AMD) treatment because of the formation of the mobile thioarsenite during sulfate reduction. In contrast, biological sulfidogenic processes based on sulfur-reducing bacteria (S[0]RB) produce sulfide without pH increase, which could achieve more effective As removal than the SRB-based process. However, the reduction ability and toxicity tolerance of S[0]RB to As remains mysterious, which may substantially affect the practical applicability of this process when treating arsenate (As(V))-containing AMD. Thus, this study aims to develop a biological sulfur reduction process driven by S[0]RB, and explore its long-term performance on As(V) removal and microbial community evolution. Operating under moderately acidic conditions (pH=4.0), the presence of 10 mg/L As(V) significantly suppressed the activity of S[0]RB, leading to the failure of As(V) removal. Surprisingly, a drop in pH to 3.0 enhanced the tolerance of S[0]RB to As toxicity, allowing for efficient sulfide production (396±102 mg S/L) through sulfur reduction. Consequently, effective and stable removal of As(V) (99.9 %) was achieved, even though the sulfidogenic bacteria were exposed to high levels of As(V) (42 mg/L) in long-term trials. Spectral and spectroscopic analysis showed that As-bearing sulfide minerals were present in the bioreactor. Remarkably, the presence of As(V) induced notable changes in the microbial community composition, with Desulfurella and Clostridium identified as predominate sulfur reducers. The qPCR result further revealed an increase in the concentration of functional genes related to As transport (asrA and arsB) in the bioreactor sludge as the pH decreased from 4.0 to 3.0. This suggests the involvement of microorganisms carrying asrA and arsB in an As transport process. Furthermore, metagenomic binning demonstrated that Desulfurella contained essential genes associated with sulfur reduction and As transportation, indicating its genetic potential for sulfide production and As tolerance. In summary, this study underscores the effectiveness of the biological sulfur reduction process driven by S[0]RB in treating As(V)-contaminated AMD. It offers insights into the role of S[0]RB in remediating As contamination and provides valuable knowledge for practical applications.}, } @article {pmid38461372, year = {2024}, author = {Ali, MJ}, title = {Alterations of Lacrimal Sac Microbiota in Failed Dacryocystorhinostomy: The Lacriome Paper 6.}, journal = {Seminars in ophthalmology}, volume = {}, number = {}, pages = {1-6}, doi = {10.1080/08820538.2024.2327481}, pmid = {38461372}, issn = {1744-5205}, abstract = {PURPOSE: To study the metagenomics of the microbes isolated from the lacrimal sac in patients with failed dacryocystorhinostomy (DCR).

METHODS: A prospective study was performed on 10 consecutive patients with failed DCR. Lacrimal sac samples were obtained for metagenomic analysis during the revision endoscopic DCR. The samples were collected intraoperatively after a full-length lacrimal sac marsupialization and immediately transported on ice to the laboratory. A whole shotgun metagenome sequencing was performed on the Illumina[TM] platform following DNA extraction and library preparation. The downstream analysis of the samples was performed using various software packaged in the Squeeze Metapipeline v1.3.0 and marker gene-based metagenomic phylogenetic analysis using MetaPhlAn4.

RESULTS: The five major phyla identified across the samples of failed DCR include Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, and Fusobacteria (Figure 1). The prevalent species include Stenotrophomonas maltophilia, Pseudomonas juntendi, Streptococcus pneumoniae, Acinetobacter ursingii, Citrobacter koseri, and Cutibacterium acnes (Figure 2). Among the other organisms identified, few were from genera candida and mezorhizobium. Among the viruses, the most abundant was the BeAn 58058 virus. It was interesting to note the occasional presence of plasmodium and toxoplasma species. The functional category distribution of KEGG (Kyoto encyclopedia of genes and genomes) data showed microbial metabolism to be the most involved function, followed by cellular processes.

CONCLUSION: This is the first whole metagenome sequencing of the lacrimal sac contents from failed DCR patients. The organisms identified varied significantly from those isolated from patients with primary acquired nasolacrimal duct obstruction (PANDO) using similar techniques and reflect altered lacrimal microbiota in surgically unsuccessful DCRs.}, } @article {pmid38461199, year = {2024}, author = {Papp, M and Tóth, AG and Békési, L and Farkas, R and Makrai, L and Maróti, G and Solymosi, N}, title = {Apis mellifera filamentous virus from a honey bee gut microbiome survey in Hungary.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {5803}, pmid = {38461199}, issn = {2045-2322}, support = {874735//European Union's Horizon 2020/ ; 874735//European Union's Horizon 2020/ ; 874735//European Union's Horizon 2020/ ; ÚNKP-22-3-II//Ministry for Culture and Innovation/ ; LP2020-5/2020//Hungarian Academy of Sciences/ ; }, abstract = {In Hungary, as part of a nationwide, climatically balanced survey for a next-generation sequencing-based study of the honey bee (Apis mellifera) gut microbiome, repeated sampling was carried out during the honey production season (March and May 2019). Among other findings, the presence of Apis mellifera filamentous virus (AmFV) was detected in all samples, some at very high levels. AmFV-derived reads were more abundant in the March samples than in the May samples. In March, a higher abundance of AmFV-originated reads was identified in samples collected from warmer areas compared to those collected from cooler areas. A lower proportion of AmFV-derived reads were identified in samples collected in March from the wetter areas than those collected from the drier areas. AmFV-read abundance in samples collected in May showed no significant differences between groups based on either environmental temperature or precipitation. The AmFV abundance correlated negatively with Bartonella apihabitans, Bartonella choladocola, and positively with Frischella perrara, Gilliamella apicola, Gilliamella sp. ESL0443, Lactobacillus apis, Lactobacillus kullabergensis, Lactobacillus sp. IBH004. De novo metagenome assembly of four samples resulted in almost the complete AmFV genome. According to phylogenetic analysis based on DNA polymerase, the Hungarian strains are closest to the strain CH-05 isolated in Switzerland.}, } @article {pmid38460819, year = {2024}, author = {Park, SY and Ardura, MI and Zhang, SX}, title = {Diagnostic Limitations and Challenges in Current Clinical Guidelines and Potential Application of Metagenomic Sequencing to Manage Pulmonary Invasive Fungal Infections in Patients with Haematological Malignancies.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2024.03.003}, pmid = {38460819}, issn = {1469-0691}, abstract = {BACKGROUND: Pulmonary invasive fungal infections (pIFI) disproportionately affect patients with haematological malignancies (HM). Establishing a rapid and accurate diagnosis of pIFI is challenging. Multiple guidelines recommend diagnostic testing of invasive fungal infections but lack consensus and may contribute to inconsistent diagnostic approaches.

OBJECTIVE: To identify key diagnostic challenges and review metagenomic sequencing data.

SOURCES: PubMed, professional consortium, and scientific society websites search to identify relevant, published, evidence-based clinical guidelines within the past five years. PubMed search for papers describing clinically relevant novel diagnostic technologies.

CONTENT: Current guidelines of patients with HM and suspected pIFI recommend chest CT imaging and specimen testing with microscopic examination (including calcofluor white stain, histopathology, cytopathology etc), Aspergillus galactomannan, beta-D-glucan, PCR, and culture, each with certain limitations. Emerging real-world data support the adjunctive use of metagenomic sequencing-based tests for the timely diagnosis of pIFI.

IMPLICATIONS: High quality evidence from robust clinical trials is needed to determine whether guidelines should be updated to include novel diagnostic technologies. Trials should ask whether the combination of powerful novel diagnostics such as pathogen-agnostic metagenomic sequencing technologies in conjunction with conventional testing can optimize the diagnostic yield for all potential pIFI pathogens that impact the health of patients with HM.}, } @article {pmid38460685, year = {2024}, author = {Zhang, Y and Ren, Y and Zhou, S and Ning, X and Wang, X and Yang, Y and Sun, S and Vinay, N and Bahn, M and Han, J and Liu, Y and Xiong, Y and Liao, Y and Mo, F}, title = {Spatio-temporal microbial regulation of aggregate-associated priming effects under contrasting tillage practices.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {171564}, doi = {10.1016/j.scitotenv.2024.171564}, pmid = {38460685}, issn = {1879-1026}, abstract = {The heterogeneous distribution and dynamic changes of soil microorganisms are important drivers of spatio-temporal patterns of SOC decomposition, which are highly sensitive to tillage intensity in agroecosystems. However, little is known about the microbial mechanisms by which tillage intensity regulates the priming effect (PE) dynamics in heterogeneous spatial environments such as aggregates. Herein, a microcosm was established by adding [13]C-labeled straw residue to three distinct aggregate-size classes (i.e., mega-, macro-, and micro-aggregates) from two long-term contrasting tillage histories (no-till [NT] and conventional plow tillage [CT]) for 160 days to observe the spatio-temporal variations in PE. Metagenomic sequencing and Fourier transform mid-infrared techniques were used to assess the relative importance of C-degrading functional genes, microbial community succession, and SOC chemical composition in aggregate-associated PE dynamics during straw decomposition. Spatially, straw addition induced a positive PE for all aggregates, with stronger PE occurring in larger aggregates, especially in CT soil compared to NT soil. Larger aggregates have more unique microbial communities enriched in genes for simple C degradation (e.g., E5.1.3.6, E2.4.1.7, pmm-pgm, and KduD in Nitrosospeera and Burkholderia), supporting the higher short-term PE; however, the CT soils harbored more genes for complex C degradation (e.g., TSTA3, fcl, pmm-pgm, and K06871 in Gammaproteobacteria and Phycicoccus), supporting a stronger long-term PE. Temporally, soil aggregates dominated early-stage PEs (i.e., < 59 days after residue addition) through co-metabolism and nitrogen (N) mining, as evidenced by the increased microbial biomass C and dissolved organic C (DOC) and reduced inorganic N with increasing aggregate-size class. At a later stage, however, the legacy effect of tillage histories controlled the PEs via microbial stoichiometry decomposition, as suggested by the higher DOC-to-inorganic N and DOC-to-available P stoichiometries in CT than NT. Our study underscores the importance of including both spatial and temporal microbial dynamics to fully understand the mechanisms of SOC priming, particularly under long-term contrasting tillage practices.}, } @article {pmid38460226, year = {2024}, author = {Liu, W and Li, J and Liu, T and Zheng, M and Meng, J and Li, J}, title = {Temperature-resilient superior performances by coupling partial nitritation/anammox and iron-based denitrification with granular formation.}, journal = {Water research}, volume = {254}, number = {}, pages = {121424}, doi = {10.1016/j.watres.2024.121424}, pmid = {38460226}, issn = {1879-2448}, abstract = {Partial nitritation-anammox (PN/A), an energy-neutral process, is widely employed in the treatment of nitrogen-rich wastewater. However, the intrinsic nitrate accumulation limits the total nitrogen (TN) removal, and the practical application of PN/A continues to face a significant challenge at low temperatures (<15 °C). Here, an integrated partial nitritation-anammox and iron-based denitrification (PNAID) system was developed to address the concern. Two up-flow bioreactors were set up and operated for 400 days, with one as the control group and the other as the experiment group with the addition of Fe[0]. In comparison to the control group, the experiment group with the Fe[0] supplement showed better nitrogen removal during the entire course of the experiment at different temperature levels. Specifically, the TN removal efficiency of the control group decreased from 82.9 % to 53.9 % when the temperature decreased from 30 to 12 °C, while in stark contrast, the experiment group consistently achieved 80 % of TN removal in the same condition. Apart from the enhanced nitrogen removal, the experiment group also exhibited better phosphorus removal (10.6 % versus 74.1 %) and organics removal (49.5 % versus 65.1 %). The enhanced and resilient nutrient removal performance of the proposed integrated process under low temperatures appeared to be attributed to the compact structure of granules and the increased microbial metabolism with Fe[0] supplement, elucidated by a comprehensive analysis including microbial-specific activity, apparent activation energy, characteristics of granular sludge, and metagenomic sequencing. These results clearly confirmed that Fe[0] supplement not only improved nitrogen removal of PN/A process, but also conferred a certain degree of robustness to the system in the face of temperature fluctuations.}, } @article {pmid38460225, year = {2024}, author = {Xu, Y and Liu, H and Geng, H and Liu, R and Dai, X}, title = {Evaporation-driven interfacial restructuring induces highly efficient methanogenesis of waste biomass.}, journal = {Water research}, volume = {254}, number = {}, pages = {121422}, doi = {10.1016/j.watres.2024.121422}, pmid = {38460225}, issn = {1879-2448}, abstract = {Methanogenesis of waste biomass (WB) is a promising method for global sustainable development, reduction of pollution and carbon emission levels, and recovering bioenergy. Unlike in the methanogenesis of organic wastewater, in which microbial cells come into direct contact with the dissolved substrate, the 'solid-liquid-solid' modes in WB and between WB and microbial cells, which involve numerous solid-liquid interfaces, greatly hinder the methanogenesis efficiency of WB. Amongst all WB, waste activated sludge is the most complex, poorly biodegradable and representative. Herein, we highlight the role of water evaporation-driven solid-liquid interfacial restructuring of sludge in determining its methanogenesis efficiency. Non-free water evaporation increased surface roughness and adhesion, and compressed pore structure with numerous capillaries in sludge, resulting in a new solid-liquid interface of sludge with great capillary force and highly ordered interfacial water molecules, which provides an extremely favourable condition for high mass transfer and proton-coupled electron transfer (PCET) in sludge. This restructuring was confirmed to induce the enhancement of solid-liquid interfacial noncovalent interactions and electron transfer efficiency in the subsequent methanogenesis process (P < 0.05), promoting the effective contact between the sludge substrate and microbial cells, thereby enriching the methanogenic consortia (i.e., Clostridia and Methanosarcina were increased by 290.0 % and 239.7 %, respectively) and improving the activities of key enzymes. Stable isotope tracing and metagenomic analysis further reveal that this restructuring promoted the participation of water molecules in the methane formation by PCET-driven release of protons from water, and enhanced main methanogenesis metabolic pathways, especially the metabolic pathway of CO2-reduction methanogenesis (+65.2 %), thereby resulting in a great advance in methane generation (+147 %, P < 0.001). The findings can provide a reference for regulating directional anaerobic biotransformation of water-rich multiphase complex substrates by interfacial restructuring inducement.}, } @article {pmid38460218, year = {2024}, author = {Zhang, X and Chen, Y and Lv, Z and Zhou, L and Guo, Y}, title = {Analysis of the effects of β-mannanase on immune function and intestinal flora in broilers fed the low energy diet based on 16S rRNA sequencing and metagenomic sequencing.}, journal = {Poultry science}, volume = {103}, number = {5}, pages = {103581}, doi = {10.1016/j.psj.2024.103581}, pmid = {38460218}, issn = {1525-3171}, abstract = {As an enzyme, β-mannanase (BM) can be widely used as feed additive to improve the growth performance of animals. This experiment aimed to determine the effect of the addition of BM to low-energy diet on the immune function and intestinal microflora of broiler chickens. In this study, 384 one-day-old Arbor Acres broilers were randomly divided into 3 groups (8 replicates per group): positive control (PC, received a corn-soybean meal basal diet), negative control (NC, received a low-energy diet with Metabolizable Energy (ME) reduced by 50 kcal/kg) and NC + BM group (NC birds + 100 mg/kg BM). All birds were raised for 42 d. The results showed that BM mitigated the damage of immune function in peripheral blood of broilers caused by the decrease of dietary energy level by increasing the Concanavalin A (Con A) index of stimulation (SI) and macrophages phagocytic activity in the peripheral blood of broilers at 42 d (P < 0.05). The analysis of cecum flora showed that the low-energy diet significantly reduced the observed_species index (P < 0.01), Chao1 index and ACE index (P < 0.05), which reduced the abundance and evenness of species in the cecum of broilers at 21 d. It also significantly reduced the relative abundance of Candidatus_Arthromitus and significantly increased the relative abundance of Pseudomonas in the cecum of broilers at 21 d, while also significantly increasing the relative abundance of Monoglobus at 42 d. BM significantly increased the relative abundance of Lachnospiraceae_UCG-001 and Lachnospiraceae_bacterium_615 in the cecum of broilers at 21 d. In addition, BM inhibited microbial Fatty acid degradation by decreasing the activity of glutaryl-CoA dehydrogenase. Collectively, BM could improve intestinal health by enhancing the immune function of broilers, promoting the proliferation of beneficial bacteria and reducing the number of harmful bacteria, regulating intestinal flora, thereby alleviating the adverse effects of lower dietary energy levels.}, } @article {pmid38459523, year = {2024}, author = {Xiong, X and Gong, J and Lu, T and Yuan, L and Lan, Y and Tu, X}, title = {Characteristics of intestinal bacteriophages and their relationship with Bacteria and serum metabolites during quail sexual maturity transition.}, journal = {BMC veterinary research}, volume = {20}, number = {1}, pages = {93}, pmid = {38459523}, issn = {1746-6148}, support = {2022JXCQZY02//Jiangxi Joint Key Project of Quail Improvement/ ; }, abstract = {BACKGROUND: Bacteriophages are prokaryotic viruses that rank among the most abundant microbes in the gut but remain among the least understood, especially in quails. In this study, we surveyed the gut bacteriophage communities in 22 quails at different ages (days 20 and 70) using shotgun metagenomic sequencing. We then systematically evaluated the relationships with gut bacteria and host serum metabolites.

RESULTS: We discovered that Myoviridae and Siphoviridae were the dominant bacteriophage families in quails. Through a random forest and LEfSe analysis, we identified 23 differential bacteriophages with overlapping presence. Of these, 21 bacteriophages (e.g., Enterococcus phage IME-EFm5 and Enterococcus phage IME-EFm1) showed higher abundances in the day 20 group, while two bacteriophages (Bacillus phage Silence and Bacillus virus WPh) were enriched in the day 70 group. These key bacteriophages can serve as biomarkers for quail sexual maturity. Additionally, the differential bacteriophages significantly correlated with specific bacterial species and shifts in the functional capacities of the gut microbiome. For example, Enterococcus phages (e.g., Enterococcus phage EFP01, Enterococcus phage IME-EFm5, and Enterococcus phage IME-EFm1) were significantly (P < 0.001, FDR) and positively correlated with Enterococcus faecalis. However, the relationships between the host serum metabolites and either bacteriophages or bacterial species varied. None of the bacteriophages significantly (P > 0.05, FDR) correlated with nicotinamide riboside and triacetate lactone. In contrast, some differential bacterial species (e.g., Christensenella massiliensis and Bacteroides neonati) significantly (P < 0.05, FDR) correlated with nicotinamide riboside and triacetate lactone. Furthermore, characteristic successional alterations in gut bacteriophages, bacteria, and host serum metabolites across different ages highlighted a sexual maturity transition coexpression network.

CONCLUSION: This study improves our understanding of the gut bacteriophage characteristics in quails and offers profound insights into the interactions among gut bacteriophages, bacteria, and host serum metabolites during the quail's sexual maturity transition.}, } @article {pmid38458994, year = {2024}, author = {Coelho, LP and Santos-Júnior, CD and de la Fuente-Nunez, C}, title = {Challenges in computational discovery of bioactive peptides in 'omics data.}, journal = {Proteomics}, volume = {}, number = {}, pages = {e2300105}, doi = {10.1002/pmic.202300105}, pmid = {38458994}, issn = {1615-9861}, support = {//Procter & Gamble Company, United Therapeutics/ ; //BBRF Young Investigator Grant/ ; //Nemirovsky Prize/ ; //Penn Health-Tech Accelerator Award/ ; //Dean's Innovation Fund from the Perelman School of Medicine at the University of Pennsylvania/ ; FT230100724//Australian Research Council/ ; //Langer Prize (AIChE Foundation)/ ; R35GM138201//National Institute of General Medical Sciences of the National Institutes of Health/ ; DTRA//Defense Threat Reduction Agency/ ; HDTRA11810041//Defense Threat Reduction Agency/ ; HDTRA1-21-1-0014//Defense Threat Reduction Agency/ ; HDTRA1-23-1-0001//Defense Threat Reduction Agency/ ; }, abstract = {Peptides have a plethora of activities in biological systems that can potentially be exploited biotechnologically. Several peptides are used clinically, as well as in industry and agriculture. The increase in available 'omics data has recently provided a large opportunity for mining novel enzymes, biosynthetic gene clusters, and molecules. While these data primarily consist of DNA sequences, other types of data provide important complementary information. Due to their size, the approaches proven successful at discovering novel proteins of canonical size cannot be naïvely applied to the discovery of peptides. Peptides can be encoded directly in the genome as short open reading frames (smORFs), or they can be derived from larger proteins by proteolysis. Both of these peptide classes pose challenges as simple methods for their prediction result in large numbers of false positives. Similarly, functional annotation of larger proteins, traditionally based on sequence similarity to infer orthology and then transferring functions between characterized proteins and uncharacterized ones, cannot be applied for short sequences. The use of these techniques is much more limited and alternative approaches based on machine learning are used instead. Here, we review the limitations of traditional methods as well as the alternative methods that have recently been developed for discovering novel bioactive peptides with a focus on prokaryotic genomes and metagenomes.}, } @article {pmid38458421, year = {2024}, author = {Liu, Y and Qin, S and Lan, C and Huang, Q and Zhang, P and Cao, W}, title = {Effectiveness of Metagenomic Next-Generation Sequencing in the Diagnosis of Infectious Diseases: A Systematic Review and Meta-Analysis.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {106996}, doi = {10.1016/j.ijid.2024.106996}, pmid = {38458421}, issn = {1878-3511}, abstract = {OBJECTIVES: Early diagnosis of infectious diseases remains a challenge. This study assessed the diagnostic value of mNGS in infections and explored the effect of various factors on the accuracy of mNGS.

METHODS: An electronic article search of PubMed, Cochrane Library, and Embase was performed. A total of 85 papers were eligible for inclusion and analysis. Stata 12.0 was used for statistical calculation to evaluate the efficacy of mNGS for the diagnosis of infectious diseases.

RESULTS: The AUC of 85 studies was 0.88 (95%CI, 0.85-0.90). The AUC of the clinical comprehensive diagnosis and conventional test groups was 0.92 (95%CI, 0.89-0.94) and 0.82 (95%CI, 0.78-0.85), respectively. The results of subgroup analysis indicated that the PLR and NLR were 12.67 (95%CI, 6.01-26.70) and 0.05 (95%CI, 0.03-0.10), respectively, in arthrosis infections. The PLR was 24.41 (95%CI, 5.70-104.58) in central system infections and the NLR of immunocompromised patients was 0.08 (95%CI, 0.01-0.62).

CONCLUSION: mNGS demonstrated satisfactory diagnostic performance for infections, especially for bone and joint infections and central system infections. Moreover, mNGS also has a high value in the exclusion of infection in immunocompromised patients.}, } @article {pmid38458256, year = {2024}, author = {Mishra, S and Tejesvi, MV and Hekkala, J and Turunen, J and Kandikanti, N and Kaisanlahti, A and Suokas, M and Leppä, S and Vihinen, P and Kuitunen, H and Sunela, K and Koivunen, J and Jukkola, A and Kalashnikov, I and Auvinen, P and Kääriäinen, OS and Peñate Medina, T and Peñate Medina, O and Saarnio, J and Meriläinen, S and Rautio, T and Aro, R and Häivälä, R and Suojanen, J and Laine, M and Erawijattari, P and Lahti, L and Karihtala, P and Ruuska, TS and Reunanen, J}, title = {Gut microbiome-derived bacterial extracellular vesicles in patients with solid tumours.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2024.03.003}, pmid = {38458256}, issn = {2090-1224}, abstract = {INTRODUCTION: Gut microbiome-derived nanoparticles, known as bacterial extracellular vesicles (bEVs), have garnered interest as promising tools for studying the link between the gut microbiome and human health. The diverse composition of bEVs, including their proteins, mRNAs, metabolites, and lipids, makes them useful for investigating diseases such as cancer. However, conventional approaches for studying gut microbiome composition alone may not be accurate in deciphering host-gut microbiome communication. In clinical microbiome research, there is a gap in the knowledge on the role of bEVs in solid tumor patients.

OBJECTIVES: Analyzing the functionality of bEVs using (meta)genomics and proteomics could highlight the unique aspects of host-gut microbiome interactions in solid tumor patients. Therefore, we performed a comparative analysis of the proteome and microbiota composition of gut microbiome-derived bEVs isolated from patients with solid tumors and healthy controls.

METHODS: After isolating bEVs from the feces of solid tumor patients and healthy controls, we performed spectrometry analysis of their proteomes and next-generation sequencing (NGS) of the 16S gene. We also investigated the gut microbiomes of feces from patients and controls using 16S sequencing and machine learning to classify the samples into patients and controls based on their bEVs and fecal microbiomes.

RESULTS: Solid tumor patients showed decreased microbiota richness and diversity in both the bEVs and feces. However, the bEV proteomes were more diverse in patients than in the controls and were enriched with proteins associated with the metabolism of amino acids and carbohydrates, nucleotide binding, and oxidoreductase activity. Metadata classification of samples was more accurate using fecal bEVs (100%) compared with fecal samples (93%).

CONCLUSION: Our findings suggest that bEVs are unique functional entities. There is a need to explore bEVs together with conventional gut microbiome analysis in functional cancer research to decipher the potential of bEVs as cancer diagnostic or therapeutic biomarkers.}, } @article {pmid38458136, year = {2024}, author = {Pragya, K and Sreya, P and Vighnesh, L and Mahima, D and Sushmita, M and Sasikala, C and Venkata Ramana, C}, title = {Phylogenomic analysis of metagenome-assembled genomes indicates new taxa in the order Spirochaetales and proposal of Thalassospirochaeta sargassi gen. nov. sp. nov. from seaweeds.}, journal = {Systematic and applied microbiology}, volume = {47}, number = {2-3}, pages = {126502}, doi = {10.1016/j.syapm.2024.126502}, pmid = {38458136}, issn = {1618-0984}, abstract = {Six metagenome-assembled genomes (JB008[Ts], JB007, JB015, JB003, JB004, and JB002) belonging to the order Spirochaetales were generated from seaweed samples collected from the Gulf of Mannar, India. The binned genomes JB008[Ts] and JB007 shared highest 16S rRNA gene identity of 94.9 % and 92.2-93.4 %, respectively with uncultivated Spirochaetaceae family members, and < 90 % identity with Marispirochaeta aestuari JC444[T]. While, the bin JB015 showed 99.1 % identity with Pleomorphochaeta naphthae SEBR 4209[T]. The phylogenomic and 16S rRNA gene-based phylogenetic analysis of the binned genomes JB007 and JB008[Ts] confirmed that these members belong to the family Spirochaetaceae and bins JB015, JB002, JB003, and JB004 belong to the genus Pleomorphochaeta within the family Sphaerochaetaceae. The AAI values of the binned genomes JB007 and JB008[Ts] compared to other members of the Spirochaetaceae family were between 53.9- 56.8 % and 53.8-57.1 %, respectively. Furthermore, the comparison of ANI, dDDH, and POCP metrics of the binned genomes JB007 and JB008[Ts], both among themselves and with the members of Spirochaetaceae, was also below the suggested thresholds for genera delineation. Consequently, the binned genome JB008[Ts] is proposed as a new genus according to the guidelines of code of nomenclature of prokaryotes described from sequence data (SeqCode) with the name Thalassospirochaeta sargassi gen. nov. sp. nov., in the family Spirochaetaceae while the bin JB007 could not be proposed as novel taxa due to low-quality estimates. The bin JB015 and its additional genomes form a distinct clade, but their taxonomic status remains ambiguous due to the absence of genomic evidence from other Pleomorphochaeta members.}, } @article {pmid38458119, year = {2024}, author = {Li, J and Luo, C and Cai, X and Dai, Y and Zhang, D and Zhang, G}, title = {Cultivation and characterization of functional-yet-uncultivable phenanthrene degraders by stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC).}, journal = {Environment international}, volume = {185}, number = {}, pages = {108555}, doi = {10.1016/j.envint.2024.108555}, pmid = {38458119}, issn = {1873-6750}, abstract = {High-throughput identification and cultivation of functional-yet-uncultivable microorganisms is a fundamental goal in environmental microbiology. It remains as a critical challenge due to the lack of routine and effective approaches. Here, we firstly proposed an approach of stable-isotope-probing and metagenomic-binning directed cultivation (SIP-MDC) to isolate and characterize the active phenanthrene degraders from petroleum-contaminated soils. From SIP and metagenome, we assembled 13 high-quality metagenomic bins from [13]C-DNA, and successfully obtained the genome of an active PHE degrader Achromobacter (genome-MB) from [13]C-DNA metagenomes, which was confirmed by gyrB gene comparison and average nucleotide/amino identity (ANI/AAI), as well as the quantification of PAH dioxygenase and antibiotic resistance genes. Thereinto, we modified the traditional cultivation medium with antibiotics and specific growth factors (e.g., vitamins and metals), and separated an active phenanthrene degrader Achromobacter sp. LJB-25 via directed isolation. Strain LJB-25 could degrade phenanthrene and its identity was confirmed by ANI/AAI values between its genome and genome-MB (>99 %). Our results hinted at the feasibility of SIP-MDC to identify, isolate and cultivate functional-yet-uncultivable microorganisms (active phenanthrene degraders) from their natural habitats. Our findings developed a state-of-the-art SIP-MDC approach, expanded our knowledge on phenanthrene biodegradation mechanisms, and proposed a strategy to mine functional-yet-uncultivable microorganisms.}, } @article {pmid38457966, year = {2024}, author = {Gajera, G and Funde, S and Palep, H and Kothari, V}, title = {Duration of fermentation affects microbiome composition and biological activity of an Indian traditional formulation - Panchagavya.}, journal = {Journal of Ayurveda and integrative medicine}, volume = {15}, number = {2}, pages = {100880}, doi = {10.1016/j.jaim.2023.100880}, pmid = {38457966}, issn = {0975-9476}, abstract = {OBJECTIVE: This study aimed at investigating whether the duration of fermenting Panchagavya (PG) preparation in copper vessel affects its biological activity and microbiome composition.

MATERIALS AND METHODS: Prophylactic potential of PG against bacterial infection was assessed through an in vivo assay employing the nematode worm Caenorhabditis elegans as a model host. Bacterial diversity of the PG samples was revealed through metagenomic analysis.

RESULTS: Duration of fermentation was found to affect biological activity as well as microbiome composition of the PG samples. PG-samples fermented ≥60 min lost their prophylactic potential, and develop anthelmintic activity. Bacterial phyla whose relative abundance was significantly different between the prophylactic and anthelmintic PG samples were Planctomycetota, Proteabacteria, Bacteroidota, Verrucomicrobiota, Patescibacteria, Acidobacteriota, Chloroflexi, Firmicutes and Campilobacterota.

CONCLUSION: This study validates the prophylactic potential of Panchagavya against bacterial pathogens, and shows that duration of the fermentation time while preparing PG can have profound effect on its biological activities. Biological activities of PG samples seem to have a correlation with their inherent microbial community. Metagenomic profiling can be an effective tool for standardization of PG formulations.}, } @article {pmid38457496, year = {2024}, author = {Pigani, E and Mele, BH and Campese, L and Ser-Giacomi, E and Ribera, M and Iudicone, D and Suweis, S}, title = {Deviation from neutral species abundance distributions unveils geographical differences in the structure of diatom communities.}, journal = {Science advances}, volume = {10}, number = {10}, pages = {eadh0477}, pmid = {38457496}, issn = {2375-2548}, abstract = {In recent years, the application of metagenomics techniques has advanced our understanding of plankton communities and their global distribution. Despite this progress, the relationship between the abundance distribution of diatom species and varying marine environmental conditions remains poorly understood. This study, leveraging data from the Tara Oceans expedition, tests the hypothesis that diatoms in sampled stations display a consistent species abundance distribution structure, as though they were sampled from a single ocean-wide metacommunity. Using a neutral sampling theory, we thus develop a framework to estimate the structure and diversity of diatom communities at each sampling station given the shape of the species abundance distribution of the metacommunity and the information of a reference station. Our analysis reveals a substantial temperature gradient in the discrepancies between predicted and observed biodiversity across the sampled stations. These findings challenge the hypothesis of a single neutral metacommunity, indicating that environmental differences substantially influence both the composition and structure of diatom communities.}, } @article {pmid38456699, year = {2024}, author = {Scilipoti, S and Molari, M}, title = {High-quality draft genome of Gammaproteobacterial SUP05 cluster from non-buoyant hydrothermal plumes of ultraslow spreading Gakkel Ridge (Central Arctic Ocean).}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0012124}, doi = {10.1128/mra.00121-24}, pmid = {38456699}, issn = {2576-098X}, abstract = {Hydrothermal plumes are an important yet understudied component of deep-sea microbial ecosystems. We report metagenome-assembled genomes (MAGs) of three Bacteria belonging to the Gammaproteobacterial SUP05 cluster (family Thioglobaceae), assembled from the metagenomes of two non-buoyant hydrothermal plumes in the ultraslow spreading Gakkel Ridge.}, } @article {pmid38169425, year = {2024}, author = {Kidani, Y and Kitagawa, Y and Hagiwara, M and Kawashima, A and Kanazawa, T and Wada, H and Uemura, M and Nonomura, N and Motooka, D and Nakamura, S and Ohkura, N and Sakaguchi, S}, title = {Downregulation of TCF7 and LEF1 is a key determinant of tumor-infiltrating regulatory T-cell function.}, journal = {International immunology}, volume = {36}, number = {4}, pages = {167-182}, doi = {10.1093/intimm/dxad053}, pmid = {38169425}, issn = {1460-2377}, support = {16H06295//Grant-in-Aid for Specially Promoted Research/ ; 18cm0106303h0003//Project for Development of Innovative Research on Cancer Therapeutics/ ; JP 19gm0010005//Core Research for Evolutional Science and Technology/ ; 18gm0010005h0001//Leading Advanced Projects for medical innovation/ ; //Osaka University/ ; }, abstract = {Forkhead box P3 (Foxp3)-expressing regulatory T (Treg) cells play essential roles in immune homeostasis but also contribute to establish a favorable environment for tumor growth by suppressing anti-tumor immune responses. It is thus necessary to specifically target tumor-infiltrating Treg cells to minimize effects on immune homeostasis in cancer immunotherapy. However, molecular features that distinguish tumor-infiltrating Treg cells from those in secondary lymphoid organs remain unknown. Here we characterize distinct features of tumor-infiltrating Treg cells by global analyses of the transcriptome and chromatin landscape. They exhibited activated phenotypes with enhanced Foxp3-dependent transcriptional regulation, yet being distinct from activated Treg cells in secondary lymphoid organs. Such differences may be attributed to the extensive clonal expansion of tumor-infiltrating Treg cells. Moreover, we found that TCF7 and LEF1 were specifically downregulated in tumor-infiltrating Treg cells both in mice and humans. These factors and Foxp3 co-occupied Treg suppressive function-related gene loci in secondary lymphoid organ Treg cells, whereas the absence of TCF7 and LEF1 accompanied altered gene expression and chromatin status at these gene loci in tumor-infiltrating Treg cells. Functionally, overexpression of TCF7 and LEF1 in Treg cells inhibited the enhancement of Treg suppressive function upon activation. Our results thus show the downregulation of TCF7 and LEF1 as markers of highly suppressive Treg cells in tumors and suggest that their absence controls the augmentation of Treg suppressive function in tumors. These molecules may be potential targets for novel cancer immunotherapy with minimum effects on immune homeostasis.}, } @article {pmid38456288, year = {2024}, author = {Adewusi, OO and Waldner, CL and Hanington, PC and Hill, JE and Freeman, CN and Otto, SJG}, title = {Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review.}, journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc}, volume = {}, number = {}, pages = {10406387241235968}, doi = {10.1177/10406387241235968}, pmid = {38456288}, issn = {1943-4936}, abstract = {Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was to synthesize knowledge on the direct application of long-read metagenomic sequencing to respiratory samples to detect bacterial pathogens and antimicrobial resistance genes (ARGs) compared to PCR, loop-mediated isothermal amplification, and recombinase polymerase amplification. Our scoping review protocol followed the Joanna Briggs Institute and PRISMA Scoping Review reporting guidelines. Included studies reported on the direct application of these methods to respiratory samples from animals or humans to detect bacterial pathogens ±ARGs and included turnaround time (TAT) and analytical sensitivity. We excluded studies not reporting these or that were focused exclusively on bioinformatics. We identified 5,636 unique articles from 5 databases. Two-reviewer screening excluded 3,964, 788, and 784 articles at 3 levels, leaving 100 articles (19 animal and 81 human), of which only 7 studied long-read sequencing (only 1 in animals). Thirty-two studies investigated ARGs (only one in animals). Reported TATs ranged from minutes to 2 d; steps did not always include sample collection to results, and analytical sensitivity varied by study. Our review reveals a knowledge gap in research for the direct detection of bacterial respiratory pathogens and ARGs in animals using long-read metagenomic sequencing. There is an opportunity to harness the rapid development in this space to detect multiple pathogens and ARGs on a single sequencing run. Long-read metagenomic sequencing tools show potential to address the urgent need for research into rapid tests to support antimicrobial stewardship in food animal production.}, } @article {pmid38455752, year = {2024}, author = {Chen, XH and Zhou, SJ and Liu, YY and Cao, H and Zheng, YR and Chen, Q}, title = {Application value of metagenomics next-generation sequencing in the diagnosis of respiratory virus infection after congenital heart surgery.}, journal = {Translational pediatrics}, volume = {13}, number = {2}, pages = {260-270}, doi = {10.21037/tp-23-341}, pmid = {38455752}, issn = {2224-4344}, abstract = {BACKGROUND: Timely and accurate pathogen diagnosis can be challenging in children who contract a respiratory virus following congenital heart surgery (CHS). This often results in suboptimal drug use and treatment delays. Metagenomics next-generation sequencing (mNGS) is a swift, efficient, and unbiased method for obtaining microbial nucleic acid sequences. This technology holds promise as a comprehensive diagnostic tool, especially for pathogens undetectable by traditional methods. However, the efficacy of mNGS in the context of congenital heart disease infections remains uncertain. This study aimed to explore the diagnostic value of mNGS for respiratory virus infections post-CHS.

METHODS: We conducted a retrospective analysis of patients who developed respiratory tract infections post-CHS and were admitted to our cardiac center between July 2021 and December 2022. The patients were categorized into the following two groups based on the diagnostic method used: (I) the mNGS group (comprising 62 patients); and (II) the conventional microbiological test (CMT) group (comprising 70 patients). Bronchoalveolar lavage fluid (BALF) samples from these patients were tested to identify pathogens.

RESULTS: The mNGS group had significantly higher detection rates for both viral infections and mixed viral infections than the CMT group (56.45% vs. 17.14%, P<0.001, and 80.00% vs. 16.67%, P<0.001, respectively). In the mNGS group, 19.35% of the patients received antiviral therapy, and 61.29% received an anti-infective regimen adjustment. Conversely, in the CMT group, only 4.29% received antiviral therapy, and 28.57% received an anti-infective regimen adjustment. A higher percentage of patients showed improved respiratory symptoms in the mNGS group than the CMT group (74.19% vs. 44.29%, P=0.001). Additionally, the mNGS group had a shorter duration of mechanical ventilation and a reduced length of stay in the cardiac intensive care unit than the CMT group (P=0.012).

CONCLUSIONS: Using mNGS for BALF enhances the detection of respiratory viral infections and coexisting viral infections post-CHS. This facilitates more precise treatment strategies and could potentially lead to improved patient outcomes.}, } @article {pmid38455360, year = {2023}, author = {Zhou, D and Chen, Y and Wang, Z and Zhu, S and Zhang, L and Song, J and Bai, T and Hou, X}, title = {Integrating clinical and cross-cohort metagenomic features: a stable and non-invasive colorectal cancer and adenoma diagnostic model.}, journal = {Frontiers in molecular biosciences}, volume = {10}, number = {}, pages = {1298679}, doi = {10.3389/fmolb.2023.1298679}, pmid = {38455360}, issn = {2296-889X}, abstract = {Background: Dysbiosis is associated with colorectal cancer (CRC) and adenomas (CRA). However, the robustness of diagnostic models based on microbial signatures in multiple cohorts remains unsatisfactory. Materials and Methods: In this study, we used machine learning models to screen metagenomic signatures from the respective cross-cohort datasets of CRC and CRA (selected from CuratedMetagenomicData, each disease included 4 datasets). Then select a CRC and CRA data set from the CuratedMetagenomicData database and meet the requirements of having both metagenomic data and clinical data. This data set will be used to verify the inference that integrating clinical features can improve the performance of microbial disease prediction models. Results: After repeated verification, we selected 20 metagenomic features that performed well and were stably expressed within cross-cohorts to represent the diagnostic role of bacterial communities in CRC/CRA. The performance of the selected cross-cohort metagenomic features was stable for multi-regional and multi-ethnic populations (CRC, AUC: 0.817-0.867; CRA, AUC: 0.766-0.833). After clinical feature combination, AUC of our integrated CRC diagnostic model reached 0.939 (95% CI: 0.932-0.947, NRI=30%), and that of the CRA integrated model reached 0.925 (95%CI: 0.917-0.935, NRI=18%). Conclusion: In conclusion, the integrated model performed significantly better than single microbiome or clinical feature models in all cohorts. Integrating cross-cohort common discriminative microbial features with clinical features could help construct stable diagnostic models for early non-invasive screening for CRC and CRA.}, } @article {pmid38455081, year = {2024}, author = {Renzi, S and Nenciarini, S and Bacci, G and Cavalieri, D}, title = {Yeast metagenomics: analytical challenges in the analysis of the eukaryotic microbiome.}, journal = {Microbiome research reports}, volume = {3}, number = {1}, pages = {2}, doi = {10.20517/mrr.2023.27}, pmid = {38455081}, issn = {2771-5965}, abstract = {Even if their impact is often underestimated, yeasts and yeast-like fungi represent the most prevalent eukaryotic members of microbial communities on Earth. They play numerous roles in natural ecosystems and in association with their hosts. They are involved in the food industry and pharmaceutical production, but they can also cause diseases in other organisms, making the understanding of their biology mandatory. The ongoing loss of biodiversity due to overexploitation of environmental resources is a growing concern in many countries. Therefore, it becomes crucial to understand the ecology and evolutionary history of these organisms to systematically classify them. To achieve this, it is essential that our knowledge of the mycobiota reaches a level similar to that of the bacterial communities. To overcome the existing challenges in the study of fungal communities, the first step should be the establishment of standardized techniques for the correct identification of species, even from complex matrices, both in wet lab practices and in bioinformatic tools.}, } @article {pmid38455080, year = {2024}, author = {Longhi, G and Argentini, C and Fontana, F and Tarracchini, C and Mancabelli, L and Lugli, GA and Alessandri, G and Lahner, E and Pivetta, G and Turroni, F and Ventura, M and Milani, C}, title = {Saponin treatment for eukaryotic DNA depletion alters the microbial DNA profiles by reducing the abundance of Gram-negative bacteria in metagenomics analyses.}, journal = {Microbiome research reports}, volume = {3}, number = {1}, pages = {4}, doi = {10.20517/mrr.2023.02}, pmid = {38455080}, issn = {2771-5965}, abstract = {Background: Recent advances in microbiome sequencing techniques have provided new insights into the role of the microbiome on human health with potential diagnostic implications. However, these developments are often hampered by the presence of a large amount of human DNA interfering with the analysis of the bacterial content. Nowadays, extensive scientific literature focuses on eukaryotic DNA depletion methods, which successfully remove host DNA in microbiome studies, even if a precise assessment of the impact on bacterial DNA is often missing. Methods: Here, we have investigated a saponin-based DNA isolation protocol commonly applied to different biological matrices to deplete the released host DNA. Results: The bacterial DNA obtained was used to assess the relative abundance of bacterial and human DNA, revealing that the inclusion of 2.5% wt/vol saponin allowed the depletion of most of the host's DNA in favor of bacterial DNA enrichment. However, shotgun metagenomic sequencing showed inaccurate microbial profiles of the DNA samples, highlighting an erroneous increase in Gram-positive DNA. Even the application of 0.0125% wt/vol saponin altered the bacterial profile by depleting Gram-negative bacteria, resulting in an overall increase of Gram-positive bacterial DNA. Conclusion: The application of the saponin-based protocol drastically changes the detection of the microbial composition of human-related biological specimens. In this context, we revealed that saponin targets not only host cells but also specific bacterial cells, thus inducing a drastic reduction in the profiling of Gram-negative bacterial DNA.}, } @article {pmid38454513, year = {2024}, author = {Lavecchia, A and Fosso, B and Engelen, AH and Borin, S and Manzari, C and Picardi, E and Pesole, G and Placido, A}, title = {Macroalgal microbiomes unveil a valuable genetic resource for halogen metabolism.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {47}, pmid = {38454513}, issn = {2049-2618}, support = {UIDB/04326/2020//Portuguese national funds from FCT/ ; 634486//European Commission/ ; 634486//European Commission/ ; 634486//European Commission/ ; }, abstract = {BACKGROUND: Macroalgae, especially reds (Rhodophyta Division) and browns (Phaeophyta Division), are known for producing various halogenated compounds. Yet, the reasons underlying their production and the fate of these metabolites remain largely unknown. Some theories suggest their potential antimicrobial activity and involvement in interactions between macroalgae and prokaryotes. However, detailed investigations are currently missing on how the genetic information of prokaryotic communities associated with macroalgae may influence the fate of organohalogenated molecules.

RESULTS: To address this challenge, we created a specialized dataset containing 161 enzymes, each with a complete enzyme commission number, known to be involved in halogen metabolism. This dataset served as a reference to annotate the corresponding genes encoded in both the metagenomic contigs and 98 metagenome-assembled genomes (MAGs) obtained from the microbiome of 2 red (Sphaerococcus coronopifolius and Asparagopsis taxiformis) and 1 brown (Halopteris scoparia) macroalgae. We detected many dehalogenation-related genes, particularly those with hydrolytic functions, suggesting their potential involvement in the degradation of a wide spectrum of halocarbons and haloaromatic molecules, including anthropogenic compounds. We uncovered an array of degradative gene functions within MAGs, spanning various bacterial orders such as Rhodobacterales, Rhizobiales, Caulobacterales, Geminicoccales, Sphingomonadales, Granulosicoccales, Microtrichales, and Pseudomonadales. Less abundant than degradative functions, we also uncovered genes associated with the biosynthesis of halogenated antimicrobial compounds and metabolites.

CONCLUSION: The functional data provided here contribute to understanding the still largely unexplored role of unknown prokaryotes. These findings support the hypothesis that macroalgae function as holobionts, where the metabolism of halogenated compounds might play a role in symbiogenesis and act as a possible defense mechanism against environmental chemical stressors. Furthermore, bacterial groups, previously never connected with organohalogen metabolism, e.g., Caulobacterales, Geminicoccales, Granulosicoccales, and Microtrichales, functionally characterized through MAGs reconstruction, revealed a biotechnologically relevant gene content, useful in synthetic biology, and bioprospecting applications. Video Abstract.}, } @article {pmid38454476, year = {2024}, author = {Li, C and Jin, S and Lv, O and Wang, G and Zhang, Y and Li, S and Zhang, W and Long, F and Shen, Z and Bai, S and Zhaxi, D and Kong, F and Yan, Q and Xiao, Z}, title = {Comparative analysis of the vaginal bacteriome and virome in healthy women living in high-altitude and sea-level areas.}, journal = {European journal of medical research}, volume = {29}, number = {1}, pages = {157}, pmid = {38454476}, issn = {2047-783X}, abstract = {The vaginal microbiota plays an important role in the health of the female reproductive tract and is closely associated with various pregnancy outcomes and sexually transmitted diseases. Plenty of internal and external factors have strong influence on the changes in a woman's vaginal microbiome. However, the effect of a high-altitude on female vaginal microbiota has not been described. In this study, we characterized the vaginal bacteriome and virome of 13 and 34 healthy women living in high-altitude and sea-level areas, using whole-metagenome shotgun sequencing of their vaginal mucus samples. The results revealed that the vaginal bacteriomes of high-altitude individuals are featured by a significant increase of species diversity, depletion of Lactobacillus crispatus, and more abundant of some anaerobic bacteria, such as Chlamydia trachomatis, Mageeibacillus indolicus, Dialister micraerophilus, and Sneathia amnii). In addition, the vagina samples of sea-level subjects harbor more Lactobacillus strains, whereas the anaerobic bacteroidetes strains mostly appeared in high-altitude subjects. Identified and assembled 191 virus operational taxonomic units (vOTUs), there were significant differences in the abundance of 107 vOTUs between the two groups. Together, the results of this study raised the understanding of bacteriome and virome in the vagina of women at different elevations, and demonstrated that the vaginal microbiome is related to the high-altitude geographic adaptation.}, } @article {pmid38454103, year = {2024}, author = {Vázquez, X and Lumbreras-Iglesias, P and Rodicio, MR and Fernández, J and Bernal, T and Moreno, AF and de Ugarriza, PL and Fernández-Verdugo, A and Margolles, A and Sabater, C}, title = {Study of the intestinal microbiota composition and the effect of treatment with intensive chemotherapy in patients recovered from acute leukemia.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {5585}, pmid = {38454103}, issn = {2045-2322}, support = {FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; FIS PI21/01590//Fondo de Investigación Sanitaria, Instituto de Salud Carlos III, Ministerio de Economía y Competitividad, Spain/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; GRUPIN IDI/2022/000033//Regional Ministry of Science of Asturias/ ; }, abstract = {A dataset comprising metagenomes of outpatients (n = 28) with acute leukemia (AL) and healthy controls (n = 14) was analysed to investigate the associations between gut microbiota composition and metabolic activity and AL. According to the results obtained, no significant differences in the microbial diversity between AL outpatients and healthy controls were found. However, significant differences in the abundance of specific microbial clades of healthy controls and AL outpatients were found. We found some differences at taxa level. The relative abundance of Enterobacteriaceae, Prevotellaceae and Rikenellaceae was increased in AL outpatients, while Bacteirodaceae, Bifidobacteriaceae and Lachnospiraceae was decreased. Interestingly, the abundances of several taxa including Bacteroides and Faecalibacterium species showed variations based on recovery time from the last cycle of chemotherapy. Functional annotation of metagenome-assembled genomes (MAGs) revealed the presence of functional domains corresponding to therapeutic enzymes including L-asparaginase in a wide range of genera including Prevotella, Ruminococcus, Faecalibacterium, Alistipes, Akkermansia. Metabolic network modelling revealed potential symbiotic relationships between Veillonella parvula and Levyella massiliensis and several species found in the microbiota of AL outpatients. These results may contribute to develop strategies for the recovery of microbiota composition profiles in the treatment of patients with AL.}, } @article {pmid38453993, year = {2024}, author = {Bergfeldt, N and Kırdök, E and Oskolkov, N and Mirabello, C and Unneberg, P and Malmström, H and Fraser, M and Sanchez-Quinto, F and Jorgensen, R and Skar, B and Lidén, K and Jakobsson, M and Storå, J and Götherström, A}, title = {Identification of microbial pathogens in Neolithic Scandinavian humans.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {5630}, pmid = {38453993}, issn = {2045-2322}, support = {2017-02503//Vetenskapsrådet/ ; 2019-00849//Vetenskapsrådet/ ; P21-0266//Riksbankens Jubileumsfond/ ; P19.0740:1//Riksbankens Jubileumsfond/ ; }, abstract = {With the Neolithic transition, human lifestyle shifted from hunting and gathering to farming. This change altered subsistence patterns, cultural expression, and population structures as shown by the archaeological/zooarchaeological record, as well as by stable isotope and ancient DNA data. Here, we used metagenomic data to analyse if the transitions also impacted the microbiome composition in 25 Mesolithic and Neolithic hunter-gatherers and 13 Neolithic farmers from several Scandinavian Stone Age cultural contexts. Salmonella enterica, a bacterium that may have been the cause of death for the infected individuals, was found in two Neolithic samples from Battle Axe culture contexts. Several species of the bacterial genus Yersinia were found in Neolithic individuals from Funnel Beaker culture contexts as well as from later Neolithic context. Transmission of e.g. Y. enterocolitica may have been facilitated by the denser populations in agricultural contexts.}, } @article {pmid38453092, year = {2024}, author = {Wang, YC and Mao, Y and Fu, HM and Wang, J and Weng, X and Liu, ZH and Xu, XW and Yan, P and Fang, F and Guo, JS and Shen, Y and Chen, YP}, title = {New insights into functional divergence and adaptive evolution of uncultured bacteria in anammox community by complete genome-centric analysis.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {171530}, doi = {10.1016/j.scitotenv.2024.171530}, pmid = {38453092}, issn = {1879-1026}, abstract = {Anaerobic ammonium-oxidation (anammox) bacteria play a crucial role in global nitrogen cycling and wastewater nitrogen removal, but they share symbiotic relationships with various other microorganisms. Functional divergence and adaptive evolution of uncultured bacteria in anammox community remain underexplored. Although shotgun metagenomics based on short reads has been widely used in anammox research, metagenome-assembled genomes (MAGs) are often discontinuous and highly contaminated, which limits in-depth analyses of anammox communities. Here, for the first time, we performed Pacific Biosciences high-fidelity (HiFi) long-read sequencing on the anammox granule sludge sample from a lab-scale bioreactor, and obtained 30 accurate and complete metagenome-assembled genomes (cMAGs). These cMAGs were obtained by selecting high-quality circular contigs from initial assemblies of long reads generated by HiFi sequencing, eliminating the need for Illumina short reads, binning, and reassembly. One new anammox species affiliated with Candidatus Jettenia and three species affiliated with novel families were found in this anammox community. cMAG-centric analysis revealed functional divergence in general and nitrogen metabolism among the anammox community members, and they might adopt a cross-feeding strategy in organic matter, cofactors, and vitamins. Furthermore, we identified 63 mobile genetic elements (MGEs) and 50 putative horizontal gene transfer (HGT) events within these cMAGs. The results suggest that HGT events and MGEs related to phage and integration or excision, particularly transposons containing tnpA in anammox bacteria, might play important roles in the adaptive evolution of this anammox community. The cMAGs generated in the present study could be used to establish of a comprehensive database for anammox bacteria and associated microorganisms. Our findings highlight the advantages of HiFi sequencing for the studies of complex mixed cultures and advance our understanding of anammox communities.}, } @article {pmid38452680, year = {2024}, author = {Cui, E and Fan, X and Cui, B and Li, S and Chen, T and Gao, F and Li, J and Zhou, Z}, title = {The introduction of influent sulfamethoxazole loads induces changes in the removal pathways of sulfamethoxazole in vertical flow constructed wetlands featuring hematite substrate.}, journal = {Journal of hazardous materials}, volume = {469}, number = {}, pages = {133964}, doi = {10.1016/j.jhazmat.2024.133964}, pmid = {38452680}, issn = {1873-3336}, abstract = {High frequent detection of sulfamethoxazole (SMX) in wastewater cannot be effectively removed by constructed wetlands (CWs) with a traditional river sand substrate. The role of emerging substrate of hematite in promoting SMX removal and the effect of influent SMX loads remain unclear. The removal efficiency of SMX in hematite CWs was significantly higher than that in river sand CWs by 12.7-13.8% by improving substrate adsorption capacity, plant uptake and microbial degradation. With increasing influent SMX load, the removal efficiency of SMX in hematite CWs slightly increased, and the removal pathways varied significantly. The contribution of plant uptake was relatively small (< 0.1%) under different influent SMX loads. Substrate adsorption (37.8%) primarily contributed to SMX removal in hematite CWs treated with low-influent SMX. Higher influent SMX loads decreased the contribution of substrate adsorption, and microbial degradation (67.0%) became the main removal pathway. Metagenomic analyses revealed that the rising influent load increased the abundance of SMX-degrading relative bacteria and the activity of key enzymes. Moreover, the abundance of high-risk ARGs and sulfonamide resistance genes in hematite CWs did not increase with the increasing influent load. This study elucidates the potential improvements in CWs with hematite introduction under different influent SMX loads.}, } @article {pmid38452676, year = {2024}, author = {Xie, X and Chen, B and Zhu, S and Yang, R and Yuan, K and Yang, Y and Chen, R and Lin, L and Chen, B}, title = {Comparative analysis of characteristics of antibiotic resistomes between Arctic soils and representative contaminated samples using metagenomic approaches.}, journal = {Journal of hazardous materials}, volume = {469}, number = {}, pages = {133943}, doi = {10.1016/j.jhazmat.2024.133943}, pmid = {38452676}, issn = {1873-3336}, abstract = {Antibiotic resistance is one of the most concerned global health issues. However, comprehensive profiles of antibiotic resistance genes (ARGs) in various environmental settings are still needed to address modern antibiotic resistome. Here, Arctic soils and representative contaminated samples from ARG pollution sources were analyzed using metagenomic approaches. The diversity and abundance of ARGs in Arctic soils were significantly lower than those in contaminated samples (p < 0.01). ARG profiles in Arctic soils were featured with the dominance of vanF, ceoB, and bacA related to multidrug and bacitracin, whereas those from ARG pollution sources were characterized by prevalent resistance to anthropogenic antibiotics such as sulfonamides, tetracyclines, and beta-lactams. Mobile genetic elements (MGEs) were found in all samples, and their abundance and relatedness to ARGs were both lower in Arctic soils than in polluted samples. Significant relationships between bacterial communities and ARGs were observed (p < 0.01). Cultural bacteria in Arctic soils had clinically-concerned resistance to erythromycin, vancomycin, ampicillin, etc., but ARGs relevant to those antibiotics were undetectable in their genomes. Our results suggested that Arctic environment could be an important reservoir of novel ARGs, and antibiotic stresses could cause ARG pollution via horizontal gene transfer and enrichment of resistant bacteria.}, } @article {pmid38452205, year = {2024}, author = {Lynes, MM and Jay, ZJ and Kohtz, AJ and Hatzenpichler, R}, title = {Methylotrophic methanogenesis in the Archaeoglobi revealed by cultivation of Ca. Methanoglobus hypatiae from a Yellowstone hot spring.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae026}, pmid = {38452205}, issn = {1751-7370}, abstract = {Over the past decade, environmental metagenomics and PCR-based marker gene surveys have revealed that several lineages beyond just a few well-established groups within the Euryarchaeota superphylum harbor the genetic potential for methanogenesis. One of these groups are the Archaeoglobi, a class of thermophilic euryarchaeotes that have long been considered to live non-methanogenic lifestyles. Here, we enriched Candidatus Methanoglobus hypatiae, a methanogen affiliated with the family Archaeoglobaceae, from a hot spring in Yellowstone National Park. The enrichment is sediment-free, grows at 64-70 °C and a pH of 7.8, and produces methane from mono-, di-, and tri-methylamine. Ca. M. hypatiae is represented by a 1.62 Mb metagenome-assembled genome with an estimated completeness of 100% and accounts for up to 67% of cells in the culture according to fluorescence in situ hybridization. Via genome-resolved metatranscriptomics and stable isotope tracing, we demonstrate that Ca. M. hypatiae expresses methylotrophic methanogenesis and energy-conserving pathways for reducing monomethylamine to methane. The detection of Archaeoglobi populations related to Ca. M. hypatiae in 36 geochemically diverse geothermal sites within Yellowstone National Park, as revealed through the examination of previously published gene amplicon datasets, implies a previously underestimated contribution to anaerobic carbon cycling in extreme ecosystems.}, } @article {pmid38452204, year = {2024}, author = {Gios, E and Mosley, OE and Hoggard, M and Handley, KM}, title = {High niche specificity and host genetic diversity of groundwater viruses.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae035}, pmid = {38452204}, issn = {1751-7370}, abstract = {Viruses are key members of microbial communities that exert control over host abundance and metabolism, thereby influencing ecosystem processes and biogeochemical cycles. Aquifers are known to host taxonomically diverse microbial life, yet little is known about viruses infecting groundwater microbial communities. Here, we analyzed 16 metagenomes from a broad range of groundwater physicochemistries. We recovered 1571 viral genomes that clustered into 468 high-quality viral operational taxonomic units (vOTUs). At least 15% were observed to be transcriptionally active, although lysis was likely constrained by the resource-limited groundwater environment. Most were unclassified (95%), and the remaining 5% were Caudoviricetes. Comparisons with viruses inhabiting other aquifers revealed no shared species, indicating substantial unexplored viral diversity. In silico predictions linked 22.4% of the viruses to microbial host populations, including to ultra-small prokaryotes, such as Patescibacteria and Nanoarchaeota. Many predicted hosts were associated with the biogeochemical cycling of carbon, nitrogen, and sulfur. Metabolic predictions revealed the presence of 205 putative auxiliary metabolic genes, involved in diverse processes associated with the utilization of the host's intracellular resources for biosynthesis and transformation reactions, including those involved in nucleotide sugar, glycan, cofactor, and vitamin metabolism. Viruses, prokaryotes overall, and predicted prokaryotic hosts exhibited narrow spatial distributions, and relative abundance correlations with the same groundwater parameters (e.g., dissolved oxygen, nitrate, and iron), consistent with host control over viral distributions. Results provide insights into underexplored groundwater viruses, and indicate the large extent to which viruses may manipulate microbial communities and biogeochemistry in the terrestrial subsurface.}, } @article {pmid38452018, year = {2024}, author = {Du, Z and Behrens, SF}, title = {Effect of target gene sequence evenness and dominance on real-time PCR quantification of artificial sulfate-reducing microbial communities.}, journal = {PloS one}, volume = {19}, number = {3}, pages = {e0299930}, doi = {10.1371/journal.pone.0299930}, pmid = {38452018}, issn = {1932-6203}, abstract = {Quantitative real-time PCR of phylogenetic and functional marker genes is among the most commonly used techniques to quantify the abundance of microbial taxa in environmental samples. However, in most environmental applications, the approach is a rough assessment of population abundance rather than an exact absolute quantification method because of PCR-based estimation biases caused by multiple factors. Previous studies on these technical issues have focused on primer or template sequence features or PCR reaction conditions. However, how target gene sequence characteristics (e.g., evenness and dominance) in environmental samples affect qPCR quantifications has not been well studied. Here, we compared three primer sets targeting the beta subunit of the dissimilatory sulfite reductase (dsrB) to investigate qPCR quantification performance under different target gene sequence evenness and dominance conditions using artificial gBlock template mixtures designed accordingly. Our results suggested that the qPCR quantification performance of all tested primer sets was determined by the comprehensive effect of the target gene sequence evenness and dominance in environmental samples. Generally, highly degenerate primer sets have equivalent or better qPCR quantification results than a more target-specific primer set. Low template concentration in this study (~105 copies/L) will exaggerate the qPCR quantification results difference among tested primer sets. Improvements to the accuracy and reproducibility of qPCR assays for gene copy number quantification in environmental microbiology and microbial ecology studies should be based on prior knowledge of target gene sequence information acquired by metagenomic analysis or other approaches, careful selection of primer sets, and proper reaction conditions optimization.}, } @article {pmid38451250, year = {2024}, author = {Bustos-Diaz, ED and Cruz-Perez, A and Garfias-Gallegos, D and D'Agostino, PM and Gehringer, MM and Cibrian-Jaramillo, A and Barona-Gomez, F}, title = {Phylometagenomics of cycad coralloid roots reveals shared symbiotic signals.}, journal = {Microbial genomics}, volume = {10}, number = {3}, pages = {}, doi = {10.1099/mgen.0.001207}, pmid = {38451250}, issn = {2057-5858}, abstract = {Cycads are known to host symbiotic cyanobacteria, including Nostocales species, as well as other sympatric bacterial taxa within their specialized coralloid roots. Yet, it is unknown if these bacteria share a phylogenetic origin and/or common genomic functions that allow them to engage in facultative symbiosis with cycad roots. To address this, we obtained metagenomic sequences from 39 coralloid roots sampled from diverse cycad species and origins in Australia and Mexico. Culture-independent shotgun metagenomic sequencing was used to validate sub-community co-cultures as an efficient approach for functional and taxonomic analysis. Our metanalysis shows a host-independent microbiome core consisting of seven bacterial orders with high species diversity within the identified taxa. Moreover, we recovered 43 cyanobacterial metagenome-assembled genomes, and in addition to Nostoc spp., symbiotic cyanobacteria of the genus Aulosira were identified for the first time. Using this robust dataset, we used phylometagenomic analysis to reveal three monophyletic cyanobiont clades, two host-generalist and one cycad-specific that includes Aulosira spp. Although the symbiotic clades have independently arisen, they are enriched in certain functional genes, such as those related to secondary metabolism. Furthermore, the taxonomic composition of associated sympatric bacterial taxa remained constant. Our research quadruples the number of cycad cyanobiont genomes and provides a robust framework to decipher cyanobacterial symbioses, with the potential of improving our understanding of symbiotic communities. This study lays a solid foundation to harness cyanobionts for agriculture and bioprospection, and assist in conservation of critically endangered cycads.}, } @article {pmid38451230, year = {2024}, author = {Eisenhofer, R and Nesme, J and Santos-Bay, L and Koziol, A and Sørensen, SJ and Alberdi, A and Aizpurua, O}, title = {A comparison of short-read, HiFi long-read, and hybrid strategies for genome-resolved metagenomics.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0359023}, doi = {10.1128/spectrum.03590-23}, pmid = {38451230}, issn = {2165-0497}, abstract = {Shotgun metagenomics enables the reconstruction of complex microbial communities at a high level of detail. Such an approach can be conducted using both short-read and long-read sequencing data, as well as a combination of both. To assess the pros and cons of these different approaches, we used 22 fecal DNA extracts collected weekly for 11 weeks from two respective lab mice to study seven performance metrics over four combinations of sequencing depth and technology: (i) 20 Gbp of Illumina short-read data, (ii) 40 Gbp of short-read data, (iii) 20 Gbp of PacBio HiFi long-read data, and (iv) 40 Gbp of hybrid (20 Gbp of short-read +20 Gbp of long-read) data. No strategy was best for all metrics; instead, each one excelled across different metrics. The long-read approach yielded the best assembly statistics, with the highest N50 and lowest number of contigs. The 40 Gbp short-read approach yielded the highest number of refined bins. Finally, the hybrid approach yielded the longest assemblies and the highest mapping rate to the bacterial genomes. Our results suggest that while long-read sequencing significantly improves the quality of reconstructed bacterial genomes, it is more expensive and requires deeper sequencing than short-read approaches to recover a comparable amount of reconstructed genomes. The most optimal strategy is study-specific and depends on how researchers assess the trade-off between the quantity and quality of recovered genomes.IMPORTANCEMice are an important model organism for understanding the gut microbiome. When studying these gut microbiomes using DNA techniques, researchers can choose from technologies that use short or long DNA reads. In this study, we perform an extensive benchmark between short- and long-read DNA sequencing for studying mice gut microbiomes. We find that no one approach was best for all metrics and provide information that can help guide researchers in planning their experiments.}, } @article {pmid38450667, year = {2024}, author = {Romey, A and Zientara, S and Kassimi, LB}, title = {[Proceedings of the International Symposium of the World Association of Veterinary Laboratory Diagnosticians, 2023].}, journal = {Virologie (Montrouge, France)}, volume = {28}, number = {1}, pages = {39-43}, doi = {10.1684/vir.2024.1036}, pmid = {38450667}, issn = {1267-8694}, abstract = {The International Symposium of the World Association of Veterinary Laboratory Diagnosticians (ISWAVLD) is the unmissable biannual meeting of all diagnostic veterinary laboratories including biologists, veterinarians and other scientists involved in laboratory diagnostics. It took place at the Lyon Convention Centre (29 June-1 July 2023). It was a pleasant and enriching moment, which allowed participants to discover and/or discuss new diagnostic methods and the epidemiology of animal diseases, around all themes involving veterinarians (animal health, but also environmental and human health, and food safety).}, } @article {pmid38450407, year = {2024}, author = {Liu, H and Ni, B and Duan, A and He, C and Zhang, J}, title = {High Frankia abundance and low diversity of microbial community are associated with nodulation specificity and stability of sea buckthorn root nodule.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1301447}, pmid = {38450407}, issn = {1664-462X}, abstract = {INTRODUCTION: Actinorhizal symbioses are gaining attention due to the importance of symbiotic nitrogen fixation in sustainable agriculture. Sea buckthorn (Hippophae L.) is an important actinorhizal plant, yet research on the microbial community and nitrogen cycling in its nodules is limited. In addition, the influence of environmental differences on the microbial community of sea buckthorn nodules and whether there is a single nitrogen-fixing actinomycete species in the nodules are still unknown.

METHODS: We investigated the diversity, community composition, network associations and nitrogen cycling pathways of the microbial communities in the root nodule (RN), nodule surface soil (NS), and bulk soil (BS) of Mongolian sea buckthorn distributed under three distinct ecological conditions in northern China using 16S rRNA gene and metagenomic sequencing. Combined with the data of environmental factors, the effects of environmental differences on different sample types were analyzed.

RESULTS: The results showed that plants exerted a clear selective filtering effect on microbiota, resulting in a significant reduction in microbial community diversity and network complexity from BS to NS to RN. Proteobacteria was the most abundant phylum in the microbiomes of BS and NS. While RN was primarily dominated by Actinobacteria, with Frankia sp. EAN1pec serving as the most dominant species. Correlation analysis indicated that the host determined the microbial community composition in RN, independent of the ecological and geographical environmental changes of the sea buckthorn plantations. Nitrogen cycle pathway analyses showed that RN microbial community primarily functions in nitrogen fixation, and Frankia sp. EAN1pec was a major contributor to nitrogen fixation genes in RN.

DISCUSSION: This study provides valuable insights into the effects of eco-geographical environment on the microbial communities of sea buckthorn RN. These findings further prove that the nodulation specificity and stability of sea buckthorn root and Frankia sp. EAN1pec may be the result of their long-term co-evolution.}, } @article {pmid38450399, year = {2024}, author = {Dumigan, CR and Deyholos, MK}, title = {Soil and seed both influence bacterial diversity in the microbiome of the Cannabis sativa seedling endosphere.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1326294}, pmid = {38450399}, issn = {1664-462X}, abstract = {INTRODUCTION: Phytobiomes have a significant impact on plant health. The microbiome of Cannabis sativa is particularly interesting both because of renewed interest in this crop and because it is commercially propagated in two different ways (i.e. clonally and by seed). Angiosperms obtain a founding population of seed-borne endophytes from their seed-bearing parent. This study examines the influence of both seed and soil-derived bacteria on the endospheres of cannabis seedlings of both hemp- and drug-types.

METHODS: A multi-factorial metagenomic study was conducted with three cannabis genotypes and two soil sources, which were tested both before and after autoclave sterilization. Seedlings were grown on soil, then rinsed and surface-sterilized, and 16S rDNA amplicons from seedling endophytes were sequenced, taxonomically classified, and used to estimate alpha- and beta-diversity in Qiime2. The statistical significance of differences in seedling microbiomes across treatments was tested, and PiCRUST2 was used to infer the functional relevance of these differences.

RESULTS: Soil was found to have a profound effect on the alpha-diversity, beta-diversity, relative abundance, and functional genes of endophytic bacteria in germinating cannabis seedlings. Additionally, there was a significant effect of cannabis genotype on beta diversity, especially when genotypes were grown in sterilized soil. Gammaproteobacteria and Bacilli were the two most abundant taxa and were found in all genotypes and soil types, including sterilized soil.

DISCUSSION: The results indicated that a component of cannabis seedling endosphere microbiomes is seed-derived and conserved across the environments tested. Functional prediction of seedling endophytes using piCRUST suggested a number of important functions of seed-borne endophytes in cannabis including nutrient and amino acid cycling, hormone regulation, and as precursors to antibiotics. This study suggested both seed and soil play a critical role in shaping the microbiome of germinating cannabis seedlings.}, } @article {pmid38449879, year = {2023}, author = {Crippen, TL and Kim, D and Poole, TL and Swiger, SL and Anderson, RC}, title = {The bacterial and archaeal communities of flies, manure, lagoons, and troughs at a working dairy.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1327841}, pmid = {38449879}, issn = {1664-302X}, abstract = {BACKGROUND: Fundamental investigations into the location, load, and persistence of microbes, whether beneficial or detrimental, are scarce. Many questions about the retention and survival of microbes on various surfaces, as well as the load necessary for spread, exist. To answer these questions, we must know more about where to find various microbes and in what concentrations, the composition of the microbial communities, and the extent of dissemination between various elements. This study investigated the diversity, composition, and relative abundance of the communities associated with manure, lagoons, troughs, house flies, and stable flies present at a dairy, implementing two different free-stall management systems: flow-through and cross-vent. Shotgun metagenomics at the community level was used to compare the microbiomes within the dairy, allowing confident interpretation at the species level.

RESULTS: The results showed that there were significant difference in microbial composition between not only each of the dairy elements but also management styles. The primary exceptions were the microbiomes of the house fly and the stable fly. Their compositions heavily overlapped with one another, but interestingly, not with the other components sampled. Additionally, both species of flies carried more pathogens than the other elements of the dairy, indicating that they may not share these organisms with the other components, or that the environments offered by the other components are unsatisfactory for the survival of some pathogens..

CONCLUSION: The lack of overlapping pathogen profiles suggests a lack of transfer from flies to other dairy elements. Dairy health data, showing a low incidence of disease, suggests minimal sharing of bacteria by the flies at a level required for infection, given the health program of this dairy. While flies did carry a multitude of pathogenic bacteria, the mere presence of the bacteria associated with the flies did not necessarily translate into high risk leading to morbidity and mortality at this dairy. Thus, using flies as the sole sentinel of dairy health may not be appropriate for all bacterial pathogens or dairies.}, } @article {pmid38449659, year = {2024}, author = {He, K and Meng, X and Su, J and Jiang, S and Chu, M and Huang, B}, title = {Oleanolic acid inhibits the tumor progression by regulating Lactobacillus through the cytokine-cytokine receptor interaction pathway in 4T1-induced mice breast cancer model.}, journal = {Heliyon}, volume = {10}, number = {5}, pages = {e27028}, pmid = {38449659}, issn = {2405-8440}, abstract = {The therapeutic mechanism of oleanolic acid (OA) in breast cancer has been widely reported, but little has been known about the combined effects of transcriptome and gut microbiome. In this study, the phenotypic effect of oleanolic acid on mice was tested at the end of the administration cycle, and RNA sequencing on murine tumor tissue and 16S-rRNA sequencing on intestinal contents were conducted to analyze gene expression profiles and microbial diversity between the control group and OA treated group using 4T1-induced mice breast cancer model. As a result, it has been confirmed that oleanolic acid would play a significant inhibitory effect on the development of breast tumors in mice. Based on the integrative analysis of the transcriptomic and metagenomic data, it was found that the abundance of Lactobacillus in the intestinal flora of mice significantly increased in the OA group. Moreover, the up-regulation of Il10 had a significant effect on inhibiting the tumor progression, which played a role through cytokine-cytokine receptor interaction pathway.}, } @article {pmid38448773, year = {2024}, author = {Batool, U and Tromas, N and Simon, DF and Sauvé, S and Shapiro, BJ and Ahmed, M}, title = {Snapshot of cyanobacterial toxins in Pakistani freshwater bodies.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38448773}, issn = {1614-7499}, support = {PIN No. IRSIP 47 BMS 18//Higher Education Commision, Pakistan/ ; PIN No. 5//Higher Education Commision, Pakistan/ ; 518-84931-2BS5-007//Higher Education Commision, Pakistan/ ; NRPU Grant 6769//Higher Education Commision, Pakistan/ ; }, abstract = {Cyanobacteria are known to produce diverse secondary metabolites that are toxic to aquatic ecosystems and human health. However, data about the cyanotoxins occurrence and cyanobacterial diversity in Pakistan's drinking water reservoirs is scarce. In this study, we first investigated the presence of microcystin, saxitoxin, and anatoxin in 12 water bodies using an enzyme-linked immunosorbent assay (ELISA). The observed cyanotoxin values for the risk quotient (RQ) determined by ELISA indicated a potential risk for aquatic life and human health. Based on this result, we made a more in-depth investigation with a subset of water bodies (served as major public water sources) to analyze the cyanotoxins dynamics and identify potential producers. We therefore quantified the distribution of 17 cyanotoxins, including 12 microcystin congeners using a high-performance liquid chromatography-high-resolution tandem mass spectrometry/mass spectrometry (HPLC-HRMS/MS). Our results revealed for the first time the co-occurrence of multiple cyanotoxins and the presence of cylindrospermopsin in an artificial reservoir (Rawal Lake) and a semi-saline lake (Kallar Kahar). We also quantified several microcystin congeners in a river (Panjnad) with MC-LR and MC-RR being the most prevalent and abundant. To identify potential cyanotoxin producers, the composition of the cyanobacterial community was characterized by shotgun metagenomics sequencing. Despite the noticeable presence of cyanotoxins, Cyanobacteria were not abundant. Synechococcus was the most abundant cyanobacterial genus found followed by a small amount of Anabaena, Cyanobium, Microcystis, and Dolichospermum. Moreover, when we looked at the cyanotoxins genes coverage, we never found a complete microcystin mcy operon. To our knowledge, this is the first snapshot sampling of water bodies in Pakistan. Our results would not only help to understand the geographical spread of cyanotoxin in Pakistan but would also help to improve cyanotoxin risk assessment strategies by screening a variety of cyanobacterial toxins and confirming that cyanotoxin quantification is not necessarily related to producer abundance.}, } @article {pmid38448687, year = {2024}, author = {Sardzikova, S and Andrijkova, K and Svec, P and Beke, G and Klucar, L and Minarik, G and Bielik, V and Kolenova, A and Soltys, K}, title = {Gut diversity and the resistome as biomarkers of febrile neutropenia outcome in paediatric oncology patients undergoing hematopoietic stem cell transplantation.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {5504}, pmid = {38448687}, issn = {2045-2322}, support = {APVV-17-0099//Agentúra na Podporu Výskumu a Vývoja/ ; APVV-17-0099//Agentúra na Podporu Výskumu a Vývoja/ ; APVV-17-0099//Agentúra na Podporu Výskumu a Vývoja/ ; APVV-17-0099//Agentúra na Podporu Výskumu a Vývoja/ ; APVV-17-0099//Agentúra na Podporu Výskumu a Vývoja/ ; APVV-17-0099//Agentúra na Podporu Výskumu a Vývoja/ ; ITMS2014+: 313021BUZ3//European Regional Development Fund/ ; ITMS2014+: 313021BUZ3//European Regional Development Fund/ ; }, abstract = {The gut microbiota of paediatric oncology patients undergoing a conditioning regimen before hematopoietic stem cell transplantation is recently considered to play role in febrile neutropenia. Disruption of commensal microbiota and evolution of opportune pathogens community carrying a plethora of antibiotic-resistance genes play crucial role. However, the impact, predictive role and association of patient´s gut resistome in the course of the therapy is still to be elucidated. We analysed gut microbiota composition and resistome of 18 paediatric oncology patients undergoing hematopoietic stem cell transplantation, including 12 patients developing febrile neutropenia, hospitalized at The Bone Marrow Transplantation Unit of the National Institute of Children´s disease in Slovak Republic and healthy individuals (n = 14). Gut microbiome of stool samples obtained in 3 time points, before hematopoietic stem cell transplantation (n = 16), one week after hematopoietic stem cell transplantation (n = 16) and four weeks after hematopoietic stem cell transplantation (n = 14) was investigated using shotgun metagenome sequencing and bioinformatical analysis. We identified significant decrease in alpha-diversity and nine antibiotic-resistance genes msr(C), dfrG, erm(T), VanHAX, erm(B), aac(6)-aph(2), aph(3)-III, ant(6)-Ia and aac(6)-Ii, one week after hematopoietic stem cell transplantation associated with febrile neutropenia. Multidrug-resistant opportune pathogens of ESKAPE, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae and Escherichia coli found in the gut carried the significant subset of patient's resistome. Over 50% of patients treated with trimethoprim/sulfamethoxazole, piperacillin/tazobactam and amikacin carried antibiotic-resistance genes to applied treatment. The alpha diversity and the resistome of gut microbiota one week after hematopoietic stem cell transplantation is relevant predictor of febrile neutropenia outcome after hematopoietic stem cell transplantation. Furthermore, the interindividual diversity of multi-drug resistant opportunistic pathogens with variable portfolios of antibiotic-resistance genes indicates necessity of preventive, personalized approach.}, } @article {pmid38444338, year = {2024}, author = {Coelho, JFR and Mendes, LF and Di Dario, F and Carvalho, PH and Dias, RM and Lima, SMQ and Verba, JT and Pereira, RJ}, title = {Integration of genomic and ecological methods inform management of an undescribed, yet highly exploited, sardine species.}, journal = {Proceedings. Biological sciences}, volume = {291}, number = {2018}, pages = {20232746}, pmid = {38444338}, issn = {1471-2954}, mesh = {Humans ; *Genomics ; *Metagenomics ; Brazil ; Salinity ; }, abstract = {Assessing genetic diversity within species is key for conservation strategies in the context of human-induced biotic changes. This is important in marine systems, where many species remain undescribed while being overfished, and conflicts between resource-users and conservation agencies are common. Combining niche modelling with population genomics can contribute to resolving those conflicts by identifying management units and understanding how past climatic cycles resulted in current patterns of genetic diversity. We addressed these issues on an undescribed but already overexploited species of sardine of the genus Harengula. We find that the species distribution is determined by salinity and depth, with a continuous distribution along the Brazilian mainland and two disconnected oceanic archipelagos. Genomic data indicate that such biogeographic barriers are associated with two divergent intraspecific lineages. Changes in habitat availability during the last glacial cycle led to different demographic histories among stocks. One coastal population experienced a 3.6-fold expansion, whereas an island-associated population contracted 3-fold, relative to the size of the ancestral population. Our results indicate that the island population should be managed separately from the coastal population, and that a Marine Protected Area covering part of the island population distribution can support the viability of this lineage.}, } @article {pmid38448159, year = {2024}, author = {Zakharevich, NV and Morozov, MD and Kanaeva, VA and Filippov, MS and Zyubko, TI and Ivanov, AB and Ulyantsev, VI and Klimina, KM and Olekhnovich, EI}, title = {Systemic metabolic depletion of gut microbiome undermines responsiveness to melanoma immunotherapy.}, journal = {Life science alliance}, volume = {7}, number = {5}, pages = {}, doi = {10.26508/lsa.202302480}, pmid = {38448159}, issn = {2575-1077}, abstract = {Immunotherapy has proven to be a boon for patients battling metastatic melanoma, significantly improving their clinical condition and overall quality of life. A compelling link between the composition of the gut microbiome and the efficacy of immunotherapy has been established in both animal models and human patients. However, the precise biological mechanisms by which gut microbes influence treatment outcomes remain poorly understood. Using a robust dataset of 680 fecal metagenomes from melanoma patients, a detailed catalog of metagenome-assembled genomes (MAGs) was constructed to explore the compositional and functional properties of the gut microbiome. Our study uncovered significant findings that deepen the understanding of the intricate relationship between gut microbes and the efficacy of melanoma immunotherapy. In particular, we discovered the specific metagenomic profile of patients with favorable treatment outcomes, characterized by a prevalence of MAGs with increased overall metabolic potential and proficiency in polysaccharide utilization, along with those responsible for cobalamin and amino acid production. Furthermore, our investigation of the biosynthetic pathways of short-chain fatty acids, known for their immunomodulatory role, revealed a differential abundance of these pathways among the specific MAGs. Among others, the cobalamin-dependent Wood-Ljungdahl pathway of acetate synthesis was directly associated with responsiveness to melanoma immunotherapy.}, } @article {pmid38448140, year = {2024}, author = {Mathur, S and Singh, D and Ranjan, R}, title = {Recent advances in plant translational genomics for crop improvement.}, journal = {Advances in protein chemistry and structural biology}, volume = {139}, number = {}, pages = {335-382}, doi = {10.1016/bs.apcsb.2023.11.009}, pmid = {38448140}, issn = {1876-1631}, abstract = {The growing population, climate change, and limited agricultural resources put enormous pressure on agricultural systems. A plateau in crop yields is occurring and extreme weather events and urbanization threaten the livelihood of farmers. It is imperative that immediate attention is paid to addressing the increasing food demand, ensuring resilience against emerging threats, and meeting the demand for more nutritious, safer food. Under uncertain conditions, it is essential to expand genetic diversity and discover novel crop varieties or variations to develop higher and more stable yields. Genomics plays a significant role in developing abundant and nutrient-dense food crops. An alternative to traditional breeding approach, translational genomics is able to improve breeding programs in a more efficient and precise manner by translating genomic concepts into practical tools. Crop breeding based on genomics offers potential solutions to overcome the limitations of conventional breeding methods, including improved crop varieties that provide more nutritional value and are protected from biotic and abiotic stresses. Genetic markers, such as SNPs and ESTs, contribute to the discovery of QTLs controlling agronomic traits and stress tolerance. In order to meet the growing demand for food, there is a need to incorporate QTLs into breeding programs using marker-assisted selection/breeding and transgenic technologies. This chapter primarily focuses on the recent advances that are made in translational genomics for crop improvement and various omics techniques including transcriptomics, metagenomics, pangenomics, single cell omics etc. Numerous genome editing techniques including CRISPR Cas technology and their applications in crop improvement had been discussed.}, } @article {pmid38448100, year = {2024}, author = {Wen, L and Lei, J and Yang, L and Kan, Q and Wang, P and Li, J and Chen, C and He, L and Fu, J and Ho, CT and Huang, Q and Cao, Y}, title = {Metagenomics and untargeted metabolomics analyses to unravel the formation mechanism of characteristic metabolites in Cantonese soy sauce during different fermentation stages.}, journal = {Food research international (Ottawa, Ont.)}, volume = {181}, number = {}, pages = {114116}, doi = {10.1016/j.foodres.2024.114116}, pmid = {38448100}, issn = {1873-7145}, abstract = {Cantonese soy sauce (CSS) is an important Chinese condiment due to its distinctive flavor. Microorganisms play a significant role in the flavor formation of CSS during fermentation. However, the correlation between microbes and flavor compounds as well as the potential fermentation mechanism remained poorly uncovered. Here we revealed the dynamic changes of microbial structure and characteristics metabolites as well as their correlation of CSS during the fermentation process. Metagenomics sequencing analysis showed that Tetragenococcus halophilus, Weissella confusa, Weissella paramesenteroides, Aspergillus oryzae, Lactiplantibacillus plantarum, Weissella cibaria were top six dominant species from day 0 to day 120. Sixty compounds were either positively or tentatively identified through untargeted metabolomics profile and they were 27 peptides, amino acids and derivatives, 8 carbohydrates and conjugates, 14 organic acids and derivatives, 5 amide compounds, 3 flavonoids and 3 nucleosides. Spearman correlation coefficient indicated that Tetragenococcus halophilus, Zygosaccharomyces rouxii, Pediococcus pentosaceus and Aspergillus oryzae were significantly related with the formation of taste amino acids and derivatives, peptides and functional substances. Additionally, the metabolisms of flavor amino acids including 13 main free amino acids were also profiled. These results provided valuable information for the production practice in the soy sauce industry.}, } @article {pmid38447722, year = {2024}, author = {Zhao, X and Niu, Z and Ma, Y and Zhang, Y and Li, Y and Zhang, R}, title = {Exploring the dynamics of antibiotic resistome on plastic debris traveling from the river to the sea along a representative estuary based on field sequential transfer incubations.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {171464}, doi = {10.1016/j.scitotenv.2024.171464}, pmid = {38447722}, issn = {1879-1026}, abstract = {The environmental risks arising from ubiquitous microplastics or plastic debris (PD) acting as carriers of antibiotic resistance genes (ARGs) have attracted widespread attention. Enormous amounts of plastic waste are transported by rivers and traverse estuaries into the sea every year. However, changes in the antibiotic resistome within the plastisphere (the biofilms formed on PD) as PD travels through estuaries are largely unknown. In this study, we performed sequential migration incubations for PD along Haihe Estuary to simulate the natural process of PD floating from rivers to the ocean. Metagenomic sequencing and analysis techniques were used to track microbial communities and antibiotic resistome on migrating PD and in seawater representing the marine environment. The total relative gene copies of ARGs on traveling PD remained stable. As migration between greatly varied waters, additional ARG subtypes were recruited to the plastisphere. Above 80 % ARG subtypes identified in the plastisphere were persistent throughout the migration, and over 30 % of these persistent ARGs were undetected in seawater. The bacterial hosts composition of ARGs on PD progressively altered as transported downstream. Human pathogenic bacteria carrying ARGs (HPBs-ARG) exhibited decreasing trends in abundance and species number during transfer. Individual HPBs-ARG persisted on transferred PD and were absent in seawater samples, comprising Enterobacter cloacae, Klebsiella pneumoniae, Mycobacterium tuberculosis, and Vibrio parahaemolyticus. Based on all detected ARGs and HPBs-ARG, the Projection Pursuit model was applied to synthetically evaluate the potential risks of antibiotic resistance on migrating PD. Diminished risks on PD were observed upon the river-to-sea journey but consistently remained significantly higher than in seawater. The potential risks posed to marine environments by drifting PD as dispersal vectors for antibiotic resistance deserve greater attention. Our results provide initial insights into the dynamics or stability of antibiotic resistome on PD crossing distinct aquatic systems in field estuaries.}, } @article {pmid38447376, year = {2024}, author = {Deng, B and Luo, J and Xu, C and Zhang, X and Li, J and Yuan, Q and Cao, H}, title = {Biotransformation of Pb and As from sewage sludge and food waste by black soldier fly larvae: Migration mechanism of bacterial community and metalloregulatory protein scales.}, journal = {Water research}, volume = {254}, number = {}, pages = {121405}, doi = {10.1016/j.watres.2024.121405}, pmid = {38447376}, issn = {1879-2448}, abstract = {The accumulation and transformation of lead (Pb) and arsenic (As) during the digestion of sewage sludge (SS) by black soldier fly larvae (BSFL) remain unclear. In this study, we used 16 s rRNA and metagenomic sequencing techniques to investigate the correlation between the microbial community, metalloregulatory proteins (MRPs), and Pb and As migration and transformation. During the 15-day test period, BSFL were able to absorb 34-48 % of Pb and 32-45 % of As into their body. Changes in bacterial community abundance, upregulation of MRPs, and redundancy analysis (RDA) results confirmed that ZntA, EfeO, CadC, ArsR, ArsB, ArsD, and ArsA play major roles in the adsorption and stabilization of Pb and As, which is mainly due to the high contribution rates of Lactobacillus (48-59 %) and Enterococcus (21-23 %). Owing to the redox reaction, the regulation of the MRPs, and the change in pH, the Pb and As in the BSFL residue were mainly the residual fraction (F4). The RDA results showed that Lactobacillus and L.koreensis could significantly (P < 0.01) reduce the reducible fraction (F2) and F4 of Pb, whereas Firmicutes and L.fermentum can significantly (P < 0.05) promote the transformation of As to F4, thus realizing the passivation Pb and As. This study contributes to the understanding of Pb and As in SS adsorbed by BSFL and provides important insights into the factors that arise during the BSFL-mediated migration of Pb and As.}, } @article {pmid38447371, year = {2024}, author = {Wang, Y and Zhang, Z and Kang, J and Chen, B and Hong, W and Lv, B and Wang, T and Qian, H}, title = {Phages in different habitats and their ability to carry antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {469}, number = {}, pages = {133941}, doi = {10.1016/j.jhazmat.2024.133941}, pmid = {38447371}, issn = {1873-3336}, abstract = {As the most abundant organisms on Earth, phages play a key role in the evolution of bacterial antibiotic resistance. Although previous studies have demonstrated the molecular mechanisms of horizontal gene transfer mediated by mobile genetic elements, our understanding of the intertwined relationships between antibiotic resistance genes (ARGs) and phages is limited. In this study, we analysed 2781 metagenomic samples to reveal the composition and species interactions of phage communities in different habitats as well as their capacity to carry ARGs with health risks. The composition of phage communities varies in different habitats and mainly depends on environmental conditions. Terrestrial habitats display more complex and robust interactions between phages than aquatic and human-associated habitats, resulting in the highest biodiversity of phages. Several types of phages in certain taxa (4.95-7.67%, mainly belonging to Caudoviricetes) have the capacity to carry specific ARGs and display a high potential risk to human health, especially in human-associated habitats. Overall, our results provide insights into the assembly mechanisms of phage communities and their effects on the dissemination of antibiotic resistance.}, } @article {pmid38448387, year = {2023}, author = {Yang, Y and Wu, J and Hu, J and Wu, T}, title = {Spondylodiscitis of lumbar complicated with spinal epidural abscess caused by Parvimonas micra: A case report and literature review.}, journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences}, volume = {48}, number = {12}, pages = {1929-1936}, doi = {10.11817/j.issn.1672-7347.2023.230139}, pmid = {38448387}, issn = {1672-7347}, support = {2022jy134//the Undergraduate Education Teaching Reform Project of Central South University/ ; 2022JGB074//the Graduate Education Teaching Reform Project of Central South University/ ; }, abstract = {Spinal infection caused by Parvimonas micra (P. micra) is a rare infection. The characteristic imageology includes spondylodiscitis, spondylitis, paravertebral abscess, and epidural abscess. One case of spondylodiscitis of lumbar complicated with spinal epidural abscess caused by P. micra was admitted to the Department of Spinal Surgery, Xiangya Hospital, Central South University on February, 2023. This case is a 60 years old man with lower back pain and left lower limb numbness. MRI showed spondylitis, spondylodiscitis, and epidural abscess. The patient underwent debridement, decompression and fusion surgery. The culture of surgical sample was negative. P. micra was detected by metagenomic next-generation sequencing (mNGS). The postoperative antibiotic treatment included intravenous infusion of linezolid and piperacillin for 1 week, then intravenous infusion of ceftazidime and oral metronidazole for 2 weeks, followed by oral metronidazole and nerofloxacin for 2 weeks. During the follow-up, the lower back pain and left lower limb numbness was complete remission. Spinal infection caused by P. micra is extremely rare, when the culture is negative, mNGS can help the final diagnosis.}, } @article {pmid38448281, year = {2024}, author = {Duong, JT and Pope, CE and Hayden, HS and Miller, C and Salipante, SJ and Rowe, SM and Solomon, GM and Nichols, D and Hoffman, LR and Narkewicz, MR and Green, N}, title = {Alterations in the fecal microbiota in patients with advanced cystic fibrosis liver disease after 6 months of elexacaftor/tezacaftor/ivacaftor.}, journal = {Journal of cystic fibrosis : official journal of the European Cystic Fibrosis Society}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jcf.2024.02.015}, pmid = {38448281}, issn = {1873-5010}, abstract = {BACKGROUND: Cystic fibrosis associated liver disease (CFLD) carries a significant disease burden with no effective preventive therapies. According to the gut-liver axis hypothesis for CFLD pathogenesis, dysbiosis and increased intestinal inflammation and permeability permit pathogenic bacterial translocation into the portal circulation, leading to hepatic inflammation and fibrosis. Evaluating the effect of CFTR (cystic fibrosis transmembrane conductance regulator) modulation with elexacaftor/tezacaftor/ivacaftor (ETI) may help determine the role of CFTR in CFLD and increase understanding of CFLD pathogenesis, which is critical for developing therapies. We aimed to characterize the fecal microbiota in participants with CF with and without advanced CFLD (aCFLD) before and after ETI.

METHODS: This is an ancillary analysis of stool samples from participants ages ≥12 y/o enrolled in PROMISE (NCT04038047). Included participants had aCFLD (cirrhosis with or without portal hypertension, or non-cirrhotic portal hypertension) or CF without liver disease (CFnoLD). Fecal microbiota were defined by shotgun metagenomic sequencing at baseline and 1 and 6 months post-ETI.

RESULTS: We analyzed 93 samples from 34 participants (11 aCFLD and 23 CFnoLD). Compared to CFnoLD, aCFLD had significantly higher baseline relative abundances of potential pathogens Streptococcus salivarius and Veillonella parvula. Four of 11 aCFLD participants had an initially abnormal fecal calprotectin that normalized 6 months post-ETI, correlating with a significant decrease in S. salivarius and a trend towards decreasing V. parvula.

CONCLUSIONS: These results support an association between dysbiosis and intestinal inflammation in CFLD with improvements in both post-ETI, lending further support to the gut-liver axis in aCFLD.}, } @article {pmid38446015, year = {2024}, author = {Rodrigues Jardim, B and Gambley, C and Tran-Nguyen, LTT and Webster, C and Kehoe, M and Kinoti, WM and Bond, S and Davis, R and Jones, L and Pathania, N and Sharman, M and Chapman, T and Rodoni, BC and Constable, FE}, title = {A metagenomic investigation of phytoplasma diversity in Australian vegetable growing regions.}, journal = {Microbial genomics}, volume = {10}, number = {3}, pages = {}, doi = {10.1099/mgen.0.001213}, pmid = {38446015}, issn = {2057-5858}, abstract = {In this study, metagenomic sequence data was used to investigate the phytoplasma taxonomic diversity in vegetable-growing regions across Australia. Metagenomic sequencing was performed on 195 phytoplasma-positive samples, originating either from historic collections (n=46) or during collection efforts between January 2015 and June 2022 (n=149). The sampled hosts were classified as crop (n=155), weed (n=24), ornamental (n=7), native plant (n=6), and insect (n=3) species. Most samples came from Queensland (n=78), followed by Western Australia (n=46), the Northern Territory (n=32), New South Wales (n=17), and Victoria (n=10). Of the 195 draft phytoplasma genomes, 178 met our genome criteria for comparison using an average nucleotide identity approach. Ten distinct phytoplasma species were identified and could be classified within the 16SrII, 16SrXII (PCR only), 16SrXXV, and 16SrXXXVIII phytoplasma groups, which have all previously been recorded in Australia. The most commonly detected phytoplasma taxa in this study were species and subspecies classified within the 16SrII group (n=153), followed by strains within the 16SrXXXVIII group ('Ca. Phytoplasma stylosanthis'; n=6). Several geographic- and host-range expansions were reported, as well as mixed phytoplasma infections of 16SrII taxa and 'Ca. Phytoplasma stylosanthis'. Additionally, six previously unrecorded 16SrII taxa were identified, including five putative subspecies of 'Ca. Phytoplasma australasiaticum' and a new putative 16SrII species. PCR and sequencing of the 16S rRNA gene was a suitable triage tool for preliminary phytoplasma detection. Metagenomic sequencing, however, allowed for higher-resolution identification of the phytoplasmas, including mixed infections, than was afforded by only direct Sanger sequencing of the 16S rRNA gene. Since the metagenomic approach theoretically obtains sequences of all organisms in a sample, this approach was useful to confirm the host family, genus, and/or species. In addition to improving our understanding of the phytoplasma species that affect crop production in Australia, the study also significantly expands the genomic sequence data available in public sequence repositories to contribute to phytoplasma molecular epidemiology studies, revision of taxonomy, and improved diagnostics.}, } @article {pmid38446011, year = {2024}, author = {Ni, Y and Chu, T and Yan, S and Wang, Y}, title = {Forty-nine metagenomic-assembled genomes from an aquatic virome expand Caudoviricetes by 45 potential new families and the newly uncovered Gossevirus of Bamfordvirae.}, journal = {The Journal of general virology}, volume = {105}, number = {3}, pages = {}, doi = {10.1099/jgv.0.001967}, pmid = {38446011}, issn = {1465-2099}, abstract = {Twenty complete genomes (29-63 kb) and 29 genomes with an estimated completeness of over 90 % (30-90 kb) were identified for novel dsDNA viruses in the Yangshan Harbor metavirome. These newly discovered viruses contribute to the expansion of viral taxonomy by introducing 46 potential new families. Except for one virus, all others belong to the class Caudoviricetes. The exception is a novel member of the recently characterized viral group known as Gossevirus. Fifteen viruses were predicted to be temperate. The predicted hosts for the viruses appear to be involved in various aspects of the nitrogen cycle, including nitrogen fixation, oxidation and denitrification. Two viruses were identified to have a host of Flavobacterium and Tepidimonas fonticaldi, respectively, by matching CRISPR spacers with viral protospacers. Our findings provide an overview for characterizing and identifying specific viruses from Yangshan Harbor. The Gossevirus-like virus uncovered emphasizes the need for further comprehensive isolation and investigation of polinton-like viruses.}, } @article {pmid38445903, year = {2024}, author = {Sun, Y and Staley, ZR and Woodbury, B and Riethoven, J-J and Li, X}, title = {Composting reduces the risks of resistome in beef cattle manure at the transcriptional level.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0175223}, doi = {10.1128/aem.01752-23}, pmid = {38445903}, issn = {1098-5336}, abstract = {Transcriptomic evidence is needed to determine whether composting is more effective than conventional stockpiling in mitigating the risk of resistome in livestock manure. The objective of this study is to compare composting and stockpiling for their effectiveness in reducing the risk of antibiotic resistance in beef cattle manure. Samples collected from the center and the surface of full-size manure stockpiling and composting piles were subject to metagenomic and metatranscriptomic analyses. While the distinctions in resistome between stockpiled and composted manure were not evident at the DNA level, the advantages of composting over stockpiling were evident at the transcriptomic level in terms of the abundance of antibiotic resistance genes (ARGs), the number of ARG subtypes, and the prevalence of high-risk ARGs (i.e., mobile ARGs associated with zoonotic pathogens). DNA and transcript contigs show that the pathogen hosts of high-risk ARGs included Escherichia coli O157:H7 and O25b:H4, Klebsiella pneumoniae, and Salmonella enterica. Although the average daily temperatures for the entire composting pile exceeded 55°C throughout the field study, more ARG and ARG transcripts were removed at the center of the composting pile than at the surface. This work demonstrates the advantage of composting over stockpiling in reducing ARG risk in active populations in beef cattle manure.IMPORTANCEProper treatment of manure before land application is essential to mitigate the spread of antibiotic resistance in the environment. Stockpiling and composting are two commonly used methods for manure treatment. However, the effectiveness of composting in reducing antibiotic resistance in manure has been debated. This work compared the ability of these two methods to reduce the risk of antibiotic resistance in beef cattle manure. Our results demonstrate that composting reduced more high-risk resistance genes at the transcriptomic level in cattle manure than conventional stockpiling. This finding not only underscores the effectiveness of composting in reducing antibiotic resistance in manure but also highlights the importance of employing RNA analyses alongside DNA analyses.}, } @article {pmid38445871, year = {2024}, author = {Cai, M and Zhang, C and Ndungu, CN and Liu, G and Liu, W and Zhang, Q}, title = {Linking ecosystem multifunctionality to microbial community features in rivers along a latitudinal gradient.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0014724}, doi = {10.1128/msystems.00147-24}, pmid = {38445871}, issn = {2379-5077}, abstract = {Microorganisms regulate numerous ecosystem functions and show considerable differences along a latitudinal gradient. Although studies have revealed the latitudinal patterns of microbial community structure and single ecosystem function, the latitudinal patterns of ecosystem multifunctionality (EMF) and how microbial communities affect EMF along a latitudinal gradient remain unclear. Here, we collected channel sediments, riparian rhizosphere soils, and riparian bulk soils from 30 rivers across China and calculated EMF using 18 variables related to nitrogen cycling, nutrient pool, plant productivity, and water quality. We also determined microbial diversity (taxonomic and functional) and microbial network complexity using metagenomic sequencing. The results showed that EMF significantly decreased with increasing latitude in riparian rhizosphere and bulk soils but not in channel sediments. Microbial taxonomic and functional richness (observed species) in channel sediments were significantly higher in the low-latitude group than in the high-latitude group. However, microbial co-occurrence networks were more complex in the high-latitude group compared with the low-latitude group. Abiotic factors, primarily geographic and climatic factors, contributed more to EMF than microbial diversity and network complexity parameters in which only betweenness centralization had a significant relationship with EMF. Together, this study provides insight into the latitudinal pattern of EMF in rivers and highlights the importance of large-scale factors in explaining such latitudinal patterns.IMPORTANCEEcosystem multifunctionality (EMF) is the capacity of an ecosystem to provide multiple functions simultaneously. Microorganisms, as dominant drivers of belowground processes, have a profound effect on ecosystem functions. Although studies have revealed the latitudinal patterns of microbial community structure and single ecosystem function, the latitudinal patterns of EMF and how microbial communities affect EMF along a latitudinal gradient remain unclear. We collected channel sediments, riparian rhizosphere soils, and riparian bulk soils from 30 rivers along a latitudinal gradient across China and calculated EMF using 18 variables related to nitrogen cycling, nutrient pool, plant productivity, and water quality. This study fills a critical knowledge gap regarding the latitudinal patterns and drivers of EMF in river ecosystems and gives new insights into how microbial diversity and network complexity affect EMF from a metagenomic perspective.}, } @article {pmid38445870, year = {2024}, author = {Yap, M and O'Sullivan, O and O'Toole, PW and Sheehan, JJ and Fenelon, MA and Cotter, PD}, title = {Seasonal and geographical impact on the Irish raw milk microbiota correlates with chemical composition and climatic variables.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0129023}, doi = {10.1128/msystems.01290-23}, pmid = {38445870}, issn = {2379-5077}, abstract = {UNLABELLED: Season and location have previously been shown to be associated with differences in the microbiota of raw milk, especially in milk from pasture-based systems. Here, we further advance research in this area by examining differences in the raw milk microbiota from several locations across Ireland over 12 months, and by investigating microbiota associations with climatic variables and chemical composition. Shotgun metagenomic sequencing was used to investigate the microbiota of raw milk collected from nine locations (n = 241). Concurrent chemical analysis of the protein, fat, lactose, total solids, nonprotein nitrogen contents, and titratable acidity (TA) of the same raw milk were performed. Although the raw milk microbiota was highly diverse, a core microbiota was found, with Pseudomonas_E, Lactococcus, Acinetobacter, and Leuconostoc present in all samples. Microbiota diversity significantly differed by season and location, with differences in seasonality and geography corresponding to 11.8% and 10.5% of the variation in the microbiota. Functional and antibiotic resistance profiles also varied across season and location. The analysis of other metadata revealed additional interactions, such as an association between mean daily air and grass temperatures with the abundance of spoilage taxa like Pseudomonas species. Correlations were identified between pathogenic, mastitis-related species, fat content, and the number of sun hours, suggesting a seasonal effect. Ultimately, this study expands our understanding of the interconnected nature of the microbiota, environment/climate variables, and chemical composition of raw milk and provides evidence of a season- and location-specific microbiota.

IMPORTANCE: The microbiota of raw milk is influenced by many factors that encourage or prevent the introduction and growth of both beneficial and undesirable microorganisms. The seasonal and geographical impacts on the microbial communities of raw milk have been previously seen, but the relationships with environmental factors and the chemical composition has yet to be investigated. In this year-long study, we found that while raw milk is highly diverse, a core microbiota was detected for Irish raw milk, with strong evidence of seasonal and geographical influence. We also found associations between groups of microorganisms, environmental factors, and milk composition, which expand current knowledge on the relationships between microbial and chemical composition and the climate. These results provide evidence for the development of a tool to allow for the prediction of raw milk quality and safety.}, } @article {pmid38445858, year = {2024}, author = {Peng, Y and Williams, MM and Xiaoli, L and Simon, A and Fueston, H and Tondella, ML and Weigand, MR}, title = {Strengthening Bordetella pertussis genomic surveillance by direct sequencing of residual positive specimens.}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {e0165323}, doi = {10.1128/jcm.01653-23}, pmid = {38445858}, issn = {1098-660X}, abstract = {Whole-genome sequencing (WGS) of microbial pathogens recovered from patients with infectious disease facilitates high-resolution strain characterization and molecular epidemiology. However, increasing reliance on culture-independent methods to diagnose infectious diseases has resulted in few isolates available for WGS. Here, we report a novel culture-independent approach to genome characterization of Bordetella pertussis, the causative agent of pertussis and a paradigm for insufficient genomic surveillance due to limited culture of clinical isolates. Sequencing libraries constructed directly from residual pertussis-positive diagnostic nasopharyngeal specimens were hybridized with biotinylated RNA "baits" targeting B. pertussis fragments within complex mixtures that contained high concentrations of host and microbial background DNA. Recovery of B. pertussis genome sequence data was evaluated with mock and pooled negative clinical specimens spiked with reducing concentrations of either purified DNA or inactivated cells. Targeted enrichment increased the yield of B. pertussis sequencing reads up to 90% while simultaneously decreasing host reads to less than 10%. Filtered sequencing reads provided sufficient genome coverage to perform characterization via whole-genome single nucleotide polymorphisms and whole-genome multilocus sequencing typing. Moreover, these data were concordant with sequenced isolates recovered from the same specimens such that phylogenetic reconstructions from either consistently clustered the same putatively linked cases. The optimized protocol is suitable for nasopharyngeal specimens with diagnostic IS481 Ct < 35 and >10 ng DNA. Routine implementation of these methods could strengthen surveillance and study of pertussis resurgence by capturing additional cases with genomic characterization.}, } @article {pmid38445660, year = {2024}, author = {Heumel, S and de Rezende Rodovalho, V and Urien, C and Specque, F and Brito Rodrigues, P and Robil, C and Delval, L and Sencio, V and Descat, A and Deruyter, L and Ferreira, S and Gomes Machado, M and Barthelemy, A and Angulo, FS and Haas, JT and Goosens, JF and Wolowczuk, I and Grangette, C and Rouillé, Y and Grimaud, G and Lenski, M and Hennart, B and Ramirez Vinolo, MA and Trottein, F}, title = {Shotgun metagenomics and systemic targeted metabolomics highlight indole-3-propionic acid as a protective gut microbial metabolite against influenza infection.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2325067}, doi = {10.1080/19490976.2024.2325067}, pmid = {38445660}, issn = {1949-0984}, abstract = {The gut-to-lung axis is critical during respiratory infections, including influenza A virus (IAV) infection. In the present study, we used high-resolution shotgun metagenomics and targeted metabolomic analysis to characterize influenza-associated changes in the composition and metabolism of the mouse gut microbiota. We observed several taxonomic-level changes on day (D)7 post-infection, including a marked reduction in the abundance of members of the Lactobacillaceae and Bifidobacteriaceae families, and an increase in the abundance of Akkermansia muciniphila. On D14, perturbation persisted in some species. Functional scale analysis of metagenomic data revealed transient changes in several metabolic pathways, particularly those leading to the production of short-chain fatty acids (SCFAs), polyamines, and tryptophan metabolites. Quantitative targeted metabolomics analysis of the serum revealed changes in specific classes of gut microbiota metabolites, including SCFAs, trimethylamine, polyamines, and indole-containing tryptophan metabolites. A marked decrease in indole-3-propionic acid (IPA) blood level was observed on D7. Changes in microbiota-associated metabolites correlated with changes in taxon abundance and disease marker levels. In particular, IPA was positively correlated with some Lactobacillaceae and Bifidobacteriaceae species (Limosilactobacillus reuteri, Lactobacillus animalis) and negatively correlated with Bacteroidales bacterium M7, viral load, and inflammation markers. IPA supplementation in diseased animals reduced viral load and lowered local (lung) and systemic inflammation. Treatment of mice with antibiotics targeting IPA-producing bacteria before infection enhanced viral load and lung inflammation, an effect inhibited by IPA supplementation. The results of this integrated metagenomic-metabolomic analysis highlighted IPA as an important contributor to influenza outcomes and a potential biomarker of disease severity.}, } @article {pmid38444804, year = {2024}, author = {Suo, B and Castro, MP and Sreenivasa, MY}, title = {Editorial: Microbiota biodiversity of traditional fermented products.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1380205}, doi = {10.3389/fmicb.2024.1380205}, pmid = {38444804}, issn = {1664-302X}, } @article {pmid38444746, year = {2024}, author = {Lu, Z and Han, J and Wang, Y and He, Z and Song, S and Liu, K and Shao, Z}, title = {Diagnosing and reintegrating traceability of infectious diseases via metagenomic next-generation sequencing: Study of a severe case of Rickettsia japonica infection.}, journal = {Infectious medicine}, volume = {3}, number = {1}, pages = {100094}, pmid = {38444746}, issn = {2772-431X}, abstract = {BACKGROUND: In this study, we present a case of Japanese spotted fever (JSF) caused by Rickettsia japonica and use this case to investigate the process of diagnosing and reintegrating traceability of infectious diseases via metagenomic next-generation sequencing (mNGS).

METHODS: From data relating to epidemiological history, clinical and laboratory examinations, and mNGS sequencing, a diagnosis of severe JSF was concluded.

RESULTS: A detailed field epidemiological investigation discovered parasitic Haemaphysalis longicornis from a host animal (dog) in the domicile of the patient, within which R. japonica was detected, along with a diverse array of other potentially pathogenic microorganisms that could cause other infectious diseases.

CONCLUSION: The mNGS provided an efficient method to diagnose JSF infection. This methodology could also be applied to field epidemiological investigations to establish the traceability of infectious diseases.}, } @article {pmid38444657, year = {2024}, author = {Rosenboom, I and Thavarasa, A and Richardson, H and Long, MB and Wiehlmann, L and Davenport, CF and Shoemark, A and Chalmers, JD and Tümmler, B}, title = {Sputum metagenomics of people with bronchiectasis.}, journal = {ERJ open research}, volume = {10}, number = {2}, pages = {}, pmid = {38444657}, issn = {2312-0541}, abstract = {BACKGROUND: The microbiota in the sputum of people with bronchiectasis has repeatedly been investigated in cohorts of different geographic origin, but so far has not been studied to the species level in comparison to control populations including healthy adults and smokers without lung disease.

METHODS: The microbial metagenome from sputa of 101 European Bronchiectasis Registry (EMBARC) study participants was examined by using whole-genome shotgun sequencing.

RESULTS: Our analysis of the metagenome of people with bronchiectasis revealed four clusters characterised by a predominance of Haemophilus influenzae, Pseudomonas aeruginosa or polymicrobial communities with varying compositions of nonpathogenic commensals and opportunistic pathogens. The metagenomes of the severely affected patients showed individual profiles characterised by low alpha diversity. Importantly, nearly 50% of patients with severe disease were grouped in a cluster characterised by commensals. Comparisons with the sputum metagenomes of healthy smokers and healthy nonsmokers revealed a gradient of depletion of taxa in bronchiectasis, most often Neisseria subflava, Fusobacterium periodonticum and Eubacterium sulci.

CONCLUSION: The gradient of depletion of commensal taxa found in healthy airways is a key feature of bronchiectasis associated with disease severity.}, } @article {pmid38444540, year = {2023}, author = {Huang, C and Chang, S and Ma, R and Shang, Y and Li, Y and Wang, Y and Feng, M and Guo, W}, title = {COVID-19 in pulmonary critically ill patients: metagenomic identification of fungi and characterization of pathogenic microorganisms.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1220012}, pmid = {38444540}, issn = {2235-2988}, abstract = {BACKGROUND: Fungal co-infection is prevalent in critically ill patients with COVID-19. The conventional approach applied to fungal identification has relatively low sensitivity and is time-consuming. The metagenomic next-generation sequencing (mNGS) technology can simultaneously detect a variety of microorganisms, and is increasingly being used for the rapid detection and diagnosis of pathogens.

METHODS: In this single-center retrospective study, we described the clinical presentation and outcomes of COVID-19 and mNGS positive for fungi in pulmonary critically ill patients during the outbreak of Omicron infection from December 2022 to January 2023.

RESULTS: Among 43 COVID-19 patients with acute respiratory distress syndrome (ARDS) on a single intensive care unit (ICU), 10 were reported to be fungal positive using the mNGS test. The number of pathogenic microorganisms detected by mNGS was significantly higher than that via traditional methods, especially in the detection of fungi and viruses. Aspergillus infection was dominant, and most of these patients also had concurrent bacterial or viral infections. Probable or possible COVID-19-associated pulmonary aspergillosis (CAPA) was diagnosed in all 10 patients, and the prognosis was poor.

CONCLUSION: Patients with COVID-19 may be at increased risk of developing fungal infections as well as concurrent bacterial or viral infections, and mNGS can be a powerful tool in identifying these infections. Clinicians should be aware of the increased risk of fungal infections in COVID-19 patients, particularly those who have underlying immunocompromising conditions, and should monitor for early signs of infection.}, } @article {pmid38444533, year = {2024}, author = {Smadi, M and Lee, E and Phelan, J and Wang, A and Bilodeau, GJ and Pernal, SF and Guarna, MM and Rott, M and Griffiths, JS}, title = {Plant virus diversity in bee and pollen samples from apple (Malus domestica) and sweet cherry (Prunus avium) agroecosystems.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1335281}, pmid = {38444533}, issn = {1664-462X}, abstract = {INTRODUCTION: Honey bee (Apis mellifera) pollination is widely used in tree fruit production systems to improve fruit set and yield. Many plant viruses can be associated with pollen or transmitted through pollination, and can be detected through bee pollination activities. Honey bees visit multiple plants and flowers in one foraging trip, essentially sampling small amounts of pollen from a wide area. Here we report metagenomics-based area-wide monitoring of plant viruses in cherry (Prunus avium) and apple (Malus domestica) orchards in Creston Valley, British Columbia, Canada, through bee-mediated pollen sampling.

METHODS: Plant viruses were identified in total RNA extracted from bee and pollen samples, and compared with profiles from double stranded RNA extracted from leaf and flower tissues. CVA, PDV, PNRSV, and PVF coat protein nucleotide sequences were aligned and compared for phylogenetic analysis.

RESULTS: A wide array of plant viruses were identified in both systems, with cherry virus A (CVA), prune dwarf virus (PDV), prunus necrotic ringspot virus (PNRSV), and prunus virus F (PVF) most commonly detected. Citrus concave gum associated virus and apple stem grooving virus were only identified in samples collected during apple bloom, demonstrating changing viral profiles from the same site over time. Different profiles of viruses were identified in bee and pollen samples compared to leaf and flower samples reflective of pollen transmission affinity of individual viruses. Phylogenetic and pairwise analysis of the coat protein regions of the four most commonly detected viruses showed unique patterns of nucleotide sequence diversity, which could have implications in their evolution and management approaches. Coat protein sequences of CVA and PVF were broadly diverse with multiple distinct phylogroups identified, while PNRSV and PDV were more conserved.

CONCLUSION: The pollen virome in fruit production systems is incredibly diverse, with CVA, PDV, PNRSV, and PVF widely prevalent in this region. Bee-mediated monitoring in agricultural systems is a powerful approach to study viral diversity and can be used to guide more targeted management approaches.}, } @article {pmid38444256, year = {2024}, author = {Shoguchi, E and Kawachi, M and Shinzato, C and Beedessee, G}, title = {Functional analyses of bacterial genomes found in Symbiodiniaceae genome assemblies.}, journal = {Environmental microbiology reports}, volume = {16}, number = {2}, pages = {e13238}, doi = {10.1111/1758-2229.13238}, pmid = {38444256}, issn = {1758-2229}, support = {20H03235//Japan Society for the Promotion of Science/ ; 20K05798//Japan Society for the Promotion of Science/ ; 23H02132//Japan Society for the Promotion of Science/ ; //OIST's support for the Marine Genomics Unit/ ; //Herchel Smith Postdoctoral Research Fellowship/ ; }, abstract = {Bacterial-algal interactions strongly influence marine ecosystems. Bacterial communities in cultured dinoflagellates of the family Symbiodiniaceae have been characterized by metagenomics. However, little is known about whole-genome analysis of marine bacteria associated with these dinoflagellates. We performed in silico analysis of four bacterial genomes from cultures of four dinoflagellates of the genera Symbiodinium, Breviolum, Cladocopium and Durusdinium. Comparative analysis showed that the former three contain the alphaproteobacterial family Parvibaculaceae and that the Durusdinium culture includes the family Sphingomonadaceae. There were no large genomic reductions in the alphaproteobacteria with genome sizes of 2.9-3.9 Mb, implying they are not obligate intracellular bacteria. Genomic annotations of three Parvibaculaceae detected the gene for diacetylchitobiose deacetylase (Dac), which may be involved in the degradation of dinoflagellate cell surfaces. They also had metabolic genes for dissimilatory nitrate reduction to ammonium (DNRA) in the nitrogen (N) cycle and cobalamin (vitamin B12) biosynthetic genes in the salvage pathway. Those three characters were not found in the Sphingomonadaceae genome. Predicted biosynthetic gene clusters for secondary metabolites indicated that the Parvibaculaceae likely produce the same secondary metabolites. Our study suggests that the Parvibaculaceae is a major resident of Symbiodiniaceae cultures with antibiotics.}, } @article {pmid38443997, year = {2024}, author = {Yerke, A and Fry Brumit, D and Fodor, AA}, title = {Proportion-based normalizations outperform compositional data transformations in machine learning applications.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {45}, pmid = {38443997}, issn = {2049-2618}, abstract = {BACKGROUND: Normalization, as a pre-processing step, can significantly affect the resolution of machine learning analysis for microbiome studies. There are countless options for normalization scheme selection. In this study, we examined compositionally aware algorithms including the additive log ratio (alr), the centered log ratio (clr), and a recent evolution of the isometric log ratio (ilr) in the form of balance trees made with the PhILR R package. We also looked at compositionally naïve transformations such as raw counts tables and several transformations that are based on relative abundance, such as proportions, the Hellinger transformation, and a transformation based on the logarithm of proportions (which we call "lognorm").

RESULTS: In our evaluation, we used 65 metadata variables culled from four publicly available datasets at the amplicon sequence variant (ASV) level with a random forest machine learning algorithm. We found that different common pre-processing steps in the creation of the balance trees made very little difference in overall performance. Overall, we found that the compositionally aware data transformations such as alr, clr, and ilr (PhILR) performed generally slightly worse or only as well as compositionally naïve transformations. However, relative abundance-based transformations outperformed most other transformations by a small but reliably statistically significant margin.

CONCLUSIONS: Our results suggest that minimizing the complexity of transformations while correcting for read depth may be a generally preferable strategy in preparing data for machine learning compared to more sophisticated, but more complex, transformations that attempt to better correct for compositionality. Video Abstract.}, } @article {pmid38443925, year = {2024}, author = {Moragues-Solanas, L and Le-Viet, T and McSorley, E and Halford, C and Lockhart, DS and Aydin, A and Kay, GL and Elumogo, N and Mullen, W and O'Grady, J and Gilmour, MW}, title = {Development and proof-of-concept demonstration of a clinical metagenomics method for the rapid detection of bloodstream infection.}, journal = {BMC medical genomics}, volume = {17}, number = {1}, pages = {71}, pmid = {38443925}, issn = {1755-8794}, support = {MR/R015937/1/MRC_/Medical Research Council/United Kingdom ; BB/CCG1860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X011011/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X011011/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: The timely and accurate diagnosis of bloodstream infection (BSI) is critical for patient management. With longstanding challenges for routine blood culture, metagenomics is a promising approach to rapidly provide sequence-based detection and characterisation of bloodborne bacteria. Long-read sequencing technologies have successfully supported the use of clinical metagenomics for syndromes such as respiratory illness, and modified approaches may address two requisite factors for metagenomics to be used as a BSI diagnostic: depletion of the high level of host DNA to then detect the low abundance of microbes in blood.

METHODS: Blood samples from healthy donors were spiked with different concentrations of four prevalent causative species of BSI. All samples were then subjected to a modified saponin-based host DNA depletion protocol and optimised DNA extraction, whole genome amplification and debranching steps in preparation for sequencing, followed by bioinformatical analyses. Two related variants of the protocol are presented: 1mL of blood processed without bacterial enrichment, and 5mL of blood processed following a rapid bacterial enrichment protocol-SepsiPURE.

RESULTS: After first identifying that a large proportion of host mitochondrial DNA remained, the host depletion process was optimised by increasing saponin concentration to 3% and scaling the reaction to allow more sample volume. Compared to non-depleted controls, the 3% saponin-based depletion protocol reduced the presence of host chromosomal and mitochondrial DNA < 10[6] and < 10[3] fold respectively. When the modified depletion method was further combined with a rapid bacterial enrichment method (SepsiPURE; with 5mL blood samples) the depletion of mitochondrial DNA improved by a further > 10X while also increasing detectable bacteria by > 10X. Parameters during DNA extraction, whole genome amplification and long-read sequencing were also adjusted, and subsequently amplicons were detected for each input bacterial species at each of the spiked concentrations, ranging from 50-100 colony forming units (CFU)/mL to 1-5 CFU/mL.

CONCLUSION: In this proof-of-concept study, four prevalent BSI causative species were detected in under 12 h to species level (with antimicrobial resistance determinants) at concentrations relevant to clinical blood samples. The use of a rapid and precise metagenomic protocols has the potential to advance the diagnosis of BSI.}, } @article {pmid38124500, year = {2024}, author = {Dinnage, R and Sarre, SD and Duncan, RP and Dickman, CR and Edwards, SV and Greenville, AC and Wardle, GM and Gruber, B}, title = {slimr: An R package for tailor-made integrations of data in population genomic simulations over space and time.}, journal = {Molecular ecology resources}, volume = {24}, number = {3}, pages = {e13916}, doi = {10.1111/1755-0998.13916}, pmid = {38124500}, issn = {1755-0998}, support = {DP180103844//Australian Research Council/ ; }, mesh = {Animals ; *Metagenomics ; *Software ; Computer Simulation ; Genomics/methods ; Biological Evolution ; Mammals ; }, abstract = {Software for realistically simulating complex population genomic processes is revolutionizing our understanding of evolutionary processes, and providing novel opportunities for integrating empirical data with simulations. However, the integration between standalone simulation software and R is currently not well developed. Here, we present slimr, an R package designed to create a seamless link between standalone software SLiM >3.0, one of the most powerful population genomic simulation frameworks, and the R development environment, with its powerful data manipulation and analysis tools. We show how slimr facilitates smooth integration between genetic data, ecological data and simulation in a single environment. The package enables pipelines that begin with data reading, cleaning and manipulation, proceed to constructing empirically based parameters and initial conditions for simulations, then to running numerical simulations and finally to retrieving simulation results in a format suitable for comparisons with empirical data - aided by advanced analysis and visualization tools provided by R. We demonstrate the use of slimr with an example from our own work on the landscape population genomics of desert mammals, highlighting the advantage of having a single integrated tool for both data analysis and simulation. slimr makes the powerful simulation ability of SLiM directly accessible to R users, allowing integrated simulation projects that incorporate empirical data without the need to switch between software environments. This should provide more opportunities for evolutionary biologists and ecologists to use realistic simulations to better understand the interplay between ecological and evolutionary processes.}, } @article {pmid38443576, year = {2024}, author = {Yu, MK and Fogarty, EC and Eren, AM}, title = {Diverse plasmid systems and their ecology across human gut metagenomes revealed by PlasX and MobMess.}, journal = {Nature microbiology}, volume = {9}, number = {3}, pages = {830-847}, pmid = {38443576}, issn = {2058-5276}, abstract = {Plasmids alter microbial evolution and lifestyles by mobilizing genes that often confer fitness in changing environments across clades. Yet our ecological and evolutionary understanding of naturally occurring plasmids is far from complete. Here we developed a machine-learning model, PlasX, which identified 68,350 non-redundant plasmids across human gut metagenomes and organized them into 1,169 evolutionarily cohesive 'plasmid systems' using our sequence containment-aware network-partitioning algorithm, MobMess. Individual plasmids were often country specific, yet most plasmid systems spanned across geographically distinct human populations. Cargo genes in plasmid systems included well-known determinants of fitness, such as antibiotic resistance, but also many others including enzymes involved in the biosynthesis of essential nutrients and modification of transfer RNAs, revealing a wide repertoire of likely fitness determinants in complex environments. Our study introduces computational tools to recognize and organize plasmids, and uncovers the ecological and evolutionary patterns of diverse plasmids in naturally occurring habitats through plasmid systems.}, } @article {pmid38443405, year = {2024}, author = {Ho, CW and Chen, PY and Liao, YT and Cheng, YF and Tsou, HH and Liu, TY and Liang, KH}, title = {Uncovering the microbiome landscape in sashimi delicacies.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {5454}, pmid = {38443405}, issn = {2045-2322}, support = {V113E-002-4//Taipei Veterans General Hospital/ ; }, abstract = {It is widely believed that a significant portion of the gut microbiota, which play crucial roles in overall health and disease, originates from the food we consume. Sashimi is a type of popular raw seafood cuisine. Its microbiome, however, remained to be thoroughly explored. The objective of this study is to explore the microbiome composition in sashimi at the time when it is served and ready to be eaten. Specifically, our tasks include investigating the diversity and characteristics of microbial profiles in sashimi with respect to the fish types. We utilized the Sanger-sequencing based DNA barcoding technology for fish species authentication and next-generation sequencing for sashimi microbiome profiling. We investigated the microbiome profiles of amberjack, cobia, salmon, tuna and tilapia sashimi, which were all identified using the MT-CO1 DNA sequences regardless of their menu offering names. Chao1 and Shannon indexes, as well as Bray-Curtis dissimilarity index were used to evaluate the alpha and beta diversities of sashimi microbiome. We successfully validated our previous observation that tilapia sashimi has a significantly higher proportions of Pseudomonas compared to other fish sashimi, using independent samples (P = 0.0010). Salmon sashimi exhibited a notably higher Chao1 index in its microbiome in contrast to other fish species (P = 0.0031), indicating a richer and more diverse microbial ecosystem. Non-Metric Multidimensional Scaling (NMDS) based on Bray-Curtis dissimilarity index revealed distinct clusters of microbiome profiles with respect to fish types. Microbiome similarity was notably observed between amberjack and tuna, as well as cobia and salmon. The relationship of microbiome similarity can be depicted as a tree which resembles partly the phylogenetic tree of host species, emphasizing the close relationship between host evolution and microbial composition. Moreover, salmon exhibited a pronounced relative abundance of the Photobacterium genus, significantly surpassing tuna (P = 0.0079), observed consistently across various restaurant sources. In conclusion, microbiome composition of Pseudomonas is significantly higher in tilapia sashimi than in other fish sashimi. Salmon sashimi has the highest diversity of microbiome among all fish sashimi that we analyzed. The level of Photobacterium is significantly higher in salmon than in tuna across all the restaurants we surveyed. These findings provide critical insights into the intricate relationship between the host evolution and the microbial composition. These discoveries deepen our understanding of sashimi microbiota, facilitating our decision in selecting raw seafood.}, } @article {pmid38443373, year = {2024}, author = {Dzofou Ngoumelah, D and Heggeset, TMB and Haugen, T and Sulheim, S and Wentzel, A and Harnisch, F and Kretzschmar, J}, title = {Effect of model methanogens on the electrochemical activity, stability, and microbial community structure of Geobacter spp. dominated biofilm anodes.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {17}, pmid = {38443373}, issn = {2055-5008}, support = {57381414//Deutscher Akademischer Austauschdienst (German Academic Exchange Service)/ ; 731101//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, abstract = {Combining anaerobic digestion (AD) and microbial electrochemical technologies (MET) in AD-MET holds great potential. Methanogens have been identified as one cause of decreased electrochemical activity and deterioration of Geobacter spp. biofilm anodes. A better understanding of the different interactions between methanogenic genera/species and Geobacter spp. biofilms is needed to shed light on the observed reduction in electrochemical activity and stability of Geobacter spp. dominated biofilms as well as observed changes in microbial communities of AD-MET. Here, we have analyzed electrochemical parameters and changes in the microbial community of Geobacter spp. biofilm anodes when exposed to three representative methanogens with different metabolic pathways, i.e., Methanosarcina barkeri, Methanobacterium formicicum, and Methanothrix soehngenii. M. barkeri negatively affected the performance and stability of Geobacter spp. biofilm anodes only in the initial batches. In contrast, M. formicicum did not affect the stability of Geobacter spp. biofilm anodes but caused a decrease in maximum current density of ~37%. M. soehngenii induced a coloration change of Geobacter spp. biofilm anodes and a decrease in the total transferred charge by ~40%. Characterization of biofilm samples after each experiment by 16S rRNA metabarcoding, whole metagenome nanopore sequencing, and shotgun sequencing showed a higher relative abundance of Geobacter spp. after exposure to M. barkeri as opposed to M. formicicum or M. soehngenii, despite the massive biofilm dispersal observed during initial exposure to M. barkeri.}, } @article {pmid38443364, year = {2024}, author = {Xie, P and Zhou, X and Li, Y and Wu, J and Zhang, H and Huang, Y and Tan, X and Wen, L and Olasunkanmi, OI and Zhou, J and Sun, Z and Liu, M and Zhang, G and Wang, Y and Xie, P and Yang, J and Zheng, P}, title = {Gut microbial CAZymes markers for depression.}, journal = {Translational psychiatry}, volume = {14}, number = {1}, pages = {135}, pmid = {38443364}, issn = {2158-3188}, support = {cstc2021jcyj-msxmX0096//Chongqing Science and Technology Commission (Chongqing Science and Technology Commission, Chongqing People's Municipal Government)/ ; }, abstract = {Major depressive disorder (MDD) is a serious mental illness, characterized by disturbances of gut microbiome, it is required to further explore how the carbohydrate-active enzymes (CAZymes) were changed in MDD. Here, using the metagenomic data from patients with MDD (n = 118) and heath controls (HC, n = 118), we found that the whole CAZymes signatures of MDD were significantly discriminated from that in HC. α-diversity indexes of the two groups were also significantly different. The patients with MDD were characterized by enriched Glycoside Hydrolases (GHs) and Polysaccharide Lyases (PLs) relative to HC. A panel of makers composed of 9 CAZymes mainly belonging to GHs enabled to discriminate the patients with MDD and HC with AUC of 0.824. In addition, this marker panel could classify blinded test samples from the two groups with an AUC of 0.736. Moreover, we found that baseline 4 CAZymes levels also could predict the antidepressant efficacy after adjusted confounding factors and times of depressive episode. Our findings showed that MDD was associated with disturbances of gut CAZymes, which may help to develop diagnostic and predictive tools for depression.}, } @article {pmid38442686, year = {2024}, author = {Sutcliffe, IC and Rodriguez-R, LM and Venter, SN and Whitman, WB}, title = {Quis custodiet ipsos custodes? A call for community participation in the governance of the SeqCode.}, journal = {Systematic and applied microbiology}, volume = {47}, number = {2-3}, pages = {126498}, doi = {10.1016/j.syapm.2024.126498}, pmid = {38442686}, issn = {1618-0984}, abstract = {Codes of nomenclature that provide well-regulated and stable frameworks for the naming of taxa are a fundamental underpinning of biological research. These Codes themselves require systems that govern their administration, interpretation and emendment. Here we review the provisions that have been made for the governance of the recently introduced Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), which provides a nomenclatural framework for the valid publication of names of Archaea and Bacteria using isolate genome, metagenome-assembled genome or single-amplified genome sequences as type material. The administrative structures supporting the SeqCode are designed to be open and inclusive. Direction is provided by the SeqCode Community, which we encourage those with an interest in prokaryotic systematics to join.}, } @article {pmid38442608, year = {2024}, author = {She, Z and Wang, J and Pan, X and Ma, D and Gao, Y and Wang, S and Chuai, X and Mu, Y and Yue, Z}, title = {Multi-omics insights into biogeochemical responses to organic matter addition in an acidic pit lake: Implications for bioremediation.}, journal = {Water research}, volume = {254}, number = {}, pages = {121404}, doi = {10.1016/j.watres.2024.121404}, pmid = {38442608}, issn = {1879-2448}, abstract = {Acidic pit lakes (APLs) emerge as reservoirs of acid mine drainage in flooded open-pit mines, representing extreme ecosystems and environmental challenges worldwide. The bioremediation of these oligotrophic waters necessitates the addition of organic matter, but the biogeochemical response of APLs to exogenous organic matter remains inadequately comprehended. This study delves into the biogeochemical impacts and remediation effects of digestate-derived organic matter within an APL, employing a multi-omics approach encompassing geochemical analyses, amplicon and metagenome sequencing, and ultra-high resolution mass spectrometry. The results indicated that digestate addition first stimulated fungal proliferation, particularly Ascomycetes and Basidiomycetes, which generated organic acids through lignocellulosic hydrolysis and fermentation. These simple compounds further supported heterotrophic growth, including Acidiphilium, Acidithrix, and Clostridium, thereby facilitating nitrate, iron, and sulfate reduction linked with acidity consumption. Nutrients derived from digestate also promoted the macroscopic development of acidophilic algae. Notably, the increased sulfate reduction-related genes primarily originated from assimilatory metabolism, thus connecting sulfate decrease to organosulfur increase. Assimilatory and dissimilatory sulfate reduction collectively contributed to sulfate removal and metal fixation. These findings yield multi-omics insights into APL biogeochemical responses to organic matter addition, enhancing the understanding of carbon-centered biogeochemical cycling in extreme ecosystems and guiding organic amendment-based bioremediation in oligotrophic polluted environments.}, } @article {pmid38442455, year = {2024}, author = {Zhu, G and Luan, L and Zhou, S and Dini-Andreote, F and Bahram, M and Yang, Y and Geisen, S and Zheng, J and Wang, S and Jiang, Y}, title = {Body size mediates the functional potential of soil organisms by diversity and community assembly across soil aggregates.}, journal = {Microbiological research}, volume = {282}, number = {}, pages = {127669}, doi = {10.1016/j.micres.2024.127669}, pmid = {38442455}, issn = {1618-0623}, abstract = {Body size is an important life-history trait that affects organism niche occupancy and ecological interactions. However, it is still unclear to what extent the assembly process of organisms with different body sizes affects soil biogeochemical cycling processes at the aggregate level. Here, we examined the diversity and community assembly of soil microorganisms (bacteria, fungi, and protists) and microfauna (nematodes) with varying body sizes. The microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism within three soil aggregate sizes (large macroaggregates, > 2 mm; small macroaggregates, 0.25-2 mm; and microaggregates, < 0.25 mm) were determined by metagenomics. We found that the smallest microbes (bacteria) had higher α-diversity and lower β-diversity and were mostly structured by stochastic processes, while all larger organisms (fungi, protists, and nematodes) had lower α-diversity and were relatively more influenced by deterministic processes. Structural equation modeling indicated that the microbial functional potential associated with carbon, nitrogen, phosphorus, and sulfur metabolism was mainly influenced by the bacterial and protist diversity in microaggregates. In contrast, the microbial functional potential was primarily mediated by the assembly processes of four organism groups, especially the nematode community in macroaggregates. This study reveals the important roles of soil organisms with different body sizes in the functional potential related to nutrient cycling, and provides new insights into the ecological processes structuring the diversity and community assembly of organisms of different body sizes at the soil aggregate level, with implications for soil nutrient cycling dynamics.}, } @article {pmid38442360, year = {2024}, author = {Yang, Y and Xu, N and Zhang, Z and Lei, C and Chen, B and Qin, G and Qiu, D and Lu, T and Qian, H}, title = {Deciphering Microbial Community and Nitrogen Fixation in the Legume Rhizosphere.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.3c09160}, pmid = {38442360}, issn = {1520-5118}, abstract = {Nitrogen is the most limiting factor in crop production. Legumes establish a symbiotic relationship with rhizobia and enhance nitrogen fixation. We analyzed 1,624 rhizosphere 16S rRNA gene samples and 113 rhizosphere metagenomic samples from three typical legumes and three non-legumes. The rhizosphere microbial community of the legumes had low diversity and was enriched with nitrogen-cycling bacteria (Sphingomonadaceae, Xanthobacteraceae, Rhizobiaceae, and Bacillaceae). Furthermore, the rhizosphere microbiota of legumes exhibited a high abundance of nitrogen-fixing genes, reflecting a stronger nitrogen-fixing potential, and Streptomycetaceae and Nocardioidaceae were the predominant nitrogen-fixing bacteria. We also identified helper bacteria and confirmed through metadata analysis and a pot experiment that the synthesis of riboflavin by helper bacteria is the key factor in promoting nitrogen fixation. Our study emphasizes that the construction of synthetic communities of nitrogen-fixing bacteria and helper bacteria is crucial for the development of efficient nitrogen-fixing microbial fertilizers.}, } @article {pmid38442029, year = {2024}, author = {Han, XY and Du, LF and Lin, ZT and Li, C and Xiong, T and Zhu, WJ and Ye, RZ and Wang, N and Wang, YF and Gao, WY and Zhao, L and Cui, XM and Cao, WC}, title = {Genomic characters of Anaplasma bovis and genetic diversity in China.}, journal = {Emerging microbes & infections}, volume = {13}, number = {1}, pages = {2323153}, doi = {10.1080/22221751.2024.2323153}, pmid = {38442029}, issn = {2222-1751}, abstract = {The emergence of Anaplasma bovis or A. bovis-like infection in humans from China and the United States of America has raised concern about the public health importance of this pathogen. Although A. bovis has been detected in a wide range of ticks and mammals in the world, no genome of the pathogen is available up to now, which has prohibited us from better understanding the genetic basis for its pathogenicity. Here we describe an A. bovis genome from metagenomic sequencing of an infected goat in China. Anaplasma bovis had the smallest genome of the genus Anaplasma, and relatively lower GC content. Phylogenetic analysis of single-copy orthologue sequence showed that A. bovis was closely related to A. platys and A. phagocytophilum, but relatively far from intraerythrocytic Anaplasma species. Anaplasma bovis had 116 unique orthogroups and lacked 51 orthogroups in comparison to other Anaplasma species. The virulence factors of A. bovis were significantly less than those of A. phagocytophilum, suggesting less pathogenicity of A. bovis. When tested by specific PCR assays, A. bovis was detected in 23 of 29 goats, with an infection rate up to 79.3% (95% CI: 64.6% ∼94.1%). The phylogenetic analyses based on partial 16S rRNA, gltA and groEL genes indicated that A. bovis had high genetic diversity. The findings of this study lay a foundation for further understanding of the biological characteristics and genetic diversity of A. bovis, and will facilitate the formulation of prevention and control strategies.}, } @article {pmid38441977, year = {2024}, author = {Chen, H and Huang, S and Zhao, Y and Sun, R and Wang, J and Yao, S and Huang, J and Yu, Z}, title = {Metagenomic analysis of the intestinal microbiome reveals the potential mechanism involved in Bacillus amyloliquefaciens in treating schistosomiasis japonica in mice.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0373523}, doi = {10.1128/spectrum.03735-23}, pmid = {38441977}, issn = {2165-0497}, abstract = {UNLABELLED: Schistosomiasis japonica is one of the neglected tropical diseases characterized by chronic hepatic, intestinal granulomatous inflammation and fibrosis, as well as dysbiosis of intestinal microbiome. Previously, the probiotic Bacillus amyloliquefaciens has been shown to alleviate the pathological injuries in mice infected with Schistosoma japonicum by improving the disturbance of the intestinal microbiota. However, the underlying mechanisms involved in this process remain unclear. In this study, metagenomics sequencing and functional analysis were employed to investigate the differential changes in taxonomic composition and functional genes of the intestinal microbiome in S. japonicum-infected mice treated with B. amyloliquefaciens. The results revealed that intervention with B. amyloliquefaciens altered the taxonomic composition of the intestinal microbiota at the species level in infected mice and significantly increased the abundance of beneficial bacteria. Moreover, the abundance of predicted genes in the intestinal microbiome was also significantly changed, and the abundance of xfp/xpk and genes translated to urease was significantly restored. Further analysis showed that Limosilactobacillus reuteri was positively correlated with several KEGG Orthology (KO) genes and metabolic reactions, which might play important roles in alleviating the pathological symptoms caused by S. japonicum infection, indicating that it has the potential to function as another effective therapeutic agent for schistosomiasis. These data suggested that treatment of murine schistosomiasis japonica by B. amyloliquefaciens might be induced by alterations in the taxonomic composition and functional gene of the intestinal microbiome in mice. We hope this study will provide adjuvant strategies and methods for the early prevention and treatment of schistosomiasis japonica.

IMPORTANCE: Targeted interventions of probiotics on gut microbiome were used to explore the mechanism of alleviating schistosomiasis japonica. Through metagenomic analysis, there were significant changes in the composition of gut microbiota in mice infected with Schistosoma japonicum and significant increase in the abundance of beneficial bacteria after the intervention of Bacillus amyloliquefaciens. At the same time, the abundance of functional genes was found to change significantly. The abundance of genes related to urease metabolism and xfp/xpk related to D-erythrose 4-phosphate production was significantly restored, highlighting the importance of Limosilactobacillus reuteri in the recovery and abundance of predicted genes of the gut microbiome. These results indicated potential regulatory mechanism between the gene function of gut microbiome and host immune response. Our research lays the foundation for elucidating the regulatory mechanism of probiotic intervention in alleviating schistosomiasis japonica, and provides potential adjuvant treatment strategies for early prevention and treatment of schistosomiasis japonica.}, } @article {pmid38441971, year = {2024}, author = {Kadlečková, D and Saláková, M and Erban, T and Tachezy, R}, title = {Discovery and characterization of novel DNA viruses in Apis mellifera: expanding the honey bee virome through metagenomic analysis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0008824}, doi = {10.1128/msystems.00088-24}, pmid = {38441971}, issn = {2379-5077}, abstract = {To date, many viruses have been discovered to infect honey bees. In this study, we used high-throughput sequencing to expand the known virome of the honey bee, Apis mellifera, by identifying several novel DNA viruses. While the majority of previously identified bee viruses are RNA, our study reveals nine new genomes from the Parvoviridae family, tentatively named Bee densoviruses 1 to 9. In addition, we characterized a large DNA virus, Apis mellifera filamentous-like virus (AmFLV), which shares limited protein identities with the known Apis mellifera filamentous virus. The complete sequence of AmFLV, obtained by a combination of laboratory techniques and bioinformatics, spans 152,678 bp. Linear dsDNA genome encodes for 112 proteins, of which 49 are annotated. Another large virus we discovered is Apis mellifera nudivirus, which belongs to a group of Alphanudivirus. The virus has a length of 129,467 bp and a circular dsDNA genome, and has 106 protein encoding genes. The virus contains most of the core genes of the family Nudiviridae. This research demonstrates the effectiveness of viral binning in identifying viruses in honey bee virology, showcasing its initial application in this field.IMPORTANCEHoney bees contribute significantly to food security by providing pollination services. Understanding the virome of honey bees is crucial for the health and conservation of bee populations and also for the stability of the ecosystems and economies for which they are indispensable. This study unveils previously unknown DNA viruses in the honey bee virome, expanding our knowledge of potential threats to bee health. The use of the viral binning approach we employed in this study offers a promising method to uncovering and understanding the vast viral diversity in these essential pollinators.}, } @article {pmid38441468, year = {2024}, author = {Xiao, Y and Wang, Y and Tong, B and Gu, Y and Zhou, X and Zhu, N and Xu, X and Yin, X and Kou, Y and Tan, Y and Wang, J and Li, W}, title = {Eubacterium rectale is a potential marker of altered gut microbiota in psoriasis and psoriatic arthritis.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0115423}, doi = {10.1128/spectrum.01154-23}, pmid = {38441468}, issn = {2165-0497}, abstract = {UNLABELLED: Previous studies have profiled the gut microbiota among psoriatic patients compared to that among healthy individuals. However, a comprehensive understanding of the magnitude, direction, and detailed compositional and functional profiles remains limited. Additionally, research exploring the gut microbiota in the context of both plaque psoriasis (PsO) and psoriatic arthritis (PsA) is lacking. To assess the taxonomic and functional characteristics of the gut microbiota in PsO and PsA patients and investigate potential links between the gut microbiota and disease pathogenesis. We collected fecal samples from 70 psoriatic patients (44 PsO and 26 PsA) and 25 age- and gender-matched healthy controls (HC) and employed deep metagenomic sequencing to characterize their gut microbiota. We noted significant alternations in the gut microbiota compositions of both PsO and PsA patients compared to those of HC. Despite limited effect sizes in alpha diversity (12.3% reduction of microbial richness but unchanged evenness in psoriatic patients) and beta diversity (disease accounts for 3.5% of total variations), we consistently observed substantial reductions of Eubacterium rectale in both PsO and PsA patients, with PsA patients exhibiting even lower levels of E. rectale than PsO patients. Additionally, two Alistipes species were also depleted in psoriatic patients. These microorganisms are known to play crucial roles in carbohydrate metabolism pathways, mainly producing short-chain fatty acids with anti-inflammatory effects. Overall, our observations supplemented the profiling of altered gut microbiota in patients with PsO and PsA at the species level and described a link between the dominant short-chain fatty acid-producing bacterial species and systemic immunity in psoriatic patients.

IMPORTANCE: In this observational clinical study with sufficient sample size and metagenomic sequencing to profile the gut microbiota, we identified consistent signals of the depleted abundance of Eubacterium rectale and related functional genes among psoriatic patients, including those with psoriatic arthritis. E. rectale may serve as an ecologically important functional unit in the gut microbiota, holding potential as a diagnostic marker and target for therapeutic interventions to achieve lasting effects. Our findings provide comprehensive gut microbiota profiling in psoriasis, resolving previous contradictions and generating new hypotheses for further investigation. These insights may significantly impact psoriasis management and related conditions.}, } @article {pmid38441466, year = {2024}, author = {Ding, Y and Er, S and Tan, A and Gounot, J-S and Saw, W-Y and Tan, LWL and Teo, YY and Nagarajan, N and Seedorf, H}, title = {Comparison of tet(X4)-containing contigs assembled from metagenomic sequencing data with plasmid sequences of isolates from a cohort of healthy subjects.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0396923}, doi = {10.1128/spectrum.03969-23}, pmid = {38441466}, issn = {2165-0497}, abstract = {Recently discovered tet(X) gene variants have provided new insights into microbial antibiotic resistance mechanisms and their potential consequences for public health. This study focused on detection, analysis, and characterization of Tet(X4)-positive Enterobacterales from the gut microbiota of a healthy cohort of individuals in Singapore using cultivation-dependent and cultivation-independent approaches. Twelve Tet(X4)-positive Enterobacterales strains that were previously obtained from the cohort were fully genome-sequenced and comparatively analyzed. A metagenomic sequencing (MS) data set of the same samples was mined for contigs that harbored the tet(X4) resistance gene. The sequences of tet(X4)-containing contigs and plasmids sequences were compared. The presence of the resistance genes floR and estT (previously annotated as catD) was detected in the same cassette in 10 and 12 out of the 12 tet(X4)-carrying plasmids, respectively. MS detected tet(X4)-containing contigs in 2 out of the 109 subjects, while cultivation-dependent analysis previously reported a prevalence of 10.1%. The tet(X4)-containing sequences assembled from MS data are relatively short (~14 to 33 kb) but show high similarity to the respective plasmid sequences of the isolates. Our findings show that MS can complement efforts in the surveillance of antibiotic resistance genes for clinical samples, while it has a lower sensitivity than a cultivation-based method when the target organism has a low abundance. Further optimization is required if MS is to be utilized in antibiotic resistance surveillance.IMPORTANCEThe global rise in antibiotic resistance makes it necessary to develop and apply new approaches to detect and monitor the prevalence of antibiotic resistance genes in human populations. In this regard, of particular interest are resistances against last-resort antibiotics, such as tigecycline. In this study, we show that metagenomic sequencing can help to detect high abundance of the tigecycline resistance gene tet(X4) in fecal samples from a cohort of healthy human subjects. However, cultivation-based approaches currently remain the most reliable and cost-effective method for detection of antibiotic-resistant bacteria.}, } @article {pmid38441032, year = {2024}, author = {Mancabelli, L and Milani, C and De Biase, R and Bocchio, F and Fontana, F and Lugli, GA and Alessandri, G and Tarracchini, C and Viappiani, A and De Conto, F and Nouvenne, A and Ticinesi, A and Bussolati, O and Meschi, T and Cecchi, R and Turroni, F and Ventura, M}, title = {Taxonomic and metabolic development of the human gut microbiome across life stages: a worldwide metagenomic investigation.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0129423}, doi = {10.1128/msystems.01294-23}, pmid = {38441032}, issn = {2379-5077}, abstract = {UNLABELLED: The human gut microbiota is a dynamic community of microorganisms that undergo variable changes over the entire life span. To thoroughly investigate the possible fluctuations of the microbiota throughout human life, we performed a pooled analysis of healthy fecal samples across different age groups covering the entire human life span. Our study integrated data from 79 publicly available studies and new stool samples from an Italian cohort, i.e., the Parma Microbiota project, resulting in 6,653 samples processed through the shotgun metagenomic approach. This approach has allowed species-level taxonomic reconstruction of the gut microbiota and investigation of its metabolic potential across the human life span. From a taxonomic point of view, our findings confirmed and detailed at species-level accuracy that the microbial richness of the gut microbiota gradually increases in the first stage of life, becoming relatively stable during adolescence. Moreover, the analysis identified the potential core microbiota representative of distinct age groups, revealing age-related bacterial patterns and the continuous rearrangement of the microbiota in terms of relative abundances across the life span rather than the acquisition and loss of taxa. Furthermore, the shotgun approach provided insights into the functional contribution of the human gut microbiome. The metagenomic analysis revealed functional age-related differences, particularly in carbohydrate and fiber metabolism, suggesting a co-evolution of the microbiome assembly with diet. Additionally, we identified correlations between vitamin synthesis, such as thiamine and niacin, and early life, suggesting a potential role of the microbiome in human physiology, in particular in the functions of the host's nervous and immune systems.

IMPORTANCE: In this study, we provided comprehensive insights into the dynamic nature of the human gut microbiota across the human life span. In detail, we analyzed a large data set based on a shotgun metagenomic approach, combining public data sets and new samples from the Parma Microbiota project and obtaining a detailed overview of the possible relationship between gut microbiota development and aging. Our findings confirmed the main stages in microbial richness development and revealed specific core microbiota associated with different age stages. Moreover, the shotgun metagenomic approach allowed the disentangling of the functional changes in the microbiome across the human life span, particularly in diet-related metabolism, which is probably correlated to bacterial co-evolution with dietary habits. Notably, our study also uncovered positive correlations with vitamin synthesis in early life, suggesting a possible impact of the microbiota on human physiology.}, } @article {pmid38441030, year = {2024}, author = {Takebe, H and Tominaga, K and Isozaki, T and Watanabe, T and Yamamoto, K and Kamikawa, R and Yoshida, T}, title = {Taxonomic difference in marine bloom-forming phytoplanktonic species affects the dynamics of both bloom-responding prokaryotes and prokaryotic viruses.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0094923}, doi = {10.1128/msystems.00949-23}, pmid = {38441030}, issn = {2379-5077}, abstract = {The production of dissolved organic matter during phytoplankton blooms and consumption by heterotrophic prokaryotes promote marine carbon biogeochemical cycling. Although prokaryotic viruses presumably affect this process, their dynamics during blooms are not fully understood. Here, we investigated the effects of taxonomic difference in bloom-forming phytoplankton on prokaryotes and their viruses. We analyzed the dynamics of coastal prokaryotic communities and viruses under the addition of dissolved intracellular fractions from taxonomically distinct phytoplankton, the diatom Chaetoceros sp. (CIF) and the raphidophycean alga Heterosigma akashiwo (HIF), using microcosm experiments. Ribosomal RNA gene amplicon and viral metagenomic analyses revealed that particular prokaryotes and prokaryotic viruses specifically increased in either CIF or HIF, indicating that taxonomic difference in bloom-forming phytoplankton promotes distinct dynamics of not only the prokaryotic community but also prokaryotic viruses. Furthermore, combining our microcosm experiments with publicly available environmental data mining, we identified both known and novel possible host-virus pairs. In particular, the growth of prokaryotes associating with phytoplanktonic organic matter, such as Bacteroidetes (Polaribacter and NS9 marine group), Vibrio spp., and Rhodobacteriales (Nereida and Planktomarina), was accompanied by an increase in viruses predicted to infect Bacteroidetes, Vibrio, and Rhodobacteriales, respectively. Collectively, our findings suggest that changes in bloom-forming species can be followed by an increase in a specific group of prokaryotes and their viruses and that elucidating these tripartite relationships among specific phytoplankton, prokaryotes, and prokaryotic viruses improves our understanding of coastal biogeochemical cycling in blooms.IMPORTANCEThe primary production during marine phytoplankton bloom and the consumption of the produced organic matter by heterotrophic prokaryotes significantly contribute to coastal biogeochemical cycles. While the activities of those heterotrophic prokaryotes are presumably affected by viral infection, the dynamics of their viruses during blooms are not fully understood. In this study, we experimentally demonstrated that intracellular fractions of taxonomically distinct bloom-forming phytoplankton species, the diatom Chaetoceros sp. and the raphidophycean alga Heterosigma akashiwo, promoted the growth of taxonomically different prokaryotes and prokaryotic viruses. Based on their dynamics and predicted hosts of those viruses, we succeeded in detecting already-known and novel possible host-virus pairs associating with either phytoplankton species. Altogether, we propose that the succession of bloom-forming phytoplankton would change the composition of the abundant prokaryotes, resulting in an increase in their viruses. These changes in viral composition, depending on bloom-forming species, would alter the dynamics and metabolism of prokaryotes, affecting biogeochemical cycling in blooms.}, } @article {pmid38440408, year = {2024}, author = {Eisenhofer, R and Wright, S and Weyrich, L}, title = {Benchmarking a targeted 16S ribosomal RNA gene enrichment approach to reconstruct ancient microbial communities.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16770}, pmid = {38440408}, issn = {2167-8359}, abstract = {The taxonomic characterization of ancient microbiomes is a key step in the rapidly growing field of paleomicrobiology. While PCR amplification of the 16S ribosomal RNA (rRNA) gene is a widely used technique in modern microbiota studies, this method has systematic biases when applied to ancient microbial DNA. Shotgun metagenomic sequencing has proven to be the most effective method in reconstructing taxonomic profiles of ancient dental calculus samples. Nevertheless, shotgun sequencing approaches come with inherent limitations that could be addressed through hybridization enrichment capture. When employed together, shotgun sequencing and hybridization capture have the potential to enhance the characterization of ancient microbial communities. Here, we develop, test, and apply a hybridization enrichment capture technique to selectively target 16S rRNA gene fragments from the libraries of ancient dental calculus samples generated with shotgun techniques. We simulated data sets generated from hybridization enrichment capture, indicating that taxonomic identification of fragmented and damaged 16S rRNA gene sequences was feasible. Applying this enrichment approach to 15 previously published ancient calculus samples, we observed a 334-fold increase of ancient 16S rRNA gene fragments in the enriched samples when compared to unenriched libraries. Our results suggest that 16S hybridization capture is less prone to the effects of background contamination than 16S rRNA amplification, yielding a higher percentage of on-target recovery. While our enrichment technique detected low abundant and rare taxa within a given sample, these assignments may not achieve the same level of specificity as those achieved by unenriched methods.}, } @article {pmid38440147, year = {2024}, author = {Xu, C and Jiang, H and Feng, LJ and Jiang, MZ and Wang, YL and Liu, SJ}, title = {Christensenella minuta interacts with multiple gut bacteria.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1301073}, pmid = {38440147}, issn = {1664-302X}, abstract = {INTRODUCTION: Gut microbes form complex networks that significantly influence host health and disease treatment. Interventions with the probiotic bacteria on the gut microbiota have been demonstrated to improve host well-being. As a representative of next-generation probiotics, Christensenella minuta (C. minuta) plays a critical role in regulating energy balance and metabolic homeostasis in human bodies, showing potential in treating metabolic disorders and reducing inflammation. However, interactions of C. minuta with the members of the networked gut microbiota have rarely been explored.

METHODS: In this study, we investigated the impact of C. minuta on fecal microbiota via metagenomic sequencing, focusing on retrieving bacterial strains and coculture assays of C. minuta with associated microbial partners.

RESULTS: Our results showed that C. minuta intervention significantly reduced the diversity of fecal microorganisms, but specifically enhanced some groups of bacteria, such as Lactobacillaceae. C. minuta selectively enriched bacterial pathways that compensated for its metabolic defects on vitamin B1, B12, serine, and glutamate synthesis. Meanwhile, C. minuta cross-feeds Faecalibacterium prausnitzii and other bacteria via the production of arginine, branched-chain amino acids, fumaric acids and short-chain fatty acids (SCFAs), such as acetic. Both metagenomic data analysis and culture experiments revealed that C. minuta negatively correlated with Klebsiella pneumoniae and 14 other bacterial taxa, while positively correlated with F. prausnitzii. Our results advance our comprehension of C. minuta's in modulating the gut microbial network.

CONCLUSIONS: C. minuta disrupts the composition of the fecal microbiota. This disturbance is manifested through cross-feeding, nutritional competition, and supplementation of its own metabolic deficiencies, resulting in the specific enrichment or inhibition of the growth of certain bacteria. This study will shed light on the application of C. minuta as a probiotic for effective interventions on gut microbiomes and improvement of host health.}, } @article {pmid38440141, year = {2024}, author = {Lumian, J and Sumner, DY and Grettenberger, CL and Jungblut, AD and Irber, L and Pierce-Ward, NT and Brown, CT}, title = {Biogeographic distribution of five Antarctic cyanobacteria using large-scale k-mer searching with sourmash branchwater.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1328083}, pmid = {38440141}, issn = {1664-302X}, abstract = {Cyanobacteria form diverse communities and are important primary producers in Antarctic freshwater environments, but their geographic distribution patterns in Antarctica and globally are still unresolved. There are however few genomes of cultured cyanobacteria from Antarctica available and therefore metagenome-assembled genomes (MAGs) from Antarctic cyanobacteria microbial mats provide an opportunity to explore distribution of uncultured taxa. These MAGs also allow comparison with metagenomes of cyanobacteria enriched communities from a range of habitats, geographic locations, and climates. However, most MAGs do not contain 16S rRNA gene sequences, making a 16S rRNA gene-based biogeography comparison difficult. An alternative technique is to use large-scale k-mer searching to find genomes of interest in public metagenomes. This paper presents the results of k-mer based searches for 5 Antarctic cyanobacteria MAGs from Lake Fryxell and Lake Vanda, assigned the names Phormidium pseudopriestleyi FRX01, Microcoleus sp. MP8IB2.171, Leptolyngbya sp. BulkMat.35, Pseudanabaenaceae cyanobacterium MP8IB2.15, and Leptolyngbyaceae cyanobacterium MP9P1.79 in 498,942 unassembled metagenomes from the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA). The Microcoleus sp. MP8IB2.171 MAG was found in a wide variety of environments, the P. pseudopriestleyi MAG was found in environments with challenging conditions, the Leptolyngbyaceae cyanobacterium MP9P1.79 MAG was only found in Antarctica, and the Leptolyngbya sp. BulkMat.35 and Pseudanabaenaceae cyanobacterium MP8IB2.15 MAGs were found in Antarctic and other cold environments. The findings based on metagenome matches and global comparisons suggest that these Antarctic cyanobacteria have distinct distribution patterns ranging from locally restricted to global distribution across the cold biosphere and other climatic zones.}, } @article {pmid38439877, year = {2024}, author = {Hua, Y and Lv, Z and Zhou, Y and Xiang, H and Sun, M and Kang, YJ}, title = {Metatranscriptomics revealed the molecular characterization of circulating enterovirus strains causing aseptic meningitis in children in Wuxi, China.}, journal = {Heliyon}, volume = {10}, number = {5}, pages = {e26847}, pmid = {38439877}, issn = {2405-8440}, abstract = {Enteroviruses are major etiological agents of aseptic meningitis globally, however information on circulating enterovirus types associated with this disease in Wuxi, China is limited. In this study, cerebrospinal fluid samples were collected from 20 pediatric aseptic meningitis cases in a Wuxi hospital in 2020 and subjected to metagenomic analysis to detect pathogens. Enterovirus B was detected in 9 cases, including 7 echovirus 18 (E18) and 2 echovirus 11 (E11) strains. The E18 strains exhibited 87.5-98.2% nucleotide identity and phylogenetically clustered with other China E18 strains, while the E11 strains showed 97.59% identity and clustered within the D5 subgroup along with other China E11 strains. One E18 strain was identified as a novel recombinants with a distinct recombination breakpoint within 3D gene. These findings expand knowledge on enteroviruses associated with pediatric aseptic meningitis in Wuxi, and highlight the circulation of genetically diverse E18 and E11 strains, including novel E18 recombinants. Characterization of enterovirus diversity by metagenomic analysis is important for molecular diagnosis and epidemiological tracking of aseptic meningitis cases. Continued surveillance of circulating enterovirus strains in Wuxi that may cause future outbreaks is warranted.}, } @article {pmid38439783, year = {2023}, author = {Hadermann, A and Jada, SR and Sebit, WJ and Deng, T and Bol, YY and Siewe Fodjo, JN and De Coninck, L and Matthijnssens, J and Mertens, I and Polman, K and Colebunders, R}, title = {Onchocerciasis-associated epilepsy: an explorative case-control study with viral metagenomic analyses on Onchocerca volvulus.}, journal = {F1000Research}, volume = {12}, number = {}, pages = {1262}, pmid = {38439783}, issn = {2046-1402}, abstract = {Background: A high prevalence of onchocerciasis-associated epilepsy (OAE) has been observed in onchocerciasis-endemic areas with high ongoing Onchocerca volvulus transmission. However, the pathogenesis of OAE remains to be elucidated. We hypothesise that the O. volvulus virome could be involved in inducing epilepsy. With this study, we aim to describe the O. volvulus virome and identify potential neurotropic viruses linked to OAE. Methods: In Maridi County, an onchocerciasis endemic area in South Sudan with a high prevalence of OAE, we will conduct an exploratory case-control study enrolling 40 persons aged 12 years and above with palpable onchocerciasis nodules. Cases will be participants with OAE (n=20), who will be age- and village-matched with controls without epilepsy (n=20). For each study participant, two skin snips at the iliac crest will be obtained to collect O. volvulus microfilariae, and one nodulectomy will be performed to obtain adult worms. A viral metagenomic study will be conducted on microfilariae and adult worms, and the O. volvulus virome of persons with and without OAE will be compared. The number, size, and localisation of onchocerciasis nodules in persons with and without OAE will be described. Moreover, the pre- and post-nodulectomy frequency of seizures in persons with OAE will be compared. Ethics and dissemination: The protocol has been approved by the Ethics Committee of the University of Antwerp and the Ministry of Health of South Sudan. Findings will be disseminated nationally and internationally via meetings and peer-reviewed publications. Registration: https://clinicaltrials.gov/ registration NCT05868551 (https://clinicaltrials.gov/study/NCT05868551) Protocol version: 1.1, dated 09/05/2023.}, } @article {pmid38439546, year = {2024}, author = {Madhav, A and Bousfield, R and Pereira-Dias, J and Cormie, C and Forrest, S and Keane, J and Kermack, L and Higginson, E and Dougan, G and Spiers, H and Massey, D and Sharkey, L and Rutter, C and Woodward, J and Russell, N and Amin, I and Butler, A and Atkinson, K and Dymond, T and Bartholdson Scott, J and Baker, S and Gkrania-Klotsas, E}, title = {A metagenomic prospective cohort study on gut microbiome composition and clinical infection in small bowel transplantation.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2323232}, doi = {10.1080/19490976.2024.2323232}, pmid = {38439546}, issn = {1949-0984}, abstract = {Two-thirds of small-bowel transplantation (SBT) recipients develop bacteremia, with the majority of infections occurring within 3 months post-transplant. Sepsis-related mortality occurs in 31% of patients and is commonly caused by bacteria of gut origin, which are thought to translocate across the implanted organ. Serial post-transplant surveillance endoscopies provide an opportunity to study whether the composition of the ileal and colonic microbiota can predict the emergence as well as the pathogen of subsequent clinical infections in the SBT patient population. Five participants serially underwent aspiration of ileal and colonic bowel effluents at transplantation and during follow-up endoscopy either until death or for up to 3 months post-SBT. We performed whole-metagenome sequencing (WMS) of 40 bowel effluent samples and compared the results with clinical infection episodes. Microbiome composition was concordant between participants and timepoint-matched ileal and colonic samples. Four out of five (4/5) participants had clinically significant infections thought to be of gut origin. Bacterial translocation from the gut was observed in 3/5 patients with bacterial infectious etiologies. In all three cases, the pathogens had demonstrably colonized the gut between 1-10 days prior to invasive clinical infection. Recipients with better outcomes received donor grafts with higher alpha diversity. There was an increase in the number of antimicrobial resistance genes associated with longer hospital stay for all participants. This metagenomic study provides preliminary evidence to support the pathogen translocation hypothesis of gut-origin sepsis in the SBT cohort. Ileal and colonic microbiome compositions were concordant; therefore, fecal metagenomic analysis could be a useful surveillance tool for impeding infection with specific gut-residing pathogens.}, } @article {pmid38438967, year = {2024}, author = {Yuan, H and Ma, X and Xu, J and Han, P and Rao, G and Chen, G and Zhang, K and Yang, R and Han, C and Jiang, M}, title = {Application of metagenomic next-generation sequencing in the clinical diagnosis of infectious diseases after allo-HSCT: a single-center analysis.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {279}, pmid = {38438967}, issn = {1471-2334}, abstract = {BACKGROUND: We investigated the value of metagenomic next-generation sequencing (mNGS) in diagnosing infectious diseases in patients receiving allogeneic hematopoietic stem cell transplantation (allo-HSCT).

METHODS: Fifty-four patients who had fever following allo-HSCT from October 2019 to February 2022 were enrolled. Conventional microbiological tests (CMTs) and mNGS, along with imaging and clinical manifestations, were used to diagnose infection following allo-HSCT. The clinical diagnostic value of mNGS was evaluated.

RESULTS: A total of 61 mNGS tests were performed, resulting in the diagnosis of 46 cases of infectious diseases. Among these cases, there were 22 cases of viral infection, 13 cases of fungal infection, and 11 cases of bacterial infection. Moreover, 27 cases (58.7%) were classified as bloodstream infections, 15 (32.6%) as respiratory infections, 2 (4.3%) as digestive system infections, and 2 (4.3%) as central nervous system infections. Additionally, there were 8 cases with non-infectious diseases (8/54, 14.81%), including 2 cases of interstitial pneumonia, 2 cases of bronchiolitis obliterans, 2 cases of engraftment syndrome, and 2 cases of acute graft-versus-host disease. The positive detection rates of mNGS and CMT were 88.9% and 33.3%, respectively, with significant differences (P < 0.001). The sensitivity of mNGS was 97.82%, the specificity was 25%, the positive predictive value was 93.75%, and the negative predictive value was 50%. Following treatment, 51 patients showed improvement, and 3 cases succumbed to multidrug-resistant bacterial infections.

CONCLUSIONS: mNGS plays an important role in the early clinical diagnosis of infectious diseases after allo-HSCT, which is not affected by immunosuppression status, empiric antibiotic therapy, and multi-microbial mixed infection.}, } @article {pmid38438919, year = {2024}, author = {Sun, D and Bian, G and Zhang, K and Liu, N and Yin, Y and Hou, Y and Xie, F and Zhu, W and Mao, S and Liu, J}, title = {Early-life ruminal microbiome-derived indole-3-carboxaldehyde and prostaglandin D2 are effective promoters of rumen development.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {64}, pmid = {38438919}, issn = {1474-760X}, support = {2021YFF1000703//National Key Research and Development Program of China/ ; 2021YFA1301300//National Key Research and Development Program of China/ ; 32172752//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The function of diverse ruminal microbes is tightly linked to rumen development and host physiology. The system of ruminal microbes is an excellent model to clarify the fundamental ecological relationships among complex nutrient-microbiome-host interactions. Here, neonatal lambs are introduced to different dietary regimes to investigate the influences of early-life crosstalk between nutrients and microbiome on rumen development.

RESULTS: We find starchy corn-soybean starter-fed lambs exhibit the thickest ruminal epithelia and fiber-rich alfalfa hay-fed lambs have the thickest rumen muscle. Metabolome and metagenome data reveal that indole-3-carboxaldehyde (3-IAld) and prostaglandin D2 (PGD2) are the top characteristic ruminal metabolites associated with ruminal epithelial and muscular development, which depend on the enhanced ruminal microbial synthesis potential of 3-IAld and PGD2. Moreover, microbial culture experiment first demonstrates that Bifidobacterium pseudolongum is able to convert tryptophan into 3-IAld and Candida albicans is a key producer for PGD2. Transcriptome sequencing of the ruminal epithelia and smooth muscle shows that ruminal epithelial and muscular development is accompanied by Wnt and Ca[2+] signaling pathway activation. Primary cell cultures further confirm that 3-IAld promotes ruminal epithelial cell proliferation depending on AhR-wnt/β-catenin signaling pathway and PGD2 accelerates ruminal smooth muscle cell proliferation via Ca[2+] signaling pathway. Furthermore, we find that 3-IAld and PGD2 infusion promote ruminal epithelial and musculature development in lambs.

CONCLUSIONS: This study demonstrates that early-life ruminal microbiome-derived 3-IAld and PGD2 are effective promoters of rumen development, which enhances our understanding of nutrient-microbiome-host interactions in early life.}, } @article {pmid38438026, year = {2024}, author = {Li, J and Chen, C and Ji, L and Wen, S and Peng, J and Yang, L and He, G}, title = {Urbanization-driven forest soil greenhouse gas emissions: Insights from the role of soil bacteria in carbon and nitrogen cycling using a metagenomic approach.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {171364}, doi = {10.1016/j.scitotenv.2024.171364}, pmid = {38438026}, issn = {1879-1026}, abstract = {Increasing population densities and urban sprawl have induced greenhouse gas (GHG) emissions from the soil, and the soil microbiota of urban forests play a critical role in the production and consumption of GHGs, supporting green development. However, the function and potential mechanism of soil bacteria in GHG emissions from forests during urbanization processes need to be better understood. Here, we measured the soil fluxes of carbon dioxide (CO2), methane (CH4), and nitrous oxide (N2O) in Cinnamomum camphora forest soils along an urbanization gradient. 16S amplicon and metagenomic sequencing approaches were employed to examine the structure and potential functions of the soil bacterial community involved in carbon (C) and nitrogen (N) cycling. In this study, the CH4 and CO2 emissions from urban forest soils (sites U and G) were significantly greater than those from suburban soils (sites S and M). The N2O emissions in the urban center (site U) were 24.0 % (G), 13.8 % (S), and 13.5 % (M) greater than those at the other three sites. These results were related to the increasing bacterial alpha diversity, interactions, and C and N cycling gene abundances (especially those involved in denitrification) in urban forest soils. Additionally, in our study areas, the soil pH and metal contents (K, Ca, Mg) affected key bacterial populations (such as Methylomirabilota, Acidobacteriota, and Proteobacteria) and indicators (napA, nosZ, nrfA, nifH) involved in reducing N2O emissions. The soil heavy metal contents (Fe, Cr, Pb) were the main contributors to CH4 emissions, possibly by affecting methanogens (Desulfobacterota) and methanotrophic bacteria (Proteobacteria, Actinobacteriota, and Patescibacteria). Our study provides new insights into the benefits of conservation-minded urban planning and close-to-nature urban forest management and construction, which are conducive to mitigating GHG emissions and supporting urban sustainable development by mediating the core bacterial population.}, } @article {pmid38438866, year = {2024}, author = {Wang, XN and Hong, J and Xu, YG and Zhang, P and Li, YY and Dou, HL and Li, HP}, title = {Epstein-Barr virus-positive iris diffuse large B-cell lymphoma detected by metagenomic next-generation sequencing.}, journal = {BMC ophthalmology}, volume = {24}, number = {1}, pages = {99}, pmid = {38438866}, issn = {1471-2415}, support = {PKU2023LCXQ013//Clinical Medicine Plus X - Young Scholars Project,Peking University, the Fundamental Research Funds for the Central Universities/ ; PKU2023LCXQ013//Clinical Medicine Plus X - Young Scholars Project,Peking University, the Fundamental Research Funds for the Central Universities/ ; PKU2023LCXQ013//Clinical Medicine Plus X - Young Scholars Project,Peking University, the Fundamental Research Funds for the Central Universities/ ; 81970768//National Natural Science Foundation: The process and mechanism of corneal endothelitis caused by cytomegalovirus infection/ ; 81970768//National Natural Science Foundation: The process and mechanism of corneal endothelitis caused by cytomegalovirus infection/ ; 81970768//National Natural Science Foundation: The process and mechanism of corneal endothelitis caused by cytomegalovirus infection/ ; 81970768//National Natural Science Foundation: The process and mechanism of corneal endothelitis caused by cytomegalovirus infection/ ; }, abstract = {PURPOSE: Epstein-Barr virus (EBV)-positive diffuse large B-cell lymphoma (DLBCL) is a relatively rare subtype of DLBCL. Herein, we report a case of a patient with EBV-positive iris DLBCL after undergoing penetrating keratoplasty and discuss its possible pathogenesis.

METHODS: A 72-year-old male patient presented to our hospital with progressive blurring of vision in the left eye for the past 4 months. Small white nodular lesions were observed on the iris and retinal surface of the left eye, with a white cloud-like opacity in the vitreous cavity.

RESULTS: The patient was eventually diagnosed with EBV-positive iris DLBCL after undergoing pathological and metagenomic tests. After injecting methotrexate in the left vitreous cavity and administering systemic and local antiviral treatments, the ocular lesions disappeared.

CONCLUSION: EBV infection, drug immunosuppression, and aging-related immune deterioration may play significant roles in the pathogenesis of EBV-positive iris DLBCL.

SYNOPSIS: Epstein-Barr virus (EBV)-positive diffuse large B-cell lymphoma (DLBCL) is a new subtype of DLBCL, which rarely occurs. Herein, we report a case of a patient with EBV-positive iris DLBCL after undergoing penetrating keratoplasty and discuss its possible pathogenesis.}, } @article {pmid38438834, year = {2024}, author = {Wentao, L and Shuxia, X and Guoxing, Z and Qiaoping, C and Peiran, C and Angela, W and Meirong, L and Songchao, Y and Peiying, F}, title = {Diagnosis of multiple tuberculous muscle abscesses in a patient with systemic lupus erythematosus by metagenomic next-generation sequencing- a case report and literature review.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {284}, pmid = {38438834}, issn = {1471-2334}, support = {No. 2020A1515011183//Natural Science Foundation of Guangdong Province of China/ ; }, abstract = {BACKGROUND: Early diagnosis of muscular tuberculosis (TB) without coexistent active skeletal involvement is often challenging because the disease is very rare and its clinical manifestation is nonspecific and misleading. To raise the awareness and emphasize early diagnosis of muscular TB, we present a case of multiple tuberculous muscle abscesses in a systemic lupus erythematosus (SLE) female, but without pulmonary tuberculosis (PTB), in order to increase awareness of and stress the need of early detection of muscular TB.

CASE PRESENTATION: A 44-year-old woman with a 6-year history of SLE who had been treated with methylprednisolone for a long time complained of erythema on her trunk and extremities for five months, along with edema and myalgia for two months, and fever for one month. The patient was first misdiagnosed as SLE overlap dermatomyositis. However, an ultrasound-guided drainage of muscle abscesses revealed positive acid-fast staining combined with positive deoxyribonucleic acid fragment of Mycobacterium tuberculosis using metagenomic next-generation sequencing (mNGS). The patient was cured and released following standard anti-tuberculosis medication, local puncture drainage, and an intravitreal injection of streptomycin. Literature search found only 19 cases of tuberculous muscle abscesses occurring in the extremities reported from 1999 to 2023.

CONCLUSIONS: Extrapulmonary TB with predominantly muscle involvement is rare and with no specific clinical presentation. Muscular tuberculosis may be disdiagnosed for dermatomyositis due to the high muscle enzyme levels, delaying diagnosis and treatment. mNGS technology is helpful in the early and rapid diagnosis of muscular TB. On the basis of traditional anti-tuberculosis treatment, an ultrasound-guided percutaneous puncture drainage and intracavitary injection of streptomycin for the treatment of tuberculous muscle abscess is easy to operate, safe and effective, which is worthy of clinical popularization and application.}, } @article {pmid38438704, year = {2024}, author = {Launes, C and Camacho, J and Pons-Espinal, M and López-Labrador, FX and Esteva, C and Cabrerizo, M and Fernández-García, MD and Fogeda, M and Masa-Calles, J and López-Perea, N and Echevarría, JE and Muñoz-Almagro, C and Tarragó, D}, title = {Hybrid capture shotgun sequencing detected unexpected viruses in the cerebrospinal fluid of children with acute meningitis and encephalitis.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {}, number = {}, pages = {}, pmid = {38438704}, issn = {1435-4373}, support = {CIBERESP21PI05//CIBER Epidemiology and Public Health, Instituto de Salud Carlos III (ES)/ ; }, abstract = {PURPOSE: Investigation of undiagnosed cases of infectious neurological diseases, especially in the paediatric population, remains a challenge. This study aimed to enhance understanding of viruses in CSF from children with clinically diagnosed meningitis and/or encephalitis (M/ME) of unknown aetiology using shotgun sequencing enhanced by hybrid capture (HCSS).

METHODS: A single-centre prospective study was conducted at Sant Joan de Déu University Hospital, Barcelona, involving 40 M/ME episodes of unknown aetiology, recruited from May 2021 to July 2022. All participants had previously tested negative with the FilmArray Meningitis/Encephalitis Panel. HCSS was used to detect viral nucleic acid in the patients' CSF. Sequencing was performed on Illumina NovaSeq platform. Raw sequence data were analysed using CZ ID metagenomics and PikaVirus bioinformatics pipelines.

RESULTS: Forty episodes of M/ME of unknown aetiology in 39 children were analysed by HCSS. A significant viral detection in 30 CSF samples was obtained, including six parechovirus A, three enterovirus ACD, four polyomavirus 5, three HHV-7, two BKV, one HSV-1, one VZV, two CMV, one EBV, one influenza A virus, one rhinovirus, and 13 HERV-K113 detections. Of these, one sample with BKV, three with HHV-7, one with EBV, and all HERV-K113 were confirmed by specific PCR. The requirement for Intensive Care Unit admission was associated with HCSS detections.

CONCLUSION: This study highlights HCSS as a powerful tool for the investigation of undiagnosed cases of M/ME. Data generated must be carefully analysed and reasonable precautions must be taken before establishing association of clinical features with unexpected or novel virus findings.}, } @article {pmid38438326, year = {2024}, author = {Pinto, GR and Carvalho Filho, PC and Carvalho, RDO and Conceição, RR and Fortuna, V and Gomes-Filho, IS and Trindade, SC and Sarmento, VA}, title = {Subgingival biofilm microbiome in individuals with asthma and periodontitis: Metagenomic analysis.}, journal = {Oral diseases}, volume = {}, number = {}, pages = {}, doi = {10.1111/odi.14913}, pmid = {38438326}, issn = {1601-0825}, support = {SUS0054/2018//PPSUS (Programa Pesquisa para o SUS) / FAPESB/ ; }, abstract = {OBJECTIVE: This observational study aimed to explore the metagenomics of subgingival biofilms in individuals with varying degrees of asthma, from severe to none, to elucidate the association between the subgingival microbiome and asthma.

MATERIALS AND METHODS: Subgingival biofilm samples were collected from thirty participants at the Asthma Control Program Outpatient Clinic in Bahia (ProAR). These samples were categorized into six groups based on the severity of asthma and the presence or absence of periodontitis. We employed next-generation sequencing (Illumina MiSeq), targeting the 16S rRNA gene, to characterize the microbial communities present. Our analysis included descriptive statistics and sequencing data, evaluated using multivariate statistical methods such as the Shannon index, principal coordinate analysis, and the Bray-Curtis dissimilarity.

RESULTS: Our findings indicate a higher prevalence of periodontally detrimental bacterial genera in individuals with severe asthma and periodontitis. Additionally, individuals with asthma, but without periodontitis, exhibited a tendency toward dysbiosis, particularly in cases of severe asthma.

CONCLUSION: This research provides new insights into the composition of the subgingival microbiome in individuals with varying severities of asthma and periodontitis. The genera identified in this study underscore the need for further investigations to build upon these findings.}, } @article {pmid38437464, year = {2024}, author = {Shen, D and Lv, X and Zhang, H and Fei, C and Feng, J and Zhou, J and Cao, L and Ying, Y and Li, N and Ma, X}, title = {Association between Clinical Characteristics and Microbiota in Bronchiectasis Patients Based on Metagenomic Next-Generation Sequencing Technology.}, journal = {Polish journal of microbiology}, volume = {73}, number = {1}, pages = {59-68}, doi = {10.33073/pjm-2024-007}, pmid = {38437464}, issn = {2544-4646}, abstract = {This study aimed to investigate the disparities between metagenomic next-generation sequencing (mNGS) and conventional culture results in patients with bronchiectasis. Additionally, we sought to investigate the correlation between the clinical characteristics of patients and their microbiome profiles. The overarching goal was to enhance the effective management and treatment of bronchiectasis patients, providing a theoretical foundation for healthcare professionals. A retrospective survey was conducted on 67 bronchiectasis patients admitted to The First Hospital of Jiaxing from October 2019 to March 2023. Clinical baseline information, inflammatory indicators, and pathogen detection reports, including mNGS, conventional blood culture, bronchoalveolar lavage fluid (BALF) culture, and sputum culture results, were collected. By comparing the results of mNGS and conventional culture, the differences in pathogen detection rate and pathogen types were explored, and the diagnostic performance of mNGS compared to conventional culture was evaluated. Based on the various pathogens detected by mNGS, the association between clinical characteristics of bronchiectasis patients and mNGS microbiota results was analyzed. The number and types of pathogens detected by mNGS were significantly larger than those detected by conventional culture. The diagnostic efficacy of mNGS was significantly superior to conventional culture for all types of pathogens, particularly in viral detection (p < 0.01). Regarding pathogen detection rate, the bacteria with the highest detection rate were Pseudomonas aeruginosa (17/58) and Haemophilus influenzae (11/58); the fungus with the highest detection rate was Aspergillus fumigatus (10/21), and the virus with the highest detection rate was human herpes virus 4 (4/11). Differences were observed between the positive and negative groups for P. aeruginosa in terms of common scoring systems for bronchiectasis and whether the main symptom of bronchiectasis manifested as thick sputum (p < 0.05). Significant distinctions were also noted between the positive and negative groups for A. fumigatus regarding Reiff score, neutrophil percentage, bronchiectasis etiology, and alterations in treatment plans following mNGS results reporting (p < 0.05). Notably, 70% of patients with positive A. fumigatus infection opted to change their treatment plans. The correlation study between clinical characteristics of bronchiectasis patients and mNGS microbiological results revealed that bacteria, such as P. aeruginosa, and fungi, such as A. fumigatus, were associated with specific clinical features of patients. This underscored the significance of mNGS in guiding personalized treatment approaches. mNGS could identify multiple pathogens in different types of bronchiectasis samples and was a rapid and effective diagnostic tool for pathogen identification. Its use was recommended for diagnosing the causes of infections in bronchiectasis patients.}, } @article {pmid38436309, year = {2024}, author = {Wang, CY and Xu, HM and Liu, G and Liu, J and Yu, H and Chen, BQ and Zheng, G and Shu, M and DU, LJ and Xu, ZW and Huang, LS and Li, HB and Wang, D and Bai, ST and Shan, QW and Zhu, CH and Tian, JM and Hao, JH and Lin, AW and Lin, DJ and Wu, JZ and Zhang, XH and Cao, Q and Tao, ZB and Chen, Y and Zhu, GL and Xue, P and Tang, ZZ and Su, XW and Qu, ZH and Zhao, SY and Pang, L and Deng, HL and Shu, SN and Chen, YH}, title = {[A multi-center epidemiological study on pneumococcal meningitis in children from 2019 to 2020].}, journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics}, volume = {26}, number = {2}, pages = {131-138}, pmid = {38436309}, issn = {1008-8830}, abstract = {OBJECTIVES: To investigate the clinical characteristics and prognosis of pneumococcal meningitis (PM), and drug sensitivity of Streptococcus pneumoniae (SP) isolates in Chinese children.

METHODS: A retrospective analysis was conducted on clinical information, laboratory data, and microbiological data of 160 hospitalized children under 15 years old with PM from January 2019 to December 2020 in 33 tertiary hospitals across the country.

RESULTS: Among the 160 children with PM, there were 103 males and 57 females. The age ranged from 15 days to 15 years, with 109 cases (68.1%) aged 3 months to under 3 years. SP strains were isolated from 95 cases (59.4%) in cerebrospinal fluid cultures and from 57 cases (35.6%) in blood cultures. The positive rates of SP detection by cerebrospinal fluid metagenomic next-generation sequencing and cerebrospinal fluid SP antigen testing were 40% (35/87) and 27% (21/78), respectively. Fifty-five cases (34.4%) had one or more risk factors for purulent meningitis, 113 cases (70.6%) had one or more extra-cranial infectious foci, and 18 cases (11.3%) had underlying diseases. The most common clinical symptoms were fever (147 cases, 91.9%), followed by lethargy (98 cases, 61.3%) and vomiting (61 cases, 38.1%). Sixty-nine cases (43.1%) experienced intracranial complications during hospitalization, with subdural effusion and/or empyema being the most common complication [43 cases (26.9%)], followed by hydrocephalus in 24 cases (15.0%), brain abscess in 23 cases (14.4%), and cerebral hemorrhage in 8 cases (5.0%). Subdural effusion and/or empyema and hydrocephalus mainly occurred in children under 1 year old, with rates of 91% (39/43) and 83% (20/24), respectively. SP strains exhibited complete sensitivity to vancomycin (100%, 75/75), linezolid (100%, 56/56), and meropenem (100%, 6/6). High sensitivity rates were also observed for levofloxacin (81%, 22/27), moxifloxacin (82%, 14/17), rifampicin (96%, 25/26), and chloramphenicol (91%, 21/23). However, low sensitivity rates were found for penicillin (16%, 11/68) and clindamycin (6%, 1/17), and SP strains were completely resistant to erythromycin (100%, 31/31). The rates of discharge with cure and improvement were 22.5% (36/160) and 66.2% (106/160), respectively, while 18 cases (11.3%) had adverse outcomes.

CONCLUSIONS: Pediatric PM is more common in children aged 3 months to under 3 years. Intracranial complications are more frequently observed in children under 1 year old. Fever is the most common clinical manifestation of PM, and subdural effusion/emphysema and hydrocephalus are the most frequent complications. Non-culture detection methods for cerebrospinal fluid can improve pathogen detection rates. Adverse outcomes can be noted in more than 10% of PM cases. SP strains are high sensitivity to vancomycin, linezolid, meropenem, levofloxacin, moxifloxacin, rifampicin, and chloramphenicol.}, } @article {pmid38436258, year = {2024}, author = {Stancheva, R and Sethuraman, A and Khadivar, H and Archambeau, J and Caughran, E and Chang, A and Hunter, B and Ihenyen, C and Onwukwe, M and Palacios, D and La Prairie, C and Read, N and Tsang, J and Vega, B and Velasquez, C and Zhang, X and Becket, E and Read, B}, title = {Characterizing the microbial metagenome of calcareous stromatolite formations in the San Felipe Creek in the Anza Borrego Desert.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0088123}, doi = {10.1128/mra.00881-23}, pmid = {38436258}, issn = {2576-098X}, abstract = {We describe the metagenome composition, community functional annotation, and prokaryote diversity in calcareous stromatolites from a dry stream bed of the San Felipe Creek in the Anza Borrego Desert. Analyses show a community capable of nitrogen fixation, assimilatory nitrate reduction, biofilm formation, quorum sensing, and potential thick-walled akinete formation for desiccation resistance.}, } @article {pmid38435684, year = {2024}, author = {Tenea, GN and Reyes, P}, title = {Bacterial community changes in strawberry fruits (Fragaria × ananassa variety "Monterey") from farm field to retail market stands, an indicator of postharvest contamination.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1348316}, pmid = {38435684}, issn = {1664-302X}, abstract = {BACKGROUND: Strawberry (Fragaria × ananassa) fruits are vulnerable to bacterial contamination; some species are pathogenic and can affect human health. Comprehending the bacterial composition and diversity at different ripe stages is a key determinant of the fruit health, productivity, and quality.

METHODOLOGY: An amplicon metagenomic approach on the 16S rRNA region was used to identify the bacterial diversity in exocarp of fruits collected from a farm field at two ripe stages: breaking (white, phase two) and ripe (red, phase four) and purchased from different retail market stands at ripe (red, phase four, ready-to-eat) stage. Besides, the fruit quality was assessed.

RESULTS: Strawberries carries a high microorganisms diversity, with Pseudomonaceae, Yearsiniaceae, and Hafniaceae being the most abundant families across the samples. Among the groups, Pseudomonaceae and Clostridiaceae were the most abundant families at breaking (phase two) and ripe (phase four), whereas Yearsiniaceae, Hafniaceae, Aeromonadaceae, and Streptococcaceae were the most abundant families in the market group. Although samples from group four-field and market were at the same ripe stage, the bacterial species composition was divergent. Serratia spp. were prevalent (above 60%) in samples collected from the market group, and Pseudomonas (above 70%) species were mostly found in the samples collected from the field settings regardless of the phase. Besides, Escherichia coli and Salmonella enterica were detected in the ready-to-eat samples from both the field and the market, while Enterococcus gallinarum was detected in the samples that originated from the market. Interestingly, Shewanella putrefaciens and Shewanella profunda, two human opportunistic pathogens, were detected in the fruits from the market only. According to alpha and beta diversity analyses, strawberry fruits displayed significant differences (P < 0.05) in bacterial communities within the ripe group, with the samples from the market showing the most bacterial diversity. Although we do not directly correlate the quality attributes with bacterial diversity, the results indicated a clear separation between groups according with their ripe stage and origin.

CONCLUSION: This study provides a comprehensive framework of the bacterial diversity throughout the transition from unripe to ripe strawberries which may aid in the development of preventative measures to manage the postharvest contamination.}, } @article {pmid38435359, year = {2023}, author = {Sun, Y and Tang, H and Du, S and Chen, Y and Ou, Z and Zhang, M and Chen, Z and Tang, Z and Zhang, D and Chen, T and Xu, Y and Li, J and Norback, D and Hashim, JH and Hashim, Z and Shao, J and Fu, X and Zhao, Z}, title = {Indoor metabolites and chemicals outperform microbiome in classifying childhood asthma and allergic rhinitis.}, journal = {Eco-Environment & Health (Online)}, volume = {2}, number = {4}, pages = {208-218}, pmid = {38435359}, issn = {2772-9850}, abstract = {Indoor microorganisms impact asthma and allergic rhinitis (AR), but the associated microbial taxa often vary extensively due to climate and geographical variations. To provide more consistent environmental assessments, new perspectives on microbial exposure for asthma and AR are needed. Home dust from 97 cases (32 asthma alone, 37 AR alone, 28 comorbidity) and 52 age- and gender-matched controls in Shanghai, China, were analyzed using high-throughput shotgun metagenomic sequencing and liquid chromatography-mass spectrometry. Homes of healthy children were enriched with environmental microbes, including Paracoccus, Pseudomonas, and Psychrobacter, and metabolites like keto acids, indoles, pyridines, and flavonoids (astragalin, hesperidin) (False Discovery Rate < 0.05). A neural network co-occurrence probability analysis revealed that environmental microorganisms were involved in producing these keto acids, indoles, and pyridines. Conversely, homes of diseased children were enriched with mycotoxins and synthetic chemicals, including herbicides, insecticides, and food/cosmetic additives. Using a random forest model, characteristic metabolites and microorganisms in Shanghai homes were used to classify high and low prevalence of asthma/AR in an independent dataset in Malaysian schools (N = 1290). Indoor metabolites achieved an average accuracy of 74.9% and 77.1% in differentiating schools with high and low prevalence of asthma and AR, respectively, whereas indoor microorganisms only achieved 51.0% and 59.5%, respectively. These results suggest that indoor metabolites and chemicals rather than indoor microbiome are potentially superior environmental indicators for childhood asthma and AR. This study extends the traditional risk assessment focusing on allergens or air pollutants in childhood asthma and AR, thereby revealing potential novel intervention strategies for these diseases.}, } @article {pmid38435306, year = {2024}, author = {Zhang, H and Liu, Z and Guan, Y and Li, D and Liu, H and Ruan, L}, title = {Case report: Metagenomics next-generation sequencing in the diagnosis of septic shock due to Fusobacterium necrophorum in a 6-year-old child.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1236630}, doi = {10.3389/fcimb.2024.1236630}, pmid = {38435306}, issn = {2235-2988}, abstract = {Fusobacterium necrophorum (F. necrophorum) infection is rare in pediatrics. In addition, the detection time of F. necrophorum by blood culture is long, and the positive rate is low. Infection with F. necrophorum bacilli usually follows rapid disease progression, resulting in high mortality. In previous reports of F. necrophorum-related cases, the most dangerous moment of the disease occurred after the appearance of Lemierre's syndrome. We report an atypical case of a 6-year-old female patient who developed septic shock within 24 h of admission due to F. necrophorum infection in the absence of Lemierre's syndrome. F. necrophorum was identified in a blood sample by metagenomics next-generation sequencing (mNGS) but not by standard blood culture. The patient was finally cured and discharged after receiving timely and effective targeted anti-infection treatment. In the present case study, it was observed that the heightened virulence and invasiveness of F. necrophorum contribute significantly to its role as a primary pathogen in pediatric septic shock. This can precipitate hemodynamic instability and multiple organ failure, even in the absence of Lemierre's syndrome. The use of mNGS can deeply and rapidly identify infectious pathogens, guide the use of targeted antibiotics, and greatly improve the survival rate of patients.}, } @article {pmid38434434, year = {2024}, author = {Xiao, Y and Zhang, S and Li, H and Teng, K and Wu, S and Liu, Y and Yu, F and He, Z and Li, L and Li, L and Meng, D and Yin, H and Wang, Y}, title = {Metagenomic insights into the response of soil microbial communities to pathogenic Ralstonia solanacearum.}, journal = {Frontiers in plant science}, volume = {15}, number = {}, pages = {1325141}, doi = {10.3389/fpls.2024.1325141}, pmid = {38434434}, issn = {1664-462X}, abstract = {Understanding the response of soil microbial communities to pathogenic Ralstonia solanacearum is crucial for preventing bacterial wilt outbreaks. In this study, we investigated the soil physicochemical and microbial community to assess their impact on the pathogenic R.solanacearum through metagenomics. Our results revealed that certain archaeal taxa were the main contributors influencing the health of plants. Additionally, the presence of the pathogen showed a strong negative correlation with soil phosphorus levels, while soil phosphorus was significantly correlated with bacterial and archaeal communities. We found that the network of microbial interactions in healthy plant rhizosphere soils was more complex compared to diseased soils. The diseased soil network had more linkages, particularly related to the pathogen occurrence. Within the network, the family Comamonadaceae, specifically Ramlibacter_tataouinensis, was enriched in healthy samples and showed a significantly negative correlation with the pathogen. In terms of archaea, Halorubrum, Halorussus_halophilus (family: Halobacteriaceae), and Natronomonas_pharaonis (family: Haloarculaceae) were enriched in healthy plant rhizosphere soils and showed negative correlations with R.solanacearum. These findings suggested that the presence of these archaea may potentially reduce the occurrence of bacterial wilt disease. On the other hand, Halostagnicola_larseniia and Haloterrigena_sp._BND6 (family: Natrialbaceae) had higher relative abundance in diseased plants and exhibited significantly positive correlations with R.solanacearum, indicating their potential contribution to the pathogen's occurrence. Moreover, we explored the possibility of functional gene sharing among the correlating bacterial pairs within the Molecular Ecological Network. Our analysis revealed 468 entries of horizontal gene transfer (HGT) events, emphasizing the significance of HGT in shaping the adaptive traits of plant-associated bacteria, particularly in relation to host colonization and pathogenicity. Overall, this work revealed key factors, patterns and response mechanisms underlying the rhizosphere soil microbial populations. The findings offer valuable guidance for effectively controlling soil-borne bacterial diseases and developing sustainable agriculture practices.}, } @article {pmid38434374, year = {2024}, author = {Li, Z and Li, W and Li, Y and Ma, F and Li, G}, title = {A case report of Balamuthia mandrillaris encephalitis.}, journal = {Heliyon}, volume = {10}, number = {5}, pages = {e26905}, doi = {10.1016/j.heliyon.2024.e26905}, pmid = {38434374}, issn = {2405-8440}, abstract = {Balamuthia amoebic encephalitis (BAE) is a rare and severe parasitic infection of the central nervous system. Its delayed diagnosis and treatment are often due to the lack of specific clinical manifestations and its poor prognosis. Reported mortality rates reach around 95%. The Balamuthia mandrillaris is also known as the "brain-eating amoeba." Recently, the use of metagenomic next-generation sequencing (mNGS) in clinical settings has led to an increase in BAE diagnoses. A case report detailing the use of mNGS to diagnose granulomatous encephalitis caused by the Baramsi amoeba has improved clinicians' understanding of this disease and helped reduce misdiagnoses and missed diagnoses.}, } @article {pmid38434258, year = {2024}, author = {Yang, S and Cheng, Y and Wang, X and Yue, S and Wang, X and Tang, L and Li, H and Zhang, J and Xiong, Q and Tan, S}, title = {Chinese herbal decoction, Yi-Qi-Jian-Pi formula exerts anti-hepatic fibrosis effects in mouse models of CCl4-induced liver fibrosis.}, journal = {Heliyon}, volume = {10}, number = {5}, pages = {e26129}, doi = {10.1016/j.heliyon.2024.e26129}, pmid = {38434258}, issn = {2405-8440}, abstract = {BACKGROUND: Yi-Qi-Jian-Pi Formula (YQJPF) is a herbal medicine that is used to treat patients with liver failure. However, scientific evidence supporting the treatment of hepatic fibrosis with YQJPF has not been forthcoming. The present study aimed to determine the mechanisms underlying the anti-fibrotic effects of YQJPF in mouse models of hepatic fibrosis.

METHODS: Mice were randomly assigned to control, hepatic fibrosis model, silymarin (positive treated), and low-, medium- and high-dose YQJPF (7.5, 15, and 30 g/kg, respectively) groups. Liver function, inflammatory cytokines, and oxygen stress were analyzed using ELISA kits. Sections were histopathologically stained with hematoxylin-eosin, Masson trichrome, and Sirius red. Macrophage polarization was measured by flow cytometry and immunofluorescence. Potential targets of YQJPF against hepatic fibrosis were analyzed by network pharmacology of Chinese herbal compound and the effects of YQJPF on the transforming growth factor-beta (TGF-β)/Suppressor of Mothers against Decapentaplegic family member 3 (Smad3) signaling pathway were assessed using qRT-PCR and immunohistochemical staining. Finally, metagenomics and LC-MS/MS were used to detect the intestinal flora and metabolites of the mice, and an in-depth correlation analysis was performed by spearman correlation analysis. The data were compared by one-way ANOVA and least significant differences (LSDs) or ANOVA-Dunnett's T3 method used when no homogeneity was detected.

RESULTS: We induced hepatic fibrosis using CCl4 to establish mouse models and found that YQJPF dose-dependently increased body weight, improved liver function, and reversed hepatic fibrosis. Elevated levels of the pro-inflammatory factors IL-1β, IL-6, and TNF-α in the model mice were substantially decreased by YQJPF, particularly at the highest dose. Levels of serum malondialdehyde and superoxide dismutase (SOD) activity were elevated and reduced, respectively. The malondialdehyde concentration decreased and SOD activity increased in the high-dose group. M1 polarized macrophages (CD86) in the mouse models were significantly decreased and M2 polarization was mildly decreased without significance. However, high-dose YQJPF increased the numbers of M2 macrophages and inhibited TGF-β/Smad3 signaling. Metagenomic and non-targeted metabolomics detection results showed that YQJPF could regulate intestinal homeostasis, and Spearman correlation analysis showed that the abundance of Calditerrivibrio_nitroreducens was significantly negatively correlated with 18β-glycyrrhetinic acid. It is suggested that Calditerrivibrio_nitroreducens may reduce the anti-fibrosis effect of licorice and other Chinese herbs by digesting 18β-glycyrrhetinic acid.

CONCLUSIONS: YQJPF can reverse liver fibrosis by inhibiting inflammation, suppressing oxidative stress, regulating the immunological response initiated by macrophages, inhibiting TGF-β/Smad3 signaling and regulating intestinal flora homeostasis. Therefore, YQJPF may be included in clinical regimens to treat hepatic fibrosis.}, } @article {pmid38434082, year = {2024}, author = {Shen, Y and Cui, SS and Teng, XB and Han, MF}, title = {Acute pneumonia due to Tropheryma whipplei diagnosed by metagenomic next-generation sequencing and pathology: A case report.}, journal = {Heliyon}, volume = {10}, number = {4}, pages = {e26747}, doi = {10.1016/j.heliyon.2024.e26747}, pmid = {38434082}, issn = {2405-8440}, abstract = {Tropheryma whipplei (TW) is a rod-shaped, gram-positive bacterium that, when chronically infects humans, can lead to multi-system pathologies, including joint pain, abdominal pain with diarrhea and weight loss, myocarditis, pericarditis, and neurologic inflammation. Moreover, acute infections can lead to bronchopulmonary infections, bacteraemia, and acute diarrhea. However, fewer cases of acute pneumonia due to TW have been reported, and this diagnosis is not well founded. Herein, we report a case of acute pneumonia caused by a TW infection. The patient, a middle-aged man, underwent bronchoscopic alveolar lavage, and the metagenomic next-generation sequencing of the lavage fluid suggested TW infection. A lung puncture biopsy tissue specimen was also positive based on periodic acid-Schiff staining. After confirming the diagnosis, the patient was administered ceftriaxone for anti-infection treatment, improving clinical symptoms and lung imaging results. Therefore, in cases where conventional anti-infective treatment is ineffective for patients with acute pneumonia, we should consider the possibility of TW infection, conduct prompt pathogenetic examination, and provide timely treatment after diagnosis to improve overall patient prognosis.}, } @article {pmid38433960, year = {2024}, author = {Banchi, E and Corre, E and Del Negro, P and Celussi, M and Malfatti, F}, title = {Genome-resolved metagenomics of Venice Lagoon surface sediment bacteria reveals high biosynthetic potential and metabolic plasticity as successful strategies in an impacted environment.}, journal = {Marine life science & technology}, volume = {6}, number = {1}, pages = {126-142}, doi = {10.1007/s42995-023-00192-z}, pmid = {38433960}, issn = {2662-1746}, abstract = {UNLABELLED: Bacteria living in sediments play essential roles in marine ecosystems and deeper insights into the ecology and biogeochemistry of these largely unexplored organisms can be obtained from 'omics' approaches. Here, we characterized metagenome-assembled-genomes (MAGs) from the surface sediment microbes of the Venice Lagoon (northern Adriatic Sea) in distinct sub-basins exposed to various natural and anthropogenic pressures. MAGs were explored for biodiversity, major marine metabolic processes, anthropogenic activity-related functions, adaptations at the microscale, and biosynthetic gene clusters. Starting from 126 MAGs, a non-redundant dataset of 58 was compiled, the majority of which (35) belonged to (Alpha- and Gamma-) Proteobacteria. Within the broad microbial metabolic repertoire (including C, N, and S metabolisms) the potential to live without oxygen emerged as one of the most important features. Mixotrophy was also found as a successful lifestyle. Cluster analysis showed that different MAGs encoded the same metabolic patterns (e.g., C fixation, sulfate oxidation) thus suggesting metabolic redundancy. Antibiotic and toxic compounds resistance genes were coupled, a condition that could promote the spreading of these genetic traits. MAGs showed a high biosynthetic potential related to antimicrobial and biotechnological classes and to organism defense and interactions as well as adaptive strategies for micronutrient uptake and cellular detoxification. Our results highlighted that bacteria living in an impacted environment, such as the surface sediments of the Venice Lagoon, may benefit from metabolic plasticity as well as from the synthesis of a wide array of secondary metabolites, promoting ecosystem resilience and stability toward environmental pressures.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-023-00192-z.}, } @article {pmid38433907, year = {2024}, author = {Rampelli, S and Gallois, S and D'Amico, F and Turroni, S and Fabbrini, M and Scicchitano, D and Candela, M and Henry, A}, title = {The gut microbiome of Baka forager-horticulturalists from Cameroon is optimized for wild plant foods.}, journal = {iScience}, volume = {27}, number = {3}, pages = {109211}, doi = {10.1016/j.isci.2024.109211}, pmid = {38433907}, issn = {2589-0042}, abstract = {The human gut microbiome is losing biodiversity, due to the "microbiome modernization process" that occurs with urbanization. To keep track of it, here we applied shotgun metagenomics to the gut microbiome of the Baka, a group of forager-horticulturalists from Cameroon, who combine hunting and gathering with growing a few crops and working for neighboring Bantu-speaking farmers. We analyzed the gut microbiome of individuals with different access to and use of wild plant and processed foods, to explore the variation of their gut microbiome along the cline from hunter-gatherer to agricultural subsistence patterns. We found that 26 species-level genome bins from our cohort were pivotal for the degradation of the wild plant food substrates. These microbes include Old Friend species and are encoded for genes that are no longer present in industrialized gut microbiome. Our results highlight the potential relevance of these genes to human biology and health, in relation to lifestyle.}, } @article {pmid38433784, year = {2024}, author = {Han, S and Yang, S and Wang, Y and Xu, Y}, title = {Case Report: Encephalitis with Initial Manifestation of Orientia Tsutsugamushi Infection Detected by Metagenomic Next-Generation Sequencing.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {749-760}, doi = {10.2147/IDR.S450693}, pmid = {38433784}, issn = {1178-6973}, abstract = {PURPOSE: Scrub typhus, caused by Orientia tsutsugamushi, is characterized by fever, eschars, lymphadenopathy, and rash. The absence of eschars in some cases makes it difficult to distinguish it from other diseases, complicating the diagnosis process. Atypical Scrub typhus is difficult to diagnose and often leads to delayed treatment. Therefore, early diagnosis and treatment through effective detection methods have high clinical value. Here, a case of scrub typhus with encephalitis symptoms is reported.

PATIENTS AND METHODS: A 64-year-old man and mNGS testing.

RESULTS: A 64-year-old man developed cough, headache, and fever, dismissing it as a respiratory tract infection. Initial treatment with cephalosporin antibiotics had minimal effect. Admission to the respiratory department showed inflammation in blood tests. Subsequent CT and further treatment provided no improvement. Multidisciplinary discussions and neurology department guidance were conducted to consider the suspected diagnosis of encephalitis in the patient. After improving the mNGS detection, the patient was diagnosed with "Orientia tsutsugamushi encephalitis". After treatment with doxycycline, the patient's symptoms were alleviated. He remained afebrile in follow-up and adhered well to medical advice.

CONCLUSION: Our case demonstrates that it is difficult to distinguish Orientia tsutsugamushi encephalitis from central nervous system infectious diseases such as meningitis and encephalitis using conventional diagnostic methods, which may affect the treatment plan for the disease. mNGS is a useful and valuable method for early diagnosis of scrub typhus.}, } @article {pmid38433268, year = {2024}, author = {Yue, H and Sun, X and Wang, T and Zhang, A and Han, D and Wei, G and Song, W and Shu, D}, title = {Host genotype-specific rhizosphere fungus enhances drought resistance in wheat.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {44}, pmid = {38433268}, issn = {2049-2618}, support = {2023-JC-QN-0218//Natural Science Foundation of Shannxi Province/ ; 2023-JC-QN-0218//Natural Science Foundation of Shannxi Province/ ; 2023-JC-QN-0218//Natural Science Foundation of Shannxi Province/ ; 32370137//National Natural Science Foundation of China/ ; U21A2029//National Natural Science Foundation of China/ ; 42077049//National Natural Science Foundation of China/ ; 2021YFD1900700//National Key Research & Development Program of China/ ; }, abstract = {BACKGROUND: The severity and frequency of drought are expected to increase substantially in the coming century and dramatically reduce crop yields. Manipulation of rhizosphere microbiomes is an emerging strategy for mitigating drought stress in agroecosystems. However, little is known about the mechanisms underlying how drought-resistant plant recruitment of specific rhizosphere fungi enhances drought adaptation of drought-sensitive wheats. Here, we investigated microbial community assembly features and functional profiles of rhizosphere microbiomes related to drought-resistant and drought-sensitive wheats by amplicon and shotgun metagenome sequencing techniques. We then established evident linkages between root morphology traits and putative keystone taxa based on microbial inoculation experiments. Furthermore, root RNA sequencing and RT-qPCR were employed to explore the mechanisms how rhizosphere microbes modify plant response traits to drought stresses.

RESULTS: Our results indicated that host plant signature, plant niche compartment, and planting site jointly contribute to the variation of soil microbiome assembly and functional adaptation, with a relatively greater effect of host plant signature observed for the rhizosphere fungi community. Importantly, drought-resistant wheat (Yunhan 618) possessed more diverse bacterial and fungal taxa than that of the drought-sensitive wheat (Chinese Spring), particularly for specific fungal species. In terms of microbial interkingdom association networks, the drought-resistant variety possessed more complex microbial networks. Metagenomics analyses further suggested that the enriched rhizosphere microbiomes belonging to the drought-resistant cultivar had a higher investment in energy metabolism, particularly in carbon cycling, that shaped their distinctive drought tolerance via the mediation of drought-induced feedback functional pathways. Furthermore, we observed that host plant signature drives the differentiation in the ecological role of the cultivable fungal species Mortierella alpine (M. alpina) and Epicoccum nigrum (E. nigrum). The successful colonization of M. alpina on the root surface enhanced the resistance of wheats in response to drought stresses via activation of drought-responsive genes (e.g., CIPK9 and PP2C30). Notably, we found that lateral roots and root hairs were significantly suppressed by co-colonization of a drought-enriched fungus (M. alpina) and a drought-depleted fungus (E. nigrum).

CONCLUSIONS: Collectively, our findings revealed host genotypes profoundly influence rhizosphere microbiome assembly and functional adaptation, as well as it provides evidence that drought-resistant plant recruitment of specific rhizosphere fungi enhances drought tolerance of drought-sensitive wheats. These findings significantly underpin our understanding of the complex feedbacks between plants and microbes during drought, and lay a foundation for steering "beneficial keystone biome" to develop more resilient and productive crops under climate change. Video Abstract.}, } @article {pmid38432054, year = {2024}, author = {Indio, V and Savini, F and Gardini, F and Barbieri, F and Prandini, L and Mekonnen, YT and Tomasello, F and Giacometti, F and Seguino, A and Serraino, A and De Cesare, A}, title = {Microbiological safety of dry-cured fish from the raw material to the end of processing.}, journal = {International journal of food microbiology}, volume = {415}, number = {}, pages = {110641}, doi = {10.1016/j.ijfoodmicro.2024.110641}, pmid = {38432054}, issn = {1879-3460}, abstract = {The commercialization of processed fish products is rising in restaurants and small to medium enterprises. However, there is a lack of data related to the microbiological safety of such products. In this study total aerobic colony count and Enterobacteriaceae, as proxy of process hygiene criteria, and detection of Listeria monocytogenes and concentration of histamine, as food safety criteria, were investigated in Salmo salar (salmon), Xiphias gladius (swordfish) and Thunnus albacares (yellowfin tuna), before, during, and at the end of a dry-curing process, performed in a dedicated cabinet, at controlled temperature, relative humidity and ventilation, up to 240 h. The microbiological parameters were investigated in the tested fish products by culture methods and shotgun metagenomic, while the presence of histamine, and other biogenic amines, was quantified by High Performance Liquid Chromatography. In the raw material, and up to the end of the dry curing process, the concentration of Enterobacteriaceae was always lower than 10 CFU/g, while total aerobic colony counts ranged between 3.9 and 5.4 Log CFU/g in salmon; 5.5 and 5.9 Log CFU/g in swordfish; 4.4 and 4.8 Log CFU/g in tuna. The pH values were significantly different between fish species, in the raw materials and during processing except for T4, occurring 70 h after the start of the process for salmon and after 114 h for swordfish and tuna. Water activity was different at specific sampling points and at the end of processing. Overall, 79 % of the sequences identified in the tested fish samples were assigned to y bacteria. The most abundant phyla were Pseudomonadota, Bacillota and Mycoplasmatota. The microbial populations identified by shotgun metagenomic in the tested fish species clustered well separated one from the other. Moreover, the microbial richness was significantly higher in salmon and tuna in comparison to swordfish. Listeria monocytogenes was not detected in the raw material by using the reference cultural method and very few reads (relative abundance <0.007) were detected in swordfish and tuna by shotgun metagenomic. Histamine producing bacteria, belonging to the genera Vibrio, Morganella, Photobacterium and Klebsiella, were identified primarily in swordfish. However, histamine and other biogenic amines were not detected in any sample. To the best of our knowledge this is the first paper reporting time point determinations of microbiological quality and safety parameters in salmon, swordfish and tuna, before, during and at the end of a dry-curing process. The data collected in this paper can help to predict the risk profile of ready to eat dry-cured fish products during storage before consumption.}, } @article {pmid38431663, year = {2024}, author = {Garmaeva, S and Sinha, T and Gulyaeva, A and Kuzub, N and Spreckels, JE and Andreu-Sánchez, S and Gacesa, R and Vich Vila, A and Brushett, S and Kruk, M and , and Dekens, J and Sikkema, J and Kuipers, F and Shkoporov, AN and Hill, C and Scherjon, S and Wijmenga, C and Fu, J and Kurilshikov, A and Zhernakova, A}, title = {Transmission and dynamics of mother-infant gut viruses during pregnancy and early life.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1945}, pmid = {38431663}, issn = {2041-1723}, abstract = {Early development of the gut ecosystem is crucial for lifelong health. While infant gut bacterial communities have been studied extensively, the infant gut virome remains under-explored. To study the development of the infant gut virome over time and the factors that shape it, we longitudinally assess the composition of gut viruses and their bacterial hosts in 30 women during and after pregnancy and in their 32 infants during their first year of life. Using shotgun metagenomic sequencing applied to dsDNA extracted from Virus-Like Particles (VLPs) and bacteria, we generate 205 VLP metaviromes and 322 total metagenomes. With this data, we show that while the maternal gut virome composition remains stable during late pregnancy and after birth, the infant gut virome is dynamic in the first year of life. Notably, infant gut viromes contain a higher abundance of active temperate phages compared to maternal gut viromes, which decreases over the first year of life. Moreover, we show that the feeding mode and place of delivery influence the gut virome composition of infants. Lastly, we provide evidence of co-transmission of viral and bacterial strains from mothers to infants, demonstrating that infants acquire some of their virome from their mother's gut.}, } @article {pmid38431030, year = {2024}, author = {Shahzad, M and Saeed, M and Amin, H and Binmadi, N and Ullah, Z and Bibi, S and Andrew, SC}, title = {The oral microbiome of newly diagnosed tuberculosis patients; a pilot study.}, journal = {Genomics}, volume = {}, number = {}, pages = {110816}, doi = {10.1016/j.ygeno.2024.110816}, pmid = {38431030}, issn = {1089-8646}, abstract = {BACKGROUND: Changes in oral microbiota composition (dysbiosis) has long been known to play a key role in the pathogenesis of oral and systemic diseases including respiratory diseases. However, till now, no study has assessed changes in oral microbiota following tuberculosis (TB) infection in humans.

AIMS: This is the first study of its kind that aimed to investigate oral microbial dysbiosis in newly diagnosed, treatment naïve, TB patients.

METHODS: Oral swab samples were collected from newly diagnosed TB patients (n = 20) and age, gender and ethnicity matched healthy controls (n = 10). DNA was extracted and microbiota analyzed by sequencing the hypervariable (V3-V4) region of the bacterial 16S rRNA gene using Illumina MiSeq platform. Bioinformatics and statistical analyses were performed using QIIME and R.

RESULTS: Bacterial richness, diversity and community composition were significantly different between TB patients and healthy controls. The two groups also exhibit differential abundance at phylum, class, genus and species levels. The LEfSe analysis revealed enrichment (LDA scores (log10) >2, P < 0.05) of Firmicutes (especially Streptococcus) and Actinobacteriota (especially Rothia) in TB patients relative to healthy controls. Gene function prediction analysis showed upregulation of metabolic pathways related to carbohydrates (butanoate, galactose) and fatty acids metabolism, antibiotics biosynthesis, proteosome and immune system signaling.

CONCLUSION: These observations suggest significant variations in diversity, relative abundance and functional potential of oral microbiota of TB patients compared to healthy controls thereby suggesting potential role of oral bacterial dysbiosis in TB pathogenesis. However, longitudinal studies using powerful metagenomic and transcriptomic approaches are crucial to identify and these findings.}, } @article {pmid38430578, year = {2024}, author = {Zhu, S and Zhao, W and Sun, S and Yang, X and Mao, H and Sheng, L and Chen, Z}, title = {Metagenomic analysis revealed N-metabolizing microbial response of Iris tectorum to Cr stress after colonization by arbuscular mycorrhizal fungi.}, journal = {Ecotoxicology and environmental safety}, volume = {273}, number = {}, pages = {116157}, doi = {10.1016/j.ecoenv.2024.116157}, pmid = {38430578}, issn = {1090-2414}, abstract = {Arbuscular mycorrhizal fungi (AMF) and plant growth-promoting bacteria enhance plant tolerance to abiotic stress and promote plant growth in contaminated soil. However, the interaction mechanism between rhizosphere microbial communities under chromium (Cr) stress remains unclear. This study conducted a greenhouse pot experiment and metagenomics analysis to reveal the comprehensive effects of the interaction between AMF (Rhizophagus intraradices) and nitrogen-N metabolizing plant growth promoters on the growth of Iris tectorum. The results showed that AMF significantly increased the biomass and nutrient levels of I. tectorum in contaminated soil and decreased the content of Cr in the soil. Metagenomics analysis revealed that the structure and composition of the rhizosphere microbial community involved in nitrogen metabolism changed significantly after inoculation with AMF under Cr stress. Functional genes related to soil nitrogen mineralization (gltB, gltD, gdhA, ureC, and glnA), nitrate reduction to ammonium (nirB, nrfA, and nasA), and soil nitrogen assimilation (NRT, nrtA, and nrtC) were up-regulated in the N-metabolizing microbial community. In contrast, the abundance of functional genes involved in denitrification (nirK and narI) was down-regulated. In addition, the inoculation of AMF regulates the synergies between the N-metabolic rhizosphere microbial communities and enhances the complexity and stability of the rhizosphere ecological network. This study provides a basis for improving plant tolerance to heavy metal stress by regulating the functional abundance of N-metabolizing plant growth-promoting bacteria through AMF inoculation. It helps to understand the potential mechanism of wetland plant remediation of Cr-contaminated soil.}, } @article {pmid38429614, year = {2024}, author = {Wang, C and Chang, J and Tian, L and Sun, Y and Wang, E and Yao, Z and Ye, L and Zhang, H and Pang, Y and Tian, C}, title = {A Synthetic Microbiome Based on Dominant Microbes in Wild Rice Rhizosphere to Promote Sulfur Utilization.}, journal = {Rice (New York, N.Y.)}, volume = {17}, number = {1}, pages = {18}, pmid = {38429614}, issn = {1939-8425}, support = {U22A20593//the National Natural Science Foundation of China/ ; U22A20593//the National Natural Science Foundation of China/ ; 41920104008//the National Natural Science Foundation of China/ ; U22A20593//the National Natural Science Foundation of China/ ; U22A20593//the National Natural Science Foundation of China/ ; U22A20593//the National Natural Science Foundation of China/ ; U22A20593//the National Natural Science Foundation of China/ ; 41920104008//the National Natural Science Foundation of China/ ; U22A20593//the National Natural Science Foundation of China/ ; U22A20593//the National Natural Science Foundation of China/ ; 2022000170//Science and Technology cooperation Project between Jilin Province and Chinese Academy of Sciences/ ; 2022000170//Science and Technology cooperation Project between Jilin Province and Chinese Academy of Sciences/ ; 2022000170//Science and Technology cooperation Project between Jilin Province and Chinese Academy of Sciences/ ; 2022000170//Science and Technology cooperation Project between Jilin Province and Chinese Academy of Sciences/ ; }, abstract = {Sulfur (S) is one of the main components of important biomolecules, which has been paid more attention in the anaerobic environment of rice cultivation. In this study, 12 accessions of rice materials, belonging to two Asian rice domestication systems and one African rice domestication system, were used by shotgun metagenomics sequencing to compare the structure and function involved in S cycle of rhizosphere microbiome between wild and cultivated rice. The sulfur cycle functional genes abundances were significantly different between wild and cultivated rice rhizosphere in the processes of sulfate reduction and other sulfur compounds conversion, implicating that wild rice had a stronger mutually-beneficial relationship with rhizosphere microbiome, enhancing sulfur utilization. To assess the effects of sulfate reduction synthetic microbiomes, Comamonadaceae and Rhodospirillaceae, two families containing the genes of two key steps in the dissimilatory sulfate reduction, aprA and dsrA respectively, were isolated from wild rice rhizosphere. Compared with the control group, the dissimilatory sulfate reduction in cultivated rice rhizosphere was significantly improved in the inoculated with different proportions groups. It confirmed that the synthetic microbiome can promote the S-cycling in rice, and suggested that may be feasible to construct the synthetic microbiome step by step based on functional genes to achieve the target functional pathway. In summary, this study reveals the response of rice rhizosphere microbial community structure and function to domestication, and provides a new idea for the construction of synthetic microbiome.}, } @article {pmid38429524, year = {2024}, author = {Gunjur, A and Shao, Y and Rozday, T and Klein, O and Mu, A and Haak, BW and Markman, B and Kee, D and Carlino, MS and Underhill, C and Frentzas, S and Michael, M and Gao, B and Palmer, J and Cebon, J and Behren, A and Adams, DJ and Lawley, TD}, title = {A gut microbial signature for combination immune checkpoint blockade across cancer types.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {38429524}, issn = {1546-170X}, support = {220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; 206194/Z/17/Z//Wellcome Trust (Wellcome)/ ; 220540/Z/20/A//Wellcome Trust (Wellcome)/ ; C9685/A25117//Cancer Research UK (CRUK)/ ; C20510/A21717//Cancer Research UK (CRUK)/ ; }, abstract = {Immune checkpoint blockade (ICB) targeting programmed cell death protein 1 (PD-1) and cytotoxic T lymphocyte protein 4 (CTLA-4) can induce remarkable, yet unpredictable, responses across a variety of cancers. Studies suggest that there is a relationship between a cancer patient's gut microbiota composition and clinical response to ICB; however, defining microbiome-based biomarkers that generalize across cohorts has been challenging. This may relate to previous efforts quantifying microbiota to species (or higher taxonomic rank) abundances, whereas microbial functions are often strain specific. Here, we performed deep shotgun metagenomic sequencing of baseline fecal samples from a unique, richly annotated phase 2 trial cohort of patients with diverse rare cancers treated with combination ICB (n = 106 discovery cohort). We demonstrate that strain-resolved microbial abundances improve machine learning predictions of ICB response and 12-month progression-free survival relative to models built using species-rank quantifications or comprehensive pretreatment clinical factors. Through a meta-analysis of gut metagenomes from a further six comparable studies (n = 364 validation cohort), we found cross-cancer (and cross-country) validity of strain-response signatures, but only when the training and test cohorts used concordant ICB regimens (anti-PD-1 monotherapy or combination anti-PD-1 plus anti-CTLA-4). This suggests that future development of gut microbiome diagnostics or therapeutics should be tailored according to ICB treatment regimen rather than according to cancer type.}, } @article {pmid38425025, year = {2024}, author = {Pereira-Marques, J and Ferreira, RM and Figueiredo, C}, title = {A metatranscriptomics strategy for efficient characterization of the microbiome in human tissues with low microbial biomass.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2323235}, doi = {10.1080/19490976.2024.2323235}, pmid = {38425025}, issn = {1949-0984}, mesh = {Humans ; Biomass ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; *Microbiota/genetics ; Bacteria/genetics ; }, abstract = {The high background of host RNA poses a major challenge to metatranscriptome analysis of human samples. Hence, metatranscriptomics has been mainly applied to microbe-rich samples, while its application in human tissues with low ratio of microbial to host cells has yet to be explored. Since there is no computational workflow specifically designed for the taxonomic and functional analysis of this type of samples, we propose an effective metatranscriptomics strategy to accurately characterize the microbiome in human tissues with a low ratio of microbial to host content. We experimentally generated synthetic samples with well-characterized bacterial and host cell compositions, and mimicking human samples with high and low microbial loads. These synthetic samples were used for optimizing and establishing the workflow in a controlled setting. Our results show that the integration of the taxonomic analysis of optimized Kraken 2/Bracken with the functional analysis of HUMAnN 3 in samples with low microbial content, enables the accurate identification of a large number of microbial species with a low false-positive rate, while improving the detection of microbial functions. The effectiveness of our metatranscriptomics workflow was demonstrated in synthetic samples, simulated datasets, and most importantly, human gastric tissue specimens, thus providing a proof of concept for its applicability on mucosal tissues of the gastrointestinal tract. The use of an accurate and reliable metatranscriptomics approach for human tissues with low microbial content will expand our understanding of the functional activity of the mucosal microbiome, uncovering critical interactions between the microbiome and the host in health and disease.}, } @article {pmid38424140, year = {2024}, author = {Rengefors, K and Annenkova, N and Wallenius, J and Svensson, M and Kremp, A and Ahrén, D}, title = {Population genomic analyses reveal that salinity and geographic isolation drive diversification in a free-living protist.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4986}, pmid = {38424140}, issn = {2045-2322}, support = {2012-3726 and 2017-03860//Vetenskapsrådet/ ; MMETSP project//Gordon & Betty Moore Foundation/ ; }, mesh = {*Salinity ; Metagenomics ; Ecosystem ; Lakes ; *Dinoflagellida/genetics ; Phylogeny ; Genetic Speciation ; }, abstract = {Protists make up the vast diversity of eukaryotic life and play a critical role in biogeochemical cycling and in food webs. Because of their small size, cryptic life cycles, and large population sizes, our understanding of speciation in these organisms is very limited. We performed population genomic analyses on 153 strains isolated from eight populations of the recently radiated dinoflagellate genus Apocalathium, to explore the drivers and mechanisms of speciation processes. Species of this genus inhabit both freshwater and saline habitats, lakes and seas, and are found in cold temperate environments across the world. RAD sequencing analyses revealed that the populations were overall highly differentiated, but morphological similarity was not congruent with genetic similarity. While geographic isolation was to some extent coupled to genetic distance, this pattern was not consistent. Instead, we found evidence that the environment, specifically salinity, is a major factor in driving ecological speciation in Apocalathium. While saline populations were unique in loci coupled to genes involved in osmoregulation, freshwater populations appear to lack these. Our study highlights that adaptation to freshwater through loss of osmoregulatory genes may be an important speciation mechanism in free-living aquatic protists.}, } @article {pmid38410449, year = {2024}, author = {Seitz, VA and McGivem, BB and Borton, MA and Chaparro, JM and Schipanski, ME and Prenni, JE and Wrighton, KC}, title = {Cover Crop Root Exudates Impact Soil Microbiome Functional Trajectories in Agricultural Soils.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {38410449}, support = {P30 CA046934/CA/NCI NIH HHS/United States ; }, abstract = {BACKGROUND: Cover cropping is an agricultural practice that uses secondary crops to support the growth of primary crops through various mechanisms including erosion control, weed suppression, nutrient management, and enhanced biodiversity. Cover crops may elicit some of these ecosystem services through chemical interactions with the soil microbiome via root exudation, or the release of plant metabolites from roots. Phytohormones are one metabolite type exuded by plants that activate the rhizosphere microbiome, yet managing this chemical interaction remains an untapped mechanism for optimizing plant-soil microbiome interactions. Currently, there is limited understanding on the diversity of cover crop phytohormone root exudation patterns and how these chemical messages selectively enrich specific microbial taxa and functionalities in agricultural soils.

RESULTS: Here, we link variability in cover crop root exudate composition to changes in soil microbiome functionality. Exudate chemical profiles from 4 cover crop species (Sorghum bicolor, Vicia villosa, Brassica napus, and Secale cereal) were used as the chemical inputs to decipher microbial responses. These distinct exudate profiles, along with a no exudate control, were amended to agricultural soil microcosms with microbial responses tracked over time using metabolomes and genome-resolved metatranscriptomes. Our findings illustrated microbial metabolic patterns were unique in response to cover crop exudate inputs over time, particularly by sorghum and cereal rye amended microcosms where we identify novel microbial members (at the genera and family level) who produced IAA and GA4 over time. We also identify broad changes in microbial nitrogen cycling in response chemical inputs.

CONCLUSIONS: We highlight that root exudate amendments alter microbial community function and phytohormone metabolisms, particularly in response to root exudates isolated from cereal rye and sorghum plants. Additionally, we constructed a soil microbial genomic catalog of microorganisms responding to commonly used cover crops, a public resource for agriculturally-relevant microbes. Many of our exudate-stimulated microorganisms are representatives from poorly characterized or novel taxa, highlighting the yet to be discovered metabolic reservoir harbored in agricultural soils. Our findings emphasize the tractability of high-resolution multiomics approaches to investigate processes relevant for agricultural soils, opening the possibility of targeting specific soil biogeochemical outcomes through biological precision agricultural practices that use cover crops and the microbiome as levers for enhanced crop production.}, } @article {pmid38428994, year = {2024}, author = {Yu, W and Luo, H and Yang, J and Zhang, S and Jiang, H and Zhao, X and Hui, X and Sun, D and Li, L and Wei, XQ and Lonardi, S and Pan, W}, title = {Comprehensive assessment of 11 de novo HiFi assemblers on complex eukaryotic genomes and metagenomes.}, journal = {Genome research}, volume = {}, number = {}, pages = {}, doi = {10.1101/gr.278232.123}, pmid = {38428994}, issn = {1549-5469}, abstract = {Pacific Biosciences (PacBio) HiFi sequencing technology generates long reads (>10 kbp) with very high accuracy (<0.01% sequencing error). Although several de novo assembly tools are available for HiFi reads, there are no comprehensive studies on the evaluation of these assemblers. We evaluated the performance of 11 de novo HiFi assemblers on (1) real data for three eukaryotic genomes; (2) 34 synthetic data sets with different ploidy, sequencing coverage levels, heterozygosity rates, and sequencing error rates; (3) one real metagenomic data set; and (4) five synthetic metagenomic data sets with different composition abundance and heterozygosity rates. The 11 assemblers were evaluated using quality assessment tool (QUAST) and benchmarking universal single-copy ortholog (BUSCO). We also used several additional criteria, namely, completion rate, single-copy completion rate, duplicated completion rate, average proportion of largest category, average distance difference, quality value, run-time, and memory utilization. Results show that hifiasm and hifiasm-meta should be the first choice for assembling eukaryotic genomes and metagenomes with HiFi data. We performed a comprehensive benchmarking study of commonly used assemblers on complex eukaryotic genomes and metagenomes. Our study will help the research community to choose the most appropriate assembler for their data and identify possible improvements in assembly algorithms.}, } @article {pmid38428600, year = {2024}, author = {Su, Y and Qian, J and Wang, J and Mi, X and Huang, Q and Zhang, Y and Jiang, Q and Wang, Q}, title = {Unraveling the mechanism of norfloxacin removal and fate of antibiotics resistance genes (ARGs) in the sulfur-mediated autotrophic denitrification via metagenomic and metatranscriptomic analyses.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {171328}, doi = {10.1016/j.scitotenv.2024.171328}, pmid = {38428600}, issn = {1879-1026}, abstract = {The co-contamination of antibiotics and nitrogen has attracted widespread concerns due to its potential harm to ecological safety and human health. Sulfur-driven autotrophic denitrification (SAD) with low sludge production rate was adopted to treat antibiotics laden-organic deficient wastewater. Herein, a lab-scale sequencing batch reactor (SBR) was established to explore the simultaneous removal of nitrate and antibiotics, i.e. Norfloxacin (NOR), as well as microbial response mechanism of SAD sludge system towards NOR exposure. About 80.78 % of NOR was removed by SAD sludge when the influent NOR level was 0.5 mg/L, in which biodegradation was dominant removal route. The nitrate removal efficiency decreased slightly from 98.37 ± 0.58 % to 96.58 ± 1.03 % in the presence of NOR. Thiobacillus and Sulfurimonas were the most abundant sulfur-oxidizing bacteria (SOB) in SAD system, but Thiobacillus was more sensitive to NOR. The up-regulated genes related to Xenobiotics biodegradation and metabolism and CYP450 indicated the occurrence of NOR biotransformation in SAD system. The resistance of SAD sludge to the exposure of NOR was mainly ascribed to antibiotic efflux. And the effect of antibiotic inactivation was enhanced after long-term fed with NOR. The NOR exposure resulted in the increased level of antibiotics resistance genes (ARGs) and mobile genetic elements (MGEs). Besides, the enhanced ARG-MGE co-existence patterns further reveals the higher horizontal mobility potential of ARGs under NOR exposure pressures. The most enriched sulfur oxidizing bacterium Thiobacillus was a potential host for most of ARGs. This study provides a new insight for the treatment of NOR-laden wastewater with low C/N ratio based on the sulfur-mediated biological process.}, } @article {pmid38428395, year = {2024}, author = {Fogarty, EC and Schechter, MS and Lolans, K and Sheahan, ML and Veseli, I and Moore, RM and Kiefl, E and Moody, T and Rice, PA and Yu, MK and Mimee, M and Chang, EB and Ruscheweyh, HJ and Sunagawa, S and Mclellan, SL and Willis, AD and Comstock, LE and Eren, AM}, title = {A cryptic plasmid is among the most numerous genetic elements in the human gut.}, journal = {Cell}, volume = {187}, number = {5}, pages = {1206-1222.e16}, doi = {10.1016/j.cell.2024.01.039}, pmid = {38428395}, issn = {1097-4172}, abstract = {Plasmids are extrachromosomal genetic elements that often encode fitness-enhancing features. However, many bacteria carry "cryptic" plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes and is 14 times as numerous as crAssphage, currently established as the most abundant extrachromosomal genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales, and although it does not appear to impact bacterial host fitness in vivo, it can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an alternative approach to track human colonic inflammatory states.}, } @article {pmid38427700, year = {2024}, author = {Schiaffino, F and Parker, CT and Garcia Bardales, PF and Huynh, S and Manzanares Villanueva, K and Mourkas, E and Pascoe, B and Peñataro Yori, P and Paredes Olortegui, M and Houpt, ER and Liu, J and Coope, KK and Kosek, MN}, title = {Novel rpsK / rpsD primer-probe assay improves detection of Campylobacter jejuni and Campylobacter coli in human stool.}, journal = {PLoS neglected tropical diseases}, volume = {18}, number = {3}, pages = {e0012018}, doi = {10.1371/journal.pntd.0012018}, pmid = {38427700}, issn = {1935-2735}, abstract = {Campylobacter causes bacterial enteritis, dysentery, and growth faltering in children in low- and middle-income countries (LMICs). Campylobacter spp. are fastidious organisms, and their detection often relies on culture independent diagnostic technologies, especially in LMICs. Campylobacter jejuni and Campylobacter coli are most often the infectious agents and in high income settings together account for 95% of Campylobacter infections. Several other Campylobacter species have been detected in LMIC children at an increased prevalence relative to high income settings. After doing extensive whole genome sequencing of isolates of C. jejuni and C. coli in Peru, we observed heterogeneity in the binding sites for the main species-specific PCR assay (cadF) and designed an alternative rpsKD-based qPCR assay to detect both C. jejuni and C. coli. The rpsKD-based qPCR assay identified 23% more C.jejuni/ C.coli samples than the cadF assay among 47 Campylobacter genus positive cadF negative samples verified to have C. jejuni and or C. coli with shotgun metagenomics. This assay can be expected to be useful in diagnostic studies of enteric infectious diseases and be useful in revising the attribution estimates of Campylobacter in LMICs.}, } @article {pmid38427308, year = {2024}, author = {Filipov, T and Teutsch, B and Szabó, A and Forintos, A and Ács, J and Váradi, A and Hegyi, P and Szarvas, T and Ács, N and Nyirády, P and Deák, PÁ}, title = {Investigating the role of ultrasound-based shear wave elastography in kidney transplanted patients: correlation between non-invasive fibrosis detection, kidney dysfunction and biopsy results-a systematic review and meta-analysis.}, journal = {Journal of nephrology}, volume = {}, number = {}, pages = {}, pmid = {38427308}, issn = {1724-6059}, abstract = {INTRODUCTION: Interstitial fibrosis and tubular atrophy are leading causes of renal allograft failure. Shear wave elastography could be a promising noninvasive method for providing information on the state of the kidney, with specific regard to fibrosis but currently available data in the literature are controversial. Our study aimed to analyze the correlation between shear wave elastography and various kidney dysfunction measures.

METHODS: This review was registered on PROSPERO (CRD42021283152). We systematically searched three major databases (MEDLINE, Embase, and CENTRAL) for articles concerning renal transplant recipients, shear wave elastography, fibrosis, and kidney dysfunction. Meta-analytical calculations for pooled Pearson and Spearman correlation coefficients (r) were interpreted with 95% confidence intervals (CIs). Heterogeneity was tested with Cochran's Q test. I[2] statistic and 95% CI were reported as a measurement of between-study heterogeneity. Study quality was assessed with the QUADAS2 tool.

RESULTS: In total, 16 studies were included in our meta-analysis. Results showed a moderate correlation between kidney stiffness and interstitial fibrosis and tubular atrophy, graded according to BANFF classification, on biopsy findings for pooled Pearson (r = 0.48; CI: 0.20, 0.69; I[2] = 84%) and Spearman correlations (r = 0.57; CI: 0.35, 0.72; I[2] = 74%). When compared to kidney dysfunction parameters, we found a moderate correlation between shear wave elastography and resistive index (r = 0.34 CI: 0.13, 0.51; I[2] = 67%) and between shear wave elastography and estimated Glomerular Filtration Rate (eGFR) (r = -0.65; CI: - 0.81, - 0.40; I[2] = 73%). All our outcomes had marked heterogeneity.

CONCLUSION: Our results showed a moderate correlation between kidney stiffness measured by shear wave elastography and biopsy results. While noninvasive assessment of kidney fibrosis after transplantation is an important clinical goal, there is insufficient evidence to support the use of elastography over the performance of a kidney biopsy.}, } @article {pmid38427084, year = {2024}, author = {Tamang, A and Kaur, A and Thakur, D and Thakur, A and Thakur, BK and Shivani, and Swarnkar, M and Pal, PK and Hallan, V and Pandey, SS}, title = {Unraveling endophytic diversity in dioecious Siraitia grosvenorii: implications for mogroside production.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {247}, pmid = {38427084}, issn = {1432-0614}, support = {MLP-0171//Council of Scientific and Industrial Research, India/ ; GAP-0269 (SRG/2020/001524)//Science and Engineering Research Board/ ; }, abstract = {Host and tissue-specificity of endophytes are important attributes that limit the endophyte application on multiple crops. Therefore, understanding the endophytic composition of the targeted crop is essential, especially for the dioecious plants where the male and female plants are different. Here, efforts were made to understand the endophytic bacterial composition of the dioecious Siraitia grosvenorii plant using 16S rRNA amplicon sequencing. The present study revealed the association of distinct endophytic bacterial communities with different parts of male and female plants. Roots of male and female plants had a higher bacterial diversity than other parts of plants, and the roots of male plants had more bacterial diversity than the roots of female plants. Endophytes belonging to the phylum Proteobacteria were abundant in all parts of male and female plants except male stems and fruit pulp, where the Firmicutes were most abundant. Class Gammaproteobacteria predominated in both male and female plants, with the genus Acinetobacter as the most dominant and part of the core microbiome of the plant (present in all parts of both, male and female plants). The presence of distinct taxa specific to male and female plants was also identified. Macrococcus, Facklamia, and Propionibacterium were the distinct genera found only in fruit pulp, the edible part of S. grosvenorii. Predictive functional analysis revealed the abundance of enzymes of secondary metabolite (especially mogroside) biosynthesis in the associated endophytic community with predominance in roots. The present study revealed bacterial endophytic communities of male and female S. grosvenorii plants that can be further explored for monk fruit cultivation, mogroside production, and early-stage identification of male and female plants. KEY POINTS: • Male and female Siraitia grosvenorii plants had distinct endophytic communities • The diversity of endophytic communities was specific to different parts of plants • S. grosvenorii-associated endophytes may be valuable for mogroside biosynthesis and monk fruit cultivation.}, } @article {pmid38426721, year = {2024}, author = {Antillon, SF and Bernhardt, TG and Chamakura, K and Young, R}, title = {Physiological characterization of single-gene lysis proteins.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0038423}, doi = {10.1128/jb.00384-23}, pmid = {38426721}, issn = {1098-5530}, abstract = {UNLABELLED: Single-strand RNA (ssRNA) and single-strand DNA phages elicit host lysis using a single gene, in each case designated as sgl. Of the 11 identified Sgls, three have been shown to be specific inhibitors of different steps in the pathway that supplies lipid II to the peptidoglycan (PG) biosynthesis machinery. These Sgls have been called "protein antibiotics" because the lytic event is a septal catastrophe indistinguishable from that caused by cell wall antibiotics. Here, we designate these as type I Sgls. In this formalism, the other eight Sgls are assigned to type II, the best-studied of which is protein L of the paradigm F-specific ssRNA phage MS2. Comparisons have suggested that type II Sgls have four sequence elements distinguished by hydrophobic and polar character. Environmental metatranscriptomics has revealed thousands of new ssRNA phage genomes, each of which presumably has an Sgl. Here, we describe methods to distinguish type I and type II Sgls. Using phase contrast microscopy, we show that both classes of Sgls cause the formation of blebs prior to lysis, but the location of the blebs differs significantly. In addition, we show that L and other type II Sgls do not inhibit the net synthesis of PG, as measured by radio-labeling of PG. Finally, we provide direct evidence that the Sgl from Pseudomonas phage PP7 is a type I Sgl, in support of a recent report based on a genetic selection. This shows that the putative four-element sequence structure suggested for L is not a reliable discriminator for the operational characterization of Sgls.

IMPORTANCE: The ssRNA phage world has recently undergone a metagenomic expansion upward of a thousandfold. Each genome likely carries at least one single-gene lysis (sgl) cistron encoding a protein that single-handedly induces host autolysis. Here, we initiate an approach to segregate the Sgls into operational types based on physiological analysis, as a first step toward the alluring goal of finding many new ways to induce bacterial death and the attendant expectations for new antibiotic development.}, } @article {pmid38426620, year = {2024}, author = {Zhang, L and Yuan, L and Wen, Y and Zhang, M and Huang, S and Wang, S and Zhao, Y and Hao, X and Li, L and Gao, Q and Wang, Y and Zhang, S and Huang, S and Liu, K and Yu, X and Li, D and Xu, J and Zhao, B and Zhang, L and Zhang, H and Zhou, W and Ai, C}, title = {Maize functional requirements drive the selection of rhizobacteria under long-term fertilization practices.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.19653}, pmid = {38426620}, issn = {1469-8137}, support = {2022YFD1900900//National Key Research and Development Program of China/ ; 32322076//National Natural Science Foundation of China/ ; 32272817//National Natural Science Foundation of China/ ; 05//Smart Fertilization Project/ ; BX20230425//Postdoctoral Innovation Talents Support Program/ ; CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; }, abstract = {Rhizosphere microbiomes are pivotal for crop fitness, but the principles underlying microbial assembly during root-soil interactions across soils with different nutrient statuses remain elusive. We examined the microbiomes in the rhizosphere and bulk soils of maize plants grown under six long-term (≥ 29 yr) fertilization experiments in three soil types across middle temperate to subtropical zones. The assembly of rhizosphere microbial communities was primarily driven by deterministic processes. Plant selection interacted with soil types and fertilization regimes to shape the structure and function of rhizosphere microbiomes. Predictive functional profiling showed that, to adapt to nutrient-deficient conditions, maize recruited more rhizobacteria involved in nutrient availability from bulk soil, although these functions were performed by different species. Metagenomic analyses confirmed that the number of significantly enriched Kyoto Encyclopedia of Genes and Genomes Orthology functional categories in the rhizosphere microbial community was significantly higher without fertilization than with fertilization. Notably, some key genes involved in carbon, nitrogen, and phosphorus cycling and purine metabolism were dominantly enriched in the rhizosphere soil without fertilizer input. In conclusion, our results show that maize selects microbes at the root-soil interface based on microbial functional traits beneficial to its own performance, rather than selecting particular species.}, } @article {pmid38426063, year = {2024}, author = {Argentini, C and Lugli, GA and Tarracchini, C and Fontana, F and Mancabelli, L and Viappiani, A and Anzalone, R and Angelini, L and Alessandri, G and Longhi, G and Bianchi, MG and Taurino, G and Bussolati, O and Milani, C and van Sinderen, D and Turroni, F and Ventura, M}, title = {Genomic and ecological approaches to identify the Bifidobacterium breve prototype of the healthy human gut microbiota.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1349391}, doi = {10.3389/fmicb.2024.1349391}, pmid = {38426063}, issn = {1664-302X}, abstract = {Members of the genus Bifidobacterium are among the first microorganisms colonizing the human gut. Among these species, strains of Bifidobacterium breve are known to be commonly transmitted from mother to her newborn, while this species has also been linked with activities supporting human wellbeing. In the current study, an in silico approach, guided by ecology- and phylogenome-based analyses, was employed to identify a representative strain of B. breve to be exploited as a novel health-promoting candidate. The selected strain, i.e., B. breve PRL2012, was found to well represent the genetic content and functional genomic features of the B. breve taxon. We evaluated the ability of PRL2012 to survive in the gastrointestinal tract and to interact with other human gut commensal microbes. When co-cultivated with various human gut commensals, B. breve PRL2012 revealed an enhancement of its metabolic activity coupled with the activation of cellular defense mechanisms to apparently improve its survivability in a simulated ecosystem resembling the human microbiome.}, } @article {pmid38426058, year = {2024}, author = {Cantin, LJ and Dunning Hotopp, JC and Foster, JM}, title = {Improved metagenome assemblies through selective enrichment of bacterial genomic DNA from eukaryotic host genomic DNA using ATAC-seq.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1352378}, doi = {10.3389/fmicb.2024.1352378}, pmid = {38426058}, issn = {1664-302X}, abstract = {Genomics can be used to study the complex relationships between hosts and their microbiota. Many bacteria cannot be cultured in the laboratory, making it difficult to obtain adequate amounts of bacterial DNA and to limit host DNA contamination for the construction of metagenome-assembled genomes (MAGs). For example, Wolbachia is a genus of exclusively obligate intracellular bacteria that live in a wide range of arthropods and some nematodes. While Wolbachia endosymbionts are frequently described as facultative reproductive parasites in arthropods, the bacteria are obligate mutualistic endosymbionts of filarial worms. Here, we achieve 50-fold enrichment of bacterial sequences using ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) with Brugia malayi nematodes, containing Wolbachia (wBm). ATAC-seq uses the Tn5 transposase to cut and attach Illumina sequencing adapters to accessible DNA lacking histones, typically thought to be open chromatin. Bacterial and mitochondrial DNA in the lysates are also cut preferentially since they lack histones, leading to the enrichment of these sequences. The benefits of this include minimal tissue input (<1 mg of tissue), a quick protocol (<4 h), low sequencing costs, less bias, correct assembly of lateral gene transfers and no prior sequence knowledge required. We assembled the wBm genome with as few as 1 million Illumina short paired-end reads with >97% coverage of the published genome, compared to only 12% coverage with the standard gDNA libraries. We found significant bacterial sequence enrichment that facilitated genome assembly in previously published ATAC-seq data sets from human cells infected with Mycobacterium tuberculosis and C. elegans contaminated with their food source, the OP50 strain of E. coli. These results demonstrate the feasibility and benefits of using ATAC-seq to easily obtain bacterial genomes to aid in symbiosis, infectious disease, and microbiome research.}, } @article {pmid38426055, year = {2024}, author = {Cai, Y and Luo, Y and Dai, N and Yang, Y and He, Y and Chen, H and Zhao, M and Fu, X and Chen, T and Xing, Z}, title = {Corrigendum: Functional metagenomic and metabolomics analysis of gut dysbiosis induced by hyperoxia.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1382290}, doi = {10.3389/fmicb.2024.1382290}, pmid = {38426055}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2023.1197970.].}, } @article {pmid38426054, year = {2024}, author = {Chen, D and Chew, D and Xiang, Q and Lam, T and Dai, Y and Liu, J and Wang, L and He, T and Strand, R and Zhang, X and Lim, L and Xu, J and Shi, Y and Dong, W}, title = {Interactions and effects of a stannous-containing sodium fluoride dentifrice on oral pathogens and the oral microbiome.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1327913}, doi = {10.3389/fmicb.2024.1327913}, pmid = {38426054}, issn = {1664-302X}, abstract = {Numerous studies have investigated the effects of stannous ions on specific microbes and their efficacy in reducing dental plaque. Nonetheless, our understanding of their impact on the oral microbiome is still a subject of ongoing exploration. Therefore, this study sought to evaluate the effects of a stannous-containing sodium fluoride dentifrice in comparison to a zinc-containing sodium fluoride dentifrice and a control group on intact, healthy oral biofilms. Utilizing the novel 2bRAD-M approach for species-resolved metagenomics, and FISH/CLSM with probes targeting periodontal and caries associated species alongside Sn[2+] and Zn[2+] ions, we collected and analyzed in situ biofilms from 15 generally healthy individuals with measurable dental plaque and treated the biofilms with dentifrices to elucidate variations in microbial distribution. Although significant shifts in the microbiome upon treatment were not observed, the use of a stannous-containing sodium fluoride dentifrice primarily led to an increase in health-associated commensal species and decrease in pathogenic species. Notably, FISH/CLSM analysis highlighted a marked reduction in representative species associated with periodontitis and caries following treatment with the use of a stannous-containing sodium fluoride dentifrice, as opposed to a zinc-containing sodium fluoride dentifrice and the control group. Additionally, Sn[2+] specific intracellular imaging reflected the colocalization of Sn[2+] ions with P. gingivalis but not with other species. In contrast, Zn[2+] ions exhibited non-specific binding, thus suggesting that Sn[2+] could exhibit selective binding toward pathogenic species. Altogether, our results demonstrate that stannous ions could help to maintain a healthy oral microbiome by preferentially targeting certain pathogenic bacteria to reverse dysbiosis and underscores the importance of the continual usage of such products as a preventive measure for oral diseases and the maintenance of health.}, } @article {pmid38425772, year = {2024}, author = {Xu, H and Wang, D and Cui, K and Wan, R and Chi, Q and Wu, T}, title = {18F-FDG PET/CT findings in fatal Balamuthia Mandrillaris encephalitis in brain stem: A case report.}, journal = {Radiology case reports}, volume = {19}, number = {5}, pages = {1851-1854}, doi = {10.1016/j.radcr.2024.02.021}, pmid = {38425772}, issn = {1930-0433}, abstract = {We presented a case of a 66-year-old female whose initial symptom was headache without obvious inducement. The patient's condition progressed rapidly to a semi-coma state after symptomatic treatment. The [18]F-FDG PET/CT scan revealed circular FDG hypermetabolism and central metabolic defect of the pons and left frontal lobe lesions. The combination of clinical findings, MRI, and Metagenomic next-generation sequencing (NGS) of cerebrospinal fluid led to the diagnosis of Balamuthia mandrillaris encephalitis. The patient died 5 days after discharge.}, } @article {pmid38425544, year = {2024}, author = {Yi, L and Zhu, J and Li, Q and Guan, X and Cheng, W and Xie, Y and Zhao, Y and Zhao, S}, title = {Panax notoginseng stems and leaves affect microbial community and function in cecum of duzang pigs.}, journal = {Translational animal science}, volume = {8}, number = {}, pages = {txad142}, doi = {10.1093/tas/txad142}, pmid = {38425544}, issn = {2573-2102}, abstract = {Panax notoginseng is a Chinese medicine with a long history in which stems and leaves are the wastes of processing Panax notoginseng and have not been effectively utilized. The effects of diets containing Panax notoginseng stems and leaves on the cecal short-chain fatty acid (SCFA) concentration and microbiome of independent pigs were studied. Diets containing Panax notoginseng stems and leaves did not affect the concentration of SCFA in the cecal contents of Duzang pigs but affected the microbial composition and diversity. Firmicutes, Proteobacteria, and Bacteroidetes dominate in the cecal of Duzang pigs. Feeding Duzang pigs with a 10% Panax notoginseng stems and leaves diet increases the abundance of Lactobacillus, Christensenellaceae R-7 group, and Akkermansia in the cecal. We found 14 genera positively associated with acetate, and they were Lactobacillus, Ruminococcaceae UCG 005, Ruminiclostridium 6; Escherichia Shigella and Family XIII AD3011 group showed negative correlations. Solobacterium, Desulfovibrio, and Erysipelatoclostridium were positively associated with propionate. Campylobacter, Clostridium sensu stricto 11, and Angelakisella were positively associated with butyrate. In conclusion, Panax notoginseng stems and leaves could affect the cecal microbial community and functional composition of Duzang pigs. Panax notoginseng stems and leaves reduce the enrichment of lipopolysaccharide biosynthetic pathway of the cecal microbiome, which may have a positive effect on intestinal health. The higher abundance of GH25 family in Duzang pig's cecal microbiome of fed Panax notoginseng stems and leaves diet. This increase may be the reason for the microbial diversity decrease.}, } @article {pmid38425506, year = {2024}, author = {Garg, D and Patel, N and Rawat, A and Rosado, AS}, title = {Cutting edge tools in the field of soil microbiology.}, journal = {Current research in microbial sciences}, volume = {6}, number = {}, pages = {100226}, doi = {10.1016/j.crmicr.2024.100226}, pmid = {38425506}, issn = {2666-5174}, abstract = {The study of the whole of the genetic material contained within the microbial populations found in a certain environment is made possible by metagenomics. This technique enables a thorough knowledge of the variety, function, and interactions of microbial communities that are notoriously difficult to research. Due to the limitations of conventional techniques such as culturing and PCR-based methodologies, soil microbiology is a particularly challenging field. Metagenomics has emerged as an effective technique for overcoming these obstacles and shedding light on the dynamic nature of the microbial communities in soil. This review focuses on the principle of metagenomics techniques, their potential applications and limitations in soil microbial diversity analysis. The effectiveness of target-based metagenomics in determining the function of individual genes and microorganisms in soil ecosystems is also highlighted. Targeted metagenomics, including high-throughput sequencing and stable-isotope probing, is essential for studying microbial taxa and genes in complex ecosystems. Shotgun metagenomics may reveal the diversity of soil bacteria, composition, and function impacted by land use and soil management. Sanger, Next Generation Sequencing, Illumina, and Ion Torrent sequencing revolutionise soil microbiome research. Oxford Nanopore Technology (ONT) and Pacific Biosciences (PacBio)'s third and fourth generation sequencing systems revolutionise long-read technology. GeoChip, clone libraries, metagenomics, and metabarcoding help comprehend soil microbial communities. The article indicates that metagenomics may improve environmental management and agriculture despite existing limitations.Metagenomics has revolutionised soil microbiology research by revealing the complete diversity, function, and interactions of microorganisms in soil. Metagenomics is anticipated to continue defining the future of soil microbiology research despite some limitations, such as the difficulty of locating the appropriate sequencing method for specific genes.}, } @article {pmid38424602, year = {2024}, author = {Chen, J and Chen, X and Zhu, Y and Yan, S and Xie, S}, title = {New insights into bioaugmented removal of sulfamethoxazole in sediment microcosms: degradation efficiency, ecological risk and microbial mechanisms.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {43}, pmid = {38424602}, issn = {2049-2618}, support = {2023J05124//Natural Science Foundation of Fujian Province/ ; 51778006//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Bioaugmentation has the potential to enhance the ability of ecological technology to treat sulfonamide-containing wastewater, but the low viability of the exogenous degraders limits their practical application. Understanding the mechanism is important to enhance and optimize performance of the bioaugmentation, which requires a multifaceted analysis of the microbial communities. Here, DNA-stable isotope probing (DNA-SIP) and metagenomic analysis were conducted to decipher the bioaugmentation mechanisms in stabilization pond sediment microcosms inoculated with sulfamethoxazole (SMX)-degrading bacteria (Pseudomonas sp. M2 or Paenarthrobacter sp. R1).

RESULTS: The bioaugmentation with both strains M2 and R1, especially strain R1, significantly improved the biodegradation rate of SMX, and its biodegradation capacity was sustainable within a certain cycle (subjected to three repeated SMX additions). The removal strategy using exogenous degrading bacteria also significantly abated the accumulation and transmission risk of antibiotic resistance genes (ARGs). Strain M2 inoculation significantly lowered bacterial diversity and altered the sediment bacterial community, while strain R1 inoculation had a slight effect on the bacterial community and was closely associated with indigenous microorganisms. Paenarthrobacter was identified as the primary SMX-assimilating bacteria in both bioaugmentation systems based on DNA-SIP analysis. Combining genomic information with pure culture evidence, strain R1 enhanced SMX removal by directly participating in SMX degradation, while strain M2 did it by both participating in SMX degradation and stimulating SMX-degrading activity of indigenous microorganisms (Paenarthrobacter) in the community.

CONCLUSIONS: Our findings demonstrate that bioaugmentation using SMX-degrading bacteria was a feasible strategy for SMX clean-up in terms of the degradation efficiency of SMX, the risk of ARG transmission, as well as the impact on the bacterial community, and the advantage of bioaugmentation with Paenarthrobacter sp. R1 was also highlighted. Video Abstract.}, } @article {pmid38424077, year = {2024}, author = {Zeng, S and Almeida, A and Li, S and Ying, J and Wang, H and Qu, Y and Paul Ross, R and Stanton, C and Zhou, Z and Niu, X and Mu, D and Wang, S}, title = {A metagenomic catalog of the early-life human gut virome.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1864}, pmid = {38424077}, issn = {2041-1723}, support = {82100590//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82241036//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Early-life human gut microbiome is a pivotal driver of gut homeostasis and infant health. However, the viral component (known as "virome") remains mostly unexplored. Here, we establish the Early-Life Gut Virome (ELGV), a catalog of 160,478 non-redundant DNA and RNA viral sequences from 8130 gut virus-like particles (VLPs) enriched or bulk metagenomes in the first three years of life. By clustering, 82,141 viral species are identified, 68.3% of which are absent in existing databases built mainly from adults, and 64 and 8 viral species based on VLPs-enriched and bulk metagenomes, respectively, exhibit potentials as biomarkers to distinguish infants from adults. With the largest longitudinal population of infants profiled by either VLPs-enriched or bulk metagenomic sequencing, we track the inherent instability and temporal development of the early-life human gut virome, and identify differential viruses associated with multiple clinical factors. The mother-infant shared virome and interactions between gut virome and bacteriome early in life are further expanded. Together, the ELGV catalog provides the most comprehensive and complete metagenomic blueprint of the early-life human gut virome, facilitating the discovery of pediatric disease-virome associations in future.}, } @article {pmid38423323, year = {2024}, author = {Liu, Z and Gu, H and Yao, Q and Jiao, F and Hu, X and Liu, J and Jin, J and Liu, X and Wang, G}, title = {Soil pH and carbon quality index regulate the biogeochemical cycle couplings of carbon, nitrogen and phosphorus in the profiles of Isohumosols.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {171269}, doi = {10.1016/j.scitotenv.2024.171269}, pmid = {38423323}, issn = {1879-1026}, abstract = {Soil biogeochemical cycles are essential for regulating ecosystem functions and services. However, little knowledge has been revealed on microbe-driven biogeochemical processes and their coupling mechanisms in soil profiles. This study investigated the vertical distribution of soil functional composition and their contribution to carbon (C), nitrogen (N) and phosphorus (P) cycling in the humus horizons (A-horizons) and parent material horizons (C-horizons) in Udic and Ustic Isohumosols using shotgun sequencing. Results showed that the diversity and relative abundance of microbial functional genes was influenced by soil horizons and soil types. In A-horizons, the relative abundances of N mineralization and liable C decomposition genes were significantly greater, but the P cycle-related genes, recalcitrant C decomposition and denitrification genes were lower compared to C-horizons. While, Ustic Isohumosols had lower relative abundances of C decomposition genes but higher relative abundances of N mineralization and P cycling-related pathways compared to Udic Isohumosols. The network analysis revealed that C-horizons had more interactions and stronger stability of functional gene networks than in A-horizons. Importantly, our results provide new insights into the potential mechanisms for the coupling processes of soil biogeochemical cycles among C, N and P, which is mediated by specific microbial taxa. Soil pH and carbon quality index (CQI) were two sensitive indicators for regulating the relative abundances and the relationships of functional genes in biogeochemical cycles. This study contributes to a deeper understanding of the ecological functions of soil microorganisms, thus providing a theoretical basis for the exploration and utilization of soil microbial resources and the development of soil ecological control strategies.}, } @article {pmid38423316, year = {2024}, author = {Xiang, Y and Yu, Y and Wang, J and Li, W and Rong, Y and Ling, H and Chen, Z and Qian, Y and Han, X and Sun, J and Yang, Y and Chen, L and Zhao, C and Li, J and Chen, K}, title = {Neural network establishes co-occurrence links between transformation products of the contaminant and the soil microbiome.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {171287}, doi = {10.1016/j.scitotenv.2024.171287}, pmid = {38423316}, issn = {1879-1026}, abstract = {It remains challenging to establish reliable links between transformation products (TPs) of contaminants and corresponding microbes. This challenge arises due to the sophisticated experimental regime required for TP discovery and the compositional nature of 16S rRNA gene amplicon sequencing and mass spectrometry datasets, which can potentially confound statistical inference. In this study, we present a new strategy by combining the use of [2]H-labeled Stable Isotope-Assisted Metabolomics ([2]H-SIAM) with a neural network-based algorithm (i.e., MMvec) to explore links between TPs of pyrene and the soil microbiome. The links established by this novel strategy were further validated using different approaches. Briefly, a metagenomic study provided indirect evidence for the established links, while the identification of pyrene degraders from soils, and a DNA-based stable isotope probing (DNA-SIP) study offered direct evidence. The comparison among different approaches, including Pearson's and Spearman's correlations, further confirmed the superior performance of our strategy. In conclusion, we summarize the unique features of the combined use of [2]H-SIAM and MMvec. This study not only addresses the challenges in linking TPs to microbes but also introduces an innovative and effective approach for such investigations. Environmental Implication: Taxonomically diverse bacteria performing successive metabolic steps of the contaminant were firstly depicted in the environmental matrix.}, } @article {pmid38423015, year = {2024}, author = {Carasso, S and Zaatry, R and Hajjo, H and Kadosh-Kariti, D and Ben-Assa, N and Naddaf, R and Mandelbaum, N and Pressman, S and Chowers, Y and Gefen, T and Jeffrey, KL and Jofre, J and Coyne, MJ and Comstock, LE and Sharon, I and Geva-Zatorsky, N}, title = {Inflammation and bacteriophages affect DNA inversion states and functionality of the gut microbiota.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2024.02.003}, pmid = {38423015}, issn = {1934-6069}, abstract = {Reversible genomic DNA inversions control the expression of numerous gut bacterial molecules, but how this impacts disease remains uncertain. By analyzing metagenomic samples from inflammatory bowel disease (IBD) cohorts, we identified multiple invertible regions where a particular orientation correlated with disease. These include the promoter of polysaccharide A (PSA) of Bacteroides fragilis, which induces regulatory T cells (Tregs) and ameliorates experimental colitis. The PSA promoter was mostly oriented "OFF" in IBD patients, which correlated with increased B. fragilis-associated bacteriophages. Similarly, in mice colonized with a healthy human microbiota and B. fragilis, induction of colitis caused a decline of PSA in the "ON" orientation that reversed as inflammation resolved. Monocolonization of mice with B. fragilis revealed that bacteriophage infection increased the frequency of PSA in the "OFF" orientation, causing reduced PSA expression and decreased Treg cells. Altogether, we reveal dynamic bacterial phase variations driven by bacteriophages and host inflammation, signifying bacterial functional plasticity during disease.}, } @article {pmid38422739, year = {2024}, author = {Cui, Z and Li, Y and Jing, X and Luan, X and Liu, N and Liu, J and Meng, Y and Xu, J and Valentine, DL}, title = {Cycloalkane degradation by an uncultivated novel genus of Gammaproteobacteria derived from China's marginal seas.}, journal = {Journal of hazardous materials}, volume = {469}, number = {}, pages = {133904}, doi = {10.1016/j.jhazmat.2024.133904}, pmid = {38422739}, issn = {1873-3336}, abstract = {The consumption of cycloalkanes is prevalent in low-temperature marine environments, likely influenced by psychrophilic microorganisms. Despite their significance, the primary active species responsible for marine cycloalkane degradation remain largely unidentified due to cultivation challenges. In this study, we provide compelling evidence indicating that the uncultured genus C1-B045 of Gammaproteobacteria is a pivotal participant in cycloalkane decomposition within China's marginal seas. Notably, the relative abundance of C1-B045 surged from 15.9% in the methylcyclohexane (MCH)-consuming starter culture to as high as 97.5% in MCH-utilizing extinction cultures following successive dilution-to-extinction and incubation cycles. We used stable isotope probing, Raman-activated gravity-driven encapsulation, and 16 S rRNA gene sequencing to link cycloalkane-metabolizing phenotype to genotype at the single-cell level. By annotating key enzymes (e.g., alkane monooxygenase, cyclohexanone monooxygenase, and 6-hexanolactone hydrolase) involved in MCH metabolism within C1-B045's representative metagenome-assembled genome, we developed a putative MCH degradation pathway.}, } @article {pmid38424056, year = {2024}, author = {Istvan, P and Birkeland, E and Avershina, E and Kværner, AS and Bemanian, V and Pardini, B and Tarallo, S and de Vos, WM and Rognes, T and Berstad, P and Rounge, TB}, title = {Exploring the gut DNA virome in fecal immunochemical test stool samples reveals associations with lifestyle in a large population-based study.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1791}, pmid = {38424056}, issn = {2041-1723}, support = {198048//Kreftforeningen (Norwegian Cancer Society)/ ; 190179//Kreftforeningen (Norwegian Cancer Society)/ ; 2022067//Ministry of Health and Care Services | Helse Sør-Øst RHF (Southern and Eastern Norway Regional Health Authority)/ ; }, abstract = {Stool samples for fecal immunochemical tests (FIT) are collected in large numbers worldwide as part of colorectal cancer screening programs. Employing FIT samples from 1034 CRCbiome participants, recruited from a Norwegian colorectal cancer screening study, we identify, annotate and characterize more than 18000 DNA viruses, using shotgun metagenome sequencing. Only six percent of them are assigned to a known taxonomic family, with Microviridae being the most prevalent viral family. Linking individual profiles to comprehensive lifestyle and demographic data shows 17/25 of the variables to be associated with the gut virome. Physical activity, smoking, and dietary fiber consumption exhibit strong and consistent associations with both diversity and relative abundance of individual viruses, as well as with enrichment for auxiliary metabolic genes. We demonstrate the suitability of FIT samples for virome analysis, opening an opportunity for large-scale studies of this enigmatic part of the gut microbiome. The diverse viral populations and their connections to the individual lifestyle uncovered herein paves the way for further exploration of the role of the gut virome in health and disease.}, } @article {pmid38424049, year = {2024}, author = {Zhong, ZP and Du, J and Köstlbacher, S and Pjevac, P and Orlić, S and Sullivan, MB}, title = {Viral potential to modulate microbial methane metabolism varies by habitat.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1857}, pmid = {38424049}, issn = {2041-1723}, support = {3790//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; 1759874//National Science Foundation (NSF)/ ; 1829831//National Science Foundation (NSF)/ ; NA//OSU | Byrd Polar and Climate Research Center, Ohio State University (Byrd Polar and Climate Research Center of The Ohio State University)/ ; }, abstract = {Methane is a potent greenhouse gas contributing to global warming. Microorganisms largely drive the biogeochemical cycling of methane, yet little is known about viral contributions to methane metabolism (MM). We analyzed 982 publicly available metagenomes from host-associated and environmental habitats containing microbial MM genes, expanding the known MM auxiliary metabolic genes (AMGs) from three to 24, including seven genes exclusive to MM pathways. These AMGs are recovered on 911 viral contigs predicted to infect 14 prokaryotic phyla including Halobacteriota, Methanobacteriota, and Thermoproteota. Of those 24, most were encoded by viruses from rumen (16/24), with substantially fewer by viruses from environmental habitats (0-7/24). To search for additional MM AMGs from an environmental habitat, we generate metagenomes from methane-rich sediments in Vrana Lake, Croatia. Therein, we find diverse viral communities, with most viruses predicted to infect methanogens and methanotrophs and some encoding 13 AMGs that can modulate host metabolisms. However, none of these AMGs directly participate in MM pathways. Together these findings suggest that the extent to which viruses use AMGs to modulate host metabolic processes (e.g., MM) varies depending on the ecological properties of the habitat in which they dwell and is not always predictable by habitat biogeochemical properties.}, } @article {pmid38421596, year = {2024}, author = {Anu, K and Kumari, S and Choudhary, G and Devi, S}, title = {Microbial diversity analysis of Chumathang geothermal spring, Ladakh, India.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {38421596}, issn = {1678-4405}, abstract = {In light of their unique and challenging environment, the high-altitude Chumathang geothermal springs in Ladakh, India, are undeniably intriguing for microbiological study. The purpose of this study was to employ a culture-independent sequencing approach to give a comprehensive characterization of the unknown bacterial and archaeal community structure, composition and networks in water and soil from the Chumathang geothermal spring. A total of 50%, and 42.86% bacterial phyla were found in the water, and soil samples respectively and this analysis also showed a total of 9.62% and 7.94% of archaeal phyla in both the samples, respectively. Further, the presence of unclassified (derived from other sequences, water: 17.31%, and soil: 19.05%) and unclassified (derived from bacteria, water: 13.46%, and soil: 12.70%) were also observed in the current metagenomics investigation. Firmicutes and Proteobacteria were the most abundant bacterial phyla in water, whereas Proteobacteria and Bacteroidetes were the most abundant bacterial phyla in geothermal soil. Crenarchaeota and Euryarchaeota dominated archeal communities in soil and water, respectively. This metagenomic study gave a detailed insight into the microbial diversity found in Chumathang geothermal spring and surrounding area, located in Ladakh, India. Surprisingly, this finding indicated the existence of geographically distinct microbial communities that were suited to various geothermal water habitats along the Himalayan Geothermal Belt. Future studies must take into account the metabolic pathways of these microbial communities that exist in these extreme environments. This will allow us to obtain a better knowledge of the microbial metabolisms that are common at these geothermal locations, which have a lot of potential for biotechnological applications. They will also enable us to establish links between the microbial community composition and the physicochemical environment of geothermal water and area.}, } @article {pmid38421266, year = {2024}, author = {Matchado, MS and Rühlemann, M and Reitmeier, S and Kacprowski, T and Frost, F and Haller, D and Baumbach, J and List, M}, title = {On the limits of 16S rRNA gene-based metagenome prediction and functional profiling.}, journal = {Microbial genomics}, volume = {10}, number = {2}, pages = {}, doi = {10.1099/mgen.0.001203}, pmid = {38421266}, issn = {2057-5858}, abstract = {Molecular profiling techniques such as metagenomics, metatranscriptomics or metabolomics offer important insights into the functional diversity of the microbiome. In contrast, 16S rRNA gene sequencing, a widespread and cost-effective technique to measure microbial diversity, only allows for indirect estimation of microbial function. To mitigate this, tools such as PICRUSt2, Tax4Fun2, PanFP and MetGEM infer functional profiles from 16S rRNA gene sequencing data using different algorithms. Prior studies have cast doubts on the quality of these predictions, motivating us to systematically evaluate these tools using matched 16S rRNA gene sequencing, metagenomic datasets, and simulated data. Our contribution is threefold: (i) using simulated data, we investigate if technical biases could explain the discordance between inferred and expected results; (ii) considering human cohorts for type two diabetes, colorectal cancer and obesity, we test if health-related differential abundance measures of functional categories are concordant between 16S rRNA gene-inferred and metagenome-derived profiles and; (iii) since 16S rRNA gene copy number is an important confounder in functional profiles inference, we investigate if a customised copy number normalisation with the rrnDB database could improve the results. Our results show that 16S rRNA gene-based functional inference tools generally do not have the necessary sensitivity to delineate health-related functional changes in the microbiome and should thus be used with care. Furthermore, we outline important differences in the individual tools tested and offer recommendations for tool selection.}, } @article {pmid38421192, year = {2024}, author = {Zhang, N and Gao, X and Li, D and Xu, L and Zhou, G and Xu, M and Peng, L and Sun, G and Pan, F and Li, Y and Ren, R and Huang, R and Yang, Y and Wang, Z}, title = {Sleep deprivation-induced anxiety-like behaviors are associated with alterations in the gut microbiota and metabolites.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0143723}, doi = {10.1128/spectrum.01437-23}, pmid = {38421192}, issn = {2165-0497}, abstract = {UNLABELLED: The present study aimed to characterize the gut microbiota and serum metabolome changes associated with sleep deprivation (SD) as well as to explore the potential benefits of multi-probiotic supplementation in alleviating SD-related mental health disorders. Rats were subjected to 7 days of SD, followed by 14 days of multi-probiotics or saline administration. Open-field tests were conducted at baseline, end of SD (day 7), and after 14 days of saline or multi-probiotic gavage (day 21). Metagenomic sequencing was conducted on fecal samples, and serum metabolites were measured by untargeted liquid chromatography tandem-mass spectrometry. At day 7, anxiety-like behaviors, including significant decreases in total movement distance (P = 0.0002) and staying time in the central zone (P = 0.021), were observed. In addition, increased levels of lipopolysaccharide (LPS; P = 0.028) and decreased levels of uridine (P = 0.018) and tryptophan (P = 0.01) were detected in rats after 7 days of SD. After SD, the richness of the gut bacterial community increased, and the levels of Akkermansia muciniphila, Muribaculum intestinale, and Bacteroides caecimuris decreased. The changes in the host metabolism and gut microbiota composition were strongly associated with the anxiety-like behaviors caused by SD. In addition, multi-probiotic supplementation for 14 days modestly improved the anxiety-like behaviors in SD rats but significantly reduced the serum level of LPS (P = 0.045). In conclusion, SD induces changes in the gut microbiota and serum metabolites, which may contribute to the development of chronic inflammatory responses and affect the gut-brain axis, causing anxiety-like behaviors. Probiotic supplementation significantly reduces serum LPS, which may alleviate the influence of chronic inflammation.

IMPORTANCE: The disturbance in the gut microbiome and serum metabolome induced by SD may be involved in anxiety-like behaviors. Probiotic supplementation decreases serum levels of LPS, but this reduction may be insufficient for alleviating SD-induced anxiety-like behaviors.}, } @article {pmid38420890, year = {2024}, author = {Long, Y and Xia, X and Feng, H and Zhao, P}, title = {Improving pulmonary infection diagnosis with metagenomic next-generation sequencing of bronchoalveolar lavage fluid.}, journal = {Journal of medical microbiology}, volume = {73}, number = {2}, pages = {}, doi = {10.1099/jmm.0.001808}, pmid = {38420890}, issn = {1473-5644}, abstract = {Introduction. Inappropriate use of antibiotics and inadequate therapeutic regimens for early-stage pulmonary infections are major contributors to increased prevalence of complications and mortality. Moreover, due to the limitations in sensitivity of conventional testing, there is an urgent need for more diagnostically efficient methods for the detection and characterization of pathogens in pulmonary infections.Hypothesis/Gap Statement. Metagenomic next-generation sequencing (mNGS) can contribute to the diagnosis and management of pulmonary infections.Aim. This study aimed to evaluate the clinical application and value of mNGS in the diagnosis of clinically suspected pulmonary infections by comparing with conventional testing.Methodology. In this study, the diagnosis performance of mNGS was evaluated using bronchoalveolar lavage fluid (BALF) samples from 143 patients with suspected lung infections. First, we conducted a prospective study on 31 patients admitted to Yuebei People's Hospital Affiliated to Shantou University Medical College to investigate the clinical value. Then a retrospective analysis was performed by including more patients (n=112) to reduce the random error. Pathogens were detected by mNGS and conventional methods (culture and PCR). Then, the types and cases of detected pathogens, as well as the specificity and sensitivity, were compared between the two methods. We evaluated the performance of mNGS in detecting bacterial, fungal, viral and mixed infections in BALF. The effect of disease severity in pulmonary infections on the integrity of mNGS pathogen detection was also explored.Results. The mNGS provided an earlier and more comprehensive pathogen profile than conventional testing, which in turn prompted a change in clinical medication, which led to improvement in eight patients (8/31=25.81 %) in the presence of other serious comorbidities. In a retrospective analysis, mNGS was much more sensitive than conventional testing in the diagnosis of pulmonary infections (95.33 % vs. 55.56 %; P<0.001), with a 39.77 % increase in sensitivity. The detection rate of mNGS for mixed infections was significantly higher than that of conventional testing methods for both common and severe pneumonia (48/67=71.64 % vs. 12/52=23.08 %, P<0.001; 44/59=74.58 % vs. 11/59=18.64 %, P<0.0001).Conclusion. The sensitivity of mNGS in the diagnosis of pathogenic microorganisms in pulmonary infections far exceeds that of conventional culture tests. As a complementary method to conventional methods, mNGS can help improve the diagnosis of pulmonary infections. In addition, mNGS pathogen integrity detection rate was similar in common and severe pneumonia. We recommend the prompt use of mNGS when mixed or rare pathogen infections are suspected, especially in immunocompromised individuals and/or critically ill individuals.}, } @article {pmid38420723, year = {2024}, author = {Zhu, K and Jin, Y and Zhao, Y and He, A and Wang, R and Cao, C}, title = {Proteomic scrutiny of nasal microbiomes: implications for the clinic.}, journal = {Expert review of proteomics}, volume = {}, number = {}, pages = {}, doi = {10.1080/14789450.2024.2323983}, pmid = {38420723}, issn = {1744-8387}, abstract = {INTRODUCTION: The nasal cavity is the initial site of the human respiratory tract and is one of the habitats where microorganisms colonize. The findings from a growing number of studies have shown that the nasal microbiome is an important factor for human disease and health. 16S rRNA sequencing and metagenomic next-generation sequencing (mNGS) are the most commonly used means of microbiome evaluation. Among them, 16S rRNA sequencing is the primary method used in previous studies of nasal microbiomes. However, neither 16S rRNA sequencing nor mNGS can be used to analyze the genes specifically expressed by nasal microorganisms and their functions. This problem can be addressed by proteomic analysis of the nasal microbiome.

AREAS COVERED: In this review, we summarize current advances in research on the nasal microbiome, introduce the methods for proteomic evaluation of the nasal microbiome, and focus on the important roles of proteomic evaluation of the nasal microbiome in the diagnosis and treatment of related diseases.

EXPERT OPINION: The detection method for microbiome-expressed proteins is known as metaproteomics. Metaproteomic analysis can help us dig deeper into the nasal microbiomes and provide new targets and ideas for clinical diagnosis and treatment of many nasal dysbiosis-related diseases.}, } @article {pmid38420673, year = {2024}, author = {Lu, Y and Zhang, L and Liu, X and Lan, Y and Wu, L and Wang, J and Wu, K and Yang, C and Lv, R and Yi, D and Zhuo, G and Li, Y and Shen, F and Hou, R and Yue, B and Fan, Z}, title = {Red pandas with different diets and environments exhibit different gut microbial functional composition and capacity.}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.12813}, pmid = {38420673}, issn = {1749-4877}, support = {2022NSFSC0126//Natural Science Foundation of Sichuan Province/ ; 2020CPB-B06//Foundation of Chengdu Research Base of Giant Panda Breeding/ ; }, abstract = {The red panda (Ailurus fulgens) is a distinctive mammal known for its reliance on a diet primarily consisting of bamboo. The gut microbiota and overall health of animals are strongly influenced by diets and environments. Therefore, conducting research to explore the taxonomical and functional variances within the gut microbiota of red pandas exposed to various dietary and environmental conditions could shed light on the dynamic complexities of their microbial communities. In this study, normal fecal samples were obtained from red pandas residing in captive and semi-free environments under different dietary regimes and used for metabolomic, 16S rRNA, and metagenomic sequencing analysis, with the pandas classified into four distinct cohorts according to diet and environment. In addition, metagenomic sequencing was conducted on mucus fecal samples to elucidate potential etiological agents of disease. Results revealed an increased risk of gastrointestinal diseases in red pandas consuming bamboo shoots due to the heightened presence of pathogenic bacteria, although an increased presence of microbiota-derived tryptophan metabolites appeared to facilitate intestinal balance. The red pandas fed bamboo leaves also exhibited a decrease in gut microbial diversity, which may be attributed to the antibacterial flavonoids and lower protein levels in leaves. Notably, red pandas residing in semi-free environments demonstrated an enriched gut microbial diversity. Moreover, the occurrence of mucus secretion may be due to an increased presence of species associated with diarrhea and a reduced level of microbiota-derived tryptophan metabolites. In summary, our findings substantiate the influential role of diet and environment in modulating the gut microbiota of red pandas, offering potential implications for improved captive breeding practices.}, } @article {pmid38420377, year = {2024}, author = {Saikh, SR and Mushtaque, MA and Pramanick, A and Prasad, JK and Roy, D and Saha, S and Das, SK}, title = {Fog caused distinct diversity of airborne bacterial communities enriched with pathogens over central Indo-Gangetic plain in India.}, journal = {Heliyon}, volume = {10}, number = {4}, pages = {e26370}, pmid = {38420377}, issn = {2405-8440}, abstract = {Fog causes enhancement of bacterial loading in the atmosphere. Current study represents the impact of occurrences of fog on the alteration of diversity of airborne bacteria and their network computed from metagenomic data of airborne samples collected at Arthauli (25.95°N, 85.10°E) situated at central Indo-Gangetic Plain (IGP) during 1-14 January 2021. A distinct bacterial diversity with a complex network is identified in foggy condition due to the enrichment of unique types of bacteria. Present investigation highlights a statistically significant enrichment of airborne pathogenic bacteria found in a unique ecosystem within air evolved due to the occurrences of fog over central IGP. In the foggy network, Cutibacterium, an opportunistic pathogen, is identified to be interacting maximum (21 edges) with other bacteria with statistically significant copresence relation, which are responsible for various infections for human beings. A 40-60% increase (p < 0.01) in the abundance of pathogenic bacteria for respiratory and skin diseases is noticed in fog period. Among the fog-enriched bacteria, Cutibacterium, Herbaspirillum, Paenibacillus, and Tsukamurella are examples of opportunistic bacteria causing various respiratory diseases, while Paenibacillus can even cause skin cancer and acute lymphoblastic leukemia.}, } @article {pmid38420205, year = {2024}, author = {Sharko, FS and Mazloum, A and Krotova, AO and Byadovskaya, OP and Prokhvatilova, LB and Chvala, IA and Zolotikov, UE and Kozlova, AD and Krylova, AS and Grosfeld, EV and Prokopenko, AV and Korzhenkov, AA and Patrushev, MV and Namsaraev, ZB and Sprygin, AV and Toshchakov, SV}, title = {Metagenomic profiling of viral and microbial communities from the pox lesions of lumpy skin disease virus and sheeppox virus-infected hosts.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1321202}, pmid = {38420205}, issn = {2297-1769}, abstract = {INTRODUCTION: It has been recognized that capripoxvirus infections have a strong cutaneous tropism with the manifestation of skin lesions in the form of nodules and scabs in the respective hosts, followed by necrosis and sloughing off. Considering that the skin microbiota is a complex community of commensal bacteria, fungi and viruses that are influenced by infections leading to pathological states, there is no evidence on how the skin microbiome is affected during capripoxvirus pathogenesis.

METHODS: In this study, shotgun metagenomic sequencing was used to investigate the microbiome in pox lesions from hosts infected with lumpy skin disease virus and sheep pox virus.

RESULTS: The analysis revealed a high degree of variability in bacterial community structures across affected skin samples, indicating the importance of specific commensal microorganisms colonizing individual hosts. The most common and abundant bacteria found in scab samples were Fusobacterium necrophorum, Streptococcus dysgalactiae, Helcococcus ovis and Trueperella pyogenes, irrespective of host. Bacterial reads belonging to the genera Moraxella, Mannheimia, Corynebacterium, Staphylococcus and Micrococcus were identified.

DISCUSSION: This study is the first to investigate capripox virus-associated changes in the skin microbiome using whole-genome metagenomic profiling. The findings will provide a basis for further investigation into capripoxvirus pathogenesis. In addition, this study highlights the challenge of selecting an optimal bioinformatics approach for the analysis of metagenomic data in clinical and veterinary practice. For example, direct classification of reads using a kmer-based algorithm resulted in a significant number of systematic false positives, which may be attributed to the peculiarities of the algorithm and database selection. On the contrary, the process of de novo assembly requires a large number of target reads from the symbiotic microbial community. In this work, the obtained sequencing data were processed by three different approaches, including direct classification of reads based on k-mers, mapping of reads to a marker gene database, and de novo assembly and binning of metagenomic contigs. The advantages and disadvantages of these techniques and their practicality in veterinary settings are discussed in relation to the results obtained.}, } @article {pmid38419630, year = {2024}, author = {Kumar, B and Lorusso, E and Fosso, B and Pesole, G}, title = {A comprehensive overview of microbiome data in the light of machine learning applications: categorization, accessibility, and future directions.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1343572}, pmid = {38419630}, issn = {1664-302X}, abstract = {Metagenomics, Metabolomics, and Metaproteomics have significantly advanced our knowledge of microbial communities by providing culture-independent insights into their composition and functional potential. However, a critical challenge in this field is the lack of standard and comprehensive metadata associated with raw data, hindering the ability to perform robust data stratifications and consider confounding factors. In this comprehensive review, we categorize publicly available microbiome data into five types: shotgun sequencing, amplicon sequencing, metatranscriptomic, metabolomic, and metaproteomic data. We explore the importance of metadata for data reuse and address the challenges in collecting standardized metadata. We also, assess the limitations in metadata collection of existing public repositories collecting metagenomic data. This review emphasizes the vital role of metadata in interpreting and comparing datasets and highlights the need for standardized metadata protocols to fully leverage metagenomic data's potential. Furthermore, we explore future directions of implementation of Machine Learning (ML) in metadata retrieval, offering promising avenues for a deeper understanding of microbial communities and their ecological roles. Leveraging these tools will enhance our insights into microbial functional capabilities and ecological dynamics in diverse ecosystems. Finally, we emphasize the crucial metadata role in ML models development.}, } @article {pmid38419121, year = {2024}, author = {Cui, N and Yang, X and Sui, H and Tan, L and Wang, W and Su, S and Qi, L and Huang, Q and Hrabchenko, N and Xu, C}, title = {Virome characterization of diarrheic red-crowned crane (G. japonensis).}, journal = {Animal microbiome}, volume = {6}, number = {1}, pages = {8}, pmid = {38419121}, issn = {2524-4671}, support = {CXGC2018E10//the High-Level Talents and Innovative Team Recruitment Program of the Shandong Academy of Agricultural Sciences/ ; ZR2020MC180//Natural Science Fund of Shandong Province/ ; ZR2021MC096//Natural Science Fund of Shandong Province/ ; 2022CXPT022//the Key Research and Development Program of Shandong province/ ; CXGC2023G03//Agricultural Scientific and Technological Innovation Project of Shandong Academy of Agricultural Sciences/ ; CARS-41-Z17//the Modern Agro-industry Technology Research System/ ; }, abstract = {BACKGROUND: The red-crowned crane is one of the vulnerable bird species. Although the captive population has markedly increased over the last decade, infectious diseases can lead to the death of young red-crowned cranes while few virological studies have been conducted.

METHODS: Using a viral metagenomics approach, we analyzed the virome of tissues of the dead captive red-crowned crane with diarrhea symptoms in Dongying Biosphere Reserve, Shandong Province, China and feces of individual birds breeding at the corresponding captive breeding center, which were pooled separately.

RESULTS: There is much more DNA and RNA viruses in the feces than that of the tissues. RNA virus belonging to the families Picornaviridae, and DNA viruses belonging to the families Parvoviridae, associated with enteric diseases were detected in the tissues and feces. Genomes of the picornavirus, genomovirus, and parvovirus identified in the study were fully characterized, which further suggested that infectious viruses of these families were possibly presented in the diseased red-crowned crane.

CONCLUSION: RNA virus belonging to the families Picornaviridae, and DNA viruses belonging to the families Genomoviridae and Parvoviridae were possibly the causative agent for diarrhea of red-crowned crane. This study has expanded our understanding of the virome of red-crowned crane and provides a baseline for elucidating the etiology for diarrhea of the birds.}, } @article {pmid38419010, year = {2024}, author = {Nooij, S and Vendrik, KEW and Zwittink, RD and Ducarmon, QR and Keller, JJ and Kuijper, EJ and Terveer, EM and , }, title = {Long-term beneficial effect of faecal microbiota transplantation on colonisation of multidrug-resistant bacteria and resistome abundance in patients with recurrent Clostridioides difficile infection.}, journal = {Genome medicine}, volume = {16}, number = {1}, pages = {37}, pmid = {38419010}, issn = {1756-994X}, abstract = {BACKGROUND: Multidrug-resistant (MDR) bacteria are a growing global threat, especially in healthcare facilities. Faecal microbiota transplantation (FMT) is an effective prevention strategy for recurrences of Clostridioides difficile infections and can also be useful for other microbiota-related diseases.

METHODS: We study the effect of FMT in patients with multiple recurrent C. difficile infections on colonisation with MDR bacteria and antibiotic resistance genes (ARG) on the short (3 weeks) and long term (1-3 years), combining culture methods and faecal metagenomics.

RESULTS: Based on MDR culture (n = 87 patients), we notice a decrease of 11.5% in the colonisation rate of MDR bacteria after FMT (20/87 before FMT = 23%, 10/87 3 weeks after FMT). Metagenomic sequencing of patient stool samples (n = 63) shows a reduction in relative abundances of ARGs in faeces, while the number of different resistance genes in patients remained higher compared to stools of their corresponding healthy donors (n = 11). Furthermore, plasmid predictions in metagenomic data indicate that patients harboured increased levels of resistance plasmids, which appear unaffected by FMT. In the long term (n = 22 patients), the recipients' resistomes are still donor-like, suggesting the effect of FMT may last for years.

CONCLUSIONS: Taken together, we hypothesise that FMT restores the gut microbiota to a composition that is closer to the composition of healthy donors, and potential pathogens are either lost or decreased to very low abundances. This process, however, does not end in the days following FMT. It may take months for the gut microbiome to re-establish a balanced state. Even though a reservoir of resistance genes remains, a notable part of which on plasmids, FMT decreases the total load of resistance genes.}, } @article {pmid38417224, year = {2024}, author = {Xie, Z and Huang, J and Sun, G and He, S and Luo, Z and Zhang, L and Li, L and Yao, M and Du, C and Yu, W and Feng, Y and Yang, D and Zhang, J and Ge, C and Li, H and Geng, M}, title = {Integrated multi-omics analysis reveals gut microbiota dysbiosis and systemic disturbance in major depressive disorder.}, journal = {Psychiatry research}, volume = {334}, number = {}, pages = {115804}, doi = {10.1016/j.psychres.2024.115804}, pmid = {38417224}, issn = {1872-7123}, abstract = {Major depressive disorder (MDD) involves systemic changes in peripheral blood and gut microbiota, but the current understanding is incomplete. Herein, we conducted a multi-omics analysis of fecal and blood samples obtained from an observational cohort including MDD patients (n = 99) and healthy control (HC, n = 50). 16S rRNA sequencing of gut microbiota showed structural alterations in MDD, as characterized by increased Enterococcus. Metagenomics sequencing of gut microbiota showed substantial functional alterations including upregulation in the superpathway of the glyoxylate cycle and fatty acid degradation and downregulation in various metabolic pathways in MDD. Plasma metabolomics revealed decreased amino acids and bile acids, together with increased sphingolipids and cholesterol esters in MDD. Notably, metabolites involved in arginine and proline metabolism were decreased while sphingolipid metabolic pathway were increased. Mass cytometry analysis of blood immune cell subtypes showed rises in proinflammatory immune subsets and declines in anti-inflammatory immune subsets in MDD. Furthermore, our findings revealed disease severity-related factors of MDD. Interestingly, we classified MDD into two immune subtypes that were highly correlated with disease relapse. Moreover, we established discriminative signatures that differentiate MDD from HC. These findings contribute to a comprehensive understanding of the MDD pathogenesis and provide valuable resources for the discovery of biomarkers.}, } @article {pmid38418769, year = {2024}, author = {Zhang, H and Zhang, P and Xiao, Z and Gao, Y and Han, N and He, X and Zhang, J and Li, Y}, title = {Hemophagocytic lymphohistiocytosis caused by herpes simplex virus type 1 in a young adult: a case report with literature review.}, journal = {Journal of hematopathology}, volume = {}, number = {}, pages = {}, pmid = {38418769}, issn = {1865-5785}, support = {2022A1515220044//Basic and Applied Basic Research Foundation of Guangdong Province/ ; }, abstract = {Hemophagocytic lymphohistiocytosis is a severe hyperinflammatory syndrome that can be potentially life-threatening without appropriate treatment. Although viral infection is the most common trigger of hemophagocytic lymphohistiocytosis, cases of herpes simplex virus type 1-induced hemophagocytic lymphohistiocytosis are rare in adults. This study aims to provide a comprehensive overview of the clinical characteristics and treatment outcomes associated with HSV-1-induced HLH. We herein report an adult case of hemophagocytic lymphohistiocytosis caused by herpes simplex virus type 1, diagnosed on the basis of peripheral blood metagenomic next-generation sequencing results. The patient exhibited a favorable response to treatment, involving dexamethasone, intravenous immunoglobulin, and acyclovir. Notably, etoposide administration was deemed unnecessary, and there has been no recurrence of the disease within the year following treatment. Early and sensitive recognition, rapid and precise diagnosis, and timely and appropriate treatment facilitated the successful treatment of this case.}, } @article {pmid38418677, year = {2024}, author = {Halleran, J and Sylvester, H and Jacob, M and Callahan, B and Baynes, R and Foster, D}, title = {Impact of florfenicol dosing regimen on the phenotypic and genotypic resistance of enteric bacteria in steers.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4920}, pmid = {38418677}, issn = {2045-2322}, support = {USDA Grants 2020-41480-32520//Food Animal Residue Avoidance Databank (FARAD)/ ; USDA Grants 2021-41480-35270//Food Animal Residue Avoidance Databank (FARAD)/ ; }, abstract = {The food animal sector's use of antimicrobials is heavily critiqued for its role in allowing resistance to develop against critically important antimicrobials in human health. The WHO recommends using lower tier antimicrobials such as florfenicol for disease treatment. The primary objective of this study was to assess the differences in resistance profiles of enteric microbes following administration of florfenicol to steers using both FDA-approved dosing regimens and two different detection methods. Our hypothesis was that we would identify an increased prevalence of resistance in the steers administered the repeated, lower dose of florfenicol; additionally, we hypothesized resistance profiles would be similar between both detection methods. Twelve steers were administered either two intramuscular (20 mg/kg q 48 h; n = 6) or a single subcutaneous dose (40 mg/kg, n = 6). Fecal samples were collected for 38 days, and E. coli and Enterococcus were isolated and tested for resistance. Fecal samples were submitted for metagenomic sequencing analysis. Metagenomics revealed genes conferring resistance to aminoglycosides as the most abundant drug class. Most multidrug resistance genes contained phenicols. The genotypic and phenotypic patterns of resistance were not similar between drug classes. Observed increases in resistant isolates and relative abundance of resistance genes peaked after drug administration and returned to baseline by the end of the sampling period. The use of a "lower tier" antimicrobial, such as florfenicol, may cause an increased amount of resistance to critically important antimicrobials for a brief period, but these changes largely resolve by the end of the drug withdrawal period.}, } @article {pmid38418624, year = {2024}, author = {Raghav, N and Saraswat, P and Kumar, S and Chaurasia, A and Ranjan, R}, title = {Metagenomics analysis of water samples collected from the Yamuna River of Agra city, India.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {4}, pages = {113}, pmid = {38418624}, issn = {1573-0972}, abstract = {Yamuna River water in Agra city of India is contaminated with toxic pollutants, including heavy metals that cause damage to the environment and human health. At present, the direct use of river water for drinking purposes and household activities lead to the direct exposure of society to the contaminants. In this study, Yamuna River water samples were collected from three different sites in Agra city during the monsoon, summer, and winter seasons. The physico-chemical parameters were estimated along with heavy metals. In physico-chemical parameter, the values found were mostly above the permissible limits. The results water samples contain high levels of cadmium, chromium, lead, and nickel above the desirable levels in most cases. The metagenomic analysis revealed that Proteobacteria, Bacteroidetes, Verrucomicrobia, Actinobacteria, and Planctobacteria were the most abundant phyla with a relative abundance of 61%, 9.34%, 5.23%, 4.64%, and 4.3%, respectively. The Comamonadaceae, the most abundant family consists of the genera involved in hydrogen oxidation, iron reduction, degraders of polycyclic aromatic hydrocarbons, and fermentation. The presence of Pseudomonas, Nitrosomonas sp., Thauera humireducens and Dechloromonas denitrificans (decomposition of sewage and organic matter) and Pseudomonas aeruginosa indicates the presence of heavy metal degrading bacteria in water sample. Functional prediction showed the presence of genes responsible for different metabolic pathways that could help developing new bioremediation strategies. The study concludes the status of water contamination, the presence of complex microbial community and suggests the futuristic use and their role in bioremediation.}, } @article {pmid38417116, year = {2024}, author = {Zheng, R and Wang, C and Sun, C}, title = {Deep-sea in situ and laboratory multi-omics provide insights into the sulfur assimilation of a deep-sea Chloroflexota bacterium.}, journal = {mBio}, volume = {}, number = {}, pages = {e0000424}, doi = {10.1128/mbio.00004-24}, pmid = {38417116}, issn = {2150-7511}, abstract = {UNLABELLED: Chloroflexota bacteria are abundant and globally distributed in various deep-sea ecosystems. It has been reported based on metagenomics data that two deep-sea Chloroflexota lineages (the SAR202 group and Dehalococcoidia class) have the potential to drive sulfur cycling. However, the absence of cultured Chloroflexota representatives is a significant bottleneck toward understanding their contribution to the deep-sea sulfur cycling. In this study, we find that Phototrophicus methaneseepsis ZRK33 isolated from deep-sea sediment has a heterotrophic lifestyle and can assimilate sulfate and thiosulfate. Using combined physiological, genomic, proteomic, and in situ transcriptomic methods, we find that strain ZRK33 can perform assimilatory sulfate reduction in both laboratory and deep-sea conditions. Metabolism of sulfate or thiosulfate by strain ZRK33 significantly promotes the transport and degradation of various macromolecules and thereby stimulates the energy production. In addition, metagenomic results show that genes associated with assimilatory and dissimilatory sulfate reduction are ubiquitously distributed in the metagenome-assembled genomes of Chloroflexota members derived from deep-sea sediments. Metatranscriptomic results also show that the expression levels of related genes are upregulated, strongly suggesting that Chloroflexota bacteria may play undocumented roles in deep-sea sulfur cycling.

IMPORTANCE: The cycling of sulfur is one of Earth's major biogeochemical processes and is closely related to the energy metabolism of microorganisms living in the deep-sea cold seep and hydrothermal vents. To date, some of the members of Chloroflexota are proposed to play a previously unrecognized role in sulfur cycling. However, the sulfur metabolic characteristics of deep-sea Chloroflexota bacteria have never been reported, and remain to be verified in cultured deep-sea representatives. Here, we show that the deep-sea Chloroflexota bacterium ZRK33 can perform sulfate assimilation in both laboratory and deep-sea conditions, which expands our knowledge of the sulfur metabolic potential of deep-sea Chloroflexota bacteria. We also show that the genes associated with assimilatory and dissimilatory sulfate reduction ubiquitously distribute in the deep-sea Chloroflexota members, providing hints to the roles of Chloroflexota bacteria in deep-sea sulfur biogeochemical cycling.}, } @article {pmid38415986, year = {2024}, author = {Genitsaris, S and Stefanidou, N and Hatzinikolaou, D and Kourkoutmani, P and Michaloudi, E and Voutsa, D and Gros, M and García-Gómez, E and Petrović, M and Ntziachristos, L and Moustaka-Gouni, M}, title = {Marine Microbiota Responses to Shipping Scrubber Effluent Assessed at Community Structure and Function Endpoints.}, journal = {Environmental toxicology and chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1002/etc.5834}, pmid = {38415986}, issn = {1552-8618}, support = {874990//Horizon 2020 Framework Programme/ ; }, abstract = {The use of novel high-throughput sequencing (HTS) technologies to examine the responses of natural multidomain microbial communities to scrubber effluent discharges to the marine environment is still limited. Thus, we applied metabarcoding sequencing targeting the planktonic unicellular eukaryotic and prokaryotic fraction (phytoplankton, bacterioplankton, and protozooplankton) in mesocosm experiments with natural microbial communities from a polluted and an unpolluted site. Furthermore, metagenomic analysis revealed changes in the taxonomic and functional dominance of multidomain marine microbial communities after scrubber effluent additions. The results indicated a clear shift in the microbial communities after such additions, which favored bacterial taxa with known oil and polycyclic aromatic hydrocarbons (PAHs) biodegradation capacities. These bacteria exhibited high connectedness with planktonic unicellular eukaryotes employing variable trophic strategies, suggesting that environmentally relevant bacteria can influence eukaryotic community structure. Furthermore, Clusters of Orthologous Genes associated with pathways of PAHs and monocyclic hydrocarbon degradation increased in numbers at treatments with high scrubber effluent additions acutely. These genes are known to express enzymes acting at various substrates including PAHs. These indications, in combination with the abrupt decrease in the most abundant PAHs in the scrubber effluent below the limit of detection-much faster than their known half-lives-could point toward a bacterioplankton-initiated rapid ultimate biodegradation of the most abundant toxic contaminants of the scrubber effluent. The implementation of HTS could be a valuable tool to develop multilevel biodiversity indicators of the scrubber effluent impacts on the marine environment, which could lead to improved impact assessment. Environ Toxicol Chem 2024;00:1-18. © 2024 The Authors. Environmental Toxicology and Chemistry published by Wiley Periodicals LLC on behalf of SETAC.}, } @article {pmid38415779, year = {2024}, author = {Bai, L and Paek, J and Shin, Y and Kim, H and Kim, SH and Shin, JH and Kook, JK and Chang, YH}, title = {Aerococcus kribbianus sp. nov., a facultatively anaerobic bacterium isolated from pig faeces.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {74}, number = {2}, pages = {}, doi = {10.1099/ijsem.0.006284}, pmid = {38415779}, issn = {1466-5034}, abstract = {Two cocci-shaped, facultatively anaerobic, Gram-positive bacteria isolated from the faeces of a pig were designated as strains YH-aer221[T] and YH-aer222. Analysis of the 16S rRNA gene sequences revealed that the isolates were most closely related to Aerococcus suis JCM 18035[T] with 96.6 % similarity. The multi-locus sequence tree revealed that the isolates formed a sub-cluster adjacent to A. suis JCM 18035[T]. The average nucleotide identity values for the isolates and their most closely related strains were 71.8 and 71.7 %, respectively; and the digital DNA-DNA hybridization values for the isolates and their most closely related strains were 25.6 and 25.5 %, respectively. The main fatty acids were C18 : 1ω9c, C16 : 0 and C18 : 0. The cell wall contained the meso-diaminopimelic acid-based peptidoglycan. The two isolates shared the same metabolic pathways. Isolates YH-aer221[T] and YH-aer222 harboured the same CRISPR array with 33 and 46 spacers, respectively. Single-genome vs. metagenome analysis showed that the genomes of the isolates were not found in the available metagenome database. Given their chemotaxonomic, phenotypic and phylogenetic properties, YH-aer221[T] (= KCTC 25571[T]=JCM 35699[T]) and YH-aer222 (=KCTC 25573=JCM 35700) represent a novel taxon. The name Aerococcus kribbianus sp. nov. is proposed.}, } @article {pmid38415690, year = {2024}, author = {Minami, S and Kotaki, T and Sakai, Y and Okamura, S and Torii, S and Ono, C and Motooka, D and Hamajima, R and Nouda, R and Nurdin, JA and Yamasaki, M and Kanai, Y and Ebina, H and Maeda, Y and Okamoto, T and Tachibana, T and Matsuura, Y and Kobayashi, T}, title = {Vero cell-adapted SARS-CoV-2 strain shows increased viral growth through furin-mediated efficient spike cleavage.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0285923}, doi = {10.1128/spectrum.02859-23}, pmid = {38415690}, issn = {2165-0497}, abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) utilizes several host proteases to cleave the spike (S) protein to enter host cells. SARS-CoV-2 S protein is cleaved into S1 and S2 subunits by furin, which is closely involved in the pathogenicity of SARS-CoV-2. However, the effects of the modulated protease cleavage activity due to S protein mutations on viral replication and pathogenesis remain unclear. Herein, we serially passaged two SARS-CoV-2 strains in Vero cells and characterized the cell-adapted SARS-CoV-2 strains in vitro and in vivo. The adapted strains showed high viral growth, effective S1/S2 cleavage of the S protein, and low pathogenicity compared with the wild-type strain. Furthermore, the viral growth and S1/S2 cleavage were enhanced by the combination of the Δ68-76 and H655Y mutations using recombinant SARS-CoV-2 strains generated by the circular polymerase extension reaction. The recombinant SARS-CoV-2 strain, which contained the mutation of the adapted strain, showed increased susceptibility to the furin inhibitor, suggesting that the adapted SARS-CoV-2 strain utilized furin more effectively than the wild-type strain. Pathogenicity was attenuated by infection with effectively cleaved recombinant SARS-CoV-2 strains, suggesting that the excessive cleavage of the S proteins decreases virulence. Finally, the high-growth-adapted SARS-CoV-2 strain could be used as the seed for a low-cost inactivated vaccine; immunization with this vaccine can effectively protect the host from SARS-CoV-2 variants. Our findings provide novel insights into the growth and pathogenicity of SARS-CoV-2 in the evolution of cell-cell transmission.IMPORTANCEThe efficacy of the S protein cleavage generally differs among the SARS-CoV-2 variants, resulting in distinct viral characteristics. The relationship between a mutation and the entry of SARS-CoV-2 into host cells remains unclear. In this study, we analyzed the sequence of high-growth Vero cell-adapted SARS-CoV-2 and factors determining the enhancement of the growth of the adapted virus and confirmed the characteristics of the adapted strain by analyzing the recombinant SARS-CoV-2 strain. We successfully identified mutations Δ68-76 and H655Y, which enhance viral growth and the S protein cleavage by furin. Using recombinant viruses enabled us to conduct a virus challenge experiment in vivo. The pathogenicity of SARS-CoV-2 introduced with the mutations Δ68-76, H655Y, P812L, and Q853L was attenuated in hamsters, indicating the possibility of the attenuation of excessive cleaved SARS-CoV-2. These findings provide novel insights into the infectivity and pathogenesis of SARS-CoV-2 strains, thereby significantly contributing to the field of virology.}, } @article {pmid38415636, year = {2024}, author = {Stewart, RD and Myers, KS and Amstadt, C and Seib, M and McMahon, KD and Noguera, DR}, title = {Refinement of the "Candidatus Accumulibacter" genus based on metagenomic analysis of biological nutrient removal (BNR) pilot-scale plants operated with reduced aeration.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0118823}, doi = {10.1128/msystems.01188-23}, pmid = {38415636}, issn = {2379-5077}, abstract = {Members of the "Candidatus Accumulibacter" genus are widely studied as key polyphosphate-accumulating organisms (PAOs) in biological nutrient removal (BNR) facilities performing enhanced biological phosphorus removal (EBPR). This diverse lineage includes 18 "Ca. Accumulibacter" species, which have been proposed based on the phylogenetic divergence of the polyphosphate kinase 1 (ppk1) gene and genome-scale comparisons of metagenome-assembled genomes (MAGs). Phylogenetic classification based on the 16S rRNA genetic marker has been difficult to attain because most "Ca. Accumulibacter" MAGs are incomplete and often do not include the rRNA operon. Here, we investigate the "Ca. Accumulibacter" diversity in pilot-scale treatment trains performing BNR under low dissolved oxygen (DO) conditions using genome-resolved metagenomics. Using long-read sequencing, we recovered medium- and high-quality MAGs for 5 of the 18 "Ca. Accumulibacter" species, all with rRNA operons assembled, which allowed a reassessment of the 16S rRNA-based phylogeny of this genus and an analysis of phylogeny based on the 23S rRNA gene. In addition, we recovered a cluster of MAGs that based on 16S rRNA, 23S rRNA, ppk1, and genome-scale phylogenetic analyses do not belong to any of the currently recognized "Ca. Accumulibacter" species for which we propose the new species designation "Ca. Accumulibacter jenkinsii" sp. nov. Relative abundance evaluations of the genus across all pilot plant operations revealed that regardless of the operational mode, "Ca. A. necessarius" and "Ca. A. propinquus" accounted for more than 40% of the "Ca. Accumulibacter" community, whereas the newly proposed "Ca. A. jenkinsii" accounted for about 5% of the "Ca. Accumulibacter" community.IMPORTANCEOne of the main drivers of energy use and operational costs in activated sludge processes is the amount of oxygen provided to enable biological phosphorus and nitrogen removal. Wastewater treatment facilities are increasingly considering reduced aeration to decrease energy consumption, and whereas successful BNR has been demonstrated in systems with minimal aeration, an adequate understanding of the microbial communities that facilitate nutrient removal under these conditions is still lacking. In this study, we used genome-resolved metagenomics to evaluate the diversity of the "Candidatus Accumulibacter" genus in pilot-scale plants operating with minimal aeration. We identified the "Ca. Accumulibacter" species enriched under these conditions, including one novel species for which we propose "Ca. Accumulibacter jenkinsii" sp. nov. as its designation. Furthermore, the MAGs obtained for five additional "Ca. Accumulibacter" species further refine the phylogeny of the "Ca. Accumulibacter" genus and provide new insight into its diversity within unconventional biological nutrient removal systems.}, } @article {pmid38415089, year = {2024}, author = {Jhaveri, TA and Weiss, ZF and Winkler, ML and Pyden, AD and Basu, SS and Pecora, ND}, title = {A decade of clinical microbiology: top 10 advances in 10 years: what every infection preventionist and antimicrobial steward should know.}, journal = {Antimicrobial stewardship & healthcare epidemiology : ASHE}, volume = {4}, number = {1}, pages = {e8}, pmid = {38415089}, issn = {2732-494X}, abstract = {The past 10 years have brought paradigm-shifting changes to clinical microbiology. This paper explores the top 10 transformative innovations across the diagnostic spectrum, including not only state of the art technologies but also preanalytic and post-analytic advances. Clinical decision support tools have reshaped testing practices, curbing unnecessary tests. Innovations like broad-range polymerase chain reaction and metagenomic sequencing, whole genome sequencing, multiplex molecular panels, rapid phenotypic susceptibility testing, and matrix-assisted laser desorption ionization time-of-flight mass spectrometry have all expanded our diagnostic armamentarium. Rapid home-based testing has made diagnostic testing more accessible than ever. Enhancements to clinician-laboratory interfaces allow for automated stewardship interventions and education. Laboratory restructuring and consolidation efforts are reshaping the field of microbiology, presenting both opportunities and challenges for the future of clinical microbiology laboratories. Here, we review key innovations of the last decade.}, } @article {pmid38414826, year = {2024}, author = {Ahsan, A and Wagner, D and Varaljay, VA and Roman, V and Kelley-Loughnane, N and Reuel, NF}, title = {Screening putative polyester polyurethane degrading enzymes with semi-automated cell-free expression and nitrophenyl probes.}, journal = {Synthetic biology (Oxford, England)}, volume = {9}, number = {1}, pages = {ysae005}, pmid = {38414826}, issn = {2397-7000}, abstract = {Cell-free expression (CFE) has shown recent utility in prototyping enzymes for discovery efforts. In this work, CFE is demonstrated as an effective tool to screen putative polyester polyurethane degrading enzyme sequences sourced from metagenomic analysis of biofilms prospected on aircraft and vehicles. An automated fluid handler with a controlled temperature block is used to assemble the numerous 30 µL CFE reactions to provide more consistent results over human assembly. In sum, 13 putative hydrolase enzymes from the biofilm organisms as well as a previously verified, polyester-degrading cutinase were expressed using in-house E. coli extract and minimal linear templates. The enzymes were then tested for esterase activity directly in extract using nitrophenyl conjugated substrates, showing highest sensitivity to shorter substrates (4-nitrophenyl hexanoate and 4-nNitrophenyl valerate). This screen identified 10 enzymes with statistically significant activities against these substrates; however, all were lower in measured relative activity, on a CFE volume basis, to the established cutinase control. This approach portends the use of CFE and reporter probes to rapidly prototype, screen and design for synthetic polymer degrading enzymes from environmental consortia. Graphical Abstract.}, } @article {pmid38414799, year = {2024}, author = {Chen, J and Guo, J and Lu, X and Yin, D and Zhou, C and Li, Y and Zhou, X}, title = {Microbiome-friendly PS/PVP electrospun fibrous membrane with antibiofilm properties for dental engineering.}, journal = {Regenerative biomaterials}, volume = {11}, number = {}, pages = {rbae011}, pmid = {38414799}, issn = {2056-3418}, abstract = {Dental caries is one of the most prevalent and biofilm-associated oral diseases in humans. Streptococcus mutans, with a high ability to form biofilms by adhering to hard surfaces, has been established as an important etiological agent for dental caries. Therefore, it is crucial to find a way to prevent the formation of cariogenic biofilm. Here, we report an electrospun fibrous membrane that could inhibit the adhesion and biofilm formation of S. mutans. Also, the polystyrene (PS)/polyvinyl pyrrolidone (PVP) electrospun fibrous membrane altered the 3D biofilm architecture and decreased water-insoluble extracellular polysaccharide production. Notably, the anti-adhesion mechanism which laid in Coulomb repulsion between the negatively charged PS/PVP electrospun fibrous membrane and S. mutans was detected by zeta potential. Furthermore, metagenomics sequencing analysis and CCK-8 assay indicated that PS/PVP electrospun fibrous membrane was microbiome-friendly and displayed no influence on the cell viability of human gingival epithelial cells and human oral keratinocytes. Moreover, an in vitro simulation experiment demonstrated that PS/PVP electrospun fibrous membrane could decrease colony-forming unit counts of S. mutans effectively, and PS/PVP electrospun fibrous membrane carrying calcium fluoride displayed better anti-adhesion ability than that of PS/PVP electrospun fibrous membrane alone. Collectively, this research showed that the PS/PVP electrospun fibrous membrane has potential applications in controlling and preventing dental caries.}, } @article {pmid38414785, year = {2024}, author = {Deng, Y and Zhang, H and Lu, J and Zhou, Z and Zhang, T and Cui, X}, title = {Whipple's disease of the respiratory system: A case report.}, journal = {Experimental and therapeutic medicine}, volume = {27}, number = {4}, pages = {133}, pmid = {38414785}, issn = {1792-1015}, abstract = {Whipple's disease (WD) is a multiple-system chronic disease caused by Tropheryma whipplei (T. whipplei) infection. The present study describes 3 cases of WD with clinical manifestations of cough, chest pain, headache, dyspnea, sputum, joint pain, abdominal pain, diarrhea and weight loss. Chest computed tomography (CT) showed signs of plaques, nodules and pleural thickening; and bronchoscopic alveolar lavage fluid metagenomic-sequencing indicated that it was T. whipplei. One patient was treated with meropenem as the starting regimen and two patients were treated with ceftriaxone as the starting regimen. Furthermore, two patients were provided with a maintenance regimen of cotrimoxazole and one was given a maintenance regimen of minocycline, which was combined with meropenem and ceftriaxone in order to improve their cough, chest pain, headache and dyspnea symptoms. To the best of our knowledge, there are few reports on WD of the respiratory system caused by T. whipplei, and differential diagnosis is the key to clinical diagnosis. When WD of the respiratory system is difficult to diagnose, metagenomic second-generation sequencing (mNGS) may be a better choice, which can achieve early diagnosis and early treatment. However, its clinical value is still limited; therefore, more research needs to be conducted in the future.}, } @article {pmid38414771, year = {2024}, author = {Song, R and Zhu, WZ and Li, H and Wang, H}, title = {Impact of wine-grape continuous cropping on soil enzyme activity and the composition and function of the soil microbial community in arid areas.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1348259}, pmid = {38414771}, issn = {1664-302X}, abstract = {INTRODUCTION: Continuous cropping affected the stability of soil enzyme activity and the structural characteristics of microbial community. Owing to challenges in the study of complex rhizosphere microbial communities, the composition and function of these microbial communities in farmland ecosystems remain elusive. Here, we studied the microbial communities of the rhizosphere of wine grapes with different years of continuous cropping and investigated their relationships with soil enzyme activity.

METHODS: Metagenomic sequencing was conducted on the rhizosphere soils from one uncultivated wasteland and four vineyards with varying durations of continuous cropping.

RESULTS: The predominant microbial were bacteria (98.39%), followed by archaea (1.15%) and eukaryotes (0.45%). Continuous cropping caused a significant increase in the relative abundance of Rhizobiales and Micrococcales but a marked decrease in Solirubrobacterales. At the genus level, 75, 88, 65, 132, and 128 microbial genera were unique to uncultivated wasteland, 5, 10, 15, and 20 years of continuous cropping, respectively. The relative abundance of genes with signal transduction function was the highest. The activity of all enzymes measured in this study peaked at 5 years of continuous cropping, and then decreased with 10 to 15 year of continuous cropping, but increased at 20 years again. In addition, soil enzyme activity, especially of alkaline phosphatase was significantly correlated with the diversity of the dominant microorganisms at the genus level. Moreover, the coupled enzyme activities had a greater impact on the diversity of the microbial community than that of individual enzymes.

CONCLUSION: Our findings reveal the composition and function of the soil microbial communities and enzymes activity in response to changes in cropping years, which has important implications for overcoming continuous cropping obstacles and optimizing land use.}, } @article {pmid38414757, year = {2024}, author = {Zhang, Y and Gong, H and Zhu, D and Lu, D and Zhou, S and Wang, Y and Dai, X}, title = {A two-stage partial nitritation-denitritation/anammox (PN-DN/A) process to treat high-solid anaerobic digestion (HSAD) reject water: Verification based on pilot-scale and full-scale projects.}, journal = {Water research X}, volume = {22}, number = {}, pages = {100213}, pmid = {38414757}, issn = {2589-9147}, abstract = {High-solid anaerobic digestion (HSAD) reject water, distinguished by elevated levels of chemical oxygen demand (COD), NH4[+]-N and an imbalanced COD/TIN, presents a significant challenge for treatment through conventional partial nitritation/ anammox (PN/A) process. This study introduced a revised two-stage PN/A process, namely partial nitritation/denitritation-anammox (PN-DN/A) process. Its effectiveness was investigated through both pilot-scale (12 t/d) and full-scale (400 t/d) operations, showcasing stable operation with an impressive total removal rate of over 90 % for total inorganic nitrogen (TIN) and exceeding 60 % for COD. Notably, 30 % of TIN was eliminated through heterotrophic denitritation in partial nitritation-denitritation (PN-DN) stage, while approximately 55 % of TIN removal occurred in the anammox stage with anaerobic ammonium oxidizing bacteria (AnAOB) enrichment (Candidatus Kuenenia, 25.9 % and 26.6 % relative abundance for pilot and full scale). In the PN-DN stage, aerobic-anaerobic alternation promoted organics elimination (around 50 % COD) and balanced nitrogen species. Microbial and metagenomic analysis verified the coupling between autotrophic and heterotrophic denitritation and demonstrated that PN-DN stage acted as a protective buffer for anammox stage. This comprehensive study highlights the PN-DN/A process's efficacy in stably treating HSAD reject water.}, } @article {pmid38414398, year = {2024}, author = {Kim, MG and Kim, S and Jeon, JY and Moon, SJ and Kwak, YG and Na, JY and Lee, S and Park, KM and Kim, HJ and Lee, SM and Choi, SY and Shin, KH}, title = {Profiling of endogenous metabolites and changes in intestinal microbiota distribution after GEN-001 (Lactococcus lactis) administration.}, journal = {The Korean journal of physiology & pharmacology : official journal of the Korean Physiological Society and the Korean Society of Pharmacology}, volume = {28}, number = {2}, pages = {153-164}, doi = {10.4196/kjpp.2024.28.2.153}, pmid = {38414398}, issn = {1226-4512}, abstract = {This study aimed to identify metabolic biomarkers and investigate changes in intestinal microbiota in the feces of healthy participants following administration of Lactococcus lactis GEN-001. GEN-001 is a single-strain L. lactis strain isolated from the gut of a healthy human volunteer. The study was conducted as a parallel, randomized, phase 1, open design trial. Twenty healthy Korean males were divided into five groups according to the GEN-001 dosage and dietary control. Groups A, B, C, and D1 received 1, 3, 6, and 9 GEN-001 capsules (1 × 10[11] colony forming units), respectively, without dietary adjustment, whereas group D2 received 9 GEN-001 capsules with dietary adjustment. All groups received a single dose. Fecal samples were collected 2 days before GEN-001 administration to 7 days after for untargeted metabolomics and gut microbial metagenomic analyses; blood samples were collected simultaneously for immunogenicity analysis. Levels of phenylalanine, tyrosine, cholic acid, deoxycholic acid, and tryptophan were significantly increased at 5-6 days after GEN-001 administration when compared with predose levels. Compared with predose, the relative abundance (%) of Parabacteroides and Alistipes significantly decreased, whereas that of Lactobacillus and Lactococcus increased; Lactobacillus and tryptophan levels were negatively correlated. A single administration of GEN-001 shifted the gut microbiota in healthy volunteers to a more balanced state as evidenced by an increased abundance of beneficial bacteria, including Lactobacillus, and higher levels of the metabolites that have immunogenic properties.}, } @article {pmid38414315, year = {2024}, author = {Torma, F and Kerepesi, C and Jókai, M and Babszki, G and Koltai, E and Ligeti, B and Kalcsevszki, R and McGreevy, KM and Horvath, S and Radák, Z}, title = {Alterations of the gut microbiome are associated with epigenetic age acceleration and physical fitness.}, journal = {Aging cell}, volume = {}, number = {}, pages = {e14101}, doi = {10.1111/acel.14101}, pmid = {38414315}, issn = {1474-9726}, support = {RRF-2.3.1-21-2022-00004//European Union/ ; 126823//Ministry of Innovation and Technology National Excellence Program/ ; OTKA142192//National Research, Development and Innovation Office/ ; OTKA146113//National Research, Development and Innovation Office/ ; TKP2021-EGA-37//Hungarian University Sport Science, Innovation and Technology Ministry, Hungary/ ; 2021-28//National Academy of Science, Hungary/ ; }, abstract = {Epigenetic clocks can measure aging and predict the incidence of diseases and mortality. Higher levels of physical fitness are associated with a slower aging process and a healthier lifespan. Microbiome alterations occur in various diseases and during the aging process, yet their relation to epigenetic clocks is not explored. To fill this gap, we collected metagenomic (from stool), epigenetic (from blood), and exercise-related data from physically active individuals and, by applying epigenetic clocks, we examined the relationship between gut flora, blood-based epigenetic age acceleration, and physical fitness. We revealed that an increased entropy in the gut microbiome of physically active middle-aged/old individuals is associated with accelerated epigenetic aging, decreased fitness, or impaired health status. We also observed that a slower epigenetic aging and higher fitness level can be linked to altered abundance of some bacterial species often linked to anti-inflammatory effects. Overall our data suggest that alterations in the microbiome can be associated with epigenetic age acceleration and physical fitness.}, } @article {pmid38414254, year = {2024}, author = {Workman, AM and Harhay, GP and Groves, JT and Vander Ley, BL}, title = {Two bovine hepacivirus genome sequences from U.S. cattle.}, journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc}, volume = {}, number = {}, pages = {10406387231225656}, doi = {10.1177/10406387231225656}, pmid = {38414254}, issn = {1943-4936}, abstract = {Bovine hepacivirus (BoHV) is closely related to the hepatitis C virus (HCV) in humans and can cause both acute and chronic liver infections in cattle. BoHV was first identified in Ghana and Germany in 2015 and since then it has been detected and characterized in other countries around the world, but no strains have been sequenced from U.S. cattle. To date, BoHV has been classified into 2 genotypes (1 and 2), with genotype 1 being further divided into 11 subtypes (A-K). However, the true genetic diversity of BoHV is likely underestimated given limited surveillance and a lack of published genome sequences. Here, we sequenced 2 nearly complete BoHV genomes from serum samples collected in 2019 from beef cattle in Missouri. Sequence comparisons and phylogenetic analysis showed that isolate MARC/2019/60 had high sequence homology with genotype 1, subtype E isolates from China. In contrast, isolate MARC/2019/50 represented a novel BoHV subtype within genotype 2. Thus, we report the first genomic characterization of BoHV isolates from U.S. cattle, and the second complete BoHV2 genome worldwide. This work increases our knowledge of the global genetic diversity of BoHV and demonstrates the co-circulation of divergent BoHV strains in U.S. cattle.}, } @article {pmid38414095, year = {2024}, author = {Mücke, MM and Hernández-Tejero, M and Gu, W and Kuhn, M and Janz, M and Keller, MI and Fullam, A and Altepeter, L and Mücke, VT and Finkelmeier, F and Schwarzkopf, KM and Cremonese, C and Hunyady, PM and Heilani, MW and Uschner, FE and Schierwagen, R and Brol, MJ and Fischer, J and Klein, S and Peiffer, KH and Hogardt, M and Shoaie, S and Coenraad, MJ and Bojunga, J and Arroyo, V and Zeuzem, S and Kempf, VAJ and Welsch, C and Laleman, W and Bork, P and Fernandez, J and Trebicka, J and , }, title = {Terlipressin therapy is associated with increased risk of colonisation with multidrug-resistant bacteria in patients with decompensated cirrhosis.}, journal = {Alimentary pharmacology & therapeutics}, volume = {}, number = {}, pages = {}, doi = {10.1111/apt.17899}, pmid = {38414095}, issn = {1365-2036}, support = {DECISION (project ID 847949)//the European Union's Horizon 2020 research and innovation program/ ; GALAXY (project ID 668031)//the European Union's Horizon 2020 research and innovation program/ ; IHMCSA (project ID 964590)//the European Union's Horizon 2020 research and innovation program/ ; LIVERHOPE (project ID 731875)//the European Union's Horizon 2020 research and innovation program/ ; MICROB-PREDICT (project ID 825694)//the European Union's Horizon 2020 research and innovation program/ ; ACLF-I cluster//Hessian Ministry of Higher Education, Research and the Arts (HMWK)/ ; DEEP-HCC//German Federal Ministry of Education and Research (BMBF)/ ; 403224013-SFB 1382 (A09)//Deutsche Forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: Patients with cirrhosis are susceptible to develop bacterial infections that trigger acute decompensation (AD) and acute-on-chronic liver failure (ACLF). Infections with multidrug-resistant organisms (MDRO) are associated with deleterious outcome. MDRO colonisation frequently proceeds MDRO infections and antibiotic therapy has been associated with MDRO colonisation.

AIM: The aim of the study was to assess the influence of non-antibiotic medication contributing to MDRO colonisation.

METHODS: Three hundred twenty-four patients with AD and ACLF admitted to the ICU of Frankfurt University Hospital with MDRO screening were included. Regression models were performed to identify drugs associated with MDRO colonisation. Another cohort (n = 129) from Barcelona was included to validate. A third multi-centre cohort (n = 203) with metagenomic sequencing data of stool was included to detect antibiotic resistance genes.

RESULTS: A total of 97 patients (30%) were identified to have MDRO colonisation and 35 of them (11%) developed MDRO infection. Patients with MDRO colonisation had significantly higher risk of MDRO infection than those without (p = 0.0098). Apart from antibiotic therapy (odds ratio (OR) 2.91, 95%-confidence interval (CI) 1.82-4.93, p < 0.0001), terlipressin therapy in the previous 14 days was the only independent covariate associated with MDRO colonisation in both cohorts, the overall (OR 9.47, 95%-CI 2.96-30.23, p < 0.0001) and after propensity score matching (OR 5.30, 95%-CI 1.22-23.03, p = 0.011). In the second cohort, prior terlipressin therapy was a risk factor for MDRO colonisation (OR 2.49, 95% CI 0.911-6.823, p = 0.075) and associated with risk of MDRO infection during follow-up (p = 0.017). The validation cohort demonstrated that antibiotic inactivation genes were significantly associated with terlipressin administration (p = 0.001).

CONCLUSIONS: Our study reports an increased risk of MDRO colonisation in patients with AD or ACLF, who recently received terlipressin therapy, while other commonly prescribed non-antibiotic co-medications had negligible influence. Future prospective trials are needed to confirm these results.}, } @article {pmid38413777, year = {2024}, author = {Lemane, T and Lezzoche, N and Lecubin, J and Pelletier, E and Lescot, M and Chikhi, R and Peterlongo, P}, title = {Indexing and real-time user-friendly queries in terabyte-sized complex genomic datasets with kmindex and ORA.}, journal = {Nature computational science}, volume = {4}, number = {2}, pages = {104-109}, pmid = {38413777}, issn = {2662-8457}, support = {ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-22-CE45-0007//Agence Nationale de la Recherche (French National Research Agency)/ ; PIA/ANR16-CONV-0005//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-P3IA-0001//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-19-CE45-0008//Agence Nationale de la Recherche (French National Research Agency)/ ; 956229//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; 872539//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 Marie Skłodowska-Curie Actions (H2020 Excellent Science - Marie Skłodowska-Curie Actions)/ ; }, abstract = {Public sequencing databases contain vast amounts of biological information, yet they are largely underutilized as it is challenging to efficiently search them for any sequence(s) of interest. We present kmindex, an approach that can index thousands of metagenomes and perform sequence searches in a fraction of a second. The index construction is an order of magnitude faster than previous methods, while search times are two orders of magnitude faster. With negligible false positive rates below 0.01%, kmindex outperforms the precision of existing approaches by four orders of magnitude. Here we demonstrate the scalability of kmindex by successfully indexing 1,393 marine seawater metagenome samples from the Tara Oceans project. Additionally, we introduce the publicly accessible web server Ocean Read Atlas, which enables real-time queries on the Tara Oceans dataset.}, } @article {pmid38413544, year = {2024}, author = {Remesh, AT and Viswanathan, R}, title = {CrAss-Like Phages: From Discovery in Human Fecal Metagenome to Application as a Microbial Source Tracking Marker.}, journal = {Food and environmental virology}, volume = {}, number = {}, pages = {}, pmid = {38413544}, issn = {1867-0342}, abstract = {CrAss-like phages are a diverse group of bacteriophages genetically similar to the prototypical crAssphage (p-crAssphage), which was discovered in the human gut microbiome through a metagenomics approach. It was identified as a ubiquitous and highly abundant bacteriophage group in the gut microbiome. Initial co-occurrence analysis postulated Bacteroides spp. as the prospective bacterial host. Subsequent studies have confirmed multiple host species under Phylum Bacteroidetes and some Firmicutes. Detection of crAss-like phages in sewage-contaminated environmental water and robust correlation with enteric viruses and bacteria has culminated in their adoption as a microbial source tracking (MST) marker. Polymerase chain reaction (PCR) and real-time PCR assays have been developed utilizing the conserved genes in the p-crAssphage genome to detect human fecal contamination of different water sources, with high specificity. Numerous investigations have examined the implications of crAss-like phages in diverse disease conditions, including ulcerative colitis, obesity and metabolic syndrome, autism spectrum disorders, rheumatoid arthritis, atopic eczema, and other autoimmune disorders. These studies have unveiled associations between certain diseases and diminished abundance and diversity of crAss-like phages. This review offers insights into the diverse aspects of research on crAss-like phages, including their discovery, genomic characteristics, structure, taxonomy, isolation, molecular detection, application as an MST marker, and role as a gut microbiome modulator with consequential health implications.}, } @article {pmid38412863, year = {2024}, author = {Xu, YX and Liu, LD and Zhu, JY and Zhu, SS and Ye, BQ and Yang, JL and Huang, JY and Huang, ZH and You, Y and Li, WK and He, JL and Xia, M and Liu, Y}, title = {Alistipes indistinctus-derived hippuric acid promotes intestinal urate excretion to alleviate hyperuricemia.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2024.02.001}, pmid = {38412863}, issn = {1934-6069}, abstract = {Hyperuricemia induces inflammatory arthritis and accelerates the progression of renal and cardiovascular diseases. Gut microbiota has been linked to the development of hyperuricemia through unclear mechanisms. Here, we show that the abundance and centrality of Alistipes indistinctus are depleted in subjects with hyperuricemia. Integrative metagenomic and metabolomic analysis identified hippuric acid as the key microbial effector that mediates the uric-acid-lowering effect of A. indistinctus. Mechanistically, A. indistinctus-derived hippuric acid enhances the binding of peroxisome-proliferator-activated receptor γ (PPARγ) to the promoter of ATP-binding cassette subfamily G member 2 (ABCG2), which in turn boosts intestinal urate excretion. To facilitate this enhanced excretion, hippuric acid also promotes ABCG2 localization to the brush border membranes in a PDZ-domain-containing 1 (PDZK1)-dependent manner. These findings indicate that A. indistinctus and hippuric acid promote intestinal urate excretion and offer insights into microbiota-host crosstalk in the maintenance of uric acid homeostasis.}, } @article {pmid38412633, year = {2024}, author = {Song, B and Guo, H and Chen, Z and Xu, Q and Chen, L and Bai, X}, title = {Analysis of landfill leachate promoting efficient application of weathered coal anaerobic fermentation.}, journal = {Ecotoxicology and environmental safety}, volume = {273}, number = {}, pages = {116151}, doi = {10.1016/j.ecoenv.2024.116151}, pmid = {38412633}, issn = {1090-2414}, abstract = {This research aimed to develop a new method for clean utilization and treatment of landfill leachate and solid waste weathered coal. Landfill leachate and weathered coal were adopted for combined anaerobic fermentation for methane production. The characteristics of microbial community, mechanism of biological methane production, and utilization characteristics of fermentation broth and solid residue for co-fermentation were analyzed through metagenomics, soluble organic matter detection and thermogravimetric (TG) analysis. The obtained results revealed that combined anaerobic fermentation increased methane production by 80.1%. Syntrophomonas, Salipiger, Methanosaeta and Methanothrix were highly correlated. Gene abundances of 2-oxoacid ferredoxin oxidoreductase and enolase were increased in methane conversion pathway mainly by acetic acid. Pyruvate-ferroredoxin oxidoreductase, 2-oxoglutarate synthase and succinate dehydrogenase acetate synthase intensified electron transfer pathways among microorganisms. Fulvic acid, tyrosine and tryptophan contents were high in fermentation broth. Volatile decomposition temperature, ignition point and residual char combustion temperature of residual coal were decreased and combustion was more stable. The obtained results showed that the co-fermentation of landfill leachate and weathered coal improved biological methane gas production, degraded weathered coal and improved combustion performance, which provided a new idea for weathered coal clean utilization.}, } @article {pmid38413462, year = {2024}, author = {Choy, WH and Adler, A and Morgan-Lang, C and Gough, EK and Hallam, SJ and Manges, AR and Chew, BH and Penniston, K and Miller, A and Lange, D}, title = {Deficient butyrate metabolism in the intestinal microbiome is a potential risk factor for recurrent kidney stone disease.}, journal = {Urolithiasis}, volume = {52}, number = {1}, pages = {38}, pmid = {38413462}, issn = {2194-7236}, abstract = {Intestinal microbiome dysbiosis is a known risk factor for recurrent kidney stone disease (KSD) with prior data suggesting a role for dysfunctional metabolic pathways other than those directly utilizing oxalate. To identify alternative mechanisms, the current study analyzed differences in the metabolic potential of intestinal microbiomes of patients (n = 17) and live-in controls (n = 17) and determined their relevance to increased risk for KSD using shotgun metagenomic sequencing. We found no differences in the abundance of genes associated with known oxalate degradation pathways, supporting the notion that dysfunction in other metabolic pathways plays a role in KSD. Further analysis showed decreased abundance of key enzymes involved in butyrate biosynthesis in patient intestinal microbiomes. Furthermore, de novo construction of microbial genomes showed that the majority of genes significantly enriched in non-stone formers are affiliated with Faecalibacterium prausnitzii, a major butyrate producer. Specifically pertaining to butyrate metabolism, the majority of abundant genes mapped back to F. prausnitzii, Alistipes spp., and Akkermansia muciniphila. No differences were observed in ascorbate or glyoxylate metabolic pathways. Collectively, these data suggest that impaired bacterial-associated butyrate metabolism may be an oxalate-independent mechanism that contributes to an increased risk for recurrent KSD. This indicates that the role of the intestinal microbiome in recurrent KSD is multi-factorial, which is representative of the highly intertwined metabolic nature of this complex environment. Future bacteria-based treatments must not be restricted to targeting only oxalate metabolism.}, } @article {pmid38412016, year = {2024}, author = {Ding, Y and Yanagi, K and Yang, F and Callaway, E and Cheng, C and Hensel, ME and Menon, R and Alaniz, RC and Lee, K and Jayaraman, A}, title = {Oral supplementation of gut microbial metabolite indole-3-acetate alleviates diet-induced steatosis and inflammation in mice.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, doi = {10.7554/eLife.87458}, pmid = {38412016}, issn = {2050-084X}, support = {Ray B. Nesbitt Endowed Chair//Texas A and M University/ ; Karol Family Professorship//Tufts University/ ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD) is the most common chronic liver disease in Western countries. There is growing evidence that dysbiosis of the intestinal microbiota and disruption of microbiota-host interactions contribute to the pathology of NAFLD. We previously demonstrated that gut microbiota-derived tryptophan metabolite indole-3-acetate (I3A) was decreased in both cecum and liver of high-fat diet-fed mice and attenuated the expression of inflammatory cytokines in macrophages and Tnfa and fatty acid-induced inflammatory responses in an aryl-hydrocarbon receptor (AhR)-dependent manner in hepatocytes. In this study, we investigated the effect of orally administered I3A in a mouse model of diet-induced NAFLD. Western diet (WD)-fed mice given sugar water (SW) with I3A showed dramatically decreased serum ALT, hepatic triglycerides (TG), liver steatosis, hepatocyte ballooning, lobular inflammation, and hepatic production of inflammatory cytokines, compared to WD-fed mice given only SW. Metagenomic analysis show that I3A administration did not significantly modify the intestinal microbiome, suggesting that I3A's beneficial effects likely reflect the metabolite's direct actions on the liver. Administration of I3A partially reversed WD-induced alterations of liver metabolome and proteome, notably, decreasing expression of several enzymes in hepatic lipogenesis and β-oxidation. Mechanistically, we also show that AMP-activated protein kinase (AMPK) mediates the anti-inflammatory effects of I3A in macrophages. The potency of I3A in alleviating liver steatosis and inflammation clearly demonstrates its potential as a therapeutic modality for preventing the progression of steatosis to non-alcoholic steatohepatitis (NASH).}, } @article {pmid38411068, year = {2024}, author = {Iwaloye, OF and Michaud, B and Alloy, T and D'Souza, N and McKay, RML and Morris, P and Gura, C and Rogers, SO}, title = {Lake Erie ice is a repository of organisms.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0109423}, doi = {10.1128/mra.01094-23}, pmid = {38411068}, issn = {2576-098X}, abstract = {Organism abundance and diversity were assessed in Lake Erie ice samples using sequences derived from a combined metagenomic and metatranscriptomic analysis. The 68,417 unique sequences were from Bacteria (77.5%), Eukarya (22.3%), and Archaea (0.2%) and indicated diverse species of organisms from 32 bacterial, 8 eukaryotic, and 2 archaeal taxonomic groups.}, } @article {pmid38411061, year = {2024}, author = {Zhang, Y and Deng, Y and Wang, C and Li, S and Lau, FTK and Zhou, J and Zhang, T}, title = {Effects of operational parameters on bacterial communities in Hong Kong and global wastewater treatment plants.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0133323}, doi = {10.1128/msystems.01333-23}, pmid = {38411061}, issn = {2379-5077}, abstract = {Wastewater treatment plants (WWTPs) are indispensable biotechnology facilities for modern cities and play an essential role in modern urban infrastructure by employing microorganisms to remove pollutants in wastewater, thus protecting public health and the environment. This study conducted a 13-month bacterial community survey of six full-scale WWTPs in Hong Kong with samples of influent, activated sludge (AS), and effluent to explore their synchronism and asynchronism of bacterial community. Besides, we compared AS results of six Hong Kong WWTPs with data from 1,186 AS amplicon data in 269 global WWTPs and a 9-year metagenomic sequencing survey of a Hong Kong WWTP. Our results showed the compositions of bacterial communities varied and the bacterial community structure of AS had obvious differences across Hong Kong WWTPs. The co-occurrence analysis identified 40 pairs of relationships that existed among Hong Kong WWTPs to show solid associations between two species and stochastic processes took large proportions for the bacterial community assembly of six WWTPs. The abundance and distribution of the functional bacteria in worldwide and Hong Kong WWTPs were examined and compared, and we found that ammonia-oxidizing bacteria had more diversity than nitrite-oxidizing bacteria. Besides, Hong Kong WWTPs could make great contributions to the genome mining of microbial dark matter in the global "wanted list." Operational parameters had important effects on OTUs' abundance, such as the temperature to the genera of Tetrasphaera, Gordonia and Nitrospira. All these results obtained from this study can deepen our understanding of the microbial ecology in WWTPs and provide foundations for further studies.IMPORTANCEWastewater treatment plants (WWTPs) are an indispensable component of modern cities, as they can remove pollutants in wastewater to prevent anthropogenic activities. Activated sludge (AS) is a fundamental wastewater treatment process and it harbors a highly complex microbial community that forms the main components and contains functional groups. Unveiling "who is there" is a long-term goal of the research on AS microbiology. High-throughput sequencing provides insights into the inventory diversity of microbial communities to an unprecedented level of detail. At present, the analysis of communities in WWTPs usually comes from a specific WWTP and lacks comparisons and verification among different WWTPs. The wide-scale and long-term sampling project and research in this study could help us evaluate the AS community more accurately to find the similarities and different results for different WWTPs in Hong Kong and other regions of the world.}, } @article {pmid38411058, year = {2024}, author = {Zhou, Y and Tang, J and Du, W and Zhang, Y and Ye, B-C}, title = {Screening potential biomarkers associated with insulin resistance in high-fat diet-fed mice by integrating metagenomics and untargeted metabolomics.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0409423}, doi = {10.1128/spectrum.04094-23}, pmid = {38411058}, issn = {2165-0497}, abstract = {Insulin resistance is the primary pathophysiological basis for metabolic syndrome and type 2 diabetes. Gut microbiota and microbiota-derived metabolites are pivotal in insulin resistance. However, identifying the specific microbes and key metabolites with causal roles is a challenging task, and the underlying mechanisms require further exploration. Here, we successfully constructed a model of insulin resistance in mice induced by a high-fat diet (HFD) and screened potential biomarkers associated with insulin resistance by integrating metagenomics and untargeted metabolomics. Our findings showed a significant increase in the abundance of 30 species of Alistipes in HFD mice compared to normal diet (ND) mice, while the abundance of Desulfovibrio and Candidatus Amulumruptor was significantly lower in HFD mice than in ND mice. Non-targeted metabolomics analysis identified 21 insulin resistance-associated metabolites, originating from the microbiota or co-metabolized by both the microbiota and the host. These metabolites were primarily enriched in aromatic amino acid metabolism (tryptophan metabolism, tyrosine metabolism, and phenylalanine metabolism) and arginine biosynthesis. Further analysis revealed a significant association between the three distinct genera and 21 differentiated metabolites in the HFD and ND mice. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis of representative genomes from 12 species of the three distinct genera further revealed the functional potential in aromatic amino acid metabolism and arginine biosynthesis. This study lays the groundwork for future investigations into the mechanisms through which the gut microbiota and its metabolites impact insulin resistance.IMPORTANCEIn this study, we aim to identify the microbes and metabolites linked to insulin resistance, some of which have not been previously reported in insulin resistance-related studies. This adds a complementary dimension to existing research. Furthermore, we establish a correlation between alterations in the gut microbiota and metabolite levels. These findings serve as a foundation for identifying the causal bacterial species and metabolites. They also offer insights that guide further exploration into the mechanisms through which these factors influence host insulin resistance.}, } @article {pmid38410723, year = {2024}, author = {Zhang, H and Liao, Y and Zhu, Z and Liu, H and Li, D and Wang, S}, title = {Assistance of next-generation sequencing for diagnosis of disseminated Bacillus Calmette-Guerin disease with X-SCID in an infant: a case report and literature review.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1341236}, pmid = {38410723}, issn = {2235-2988}, abstract = {Bacille Calmette-Guérin (BCG) is a live strain of Mycobacterium bovis (M.bovis) for use as an attenuated vaccine to prevent tuberculosis (TB) infection, while it could also lead to an infection in immunodeficient patients. M.bovis could infect patients with immunodeficiency via BCG vaccination. Disseminated BCG disease (BCGosis) is extremely rare and has a high mortality rate. This article presents a case of a 3-month-old patient with disseminated BCG infection who was initially diagnosed with hemophagocytic syndrome (HPS) and eventually found to have X-linked severe combined immunodeficiency (X-SCID). M.bovis and its drug resistance genes were identified by metagenomics next-generation sequencing (mNGS) combined with targeted next-generation sequencing (tNGS) in blood and cerebrospinal fluid. Whole exome sequencing (WES) revealed a pathogenic variant in the common γ-chain gene (IL2RG), confirming X-SCID. Finally, antituberculosis therapy and umbilical cord blood transplantation were given to the patient. He was successfully cured of BCGosis, and his immune function was restored. The mNGS combined with the tNGS provided effective methods for diagnosing rare BCG infections in children. Their combined application significantly improved the sensitivity and specificity of the detection of M.bovis.}, } @article {pmid38410647, year = {2024}, author = {Zhou, Z and Wu, W and Ho, H and Wang, J and Shi, L and Davuluri, RV and Wang, Z and Liu, H}, title = {DNABERT-S: Learning Species-Aware DNA Embedding with Genome Foundation Models.}, journal = {ArXiv}, volume = {}, number = {}, pages = {}, pmid = {38410647}, issn = {2331-8422}, abstract = {Effective DNA embedding remains crucial in genomic analysis, particularly in scenarios lacking labeled data for model fine-tuning, despite the significant advancements in genome foundation models. A prime example is metagenomics binning, a critical process in microbiome research that aims to group DNA sequences by their species from a complex mixture of DNA sequences derived from potentially thousands of distinct, often uncharacterized species. To fill the lack of effective DNA embedding models, we introduce DNABERT-S, a genome foundation model that specializes in creating species-aware DNA embeddings. To encourage effective embeddings to error-prone long-read DNA sequences, we introduce Manifold Instance Mixup (MI-Mix), a contrastive objective that mixes the hidden representations of DNA sequences at randomly selected layers and trains the model to recognize and differentiate these mixed proportions at the output layer. We further enhance it with the proposed Curriculum Contrastive Learning (C$^2$LR) strategy. Empirical results on 18 diverse datasets showed DNABERT-S's remarkable performance. It outperforms the top baseline's performance in 10-shot species classification with just a 2-shot training while doubling the Adjusted Rand Index (ARI) in species clustering and substantially increasing the number of correctly identified species in metagenomics binning. The code, data, and pre-trained model are publicly available at https://github.com/Zhihan1996/DNABERT_S.}, } @article {pmid38410192, year = {2024}, author = {Lim, TW and Huang, S and Jiang, Y and Zhang, Y and Burrow, MF and McGrath, C}, title = {Characterization of pathogenic microbiome on removable prostheses with different levels of cleanliness using 2bRAD-M metagenomic sequencing.}, journal = {Journal of oral microbiology}, volume = {16}, number = {1}, pages = {2317059}, pmid = {38410192}, issn = {2000-2297}, abstract = {BACKGROUND: The microbiomes on the surface of unclean removable prostheses are complex and yet largely underexplored using metagenomic sequencing technology.

OBJECTIVES: To characterize the microbiome of removable prostheses with different levels of cleanliness using Type IIB Restriction-site Associated DNA for Microbiome (2bRAD-M) sequencing and compare the Microbial Index of Pathogenic Bacteria (MIP) between clean and unclean prostheses.

MATERIALS AND METHODS: Ninety-seven removable prostheses were classified into 'clean' and 'unclean' groups. All prosthesis plaque samples underwent 2bRAD metagenomic sequencing to characterize the species-resolved microbial composition. MIPs for clean and unclean prostheses were calculated based on the sum of the relative abundance of pathogenic bacteria in a microbiome using a reference database that contains opportunistic pathogenic bacteria and disease-associated information.

RESULTS: Beta diversity analyses based on Jaccard qualitative and Bray-Curtis quantitative distance matrices identified significant differences between the two groups (p < 0.05). There was a significant enrichment of many pathogenic bacteria in the unclean prosthesis group. The MIP for unclean prostheses (0.47 ± 0.25) was significantly higher than for clean prostheses (0.37 ± 0.29), p = 0.029.

CONCLUSIONS: The microbial community of plaque samples from 'unclean' prostheses demonstrated compositional differences compared with 'clean' prostheses. In addition, the pathogenic microbiome in the 'unclean' versus 'clean' group differed.}, } @article {pmid38409166, year = {2024}, author = {Li, X and Bei, Q and Rabiei Nematabad, M and Peng, J and Liesack, W}, title = {Time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies predominates the methanogen dynamics in Philippine rice field soil.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {39}, pmid = {38409166}, issn = {2049-2618}, support = {41977038//National Natural Science Foundation of China/ ; Collaborative Research Center SFB 987//Deutsche Forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: The final step in the anaerobic decomposition of biopolymers is methanogenesis. Rice field soils are a major anthropogenic source of methane, with straw commonly used as a fertilizer in rice farming. Here, we aimed to decipher the structural and functional responses of the methanogenic community to rice straw addition during an extended anoxic incubation (120 days) of Philippine paddy soil. The research combined process measurements, quantitative real-time PCR and RT-PCR of particular biomarkers (16S rRNA, mcrA), and meta-omics (environmental genomics and transcriptomics).

RESULTS: The analysis methods collectively revealed two major bacterial and methanogenic activity phases: early (days 7 to 21) and late (days 28 to 60) community responses, separated by a significant transient decline in microbial gene and transcript abundances and CH4 production rate. The two methanogenic activity phases corresponded to the greatest rRNA and mRNA abundances of the Methanosarcinaceae but differed in the methanogenic pathways expressed. While three genetically distinct Methanosarcina populations contributed to acetoclastic methanogenesis during the early activity phase, the late activity phase was defined by methylotrophic methanogenesis performed by a single Methanosarcina genomospecies. Closely related to Methanosarcina sp. MSH10X1, mapping of environmental transcripts onto metagenome-assembled genomes (MAGs) and population-specific reference genomes revealed this genomospecies as the key player in acetoclastic and methylotrophic methanogenesis. The anaerobic food web was driven by a complex bacterial community, with Geobacteraceae and Peptococcaceae being putative candidates for a functional interplay with Methanosarcina. Members of the Methanocellaceae were the key players in hydrogenotrophic methanogenesis, while the acetoclastic activity of Methanotrichaceae members was detectable only during the very late community response.

CONCLUSIONS: The predominant but time-shifted expression of acetoclastic and methylotrophic methanogenesis by a single Methanosarcina genomospecies represents a novel finding that expands our hitherto knowledge of the methanogenic pathways being highly expressed in paddy soils. Video Abstract.}, } @article {pmid38408616, year = {2024}, author = {Xiong, D and Zhang, X and Xu, B and Shi, M and Chen, M and Dong, Z and Zhong, J and Gong, R and Wu, C and Li, J and Wei, H and Yu, J}, title = {PHDtools: A platform for pathogen detection and multi-dimensional genetic signatures decoding to realize pathogen genomics data analyses online.}, journal = {Gene}, volume = {909}, number = {}, pages = {148306}, doi = {10.1016/j.gene.2024.148306}, pmid = {38408616}, issn = {1879-0038}, abstract = {OBJECTIVES: Facing the emerging diseases, rapid identification of the pathogen and multi-dimensional characterization of the genomic features at both isolate-level and population-level through high-throughput sequencing data can provide invaluable information to guide the development of antiviral agents and strategies. However, a user-friendly program is in urgent need for clinical laboratories without bioinformatics background to decode the complex big genomics data.

METHODS: In this study, we developed an interactive online platform named PHDtools with a total of 15 functions to analyze metagenomics data to identify the potential pathogen and decode multi-dimensional genetic signatures including intra-/inter-host variations and lineage-level variations. The platform was applied to analyze the meta-genomic data of the samples collected from the 172 imported COVID-19 cases.

RESULTS: According to the analytical results of mNGS, 27 patients were found to have the co-infections of SARS-CoV-2 with either influenza virus (n = 9) or human picobirnavirus (n = 19). Enough coverages of all the assembled SARS-CoV-2 genomes provided the sub-lineages of Omicron variant, and the number of mutations in the non-structural genes and M gene was increased, as well as the intra-host variations occurred in E and M gene were under positive selection (Ka/Ks > 1). These findings of increased or changed mutations in the SARS-CoV-2 genome characterized the current adaptive evolution patterns of Omicron sub-lineages, and revealed the evolution speed of these sub-lineages might increase.

CONCLUSIONS: Consequently, the application of PHDtools has proved that this platform is accurate, user-friendly and convenient for clinical users who are deficient in bioinformatics, and the clinical monitor of SARS-CoV-2 genomes by PHDtools also highlighted the potential evolution features of current SARS-CoV-2 and indicated that the development of anti-SARS-CoV-2 agents and new-designed vaccines should incorporate the gene variations other than S gene.}, } @article {pmid38408506, year = {2024}, author = {Ranauda, MA and Zuzolo, D and Maisto, M and Tartaglia, M and Scarano, P and Prigioniero, A and Sciarrillo, R and Guarino, C}, title = {Microplastics affect soil-plant system: Implications for rhizosphere biology and fitness of sage (Salvia officinalis L.).}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {123656}, doi = {10.1016/j.envpol.2024.123656}, pmid = {38408506}, issn = {1873-6424}, abstract = {A mesocosm experiment was set-up to investigate the effects of low-density polyethylene (LDPE) fragments deriving from plastic film on soil ecology, rhizosphere and plant (Salvia officinalis L.) fitness. The internal transcribed spacer (ITS) and 16S metagenomic analysis was adopted to evaluate taxonomic and functional shifts of both soil and rhizosphere under the influence of microplastics (MPs). Photosynthetic parameters and enzymes involved in oxidative stress were assessed to unveil the plant physiological state. MP fragments were analysed by scanning electron microscope (SEM) and metagenomics to investigate the plastisphere. Microbial biomarkers of MPs pollution were identified in soil and rhizosphere, reinforcing the concept of molecular biomonitoring. Overall, Bacillus, Nocardioides and Streptomyces genera are bacterial biomarkers of MPs pollution in soil whereas Aspergillus, Fusarium and Trichoderma genera, and Nectriaceae family are fungal biomarkers of MPs polluted soil. The data show that the presence of MPs promotes the abundance of taxa involved in the soil N cycle, but simultaneously reduces the endophytic interaction capability and enhances pathogen related functions at the rhizosphere level. A significant decrease in chlorophyll levels and increase of oxidative stress enzymes was observed in plants grown in MPs-polluted soil. The SEM observations of MPs fragments revealed a complex colonisation, where bacteria (Bacillus in MPSo and Microvirga in MPRz) and fungi (Aspergillus in MPSo and Trichoderma in MPRz) represent the main colonisers. The results demonstrate that the presence of MPs causes changes in the soil and rhizosphere microbial community and functions leading to negative effects on plant fitness.}, } @article {pmid38407923, year = {2024}, author = {Mishra, R and Modi, A and Pandit, R and Sadhwani, J and Joshi, C and Patel, AK}, title = {Cloning and characterization of FMN dependent azoreductases from textile industry effluent identified through metagenomic sequencing.}, journal = {Journal of the Air & Waste Management Association (1995)}, volume = {}, number = {}, pages = {}, doi = {10.1080/10962247.2024.2322513}, pmid = {38407923}, issn = {2162-2906}, abstract = {Azo dyes, when released untreated in the environment, cause detrimental effects on flora and fauna. Azoreductases are enzymes capable of cleaving commercially used azo dyes, sometimes in less toxic by-products which can be further degraded via synergistic microbial cometabolism. In this study, azoreductases encoded by FMN1 and FMN2 genes were screened from metagenome shotgun sequences generated from the samples of textile dye industries' effluents, cloned, expressed, and evaluated for its azo dye decolorization efficacy. At pH 7 and 45°C temperature, both recombinant enzymes, FMN1 and FMN2 were able to decolorize methyl red at 20 and 100ppm concentrations, respectively. FMN2 was found to be more efficient in decolorization/degradation of methyl red than FMN1. This study offers valuable insights into possible application of azoreductases to reduce the environmental damage caused by azo dyes, with the hope of contributing to sustainable and eco-friendly practices for the environment management. This enzymatic approach offers a promising solution for the bioremediation of textile industrial effluents. However, the study acknowledges the need for further process optimization to enhance the efficacy of these enzymes in large-scale applications.}, } @article {pmid38407781, year = {2024}, author = {Vishwakarma, A and Verma, D}, title = {16S rDNA-Based Amplicon Analysis Unveiled a Correlation Between the Bacterial Diversity and Antibiotic Resistance Genes of Bacteriome of Commercial Smokeless Tobacco Products.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {38407781}, issn = {1559-0291}, support = {UGC-BSR (F 30.442/2018/BSR)//University Grants Commission - South Eastern Regional Office/ ; }, abstract = {The distribution of bacterial-derived antibiotic resistance genes (ARGs) in smokeless tobacco products is less explored and encourages understanding of the ARG profile of Indian smokeless tobacco products. Therefore, in the present investigation, ten commercial smokeless tobacco products were assessed for their bacterial diversity to understand the correlation between the inhabitant bacteria and predicted ARGs using a 16S rDNA-based metagenome analysis. Overall analysis showed the dominance of two phyla, i.e., Firmicutes (43.07%) and Proteobacteria (8.13%) among the samples, where Bacillus (9.76%), Terribacillus (8.06%), Lysinibacillus (5.8%), Alkalibacterium (5.6%), Oceanobacillus (3.52%), and Dickeya (3.1%) like genera were prevalent among these phyla. The phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt)-based analysis revealed 217 ARGs which were categorized into nine groups. Cationic antimicrobial polypeptides (CAMP, 33.8%), vancomycin (23.4%), penicillin-binding protein (13.8%), multidrug resistance MDR (10%), and β-lactam (9.3%) were among the top five contributors to ARGs. Staphylococcus, Dickeya, Bacillus, Aerococcus, and Alkalibacterium showed their strong and significant correlation (p value < 0.05) with various antibiotic resistance mechanisms. ARGs of different classes (blaTEM, blaSHV, blaCTX, tetX, vanA, aac3-II, mcr-1, intI-1, and intI2) were also successfully amplified in the metagenomes of SMT samples using their specific primers. The prevalence of ARGs in inhabitant bacteria of smokeless tobacco products suggests making steady policies to regulate the hygiene of commercial smokeless tobacco products.}, } @article {pmid38407280, year = {2024}, author = {Sandås, K and Lewerentz, J and Karlsson, E and Karlsson, L and Sundell, D and Simonyté-Sjödin, K and Sjödin, A}, title = {Nanometa live: a user-friendly application for real-time metagenomic data analysis and pathogen identification.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btae108}, pmid = {38407280}, issn = {1367-4811}, abstract = {SUMMARY: Nanometa Live presents a user-friendly interface designed for real-time metagenomic data analysis and pathogen identification utilizing Oxford Nanopore Technologies' MinION and Flongle flow cells. It offers an efficient workflow and graphical interface for the visualization and interpretation of metagenomic data as it is being generated. Key features include automated BLAST validation, streamlined handling of custom Kraken2 databases, and a simplified graphical user interface (GUI) for enhanced user experience. Nanometa Live is particularly notable for its capability to run without constant internet or server access once installed, setting it apart from similar tools. It provides a comprehensive view of taxonomic composition and facilitates the detection of user-defined pathogens or other species of interest, catering to both researchers and clinicians.

Nanometa Live has been implemented as a local web application using the Dash framework with Snakemake handling the data processing. The source code is freely accessible on the GitHub repository at https://github.com/FOI-Bioinformatics/nanometa_live and it is easily installable using Bioconda. It includes containerization support via Docker and Singularity, ensuring ease of use, reproducibility, and portability.}, } @article {pmid38406876, year = {2024}, author = {Li, A and Liu, A and Wang, J and Song, H and Luo, P and Zhan, M and Zhou, X and Chen, L and Zhang, L}, title = {The prophylaxis functions of lactobacillus fermentum GLF-217 and lactobacillus plantarum FLP-215 on ulcerative colitis via modulating gut microbiota of mice.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.13410}, pmid = {38406876}, issn = {1097-0010}, abstract = {BACKGROUND: The strong connection between gut microbes and human health has been confirmed by an increasing number of studies. Although probiotics have been found to relieve ulcerative colitis, the mechanism varies by the species involved. In this study, the physiological, immune and pathological factors of mice were measured and shotgun metagenomic was conducted to investigate the potential mechanisms in preventing ulcerative colitis.

RESULTS: The results demonstrated that ingestion of Lactobacillus fermentum GLF-217 and Lactobacillus plantarum FLP-215 significantly alleviated ulcerative colitis induced by dextran sulfate sodium (DSS), as evidenced by the increase in body weight, food intake, water intake and colon length as well as the decreased in disease activity index, histopathological score and inflammatory factor. Both strains not only improved intestinal mucosa by increasing mucin-2 and zonula occludens-1, but also improved the immune system response by elevating interleukin-10 levels and decreasing the levels of interleukin-1β, interleukin-6, tumor necrosis factor-α and interferon-γ. Moreover, L. fermentum GLF-217 and L. plantarum FLP-215 play a role in preventing DSS-induced colitis by regulating the structure of gut microbiota and promoting the formation of short-chain fatty acids.

CONCLUSIONS: This study may provide reference for the prevention strategy of ulcerative colitis. This article is protected by copyright. All rights reserved.}, } @article {pmid38406289, year = {2024}, author = {Banar, M and Rokaya, D and Azizian, R and Khurshid, Z and Banakar, M}, title = {Oral bacteriophages: metagenomic clues to interpret microbiomes.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16947}, pmid = {38406289}, issn = {2167-8359}, abstract = {Bacteriophages are bacterial viruses that are distributed throughout the environment. Lytic phages and prophages in saliva, oral mucosa, and dental plaque interact with the oral microbiota and can change biofilm formation. The interactions between phages and bacteria can be considered a portion of oral metagenomics. The metagenomic profile of the oral microbiome indicates various bacteria. Indeed, there are various phages against these bacteria in the oral cavity. However, some other phages, like phages against Absconditabacteria, Chlamydiae, or Chloroflexi, have not been identified in the oral cavity. This review gives an overview of oral bacteriophage and used for metagenomics. Metagenomics of these phages deals with multi-drug-resistant bacterial plaques (biofilms) in oral cavities and oral infection. Hence, dentists and pharmacologists should know this metagenomic profile to cope with predental and dental infectious diseases.}, } @article {pmid38406269, year = {2024}, author = {Xiong, C and Wu, J and Ma, Y and Li, N and Wang, X and Li, Y and Ding, X}, title = {Effects of Glucagon-Like Peptide-1 Receptor Agonists on Gut Microbiota in Dehydroepiandrosterone-Induced Polycystic Ovary Syndrome Mice: Compared Evaluation of Liraglutide and Semaglutide Intervention.}, journal = {Diabetes, metabolic syndrome and obesity : targets and therapy}, volume = {17}, number = {}, pages = {865-880}, pmid = {38406269}, issn = {1178-7007}, abstract = {PURPOSE: Polycystic ovary syndrome (PCOS) is a frequent cause of infertility in reproductive-age women. Our work aims to evaluate the effects of glucagon-like peptide-1 receptor agonists (GLP-1RAs) on gut microbiota, with metabolic parameters including body weight and the hormone profile in PCOS.

PATIENTS AND METHODS: Dehydroepiandrosterone (DHEA)-induced PCOS mice were established and then treated with two GLP-1RAs: liraglutide and novel form semaglutide for four weeks. Changes in body weight and metabolic parameters were measured. Fecal samples were collected and analyzed using metagenomic sequencing.

RESULTS: Liraglutide and semaglutide modulated both alpha and beta diversity of the gut microbiota in PCOS. Liraglutide increased the Bacillota-to-Bacteroidota ratio through up-regulating the abundance of butyrate-producing members of Bacillota like Lachnospiraceae. Moreover, liraglutide showed the ability to reverse the altered microbial composition and the disrupted microbiota functions caused by PCOS. Semaglutide increased the abundance of Helicobacter in PCOS mice (p < 0.01) which was the only bacteria found negatively correlated with body weight. Moreover, pathways involving porphyrin and flavonoids were increased after semaglutide intervention.

CONCLUSION: Liraglutide and semaglutide improved reproductive and metabolic disorders by modulating the whole structure of gut microbiota in PCOS. The greater efficacy in weight loss compared with liraglutide observed after semaglutide intervention was positively related with Helicobacter. The study may provide new ideas in the treatment and the underlying mechanisms of GLP-1RAs to improve PCOS.}, } @article {pmid38405982, year = {2024}, author = {Sabsay, K and Te Velthuis, AJW}, title = {Using structure prediction of negative sense RNA virus nucleoproteins to assess evolutionary relationships.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.02.16.580771}, pmid = {38405982}, abstract = {Negative sense RNA viruses (NSV) include some of the most detrimental human pathogens, including the influenza, Ebola and measles viruses. NSV genomes consist of one or multiple single-stranded RNA molecules that are encapsidated into one or more ribonucleoprotein (RNP) complexes. Current evolutionary relationships within the NSV phylum are based on alignment of conserved RNA-dependent RNA polymerase (RdRp) domain amino acid sequences. However, the RdRp-based phylogeny does not address whether other core proteins in the NSV genome evolved along the same trajectory. Moreover, the current classification of NSVs does not consistently match the segmented and non-segmented nature of negative-sense virus genomes. Viruses belonging to e.g. the Serpentovirales have a segmented genome but are classified among the non-segmented negative-sense RNA viruses. We hypothesized that RNA genome segmentation is not coupled to the RdRp domain, but rather to the nucleocapsid protein (NP) that forms RNP complexes with the viral RNA. Because NP sequences are too short to infer robust phylogenetic relationships, we here used experimentally-obtained and AlphaFold 2.0-predicted NP structures to probe whether evolutionary relationships can be estimated using NSV NP sequences and potentially improve our understanding of the relationships between NSV subphyla and the NSV genome organization. Following flexible structure alignments of modeled structures, we find that the structural homology of the NSV NPs reveals phylogenetic clusters that are consistent with the currently accepted NSV taxonomy based on RdRp sequences with one key difference: the NPs of the segmented Serpentovirales cluster with the other segmented NSV. In addition, we were able to assign viruses for which RdRp sequences are currently missing to phylogenetic clusters. Overall, our results suggest that the NSV RdRp and NP genes largely evolved along similar trajectories, that NP-based clustering is better correlated with the NSV genome structure organization, and that even short pieces of genetic, protein-coding information can be used to infer evolutionary relationships, potentially making metagenomic analyses more valuable.}, } @article {pmid38405898, year = {2024}, author = {Tuladhar, ET and Shrestha, S and Vernon, S and Droit, L and Mihindukulasuriya, KA and Tamang, M and Karki, L and Ngono, AE and Jha, B and Awal, BK and Chalise, BS and Jha, R and Shresta, S and Wang, D and Manandhar, KD}, title = {Gemykibivirus detection in acute encephalitis patients from Nepal.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.02.13.24302648}, pmid = {38405898}, abstract = {Acute Encephalitis Syndrome (AES) causes significant morbidity and mortality worldwide. In Nepal, Japanese encephalitis virus (JEV) accounts for ∼ 5-20% of AES cases, but ∼75% of AES cases are of unknown etiology. We identified a gemykibivirus in CSF collected in 2020 from a male child with AES using metagenomic next-generation sequencing. Gemykibiviruses are single stranded, circular DNA viruses in the family Genomoviridae . The complete genome of 2211 nucleotides was sequenced which shared 98.69% nucleotide identity to its closest relative, Human associated gemykibivirus 2 isolate SAfia-449D. Two real-time PCR assays were designed, and screening of 337 CSF and 164 serum samples from AES patients in Nepal collected in 2020 and 2022 yielded 11 CSF and 1 serum sample that were positive in both PCR assays. Complete genomes of 7 of the positives were sequenced. These results identify a candidate etiologic agent of encephalitis in Nepal.}, } @article {pmid38405713, year = {2024}, author = {Hallberg, ZF and Nicolas, AM and Alvarez-Aponte, ZI and Mok, KC and Sieradzki, ET and Pett-Ridge, J and Banfield, JF and Carlson, HK and Firestone, MK and Taga, ME}, title = {Vitamin B 12 variants structure soil microbial communities despite soil's vast reservoir of B 12.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.02.12.580003}, pmid = {38405713}, abstract = {Soil microbial communities perform critical ecosystem services through the collective metabolic activities of numerous individual organisms. Most microbes use corrinoids, a structurally diverse family of cofactors related to vitamin B 12 . Corrinoid structure influences the growth of individual microbes, yet how these growth responses scale to the community level remains unknown. Analysis of metagenome-assembled genomes suggests corrinoids are supplied to the community by members of the archaeal and bacterial phyla Thermoproteota, Actinobacteria, and Proteobacteria. Corrinoids were found largely adhered to the soil matrix in a grassland soil, at levels exceeding those required by cultured bacteria. Enrichment cultures and soil microcosms seeded with different corrinoids show distinct shifts in bacterial 16S composition, supporting the hypothesis that corrinoid structure can shape communities. Environmental context influenced both community and taxon-specific responses to specific corrinoids. These results implicate corrinoids as key determinants of soil microbiome structure and suggest that environmental micronutrient reservoirs promote community stability.}, } @article {pmid38405403, year = {2024}, author = {Del Amo, LL and Durán-González, E and Ramírez-Tejero, JA and Martínez-Lara, A and Cotán, D}, title = {Corrigendum: Study protocol for FIBROKIT: a new tool for fibromyalgia diagnosis and patient follow-up.}, journal = {Frontiers in neurology}, volume = {15}, number = {}, pages = {1375764}, doi = {10.3389/fneur.2024.1375764}, pmid = {38405403}, issn = {1664-2295}, abstract = {[This corrects the article DOI: 10.3389/fneur.2023.1286539.].}, } @article {pmid38405056, year = {2024}, author = {Liu, K and Wu, L and Chen, G and Zeng, D and Zhong, Q and Luo, L and Song, B and Ying, X and Ni, F and Yu, L and Xu, L and Lin, X and Chen, X and Zou, X and Xiao, J and Hu, Y}, title = {Clinical Characteristics of Chlamydia psittaci Infection Diagnosed by Metagenomic Next-Generation Sequencing: A Retrospective Multi-Center Study in Fujian, China.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {697-708}, pmid = {38405056}, issn = {1178-6973}, abstract = {OBJECTIVE: This study aimed to describe and compare the epidemiological, demographic, clinical, laboratory and radiological characteristics as well as the complications, treatments, and outcomes of these patients.

METHODS: We retrospectively investigated clinical data of patients with C. psittaci infection (psittacosis) in eight Grade IIIA hospitals of Fujian. Metagenomic next-generation sequencing (mNGS) was used identify C. psittaci in clinical samples of all included patients.

RESULTS: A total of 74 patients (39 severe/35 non-severe) was diagnosed with psittacosis, 25 (33.8%) of whom had history of poultry exposure. Common symptoms included high fever (98% [37/74]), fatigue (52.7% [39/74]), and dyspnea (51.4% [38/74]). Common manifestations in imaging included consolidation (89.2%), pleural effusion (77.0%), and air bronchogram (66.2%). Common complications included acute respiratory distress syndrome (55.4% [41/74]), type I respiratory failure (52.7% [39/74]), acute liver injury (41.9% [31/74]), and secondary infection (27.0% [20/74]). The in-hospital mortality rate was 8.11% (6/74).

CONCLUSION: C. psittaci infection is represents an underestimated cause of CAP. For SCAP patients with poultry and bird contact history, specimens were encouraged to be sended for mNGS test in time. C. psittaci infection can lead to severe, multiple system involvement, and several complications. mNGS facilitate timely diagnosis of C. psittaci infection.}, } @article {pmid38404751, year = {2024}, author = {Williams, A and Webster, WZ and Cai, C and Milgrom, A and Al-Hasan, M and Bookstaver, PB}, title = {Evaluation of the diagnostic utility of metagenomic next-generation sequencing testing for pathogen identification in infected hosts: a retrospective cohort study.}, journal = {Therapeutic advances in infectious disease}, volume = {11}, number = {}, pages = {20499361241232854}, pmid = {38404751}, issn = {2049-9361}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) testing identifies thousands of potential pathogens in a single blood test, though data on its real-world diagnostic utility are lacking.

OBJECTIVES: Determine the diagnostic utility of mNGS testing in practice and factors associated with high clinical utility.

DESIGN: Retrospective cohort study of mNGS tests ordered from June 2018 through May 2020 at a community teaching hospital.

METHODS: Tests were included if ordered for diagnostic purposes in patients with probable or high clinical suspicion of infection. Exclusions included patient expiration, hospice care, or transfer outside of the institution. Utility criteria were established a priori by the research team. Two investigators independently reviewed each test and categorized it to either high or low diagnostic utility. Reviewer discordance was referred to a third investigator. The stepwise multiple regression method was used to identify clinical factors associated with high diagnostic utility.

RESULTS: Among 96 individual tests from 82 unique patients, 80 tests met the inclusion criteria for analysis. At least one potential pathogen was identified in 58% of tests. Among 112 pathogens identified, there were 74 bacteria, 25 viruses, 12 fungi, and 1 protozoon. In all, 46 tests (57.5%) were determined to be of high diagnostic utility. Positive mNGS tests were identified in 36 (78.3%) and 11 (32.4%) of high and low diagnostic utility tests, respectively (p < 0.001). Antimicrobials were changed after receiving test results in 31 (67.4%) of high utility tests and 4 (11.8%) of low utility tests (p < 0.0001). In the multiple regression model, a positive test [odds ratio (OR) = 10.9; 95% confidence interval (CI), 3.2-44.4] and consultation with the company medical director (OR = 3.6; 95% CI, 1.1-13.7) remained significantly associated with high diagnostic utility.

CONCLUSION: mNGS testing resulted in high clinical utility in most cases. Positive mNGS tests were associated with high diagnostic utility. Consultation with the Karius[®] medical director is recommended to maximize utility.}, } @article {pmid38404539, year = {2024}, author = {Yasir, M and Al-Zahrani, IA and Khan, R and Soliman, SA and Turkistani, SA and Alawi, M and Azhar, EI}, title = {Microbiological risk assessment and resistome analysis from shotgun metagenomics of bovine colostrum microbiome.}, journal = {Saudi journal of biological sciences}, volume = {31}, number = {4}, pages = {103957}, pmid = {38404539}, issn = {1319-562X}, abstract = {Colostrum is known for its nutraceutical qualities, probiotic attributes, and health benefits. The aim of this study was to profile colostrum microbiome from bovine in rural sites of a developing country. The focus was on microbiological safety assessments and antimicrobial resistance, taking into account the risks linked with the consumption of raw colostrum. Shotgun sequencing was employed to analyze microbiome in raw buffalo and cow colostrum. Alpha and beta diversity analyses revealed increased inter and intra-variability within colostrum samples' microbiome from both livestock species. The colostrum microbiome was mainly comprised of bacteria, with over 90% abundance, whereas fungi and viruses were found in minor abundance. Known probiotic species, such as Leuconostoc mesenteroides, Lactococcus lactis, Streptococcus thermophilus, and Lactobacillus paracasei, were found in the colostrum samples. A relatively higher number of pathogenic and opportunistic pathogenic bacteria were identified in colostrum from both animals, including clinically significant bacteria like Clostridium botulinum, Pseudomonas aeruginosa, Escherichia coli, and Listeria monocytogenes. Binning retrieved 11 high-quality metagenome-assembled genomes (MAGs), with three MAGs potentially representing novel species from the genera Psychrobacter and Pantoea. Notably, 175 antimicrobial resistance genes (ARGs) and variants were detected, with 55 of them common to both buffalo and cow colostrum metagenomes. These ARGs confer resistance against aminoglycoside, fluoroquinolone, tetracycline, sulfonamide, and peptide antibiotics. In conclusion, this study describes a thorough overview of microbial communities in buffalo and cow colostrum samples. It emphasizes the importance of hygienic processing and pasteurization in minimizing the potential transmission of harmful microorganisms linked to the consumption of colostrum.}, } @article {pmid38404538, year = {2024}, author = {Alshareef, SA}, title = {Metabolic analysis of the CAZy class glycosyltransferases in rhizospheric soil fungiome of the plant species Moringa oleifera.}, journal = {Saudi journal of biological sciences}, volume = {31}, number = {4}, pages = {103956}, pmid = {38404538}, issn = {1319-562X}, abstract = {The target of the present work is to study the most abundant carbohydrate-active enzymes (CAZymes) of glycosyltransferase (GT) class, which are encoded by fungiome genes present in the rhizospheric soil of the plant species Moringa oleifera. The datasets of this CAZy class were recovered using metagenomic whole shotgun genome sequencing approach, and the resultant CAZymes were searched against the KEGG pathway database to identify function. High emphasis was given to the two GT families, GT4 and GT2, which were the highest within GT class in the number and abundance of gene queries in this soil compartment. These two GT families harbor CAZymes playing crucial roles in cell membrane and cell wall processes. These CAZymes are responsible for synthesizing essential structural components such as cellulose and chitin, which contribute to the integrity of cell walls in plants and fungi. The CAZyme beta-1,3-glucan synthase of GT2 family accumulates 1,3-β-glucan, which provides elasticity as well as tensile strength to the fungal cell wall. Other GT CAZymes contribute to the biosynthesis of several compounds crucial for cell membrane and wall integrity, including lipopolysaccharide, e.g., lipopolysaccharide N-acetylglucosaminyltransferase, cell wall teichoic acid, e.g., alpha-glucosyltransferase, and cellulose, e.g., cellulose synthase. These compounds also play pivotal roles in ion homeostasis, organic carbon mineralization, and osmoprotection against abiotic stresses in plants. This study emphasizes the major roles of these two CAZy GT families in connecting the structure and function of cell membranes and cell walls of fungal and plant cells. The study also sheds light on the potential occurrence of tripartite symbiotic relationships involving the plant, rhizospheric bacteriome, and fungiome via the action of CAZymes of GT4 and GT2 families. These findings provide valuable insights towards the generation of innovative agricultural practices to enhance the performance of crop plants in the future.}, } @article {pmid38404111, year = {2024}, author = {Conrad, MA and Bittinger, K and Ren, Y and Kachelries, K and Vales, J and Li, H and Wu, GD and Bushman, FD and Devoto, M and Baldassano, RN and Kelsen, JR}, title = {The intestinal microbiome of inflammatory bowel disease across the pediatric age range.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2317932}, doi = {10.1080/19490976.2024.2317932}, pmid = {38404111}, issn = {1949-0984}, abstract = {Dysbiosis is associated with pediatric and adult-onset inflammatory bowel disease (IBD), but the role of dysbiosis and the microbiome in very early onset IBD (VEO-IBD) has not yet been described. Here, we aimed to demonstrate the impact of age and inflammation on microbial community structure using shotgun metagenomic sequencing in children with VEO-IBD, pediatric-onset IBD, and age-matched pediatric healthy controls (HC) observed longitudinally over the course of 8 weeks. We found disease-related differences in alpha and beta diversity between HC and children with IBD or VEO-IBD. Using a healthy microbial maturity index modeled from HC across the age range to characterize their gut microbiota, we found that children with pediatric-onset IBD and VEO-IBD had lower maturity than their age-matched HC groups, suggesting a disease effect on the microbial community. In addition, patients with pediatric IBD had significantly lower maturity than those with VEO-IBD, who had more heterogeneity at the youngest ages, highlighting differences in these two cohorts that were not captured in standard comparisons of alpha and beta diversity. These results demonstrate that young age and inflammation independently impact microbial community structure. However, the effect is not additive in the youngest patients, likely because of the heterogeneous and dynamic stool microbiome in this population.}, } @article {pmid38403655, year = {2024}, author = {Ren, Y and Chen, L and Guo, R and Ma, S and Li, S and Zhang, Y and Jiang, H and Shi, H and Zhang, P}, title = {Altered gut mycobiome in patients with end-stage renal disease and its correlations with serum and fecal metabolomes.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {202}, pmid = {38403655}, issn = {1479-5876}, support = {Program No. 2023-ZDLSF-45//Key Research and Development Projects of Shaanxi Province/ ; }, abstract = {BACKGROUND: The relationship between the gut mycobiome and end-stage renal disease (ESRD) remains largely unexplored.

METHODS: In this study, we compared the gut fungal populations of 223 ESRD patients and 69 healthy controls (HCs) based on shotgun metagenomic sequencing data, and analyzed their associations with host serum and fecal metabolites.

RESULTS: Our findings revealed that ESRD patients had a higher diversity in the gut mycobiome compared to HCs. Dysbiosis of the gut mycobiome in ESRD patients was characterized by a decrease of Saccharomyces cerevisiae and an increase in various opportunistic pathogens, such as Aspergillus fumigatus, Cladophialophora immunda, Exophiala spinifera, Hortaea werneckii, Trichophyton rubrum, and others. Through multi-omics analysis, we observed a substantial contribution of the gut mycobiome to host serum and fecal metabolomes. The opportunistic pathogens enriched in ESRD patients were frequently and positively correlated with the levels of creatinine, homocysteine, and phenylacetylglycine in the serum. The populations of Saccharomyces, including the HC-enriched Saccharomyces cerevisiae, were frequently and negatively correlated with the levels of various toxic metabolites in the feces.

CONCLUSIONS: Our results provided a comprehensive understanding of the associations between the gut mycobiome and the development of ESRD, which had important implications for guiding future therapeutic studies in this field.}, } @article {pmid38403443, year = {2024}, author = {Román-Camacho, JJ and Mauricio, JC and Santos-Dueñas, IM and García-Martínez, T and García-García, I}, title = {Recent advances in applying omic technologies for studying acetic acid bacteria in industrial vinegar production: A comprehensive review.}, journal = {Biotechnology journal}, volume = {19}, number = {2}, pages = {e2300566}, doi = {10.1002/biot.202300566}, pmid = {38403443}, issn = {1860-7314}, support = {//Universidad de Córdoba/ ; PID2021-127766OB-I00//Ministry of Science and Innovation/ ; PY20_00590//Junta de Andalucía/ ; }, abstract = {Vinegar and related bioproducts containing acetic acid as the main component are among the most appreciated fermented foodstuffs in numerous European and Asian countries because of their exceptional organoleptic and bio-healthy properties. Regarding the acetification process and obtaining of final products, there is still a lack of knowledge on fundamental aspects, especially those related to the study of biodiversity and metabolism of the present microbiota. In this context, omic technologies currently allow for the massive analysis of macromolecules and metabolites for the identification and characterization of these microorganisms working in their natural media without the need for isolation. This review approaches comprehensive research on the application of omic tools for the identification of vinegar microbiota, mainly acetic acid bacteria, with subsequent emphasis on the study of the microbial diversity, behavior, and key molecular strategies used by the predominant groups throughout acetification. The current omics tools are enabling both the finding of new vinegar microbiota members and exploring underlying strategies during the elaboration process. The species Komagataeibacter europaeus may be a model organism for present and future research in this industry; moreover, the development of integrated meta-omic analysis may facilitate the achievement of numerous of the proposed milestones. This work might provide useful guidance for the vinegar industry establishing the first steps towards the improvement of the acetification conditions and the development of new products with sensory and bio-healthy profiles adapted to the agri-food market.}, } @article {pmid38397160, year = {2024}, author = {da Fonseca, RR and Campos, PF and Rey-Iglesia, A and Barroso, GV and Bergeron, LA and Nande, M and Tuya, F and Abidli, S and Pérez, M and Riveiro, I and Carrera, P and Jurado-Ruzafa, A and G Santamaría, MT and Faria, R and Machado, AM and Fonseca, MM and Froufe, E and C Castro, LF}, title = {Population Genomics Reveals the Underlying Structure of the Small Pelagic European Sardine and Suggests Low Connectivity within Macaronesia.}, journal = {Genes}, volume = {15}, number = {2}, pages = {}, pmid = {38397160}, issn = {2073-4425}, support = {VKR023446//Villum Fonden/ ; CEECIND/00627/2017//Fundação para a Ciência e Tecnologia/ ; CEECIND/01799/2017//Fundação para a Ciência e Tecnologia/ ; 25925//Villum Fonden/ ; IN607B 2018/14//Axencia Galega de Innovacion/ ; IN607-A 2018/4//Axencia Galega de Innovacion/ ; RTI2018-099868-B-I00//Ministerio de Ciencia e Innovación/ ; PTDC/BIA-EVL/30628/2017//Programa Operacional Temático Factores de Competitividade/ ; POCI-01-0145-FEDER-030628//Programa Operacional Temático Factores de Competitividade/ ; 24517//Programa Operacional Temático Factores de Competitividade/ ; UIDB/04423/2020//European Regional Development Fund/ ; }, mesh = {Humans ; Animals ; *Metagenomics ; *Fishes/genetics ; Portugal ; Genome/genetics ; Spain ; }, abstract = {The European sardine (Sardina pilchardus, Walbaum 1792) is indisputably a commercially important species. Previous studies using uneven sampling or a limited number of makers have presented sometimes conflicting evidence of the genetic structure of S. pilchardus populations. Here, we show that whole genome data from 108 individuals from 16 sampling areas across 5000 km of the species' distribution range (from the Eastern Mediterranean to the archipelago of Azores) support at least three genetic clusters. One includes individuals from Azores and Madeira, with evidence of substructure separating these two archipelagos in the Atlantic. Another cluster broadly corresponds to the center of the distribution, including the sampling sites around Iberia, separated by the Almeria-Oran front from the third cluster that includes all of the Mediterranean samples, except those from the Alboran Sea. Individuals from the Canary Islands appear to belong to the Mediterranean cluster. This suggests at least two important geographical barriers to gene flow, even though these do not seem complete, with many individuals from around Iberia and the Mediterranean showing some patterns compatible with admixture with other genetic clusters. Genomic regions corresponding to the top outliers of genetic differentiation are located in areas of low recombination indicative that genetic architecture also has a role in shaping population structure. These regions include genes related to otolith formation, a calcium carbonate structure in the inner ear previously used to distinguish S. pilchardus populations. Our results provide a baseline for further characterization of physical and genetic barriers that divide European sardine populations, and information for transnational stock management of this highly exploited species towards sustainable fisheries.}, } @article {pmid38370726, year = {2024}, author = {Mercado-Evans, V and Chew, C and Serchejian, C and Saltzman, A and Mejia, ME and Zulk, JJ and Cornax, I and Nizet, V and Patras, KA}, title = {Tamm-Horsfall protein augments neutrophil NETosis during urinary tract infection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38370726}, support = {F31 AI167538/AI/NIAID NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; F31 DK136201/DK/NIDDK NIH HHS/United States ; S10 OD026804/OD/NIH HHS/United States ; R01 DK128053/DK/NIDDK NIH HHS/United States ; F31 AI167547/AI/NIAID NIH HHS/United States ; }, abstract = {Urinary neutrophils are a hallmark of urinary tract infection (UTI), yet the mechanisms governing their activation, function, and efficacy in controlling infection remain incompletely understood. Tamm-Horsfall glycoprotein (THP), the most abundant protein in urine, uses terminal sialic acids to bind an inhibitory receptor and dampen neutrophil inflammatory responses. We hypothesized that neutrophil modulation is an integral part of THP-mediated host protection. In a UTI model, THP-deficient mice showed elevated urinary tract bacterial burdens, increased neutrophil recruitment, and more severe tissue histopathological changes compared to WT mice. Furthermore, THP-deficient mice displayed impaired urinary NETosis during UTI. To investigate the impact of THP on NETosis, we coupled in vitro fluorescence-based NET assays, proteomic analyses, and standard and imaging flow cytometry with peripheral human neutrophils. We found that THP increases proteins involved in respiratory chain, neutrophil granules, and chromatin remodeling pathways, enhances NETosis in an ROS-dependent manner, and drives NET-associated morphologic features including nuclear decondensation. These effects were observed only in the presence of a NETosis stimulus and could not be solely replicated with equivalent levels of sialic acid alone. We conclude that THP is a critical regulator of NETosis in the urinary tract, playing a key role in host defense against UTI.}, } @article {pmid38402921, year = {2024}, author = {Molina-Hoyos, K and Montoya-Ruíz, C and Aguilar, PV and Pérez-Doria, A and Díaz, FJ and Rodas, JD}, title = {Virome analyses of Amblyomma cajennense and Rhipicephalus microplus ticks collected in Colombia.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {107158}, doi = {10.1016/j.actatropica.2024.107158}, pmid = {38402921}, issn = {1873-6254}, abstract = {Tick-borne viruses (TBV) have gained public health relevance in recent years due to the recognition of human-associated fatal cases and the increase in tick-borne disease and transmission. However, many tick species have not been studied for their potential to transmit pathogenic viruses, especially those found in Latin America. To gain better understanding of the tick virome, we conducted targeted amplification using broadly-reactive consensus-degenerate pan-viral targeting viruses from the genera Flavivirus, Bandavirus, Uukuvirus, and Orthonairovirus genus. Additionally, we conducted unbiased metagenomic analyses to investigate the presence of viral RNA sequences in Amblyomma cajennense, A. patinoi and Rhipicephalus microplus ticks collected from a horse slaughter plant in Medellín, Colombia. While no viral products were detected by PCR, results of the metagenomic analyses revealed the presence of viral genomes belonging to the genera Phlebovirus, Bandavirus, and Uukuvirus, including Lihan Tick Virus (LTV), which was previously reported in Rhipicephalus microplus from Colombia. Overall, the results emphasized the enormous utility of the next-generation sequencing in identifying virus genetic diversity presents in ticks and other species of vectors and reservoirs.}, } @article {pmid38402727, year = {2024}, author = {Wang, R and Li, X and Lv, F and He, J and Lv, R and Wei, L}, title = {Sesame bacterial wilt significantly alters rhizosphere soil bacterial community structure, function, and metabolites in continuous cropping systems.}, journal = {Microbiological research}, volume = {282}, number = {}, pages = {127649}, doi = {10.1016/j.micres.2024.127649}, pmid = {38402727}, issn = {1618-0623}, abstract = {Bacterial wilt is the leading disease of sesame and alters the bacterial community composition, function, and metabolism of sesame rhizosphere soil. However, its pattern of change is unclear. Here, the purpose of this study was to investigate how these communities respond to three differing severities of bacterial wilt in mature continuously cropped sesame plants by metagenomic and metabolomic techniques, namely, absence (WH), moderate (WD5), and severe (WD9) wilt. The results indicated that bacterial wilt could significantly change the bacterial community structure in the rhizosphere soil of continuously cropped sesame plants. The biomarker species with significant differences will also change with increasing disease severity. In particular, the gene expression levels of Ralstonia solanacearum in the WD9 and WD5 treatments increased by 25.29% and 33.61%, respectively, compared to those in the WH treatment (4.35 log10 copies g-1). The occurrence of bacterial wilt significantly altered the functions of the bacterial community in rhizosphere soil. KEEG and CAZy functional annotations revealed that the number of significantly different functions in WH was greater than that in WD5 and WD9. Bacterial wilt significantly affected the relative content of metabolites, especially acids, in the rhizosphere soil, and compared with those in the rhizosphere soil from WH, 10 acids (including S-adenosylmethionine, N-acetylleucine, and desaminotyrosine, etc.) in the rhizosphere soil from WD5 or WD9 significantly increased. In comparison, the changes in the other 10 acids (including hypotaurine, erucic acid, and 6-hydroxynicotinic acid, etc.) were reversed. The occurrence of bacterial wilt also significantly inhibited metabolic pathways such as ABC transporter and amino acid biosynthesis pathways in rhizosphere soil and had a significant impact on two key enzymes (1.1.1.11 and 2.6.1.44). In conclusion, sesame bacterial wilt significantly alters the rhizosphere soil bacterial community structure, function, and metabolites. This study enhances the understanding of sesame bacterial wilt mechanisms and lays the groundwork for future prevention and control strategies against this disease.}, } @article {pmid38402605, year = {2024}, author = {Ijeomah, IM and Temitope, FOC and Lander, C and Sheriff, AT and Uwem, GE and Bernard, OA and Oluseyi, OA and Elijah, OI and Toluwani, AG and Arthur, OO and Toluwanimi, AE and Bolutife, PO and Damilola, OG and Titilola, OO and Oluwadamilola, GA and Muhammad, AI and Omotosho, KI and Johnson, AA and Jelle, M and Olubusuyi, AM}, title = {Classic human astrovirus 4, 8, MLB-3, and likely new genotype 5 sublineage in stool samples of children in Nigeria.}, journal = {Journal of medical virology}, volume = {96}, number = {3}, pages = {e29489}, doi = {10.1002/jmv.29489}, pmid = {38402605}, issn = {1096-9071}, abstract = {Human astrovirus (HAstV) is a nonenveloped RNA virus and has been implicated in acute gastroenteritis among children and elderly. However, there exists a substantial dearth of information on HAstV strains circulating in Nigeria. Viral-like particles were purified from archived 254 stool samples of children with acute flaccid paralysis between January and December 2020 from five states in Nigeria, using the NetoVIR protocol. Extracted viral RNA and DNA were subjected to a reverse transcription step and subsequent random polymerase chain reaction amplification. Library preparation and Illumina sequencing were performed. Using the virome paired-end reads pipeline, raw reads were processed into genomic contigs. Phylogenetic and pairwise identity analysis of the recovered HAstV genomes was performed. Six near-complete genome sequences of HAstV were identified and classified as HAstV4 (n = 1), HAstV5 (n = 1), HAstV8 (n = 1), and MLB-3 (n = 3). The HAstV5 belonged to a yet unclassified sublineage, which we tentatively named HAstV-5d. Phylogenetic analysis of open reading frames 1a, 1b, and 2 suggested recombination events inside the MAstV1 species. Furthermore, phylogenetic analysis implied a geographic linkage between the HAstV5 strain from this study with two strains from Cameroon across all the genomic regions. We report for the first time the circulation of HAstV genotypes 4, 8, and MLB-3 in Nigeria and present data suggestive for the existence of a new sublineage of HAstV5. To further understand the burden, diversity, and evolution of HAstV, increased research interest as well as robust HAstV surveillance in Nigeria is essential.}, } @article {pmid38401756, year = {2024}, author = {Li, C and Xiao, NS and Ke, BY and Li, S and Lin, Y}, title = {Application of metagenomic next-generation sequencing in suspected spinal infectious diseases.}, journal = {World neurosurgery}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.wneu.2024.02.071}, pmid = {38401756}, issn = {1878-8769}, abstract = {OBJECTIVE: This study aimed to explore the clinical efficacy of metagenomic next-generation sequencing (mNGS) in diagnosing and treating suspected spinal infectious diseases.

METHODS: Between October 2022 to December 2023, a retrospective analysis was performed on patient records within the Department of Spinal Surgery at Guilin People's Hospital. The analysis included comprehensive data on patients with presumed spinal infectious diseases, incorporating results from mNGS tests conducted externally, conventional pathogen detection results, laboratory examination results, and imaging findings. The study aimed to assess the applicability of mNGS in the context of suspected spinal infectious lesions.

RESULTS: Twenty-seven patients were included in the final analysis. Pathogenic microorganisms were identified in 23 cases. The included cases encompassed one case of tuberculous spondylitis, one case of fungal infection, three cases of Brucella spondylitis, three cases of viral infection, nine cases of bacterial infection, and six cases of mixed infections. Pathogenic microorganisms remained elusive in four cases. The application of the mNGS method demonstrated a significantly elevated positive detection rate compared to conventional methods (85.19% vs. 48.15%, P < 0.05). Moreover, the mNGS method detected a greater variety of pathogen species than traditional methods (Z = 10.69, P < 0.05). Additionally, the mNGS method exhibited a shorter detection time.

CONCLUSION: mNGS demonstrated significantly higher detection rates for bacterial, fungal, viral, and mixed infections in cases of suspected spinal infectious diseases. The clinical implementation of mNGS could further enhance the efficiency of diagnosing and treating suspected spinal infectious diseases.}, } @article {pmid38400721, year = {2024}, author = {Liu, X and Fang, H and Pan, L and Zhang, P and Lin, H and Gao, H and Ye, C and Mao, D and Luo, Y}, title = {S-amlodipine induces liver inflammation and dysfunction through the alteration of intestinal microbiome in a rat model.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2316923}, doi = {10.1080/19490976.2024.2316923}, pmid = {38400721}, issn = {1949-0984}, abstract = {S-amlodipine, a commonly prescribed antihypertensive agent, is widely used in clinical settings to treat hypertension. However, the potential adverse effects of long-term S-amlodipine treatment on the liver remain uncertain, given the cautionary recommendations from clinicians regarding its administration in individuals with impaired liver function. To address this, we conducted a study using an eight-week-old male rat model and administered a daily dose of 0.6 ~ 5 mg/kg of S-amlodipine for 7 weeks. Our findings demonstrated that 1.2 ~ 5 mg/kg of S-amlodipine treatment induced liver inflammation and associated dysfunction in rats, further in vitro experiments revealed that the observed liver inflammation and dysfunction were not attributable to direct effects of S-amlodipine on the liver. Metagenome sequencing analysis revealed that S-amlodipine treatment led to alterations in the gut microbiome of rats, with the bloom of E. coli (4.5 ~ 6.6-fold increase) and a decrease in A. muciniphila (1,613.4 ~ 2,000-fold decrease) and B. uniformis (20.6 ~ 202.7-fold decrease), subsequently causing an increase in the gut bacterial lipopolysaccharide (LPS) content (1.4 ~ 1.5-fold increase in feces). S-amlodipine treatment also induced damage to the intestinal barrier and increased intestinal permeability, as confirmed by elevated levels of fecal albumin; furthermore, the flux of gut bacterial LPS into the bloodstream through the portal vein resulted in an increase in serum LPS content (3.3 ~ 4-fold increase). LPS induces liver inflammation and subsequent dysfunction in rats by activating the TLR4 pathway. This study is the first to show that S-amlodipine induces liver inflammation and dysfunction by perturbing the rat gut microbiome. These results indicate the adverse effects of S-amlodipine on the liver and provide a rich understanding of the safety of long-term S-amlodipine administration.}, } @article {pmid38400535, year = {2024}, author = {Cui, X and Qiu, J and Huang, F and Zhang, C and Shao, T and Wang, Y}, title = {Herpes Simplex Keratitis as a Complication of Pterygium Surgery.}, journal = {The American journal of case reports}, volume = {25}, number = {}, pages = {e942401}, doi = {10.12659/AJCR.942401}, pmid = {38400535}, issn = {1941-5923}, abstract = {BACKGROUND Infectious keratitis after pterygium surgery is a rare but potentially devastating complication. The present study presents 5 cases of herpes simplex keratitis (HSK) after pterygium surgery. CASE REPORT This study was conducted in our clinic in a 5-year period from February 2017 to September 2021. The 5 patients were men, aged between 42 and 73 years, with no prior history of herpes simplex virus (HSV) infections. Symptoms appeared near 1 month (median 30 days, range 10 to 70 days) after primary pterygium surgery. Diagnosis was based on clinical symptoms and laboratory test results, such as tear HSV-sIgA, corneal tissue polymerase chain reaction, and next-generation sequencing of metagenomics. The epithelial (1/5) and stromal (4/5) subtypes of HSK were identified. The patients received topical ganciclovir gel, immunosuppressive eyedrops, and oral acyclovir tablets, along with additional surgical interventions if necessary. Three were healed with conservative therapy, 1 eye required amniotic membrane transplantation due to corneal melt, and 1 was perforated and followed by corneal grafting. Finally, a literature review of previous publications on HSK after ocular surgeries was conducted. CONCLUSIONS HSK is a rare but serious complication that can arise after uneventful pterygium surgery. It is worthy of attention that both epithelial and stromal forms can occur. Timely diagnosis and treatment are crucial to prevent unfavorable outcomes. Consequently, routine corneal fluorescein staining, tear sIgA examination, and corneal scraping for polymerase chain reaction or next-generation sequencing of metagenomics should be performed in any suspected cases.}, } @article {pmid38400074, year = {2024}, author = {Desmecht, S and Latka, A and Ceyssens, PJ and Garcia-Pino, A and Gillis, A and Lavigne, R and Lima-Mendez, G and Matthijnssens, J and Vázquez, R and Venneman, J and Wagemans, J and Briers, Y and Thiry, D}, title = {Meeting Report of the Second Symposium of the Belgian Society for Viruses of Microbes and Launch of the Phage Valley.}, journal = {Viruses}, volume = {16}, number = {2}, pages = {}, doi = {10.3390/v16020299}, pmid = {38400074}, issn = {1999-4915}, abstract = {The second symposium of the Belgian Society for Viruses of Microbes (BSVoM) took place on 8 September 2023 at the University of Liège with 141 participants from 10 countries. The meeting program covered three thematic sessions opened by international keynote speakers: two sessions were devoted to "Fundamental research in phage ecology and biology" and the third one to the "Present and future applications of phages". During this one day symposium, four invited keynote lectures, nine selected talks and eight student pitches were given along with thirty presented posters. The president of the Belgian Society for Viruses of Microbes, Prof. Yves Briers, took advantage of this symposium to launch the Phage Valley concept that will put the spotlight on the exceptionally high density of researchers investigating viruses of microbes as well as the successful triple helix approach between academia, industry and government in Belgium.}, } @article {pmid38400004, year = {2024}, author = {Zhu, P and Liu, C and Liu, GF and Liu, H and Xie, KM and Zhang, HS and Xu, X and Xiao, J and Jiang, JZ}, title = {Unveiling CRESS DNA Virus Diversity in Oysters by Virome.}, journal = {Viruses}, volume = {16}, number = {2}, pages = {}, doi = {10.3390/v16020228}, pmid = {38400004}, issn = {1999-4915}, support = {2022B1111030001//Key-Area Research and Development Program of Guangdong Province/ ; 31972847//National Natural Science Foundation of China/ ; 2023TD44//Central Public-Interest Scientific Institution Basal Research Fund, CAFS/ ; 2021SD05//Central Public-Interest Scientific Institution Basal Research Fund, CAFS/ ; }, abstract = {Oysters that filter feed can accumulate numerous pathogens, including viruses, which can serve as a valuable viral repository. As oyster farming becomes more prevalent, concerns are mounting about diseases that can harm both cultivated and wild oysters. Unfortunately, there is a lack of research on the viruses and other factors that can cause illness in shellfish. This means that it is harder to find ways to prevent these diseases and protect the oysters. This is part of a previously started project, the Dataset of Oyster Virome, in which we further study 30 almost complete genomes of oyster-associated CRESS DNA viruses. The replication-associated proteins and capsid proteins found in CRESS DNA viruses display varying evolutionary rates and frequently undergo recombination. Additionally, some CRESS DNA viruses have the capability for cross-species transmission. A plethora of unclassified CRESS DNA viruses are detectable in transcriptome libraries, exhibiting higher levels of transcriptional activity than those found in metagenome libraries. The study significantly enhances our understanding of the diversity of oyster-associated CRESS DNA viruses, emphasizing the widespread presence of CRESS DNA viruses in the natural environment and the substantial portion of CRESS DNA viruses that remain unidentified. This study's findings provide a basis for further research on the biological and ecological roles of viruses in oysters and their environment.}, } @article {pmid38399807, year = {2024}, author = {Liu, Z and Zhang, C and Ma, J and Peng, Q and Du, X and Sun, S and Cheng, J and Peng, W and Chen, L and Gu, Z and Zhang, W and Su, P and Zhang, D}, title = {Extraction Methods Determine the Quality of Soil Microbiota Acquisition.}, journal = {Microorganisms}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/microorganisms12020403}, pmid = {38399807}, issn = {2076-2607}, support = {ZDKJ202001//2020 Hainan Science and Technology Major Project/ ; 2023CX18//Hunan agricultural science and technology innovation fund/ ; 32302316//the National Natural Science Foundation of China/ ; 31901854//the National Natural Science Foundation of China/ ; 2023MS02//independent research project of State Key Laboratory of Hybrid Rice/ ; 2023MS03//independent research project of State Key Laboratory of Hybrid Rice/ ; }, abstract = {The soil microbiome plays a key role in plant health. Native soil microbiome inoculation, metagenomic profiling, and high-throughput cultivation require efficient microbe extraction. Sonication and oscillation are the most common methods used to extract soil microbiomes. However, the extraction efficiency of these methods has not been investigated in full. In this study, we compared the culturable microbe numbers, community structures, and alpha diversities among the different methods, including sonication, oscillation, and centrifugation, and their processing times. The study results showed that sonication significantly increases the culturable colony number compared with oscillation and centrifugation. Furthermore, the sonication strategy was found to be the main factor influencing extraction efficiency, but increased sonication time can aid in recovery from this impact. Finally, the extraction processing times were found to have a significant negative relationship with α-diversity among the extracted microbiota. In conclusion, sonication is the main factor for enriching in situ microbiota, and increased extraction time significantly decreases the α-diversity of the extracted microbiota. The results of this study provide insights into the isolation and utilization of different microorganism sources.}, } @article {pmid38399800, year = {2024}, author = {Rui, Y and Qiu, G}, title = {Analysis of Antibiotic Resistance Genes in Water Reservoirs and Related Wastewater from Animal Farms in Central China.}, journal = {Microorganisms}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/microorganisms12020396}, pmid = {38399800}, issn = {2076-2607}, support = {FCL202013//the Foundation of Central Laboratory of Xinyang Agriculture and Forestry University/ ; }, abstract = {This study aimed to explore the phenotype and relationship of drug resistance genes in livestock and poultry farm wastewater and drinking water reservoirs to provide evidence for the transmission mechanisms of drug resistance genes, in order to reveal the spread of drug resistance genes in wastewater from intensive farms in Central China to urban reservoirs that serve as drinking water sources and provide preliminary data for the treatment of wastewater from animal farms to reduce the threat to human beings. DNA extraction and metagenomic sequencing were performed on eight groups of samples collected from four water reservoirs and four related wastewaters from animal farms in Central China. Metagenomic sequencing showed that the top 20 AROs with the highest abundance were vanT_gene, vanY_gene, adeF, qacG, Mtub_rpsL_STR, vanY_gene_, vanW_gene, Mtub_murA_FOF, vanY_gene, vanH_gene, FosG, rsmA, qacJ, RbpA, vanW_gene, aadA6, vanY_gene, sul4, sul1, and InuF. The resistance genes mentioned above belong to the following categories of drug resistance mechanisms: antibiotic target replacement, antibiotic target protection, antibiotic inactivation, and antibiotic efflux. The resistomes that match the top 20 genes are Streptococcus agalactiae and Streptococcus anginosus; Enterococcus faecalis; Enterococcus faecium; Actinomyces viscosus and Bacillus cereus. Enterococcus faecium; Clostridium tetani; Streptococcus agalactiae and Streptococcus anginosus; Streptococcus agalactiae and Streptococcus anginosus; Acinetobacter baumannii, Bifidobacterium bifidum, Bifidobacterium breve, Bifidobacterium longum, Corynebacterium jeikeium, Corynebacterium urealyticum, Mycobacterium kansasii, Mycobacterium tuberculosis, Schaalia odontolytica, and Trueperella pyogenes; Mycobacterium avium and Mycobacterium tuberculosis; Aeromonas caviae, Enterobacter hormaechei, Vibrio cholerae, Vibrio metoecus, Vibrio parahaemolyticus, and Vibrio vulnificus; Pseudomonas aeruginosa and Pseudomonas fluorescens; Staphylococcus aureus and Staphylococcus equorum; M. avium, Achromobacter xylosoxidans, and Acinetobacter baumannii; Sphingobium yanoikuyae, Acinetobacter indicus, Morganella morganii, Proteus mirabilis, Proteus vulgaris, Providencia rettgeri, and Providencia stuartii. Unreported drug resistance genes and drug-resistant bacteria in Central China were identified in 2023. In the transmission path of drug resistance genes, the transmission path from aquaculture wastewater to human drinking water sources cannot be ignored. For the sake of human health and ecological balance, the treatment of aquaculture wastewater needs to be further strengthened, and the effective blocking of drug resistance gene transmission needs to be considered.}, } @article {pmid38399795, year = {2024}, author = {Cho, WY and Lee, PC}, title = {Metagenomic Analysis of Antarctic Ocean near the King Sejong Station Reveals the Diversity of Carotenoid Biosynthetic Genes.}, journal = {Microorganisms}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/microorganisms12020390}, pmid = {38399795}, issn = {2076-2607}, support = {20220258//Korea Institute of Marine Science and Technology Promotion/ ; }, abstract = {Carotenoids, biotechnologically significant pigments, play crucial biological roles in marine microorganisms. While various environments have been explored to understand the diversity of carotenoids and their biosynthesis, the Antarctic Ocean remains relatively under-investigated. This study conducted a metagenomic analysis of seawater from two depths (16 and 25 m) near the King Sejong Station in the Antarctic Ocean. The analysis revealed a rich genetic diversity underlying C40 (astaxanthin, myxol, okenone, spheroidene, and spirilloxanthin), C30 (diaponeurosporene, diapolycopene, and staphyloxanthin), and C50 (C.p. 450) carotenoid biosynthesis in marine microorganisms, with notable differential gene abundances between depth locations. Exploring carotenoid pathway genes offers the potential for discovering diverse carotenoid structures of biotechnological value and better understanding their roles in individual microorganisms and broader ecosystems.}, } @article {pmid38399785, year = {2024}, author = {Wang, H and Dang, D and Zhu, L and Pan, M and Zhu, J and Lu, W and Lu, S and Zhao, J}, title = {Effects of Varied Sulfamethazine Dosage and Exposure Durations on Offspring Mice.}, journal = {Microorganisms}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/microorganisms12020381}, pmid = {38399785}, issn = {2076-2607}, support = {31972085//National Natural Science Foundation of China/ ; 2022YFF1100403//National Key Research and Development Program of China/ ; }, abstract = {The development of antibiotics was a turning point in the history of medicine; however, their misuse and overuse have contributed to the current global epidemic of antibiotic resistance. According to epidemiological studies, early antibiotic exposure increases the risk of immunological and metabolic disorders. This study investigated the effects of exposure to different doses of sulfamethazine (SMZ) on offspring mice and compared the effects of exposure to SMZ on offspring mice in prenatal and early postnatal periods and continuous periods. Furthermore, the effects of SMZ exposure on the gut microbiota of offspring mice were analyzed using metagenome. According to the results, continuous exposure to high-dose SMZ caused weight gain in mice. IL-6, IL-17A, and IL-10 levels in the female offspring significantly increased after high-dose SMZ exposure. In addition, there was a significant gender difference in the impact of SMZ exposure on the gut microbiota of offspring: Continuous high-dose SMZ exposure significantly decreased the relative abundance of Ligilactobacillus murinus, Limosilactobacillus reuteri, Lactobacillus johnsonii, and Bifidobacterium pseudolongum (p < 0.05) in female offspring mice; however, these significant changes were not observed in male offspring mice.}, } @article {pmid38399738, year = {2024}, author = {Straková, D and Sánchez-Porro, C and de la Haba, RR and Ventosa, A}, title = {Decoding the Genomic Profile of the Halomicroarcula Genus: Comparative Analysis and Characterization of Two Novel Species.}, journal = {Microorganisms}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/microorganisms12020334}, pmid = {38399738}, issn = {2076-2607}, support = {PID2020-118136GB-I00//MCIN/AEI/10.13039/501100011033/ ; P20_01066 and BIO-213//Junta de Andalucía/ ; }, abstract = {The genus Halomicroarcula, classified within the family Haloarculaceae, presently comprises eight haloarchaeal species isolated from diverse saline habitats, such as solar salterns, hypersaline soils, marine salt, and marine algae. Here, a detailed taxogenomic study and comparative genomic analysis of the genus Halomicroarcula was carried out. In addition, two strains, designated S1CR25-12[T] and S3CR25-11[T], that were isolated from hypersaline soils located in the Odiel Saltmarshes in Huelva (Spain) were included in this study. The 16S rRNA and rpoB' gene sequence analyses affiliated the two strains to the genus Halomicroarcula. Typically, the species of the genus Halomicroarcula possess multiple heterogeneous copies of the 16S rRNA gene, which can lead to misclassification of the taxa and overestimation of the prokaryotic diversity. In contrast, the application of overall genome relatedness indexes (OGRIs) augments the capacity for the precise taxonomic classification and categorization of prokaryotic organisms. The relatedness indexes of the two new isolates, particularly digital DNA-DNA hybridization (dDDH), orthologous average nucleotide identity (OrthoANI), and average amino acid identity (AAI), confirmed that strains S1CR25-12[T] (= CECT 30620[T] = CCM 9252[T]) and S3CR25-11[T] (= CECT 30621[T] = CCM 9254[T]) constitute two novel species of the genus Halomicroarcula. The names Halomicroarcula saliterrae sp. nov. and Halomicroarcula onubensis sp. nov. are proposed for S1CR25-12[T] and S3CR25-11[T], respectively. Metagenomic fragment recruitment analysis, conducted using seven shotgun metagenomic datasets, revealed that the species belonging to the genus Halomicroarcula were predominantly recruited from hypersaline soils found in the Odiel Saltmarshes and the ponds of salterns with high salt concentrations. This reinforces the understanding of the extreme halophilic characteristics associated with the genus Halomicroarcula. Finally, comparing pan-genomes across the twenty Halomicroarcula and Haloarcula species allowed for the identification of commonalities and differences between the species of these two related genera.}, } @article {pmid38399723, year = {2024}, author = {Abdulkhakov, S and Markelova, M and Safina, D and Siniagina, M and Khusnutdinova, D and Abdulkhakov, R and Grigoryeva, T}, title = {Butyric Acid Supplementation Reduces Changes in the Taxonomic and Functional Composition of Gut Microbiota Caused by H. pylori Eradication Therapy.}, journal = {Microorganisms}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/microorganisms12020319}, pmid = {38399723}, issn = {2076-2607}, support = {No. FZSM-2023-0013//Ministry of Education of Russian Federation/ ; }, abstract = {UNLABELLED: H. pylori eradication therapy leads to significant changes in the gut microbiome, including influence on the gut microbiome's functional potential. Probiotics are one of the most studied potential methods for reducing the microbiota-related consequences of antibiotics. However, the beneficial effects of probiotics are still under discussion. In addition, there are some concerns about the safety of probiotics, emphasizing the need for research of other therapeutic interventions. The aim of our study was to evaluate the influence of butyric acid+inulin supplements on gut microbiota changes (the gut microbiota composition, abundance of metabolic pathways, and gut resistome) caused by H. pylori eradication therapy.

MATERIALS AND METHODS: Twenty two H. pylori-positive patients, aged 19 to 64 years, were enrolled in the study and randomized into two treatment groups, as follows: (1) ECAB-14 (n = 11), with esomeprazole 20 mg, clarithromycin 500 mg, amoxicillin 1000 mg, and bismuthate tripotassium dicitrate 240 mg, twice daily, per os, for 14 days, and (2), ECAB-Z-14 (n = 11), with esomeprazole 20 mg, clarithromycin 500 mg, amoxicillin 1000 mg, and bismuthate tripotassium dicitrate 240 mg, twice daily, along with butyric acid+inulin (Zacofalk), two tablets daily, each containing 250 mg of butyric acid, and 250 mg of inulin, per os, for 14 days. Fecal samples were collected from each subject prior to eradication therapy (time point I), after the end of eradication therapy (time point II), and a month after the end of eradication therapy (time point III). The total DNA from the fecal samples was isolated for whole genome sequencing using the Illumina NextSeq 500 platform. Qualitative and quantitative changes in gut microbiota were assessed, including alpha and beta diversity, functional potential and antibiotic resistance gene profiling.

RESULTS: Gut microbiota alpha diversity significantly decreased compared with the baseline immediately after eradication therapy in both treatment groups (ECAB-14 and ECAB-Z-14). This diversity reached its baseline in the ECAB-Z-14 treatment group a month after the end of eradication therapy. However, in the ECAB-14 treatment arm, a reduction in the Shannon index was observed up to a month after the end of H. pylori eradication therapy. Fewer alterations in the gut microbiota functional potential were observed in the ECAB-Z-14 treatment group. The abundance of genes responsible for the metabolic pathway associated with butyrate production decreased only in the ECAB-14 treatment group. The prevalence of antibiotic-resistant genes in the gut microbiota increased significantly in both treatment groups by the end of treatment. However, more severe alterations were noted in the ECAB-14 treatment group.

CONCLUSIONS: H. pylori eradication therapy leads to taxonomic changes, a reduction in the alpha diversity index, and alterations in the functional potential of the gut microbiota and gut resistome. Taking butyric acid+inulin supplements during H. pylori eradication therapy could help maintain the gut microbiota in its initial state and facilitate its recovery after H. pylori eradication.}, } @article {pmid38399681, year = {2024}, author = {Kim, KE and Joo, HM and Kim, YJ and Kang, D and Lee, TK and Jung, SW and Ha, SY}, title = {Ecological Interaction between Bacteriophages and Bacteria in Sub-Arctic Kongsfjorden Bay, Svalbard, Norway.}, journal = {Microorganisms}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/microorganisms12020276}, pmid = {38399681}, issn = {2076-2607}, support = {20210466//Ministry of Oceans and Fisheries/ ; NRF2020R1A2C2005970//National Research Foundation of Korea/ ; }, abstract = {Marine virus diversity and their relationships with their hosts in the marine environment remain unclear. This study investigated the co-occurrence of marine DNA bacteriophages (phages) and bacteria in the sub-Arctic area of Kongsfjorden Bay in Svalbard (Norway) in April and June 2018 using metagenomics tools. Of the marine viruses identified, 48-81% were bacteriophages of the families Myoviridae, Siphoviridae, and Podoviridae. Puniceispirillum phage HMO-2011 was dominant (7.61%) in April, and Puniceispirillum phage HMO-2011 (3.32%) and Pelagibacter phage HTVC008M (3.28%) were dominant in June. Gammaproteobacteria (58%), including Eionea flava (14.3%) and Pseudomonas sabulinigri (12.2%), were dominant in April, whereas Alphaproteobacteria (87%), including Sulfitobacter profundi (51.5%) and Loktanella acticola (32.4%), were dominant in June. The alpha diversity of the bacteriophages and bacterial communities exhibited opposite patterns. The diversity of the bacterial community was higher in April and lower in June. Changes in water temperature and light can influence the relationship between bacteria and bacteriophages.}, } @article {pmid38399658, year = {2024}, author = {Ishola, OA and Kublik, S and Durai Raj, AC and Ohnmacht, C and Schulz, S and Foesel, BU and Schloter, M}, title = {Comparative Metagenomic Analysis of Bacteriophages and Prophages in Gnotobiotic Mouse Models.}, journal = {Microorganisms}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/microorganisms12020255}, pmid = {38399658}, issn = {2076-2607}, support = {Helmholtz Munich Allergy Program//Helmholtz Munich Allergy Program/ ; }, abstract = {Gnotobiotic murine models are important to understand microbiota-host interactions. Despite the role of bacteriophages as drivers for microbiome structure and function, there is no information about the structure and function of the gut virome in gnotobiotic models and the link between bacterial and bacteriophage/prophage diversity. We studied the virome of gnotobiotic murine Oligo-MM12 (12 bacterial species) and reduced Altered Schaedler Flora (ASF, three bacterial species). As reference, the virome of Specific Pathogen-Free (SPF) mice was investigated. A metagenomic approach was used to assess prophages and bacteriophages in the guts of 6-week-old female mice. We identified a positive correlation between bacteria diversity, and bacteriophages and prophages. Caudoviricetes (82.4%) were the most prominent class of phages in all samples with differing relative abundance. However, the host specificity of bacteriophages belonging to class Caudoviricetes differed depending on model bacterial diversity. We further studied the role of bacteriophages in horizontal gene transfer and microbial adaptation to the host's environment. Analysis of mobile genetic elements showed the contribution of bacteriophages to the adaptation of bacterial amino acid metabolism. Overall, our results implicate virome "dark matter" and interactions with the host system as factors for microbial community structure and function which determine host health. Taking the importance of the virome in the microbiome diversity and horizontal gene transfer, reductions in the virome might be an important factor driving losses of microbial biodiversity and the subsequent dysbiosis of the gut microbiome.}, } @article {pmid38399650, year = {2024}, author = {Muter, O and Gudrā, D and Daumova, G and Idrisheva, Z and Rakhymberdina, M and Tabors, G and Dirnēna, B and Dobkeviča, L and Petrova, O and Apshikur, B and Luņģe, M and Fridmanis, D and Denissov, I and Bekishev, Y and Kasparinskis, R and Mukulysova, Z and Polezhayev, S}, title = {Impact of Anthropogenic Activities on Microbial Community Structure in Riverbed Sediments of East Kazakhstan.}, journal = {Microorganisms}, volume = {12}, number = {2}, pages = {}, doi = {10.3390/microorganisms12020246}, pmid = {38399650}, issn = {2076-2607}, support = {IRN BR21881921//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; Contract for the provision of services (O.Muter), Ust-Kamenogorsk, No 13-12, 23.06.2023//Ministry of Science and Higher Education of the Republic of Kazakhstan/ ; }, abstract = {Heavy metal (HMe) pollution in regions with mining and metallurgy activities is known to be a serious environmental problem worldwide. Hydrological processes contribute to the dissemination of HMes (drainage, precipitation, flow rate). The aim of the present study is to investigate the microbial community structure in ten river sediments sampled in different regions of East Kazakhstan, which are contaminated with HMes. The overall degree of sediment contamination with HMes (Cr, Cu, Zn, Pb, and Cd) was assessed using the pollution index Zc, which ranged from 0.43 to 21.6, with the highest in Ridder City (Zc = 21.6) and Ust-Kamenogorsk City, 0.8 km below the dam of the hydroelectric power station (Zc = 19.6). The tested samples considerably differed in organic matter, total carbon, nitrogen, and phosphorus content, as well as in the abundance of HMe-related functional gene families and antibiotic resistance genes. Metagenomic analysis of benthic microorganisms showed the prevalence of Proteobacteria (88.84-97.61%) and Actinobacteria (1.21-5.98%) at the phylum level in all samples. At the class level, Actinobacteria (21.68-57.48%), Betaproteobacteria (19.38-41.17%), and Alphaproteobacteria (10.0-39.78%) were the most common among the classified reads. To the best of our knowledge, this is the first study on the metagenomic characteristics of benthic microbial communities exposed to chronic HMe pressure in different regions of East Kazakhstan.}, } @article {pmid38398787, year = {2024}, author = {Doytchinov, VV and Peykov, S and Dimov, SG}, title = {Study of the Bacterial, Fungal, and Archaeal Communities Structures near the Bulgarian Antarctic Research Base "St. Kliment Ohridski" on Livingston Island, Antarctica.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/life14020278}, pmid = {38398787}, issn = {2075-1729}, support = {№ 70-25-72 from 03.08.2021//National Center for Polar Studies - Sofia University "St. Kliment Ohridski"/ ; }, abstract = {As belonging to one of the most isolated continents on our planet, the microbial composition of different environments in Antarctica could hold a plethora of undiscovered species with the potential for biotechnological applications. This manuscript delineates our discoveries after an expedition to the Bulgarian Antarctic Base "St. Kliment Ohridski" situated on Livingston Island, Antarctica. Amplicon-based metagenomics targeting the 16S rRNA genes and ITS2 region were employed to assess the metagenomes of the bacterial, fungal, and archaeal communities across diverse sites within and proximal to the research station. The predominant bacterial assemblages identified included Oxyphotobacteria, Bacteroidia, Gammaprotobacteria, and Alphaprotobacteria. A substantial proportion of cyanobacteria reads were attributed to a singular uncultured taxon within the family Leptolyngbyaceae. The bacterial profile of a lagoon near the base exhibited indications of penguin activity, characterized by a higher abundance of Clostridia, similar to lithotelm samples from Hannah Pt. Although most fungal reads in the samples could not be identified at the species level, noteworthy genera, namely Betamyces and Tetracladium, were identified. Archaeal abundance was negligible, with prevalent groups including Woesearchaeales, Nitrosarchaeum, Candidatus Nitrosopumilus, and Marine Group II.}, } @article {pmid38398700, year = {2024}, author = {Huang, K and Yan, X and Li, Z and Liu, F and Cui, K and Liu, Q}, title = {Construction and Identification of a Breast Bioreactor for Human-Derived Hypoglycemic Protein Amylin.}, journal = {Life (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/life14020191}, pmid = {38398700}, issn = {2075-1729}, support = {U20A2051//National Natural Science Foundation of China/ ; 2022B02//Guangdong Provincial Key Laboratory of Molecular Design and Precision Breeding/ ; }, abstract = {The mammary gland of mammals can generate numerous bioactive proteins. To express the human amylin protein in the mammary glands of domestic animals, we engineered a transgenic mammary gland bioreactor. For this study, we produced transgenic mice through prokaryotic microinjection. RT-PCR, qPCR, and Western blotting confirmed the presence of transgenes in the mice. The ELISA assay indicated an amylin yield of approximately 1.44 μg/mL in the mice milk. Further research revealed that consuming milk containing amylin resulted in a slight, but insignificant enhancement in food consumption, blood sugar equilibrium, and glucose tolerance. The influence of amylin-fortified milk on the abundance of fecal strains in mice was examined, and a significant difference in the quantity of strains needed for fatty acid synthesis and metabolism was discovered. The amylin protein gathered from humans is safe to consume, as no harmful effects were detected in the mice. Our study examined the production of human amylin using a new safety strategy that could potentially alleviate diabetic symptoms in the future through oral administration of milk containing amylin.}, } @article {pmid38397811, year = {2024}, author = {Yu, T and Yan, J and Wang, R and Zhang, L and Hu, X and Xu, J and Li, F and Sun, Q}, title = {Integrative Multiomics Profiling Unveils the Protective Function of Ulinastatin against Dextran Sulfate Sodium-Induced Colitis.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/antiox13020214}, pmid = {38397811}, issn = {2076-3921}, support = {82073271//National Natural Science Foundation of China/ ; 81803026//National Natural Science Foundation of China/ ; 2023KJXX-031//Science and Technology Program of Shaanxi Province/ ; xzy012023108//Fundamental Research Funds of Xi'an Jiaotong University/ ; YXJLRH2022044//Institutional Foundation of The First Affiliated Hospital of Xi'an Jiaotong University/ ; 2022YQPY07//Institutional Foundation of The First Affiliated Hospital of Xi'an Jiaotong University/ ; 2022MS-18//Institutional Foundation of The First Affiliated Hospital of Xi'an Jiaotong University/ ; }, abstract = {Ulcerative colitis is an inflammatory bowel disease with multiple pathogeneses. Here, we aimed to study the therapeutic role of ulinastatin (UTI), an anti-inflammatory bioagent, and its associated mechanisms in treating colitis. Dextran sulfate sodium was administrated to induce colitis in mice, and a subgroup of colitis mice was treated with UTI. The gut barrier defect and inflammatory manifestations of colitis were determined via histological and molecular experiments. In addition, transcriptomics, metagenomics, and metabolomics were employed to explore the possible mechanisms underlying the effects of UTI. We found that UTI significantly alleviated the inflammatory manifestations and intestinal barrier damage in the mice with colitis. Transcriptome sequencing revealed a correlation between the UTI treatment and JAK-STAT signaling pathway. UTI up-regulated the expression of SOCS1, which subsequently inhibited the phosphorylation of JAK2 and STAT3, thus limiting the action of inflammatory mediators. In addition, 16S rRNA sequencing illustrated that UTI maintained a more stable intestinal flora, protecting the gut from dysbiosis in colitis. Moreover, metabolomics analysis demonstrated that UTI indeed facilitated the production of some bile acids and short-chain fatty acids, which supported intestinal homeostasis. Our data provide evidence that UTI is effective in treating colitis and support the potential use of UTI treatment for patients with ulcerative colitis.}, } @article {pmid38396952, year = {2024}, author = {Vaglio-Garro, A and Kozlov, AV and Smirnova, YD and Weidinger, A}, title = {Pathological Interplay between Inflammation and Mitochondria Aggravates Glutamate Toxicity.}, journal = {International journal of molecular sciences}, volume = {25}, number = {4}, pages = {}, doi = {10.3390/ijms25042276}, pmid = {38396952}, issn = {1422-0067}, support = {FWF P-33799//FWF Austrian Science Fund/ ; }, abstract = {Mitochondrial dysfunction and glutamate toxicity are associated with neural disorders, including brain trauma. A review of the literature suggests that toxic and transmission actions of neuronal glutamate are spatially and functionally separated. The transmission pathway utilizes synaptic GluN2A receptors, rapidly released pool of glutamate, evoked release of glutamate mediated by Synaptotagmin 1 and the amount of extracellular glutamate regulated by astrocytes. The toxic pathway utilizes extrasynaptic GluN2B receptors and a cytoplasmic pool of glutamate, which results from the spontaneous release of glutamate mediated by Synaptotagmin 7 and the neuronal 2-oxoglutarate dehydrogenase complex (OGDHC), a tricarboxylic acid (TCA) cycle enzyme. Additionally, the inhibition of OGDHC observed upon neuro-inflammation is due to an excessive release of reactive oxygen/nitrogen species by immune cells. The loss of OGDHC inhibits uptake of glutamate by mitochondria, thus facilitating its extracellular accumulation and stimulating toxic glutamate pathway without affecting transmission. High levels of extracellular glutamate lead to dysregulation of intracellular redox homeostasis and cause ferroptosis, excitotoxicity, and mitochondrial dysfunction. The latter affects the transmission pathway demanding high-energy supply and leading to cell death. Mitochondria aggravate glutamate toxicity due to impairments in the TCA cycle and become a victim of glutamate toxicity, which disrupts oxidative phosphorylation. Thus, therapies targeting the TCA cycle in neurological disorders may be more efficient than attempting to preserve mitochondrial oxidative phosphorylation.}, } @article {pmid38396905, year = {2024}, author = {Tuchscherr, L and Wendler, S and Santhanam, R and Priese, J and Reissig, A and Müller, E and Ali, R and Müller, S and Löffler, B and Monecke, S and Ehricht, R and Guntinas-Lichius, O}, title = {Reduced Glycolysis and Cytotoxicity in Staphylococcus aureus Isolates from Chronic Rhinosinusitis as Strategies for Host Adaptation.}, journal = {International journal of molecular sciences}, volume = {25}, number = {4}, pages = {}, doi = {10.3390/ijms25042229}, pmid = {38396905}, issn = {1422-0067}, support = {ADA (13GW0456C); ResiCheck (13GW0422C)//Federal Ministry of Education and Research/ ; MESINFLAME (01EC1901B)//Federal Ministry of Education and Research/ ; 01K12306 StopStphGrowth//Bundesministeriums für Bildung und Forschung zur Projektförderung (NABF)/ ; }, abstract = {Chronic rhinosinusitis (CRS) is a multifactorial infection of the nasal cavity and sinuses. In this study, nasal swabs from control donors (N = 128) and patients with CRS (N = 246) were analysed. Culture methods and metagenomics revealed no obvious differences in the composition of the bacterial communities between the two groups. However, at the functional level, several metabolic pathways were significantly enriched in the CRS group compared to the control group. Pathways such as carbohydrate transport metabolism, ATP synthesis, cofactors and vitamins, photosynthesis and transcription were highly enriched in CRS. In contrast, pathways related to lipid metabolism were more representative in the control microbiome. As S. aureus is one of the main species found in the nasal cavity, staphylococcal isolates from control and CRS samples were analysed by microarray and functional assays. Although no significant genetic differences were detected by microarray, S. aureus from CRS induced less cytotoxicity to lung cells and lower rates of glycolysis in host cells than control isolates. These results suggest the differential modulation of staphylococcal virulence by the environment created by other microorganisms and their interactions with host cells in control and CRS samples. These changes were reflected in the differential expression of cytokines and in the expression of Agr, the most important quorum-sensing regulator of virulence in S. aureus. In addition, the CRS isolates remained stable in their cytotoxicity, whereas the cytotoxic activity of S. aureus isolated from control subjects decreased over time during in vitro passage. These results suggest that host factors influence the virulence of S. aureus and promote its adaptation to the nasal environment during CRS.}, } @article {pmid38396863, year = {2024}, author = {Yuan, H and Wu, X and Wang, X and Zhou, JY and Park, S}, title = {Microbial Dysbiosis Linked to Metabolic Dysfunction-Associated Fatty Liver Disease in Asians: Prevotella copri Promotes Lipopolysaccharide Biosynthesis and Network Instability in the Prevotella Enterotype.}, journal = {International journal of molecular sciences}, volume = {25}, number = {4}, pages = {}, doi = {10.3390/ijms25042183}, pmid = {38396863}, issn = {1422-0067}, support = {RS202300208567//the National Research Foundation of Korea/ ; }, abstract = {Metabolic dysfunction-associated fatty liver disease (MAFLD), formerly known as non-alcoholic fatty liver disease (NAFLD), is characterized by hepatic fat accumulation by metabolic dysfunction. The rising prevalence of MAFLD, especially among Asians, may be associated with changes in gut microbiota. We investigated gut microbiota characteristics and potential mechanisms leading to MAFLD development according to enterotypes. Case-control studies examining the gut microbiota composition between MAFLD and non-MAFLD participants were searched in public databases until July 2023. Gut microbiota was categorized into two enterotypes by principal component analysis. According to the enterotypes, LEfSe, ALDEx2, XGBoost, and DCiPatho were utilized to identify differential abundances and pathogenic microbes in the gut between the MAFLD and non-MAFLD groups. We analyzed microbial community networks with the SprCC module and predicted microbial functions. In the Prevotella enterotype (ET-P), 98.6% of Asians and 65.1% of Caucasians were associated with MAFLD (p = 0.049). MAFLD incidence was correlated with enterotype, age, obesity, and ethnicity (p < 0.05). Asian MAFLD patients exhibited decreased Firmicutes and Akkermansia muciniphila and increased Bacteroidetes and P. copri. The pathogenicity scores were 0.006 for A. muciniphila and 0.868 for P. copri. The Asian MAFLD group showed decreased stability and complexity in the gut microbiota network. Metagenome function analysis revealed higher fructose metabolism and lipopolysaccharide (LPS) biosynthesis and lower animal proteins and α-linolenic acid metabolism in Asians with MAFLD compared with the non-MAFLD group. LPS biosynthesis was positively correlated with P. copri (p < 0.05). In conclusion, P. copri emerged as a potential microbial biomarker for MAFLD. These findings enhance our understanding of the pathological mechanisms of MAFLD mediated through the gut microbiota, providing insights for future interventions.}, } @article {pmid38396840, year = {2024}, author = {Blondeaux, A and Valibouze, C and Speca, S and Rousseaux, C and Dubuquoy, C and Blanquart, H and Zerbib, P and Desreumaux, P and Foligné, B and Titécat, M}, title = {Changes in HLA-B27 Transgenic Rat Fecal Microbiota Following Tofacitinib Treatment and Ileocecal Resection Surgery: Implications for Crohn's Disease Management.}, journal = {International journal of molecular sciences}, volume = {25}, number = {4}, pages = {}, doi = {10.3390/ijms25042164}, pmid = {38396840}, issn = {1422-0067}, support = {59223519//Pfizer (France)/ ; }, abstract = {The therapeutic management of Crohn's disease (CD), a chronic relapsing-remitting inflammatory bowel disease (IBD), is highly challenging. Surgical resection is sometimes a necessary procedure even though it is often associated with postoperative recurrences (PORs). Tofacitinib, an orally active small molecule Janus kinase inhibitor, is an anti-inflammatory drug meant to limit PORs in CD. Whereas bidirectional interactions between the gut microbiota and the relevant IBD drug are crucial, little is known about the impact of tofacitinib on the gut microbiota. The HLA-B27 transgenic rat is a good preclinical model used in IBD research, including for PORs after ileocecal resection (ICR). In the present study, we used shotgun metagenomics to first delineate the baseline composition and determinants of the fecal microbiome of HLA-B27 rats and then to evaluate the distinct impact of either tofacitinib treatment, ileocecal resection or the cumulative effect of both interventions on the gut microbiota in these HLA-B27 rats. The results confirmed that the microbiome of the HLA-B27 rats was fairly different from their wild-type littermates. We demonstrated here that oral treatment with tofacitinib does not affect the gut microbial composition of HLA-B27 rats. Of note, we showed that ICR induced an intense loss of bacterial diversity together with dramatic changes in taxa relative abundances. However, the oral treatment with tofacitinib neither modified the alpha-diversity nor exacerbated significant modifications in bacterial taxa induced by ICR. Collectively, these preclinical data are rather favorable for the use of tofacitinib in combination with ICR to address Crohn's disease management when considering microbiota.}, } @article {pmid38396543, year = {2024}, author = {Zheng, L and Han, Z and Zhang, J and Kang, J and Li, C and Pang, Q and Liu, S}, title = {Lactiplantibacillus plantarum and Saccharomyces cerevisiae-Fermented Coconut Water Alleviates Dextran Sodium Sulfate-Induced Enteritis in Wenchang Chicken: A Gut Microbiota and Metabolomic Approach.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {4}, pages = {}, doi = {10.3390/ani14040575}, pmid = {38396543}, issn = {2076-2615}, support = {ZDYF2020102//the Key Research and Development Program of Hainan Province/ ; 32060529//the National Natural Science Foundation of China/ ; }, abstract = {In order to investigate the potential mechanisms of probiotic-fermented coconut water in treating enteritis, this study conducted a comprehensive analysis of the effects of probiotic intervention on the recovery from Dextran Sodium Sulfate-induced acute enteritis in Wenchang chicks. The analysis encompassed the assessment of growth performance, serum indicators, intestinal tissue structure, and metagenomic and metabolomic profiles of cecal contents in 60 Wenchang chicks subjected to intervention. This approach aimed to elucidate the impact of probiotic intervention on the recovery process from acute enteritis at both the genetic and metabolic levels in the avian model. The results revealed that intervention with Saccharomyces cerevisiae Y301 improved the growth rate of chicks. and intervention with Lactiplantibacillus plantarum MS2c regulated the glycerophospholipid metabolism pathway and reshaped the gut microbiota structure in modeling chicks with acute enteritis, reducing the abundance of potentially pathogenic bacteria from the Alistipes and increasing the abundance of potentially beneficial species from the Christensenellaceae. This intervention resulted in the production of specific gut metabolites, including Gentamicin C and polymyxin B2, recognized for their therapeutic effects on acute enteritis. The combined intervention of S. cerevisiae Y301 and L. plantarum MS2c not only enhanced growth performance but also mitigated intestinal wall damage and increased the abundance of gut metabolites such as gentamicin C and polymyxin B2, thereby mitigating symptoms of enteritis. Furthermore, this combined intervention reduced the levels of serum immune markers, including IL-10, IL-6, TNF-α, IFN-γ, and D-lactic acid, thus mitigating intestinal epithelial cell damage and promoting acute enteritis recovery. This study provides crucial insights into the mechanisms of action of probiotics and probiotic-fermented coconut water in acute enteritis recovery, offering new perspectives for sustainable farming practices for Wenchang chicken.}, } @article {pmid38395948, year = {2024}, author = {Alves Costa Silva, C and Piccinno, G and Suissa, D and Bourgin, M and Schreibelt, G and Durand, S and Birebent, R and Fidelle, M and Sow, C and Aprahamian, F and Manghi, P and Punčochář, M and Asnicar, F and Pinto, F and Armanini, F and Terrisse, S and Routy, B and Drubay, D and Eggermont, AMM and Kroemer, G and Segata, N and Zitvogel, L and Derosa, L and Bol, KF and de Vries, IJM}, title = {Influence of microbiota-associated metabolic reprogramming on clinical outcome in patients with melanoma from the randomized adjuvant dendritic cell-based MIND-DC trial.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1633}, pmid = {38395948}, issn = {2041-1723}, abstract = {Tumor immunosurveillance plays a major role in melanoma, prompting the development of immunotherapy strategies. The gut microbiota composition, influencing peripheral and tumoral immune tonus, earned its credentials among predictors of survival in melanoma. The MIND-DC phase III trial (NCT02993315) randomized (2:1 ratio) 148 patients with stage IIIB/C melanoma to adjuvant treatment with autologous natural dendritic cell (nDC) or placebo (PL). Overall, 144 patients collected serum and stool samples before and after 2 bimonthly injections to perform metabolomics (MB) and metagenomics (MG) as prespecified exploratory analysis. Clinical outcomes are reported separately. Here we show that different microbes were associated with prognosis, with the health-related Faecalibacterium prausnitzii standing out as the main beneficial taxon for no recurrence at 2 years (p = 0.008 at baseline, nDC arm). Therapy coincided with major MB perturbations (acylcarnitines, carboxylic and fatty acids). Despite randomization, nDC arm exhibited MG and MB bias at baseline: relative under-representation of F. prausnitzii, and perturbations of primary biliary acids (BA). F. prausnitzii anticorrelated with BA, medium- and long-chain acylcarnitines. Combined, these MG and MB biomarkers markedly determined prognosis. Altogether, the host-microbial interaction may play a role in localized melanoma. We value systematic MG and MB profiling in randomized trials to avoid baseline differences attributed to host-microbe interactions.}, } @article {pmid38395946, year = {2024}, author = {Jin, C and Wu, S and Liang, Z and Zhang, J and Lei, X and Bai, H and Liang, G and Su, X and Chen, X and Wang, P and Wang, Y and Guan, L and Yao, J}, title = {Multi-omics reveal mechanisms of high enteral starch diet mediated colonic dysbiosis via microbiome-host interactions in young ruminant.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {38}, pmid = {38395946}, issn = {2049-2618}, support = {2022YFD1600101//National Key Research and Development Program of China/ ; 2022YFD1600101//National Key Research and Development Program of China/ ; 20220203//Shaanxi Provincial Science and Technology Association Young Talents Lifting Program Project/ ; 32272829//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Although rumen development is crucial, hindgut undertakes a significant role in young ruminants' physiological development. High-starch diet is usually used to accelerate rumen development for young ruminants, but always leading to the enteral starch overload and hindgut dysbiosis. However, the mechanism behind remains unclear. The combination of colonic transcriptome, colonic luminal metabolome, and metagenome together with histological analysis was conducted using a goat model, with the aim to identify the potential molecular mechanisms behind the disrupted hindgut homeostasis by overload starch in young ruminants.

RESULT: Compared with low enteral starch diet (LES), high enteral starch diet (HES)-fed goats had significantly higher colonic pathology scores, and serum diamine oxidase activity, and meanwhile significantly decreased colonic mucosal Mucin-2 (MUC2) protein expression and fecal scores, evidencing the HES-triggered colonic systemic inflammation. The bacterial taxa Prevotella sp. P4-67, Prevotella sp. PINT, and Bacteroides sp. CAG:927, together with fungal taxa Fusarium vanettenii, Neocallimastix californiae, Fusarium sp. AF-8, Hypoxylon sp. EC38, and Fusarium pseudograminearum, and the involved microbial immune pathways including the "T cell receptor signaling pathway" were higher in the colon of HES goats. The integrated metagenome and host transcriptome analysis revealed that these taxa were associated with enhanced pathogenic ability, antigen processing and presentation, and stimulated T helper 2 cell (TH2)-mediated cytokine secretion functions in the colon of HES goats. Further luminal metabolomics analysis showed increased relative content of chenodeoxycholic acid (CDCA) and deoxycholic acid (DCA), and decreased the relative content of hypoxanthine in colonic digesta of HES goats. These altered metabolites contributed to enhancing the expression of TH2-mediated inflammatory-related cytokine secretion including GATA Binding Protein 3 (GATA3), IL-5, and IL-13. Using the linear mixed effect model, the variation of MUC2 biosynthesis explained by the colonic bacteria, bacterial functions, fungi, fungal functions, and metabolites were 21.92, 20.76, 19.43, 12.08, and 44.22%, respectively. The variation of pathology scores explained by the colonic bacterial functions, fungal functions, and metabolites were 15.35, 17.61, and 57.06%.

CONCLUSIONS: Our findings revealed that enteral starch overload can trigger interrupted hindgut host-microbiome homeostasis that led to impaired mucosal, destroyed colonic water absorption, and TH2-mediated inflammatory process. Except for the colonic metabolites mostly contribute to the impaired mucosa, the nonnegligible contribution from fungi deserves more future studies focused on the fungal functions in hindgut dysbiosis of young ruminants. Video Abstract.}, } @article {pmid38395368, year = {2024}, author = {Lin, Z and Wu, W and Yang, C and Yang, G and Wu, W and Wei, T and Huang, F and Li, H and Ren, L and Liang, Y and Zhang, D and Li, Z and Zhen, Z}, title = {Mechanisms of biochar assisted di-2-ethylhexyl phthalate (DEHP) biodegradation in tomato rhizosphere by metabolic and metagenomic analysis.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {141520}, doi = {10.1016/j.chemosphere.2024.141520}, pmid = {38395368}, issn = {1879-1298}, abstract = {The intensive accumulation of di-2-ethylhexyl phthalate (DEHP) in agricultural soils has resulted in severe environmental pollution that endangers ecosystem and human health. Biochar is an eco-friendly material that can help in accelerating organic pollutant degradation; nevertheless, its roles in enhancing DEHP removal in rhizosphere remain unclear. This work investigated the impacts of biochar dosage (0%-2.0%) on DEHP degradation performance in tomato rhizosphere by comprehensively exploring the change in DEHP metabolites, bacterial communities and DEHP-degrading genes. Our results showed a significant increase of rhizosphere pH, organic matter and humus by biochar amendment, which achieved a satisfactorily higher DEHP removal efficiency, maximally 77.53% in treatments with 1.0% of biochar. Biochar addition also remarkably changed rhizosphere bacterial communities by enriching some potential DEHP degraders of Nocardioides, Sphingomonas, Bradyrhizobium and Rhodanobacter. The abundance of genes encoding key enzymes (hydrolase, esterase and cytochrome P450) and DEHP-degrading genes (pht3, pht4, pht5, benC-xylZ and benD-xylL) were increased after biochar amendment, leading to the change in DEHP degradation metabolism, primarily from benzoic acid pathway to protocatechuic acid pathway. Our findings evidenced that biochar amendment could accelerate DEHP degradation by altering rhizosphere soil physicochemical variables, bacterial community composition and metabolic genes, providing clues for the mechanisms of biochar-assisted DEHP degradation in organic contaminated farmland soils.}, } @article {pmid38395220, year = {2024}, author = {Huang, L and Tong, X and Cui, J and Du, X and Liao, Y and Tan, X and Ju, Y and Zhong, X and Zhou, W and Xu, X and Li, Y}, title = {Recurrent and persistent fever after SARS-CoV-2 infection in patients with follicular lymphoma: a case series.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ijid.2024.02.016}, pmid = {38395220}, issn = {1878-3511}, abstract = {Whilst persistent or recurrent COVID-19 infection is well described among some immunosuppressed patient cohort, to date there have been no reports of this phenomenon in the context of repeatedly negative SARS-CoV-2 testing in the upper respiratory tract. We reported 6 follicular lymphoma developed recurrent symptomatic COVID-19 infection. They tested persistently negative for SARS-CoV-2 on pharyngeal swabs and ultimately confirmed by BALF metagenomics next generation sequencing. All 6 patients presented with lymphopenia and B-cell depletion, and 5 of them received the anti-CD 20 treatment in the last year. Persistent fever was the most common symptom and bilateral ground glass opacities were the primary pattern on chest computed tomography. A relatively long course of unnecessary and ineffective antibacterial and/or antifungal treatments was administered until the definitive diagnosis. Persistent fever subsided rapidly with nirmatrelvir/ritonavir treatment. Our case highlighted that recurrent COVID-19 infection should be suspected in immunocompromised patients with persistent fever despite negative pharyngeal swabs, and urgent BALF testing is necessary. Treatment with nirmatrelvir/ritonavir appeared to be very effective in these patients.}, } @article {pmid38394893, year = {2024}, author = {Chen, T and Mo, C and Yuan, Y and Li, S and Wu, Y and Liao, X and Yang, Y}, title = {Short-, long-read metagenome and virome reveal the profile of phage-mediated ARGs in anoxic-oxic processes for swine wastewater treatment.}, journal = {Journal of hazardous materials}, volume = {468}, number = {}, pages = {133789}, doi = {10.1016/j.jhazmat.2024.133789}, pmid = {38394893}, issn = {1873-3336}, abstract = {Phages are among the most widely spread viruses, but their profiles and the antibiotic resistance genes (ARGs) they carry in swine wastewater remain underexplored. The present study investigated the distribution characteristics of phages and their ARG risk in anoxic/oxic (A/O) wastewater treatment processes of swine farms using short- and long-read metagenome and virome. The results demonstrated that the virome could extract more phage sequences than the total metagenome; thus, it was more suited for studying phages in wastewater settings. Intriguingly, phages had significantly lower abundance of ARG than ARGs harbored by total microorganisms (P < 0.01). Eleven ARGs co-occurred with phages and bacteria (R > 0.6 and P < 0.05), with Siphoviridae being the phage co-occurring with the most ARGs (5). Horizontal gene transfer (HGT) events were observed between Proteobacteria and the major phyla except for Bacteroidota. Furthermore, there were prophage sequences and ARGs on the same contig in bacterial MAGs. These data strongly demonstrate that phages promote horizontal transfer of ARG between bacterial hosts in A/O processes for swine wastewater treatment. Therefore, the risk of phage-mediated horizontal transfer of ARGs cannot be overlooked despite the low abundance of phage ARGs (pARG).}, } @article {pmid38394877, year = {2024}, author = {Ji, Y and Zhuo, B and Jiang, T and Chen, M and Xu, W and Shen, Y and Cheng, D and Ge, Y}, title = {Talaromyces marneffei endocarditis initially detected by Next Generation Sequencing: A case report.}, journal = {International journal of medical microbiology : IJMM}, volume = {314}, number = {}, pages = {151615}, doi = {10.1016/j.ijmm.2024.151615}, pmid = {38394877}, issn = {1618-0607}, abstract = {BACKGROUND: Talaromyces marneffei (T. marneffei) is a thermal dimorphic fungus, which can cause lung or blood stream infection in patients, often life-threatening. However, endocarditis caused by T. marneffei has not been reported. For elderly patients with implanted cardiac devices or artificial valves, the prevention and treatment of infective endocarditis should not be ignored.

METHODS: This is a descriptive study of a T. marneffei endocarditis by joint detection of cardiac ultrasound examination, peripheral blood DNA metagenomics Next Generation Sequencing (mNGS), and in vitro culture.

RESULTS: We describe an 80-year-old female patient with an unusual infection of T. marneffei endocarditis. After intravenous drip of 0.2 g voriconazole twice a day for antifungal treatment, the patient showed no signs of improvement and their family refused further treatment.

CONCLUSION: Infective endocarditis is becoming more and more common in the elderly due to the widely use of invasive surgical procedures and implantation of intracardiac devices. The diagnosis and treatment of T. marneffei endocarditis is challenging because of its rarity. Here, we discussed a case of T. marneffei endocarditis, and emphasized the role of mNGS in early diagnosis, which is of great significance for treatment and survival rate of patients.}, } @article {pmid38394797, year = {2024}, author = {Patel, ZZ and Joshi, H and Puvar, A and Pandit, R and Joshi, C and Joshi, M and Tipre, DR}, title = {A study into the diversity of coral-associated bacteria using culture-dependent and culture-independent approaches in coral Dipsastraea favus from the Gulf of Kutch.}, journal = {Marine pollution bulletin}, volume = {201}, number = {}, pages = {116172}, doi = {10.1016/j.marpolbul.2024.116172}, pmid = {38394797}, issn = {1879-3363}, abstract = {Corals harbour ~25 % of the marine diversity referring to biodiversity hotspots in marine ecosystems. Global efforts to find ways to restore the coral reef ecosystem from various threats can be complemented by studying coral-associated bacteria. Coral-associated bacteria are vital components of overall coral wellbeing. We explored the bacterial diversity associated with coral Dipsastraea favus (D. favus) collected from the Gulf of Kutch, India, using both culture-dependent and metagenomic approaches. In both approaches, phylum Proteobacteria, Firmicutes, and Actinobacteria predominated, comprising the genera Vibrio, Bacillus, Shewanella, Pseudoalteromonas, Exiguobacterium and Streptomyces. Moreover, the majority of culturable isolates showed multiple antibiotic resistance index ≥0.2. In this study, specific bacterial diversity associated with coral sp. D. favus and its possible role in managing coral health was established. Almost 43 strains from the samples were successfully cultured, creating a base for exploring these microbes for their potential use in coral conservation methods.}, } @article {pmid38393114, year = {2024}, author = {Yu, JS and Kim, M and Cho, IH and Sim, YM and Hwang, YS}, title = {Evidence Supporting Oral Hygiene Management by Owners through a Genetic Analysis of Dental Plaque Bacteria in Dogs.}, journal = {Veterinary sciences}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/vetsci11020096}, pmid = {38393114}, issn = {2306-7381}, support = {2023//Eulji University/ ; }, abstract = {With the increase in the number of households raising dogs and the reports of human-to-dog transmission of oral bacteria, concerns about dogs' oral health and the need for oral hygiene management are increasing. In this study, the owners' perceptions about their dogs' oral health and the frequency of oral hygiene were determined along with the analysis of dog dental plaque bacteria through metagenomic amplicon sequencing so as to support the need for oral hygiene management for dogs. Although the perception of 63.2% of the owners about their dogs' oral health was consistent with the veterinarian's diagnosis, the owners' oral hygiene practices regarding their dogs were very poor. The calculi index (CI) and gingiva index (GI) were lower in dogs who had their teeth brushed more than once a week (57.89%) than in dogs brushed less than once a month (42.10%); however, the difference was nonsignificant (CI: p = 0.479, GI: p = 0.840). Genomic DNA was extracted from dental plaque bacteria removed during dog teeth scaling, and metagenomic amplicons were sequenced. The 16S amplicons of 73 species were identified from among the plaque bacteria of the dogs. These amplicons were of oral disease-causing bacteria in humans and dogs. The 16S amplicon of Streptococcus mutans matched that of the human S. mutans, with type c identified as the main serotype. This result suggests that human oral bacteria can be transmitted to dogs. Therefore, considering the high frequency of contact between dogs and humans because of communal living and the current poor oral health of dogs, owners must improve the oral hygiene management of their dogs.}, } @article {pmid38393105, year = {2024}, author = {Shao, Y and Qi, Z and Sang, J and Yu, Z and Li, M and Wang, Z and Tu, J and Song, X and Qi, K}, title = {Metagenome-Based Analysis of the Microbial Community Structure and Drug-Resistance Characteristics of Livestock Feces in Anhui Province, China.}, journal = {Veterinary sciences}, volume = {11}, number = {2}, pages = {}, doi = {10.3390/vetsci11020087}, pmid = {38393105}, issn = {2306-7381}, support = {32202891//National Science Fund for Distinguished Young Scholars of China/ ; 32372955//National Natural Science Foundation of China/ ; }, abstract = {We analyzed metagenome data of feces from sows at different physiological periods reared on large-scale farms in Anhui Province, China, to provide a better understanding of the microbial diversity of the sow intestinal microbiome and the structure of antibiotic-resistance genes (ARGs) and virulence genes it carries. Species annotation of the metagenome showed that in the porcine intestinal microbiome, bacteria were dominant, representing >97% of the microorganisms at each physiological period. Firmicutes and Proteobacteria dominated the bacterial community. In the porcine gut microbiome, the viral component accounted for an average of 0.65%, and the species annotation results indicated that most viruses were phages. In addition, we analyzed the microbiome for ARGs and virulence genes. Multidrug-like, MLS-like, and tetracycline-like ARGs were most abundant in all samples. Evaluation of the resistance mechanisms indicated that antibiotic inactivation was the main mechanism of action in the samples. It is noteworthy that there was a significant positive correlation between ARGs and the total microbiome. Moreover, comparative analysis with the Virulence Factor Database showed that adhesion virulence factors were most abundant.}, } @article {pmid38393013, year = {2024}, author = {Riggen-Bueno, V and Del Toro-Arreola, S and Baltazar-Díaz, TA and Vega-Magaña, AN and Peña-Rodríguez, M and Castaño-Jiménez, PA and Sánchez-Orozco, LV and Vera-Cruz, JM and Bueno-Topete, MR}, title = {Intestinal Dysbiosis in Subjects with Obesity from Western Mexico and Its Association with a Proinflammatory Profile and Disturbances of Folate (B9) and Carbohydrate Metabolism.}, journal = {Metabolites}, volume = {14}, number = {2}, pages = {}, pmid = {38393013}, issn = {2218-1989}, support = {IECD 271879//University of Guadalajara/ ; }, abstract = {Obesity is a public health problem with a growing prevalence worldwide. In Mexico, it is estimated that one out of three adults suffer from obesity. In these patients, the intestinal microbiota (IM) undergoes pathological changes that are associated with a dysbiotic state; however, the microbiota profile of adult subjects with obesity from western Mexico has not been described. To assess this, fecal samples were obtained from 65 participants (Obese = 38; Control = 27). The microbial composition was characterized by 16S rRNA amplicon sequencing. The IM of the group with obesity revealed a clear decrease in richness and diversity (p < 0.001), as well as a significant increase in proinflammatory bacterial groups, mainly genera belonging to the Negativicutes class, Escherichia/Shigella, and Prevotella. Likewise, an increase in short-chain fatty acid-producing bacteria was found, especially the genus Lachnoclostridium. Additionally, PICRUSt2 analysis showed a depletion of vitamin B9 metabolism and an increase in saccharolytic pathways. The IM of patients with obesity possesses a dysbiotic, proinflammatory environment, possibly contributing to lipogenesis and adiposity. Thus, assessing the IM will allow for a better understanding of the pathophysiology of metabolic diseases of high prevalence, such as obesity. These findings are described for the first time in the adult population of western Mexico.}, } @article {pmid38393009, year = {2024}, author = {Zulfiqar, M and Crusoe, MR and König-Ries, B and Steinbeck, C and Peters, K and Gadelha, L}, title = {Implementation of FAIR Practices in Computational Metabolomics Workflows-A Case Study.}, journal = {Metabolites}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/metabo14020118}, pmid = {38393009}, issn = {2218-1989}, support = {390713860//Deutsche Forschungsgemeinschaft/ ; }, abstract = {Scientific workflows facilitate the automation of data analysis tasks by integrating various software and tools executed in a particular order. To enable transparency and reusability in workflows, it is essential to implement the FAIR principles. Here, we describe our experiences implementing the FAIR principles for metabolomics workflows using the Metabolome Annotation Workflow (MAW) as a case study. MAW is specified using the Common Workflow Language (CWL), allowing for the subsequent execution of the workflow on different workflow engines. MAW is registered using a CWL description on WorkflowHub. During the submission process on WorkflowHub, a CWL description is used for packaging MAW using the Workflow RO-Crate profile, which includes metadata in Bioschemas. Researchers can use this narrative discussion as a guideline to commence using FAIR practices for their bioinformatics or cheminformatics workflows while incorporating necessary amendments specific to their research area.}, } @article {pmid38392888, year = {2024}, author = {Ford, CE and Dunn, CD and Leis, EM and Thiel, WA and Goldberg, TL}, title = {Five Species of Wild Freshwater Sport Fish in Wisconsin, USA, Reveal Highly Diverse Viromes.}, journal = {Pathogens (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/pathogens13020150}, pmid = {38392888}, issn = {2076-0817}, support = {R/SFA-24//University of Wisconsin Sea Grant Institute/ ; }, abstract = {Studies of marine fish have revealed distant relatives of viruses important to global fish and animal health, but few such studies exist for freshwater fish. To investigate whether freshwater fish also host such viruses, we characterized the viromes of five wild species of freshwater fish in Wisconsin, USA: bluegill (Lepomis macrochirus), brown trout (Salmo trutta), lake sturgeon (Acipenser fulvescens), northern pike (Esox lucius), and walleye (Sander vitreus). We analyzed 103 blood serum samples collected during a state-wide survey from 2016 to 2020 and used a metagenomic approach for virus detection to identify known and previously uncharacterized virus sequences. We then characterized viruses phylogenetically and quantified prevalence, richness, and relative abundance for each virus. Within these viromes, we identified 19 viruses from 11 viral families: Amnoonviridae, Circoviridae, Coronaviridae, Hepadnaviridae, Peribunyaviridae, Picobirnaviridae, Picornaviridae, Matonaviridae, Narnaviridae, Nudnaviridae, and Spinareoviridae, 17 of which were previously undescribed. Among these viruses was the first fish-associated coronavirus from the Gammacoronavirus genus, which was present in 11/15 (73%) of S. vitreus. These results demonstrate that, similar to marine fish, freshwater fish also harbor diverse relatives of viruses important to the health of fish and other animals, although it currently remains unknown what effect, if any, the viruses we identified may have on fish health.}, } @article {pmid38392689, year = {2024}, author = {Tronel, A and Silvent, AS and Buelow, E and Giai, J and Leroy, C and Proust, M and Martin, D and Le Gouellec, A and Soranzo, T and Mathieu, N}, title = {Pilot Study: Safety and Performance Validation of an Ingestible Medical Device for Collecting Small Intestinal Liquid in Healthy Volunteers.}, journal = {Methods and protocols}, volume = {7}, number = {1}, pages = {}, doi = {10.3390/mps7010015}, pmid = {38392689}, issn = {2409-9279}, support = {i-Lab DOS0172081/00//BPIFrance/ ; CIFRE 2021-0931//Association Nationale de la Recherche et de la Technologie (ANRT)/ ; }, abstract = {The connection between imbalances in the human gut microbiota, known as dysbiosis, and various diseases has been well established. Current techniques for sampling the small intestine are both invasive for patients and costly for healthcare facilities. Most studies on human gut microbiome are conducted using faecal samples, which do not accurately represent the microbiome in the upper intestinal tract. A pilot clinical investigation, registered as NCT05477069 and sponsored by the Grenoble Alpes University Hospital, is currently underway to evaluate a novel ingestible medical device (MD) designed for collecting small intestinal liquids by Pelican Health. This study is interventional and monocentric, involving 15 healthy volunteers. The primary objective of the study is to establish the safety and the performance of the MD when used on healthy volunteers. Secondary objectives include assessing the device's performance and demonstrating the difference between the retrieved sample from the MD and the corresponding faecal sample. Multi-omics analysis will be performed, including metagenomics, metabolomics, and culturomics. We anticipate that the MD will prove to be safe without any reported adverse effects, and we collected samples suitable for the proposed omics analyses in order to demonstrate the functionality of the MD and the clinical potential of the intestinal content.}, } @article {pmid38391568, year = {2024}, author = {Mena Navarro, MP and Espinosa Bernal, MA and Alvarado Osuna, C and Ramos López, MÁ and Amaro Reyes, A and Arvizu Gómez, JL and Pacheco Aguilar, JR and Saldaña Gutiérrez, C and Pérez Moreno, V and Rodríguez Morales, JA and García Gutiérrez, MC and Álvarez Hidalgo, E and Nuñez Ramírez, J and Hernández Flores, JL and Campos Guillén, J}, title = {A Study of Resistome in Mexican Chili Powder as a Public Health Risk Factor.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/antibiotics13020182}, pmid = {38391568}, issn = {2079-6382}, support = {FONDEC-UAQ-2022; FOPES 2023; FOPER-2023//Autonomous University of Queretaro/ ; }, abstract = {Chili powder is an important condiment around the world. However, according to various reports, the presence of pathogenic microorganisms could present a public health risk factor during its consumption. Therefore, microbiological quality assessment is required to understand key microbial functional traits, such as antibiotic resistance genes (ARGs). In this study, metagenomic next-generation sequencing (mNGS) and bioinformatics analysis were used to characterize the comprehensive profiles of the bacterial community and antibiotic resistance genes (ARGs) in 15 chili powder samples from different regions of Mexico. The initial bacterial load showed aerobic mesophilic bacteria (AMB) ranging between 6 × 10[3] and 7 × 10[8] CFU/g, sporulated mesophilic bacteria (SMB) from 4.3 × 10[3] to 2 × 10[9] CFU/g, and enterobacteria (En) from <100 to 2.3 × 10[6] CFU/g. The most representative families in the samples were Bacillaceae and Enterobacteriaceae, in which 18 potential pathogen-associated species were detected. In total, the resistome profile in the chili powder contained 68 unique genes, which conferred antibiotic resistance distributed in 13 different classes. Among the main classes of antibiotic resistance genes with a high abundance in almost all the samples were those related to multidrug, tetracycline, beta-lactam, aminoglycoside, and phenicol resistance. Our findings reveal the utility of mNGS in elucidating microbiological quality in chili powder to reduce the public health risks and the spread of potential pathogens with antibiotic resistance mechanisms.}, } @article {pmid38391513, year = {2024}, author = {Hanafiah, A and Sukri, A and Yusoff, H and Chan, CS and Hazrin-Chong, NH and Salleh, SA and Neoh, HM}, title = {Insights into the Microbiome and Antibiotic Resistance Genes from Hospital Environmental Surfaces: A Prime Source of Antimicrobial Resistance.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/antibiotics13020127}, pmid = {38391513}, issn = {2079-6382}, support = {GUP-2019-083//National University of Malaysia/ ; }, abstract = {Hospital environmental surfaces are potential reservoirs for transmitting hospital-associated pathogens. This study aimed to profile microbiomes and antibiotic resistance genes (ARGs) from hospital environmental surfaces using 16S rRNA amplicon and metagenomic sequencing at a tertiary teaching hospital in Malaysia. Samples were collected from patient sinks and healthcare staff counters at surgery and orthopaedic wards. The samples' DNA were subjected to 16S rRNA amplicon and shotgun sequencing to identify bacterial taxonomic profiles, antibiotic resistance genes, and virulence factor pathways. The bacterial richness was more diverse in the samples collected from patient sinks than those collected from staff counters. Proteobacteria and Verrucomicrobia dominated at the phylum level, while Bacillus, Staphylococcus, Pseudomonas, and Acinetobacter dominated at the genus level. Staphylococcus epidermidis and Staphylococcus aureus were prevalent on sinks while Bacillus cereus dominated the counter samples. The highest counts of ARGs to beta-lactam were detected, followed by ARGs against fosfomycin and cephalosporin. We report the detection of mcr-10.1 that confers resistance to colistin at a hospital setting in Malaysia. The virulence gene pathways that aid in antibiotic resistance gene transfer between bacteria were identified. Environmental surfaces serve as potential reservoirs for nosocomial infections and require mitigation strategies to control the spread of antibiotic resistance bacteria.}, } @article {pmid38391155, year = {2024}, author = {Khattak, F and Galgano, S and Pedersen, NR and Hui, Y and Matthiesen, R and Houdijk, J}, title = {Supplementation of lactobacillus fermented rapeseed meal in broiler diet reduces Campylobacter Jejuni caecal colonisation and limits the L-tryptophan and L-histidine biosynthesis pathways.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.13378}, pmid = {38391155}, issn = {1097-0010}, abstract = {BACKGROUND: Campylobacter jejuni (C. jejuni), a widely distributed global foodborne pathogen primarily linked with contaminated chicken meat, poses a significant health risk. Lowering this pathogen abundance in poultry meat is challenging but essential. This study assessed the impact of lactobacillus-fermented rapeseed meal (LFRM) on broilers exposed to C. jejuni contaminated litter, evaluating growth performance, Campylobacter levels, and metagenomic profile.

RESULTS: By day 35, the litter contamination successfully colonised broilers with Campylobacter spp., particularly C. jejuni. In the grower phase, LFRM improved (P < 0.05) body weight and daily weight gain, resulting in a 9.2% better feed conversion ratio during the pre-challenged period (days 13 to 20). LFRM also reduced C. jejuni concentration in the caeca (P < 0.05), without altering alfa and beta diversity. However, metagenomic data analysis revealed LFRM targeted reduction in the abundance of C. jejuni biosynthetic pathways of L-tryptophan and L-histidine and gene families associated with transcription and virulence factors whilst also possibly leading to a selected stress-induced resistance mechanisms.

CONCLUSION: The study demonstrated that LFRM inclusion improved growth and decreased caecal Campylobacter spp. concentration and relative abundance of pivotal C. jejuni genes. Performance benefits likely resulted from LFRM metabolites. At the molecular level, LFRM may have reduced C. jejuni colonisation, likely by decreasing abundance of energy transduction and L-histidine and L-tryptophan biosynthesis genes, otherwise required for bacterial survival and increased virulence. This article is protected by copyright. All rights reserved.}, } @article {pmid38390939, year = {2024}, author = {Xu, ZF and Yuan, L and Zhang, Y and Zhang, W and Wei, C and Wang, W and Zhao, D and Zhou, D and Li, J}, title = {The Gut Microbiome Correlated to Chemotherapy Efficacy in Diffuse Large B-Cell Lymphoma Patients.}, journal = {Hematology reports}, volume = {16}, number = {1}, pages = {63-75}, doi = {10.3390/hematolrep16010007}, pmid = {38390939}, issn = {2038-8322}, support = {81970188//National Natural Science Foundation of China/ ; 2021-I2M-1-041//CAMS Innovation Fund for Medical Sciences/ ; }, abstract = {The gut microbiome (GMB) has been extensively reported to be associated with the development and prognosis of human diseases. This study aims to investigate the relationship between GMB composition and chemotherapy efficacy in diffuse large B-cell lymphoma (DLBCL). We demonstrated that DLBCL patients at diagnosis have altered GMB compositions. Significant enrichment of the Proteobacteria phylum in DLBCL patients was observed. Gene analysis showed a high abundance of virulence factors genes. We found baseline GMB to be associated with clinical outcomes. The emergence of Lactobacillus fermentum was correlated with better treatment outcome. Our pilot results suggested a correlation between GMB composition and DLBCL development and prognosis. Clues from our study, together with previous research, provided a rational foundation for further investigation on the pathogenesis, prognosis value, and targeted therapy of GMB in DLBCL.}, } @article {pmid38390522, year = {2024}, author = {Bech, PK and Jarmusch, SA and Rasmussen, JA and Limborg, MT and Gram, L and Henriksen, NNSE}, title = {Succession of microbial community composition and secondary metabolism during marine biofilm development.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycae006}, pmid = {38390522}, issn = {2730-6151}, abstract = {In nature, secondary metabolites mediate interactions between microorganisms residing in complex microbial communities. However, the degree to which community dynamics can be linked to secondary metabolite potential remains largely unknown. In this study, we address the relationship between community succession and secondary metabolism variation. We used 16S and 18S rRNA gene and adenylation domain amplicon sequencing, genome-resolved metagenomics, and untargeted metabolomics to track the taxons, biosynthetic gene clusters, and metabolome dynamics in situ of microorganisms during marine biofilm succession over 113 days. Two phases were identified during the community succession, with a clear shift around Day 29, where the alkaloid secondary metabolites, pseudanes, were also detected. The microbial secondary metabolite potential changed between the phases, and only a few community members, including Myxococotta spp., were responsible for the majority of the biosynthetic gene cluster potential in the early succession phase. In the late phase, bryozoans and benthic copepods were detected, and the microbial nonribosomal peptide potential drastically decreased in association with a reduction in the relative abundance of the prolific secondary metabolite producers. Conclusively, this study provides evidence that the early succession of the marine biofilm community favors prokaryotes with high nonribosomal peptide synthetase potential. In contrast, the late succession is dominated by multicellular eukaryotes and a reduction in bacterial nonribosomal peptide synthetase potential.}, } @article {pmid38390520, year = {2024}, author = {Bittner, MJ and Bannon, CC and Rowland, E and Sundh, J and Bertrand, EM and Andersson, AF and Paerl, RW and Riemann, L}, title = {New chemical and microbial perspectives on vitamin B1 and vitamer dynamics of a coastal system.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycad016}, pmid = {38390520}, issn = {2730-6151}, abstract = {Vitamin B1 (thiamin, B1) is an essential micronutrient for cells, yet intriguingly in aquatic systems most bacterioplankton are unable to synthesize it de novo (auxotrophy), requiring an exogenous source. Cycling of this valuable metabolite in aquatic systems has not been fully investigated and vitamers (B1-related compounds) have only begun to be measured and incorporated into the B1 cycle. Here, we identify potential key producers and consumers of B1 and gain new insights into the dynamics of B1 cycling through measurements of B1 and vitamers (HMP: 4-amino-5-hydroxymethyl-2-methylpyrimidine, HET: 4-methyl-5-thiazoleethanol, FAMP: N-formyl-4-amino-5-aminomethyl-2-methylpyrimidine) in the particulate and dissolved pool in a temperate coastal system. Dissolved B1 was not the primary limiting nutrient for bacterial production and was relatively stable across seasons with concentrations ranging from 74-117 pM, indicating a balance of supply and demand. However, vitamer concentration changed markedly with season as did transcripts related to vitamer salvage and transport suggesting use of vitamers by certain bacterioplankton, e.g. Pelagibacterales. Genomic and transcriptomic analyses showed that up to 78% of the bacterioplankton taxa were B1 auxotrophs. Notably, de novo B1 production was restricted to a few abundant bacterioplankton (e.g. Vulcanococcus, BACL14 (Burkholderiales), Verrucomicrobiales) across seasons. In summer, abundant picocyanobacteria were important putative B1 sources, based on transcriptional activity, leading to an increase in the B1 pool. Our results provide a new dynamic view of the players and processes involved in B1 cycling over time in coastal waters, and identify specific priority populations and processes for future study.}, } @article {pmid38390220, year = {2023}, author = {Dou, S and Ma, G and Liang, Y and Fu, G and Shen, J and Fu, L and Wang, Q and Li, T and Cong, B and Li, S}, title = {Preliminary exploratory research on the application value of oral and intestinal meta-genomics in predicting subjects' occupations-A case study of the distinction between students and migrant workers.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1330603}, doi = {10.3389/fmicb.2023.1330603}, pmid = {38390220}, issn = {1664-302X}, abstract = {BACKGROUND: In the field of forensic science, accurately determining occupation of an individual can greatly assist in resolving cases such as criminal investigations or disaster victim identifications. However, estimating occupation can be challenging due to the intricate relationship between occupation and various factors, including gender, age, living environment, health status, medication use, and lifestyle habits such as alcohol consumption and smoking. All of these factors can impact the composition of oral or gut microbial community of an individual.

METHODS AND RESULTS: In this study, we collected saliva and feces samples from individuals representing different occupational sectors, specifically students and manual laborers. We then performed metagenomic sequencing on the DNA extracted from these samples to obtain data that could be analyzed for taxonomic and functional annotations in five different databases. The correlation between occupation with microbial information was assisted from the perspective of α and β diversity, showing that individuals belonging to the two occupations hold significantly different oral and gut microbial communities, and that this correlation is basically not affected by gender, drinking, and smoking in our datasets. Finally, random forest (RF) models were built with recursive feature elimination (RFE) processes. Models with 100% accuracy in both training and testing sets were constructed based on three species in saliva samples or on a single pathway annotated by the KEGG database in fecal samples, namely, "ko04145" or Phagosome.

CONCLUSION: Although this study may have limited representativeness due to its small sample size, it provides preliminary evidence of the potential of using microbiome information for occupational inference.}, } @article {pmid38389952, year = {2023}, author = {Shao, A and He, Q and Jiao, X and Liu, J}, title = {Hemoptysis caused by Parvimonas micra: case report and literature review.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1307902}, doi = {10.3389/fpubh.2023.1307902}, pmid = {38389952}, issn = {2296-2565}, abstract = {BACKGROUND: Parvimonas micra (P. micra), a Gram-positive anaerobic bacterium, exhibits colonization tendencies on oral mucosal and skin surfaces, potentially evolving into a pathogenic entity associated with diverse diseases. The diagnostic trajectory for P. micra-related diseases encounters delays, often with severe consequences, including fatality, attributed to the absence of symptom specificity and challenges in culture. The absence of a consensus on the diagnostic and therapeutic approaches to P. micra exacerbates the complexity of addressing associated conditions. This study aims to elucidate and scrutinize the clinical manifestations linked to P. micra, drawing insights from an extensive literature review of pertinent case reports.

CASE PRESENTATION: A 53-year-old male sought medical attention at our institution presenting with recurrent hemoptysis. Empirical treatment was initiated while awaiting pathogen culture results; however, the patient's symptoms persisted. Subsequent metagenomic next-generation sequencing (mNGS) analysis revealed a pulmonary infection attributable to P. micra. Resolution of symptoms occurred following treatment with piperacillin sulbactam sodium and moxifloxacin hydrochloride. A comprehensive literature review, utilizing the PubMed database, was conducted to assess case reports over the last decade where P. micra was identified as the causative agent.

CONCLUSION: The literature analysis underscores the predilection of P. micra for immunocompromised populations afflicted by cardiovascular diseases, diabetes, orthopedic conditions, and tumors. Risk factors, including oral and periodontal hygiene, smoking, and alcohol consumption, were found to be associated with P. micra infections. Clinical manifestations encompassed fever, cough, sputum production, and back pain, potentially leading to severe outcomes such as Spondylodiscitis, septic arthritis, lung abscess, bacteremia, sepsis, and mortality. While conventional bacterial culture remains the primary diagnostic tool, emerging technologies like mNGS offer alternative considerations. In terms of treatment modalities, β-lactam antibiotics and nitroimidazoles predominated, exhibiting recovery rates of 56.10% (46/82) and 23.17% (19/82), respectively. This case report and literature review collectively aim to enhance awareness among clinicians and laboratory medicine professionals regarding the intricacies of P. micra-associated infections.}, } @article {pmid38388811, year = {2024}, author = {de Carvalho, FM and Laux, M and Ciapina, LP and Gerber, AL and Guimarães, APC and Kloh, VP and Apolinário, M and Paes, JES and Jonck, CR and de Vasconcelos, ATR}, title = {Finding microbial composition and biological processes as predictive signature to access the ongoing status of mangrove preservation.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {38388811}, issn = {1618-1905}, support = {2018/00190-8//Petrobras/ ; 2018/00190-8//Petrobras/ ; 2018/00190-8//Petrobras/ ; E-26/201.046/2022//Fundação Carlos Chagas Filho de Amparo à Pesquisa do Estado do Rio de Janeiro/ ; 307145/2021-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {Mangroves are complex land-sea transition ecosystems whose microbiota are essential for their nutrient recycling and conservation. Brazil is the third-largest estuarine area in the world and "Baía de Todos os Santos" (BTS) is one of the largest bays of the country, with wide anthropogenic exploration. Using a metagenomic approach, we investigated composition and functional adaptability as signatures of the microbiome of pristine and anthropized areas of BTS, including those under petroleum refinery influence. The taxonomic analysis showed dominance of sulfate-reducing Desulfobacteraceae, Rhodobacteraceae, and Flavobacteriaceae. Taxa were significantly diverse between pristine and disturbed areas. Disturbed mangroves showed a notary increase in abundance of halophilic, sulfur-related, and hydrocarbon-degrading genera and a decrease in diatoms compared to pristine area. The metabolic profile of BTS mangroves was correlated with the differentially abundant microbiota. Two ecological scenarios were observed: one marked by functions of central metabolism associated with biomass degradation and another by mechanisms of microbial adaptability to pollution conditions and environmental degradation. Part of the microbiome was distinct and not abundant in Brazilian estuarine soils. The microbiome signature observed in each BTS mangrove reflects how human actions impact the diversity of these ecosystems and also emphasize their role in attempting to restore disturbed mangroves. The microbiome may act as a potential biological indicator of the preservation status of these soils, despite the limitation of soil property conditions. Additionally, our data pointed to metagenomics as an additional tool for environmental assessment and reinforced the need for protective measures for the mangroves under study.}, } @article {pmid38388732, year = {2024}, author = {Maruyama, R and Yasumoto, K and Mizusawa, N and Iijima, M and Yasumoto-Hirose, M and Iguchi, A and Hermawan, OR and Hosono, T and Takada, R and Song, KH and Shinjo, R and Watabe, S and Yasumoto, J}, title = {Metagenomic analysis of the microbial communities and associated network of nitrogen metabolism genes in the Ryukyu limestone aquifer.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4356}, pmid = {38388732}, issn = {2045-2322}, support = {20H03077//Grants-in-Aid from the Japan Society for the Promotion of Science/ ; 19K12310//Grants-in-Aid from the Japan Society for the Promotion of Science/ ; JPMEERF20194007//Environment Research and Technology Development Fund/ ; RIHN14200145//Research Institute for Humanity and Nature/ ; JPMJRX19IA//Solution-Driven Co-creative R&D Program for SDGs Program/ ; }, abstract = {While microbial biogeochemical activities such as those involving denitrification and sulfate reduction have been considered to play important roles in material cycling in various aquatic ecosystems, our current understanding of the microbial community in groundwater ecosystems is remarkably insufficient. To assess the groundwater in the Ryukyu limestone aquifer of Okinawa Island, which is located in the southernmost region of Japan, we performed metagenomic analysis on the microbial communities at the three sites and screened for functional genes associated with nitrogen metabolism. 16S rRNA amplicon analysis showed that bacteria accounted for 94-98% of the microbial communities, which included archaea at all three sites. The bacterial communities associated with nitrogen metabolism shifted by month at each site, indicating that this metabolism was accomplished by the bacterial community as a whole. Interestingly, site 3 contained much higher levels of the denitrification genes such as narG and napA than the other two sites. This site was thought to have undergone denitrification that was driven by high quantities of dissolved organic carbon (DOC). In contrast, site 2 was characterized by a high nitrate-nitrogen (NO3-N) content and a low amount of DOC, and this site yielded a moderate amount of denitrification genes. Site 1 showed markedly low amounts of all nitrogen metabolism genes. Overall, nitrogen metabolism in the Ryukyu limestone aquifer was found to change based on environmental factors.}, } @article {pmid38388542, year = {2024}, author = {Jia, L and Jiang, Y and Wu, L and Fu, J and Du, J and Luo, Z and Guo, L and Xu, J and Liu, Y}, title = {Porphyromonas gingivalis aggravates colitis via a gut microbiota-linoleic acid metabolism-Th17/Treg cell balance axis.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1617}, pmid = {38388542}, issn = {2041-1723}, support = {81991504//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81974149//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82101009//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82122015//National Natural Science Foundation of China (National Science Foundation of China)/ ; ZYLX202121//Beijing Municipal Administration of Hospitals Clinical Medicine Development of Special Funding Support/ ; }, abstract = {Periodontitis is closely related to inflammatory bowel disease (IBD). An excessive and non-self-limiting immune response to the dysbiotic microbiome characterizes the two. However, the underlying mechanisms that overlap still need to be clarified. We demonstrate that the critical periodontal pathogen Porphyromonas gingivalis (Pg) aggravates intestinal inflammation and Th17/Treg cell imbalance in a gut microbiota-dependent manner. Specifically, metagenomic and metabolomic analyses shows that oral administration of Pg increases levels of the Bacteroides phylum but decreases levels of the Firmicutes, Verrucomicrobia, and Actinobacteria phyla. Nevertheless, it suppresses the linoleic acid (LA) pathway in the gut microbiota, which was the target metabolite that determines the degree of inflammation and functions as an aryl hydrocarbon receptor (AHR) ligand to suppress Th17 differentiation while promoting Treg cell differentiation via the phosphorylation of Stat1 at Ser727. Therapeutically restoring LA levels in colitis mice challenged with Pg exerts anti-colitis effects by decreasing the Th17/Treg cell ratio in an AHR-dependent manner. Our study suggests that Pg aggravates colitis via a gut microbiota-LA metabolism-Th17/Treg cell balance axis, providing a potential therapeutically modifiable target for IBD patients with periodontitis.}, } @article {pmid38383537, year = {2024}, author = {Haeussermann, I and Hasselmann, M}, title = {Complex European invasion history of Anoplophora glabripennis (Motschulsky): new insights in its population genomic differentiation using genotype-by-sequencing.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4263}, pmid = {38383537}, issn = {2045-2322}, support = {2814905615//Federal Office for Agriculture and Food Germany (BLE)/ ; }, mesh = {Animals ; Phylogeny ; *Metagenomics ; Europe ; *Coleoptera/genetics ; Genotype ; }, abstract = {Anthropogenic activities like trade facilitate increasing rates of biological invasions. Asian long-horned beetle (ALB), which is naturally distributed in eastern Asia (China, Korean peninsula), was introduced via wood packing materials (WPM) used in trade to North America (1996) and Europe (2001). We used 7810 single nucleotide polymorphisms (SNPs) derived by a genotype-by-sequencing (GBS) approach to decipher the introduction patterns into Europe. This is applied for the first time on European ALB outbreaks from Germany, Switzerland, and Italy, both from still active and already eradicated infestations. The genome-wide SNPs detected signs of small and highly structured populations within Europe, showing clear founder effects. The very high population differentiation is presumably derived from multiple independent introductions to Europe, which are spatially restricted in mating. By admixture and phylogenetic analyses, some cases of secondary dispersal were observed. Furthermore, some populations suggest admixture, which might have been originated by either multiple introductions from different sources into the new sites or recurrent introductions from an admixed source population. Our results confirmed a complex invasion history of the ALB into Europe and the usability of GBS obtained SNPs in invasion science even without source populations.}, } @article {pmid38388166, year = {2024}, author = {Kaspersen, H and Urdahl, AM and Ilag, HK and Franklin-Alming, FV and Haverkamp, THA and Sunde, M}, title = {Detection of Klebsiella pneumoniae in healthy poultry: Insights and perspectives from culturing and metagenomics.}, journal = {Environmental microbiology reports}, volume = {16}, number = {1}, pages = {e13240}, doi = {10.1111/1758-2229.13240}, pmid = {38388166}, issn = {1758-2229}, support = {TMS2019TMT03//Trond Mohn stiftelse/ ; //Norwegian Veterinary Institute/ ; }, abstract = {Previously, Klebsiella pneumoniae was found to occur more frequently in healthy turkey flocks than in healthy broiler flocks in Norway. This study aimed to investigate whether this higher occurrence could be attributed to a greater abundance of K. pneumoniae in turkey flocks. We compared culturing, qPCR, and shotgun metagenomic sequencing for the detection and quantification of K. pneumoniae. Using qPCR, we found that 20.7% of broiler flock samples and 63.9% of turkey flock samples were positive for K. pneumoniae. Culturing revealed a significantly higher abundance of K. pneumoniae in turkey flocks compared to broiler flocks. However, metagenomic analysis showed no difference in the relative abundance of Klebsiella spp. between broiler and turkey flocks, and no correlation between the results of culturing and metagenomic quantification. Interestingly, the differential abundance of K. quasipneumoniae was significantly different between the two hosts. Our results indicate that Klebsiella spp. are present in both turkey and broiler flocks at relatively low levels but with a higher abundance in turkey flocks. Our findings also suggest that shotgun metagenomic studies targeting low-abundance taxa such as Klebsiella have poor sensitivity when comparing groups, indicating that reliance on results from metagenomic analysis without experimental validation should be done with caution.}, } @article {pmid38388067, year = {2024}, author = {Muñoz-Juan, A and Assié, A and Esteve-Codina, A and Gut, M and Benseny-Cases, N and Samuel, BS and Dalfó, E and Laromaine, A}, title = {Caenorhabditis elegans endorse bacterial nanocellulose fibers as functional dietary Fiber reducing lipid markers.}, journal = {Carbohydrate polymers}, volume = {331}, number = {}, pages = {121815}, doi = {10.1016/j.carbpol.2024.121815}, pmid = {38388067}, issn = {1879-1344}, abstract = {Bacterial nanocellulose (BNC) is a promising dietary fiber with potential as a functional food additive. We evaluated BNC fibers (BNCf) in the Caenorhabditis elegans model to obtain insight into the BNCf's biointeraction with its gastrointestinal tract while reducing the variables of higher complex animals. BNCf were uptaken and excreted by worms without crossing the intestinal barrier, confirming its biosafety regarding survival rate, reproduction, and aging for concentrations up to 34 μg/ml BNCf. However, a slight decrease in the worms' length was detected. A possible nutrient shortage or stress produced by BNCf was discarded by measuring stress and chemotactic response pathways. Besides, we detected a lipid-lowering effect of BNCf in N2 C. elegans in normal and high-caloric diets. Oxidative damage was computed in N2 worms and Rac1/ced-10 mutants. The GTPase Rac1 is involved in neurological diseases, where its dysregulation enhances ROS production and neuronal damage. BNCf reduced the lipid oxidative markers produced by ROS species in this worm strain. Finally, we detected that BNCf activated the genetic expression of the immunological response and lipid catabolic process. These results strengthen the use of BNCf as a functional dietary fiber and encourage the potential treatment of neurological disease by modulating diet.}, } @article {pmid38387349, year = {2024}, author = {Chaudhary, V and Kumar, M and Chauhan, C and Sirohi, U and Srivastav, AL and Rani, L}, title = {Strategies for mitigation of pesticides from the environment through alternative approaches: A review of recent developments and future prospects.}, journal = {Journal of environmental management}, volume = {354}, number = {}, pages = {120326}, doi = {10.1016/j.jenvman.2024.120326}, pmid = {38387349}, issn = {1095-8630}, abstract = {Chemical-based peticides are having negative impacts on both the healths of human beings and plants as well. The World Health Organisation (WHO), reported that each year, >25 million individuals in poor nations are having acute pesticide poisoning cases along with 20,000 fatal injuries at global level. Normally, only ∼0.1% of the pesticide reaches to the intended targets, and rest amount is expected to come into the food chain/environment for a longer period of time. Therefore, it is crucial to reduce the amounts of pesticides present in the soil. Physical or chemical treatments are either expensive or incapable to do so. Hence, pesticide detoxification can be achieved through bioremediation/biotechnologies, including nano-based methodologies, integrated approaches etc. These are relatively affordable, efficient and environmentally sound methods. Therefore, alternate strategies like as advanced biotechnological tools like as CRISPR Cas system, RNAi and genetic engineering for development of insects and pest resistant plants which are directly involved in the development of disease- and pest-resistant plants and indirectly reduce the use of pesticides. Omics tools and multi omics approaches like metagenomics, genomics, transcriptomics, proteomics, and metabolomics for the efficient functional gene mining and their validation for bioremediation of pesticides also discussed from the literatures. Overall, the review focuses on the most recent advancements in bioremediation methods to lessen the effects of pesticides along with the role of microorganisms in pesticides elimination. Further, pesticide detection is also a big challenge which can be done by using HPLC, GC, SERS, and LSPR ELISA etc. which have also been described in this review.}, } @article {pmid38387264, year = {2024}, author = {Wang, G and Feng, Z and Yin, X and Chen, D and Zhao, N and Yuan, Y and Chen, C and Liu, C and Ao, M and Chen, L and Chen, Z and Yang, W and Li, D and Morel, JL and Chao, Y and Wang, P and Tang, Y and Qiu, R and Wang, S}, title = {Biogenic manganese oxides promote metal(loid) remediation by shaping microbial communities in biological aqua crust.}, journal = {Water research}, volume = {253}, number = {}, pages = {121287}, doi = {10.1016/j.watres.2024.121287}, pmid = {38387264}, issn = {1879-2448}, abstract = {Biological aqua crust (biogenic aqua crust-BAC) is a potentially sustainable solution for metal(loid) bioremediation in global water using solar energy. However, the key geochemical factors and underlying mechanisms shaping microbial communities in BAC remain poorly understood. The current study aimed at determining the in situ metal(loid) distribution and the key geochemical factors related to microbial community structure and metal(loid)-related genes in BAC of a representative Pb/Zn tailing pond. Here we showed that abundant metal(loid)s (e.g. Pb, As) were co-distributed with Mn/Fe-rich minerals (e.g. biogenic Mn oxide, FeOOH) in BAC. Biogenic Mn oxide (i.e. Mn) was the most dominant factor in shaping microbial community structure in BAC and source tailings. Along with the fact that keystone species (e.g. Burkholderiales, Haliscomenobacter) have the potential to promote Mn ion oxidization and particle agglomeration, as well as Mn is highly associated with metal(loid)-related genes, especially genes related to As redox (e.g. arsC, aoxA), and Cd transport (e.g. zipB), biogenic Mn oxides thus effectively enhance metal(loid) remediation by accelerating the formation of organo-mineral aggregates in biofilm-rich BAC system. Our study indicated that biogenic Mn oxides may play essential roles in facilitating in situ metal(loid) bioremediation in BAC of mine drainage.}, } @article {pmid38387163, year = {2024}, author = {Cotes-Perdomo, AP and Sánchez-Vialas, A and Thomas, R and Jenkins, A and Uribe, JE}, title = {New insights into the systematics of the afrotropical Amblyomma marmoreum complex (Acari: Ixodidae) and the genome of a novel Rickettsia africae strain using morphological and metagenomic approaches.}, journal = {Ticks and tick-borne diseases}, volume = {15}, number = {3}, pages = {102323}, doi = {10.1016/j.ttbdis.2024.102323}, pmid = {38387163}, issn = {1877-9603}, abstract = {The Amblyomma marmoreum complex includes afrotropical species, such as Amblyomma sparsum, a three-host tick that parasitizes reptiles, birds, and mammals, and is a recognized vector of Ehrlichia ruminantium. However, the lack of morphological, genetic and ecological data on A. sparsum has caused considerable confusion in its identification. In this study, we used microscopy and metagenomic approaches to analyze A. sparsum ticks collected from a puff adder snake (Bitis arietans) in southwest Senegal (an endemic rickettsioses area) in order to supplement previous morphological descriptions, provide novel genomic data for the A. marmoreum complex, and describe the genome of a novel spotted fever group Rickettsia strain. Based on stereoscope and scanning electron microscopy (SEM) morphological evaluations, we provide high-quality images and new insights about punctation and enameling in the adult male of A. sparsum to facilitate identification for future studies. The metagenomic approach allowed us assembly the complete mitochondrial genome of A. sparsum, as well as the nearly entire chromosome and complete plasmid sequences of a novel Rickettsia africae strain. Phylogenomic analyses demonstrated a close relationship between A. sparsum and Amblyomma nuttalli for the first time and confirmed the position of A. sparsum within the A. marmoreum complex. Our results provide new insights into the systematics of A. sparsum and A. marmoreum complex, as well as the genetic diversity of R. africae in the Afrotropical region. Future studies should consider the possibility that A. sparsum may be a vector for R. africae.}, } @article {pmid38387153, year = {2024}, author = {Yi, B and Zhao, Y and Yan, H and Li, Z and Zhang, P and Fang, Z and Zhao, Y and Yang, H and Guo, N}, title = {Targeted arginine metabolomics combined with metagenomics revealed the potential mechanism of Pueraria lobata extract in treating myocardial infarction.}, journal = {Journal of chromatography. A}, volume = {1719}, number = {}, pages = {464732}, doi = {10.1016/j.chroma.2024.464732}, pmid = {38387153}, issn = {1873-3778}, abstract = {The extraction methods for traditional Chinese medicine (TCM) may have varying therapeutic effects on diseases. Currently, Pueraria lobata (PL) is mostly extracted with ethanol, but decoction, as a TCM extraction method, is not widely adopted. In this study, we present a strategy that integrates targeted metabolomics, 16 s rDNA sequencing technology and metagenomics for exploring the potential mechanism of the water extract of PL (PLE) in treating myocardial infarction (MI). Using advanced analytical techniques like ultra-high performance liquid chromatography with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS) and ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), we comprehensively characterized PLE's chemical composition. Further, we tested its efficacy in a rat model of MI induced by ligation of the left anterior descending branch of the coronary artery (LAD). We assessed cardiac enzyme levels and conducted echocardiograms. UPLC-MS/MS was used to compare amino acid differences in serum. Furthermore, we investigated fecal samples using 16S rDNA sequencing and metagenomic sequencing to study intestinal flora diversity and function. This study demonstrated PLE's effectiveness in reducing cardiac injury in LAD-ligated rats. Amino acid metabolomics revealed significant improvements in serum levels of arginine, citrulline, proline, ornithine, creatine, creatinine, and sarcosine in MI rats, which are key compounds in the arginine metabolism pathway. Enzyme-linked immunosorbent assay (ELISA) results showed that PLE significantly improved arginase (Arg), nitric oxide synthase (NOS), and creatine kinase (CK) contents in the liver tissue of MI rats. 16 s rDNA and metagenome sequencing revealed that PLE significantly improved intestinal flora imbalance in MI rats, particularly in taxa such as Tuzzerella, Desulfovibrio, Fournierella, Oscillibater, Harryflintia, and Holdemania. PLE also improved the arginine metabolic pathway in the intestinal microorganisms of MI rats. The findings indicate that PLE effectively modulates MI-induced arginine levels and restores intestinal flora balance. This study, the first to explore the mechanism of action of PLE in MI treatment considering amino acid metabolism and intestinal flora, expands our understanding of the potential of PL in MI treatment. It offers fresh insights into the mechanisms of PL, guiding further research and development of PL-based medicines.}, } @article {pmid38386620, year = {2024}, author = {Ergunay, K and Bourke, BP and Achee, N and Jiang, L and Grieco, J and Linton, YM}, title = {Vector-borne pathogen surveillance in a metagenomic world.}, journal = {PLoS neglected tropical diseases}, volume = {18}, number = {2}, pages = {e0011943}, doi = {10.1371/journal.pntd.0011943}, pmid = {38386620}, issn = {1935-2735}, } @article {pmid38385832, year = {2024}, author = {Chen, YW and Hou, YW and Wang, CW and Cheng, SJ and Kuo, WT and Lin, CP and Hou, HH}, title = {Oral Lactobacillus zeae exacerbates the pathological manifestation of periodontitis in a mouse model.}, journal = {Molecular oral microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/omi.12455}, pmid = {38385832}, issn = {2041-1014}, support = {109-2314-B-002-027-MY2//National Science and Technology Council/ ; 109-2314-B-002-181-MY3//National Science and Technology Council/ ; 111-2314-B-002-119//National Science and Technology Council/ ; 112-2314-B-002-229-MY3//National Science and Technology Council/ ; 110-S5072 111-S0255//National Taiwan University Hospital/ ; 112-S1080//National Taiwan University Hospital/ ; 10912041001//National Taiwan University System/ ; }, abstract = {INTRODUCTION: The worldwide prevalence of periodontitis is considerably high, and its pathogenic mechanisms must be investigated and understood in order to improve clinical treatment outcomes and reduce the disease prevalence and burden. The exacerbation of the host immune system induced by oral microbial dysbiosis and the subsequent tissue destruction are the hallmarks of the periodontitis. However, the oral bacteria involved in periodontitis are not fully understood. We used the Oxford Nanopore Technologies (ONT) sequencing system to analyze metagenomic information in subgingival dental plaque from periodontitis and non-periodontitis patients. The number of Lactobacillus zeae (L. zeae) in the periodontitis patients was 17.55-fold higher than in the non-periodontitis patients, suggesting that L. zeae is a novel periodontitis-associated pathogen. Although several Lactobacillus species are used in vivo as probiotics to treat periodontitis and compete with Porphyromonas gingivalis (P. gingivalis), the roles of L. zeae in periodontitis progression, and the relationship between L. zeae and P. gingivalis needs to be investigated.

METHODS: Both L. zeae and P. gingivalis were inoculated in the ligature-implant site of periodontitis mice. We collected mouse gingival crevicular fluid to analyze inflammatory cytokine secretion using a multiplex assay. Intact or sliced mouse maxilla tissue was used for micro-computed tomography analysis or hematoxylin and eosin staining, immunohistochemistry, and tartrate-resistant acid phosphatase staining to evaluate alveolar bone loss, neutrophil infiltration, and osteoclast activation, respectively.

RESULTS: We observed that L. zeae competed with P. gingivalis, and it increased inflammatory cytokine secretion at the ligature-implant site. Similar to P. gingivalis, L. zeae promoted ligature-induced neutrophile infiltration, osteoclast activation, and alveolar bone loss.

DISCUSSION: We, therefore, concluded that L. zeae accelerated the progression of periodontitis in the ligature-induced periodontitis mouse model.}, } @article {pmid38385739, year = {2024}, author = {Hong, J-C and Chen, J-S and Jiang, Z-J and Chen, Z-C and Ruan, N and Yao, X-P}, title = {Microbiota in adult perianal abscess revealed by metagenomic next-generation sequencing.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0347423}, doi = {10.1128/spectrum.03474-23}, pmid = {38385739}, issn = {2165-0497}, abstract = {The microbiota of perianal abscesses is scarcely investigated. Identifying causative bacteria is essential to develop antibiotic therapy. However, culture-based methods and molecular diagnostics through 16S PCR technology are often hampered by the polymicrobial nature of perianal abscesses. We sought to characterize the microbiota composition of perianal abscesses via metagenomic next-generation sequencing (mNGS). Fourteen patients suffering from perianal abscesses between March 2023 and August 2023 underwent retrospective assessment. Information from medical records was used, including clinical information, laboratory data, and culture and mNGS results. Forty bacterial taxa were identified from perianal abscesses through mNGS, with Bilophila wadsworthia (71.4%), Bacteroides fragilis (57.1%), and Escherichia coli (50.0%) representing the most prevalent species. mNGS identified an increased number of bacterial taxa, with an average of 6.1 compared to a traditional culture-based method which only detected an average of 1.1 in culture-positive perianal abscess patients, predominantly E. coli (75.0%), revealing the polymicrobial nature of perianal abscesses. Our study demonstrates that a more diverse bacterial profile is detected by mNGS in perianal abscesses, and that Bilophila wadsworthia is the most prevalent microorganism, potentially serving as a potential biomarker for perianal abscess.IMPORTANCEAccurately, identifying the bacteria causing perianal abscesses is crucial for effective antibiotic therapy. However, traditional culture-based methods and 16S PCR technology often struggle with the polymicrobial nature of these abscesses. This study employed metagenomic next-generation sequencing (mNGS) to comprehensively analyze the microbiota composition. Results revealed 40 bacterial taxa, with Bilophila wadsworthia (71.4%), Bacteroides fragilis (57.1%), and Escherichia coli (50.0%) being the most prevalent species. Compared to the culture-based approach, mNGS detected a significantly higher number of bacterial taxa (average 6.1 vs 1.1), highlighting the complex nature of perianal abscesses. Notably, Bilophila wadsworthia emerged as a potential biomarker for these abscesses. This research emphasizes the importance of mNGS in understanding perianal abscesses and suggests its potential for improving diagnostic accuracy and guiding targeted antibiotic therapy in the future.}, } @article {pmid38385646, year = {2024}, author = {Hou, Z and Zhang, T and Ding, Z and Qian, T and Wang, P and Wu, B and Pan, X and Li, X}, title = {Analysis on the change of gut microbiota and metabolome in lung transplant patients.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0314223}, doi = {10.1128/spectrum.03142-23}, pmid = {38385646}, issn = {2165-0497}, abstract = {Previous studies have shown that the gut microbiota and its metabolites are associated with the success of organ transplantation. However, the specific changes in the gut microbiota of lung transplant patients remain unclear. Hence, this study aimed to elucidate the interplay between the gut microbiota, metabolome, and lung transplantation outcomes. Using 16S metagenomics sequencing and untargeted metabolic profiling, we conducted a comprehensive analysis of gut microbial and metabolic alterations in lung transplant recipients relative to non-transplant group. Our findings revealed the predominance of Enterococcus and Streptococcus genera within the lung transplant cohort, accompanied by the significant reduction in Bacteroides, Epulopiscium, Faecalibacterium, and Prevotella abundance. In addition, a significant reduction in ATRA (all-trans retinoic acid) levels and suppression of IgA production were observed in lung transplant recipients, which were found to be closely associated with the Enterococcus genus. It was speculated that the association might have implications for the prognosis of lung transplant patients. Notably, the differences in gut microbial composition and metabolomic profiles between successful transplant recipients and those experiencing chronic rejection were not statistically significant. These novel insights shed light on the putative implications of the gut microbiota and metabolome in shaping lung transplantation outcomes, and provide a foundation for future investigations and targeted therapeutic interventions.IMPORTANCEThis study has profound implications for lung transplantation as it uncovers the important role of gut microbiota and metabolome in shaping transplantation outcomes. The identification of dominant bacterial genera, such as Enterococcus and Streptococcus, within the lung transplant cohort, along with the significant decrease in Bacteroides, Epulopiscium, Faecalibacterium, and Prevotella abundance, reveals potential microbial imbalances associated with lung transplantation. In addition, a significant reduction in ATRA (all-trans retinoic acid) levels and suppression of IgA production were observed in lung transplant recipients, which were found to be closely associated with the Enterococcus genus. It was speculated that the association might have implications for the prognosis of lung transplant patients. These findings hold immense clinical significance as they lay the groundwork for future research and targeted therapeutic interventions. Understanding the impact of the gut microbiota and metabolome on lung transplantation outcomes offers promising avenues for improving transplantation patient prognosis.}, } @article {pmid38385313, year = {2024}, author = {Iqbal, S and Begum, F and Ullah, I and Jalal, N and Shaw, P}, title = {Peeling off the layers from microbial dark matter (MDM): recent advances, future challenges, and opportunities.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-21}, doi = {10.1080/1040841X.2024.2319669}, pmid = {38385313}, issn = {1549-7828}, abstract = {Microbes represent the most common organisms on Earth; however, less than 2% of microbial species in the environment can undergo cultivation for study under laboratory conditions, and the rest of the enigmatic, microbial world remains mysterious, constituting a kind of "microbial dark matter" (MDM). In the last two decades, remarkable progress has been made in culture-dependent and culture-independent techniques. More recently, studies of MDM have relied on culture-independent techniques to recover genetic material through either unicellular genomics or shotgun metagenomics to construct single-amplified genomes (SAGs) and metagenome-assembled genomes (MAGs), respectively, which provide information about evolution and metabolism. Despite the remarkable progress made in the past decades, the functional diversity of MDM still remains uncharacterized. This review comprehensively summarizes the recently developed culture-dependent and culture-independent techniques for characterizing MDM, discussing major challenges, opportunities, and potential applications. These activities contribute to expanding our knowledge of the microbial world and have implications for various fields including Biotechnology, Bioprospecting, Functional genomics, Medicine, Evolutionary and Planetary biology. Overall, this review aims to peel off the layers from MDM, shed light on recent advancements, identify future challenges, and illuminate the exciting opportunities that lie ahead in unraveling the secrets of this intriguing microbial realm.}, } @article {pmid38384949, year = {2024}, author = {Cao, Z and Yi, M and Zhou, J and Zhang, Z and Liu, Z and Yang, C and Sun, S and Wang, L and Ling, Y and Zhang, Z and Cao, H}, title = {Multi-omics analysis on the mechanism of the effect of Isatis leaf on the growth performance of fattening sheep.}, journal = {Frontiers in veterinary science}, volume = {11}, number = {}, pages = {1332457}, pmid = {38384949}, issn = {2297-1769}, abstract = {INTRODUCTION: This study evaluated the effects of Isatis Leaf (ISL) on the growth performance, gastrointestinal tissue morphology, rumen and intestinal microbiota, rumen, serum and urine metabolites, and rumen epithelial tissue transcriptome of fattening sheep.

METHODS: Twelve 3.5-month-old healthy fattening sheep were randomly divided into two groups, each with 6 replicates, and fed with basal diet (CON) and basal diet supplemented with 80 g/kg ISL for 2.5 months. Gastrointestinal tract was collected for histological analysis, rumen fluid and feces were subjected to metagenomic analysis, rumen fluid, serum, and urine for metabolomics analysis, and rumen epithelial tissue for transcriptomics analysis.

RESULTS: The results showed that in the ISL group, the average daily gain and average daily feed intake of fattening sheep were significantly lower than those of the CON group (P < 0.05), and the rumen ammonia nitrogen level was significantly higher than that of the CON group (P < 0.01). The thickness of the reticulum and abomasum muscle layer was significantly increased (P < 0.05). At the genus level, the addition of ISL modified the composition of rumen and fecal microorganisms, and the relative abundance of Methanobrevibacter and Centipeda was significantly upregulated in rumen microorganisms, The relative abundance of Butyrivibrio, Saccharofermentans, Mogibacterium, and Pirellula was significantly downregulated (P < 0.05). In fecal microorganisms, the relative abundance of Papillibacter, Pseudoflavonifractor, Butyricicoccus, Anaerovorax, and Methanocorpusculum was significantly upregulated, while the relative abundance of Roseburia, Coprococcus, Clostridium XVIII, Butyrivibrio, Parasutterella, Macellibacteroides, and Porphyromonas was significantly downregulated (P < 0.05). There were 164, 107, and 77 different metabolites in the rumen, serum, and urine between the ISL and CON groups (P < 0.05). The differential metabolic pathways mainly included thiamine metabolism, niacin and nicotinamide metabolism, vitamin B6 metabolism, taurine and taurine metabolism, beta-Alanine metabolism and riboflavin metabolism. These metabolic pathways were mainly involved in the regulation of energy metabolism and immune function in fattening sheep. Transcriptome sequencing showed that differentially expressed genes were mainly enriched in cellular physiological processes, development, and immune regulation.

CONCLUSION: In summary, the addition of ISL to the diet had the effect of increasing rumen ammonia nitrogen levels, regulating gastrointestinal microbiota, promoting body fat metabolism, and enhancing immunity in fattening sheep.}, } @article {pmid38384305, year = {2024}, author = {Liu, X and Li, K and Yang, Y and Cao, D and Xu, X and He, Z and Wu, W}, title = {Gut resistome profiling reveals high diversity and fluctuations in pancreatic cancer cohorts.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1354234}, pmid = {38384305}, issn = {2235-2988}, abstract = {BACKGROUND: Pancreatic cancer is one of the deadliest cancer, with a 5-year overall survival rate of 11%. Unfortunately, most patients are diagnosed with advanced stage by the time they present with symptoms. In the past decade, microbiome studies have explored the association of pancreatic cancer with the human oral and gut microbiomes. However, the gut microbial antibiotic resistance genes profiling of pancreatic cancer patients was never reported compared to that of the healthy cohort.

RESULTS: In this study, we addressed the gut microbial antibiotic resistance genes profile using the metagenomic data from two online public pancreatic cancer cohorts. We found a high degree of data concordance between the two cohorts, which can therefore be used for cross-sectional comparisons. Meanwhile, we used two strategies to predict antibiotic resistance genes and compared the advantages and disadvantages of these two approaches. We also constructed microbe-antibiotic resistance gene networks and found that most of the hub nodes in the networks were antibiotic resistance genes.

CONCLUSIONS: In summary, we describe the panorama of antibiotic resistance genes in the gut microbes of patients with pancreatic cancer. We hope that our study will provide new perspectives on treatment options for the disease.}, } @article {pmid38384302, year = {2024}, author = {Ortiz Sanjuán, JM and Manzanilla, EG and Cabrera-Rubio, R and Crispie, F and Cotter, PD and Garrido, JJ and Ekhlas, D and O'Neill, L and Argüello, H}, title = {Fine-tuning of post-weaning pig microbiome structure and functionality by in-feed zinc oxide and antibiotics use.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1354449}, pmid = {38384302}, issn = {2235-2988}, abstract = {INTRODUCTION: Post-weaning diarrhoea (PWD) is a multifactorial disease that affects piglets after weaning, contributing to productive and economic losses. Its control includes the use of in-feed prophylactic antibiotics and therapeutic zinc oxide (ZnO), treatments that, since 2022, are no longer permitted in the European Union due to spread of antimicrobial resistance genes and pollution of soil with heavy metals. A dysbiosis in the microbiota has been suggested as a potential risk factor of PWD onset. Understanding pig's microbiota development around weaning and its changes in response to ZnO and antibiotics is crucial to develop feasible alternatives to prophylactic and metaphylactic antimicrobial use.

METHODS: This study used shotgun metagenomic sequencing to investigate the environmental and faecal microbiota on 10 farms using (Treated) or not using (ZnO-free) in-feed antibiotics and ZnO during the first 14 days post-weaning (dpw). Environmental samples from clean pens were collected at weaning day (0dpw), and faecal samples at 0, 7 and 14dpw. Diarrhoeic faecal samples were collected at 7dpw when available.

RESULTS: The analysis of data revealed that the faecal microbiota composition and its functionality was impacted by the sampling time point (microbiota maturation after weaning) but not by the farm environment. Treatment with antibiotics and ZnO showed no effects on diversity indices while the analyses of microbiota taxonomic and functional profiles revealed increased abundance of taxa and metabolic functions associated with Phascolarctobacterium succinatutens or different species of Prevotella spp. on the Treated farms, and with Megasphaera elsdenii and Escherichia coli on the ZnO-free farms. The analysis of diarrhoea samples revealed that the treatment favoured the microbiota transition or maturation from 0dpw to 14dpw in Treated farms, resembling the composition of healthy animals, when compared to diarrhoea from ZnO-free farms, which were linked in composition to 0dpw samples.

DISCUSSION: The results provide a comprehensive overview of the beneficial effects of ZnO and antibiotics in PWD in the microbiota transition after weaning, preventing the overgrowth of pathogens such as pathogenic E. coli and revealing the key aspects in microbiota maturation that antibiotics or ZnO alternatives should fulfil.}, } @article {pmid38384270, year = {2024}, author = {Jiang, L and Wang, H and Luo, L and Pang, X and Liu, T and Sun, L and Zhang, G}, title = {Urogenital microbiota-driven virulence factor genes associated with recurrent urinary tract infection.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1344716}, pmid = {38384270}, issn = {1664-302X}, abstract = {Urinary tract infections (UTIs) are a common health issue affecting individuals worldwide. Recurrent urinary tract infections (rUTI) pose a significant clinical challenge, with limited understanding of the underlying mechanisms. Recent research suggests that the urobiome, the microbial community residing in the urinary tract, may play a crucial role in the development and recurrence of urinary tract infections. However, the specific virulence factor genes (VFGs) driven by urobiome contributing to infection recurrence remain poorly understood. Our study aimed to investigate the relationship between urobiome driven VFGs and recurrent urinary tract infections. By analyzing the VFGs composition of the urinary microbiome in patients with rUTI compared to a control group, we found higher alpha diversity in rUTI patients compared with healthy control. And then, we sought to identify specific VFGs features associated with infection recurrence. Specifically, we observed an increased abundance of certain VGFs in the recurrent infection group. We also associated VFGs and clinical data. We then developed a diagnostic model based on the levels of these VFGs using random forest and support vector machine analysis to distinguish healthy control and rUIT, rUTI relapse and rUTI remission. The diagnostic accuracy of the model was assessed using receiver operating characteristic curve analysis, and the area under the ROC curve were 0.83 and 0.75. These findings provide valuable insights into the complex interplay between the VFGs of urobiome and recurrent urinary tract infections, highlighting potential targets for therapeutic interventions to prevent infection recurrence.}, } @article {pmid38383926, year = {2024}, author = {Sun, S and Chen, W and Peng, K and Chen, X and Chen, J}, title = {Characterization of a novel amidohydrolase with promiscuous esterase activity from a soil metagenomic library and its application in degradation of amide herbicides.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38383926}, issn = {1614-7499}, support = {KYCX21_0581//Postgraduate Research & Practice Innovation Program of Jiangsu Province/ ; }, abstract = {Amide herbicides have been extensively used worldwide and have received substantial attention due to their adverse environmental effects. Here, a novel amidohydrolase gene was identified from a soil metagenomic library using diethyl terephthalate (DET) as a screening substrate. The recombinant enzyme, AmiH52, was heterologously expressed in Escherichia coli and later purified and characterized, with the highest activity occurring at 40 ℃ and pH 8.0. AmiH52 was demonstrated to have both esterase and amidohydrolase activities, which exhibited highly specific activity for p-nitrophenyl butyrate (2669 U/mg) and degrading activity against several amide herbicides. In particular, it displayed the strongest activity against propanil, with a high degradation rate of 84% at 8 h. A GC-MS analysis revealed that propanil was transformed into 3,4-dichloroaniline (3,4-DCA) during this degradation. The molecular interactions and binding stability were then analyzed by molecular docking and molecular dynamics simulation, which revealed that several key amino acid residues, including Tyr164, Trp66, Ala59, Val283, Arg58, His33, His191, and His226, are involved in the specific interactions with propanil. This study provides a function-driven screening method for amide herbicide hydrolase from the metagenomic libraries and a promising propanil-degrading enzyme (AmiH52) for potential applications in environmental remediation.}, } @article {pmid38383853, year = {2024}, author = {Ma, B and Wang, Y and Zhao, K and Stirling, E and Lv, X and Yu, Y and Hu, L and Tang, C and Wu, C and Dong, B and Xue, R and Dahlgren, RA and Tan, X and Dai, H and Zhu, YG and Chu, H and Xu, J}, title = {Biogeographic patterns and drivers of soil viromes.}, journal = {Nature ecology & evolution}, volume = {}, number = {}, pages = {}, pmid = {38383853}, issn = {2397-334X}, support = {41721007//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42090060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42277283//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41991334//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41721007//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42090060//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42277283//National Natural Science Foundation of China (National Science Foundation of China)/ ; 41991334//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Viruses are crucial in shaping soil microbial functions and ecosystems. However, studies on soil viromes have been limited in both spatial scale and biome coverage. Here we present a comprehensive synthesis of soil virome biogeographic patterns using the Global Soil Virome dataset (GSV) wherein we analysed 1,824 soil metagenomes worldwide, uncovering 80,750 partial genomes of DNA viruses, 96.7% of which are taxonomically unassigned. The biogeography of soil viral diversity and community structure varies across different biomes. Interestingly, the diversity of viruses does not align with microbial diversity and contrasts with it by showing low diversity in forest and shrubland soils. Soil texture and moisture conditions are further corroborated as key factors affecting diversity by our predicted soil viral diversity atlas, revealing higher diversity in humid and subhumid regions. In addition, the binomial degree distribution pattern suggests a random co-occurrence pattern of soil viruses. These findings are essential for elucidating soil viral ecology and for the comprehensive incorporation of viruses into soil ecosystem models.}, } @article {pmid38383848, year = {2024}, author = {Megaw, J and Skvortsov, T and Gori, G and Dabai, AI and Gilmore, BF and Allen, CCR}, title = {A novel bioinformatic method for the identification of antimicrobial peptides in metagenomes.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxae045}, pmid = {38383848}, issn = {1365-2672}, abstract = {AIMS: This study aimed to develop a new bioinformatic approach for the identification of novel antimicrobial peptides (AMPs), which did not depend on sequence similarity to known AMPs held within databases, but on structural mimicry of another antimicrobial compound, in this case an ultrashort, synthetic, cationic lipopeptide (C12-OOWW-NH2).

METHODS AND RESULTS: When applied to a collection of metagenomic datasets, our outlined bioinformatic method successfully identified several short (8-10aa) functional AMPs, the activity of which was verified via disk diffusion and minimum inhibitory concentration (MIC) assays against a panel of 12 bacterial strains. Some peptides had activity comparable to, or in some cases greater than those from published studies that identified AMPs using more conventional methods. We also explored the effects of modifications, including extension of the peptides, observing an activity peak at 9-12aa. Additionally, the inclusion of a C-terminal amide enhanced activity in most cases. Our most promising candidate (named PB2-10aa-NH2) was thermally stable, lipid soluble, and possessed synergistic activity with ethanol, but not with a conventional antibiotic (streptomycin).

CONCLUSIONS: While several bioinformatic methods exist to predict AMPs, the approach outlined here is much simpler and can be used to quickly scan huge datasets. Searching for peptide sequences bearing structural similarity to other antimicrobial compounds may present a further opportunity to identify novel AMPs with clinical relevance, and provide a meaningful contribution to the pressing global issue of AMR.}, } @article {pmid38382768, year = {2024}, author = {Qin, L and Xiang, Y and Wu, Z and Zhang, H and Wu, X and Chen, Q}, title = {Metagenomic next-generation sequencing for diagnosis of fatal Balamuthia amoebic encephalitis.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105570}, doi = {10.1016/j.meegid.2024.105570}, pmid = {38382768}, issn = {1567-7257}, abstract = {INTRODUCTION: Balamuthia amoebic encephalitis (BAE), caused by Balamuthia mandrillaris, is a rare and life-threatening infectious disease with no specific and effective treatments available. The diagnosis of BAE at an early stage is difficult because of the non-specific clinical manifestations and neuroimaging.

CASE DESCRIPTION: A 52-year-old male patient, who had no previous history of skin lesions, presented to the emergency department with an acute headache, walking difficulties, and disturbance of consciousness. The patient underwent a series of examinations, including regular cerebrospinal fluid (CSF) studies and magnetic resonance imaging, and tuberculous meningoencephalitis was suspected. Despite being treated with anti-TB drugs, no clinical improvement was observed in the patient. Following corticosteroid therapy, the patient developed a rapid deterioration in consciousness with dilated pupils. Metagenomic next-generation sequencing (mNGS) revealed an unexpected central nervous system (CNS) amoebic infection, and the patient died soon after the confirmed diagnosis.

CONCLUSION: This study highlights the application of mNGS for the diagnosis of patients with suspected encephalitis or meningitis, especially those caused by rare opportunistic infections.}, } @article {pmid38382662, year = {2024}, author = {Yang, S and Sun, J and Wang, C and Li, S and Li, Z and Luo, W and Wei, G and Chen, W}, title = {Residue quality drives SOC sequestration by altering microbial taxonomic composition and ecophysiological function in desert ecosystem.}, journal = {Environmental research}, volume = {}, number = {}, pages = {118518}, doi = {10.1016/j.envres.2024.118518}, pmid = {38382662}, issn = {1096-0953}, abstract = {Plant residues are important sources of soil organic carbon in terrestrial ecosystems. The degradation of plant residue by microbes can influence the soil carbon cycle and sequestration. However, little is known about the microbial composition and function, as well as the accumulation of soil organic carbon (SOC) in response to the inputs of different quality plant residues in the desert environment. The present study evaluated the effects of plant residue addition from Pinus sylvestris var. mongolica (Pi), Artemisia desertorum (Ar) and Amorpha fruticosa (Am) on desert soil microbial community composition and function in a field experiment in the Mu Us Desert. The results showed that the addition of the three plant residues with different C/N ratios induced significant variation in soil microbial communities. The Am treatment (low C/N ratio) improved microbial diversity compared with the Ar and Pi treatments (medium and high C/N ratios). The variations in the taxonomic and functional compositions of the dominant phyla Actinobacteria and Proteobacteria were higher than those of the other phyla among the different treatments. Moreover, the network links between Proteobacteria and other phyla and the CAZyme genes abundances from Proteobacteria increased with increasing residue C/N, whereas those decreased for Actinobacteria. The SOC content of the Am, Ar and Pi treatments increased by 45.73%, 66.54% and 107.99%, respectively, as compared to the original soil. The net SOC accumulation was positively correlated with Proteobacteria abundance and negatively correlated with Actinobacteria abundance. These findings showed that changing the initial quality of plant residue from low C/N to high C/N can result in shifts in taxonomic and functional composition from Actinobacteria to Proteobacteria, which favors SOC accumulation. This study elucidates the ecophysiological roles of Actinobacteria and Proteobacteria in the desert carbon cycle, expands our understanding of the potential microbial-mediated mechanisms by which plant residue inputs affect SOC sequestration in desert soils, and provides valuable guidance for species selection in desert vegetation reconstruction.}, } @article {pmid38382601, year = {2024}, author = {Moreno, Y and Moreno-Mesonero, L and Soler, P and Zornoza, A and Soriano, A}, title = {Influence of drinking water biofilm microbiome on water quality: Insights from a real-scale distribution system.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {171086}, doi = {10.1016/j.scitotenv.2024.171086}, pmid = {38382601}, issn = {1879-1026}, abstract = {Biofilms, constituting over 95 % of the biomass in drinking water distribution systems, form an ecosystem impacting both the aesthetic and microbiological quality of water. This study investigates the microbiome of biofilms within a real-scale drinking water distribution system in eastern Spain, utilizing amplicon-based metagenomics. Forty-one biofilm samples underwent processing and sequencing to analyze both bacterial and eukaryotic microbiomes, with an assessment of active biomass. Genus-level analysis revealed considerable heterogeneity, with Desulfovibrio, Ralstonia, Bradyrhizobium, Methylocystis, and Bacillus identified as predominant genera. Notably, bacteria associated with corrosion processes, including Desulfovibrio, Sulfuricella, Hyphomicrobium, and Methylobacterium, were prevalent. Potentially pathogenic bacteria such as Helicobacter, Pseudomonas, and Legionella were also detected. Among protozoa, Opisthokonta and Archaeplastida were the most abundant groups in biofilm samples, with potential pathogenic eukaryotes (Acanthamoeba, Naegleria, Blastocystis) identified. Interestingly, no direct correlation between microbiota composition and pipe materials was observed. The study suggests that the usual concentration of free chlorine in bulk water proved insufficient to prevent the presence of undesirable bacteria and protozoa in biofilms, which exhibited a high concentration of active biomass.}, } @article {pmid38378556, year = {2024}, author = {Wang, P and Jin, M and Wu, C and Peng, Y and He, Y and Wang, H and Xiao, Y}, title = {Population genomics of Agrotis segetum provide insights into the local adaptive evolution of agricultural pests.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {42}, pmid = {38378556}, issn = {1741-7007}, support = {2022ZD04021//Sci-Tech Innovation 2030 Agenda/ ; }, mesh = {Animals ; *Metagenomics ; *Moths/genetics ; China ; }, abstract = {BACKGROUND: The adaptive mechanisms of agricultural pests are the key to understanding the evolution of the pests and to developing new control strategies. However, there are few studies on the genetic basis of adaptations of agricultural pests. The turnip moth, Agrotis segetum (Lepidoptera: Noctuidae) is an important underground pest that affects a wide range of host plants and has a strong capacity to adapt to new environments. It is thus a good model for studying the adaptive evolution of pest species.

RESULTS: We assembled a high-quality reference genome of A. segetum using PacBio reads. Then, we constructed a variation map of A. segetum by resequencing 98 individuals collected from six natural populations in China. The analysis of the population structure showed that all individuals were divided into four well-differentiated populations, corresponding to their geographical distribution. Selective sweep analysis and environmental association studies showed that candidate genes associated with local adaptation were functionally correlated with detoxification metabolism and glucose metabolism.

CONCLUSIONS: Our study of A. segetum has provided insights into the genetic mechanisms of local adaptation and evolution; it has also produced genetic resources for developing new pest management strategies.}, } @article {pmid38382547, year = {2024}, author = {Jin, MK and Zhang, Q and Xu, N and Zhang, Z and Guo, HQ and Li, J and Ding, K and Sun, X and Yang, XR and Zhu, D and Su, X and Qian, H and Zhu, YG}, title = {Lipid Metabolites as Potential Regulators of the Antibiotic Resistome in Tetramorium caespitum.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c05741}, pmid = {38382547}, issn = {1520-5851}, abstract = {Antibiotic resistance genes (ARGs) are ancient but have become a modern critical threat to health. Gut microbiota, a dynamic reservoir for ARGs, transfer resistance between individuals. Surveillance of the antibiotic resistome in the gut during different host growth phases is critical to understanding the dynamics of the resistome in this ecosystem. Herein, we disentangled the ARG profiles and the dynamic mechanism of ARGs in the egg and adult phases of Tetramorium caespitum. Experimental results showed a remarkable difference in both gut microbiota and gut resistome with the development of T. caespitum. Meta-based metagenomic results of gut microbiota indicated the generalizability of gut antibiotic resistome dynamics during host development. By using Raman spectroscopy and metabolomics, the metabolic phenotype and metabolites indicated that the biotic phase significantly changed lipid metabolism as T. caespitum aged. Lipid metabolites were demonstrated as the main factor driving the enrichment of ARGs in T. caespitum. Cuminaldehyde, the antibacterial lipid metabolite that displayed a remarkable increase in the adult phase, was demonstrated to strongly induce ARG abundance. Our findings show that the gut resistome is host developmental stage-dependent and likely modulated by metabolites, offering novel insights into possible steps to reduce ARG dissemination in the soil food chain.}, } @article {pmid38382437, year = {2024}, author = {Yuan, N and Li, Z and Shang, Q and Liu, X and Deng, C and Wang, C}, title = {High efficiency of drinking water treatment residual-based sintered ceramsite in biofilter for domestic wastewater treatment.}, journal = {Journal of environmental management}, volume = {354}, number = {}, pages = {120401}, doi = {10.1016/j.jenvman.2024.120401}, pmid = {38382437}, issn = {1095-8630}, abstract = {Aluminum (Al)-based drinking water treatment residue (DWTR) has often been attempted to be recycled as dominant ingredient to produce sintered ceramsite for water treatment. This study aimed to determine the long-term performance of DWTR-based ceramsite in treating domestic wastewater based on a 385-d biofilter test and by using physicochemical, metagenomic, and metatranscriptomic analyses. The results showed that the ceramsite-packed biofilter exhibited high and stable capability in removing phosphorus (P) and chemical oxygen demand (COD), with removal efficiencies of 92.6 ± 3.97% and 81.1 ± 14.0% for total P and COD, respectively; moreover, 88-100% of ammonium-nitrogen (N) was normally converted, and the total N removal efficiency reached 80-86% under proper aeration. Further analysis suggested that the forms of the removed P in the ceramsite were mainly NH4F- and NaOH-extractable. Microbial communities in the ceramsite biofilter exhibited relatively high activity. Typically, various organic matter degradation-related genes (e.g., hemicellulose and starch degradations) were enriched, and a complete N-cycling pathway was established, which is beneficial for enriching microbes involved in ammonium-N conversion, especially Candidatus Brocadia, Candidatus Jettenia, Nitrosomonas, and Nitrospira. In addition, the structures of the ceramsite had high stability (e.g., compressive strength and major compositions). The ceramsites showed limited metal and metalloid pollution risks and even accumulated copper from the wastewater. These results demonstrate the high feasibility of applying ceramsite prepared from Al-based DWTR for water treatment.}, } @article {pmid38382341, year = {2024}, author = {Xiao, X and He, M and Ma, L and Lv, W and Huang, K and Yang, H and Li, Y and Zou, L and Xiao, Y and Wang, W}, title = {Insights into microbial contamination and antibiotic resistome traits in pork wholesale market: An evaluation of the disinfection effect of sodium hypochlorite.}, journal = {Journal of hazardous materials}, volume = {468}, number = {}, pages = {133811}, doi = {10.1016/j.jhazmat.2024.133811}, pmid = {38382341}, issn = {1873-3336}, abstract = {Chlorine and its derivatives, such as sodium hypochlorite (NaClO) and chlorine dioxide, are frequently employed as disinfectants throughout the pork supply chain in China. Nevertheless, the extensive use of NaClO has the potential to cause the creation of 'chlorine-tolerant bacteria' and accelerate the evolution of antibiotic resistance. This study evaluated the efficacy of NaClO disinfection by examining alterations in the microbiome and resistome of a pork wholesale market (PWM), and bacteria isolation and analysis were performed to validate the findings. As expected, the taxonomic compositions of bacteria was significantly different before and after disinfection. Notably, Salmonella enterica (S. enterica), Salmonella bongori (S. bongori), Escherichia coli (E. coli), Klebsiella pneumoniae (K. pneumoniae), and Pseudomonas aeruginosa (P. aeruginosa) were observed on all surfaces, indicating that the application of NaClO disinfection treatment in PWM environments for pathogenic bacteria is limited. Correlations were identified between antibiotic resistance genes (ARGs) associated with aminoglycosides (aph(3'')-I, aph(6')-I), quinolone (qnrB, abaQ), polymyxin (arnA, mcr-4) and disinfectant resistance genes (emrA/BD, mdtA/B/C/E/F). Furthermore, correlations were found between risk Rank I ARGs associated with aminoglycoside (aph(3')-I), tetracycline (tetH), beta_lactam (TEM-171), and disinfectant resistance genes (mdtB/C/E/F, emrA, acrB, qacG). Importantly, we found that Acinetobacter and Salmonella were the main hosts of disinfectant resistance genes. The resistance mechanisms of the ARGs identified in PWM were dominated by antibiotic deactivation (38.7%), antibiotic efflux (27.2%), and antibiotic target protection (14.4%). The proportion of genes encoding efflux pumps in the PWM resistome increased after disinfection. Microbial cultures demonstrated that the traits of microbial contamination and antibiotic resistane were consistent with those observed by metagenomic sequencing. This study highlights the possibility of cross-resistance between NaClO disinfectants and antibiotics, which should not be ignored.}, } @article {pmid38382338, year = {2024}, author = {Wang, JT and Hu, W and Xue, Z and Cai, X and Zhang, SY and Li, FQ and Lin, LS and Chen, H and Miao, Z and Xi, Y and Guo, T and Zheng, JS and Chen, YM and Lin, HL}, title = {Mapping multi-omics characteristics related to short-term PM2.5 trajectory and their impact on type 2 diabetes in middle-aged and elderly adults in Southern China.}, journal = {Journal of hazardous materials}, volume = {468}, number = {}, pages = {133784}, doi = {10.1016/j.jhazmat.2024.133784}, pmid = {38382338}, issn = {1873-3336}, abstract = {The relationship between PM2.5 and metabolic diseases, including type 2 diabetes (T2D), has become increasingly prominent, but the molecular mechanism needs to be further clarified. To help understand the mechanistic association between PM2.5 exposure and human health, we investigated short-term PM2.5 exposure trajectory-related multi-omics characteristics from stool metagenome and metabolome and serum proteome and metabolome in a cohort of 3267 participants (age: 64.4 ± 5.8 years) living in Southern China. And then integrate these features to examine their relationship with T2D. We observed significant differences in overall structure in each omics and 193 individual biomarkers between the high- and low-PM2.5 groups. PM2.5-related features included the disturbance of microbes (carbohydrate metabolism-associated Bacteroides thetaiotaomicron), gut metabolites of amino acids and carbohydrates, serum biomarkers related to lipid metabolism and reducing n-3 fatty acids. The patterns of overall network relationships among the biomarkers differed between T2D and normal participants. The subnetwork membership centered on the hub nodes (fecal rhamnose and glycylproline, serum hippuric acid, and protein TB182) related to high-PM2.5, which well predicted higher T2D prevalence and incidence and a higher level of fasting blood glucose, HbA1C, insulin, and HOMA-IR. Our findings underline crucial PM2.5-related multi-omics biomarkers linking PM2.5 exposure and T2D in humans.}, } @article {pmid38382292, year = {2024}, author = {Li, ZT and Song, X and Yuan, S and Zhao, HP}, title = {Unveiling the inhibitory mechanisms of chromium exposure on microbial reductive dechlorination: Kinetics and microbial responses.}, journal = {Water research}, volume = {253}, number = {}, pages = {121328}, doi = {10.1016/j.watres.2024.121328}, pmid = {38382292}, issn = {1879-2448}, abstract = {Chromium and organochlorine solvents, particularly trichloroethene (TCE), are pervasive co-existing contaminants in subsurface aquifers due to their extensive industrial use and improper disposal practices. In this study, we investigated the microbial dechlorination kinetics under different TCE-Cr(Ⅲ/VI) composite pollution conditions and elucidated microbial response mechanisms based on community shift patterns and metagenomic analysis. Our results revealed that the reductive dechlorinating consortium had high resistance to Cr(III) but extreme sensitivity to Cr(VI) disturbance, resulting in a persistent inhibitory effect on subsequent dechlorination. Interestingly, the vinyl chloride-respiring organohalide-respiring bacteria (OHRB) was notably more susceptible to Cr(III/VI) exposure than the trichloroethene-respiring one, possibly due to inferior competition for growth substrates, such as electron donors. In terms of synergistic non-OHRB populations, Cr(III/VI) exposure had limited impacts on lactate fermentation but significantly interfered with H2-producing acetogenesis, leading to inhibited microbial dechlorination due to electron donor deficiencies. However, this inhibition can be effectively mitigated by the amendment of exogenous H2 supply. Furthermore, being the predominant OHRB, Dehalococcoides have inherent Cr(VI) resistance defects and collaborate with synergistic non-OHRB populations to achieve concurrent bio-detoxication of Cr(VI) and TCE. Our findings expand the understanding of the response patterns of different functional populations towards Cr(III/VI) stress, and provide valuable insights for the development of in situ bioremediation strategies for sites co-contaminated with chloroethene and chromium.}, } @article {pmid38381609, year = {2024}, author = {Camprubí-Ferrer, D and Tomazatos, A and Balerdi-Sarasola, L and Cobuccio, LG and Van Den Broucke, S and Horváth, B and Van Esbroeck, M and Martinez, MJ and Gandasegui, J and Subirà, C and Saloni, M and Genton, B and Bottieau, E and Cadar, D and Muñoz, J}, title = {Assessing viral metagenomics for the diagnosis of acute undifferentiated fever in returned travellers: a multicenter cohort study.}, journal = {Journal of travel medicine}, volume = {}, number = {}, pages = {}, doi = {10.1093/jtm/taae029}, pmid = {38381609}, issn = {1708-8305}, support = {13N15449//German Federal Ministry of Education and Research/ ; }, abstract = {BACKGROUND: Up to 45% of febrile returning travellers remain undiagnosed after a thorough diagnostic work-up, even at referral centers. Although metagenomic next-generation sequencing (mNGS) has emerged as a promising tool, evidence of its usefulness in imported fever is very limited.

METHODS: Travellers returning with fever were prospectively recruited in three referral clinics from November 2017 to November 2019. Unbiased mNGS optimized for virus detection was performed on serum samples of participants with acute undifferentiated febrile illness (AUFI) and results were compared to those obtained by reference diagnostic methods (RDM).

RESULTS: Among 507 returned febrile travellers, 433(85.4%) presented with AUFI. Dengue virus (n=86) and Plasmodium spp. (n=83) were the most common causes of fever. 103/433(23.8%)AUFI remained undiagnosed at the end of the follow-up.mNGS unveiled potentially pathogenic microorganisms in 196/433(38.7%) AUFI. mNGS identifications were more common in patients with shorter duration of fever (42.3% in ≤5 days vs. 28.7% in >5 days, p=0.005). Potential causes of fever were revealed in 25/103(24.2%) undiagnosed AUFI and 5/23(21.7%) travellers with severe undiagnosed AUFI. Missed severe aetiologies included 8 bacterial identifications and one co-infection of B19 parvovirus and Aspergillus spp.Additional identifications indicating possible co-infections occurred in 29/316(9.2%) travellers with AUFI, and in 11/128(8.6%) travellers with severe AUFI, who had received a diagnosis through RDM. Most common co-infections detected in severe AUFI were caused by Gram-negative bacteria. Serum mNGS was unable to detect >50% of infectious diagnoses achieved by RDM and also yielded 607 non-pathogenic identifications.

DISCUSSION: mNGS of serum can be a valuable diagnostic tool for selected travellers with undiagnosed AUFI or severe disease in addition to reference diagnostic techniques, especially during the first days of symptoms. Nevertheless, mNGS results interpretation presents a great challenge. Further studies evaluating the performance of mNGS using different sample types and protocols tailored to non-viral agents are needed.}, } @article {pmid38381034, year = {2024}, author = {Wang, X and Ding, Z and Yang, Y and Liang, L and Sun, Y and Hou, C and Zheng, Y and Xia, Y and Dong, L}, title = {ViromeFlowX: a Comprehensive Nextflow-based Automated Workflow for Mining Viral Genomes from Metagenomic Sequencing Data.}, journal = {Microbial genomics}, volume = {10}, number = {2}, pages = {}, doi = {10.1099/mgen.0.001202}, pmid = {38381034}, issn = {2057-5858}, abstract = {Understanding the link between the human gut virome and diseases has garnered significant interest in the research community. Extracting virus-related information from metagenomic sequencing data is crucial for unravelling virus composition, host interactions, and disease associations. However, current metagenomic analysis workflows for viral genomes vary in effectiveness, posing challenges for researchers seeking the most up-to-date tools. To address this, we present ViromeFlowX, a user-friendly Nextflow workflow that automates viral genome assembly, identification, classification, and annotation. This streamlined workflow integrates cutting-edge tools for processing raw sequencing data for taxonomic annotation and functional analysis. Application to a dataset of 200 metagenomic samples yielded high-quality viral genomes. ViromeFlowX enables efficient mining of viral genomic data, offering a valuable resource to investigate the gut virome's role in virus-host interactions and virus-related diseases.}, } @article {pmid38380943, year = {2024}, author = {Zhang, IH and Borer, B and Zhao, R and Wilbert, S and Newman, DK and Babbin, AR}, title = {Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen-deficient zones with diverse metabolic potential.}, journal = {mBio}, volume = {}, number = {}, pages = {e0291823}, doi = {10.1128/mbio.02918-23}, pmid = {38380943}, issn = {2150-7511}, abstract = {Archaea belonging to the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have been found in an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise a sizeable fraction of the archaeal community within marine oxygen-deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes (MAGs) belonging to the DPANN phyla Nanoarchaeota, Pacearchaeota, Woesearchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and the Arabian Sea. We find these archaea to be permanent, stable residents of all three major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25%-50% of archaea as estimated from read mapping to MAGs. ODZ DPANN appear to be capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.IMPORTANCEArchaea from the DPANN (Diapherotrites, Parvarchaeota, Aenigmarchaeota, Nanoarchaeota, and Nanohaloarchaeota) superphylum have diverse metabolic capabilities and participate in multiple biogeochemical cycles. While metagenomics and enrichments have revealed that many DPANN are characterized by ultrasmall genomes, few biosynthetic genes, and episymbiotic lifestyles, much remains unknown about their biology. We report 33 new DPANN metagenome-assembled genomes originating from the three global marine oxygen-deficient zones (ODZs), the first from these regions. We survey DPANN abundance and distribution within the ODZ water column, investigate their biosynthetic capabilities, and report potential roles in the cycling of organic carbon, methane, and nitrogen. We test the hypothesis that nitrous oxide reductases found within several ODZ DPANN genomes may enable ultrasmall episymbionts to serve as nitrous oxide consumers when attached to a host nitrous oxide producer. Our results indicate DPANN archaea as ubiquitous residents within the anoxic core of ODZs with the potential to produce or consume key compounds.}, } @article {pmid38380923, year = {2024}, author = {Zhong, J and Osborn, T and Del Rosario Hernández, T and Kyrysyuk, O and Tully, BJ and Anderson, RE}, title = {Increasing transposase abundance with ocean depth correlates with a particle-associated lifestyle.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0006724}, doi = {10.1128/msystems.00067-24}, pmid = {38380923}, issn = {2379-5077}, abstract = {Transposases are mobile genetic elements that move within and between genomes, promoting genomic plasticity in microorganisms. In marine microbial communities, the abundance of transposases increases with depth, but the reasons behind this trend remain unclear. Our analysis of metagenomes from the Tara Oceans and Malaspina Expeditions suggests that a particle-associated lifestyle is the main covariate for the high occurrence of transposases in the deep ocean, and this trend holds true for individual genomes as well as in a community-wide sense. We observed a strong and depth-independent correlation between transposase abundance and the presence of biofilm-associated genes, as well as the prevalence of secretory enzymes. This suggests that mobile genetic elements readily propagate among microbial communities within crowded biofilms. Furthermore, we show that particle association positively correlates with larger genome size, which is in turn associated with higher transposase abundance. Cassette sequences associated with transposons are enriched with genes related to defense mechanisms, which are more highly expressed in the deep sea. Thus, while transposons spread at the expense of their microbial hosts, they also introduce novel genes and potentially benefit the hosts in helping to compete for limited resources. Overall, our results suggest a new understanding of deep ocean particles as highways for gene sharing among defensively oriented microbial genomes.IMPORTANCEGenes can move within and between microbial genomes via mobile genetic elements, which include transposases and transposons. In the oceans, there is a puzzling increase in transposase abundance in microbial genomes as depth increases. To gain insight into this trend, we conducted an extensive analysis of marine microbial metagenomes and metatranscriptomes. We found a significant correlation between transposase abundance and a particle-associated lifestyle among marine microbes at both the metagenome and genome-resolved levels. We also observed a link between transposase abundance and genes related to defense mechanisms. These results suggest that as microbes become densely packed into crowded particles, mobile genes are more likely to spread and carry genetic material that provides a competitive advantage in crowded habitats. This may enable deep sea microbes to effectively compete in such environments.}, } @article {pmid38380907, year = {2024}, author = {Xiong, Q and Sopko, B and Klimov, PB and Hubert, J}, title = {A novel Bartonella-like bacterium forms an interdependent mutualistic symbiosis with its host, the stored-product mite Tyrophagus putrescentiae.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0082923}, doi = {10.1128/msystems.00829-23}, pmid = {38380907}, issn = {2379-5077}, abstract = {A novel Bartonella-like symbiont (BLS) of Tyrophagus putrescentiae was characterized. BLS formed a separate cluster from the Bartonella clade together with an ant symbiont. BLS was present in mite bodies (103 16S DNA copies/mite) and feces but was absent in eggs. This indicated the presence of the BLS in mite guts. The BLS showed a reduction in genome size (1.6 Mb) and indicates gene loss compared to Bartonella apis. The BLS can be interacted with its host by using host metabolic pathways (e.g., the histidine and arginine metabolic pathways) as well as by providing its own metabolic pathways (pantothenate and lipoic acid) to the host, suggesting the existence of a mutualistic association. Our experimental data further confirmed these potential mutualistic nutritional associations, as cultures of T. putrescentiae with low BLS abundance showed the strongest response after the addition of vitamins. Despite developing an arguably tight dependency on its host, the BLS has probably retained flagellar mobility, as evidenced by the 32 proteins enriched in KEGG pathways associated with flagellar assembly or chemotaxis (e.g., fliC, flgE, and flgK, as highly expressed genes). Some of these proteins probably also facilitate adhesion to host gut cells. The microcin C transporter was identified in the BLS, suggesting that microcin C may be used in competition with other gut bacteria. The 16S DNA sequence comparison indicated a mite clade of BLSs with a broad host range, including house dust and stored-product mites. Our phylogenomic analyses identified a unique lineage of arachnid specific BLSs in mites and scorpions.IMPORTANCEA Bartonella-like symbiont was found in an astigmatid mite of allergenic importance. We assembled the genome of the bacterium from metagenomes of different stored-product mite (T. putrescentiae) cultures. The bacterium provides pantothenate and lipoic acid to the mite host. The vitamin supply explains the changes in the relative abundance of BLSs in T. putrescentiae as the microbiome response to nutritional or pesticide stress, as observed previously. The phylogenomic analyses of available 16S DNA sequences originating from mite, scorpion, and insect samples identified a unique lineage of arachnid specific forming large Bartonella clade. BLSs associated with mites and a scorpion. The Bartonella clade included the previously described Ca. Tokpelaia symbionts of ants.}, } @article {pmid38380878, year = {2024}, author = {Galli, BD}, title = {Sustainability implications and relevance of using omics sciences to investigate cheeses with protected designation of origin (PDO).}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.13403}, pmid = {38380878}, issn = {1097-0010}, abstract = {Cheese, a fundamental component of the human diet and a cornerstone of the global food economy, holds significance beyond its role as a market commodity, playing a crucial part in the cultural identity of various social communities. The intricate natural aging process, known as maturation, involves a series of reactions that induce changes in physical, biochemical, microbiological, and particularly sensory characteristics, making it a complex aspect of cheese production. Recently, the adoption of omics sciences (e.g., metagenomics, metabolomics, proteomics) in PDO cheese studies has emerged as a new trend. This mini-summary aims to outline the relationship between omics studies in these food matrices and all the sustainability facets of the production chain in general, as well as discuss and recognize that the importance of these studies goes beyond comprehending the cheesebiome; it extends to fostering and ensuring the sustainability of the production chain. In this context, numerous studies in recent years have linked the identification of intrinsic characteristics of PDO cheeses through omics sciences to crucial sustainability themes such as territoriality, biodiversity, and the preservation of product authenticity. The trajectory suggests that increasingly multidisciplinary studies, spanning various omics sciences, will not only contribute to characterizing these products but also address sustainability aspects directly related to the production chain (e.g., authenticity, microbial biodiversity, functionality). This expansion underscores the multidisciplinary nature of these studies, broadening their social impact beyond the academic realm. Consequently, these pivotal studies play a crucial role in advancing discussions on PDO products and sustainability. This article is protected by copyright. All rights reserved.}, } @article {pmid38380347, year = {2024}, author = {Visconti, V and Wirtz, S and Schiffer, M and Müller-Deile, J}, title = {Distinct Changes in Gut Microbiota of Patients With Kidney Graft Rejection.}, journal = {Transplantation direct}, volume = {10}, number = {3}, pages = {e1582}, pmid = {38380347}, issn = {2373-8731}, abstract = {BACKGROUND: Kidney graft rejection still represents the major cause of graft loss in kidney transplant recipients. Of growing interest is the bidirectional relationship between gut microbiome and immune system suggesting that gut microbiota can affect allograft outcome.

METHODS: In this cross-sectional case-control study, we characterized the gut microbial profile of adult renal transplant recipients with and without graft rejection to define a cohort-specific microbial fingerprint through 16S ribosomal RNA gene sequencing. We used very strict inclusion and exclusion criteria to address confounder of microbiota composition.

RESULTS: Different relative abundances in several gut microbial taxa were detectable in control patients compared with patients with kidney allograft rejection. Alpha diversity was lower in the rejection group and beta diversity revealed dissimilarity between patients with and without kidney graft rejection (P < 0.01). When the rejection group was stratified according to different types of allograft rejection, major changes were identified between patients with chronic T-cellular-mediated rejection and controls. Changes in alpha diversity within the gut microbiome were related to the probability of chronic T-cellular-mediated rejection (P < 0.05). Kidney transplant patients without rejection showed significant enrichment of rather anti-inflammatory taxa whereas in the rejection group bacteria well known for their role in chronic inflammation were increased. For example, amplicon sequence variant (ASV) 362 belonging to the genus Bacteroides and ASV 312 belonging to Tannerellaceae were enriched in no rejection (P < 0.001 and P < 0.01), whereas ASV 365 was enriched in patients with allograft rejection (P = 0.04). Looking at metagenomic functions, a higher abundance of genes coding for enzymes involved in bacterial multidrug resistance and processing of short-chain fatty acids was found in patients without rejection but an increase in enzymes involved in nicotinamide adenine dinucleotide phosphate production was seen in patients with allograft rejection.

CONCLUSIONS: A distinct microbial fingerprint of patients with allograft rejection might serve as noninvasive biomarker in the future.}, } @article {pmid38380092, year = {2024}, author = {Pramono, AK and Hidayanti, AK and Tagami, Y and Ando, H}, title = {Bacterial community and genome analysis of cytoplasmic incompatibility-inducing Wolbachia in American serpentine leafminer, Liriomyza trifolii.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1304401}, pmid = {38380092}, issn = {1664-302X}, abstract = {Liriomyza trifolii, an agricultural pest, is occasionally infected by Wolbachia. A Wolbachia strain present in Liriomyza trifolii is associated with cytoplasmic incompatibility (CI) effects, leading to the death of embryos resulting from incompatible crosses between antibiotic-treated or naturally Wolbachia-free strain females and Wolbachia-infected males. In this study, high-throughput sequencing of hypervariable rRNA genes was employed to characterize the bacterial community in Wolbachia-infected L. trifolii without antibiotic treatment. The analysis revealed that Wolbachia dominates the bacterial community in L. trifolii, with minor presence of Acinetobacter, Pseudomonas, and Limnobacter. To elucidate the genetic basis of the CI phenotype, metagenomic sequencing was also conducted to assemble the genome of the Wolbachia strain. The draft-genome of the Wolbachia strain wLtri was 1.35 Mbp with 34% GC content and contained 1,487 predicted genes. Notably, within the wLtri genome, there are three distinct types of cytoplasmic incompatibility factor (cif) genes: Type I, Type III, and Type V cifA;B. These genes are likely responsible for inducing the strong cytoplasmic incompatibility observed in L. trifolii.}, } @article {pmid38379885, year = {2024}, author = {Yahaya, N and Mohamed Rehan, M and Hamdan, NH and Nasaruddin, SM}, title = {Metagenomic data of microbiota in mangrove soil from Lukut River, Malaysia.}, journal = {Data in brief}, volume = {53}, number = {}, pages = {110155}, pmid = {38379885}, issn = {2352-3409}, abstract = {The mangrove ecosystem contains sediment microorganisms that play a crucial part in the decomposition of organic matter and the cycling of water and nutrients in the mangrove. Here we present the metagenomics whole genome shotgun (mWGS) sequence data analysis from three soil samples that were collected at the freshwater riverine mangrove at Lukut River, Negeri Sembilan, Malaysia. Data analysis shows different distributions of bacteria of the genera Bradyrhizobium, Methyloceanibacter and Desulfobacteaceae were detected in soil samples collected at freshwater riverine mangrove. In the data analysis, we report the existence of a large number of Carbohydrate-Active genes in metagenomes collected from mangrove soil. An in-depth exploration of functional annotation analysis based on the KEGG database also showed that the most abundant genes found in these three soils are those that function in carbon fixation pathways, followed by methane, nitrogen, sulfur metabolisms, atrazine and dioxin degradations.}, } @article {pmid38378498, year = {2024}, author = {Wang, S and Tian, Y and Wu, Y and Yu, Z and Zhang, J and Zhang, J and Liu, S}, title = {Fusobacterium nucleatum bacteremia complicated with intracranial Porphyromonas gingivalis and HSV-1 infection: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {225}, pmid = {38378498}, issn = {1471-2334}, support = {22JCQNJC01590//Tianjin Applied Basic Research Project/ ; TJYXZDXK-047A//Tianjin Key Medical Discipline (Specialty) Construction Project/ ; }, abstract = {BACKGROUND: Fusobacterium nucleatum (F. nucleatum) belongs to the genus Fusobacterium, which is a gram-negative obligate anaerobic bacterium. Bacteremia associated with F. nucleatum is a serious complication, which is not common in clinic, especially when it is combined with other intracranial pathogenic microorganism infection. We reported for the first time a case of F. nucleatum bacteremia combined with intracranial Porphyromonas gingivalis (P. gingivalis) and herpes simplex virus type 1(HSV-1) infection.

CASE PRESENTATION: A 60-year-old woman was admitted to our hospital with a headache for a week that worsened for 2 days. Combined with history, physical signs and examination, it was characterized as ischemic cerebrovascular disease (ICVD). F. nucleatum was detected in blood by matrix-assisted laser desorption/ionization time-offight mass spectrometry (MALDI-TOF-MS). Meanwhile, P. gingivalis and HSV-1 in cerebrospinal fluid (CSF) were identified by metagenome next generation sequencing (mNGS). After a quick diagnosis and a combination of antibiotics and antiviral treatment, the patient recovered and was discharged.

CONCLUSION: To our knowledge, this is the first report of intracranial P. gingivalis and HSV-1 infection combined with F. nucleatum bacteremia.}, } @article {pmid38378443, year = {2024}, author = {Li, J and Li, Y and Zhou, L and Li, H and Wan, T and Tang, J and Zhou, L and Xie, H and Wang, L}, title = {Microbiome analysis reveals the inducing effect of Pseudomonas on prostatic hyperplasia via activating NF-κB signalling.}, journal = {Virulence}, volume = {15}, number = {1}, pages = {2313410}, doi = {10.1080/21505594.2024.2313410}, pmid = {38378443}, issn = {2150-5608}, abstract = {Benign prostatic hyperplasia (BPH) is a prevalent disease among middle-aged and elderly males, but its pathogenesis remains unclear. Dysbiosis of the microbiome is increasingly recognized as a significant factor in various human diseases. Prostate tissue also contains a unique microbiome, and its dysbiosis has been proposed to contribute to prostate diseases. Here, we obtained prostate tissues and preoperative catheterized urine from 24 BPH individuals, and 8 normal prostate samples as controls, which followed strict aseptic measures. Using metagenomic next-generation sequencing (mNGS), we found the disparities in the microbiome composition between normal and BPH tissues, with Pseudomonas significantly enriched in BPH tissues, as confirmed by fluorescence in situ hybridization (FISH). Additionally, we showed that the prostate microbiome differed from the urine microbiome. In vitro experiments revealed that lipopolysaccharide (LPS) of Pseudomonas activated NF-κB signalling, leading to inflammation, proliferation, and EMT processes, while inhibiting apoptosis in prostatic cells. Overall, our research determines the presence of microbiome dysbiosis in BPH, and suggests that Pseudomonas, as the dominant microflora, may promote the progression of BPH through LPS activation of NF-κB signalling.}, } @article {pmid38378054, year = {2024}, author = {Wang, S and Yuan, X and Li, T and Yang, J and Zhao, L and Yuan, D and Guo, Z and Liu, C and Duan, C}, title = {Changes in soil microbe-mediated carbon, nitrogen and phosphorus cycling during spontaneous succession in abandoned PbZn mining areas.}, journal = {The Science of the total environment}, volume = {920}, number = {}, pages = {171018}, doi = {10.1016/j.scitotenv.2024.171018}, pmid = {38378054}, issn = {1879-1026}, abstract = {The mechanism through which soil microorganisms mediate carbon and nutrient cycling during mine wasteland restoration remained unknown. Using soil metagenome sequencing, we investigated the dynamic changes in soil microbial potential metabolic functions during the transition from biological soil crusts (BSC) to mixed broad-conifer forest (MBF) in a typical PbZn mine. The results showed soil microorganisms favored carbon sequestration through anaerobic and microaerobic pathways, predominantly using efficient, low-energy pathways during succession. Genes governing carbon degradation and aerobic respiration increased by 19.56 % and 24.79 %, respectively, reflecting change toward more efficient and intensive soil carbon utilization in late succession. Nitrogen-cycling genes mediated by soil microorganisms met their maximum influence during early succession (sparse grassland, SGL), leading to a respective increase of 75.29 % and 76.81 % in the net potential nitrification rate and total nitrogen content. Mantel and correlation analyses indicated that TOC, TN, Zn and Cd contents were the main factors affecting the soil carbon and phosphorus cycles. Soil AP content emerged as the primary influencer of genes associated with the nitrogen cycle. These results shed light on the dynamic shifts in microbial metabolic activities during succession, providing a genetic insight into biogeochemical cycling mechanisms and underscoring crucial factors influencing soil biogeochemical processes in mining regions.}, } @article {pmid38378003, year = {2024}, author = {Li, J and Chen, Z and Wang, Q and Du, L and Yang, Y and Guo, F and Li, X and Chao, Y and Ma, Y}, title = {Microbial and metabolic profiles unveil mutualistic microbe-microbe interaction in obesity-related colorectal cancer.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {101429}, doi = {10.1016/j.xcrm.2024.101429}, pmid = {38378003}, issn = {2666-3791}, abstract = {Obesity is a risk factor for colorectal cancer (CRC), and the involvement of gut microbiota in the pathogenesis of obesity and CRC is widely recognized. However, the landscape of fecal microbiome and metabolome distinguishing patients with obesity-related CRC from obesity remains unknown. Here, we utilize metagenomic sequencing and metabolomics from 522 patients with CRC and healthy controls to identify the characteristics of obese CRC. Our integrated analysis reveals that obesity-related CRC is characterized by elevated Peptostreptococcus stomatis, dysregulated fatty acids and phospholipids, and altered Kyoto Encyclopedia of Genes and Genomes pathways involving glycerophospholipid metabolism and lipopolysaccharide synthesis. Correlation analysis unveils microbial interactions in obesity, where the probiotic Faecalibacterium prausnitzii and the tumor-promoting species P. stomatis may engage in cross-feeding, thereby promoting tumorigenesis. In vitro experiments affirm enhanced growth under cross-feeding conditions. The mutualistic microbe-microbe interaction may contribute to the association between obesity and elevated CRC risk. Additionally, diagnostic models incorporating BMI-specific microbial biomarkers display promise for precise CRC screening.}, } @article {pmid38377920, year = {2024}, author = {Egli, T and Campostrini, L and Leifels, M and Füchslin, HP and Kolm, C and Dan, C and Zimmermann, S and Hauss, V and Guiller, A and Grasso, L and Shajkofci, A and Farnleitner, AH and Kirschner, AKT}, title = {Domestic hot-water boilers harbour active thermophilic bacterial communities distinctly different from those in the cold-water supply.}, journal = {Water research}, volume = {253}, number = {}, pages = {121109}, doi = {10.1016/j.watres.2024.121109}, pmid = {38377920}, issn = {1879-2448}, abstract = {Running cold and hot water in buildings is a widely established commodity. However, interests regarding hygiene and microbiological aspects had so far been focussed on cold water. Little attention has been given to the microbiology of domestic hot-water installations (DHWIs), except for aspects of pathogenic Legionella. World-wide, regulations consider hot (or warm) water as 'heated drinking water' that must comply (cold) drinking water (DW) standards. However, the few reports that exist indicate presence and growth of microbial flora in DHWIs, even when supplied with water with disinfectant residual. Using flow cytometric (FCM) total cell counting (TCC), FCM-fingerprinting, and 16S rRNA-gene-based metagenomic analysis, the characteristics and composition of bacterial communities in cold drinking water (DW) and hot water from associated boilers (operating at 50 - 60 °C) was studied in 14 selected inhouse DW installations located in Switzerland and Austria. A sampling strategy was applied that ensured access to the bulk water phase of both, supplied cold DW and produced hot boiler water. Generally, 1.3- to 8-fold enhanced TCCs were recorded in hot water compared to those in the supplied cold DW. FCM-fingerprints of cold and corresponding hot water from individual buildings indicated different composition of cold- and hot-water microbial floras. Also, hot waters from each of the boilers sampled had its own individual FCM-fingerprint. 16S rRNA-gene-based metagenomic analysis confirmed the marked differences in composition of microbiomes. E.g., in three neighbouring houses supplied from the same public network pipe each hot-water boiler contained its own thermophilic bacterial flora. Generally, bacterial diversity in cold DW was broad, that in hot water was restricted, with mostly thermophilic strains from the families Hydrogenophilaceae, Nitrosomonadaceae and Thermaceae dominating. Batch growth assays, consisting of cold DW heated up to 50 - 60 °C and inoculated with hot water, resulted in immediate cell growth with doubling times between 5 and 10 h. When cold DW was used as an inoculum no significant growth was observed. Even boilers supplied with UVC-treated cold DW contained an actively growing microbial flora, suggesting such hot-water systems as autonomously operating, thermophilic bioreactors. The generation of assimilable organic carbon from dissolved organic carbon due to heating appears to be the driver for growth of thermophilic microbial communities. Our report suggests that a man-made microbial ecosystem, very close to us all and of potential hygienic importance, may have been overlooked so far. Despite consumers having been exposed to microbial hot-water flora for a long time, with no major pathogens so far been associated specifically with hot-water usage (except for Legionella), the role of harmless thermophiles and their interaction with potential human pathogens able to grow at elevated temperatures in DHWIs remains to be investigated.}, } @article {pmid38377397, year = {2024}, author = {Martiny, HM and Pyrounakis, N and Petersen, TN and Lukjančenko, O and Aarestrup, FM and Clausen, PTLC and Munk, P}, title = {ARGprofiler-a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btae086}, pmid = {38377397}, issn = {1367-4811}, abstract = {MOTIVATION: Analyzing metagenomic data can be highly valuable for understanding the function and distribution of antimicrobial resistance genes (ARGs). However, there is a need for standardized and reproducible workflows to ensure the comparability of studies, as the current options involve various tools and reference databases, each designed with a specific purpose in mind.

RESULTS: In this work, we have created the workflow ARGprofiler to process large amounts of raw sequencing reads for studying the composition, distribution, and function of ARGs. ARGprofiler tackles the challenge of deciding which reference database to use by providing the PanRes database of 14,078 unique ARGs that combines several existing collections into one. Our pipeline is designed to not only produce abundance tables of genes and microbes but also to reconstruct the flanking regions of ARGs with ARGextender. ARGextender is a bioinformatic approach combining KMA and SPAdes to recruit reads for a targeted de novo assembly. While our aim is on ARGs, the pipeline also creates Mash sketches for fast searching and comparisons of sequencing runs.

AVAILABILITY: The ARGprofiler pipeline is a Snakemake workflow that supports the reuse of metagenomic sequencing data and is easily installable and maintained at https://github.com/genomicepidemiology/ARGprofiler.}, } @article {pmid38377278, year = {2024}, author = {Dindhoria, K and Kumar, R and Bhargava, B and Kumar, R}, title = {Metagenomic assembled genomes indicated the potential application of hypersaline microbiome for plant growth promotion and stress alleviation in salinized soils.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0105023}, doi = {10.1128/msystems.01050-23}, pmid = {38377278}, issn = {2379-5077}, abstract = {Climate change is causing unpredictable seasonal variations globally. Due to the continuously increasing earth's surface temperature, the rate of water evaporation is enhanced, conceiving a problem of soil salinization, especially in arid and semi-arid regions. The accumulation of salt degrades soil quality, impairs plant growth, and reduces agricultural yields. Salt-tolerant, plant-growth-promoting microorganisms may offer a solution, enhancing crop productivity and soil fertility in salinized areas. In the current study, genome-resolved metagenomic analysis has been performed to investigate the salt-tolerating and plant growth-promoting potential of two hypersaline ecosystems, Sambhar Lake and Drang Mine. The samples were co-assembled independently by Megahit, MetaSpades, and IDBA-UD tools. A total of 67 metagenomic assembled genomes (MAGs) were reconstructed following the binning process, including 15 from Megahit, 26 from MetaSpades, and 26 from IDBA_UD assembly tools. As compared to other assemblers, the MAGs obtained by MetaSpades were of superior quality, with a completeness range of 12.95%-96.56% and a contamination range of 0%-8.65%. The medium and high-quality MAGs from MetaSpades, upon functional annotation, revealed properties such as salt tolerance (91.3%), heavy metal tolerance (95.6%), exopolysaccharide (95.6%), and antioxidant (60.86%) biosynthesis. Several plant growth-promoting attributes, including phosphate solubilization and indole-3-acetic acid (IAA) production, were consistently identified across all obtained MAGs. Conversely, characteristics such as iron acquisition and potassium solubilization were observed in a substantial majority, specifically 91.3%, of the MAGs. The present study indicates that hypersaline microflora can be used as bio-fertilizing agents for agricultural practices in salinized areas by alleviating prevalent stresses.IMPORTANCEThe strategic implementation of metagenomic assembled genomes (MAGs) in exploring the properties and harnessing microorganisms from ecosystems like hypersaline niches has transformative potential in agriculture. This approach promises to redefine our comprehension of microbial diversity and its ecosystem roles. Recovery and decoding of MAGs unlock genetic resources, enabling the development of new solutions for agricultural challenges. Enhanced understanding of these microbial communities can lead to more efficient nutrient cycling, pest control, and soil health maintenance. Consequently, traditional agricultural practices can be improved, resulting in increased yields, reduced environmental impacts, and heightened sustainability. MAGs offer a promising avenue for sustainable agriculture, bridging the gap between cutting-edge genomics and practical field applications.}, } @article {pmid38377089, year = {2024}, author = {Yang, Q and Wu, B and Wang, W and Tan, N and Huang, H}, title = {Metagenomic sequencing expedites diagnosis of disseminated BCG in an infant with BRAFV600E mutation.}, journal = {Journal of infection in developing countries}, volume = {18}, number = {1}, pages = {162-167}, doi = {10.3855/jidc.18628}, pmid = {38377089}, issn = {1972-2680}, abstract = {INTRODUCTION: Disseminated bacillus Calmette-Guérin (BCG) disease is a rare but serious BCG complication in children. Early diagnosis and timely interventions are essential to improve prognosis. However, its manifestations can closely mimic those of Langerhans cell histiocytosis (LCH), which usually leads to a high rate of misdiagnoses. Herein we report the first case of successful application of biopsy tissue metagenomic next-generation sequencing (mNGS) in the differential diagnosis of disseminated BCG disease and LCH.

CASE STUDY: A 5-month-old female infant was transferred to our center for the treatment of paroxysmal cough, intermittent hematochezia and trunk rash. Examination on admission showed moderate anemia, erythropenia, thrombocytopenia and hepatosplenomegaly. The immunohistochemistry of her intestinal biopsy samples showed CD1a (+) and Langerin (+). Genetic testing of both peripheral blood and bone marrow samples suggested BRAFV600E mutation. Hence, she was initially diagnosed with LCH. However, no improvement was observed after a course of systemic chemotherapy. The left axillary lymph node and colonic mucosal biopsy specimens were sent for mNGS which resulted in sequence reads of Mycobacterium bovis-BCG. Triple antimycobacterial therapy was started according to the diagnosis.

RESULTS: The diagnosis of this case was corrected as disseminated BCG disease by mNGS. Currently, she is doing well clinically and continues to follow-up at our outpatient clinic.

CONCLUSIONS: This case suggests that mNGS is a valuable tool in the differential diagnosis of disseminated BCG disease and LCH, which can improve the early diagnosis rate of disseminated BCG disease.}, } @article {pmid38205997, year = {2024}, author = {Shi, Z and Zhang, C and Tan, X and Xie, L and Luo, G}, title = {Syntrophic microbes involved in the oxidation of short-chain fatty acids in continuous-flow anaerobic digesters treating waste activated sludge with hydrochar.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {2}, pages = {e0204723}, doi = {10.1128/aem.02047-23}, pmid = {38205997}, issn = {1098-5336}, support = {22ZR1405900//Science and Technology Commission of Shanghai Municipality (STCSM)/ ; 52300154//MOST | National Natural Science Foundation of China (NSFC)/ ; 2022M720796//China Postdoctoral Science Foundation (China Postdoctoral Foundation Project)/ ; }, abstract = {The rapid degradation of short-chain fatty acids (SCFAs) is an essential issue of anaerobic digestion (AD), in which SCFA oxidizers could generally metabolize in syntrophy with methanogens. The dynamic responses of active metagenome-assembled genomes to low concentrations of propionate and acetate were analyzed to identify specific syntrophic SCFA oxidizers and their metabolic characteristics in continuous-flow AD systems treating waste activated sludge with and without hydrochar. In this study, hydrochar increased methane production by 19%, possibly due to hydrochar enhancing acidification and methanogenesis processes. A putative syntrophic propionate oxidizer and two acetate oxidizers contributed substantially to the syntrophic degradation of SCFAs, and hydrochar positively regulated their functional gene expressions. A significant relationship was established between the replication rate of SCFA oxidizers and their stimulation-related transcriptional activity. Acetate was degraded in the hydrochar group, which might be mainly through the syntrophic acetate oxidizer from the genus Desulfallas and methanogens from the genus Methanosarcina.IMPORTANCEShort-chain fatty acid (SCFA) degradation is an important process in the methanogenic ecosystem. However, current knowledge of this microbial mechanism is mainly based on studies on a few model organisms incubated as mono- or co-cultures or in enrichments, which cannot provide appropriate evidence in complex environments. Here, this study revealed the microbial mechanism of a hydrochar-mediated anaerobic digestion (AD) system promoting SCFA degradation at the species level and identified key SCFA oxidizing bacteria. Our analysis provided new insights into the SCFA oxidizers involved in the AD of waste activated sludge facilitated by hydrochar.}, } @article {pmid38377081, year = {2024}, author = {Zhang, K and Xu, J and Chen, G and Yang, R and Jiang, M and Yuan, H}, title = {Metagenomic Next-Generation Sequencing (mNGS) of cerebrospinal fluid for diagnosis of human herpesvirus 6B encephalitis following transplantation for severe aplastic anemia.}, journal = {Journal of infection in developing countries}, volume = {18}, number = {1}, pages = {152-157}, doi = {10.3855/jidc.18152}, pmid = {38377081}, issn = {1972-2680}, abstract = {INTRODUCTION: Human herpesvirus 6B (HHV-6B) encephalitis is common in immunosuppressed patients and presents a diagnostic challenge for physicians. Metagenomic next-generation sequencing (mNGS) may facilitate early diagnosis of HHV-6B encephalitis. Herein, we described a case of HHV-6B encephalitis following transplantation for severe aplastic anemia (SAA) diagnosed by mNGS.

CASE SUMMARY: A 31-year-old male underwent myeloablative haploid hematopoietic stem cell transplantation for the treatment of SAA. On day + 21 after transplantation, the patient developed symptoms such as sudden epilepsy, drowsiness, memory dislocation, and memory loss. HHV-6B encephalitis was confirmed based on cranial MRI and mNGS of cerebrospinal fluid. Following antiviral therapy with sodium foscarnet, the symptoms improved and HHV-6B was negative by mNGS. There were no serious sequelae. Currently, the patient is in good health and is still under follow-up.

CONCLUSIONS: A case of HHV-6B encephalitis after SAA transplantation was diagnosed by mNGS of cerebrospinal fluid in time and was effectively treated with sodium foscarnet.}, } @article {pmid38376627, year = {2024}, author = {Isali, I and Helstrom, EK and Uzzo, N and Lakshmanan, A and Nandwana, D and Valentine, H and Sindhani, M and Abbosh, P and Bukavina, L}, title = {Current Trends and Challenges of Microbiome Research in Bladder Cancer.}, journal = {Current oncology reports}, volume = {}, number = {}, pages = {}, pmid = {38376627}, issn = {1534-6269}, abstract = {PURPOSE OF THE REVIEW: Microbiome research has provided valuable insights into the associations between microbial communities and bladder cancer. However, this field faces significant challenges that hinder the interpretation, generalization, and translation of findings into clinical practice. This review aims to elucidate these challenges and highlight the importance of addressing them for the advancement of microbiome research in bladder cancer.

RECENT FINDINGS: Recent findings underscore the complexities involved in microbiome research, particularly in the context of bladder cancer. Challenges include low microbial biomass in urine samples, potential contamination issues during collection and processing, variability in sequencing methods and primer selection, and the difficulty of establishing causality between microbiota and bladder cancer. Studies have shown the impact of sample storage conditions and DNA isolation kits on microbiome analysis, emphasizing the need for standardization. Additionally, variations in urine collection methods can introduce contamination and affect results. The choice of 16S rRNA gene amplicon sequencing or shotgun metagenomic sequencing introduces technical challenges, including primer selection and sequencing read length. Establishing causality between the microbiota and bladder cancer requires experimental methods like fecal microbiota transplantation and human microbiota-associated murine models, which face their own set of challenges. Translating microbiome research into therapeutic applications is hindered by methodological variability, incomplete understanding of bioactive molecules, imperfect animal models, and the inherent heterogeneity of microbiome communities among individuals. Microbiome research in bladder cancer presents significant challenges stemming from technical and conceptual complexities. Addressing these challenges through standardization, improved experimental models, and advanced analytical approaches is essential for advancing our understanding of the microbiome's role in bladder cancer and its potential clinical applications. Achieving this goal can lead to improved patient outcomes and novel therapeutic strategies in the future.}, } @article {pmid38376411, year = {2024}, author = {François, S and Hill, SC and Perrins, CM and Pybus, OG}, title = {Characterization of the genomic sequence of a circo-like virus and of three chaphamaparvoviruses detected in mute swan (Cygnus olor).}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0118623}, doi = {10.1128/mra.01186-23}, pmid = {38376411}, issn = {2576-098X}, abstract = {We report the complete genomes of four ssDNA viruses: a circular replication-associated protein-encoding single-stranded DNA virus belonging to a clade previously detected only in mammals, and three chaphamaparvoviruses, which were detected by viromic surveillance of mute swan (Cygnus olor) fecal samples from the United Kingdom.}, } @article {pmid38376381, year = {2024}, author = {Hiralal, A and Geelhoed, JS and Hidalgo-Martinez, S and Smets, B and van Dijk, JR and Meysman, FJR}, title = {Closing the genome of unculturable cable bacteria using a combined metagenomic assembly of long and short sequencing reads.}, journal = {Microbial genomics}, volume = {10}, number = {2}, pages = {}, doi = {10.1099/mgen.0.001197}, pmid = {38376381}, issn = {2057-5858}, abstract = {Many environmentally relevant micro-organisms cannot be cultured, and even with the latest metagenomic approaches, achieving complete genomes for specific target organisms of interest remains a challenge. Cable bacteria provide a prominent example of a microbial ecosystem engineer that is currently unculturable. They occur in low abundance in natural sediments, but due to their capability for long-distance electron transport, they exert a disproportionately large impact on the biogeochemistry of their environment. Current available genomes of marine cable bacteria are highly fragmented and incomplete, hampering the elucidation of their unique electrogenic physiology. Here, we present a metagenomic pipeline that combines Nanopore long-read and Illumina short-read shotgun sequencing. Starting from a clonal enrichment of a cable bacterium, we recovered a circular metagenome-assembled genome (5.09 Mbp in size), which represents a novel cable bacterium species with the proposed name Candidatus Electrothrix scaldis. The closed genome contains 1109 novel identified genes, including key metabolic enzymes not previously described in incomplete genomes of cable bacteria. We examined in detail the factors leading to genome closure. Foremost, native, non-amplified long reads are crucial to resolve the many repetitive regions within the genome of cable bacteria, and by analysing the whole metagenomic assembly, we found that low strain diversity is key for achieving genome closure. The insights and approaches presented here could help achieve genome closure for other keystone micro-organisms present in complex environmental samples at low abundance.}, } @article {pmid38376378, year = {2024}, author = {Kitamura, N and Kajihara, T and Volpiano, CG and Naung, M and Méric, G and Hirabayashi, A and Yano, H and Yamamoto, M and Yoshida, F and Kobayashi, T and Yamanashi, S and Kawamura, T and Matsunaga, N and Okochi, J and Sugai, M and Yahara, K}, title = {Exploring the effects of antimicrobial treatment on the gut and oral microbiomes and resistomes from elderly long-term care facility residents via shotgun DNA sequencing.}, journal = {Microbial genomics}, volume = {10}, number = {2}, pages = {}, doi = {10.1099/mgen.0.001180}, pmid = {38376378}, issn = {2057-5858}, abstract = {Monitoring antibiotic-resistant bacteria (ARB) and understanding the effects of antimicrobial drugs on the human microbiome and resistome are crucial for public health. However, no study has investigated the association between antimicrobial treatment and the microbiome-resistome relationship in long-term care facilities, where residents act as reservoirs of ARB but are not included in the national surveillance for ARB. We conducted shotgun metagenome sequencing of oral and stool samples from long-term care facility residents and explored the effects of antimicrobial treatment on the human microbiome and resistome using two types of comparisons: cross-sectional comparisons based on antimicrobial treatment history in the past 6 months and within-subject comparisons between stool samples before, during and 2-4 weeks after treatment using a single antimicrobial drug. Cross-sectional analysis revealed two characteristics in the group with a history of antimicrobial treatment: the archaeon Methanobrevibacter was the only taxon that significantly increased in abundance, and the total abundance of antimicrobial resistance genes (ARGs) was also significantly higher. Within-subject comparisons showed that taxonomic diversity did not decrease during treatment, suggesting that the effect of the prescription of a single antimicrobial drug in usual clinical treatment on the gut microbiota is likely to be smaller than previously thought, even among very elderly people. Additional analysis of the detection limit of ARGs revealed that they could not be detected when contig coverage was <2.0. This study is the first to report the effects of usual antimicrobial treatments on the microbiome and resistome of long-term care facility residents.}, } @article {pmid38376377, year = {2024}, author = {Cook, R and Brown, N and Rihtman, B and Michniewski, S and Redgwell, T and Clokie, M and Stekel, DJ and Chen, Y and Scanlan, DJ and Hobman, JL and Nelson, A and Jones, MA and Smith, D and Millard, A}, title = {The long and short of it: benchmarking viromics using Illumina, Nanopore and PacBio sequencing technologies.}, journal = {Microbial genomics}, volume = {10}, number = {2}, pages = {}, doi = {10.1099/mgen.0.001198}, pmid = {38376377}, issn = {2057-5858}, abstract = {Viral metagenomics has fuelled a rapid change in our understanding of global viral diversity and ecology. Long-read sequencing and hybrid assembly approaches that combine long- and short-read technologies are now being widely implemented in bacterial genomics and metagenomics. However, the use of long-read sequencing to investigate viral communities is still in its infancy. While Nanopore and PacBio technologies have been applied to viral metagenomics, it is not known to what extent different technologies will impact the reconstruction of the viral community. Thus, we constructed a mock bacteriophage community of previously sequenced phage genomes and sequenced them using Illumina, Nanopore and PacBio sequencing technologies and tested a number of different assembly approaches. When using a single sequencing technology, Illumina assemblies were the best at recovering phage genomes. Nanopore- and PacBio-only assemblies performed poorly in comparison to Illumina in both genome recovery and error rates, which both varied with the assembler used. The best Nanopore assembly had errors that manifested as SNPs and INDELs at frequencies 41 and 157 % higher than found in Illumina only assemblies, respectively. While the best PacBio assemblies had SNPs at frequencies 12 and 78 % higher than found in Illumina-only assemblies, respectively. Despite high-read coverage, long-read-only assemblies recovered a maximum of one complete genome from any assembly, unless reads were down-sampled prior to assembly. Overall the best approach was assembly by a combination of Illumina and Nanopore reads, which reduced error rates to levels comparable with short-read-only assemblies. When using a single technology, Illumina only was the best approach. The differences in genome recovery and error rates between technology and assembler had downstream impacts on gene prediction, viral prediction, and subsequent estimates of diversity within a sample. These findings will provide a starting point for others in the choice of reads and assembly algorithms for the analysis of viromes.}, } @article {pmid38376339, year = {2024}, author = {Brown, KM and Ward, CS and Bullerjahn, GS}, title = {Metagenome-assembled genome sequences of two cyanobacterial cultures from Homa Bay County, Kenya.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0120523}, doi = {10.1128/mra.01205-23}, pmid = {38376339}, issn = {2576-098X}, abstract = {Metagenome-assembled genomes were generated for two xenic cyanobacterial strains collected from aquatic sources in Kenya and sequenced by NovaSeq S4. Here, we report the classification and genome statistics of Microcystis panniformis WG22 and Limnospira fusiformis LS22.}, } @article {pmid38376235, year = {2024}, author = {Huang, J and Wu, Y and Gao, Q and Li, X and Zeng, Y and Guo, Y and Zhang, H and Qin, Z}, title = {Metagenomic exploration of the rhizosphere soil microbial community and their significance in facilitating the development of wild-simulated ginseng.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0233523}, doi = {10.1128/aem.02335-23}, pmid = {38376235}, issn = {1098-5336}, abstract = {Panax ginseng, a prized medicinal herb, has faced increasingly challenging field production due to soil degradation and fungal diseases in Northeast China. Wild-simulated cultivation has prevailed because of its sustainable soil management and low disease incidence. Despite the recognized benefits of rhizosphere microorganisms in ginseng cultivation, their genomic and functional diversity remain largely unexplored. In this work, we utilized shotgun metagenomic analysis to reveal that Pseudomonadota, Actinomycetota, and Acidobacteriota were dominant in the ginseng rhizobiome and recovered 14 reliable metagenome-assembled genomes. Functional analysis indicated an enrichment of denitrification-associated genes, potentially contributing to the observed decline in soil fertility, while genes associated with aromatic carbon degradation may be linked to allelochemical degradation. Further analysis demonstrated enrichment of Actinomycetota in 9-year-old wild-simulated ginseng (WSG), suggesting the need for targeted isolation of Actinomycetota bacteria. Among these, at least three different actinomycete strains were found to play a crucial role in fungal disease resistance, with Streptomyces spp. WY144 standing out for its production of actinomycin natural products active against the pathogenic fungus Ilyonectria robusta. These findings not only enhance our understanding of the rhizobiome of WSG but also present promising avenues for combating detrimental fungal pathogens, underscoring the importance of ginseng in both medicinal and agricultural contexts.IMPORTANCEWild-simulated ginseng, growing naturally without human interference, is influenced by its soil microbiome. Using shotgun metagenomics, we analyzed the rhizospheric soil microbiome of 7- and 9-year-old wild-simulated ginseng. The study aimed to reveal its composition and functions, exploring the microbiome's key roles in ginseng growth. Enrichment analysis identified Streptomycetes in ginseng soil, with three strains inhibiting plant pathogenic fungi. Notably, one strain produced actinomycins, suppressing the ginseng pathogenic fungus Ilyonectria robusta. This research accelerates microbiome application in wild-simulated ginseng cultivation, offering insights into pathogen protection and supporting microbiome utilization in agriculture.}, } @article {pmid38376220, year = {2024}, author = {Saito, D and Saito, CPB and Cannavan, FdS and Tsai, SM}, title = {Draft genome sequences of 13 putatively novel Haemophilus species and strains assembled from human saliva.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0094523}, doi = {10.1128/mra.00945-23}, pmid = {38376220}, issn = {2576-098X}, abstract = {We present the draft metagenome-assembled genomes (MAGs) of 13 Haemophilus representatives from human saliva. MAGs were reconstructed by a streamlined pre-assembly mapping approach performed against 9 clinically relevant reference genomes. Overall, genomes belonging to 2 potentially novel Haemophilus species and 11 strains were recovered, as determined by genome-wide ANI analysis.}, } @article {pmid38376207, year = {2024}, author = {Xu, Q and Li, L and Guo, J and Guo, H and Liu, M and Guo, S and Kuzyakov, Y and Ling, N and Shen, Q}, title = {Active microbial population dynamics and life strategies drive the enhanced carbon use efficiency in high-organic matter soils.}, journal = {mBio}, volume = {}, number = {}, pages = {e0017724}, doi = {10.1128/mbio.00177-24}, pmid = {38376207}, issn = {2150-7511}, abstract = {Microbial carbon use efficiency (CUE) is a critical parameter that controls carbon storage in soil, but many uncertainties remain concerning adaptations of microbial communities to long-term fertilization that impact CUE. Based on H2[18]O quantitative stable isotope probing coupled with metagenomic sequencing, we disentangled the roles of active microbial population dynamics and life strategies for CUE in soils after a long-term (35 years) mineral or organic fertilization. We found that the soils rich in organic matter supported high microbial CUE, indicating a more efficient microbial biomass formation and a greater carbon sequestration potential. Organic fertilizers supported active microbial communities characterized by high diversity and a relative increase in net growth rate, as well as an anabolic-biased carbon cycling, which likely explains the observed enhanced CUE. Overall, these results highlight the role of population dynamics and life strategies in understanding and predicting microbial CUE and sequestration in soil.IMPORTANCEMicrobial CUE is a major determinant of global soil organic carbon storage. Understanding the microbial processes underlying CUE can help to maintain soil sustainable productivity and mitigate climate change. Our findings indicated that active microbial communities, adapted to long-term organic fertilization, exhibited a relative increase in net growth rate and a preference for anabolic carbon cycling when compared to those subjected to chemical fertilization. These shifts in population dynamics and life strategies led the active microbes to allocate more carbon to biomass production rather than cellular respiration. Consequently, the more fertile soils may harbor a greater microbially mediated carbon sequestration potential. This finding is of great importance for manipulating microorganisms to increase soil C sequestration.}, } @article {pmid38376180, year = {2024}, author = {Schaan, AP and Vidal, A and Zhang, A-N and Poyet, M and Alm, EJ and Groussin, M and Ribeiro-Dos-Santos, Â}, title = {Temporal dynamics of gut microbiomes in non-industrialized urban Amazonia.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0070723}, doi = {10.1128/msystems.00707-23}, pmid = {38376180}, issn = {2379-5077}, abstract = {Increasing levels of industrialization have been associated with changes in gut microbiome structure and loss of features thought to be crucial for maintaining gut ecological balance. The stability of gut microbial communities over time within individuals seems to be largely affected by these changes but has been overlooked among transitioning populations from low- to middle-income countries. Here, we used metagenomic sequencing to characterize the temporal dynamics in gut microbiomes of 24 individuals living an urban non-industrialized lifestyle in the Brazilian Amazon. We further contextualized our data with 165 matching longitudinal samples from an urban industrialized and a rural non-industrialized population. We show that gut microbiome composition and diversity have greater variability over time among non-industrialized individuals when compared to industrialized counterparts and that taxa may present diverse temporal dynamics across human populations. Enterotype classifications show that community types are generally stable over time despite shifts in microbiome structure. Furthermore, by tracking genomes over time, we show that levels of bacterial population replacements are more frequent among Amazonian individuals and that non-synonymous variants accumulate in genes associated with degradation of host dietary polysaccharides. Taken together, our results suggest that the stability of gut microbiomes is influenced by levels of industrialization and that tracking microbial population dynamics is important to understand how the microbiome will adapt to these transitions.IMPORTANCEThe transition from a rural or non-industrialized lifestyle to urbanization and industrialization has been linked to changes in the structure and function of the human gut microbiome. Understanding how the gut microbiomes changes over time is crucial to define healthy states and to grasp how the gut microbiome interacts with the host environment. Here, we investigate the temporal dynamics of gut microbiomes from an urban and non-industrialized population in the Amazon, as well as metagenomic data sets from urban United States and rural Tanzania. We showed that healthy non-industrialized microbiomes experience greater compositional shifts over time compared to industrialized individuals. Furthermore, bacterial strain populations are more frequently replaced in non-industrialized microbiomes, and most non-synonymous mutations accumulate in genes associated with the degradation of host dietary components. This indicates that microbiome stability is affected by transitions to industrialization, and that strain tracking can elucidate the ecological dynamics behind such transitions.}, } @article {pmid38376167, year = {2024}, author = {Hegarty, B and Riddell V, J and Bastien, E and Langenfeld, K and Lindback, M and Saini, JS and Wing, A and Zhang, J and Duhaime, M}, title = {Benchmarking informatics approaches for virus discovery: caution is needed when combining in silico identification methods.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0110523}, doi = {10.1128/msystems.01105-23}, pmid = {38376167}, issn = {2379-5077}, abstract = {Understanding the ecological impacts of viruses on natural and engineered ecosystems relies on the accurate identification of viral sequences from community sequencing data. To maximize viral recovery from metagenomes, researchers frequently combine viral identification tools. However, the effectiveness of this strategy is unknown. Here, we benchmarked combinations of six widely used informatics tools for viral identification and analysis (VirSorter, VirSorter2, VIBRANT, DeepVirFinder, CheckV, and Kaiju), called "rulesets." Rulesets were tested against mock metagenomes composed of taxonomically diverse sequence types and diverse aquatic metagenomes to assess the effects of the degree of viral enrichment and habitat on tool performance. We found that six rulesets achieved equivalent accuracy [Matthews Correlation Coefficient (MCC) = 0.77, Padj ≥ 0.05]. Each contained VirSorter2, and five used our "tuning removal" rule designed to remove non-viral contamination. While DeepVirFinder, VIBRANT, and VirSorter were each found once in these high-accuracy rulesets, they were not found in combination with each other: combining tools does not lead to optimal performance. Our validation suggests that the MCC plateau at 0.77 is partly caused by inaccurate labeling within reference sequence databases. In aquatic metagenomes, our highest MCC ruleset identified more viral sequences in virus-enriched (44%-46%) than in cellular metagenomes (7%-19%). While improved algorithms may lead to more accurate viral identification tools, this should be done in tandem with careful curation of sequence databases. We recommend using the VirSorter2 ruleset and our empirically derived tuning removal rule. Our analysis provides insight into methods for in silico viral identification and will enable more robust viral identification from metagenomic data sets.IMPORTANCEThe identification of viruses from environmental metagenomes using informatics tools has offered critical insights in microbial ecology. However, it remains difficult for researchers to know which tools optimize viral recovery for their specific study. In an attempt to recover more viruses, studies are increasingly combining the outputs from multiple tools without validating this approach. After benchmarking combinations of six viral identification tools against mock metagenomes and environmental samples, we found that these tools should only be combined cautiously. Two to four tool combinations maximized viral recovery and minimized non-viral contamination compared with either the single-tool or the five- to six-tool ones. By providing a rigorous overview of the behavior of in silico viral identification strategies and a pipeline to replicate our process, our findings guide the use of existing viral identification tools and offer a blueprint for feature engineering of new tools that will lead to higher-confidence viral discovery in microbiome studies.}, } @article {pmid38375831, year = {2024}, author = {Reuter, MA and Tucker, M and Marfori, Z and Shishani, R and Bustamante, JM and Moreno, R and Goodson, ML and Ehrlich, A and Taha, AY and Lein, PJ and Joshi, N and Brito, I and Durbin-Johnson, B and Nandakumar, R and Cummings, BP}, title = {Dietary resistant starch supplementation increases gut luminal deoxycholic acid abundance in mice.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2315632}, doi = {10.1080/19490976.2024.2315632}, pmid = {38375831}, issn = {1949-0984}, abstract = {Bile acids (BA) are among the most abundant metabolites produced by the gut microbiome. Primary BAs produced in the liver are converted by gut bacterial 7-α-dehydroxylation into secondary BAs, which can differentially regulate host health via signaling based on their varying affinity for BA receptors. Despite the importance of secondary BAs in host health, the regulation of 7-α-dehydroxylation and the role of diet in modulating this process is incompletely defined. Understanding this process could lead to dietary guidelines that beneficially shift BA metabolism. Dietary fiber regulates gut microbial composition and metabolite production. We tested the hypothesis that feeding mice a diet rich in a fermentable dietary fiber, resistant starch (RS), would alter gut bacterial BA metabolism. Male and female wild-type mice were fed a diet supplemented with RS or an isocaloric control diet (IC). Metabolic parameters were similar between groups. RS supplementation increased gut luminal deoxycholic acid (DCA) abundance. However, gut luminal cholic acid (CA) abundance, the substrate for 7-α-dehydroxylation in DCA production, was unaltered by RS. Further, RS supplementation did not change the mRNA expression of hepatic BA producing enzymes or ileal BA transporters. Metagenomic assessment of gut bacterial composition revealed no change in the relative abundance of bacteria known to perform 7-α-dehydroxylation. P. ginsenosidimutans and P. multiformis were positively correlated with gut luminal DCA abundance and increased in response to RS supplementation. These data demonstrate that RS supplementation enriches gut luminal DCA abundance without increasing the relative abundance of bacteria known to perform 7-α-dehydroxylation.}, } @article {pmid38375275, year = {2024}, author = {Qian, L and Zhuang, Z and Lu, J and Wang, H and Wang, X and Yang, S and Ji, L and Shen, Q and Zhang, W and Shan, T}, title = {Metagenomic survey of viral diversity obtained from feces of piglets with diarrhea.}, journal = {Heliyon}, volume = {10}, number = {4}, pages = {e25616}, pmid = {38375275}, issn = {2405-8440}, abstract = {Pigs are natural host to various zoonotic pathogens including viruses. In this study, we analyzed the viral communities in the feces of 89 piglets with diarrhea under one month old which were collected from six farms in Jiangsu Province of the Eastern China, using the unbiased virus metagenomic method. A total of 89 libraries were constructed, and 46937894 unique sequence reads were generated by Illumina sequencing. Overall, the family Picornaviridae accounted for the majority of the total reads of putative mammalian viruses. Ten novel virus genomes from different family members were discovered, including Parvoviridae (n = 2), Picobirnaviridae (n = 4) and CRESS DNA viruses (n = 4). A large number of phages were identified, which mainly belonged to the order Caudovirales and the family Microviridae. Moreover, some identified viruses were closely related to viruses found in non-porcine hosts, highlighting the potential for cross-species virus dissemination. This study increased our understanding of the fecal virus communities of diarrhea piglets and provided valuable information for virus monitoring and preventing.}, } @article {pmid38375239, year = {2024}, author = {Peeters, J and Bot, DM and Rovelo Ruiz, G and Aerts, J}, title = {Snowflake: visualizing microbiome abundance tables as multivariate bipartite graphs.}, journal = {Frontiers in bioinformatics}, volume = {4}, number = {}, pages = {1331043}, pmid = {38375239}, issn = {2673-7647}, abstract = {Current visualizations in microbiome research rely on aggregations in taxonomic classifications or do not show less abundant taxa. We introduce Snowflake: a new visualization method that creates a clear overview of the microbiome composition in collected samples without losing any information due to classification or neglecting less abundant reads. Snowflake displays every observed OTU/ASV in the microbiome abundance table and provides a solution to include the data's hierarchical structure and additional information obtained from downstream analysis (e.g., alpha- and beta-diversity) and metadata. Based on the value-driven ICE-T evaluation methodology, Snowflake was positively received. Experts in microbiome research found the visualizations to be user-friendly and detailed and liked the possibility of including and relating additional information to the microbiome's composition. Exploring the topological structure of the microbiome abundance table allows them to quickly identify which taxa are unique to specific samples and which are shared among multiple samples (i.e., separating sample-specific taxa from the core microbiome), and see the compositional differences between samples. An R package for constructing and visualizing Snowflake microbiome composition graphs is available at https://gitlab.com/vda-lab/snowflake.}, } @article {pmid38375206, year = {2023}, author = {Sadeghi, M and Mestivier, D and Carbonnelle, E and Benamouzig, R and Khazaie, K and Sobhani, I}, title = {Loss of symbiotic and increase of virulent bacteria through microbial networks in Lynch syndrome colon carcinogenesis.}, journal = {Frontiers in oncology}, volume = {13}, number = {}, pages = {1313735}, pmid = {38375206}, issn = {2234-943X}, abstract = {PURPOSE: Through a pilot study, we performed whole gut metagenomic analysis in 17 Lynch syndrome (LS) families, including colorectal cancer (CRC) patients and their healthy first-degree relatives. In a second asymptomatic LS cohort (n=150) undergoing colonoscopy-screening program, individuals with early precancerous lesions were compared to those with a normal colonoscopy. Since bacteria are organized into different networks within the microbiota, we compared related network structures in patients and controls.

EXPERIMENTAL DESIGN: Fecal prokaryote DNA was extracted prior to colonoscopy for whole metagenome (n=34, pilot study) or 16s rRNA sequencing (validation study). We characterized bacteria taxonomy using Diamond/MEGAN6 and DADA2 pipelines and performed differential abundances using Shaman website. We constructed networks using SparCC inference tools and validated the construction's accuracy by performing qPCR on selected bacteria.

RESULTS: Significant differences in bacterial communities in LS-CRC patients were identified, with an enrichment of virulent bacteria and a depletion of symbionts compared to their first-degree relatives. Bacteria taxa in LS asymptomatic individuals with colonic precancerous lesions (n=79) were significantly different compared to healthy individuals (n=71). The main bacterial network structures, constructed based on bacteria-bacteria correlations in CRC (pilot study) and in asymptomatic precancerous patients (validation-study), showed a different pattern than in controls. It was characterized by virulent/symbiotic co-exclusion in both studies and illustrated (validation study) by a higher Escherichia/Bifidobacterium ratio, as assessed by qPCR.

CONCLUSION: Enhanced fecal virulent/symbiotic bacteria ratios influence bacterial network structures. As an early event in colon carcinogenesis, these ratios can be used to identify asymptomatic LS individual with a higher risk of CRC.}, } @article {pmid38375198, year = {2024}, author = {Liu, C and Xu, Q and Dong, S and Ding, H and Li, B and Zhang, D and Liang, Y and Li, L and Liu, Q and Cheng, Y and Wu, J and Zhu, J and Zhong, M and Cao, Y and Zhang, G}, title = {New mechanistic insights of anti-obesity by sleeve gastrectomy-altered gut microbiota and lipid metabolism.}, journal = {Frontiers in endocrinology}, volume = {15}, number = {}, pages = {1338147}, pmid = {38375198}, issn = {1664-2392}, abstract = {BACKGROUND: The obesity epidemic has been on the rise due to changes in living standards and lifestyles. To combat this issue, sleeve gastrectomy (SG) has emerged as a prominent bariatric surgery technique, offering substantial weight reduction. Nevertheless, the mechanisms that underlie SG-related bodyweight loss are not fully understood.

METHODS: In this study, we conducted a collection of preoperative and 3-month postoperative serum and fecal samples from patients who underwent laparoscopic SG at the First Affiliated Hospital of Shandong First Medical University (Jinan, China). Here, we took an unbiased approach of multi-omics to investigate the role of SG-altered gut microbiota in anti-obesity of these patients. Non-target metabolome sequencing was performed using the fecal and serum samples.

RESULTS: Our data show that SG markedly increased microbiota diversity and Rikenellaceae, Alistipes, Parabacteroides, Bactreoidales, and Enterobacteraies robustly increased. These compositional changes were positively correlated with lipid metabolites, including sphingolipids, glycerophospholipids, and unsaturated fatty acids. Increases of Rikenellaceae, Alistipes, and Parabacteroide were reversely correlated with body mass index (BMI).

CONCLUSION: In conclusion, our findings provide evidence that SG induces significant alterations in the abundances of Rikenellaceae, Alistipes, Parabacteroides, and Bacteroidales, as well as changes in lipid metabolism-related metabolites. Importantly, these changes were found to be closely linked to the alleviation of obesity. On the basis of these findings, we have identified a number of microbiotas that could be potential targets for treatment of obesity.}, } @article {pmid38375100, year = {2024}, author = {Shen, B and Tong, L and Qiu, J and Zhong, J and Tong, Z and Li, X}, title = {Suppurative Meningitis Complicated with Arthritis Caused by Streptococcus Suis Infection: A Case Report.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {561-569}, pmid = {38375100}, issn = {1178-6973}, abstract = {BACKGROUND: Streptococcus suis (S. suis) is a common gram-positive bacterium in pigs. Its natural infection sites are the upper respiratory tract (especially tonsils and nasal cavity), reproductive tract and digestive tract of pigs. It is a new emerging human and animal disease. A co-morbid pathogen that can cause serious infections in humans, including meningitis, sepsis, septic arthritis, and sometimes deafness. No cases have been reported in Huzhou City, Zhejiang Province, China.

CASE PRESENTATION: A 50-year-old male patient who had Worked as a butcher in a slaughterhouse for 20 years. Admitted to the hospital due to abdominal pain, joint pain, fever, and headache.His condition rapidly worsened causing altered consciousness, drowsiness and developed hearing loss. S. suis induced pyogenic meningitis complicated by arthritis was suspected based on the results of biochemical and culture analysis of the cerebrospinal fluid, and metagenomic next-generation sequencing, The patient's symptoms significantly improved after treatment with antibiotics such as ceftriaxone, meropenem, and linezolid, as well as supportive therapies including steroids and hyperbaric oxygen therapy, and his hearing improved significantly.After about 2 years of follow-up, the hearing was significantly better than before, but hearing impairment still remained.

CONCLUSION: Streptococcus suis is endemic in pork-consuming and pig-raising countries, but can occur throughout the world, especially among individuals with occupational exposure to pigs and/or pork, such as slaughterhouse workers, butchers, farmers, etc. Strengthen science education among key groups. This case was diagnosed as Streptococcus suis meningitis combined with arthritis. However, abdominal pain in the early stage of the disease is very rare and is easy to be misdiagnosed. It is necessary to identify whether it is complicated by peritonitis. For hearing loss caused by Streptococcus suis infection, the use of hyperbaric oxygen chamber treatment has obvious therapeutic effects.}, } @article {pmid38374958, year = {2024}, author = {Panyako, PM and Ommeh, SC and Kuria, SN and Lichoti, JK and Musina, J and Nair, V and Nene, V and Munir, M and Oyola, SO}, title = {Metagenomic Characterization of Poultry Cloacal and Oropharyngeal Swabs in Kenya Reveals Bacterial Pathogens and Their Antimicrobial Resistance Genes.}, journal = {International journal of microbiology}, volume = {2024}, number = {}, pages = {8054338}, pmid = {38374958}, issn = {1687-918X}, abstract = {Poultry enteric bacterial diseases are of significant economic importance because they are responsible for production losses due to weight loss, increased morbidity and mortality, and increased cost of production arising from poor feed conversion and treatment. This cross-sectional purposive study characterized enteric bacterial pathogens in poultry from selected agroclimatic regions in Kenya and investigated their antimicrobial resistance gene profiles. Cloacal (n = 563) and oropharyngeal (n = 394) swabs were collected and pooled into 16 and 14 samples, respectively, to characterize bacterial pathogens and their antimicrobial resistance gene profiles. We report that Proteobacteria, Chlamydiae, and Firmicutes are the most dominant phyla present in both cloacal and oropharyngeal swabs of the six poultry species studied, indicating the colonization of the poultry gut by many pathogenic bacteria. Using KEGG and COG databases, some pathways related to metabolism, genetic information, and cellular processing were detected. We also report the abundance of antimicrobial resistance genes that confer resistance to β-lactamases, aminoglycosides, and tetracycline in most of the poultry analyzed, raising concern about the dangers associated with continuous and inappropriate use of these antibiotics in poultry production. The antimicrobial resistance gene data generated in this study provides a valuable indicator of the use of antimicrobials in poultry in Kenya. The information generated is essential for managing bacterial diseases, especially in backyard poultry raised under scavenging conditions.}, } @article {pmid38374918, year = {2024}, author = {Zhang, L and Bai, J and Zhai, Y and Zhang, K and Wang, Y and Tang, R and Xiao, R and Jorquera, MA}, title = {Seasonal changes in N-cycling functional genes in sediments and their influencing factors in a typical eutrophic shallow lake, China.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1363775}, pmid = {38374918}, issn = {1664-302X}, abstract = {N-cycling processes mediated by microorganisms are directly linked to the eutrophication of lakes and ecosystem health. Exploring the variation and influencing factors of N-cycling-related genes is of great significance for controlling the eutrophication of lakes. However, seasonal dynamics of genomic information encoding nitrogen (N) cycling in sediments of eutrophic lakes have not yet been clearly addressed. We collected sediments in the Baiyangdian (BYD) Lake in four seasons to explore the dynamic variation of N-cycling functional genes based on a shotgun metagenome sequencing approach and to reveal their key influencing factors. Our results showed that dissimilatory nitrate reduction (DNRA), assimilatory nitrate reduction (ANRA), and denitrification were the dominant N-cycling processes, and the abundance of nirS and amoC were higher than other functional genes by at least one order of magnitude. Functional genes, such as nirS, nirK and amoC, generally showed a consistent decreasing trend from the warming season (i.e., spring, summer, fall) to the cold season (i.e., winter). Furthermore, a significantly higher abundance of nitrification functional genes (e.g., amoB, amoC and hao) in spring and denitrification functional genes (e.g., nirS, norC and nosZ) in fall were observed. N-cycling processes in four seasons were influenced by different dominant environmental factors. Generally, dissolved organic carbon (DOC) or sediment organic matter (SOM), water temperature (T) and antibiotics (e.g., Norfloxacin and ofloxacin) were significantly correlated with N-cycling processes. The findings imply that sediment organic carbon and antibiotics may be potentially key factors influencing N-cycling processes in lake ecosystems, which will provide a reference for nitrogen management in eutrophic lakes.}, } @article {pmid38374327, year = {2024}, author = {Verma, LM and Kumar, A and Kumar, A and Singh, G and Singh, U and Chaudhary, S and Kumar, S and Sanwaria, AR and Ingole, PP and Sharma, S}, title = {Green chemistry routed sugar press mud for (2D) ZnO nanostructure fabrication, mineral fortification, and climate-resilient wheat crop productivity.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4074}, pmid = {38374327}, issn = {2045-2322}, abstract = {Nanotechnology appears to be a promising tool to redefine crop nutrition in the coming decades. However, the crucial interactions of nanomaterials with abiotic components of the environment like soil organic matter (SOM) and carbon‒sequestration may hold the key to sustainable crop nutrition, fortification, and climate change. Here, we investigated the use of sugar press mud (PM) mediated ZnO nanosynthesis for soil amendment and nutrient mobilisation under moderately alkaline conditions. The positively charged (+ 7.61 mv) ZnO sheet-like nanoparticles (~ 17 nm) from zinc sulphate at the optimum dose of (75 mg/kg blended with PM (1.4% w/w) were used in reinforcing the soil matrix for wheat growth. The results demonstrated improved agronomic parameters with (~ 24%) and (~ 19%) relative increases in yield and plant Zn content. Also, the soil solution phase interactions of the ZnO nanoparticles with the PM-induced soil colloidal carbon (- 27.9 mv and diameter 0.4864 μm) along with its other components have influenced the soil nutrient dynamics and mineral ecology at large. Interestingly, one such interaction seems to have reversed the known Zn-P interaction from negative to positive. Thus, the study offers a fresh insight into the possible correlations between nutrient interactions and soil carbon sequestration for climate-resilient crop productivity.}, } @article {pmid38374282, year = {2024}, author = {Spohr, P and Scharf, S and Rommerskirchen, A and Henrich, B and Jäger, P and Klau, GW and Haas, R and Dilthey, A and Pfeffer, K}, title = {Insights into gut microbiomes in stem cell transplantation by comprehensive shotgun long-read sequencing.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4068}, pmid = {38374282}, issn = {2045-2322}, abstract = {The gut microbiome is a diverse ecosystem, dominated by bacteria; however, fungi, phages/viruses, archaea, and protozoa are also important members of the gut microbiota. Exploration of taxonomic compositions beyond bacteria as well as an understanding of the interaction between the bacteriome with the other members is limited using 16S rDNA sequencing. Here, we developed a pipeline enabling the simultaneous interrogation of the gut microbiome (bacteriome, mycobiome, archaeome, eukaryome, DNA virome) and of antibiotic resistance genes based on optimized long-read shotgun metagenomics protocols and custom bioinformatics. Using our pipeline we investigated the longitudinal composition of the gut microbiome in an exploratory clinical study in patients undergoing allogeneic hematopoietic stem cell transplantation (alloHSCT; n = 31). Pre-transplantation microbiomes exhibited a 3-cluster structure, characterized by Bacteroides spp. /Phocaeicola spp., mixed composition and Enterococcus abundances. We revealed substantial inter-individual and temporal variabilities of microbial domain compositions, human DNA, and antibiotic resistance genes during the course of alloHSCT. Interestingly, viruses and fungi accounted for substantial proportions of microbiome content in individual samples. In the course of HSCT, bacterial strains were stable or newly acquired. Our results demonstrate the disruptive potential of alloHSCTon the gut microbiome and pave the way for future comprehensive microbiome studies based on long-read metagenomics.}, } @article {pmid38374154, year = {2024}, author = {Wang, FQ and Bartosik, D and Sidhu, C and Siebers, R and Lu, DC and Trautwein-Schult, A and Becher, D and Huettel, B and Rick, J and Kirstein, IV and Wiltshire, KH and Schweder, T and Fuchs, BM and Bengtsson, MM and Teeling, H and Amann, RI}, title = {Particle-attached bacteria act as gatekeepers in the decomposition of complex phytoplankton polysaccharides.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {32}, pmid = {38374154}, issn = {2049-2618}, support = {AM 73/9-3//Deutsche Forschungsgemeinschaft,Germany/ ; SCHW 595/10-3//Deutsche Forschungsgemeinschaft,Germany/ ; TE 813/2-3//Deutsche Forschungsgemeinschaft,Germany/ ; RI 969/9-2//Deutsche Forschungsgemeinschaft,Germany/ ; BE 3869/4-3//Deutsche Forschungsgemeinschaft,Germany/ ; SCHW 595/11-3//Deutsche Forschungsgemeinschaft,Germany/ ; FU 627/2-3//Deutsche Forschungsgemeinschaft,Germany/ ; RI 969/9-2//Deutsche Forschungsgemeinschaft,Germany/ ; TE 813/2-3//Deutsche Forschungsgemeinschaft,Germany/ ; AM 73/9-3//Deutsche Forschungsgemeinschaft,Germany/ ; AWI_BAH_o 1//Biological Station Helgoland, Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research/ ; AWI_BAH_o 1//Biological Station Helgoland, Alfred Wegener Institute, Helmholtz Center for Polar and Marine Research/ ; }, abstract = {BACKGROUND: Marine microalgae (phytoplankton) mediate almost half of the worldwide photosynthetic carbon dioxide fixation and therefore play a pivotal role in global carbon cycling, most prominently during massive phytoplankton blooms. Phytoplankton biomass consists of considerable proportions of polysaccharides, substantial parts of which are rapidly remineralized by heterotrophic bacteria. We analyzed the diversity, activity, and functional potential of such polysaccharide-degrading bacteria in different size fractions during a diverse spring phytoplankton bloom at Helgoland Roads (southern North Sea) at high temporal resolution using microscopic, physicochemical, biodiversity, metagenome, and metaproteome analyses.

RESULTS: Prominent active 0.2-3 µm free-living clades comprised Aurantivirga, "Formosa", Cd. Prosiliicoccus, NS4, NS5, Amylibacter, Planktomarina, SAR11 Ia, SAR92, and SAR86, whereas BD1-7, Stappiaceae, Nitrincolaceae, Methylophagaceae, Sulfitobacter, NS9, Polaribacter, Lentimonas, CL500-3, Algibacter, and Glaciecola dominated 3-10 µm and > 10 µm particles. Particle-attached bacteria were more diverse and exhibited more dynamic adaptive shifts over time in terms of taxonomic composition and repertoires of encoded polysaccharide-targeting enzymes. In total, 305 species-level metagenome-assembled genomes were obtained, including 152 particle-attached bacteria, 100 of which were novel for the sampling site with 76 representing new species. Compared to free-living bacteria, they featured on average larger metagenome-assembled genomes with higher proportions of polysaccharide utilization loci. The latter were predicted to target a broader spectrum of polysaccharide substrates, ranging from readily soluble, simple structured storage polysaccharides (e.g., laminarin, α-glucans) to less soluble, complex structural, or secreted polysaccharides (e.g., xylans, cellulose, pectins). In particular, the potential to target poorly soluble or complex polysaccharides was more widespread among abundant and active particle-attached bacteria.

CONCLUSIONS: Particle-attached bacteria represented only 1% of all bloom-associated bacteria, yet our data suggest that many abundant active clades played a pivotal gatekeeping role in the solubilization and subsequent degradation of numerous important classes of algal glycans. The high diversity of polysaccharide niches among the most active particle-attached clades therefore is a determining factor for the proportion of algal polysaccharides that can be rapidly remineralized during generally short-lived phytoplankton bloom events. Video Abstract.}, } @article {pmid38374121, year = {2024}, author = {Sun, J and Xie, F and Wang, J and Luo, J and Chen, T and Jiang, Q and Xi, Q and Liu, GE and Zhang, Y}, title = {Integrated meta-omics reveals the regulatory landscape involved in lipid metabolism between pig breeds.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {33}, pmid = {38374121}, issn = {2049-2618}, support = {2023ZD04044//the Sci-Tech Innovation 2030 Agenda/ ; 32072714, 31802032//Natural Science Foundation of China Program/ ; 2023GZ20//the Opening Foundation of State Key Laboratory of Swine and Poultry Breeding Industry/ ; 2020A1515010062//the Natural Science Foundation of Guangdong Province/ ; 202002030037//the Science and Technology Project of Guangzhou/ ; }, abstract = {BACKGROUND: Domesticated pigs serve as an ideal animal model for biomedical research and also provide the majority of meat for human consumption in China. Porcine intramuscular fat content associates with human health and diseases and is essential in pork quality. The molecular mechanisms controlling lipid metabolism and intramuscular fat accretion across tissues in pigs, and how these changes in response to pig breeds, remain largely unknown.

RESULTS: We surveyed the tissue-resident cell types of the porcine jejunum, colon, liver, and longissimus dorsi muscle between Lantang and Landrace breeds by single-cell RNA sequencing. Combining lipidomics and metagenomics approaches, we also characterized gene signatures and determined key discriminating markers of lipid digestibility, absorption, conversion, and deposition across tissues in two pig breeds. In Landrace, lean-meat swine mainly exhibited breed-specific advantages in lipid absorption and oxidation for energy supply in small and large intestinal epitheliums, nascent high-density lipoprotein synthesis for reverse cholesterol transport in enterocytes and hepatocytes, bile acid formation, and secretion for fat emulsification in hepatocytes, as well as intestinal-microbiota gene expression involved in lipid accumulation product. In Lantang, obese-meat swine showed a higher synthesis capacity of chylomicrons responsible for high serum triacylglycerol levels in small intestinal epitheliums, the predominant characteristics of lipid absorption in muscle tissue, and greater intramuscular adipcytogenesis potentials from muscular fibro-adipogenic progenitor subpopulation.

CONCLUSIONS: The findings enhanced our understanding of the cellular biology of lipid metabolism and opened new avenues to improve animal production and human diseases. Video Abstract.}, } @article {pmid38374114, year = {2024}, author = {Bazzani, D and Heidrich, V and Manghi, P and Blanco-Miguez, A and Asnicar, F and Armanini, F and Cavaliere, S and Bertelle, A and Dell'Acqua, F and Dellasega, E and Waldner, R and Vicentini, D and Bolzan, M and Tomasi, C and Segata, N and Pasolli, E and Ghensi, P}, title = {Favorable subgingival plaque microbiome shifts are associated with clinical treatment for peri-implant diseases.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {12}, pmid = {38374114}, issn = {2055-5008}, abstract = {We performed a longitudinal shotgun metagenomic investigation of the plaque microbiome associated with peri-implant diseases in a cohort of 91 subjects with 320 quality-controlled metagenomes. Through recently improved taxonomic profiling methods, we identified the most discriminative species between healthy and diseased subjects at baseline, evaluated their change over time, and provided evidence that clinical treatment had a positive effect on plaque microbiome composition in patients affected by mucositis and peri-implantitis.}, } @article {pmid38373501, year = {2024}, author = {Chen, X and Gong, Y and Li, Z and Guo, Y and Zhang, H and Hu, B and Yang, W and Cao, Y and Mu, R}, title = {Key function of Kouleothrix in stable formation of filamentous aerobic granular sludge at low superficial gas velocity with polymeric substrates.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {130466}, doi = {10.1016/j.biortech.2024.130466}, pmid = {38373501}, issn = {1873-2976}, abstract = {Forming and maintaining stable aerobic granular sludge (AGS) at a low superficial gas velocity (SGV) is challenging, particularly with polymeric substrates. This study cultivated filamentous aerobic granular sludge (FAGS) with filamentous Kouleothrix (Type 1851) at low SGV (0.15 cm/s) utilizing mixed acetate-soluble starch. Within approximately 260 days, notable increases in the relative abundance of Kouleothrix (from 4 % to 10 %) and Ca. Competibacter (from 1 % to 26 %) were observed through 16S rRNA gene analysis. Metagenomic analysis revealed increased expression of functional genes involved in volatile fatty acid (VFA) production (e.g., ackA and pta) and polyhydroxyalkanoate synthesis (e.g., phbB and phbC). Kouleothrix acted as a skeleton for bacterial attachment and was the key fermenting bacteria promoting granulation and maintaining granule stability. This study provides insight into the formation of FAGS with low-energy and non-VFA substrates.}, } @article {pmid38373261, year = {2024}, author = {Dumonteil, E and Tu, W and Jiménez, FA and Herrera, C}, title = {Ecological interactions of Triatoma sanguisuga (Hemiptera: Reduviidae) and risk for human infection with Trypanosoma cruzi (Kinetoplastida: Trypanosomatidae) in Illinois and Louisiana.}, journal = {Journal of medical entomology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jme/tjae017}, pmid = {38373261}, issn = {1938-2928}, abstract = {Triatoma sanguisuga (Leconte) is one of the most widely distributed kissing bugs in the United States, associated with an extensive zoonotic circulation of Trypanosoma cruzi, the agent of Chagas disease, in a large part of the country. However, the actual risk for human infection in the United States is poorly understood. Here, we further assessed the ecology of T. sanguisuga bugs collected in residents' houses in Illinois and Louisiana, using a metagenomic approach to identify their blood-feeding sources, T. cruzi parasites and gut microbiota. Blood meal analysis revealed feeding on domestic animals (dogs, cats, pigs, goats, and turkeys), synanthropic species (raccoons, opossums, and squirrels), as well as the more sylvatic white-tail deer. Human blood was identified in 11/14 (78%) of bugs, highlighting a frequent vector-human contact. The infection rate with T. cruzi was 53% (8/15), and most infected bugs (6/8) had fed on humans. A total of 41 bacterial families were identified, with significant differences in microbiota alpha and beta diversity between bugs from Louisiana and Illinois. However, predicted metabolic functions remained highly conserved, suggesting important constraints to fulfill their role in bug biology. These results confirmed a significant risk for vector-borne transmission of T. cruzi to humans in Louisiana and Illinois, which warrants more active screening for human infections. Also, while there is broad plasticity in the bacterial composition of T. sanguisuga microbiota, there are strong constraints to preserve metabolic profile and function, making it a good target for novel vector control strategies.}, } @article {pmid38373115, year = {2024}, author = {Xie, N and Lin, Y and Li, P and Zhao, J and Li, J and Wang, K and Yang, L and Jia, L and Wang, Q and Li, P and Song, H}, title = {Simultaneous identification of DNA and RNA pathogens using metagenomic sequencing in cases of severe acute respiratory infection.}, journal = {Journal of medical virology}, volume = {96}, number = {2}, pages = {e29406}, doi = {10.1002/jmv.29406}, pmid = {38373115}, issn = {1096-9071}, support = {//2021YFC2301000,2017ZX10303405 and 2018ZX10201001/ ; 2021YFC2301000//National Key Research and Development Program of China/ ; 2017ZX10303405//National Science and Technology Major Project/ ; 2018ZX10201001//National Science and Technology Major Project/ ; }, abstract = {Metagenomic next-generation sequencing (mNGS) is a valuable technique for identifying pathogens. However, conventional mNGS requires the separate processing of DNA and RNA genomes, which can be resource- and time-intensive. To mitigate these impediments, we propose a novel method called DNA/RNA cosequencing that aims to enhance the efficiency of pathogen detection. DNA/RNA cosequencing uses reverse transcription of total nucleic acids extracted from samples by using random primers, without removing DNA, and then employs mNGS. We applied this method to 85 cases of severe acute respiratory infections (SARI). Influenza virus was identified in 13 cases (H1N1: seven cases, H3N2: three cases, unclassified influenza type: three cases) and was not detected in the remaining 72 samples. Bacteria were present in all samples. Pseudomonas aeruginosa, Klebsiella pneumoniae, and Acinetobacter baumannii were detected in four influenza-positive samples, suggesting coinfections. The sensitivity and specificity for detecting influenza A virus were 73.33% and 95.92%, respectively. A κ value of 0.726 indicated a high level of concordance between the results of DNA/RNA cosequencing and SARI influenza virus monitoring. DNA/RNA cosequencing enhanced the efficiency of pathogen detection, providing a novel capability to strengthen surveillance and thereby prevent and control infectious disease outbreaks.}, } @article {pmid38372665, year = {2024}, author = {Gu, X and Fu, L and Wang, Z and Cao, Z and Zhao, L and Seswita-Zilda, D and Zhang, A and Zhang, Q and Li, J}, title = {A Novel Bifunctional Alginate Lyase and Antioxidant Activity of the Enzymatic Hydrolysates.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.3c08638}, pmid = {38372665}, issn = {1520-5118}, abstract = {Alginate lyase Aly448, a potential new member of the polysaccharide lyase (PL) 7 family, which was cloned and identified from the macroalgae-associated bacterial metagenomic library, showed bifunctionality. The molecular docking results revealed that Aly448 has two completely different binding sites for alginate (polyMG), poly-α-l-guluronic acid (polyG), and poly-β-d-mannuronic acid (polyM) substrates, respectively, which might be the molecular basis for the enzyme's bifunctionality. Truncational results confirmed that predicted key residues affected the bifunctionality of Aly448, but did not wholly explain. Besides, Aly448 presented excellent biochemical characteristics, such as higher thermal stability and pH tolerance. Degradation of polyMG, polyM, and polyG substrates by Aly448 produced tetrasaccharide (DP4), disaccharide (DP2), and galactose (DP1), which exhibited excellent antioxidant activity. These findings provide novel insights into the substrate recognition mechanism of bifunctional alginate lyases and pave a new path for the exploitation of natural antioxidant agents.}, } @article {pmid38372512, year = {2024}, author = {Williams, TJ and Allen, MA and Ray, AE and Benaud, N and Chelliah, DS and Albanese, D and Donati, C and Selbmann, L and Coleine, C and Ferrari, BC}, title = {Novel endolithic bacteria of phylum Chloroflexota reveal a myriad of potential survival strategies in the Antarctic desert.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0226423}, doi = {10.1128/aem.02264-23}, pmid = {38372512}, issn = {1098-5336}, abstract = {The ice-free McMurdo Dry Valleys of Antarctica are dominated by nutrient-poor mineral soil and rocky outcrops. The principal habitat for microorganisms is within rocks (endolithic). In this environment, microorganisms are provided with protection against sub-zero temperatures, rapid thermal fluctuations, extreme dryness, and ultraviolet and solar radiation. Endolithic communities include lichen, algae, fungi, and a diverse array of bacteria. Chloroflexota is among the most abundant bacterial phyla present in these communities. Among the Chloroflexota are four novel classes of bacteria, here named Candidatus Spiritibacteria class. nov. (=UBA5177), Candidatus Martimicrobia class. nov. (=UBA4733), Candidatus Tarhunnaeia class. nov. (=UBA6077), and Candidatus Uliximicrobia class. nov. (=UBA2235). We retrieved 17 high-quality metagenome-assembled genomes (MAGs) that represent these four classes. Based on genome predictions, all these bacteria are inferred to be aerobic heterotrophs that encode enzymes for the catabolism of diverse sugars. These and other organic substrates are likely derived from lichen, algae, and fungi, as metabolites (including photosynthate), cell wall components, and extracellular matrix components. The majority of MAGs encode the capacity for trace gas oxidation using high-affinity uptake hydrogenases, which could provide energy and metabolic water required for survival and persistence. Furthermore, some MAGs encode the capacity to couple the energy generated from H2 and CO oxidation to support carbon fixation (atmospheric chemosynthesis). All encode mechanisms for the detoxification and efflux of heavy metals. Certain MAGs encode features that indicate possible interactions with other organisms, such as Tc-type toxin complexes, hemolysins, and macroglobulins.IMPORTANCEThe ice-free McMurdo Dry Valleys of Antarctica are the coldest and most hyperarid desert on Earth. It is, therefore, the closest analog to the surface of the planet Mars. Bacteria and other microorganisms survive by inhabiting airspaces within rocks (endolithic). We identify four novel classes of phylum Chloroflexota, and, based on interrogation of 17 metagenome-assembled genomes, we predict specific metabolic and physiological adaptations that facilitate the survival of these bacteria in this harsh environment-including oxidation of trace gases and the utilization of nutrients (including sugars) derived from lichen, algae, and fungi. We propose that such adaptations allow these endolithic bacteria to eke out an existence in this cold and extremely dry habitat.}, } @article {pmid38371940, year = {2024}, author = {Nguyen, VG and Kim, HK and Na, W}, title = {Editorial: Advanced bioinformatic approaches in veterinary virology.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1354424}, doi = {10.3389/fmicb.2024.1354424}, pmid = {38371940}, issn = {1664-302X}, } @article {pmid38371920, year = {2024}, author = {Verma, B and Parkinson, J}, title = {HiTaxon: a hierarchical ensemble framework for taxonomic classification of short reads.}, journal = {Bioinformatics advances}, volume = {4}, number = {1}, pages = {vbae016}, pmid = {38371920}, issn = {2635-0041}, abstract = {MOTIVATION: Whole microbiome DNA and RNA sequencing (metagenomics and metatranscriptomics) are pivotal to determining the functional roles of microbial communities. A key challenge in analyzing these complex datasets, typically composed of tens of millions of short reads, is accurately classifying reads to their taxa of origin. While still performing worse relative to reference-based short-read tools in species classification, ML algorithms have shown promising results in taxonomic classification at higher ranks. A recent approach exploited to enhance the performance of ML tools, which can be translated to reference-dependent classifiers, has been to integrate the hierarchical structure of taxonomy within the tool's predictive algorithm.

RESULTS: Here, we introduce HiTaxon, an end-to-end hierarchical ensemble framework for taxonomic classification. HiTaxon facilitates data collection and processing, reference database construction and optional training of ML models to streamline ensemble creation. We show that databases created by HiTaxon improve the species-level performance of reference-dependent classifiers, while reducing their computational overhead. In addition, through exploring hierarchical methods for HiTaxon, we highlight that our custom approach to hierarchical ensembling improves species-level classification relative to traditional strategies. Finally, we demonstrate the improved performance of our hierarchical ensembles over current state-of-the-art classifiers in species classification using datasets comprised of either simulated or experimentally derived reads.

HiTaxon is available at: https://github.com/ParkinsonLab/HiTaxon.}, } @article {pmid38371901, year = {2024}, author = {Nandakumar, K and Anto, PV and Antony, I}, title = {Diversity of soil fungi from sacred groves of Kerala, India revealed by comparative metagenomics analysis using illumina sequencing.}, journal = {3 Biotech}, volume = {14}, number = {3}, pages = {79}, pmid = {38371901}, issn = {2190-572X}, abstract = {The diversity, composition, and abundance of soil fungi from three sacred groves in Kerala, namely Iringole kavu of Ernakulam District, Kollakal Thapovanam of Alappuzha District, and Poyilkavu of Kozhikode District were analysed using Metagenomics analysis and Illumina sequencing. A total of 30,584, 78,323, and 55,640 reads were obtained from these groves, respectively. Ascomycota constitutes over 96% of the total fungi, making it the most abundant phylum, followed by Mortierellomycota, Basidiomycota, Chytridiomycota, and Rozellomycota. These phyla were subdivided into 20 classes, 40 orders, 83 families, 119 genera, and 135 species, while 1269 OTUs remained unidentified at the species level. Eurotiomycetes predominates the class, while the genus Talaromyces from the family Trichomaceae dominates the genera. Neocarmospora falciformis, Trichoderma lixii, and Candida ethanolic are the most abundant fungal species. Diversity analysis shows that Kollakal Thapovanam is rich in fungal species, while Poyilkavu is rich in biodiversity, with a high degree of dominance. Several species were found only in a particular grove and were absent in others and vice-versa, indicating high fungal specificity. Therefore, fungi have to be preserved in their original habitat. The Principal Coordinate Analysis revealed that each grove is distinct highlighting the importance of preserving the unique diversity of each sacred grove. In conclusion, this research provides valuable information about the soil fungal genera in their natural habitat. It emphasizes the need for more systematic research to understand the actual diversity and ecological role of fungi in sacred groves. This study is the first of its kind to analyse and compare soil fungal diversity in sacred groves using the metagenomics approach.}, } @article {pmid38371896, year = {2023}, author = {Gregorczyk-Maga, I and Kania, M and Dąbrowska, M and Samborowska, E and Żeber-Lubecka, N and Kulecka, M and Klupa, T}, title = {The interplay between gingival crevicular fluid microbiome and metabolomic profile in intensively treated people with type 1 diabetes - a combined metagenomic/metabolomic approach cross-sectional study.}, journal = {Frontiers in endocrinology}, volume = {14}, number = {}, pages = {1332406}, pmid = {38371896}, issn = {1664-2392}, abstract = {AIMS: This study aimed to assess the gingival crevicular fluid (GCF) microbiome and metabolome of adults with type 1 diabetes (T1D) treated with continuous subcutaneous insulin infusion (CSII).

METHODS: In this cross-sectional study, the GCF of adults with T1D treated with CSII and non-diabetic controls were sampled, and metagenomic/metabolomic analyses were performed.

RESULTS: In total, 65 participants with T1D and 45 healthy controls with a mean age of 27.05 ± 5.95 years were investigated. There were 22 cases of mild gingivitis (G) in the T1D group. There were no differences considering the Shannon and Chao indices and β-diversity between people with T1D and G, with T1D without G, and healthy controls. Differential taxa were identified, which were mainly enriched in people with T1D and G. Acetic acid concentration was higher in people with T1D, regardless of the presence of G, than in healthy controls. Propionic acid was higher in people with T1D and G than in healthy controls. Isobutyric and isovaleric acid levels were higher in individuals with T1D and G than in the other two subgroups. The concentration of valeric acid was lower and that of caproic acid was higher in people with T1D (regardless of gingival status) than in healthy controls.

CONCLUSIONS: The identification of early changes in periodontal tissues by targeting the microbiome and metabolome could potentially enable effective prevention and initial treatment of periodontal disease in people with T1D.}, } @article {pmid38371477, year = {2024}, author = {Zhang, X and Xu, H and Gong, L and Wang, J and Fu, J and Lv, Z and Zhou, L and Li, X and Liu, Q and Xia, P and Guo, Y}, title = {Mannanase improves the growth performance of broilers by alleviating inflammation of the intestinal epithelium and improving intestinal microbiota.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {16}, number = {}, pages = {376-394}, pmid = {38371477}, issn = {2405-6383}, abstract = {This experiment aimed to discuss and reveal the effect and mechanism of mannanase on intestinal inflammation in broilers triggered by a soybean meal diet. In this experiment, 384 Arbor Acres broilers at 1 d old were randomly divided into 3 treatment groups. The broilers were fed a corn-soybean meal basal diet, a low-energy diet (metabolizable energy reduced by 50 kcal/kg), and a low-energy diet supplemented with 100 mg/kg mannanase for 42 d. The low-energy diet increased feed conversion ratio from 0 to 42 d, reduced ileal villus height and villus height-to-crypt depth ratio and upregulated the expression of nuclear factor kappa B (NF-κB) in the ileum (P < 0.05). It also reduced cecal short-chain fatty acids (SCFA), such as acetic acid (P < 0.05). Compared with low-energy diets, the addition of mannanase increased body weight at 42 d, promoted the digestibility of nutrients, and maintained the morphology and integrity of the intestinal epithelium of broilers (P < 0.05). In addition, mannanase upregulated the expression of claudin-1 (CLDN1) and zonula occludens-1 (ZO-1) in the jejunum at 21 d, downregulated the expression of ileal NF-κB, and increased the content of isobutyric acid in the cecum of broilers (P < 0.05). The results for the ileal microbiota showed that a low-energy diet led to a decrease in the relative abundance of Lactobacillus reuteri in the ileum of broilers. The addition of mannanase increased the relative abundance of Lactobacillus-KC45b and Lactobacillus johnsonii in broilers. Furthermore, a low-energy diet reduced the relative abundance of Butyricicoccus in the intestine of broilers and inhibited oxidative phosphorylation and phosphoinositol metabolism. Mannanase increased the relative abundance of Odoribacter, promoted energy metabolism and N-glycan biosynthesis, and increased the activities of GH3 and GH18. It is concluded that mannanase could improve the growth performance of broilers by reducing the expression of NF-κB in the ileum, increasing the production of SCFA in the cecum, suppressing intestinal inflammation, balancing the intestinal microbiota, reducing damage to the intestinal barrier, and improving the efficiency of nutrient utilization to alleviate the adverse effects caused by the decrease in dietary energy level.}, } @article {pmid38371394, year = {2024}, author = {Bodilis, J and Simenel, O and Michalet, S and Brothier, E and Meyer, T and Favre-Bonté, S and Nazaret, S}, title = {HME, NFE, and HAE-1 efflux pumps in Gram-negative bacteria: a comprehensive phylogenetic and ecological approach.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycad018}, pmid = {38371394}, issn = {2730-6151}, abstract = {The three primary resistance-nodulation-cell division (RND) efflux pump families (heavy metal efflux [HME], nodulation factor exporter [NFE], and hydrophobe/amphiphile efflux-1 [HAE-1]) are almost exclusively found in Gram-negative bacteria and play a major role in resistance against metals and bacterial biocides, including antibiotics. Despite their significant societal interest, their evolutionary history and environmental functions are poorly understood. Here, we conducted a comprehensive phylogenetic and ecological study of the RND permease, the subunit responsible for the substrate specificity of these efflux pumps. From 920 representative genomes of Gram-negative bacteria, we identified 6205 genes encoding RND permeases with an average of 6.7 genes per genome. The HME family, which is involved in metal resistance, corresponds to a single clade (21.8% of all RND pumps), but the HAE-1 and NFE families had overlapping distributions among clades. We propose to restrict the HAE-1 family to two phylogenetic sister clades, representing 41.8% of all RND pumps and grouping most of the RND pumps involved in multidrug resistance. Metadata associated with genomes, analyses of previously published metagenomes, and quantitative Polymerase Chain Reaction (qPCR) analyses confirmed a significant increase in genes encoding HME permeases in metal-contaminated environments. Interestingly, and possibly related to their role in root colonization, genes encoding HAE-1 permeases were particularly abundant in the rhizosphere. In addition, we found that the genes encoding these HAE-1 permeases are significantly less abundant in marine environments, whereas permeases of a new proposed HAE-4 family are predominant in the genomes of marine strains. These findings emphasize the critical role of the RND pumps in bacterial resistance and adaptation to diverse ecological niches.}, } @article {pmid38371300, year = {2024}, author = {Chen, Y and Wang, J and Gan, X and Li, M and Liao, Y and Zhou, Y and Niu, T}, title = {Application of plasma metagenomic next-generation sequencing improves prognosis in hematology patients with neutropenia or hematopoietic stem cell transplantation for infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1338307}, pmid = {38371300}, issn = {2235-2988}, abstract = {INTRODUCTION: Metagenomic next-generation sequencing (mNGS) is a novel technique for detecting pathogens. This retrospective study evaluated the diagnostic value of mNGS using plasma for infections in hematology patients and its impact on clinical treatment and prognosis in different subgroups of hematology patients.

METHODS: A total of 153 hematology patients with suspected infection who underwent mNGS using plasma were enrolled in the study. Their clinical histories, conventional microbiological test (CMT) results, mNGS results, treatment and prognosis were retrospectively analyzed.

RESULTS: In 153 plasma samples, mNGS yielded a higher positivity rate than CMT (total: 88.24% vs. 40.52%, P<0.001; bacteria: 35.95% vs. 21.57%, P < 0.01; virus: 69.93% vs. 21.57%, P<0.001; fungi: 20.26% vs. 7.84%, P<0.01). mNGS had a higher positivity rate for bacteria and fungi in the neutropenia group than in the non-neutropenia group (bacteria: 48.61% vs. 24.69%, P<0.01; fungi: 27.78% vs. 13.58%, P<0.05). mNGS demonstrated a greater advantage in the group of patients with hematopoietic stem cell transplantation (HSCT). Both the 3-day and 7-day efficacy rates in the HSCT group were higher than those in the non-HSCT group (3-day: 82.22% vs. 58.65%, P < 0.01; 7-day: 88.89% vs. 67.31%, P < 0.01), and the 28-day mortality rate was lower in the HSCT group than in the non-HSCT group (6.67% vs. 38.89%, P < 0.000). The neutropenia group achieved similar efficacy and mortality rates to the non-neutropenia group (7-day efficiency rate: 76.39% vs. 71.43%, P > 0.05; mortality rate: 29.17% vs. 29.63%, P > 0.05) with more aggressive antibiotic adjustments (45.83% vs. 22.22%, P < 0.01).

CONCLUSION: mNGS can detect more microorganisms with higher positive rates, especially in patients with neutropenia. mNGS had better clinical value in patients with hematopoietic stem cell transplantation (HSCT) or neutropenia, which had a positive effect on treatment and prognosis.}, } @article {pmid38370893, year = {2023}, author = {Marlida, Y and Susalam, MK and Harnentis, H and Jamsari, J and Huda, N and Noordin, WNM and Anggraini, L and Ardani, LR}, title = {Metagenomic analysis and biodiversity of bacteria in traditional fermented fish or Budu from West Sumatera, Indonesia.}, journal = {Journal of advanced veterinary and animal research}, volume = {10}, number = {4}, pages = {801-808}, pmid = {38370893}, issn = {2311-7710}, abstract = {OBJECTIVE: This research aims to investigate the microbial diversity of Budu prepared from fresh and frozen fish from the Pariaman and Pasaman districts in West Sumatra Province, Indonesia, as well as provide basic information about Budu quality.

MATERIALS AND METHODS: To obtain the bacterial microbial composition, deoxyribonucleic acid extraction was carried out using amplicon-sequencing of the 16S-rRNA gene in the V3-V4 region from two types of Budu and carried out in duplicate.

RESULTS: Budu prepared with fresh (Pariaman) or frozen (Pasaman) fish was dominated by Firmicutes (78.455%-92.37%) and Proteobacteria (6.477%-7.23%) phyla. The total microbial species in Budu from Pariaman were higher (227 species) than in Pasaman (153 species). The bacterial species found are Lentibacillus kimchi (1.878%-2.21%), Staphylococcus cohnii (0.597%-0.70%), Peptostreptococcus russeli (0.00%-0.002%), Clostridium disporicum (0.073%-0.09%), Clostridium novyi (0.00%-0.01%), Nioella sediminis (0.00%-0.001%), and Shewanella baltica (0.00%-0.003%). Lentibacillus kimchi, S. cohnii, and C. disporicum are found in both Budu. Nioella sediminis and S. baltica are found in Budu Pariaman. Peptostreptococcus russeli and C. novyi were found in Budu Pasaman.

CONCLUSION: Metagenomic analysis of Budu from different fish, Pariaman (fresh fish) and Pasaman (frozen fish) showed that the biodiversity of bacteria was barely different. Both Budu found lactic acid bacteria from the Enterococcaceae family, genus Vagococcus, and pathogenic bacteria, such as S. cohnii, P. russeli, C. disporicum, and S. baltica. The discovery of various species of pathogenic bacteria indicates that development is still needed in the Budu production process to improve Budu quality.}, } @article {pmid38370838, year = {2024}, author = {McMillan, AS and Zhang, G and Dougherty, MK and McGill, SK and Gulati, AS and Baker, ES and Theriot, CM}, title = {Metagenomic, metabolomic, and lipidomic shifts associated with fecal microbiota transplantation for recurrent Clostridioides difficile infection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.02.07.579219}, pmid = {38370838}, abstract = {Recurrent C. difficile infection (rCDI) is an urgent public health threat for which the last resort and lifesaving treatment is a fecal microbiota transplant (FMT). However, the exact mechanisms which mediate a successful FMT are not well understood. Here we use longitudinal stool samples collected from patients undergoing FMT to evaluate changes in the microbiome, metabolome, and lipidome after successful FMTs. We show changes in the abundance of many lipids, specifically acylcarnitines and bile acids, in response to FMT. These changes correlate with Enterobacteriaceae, which encode carnitine metabolism genes, and Lachnospiraceae, which encode bile salt hydrolases and baiA genes. LC-IMS-MS revealed a shift from microbial conjugation of primary bile acids pre-FMT to secondary bile acids post-FMT. Here we define the structural and functional changes in successful FMTs. This information will help guide targeted Live Biotherapeutic Product development for the treatment of rCDI and other intestinal diseases.}, } @article {pmid38370794, year = {2024}, author = {Rohwer, RR and Kirkpatrick, M and Garcia, SL and Kellom, M and McMahon, KD and Baker, BJ}, title = {Bacterial ecology and evolution converge on seasonal and decadal scales.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.02.06.579087}, pmid = {38370794}, abstract = {Ecology and evolution are distinct theories, but the short lifespans and large population sizes of microbes allow evolution to unfold along contemporary ecological time scales. To document this in a natural system, we collected a two-decade, 471-metagenome time series from a single site in a freshwater lake, which we refer to as the TYMEFLIES dataset. This massive sampling and sequencing effort resulted in the reconstruction of 30,389 metagenomic-assembled genomes (MAGs) over 50% complete, which dereplicated into 2,855 distinct genomes (>96% nucleotide sequence identity). We found both ecological and evolutionary processes occurred at seasonal time scales. There were recurring annual patterns at the species level in abundances, nucleotide diversities (π), and single nucleotide variant (SNV) profiles for the majority of all taxa. During annual blooms, we observed both higher and lower nucleotide diversity, indicating that both ecological differentiation and competition drove evolutionary dynamics. Overlayed upon seasonal patterns, we observed long-term change in 20% of the species' SNV profiles including gradual changes, step changes, and disturbances followed by resilience. Most abrupt changes occurred in a single species, suggesting evolutionary drivers are highly specific. Nevertheless, seven members of the abundant Nanopelagicaceae family experienced abrupt change in 2012, an unusually hot and dry year. This shift coincided with increased numbers of genes under selection involved in amino acid and nucleic acid metabolism, suggesting fundamental organic nitrogen compounds drive strain differentiation in the most globally abundant freshwater family. Overall, we observed seasonal and decadal trends in both interspecific ecological and intraspecific evolutionary processes. The convergence of microbial ecology and evolution on the same time scales demonstrates that understanding microbiomes requires a new unified approach that views ecology and evolution as a single continuum.}, } @article {pmid38370680, year = {2024}, author = {Elmassry, MM and Sugihara, K and Chankhamjon, P and Camacho, FR and Wang, S and Sugimoto, Y and Chatterjee, S and Chen, LA and Kamada, N and Donia, MS}, title = {A meta-analysis of the gut microbiome in inflammatory bowel disease patients identifies disease-associated small molecules.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.02.07.579278}, pmid = {38370680}, abstract = {Changes in the gut microbiome have been associated with several human diseases, but the molecular and functional details underlying these associations remain largely unknown. Here, we performed a multi-cohort analysis of small molecule biosynthetic gene clusters (BGCs) in 5,306 metagenomic samples of the gut microbiome from 2,033 Inflammatory Bowel Disease (IBD) patients and 833 matched healthy subjects and identified a group of Clostridia-derived BGCs that are significantly associated with IBD. Using synthetic biology, we discovered and solved the structures of six fatty acid amides as the products of the IBD-enriched BGCs. Using two mouse models of colitis, we show that the discovered small molecules disrupt gut permeability and exacerbate inflammation in chemically and genetically susceptible mice. These findings suggest that microbiome-derived small molecules may play a role in the etiology of IBD and represent a generalizable approach for discovering molecular mediators of microbiome-host interactions in the context of microbiome-associated diseases.}, } @article {pmid38370672, year = {2024}, author = {Diener, C and Gibbons, SM}, title = {Metagenomic estimation of dietary intake from human stool.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.02.02.578701}, pmid = {38370672}, abstract = {Dietary intake is tightly coupled to gut microbiota composition, human metabolism, and to the incidence of virtually all major chronic diseases. Dietary and nutrient intake are usually quantified using dietary questionnaires, which tend to focus on broad food categories, suffer from self-reporting biases, and require strong compliance from study participants. Here, we present MEDI (Metagenomic Estimation of Dietary Intake): a method for quantifying dietary intake using food-derived DNA in stool metagenomes. We show that food items can be accurately detected in metagenomic shotgun sequencing data, even when present at low abundances (>10 reads). Furthermore, we show how dietary intake, in terms of DNA abundance from specific organisms, can be converted into a detailed metabolic representation of nutrient intake. MEDI could identify the onset of solid food consumption in infants and it accurately predicted food questionnaire responses in an adult population. Additionally, we were able to identify specific dietary features associated with metabolic syndrome in a large clinical cohort, providing a proof-of-concept for detailed quantification of individual-specific dietary patterns without the need for questionnaires.}, } @article {pmid38370187, year = {2024}, author = {Hai, L and Li, P and Xiao, Z and Zhou, J and Xiao, B and Zhou, L}, title = {Rhizopus microsporus and Mucor racemosus coinfection following COVID-19 detected by metagenomics next-generation sequencing: A case of disseminated mucormycosis.}, journal = {Heliyon}, volume = {10}, number = {4}, pages = {e25840}, pmid = {38370187}, issn = {2405-8440}, abstract = {Mucormycosis is an invasive opportunistic fungal infection, which may be lethal and mostly affects patients with immunodeficiency or diabetes mellitus. Among Mucorales fungi, Rhizopus spp. is the most common cause of mucormycosis, followed by genera such as Mucor and Lichtheimia. Here we report a patient with severe COVID-19 infection who developed nasal pain, facial swelling, prominent black eschar on the nasal root. CT scan revealed pansinusitis along the maxillary, ethmoidal, and sphenoid sinuses. Mixed mold infection with Rhizopus microsporus and Mucor racemosus was detected by blood metagenomics next-generation sequencing (mNGS) and later nasal mucosa histological investigation confirmed mucormycosis. Severe COVID-19 infection led to the patient's thrombocytopenia and leukopenia. Later disseminated mucormycosis aggravated the infection and sepsis eventually resulted in death. It is the first case report of mucormycosis in which R. microsporus and M. racemosus as the etiologic agents were found simultaneously in one patient. COVID-19 infection combined with disseminated mucormycosisis can be fatal and mNGS is a fast, sensitive and accurate diagnostic method for fungi detection.}, } @article {pmid38369656, year = {2024}, author = {Chang, X and Zhang, Y and Chen, X and Li, S and Mei, H and Xiao, H and Ma, X and Liu, Z and Li, R}, title = {Gut microbiome and serum amino acid metabolome alterations in autism spectrum disorder.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {4037}, pmid = {38369656}, issn = {2045-2322}, support = {the Knowledge Innovation Program of Wuhan-Shugung Project//the Knowledge Innovation Program of Wuhan-Shugung Project/ ; 2022DCC020//the Hubei Provincial Science and Technology Plan Project for Clinical Research Center of Neurodevelopmental Disorders in Children/ ; 2019ZYYD051//the Special Projects for the Central Government to Guide the Development of Local Science and Technology/ ; }, abstract = {Gut microbiota and their metabolic products might play important roles in regulating the pathogenesis of autism spectrum disorder (ASD). The purpose of this study was to characterize gut microbiota and serum amino acid metabolome profiles in children with ASD. A non-randomized controlled study was carried out to analyze the alterations in the intestinal microbiota and their metabolites in patients with ASD (n = 30) compared with neurotypical controls (NC) (n = 30) by metagenomic sequencing to define the gut microbiota community and liquid chromatography/mass spectrometry (LC/MS) analysis to characterize the metabolite profiles. Compared with children in the NC group, those in the ASD group showed lower richness, higher evenness, and an altered microbial community structure. At the class level, Deinococci and Holophagae were significantly lower in children with ASD compared with TD. At the phylum level, Deinococcus-Thermus was significantly lower in children with ASD compared with TD. In addition, the functional properties (such as galactose metabolism) displayed significant differences between the ASD and NC groups. Five dominant altered species were identified and analyzed (LDA score > 2.0, P < 0.05), including Subdoligranulum, Faecalibacterium_praushitzii, Faecalibacterium, Veillonellaceae, and Rumminococcaceae. The peptides/nickel transport system was the main metabolic pathway involved in the differential species in the ASD group. Decreased ornithine levels and elevated valine levels may increase the risk of ASD through a metabolic pathway known as the nickel transport system. The microbial metabolism in diverse environments was negatively correlated with phascolarctobacterium succinatutens. Our study provides novel insights into compositional and functional alterations in the gut microbiome and metabolite profiles in ASD and the underlying mechanisms between metabolite and ASD.}, } @article {pmid38369542, year = {2024}, author = {Zou, S and Yang, C and Zhang, J and Zhong, D and Meng, M and Zhang, L and Chen, H and Fang, L}, title = {Multi-omic profiling reveals associations between the gut microbiome, host genome and transcriptome in patients with colorectal cancer.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {175}, pmid = {38369542}, issn = {1479-5876}, support = {82373512//National Natural Science Foundation of China/ ; 82222056//National Natural Science Foundation of China/ ; 82302910//National Natural Science Foundation of China/ ; 2022A1515012316//Natural Science Foundation of Guangdong Province/ ; 2021B1212010004//Natural Science Foundation of Guangdong Province/ ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is the leading cancer worldwide. Microbial agents have been considered to contribute to the pathogenesis of different disease. But the underlying relevance between CRC and microbiota remain unclear.

METHODS: We dissected the fecal microbiome structure and genomic and transcriptomic profiles of matched tumor and normal mucosa tissues from 41 CRC patients. Of which, the relationship between CRC-associated bacterial taxa and their significantly correlated somatic mutated gene was investigated by exome sequencing technology. Differentially expressed functional genes in CRC were clustered according to their correlation with differentially abundant species, following by annotation with DAVID. The composition of immune and stromal cell types was identified by XCELL.

RESULTS: We identified a set of 22 microbial gut species associated with CRC and estimate the relative abundance of KEGG ontology categories. Next, the interactions between CRC-related gut microbes and clinical phenotypes were evaluated. 4 significantly mutated gene: TP53, APC, KRAS, SMAD4 were pointed out and the associations with cancer related microbes were identified. Among them, Fusobacterium nucleatum positively corelated with different host metabolic pathways. Finally, we revealed that Fusobacterium nucleatum modified the tumor immune environment by TNFSF9 gene expression.

CONCLUSION: Collectively, our multi-omics data could help identify novel biomarkers to inform clinical decision-making in the detection and diagnosis of CRC.}, } @article {pmid38369453, year = {2024}, author = {Voutsinos, MY and West-Roberts, JA and Sachdeva, R and Moreau, JW and Banfield, JF}, title = {Weathered granites and soils harbour microbes with lanthanide-dependent methylotrophic enzymes.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {41}, pmid = {38369453}, issn = {1741-7007}, abstract = {BACKGROUND: Prior to soil formation, phosphate liberated by rock weathering is often sequestered into highly insoluble lanthanide phosphate minerals. Dissolution of these minerals releases phosphate and lanthanides to the biosphere. Currently, the microorganisms involved in phosphate mineral dissolution and the role of lanthanides in microbial metabolism are poorly understood.

RESULTS: Although there have been many studies of soil microbiology, very little research has investigated microbiomes of weathered rock. Here, we sampled weathered granite and associated soil to identify the zones of lanthanide phosphate mineral solubilisation and genomically define the organisms implicated in lanthanide utilisation. We reconstructed 136 genomes from 11 bacterial phyla and found that gene clusters implicated in lanthanide-based metabolism of methanol (primarily xoxF3 and xoxF5) are surprisingly common in microbial communities in moderately weathered granite. Notably, xoxF3 systems were found in Verrucomicrobia for the first time, and in Acidobacteria, Gemmatimonadetes and Alphaproteobacteria. The xoxF-containing gene clusters are shared by diverse Acidobacteria and Gemmatimonadetes, and include conserved hypothetical proteins and transporters not associated with the few well studied xoxF systems. Given that siderophore-like molecules that strongly bind lanthanides may be required to solubilise lanthanide phosphates, it is notable that candidate metallophore biosynthesis systems were most prevalent in bacteria in moderately weathered rock, especially in Acidobacteria with lanthanide-based systems.

CONCLUSIONS: Phosphate mineral dissolution, putative metallophore production and lanthanide utilisation by enzymes involved in methanol oxidation linked to carbonic acid production co-occur in the zone of moderate granite weathering. In combination, these microbial processes likely accelerate the conversion of granitic rock to soil.}, } @article {pmid38365587, year = {2024}, author = {Kvapilova, K and Misenko, P and Radvanszky, J and Brzon, O and Budis, J and Gazdarica, J and Pos, O and Korabecna, M and Kasny, M and Szemes, T and Kvapil, P and Paces, J and Kozmik, Z}, title = {Validated WGS and WES protocols proved saliva-derived gDNA as an equivalent to blood-derived gDNA for clinical and population genomic analyses.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {187}, pmid = {38365587}, issn = {1471-2164}, mesh = {Humans ; Exome Sequencing ; *Saliva ; *Metagenomics ; Exome ; Genome, Human ; Whole Genome Sequencing ; Genomics ; DNA/genetics ; }, abstract = {BACKGROUND: Whole exome sequencing (WES) and whole genome sequencing (WGS) have become standard methods in human clinical diagnostics as well as in population genomics (POPGEN). Blood-derived genomic DNA (gDNA) is routinely used in the clinical environment. Conversely, many POPGEN studies and commercial tests benefit from easy saliva sampling. Here, we evaluated the quality of variant call sets and the level of genotype concordance of single nucleotide variants (SNVs) and small insertions and deletions (indels) for WES and WGS using paired blood- and saliva-derived gDNA isolates employing genomic reference-based validated protocols.

METHODS: The genomic reference standard Coriell NA12878 was repeatedly analyzed using optimized WES and WGS protocols, and data calls were compared with the truth dataset published by the Genome in a Bottle Consortium. gDNA was extracted from the paired blood and saliva samples of 10 participants and processed using the same protocols. A comparison of paired blood-saliva call sets was performed in the context of WGS and WES genomic reference-based technical validation results.

RESULTS: The quality pattern of called variants obtained from genomic-reference-based technical replicates correlates with data calls of paired blood-saliva-derived samples in all levels of tested examinations despite a higher rate of non-human contamination found in the saliva samples. The F1 score of 10 blood-to-saliva-derived comparisons ranged between 0.8030-0.9998 for SNVs and between 0.8883-0.9991 for small-indels in the case of the WGS protocol, and between 0.8643-0.999 for SNVs and between 0.7781-1.000 for small-indels in the case of the WES protocol.

CONCLUSION: Saliva may be considered an equivalent material to blood for genetic analysis for both WGS and WES under strict protocol conditions. The accuracy of sequencing metrics and variant-detection accuracy is not affected by choosing saliva as the gDNA source instead of blood but much more significantly by the genomic context, variant types, and the sequencing technology used.}, } @article {pmid37432099, year = {2024}, author = {Subedi, A and Barrera, LBT and Ivey, ML and Egel, DS and Kebede, M and Kara, S and Aysan, Y and Minsavage, GV and Roberts, PD and Jones, JB and Goss, EM}, title = {Population Genomics Reveals an Emerging Lineage of Xanthomonas perforans on Pepper.}, journal = {Phytopathology}, volume = {114}, number = {1}, pages = {241-250}, doi = {10.1094/PHYTO-04-23-0128-R}, pmid = {37432099}, issn = {0031-949X}, mesh = {*Metagenomics ; Phylogeny ; Plant Diseases/microbiology ; Genomics ; *Xanthomonas/genetics ; }, abstract = {Xanthomonas perforans-the dominant causal agent of bacterial leaf spot of tomato-is an emerging pathogen of pepper, indicative of a potential host expansion across the southeastern United States. However, studies of the genetic diversity and evolution of X. perforans from pepper remain limited. In this study, the whole-genome sequences of 35 X. perforans strains isolated from pepper from four fields and two transplant facilities across southwest Florida between 2019 and 2021 were used to compare genomic divergence, evolution, and variation in type III secreted effectors. Phylogenetic analysis based on core genes revealed that all 35 X. perforans strains formed one genetic cluster with pepper and tomato strains from Alabama and Turkey and were closely related to strains isolated from tomato in Indiana, Mexico, and Louisiana. The in planta population growth of tomato strains isolated from Indiana, Mexico, Louisiana, and Turkey in pepper leaf mesophyll was on par with pepper X. perforans and X. euvesicatoria strains. Molecular clock analysis of the 35 Florida strains dated their emergence to approximately 2017. While strains varied in copper tolerance, all sequenced strains harbored the avrHah1 transcription activation-like effector located on a conjugative plasmid, not previously reported in Florida. Our findings suggest that there is a geographically distributed lineage of X. perforans strains on tomato that has the genetic background to cause disease on pepper. Moreover, this study clarifies potential adaptive variants of X. perforans on pepper that could help forecast the emergence of such strains and enable immediate or preemptive intervention.}, } @article {pmid38369215, year = {2024}, author = {Lin, K and Zheng, W and Guo, M and Zhou, R and Zhang, M and Liu, T}, title = {The intestinal microbial metabolite acetyl l-carnitine improves gut inflammation and immune homeostasis via CADM2.}, journal = {Biochimica et biophysica acta. Molecular basis of disease}, volume = {}, number = {}, pages = {167089}, doi = {10.1016/j.bbadis.2024.167089}, pmid = {38369215}, issn = {1879-260X}, abstract = {Intestinal symbiotic bacteria play a key role in the regulation of immune tolerance in inflammatory bowel disease (IBD) hosts. However, the bacterial strains directly involved in this regulation and their related metabolites are largely unknown. We sought to investigate the effects of intestinal microbial metabolites on intestinal epithelium and to elucidate their therapeutic potential in regulating intestinal mucosal inflammation and immune homeostasis. Here, we used metagenomic data from Crohn's disease (CD) patients to analyze the composition of intestinal flora and identify metabolite profiles associated with disease behavior, and used the mouse model of dextran sodium sulfate (DSS)-induced colitis to characterize the therapeutic effects of the flora metabolite acetyl l-carnitine (ALC) on DSS-induced colitis. We found that intraperitoneal injection of ALC treatment could significantly alleviate the symptoms of DSS-induced colitis in mice, including prevention of weight loss, reduction in disease activity index (DAI) scores, increasing of colonic length, reduction in histological scores, and improvement in intestinal barrier function. Further, transcriptome sequencing analysis and gene silencing experiments revealed that the absence of CADM2 abolished the inhibitory effect of ALC on the TLR-MyD88 pathway in colonic epithelial cells, thereby reducing the release of inflammatory factors in colon epithelial cells. And we confirmed a significant downregulation of CADM2 expression in intestinal tissues of CD patients compared to healthy people in a population cohort. In addition, we also found that ALC increased the ratio of Treg cells in colon, and decreased the ratio of Th17 cells and macrophages, thereby improving the immune tolerance of the organism. The proposed study could be a potential approach for the treatment of CD.}, } @article {pmid38369136, year = {2024}, author = {Singh, JP and Bottos, EM and Van Hamme, JD and Fraser, LH}, title = {Microbial composition and function in reclaimed mine sites along a reclamation chronosequence become increasingly similar to undisturbed reference sites.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170996}, doi = {10.1016/j.scitotenv.2024.170996}, pmid = {38369136}, issn = {1879-1026}, abstract = {Mine reclamation historically focuses on enhancing plant coverage to improve below and aboveground ecology. However, there is a great need to study the role of soil microorganisms in mine reclamation, particularly long-term studies that track the succession of microbial communities. Here, we investigate the trajectory of microbial communities of mining sites reclaimed between three and 26 years. We used high-throughput amplicon sequencing to characterize the bacterial and fungal communities. We quantified how similar the reclaimed sites were to unmined, undisturbed reference sites and explored the trajectory of microbial communities along the reclamation chronosequence. We also examined the ecological processes that shape the assembly of bacterial communities. Finally, we investigated the functional potential of the microbial communities through metagenomic sequencing. Our results reveal that the reclamation age significantly impacted the community compositions of bacterial and fungal communities. As the reclamation age increases, bacterial and fungal communities become similar to the unmined, undisturbed reference site, suggesting a favorable succession in microbial communities. The bacterial community assembly was also significantly impacted by reclamation age and was primarily driven by stochastic processes, indicating a lesser influence of environmental properties on the bacterial community. Furthermore, our read-based metagenomic analysis showed that the microbial communities' functional potential increasingly became similar to the reference sites. Additionally, we found that the plant richness increased with the reclamation age. Overall, our study shows that both above- and belowground ecological properties of reclaimed mine sites trend towards undisturbed sites with increasing reclamation age. Further, it demonstrates the importance of microbial genomics in tracking the trajectory of ecosystem reclamation.}, } @article {pmid38369119, year = {2024}, author = {McGovern, CJ and González-Orozco, BD and Jiménez-Flores, R}, title = {Evaluation of Kefir Grain Microbiota, Grain Viability, and Kefir Bioactivity from Fermenting Dairy Processing By-Products.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2023-24364}, pmid = {38369119}, issn = {1525-3198}, abstract = {Four dairy foods processing by-products (acid whey permeate (AWP), buttermilk (BM), sweet whey permeate (SWP), and sweet whey permeate with added milk fat globule ingredient (SWP+MFGM)) were fermented for 4 weeks and compared with traditional kefir milks for production of novel kefir-like dairy products. AU: Sweet whey permeates and SWP supplemented with 1.5% milk fat globule membrane (MFGM) showed to be the most viable by-products for kefir grain fermentation, exhibiting diverse abundance of traditional kefir microorganisms and positive indicators of bioactive properties. Grain viability was assessed with shotgun metagenomics, texture profile analysis, live cell counts, and scanning electron microscopy. Assessed bioactivities of the kefir-like products included antibacterial, antioxidant, potential anticancerogenic properties, and membrane barrier effect on human colorectal adenocarcinoma Caco-2 cells. All kefir grains were most abundant in Lactobacillus kefiranofaciens when analyzed with shotgun metagenomics. When analyzed with live cell counts on selective media, AWP kefir-like product had no countable Lactococcus spp. indicating suboptimal conditions for kefir grain microbiota survival and application for fermented dairy starter culture bacterium. Live cell counts were affirmed with kefir grain surface scanning electron microscopy images. SWP had the most adhesive kefir grain surface while SWP+MFGM had the largest exopolysaccharide (EPS) yield from grain extraction. All kefir and kefir-like products were able to achieve a 6-log reduction against Listeria innocua and Escherichia coli. Traditional milk kefirs had the highest antioxidant capacity for 2,2-diphenyl-1-picrylhydrazyl (DPPH) and the 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulfonic acid) (ABTS) assay. AWP had a significantly higher DPPH antioxidant activity and SWP had the lowest Trolox equivalence concentration in the ABTS assay. Sweet whey and supplemented milk fat sweet whey had upregulation of Cldn-1 and Ocln-1 gene expression, which correspond with a significant increase in transepithelial electrical resistance.}, } @article {pmid38368734, year = {2024}, author = {Deng, C and Chen, T and Qiu, Z and Zhou, H and Li, B and Zhang, Y and Xu, X and Lian, C and Qiao, X and Yu, K}, title = {A mixed blessing of influent leachate microbes in downstream biotreatment systems of a full-scale landfill leachate treatment plant.}, journal = {Water research}, volume = {253}, number = {}, pages = {121310}, doi = {10.1016/j.watres.2024.121310}, pmid = {38368734}, issn = {1879-2448}, abstract = {In landfill leachate treatment plants (LLTPs), the microbiome plays a pivotal role in the decomposition of organic compounds, reduction in nutrient levels, and elimination of toxins. However, the effects of microbes in landfill leachate influents on downstream treatment systems remain poorly understood. To address this knowledge gap, we collected 23 metagenomic and 12 metatranscriptomic samples from landfill leachate and activated sludge from various treatment units in a full-scale LLTP. We successfully recovered 1,152 non-redundant metagenome-assembled genomes (MAGs), encompassing a wide taxonomic range, including 48 phyla, 95 classes, 166 orders, 247 families, 238 genera, and 1,152 species. More diverse microbes were observed in the influent leachate than in the downstream biotreatment systems, among which, an unprecedented ∼30 % of microbes with transcriptional expression migrated from the influent to the biological treatment units. Network analysis revealed that 399 shared MAGs across the four units exhibited high node centrality and degree, thus supporting enhanced interactions and increased stability of microbial communities. Functional reconstruction and genome characterization of MAGs indicated that these shared MAGs possessed greater capabilities for carbon, nitrogen, sulfur, and arsenic metabolism compared to non-shared MAGs. We further identified a novel species of Zixibacteria in the leachate influent with discrete lineages from those in other environments that accounted for up to 17 % of the abundance of the shared microbial community and exhibited notable metabolic versatility. Meanwhile, we presented groundbreaking evidence of the involvement of Zixibacteria-encoded genes in the production of harmful gas emissions, such as N2O and H2S, at the transcriptional level, thus suggesting that influent microbes may pose safety risks to downstream treatment systems. In summary, this study revealed the complex impact of the influent microbiome on LLTP and emphasizes the need to consider these microbial characteristics when designing treatment technologies and strategies for landfill leachate management.}, } @article {pmid38368689, year = {2024}, author = {Shuai, X and Zhou, Z and Zhu, L and Achi, C and Lin, Z and Liu, Z and Yu, X and Zhou, J and Lin, Y and Chen, H}, title = {Ranking the risk of antibiotic resistance genes by metagenomic and multifactorial analysis in hospital wastewater systems.}, journal = {Journal of hazardous materials}, volume = {468}, number = {}, pages = {133790}, doi = {10.1016/j.jhazmat.2024.133790}, pmid = {38368689}, issn = {1873-3336}, abstract = {Antimicrobial resistance poses a serious threat to human health. Hospital wastewater system (HWS) is an important source of antibiotic resistance genes (ARGs). The risk of ARGs in HWS is still an under-researched area. In this study, we collected publicly metagenomic datasets of 71 hospital wastewater samples from 18 hospitals in 13 cities. A total of 9838 contigs were identified to carry 383 unique ARGs across all samples, of which 2946 contigs were plasmid-like sequences. Concurrently, the primary hosts of ARGs within HWS were found to be Escherichia coli and Klebsiella pneumoniae. To further evaluate the risk of each ARG subtype, we proposed a risk assessment framework based on the importance of corresponding antibiotics as defined by the WHO and three other indicators - ARG abundance (A), mobility (M), and host pathogenicity (P). Ninety ARGs were identified as R1 ARGs having high-risk scores, which meant having a high abundance, high mobility, and carried by pathogens in HWS. Furthermore, 25% to 49% of genomes from critically important pathogens accessed from NCBI carried R1 ARGs. A significantly higher number of R1 ARGs was carried by pathogens in the effluents of municipal wastewater treatment plants from NCBI, highlighting the role of R1 ARGS in accelerating health and environmental risks.}, } @article {pmid38368638, year = {2024}, author = {Zheng, W and Teng, X and Jiang, T and Tang, W and Jiang, L and Zhu, H and Yu, X and Chen, G and Wang, J and Zhang, J and Qu, M and Zhang, X}, title = {Genome analysis of a novel avian atadenovirus reveals a possible horizontal gene transfer.}, journal = {Virology}, volume = {593}, number = {}, pages = {109999}, doi = {10.1016/j.virol.2024.109999}, pmid = {38368638}, issn = {1096-0341}, abstract = {We report the discovery and characterization of a novel adenovirus, Zoothera dauma adenovirus (ZdAdV), from a wild bird species, Zoothera dauma (Scaly thrush). This new atadenovirus was discovered by metagenomic sequencing without virus cultivation. Analyses of the full genome sequence revealed that this new virus is a distinct member of the genus Atadenovirus and represents a novel species. ZdAdV has a genome of 34,760 bp with 28 predicted genes and 39% GC content. ZdAdV is the first atadenovirus to contain ORF19, a gene previously found only in aviadenoviruses. Phylogenetic analysis of ORF19 suggests that it was acquired by ZdAdV through horizontal gene transfer from an aviadenovirus. By analyzing all orthologous genes of aviadenovirus, mastadenovirus, atadenovirus, and siadenovirus, we also found potential horizontal gene transfer for the E4 gene in Pigeon aviadenovirus B. Our study widens our knowledge concerning the genetic diversity and evolutionary history of atadenoviruses and their potential for cross-species transmission.}, } @article {pmid38368447, year = {2024}, author = {Ouboter, HT and Mesman, R and Sleutels, T and Postma, J and Wissink, M and Jetten, MSM and Ter Heijne, A and Berben, T and Welte, CU}, title = {Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1477}, pmid = {38368447}, issn = {2041-1723}, support = {024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; VI.Vidi.223.012//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; 854088//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; }, abstract = {Anaerobic methanotrophic (ANME) archaea are environmentally important, uncultivated microorganisms that oxidize the potent greenhouse gas methane. During methane oxidation, ANME archaea engage in extracellular electron transfer (EET) with other microbes, metal oxides, and electrodes through unclear mechanisms. Here, we cultivate ANME-2d archaea ('Ca. Methanoperedens') in bioelectrochemical systems and observe strong methane-dependent current (91-93% of total current) associated with high enrichment of 'Ca. Methanoperedens' on the anode (up to 82% of the community), as determined by metagenomics and transmission electron microscopy. Electrochemical and metatranscriptomic analyses suggest that the EET mechanism is similar at various electrode potentials, with the possible involvement of an uncharacterized short-range electron transport protein complex and OmcZ nanowires.}, } @article {pmid38368431, year = {2024}, author = {Laczkó, L and Jordán, S and Póliska, S and Rácz, HV and Nagy, NA and Molnár V, A and Sramkó, G}, title = {The draft genome of Spiraea crenata L. (Rosaceae) - the first complete genome in tribe Spiraeeae.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {219}, pmid = {38368431}, issn = {2052-4463}, abstract = {Spiraea crenata L. is a deciduous shrub distributed across the Eurasian steppe zone. The species is of cultural and horticultural importance and occurs in scattered populations throughout its westernmost range. Currently, there is no genomic information on the tribe of Spiraeeae. Therefore we sequenced and assembled the whole genome of S. crenata using second- and third-generation sequencing and a hybrid assembly approach to expand genomic resources for conservation and support research on this horticulturally important lineage. In addition to the organellar genomes (the plastome and the mitochondrion), we present the first draft genome of the species with an estimated size of 220 Mbp, an N50 value of 7.7 Mbp, and a BUSCO score of 96.0%. Being the first complete genome in tribe Spiraeeae, this may not only be the first step in the genomic study of a rare plant but also a contribution to genomic resources supporting the study of biodiversity and evolutionary history of Rosaceae.}, } @article {pmid38368306, year = {2024}, author = {Lv, T and Zhao, Q and Liu, J and Wang, S and Wu, W and Miao, L and Zhan, P and Chen, X and Huang, M and Ye, M and Ou, Q and Zhang, Y}, title = {Utilizing metagenomic next-generation sequencing for pathogen detection and diagnosis in lower respiratory tract infections in real-world clinical practice.}, journal = {Infection}, volume = {}, number = {}, pages = {}, pmid = {38368306}, issn = {1439-0973}, abstract = {BACKGROUND: Infectious etiologies of lower respiratory tract infections (LRTIs) by the conventional microbiology tests (CMTs) can be challenging. Metagenomic next-generation sequencing (mNGS) has great potential in clinical use for its comprehensiveness in identifying pathogens, particularly those difficult-to-culture organisms.

METHODS: We analyzed a total of 205 clinical samples from 201 patients with suspected LRTIs using mNGS in parallel with CMTs. mNGS results were used to guide treatment adjustments for patients who had negative CMT results. The efficacy of treatment was subsequently evaluated in these patients.

RESULTS: mNGS-detected microorganisms in 91.7% (188/205) of the clinical samples, whereas CMTs demonstrated a lower detection rate, identifying microorganisms in only 37.6% (77/205) of samples. Compared to CMT results, mNGS exhibited a detection sensitivity of 93.5% and 95.4% in all 205 clinical samples and 180 bronchoalveolar lavage fluid (BALF) samples, respectively. A total of 114 patients (114/201; 56.7%) showed negative CMT results, among which 92 received treatment adjustments guided by their positive mNGS results. Notably, 67.4% (62/92) of patients demonstrated effective treatment, while 25% (23/92) experienced a stabilized condition. Subgroup analysis of cancer patients revealed that 41.9% (13/31) exhibited an effective response to treatment, and 35.5% (11/31) maintained a stable condition following medication adjustments guided by mNGS.

CONCLUSION: mNGS demonstrated great potential in identifying microorganisms of clinical significance in LRTIs. The rapid turnaround time and reduced susceptibility to the impact of antimicrobial administration make mNGS a valuable supplementary tool for diagnosis and treatment decision-making for suspected LRTIs in clinical practice.}, } @article {pmid38367621, year = {2024}, author = {Chen, Q and Wu, C and Xu, J and Ye, C and Chen, X and Tian, H and Zong, N and Zhang, S and Li, L and Gao, Y and Zhao, D and Lv, X and Yang, Q and Wang, L and Cui, J and Lin, Z and Lu, J and Yang, R and Yin, F and Qin, N and Li, N and Xu, Q and Qin, H}, title = {Donor-recipient intermicrobial interactions impact transfer of subspecies and fecal microbiota transplantation outcome.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2024.01.013}, pmid = {38367621}, issn = {1934-6069}, abstract = {Studies on fecal microbiota transplantation (FMT) have reported inconsistent connections between clinical outcomes and donor strain engraftment. Analyses of subspecies-level crosstalk and its influences on lineage transfer in metagenomic FMT datasets have proved challenging, as single-nucleotide polymorphisms (SNPs) are generally not linked and are often absent. Here, we utilized species genome bin (SGB), which employs co-abundance binning, to investigate subspecies-level microbiome dynamics in patients with autism spectrum disorder (ASD) who had gastrointestinal comorbidities and underwent encapsulated FMT (Chinese Clinical Trial: 2100043906). We found that interactions between donor and recipient microbes, which were overwhelmingly phylogenetically divergent, were important for subspecies transfer and positive clinical outcomes. Additionally, a donor-recipient SGB match was indicative of a high likelihood of strain transfer. Importantly, these ecodynamics were shared across FMT datasets encompassing multiple diseases. Collectively, these findings provide detailed insight into specific microbial interactions and dynamics that determine FMT success.}, } @article {pmid38367443, year = {2024}, author = {Wang, M and Zhao, J and Liu, Y and Huang, S and Zhao, C and Jiang, Z and Gu, Y and Xiao, J and Wu, Y and Ying, R and Zhang, J and Tian, W}, title = {Deciphering soil resistance and virulence gene risks in conventional and organic farming systems.}, journal = {Journal of hazardous materials}, volume = {468}, number = {}, pages = {133788}, doi = {10.1016/j.jhazmat.2024.133788}, pmid = {38367443}, issn = {1873-3336}, abstract = {Organic farming is a sustainable agricultural practice emphasizing natural inputs and ecological balance, and has garnered significant attention for its potential health and environmental benefits. However, a comprehensive evaluation of the emergent contaminants, particularly resistance and virulence genes within organic farming system, remains elusive. Here, a total of 36 soil samples from paired conventional and organic vegetable farms were collected from Jiangsu province, China. A systematic metagenomic approach was employed to investigate the prevalence, dispersal capability, pathogenic potential, and drivers of resistance and virulence genes across both organic and conventional systems. Our findings revealed a higher abundance of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and virulence factor genes (VFGs) in organic farming system, with ARGs exhibiting a particularly notable increase of 10.76% compared to the conventional one. Pathogens such as Pseudomonas aeruginosa, Escherichia coli, and Mycobacterium tuberculosis were hosts carrying all four gene categories, highlighting their potential health implications. The neutral community model captured 77.1% and 71.9% of the variance in community dynamics within the conventional and organic farming systems, respectively, indicating that stochastic process was the predominant factor shaping gene communities. The relative smaller m value calculated in organic farming system (0.021 vs 0.023) indicated diminished gene exchange with external sources. Moreover, farming practices were observed to influence the resistance and virulence gene landscape by modifying soil properties, managing heavy metal stress, and steering mobile genetic elements (MGEs) dynamics. The study offers insights that can guide agricultural strategies to address potential health and ecological concerns.}, } @article {pmid38367442, year = {2024}, author = {Liu, Q and Jia, J and Hu, H and Li, X and Zhao, Y and Wu, C}, title = {Nitrogen and phosphorus limitations promoted bacterial nitrate metabolism and propagation of antibiotic resistome in the phycosphere of Auxenochlorella pyrenoidosa.}, journal = {Journal of hazardous materials}, volume = {468}, number = {}, pages = {133786}, doi = {10.1016/j.jhazmat.2024.133786}, pmid = {38367442}, issn = {1873-3336}, abstract = {Despite that nitrogen (N) and phosphorus (P) play critical roles in the lifecycle of microalgae, how N and P further affect the distribution of bacteria and antibiotic resistance genes (ARGs) in the phycosphere is still poorly understood. In this study, the effects of N and P on the distribution of ARGs in the phycosphere of Auxenochlorella pyrenoidosa were investigated. Results showed that the growth and chlorophyll synthesis of microalgae were inhibited when N or P was limited, regardless of the N/P ratios, but the extracellular polymeric substances content and nitrate assimilation efficiency were enhanced in contrast. Metagenomic sequencing revealed that N or P limitation resulted in the recruitment of specific bacteria that highly contribute to the nitrate metabolism in the phycosphere. Besides, N or P limitation promoted the propagation of phycosphere ARGs, primarily through horizontal gene transfer mediated by mobile genetic elements. The enrichment of specific bacteria induced by changes in the algal physiology also contributed to the ARGs proliferation under nutrient limitation. Our results demonstrated that the reduction of algal cells caused by nutrient limitation could promote the propagation of ARGs, which provides new insights into the occurrence and spread of ARGs in the phycosphere.}, } @article {pmid38367384, year = {2024}, author = {Zhao, Q and Li, X and Zhang, L and Li, J and Jia, T and Zhao, Y and Wang, L and Peng, Y}, title = {Partial denitrifying phosphorus removal coupling with anammox (PDPRA) enables synergistic removal of C, N, and P nutrients from municipal wastewater: A year-round pilot-scale evaluation.}, journal = {Water research}, volume = {253}, number = {}, pages = {121321}, doi = {10.1016/j.watres.2024.121321}, pmid = {38367384}, issn = {1879-2448}, abstract = {Applying anaerobic ammonium oxidation (anammox) in municipal wastewater treatment plants (MWWTPs) can unlock significant energy and resource savings. However, its practical implementation encounters significant challenges, particularly due to its limited compatibility with carbon and phosphorus removal processes. This study established a pilot-scale plant featuring a modified anaerobic-anoxic-oxic (A[2]O) process and operated continuously for 385 days, treating municipal wastewater of 50 m[3]/d. For the first time, we propose a novel concept of partial denitrifying phosphorus removal coupling with anammox (PDPRA), leveraging denitrifying phosphorus-accumulating organisms (DPAOs) as NO2[-] suppliers for anammox. [15]N stable isotope tracing revealed that the PDPRA enabled an anammox reaction rate of 6.14 ± 0.18 μmol-N/(L·h), contributing 57.4 % to total inorganic nitrogen (TIN) removal. Metagenomic sequencing and 16S rRNA amplicon sequencing unveiled the co-existence and co-prosperity of anammox bacteria and DPAOs, with Candidatus Brocadia being highly enriched in the anoxic biofilms at a relative abundance of 2.46 ± 0.52 %. Finally, the PDPRA facilitated the synergistic conversion and removal of carbon, nitrogen, and phosphorus nutrients, achieving remarkable removal efficiencies of chemical oxygen demand (COD, 83.5 ± 5.3 %), NH4[+] (99.8 ± 0.7 %), TIN (77.1 ± 3.6 %), and PO4[3-] (99.3 ± 1.6 %), even under challenging operational conditions such as low temperature of 11.7 °C. The PDPRA offers a promising solution for reconciling the mainstream anammox and the carbon and phosphorus removal, shedding fresh light on the paradigm shift of MWWTPs in the near future.}, } @article {pmid38367382, year = {2024}, author = {He, Z and Shen, J and Zhao, Y and Ru, Y and Zhang, D and Pan, X}, title = {Microbial antagonistic mechanisms of Hg(II) and Se(IV) in efficient wastewater treatment using granular sludge.}, journal = {Water research}, volume = {253}, number = {}, pages = {121311}, doi = {10.1016/j.watres.2024.121311}, pmid = {38367382}, issn = {1879-2448}, abstract = {The antagonistic effects of mercury (Hg) and selenium (Se) have been extensively studied in higher animals and plants. In this study, the microbial antagonistic effects of Hg and Se were utilized for wastewater treatment. We developed and optimized a new granular sludge approach to efficiently remove Hg(II) and Se(IV) from wastewater. Under anaerobic-oxic-anaerobic (AOA) conditions, the removal rates of Hg(II) and Se(IV) reached up to 99.91±0.07 % and 97.7 ± 0.8 %, respectively. The wastewater Hg(II) was mostly (97.43±0.01 %) converted to an inert mineral called tiemannite (HgSe) in the sludge, and no methylmercury (MeHg) was detected. The HgSe in sludge is less toxic, with almost no risk of secondary release, and it can be recovered with high purity. An inhibition experiment of mercury reduction and the high expression of the mer operon indicated that most Hg(II) (∼71 %) was first reduced to Hg[0], and then Hg[0] reacted with Se[0] to synthesize HgSe. Metagenomic results showed that the final sludge (day 182) was dominated by two unclassified bacteria in the orders Rhodospirillales (27.7 %) and Xanthomonadales (6.3 %). Their metagenome-assembled genomes (MAGs) were recovered, suggesting that both of them can reduce Hg(II) and Se(IV). Metatranscriptomic analyses indicate that they can independently and cooperatively synthesize HgSe. In summary, granular sludge under AOA conditions is an efficient method for removing and recovering Hg from wastewater. The microbial transformation of Hg[2+]to Hg[0] to HgSe may occur widely in both engineering and natural ecosystems.}, } @article {pmid38367110, year = {2024}, author = {Yadav, R and Dharne, M}, title = {Utility of metagenomics for bioremediation: a comprehensive review on bioremediation mechanisms and microbial dynamics of river ecosystem.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38367110}, issn = {1614-7499}, abstract = {Global industrialization has contributed substantial amounts of chemical pollutants in rivers, resulting in an uninhabitable state and impacting different life forms. Moreover, water macrophytes, such as water hyacinths, are abundantly present in polluted rivers, significantly affecting the overall water biogeochemistry. Bioremediation involves utilizing microbial metabolic machinery and is one of the most viable approaches for removing toxic pollutants. Conventional techniques generate limited information on the indigenous microbial population and their xenobiotic metabolism, failing the bioremediation process. Metagenomics can overcome these limitations by providing in-depth details of microbial taxa and functionality-related information required for successful biostimulation and augmentation. An in-depth summary of the findings related to pollutant metabolizing genes and enzymes in rivers still needs to be collated. The present study details bioremediation genes and enzymes functionally mined from polluted river ecosystems worldwide using a metagenomic approach. Several studies reported a wide variety of pollutant-degrading enzymes involved in the metabolism of dyes, plastics, persistent organic pollutants, and aromatic hydrocarbons. Additionally, few studies also noted a shift in the microbiome of the rivers upon exposure to contaminants, crucially affecting the ecological determinant processes. Furthermore, minimal studies have focused on the role of water-hyacinth-associated microbes in the bioremediation potentials, suggesting the need for the bioprospecting of these lesser-studied microbes. Overall, our study summarizes the prospects and utilities of the metagenomic approach and proposes the need to employ it for efficient bioremediation.}, } @article {pmid38367105, year = {2024}, author = {Domínguez-Maldonado, JA and Solís-Pereira, SE and Valle-Gough, RE and Álvarez, AAM and Olguín-Maciel, E and Alzate-Gaviria, L and Tapia-Tussell, R}, title = {Microbial communities present in Sargassum spp. leachates from the Mexican Caribbean which are involved in their degradation in the environment, a tool to tackle the problem.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38367105}, issn = {1614-7499}, support = {305292.//Consejo Nacional de Ciencia y Tecnología/ ; }, abstract = {The Sargassum phenomenon is currently affecting the Caribbean in several ways; one of them is the increase of greenhouse gases due to the decomposition process of this macroalgae; these processes also produce large amounts of pollutant leachates, in which several microbial communities are involved. To understand these processes, we conducted a 150-day study on the Sargassum spp environmental degradation under outdoor conditions, during which leachates were collected at 0, 30, 90, and 150 days. Subsequently, a metagenomic study of the microorganisms found in the leachates was carried out, in which changes in the microbial community were observed over time. The results showed that anaerobic bacterial genera such as Thermofilum and Methanopyrus were predominant at the beginning of this study (0 and 30 days), degrading sugars of sulfur polymers such as fucoidan, but throughout the experiment, the microbial communities were changed also, with the genera Fischerella and Dolichospermum being the most predominant at days 90 and 150, respectively. A principal component analysis (PCA) indicated, with 94% variance, that genera were positively correlated at 30 and 90 days, but not with initial populations, indicating changes in community structure due to sargassum degradation were present. Finally, at 150 days, the leachate volume decreased by almost 50% and there was a higher abundance of the genera Desulfobacter and Dolichospemum. This is the first work carried out to understand the degradation of Sargassum spp, which will serve, together with other works, to understand and provide a solution to this serious environmental problem in the Caribbean.}, } @article {pmid38367043, year = {2024}, author = {LeBlanc, NR and Harrigian, FC}, title = {Green Waste Compost Impacts Microbial Functions Related to Carbohydrate Use and Active Dispersal in Plant Pathogen-Infested Soil.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {44}, pmid = {38367043}, issn = {1432-184X}, support = {2038-22430-003-000-D//Agricultural Research Service/ ; }, abstract = {The effects of compost on physical and chemical characteristics of soil are well-studied but impacts on soil microbiomes are poorly understood. This research tested effects of green waste compost on bacterial communities in soil infested with the plant pathogen Fusarium oxysporum. Compost was added to pathogen-infested soil and maintained in mesocosms in a greenhouse experiment and replicated growth chamber experiments. Bacteria and F. oxysporum abundance were quantified using quantitative PCR. Taxonomic and functional characteristics of bacterial communities were measured using shotgun metagenome sequencing. Compost significantly increased bacterial abundance 8 weeks after amendment in one experiment. Compost increased concentrations of chemical characteristics of soil, including phosphorus, potassium, organic matter, and pH. In all experiments, compost significantly reduced abundance of F. oxysporum and altered the taxonomic composition of soil bacterial communities. Sixteen bacterial genera were significantly increased from compost in every experiment, potentially playing a role in pathogen suppression. In all experiments, there was a consistent negative effect of compost on functions related to carbohydrate use and a positive effect on bacteria with flagella. Results from this work demonstrate that compost can reduce the abundance of soilborne plant pathogens and raise questions about the role of microbes in plant pathogen suppression.}, } @article {pmid38366600, year = {2024}, author = {Huang, KD and Amend, L and Gálvez, EJC and Lesker, TR and de Oliveira, R and Bielecka, A and Blanco-Míguez, A and Valles-Colomer, M and Ruf, I and Pasolli, E and Buer, J and Segata, N and Esser, S and Strowig, T and Kehrmann, J}, title = {Establishment of a non-Westernized gut microbiota in men who have sex with men is associated with sexual practices.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {101426}, doi = {10.1016/j.xcrm.2024.101426}, pmid = {38366600}, issn = {2666-3791}, abstract = {The human gut microbiota is influenced by various factors, including health status and environmental conditions, yet considerable inter-individual differences remain unexplained. Previous studies identified that the gut microbiota of men who have sex with men (MSM) is distinct from that of non-MSM. Here, we reveal through species-level microbiota analysis using shotgun metagenomics that the gut microbiota of many MSM with Western origin resembles gut microbial communities of non-Westernized populations. Specifically, MSM gut microbiomes are frequently dominated by members of the Prevotellaceae family, including co-colonization of species from the Segatella copri complex and unknown Prevotellaceae members. Questionnaire-based analysis exploring inter-individual differences in MSM links specific sexual practices to microbiota composition. Moreover, machine learning identifies microbial features associated with sexual activities in MSM. Together, this study shows associations of sexual activities with gut microbiome alterations in MSM, which may have a large impact on population-based microbiota studies.}, } @article {pmid38366262, year = {2024}, author = {Wang, J and Zhu, YG and Tiedje, JM and Ge, Y}, title = {Global biogeography and ecological implications of cobamide-producing prokaryotes.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae009}, pmid = {38366262}, issn = {1751-7370}, abstract = {Cobamides, a class of essential coenzymes synthesized only by a subset of prokaryotes, are model nutrients in microbial interaction studies and play significant roles in global ecosystems. Yet, their spatial patterns and functional roles remain poorly understood. Herein, we present an in-depth examination of cobamide-producing microorganisms, drawn from a comprehensive analysis of 2862 marine and 2979 soil metagenomic samples. A total of 1934 non-redundant Metagenome-Assembled Genomes (MAGs) potentially capable of producing cobamides de novo were identified. The cobamide-producing MAGs are taxonomically diverse but habitat specific. They constituted only a fraction of all the recovered MAGs, with the majority of MAGs being potential cobamide users. By mapping the distribution of cobamide producers in marine and soil environments, distinct latitudinal gradients were observed: the marine environment showed peak abundance at the equator, whereas soil environments peaked at mid-latitudes. Importantly, significant and positive links between the abundance of cobamide producers and the diversity and functions of microbial communities was observed, as well as their promotional roles in essential biogeochemical cycles. These associations were more pronounced in marine samples than in soil samples, which suggests a heightened propensity for microorganisms to engage in cobamide sharing in fluid environments relative to the more spatially restricted soil environment. These findings shed light on the global patterns and potential ecological roles of cobamide-producing microorganisms in marine and soil ecosystems, enhancing our understanding of large-scale microbial interactions.}, } @article {pmid38366248, year = {2024}, author = {Zhao, D and Zhang, S and Chen, J and Zhao, J and An, P and Xiang, H}, title = {Members of the class Candidatus Ordosarchaeia imply an alternative evolutionary scenario from methanogens to haloarchaea.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrad033}, pmid = {38366248}, issn = {1751-7370}, support = {92251302//National Natural Science Foundation of China/ ; CAM202202//Central Asian Drug Discovery and Development Center of Chinese Academy of Sciences/ ; }, abstract = {The origin of methanogenesis can be traced to the common ancestor of non-DPANN archaea, whereas haloarchaea (or Halobacteria) are believed to have evolved from a methanogenic ancestor through multiple evolutionary events, including the loss of genes associated with methanogenesis. However, due to the accelerated evolution and compositional bias of proteins adapting to hypersaline habitats, Halobacteria exhibit substantial evolutionary divergence from methanogens, and the identification of the closest methanogen (either Methanonatronarchaeia or other related taxa) to Halobacteria remains a subject of debate. Here, we obtained five metagenome-assembled genomes with high completeness from soda-saline lakes on the Ordos Plateau in Inner Mongolia, China, and we proposed the name Candidatus Ordosarchaeia for this novel class. Phylogenetic analyses revealed that Ca. Ordosarchaeia is firmly positioned near the median position between the Methanonatronarchaeia and Halobacteria-Hikarchaeia lineages. Functional predictions supported the transitional status of Ca. Ordosarchaeia with the metabolic potential of nonmethanogenic and aerobic chemoheterotrophy, as did remnants of the gene sequences of methylamine/dimethylamine/trimethylamine metabolism and coenzyme M biosynthesis. Based on the similarity of the methyl-coenzyme M reductase genes mcrBGADC in Methanonatronarchaeia with the phylogenetically distant methanogens, an alternative evolutionary scenario is proposed, in which Methanonatronarchaeia, Ca. Ordosarchaeia, Ca. Hikarchaeia and Halobacteria share a common ancestor that initially lost mcr genes. However, certain members of Methanonatronarchaeia subsequently acquired mcr genes through horizontal gene transfer from distantly related methanogens. This hypothesis is supported by amalgamated likelihood estimation, phylogenetic analysis, and gene arrangement patterns. Altogether, Ca. Ordosarchaeia genomes clarify the sisterhood of Methanonatronarchaeia with Halobacteria and provide new insights into the evolution from methanogens to haloarchaea.}, } @article {pmid38366198, year = {2024}, author = {Liu, HB and Sun, HX and Du, LQ and Jiang, LL and Zhang, LA and Qi, YY and Cai, J and Yu, F}, title = {Rice receptor kinase FLR7 regulates rhizosphere oxygen levels and enriches the dominant Anaeromyxobacter that improves submergence tolerance in rice.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae006}, pmid = {38366198}, issn = {1751-7370}, abstract = {Oxygen is one of the determinants of root microbiome formation. However, whether plants regulate rhizosphere oxygen levels to affect microbiota composition and the underlying molecular mechanisms remain elusive. The receptor-like kinase (RLK) family member FERONIA modulates the growth-defense tradeoff in Arabidopsis. Here, we established that rice FERONIA-like RLK 7 (FLR7) controls rhizosphere oxygen levels by methylene blue staining, oxygen flux and potential measurements. The formation of oxygen-transporting aerenchyma in roots is negatively regulated by FLR7. We further characterized the root microbiota of 11 FLR mutants including flr7 and wild-type Nipponbare (Nip) grown in the field by 16S ribosomal RNA gene profiling and demonstrated that the 11 FLRs are involved in regulating rice root microbiome formation. The most abundant anaerobic-dependent genus Anaeromyxobacter in the Nip root microbiota was less abundant in the root microbiota of all these mutants, and this contributed the most to the community differences between most mutants and Nip. Metagenomic sequencing revealed that flr7 increases aerobic respiration and decreases anaerobic respiration in the root microbiome. Finally, we showed that a representative Anaeromyxobacter strain improved submergence tolerance in rice via FLR7. Collectively, our findings indicate that FLR7 mediates changes in rhizosphere oxygen levels and enriches the beneficial dominant genus Anaeromyxobacter and may provide insights for developing plant flood prevention strategies via the use of environment-specific functional soil microorganisms.}, } @article {pmid38366194, year = {2024}, author = {Hu, J and Chen, J and Ma, L and Hou, Q and Zhang, Y and Kong, X and Huang, X and Tang, Z and Wei, H and Wang, X and Yan, X}, title = {Characterizing core microbiota and regulatory functions of the pig gut microbiome.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrad037}, pmid = {38366194}, issn = {1751-7370}, abstract = {Domestic pigs (Sus scrofa) are the leading terrestrial animals used for meat production. The gut microbiota significantly affect host nutrition, metabolism, and immunity. Hence, characterization of the gut microbial structure and function will improve our understanding of gut microbial resources and the mechanisms underlying host-microbe interactions. Here, we investigated the gut microbiomes of seven pig breeds using metagenomics and 16S rRNA gene amplicon sequencing. We established an expanded gut microbial reference catalog comprising 17 020 160 genes and identified 4910 metagenome-assembled genomes (MAGs). We also analyzed the gut resistome to provide an overview of the profiles of the antimicrobial resistance genes in pigs. By analyzing the relative abundances of microbes, we identified three core-predominant gut microbes (Phascolarctobacterium succinatutens, Prevotella copri, and Oscillibacter valericigenes) in pigs used in this study. Oral administration of the three core-predominant gut microbes significantly increased the organ indexes (including the heart, spleen, and thymus), but decreased the gastrointestinal lengths in germ-free (GF) mice. The three core microbes significantly enhanced intestinal epithelial barrier function and altered the intestinal mucosal morphology, as was evident from the increase in crypt depths in the duodenum and ileum. Furthermore, the three core microbes significantly affected several metabolic pathways (such as "steroid hormone biosynthesis", "primary bile acid biosynthesis", "phenylalanine, tyrosine and tryptophan biosynthesis", and "phenylalanine metabolism") in GF mice. These findings provide a panoramic view of the pig gut microbiome and insights into the functional contributions of the core-predominant gut microbes to the host.}, } @article {pmid38366190, year = {2024}, author = {Rubio-Portillo, E and Robertson, S and Antón, J}, title = {Coral mucus as a reservoir of bacteriophages targeting Vibrio pathogens.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae017}, pmid = {38366190}, issn = {1751-7370}, abstract = {The increasing trend in sea surface temperature promotes the spread of Vibrio species, which are known to cause diseases in a wide range of marine organisms. Among these pathogens, Vibrio mediterranei has emerged as a significant threat, leading to bleaching in the coral species Oculina patagonica. Bacteriophages, or phages, are viruses that infect bacteria, thereby regulating microbial communities and playing a crucial role in the coral's defense against pathogens. However, our understanding of phages that infect V. mediterranei is limited. In this study, we identified two phage species capable of infecting V. mediterranei, utilizing a combination of cultivation and metagenomic approaches. These phages are low-abundance specialists within the coral mucus layer that exhibit rapid proliferation in the presence of their hosts, suggesting a potential role in coral defense. Additionally, one of these phages possesses a conserved domain of a leucine-rich repeat protein, similar to those harbored in the coral genome, that plays a key role in pathogen recognition, hinting at potential coral-phage coevolution. Furthermore, our research suggests that lytic Vibrio infections could trigger prophage induction, which may disseminate genetic elements, including virulence factors, in the coral mucus layer. Overall, our findings underscore the importance of historical coral-phage interactions as a form of coral immunity against invasive Vibrio pathogens.}, } @article {pmid38366085, year = {2024}, author = {Fernández-Pato, A and Sinha, T and Gacesa, R and Andreu-Sánchez, S and Gois, MFB and Gelderloos-Arends, J and Jansen, DBH and Kruk, M and Jaeger, M and Joosten, LAB and Netea, MG and Weersma, RK and Wijmenga, C and Harmsen, HJM and Fu, J and Zhernakova, A and Kurilshikov, A}, title = {Choice of DNA extraction method affects stool microbiome recovery and subsequent phenotypic association analyses.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {3911}, pmid = {38366085}, issn = {2045-2322}, support = {LSHM18057-SGF//TIMID project/ ; 2018-27//Netherlands Heart Foundation CVON grant/ ; 16-14//Seerave Foundation and the Dutch Digestive Foundation/ ; 024.003.001//NWO Gravitation grant Netherlands Organ-on-Chip Initiative/ ; SPI 92-266//NWO Spinoza Prize/ ; 101001678//ERC Consolidator grant/ ; VI.C.202.022//NWO VICI grant/ ; 715772//European Research Council (ERC) Starting Grant/ ; 016.178.056//Netherlands Organization for Scientific Research (NWO) VIDI grant/ ; 024.004.017//NWO Gravitation grant ExposomeNL/ ; 101094099//EU Horizon Europe Program grant INITIALISE/ ; }, abstract = {The lack of standardization in the methods of DNA extraction from fecal samples represents the major source of experimental variation in the microbiome research field. In this study, we aimed to compare the metagenomic profiles and microbiome-phenotype associations obtained by applying two commercially available DNA extraction kits: the AllPrep DNA/RNA Mini Kit (APK) and the QIAamp Fast DNA Stool Mini Kit (FSK). Using metagenomic sequencing data available from 745 paired fecal samples from two independent population cohorts, Lifelines-DEEP (LLD, n = 292) and the 500 Functional Genomics project (500FG, n = 453), we confirmed significant differences in DNA yield and the recovered microbial communities between protocols, with the APK method resulting in a higher DNA concentration and microbial diversity. Further, we observed a massive difference in bacterial relative abundances at species-level between the APK and the FSK protocols, with > 75% of species differentially abundant between protocols in both cohorts. Specifically, comparison with a standard mock community revealed that the APK method provided higher accuracy in the recovery of microbial relative abundances, with the absence of a bead-beating step in the FSK protocol causing an underrepresentation of gram-positive bacteria. This heterogeneity in the recovered microbial composition led to remarkable differences in the association with anthropometric and lifestyle phenotypes. The results of this study further reinforce that the choice of DNA extraction method impacts the metagenomic profile of human gut microbiota and highlight the importance of harmonizing protocols in microbiome studies.}, } @article {pmid38366050, year = {2024}, author = {Baquero, DP and Bignon, EA and Krupovic, M}, title = {Pleomorphic viruses establish stable relationship with marine hyperthermophilic archaea.}, journal = {The ISME journal}, volume = {}, number = {}, pages = {}, doi = {10.1093/ismejo/wrae008}, pmid = {38366050}, issn = {1751-7370}, abstract = {Non-lytic viruses with enveloped pleomorphic virions (family Pleolipoviridae) are ubiquitous in hypersaline environments across the globe and are associated with nearly all major lineages of halophilic archaea. However, their existence in other ecosystems remains largely unknown. Here, we show that evolutionarily related viruses also infect hyperthermophilic archaea thriving in deep-sea hydrothermal vents. Archaeoglobus veneficus pleomorphic virus 1 (AvPV1), the first virus described for any member of the class Archaeoglobi, encodes a morphogenetic module typical of pleolipoviruses, including the characteristic VP4-like membrane fusion protein. We show that AvPV1 is a non-lytic virus chronically produced in liquid cultures without substantially affecting the growth dynamics of its host with a stable virus-to-host ratio of ~1. Mining of genomic and metagenomic databases revealed broad distribution of AvPV1-like viruses in geographically remote hydrothermal vents. Comparative genomics, coupled with phylogenetic analysis of VP4-like fusogens revealed deep divergence of pleomorphic viruses infecting halophilic, methanogenic, and hyperthermophilic archaea, signifying niche separation and coevolution of the corresponding virus-host pairs. Hence, we propose a new virus family, "Thalassapleoviridae", for classification of the marine hyperthermophilic virus AvPV1 and its relatives. Collectively, our results provide insights into the diversity and evolution of pleomorphic viruses beyond hypersaline environments.}, } @article {pmid38365827, year = {2024}, author = {Bosch, ME and Dodiya, HB and Michalkiewicz, J and Lee, C and Shaik, SM and Weigle, IQ and Zhang, C and Osborn, J and Nambiar, A and Patel, P and Parhizkar, S and Zhang, X and Laury, ML and Mondal, P and Gomm, A and Schipma, MJ and Mallah, D and Butovsky, O and Chang, EB and Tanzi, RE and Gilbert, JA and Holtzman, DM and Sisodia, SS}, title = {Sodium oligomannate alters gut microbiota, reduces cerebral amyloidosis and reactive microglia in a sex-specific manner.}, journal = {Molecular neurodegeneration}, volume = {19}, number = {1}, pages = {18}, pmid = {38365827}, issn = {1750-1326}, support = {T32AG05851804/AG/NIA NIH HHS/United States ; }, abstract = {It has recently become well-established that there is a connection between Alzheimer's disease pathology and gut microbiome dysbiosis. We have previously demonstrated that antibiotic-mediated gut microbiota perturbations lead to attenuation of Aβ deposition, phosphorylated tau accumulation, and disease-associated glial cell phenotypes in a sex-dependent manner. In this regard, we were intrigued by the finding that a marine-derived oligosaccharide, GV-971, was reported to alter gut microbiota and reduce Aβ amyloidosis in the 5XFAD mouse model that were treated at a point when Aβ burden was near plateau levels. Utilizing comparable methodologies, but with distinct technical and temporal features, we now report on the impact of GV-971 on gut microbiota, Aβ amyloidosis and microglial phenotypes in the APPPS1-21 model, studies performed at the University of Chicago, and independently in the 5X FAD model, studies performed at Washington University, St. Louis.Methods To comprehensively characterize the effects of GV-971 on the microbiota-microglia-amyloid axis, we conducted two separate investigations at independent institutions. There was no coordination of the experimental design or execution between the two laboratories. Indeed, the two laboratories were not aware of each other's experiments until the studies were completed. Male and female APPPS1-21 mice were treated daily with 40, 80, or 160 mg/kg of GV-971 from 8, when Aβ burden was detectable upto 12 weeks of age when Aβ burden was near maximal levels. In parallel, and to corroborate existing published studies and further investigate sex-related differences, male and female 5XFAD mice were treated daily with 100 mg/kg of GV-971 from 7 to 9 months of age when Aβ burden was near peak levels. Subsequently, the two laboratories independently assessed amyloid-β deposition, metagenomic, and neuroinflammatory profiles. Finally, studies were initiated at the University of Chicago to evaluate the metabolites in cecal tissue from vehicle and GV-971-treated 5XFAD mice.Results These studies showed that independent of the procedural differences (dosage, timing and duration of treatment) between the two laboratories, cerebral amyloidosis was reduced primarily in male mice, independent of strain. We also observed sex-specific microbiota differences following GV-971 treatment. Interestingly, GV-971 significantly altered multiple overlapping bacterial species at both institutions. Moreover, we discovered that GV-971 significantly impacted microbiome metabolism, particularly by elevating amino acid production and influencing the tryptophan pathway. The metagenomics and metabolomics changes correspond with notable reductions in peripheral pro-inflammatory cytokine and chemokine profiles. Furthermore, GV-971 treatment dampened astrocyte and microglia activation, significantly decreasing plaque-associated reactive microglia while concurrently increasing homeostatic microglia only in male mice. Bulk RNAseq analysis unveiled sex-specific changes in cerebral cortex transcriptome profiles, but most importantly, the transcriptome changes in the GV-971-treated male group revealed the involvement of microglia and inflammatory responses.Conclusions In conclusion, these studies demonstrate the connection between the gut microbiome, neuroinflammation, and Alzheimer's disease pathology while highlighting the potential therapeutic effect of GV-971. GV-971 targets the microbiota-microglia-amyloid axis, leading to the lowering of plaque pathology and neuroinflammatory signatures in a sex-dependent manner when given at the onset of Aβ deposition or when given after Aβ deposition is already at higher levels.}, } @article {pmid38365793, year = {2024}, author = {Cheng, M and Luo, S and Zhang, P and Xiong, G and Chen, K and Jiang, C and Yang, F and Huang, H and Yang, P and Liu, G and Zhang, Y and Ba, S and Yin, P and Xiong, J and Miao, W and Ning, K}, title = {A genome and gene catalog of the aquatic microbiomes of the Tibetan Plateau.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1438}, pmid = {38365793}, issn = {2041-1723}, abstract = {The Tibetan Plateau supplies water to nearly 2 billion people in Asia, but climate change poses threats to its aquatic microbial resources. Here, we construct the Tibetan Plateau Microbial Catalog by sequencing 498 metagenomes from six water ecosystems (saline lakes, freshwater lakes, rivers, hot springs, wetlands and glaciers). Our catalog expands knowledge of regional genomic diversity by presenting 32,355 metagenome-assembled genomes that de-replicated into 10,723 representative genome-based species, of which 88% were unannotated. The catalog contains nearly 300 million non-redundant gene clusters, of which 15% novel, and 73,864 biosynthetic gene clusters, of which 50% novel, thus expanding known functional diversity. Using these data, we investigate the Tibetan Plateau aquatic microbiome's biogeography along a distance of 2,500 km and >5 km in altitude. Microbial compositional similarity and the shared gene count with the Tibetan Plateau microbiome decline along with distance and altitude difference, suggesting a dispersal pattern. The Tibetan Plateau Microbial Catalog stands as a substantial repository for high-altitude aquatic microbiome resources, providing potential for discovering novel lineages and functions, and bridging knowledge gaps in microbiome biogeography.}, } @article {pmid38365303, year = {2024}, author = {Xu, T and Lu, Y and Chen, B and Deng, C and Zhang, Y and Wang, M and Ling, H and Huang, Y and Yuan, J and Jin, X and Ruan, L and Li, T and Zhang, CT}, title = {Cohort profile for the Tongji Cardiovascular Health Study: a prospective multiomics cohort study.}, journal = {BMJ open}, volume = {14}, number = {2}, pages = {e074768}, doi = {10.1136/bmjopen-2023-074768}, pmid = {38365303}, issn = {2044-6055}, abstract = {PURPOSE: The Tongji Cardiovascular Health Study aimed to further explore the onset and progression mechanisms of cardiovascular disease (CVD) through a combination of traditional cohort studies and multiomics analysis, including genomics, metabolomics and metagenomics.

STUDY DESIGN AND PARTICIPANTS: This study included participants aged 20-70 years old from the Geriatric Health Management Centre of Tongji Hospital of Tongji Medical College of Huazhong University of Science and Technology. After enrollment, each participant underwent a comprehensive series of traditional and novel cardiovascular risk factor assessments at baseline, including questionnaires, physical examinations, laboratory tests, cardiovascular health assessments and biological sample collection for subsequent multiomics analysis (whole genome sequencing, metabolomics study from blood samples and metagenomics study from stool samples). A biennial follow-up will be performed for 10 years to collect the information above and the outcome data.

FINDINGS TO DATE: A total of 2601 participants were recruited in this study (73.4% men), with a mean age of 51.5±11.5 years. The most common risk factor is overweight or obesity (54.8%), followed by hypertension (39.7%), hyperlipidaemia (32.4%), current smoking (23.9%) and diabetes (12.3%). Overall, 13.1% and 48.7% of men and women, respectively, did not have any of the CVD risk factors (hypertension, hyperlipidaemia, diabetes, cigarette smoking and overweight or obesity). Additionally, multiomics analyses of a subsample of the participants (n=938) are currently ongoing.

FUTURE PLANS: With the progress of the cohort follow-up work, it is expected to provide unique multidimensional and longitudinal data on cardiovascular health in China.}, } @article {pmid38365259, year = {2024}, author = {Jiao, J and Wu, J and Zhou, C and He, Z and Tan, Z and Wang, M}, title = {Ecological niches and assembly dynamics of diverse microbial consortia in the gastrointestine of goat kids.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, doi = {10.1093/ismejo/wrae002}, pmid = {38365259}, issn = {1751-7370}, support = {31972992//National Natural Science Foundation of China/ ; 161343KYSB20200015//International Partnership Program of Chinese Academy of Sciences/ ; 2023JJ10047//Hunan Provincial Natural Science Foundation of China/ ; U22A20512//National Natural Science Foundation of China/ ; 2023382//Youth Innovation Promotion Association CAS/ ; }, abstract = {Goats are globally invaluable ruminants that balance food security and environmental impacts, and their commensal microbiome residing in the gastrointestinal tract (GIT) is associated with animal health and productivity. However, the reference genomes and functional repertoires of GIT microbes in goat kids have not been fully elucidated. Herein, we performed a comprehensive landscape survey of the GIT microbiome of goat kids using metagenomic sequencing and binning, spanning a dense sampling regime covering three gastrointestinal compartments spatially and five developmental ages temporally. We recovered 1002 high-quality metagenome-assembled genomes (termed the goat kid GIT microbial catalog [GKGMC]), 618 of which were novel. They encode more than 2.3 million nonredundant proteins, and represent a variety of carbohydrate-degrading enzymes and metabolic gene clusters. The GKGMC-enriched microbial taxa, particularly Sodaliphilus, expanded the microbial tree of life in goat kids. Using this GKGMC, we first deciphered the prevalence of fiber-degrading bacteria for carbohydrate decomposition in the rumen and colon, while the ileal microbiota specialized in the uptake and conversion of simple sugars. Moreover, GIT microorganisms were rapidly assembled after birth, and their carbohydrate metabolic adaptation occurred in three phases of progression. Finally, phytobiotics modified the metabolic cascades of the ileal microbiome, underpinned by the enrichment of Sharpea azabuensis and Olsenella spp. implicated in lactate formation and utilization. This GKGMC reference provides novel insights into the early-life microbial developmental dynamics in distinct compartments, and offers expanded resources for GIT microbiota-related research in goat kids.}, } @article {pmid38365257, year = {2024}, author = {Dong, Q and Hua, D and Wang, X and Jiao, Y and Liu, L and Deng, Q and Wu, T and Zou, H and Zhao, C and Wang, C and Reng, J and Ding, L and Hu, S and Shi, J and Wang, Y and Zhang, H and Sheng, Y and Sun, W and Shen, Y and Tang, L and Kong, X and Chen, L}, title = {Temporal colonization and metabolic regulation of the gut microbiome in neonatal oxen at single nucleotide resolution.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, doi = {10.1093/ismejo/wrad022}, pmid = {38365257}, issn = {1751-7370}, support = {32394052//National Natural Science Foundation of China/ ; JSSCBS20221815//Jiangsu Shuangchuang Project/ ; BK20220709//Natural Science Foundation of Jiangsu/ ; C2022204247//Natural Science Foundation of Hebei/ ; CMCM202204//Nanjing Medical University/ ; //Development of Jiangsu Higher Education Institutions Priority Academic Program/ ; }, abstract = {The colonization of microbes in the gut is key to establishing a healthy host-microbiome symbiosis for newborns. We longitudinally profiled the gut microbiome in a model consisting of 36 neonatal oxen from birth up to 2 months postpartum and carried out microbial transplantation to reshape their gut microbiome. Genomic reconstruction of deeply sequenced fecal samples resulted in a total of 3931 metagenomic-assembled genomes from 472 representative species, of which 184 were identified as new species when compared with existing databases of oxen. Single nucleotide level metagenomic profiling shows a rapid influx of microbes after birth, followed by dynamic shifts during the first few weeks of life. Microbial transplantation was found to reshape the genetic makeup of 33 metagenomic-assembled genomes (FDR < 0.05), mainly from Prevotella and Bacteroides species. We further linked over 20 million microbial single nucleotide variations to 736 plasma metabolites, which enabled us to characterize 24 study-wide significant associations (P < 4.4 × 10-9) that identify the potential microbial genetic regulation of host immune and neuro-related metabolites, including glutathione and L-dopa. Our integration analyses further revealed that microbial genetic variations may influence the health status and growth performance by modulating metabolites via structural regulation of their encoded proteins. For instance, we found that the albumin levels and total antioxidant capacity were correlated with L-dopa, which was determined by single nucleotide variations via structural regulations of metabolic enzymes. The current results indicate that temporal colonization and transplantation-driven strain replacement are crucial for newborn gut development, offering insights for enhancing newborn health and growth.}, } @article {pmid38365254, year = {2024}, author = {Layoun, P and López-Pérez, M and Haro-Moreno, JM and Haber, M and Thrash, JC and Henson, MW and Kavagutti, VS and Ghai, R and Salcher, MM}, title = {Flexible genomic island conservation across freshwater and marine Methylophilaceae.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, doi = {10.1093/ismejo/wrad036}, pmid = {38365254}, issn = {1751-7370}, support = {19-23469S//Czech Science Foundation/ ; KA131//University of South Bohemia, Faculty of Science, Department of Ecosystem Biology/ ; 116/2019/P//Grant Agency of the University of South Bohemia in České Budějovice/ ; }, abstract = {The evolutionary trajectory of Methylophilaceae includes habitat transitions from freshwater sediments to freshwater and marine pelagial that resulted in genome reduction (genome-streamlining) of the pelagic taxa. However, the extent of genetic similarities in the genomic structure and microdiversity of the two genome-streamlined pelagic lineages (freshwater "Ca. Methylopumilus" and the marine OM43 lineage) has so far never been compared. Here, we analyzed complete genomes of 91 "Ca. Methylopumilus" strains isolated from 14 lakes in Central Europe and 12 coastal marine OM43 strains. The two lineages showed a remarkable niche differentiation with clear species-specific differences in habitat preference and seasonal distribution. On the other hand, we observed a synteny preservation in their genomes by having similar locations and types of flexible genomic islands (fGIs). Three main fGIs were identified: a replacement fGI acting as phage defense, an additive fGI harboring metabolic and resistance-related functions, and a tycheposon containing nitrogen-, thiamine-, and heme-related functions. The fGIs differed in relative abundances in metagenomic datasets suggesting different levels of variability ranging from strain-specific to population-level adaptations. Moreover, variations in one gene seemed to be responsible for different growth at low substrate concentrations and a potential biogeographic separation within one species. Our study provides a first insight into genomic microdiversity of closely related taxa within the family Methylophilaceae and revealed remarkably similar dynamics involving mobile genetic elements and recombination between freshwater and marine family members.}, } @article {pmid38365253, year = {2024}, author = {Buchwald, SZ and Herzschuh, U and Nürnberg, D and Harms, L and Stoof-Leichsenring, KR}, title = {Plankton community changes during the last 124 000 years in the subarctic Bering Sea derived from sedimentary ancient DNA.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, doi = {10.1093/ismejo/wrad006}, pmid = {38365253}, issn = {1751-7370}, support = {03G0672A//German Ministry of Education and Research/ ; }, abstract = {Current global warming results in rising sea-water temperatures, and the loss of sea ice in Arctic and subarctic oceans impacts the community composition of primary producers with cascading effects on the food web and potentially on carbon export rates. This study analyzes metagenomic shotgun and diatom rbcL amplicon sequencing data from sedimentary ancient DNA of the subarctic western Bering Sea that records phyto- and zooplankton community changes over the last glacial-interglacial cycles, including the last interglacial period (Eemian). Our data show that interglacial and glacial plankton communities differ, with distinct Eemian and Holocene plankton communities. The generally warm Holocene period is dominated by picosized cyanobacteria and bacteria-feeding heterotrophic protists, while the Eemian period is dominated by eukaryotic picosized chlorophytes and Triparmaceae. By contrast, the glacial period is characterized by microsized phototrophic protists, including sea ice-associated diatoms in the family Bacillariaceae and co-occurring diatom-feeding crustaceous zooplankton. Our deep-time record of plankton community changes reveals a long-term decrease in phytoplankton cell size coeval with increasing temperatures, resembling community changes in the currently warming Bering Sea. The phytoplankton community in the warmer-than-present Eemian period is distinct from modern communities and limits the use of the Eemian as an analog for future climate scenarios. However, under enhanced future warming, the expected shift toward the dominance of small-sized phytoplankton and heterotrophic protists might result in an increased productivity, whereas the community's potential of carbon export will be decreased, thereby weakening the subarctic Bering Sea's function as an effective carbon sink.}, } @article {pmid38365243, year = {2024}, author = {Li, Q and Ma, Z and Huo, J and Zhang, X and Wang, R and Zhang, S and Jiao, J and Dong, X and Janssen, PH and Ungerfeld, EM and Greening, C and Tan, Z and Wang, M}, title = {Distinct microbial hydrogen and reductant disposal pathways explain interbreed variations in ruminant methane yield.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, doi = {10.1093/ismejo/wrad016}, pmid = {38365243}, issn = {1751-7370}, support = {2023YFD1300900//National Key Research and Development Program of China/ ; 32161143028//National Natural Science Foundation of China/ ; 2022NK2021//Hunan Province Science and Technology Plan/ ; 2021BEF02020//Ningxia Province Science and Technology Plan/ ; //China Agriculture Research System of MOF and MARA/ ; ISA2021203//Open Fund of Key Laboratory of Agro-ecological Processes in Subtropical Region Chinese Academy of Sciences/ ; }, abstract = {Ruminants are essential for global food security, but these are major sources of the greenhouse gas methane. Methane yield is controlled by the cycling of molecular hydrogen (H2), which is produced during carbohydrate fermentation and is consumed by methanogenic, acetogenic, and respiratory microorganisms. However, we lack a holistic understanding of the mediators and pathways of H2 metabolism and how this varies between ruminants with different methane-emitting phenotypes. Here, we used metagenomic, metatranscriptomic, metabolomics, and biochemical approaches to compare H2 cycling and reductant disposal pathways between low-methane-emitting Holstein and high-methane-emitting Jersey dairy cattle. The Holstein rumen microbiota had a greater capacity for reductant disposal via electron transfer for amino acid synthesis and propionate production, catalyzed by enzymes such as glutamate synthase and lactate dehydrogenase, and expressed uptake [NiFe]-hydrogenases to use H2 to support sulfate and nitrate respiration, leading to enhanced coupling of H2 cycling with less expelled methane. The Jersey rumen microbiome had a greater proportion of reductant disposal via H2 production catalyzed by fermentative hydrogenases encoded by Clostridia, with H2 mainly taken up through methanogenesis via methanogenic [NiFe]-hydrogenases and acetogenesis via [FeFe]-hydrogenases, resulting in enhanced methane and acetate production. Such enhancement of electron incorporation for metabolite synthesis with reduced methanogenesis was further supported by two in vitro measurements of microbiome activities, metabolites, and public global microbiome data of low- and high-methane-emitting beef cattle and sheep. Overall, this study highlights the importance of promoting alternative H2 consumption and reductant disposal pathways for synthesizing host-beneficial metabolites and reducing methane production in ruminants.}, } @article {pmid38365241, year = {2024}, author = {Luo, ZH and Li, Q and Xie, YG and Lv, AP and Qi, YL and Li, MM and Qu, YN and Liu, ZT and Li, YX and Rao, YZ and Jiao, JY and Liu, L and Narsing Rao, MP and Hedlund, BP and Evans, PN and Fang, Y and Shu, WS and Huang, LN and Li, WJ and Hua, ZS}, title = {Temperature, pH, and oxygen availability contributed to the functional differentiation of ancient Nitrososphaeria.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, doi = {10.1093/ismejo/wrad031}, pmid = {38365241}, issn = {1751-7370}, support = {32300001//National Natural Science Foundation of China/ ; 2021A1515012468//National Science Foundation of Guangdong Province/ ; 2021M703757//China Postdoctoral Science Foundation/ ; }, abstract = {Ammonia-oxidizing Nitrososphaeria are among the most abundant archaea on Earth and have profound impacts on the biogeochemical cycles of carbon and nitrogen. In contrast to these well-studied ammonia-oxidizing archaea (AOA), deep-branching non-AOA within this class remain poorly characterized because of a low number of genome representatives. Here, we reconstructed 128 Nitrososphaeria metagenome-assembled genomes from acid mine drainage and hot spring sediment metagenomes. Comparative genomics revealed that extant non-AOA are functionally diverse, with capacity for carbon fixation, carbon monoxide oxidation, methanogenesis, and respiratory pathways including oxygen, nitrate, sulfur, or sulfate, as potential terminal electron acceptors. Despite their diverse anaerobic pathways, evolutionary history inference suggested that the common ancestor of Nitrososphaeria was likely an aerobic thermophile. We further surmise that the functional differentiation of Nitrososphaeria was primarily shaped by oxygen, pH, and temperature, with the acquisition of pathways for carbon, nitrogen, and sulfur metabolism. Our study provides a more holistic and less biased understanding of the diversity, ecology, and deep evolution of the globally abundant Nitrososphaeria.}, } @article {pmid38365239, year = {2024}, author = {Maire, J and Tsang Min Ching, SJ and Damjanovic, K and Epstein, HE and Judd, LM and Blackall, LL and van Oppen, MJH}, title = {Tissue-associated and vertically transmitted bacterial symbiont in the coral Pocillopora acuta.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, doi = {10.1093/ismejo/wrad027}, pmid = {38365239}, issn = {1751-7370}, support = {FL180100036//Australian Research Council/ ; //Native Australian Animals Trust/ ; //Paul G. Allen Philanthropies/ ; //James Cook University/ ; //Australian Institute of Marine Science/ ; }, abstract = {Coral microhabitats are colonized by a myriad of microorganisms, including diverse bacteria which are essential for host functioning and survival. However, the location, transmission, and functions of individual bacterial species living inside the coral tissues remain poorly studied. Here, we show that a previously undescribed bacterial symbiont of the coral Pocillopora acuta forms cell-associated microbial aggregates (CAMAs) within the mesenterial filaments. CAMAs were found in both adults and larval offspring, suggesting vertical transmission. In situ laser capture microdissection of CAMAs followed by 16S rRNA gene amplicon sequencing and shotgun metagenomics produced a near complete metagenome-assembled genome. We subsequently cultured the CAMA bacteria from Pocillopora acuta colonies, and sequenced and assembled their genomes. Phylogenetic analyses showed that the CAMA bacteria belong to an undescribed Endozoicomonadaceae genus and species, which we propose to name Candidatus Sororendozoicomonas aggregata gen. nov sp. nov. Metabolic pathway reconstruction from its genome sequence suggests this species can synthesize most amino acids, several B vitamins, and antioxidants, and participate in carbon cycling and prey digestion, which may be beneficial to its coral hosts. This study provides detailed insights into a new member of the widespread Endozoicomonadaceae family, thereby improving our understanding of coral holobiont functioning. Vertically transmitted, tissue-associated bacteria, such as Sororendozoicomonas aggregata may be key candidates for the development of microbiome manipulation approaches with long-term positive effects on the coral host.}, } @article {pmid38365236, year = {2024}, author = {Koonin, EV and Kuhn, JH and Dolja, VV and Krupovic, M}, title = {Megataxonomy and global ecology of the virosphere.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, doi = {10.1093/ismejo/wrad042}, pmid = {38365236}, issn = {1751-7370}, support = {/NH/NIH HHS/United States ; /LM/NLM NIH HHS/United States ; HHSN272201800013C/AI/NIAID NIH HHS/United States ; HHSN272201800013C/AI/NIAID NIH HHS/United States ; }, abstract = {Nearly all organisms are hosts to multiple viruses that collectively appear to be the most abundant biological entities in the biosphere. With recent advances in metagenomics and metatranscriptomics, the known diversity of viruses substantially expanded. Comparative analysis of these viruses using advanced computational methods culminated in the reconstruction of the evolution of major groups of viruses and enabled the construction of a virus megataxonomy, which has been formally adopted by the International Committee on Taxonomy of Viruses. This comprehensive taxonomy consists of six virus realms, which are aspired to be monophyletic and assembled based on the conservation of hallmark proteins involved in capsid structure formation or genome replication. The viruses in different major taxa substantially differ in host range and accordingly in ecological niches. In this review article, we outline the latest developments in virus megataxonomy and the recent discoveries that will likely lead to reassessment of some major taxa, in particular, split of three of the current six realms into two or more independent realms. We then discuss the correspondence between virus taxonomy and the distribution of viruses among hosts and ecological niches, as well as the abundance of viruses versus cells in different habitats. The distribution of viruses across environments appears to be primarily determined by the host ranges, i.e. the virome is shaped by the composition of the biome in a given habitat, which itself is affected by abiotic factors.}, } @article {pmid38365235, year = {2024}, author = {Zhu, W and Chang, L and Shi, S and Lu, N and Du, S and Li, J and Jiang, J and Wang, B}, title = {Gut microbiota reflect adaptation of cave-dwelling tadpoles to resource scarcity.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, doi = {10.1093/ismejo/wrad009}, pmid = {38365235}, issn = {1751-7370}, support = {2019QZKK05010203//Second Tibetan Plateau Scientific Expedition and Research Program/ ; 31900327//National Natural Science Foundation of China/ ; }, abstract = {Gut microbiota are significant to the host's nutrition and provide a flexible way for the host to adapt to extreme environments. However, whether gut microbiota help the host to colonize caves, a resource-limited environment, remains unknown. The nonobligate cave frog Oreolalax rhodostigmatus completes its metamorphosis within caves for 3-5 years before foraging outside. Their tadpoles are occasionally removed from the caves by floods and utilize outside resources, providing a contrast to the cave-dwelling population. For both cave and outside tadpoles, the development-related reduction in their growth rate and gut length during prometamorphosis coincided with a shift in their gut microbiota, which was characterized by decreased Lactobacillus and Cellulosilyticum and Proteocatella in the cave and outside individuals, respectively. The proportion of these three genera was significantly higher in the gut microbiota of cave-dwelling individuals compared with those outside. The cave-dwellers' gut microbiota harbored more abundant fibrolytic, glycolytic, and fermentative enzymes and yielded more short-chain fatty acids, potentially benefitting the host's nutrition. Experimentally depriving the animals of food resulted in gut atrophy for the individuals collected outside the cave, but not for those from inside the cave. Imitating food scarcity reproduced some major microbial features (e.g. abundant Proteocatella and fermentative genes) of the field-collected cave individuals, indicating an association between the cave-associated gut microbiota and resource scarcity. Overall, the gut microbiota may reflect the adaptation of O. rhodostigmatus tadpoles to resource-limited environments. This extends our understanding of the role of gut microbiota in the adaptation of animals to extreme environments.}, } @article {pmid38365233, year = {2024}, author = {Stephens, BM and Durkin, CA and Sharpe, G and Nguyen, TTH and Albers, J and Estapa, ML and Steinberg, DK and Levine, NM and Gifford, SM and Carlson, CA and Boyd, PW and Santoro, AE}, title = {Direct observations of microbial community succession on sinking marine particles.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, doi = {10.1093/ismejo/wrad010}, pmid = {38365233}, issn = {1751-7370}, support = {80NSSC17K0662/NASA/NASA/United States ; }, abstract = {Microbial community dynamics on sinking particles control the amount of carbon that reaches the deep ocean and the length of time that carbon is stored, with potentially profound impacts on Earth's climate. A mechanistic understanding of the controls on sinking particle distributions has been hindered by limited depth- and time-resolved sampling and methods that cannot distinguish individual particles. Here, we analyze microbial communities on nearly 400 individual sinking particles in conjunction with more conventional composite particle samples to determine how particle colonization and community assembly might control carbon sequestration in the deep ocean. We observed community succession with corresponding changes in microbial metabolic potential on the larger sinking particles transporting a significant fraction of carbon to the deep sea. Microbial community richness decreased as particles aged and sank; however, richness increased with particle size and the attenuation of carbon export. This suggests that the theory of island biogeography applies to sinking marine particles. Changes in POC flux attenuation with time and microbial community composition with depth were reproduced in a mechanistic ecosystem model that reflected a range of POC labilities and microbial growth rates. Our results highlight microbial community dynamics and processes on individual sinking particles, the isolation of which is necessary to improve mechanistic models of ocean carbon uptake.}, } @article {pmid38365232, year = {2024}, author = {Zheng, Y and Wang, B and Gao, P and Yang, Y and Xu, B and Su, X and Ning, D and Tao, Q and Li, Q and Zhao, F and Wang, D and Zhang, Y and Li, M and Winkler, MH and Ingalls, AE and Zhou, J and Zhang, C and Stahl, DA and Jiang, J and Martens-Habbena, W and Qin, W}, title = {Novel order-level lineage of ammonia-oxidizing archaea widespread in marine and terrestrial environments.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, doi = {10.1093/ismejo/wrad002}, pmid = {38365232}, issn = {1751-7370}, support = {548565//Simons Postdoctoral Fellowship in Marine Microbial Ecology/ ; //Florida Agricultural Experiment Station Hatch project/ ; //National Natural Science Foundation of China/ ; 2020Z01//Shanghai Sheshan National Geophysical Observatory/ ; 20200925173954005//Stable Support Plan Program of Shenzhen Natural Science Fund/ ; ZDSYS201802081843490//Southern University of Science and Technology/ ; //Shenzhen Key Laboratory of Marine Archaea Geo-Omics/ ; 2020KCXTD023//the Innovation Team Project of Universities/ ; //National Natural Science Foundation of China/ ; //Fundamental Research Funds for the Central Universities of China/ ; 92051114//National Natural Science Foundation of China/ ; }, abstract = {Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant archaea on Earth, widely distributed in marine, terrestrial, and geothermal ecosystems. However, the genomic diversity, biogeography, and evolutionary process of AOA populations in subsurface environments are vastly understudied compared to those in marine and soil systems. Here, we report a novel AOA order Candidatus (Ca.) Nitrosomirales which forms a sister lineage to the thermophilic Ca. Nitrosocaldales. Metagenomic and 16S rRNA gene-read mapping demonstrates the abundant presence of Nitrosomirales AOA in various groundwater environments and their widespread distribution across a range of geothermal, terrestrial, and marine habitats. Terrestrial Nitrosomirales AOA show the genetic capacity of using formate as a source of reductant and using nitrate as an alternative electron acceptor. Nitrosomirales AOA appear to have acquired key metabolic genes and operons from other mesophilic populations via horizontal gene transfer, including genes encoding urease, nitrite reductase, and V-type ATPase. The additional metabolic versatility conferred by acquired functions may have facilitated their radiation into a variety of subsurface, marine, and soil environments. We also provide evidence that each of the four AOA orders spans both marine and terrestrial habitats, which suggests a more complex evolutionary history for major AOA lineages than previously proposed. Together, these findings establish a robust phylogenomic framework of AOA and provide new insights into the ecology and adaptation of this globally abundant functional guild.}, } @article {pmid38365230, year = {2024}, author = {Benito Merino, D and Lipp, JS and Borrel, G and Boetius, A and Wegener, G}, title = {Anaerobic hexadecane degradation by a thermophilic Hadarchaeon from Guaymas Basin.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, doi = {10.1093/ismejo/wrad004}, pmid = {38365230}, issn = {1751-7370}, support = {//Census of Deep Life Phase 14 call (Deep Carbon Observatory)/ ; 1357238//National Science Foundation, Biological Oceanography/ ; 390741601//DFG under Germany's Excellence Initiative/Strategy through the Clusters of Excellence EXC 2077 "The Ocean Floor-Earth's Uncharted Interface"/ ; //Max Planck Society/ ; }, abstract = {Hadarchaeota inhabit subsurface and hydrothermally heated environments, but previous to this study, they had not been cultured. Based on metagenome-assembled genomes, most Hadarchaeota are heterotrophs that grow on sugars and amino acids, or oxidize carbon monoxide or reduce nitrite to ammonium. A few other metagenome-assembled genomes encode alkyl-coenzyme M reductases (Acrs), β-oxidation, and Wood-Ljungdahl pathways, pointing toward multicarbon alkane metabolism. To identify the organisms involved in thermophilic oil degradation, we established anaerobic sulfate-reducing hexadecane-degrading cultures from hydrothermally heated sediments of the Guaymas Basin. Cultures at 70°C were enriched in one Hadarchaeon that we propose as Candidatus Cerberiarchaeum oleivorans. Genomic and chemical analyses indicate that Ca. C. oleivorans uses an Acr to activate hexadecane to hexadecyl-coenzyme M. A β-oxidation pathway and a tetrahydromethanopterin methyl branch Wood-Ljungdahl (mWL) pathway allow the complete oxidation of hexadecane to CO2. Our results suggest a syntrophic lifestyle with sulfate reducers, as Ca. C. oleivorans lacks a sulfate respiration pathway. Comparative genomics show that Acr, mWL, and β-oxidation are restricted to one family of Hadarchaeota, which we propose as Ca. Cerberiarchaeaceae. Phylogenetic analyses further indicate that the mWL pathway is basal to all Hadarchaeota. By contrast, the carbon monoxide dehydrogenase/acetyl-coenzyme A synthase complex in Ca. Cerberiarchaeaceae was horizontally acquired from Bathyarchaeia. The Acr and β-oxidation genes of Ca. Cerberiarchaeaceae are highly similar to those of other alkane-oxidizing archaea such as Ca. Methanoliparia and Ca. Helarchaeales. Our results support the use of Acrs in the degradation of petroleum alkanes and suggest a role of Hadarchaeota in oil-rich environments.}, } @article {pmid38365229, year = {2024}, author = {Miksch, S and Orellana, LH and Oggerin de Orube, M and Vidal-Melgosa, S and Solanki, V and Hehemann, JH and Amann, R and Knittel, K}, title = {Taxonomic and functional stability overrules seasonality in polar benthic microbiomes.}, journal = {The ISME journal}, volume = {18}, number = {1}, pages = {}, doi = {10.1093/ismejo/wrad005}, pmid = {38365229}, issn = {1751-7370}, support = {//Max Planck Society/ ; //MARUM Center for Marine Environmental Science/ ; //Andreas Rühl foundation/ ; 2077//DFG Exzellenzcluster/ ; HE 7217/5-1//DFG Heisenberg program/ ; HE 7217/1-1//DFG Emmy Noether program/ ; }, abstract = {Coastal shelf sediments are hot spots of organic matter mineralization. They receive up to 50% of primary production, which, in higher latitudes, is strongly seasonal. Polar and temperate benthic bacterial communities, however, show a stable composition based on comparative 16S rRNA gene sequencing despite different microbial activity levels. Here, we aimed to resolve this contradiction by identifying seasonal changes at the functional level, in particular with respect to algal polysaccharide degradation genes, by combining metagenomics, metatranscriptomics, and glycan analysis in sandy surface sediments from Isfjorden, Svalbard. Gene expressions of diverse carbohydrate-active enzymes changed between winter and spring. For example, β-1,3-glucosidases (e.g. GH30, GH17, GH16) degrading laminarin, an energy storage molecule of algae, were elevated in spring, while enzymes related to α-glucan degradation were expressed in both seasons with maxima in winter (e.g. GH63, GH13_18, and GH15). Also, the expression of GH23 involved in peptidoglycan degradation was prevalent, which is in line with recycling of bacterial biomass. Sugar extractions from bulk sediments were low in concentrations during winter but higher in spring samples, with glucose constituting the largest fraction of measured monosaccharides (84% ± 14%). In porewater, glycan concentrations were ~18-fold higher than in overlying seawater (1107 ± 484 vs. 62 ± 101 μg C l-1) and were depleted in glucose. Our data indicate that microbial communities in sandy sediments digest and transform labile parts of photosynthesis-derived particulate organic matter and likely release more stable, glucose-depleted residual glycans of unknown structures, quantities, and residence times into the ocean, thus modulating the glycan composition of marine coastal waters.}, } @article {pmid38364918, year = {2024}, author = {Wang, S and Zhang, M and Chen, X and Bi, Y and Meng, F and Wang, C and Liu, L and Wang, S}, title = {Effect of biochar on the SPNA system at the ambient temperature.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {141465}, doi = {10.1016/j.chemosphere.2024.141465}, pmid = {38364918}, issn = {1879-1298}, abstract = {Biochar has been extensively studied in wastewater treatment systems. However, role of biochar in the single-stage partial nitritation anammox (SPNA) system remains not fully understood. This study explored the impact of biochar on the SPNA at ambient temperatures (20 °C and 15 °C). The nitrogen removal rate of the system raised from 0.43 to 0.50 g N/(L·d) as the biochar addition was raised from 2 to 4 g/L. Metagenomic analysis revealed that gene abundances of amino sugar metabolism and nucleotide sugar metabolism, amino acid metabolism, and quorum sensing were decreased after the addition of biochar. However, the gene abundance of enzymes synthesizing NADH and trehalose increased, suggesting that biochar could stimulate electron transfer reactions in microbial metabolism and help microorganisms to maintain steady state at lower temperature. The findings of this study offer valuable insights into the mechanism behind the improved nitrogen removal facilitated by biochar in the single-stage partial nitritation anammox system.}, } @article {pmid38364580, year = {2024}, author = {Cai, Q and Shi, C and Cao, Z and Li, Z and Zhao, HP and Yuan, S}, title = {Electrokinetic bioremediation of trichloroethylene and Cr/As co-contaminated soils with elevated sulfate.}, journal = {Journal of hazardous materials}, volume = {468}, number = {}, pages = {133761}, doi = {10.1016/j.jhazmat.2024.133761}, pmid = {38364580}, issn = {1873-3336}, abstract = {Co-contaminants and complex subsurface conditions pose great challenges to site remediation. This study demonstrates the potential of electrokinetic bioremediation (EK-BIO) in treating co-contaminants of chlorinated solvents and heavy metals in low-permeability soils with elevated sulfate. EK-BIO columns were filled with field soils, and were fed by the electrolyte containing 20 mg/L trichloroethylene (TCE), 250 μM Cr(VI), 25 μM As(III), 10 mM lactate, and 10 mM sulfate. A dechlorinating consortium containing Dehalococcoides (Dhc) was injected several times during a 199-d treatment at ∼1 V/cm. Sulfate reduction, Cr/As immobilization, and complete TCE biodechlorination were observed sequentially. EK-BIO facilitated the delivery of lactate, Cr(VI)/As(III), and sulfate to the soils, creating favorable reductive conditions for contaminant removal. Supplementary batch experiments and metagenomic/transcriptomic analysis suggested that sulfate promoted the reductive immobilization of Cr(VI) by generating sulfide species, which subsequently enhanced TCE biodechlorination by alleviating Cr(VI) toxicity. The dechlorinating community displayed a high As(III) tolerance. Metagenomic binning analysis revealed the dechlorinating activity of Dhc and the potential synergistic effects from other bacteria in mitigating heavy metal toxicity. This study justified the feasibility of EK-BIO for co-contaminant treatment and provided mechanistic insights into EK-BIO treatment.}, } @article {pmid38364107, year = {2024}, author = {Song, J and Dong, X and Lan, Y and Lu, Y and Liu, X and Kang, X and Huang, Z and Yue, B and Liu, Y and Ma, W and Zhang, L and Yan, H and He, M and Fan, Z and Guo, T}, title = {Interpretation of vaginal metagenomic characteristics in different types of vaginitis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0137723}, doi = {10.1128/msystems.01377-23}, pmid = {38364107}, issn = {2379-5077}, abstract = {Although vaginitis is closely related to vaginal microecology in females, the precise composition and functional potential of different types of vaginitis remain unclear. Here, metagenomic sequencing was applied to analyze the vaginal flora in patients with various forms of vaginitis, including cases with a clue cell proportion ranging from 1% to 20% (Clue1_20), bacterial vaginitis (BV), vulvovaginal candidiasis (VVC), and BV combined with VVC (VVC_BV). Our results identified Prevotella as an important biomarker between BV and Clue1_20. Moreover, a gradual decrease was observed in the relative abundance of shikimic acid metabolism associated with bacteria producing indole as well as a decline in the abundance of Gardnerella vaginalis in patients with BV, Clue1_20, and healthy women. Interestingly, the vaginal flora of patients in the VVC_BV group exhibited structural similarities to that of the VVC group, and its potentially functional characteristics resembled those of the BV and VVC groups. Finally, Lactobacillus crispatus was found in high abundance in healthy samples, greatly contributing to the stability of the vaginal environment. For the further study of L. crispatus, we isolated five strains of L. crispatus from healthy samples and evaluated their capacity to inhibit G. vaginalis biofilms and produce lactic acid in vitro to select the potential probiotic candidate for improving vaginitis in future clinical studies. Overall, we successfully identified bacterial biomarkers of different vaginitis and characterized the dynamic shifts in vaginal flora between patients with BV and healthy females. This research advances our understanding and holds great promise in enhancing clinical approaches for the treatment of vaginitis.IMPORTANCEVaginitis is one of the most common gynecological diseases, mostly caused by infections of pathogens such as Candida albicans and Gardnerella vaginalis. In recent years, it has been found that the stability of the vaginal flora plays an important role in vaginitis. Furthermore, the abundant Lactobacillus-producing rich lactic acid in the vagina provides a healthy acidic environment such as Lactobacillus crispatus. The metabolites of Lactobacillus can inhibit the colonization of pathogens. Here, we collected the vaginal samples of patients with bacterial vaginitis (BV), vulvovaginal candidiasis (VVC), and BV combined with VVC to discover the differences and relationships among the different kinds of vaginitis by metagenomic sequencing. Furthermore, because of the importance of L. crispatus in promoting vaginal health, we isolated multiple strains from vaginal samples of healthy females and chose the most promising strain with potential probiotic benefits to provide clinical implications for treatment strategies.}, } @article {pmid38363904, year = {2024}, author = {Xia, Q and Gu, M and Xu, Y and Sang, H and Lin, W and Wang, Y and Liu, K}, title = {Unmasking the invisible enemy: A case report of metagenomics-guided diagnosis and treatment of neonatal septic meningitis caused by Corynebacterium aurimucosum in a preterm infant with neonatal lupus erythematosus.}, journal = {Medicine}, volume = {103}, number = {7}, pages = {e35968}, pmid = {38363904}, issn = {1536-5964}, abstract = {RATIONALE: Neonatal septic meningitis is a serious condition that can be caused by various pathogens, including Corynebacterium aurimucosum, a rare and opportunistic bacterium. We reports a case of infectious meningitis in a premature infant with neonatal lupus erythematosus caused by C aurimucosum. The purpose of this study is to explore the occurrence of meningitis caused by C aurimucosum in preterm infants with neonatal lupus erythematosus. We found that early diagnosis and treatment are crucial for this type of meningitis, especially for infants with impaired immunity or mothers receiving immunosuppressive therapy. This bacterium is rare in clinical practice, but it needs to be taken seriously.

PATIENT CONCERNS: The infant was born to a mother with systemic lupus erythematosus who had a history of long-term immunosuppressive therapy. The infant presented with preterm birth, purplish-red skin, fever, and widespread scarlet dermatitis. He also had positive anti-Ro/SSA and anti-La/SSB antibodies.

DIAGNOSIS: The infant was diagnosed with neonatal lupus erythematosus based on clinical and serological features. A lumbar puncture revealed septic meningitis with high levels of total nucleated cells, protein, and Pan's test in the CSF. The macrogenic examination identified C aurimucosum as the causative agent. The culture of the mother's vaginal secretion also revealed the same bacterium.

INTERVENTIONS: The infant was treated with anti-infective therapy with ceftriaxone, ampicillin, vancomycin, and meropenem. He also received prednisone and gammaglobulin infusion for neonatal lupus erythematosus.

OUTCOMES: The infant's temperature returned to normal, and his general condition and responsiveness improved. The CSF cytology and biochemistry normalized, and the culture was negative. The cranial MRI examination showed no abnormalities. The red rash disappeared, and the follow-ups after discharge revealed no complications.

LESSONS: This case highlights the importance of early diagnosis and treatment of neonatal septic meningitis caused by C aurimucosum, especially in infants with immunocompromised conditions or maternal history of immunosuppressive therapy. C aurimucosum should not be overlooked as a potential pathogen in neonatal septic meningitis.}, } @article {pmid38363349, year = {2024}, author = {Yang, W and Cui, H and Liu, Q and Wang, F and Liao, H and Lu, P and Qin, S}, title = {Effect of nitrogen reduction by chemical fertilization with green manure (Vicia sativa L.) on soil microbial community, nitrogen metabolism and and yield of Uncaria rhynchophylla by metagenomics.}, journal = {Archives of microbiology}, volume = {206}, number = {3}, pages = {106}, pmid = {38363349}, issn = {1432-072X}, support = {[2020]4Y100 and [2018]5768-06//Department of Science and Technology of Guizhou Province and Guizhou Academy of Agricultural Sciences/ ; CARS-22//China Agriculture Research System-Green Manure/ ; }, abstract = {Uncaria rhynchophylla is an important herbal medicine, and the predominant issues affecting its cultivation include a single method of fertilizer application and inappropriate chemical fertilizer application. To reduce the use of inorganic nitrogen fertilization and increase the yield of Uncaria rhynchophylla, field experiments in 2020-2021 were conducted. The experimental treatments included the following categories: S1, no fertilization; S2, application of chemical NPK fertilizer; and S3-S6, application of chemical fertilizers and green manures, featuring nitrogen fertilizers reductions of 0%, 15%, 30%, and 45%, respectively. The results showed that a moderate application of nitrogen fertilizer when combined with green manure, can help alleviate soil acidification and increase urease activity. Specifically, the treatment with green manure provided in a 14.71-66.67% increase in urease activity compared to S2. Metagenomics sequencing results showed a decrease in diversity in S3, S4, S5, and S6 compared to S2, but the application of chemical fertilizer with green manure promoted an increase in the relative abundance of Acidobacteria and Chloroflexi. In addition, the nitrification pathway displayed a progressive augmentation in tandem with the reduction in nitrogen fertilizer and application of green manure, reaching its zenith at S5. Conversely, other nitrogen metabolism pathways showed a decline in correlation with diminishing nitrogen fertilizer dosages. The rest of the treatments showed an increase in yield in comparison to S1, S5 showing significant differences (p < 0.05). In summary, although S2 demonstrate the ability to enhance soil microbial diversity, it is important to consider the long-term ecological impacts, and S5 may be a better choice.}, } @article {pmid38362324, year = {2023}, author = {Marín, MDC and Jaffe, AL and West, PT and Konno, M and Banfield, JF and Inoue, K}, title = {Biophysical characterization of microbial rhodopsins with DSE motif.}, journal = {Biophysics and physicobiology}, volume = {20}, number = {Supplemental}, pages = {e201023}, doi = {10.2142/biophysico.bppb-v20.s023}, pmid = {38362324}, issn = {2189-4779}, abstract = {Microbial rhodopsins are photoreceptive transmembrane proteins that transport ions or regulate other intracellular biological processes. Recent genomic and metagenomic analyses found many microbial rhodopsins with unique sequences distinct from known ones. Functional characterization of these new types of microbial rhodopsins is expected to expand our understanding of their physiological roles. Here, we found microbial rhodopsins having a DSE motif in the third transmembrane helix from members of the Actinobacteria. Although the expressed proteins exhibited blue-green light absorption, either no or extremely small outward H[+] pump activity was observed. The turnover rate of the photocycle reaction of the purified proteins was extremely slow compared to typical H[+] pumps, suggesting these rhodopsins would work as photosensors or H[+] pumps whose activities are enhanced by an unknown regulatory system in the hosts. The discovery of this rhodopsin group with the unique motif and functionality expands our understanding of the biological role of microbial rhodopsins.}, } @article {pmid38362158, year = {2023}, author = {Pang, F and Xu, W and Zhao, H and Chen, S and Tian, Y and Fu, J and You, Z and Song, P and Xian, Q and Zhao, Q and Wang, C and Jia, X}, title = {Comprehensive evaluation of plasma microbial cell-free DNA sequencing for predicting bloodstream and local infections in clinical practice: a multicenter retrospective study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1256099}, doi = {10.3389/fcimb.2023.1256099}, pmid = {38362158}, issn = {2235-2988}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) of plasma cell-free DNA (cfDNA) shows promising application for complicated infections that cannot be resolved by conventional microbiological tests (CMTs). The criteria for cfDNA sequencing are currently in need of agreement and standardization.

METHODS: We performed a retrospective cohort observation of 653 patients who underwent plasma cfDNA mNGS, including 431 with suspected bloodstream infections (BSI) and 222 with other suspected systemic infections. Plasma mNGS and CMTs were performed simultaneously in clinical practice. The diagnostic efficacy of plasma mNGS and CMTs in the diagnosis of blood-borne and other systemic infections was evaluated using receiver operating characteristic (ROC) curves. The sensitivity and specificity of the two methods were analyzed based on the final clinical outcome as the gold standard.

RESULTS: The mNGS test showed an overall positive rate of 72.3% (472/653) for detecting microorganisms in plasma cfDNA, with a range of 2 to 6 different microorganisms detected in 171 patient specimens. Patients with positive mNGS results were more immunocompromised and had a higher incidence of severe disease (P<0·05). The sensitivity of mNGS was higher for BSI (93·5%) and other systemic infections (83·6%) compared to CMTs (37·7% and 14·3%, respectively). The mNGS detected DNA from a total of 735 microorganisms, with the number of microbial DNA reads ranging from 3 to 57,969, and a higher number of reads being associated with clinical infections (P<0·05). Of the 472 patients with positive mNGS results, clinical management was positively affected in 203 (43%) cases. Negative mNGS results led to a modified clinical management regimen in 92 patients (14.1%). The study also developed a bacterial and fungal library for plasma mNGS and obtained comparisons of turnaround times and detailed processing procedures for rare pathogens.

CONCLUSION: Our study evaluates the clinical use and analytic approaches of mNGS in predicting bloodstream and local infections in clinical practice. Our results suggest that mNGS has higher positive predictive values (PPVs) for BSI and systemic infections compared to CMTs, and can positively affect clinical management in a significant number of patients. The standardized whole-process management procedure for plasma mNGS developed in this study will ensure improved pre-screening probabilities and yield clinically valuable data.}, } @article {pmid38361822, year = {2024}, author = {Howell, AA and Versoza, CJ and Pfeifer, SP}, title = {Computational host range prediction-The good, the bad, and the ugly.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {vead083}, doi = {10.1093/ve/vead083}, pmid = {38361822}, issn = {2057-1577}, abstract = {The rapid emergence and spread of antimicrobial resistance across the globe have prompted the usage of bacteriophages (i.e. viruses that infect bacteria) in a variety of applications ranging from agriculture to biotechnology and medicine. In order to effectively guide the application of bacteriophages in these multifaceted areas, information about their host ranges-that is the bacterial strains or species that a bacteriophage can successfully infect and kill-is essential. Utilizing sixteen broad-spectrum (polyvalent) bacteriophages with experimentally validated host ranges, we here benchmark the performance of eleven recently developed computational host range prediction tools that provide a promising and highly scalable supplement to traditional, but laborious, experimental procedures. We show that machine- and deep-learning approaches offer the highest levels of accuracy and precision-however, their predominant predictions at the species- or genus-level render them ill-suited for applications outside of an ecosystems metagenomics framework. In contrast, only moderate sensitivity (<80 per cent) could be reached at the strain-level, albeit at low levels of precision (<40 per cent). Taken together, these limitations demonstrate that there remains room for improvement in the active scientific field of in silico host prediction to combat the challenge of guiding experimental designs to identify the most promising bacteriophage candidates for any given application.}, } @article {pmid38361820, year = {2024}, author = {Débarre, F}, title = {What we can and cannot learn from SARS-CoV-2 and animals in metagenomic samples from the Huanan market.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {vead077}, doi = {10.1093/ve/vead077}, pmid = {38361820}, issn = {2057-1577}, abstract = {While the exact context of the emergence of SARS-CoV-2 remains uncertain, data accumulated since 2020 have provided an increasingly more precise picture of Wuhan's Huanan Seafood Wholesale Market, to which the earliest clusters of human cases of Covid-19 were linked. After the market closed on January 1st 2020, teams from the Chinese Center for Disease Control and Prevention collected environmental samples, and sequenced them. Metagenomic sequencing data from these samples were shared in early 2023. These data confirmed that non-human animals susceptible to SARS-CoV-2 were present in the market before it closed, but also that these animals were located in the side of the market with most human cases, and in a corner with comparatively more SARS-CoV-2-positive environmental samples. The environmental samples were however collected after abundant human-to-human transmission had taken place in the market, precluding any identification of a non-human animal host. Jesse Bloom recently investigated associations between SARS-CoV-2 and non-human animals, concluding that the data failed to indicate whether non-human animals were infected by SARS-CoV-2, despite this being an already acknowledged limitation of the data. Here I explain why a correlation analysis could not confidently conclude which hosts(s) may have shed SARS-CoV-2 in the market, and I rebut the suggestion that such analyses had been encouraged. I show that Bloom's investigation ignores the temporal and spatial structure of the data, which led to incorrect interpretations. Finally, I show that criteria put forward by Bloom to identify the host(s) that shed environmental SARS-CoV-2 would also exclude humans. Progress on the topic of SARS-CoV-2's origin requires a clear distinction between scientific studies and news articles (mis)interpreting them.}, } @article {pmid38361815, year = {2024}, author = {Bloom, JD}, title = {Importance of quantifying the number of viral reads in metagenomic sequencing of environmental samples from the Huanan Seafood Market.}, journal = {Virus evolution}, volume = {10}, number = {1}, pages = {vead089}, doi = {10.1093/ve/vead089}, pmid = {38361815}, issn = {2057-1577}, abstract = {In March 2023, the Chinese CDC publicly released raw metagenomic sequencing data for environmental samples collected in early 2020 from the Huanan Seafood Market. Prior to that data release, some scientists had suggested that these samples could be informative for establishing if animals such as raccoon dogs had been infected with severe acute respiratory syndrome virus 2 (SARS-CoV-2). However, no one had analyzed how much SARS-CoV-2 was actually present in the metagenomic sequencing data. After the raw data became available, I fully analyzed the abundance of both viral and animal genetic material in the samples. That analysis, which was published in Virus Evolution, found that the SARS-CoV-2 content of most samples was very low and that the abundance of SARS-CoV-2 was most strongly associated with animals such as largemouth bass that are not plausible candidates for having been infected. Based on these results, I concluded that the metagenomic content of the samples was not informative for determining if any non-human animals in the market had been infected with SARS-CoV-2. One of the authors of an earlier study of these samples, Florence Débarre, recently submitted a response to my paper. Here, I reply in turn to explain why it is important to quantify the abundance of viral material before drawing conclusions from metagenomic sequencing. I also report new analyses of other animal coronaviruses in the samples and show that material from some other animal coronaviruses is much more abundant than SARS-CoV-2 in samples collected on the date when most wildlife stall sampling was performed. I further show that material from some of these animal coronaviruses is associated with the animals they probably infect but that no such association exists for SARS-CoV-2. Overall, these new analyses further emphasize the importance of quantifying the actual amount of viral material in metagenomic samples and underscore why the environmental samples from the Huanan Seafood Market are not informative for determining if any non-human animals were infected with SARS-CoV-2.}, } @article {pmid38361648, year = {2024}, author = {Pessi, IS and Rutanen, A and Hultman, J}, title = {Metagenome-assembled genomes from mineral tundra soils in Rásttigáisá, northern Norway.}, journal = {Access microbiology}, volume = {6}, number = {1}, pages = {}, pmid = {38361648}, issn = {2516-8290}, abstract = {Microbial communities in tundra soils remain largely unknown despite their important roles in the cycling of greenhouse gases. Here, we report 59 non-redundant metagenome-assembled genomes (MAGs) recovered from mineral tundra soils in Rásttigáisá, northern Norway. The MAGs were obtained by clustering contigs according to tetranucleotide frequency and differential coverage and were manually curated to remove contigs with outlying GC content and/or mean coverage. Most MAGs were assigned to the bacterial phyla Candidatus Dormibacterota (n=12), Verrucomicrobiota (n=10), and Acidobacteriota (n=9). All archaeal MAGs (n=4) belong to the genus Candidatus Nitrosopolaris (phylum Thermoproteota). The 59 Rásttigáisá MAGs expand our knowledge of the diversity and ecological roles of tundra microbiomes.}, } @article {pmid38361608, year = {2024}, author = {Gustafson, KL and McAdams, ZL and Russell, AL and Dorfmeyer, RA and Turner, GM and Ericsson, AC}, title = {Effect size of delayed freezing, diurnal variation, and hindgut location on the mouse fecal microbiome.}, journal = {iScience}, volume = {27}, number = {3}, pages = {109090}, doi = {10.1016/j.isci.2024.109090}, pmid = {38361608}, issn = {2589-0042}, abstract = {Practical considerations in fecal sample collection for microbiome research include time to sample storage, time of collection, and hindgut position during terminal collections. Here, parallel experiments were performed to investigate the relative effect of these factors on microbiome composition in mice colonized with two different vendor-origin microbiomes. 16S rRNA amplicon sequencing of immediately flash-frozen feces showed no difference in alpha or beta diversity compared to samples incubated up to 9 h at room temperature. Samples collected in the morning showed greater alpha diversity compared to samples collected in the afternoon. While a significant effect of time was detected in all hindgut regions, the effect increased from cecum to distal colon. This study highlights common scenarios in microbiome research that may affect outcome measures of microbial community analysis. However, we demonstrate a relatively low effect size of these technical factors when compared to a primary experimental factor with large intergroup variability.}, } @article {pmid38360413, year = {2024}, author = {Wang, W and Jiang, T and Wang, S and Wang, L and Li, Z and Li, W and Wang, B}, title = {Low alkalinity, free ammonia, and free nitrous acid cooperatively stabilize partial nitrification under excessive aeration condition.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {141447}, doi = {10.1016/j.chemosphere.2024.141447}, pmid = {38360413}, issn = {1879-1298}, abstract = {In this study, a lab-scale sequencing batch reactor (SBR) was established to assess the feasibility of maintaining partial nitrification in treating high-ammonium wastewater under the condition of excessive aeration (1 L/min, 1289 min). Results showed that the average ammonia (NH4[+]-N) removal efficiency (ARE) was 93.4 ± 2.7% and the average nitrite accumulation ratio (NAR) was 90.7 ± 2.8% during 15-50 d. In a typical cycle, free ammonia (FA) and free nitrous acid (FNA) alternately inhibited the activity of nitrite oxidizing bacteria (NOB), while low alkalinity limited further nitrification at even excessive aeration. Metagenomic analysis revealed that the relative abundance of Nitrosomonas, as the ammonia oxidizing bacteria (AOB), was up to 1.61%, while NOB were not detected. Taken together, this study indicated partial nitrification was almost not affected by excessive aeration, demonstrating its robustness depending on the cooperative strategy of the low alkalinity limitation and the inhibition of FA and FNA.}, } @article {pmid38360319, year = {2024}, author = {Liu, Y and Liu, R and Feng, Z and Hu, R and Zhao, F and Wang, J}, title = {Regulation of wheat growth by soil multifunctionality and metagenomic-based microbial functional profiles under mulching treatments.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170881}, doi = {10.1016/j.scitotenv.2024.170881}, pmid = {38360319}, issn = {1879-1026}, abstract = {Soil microbial functional genes play key roles in biogeochemical processes that are closely related to crop development. However, the regulation of crop growth by the composition and potential interactions of metagenomic-based functional genes is poorly understood. Therefore, in a long-term mulching experiment, the regulation of wheat growth by soil multifunctionality, microbial functional profiles driven by soil properties and microbial activity was studied. Soil properties and microbial activity were significantly separated into distinct mulching treatments, and were significantly declined by plastic film mulching treatment, similar to soil multifunctionality. Only carbon (C) and phosphorus (P) cycling gene compositions were divided significantly into distinct mulching treatments to varying degrees. Similarly, intra- and inter-connected sub-networks associated with C and P cycling genes were more complex and stable than the sub-networks containing nitrogen cycling genes. Despite core functional genes being located in the middle of each network, they were rarely observed in the metagenomic assembly genomes. Subsequently, the dominant soil properties and microbial activity had greater effects on C cycling gene composition and network, which played essential roles in wheat growth regulation. Overall, wheat yield and biomass were affected differently by straw and plastic film mulching treatments, and were mainly regulated by C cycling gene network and soil multifunctionality, respectively. The results of the present study provide novel insights into wheat growth regulation by soil microbial functional profiles, with potential implications for sustainable crop production in mulching conservation agroecosystems.}, } @article {pmid37906837, year = {2024}, author = {Andersson, L and Bekkevold, D and Berg, F and Farrell, ED and Felkel, S and Ferreira, MS and Fuentes-Pardo, AP and Goodall, J and Pettersson, M}, title = {How Fish Population Genomics Can Promote Sustainable Fisheries: A Road Map.}, journal = {Annual review of animal biosciences}, volume = {12}, number = {}, pages = {1-20}, doi = {10.1146/annurev-animal-021122-102933}, pmid = {37906837}, issn = {2165-8110}, mesh = {Animals ; *Ecosystem ; *Fisheries ; Metagenomics ; Whole Genome Sequencing/veterinary ; }, abstract = {Maintenance of genetic diversity in marine fishes targeted by commercial fishing is a grand challenge for the future. Most of these species are abundant and therefore important for marine ecosystems and food security. Here, we present a road map of how population genomics can promote sustainable fisheries. In these species, the development of reference genomes and whole genome sequencing is key, because genetic differentiation at neutral loci is usually low due to large population sizes and gene flow. First, baseline allele frequencies representing genetically differentiated populations within species must be established. These can then be used to accurately determine the composition of mixed samples, forming the basis for population demographic analysis to inform sustainably set fish quotas. SNP-chip analysis is a cost-effective method for determining baseline allele frequencies and for population identification in mixed samples. Finally, we describe how genetic marker analysis can transform stock identification and management.}, } @article {pmid38359904, year = {2024}, author = {Parvin, N and Mandal, S and Rath, J}, title = {Microbiome of seventh-century old Parsurameswara stone monument of India and role of desiccation-tolerant cyanobacterium Lyngbya corticicola on its biodeterioration.}, journal = {Biofouling}, volume = {}, number = {}, pages = {1-14}, doi = {10.1080/08927014.2024.2305381}, pmid = {38359904}, issn = {1029-2454}, abstract = {The Parsurameswara stone monument, built in the seventh century, is one of the oldest stone monuments in Odisha, India. Metagenomic analysis of the biological crust samples collected from the stone monument revealed 17 phyla in the microbiome, with Proteobacteria being the most dominant phylum, followed by cyanobacteria. Eight cyanobacteria were isolated. Lyngbya corticicola was the dominant cyanobacterium in all crust samples and could tolerate six months of desiccation in vitro. With six months of desiccation, chlorophyll-a decreased; however, carotenoid and cellular carbohydrate contents of this organism increased in the desiccated state. Resistance to desiccation, high carotenoid content, and effective trehalose biosynthesis in this cyanobacterium provide a distinct advantage over other microbiomes. Comparative metabolic profiles of the biological crust and L. corticicola show strongly corrosive organic acids such as dichloroacetic acid, which might be responsible for the biocorrosion of stone monuments.}, } @article {pmid38359677, year = {2024}, author = {Yu, Y and Zhou, B and Xu, W and Li, L and Jin, X and Ji, Y and Ge, Y}, title = {Diagnosis of an immunocompetent adult with acute headache and fever as Epstein-Barr virus encephalitis by mNGS of cerebrospinal fluid.}, journal = {Diagnostic microbiology and infectious disease}, volume = {109}, number = {1}, pages = {116213}, doi = {10.1016/j.diagmicrobio.2024.116213}, pmid = {38359677}, issn = {1879-0070}, abstract = {Complicated case with fever or headache of unknown origin is currently one of the main challenges in clinical diagnosis. A retrospective analysis was conducted on a 27-year-old female patient hospitalized with headache and fever, and the pathogen species were ultimately determined by metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF). The culture results of CSF showed no bacterial or fungal growth. CSF cytology showed a significant increase in nucleated cells. Pathogenic index (corresponded to human gamma herpesvirus 4) of the microorganism after correcting for human background was 12846.77 with a host index (human resource) of 27822.48 by mNGS of CSF. The patient improved through antiviral treatment with ganciclovir. Epstein-Barr virus encephalitis is rare in immunocompetent adults, which can easily cause misdiagnosis and should be paid attention to. mNGS of CSF has significant advantages in the diagnosis of Epstein-Barr virus encephalitis.}, } @article {pmid38359595, year = {2024}, author = {Cha, G and Zhu, KJ and Fischer, JM and Flores, CI and Brown, J and Pinto, A and Hatt, JK and Konstantinidis, KT and Graham, KE}, title = {Metagenomic evaluation of the performance of passive Moore swabs for sewage monitoring relative to composite sampling over time resolved deployments.}, journal = {Water research}, volume = {253}, number = {}, pages = {121269}, doi = {10.1016/j.watres.2024.121269}, pmid = {38359595}, issn = {1879-2448}, abstract = {Moore swabs have re-emerged as a versatile tool in the field of wastewater-based epidemiology during the COVID-19 pandemic and offer unique advantages for monitoring pathogens in sewer systems, especially at the neighborhood-level. However, whether Moore swabs provide comparable results to more commonly used composite samples remains to be rigorously tested including the optimal duration of Moore swab deployment. This study provides new insights into these issues by comparing the results from Moore swab samples to those of paired composite samples collected from the same sewer lines continuously over six to seventy-two hours post-deployment, during low COVID-19 prevalence periods. Our results show that Moore swabs accumulated approximately 10-fold higher PMMoV concentrations (on a basis of mL of Moore swab squeezed filtrate to mL of composite sewage) and showed comparable trends in terms of bacterial species abundance when compared to composite samples. Moore swabs also generally captured higher SARS-CoV-2 N1/N2 RNA concentrations than composite samples. Moore swabs showed comparable trends in terms of abundance dynamics of the sewage microbiome to composite samples and variable signs of saturation over time that were site and/or microbial population-specific. Based on our dual ddRT-PCR and shotgun metagenomic approach, we find that Moore swabs at our sites were optimally deployed for 6 h at a time at two sites.}, } @article {pmid38359594, year = {2024}, author = {Wang, C and Yin, X and Xu, X and Wang, D and Liu, L and Zhang, X and Yang, C and Zhang, X and Zhang, T}, title = {Metagenomic absolute quantification of antibiotic resistance genes and virulence factor genes-carrying bacterial genomes in anaerobic digesters.}, journal = {Water research}, volume = {253}, number = {}, pages = {121258}, doi = {10.1016/j.watres.2024.121258}, pmid = {38359594}, issn = {1879-2448}, abstract = {Sewage treatment works have been considered as hotspots for the dissemination of antibiotic resistance genes (ARGs). Anaerobic digestion (AD) has emerged as a promising approach for controlling the spread of ARGs while destroying biomass in sludge. Evaluating the impact of AD on ARG removal relies on the absolute quantification of ARGs. In this study, we quantified the ARG concentrations in both full-scale and lab-scale AD systems using a cellular spike-ins based absolute quantification approach. Results demonstrated that AD effectively removed 68 ± 18 %, 55 ± 12 %, and 57 ± 19 % of total ARGs in semi-continuous AD digesters, with solid retention times of 15, 20, and 25 days, respectively. The removal efficiency of total ARGs increased as the AD process progressed in the batch digesters over 40 days. A significant negative correlation was observed between digestion time and the concentrations of certain ARG types, such as beta-lactam, sulfonamide, and tetracycline. However, certain potential pathogenic antibiotic resistant bacteria (PARB) and multi-resistant high-risk ARGs-carrying populations robustly persisted throughout the AD process, regardless of the operating conditions. This study highlighted the influence of the AD process and its operating parameters on ARG removal, and revealed the broad spectrum and persistence of PARB in AD systems. These findings provided critical insights for the management of microbial hazards.}, } @article {pmid38359578, year = {2024}, author = {Zhou, K and Zhou, H}, title = {Distribution patterns and functional diversity of DNA viruses determined by ecological niches in huge river ecosystems.}, journal = {Virology}, volume = {593}, number = {}, pages = {110015}, doi = {10.1016/j.virol.2024.110015}, pmid = {38359578}, issn = {1096-0341}, abstract = {While the vast number of DNA and RNA viruses participate in biogeochemical cycles in natural systems, little is known about virome in river ecosystems. Here, we analyzed the DNA viral composition and its metabolic potential in the Yangtze River, including freshwater (FW) and freshwater sediments (FWS). A total of 1237 river-derived virus contigs (RVCs) were obtained following de novo assembly from 62 metagenomics. We found that the viral diversity is significantly positively correlated longitudinally. Moreover, FW exhibited a greater viral variety and significantly different composition than FWS. The viral co-occurrence network suggested that positive correlations predominate between RVCs. Lastly, 1657 viral functions were predicted by gene ontology. Notably, 96 of 150 RVCs with higher weights identified by random-forest classier were more abundant in FW, which most engage organic cyclic compound metabolic processes and hydrolase activity. Together, this study highlights the previously unrecognized viruses and the importance of their distributions and functions in major river systems.}, } @article {pmid38359396, year = {2024}, author = {Li, Y and Qian, Z and Chen, H and Zhang, S and Wang, R and Yu, S and Chen, L and Wang, L and Xu, S and Tao, Y}, title = {The clinical value of β-D-glucan testing and next-generation metagenomic sequencing for the diagnosis of fungal endophthalmitis.}, journal = {Retina (Philadelphia, Pa.)}, volume = {}, number = {}, pages = {}, doi = {10.1097/IAE.0000000000004073}, pmid = {38359396}, issn = {1539-2864}, abstract = {PURPOSE: To explore the clinical value of β-D-glucan (BDG) testing and next-generation metagenomic sequencing (mNGS) for detecting the pathogens of fungal endophthalmitis (FE).

METHODS: This study included 32 cases (32 eyes) with FE and 20 cases (20 eyes) with intraocular inflammation caused by other etiologies. All patients underwent extraction of aqueous humor or vitreous fluid samples for BDG testing and mNGS. The diagnostic performance and total clinical concordance rate (TCCR) of BDG testing and mNGS for FE were evaluated and calculated based on the results of the clinical diagnosis.

RESULTS: Among the clinically diagnosed FE, the positivity rates of BDG testing and mNGS (90.63%) were both significantly higher (P<0.001) than that of microbial cultures (53.13%). There was 100% consistency in pathogen identification using mNGS and culture identification for culture-positive cases. The area under the curve (AUC) was 0.927 for BDG testing and 0.853 for mNGS. When the 2 tests were combined, the sensitivity (93.75%), specificity (100.00%), and TCCR (96.15%) were all improved compared with the single tests.

CONCLUSIONS: The positive rates of BDG test and mNGS were markedly higher than those of cultures in FE identification. The combination of these 2 tests showed improved performance when compared with individual tests.}, } @article {pmid38359370, year = {2024}, author = {Nguyen, SM and Tran, HTT and Long, J and Shrubsole, MJ and Cai, H and Yang, Y and Nguyen, LM and Nguyen, GH and Nguyen, CV and Ta, TV and Wu, J and Cai, Q and Zheng, W and Tran, TV and Shu, XO}, title = {Gut Microbiome of Patients With Breast Cancer in Vietnam.}, journal = {JCO global oncology}, volume = {10}, number = {}, pages = {e2300234}, doi = {10.1200/GO.23.00234}, pmid = {38359370}, issn = {2687-8941}, abstract = {PURPOSE: Gut microbiota play an important role in human health, including cancer. Cancer and its treatment, in turn, may alter the gut microbiome. To understand this complex relationship, we profiled the gut microbiome of 356 Vietnamese patients with breast cancer.

MATERIALS AND METHODS: Stool samples were collected before chemotherapy, with 162 pre- and 194 postsurgery. The gut microbiome was measured by shotgun metagenomic sequencing. Associations of gut microbial diversity, taxa abundance, and gut microbiome health index (GMHI) with sociodemographic, clinical factors, and tumor characteristics were evaluated.

RESULTS: Postsurgery samples were associated with significantly lower α- and β-diversities (P < .001) and showed significant differences in the abundance of 15% of 2,864 investigated taxa (false discovery rate [FDR] <0.1) compared with presurgery samples. An unhealthy gut microbiome was prevalent among patients with breast cancer, with a mean GMHI of -0.79 and -2.81 in pre- and postsurgery stool samples, respectively. In an analysis of 162 presurgery stool samples, diagnosis delay was significantly associated with lower α-diversity, variation in β-diversity, an increased abundance of species Enorma massiliensis, and a decreased abundance of Faecalicoccus pleomorphus. High intake of fiber was significantly associated with lower α-diversity and a higher abundance of species belonging to Bifidobacterium, Prevotella, and Bacteroides gena (FDR < 0.1). We did not find that cancer stage and subtype, menopausal status, comorbidity, antibiotic use during 3 months before stool collection, or physical activity was significantly associated with α- and β-diversities or GMHI although a few significant differences were observed in taxa abundance.

CONCLUSION: Our study revealed that diagnosis delay, high fiber intake, and breast cancer surgery, which is always followed by antibiotic prophylaxis in Vietnam, led to a less diverse and unhealthy gut microbiome among patients with breast cancer.}, } @article {pmid38358316, year = {2024}, author = {Wanghu, H and Li, Y and Huang, J and Pu, K and Guo, F and Zhong, P and Wang, T and Yuan, J and Yu, Y and Chen, J and Liu, J and Chen, JJ and Hu, C}, title = {A novel synthetic nucleic acid mixture for quantification of microbes by mNGS.}, journal = {Microbial genomics}, volume = {10}, number = {2}, pages = {}, doi = {10.1099/mgen.0.001199}, pmid = {38358316}, issn = {2057-5858}, abstract = {Metagenomic next-generation sequencing (mNGS) provides considerable advantages in identifying emerging and re-emerging, difficult-to-detect and co-infected pathogens; however, the clinical application of mNGS remains limited primarily due to the lack of quantitative capabilities. This study introduces a novel approach, KingCreate-Quantification (KCQ) system, for quantitative analysis of microbes in clinical specimens by mNGS, which co-sequence the target DNA extracted from the specimens along with a set of synthetic dsDNA molecules used as Internal-Standard (IS). The assay facilitates the conversion of microbial reads into their copy numbers based on IS reads utilizing a mathematical model proposed in this study. The performance of KCQ was systemically evaluated using commercial mock microbes with varying IS input amounts, different proportions of human genomic DNA, and at varying amounts of sequence analysis data. Subsequently, KCQ was applied in microbial quantitation in 36 clinical specimens including blood, bronchoalveolar lavage fluid, cerebrospinal fluid and oropharyngeal swabs. A total of 477 microbe genetic fragments were screened using the bioinformatic system. Of these 83 fragments were quantitatively compared with digital droplet PCR (ddPCR), revealing a correlation coefficient of 0.97 between the quantitative results of KCQ and ddPCR. Our study demonstrated that KCQ presents a practical approach for the quantitative analysis of microbes by mNGS in clinical samples.}, } @article {pmid38358269, year = {2024}, author = {Carter, KA and France, MT and Rutt, L and Bilski, L and Martinez-Greiwe, S and Regan, M and Brotman, RM and Ravel, J}, title = {Sexual transmission of urogenital bacteria: whole metagenome sequencing evidence from a sexual network study.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0003024}, doi = {10.1128/msphere.00030-24}, pmid = {38358269}, issn = {2379-5042}, abstract = {Sexual transmission of the urogenital microbiota may contribute to adverse sexual and reproductive health outcomes. The extent of sexual transmission of the urogenital microbiota is unclear as prior studies largely investigated specific pathogens. We used epidemiologic data and whole metagenome sequencing to characterize urogenital microbiota strain concordance between participants of a sexual network study. Individuals who screened positive for genital Chlamydia trachomatis were enrolled and referred their sexual contacts from the prior 60-180 days. Snowball recruitment of sexual contacts continued for up to four waves. Vaginal swabs and penile urethral swabs were collected for whole metagenome sequencing. We evaluated bacterial strain concordance using inStrain and network analysis. We defined concordance as ≥99.99% average nucleotide identity over ≥50% shared coverage; we defined putative sexual transmission as concordance between sexual contacts with <5 single-nucleotide polymorphisms per megabase. Of 138 participants, 74 (54%) were female; 120 (87%) had genital chlamydia; and 43 (31%) were recruited contacts. We identified 115 strain-concordance events among 54 participants representing 25 bacterial species. Seven events (6%) were between sexual contacts including putative heterosexual transmission of Fannyhessea vaginae, Gardnerella leopoldii, Prevotella amnii, Sneathia sanguinegens, and Sneathia vaginalis (one strain each), and putative sexual transmission of Lactobacillus iners between female contacts. Most concordance events (108, 94%) were between non-contacts, including eight female participants connected through 18 Lactobacillus crispatus and 3 Lactobacillus jensenii concordant strains, and 14 female and 2 male participants densely interconnected through 52 Gardnerella swidsinskii concordance events.IMPORTANCEEpidemiologic evidence consistently indicates bacterial vaginosis (BV) is sexually associated and may be sexually transmitted, though sexual transmission remains subject to debate. This study is not capable of demonstrating BV sexual transmission; however, we do provide strain-level metagenomic evidence that strongly supports heterosexual transmission of BV-associated species. These findings strengthen the evidence base that supports ongoing investigations of concurrent male partner treatment for reducing BV recurrence. Our data suggest that measuring the impact of male partner treatment on F. vaginae, G. leopoldii, P. amnii, S. sanguinegens, and S. vaginalis may provide insight into why a regimen does or does not perform well. We also observed a high degree of strain concordance between non-sexual-contact female participants. We posit that this may reflect limited dispersal capacity of vaginal bacteria coupled with individuals' comembership in regional transmission networks where transmission may occur between parent and child at birth, cohabiting individuals, or sexual contacts.}, } @article {pmid38358052, year = {2024}, author = {Kakouridis, A and Yuan, M and Nuccio, EE and Hagen, JA and Fossum, CA and Moore, ML and Estera-Molina, KY and Nico, PS and Weber, PK and Pett-Ridge, J and Firestone, MK}, title = {Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral-associated organic matter.}, journal = {The New phytologist}, volume = {}, number = {}, pages = {}, doi = {10.1111/nph.19560}, pmid = {38358052}, issn = {1469-8137}, support = {DE-AC52-07NA27344//US Department of Energy/ ; DE-SC0016247//US Department of Energy, Awards to UC Berkeley/ ; DE-SC0020163//US Department of Energy, Awards to UC Berkeley/ ; SCW1589//US Department of Energy, Awards to LLNL:/ ; SCW1678//US Department of Energy, Awards to LLNL:/ ; }, abstract = {Arbuscular mycorrhizal fungi (AMF) transport substantial plant carbon (C) that serves as a substrate for soil organisms, a precursor of soil organic matter (SOM), and a driver of soil microbial dynamics. Using two-chamber microcosms where an air gap isolated AMF from roots, we [13] CO2 -labeled Avena barbata for 6 wk and measured the C Rhizophagus intraradices transferred to SOM and hyphosphere microorganisms. NanoSIMS imaging revealed hyphae and roots had similar [13] C enrichment. SOM density fractionation, [13] C NMR, and IRMS showed AMF transferred 0.77 mg C g[-1] of soil (increasing total C by 2% relative to non-mycorrhizal controls); 33% was found in occluded or mineral-associated pools. In the AMF hyphosphere, there was no overall change in community diversity but 36 bacterial ASVs significantly changed in relative abundance. With stable isotope probing (SIP)-enabled shotgun sequencing, we found taxa from the Solibacterales, Sphingobacteriales, Myxococcales, and Nitrososphaerales (ammonium oxidizing archaea) were highly enriched in AMF-imported [13] C (> 20 atom%). Mapping sequences from [13] C-SIP metagenomes to total ASVs showed at least 92 bacteria and archaea were significantly [13] C-enriched. Our results illustrate the quantitative and ecological impact of hyphal C transport on the formation of potentially protective SOM pools and microbial roles in the AMF hyphosphere soil food web.}, } @article {pmid38357923, year = {2024}, author = {Rodino, KG and Simner, PJ}, title = {Status check: next-generation sequencing for infectious-disease diagnostics.}, journal = {The Journal of clinical investigation}, volume = {134}, number = {4}, pages = {}, pmid = {38357923}, issn = {1558-8238}, abstract = {Next-generation sequencing (NGS) applications for the diagnostics of infectious diseases has demonstrated great potential with three distinct approaches: whole-genome sequencing (WGS), targeted NGS (tNGS), and metagenomic NGS (mNGS, also known as clinical metagenomics). These approaches provide several advantages over traditional microbiologic methods, though challenges still exist.}, } @article {pmid38357732, year = {2024}, author = {Virendra, A and Gulavane, SU and Ahmed, ZA and Reddy, R and Chaudhari, RJ and Gaikwad, SM and Shelar, RR and Ingole, SD and Thorat, VD and Khanam, A and Khan, FA}, title = {Metagenomic analysis unravels novel taxonomic differences in the uterine microbiome between healthy mares and mares with endometritis.}, journal = {Veterinary medicine and science}, volume = {10}, number = {2}, pages = {e1369}, doi = {10.1002/vms3.1369}, pmid = {38357732}, issn = {2053-1095}, abstract = {BACKGROUND: The application of high throughput technologies has enabled unravelling of unique differences between healthy mares and mares with endometritis at transcriptomic and proteomic levels. However, differences in the uterine microbiome are yet to be investigated.

OBJECTIVES: The present study was aimed at evaluating the differences in uterine microbiome between healthy mares and mares with endometritis.

METHODS: Low-volume lavage (LVL) samples were collected from the uterus of 30 mares classified into healthy (n = 15) and endometritis (n = 15) based on their reproductive history, intrauterine fluid accumulation, gross appearance of LVL samples, endometrial cytology and bacterial culture. The samples were subjected to 16S rRNA sequencing.

RESULTS: Notable differences in the uterine microbiome were observed between healthy mares and mares with endometritis at various taxonomic levels. In healthy mares, the most abundant phylum, class, order and family were Firmicutes, Bacilli, Bacillales and Paenibacillaceae, respectively. In contrast, the most abundant corresponding taxonomic levels in mares with endometritis were Proteobacteria, Gammaproteobacteria, Enterobacterales and Enterobacteriaceae, respectively. At the genus level, Brevibacillus and Paenibacillus were more abundant in healthy mares, whereas Escherichia, Salmonella and Klebsiella were more abundant in mares with endometritis. In healthy mares, Brevibacillus brevis was the most abundant species, followed by Brevibacillus choshinensis and Paenibacillus sp JDR-2. However, in mares with endometritis, Escherichia coli was the most abundant species, followed by Salmonella enterica and Klebsiella pneumoniae.

CONCLUSIONS: These results confirmed the previously reported presence of a uterine microbiome in healthy mares and helped unravel some alterations that occur in mares with endometritis. The findings can potentially help formulate new approaches to prevent or treat equine endometritis.}, } @article {pmid38357351, year = {2024}, author = {Antunes, A and de la Haba, RR and Jebbar, M and Hedlund, BP}, title = {Editorial: Community series-extremophiles: microbial genomics and taxogenomics, volume II.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1371210}, pmid = {38357351}, issn = {1664-302X}, } @article {pmid38356583, year = {2024}, author = {Pattarach, K and Surachat, K and Liu, SL and Mayakun, J}, title = {Water depth outweighs reef condition in shaping non-geniculate coralline algae-associated microbial communities in coral reefs: A case study from Thailand.}, journal = {Heliyon}, volume = {10}, number = {3}, pages = {e25486}, pmid = {38356583}, issn = {2405-8440}, abstract = {Red calcified non-geniculate coralline algae (NGCA) provide habitat structures, stabilize reef structures, and foster coral larval settlement and metamorphosis. Moreover, the microbes associated with NGCA are dependent on the NGCA host species and are affected by environmental factors; however, little is known about the influence of reef conditions and depth gradients on the associated microbial communities and NGCA. In this study, we collected NGCA under different reef conditions and depth gradients and characterized the microbial communities using the V3-V4 hypervariable regions of the 16S rRNA gene. Metagenomic analysis revealed 2 domains, 51 phyla, 123 classes, and 210 genera. The NGCA-associated bacterial communities were dominated by Proteobacteria, Bacteroidetes, Chloroflexi, Actinobacteria, and Acidobacteriota. Gammaproteobacteria and Alphaproteobacteria were the most abundant bacterial classes. Differences in microbial diversity and richness were not apparent between reef conditions and depth gradients. However, there was a significant difference in bacterial evenness among the depth gradients. The bacterial abundance associated with NGCA was greater in deep zones than in shallow zones. The shallow zone exhibited a greater relative abundance of all gene functions than the deep zone, indicating differences in the distribution of gene functions. This study showed that the microbial communities associated with red calcified NGCA are diverse, and that the depth gradient affects their abundance and evenness, highlighting the need for further research to understand the functional roles of these microbial communities in coral reef conservation.}, } @article {pmid38356108, year = {2024}, author = {Nweze, JE and Schweichhart, JS and Angel, R}, title = {Viral communities in millipede guts: Insights into the diversity and potential role in modulating the microbiome.}, journal = {Environmental microbiology}, volume = {26}, number = {2}, pages = {e16586}, doi = {10.1111/1462-2920.16586}, pmid = {38356108}, issn = {1462-2920}, support = {21-04987S//Czech Science Foundation (GA ČR)/ ; 19-24309Y//Grantová Agentura České Republiky/ ; }, abstract = {Millipedes are important detritivores harbouring a diverse microbiome. Previous research focused on bacterial and archaeal diversity, while the virome remained neglected. We elucidated the DNA and RNA viral diversity in the hindguts of two model millipede species with distinct microbiomes: the tropical Epibolus pulchripes (methanogenic, dominated by Bacillota) and the temperate Glomeris connexa (non-methanogenic, dominated by Pseudomonadota). Based on metagenomic and metatranscriptomic assembled viral genomes, the viral communities differed markedly and preferentially infected the most abundant prokaryotic taxa. The majority of DNA viruses were Caudoviricetes (dsDNA), Cirlivirales (ssDNA) and Microviridae (ssDNA), while RNA viruses consisted of Leviviricetes (ssRNA), Potyviridae (ssRNA) and Eukaryotic viruses. A high abundance of subtypes I-C, I-B and II-C CRISPR-Cas systems was found, primarily from Pseudomonadota, Bacteroidota and Bacillota. In addition, auxiliary metabolic genes that modulate chitin degradation, vitamins and amino acid biosynthesis and sulphur metabolism were also detected. Lastly, we found low virus-to-microbe-ratios and a prevalence of lysogenic viruses, supporting a Piggyback-the-Winner dynamic in both hosts.}, } @article {pmid38355611, year = {2024}, author = {Górecki, P and Rutecka, N and Mykowiecka, A and Paszek, J}, title = {Unifying duplication episode clustering and gene-species mapping inference.}, journal = {Algorithms for molecular biology : AMB}, volume = {19}, number = {1}, pages = {7}, pmid = {38355611}, issn = {1748-7188}, support = {#2017/27/B/ST6/02720//National Science Centre, Poland/ ; }, abstract = {We present a novel problem, called MetaEC, which aims to infer gene-species assignments in a collection of partially leaf-labeled gene trees labels by minimizing the size of duplication episode clustering (EC). This problem is particularly relevant in metagenomics, where incomplete data often poses a challenge in the accurate reconstruction of gene histories. To solve MetaEC, we propose a polynomial time dynamic programming (DP) formulation that verifies the existence of a set of duplication episodes from a predefined set of episode candidates. In addition, we design a method to infer distributions of gene-species mappings. We then demonstrate how to use DP to design an algorithm that solves MetaEC. Although the algorithm is exponential in the worst case, we introduce a heuristic modification of the algorithm that provides a solution with the knowledge that it is exact. To evaluate our method, we perform two computational experiments on simulated and empirical data containing whole genome duplication events, showing that our algorithm is able to accurately infer the corresponding events.}, } @article {pmid38355595, year = {2024}, author = {Chakoory, O and Barra, V and Rochette, E and Blanchon, L and Sapin, V and Merlin, E and Pons, M and Gallot, D and Comtet-Marre, S and Peyret, P}, title = {DeepMPTB: a vaginal microbiome-based deep neural network as artificial intelligence strategy for efficient preterm birth prediction.}, journal = {Biomarker research}, volume = {12}, number = {1}, pages = {25}, pmid = {38355595}, issn = {2050-7771}, support = {MIA: Artificial Intelligence for clerMont//ANR/ ; MIA: Artificial Intelligence for clerMont//ANR/ ; MIA: Artificial Intelligence for clerMont//ANR/ ; MIA: Artificial Intelligence for clerMont//ANR/ ; MIA: Artificial Intelligence for clerMont//ANR/ ; MIA: Artificial Intelligence for clerMont//ANR/ ; MIA: Artificial Intelligence for clerMont//ANR/ ; MIA: Artificial Intelligence for clerMont//ANR/ ; MIA: Artificial Intelligence for clerMont//ANR/ ; MIA: Artificial Intelligence for clerMont//ANR/ ; Intelligence Artificielle//FEDER/ ; Intelligence Artificielle//FEDER/ ; Intelligence Artificielle//FEDER/ ; }, abstract = {In recent decades, preterm birth (PTB) has become a significant research focus in the healthcare field, as it is a leading cause of neonatal mortality worldwide. Using five independent study cohorts including 1290 vaginal samples from 561 pregnant women who delivered at term (n = 1029) or prematurely (n = 261), we analysed vaginal metagenomics data for precise microbiome structure characterization. Then, a deep neural network (DNN) was trained to predict term birth (TB) and PTB with an accuracy of 84.10% and an area under the receiver operating characteristic curve (AUROC) of 0.875 ± 0.11. During a benchmarking process, we demonstrated that our DL model outperformed seven currently used machine learning algorithms. Finally, our results indicate that overall diversity of the vaginal microbiota should be taken in account to predict PTB and not specific species. This artificial-intelligence based strategy should be highly helpful for clinicians in predicting preterm birth risk, allowing personalized assistance to address various health issues. DeepMPTB is open source and free for academic use. It is licensed under a GNU Affero General Public License 3.0 and is available at https://deepmptb.streamlit.app/ . Source code is available at https://github.com/oschakoory/DeepMPTB and can be easily installed using Docker (https://www.docker.com/).}, } @article {pmid38355463, year = {2024}, author = {Zhang, D and Cheng, Y and Ji, Y and Miao, Q and Chen, B and Wang, J and Wu, G and Yuan, C and Zheng, G and Liu, H and Qiu, X and Gong, J and Ba, H and Pan, L and Ma, X and Qi, Y and Shi, Y and Zhang, Q and Li, D and Xu, Y}, title = {A training program for improving the capacity of infection high-throughput sequencing and diagnosis in China.}, journal = {BMC medical education}, volume = {24}, number = {1}, pages = {142}, pmid = {38355463}, issn = {1472-6920}, support = {2022-PUMCH-B-074//National High Level Hospital Clinical Research Funding/ ; 2022-PUMCH-B-074//National High Level Hospital Clinical Research Funding/ ; }, abstract = {BACKGROUND: Infectious diseases are a serious threat to human especially since the COVID-19 outbreak has proved the importance and urgency of their diagnosis and treatment again. Metagenomic next-generation sequencing (mNGS) has been widely used and recognized in clinical and carried out localized testing in hospitals. Increasing the training of mNGS detection technicians can enhance their professional quality and more effectively realize the application value of the hospital platform.

METHODS: Based on the initial theoretical understanding and practice of the mNGS platform for localization construction, we have designed a training program to enhance the ability of technicians to detect pathogens by utilizing mNGS, and hence to conduct training practices nationwide.

RESULTS: Until August 30, 2022, the page views of online classes have reached 51,500 times and 6 of offline small-scale training courses have been conducted. A total of 67 trainees from 67 hospitals have participated in the training with a qualified rate of 100%. After the training course, the localization platform of 1 participating hospital has been put into use, 2 have added the mNGS localization platform for admission, among which 3 have expressed strong intention of localization.

CONCLUSIONS: This study focuses on the training procedures and practical experience of the project which is the first systematic standardized program of mNGS in the world. It solves the training difficulties in the current industry, and effectively promotes the localization construction and application of mNGS in hospitals. It has great development potential in the future and is worth further promotion.}, } @article {pmid38355084, year = {2024}, author = {Ahmed, T and Junning, G and Noman, M and Luqiong, L and Manzoor, N and Qi, X and Li, B}, title = {Metagenomic and biochemical analyses reveal the potential of silicon to alleviate arsenic toxicity in rice (Oryza sativa L.).}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {123537}, doi = {10.1016/j.envpol.2024.123537}, pmid = {38355084}, issn = {1873-6424}, abstract = {Arsenic (As) pollution in agricultural systems poses a serious threat to crop productivity and food safety. Silicon (Si) has been reported to mitigate toxic effects of heavy metals in plants. However, the mechanisms behind Si-mediated alleviation of As toxicity in rice (Oryza sativa L.) remain poorly understood. Here, we performed metagenomic and biochemical analyses to investigate the potential of Si in alleviating As toxicity to rice plants. As exposure reduced plant growth, chlorophyll contents, antioxidant enzyme levels and soil enzymes activity, while increasing reactive oxygen species (ROS) activity and inducing alterations in the rhizosphere microbiome of rice seedlings. Silicon amendments enhanced rice growth (24%), chlorophyll a (25%), and chlorophyll b (26.7%), indicating enhanced photosynthetic capacity. Si amendments also led to the upregulation of antioxidant enzymes viz., superoxide dismutase (15.4%), and peroxidase (15.6%), resulting in reduced ROS activity and oxidative stress compared to the As-treated control. Furthermore, Si treatment reduced uptake and translocation of As in rice plants, as evidenced by the analysis of elemental contents. Microscopic examination of leaf and root ultrastructure showed that Si mitigated As-induced cellular damage and maintained normal morphology. Metagenomic analysis of the rice rhizosphere microbiome revealed that Si application modulated composition and diversity of microbial communities e.g., Proteobacteria, Actinobacteria, and Firmicutes. Additionally, Si amendments upregulated the relative expression levels of OsGSH, OsPCs, OsNIP1;1 and OsNIP3;3 genes, while the expression levels of the OsLis1 and OsLis2 genes were significantly downregulated compared with As-treated rice plants. Overall, these findings contribute to our understanding of Si-mediated plant resilience to As stress and offer potential strategies for sustainable agriculture in As-contaminated regions.}, } @article {pmid38354633, year = {2024}, author = {Ma, C and Huang, Z and Feng, X and Memon, FU and Cui, Y and Duan, X and Zhu, J and Tettamanti, G and Hu, W and Tian, L}, title = {Selective breeding of cold-tolerant black soldier fly (Hermetia illucens) larvae: Gut microbial shifts and transcriptional patterns.}, journal = {Waste management (New York, N.Y.)}, volume = {177}, number = {}, pages = {252-265}, doi = {10.1016/j.wasman.2024.02.007}, pmid = {38354633}, issn = {1879-2456}, abstract = {The larvae of black soldier fly (BSFL) convert organic waste into insect proteins used as feedstuff for livestock and aquaculture. BSFL production performance is considerably reduced during winter season. Herein, the intraspecific diversity of ten commercial BSF colonies collected in China was evaluated. The Bioforte colony was subjected to selective breeding at 12 °C and 16 °C to develop cold-tolerant BSF with improved production performance. After breeding for nine generations, the weight of larvae, survival rate, and the dry matter conversion rate significantly increased. Subsequently, intestinal microbiota in the cold-tolerant strain showed that bacteria belonging to Morganella, Dysgonomonas, Salmonella, Pseudochrobactrum, and Klebsiella genera were highly represented in the 12 °C bred, while those of Acinetobacter, Pseudochrobactrum, Enterococcus, Comamonas, and Leucobacter genera were significantly represented in the 16 °C bred group. Metagenomic revealed that several animal probiotics of the Enterococcus and Vagococcus genera were greatly enriched in the gut of larvae bred at 16 °C. Moreover, bacterial metabolic pathways including carbohydrate, lipid, amino acids, and cofactors and vitamins, were significantly increased, while organismal systems and human diseases was decreased in the 16 °C bred group. Transcriptomic analysis revealed that the upregulated differentially expressed genes in the 16 °C bred groups mainly participated in Autophagy-animal, AMPK signaling pathway, mTOR signaling pathway, Wnt signaling pathway, FoxO signaling pathway, Hippo signaling pathway at day 34 under 16 °C conditions, suggesting their significant role in the survival of BSFL. Taken together, these results shed lights on the role of intestinal microflora and gene pathways in the adaptation of BSF larvae to cold stress.}, } @article {pmid38354254, year = {2024}, author = {Doré, H and Eisenberg, AR and Junkins, EN and Leventhal, GE and Ganesh, A and Cordero, OX and Paul, BG and Valentine, DL and O'Malley, MA and Wilbanks, EG}, title = {Targeted hypermutation of putative antigen sensors in multicellular bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {9}, pages = {e2316469121}, doi = {10.1073/pnas.2316469121}, pmid = {38354254}, issn = {1091-6490}, support = {W911NF-19-2-0026//DOD | USA | AFC | CCDC | Army Research Office (ARO)/ ; W911NF-19-D-0001//DOD | USA | AFC | CCDC | Army Research Office (ARO)/ ; 508543//Joint Genome Institute (JGI)/ ; }, abstract = {Diversity-generating retroelements (DGRs) are used by bacteria, archaea, and viruses as a targeted mutagenesis tool. Through error-prone reverse transcription, DGRs introduce random mutations at specific genomic loci, enabling rapid evolution of these targeted genes. However, the function and benefits of DGR-diversified proteins in cellular hosts remain elusive. We find that 82% of DGRs from one of the major monophyletic lineages of DGR reverse transcriptases are encoded by multicellular bacteria, which often have two or more DGR loci in their genomes. Using the multicellular purple sulfur bacterium Thiohalocapsa sp. PB-PSB1 as an example, we characterized nine distinct DGR loci capable of generating 10[282] different combinations of target proteins. With environmental metagenomes from individual Thiohalocapsa aggregates, we show that most of PB-PSB1's DGR target genes are diversified across its biogeographic range, with spatial heterogeneity in the diversity of each locus. In Thiohalocapsa PB-PSB1 and other bacteria hosting this lineage of cellular DGRs, the diversified target genes are associated with NACHT-domain anti-phage defenses and putative ternary conflict systems previously shown to be enriched in multicellular bacteria. We propose that these DGR-diversified targets act as antigen sensors that confer a form of adaptive immunity to their multicellular consortia, though this remains to be experimentally tested. These findings could have implications for understanding the evolution of multicellularity, as the NACHT-domain anti-phage systems and ternary systems share both domain homology and conceptual similarities with the innate immune and programmed cell death pathways of plants and metazoans.}, } @article {pmid38353611, year = {2024}, author = {Li, LJ and Xu, F and Xu, JX and Yan, Y and Su, JQ and Zhu, YG and Li, H}, title = {Spatiotemporal Changes of Antibiotic Resistance, Potential Pathogens, and Health Risk in Kindergarten Dust.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c07935}, pmid = {38353611}, issn = {1520-5851}, abstract = {The microorganisms present in kindergartens are extremely important for children's health during their three-year preschool education. To assess the risk of outdoor dust in kindergartens, the antibiotic resistome and potential pathogens were investigated in dust samples collected from 59 kindergartens in Xiamen, southeast China in both the winter and summer. Both high-throughput quantitative PCR and metagenome analysis revealed a higher richness and abundance of antibiotic resistance genes (ARGs) in winter (P < 0.05). Besides, the bloom of ARGs and potential pathogens was evident in the urban kindergartens. The co-occurrence patterns among ARGs, mobile genetic elements (MGEs), and potential pathogens suggested some bacterial pathogens were potential hosts of ARGs and MGEs. We found a large number of high-risk ARGs in the dust; the richness and abundance of high-risk ARGs were higher in winter and urban kindergartens compared to in summer and peri-urban kindergartens, respectively. The results of the co-occurrence patterns and high-risk ARGs jointly reveal that urbanization will significantly increase the threat of urban dust to human beings and their risks will be higher in winter. This study unveils the close association between ARGs/mobile ARGs and potential pathogens and emphasizes that we should pay more attention to the health risks induced by their combination.}, } @article {pmid38353022, year = {2024}, author = {Schwenger, KJP and Sharma, D and Ghorbani, Y and Xu, W and Lou, W and Comelli, EM and Fischer, SE and Jackson, TD and Okrainec, A and Allard, JP}, title = {Links between gut microbiome, metabolome, clinical variables and non-alcoholic fatty liver disease severity in bariatric patients.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {}, number = {}, pages = {}, doi = {10.1111/liv.15864}, pmid = {38353022}, issn = {1478-3231}, support = {/CAPMC/CIHR/Canada ; }, abstract = {BACKGROUND AND AIMS: Bacterial species and microbial pathways along with metabolites and clinical parameters may interact to contribute to non-alcoholic fatty liver disease (NAFLD) and disease severity. We used integrated machine learning models and a cross-validation approach to assess this interaction in bariatric patients.

METHODS: 113 patients undergoing bariatric surgery had clinical and biochemical parameters, blood and stool metabolite measurements as well as faecal shotgun metagenome sequencing to profile the intestinal microbiome. Liver histology was classified as normal liver obese (NLO; n = 30), simple steatosis (SS; n = 41) or non-alcoholic steatohepatitis (NASH; n = 42); fibrosis was graded F0 to F4.

RESULTS: We found that those with NASH versus NLO had an increase in potentially harmful E. coli, a reduction of potentially beneficial Alistipes putredinis and an increase in ALT and AST. There was higher serum glucose, faecal 3-(3-hydroxyphenyl)-3-hydroxypropionic acid and faecal cholic acid and lower serum glycerophospholipids. In NAFLD, those with severe fibrosis (F3-F4) versus F0 had lower abundance of anti-inflammatory species (Eubacterium ventriosum, Alistipes finegoldii and Bacteroides dorei) and higher AST, serum glucose, faecal acylcarnitines, serum isoleucine and homocysteine as well as lower serum glycerophospholipids. Pathways involved with amino acid biosynthesis and degradation were significantly more represented in those with NASH compared to NLO, with severe fibrosis having an overall stronger significant association with Superpathway of menaquinol-10 biosynthesis and Peptidoglycan biosynthesis IV.

CONCLUSIONS: In bariatric patients, NASH and severe fibrosis were associated with specific bacterial species, metabolic pathways and metabolites that may contribute to NAFLD pathogenesis and disease severity.}, } @article {pmid38352454, year = {2024}, author = {Curry, KD and Yu, FB and Vance, SE and Segarra, S and Bhaya, D and Chikhi, R and Rocha, EPC and Treangen, TJ}, title = {Reference-free Structural Variant Detection in Microbiomes via Long-read Coassembly Graphs.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.01.25.577285}, pmid = {38352454}, abstract = {Bacterial genome dynamics are vital for understanding the mechanisms underlying microbial adaptation, growth, and their broader impact on host phenotype. Structural variants (SVs), genomic alterations of 10 base pairs or more, play a pivotal role in driving evolutionary processes and maintaining genomic heterogeneity within bacterial populations. While SV detection in isolate genomes is relatively straightforward, metagenomes present broader challenges due to absence of clear reference genomes and presence of mixed strains. In response, our proposed method rhea, forgoes reference genomes and metagenome-assembled genomes (MAGs) by encompassing a single metagenome coassembly graph constructed from all samples in a series. The log fold change in graph coverage between subsequent samples is then calculated to call SVs that are thriving or declining throughout the series. We show rhea to outperform existing methods for SV and horizontal gene transfer (HGT) detection in two simulated mock metagenomes, which is particularly noticeable as the simulated reads diverge from reference genomes and an increase in strain diversity is incorporated. We additionally demonstrate use cases for rhea on series metagenomic data of environmental and fermented food microbiomes to detect specific sequence alterations between subsequent time and temperature samples, suggesting host advantage. Our innovative approach leverages raw read patterns rather than references or MAGs to include all sequencing reads in analysis, and thus provide versatility in studying SVs across diverse and poorly characterized microbial communities for more comprehensive insights into microbial genome dynamics.}, } @article {pmid38352442, year = {2024}, author = {Shin, A and Xing, Y and Waseem, MR and Siwiec, R and James-Stevenson, T and Rogers, N and Bohm, M and Wo, J and Lockett, C and Gupta, A and Gupta, A and Kadariya, J and Toh, E and Anderson, R and Xu, H and Gao, X}, title = {Microbiota-Short Chain Fatty Acid Relationships and Microbial Substrate Preferences Vary Across the Spectrum of Irritable Bowel Syndrome (IBS).}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.01.31.24302084}, pmid = {38352442}, abstract = {OBJECTIVE: Identifying microbial targets in irritable bowel syndrome (IBS) is challenged by dynamic microbiota-metabolite-host interactions. We aimed to assess microbial features associated with short chain fatty acids (SCFA) and determine if features were related to IBS symptoms, subtypes, and endophenotypes.

DESIGN: We performed an observational study of stool microbial metagenomes, stool SCFA, and IBS traits (stool form, stool bile acids, and colonic transit) in patients with IBS (IBS with constipation [IBS-C] IBS with diarrhea [IBS-D]) and healthy controls. We analyzed associations of microbiome composition with stool SCFA to identify microbe-SCFA relationships that were shared and distinct across groups. We compared gut microbiome-encoded potential for substrate utilization across groups and within a subset of participants selected by stool characteristics. In IBS-D, we compared stool microbiomes of patients with and without bile acid malabsorption (BAM).

RESULTS: Overall stool microbiome composition and abundances of individual taxa differed between groups. Increased abundances of several bacterial species were observed in IBS-D including Dorea sp. CAG:317.. Microbes-SCFA relationships varied across groups after accounting for transit and bile acids. Significant microbe-SCFA were common in IBS-D and several SCFA-producing species were inversely correlated with SCFA. Among participants selected by stool form characteristics, functional profiling demonstrated differential abundances of microbial genes/pathways for SCFA metabolism and degradation of carbohydrates and mucin across groups. SCFA-producing taxa were reduced in IBS-D with BAM.

CONCLUSION: Microbe-SCFA associations differ across IBS subtypes and traits. Altered substrate preferences offer insights into functional microbiome traits and could be used as novel microbial IBS biomarkers.

KEY MESSAGES: What is already known on this topic: The intestinal microbiota and its metabolites (e.g., short chain fatty acids [SCFA]) modulate irritable bowel syndrome (IBS) pathophysiology. What this study adds: We studied microbe-SCFA associations across IBS subtypes and endophenotypes to demonstrate (1) the intestinal microbiome plays distinct roles across IBS subtypes, (2) microbial substrate preferences vary between IBS subtypes and influences stool form, and (3) microbe-SCFA patterns may reveal key taxa that underlie shared and distinct microbial mechanisms across the IBS spectrum. How this study might affect research, practice or policy: Findings demonstrate that structural and functional features of the intestinal microbiome may represent unbiased microbial biomarkers for clinical and mechanistic IBS subtypes. Further study of these putative microbial targets as well as their interactions with diet- and host-specific traits should be pursued to develop individualized microbiome-based approached to IBS management.}, } @article {pmid38352054, year = {2024}, author = {Zhao, M and Zhang, Y and Chen, L and Yan, X and Xu, T and Fu, M and Han, Y and Zhang, Y and Zhang, B and Cao, J and Lin, J and Shen, D and Li, S and Zhu, C and Zhao, W}, title = {Nanopore sequencing of infectious fluid is a promising supplement for gold-standard culture in real-world clinical scenario.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1330788}, pmid = {38352054}, issn = {2235-2988}, abstract = {INTRODUCTION: Infectious diseases are major causes of morbidity and mortality worldwide, necessitating the rapid identification and accurate diagnosis of pathogens. While unbiased metagenomic next-generation sequencing (mNGS) has been extensively utilized in clinical pathogen identification and scientific microbiome detection, there is limited research about the application of nanopore platform-based mNGS in the diagnostic performance of various infectious fluid samples.

METHODS: In this study, we collected 297 suspected infectious fluids from 10 clinical centers and detected them with conventional microbiology culture and nanopore platform-based mNGS. The objective was to assess detective and diagnostic performance of nanopore-sequencing technology (NST) in real-world scenarios.

RESULTS: Combined with gold-standard culture and clinical adjudication, nanopore sequencing demonstrated nearly 100% positive predictive agreements in microbial-colonized sites, such as the respiratory and urinary tracts. For samples collected from initially sterile body sites, the detected microorganisms were highly suspected pathogens, and the negative predictive agreements were relatively higher than those in the microbial-colonized sites, particularly with 100% in abscess and 95.7% in cerebrospinal fluid. Furthermore, consistent performance was also observed in the identification of antimicrobial resistance genes and drug susceptibility testing of pathogenic strains of Escherichia coli, Staphylococcus aureus, and Acinetobacter baumannii.

DISCUSSION: Rapid NST is a promising clinical tool to supplement gold-standard culture, and it has the potential improve patient prognosis and facilitate clinical treatment of infectious diseases.}, } @article {pmid38351919, year = {2024}, author = {Wang, JH and Lim, DW and Yadav, MK and Zheng, X}, title = {Editorial: The role of commensal microbiota in drug metabolism: friend or foe?.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1364747}, pmid = {38351919}, issn = {1664-302X}, } @article {pmid38351916, year = {2024}, author = {Yao, A and Wang, J and Xu, Q and Shah, BK and Sun, K and Hu, F and Wang, C and Xie, S}, title = {Higher diagnostic value of metagenomic next-generation sequencing in acute infection than chronic infection: a multicenter retrospective study.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1295184}, pmid = {38351916}, issn = {1664-302X}, abstract = {BACKGROUND: The aim of this study is to compare the diagnostic value of metagenomic next-generation sequencing (mNGS) vs. conventional culture methods (CM) in chronic infection and acute infection.

METHODS: We retrospectively analyzed the bronchoalveolar lavage fluid (BALF) of 88 patients with acute infection and 105 patients with chronic infection admitted to three hospitals from 2017 to 2022.

RESULTS: The results showed that the sensitivity and specificity of mNGS were higher than those of CM. The number of patients who changed the antibiotic treatment in the mNGS positive group was larger than that of patients in the mNGS negative group in both the acute infection group (60.5 vs. 28.0%, P = 0.0022) and chronic infection group (46.2 vs. 22.6%, P = 0.01112). High levels of temperature (OR: 2.02, 95% CI: 1.18-3.70, P: 0.015), C-reactive protein (CRP) (OR: 15, 95% CI: 2.74-280.69, P: 0.011), neutrophil count (OR: 3.09, 95% CI: 1.19-8.43, P: 0.023), and low levels of lymphocyte count (OR: 3.43, 95% CI:1.26-10.21, P: 0.020) may lead to positive mNGS results in the acute infection group while no significant factor was identified to predict positive results in the chronic infection group.

CONCLUSION: mNGS could provide useful guidance on antibiotic strategies in infectious diseases and may be more valuable for the diagnosis and treatment of acute infection vs. chronic infection.}, } @article {pmid38351104, year = {2024}, author = {Xu, S and Huang, H and Chen, S and Muhammad, ZUA and Wei, W and Xie, W and Jiang, H and Hou, S}, title = {Recovery of 1887 metagenome-assembled genomes from the South China Sea.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {197}, pmid = {38351104}, issn = {2052-4463}, support = {42276163//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92051117//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32170108//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42188102//National Natural Science Foundation of China (National Science Foundation of China)/ ; JCYJ20220530115401003//Shenzhen Science and Technology Innovation Commission/ ; }, abstract = {The South China Sea (SCS) is a marginal sea characterized by strong land-sea biogeochemical interactions. SCS has a distinctive landscape with a multitude of seamounts in its basin. Seamounts create "seamount effects" that influence the diversity and distribution of planktonic microorganisms in the surrounding oligotrophic waters. Although the vertical distribution and community structure of marine microorganisms have been explored in certain regions of the global ocean, there is a lack of comprehensive microbial genomic surveys for uncultured microorganisms in SCS, particularly in the seamount regions. Here, we employed a metagenomic approach to study the uncultured microbial communities sampled from the Xianbei seamount region to the North Coast waters of SCS. A total of 1887 non-redundant prokaryotic metagenome-assembled genomes (MAGs) were reconstructed, of which, 153 MAGs were classified as high-quality MAGs based on the MIMAG standards. The community structure and genomic information provided by this dataset could be used to analyze microbial distribution and metabolism in the SCS.}, } @article {pmid38191839, year = {2024}, author = {Beer, MA and Proft, KM and Veillet, A and Kozakiewicz, CP and Hamilton, DG and Hamede, R and McCallum, H and Hohenlohe, PA and Burridge, CP and Margres, MJ and Jones, ME and Storfer, A}, title = {Disease-driven top predator decline affects mesopredator population genomic structure.}, journal = {Nature ecology & evolution}, volume = {8}, number = {2}, pages = {293-303}, pmid = {38191839}, issn = {2397-334X}, support = {NSF DEB 2027446//NSF | BIO | Division of Environmental Biology (DEB)/ ; R01-GM126563-01//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; R01-GM126563//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {Animals ; *Marsupialia/genetics ; Metagenomics ; Population Dynamics ; Food Chain ; }, abstract = {Top predator declines are pervasive and often have dramatic effects on ecological communities via changes in food web dynamics, but their evolutionary consequences are virtually unknown. Tasmania's top terrestrial predator, the Tasmanian devil, is declining due to a lethal transmissible cancer. Spotted-tailed quolls benefit via mesopredator release, and they alter their behaviour and resource use concomitant with devil declines and increased disease duration. Here, using a landscape community genomics framework to identify environmental drivers of population genomic structure and signatures of selection, we show that these biotic factors are consistently among the top variables explaining genomic structure of the quoll. Landscape resistance negatively correlates with devil density, suggesting that devil declines will increase quoll genetic subdivision over time, despite no change in quoll densities detected by camera trap studies. Devil density also contributes to signatures of selection in the quoll genome, including genes associated with muscle development and locomotion. Our results provide some of the first evidence of the evolutionary impacts of competition between a top predator and a mesopredator species in the context of a trophic cascade. As top predator declines are increasing globally, our framework can serve as a model for future studies of evolutionary impacts of altered ecological interactions.}, } @article {pmid38073491, year = {2024}, author = {Young, SM and Woode, RA and Williams, EC and Ericsson, AC and Clarke, LL}, title = {Fecal dysbiosis and inflammation in intestinal-specific Cftr knockout mice on regimens preventing intestinal obstruction.}, journal = {Physiological genomics}, volume = {56}, number = {3}, pages = {247-264}, doi = {10.1152/physiolgenomics.00077.2023}, pmid = {38073491}, issn = {1531-2267}, support = {1/CX/CSRD VA/United States ; }, abstract = {Chronic intestinal inflammation is a poorly understood manifestation of cystic fibrosis (CF), which may be refractory to ion channel CF transmembrane conductance regulator (CFTR) modulator therapy. People with CF exhibit intestinal dysbiosis, which has the potential for stimulating intestinal and systemic inflammation. CFTR is expressed in organ epithelia, leukocytes, and other tissues. Here, we investigate the contribution of intestinal epithelium-specific loss of Cftr [iCftr knockout (KO)] to dysbiosis and inflammation in mice treated with either of two antiobstructive dietary regimens necessary to maintain CF mouse models [polyethylene glycol (PEG) laxative or a liquid diet (LiqD)]. Feces collected from iCftr KO mice and their wild-type (WT) sex-matched littermates were used to measure fecal calprotectin to evaluate inflammation and to perform 16S rRNA sequencing to characterize the gut microbiome. Fecal calprotectin was elevated in iCftr KO relative to WT mice that consumed either PEG or LiqD. PEG iCftr KO mice did not show a change in α diversity versus WT mice but demonstrated a significant difference in microbial composition (β diversity) with included increases in the phylum Proteobacteria, the family Peptostreptococcaceae, four genera of Clostridia including C. innocuum, and the mucolytic genus Akkermansia. Fecal microbiome analysis of LiqD-fed iCftr KO mice showed both decreased α diversity and differences in microbial composition with increases in the Proteobacteria family Enterobacteriaceae, Firmicutes families Clostridiaceae and Peptostreptococcaceae, and enrichment of Clostridium perfringens, C. innocuum, C. difficile, mucolytic Ruminococcus gnavus, and reduction of Akkermansia. It was concluded that epithelium-specific loss of Cftr is a major driver of CF intestinal dysbiosis and inflammation with significant similarities to previous studies of pan Cftr KO mice.NEW & NOTEWORTHY Chronic intestinal inflammation is a manifestation of cystic fibrosis (CF), a disease caused by loss of the anion channel CF transmembrane conductance regulator (CFTR) that is expressed in many tissues. This study shows that intestinal epithelial cell-specific loss of CFTR [inducible Cftr knockout (KO)] in mice is sufficient to induce intestinal dysbiosis and inflammation. Experiments were performed on mice consuming two dietary regimens routinely used to prevent obstruction in CF mice.}, } @article {pmid38350856, year = {2024}, author = {Hui, TKL and Lo, ICN and Wong, KKW and Tsang, CTT and Tsang, LM}, title = {Metagenomic analysis of gut microbiome illuminates the mechanisms and evolution of lignocellulose degradation in mangrove herbivorous crabs.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {57}, pmid = {38350856}, issn = {1471-2180}, support = {CUHK14119419//Research Grants Council, University Grants Committee/ ; }, abstract = {BACKGROUND: Sesarmid crabs dominate mangrove habitats as the major primary consumers, which facilitates the trophic link and nutrient recycling in the ecosystem. Therefore, the adaptations and mechanisms of sesarmid crabs to herbivory are not only crucial to terrestrialization and its evolutionary success, but also to the healthy functioning of mangrove ecosystems. Although endogenous cellulase expressions were reported in crabs, it remains unknown if endogenous enzymes alone can complete the whole lignocellulolytic pathway, or if they also depend on the contribution from the intestinal microbiome. We attempt to investigate the role of gut symbiotic microbes of mangrove-feeding sesarmid crabs in plant digestion using a comparative metagenomic approach.

RESULTS: Metagenomics analyses on 43 crab gut samples from 23 species of mangrove crabs with different dietary preferences revealed a wide coverage of 127 CAZy families and nine KOs targeting lignocellulose and their derivatives in all species analyzed, including predominantly carnivorous species, suggesting the crab gut microbiomes have lignocellulolytic capacity regardless of dietary preference. Microbial cellulase, hemicellulase and pectinase genes in herbivorous and detritivorous crabs were differentially more abundant when compared to omnivorous and carnivorous crabs, indicating the importance of gut symbionts in lignocellulose degradation and the enrichment of lignocellulolytic microbes in response to diet with higher lignocellulose content. Herbivorous and detritivorous crabs showed highly similar CAZyme composition despite dissimilarities in taxonomic profiles observed in both groups, suggesting a stronger selection force on gut microbiota by functional capacity than by taxonomy. The gut microbiota in herbivorous sesarmid crabs were also enriched with nitrogen reduction and fixation genes, implying possible roles of gut microbiota in supplementing nitrogen that is deficient in plant diet.

CONCLUSIONS: Endosymbiotic microbes play an important role in lignocellulose degradation in most crab species. Their abundance is strongly correlated with dietary preference, and they are highly enriched in herbivorous sesarmids, thus enhancing their capacity in digesting mangrove leaves. Dietary preference is a stronger driver in determining the microbial CAZyme composition and taxonomic profile in the crab microbiome, resulting in functional redundancy of endosymbiotic microbes. Our results showed that crabs implement a mixed mode of digestion utilizing both endogenous and microbial enzymes in lignocellulose degradation, as observed in most of the more advanced herbivorous invertebrates.}, } @article {pmid38350645, year = {2024}, author = {Soufi, HH and Tran, D and Louca, S}, title = {Microbiology of Big Soda Lake, a multi-extreme meromictic volcanic crater lake in the Nevada desert.}, journal = {Environmental microbiology}, volume = {26}, number = {2}, pages = {e16578}, doi = {10.1111/1462-2920.16578}, pmid = {38350645}, issn = {1462-2920}, support = {//Alfred P. Sloan Foundation/ ; }, abstract = {Big Soda Lake, Nevada, is a multi-extreme meromictic lake, whose hypersaline hyperalkaline bottom waters feature permanent anoxia and high concentrations of arsenic, sulphide and ammonia. These properties make Big Soda Lake-and the adjacent Little Soda Lake-a fascinating system for exploring life's boundaries, discovering novel microbial taxa and identifying biotechnologically useful strains. To date, the taxonomic diversity and metabolic capabilities of microorganisms in this system remain largely unknown. Here, we fill this gap using microbiome surveys across the Big and Little Soda Lake water columns, including 16S rRNA sequencing, fungal ITS2 sequencing and gene- and genome-resolved metagenomics. We accompany these surveys with measurements of salinity, pH, temperature, oxygen, ammonium and ammonia concentrations. Our analyses reveal rich bacterial communities, taxonomically and functionally differentiated along Big Soda Lake's oxycline and, to lesser extent, between lakes. Fungal communities were dominated by a small number of families, while nearly no archaea were detected. Pathways related to perchlorate reduction, anoxygenic phototrophy, fermentation, dissimilatory metabolism of arsenite/arsenate, sulphur compounds, nitrogen compounds and hydrogen, were particularly prevalent. A total of 129 high-quality bacterial and archaeal metagenome-assembled genomes (completeness ≥ 80%, contamination ≤ 5%) were recovered, yielding insight into the taxonomic distribution of microbial metabolic pathways.}, } @article {pmid38350567, year = {2024}, author = {Ge, Y and Chen, J and Xue, Y and Xing, W and Zhang, L and Lu, X and Liu, J and Li, F and Yang, Q}, title = {Elimination of inhibitory effects of dodecyl dimethyl benzyl ammonium chloride on microalgae in wastewater by cocultivation with a newly screened microbial consortium.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170676}, doi = {10.1016/j.scitotenv.2024.170676}, pmid = {38350567}, issn = {1879-1026}, abstract = {As one of the most commonly used biocidal cationic surfactants, benzalkonium chlorides (BACs) have been an increasing concern as emerging contaminants. Wastewater has been claimed the main point for BACs to enter into the environment, but to date, it is still largely unknown how the BACs affect the microbes (especially microalgae) in the practical wastewater and how to cost-effectively remove them. In this study, the inhibitory effects of a typical BACs, dodecyl dimethyl benzyl ammonium chloride (DDBAC), on a green microalga Chlorella sp. in oxidation pond wastewater were investigated. The results showed that though a hermetic effect at the first 2 days was observed with the DDBAC at low concentration (<6 mg/L), the algal growth and photosynthesis were significantly inhibited by the DDBAC at all the tested concentrations (3 to 48 mg/L). Fortunately, a new microbial consortium (MC) capable of degrading DDBAC was screened through a gradient domestication method. The MC mainly composed of Wickerhamomyces sp., Purpureocillium sp., and Achromobacter sp., and its maximum removal efficiency and removal rate of DDBAC (48 mg/L) respectively reached 98.1 % and 46.32 mg/L/d. Interestingly, a microbial-microalgal system (MMS) was constructed using the MC and Chlorella sp., and a synergetic effect between the two kinds of microorganisms was proposed: microalga provided oxygen and extracellular polysaccharides as co-metabolic substrates to help the MC to degrade DDBAC, while the MC helped to eliminate the DDBAC-induced inhibition on the alga. Further, by observing the seven kinds of degradation products (mainly including CH5O3P, C6H5CH2-, and C8H11N), two possible chemical pathways of the DDBAC degradation were proposed. In addition, the metagenomic sequencing results showed that the main functional genes of the MMS included antibiotic-resistant genes, ABC transporter genes, quorum sensing genes, two-component regulatory system genes, etc. This study provided some theoretical and application findings for the cost-effective pollution prevention of BACs in wastewater.}, } @article {pmid38350466, year = {2023}, author = {Nguyen, TT and Bui, ATP and Le, NTH and Vo, HTN and Nguyen, AH and Pham, TD and Hara, T and Yokota, K and Matsutani, M and Takatsuka, Y and Nguyen, ATV}, title = {Heat-stable spores of carotenoid-producing Bacillus marisflavi and non-pigmented Bacillus subtilis cooperatively promote growth, quality, and gut microbiota of white-leg shrimp.}, journal = {Beneficial microbes}, volume = {14}, number = {6}, pages = {623-640}, doi = {10.1163/18762891-20230041}, pmid = {38350466}, issn = {1876-2891}, abstract = {We evaluated the benefits of heat-stable carotenoid-producing Bacillus marisflavi SH8 spores individually and in combination with non-pigmented Bacillus subtilis SH23 spores on growth, colour change, nutritional content, innate immunity, and gut microbiota of white-leg shrimp. White-leg shrimp (Litopenaeus vannamei; n = 30 per tank; 2 tanks per group) were provided feed without (control group) or with SH8, SH23, or mixed spores (total, 1 × 106 cfu/g pellet) for 28 d. The SH8 and SH8-23 combination groups had significantly higher specific growth rates (9.6 and 11.0%), improved red-colour score (4 scores), astaxanthin concentration (1.8- and 2.3-fold), lipid contents (30 and 50%), and superoxidase dismutase activity (8.5 and 12.3%) than that of the control group. Analysis of shrimp's gut microbiome using 16S rRNA metagenome sequencing revealed increased abundance of four useful species and reduced abundance of four harmful species in the combination group than in the control group. Heat-stable Bacillus spore combination improved growth parameters, nutrient content, red-colour score, live counts, and abundance of useful bacteria in the gut of L. vannamei. This is the first study to show the benefits of combining highly heat-stable pigmented and non-pigmented Bacillus spores and their possible mechanisms in a shrimp model.}, } @article {pmid38350318, year = {2024}, author = {Yang, Y and Kang, Z and Wang, J and Xu, G and Yu, Y}, title = {Simultaneous achievement of removing bensulfuron-methyl and reducing CO2 emission in paddy soil by Acinetobacter YH0317 immobilized boron-doping biochar.}, journal = {Journal of hazardous materials}, volume = {467}, number = {}, pages = {133758}, doi = {10.1016/j.jhazmat.2024.133758}, pmid = {38350318}, issn = {1873-3336}, abstract = {Herbicide residue and greenhouse gas (GHG) emission are two main problems in the paddy rice field, which have barely been considered simultaneously. Herein, a bensulfuron-methyl (BSM)-degrading bacterium named Acinetobacter YH0317 was successfully immobilized on two kinds of biochars and subsequently applied in the paddy soil. The BSM removal rate of Acinetobacter YH0317 immobilized boron-doping biochar (BBC) was 80.42% after 30 d, which was significantly higher than that of BBC (39.05%) and Acinetobacter YH0317 (49.10%) applied alone. BBC acting as an immobilized carrier could enable Acinetobacter YH0317 to work in harsh and complex environment and thus improve the BSM removal efficiency. The addition of Acinetobacter YH0317 immobilized BBC (TP5) significantly improved the soil physicochemical properties (pH, SOC, and NH4[+]-N) and increased the diversity of soil microbial community compared to control group (CG). Meanwhile, Acinetobacter YH0317 immobilized BBC reduced the CO2-equivalent emission by 41.0%. Metagenomic sequencing results revealed that the decreasing CO2 emission in TP5 was correlated with carbon fixation gene (fhs), indicating that fhs gene may play an important role in reducing CO2 emission. The work presents a practical and supportive technique for the simultaneous achievement on the soil purification and GHG emission reduction in paddy soil.}, } @article {pmid38350193, year = {2024}, author = {Wang, B and Ma, B and Zhang, Y and Stirling, E and Yan, Q and He, Z and Liu, Z and Yuan, X and Zhang, H}, title = {Global diversity, coexistence and consequences of resistome in inland waters.}, journal = {Water research}, volume = {253}, number = {}, pages = {121253}, doi = {10.1016/j.watres.2024.121253}, pmid = {38350193}, issn = {1879-2448}, abstract = {Human activities have long impacted the health of Earth's rivers and lakes. These inland waters, crucial for our survival and productivity, have suffered from contamination which allows the formation and spread of antibiotic-resistant genes (ARGs) and consequently, ARG-carrying pathogens (APs). Yet, our global understanding of waterborne pathogen antibiotic resistance remains in its infancy. To shed light on this, our study examined 1240 metagenomic samples from both open and closed inland waters. We identified 22 types of ARGs, 19 types of mobile genetic elements (MGEs), and 14 types of virulence factors (VFs). Our findings showed that open waters have a higher average abundance and richness of ARGs, MGEs, and VFs, with more robust co-occurrence network compared to closed waters. Out of the samples studied, 321 APs were detected, representing a 43 % detection rate. Of these, the resistance gene 'bacA' was the most predominant. Notably, AP hotspots were identified in regions including East Asia, India, Western Europe, the eastern United States, and Brazil. Our research underscores how human activities profoundly influence the diversity and spread of resistome. It also emphasizes that both abiotic and biotic factors play pivotal roles in the emergence of ARG-carrying pathogens.}, } @article {pmid38349445, year = {2024}, author = {López-Sánchez, R and Rebollar, EA and Gutiérrez-Ríos, RM and Garciarrubio, A and Juarez, K and Segovia, L}, title = {Metagenomic analysis of carbohydrate-active enzymes and their contribution to marine sediment biodiversity.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {3}, pages = {95}, pmid = {38349445}, issn = {1573-0972}, support = {756092//Consejo Nacional de Ciencia y Tecnología/ ; 269435//Consejo Nacional de Ciencia y Tecnología/ ; IN209921//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; }, abstract = {Marine sediments constitute the world's most substantial long-term carbon repository. The microorganisms dwelling in these sediments mediate the transformation of fixed oceanic carbon, but their contribution to the carbon cycle is not fully understood. Previous culture-independent investigations into sedimentary microorganisms have underscored the significance of carbohydrates in the carbon cycle. In this study, we employ a metagenomic methodology to investigate the distribution and abundance of carbohydrate-active enzymes (CAZymes) in 37 marine sediments sites. These sediments exhibit varying oxygen availability and were isolated in diverse regions worldwide. Our comparative analysis is based on the metabolic potential for oxygen utilisation, derived from genes present in both oxic and anoxic environments. We found that extracellular CAZyme modules targeting the degradation of plant and algal detritus, necromass, and host glycans were abundant across all metagenomic samples. The analysis of these results indicates that the oxic/anoxic conditions not only influence the taxonomic composition of the microbial communities, but also affect the occurrence of CAZyme modules involved in the transformation of necromass, algae and plant detritus. To gain insight into the sediment microbial taxa, we reconstructed metagenome assembled genomes (MAG) and examined the presence of primary extracellular carbohydrate active enzyme (CAZyme) modules. Our findings reveal that the primary CAZyme modules and the CAZyme gene clusters discovered in our metagenomes were prevalent in the Bacteroidia, Gammaproteobacteria, and Alphaproteobacteria classes. We compared those MAGs to organisms from the same taxonomic classes found in soil, and we found that they were similar in its CAZyme repertoire, but the soil MAG contained a more abundant and diverse CAZyme content. Furthermore, the data indicate that abundant classes in our metagenomic samples, namely Alphaproteobacteria, Bacteroidia and Gammaproteobacteria, play a pivotal role in carbohydrate transformation within the initial few metres of the sediments.}, } @article {pmid38349437, year = {2024}, author = {Gu, L and Alemasi, A and Chen, Y and Li, X and Mei, Y and Zhou, J and He, D and Zeng, J}, title = {Gut Microbiota Disorders in Obesity-Associated Benign Prostatic Hyperplasia in Rats.}, journal = {Biochemical genetics}, volume = {}, number = {}, pages = {}, pmid = {38349437}, issn = {1573-4927}, support = {82172684//National Natural Science Foundation of China/ ; 82073304//National Natural Science Foundation of China/ ; 2019YFC0121501//National Key Research and Development Program of China/ ; }, abstract = {UNLABELLED: Benign prostatic hyperplasia (BPH), commonly seen in older men, can cause symptoms of discomfort, and may even need surgical intervention. Studies have shown the potential link between gut microbes and BPH, but the molecular association is not fully understood.

METHODS: Four-week-old male Sprague-Dawley rats (n = 16) were randomly allocated to normal control diet (ND, 10% fat) and high-fat diet-induced BPH (HFD, 45% fat) groups. Metagenomic analysis was used to examine the abundance and discrepancies in gut microbiota within the two groups after 24 weeks of feeding. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis was conducted to assess the biological functions of the differentially expressed genes.

RESULTS: Rats with HFD-induced obesity exhibited morphological abnormalities in their prostate tissues. Metagenomic analysis of the gut revealed that Firmicutes were the dominant phyla in the HFD group, whereas the ND group had a higher abundance of Spirochaetes. At the genus level, Ruminococcus spp exhibited greater abundance in the HFD group, whereas Treponema spp were more abundant in the ND group. KEGG analysis demonstrated that the differentially expressed genes were mainly enriched in the NOD-like receptor (NLR) signaling, PI3K-Akt signaling, estrogen-signaling, signalings associated with GABAergic synapses, pantothenate and CoA biosynthesis.

CONCLUSION: The findings of our study indicated that there was a notable variation in the microbiota abundance within the intestinal tract of obese rats suffering from prostate hyperplasia. It is plausible that these differentially abundant bacteria played a role in the development of pathological alterations in the prostate through the facilitation of inflammatory responses; however, additional research is required to validate the findings.}, } @article {pmid38349163, year = {2024}, author = {Xiao, Y and Sheng, Z-M and Williams, SL and Taubenberger, JK}, title = {Two complete 1918 influenza A/H1N1 pandemic virus genomes characterized by next-generation sequencing using RNA isolated from formalin-fixed, paraffin-embedded autopsy lung tissue samples along with evidence of secondary bacterial co-infection.}, journal = {mBio}, volume = {}, number = {}, pages = {e0321823}, doi = {10.1128/mbio.03218-23}, pmid = {38349163}, issn = {2150-7511}, abstract = {The 1918 influenza pandemic was the most devastating respiratory pandemic in modern human history, with 50-100 million deaths worldwide. Here, we characterized the complete genomes of influenza A virus (IAV) from two fatal cases during the fall wave of 1918 influenza A (H1N1) pandemic in the United States, one from Walter Reed Army Hospital in Washington, DC, and the other from Camp Jackson, SC. The two complete IAV genomes were obtained by combining Illumina deep sequencing data from both total RNA and influenza viral genome-enriched libraries along with Sanger sequencing data from PCR across the sequencing gaps. This study confirms the previously reported 1918 IAV genomes and increases the total number of available complete or near-complete influenza viral genomes of the 1918 pandemic from four to six. Sequence comparisons among them confirm that the genomes of the 1918 pandemic virus were highly conserved during the main wave of the pandemic with geographic separation in North America and Europe. Metagenomic analyses revealed bacterial co-infections in both cases. Interestingly, in the Washington, DC, case, evidence is presented of the first reported Rhodococcus-influenza virus co-infection.IMPORTANCEThis study applied modern molecular biotechnology and high-throughput sequencing to formalin-fixed, paraffin-embedded autopsy lung samples from two fatal cases during the fall wave of the 1918 influenza A (H1N1) pandemic in the United States. Complete influenza genomes were obtained from both cases, which increases the total number of available complete or near-complete influenza genomes of the 1918 pandemic virus from four to six. Sequence analysis confirms that the 1918 pandemic virus was highly conserved during the main wave of the pandemic with geographic separation in North America and Europe. Metagenomic analyses revealed bacterial co-infections in both cases, including the first reported evidence of Rhodococcus-influenza co-infection. Overall, this study offers a detailed view at the molecular level of the very limited samples from the most devastating influenza pandemic in modern human history.}, } @article {pmid38349151, year = {2024}, author = {Zhang, Y and Si, L and Gao, J and Shu, X and Qiu, C and Zhang, Y and Zu, S and Hu, H}, title = {Serial passage of PDCoV in cell culture reduces its pathogenicity and its damage of gut microbiota homeostasis in piglets.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0134623}, doi = {10.1128/msystems.01346-23}, pmid = {38349151}, issn = {2379-5077}, abstract = {Porcine deltacoronavirus (PDCoV) is an enteropathogenic coronavirus that mainly causes diarrhea in suckling piglets, and also has the potential for cross-species transmission. However, there are still no commercial vaccines available to prevent and control PDCoV infection. In this study, PDCoV strain HNZK-02 was serially propagated in vitro for up to 150 passages and the amino acid changes have mainly occurred in the S protein during serial passage which caused structure change. PDCoV HNZK-02-passage 5 (P5)-infected piglets exhibited acute and severe watery diarrhea, an obvious intestinal damage, while the piglets infected with PDCoV HNZK-02-P150 showed no obvious clinical signs, weak intestinal lesions, and lower viral loads in rectal swabs and various tissues. Compared with the PDCoV HNZK-02-P5 infection, HNZK-02-P150 infection resulted in a decrease in intestinal mucosal permeability and pro-inflammatory cytokines. Moreover, PDCoV HNZK-02-P5 infection had significantly reduced bacterial diversity and increased relative abundance of opportunistic pathogens, while PDCoV HNZK-02-P150 infection did not significantly affect the bacterial diversity, and the relative abundance of probiotics increased. Furthermore, the alterations of gut microbiota were closely related to the change of pro-inflammatory factor. Metagenomics prediction analysis demonstrated that HNZK-02-P150 modulated the tyrosine metabolism, Nucleotide-binding and oligomerization domain (NOD)-like receptor signaling pathway, and lipopolysaccharide biosynthesis, which coincided with lower inflammatory response and intestinal permeability in the piglets infected with HNZK-02-P150. In conclusion, the PDCoV HNZK-02 was successfully attenuated by serial passage in vitro, and the changes of S gene, metabolic function, and gut microbiota may contribute to the attenuation. The PDCoV HNZK-02-P150 may have the potential for developing live-attenuated vaccine.IMPORTANCEPorcine deltacoronavirus (PDCoV) is an enteropathogen causing severe diarrhea, dehydration, and death in nursing piglets, devastating great economic losses for the global swine industry, and has cross-species transmission and zoonotic potential. There are currently no approved treatments or vaccines available for PDCoV. In addition, gut microbiota has an important relationship with the development of many diseases. Here, the PDCoV virulent HNZK-02 strain was successfully attenuated by serial passage on cell cultures, and the pathogenesis and effects on the gut microbiota composition and metabolic function of the PDCoV HNZK-02-P5 and P150 strains were investigated in piglets. We also found the genetic changes in the S protein during passage in vitro and the gut microbiota may contribute to the pathogenesis of PDCoV, while their interaction molecular mechanism would need to be explored further.}, } @article {pmid38348834, year = {2024}, author = {Lin, C and Li, J and Liu, B and Hong, X and Luo, T and Ye, J and Yu, Y and Peng, X and Gou, S and Tang, H and Yuan, T and Luo, J and Yang, M and Feng, B and Zhao, Z and Ning, C and Sun, Z and Zhu, S and Chen, L and Shen, D and Huang, G}, title = {Metagenomic next-generation sequencing, instead of procalcitonin, could guide antibiotic usage in patients with febrile acute necrotizing pancreatitis: a multicenter, prospective cohort study.}, journal = {International journal of surgery (London, England)}, volume = {}, number = {}, pages = {}, doi = {10.1097/JS9.0000000000001162}, pmid = {38348834}, issn = {1743-9159}, abstract = {BACKGROUNDS: The effectiveness of procalcitonin-based algorithms in guiding antibiotic usage for febrile acute necrotizing pancreatitis (ANP) remains controversial. Metagenomic next-generation sequencing (mNGS) has been applied to diagnose infectious diseases. We aimed to evaluate the effectiveness of blood mNGS in guiding antibiotic stewardship for febrile ANP.

MATERIALS AND METHODS: The prospective multicenter clinical trial was conducted at seven hospitals in China. Blood samples were collected during fever (T ≥38.5°C) from ANP patients. The effectiveness of blood mNGS, procalcitonin, and blood culture in diagnosing pancreatic infection was evaluated and compared. Additionally, the real-world utilization of antibiotics and the potential mNGS-guided antimicrobial strategy in febrile ANP were also analyzed.

RESULTS: From May 2023 to October 2023, a total of 78 patients with febrile ANP were enrolled and 30 patients (38.5%) were confirmed infected pancreatic necrosis (IPN). Compared with procalcitonin and blood culture, mNGS showed a significantly higher sensitivity rate (86.7% vs. 56.7% vs. 26.7%, P<0.001). Moreover, mNGS outperformed procalcitonin (89.5% vs. 61.4%, P<0.01) and blood culture (89.5% vs. 69.0%, P<0.01) in terms of negative predictive value. Blood mNGS exhibited the highest accuracy (85.7%) in diagnosing IPN and sterile pancreatic necrosis (SPN), significantly superior to both procalcitonin (65.7%) and blood culture (61.4%). In the multivariate analysis, positive blood mNGS (OR=60.2, P<0.001) and lower fibrinogen level (OR=2.0, P<0.05) were identified as independent predictors associated with IPN, whereas procalcitonin was not associated with IPN, but with increased mortality (OR=11.7, P=0.006). Overall, the rate of correct use of antibiotics in the cohort was only 18.6% (13/70) and would be improved to 81.4% (57/70) if adjusted according to the mNGS results.

CONCLUSION: Blood mNGS represents important progress in the early diagnosis of IPN, with particular importance in guiding antibiotic usage for patients with febrile ANP.}, } @article {pmid38348306, year = {2023}, author = {Prakash, O and Dewala, SR and Nimonkar, Y and Patil, SK and Chauhan, A and Yadav, A and Dhotre, DP and Ranade, DR}, title = {Culture-based and culture-independent approach for the study of the methanogens and obligate anaerobes from different landfill sites.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1273037}, pmid = {38348306}, issn = {1664-302X}, abstract = {The landfill is a cheap way of solid waste management in developing countries. The majority of landfills are non-sanitary and work as open garbage dumping sites and pose threats to public and environmental health. Therefore, an in-depth understanding of the chemistry and microbiology of landfills is imperative to develop the right policies for landfill management. In the current study, we investigated the chemistry and microbiology of three Indian landfill sites using culture-based and culture-independent molecular approaches. Our data indicate that the nature of landfills varies from site to site in terms of chemistry, pollutants, and pathogens. We also enriched and cultivated three methanogens using an optimized medium and constructed two high-quality draft genomes from enriched microbiomes using metagenome-assembled genome approaches. The phylogenomic study of one draft genome showed the highest 93% sequence similarity with members of Methanomassiliicoccaceae and was always enriched with Acholoplasma and Anaerohalosphaera lusitana. Despite all the efforts, we did not isolate it in pure culture and hypothesized that for the cultivation of some not-yet-cultured methanogen, the presence of other organisms plays an important role, and their syntrophic interaction must be discerned for its successful cultivation in the future. Co-cultivation of amino acid-degrading organisms indicates that their co-culture can assist in boosting the growth of methanogens. In addition, our data indicated that landfill leachate contains a heavy load of pollutants and treatment is a must before discharge in nature or use in irrigation or biofertilizer.}, } @article {pmid38347962, year = {2024}, author = {Li, M and Guo, K and He, Y and Li, H and Sun, W and Yuan, X and Liu, Z and Li, X and Merriman, TR and Li, C and Zhang, H}, title = {Natural Changbai mineral water reduces obesity risk through regulating metabolism and gut microbiome in a hyperuricemia male mouse model.}, journal = {Frontiers in nutrition}, volume = {11}, number = {}, pages = {1308882}, pmid = {38347962}, issn = {2296-861X}, abstract = {Access to clean and safe drinking water is essential. This study aimed to evaluate the effect of a kind of small molecular natural mineral water, C-cell mineral water on hyperuricemia male mice metabolism condition. A 13-week drinking water intervention study was conducted in Uox-knockout mice (KO). The hepatic metabolite profiling and related genes expression were detected by UPLC-TOF-MS and transcriptomic, and the gut microbiota of KO mice was determined by metagenomics sequencing. Results showed that the body weight of mice fed with C-cell water was remarkably lower than that of control mice on D 77 and D 91. Hepatic metabolite profiling revealed a shift in the pathway of glycine, serine and threonine metabolism, pantothenate and CoA biosynthesis, and biosynthesis of cofactors in KO mice fed with C-cell mineral water. Increased energy metabolism levels were related to increased hepatic expression of genes responsible for coenzyme metabolism and lipid metabolism. Gut microbiota was characterized by increasing activity of beneficial bacteria Blautia, and reducing activity of pathobiont bacteria Parasutterella. These genera have been reported to be associated with obesity. Small molecular mineral-rich natural water ingestion regulates metabolism and gut microbiota, protecting against obesity induced by hyperuricemia through mediating a microbiota-liver axis.}, } @article {pmid38347797, year = {2024}, author = {Zhao, L and Formslag, CR and Zhang, Q and Cowan, BC and Mayberry, TG and Barnhill, AR and Wang, Y and Fang, Y}, title = {Determination of Ideal Factors for Early Adoption and Standardization of Metagenomic Next-Generation Sequencing for Respiratory System Infections.}, journal = {Current pharmaceutical biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.2174/0113892010246350231030042340}, pmid = {38347797}, issn = {1873-4316}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) demonstrates great promise as a diagnostic tool for determining the cause of pathogenic infections. The standard diagnostic procedures (SDP) include smears and cultures and are typically viewed as less sensitive and more time-consuming when compared to mNGS. There are concerns about the logistics and ease of transition from SDP to mNGS. mNGS lacks standardization of collection processes, databases, and sequencing. Additionally, there is the burden of training clinicians on interpreting mNGS results.

OBJECTIVE: Until now, few studies have explored factors that could be used as early adoption candidates to ease the transition between SDP and mNGS. This study evaluated 123 patients who had received both SDP and mNGS and compared several variables across a diagnostic test evaluation.

METHODS: The diagnostic test evaluation observed metrics such as sensitivity, specificity, positive and negative likelihood ratios (PLR, NLR), positive and negative predictive values (PPV, NPV), and accuracy. Factors included various sample sources such as bronchoalveolar lavage fluid (BALF), lung tissue, and cerebral spinal fluid (CSF). An additional factor observed was the patient's immune status.

RESULTS: Pathogen detection was found to be significantly greater for mNGS for total patients, BALF sample source, CSF sample source, and non-immunocompromised patients (p<0.05). Pathogen detection was found to be insignificant for lung tissue sample sources and immunocompromised patients. Sensitivity, PLR, NLR, PPV, NPV, and accuracy appeared to be higher with mNGS for the total patients, BALF sample source, and non-immunocompromised patients when compared with SDP (p<0.05).

CONCLUSION: With higher metrics in sensitivity, specificity, PLR, NLR, PPV, NPV, and accuracy for overall patients, mNGS may prove a better diagnostic tool than SDP. When addressing sample sources, mNGS for BALF-collected samples appeared to have higher scores than SDP for the same metrics. When patients were in a non-immunocompromised state, mNGS also demonstrated greater diagnostic benefits to BALF and overall patients compared to SDP. This study demonstrates that using BALF as a sample source and selecting non-immunocompromised patients may prove beneficial as early adoption factors for mNGS standard protocol. Such a study may pave the road for mNGS as a routine clinical method for determining the exact pathogenic etiology of lung infections.}, } @article {pmid38347627, year = {2024}, author = {Behling, AH and Wilson, BC and Ho, D and Cutfield, WS and Vatanen, T and O'Sullivan, JM}, title = {Horizontal gene transfer after faecal microbiota transplantation in adolescents with obesity.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {26}, pmid = {38347627}, issn = {2049-2618}, abstract = {BACKGROUND: Horizontal gene transfer (HGT) describes the transmission of DNA outside of direct ancestral lineages. The process is best characterised within the bacterial kingdom and can enable the acquisition of genetic traits that support bacterial adaptation to novel niches. The adaptation of bacteria to novel niches has particular relevance for faecal microbiota transplantation (FMT), a therapeutic procedure which aims to resolve gut-related health conditions of individuals, through transplanted gut microbiota from healthy donors.

RESULTS: Three hundred eighty-one stool metagenomic samples from a placebo-controlled FMT trial for obese adolescents (the Gut Bugs Trial) were analysed for HGT, using two complementary methodologies. First, all putative HGT events, including historical HGT signatures, were quantified using the bioinformatics application WAAFLE. Second, metagenomic assembly and gene clustering were used to assess and quantify donor-specific genes transferred to recipients following the intervention. Both methodologies found no difference between the level of putative HGT events in the gut microbiomes of FMT and placebo recipients, post-intervention. HGT events facilitated by engrafted donor species in the FMT recipient gut at 6 weeks post-intervention were identified and characterised. Bacterial strains contributing to this subset of HGT events predominantly belonged to the phylum Bacteroidetes. Engraftment-dependent horizontally transferred genes were retained within recipient microbiomes at 12 and 26 weeks post-intervention.

CONCLUSION: Our study suggests that novel microorganisms introduced into the recipient gut following FMT have no impact on the basal rate of HGT within the human gut microbiome. Analyses of further FMT studies are required to assess the generalisability of this conclusion across different FMT study designs and for the treatment of different gut-related conditions. Video Abstract.}, } @article {pmid38347598, year = {2024}, author = {Shen, H and Wang, T and Dong, W and Sun, G and Liu, J and Peng, N and Zhao, S}, title = {Metagenome-assembled genome reveals species and functional composition of Jianghan chicken gut microbiota and isolation of Pediococcus acidilactic with probiotic properties.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {25}, pmid = {38347598}, issn = {2049-2618}, support = {2021hszd022//Foundation of Hubei Hongshan Laboratory/ ; 2020BBA054//Key Research and Development Program of Hubei Province/ ; }, abstract = {BACKGROUND: Chickens are one of the most widely farmed animals worldwide and play a crucial role in meat and egg production. Gut microbiota is essential for chickens' health, disease, growth, and egg production. However, native chickens such as Jianghan chickens have better meat and egg production quality than centralized chickens, their intestinal microbial diversity is richer, and the potential gut microbial resources may bring health benefits to the host.

RESULTS: The bacterial species composition in the gut microbiota of Jianghan chickens is similar to that of other chicken breeds, with Phocaeicola and Bacteroides being the most abundant bacterial genera. The LEfSe analysis revealed significant differences in species composition and functional profiles between samples from Jingzhou and the other three groups. Functional annotation indicated that the gut microbiota of Jianghan chickens were dominated by metabolic genes, with the highest number of genes related to carbohydrate metabolism. Several antibiotic resistance genes (ARGs) were found, and the composition of ARGs was similar to that of factory-farmed chickens, suggesting that antibiotics were widely present in the gut microbiota of Jianghan chickens. The resistance genes of Jianghan chickens are mainly carried by microorganisms of the Bacteroidota and Bacillota phylum. In addition, more than 829 isolates were selected from the microbiota of Jianghan chickens. Following three rounds of acid and bile tolerance experiments performed on all the isolated strains, it was determined that six strains of Pediococcus acidilactici exhibited consistent tolerance. Further experiments confirmed that three of these strains (A4, B9, and C2) held substantial probiotic potential, with P. acidilactici B9 displaying the highest probiotic potential.

CONCLUSIONS: This study elucidates the composition of the intestinal microbiota and functional gene repertoire in Jianghan chickens. Despite the absence of antibiotic supplementation, the intestinal microbial community of Jianghan chickens still demonstrates a profile of antibiotic resistance genes similar to that of intensively reared chickens, suggesting resistance genes are prevalent in free-ranging poultry. Moreover, Jianghan and intensively reared chickens host major resistance genes differently, an aspect seldom explored between free-range and pastured chickens. Furthermore, among the 829 isolates, three strains of P. acidilatici exhibited strong probiotic potential. These findings provide insights into the unique gut microbiota of Jianghan chickens and highlight potential probiotic strains offering benefits to the host. Video Abstract.}, } @article {pmid38347444, year = {2024}, author = {Zhang, H and Liang, R and Zhu, Y and Hu, L and Xia, H and Li, J and Ye, Y}, title = {Metagenomic next-generation sequencing of plasma cell-free DNA improves the early diagnosis of suspected infections.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {187}, pmid = {38347444}, issn = {1471-2334}, support = {no. 82304209//the National Natural Science Foundation of China/ ; no. 81973983//the National Natural Science Foundation of China/ ; No.2022-SXKXJ-005//Shaanxi Qinchuangyuan＂Chief Scientist＂Project/ ; No. AHWJ 2021b096//the Scientific Research Project of Anhui Provincial Health Committee/ ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) could improve the diagnosed efficiency of pathogens in bloodstream infections or sepsis. Little is known about the clinical impact of mNGS test when used for the early diagnosis of suspected infections. Herein, our main objective was to assess the clinical efficacy of utilizing blood samples to perform mNGS for early diagnosis of suspected infections, as well as to evaluate its potential in guiding antimicrobial therapy decisions.

METHODS: In this study, 212 adult hospitalized patients who underwent blood mNGS test in the early stage of suspected infections were enrolled. Diagnostic efficacy of mNGS test and blood culture was compared, and the clinical impact of mNGS on clinical care was analyzed.

RESULTS: In our study, the total detection rate of blood mNGS was significantly higher than that of culture method (74.4% vs. 12.1%, P < 0.001) in the paired mNGS test and blood culture. Blood stream infection (107, 67.3%) comprised the largest component of all the diseases in our patients, and the detection rate of single blood sample subgroup was similar with that of multiple type of samples subgroup. Among the 187 patients complained with fever, there was no difference in the diagnostic efficacy of mNGS when blood specimens or additional other specimens were used in cases presenting only with fever. While, when patients had other symptoms except fever, the performance of mNGS was superior in cases with specimens of suspected infected sites and blood collected at the same time. Guided by mNGS results, therapeutic regimens for 70.3% cases (149/212) were changed, and the average hospitalized days were significantly shortened in cases with the earlier sampling time of admission.

CONCLUSION: In this study, we emphasized the importance of blood mNGS in early infectious patients with mild and non-specific symptoms. Blood mNGS can be used as a supplement to conventional laboratory examination, and should be performed as soon as possible to guide clinicians to perform appropriate anti-infection treatment timely and effectively. Additionally, combining the contemporaneous samples from suspected infection sites could improve disease diagnosis and prognoses. Further research needs to be better validated in large-scale clinical trials to optimize diagnostic protocol, and the cost-utility analysis should be performed.}, } @article {pmid38347104, year = {2024}, author = {Burcham, ZM and Belk, AD and McGivern, BB and Bouslimani, A and Ghadermazi, P and Martino, C and Shenhav, L and Zhang, AR and Shi, P and Emmons, A and Deel, HL and Xu, ZZ and Nieciecki, V and Zhu, Q and Shaffer, M and Panitchpakdi, M and Weldon, KC and Cantrell, K and Ben-Hur, A and Reed, SC and Humphry, GC and Ackermann, G and McDonald, D and Chan, SHJ and Connor, M and Boyd, D and Smith, J and Watson, JMS and Vidoli, G and Steadman, D and Lynne, AM and Bucheli, S and Dorrestein, PC and Wrighton, KC and Carter, DO and Knight, R and Metcalf, JL}, title = {A conserved interdomain microbial network underpins cadaver decomposition despite environmental variables.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {38347104}, issn = {2058-5276}, support = {2015-DN-BX-K016//United States Department of Justice | National Institute of Justice (NIJ)/ ; 2016-DN-BX-0194//United States Department of Justice | National Institute of Justice (NIJ)/ ; T32GM132057//Foundation for the National Institutes of Health (Foundation for the National Institutes of Health, Inc.)/ ; }, abstract = {Microbial breakdown of organic matter is one of the most important processes on Earth, yet the controls of decomposition are poorly understood. Here we track 36 terrestrial human cadavers in three locations and show that a phylogenetically distinct, interdomain microbial network assembles during decomposition despite selection effects of location, climate and season. We generated a metagenome-assembled genome library from cadaver-associated soils and integrated it with metabolomics data to identify links between taxonomy and function. This universal network of microbial decomposers is characterized by cross-feeding to metabolize labile decomposition products. The key bacterial and fungal decomposers are rare across non-decomposition environments and appear unique to the breakdown of terrestrial decaying flesh, including humans, swine, mice and cattle, with insects as likely important vectors for dispersal. The observed lockstep of microbial interactions further underlies a robust microbial forensic tool with the potential to aid predictions of the time since death.}, } @article {pmid38346849, year = {2024}, author = {Kuruwa, S and Zade, A and Shah, S and Moidu, R and Lad, S and Chande, C and Joshi, A and Hirani, N and Nikam, C and Bhattacharya, S and Poojary, A and Kapoor, M and Kondabagil, K and Chatterjee, A}, title = {An integrated method for targeted Oxford Nanopore sequencing and automated bioinformatics for the simultaneous detection of bacteria, fungi and ARG.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxae037}, pmid = {38346849}, issn = {1365-2672}, abstract = {BACKGROUND: Metagenomics of clinical samples and microbiomes have enabled a better understanding of the role of pathogens. However, the use of metagenomics in clinical practice has been limited due to non-standardized methods of sample processing and need of expertise for the bioinformatic analysis of next generation sequencing (NGS) data.

AIM: Here we describe a workflow to encourage the clinical utility and potential of NGS for the screening of bacteria, fungi and antimicrobial resistance genes (ARGs).

METHODS: The method includes target enrichment, long-read sequencing and automated bioinformatics. Evaluation of several tools and databases was undertaken across standard organisms (n = 12), clinical isolates (n = 114) and blood samples from patients with suspected bloodstream infections (n = 33).

RESULTS: The strategy used could offset the presence of host background DNA, error rates of long read sequencing, and provide accurate and reproducible detection of pathogens. Eleven targets could be successfully tested in a single assay. Organisms could be confidently identified considering ≥ 60% of best hits of a BLAST-based threshold of e-value 0.001 and a % identity of > 80%. For ARGs, reads with % identity of > 90% and > 60% overlap of the complete gene could be confidently annotated. A kappa of 0.83 was observed compared to standard diagnostic methods. Thus, a workflow for the direct-from-sample, on-site sequencing combined with automated genomics was demonstrated to be reproducible.

CONCLUSION: NGS-based technologies overcome several limitations of current day diagnostics. Highly sensitive and comprehensive methods of pathogen screening are the need of the hour. We developed a framework for reliable, on-site, screening of pathogens.}, } @article {pmid38346660, year = {2024}, author = {Durán-Viseras, A and Lindner, BG and Hatt, JK and Lai, A and Wallace, R and Ginn, O and Brown, J and Konstantinidis, KT}, title = {Metagenomic insights into the impact of litter from poultry concentrated animal feeding operations (CAFOs) to adjacent soil and water microbial communities.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170772}, doi = {10.1016/j.scitotenv.2024.170772}, pmid = {38346660}, issn = {1879-1026}, abstract = {In recent decades, human food consumption has led to an increased demand for animal-based foods, particularly chicken meat production. The state of Georgia, USA is one of the top broiler chicken producers in the United States, where animals are raised in Concentrated Animal Feeding Operations (CAFOs). Without proper management, CAFOs could negatively impact the environment and become a public health risk as a source of water and air pollution and/or by spreading antimicrobial resistance genes. In this study, we used metagenome sequencing to investigate the impact of the application of the CAFO's litter on adjacent soils and downstream creek waters in terms of microbial diversity and antimicrobial resistance profile changes. Our data indicate that while a few microbial groups increased in abundance within a short period of time after litter application, these populations subsequently decreased to levels similar to those found prior to the litter application or to below the detection limit of our metagenome sequencing effort. Microbial taxonomic composition analyses, relative abundance of Metagenome-Assembled Genomes (MAGs) and detection of Antimicrobial Resistance Genes (ARGs) allow us to conclude that this practice of litter application had a negligible effect on the microbiome or resistome profile of these soils and nearby waterways, likely due to its dilution in the field revealing a minimal impact of these poultry facilities on the natural microbial communities.}, } @article {pmid38345985, year = {2024}, author = {Chen, K and Zhao, T and Sun, H and Geng, Y and Xu, Y and Shan, C and Chen, Y}, title = {Comparison of Three Detection Methods for Seoul Virus Causing Hemorrhagic Fever with Renal Syndrome.}, journal = {Clinical laboratory}, volume = {70}, number = {2}, pages = {}, doi = {10.7754/Clin.Lab.2023.230821}, pmid = {38345985}, issn = {1433-6510}, abstract = {BACKGROUND: Seoul virus (SEOV) is a significant causative pathogen of hemorrhagic fever with renal syndrome (HFRS). Accurate discrimination of SEOV infection from other viral or bacterial infections holds vital clinical importance.

METHODS: Our study utilized quantitative real-time PCR (qRT-PCR), metagenomic next-generation sequencing (mNGS), and immunological assays to identify the pathogen causing HFRS.

RESULTS: For the case, mNGS identified SEOV and suspected host or environmental microorganisms at 5 days from symptom onset. qRT-PCR detected SEOV between 5 to 8 days from symptom onset. Anti-hantavirus IgM antibodies reached positive criteria at 7 days and IgG antibodies at 9 days from symptom onset.

CONCLUSIONS: qRT-PCR, mNGS, and immunological assays each have merits and drawbacks. Optimal selection depends on laboratory conditions and clinical requirements.}, } @article {pmid38345467, year = {2024}, author = {Mwakibete, L and Greening, SS and Kalantar, K and Ahyong, V and Anis, E and Miller, EA and Needle, DB and Oglesbee, M and Thomas, WK and Sevigny, JL and Gordon, LM and Nemeth, NM and Ogbunugafor, CB and Ayala, AJ and Faith, SA and Neff, N and Detweiler, AM and Baillargeon, T and Tanguay, S and Simpson, SD and Murphy, LA and Ellis, JC and Tato, CM and Gagne, RB}, title = {Metagenomics for Pathogen Detection During a Mass Mortality Event in Songbirds.}, journal = {Journal of wildlife diseases}, volume = {}, number = {}, pages = {}, doi = {10.7589/JWD-D-23-00109}, pmid = {38345467}, issn = {1943-3700}, abstract = {Mass mortality events in wildlife can be indications of an emerging infectious disease. During the spring and summer of 2021, hundreds of dead passerines were reported across the eastern US. Birds exhibited a range of clinical signs including swollen conjunctiva, ocular discharge, ataxia, and nystagmus. As part of the diagnostic investigation, high-throughput metagenomic next-generation sequencing was performed across three molecular laboratories on samples from affected birds. Many potentially pathogenic microbes were detected, with bacteria forming the largest proportion; however, no singular agent was consistently identified, with many of the detected microbes also found in unaffected (control) birds and thus considered to be subclinical infections. Congruent results across laboratories have helped drive further investigation into alternative causes, including environmental contaminants and nutritional deficiencies. This work highlights the utility of metagenomic approaches in investigations of emerging diseases and provides a framework for future wildlife mortality events.}, } @article {pmid38345372, year = {2024}, author = {Campbell, BC and Greenfield, P and Barnhart, EP and Gong, S and Midgley, DJ and Paulsen, IT and George, SC}, title = {Krumholzibacteriota and Deltaproteobacteria contain rare genetic potential to liberate carbon from monoaromatic compounds in subsurface coal seams.}, journal = {mBio}, volume = {}, number = {}, pages = {e0173523}, doi = {10.1128/mbio.01735-23}, pmid = {38345372}, issn = {2150-7511}, abstract = {Biogenic methane in subsurface coal seam environments is produced by diverse consortia of microbes. Although this methane is useful for global energy security, it remains unclear which microbes can liberate carbon from the coal. Most of this carbon is relatively resistant to biodegradation, as it is contained within aromatic rings. Thus, to explore for coal-degrading taxa in the subsurface, this study reconstructed relevant metagenome-assembled genomes (MAGs) from coal seams by using a key genomic marker for the anaerobic degradation of monoaromatic compounds as a guide: the benzoyl-CoA reductase gene (bcrABCD). Three MAGs were identified with this genetic potential. The first represented a novel taxon from the Krumholzibacteriota phylum, which this study is the first to describe. This Krumholzibacteriota MAG contained a full set of genes for benzoyl-CoA dearomatization, in addition to other genes for anaerobic catabolism of monoaromatics. Analysis of Krumholzibacteriota MAGs from other environments revealed that this genetic potential may be common, and thus, Krumholzibacteriota may be important organisms for the liberation of recalcitrant carbon in a broad range of environments. Moreover, the assembly and characterization of two Syntrophorhabdus aromaticivorans MAGs from different continents and a Syntrophaceae sp. MAG implicate the Deltaproteobacteria class in coal seam monoaromatic degradation. Each of these taxa are potential rate-limiting organisms for subsurface coal-to-methane biodegradation. Their description here provides some understanding of their function within the coal seam microbiome and will help inform future efforts in coal bed methane stimulation, anoxic bioremediation of organic pollutants, and assessments of anoxic, subsurface carbon cycling and emissions.IMPORTANCESubsurface coal seams are highly anoxic, oligotrophic environments, where the main source of carbon is "locked away" within aromatic rings. Despite these challenges, many coal seams accumulate biogenic methane, implying that the coal seam microbiome is "unlocking" this carbon source in situ. For over two decades, researchers have endeavored to understand which organisms perform these processes. This study provides the first descriptions of organisms with this genetic potential from the coal seam environment. Here, we report metagenomic insights into carbon liberation from aromatic molecules and the degradation pathways involved and describe a Krumholzibacteriota, two Syntrophorhabdus aromaticivorans, and a Syntrophaceae MAG that contain this genetic potential. This is also the first time that the Krumholzibacteriota phylum has been implicated in anaerobic dearomatization of aromatic hydrocarbons. This potential is identified here in numerous MAGs from other terrestrial and marine subsurface habitats, implicating the Krumholzibacteriota in carbon-cycling processes across a broad range of environments.}, } @article {pmid38345108, year = {2024}, author = {Shih, KC and Tong, L}, title = {The Conjunctival Microbiome and Dry Eye: What We Know and Controversies.}, journal = {Eye & contact lens}, volume = {}, number = {}, pages = {}, doi = {10.1097/ICL.0000000000001077}, pmid = {38345108}, issn = {1542-233X}, abstract = {Dry eye disease is a common multifactorial condition that may be idiopathic or associated with autoimmune conditions, such as Sjogren syndrome. Commensal microorganisms modify immune responses, so it is relevant to understand how they modify such immune-mediated diseases. Microbiota in the gut regulate inflammation in the eye, and conversely, severe inflammation of the ocular surface results in alteration of gut microbiome. The conjunctiva microbiome can be analyzed using 16S or shotgun metagenomics. The amount of microbial DNA in ocular surface mucosa relative to human DNA is limited compared with the case of the intestinal microbiome. There are challenges in defining, harvesting, processing, and analyzing the microbiome in the ocular surface mucosa. Recent studies have shown that the conjunctiva microbiome depends on age, presence of local and systemic inflammation, and environmental factors. Microbiome-based therapy, such as the use of oral probiotics to manage dry eye disease, has initial promising results. Further longitudinal studies are required to investigate the alteration of the conjunctival microbiome after local therapy and surgery.}, } @article {pmid38343829, year = {2024}, author = {Kim, M and Ii, RCP and Shah, VS and Ross, M and Cormier, J and Baig, A and Huang, CY and Brenner, L and Neuringer, I and Whiteson, K and Harris, JK and Willis, AD and Lai, PS}, title = {Host DNA depletion on frozen human respiratory samples enables successful metagenomic sequencing for microbiome studies.}, journal = {Research square}, volume = {}, number = {}, pages = {}, doi = {10.21203/rs.3.rs-3638876/v1}, pmid = {38343829}, abstract = {Background Most respiratory microbiome studies have focused on amplicon rather than metagenomics sequencing due to high host DNA content. We evaluated efficacy of five host DNA depletion methods on previously frozen human bronchoalveolar lavage (BAL), nasal swabs, and sputum prior to metagenomic sequencing. Results Median sequencing depth was 76.4 million reads per sample. Untreated nasal, sputum and BAL samples had 94.1%, 99.2%, and 99.7% host-reads. The effect of host depletion differed by sample type. Most treatment methods increased microbial reads, species richness and predicted functional richness; the increase in species and predicted functional richness was mediated by higher effective sequencing depth. For BAL and nasal samples, most methods did not change Morisita-Horn dissimilarity suggesting limited bias introduced by host depletion. Conclusions Metagenomics sequencing without host depletion will underestimate microbial diversity of most respiratory samples due to shallow effective sequencing depth and is not recommended. Optimal host depletion methods vary by sample type.}, } @article {pmid38343326, year = {2024}, author = {Miao, Y and Sun, Z and Ma, C and Lin, C and Wang, G and Yang, C}, title = {VirGrapher: a graph-based viral identifier for long sequences from metagenomes.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {2}, pages = {}, doi = {10.1093/bib/bbae036}, pmid = {38343326}, issn = {1477-4054}, support = {62301139//Fundamental Research Funds for the Central Universities/ ; 62225109//National Natural Science Foundation of China/ ; }, abstract = {Viruses are the most abundant biological entities on earth and are important components of microbial communities. A metagenome contains all microorganisms from an environmental sample. Correctly identifying viruses from these mixed sequences is critical in viral analyses. It is common to identify long viral sequences, which has already been passed thought pipelines of assembly and binning. Existing deep learning-based methods divide these long sequences into short subsequences and identify them separately. This makes the relationships between them be omitted, leading to poor performance on identifying long viral sequences. In this paper, VirGrapher is proposed to improve the identification performance of long viral sequences by constructing relationships among short subsequences from long ones. VirGrapher see a long sequence as a graph and uses a Graph Convolutional Network (GCN) model to learn multilayer connections between nodes from sequences after a GCN-based node embedding model. VirGrapher achieves a better AUC value and accuracy on validation set, which is better than three benchmark methods.}, } @article {pmid38342563, year = {2024}, author = {Shen, Y and Liu, N and Wang, Z}, title = {Recent advances in the culture-independent discovery of natural products using metagenomic approaches.}, journal = {Chinese journal of natural medicines}, volume = {22}, number = {2}, pages = {100-111}, doi = {10.1016/S1875-5364(24)60585-6}, pmid = {38342563}, issn = {1875-5364}, abstract = {Natural products derived from bacterial sources have long been pivotal in the discovery of drug leads. However, the cultivation of only about 1% of bacteria in laboratory settings has left a significant portion of biosynthetic diversity hidden within the genomes of uncultured bacteria. Advances in sequencing technologies now enable the exploration of genetic material from these metagenomes through culture-independent methods. This approach involves extracting genetic sequences from environmental DNA and applying a hybrid methodology that combines functional screening, sequence tag-based homology screening, and bioinformatic-assisted chemical synthesis. Through this process, numerous valuable natural products have been identified and synthesized from previously uncharted metagenomic territories. This paper provides an overview of the recent advancements in the utilization of culture-independent techniques for the discovery of novel biosynthetic gene clusters and bioactive small molecules within metagenomic libraries.}, } @article {pmid38342543, year = {2024}, author = {Jin, YH and Mah, JH}, title = {Culture-dependent and -independent analyses of bacterial compositions and its contributions to formation of γ-aminobutyric acid and poly-γ-glutamic acid in Cheonggukjang.}, journal = {Food research international (Ottawa, Ont.)}, volume = {179}, number = {}, pages = {114026}, doi = {10.1016/j.foodres.2024.114026}, pmid = {38342543}, issn = {1873-7145}, abstract = {This study was performed to unveil bacterial compositions and their contributions to the formation of γ-aminobutyric acid (GABA) and poly-γ-glutamic acid (γ-PGA) in Cheonggukjang. To predict possible key factors contributing to the content of the bioactive compounds in Cheonggukjang, commercial products were analyzed for various parameters. The content of GABA and γ-PGA showed a negative (R[2] = 0.61 - 0.73) and positive correlation (R[2] = 0.53 - 0.96) with antioxidative activity. Consistently, GABA content showed a moderate negative correlation with γ-PGA content (R[2] = 0.58). Among the physicochemical and microbial parameters, only salinity showed a moderate negative correlation with γ-PGA content (R[2] = 0.75), which might be due to the inhibition of bacterial growth. It was also suggested that multiple factors (including bacterial species) were involved in the formation of GABA and γ-PGA in Cheonggukjang. To reveal dominant bacterial species and further presume their contributions to the bioactive compound formation in Cheonggukjang, both culture-independent (metagenomic) and -dependent (culturomic) methods were used. Culture-independent method showed that Bacillus piscis was dominant (23.37 - 94.89 %), followed by B. hisashii (0.00 - 62.45 %) and B. coagulans (0.00 - 13.82 %). Considering the quantitative speciation data on the bioactive compound content in Cheonggukjang (and bacterial production capability) together, it was further elucidated that B. piscis contributed primarily to the bioactive compound formation. Unlike this, culture-dependent analysis revealed that B. licheniformis and B. subtilis were dominant (30.0 - 47.6 and 17.5 - 39.5 %, respectively). Based on the quantitative speciation data on the bacterial production capability of GABA and γ-PGA, B. subtilis was the primarily contributing bacterial species to the bioactive compound formation. Consequently, it was observed that the bacterial compositions and their contributions to the bioactive compound formation determined by the two methods differed considerably, i.e., B. piscis and B. subtilis were identified to be prominent bacterial contributors, respectively, depending on the method used.}, } @article {pmid38342281, year = {2024}, author = {Zhang, J and Wang, Q and Yu, H and Lin, L and Zhang, Z and Song, Y}, title = {Metagenomic insights into protein degradation mechanisms in natural fermentation of cassava leaves.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {130433}, doi = {10.1016/j.biortech.2024.130433}, pmid = {38342281}, issn = {1873-2976}, abstract = {Cassava (Manihot esculenta Crantz) leaves, the primary by-product of cassava processing, constitute a significant protein source, accounting for 18 to 38 percent on a dry weight basis. Despite their nutritional value, a substantial portion of these leaves is often discarded post-harvest, resulting in notable resource waste. This study employs metagenomic technology to investigate the protein degradation mechanism in cassava leaves, aiming to provide a technical reference for value-added of this by-product. Following a 36-hour period of natural fermentation, the protein degradation rate reached 58%, a phenomenon intricately linked to both the microbial community structure and its functional properties. Notably, Lactococcus and Enterobacter, recognized for their abundant protease activity, were predominant. Metagenomically assembled genomes further revealed Lactococcus's substantial role in producing flavors and active compounds, including amino acids and peptides. This study offers novel perspectives to the foodization and high-value utilization of cassava by-products, emphasizing the sustainable exploitation of biomass resources.}, } @article {pmid38341975, year = {2024}, author = {Li, Z and Guo, X and Liu, B and Huang, T and Liu, R and Liu, X}, title = {Metagenome sequencing reveals shifts in phage-associated antibiotic resistance genes from influent to effluent in wastewater treatment plants.}, journal = {Water research}, volume = {253}, number = {}, pages = {121289}, doi = {10.1016/j.watres.2024.121289}, pmid = {38341975}, issn = {1879-2448}, abstract = {Antibiotic resistance poses a significant threat to global health, and the microbe-rich activated sludge environment may contribute to the dissemination of antibiotic resistance genes (ARGs). ARGs spread across various bacterial populations via multiple dissemination routes, including horizontal gene transfer mediated by bacteriophages (phages). However, the potential role of phages in spreading ARGs in wastewater treatment systems remains unclear. This study characterized the core resistome, mobile genetic elements (MGEs), and virus-associated ARGs (vir_ARGs) in influents (Inf) and effluents (Eff) samples from nine WWTPs in eastern China. The abundance of ARGs in the Inf samples was higher than that in the Eff samples. A total of 21 core ARGs were identified, accounting for 38.70 %-83.70 % of the different samples. There was an increase in MGEs associated with phage-related processes from influents to effluents (from 12.68 % to 21.10 %). These MGEs showed strong correlations in relative abundance and composition with the core ARGs in the Eff samples. Across the Inf and Eff samples, 58 unique vir_ARGs were detected, with the Eff samples exhibiting higher diversity of vir_ARGs than the Inf samples. Statistical analyses indicated a robust relationship between core ARG profile, MGEs associated with phage-related processes, and vir_ARG composition in the Eff samples. Additionally, the co-occurrence of MGEs and ARGs in viral genomes was observed, ranging from 22.73 % to 68.75 %. This co-occurrence may exacerbate the persistence and spread of ARGs within WWTPs. The findings present new information on the changes in core ARGs, MGEs, and phage-associated ARGs from influents to effluents in WWTPs and provide new insights into the role of phage-associated ARGs in these systems.}, } @article {pmid38341972, year = {2024}, author = {Kuroda, K and Maeda, R and Shinshima, F and Urasaki, K and Kubota, K and Nobu, MK and Noguchi, TQP and Satoh, H and Yamauchi, M and Narihiro, T and Yamada, M}, title = {Microbiological insights into anaerobic phenol degradation mechanisms and bulking phenomenon in a mesophilic upflow anaerobic sludge blanket reactor in long-term operation.}, journal = {Water research}, volume = {253}, number = {}, pages = {121271}, doi = {10.1016/j.watres.2024.121271}, pmid = {38341972}, issn = {1879-2448}, abstract = {In this study, a long-term operation of 2,747 days was conducted to evaluate the performance of the upflow anaerobic sludge blanket (UASB) reactor and investigated the degradation mechanisms of high-organic loading phenol wastewater. During the reactor operation, the maximum chemical oxygen demand (COD) removal rate of 6.1 ± 0.6 kg/m[3]/day under 1,680 mg/L phenol concentration was achieved in the mesophilic UASB reactor. After a significant change in the operating temperature from 24.0 ± 4.1 °C to 35.9 ± 0.6 °C, frequent observations of floating and washout of the bloated granular sludge (novel types of the bulking phenomenon) were made in the UASB reactor, suggesting that the change in operating temperature could be a trigger for the bulking phenomenon. Through the metagenomic analysis, phenol degradation mechanisms were predicted that phenol was converted to 4-hydroxybenzoate via two possible routes by Syntrophorhabdaceae and Pelotomaculaceae bacteria. Furthermore, the degradation of 4-hydroxybenzoate to benzoyl-CoA was carried out by members of Syntrophorhabdaceae and Smithellaceae. In the bulking sludge, a predominant presence of Nanobdellota, belonging to DPANN archaea, was detected. The metagenome-assembled genome of the Nanobdellota lacks many biosynthetic pathways and has several genes for the symbiotic lifestyle such as trimeric autotransporter adhesin-related protein. Furthermore, the Nanobdellota have significant correlations with several methanogenic archaea that are predominantly present in the UASB reactor. Considering the results of this study, the predominant Nanobdellota may negatively affect the growth of the methanogens through the parasitic lifestyle and change the balance of microbial interactions in the granular sludge ecosystem.}, } @article {pmid38341971, year = {2024}, author = {Zhu, Z and Ding, J and Du, R and Zhang, Z and Guo, J and Li, X and Jiang, L and Chen, G and Bu, Q and Tang, N and Lu, L and Gao, X and Li, W and Li, S and Zeng, G and Liang, J}, title = {Systematic tracking of nitrogen sources in complex river catchments: Machine learning approach based on microbial metagenomics.}, journal = {Water research}, volume = {253}, number = {}, pages = {121255}, doi = {10.1016/j.watres.2024.121255}, pmid = {38341971}, issn = {1879-2448}, abstract = {Tracking nitrogen pollution sources is crucial for the effective management of water quality; however, it is a challenging task due to the complex contaminative scenarios in the freshwater systems. The contaminative pattern variations can induce quick responses of aquatic microorganisms, making them sensitive indicators of pollution origins. In this study, the soil and water assessment tool, accompanied by a detailed pollution source database, was used to detect the main nitrogen pollution sources in each sub-basin of the Liuyang River watershed. Thus, each sub-basin was assigned to a known class according to SWAT outputs, including point source pollution-dominated area, crop cultivation pollution-dominated area, and the septic tank pollution-dominated area. Based on these outputs, the random forest (RF) model was developed to predict the main pollution sources from different river ecosystems using a series of input variable groups (e.g., natural macroscopic characteristics, river physicochemical properties, 16S rRNA microbial taxonomic composition, microbial metagenomic data containing taxonomic and functional information, and their combination). The accuracy and the Kappa coefficient were used as the performance metrics for the RF model. Compared with the prediction performance among all the input variable groups, the prediction performance of the RF model was significantly improved using metagenomic indices as inputs. Among the metagenomic data-based models, the combination of the taxonomic information with functional information of all the species achieved the highest accuracy (0.84) and increased median Kappa coefficient (0.70). Feature importance analysis was used to identify key features that could serve as indicators for sudden pollution accidents and contribute to the overall function of the river system. The bacteria Rhabdochromatium marinum, Frankia, Actinomycetia, and Competibacteraceae were the most important species, whose mean decrease Gini indices were 0.0023, 0.0021, 0.0019, and 0.0018, respectively, although their relative abundances ranged only from 0.0004 to 0.1 %. Among the top 30 important variables, functional variables constituted more than half, demonstrating the remarkable variation in the microbial functions among sites with distinct pollution sources and the key role of functionality in predicting pollution sources. Many functional indicators related to the metabolism of Mycobacterium tuberculosis, such as K24693, K25621, K16048, and K14952, emerged as significant important factors in distinguishing nitrogen pollution origins. With the shortage of pollution source data in developing regions, this suggested approach offers an economical, quick, and accurate solution to locate the origins of water nitrogen pollution using the metagenomic data of microbial communities.}, } @article {pmid38341816, year = {2024}, author = {Chen, Z and Ye, T and He, Y and Pan, A and Mei, Q}, title = {Use of pus metagenomic next-generation sequencing for efficient identification of pathogens in patients with sepsis.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {38341816}, issn = {1874-9356}, abstract = {The positive detection rate of blood metagenomic next-generation sequencing (mNGS) was still too low to meet clinical needs, while pus from the site of primary infection may be advantageous for identification of pathogens. To assess the value of mNGS using pus in patients with sepsis, thirty-five samples were collected. Pathogen identification and mixed infection diagnosis obtained by use of mNGS or cultivation methods were compared. Fifty-three aerobic or facultative anaerobes, 59 obligate anaerobes and 7 fungi were identified by the two methods. mNGS increased the accuracy rate of diagnosing aerobic or facultative anaerobic infections from 44.4% to 94.4%; mNGS also increased the sensitivity of diagnosing obligate anaerobic infections from 52.9% to 100.0%; however, mNGS did not show any advantage in terms of fungal infections. Culture and mNGS identified 1 and 24 patients with mixed infection, respectively. For obligate anaerobes, source of microorganisms was analyzed. The odontogenic bacteria all caused empyema (n = 7) or skin and soft tissue infections (n = 5), whereas the gut-derived microbes all caused intra-abdominal infections (n = 7). We also compared the clinical characteristics of non-obligate anaerobic and obligate anaerobic infection groups. The SOFA score [9.0 (7.5, 14.3) vs. 5.0 (3.0, 8.0), P = 0.005], procalcitonin value [4.7 (1.8, 39.9) vs. 2.50 (0.7, 8.0), P = 0.035], the proportion of septic shock (66.7% vs. 35.3%, P = 0.044) and acute liver injury (66.7% vs. 23.5%, P = 0.018) in the non-obligate anaerobic infection group were significantly higher than those in the obligate anaerobic infection group. In patients with sepsis caused by purulent infection, mNGS using pus from the primary lesion may yield more valuable microbiological information.}, } @article {pmid38344319, year = {2022}, author = {Mousavi Maleki, MS and Yakhchali, B and Karkhaneh, AA and Rezvani, M and Ahmadpour, F}, title = {A Cross-section Metagenomics and 16S Ribosomal DNA Based Evaluation of the Bacterial and Archaeal Communities Resident in the Forumad Chromite Mine, Northeastern of Iran.}, journal = {Iranian journal of biotechnology}, volume = {20}, number = {4}, pages = {e2818}, pmid = {38344319}, issn = {1728-3043}, abstract = {BACKGROUND: The Forumad chromite area from Sabzevar ophiolite belt, Northeastern Iran, is an environment with high concentration of heavy metals, particularly chromite and magnesite minerals, containing chromium and magnesium.

OBJECTIVES: In this study for the first time, we analyzed and report the diversity of microbial (bacterial and archaeal) community inhabiting in Forumad chromite mine environment using metagenomics approach.

MATERIALS AND METHODS: Samples were obtained from different areas of the mine, and total DNA was extracted from water and soil samples. 16S rDNA was amplified using universal primers and the PCR products were cloned in pTz57R/T plasmid. Then, 43% of the positive clones were randomly sequenced. BLAST program in NCBI and EzTaxon databases were used to identify similar 16S rDNA sequences. Phylogenetic analysis was performed using the MEGA5 software and multiple alignments of sequences.

RESULTS: In the phylogenetic analyses, proteobacteria, which contains many heavy metals tolerant bacteria especially chromium, were the dominant population in bacterial libraries with Rheinheimera and Cedecaeas the most abundant genuses. Other phyla were Bacteroidetes, Firmicutes, Verrucomicrobia, Chloroflexi, Actinobacteria, Acidobacteria, Cyanobacteria, Gemmatimonadetes, and Planctomycetes. In the archaeal clone library, all the sequences were related to the phylum Thaumarchaeota. Further, 68.6% of the sequences had less than 98.7℅ similarity with the recorded strains which could represent new taxons.

CONCLUSIONS: The results showed that there was a high microbial diversity in the Forumad chromite area. These results can be used for detoxification and bioremediation of regions contaminated with heavy metals, although more studies are needed.}, } @article {pmid38341424, year = {2024}, author = {Gao, SM and Fei, HL and Li, Q and Lan, LY and Huang, LN and Fan, PF}, title = {Eco-evolutionary dynamics of gut phageome in wild gibbons (Hoolock tianxing) with seasonal diet variations.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1254}, pmid = {38341424}, issn = {2041-1723}, support = {2022YFF1301500//Ministry of Science and Technology of the People's Republic of China (Chinese Ministry of Science and Technology)/ ; 31822049//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31770421//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32201269//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2021A1515110523//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; 2023A1515010695//Natural Science Foundation of Guangdong Province (Guangdong Natural Science Foundation)/ ; 2021M703754//China Postdoctoral Science Foundation/ ; }, abstract = {It has been extensively studied that the gut microbiome provides animals flexibility to adapt to food variability. Yet, how gut phageome responds to diet variation of wild animals remains unexplored. Here, we analyze the eco-evolutionary dynamics of gut phageome in six wild gibbons (Hoolock tianxing) by collecting individually-resolved fresh fecal samples and parallel feeding behavior data for 15 consecutive months. Application of complementary viral and microbial metagenomics recovers 39,198 virulent and temperate phage genomes from the feces. Hierarchical cluster analyses show remarkable seasonal diet variations in gibbons. From high-fruit to high-leaf feeding period, the abundances of phage populations are seasonally fluctuated, especially driven by the increased abundance of virulent phages that kill the Lachnospiraceae hosts, and a decreased abundance of temperate phages that piggyback the Bacteroidaceae hosts. Functional profiling reveals an enrichment through horizontal gene transfers of toxin-antitoxin genes on temperate phage genomes in high-leaf season, potentially conferring benefits to their prokaryotic hosts. The phage-host ecological dynamics are driven by the coevolutionary processes which select for tail fiber and DNA primase genes on virulent and temperate phage genomes, respectively. Our results highlight complex phageome-microbiome interactions as a key feature of the gibbon gut microbial ecosystem responding to the seasonal diet.}, } @article {pmid38341044, year = {2024}, author = {Tian, G and Kong, Z and Zhang, Y and Qiu, L and Wang, H and Yan, Q}, title = {Simultaneous ammonia and nitrate removal by novel integrated partial denitrification-anaerobic ammonium oxidation-bioelectrochemical system.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {130428}, doi = {10.1016/j.biortech.2024.130428}, pmid = {38341044}, issn = {1873-2976}, abstract = {The current study explored the performance of an integrated partial denitrification-anaerobic ammonium oxidation (anammox)-bioelectrochemical system on simultaneous removal of ammonia nitrogen and nitrate nitrogen. Different operational conditions were selected to optimize critical parameters of the process for improving nitrogen removal. The results indicated that more than 90 % of total inorganic nitrogen removal efficiency was achieved under the optimal conditions: ammonia nitrogen/nitrate nitrogen ratio of 1:2, external resistance of 200 Ω and inoculation volume ratio of anammox bacteria/denitrifying at 2:1. Improved nitrogen removal under the optimal conditions were confirmed by microbial community changes (Candidatus Brocadia and Thiobacillus) and enhanced of nitrogen metabolism-related genes (hao, hzsA/C and hdh). Increases of Limnobacter indicated an enhanced electron transfer efficiency. Overall, high-efficiency and stable nitrogen removal efficiency without nitrite nitrogen accumulation could be achieved by the integrated system under the optimal conditions, providing novel insights for simultaneous treatment of domestic wastewater and groundwater.}, } @article {pmid38340855, year = {2024}, author = {Xiang, Y and Xiong, W and Yang, Z and Xu, R and Zhang, Y and Wu, M and Ye, Y and Peng, H and Sun, W and Wang, D}, title = {Metagenomic insights into the toxicity of carbamazepine to functional microorganisms in sludge anaerobic digestion.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170780}, doi = {10.1016/j.scitotenv.2024.170780}, pmid = {38340855}, issn = {1879-1026}, abstract = {Contaminants of emerging concern (CECs) contained in sludge, such as carbamazepine, may be toxic to microorganisms and affect the biogenesis of methane during anaerobic digestion. In this study, different scales of anaerobic digesters were constructed to investigate the inhibitory effect of carbamazepine. Results showed that carbamazepine reduced methane production by 11.3 % and 62.1 % at concentrations of 0.4 and 2 mg/g TS, respectively. Carbamazepine hindered the dissolution of organic matter and the degradation of protein. Carbamazepine inhibited some fermentative bacteria, especially uncultured Aminicenantales, whose abundance decreased by 9.5-93.4 % under carbamazepine stress. It is worth noting that most prior studies investigated the effects of CECs only based on well-known microorganisms, ignoring the metabolisms of uncultured microorganisms. Genome-predicted metabolic potential suggested that 54 uncultured metagenome-assembled genomes (MAGs) associated with acidogenesis or acetogenesis. Therein, uncultured Aminicenantales related MAGs were proved to be acetogenic fermenters, their significant reduction may be an important reason for the decrease of methane production under carbamazepine stress. The toxicity of carbamazepine to microorganisms was mainly related to the overproduction of reactive oxygen species. This study elucidates the inhibition mechanism of carbamazepine and emphasizes the indispensable role of uncultured microorganisms in anaerobic digestion.}, } @article {pmid38340836, year = {2024}, author = {Gao, D and Xu, A and Zhang, Y and Fengqin, L and Li, H and Liang, H}, title = {Metagenomic insights into carbon and nitrogen cycling in the water-land transition zone of inland alkaline wetlands.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170856}, doi = {10.1016/j.scitotenv.2024.170856}, pmid = {38340836}, issn = {1879-1026}, abstract = {Inland alkaline wetlands play a crucial role in maintaining ecological functions. However, these wetlands are becoming more vulnerable to the effects of water level fluctuations caused by global climate change, especially concerning carbon (C) and nitrogen (N) cycling. Here, metagenomics sequencing was used to investigate microorganism diversity, C and N cycling gene abundance at three water level types (D (dry), MF (Middle flooded), HF (high flooded)) along an inland alkaline wetland. Our findings reveal that water level was the most important factor in regulating the microbial communities. Distinct shifts in community composition were found along the water level increases, without fundamentally altering their composition. With the increase of water level, the relative abundance of pmoA decreased from 2.5 × 10[-5] to 5.1 × 10[-6]. The C cycling processes shift from predominantly CO2-generated processes under low water levels to CO2 and CH4 co-generated processes under high water levels. The relative abundance of nosZ reached 4.9 × 10[-5] in HF, while in D and MF, it is recorded at 4.5 × 10[-5] and 3.4 × 10[-5], respectively. Water levels accelerate N cycling and generating N2O intermediates. Furthermore, our study highlights the dynamic competition and cooperation between C and N cycling processes. This research provides a comprehensive biological understanding of the influence of varying water levels on soil C and N cycling processes in wetland.}, } @article {pmid38340614, year = {2024}, author = {Mahnic, A and Rak, M and Trebše, R and Rupnik, M and Cőr, A}, title = {Identification of prosthetic joint infections with 16S amplicon metagenomic sequencing - comparison with standard cultivation approach.}, journal = {Diagnostic microbiology and infectious disease}, volume = {109}, number = {1}, pages = {116188}, doi = {10.1016/j.diagmicrobio.2024.116188}, pmid = {38340614}, issn = {1879-0070}, abstract = {Prosthetic joint infections (PJIs) are commonly diagnosed via culture-based methods, which may miss hard-to-grow pathogens. This study contrasts amplicon metagenomic sequencing (16S AS) with traditional culture techniques for enhanced clinical decision-making. We analyzed sonicate fluid from 27 patients undergoing revision arthroplasty using both methods, emphasizing the distinction between contaminants and true positives. Our findings show moderate agreement between the two methods, with a Cohen's kappa of 0.490, varying across bacterial genera (Cohen's kappa -0.059 to 1). The sensitivity of 16S AS compared to culture was 81% (95% CI, 68% to 94%). Sequencing revealed greater microbial diversity, including anaerobic genera like Anaerococcus and Citrobacter. Interestingly, several culture-negative PJI samples showed diverse bacteria via 16S AS. Despite rigorous controls and algorithms to eliminate contaminants, confirming bacteria presence with 16S AS remains a challenge. This highlights the need for improved PJI diagnostic methods, while also pointing out the limitations of next-generation sequencing (NGS) as a clinical diagnostic tool.}, } @article {pmid38340561, year = {2024}, author = {Jing, Z and Tu, S and Yuan, P and Liu, X and Wang, S and Dong, B and Li, Q and Gao, H}, title = {The ecological role of microbiome at community-, taxonomic - and genome-levels in black-odorous waters.}, journal = {Journal of hazardous materials}, volume = {467}, number = {}, pages = {133673}, doi = {10.1016/j.jhazmat.2024.133673}, pmid = {38340561}, issn = {1873-3336}, abstract = {Black-odorous waters (BOWs) are heavily polluted waters where microbial information remains elusive mechanistically. Based on gene amplicon and metagenomics sequencing, a comprehensive study was conducted to investigate the microbial communities in urban and rural BOWs. The results revealed that microbial communities' assembly in urban and rural BOWs was predominantly governed by stochastic factors at the community level. At the taxonomic level, there were 62 core species (58.48%) in water and 207 core species (44.56%) in sediment across urban and rural areas. Notably, significant differences were observed in the functional genetic composition of BOWs between urban and rural areas. Specifically, rural areas exhibited an enhanced abundance of genes involved in nitrogen fixation, Fe[2+] transport, and sulfate reduction. Conversely, urban areas showed higher abundances of some genes associated with carbon fixation, nitrification and denitrification. A sulfur-centered ecological model of microbial communities was constructed by integrating data from the three levels of analysis, and 14 near-complete draft genomes were generated, representing a substantial portion of the microbial community (35.04% in rural BOWs and 29.97% in urban BOWs). This research provides significant insights into the sustainable management and preservation of aquatic ecosystems affected by BOWs.}, } @article {pmid38339197, year = {2024}, author = {Laske, C and Müller, S and Munk, MHJ and Honold, I and Willmann, M and Peter, S and Schoppmeier, U}, title = {Prognostic Value of Gut Microbiome for Conversion from Mild Cognitive Impairment to Alzheimer's Disease Dementia within 4 Years: Results from the AlzBiom Study.}, journal = {International journal of molecular sciences}, volume = {25}, number = {3}, pages = {}, doi = {10.3390/ijms25031906}, pmid = {38339197}, issn = {1422-0067}, support = {374-1-0//University of Tübingen/ ; 32-5400/58/3//Forum Gesundheitsstandort BW/ ; D3030814//Faber Foundation/ ; }, abstract = {Alterations in the gut microbiome are associated with the pathogenesis of Alzheimer's disease (AD) and can be used as a diagnostic measure. However, longitudinal data of the gut microbiome and knowledge about its prognostic significance for the development and progression of AD are limited. The aim of the present study was to develop a reliable predictive model based on gut microbiome data for AD development. In this longitudinal study, we investigated the intestinal microbiome in 49 mild cognitive impairment (MCI) patients over a mean (SD) follow-up of 3.7 (0.6) years, using shotgun metagenomics. At the end of the 4-year follow-up (4yFU), 27 MCI patients converted to AD dementia and 22 MCI patients remained stable. The best taxonomic model for the discrimination of AD dementia converters from stable MCI patients included 24 genera, yielding an area under the receiver operating characteristic curve (AUROC) of 0.87 at BL, 0.92 at 1yFU and 0.95 at 4yFU. The best models with functional data were obtained via analyzing 25 GO (Gene Ontology) features with an AUROC of 0.87 at BL, 0.85 at 1yFU and 0.81 at 4yFU and 33 KO [Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog] features with an AUROC of 0.79 at BL, 0.88 at 1yFU and 0.82 at 4yFU. Using ensemble learning for these three models, including a clinical model with the four parameters of age, gender, body mass index (BMI) and Apolipoprotein E (ApoE) genotype, yielded an AUROC of 0.96 at BL, 0.96 at 1yFU and 0.97 at 4yFU. In conclusion, we identified novel and timely stable gut microbiome algorithms that accurately predict progression to AD dementia in individuals with MCI over a 4yFU period.}, } @article {pmid38242208, year = {2024}, author = {Miesbach, W and Konkle, B and Chowdary, P and Kaczmarek, R and Leebeek, F and Mahlangu, J and Makris, M and Pipe, SW and Srivastava, A and Voorberg, J and Pierce, GF and Peyvandi, F}, title = {Recommendations for a minimum data set for monitoring gene therapy in hemophilia: communication from the ISTH SSC Working Group on Gene Therapy.}, journal = {Journal of thrombosis and haemostasis : JTH}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jtha.2023.12.039}, pmid = {38242208}, issn = {1538-7836}, abstract = {Independent data collection is crucial in addressing the challenges associated with gene therapy for hemophilia, which is a promising treatment option but requires careful monitoring and management of short-term and potential long-term safety concerns. The International Society on Thrombosis and Haemostasis has identified a minimum efficacy and safety data set included in the World Federation of Hemophilia Gene Therapy Registry that should be collected on a national basis at specific time points for each patient who has been treated with the gene therapy products. This Gene Therapy Minimum Data Set (GT-MDS) was developed to facilitate data collection and to ensure capturing the most relevant data and most known and unknown safety and efficacy parameters recently cited by the European Medicine Agencies. The concept of assembling a minimum data set is not about creating a new data set but rather about identifying a subset of critical and essential topics that should always be included. The GT-MDS is structured into 3 sections and comprises an abridged list of 6 topics during routine gene therapy follow-up, keeping the number of data points low but allowing for rapid and independent data evaluation. The World Federation of Hemophilia Gene Therapy Registry data set, developed by the World Federation of Hemophilia, the International Society on Thrombosis and Haemostasis, and other organizations, including industry partners in 2020, is comprehensive. The GT-MDS reports the minimum relevant information that should not be lost and is mandatory to be collected for all patients who undergo gene therapy. Therefore, the implementation of the gene therapy registry and the minimum data set empowers and enhances data collection at a global level.}, } @article {pmid38338789, year = {2024}, author = {Benedetto, A and Robotti, E and Belay, MH and Ghignone, A and Fabbris, A and Goggi, E and Cerruti, S and Manfredi, M and Barberis, E and Peletto, S and Arillo, A and Giaccio, N and Masini, MA and Brandi, J and Cecconi, D and Marengo, E and Brizio, P}, title = {Multi-Omics Approaches for Freshness Estimation and Detection of Illicit Conservation Treatments in Sea Bass (Dicentrarchus Labrax): Data Fusion Applications.}, journal = {International journal of molecular sciences}, volume = {25}, number = {3}, pages = {}, doi = {10.3390/ijms25031509}, pmid = {38338789}, issn = {1422-0067}, support = {GR-2016-02363722//Ministero della Salute/ ; }, abstract = {Fish freshness consists of complex endogenous and exogenous processes; therefore, the use of a few parameters to unravel illicit practices could be insufficient. Moreover, the development of strategies for the identification of such practices based on additives known to prevent and/or delay fish spoilage is still limited. The paper deals with the identification of the effect played by a Cafodos solution on the conservation state of sea bass at both short-term (3 h) and long-term (24 h). Controls and treated samples were characterized by a multi-omic approach involving proteomics, lipidomics, metabolomics, and metagenomics. Different parts of the fish samples were studied (muscle, skin, eye, and gills) and sampled through a non-invasive procedure based on EVA strips functionalized by ionic exchange resins. Data fusion methods were then applied to build models able to discriminate between controls and treated samples and identify the possible markers of the applied treatment. The approach was effective in the identification of the effect played by Cafodos that proved to be different in the short- and long-term and complex, involving proteins, lipids, and small molecules to a different extent.}, } @article {pmid38338730, year = {2024}, author = {Kong, D and Ye, Z and Dai, M and Ma, B and Tan, X}, title = {Light Intensity Modulates the Functional Composition of Leaf Metabolite Groups and Phyllosphere Prokaryotic Community in Garden Lettuce (Lactuca sativa L.) Plants at the Vegetative Stage.}, journal = {International journal of molecular sciences}, volume = {25}, number = {3}, pages = {}, doi = {10.3390/ijms25031451}, pmid = {38338730}, issn = {1422-0067}, support = {2022C02026; 2022C02003//Key R&D Program of Zhejiang Province, China/ ; 42107314//National Natural Science Foundation of China/ ; }, abstract = {Light intensity primarily drives plant growth and morphogenesis, whereas the ecological impact of light intensity on the phyllosphere (leaf surface and endosphere) microbiome is poorly understood. In this study, garden lettuce (Lactuca sativa L.) plants were grown under low, medium, and high light intensities. High light intensity remarkably induced the leaf contents of soluble proteins and chlorophylls, whereas it reduced the contents of leaf nitrate. In comparison, medium light intensity exhibited the highest contents of soluble sugar, cellulose, and free amino acids. Meanwhile, light intensity resulted in significant changes in the composition of functional genes but not in the taxonomic compositions of the prokaryotic community (bacteria and archaea) in the phyllosphere. Notably, garden lettuce plants under high light intensity treatment harbored more sulfur-cycling mdh and carbon-cycling glyA genes than under low light intensity, both of which were among the 20 most abundant prokaryotic genes in the leaf phyllosphere. Furthermore, the correlations between prokaryotic functional genes and lettuce leaf metabolite groups were examined to disclose their interactions under varying light intensities. The relative abundance of the mdh gene was positively correlated with leaf total chlorophyll content but negatively correlated with leaf nitrate content. In comparison, the relative abundance of the glyA gene was positively correlated with leaf total chlorophyll and carotenoids. Overall, this study revealed that the functional composition of the phyllosphere prokaryotic community and leaf metabolite groups were tightly linked in response to changing light intensities. These findings provided novel insights into the interactions between plants and prokaryotic microbes in indoor farming systems, which will help optimize environmental management in indoor farms and harness beneficial plant-microbe relationships for crop production.}, } @article {pmid38338088, year = {2024}, author = {Álvarez Narváez, S and Beaudry, MS and Norris, CG and Bartlett, PB and Glenn, TC and Sanchez, S}, title = {Improved Equine Fecal Microbiome Characterization Using Target Enrichment by Hybridization Capture.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/ani14030445}, pmid = {38338088}, issn = {2076-2615}, support = {Animal Health Capacity Grant SNIFA0001344201//United States Department of Agriculture/ ; }, abstract = {GITDs are among the most common causes of death in adult and young horses in the United States (US). Previous studies have indicated a connection between GITDs and the equine gut microbiome. However, the low taxonomic resolution of the current microbiome sequencing methods has hampered the identification of specific bacterial changes associated with GITDs in horses. Here, we have compared TEHC, a new approach for 16S rRNA gene selection and sequencing, with conventional 16S rRNA gene amplicon sequencing for the characterization of the equine fecal microbiome. Both sequencing approaches were used to determine the fecal microbiome of four adult horses and one commercial mock microbiome. Our results show that TEHC yielded significantly more operational taxonomic units (OTUs) than conventional 16S amplicon sequencing when the same number of reads were used in the analysis. This translated into a deeper and more accurate characterization of the fecal microbiome when the samples were sequenced with TEHC according to the relative abundance analysis. Alpha and beta diversity metrics corroborated these findings and demonstrated that the microbiome of the fecal samples was significantly richer when sequenced with TEHC compared to 16S amplicon sequencing. Altogether, our study suggests that the TEHC strategy provides a more extensive characterization of the fecal microbiome of horses than the current alternative based on the PCR amplification of a portion of the 16S rRNA gene.}, } @article {pmid38337180, year = {2024}, author = {Finn, DR}, title = {A metagenomic alpha-diversity index for microbial functional biodiversity.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiae019}, pmid = {38337180}, issn = {1574-6941}, abstract = {Alpha-diversity indices are an essential tool for describing and comparing biodiversity. Microbial ecologists apply indices originally intended for, or adopted by, macroecology to address questions relating to taxonomy (conserved marker) and function (metagenome-based data). In this Perspective piece, I begin by discussing the nature and mathematical quirks important for interpreting routinely employed alpha-diversity indices. Secondly, I propose a metagenomic alpha-diversity index (MD) that measures the (dis)similarity of protein-encoding genes within a community. MD has defined limits, whereby a community comprised mostly of similar, poorly diverse protein-encoding genes pulls the index to the lower limit, while a community rich in divergent homologs and unique genes drives it toward the upper limit. With data acquired from an in silico and three in situ metagenome studies, I derive MD and typical alpha-diversity indices applied to taxonomic (ribosomal rRNA) and functional (all protein-encoding) genes, and discuss their relationships with each other. Not all alpha-diversity indices detect biological trends, and taxonomic does not necessarily follow functional biodiversity. Throughout, I explain that protein Richness and MD provide complementary and easily interpreted information, while probability-based indices do not. Finally, considerations regarding the unique nature of microbial metagenomic data and its relevance for describing functional biodiversity are discussed.}, } @article {pmid38336904, year = {2024}, author = {Cacaci, M and De Maio, F and Matteo, MV and Posteraro, B and Di Vito, M and Menchinelli, G and Tringali, A and Monzo, FR and Torelli, R and Costamagna, G and Spada, C and Bugli, F and Sanguinetti, M and Boskoski, I}, title = {Pilot study on cultural and metagenomic analysis of bile and biliary stentslead to unveiling the key players in stent occlusion.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {3344}, pmid = {38336904}, issn = {2045-2322}, support = {grant number: SG-2018-12366369, awarded to Margherita Cacaci.//Ministero della Salute/ ; EU funding within the MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases (Project no. PE00000007, INF-ACT).//Ministero dell'Università e della Ricerca/ ; }, abstract = {Endoscopic Retrograde Cholangio-Pancreatography (ERCP) with biliary stenting is a minimally invasive medical procedure employed to address both malignant and benign obstructions within the biliary tract. Benign biliary strictures (BBSs), typically arising from surgical interventions such as liver transplants and cholecystectomy, as well as chronic inflammatory conditions, present a common clinical challenge. The current gold standard for treating BBSs involves the periodic insertion of plastic stents at intervals of 3-4 months, spanning a course of approximately one year. Unfortunately, stent occlusion emerges as a prevalent issue within this treatment paradigm, leading to the recurrence of symptoms and necessitating repeated ERCPs. In response to this clinical concern, we initiated a pilot study, delving into the microbial composition present in bile and on the inner surfaces of plastic stents. This investigation encompassed 22 patients afflicted by BBSs who had previously undergone ERCP with plastic stent placement. Our preliminary findings offered promising insights into the microbial culprits behind stent occlusion, with Enterobacter and Lactobacillus spp. standing out as prominent bacterial species known for their biofilm-forming tendencies on stent surfaces. These revelations hold promise for potential interventions, including targeted antimicrobial therapies aimed at curtailing bacterial growth on stents and the development of advanced stent materials boasting anti-biofilm properties.}, } @article {pmid38336233, year = {2024}, author = {Osadchiy, V and Belarmino, A and Kianian, R and Sigalos, JT and Furtado, TP and Ancira, JS and Kanie, T and Mangum, SF and Tipton, CD and Hsieh, TM and Mills, JN and Eleswarapu, SV}, title = {Urine microbes and predictive metagenomic profiles associate with abnormalities in sperm parameters: Implications for male subfertility.}, journal = {F&S science}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.xfss.2024.01.002}, pmid = {38336233}, issn = {2666-335X}, abstract = {OBJECTIVE: To explore the taxonomic and predicted functional relationship between the urine microbiome and alterations of semen analysis (SA) parameters.

DESIGN: Cross-sectional study.

SETTING: Academic medical center.

SUBJECTS: Men presenting for fertility evaluation or men presenting for vasectomy consultation with proven biological paternity were recruited and stratified based on alterations, or lack thereof, in SA parameters.

MAIN OUTCOME MEASURE: Changes in the functional and taxonomic urine microbiome profiles of participants with or without alterations in SA parameters.

RESULTS: Seventy-three participants were included in our study. Men with abnormal sperm motility (N=27) showed a nearly fifty-fold higher abundance of Dialister micraerophilus (p=0.032) compared to those with normal sperm motility (N=46). This relationship persisted on canonical correlational analysis (r=0.439, p=0.014). Men with abnormal sperm concentration (N=20) showed a lower abundance of Enterococcus faecalis (p=0.012) and Staphylococcus aureus (p=0.037), compared to those with normal sperm concentration (N=53). Urine of participants with impaired sperm motility demonstrated dramatic differences in predictive functional profiles in pathways involved in oxidation-reduction balance and cell longevity (all p<0.05).

CONCLUSIONS: Our findings underscore differences in the urinary microbiome and abnormalities in semen parameters, especially sperm motility. By incorporating predictive functional profiling, we also highlight possible mechanisms that may drive the observed differences in sperm parameters.}, } @article {pmid38336206, year = {2024}, author = {Carias, C and Hartwig, S and Kanibir, N and Matthijnssens, J and Tu, Y}, title = {Letter to the editor on cross-protection of RotaTeq[TM].}, journal = {The Journal of pediatrics}, volume = {}, number = {}, pages = {113952}, doi = {10.1016/j.jpeds.2024.113952}, pmid = {38336206}, issn = {1097-6833}, } @article {pmid38336077, year = {2024}, author = {Xu, J and Wang, H and Xu, R and Li, Q and Li, L and Su, Y and Liu, J and Zhu, W}, title = {Daily fluctuation of Lactobacillus species and their antibiotic resistome in the colon of growing pigs.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170821}, doi = {10.1016/j.scitotenv.2024.170821}, pmid = {38336077}, issn = {1879-1026}, abstract = {There are various types of bacteria inhabiting the intestine that help maintain the balance of the intestinal microbiota. Lactobacillus is one of the important beneficial bacteria and is widely used as a food starter and probiotic. In this study, we investigated the daily fluctuation of the colonic Lactobacillus species and their distribution of antibiotic resistance genes (ARGs) as well as antibiotic susceptibility in pigs. Metagenomic analysis revealed that genus Lactobacillus was one of the most dominant genera in the colon of growing pigs. Rhythmicity analysis revealed that 84 out of 285 Lactobacillus species exhibited rhythmic patterns. Lactobacillus johnsonii and Lactobacillus reuteri were the two most abundant lactobacilli with circadian oscillation, which increased during the day and decreased at night. The profile of the antibiotic resistome was modified over time within 24-h period. Elfamycin resistance genes were the most enriched class found in Lactobacillus. Furthermore, the seven strains of Lactobacillus isolated from the pig intestine mainly exhibited resistance to gentamicin, erythromycin, and lincomycin. The whole genome annotation of four Lactobacillus strains indicated the presence of multiple ARGs, including elfamycin resistance genes, however, the most abundant ARG was optrA in genome of four strains. These results indicate the presence of various Lactobacillus species harboring a large number of ARGs in the swine intestine. This implies that when using animal-derived lactobacilli, it is essential to assess antibiotic resistance to prevent further transmission between animals and the environment.}, } @article {pmid38335748, year = {2024}, author = {Gu, Z and Yan, H and Zhang, Q and Wang, Y and Liu, C and Cui, X and Liu, Y and Yu, Z and Wu, X and Ruan, R}, title = {Elimination of copper obstacle factor in anaerobic digestion effluent for value-added utilization: Performance and resistance mechanisms of indigenous bacterial consortium.}, journal = {Water research}, volume = {252}, number = {}, pages = {121217}, doi = {10.1016/j.watres.2024.121217}, pmid = {38335748}, issn = {1879-2448}, abstract = {The presence of excessive residual Cu(II), a high-risk heavy metal with potential toxicity and biomagnification property, substantially impede the value-added utilization of anaerobic digestion effluent (ADE). This study adapted indigenous bacterial consortium (IBCs) to eliminate Cu(II) from ADE, and their performances and resistance mechanisms against Cu(II) were analyzed. Results demonstrated that when the Cu(II) exposure concentration exceeded 7.5 mg/L, the biomass of IBCs decreased significantly, cells produced a substantial amount of ROS and EPS, at which time the intracellular Cu(II) content gradually decreased, while Cu(II) accumulation within the EPS substantially increased. The combined features of a high PN/PS ratio, a reversed Zeta potential gradient, and abundant functional groups within EPS collectively render EPS a primary diffusion barrier against Cu(II) toxicity. Mutual physiological and metagenomics analyses reveal that EPS synthesis and secretion, efflux, DNA repair along with coordination between each other were the primary resistance mechanisms of IBCs against Cu(II) toxicity. Furthermore, IBCs exhibited enhanced resistance by enriching bacteria carrying relevant resistance genes. Continuous pretreatment of actual ADE with IBCs at a 10-day hydraulic retention time (HRT) efficiently eliminated Cu(II) concentration from 5.01 mg/L to ∼0.68 mg/L by day 2. This elimination remained stable for the following 8 days of operation, further validated their good Cu(II) elimination stability. Notably, supplementing IBCs with 200 mg/L polymerized ferrous sulfate significantly enhanced their settling performance. By elucidating the intricate interplay of Cu(II) toxicity and IBC resistance mechanisms, this study provides a theoretical foundation for eliminating heavy metal barriers in ADE treatment.}, } @article {pmid38335438, year = {2024}, author = {Meng, D and Zou, Y and Li, J and Zhai, J and Guo, R and Jin, X}, title = {Invasive pulmonary and central nervous system aspergillosis in a child: A case report and literature review.}, journal = {Medicine}, volume = {103}, number = {6}, pages = {e37160}, doi = {10.1097/MD.0000000000037160}, pmid = {38335438}, issn = {1536-5964}, abstract = {RATIONALE: Children with haematological malignancies have a higher risk of developing aggressive pulmonary aspergillosis and a higher mortality rate. The most common site of extrapulmonary aspergillosis in children is the central nervous system (CNS), and the death rate is higher when CNS is affected. Therefore, early diagnosis and treatment of invasive aspergillosis are essential for reducing mortality.

PATIENT CONCERNS: We report a case of an 8-year-old girl with acute lymphoblastic leukaemia who developed invasive pulmonary aspergillosis complicated by CNS aspergillosis. Aspergillus was confirmed by metagenomic sequencing of pathogenic microorganisms.

DIAGNOSES: Invasive pulmonary and central nervous system aspergillosis.

INTERVENTIONS: The patient was treated with combined systemic antifungal agents (voriconazole and liposomal amphotericin B) and intrathecal injection of amphotericin B.

OUTCOMES: The treatment was well tolerated and resulted in remarkable clinical and radiological head improvements.

LESSONS: Invasive aspergillosis has a high mortality rate and requires early diagnosis and treatment. Pathogenic microbial metagenomic sequencing is a convenient method to assist in the early diagnosis of aspergillosis. Voriconazole is the drug of choice for the treatment of invasive aspergillosis. When CNS aspergillosis occurs, it can be combined with other systemic antifungal drugs and intrathecal injection of amphotericin B.}, } @article {pmid38334873, year = {2024}, author = {Gao, Q and Li, D and Wang, Y and Zhao, C and Li, M and Xiao, J and Kang, Y and Lin, H and Wang, N}, title = {Analysis of intestinal flora and cognitive function in maintenance hemodialysis patients using combined 16S ribosome DNA and shotgun metagenome sequencing.}, journal = {Aging clinical and experimental research}, volume = {36}, number = {1}, pages = {28}, pmid = {38334873}, issn = {1720-8319}, support = {LJKZZ20220099//Key research project of basic scientific research projects of the educational department of Liaoning province/ ; }, abstract = {BACKGROUND: Cognitive impairment is widely prevalent in maintenance hemodialysis (MHD) patients, and seriously affects their quality of life. The intestinal flora likely regulates cognitive function, but studies on cognitive impairment and intestinal flora in MHD patients are lacking.

METHODS: MHD patients (36) and healthy volunteers (18) were evaluated using the Montreal Cognitive Function Scale, basic clinical data, and 16S ribosome DNA (rDNA) sequencing. Twenty MHD patients and ten healthy volunteers were randomly selected for shotgun metagenomic analysis to explore potential metabolic pathways of intestinal flora. Both16S rDNA sequencing and shotgun metagenomic sequencing were conducted on fecal samples.

RESULTS: Roseburia were significantly reduced in the MHD group based on both 16S rDNA and shotgun metagenomic sequencing analyses. Faecalibacterium, Megamonas, Bifidobacterium, Parabacteroides, Collinsella, Tyzzerella, and Phascolarctobacterium were positively correlated with cognitive function or cognitive domains. Enriched Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways included oxidative phosphorylation, photosynthesis, retrograde endocannabinoid signaling, flagellar assembly, and riboflavin metabolism.

CONCLUSION: Among the microbiota, Roseburia may be important in MHD patients. We demonstrated a correlation between bacterial genera and cognitive function, and propose possible mechanisms.}, } @article {pmid38334585, year = {2024}, author = {Yadav, B and Bhattacharya, SS and Rosen, L and Nagpal, R and Yadav, H and Yadav, JS}, title = {Oro-Respiratory Dysbiosis and Its Modulatory Effect on Lung Mucosal Toxicity during Exposure or Co-Exposure to Carbon Nanotubes and Cigarette Smoke.}, journal = {Nanomaterials (Basel, Switzerland)}, volume = {14}, number = {3}, pages = {}, doi = {10.3390/nano14030314}, pmid = {38334585}, issn = {2079-4991}, support = {P30ES006096/ES/NIEHS NIH HHS/United States ; }, abstract = {The oro-respiratory microbiome is impacted by inhalable exposures such as smoking and has been associated with respiratory health conditions. However, the effect of emerging toxicants, particularly engineered nanoparticles, alone or in co-exposure with smoking, is poorly understood. Here, we investigated the impact of sub-chronic exposure to carbon nanotube (CNT) particles, cigarette smoke extract (CSE), and their combination. The oral, nasal, and lung microbiomes were characterized using 16S rRNA-based metagenomics. The exposures caused the following shifts in lung microbiota: CNT led to a change from Proteobacteria and Bacteroidetes to Firmicutes and Tenericutes; CSE caused a shift from Proteobacteria to Bacteroidetes; and co-exposure (CNT+CSE) had a mixed effect, maintaining higher numbers of Bacteroidetes (due to the CNT effect) and Tenericutes (due to the CSE effect) compared to the control group. Oral microbiome analysis revealed an abundance of the following genera: Acinetobacter (CNT), Staphylococcus, Aggregatibacter, Allobaculum, and Streptococcus (CSE), and Alkalibacterium (CNT+CSE). These proinflammatory microbial shifts correlated with changes in the relative expression of lung mucosal homeostasis/defense proteins, viz., aquaporin 1 (AQP-1), surfactant protein A (SP-A), mucin 5b (MUC5B), and IgA. Microbiota depletion reversed these perturbations, albeit to a varying extent, confirming the modulatory role of oro-respiratory dysbiosis in lung mucosal toxicity. This is the first demonstration of specific oro-respiratory microbiome constituents as potential modifiers of toxicant effects in exposed lungs.}, } @article {pmid38334291, year = {2024}, author = {White, K and Eraclio, G and McDonnell, B and Bottacini, F and Lugli, GA and Ventura, M and Volontè, F and Dal Bello, F and Mahony, J and van Sinderen, D}, title = {A multifaceted investigation of lactococcal strain diversity in undefined mesophilic starter cultures.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0215223}, doi = {10.1128/aem.02152-23}, pmid = {38334291}, issn = {1098-5336}, abstract = {The dairy fermentation industry relies on the activity of lactic acid bacteria in robust starter cultures to accomplish milk acidification. Maintenance of the composition of these starter cultures, whether defined or undefined, is essential to ensure consistent and high-quality fermentation end products. To date, limited information exists regarding the microbial composition of undefined starter culture systems. Here, we describe a culture-based analysis combined with a metagenomics approach to evaluate the composition of two undefined mesophilic starter cultures. In addition, we describe a qPCR-based genotype detection assay, which is capable of discerning nine distinct lactococcal genotypes to characterize these undefined starter cultures, and which can be applied to monitor compositional changes in an undefined starter culture during a fermentation.IMPORTANCEThis study reports on the development of a combined culture-based analysis and metagenomics approach to evaluate the composition of two undefined mesophilic starter cultures. In addition, a novel qPCR-based genotype detection assay, capable of discerning nine distinct lactococcal genotypes (based on lactococcal cell wall polysaccharide biosynthesis gene clusters), was used to monitor compositional changes in an undefined starter culture following phage attack. These analytical approaches facilitate a multifaceted assessment of starter culture compositional stability during milk fermentation, which has become an important QC aspect due to the increasing demand for consistent and high-quality dairy products.}, } @article {pmid38333588, year = {2024}, author = {Galgano, S and Conway, L and Fellows, A and Houdijk, J}, title = {Impact of precursor-derived peracetic acid on post-weaning diarrhea, intestinal microbiota, and predicted microbial functional genes in weaned pigs.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1356538}, doi = {10.3389/fmicb.2024.1356538}, pmid = {38333588}, issn = {1664-302X}, abstract = {Post-weaning diarrhea affects piglets in the nursery phase of production, leading to a substantial impact both at the farm and financial levels. The multifactorial etiology of this disease includes housing conditions, pig genetics, microbial composition, and metagenomic assets. Among the common therapeutic approaches, the widely used zinc oxide underwent a European Union ban in 2022 due to its negative environmental impact and correlation to increased antimicrobial resistance. During this study, we have tested two levels of inclusion of the potential antimicrobial alternative peracetic acid, delivered in water via the hydrolysis of the precursors sodium percarbonate and tetraacetylethylenediamine, in comparison to zinc oxide and an untreated control during a 2-week animal study. We assessed the microbial composition and predicted the metagenome, together with performance and physiological parameters, in order to describe the microbial functional role in etiopathology. Both zinc oxide and peracetic acid resulted in amelioration of the diarrheal status by the end of the trial period, with noticeable zinc oxide effects visible from the first week. This was accompanied by improved performance when compared to the first-week figures and a decreased stomach pH in both peracetic acid levels. A significant reduction in both stomach and caecal Proteobacteria was recorded in the zinc oxide group, and a significant reduction of Campylobacter in the stomach was reported for both zinc oxide and one of the peracetic acid concentrations. Among other functional differences, we found that the predicted ortholog for the zonula occludens toxin, a virulence factor present in pathogens like Escherichia coli and Campylobacter jejuni, was less abundant in the stomach of treated pigs compared to the control group. In water, peracetic acid delivered via precursor hydrolysis has the potential to be a valid intervention, an alternative to antimicrobial, to assist the weaning of piglets. Our findings support the view that post-weaning diarrhea is a complex multifactorial disease with an important metagenomic component characterized by the differential abundance of specific predicted orthologs and microbial genera in the stomach and caecum of pigs.}, } @article {pmid38332701, year = {2024}, author = {Li, P and Zhang, R and Zhou, J and Guo, P and Liu, Y and Shi, S}, title = {Vancomycin relieves tacrolimus-induced hyperglycemia by eliminating gut bacterial beta-glucuronidase enzyme activity.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2310277}, doi = {10.1080/19490976.2024.2310277}, pmid = {38332701}, issn = {1949-0984}, abstract = {Up to 40% of transplant recipients treated long-term with tacrolimus (TAC) develop post-transplant diabetes mellitus (PTDM). TAC is an important risk factor for PTDM, but is also essential for immunosuppression after transplantation. Long-term TAC treatment alters the gut microbiome, but the mechanisms of TAC-induced gut microbiota in the pathogenesis of PTDM are poorly characterized. Here, we showed that vancomycin, an inhibitor of bacterial beta-glucuronidase (GUS), prevents TAC-induced glucose disorder and insulin resistance in mice. Metagenomics shows that GUS-producing bacteria are predominant and flourish in the TAC-induced hyperglycemia mouse model, with upregulation of intestinal GUS activity. Targeted metabolomics analysis revealed that in the presence of high GUS activity, the hydrolysis of bile acid (BAs)-glucuronic conjugates is increased and most BAs are overproduced in the serum and liver, which, in turn, activates the ileal farnesoid X receptor (FXR) and suppresses GLP-1 secretion by L-cells. The GUS inhibitor vancomycin significantly eliminated GUS-producing bacteria and inhibited bacterial GUS activity and BAs levels, thereby enhancing L-cell GLP-1 secretion and preventing hyperglycemia. Our results propose a novel clinical strategy for inhibiting the bacterial GUS enzyme to prevent hyperglycemia without requiring withdrawal of TAC treatment. This strategy exerted its effect through the ileal bile acid-FXR-GLP-1 pathway.}, } @article {pmid38331563, year = {2024}, author = {Budden, KF and Shukla, SD and Bowerman, KL and Vaughan, A and Gellatly, SL and Wood, DLA and Lachner, N and Idrees, S and Rehman, SF and Faiz, A and Patel, VK and Donovan, C and Alemao, CA and Shen, S and Amorim, N and Majumder, R and Vanka, KS and Mason, J and Haw, TJ and Tillet, B and Fricker, M and Keely, S and Hansbro, N and Belz, GT and Horvat, J and Ashhurst, T and van Vreden, C and McGuire, H and Fazekas de St Groth, B and King, NJC and Crossett, B and Cordwell, SJ and Bonaguro, L and Schultze, JL and Hamilton-Williams, EE and Mann, E and Forster, SC and Cooper, MA and Segal, LN and Chotirmall, SH and Collins, P and Bowman, R and Fong, KM and Yang, IA and Wark, PAB and Dennis, PG and Hugenholtz, P and Hansbro, PM}, title = {Faecal microbial transfer and complex carbohydrates mediate protection against COPD.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2023-330521}, pmid = {38331563}, issn = {1468-3288}, abstract = {OBJECTIVE: Chronic obstructive pulmonary disease (COPD) is a major cause of global illness and death, most commonly caused by cigarette smoke. The mechanisms of pathogenesis remain poorly understood, limiting the development of effective therapies. The gastrointestinal microbiome has been implicated in chronic lung diseases via the gut-lung axis, but its role is unclear.

DESIGN: Using an in vivo mouse model of cigarette smoke (CS)-induced COPD and faecal microbial transfer (FMT), we characterised the faecal microbiota using metagenomics, proteomics and metabolomics. Findings were correlated with airway and systemic inflammation, lung and gut histopathology and lung function. Complex carbohydrates were assessed in mice using a high resistant starch diet, and in 16 patients with COPD using a randomised, double-blind, placebo-controlled pilot study of inulin supplementation.

RESULTS: FMT alleviated hallmark features of COPD (inflammation, alveolar destruction, impaired lung function), gastrointestinal pathology and systemic immune changes. Protective effects were additive to smoking cessation, and transfer of CS-associated microbiota after antibiotic-induced microbiome depletion was sufficient to increase lung inflammation while suppressing colonic immunity in the absence of CS exposure. Disease features correlated with the relative abundance of Muribaculaceae, Desulfovibrionaceae and Lachnospiraceae family members. Proteomics and metabolomics identified downregulation of glucose and starch metabolism in CS-associated microbiota, and supplementation of mice or human patients with complex carbohydrates improved disease outcomes.

CONCLUSION: The gut microbiome contributes to COPD pathogenesis and can be targeted therapeutically.}, } @article {pmid38331298, year = {2024}, author = {Farrell, CT and Hunter, E and Wilson, PB and White, SJ}, title = {Genomic characterisation of bioaerosols within livestock facilities: A systematic review.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170722}, doi = {10.1016/j.scitotenv.2024.170722}, pmid = {38331298}, issn = {1879-1026}, abstract = {Livestock facilities are widely regarded as reservoirs of infectious disease, owing to their abundance in particulate matter (PM) and microbial bioaerosols. Over the past decade, bioaerosol studies have increasingly utilised high throughput sequencing (HTS) to achieve superior throughput, taxonomic resolution, and the detection of unculturable organisms. However, the prevailing focus on amplicon sequencing has limited the identification of viruses and microbial taxa at the species-level. Herein, a literature search was conducted to identify methods capable of overcoming the aforementioned limitations. Screening 1531 international publications resulted in 29 eligible for review. Metagenomics capable of providing rich insights were identified in only three instances. Notably, long-read sequencing was not utilised for metagenomics. This review also identified that sample collection methods lack a uniform approach, highlighted by the differences in sampling equipment, flow rates and durations. Further heterogeneity was introduced by the unique sampling conditions, which makes it challenging to ground new findings within the established literature. For instance, winter was associated with increased microbial abundance and antimicrobial resistance, yet less alpha diversity. Researchers implementing metagenomics into the livestock environment should consider season, the microclimate, and livestock growth stage as influential upon their findings. Considering the increasing accessibility of long-read sequencing, future research should explore its viability within a novel uniform testing protocol for bioaerosol emissions.}, } @article {pmid38330916, year = {2024}, author = {Kallifidas, D and Dhakal, D and Chen, M and Chen, QY and Kokkaliari, S and Colon Rosa, NA and Ratnayake, R and Bruner, SD and Paul, VJ and Ding, Y and Luesch, H}, title = {Biosynthesis of Dolastatin 10 in Marine Cyanobacteria, a Prototype for Multiple Approved Cancer Drugs.}, journal = {Organic letters}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.orglett.3c04083}, pmid = {38330916}, issn = {1523-7052}, abstract = {Dolastatin 10, a potent tubulin-targeting marine anticancer natural product, provided the basis for the development of six FDA-approved antibody-drug conjugates. Through the screening of cyanobacterial Caldora penicillata environmental DNA libraries and metagenome sequencing, we identified its biosynthetic gene cluster. Functional prediction of 10 enzymes encoded in the 39 kb cluster supports the dolastatin 10 biosynthesis. The nonheme diiron monooxygenase DolJ was biochemically characterized to mediate the terminal thiazole formation in dolastatin 10.}, } @article {pmid38330717, year = {2024}, author = {Doloman, A and de Bruin, S and van Loosdrecht, MCM and Sousa, DZ and Lin, Y}, title = {Coupling extracellular glycan composition with metagenomic data in papermill and brewery anaerobic granular sludges.}, journal = {Water research}, volume = {252}, number = {}, pages = {121240}, doi = {10.1016/j.watres.2024.121240}, pmid = {38330717}, issn = {1879-2448}, abstract = {Glycans are crucial for the structure and function of anaerobic granular sludge in wastewater treatment. Yet, there is limited knowledge regarding the microorganisms and biosynthesis pathways responsible for glycan production. In this study, we analysed samples from anaerobic granular sludges treating papermill and brewery wastewater, examining glycans composition and using metagenome-assembled genomes (MAGs) to explore potential biochemical pathways associated with their production. Uronic acids were the predominant constituents of the glycans in extracellular polymeric substances (EPS) produced by the anaerobic granular sludges, comprising up to 60 % of the total polysaccharide content. MAGs affiliated with Anaerolineacae, Methanobacteriaceae and Methanosaetaceae represented the majority of the microbial community (30-50 % of total reads per MAG). Based on the analysis of MAGs, it appears that Anaerolinea sp. and members of the Methanobacteria class are involved in the production of exopolysaccharides within the analysed granular sludges. These findings shed light on the functional roles of microorganisms in glycan production in industrial anaerobic wastewater treatment systems.}, } @article {pmid38330645, year = {2024}, author = {Liu, F and Ding, J and Zeng, J and Wang, C and Wu, B and Yan, Q and He, Z and Shu, L}, title = {Mangrove sediments are environmental hotspots for pathogenic protists.}, journal = {Journal of hazardous materials}, volume = {467}, number = {}, pages = {133643}, doi = {10.1016/j.jhazmat.2024.133643}, pmid = {38330645}, issn = {1873-3336}, abstract = {Mangrove sediments are unique ecosystems providing habitats for diverse organisms, especially microbial communities. However, little is known about the diversity and environmental risk of a critical group of microorganisms, the protists. To address this gap, we employed metagenome sequencing technologies to provide the first comprehensive view of the protistan community in the mangrove sediment. Our results surprisingly showed that parasitic protists dominated the protistan community in mangrove sediments, with an average abundance of 59.67%, one of the highest in all ecosystems on Earth. We also found that the relative abundance of protists decreased significantly (R = -0.21, p = 0.045) with latitude but increased with depths (R = 0.7099, p < 0.001). The parasitic communities were positively influenced by microbial (bacteria, fungi, and archaea) communities, including horizontal-scale and vertical-scale. In addition, sulfate and salinity had the most significant influence on the protistan community. Our findings provide new insights into our understanding of protistan variation in mangrove sediments, including abundance, composition, and possible functions, and indicate that mangrove sediments are hotspots for environmental pathogens, posing a potential risk to human health.}, } @article {pmid38330476, year = {2024}, author = {Fletcher, AM and Bhattacharyya, S}, title = {Infectious Myelopathies.}, journal = {Continuum (Minneapolis, Minn.)}, volume = {30}, number = {1}, pages = {133-159}, pmid = {38330476}, issn = {1538-6899}, abstract = {OBJECTIVE: Infectious myelopathy of any stage and etiology carries the potential for significant morbidity and mortality. This article details the clinical presentation, risk factors, and key diagnostic components of infectious myelopathies with the goal of improving the recognition of these disorders and guiding subsequent management.

LATEST DEVELOPMENTS: Despite our era of advanced multimodal imaging and laboratory diagnostic technology, a causative organism often remains unidentified in suspected infectious and parainfectious myelopathy cases. To improve diagnostic capability, newer technologies such as metagenomics are being harnessed to develop diagnostic assays with a greater breadth of data from each specimen and improvements in infection identification. Conventional assays have been optimized for improved sensitivity and specificity.

ESSENTIAL POINTS: Prompt recognition and treatment of infectious myelopathy decreases morbidity and mortality. The key diagnostic tools include serologies, CSF analysis, and imaging; however clinical presentation, epidemiologic risk factors, and history of recent illness are all vital to making the proper diagnosis because current laboratory and imaging modalities are often inconclusive. The cornerstone of recommended treatment is targeted antimicrobials with appropriate immune modulation, surgical intervention, supportive care, and interdisciplinary involvement, all of which further improve outcomes for patients with infectious myelopathy.}, } @article {pmid38329942, year = {2024}, author = {Zhan, K and Wu, H and Xu, Y and Rao, K and Zheng, H and Qin, S and Yang, Y and Jia, R and Chen, W and Huang, S}, title = {The function of the gut microbiota-bile acid-TGR5 axis in diarrhea-predominant irritable bowel syndrome.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0129923}, doi = {10.1128/msystems.01299-23}, pmid = {38329942}, issn = {2379-5077}, abstract = {Imbalanced gut microbiota (GM) and abnormal fecal bile acid (BA) are thought to be the key factors for diarrhea-predominant irritable bowel syndrome (IBS-D), but the underlying mechanism remains unclear. Herein, we explore the influence of the GM-BA-Takeda G-protein-coupled receptor 5 (TGR5) axis on IBS-D. Twenty-five IBS-D patients and fifteen healthy controls were recruited to perform BA-related metabolic and metagenomic analyses. Further, the microbiota-humanized IBS-D rat model was established by fecal microbial transplantation (FMT) to investigate the GM-BA-TGR5 axis effects on the colonic barrier and visceral hypersensitivity (VH) in IBS-D. Finally, we used chenodeoxycholic acid (CDCA), an important BA screened out by metabolome, to evaluate whether it affected diarrhea and VH via the TGR5 pathway. Clinical research showed that GM associated with bile salt hydrolase (BSH) activity such as Bacteroides ovatus was markedly reduced in the GM of IBS-D, accompanied by elevated total and primary BA levels. Moreover, we found that CDCA not only was increased as the most important primary BA in IBS-D patients but also could induce VH through upregulating TGR5 in the colon and ileum of normal rats. TGR5 inhibitor could reverse the phenotype, depression-like behaviors, pathological change, and level of fecal BSH in a microbiota-humanized IBS-D rat model. Our findings proved that human-associated FMT could successfully induce the IBS-D rat model, and the imbalanced GM-BA-TGR5 axis may promote colonic mucosal barrier dysfunction and enhance VH in IBS-D. IMPORTANCE Visceral hypersensitivity and intestinal mucosal barrier damage are important factors that cause abnormal brain-gut interaction in diarrhea-predominant irritable bowel syndrome (IBS-D). Recently, it was found that the imbalance of the gut microbiota-bile acid axis is closely related to them. Therefore, understanding the structure and function of the gut microbiota and bile acids and the underlying mechanisms by which they shape visceral hypersensitivity and mucosal barrier damage in IBS-D is critical. An examination of intestinal feces from IBS-D patients revealed that alterations in gut microbiota and bile acid metabolism underlie IBS-D and symptom onset. We also expanded beyond existing knowledge of well-studied gut microbiota and bile acid and found that Bacteroides ovatus and chenodeoxycholic acid may be potential bacteria and bile acid involved in the pathogenesis of IBS-D. Moreover, our data integration reveals the influence of the microbiota-bile acid-TGR5 axis on barrier function and visceral hypersensitivity.}, } @article {pmid38329355, year = {2024}, author = {Nguyen, TM and Pombubpa, N and Huntemann, M and Clum, A and Foster, B and Foster, B and Roux, S and Palaniappan, K and Varghese, N and Mukherjee, S and Reddy, TBK and Daum, C and Copeland, A and Chen, I-MA and Ivanova, NN and Kyrpides, NC and Harmon-Smith, M and Eloe-Fadrosh, EA and Pietrasiak, N and Stajich, JE and Hom, EFY}, title = {Whole community shotgun metagenomes of two biological soil crust types from the Mojave Desert.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0098023}, doi = {10.1128/mra.00980-23}, pmid = {38329355}, issn = {2576-098X}, abstract = {We present six whole community shotgun metagenomic sequencing data sets of two types of biological soil crusts sampled at the ecotone of the Mojave Desert and Colorado Desert in California. These data will help us understand the diversity and function of biocrust microbial communities, which are essential for desert ecosystems.}, } @article {pmid38329353, year = {2024}, author = {Dong, J-H and Xu, X and Ren, Z-X and Zhao, Y-H and Zhang, Y and Chen, L and Wu, Y and Chen, G and Cao, R and Wu, Q and Wang, H}, title = {The adaptation of bumblebees to extremely high elevation associated with their gut microbiota.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0121923}, doi = {10.1128/msystems.01219-23}, pmid = {38329353}, issn = {2379-5077}, abstract = {Bumblebees are among the most abundant and important pollinators for sub-alpine and alpine flowering plant species in the Northern Hemisphere, but little is known about their adaptations to high elevations. In this article, we focused on two bumblebee species, Bombus friseanus and Bombus prshewalskyi, and their respective gut microbiota. The two species, distributed through the Hengduan Mountains of southwestern China, show species replacement at different elevations. We performed genome sequencing based on 20 worker bee samples of each species. Applying evolutionary population genetics and metagenomic approaches, we detected genes under selection and analyzed functional pathways between bumblebees and their gut microbes. We found clear genetic differentiation between the two host species and significant differences in their microbiota. Species replacement occurred in both hosts and their bacteria (Snodgrassella) with an increase in elevation. These extremely high-elevation bumblebees show evidence of positive selection related to diverse biological processes. Positively selected genes involved in host immune systems probably contributed to gut microbiota changes, while the butyrate generated by gut microbiota may influence both host energy metabolism and immune systems. This suggests a close association between the genomes of the host species and their microbiomes based on some degree of natural selection.IMPORTANCETwo closely related and dominant bumblebee species, distributed at different elevations through the Hengduan Mountains of southwestern China, showed a clear genomic signature of adaptation to elevation at the molecular level and significant differences in their respective microbiota. Species replacement occurred in both hosts and their bacteria (Snodgrassella) with an increase in elevation. Bumblebees' adaptations to higher elevations are closely associated with their gut microbiota through two biological processes: energy metabolism and immune response. Information allowing us to understand the adaptive mechanisms of species to extreme conditions is implicit if we are to conserve them as their environments change.}, } @article {pmid38329258, year = {2024}, author = {Euzen, V and Ghelfenstein-Ferreira, T and Le Goff, J and Salmona, M}, title = {[Interests of clinical metagenomic in infectious diseases].}, journal = {La Revue du praticien}, volume = {74}, number = {1}, pages = {63-68}, pmid = {38329258}, issn = {2101-017X}, abstract = {INTERESTS OF CLINICAL METAGENOMICS IN INFECTIOUS DISEASES. Clinical metagenomics (CM) is a cutting-edge molecular biology technique that is now a valuable diagnostic tool for microbiologists. It enables the detection of all microorganisms present in a sample, without any prior assumption or bias. The CM approach can be applied to various types of samples and involves multiple steps, such as extraction, library preparation, Next Generation Sequencing, and bioinformatics analysis. CM has been implemented in the diagnosis of various conditions, including infections of the central nervous system, respiratory, digestive, ocular, skin infection, and sepsis. Moreover, CM provides a comprehensive analysis of the microbiome present in the sample, microbial transcripts, and the host response in a single analysis. However, further studies are necessary to determine its place in the diagnostic algorithm. Besides diagnosis, CM has proven useful in identifying resistance to antimicrobial treatments and in epidemiology. Although the cost of CM is still higher than conventional methods, the emergence of more affordable sequencers and commercial tests will enable its implementation in a larger number of laboratories in the future.}, } @article {pmid38328669, year = {2024}, author = {Yu, J and Zhang, L and Gao, D and Wang, J and Li, Y and Sun, N}, title = {Comparison of metagenomic next-generation sequencing and blood culture for diagnosis of bloodstream infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1338861}, doi = {10.3389/fcimb.2024.1338861}, pmid = {38328669}, issn = {2235-2988}, abstract = {OBJECTIVES: This study aimed to evaluate the clinical performance of plasma cell-free DNA (cfDNA) next-generation sequencing (NGS) for pathogen detection in patients with sepsis.

METHODS: A total of 43 pairs of blood and plasma samples form 33 blood culture-positive patients were used as testing samples in metagenomic NGS (mNGS) and NGS of 16S ribosomal RNA gene amplicons (16S rRNA NGS). The results of routine tests, including microbial culture, complete blood count, and biochemical tests, were collected from electronic medical records.

RESULTS: Using blood as an mNGS testing sample, the proportion of host DNA was 99.9%, with only three bacteria and no fungi detected. When using plasma in mNGS, the proportion of host DNA was approximately 97%, with 84 bacteria and two fungi detected. Notably, 16S rRNA NGS detected 15 and 16 bacteria in 43 pairs of blood and plasma samples, respectively. Blood culture detected 49 bacteria (23 gram-negative bacilli and 26 gram-positive cocci) and four fungi, with 14 bacteria considered contaminants by clinical microbiologists. For all blood cultures, plasma cfDNA mNGS detected 78.26% (19/23) gram-negative rods, 17% (2/12) gram-positive cocci, and no fungi. Compared to blood cultures, the sensitivity and specificity of plasma cfDNA mNGS for detecting bacteria and fungi were 62.07% and 57.14%, respectively.

CONCLUSION: Compared to blood, plasma is more suitable for the detection of bloodstream infections using mNGS and is less affected by host DNA. The positive detection rate of plasma cfDNA mNGS for bloodstream infections caused by gram-negative bacteria was higher than that caused by gram-positive cocci.}, } @article {pmid38328509, year = {2024}, author = {Xue, B and Tian, L and Liu, Y and Peng, L and Iqbal, W and Li, L and Mao, Y}, title = {Enhanced nitrate reduction in hypotrophic waters with integrated photocatalysis and biodegradation.}, journal = {Environmental science and ecotechnology}, volume = {21}, number = {}, pages = {100390}, doi = {10.1016/j.ese.2024.100390}, pmid = {38328509}, issn = {2666-4984}, abstract = {Addressing nitrate contamination in water bodies is a critical environmental challenge, and Intimately Coupling Photocatalysis and Biodegradation (ICPB) presents a promising solution. However, there is still debate about the effectiveness of ICPB in reducing nitrate under hypotrophic conditions. Further research is needed to understand its microbial metabolic mechanism and the functional changes in bacterial structure. Here we explored microbial metabolic mechanisms and changes in bacterial structure in ICPB reactors integrating a meticulously screened TiO2/g-C3N4 photocatalyst with biofilm. We achieved a 26.3% increase in nitrate reduction using 12.2% less organic carbon compared to traditional biodegradation methods. Metagenomic analysis of the microbial communities in ICPB reactors revealed evolving metabolic pathways conducive to nitrate reduction. This research not only elucidates the photocatalytic mechanism behind nitrate reduction in hypotrophic conditions but also provides genomic insights that pave the way for alternative approaches in water remediation technologies.}, } @article {pmid38328472, year = {2024}, author = {Sato, A and Arai, S and Sumi, K and Fukamachi, H and Miyake, S and Ozawa, M and Myers, M and Maruoka, Y and Shimizu, K and Mizutani, T and Kuwata, H}, title = {Metagenomic Analysis of Bacterial Microflora in Dental and Atherosclerotic Plaques of Patients With Internal Carotid Artery Stenosis.}, journal = {Clinical Medicine Insights. Cardiology}, volume = {18}, number = {}, pages = {11795468231225852}, doi = {10.1177/11795468231225852}, pmid = {38328472}, issn = {1179-5468}, abstract = {BACKGROUND: Internal carotid artery stenosis is primarily attributed to atherosclerosis in the carotid artery bifurcation. Previous studies have detected oral bacteria in atherosclerotic lesions, suggesting an association between oral bacteria and atherosclerosis. In this study, we compared the bacterial flora of the atherosclerotic plaque in the carotid artery and dental plaque of patients with internal carotid artery stenosis using 16S ribosomal RNA (16S rRNA) metagenomic sequencing.

METHODS: Fifty-four patients who underwent internal carotid endarterectomy for internal carotid artery stenosis at the Showa University Hospital between April 2016 and February 2018 were included. Polymerase chain reaction targeting the 16S rRNA gene detected bacterial DNA in the carotid plaques of 11 cases, of which only 5 could be further analyzed. Thereafter, DNA extracted from the carotid and oral plaques of these 5 cases were analyzed using metagenomic sequencing targeting 16S rRNA. In addition, their general condition and oral conditions were evaluated. The patients were classified into symptomatic and asymptomatic groups based on the presence or absence of symptoms of transient ischemic attack, and their bacterial flora was evaluated.

RESULTS: The results demonstrated that the microflora of carotid plaques (n = 5) contained bacterial species from 55 families and 78 genera. In addition, 86.5% of the bacteria detected in the carotid plaques were also detected in oral plaques. Cariogenic and periodontopathic bacteria accounted for 27.7% and 4.7% of the bacteria in the carotid plaques, respectively.

CONCLUSIONS: These results suggest that oral bacteria are directly or indirectly involved in the pathogenesis of atherosclerosis. More extensive studies of oral commensal bacteria detected in extra-oral lesions are warranted to comprehensively investigate the role of oral bacteria in the pathogenesis of systemic diseases.}, } @article {pmid38328448, year = {2024}, author = {Duan, C and Liu, Y and Liu, Y and Liu, L and Cai, M and Zhang, R and Zeng, Q and Koonin, EV and Krupovic, M and Li, M}, title = {Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycad011}, doi = {10.1093/ismeco/ycad011}, pmid = {38328448}, issn = {2730-6151}, abstract = {Bathyarchaeia represent a class of archaea common and abundant in sedimentary ecosystems. Here we report 56 metagenome-assembled genomes of Bathyarchaeia viruses identified in metagenomes from different environments. Gene sharing network and phylogenomic analyses led to the proposal of four virus families, including viruses of the realms Duplodnaviria and Adnaviria, and archaea-specific spindle-shaped viruses. Genomic analyses uncovered diverse CRISPR elements in these viruses. Viruses of the proposed family "Fuxiviridae" harbor an atypical Type IV-B CRISPR-Cas system and a Cas4 protein that might interfere with host immunity. Viruses of the family "Chiyouviridae" encode a Cas2-like endonuclease and two mini-CRISPR arrays, one with a repeat identical to that in the host CRISPR array, potentially allowing the virus to recruit the host CRISPR adaptation machinery to acquire spacers that could contribute to competition with other mobile genetic elements or to inhibit host defenses. These findings present an outline of the Bathyarchaeia virome and offer a glimpse into their counter-defense mechanisms.}, } @article {pmid38328429, year = {2024}, author = {Li, C and Song, J and Chen, Q and Ge, D and Li, Q and Yang, Y}, title = {Whole-genome shotgun sequencing unravels the influence of environmental microbial co-infections on the treatment efficacy for severe pediatric infectious diseases.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1308871}, doi = {10.3389/fmicb.2024.1308871}, pmid = {38328429}, issn = {1664-302X}, abstract = {BACKGROUND: The microbiome plays a pivotal role in mediating immune deviation during the development of early-life viral infections. Recurrent infections in children are considered a risk factor for disease development. This study delves into the metagenomics of the microbiome in children suffering from severe infections, seeking to identify potential sources of these infections.

AIMS: The aim of this study was to identify the specific microorganisms and factors that significantly influence the treatment duration in patients suffering from severe infections. We sought to understand how these microbial communities and other variables may affect the treatment duration and the use of antibiotics of these patients with severe infections.

METHOD: Whole-genome shotgun sequencing was conducted on samples collected from children aged 0-14 years with severe infections, admitted to the Pediatrics Department of Xiamen First Hospital. The Kraken2 algorithm was used for taxonomic identification from sequence reads, and linear mixed models were employed to identify significant microorganisms influencing treatment duration. Colwellia, Cryptococcus, and Citrobacter were found to significantly correlate with the duration of clinical treatment. Further analysis using propensity score matching (PSM) and rank-sum test identified clinical indicators significantly associated with the presence of these microorganisms.

RESULTS: Using a linear mixed model after removed the outliers, we identified that the abundance of Colwellia, Cryptococcus, and Citrobacter significantly influences the treatment duration. The presence of these microorganisms is associated with a longer treatment duration for patients. Furthermore, these microorganisms were found to impact various clinical measures. Notably, an increase in hospitalization durations and medication costs was observed in patients with these microorganisms. In patients with Colwellia, Cryptococcus, and Citrobacter, we discover significant differences in platelets levels. We also find that in patients with Cryptococcus, white blood cells, hemoglobin, and neutrophils levels are lower.

CONCLUSION: These findings suggest that Colwellia, Cryptococcus, and Citrobacter, particularly Cryptococcus, could potentially contribute to the severity of infections observed in this cohort, possibly as co-infections. These microorganisms warrant further investigation into their pathogenic roles and mechanisms of action, as their presence in combination with disease-causing organisms may have a synergistic effect on disease severity. Understanding the interplay between these microorganisms and pathogenic agents could provide valuable insights into the complex nature of severe pediatric infections and guide the development of targeted therapeutic strategies.}, } @article {pmid38328355, year = {2023}, author = {Burakova, I and Gryaznova, M and Smirnova, Y and Morozova, P and Mikhalev, V and Zimnikov, V and Latsigina, I and Shabunin, S and Mikhailov, E and Syromyatnikov, M}, title = {Association of milk microbiome with bovine mastitis before and after antibiotic therapy.}, journal = {Veterinary world}, volume = {16}, number = {12}, pages = {2389-2402}, doi = {10.14202/vetworld.2023.2389-2402}, pmid = {38328355}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: Mastitis is recognized as the most common disease in cattle and causes economic losses in the dairy industry. A number of opportunistic bacterial taxa have been identified as causative agents for this disease. Conventionally, antibiotics are used to treat mastitis; however, most bacteria are resistant to the majority of antibiotics. This study aimed to use molecular methods to identify milk microbiome patterns characteristic of mastitis that can help in the early diagnosis of this disease and in the development of new treatment strategies.

MATERIALS AND METHODS: To evaluate the microbiome composition, we performed NGS sequencing of the 16S rRNA gene of the V3 region.

RESULTS: An increase in the abundance of the bacterial genera Hymenobacter and Lachnospiraceae NK4A136 group is associated with the development of subclinical and clinical mastitis in dairy cows. These bacteria can be added to the list of markers used to detect mastitis in cows. Furthermore, a decrease in the abundance of Ralstonia, Lachnospiraceae NK3A20 group, Acetitomaculum, Massilia, and Atopostipes in cows with mastitis may indicate their role in maintaining a healthy milk microbiome. Antibiotics reduced the levels of Streptococcus in milk compared to those in the healthy group and cows before antibiotic treatment. Antibiotic therapy also contributed to an increase in the abundance of beneficial bacteria of the genus Asticcacaulis.

CONCLUSION: This study expands our understanding of the association between milk microbiota and mastitis.}, } @article {pmid38328166, year = {2024}, author = {Allert, M and Ferretti, P and Johnson, KE and Heisel, T and Gonia, S and Knights, D and Fields, DA and Albert, FW and Demerath, EW and Gale, CA and Blekhman, R}, title = {Assembly, stability, and dynamics of the infant gut microbiome are linked to bacterial strains and functions in mother's milk.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.01.28.577594}, pmid = {38328166}, abstract = {The establishment of the gut microbiome in early life is critical for healthy infant development. Although human milk is recommended as the sole source of nutrition for the human infant, little is known about how variation in milk composition, and especially the milk microbiome, shapes the microbial communities in the infant gut. Here, we quantified the similarity between the maternal milk and the infant gut microbiome using 507 metagenomic samples collected from 195 mother-infant pairs at one, three, and six months postpartum. We found that the microbial taxonomic overlap between milk and the infant gut was driven by bifidobacteria, in particular by B. longum . Infant stool samples dominated by B. longum also showed higher temporal stability compared to samples dominated by other species. We identified two instances of strain sharing between maternal milk and the infant gut, one involving a commensal (B. longum) and one a pathobiont (K. pneumoniae). In addition, strain sharing between unrelated infants was higher among infants born at the same hospital compared to infants born in different hospitals, suggesting a potential role of the hospital environment in shaping the infant gut microbiome composition. The infant gut microbiome at one month compared to six months of age was enriched in metabolic pathways associated with de-novo molecule biosynthesis, suggesting that early colonisers might be more versatile and metabolically independent compared to later colonizers. Lastly, we found a significant overlap in antimicrobial resistance genes carriage between the mother's milk and their infant's gut microbiome. Taken together, our results suggest that the human milk microbiome has an important role in the assembly, composition, and stability of the infant gut microbiome.}, } @article {pmid38327879, year = {2024}, author = {Zhang, J and Liu, Y and Wu, H and Zhou, L}, title = {Is Shigella an under-recognized pathogen? A case of pyogenic cervical spondylitis caused by Escherichia coli and Shigella flexneri infection.}, journal = {IDCases}, volume = {35}, number = {}, pages = {e01930}, doi = {10.1016/j.idcr.2024.e01930}, pmid = {38327879}, issn = {2214-2509}, abstract = {Shigella typically causes gastrointestinal infections, and extra-intestinal manifestations are rare. We report the first known case of pyogenic cervical spondylitis co-infected with Escherichia coli and Shigella flexneri, highlighting the diagnostic challenges and clinical implications. A 53-year-old woman presented with neck pain for one month. MRI revealed C6 and C7 vertebrae abscesses. The patient underwent anterior cervical debridement and bone-graft fusion. Intraoperative pus culture grew Escherichia coli, while metagenomic next-generation sequencing detected both Escherichia coli and Shigella species. Intravenous imipenem 500 mg every 6 h was administered, leading to full wound healing at a 6-month follow-up. This case emphasizes the importance of considering Shigella infection in the differential diagnosis of pyogenic spondylitis and demonstrates the utility of a multi-pronged diagnostic approach.}, } @article {pmid38327745, year = {2024}, author = {Zeber-Lubecka, N and Kulecka, M and Jagiełło-Gruszfeld, A and Dąbrowska, M and Kluska, A and Piątkowska, M and Bagińska, K and Głowienka, M and Surynt, P and Tenderenda, M and Mikula, M and Ostrowski, J}, title = {Breast cancer but not the menopausal status is associated with small changes of the gut microbiota.}, journal = {Frontiers in oncology}, volume = {14}, number = {}, pages = {1279132}, doi = {10.3389/fonc.2024.1279132}, pmid = {38327745}, issn = {2234-943X}, abstract = {BACKGROUND: Possible relationships between gut dysbiosis and breast cancer (BC) development and progression have been previously reported. However, the results of these metagenomics studies are inconsistent. Our study involved 88 patients diagnosed with breast cancer and 86 cancer-free control women. Participants were divided into groups based on their menopausal status. Fecal samples were collected from 47 and 41 pre- and postmenopausal newly diagnosed breast cancer patients and 51 and 35 pre- and postmenopausal controls, respectively. In this study, we performed shotgun metagenomic analyses to compare the gut microbial community between pre- and postmenopausal BC patients and the corresponding controls.

RESULTS: Firstly, we identified 12, 64, 158, and 455 bacterial taxa on the taxonomy level of phyla, families, genera, and species, respectively. Insignificant differences of the Shannon index and β-diversity were found at the genus and species levels between pre- and postmenopausal controls; the differences concerned only the Chao index at the species level. No differences in α-diversity indexes were found between pre- and postmenopausal BC patients, although β-diversity differed these subgroups at the genus and species levels. Consistently, only the abundance of single taxa differed between pre- and postmenopausal controls and cases, while the abundances of 14 and 23 taxa differed or tended to differ between premenopausal cases and controls, and between postmenopausal cases and controls, respectively. There were similar differences in the distribution of enterotypes. Of 460 bacterial MetaCyc pathways discovered, no pathways differentiated pre- and postmenopausal controls or BC patients, while two and one pathways differentiated cases from controls in the pre- and postmenopausal subgroups, respectively.

CONCLUSION: While our findings did not reveal an association of changes in the overall microbiota composition and selected taxa with the menopausal status in cases and controls, they confirmed differences of the gut microbiota between pre- and postmenopausal BC patients and the corresponding controls. However, these differences were less extensive than those described previously.}, } @article {pmid38327077, year = {2024}, author = {Wang, N and Wang, H and Bai, Y and Zhao, Y and Zheng, X and Gao, X and Zhang, Z and Yang, L}, title = {Metagenomic Analysis Reveals Difference of Gut Microbiota in ADHD.}, journal = {Journal of attention disorders}, volume = {}, number = {}, pages = {10870547231225491}, doi = {10.1177/10870547231225491}, pmid = {38327077}, issn = {1557-1246}, abstract = {OBJECTIVE: Although ADHD is highly heritable, some environmental factors contribute to its development. Given the growing evidence that gut microbiota was involved in psychiatric disorders, we aimed to identify the characteristic composition of the gut microbiota in ADHD.

METHODS: We recruited 47 medication-naive children and adolescents with ADHD, and 60 healthy controls (HCs). We used shotgun metagenomics to measure the structure of the gut microbiota and analyzed the difference in bacterial taxa between ADHD and HCs.

RESULTS: Significant differences were found between the ADHD and HC groups in both alpha diversity indices (Simpson index, p = .025 and Shannon index, p = .049) and beta diversity indices (Euclidean distance, Bray-Curtis distance, and JSD distance, p < 2.2e-16). Nine representative species best explain the difference.

CONCLUSION: Patients with ADHD showed significant differences in the composition of the gut microbiota compared with HCs. These results may help identify potential biomarkers of ADHD.}, } @article {pmid38326763, year = {2024}, author = {Chen, Y and Wang, J and Niu, T}, title = {Clinical and diagnostic values of metagenomic next-generation sequencing for infection in hematology patients: a systematic review and meta-analysis.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {167}, pmid = {38326763}, issn = {1471-2334}, abstract = {OBJECTIVES: This meta-analysis focused on systematically assessing the clinical value of mNGS for infection in hematology patients.

METHODS: We searched for studies that assessed the clinical value of mNGS for infection in hematology patients published in Embase, PubMed, Cochrane Library, Web of Science, and CNKI from inception to August 30, 2023. We compared the detection positive rate of pathogen for mNGS and conventional microbiological tests (CMTs). The diagnostic metrics, antibiotic adjustment rate and treatment effective rate were combined.

RESULTS: Twenty-two studies with 2325 patients were included. The positive rate of mNGS was higher than that of CMT (blood: 71.64% vs. 24.82%, P < 0.001; BALF: 89.86% vs. 20.78%, P < 0.001; mixed specimens: 82.02% vs. 28.12%, P < 0.001). The pooled sensitivity and specificity were 87% (95%CI: 81-91%) and 59% (95%CI: 43-72%), respectively. The reference standard/neutropenia and research type/reference standard may be sources of heterogeneity in sensitivity and specificity, respectively. The pooled antibiotic adjustment rate according to mNGS was 49.6% (95% CI: 41.8-57.4%), and the pooled effective rate was 80.9% (95% CI: 62.4-99.3%).

CONCLUSION: mNGS has high positive detection rates in hematology patients. mNGS can guide clinical antibiotic adjustments and improve prognosis, especially in China.}, } @article {pmid38320475, year = {2024}, author = {Jaffe, AL and Banfield, JF}, title = {Candidate Phyla Radiation bacteria.}, journal = {Current biology : CB}, volume = {34}, number = {3}, pages = {R80-R81}, doi = {10.1016/j.cub.2023.12.024}, pmid = {38320475}, issn = {1879-0445}, mesh = {*Metagenomics ; Phylogeny ; *Bacteria ; }, abstract = {Discovery of microbial diversity has been increasing at an astonishing rate. In this quick guide, Jaffe and Banfield provide an introduction to one major group of recently discovered microbes - the 'Candidate Phyla Radiation' bacteria.}, } @article {pmid38155570, year = {2024}, author = {Yan, M and Li, M and Wang, Y and Wang, X and Moeinzadeh, MH and Quispe-Huamanquispe, DG and Fan, W and Fang, Y and Wang, Y and Nie, H and Wang, Z and Tanaka, A and Heider, B and Kreuze, JF and Gheysen, G and Wang, H and Vingron, M and Bock, R and Yang, J}, title = {Haplotype-based phylogenetic analysis and population genomics uncover the origin and domestication of sweetpotato.}, journal = {Molecular plant}, volume = {17}, number = {2}, pages = {277-296}, doi = {10.1016/j.molp.2023.12.019}, pmid = {38155570}, issn = {1752-9867}, mesh = {Phylogeny ; *Genome, Plant ; *Metagenomics ; Tetraploidy ; Haplotypes ; Domestication ; }, abstract = {The hexaploid sweetpotato (Ipomoea batatas) is one of the most important root crops worldwide. However, its genetic origin remains controversial, and its domestication history remains unknown. In this study, we used a range of genetic evidence and a newly developed haplotype-based phylogenetic analysis to identify two probable progenitors of sweetpotato. The diploid progenitor was likely closely related to Ipomoea aequatoriensis and contributed the B1 subgenome, IbT-DNA2, and the lineage 1 type of chloroplast genome to sweetpotato. The tetraploid progenitor of sweetpotato was most likely I. batatas 4x, which donated the B2 subgenome, IbT-DNA1, and the lineage 2 type of chloroplast genome. Sweetpotato most likely originated from reciprocal crosses between the diploid and tetraploid progenitors, followed by a subsequent whole-genome duplication. In addition, we detected biased gene exchanges between the subgenomes; the rate of B1 to B2 subgenome conversions was nearly three times higher than that of B2 to B1 subgenome conversions. Our analyses revealed that genes involved in storage root formation, maintenance of genome stability, biotic resistance, sugar transport, and potassium uptake were selected during the speciation and domestication of sweetpotato. This study sheds light on the evolution of sweetpotato and paves the way for improvement of this crop.}, } @article {pmid38326388, year = {2024}, author = {Chan, OM and Xu, W and Cheng, NS and Leung, ASY and Ching, JYL and Fong, BLY and Cheong, PK and Zhang, L and Chan, FKL and Ng, SC and Leung, TF}, title = {A novel infant microbiome formula (SIM03) improved eczema severity and quality of life in preschool children.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {3168}, pmid = {38326388}, issn = {2045-2322}, abstract = {Altered gut microbiome composition has been reported in children with eczema and interventions that restore beneficial bacteria in the gut may improve eczema. This open-label pilot study aimed to investigate the efficacy of a novel infant microbiome formula (SIM03) in young children with eczema. Pre-school Chinese children aged 1-5 years old with eczema received SIM03 twice daily for three months. The novelty of SIM03 consists of both the use of a patented microencapsulation technology to protect the viability of unique Bifidobacterium bifidum and Bifidobacterium breve strains identified through big data analysis of large metagenomic datasets of young Chinese children. Paired stool samples at baseline and following SIM03 were analyzed by metagenomics sequencing. Generalized estimating equation was used to analyze changes in eczema severity, skin biophysical parameters, quality of life and stool microbiome. Twenty children aged 3.0 ± 1.6 years (10 with severe eczema) were recruited. Treatment compliance was ≥ 98%. SCORing Atopic Dermatitis score decreased significantly at two months (P = 0.008) and three months (P < 0.001), while quality of life improved significantly at 1, 2, and 3 months. The relative abundance of B. breve and microbial pathways on acetate and acetyl-CoA synthesis were enriched in stool samples at one month (P = 0.0014). Children who demonstrated increased B. bifidum after SIM03 showed improvement in sleep loss (P = 0.045). Relative abundance of B. breve correlated inversely with eczema extent (P = 0.023) and intensity (P = 0.019) only among patients with increased B. breve at Month 3. No serious adverse event was observed. In conclusion, SIM03 is well tolerated. This patented microbiome formula improves disease severity and quality of life in young eczematous children by enhancing the delivery of B. bifidum and B. breve in the gut. SIM03 is a potential treatment option for childhood eczema.}, } @article {pmid38325494, year = {2024}, author = {Forsmark, B and Bizjak, T and Nordin, A and Rosenstock, NP and Wallander, H and Gundale, MJ}, title = {Shifts in microbial community composition and metabolism correspond with rapid soil carbon accumulation in response to 20 years of simulated nitrogen deposition.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170741}, doi = {10.1016/j.scitotenv.2024.170741}, pmid = {38325494}, issn = {1879-1026}, abstract = {Anthropogenic nitrogen (N) deposition and fertilization in boreal forests frequently reduces decomposition and soil respiration and enhances C storage in the topsoil. This enhancement of the C sink can be as strong as the aboveground biomass response to N additions and has implications for the global C cycle, but the mechanisms remain elusive. We hypothesized that this effect would be associated with a shift in the microbial community and its activity, and particularly by fungal taxa reported to be capable of lignin degradation and organic N acquisition. We sampled the organic layer below the intact litter of a Norway spruce (Picea abies (L.) Karst) forest in northern Sweden after 20 years of annual N additions at low (12.5 kg N ha[-1] yr[-1]) and high (50 kg N ha[-1] yr[-1]) rates. We measured microbial biomass using phospholipid fatty-acid analysis (PLFA) and ergosterol measurements and used ITS metagenomics to profile the fungal community of soil and fine-roots. We probed the metabolic activity of the soil community by measuring the activity of extracellular enzymes and evaluated its relationships with the most N responsive soil fungal species. Nitrogen addition decreased the abundance of fungal PLFA markers and changed the fungal community in humus and fine-roots. Specifically, the humus community changed in part due to a shift from Oidiodendron pilicola, Cenococcum geophilum, and Cortinarius caperatus to Tylospora fibrillosa and Russula griseascens. These microbial community changes were associated with decreased activity of Mn-peroxidase and peptidase, and an increase in the activity of C acquiring enzymes. Our results show that the rapid accumulation of C in the humus layer frequently observed in areas with high N deposition is consistent with a shift in microbial metabolism, where decomposition associated with organic N acquisition is downregulated when inorganic N forms are readily available.}, } @article {pmid38325477, year = {2024}, author = {Liu, S and Liu, J and She, J and Xie, Z and Zhou, L and Dai, Q and Zhang, X and Wan, Y and Yin, M and Dong, X and Zhao, M and Chen, D and Wang, J}, title = {Microbial features with uranium pollution in artificial reservoir sediments at different depths under drought stress.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170694}, doi = {10.1016/j.scitotenv.2024.170694}, pmid = {38325477}, issn = {1879-1026}, abstract = {The discharge of uranium (U) (1185 μg/L) containing leachate from uranium tailings dam into the natural settings, may greatly affect the downstream environment. To reveal such relationship between uranium contamination and microbial communities in the most affected downstream environment under drought stress, a 180 cm downstream artificial reservoir depth sediment profile was collected, and the microbial communities and related genes were analyzed by 16S rDNA and metagenomics. Besides, the sequential extraction scheme was employed to shed light on the distinct role of U geochemical speciations in shaping microbial community structures. The results showed that U content ranged from 28.1 to 70.1 mg/kg, with an average content of 44.9 mg/kg, significantly exceeding the value of background sediments. Further, U in all the studied sediments was related to remarkably high portions of mobile fractions, and U was likely deposited layer by layer depending on the discharge/leachate inputs from uranium tailings dam upstream. The nexus between U speciation, physico-chemical indicators and microbial composition showed that Fe, S, and N metabolism played a vital role in microbial adaptation to U-enriched environment; meanwhile, the fraction of Ureducible and the Fe and S contents had the most significant effects on microbial community composition in the sediments under drought stress.}, } @article {pmid38325450, year = {2024}, author = {Lin, W and Cao, S and Wu, Q and Xu, F and Li, R and Cui, L}, title = {Size effects of microplastics on antibiotic resistome and core microbiome in an urban river.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170716}, doi = {10.1016/j.scitotenv.2024.170716}, pmid = {38325450}, issn = {1879-1026}, abstract = {Microplastics (MPs) in aquatic environments provide a new ecological niche that facilitates the attachment of antibiotic-resistance genes (ARGs) and pathogens. However, the effect of particle size on the colonization of antibiotic resistomes and pathogens remains poorly understood. To address this knowledge gap, this study explored the antibiotic resistome and core microbiomes on three distinct types of MPs including polyethylene, polypropylene, and polystyrene (PS), with varying sizes of 30, 200, and 3000 μm by metagenomic sequencing. Our finding showed that the ARG abundances of the PS type increased by 4-folds with increasing particle size from 30 to 3000 μm, and significant differences in ARG profiles were found across the three MP types. In addition, the concentrations of ARGs and mobile genetic elements (MGEs) were markedly higher in the MPs than in the surrounding water, indicating their enrichment at these artificial interfaces. Notably, several pathogens such as Pseudomonas aeruginosa, Mycobacterium tuberculosis, and Legionella pneumophila were enriched in MP biofilms, and the co-occurrence of ARGs and virulence factor genes (VFGs)/MGEs suggested the presence of pathogenic antibiotic-resistant microbes with potential mobility. Both redundancy analysis (RDA) and structural equation modeling (SEM) demonstrated that physicochemical properties such as zeta potential, MP size, and contact angle were the most significant contributors to the antibiotic resistome. Strikingly, no significant differences were observed in the health risk scores of the ARG profiles among different sizes and types of MPs. This study expands our knowledge on the impact of MP size on microbial risks, thus enhancing our understanding of the potential health hazards they pose.}, } @article {pmid38325080, year = {2024}, author = {Yu, X and Gu, C and Guo, X and Guo, R and Zhu, L and Qiu, X and Chai, J and Liu, F and Feng, Z}, title = {Dynamic changes of microbiota and metabolite of traditional Hainan dregs vinegar during fermentation based on metagenomics and metabolomics.}, journal = {Food chemistry}, volume = {444}, number = {}, pages = {138641}, doi = {10.1016/j.foodchem.2024.138641}, pmid = {38325080}, issn = {1873-7072}, abstract = {Hainan dregs vinegar (HNDV) is a traditional fermented food in China that is renowned for its unique flavor. HNDV is one of the most popular vinegars in Southeast Asia. However, research on the microorganisms and characteristic metabolites specific to HNDV is lacking. This study investigated the changes in microbial succession, volatile flavor compounds and characteristic non-volatile flavor compounds during HNDV fermentation based on metagenomics and metabolomics. The predominant microbial genera were Lactococcus, Limosilactobacillus, Lactiplantibacillus, and Saccharomyces. Unlike traditional vinegar, l-lactic acid was identified as the primary organic acid in HNDV. Noteworthy flavor compounds specific to HNDV included 3-methylthiopropanol and dl-phenylalanine. Significant associations were observed between six predominant microorganisms and six characteristic volatile flavor compounds, as well as seven characteristic non-volatile flavor compounds. The present results contribute to the development of starter cultures and the enhancement of HNDV quality.}, } @article {pmid38324986, year = {2024}, author = {Wang, M and Sun, H and Ma, X and Wang, H and Shi, B}, title = {Metabolic response of bacterial community to sodium hypochlorite and ammonia nitrogen affected the antibiotic resistance genes in pipelines biofilm.}, journal = {Water research}, volume = {252}, number = {}, pages = {121179}, doi = {10.1016/j.watres.2024.121179}, pmid = {38324986}, issn = {1879-2448}, abstract = {The biofilm is important for the antibiotic resistance genes (ARGs) propagation in drinking water pipelines. This study investigated the influence of chlorine disinfection and ammonia nitrogen on the ARGs in pipelines biofilm using metagenomic and metabolomics analysis. Chlorine disinfection reduced the relative abundance of unclassified_c_Actinobacteria, Acidimicrobium, and Candidatus_Pelagibacter to 394-430 TPM, 114-123 TPM, and 49-54 TPM, respectively. Correspondingly, the ARGs Saur_rpoC_DAP, macB, and mfd was reduced to 8-12 TPM, 81-92 TPM and 30-35 TPM, respectively. The results of metabolomics suggested that chlorine disinfection suppressed the pathways of ABC transporters, fatty acid biosynthesis, biosynthesis of unsaturated fatty acids, and biosynthesis of amino acids. These pathways were related to the cell membrane integrality and extracellular polymeric substances (EPS) secretion. Chlorine disinfection induced the decrease of EPS-related genes, resulting in the lower relative abundance of bacterial community and their antibiotic resistance. However, added approximately 0.5 mg/L NH3-N induced up-regulation of these metabolic pathways. In addition, NH3-N addition increased the relative abundance of enzymes related to inorganic and organic nitrogen metabolic pathway significantly, such as ammonia monooxygenase, glutamine synthetase, and glutamate synthase. Due to the EPS protection and nitrogen metabolism, the relative abundance of the main bacterial genera and the related ARGs increased to the level equal to that in pipelines biofilm with no disinfection. Therefore, NH3-N reduced the ARGs removal efficiency of chlorine disinfection. It is necessary to take measures to improve the removal rate of NH3-N and ARGs for preventing their risks in drinking water.}, } @article {pmid38324929, year = {2024}, author = {Ren, Z and Gao, H}, title = {Antibiotic resistance genes in integrated surface ice, cryoconite, and glacier-fed stream in a mountain glacier in Central Asia.}, journal = {Environment international}, volume = {184}, number = {}, pages = {108482}, doi = {10.1016/j.envint.2024.108482}, pmid = {38324929}, issn = {1873-6750}, abstract = {Glacier ice, cryoconite, and glacier-fed streams are interconnected features that have important implications for the dynamics and distribution of abiotic and biotic materials. However, the presence and behavior of antibiotic resistance genes (ARGs) within these glacial environments remained largely unexplored. Addressing this gap, we hypothesized that ARGs are widely distributed and exhibit distinct yet interconnected patterns of diversity and dynamics in these glacial environments. Here, we investigated ARGs in a mountain glacier in Central Asia. A total of 944 ARGs, spanning 22 antibiotic classes, were identified, with 633 ARGs shared across all three environments. Cryoconite exhibited the highest ARG richness, followed by ice, while stream biofilm displayed the lowest value. Exploring ARG profiles, we observed a consistent pattern in terms of antibiotic class and resistance mechanism across all three environments. Beta-lactam resistance genes exhibited the highest diversity, followed by multidrug, glycopeptide, and MLS. The predominant mechanisms were antibiotic inactivation, antibiotic efflux, and target alteration. The most prevalent ARG is cls, followed by mdfA, ropB, fabI, and macB. The similarity in ARG profiles between surface ice and cryoconite samples was more pronounced than their resemblance to stream biofilm samples. The variations of ARG profiles between any pair of environments were largely contributed by turnover component. Further insights into microbial interactions revealed 2328 significant associations between 80 OTUs and 356 ARGs, indicating complex relationships. Certain OTUs, including those from the genera Polaromonas, Ferruginibacter, Hymenobacter, Phormidesmis, Novosphingobium, and Polymorphobacter, were speculated as potential hosts for a variety of ARGs. Our findings underscore the intricate dynamics of antibiotic resistance in glacial ecosystems, emphasizing the need for a holistic understanding of ARG distribution, diversity, and associations across diverse environmental compartments. This research contributes valuable insights into the potential ecological implications of antibiotic resistance dissemination in cold environments, particularly as influenced by increasing climate change.}, } @article {pmid38324928, year = {2024}, author = {You, X and Wang, S and Chen, J}, title = {Magnetic biochar accelerates microbial succession and enhances assimilatory nitrate reduction during pig manure composting.}, journal = {Environment international}, volume = {184}, number = {}, pages = {108469}, doi = {10.1016/j.envint.2024.108469}, pmid = {38324928}, issn = {1873-6750}, abstract = {Biochar promotes microbial metabolic activities and reduces N2O on aerobic composting. However, the effects of magnetic biochar (MBC) on the microbial succession and N2O emissions during pig manure composting remain unclear. Herein, a 42-day composting experiment was conducted with five treatment regimes: pig manure without biochar (CK), 5 % pig manure-based biochar (5 % PBC), 2 % MBC (2 % MBC), 5 % MBC (5 % MBC) and 7.5 % MBC (7.5 % MBC)), to clarify the variation in functional microorganisms and genes associated with nitrogen and direct interspecies electron transfer via metagenomics. Fourier-transform infrared spectroscopy showed that MBC possessed more stable aromatic structures than pig manure-based biochar (PBC), indicating its greater potential for nitrous oxide reduction. MBC treatments were more effective in composting organic matter and improving the carbon/nitrogen ratio than PBC. The microbial composition during composting varied significantly, with the dominant phyla shifting from Firmicutes to Proteobacteria, Actinobacteria, and Bacteroidota. Network and hierarchical clustering analyses showed that the MBC treatment enhanced the interactions of dominant microbes (Proteobacteria and Bacteroidota) and accelerated the composting process. The biochar addition accelerated assimilatory nitrate reduction and slowed dissimilatory nitrate reduction and denitrification. The Mantel test demonstrated that magnetic biochar potentially helped regulate composting nutrients and affected functional nitrogen genes. These findings shed light on the role of MBC in mitigating greenhouse gas emissions during aerobic composting.}, } @article {pmid38323850, year = {2024}, author = {Egas, RA and Kurth, JM and Boeren, S and Sousa, DZ and Welte, CU and Sánchez-Andrea, I}, title = {A novel mechanism for dissimilatory nitrate reduction to ammonium in Acididesulfobacillus acetoxydans.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0096723}, doi = {10.1128/msystems.00967-23}, pmid = {38323850}, issn = {2379-5077}, abstract = {The biological route of nitrate reduction has important implications for the bioavailability of nitrogen within ecosystems. Nitrate reduction via nitrite, either to ammonium (ammonification) or to nitrous oxide or dinitrogen (denitrification), determines whether nitrogen is retained within the system or lost as a gas. The acidophilic sulfate-reducing bacterium (aSRB) Acididesulfobacillus acetoxydans can perform dissimilatory nitrate reduction to ammonium (DNRA). While encoding a Nar-type nitrate reductase, A. acetoxydans lacks recognized nitrite reductase genes. In this study, A. acetoxydans was cultivated under conditions conducive to DNRA. During cultivations, we monitored the production of potential nitrogen intermediates (nitrate, nitrite, nitric oxide, hydroxylamine, and ammonium). Resting cell experiments were performed with nitrate, nitrite, and hydroxylamine to confirm their reduction to ammonium, and formed intermediates were tracked. To identify the enzymes involved in DNRA, comparative transcriptomics and proteomics were performed with A. acetoxydans growing under nitrate- and sulfate-reducing conditions. Nitrite is likely reduced to ammonia by the previously undescribed nitrite reductase activity of the NADH-linked sulfite reductase AsrABC, or by a putatively ferredoxin-dependent homolog of the nitrite reductase NirA (DEACI_1836), or both. We identified enzymes and intermediates not previously associated with DNRA and nitrosative stress in aSRB. This increases our knowledge about the metabolism of this type of bacteria and helps the interpretation of (meta)genome data from various ecosystems on their DNRA potential and the nitrogen cycle.IMPORTANCENitrogen is crucial to any ecosystem, and its bioavailability depends on microbial nitrogen-transforming reactions. Over the recent years, various new nitrogen-transforming reactions and pathways have been identified, expanding our view on the nitrogen cycle and metabolic versatility. In this study, we elucidate a novel mechanism employed by Acididesulfobacillus acetoxydans, an acidophilic sulfate-reducing bacterium, to reduce nitrate to ammonium. This finding underscores the diverse physiological nature of dissimilatory reduction to ammonium (DNRA). A. acetoxydans was isolated from acid mine drainage, an extremely acidic environment where nitrogen metabolism is poorly studied. Our findings will contribute to understanding DNRA potential and variations in extremely acidic environments.}, } @article {pmid38322857, year = {2024}, author = {Astuti, PK and Ayoob, A and Strausz, P and Vakayil, B and Kumar, SH and Kusza, S}, title = {Climate change and dairy farming sustainability; a causal loop paradox and its mitigation scenario.}, journal = {Heliyon}, volume = {10}, number = {3}, pages = {e25200}, doi = {10.1016/j.heliyon.2024.e25200}, pmid = {38322857}, issn = {2405-8440}, abstract = {It is arguable at this time whether climate change is a cause or effect of the disruption in dairy farming. Climate change drastically affects the productive performance of livestock, including milk and meat production, and this could be attributed to the deviation of energy resources towards adaptive mechanisms. However, livestock farming also contributes substantially to the existing greenhouse gas pool, which is the causal of the climate change. We gathered relevant information from the recent publication and reviewed it to elaborate on sustainable dairy farming management in a changing climatic scenario, and efforts are needed to gather this material to develop methods that could help to overcome the adversities associated with livestock industries. We summarize the intervention points to reverse these adversities, such as application of genetic technology, nutrition intervention, utilization of chemical inhibitors, immunization, and application of metagenomics, which may help to sustain farm animal production in the changing climate scenario.}, } @article {pmid38322466, year = {2024}, author = {Zhu, XM and Dong, CX and Xie, L and Liu, HX and Hu, HQ}, title = {Brain abscess from oral microbiota approached by metagenomic next-generation sequencing: A case report and review of literature.}, journal = {World journal of clinical cases}, volume = {12}, number = {3}, pages = {616-622}, doi = {10.12998/wjcc.v12.i3.616}, pmid = {38322466}, issn = {2307-8960}, abstract = {BACKGROUND: Brain abscess is a serious and potentially fatal disease caused primarily by microbial infection. Although progress has been made in the diagnosis and treatment of brain abscesses, the diagnostic timeliness of pathogens needs to be improved.

CASE SUMMARY: We report the case of a 54-year-old male with a brain abscess caused by oral bacteria. The patient recovered well after receiving a combination of metagenomic next-generation sequencing (mNGS)-assisted guided medication and surgery.

CONCLUSION: Therefore, mNGS may be widely applied to identify the pathogenic microorganisms of brain abscesses and guide precision medicine.}, } @article {pmid38322128, year = {2024}, author = {Yang, S and Kozyreva, VK and Timme, RE and Hemarajata, P}, title = {Editorial: Integration of NGS in clinical and public health microbiology workflows: applications, compliance, quality considerations.}, journal = {Frontiers in public health}, volume = {12}, number = {}, pages = {1357098}, doi = {10.3389/fpubh.2024.1357098}, pmid = {38322128}, issn = {2296-2565}, } @article {pmid38321565, year = {2024}, author = {Marinelli, T and Masters, J and Buckland, ME and Lee, M and Rawlinson, W and Kim, KW and Urriola, N and van Hal, S}, title = {Chronic and neurotropic: A paradigm-challenging case of dengue virus encephalitis in patient with advanced human immunodeficiency virus infection.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciae061}, pmid = {38321565}, issn = {1537-6591}, abstract = {A 32-year-old female with advanced HIV infection presented to an Australian hospital with subacute but worsening symptoms of encephalitis. Metagenomic sequencing and Dengue NS3 antigen staining of brain tissue confirmed active Dengue virus (DENV) encephalitis. The most recent possible DENV exposure was months prior in West Africa, indicating chronicity.}, } @article {pmid38315173, year = {2024}, author = {Rafiqullah, IM and Varghese, R and Hellmann, KT and Velmurugan, A and Neeravi, A and Kumar Daniel, JL and Vidal, JE and Kompithra, RZ and Verghese, VP and Veeraraghavan, B and Robinson, DA}, title = {Pneumococcal population genomics changes during the early time period of conjugate vaccine uptake in southern India.}, journal = {Microbial genomics}, volume = {10}, number = {2}, pages = {}, doi = {10.1099/mgen.0.001191}, pmid = {38315173}, issn = {2057-5858}, mesh = {Child ; Humans ; Child, Preschool ; *Streptococcus pneumoniae ; Vaccines, Conjugate ; Trimethoprim, Sulfamethoxazole Drug Combination ; Metagenomics ; *Pneumococcal Infections/epidemiology/prevention & control ; Pneumococcal Vaccines ; Anti-Bacterial Agents/pharmacology/therapeutic use ; India/epidemiology ; }, abstract = {Streptococcus pneumoniae is a major cause of invasive disease of young children in low- and middle-income countries. In southern India, pneumococcal conjugate vaccines (PCVs) that can prevent invasive pneumococcal disease began to be used more frequently after 2015. To characterize pneumococcal evolution during the early time period of PCV uptake in southern India, genomes were sequenced and selected characteristics were determined for 402 invasive isolates collected from children <5 years of age during routine surveillance from 1991 to 2020. Overall, the prevalence and diversity of vaccine type (VT) and non-vaccine type (NVT) isolates did not significantly change post-uptake of PCV. Individually, serotype 1 and global pneumococcal sequence cluster (GPSC or strain lineage) 2 significantly decreased, whereas serotypes 6B, 9V and 19A and GPSCs 1, 6, 10 and 23 significantly increased in proportion post-uptake of PCV. Resistance determinants to penicillin, erythromycin, co-trimoxazole, fluoroquinolones and tetracycline, and multidrug resistance significantly increased in proportion post-uptake of PCV and especially among VT isolates. Co-trimoxazole resistance determinants were common pre- and post-uptake of PCV (85 and 93 %, respectively) and experienced the highest rates of recombination in the genome. Accessory gene frequencies were seen to be changing by small amounts across the frequency spectrum specifically among VT isolates, with the largest changes linked to antimicrobial resistance determinants. In summary, these results indicate that as of 2020 this pneumococcal population was not yet approaching a PCV-induced equilibrium and they highlight changes related to antimicrobial resistance. Augmenting PCV coverage and prudent use of antimicrobials are needed to counter invasive pneumococcal disease in this region.}, } @article {pmid38214523, year = {2024}, author = {Wang, H and Zheng, K and Wang, M and Ma, K and Ren, L and Guo, R and Ma, L and Zhang, H and Liu, Y and Xiong, Y and Wu, M and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Liang, Y}, title = {Shewanella phage encoding a putative anti-CRISPR-like gene represents a novel potential viral family.}, journal = {Microbiology spectrum}, volume = {12}, number = {2}, pages = {e0336723}, pmid = {38214523}, issn = {2165-0497}, abstract = {Shewanella is a prevalent bacterial genus in deep-sea environments including marine sediments, exhibiting diverse metabolic capabilities that indicate its significant contributions to the marine biogeochemical cycles. However, only a few Shewanella phages were isolated and deposited in the NCBI database. In this study, we report the isolation and characterization of a novel Shewanella phage, vB_SbaS_Y11, that infects Shewanella KR11 and was isolated from the sewage in Qingdao, China. Transmission electron microscopy revealed that vB_SbaS_Y11 has an icosahedral head and a long tail. The genome of vB_SbaS_Y11 is a linear, double-stranded DNA with a length of 62,799 bp and a G+C content of 46.9%, encoding 71 putative open reading frames. No tRNA genes or integrase-related feature genes were identified. An uncharacterized anti-CRISPR AcrVA2 gene was detected in its genome. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analyses indicate that vB_SbaS_Y11 has a novel genomic architecture and shares low similarity to Pseudomonas virus H66 and Pseudomonas phage F116. vB_SbaS_Y11 represents a potential new family-level virus cluster with eight metagenomic assembled viral genomes named Ranviridae.IMPORTANCEThe Gram-negative Shewanella bacterial genus currently includes about 80 species of mostly aquatic Gammaproteobacteria, which were isolated around the globe in a multitude of environments, such as freshwater, seawater, coastal sediments, and the deepest trenches. Here, we present a Shewanella phage vB_SbaS_Y11 that contains an uncharacterized anti-CRISPR AcrVA2 gene and belongs to a potential virus family, Ranviridae. This study will enhance the knowledge about the genome, diversity, taxonomic classification, and global distribution of Shewanella phage populations.}, } @article {pmid37985738, year = {2024}, author = {Batalha-Filho, H and Barreto, SB and Silveira, MHB and Miyaki, CY and Afonso, S and Ferrand, N and Carneiro, M and Sequeira, F}, title = {Disentangling the contemporary and historical effects of landscape on the population genomic variation of two bird species restricted to the highland forest enclaves of northeastern Brazil.}, journal = {Heredity}, volume = {132}, number = {2}, pages = {77-88}, pmid = {37985738}, issn = {1365-2540}, mesh = {Animals ; *Genetic Variation ; Brazil ; *Metagenomics ; Forests ; Birds/genetics ; Genetics, Population ; Phylogeny ; Ecosystem ; }, abstract = {Investigating the impact of landscape features on patterns of genetic variation is crucial to understand spatially dependent evolutionary processes. Here, we assess the population genomic variation of two bird species (Conopophaga cearae and Sclerurus cearensis) through the Caatinga moist forest enclaves in northeastern Brazil. To infer the evolutionary dynamics of bird populations through the Late Quaternary, we used genome-wide polymorphism data obtained from double-digestion restriction-site-associated DNA sequencing (ddRADseq), and integrated population structure analyses, historical demography models, paleodistribution modeling, and landscape genetics analyses. We found the population differentiation among enclaves to be significantly related to the geographic distance and historical resistance across the rugged landscape. The climate changes at the end of the Pleistocene to the Holocene likely triggered synchronic population decline in all enclaves for both species. Our findings revealed that both geographic distance and historical connectivity through highlands are important factors that can explain the current patterns of genetic variation. Our results further suggest that levels of population differentiation and connectivity cannot be explained purely on the basis of contemporary environmental conditions. By combining historical demographic analyses and niche modeling predictions in a historical framework, we provide strong evidence that climate fluctuations of the Quaternary promoted population differentiation and a high degree of temporal synchrony among population size changes in both species.}, } @article {pmid38320576, year = {2023}, author = {Salas-Espejo, E and Terrón-Camero, LC and Ruiz, JL and Molina, NM and Andrés-León, E}, title = {Exploring the Microbiome in Human Reproductive Tract: High-Throughput Methods for the Taxonomic Characterization of Microorganisms.}, journal = {Seminars in reproductive medicine}, volume = {41}, number = {5}, pages = {125-143}, doi = {10.1055/s-0044-1779025}, pmid = {38320576}, issn = {1526-4564}, abstract = {Microorganisms are important due to their widespread presence and multifaceted roles across various domains of life, ecology, and industries. In humans, they underlie the proper functioning of multiple systems crucial to well-being, including immunological and metabolic functions. Emerging research addressing the presence and roles of microorganisms within human reproduction is increasingly relevant. Studies implementing new methodologies (e.g., to investigate vaginal, uterine, and semen microenvironments) can now provide relevant insights into fertility, reproductive health, or pregnancy outcomes. In that sense, cutting-edge sequencing techniques, as well as others such as meta-metabolomics, culturomics, and meta-proteomics, are becoming more popular and accessible worldwide, allowing the characterization of microbiomes at unprecedented resolution. However, they frequently involve rather complex laboratory protocols and bioinformatics analyses, for which researchers may lack the required expertise. A suitable pipeline would successfully enable both taxonomic classification and functional profiling of the microbiome, providing easy-to-understand biological interpretations. However, the selection of an appropriate methodology would be crucial, as it directly impacts the reproducibility, accuracy, and quality of the results and observations. This review focuses on the different current microbiome-related techniques in the context of human reproduction, encompassing niches like vagina, endometrium, and seminal fluid. The most standard and reliable methods are 16S rRNA gene sequencing, metagenomics, and meta-transcriptomics, together with complementary approaches including meta-proteomics, meta-metabolomics, and culturomics. Finally, we also offer case examples and general recommendations about the most appropriate methods and workflows and discuss strengths and shortcomings for each technique.}, } @article {pmid38320392, year = {2024}, author = {Lyte, JM and Eckenberger, J and Keane, J and Robinson, K and Bacon, T and Assumpcao, ALFV and Donoghue, AM and Liyanage, R and Daniels, KM and Caputi, V and Lyte, M}, title = {Cold stress initiates catecholaminergic and serotonergic responses in the chicken gut that are associated with functional shifts in the microbiome.}, journal = {Poultry science}, volume = {103}, number = {3}, pages = {103393}, doi = {10.1016/j.psj.2023.103393}, pmid = {38320392}, issn = {1525-3171}, abstract = {Climate change is one of the most significant challenges facing the sustainability of global poultry production. Stress resulting from extreme temperature swings, including cold snaps, is a major concern for food production birds. Despite being well-documented in mammals, the effect of environmental stress on enteric neurophysiology and concomitant impact on host-microbiome interactions remains poorly understood in birds. As early life stressors may imprint long-term adaptive changes in the host, the present study sought to determine whether cold temperature stress, a prominent form of early life stress in chickens, elicits changes in enteric stress-related neurochemical concentrations that coincide with compositional and functional changes in the microbiome that persist into the later life of the bird. Chicks were, or were not, subjected to cold ambient temperature stress during the first week post-hatch and then remained at normal temperature for the remainder of the study. 16S rRNA gene and shallow shotgun metagenomic analyses demonstrated taxonomic and functional divergence between the cecal microbiomes of control and cold stressed chickens that persisted for weeks following cessation of the stressor. Enteric concentrations of serotonin, norepinephrine, and other monoamine neurochemicals were elevated (P < 0.05) in both cecal tissue and luminal content of cold stressed chickens. Significant (P < 0.05) associations were identified between cecal neurochemical concentrations and microbial taxa, suggesting host enteric neurochemical responses to environmental stress may shape the cecal microbiome. These findings demonstrate for the first time that early life exposure to environmental temperature stress can change the developmental trajectory of both the chicken cecal microbiome and host neuroendocrine enteric physiology. As many neurochemicals serve as interkingdom signaling molecules, the relationships identified here could be exploited to control the impact of climate change-driven stress on avian enteric host-microbe interactions.}, } @article {pmid38321488, year = {2024}, author = {Li, Y and Miyani, B and Faust, RA and David, RE and Xagoraraki, I}, title = {A broad wastewater screening and clinical data surveillance for virus-related diseases in the metropolitan Detroit area in Michigan.}, journal = {Human genomics}, volume = {18}, number = {1}, pages = {14}, pmid = {38321488}, issn = {1479-7364}, abstract = {BACKGROUND: Periodic bioinformatics-based screening of wastewater for assessing the diversity of potential human viral pathogens circulating in a given community may help to identify novel or potentially emerging infectious diseases. Any identified contigs related to novel or emerging viruses should be confirmed with targeted wastewater and clinical testing.

RESULTS: During the COVID-19 pandemic, untreated wastewater samples were collected for a 1-year period from the Great Lakes Water Authority Wastewater Treatment Facility in Detroit, MI, USA, and viral population diversity from both centralized interceptor sites and localized neighborhood sewersheds was investigated. Clinical cases of the diseases caused by human viruses were tabulated and compared with data from viral wastewater monitoring. In addition to Betacoronavirus, comparison using assembled contigs against a custom Swiss-Prot human virus database indicated the potential prevalence of other pathogenic virus genera, including: Orthopoxvirus, Rhadinovirus, Parapoxvirus, Varicellovirus, Hepatovirus, Simplexvirus, Bocaparvovirus, Molluscipoxvirus, Parechovirus, Roseolovirus, Lymphocryptovirus, Alphavirus, Spumavirus, Lentivirus, Deltaretrovirus, Enterovirus, Kobuvirus, Gammaretrovirus, Cardiovirus, Erythroparvovirus, Salivirus, Rubivirus, Orthohepevirus, Cytomegalovirus, Norovirus, and Mamastrovirus. Four nearly complete genomes were recovered from the Astrovirus, Enterovirus, Norovirus and Betapolyomavirus genera and viral species were identified.

CONCLUSIONS: The presented findings in wastewater samples are primarily at the genus level and can serve as a preliminary "screening" tool that may serve as indication to initiate further testing for the confirmation of the presence of species that may be associated with human disease. Integrating innovative environmental microbiology technologies like metagenomic sequencing with viral epidemiology offers a significant opportunity to improve the monitoring of, and predictive intelligence for, pathogenic viruses, using wastewater.}, } @article {pmid38321233, year = {2024}, author = {Jin, L and Diaz-Canestro, C and Wang, Y and Tse, MA and Xu, A}, title = {Exerkines and cardiometabolic benefits of exercise: from bench to clinic.}, journal = {EMBO molecular medicine}, volume = {}, number = {}, pages = {}, pmid = {38321233}, issn = {1757-4684}, support = {82070860//MOST | National Natural Science Foundation of China (NSFC)/ ; 82161138026//MOST | National Natural Science Foundation of China (NSFC)/ ; 17127518//General Research Fund from the Research Grant Council of Hong Kong/ ; AOE/M/707-18//Area of Excellence from the Research Grant Council of Hong Kong/ ; 09201676//Health and Medical Research Fund from the Research Grant Council of Hong Kong/ ; }, abstract = {Regular exercise has both immediate and long-lasting benefits on cardiometabolic health, and has been recommended as a cornerstone of treatment in the management of diabetes and cardiovascular conditions. Exerkines, which are defined as humoral factors responsive to acute or chronic exercise, have emerged as important players conferring some of the multiple cardiometabolic benefits of exercise. Over the past decades, hundreds of exerkines released from skeletal muscle, heart, liver, adipose tissue, brain, and gut have been identified, and several exerkines (such as FGF21, IL-6, and adiponectin) have been exploited therapeutically as exercise mimetics for the treatment of various metabolic and cardiovascular diseases. Recent advances in metagenomics have led to the identification of gut microbiota, a so-called "hidden" metabolic organ, as an additional class of exerkines determining the efficacy of exercise in diabetes prevention, cardiac protection, and exercise performance. Furthermore, multiomics-based studies have shown the feasibility of using baseline exerkine signatures to predict individual responses to exercise with respect to metabolic and cardiorespiratory health. This review aims to explore the molecular pathways whereby exerkine networks mediate the cardiometabolic adaptations to exercise by fine-tuning inter-organ crosstalk, and discuss the roadmaps for translating exerkine-based discovery into the therapeutic application and personalized medicine in the management of the cardiometabolic disease.}, } @article {pmid38321183, year = {2024}, author = {Chen, L and Banfield, JF}, title = {COBRA improves the completeness and contiguity of viral genomes assembled from metagenomes.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {38321183}, issn = {2058-5276}, abstract = {Viruses are often studied using metagenome-assembled sequences, but genome incompleteness hampers comprehensive and accurate analyses. Contig Overlap Based Re-Assembly (COBRA) resolves assembly breakpoints based on the de Bruijn graph and joins contigs. Here we benchmarked COBRA using ocean and soil viral datasets. COBRA accurately joined the assembled sequences and achieved notably higher genome accuracy than binning tools. From 231 published freshwater metagenomes, we obtained 7,334 bacteriophage clusters, ~83% of which represent new phage species. Notably, ~70% of these were circular, compared with 34% before COBRA analyses. We expanded sampling of huge phages (≥200 kbp), the largest of which was curated to completion (717 kbp). Improved phage genomes from Rotsee Lake provided context for metatranscriptomic data and indicated the in situ activity of huge phages, whiB-encoding phages and cysC- and cysH-encoding phages. COBRA improves viral genome assembly contiguity and completeness, thus the accuracy and reliability of analyses of gene content, diversity and evolution.}, } @article {pmid38321113, year = {2024}, author = {Castelli, M and Nardi, T and Gammuto, L and Bellinzona, G and Sabaneyeva, E and Potekhin, A and Serra, V and Petroni, G and Sassera, D}, title = {Host association and intracellularity evolved multiple times independently in the Rickettsiales.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1093}, pmid = {38321113}, issn = {2041-1723}, abstract = {The order Rickettsiales (Alphaproteobacteria) encompasses multiple diverse lineages of host-associated bacteria, including pathogens, reproductive manipulators, and mutualists. Here, in order to understand how intracellularity and host association originated in this order, and whether they are ancestral or convergently evolved characteristics, we built a large and phylogenetically-balanced dataset that includes de novo sequenced genomes and a selection of published genomic and metagenomic assemblies. We perform detailed functional reconstructions that clearly indicates "late" and parallel evolution of obligate host-association in different Rickettsiales lineages. According to the depicted scenario, multiple independent horizontal acquisitions of transporters led to the progressive loss of biosynthesis of nucleotides, amino acids and other metabolites, producing distinct conditions of host-dependence. Each clade experienced a different pattern of evolution of the ancestral arsenal of interaction apparatuses, including development of specialised effectors involved in the lineage-specific mechanisms of host cell adhesion and/or invasion.}, } @article {pmid38319625, year = {2024}, author = {Ortega Parra, N and Zisi, Z and Vogel, E and Vos, C and Hanssen, I}, title = {First report of infections with isolates of the Asian genotype of Cucumber green mottle mosaic virus in cucumber crops in Belgium.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-11-23-2532-PDN}, pmid = {38319625}, issn = {0191-2917}, abstract = {In July 2019, four rows of cucumber plants (Cucumis sativus) in a commercial glasshouse in the north of Belgium showed severe mosaic, blistering and distortion of the leaves, with symptoms resembling those caused by Cucumber green mottle mosaic virus (CGMMV). CGMMV is a Tobamovirus that mainly affects cucurbit crops worldwide (Dombrovsky et al., 2017). Phylogenetic analyses in previous studies have shown two major clades, one including isolates that were initially identified in Europe and Russia (European genotype) and the second one with isolates initially identified in Asia and Israel (Asian genotype) (Dombrovsky et al., 2017; Pitman et al., 2022; Mackie et al., 2023). A symptomatic leaf sample was collected and total RNA was isolated from 100 mg of leaf tissue (Spectrum™ Plant Total RNA kit, Sigma-Aldrich). CGMMV was detected using a one-step TaqMan RT-qPCR (Hongyun et al., 2008). High-throughput sequencing (HTS) confirmed the presence of CGMMV. The sample was prepared using the Novel enrichment technique of viromes protocol (NETOVIR protocol, Conceição-Neto et al., 2015). The leaf material was homogenized, enriched for virus-like particles and the RNA was extracted (QIAamp Viral RNA mini kit, QIAGEN). The extract was randomly amplified (Whole Transcriptome Amplification kit, Sigma Aldrich), used for library preparation (Nextera XT DNA library preparation kit, Illumina) and sequenced on a NovaSeq platform. HTS data analysis was performed using Geneious Prime software (Biomatters, Auckland, New Zealand, version 2023.2). After quality filtering and trimming, 26.7M reads were obtained (132 nt mean length). In total, 20.6M reads were mapped to two genomes KP772568 and GQ411361 (considered as reference for the Asian and European genotypes respectively) with Geneious. This revealed 100% coverage of the full sequences (6422 nt) with 99.4% and 90% nucleotide identities to the reference genomes of Asian and European genotypes, respectively. Phylogenetic analyses confirmed that isolate 2019-26A-BE, with GenBank ID OR724740, relates to the Asian genotype. The HTS data were additionally processed using the ViPER pipeline (De Coninck, 2021). The raw reads were quality filtered and trimmed, (Trimmomatic) and then used to perform de novo assembly (metaSPAdes). The produced contigs were classified using DIAMOND and visualized with KronaTools. The results showed that no other virus was detected in the sample. Finally, cucumber seedlings were inoculated using the original symptomatic sample and were grown in a research glasshouse. After 3 weeks, severe CGMMV symptoms, similar to the original symptoms observed in the commercial glasshouse, were observed in the inoculated plants. Infection with CGMMV was verified via RT-qPCR, and the isolate present in the inoculated plants was confirmed to belong to the Asian genotype via RT-PCR-RFLP (Crespo et al., 2017). Later samplings of symptomatic leaves confirmed the presence of isolates belonging to the Asian genotype of CGMMV at four other commercial glasshouse locations, specializing in cucumber crop, in Belgium in 2020, 2021 and 2023 by RT-PCR-RFLP. While the Asian genotype was previously found elsewhere in Europe (Pitman et al., 2022), to our knowledge, this is the first report of infections with isolates of this genotype in glasshouse cucumber crops in Belgium. Further investigation is required to determine the spread and impact of infections with isolates of the Asian genotype in cucumber crops in Belgium.}, } @article {pmid38319284, year = {2024}, author = {Nguyen, SM and Tran, HTT and Long, J and Shrubsole, MJ and Cai, H and Yang, Y and Cai, Q and Tran, TV and Zheng, W and Shu, XO}, title = {Gut microbiome in association with chemotherapy-induced toxicities among patients with breast cancer.}, journal = {Cancer}, volume = {}, number = {}, pages = {}, doi = {10.1002/cncr.35229}, pmid = {38319284}, issn = {1097-0142}, support = {D43 TW009337/TW/FIC NIH HHS/United States ; P20 CA210300/CA/NCI NIH HHS/United States ; /GH/CGH CDC HHS/United States ; /CA/NCI NIH HHS/United States ; /TW/FIC NIH HHS/United States ; }, abstract = {BACKGROUND: Little research has focused on the relationship between gut microbiome and chemotherapy-induced toxicity.

METHODS: This prospective study involves 301 patients with breast cancer who had prechemotherapy stool samples collected. Gut microbiome was sequenced by shotgun metagenomics; associations with chemotherapy-induced toxicities during first-line treatment by gut microbial diversity, composition, and metabolic pathways with severe (i.e., grade ≥3) hematological and gastrointestinal toxicities were evaluated via multivariable logistic regression.

RESULTS: High prechemotherapy α-diversity was associated with a significantly reduced risk of both severe hematological toxicity (odds ratio [OR] = 0.94; 95% CI, 0.89-0.99; p = .048) and neutropenia (OR = 0.94; 95% CI, 0.89-0.99; p = .016). A high abundance of phylum Synergistota, class Synergistia, and order Synergistales were significantly associated with a reduced risk of severe neutropenia; conversely, enrichment of phylum Firmicutes C, class Negativicutes, phylum Firmicutes I, and class Bacilli A, order Paenibacillales were significantly associated with an increased risk of severe neutropenia (p range: 0.012-2.32 × 10[-3] ; false discovery rate <0.1). Significant positive associations were also observed between severe nausea/vomiting and high Chao1 indexes, β-diversity (p < .05), 20 species belonging to the family Lachnospiraceae, Oscillospiraceae, and Ruminococcaceae (p value range: 6.14 × 10[-3] to 1.33 × 10[-5] ; false discovery rate <0.1), and three metabolic pathways involved in reductive tricarboxylic acid cycle I and cycle II, and an incomplete reductive tricarboxylic acid cycle (p < .01). Conversely, a high abundance of species Odoribacter laneus and the pathway related to the L-proline biosynthesis II were inversely associated with severe nausea/vomiting.

CONCLUSIONS: Our study suggests that gut microbiota may be a potential preventive target to reduce chemotherapy-induced toxicity.}, } @article {pmid38319095, year = {2024}, author = {Xie, J and Yap, G and Simpson, D and Gänzle, M}, title = {The effect of seed germination and Bacillus spp. on the ripening of plant cheese analogs.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0227623}, doi = {10.1128/aem.02276-23}, pmid = {38319095}, issn = {1098-5336}, abstract = {Consumer demand for plant cheeses is increasing, but challenges of improving both flavor and quality remain. This study investigated the microbiological and physicochemical impact of seed germination and fermentation with Bacillus velezensis and Bacillus amyloliquefaciens on the ripening of plant cheese analogs. Chlorine treatment or addition of Lactiplantibacillus plantarum and Lactococcus lactis controlled microbial growth during seed germination. Lp. plantarum and Lc. lactis also served as starter cultures for the acidification of soy and lupine milk and were subsequently present in the unripened plant cheese as dominant microbes. Acidification also inhibited the growth and metabolic activity of bacilli but Bacillus spores remained viable throughout ripening. During plant cheese ripening, Lc. lactis was inactivated before Lp. plantarum and the presence of bacilli during seed germination delayed Lc. lactis inactivation. Metagenomic sequencing of full-length 16S rRNA gene amplicons confirmed that the relative abundance of the inoculated strains in each ripened cheese sample exceeded 99%. Oligosaccharides including raffinose, stachyose, and verbascose were rapidly depleted in the initial stage of ripening. Both germination and the presence of bacilli during seed germination had impact on polysaccharide hydrolysis during ripening. Bacilli but not seed germination enhanced proteolysis of plant cheese during ripening. In conclusion, the use of germination with lactic acid bacteria in combination with Bacillus spp. exhibited the potential to improve the quality of ripened plant cheeses with a positive effect on the reduction of hygienic risks.IMPORTANCEThe development of novel plant-based fermented food products for which no traditional templates exist requires the development of starter cultures. Although the principles of microbial flavor formation in plant-based analogs partially overlap with dairy fermentations, the composition of the raw materials and thus likely the selective pressure on the activity of starter cultures differs. Experiments that are described in this study explored the use of seed germination, the use of lactic acid bacteria, and the use of bacilli to reduce hygienic risks, to acidify plant milk, and to generate taste-active compounds through proteolysis and fermentative conversion of carbohydrates. The characterization of fermentation microbiota by culture-dependent and culture-independent methods also confirmed that the starter cultures used were able to control microbial communities throughout 90 d of ripening. Taken together, the results provide novel tools for the development of plant-based analogs of fermented dairy products.}, } @article {pmid38318812, year = {2024}, author = {Li, Z and Feng, C and Lei, J and He, X and Wang, Q and Zhao, Y and Qian, Y and Zhan, X and Shen, Z}, title = {Farmland Microhabitat Mediated by a Residual Microplastic Film: Microbial Communities and Function.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c07717}, pmid = {38318812}, issn = {1520-5851}, abstract = {How the plastisphere mediated by the residual microplastic film in farmlands affects microhabitat systems is unclear. Here, microbial structure, assembly, and biogeochemical cycling in the plastisphere and soil in 33 typical farmland sites were analyzed by amplicon sequencing of 16S rRNA genes and ITS and metagenome analysis. The results indicated that residual microplastic film was colonized by microbes, forming a unique niche called the plastisphere. Notable differences in the microbial community structure and function were observed between soil and plastisphere. Residual microplastic film altered the microbial symbiosis and assembly processes. Stochastic processes significantly dominated the assembly of the bacterial community in the plastisphere and soil but only in the plastisphere for the fungal community. Deterministic processes significantly dominated the assembly of fungal communities only in soil. Moreover, the plastisphere mediated by the residual microplastic film acted as a preferred vector for pathogens and microorganisms associated with plastic degradation and the nitrogen and sulfur cycle. The abundance of genes associated with denitrification and sulfate reduction activity in the plastisphere was pronouncedly higher than that of soil, which increase the potential risk of nitrogen and sulfur loss. The results will offer a scientific understanding of the harm caused by the residual microplastic film in farmlands.}, } @article {pmid38318165, year = {2024}, author = {Jiang, J and Li, Y and Wang, Q and Zeng, H and Yang, W and Wu, Y and Peng, W and Pan, P and Hu, C and Deng, P}, title = {Clinical implications of trichomonads detected in bronchoalveolar fluid by metagenomic next-generation sequencing: a multicenter retrospective study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1289231}, doi = {10.3389/fcimb.2024.1289231}, pmid = {38318165}, issn = {2235-2988}, abstract = {BACKGROUND: Pulmonary trichomoniasis is considered a neglected disease due to failures in recognizing it, stemming from insensitive microbial methods and a lack of specific clinical features. This study aims to analyze the clinical implications of trichomonads detected in bronchoalveolar lavage fluid (BALF) by metagenomic next-generation sequencing (mNGS).

METHODS: This multicenter retrospective study included patients diagnosed with pneumonia, admitted to three tertiary hospitals in China from July 2018 to September 2022, with trichomonads detected in BALF through mNGS. The analysis covered demographics, comorbidities, symptoms, laboratory findings, mNGS results, clinical treatment, and outcomes of these patients.

RESULTS: A total of 17 patients were enrolled, comprising 14 males and 3 females. Trichomonas tenax and Trichomonas vaginalis were detected by mNGS in BALF samples of 15 and 2 patients, respectively. Patients were categorized into two groups based on the presence of risk factors for trichomonad infection, including immunocompromised conditions, uncontrolled diabetes mellitus, oral/periodontal diseases, and aspiration. Among 11 patients with risk factors (Case 1-11), 4 received nitromidazoles as part of comprehensive treatment, achieving a 100% treatment success rate. The remaining 7 patients, who did not receive nitromidazoles, had only one achieving relief after broad-spectrum antimicrobial therapy, resulting in a 14.3% treatment success rate. For the 6 patients without any risk factors for trichomonad infection (Case 12-17), none received nitromidazoles during hospitalization. However, 4 out of these 6 patients (66.7%) eventually recovered.

CONCLUSION: mNGS proves to be an efficient tool for detecting trichomonads in BALF samples. Comprehensive analysis of clinical features and laboratory indicators is essential to distinguish between infection and colonization of trichomonads. Pulmonary trichomoniasis should not be overlooked when trichomonads are detected in BALF from patients with risk factors.}, } @article {pmid38318164, year = {2024}, author = {Piazzesi, A and Pane, S and Del Chierico, F and Romani, L and Campana, A and Palma, P and Putignani, L}, title = {The pediatric gut bacteriome and virome in response to SARS-CoV-2 infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {14}, number = {}, pages = {1335450}, doi = {10.3389/fcimb.2024.1335450}, pmid = {38318164}, issn = {2235-2988}, abstract = {INTRODUCTION: Since the beginning of the SARS-CoV-2 pandemic in early 2020, it has been apparent that children were partially protected from both infection and the more severe forms of the disease. Many different mechanisms have been proposed to explain this phenomenon, including children's frequent exposure to other upper respiratory infections and vaccines, and which inflammatory cytokines they are more likely to produce in response to infection. Furthermore, given the presence of SARS-CoV-2 in the intestine and its ability to infect enterocytes, combined with the well described immunomodulatory capabilities of the microbiome, another potential contributing factor may be the presence of certain protective microbial members of the gut microbiota (GM).

METHODS: We performed shotgun metagenomic sequencing and profiled both the bacteriome and virome of the GM of pediatric SARS-CoV-2 patients compared to healthy, age-matched subjects.

RESULTS: We found that, while pediatric patients do share some pro-inflammatory microbial signatures with adult patients, they also possess a distinct microbial signature of protective bacteria previously found to be negatively correlated with SARS-CoV-2 infectivity and COVID-19 severity. COVID-19 was also associated with higher fecal Cytomegalovirus load, and with shifts in the relative abundances of bacteriophages in the GM. Furthermore, we address how the preventative treatment of COVID-19 patients with antibiotics, a common practice especially in the early days of the pandemic, affected the bacteriome and virome, as well as the abundances of antimicrobial resistance and virulence genes in these patients.

DISCUSSION: To our knowledge, this is the first study to address the bacteriome, virome, and resistome of pediatric patients in response to COVID-19 and to preventative antibiotics use.}, } @article {pmid38317822, year = {2024}, author = {Kop, LFM and Koch, H and Jetten, MSM and Daims, H and Lücker, S}, title = {Metabolic and phylogenetic diversity in the phylum Nitrospinota revealed by comparative genome analyses.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycad017}, doi = {10.1093/ismeco/ycad017}, pmid = {38317822}, issn = {2730-6151}, abstract = {The most abundant known nitrite-oxidizing bacteria in the marine water column belong to the phylum Nitrospinota. Despite their importance in marine nitrogen cycling and primary production, there are only few cultured representatives that all belong to the class Nitrospinia. Moreover, although Nitrospinota were traditionally thought to be restricted to marine environments, metagenome-assembled genomes have also been recovered from groundwater. Over the recent years, metagenomic sequencing has led to the discovery of several novel classes of Nitrospinota (UBA9942, UBA7883, 2-12-FULL-45-22, JACRGO01, JADGAW01), which remain uncultivated and have not been analyzed in detail. Here, we analyzed a nonredundant set of 98 Nitrospinota genomes with focus on these understudied Nitrospinota classes and compared their metabolic profiles to get insights into their potential role in biogeochemical element cycling. Based on phylogenomic analysis and average amino acid identities, the highly diverse phylum Nitrospinota could be divided into at least 33 different genera, partly with quite distinct metabolic capacities. Our analysis shows that not all Nitrospinota are nitrite oxidizers and that members of this phylum have the genomic potential to use sulfide and hydrogen for energy conservation. This study expands our knowledge of the phylogeny and potential ecophysiology of the phylum Nitrospinota and offers new avenues for the isolation and cultivation of these elusive bacteria.}, } @article {pmid38317726, year = {2024}, author = {Fitak, RR}, title = {The magneto-microbiome: A dataset of the metagenomic distribution of magnetotactic bacteria.}, journal = {Data in brief}, volume = {53}, number = {}, pages = {110073}, doi = {10.1016/j.dib.2024.110073}, pmid = {38317726}, issn = {2352-3409}, abstract = {Magnetotactic bacteria (MTB) are diverse prokaryotes characterized by their ability to generate biogenic magnetic iron crystals. MTB are ubiquitous across aquatic environments, and growing evidence has indicated they may be present in association with animal microbiomes. Unfortunately, they are difficult to culture in vitro and more studies understanding their biogeographical distribution and ecological roles are needed. To provide data regarding the patterns of diversity and distribution of MTB, we screened the entire Sequence Read Archive (SRA) from the National Center for Biotechnology Information for DNA sequencing reads matching known MTB taxa. The dataset summarizes the count of reads assigned to MTB from more than 26 million SRA accessions comprising approximately 80 petabases (7.98 × 10[16]) of DNA. More than 396 million DNA sequencing reads were assigned to 214 MTB taxa in 691,086 (2.65 %) SRA accessions. The final dataset can be utilized by researchers to narrow their efforts in examination of both environmental and ecological roles of specific MTB or to identify potential host organisms. These data will be instrumental to further elucidating the importance and utility of these enigmatic bacteria.}, } @article {pmid38317381, year = {2024}, author = {Xiu, W and Gai, R and Chen, S and Ren, C and Lloyd, JR and Bassil, NM and Nixon, SL and Polya, DA and Hou, S and Guo, H}, title = {Ammonium-Enhanced Arsenic Mobilization from Aquifer Sediments.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c09640}, pmid = {38317381}, issn = {1520-5851}, abstract = {Ammonium-related pathways are important for groundwater arsenic (As) enrichment, especially via microbial Fe(III) reduction coupled with anaerobic ammonium oxidation; however, the key pathways (and microorganisms) underpinning ammonium-induced Fe(III) reduction and their contributions to As mobilization in groundwater are still unknown. To address this gap, aquifer sediments hosting high As groundwater from the western Hetao Basin were incubated with [15]N-labeled ammonium and external organic carbon sources (including glucose, lactate, and lactate/acetate). Decreases in ammonium concentrations were positively correlated with increases in the total produced Fe(II) (Fe(II)tot) and released As. The molar ratios of Fe(II)tot to oxidized ammonium ranged from 3.1 to 3.7 for all incubations, and the δ[15]N values of N2 from the headspace increased in [15]N-labeled ammonium-treated series, suggesting N2 as the key end product of ammonium oxidation. The addition of ammonium increased the As release by 16.1% to 49.6%, which was more pronounced when copresented with organic electron donors. Genome-resolved metagenomic analyses (326 good-quality MAGs) suggested that ammonium-induced Fe(III) reduction in this system required syntrophic metabolic interactions between bacterial Fe(III) reduction and archaeal ammonium oxidation. The current results highlight the significance of syntrophic ammonium-stimulated Fe(III) reduction in driving As mobilization, which is underestimated in high As groundwater.}, } @article {pmid38317217, year = {2024}, author = {Xing, JH and Niu, TM and Zou, BS and Yang, GL and Shi, CW and Yan, QS and Sun, MJ and Yu, T and Zhang, SM and Feng, XZ and Fan, SH and Huang, HB and Wang, JH and Li, MH and Jiang, YL and Wang, JZ and Cao, X and Wang, N and Zeng, Y and Hu, JT and Zhang, D and Sun, WS and Yang, WT and Wang, CF}, title = {Gut microbiota-derived LCA mediates the protective effect of PEDV infection in piglets.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {20}, pmid = {38317217}, issn = {2049-2618}, support = {U21A20261， 721 32202819, 31941018, 31972696 and 32072888//National Natural Science Foundation of China/ ; CARS-35//China Agriculture Research System of MOF 722 and MARA/ ; 20190301042NY, YDZJ202102CXJD029, and 20210202102NC//Science and Technology Development Program of Jilin Province/ ; }, abstract = {BACKGROUND: The gut microbiota is a critical factor in the regulation of host health, but the relationship between the differential resistance of hosts to pathogens and the interaction of gut microbes is not yet clear. Herein, we investigated the potential correlation between the gut microbiota of piglets and their disease resistance using single-cell transcriptomics, 16S amplicon sequencing, metagenomics, and untargeted metabolomics.

RESULTS: Porcine epidemic diarrhea virus (PEDV) infection leads to significant changes in the gut microbiota of piglets. Notably, Landrace pigs lose their resistance quickly after being infected with PEDV, but transplanting the fecal microbiota of Min pigs to Landrace pigs alleviated the infection status. Macrogenomic and animal protection models identified Lactobacillus reuteri and Lactobacillus amylovorus in the gut microbiota as playing an anti-infective role. Moreover, metabolomic screening of the secondary bile acids' deoxycholic acid (DCA) and lithocholic acid (LCA) correlated significantly with Lactobacillus reuteri and Lactobacillus amylovorus, but only LCA exerted a protective function in the animal model. In addition, LCA supplementation altered the distribution of intestinal T-cell populations and resulted in significantly enriched CD8[+] CTLs, and in vivo and in vitro experiments showed that LCA increased SLA-I expression in porcine intestinal epithelial cells via FXR receptors, thereby recruiting CD8[+] CTLs to exert antiviral effects.

CONCLUSIONS: Overall, our findings indicate that the diversity of gut microbiota influences the development of the disease, and manipulating Lactobacillus reuteri and Lactobacillus amylovorus, as well as LCA, represents a promising strategy to improve PEDV infection in piglets. Video Abstract.}, } @article {pmid38316431, year = {2024}, author = {Johnson, BA and Clark, KA and Bushin, LB and Spolar, CN and Seyedsayamdost, MR}, title = {Expanding the Landscape of Noncanonical Amino Acids in RiPP Biosynthesis.}, journal = {Journal of the American Chemical Society}, volume = {}, number = {}, pages = {}, doi = {10.1021/jacs.3c10824}, pmid = {38316431}, issn = {1520-5126}, abstract = {Advancements in DNA sequencing technologies and bioinformatics have enabled the discovery of new metabolic reactions from overlooked microbial species and metagenomic sequences. Using a bioinformatic co-occurrence strategy, we previously generated a network of ∼600 uncharacterized quorum-sensing-regulated biosynthetic gene clusters that code for ribosomally synthesized and post-translationally modified peptide (RiPP) natural products and are tailored by radical S-adenosylmethionine (RaS) enzymes in streptococci. The most complex of these is the GRC subfamily, named after a conserved motif in the precursor peptide and found exclusively in Streptococcus pneumoniae, the causative agent of bacterial pneumonia. In this study, using both in vivo and in vitro approaches, we have elucidated the modifications installed by the grc biosynthetic enzymes, including a ThiF-like adenylyltransferase/cyclase that generates a C-terminal Glu-to-Cys thiolactone macrocycle, and two RaS enzymes, which selectively epimerize the β-carbon of threonine and desaturate histidine to generate the first instances of l-allo-Thr and didehydrohistidine in RiPP biosynthesis. RaS-RiPPs that have been discovered thus far have stood out for their exotic macrocycles. The product of the grc cluster breaks this trend by generating two noncanonical residues rather than an unusual macrocycle in the peptide substrate. These modifications expand the landscape of nonproteinogenic amino acids in RiPP natural product biosynthesis and motivate downstream biocatalytic applications of the corresponding enzymes.}, } @article {pmid38316151, year = {2024}, author = {Li, R and Zhou, J}, title = {Sepsis and multi-organ failure due to genital herpes in a healthy person.}, journal = {International journal of STD & AIDS}, volume = {}, number = {}, pages = {9564624241229465}, doi = {10.1177/09564624241229465}, pmid = {38316151}, issn = {1758-1052}, abstract = {Herpes simplex virus type 2 (HSV-2) is highly prevalent in several regions of the world and is the main pathogen causing genital herpes, which is transmitted almost exclusively through sexual contact. Systemically disseminated infections caused by HSV-2 are rare and most often seen in newborns, pregnant women, or immunocompromised populations. The virus can invade multiple organs and cause damage. In this paper, we present an extremely rare case of an immunocompetent 36-year-old male who came to our hospital with a high fever with abdominal pain and died of sepsis and multiple organ dysfunction syndrome within a short period. After the exclusion of common pathogens such as bacterial and fungal infections during hospitalization, metagenomic next generation sequencing of the patient's peripheral blood and ascites gave us the answer, and very high nucleic acid sequence counts of HSV-2 were detected in both his peripheral blood and ascites, confirming HSV-2 as the causative virus. In addition, this paper provides a brief review of the relevant literature.}, } @article {pmid38316105, year = {2024}, author = {Benvenuti, E and Ferriani, R and Gianella, P and Ruggiero, P and Cagnasso, F and Borrelli, A and Benvenuto, G and Bertoldi, L and Bottero, E}, title = {The fecal bacterial microbiota is not useful for discriminating between lymphoplasmacytic enteritis and low-grade intestinal T-cell lymphoma in cats nor for predicting therapeutic response.}, journal = {American journal of veterinary research}, volume = {}, number = {}, pages = {1-9}, doi = {10.2460/ajvr.23.11.0251}, pmid = {38316105}, issn = {1943-5681}, abstract = {OBJECTIVE: To evaluate the fecal bacterial microbiota at the time of diagnosis (T0) and after 1 month of therapy (T1) in cats diagnosed with lymphoplasmacytic enteritis (LPE) or cats with low-grade intestinal T-cell lymphoma (LGITL) and to compare these findings with those of healthy cats.

ANIMALS: 5 healthy cats, 13 cats with LPE, and 7 cats with LGITL were prospectively enrolled between June 2020 and June 2021.

METHODS: Fecal samples were collected at T0 and T1, and DNA was extracted for 16S ribosomal amplicon sequencing. Alpha diversity and beta diversity were computed. The taxonomic assignment was performed using sequences from the Silva v138 formatted reference database. Differential abundant taxa were selected in each taxonomic level, with the P value adjusted < .05, as the cut-off.

RESULTS: No significant differences in alpha and beta diversity were found either at T0 or T1 between healthy and diseased cats or between cats with LPE and LGITL. Beta-diversity analysis showed an increase in the Fusobacteriaceae family in cats with LGITL at T0, compared to cats with LPE. Regardless of histological diagnosis, several microbiota differences were found at T0 based on serum cobalamin levels.

CLINICAL RELEVANCE: Fecal samples were successfully used to characterize the bacteriome of the intestinal tract in cats by 16S rRNA gene sequencing. However, results highlighted that the metagenomic evaluation was not useful to discriminate between LPE and LGITL nor to predict the therapeutic response in this study population.}, } @article {pmid38317206, year = {2024}, author = {Wang, C and Yin, X and Ma, W and Zhao, L and Wu, X and Ma, N and Cao, Y and Zhang, Q and Ma, S and Xu, L and Wang, X}, title = {Clinical application of bronchoalveolar lavage fluid metagenomics next-generation sequencing in cancer patients with severe pneumonia.}, journal = {Respiratory research}, volume = {25}, number = {1}, pages = {68}, pmid = {38317206}, issn = {1465-993X}, support = {ZDXYS202203//Jiangsu Province Capability Improvement Project through Science, Technology and Education, Jiangsu Provincial Medical Key Laboratory/ ; 81972763//National Natural Science Foundation of China/ ; }, abstract = {OBJECTIVE: Metagenomic next-generation sequencing (mNGS), as an emerging technique for pathogen detection, has been widely used in clinic. However, reports on the application of mNGS in cancer patients with severe pneumonia remain limited. This study aims to evaluate the diagnostic performance of bronchoalveolar lavage fluid (BALF) mNGS in cancer patients complicated with severe pneumonia.

METHODS: A total of 62 cancer patients with severe pneumonia simultaneously received culture and mNGS of BALF were enrolled in this study. We systematically analyzed the diagnostic significance of BALF mNGS. Subsequently, optimization of anti-infective therapy based on the distribution of pathogens obtained from BALF mNGS was also assessed.

RESULTS: For bacteria and fungi, the positive detection rate of mNGS was significantly higher than culture method (91.94% versus 51.61%, P < 0.001), especially for poly-microbial infections (70.97% versus 12.90%, P < 0.001). Compared with the culture method, mNGS exhibited a diagnostic sensitivity of 100% and a specificity of 16.67%, with the positive predictive value (PPV) and negative predictive value (NPV) being 56.14% and 100%, respectively. The agreement rate between these two methods was 59.68%, whereas kappa consensus analysis indicated a poor concordance (kappa = 0.171). After receipt of BALF mNGS results, anti-infective treatment strategies in 39 out of 62 cases (62.90%) were optimized. Moreover, anti-tumor therapy was a high-risk factor for mixed infections (87.18% versus 65.22%, P = 0.04).

CONCLUSIONS: The present study showed that cancer patients with severe pneumonia, especially those received anti-tumor therapy, were more likely to have poly-microbial infections. BALF mNGS can provide a rapid and comprehensive pathogen distribution of pulmonary infection, making it a promising technique in clinical practice, especially for optimizing therapeutic strategies for cancer patients.}, } @article {pmid38316929, year = {2024}, author = {Ritz, NL and Draper, LA and Bastiaanssen, TFS and Turkington, CJR and Peterson, VL and van de Wouw, M and Vlckova, K and Fülling, C and Guzzetta, KE and Burokas, A and Harris, H and Dalmasso, M and Crispie, F and Cotter, PD and Shkoporov, AN and Moloney, GM and Dinan, TG and Hill, C and Cryan, JF}, title = {The gut virome is associated with stress-induced changes in behaviour and immune responses in mice.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {38316929}, issn = {2058-5276}, support = {12/RC/2273_P2//Science Foundation Ireland (SFI)/ ; }, abstract = {The microbiota-gut-brain axis has been shown to play an important role in the stress response, but previous work has focused primarily on the role of the bacteriome. The gut virome constitutes a major portion of the microbiome, with bacteriophages having the potential to remodel bacteriome structure and activity. Here we use a mouse model of chronic social stress, and employ 16S rRNA and whole metagenomic sequencing on faecal pellets to determine how the virome is modulated by and contributes to the effects of stress. We found that chronic stress led to behavioural, immune and bacteriome alterations in mice that were associated with changes in the bacteriophage class Caudoviricetes and unassigned viral taxa. To determine whether these changes were causally related to stress-associated behavioural or physiological outcomes, we conducted a faecal virome transplant from mice before stress and autochthonously transferred it to mice undergoing chronic social stress. The transfer of the faecal virome protected against stress-associated behaviour sequelae and restored stress-induced changes in select circulating immune cell populations, cytokine release, bacteriome alterations and gene expression in the amygdala. These data provide evidence that the virome plays a role in the modulation of the microbiota-gut-brain axis during stress, indicating that these viral populations should be considered when designing future microbiome-directed therapies.}, } @article {pmid38315959, year = {2024}, author = {Meldrum, OW and Donaldson, GC and Narayana, JK and Xaverius Ivan, F and Jaggi, TK and Mac Aogáin, M and Finney, LJ and Allinson, JP and Wedzicha, JA and Chotirmall, SH}, title = {Accelerated Lung Function Decline and Mucus-Microbe Evolution in Chronic Obstructive Pulmonary Disease.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1164/rccm.202306-1060OC}, pmid = {38315959}, issn = {1535-4970}, abstract = {RATIONALE: Progressive lung function loss is recognized in COPD; however, no study concurrently evaluates how accelerated lung function decline relates to mucus properties and the microbiome in COPD.

OBJECTIVE: Longitudinal assessment of mucus and microbiome changes accompanying accelerated lung function decline in COPD patients.

METHODS: Prospective, longitudinal assessment of the London COPD cohort exhibiting the greatest FEV1 decline (n=30; "accelerated decline"; 156 mL/year FEV1 loss) and with no FEV1 decline (n=28; "non-decline"; 49 mL/year FEV1 gain) over time. Lung microbiomes from "paired" sputum (total 116 specimens) were assessed by shotgun metagenomics and corresponding mucus profiles evaluated for biochemical and biophysical properties.

RESULTS: Biochemical and biophysical mucus properties are significantly altered in the accelerated decline group. Unsupervised principal component analysis showed clear separation, with mucus biochemistry associated with accelerated decline, while biophysical mucus characteristics contributed to inter-individual variability. When mucus and microbes are considered together, an accelerated decline mucus-microbiome association emerges, characterized by increased mucin (MUC5AC and MUC5B) concentration and the presence of Achromobacter and Klebsiella. As COPD progresses, mucus-microbiome shifts occur, initially characterized by low mucin concentration and transition from viscous to elastic dominance accompanied by the commensals Veillonella, Gemella, Rothia and Prevotella (GOLD A and B) before transition to increased mucus viscosity, mucins, and DNA concentration along with the emergence of pathogenic microorganisms including Haemophilus, Moraxella and Pseudomonas (GOLD E).

CONCLUSION: Mucus-microbiome associations evolve over time with accelerated lung function decline, symptom progression and exacerbations affording fresh therapeutic opportunities for early intervention.}, } @article {pmid38315946, year = {2024}, author = {Bai, X and Xiang, J and Deng, J and Ding, WH and Luan, X and Geng, Z}, title = {Clinical Reasoning: A 30-Year-Old Woman Presenting With Rapidly Progressive Dementia and Extreme Hypoglycorrhachia.}, journal = {Neurology}, volume = {102}, number = {5}, pages = {e209188}, doi = {10.1212/WNL.0000000000209188}, pmid = {38315946}, issn = {1526-632X}, abstract = {A 30-year-old woman presented with rapidly progressive dementia 1 month after the coronavirus disease 2019 infection. Repeated CSF analysis showed extreme hypoglycorrhachia, while cultures, metagenomic next-generation sequencing, and cytopathology testing of CSF were negative. Laboratory investigations for possible etiologies revealed elevated blood ammonia and cancer antigen 125. Brain MRI demonstrated bilateral symmetric diffuse cortical lesions with mild hyperintensity on T1-weighted image and postcontrast enhancement. A more thorough history and specific examinations subsequently indicated an underlying etiology. This case provides an approach for evaluating young patients with rapidly progressive dementia, extreme hypoglycorrhachia, and diffuse CNS lesions, highlighting the importance of considering a broad differential diagnosis.}, } @article {pmid38315309, year = {2024}, author = {Macharoen, P and Mhuantong, W and Wannawong, T and Leesutthiphonchai, W and Tanasupawat, S and Suwannarach, N and Kuncharoen, N}, title = {Bacterial diversity, community structure and function in association of potato scabby tubers during storage in northern Thailand.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {38315309}, issn = {1874-9356}, support = {N42A650203//National Research Council of Thailand/ ; }, abstract = {Potato scab is a common potato tuber disease that affects quality and cost in the marketplace, shortening storage, and increasing the chance for secondary infection. The tubers with disease severity of 1 to 4 are accepted and stored in potato storage for cheap selling in Thailand. However, there are few studies of the bacterial community of the scabby tuber during storage. Thus, we aim to elucidate the diversity, structure, and function of the bacterial community of 30-day storage potato scabby tubers stored in different temperatures using 16S amplicon metagenomic sequencing. Bacterial communities of storage potato scabby tubers (Spunta cultivar) collected from different storage temperatures, 4 °C (MEP1) and 6 °C (MEP2), were characterized using 16S rRNA amplicon metagenomic sequencing. The alpha-diversity abundance in the bacteriome of the scabby tubers stored at 6 °C was higher than in those stored at 4 °C. Actinobacteria (34.7%) was a dominant phylum in MEP1, while Proteobacteria (39.9%) was predominant in MEP2. The top 10 genera of both communities were Rhizobium group, Streptomyces, Pectobacterium, Ruminococcus, Cellulomonas, Promicromonospora, Prevotella, Enterobacter, Pedobacter, and Paenarthrobacter. Moreover, functional profile prediction of both communities reveals essential genes in the pathosystem: nos, bglA, and cebEFG-msiK for potato scab disease and phc and peh operons for rot disease. Our findings are the first study to explore details of the bacteriome of the accepted potato scabby tubers for selling during storage in Thailand and strongly indicate that although potatoes were stored at low temperatures, diseases still occur by secondary pathogens.}, } @article {pmid38315121, year = {2024}, author = {Han, K and Li, J and Yang, D and Zhuang, Q and Zeng, H and Rong, C and Yue, J and Li, N and Gu, C and Chen, L and Chen, C}, title = {Detecting horizontal gene transfer with metagenomics co-barcoding sequencing.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0360223}, doi = {10.1128/spectrum.03602-23}, pmid = {38315121}, issn = {2165-0497}, abstract = {Horizontal gene transfer (HGT) is the process through which genetic information is transferred between different genomes and that played a crucial role in bacterial evolution. HGT can enable bacteria to rapidly acquire antibiotic resistance and bacteria that have acquired resistance is spreading within the microbiome. Conventional methods of characterizing HGT patterns include short-read metagenomic sequencing (short-reads mNGS), long-read sequencing, and single-cell sequencing. These approaches present several limitations, such as short-read fragments, high amounts of input DNA, and sequencing costs, respectively. Here, we attempt to circumvent present limitations to detect HGT by developing a metagenomics co-barcode sequencing workflow (MECOS) and applying it to the human and mouse gut microbiomes. In addition to that, we have over 10-fold increased contig length compared to short-reads mNGS; we also obtained exceeding 30 million paired reads with co-barcode information. Applying the novel bioinformatic pipeline, we integrated this co-barcoding information and the context information from long reads, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Specifically, we detected approximately 3,000 HGT blocks in individual samples, encompassing ~6,000 genes and ~100 taxonomic groups, including loci conferring tetracycline resistance through ribosomal protection. MECOS provides a valuable tool for investigating HGT and advance our understanding on the evolution of natural microbial communities within hosts.IMPORTANCEIn this study, to better identify horizontal gene transfer (HGT) in individual samples, we introduce a new co-barcoding sequencing system called metagenomics co-barcoding sequencing (MECOS), which has three significant improvements: (i) long DNA fragment extraction, (ii) a special transposome insertion, (iii) hybridization of DNA to barcode beads, and (4) an integrated bioinformatic pipeline. Using our approach, we have over 10-fold increased contig length compared to short-reads mNGS, and observed over 50-fold HGT events after we corrected the potential wrong HGT events. Our results indicate the presence of approximately 3,000 HGT blocks, involving roughly 6,000 genes and 100 taxonomic groups in individual samples. Notably, these HGT events are predominantly enriched in genes that confer tetracycline resistance via ribosomal protection. MECOS is a useful tool for investigating HGT and the evolution of natural microbial communities within hosts, thereby advancing our understanding of microbial ecology and evolution.}, } @article {pmid38314824, year = {2024}, author = {Gebert, JT and Scribano, FJ and Engevik, KA and Hyser, JM}, title = {Live Calcium Imaging of Virus-Infected Human Intestinal Organoid Monolayers Using Genetically Encoded Calcium Indicators.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {203}, pages = {}, doi = {10.3791/66132}, pmid = {38314824}, issn = {1940-087X}, abstract = {Calcium signaling is an integral regulator of nearly every tissue. Within the intestinal epithelium, calcium is involved in the regulation of secretory activity, actin dynamics, inflammatory responses, stem cell proliferation, and many other uncharacterized cellular functions. As such, mapping calcium signaling dynamics within the intestinal epithelium can provide insight into homeostatic cellular processes and unveil unique responses to various stimuli. Human intestinal organoids (HIOs) are a high-throughput, human-derived model to study the intestinal epithelium and thus represent a useful system to investigate calcium dynamics. This paper describes a protocol to stably transduce HIOs with genetically encoded calcium indicators (GECIs), perform live fluorescence microscopy, and analyze imaging data to meaningfully characterize calcium signals. As a representative example, 3-dimensional HIOs were transduced with lentivirus to stably express GCaMP6s, a green fluorescent protein-based cytosolic GECI. The engineered HIOs were then dispersed into a single-cell suspension and seeded as monolayers. After differentiation, the HIO monolayers were infected with rotavirus and/or treated with drugs known to stimulate a calcium response. An epifluorescence microscope fitted with a temperature-controlled, humidified live-imaging chamber allowed for long-term imaging of infected or drug-treated monolayers. Following imaging, acquired images were analyzed using the freely available analysis software, ImageJ. Overall, this work establishes an adaptable pipeline for characterizing cellular signaling in HIOs.}, } @article {pmid38314433, year = {2024}, author = {Wu, Z and Guo, Y and Hayakawa, M and Yang, W and Lu, Y and Ma, J and Li, L and Li, C and Liu, Y and Niu, J}, title = {Artificial intelligence-driven microbiome data analysis for estimation of postmortem interval and crime location.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1334703}, doi = {10.3389/fmicb.2024.1334703}, pmid = {38314433}, issn = {1664-302X}, abstract = {Microbial communities, demonstrating dynamic changes in cadavers and the surroundings, provide invaluable insights for forensic investigations. Conventional methodologies for microbiome sequencing data analysis face obstacles due to subjectivity and inefficiency. Artificial Intelligence (AI) presents an efficient and accurate tool, with the ability to autonomously process and analyze high-throughput data, and assimilate multi-omics data, encompassing metagenomics, transcriptomics, and proteomics. This facilitates accurate and efficient estimation of the postmortem interval (PMI), detection of crime location, and elucidation of microbial functionalities. This review presents an overview of microorganisms from cadavers and crime scenes, emphasizes the importance of microbiome, and summarizes the application of AI in high-throughput microbiome data processing in forensic microbiology.}, } @article {pmid38313584, year = {2023}, author = {Wu, J and Singleton, SS and Bhuiyan, U and Krammer, L and Mazumder, R}, title = {Multi-omics approaches to studying gastrointestinal microbiome in the context of precision medicine and machine learning.}, journal = {Frontiers in molecular biosciences}, volume = {10}, number = {}, pages = {1337373}, doi = {10.3389/fmolb.2023.1337373}, pmid = {38313584}, issn = {2296-889X}, abstract = {The human gastrointestinal (gut) microbiome plays a critical role in maintaining host health and has been increasingly recognized as an important factor in precision medicine. High-throughput sequencing technologies have revolutionized -omics data generation, facilitating the characterization of the human gut microbiome with exceptional resolution. The analysis of various -omics data, including metatranscriptomics, metagenomics, glycomics, and metabolomics, holds potential for personalized therapies by revealing information about functional genes, microbial composition, glycans, and metabolites. This multi-omics approach has not only provided insights into the role of the gut microbiome in various diseases but has also facilitated the identification of microbial biomarkers for diagnosis, prognosis, and treatment. Machine learning algorithms have emerged as powerful tools for extracting meaningful insights from complex datasets, and more recently have been applied to metagenomics data via efficiently identifying microbial signatures, predicting disease states, and determining potential therapeutic targets. Despite these rapid advancements, several challenges remain, such as key knowledge gaps, algorithm selection, and bioinformatics software parametrization. In this mini-review, our primary focus is metagenomics, while recognizing that other -omics can enhance our understanding of the functional diversity of organisms and how they interact with the host. We aim to explore the current intersection of multi-omics, precision medicine, and machine learning in advancing our understanding of the gut microbiome. A multidisciplinary approach holds promise for improving patient outcomes in the era of precision medicine, as we unravel the intricate interactions between the microbiome and human health.}, } @article {pmid38312103, year = {2024}, author = {Han, B and Tang, D and Lv, X and Fan, J and Li, S and Zhu, H and Zhang, J and Xu, S and Xu, X and Huang, Z and Huang, Z and Lin, G and Zhan, L and Lv, X}, title = {Integrated multi-omics reveal gut microbiota-mediated bile acid metabolism alteration regulating immunotherapy responses to anti-α4β7-integrin in Crohn's disease.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2310894}, doi = {10.1080/19490976.2024.2310894}, pmid = {38312103}, issn = {1949-0984}, abstract = {Gut microbiota and related metabolites are both crucial factors that significantly influence how individuals with Crohn's disease respond to immunotherapy. However, little is known about the interplay among gut microbiota, metabolites, Crohn's disease, and the response to anti-α4β7-integrin in current studies. Our research utilized 2,4,6-trinitrobenzene sulfonic acid to induce colitis based on the humanized immune system mouse model and employed a combination of whole-genome shotgun metagenomics and non-targeted metabolomics to investigate immunotherapy responses. Additionally, clinical cases with Crohn's disease initiating anti-α4β7-integrin therapy were evaluated comprehensively. Particularly, 16S-rDNA gene high-throughput sequencing and targeted bile acid metabolomics were conducted at weeks 0, 14, and 54. We found that anti-α4β7-integrin therapy has shown significant potential for mitigating disease phenotypes in remission-achieving colitis mice. Microbial profiles demonstrated that not only microbial composition but also microbially encoded metabolic pathways could predict immunotherapy responses. Metabonomic signatures revealed that bile acid metabolism alteration, especially elevated secondary bile acids, was a determinant of immunotherapy responses. Especially, the remission mice significantly enriched the proportion of the beneficial Lactobacillus and Clostridium genera, which were correlated with increased gastrointestinal levels of BAs involving lithocholic acid and deoxycholic acid. Moreover, most of the omics features observed in colitis mice were replicated in clinical cases. Notably, anti-α4β7 integrin provided sustained therapeutic benefits in clinical remitters during follow-up, and long-lasting remission was linked to persistent changes in the microbial-related bile acids. In conclusion, gut microbiota-mediated bile acid metabolism alteration could play a crucial role in regulating immunotherapy responses to anti-α4β7-integrin in Crohn's disease. Therefore, the identification of prognostic microbial signals facilitates the advancement of targeted probiotics that activate anti-inflammatory bile acid metabolic pathways, thereby improving immunotherapy responses. The integrated multi-omics established in our research provide valuable insights into potential mechanisms that impact treatment responses in complex diseases.}, } @article {pmid38311076, year = {2024}, author = {Jenkins, JA and Draugelis-Dale, RO and Hoffpauir, NM and Baudoin, BA and Matkin, C and Driver, L and Hodges, S and Brown, BL}, title = {Flow cytometric assessments of metabolic activity in bacterial assemblages provide insight into ecosystem condition along the Buffalo National River, Arkansas.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170462}, doi = {10.1016/j.scitotenv.2024.170462}, pmid = {38311076}, issn = {1879-1026}, abstract = {The Buffalo National River (BNR) on karst terrain in Arkansas is considered an extraordinary water resource. Water collected in Spring 2017 along BNR were metagenomically analyzed using 16S rDNA, and for 17 months (5/2017-11/2018), bacterial responses were measured in relation to nutrients sampled along a stretch of BNR near a concentrated animal feed operation (CAFO) on Big Creek. Because cell count and esterase activity can increase proportionally with organic enrichment, they were hypothesized to be elevated near the CAFO. Counts (colony forming units; CFUs) were different among sites for 73 % of the months; Big Creek generated highest CFUs 27 % of the time, with the close downstream site at 13.3 %. Esterase activity was different among sites 94 % of the time, with Big Creek exhibiting lowest activity 71 % of the time. Over the months, activity was similar across sites at ~70 % active, except at Big Creek (56 %). The α-diversity of BNR microbial consortia near a wastewater treatment plant (WWTP) and the CAFO was related to distance from the WWTP and CAFO. The inverse relationship between high CFUs and low esterase activity at Big Creek (r = -0.71) actuated in vitro exposures of bacteria to organic wastewater contaminants (OWC) previously identified in the watershed. Exponential-phase Escherichia coli (stock strain), Streptococcus suis (avirulent, from swine), and S. dysgalactiae (virulent, from silver carp, Hypophthalmichthys molitrix) were incubated with atrazine, pharmaceuticals (17 α-ethynylestradiol and trenbolone), and antimicrobials (tylosin and butylparaben). Bacteria were differentially responsive. Activity varied with exposure time and OWC type but not concentration; atrazine decreased it most. Taken together - the metagenomic taxonomic similarities along BNR, slightly higher bacterial growth and lower bacterial esterase at the CAFO, and the lab exposures of bacterial strains showing that OWC altered metabolism - results indicated that bioactive OWC entering the watershed can strongly influence microbial processes in the aquatic ecosystem.}, } @article {pmid38310979, year = {2024}, author = {Chen, Z and Shi, Z and Zhang, Y and Shi, Y and Sun, M and Cui, Y and Zhang, S and Luo, G}, title = {Metagenomic analysis towards understanding the effects of ammonia on chain elongation process for medium chain fatty acids production.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {130413}, doi = {10.1016/j.biortech.2024.130413}, pmid = {38310979}, issn = {1873-2976}, abstract = {The production of medium chain fatty acids (MCFAs) through chain elongation (CE) from organic wastes/wastewater has attracted much attention, while the effects of a common inhibitor-ammonia has not been elucidated. The mechanism of ammonia affecting CE was studied by metagenomic. The lag phase duration of caproate production was increased, and the maximum caproate production rate was decreased by 43.4 % at 4 g-N/L, as compared to 0 g-N/L. And hydrochar (HC) alleviated the inhibition of ammonia at 4 g-N/L. Metagenomic analysis indicated that ammonia induced UBA4085 sp.FDU78 as the dominant microorganism, and metabolic reconstruction revealed its potential CE ability. Furthermore, ammonia inhibited the reverse β oxidation pathway and Acetyl-CoA production pathway. The tolerance of UBA4085 sp.FDU78 to ammonia was associated with the uptake of inorganic ions, energy conservation, and synthesis of osmoprotectants. The present study provided a deep-insight on the ammonia tolerance mechanism on the CE process.}, } @article {pmid38310777, year = {2024}, author = {Domingues Galli, B and Trossolo, E and Carafa, I and Squara, S and Caratti, A and Filannino, P and Cordero, C and Gobbetti, M and Di Cagno, R}, title = {Effectiveness of modified atmosphere and vacuum packaging in preserving the volatilome of Stelvio PDO cheese over time.}, journal = {Food chemistry}, volume = {444}, number = {}, pages = {138544}, doi = {10.1016/j.foodchem.2024.138544}, pmid = {38310777}, issn = {1873-7072}, abstract = {We aimed to assay the effectiveness of vacuum or modified atmosphere packaging in preserving the organoleptic characteristics of already ripened slices of Stelvio Protected Designation of Origin cheese during 3 months of storage. A multi-omics panel, including metagenomic and metabolomic analyses, was implemented together with physicochemical and sensory analyses. Among the 177 volatiles identified, 30 out of the 50 potent odorants were found to be prevalent, regardless of packaging. Isovaleric acid showed the highest relative intensity in all samples. Caproic and caprylic acids always increased during storage, while metabolites such as dodecane and 2,3-butanediol always decreased. Slow proteolysis occurred during storage, but did not differentiate cheese samples. The type of packaging differentiated the microbiota and volatile profile, with modified atmosphere packaging keeping the volatilome more stable. Out of the 50 potent odorants, 9 were relevant to sample discrimination, with 8-nonen-2-one, 2-nonanone, and caproic acid being more abundant in stored samples.}, } @article {pmid38310316, year = {2024}, author = {Patangia, DV and Grimaud, G and O'Shea, CA and Ryan, CA and Dempsey, E and Stanton, C and Ross, RP}, title = {Early life exposure of infants to benzylpenicillin and gentamicin is associated with a persistent amplification of the gut resistome.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {19}, pmid = {38310316}, issn = {2049-2618}, support = {12/RC/2273_P2 and 19/SP/6989/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273_P2 and 19/SP/6989/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273_P2 and 19/SP/6989/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273_P2 and 19/SP/6989/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273_P2 and 19/SP/6989/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273_P2 and 19/SP/6989/SFI_/Science Foundation Ireland/Ireland ; 12/RC/2273_P2 and 19/SP/6989/SFI_/Science Foundation Ireland/Ireland ; 101054719/ERC_/European Research Council/International ; }, abstract = {BACKGROUND: Infant gut microbiota is highly malleable, but the long-term longitudinal impact of antibiotic exposure in early life, together with the mode of delivery on infant gut microbiota and resistome, is not extensively studied.

METHODS: Two hundred and eight samples from 45 infants collected from birth until 2 years of age over five time points (week 1, 4, 8, 24, year 2) were analysed. Based on shotgun metagenomics, the gut microbial composition and resistome profile were compared in the early life of infants divided into three groups: vaginal delivery/no-antibiotic in the first 4 days of life, C-section/no-antibiotic in the first 4 days of life, and C-section/antibiotic exposed in first 4 days of life. Gentamycin and benzylpenicillin were the most commonly administered antibiotics during this cohort's first week of life.

RESULTS: Newborn gut microbial composition differed in all three groups, with higher diversity and stable composition seen at 2 years of age, compared to week 1. An increase in microbial diversity from week 1 to week 4 only in the C-section/antibiotic-exposed group reflects the effect of antibiotic use in the first 4 days of life, with a gradual increase thereafter. Overall, a relative abundance of Actinobacteria and Bacteroides was significantly higher in vaginal delivery/no-antibiotic while Proteobacteria was higher in C-section/antibiotic-exposed infants. Strains from species belonging to Bifidobacterium and Bacteroidetes were generally persistent colonisers, with Bifidobacterium breve and Bifidobacterium bifidum species being the major persistent colonisers in all three groups. Bacteroides persistence was dominant in the vaginal delivery/no-antibiotic group, with species Bacteroides ovatus and Phocaeicola vulgatus found to be persistent colonisers in the no-antibiotic groups. Most strains carrying antibiotic-resistance genes belonged to phyla Proteobacteria and Firmicutes, with the C-section/antibiotic-exposed group presenting a higher frequency of antibiotic-resistance genes (ARGs).

CONCLUSION: These data show that antibiotic exposure has an immediate and persistent effect on the gut microbiome in early life. As such, the two antibiotics used in the study selected for strains (mainly Proteobacteria) which were multiple drug-resistant (MDR), presumably a reflection of their evolutionary lineage of historical exposures-leading to what can be an extensive and diverse resistome. Video Abstract.}, } @article {pmid38310089, year = {2024}, author = {Mercado-Evans, V and Mejia, ME and Zulk, JJ and Ottinger, S and Hameed, ZA and Serchejian, C and Marunde, MG and Robertson, CM and Ballard, MB and Ruano, SH and Korotkova, N and Flores, AR and Pennington, KA and Patras, KA}, title = {Gestational diabetes augments group B Streptococcus infection by disrupting maternal immunity and the vaginal microbiota.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {1035}, pmid = {38310089}, issn = {2041-1723}, support = {DK128053//U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)/ ; AI157981//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; AI173448//U.S. Department of Health & Human Services | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; NGP10103//Burroughs Wellcome Fund (BWF)/ ; }, abstract = {Group B Streptococcus (GBS) is a pervasive perinatal pathogen, yet factors driving GBS dissemination in utero are poorly defined. Gestational diabetes mellitus (GDM), a complication marked by dysregulated immunity and maternal microbial dysbiosis, increases risk for GBS perinatal disease. Using a murine GDM model of GBS colonization and perinatal transmission, we find that GDM mice display greater GBS in utero dissemination and subsequently worse neonatal outcomes. Dual-RNA sequencing reveals differential GBS adaptation to the GDM reproductive tract, including a putative glycosyltransferase (yfhO), and altered host responses. GDM immune disruptions include reduced uterine natural killer cell activation, impaired recruitment to placentae, and altered maternofetal cytokines. Lastly, we observe distinct vaginal microbial taxa associated with GDM status and GBS invasive disease status. Here, we show a model of GBS dissemination in GDM hosts that recapitulates several clinical aspects and identifies multiple host and bacterial drivers of GBS perinatal disease.}, } @article {pmid38309918, year = {2024}, author = {Cardin, M and Mounier, J and Coton, E and Cardazzo, B and Perini, M and Bertoldi, D and Pianezze, S and Segato, S and Di Camillo, B and Cappellato, M and Coton, M and Carraro, L and Currò, S and Lucchini, R and Mohammadpour, H and Novelli, E}, title = {Discriminative power of DNA-based, volatilome, near infrared spectroscopy, elements and stable isotopes methods for the origin authentication of typical Italian mountain cheese using sPLS-DA modeling.}, journal = {Food research international (Ottawa, Ont.)}, volume = {178}, number = {}, pages = {113975}, doi = {10.1016/j.foodres.2024.113975}, pmid = {38309918}, issn = {1873-7145}, abstract = {Origin authentication methods are pivotal in counteracting frauds and provide evidence for certification systems. For these reasons, geographical origin authentication methods are used to ensure product origin. This study focused on the origin authentication (i.e. at the producer level) of a typical mountain cheese origin using various approaches, including shotgun metagenomics, volatilome, near infrared spectroscopy, stable isotopes, and elemental analyses. DNA-based analysis revealed that viral communities achieved a higher classification accuracy rate (97.4 ± 2.6 %) than bacterial communities (96.1 ± 4.0 %). Non-starter lactic acid bacteria and phages specific to each origin were identified. Volatile organic compounds exhibited potential clusters according to cheese origin, with a classification accuracy rate of 90.0 ± 11.1 %. Near-infrared spectroscopy showed lower discriminative power for cheese authentication, yielding only a 76.0 ± 31.6 % classification accuracy rate. Model performances were influenced by specific regions of the infrared spectrum, possibly associated with fat content, lipid profile and protein characteristics. Furthermore, we analyzed the elemental composition of mountain Caciotta cheese and identified significant differences in elements related to dairy equipment, macronutrients, and rare earth elements among different origins. The combination of elements and isotopes showed a decrease in authentication performance (97.0 ± 3.1 %) compared to the original element models, which were found to achieve the best classification accuracy rate (99.0 ± 0.01 %). Overall, our findings emphasize the potential of multi-omics techniques in cheese origin authentication and highlight the complexity of factors influencing cheese composition and hence typicity.}, } @article {pmid38309691, year = {2024}, author = {Yuan, Q and Liu, W and Hao, W and Chen, Y and Xiao, Y and Li, H and Shui, M and Wu, DT and Wang, S}, title = {Glycosidic linkages of fungus polysaccharides influence the anti-inflammatory activity in mice.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2024.01.037}, pmid = {38309691}, issn = {2090-1224}, abstract = {INTRODUCTION: Over decades, the source-function relationships of bioactive polysaccharides have been progressively investigated, however, it is still unclear how a defined structure may conduce to the bioactivities of polysaccharides.

OBJECTIVES: To explore the structure-function relationship of fungus polysaccharides, we employed a dextran sulfate sodium (DSS)-induced colitis mouse model to compare the anti-inflammatory activity of two fungus polysaccharides from Dictyophora indusiata (DIP) and Tremella fuciformis (TFP), which exhibit distinct glycosidic linkages.

METHODS: The structures of DIP and TFP were characterized through molecular weight detection, molecular morphology analysis, methylation analysis, and NMR analysis. Subsequently, we employed a DSS-induced colitis model to assess the anti-inflammatory efficacy of DIP and TFP. The colitis symptoms, histological morphology, intestinal inflammatory cytokines, and the composition and function of gut microbiota before and after polysaccharides treatment in colitis mice were also investigated.

RESULTS: DIP, l,3-β-D-glucan with 1,4-β and 1,6-β-D-Glcp as branched chains, exhibited superior therapeutic effect than that of TFP consisted of a linear 1,3-α-D-mannose backbone with D-xylose and L-fucose in the side chains. Both DIP and TFP relieved DSS-induced colitis in a gut microbiota dependent manner. Furthermore, metagenomics showed that DIP and TFP could partially reverse the bacterial function in colitis mice. Glycoside Hydrolase 1 (GH1) and GH3 were shown to cleave the glucose linkages in DIP, while GH92 and GH29 were likely active on the α-1,3-linked mannose linkages and the glycosidic bonds of L-fucose residues in TFP.

CONCLUSION: Our findings highlight the pivotal role of glycosidic linkages in anti-inflammatory activities of fungus polysaccharides and would promote the design and discovery of polysaccharides with designated activity to be used as functional foods and/or therapeutics.}, } @article {pmid38309618, year = {2024}, author = {Bouzid, F and Gtif, I and Charfeddine, S and Abid, L and Kharrat, N}, title = {Polyphasic molecular approach to the characterization of methanogens in the saliva of Tunisian adults.}, journal = {Anaerobe}, volume = {}, number = {}, pages = {102820}, doi = {10.1016/j.anaerobe.2024.102820}, pmid = {38309618}, issn = {1095-8274}, abstract = {BACKGROUND: Methanogenic archaea are a minor component of human oral microbiota. Due to their relatively low abundance, the detection of these neglected microorganisms is challenging.

OBJECTIVE: This study concerns the presence of methanogens in salivary samples collected from Tunisian adults to evaluate their prevalence and burden using a polyphasic molecular approach.

METHODS: A total of 43 saliva samples were included. Metagenomic and standard 16S rRNA sequencing were performed as an initial screening to detect the presence of methanogens in the oral microbiota of Tunisian adults. Further investigations were performed using specific quantitative real-time PCR targeting Methanobrevibacter oralis and Methanobrevibacter smithii.

RESULTS: Methanobrevibacter was detected in 5/43 (11.62 %) saliva samples after metagenomic 16S rRNA data analysis. The presence of M. oralis was confirmed in 6/43 samples by standard 16S rRNA sequencing. Using real-time PCR, methanogens were detected in 35/43 (81.39 %) samples, including 62.79 % positive for M. oralis and 76.74 % positive for M. smithii. These findings reflect the high prevalence of both methanogens, revealed by the high sensitivity of the real-time PCR approach. Interestingly, we also noted a significant statistical association between the detection of M. smithii and poor adherence to a Mediterranean diet, indicating the impact of diet on M. smithii prevalence.

CONCLUSION: Our study showed the presence of methanogens in the oral microbiota of Tunisian adults with an unprecedented relatively high prevalence. Choice of methodology is also central to picturing the real prevalence and diversity of such minor taxa in the oral microbiota.}, } @article {pmid38309356, year = {2024}, author = {Cui, X and Yuan, J and Yang, X and Wei, C and Bi, Y and Sun, Q and Meng, J and Han, X}, title = {Biochar application alters soil metabolites and nitrogen cycle-related microorganisms in a soybean continuous cropping system.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170522}, doi = {10.1016/j.scitotenv.2024.170522}, pmid = {38309356}, issn = {1879-1026}, abstract = {Biochar application is a promising practice to enhance soil fertility. However, it is unclear how field-aged biochar affects the soil metabolites and microbial communities in soybean fields. Here, the rhizosphere soil performance after amending with biochar addition rates at 0 (CK), 20 (B20), 40 (B40), and 60 t ha[-1] (B60) was examined via a five-year in-situ field experiment based on a soybean continuous cropping system. Untargeted metabolomics and metagenomics analysis techniques were applied to study the regulatory mechanism of biochar on soybean growth from metabolomics and N cycle microbiology perspectives. We found that the contents of soil total N (TN), available N (Ava N), NH4[+]-N, and NO3[-]-N were significantly increased with biochar addition amounts by 20.0-65.7 %, 3.6-10.7 %, 29.5-57.1 %, and 24.4-46.7 %, respectively. The B20, B40, and B60 triggered 259 (236 were up-regulated and 23 were down-regulated), 236 (220 were up-regulated and 16 were down-regulated), and 299 (264 were up-regulated and 35 were down-regulated) differential metabolites, respectively. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis and topology analysis demonstrated that differential metabolites were highly enriched in seven metabolic pathways such as Oxidative phosphorylation and Benzoxazinoid biosynthesis. Moreover, ten differential metabolites were up-regulated in all three treatments with biochar. Biochar treatments decreased the Nitrospirae abundance in soybean rhizosphere soil while increasing Bradyrhizobium abundance significantly in B60. Mantel test revealed that as the biochar addition rate grows, the correlation between Nitrospirae and soil properties other than NO3[-]-N became stronger. In conclusion, the co-application of biochar with fertilizers is a feasible and effective way to improve soil N supply, even though biochar has undergone field aging. This work offers new insights into the variations in soil metabolites and microbial communities associated with N metabolism processes under biochar addition in soybean continuous cropping soils.}, } @article {pmid38309340, year = {2024}, author = {Yu, K and Song, Y and Wang, N and Yu, X and Sun, T and Yu, H and Ruan, Z and Qiu, Y}, title = {Exposure of Danio rerio to environmental sulfamethoxazole may contribute to neurobehavioral abnormalities via gut microbiome disturbance.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170546}, doi = {10.1016/j.scitotenv.2024.170546}, pmid = {38309340}, issn = {1879-1026}, abstract = {The neurotoxic effects and mechanisms of low-dose and long-term sulfamethoxazole (SMZ) exposure remain unknown. This study exposed zebrafish to environmental SMZ concentrations and observed behavioral outcomes. SMZ exposure increased hyperactivity and altered the transcript levels of 17 genes associated with neurological function. It impaired intestinal function by reducing the number of intestinal goblet cells and lipid content. Metabolomic results indicated that the contents of several lipids and amino acids in the gut were altered, which might affect the expression levels of neurological function-related genes. Metagenomic results demonstrated that SMZ exposure substantially altered the composition of the gut microbiome. Zebrafish receiving a transplanted fecal microbiome from the SMZ group were also found to exhibit abnormal behavior, suggesting that the gut microbiome is an important target for SMZ exposure-induced neurobehavioral abnormalities. Multi-omics correlation analysis revealed that gut micrometabolic function was related to differential gut metabolite levels, which may affect neurological function through the gut-brain-axis. Reduced abundance of Lefsonia and Microbacterium was strongly correlated with intestinal metabolic function and may be the key bacterial genera in neurobehavioral changes. This study confirms for the first time that SMZ-induced neurotoxicity in zebrafish is closely mediated by alterations in the gut microbiome.}, } @article {pmid38309231, year = {2024}, author = {Xu, J and Dong, Y}, title = {Analysis of the gut microbiome associated to PVC biodegradation in yellow mealworms.}, journal = {Ecotoxicology and environmental safety}, volume = {272}, number = {}, pages = {116046}, doi = {10.1016/j.ecoenv.2024.116046}, pmid = {38309231}, issn = {1090-2414}, abstract = {The potential of invertebrates in the biodegradation of plastic polymers such as polyvinyl chloride (PVC) is receiving increasing attention. The present study is aimed to identify the gut microbiome involved in this degradation in yellow mealworms, i.e., the larvae of Tenebrio molitor Linnaeus. The egested PVC polymer experienced a dramatic reduction in both number average molecular weight (Mn) and weight average molecular weight (Mw) of 99.3% and 99.6%, respectively, whereas FTIR analysis revealed chemical alterations. Mass spectrometry analysis identified two potential degradation products: phthalic acid, di(2-propylpentyl) ester and 2-Propenoic acid, tridecyl ester. Further, we used metagenomic sequencing to elucidate the response of the gut microbiome when transitioning from bran to PVC as a food source, identifying four microorganisms actively involved in PVC degradation. Additionally, metagenomic functional analysis of the gut microbiome identified 111 key gene modules that were significantly enriched. In summary, our findings suggest that yellow mealworms adapt to PVC degradation by modifying their gut microbiome both structurally and functionally.}, } @article {pmid38309072, year = {2024}, author = {Hu, X and Wang, H and Ji, B and Wang, B and Guo, W and Chen, R and Jiang, C and Chen, Y and Zhou, D and Zhang, Q}, title = {Metagenomic insights into the mechanism for the rapid enrichment and high stability of Candidatus Brocadia facilitated by Fe(Ⅲ).}, journal = {Water research}, volume = {252}, number = {}, pages = {121224}, doi = {10.1016/j.watres.2024.121224}, pmid = {38309072}, issn = {1879-2448}, abstract = {The rapid enrichment of anammox bacteria and its fragile resistance to adverse environment are the critical problems facing of anammox processes. As an abundant component in anammox bacteria, iron has been proved to promote the activity and growth of anammox bacteria in the mature anammox systems, but the functional and metabolic profiles in Fe(III) enhanced emerging anammox systems have not been evaluated. Results indicated that the relative abundance of functional genes involved in oxidative phosphorylation, nitrogen metabolism, cofactors synthesis, and extracellular polymers synthesis pathways was significantly promoted in the system added with 5 mg/L Fe(III) (R5). These enhanced pathways were crucial to energy generation, nitrogen removal, cell activity and proliferation, and microbial self-defense, thereby accelerating the enrichment of anammox bacteria Ca. Brocadia and facilitating their resistance to adverse environments. Microbial community analysis showed that the proportion of Ca. Brocadia in R5 also increased to 64.42 %. Hence, R5 could adapt rapidly to the increased nitrogen loading rate and increase the nitrogen removal rate by 108 % compared to the system without Fe(III) addition. However, the addition of 10 and 20 mg/L Fe(III) showed inhibitory effects on the growth and activity of anammox bacteria, which exhibited the lower relative abundance of Ca. Brocadia and unstable or even collapsed nitrogen removal performance. This study not only clarified the concentration range of Fe(III) that promoted and inhibited the enrichment of anammox bacteria, but also deepened our understanding of the functional and metabolic mechanisms underlying enhanced enrichment of anammox bacteria by Fe(III), providing a potential strategy to hasten the start-up of anammox from conventional activated sludge.}, } @article {pmid38308006, year = {2024}, author = {Villiger, L and Joung, J and Koblan, L and Weissman, J and Abudayyeh, OO and Gootenberg, JS}, title = {CRISPR technologies for genome, epigenome and transcriptome editing.}, journal = {Nature reviews. Molecular cell biology}, volume = {}, number = {}, pages = {}, pmid = {38308006}, issn = {1471-0080}, abstract = {Our ability to edit genomes lags behind our capacity to sequence them, but the growing understanding of CRISPR biology and its application to genome, epigenome and transcriptome engineering is narrowing this gap. In this Review, we discuss recent developments of various CRISPR-based systems that can transiently or permanently modify the genome and the transcriptome. The discovery of further CRISPR enzymes and systems through functional metagenomics has meaningfully broadened the applicability of CRISPR-based editing. Engineered Cas variants offer diverse capabilities such as base editing, prime editing, gene insertion and gene regulation, thereby providing a panoply of tools for the scientific community. We highlight the strengths and weaknesses of current CRISPR tools, considering their efficiency, precision, specificity, reliance on cellular DNA repair mechanisms and their applications in both fundamental biology and therapeutics. Finally, we discuss ongoing clinical trials that illustrate the potential impact of CRISPR systems on human health.}, } @article {pmid38307921, year = {2024}, author = {Ho, SX and Law, JH and Png, CW and Alberts, R and Zhang, Y and Chu, JJH and Tan, KK}, title = {Alterations in colorectal cancer virome and its persistence after surgery.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2819}, pmid = {38307921}, issn = {2045-2322}, support = {NUHSRO/2020/142/RO5+6/Seed-Sep/02//National University Health System/ ; }, abstract = {Viruses are a key component of the colon microbiome, but the relationship between virome and colorectal cancer (CRC) remains poorly understood. We seek to identify alterations in the viral community that is characteristic of CRC and examine if they persist after surgery. Forty-nine fecal samples from 25 non-cancer (NC) individuals and 12 CRC patients, before and 6-months after surgery, were collected for metagenomic analysis. The fecal virome of CRC patients demonstrated an increased network connectivity as compared to NC individuals. Co-exclusion of influential viruses to bacterial species associated with healthy gut status was observed in CRC, suggesting an altered virome induced a change in the healthy gut bacteriome. Network analysis revealed lower connectivity within the virome and trans-kingdom interactions in NC. After surgery, the number of strong correlations decreased for trans-kingdom and within the bacteria and virome networks, indicating lower connectivity within the microbiome. Some co-occurrence patterns between dominant viruses and bacteria were also lost after surgery, suggesting a possible return to the healthy state of gut microbiome. Microbial signatures characteristic of CRC include an altered virome besides an altered bacterial composition. Elevated viral correlations and network connectivity were observed in CRC patients relative to healthy individuals, alongside distinct changes in the cross-kingdom correlation network unique to CRC patients. Some patterns of dysbiosis persist after surgery. Future studies should seek to verify if dysbiosis truly persists after surgery in a larger sample size with microbiome data collected at various time points after surgery to explore if there is field-change in the remaining colon, as well as to examine if persistent dysbiosis correlates with patient outcomes.}, } @article {pmid38307768, year = {2024}, author = {Thenmozhi Kulasekaran, N and Sankara Subramanian, SH and Thilakam, ML and Gopal, D and Lee, JK and Marimuthu, J}, title = {Functional analysis of a putative type III polyketide synthase from deep-sea sediment metagenome.}, journal = {Journal of bioscience and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jbiosc.2023.12.019}, pmid = {38307768}, issn = {1347-4421}, abstract = {Type III polyketide synthases (type III PKSs) are single homodimeric enzymes that produce diverse products such as phloroglucinol, pyrones, resorcinols and chalcones which are biotechnologically important molecules. In an attempt to identify new type III PKS from extreme environments, the deep-sea sediment metagenome from Bay of Bengal was screened for type III PKS genes. BLASTX analyses of Nanopore sequence derived metagenome with the in-house created PKS database revealed a full length type III PKS from a 5 kb fragment. The annotated full length type III PKS, S9PKS showed 25-30 % sequence identity towards previously characterized enzymes. To functionally characterize the gene, it was synthesized, cloned into pET28a and pColdI vectors under T7 and csp promoters, respectively, and expressed in Escherichia coli Rosetta(DE3) pLysS. The optimized PKS (OptiPKS) was expressed as inclusion bodies under both promoters. The inclusion bodies were successfully solubilised using low concentration of urea, refolded and purified using Ni-NTA Agarose resin. The purified OptiPKS was tested for functionality using fatty acyl-CoA substrates at various temperatures. High performance liquid chromatography (HPLC) analyses revealed that OptiPKS produced tri and tetraketide pyrones using C4 to C10 acyl-CoA starter substrates. Further characterization and mutation of the enzyme would reveal its functional significance. Thus, the study could be a lead for the annotation and functional characterization of putative type III PKS from environmental metagenome data.}, } @article {pmid38307363, year = {2024}, author = {Intirach, J and Lv, X and Sutthanont, N and Cai, B and Champakaew, D and Chen, T and Han, Q and Lv, Z}, title = {Molecular and Next-Generation Sequencing Analysis of Tick-Borne Pathogens of Rhipicephalus Ticks (Acari: Ixodidae) in cattle and dogs.}, journal = {Acta tropica}, volume = {}, number = {}, pages = {107138}, doi = {10.1016/j.actatropica.2024.107138}, pmid = {38307363}, issn = {1873-6254}, abstract = {Ticks are small and adaptable arachnid ectoparasites and global carriers of various pathogens that threaten both human and animal health. They are present in many parts of China. A total of 858 ticks were collected from various regions and hosts, then subjected to species identification based on morphological and molecular characteristics, as described in the authors' previous study. Eighty-three individual tick samples were selected for screening pathogens based on metagenomic next-generation sequencing (mNGS) and polymerase chain reaction (PCR) assays. The genomic DNA of tick species was extracted, and amplification of the bacterial 16S rRNA gene was carried out from DNA of individual ticks using V3-V4 hypervariable regions, before subjecting to metagenomic analysis. Each tick underwent specific PCR tests for identifying the bacterial species present, including Anaplasma, Ehrlichia, Coxiella, and Rickettsia, and also protozoans such as Babesia, Theileria, and Hepatozoon. Illumina NovaSeq sequencing results revealed that the dominant phylum and family in Rhipicephalus spp. were Bacteroidota and Muribaculaceae, respectively. Alpha diversity patterns varied depending on tick sex (R. linnaei only), species and location, but not on host. Furthermore, bacterial pathogens, including A. marginale (58%, 29/50), A. platys (6%, 3/50), E. minasensis (2%, 1/50), Ehrlichia sp. (10%, 5/50), T. sinensis (24%, 12/50), T. orientalis (54%, 27/50) and Coxiella-like bacteria (CLB) (80%, 40/50) were detected in R. microplus, while E. canis (33.33%, 10/30), H. canis (20%, 6/30) and CLB (100%, 30/30) were detected in R. linnaei. Also, Anaplasma sp. (33.33%, 1/3), A. marginale (33.33%, 1/3), R. felis (33.33%, 1/3) and CLB (100%, 3/3) were detected in R. haemaphysaloides. Dual and triple co-infections involving pathogens or CLB were detected in 84.00% of R. microplus, 66.66% of R. haemaphysaloides, and 33.00% of R. linnaei. The report on microbial communities and pathogens, which found from Rhipicephalus spp. in Hainan Island, is an important step towards a better understanding of tick-borne disease transmission. This is the first report in the area on the presence of Anaplasma sp., A. marginale, R. felis and Coxiella, in R. haemaphysaloides.}, } @article {pmid38307295, year = {2024}, author = {Ding, X and Lan, W and Li, J and Deng, M and Li, Y and Katayama, Y and Gu, JD}, title = {Metagenomic insight into the pathogenic-related characteristics and resistome profiles within microbiome residing on the Angkor sandstone monuments in Cambodia.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170402}, doi = {10.1016/j.scitotenv.2024.170402}, pmid = {38307295}, issn = {1879-1026}, abstract = {To reveal the characteristics of indigenous microbiome including the pathogenic-related ones on Angkor monuments in Cambodia and the distribution pattern of resistome at different locations, several sites, namely Angkor Wat, Bayon of Angkor Thom, and Prasat Preah Vihear with different exposure levels to tourists were selected to conduct the metagenomic analysis in this study. The general characteristics of the microbiome on these monuments were revealed, and the association between the environmental geo-ecological feature and the indigenous microbiome was delineated. The most common microbial groups included 6 phyla, namely Acidobacteria, Actinobacteria, Gemmatimonadetes, Nitrospirae, Proteobacteria and Verrucomicrobia on the monuments, but Firmicutes and Chlamydiae were the most dominant phyla found in bats droppings. The taxonomic family of Chitinophagaceae could serve as a signature microbial group for Preah Vihear, the less visited site. More importantly, the pathogenic-related characteristics of the microbiome residing on Angkor monuments were uncovered. A set of specific antibiotic resistance genes (ARGs) with cross-niches dispersal capacity (between the environmental microbiome and the microbiome within warm blood fauna) was identified to be high by the source tracking analysis based on ARGs profile varies in this study. Among the 10 ARG-types detected in this study, 6 of them are confined to resistance mechanism of antibiotic efflux-pump. The findings of this study provide new a new direction on public health management and implication globally at archaeological sites for tourism.}, } @article {pmid38307030, year = {2024}, author = {Wan, Y and Zhang, L and Xu, Z and Su, Q and Leung, TF and Chan, D and Wong, OWH and Chan, S and Chan, FKL and Tun, HM and Ng, SC}, title = {Alterations in fecal virome and bacteriome virome interplay in children with autism spectrum disorder.}, journal = {Cell reports. Medicine}, volume = {}, number = {}, pages = {101409}, doi = {10.1016/j.xcrm.2024.101409}, pmid = {38307030}, issn = {2666-3791}, abstract = {Emerging evidence suggests autism spectrum disorder (ASD) is associated with altered gut bacteria. However, less is known about the gut viral community and its role in shaping microbiota in neurodevelopmental disorders. Herein, we perform a metagenomic analysis of gut-DNA viruses in 60 children with ASD and 64 age- and gender-matched typically developing children to investigate the effect of the gut virome on host bacteria in children with ASD. ASD is associated with altered gut virome composition accompanied by the enrichment of Clostridium phage, Bacillus phage, and Enterobacteria phage. These ASD-enriched phages are largely associated with disrupted viral ecology in ASD. Importantly, changes in the interplay between the gut bacteriome and virome seen in ASD may influence the encoding capacity of microbial pathways for neuroactive metabolite biosynthesis. These findings suggest an impaired bacteriome-virome ecology in ASD, which sheds light on the importance of bacteriophages in pathogenesis and the development of microbial therapeutics in ASD.}, } @article {pmid38306858, year = {2024}, author = {Zhu, L and Li, W and Huang, C and Tian, Y and Xi, B and Wu, W and Yan, Y}, title = {Contribution of sulfur-containing precursors to release of hydrogen sulfide in sludge composting.}, journal = {Journal of environmental management}, volume = {353}, number = {}, pages = {120195}, doi = {10.1016/j.jenvman.2024.120195}, pmid = {38306858}, issn = {1095-8630}, abstract = {Hydrogen sulfide (H2S) production during composting can impact the environment and human health. Especially during the thermophilic phase, H2S is discharged in large quantities. However, in sludge composting, the contributions of different sulfur-containing precursors to H2S fluxes, key functional microorganisms, and key environmental parameters for reducing H2S flux remain unclear. Analysis of cysteine (Cys), methionine (Met), and sulfate (SO4[2-]) concentrations, multiple stepwise regression analysis, and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analysis of metagenomes showed that Cys was the main contributor to the production of H2S and that Met was among the main sources during the first three days of composting, while the SO4[2-] contribution to H2S was negligible. Fifteen functional genera involved in the conversion of precursors to H2S were identified by co-occurrence network analysis. Only Bacillus showed high temperature resistance (>50 °C) and the ability to reduce H2S. Redundancy analysis showed that total carbon (64.0 %) and pH (23.3 %) had significant effects on functional bacteria. H2S had a quadratic relationship with sulfur-containing precursors. All microbial network sulfur-containing precursors metabolism modules showed a highly significant relationship with Cys.}, } @article {pmid38306774, year = {2024}, author = {Li, X and Wang, H and Abdelrahman, H and Kelly, A and Roy, L and Wang, L}, title = {Profiling and source tracking of the microbial populations and resistome present in fish products.}, journal = {International journal of food microbiology}, volume = {413}, number = {}, pages = {110591}, doi = {10.1016/j.ijfoodmicro.2024.110591}, pmid = {38306774}, issn = {1879-3460}, abstract = {Microorganisms in processing environments significantly impact the quality and safety of food products and can serve as potential reservoirs for antibiotic-resistant genes, contributing to public health concerns about antimicrobial resistance (AMR). Fish processing plants represent an understudied environment for microbiome mapping. This study investigated the microbial composition, prevalence of Listeria spp., and resistome structures in three catfish processing facilities in the southeastern United States. The 16S rRNA gene sequencing revealed that the observed richness and Shannon diversity index increased significantly from fish to fillet. Beta diversity analysis showed distinct clustering of microbial communities between fish, environment, and fillet samples. Fast expectation-maximization microbial source tracking (FEAST) algorithm demonstrated that the microbiota presents in the processing environment contributed 48.2 %, 62.4 %, and 53.7 % to the microbiota present on fillet in Facility 1 (F1), F2, and F3, respectively. Food contact surfaces made larger contributions compared to the non-food contact surfaces. The linear discriminant analysis of effect size (LEfSe) identified specific microbial genera (e.g., Plesiomohas, Brochothrix, Chryseobacterium and Cetobacterium) that significantly varied between Listeria spp. positive and negative samples in all three processing plants. The metagenomic sequencing results identified 212 antimicrobial resistance genes (ARGs) belonging to 72 groups from the raw fish and fish fillet samples collected from three processing plants. Although there was a significant decrease in the overall diversity of ARGs from fish to fillet samples, the total abundance of ARGs did not change significantly (P > 0.05). ARGs associated with resistance to macrolide-lincosamide-streptogramin (MLS), cationic antimicrobial peptides, aminoglycosides, and beta-lactams were found to be enriched in the fillet samples when compared to fish samples. Results of this study highlight the profound impact of processing environment on shaping the microbial populations present on the final fish product and the need for additional strategies to mitigate AMR in fish products.}, } @article {pmid38306604, year = {2024}, author = {Zheng, YR and Chen, XH and Chen, Q and Cao, H}, title = {Metagenomic Next-generation Sequencing for Pathogen Identification in Bronchoalveolar Lavage Fluid From Neonates Receiving Extracorporeal Membrane Oxygenation.}, journal = {The Pediatric infectious disease journal}, volume = {}, number = {}, pages = {}, doi = {10.1097/INF.0000000000004250}, pmid = {38306604}, issn = {1532-0987}, abstract = {BACKGROUND: Neonates on extracorporeal membrane oxygenation (ECMO) are at high risk of infection. Rapid and accurate identification of pathogens is essential to improve the prognosis of children on ECMO. Metagenome next-generation sequencing (mNGS) has been used in recent years to detect pathogenic bacteria, but evidence for its use in neonates on ECMO is lacking.

METHODS: This retrospective study was conducted using an electronic medical record system. We analyzed the results of mNGS and conventional microbiological tests (CMTs) in bronchoalveolar lavage fluid of neonates receiving ECMO support with pulmonary infections in our hospital from July 2021 to January 2023.

RESULTS: We screened 18 ECMO-supported neonates with pneumonia for inclusion in the study. The median age of the included children was 2 (1-4) days, the median gestational age was 38.3 (33-40+4) weeks, and the median weight was 3.3 (2.2-4.8) kg. The detection rate of mNGS was 77.8% (14/18), higher than the 44.4% (8/18) of CMT (P = 0.04). A total of 20 pathogens were detected in mNGS, with the top 3 most common pathogens being Klebsiella pneumoniae, Acinetobacter baumannii and Escherichia coli. Mixed infections were found in 14 cases (77.8%), including 13 cases (72.2%) with mixed infections detected by mNGS and 7 cases (27.8%) with mixed infections detected by CMT. A total of 9 children underwent treatment changes based on mNGS results and all of them experienced relief of symptoms.

CONCLUSION: Compared with CMT, mNGS can detect pathogens earlier and more sensitively, and may play an important role in ECMO-supported neonatal pneumonia pathogen detection and optimization of antibiotic therapy.}, } @article {pmid38306578, year = {2024}, author = {Kitsios, GD and Bain, W}, title = {"Now We Got Bad Blood:" Beyond Phenotype Labels in an "Era" of Meta-Omics in Critical Illness.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1164/rccm.202401-0004ED}, pmid = {38306578}, issn = {1535-4970}, } @article {pmid38306531, year = {2024}, author = {Wang, M and Xiao, Q and Wang, K}, title = {Empyema caused by Actinomyces odontolyticus: A case report.}, journal = {Medicine}, volume = {103}, number = {5}, pages = {e37003}, doi = {10.1097/MD.0000000000037003}, pmid = {38306531}, issn = {1536-5964}, abstract = {RATIONALE: Actinomyces odontolyticus causes a rare, chronic granulomatous infection that is frequently associated with immunocompromised states. A odontolyticus can cause infection in multiple organs, but empyema is rare.

PATIENT CONCERNS: We report a case of empyema caused by A odontolyticus. The patient was a 64-year-old man. He was admitted to the hospital with a 5-day history of fever and dyspnea. He had caries and sequelae of cerebral apoplexy.

DIAGNOSES: Metagenome next generation sequencing of pleural effusion was positive for A odontolyticus. Pathogen was identified by biphasic culture of pleural effusion fluid.

INTERVENTIONS: According to the drug sensitivity test, linezolid 0.6 g twice daily and clindamycin 0.6 g 3 times a day were administered intravenously. Thoracic drainage was initially performed, but the drainage was not sufficient. Medical thoracoscopy was performed to fully drain the pleural effusion.

OUTCOMES: After anti-infection and medical thoracoscopic therapy, the symptoms of this patient improved.

LESSONS: Microbial metagenome sequencing can find pathogens that are difficult to culture by traditional methods. Adequate drainage was the key to the treatment of empyema. Medical thoracoscopy was recommended to remove the pleural effusion and spoilage when thoracic drainage is difficult. The common clinical features of A odontolyticus include a mass or swelling, abdominal disease, dental disease, and subcutaneous abscesses. Microbial metagenome sequencing can find pathogens that are difficult to culture by traditional methods. Adequate drainage was the key to the treatment of empyema. Medical thoracoscopy was recommended to remove the pleural effusion and spoilage when thoracic drainage is difficult.}, } @article {pmid38306257, year = {2024}, author = {Song, J and Zheng, C and Qiu, M and Zhan, XP and Zhang, Z and Zhang, H and Shi, N and Zhang, L and Yu, Y and Nicolaisen, M and Xu, L and Fang, H}, title = {Mechanisms Underlying the Overlooked Chiral Fungicide-Driven Enantioselective Proliferation of Antibiotic Resistance in Earthworm Intestinal Microbiome.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c07761}, pmid = {38306257}, issn = {1520-5851}, abstract = {From a "One Health" perspective, the global threat of antibiotic resistance genes (ARGs) is associated with modern agriculture practices including agrochemicals application. Chiral fungicides account for a considerable proportion of wildly used agrochemicals; however, whether and how their enantiomers lead to differential proliferation of antibiotic resistance in agricultural environments remain overlooked. Focused on the soil-earthworm ecosystem, we for the first time deciphered the mechanisms underlying the enantioselective proliferation of antibiotic resistance driven by the enantiomers of a typical chiral fungicide mandipropamid (i.e., R-MDP and S-MDP) utilizing a multiomic approach. Time-series metagenomic analysis revealed that R-MDP led to a significant enhancement of ARGs with potential mobility (particularly the plasmid-borne ARGs) in the earthworm intestinal microbiome. We further demonstrated that R-MDP induced a concentration-dependent facilitation of plasmid-mediated ARG transfer among microbes. In addition, transcriptomic analysis with verification identified the key aspects involved, where R-MDP enhanced cell membrane permeability, transfer ability, biofilm formation and quorum sensing, rebalanced energy production, and decreased cell mobility versus S-MDP. Overall, the findings provide novel insights into the enantioselective disruption of microbiome and resistome in earthworm gut by chiral fungicides and offer significant contributions to the comprehensive risk assessment of chiral agrochemicals in agroecosystems.}, } @article {pmid38305171, year = {2024}, author = {Ning, R and Li, C and Xia, M and Zhang, Y and Gan, Y and Huang, Y and Zhang, T and Song, H and Zhang, S and Guo, W}, title = {Pseudomonas-associated bacteria play a key role in obtaining nutrition from bamboo for the giant panda (Ailuropoda melanoleuca).}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0381923}, doi = {10.1128/spectrum.03819-23}, pmid = {38305171}, issn = {2165-0497}, abstract = {Gut microbiota plays a vital role in obtaining nutrition from bamboo for giant pandas. However, low cellulase activity has been observed in the panda's gut. Besides, no specific pathway has been implicated in lignin digestion by gut microbiota of pandas. Therefore, the mechanism by which they obtain nutrients is still controversial. It is necessary to elucidate the precise pathways employed by gut microbiota of pandas to degrade lignin. Here, the metabolic pathways for lignin degradation in pandas were explored by comparing 209 metagenomic sequencing data from wild species with different feeding habits. Lignin degradation central pathways, including beta-ketoadipate and homogentisate pathway, were enriched in the gut of wild bamboo-eating pandas. The gut microbiome of wild bamboo-eating specialists was enriched with genes from pathways implicated in degrading ferulate and p-coumarate into acetyl-CoA and succinyl-CoA, which can potentially provide the raw materials for metabolism in pandas. Specifically, Pseudomonas, as the most dominant gut bacteria genus, was found to be the main bacteria to provide genes involved in lignin or lignin derivative degradation. Herein, three Pseudomonas-associated strains isolated from the feces of wild pandas showed the laccase, lignin peroxidase, and manganese peroxidase activity and extracellular lignin degradation ability in vitro. A potential mechanism for pandas to obtain nutrition from bamboo was proposed based on the results. This study provides novel insights into the adaptive evolution of pandas from the perspective of lignin metabolism.IMPORTANCEAlthough giant pandas only feed on bamboo, the mechanism of lignin digestion in pandas is unclear. Here, the metabolic pathways for lignin degradation in wild pandas were explored by comparing gut metagenomic from species with different feeding habits. Results showed that lignin degradation central pathways, including beta-ketoadipate and homogentisate pathway, were enriched in the gut of wild bamboo-eating pandas. Genes from pathways involved in degrading ferulate and p-coumarate via beta-ketoadipate pathway were also enriched in bamboo-eating pandas. The final products of the above process, such as acetyl-CoA, can potentially provide the raw materials for metabolism in pandas. Specifically, Pseudomonas, as the most dominant gut bacteria genus, mainly provides genes involved in lignin degradation. Herein, Pseudomonas-associated strains isolated from the feces of pandas could degrade extracellular lignin. These findings suggest that gut microbiome of pandas is crucial in obtaining nutrition from lignin via Pseudomonas, as the main lignin-degrading bacteria.}, } @article {pmid38305149, year = {2024}, author = {Mukhia, S and Kumar, A and Kumar, R}, title = {Bacterial community distribution and functional potentials provide key insights into their role in the ecosystem functioning of a retreating Eastern Himalayan glacier.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiae012}, pmid = {38305149}, issn = {1574-6941}, abstract = {Himalayan glaciers are receding at an exceptional rate, perturbing the local biome and ecosystem processes. Understanding the microbial ecology of an exclusively microbe-driven biome provides insights into their contributions to the ecosystem functioning through biogeochemical fluxes. Here, we investigated the bacterial communities and their functional potential in the retreating East Rathong Glacier (ERG) of Sikkim Himalaya. Amplicon-based taxonomic classification revealed the dominance of the phyla Proteobacteria, Bacteroidota and candidate Patescibacteria in the glacial sites. Further, eight good-quality metagenome-assembled genomes (MAGs) of Proteobacteria, Patescibacteria, Acidobacteriota, and Choloflexota retrieved from the metagenomes elucidated the microbial contributions to nutrient cycling. The ERG MAGs showed aerobic respiration as a primary metabolic feature, accompanied by carbon fixation and complex carbon degradation potentials. Pathways for nitrogen metabolism, chiefly dissimilatory nitrate reduction and denitrification, and a complete sulfur oxidation enzyme complex for sulfur metabolism were identified in the MAGs. We observed that DNA repair and oxidative stress response genes complemented with osmotic and periplasmic stress and protein chaperones were vital for adaptation against the intense radiation and stress conditions of the extreme Himalayan niche. Current findings elucidate the microbiome and associated functional potentials of a vulnerable glacier, emphasizing their significant ecological roles in a changing glacial ecosystem.}, } @article {pmid38305096, year = {2024}, author = {Linnehan, BK and Kodera, SM and Allard, SM and Brodie, EC and Allaband, C and Knight, R and Lutz, HL and Carroll, MC and Meegan, JM and Jensen, ED and Gilbert, JA}, title = {Evaluation of the safety and efficacy of fecal microbiota transplantations in bottlenose dolphins (Tursiops truncatus) using metagenomic sequencing.}, journal = {Journal of applied microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/jambio/lxae026}, pmid = {38305096}, issn = {1365-2672}, abstract = {AIMS: Gastrointestinal disease is a leading cause of morbidity in bottlenose dolphins (Tursiops truncatus) under managed care. Fecal microbiota transplantation (FMT) holds promise as a therapeutic tool to restore gut microbiota without antibiotic use. This prospective clinical study aimed to develop a screening protocol for FMT donors to ensure safety, determine an effective FMT administration protocol for managed dolphins, and evaluate the FMT's efficacy in four recipient dolphins.

METHODS AND RESULTS: Comprehensive health monitoring was performed on donor and recipient dolphins. Fecal samples were collected before, during, and after FMT therapy. Screening of donor and recipient fecal samples was accomplished by in-house and reference lab diagnostic tests. Shotgun metagenomics was used for sequencing. Following FMT treatment, all four recipient communities experienced engraftment of novel microbial species from donor communities. Engraftment coincided with resolution of clinical signs and a sustained increase in alpha diversity.

CONCLUSION: The donor screening protocol proved to be safe in this study and no adverse effects were observed in four recipient dolphins. Treatment coincided with improvement in clinical signs.}, } @article {pmid38304712, year = {2024}, author = {Chen, P and Wang, S and Li, H and Qi, X and Hou, Y and Ma, T}, title = {Comparative genomic analyses of Cutibacterium granulosum provide insights into genomic diversity.}, journal = {Frontiers in microbiology}, volume = {15}, number = {}, pages = {1343227}, doi = {10.3389/fmicb.2024.1343227}, pmid = {38304712}, issn = {1664-302X}, abstract = {Cutibacterium granulosum, a commensal bacterium found on human skin, formerly known as Propionibacterium granulosum, rarely causes infections and is generally considered non-pathogenic. Recent research has revealed the transferability of the multidrug-resistant plasmid pTZC1 between C. granulosum and Cutibacterium acnes, the latter being an opportunistic pathogen in surgical site infections. However, there is a noticeable lack of research on the genome of C. granulosum, and the genetic landscape of this species remains largely uncharted. We investigated the genomic features and evolutionary structure of C. granulosum by analyzing a total of 30 Metagenome-Assembled Genomes (MAGs) and isolate genomes retrieved from public databases, as well as those generated in this study. A pan-genome of 6,077 genes was identified for C. granulosum. Remarkably, the 'cloud genes' constituted 62.38% of the pan-genome. Genes associated with mobilome: prophages, transposons [X], defense mechanisms [V] and replication, recombination and repair [L] were enriched in the cloud genome. Phylogenomic analysis revealed two distinct mono-clades, highlighting the genomic diversity of C. granulosum. The genomic diversity was further confirmed by the distribution of Average Nucleotide Identity (ANI) values. The functional profiles analysis of C. granulosum unveiled a wide range of potential Antibiotic Resistance Genes (ARGs) and virulence factors, suggesting its potential tolerance to various environmental challenges. Subtype I-E of the CRISPR-Cas system was the most abundant in these genomes, a feature also detected in C. acnes genomes. Given the widespread distribution of C. granulosum strains within skin microbiome, our findings make a substantial contribution to our broader understanding of the genetic diversity, which may open new avenues for investigating the mechanisms and treatment of conditions such as acne vulgaris.}, } @article {pmid38304082, year = {2024}, author = {Wood, C and Bruinink, A and Trembath-Reichert, E and Wilhelm, MB and Vidal, C and Balaban, E and McKay, CP and Swan, R and Swan, B and Goordial, J}, title = {Active microbiota persist in dry permafrost and active layer from Elephant Head, Antarctica.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycad002}, doi = {10.1093/ismeco/ycad002}, pmid = {38304082}, issn = {2730-6151}, abstract = {Dry permafrost is a challenging environment for microbial life due to cold, dry, and often oligotrophic conditions. In 2016, Elephant Head, Antarctica, was confirmed as the second site on Earth to contain dry permafrost. It is geographically distinct from the McMurdo Dry Valleys where dry permafrost has been studied previously. Here, we present the first study of the microbial activity, diversity, and functional potential of Elephant Head dry permafrost. Microbial activity was measured using radiorespiration assays with radiolabeled acetate as a carbon source at 5, 0, and -5°C. Low, but detectable, rates of microbial activity were measured in some samples at 0 and -5°C. This is distinct from previous studies of McMurdo Dry Valley dry permafrost which concluded that dry permafrost represents a cold-arid limit to life on the planet. The isolation of cold-adapted organisms from these soils, including one capable of subzero growth, further supports that the Elephant Head dry active layer and dry permafrost harbor viable microbial life, which may be active in situ. Metagenomic, 16S rRNA gene, and internal transcribed spacer and amplicon sequencing identified similar microbial communities to other Antarctic and cold environments. The Elephant Head microbial community appears to be adapted for survival in cold, dry, and oligotrophic conditions based on the presence of cold adaptation and stress response genes in the metagenomes. Together, our results show that dry permafrost environments do not exclude active microbial life at subzero temperatures, suggesting that the cold, dry soils of Mars may also not be as inhospitable as previously thought.}, } @article {pmid38304081, year = {2024}, author = {Oshiki, M and Morimoto, E and Kobayashi, K and Satoh, H and Okabe, S}, title = {Collaborative metabolisms of urea and cyanate degradation in marine anammox bacterial culture.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycad007}, doi = {10.1093/ismeco/ycad007}, pmid = {38304081}, issn = {2730-6151}, abstract = {Anammox process greatly contributes to nitrogen loss occurring in oceanic oxygen minimum zones (OMZs), where the availability of NH4[+] is scarce as compared with NO2[-]. Remineralization of organic nitrogen compounds including urea and cyanate (OCN[-]) into NH4[+] has been believed as an NH4[+] source of the anammox process in oxygen minimum zones. However, urea- or OCN[-]- dependent anammox has not been well examined due to the lack of marine anammox bacterial culture. In the present study, urea and OCN[-] degradation in a marine anammox bacterial consortium were investigated based on [15]N-tracer experiments and metagenomic analysis. Although a marine anammox bacterium, Candidatus Scalindua sp., itself was incapable of urea and OCN[-] degradation, urea was anoxically decomposed to NH4[+] by the coexisting ureolytic bacteria (Rhizobiaceae, Nitrosomonadaceae, and/or Thalassopiraceae bacteria), whereas OCN[-] was abiotically degraded to NH4[+]. The produced NH4[+] was subsequently utilized in the anammox process. The activity of the urea degradation increased under microaerobic condition (ca. 32-42 μM dissolved O2, DO), and the contribution of the anammox process to the total nitrogen loss also increased up to 33.3% at 32 μM DO. Urea-dependent anammox activities were further examined in a fluid thioglycolate media with a vertical gradient of O2 concentration, and the active collaborative metabolism of the urea degradation and anammox was detected at the lower oxycline (21 μM DO).}, } @article {pmid38303501, year = {2024}, author = {Oliphant, K and Cruz Ayala, W and Ilyumzhinova, R and Mbayiwa, K and Sroka, A and Xie, B and Andrews, B and Keenan, K and Claud, EC}, title = {Microbiome function and neurodevelopment in Black infants: vitamin B12 emerges as a key factor.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2298697}, doi = {10.1080/19490976.2023.2298697}, pmid = {38303501}, issn = {1949-0984}, abstract = {The early life gut microbiome affects the developing brain, and therefore may serve as a target to support neurodevelopment of children living in stressful and under-resourced environments, such as Black youth living on the South Side of Chicago, for whom we observe racial disparities in health. Microbiome compositions/functions key to multiple neurodevelopmental facets have not been studied in Black children, a vulnerable population due to racial disparities in health; thus, a subsample of Black infants living in urban, low-income neighborhoods whose mothers participated in a prenatal nutrition study were recruited for testing associations between composition and function of the gut microbiome (16S rRNA gene sequencing, shotgun metagenomics, and targeted metabolomics of fecal samples) and neurodevelopment (developmental testing, maternal report of temperament, and observed stress regulation). Two microbiome community types, defined by high Lachnospiraceae or Enterobacteriaceae abundance, were discovered in this cohort from 16S rRNA gene sequencing analysis; the Enterobacteriaceae-dominant community type was significantly negatively associated with cognition and language scores, specifically in male children. Vitamin B12 biosynthesis emerged as a key microbiome function from shotgun metagenomics sequencing analysis, showing positive associations with all measured developmental skills (i.e., cognition, language, motor, surgency, effortful control, and observed stress regulation). Blautia spp. also were identified as substantial contributors of important microbiome functions, including vitamin B12 biosynthesis and related vitamin B12-dependent microbiome functions, anti-inflammatory microbial surface antigens, competitive mechanisms against pathobionts, and production of antioxidants. The results are promising with respect to the potential for exploring therapeutic candidates, such as vitamin B12 nutritional or Blautia spp. probiotic supplementation, to support the neurodevelopment of infants at risk for experiencing racial disparities in health.}, } @article {pmid38303006, year = {2024}, author = {Asher, EE and Bashan, A}, title = {Model-free prediction of microbiome compositions.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {17}, pmid = {38303006}, issn = {2049-2618}, support = {1258/21//Israel Science Foundation/ ; I-1523-500.15/2021//German-Israeli Foundation for Scientific Research and Development/ ; }, abstract = {BACKGROUND: The recent recognition of the importance of the microbiome to the host's health and well-being has yielded efforts to develop therapies that aim to shift the microbiome from a disease-associated state to a healthier one. Direct manipulation techniques of the species' assemblage are currently available, e.g., using probiotics or narrow-spectrum antibiotics to introduce or eliminate specific taxa. However, predicting the species' abundances at the new state remains a challenge, mainly due to the difficulties of deciphering the delicate underlying network of ecological interactions or constructing a predictive model for such complex ecosystems.

RESULTS: Here, we propose a model-free method to predict the species' abundances at the new steady state based on their presence/absence configuration by utilizing a multi-dimensional k-nearest-neighbors (kNN) regression algorithm. By analyzing data from numeric simulations of ecological dynamics, we show that our predictions, which consider the presence/absence of all species holistically, outperform both the null model that uses the statistics of each species independently and a predictive neural network model. We analyze real metagenomic data of human-associated microbial communities and find that by relying on a small number of "neighboring" samples, i.e., samples with similar species assemblage, the kNN predicts the species abundance better than the whole-cohort average. By studying both real metagenomic and simulated data, we show that the predictability of our method is tightly related to the dissimilarity-overlap relationship of the training data.

CONCLUSIONS: Our results demonstrate how model-free methods can prove useful in predicting microbial communities and may facilitate the development of microbial-based therapies. Video Abstract.}, } @article {pmid38302964, year = {2024}, author = {Liang, W and Zhang, Q and Qian, Q and Wang, M and Ding, Y and Zhou, J and Zhu, Y and Jin, Y and Chen, X and Kong, H and Song, W and Lu, X and Wu, X and Xu, X and Dai, S and Sun, W}, title = {Diagnostic strategy of metagenomic next-generation sequencing for gram negative bacteria in respiratory infections.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {23}, number = {1}, pages = {10}, pmid = {38302964}, issn = {1476-0711}, abstract = {OBJECTIVE: This study aims to identify the most effective diagnostic method for distinguishing pathogenic and non-pathogenic Gram-negative bacteria (GNB) in suspected pneumonia cases using metagenomic next-generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) samples.

METHODS: The effectiveness of mNGS was assessed on BALF samples collected from 583 patients, and the results were compared with those from microbiological culture and final clinical diagnosis. Three interpretational approaches were evaluated for diagnostic accuracy.

RESULTS: mNGS outperformed culture significantly. Among the interpretational approaches, Clinical Interpretation (CI) demonstrated the best diagnostic performance with a sensitivity of 87.3%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 98.3%. CI's specificity was significantly higher than Simple Interpretation (SI) at 37.9%. Additionally, CI excluded some microorganisms identified as putative pathogens by SI, including Haemophilus parainfluenzae, Haemophilus parahaemolyticus, and Klebsiella aerogenes.

CONCLUSION: Proper interpretation of mNGS data is crucial for accurately diagnosing respiratory infections caused by GNB. CI is recommended for this purpose.}, } @article {pmid38302952, year = {2024}, author = {Kim, HY and Jung, YS and Park, W and Choi, YJ and Kim, JY}, title = {Can medication-related osteonecrosis of the jaw be attributed to specific microorganisms through oral microbiota analyses? A preliminary study.}, journal = {BMC oral health}, volume = {24}, number = {1}, pages = {160}, pmid = {38302952}, issn = {1472-6831}, abstract = {BACKGROUND: Medication-related osteonecrosis of the jaw (MRONJ) can cause significant pain and loss of aesthetics and function if not treated properly. However, diagnosis still relies on detailed intraoral examinations and imaging. Prognosis varies even among patients with similar stages or conditions of MRONJ, emphasizing the need for a deeper understanding of its complex mechanisms. Thus, this study aimed to identify the oral microbiota of patients with MRONJ.

METHODS: This single-center prospective cohort study included patients with confirmed MRONJ who visited the Department of Oral and Maxillofacial Surgery at Yonsei University Dental Hospital between 2021 and 2022. Oral swab samples were collected from the affected and unaffected sides of each patient. The composition and enumeration of the microbial communities were analyzed, and the diversity was compared to verify ecological changes in the groups using a next-generation sequencing-based 16S metagenomic analysis. A statistical analysis was performed using Wilcoxon signed-rank test with SPSS version 22, and values of P less than 0.05 were considered statistically significant.

RESULTS: The final study sample included 12 patients. The mean age was 82.67 ± 5.73 (range, 72-90) years. Changes in microbial composition were observed at different taxonomic levels (phylum, genus, and species). The identified microorganisms were commonly associated with periodontitis, gingival disease, and endodontic infection, suggesting a multifactorial etiology of MRONJ.

CONCLUSIONS: Although this study is based on a small number of cases, it shows that MRONJ is not caused by a specific microorganism but can rather be caused by a variety of factors. By addressing these findings in large-scale studies, the significance of oral microbiome in pathogenesis can be further elucidated and can facilitate the development of effective therapeutic interventions for patients with MRONJ.}, } @article {pmid38302869, year = {2024}, author = {Ahmed, N and Azab, M and Enany, S and Hanora, A}, title = {Draft genome sequence of novel Candidatus Ornithobacterium hominis carrying antimicrobial resistance genes in Egypt.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {47}, pmid = {38302869}, issn = {1471-2180}, support = {85D/2021//Academy of Scientific Research and Technology/ ; 85D/2021//Academy of Scientific Research and Technology/ ; }, abstract = {BACKGROUND: Candidatus Ornithobacterium hominis (O. hominis), which was identified in nasopharyngeal swabs from Egypt, has been associated with respiratory disorders in humans. O. hominis, a recently identified member of the Flavobacteriaceae family, belongs to the largest family within the Bacteroidetes phylum. This family includes hundreds of species and 90 genera, including major human pathogens such as Capnocytophaga canimorsus and Elizabethkingia meningoseptica. Herein, we presented two draft genome assemblies of O. hominis that were extracted from metagenomic data using the Illumina sequencing method. The alignment of reads against the O. hominis genome was accomplished using BLASTN, and the reads with significant hits were extracted using Seqtk and assembled using SPAdes. The primary goal of this study was to obtain a more profound understanding of the genomic landscape of O. hominis, with an emphasis on identifying the associated virulence, antimicrobial genes, and distinct defense mechanisms to shed light on the potential role of O. hominis in human respiratory infections.

RESULTS: The genome size was estimated to be 1.84 Mb, including 1,931,660 base pairs (bp), with 1,837 predicted coding regions and a G+C content of 35.62%. Genes encoding gliding motility, antibiotic resistance (20 genes), and the toxA gene were all included in the genome assembly. Gliding motility lipoproteins (GldD, GldJ, GldN, and GldH) and the gliding motility-associated ABC transporter substrate-binding protein, which acts as a crucial virulence mechanism in Flavobacterium species, were identified. The genome contained unique genes encoding proteins, such as the ParE1 toxin that defend against the actions of quinolone and other antibiotics. The cobalt-zinc-cadmium resistance gene encoding the protein CzcB, which is necessary for metal resistance, urease regulation, and colonization, was also detected. Several multidrug resistance genes encoding proteins were identified, such as MexB, MdtK, YheI, and VanC.

CONCLUSION: Our study focused on identifying virulence factors, and antimicrobial resistance genes present in the core genome of O. hominis. These findings provide valuable insights into the potential pathogenicity and antibiotic susceptibility of O. hominis.}, } @article {pmid38302544, year = {2024}, author = {Prasoodanan P K, V and Kumar, S and Dhakan, DB and Waiker, P and Saxena, R and Sharma, VK}, title = {Metagenomic exploration of Andaman region of the Indian Ocean.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2717}, pmid = {38302544}, issn = {2045-2322}, abstract = {Ocean microbiome is crucial for global biogeochemical cycles and primary productivity. Despite numerous studies investigating the global ocean microbiomes, the microbiome composition of the Andaman region of the Indian Ocean remains largely unexplored. While this region harbors pristine biological diversity, the escalating anthropogenic activities along coastal habitats exert an influence on the microbial ecology and impact the aquatic ecosystems. We investigated the microbiome composition in the coastal waters of the Andaman Islands by 16S rRNA gene amplicon and metagenomic shotgun sequencing approaches and compared it with the Tara Oceans Consortium. In the coastal waters of the Andaman Islands, a significantly higher abundance and diversity of Synechococcus species was observed with a higher abundance of photosynthesis pigment-related genes to adapt to variable light conditions and nutrition. In contrast, Prochlorococcus species showed higher abundance in open ocean water samples of the Indian Ocean region, with a relatively limited functional diversity. A higher abundance of antibiotic-resistance genes was also noted in the coastal waters region. We also updated the ocean microbiome gene catalog with 93,172 unique genes from the Andaman coastal water microbiome. This study provides valuable insights into the Indian Ocean microbiome and supplements the global marine microbial ecosystem studies.}, } @article {pmid38302528, year = {2024}, author = {Sánchez, P and Coutinho, FH and Sebastián, M and Pernice, MC and Rodríguez-Martínez, R and Salazar, G and Cornejo-Castillo, FM and Pesant, S and López-Alforja, X and López-García, EM and Agustí, S and Gojobori, T and Logares, R and Sala, MM and Vaqué, D and Massana, R and Duarte, CM and Acinas, SG and Gasol, JM}, title = {Marine picoplankton metagenomes and MAGs from eleven vertical profiles obtained by the Malaspina Expedition.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {154}, pmid = {38302528}, issn = {2052-4463}, support = {BCV-20132-0001//Barcelona Supercomputing Center (Centro Nacional de Supercomputación)/ ; CSD2008-00077//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/ ; CTM2011-15461-E//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/ ; CTM2017-87736-R//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/ ; OSR #3362//King Abdullah University of Science and Technology (KAUST)/ ; }, abstract = {The Ocean microbiome has a crucial role in Earth's biogeochemical cycles. During the last decade, global cruises such as Tara Oceans and the Malaspina Expedition have expanded our understanding of the diversity and genetic repertoire of marine microbes. Nevertheless, there are still knowledge gaps regarding their diversity patterns throughout depth gradients ranging from the surface to the deep ocean. Here we present a dataset of 76 microbial metagenomes (MProfile) of the picoplankton size fraction (0.2-3.0 µm) collected in 11 vertical profiles covering contrasting ocean regions sampled during the Malaspina Expedition circumnavigation (7 depths, from surface to 4,000 m deep). The MProfile dataset produced 1.66 Tbp of raw DNA sequences from which we derived: 17.4 million genes clustered at 95% sequence similarity (M-GeneDB-VP), 2,672 metagenome-assembled genomes (MAGs) of Archaea and Bacteria (Malaspina-VP-MAGs), and over 100,000 viral genomic sequences. This dataset will be a valuable resource for exploring the functional and taxonomic connectivity between the photic and bathypelagic tropical and sub-tropical ocean, while increasing our general knowledge of the Ocean microbiome.}, } @article {pmid38302438, year = {2024}, author = {Eberhart, T and Stanley, FU and Ricci, L and Chirico, T and Ferrarese, R and Sisti, S and Scagliola, A and Baj, A and Badurek, S and Sommer, A and Culp-Hill, R and Dzieciatkowska, M and Shokry, E and Sumpton, D and D'Alessandro, A and Clementi, N and Mancini, N and Cardaci, S}, title = {ACOD1 deficiency offers protection in a mouse model of diet-induced obesity by maintaining a healthy gut microbiota.}, journal = {Cell death & disease}, volume = {15}, number = {2}, pages = {105}, pmid = {38302438}, issn = {2041-4889}, support = {Start-Up 2017 - ID. 20464 project//Associazione Italiana per la Ricerca sul Cancro (Italian Association for Cancer Research)/ ; GR-2018-12365954//Ministero della Salute (Ministry of Health, Italy)/ ; }, abstract = {Aconitate decarboxylase 1 (ACOD1) is the enzyme synthesizing itaconate, an immuno-regulatory metabolite tuning host-pathogen interactions. Such functions are achieved by affecting metabolic pathways regulating inflammation and microbe survival. However, at the whole-body level, metabolic roles of itaconate remain largely unresolved. By using multiomics-integrated approaches, here we show that ACOD1 responds to high-fat diet consumption in mice by promoting gut microbiota alterations supporting metabolic disease. Genetic disruption of itaconate biosynthesis protects mice against obesity, alterations in glucose homeostasis and liver metabolic dysfunctions by decreasing meta-inflammatory responses to dietary lipid overload. Mechanistically, fecal metagenomics and microbiota transplantation experiments demonstrate such effects are dependent on an amelioration of the intestinal ecosystem composition, skewed by high-fat diet feeding towards obesogenic phenotype. In particular, unbiased fecal microbiota profiling and axenic culture experiments point towards a primary role for itaconate in inhibiting growth of Bacteroidaceae and Bacteroides, family and genus of Bacteroidetes phylum, the major gut microbial taxon associated with metabolic health. Specularly to the effects imposed by Acod1 deficiency on fecal microbiota, oral itaconate consumption enhances diet-induced gut dysbiosis and associated obesogenic responses in mice. Unveiling an unrecognized role of itaconate, either endogenously produced or exogenously administered, in supporting microbiota alterations underlying diet-induced obesity in mice, our study points ACOD1 as a target against inflammatory consequences of overnutrition.}, } @article {pmid38301483, year = {2024}, author = {Baldanzi, G and Sayols-Baixeras, S and Ekblom-Bak, E and Ekblom, Ö and Dekkers, KF and Hammar, U and Nguyen, D and Ahmad, S and Ericson, U and Arvidsson, D and Börjesson, M and Johanson, PJ and Smith, JG and Bergström, G and Lind, L and Engström, G and Ärnlöv, J and Kennedy, B and Orho-Melander, M and Fall, T}, title = {Accelerometer-based physical activity is associated with the gut microbiota in 8416 individuals in SCAPIS.}, journal = {EBioMedicine}, volume = {100}, number = {}, pages = {104989}, doi = {10.1016/j.ebiom.2024.104989}, pmid = {38301483}, issn = {2352-3964}, abstract = {BACKGROUND: Previous population-based studies investigating the relationship between physical activity and the gut microbiota have relied on self-reported activity, prone to reporting bias. Here, we investigated the associations of accelerometer-based sedentary (SED), moderate-intensity (MPA), and vigorous-intensity (VPA) physical activity with the gut microbiota using cross-sectional data from the Swedish CArdioPulmonary bioImage Study.

METHODS: In 8416 participants aged 50-65, time in SED, MPA, and VPA were estimated with hip-worn accelerometer. Gut microbiota was profiled using shotgun metagenomics of faecal samples. We applied multivariable regression models, adjusting for sociodemographic, lifestyle, and technical covariates, and accounted for multiple testing.

FINDINGS: Overall, associations between time in SED and microbiota species abundance were in opposite direction to those for MPA or VPA. For example, MPA was associated with lower, while SED with higher abundance of Escherichia coli. MPA and VPA were associated with higher abundance of the butyrate-producers Faecalibacterium prausnitzii and Roseburia spp. We observed discrepancies between specific VPA and MPA associations, such as a positive association between MPA and Prevotella copri, while no association was detected for VPA. Additionally, SED, MPA and VPA were associated with the functional potential of the microbiome. For instance, MPA was associated with higher capacity for acetate synthesis and SED with lower carbohydrate degradation capacity.

INTERPRETATION: Our findings suggest that sedentary and physical activity are associated with a similar set of gut microbiota species but in opposite directions. Furthermore, the intensity of physical activity may have specific effects on certain gut microbiota species.

FUNDING: European Research Council, Swedish Heart-Lung Foundation, Swedish Research Council, Knut and Alice Wallenberg Foundation.}, } @article {pmid38301118, year = {2024}, author = {Hessler, T and Harrison, STL and Banfield, JF and Huddy, RJ}, title = {Harnessing Fermentation May Enhance the Performance of Biological Sulfate-Reducing Bioreactors.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c04187}, pmid = {38301118}, issn = {1520-5851}, abstract = {Biological sulfate reduction (BSR) represents a promising strategy for bioremediation of sulfate-rich waste streams, yet the impact of metabolic interactions on performance is largely unexplored. Here, genome-resolved metagenomics was used to characterize 17 microbial communities in reactors treating synthetic sulfate-contaminated solutions. Reactors were supplemented with lactate or acetate and a small amount of fermentable substrate. Of the 163 genomes representing all the abundant bacteria, 130 encode 321 NiFe and FeFe hydrogenases and all genomes of the 22 sulfate-reducing microorganisms (SRM) encode genes for H2 uptake. We observed lactate oxidation solely in the first packed bed reactor zone, with propionate and acetate oxidation in the middle and predominantly acetate oxidation in the effluent zone. The energetics of these reactions are very different, yet sulfate reduction kinetics were unaffected by the type of electron donor available. We hypothesize that the comparable rates, despite the typically slow growth of SRM on acetate, are a result of the consumption of H2 generated by fermentation. This is supported by the sustained performance of a predominantly acetate-supplemented stirred tank reactor dominated by diverse fermentative bacteria encoding FeFe hydrogenase genes and SRM capable of acetate and hydrogen consumption and CO2 assimilation. Thus, addition of fermentable substrates to stimulate syntrophic relationships may improve the performance of BSR reactors supplemented with inexpensive acetate.}, } @article {pmid38300968, year = {2024}, author = {Cisneros-Martínez, AM and Rodriguez-Cruz, UE and Alcaraz, LD and Becerra, A and Eguiarte, LE and Souza, V}, title = {Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Ciénegas Basin, Mexico.}, journal = {PloS one}, volume = {19}, number = {2}, pages = {e0291402}, doi = {10.1371/journal.pone.0291402}, pmid = {38300968}, issn = {1932-6203}, abstract = {Due to the enormous diversity of non-culturable viruses, new viruses must be characterized using culture-independent techniques. The associated host is an important phenotypic feature that can be inferred from metagenomic viral contigs thanks to the development of several bioinformatic tools. Here, we compare the performance of recently developed virus-host prediction tools on a dataset of 1,046 virus-host pairs and then apply the best-performing tools to a metagenomic dataset derived from a highly diverse transiently hypersaline site known as the Archaean Domes (AD) within the Cuatro Ciénegas Basin, Coahuila, Mexico. Among host-dependent methods, alignment-based approaches had a precision of 66.07% and a sensitivity of 24.76%, while alignment-free methods had an average precision of 75.7% and a sensitivity of 57.5%. RaFAH, a virus-dependent alignment-based tool, had the best overall performance (F1_score = 95.7%). However, when predicting the host of AD viruses, methods based on public reference databases (such as RaFAH) showed lower inter-method agreement than host-dependent methods run against custom databases constructed from prokaryotes inhabiting AD. Methods based on custom databases also showed the greatest agreement between the source environment and the predicted host taxonomy, habitat, lifestyle, or metabolism. This highlights the value of including custom data when predicting hosts on a highly diverse metagenomic dataset, and suggests that using a combination of methods and qualitative validations related to the source environment and predicted host biology can increase the number of correct predictions. Finally, these predictions suggest that AD viruses infect halophilic archaea as well as a variety of bacteria that may be halophilic, halotolerant, alkaliphilic, thermophilic, oligotrophic, sulfate-reducing, or marine, which is consistent with the specific environment and the known geological and biological evolution of the Cuatro Ciénegas Basin and its microorganisms.}, } @article {pmid38299854, year = {2024}, author = {Podar, NA and Carrell, AA and Cassidy, KA and Klingeman, DM and Yang, Z and Stahler, EA and Smith, DW and Stahler, DR and Podar, M}, title = {From wolves to humans: oral microbiome resistance to transfer across mammalian hosts.}, journal = {mBio}, volume = {}, number = {}, pages = {e0334223}, doi = {10.1128/mbio.03342-23}, pmid = {38299854}, issn = {2150-7511}, abstract = {The mammalian mouth is colonized by complex microbial communities, adapted to specific niches, and in homeostasis with the host. Individual microbes interact metabolically and rely primarily on nutrients provided by the host, with which they have potentially co-evolved along the mammalian lineages. The oral environment is similar across mammals, but the diversity, specificity, and evolution of community structure in related or interacting mammals are little understood. Here, we compared the oral microbiomes of dogs with those of wild wolves and humans. In dogs, we found an increased microbial diversity relative to wolves, possibly related to the transition to omnivorous nutrition following domestication. This includes a larger diversity of Patescibacteria than previously reported in any other oral microbiota. The oral microbes are most distinct at bacterial species or strain levels, with few if any shared between humans and canids, while the close evolutionary relationship between wolves and dogs is reflected by numerous shared taxa. More taxa are shared at higher taxonomic levels including with humans, supporting their more ancestral common mammalian colonization followed by diversification. Phylogenies of selected oral bacterial lineages do not support stable human-dog microbial transfers but suggest diversification along mammalian lineages (apes and canids). Therefore, despite millennia of cohabitation and close interaction, the host and its native community controls and limits the assimilation of new microbes, even if closely related. Higher resolution metagenomic and microbial physiological studies, covering a larger mammalian diversity, should help understand how oral communities assemble, adapt, and interact with their hosts.IMPORTANCENumerous types of microbes colonize the mouth after birth and play important roles in maintaining oral health. When the microbiota-host homeostasis is perturbed, proliferation of some bacteria leads to diseases such as caries and periodontitis. Unlike the gut microbiome, the diversity of oral microbes across the mammalian evolutionary space is not understood. Our study compared the oral microbiomes of wild wolves, dogs, and apes (humans, chimpanzees, and bonobos), with the aim of identifying if microbes have been potentially exchanged between humans and dogs as a result of domestication and cohabitation. We found little if any evidence for such exchanges. The significance of our research is in finding that the oral microbiota and/or the host limit the acquisition of exogenous microbes, which is important in the context of natural exclusion of potential novel pathogens. We provide a framework for expanded higher-resolution studies across domestic and wild animals to understand resistance/resilience.}, } @article {pmid38298647, year = {2024}, author = {Jin, W and Liu, Y and Ning, Q and Wu, S and Su, S and Zheng, D and Ma, S and Zou, J and Yang, M and Hu, D and Ding, H}, title = {A case of chronic wounds caused by Sporothrix schenckii infection was rapidly detected by metagenomic next generation sequencing.}, journal = {Heliyon}, volume = {10}, number = {2}, pages = {e24420}, doi = {10.1016/j.heliyon.2024.e24420}, pmid = {38298647}, issn = {2405-8440}, abstract = {The dimorphic fungus Sporothrix schenckii is widely distributed in soil, vegetation, and decaying organic matter, and can cause sporotrichosis when the patient's skin trauma was exposed to contaminated material with Sporothrix spp. The cases of Sporothrix schenckii infection in chronic wounds are rarely reported. Here we reported a 53-year-old male construction worker who was admitted to our hospital on July 9, 2022, without underlying disease presented with a painless subcutaneous hard nodule on his right calf, which later ulcerated and oozed, with an enlarged wound and no fever during the course of the disease. His procalcitonin, C-reactive protein, erythrocyte sedimentation rate increased, and necrotic histopathology suggested chronic granulomatous inflammation. Then his necrotic tissue and pus were sent for metagenomic next generation sequencing(mNGS), the result reported Sporothrix schenckii after 43 hours, which was consistent with the result of culture after 18 days. mNGS might be more useful and valuable in diseases such as sporotrichosis where it is difficult to see the yeast cells in the tissues.}, } @article {pmid38297252, year = {2024}, author = {Vályi, P and Wirth, R and Minárovits, J and Strang, O and Maróti, G and Kovács, KL}, title = {The oral microbiome of a family including Papillon-Lefèvre-syndrome patients and clinically healthy members.}, journal = {BMC oral health}, volume = {24}, number = {1}, pages = {158}, pmid = {38297252}, issn = {1472-6831}, abstract = {AIMS: The oral microbiota composition of patients diagnosed with Papillon-Lefèvre-syndrome and treated for several years were compared to those existing in the oral cavity of the clinically healthy family members and a cohort of patients having various stages of chronic periodontitis.

MATERIALS AND METHODS: A family with two sisters affected with severe periodontitis and with the typical skin symptoms of Papillon-Lefèvre-syndrome, and symptomless parents and third sibling were investigated. The Patients received periodontal treatment for several years and their oral microbiome was analysed by amplicon sequencing. Data were evaluated by microbial cluster analysis.

RESULTS: The microbiome of the patients with Papillon-Lefèvre-syndrome was predominated with Aggregatibacter actinomycetemcomitans and associated oral periodontopathogens. Although the clinically healthy family members showed no oral disorder, their microbiome resembled that of subjects having mild periodontitis.

CONCLUSIONS: Predominance of A. actinomycetemcomitans in the subgingival microbiome of patients with Papillon-Lefèvre-syndrome suggests that specific treatment strategies directed against this pathobiont may improve the oral health status of the affected individuals.

TRIAL REGISTRATION: The study was conducted in accordance with the Declaration of Helsinki and the ethical permission has been issued by the Human Investigation Review Board of the University of Szeged, Albert Szent-Györgyi Clinical Centre (Permission No. 63/2017-SZTE). September 19, 2017.  https://u-szeged.hu/klinikaikutatas/rkeb-altal-jovahagyott/rkeb-2017 .}, } @article {pmid38296309, year = {2024}, author = {Kragsnaes, MS and Jensen, JRB and Nilsson, AC and Malik, MI and Munk, HL and Pedersen, JK and Horn, HC and Kruhøffer, M and Kristiansen, K and Mullish, BH and Marchesi, JR and Kjeldsen, J and Röttger, R and Ellingsen, T}, title = {Dynamics of inflammation-associated plasma proteins following faecal microbiota transplantation in patients with psoriatic arthritis and healthy controls: exploratory findings from the FLORA trial.}, journal = {RMD open}, volume = {10}, number = {1}, pages = {}, doi = {10.1136/rmdopen-2023-003750}, pmid = {38296309}, issn = {2056-5933}, abstract = {OBJECTIVES: The gut microbiota can mediate both pro and anti-inflammatory responses. In patients with psoriatic arthritis (PsA), we investigated the impact of faecal microbiota transplantation (FMT), relative to sham transplantation, on 92 inflammation-associated plasma proteins.

METHODS: This study relates to the FLORA trial cohort, where 31 patients with moderate-to-high peripheral PsA disease activity, despite at least 3 months of methotrexate treatment, were included in a 26-week, double-blind, randomised, sham-controlled trial. Participants were allocated to receive either one gastroscopic-guided healthy donor FMT (n=15) or sham (n=16). Patient plasma samples were collected at baseline, week 4, 12 and 26 while samples from 31 age-matched and sex-matched healthy controls (HC) were collected at baseline. Samples were analysed using proximity extension assay technology (Olink Target-96 Inflammation panel).

RESULTS: Levels of 26 proteins differed significantly between PsA and HC pre-FMT (adjusted p<0.05), of which 10 proteins were elevated in PsA: IL-6, CCL20, CCL19, CDCP1, FGF-21, HGF, interferon-γ (IFN-γ), IL-18R1, monocyte chemotactic protein 3, and IL-2. In the FMT group, levels of 12 proteins changed significantly across all timepoints (tumour necrosis factor (TNF), CDCP1, IFN-γ, TWEAK, signalling lymphocytic activation molecule (SLAMF1), CD8A, CD5, Flt3L, CCL25, FGF-23, CD6, caspase-8). Significant differences in protein levels between FMT and sham-treated patients were observed for TNF (p=0.002), IFN-γ (p=0.011), stem cell factor (p=0.024), matrix metalloproteinase-1 (p=0.038), and SLAMF1 (p=0.042). FMT had the largest positive effect on IFN-γ, Axin-1 and CCL25 and the largest negative effect on CCL19 and IL-6.

CONCLUSIONS: Patients with active PsA have a distinct immunological plasma protein signature compared with HC pre-FMT. FMT affects several of these disease markers, including sustained elevation of IFN-γ.

TRIAL REGISTRATION NUMBER: NCT03058900.}, } @article {pmid38295682, year = {2024}, author = {Klontz, EH and Solomon, IH and Turbett, SE and Lemieux, JE and Branda, JA}, title = {Cerebrospinal fluid metagenomics has greatest added value as a test for Powassan virus among patients in New England with suspected central nervous system infection.}, journal = {Diagnostic microbiology and infectious disease}, volume = {108}, number = {4}, pages = {116169}, doi = {10.1016/j.diagmicrobio.2023.116169}, pmid = {38295682}, issn = {1879-0070}, abstract = {Cerebrospinal fluid (CSF) metagenomic next generation sequencing (mNGS) can detect diverse pathogens in patients with central nervous system infection. Due to its high cost and unclear clinical utility, it is typically reserved for patients with unrevealing routine workups. A multi-center retrospective analysis of real-world CSF mNGS was performed involving orders between 2017 and 2022 at a large New England healthcare system. CSF mNGS was performed 64 times with 17 positive results (27 %). In 11/17 positive samples (65 %), the infectious agent had not been previously detected using routine methods. Arboviruses (n = 8) were the most frequently detected agents, particularly Powassan virus (n = 6). Results changed therapy in 3/64 cases (5 %). Positive results were associated with immunodeficiency (p = 0.06), especially anti-B-cell therapy (p = 0.02), and earlier sample collection (p = 0.06). The association with compromised humoral immunity was stronger in the arbovirus and Powassan virus subgroups (p = 0.001), whose constituents were older than the overall cohort and had higher mortality rates.}, } @article {pmid38295644, year = {2024}, author = {Luan, YN and Yin, Y and Guo, Z and Wang, Q and Xu, Y and Zhang, F and Xiao, Y and Liu, C}, title = {Partial nitrification-denitrification and enrichment of paracoccus induced by iron-chitosan beads addition in an intermittently-aerated activated sludge system.}, journal = {Journal of environmental management}, volume = {353}, number = {}, pages = {120189}, doi = {10.1016/j.jenvman.2024.120189}, pmid = {38295644}, issn = {1095-8630}, abstract = {Insufficient carbon source has become the main limiting factor for efficient nitrogen removal in wastewater treatment. In this study, an intermittently-aerated activated sludge system with iron-chitosan (Fe-CS) beads addition was proposed for nitrogen removal from low C/N wastewater. By adding Fe-CS beads, partial nitrification-denitrification (PND) process and significant enrichment of Paracoccus (with ability of iron reduction/ammonium oxidation/aerobic denitrification) were observed in the reactor. The accumulation rate of NO2[-]-N reached 81.9 %, and the total nitrogen removal efficiency was improved to 93.9 % by shortening the aeration time. The higher activity of ammonium oxidizing bacteria and inhibited activity of nitrite-oxidizing bacteria in Fe-CS assisted system mediated the occurrence of PND. In contrast, the traditional nitrification and denitrification process occurred in the control group. The high-throughput sequencing analysis and metagenomic results confirmed that the addition of Fe-CS induced 77.8 % and 54.9 % enrichment of Paracoccus in sludge and Fe-CS beads, respectively, while almost no enrichment was observed in control group. Furthermore, with the addition of Fe-CS beads, the expression of genes related to outer membrane porin, cytochrome c, and TCA was strengthened, thereby enhancing the electron transport of Fe(Ⅱ) (electron donor) and Fe(Ⅲ) (electron acceptor) with pollutants in the periplasm. This study provides new insights into the direct enrichment of iron-reducing bacteria and its PND performance induced by the Fe-CS bead addition. It therefore offers an appealing strategy for low C/N wastewater treatment.}, } @article {pmid38295603, year = {2024}, author = {Plum-Jensen, LE and Schramm, A and Marshall, IPG}, title = {First single-strain enrichments of Electrothrix cable bacteria, description of E. aestuarii sp. nov. and E. rattekaaiensis sp. nov., and proposal of a cable bacteria taxonomy following the rules of the SeqCode.}, journal = {Systematic and applied microbiology}, volume = {47}, number = {1}, pages = {126487}, doi = {10.1016/j.syapm.2024.126487}, pmid = {38295603}, issn = {1618-0984}, abstract = {Cable bacteria are electrically conductive, filamentous Desulfobulbaceae, which are morphologically, functionally, and phylogenetically distinct from the other members of this family. Cable bacteria have not been obtained in pure culture and were therefore previously described as candidate genera, Candidatus Electrothrix and Ca. Electronema; a representative of the latter is available as single-strain sediment enrichment. Here we present an improved workflow to obtain the first single-strain enrichments of Ca. Electrothrix and report their metagenome-assembled genomes (MAGs) and morphology. Based on these results and on previously published high-quality MAGs and morphological data of cable bacteria from both candidate genera, we propose to adopt the genus names Electrothrix and Electronema following the rules of the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), with Electrothrix communis RB[TS] and Electronema aureum GS[TS], respectively, as the nomenclatural types of the genera. Furthermore, based on average nucleotide identity (ANI) values < 95 % with any described species, we propose two of our three single-strain enrichment cultures as novel species of the genus Electrothrix, with the names E. aestuarii sp. nov. and E. rattekaaiensis sp. nov., according to the SeqCode.}, } @article {pmid38295518, year = {2024}, author = {Maddock, KJ and Burbick, CR and Cole, SD and Daniels, JB and LeCuyer, TE and Li, XZ and Loy, JD and Sanchez, S and Stenger, BLS and Diaz-Campos, D}, title = {A One Health perspective on the use of genotypic methods for antimicrobial resistance prediction.}, journal = {Journal of the American Veterinary Medical Association}, volume = {}, number = {}, pages = {1-10}, doi = {10.2460/javma.23.12.0687}, pmid = {38295518}, issn = {1943-569X}, abstract = {Antimicrobial resistance is a global One Health concern with critical implications for the health of humans, animals, and the environment. Phenotypic methods of bacterial culture and antimicrobial susceptibility testing remain the gold standards for the detection of antimicrobial resistance and appropriate patient care; however, genotypic-based methods, such as PCR, whole genome sequencing, and metagenomic sequencing, for detection of genes conferring antimicrobial resistance are increasingly available without inclusion of appropriate standards for quality or interpretation. Misleading test results may lead to inappropriate antimicrobial treatment and, in turn, poor patient outcomes and the potential for increased incidence of antimicrobial resistance. This article explores the current landscape of clinical and methodological aspects of antimicrobial susceptibility testing and genotypic antimicrobial resistance test methods. Additionally, it describes the limitations associated with employing genotypic-based test methods in the management of veterinary patients from a One Health perspective. The companion Currents in One Health by Maddock et al, AJVR, March 2024, addresses current and future needs for veterinary antimicrobial resistance research.}, } @article {pmid38297006, year = {2024}, author = {Maza-Márquez, P and Lee, MD and Bebout, BM}, title = {Community ecology and functional potential of bacteria, archaea, eukarya and viruses in Guerrero Negro microbial mat.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {2561}, pmid = {38297006}, issn = {2045-2322}, abstract = {In this study, the microbial ecology, potential environmental adaptive mechanisms, and the potential evolutionary interlinking of genes between bacterial, archaeal and viral lineages in Guerrero Negro (GN) microbial mat were investigated using metagenomic sequencing across a vertical transect at millimeter scale. The community composition based on unique genes comprised bacteria (98.01%), archaea (1.81%), eukarya (0.07%) and viruses (0.11%). A gene-focused analysis of bacteria archaea, eukarya and viruses showed a vertical partition of the community. The greatest coverages of genes of bacteria and eukarya were detected in first layers, while the highest coverages of genes of archaea and viruses were found in deeper layers. Many genes potentially related to adaptation to the local environment were detected, such as UV radiation, multidrug resistance, oxidative stress, heavy metals, salinity and desiccation. Those genes were found in bacterial, archaeal and viral lineages with 6477, 44, and 1 genes, respectively. The evolutionary histories of those genes were studied using phylogenetic analysis, showing an interlinking between domains in GN mat.}, } @article {pmid38296951, year = {2024}, author = {Bálint, B and Merényi, Z and Hegedüs, B and Grigoriev, IV and Hou, Z and Földi, C and Nagy, LG}, title = {ContScout: sensitive detection and removal of contamination from annotated genomes.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {936}, pmid = {38296951}, issn = {2041-1723}, support = {758161//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Priority Excellent Science | H2020 European Research Council (H2020 Excellent Science - European Research Council)/ ; LP2019-13/2019//Magyar Tudományos Akadémia (Hungarian Academy of Sciences)/ ; }, abstract = {Contamination of genomes is an increasingly recognized problem affecting several downstream applications, from comparative evolutionary genomics to metagenomics. Here we introduce ContScout, a precise tool for eliminating foreign sequences from annotated genomes. It achieves high specificity and sensitivity on synthetic benchmark data even when the contaminant is a closely related species, outperforms competing tools, and can distinguish horizontal gene transfer from contamination. A screen of 844 eukaryotic genomes for contamination identified bacteria as the most common source, followed by fungi and plants. Furthermore, we show that contaminants in ancestral genome reconstructions lead to erroneous early origins of genes and inflate gene loss rates, leading to a false notion of complex ancestral genomes. Taken together, we offer here a tool for sensitive removal of foreign proteins, identify and remove contaminants from diverse eukaryotic genomes and evaluate their impact on phylogenomic analyses.}, } @article {pmid38295455, year = {2024}, author = {Liu, L and Wang, H and Guo, Y and Yan, Q and Chen, J}, title = {Human-induced homogenization of microbial taxa and function in a subtropical river and its impacts on community stability.}, journal = {Water research}, volume = {252}, number = {}, pages = {121198}, doi = {10.1016/j.watres.2024.121198}, pmid = {38295455}, issn = {1879-2448}, abstract = {Combination of taxa and function can provide a more comprehensive picture on human-induced microbial homogenization. Here, we obtained 2.58 billion high-throughput sequencing reads and 479 high-quality metagenome-assembled genomes (MAGs) of planktonic microbial communities in a subtropical river for 5 years. We found the microbial taxa homogenization and functional homogenization were uncoupled. Although human activities in downstream sites significantly decreased the taxonomic diversity of non-abundant ASV communities (16S rRNA gene amplicon sequence variants), they did not significantly decrease the taxonomic diversity of abundant ASV and total observed MAG communities. However, the total observed MAG communities in downstream sites tended to homogenize into some specific taxa which encode human-activity-related functional genes, such as nutrient cycles, greenhouse gas emission, antibiotic and arsenic resistance. Those specific MAGs with high taxonomic diversity caused the weak heterogenization of total observed MAG communities in downstream sites. Moreover, functional homogenization promoted the synchrony among downstream MAGs, and these MAGs constructed some specific network modules might to synergistically execute or resist the human-activity-related functions. High synchrony also led to the tandem effects among MAGs and thus decreased community stability. Overall, our findings revealed the links of microbial taxa, functions and stability under human activity impacts, and provided a strong evidence to encourage us re-thinking biotic homogenization based on microbial taxa and their functional attributes.}, } @article {pmid38294805, year = {2024}, author = {Vasileva, SS and Yang, Y and Baker, A and Siskind, D and Gratten, J and Eyles, D}, title = {Associations of the Gut Microbiome With Treatment Resistance in Schizophrenia.}, journal = {JAMA psychiatry}, volume = {}, number = {}, pages = {}, doi = {10.1001/jamapsychiatry.2023.5371}, pmid = {38294805}, issn = {2168-6238}, abstract = {IMPORTANCE: There is growing interest in the role of gut microbiome composition in schizophrenia. However, lifestyle factors are often neglected, and few studies have investigated microbiome composition in treatment-resistant schizophrenia.

OBJECTIVE: To explore associations between the gut microbiome and schizophrenia diagnosis, treatment resistance, clozapine response, and treatment-related adverse effects while adjusting for demographic and lifestyle factors.

In this case-control study of adults aged 20 to 63 years, stool samples and data on demographic characteristics, lifestyle, and medication use were collected and gut microbiome measures obtained using shotgun metagenomics. Participants with a schizophrenia diagnosis were referred through psychiatric inpatient units and outpatient clinics. Data were collected for 4 distinct groups: control individuals without a psychiatric diagnosis (past or present), individuals with treatment-responsive schizophrenia taking nonclozapine antipsychotic medications, clozapine-responsive individuals with treatment-resistant schizophrenia, and clozapine-nonresponsive individuals with treatment-resistant schizophrenia. Participants were recruited between November 2020 and November 2021. Control individuals were recruited in parallel through posters and online advertisements and matched for age, sex, and body mass index (BMI) to the individuals with schizophrenia. Participants were excluded if taking antibiotics in the past 2 months, if unable to communicate in English or otherwise follow study instructions, were pregnant or planning to become pregnant, or had any concomitant disease or condition making them unsuited to the study per investigator assessment. Data were analyzed from January 2022 to March 2023.

MAIN OUTCOMES AND MEASURES: Omics relationship matrices, α and β diversity, and relative abundance of microbiome features.

RESULTS: Data were collected for 97 individuals (71 [74%] male; mean [SD] age, 40.4 [10.3] years; mean [SD] BMI, 32.8 [7.4], calculated as weight in kilograms divided by height in meters squared). Significant microbiome associations with schizophrenia were observed at multiple taxonomic and functional levels (eg, common species: b2, 30%; SE, 13%; adjusted P = .002) and treatment resistance (eg, common species: b2, 27%; SE, 16%; adjusted P = .03). In contrast, limited evidence was found for microbiome associations with clozapine response, constipation, or metabolic syndrome. Significantly decreased microbial richness was found in individuals with schizophrenia compared to control individuals (t95 = 4.25; P < .001; mean [SD] for control individuals, 151.8 [32.31]; mean [SD] for individuals with schizophrenia, 117.00 [36.2]; 95% CI, 18.6-51.0), which remained significant after a covariate and multiple comparison correction. However, limited evidence was found for differences in β diversity (weighted UniFrac) for schizophrenia diagnosis (permutational multivariate analysis of variance [PERMANOVA]: R2, 0.03; P = .02), treatment resistance (R2, 0.02; P = .18), or clozapine response (R2, 0.04; P = .08). Multiple differentially abundant bacterial species (19) and metabolic pathways (162) were found in individuals with schizophrenia, which were primarily associated with treatment resistance and clozapine exposure.

CONCLUSIONS AND RELEVANCE: The findings in this study are consistent with the idea that clozapine induces alterations to gut microbiome composition, although the possibility that preexisting microbiome differences contribute to treatment resistance cannot be ruled out. These findings suggest that prior reports of microbiome alterations in individuals with chronic schizophrenia may be due to medication or lifestyle factors and that future studies should incorporate these variables in their design and interpretation.}, } @article {pmid38294254, year = {2024}, author = {Brealey, JC and Kodama, M and Rasmussen, JA and Hansen, SB and Santos-Bay, L and Lecaudey, LA and Hansen, M and Fjære, E and Myrmel, LS and Madsen, L and Bernhard, A and Sveier, H and Kristiansen, K and Gilbert, MTP and Martin, MD and Limborg, MT}, title = {Host-gut microbiota interactions shape parasite infections in farmed Atlantic salmon.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0104323}, doi = {10.1128/msystems.01043-23}, pmid = {38294254}, issn = {2379-5077}, abstract = {Animals and their associated microbiota share long evolutionary histories. However, it is not always clear how host genotype and microbiota interact to affect phenotype. We applied a hologenomic approach to explore how host-microbiota interactions shape lifetime growth and parasite infection in farmed Atlantic salmon (Salmo salar). Multi-omics data sets were generated from the guts of 460 salmon, 82% of which were naturally infected with an intestinal cestode. A single Mycoplasma bacterial strain, MAG01, dominated the gut metagenome of large, non-parasitized fish, consistent with previous studies showing high levels of Mycoplasma in the gut microbiota of healthy salmon. While small and/or parasitized salmon also had high abundance of MAG01, we observed increased alpha diversity in these individuals, driven by increased frequency of low-abundance Vibrionaceae and other Mycoplasma species that carried known virulence genes. Colonization by one of these cestode-associated Mycoplasma strains was associated with host individual genomic variation in long non-coding RNAs. Integrating the multi-omic data sets revealed coordinated changes in the salmon gut mRNA transcriptome and metabolome that correlated with shifts in the microbiota of smaller, parasitized fish. Our results suggest that the gut microbiota of small and/or parasitized fish is in a state of dysbiosis that partly depends on the host genotype, highlighting the value of using a hologenomic approach to incorporate the microbiota into the study of host-parasite dynamics.IMPORTANCEStudying host-microbiota interactions through the perspective of the hologenome is gaining interest across all life sciences. Intestinal parasite infections are a huge burden on human and animal health; however, there are few studies investigating the role of the hologenome during parasite infections. We address this gap in the largest multi-omics fish microbiota study to date using natural cestode infection of farmed Atlantic salmon. We find a clear association between cestode infection, salmon lifetime growth, and perturbation of the salmon gut microbiota. Furthermore, we provide the first evidence that the genetic background of the host may partly determine how the gut microbiota changes during parasite-associated dysbiosis. Our study therefore highlights the value of a hologenomic approach for gaining a more in-depth understanding of parasitism.}, } @article {pmid38294252, year = {2024}, author = {Argentini, C and Lugli, GA and Tarracchini, C and Fontana, F and Mancabelli, L and Viappiani, A and Anzalone, R and Angelini, L and Alessandri, G and Bianchi, MG and Taurino, G and Bussolati, O and Milani, C and van Sinderen, D and Turroni, F and Ventura, M}, title = {Ecology- and genome-based identification of the Bifidobacterium adolescentis prototype of the healthy human gut microbiota.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0201423}, doi = {10.1128/aem.02014-23}, pmid = {38294252}, issn = {1098-5336}, abstract = {Bifidobacteria are among the first microbial colonizers of the human gut, being frequently associated with human health-promoting activities. In the current study, an in silico methodology based on an ecological and phylogenomic-driven approach allowed the selection of a Bifidobacterium adolescentis prototype strain, i.e., B. adolescentis PRL2023, which best represents the overall genetic content and functional features of the B. adolescentis taxon. Such features were confirmed by in vitro experiments aimed at evaluating the ability of this strain to survive in the gastrointestinal tract of the host and its ability to interact with human intestinal cells and other microbial gut commensals. In this context, co-cultivation of B. adolescentis PRL2023 and several gut commensals revealed various microbe-microbe interactions and indicated co-metabolism of particular plant-derived glycans, such as xylan.IMPORTANCEThe use of appropriate bacterial strains in experimental research becomes imperative in order to investigate bacterial behavior while mimicking the natural environment. In the current study, through in silico and in vitro methodologies, we were able to identify the most representative strain of the Bifidobacterium adolescentis species. The ability of this strain, B. adolescentis PRL2023, to cope with the environmental challenges imposed by the gastrointestinal tract, together with its ability to switch its carbohydrate metabolism to compete with other gut microorganisms, makes it an ideal choice as a B. adolescentis prototype and a member of the healthy microbiota of adults. This strain possesses a genetic blueprint appropriate for its exploitation as a candidate for next-generation probiotics.}, } @article {pmid38294243, year = {2024}, author = {Omondi, VO and Bosire, GO and Onyari, JM and Kibet, C and Mwasya, S and Onyonyi, VN and Getahun, MN}, title = {Multi-omics analyses reveal rumen microbes and secondary metabolites that are unique to livestock species.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0122823}, doi = {10.1128/msystems.01228-23}, pmid = {38294243}, issn = {2379-5077}, abstract = {Ruminant livestock, including cattle, sheep, goats, and camels, possess a distinctive digestive system with complex microbiota communities critical for feed conversion and secondary metabolite production, including greenhouse gases. Yet, there is limited knowledge regarding the diversity of rumen microbes and metabolites benefiting livestock physiology, productivity, climate impact, and defense mechanisms across ruminant species. In this study, we utilized metataxonomics and metabolomics data from four evolutionarily distinct livestock species, which had fed on diverse plant materials like grass, shrubs, and acacia trees, to uncover the unique signature microbes and secondary metabolites. We established the presence of a distinctive anaerobic fungus called Oontomyces in camels, while cattle exhibited a higher prevalence of unique microbes like Psychrobacter, Anaeromyces, Cyllamyces, and Orpinomyces. Goats hosted Cleistothelebolus, and Liebetanzomyces was unique to sheep. Furthermore, we identified a set of conserved core microbes, including Prevotella, Rickenellaceae, Cladosporium, and Pecoramyces, present in all the ruminants, irrespective of host genetics and dietary composition. This underscores their indispensable role in maintaining crucial physiological functions. Regarding secondary metabolites, camel's rumen is rich in organic acids, goat's rumen is rich in alcohols and hydrocarbons, sheep's rumen is rich in indoles, and cattle's rumen is rich in sesquiterpenes. Additionally, linalool propionate and terpinolene were uniquely found in sheep rumen, while valencene was exclusive to cattle. This may suggest the existence of species-specific microbes and metabolites that require host rumen-microbes' environment balance. These results have implications for manipulating the rumen environment to target specific microbes and secondary metabolite networks, thereby enhancing livestock productivity, resilience, reducing susceptibility to vectors, and environmentally preferred livestock husbandry.IMPORTANCERumen fermentation, which depends on feed components and rumen microbes, plays a crucial role in feed conversion and the production of various metabolites important for the physiological functions, health, and environmental smartness of ruminant livestock, in addition to providing food for humans. However, given the complexity and variation of the rumen ecosystem and feed of these various livestock species, combined with inter-individual differences between gut microbial communities, how they influence the rumen secondary metabolites remains elusive. Using metagenomics and metabolomics approaches, we show that each livestock species has a signature microbe(s) and secondary metabolites. These findings may contribute toward understanding the rumen ecosystem, microbiome and metabolite networks, which may provide a gateway to manipulating rumen ecosystem pathways toward making livestock production efficient, sustainable, and environmentally friendly.}, } @article {pmid38294222, year = {2024}, author = {Fu, Y and Gu, J and Chen, L-J and Xiong, M and Zhao, J and Xiao, X and Zhou, J and Li, Z and Li, Y}, title = {A prospective study of nanopore-targeted sequencing in the diagnosis of central nervous system infections.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0331723}, doi = {10.1128/spectrum.03317-23}, pmid = {38294222}, issn = {2165-0497}, abstract = {Central nervous system (CNS) infections are a leading cause of death in patients. Nanopore-targeted sequencing (NTS) has begun to be used for pathogenic microbial detection. This study aims to evaluate the ability of NTS in the detection of pathogens in cerebrospinal fluid (CSF) through a prospective study. Fifty CSF specimens collected from 50 patients with suspected CNS infections went through three methods including NTS, metagenomic next-generation sequencing (mNGS), and microbial culture in parallel. When there was an inconsistency between NTS results and the results of the mNGS, the 16S rDNA gene was amplified followed by Sanger sequencing to further verify pathogens detected by NTS. Among 50 CSF specimens, 76% were NTS-positive, which is lower than mNGS (94.0%), yet higher than microbial culture (16.0%). The overall validation rate, diagnostic accordance rate (DAR), sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) of NTS were 86.7%, 50.0%, 71.0%, 15.8%, 57.9%, and 25.0%, respectively. In the CSF total nucleated cell (TNC) number ≤10 cells/µL, DAR, specificity, and PPV were 20%, 11.1%, and 11.1%, whereas in that with CSF TNC number >10 cells/µL, DAR, sensitivity, specificity, PPV, and NPV were 57.5%, 70.0%, 20.0%, 72.4%, and 18.2%, respectively. Although NTS has a higher microbial detection rate than microbial culture, it should combine CSF TNC result to evaluate the value of NTS for the diagnosis of CNS infections.IMPORTANCEThis study aims to prospectively evaluate the ability of nanopore-targeted sequencing (NTS) in the detection of pathogens in cerebrospinal fluid (CSF). It was the first time combining mNGS and microbial culture to verify the NTS-positive results also using 16S rDNA amplification with Sanger sequencing. Although microbial culture was thought to be the gold standard for pathogens detection and diagnosis of infectious diseases, this study suggested that microbial culture of CSF is not the most appropriate way for diagnosing central nervous system (CNS) infection. NTS should be recommended to be used in CSF for diagnosing CNS infection. When evaluating the value of NTS for diagnosis of CNS infections, the results of CSF TNC should be combined, and NTS-positive result is observed to be more reliable in patients with CSF TNC level >10 cells/μL.}, } @article {pmid38293856, year = {2023}, author = {Díaz-Velis, L and Álvarez-Echeverría, F and Garrido, G}, title = {[Culture and metagenomics as bacterial identification methods in patients with diabetic foot ulcers: a systematic review].}, journal = {Revista medica de Chile}, volume = {151}, number = {2}, pages = {206-221}, doi = {10.4067/s0034-98872023000200206}, pmid = {38293856}, issn = {0717-6163}, abstract = {BACKGROUND: Diabetic foot osteomyelitis (DFO) is a serious complication of infected ulcers in a diabetic patient. The identification of the infecting microorganisms is generally by culture, which causes a bias. Recently, metagenomics has been used for microbial identification.

AIM: To systematically review the scientific literature related to DFO in the last 10 years to evaluate if culture and metagenomics are complementary.

MATERIAL AND METHODS: To carry out the systematic review, PRISMA and Rayyan were used for the selection of studies, using three databases, using the keywords diabetes, osteomyelitis, culture and microbiome. Articles in English or Spanish were included, containing information related to bacterial identification in DFO. Characteristics of the technique, patients and frequency of bacterial appearance were collected.

RESULTS: Twenty six articles were included, 19 used culture and 7 metagenomics. The patients were predominantly men (68%), with an average age of 61 years, 83% had type 2 diabetes and comorbidities, mainly vascular and neuropathy. The Families with the highest frequency of appearance using the culture technique were Enterobacteriaceae (29.3%) and Staphylococcaceae(28.3%) and with metagenomics Peptoniphilaceae (22.1%) and Staphylococcaceae (9.4%). Peptoniphilaceae were not identified in culture, although they were frequently identified by metagenomics. Methicillin- resistant Staphylococcus aureus, regularly identified by culture, was not identified using metagenomics.

CONCLUSIONS: Comparing results, there is a certain complementarity between microbiological culture and sequencing to identify bacteria present in DFO.}, } @article {pmid38293582, year = {2024}, author = {Tran, DM and Nguyen, TH}, title = {16S rRNA metagenomic dataset on endophytic bacterial community of the cashew plant (Anacardium occidentale L.) grown in Dak Lak Province of Vietnam.}, journal = {Data in brief}, volume = {52}, number = {}, pages = {110039}, doi = {10.1016/j.dib.2024.110039}, pmid = {38293582}, issn = {2352-3409}, abstract = {Vietnam is currently one of the largest producers and exporters of cashew nuts in the world. Cashew (Anacardium occidentale L.) is one of the main industrial crops cultivated in Dak Lak Province of Vietnam. Comprehending the endophytic bacteria of this plant, a new biofertilizer for sustainable cashew nut production can be progressed. In this report, the cashew root sample was collected from cashew fields in 2021 in Dak Lak. The DNeasy Powersoil kit was used to extract the genomic DNA of endophytic bacteria from the root sample. The 16S rRNA genes (V1-V9 regions) were amplified by PCR, and libraries of amplicons were prepared using the Swift amplicon 16S plus ITS panel kit. The Illumina MiSeq platform was applied to sequence amplicon libraries using 16S rRNA metagenomics. Taxonomic analyses showed that Gammaproteobacteria (38.77 %) and Alphaproteobacteria (37.76 %) were the predominant classes among the endophytic bacteria. Functional analyses revealed that biosynthesis (72.78 %) was the primary function of the endophytic bacterial community. Raw sequences (Fastq files) have been deposited in Mendeley Data [1]. The obtained data provide insight into the endophytic bacterial community of cashews cultivated in Dak Lak Province of Vietnam. The data are valuable for further developing a new biofertilizer for cashew nut production using endophytic bacteria. Ours is the first report about endophytic bacterial communities of cashews cultivated in this province as well as the Central Highlands of Vietnam.}, } @article {pmid38293554, year = {2023}, author = {Grion, BAR and Fonseca, PLC and Kato, RB and García, GJY and Vaz, ABM and Jiménez, BN and Dambolenea, AL and Garcia-Etxebarria, K and Brenig, B and Azevedo, V and Bujanda, L and Banales, JM and Góes-Neto, A}, title = {Identification of taxonomic changes in the fecal bacteriome associated with colorectal polyps and cancer: potential biomarkers for early diagnosis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1292490}, doi = {10.3389/fmicb.2023.1292490}, pmid = {38293554}, issn = {1664-302X}, abstract = {Colorectal cancer (CRC) commonly arises in individuals with premalignant colon lesions known as polyps, with both conditions being influenced by gut microbiota. Host-related factors and inherent characteristics of polyps and tumors may contribute to microbiome variability, potentially acting as confounding factors in the discovery of taxonomic biomarkers for both conditions. In this study we employed shotgun metagenomics to analyze the taxonomic diversity of bacteria present in fecal samples of 90 clinical subjects (comprising 30 CRC patients, 30 with polyps and 30 controls). Our findings revealed a decrease in taxonomic richness among individuals with polyps and CRC, with significant dissimilarities observed among the study groups. We identified significant alterations in the abundance of specific taxa associated with polyps (Streptococcaceae, Lachnoclostridium, and Ralstonia) and CRC (Lactobacillales, Clostridiaceae, Desulfovibrio, SFB, Ruminococcus, and Faecalibacterium). Clostridiaceae exhibited significantly lower abundance in the early stages of CRC. Additionally, our study revealed a positive co-occurrence among underrepresented genera in CRC, while demonstrating a negative co-occurrence between Faecalibacterium and Desulfovibrio, suggesting potential antagonistic relationships. Moreover, we observed variations in taxonomic richness and/or abundance within the polyp and CRC bacteriome linked to polyp size, tumor stage, dyslipidemia, diabetes with metformin use, sex, age, and family history of CRC. These findings provide potential new biomarkers to enhance early CRC diagnosis while also demonstrating how intrinsic host factors contribute to establishing a heterogeneous microbiome in patients with CRC and polyps.}, } @article {pmid38293370, year = {2024}, author = {Qin, F and Hu, X and Wang, X and Liu, W and Deng, Q and Zhao, Y and Li, C and Liu, C and Huang, Z and Gu, B}, title = {Utility of metagenomic Next-Generation Sequencing for simultaneously detecting pathogens and neoplasms.}, journal = {Heliyon}, volume = {10}, number = {2}, pages = {e24399}, doi = {10.1016/j.heliyon.2024.e24399}, pmid = {38293370}, issn = {2405-8440}, abstract = {OBJECTIVES: Clinicians often face the challenge of differentially diagnosing febrile patients who are suspected of infectious diseases, since the clinical manifestations of infection and cancer may overlap. A single test that can detect both pathogens and tumor could provide timely and accurate diagnostic clues to aid the treatment and management of these patients.

METHODS: We enrolled eight patients to evaluate the utility of metagenomic Next-Generation Sequencing for simultaneously detecting pathogens and neoplasms using body fluids and tissue samples. Patients were selected by the following criteria: 1) Tumor was not considered upon hospitalization, but mNGS testing indicated neoplasm; 2) Tumor was not excluded, but microbial infection was primarily suspected according to initial clinical assessment.

RESULTS: We detected potential pathogens in five patients, three of whom had progressed into critical infections. Moreover, abnormal chromosomal copy numbers were identified in all patients that indicated presence of neoplasms, which were pathologically confirmed.

CONCLUSIONS: Although copy number variations do not render a definitive cancer diagnosis, it can prompt clinicians to conduct more focused diagnostic testing for cancer, potentially saving time and cost. As a result, integrating copy number analysis with pathogen detection in mNGS may help establish rapid and accurate diagnosis for febrile patients.}, } @article {pmid38293090, year = {2024}, author = {Zhao, H and Meng, L and Hikida, H and Ogata, H}, title = {Eukaryotic genomic data uncover an extensive host range of mirusviruses.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.01.18.576163}, pmid = {38293090}, abstract = {UNLABELLED: A recent marine metagenomic study has revealed the existence of a novel group of viruses designated mirusviruses, which are proposed to form an evolutionary link between two realms of double-stranded DNA viruses, Varidnaviria and Duplodnaviria . Metagenomic data suggest that mirusviruses infect microeukaryotes in the photic layer of the ocean, but their host range remains largely unknown. In this study, we investigated the presence of mirusvirus marker genes in publicly available 1,901 eukaryotic genome assemblies, mainly derived from unicellular eukaryotes, to identify potential hosts of mirusviruses. Mirusvirus marker sequences were identified in 1,348 assemblies spanning 284 genera across eight supergroups of eukaryotes. The habitats of the putative mirusvirus hosts included not only marine but also other diverse environments. Among the major capsid protein (MCP) signals in the genome assemblies, we identified 85 sequences that showed high sequence and structural similarities to reference mirusvirus MCPs. A phylogenetic analysis of these sequences revealed their distant evolutionary relationships with the seven previously reported mirusvirus clades. Most of the scaffolds with these MCP sequences encoded multiple mirusvirus homologs, underscoring the impact of mirusviral infection on the evolution of the host genome. We also identified three circular mirusviral genomes within the genomic data of the oil producing thraustochytrid Schizochytrium sp. and the endolithic green alga Ostreobium quekettii . Overall, mirusviruses probably infect a wide spectrum of eukaryotes and are more diverse than previously reported.

HIGHLIGHTS: Mirusvirus signals detected in genomic data from eight eukaryotic supergroups.Habits of putative mirusvirus hosts not limited to marine environments.Major capsid sequences from these assemblies show new mirusviral lineages.Three circular mirusvirus genomes were identified.}, } @article {pmid38292760, year = {2024}, author = {Candeliere, F and Sola, L and Raimondi, S and Rossi, M and Amaretti, A}, title = {Good and bad dispositions between archaea and bacteria in the human gut: New insights from metagenomic survey and co-occurrence analysis.}, journal = {Synthetic and systems biotechnology}, volume = {9}, number = {1}, pages = {88-98}, doi = {10.1016/j.synbio.2023.12.007}, pmid = {38292760}, issn = {2405-805X}, abstract = {Archaea are an understudied component of the human microbiome. In this study, the gut archaeome and bacteriome of 60 healthy adults from different region were analyzed by whole-genome shotgun sequencing. Archaea were ubiquitously found in a wide range of abundances, reaching up to 7.2 %. The dominant archaeal phylum was Methanobacteriota, specifically the family Methanobacteriaceae, encompassing more than 50 % of Archaea in 50 samples. The previously underestimated Thermoplasmatota, mostly composed of Methanomassiliicoccaceae, dominated in 10 subjects (>50 %) and was present in all others except one. Halobacteriota, the sole other archaeal phylum, occurred in negligible concentration, except for two samples (4.6-4.8 %). This finding confirmed that the human gut archaeome is primarily composed of methanogenic organisms and among the known methanogenic pathway: i) hydrogenotrophic reduction of CO2 is the predominant, being the genus Methanobrevibacter and the species Methanobrevibacter smithii the most abundant in the majority of the samples; ii) the second pathway, that involved Methanomassiliicoccales, was the hydrogenotrophic reduction of methyl-compounds; iii) dismutation of acetate or methyl-compounds seemed to be absent. Co-occurrence analysis allowed to unravel correlations between Archaea and Bacteria that shapes the overall structure of the microbial community, allowing to depict a clearer picture of the human gut archaeome.}, } @article {pmid38292670, year = {2024}, author = {Qasim, S and Gul, S and Buriro, AH and Shafiq, F and Ismail, T}, title = {Biochar-based organic fertilizers: Influence on yield and concentration of antioxidants in the stigma of saffron and rhizosphere bacterial diversity of slightly saline and non-saline soils.}, journal = {Saudi journal of biological sciences}, volume = {31}, number = {3}, pages = {103922}, doi = {10.1016/j.sjbs.2023.103922}, pmid = {38292670}, issn = {1319-562X}, abstract = {Being the most expensive spice, saffron has great economic importance. This crop grows well in cold arid deserts. Salinity is one of the important limiting factors for the cultivation of this crop. However, the use of composted manured and co-composted biochar and fertilizers can play a role in attenuating the salinity stress on this crop. In this two-year field study, manures from three sources: sheep and goat (SG), cow and buffalo (FYM), and poultry (PM) farms, and their co-compost with slow-pyrolyzed wood-derived biochar (B) were used for saffron cultivation in slightly saline (electrical conductivity 1.95 dS m[-1]) and non-saline soils. Yield and concentration of antioxidants of stigma and bacterial diversity in the rhizosphere of this crop, under salinity and non-salinity conditions, were evaluated. Results revealed that in non-saline soil of first-year crops, all fertilizers decreased the yield of stigma than control by 15-49 % (P ≤ 0.05) but increased the concentration of carotenoids and total polyphenolics (P ≤ 0.05). In saline soil, no difference in yield was observed between treatments for the first-year crop; however, for the second-year crop, as compared to control, PM and FYM significantly increased yield by 41 % and 44 % respectively, whereas FYM also increased the concentration of total polyphenolics (P ≤ 0.05). The FYM fertilizer was found suitable for the yield and quality of saffron stigma for second-year crops in both soils (non-saline and saline). The observed OTUs, Chao1, Fischer, and ACE indexes based on 16 s rRNA metagenomic analysis revealed 2-4 times greater bacterial diversity in the rhizosphere soil of PM-B and SG-B treatments than in the control. Furthermore, 347 bacterial species were found in PM-B- or SG-B-amended soils absent in control treatments.}, } @article {pmid38292625, year = {2024}, author = {Liang, GF and Chao, S and Sun, Z and Zhu, KJ and Chen, Q and Jia, L and Niu, YL}, title = {Pleural empyema with endobronchial mass due to Rhodococcus equi infection after renal transplantation: A case report and review of literature.}, journal = {World journal of clinical cases}, volume = {12}, number = {1}, pages = {224-231}, doi = {10.12998/wjcc.v12.i1.224}, pmid = {38292625}, issn = {2307-8960}, abstract = {BACKGROUND: Kidney transplantation is the best option for patients with end-stage renal disease. However, the need for lifelong immunosuppression results in renal transplant recipients being susceptible to various infections. Rhodococcus equi (R. equi) is a rare opportunistic pathogen in humans, and there are limited reports of infection with R. equi in post-renal transplant recipients and no uniform standard of treatment. This article reports on the diagnosis and treatment of a renal transplant recipient infected with R. equi 21 mo postoperatively and summarizes the characteristics of infection with R. equi after renal transplantation, along with a detailed review of the literature.

CASE SUMMARY: Here, we present the case of a 25-year-old man who was infected with R. equi 21 mo after renal transplantation. Although the clinical features at the time of presentation were not specific, chest computed tomography (CT) showed a large volume of pus in the right thoracic cavity and right middle lung atelectasis, and fiberoptic bronchoscopy showed an endobronchial mass in the right middle and lower lobe orifices. Bacterial culture and metagenomic next-generation sequencing sequencing of the pus were suggestive of R. equi infection. The immunosuppressive drugs were immediately suspended and intravenous vancomycin and azithromycin were administered, along with adequate drainage of the abscess. The endobronchial mass was then resected. After the patient's clinical symptoms and chest CT presentation resolved, he was switched to intravenous ciprofloxacin and azithromycin, followed by oral ciprofloxacin and azithromycin. The patient was re-hospitalized 2 wk after discharge for recurrence of R. equi infection. He recovered after another round of adequate abscess drainage and intravenous ciprofloxacin and azithromycin.

CONCLUSION: Infection with R. equi in renal transplant recipients is rare and complex, and the clinical presentation lacks specificity. Elaborate antibiotic therapy is required, and adequate abscess drainage and surgical excision are necessary. Given the recurrent nature of R. equi, patients need to be followed-up closely.}, } @article {pmid38292428, year = {2024}, author = {Shkoporov, AN and O'Regan, O and Smith, L and Khokhlova, EV and Draper, LA and Ross, RP and Hill, C}, title = {Dynamic nature of viral and bacterial communities in human faeces.}, journal = {iScience}, volume = {27}, number = {2}, pages = {108778}, doi = {10.1016/j.isci.2023.108778}, pmid = {38292428}, issn = {2589-0042}, abstract = {Bacteriophages are a major component of the gut microbiome and are believed to play a role in establishment and stabilization of microbial communities by influencing taxonomic and functional diversity. We show that the activity of lytic and temperate phages can also significantly affect bacterial community structure in a model of extended colonic retention. Intact fresh human feces were incubated anaerobically at 37°C without homogenization and subjected to metagenomic sequencing. We observed subject-specific blooms and collapses of selected bacteriophage and bacterial populations within some individuals. Most notable were striking collapses of Prevotella populations accompanied by increases in specific bacteriophages. In a number of cases, we even observed a shift from one bacterial "enterotype" to another within 48 h. These results confirm that intact feces represents a highly dynamic ecological system and suggests that colonic retention time could have a profound effect on microbiome composition, including a significant impact by bacteriophages.}, } @article {pmid38291926, year = {2024}, author = {Danckert, NP and Freidin, MB and Smith, IG and Wells, PM and Naeini, MK and Visconti, A and Compte, R and MacGregor, A and Williams, FMK}, title = {Treatment response in rheumatoid arthritis is predicted by the microbiome: a large observational study in UK DMARD-naïve patients.}, journal = {Rheumatology (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/rheumatology/keae045}, pmid = {38291926}, issn = {1462-0332}, abstract = {OBJECTIVES: Disease-modifying antirheumatic drugs (DMARDs) are first line treatment in rheumatoid arthritis (RA). Treatment response to DMARDs is patient-specific, dose efficacy is difficult to predict and long-term results variable. The gut microbiota are known to play a pivotal role in prodromal and early-disease RA, manifested by Prevotella spp. enrichment. The clinical response to therapy may be mediated by microbiota, and large-scale studies assessing the microbiome are few. This study assessed whether microbiome signals were associated with, and predictive of, patient response to DMARD-treatment. Accurate early identification of those who will respond poorly to DMARD therapy would allow selection of alternative treatment (e.g. biologic therapy), and potentially improve patient outcome.

METHODS: A multicentre, longitudinal, observational study of stool- and saliva microbiome was performed in DMARD-naïve, newly diagnosed RA patients during introduction of DMARD treatment. Clinical data and samples were collected at baseline (n = 144) in DMARD-naïve patients and at six weeks (n = 117) and 12 weeks (n = 95) into DMARD-therapy. Samples collected (n = 365 stool, n = 365 saliva) underwent shotgun sequencing. Disease activity measures were collected at each timepoint and minimal clinically important improvement determined.

RESULTS: In total, 26 stool microbes were found to decrease in those manifesting a minimal clinically important improvement. Prevotella spp. and Streptococcus spp. were the predominant taxa to decline following six weeks and 12 weeks of DMARDs, respectively. Furthermore, baseline microbiota of DMARD-naïve patients were indicative of future response.

CONCLUSION: DMARDs appear to restore a perturbed microbiome to a eubiotic state. Moreover, microbiome status can be used to predict likelihood of patient response to DMARD.}, } @article {pmid38291480, year = {2024}, author = {Ghaly, TM and Focardi, A and Elbourne, LDH and Sutcliffe, B and Humphreys, WF and Jaschke, PR and Tetu, SG and Paulsen, IT}, title = {Exploring virus-host-environment interactions in a chemotrophic-based underground estuary.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {9}, pmid = {38291480}, issn = {2524-6372}, support = {FL140100021//Australian Resuscitation Council/ ; }, abstract = {BACKGROUND: Viruses play important roles in modulating microbial communities and influencing global biogeochemistry. There is now growing interest in characterising their ecological roles across diverse biomes. However, little is known about viral ecology in low-nutrient, chemotrophic-based environments. In such ecosystems, virus-driven manipulation of nutrient cycles might have profound impacts across trophic levels. In particular, anchialine environments, which are low-energy underground estuaries sustained by chemotrophic processes, represent ideal model systems to study novel virus-host-environment interactions.

RESULTS: Here, we employ metagenomic sequencing to investigate the viral community in Bundera Sinkhole, an anchialine ecosystem rich in endemic species supported by microbial chemosynthesis. We find that the viruses are highly novel, with less than 2% representing described viruses, and are hugely abundant, making up as much as 12% of microbial intracellular DNA. These highly abundant viruses largely infect important prokaryotic taxa that drive key metabolic processes in the sinkhole. Further, the abundance of viral auxiliary metabolic genes (AMGs) involved in nucleotide and protein synthesis was strongly correlated with declines in environmental phosphate and sulphate concentrations. These AMGs encoded key enzymes needed to produce sulphur-containing amino acids, and phosphorus metabolic enzymes involved in purine and pyrimidine nucleotide synthesis. We hypothesise that this correlation is either due to selection of these AMGs under low phosphate and sulphate concentrations, highlighting the dynamic interactions between viruses, their hosts, and the environment; or, that these AMGs are driving increased viral nucleotide and protein synthesis via manipulation of host phosphorus and sulphur metabolism, consequently driving nutrient depletion in the surrounding water.

CONCLUSION: This study represents the first metagenomic investigation of viruses in anchialine ecosystems, and provides new hypotheses and insights into virus-host-environment interactions in such 'dark', low-energy environments. This is particularly important since anchialine ecosystems are characterised by diverse endemic species, both in their microbial and faunal assemblages, which are primarily supported by microbial chemosynthesis. Thus, virus-host-environment interactions could have profound effects cascading through all trophic levels.}, } @article {pmid37821326, year = {2023}, author = {Muñoz-Tamayo, R and Davoudkhani, M and Fakih, I and Robles-Rodriguez, CE and Rubino, F and Creevey, CJ and Forano, E}, title = {Review: Towards the next-generation models of the rumen microbiome for enhancing predictive power and guiding sustainable production strategies.}, journal = {Animal : an international journal of animal bioscience}, volume = {17 Suppl 5}, number = {}, pages = {100984}, doi = {10.1016/j.animal.2023.100984}, pmid = {37821326}, issn = {1751-732X}, mesh = {Animals ; *Rumen/metabolism ; *Microbiota ; Ruminants/metabolism ; Metagenome ; Fermentation ; Methane/metabolism ; }, abstract = {The rumen ecosystem harbours a galaxy of microbes working in syntrophy to carry out a metabolic cascade of hydrolytic and fermentative reactions. This fermentation process allows ruminants to harvest nutrients from a wide range of feedstuff otherwise inaccessible to the host. The interconnection between the ruminant and its rumen microbiota shapes key animal phenotypes such as feed efficiency and methane emissions and suggests the potential of reducing methane emissions and enhancing feed conversion into animal products by manipulating the rumen microbiota. Whilst significant technological progress in omics techniques has increased our knowledge of the rumen microbiota and its genome (microbiome), translating omics knowledge into effective microbial manipulation strategies remains a great challenge. This challenge can be addressed by modelling approaches integrating causality principles and thus going beyond current correlation-based approaches applied to analyse rumen microbial genomic data. However, existing rumen models are not yet adapted to capitalise on microbial genomic information. This gap between the rumen microbiota available omics data and the way microbial metabolism is represented in the existing rumen models needs to be filled to enhance rumen understanding and produce better predictive models with capabilities for guiding nutritional strategies. To fill this gap, the integration of computational biology tools and mathematical modelling frameworks is needed to translate the information of the metabolic potential of the rumen microbes (inferred from their genomes) into a mathematical object. In this paper, we aim to discuss the potential use of two modelling approaches for the integration of microbial genomic information into dynamic models. The first modelling approach explores the theory of state observers to integrate microbial time series data into rumen fermentation models. The second approach is based on the genome-scale network reconstructions of rumen microbes. For a given microorganism, the network reconstruction produces a stoichiometry matrix of the metabolism. This matrix is the core of the so-called genome-scale metabolic models which can be exploited by a plethora of methods comprised within the constraint-based reconstruction and analysis approaches. We will discuss how these methods can be used to produce the next-generation models of the rumen microbiome.}, } @article {pmid38291301, year = {2024}, author = {Link, VM and Subramanian, P and Cheung, F and Han, KL and Stacy, A and Chi, L and Sellers, BA and Koroleva, G and Courville, AB and Mistry, S and Burns, A and Apps, R and Hall, KD and Belkaid, Y}, title = {Differential peripheral immune signatures elicited by vegan versus ketogenic diets in humans.}, journal = {Nature medicine}, volume = {}, number = {}, pages = {}, pmid = {38291301}, issn = {1546-170X}, abstract = {Nutrition has broad impacts on all physiological processes. However, how nutrition affects human immunity remains largely unknown. Here we explored the impact of a dietary intervention on both immunity and the microbiota by performing a post hoc analysis of a clinical trial in which each of the 20 participants sequentially consumed vegan or ketogenic diets for 2 weeks (NCT03878108). Using a multiomics approach including multidimensional flow cytometry, transcriptomic, proteomic, metabolomic and metagenomic datasets, we assessed the impact of each diet, and dietary switch, on host immunity and the microbiota. Our data revealed that overall, a ketogenic diet was associated with a significant upregulation of pathways and enrichment in cells associated with the adaptive immune system. In contrast, a vegan diet had a significant impact on the innate immune system, including upregulation of pathways associated with antiviral immunity. Both diets significantly and differentially impacted the microbiome and host-associated amino acid metabolism, with a strong downregulation of most microbial pathways following ketogenic diet compared with baseline and vegan diet. Despite the diversity of participants, we also observed a tightly connected network between datasets driven by compounds associated with amino acids, lipids and the immune system. Collectively, this work demonstrates that in diverse participants 2 weeks of controlled dietary intervention is sufficient to significantly and divergently impact host immunity, which could have implications for precision nutritional interventions. ClinicalTrials.gov registration: NCT03878108 .}, } @article {pmid38291208, year = {2024}, author = {Raj, A and Kumar, A and Khare, PK}, title = {The looming threat of profenofos organophosphate and microbes in action for their sustainable degradation.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38291208}, issn = {1614-7499}, support = {Grant No. 3/1/2 (10) Env/2021- NCD-II//ICMR New Delhi, India/ ; }, abstract = {Organophosphates are the most extensively used class of pesticides to deal with increasing pest diversity and produce more on limited terrestrial areas to feed the ever-expanding global population. Profenofos, an organophosphate group of non-systematic insecticides and acaricides, is used to combat aphids, cotton bollworms, tobacco budworms, beet armyworms, spider mites, and lygus bugs. Profenofos was inducted into the system as a replacement for chlorpyrifos due to its lower toxicity and half-life. It has become a significant environmental concern due to its widespread presence. It accumulates in various environmental components, contaminating food, water, and air. As a neurotoxic poison, it inhibits acetylcholinesterase receptor activity, leading to dizziness, paralysis, and pest death. It also affects other eukaryotes, such as pollinators, birds, mammals, and invertebrates, affecting ecosystem functioning. Microbes directly expose themselves to profenofos and adapt to these toxic compounds over time. Microbes use these toxic compounds as carbon and energy sources and it is a sustainable and economical method to eliminate profenofos from the environment. This article explores the studies and developments in the bioremediation of profenofos, its impact on plants, pollinators, and humans, and the policies and laws related to pesticide regulation. The goal is to raise awareness about the global threat of profenofos and the role of policymakers in managing pesticide mismanagement.}, } @article {pmid38291185, year = {2024}, author = {Liu, X and Tong, X and Zou, L and Ju, Y and Liu, M and Han, M and Lu, H and Yang, H and Wang, J and Zong, Y and Liu, W and Xu, X and Jin, X and Xiao, L and Jia, H and Guo, R and Zhang, T}, title = {A genome-wide association study reveals the relationship between human genetic variation and the nasal microbiome.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {139}, pmid = {38291185}, issn = {2399-3642}, support = {32200548//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {The nasal cavity harbors diverse microbiota that contributes to human health and respiratory diseases. However, whether and to what extent the host genome shapes the nasal microbiome remains largely unknown. Here, by dissecting the human genome and nasal metagenome data from 1401 healthy individuals, we demonstrated that the top three host genetic principal components strongly correlated with the nasal microbiota diversity and composition. The genetic association analyses identified 63 genome-wide significant loci affecting the nasal microbial taxa and functions, of which 2 loci reached study-wide significance (p < 1.7 × 10[-10]): rs73268759 within CAMK2A associated with genus Actinomyces and family Actinomycetaceae; and rs35211877 near POM121L12 with Gemella asaccharolytica. In addition to respiratory-related diseases, the associated loci are mainly implicated in cardiometabolic or neuropsychiatric diseases. Functional analysis showed the associated genes were most significantly expressed in the nasal airway epithelium tissue and enriched in the calcium signaling and hippo signaling pathway. Further observational correlation and Mendelian randomization analyses consistently suggested the causal effects of Serratia grimesii and Yokenella regensburgei on cardiometabolic biomarkers (cystine, glutamic acid, and creatine). This study suggested that the host genome plays an important role in shaping the nasal microbiome.}, } @article {pmid38290350, year = {2024}, author = {Wen, X and Chen, M and Ma, B and Xu, J and Zhu, T and Zou, Y and Liao, X and Wang, Y and Worrich, A and Wu, Y}, title = {Removal of antibiotic resistance genes during swine manure composting is strongly impaired by high levels of doxycycline residues.}, journal = {Waste management (New York, N.Y.)}, volume = {177}, number = {}, pages = {76-85}, doi = {10.1016/j.wasman.2024.01.037}, pmid = {38290350}, issn = {1879-2456}, abstract = {Antibiotic resistance genes (ARGs) are emerging pollutants that enter the farm and surrounding environment via the manure of antibiotic-treated animals. Pretreatment of livestock manure by composting decreases ARGs abundance, but how antibiotic residues affect ARGs removal efficiency remains poorly understood. Here, we explored the fate of the resistome under different doxycycline residue levels during aerobic swine manure composting. Metagenomic sequencing showed that the presence of high levels of doxycycline generally had a higher abundance of tetracycline ARGs, and their dominant host bacteria of Firmicutes, especially Clostridium and Streptococcus, also had limited elimination in composting under high levels of doxycycline stress. Moreover, high levels of doxycycline impaired the removal of the total ARGs number in finished composts, with a removal rate of 51.74 % compared to 63.70 % and 71.52 % for the control and low-level doxycycline manure, respectively. Horizontal gene transfer and strengthened correlations among the bacterial community fostered ARGs preservation at high doxycycline levels during composting. In addition, ARGs carried by both plasmids and chromosomes, such as multidrug ARGs, showed wide host characteristics and rebound during compost maturation. Compared with chromosomes, a greater variety of ARGs on plasmids suggested that the majority of ARGs were characterized by horizontal mobility during composting, and the cross-host characteristics of ARGs during composting deserve further attention. This study provided deep insight into the fate of ARGs under residual antibiotic stress during manure composting and reminded the associated risk for environmental and public health.}, } @article {pmid38290262, year = {2024}, author = {Zhang, J and Yu, X and Ding, S and Zou, Y}, title = {Lignite-steel slag constructed wetland with multi-functionality and effluent reuse.}, journal = {Journal of environmental management}, volume = {353}, number = {}, pages = {120183}, doi = {10.1016/j.jenvman.2024.120183}, pmid = {38290262}, issn = {1095-8630}, abstract = {Constructed wetlands (CWs) are widely used to treat wastewater, while innovative studies are needed to support resource conservation, enhance multi-functionality, and improve the effectiveness of effluent usage. This study assessed the potential of CW's multiple functions by combining low-rank coal (lignite) and industrial waste (steel slag) in different configurations as CW substrates. The results of scanning electron microscope (SEM), energy dispersive spectroscopy (EDS), X-ray photoelectron spectroscopy (XPS), and metagenomic sequencing showed that the experimental treatment with lignite and steel slag mixtures had the highest multi-functionality, including efficient nutrient removal and carbon sequestration, as well as hydroponic crop production. Lignite and steel slag were mixed to form lignite-steel slag particle clusters, where Ca[2+] dissolved on the surface of steel slag was combined with PO4[3-] in wastewater to form Ca3(PO4)2 precipitation for phosphorus removal. A biofilm grew on the surface of lignite in this cluster, and OH[-] released from steel slag promoted lignite to release fulvic acid, which provided a carbon source for heterotrophic microorganisms and promoted denitrification. Moreover, fulvic acid enhanced carbon sequestration in CWs by increasing the biomass of Phragmites australis. The effluent from lignite-steel slag CW increased cherry tomato yield and quality while saving N and P applications. These results provide new ideas for the "green" and economic development of CW technology.}, } @article {pmid38289284, year = {2024}, author = {Wang, H and Chen, Y and Feng, L and Lu, S and Zhu, J and Zhao, J and Zhang, H and Chen, W and Lu, W}, title = {A gut aging clock using microbiome multi-view profiles is associated with health and frail risk.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2297852}, doi = {10.1080/19490976.2023.2297852}, pmid = {38289284}, issn = {1949-0984}, abstract = {Age-related changes in the microbiome have been reported in previous studies; however, direct evidence for their association with frailty is lacking. Here, we introduce biological age based on gut microbiota (gAge), an integrated prediction model that integrates gut microbiota data from different perspectives with potential background factors for aging assessment. Simulation results show that, compared with a single model, the ensemble model can not only significantly improve the prediction accuracy, but also make full use of the data in unpaired samples. From this, we identified markers associated with age development and grouped markers into accelerated aging and mitigated aging according to their effect on the prediction. Importantly, the application of gAge to an elderly cohort with different frailty levels confirmed that gAge and its predictive residuals are closely related to the individual's health status and frailty stage, and age-related markers overlap significantly with disease and frailty characteristics. Furthermore, we applied the gAge prediction model to another independent cohort of the elderly population for aging assessment and found that gAge could effectively represent the aging population. Overall, our study explains the association between the gut microbiota and frailty, providing potential targets for the development of gut microbiota-based targeted intervention strategies for aging.}, } @article {pmid38289113, year = {2024}, author = {Abdulkadir, N and Saraiva, JP and Zhang, J and Stolte, S and Gillor, O and Harms, H and Rocha, U}, title = {Genome-centric analyses of 165 metagenomes show that mobile genetic elements are crucial for the transmission of antimicrobial resistance genes to pathogens in activated sludge and wastewater.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0291823}, doi = {10.1128/spectrum.02918-23}, pmid = {38289113}, issn = {2165-0497}, abstract = {Wastewater is considered a reservoir of antimicrobial resistance genes (ARGs), where the abundant antimicrobial-resistant bacteria and mobile genetic elements facilitate horizontal gene transfer. However, the prevalence and extent of these phenomena in different taxonomic groups that inhabit wastewater are still not fully understood. Here, we determined the presence of ARGs in metagenome-assembled genomes (MAGs) and evaluated the risks of MAG-carrying ARGs in potential human pathogens. The potential of these ARGs to be transmitted horizontally or vertically was also determined. A total of 5,916 MAGs (completeness >50%, contamination <10%) were recovered, covering 68 phyla and 279 genera. MAGs were dereplicated into 1,204 genome operational taxonomic units (gOTUs) as a proxy for species (average nucleotide identity >0.95). The dominant ARG classes detected were bacitracin, multi-drug, macrolide-lincosamide-streptogramin (MLS), glycopeptide, and aminoglycoside, and 10.26% of them were located on plasmids. The main hosts of ARGs belonged to Escherichia, Klebsiella, Acinetobacter, Gresbergeria, Mycobacterium, and Thauera. Our data showed that 253 MAGs carried virulence factor genes (VFGs) divided into 44 gOTUs, of which 45 MAGs were carriers of ARGs, indicating that potential human pathogens carried ARGs. Alarmingly, the MAG assigned as Escherichia coli contained 159 VFGs, of which 95 were located on chromosomes and 10 on plasmids. In addition to shedding light on the prevalence of ARGs in individual genomes recovered from activated sludge and wastewater, our study demonstrates a workflow that can identify antimicrobial-resistant pathogens in complex microbial communities.IMPORTANCEAntimicrobial resistance (AMR) threatens the health of humans, animals, and natural ecosystems. In our study, an analysis of 165 metagenomes from wastewater revealed antibiotic-targeted alteration, efflux, and inactivation as the most prevalent AMR mechanisms. We identified several genera correlated with multiple ARGs, including Klebsiella, Escherichia, Acinetobacter, Nitrospira, Ottowia, Pseudomonas, and Thauera, which could have significant implications for AMR transmission. The abundance of bacA, mexL, and aph(3")-I in the genomes calls for their urgent management in wastewater. Our approach could be applied to different ecosystems to assess the risk of potential pathogens containing ARGs. Our findings highlight the importance of managing AMR in wastewater and can help design measures to reduce the transmission and evolution of AMR in these systems.}, } @article {pmid38289047, year = {2024}, author = {Romani, L and Del Chierico, F and Pane, S and Ristori, MV and Pirona, I and Guarrasi, V and Cotugno, N and Bernardi, S and Lancella, L and Perno, CF and Rossi, P and Villani, A and Campana, A and Palma, P and Putignani, L and , }, title = {Exploring nasopharyngeal microbiota profile in children affected by SARS-CoV-2 infection.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0300923}, doi = {10.1128/spectrum.03009-23}, pmid = {38289047}, issn = {2165-0497}, abstract = {The relationship between COVID-19 and nasopharyngeal (NP) microbiota has been investigated mainly in the adult population. We explored the NP profile of children affected by COVID-19, compared to healthy controls (CTRLs). NP swabs of children with COVID-19, collected between March and September 2020, were investigated at the admission (T0), 72 h to 7 days (T1), and at the discharge (T2) of the patients. NP microbiota was analyzed by 16S rRNA targeted-metagenomics. Data from sequencing were investigated by QIIME 2.0 and PICRUSt 2. Multiple machine learning (ML) models were exploited to classify patients compared to CTRLs. The NP microbiota of COVID-19 patients (N = 71) was characterized by reduction of α-diversity compared to CTRLs (N = 59). The NP microbiota of COVID-19 cohort appeared significantly enriched in Streptococcus, Haemophilus, Staphylococcus, Veillonella, Enterococcus, Neisseria, Moraxella, Enterobacteriaceae, Gemella, Bacillus, and reduced in Faecalibacterium, Akkermansia, Blautia, Bifidobacterium, Ruminococcus, and Bacteroides, compared to CTRLs (FDR < 0.001). Exploiting ML models, Enterococcus, Pseudomonas, Streptococcus, Capnocytopagha, Tepidiphilus, Porphyromonas, Staphylococcus, and Veillonella resulted as NP microbiota biomarkers, in COVID-19 patients. No statistically significant differences were found comparing the NP microbiota profile of COVID-19 patients during the time-points or grouping patients on the basis of high, medium, and low viral load (VL). This evidence provides specific pathobiont signatures of the NP microbiota in pediatric COVID-19 patients, and the reduction of anaerobic protective commensals. Our data suggest that the NP microbiota may have a specific disease-related signature since infection onset without changes during disease progression, regardless of the SARS-CoV-2 VL.IMPORTANCESince the beginning of pandemic, we know that children are less susceptible to severe COVID-19 disease. A potential role of the nasopharyngeal (NP) microbiota has been hypothesized but to date, most of the studies have been focused on adults. We studied the NP microbiota modifications in children affected by SARS-CoV-2 infection showing a specific NP microbiome profile, mainly composed by pathobionts and almost missing protective anaerobic commensals. Moreover, in our study, specific microbial signatures appear since the first days of infection independently from SARS-CoV-2 viral load.}, } @article {pmid38288819, year = {2024}, author = {Lou, D and Cao, Y and Duan, H and Tan, J and Li, B and Zhou, Y and Wang, D}, title = {Characterization of a Novel Thermostable 7α-hydroxysteroid Dehydrogenase.}, journal = {Protein and peptide letters}, volume = {}, number = {}, pages = {}, doi = {10.2174/0109298665279004231229100320}, pmid = {38288819}, issn = {1875-5305}, abstract = {BACKGROUND: 7α-Hydroxysteroid dehydrogenase (7α-HSDH) plays a pivotal role in vivo in the biotransformation of secondary bile acids and has great potential in industrial biosynthesis due to its broad substrate specificity. In this study, we expressed and characterized a novel thermostable 7α-HSDH (named Sa 7α-HSDH).

METHODS: The DNA sequence was derived from the black bear gut microbiome metagenomic sequencing data, and the coding sequence of Sa 7α-HSDH was chemically synthesized. The heterologous expression of the enzyme was carried out using the pGEX-6p-1 vector. Subsequently, the activity of the purified enzyme was studied by measuring the absorbance change at 340 nm. Finally, the three-dimensional structure was predicted with AlphaFold2.

RESULTS: Coenzyme screening results confirmed it to be NAD(H) dependent. Substrate specificity test revealed that Sa 7α-HSDH could catalyze taurochenodeoxycholic acid (TCDCA) with catalytic efficiency (kcat/Km) 3.81 S-1 mM-1. The optimum temperature of Sa 7α-HSDH was measured to be 75°C, confirming that it belongs to thermophilic enzymes. Additionally, its thermostability was assessed using an accelerated stability test over 32 hours. The catalytic activity of Sa 7α-HSDH remained largely unchanged for the first 24 hours and retained over 90% of its functionality after 32 hours at 50°C. Sa 7α-HSDH exhibited maximal activity at pH 10. The effect of metal ions-K+, Na+, Mg2+ and Cu2+-on the enzymatic activity of Sa 7α-HSDH was investigated. Only Mg2+ was observed to enhance the enzyme's activity by 27% at a concentration of 300 mM. Neither K+ nor Na+ had a significant influence on activity. Only Cu2+ was found to reduce enzyme activity.

CONCLUSION: We characterized the thermostable 7α-HSDH, which provides a promising biocatalyst for bioconversion of steroids at high reaction temperatures.}, } @article {pmid38287977, year = {2023}, author = {Zhou, T and Zheng, Y and Zhang, H and Liu, Y}, title = {A case report of diagnosis of cat-scratch disease using metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1322651}, doi = {10.3389/fcimb.2023.1322651}, pmid = {38287977}, issn = {2235-2988}, abstract = {Cat-scratch disease (CSD) is an anthropozoonotic infection caused by Bartonella henselae, and it is one of the most common causes of lymph node infections in children and adolescents. B. henselae, belonging to the genus Bartonella, is a common human pathogen of human beings. CSD commonly develops as a result of cat scratches and bites or when injured skin comes into contact with cat saliva. The manifestation of CSD clinically differs for each patient based on their immune system. Individuals who have healthy immune systems generally manifest minimal clinical symptoms and do not necessitate any form of treatment. However, patients who have hypo-immunity require prompt medical attention due to the potential manifestation of severe symptoms that affect multiple systems of the body. Long latency and atypical clinical manifestations are characteristics of CSD. Bartonella isolation and identification are challenging procedures that require specialized equipment. There is no gold standard method for CSD diagnosis, and misdiagnosis and missed diagnosis rates are typically high. We present the case of a middle-aged male patient who developed fever, chills, anal distension, dizziness, and muscle pain for 10 days. The patient had a documented history of cat bites 1 month prior to the onset of symptoms. Following admission, he underwent an examination to determine superficial lymphadenopathy and hypoimmunity. Additionally, he had a fever during the disease. As the patient refused a needle biopsy of lymph nodes, metagenomic next-generation sequencing (mNGS) was employed and B. henselae was detected in the peripheral blood. The patient was diagnosed with CSD and treated with a combination of azithromycin and doxycycline. The fever symptoms were alleviated, and the patient was ultimately discharged. As a result of this case, we suggest that mNGS be used as a crucial supplementary diagnostic tool for individuals with compromised immune systems who may have CSD, especially when conventional diagnostic methods are inconclusive.}, } @article {pmid38287955, year = {2023}, author = {Hu, M and Zhou, S and Xiong, X and Wang, X and Sun, Y and Meng, Z and Hui, D and Li, J and Zhang, D and Deng, Q}, title = {Dynamics of soil microbial communities involved in carbon cycling along three successional forests in southern China.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1326057}, doi = {10.3389/fmicb.2023.1326057}, pmid = {38287955}, issn = {1664-302X}, abstract = {Dynamics of plant communities during forest succession have been received great attention in the past decades, yet information about soil microbial communities that are involved in carbon cycling remains limited. Here we investigated soil microbial community composition and carbohydrate degradation potential using metagenomic analysis and examined their influencing factors in three successional subtropical forests in southern China. Results showed that the abundances of soil bacteria and fungi increased (p ≤ 0.05 for both) with forest succession in relation to both soil and litter characteristics, whereas the bacterial diversity did not change (p > 0.05) and the fungal diversity of Shannon-Wiener index even decreased (p ≤ 0.05). The abundances of microbial carbohydrate degradation functional genes of cellulase, hemicellulase, and pectinase also increased with forest succession (p ≤ 0.05 for all). However, the chitinase gene abundance did not change with forest succession (p > 0.05) and the amylase gene abundance decreased firstly in middle-succession forest and then increased in late-succession forest. Further analysis indicated that changes of functional gene abundance in cellulase, hemicellulase, and pectinase were primarily affected by soil organic carbon, soil total nitrogen, and soil moisture, whereas the variation of amylase gene abundance was well explained by soil phosphorus and litterfall. Overall, we created a metagenome profile of soil microbes in subtropical forest succession and fostered our understanding of microbially-mediated soil carbon cycling.}, } @article {pmid38287457, year = {2024}, author = {Nweze, JE and Šustr, V and Brune, A and Angel, R}, title = {Functional similarity, despite taxonomical divergence in the millipede gut microbiota, points to a common trophic strategy.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {16}, pmid = {38287457}, issn = {2049-2618}, support = {19-24309Y//Grantová Agentura České Republiky/ ; 19-24309Y//Grantová Agentura České Republiky/ ; }, abstract = {BACKGROUND: Many arthropods rely on their gut microbiome to digest plant material, which is often low in nitrogen but high in complex polysaccharides. Detritivores, such as millipedes, live on a particularly poor diet, but the identity and nutritional contribution of their microbiome are largely unknown. In this study, the hindgut microbiota of the tropical millipede Epibolus pulchripes (large, methane emitting) and the temperate millipede Glomeris connexa (small, non-methane emitting), fed on an identical diet, were studied using comparative metagenomics and metatranscriptomics.

RESULTS: The results showed that the microbial load in E. pulchripes is much higher and more diverse than in G. connexa. The microbial communities of the two species differed significantly, with Bacteroidota dominating the hindguts of E. pulchripes and Proteobacteria (Pseudomonadota) in G. connexa. Despite equal sequencing effort, de novo assembly and binning recovered 282 metagenome-assembled genomes (MAGs) from E. pulchripes and 33 from G. connexa, including 90 novel bacterial taxa (81 in E. pulchripes and 9 in G. connexa). However, despite this taxonomic divergence, most of the functions, including carbohydrate hydrolysis, sulfate reduction, and nitrogen cycling, were common to the two species. Members of the Bacteroidota (Bacteroidetes) were the primary agents of complex carbon degradation in E. pulchripes, while members of Proteobacteria dominated in G. connexa. Members of Desulfobacterota were the potential sulfate-reducing bacteria in E. pulchripes. The capacity for dissimilatory nitrate reduction was found in Actinobacteriota (E. pulchripes) and Proteobacteria (both species), but only Proteobacteria possessed the capacity for denitrification (both species). In contrast, some functions were only found in E. pulchripes. These include reductive acetogenesis, found in members of Desulfobacterota and Firmicutes (Bacillota) in E. pulchripes. Also, diazotrophs were only found in E. pulchripes, with a few members of the Firmicutes and Proteobacteria expressing the nifH gene. Interestingly, fungal-cell-wall-degrading glycoside hydrolases (GHs) were among the most abundant carbohydrate-active enzymes (CAZymes) expressed in both millipede species, suggesting that fungal biomass plays an important role in the millipede diet.

CONCLUSIONS: Overall, these results provide detailed insights into the genomic capabilities of the microbial community in the hindgut of millipedes and shed light on the ecophysiology of these essential detritivores. Video Abstract.}, } @article {pmid38287147, year = {2024}, author = {Flamholz, ZN and Biller, SJ and Kelly, L}, title = {Large language models improve annotation of prokaryotic viral proteins.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {38287147}, issn = {2058-5276}, support = {R01HL069438//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; 1T32GM149364//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; OCE-2049004//National Science Foundation (NSF)/ ; OCE-2304066//National Science Foundation (NSF)/ ; 917971//Simons Foundation/ ; }, abstract = {Viral genomes are poorly annotated in metagenomic samples, representing an obstacle to understanding viral diversity and function. Current annotation approaches rely on alignment-based sequence homology methods, which are limited by the paucity of characterized viral proteins and divergence among viral sequences. Here we show that protein language models can capture prokaryotic viral protein function, enabling new portions of viral sequence space to be assigned biologically meaningful labels. When applied to global ocean virome data, our classifier expanded the annotated fraction of viral protein families by 29%. Among previously unannotated sequences, we highlight the identification of an integrase defining a mobile element in marine picocyanobacteria and a capsid protein that anchors globally widespread viral elements. Furthermore, improved high-level functional annotation provides a means to characterize similarities in genomic organization among diverse viral sequences. Protein language models thus enhance remote homology detection of viral proteins, serving as a useful complement to existing approaches.}, } @article {pmid38085017, year = {2024}, author = {Yang, L and Guo, Y and Yang, H and Li, S and Zhang, Y and Hao, L}, title = {Taxonomic and functional assembly cues enrich the endophytic tobacco microbiota across epiphytic compartments.}, journal = {mSphere}, volume = {9}, number = {1}, pages = {e0060723}, doi = {10.1128/msphere.00607-23}, pmid = {38085017}, issn = {2379-5042}, support = {E2DF028//Guizhou Provincial Department of Science and Technology/ ; 2017-020//Startup Funding of the Chinese Academy of Sciences/ ; 41877400//MOST | National Natural Science Foundation of China (NSFC)/ ; 2018YFC1802601//MOST | National Key Research and Development Program of China (NKPs)/ ; XDB40020300//Strategic Priority Research Program of Chinese Academy Sciences/ ; SKLEG2018911//CAS | State Key Laboratory of Environmental Geochemistry, Chinese Academy of Sciences (SKLEG)/ ; }, abstract = {The plant microbiome plays a critical role in plant growth, development, and health, with endophytes being recognized as essential members due to their close interactions with host plants. However, knowledge gaps remain in understanding the mechanisms driving the colonization and establishment of endophytic communities. To address this issue, we investigated the microbiota of tobacco roots and leaves, including both epiphytic and endophytic microorganisms. We found that Actinobacteria and Alphaproteobacteria were significantly enriched in the root endosphere. Additionally, we identified higher abundances of functional traits involved in antibiotic synthesis, plant cell wall degradation, iron metabolism, secretion systems, and nicotine degradation enzymes in the endosphere. We further studied metagenome-assembled genomes from the rhizosphere and root endosphere, revealing a greater diversity of secondary metabolites in bacteria within the root endosphere. Together, this study provides insights into the taxonomic and functional assembly cues that may contribute to shaping the endophytic plant microbiota.IMPORTANCEThe presence of diverse microorganisms within plant tissues under natural conditions is a well-established fact. However, due to the plant immune system's barrier and the unique microhabitat of the plant interior, it remains unclear what specific characteristics bacteria require to successfully colonize and thrive in the plant endosphere. Recognizing the significance of unraveling these functional features, our study focused on investigating the enriched traits in the endophytic microbiota compared to the epiphytes. Through our research, we have successfully identified the taxonomic and functional assembly cues that drive the enrichment of the endophytic microbiota across the epiphytic compartments. These findings shed new light on the intricate mechanisms of endophyte colonization, thereby deepening our understanding of plant-microbe interactions and paving the way for further advancements in microbiome manipulation.}, } @article {pmid38287146, year = {2024}, author = {Achberger, AM and Jones, R and Jamieson, J and Holmes, CP and Schubotz, F and Meyer, NR and Dekas, AE and Moriarty, S and Reeves, EP and Manthey, A and Brünjes, J and Fornari, DJ and Tivey, MK and Toner, BM and Sylvan, JB}, title = {Inactive hydrothermal vent microbial communities are important contributors to deep ocean primary productivity.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {38287146}, issn = {2058-5276}, support = {OCE 1756339//National Science Foundation (NSF)/ ; OCE 1756558//National Science Foundation (NSF)/ ; OCE 1756339//National Science Foundation (NSF)/ ; ECCS-2026822//National Science Foundation (NSF)/ ; ECCS-2026822//National Science Foundation (NSF)/ ; OCE-1949485//National Science Foundation (NSF)/ ; OCE-1756419//National Science Foundation (NSF)/ ; OCE-1756558//National Science Foundation (NSF)/ ; OCE-1756339//National Science Foundation (NSF)/ ; CRC-2020-001165//Canada Research Chairs (Chaires de recherche du Canada)/ ; EXC 2077 - 390741603//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2077 - 390741603//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EXC 2077 - 390741603//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Active hydrothermal vents are oases for productivity in the deep ocean, but the flow of dissolved substrates that fuel such abundant life ultimately ceases, leaving behind inactive mineral deposits. The rates of microbial activity on these deposits are largely unconstrained. Here we show primary production occurs on inactive hydrothermal deposits and quantify its contribution to new organic carbon production in the deep ocean. Measured incorporation of [14]C-bicarbonate shows that microbial communities on inactive deposits fix inorganic carbon at rates comparable to those on actively venting deposits. Single-cell uptake experiments and nanoscale secondary ion mass spectrometry showed chemoautotrophs comprise a large fraction (>30%) of the active microbial cells. Metagenomic and lipidomic surveys of inactive deposits further revealed that the microbial communities are dominated by Alphaproteobacteria and Gammaproteobacteria using the Calvin-Benson-Bassham pathway for carbon fixation. These findings establish inactive vent deposits as important sites for microbial activity and organic carbon production on the seafloor.}, } @article {pmid38286834, year = {2024}, author = {Wang, X and Liu, Y and Qing, C and Zeng, J and Dong, J and Xia, P}, title = {Analysis of diversity and function of epiphytic bacterial communities associated with macrophytes using a metagenomic approach.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {37}, pmid = {38286834}, issn = {1432-184X}, abstract = {Epiphytic bacteria constitute a vital component of aquatic ecosystems, pivotal in regulating elemental cycling. Despite their significance, the diversity and functions of epiphytic bacterial communities adhering to various submerged macrophytes remain largely unexplored. In this study, we employed a metagenomic approach to investigate the diversity and function of epiphytic bacterial communities associated with six submerged macrophytes: Ceratophyllum demersum, Hydrilla verticillata, Myriophyllum verticillatum, Potamogeton lucens, Stuckenia pectinata, and Najas marina. The results revealed that the predominant epiphytic bacterial species for each plant type included Pseudomonas spp., Microbacterium spp., and Stenotrophomonas rhizophila. Multiple comparisons and linear discriminant analysis effect size indicated a significant divergence in the community composition of epiphytic bacteria among the six submerged macrophytes, with 0.3-1% of species uniquely identified. Epiphytic bacterial richness associated with S. pectinata significantly differed from that of both C. demersum and H. verticillata, although no significant differences were observed in diversity and evenness. Functionally, notable variations were observed in the relative abundances of genes associated with carbon, nitrogen, and phosphorus cycling within epiphytic bacterial communities on the submerged macrophyte hosts. Among these communities, H. verticillata exhibited enrichment in genes related to the 3-hydroxypropionate bicycle and nitrogen assimilation, translocation, and denitrification. Conversely, M. verticillatum showcased enrichment in genes linked to the reductive citric acid cycle (Arnon-Buchanan cycle), reductive pentose phosphate cycle (Calvin cycle), polyphosphate degradation, and organic nitrogen metabolism. In summary, our findings offer valuable insights into the diversity and function of epiphytic bacteria on submerged macrophyte leaves, shedding light on their roles in lake ecosystems.}, } @article {pmid38286361, year = {2024}, author = {Pourafshar, S and Sharma, B and Allen, J and Hoang, M and Lee, H and Dressman, H and Tyson, CC and Mallawaarachchi, I and Kumar, P and Ma, JZ and Lin, PH and Scialla, JJ}, title = {Longitudinal Pilot Evaluation of the Gut Microbiota Comparing Patients with and without Chronic Kidney Disease.}, journal = {Journal of renal nutrition : the official journal of the Council on Renal Nutrition of the National Kidney Foundation}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.jrn.2024.01.003}, pmid = {38286361}, issn = {1532-8503}, abstract = {OBJECTIVE: The gut microbiota contributes to metabolic diseases, such as diabetes and hypertension, but is poorly characterized in chronic kidney disease (CKD).

DESIGN AND METHODS: We enrolled 24 adults within household pairs, in which at least one member had self-reported kidney disease, diabetes, or hypertension. CKD was classified based on estimated glomerular filtration rate (eGFR) <60 ml/min/1.73m[2] or urine-albumin-to-creatinine ratio (UACR) of ≥30 mg/g. Participants collected stool and dietary recalls seasonally over a year. Gut microbiota was characterized using 16s rRNA and metagenomic sequencing.

RESULTS: 10 participants had CKD (42%) with a median (IQR) eGFR of 49 (44, 54) ml/min/1.73 m[2]. By 16s rRNA sequencing, there was moderate to high intra-class correlation (ICC=0.6) for seasonal alpha diversity (Shannon index) within-individuals and modest differences by season (p<0.01). ICC was lower with metagenomics, which has resolution at the species level (ICC=0.2). There were no differences in alpha or beta diversity by CKD with either method. Among 79 genera, Frisingicoccus, Tuzzerella, Faecalitalea, and Lachnoclostridium had lower abundance in CKD, while Collinsella, Lachnospiraceae_ND3007, Veillonella, and Erysipelotrichaceae_UCG_003 were more abundant in CKD (each nominal p<0.05) using 16s rRNA sequencing. Higher Collinsella and Veillonella and lower Lachnoclostridium in CKD were also identified by metagenomics. By metagenomics, Coprococcus catus and Bacteroides stercoris were more and less abundant in CKD, respectively, at false discovery rate corrected p=0.02.

CONCLUSIONS: We identified candidate taxa in the gut microbiota associated with CKD. High ICC in individuals with modest seasonal impacts imply that follow up studies may use less frequent sampling.}, } @article {pmid38286261, year = {2024}, author = {Xiao, Z and Qin, Y and Han, L and Liu, Y and Wang, Z and Huang, Y and Ma, Y and Zou, Y}, title = {Effects of wastewater treatment plant effluent on microbial risks of pathogens and their antibiotic resistance in the receiving river.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {}, number = {}, pages = {123461}, doi = {10.1016/j.envpol.2024.123461}, pmid = {38286261}, issn = {1873-6424}, abstract = {The increase in effluent discharge from wastewater treatment plants (WWTPs) into urban rivers has raised concerns about the potential effects on pathogen risks. This study utilized metagenomic sequencing combined with flow cytometry to analyze pathogen concentrations and antibiotic resistance in a typical effluent-receiving river. Quantitative microbial risk assessment (QMRA) was employed to assess the microbial risks of pathogens. The results indicated obvious spatial-temporal differences (i.e., summer vs. winter and effluent vs. river) in microbial composition. Microcystis emerged as a crucial species contributing to these variations. Pathogen concentrations were found to be higher in the river than in the effluent, with the winter exhibiting higher concentrations compared to the summer. The effluent discharge slightly increased the pathogen concentrations in the river in summer but dramatically reduced them in winter. The combined effects of cyanobacterial bloom and high temperature were considered key factors suppressing pathogen concentrations in summer. Moreover, the prevalence of antibiotic resistance of pathogens in the river was inferior to that in the effluent, with higher levels in winter than in summer. Three high-concentration pathogens (Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa) were selected for QMRA. The results showed that the risks of pathogens exceeded the recommended threshold value. Escherichia coli posed the highest risks. And the fishing scenario posed significantly higher risks than the walking scenario. Importantly, the effluent discharge helped reduce the microbial risks in the receiving river in winter. The study contributes to the management and decision-making regarding microbial risks in the effluent-receiving river.}, } @article {pmid38285456, year = {2024}, author = {Ramachandran, PS and Okaty, BW and Riehs, M and Wapniarski, A and Hershey, D and Harb, H and Zia, M and Haas, EA and Alexandrescu, S and Sleeper, LA and Vargas, SO and Gorman, MP and Campman, S and Mena, OJ and Levert, K and Hyland, K and Goldstein, RD and Wilson, MR and Haynes, RL}, title = {Multiomic Analysis of Neuroinflammation and Occult Infection in Sudden Infant Death Syndrome.}, journal = {JAMA neurology}, volume = {}, number = {}, pages = {}, doi = {10.1001/jamaneurol.2023.5387}, pmid = {38285456}, issn = {2168-6157}, abstract = {IMPORTANCE: Antemortem infection is a risk factor for sudden infant death syndrome (SIDS)-the leading postneonatal cause of infant mortality in the developed world. Manifestations of infection and inflammation are not always apparent in clinical settings or by standard autopsy; thus, enhanced resolution approaches are needed.

OBJECTIVE: To ascertain whether a subset of SIDS cases is associated with neuroinflammation and occult infection.

In this case-control study, postmortem fluids from SIDS cases and controls collected between July 2011 and November 2018 were screened for elevated inflammatory markers, specifically cerebrospinal fluid (CSF) neopterin and CSF and serum cytokines. CSF, liver, and brain tissue from SIDS cases with elevated CSF neopterin were subjected to metagenomic next-generation sequencing (mNGS) to probe for infectious pathogens. Brainstem tissue from a subset of these cases was analyzed by single-nucleus RNA sequencing (snRNAseq) to measure cell type-specific gene expression associated with neuroinflammation and infection. All tissue and fluid analyses were performed from April 2019 to January 2023 in a pathology research laboratory. Included was autopsy material from infants dying of SIDS and age-matched controls dying of known causes.

EXPOSURES: There were no interventions or exposures.

MAIN OUTCOMES AND MEASURES: CSF neopterin levels were measured by high-performance liquid chromatography. Cytokines were measured by multiplex fluorometric assay. mNGS was performed on liver, CSF, brain, and brainstem tissue. snRNAseq was performed on brainstem tissue.

RESULTS: A cohort of 71 SIDS cases (mean [SD] age, 55.2 [11.4] postconceptional weeks; 42 male [59.2%]) and 20 controls (mean [SD] age, 63.2 [16.9] postconceptional weeks; 11 male [55.0%]) had CSF and/or serum available. CSF neopterin was screened in 64 SIDS cases and 15 controls, with no exclusions. Tissues from 6 SIDS cases were further analyzed. For CSF neopterin measures, SIDS samples were from infants with mean (SD) age of 54.5 (11.3) postconceptional weeks (38 male [59.4%]) and control samples were from infants with mean (SD) age of 61.5 (17.4) postconceptional weeks (7 male [46.7%]). A total of 6 SIDS cases (9.3%) with high CSF neopterin were identified, suggestive of neuroinflammation. mNGS detected human parechovirus 3 (HPeV3) in tissue and CSF from 1 of these 6 cases. snRNAseq of HPeV3-positive brainstem tissue (medulla) revealed dramatic enrichment of transcripts for genes with predominately inflammatory functions compared with 3 age-matched SIDS cases with normal CSF neopterin levels.

CONCLUSIONS AND RELEVANCE: Next-generation molecular tools in autopsy tissue provide novel insight into pathogens that go unrecognized by normal autopsy methodology, including in infants dying suddenly and unexpectedly.}, } @article {pmid38285123, year = {2024}, author = {Rana, S and Singh, P and Bhardwaj, T and Somvanshi, P}, title = {A Comprehensive Metagenome Study Identifies Distinct Biological Pathways in Asthma Patients: An In-Silico Approach.}, journal = {Biochemical genetics}, volume = {}, number = {}, pages = {}, pmid = {38285123}, issn = {1573-4927}, abstract = {Asthma is a multifactorial disease with phenotypes and several clinical and pathophysiological characteristics. Besides innate and adaptive immune responses, the gut microbiome generates Treg cells, mediating the allergic response to environmental factors and exposure to allergens. Because of the complexity of asthma, microbiome analysis and other precision medicine methods are now widely regarded as essential elements of efficient disease therapy. An in-silico pipeline enables the comparative taxonomic profiling of 16S rRNA metagenomic profiles of 20 asthmatic patients and 15 healthy controls utilizing QIIME2. Further, PICRUSt supports downstream gene enrichment and pathway analysis, inferring the enriched pathways in a diseased state. A significant abundance of the phylum Proteobacteria, Sutterella, and Megamonas is identified in asthma patients and a diminished genus Akkermansia. Nasal samples reveal a high relative abundance of Mycoplasma in the nasal samples. Further, differential functional profiling identifies the metabolic pathways related to cofactors and amino acids, secondary metabolism, and signaling pathways. These findings support that a combination of bacterial communities is involved in mediating the responses involved in chronic respiratory conditions like asthma by exerting their influence on various metabolic pathways.}, } @article {pmid38284378, year = {2024}, author = {Samuchiwal, S and Sahu, A and Selvaraju, K and Singh, S and Malik, A}, title = {Unveiling the azo-reductase mechanism in Pseudomonas putida for efficient decolorization of textile Reactive dyes: an in-silico study.}, journal = {Journal of biomolecular structure & dynamics}, volume = {}, number = {}, pages = {1-14}, doi = {10.1080/07391102.2024.2308768}, pmid = {38284378}, issn = {1538-0254}, abstract = {The textile industry utilizing affordable azo dyes is a high threat to aquatic life and causes environmental problems due to their toxicity. Biodegradation of azo dyes employing microbes and enzymes has proved to be an efficient method for treating industrial effluent. This study used the novel microbial consortium to decolorize reactive azo dyes (Reactive Red 120; Reactive Black 5 and Reactive Blue 13), and its azo-reductase activity was evaluated. The metagenomic analysis of the consortium identified azo-reductase-producing bacterial species. The molecular docking revealed that PpAzoR from Pseudomonas putida had the highest binding affinities for all the three dyes such as Reactive Black 5 (-9.3 kcal/mol), Reactive Blue 13 (-9.8 kcal/mol) and Reactive Red 120 (-10.7 kcal/mol). The structural rigidity and stability of the docked complex were confirmed through MD simulations evaluated across multiple descriptors from the simulation trajectories. Further, MMPBSA analysis validated the results that binding of the ligands, i.e. dye molecules Reactive Black (RB5), Reactive Blue (RB13) and Reactive Red (RR120) binding with the Azoreductase (PpAzoR) to the screened Azo-dyes was spontaneous. Based on molecular dynamics simulations for 100 ns, RR 120 showed the highest binding affinity (-411.336 ± 46.799 KJ/mol), followed by RB5 (-288.012 ± 33.371 KJ/mol). The dyes (RR120 and RB5) exhibited stable interactions with the target azoreductase (PpAzoR). The present study provides insights that PpAzoR shows the highest decolorization potency, which could be interpreted as a potential dye-degrading protein based on dye-degrading assay findings.Communicated by Ramaswamy H. Sarma.}, } @article {pmid38283887, year = {2024}, author = {Wei, H and Xiong, T and Wang, SS and Wang, BH and Du, LF and Xu, Q and Zheng, JJ and Cui, XM and Jia, N and Jiang, JF and Shi, W and Zhao, L and Cao, WC}, title = {Investigating the pathogens associated with Dermacentor nuttalli and its global distribution: A study integrating metagenomic sequencing, meta-analysis and niche modeling.}, journal = {International journal for parasitology. Parasites and wildlife}, volume = {23}, number = {}, pages = {100907}, doi = {10.1016/j.ijppaw.2024.100907}, pmid = {38283887}, issn = {2213-2244}, abstract = {Dermacentor nuttalli, a member of family Ixodidae and genus Dermacentor, is predominantly found in North Asia. It transmits various pathogens of human and animal diseases, such as Lymphocytic choriomeningitis mammarenavirus and Brucella ovis, leading to severe symptoms in patients and posing serious hazards to livestock husbandry. To profile pathogen abundances of wild D. nuttalli, metagenomic sequencing was performed of four field-collected tick samples, revealing that Rickettsia, Streptomyces, and Pseudomonas were the most abundant bacterial genera in D. nuttalli. Specifically, four nearly complete Rickettsia genomes were assembled, closely relative to Rickettsia conorii subsp. raoultii. Then, a comprehensive meta-analysis was performed to evaluate its potential threats based on detected pathogens and geographical distribution positions reported in literature, reference books, related websites, and field surveys. At least 48 pathogens were identified, including 20 species of bacteria, seven species of eukaryota, and 21 species of virus. Notably, Rickettsia conorii subsp. raoultii, Coxiella burnetii, and Brucella ovis displayed remarkably high positivity rates, which were known to cause infectious diseases in both humans and livestock. Currently, the primary distribution of D. nuttalli spans China, Mongolia, and Russia. However, an additional 14 countries in Asia and America that may also be affected by D. nuttalli were identified in our niche model, despite no previous reports of its presence in these areas. This study provides comprehensive data and analysis on the pathogens carried by D. nuttalli, along with documented and potential distribution, suggesting an emerging threat to public health and animal husbandry. Therefore, there is a need for heightened surveillance and thorough investigation of D. nuttalli.}, } @article {pmid38283642, year = {2023}, author = {Teh, HE and Pung, CK and Arasoo, VJT and Yap, PSX}, title = {A Landscape View of the Female Genital Tract Microbiome in Healthy Controls and Women With Reproductive Health Conditions Associated With Ectopic Pregnancy.}, journal = {British journal of biomedical science}, volume = {80}, number = {}, pages = {12098}, doi = {10.3389/bjbs.2023.12098}, pmid = {38283642}, issn = {2474-0896}, abstract = {Disruption of the female genital microbiome is associated with several pregnancy complications, including miscarriage, preterm onset of labour, and tubal pregnancy. Ectopic pregnancy is a known cause of maternal morbidity and mortality, but early diagnosis and treatment of ectopic pregnancy remain a challenge. Despite growing established associations between genital microbiome and female reproductive health, few studies have specifically focused on its link with ectopic pregnancy. Therefore, the current review aims to provide a comprehensive account of the female genital microbiome in healthy and fertile women compared to those in ectopic pregnancy and its associated risk factors. The microbial diversity from various sites of the female genital tract was explored for a reliable proxy of female reproductive health in sequencing-based ectopic pregnancy research. Our report confirmed the predominance of Lactobacillus in the vagina and the cervix among healthy women. The relative abundance decreased in the vaginal and cervical microbiome in the disease state. In contrast, there were inconsistent findings on the uterine microbiome across studies. Additionally, we explore a spectrum of opportunities to enhance our understanding of the female genital tract microbiome and reproductive conditions. In conclusion, this study identifies gaps within the field and emphasises the need for visionary solutions in metagenomic tools for the early detection of ectopic pregnancy and other gynaecological diseases.}, } @article {pmid38283387, year = {2024}, author = {Zheng, Y and Yang, Y and Liu, X and Liu, P and Li, X and Zhang, M and Zhou, E and Zhao, Z and Wang, X and Zhang, Y and Zheng, B and Yan, Y and Liu, Y and Xu, D and Cao, L}, title = {Accelerated corrosion of 316L stainless steel in a simulated oral environment via extracellular electron transfer and acid metabolites of subgingival microbiota.}, journal = {Bioactive materials}, volume = {35}, number = {}, pages = {56-66}, doi = {10.1016/j.bioactmat.2024.01.007}, pmid = {38283387}, issn = {2452-199X}, abstract = {316L stainless steel (SS) is widely applied as microimplant anchorage (MIA) due to its excellent mechanical properties. However, the risk that the oral microorganisms can corrode 316L SS is fully neglected. Microbiologically influenced corrosion (MIC) of 316L SS is essential to the health and safety of all patients because the accelerated corrosion caused by the oral microbiota can trigger the release of Cr and Ni ions. This study investigated the corrosion behavior and mechanism of subgingival microbiota on 316L SS by 16S rRNA and metagenome sequencing, electrochemical measurements, and surface characterization techniques. Multispecies biofilms were formed by the oral subgingival microbiota in the simulated oral anaerobic environment on 316L SS surfaces, significantly accelerating the corrosion in the form of pitting. The microbiota samples collected from the subjects differed in biofilm compositions, corrosion behaviors, and mechanisms. The oral subgingival microbiota contributed to the accelerated corrosion of 316L SS via acidic metabolites and extracellular electron transfer. Our findings provide a new insight into the underlying mechanisms of oral microbial corrosion and guide the design of oral microbial corrosion-resistant materials.}, } @article {pmid38283142, year = {2024}, author = {Skaraki, K and Pavloudi, C and Dailianis, T and Lagnel, J and Pantazidou, A and Magoulas, A and Kotoulas, G}, title = {Microbial diversity in four Mediterranean irciniid sponges.}, journal = {Biodiversity data journal}, volume = {12}, number = {}, pages = {e114809}, doi = {10.3897/BDJ.12.e114809}, pmid = {38283142}, issn = {1314-2828}, abstract = {This paper describes a dataset of microbial communities from four different sponge species: Irciniaoros (Schmidt, 1864), Irciniavariabilis (Schmidt, 1862), Sarcotragusspinosulus Schmidt, 1862 and Sarcotragusfasciculatus (Pallas, 1766). The examined sponges all belong to Demospongiae (Class); Keratosa (Subclass); Dictyoceratida (Order); Irciniidae (Family). Samples were collected by scuba diving at depths between 6-14 m from two sampling sites of rocky formations at the northern coast of Crete (Cretan Sea, eastern Mediterranean) and were subjected to metabarcoding for the V5-V6 region of the 16S rRNA gene.}, } @article {pmid38283113, year = {2024}, author = {Wu, M and Zhao, J and Liu, Z and Zhang, H}, title = {Intrathecal Injection of Polymyxin B in a Child with Meningitis Caused by Carbapenem-Resistant Pseudomonas aeruginosa: A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {249-258}, doi = {10.2147/IDR.S445416}, pmid = {38283113}, issn = {1178-6973}, abstract = {BACKGROUND: Clinically, Carbapenem-resistant Pseudomonas aeruginosa (CRPA) meningitis is extremely difficult to cure and has a high mortality rate. Intrathecal injection of polymyxins B is suggested to be an effective anti-infective means to treat intracranial infection with CRPA. However, due to the potential drug toxicity of polymyxin B in children, this regimen has rarely been reported in pediatrics.

CASE DESCRIPTION: A 5-year-old male patient diagnosed with Epstein-Barr virus-induced hemophagocytic syndrome (HPS) exhibited persistent fever for over a month despite antibacterial and chemotherapy regimens. During hospitalization, the patient presented with unconsciousness, nystagmus, and myasthenia. Cerebrospinal fluid (CSF) analysis indicated elevated leukocyte counts and protein levels. Sputum and blood cultures, as well as metagenomic next-generation sequencing (mNGS) of CSF, identified CRPA. Intravenous and intrathecal polymyxin B administration resulted in temperature normalization and amelioration of consciousness disturbances and nystagmus. Subsequent CSF analysis yielded normal results, while polymyxin B treatment exhibited no nephrotoxicity or neurotoxicity.

CONCLUSION: Intrathecal injection of polymyxin B in children with meningitis caused by CRPA is an effective treatment without remarkable adverse events.}, } @article {pmid38282730, year = {2023}, author = {Lumian, J and Grettenberger, C and Jungblut, AD and Mackey, TJ and Hawes, I and Alatorre-Acevedo, E and Sumner, DY}, title = {Genomic profiles of four novel cyanobacteria MAGs from Lake Vanda, Antarctica: insights into photosynthesis, cold tolerance, and the circadian clock.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1330602}, doi = {10.3389/fmicb.2023.1330602}, pmid = {38282730}, issn = {1664-302X}, abstract = {Cyanobacteria in polar environments face environmental challenges, including cold temperatures and extreme light seasonality with small diurnal variation, which has implications for polar circadian clocks. However, polar cyanobacteria remain underrepresented in available genomic data, and there are limited opportunities to study their genetic adaptations to these challenges. This paper presents four new Antarctic cyanobacteria metagenome-assembled genomes (MAGs) from microbial mats in Lake Vanda in the McMurdo Dry Valleys in Antarctica. The four MAGs were classified as Leptolyngbya sp. BulkMat.35, Pseudanabaenaceae cyanobacterium MP8IB2.15, Microcoleus sp. MP8IB2.171, and Leptolyngbyaceae cyanobacterium MP9P1.79. The MAGs contain 2.76 Mbp - 6.07 Mbp, and the bin completion ranges from 74.2-92.57%. Furthermore, the four cyanobacteria MAGs have average nucleotide identities (ANIs) under 90% with each other and under 77% with six existing polar cyanobacteria MAGs and genomes. This suggests that they are novel cyanobacteria and demonstrates that polar cyanobacteria genomes are underrepresented in reference databases and there is continued need for genome sequencing of polar cyanobacteria. Analyses of the four novel and six existing polar cyanobacteria MAGs and genomes demonstrate they have genes coding for various cold tolerance mechanisms and most standard circadian rhythm genes with the Leptolyngbya sp. BulkMat.35 and Leptolyngbyaceae cyanobacterium MP9P1.79 contained kaiB3, a divergent homolog of kaiB.}, } @article {pmid38282655, year = {2024}, author = {Cosier, D and Lambert, K and Batterham, M and Sanderson-Smith, M and Mansfield, KJ and Charlton, K}, title = {The INHABIT (synergIstic effect of aNtHocyAnin and proBIoTics in) Inflammatory Bowel Disease trial: a study protocol for a double-blind, randomised, controlled, multi-arm trial.}, journal = {Journal of nutritional science}, volume = {13}, number = {}, pages = {e1}, doi = {10.1017/jns.2023.113}, pmid = {38282655}, issn = {2048-6790}, abstract = {Ulcerative Colitis (UC), a type of Inflammatory Bowel Disease (IBD), is a chronic, relapsing gastrointestinal condition with increasing global prevalence. The gut microbiome profile of people living with UC differs from healthy controls and this may play a role in the pathogenesis and clinical management of UC. Probiotics have been shown to induce remission in UC; however, their impact on the gut microbiome and inflammation is less clear. Anthocyanins, a flavonoid subclass, have shown anti-inflammatory and microbiota-modulating properties; however, this evidence is largely preclinical. To explore the combined effect and clinical significance of anthocyanins and a multi-strain probiotic, a 3-month randomised controlled trial will be conducted in 100 adults with UC. Participants will be randomly assigned to one of four groups: anthocyanins (blackcurrant powder) + placebo probiotic, probiotic + placebo fruit powder, anthocyanin + probiotic, or double placebo. The primary outcome is a clinically significant change in the health-related quality-of-life measured with the Inflammatory Bowel Disease Questionnaire-32. Secondary outcomes include shotgun metagenomic sequencing of the faecal microbiota, faecal calprotectin, symptom severity, and mood and cognitive tests. This research will identify the role of adjuvant anti-inflammatory dietary treatments in adults with UC and elucidate the relationship between the gut microbiome and inflammatory biomarkers in this disease, to help identify targeted individualised microbial therapies. ANZCTR registration ACTRN12623000630617.}, } @article {pmid38282647, year = {2024}, author = {Chan, AA and Tran, PT and Lee, DJ}, title = {Quantitative Aggregation of Microbiome Sequencing Data Provides Insights into the Associations between the Skin Microbiome and Psoriasis.}, journal = {JID innovations : skin science from molecules to population health}, volume = {4}, number = {1}, pages = {100249}, doi = {10.1016/j.xjidi.2023.100249}, pmid = {38282647}, issn = {2667-0267}, abstract = {Although prior studies have reported distinct skin microbiome profiles associated with psoriasis, differences in methods and analyses limit generalizable conclusions. Individual studies have actually reported conflicting findings; for example, Propionibacterium and Staphylococcus have been significantly associated with both psoriatic lesions and healthy skin. Qualitative reviews have attempted to summarize this body of work, but there is great variability across the studies' findings and methods. To better unify these data, we created a meta-analysis of all publicly available datasets by utilizing a uniform bioinformatics pipeline and reference database to investigate associations of the skin microbiome in psoriasis. A total of 977 skin swab samples (341 lesional, 295 nonlesional, and 341 healthy) from 6 studies were analyzed. The aggregated analysis revealed a higher relative abundance of microorganisms, including Staphylococcus aureus and Corynebacterium simulans, among others, from patients with psoriasis than those from healthy swab samples; in addition, Cutibacterium acnes, Lawsonella unclassified, and S warneri were significantly higher in healthy samples. Furthermore, comparison of functional pathways predicted from 16S gene markers showed that L-ornithine biosynthesis and L-histidine biosynthesis were lower in psoriatic lesions than in healthy controls. Taken together, this meta-analysis allows for a more generalizable association between the skin microbiome and psoriasis.}, } @article {pmid38282644, year = {2024}, author = {Schauberger, C and Thamdrup, B and Lemonnier, C and Trouche, B and Poulain, J and Wincker, P and Arnaud-Haond, S and Glud, RN and Maignien, L}, title = {Metagenome-assembled genomes of deep-sea sediments: changes in microbial functional potential lag behind redox transitions.}, journal = {ISME communications}, volume = {4}, number = {1}, pages = {ycad005}, doi = {10.1093/ismeco/ycad005}, pmid = {38282644}, issn = {2730-6151}, abstract = {Hadal sediments are hotspots of microbial activity in the deep sea and exhibit strong biogeochemical gradients. But although these gradients are widely assumed to exert selective forces on hadal microbial communities, the actual relationship between biogeochemistry, functional traits, and microbial community structure remains poorly understood. We tested whether the biogeochemical conditions in hadal sediments select for microbes based on their genomic capacity for respiration and carbohydrate utilization via a metagenomic analysis of over 153 samples from the Atacama Trench region (max. depth = 8085 m). The obtained 1357 non-redundant microbial genomes were affiliated with about one-third of all known microbial phyla, with more than half belonging to unknown genera. This indicated that the capability to withstand extreme hydrostatic pressure is a phylogenetically widespread trait and that hadal sediments are inhabited by diverse microbial lineages. Although community composition changed gradually over sediment depth, these changes were not driven by selection for respiratory or carbohydrate degradation capability in the oxic and nitrogenous zones, except in the case of anammox bacteria and nitrifying archaea. However, selection based on respiration and carbohydrate degradation capacity did structure the communities of the ferruginous zone, where aerobic and nitrogen respiring microbes declined exponentially (half-life = 125-419 years) and were replaced by subsurface communities. These results highlight a delayed response of microbial community composition to selective pressure imposed by redox zonation and indicated that gradual changes in microbial composition are shaped by the high-resilience and slow growth of microbes in the seafloor.}, } @article {pmid38282030, year = {2024}, author = {Kim, C and Pongpanich, M and Porntaveetus, T}, title = {Unraveling metagenomics through long-read sequencing: a comprehensive review.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {111}, pmid = {38282030}, issn = {1479-5876}, support = {66-101//Health systems research institute/ ; N42A650229//National Research Council of Thailand/ ; DRF67_012//Faculty of Dentistry, Chulalongkorn University/ ; Meta_66_005_3200_002//Chulalongkorn University/ ; }, abstract = {The study of microbial communities has undergone significant advancements, starting from the initial use of 16S rRNA sequencing to the adoption of shotgun metagenomics. However, a new era has emerged with the advent of long-read sequencing (LRS), which offers substantial improvements over its predecessor, short-read sequencing (SRS). LRS produces reads that are several kilobases long, enabling researchers to obtain more complete and contiguous genomic information, characterize structural variations, and study epigenetic modifications. The current leaders in LRS technologies are Pacific Biotechnologies (PacBio) and Oxford Nanopore Technologies (ONT), each offering a distinct set of advantages. This review covers the workflow of long-read metagenomics sequencing, including sample preparation (sample collection, sample extraction, and library preparation), sequencing, processing (quality control, assembly, and binning), and analysis (taxonomic annotation and functional annotation). Each section provides a concise outline of the key concept of the methodology, presenting the original concept as well as how it is challenged or modified in the context of LRS. Additionally, the section introduces a range of tools that are compatible with LRS and can be utilized to execute the LRS process. This review aims to present the workflow of metagenomics, highlight the transformative impact of LRS, and provide researchers with a selection of tools suitable for this task.}, } @article {pmid38279118, year = {2024}, author = {Hanage, WP}, title = {Two decades of population genomics: will we ever agree on bacterial species?.}, journal = {BMC biology}, volume = {22}, number = {1}, pages = {20}, pmid = {38279118}, issn = {1741-7007}, mesh = {*Metagenomics ; *Bacteria/genetics ; Genomics ; Genome, Bacterial ; }, abstract = {We have never known more about the genetic variation that characterizes life on earth, which is stored in ever-growing databases, many of which are publicly accessible. Yet, an accessible database does not mean that information is readily usable or interpretable. Here, I consider how the last two decades of gene and genome sequencing have advanced our understanding specifically of pathogen variation and how the field might be revolutionized all over again — provided we are able to solve the challenges that have become evident as with the size of our databases.}, } @article {pmid38273486, year = {2024}, author = {Benham, PM and Walsh, J and Bowie, RCK}, title = {Spatial variation in population genomic responses to over a century of anthropogenic change within a tidal marsh songbird.}, journal = {Global change biology}, volume = {30}, number = {1}, pages = {e17126}, doi = {10.1111/gcb.17126}, pmid = {38273486}, issn = {1365-2486}, support = {PRFB 1812282//Division of Environmental Biology/ ; }, mesh = {Animals ; Humans ; *Wetlands ; Metagenomics ; Ecosystem ; *Sparrows/genetics ; Fresh Water ; Genetic Variation ; }, abstract = {Combating the current biodiversity crisis requires the accurate documentation of population responses to human-induced ecological change. However, our ability to pinpoint population responses to human activities is often limited to the analysis of populations studied well after the fact. Museum collections preserve a record of population responses to anthropogenic change that can provide critical baseline data on patterns of genetic diversity, connectivity, and population structure prior to the onset of human perturbation. Here, we leverage a spatially replicated time series of specimens to document population genomic responses to the destruction of nearly 90% of coastal habitats occupied by the Savannah sparrow (Passerculus sandwichensis) in California. We sequenced 219 sparrows collected from 1889 to 2017 across the state of California using an exome capture approach. Spatial-temporal analyses of genetic diversity found that the amount of habitat lost was not predictive of genetic diversity loss. Sparrow populations from southern California historically exhibited lower levels of genetic diversity and experienced the most significant temporal declines in genetic diversity. Despite experiencing the greatest levels of habitat loss, we found that genetic diversity in the San Francisco Bay area remained relatively high. This was potentially related to an observed increase in gene flow into the Bay Area from other populations. While gene flow may have minimized genetic diversity declines, we also found that immigration from inland freshwater-adapted populations into tidal marsh populations led to the erosion of divergence at loci associated with tidal marsh adaptation. Shifting patterns of gene flow through time in response to habitat loss may thus contribute to negative fitness consequences and outbreeding depression. Together, our results underscore the importance of tracing the genomic trajectories of multiple populations over time to address issues of fundamental conservation concern.}, } @article {pmid38281639, year = {2024}, author = {Sharma, A and Taubert, M and Carasscal, OMP and Lehmann, R and Ritschel, T and Totsche, KU and Lazar, CS and Küsel, K}, title = {Iron coatings on carbonate rocks shape the attached bacterial aquifer community.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170384}, doi = {10.1016/j.scitotenv.2024.170384}, pmid = {38281639}, issn = {1879-1026}, abstract = {Most studies of groundwater ecosystems target planktonic microbes, which are easily obtained via water samples. In contrast, little is known about the diversity and function of microbes adhering to rock surfaces, particularly to consolidated rocks. To investigate microbial attachment to rock surfaces, we incubated rock chips from fractured aquifers in limestone-mudstone alternations in bioreactors fed with groundwater from two wells representing oxic and anoxic conditions. Half of the chips were coated with iron oxides, representing common secondary mineralization in fractured rock. Our time-series analysis showed bacteria colonizing the chips within two days, reaching cell numbers up to 4.16 × 10[5] cells/mm[2] after 44 days. Scanning electron microscopy analyses revealed extensive colonization but no multi-layered biofilms, with chips from oxic bioreactors more densely colonized than from anoxic ones. Estimated attached-to-planktonic cell ratios yielded values of up to 10[6]: 1 and 10[3]: 1, for oxic and anoxic aquifers, respectively. We identified distinct attached and planktonic communities with an overlap between 17 % and 42 %. Oxic bioreactors were dominated by proteobacterial genera Aquabacterium and Rhodoferax, while Rheinheimera and Simplicispira were the key players of anoxic bioreactors. Motility, attachment, and biofilm formation traits were predicted in major genera based on groundwater metagenome-assembled genomes and reference genomes. Early rock colonizers appeared to be facultative autotrophs, capable of fixing CO2 to synthesize biomass and a biofilm matrix. Late colonizers were predicted to possess biofilm degrading enzymes such as beta-glucosidase, beta-galactosidase, amylases. Fe-coated chips of both bioreactors featured more potential iron reducers and oxidizers than bare rock chips. As secondary minerals can also serve as energy source, they might favor primary production and thus contribute to subsurface ecosystem services like carbon fixation. Since most subsurface microbes seem to be attached, their contribution to ecosystem services should be considered in future studies.}, } @article {pmid38281357, year = {2024}, author = {Kang, Y and Wang, J and Li, Z}, title = {Meta-analysis addressing the characterization of antibiotic resistome in global hospital wastewater.}, journal = {Journal of hazardous materials}, volume = {466}, number = {}, pages = {133577}, doi = {10.1016/j.jhazmat.2024.133577}, pmid = {38281357}, issn = {1873-3336}, abstract = {Hospital wastewater (HWW) is a significant environmental reservoir of antibiotic resistance genes (ARGs). However, currently, no comprehensive understanding exists of the antibiotic resistome in global HWW. In this study, we attempted to address this knowledge gap through an in silico reanalysis of publicly accessible global HWW metagenomic data. We reanalyzed ARGs in 338 HWW samples from 13 countries in Africa, Asia, and Europe. In total, 2420 ARG subtypes belonging to 30 ARG types were detected, dominated by multidrug, beta-lactam, and aminoglycoside resistance genes. ARG composition in Europe differed from that in Asia and Africa. Notably, the ARGs presented co-occurrence with mobile genetic elements (MGEs), metal resistance genes (MRGs), and human bacterial pathogens (HBP), indicating a potential dissemination risk of ARGs in the HWW. Multidrug resistance genes presented co-occurrence with MGEs, MRGs, and HBP, is particularly pronounced. The abundance of contigs that contained ARG, contigs that contained ARG and HBP, contigs that contained ARG and MGE, contigs that contained ARG and MRG were used for health and transmission risk assessment of antibiotic resistome and screened out 40 high risk ARGs in the global HWW. This study first provides a comprehensive characterization and risk of the antibiotic resistome in global HWW.}, } @article {pmid38281336, year = {2024}, author = {Wang, L and Wang, Z and Li, Y and Cai, W and Zou, Y and Hui, C}, title = {Deciphering solute transport, microbiota assembly patterns and metabolic functions in the hyporheic zone of an effluent-dominated river.}, journal = {Water research}, volume = {251}, number = {}, pages = {121190}, doi = {10.1016/j.watres.2024.121190}, pmid = {38281336}, issn = {1879-2448}, abstract = {We lack a clear understanding of how anthropogenic pressures, exemplified by effluent discharge from wastewater treatment plants, destabilize microbial communities in the hyporheic zone (HZ) of receiving rivers. In this study, the spatiotemporal characteristics of hydrological parameters, and the physicochemical properties of surface and subsurface water in a representative effluent-dominated river were monitored. Sequencing of 16S rRNA amplicons and metagenomes revealed the microbial community structure in the HZ of both effluent discharge area and downstream region. The keystone taxa (taxa vital in determining the composition of each microbial cluster) and the keystone functions they controlled were subsequently identified. Effluent discharge amplified the depth of the oxic/suboxic zone and the hyporheic exchange fluxes in the effluent discharge area, which was 50-120% and 40-300% higher than in the downstream region, respectively. Microbial community structure pattern analysis demonstrated an enhancement in the rate of dispersal, an increase in microbial diversity, and an improved community network complexity in the effluent discharge area. By contrast, the number of keystone taxa in the effluent discharge area was 50-70% lower than that of the downstream region, resulting in reduced community network stability and functionality. The keystone taxa controlling metabolic functions in the networks categorized to effluent discharge area were comprised of more genera related to nitrogen and sulfur cycling, e.g., Dechloromonas, Desulfobacter, Flavobacterium, Nitrosomonas, etc., highlighting a research need in monitoring species associated with nutrient element cycling in the HZ of receiving waterbodies. The results showed that the keystone taxa could contribute positively to network stability, which was negatively correlated to hyporheic exchange fluxes and redox gradients. This study provides valuable insights that will improve our understanding of how river ecosystems respond to changes in anthropogenic pressures.}, } @article {pmid38280799, year = {2024}, author = {Costales, C and Dien Bard, J}, title = {The Report Says What?: How the Medical Microbiologist can aid in the Interpretation of Next-Generation Sequencing Results.}, journal = {Clinics in laboratory medicine}, volume = {44}, number = {1}, pages = {75-84}, doi = {10.1016/j.cll.2023.10.006}, pmid = {38280799}, issn = {1557-9832}, abstract = {The applications of next-generation sequencing (NGS) in the clinical microbiology laboratory are expanding at a rapid pace. The medical microbiologist thus plays a key role in translating the results of these emerging technologies to the practicing clinician. Here we discuss the factors to consider to successfully develop standardized reporting for microbial targeted or metagenomic NGS testing in the clinical laboratory.}, } @article {pmid38280793, year = {2024}, author = {Craney, A and Miller, S}, title = {Present and Future Non-Culture-Based Diagnostics: Stewardship Potentials and Considerations.}, journal = {Clinics in laboratory medicine}, volume = {44}, number = {1}, pages = {109-122}, doi = {10.1016/j.cll.2023.10.003}, pmid = {38280793}, issn = {1557-9832}, abstract = {The medical microbiologist plays a key role in the transition from culture-based to molecular test methods for diagnosis of infectious diseases. They must understand the scientific and technical bases underlying these tests along with their associated benefits and limitations and be able to educate administrators and patient providers on their proper use. Coordination of testing practices between clinical departments and the spectrum of public health and research laboratories is essential to optimize health care delivery.}, } @article {pmid38280666, year = {2024}, author = {Breno Zampieri Lima, M and Giovana Pereira Daniel, T and Tayaná Oliveira Bitencourt, H and Carlos Junior Alcantara, L and Haddad, R and Kashima, S and Carolina Elias, M and Giovanetti, M and Coccuzzo Sampaio, S and Nanev Slavov, S}, title = {MOLECULAR FREQUENCY OF HUMAN GEMYCIRCULARVIRUS (GCYV) DNA AMONG BLOOD DONORS FROM THE BRAZILIAN AMAZON.}, journal = {Transfusion clinique et biologique : journal de la Societe francaise de transfusion sanguine}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tracli.2024.01.009}, pmid = {38280666}, issn = {1953-8022}, abstract = {It has been recently reported that genetic material of human gemycircularviruses (GCYV) can be detected by metagenomics in clinical samples. However, the potential clinical impact of these viruses is still unknown. In this study, we evaluated the molecular prevalence of GCYV DNA among asymptomatic blood donors from the city of Macapa, Amapa State, Brazilian Amazon. During 2015, plasma samples obtained from 348 asymptomatic blood donors were submitted to molecular detection of GYCV using nested-PCR. From these samples, six were found to be positive for GYCV DNA (frequency 1.7%). Positive samples were also sequenced for amplicon confirmation. Currently, there is no data regarding the impact of the GCYV DNA presence on healthy donors and transfusion medicine. Comprehensive investigations, including broader prevalence studies, are essential to assess the spread of these viruses within the human population. Moreover, it is crucial to determine any potential clinical implications of this virus, if such exist. RÉSUMÉ La métagénomique a permis récemment de découvrir que le génome de Gemycircularviruses (GCYV) pouvait être détecté dans des échantillons cliniques. Cependant, l'impact clinique potentiel de ces virus est encore inconnu. Dans cette étude, nous avons évalué la prévalence moléculaire de l'ADN appartenant aux GCYV parmi les donneurs de sang asymptomatiques de la ville de Macapa, dans l'État d'Amapa, en Amazonie brésilienne. Au cours de 2015, des échantillons de plasma obtenus auprès de 348 donneurs de sang asymptomatiques ont été soumis à la détection moléculaire du GYCV par nested-PCR. Parmi ces échantillons, 6 se sont révélés positifs pour l'ADN du GYCV (prévalence 1,7 %). Les échantillons positifs ont également été séquencés pour la confirmation des amplicons. Actuellement, il n'existe aucune donnée concernant l'impact de la présence d'ADN du GCYV chez des donneurs de sang asymptomatiques. Des recherches approfondies, et aussi des études de prévalence plus larges, sont essentielles pour évaluer la propagation de ce virus au sein de la population humaine. De plus, il est crucial de déterminer les éventuelles implications cliniques de ce virus, si elles existent.}, } @article {pmid38280535, year = {2024}, author = {Stiernborg, M and Prast-Nielsen, S and Melas, PA and Skott, M and Millischer, V and Boulund, F and Forsell, Y and Lavebratt, C}, title = {Differences in the gut microbiome of young adults with schizophrenia spectrum disorder: using machine learning to distinguish cases from controls.}, journal = {Brain, behavior, and immunity}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.bbi.2024.01.218}, pmid = {38280535}, issn = {1090-2139}, abstract = {While an association between the gut microbiome and schizophrenia spectrum disorders (SSD) has been suggested, the existing evidence is still inconclusive. To this end, we analyzed bacteria and bacterial genes in feces from 52 young adult SSD patients and 52 controls using fecal shotgun metagenomic sequencing. Compared to controls, young SSD patients were found to have significantly lower α-diversity and different β-diversity both regarding bacterial species (i.e., taxonomic diversity) and bacterial genes (i.e., functional diversity). Furthermore, the α-diversity measures 'Pielou's evenness' and 'Shannon' were significantly higher for both bacterial species, bacterial genes encoding enzymes and gut brain modules in young SSD patients on antipsychotic treatment (young SSDnnot on antipsychotics=9, young SSDn on antipsychotics=43). We also applied machine learning classifiers to distinguish between young SSD patients and healthy controls based on their gut microbiome. Results showed that taxonomic and functional data classified young SSD individuals with an accuracy of ≥ 70% and with an area under the receiver operating characteristic curve (AUROC) of ≥ 0.75. Differential abundance analysis on the most important features in the classifier models revealed that most of the species with higher abundance in young SSD patients had their natural habitat in the oral cavity. In addition, many of the modules with higher abundance in young SSD patients were amino acid biosynthesis modules. Moreover, abundance of gut-brain modules of butyrate synthesis and acetate degradation were lower in the SSD patients compared to controls. Collectively, our findings continue to support the presence of gut microbiome alterations in SSD and provide support for the use of machine learning algorithms to distinguish patients from controls based on microbiome profiles.}, } @article {pmid38280321, year = {2024}, author = {Wang, S and Zhuang, Y and Gao, L and Huang, H and Zhang, X and Jia, S and Shi, P and Zhang, XX}, title = {Deciphering the dynamics and driving mechanisms of high-risk antibiotic resistome in size-fractionated bacterial community during drinking water chlorination via metagenomic analysis.}, journal = {Journal of hazardous materials}, volume = {466}, number = {}, pages = {133572}, doi = {10.1016/j.jhazmat.2024.133572}, pmid = {38280321}, issn = {1873-3336}, abstract = {To reveal the impact of chlorination on the high-risk resistome in size-fractionated bacterial community, we employed metagenomic approaches to decipher dynamics of high-risk antibiotic resistance genes (ARGs) and driving mechanisms in the free-living and particle-associated fractions within a full-scale drinking water treatment system. Our results revealed that chlorination significantly increased the relative abundance of high-risk ARGs in the free-living fraction to 0.33 ± 0.005 copies/cell (cpc), bacitracin and chloramphenicol resistance types were major contributors. Furthermore, chlorination significantly increased the relative abundance of mobile genetic elements (MGEs) in the free-living fraction, while decreasing it in the particle-associated fraction. During chlorination, size-fractionated bacterial communities varied considerably. Multiple statistical analyses highlighted the pivotal role of the bacterial community in altering high-risk ARGs in both the free-living and particle-associated fractions, while MGEs had a more pronounced impact on high-risk ARGs in the free-living fraction. Specifically, the enrichment of pathogenic hosts, such as Comamonas and Pseudomonas, led to an increase in the abundance of high-risk ARGs. Concurrently, MGEs exhibited significant correlations with high-risk ARGs, indicating the potential of horizontal transfer of high-risk ARGs. These findings provide novel insights for mitigating antibiotic resistance risk by considering different bacterial fractions and respective risk ranks in drinking water.}, } @article {pmid38280177, year = {2024}, author = {Liberato, MV and Paixao, DAA and Tomazetto, G and Ndeh, D and Bolam, DN and Squina, FM}, title = {Discovery, structural characterization, and functional insights into a novel apiosidase from the GH140 family, isolated from a lignocellulolytic-enriched mangrove microbial community.}, journal = {Biotechnology letters}, volume = {}, number = {}, pages = {}, pmid = {38280177}, issn = {1573-6776}, support = {2022/08958-8//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 306279/2020-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, abstract = {OBJECTIVES: Apiosidases are enzymes that cleave the glycosidic bond between the monosaccharides linked to apiose, a branched chain furanose found in the cell walls of vascular plants and aquatic monocots. There is biotechnological interest in this enzyme group because apiose is the flavor-active compound of grapes, fruit juice, and wine, and the monosaccharide is found to be a plant secondary metabolite with pharmaceutical properties. However, functional and structural studies of this enzyme family are scarce. Recently, a glycoside hydrolase family member GH140 was isolated from Bacteroides thetaiotaomicron and identified as an endo-apiosidase.

RESULTS: The structural characterization and functional identification of a second GH140 family enzyme, termed MmApi, discovered through mangrove soil metagenomic approach, are described. Among the various substrates tested, MmApi exhibited activity on an apiose-containing oligosaccharide derived from the pectic polysaccharide rhamnogalacturonan-II. While the crystallographic model of MmApi was similar to the endo-apiosidase from Bacteroides thetaiotaomicron, differences in the shape of the binding sites indicated that MmApi could cleave apioses within oligosaccharides of different compositions.

CONCLUSION: This enzyme represents a novel tool for researchers interested in studying the physiology and structure of plant cell walls and developing biocatalytic strategies for drug and flavor production.}, } @article {pmid38280093, year = {2024}, author = {Jasmin, MY and Isa, NM and Kamarudin, MS and Lim, KC and Karim, M}, title = {Evaluating Bacillus flexus as bioremediators for ammonia removal in shrimp culture water and wastewater and characterizing microbial communities in shrimp pond sludge.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {38280093}, issn = {1678-4405}, abstract = {The accumulation of nitrogen compounds in shrimp farming water and effluent presents a major challenge. Ammonia is a form of nitrogen that limits shrimp growth due to its potential toxicity and effects on shrimp health and water quality. This study is aimed at identifying promising bioremediators from shrimp pond sludge to mitigate ammonia levels in both culture water and wastewater and at determining major bacterial communities in sludge using metagenomic analysis. A sludge sample was collected from a shrimp pond in Selangor, Malaysia, to isolate potential ammonia-removing bacteria. Out of 64 isolated strains, Bacillus flexus SS2 showed the highest growth in synthetic basal media (SBM) containing ammonium sulfate at a concentration of 70 mg/L as the sole nitrogen source. The strain was then incubated in SBM with varying pH levels and showed optimal growth at pH 6.5-7. After 24 h of incubation, B. flexus SS2 reduced the ammonia concentration from an initial concentration of 5 to 0.01 mg/L, indicating a 99.61% reduction rate, which was highest in SBM at pH 7. Moreover, the strain showed ammonia removal ability at concentrations ranging from 5 to 70 mg/L. Metagenomic analysis revealed that Proteobacteria was the most abundant phylum in the sludge, followed by Cyanobacteria, Actinobacteria, Chloraflexi, Firmicutes, and Campilobacterota. Bacillus flexus SS2 belongs to the Bacillota phylum and has the potential to serve as a bioremediator for removing ammonia from shrimp culture water and wastewater.}, } @article {pmid38280026, year = {2024}, author = {Otsuka, K and Isobe, J and Asai, Y and Nakano, T and Hattori, K and Ariyoshi, T and Yamashita, T and Motegi, K and Saito, A and Kohmoto, M and Hosonuma, M and Kuramasu, A and Baba, Y and Murayama, M and Narikawa, Y and Toyoda, H and Funayama, E and Tajima, K and Shida, M and Hirasawa, Y and Tsurui, T and Ariizumi, H and Ishiguro, T and Suzuki, R and Ohkuma, R and Kubota, Y and Sambe, T and Tsuji, M and Wada, S and Kiuchi, Y and Kobayashi, S and Horiike, A and Goto, S and Murakami, M and Kim, YG and Tsunoda, T and Yoshimura, K}, title = {Butyricimonas is a key gut microbiome component for predicting postoperative recurrence of esophageal cancer.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {73}, number = {2}, pages = {23}, pmid = {38280026}, issn = {1432-0851}, abstract = {BACKGROUND: Recently, intestinal bacteria have attracted attention as factors affecting the prognosis of patients with cancer. However, the intestinal microbiome is composed of several hundred types of bacteria, necessitating the development of an analytical method that can allow the use of this information as a highly accurate biomarker. In this study, we investigated whether the preoperative intestinal bacterial profile in patients with esophageal cancer who underwent surgery after preoperative chemotherapy could be used as a biomarker of postoperative recurrence of esophageal cancer.

METHODS: We determined the gut microbiome of the patients using 16S rRNA metagenome sequencing, followed by statistical analysis. Simultaneously, we performed a machine learning analysis using a random forest model with hyperparameter tuning and compared the data obtained.

RESULTS: Statistical and machine learning analyses revealed two common bacterial genera, Butyricimonas and Actinomyces, which were abundant in cases with recurrent esophageal cancer. Butyricimonas primarily produces butyrate, whereas Actinomyces are oral bacteria whose function in the gut is unknown.

CONCLUSION: Our results indicate that Butyricimonas spp. may be a biomarker of postoperative recurrence of esophageal cancer. Although the extent of the involvement of these bacteria in immune regulation remains unknown, future research should investigate their presence in other pathological conditions. Such research could potentially lead to a better understanding of the immunological impact of these bacteria on patients with cancer and their application as biomarkers.}, } @article {pmid38279971, year = {2024}, author = {Patel, V and Patil, K and Patel, D and Kikani, B and Madamwar, D and Desai, C}, title = {Distribution of bacterial community structures and spread of antibiotic resistome at industrially polluted sites of Mini River, Vadodara, Gujarat, India.}, journal = {Environmental monitoring and assessment}, volume = {196}, number = {2}, pages = {208}, pmid = {38279971}, issn = {1573-2959}, abstract = {The influence of anthropogenic pollution on the distribution of bacterial diversity, antibiotic-resistant bacteria (ARBs), and antibiotic resistance genes (ARGs) was mapped at various geo-tagged sites of Mini River, Vadodara, Gujarat, India. The high-throughput 16S rRNA gene amplicon sequencing analysis revealed a higher relative abundance of Planctomycetota at the polluted sites, compared to the pristine site. Moreover, the relative abundance of Actinobacteriota increased, whereas Chloroflexi decreased in the water samples of polluted sites than the pristine site. The annotation of functional genes in the metagenome samples of Mini River sites indicated the presence of genes involved in the defence mechanisms against bacitracin, aminoglycosides, cephalosporins, chloramphenicol, streptogramin, streptomycin, methicillin, and colicin. The analysis of antibiotic resistome at the polluted sites of Mini River revealed the abundance of sulfonamide, beta-lactam, and aminoglycoside resistance. The presence of pathogens and ARB was significantly higher in water and sediment samples of polluted sites compared to the pristine site. The highest resistance of bacterial populations in the Mini River was recorded against sulfonamide (≥ 7.943 × 10[3] CFU/mL) and ampicillin (≥ 8.128 × 10[3] CFU/mL). The real-time PCR-based quantification of ARGs revealed the highest abundance of sulfonamide resistance genes sul1 and sul2 at the polluted sites of the Mini River. Additionally, the antimicrobial resistance genes aac(6')-Ib-Cr and blaTEM were also found abundantly at polluted sites of the Mini River. The findings provide insights into how anthropogenic pollution drives the ARG and ARB distribution in the riverine ecosystem, which may help with the development of antimicrobial resistance mitigation strategies.}, } @article {pmid38279288, year = {2024}, author = {Lanzavecchia, G and Frascarelli, G and Rocchetti, L and Bellucci, E and Bitocchi, E and Di Vittori, V and Sillo, F and Ferraris, I and Carta, G and Delledonne, M and Nanni, L and Papa, R}, title = {Genotype Combinations Drive Variability in the Microbiome Configuration of the Rhizosphere of Maize/Bean Intercropping System.}, journal = {International journal of molecular sciences}, volume = {25}, number = {2}, pages = {}, pmid = {38279288}, issn = {1422-0067}, support = {Strategic University Projects: "Novel strategies for innovative plant breeding: from monocolture to crop associations"//Marche Polytechnic University/ ; H2020 SFS-01-2020 subtopic c: From Agrobiodiversity to Dynamic Value Chains, Project title: "RADIANT: Realising Dynamic Value Chains for Underutilised Crops"//European Commission/ ; }, abstract = {In an intercropping system, the interplay between cereals and legumes, which is strongly driven by the complementarity of below-ground structures and their interactions with the soil microbiome, raises a fundamental query: Can different genotypes alter the configuration of the rhizosphere microbial communities? To address this issue, we conducted a field study, probing the effects of intercropping and diverse maize (Zea mays L.) and bean (Phaseolus vulgaris L., Phaseolus coccineus L.) genotype combinations. Through amplicon sequencing of bacterial 16S rRNA genes from rhizosphere samples, our results unveil that the intercropping condition alters the rhizosphere bacterial communities, but that the degree of this impact is substantially affected by specific genotype combinations. Overall, intercropping allows the recruitment of exclusive bacterial species and enhances community complexity. Nevertheless, combinations of maize and bean genotypes determine two distinct groups characterized by higher or lower bacterial community diversity and complexity, which are influenced by the specific bean line associated. Moreover, intercropped maize lines exhibit varying propensities in recruiting bacterial members with more responsive lines showing preferential interactions with specific microorganisms. Our study conclusively shows that genotype has an impact on the rhizosphere microbiome and that a careful selection of genotype combinations for both species involved is essential to achieve compatibility optimization in intercropping.}, } @article {pmid38279125, year = {2024}, author = {Rahnavard, A and Chatterjee, R and Wen, H and Gaylord, C and Mugusi, S and Klatt, KC and Smith, ER}, title = {Molecular epidemiology of pregnancy using omics data: advances, success stories, and challenges.}, journal = {Journal of translational medicine}, volume = {22}, number = {1}, pages = {106}, pmid = {38279125}, issn = {1479-5876}, support = {INV-016930/GATES/Bill & Melinda Gates Foundation/United States ; }, abstract = {Multi-omics approaches have been successfully applied to investigate pregnancy and health outcomes at a molecular and genetic level in several studies. As omics technologies advance, research areas are open to study further. Here we discuss overall trends and examples of successfully using omics technologies and techniques (e.g., genomics, proteomics, metabolomics, and metagenomics) to investigate the molecular epidemiology of pregnancy. In addition, we outline omics applications and study characteristics of pregnancy for understanding fundamental biology, causal health, and physiological relationships, risk and prediction modeling, diagnostics, and correlations.}, } @article {pmid38278977, year = {2024}, author = {Cho, EJ and Kim, B and Yu, SJ and Hong, SK and Choi, Y and Yi, NJ and Lee, KW and Suh, KS and Yoon, JH and Park, T}, title = {Urinary microbiome-based metagenomic signature for the noninvasive diagnosis of hepatocellular carcinoma.}, journal = {British journal of cancer}, volume = {}, number = {}, pages = {}, pmid = {38278977}, issn = {1532-1827}, support = {NRF-2020R1C1C1012749//National Research Foundation of Korea (NRF)/ ; 05-2021-0010//Seoul National University Hospital (SNUH)/ ; HI16C2037//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; }, abstract = {BACKGROUND: Gut microbial dysbiosis is implicated in chronic liver disease and hepatocellular carcinoma (HCC), but the role of microbiomes from various body sites remains unexplored. We assessed disease-specific alterations in the urinary microbiome in HCC patients, investigating their potential as diagnostic biomarkers.

METHODS: We performed cross-sectional analyses of urine samples from 471 HCC patients and 397 healthy controls and validated the results in an independent cohort of 164 HCC patients and 164 healthy controls. Urinary microbiomes were analyzed by 16S rRNA gene sequencing. A microbial marker-based model distinguishing HCC from controls was built based on logistic regression, and its performance was tested.

RESULTS: Microbial diversity was significantly reduced in the HCC patients compared with the controls. There were significant differences in the abundances of various bacteria correlated with HCC, thus defining a urinary microbiome-derived signature of HCC. We developed nine HCC-associated genera-based models with robust diagnostic accuracy (area under the curve [AUC], 0.89; balanced accuracy, 81.2%). In the validation, this model detected HCC with an AUC of 0.94 and an accuracy of 88.4%.

CONCLUSIONS: The urinary microbiome might be a potential biomarker for the detection of HCC. Further clinical testing and validation of these results are needed in prospective studies.}, } @article {pmid38278791, year = {2024}, author = {Omura, T and Isobe, N and Miura, T and Ishii, S and Mori, M and Ishitani, Y and Kimura, S and Hidaka, K and Komiyama, K and Suzuki, M and Kasuya, KI and Nomaki, H and Nakajima, R and Tsuchiya, M and Kawagucci, S and Mori, H and Nakayama, A and Kunioka, M and Kamino, K and Iwata, T}, title = {Microbial decomposition of biodegradable plastics on the deep-sea floor.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {568}, pmid = {38278791}, issn = {2041-1723}, support = {JPNP18016//New Energy and Industrial Technology Development Organization (NEDO)/ ; PJ-ID 20001845//New Energy and Industrial Technology Development Organization (NEDO)/ ; }, abstract = {Microbes can decompose biodegradable plastics on land, rivers and seashore. However, it is unclear whether deep-sea microbes can degrade biodegradable plastics in the extreme environmental conditions of the seafloor. Here, we report microbial decomposition of representative biodegradable plastics (polyhydroxyalkanoates, biodegradable polyesters, and polysaccharide esters) at diverse deep-sea floor locations ranging in depth from 757 to 5552 m. The degradation of samples was evaluated in terms of weight loss, reduction in material thickness, and surface morphological changes. Poly(L-lactic acid) did not degrade at either shore or deep-sea sites, while other biodegradable polyesters, polyhydroxyalkanoates, and polysaccharide esters were degraded. The rate of degradation slowed with water depth. We analysed the plastic-associated microbial communities by 16S rRNA gene amplicon sequencing and metagenomics. Several dominant microorganisms carried genes potentially encoding plastic-degrading enzymes such as polyhydroxyalkanoate depolymerases and cutinases/polyesterases. Analysis of available metagenomic datasets indicated that these microorganisms are present in other deep-sea locations. Our results confirm that biodegradable plastics can be degraded by the action of microorganisms on the deep-sea floor, although with much less efficiency than in coastal settings.}, } @article {pmid38278456, year = {2024}, author = {Wang, X and Qin, S and Zhao, L and Wang, J and Yang, H}, title = {Mechanism of gel immobilization driving efficient anammox in mainstream partial nitritation/anammox process: Structural characterization and multi-perspective microbial analysis.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {130375}, doi = {10.1016/j.biortech.2024.130375}, pmid = {38278456}, issn = {1873-2976}, abstract = {Here, the mechanism of encapsulated anammox bacteria (AnAOB) driving efficient nitrogen removal in the mainstream partial nitritation/anammox process is revealed. The results show that a high nitrogen removal rate (1.21±0.02 kgN·(m[3]·d)[-1]) was achieved due to the abundant micropore structure inside the anammox immobilized filler, ensuring good connectivity, and a stable aggregation capacity, reducing dependence on extracellular polymeric substances. AnAOB were uniformly distributed throughout all regions of the immobilized filler, and their abundance was higher than that of the control anammox granular sludge (AnGS). Conversely, cracks appeared on the surface of the AnGS, and hollows formed inside. The metagenome analysis revealed that the immobilized filler supported the coexistence of multiple AnAOB, and the appropriate niche enhanced coordination between the AnAOB and dominant companion microorganisms. In contrast, AnGS exhibited stronger NH4[+]-N and NO2[-]-N loops, potentially reducing the total nitrogen removal efficiency. This study promotes the mainstream application of anammox.}, } @article {pmid38278266, year = {2024}, author = {Xu, J and Zhao, R and Liu, A and Li, L and Li, S and Li, Y and Qu, M and Di, Y}, title = {To live or die: "Fine-tuning" adaptation revealed by systemic analyses in symbiotic bathymodiolin mussels from diverse deep-sea extreme ecosystems.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170434}, doi = {10.1016/j.scitotenv.2024.170434}, pmid = {38278266}, issn = {1879-1026}, abstract = {Hydrothermal vents (HVs) and cold seeps (CSs) are typical deep-sea extreme ecosystems with their own geochemical characteristics to supply the unique living conditions for local communities. Once HVs or CSs stop emission, the dramatic environmental change would pose survival risks to deep-sea organisms. Up to now, limited knowledge has been available to understand the biological responses and adaptive strategy to the extreme environments and their transition from active to extinct stage, mainly due to the technical difficulties and lack of representative organisms. In this study, bathymodiolin mussels, the dominant and successful species surviving in diverse deep-sea extreme ecosystems, were collected from active and extinct HVs (Southwest Indian Ocean) or CSs (South China Sea) via two individual cruises. The transcriptomic analysis and determination of multiple biological indexes in stress defense and metabolic systems were conducted in both gills and digestive glands of mussels, together with the metagenomic analysis of symbionts in mussels. The results revealed the ecosystem- and tissue-specific transcriptional regulation in mussels, addressing the autologous adaptations in antioxidant defense, energy utilization and key compounds (i.e. sulfur) metabolism. In detail, the successful antioxidant defense contributed to conquering the oxidative stress induced during the unavoidable metabolism of xenobiotics commonly existing in the extreme ecosystems; changes in metabolic rate functioned to handle toxic matters in different surroundings; upregulated gene expression of sulfide:quinone oxidoreductase indicated an active sulfide detoxification in mussels from HVs and active stage of HVs & CSs. Coordinately, a heterologous adaptation, characterized by the functional compensation between symbionts and mussels in energy utilization, sulfur and carbon metabolism, was also evidenced by the bacterial metagenomic analysis. Taken together, a new insight was proposed that symbiotic bathymodiolin mussels would develop a "finetuning" strategy combining the autologous and heterologous regulations to fulfill the efficient and effective adaptations for successful survival.}, } @article {pmid38278245, year = {2024}, author = {Midya, V and Nagdeo, K and Lane, JM and Torres-Olascoaga, LA and Torres-Calapiz, M and Gennings, C and Horton, MK and Téllez-Rojo, MM and Wright, RO and Arora, M and Eggers, S}, title = {Prenatal metal exposures and childhood gut microbial signatures are associated with depression score in late childhood.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170361}, doi = {10.1016/j.scitotenv.2024.170361}, pmid = {38278245}, issn = {1879-1026}, abstract = {BACKGROUND: Childhood depression is a major public health issue worldwide. Previous studies have linked both prenatal metal exposures and the gut microbiome to depression in children. However, few, if any, have studied their interacting effect in specific subgroups of children.

OBJECTIVES: Using an interpretable machine-learning method, this study investigates whether children with specific combinations of prenatal metals and childhood microbial signatures (cliques or groups of metals and microbes) were more likely to have higher depression scores at 9-11 years of age.

METHODS: We leveraged data from a well-characterized pediatric longitudinal birth cohort in Mexico City and its microbiome substudy (n = 112). Eleven metal exposures were measured in maternal whole blood samples in the second and third trimesters of pregnancy. The gut microbial abundances were measured at 9-11-year-olds using shotgun metagenomic sequencing. Depression symptoms were assessed using the Child Depression Index (CDI) t-scores at 9-11 years of age. We used Microbial and Chemical Exposure Analysis (MiCxA), which combines interpretable machine-learning into a regression framework to identify and estimate joint associations of metal-microbial cliques in specific subgroups. Analyses were adjusted for relevant covariates.

RESULTS: We identified a subgroup of children (11.6 % of the sample) characterized by a four-component metal-microbial clique that had a significantly high depression score (15.4 % higher than the rest) in late childhood. This metal-microbial clique consisted of high Zinc in the second trimester, low Cobalt in the third trimester, a high abundance of Bacteroides fragilis, a high abundance of Faecalibacterium prausnitzii. All combinations of cliques (two-, three-, and four-components) were significantly associated with increased log-transformed t-scored CDI (β = 0.14, 95%CI = [0.05,0.23], P < 0.01 for the four-component clique).

SIGNIFICANCE: This study offers a new approach to chemical-microbial analysis and a novel demonstration that children with specific gut microbiome cliques and metal exposures during pregnancy may have a higher likelihood of elevated depression scores.}, } @article {pmid38278240, year = {2024}, author = {Wang, X and Zhu, J and Liu, Q and Fu, Q and Hu, H and Huang, Q}, title = {Role of genes encoding microbial carbohydrate-active enzymes in the accumulation and dynamics of organic carbon in subtropical forest soils.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170295}, doi = {10.1016/j.scitotenv.2024.170295}, pmid = {38278240}, issn = {1879-1026}, abstract = {Microbial anabolism and catabolism regulate the accumulation and dynamics of soil organic carbon (SOC). However, very little attention has been paid to the role of microbial functional traits in the accumulation and dynamics of SOC in forest soils. In this study, nine forest soils were selected at three altitudes (600 m, 1200 m, and 1500 m) and three soil depths (0-15 cm, 15-30 cm, and 30-45 cm) located in Jiugong Mountain. Vertical traits of functional genes encoding microbial carbohydrate-active enzymes (CAZymes) were observed using metagenomic sequencing. Soil amino sugars were used as biomarkers to indicate microbial residue carbon (MRC). The results showed that GH1 (β-glucosidase: 147.49 TPM) and GH3 (β-glucosidase: 109.09 TPM) were the dominant genes for plant residue decomposition, and their abundance increased with soil depth and peaked in the deep soil at 600 m (GH1: 147.89 TPM; GH3: 109.59 TPM). The highest abundance of CAZymes for fungal and bacterial residue decomposition were GH18 (chitinase: 30.81 TPM) and GH23 (lysozyme: 58.02 TPM), respectively. The abundance of GH18 increased with soil depth, while GH23 showed the opposite trend. Moreover, MRC accumulation was significantly positively correlated with CAZymes involved in the degradation of hemicellulose (r = 0.577, p = 0.002). Compared with the soil before incubation, MRC in the topsoil at the low and middle altitudes after incubation increased by 4 % and 8 %, respectively, while MRC in the soils at 1500 m tended to decrease (p > 0.05). The mineralization capacity of SOC at 1500 m was significantly higher than that at 1200 m and 600 m (p < 0.05). Our results suggested that microbial function for degrading plant residue components, especially hemicellulose and lignin, contributed greatly to SOC accumulation and dynamics. These results were vital for understanding the roles of microbial functional traits in C cycling in forest.}, } @article {pmid38278071, year = {2023}, author = {Ma, L and Banda, JF and Wang, Y and Yang, Q and Zhao, L and Hao, C and Dong, H}, title = {Metagenomic insight into the acidophilic functional communities driving elemental geochemical cycles in an acid mine drainage lake.}, journal = {Journal of hazardous materials}, volume = {466}, number = {}, pages = {133070}, doi = {10.1016/j.jhazmat.2023.133070}, pmid = {38278071}, issn = {1873-3336}, abstract = {Acidophiles play a key role in the generation, evolution and attenuation of acid mine drainage (AMD), which is characterized by strong acidity (pH<3.5) and high metal concentrations. In this study, the seasonal changes of acidophilic communities and their roles in elemental cycling in an AMD lake (pH∼3.0) in China were analyzed through metagenomics. The results showed eukaryotic algae thrived in the lake, and Coccomyxa was dominant in January (38.1%) and May (33.9%), while Chlorella in July (9.5%). The extensive growth of Chlamydomonas in December (22.7%) resulted in an ultrahigh chlorophyll a concentration (587 μg/L), providing abundant organic carbon for the ecosystem. In addition, the iron-oxidizing and nitrogen-fixing bacterium Ferrovum contributed to carbon fixation. Ammonia oxidation likely occurred in the acidic lake, as was revealed by archaea Ca. Nitrosotalea. To gain a competitive advantage in the nutrient-poor environment, some acidophiles exhibited facultative characteristics, e.g. the most abundant bacterium Acidiphilium utilized both organic and inorganic carbon, and obtained energy from organic matter, inorganic sulfur, and sunlight simultaneously. It was suggested that sunlight, rather than chemical energy of reduced iron-sulfur was the major driver of elemental cycling in the AMD lake. The results are beneficial to the development of bioremediation strategies for AMD.}, } @article {pmid38277936, year = {2024}, author = {Liu, M and Deng, N and Hou, X and Zhang, B and Li, H and Wang, J}, title = {Characterisation of flavour profiles and microbial communities of fermented peppers with different fermentation years by combining flavouromics and metagenomics.}, journal = {Food chemistry}, volume = {443}, number = {}, pages = {138550}, doi = {10.1016/j.foodchem.2024.138550}, pmid = {38277936}, issn = {1873-7072}, abstract = {The changes in flavours, volatile aromas and microbial communities of fermented peppers with different fermentation years and their relationships were investigated in this study. Results indicated a gradual increase in organic acids during fermentation, whereas free amino acids and capsaicinoids reached stability after 1 year of fermentation. Overall, the analysis detected 340 volatile compounds in fermented peppers and regarded 69 of them as differential compounds. Peppers fermented for 2 (FY2) and 4 years (FY4) possessed a greater number of differential volatiles with large odour activity values, thus endowing them with more favourable flavours. Hence, metagenomic analysis compared their microbial communities and functional annotations. Results revealed that Lactiplantibacillus plantarum and Zygosaccharomyces rouxii were the dominant bacterium and fungus, and metabolism was the main Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway in FY2. Correlation analysis demonstrated that Hyphopichia, Kazachstania and Clavispora were highly positively correlated with 12 key aroma flavours.}, } @article {pmid38277823, year = {2023}, author = {Yan, Y and Han, IL and Lee, J and Li, G and Srinivasan, V and McCullough, K and Klaus, S and Kang, D and Wang, D and He, P and Patel, A and Bott, C and Gu, AZ}, title = {Revisiting the role of Acinetobacter spp. in side-stream enhanced biological phosphorus removal (S2EBPR) systems.}, journal = {Water research}, volume = {251}, number = {}, pages = {121089}, doi = {10.1016/j.watres.2023.121089}, pmid = {38277823}, issn = {1879-2448}, abstract = {We piloted the incorporation of side-stream enhanced biological phosphorus removal (S2EBPR) with A/B stage short-cut nitrogen removal processes to enable simultaneous carbon-energy-efficient nutrients removal. This unique configuration and system conditions exerted selective force on microbial populations distinct from those in conventional EBPR. Interestingly, effective P removal was achieved with the predominance of Acinetobacter (21.5 ± 0.1 %) with nearly negligible level of known conical PAOs (Ca. Accumulibacter and Tetrasphaera were 0.04 ± 0.10 % and 0.47 ± 0.32 %, respectively). Using a combination of techniques, such as fluorescence in situ hybridization (FISH) coupled with single cell Raman spectroscopy (SCRS), the metabolic tracing of Acinetobacter-like cells exerted PAO-like phenotypic profiling. In addition, comparative metagenomics analysis of the closely related Acinetobacter spp. revealed the EBPR relevant metabolic pathways. Further oligotyping analysis of 16s rRNA V4 region revealed sub-clusters (microdiversity) of the Acinetobacter and revealed that the sub-group (oligo type 1, identical (100 % alignment identity) hits from Acinetobacter_midas_s_49494, and Acinetobacter_midas_s_55652) correlated with EBPR activities parameters, provided strong evidence that the identified Acinetobacter most likely contributed to the overall P removal in our A/B-shortcut N-S2EBPR system. To the best of our knowledge, this is the first study to confirm the in situ EBPR activity of Acinetobacter using combined genomics and SCRS Raman techniques. Further research is needed to identify the specific taxon, and phenotype of the Acinetobacter that are responsible for the P-removal.}, } @article {pmid38277707, year = {2024}, author = {Zheng, W and Zhou, H and Fu, Z and Feng, L and Wen, D and Liang, X and Cao, L}, title = {Integration of 16 S rRNA gene sequencing, metabonomics and metagenome analysis to investigate the mechanism of Sparganium stoloniferum-Curcuma phaeocaulis in treating of endometriosis in rats.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {241}, number = {}, pages = {115970}, doi = {10.1016/j.jpba.2024.115970}, pmid = {38277707}, issn = {1873-264X}, abstract = {BACKGROUND: Endometriosis is a gynecological disease that causes severe chronic pelvic pain and infertility in women. The therapeutic efficacy of the traditional herbal combination of Sparganium stoloniferum-Curcuma phaeocaulis (Sangleng-Ezhu, SL-EZ) in the treatment of endometriosis has been established. However, the precise mechanism by which this treatment exerts its effects remains elusive.

METHODS: To gain further insights, UPLC-MS/MS was employed to identify the primary chemical constituents of SL-EZ in serum. Additionally, network pharmacology was utilized to analyze the active ingredients and their corresponding targets. Furthermore, the impact of SL-EZ on ectopic endometrial growth in endometrial implants was assessed using a rat model. The therapeutic mechanism of SL-EZ in rats with endometriosis was further investigated through the application of 16 S rRNA gene sequencing, metagenomic sequencing, and metabolomics.

RESULTS: The primary compounds in serum were zederone, p-coumaric acid, dehydrocostus lactone, curdione, curcumol. The growth of ectopic lesions in a rat model was effectively inhibited by SL-EZ. In comparison to the control group, the endometriotic rats exhibited a decrease in α-diversity of the gut microbiota, an increase in the Firmicutes/Bacteroidetes ratio, and a reduction in the abundance of Ruminococcaceae. Following SL-EZ intervention, the potential probiotic strains Lactobacillus gasseri and Lactobacillus johnsonii were able to restore the intestinal microenvironment at the species level. The altered metabolites were significantly correlated with Verrucomicrobia, Proteobacteria, and Bacteroidetes. The metabolomic analysis demonstrated significant alterations in intestinal metabolites. And SL-EZ intervention also exerted regulatory effects on various metabolic pathways in gut microbiota, including aminoacyl-tRNA biosynthesis, monobactam biosynthesis, cyanoamino acid metabolism, glycine, serine and threonine metabolism, plant secondary metabolite biosynthesis, and amino acid biosynthesis.

CONCLUSION: The identification of novel treatment formulations for endometriosis was achieved through the utilization of network pharmacology and gut microbiota analyses. Our findings revealed simultaneous alterations in the microbiota within the rat model of endometriosis. The therapeutic efficacy of SL-EZ in treating endometriosis is attributed to its ability to restore the gut microbiota and regulate metabolism. This investigation offers valuable insights into the therapeutic mechanisms of traditional Chinese medicine (TCM) for endometriosis.}, } @article {pmid38277518, year = {2024}, author = {Zhang, H and Zhou, F and Liu, X and Huang, J}, title = {Clinical application of metagenomic next-generation sequencing in patients with different organ system infection: A retrospective observational study.}, journal = {Medicine}, volume = {103}, number = {4}, pages = {e36745}, doi = {10.1097/MD.0000000000036745}, pmid = {38277518}, issn = {1536-5964}, abstract = {Microbiological identification is essential for appropriate treatment, but conventional methods are time-consuming and have a low sensitivity. In contrast, metagenomic next-generation sequencing (mNGS) is a culture-free and hypothesis-free technique that can detect a wide array of potential pathogens. This study aimed to reveal the overall diagnostic value of mNGS for infectious diseases of different organ systems and compare the sensitivity and specificity of mNGS with conventional methods. In a retrospective cohort study, 94 patients with mNGS results were enrolled, and clinical data were recorded and analyzed to compare the positive rate of mNGS with traditional methods including as smears, serological tests, and traditional PCR, etc. In this study, mNGS and culture were both positive in 12.77% cases and were both negative in 23.4% cases. There were positive results in 56 cases (54.26%) only by mNGS and 4 cases (4.26%) were positive only by culture. There were significant differences in sensitivity of pathogen detection between of ID and NID group for mNGS (χ2 = 10.461, P = .001)and conventional methods(χ2 = 7.963, P = .005). The positive predictive values and negative predictive values of diagnosing infectious disease by mNGS were 94.12% and 30.77%, respectively. mNGS increased the sensitivity rate by approximately 53.66% compared with that of culture (78.05% vs24.39%; χ2 = 47.248, P < .001) and decreased the specificity rate by 12.5% compared with that of culture (66.67% vs 100.0%; χ2 = 4.8, P = .028). mNGS can identify emerging or rare pathogen and further guide treatment regimens. mNGS has advantages in identifying overall pathogens and bacteria, however, there was no obvious advantage in identifying fungi, virus and tuberculosis. mNGS has higher specificity than conventional methods in identifying pathogens and advantages in detecting emerging or rare pathogens.}, } @article {pmid38277270, year = {2024}, author = {Huang, X and Li, L and Chen, H}, title = {Protocol to identify fungal profile from fecal metagenomes in cancer patients prior to immunotherapy.}, journal = {STAR protocols}, volume = {5}, number = {1}, pages = {102847}, doi = {10.1016/j.xpro.2024.102847}, pmid = {38277270}, issn = {2666-1667}, abstract = {Identifying fungal profiles from metagenomes is challenging due to an incomplete fungal database and limitations in the understanding of software. Here, we describe a protocol for analyzing the fecal metagenome of cancer patients prior to immunotherapy. We describe steps for raw metagenomic sequencing data retrieval, human genome and contaminants elimination, and assigning taxonomy labels to fungal reads. We then detail measures for assessing fungal alpha diversity and beta diversity, along with differential analysis. For complete details on the use and execution of this protocol, please refer to Xiaowen Huang et al.[1].}, } @article {pmid38276213, year = {2024}, author = {Parkin, K and Palmer, DJ and Verhasselt, V and Amenyogbe, N and Cooper, MN and Christophersen, CT and Prescott, SL and Silva, D and Martino, D}, title = {Metagenomic Characterisation of the Gut Microbiome and Effect of Complementary Feeding on Bifidobacterium spp. in Australian Infants.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/microorganisms12010228}, pmid = {38276213}, issn = {2076-2607}, abstract = {Complementary feeding induces dramatic ecological shifts in the infant gut microbiota toward more diverse compositions and functional metabolic capacities, with potential implications for immune and metabolic health. The aim of this study was to examine whether the age at which solid foods are introduced differentially affects the microbiota in predominantly breastfed infants compared with predominantly formula-fed infants. We performed whole-genome shotgun metagenomic sequencing of infant stool samples from a cohort of six-month-old Australian infants enrolled in a nested study within the ORIGINS Project longitudinal birth cohort. Infants born preterm or those who had been administered antibiotics since birth were excluded. The taxonomic composition was highly variable among individuals at this age. Predominantly formula-fed infants exhibited a higher microbiome diversity than predominantly breastfed infants. Among the predominantly breastfed infants, the introduction of solid foods prior to five months of age was associated with higher alpha diversity than solid food introduction after six months of age, primarily due to the loss of Bifidobacterium infantis. In contrast, the age at which solid food was introduced was not associated with the overall change in diversity among predominantly formula-fed infants but was associated with compositional changes in Escherichia abundance. Examining the functional capacity of the microbiota in relation to these changes, we found that the introduction of solid foods after six months of age was associated with elevated one-carbon compound metabolic pathways in both breastfed and formula-fed infants, although the specific metabolic sub-pathways differed, likely reflecting different taxonomic compositions. Our findings suggest that the age of commencement of solid foods influences the gut microbiota composition differently in predominantly breastfed infants than in predominantly formula-fed infants.}, } @article {pmid38276191, year = {2024}, author = {Couto, RDS and Ramos, EDSF and Abreu, WU and Rodrigues, LRR and Marinho, LF and Morais, VDS and Villanova, F and Pandey, RP and Deng, X and Delwart, E and Costa, ACD and Leal, E}, title = {Metagenomic of Liver Tissue Identified at Least Two Genera of Totivirus-like Viruses in Molossus molossus Bats.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/microorganisms12010206}, pmid = {38276191}, issn = {2076-2607}, abstract = {The Totiviridae family of viruses has a unique genome consisting of double-stranded RNA with two open reading frames that encode the capsid protein (Cap) and the RNA-dependent RNA polymerase (RdRpol). Most virions in this family are isometric in shape, approximately 40 nm in diameter, and lack an envelope. There are five genera within this family, including Totivirus, Victorivirus, Giardiavirus, Leishmaniavirus, and Trichomonasvirus. While Totivirus and Victorivirus primarily infect fungi, Giardiavirus, Leishmaniavirus, and Trichomonasvirus infect diverse hosts, including protists, insects, and vertebrates. Recently, new totivirus-like species have been discovered in fish and plant hosts, and through metagenomic analysis, a novel totivirus-like virus (named Tianjin totivirus) has been isolated from bat guano. Interestingly, Tianjin totivirus causes cytopathic effects in insect cells but cannot grow in mammalian cells, suggesting that it infects insects consumed by insectivorous bats. In this study, we used next-generation sequencing and identified totivirus-like viruses in liver tissue from Molossus molossus bats in the Amazon region of Brazil. Comparative phylogenetic analysis based on the RNA-dependent RNA polymerase region revealed that the viruses identified in Molossus bats belong to two distinct phylogenetic clades, possibly comprising different genera within the Totiviridae family. Notably, the mean similarity between the Tianjin totivirus and the totiviruses identified in Molossus bats is less than 18%. These findings suggest that the diversity of totiviruses in bats is more extensive than previously recognized and highlight the potential for bats to serve as reservoirs for novel toti-like viruses.}, } @article {pmid38276185, year = {2023}, author = {Elcheninov, AG and Zayulina, KS and Klyukina, AA and Kremneva, MK and Kublanov, IV and Kochetkova, TV}, title = {Metagenomic Insights into the Taxonomic and Functional Features of Traditional Fermented Milk Products from Russia.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/microorganisms12010016}, pmid = {38276185}, issn = {2076-2607}, support = {Federal scientific-technical program of the genetic technologies development for 2019-2027 (Agreement № 075-15-2021-1401, 03 November 2021)//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Fermented milk products (FMPs) contain probiotics that are live bacteria considered to be beneficial to human health due to the production of various bioactive molecules. In this study, nine artisanal FMPs (kefir, ayran, khurunga, shubat, two cottage cheeses, bryndza, khuruud and suluguni-like cheese) from different regions of Russia were characterized using metagenomics. A metagenomic sequencing of ayran, khurunga, shubat, khuruud and suluguni-like cheese was performed for the first time. The taxonomic profiling of metagenomic reads revealed that Lactococcus species, such as Lc. lactis and Lc. cremoris prevailed in khuruud, bryndza, one sample of cottage cheese and khurunga. The latter one together with suluguni-like cheese microbiome was dominated by bacteria, affiliated to Lactobacillus helveticus (32-35%). In addition, a high proportion of sequences belonging to the genera Lactobacillus, Lactococcus and Streptococcus but not classified at the species level were found in the suluguni-like cheese. Lactobacillus delbrueckii, as well as Streptococcus thermophilus constituted the majority in another cottage cheese, kefir and ayran metagenomes. The microbiome of shubat, produced from camel's milk, was significantly distinctive, and Lentilactobacillus kefiri, Lactobacillus kefiranofaciens and Bifidobacterium mongoliense represented the dominant components (42, 7.4 and 5.6%, respectively). In total, 78 metagenome-assembled genomes with a completeness ≥ 50.2% and a contamination ≤ 8.5% were recovered: 61 genomes were assigned to the Enterococcaceae, Lactobacillaceae and Streptococcaceae families (the Lactobacillales order within Firmicutes), 4 to Bifidobacteriaceae (the Actinobacteriota phylum) and 2 to Acetobacteraceae (the Proteobacteria phylum). A metagenomic analysis revealed numerous genes, from 161 to 1301 in different products, encoding glycoside hydrolases and glycosyltransferases predicted to participate in lactose, alpha-glucans and peptidoglycan hydrolysis as well as exopolysaccharides synthesis. A large number of secondary metabolite biosynthetic gene clusters, such as lanthipeptides, unclassified bacteriocins, nonribosomal peptides and polyketide synthases were also detected. Finally, the genes involved in the synthesis of bioactive compounds like β-lactones, terpenes and furans, nontypical for fermented milk products, were also found. The metagenomes of kefir, ayran and shubat was shown to contain either no or a very low count of antibiotic resistance genes. Altogether, our results show that traditional indigenous fermented products are a promising source of novel probiotic bacteria with beneficial properties for medical and food industries.}, } @article {pmid38276173, year = {2023}, author = {Lücking, D and Alarcón-Schumacher, T and Erdmann, S}, title = {Distribution and Implications of Haloarchaeal Plasmids Disseminated in Self-Encoded Plasmid Vesicles.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/microorganisms12010005}, pmid = {38276173}, issn = {2076-2607}, support = {Max-Planck Research Group Archaeal Virology//Max-Planck Society/ ; 98 190//Volkswagen Foundation/ ; }, abstract = {Even though viruses and plasmids are both drivers of horizontal gene transfer, they differ fundamentally in their mode of transfer. Virus genomes are enclosed in virus capsids and are not dependent on cell-to-cell contacts for their dissemination. In contrast, the transfer of plasmids most often requires physical contact between cells. However, plasmid pR1SE of Halorubrum lacusprofundi is disseminated between cells, independent of cell-cell contacts, in specialized membrane vesicles that contain plasmid proteins. In this study, we searched for pR1SE-like elements in public databases and a metagenomics dataset from Australian salt lakes and identified 40 additional pR1SE-like elements in hypersaline environments worldwide. Herein, these elements are named apHPVs (archaeal plasmids of haloarchaea potentially transferred in plasmid vesicles). They share two sets of closely related proteins with conserved synteny, strongly indicating an organization into different functional clusters. We find that apHPVs, besides transferring themselves, have the potential to transfer large fragments of DNA between host cells, including virus defense systems. Most interestingly, apHPVs likely play an important role in the evolution of viruses and plasmids in haloarchaea, as they appear to recombine with both of them. This further supports the idea that plasmids and viruses are not distinct but closely related mobile genetic elements.}, } @article {pmid38275746, year = {2023}, author = {Seppi, M and Pasqualini, J and Facchin, S and Savarino, EV and Suweis, S}, title = {Emergent Functional Organization of Gut Microbiomes in Health and Diseases.}, journal = {Biomolecules}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/biom14010005}, pmid = {38275746}, issn = {2218-273X}, abstract = {Continuous and significant progress in sequencing technologies and bioinformatics pipelines has revolutionized our comprehension of microbial communities, especially for human microbiomes. However, most studies have focused on studying the taxonomic composition of the microbiomes and we are still not able to characterize dysbiosis and unveil the underlying ecological consequences. This study explores the emergent organization of functional abundances and correlations of gut microbiomes in health and disease. Leveraging metagenomic sequences, taxonomic and functional tables are constructed, enabling comparative analysis. First, we show that emergent taxonomic and functional patterns are not useful to characterize dysbiosis. Then, through differential abundance analyses applied to functions, we reveal distinct functional compositions in healthy versus unhealthy microbiomes. In addition, we inquire into the functional correlation structure, revealing significant differences between the healthy and unhealthy groups, which may significantly contribute to understanding dysbiosis. Our study demonstrates that scrutinizing the functional organization in the microbiome provides novel insights into the underlying state of the microbiome. The shared data structure underlying the functional and taxonomic compositions allows for a comprehensive macroecological examination. Our findings not only shed light on dysbiosis, but also underscore the importance of studying functional interrelationships for a nuanced understanding of the dynamics of the microbial community. This research proposes a novel approach, bridging the gap between microbial ecology and functional analyses, promising a deeper understanding of the intricate world of the gut microbiota and its implications for human health.}, } @article {pmid38275326, year = {2023}, author = {Bonaldo, F and Avot, BJP and De Cesare, A and Aarestrup, FM and Otani, S}, title = {Foodborne Pathogen Dynamics in Meat and Meat Analogues Analysed Using Traditional Microbiology and Metagenomic Sequencing.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/antibiotics13010016}, pmid = {38275326}, issn = {2079-6382}, abstract = {Meat analogues play an increasing role in meeting global nutritional needs. However, while it is well known that meat possesses inherent characteristics that create favourable conditions for the growth of various pathogenic bacteria, much less is known about meat analogues. This study aimed to compare the growth and survival of Escherichia coli HEHA16, Listeria monocytogenes, Salmonella enterica Typhi, Cronobacter sakazakii, and a cocktail of these bacteria in sterile juices from minced chicken, pig, and beef, as well as pea-based and soy-based minced meat. Traditional microbiology and next-generation sequencing of those metagenomes were employed to analyse the pathogen variability, abundance, and survival after an incubation period. Our findings show that all the meat juices provided favourable conditions for the growth and proliferation of the studied bacteria, with the exception of E. coli HEHA16, which showed lower survival rates in the chicken matrix. Meat analogue juice mainly supported L. monocytogenes survival, with C. sakazakii survival supported to a lesser extent. A correlation was observed between the traditional culturing and metagenomic analysis results, suggesting that further work is needed to compare these technologies in foodborne setups. Our results indicate that plant-based meats could serve as vectors for the transmission of certain, but likely not all, foodborne pathogens, using two accurate detection methods. This warrants the need for additional research to better understand and characterise their safety implications, including their potential association with additional pathogens.}, } @article {pmid38275294, year = {2024}, author = {Reasoner, SA and Bernard, R and Waalkes, A and Penewit, K and Lewis, J and Sokolow, AG and Brown, RF and Edwards, KM and Salipante, SJ and Hadjifrangiskou, M and Nicholson, MR}, title = {Longitudinal profiling of the intestinal microbiome in children with cystic fibrosis treated with elexacaftor-tezacaftor-ivacaftor.}, journal = {mBio}, volume = {}, number = {}, pages = {e0193523}, doi = {10.1128/mbio.01935-23}, pmid = {38275294}, issn = {2150-7511}, abstract = {The intestinal microbiome influences growth and disease progression in children with cystic fibrosis (CF). Elexacaftor-tezacaftor-ivacaftor (ELX/TEZ/IVA), the newest pharmaceutical modulator for CF, restores the function of the pathogenic mutated CF transmembrane conductance regulator (CFTR) channel. We performed a single-center longitudinal analysis of the effect of ELX/TEZ/IVA on the intestinal microbiome, intestinal inflammation, and clinical parameters in children with CF. Following ELX/TEZ/IVA, children with CF had significant improvements in body mass index and percent predicted forced expiratory volume in one second, and required fewer antibiotics for respiratory infections. Intestinal microbiome diversity increased following ELX/TEZ/IVA coupled with a decrease in the intestinal carriage of Staphylococcus aureus, the predominant respiratory pathogen in children with CF. There was a reduced abundance of microbiome-encoded antibiotic resistance genes. Microbial pathways for aerobic respiration were reduced after ELX/TEZ/IVA. The abundance of microbial acid tolerance genes was reduced, indicating microbial adaptation to increased CFTR function. In all, this study represents the first comprehensive analysis of the intestinal microbiome in children with CF receiving ELX/TEZ/IVA.IMPORTANCECystic fibrosis (CF) is an autosomal recessive disease with significant gastrointestinal symptoms in addition to pulmonary complications. Recently approved treatments for CF, CF transmembrane conductance regulator (CFTR) modulators, are anticipated to substantially improve the care of people with CF and extend their lifespans. Prior work has shown that the intestinal microbiome correlates with health outcomes in CF, particularly in children. Here, we study the intestinal microbiome of children with CF before and after the CFTR modulator, ELX/TEZ/IVA. We identify promising improvements in microbiome diversity, reduced measures of intestinal inflammation, and reduced antibiotic resistance genes. We present specific bacterial taxa and protein groups which change following ELX/TEZ/IVA. These results will inform future mechanistic studies to understand the microbial improvements associated with CFTR modulator treatment. This study demonstrates how the microbiome can change in response to a targeted medication that corrects a genetic disease.}, } @article {pmid38274799, year = {2023}, author = {Nguyen, WQ and Chrisman, LP and Enriquez, GL and Hooper, MJ and Griffin, TL and Ahmad, M and Rahman, S and Green, SJ and Seed, PC and Guitart, J and Burns, MB and Zhou, XA}, title = {Gut microbiota analyses of cutaneous T-cell lymphoma patients undergoing narrowband ultraviolet B therapy reveal alterations associated with disease treatment.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1280205}, doi = {10.3389/fimmu.2023.1280205}, pmid = {38274799}, issn = {1664-3224}, abstract = {Recent studies have shown a close relationship between cutaneous T-cell lymphoma (CTCL) and its microbiome. CTCL disease progression is associated with gut dysbiosis and alterations in bacterial taxa parallel those observed in immunologically similar atopic dermatitis. Moreover, the microbial profile of lesional skin may predict response to narrowband ultraviolet B (nbUVB), a common skin-directed therapy. However, the relationship between the gut microbiome, an immunologically vital niche, and nbUVB remains unexplored in CTCL. Herein, we performed 16S rRNA sequencing and PICRUSt2 predictive metagenomics on DNA extracted from stool swabs of 13 CTCL patients treated with nbUVB, 8 non-treated patients, and 13 healthy controls. Disease response was assessed with modified Severity Weighted Assessment Tool (mSWAT); of nbUVB-treated patients, 6 improved (decreased mSWAT), 2 remained stable, and 5 worsened (increased mSWAT). Protective commensal bacteria including Lactobacillaceae and Erysipelatoclostridiaceae were significantly less abundant in CTCL patients compared to controls. With treatment, the CTCL gut microbiome exhibited decreased phylogenetic diversity and lower relative abundance of pro-inflammatory Sutterellaceae. Sutterellaceae was also significantly more abundant in patients who worsened, and Eggerthellaceae and Erysipelotrichaceae trended higher in patients who improved. Finally, PICRUSt2 functional predictions based on shifts in abundance of bacterial sequences repeatedly identified alterations in inositol degradation, which plays a key role in host immunomodulation, including inositol phospholipid signaling relevant to T-cell survival and proliferation. Our results bolster the paradigm of gut dysbiosis in CTCL and its functional implications in disease pathogenesis, and further delineate bacterial taxa associated with nbUVB response and with nbUVB treatment itself.}, } @article {pmid38274764, year = {2023}, author = {Hu, X and Yang, L and Zhang, Y and Yang, M and Li, J and Fan, Y and Guo, P and Tian, Z}, title = {Fecal and oral microbiome analysis of snakes from China reveals a novel natural emerging disease reservoir.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1339188}, doi = {10.3389/fmicb.2023.1339188}, pmid = {38274764}, issn = {1664-302X}, abstract = {INTRODUCTION: The gastrointestinal tract and oral cavity of animal species harbor complex microbial communities, the composition of which is indicative of the behavior, co-evolution, diet, and immune system of the host.

METHODS: This study investigated the microbial composition in snakes from varying altitudinal ranges by assessing the fecal and oral bacterial communities in Protobothrops mucrosquamatus, Elaphe dione, and Gloydius angusticeps from Sichuan Province, China, using metagenomic sequencing.

RESULTS AND DISCUSSION: It was revealed that Bacteroidetes, Proteobacteria, Firmicutes, and Fusobacteria were the core microbial phyla in fecal samples across all three species, while Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes were the core microbial phyla in oral samples across all three species. Notably, the dominance of Armatimonadetes was documented for the first time in the feces of all three species. Comparative analysis of the microbiomes of the three species indicated distinct microbiological profiles between snakes living at low- and high-altitude regions. Furthermore, 12 to 17 and 22 to 31 bacterial pathogens were detected in the oral and fecal samples, respectively, suggesting that snakes may serve as a novel reservoir for emerging diseases. Overall, this study provides a comparative analysis of the fecal and oral microbiomes in three snake species. Future investigations are anticipated to further elucidate the influence of age, genetics, behavior, diet, environment, ecology, and evolution on the gut and oral microbial communities of snakes.}, } @article {pmid38274751, year = {2023}, author = {Barba, M and Toquet, M and García-Roselló, E and Gomis, J and Quereda, JJ and González-Torres, P and Carbonetto, B and Gómez-Martín, Á}, title = {Description of the vaginal microbiota in nulliparous ewes during natural mating and pregnancy: preliminary signs of the male preputial microbiota modulation.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1224910}, doi = {10.3389/fmicb.2023.1224910}, pmid = {38274751}, issn = {1664-302X}, abstract = {The vaginal microbiota plays a key role in animals' health. Understanding its diversity and composition and associated changes occurring through the reproductive cycle represents valuable knowledge to disclose the mechanisms leading to dysbiosis and eventually to infection. Even if the human vaginal microbiota has been thoroughly studied, scarce research has been conducted on the vaginal microbiota of livestock. In this study, 16S rRNA gene-based sequencing was performed on vaginal samples of ten nulliparous ewes at three different sampling points: before the estrus synchronization protocol (T0), at the time of estrus before mating (Testrus), and the day of the pregnancy diagnosis (Tpreg). Preputial samples from the three males collected pre and post-mating were also analyzed. Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria were the most abundant phyla in vaginal samples. The most abundant genera were Porphyromonas, Anaerococcus, and Peptinophilius. Vaginal microbiota biodiversity decreased during pregnancy. Tenericutes (Ureaplasma spp.) increased significantly at Tpreg in both pregnant and non-pregnant ewes. Differences were observed between pregnant and non-pregnant ewes at Tpreg where pregnant ewes had a significantly higher abundance of Actinobacillus spp. and Ureaplasma spp. Ewes that were diagnosed with pregnancy at Tpreg showed a decreased abundance of gram-negative bacteria such as Bacteroidales, Campylobacterales, and Enterobacteriales. In addition, a significant decrease in the relative abundances of genera within Firmicutes, such as Alloicoccus (Lactobacillales), Atopostipes (Lactobacillales), and an uncultured bacteria W5053 from Family XI (Firmicutes, Clostridiales) was observed in non-pregnant ewes at Tpreg. The four most abundant phyla in the rams' prepuce were the same as in the ewes' vagina. The most abundant genus was Corynebacterium. No major differences were observed in the ram's preputial microbiota between pre and post-mating samples. Nevertheless, the differences in the taxonomic composition of ewes' vaginal microbiota between Testrus and Tpreg could be explained by the exposure to the preputial microbiota. This study offers new insights into the effects of several key steps of the ewe's reproductive cycle such as estrus-synchronization protocol, mating, and pregnancy on ovine vaginal microbiota. The knowledge of the microbiota dynamics during the reproductive cycle can help improve the reproductive outcomes of dams by identifying biomarkers and putative probiotics.}, } @article {pmid38274732, year = {2023}, author = {Hao, L and Bian, W and Qing, Z and Ma, T and Li, H and Xu, P and Wen, P}, title = {Will previous antimicrobial therapy reduce the positivity rate of metagenomic next-generation sequencing in periprosthetic joint infections? A clinical study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1295962}, doi = {10.3389/fcimb.2023.1295962}, pmid = {38274732}, issn = {2235-2988}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a culture-independent massively parallel DNA sequencing technology and it has been widely used for rapid etiological diagnosis with significantly high positivity rate. Currently, clinical studies on evaluating the influence of previous antimicrobial therapy on positivity rate of mNGS in PJIs are rarely reported. The present study aimed to investigate whether the positivity rate of mNGS is susceptible to previous antimicrobial therapy.

METHODS: We performed a prospective trial among patients who undergone hip or knee surgery due to periprosthetic joint infection (PJI) to compare the positivity rate of culture and mNGS between cases with and without previous antimicrobial therapy, and the positivity rates between cases with different antimicrobial-free intervals were also analysed.

RESULTS: Among 131 included PJIs, 91 (69.5%) had positive cultures and 115 (87.8%) had positive mNGS results. There was no significant difference in the positivity rate of deep-tissue culture and synovial fluid mNGS between cases with and without previous antimicrobial therapy. The positivity rate of synovial fluid culture was higher in cases with previous antimicrobial therapy. The positivity rates of mNGS in synovial fluid decreased as the antimicrobial-free interval ranged from 4 to 14 days to 0 to 3 days.

CONCLUSION: mNGS is more advantageous than culture with a higher pathogen detection rate. However, our data suggested that antimicrobial agents may need to be discontinued more than 3 days before sampling to further increase the positivity rate of mNGS for PJIs.}, } @article {pmid38274454, year = {2023}, author = {Tan, Y and Yang, M and Wan, C and Tang, S and Liu, L and Chen, L}, title = {Nocardia farcinica infection presenting as a solitary bronchial neoplasm in an immunocompetent adult: a case report.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1337303}, doi = {10.3389/fmed.2023.1337303}, pmid = {38274454}, issn = {2296-858X}, abstract = {Nocardia species are gram-positive, acid-fast, saprophytic, aerobic bacilli, predominantly resulting in opportunistic infections in immunocompromised individuals. Here, we reported a case of Nocardia infection in a 27-year-old woman with normal immunocompetence, who presented as a solitary neoplasm in the left principal bronchus with a chief complaint of postural dyspnea. By electrotomy via bronchoscopy, the neoplasm was successfully removed, and it was further identified as Nocardia farcinica by metagenomic next-generation sequencing.}, } @article {pmid38274111, year = {2023}, author = {Gorecki, A and Ostapczuk, P and Dziewit, L}, title = {Diversity of antibiotic resistance gene variants at subsequent stages of the wastewater treatment process revealed by a metagenomic analysis of PCR amplicons.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1334646}, doi = {10.3389/fgene.2023.1334646}, pmid = {38274111}, issn = {1664-8021}, abstract = {Wastewater treatment plants have been recognised as point sources of various antibiotic-resistant bacteria (ARB) and antibiotic resistance genes (ARG) which are considered recently emerging biological contaminants. So far, culture-based and molecular-based methods have been successfully applied to monitor antimicrobial resistance (AMR) in WWTPs. However, the methods applied do not permit the comprehensive identification of the true diversity of ARGs. In this study we applied next-generation sequencing for a metagenomic analysis of PCR amplicons of ARGs from the subsequent stages of the analysed WWTP. The presence of 14 genes conferring resistance to different antibiotic families was screened by PCR. In the next step, three genes were selected for detailed analysis of changes of the profile of ARG variants along the process. A relative abundance of 79 variants was analysed. The highest diversity was revealed in the ermF gene, with 52 variants. The relative abundance of some variants changed along the purification process, and some ARG variants might be present in novel hosts for which they were currently unassigned. Additionally, we identified a pool of novel ARG variants present in the studied WWTP. Overall, the results obtained indicated that the applied method is sufficient for analysing ARG variant diversity.}, } @article {pmid38273942, year = {2023}, author = {Pais, A and Ristaino, J and Whetten, R and Xiang, QJ}, title = {Metagenomic study reveals hidden relationships among fungal diversity, variation of plant disease, and genetic distance in Cornus florida (Cornaceae).}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1282188}, doi = {10.3389/fpls.2023.1282188}, pmid = {38273942}, issn = {1664-462X}, abstract = {INTRODUCTION: Understanding patterns of plant-microbe interactions across plant species and populations is a critical yet poorly characterized aspect in the field of plant pathology. Microbial DNA sequences present as contaminants in omics data of plants obtained using next-generation sequencing methods provide a valuable source to explore the relationships among endophytic microbial diversity, disease and genetic differentiation of host plants, and environmental variation, but few such studies have been conducted. The flowering dogwood tree (Cornus florida L.), an ecologically important species in North America, is threatened by powdery mildew and dogwood anthracnose diseases, and knowledge of the microbial diversity harbored within genetically and environmental distinct populations of this species remains largely unknown.

METHODS: We conducted a metagenomics study utilizing the sequences of RAD-tag/genotype-by-sequence libraries from leaf tissues of C. florida to examine such host-fungus interactions across the dogwood's US range. We performed various combinations of alignments to both host and pathogen genomes to obtain filtered sets sequences for metagenomics analysis. Taxonomic assignments were determined on each filtered set of sequences, followed by estimation of microbial diversity and correlation to environment and host-genetic variation.

RESULTS: Our data showed that microbial community composition significantly differed between visually healthy and diseased sites. Several microbial taxa known to interact with dogwood were identified from these sequences. We found no correlation between microbial diversity and relative abundances of sequences aligning to draft genomes of either pathogen causing powdery mildew or dogwood anthracnose. We found a significant relationship between differences of fungal communities and geographic distances of plant populations, suggesting roles of environments in shaping fungal communities in leaf tissues. Significant correlations between the genetic differentiation of plant samples and fungal community dissimilarity (beta diversity) were also observed in certain sets of our analyses-suggesting the possibility of a relationship between microbial community composition and plant genetic distance. This relationship persisted in significance even after controlling for significant effects of geographic-bioclimatic variation of microbial diversity.

DISCUSSION: Our results suggest that both genetics and the environment play a significant role in shaping foliar fungal communities. Our findings underscore the power of leveraging hidden microbial sequences within datasets originally collected for plant genetic studies to understand plant-pathogen interactions.}, } @article {pmid38273328, year = {2024}, author = {Valentin-Alvarado, LE and Fakra, SC and Probst, AJ and Giska, JR and Jaffe, AL and Oltrogge, LM and West-Roberts, J and Rowland, J and Manga, M and Savage, DF and Greening, C and Baker, BJ and Banfield, JF}, title = {Autotrophic biofilms sustained by deeply sourced groundwater host diverse bacteria implicated in sulfur and hydrogen metabolism.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {15}, pmid = {38273328}, issn = {2049-2618}, support = {1R01GM12763/NH/NIH HHS/United States ; 1R01GM12763/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Biofilms in sulfide-rich springs present intricate microbial communities that play pivotal roles in biogeochemical cycling. We studied chemoautotrophically based biofilms that host diverse CPR bacteria and grow in sulfide-rich springs to investigate microbial controls on biogeochemical cycling.

RESULTS: Sulfide springs biofilms were investigated using bulk geochemical analysis, genome-resolved metagenomics, and scanning transmission X-ray microscopy (STXM) at room temperature and 87 K. Chemolithotrophic sulfur-oxidizing bacteria, including Thiothrix and Beggiatoa, dominate the biofilms, which also contain CPR Gracilibacteria, Absconditabacteria, Saccharibacteria, Peregrinibacteria, Berkelbacteria, Microgenomates, and Parcubacteria. STXM imaging revealed ultra-small cells near the surfaces of filamentous bacteria that may be CPR bacterial episymbionts. STXM and NEXAFS spectroscopy at carbon K and sulfur L2,3 edges show that filamentous bacteria contain protein-encapsulated spherical elemental sulfur granules, indicating that they are sulfur oxidizers, likely Thiothrix. Berkelbacteria and Moranbacteria in the same biofilm sample are predicted to have a novel electron bifurcating group 3b [NiFe]-hydrogenase, putatively a sulfhydrogenase, potentially linked to sulfur metabolism via redox cofactors. This complex could potentially contribute to symbioses, for example, with sulfur-oxidizing bacteria such as Thiothrix that is based on cryptic sulfur cycling. One Doudnabacteria genome encodes adjacent sulfur dioxygenase and rhodanese genes that may convert thiosulfate to sulfite. We find similar conserved genomic architecture associated with CPR bacteria from other sulfur-rich subsurface ecosystems.

CONCLUSIONS: Our combined metagenomic, geochemical, spectromicroscopic, and structural bioinformatics analyses of biofilms growing in sulfide-rich springs revealed consortia that contain CPR bacteria and sulfur-oxidizing Proteobacteria, including Thiothrix, and bacteria from a new family within Beggiatoales. We infer roles for CPR bacteria in sulfur and hydrogen cycling. Video Abstract.}, } @article {pmid38272885, year = {2024}, author = {Levine, ZC and Sene, A and Mkandawire, W and Deme, AB and Ndiaye, T and Sy, M and Gaye, A and Diedhiou, Y and Mbaye, AM and Ndiaye, IM and Gomis, J and Ndiop, M and Sene, D and Faye Paye, M and MacInnis, BL and Schaffner, SF and Park, DJ and Badiane, AS and Colubri, A and Ndiaye, M and Sy, N and Sabeti, PC and Ndiaye, D and Siddle, KJ}, title = {Investigating the etiologies of non-malarial febrile illness in Senegal using metagenomic sequencing.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {747}, pmid = {38272885}, issn = {2041-1723}, support = {U54HG007480//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; U01HG007480//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; U01AI151812//U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; Centennial Award to K.J.S.//American Society of Tropical Medicine and Hygiene (American Society of Tropical Medicine & Hygiene)/ ; T32GM007753//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32GM144273//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; Investigator award to P.C.S.//Howard Hughes Medical Institute (HHMI)/ ; }, abstract = {The worldwide decline in malaria incidence is revealing the extensive burden of non-malarial febrile illness (NMFI), which remains poorly understood and difficult to diagnose. To characterize NMFI in Senegal, we collected venous blood and clinical metadata in a cross-sectional study of febrile patients and healthy controls in a low malaria burden area. Using 16S and untargeted sequencing, we detected viral, bacterial, or eukaryotic pathogens in 23% (38/163) of NMFI cases. Bacteria were the most common, with relapsing fever Borrelia and spotted fever Rickettsia found in 15.5% and 3.8% of cases, respectively. Four viral pathogens were found in a total of 7 febrile cases (3.5%). Sequencing also detected undiagnosed Plasmodium, including one putative P. ovale infection. We developed a logistic regression model that can distinguish Borrelia from NMFIs with similar presentation based on symptoms and vital signs (F1 score: 0.823). These results highlight the challenge and importance of improved diagnostics, especially for Borrelia, to support diagnosis and surveillance.}, } @article {pmid38272816, year = {2024}, author = {Morsli, M and Salipante, F and Gelis, A and Magnan, C and Guigon, G and Lavigne, JP and Sotto, A and Dunyach-Remy, C}, title = {Evolution of the urinary microbiota in spinal cord injury patients with decubitus ulcer: A snapshot study.}, journal = {International wound journal}, volume = {21}, number = {1}, pages = {e14626}, doi = {10.1111/iwj.14626}, pmid = {38272816}, issn = {1742-481X}, support = {//Centre Hospitalier Universitaire de Nîmes/ ; //French Society of Pressure Ulcer/ ; }, abstract = {Current microbiome investigations of patients with pressure ulcers (PU) are mainly based on wound swabs and/or biopsy sequencing, leaving the colonization scenario unclear. Urinary microbiota has been never studied. As a part of the prospective ESCAFLOR study, we studied urinary microbiota of spinal cord injury (SCI) patients with PU without any urinary tract infection at the inclusion, collected at two times (at admission [D0] and after 28 days [D28]) during the patient's care, investigated by 16S rDNA metagenomics next generation sequencing. Subgroup analyses were carried out between patients with wounds showing improved evolution versus stagnated/worsened wounds at D28. Analysis was done using EPISEQ® 16S and R software. Among the 12 studied patients, the urinary microbiota of patients with improved wound evolution at D28 (n = 6) presented a significant decrease of microbial diversity. This modification was associated with the presence of Proteobacteria phylum and an increase of Escherichia-Shigella (p = 0.005), as well as the presence of probiotic anaerobic bacteria Lactobacillus and Bifidobacterium. In contrast, Proteus abundance was significantly increased in urine of patients with stagnated/worsened wound evolution (n = 6) (p = 0.003). This study proposes urinary microbiota as a complementary factor indirectly associated with the wound evolution and patient cure. It opens new perspectives for further investigations based on multiple body microbiome comparison to describe the complete scenario of the transmission dynamics of wound-colonizing microorganisms.}, } @article {pmid38272730, year = {2024}, author = {Rodríguez, MA and Fernández, LA and Díaz, ML and Gallo, CA and Corona, M and Evans, JD and Reynaldi, FJ}, title = {Bacterial diversity using metagenomics of 16s rDNA in water kefir, an innovative source of probiotics for bee nutrition.}, journal = {Revista Argentina de microbiologia}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ram.2023.12.002}, pmid = {38272730}, issn = {0325-7541}, abstract = {Water kefir is a sparkling, slightly acidic fermented beverage made from sugar, water, and water kefir grains, which are a mixture of yeast and bacteria. These grains produce a variety of fermentation compounds such as lactic acid, acetaldehyde, acetoin, ethanol and carbon dioxide. In this study, a high-throughput sequencing technique was used to characterize the bacterial composition of the original water kefir from which potential probiotics were obtained. We studied the bacterial diversity of both water kefir grains and beverages. DNA was extracted from three replicate samples of both grains and beverages using the Powerlyzer Microbial Kit. The hypervariable V1-V2 region of the bacterial 16S ribosomal RNA gene was amplified to prepare six DNA libraries. Between 1.4M and 2.4M base-pairs were sequenced for the library. In total, 28721971 raw reads were obtained from all the samples. Estimated species richness was higher in kefir beverage samples compared to grain samples. Moreover, a higher level of microbial alpha diversity was observed in the beverage samples. Particularly, the predominant bacteria in beverages were Anaerocolumna and Ralstonia, while in grains Liquorilactobacillus dominated, with lower levels of Leuconostoc and Oenococcus. Although the bacterial diversity in kefir grains was low because only three genera were the most represented, all of them are LAB bacteria with the potential to serve as probiotics in the artificial feeding of bees.}, } @article {pmid38271608, year = {2024}, author = {Mac Aogáin, M and Xaverius Ivan, F and Jaggi, TK and Richardson, H and Shoemark, A and Narayana, JK and Dicker, AJ and Koh, MS and Lee, KCH and Thun How, O and Poh, ME and Chin, KK and Hou, ALY and Ser Hon, P and Low, TB and Abisheganaden, JA and Dimakou, K and Digalaki, A and Kosti, C and Gkousiou, A and Hansbro, PM and Blasi, F and Aliberti, S and Chalmers, JD and Chotirmall, SH}, title = {Airway 'Resistotypes' and Clinical Outcomes in Bronchiectasis.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1164/rccm.202306-1059OC}, pmid = {38271608}, issn = {1535-4970}, abstract = {INTRODUCTION: Application of whole-genome shotgun metagenomics to the airway microbiome in bronchiectasis highlights a diverse pool of antimicrobial resistance genes: the 'resistome', the clinical significance of which remains unclear.

METHODS: Individuals with bronchiectasis were prospectively recruited into cross-sectional and longitudinal cohorts (n=280) including the international multicentre cross-sectional Cohort of Asian and Matched European Bronchiectasis 2 study (CAMEB 2; n=251) and two independent cohorts, one describing patients experiencing acute exacerbation and a further cohort of patients undergoing P. aeruginosa eradication treatment. Sputum was subjected to metagenomic sequencing and the bronchiectasis resistome evaluated in association with clinical outcomes and underlying host microbiomes.

RESULTS: The bronchiectasis resistome features a unique resistance gene profile and elevated counts of aminoglycoside, bicyclomycin, phenicol, triclosan and multi-drug resistance genes. Longitudinally, it exhibits within-patient stability over time and during exacerbations despite between-patient heterogeneity. Proportional differences in baseline resistome profiles including increased macrolide and multi-drug resistance genes associate with shorter intervals to next exacerbation, while distinct resistome archetypes associate with frequent exacerbations, poorer lung function, geographic origin, and the host microbiome. Unsupervised analysis of resistome profiles identified two clinically relevant 'resistotypes' RT1 and RT2, the latter characterized by poor clinical outcomes, increased multi-drug resistance and P. aeruginosa. Successful targeted eradication in P. aeruginosa-colonized individuals mediated reversion from RT2 to RT1, a more clinically favourable resistome profile demonstrating reduced resistance gene diversity.

CONCLUSION: The bronchiectasis resistome associates with clinical outcomes, geographic origin, and the underlying host microbiome. Bronchiectasis 'resistotypes' link to clinical disease and are modifiable through targeted antimicrobial therapy.}, } @article {pmid38271603, year = {2024}, author = {Wicaksono, WA and Mora, M and Bickel, S and Berg, C and Kühn, I and Cernava, T and Berg, G}, title = {Rhizosphere assembly alters along a chronosequence in the Hallstätter glacier forefield (Dachstein, Austria).}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiae005}, pmid = {38271603}, issn = {1574-6941}, abstract = {Rhizosphere microbiome assembly is essential for plant health, but the temporal dimension of this process remains unexplored. We used a chronosequence of 150 years of the retreating Hallstätter glacier (Dachstein, Austria) to disentangle this exemplarily for the rhizosphere of three pioneer alpine plants. Time of deglaciation was an important factor shaping the rhizosphere microbiome. Microbiome functions i.e., nutrient uptake and stress protection were carried out by ubiquitous and cosmopolitan bacteria. The rhizosphere succession along the chronosequence was characterized by decreasing microbial richness but increasing specificity in plant associated bacterial community. Environmental selection is a critical factor in shaping the ecosystem, particularly in terms of plant-driven recruitment from the available edaphic pool. A higher rhizosphere microbial richness during early succession compared to late succession can be explained by the occurrence of cold-acclimated bacteria recruited from the surrounding soils. These taxa might be sensitive to changing habitat conditions that occurred at the later stages. A stronger influence of the plant host on the rhizosphere microbiome assembly was observed with increased time since deglaciation. Overall, this study indicated that well-adapted, ubiquitous microbes potentially support pioneer plants to colonize new ecosystems, while plant-specific microbes may be associated with the long-term establishment of their hosts.}, } @article {pmid38270209, year = {2023}, author = {Laovechprasit, W and Young, KT and Stacy, BA and Tillis, SB and Ossiboff, RJ and Vann, JA and Subramaniam, K and Agnew, DW and Howerth, EW and Zhang, J and Whitaker, S and Walker, A and Orgill, AM and Howell, LN and Shaver, DJ and Donnelly, K and Foley, AM and Stanton, JB}, title = {Piscichuvirus-Associated Severe Meningoencephalomyelitis in Aquatic Turtles, United States, 2009-2021.}, journal = {Emerging infectious diseases}, volume = {30}, number = {2}, pages = {280-288}, doi = {10.3201/eid3002.231142}, pmid = {38270209}, issn = {1080-6059}, abstract = {Viruses from a new species of piscichuvirus were strongly associated with severe lymphocytic meningoencephalomyelitis in several free-ranging aquatic turtles from 3 coastal US states during 2009-2021. Sequencing identified 2 variants (freshwater turtle neural virus 1 [FTuNV1] and sea turtle neural virus 1 [STuNV1]) of the new piscichuvirus species in 3 turtles of 3 species. In situ hybridization localized viral mRNA to the inflamed region of the central nervous system in all 3 sequenced isolates and in 2 of 3 additional nonsequenced isolates. All 3 sequenced isolates phylogenetically clustered with other vertebrate chuvirids within the genus Piscichuvirus. FTuNV1 and STuNV1 shared ≈92% pairwise amino acid identity of the large protein, which narrowly places them within the same novel species. The in situ association of the piscichuviruses in 5 of 6 turtles (representing 3 genera) with lymphocytic meningoencephalomyelitis suggests that piscichuviruses are a likely cause of lymphocytic meningoencephalomyelitis in freshwater and marine turtles.}, } @article {pmid38269573, year = {2024}, author = {Sun, Y and Zhang, D and Liu, H and Ruan, C and Dou, X and Ren, Z and Ge, Z and Du, Z and Jin, H and Li, D and Xue, H and Liu, W and Chen, Z and Wang, Q}, title = {The first reported cases of severe fever with thrombocytopenia syndrome virus from domestic sick camel to humans in China.}, journal = {Emerging microbes & infections}, volume = {}, number = {}, pages = {2309990}, doi = {10.1080/22221751.2024.2309990}, pmid = {38269573}, issn = {2222-1751}, abstract = {ABSTRACTSevere fever with thrombocytopenia syndrome (SFTS) is an emerging tick-borne disease with an increasing annual incidence rate. In this case report, we presented two patients infected with the SFTS virus, suggesting a potential direct transmission route from camels to humans through blood contact. Both patients developed symptoms after engaging in the slaughtering of one sick camel, while their family members living in the same environment or co-diners remained unaffected. Subsequent detection revealed a high viral load of SFTS virus, reaching 10[10] viral RNA copies/ml, in the sample obtained from the sick camel. Metagenomic sequencing did not identify any other pathogens. The SFTS virus was successfully isolated from both patient and camel samples. The complete nucleotide sequences obtained from the infected patients demonstrated a remarkable 100% similarity to those found in the camel, and genetic evolution analysis classified the virus as genotype A. Additionally, partial sequences of the SFTS virus were identified in ticks captured from the camel rearing environment, however, these sequences showed only 95.9% similarity to those found in camel and humans. Furthermore, immunoglobulin M and immunoglobulin G antibodies were detected in serum samples collected from the patient. Our findings provide evidence that camel may serve as a competent reservoir for transmitting the SFTS virus to humans. Further in vitro investigations into SFTS virus infections in large animals are warranted to understand their role in viral maintenance and transmission.}, } @article {pmid38269051, year = {2024}, author = {Han, D and Yu, F and Zhang, D and Yang, Q and Shen, R and Zheng, S and Chen, Y}, title = {Applicability of Bronchoalveolar Lavage Fluid and Plasma Metagenomic Next-Generation Sequencing Assays in the Diagnosis of Pneumonia.}, journal = {Open forum infectious diseases}, volume = {11}, number = {1}, pages = {ofad631}, pmid = {38269051}, issn = {2328-8957}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) provides innovative solutions for predicting complex infections. A comprehensive understanding of its strengths and limitations in real-world clinical settings is necessary to ensure that it is not overused or misinterpreted.

METHODS: Two hundred nine cases with suspected pneumonia were recruited to compare the capabilities of 2 available mNGS assays (bronchoalveolar lavage fluid [BALF] mNGS and plasma mNGS) to identify pneumonia-associated DNA/RNA pathogens and predict antibiotic resistance.

RESULTS: Compared to clinical diagnosis, BALF mNGS demonstrated a high positive percent agreement (95.3%) but a low negative percent agreement (63.1%). Plasma mNGS revealed a low proportion of true negatives (30%) in predicting pulmonary infection. BALF mNGS independently diagnosed 65.6% (61/93) of coinfections and had a remarkable advantage in detecting caustic, rare, or atypical pathogens. Pathogens susceptible to invasive infection or bloodstream transmission, such as Aspergillus spp, Rhizopus spp, Chlamydia psittaci, and human herpesviruses, are prone to be detected by plasma mNGS. BALF mNGS tests provided a positive impact on the diagnosis and treatment of 128 (61.2%) patients. Plasma mNGS, on the other hand, turned out to be more suitable for diagnosing patients who received mechanical ventilation, developed severe pneumonia, or developed sepsis (all P < .01). BALF mNGS was able to identify resistance genes that matched the phenotypic resistance of 69.4% (25/36) of multidrug-resistant pathogens.

CONCLUSIONS: Our data reveal new insights into the advantages and disadvantages of 2 different sequencing modalities in pathogen identification and antibiotic resistance prediction for patients with suspected pneumonia.}, } @article {pmid38268844, year = {2024}, author = {Yul Lee, H and Haque, MA and Yong Cho, D and Bin Jeong, J and Ho Lee, J and Young Lee, G and Yeun Jang, M and Hwan Lee, J and Man Cho, K}, title = {Comparison of microbial diversity and metabolites on household and commercial doenjang.}, journal = {Food chemistry: X}, volume = {21}, number = {}, pages = {101101}, pmid = {38268844}, issn = {2590-1575}, abstract = {In this study, the microbial diversity, free amino acid (FAA), and biological activities of household doenjang (HDJ) from four different regions and commercial doenjang (CDJ) four manufacturers were analyzed. And volatile flavor compound (VFC) and isoflavone profiles were analyzed using gas chromatograph-mass spectrometer (GC-MS) and high performance liquid chromatography (HPLC), respectively. The major bacterial genus in 1HDJ and 2HDJ was Bacillus (97.5%), while in 3HDJ and 4HDJ, it was Enterobacter (47.5%) and Pseudomonas (80%), respectively. Tetragenococcus was the main bacterial genus of CDJ. The Zygosaccharomyces genus among yeast was comparatively high in all samples. In all samples, glutamic acid predominated among the FAAs, and the 3-methyl butanal, benzeneacetaldehyde, and diallyl disulphide were major VFCs. CDJ contained higher levels of isoflavone-glycoside and total phenolics. Except for 3HDJ and 4CDJ, the isoflavone-aglycone and total flavonoid contents were higher in HDJ. The correlation between bacterial genus and metabolited of doenjang showed that Tetragenococcus was closely related to glutamic acid, Bacillus was related to aglycones and ammonia, and Pseudomonas was highly related to isovaleric acid. While, correlation between yeast genus and metabolited of doenjang confirmed that Candida, Hanseniaspora, and Saccharomyces were related with furfural, benzeneacetaldehyde, and 3-methyl butanal, respectively. The results of this study can be utilized as basic data for the industrialization and development of doenjang.}, } @article {pmid38268789, year = {2023}, author = {Lu, Y and Wang, C and Wang, Y and Chen, Y and Zhao, L and Li, Y}, title = {Case report: Enhancing prognosis in severe COVID-19 through human herpes virus coinfection treatment strategies.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1320933}, pmid = {38268789}, issn = {2235-2988}, abstract = {BACKGROUND: In the context of increasing reports of co-infection with coronavirus disease 2019 (COVID-19), particularly with human herpes viruses (HHVs), it is important to consider the appropriate treatment options for HHVs that have been reactivated by COVID-19.

CASE PRESENTATION: This study presents two cases of severe COVID-19 with HHV co-infection. The first case involved a critically ill patient with COVID-19 co-infected with herpes simplex virus type 1, confirmed using metagenomic next-generation sequencing, and another patient with severe COVID-19 experiencing Epstein-Barr virus (EBV) reactivation, as evidenced by elevated EBV-DNA levels in the serum. Treatment included high-dose glucocorticoids and sivelestat sodium, with notable improvements observed after initiating ganciclovir anti-herpesvirus therapy.

CONCLUSION: This study underscores the significance of recognizing HHV co-infections in severe COVID-19 cases and highlights the potential of combining anti-HHV treatment, increased glucocorticoid dosages, and anti-cytokine storm therapy to enhance prognosis.}, } @article {pmid38268584, year = {2024}, author = {Eladham, MW and Selvakumar, B and Saheb Sharif-Askari, N and Saheb Sharif-Askari, F and Ibrahim, SM and Halwani, R}, title = {Unraveling the gut-Lung axis: Exploring complex mechanisms in disease interplay.}, journal = {Heliyon}, volume = {10}, number = {1}, pages = {e24032}, pmid = {38268584}, issn = {2405-8440}, abstract = {The link between gut and lung starts as early as during organogenesis. Even though they are anatomically distinct, essential bidirectional crosstalk via complex mechanisms supports GLA. Emerging studies have demonstrated the association of gut and lung diseases via multifaceted mechanisms. Advancements in omics and metagenomics technologies revealed a potential link between gut and lung microbiota, adding further complexity to GLA. Despite substantial studies on GLA in various disease models, mechanisms beyond microbial dysbiosis regulating the interplay between gut and lung tissues during disease conditions are not thoroughly reviewed. This review outlines disease specific GLA mechanisms, emphasizing research gaps with a focus on gut-to-lung direction based on current GLA literature. Moreover, the review discusses potential gut microbiota and their products like metabolites, immune modulators, and non-bacterial contributions as a basis for developing treatment strategies for lung diseases. Advanced experimental methods, modern diagnostic tools, and technological advancements are also highlighted as crucial areas for improvement in developing novel therapeutic approaches for GLA-related diseases. In conclusion, this review underscores the importance of exploring additional mechanisms within the GLA to gain a deeper understanding that could aid in preventing and treating a wide spectrum of lung diseases.}, } @article {pmid38268451, year = {2024}, author = {Koslicki, D and White, S and Ma, C and Novikov, A}, title = {YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample.}, journal = {Bioinformatics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/bioinformatics/btae047}, pmid = {38268451}, issn = {1367-4811}, abstract = {MOTIVATION: In metagenomics, the study of environmentally associated microbial communities from their sampled DNA, one of the most fundamental computational tasks is that of determining which genomes from a reference database are present or absent in a given sample metagenome. Existing tools generally return point estimates, with no associated confidence or uncertainty associated with it. This has led to practitioners experiencing difficulty when interpreting the results from these tools, particularly for low abundance organisms as these often reside in the "noisy tail" of incorrect predictions. Furthermore, few tools account for the fact that reference databases are often incomplete and rarely, if ever, contain exact replicas of genomes present in an environmentally derived metagenome.

RESULTS: We present solutions for these issues by introducing the algorithm YACHT: Yes/No Answers to Community membership via Hypothesis Testing. This approach introduces a statistical framework that accounts for sequence divergence between the reference and sample genomes, in terms of average nucleotide identity (ANI), as well as incomplete sequencing depth, thus providing a hypothesis test for determining the presence or absence of a reference genome in a sample. After introducing our approach, we quantify its statistical power and how this changes with varying parameters. Subsequently, we perform extensive experiments using both simulated and real data to confirm the accuracy and scalability of this approach.

AVAILABILITY: The source code implementing this approach is available via Conda and at https://github.com/KoslickiLab/YACHT. We also provide the code for reproducing experiments at https://github.com/KoslickiLab/YACHT-reproducibles.

SUPPLEMENTARY INFORMATION: available at Bioinformatics online.}, } @article {pmid38268397, year = {2024}, author = {Wietz, M and Engel, A and Ramondenc, S and Niwano, M and von Appen, WJ and Priest, T and von Jackowski, A and Metfies, K and Bienhold, C and Boetius, A}, title = {The Arctic summer microbiome across Fram Strait: Depth, longitude, and substrate concentrations structure microbial diversity in the euphotic zone.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1462-2920.16568}, pmid = {38268397}, issn = {1462-2920}, support = {//Max-Planck-Gesellschaft/ ; //Natural Environment Research Council/ ; 03F0802A//Bundesministerium für Bildung, Wissenschaft und Kultur/ ; //Helmholtz Association; Helmholtz Program-Oriented Funding (POF-IV)/ ; //AWI program "International Science Program for Integrative Research in Earth Systems" (INSPIRES)/ ; 294757//European Research Council; (FP7/2007-2013) research project ABYSS/ ; }, abstract = {The long-term dynamics of microbial communities across geographic, hydrographic, and biogeochemical gradients in the Arctic Ocean are largely unknown. To address this, we annually sampled polar, mixed, and Atlantic water masses of the Fram Strait (2015-2019; 5-100 m depth) to assess microbiome composition, substrate concentrations, and oceanographic parameters. Longitude and water depth were the major determinants (~30%) of microbial community variability. Bacterial alpha diversity was highest in lower-photic polar waters. Community composition shifted from west to east, with the prevalence of, for example, Dadabacteriales and Thiotrichales in Arctic- and Atlantic-influenced waters, respectively. Concentrations of dissolved organic carbon peaked in the western, compared to carbohydrates in the chlorophyll-maximum of eastern Fram Strait. Interannual differences due to the time of sampling, which varied between early (June 2016/2018) and late (September 2019) phytoplankton bloom stages, illustrated that phytoplankton composition and resulting availability of labile substrates influence bacterial dynamics. We identified 10 species clusters with stable environmental correlations, representing signature populations of distinct ecosystem states. In context with published metagenomic evidence, our microbial-biogeochemical inventory of a key Arctic region establishes a benchmark to assess ecosystem dynamics and the imprint of climate change.}, } @article {pmid38078558, year = {2024}, author = {Fusco, NA and Cosentino, BJ and Gibbs, JP and Allen, ML and Blumenfeld, AJ and Boettner, GH and Carlen, EJ and Collins, M and Dennison, C and DiGiacopo, D and Drapeau Picard, AP and Edmonson, J and Fisher-Reid, MC and Fyffe, R and Gallo, T and Grant, A and Harbold, W and Heard, SB and Lafferty, DJR and Lehtinen, RM and Marino, S and McDonald, JE and Mortelliti, A and Murray, M and Newman, A and Oswald, KN and Ott-Conn, C and Richardson, JL and Rimbach, R and Salaman, P and Steele, M and Stothart, MR and Urban, MC and Vandegrift, K and Vanek, JP and Vanderluit, SN and Vezina, L and Caccone, A}, title = {Population genomic structure of a widespread, urban-dwelling mammal: The eastern grey squirrel (Sciurus carolinensis).}, journal = {Molecular ecology}, volume = {33}, number = {3}, pages = {e17230}, doi = {10.1111/mec.17230}, pmid = {38078558}, issn = {1365-294X}, support = {DEB 2017987//National Science Foundation/ ; DEB 2018140//National Science Foundation/ ; DEB 2018249//National Science Foundation/ ; }, mesh = {Animals ; Humans ; *Metagenomics ; Urban Population ; *Animals, Wild ; Ecosystem ; Sciuridae/genetics ; }, abstract = {Urbanization is a persistent and widespread driver of global environmental change, potentially shaping evolutionary processes due to genetic drift and reduced gene flow in cities induced by habitat fragmentation and small population sizes. We tested this prediction for the eastern grey squirrel (Sciurus carolinensis), a common and conspicuous forest-dwelling rodent, by obtaining 44K SNPs using reduced representation sequencing (ddRAD) for 403 individuals sampled across the species' native range in eastern North America. We observed moderate levels of genetic diversity, low levels of inbreeding, and only a modest signal of isolation-by-distance. Clustering and migration analyses show that estimated levels of migration and genetic connectivity were higher than expected across cities and forested areas, specifically within the eastern portion of the species' range dominated by urbanization, and genetic connectivity was less than expected within the western range where the landscape is fragmented by agriculture. Landscape genetic methods revealed greater gene flow among individual squirrels in forested regions, which likely provide abundant food and shelter for squirrels. Although gene flow appears to be higher in areas with more tree cover, only slight discontinuities in gene flow suggest eastern grey squirrels have maintained connected populations across urban areas in all but the most heavily fragmented agricultural landscapes. Our results suggest urbanization shapes biological evolution in wildlife species depending strongly on the composition and habitability of the landscape matrix surrounding urban areas.}, } @article {pmid38267717, year = {2024}, author = {Barcenilla, C and Cobo-Díaz, JF and De Filippis, F and Valentino, V and Cabrera Rubio, R and O'Neil, D and Mahler de Sanchez, L and Armanini, F and Carlino, N and Blanco-Míguez, A and Pinto, F and Calvete-Torre, I and Sabater, C and Delgado, S and Ruas-Madiedo, P and Quijada, NM and Dzieciol, M and Skírnisdóttir, S and Knobloch, S and Puente, A and López, M and Prieto, M and Marteinsson, VT and Wagner, M and Margolles, A and Segata, N and Cotter, PD and Ercolini, D and Alvarez-Ordóñez, A}, title = {Improved sampling and DNA extraction procedures for microbiome analysis in food-processing environments.}, journal = {Nature protocols}, volume = {}, number = {}, pages = {}, pmid = {38267717}, issn = {1750-2799}, support = {818368//European Commission (EC)/ ; 818368//European Commission (EC)/ ; 818368//European Commission (EC)/ ; 818368//European Commission (EC)/ ; 818368//European Commission (EC)/ ; 818368//European Commission (EC)/ ; 818368//European Commission (EC)/ ; 818368//European Commission (EC)/ ; }, abstract = {Deep investigation of the microbiome of food-production and food-processing environments through whole-metagenome sequencing (WMS) can provide detailed information on the taxonomic composition and functional potential of the microbial communities that inhabit them, with huge potential benefits for environmental monitoring programs. However, certain technical challenges jeopardize the application of WMS technologies with this aim, with the most relevant one being the recovery of a sufficient amount of DNA from the frequently low-biomass samples collected from the equipment, tools and surfaces of food-processing plants. Here, we present the first complete workflow, with optimized DNA-purification methodology, to obtain high-quality WMS sequencing results from samples taken from food-production and food-processing environments and reconstruct metagenome assembled genomes (MAGs). The protocol can yield DNA loads >10 ng in >98% of samples and >500 ng in 57.1% of samples and allows the collection of, on average, 12.2 MAGs per sample (with up to 62 MAGs in a single sample) in ~1 week, including both laboratory and computational work. This markedly improves on results previously obtained in studies performing WMS of processing environments and using other protocols not specifically developed to sequence these types of sample, in which <2 MAGs per sample were obtained. The full protocol has been developed and applied in the framework of the European Union project MASTER (Microbiome applications for sustainable food systems through technologies and enterprise) in 114 food-processing facilities from different production sectors.}, } @article {pmid38267392, year = {2024}, author = {Zhang, J and Lu, T and Song, Y and Rocha, UND and Liu, J and Nikolausz, M and Wei, Y and Richnow, HH}, title = {Viral Communities Contribute More to the Lysis of Antibiotic-Resistant Bacteria than the Transduction of Antibiotic Resistance Genes in Anaerobic Digestion Revealed by Metagenomics.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c07664}, pmid = {38267392}, issn = {1520-5851}, abstract = {Ecological role of the viral community on the fate of antibiotic resistance genes (ARGs) (reduction vs proliferation) remains unclear in anaerobic digestion (AD). Metagenomics revealed a dominance of Siphoviridae and Podoviridae among 13,895 identified viral operational taxonomic units (vOTUs) within AD, and only 21 of the vOTUs carried ARGs, which only accounted for 0.57 ± 0.43% of AD antibiotic resistome. Conversely, ARGs locating on plasmids and integrative and conjugative elements accounted for above 61.0%, indicating a substantial potential for conjugation in driving horizontal gene transfer of ARGs within AD. Virus-host prediction based on CRISPR spacer, tRNA, and homology matches indicated that most viruses (80.2%) could not infect across genera. Among 480 high-quality metagenome assembly genomes, 95 carried ARGs and were considered as putative antibiotic-resistant bacteria (pARB). Furthermore, lytic phages of 66 pARBs were identified and devoid of ARGs, and virus/host abundance ratios with an average value of 71.7 indicated extensive viral activity and lysis. The infectivity of lytic phage was also elucidated through laboratory experiments concerning changes of the phage-to-host ratio, pH, and temperature. Although metagenomic evidence for dissemination of ARGs by phage transduction was found, the higher proportion of lytic phages infecting pARBs suggested that the viral community played a greater role in reducing ARB numbers than spreading ARGs in AD.}, } @article {pmid38267389, year = {2024}, author = {Zhang, L and Zhao, H and Qin, S and Hu, C and Shen, Y and Qu, B and Bai, Y and Liu, B}, title = {Genome-Resolved Metagenomics and Denitrifying Strain Isolation Reveal New Insights into Microbial Denitrification in the Deep Vadose Zone.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c06466}, pmid = {38267389}, issn = {1520-5851}, abstract = {The heavy use of nitrogen fertilizer in intensive agricultural areas often leads to nitrate accumulation in subsurface soil and nitrate contamination in groundwater, which poses a serious risk to public health. Denitrifying microorganisms in the subsoil convert nitrate to gaseous forms of nitrogen, thereby mitigating the leaching of nitrate into groundwater. Here, we investigated denitrifying microorganisms in the deep vadose zone of a typical intensive agricultural area in China through microcosm enrichment, genome-resolved metagenomic analysis, and denitrifying bacteria isolation. A total of 1000 metagenome-assembled genomes (MAGs) were reconstructed, resulting in 98 high-quality, dereplicated MAGs that contained denitrification genes. Among them, 32 MAGs could not be taxonomically classified at the genus or species level, indicating that a broader spectrum of taxonomic groups is involved in subsoil denitrification than previously recognized. A denitrifier isolate library was constructed by using a strategy combining high-throughput and conventional cultivation techniques. Assessment of the denitrification characteristics of both the MAGs and isolates demonstrated the dominance of truncated denitrification. Functional screening revealed the highest denitrification activity in two complete denitrifiers belonging to the genus Pseudomonas. These findings greatly expand the current knowledge of the composition and function of denitrifying microorganisms in subsoils. The constructed isolate library provided the first pool of subsoil-denitrifying microorganisms that could facilitate the development of microbe-based technologies for nitrate attenuation in groundwater.}, } @article {pmid38267279, year = {2024}, author = {Koh, C and Saleh, MC}, title = {Mosquito core viromes: do they exist?.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2024.01.003}, pmid = {38267279}, issn = {1471-5007}, } @article {pmid38266905, year = {2024}, author = {Ning, Z and Cai, P and Zhang, M}, title = {Metagenomic analysis revealed highly diverse carbon fixation microorganisms in a petroleum-hydrocarbon-contaminated aquifer.}, journal = {Environmental research}, volume = {}, number = {}, pages = {118289}, doi = {10.1016/j.envres.2024.118289}, pmid = {38266905}, issn = {1096-0953}, abstract = {As one of the ultimate products of hydrocarbon biodegradation, inorganic carbon always be used to evaluate hydrocarbon biodegradation rates in petroleum-hydrocarbon-contaminated (PHC) aquifers. The evaluation method was challenged because of the existence of carbon fixation microorganisms, which may uptake inorganic carbons and consequently cause the biodegradation rates to be underestimated. We wonder if there are carbon fixation microorganisms in PHC aquifers. Although an extremely limited number of carbon fixation microorganisms in PHC sites have been studied in previous studies, the vast majority of microorganisms that participate in carbon fixation have not been systematically identified. To systematically reveal carbon fixation microorganisms and their survival environmental conditions, high-throughput metagenomic sequencing technologies, which are characterized by culture-independent, unbiased, and comprehensive methods for the detection and taxonomic characterization of microorganisms, were introduced to analyze the groundwater samples collected from a PHC aquifer. Results showed that 1041 genera were annotated as carbon fixation microorganisms, which accounted for 49% of the total number of genera in the PHC aquifer. Carbon fixation genes involved in Calvin-Benson-Bassham (CBB), 3-hydroxy propionate (3HP), reductive tricarboxylic acid (rTCA), and Wood-Ljungdahl (WL) cycles accounted for 2%, 41%, 34%, and 23% of the total carbon fixation genes, respectively, and 3HP, rTCA, and WL can be deemed as the dominant carbon fixation pathways. Most of the identified carbon fixation microorganisms are potential hydrocarbon biodegraders, and the most abundant carbon fixation microorganisms, such as Microbacterium, Novosphingobium, and Reyranella, were just the most abundant microorganisms in the aquifer system. It's deduced that most of the microorganisms in the aquifer were facultative autotrophic, and undertaking the dual responsibilities of degrading hydrocarbons to inorganic carbon and uptaking inorganic carbon to biomass.}, } @article {pmid38266788, year = {2024}, author = {Jiang, Q and Feng, L and Luo, J and Wu, Y and Dong, H and Mustafa, AM and Su, Y and Zhao, Y and Chen, Y}, title = {Simultaneous volatile fatty acids promotion and antibiotic resistance genes reduction in fluoranthene-induced sludge alkaline fermentation: Regulation of microbial consortia and cell functions.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {130367}, doi = {10.1016/j.biortech.2024.130367}, pmid = {38266788}, issn = {1873-2976}, abstract = {The impact and mechanism of fluoranthene (Flr), a typical polycyclic aromatic hydrocarbon highly detected in sludge, on alkaline fermentation for volatile fatty acids (VFAs) recovery and antibiotic resistance genes (ARGs) transfer were studied. The results demonstrated that VFAs production increased from 2189 to 4272 mg COD/L with a simultaneous reduction of ARGs with Flr. The hydrolytic enzymes and genes related to glucose and amino acid metabolism were provoked. Also, Flr benefited for the enrichment of hydrolytic-acidifying consortia (i.e., Parabacteroides and Alkalibaculum) while reduced VFAs consumers (i.e., Rubrivivax) and ARGs potential hosts (i.e., Rubrivivax and Pseudomonas). Metagenomic analysis indicated that the genes related to cell wall synthesis, biofilm formation and substrate transporters to maintain high VFAs-producer activities were upregulated. Moreover, cell functions of efflux pump and Type Ⅳ secretion system were suppressed to inhibit ARGs proliferation. This study provided intrinsic mechanisms of Flr-induced VFAs promotion and ARGs reduction during alkaline fermentation.}, } @article {pmid38266376, year = {2024}, author = {Liu, MK and Tian, XH and Liu, CY and Liu, Y and Tang, YM}, title = {Microbiologic surveys for Baijiu fermentation are affected by experimental design.}, journal = {International journal of food microbiology}, volume = {413}, number = {}, pages = {110588}, doi = {10.1016/j.ijfoodmicro.2024.110588}, pmid = {38266376}, issn = {1879-3460}, abstract = {The traditional Chinese alcoholic beverage Baijiu is produced by spontaneous fermentation of grains under anaerobic conditions. While numerous studies have used metagenomic technology to investigate the microbiome of Baijiu brewing, the microbial succession mechanism of Baijiu brewing has not been fully clarified, and metagenomic strategies for microecology surveys have not been comprehensively evaluated. Using the fermentation process of strong-flavor Baijiu as a model, we compared the data for bacterial communities based on short read 16S rRNA variable regions, V3-V4, and full-length 16S regions, V1-V9, to whole metagenomic shotgun sequencing (WMS) to measure the effect of technology selection on phylogenetic and functional profiles. The results showed differences in bacterial compositions and their relation to volatiles and physicochemical variables between sequencing methods. Furthermore, the percentage of V3-V4 sequences assigned to species level was higher than the percentage of V1-V9 sequences according to SILVA taxonomy, but lower according to NCBI taxonomy (P < 0.05). In both SILVA and NCBI taxonomies, the relative abundances of bacterial communities at both the genus and family levels were more positively correlated with WMS data in the V3-V4 dataset than in the V1-V9 dataset. The WMS identified changes in abundances of multiple metabolic pathways during fermentation (P < 0.05), including "starch and sucrose metabolism," "galactose metabolism," and "fatty acid biosynthesis." Although functional predictions derived from 16S data show similar patterns to WMS, most metabolic pathway changes are uncorrelated (P > 0.05). This study provided new technical and biological insights into Baijiu production that may assist in selection of methodologies for studies of fermentation systems.}, } @article {pmid38266051, year = {2024}, author = {Camacho-Mateu, J and Lampo, A and Sireci, M and Muñoz, MA and Cuesta, JA}, title = {Sparse species interactions reproduce abundance correlation patterns in microbial communities.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {5}, pages = {e2309575121}, doi = {10.1073/pnas.2309575121}, pmid = {38266051}, issn = {1091-6490}, support = {PGC2018-098186-B-I00//Ministerio de Ciencia e Innovación (MCIN)/ ; PID2021-128966NB-I00//Ministerio de Ciencia e Innovación (MCIN)/ ; PID2020-113681GB-I00//Ministerio de Ciencia e Innovación (MCIN)/ ; B-FQM-366-UGR20//Consejería de Conocimiento, Investigación y Universidad, Junta de Andalucía (Ministry of Knowledge, Research and University, Andalusia)/ ; PGC2022-141802NB-I00//Ministerio de Ciencia e Innovación (MCIN)/ ; }, abstract = {During the last decades, macroecology has identified broad-scale patterns of abundances and diversity of microbial communities and put forward some potential explanations for them. However, these advances are not paralleled by a full understanding of the dynamical processes behind them. In particular, abundance fluctuations of different species are found to be correlated, both across time and across communities in metagenomic samples. Reproducing such correlations through appropriate population models remains an open challenge. The present paper tackles this problem and points to sparse species interactions as a necessary mechanism to account for them. Specifically, we discuss several possibilities to include interactions in population models and recognize Lotka-Volterra constants as a successful ansatz. For this, we design a Bayesian inference algorithm to extract sets of interaction constants able to reproduce empirical probability distributions of pairwise correlations for diverse biomes. Importantly, the inferred models still reproduce well-known single-species macroecological patterns concerning abundance fluctuations across both species and communities. Endorsed by the agreement with the empirically observed phenomenology, our analyses provide insights into the properties of the networks of microbial interactions, revealing that sparsity is a crucial feature.}, } @article {pmid38265980, year = {2024}, author = {Nishimura, L and Tanino, A and Ajimoto, M and Katsumura, T and Ogawa, M and Koganebuchi, K and Waku, D and Kumagai, M and Sugimoto, R and Nakaoka, H and Oota, H and Inoue, I}, title = {Metagenomic analyses of 7000 to 5500 years old coprolites excavated from the Torihama shell-mound site in the Japanese archipelago.}, journal = {PloS one}, volume = {19}, number = {1}, pages = {e0295924}, doi = {10.1371/journal.pone.0295924}, pmid = {38265980}, issn = {1932-6203}, abstract = {Coprolites contain various kinds of ancient DNAs derived from gut micro-organisms, viruses, and foods, which can help to determine the gut environment of ancient peoples. Their genomic information should be helpful in elucidating the interaction between hosts and microbes for thousands of years, as well as characterizing the dietary behaviors of ancient people. We performed shotgun metagenomic sequencing on four coprolites excavated from the Torihama shell-mound site in the Japanese archipelago. The coprolites were found in the layers of the Early Jomon period, corresponding stratigraphically to 7000 to 5500 years ago. After shotgun sequencing, we found that a significant number of reads showed homology with known gut microbe, viruses, and food genomes typically found in the feces of modern humans. We detected reads derived from several types of phages and their host bacteria simultaneously, suggesting the coexistence of viruses and their hosts. The food genomes provide biological evidence for the dietary behavior of the Jomon people, consistent with previous archaeological findings. These results indicate that ancient genomic analysis of coprolites is useful for understanding the gut environment and lifestyle of ancient peoples.}, } @article {pmid38265708, year = {2024}, author = {Scribano, FJ and Engevik, KA and Gebert, JT and Hyser, JM}, title = {Live-Cell Fluorescence Imaging for Virus-Host Interactions.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2751}, number = {}, pages = {33-46}, pmid = {38265708}, issn = {1940-6029}, abstract = {Recent technological advances in microscopy have facilitated novel approaches to investigate host-pathogen interactions. In particular, improvements in both microscope hardware and engineered biosensors have helped to overcome barriers to live-cell imaging with fluorescence microscopy. Live fluorescent microscopy allows for the detection of discrete signaling events and protein localization, improving our ability to assess the effects of pharmacologic agents, microbes, or infection with high temporal resolution. Here we describe a protocol for long-term live-cell fluorescence imaging of virus infected cell lines.}, } @article {pmid38265338, year = {2024}, author = {Chanda, D and De, D}, title = {Meta-analysis reveals obesity associated gut microbial alteration patterns and reproducible contributors of functional shift.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2304900}, doi = {10.1080/19490976.2024.2304900}, pmid = {38265338}, issn = {1949-0984}, abstract = {The majority of cohort-specific studies associating gut microbiota with obesity are often contradictory; thus, the replicability of the signature remains questionable. Moreover, the species that drive obesity-associated functional shifts and their replicability remain unexplored. Thus, we aimed to address these questions by analyzing gut microbial metagenome sequencing data to develop an in-depth understanding of obese host-gut microbiota interactions using 3329 samples (Obese, n = 1494; Control, n = 1835) from 17 different countries, including both 16S rRNA gene and metagenomic sequence data. Fecal metagenomic data from diverse geographical locations were curated, profiled, and pooled using a machine learning-based approach to identify robust global signatures of obesity. Furthermore, gut microbial species and pathways were systematically integrated through the genomic content of the species to identify contributors to obesity-associated functional shifts. The community structure of the obese gut microbiome was evaluated, and a reproducible depletion of diversity was observed in the obese compared to the lean gut. From this, we infer that the loss of diversity in the obese gut is responsible for perturbations in the healthy microbial functional repertoire. We identified 25 highly predictive species and 37 pathway associations as signatures of obesity, which were validated with remarkably high accuracy (AUC, Species: 0.85, and pathway: 0.80) with an independent validation dataset. We observed a reduction in short-chain fatty acid (SCFA) producers (several Alistipes species, Odoribacter splanchnicus, etc.) and depletion of promoters of gut barrier integrity (Akkermansia muciniphila and Bifidobacterium longum) in obese guts. Our analysis underlines SCFAs and purine/pyrimidine biosynthesis, carbohydrate metabolism pathways in control individuals, and amino acid, enzyme cofactor, and peptidoglycan biosynthesis pathway enrichment in obese individuals. We also mapped the contributors to important obesity-associated functional shifts and observed that these are both dataset-specific and shared across the datasets. In summary, a comprehensive analysis of diverse datasets unveils species specifically contributing to functional shifts and consistent gut microbial patterns associated to obesity.}, } @article {pmid38265223, year = {2024}, author = {Bollmann, A and Sedlacek, CJ and Sayavedra-Soto, L and Norton, JM}, title = {Metagenome-assembled genomes of two nitrifying microorganisms from the freshwater archaeal ammonia-oxidizing enrichment culture BO1.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0090023}, doi = {10.1128/mra.00900-23}, pmid = {38265223}, issn = {2576-098X}, abstract = {Two metagenome-assembled genomes (MAGs) were recovered from the ammonia-oxidizing enrichment culture BO1 obtained from the sediment of the freshwater reservoir Lake Burr Oak, Ohio, USA. High quality MAGs were assembled for the archaeal ammonia oxidizer Nitrosarchaeum sp. BO1 and the canonical nitrite oxidizer Nitrospira sp. BO1.}, } @article {pmid38264726, year = {2023}, author = {Wang, JZ and Yuan, D and Yang, XH and Sun, CH and Hou, LL and Zhang, Y and Gao, YX}, title = {Etiology of lower respiratory tract in pneumonia based on metagenomic next-generation sequencing: a retrospective study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1291980}, pmid = {38264726}, issn = {2235-2988}, abstract = {INTRODUCTION: Pneumonia are the leading cause of death worldwide, and antibiotic treatment remains fundamental. However, conventional sputum smears or cultures are still inefficient for obtaining pathogenic microorganisms.Metagenomic next-generation sequencing (mNGS) has shown great value in nucleic acid detection, however, the NGS results for lower respiratory tract microorganisms are still poorly studied.

METHODS: This study dealt with investigating the efficacy of mNGS in detecting pathogens in the lower respiratory tract of patients with pulmonary infections. A total of 112 patients admitted at the First Affiliated Hospital of Zhengzhou University between April 30, 2018, and June 30, 2020, were enrolled in this retrospective study. The bronchoalveolar lavage fluid (BALF) was obtained from lower respiratory tract from each patient. Routine methods (bacterial smear and culture) and mNGS were employed for the identification of pathogenic microorganisms in BALF.

RESULTS: The average patient age was 53.0 years, with 94.6% (106/112) obtaining pathogenic microorganism results. The total mNGS detection rate of pathogenic microorganisms significantly surpassed conventional methods (93.7% vs. 32.1%, P < 0.05). Notably, 75% of patients (84/112) were found to have bacteria by mNGS, but only 28.6% (32/112) were found to have bacteria by conventional approaches. The most commonly detected bacteria included Acinetobacter baumannii (19.6%), Klebsiella pneumoniae (17.9%), Pseudomonas aeruginosa (14.3%), Staphylococcus faecium (12.5%), Enterococcus faecium (12.5%), and Haemophilus parainfluenzae (11.6%). In 29.5% (33/112) of patients, fungi were identified using mNGS, including 23 cases of Candida albicans (20.5%), 18 of Pneumocystis carinii (16.1%), and 10 of Aspergillus (8.9%). However, only 7.1 % (8/112) of individuals were found to have fungi when conventional procedures were used. The mNGS detection rate of viruses was significantly higher than the conventional method rate (43.8% vs. 0.9%, P < 0.05). The most commonly detected viruses included Epstein-Barr virus (15.2%), cytomegalovirus (13.4%), circovirus (8.9%), human coronavirus (4.5%), and rhinovirus (4.5%). Only 29.4% (33/112) of patients were positive, whereas 5.4% (6/112) of patients were negative for both detection methods as shown by Kappa analysis, indicating poor consistency between the two methods (P = 0.340; Kappa analysis).

CONCLUSION: Significant benefits of mNGS have been shown in the detection of pathogenic microorganisms in patients with pulmonary infection. For those with suboptimal therapeutic responses, mNGS can provide an etiological basis, aiding in precise anti-infective treatment.}, } @article {pmid38264487, year = {2023}, author = {Ma, X and La, Y and Yang, G and Dai, R and Zhang, J and Zhang, Y and Jin, J and Ma, X and Guo, X and Chu, M and Yan, P and Zhang, Q and Liang, C}, title = {Multi-omics revealed the effects of dietary energy levels on the rumen microbiota and metabolites in yaks under house-feeding conditions.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1309535}, pmid = {38264487}, issn = {1664-302X}, abstract = {Yak (Bos grunniens) is a unique large ruminant species in the Qinghai-Tibetan Plateau (QTP). Changing the energy levels of their rations can significantly improve their growth performance. Therefore, studying the effects of dietary energy levels on the rumen microflora and metabolites of yak is crucial for enhancing the development of the yak industry. Currently, there is a lack of understanding regarding the impact of feeding energy diets on rumen fermentation parameters, microbial functions, and metabolites. This study was designed to determine the appropriate energy level for feeding yak. Three test diets with metabolizable energy levels of 7.57 MJ/kg, 9.44 MJ/kg, and 11.9 MJ/kg were used and the concentration of volatile fatty acids (VFA) in rumen fluid was measured. The microbial communities, functions, and metabolites in yaks were studied by 16S rRNA sequencing, metagenome, and LC-MS non-targeted metabolomics to investigate the relationships among rumen fermentation parameters, microbial diversity, and metabolites. Ration energy levels significantly affect total VFA, acetate, propionate, butyrate, iso-valerate, valerate, and acetate/propionate (p < 0.05). At the phylum level, the dominant phyla in all three treatment groups were Bacteroidota, Firmicutes, and Actinobacteriota. At the genus level, the abundance of the unclassified_o__Bacteroidales, norank_f_Muribaculaceae, Lachnospiraceae_NK4A136_group, and Family _XIII_AD3011_group showed significant differences (p < 0.05) and were significantly correlated with differential metabolites screened for phosphatidylcholine [PC(16:0/0:0), PC(18:3/0:0)], uridine 3'-monophosphate, and adenosine monophosphate, etc. CAZymes family analysis showed that GHs and CEs differed significantly among the three groups. In addition, differential metabolites were mainly enriched in the pathways of lipid metabolism, nucleotide metabolism, and biosynthesis of other secondary metabolites, and the concentrations of differential metabolites were correlated with microbial abundance. In summary, this study analyzed the effects of ration energy levels on rumen microorganisms and metabolites of yaks and their relationships. The results provided a scientific basis for the selection of dietary energy for yaks in the house feeding period in the future.}, } @article {pmid38264162, year = {2024}, author = {Dungan, AM and Tandon, K and Jameson, V and Gotze, CR and Blackall, LL and van Oppen, MJH}, title = {A targeted approach to enrich host-associated bacteria for metagenomic sequencing.}, journal = {FEMS microbes}, volume = {5}, number = {}, pages = {xtad021}, pmid = {38264162}, issn = {2633-6685}, abstract = {Multicellular eukaryotic organisms are hosts to communities of bacteria that reside on or inside their tissues. Often the eukaryotic members of the system contribute to high proportions of metagenomic sequencing reads, making it challenging to achieve sufficient sequencing depth to evaluate bacterial ecology. Stony corals are one such complex community; however, separation of bacterial from eukaryotic (primarily coral and algal symbiont) cells has so far not been successful. Using a combination of hybridization chain reaction fluorescence in situ hybridization and fluorescence activated cell sorting (HCR-FISH + FACS), we sorted two populations of bacteria from five genotypes of the coral Acropora loripes, targeting (i) Endozoicomonas spp, and (ii) all other bacteria. NovaSeq sequencing resulted in 67-91 M reads per sample, 55%-90% of which were identified as bacterial. Most reads were taxonomically assigned to the key coral-associated family, Endozoicomonadaceae, with Vibrionaceae also abundant. Endozoicomonadaceae were 5x more abundant in the 'Endozoicomonas' population, highlighting the success of the dual-labelling approach. This method effectively enriched coral samples for bacteria with <1% contamination from host and algal symbionts. The application of this method will allow researchers to decipher the functional potential of coral-associated bacteria. This method can also be adapted to accommodate other host-associated communities.}, } @article {pmid38264056, year = {2023}, author = {Wang, DX and Xiao, LX and Deng, XY and Deng, W}, title = {Omadacycline for the treatment of severe pneumonia caused by Chlamydia psittaci complicated with acute respiratory distress syndrome during the COVID-19 pandemic.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1207534}, pmid = {38264056}, issn = {2296-858X}, abstract = {INTRODUCTION: Chlamydia psittaci infection in humans is a rare cause that mainly present as community-acquired pneumonia. Severe Chlamydia psittaci pneumonia can lead to acute respiratory distress syndrome (ARDS), septic shock, or multiple organ dysfunction with a mortality rate of 15%-20% before accurate diagnosis and targeted treatment. Metagenomic next-generation sequencing (mNGS) has an advantage in achieving early diagnosis. In the study, omadacycline implementation was described to provide a better understanding of effectiveness in severe psittacosis pneumonia with ARDS.

METHODS: Sixteen patients with severe psittacosis pneumonia with ARDS were selected between September 2021 and October 2022. They were diagnosed using mNGS and treated with omadacycline. Retrospective analysis of clinical manifestations, laboratory data, disease progression, diagnostic tool, treatment, and prognosis was summarized.

RESULTS: Common symptoms included fever, dyspnea, and cough. All patients developed ARDS, accompanied by septic shock (43.7%) and pulmonary embolism (43.7%). Laboratory data showed normal leucocytes, increased creatine kinase isoenzyme, and decreased albumin with liver dysfunction in most patients. All patients had increased neutrophils, C-reactive protein, procalcitonin, and D-dimer with decreased lymphocytes. Airspace consolidation, ground glass opacity, and pleural effusion were found on chest CT. mNGS results were obtained in 24-48 h to identify the diagnosis of Chlamydia psittacosis. All patients received mechanical ventilation with omadacycline treatment. Fourteen patients experienced complete recovery, while the other two patients died from multidrug-resistant bacterial infection and renal failure.

CONCLUSION: mNGS has a significant value in the diagnosis of Chlamydia psittaci infection. Timely treatment of omadacycline can improve prognosis and provide a promising new option for the treatment of severe Chlamydia psittaci pneumonia with ARDS.}, } @article {pmid38263937, year = {2024}, author = {Arıkan, M and Kahraman Demir, T and Yıldız, Z and Helvacı Yılmaz, N and Şen, A and Hanoğlu, L and Yıldırım, S}, title = {[Investigation of the Relationship Between Akkermansia Genomic Diversity in Gut Microbiota and Parkinson's Disease Dementia].}, journal = {Mikrobiyoloji bulteni}, volume = {58}, number = {1}, pages = {13-28}, doi = {10.5578/mb.20249951}, pmid = {38263937}, issn = {0374-9096}, abstract = {Although it is known that the relative abundance of Akkermansia, a bacterial genus commonly associated with health, increases in the gut microbiota of Parkinson's disease (PD) patients, the exact reason for this increase remains unclear. This study was aimed to identify potential changes in Akkermansia within the gut microbiota of PD patients in Türkiye. For this purpose, shotgun metagenomics and a novel Akkermansia genus-specific amplicon sequencing technique was used to investigate the presence of specific Akkermansia strains associated with cognitive impairment (CI) stages in PD and to examine potential genes within these strains. In this context, four gut microbiota samples from Türkiye -three PD with dementia (PDD) and one healthy control without CI (HC)- were analyzed by shotgun metagenomics and metagenome-assembled genomes assigned to Akkermansia genus were reconstructed. Then, a custom database was created by combining these genomes with the Akkermansia genomes in public databases and next generation sequencing (NGS) compatible primers specific to the genus Akkermansia were designed using this database. After optimization of amplification and library preparation steps for genus-specific next generation sequencing, gut microbiota samples from 64 PD patients [32 PDD and 32 PD with mild CI (PD-MCI)] and 26 HCs were analyzed by genus-specific amplicon sequencing. The results revealed the presence of seven strains assigned to Akkermansia muciniphila in gut microbiota samples, two of which showed significant distribution differences (p< 0.05) between demented (PDD) and non-demented groups (PD-MCI, HC). When gene contents of the detected Akkermansia genomes were examined through comparative genomic analysis, the presence of 12 genes only in Akkermansia genomes specific to non-demented groups were predicted. The annotations of these genes showed that they were not reported before with unknown functions. In this study, for the first time, gut microbiota samples from PD patients in Türkiye were analyzed using shotgun metagenomics, a novel genus-specific amplicon sequencing method was developed specifically for the analysis of Akkermansia genus, and then Akkermansia strains and genes potentially associated with CI stages in PD were identified using this method. The results underscore that investigating the species or strain level differences could help better understanding of the changes associated with PD in the human gut microbiota.}, } @article {pmid38263620, year = {2024}, author = {Qiao, J and Chen, M and Zhong, S and Tong, H and Li, F}, title = {Soil Humic Acid Stimulates Potentially Active Dissimilatory Arsenate-Reducing Bacteria in Flooded Paddy Soil as Revealed by Metagenomic Stable Isotope Probing.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c07753}, pmid = {38263620}, issn = {1520-5851}, abstract = {Dissimilatory arsenate reduction contributes a large proportion of arsenic flux from flooded paddy soil, which is closely linked to soil organic carbon input and efflux. Humic acid (HA) represents a natural ingredient in soil and is shown to enhance microbial arsenate respiration to promote arsenic mobility. However, the community and function profiles of metabolically active arsenate-respiring bacteria and their interactions with HA in paddy soil remain unclear. To probe this linkage, we performed a genome-centric comparison of potentially active arsenate-respiring bacteria in anaerobic microcosms amended with [13]C-lactate and HA by combining stable-isotope probing with genome-resolved metagenomics. Indeed, HA greatly accelerated the microbial reduction of arsenate to arsenite. Enrichment of bacteria that harbor arsenate-respiring reductase genes (arrA) in HA-enriched [13]C-DNA was confirmed by metagenomic binning, which are affiliated with Firmicutes (mainly Desulfitobacterium, Bacillus, Brevibacillus, and Clostridia) and Acidobacteria. Characterization of reference extracellular electron transfer (EET)-related genes in these arrA-harboring bacteria supports the presence of EET-like genes, with partial electron-transport chain genes identified. This suggests that Gram-positive Firmicutes- and Acidobacteria-related members may harbor unspecified EET-associated genes involved in metal reduction. Our findings highlight the link between soil HA and potentially active arsenate-respiring bacteria, which can be considered when using HA for arsenic removal.}, } @article {pmid38112444, year = {2024}, author = {Sato, Y and Takebe, H and Tominaga, K and Yasuda, J and Kumagai, H and Hirooka, H and Yoshida, T}, title = {A rumen virosphere with implications of contribution to fermentation and methane production, and endemism in cattle breeds and individuals.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {1}, pages = {e0158123}, doi = {10.1128/aem.01581-23}, pmid = {38112444}, issn = {1098-5336}, support = {//Kieikai Research Foundation/ ; JP21H05057//Japan Society for the Promotion of Science (JSPS)/ ; }, abstract = {Viruses have a potential to modify the ruminal digestion via infection and cell lysis of prokaryotes, suggesting that viruses are related to animal performance and methane production. This study aimed to elucidate the genome-based diversity of rumen viral communities and the differences in virus structure between individuals and cattle breeds and to understand how viruses influence on the rumen. To these ends, a metagenomic sequencing of virus-like particles in the rumen of 22 Japanese cattle, including Japanese Black (JB, n = 8), Japanese Shorthorn (n = 2), and Japanese Black sires × Holstein dams crossbred steers (F1, n = 12) was conducted. Additionally, the rumen viromes of six JB and six F1 that were fed identical diets and kept in a single barn were compared. A total of 8,232 non-redundant viral genomes (≥5-kb length and ≥50% completeness), including 982 complete genomes, were constructed, and rumen virome exhibited lysogenic signatures. Furthermore, putative hosts of 1,223 viral genomes were predicted using tRNA and clustered regularly interspaced short palindromic repeat (CRISPR)-spacer matching. The genomes included 1 and 10 putative novel complete genomes associated with Fibrobacter and Ruminococcus, respectively, which are the main rumen cellulose-degrading bacteria. Additionally, the hosts of 22 viral genomes, including 2 complete genomes, were predicted as methanogens, such as Methanobrevibacter and Methanomethylophilus. Most rumen viruses were highly rumen and individual specific and related to rumen-specific prokaryotes. Furthermore, the rumen viral community structure was significantly different between JB and F1 steers, indicating that cattle breed is one of the factors influencing the rumen virome composition.IMPORTANCEHere, we investigated the individual and breed differences of the rumen viral community in Japanese cattle. In the process, we reconstructed putative novel complete viral genomes related to rumen fiber-degrading bacteria and methanogen. The finding strongly suggests that rumen viruses contribute to cellulose and hemicellulose digestion and methanogenesis. Notably, this study also found that rumen viruses are highly rumen and individual specific, suggesting that rumen viruses may not be transmitted through environmental exposure. More importantly, we revealed differences of viral communities between JB and F1 cattle, indicating that cattle breed is a factor that influences the establishment of rumen virome. These results suggest the possibility of rumen virus transmission from mother to offspring and its potential to influence beef production traits. These rumen viral genomes and findings provide new insights into the characterizations of the rumen viruses.}, } @article {pmid38088552, year = {2024}, author = {Konstanti, P and Ligthart, K and Fryganas, C and Constantinos, P and Smidt, H and de Vos, WM and Belzer, C}, title = {Physiology of γ-aminobutyric acid production by Akkermansia muciniphila.}, journal = {Applied and environmental microbiology}, volume = {90}, number = {1}, pages = {e0112123}, doi = {10.1128/aem.01121-23}, pmid = {38088552}, issn = {1098-5336}, support = {024.00.002//Soehngen Institute of Anaerobic Microbiology (SIAM)/ ; Union's Horizon 2020 grant//Eat2beNICE/ ; }, abstract = {Gut bacteria hold the potential to produce a broad range of metabolites that can modulate human functions, including molecules with neuroactive potential. One such molecule is γ-aminobutyric acid (GABA), the main inhibitory neurotransmitter of the central nervous system in animals. Metagenomic analyses suggest that the genomes of many gut bacteria encode glutamate decarboxylase (GAD), the enzyme that catalyzes GABA production. The genome of Akkermansia muciniphila, a mucin specialist and potential next-generation probiotic from the human gut, is predicted to encode GAD, suggesting a contributing role in GABA production in the human gut. In this study, A. muciniphila was grown in batch cultures with and without pH control. In both experiments, A. muciniphila was found to produce GABA as a response to acid (pH <5.5), although only when GABA precursors, either glutamate or glutamine, were present in the medium. Proteomic analysis comparing A. muciniphila grown with and without precursors at pH 4 did not show a difference in GAD expression, suggesting that it is expressed regardless of the presence of GABA precursors. To further investigate the function of A. muciniphila GAD, we heterologously expressed the gad gene (encoded by locus tag Amuc_0372) with a His tag in Escherichia coli and purified the GAD protein. Enzyme assays showed GAD activity in a pH range between 4 and 6, with the highest specific activity at pH 5 of 144 ± 16 µM GABA/min/mg. Overall, our results demonstrate the ability of A. muciniphila to produce GABA as an acid response and unravel the conditions under which GABA production in A. muciniphila occurs.IMPORTANCEAkkermansia muciniphila is considered to be a beneficial bacterium from the human gut, but the exact mechanisms by which A. muciniphila influences its host are not yet fully understood. To this end, it is important to identify which metabolites are produced and consumed by A. muciniphila that may contribute to a healthy gut. In the present study, we demonstrate the ability of A. muciniphila to produce γ-aminobutyric acid (GABA) when grown in an acidic environment, which often occurs in the gut. GABA is the major inhibitory neurotransmitter in the central nervous system and is present in the human gut. For this reason, it is considered an important bacterial metabolite. Our finding that A. muciniphila produces GABA in acidic environments adds to the growing body of understanding of its relationship with host health and provides an explanation on how it can survive acid stress in the human gut.}, } @article {pmid38263062, year = {2024}, author = {Xie, F and Zhao, S and Zhan, X and Zhou, Y and Li, Y and Zhu, W and Pope, PB and Attwood, GT and Jin, W and Mao, S}, title = {Unraveling the phylogenomic diversity of Methanomassiliicoccales and implications for mitigating ruminant methane emissions.}, journal = {Genome biology}, volume = {25}, number = {1}, pages = {32}, pmid = {38263062}, issn = {1474-760X}, abstract = {BACKGROUND: Methanomassiliicoccales are a recently identified order of methanogens that are diverse across global environments particularly the gastrointestinal tracts of animals; however, their metabolic capacities are defined via a limited number of cultured strains.

RESULTS: Here, we profile and analyze 243 Methanomassiliicoccales genomes assembled from cultured representatives and uncultured metagenomes recovered from various biomes, including the gastrointestinal tracts of different animal species. Our analyses reveal the presence of numerous undefined genera and genetic variability in metabolic capabilities within Methanomassiliicoccales lineages, which is essential for adaptation to their ecological niches. In particular, gastrointestinal tract Methanomassiliicoccales demonstrate the presence of co-diversified members with their hosts over evolutionary timescales and likely originated in the natural environment. We highlight the presence of diverse clades of vitamin transporter BtuC proteins that distinguish Methanomassiliicoccales from other archaeal orders and likely provide a competitive advantage in efficiently handling B12. Furthermore, genome-centric metatranscriptomic analysis of ruminants with varying methane yields reveal elevated expression of select Methanomassiliicoccales genera in low methane animals and suggest that B12 exchanges could enable them to occupy ecological niches that possibly alter the direction of H2 utilization.

CONCLUSIONS: We provide a comprehensive and updated account of divergent Methanomassiliicoccales lineages, drawing from numerous uncultured genomes obtained from various habitats. We also highlight their unique metabolic capabilities involving B12, which could serve as promising targets for mitigating ruminant methane emissions by altering H2 flow.}, } @article {pmid38262517, year = {2024}, author = {Peng, W and Lu, J and Kuang, J and Tang, R and Guan, F and Xie, K and Zhou, L and Yuan, Y}, title = {Enhancement of hydrogenotrophic methanogenesis for methane production by nano zero-valent iron in soils.}, journal = {Environmental research}, volume = {}, number = {}, pages = {118232}, doi = {10.1016/j.envres.2024.118232}, pmid = {38262517}, issn = {1096-0953}, abstract = {Nanoscale zero-valent iron (nZVI) is attracting increasing attention as the most commonly used environmental remediation material. However, given the high surface area and strong reducing capabilities of nZVI, there is a lack of understanding regarding its effects on the complex anaerobic methane production process in flooded soils. To elucidate the mechanism of CH4 production in soil exposed to nZVI, paddy soil was collected and subjected to anaerobic culture under continuous flooding conditions, with various dosages of nZVI applied. The results showed that the introduction of nZVI into anaerobic flooded rice paddy systems promoted microbial utilization of acetate and carbon dioxide as carbon sources for methane production, ultimately leading to increased methane production. Following the introduction of nZVI into the soil, there was a rapid increase in hydrogen levels in the headspace, surpassing that of the control group. The hydrogen levels in both the experimental and control groups were depleted by the 29th day of culture. These findings suggest that nZVI exposure facilitates the enrichment of hydrogenotrophic methanogens, providing them with a favorable environment for growth. Additionally, it affected soil physicochemical properties by increasing pH and electrical conductivity. The metagenomic analysis further indicates that under exposure to nZVI, hydrogenotrophic methanogens, particularly Methanobacteriaceae and Methanocellaceae, were enriched. The relative abundance of genes such as mcrA and mcrB associated with methane production was increased. This study provides important theoretical insights into the response of key microbes, functional genes, and methane production pathways to nZVI during anaerobic methane production in rice paddy soils, offering fundamental insights into the long-term fate and risks associated with the introduction of nZVI into soils.}, } @article {pmid38262490, year = {2024}, author = {Parida, D and Katare, K and Ganguly, A and Chakraborty, D and Konar, O and Nogueira, R and Bala, K}, title = {Molecular docking and metagenomics assisted mitigation of microplastic pollution.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {141271}, doi = {10.1016/j.chemosphere.2024.141271}, pmid = {38262490}, issn = {1879-1298}, abstract = {Microplastics, tiny, flimsy, and direct progenitors of principal and subsidiary plastics, cause environmental degradation in aquatic and terrestrial entities. Contamination concerns include irrevocable impacts, potential cytotoxicity, and negative health effects on mortals. The detection, recovery, and degradation strategies of these pollutants in various biota and ecosystems, as well as their impact on plants, animals, and humans, have been a topic of significant interest. But the natural environment is infested with several types of plastics, all having different chemical makeup, structure, shape, and origin. Plastic trash acts as a substrate for microbial growth, creating biofilms on the plastisphere surface. This colonizing microbial diversity can be glimpsed with meta-genomics, a culture-independent approach. Owing to its comprehensive description of microbial communities, genealogical evidence on unconventional biocatalysts or enzymes, genomic correlations, evolutionary profile, and function, it is being touted as one of the promising tools in identifying novel enzymes for the degradation of polymers. Additionally, computational tools such as molecular docking can predict the binding of these novel enzymes to the polymer substrate, which can be validated through in vitro conditions for its environmentally feasible applications. This review mainly deals with the exploration of metagenomics along with computational tools to provide a clearer perspective into the microbial potential in the biodegradation of microplastics. The computational tools due to their polymathic nature will be quintessential in identifying the enzyme structure, binding affinities of the prospective enzymes to the substrates, and foretelling of degradation pathways involved which can be quite instrumental in the furtherance of the plastic degradation studies.}, } @article {pmid38262322, year = {2024}, author = {Zhang, L and Yan, C and Wen, C}, title = {Vertical distribution characteristics and transport paths of antibiotic resistance genes in constructed wetland system.}, journal = {Journal of hazardous materials}, volume = {466}, number = {}, pages = {133555}, doi = {10.1016/j.jhazmat.2024.133555}, pmid = {38262322}, issn = {1873-3336}, abstract = {Although the migration and diffusion of antibiotic resistance genes (ARGs) in soil-plant systems have attracted much attention, the migration and diffusion characteristics between constructed wetlands and soil-plant systems differ greatly. Therefore, it is necessary to conduct research on vertical transmission and diffusion of ARGs in constructed wetlands. The vertical distribution and transmission of ARGs in constructed wetlands were explored via metagenomic analysis. The results showed that the proportion of multidrug ARGs was the largest, ranging from 24.2% to 47.5%. The shared characteristics of ARGs were similar to those of bacteria, and there were fewer unique ARGs and microbial species in mesophyll tissue. Sourcetracker analysis revealed that ARGs transfer between plants and atmosphere was bidirectional, but the diffusion of ARGs to atmosphere through plants was relatively weak. ARGs were mainly transmitted to atmosphere/surrounding environment through substrate and influent, and the contributions of substrate to ARGs in atmosphere/surrounding environment were 59.2% and 78.6%, respectively. ARGs involved in foliar attachment mainly originated from peripheral inputs. ARGs showed nonspecific selection for the host at phylum, class and order levels. These findings suggest that more attention should be given to the potential risks of ARGs in constructed wetlands, to formulate effective control and management strategies.}, } @article {pmid38261263, year = {2024}, author = {Cao, L and Song, X and Qian, Y and Li, Y and Xu, J and Chen, X and Wang, X and Chen, J}, title = {Identification of a novel adenovirus in liver tissue sample of the Great Himalayan leaf-nosed bat (Hipposideros armiger).}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {38261263}, issn = {1678-4405}, support = {2017YFC1200201//the National Key Research and Development Programs of China/ ; BE2017693//Jiangsu Provincial Key Research and Development Program/ ; 81741062//National Natural Science Foundation of China/ ; }, abstract = {Bats are important reservoirs for many zoonotic viruses. To explore and monitor potential novel viruses carried by bats, 21 liver samples of bats (Hipposideros armiger) were collected from Yunnan Province in southern China. Only one (4.8%) of all models was detected with adenovirus. The whole genome strain obtained by the viral metagenomics method combined with PCR was temporarily named YN01. The complete genome of YN01 was 37,676 bp, with a G + C content of 55.20% and 28 open reading frames. Phylogenetic analysis indicated that the strain YN01 can be classified as genus Mastadenovirus and was the most similar to the adenovirus isolated from Rhinolophus sinicus in China in 2016. The analysis is needed to verify the possibility of cross-species transmission. This virological investigation has increased our understanding of the ecology of bat-borne viruses in this area and provided a reference for possible future infectious diseases.}, } @article {pmid38260892, year = {2023}, author = {Agrawal, N and Fontana, F and Tarracchini, C and Lommi, S and Ventura, M and Milani, C and Viljakainen, H}, title = {Associations of central obesity and habitual food consumption with saliva microbiota and its enzymatic profiles - a pilot study in Finnish children.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1323346}, pmid = {38260892}, issn = {1664-302X}, abstract = {BACKGROUND: Variation in diversity and composition of saliva microbiota has been linked to weight status, but findings have been inconsistent. Focusing on clinically relevant conditions such as central obesity and using advanced sequencing techniques might fill in the gaps of knowledge.

AIMS: We investigated saliva microbiota with shallow metagenome sequencing in children with (n = 14) and without (n = 36) central obesity. Additionally, we examined the role of habitual food consumption on microbial enzymatic repertoire.

METHODS: Data comprised 50 children (50% male) with a mean age of 14.2 (SD 0.3) years, selected from the Finnish Health in Teens (Fin-HIT) cohort. Dietary scores for consumption frequency of sweet treats (STI), dairy products (DCI) and plants (PCI) were derived based on a self-administered food frequency questionnaire. Central obesity was defined based on waist-height ratio using the cut-off 0.5. Saliva samples were subjected to whole-metagenome shotgun sequencing, and taxonomic and functional profiling was achieved with METAnnotatorX2 bioinformatics platform.

RESULTS: Groups had an average 20 (95% CI 14-27) cm difference in waist circumference. We identified the lack of Pseudomonas guguagenesis and Prevotella scopos, oulorum and oris as putative biomarkers associated with central obesity and observed a total of 16 enzymatic reactions differing between the groups. DCI was associated with the highest number of enzyme profiles (122), followed by STI (60) and DCI (25) (Pearson correlation p < 0.05). Intriguingly, STI showed a high positive/negative correlation ratio (5.09), while DCI and PCI showed low ratios (0.54 and 0.33, respectively). Thus, the main driver of enzymatic reactions was STI, and the related pathways involved nitrate metabolism induced by Haemophilus parainfluenzae and Veilonella dispar among others.

CONCLUSION: Clinically relevant differences in central obesity were only modestly reflected in the composition of saliva microbiota. Habitual consumption of sweet treats was a strong determinant of enzymatic reactions of saliva microbiota in children with and without central obesity. The clinical relevance of these findings warrants further studies.}, } @article {pmid38260883, year = {2023}, author = {Sun, X and Jiang, H and Zhang, S}, title = {Diversities and interactions of phages and bacteria in deep-sea sediments as revealed by metagenomics.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1337146}, pmid = {38260883}, issn = {1664-302X}, abstract = {Phages are found virtually everywhere, even in extreme environments, and are extremely diverse both in their virion structures and in their genomic content. They are thought to shape the taxonomic and functional composition of microbial communities as well as their stability. A number of studies on laboratory culture and viral metagenomic research provide deeper insights into the abundance, diversity, distribution, and interaction with hosts of phages across a wide range of ecosystems. Although most of these studies focus on easily accessible samples, such as soils, lakes, and shallow oceans, little is known about bathypelagic phages. In this study, through analyzing the 16S rRNA sequencing and viral metagenomic sequencing data of 25 samples collected from five different bathypelagic ecosystems, we detected a high diversity of bacteria and phages, particularly in the cold seep and hydrothermal vent ecosystems, which have stable chemical energy. The relative abundance of phages in these ecosystems was higher than in other three abyssal ecosystems. The low phage/host ratios obtained from host prediction were different from shallow ecosystems and indicated the prevalence of prophages, suggesting the complexity of phage-bacteria interactions in abyssal ecosystems. In the correlation analysis, we revealed several phages-bacteria interaction networks of potential ecological relevance. Our study contributes to a better understanding of the interactions between bathypelagic bacteria and their phages.}, } @article {pmid38260564, year = {2024}, author = {Singh, V and West, G and Fiocchi, C and Good, CE and Katz, J and Jacobs, MR and Dichosa, AEK and Flask, C and Wesolowski, M and McColl, C and Grubb, B and Ahmed, S and Bank, NC and Thamma, K and Bederman, I and Erokwu, B and Yang, X and Sundrud, MS and Menghini, P and Basson, AR and Ezeji, J and Viswanath, SE and Veloo, A and Sykes, DB and Cominelli, F and Rodriguez-Palacios, A}, title = {Clonal Parabacteroides from Gut Microfistulous Tracts as Transmissible Cytotoxic Succinate-Commensal Model of Crohn's Disease Complications.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.01.09.574896}, pmid = {38260564}, abstract = {Crohn's disease (CD) has been traditionally viewed as a chronic inflammatory disease that cause gut wall thickening and complications, including fistulas, by mechanisms not understood. By focusing on Parabacteroides distasonis (presumed modern succinate-producing commensal probiotic), recovered from intestinal microfistulous tracts (cavernous fistulous micropathologies CavFT proposed as intermediate between 'mucosal fissures' and 'fistulas') in two patients that required surgery to remove CD-damaged ilea, we demonstrate that such isolates exert pathogenic/pathobiont roles in mouse models of CD. Our isolates are clonally-related; potentially emerging as transmissible in the community and mice; proinflammatory and adapted to the ileum of germ-free mice prone to CD-like ileitis (SAMP1/YitFc) but not healthy mice (C57BL/6J), and cytotoxic/ATP-depleting to HoxB8-immortalized bone marrow derived myeloid cells from SAMP1/YitFc mice when concurrently exposed to succinate and extracts from CavFT-derived E. coli , but not to cells from healthy mice. With unique genomic features supporting recent genetic exchange with Bacteroides fragilis -BGF539, evidence of international presence in primarily human metagenome databases, these CavFT Pdis isolates could represent to a new opportunistic Parabacteroides species, or subspecies (' cavitamuralis') adapted to microfistulous niches in CD.}, } @article {pmid38260425, year = {2024}, author = {Heinz, JM and Sommer, M and Rosales, SM and Lu, J and Huebner, LK and Salzberg, SL}, title = {Novel metagenomics analysis suggests a Vibrio species is associated with stony coral tissue loss disease.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.01.02.573916}, pmid = {38260425}, abstract = {UNLABELLED: Stony coral tissue loss disease (SCTLD) has devastated coral reefs off the coast of Florida and continues to spread throughout the Caribbean. Although a number of bacterial taxa have consistently been associated with SCTLD, no pathogen has been definitively implicated in the etiology of SCTLD. Previous studies have predominantly focused on the prokaryotic community through 16S rRNA sequencing of healthy and infected tissues. Here, we provide a different analytical approach by applying a bioinformatics pipeline to publicly available whole genome sequencing samples of SCTLD lesions and healthy tissues from four stony coral species. To compensate for the lack of coral reference genomes, we used data from apparently healthy coral samples to approximate a host genome and healthy microbiome reference. The healthy reference reads were then used to filter the reads from diseased lesion tissue samples, and the remaining data were taxonomically classified at the DNA and protein levels. For DNA classifications, we used a pathogen identification protocol originally designed to identify pathogens in human tissue samples, and for protein classifications, we used a fast protein sequence aligner. Although these data were previously analyzed, our approach revealed unique patterns that were not identified in the previous work. We found a relatively high abundance of the Vibrio genus across diseased samples as well as a number of enriched Vibrio phages that further support the presence of this genus in diseased samples, suggesting that a member of the Vibrio genus may be involved in the visual lesion formation stage of SCTLD.

ARTICLE SUMMARY: Studies of stony coral tissue loss disease (SCTLD), a devastating coral disease, have primary used 16S rRNA sequencing approaches to identify putative pathogens. This study applied human tissue pathogen identification protocols to SCTLD whole genome DNA samples. A k-mer based filtering method for diseased samples was utilized to compensate for the lack of host reference genomes. DNA and protein level classifications revealed a relatively abundant member of the Vibrio genus associated with SCTLD across four stony coral species.}, } @article {pmid38260404, year = {2024}, author = {Baker, JS and Qu, E and Mancuso, CP and Tripp, AD and Conwill, A and Lieberman, TD}, title = {Highly-resolved within-species dynamics in the human facial skin microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.01.10.575018}, pmid = {38260404}, abstract = {UNLABELLED: Human facial skin microbiomes (FSMs) on adults are dominated by just two bacterial species, Cutibacterium acnes and Staphylococcus epidermidis. Underlying this apparent simplicity, each FSM harbors multiple strains of both species whose assembly dynamics on individuals are unknown. Here, we use 4,055 isolate genomes and 360 metagenomes to trace the dynamics of strains on individuals and their transmission. Strains are shared amongst family members of all ages, but each individual harbors unique strain consortia. Strain stability changes upon formation of the adult-type FSM: S. epidermidis lineage turnover slows, and the rate of C. acnes colonization increases before stabilizing, suggesting this transitional window could facilitate engraftment of therapeutic strains. Our work reveals previously undetectable community dynamics and informs the design of therapeutic interventions.

ONE-SENTENCE SUMMARY: Previously undetectable gain and loss of individual strains underlies the species stability of important microbiome bacteria.}, } @article {pmid38260309, year = {2024}, author = {Zheng, J and Huang, L and Yi, H and Yan, Y and Zhang, X and Akresi, J and Yin, Y}, title = {Carbohydrate-active enzyme annotation in microbiomes using dbCAN.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2024.01.10.575125}, pmid = {38260309}, abstract = {CAZymes or carbohydrate-active enzymes are critically important for human gut health, lignocellulose degradation, global carbon recycling, soil health, and plant disease. We developed dbCAN as a web server in 2012 and actively maintain it for automated CAZyme annotation. Considering data privacy and scalability, we provide run_dbcan as a standalone software package since 2018 to allow users perform more secure and scalable CAZyme annotation on their local servers. Here, we offer a comprehensive computational protocol on automated CAZyme annotation of microbiome sequencing data, covering everything from short read pre-processing to data visualization of CAZyme and glycan substrate occurrence and abundance in multiple samples. Using a real-world metagenomic sequencing dataset, this protocol describes commands for dataset and software preparation, metagenome assembly, gene prediction, CAZyme prediction, CAZyme gene cluster (CGC) prediction, glycan substrate prediction, and data visualization. The expected results include publication-quality plots for the abundance of CAZymes, CGCs, and substrates from multiple CAZyme annotation routes (individual sample assembly, co-assembly, and assembly-free). For the individual sample assembly route, this protocol takes ∼33h on a Linux computer with 40 CPUs, while other routes will be faster. This protocol does not require programming experience from users, but it does assume a familiarity with the Linux command-line interface and the ability to run Python scripts in the terminal. The target audience includes the tens of thousands of microbiome researchers who routinely use our web server. This protocol will encourage them to perform more secure, rapid, and scalable CAZyme annotation on their local computer servers.}, } @article {pmid38260197, year = {2023}, author = {Jakab, S and Bálint, Á and Cseri, K and Bali, K and Kaszab, E and Domán, M and Halas, M and Szarka, K and Bányai, K}, title = {Genome stability assessment of PRRS vaccine strain with new ARTIC-style sequencing protocol.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1327725}, pmid = {38260197}, issn = {2297-1769}, abstract = {A tiling amplicon sequencing protocol was developed to analyse the genome sequence stability of the modified live PRRSV vaccine strain, Porcilis MLV. The backbone of the ARTIC-style protocol was formed by 34 individual primer pairs, which were divided into two primer pools. Primer pairs were designed to amplify 532 to 588 bp fragments of the corresponding genomic region. The amplicons are suitable for sequencing on Illumina DNA sequencers with available 600-cycle sequencing kits. The concentration of primer pairs in the pools was optimized to obtain a balanced sequencing depth along the genome. Deep sequencing data of three vaccine batches were also analysed. All three vaccine batches were very similar to each other, although they also showed single nucleotide variations (SNVs) affecting less than 1 % of the genome. In the three vaccine strains, 113 to 122 SNV sites were identified; at these sites, the minority variants represented a frequency range of 1 to 48.7 percent. Additionally, the strains within the batches contained well-known length polymorphisms; the genomes of these minority deletion mutants were 135 to 222 bp shorter than the variant with the complete genome. Our results show the usefulness of ARTIC-style protocols in the evaluation of the genomic stability of PRRS MLV strains.}, } @article {pmid38259958, year = {2024}, author = {Lin, Y and Pascall, DJ}, title = {Characterisation of putative novel tick viruses and zoonotic risk prediction.}, journal = {Ecology and evolution}, volume = {14}, number = {1}, pages = {e10814}, pmid = {38259958}, issn = {2045-7758}, abstract = {Tick-associated viruses remain a substantial zoonotic risk worldwide, so knowledge of the diversity of tick viruses has potential health consequences. Despite their importance, large amounts of sequences in public data sets from tick meta-genomic and -transcriptomic projects remain unannotated, sequence data that could contain undocumented viruses. Through data mining and bioinformatic analysis of more than 37,800 public meta-genomic and -transcriptomic data sets, we found 83 unannotated contigs exhibiting high identity with known tick viruses. These putative viral contigs were classified into three RNA viral families (Alphatetraviridae, Orthomyxoviridae and Chuviridae) and one DNA viral family (Asfarviridae). After manual checking of quality and dissimilarity towards other sequences in the data set, these 83 contigs were reduced to five contigs in the Alphatetraviridae from four putative viruses, four in the Orthomyxoviridae from two putative viruses and one in the Chuviridae which clustered with known tick-associated viruses, forming a separate clade within the viral families. We further attempted to assess which previously known tick viruses likely represent zoonotic risks and thus deserve further investigation. We ranked the human infection potential of 133 known tick-associated viruses using a genome composition-based machine learning model. We found five high-risk tick-associated viruses (Langat virus, Lonestar tick chuvirus 1, Grotenhout virus, Taggert virus and Johnston Atoll virus) that have not been known to infect human and two viral families (Nairoviridae and Phenuiviridae) that contain a large proportion of potential zoonotic tick-associated viruses. This adds to the knowledge of tick virus diversity and highlights the importance of surveillance of newly emerging tick-associated diseases.}, } @article {pmid38259673, year = {2024}, author = {Meiller, TF and Fraser, CM and Grant-Beurmann, S and Humphrys, M and Tallon, L and Sadzewicz, LD and Jabra-Rizk, MA and Alfaifi, A and Kensara, A and Molitoris, JK and Witek, M and Mendes, WS and Regine, WF and Tran, PT and Miller, RC and Sultan, AS}, title = {A Longitudinal Metagenomic Comparative Analysis of Oral Microbiome Shifts in Patients Receiving Proton Radiation versus Photon Radiation for Head and Neck Cancer.}, journal = {Journal of cancer & allied specialties}, volume = {10}, number = {1}, pages = {579}, pmid = {38259673}, issn = {2411-989X}, abstract = {INTRODUCTION: Due to the radiation-sparing effects on salivary gland acini, changes in the composition of the oral microbiome may be a driver for improved outcomes in patients receiving proton radiation, with potentially worse outcomes in patients exposed to photon radiation therapy. To date, a head-to-head comparison of oral microbiome changes at a metagenomic level with longitudinal sampling has yet to be performed in these patient cohorts.

METHODS AND MATERIALS: To comparatively analyze oral microbiome shifts during head and neck radiation therapy, a prospective pilot cohort study was performed at the Maryland Proton Treatment Center and the University of Maryland Marlene and Stewart Greenebaum Comprehensive Cancer Center. A longitudinal metagenomic comparative analysis of oral microbiome shifts was performed at three time points (pre-radiation, during radiation, and immediately post-radiation). Head and neck cancer patients receiving proton radiation (n = 4) were compared to photon radiation (n = 4). Additional control groups included healthy age- and sex-matched controls (n = 5), head and neck cancer patients who never received radiation therapy (n = 8), and patients with oral inflammatory disease (n = 3).

RESULTS: Photon therapy patients presented with lower microbial alpha diversity at all timepoints, and there was a trend towards reduced species richness as compared with proton therapy. Healthy controls and proton patients exhibited overall higher and similar diversity. A more dysbiotic state was observed in patients receiving photon therapy as compared to proton therapy, in which oral microbial homeostasis was maintained. Mucositis was observed in 3/4 photon patients and was not observed in any proton patients during radiation therapy. The bacterial de novo pyrimidine biosynthesis pathway and the nitrate reduction V pathway were comparatively higher following photon exposure. These functional changes in bacterial metabolism may suggest that photon exposure produces a more permissive environment for the proliferation of pathogenic bacteria.

CONCLUSION: Oral microbiome dysbiosis in patients receiving photon radiation may be associated with increased mucositis occurrence. Proton radiation therapy for head and neck cancer demonstrates a safer side effect profile in terms of oral complications, oral microbiome dysbiosis, and functional metabolic status.}, } @article {pmid38259106, year = {2024}, author = {Wei, W and Li, J and Tang, B and Deng, Y and Li, Y and Chen, Q}, title = {Metabolomics and metagenomics reveal the impact of γδ T inhibition on gut microbiota and metabolism in periodontitis-promoting OSCC.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0077723}, doi = {10.1128/msystems.00777-23}, pmid = {38259106}, issn = {2379-5077}, abstract = {During the process of periodontitis-promoting oral squamous cell carcinoma (OSCC), the periodontitis microbiota can facilitate OSCC development by activating γδ T cells. Inhibiting γδ T cells through immunotherapy has been shown to significantly alleviate various types of cancer. However, the underlying mechanism by which inhibiting γδ T cells influenced cancer treatment has not been fully elucidated. In this study, a mouse model of OSCC with periodontitis was established, and γδ T cells were inhibited by antibodies. Gut samples from the mice were collected and analyzed by metabolomics, metagenomics, and 16S rRNA. Integrative analysis of the gut metabolome and microbiome revealed that targeting γδ T resulted in changes in the levels of metabolites associated with cancer in the gut. Although there was no difference in the α diversity of microbiota, β diversity was significantly different, with a more heterogeneous community structure in the mice receiving targeted γδ T immunotherapy. Statistical analysis of the gut microbiota at the species level revealed a significant enrichment of Lactobacillus murinus, which was significantly correlated with γδ T abundance. The functional analysis revealed that inhibiting γδ T could impact the functional gene. A comprehensive analysis revealed that L. murinus is especially associated with changes in adenine, which also had connection with the concentration of IL-17 and the abundance of γδ T.IMPORTANCEThis study revealed the effect of γδ T cells on gut microbial dysbiosis and identify potential links between gut microbiota and metabolism, providing new insights into the role of γδ T during the process of periodontitis-induced OSCC, and identifying relevant biomarkers for future research and clinical monitoring protocol development.}, } @article {pmid38259104, year = {2024}, author = {Fadeev, E and Hennenfeind, JH and Amano, C and Zhao, Z and Klun, K and Herndl, GJ and Tinta, T}, title = {Bacterial degradation of ctenophore Mnemiopsis leidyi organic matter.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0126423}, doi = {10.1128/msystems.01264-23}, pmid = {38259104}, issn = {2379-5077}, abstract = {Blooms of gelatinous zooplankton, an important source of protein-rich biomass in coastal waters, often collapse rapidly, releasing large amounts of labile detrital organic matter (OM) into the surrounding water. Although these blooms have the potential to cause major perturbations in the marine ecosystem, their effects on the microbial community and hence on the biogeochemical cycles have yet to be elucidated. We conducted microcosm experiments simulating the scenario experienced by coastal bacterial communities after the decay of a ctenophore (Mnemiopsis leidyi) bloom in the northern Adriatic Sea. Within 24 h, a rapid response of bacterial communities to the M. leidyi OM was observed, characterized by elevated bacterial biomass production and respiration rates. However, compared to our previous microcosm study of jellyfish (Aurelia aurita s.l.), M. leidyi OM degradation was characterized by significantly lower bacterial growth efficiency, meaning that the carbon stored in the OM was mostly respired. Combined metagenomic and metaproteomic analysis indicated that the degradation activity was mainly performed by Pseudoalteromonas, producing a large amount of proteolytic extracellular enzymes and exhibiting high metabolic activity. Interestingly, the reconstructed metagenome-assembled genome (MAG) of Pseudoalteromonas phenolica was almost identical (average nucleotide identity >99%) to the MAG previously reconstructed in our A. aurita microcosm study, despite the fundamental genetic and biochemical differences of the two gelatinous zooplankton species. Taken together, our data suggest that blooms of different gelatinous zooplankton are likely triggering a consistent response from natural bacterial communities, with specific bacterial lineages driving the remineralization of the gelatinous OM.IMPORTANCEJellyfish blooms are increasingly becoming a recurring seasonal event in marine ecosystems, characterized by a rapid build-up of gelatinous biomass that collapses rapidly. Although these blooms have the potential to cause major perturbations, their impact on marine microbial communities is largely unknown. We conducted an incubation experiment simulating a bloom of the ctenophore Mnemiopsis leidyi in the Northern Adriatic, where we investigated the bacterial response to the gelatinous biomass. We found that the bacterial communities actively degraded the gelatinous organic matter, and overall showed a striking similarity to the dynamics previously observed after a simulated bloom of the jellyfish Aurelia aurita s.l. In both cases, we found that a single bacterial species, Pseudoalteromonas phenolica, was responsible for most of the degradation activity. This suggests that blooms of different jellyfish are likely to trigger a consistent response from natural bacterial communities, with specific bacterial species driving the remineralization of gelatinous biomass.}, } @article {pmid38259099, year = {2024}, author = {Caesar, L and Rice, DW and McAfee, A and Underwood, R and Ganote, C and Tarpy, DR and Foster, LJ and Newton, ILG}, title = {Metagenomic analysis of the honey bee queen microbiome reveals low bacterial diversity and Caudoviricetes phages.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0118223}, doi = {10.1128/msystems.01182-23}, pmid = {38259099}, issn = {2379-5077}, abstract = {In eusocial insects, the health of the queens-the colony founders and sole reproductive females-is a primary determinant for colony success. Queen failure in the honey bee Apis mellifera, for example, is a major concern of beekeepers who annually suffer colony losses, necessitating a greater knowledge of queen health. Several studies on the microbiome of honey bees have characterized its diversity and shown its importance for the health of worker bees, the female non-reproductive caste. However, the microbiome of workers differs from that of queens, which, in comparison, is still poorly studied. Thus, direct investigations of the queen microbiome are required to understand colony-level microbiome assembly, functional roles, and evolution. Here, we used metagenomics to comprehensively characterize the honey bee queen microbiome. Comparing samples from different geographic locations and breeder sources, we show that the microbiome of queens is mostly shaped by the environment experienced since early life and is predicted to play roles in the breakdown of the diet and protection from pathogens and xenobiotics. We also reveal that the microbiome of queens comprises only four candidate core bacterial species, Apilactobacillus kunkeei, Lactobacillus apis, Bombella apis, and Commensalibacter sp. Interestingly, in addition to bacteria, we show that bacteriophages infect the queen microbiome, for which Lactobacillaceae are predicted to be the main reservoirs. Together, our results provide the basis to understand the honey bee colony microbiome assemblage, can guide improvements in queen-rearing processes, and highlight the importance of considering bacteriophages for queen microbiome health and microbiome homeostasis in eusocial insects.IMPORTANCEThe queen caste plays a central role in colony success in eusocial insects, as queens lay eggs and regulate colony behavior and development. Queen failure can cause colonies to collapse, which is one of the major concerns of beekeepers. Thus, understanding the biology behind the queen's health is a pressing issue. Previous studies have shown that the bee microbiome plays an important role in worker bee health, but little is known about the queen microbiome and its function in vivo. Here, we characterized the queen microbiome, identifying for the first time the present species and their putative functions. We show that the queen microbiome has predicted nutritional and protective roles in queen association and comprises only four consistently present bacterial species. Additionally, we bring to attention the spread of phages in the queen microbiome, which increased in abundance in failing queens and may impact the fate of the colony.}, } @article {pmid38259081, year = {2024}, author = {Vineis, JH and Reznikoff, WS and Antonopoulos, DA and Koval, J and Chang, E and Fallon, BR and Paul, BG and Morrison, HG and Sogin, ML}, title = {A novel conjugative transposon carrying an autonomously amplified plasmid.}, journal = {mBio}, volume = {}, number = {}, pages = {e0278723}, doi = {10.1128/mbio.02787-23}, pmid = {38259081}, issn = {2150-7511}, abstract = {Tetracyclines serve as broad-spectrum antibiotics to treat bacterial infections. The discovery of new tetracycline resistance genes has led to new questions about the underlying mechanisms of resistance, gene transfer, and their relevance to human health. We tracked changes in the abundance of a 55-kbp conjugative transposon (CTn214) carrying tetQ, a tetracycline resistance gene, within a Bacteroides fragilis metagenome-assembled genome derived from shotgun sequencing of microbial DNA extracted from the ileal pouch of a patient with ulcerative colitis. The mapping of metagenomic reads to CTn214 revealed the multi-copy nature of a 17,044-nt region containing tetQ in samples collected during inflammation and uninflamed visits. B. fragilis cultivars isolated from the same patient during periods of inflammation harbored CTn214 integrated into the chromosome or both a circular, multi-copy, extrachromosomal region of the CTn214 containing tetQ and the corresponding integrated form. The tetracycline-dependent mechanism for the transmission of CTn214 is nearly identical to a common conjugative transposon found in the genome of B. fragilis (CTnDOT), but the autonomously amplified nature of a circular 17,044-nt region of CTn214 that codes for tetQ and the integration of the same sequence in the linear chromosome within the same cell is a novel observation. Genome and transcriptome sequencing of B. fragilis cultivars grown under different concentrations of tetracycline and ciprofloxacin indicates that tetQ in strains containing the circular form remains actively expressed regardless of treatment, while the expression of tetQ in strains containing the linear form increases only in the presence of tetracycline.IMPORTANCEThe exchange of antibiotic production and resistance genes between microorganisms can lead to the emergence of new pathogens. In this study, short-read mapping of metagenomic samples taken over time from the illeal pouch of a patient with ulcerative colitis to a Bacteroides fragilis metagenome-assembled genome revealed two distinct genomic arrangements of a novel conjugative transposon, CTn214, that encodes tetracycline resistance. The autonomous amplification of a plasmid-like circular form from CTn214 that includes tetQ potentially provides consistent ribosome protection against tetracycline. This mode of antibiotic resistance offers a novel mechanism for understanding the emergence of pathobionts like B. fragilis and their persistence for extended periods of time in patients with inflammatory bowel disease.}, } @article {pmid38259075, year = {2024}, author = {Zeng, Y and Zheng, D and Li, L-P and Wang, M and Gou, M and Kamagata, Y and Chen, Y-T and Nobu, MK and Tang, Y-Q}, title = {Metabolism of novel potential syntrophic acetate-oxidizing bacteria in thermophilic methanogenic chemostats.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0109023}, doi = {10.1128/aem.01090-23}, pmid = {38259075}, issn = {1098-5336}, abstract = {Acetate is a major intermediate in the anaerobic digestion of organic waste to produce CH4. In methanogenic systems, acetate degradation is carried out by either acetoclastic methanogenesis or syntrophic degradation by acetate oxidizers and hydrogenotrophic methanogens. Due to challenges in the isolation of syntrophic acetate-oxidizing bacteria (SAOB), the diversity and metabolism of SAOB and the mechanisms of their interactions with methanogenic partners are not fully characterized. In this study, the in situ activity and metabolic characteristics of potential SAOB and their interactions with methanogens were elucidated through metagenomics and metatranscriptomics. In addition to the reported SAOB classified in the genera Tepidanaerobacter, Desulfotomaculum, and Thermodesulfovibrio, we identified a number of potential SAOB that are affiliated with Clostridia, Thermoanaerobacteraceae, Anaerolineae, and Gemmatimonadetes. The potential SAOB possessing the glycine-mediated acetate oxidation pathway dominates SAOB communities. Moreover, formate appeared to be the main product of the acetate degradation by the most active potential SAOB. We identified the methanogen partner of these potential SAOB in the acetate-fed chemostat as Methanosarcina thermophila. The dominated potential SAOB in each chemostat had similar metabolic characteristics, even though they were in different fatty-acid-fed chemostats. These novel syntrophic lineages are prevalent and may play critical roles in thermophilic methanogenic reactors. This study expands our understanding of the phylogenetic diversity and in situ biological functions of uncultured syntrophic acetate degraders and presents novel insights into how they interact with methanogens.IMPORTANCECombining reactor operation with omics provides insights into novel uncultured syntrophic acetate degraders and how they perform in thermophilic anaerobic digesters. This improves our understanding of syntrophic acetate degradation and contributes to the background knowledge necessary to better control and optimize anaerobic digestion processes.}, } @article {pmid38259074, year = {2024}, author = {Zhang, Y-S and Zhang, Y-Q and Zhao, X-M and Liu, X-L and Qin, Q-L and Liu, N-H and Xu, F and Chen, X-L and Zhang, Y-Z and Li, P-Y}, title = {Metagenomic insights into the dynamic degradation of brown algal polysaccharides by kelp-associated microbiota.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0202523}, doi = {10.1128/aem.02025-23}, pmid = {38259074}, issn = {1098-5336}, abstract = {Marine bacteria play important roles in the degradation and cycling of algal polysaccharides. However, the dynamics of epiphytic bacterial communities and their roles in algal polysaccharide degradation during kelp decay are still unclear. Here, we performed metagenomic analyses to investigate the identities and predicted metabolic abilities of epiphytic bacterial communities during the early and late decay stages of the kelp Saccharina japonica. During kelp decay, the dominant epiphytic bacterial communities shifted from Gammaproteobacteria to Verrucomicrobia and Bacteroidetes. In the early decay stage of S. japonica, epiphytic bacteria primarily targeted kelp-derived labile alginate for degradation, among which the gammaproteobacterial Vibrionaceae (particularly Vibrio) and Psychromonadaceae (particularly Psychromonas), abundant in alginate lyases belonging to the polysaccharide lyase (PL) families PL6, PL7, and PL17, were key alginate degraders. More complex fucoidan was preferred to be degraded in the late decay stage of S. japonica by epiphytic bacteria, predominantly from Verrucomicrobia (particularly Lentimonas), Pirellulaceae of Planctomycetes (particularly Rhodopirellula), Pontiellaceae of Kiritimatiellota, and Flavobacteriaceae of Bacteroidetes, which depended on using glycoside hydrolases (GHs) from the GH29, GH95, and GH141 families and sulfatases from the S1_15, S1_16, S1_17, and S1_25 families to depolymerize fucoidan. The pathways for algal polysaccharide degradation in dominant epiphytic bacterial groups were reconstructed based on analyses of metagenome-assembled genomes. This study sheds light on the roles of different epiphytic bacteria in the degradation of brown algal polysaccharides.IMPORTANCEKelps are important primary producers in coastal marine ecosystems. Polysaccharides, as major components of brown algal biomass, constitute a large fraction of organic carbon in the ocean. However, knowledge of the identities and pathways of epiphytic bacteria involved in the degradation process of brown algal polysaccharides during kelp decay is still elusive. Here, based on metagenomic analyses, the succession of epiphytic bacterial communities and their metabolic potential were investigated during the early and late decay stages of Saccharina japonica. Our study revealed a transition in algal polysaccharide-degrading bacteria during kelp decay, shifting from alginate-degrading Gammaproteobacteria to fucoidan-degrading Verrucomicrobia, Planctomycetes, Kiritimatiellota, and Bacteroidetes. A model for the dynamic degradation of algal cell wall polysaccharides, a complex organic carbon, by epiphytic microbiota during kelp decay was proposed. This study deepens our understanding of the role of epiphytic bacteria in marine algal carbon cycling as well as pathogen control in algal culture.}, } @article {pmid38258025, year = {2024}, author = {Nomoto, R and Osawa, K and Kinoshita, S and Kitagawa, K and Nakanishi, N and Sarassari, R and Raharjo, D and Fujisawa, M and Kuntaman, K and Shirakawa, T}, title = {Metagenome and Resistome Analysis of Beta-Lactam-Resistant Bacteria Isolated from River Waters in Surabaya, Indonesia.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/microorganisms12010199}, pmid = {38258025}, issn = {2076-2607}, support = {1149/UN3/2018//Tahir Professorship of Airlangga University/ ; P23wm0125009 for T.S., JP22fk0108636 and JP23fk0108636 for R.N//The Japan Agency for Medical Research and Development (AMED)/ ; 21K10423 for K.O//Japan Society for the Promotion of Science (JSPS) KAKENHI/ ; }, abstract = {Antimicrobial agents are administered to humans and livestock, and bacterial antimicrobial resistance (AMR) and antimicrobial agents are released into the environment. In this study, to investigate the trend of AMR in humans, livestock, and the environment, we performed a metagenomic analysis of multidrug-resistant bacteria with CHROMagar ESBL in environmental river water samples, which were collected using syringe filter units from waters near hospitals, downtown areas, residential areas, and water treatment plants in Surabaya, Indonesia. Our results showed that Acinetobacter, Pseudomonas, Aeromonas, Enterobacter, Escherichia, and Klebsiella grew in CHROMagar ESBL; they were most frequently detected in water samples from rivers surrounding hospitals contaminated with various AMR genes (ARGs) in high levels. These results identified bacteria as ARG reservoirs and revealed that hospitals could be sources for various ARGs disseminated into the environment. In conclusion, this study details a novel metagenomic analysis of collected bacteria in environmental water samples using a syringe filter unit for an AMR epidemiological study based on the One Health approach.}, } @article {pmid38258021, year = {2024}, author = {Olivo, D and Khalifeh, A and Custer, JM and Kraberger, S and Varsani, A}, title = {Diverse Small Circular DNA Viruses Identified in an American Wigeon Fecal Sample.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/microorganisms12010196}, pmid = {38258021}, issn = {2076-2607}, abstract = {American wigeons (Mareca americana) are waterfowls that are widely distributed throughout North America. Research of viruses associated with American wigeons has been limited to orthomyxoviruses, coronaviruses, and circoviruses. To address this poor knowledge of viruses associated with American wigeons, we undertook a pilot study to identify small circular DNA viruses in a fecal sample collected in January 2021 in the city of Tempe, Arizona (USA). We identified 64 diverse circular DNA viral genomes using a viral metagenomic workflow biased towards circular DNA viruses. Of these, 45 belong to the phylum Cressdnaviricota based on their replication-associated protein sequence, with 3 from the Genomoviridae family and the remaining 42 which currently cannot be assigned to any established virus group. It is most likely that these 45 viruses infect various organisms that are associated with their diet or environment. The remaining 19 virus genomes are part of the Microviridae family and likely associated with the gut enterobacteria of American wigeons.}, } @article {pmid38258019, year = {2024}, author = {Sbaghdi, T and Garneau, JR and Yersin, S and Chaucheyras-Durand, F and Bocquet, M and Moné, A and El Alaoui, H and Bulet, P and Blot, N and Delbac, F}, title = {The Response of the Honey Bee Gut Microbiota to Nosema ceranae Is Modulated by the Probiotic Pediococcus acidilactici and the Neonicotinoid Thiamethoxam.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/microorganisms12010192}, pmid = {38258019}, issn = {2076-2607}, abstract = {The honey bee Apis mellifera is exposed to a variety of biotic and abiotic stressors, such as the highly prevalent microsporidian parasite Nosema (Vairimorpha) ceranae and neonicotinoid insecticides. Both can affect honey bee physiology and microbial gut communities, eventually reducing its lifespan. They can also have a combined effect on the insect's survival. The use of bacterial probiotics has been proposed to improve honey bee health, but their beneficial effect remains an open question. In the present study, western honey bees were experimentally infected with N. ceranae spores, chronically exposed to the neonicotinoid thiamethoxam, and/or supplied daily with the homofermentative bacterium Pediococcus acidilactici MA18/5M thought to improve the honey bees' tolerance to the parasite. Deep shotgun metagenomic sequencing allowed the response of the gut microbiota to be investigated with a taxonomic resolution at the species level. All treatments induced significant changes in honey bee gut bacterial communities. Nosema ceranae infection increased the abundance of Proteus mirabilis, Frischella perrara, and Gilliamella apicola and reduced the abundance of Bifidobacterium asteroides, Fructobacillus fructosus, and Lactobacillus spp. Supplementation with P. acidilactici overturned some of these alterations, bringing back the abundance of some altered species close to the relative abundance found in the controls. Surprisingly, the exposure to thiamethoxam also restored the relative abundance of some species modulated by N. ceranae. This study shows that stressors and probiotics may have an antagonistic impact on honey bee gut bacterial communities and that P. acidilactici may have a protective effect against the dysbiosis induced by an infection with N. ceranae.}, } @article {pmid38257988, year = {2024}, author = {Soria-Villalba, A and Pesantes, N and Jiménez-Hernández, N and Pons, J and Moya, A and Pérez-Brocal, V}, title = {Comparison of Experimental Methodologies Based on Bulk-Metagenome and Virus-like Particle Enrichment: Pros and Cons for Representativeness and Reproducibility in the Study of the Fecal Human Virome.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/microorganisms12010162}, pmid = {38257988}, issn = {2076-2607}, support = {CDEI-06/20-E//Conselleria de Sanitat Universal i Salut Pública/ ; AECC 2017-1485//Asociación Española Contra el Cáncer/ ; CIPROM/2021/042//Generalitat Valenciana/ ; }, abstract = {Studies on the human virome based on the application of metagenomic approaches involve overcoming a series of challenges and limitations inherent not only to the biological features of viruses, but also to methodological pitfalls which different approaches have tried to minimize. These approaches fall into two main categories: bulk-metagenomes and virus-like particle (VLP) enrichment. In order to address issues associated with commonly used experimental procedures to assess the degree of reliability, representativeness, and reproducibility, we designed a comparative analysis applied to three experimental protocols, one based on bulk-metagenomes and two based on VLP enrichment. These protocols were applied to stool samples from 10 adult participants, including two replicas per protocol and subject. We evaluated the performances of the three methods, not only through the analysis of the resulting composition, abundance, and diversity of the virome via taxonomical classification and type of molecule (DNA versus RNA, single stranded vs. double stranded), but also according to how the a priori identical replicas differed from each other according to the extraction methods used. Our results highlight the strengths and weaknesses of each approach, offering valuable insights and tailored recommendations for drawing reliable conclusions based on specific research goals.}, } @article {pmid38257987, year = {2024}, author = {Chen, T and Zhang, S and Yang, J and Li, Y and Kogure, E and Zhu, Y and Xiong, W and Chen, E and Shi, G}, title = {Metabarcoding Analysis of Microorganisms Inside Household Washing Machines in Shanghai, China.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/microorganisms12010160}, pmid = {38257987}, issn = {2076-2607}, support = {KCRC-20220225//KAO (China) Research and Development Center Co., LTD/ ; }, abstract = {Washing machines are one of the tools that bring great convenience to people's daily lives. However, washing machines that have been used for a long time often develop issues such as odor and mold, which can pose health hazards to consumers. There exists a conspicuous gap in our understanding of the microorganisms that inhabit the inner workings of washing machines. In this study, samples were collected from 22 washing machines in Shanghai, China, including both water eluted from different parts of washing machines and biofilms. Quantitative qualitative analysis was performed using fluorescence PCR quantification, and microbial communities were characterized by high-throughput sequencing (HTS). This showed that the microbial communities in all samples were predominantly composed of bacteria. HTS results showed that in the eluted water samples, the bacteria mainly included Pseudomonas, Enhydrobacter, Brevibacterium, and Acinetobacter. Conversely, in the biofilm samples, Enhydrobacter and Brevibacterium were the predominant bacterial microorganisms. Correlation analysis results revealed that microbial colonies in washing machines were significantly correlated with years of use and the type of detergent used to clean the washing machine. As numerous pathogenic microorganisms can be observed in the results, effective preventive measures and future research are essential to mitigate these health problems and ensure the continued safe use of these household appliances.}, } @article {pmid38257986, year = {2024}, author = {Ghenciu, LA and Faur, AC and Bolintineanu, SL and Salavat, MC and Maghiari, AL}, title = {Recent Advances in Diagnosis and Treatment Approaches in Fungal Keratitis: A Narrative Review.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/microorganisms12010161}, pmid = {38257986}, issn = {2076-2607}, abstract = {Fungal keratitis represents a potentially sight-threatening infection associated with poor prognosis, as well as financial burden. Novel diagnostic methods include polymerase-chain-reaction (PCR)-based approaches, metagenomic deep sequences, in vivo confocal microscopy, and antifungal susceptibility testing. The ideal therapeutic approaches and outcomes have been widely discussed in recent times, with early therapy being of the utmost importance for the preservation of visual acuity, minimizing corneal damage and reducing the scar size. However, combination therapy can be more efficacious compared to monotherapy. Understanding the pathogenesis, early diagnosis, and prevention strategies can be of great importance. In this narrative, we discuss the recent progress that may aid our understanding of the diagnosis, treatment, and prevention of mycotic keratitis.}, } @article {pmid38257974, year = {2024}, author = {Filippidou, S and Price, A and Spencer-Jones, C and Scales, A and Macey, MC and Franchi, F and Lebogang, L and Cavalazzi, B and Schwenzer, SP and Olsson-Francis, K}, title = {Diversity of Microbial Mats in the Makgadikgadi Salt Pans, Botswana.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/microorganisms12010147}, pmid = {38257974}, issn = {2076-2607}, support = {124.18//Research England/ ; }, abstract = {The Makgadikgadi Salt Pans are the remnants of a mega paleo-lake system in the central Kalahari, Botswana. Today, the Makgadikgadi Basin is an arid to semi-arid area receiving water of meteoric origin during the short, wet season. Large microbial mats, which support primary production, are formed due to desiccation during the dry season. This study aimed to characterise the microbial diversity of the microbial mats and the underlying sediment. The focus was the Ntwetwe Pan, located west of the Makgadikgadi Basin. Metagenomic analyses demonstrated that the mats consisted of a high relative abundance of Cyanobacteriota (synonym Cyanobacteria) (20.50-41.47%), Pseudomonadota (synonym Proteobacteria) (15.71 to 32.18%), and Actinomycetota (synonym Actinobacteria) (8.53-32.56%). In the underlying sediments, Pseudomonadota, Actinomycetota, and Euryarchaeota represented over 70% of the community. Localised fluctuations in water content and pH did not significantly affect the microbial diversity of the sediment or the mats.}, } @article {pmid38257969, year = {2024}, author = {Fernández, FD and Yan, XH and Kuo, CH and Marcone, C and Conci, LR}, title = {Improving the Comprehension of Pathogenicity and Phylogeny in 'Candidatus Phytoplasma meliae' through Genome Characterization.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/microorganisms12010142}, pmid = {38257969}, issn = {2076-2607}, support = {PICT2016-0862//Agencia Nacional de Promoción Científica y Tecnológica FONCyT/ ; PICT2020-0230//Agencia Nacional de Promoción Científica y Tecnológica FONCyT/ ; PICT2017-3068//Agencia Nacional de Promoción Científica y Tecnológica FONCyT/ ; 2019-PD-E4-I090-001//INTA/ ; }, abstract = {'Candidatus Phytoplasma meliae' is a pathogen associated with chinaberry yellowing disease, which has become a major phytosanitary problem for chinaberry forestry production in Argentina. Despite its economic impact, no genome information of this phytoplasma has been published, which has hindered its characterization at the genomic level. In this study, we used a metagenomics approach to analyze the draft genome of the 'Ca. P. meliae' strain ChTYXIII. The draft assembly consisted of twenty-one contigs with a total length of 751.949 bp, and annotation revealed 669 CDSs, 34 tRNAs, and 1 set of rRNA operons. The metabolic pathways analysis showed that ChTYXIII contains the complete core genes for glycolysis and a functional Sec system for protein translocation. Our phylogenomic analysis based on 133 single-copy genes and genome-to-genome metrics supports the classification as unique 'Ca. P. species' within the MPV clade. We also identified 31 putative effectors, including a homolog to SAP11 and others that have only been described in this pathogen. Our ortholog analysis revealed 37 PMU core genes in the genome of 'Ca. P. meliae' ChTYXIII, leading to the identification of 2 intact PMUs. Our work provides important genomic information for 'Ca. P. meliae' and others phytoplasmas for the 16SrXIII (MPV) group.}, } @article {pmid38257962, year = {2024}, author = {Baud, A and Kennedy, SP}, title = {Targeted Metagenomic Databases Provide Improved Analysis of Microbiota Samples.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/microorganisms12010135}, pmid = {38257962}, issn = {2076-2607}, support = {DOS0053477 SUB et DOS0053473 AR//bpifrance (Structuring R&D Project for Competitiveness - PSPC)/ ; NA//Programme d'Investissements d'avenir/ ; }, abstract = {We report on Moonbase, an innovative pipeline that builds upon the established tools of MetaPhlAn and Kraken2, enhancing their capabilities for more precise taxonomic detection and quantification in diverse microbial communities. Moonbase enhances the performance of Kraken2 mapping by providing an efficient method for constructing project-specific databases. Moonbase was evaluated using synthetic metagenomic samples and compared against MetaPhlAn3 and generalized Kraken2 databases. Moonbase significantly improved species precision and quantification, outperforming marker genes and generalized databases. Construction of a phylogenetic tree from 16S genome data in Moonbase allowed for the incorporation of UniFrac-type phylogenetic information into diversity calculations of samples. We demonstrated that the resulting analysis increased statistical power in distinguishing microbial communities. This study highlights the continual evolution of metagenomic tools with the goal of improving metagenomic analysis and highlighting the potential of the Moonbase pipeline.}, } @article {pmid38257948, year = {2024}, author = {Spatafora, G and Li, Y and He, X and Cowan, A and Tanner, ACR}, title = {The Evolving Microbiome of Dental Caries.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/microorganisms12010121}, pmid = {38257948}, issn = {2076-2607}, support = {DE014711/NH/NIH HHS/United States ; DE019455/NH/NIH HHS/United States ; DE023810/NH/NIH HHS/United States ; DE020102/NH/NIH HHS/United States ; DE026186/NH/NIH HHS/United States ; }, abstract = {Dental caries is a significant oral and public health problem worldwide, especially in low-income populations. The risk of dental caries increases with frequent intake of dietary carbohydrates, including sugars, leading to increased acidity and disruption of the symbiotic diverse and complex microbial community of health. Excess acid production leads to a dysbiotic shift in the bacterial biofilm composition, demineralization of tooth structure, and cavities. Highly acidic and acid-tolerant species associated with caries include Streptococcus mutans, Lactobacillus, Actinomyces, Bifidobacterium, and Scardovia species. The differences in microbiotas depend on tooth site, extent of carious lesions, and rate of disease progression. Metagenomics and metatranscriptomics not only reveal the structure and genetic potential of the caries-associated microbiome, but, more importantly, capture the genetic makeup of the metabolically active microbiome in lesion sites. Due to its multifactorial nature, caries has been difficult to prevent. The use of topical fluoride has had a significant impact on reducing caries in clinical settings, but the approach is costly; the results are less sustainable for high-caries-risk individuals, especially children. Developing treatment regimens that specifically target S. mutans and other acidogenic bacteria, such as using nanoparticles, show promise in altering the cariogenic microbiome, thereby combatting the disease.}, } @article {pmid38257907, year = {2023}, author = {Melekhina, EN and Belykh, ES and Kanev, VA and Taskaeva, AA and Tarabukin, DV and Zinovyeva, AN and Velegzhaninov, IO and Rasova, EE and Baturina, OA and Kabilov, MR and Markarova, MY}, title = {Soil Microbiome in Conditions of Oil Pollution of Subarctic Ecosystems.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/microorganisms12010080}, pmid = {38257907}, issn = {2076-2607}, support = {Registration No. 122040600025-2//The State Assignment of the Institute of Biology of the Federal Research Center of the Komi Scientific Center of the Ural Branch of the Russian Academy of Sciences/ ; 18-29-05028 mk//The Russian Foundation for Basic Research/ ; }, abstract = {The present study aimed to investigate the recovery of soil quality and the bacterial and fungal communities following various recultivation methods in areas contaminated with oil. Oil spills are known to have severe impacts on ecosystems; thus, the restoration of contaminated soils has become a significant challenge nowadays. The study was conducted in the forest-tundra zone of the European North-East, where 39 soil samples from five oil-contaminated sites and reference sites were subjected to metagenomic analyses. The contaminated sites were treated with different biopreparations, and the recovery of soil quality and microbial communities were analyzed. The analysis of bacteria and fungi communities was carried out using 16S rDNA and ITS metabarcoding. It was found that 68% of bacterial OTUs and 64% of fungal OTUs were unique to the reference plot and not registered in any of the recultivated plots. However, the species diversity of recultivated sites was similar, with 50-80% of bacterial OTUs and 44-60% of fungal OTUs being common to all sites. New data obtained through soil metabarcoding confirm our earlier conclusions about the effectiveness of using biopreparations with indigenous oil-oxidizing micro-organisms also with mineral fertilizers, and herbaceous plant seeds for soil remediation. It is possible that the characteristics of microbial communities will be informative in the bioindication of soils reclaimed after oil pollution.}, } @article {pmid38257874, year = {2023}, author = {Malik, PK and Trivedi, S and Kolte, AP and Mohapatra, A and Biswas, S and Bhattar, AVK and Bhatta, R and Rahman, H}, title = {Comparative Rumen Metagenome and CAZyme Profiles in Cattle and Buffaloes: Implications for Methane Yield and Rumen Fermentation on a Common Diet.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/microorganisms12010047}, pmid = {38257874}, issn = {2076-2607}, support = {DARE Window III//International Livestock Research Institute/ ; }, abstract = {A study was undertaken to compare the rumen microbial community composition, methane yield, rumen fermentation, and CAZyme profiles between cattle and buffaloes. The primary aim of this study was to ascertain the impact of the host species on the above when diet and environmental factors are fixed. A total of 43 phyla, 200 orders, 458 families, and 1722 microbial genera were identified in the study. Bacteroidetes was the most prominent bacterial phylum and constituted >1/3rd of the ruminal microbiota; however, their abundances were comparable between cattle and buffaloes. Firmicutes were the second most abundant bacteria, found to be negatively correlated with the Bacteroidetes. The abundances of Firmicutes as well as the F/B ratio were not different between the two host species. In this study, archaea affiliated with the nine phyla were identified, with Euryarchaeota being the most prominent. Like bacterial phyla, the abundances of Euryarchaeota methanogens were also similar between the cattle and buffaloes. At the order level, Methanobacteriales dominated the archaea. Methanogens from the Methanosarcinales, Methanococcales, Methanomicrobiales, and Methanomassiliicoccales groups were also identified, but at a lower frequency. Methanobrevibacter was the most prevalent genus of methanogens, accounting for approximately three percent of the rumen metagenome. However, their distribution was not different between the two host species. CAZymes affiliated with five classes, namely CBM, CE, GH, GT, and PL, were identified in the metagenome, where the GH class was the most abundant and constituted ~70% of the total CAZymes. The protozoal numbers, including Entodiniomorphs and Holotrichs, were also comparable between the cattle and buffaloes. Results from the study did not reveal any significant difference in feed intake, nutrient digestibility, and rumen fermentation between cattle and buffaloes fed on the same diet. As methane yield due to the similar diet composition, feed ingredients, rumen fermentation, and microbiota composition did not vary, these results indicate that the microbiota community structure and methane emissions are under the direct influence of the diet and environment, and the host species may play only a minor role until the productivity does not vary. More studies are warranted to investigate the effect of different diets and environments on microbiota composition and methane yield. Further, the impact of variable productivity on both the cattle and buffaloes when the diet and environmental factors are fixed needs to be ascertained.}, } @article {pmid38257861, year = {2023}, author = {Neal, K and Amachawadi, RG and White, BJ and Shippy, TD and Theurer, ME and Larson, RL and Lubbers, BV and Kleinhenz, M}, title = {Nasopharyngeal Bacterial Prevalence and Microbial Diversity at First Treatment for Bovine Respiratory Disease (BRD) and Its Associations with Health and Mortality Outcomes in Feedyard Cattle.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/microorganisms12010033}, pmid = {38257861}, issn = {2076-2607}, abstract = {Bovine respiratory disease (BRD) is an economically important disease in feedyards influencing both animal welfare and antimicrobial utilization. Major pathogens associated with BRD have been identified in previous research, but little information is available on the relationship between nasopharyngeal microbiota and health outcomes. The objective of this study was to identify potential associations between nasopharyngeal microbiota and antimicrobial resistance patterns of clinical cases that lived or died compared to non-diseased controls. Enrolled animals were subdivided based on clinical disease status and case outcome (subsequent mortality). Deep nasopharyngeal swabs were collected on enrolled animals and submitted for bacterial isolation, antimicrobial susceptibility determination, and metagenomics analysis. Enrolled cattle were represented in three groups: animals at first treatment for BRD that subsequently died (BRDM, n = 9), animals at first treatment for BRD that subsequently lived (BRDL, n = 15), and animals that were never treated for BRD during the feeding phase (CONT, n = 11). Antimicrobial resistance patterns for Pasteurella multocida illustrated cattle in each outcome category had isolates that were pan-susceptible or only showed resistance to oxytetracycline. The relative abundance of species and genera illustrated few differences among the three outcomes. Higher alpha diversity was identified in BRDL compared to CONT at the species level, and both BRDL and BRDM showed increased alpha diversity compared to CONT at the general level. Overall, this work illustrated nasopharyngeal microbiota showed relatively few differences among BRD cases that lived or died compared to animals without BRD.}, } @article {pmid38257846, year = {2023}, author = {Carmona, RCC and Cilli, A and da Costa, AC and Reis, FC and Leal, É and Dos Santos, FCP and Machado, BC and Lopes, CS and Afonso, AMS and Timenetsky, MDCST}, title = {Pegivirus Detection in Cerebrospinal Fluid from Patients with Central Nervous System Infections of Unknown Etiology in Brazil by Viral Metagenomics.}, journal = {Microorganisms}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/microorganisms12010019}, pmid = {38257846}, issn = {2076-2607}, support = {#2018/21193-5 e #2017/50333-7//São Paulo Research Foundation/ ; Fundo Especial de Saúde para Imunização em Massa e Controle de Doenças (FESIMA) SES-PRC-2020/42261 (#CAF107/2020, #CAF 050/2021 and #CAF 060/2022)//Governo do Estado de São Paulo/ ; }, abstract = {Metagenomic next-generation sequencing (mNGS) methodology serves as an excellent supplement in cases where diagnosis is challenging to establish through conventional laboratory tests, and its usage is increasingly prevalent. Examining the causes of infectious diseases in the central nervous system (CNS) is vital for understanding their spread, managing outbreaks, and effective patient care. In a study conducted in the state of São Paulo, Brazil, cerebrospinal fluid (CSF) samples from 500 patients with CNS diseases of indeterminate etiology, collected between 2017 and 2021, were analyzed. Employing a mNGS approach, we obtained the complete coding sequence of Pegivirus hominis (HPgV) genotype 2 in a sample from a patient with encephalitis (named IAL-425/BRA/SP/2019); no other pathogen was detected. Subsequently, to determine the extent of this virus's presence, both polymerase chain reaction (PCR) and/or real-time PCR assays were utilized on the entire collection. The presence of the virus was identified in 4.0% of the samples analyzed. This research constitutes the first report of HPgV detection in CSF samples in South America. Analysis of the IAL-425 genome (9107 nt) revealed a 90% nucleotide identity with HPgV strains from various countries. Evolutionary analyses suggest that HPgV is both endemic and extensively distributed. The direct involvement of HPgV in CNS infections in these patients remains uncertain.}, } @article {pmid38257834, year = {2024}, author = {Veldsman, WP and Yang, C and Zhang, Z and Huang, Y and Chowdhury, D and Zhang, L}, title = {Structural and Functional Disparities within the Human Gut Virome in Terms of Genome Topology and Representative Genome Selection.}, journal = {Viruses}, volume = {16}, number = {1}, pages = {}, doi = {10.3390/v16010134}, pmid = {38257834}, issn = {1999-4915}, support = {BGIRSZ20220014//BGI Group (China)/ ; HKBU 22201419//Hong Kong Research Grant Council Early Career Scheme/ ; RC-SGT2/19-20/SCI/007//HKBU Start-up Grant Tier 2/ ; IRCMS/19-20/D02//HKBU IRCMS/ ; 2021A1515012226//Guangdong Basic and Applied Basic Research Foundation/ ; }, abstract = {Circularity confers protection to viral genomes where linearity falls short, thereby fulfilling the form follows function aphorism. However, a shift away from morphology-based classification toward the molecular and ecological classification of viruses is currently underway within the field of virology. Recent years have seen drastic changes in the International Committee on Taxonomy of Viruses' operational definitions of viruses, particularly for the tailed phages that inhabit the human gut. After the abolition of the order Caudovirales, these tailed phages are best defined as members of the class Caudoviricetes. To determine the epistemological value of genome topology in the context of the human gut virome, we designed a set of seven experiments to assay the impact of genome topology and representative viral selection on biological interpretation. Using Oxford Nanopore long reads for viral genome assembly coupled with Illumina short-read polishing, we showed that circular and linear virus genomes differ remarkably in terms of genome quality, GC skew, transfer RNA gene frequency, structural variant frequency, cross-reference functional annotation (COG, KEGG, Pfam, and TIGRfam), state-of-the-art marker-based classification, and phage-host interaction. Furthermore, the disparity profile changes during dereplication. In particular, our phage-host interaction results demonstrated that proportional abundances cannot be meaningfully compared without due regard for genome topology and dereplication threshold, which necessitates the need for standardized reporting. As a best practice guideline, we recommend that comparative studies of the human gut virome always report the ratio of circular to linear viral genomes along with the dereplication threshold so that structural and functional metrics can be placed into context when assessing biologically relevant metagenomic properties such as proportional abundance.}, } @article {pmid38257809, year = {2024}, author = {Gangopadhayya, A and Lole, K and Ghuge, O and Ramdasi, A and Kamble, A and Roy, D and Thakar, S and Nath, A and Sudeep, AB and Cherian, S}, title = {Metagenomic Analysis of Viromes of Aedes Mosquitoes across India.}, journal = {Viruses}, volume = {16}, number = {1}, pages = {}, doi = {10.3390/v16010109}, pmid = {38257809}, issn = {1999-4915}, support = {6/9-7(209)/2019-ECD-II//Indian Council of Medical Research/ ; }, abstract = {Metagenomic analysis of Aedes aegypti and Ae. albopictus mosquitoes from diverse geographical regions of India revealed the presence of several insect viruses of human interest. Most abundant reads found in Ae. aegypti mosquitoes were of Phasi Charoen-like virus (PCLV), Choristoneura fumiferana granulovirus (CfGV), Cell fusing agent virus (CFAV), and Wenzhou sobemo-like virus 4 (WSLV4), whereas WSLV4 and CfGV constituted the highest percentage of reads in Ae. albopictus viromes. Other reads that were of low percentage included Hubei mosquito virus 2 (HMV2), Porcine astrovirus 4 (PAstV4), and Wild Boar astrovirus (WBAstV). PCLV and CFAV, which were found to be abundant in Ae. aegypti viromes were absent in Ae. albopictus viromes. Among the viromes analyzed, Ae. aegypti sampled from Pune showed the highest percentage (79.82%) of viral reads, while Ae. aegypti mosquitoes sampled from Dibrugarh showed the lowest percentage (3.47%). Shamonda orthobunyavirus (SHAV), African swine fever virus (ASFV), Aroa virus (AROAV), and Ilheus virus (ILHV), having the potential to infect vertebrates, including humans, were also detected in both mosquito species, albeit with low read numbers. Reads of gemykibivirus, avian retrovirus, bacteriophages, herpesviruses, and viruses infecting protozoans, algae, etc., were also detected in the mosquitoes. A high percentage of reads in the Ae. albopictus mosquito samples belonged to unclassified viruses and warrant further investigation. The data generated in the present work may not only lead to studies to explain the influence of these viruses on the replication and transmission of viruses of clinical importance but also to find applications as biocontrol agents against pathogenic viruses.}, } @article {pmid38257241, year = {2024}, author = {Zheng, A and Wei, C and Liu, J and Bu, N and Liu, D}, title = {Deciphering the Mechanism by Which Carbon Dioxide Extends the Shelf Life of Raw Milk: A Microbiomics- and Metabolomics-Based Approach.}, journal = {Molecules (Basel, Switzerland)}, volume = {29}, number = {2}, pages = {}, doi = {10.3390/molecules29020329}, pmid = {38257241}, issn = {1420-3049}, support = {2021AAC02019, 2021AAC03050//Ningxia University/ ; }, abstract = {Microbial community succession in raw milk determines its quality and storage period. In this study, carbon dioxide (CO2) at 2000 ppm was used to treat raw milk to investigate the mechanism of extending the shelf life of raw milk by CO2 treatment from the viewpoint of microbial colonies and metabolites. The results showed that the shelf life of CO2-treated raw milk was extended to 16 days at 4 °C, while that of the control raw milk was only 6 days. Microbiomics analysis identified 221 amplicon sequence variants (ASVs) in raw milk, and the alpha diversity of microbial communities increased (p < 0.05) with the extension of storage time. Among them, Pseudomonas, Actinobacteria and Serratia were the major microbial genera responsible for the deterioration of raw milk, with a percentage of 85.7%. A combined metagenomics and metabolomics analysis revealed that microorganisms altered the levels of metabolites, such as pyruvic acid, glutamic acid, 5'-cmp, arginine, 2-propenoic acid and phenylalanine, in the raw milk through metabolic activities, such as ABC transporters, pyrimidine metabolism, arginine and proline metabolism and phenylalanine metabolism, and reduced the shelf life of raw milk. CO2 treatment prolonged the shelf life of raw milk by inhibiting the growth of Gram-negative aerobic bacteria, such as Acinetobacter guillouiae, Pseudomonas fluorescens, Serratia liquefaciens and Pseudomonas simiae.}, } @article {pmid38256358, year = {2024}, author = {Hsia, NY and Bair, H and Lin, CY and Lin, CJ and Lai, CT and Chang, CM and Lin, JM and Tsai, YY}, title = {Epstein-Barr Virus Uveitis Confirmed via Aqueous Humor Polymerase Chain Reaction and Metagenomics-A Case Report.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {60}, number = {1}, pages = {}, doi = {10.3390/medicina60010097}, pmid = {38256358}, issn = {1648-9144}, abstract = {This is a case report of Epstein-Barr virus (EBV) uveitis confirmed via aqueous humor polymerase chain reaction (PCR) and metagenomics. This 72-year-old male with a history of diabetes and herpes zoster complained of redness and blurred vision in his right eye for eight months. Mild conjunctival injection, anterior chamber cells, mutton-fat keratic precipitates, and vitreous haze were noted. Fluorescein angiography revealed dye leakage from retinal vessels without retinal ischemic changes. Only the serum anti-cytomegalovirus (CMV) IgG was positive while the aqueous humor PCR for VZV (Varicella-zoster virus), HSV (Herpes simplex viruses), CMV, and EBV was initially negative. Inflammation recurred and vitreous haze worsened after discontinuing nine-month topical ganciclovir and oral prednisolone. the aqueous humor PCR was repeated due to persistent low-grade inflammation. The EBV PCR turned out to be positive. Shotgun metagenomics revealed 1459 classified sequences (1.62%) and confirmed the EBV infection. Topical ganciclovir and methylprednisolone treatment was resumed. Conjunctival injection improved while pigmented keratic precipitates lessened. Elderly patients with diabetes or under immunosuppression may be susceptible to chronic uveitis associated with subsequent EBV infection. Repeated aqueous humor PCR and shotgun metagenomics are important tools in the diagnosis of this case of chronic indolent panuveitis.}, } @article {pmid38256252, year = {2024}, author = {Ramon, E and Obón-Santacana, M and Khannous-Lleiffe, O and Saus, E and Gabaldón, T and Guinó, E and Bars-Cortina, D and Ibáñez-Sanz, G and Rodríguez-Alonso, L and Mata, A and García-Rodríguez, A and Moreno, V}, title = {Performance of a Shotgun Prediction Model for Colorectal Cancer When Using 16S rRNA Sequencing Data.}, journal = {International journal of molecular sciences}, volume = {25}, number = {2}, pages = {}, doi = {10.3390/ijms25021181}, pmid = {38256252}, issn = {1422-0067}, support = {PI17-00092 and PI20-01439//Instituto de Salud Carlos III/ ; GCTRA18022MORE//Spanish Association Against Cancer (AECC) Scientific Foundation/ ; action Genrisk//Consortium for Biomedical Research in Epidemiology and Public Health (CIBERESP)/ ; A18131 Ml4Microbiome//COST action/ ; PID2021-126067NB-I00, CPP2021-008552, PCI2022-135066-2 and PDC2022-133266-I00//Spanish Ministry of Science and Innovation, cofounded by ERDF "A way of making Europe"/ ; SGR01551//Catalan Research Agency (AGAUR)/ ; ERC-2016-724173//European Union's Horizon 2020 research and innovation programme/ ; GBMF9742//Gordon and Betty Moore Foundation/ ; LCF/PR/HR21/00737//"La Caixa" foundation/ ; IMPACT Grant IMP/00019 and CIBERINFEC CB21/13/00061- ISCIII-SGEFI/ERDF//Instituto de Salud Carlos III/ ; 875/C/2021//Fundació Marató TV3/ ; CD21/00094//Instituto de Salud Carlos III Sara Borrell/ ; FPU2020-02907//Spanish Ministerio de Universidades/ ; }, abstract = {Colorectal cancer (CRC), the third most common cancer globally, has shown links to disturbed gut microbiota. While significant efforts have been made to establish a microbial signature indicative of CRC using shotgun metagenomic sequencing, the challenge lies in validating this signature with 16S ribosomal RNA (16S) gene sequencing. The primary obstacle is reconciling the differing outputs of these two methodologies, which often lead to divergent statistical models and conclusions. In this study, we introduce an algorithm designed to bridge this gap by mapping shotgun-derived taxa to their 16S counterparts. This mapping enables us to assess the predictive performance of a shotgun-based microbiome signature using 16S data. Our results demonstrate a reduction in performance when applying the 16S-mapped taxa in the shotgun prediction model, though it retains statistical significance. This suggests that while an exact match between shotgun and 16S data may not yet be feasible, our approach provides a viable method for comparative analysis and validation in the context of CRC-associated microbiome research.}, } @article {pmid38256164, year = {2024}, author = {Bombardi, L and Salini, A and Aulitto, M and Zuliani, L and Andreolli, M and Bordoli, P and Coltro, A and Vitulo, N and Zaccone, C and Lampis, S and Fusco, S}, title = {Lignocellulolytic Potential of Microbial Consortia Isolated from a Local Biogas Plant: The Case of Thermostable Xylanases Secreted by Mesophilic Bacteria.}, journal = {International journal of molecular sciences}, volume = {25}, number = {2}, pages = {}, doi = {10.3390/ijms25021090}, pmid = {38256164}, issn = {1422-0067}, support = {CUP B31I18000230006//MUR - Italian Ministry of University and Research/ ; CUP B33C22000660001//NextGenerationEU - European Union/ ; }, abstract = {Lignocellulose biomasses (LCB), including spent mushroom substrate (SMS), pose environmental challenges if not properly managed. At the same time, these renewable resources hold immense potential for biofuel and chemicals production. With the mushroom market growth expected to amplify SMS quantities, repurposing or disposal strategies are critical. This study explores the use of SMS for cultivating microbial communities to produce carbohydrate-active enzymes (CAZymes). Addressing a research gap in using anaerobic digesters for enriching microbiomes feeding on SMS, this study investigates microbial diversity and secreted CAZymes under varied temperatures (37 °C, 50 °C, and 70 °C) and substrates (SMS as well as pure carboxymethylcellulose, and xylan). Enriched microbiomes demonstrated temperature-dependent preferences for cellulose, hemicellulose, and lignin degradation, supported by thermal and elemental analyses. Enzyme assays confirmed lignocellulolytic enzyme secretion correlating with substrate degradation trends. Notably, thermogravimetric analysis (TGA), coupled with differential scanning calorimetry (TGA-DSC), emerged as a rapid approach for saccharification potential determination of LCB. Microbiomes isolated at mesophilic temperature secreted thermophilic hemicellulases exhibiting robust stability and superior enzymatic activity compared to commercial enzymes, aligning with biorefinery conditions. PCR-DGGE and metagenomic analyses showcased dynamic shifts in microbiome composition and functional potential based on environmental conditions, impacting CAZyme abundance and diversity. The meta-functional analysis emphasised the role of CAZymes in biomass transformation, indicating microbial strategies for lignocellulose degradation. Temperature and substrate specificity influenced the degradative potential, highlighting the complexity of environmental-microbial interactions. This study demonstrates a temperature-driven microbial selection for lignocellulose degradation, unveiling thermophilic xylanases with industrial promise. Insights gained contribute to optimizing enzyme production and formulating efficient biomass conversion strategies. Understanding microbial consortia responses to temperature and substrate variations elucidates bioconversion dynamics, emphasizing tailored strategies for harnessing their biotechnological potential.}, } @article {pmid38255883, year = {2024}, author = {Krupinskaitė, A and Stanislauskienė, R and Serapinas, P and Rutkienė, R and Gasparavičiūtė, R and Meškys, R and Stankevičiūtė, J}, title = {α-L-Fucosidases from an Alpaca Faeces Metagenome: Characterisation of Hydrolytic and Transfucosylation Potential.}, journal = {International journal of molecular sciences}, volume = {25}, number = {2}, pages = {}, doi = {10.3390/ijms25020809}, pmid = {38255883}, issn = {1422-0067}, support = {No. 01.2.2-LMT-K-718-03-0045//Lietuvos Mokslo Taryba/ ; }, abstract = {In various life forms, fucose-containing glycans play vital roles in immune recognition, developmental processes, plant immunity, and host-microbe interactions. Together with glucose, galactose, N-acetylglucosamine, and sialic acid, fucose is a significant component of human milk oligosaccharides (HMOs). Fucosylated HMOs benefit infants by acting as prebiotics, preventing pathogen attachment, and potentially protecting against infections, including HIV. Although the need for fucosylated derivatives is clear, their availability is limited. Therefore, synthesis methods for various fucosylated oligosaccharides are explored, employing enzymatic approaches and α-L-fucosidases. This work aimed to characterise α-L-fucosidases identified in an alpaca faeces metagenome. Based on bioinformatic analyses, they were confirmed as members of the GH29A subfamily. The recombinant α-L-fucosidases were expressed in Escherichia coli and showed hydrolytic activity towards p-nitrophenyl-α-L-fucopyranoside and 2'-fucosyllactose. Furthermore, the enzymes' biochemical properties and kinetic characteristics were also determined. All four α-L-fucosidases could catalyse transfucosylation using a broad diversity of fucosyl acceptor substrates, including lactose, maltotriose, L-serine, and L-threonine. The results contribute insights into the potential use of α-L-fucosidases for synthesising fucosylated amino acids.}, } @article {pmid38255816, year = {2024}, author = {Smutin, D and Taldaev, A and Lebedev, E and Adonin, L}, title = {Shotgun Metagenomics Reveals Minor Micro"bee"omes Diversity Defining Differences between Larvae and Pupae Brood Combs.}, journal = {International journal of molecular sciences}, volume = {25}, number = {2}, pages = {}, doi = {10.3390/ijms25020741}, pmid = {38255816}, issn = {1422-0067}, support = {agreement №075-15-2021-1345, unique identifier RF-193021X0012//the Ministry of Science and Higher Education of the Russian Federation within the framework of the Federal Scientific and Technical Program for the Development of Genetic Technologies for 2019-2027./ ; }, abstract = {Bees represent not only a valuable asset in agriculture, but also serve as a model organism within contemporary microbiology. The metagenomic composition of the bee superorganism has been substantially characterized. Nevertheless, traditional cultural methods served as the approach to studying brood combs in the past. Indeed, the comb microbiome may contribute to determining larval caste differentiation and hive immunity. To further this understanding, we conducted a shotgun sequencing analysis of the brood comb microbiome. While we found certain similarities regarding species diversity, it exhibits significant differentiation from all previously described hive metagenomes. Many microbiome members maintain a relatively constant ratio, yet taxa with the highest abundance level tend to be ephemeral. More than 90% of classified metagenomes were Gammaproteobacteria, Bacilli and Actinobacteria genetic signatures. Jaccard dissimilarity between samples based on bacteria genus classifications hesitate from 0.63 to 0.77, which for shotgun sequencing indicates a high consistency in bacterial composition. Concurrently, we identified antagonistic relationships between certain bacterial clusters. The presence of genes related to antibiotic synthesis and antibiotic resistance suggests potential mechanisms underlying the stability of comb microbiomes. Differences between pupal and larval combs emerge in the total metagenome, while taxa with the highest abundance remained consistent. All this suggests that a key role in the functioning of the comb microbiome is played by minor biodiversity, the function of which remains to be established experimentally.}, } @article {pmid38254996, year = {2024}, author = {Silva, I and Alves, M and Malheiro, C and Silva, ARR and Loureiro, S and Henriques, I and González-Alcaraz, MN}, title = {Structural and Functional Shifts in the Microbial Community of a Heavy Metal-Contaminated Soil Exposed to Short-Term Changes in Air Temperature, Soil Moisture and UV Radiation.}, journal = {Genes}, volume = {15}, number = {1}, pages = {}, doi = {10.3390/genes15010107}, pmid = {38254996}, issn = {2073-4425}, support = {PTDC/CTA-AMB/29557/2017//Fundação para a Ciência e Tecnologia/ ; UIDP/50017/2020+UIDB/50017/2020 + LA/P/0094/2020//Fundação para a Ciência e Tecnologia/ ; UIDB/04004/2020//Fundação para a Ciência e Tecnologia/ ; BI/CESAM/0063/METOXCLIM/2018//Fundação para a Ciência e Tecnologia/ ; BI/CESAM/00060/METOXCLIM/2018//Fundação para a Ciência e Tecnologia/ ; PD/BD/135577/2018//Fundação para a Ciência e Tecnologia/ ; RYC2020-029322-I//Government of Spain/ ; MICROCLIM//Analyses et Expérimentations pour les Ecosystèmes/ ; }, abstract = {The interplay between metal contamination and climate change may exacerbate the negative impact on the soil microbiome and, consequently, on soil health and ecosystem services. We assessed the response of the microbial community of a heavy metal-contaminated soil when exposed to short-term (48 h) variations in air temperature, soil humidity or ultraviolet (UV) radiation in the absence and presence of Enchytraeus crypticus (soil invertebrate). Each of the climate scenarios simulated significantly altered at least one of the microbial parameters measured. Irrespective of the presence or absence of invertebrates, the effects were particularly marked upon exposure to increased air temperature and alterations in soil moisture levels (drought and flood scenarios). The observed effects can be partly explained by significant alterations in soil properties such as pH, dissolved organic carbon, and water-extractable heavy metals, which were observed for all scenarios in comparison to standard conditions. The occurrence of invertebrates mitigated some of the impacts observed on the soil microbial community, particularly in bacterial abundance, richness, diversity, and metabolic activity. Our findings emphasize the importance of considering the interplay between climate change, anthropogenic pressures, and soil biotic components to assess the impact of climate change on terrestrial ecosystems and to develop and implement effective management strategies.}, } @article {pmid38254505, year = {2024}, author = {Dridi, C and Millette, M and Salmieri, S and Aguilar Uscanga, BR and Lacroix, S and Venneri, T and Sarmast, E and Allahdad, Z and Di Marzo, V and Silvestri, C and Lacroix, M}, title = {Effect of a Probiotic Beverage Enriched with Cricket Proteins on the Gut Microbiota: Composition of Gut and Correlation with Nutritional Parameters.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/foods13020204}, pmid = {38254505}, issn = {2304-8158}, support = {PSR-SIIRI-984//Ministry of Economy and Innovation (MEI) of Quebec/ ; CRDPJ/505365-2016//Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; PSR-SIIRI-984//Bio-K+, a Kerry company/ ; n/d//International Atomic Energy Agency (IAEA)/ ; }, abstract = {The health and balance of the gut microbiota are known to be linked to diet composition and source, with fermented products and dietary proteins potentially providing an exceptional advantage for the gut. The purpose of this study was to evaluate the effect of protein hydrolysis, using a probiotic beverage enriched with either cricket protein (CP) or cricket protein hydrolysates (CP.Hs), on the composition of the gut microbiota of rats. Taxonomic characterization of the gut microbiota in fecal samples was carried out after a 14-day nutritional study to identify modifications induced by a CP- and CP.H-enriched fermented probiotic product. The results showed no significant differences (p > 0.05) in the diversity and richness of the gut microbiota among the groups fed with casein (positive control), CP-enriched, and fermented CP.H-enriched probiotic beverages; however, the overall composition of the microbiota was altered, with significant modifications in the relative abundance of several bacterial families and genera. In addition, fermented CP.H-enriched probiotic beverages could be related to the decrease in the number of potential pathogens such as Enterococcaceae. The association of gut microbiota with the nutritional parameters was determined and the results showed that digestibility and the protein efficiency ratio (PER) were highly associated with the abundance of several taxa.}, } @article {pmid38254494, year = {2024}, author = {Shu, S and Jing, R and Li, L and Wang, W and Zhang, J and Luo, Z and Shan, Y and Liu, Z}, title = {Effects of Different Heat Treatments on Yak Milk Proteins on Intestinal Microbiota and Metabolism.}, journal = {Foods (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, doi = {10.3390/foods13020192}, pmid = {38254494}, issn = {2304-8158}, support = {32160561//National Natural Science Foundation of China/ ; }, abstract = {Dairy products are susceptible to modifications in protein oxidation during heat processing, which can lead to changes in protein function, subsequently affecting intestinal health. Despite being a unique nutritional source, yak milk has not been thoroughly examined for the effects of its oxidized proteins on intestinal microbiota and metabolism. Hence, this study employed different heat treatment methods (low-temperature pasteurization, high-temperature pasteurization, and high-temperature sterilization) to induce oxidation in yak milk proteins. The study then assessed the degree of oxidation in these proteins and utilized mice as research subjects. Using metagenomics and metabolomics methods, this study examined the structure of intestinal microbial communities and metabolic products in mice consuming oxidized yak milk. The results showed a decrease in carbonyl and total thiol contents of yak milk proteins after different heat treatments, indicating that heat treatment causes oxidation in yak milk proteins. Metagenomic analysis of mouse intestinal microbiota revealed significant changes in 66 genera. In the high-temperature sterilization group (H), key differential genera included Verrucomicrobiales, Verrucomicrobiae, Akkermansiaceae, and 28 others. The high-temperature pasteurization group (M) mainly consisted of Latilactobacillus, Bacillus, and Romboutsia. The low-temperature pasteurization group (L) primarily comprised of Faecalibacterium, Chaetomium, Paenibacillaceae, Eggerthella, Sordariales, and 33 others. Functionally, compared to the control group (C), the H group upregulated translation and energy metabolism functions, the L group the M group significantly upregulated metabolism of other amino acids, translation, and cell replication and repair functions. Based on metabolomic analysis, differential changes in mouse metabolites could affect multiple metabolic pathways in the body. The most significantly affected metabolic pathways were phenylalanine metabolism, vitamin B6 metabolism, steroid hormone biosynthesis, and pantothenate and CoA biosynthesis. The changes were similar to the functional pathway analysis of mouse metagenomics, affecting amino acid and energy metabolism in mice. In summary, moderate oxidation of yak milk proteins exhibits a positive effect on mouse intestinal microbiota and metabolism. In conclusion, yak milk has a positive effect on mouse intestinal microflora and metabolism, and this study provides a scientific basis for optimizing dairy processing technology and further developing and applying yak milk.}, } @article {pmid38254416, year = {2024}, author = {Hetterich, J and Mirolo, M and Kaiser, F and Ludlow, M and Reineking, W and Zdora, I and Hewicker-Trautwein, M and Osterhaus, ADME and Pees, M}, title = {Concurrent Detection of a Papillomatous Lesion and Sequence Reads Corresponding to a Member of the Family Adintoviridae in a Bell's Hinge-Back Tortoise (Kinixys belliana).}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/ani14020247}, pmid = {38254416}, issn = {2076-2615}, abstract = {An adult male Bell's hinge-back tortoise (Kinixys belliana) was admitted to a veterinary clinic due to a swelling in the oral cavity. Physical examination revealed an approximately 2.5 × 1.5 cm sized, irregularly shaped tissue mass with villiform projections extending from its surface located in the oropharyngeal cavity. An initial biopsy was performed, and the lesion was diagnosed as squamous papilloma. Swabs taken for virological examination tested negative with specific PCRs for papillomavirus and herpesvirus. Further analysis of the oropharyngeal mass via metagenomic sequencing revealed sequence reads corresponding to a member of the family Adintoviridae. The tissue mass was removed one week after the initial examination. The oral cavity remained unsuspicious in follow-up examinations performed after one, five and twenty weeks. However, a regrowth of the tissue was determined 23 months after the initial presentation. The resampled biopsy tested negative for sequence reads of Adintoviridae. Conclusively, this report presents the diagnostic testing and therapy of an oral cavity lesion of unknown origin. The significance of concurrent metagenomic determination of adintovirus sequence reads within the tissue lesion is discussed.}, } @article {pmid38254406, year = {2024}, author = {Kaszab, E and Bali, K and Marton, S and Ursu, K and Farkas, SL and Fehér, E and Domán, M and Martella, V and Bányai, K}, title = {Metagenomic Identification of Novel Eukaryotic Viruses with Small DNA Genomes in Pheasants.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/ani14020237}, pmid = {38254406}, issn = {2076-2615}, support = {National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety (RRF- 2.3.1-21-2022-00001)//National Research, Development and Innovation Office/ ; TKP2021-EGA-01//National Research, Development and Innovation Office/ ; NKFI-OTKA K124655//National Research, Development and Innovation Office/ ; }, abstract = {A panel of intestinal samples collected from common pheasants (Phasianus colchicus) between 2008 and 2017 was used for metagenomic investigation using an unbiased enrichment protocol and different bioinformatic pipelines. The number of sequence reads in the metagenomic analysis ranged from 1,419,265 to 17,507,704 with a viral sequence read rate ranging from 0.01% to 59%. When considering the sequence reads of eukaryotic viruses, RNA and DNA viruses were identified in the samples, including but not limited to coronaviruses, reoviruses, parvoviruses, and CRESS DNA viruses (i.e., circular Rep-encoding single-stranded DNA viruses). Partial or nearly complete genome sequences were reconstructed of at least three different parvoviruses (dependoparvovirus, aveparvovirus and chaphamaparvovirus), as well as gyroviruses and diverse CRESS DNA viruses. Generating information of virus diversity will serve as a basis for developing specific diagnostic tools and for structured epidemiological investigations, useful to assess the impact of these novel viruses on animal health.}, } @article {pmid38254181, year = {2024}, author = {Chai, J and Zhuang, Y and Cui, K and Bi, Y and Zhang, N}, title = {Metagenomics reveals the temporal dynamics of the rumen resistome and microbiome in goat kids.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {14}, pmid = {38254181}, issn = {2049-2618}, support = {31872385//National Natural Science Foundation of China/ ; 31872385//National Natural Science Foundation of China/ ; 2021SZD0014//Inner Mongolia Science and Technology Key Project/ ; 2018YFD0501902//National Key R&D Program Projects/ ; }, abstract = {BACKGROUND: The gut microbiome of domestic animals carries antibiotic resistance genes (ARGs) which can be transmitted to the environment and humans, resulting in challenges of antibiotic resistance. Although it has been reported that the rumen microbiome of ruminants may be a reservoir of ARGs, the factors affecting the temporal dynamics of the rumen resistome are still unclear. Here, we collected rumen content samples of goats at 1, 7, 14, 28, 42, 56, 70, and 84 days of age, analyzed their microbiome and resistome profiles using metagenomics, and assessed the temporal dynamics of the rumen resistome in goats at the early stage of life under a conventional feeding system.

RESULTS: In our results, the rumen resistome of goat kids contained ARGs to 41 classes, and the richness of ARGs decreased with age. Four antibiotic compound types of ARGs, including drugs, biocides, metals, and multi-compounds, were found during milk feeding, while only drug types of ARGs were observed after supplementation with starter feed. The specific ARGs for each age and their temporal dynamics were characterized, and the network inference model revealed that the interactions among ARGs were related to age. A strong correlation between the profiles of rumen resistome and microbiome was found using Procrustes analysis. Ruminal Escherichia coli within Proteobacteria phylum was the main carrier of ARGs in goats consuming colostrum, while Prevotella ruminicola and Fibrobacter succinogenes associated with cellulose degradation were the carriers of ARGs after starter supplementation. Milk consumption was likely a source of rumen ARGs, and the changes in the rumen resistome with age were correlated with the microbiome modulation by starter supplementation.

CONCLUSIONS: Our data revealed that the temporal dynamics of the rumen resistome are associated with the microbiome, and the reservoir of ARGs in the rumen during early life is likely related to age and diet. It may be a feasible strategy to reduce the rumen and its downstream dissemination of ARGs in ruminants through early-life dietary intervention. Video Abstract.}, } @article {pmid38254124, year = {2024}, author = {Fan, J and Khan, J and Singh, NP and Pibiri, GE and Patro, R}, title = {Fulgor: a fast and compact k-mer index for large-scale matching and color queries.}, journal = {Algorithms for molecular biology : AMB}, volume = {19}, number = {1}, pages = {3}, pmid = {38254124}, issn = {1748-7188}, support = {R01HG009937/NH/NIH HHS/United States ; }, abstract = {The problem of sequence identification or matching-determining the subset of reference sequences from a given collection that are likely to contain a short, queried nucleotide sequence-is relevant for many important tasks in Computational Biology, such as metagenomics and pangenome analysis. Due to the complex nature of such analyses and the large scale of the reference collections a resource-efficient solution to this problem is of utmost importance. This poses the threefold challenge of representing the reference collection with a data structure that is efficient to query, has light memory usage, and scales well to large collections. To solve this problem, we describe an efficient colored de Bruijn graph index, arising as the combination of a k-mer dictionary with a compressed inverted index. The proposed index takes full advantage of the fact that unitigs in the colored compacted de Bruijn graph are monochromatic (i.e., all k-mers in a unitig have the same set of references of origin, or color). Specifically, the unitigs are kept in the dictionary in color order, thereby allowing for the encoding of the map from k-mers to their colors in as little as 1 + o(1) bits per unitig. Hence, one color per unitig is stored in the index with almost no space/time overhead. By combining this property with simple but effective compression methods for integer lists, the index achieves very small space. We implement these methods in a tool called Fulgor, and conduct an extensive experimental analysis to demonstrate the improvement of our tool over previous solutions. For example, compared to Themisto-the strongest competitor in terms of index space vs. query time trade-off-Fulgor requires significantly less space (up to 43% less space for a collection of 150,000 Salmonella enterica genomes), is at least twice as fast for color queries, and is 2-6[Formula: see text] faster to construct.}, } @article {pmid38108668, year = {2024}, author = {Ye, H-L and Zhi, M-F and Chen, B-Y and Lin, W-Z and Li, Y-L and Huang, S-J and Zhou, L-J and Xu, S and Zhang, J and Zhang, W-C and Feng, Q and Duan, S-Z}, title = {Alterations of oral and gut viromes in hypertension and/or periodontitis.}, journal = {mSystems}, volume = {9}, number = {1}, pages = {e0116923}, doi = {10.1128/msystems.01169-23}, pmid = {38108668}, issn = {2379-5077}, support = {81991503 81725003 81921002//MOST | National Natural Science Foundation of China (NSFC)/ ; SHSMU-ZDCX20212500//Innovative Research Team of High-level Local University in Shanghai (Innovative Research Team of High-level Local Universities in Shanghai)/ ; }, abstract = {The microbiota plays an important role in both hypertension (HTN) and periodontitis (PD), and PD exacerbates the development of HTN by oral and gut microbiota. Previous studies have focused on exploring the importance of the bacteriome in HTN and PD but overlooked the impact of the virome, which is also a member of the microbiota. We collected 180 samples of subgingival plaques, saliva, and feces from a cohort of healthy subjects (nHTNnPD), subjects with HTN (HTNnPD) or PD (PDnHTN), and subjects with both HTN and PD (HTNPD). We performed metagenomic sequencing to assess the roles of the oral and gut viromes in HTN and PD. The HTNnPD, PDnHTN, and HTNPD groups all showed significantly distinct beta diversity from the nHTNnPD group in saliva. We analyzed alterations in oral and gut viral composition in HTN and/or PD and identified significantly changed viruses in each group. Many viruses across three sites were significantly associated with blood pressure and other clinical parameters. Combined with these clinical associations, we found that Gillianvirus in subgingival plaques was negatively associated with HTN and that Torbevirus in saliva was positively associated with HTN. We found that Pepyhexavirus from subgingival plaques was indicated to be transferred to the gut. We finally evaluated viral-bacterial transkingdom interactions and found that viruses and bacteria may cooperate to affect HTN and PD. Correspondingly, HTN and PD may synergize to improve communications between viruses and bacteria.IMPORTANCEPeriodontitis (PD) and hypertension (HTN) are both highly prevalent worldwide and cause serious adverse outcomes. Increasing studies have shown that PD exacerbates HTN by oral and gut microbiota. Previous studies have focused on exploring the importance of the bacteriome in HTN and PD but overlooked the impact of the virome, even though viruses are common inhabitants in humans. Alterations in oral and gut viral diversity and composition contribute to diseases. The present study, for the first time, profiled the oral and gut viromes in HTN and/or PD. We identified key indicator viruses and their clinical implications in HTN and/or PD. We also investigated interactions between viruses and bacteria. This work improved the overall understanding of the viromes in HTN and PD, providing vital insights into the role of the virome in the development of HTN and PD.}, } @article {pmid38085089, year = {2024}, author = {Zhang, T and Mu, Y and Gao, Y and Tang, Y and Mao, S and Liu, J}, title = {Fecal microbial gene transfer contributes to the high-grain diet-induced augmentation of aminoglycoside resistance in dairy cattle.}, journal = {mSystems}, volume = {9}, number = {1}, pages = {e0081023}, doi = {10.1128/msystems.00810-23}, pmid = {38085089}, issn = {2379-5077}, support = {32372904//MOST | National Natural Science Foundation of China (NSFC)/ ; RENCAI2023008//MOST | NSFC | National Science Fund for Distinguished Young Scholars (National Science Foundation for Distinguished Young Scholars)/ ; BK20210402//JST | Natural Science Foundation of Jiangsu Province (Jiangsu Natural Science Foundation)/ ; }, abstract = {A high-grain (HG) diet can rapidly lower the rumen pH and thus modify the gastrointestinal microbiome in dairy cattle. Although the prevalence of antibiotic resistance is strongly linked with the gut microbiome, the influences of HG diet on animals' gut resistome remain largely unexplored. Here, we examined the impact and mechanism of an HG diet on the fecal resistome in dairy cattle by metagenomically characterizing the gut microbiome. Eight lactating Holstein cattle were randomly allocated into two groups and fed either a conventional (CON) or HG diet for 3 weeks. The fecal microbiome and resistome were significantly altered in dairy cattle from HG, demonstrating an adaptive response that peaks at day 14 after the dietary transition. Importantly, we determined that feeding an HG diet specifically elevated the prevalence of resistance to aminoglycosides (0.11 vs 0.24 RPKG, P < 0.05). This diet-induced resistance increase is interrelated with the disproportional propagation of microbes in Lachnospiraceae, indicating a potential reservoir of aminoglycosides resistance. We further showed that the prevalence of acquired resistance genes was also modified by introducing a different diet, likely due to the augmented frequency of lateral gene transfer (LGT) in microbes (CON vs HG: 254 vs 287 taxa) such as Lachnospiraceae. Consequently, we present that diet transition is associated with fecal resistome modification in dairy cattle and an HG diet specifically enriched aminoglycosides resistance that is likely by stimulating microbial LGT.IMPORTANCEThe increasing prevalence of antimicrobial resistance is one of the most severe threats to public health, and developing novel mitigation strategies deserves our top priority. High-grain (HG) diet is commonly applied in dairy cattle to enhance animals' performance to produce more high-quality milk. We present that despite such benefits, the application of an HG diet is correlated with an elevated prevalence of resistance to aminoglycosides, and this is a combined effect of the expansion of antibiotic-resistant bacteria and increased frequency of lateral gene transfer in the fecal microbiome of dairy cattle. Our results provided new knowledge in a typically ignored area by showing an unexpected enrichment of antibiotic resistance under an HG diet. Importantly, our findings laid the foundation for designing potential dietary intervention strategies to lower the prevalence of antibiotic resistance in dairy production.}, } @article {pmid38063415, year = {2024}, author = {Ellenbogen, JB and Borton, MA and McGivern, BB and Cronin, DR and Hoyt, DW and Freire-Zapata, V and McCalley, CK and Varner, RK and Crill, PM and Wehr, RA and Chanton, JP and Woodcroft, BJ and Tfaily, MM and Tyson, GW and Rich, VI and Wrighton, KC}, title = {Methylotrophy in the Mire: direct and indirect routes for methane production in thawing permafrost.}, journal = {mSystems}, volume = {9}, number = {1}, pages = {e0069823}, doi = {10.1128/msystems.00698-23}, pmid = {38063415}, issn = {2379-5077}, support = {2022070//NSF Biology Integration Institutes Program/ ; 1912915//National Science Foundation (NSF)/ ; NSF EF 1241037//US NSF Macrosystems Program/ ; DE-SC0023084//US DOE BER/ ; 10.46936/sarr.proj.2018.50229/60000028//US DOE BER EMSL/FICUS Initiative/ ; 10.46936/lser.proj.2021.51858/60000347//US DOE BER EMSL /FICUS Initiative/ ; DE-SC0023456//US DOE BER/ ; NT 2007-4547//Swedish Research Council/ ; NT 2013-5562//Swedish Research Council/ ; }, abstract = {While wetlands are major sources of biogenic methane (CH4), our understanding of resident microbial metabolism is incomplete, which compromises the prediction of CH4 emissions under ongoing climate change. Here, we employed genome-resolved multi-omics to expand our understanding of methanogenesis in the thawing permafrost peatland of Stordalen Mire in Arctic Sweden. In quadrupling the genomic representation of the site's methanogens and examining their encoded metabolism, we revealed that nearly 20% of the metagenome-assembled genomes (MAGs) encoded the potential for methylotrophic methanogenesis. Further, 27% of the transcriptionally active methanogens expressed methylotrophic genes; for Methanosarcinales and Methanobacteriales MAGs, these data indicated the use of methylated oxygen compounds (e.g., methanol), while for Methanomassiliicoccales, they primarily implicated methyl sulfides and methylamines. In addition to methanogenic methylotrophy, >1,700 bacterial MAGs across 19 phyla encoded anaerobic methylotrophic potential, with expression across 12 phyla. Metabolomic analyses revealed the presence of diverse methylated compounds in the Mire, including some known methylotrophic substrates. Active methylotrophy was observed across all stages of a permafrost thaw gradient in Stordalen, with the most frozen non-methanogenic palsa found to host bacterial methylotrophy and the partially thawed bog and fully thawed fen seen to house both methanogenic and bacterial methylotrophic activities. Methanogenesis across increasing permafrost thaw is thus revised from the sole dominance of hydrogenotrophic production and the appearance of acetoclastic at full thaw to consider the co-occurrence of methylotrophy throughout. Collectively, these findings indicate that methanogenic and bacterial methylotrophy may be an important and previously underappreciated component of carbon cycling and emissions in these rapidly changing wetland habitats.IMPORTANCEWetlands are the biggest natural source of atmospheric methane (CH4) emissions, yet we have an incomplete understanding of the suite of microbial metabolism that results in CH4 formation. Specifically, methanogenesis from methylated compounds is excluded from all ecosystem models used to predict wetland contributions to the global CH4 budget. Though recent studies have shown methylotrophic methanogenesis to be active across wetlands, the broad climatic importance of the metabolism remains critically understudied. Further, some methylotrophic bacteria are known to produce methanogenic by-products like acetate, increasing the complexity of the microbial methylotrophic metabolic network. Prior studies of Stordalen Mire have suggested that methylotrophic methanogenesis is irrelevant in situ and have not emphasized the bacterial capacity for metabolism, both of which we countered in this study. The importance of our findings lies in the significant advancement toward unraveling the broader impact of methylotrophs in wetland methanogenesis and, consequently, their contribution to the terrestrial global carbon cycle.}, } @article {pmid37652224, year = {2024}, author = {Gandasegui, J and Power, RI and Curry, E and Lau, DC and O'Neill, CM and Wolstenholme, A and Prichard, R and Šlapeta, J and Doyle, SR}, title = {Genome structure and population genomics of the canine heartworm Dirofilaria immitis.}, journal = {International journal for parasitology}, volume = {54}, number = {2}, pages = {89-98}, doi = {10.1016/j.ijpara.2023.07.006}, pmid = {37652224}, issn = {1879-0135}, mesh = {Dogs ; Animals ; *Dirofilaria immitis/genetics ; Metagenomics ; Genome, Helminth ; Lactones ; Australia ; *Dirofilariasis/epidemiology ; *Dog Diseases/parasitology ; }, abstract = {The heartworm, Dirofilaria immitis, is a filarial parasitic nematode responsible for significant morbidity and mortality in wild and domesticated canids. Resistance to macrocyclic lactone drug prevention represents a significant threat to parasite control and has prompted investigations to understand the genetic determinants of resistance. This study aimed to improve the genomic resources of D. immitis to enable a more precise understanding of how genetic variation is distributed within and between parasite populations worldwide, which will inform the likelihood and rate by which parasites, and in turn, resistant alleles, might spread. We have guided the scaffolding of a recently published genome assembly for D. immitis (ICBAS_JMDir_1.0) using the chromosomal-scale reference genomes of Brugia malayi and Onchocerca volvulus, resulting in an 89.5 Mb assembly composed of four autosomal- and one sex-linked chromosomal-scale scaffolds representing 99.7% of the genome. Publicly available and new whole-genome sequencing data from 32 D. immitis samples from Australia, Italy and the USA were assessed using principal component analysis, nucleotide diversity (Pi) and absolute genetic divergence (Dxy) to characterise the global genetic structure and measure within- and between-population diversity. These population genetic analyses revealed broad-scale genetic structure among globally diverse samples and differences in genetic diversity between populations; however, fine-scale subpopulation analysis was limited and biased by differences between sample types. Finally, we mapped single nucleotide polymorphisms previously associated with macrocyclic lactone resistance in the new genome assembly, revealing the physical linkage of high-priority variants on chromosome 3, and determined their frequency in the studied populations. This new chromosomal assembly for D. immitis now allows for a more precise investigation of selection on genome-wide genetic variation and will enhance our understanding of parasite transmission and the spread of genetic variants responsible for resistance to treatment.}, } @article {pmid38254005, year = {2024}, author = {Larin, AK and Klimina, KM and Veselovsky, VA and Olekhnovich, EI and Morozov, MD and Boldyreva, DI and Yunes, RA and Manolov, AI and Fedorov, DE and Pavlenko, AV and Galeeva, YS and Starikova, EV and Ilina, EN}, title = {An improved and extended dual-index multiplexed 16S rRNA sequencing for the Illumina HiSeq and MiSeq platform.}, journal = {BMC genomic data}, volume = {25}, number = {1}, pages = {8}, doi = {10.1186/s12863-024-01192-3}, pmid = {38254005}, issn = {2730-6844}, support = {21-15-00431//Russian Science Foundation/ ; }, abstract = {BACKGROUND: Recent advancements in next-generation sequencing (NGS) technology have ushered in significant improvements in sequencing speed and data throughput, thereby enabling the simultaneous analysis of a greater number of samples within a single sequencing run. This technology has proven particularly valuable in the context of microbial community profiling, offering a powerful tool for characterizing the microbial composition at the species level within a given sample. This profiling process typically involves the sequencing of 16S ribosomal RNA (rRNA) gene fragments. By scaling up the analysis to accommodate a substantial number of samples, sometimes as many as 2,000, it becomes possible to achieve cost-efficiency and minimize the introduction of potential batch effects. Our study was designed with the primary objective of devising an approach capable of facilitating the comprehensive analysis of 1,711 samples sourced from diverse origins, including oropharyngeal swabs, mouth cavity swabs, dental swabs, and human fecal samples. This analysis was based on data obtained from 16S rRNA metagenomic sequencing conducted on the Illumina MiSeq and HiSeq sequencing platforms.

RESULTS: We have designed a custom set of 10-base pair indices specifically tailored for the preparation of libraries from amplicons derived from the V3-V4 region of the 16S rRNA gene. These indices are instrumental in the analysis of the microbial composition in clinical samples through sequencing on the Illumina MiSeq and HiSeq platforms. The utilization of our custom index set enables the consolidation of a significant number of libraries, enabling the efficient sequencing of these libraries in a single run.

CONCLUSIONS: The unique array of 10-base pair indices that we have developed, in conjunction with our sequencing methodology, will prove highly valuable to laboratories engaged in sequencing on Illumina platforms or utilizing Illumina-compatible kits.}, } @article {pmid38253478, year = {2024}, author = {Kean, IRL and Clark, JA and Zhang, Z and Daubney, E and White, D and Ferrando-Vivas, P and Milla, G and Cuthbertson, B and Pappachan, J and Klein, N and Mouncey, P and Rowan, K and Myburgh, J and Gouliouris, T and Baker, S and Parkhill, J and Pathan, N and Arctic Research Team, }, title = {Short-duration selective decontamination of the digestive tract infection control does not contribute to increased antimicrobial resistance burden in a pilot cluster randomised trial (the ARCTIC Study).}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2023-330851}, pmid = {38253478}, issn = {1468-3288}, abstract = {OBJECTIVE: Selective decontamination of the digestive tract (SDD) is a well-studied but hotly contested medical intervention of enhanced infection control. Here, we aim to characterise the changes to the microbiome and antimicrobial resistance (AMR) gene profiles in critically ill children treated with SDD-enhanced infection control compared with conventional infection control.

DESIGN: We conducted shotgun metagenomic microbiome and resistome analysis on serial oropharyngeal and faecal samples collected from critically ill, mechanically ventilated patients in a pilot multicentre cluster randomised trial of SDD. The microbiome and AMR profiles were compared for longitudinal and intergroup changes. Of consented patients, faecal microbiome baseline samples were obtained in 89 critically ill children. Additionally, samples collected during and after critical illness were collected in 17 children treated with SDD-enhanced infection control and 19 children who received standard care.

RESULTS: SDD affected the alpha and beta diversity of critically ill children to a greater degree than standard care. At cessation of treatment, the microbiome of SDD patients was dominated by Actinomycetota, specifically Bifidobacterium, at the end of mechanical ventilation. Altered gut microbiota was evident in a subset of SDD-treated children who returned late longitudinal samples compared with children receiving standard care. Clinically relevant AMR gene burden was unaffected by the administration of SDD-enhanced infection control compared with standard care. SDD did not affect the composition of the oral microbiome compared with standard treatment.

CONCLUSION: Short interventions of SDD caused a shift in the microbiome but not of the AMR gene pool in critically ill children at the end mechanical ventilation, compared with standard antimicrobial therapy.}, } @article {pmid38253195, year = {2024}, author = {Wang, H and Wang, Z and Yu, J and Ma, C and Liu, L and Xu, D and Zhang, J}, title = {The function and keystone microbiota in typical habitats under the influence of anthropogenic activities in Baiyangdian Lake.}, journal = {Environmental research}, volume = {}, number = {}, pages = {118196}, doi = {10.1016/j.envres.2024.118196}, pmid = {38253195}, issn = {1096-0953}, abstract = {Microbe is an essential driver in regulating the biochemical cycles of carbon, nitrogen, and sulfur. In freshwater lake, microbial communities and functions are influenced by multiple factors, especially anthropogenic activities. Baiyangdian Lake consisted of various habitats, and was frequently interfered with human activities. In this study, 16 S rRNA sequencing and metagenomic sequencing were performed to characterize the microbial communities, determine keystone taxa and reveal dominated metabolic functions in typical habitats in Baiyangdian Lake. The results showed that the diversity of microbial community was significantly higher in sediment compared with corresponding water sample. Microbial community showed strong spatial heterogeneity in sediment, and temporal heterogeneity in water. As for different habitats, significantly higher alpha diversity was observed in ecotone, where the interference of human activities was relatively weak. The shared OTUs were distinguished from the keystone taxa, which indicated the uniqueness of microbiota in different ecological habitat. Moreover, the interactions of microbial in ecological restoration area (abandoned fish pond) were relatively simple, suggesting that this ecosystem was relatively fragile compared with others. Based on the metagenomic sequencing, we recognized that the canal, open water, and abandoned fish pond were beneficial for methanogenic and the ecotone might be a hot zone for the oxidation of methane. Notably, most of the microbes that participated in these predominant metabolisms were unclassified, which indicated the hug potential for exploring functional microorganisms in Baiyangdian Lake. This study provided a comprehensive understanding of the ecology characteristics of microbiota in habitats undergoing various human interference in Baiyangdian Lake.}, } @article {pmid38253098, year = {2024}, author = {Yu, W and Yang, H and Chen, J and Liao, P and Wu, J and Jiang, L and Guo, W}, title = {Molecular insights into the microbial degradation of sediment-derived DOM in a macrophyte-dominated lake under aerobic and hypoxic conditions.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170257}, doi = {10.1016/j.scitotenv.2024.170257}, pmid = {38253098}, issn = {1879-1026}, abstract = {The mineralization of dissolved organic matter (DOM) in sediments is an important factor leading to the eutrophication of macrophyte-dominated lakes. However, the changes in the molecular characteristics of sediment-derived DOM during microbial degradation in macrophyte-dominated lakes are not well understood. In this study, the microbial degradation process of sediment-derived DOM in Lake Caohai under aerobic and hypoxic conditions was investigated using Fourier transform ion cyclotron resonance mass spectrometry (FT-ICR MS) and metagenomics. The results revealed that the microbial degradation of sediment-derived DOM in macrophyte-dominated lakes was more intense under aerobic conditions. The microorganisms mainly metabolized the protein-like substances in the macrophyte-dominated lakes, and the carbohydrate-active enzyme genes and protein/lipid-like degradation genes played key roles in sediment-derived DOM degradation. Organic compounds with high H/C ratios such as lipids, carbohydrates, and protein/lipid-like compounds were preferentially removed by microorganisms during microbial degradation. Meanwhile, there was an increase in the abundance of organic molecular formula with a high aromaticity such as tannins and unsaturated hydrocarbons with low molecular weight and low double bond equivalent. In addition, aerobic/hypoxic environments can alter microbial metabolic pathways of sediment-derived DOM by affecting the relative abundance of microbial communities (e.g., Gemmatimonadetes and Acidobacteria) and functional genes (e.g., ABC.PE.P1 and ABC.PE.P) in macrophyte-dominated lakes. The abundances of lipids, unsaturated hydrocarbons, and protein compounds in aerobic environments decreased by 58 %, 50 %, and 44 %, respectively, compared to in hypoxic environments under microbial degradation. The results of this study deepen our understanding of DOM biodegradation in macrophyte-dominated lakes under different redox environments and provide new insights into nutrients releases from sediment and continuing eutrophication in macrophyte-dominated lakes.}, } @article {pmid38252132, year = {2024}, author = {Pantiora, PD and Georgakis, ND and Premetis, GE and Labrou, NE}, title = {Metagenomic analysis of hot spring soil for mining a novel thermostable enzybiotic.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {163}, pmid = {38252132}, issn = {1432-0614}, support = {4036//Hellenic Foundation for Research and Innovation/ ; }, abstract = {The misuse and overuse of antibiotics have contributed to a rapid emergence of antibiotic-resistant bacterial pathogens. This global health threat underlines the urgent need for innovative and novel antimicrobials. Endolysins derived from bacteriophages or prophages constitute promising new antimicrobials (so-called enzybiotics), exhibiting the ability to break down bacterial peptidoglycan (PG). In the present work, metagenomic analysis of soil samples, collected from thermal springs, allowed the identification of a prophage-derived endolysin that belongs to the N-acetylmuramoyl-L-alanine amidase type 2 (NALAA-2) family and possesses a LysM (lysin motif) region as a cell wall binding domain (CWBD). The enzyme (Ami1) was cloned and expressed in Escherichia coli, and its bactericidal and lytic activity was characterized. The results indicate that Ami1 exhibits strong bactericidal and antimicrobial activity against a broad range of bacterial pathogens, as well as against isolated peptidoglycan (PG). Among the examined bacterial pathogens, Ami1 showed highest bactericidal activity against Staphylococcus aureus sand Staphylococcus epidermidis cells. Thermostability analysis revealed a melting temperature of 64.2 ± 0.6 °C. Overall, these findings support the potential that Ami1, as a broad spectrum antimicrobial agent, could be further assessed as enzybiotic for the effective treatment of bacterial infections. KEY POINTS: • Metagenomic analysis allowed the identification of a novel prophage endolysin • The endolysin belongs to type 2 amidase family with lysin motif region • The endolysin displays high thermostability and broad bactericidal spectrum.}, } @article {pmid38252058, year = {2024}, author = {Caesar, L and Haag, KL}, title = {Tailed bacteriophages (Caudoviricetes) dominate the microbiome of a diseased stingless bee.}, journal = {Genetics and molecular biology}, volume = {46}, number = {3 Suppl 1}, pages = {e20230120}, doi = {10.1590/1678-4685-GMB-2023-0120}, pmid = {38252058}, issn = {1415-4757}, abstract = {Bacteriophages, viruses that infect bacterial hosts, are known to rule the dynamics and diversity of bacterial populations in a number of ecosystems. Bacterial communities residing in the gut of animals, known as the gut microbiome, have revolutionized our understanding of many diseases. However, the gut phageome, while of apparent importance in this context, remains an underexplored area of research. Here we identify for the first time genomic sequences from tailed viruses (Caudoviricetes) that are associated with the microbiome of stingless bees (Melipona quadrifasciata). Both DNA and RNA were extracted from virus particles isolated from healthy and diseased forager bees, the latter showing symptoms from an annual syndrome that only affects M. quadrifasciata. Viral contigs from previously sequenced metagenomes of healthy and diseased forager bees were used for the analyses. Using conserved proteins deduced from their genomes, we found that Caudoviricetes were only present in the worker bee gut microbiome from diseased stingless bees. The most abundant phages are phylogenetically related to phages that infect Gram-positive bacteria from the order Lactobacillales and Gram-negative bacteria from the genus Gilliamella and Bartonella, that are common honey bee symbionts. The potential implication of these viruses in the M. quadrifasciata syndrome is discussed.}, } @article {pmid38252055, year = {2024}, author = {Cheng, B and Wang, J and Lin, L and Yang, D and Liu, X and Wu, H}, title = {Clinical characteristics of 14 cases of Chlamydia psittaci pneumonia.}, journal = {The new microbiologica}, volume = {46}, number = {4}, pages = {416-423}, pmid = {38252055}, issn = {1121-7138}, abstract = {Among 14 patients with C. psittaci pneumonia, there were 9 critical and 5 non-critical cases. Ten patients improved clinically and were discharged to home; however, four patients died. Seven patients had a history of contact with birds or poultry. All 14 patients had a high fever as the presenting symptom, but most had a normal white blood cell count. Most of the patients had a significant increase in high-sensitivity C-reactive protein and procalcitonin levels. The lymphocyte count in the critical group was considerably lower than in the non-critical group. Patients in the critical group were more advanced in age than in the non-critical group. In addition, serum urea nitrogen, creatinine, procalcitonin, and lactate dehydrogenase levels were significantly higher in the critical group than in the non-critical group (P<0.05). The 4 patients who died had significantly increased procalcitonin levels compared to the 10 patients who survived (P<0.05). In summary, a high fever is usually the presenting complaint of patients with C. psittaci pneumonia. Such patients often progress to severe disease; however, early diagnostic confirmation by mNGS and appropriate treatment dramatically improve the prognosis. Age, lymphocyte count, procalcitonin, blood urea nitrogen, creatinine, and lactate dehydrogenase levels were shown to predict disease severity.}, } @article {pmid38252043, year = {2024}, author = {Xu, Y and Hu, D and Cheng, H and Peng, F and Gao, Q}, title = {Research on the Artemia nauplii microorganism compositions based on metagenomics next-generation sequencing.}, journal = {The new microbiologica}, volume = {46}, number = {4}, pages = {332-339}, pmid = {38252043}, issn = {1121-7138}, abstract = {Vibrio species represent the predominant and significant pathogen in global marine fish and shellfish aquaculture. Vibrio species are ubiquitously presented in Artemia cyst hatcheries, and their notable colonization in live prey, particularly Artemia nauplii, leads to the transmission of these pathogens into the digestive system of larval organisms, causing serious problems in Vibriosis in marine aquaculture. To eliminate the Vibriospecies in Artemia nauplii, trichloroisocyanuric acid (TCCA) was used for sterilization of the nauplii. In this study, 3 different concentrations, including 0.5 ppm (FA group), 1.0 ppm (FB group) and 1.5 ppm (FC group) of TCCA were used to treat nauplii for 25 min, and then genomic DNA of the different groups were extracted followed by metagenomic next-generation sequencing (NGS). Bioinformatics analysis was applied and the results indicated that Proteobacter constituted the predominant component within each group at the phylum level, albeit accounting for only 58.68% in the FB group, which was significantly lower than in other groups (>86%). The relative abundance of Vibrio species at genus level showed that when compared with the control group, the FB group (15.8%) was reduced by 25.5%. Beta diversity showed differences between the FB group and the other groups, suggesting that treatment with 1.0ppm TCCA for 25 min would obviously reduce the Vibrio in Artemia nauplii. In conclusion, the Vibrio species were significantly reduced after treatment with TCCA, indicating that TCCA might be an alternative to antibiotics used for live food sterilization in marine aquaculture.}, } @article {pmid38251472, year = {2023}, author = {Shen, D and Lin, C and Hong, X and Li, J and Huang, G}, title = {Diagnostic performance of plasma metagenomic next-generation sequencing for infected pancreatic necrosis: A prospective multicenter study.}, journal = {The Journal of infection}, volume = {87}, number = {6}, pages = {e104-e106}, doi = {10.1016/j.jinf.2023.10.014}, pmid = {38251472}, issn = {1532-2742}, } @article {pmid38250179, year = {2024}, author = {Bhagat, N and Vakhlu, J}, title = {Effects of biocontrol Bacillus sp. strain D5 on the pathogenic Fusarium oxysporum R1 at the microscopic and molecular level in Crocus sativus L. (saffron) corm.}, journal = {FEMS microbes}, volume = {5}, number = {}, pages = {xtad025}, pmid = {38250179}, issn = {2633-6685}, abstract = {Corm rot of saffron caused by Fusarium oxysporum is a major threat to saffron cultivation the world over. To minimize the ill effects of chemical fungicides, attention has been shifted to the use of biocontrol agents for disease management in a sustainable way. In saffron, various biocontrol agents against corm rot disease have been reported and characterized but no study has been done so far to understand their interaction at the molecular level. The present study was conducted to unravel the mechanism of action of an already characterized native biocontrol agent i.e. Bacillus sp. strain D5 (Bar D5) against F. oxsporum R1 (Fox R1) in the saffron corm. The growth inhibition of Fox R1 was observed in vitro and in planta (saffron corm) by real time imaging. Bacillus sp. strain D5 reduced Fox R1 load in infected corms by 50% as quantified by q-PCR and the colony-forming unit method. Comparative transcriptome analysis revealed upregulation and downregulation of various Fox R1 genes in presence of Bar D5. The genes related to carbon metabolism, cell wall and membrane synthesis, and growth of Fox R1 were significantly downregulated in Bar D5-primed and Fox R1-inoculated corms as compared to only Fox R1-inoculated corms.}, } @article {pmid38249485, year = {2023}, author = {Xing, Y and Zhang, P and Zhang, W and Yu, C and Luo, Z}, title = {Continuous cropping of potato changed the metabolic pathway of root exudates to drive rhizosphere microflora.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1318586}, pmid = {38249485}, issn = {1664-302X}, abstract = {For potato production, continuous cropping (CC) could lead to autotoxicity buildup and microflora imbalance in the field soil, which may result in failure of crops and reduction in yield. In this study, non-targeted metabolomics (via liquid chromatography with tandem mass spectrometry (LC-MS/MS)) combined with metagenomic profiling (via high-throughput amplicon sequencing) were used to evaluate correlations between metabolomics of potato root exudates and communities of bacteria and fungi around potato plants to illustrate the impacts of CC. Potato plants were grown in soil collected from fields with various CC years (0, 1, 4, and 7 years). Metabolomic analysis showed that the contents and types of potential autotoxins in potato root exudates increased significantly in CC4 and CC7 plants (i.e., grown in soils with 4 and 7 years of CC). The differentially expressed metabolites were mainly produced via alpha-linolenic acid metabolism in plant groups CC0 and CC1 (i.e., no CC or 1 year CC). The metabolomics of the groups CC4 and CC7 became dominated by styrene degradation, biosynthesis of siderophore group non-ribosomal peptides, phenylpropanoid biosynthesis, and biosynthesis of various plant secondary metabolites. Continuous cropping beyond 4 years significantly changed the bacterial and fungal communities in the soil around the potato crops, with significant reduction of beneficial bacteria and accumulation of harmful fungi. Correlations between DEMs and microflora biomarkers were established with strong significances. These results suggested that continuous cropping of potato crops changed their metabolism as reflected in the plant root exudates and drove rhizosphere microflora to directions less favorable to plant growth, and it needs to be well managed to assure potato yield.}, } @article {pmid38249484, year = {2023}, author = {Myeong, NR and Kwon, MJ and Göckede, M and Tripathi, BM and Kim, M}, title = {Responses of soil micro-eukaryotic communities to decadal drainage in a Siberian wet tussock tundra.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1227909}, pmid = {38249484}, issn = {1664-302X}, abstract = {Climate warming holds the potential to cause extensive drying of wetlands in the Arctic, but the warming-drying effects on belowground ecosystems, particularly micro-eukaryotes, remain poorly understood. We investigated the responses of soil micro-eukaryotic communities, including fungi, protists, and microbial metazoa, to decadal drainage manipulation in a Siberian wet tundra using both amplicon and shotgun metagenomic sequencing. Our results indicate that drainage treatment increased the abundance of both fungal and non-fungal micro-eukaryotic communities, with key groups such as Ascomycota (mostly order Helotiales), Nematoda, and Tardigrada being notably abundant in drained sites. Functional traits analysis showed an increase in litter saprotrophic fungi and protistan consumers, indicating their increased activities in drained sites. The effects of drainage were more pronounced in the surface soil layer than the deeper layer, as soils dry and warm from the surface. Marked compositional shifts were observed for both communities, with fungal communities being more strongly influenced by drainage-induced vegetation change than the lowered water table itself, while the vegetation effect on non-fungal micro-eukaryotes was moderate. These findings provide insights into how belowground micro-eukaryotic communities respond to the widespread drying of wetlands in the Arctic and improve our predictive understanding of future ecosystem changes.}, } @article {pmid38249472, year = {2023}, author = {Li, S and Liu, T and Liu, C and Sun, D and Yan, Q and Gao, D and Zhang, Z}, title = {Impact of soil inorganic nitrogen on bacterial phylogeny in estuarine intertidal zones: a study of nitrogen metabolism.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1341564}, pmid = {38249472}, issn = {1664-302X}, abstract = {Here we investigated the potential impacts of soil inorganic nitrogen (SIN) content on the phylogenetic characteristics and ecological functions of soil bacterial communities in estuarine intertidal zones in China, aiming to comprehend the response mechanism of soil microorganisms to variations in SIN content within estuarine wetlands. Our results show that SIN in estuarine areas has a significant spatiotemporal variation on spatial and seasonal scales, in this study and is significantly associated with the phylogenetic diversity and phylogenetic turnover of soil bacterial communities. In addition, the results of the metagenomic analysis showed that the relative abundance of nitrogen-cycling functional genes in bacterial communities did not differ significantly in sampling sites and seasons, and weakly correlated with SIN content. Further, the results based on structural equation modeling (SEM) analysis showed that SIN directly and significantly regulated the phylogenetic characteristics of bacterial communities, thereby indirectly affecting the potential of bacterial nitrogen metabolism. This study emphasizes the key influence of SIN variations on the phylogenetic dissimilarity in soil bacterial communities. Moreover, although there was a weak direct relationship between the functional characteristics of the bacterial nitrogen metabolism and SIN content, the spatiotemporal variation of bacterial nitrogen metabolic potential may be indirectly regulated by SIN content by influencing the phylogenetic diversity in bacterial communities. Our study unravels the pivotal mechanisms through which SIN content influences bacterial communities, thereby offering novel insights into the microbial intricacies governing nitrogen metabolism within estuaries.}, } @article {pmid38249461, year = {2023}, author = {Potekhin, A and Plotnikov, AO and Gogoleva, N and Sonntag, B}, title = {Editorial: Microbial associations formed and hosted by protists, algae, and fungi.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1341058}, pmid = {38249461}, issn = {1664-302X}, } @article {pmid38249456, year = {2023}, author = {Wang, X and Feng, X}, title = {Challenges in estimating effective population sizes from metagenome-assembled genomes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1331583}, pmid = {38249456}, issn = {1664-302X}, abstract = {Effective population size (Ne) plays a critical role in shaping the relative efficiency between natural selection and genetic drift, thereby serving as a cornerstone for understanding microbial ecological dynamics. Direct Ne estimation relies on neutral genetic diversity within closely related genomes, which is, however, often constrained by the culturing difficulties for the vast majority of prokaryotic lineages. Metagenome-assembled genomes (MAGs) offer a high-throughput alternative for genomic data acquisition, yet their accuracy in Ne estimation has not been fully verified. This study examines the Thermococcus genus, comprising 66 isolated strains and 29 MAGs, to evaluate the reliability of MAGs in Ne estimation. Despite the even distribution across the Thermococcus phylogeny and the comparable internal average nucleotide identity (ANI) between isolate populations and MAG populations, our results reveal consistently lower Ne estimates from MAG populations. This trend of underestimation is also observed in various MAG populations across three other bacterial genera. The underrepresentation of genetic variation in MAGs, including loss of allele frequency data and variable genomic segments, likely contributes to the underestimation of Ne. Our findings underscore the necessity for caution when employing MAGs for evolutionary studies, which often depend on high-quality genome assemblies and nucleotide-level diversity.}, } @article {pmid38249446, year = {2023}, author = {Trevelline, BK and Sprockett, D and DeLuca, WV and Andreadis, CR and Moeller, AH and Tonra, CM}, title = {Convergent remodelling of the gut microbiome is associated with host energetic condition over long-distance migration.}, journal = {Functional ecology}, volume = {37}, number = {11}, pages = {2840-2854}, pmid = {38249446}, issn = {0269-8463}, abstract = {The gut microbiome can be thought of as a virtual organ given its immense metabolic capacity and profound effects on host physiology. Migratory birds are capable of adaptively modulating many aspects of their physiology to facilitate long-distance movements, raising the hypothesis that their microbiome may undergo a parallel remodeling process that helps to meet the energetic demands of migration.To test this hypothesis, we investigated changes in gut microbiome composition and function over the fall migration of the Blackpoll Warbler (Setophaga striata), which exhibits one of the longest known autumnal migratory routes of any songbird and rapidly undergoes extensive physiological remodeling during migration.Overall, our results showed that the Blackpoll Warbler microbiome differed significantly across phases of fall migration. This pattern was driven by a dramatic increase in the relative abundance of Proteobacteria, and more specifically a single 16S rRNA gene amplicon sequence variant belonging to the family Enterobacteriaceae. Further, Blackpoll Warblers exhibited a progressive reduction in microbiome diversity and within-group variance over migration, indicating convergence of microbiome composition among individuals during long-distance migration. Metagenomic analysis revealed that the gut microbiome of staging individuals was enriched in bacterial pathways involved in vitamin, amino acid, and fatty acid biosynthesis, as well as carbohydrate metabolism, and that these pathways were in turn positively associated with host body mass and subcutaneous fat deposits.Together, these results provide evidence that the gut microbiome of migratory birds may undergo adaptive remodeling to meet the physiological and energetic demands of long-distance migration.}, } @article {pmid38248835, year = {2024}, author = {Claypool, DJ and Zhang, YG and Xia, Y and Sun, J}, title = {Conditional Vitamin D Receptor Deletion Induces Fungal and Archaeal Dysbiosis and Altered Metabolites.}, journal = {Metabolites}, volume = {14}, number = {1}, pages = {}, doi = {10.3390/metabo14010032}, pmid = {38248835}, issn = {2218-1989}, support = {1 I101BX004824-01/VA/VA/United States ; R01DK134343, R01 DK105118, and R01DK114126/GF/NIH HHS/United States ; }, abstract = {A vitamin D receptor (VDR) deficiency leads to the dysbiosis of intestinal bacteria and is associated with various diseases, including cancer, infections, and inflammatory bowel disease. However, the impact of a VDR deficiency on fungi and archaea is unknown. We conditionally deleted the VDR in Paneth cells (VDR[ΔPC]), intestinal epithelial cells (VDR[ΔIEC]), or myeloid cells (VDR[ΔLyz]) in mice and collected feces for shotgun metagenomic sequencing and untargeted metabolomics. We found that fungi were significantly altered in each knockout (KO) group compared to the VDR[Loxp] control. The VDR[ΔLyz] mice had the most altered fungi species (three depleted and seven enriched), followed by the VDR[ΔPC] mice (six depleted and two enriched), and the VDR[ΔIEC] mice (one depleted and one enriched). The methanogen Methanofollis liminatans was enriched in the VDR[ΔPC] and VDR[ΔLyz] mice and two further archaeal species (Thermococcus piezophilus and Sulfolobus acidocaldarius) were enriched in the VDR[ΔLyz] mice compared to the Loxp group. Significant correlations existed among altered fungi, archaea, bacteria, and viruses in the KO mice. Functional metagenomics showed changes in several biologic functions, including decreased sulfate reduction and increased biosynthesis of cobalamin (vitamin B12) in VDR[ΔLyz] mice relative to VDR[Loxp] mice. Fecal metabolites were analyzed to examine the involvement of sulfate reduction and other pathways. In conclusion, a VDR deficiency caused the formation of altered fungi and archaea in a tissue- and sex-dependent manner. These results provide a foundation about the impact of a host factor (e.g., VDR deficiency) on fungi and archaea. It opens the door for further studies to determine how mycobiome and cross-kingdom interactions in the microbiome community and metabolites contribute to the risk of certain diseases.}, } @article {pmid38248446, year = {2023}, author = {Órdenes, P and Carril Pardo, C and Elizondo-Vega, R and Oyarce, K}, title = {Current Research on Molecular Biomarkers for Colorectal Cancer in Stool Samples.}, journal = {Biology}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/biology13010015}, pmid = {38248446}, issn = {2079-7737}, support = {VRID PDO C22//Universidad San Sebastián/ ; }, abstract = {Colorectal cancer (CRC) is one of the most diagnosed cancers worldwide, with a high incidence and mortality rate when diagnosed late. Currently, the methods used in healthcare to diagnose CRC are the fecal occult blood test, flexible sigmoidoscopy, and colonoscopy. However, the lack of sensitivity and specificity and low population adherence are driving the need to implement other technologies that can identify biomarkers that not only help with early CRC detection but allow for the selection of more personalized treatment options. In this regard, the implementation of omics technologies, which can screen large pools of biological molecules, coupled with molecular validation, stands out as a promising tool for the discovery of new biomarkers from biopsied tissues or body fluids. This review delves into the current state of the art in the identification of novel CRC biomarkers that can distinguish cancerous tissue, specifically from fecal samples, as this could be the least invasive approach.}, } @article {pmid38248338, year = {2024}, author = {Kirby, TO and Sapp, PA and Townsend, JR and Govaert, M and Duysburgh, C and Marzorati, M and Marshall, TM and Esposito, R}, title = {AG1[®] Induces a Favorable Impact on Gut Microbial Structure and Functionality in the Simulator of Human Intestinal Microbial Ecosystem[®] Model.}, journal = {Current issues in molecular biology}, volume = {46}, number = {1}, pages = {557-569}, doi = {10.3390/cimb46010036}, pmid = {38248338}, issn = {1467-3045}, support = {N/A//Athletic Greens International/ ; }, abstract = {Modulation of the human gut microbiome has become an area of interest in the nutraceutical space. We explored the effect of the novel foundational nutrition supplement AG1[®] on the composition of human microbiota in an in vitro experimental design. Employing the Simulator of Human Intestinal Microbial Ecosystem (SHIME[®]) model, AG1[®] underwent digestion, absorption, and subsequent colonic microenvironment simulation under physiologically relevant conditions in healthy human fecal inocula. Following 48 h of colonic simulation, the gut microbiota were described using shallow shotgun, whole genome sequencing. Metagenomic data were used to describe changes in community structure (alpha diversity, beta diversity, and changes in specific taxa) and community function (functional heterogeneity and changes in specific bacterial metabolic pathways). Results showed no significant change in alpha diversity, but a significant effect of treatment and donor and an interaction between the treatment and donor effect on structural heterogeneity likely stemming from the differential enrichment of eight bacterial taxa. Similar findings were observed for community functional heterogeneity likely stemming from the enrichment of 20 metabolic pathways characterized in the gene ontology term database. It is logical to conclude that an acute dose of AG1 has significant effects on gut microbial composition that may translate into favorable effects in humans.}, } @article {pmid38248224, year = {2024}, author = {Yamamoto, Y and Yamamoto, T and Miyamoto, N and Kinoshita, K and Nishikawa, S and Adachi, T and Takizawa, S and Inoue, R and Matoba, S and Kanamura, N}, title = {Oral Function and the Oral Microbiome in the Elderly in the Kyotango Area.}, journal = {Dentistry journal}, volume = {12}, number = {1}, pages = {}, doi = {10.3390/dj12010016}, pmid = {38248224}, issn = {2304-6767}, support = {18-2-03, 20-02-01, 22-02-05//8020 Promotion Foundation/ ; JP23K09485//JSPS scientific research funding/ ; JPMJCE1302//COI program/ ; JPMJCA2201//COI program acceleration support in 2022/ ; JPMJPF2210//COI-NEXT program/ ; }, abstract = {INTRODUCTION: Prevention of tooth loss contributes to an extended life expectancy, namely longevity. Aging-related oral hypofunction, including tooth loss, markedly increases the risks of functional disorder and mortality. Dysbiosis of the oral microbiome has recently been associated with various diseases, such as liver cirrhosis, pancreatic cancer, colorectal cancer, and inflammatory bowel disease. Therefore, the relationship between the oral microbiome and systemic health has been attracting increasing attention. In the present study, we examined oral function and the oral microbiome in the elderly in a world-leading longevity area.

MATERIALS AND METHODS: An oral examination, chewing ability/tongue-lip motor function/saliva tests, and a metagenomic analysis with a 16S rRNA gene-targeting next-generation sequencer were conducted on 78 subjects aged ≥80 years. Twenty-six healthy individuals aged between 20 and 39 years were also investigated as controls. The data obtained were statistically analyzed. The protocol of the present study was approved by the Ethics Review Board of our university (ERB-C-885).

RESULTS: Chewing ability, tongue-lip motor function, and saliva volume were normal in elderly subjects with a current tooth number ≥20, but were significantly lower in those with a current tooth number <20. The oral microbiome in elderly subjects with a current tooth number ≥20 and young controls differed from that in elderly subjects with a current tooth number <20.

CONCLUSION: Tooth number ≥20 in elderly subjects in the longevity area contributed to the maintenance of both oral function and the diversity of the oral microbiome.}, } @article {pmid38248064, year = {2024}, author = {Gouello, A and Henry, L and Chadli-Benhemani, D and Salipante, F and Gibert, J and Boutet-Dubois, A and Lavigne, JP}, title = {Evaluation of the Microbiome Identification of Forensically Relevant Biological Fluids: A Pilot Study.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {14}, number = {2}, pages = {}, doi = {10.3390/diagnostics14020187}, pmid = {38248064}, issn = {2075-4418}, abstract = {In forensic sciences, body fluids, or biological traces, are a major source of information, and their identification can play a decisive role in criminal investigations. Currently, the nature of biological fluids is assessed using immunological, physico-chemical, mRNA and epigenetic methods, but these have limits in terms of sensitivity and specificity. The emergence of next-generation sequencing technologies offers new opportunities to identify the nature of body fluids by determining bacterial communities. The aim of this pilot study was to assess whether analysis of the bacterial communities in isolated and mixed biological fluids could reflect the situation observed in real forensics labs. Several samples commonly encountered in forensic sciences were tested from healthy volunteers: saliva, vaginal fluid, blood, semen and skin swabs. These samples were analyzed alone or in combination in a ratio of 1:1. Sequencing was performed on the Ion Gene Studio[TM] S5 automated sequencer. Fluids tested alone revealed a typical bacterial signature with specific bacterial orders, enabling formal identification of the fluid of interest, despite inter-individual variations. However, in biological fluid mixtures, the predominance of some bacterial microbiomes inhibited interpretation. Oral and vaginal microbiomes were clearly preponderant, and the relative abundance of their bacterial communities and/or the presence of common species between samples made it impossible to detect bacterial orders or genera from other fluids, although they were distinguishable from one another. However, using the beta diversity, salivary fluids were identified and could be distinguished from fluids in combination. While this method of fluid identification is promising, further analyses are required to consolidate the protocol and ensure reliability.}, } @article {pmid38247491, year = {2024}, author = {Hernandez-Baixauli, J and Chomiciute, G and Tracey, H and Mora, I and Cortés-Espinar, AJ and Ávila-Román, J and Abasolo, N and Palacios-Jordan, H and Foguet-Romero, E and Suñol, D and Galofré, M and Alcaide-Hidalgo, JM and Baselga-Escudero, L and Del Bas, JM and Mulero, M}, title = {Exploring Metabolic and Gut Microbiome Responses to Paraquat Administration in Male Wistar Rats: Implications for Oxidative Stress.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {13}, number = {1}, pages = {}, doi = {10.3390/antiox13010067}, pmid = {38247491}, issn = {2076-3921}, support = {ACCIÓ-Eurecat (PRIV2019-PREVENTOMICS)//Catalan Government/ ; DOCTORAT INDUSTRIAL 2020-DI-109//AGAUR/ ; Marie Skłodowska-Curie grant agreement No 101034328//European Union's Horizon 2020/ ; TECNOMIFOOD project. CER-20191010//Ministry of Science and Innovation/ ; TECNOMIFOOD project. CER-20191010//Centre for the Development of Industrial Technology (CDTI) of the Spanish Ministry of Science and Innovation/ ; }, abstract = {In this study, we examined the metabolic and gut microbiome responses to paraquat (PQ) in male Wistar rats, focusing on oxidative stress effects. Rats received a single intraperitoneal injection of PQ at 15 and 30 mg/kg, and various oxidative stress parameters (i.e., MDA, SOD, ROS, 8-isoprostanes) were assessed after three days. To explore the omic profile, GC-qTOF and UHPLC-qTOF were performed to assess the plasma metabolome; [1]H-NMR was used to assess the urine metabolome; and shotgun metagenomics sequencing was performed to study the gut microbiome. Our results revealed reductions in body weight and tissue changes, particularly in the liver, were observed, suggesting a systemic effect of PQ. Elevated lipid peroxidation and reactive oxygen species levels in the liver and plasma indicated the induction of oxidative stress. Metabolic profiling revealed changes in the tricarboxylic acid cycle, accumulation of ketone body, and altered levels of key metabolites, such as 3-hydroxybutyric acid and serine, suggesting intricate links between energy metabolism and redox reactions. Plasma metabolomic analysis revealed alterations in mitochondrial metabolism, nicotinamide metabolism, and tryptophan degradation. The gut microbiome showed shifts, with higher PQ doses influencing microbial populations (e.g., Escherichia coli and Akkermansia muciniphila) and metagenomic functions (pyruvate metabolism, fermentation, nucleotide and amino acid biosynthesis). Overall, this study provides comprehensive insights into the complex interplay between PQ exposure, metabolic responses, and gut microbiome dynamics. These findings enhance our understanding of the mechanisms behind oxidative stress-induced metabolic alterations and underscore the connections between xenobiotic exposure, gut microbiota, and host metabolism.}, } @article {pmid38247211, year = {2024}, author = {Jo, E and Lee, H and Song, Y and Cha, J}, title = {Taxonomic Variations of Bacterial and Fungal Communities Depending on Fermentation Temperature in Traditional Korean Fermented Soybean Food, Doenjang.}, journal = {Journal of microbiology and biotechnology}, volume = {34}, number = {4}, pages = {1-10}, doi = {10.4014/jmb.2312.12024}, pmid = {38247211}, issn = {1738-8872}, abstract = {Meju, a fermented soybean brick, is a key component in soybean foods like doenjang and ganjang, harboring a variety of microorganisms, including bacteria and fungi. These microorganisms significantly contribute to the nutritional and sensory characteristics of doenjang and ganjang. Amplicon-based next-generation sequencing was applied to investigate how the microbial communities of meju fermented at low and high temperatures differ and how this variation affects the microbial communities of doenjang, a subsequently fermented soybean food. Our metagenomic data showed distinct patterns depending on the fermentation temperature. The microbial abundance in the bacterial community was increased under both temperatures during the fermentation of meju and doenjang. Weissella was the most abundant genus before the fermentation of meju, however, it was replaced by Bacillus at high temperature-fermented meju and lactic acid bacteria such as Weissella and Latilactobacillus at low temperature-fermented meju. Leuconostoc, Logiolactobacillus, and Tetragenococcus gradually took over the dominant role during the fermentation process of doenjang, replacing the previous dominant microorganisms. Mucor was dominant in the fungal community before and after meju fermentation, whereas Debaryomyces was dominant under both temperatures during doenjang fermentation. The dominant fungal genus of doenjang was not affected regardless of the fermentation temperature of meju. Strong correlations were shown for specific bacteria and fungi linked to specific fermentation temperatures. This study helps our understanding of meju fermentation process at different fermentation temperatures and highlights different bacteria and fungi associated with specific fermentation periods which may influence the nutritional and organoleptic properties of the final fermented soybean foods doenjang.}, } @article {pmid38179946, year = {2024}, author = {Bian, G and Yu, S and Cheng, C and Huang, H and Liu, J}, title = {Ruminal microbiota-host crosstalks promote ruminal epithelial development in neonatal lambs with alfalfa hay introduction.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0103423}, doi = {10.1128/msystems.01034-23}, pmid = {38179946}, issn = {2379-5077}, abstract = {Ruminal microbiota is gradually established after birth, while microbiota maturation could be highly diverse because of varied solid dietary accessibility. However, how the ruminal microbiota accreted from postnatal hay diets alters rumen epithelial development, and how this affects animal health remains largely unknown. Here, neonatal lambs were introduced to starchy corn-soybean starter or corn-soybean starter + alfalfa hay (AH) to investigate the influences of early life ruminal microbiome on rumen epithelial development using integrated 16s rRNA sequencing-metagenome-transcriptome approaches. The results showed that AH introduction elevated average daily weight gain, rumen weight and volume, rumen epithelial papillae length, and rumen muscle layer thickness. Meanwhile, the relative abundance of fibrolytic bacteria (Christensenellaceae R-7 group, Prevotellaceae UCG-001, and Succinivibrio), acetate producer (Acetitomaculum and Mitsuokella), and propionate producer Succiniclasticum was increased in the rumen content by AH supplementation (P < 0.05). Moreover, AH introduction decreased the relative abundance of total CAZymes, CBM, and GH and increased the abundance of KO genes related to volatile fatty acid (VFA) generation in the rumen content. AH lambs had a higher relative abundance of Succiniclasticum, Megasphaera, Succinivibrio, and Suttonella (P < 0.05), while a lower relative abundance of Cloacibacillus, Desulfovibrio, Dialister, Intestinimonas, Parabacteroides, and Pseudoscardovia (P < 0.05) in the rumen epithelial samples. Furthermore, these alterations in ruminal microbial structure and function resulted in ruminal epithelial cell proliferation and development pathways activation. In summary, AH introduction benefited ruminal fiber degradation and VFA generation bacteria colonization and promoted ruminal epithelial development. These findings provide new insights into ruminal microbial-host interactions in the early life.IMPORTANCEWhile it is established that a fiber-rich diet promotes rumen development in lambs, further research is needed to investigate the precise response of rumen microbiota and epithelium to high-quality alfalfa hay. Here, we observed that the inclusion of alfalfa hay led to a discernible alteration in the developmental trajectory of the rumen. Notably, there was a favorable shift in the rumen's volume, morphology, and the development of rumen papillae. Furthermore, ruminal microbial structure and function resulted in ruminal epithelial cell proliferation and development pathways activation, collectively provide compelling evidence supporting the capacity of alfalfa hay to enhance rumen development and health through ruminal micrbiota-host crosstalks. Our findings elucidate the functional response of the rumen to alfalfa hay introduction, providing new insights into strategies for promoting healthy development of the rumen in young ruminants.}, } @article {pmid38246555, year = {2024}, author = {Qu, T and Wang, P and Zhao, X and Liang, L and Ge, Y and Chen, Y}, title = {Metagenomics reveals differences in the composition of bacterial antimicrobial resistance and antibiotic resistance genes in pasteurized yogurt and probiotic bacteria yogurt from China.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2023-23983}, pmid = {38246555}, issn = {1525-3198}, abstract = {Antimicrobial resistance has become a global public health concern, and antibiotic resistance genes (ARGs) in food are a research focus. In China, probiotics and pasteurized yogurts are the 2 main types of commercially available yogurt, but the distribution and differences of antibiotic-resistant bacteria and gene types in these products are not well known. This study used a shotgun metagenomic approach to analyze 22 different types of yogurt collected from 9 main yogurt-producing areas in China, each type of yogurt includes 8 different batches of samples. The abundance and diversity of bacteria identified in probiotic yogurt were significantly higher than those in pasteurized yogurt, with Acetobacter, Raoultella, and Burkholderia identified as unique and highly abundant genera in probiotic yogurt. Similarly, ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) abundance was higher than that in pasteurized yogurt. A total of 1149 ARG subtypes belonging to 16 ARG types were identified, with the highest abundance of rifampicin, multidrug efflux pumps, and quinolone resistance genes detected. Network analysis revealed significant non-random co-occurrence relationships between different types and subtypes of ARGs in yogurt samples. Forty-four ARG subtypes in pasteurized yogurt were potentially hosted by 36 bacterial genera, and in probiotic yogurt, 63 ARGs were expected to be hosted by 86 bacterial species from 37 genera. These findings speculate on potential safety issues in fermented dairy products and emphasize the need for a more hygienic environment when processing probiotic yogurt.}, } @article {pmid38246376, year = {2024}, author = {Wang, L and He, Y and Zhu, Y and Ping, Q and Li, Y}, title = {Insight into using hydrochar to alleviate ammonia nitrogen inhibition during anaerobic digestion of waste activated sludge: Performance, metagenomic and metabolomic signatures.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170196}, doi = {10.1016/j.scitotenv.2024.170196}, pmid = {38246376}, issn = {1879-1026}, abstract = {In this study, hydrochar (HCR) was used to alleviate high ammonia inhibition to the anaerobic digestion (AD) of waste activated sludge (WAS) and to elucidate the inner microorganism mechanism. After HCR addition, the cumulative methane yield increased by 73.6 % and 35.6 % under ammonia inhibition levels of 3000 and 6000 mg/L, respectively. Metagenomic analysis showed that HCR enriched the diversity of hydrogenotrophic methanotrophs, and the relative abundances of functional microorganisms with electron transfer capabilities (Geobacteraceae bacterium etc.) were 1.5-7.8 times higher than those without HCR addition. Metabolomics analysis implied that metabolites related to fatty acid degradation, such as glutaric acid and hexadecanal, were downregulated (2.9-15.7 %) under ammonia inhibition conditions and that HCR regulates metabolites in the methane metabolic pathway. Moreover, HCR changed the methanogenic pathway from hydrogenotrophic methanogenesis to multiple pathways under ammonia inhibition conditions, especially methanolic and methylotrophic methanogenesis, which facilitated the methane yield. This study provides valuable information for understanding the inner microbial mechanism of HCR addition on alleviating high ammonia inhibition to AD of WAS, and gives basic knowledge for the application of AD of WAS under ammonia inhibition conditions.}, } @article {pmid38246373, year = {2024}, author = {Ren, Z and Li, H and Luo, W}, title = {Unraveling the mystery of antibiotic resistance genes in green and red Antarctic snow.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170148}, doi = {10.1016/j.scitotenv.2024.170148}, pmid = {38246373}, issn = {1879-1026}, abstract = {Antarctic snow is a thriving habitat for a diverse array of complex microorganisms, and can present in different colors due to algae blooms. However, the potential role of Antarctic snow as reservoirs for antibiotic resistance genes (ARGs) has not been studied. Using metagenomic sequencing, we studied ARGs in green-snow and red-snow on the Fildes Peninsula, Antarctica. Alpha and beta diversities of ARGs, as well as co-occurrence between ARGs and bacteria were assessed. The results showed that a total of 525 ARGs conferring resistance to 30 antibiotic classes were detected across the samples, with half of the ARGs presented in all samples. Green-snow exhibited a higher number of ARGs compared to red-snow. The most abundant ARGs conferring resistance to commonly used antibiotics, including disinfecting agents and antiseptics, peptide, isoniazid, MLS, fluoroquinolone, aminocoumarin, etc. Multidrug resistance genes stood out as the most diverse and abundant, with antibiotic efflux emerging as the dominant resistance mechanism. Interestingly, the composition of ARGs in green-snow markedly differed from that in red-snow, highlighting distinct ARG profiles. Beta-diversity partitioning showed a higher contribution of nestedness for ARG's variation in green-snow, while higher contribution of turnover in red-snow. Furthermore, the co-occurrence analysis between ARGs and bacteria unveiled intricate relationships, indicating that certain ARGs may have multiple potential hosts. The observed differences in co-occurrence networks between green-snow and red-snow suggested distinct host relationships between ARGs and bacteria in these colored snows. Given the increasing appearance of the colored snow around the world due to the climate change, the results shed light on the mystery and potential implication of ARGs in green and red Antarctic snow.}, } @article {pmid38246133, year = {2024}, author = {Chulenbayeva, L and Ganzhula, Y and Kozhakhmetov, S and Jarmukhanov, Z and Nurgaziyev, M and Nurgozhina, A and Muhanbetzhanov, N and Sergazy, S and Zhetkenev, S and Borykbay, Z and Tkachev, V and Urazova, S and Vinogradova, E and Kushugulova, A}, title = {The Trajectory of Successful Aging: Insights from Metagenome and Cytokine Profiling.}, journal = {Gerontology}, volume = {}, number = {}, pages = {}, doi = {10.1159/000536082}, pmid = {38246133}, issn = {1423-0003}, abstract = {INTRODUCTION: The longevity is influenced by of genetic, environmental, and lifestyle factors. The specific changes that occur in the gut microbiome during the aging process, and their relationship to longevity and immune function, have not yet been fully understood. The ongoing research other microbiome based to longevity cohort in Kazakhstan, provides preliminary information on longevity-related aging, where cytokine expression is associated with specific microbial communities and microbial functions.

METHODS: Metagenomic shotgun sequencing study of 40 long-lived individuals aged 90 years and over were carried out, who were conditionally healthy and active, able to served themselves, without a history of serious infection and cancer, who had not taken any antimicrobials, including probiotics. Blood serum weas analyzed to clinical and laboratory characteristics. The cytokine and chemokine profile in serum and stool samples was assessed using Multiplex analysis.

RESULTS: We found a significant increase in the expression of pro-inflammatory cytokines IL-1a, IL-6, 12p70, IP-10, IFN-α2, IL-15 TNFa, as well as chemokines MIP-1a/CCL3 and MIP-1b/CCL4, chemokine motif ligands MCP-3/CCL7 and MDC/CCL22(1c). Nonagenerians and centenarians demonstrated a greater diversity of core microbiota genera and showed an elevated prevalence of the genera Bacteroides, Clostridium, Escherichia and Alistipes. Conversely, there was a decrease in the abundance of the genera Ruminococcaceae, Fusicatenibacter, Dorea, as well as the species Fusicatenibacter saccharivorans. Furthermore, functional analysis revealed that the microbiome in long-lived group has a high capacity for lipid metabolism, amino acid degradation, and potential signs of chronic inflammatory status.

CONCLUSION: Long-lived individuals exhibit an immune system imbalance and observed changes in the composition of the gut microbiota at the genus level between to the two age groups. Age-related changes in the gut microbiome, metabolic functions of the microbial community, and chronic inflammation all contribute to immunosenescence. In turn, the inflammatory state and microbial composition of the gut is related to nutritional status.}, } @article {pmid38246125, year = {2024}, author = {Mahony, J}, title = {Biological and bioinformatic tools for the discovery of unknown phage-host combinations.}, journal = {Current opinion in microbiology}, volume = {77}, number = {}, pages = {102426}, doi = {10.1016/j.mib.2024.102426}, pmid = {38246125}, issn = {1879-0364}, abstract = {The field of microbial ecology has been transformed by metagenomics in recent decades and has culminated in vast datasets that facilitate the bioinformatic dissection of complex microbial communities. Recently, attention has turned from defining the microbiota composition to the interactions and relationships that occur between members of the microbiota. Within complex microbiota, the identification of bacteriophage-host combinations has been a major challenge. Recent developments in artificial intelligence tools to predict protein structure and function as well as the relationships between bacteria and their infecting bacteriophages allow a strategic approach to identifying and validating phage-host relationships. However, biological validation of these predictions remains essential and will serve to improve the existing predictive tools. In this review, I provide an overview of the most recent developments in both bioinformatic and experimental approaches to predicting and experimentally validating unknown phage-host combinations.}, } @article {pmid38246077, year = {2024}, author = {Tang, M and Chen, Q and Zhong, H and Liu, S and Sun, W}, title = {CPR bacteria and DPANN archaea play pivotal roles in response of microbial community to antibiotic stress in groundwater.}, journal = {Water research}, volume = {251}, number = {}, pages = {121137}, doi = {10.1016/j.watres.2024.121137}, pmid = {38246077}, issn = {1879-2448}, abstract = {The accumulation of antibiotics in the natural environment can disrupt microbial population dynamics. However, our understanding of how microbial communities adapt to the antibiotic stress in groundwater ecosystems remains limited. By recovering 2675 metagenome-assembled genomes (MAGs) from 66 groundwater samples, we explored the effect of antibiotics on bacterial, archaeal, and fungal communities, and revealed the pivotal microbes and their mechanisms in coping with antibiotic stress. The results indicated that antibiotics had the most significant influence on bacterial and archaeal communities, while the impact on the fungal community was minimal. Analysis of co-occurrence networks between antibiotics and microbes revealed the critical roles of Candidate Phyla Radiation (CPR) bacteria and DPANN archaea, two representative microbial groups in groundwater ecosystem, in coping with antibiotic resistance and enhancing network connectivity and complexity. Further genomic analysis demonstrated that CPR bacteria carried approximately 6 % of the identified antibiotic resistance genes (ARGs), indicating their potential to withstand antibiotics on their own. Meanwhile, the genomes of CPR bacteria and DPANN archaea were found to encode diverse biosynthetic gene clusters (BGCs) responsible for producing antimicrobial metabolites, which could not only assist CPR and DPANN organisms but also benefit the surrounding microbes in combating antibiotic stress. These findings underscore the significant impact of antibiotics on prokaryotic microbial communities in groundwater, and highlight the importance of CPR bacteria and DPANN archaea in enhancing the overall resilience and functionality of the microbial community in the face of antibiotic stress.}, } @article {pmid38246038, year = {2024}, author = {Phulpoto, IA and Qi, Z and Qazi, MA and Yu, Z}, title = {Biosurfactants-based mixed polycyclic aromatic hydrocarbon degradation: From microbial community structure toward non-targeted metabolomic profile determination.}, journal = {Environment international}, volume = {184}, number = {}, pages = {108448}, doi = {10.1016/j.envint.2024.108448}, pmid = {38246038}, issn = {1873-6750}, abstract = {Biosurfactants-based bioremediation is considered an efficient technology to eliminate environmental pollutants including polycyclic aromatic hydrocarbons (PAHs). However, the precise role of rhamnolipids or lipopeptide-biosurfactants in mixed PAH dissipation, shaping microbial community structure, and influencing metabolomic profile remained unclear. In this study, results showed that the maximum PAH degradation was achieved in lipopeptide-assisted treatment (SPS), where the pyrene and phenanthrene were substantially degraded up to 74.28 % and 63.05 % respectively, as compared to rhamnolipids (SPR) and un-aided biosurfactants (SP). Furthermore, the high throughput sequencing analysis revealed a significant change in the PAH-degrading microbial community, with Proteobacteria being the predominant phylum (>98 %) followed by Bacteroidota and Firmicutes in all the treatments. Moreover, Pseudomonas and Pannonibacter were found as highly potent bacterial genera for mixed PAH degradation in SPR, SPS, and SP treatments, nevertheless, the abundance of the genus Pseudomonas was significantly enhanced (>97 %) in SPR treatment groups. On the other hand, the non-targeted metabolomic profile through UHPLC-MS/MS exhibited a remarkable change in the metabolites of amino acids, carbohydrates, and lipid metabolisms by the input of rhamnolipids or lipopeptide-biosurfactants whereas, the maximum intensities of metabolites (more than two-fold) were observed in SPR treatment. The findings of this study suggested that the aforementioned biosurfactants can play an indispensable role in mixed PAH degradation as well as seek to offer new insights into shifts in PAH-degrading microbial communities and their metabolic function, which can guide the development of more efficient and targeted strategies for complete removal of organic pollutants such as PAH from the contaminated environment.}, } @article {pmid38246037, year = {2024}, author = {Adhikari, BN and Paskey, AC and Frey, KG and Bennett, AJ and Long, KA and Kuhn, JH and Hamilton, T and Glang, L and Cer, RZ and Goldberg, TL and Bishop-Lilly, KA}, title = {Virome profiling of fig wasps (Ceratosolen spp.) reveals virus diversity spanning four realms.}, journal = {Virology}, volume = {591}, number = {}, pages = {109992}, doi = {10.1016/j.virol.2024.109992}, pmid = {38246037}, issn = {1096-0341}, abstract = {We investigated the virome of agaonid fig wasps (Ceratosolen spp.) inside syconia ("fruits") of various Ficus trees fed upon by frugivores such as pteropodid bats in Sub-Saharan Africa. This virome includes representatives of viral families spanning four realms and includes near-complete genome sequences of three novel viruses and fragments of five additional potentially novel viruses evolutionarily associated with insects, fungi, plants, and vertebrates. Our study provides evidence that frugivorous animals are exposed to a plethora of viruses by coincidental consumption of fig wasps, which are obligate pollinators of figs worldwide.}, } @article {pmid38246927, year = {2024}, author = {Bhagat, N and Mansotra, R and Patel, K and Ambardar, S and Vakhlu, J}, title = {Molecular warfare between pathogenic Fusarium oxysporum R1 and host Crocus sativus L. unraveled by dual transcriptomics.}, journal = {Plant cell reports}, volume = {43}, number = {2}, pages = {42}, pmid = {38246927}, issn = {1432-203X}, support = {F.No.Z18017/187/CSS/R&D/JK-01/2018-19-NMPB-IV A//National Medicinal Plants Board, Ministry of AYUSH, Government of India/ ; }, abstract = {Phenylpropanoid biosynthesis and plant-pathogen interaction pathways in saffron and cell wall degrading enzymes in Fusarium oxysporum R1 are key players involved in the interaction. Fusarium oxysporum causes corm rot in saffron (Crocus sativus L.), which is one of the most devastating fungal diseases impacting saffron yield globally. Though the corm rot agent and its symptoms are known widely, little is known about the defense mechanism of saffron in response to Fusarium oxysporum infection at molecular level. Therefore, the current study reports saffron-Fusarium oxysporum R1 (Fox R1) interaction at the molecular level using dual a transcriptomics approach. The results indicated the activation of various defense related pathways such as the mitogen activated protein kinase pathway (MAPK), plant-hormone signaling pathways, plant-pathogen interaction pathway, phenylpropanoid biosynthesis pathway and PR protein synthesis in the host during the interaction. The activation of pathways is involved in the hypersensitive response, production of various secondary metabolites, strengthening of the host cell wall, systemic acquired resistance etc. Concurrently, in the pathogen, 60 genes reported to be linked to pathogenicity and virulence has been identified during the invasion. The expression of genes encoding plant cell wall degrading enzymes, various transcription factors and effector proteins indicated the strong pathogenicity of Fusarium oxysporum R1. Based on the results obtained, the putative molecular mechanism of the saffron-Fox R1 interaction was identified. As saffron is a male sterile plant, and can only be improved by genetic manipulation, this work will serve as a foundation for identifying genes that can be used to create saffron varieties, resistant to Fusarium oxysporum infection.}, } @article {pmid38246848, year = {2024}, author = {Liu, Y and Fachrul, M and Inouye, M and Méric, G}, title = {Harnessing human microbiomes for disease prediction.}, journal = {Trends in microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.tim.2023.12.004}, pmid = {38246848}, issn = {1878-4380}, abstract = {The human microbiome has been increasingly recognized as having potential use for disease prediction. Predicting the risk, progression, and severity of diseases holds promise to transform clinical practice, empower patient decisions, and reduce the burden of various common diseases, as has been demonstrated for cardiovascular disease or breast cancer. Combining multiple modifiable and non-modifiable risk factors, including high-dimensional genomic data, has been traditionally favored, but few studies have incorporated the human microbiome into models for predicting the prospective risk of disease. Here, we review research into the use of the human microbiome for disease prediction with a particular focus on prospective studies as well as the modulation and engineering of the microbiome as a therapeutic strategy.}, } @article {pmid38182051, year = {2024}, author = {Huang, XY and Kuang, YK and Liu, QH and Liao, H}, title = {Pleural aspergillosis in an otherwise healthy patient diagnosed by medical thoracoscopy.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cmi.2023.12.031}, pmid = {38182051}, issn = {1469-0691}, } @article {pmid38245666, year = {2024}, author = {Cooper, AL and Low, A and Wong, A and Tamber, S and Blais, BW and Carrillo, CD}, title = {Modeling the limits of detection for antimicrobial resistance genes in agri-food samples: a comparative analysis of bioinformatics tools.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {31}, pmid = {38245666}, issn = {1471-2180}, abstract = {BACKGROUND: Although the spread of antimicrobial resistance (AMR) through food and its production poses a significant concern, there is limited research on the prevalence of AMR bacteria in various agri-food products. Sequencing technologies are increasingly being used to track the spread of AMR genes (ARGs) in bacteria, and metagenomics has the potential to bypass some of the limitations of single isolate characterization by allowing simultaneous analysis of the agri-food product microbiome and associated resistome. However, metagenomics may still be hindered by methodological biases, presence of eukaryotic DNA, and difficulties in detecting low abundance targets within an attainable sequence coverage. The goal of this study was to assess whether limits of detection of ARGs in agri-food metagenomes were influenced by sample type and bioinformatic approaches.

RESULTS: We simulated metagenomes containing different proportions of AMR pathogens and analysed them for taxonomic composition and ARGs using several common bioinformatic tools. Kraken2/Bracken estimates of species abundance were closest to expected values. However, analysis by both Kraken2/Bracken indicated presence of organisms not included in the synthetic metagenomes. Metaphlan3/Metaphlan4 analysis of community composition was more specific but with lower sensitivity than the Kraken2/Bracken analysis. Accurate detection of ARGs dropped drastically below 5X isolate genome coverage. However, it was sometimes possible to detect ARGs and closely related alleles at lower coverage levels if using a lower ARG-target coverage cutoff (< 80%). While KMA and CARD-RGI only predicted presence of expected ARG-targets or closely related gene-alleles, SRST2 (which allows read to map to multiple targets) falsely reported presence of distantly related ARGs at all isolate genome coverage levels. The presence of background microbiota in metagenomes influenced the accuracy of ARG detection by KMA, resulting in mcr-1 detection at 0.1X isolate coverage in the lettuce but not in the beef metagenome.

CONCLUSIONS: This study demonstrates accurate detection of ARGs in synthetic metagenomes using various bioinformatic methods, provided that reads from the ARG-encoding organism exceed approximately 5X isolate coverage (i.e. 0.4% of a 40 million read metagenome). While lowering thresholds for target gene detection improved sensitivity, this led to the identification of alternative ARG-alleles, potentially confounding the identification of critical ARGs in the resistome. Further advancements in sequencing technologies providing increased coverage depth or extended read lengths may improve ARG detection in agri-food metagenomic samples, enabling use of this approach for tracking clinically important ARGs in agri-food samples.}, } @article {pmid38245560, year = {2024}, author = {Duan, N and Hand, E and Pheko, M and Sharma, S and Emiola, A}, title = {Structure-guided discovery of anti-CRISPR and anti-phage defense proteins.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {649}, pmid = {38245560}, issn = {2041-1723}, abstract = {Bacteria use a variety of defense systems to protect themselves from phage infection. In turn, phages have evolved diverse counter-defense measures to overcome host defenses. Here, we use protein structural similarity and gene co-occurrence analyses to screen >66 million viral protein sequences and >330,000 metagenome-assembled genomes for the identification of anti-phage and counter-defense systems. We predict structures for ~300,000 proteins and perform large-scale, pairwise comparison to known anti-CRISPR (Acr) and anti-phage proteins to identify structural homologs that otherwise may not be uncovered using primary sequence search. This way, we identify a Bacteroidota phage Acr protein that inhibits Cas12a, and an Akkermansia muciniphila anti-phage defense protein, termed BxaP. Gene bxaP is found in loci encoding Bacteriophage Exclusion (BREX) and restriction-modification defense systems, but confers immunity independently. Our work highlights the advantage of combining protein structural features and gene co-localization information in studying host-phage interactions.}, } @article {pmid38245554, year = {2024}, author = {Tang, Q and Huang, H and Xu, H and Xia, H and Zhang, C and Ye, D and Bi, F}, title = {Endogenous Coriobacteriaceae enriched by a high-fat diet promotes colorectal tumorigenesis through the CPT1A-ERK axis.}, journal = {NPJ biofilms and microbiomes}, volume = {10}, number = {1}, pages = {5}, pmid = {38245554}, issn = {2055-5008}, abstract = {A high-fat diet (HFD) may be linked to an increased colorectal cancer (CRC) risk. Stem cell proliferation and adipokine release under inflammatory and obese conditions are the main factors regulating CRC progression. Furthermore, alterations in intestinal flora have been linked to tumorigenesis and tumour progression. However, whether a HFD can promote CRC occurrence by altering intestinal flora remains unclear. The objective of this study was to identify bacterial strains enriched by a HFD and investigate the association and mechanism by which a HFD and bacterial enrichment promote CRC occurrence and development. In this study, the intestinal microbiota of mice was assessed using 16S rRNA and metagenomic sequencing. Serum metabolites of HFD-fed mice were assessed using tandem liquid chromatography-mass spectrometry. CRC cell lines and organoids were co-cultured with Coriobacteriaceae to evaluate the effect of these bacteria on the CPT1A-ERK signalling pathway. We found that Coriobacteriaceae were enriched in the colons of HFD-fed mice. An endogenous Coriobacteriaceae strain, designated as Cori.ST1911, was successfully isolated and cultured from the stools of HFD-fed mice, and the tumorigenic potential of Cori.ST1911 in CRC was validated in several CRC mouse models. Furthermore, Cori.ST1911 increased acylcarnitine levels by activating CPT1A, demonstrating the involvement of the CPT1A-ERK axis. We also found that the endogenous Lactobacillus strain La.mu730 can interfere with Cori.ST1911 colonisation and restore gut barrier function. In conclusion, we identified a novel endogenous intestinal Coriobacteriaceae, Cori.ST1911, which might lead to a new gut microbiota intervention strategy for the prevention and treatment of CRC.}, } @article {pmid38245349, year = {2024}, author = {Shama, S and Ranade, AV and Qaisar, R and Khan, NA and Tauseef, I and Elmoselhi, A and Siddiqui, R}, title = {Enhancing microbial diversity as well as multi-organ health in hind-limb unloaded mice.}, journal = {Life sciences in space research}, volume = {40}, number = {}, pages = {62-71}, doi = {10.1016/j.lssr.2023.08.006}, pmid = {38245349}, issn = {2214-5532}, abstract = {During space travel, the gut microbiota is changed which can lead to health-related issues. Previously, we utilized the hind-limb unloaded (HU) mouse, which is an established ground-based in-vivo model of microgravity and observed altered gut microbiota. In this study, we evaluated the beneficial effects of novel bacterial conditioned media in HU mice to understand if they can offset the effects of unloading in the HU mouse model. We aimed to explore the influence of bacterial conditioned media on diversity and quantity of intestinal microbes in HU mice, and investigated the microarchitecture of mice retinas and kidneys to evaluate the potential systemic effects of bacterial conditioned media in HU mice. Four-month-old, male C57/Bl6 mice were separated into groups: including the ground-based control group, the HU group mice fed with vehicle as placebo (HU-placebo mice), and the HU group fed with bacterial conditioned media (HU-CP mice) and kept under controlled environmental conditions for three weeks. Next, mice were sacrificed; gut dissections were conducted, and metagenomic analysis of bacterial species was performed via DNA extraction and 16S rRNA analysis. The results revealed an HU-induced reduction in intestinal microbial diversity, and an increase in pathogenic bacteria dominated by Firmicutes (45%). In contrast, supplementation with bacterial conditioned media for three weeks led to a significant increase in gut microbial diversity with noticeable changes in the OTUs abundance in the HU mice. Additionally, HU-induced muscle weakness and structural abnormalities in the retina and kidney were partially prevented with bacterial conditioned media. Moreover, a greater diversity of several bacteria in the HU-CP was observed including, Bacteriodota, Firmicutes, Proteobacteria, Actionobacteriota, Verrucomicorbiota, Cyanobacteria, Gemmatimonadota, Acidobacteriota, Chloroflexi, Myxococcota, and others. Prospective research involving molecular mechanistic studies are needed to comprehend the systemic effects of bacterial metabolites conditioned media on experimental animal models under chronic stress.}, } @article {pmid38244622, year = {2024}, author = {Coleine, C and Albanese, D and Ray, AE and Delgado-Baquerizo, M and Stajich, JE and Williams, TJ and Larsen, S and Tringe, S and Pennacchio, C and Ferrari, BC and Donati, C and Selbmann, L}, title = {Metagenomics untangles potential adaptations of Antarctic endolithic bacteria at the fringe of habitability.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170290}, doi = {10.1016/j.scitotenv.2024.170290}, pmid = {38244622}, issn = {1879-1026}, abstract = {Survival and growth strategies of Antarctic endolithic microbes residing in Earth's driest and coldest desert remain virtually unknown. From 109 endolithic microbiomes, 4539 metagenome-assembled genomes were generated, 49.3 % of which were novel candidate bacterial species. We present evidence that trace gas oxidation and atmospheric chemosynthesis may be the prevalent strategies supporting metabolic activity and persistence of these ecosystems at the fringe of life and the limits of habitability.}, } @article {pmid38244412, year = {2024}, author = {Liu, X and Wang, L and Zheng, J and Mao, W and Liu, W and Zhu, G and Ji, XM and Zhang, Q}, title = {Multi-omics analysis reveals the collaboration and metabolisms of the anammox consortia driven by soluble/non-soluble Fe(III) as the sole iron element.}, journal = {Journal of environmental management}, volume = {352}, number = {}, pages = {120124}, doi = {10.1016/j.jenvman.2024.120124}, pmid = {38244412}, issn = {1095-8630}, abstract = {Iron is recognized as a physiological requirement for anammox bacteria (AnAOB), with Fe(II) considered to be the most effective form. However, Fe(III), instead of Fe(II) is the common iron form in natural and artificial ecosystems. In this study, the nitrogen removal performance and metabolic mechanisms in anammox consortia with soluble and non-soluble Fe(III) as the sole iron element were investigated. After the 150-day operation, the soluble (FeCl3) and insoluble (Fe2O3) Fe(III)-fed anammox systems reached nitrogen removal rates of 71.84 ± 0.80% and 50.20 ± 0.98%, respectively. AnAOB could survive with soluble (FeCl3) or insoluble (Fe2O3) Fe(III) as the sole iron element, reaching relative abundances of 18.49% and 13.16%, respectively. The results show that the formation of anammox core consortia can enable AnAOB's survival to adverse external conditions of Fe(II) deficiency. Metagenomic and metatranscriptomic analysis reveal that Ca. Kuenenia can only uptake Fe(II) into the cell for metabolisms either independently through the extracellular electron transfer or with the cross-feeding of symbiotic microbes. This study provides insight into the utilization and metabolic mechanisms of Fe(III) in Ca. Kuenenia-dominated consortia, and deepens the understanding of anammox core consortia in the nitrogen, carbon, and iron cycling, further promoting the practical applications of anammox processes.}, } @article {pmid38244232, year = {2024}, author = {Wu, IW and Chang, LC and Wu, YL and Yang, HY and Twu, YC and Tsai, PY and Paulus, S and Resnick, R and Chung, WH and Yang, CW and Hsieh, WP and Su, SC}, title = {Gut flora metagenomic analysis coupled with metabolic and deep immune profiling in chronic kidney disease.}, journal = {Nephrology, dialysis, transplantation : official publication of the European Dialysis and Transplant Association - European Renal Association}, volume = {}, number = {}, pages = {}, doi = {10.1093/ndt/gfae013}, pmid = {38244232}, issn = {1460-2385}, abstract = {BACKGROUND AND HYPOTHESIS: Perturbation of gut microbiota has been linked to chronic kidney disease (CKD), which was correlated with a sophisticated milieu of metabolic and immune dysregulation.

METHODS: To clarify the underlying host-microbe interaction in CKD, we performed multi-omics measurements, including systems-level gut microbiome, targeted serum metabolome, and deep immunotyping, in a cohort of patients and non-CKD controls.

RESULTS: Our analyses on functional profiles of gut microbiome showed a decrease in the diversity and abundance of carbohydrate-active enzyme (CAZyme) genes but an increase in the abundance of antibiotic resistance, nitrogen cycling enzyme, and virulence factor genes in CKD. Moreover, models generated using measurements of serum metabolites (amino acids, bile acids, and short-chain fatty acids) or immunotypes were predictive of renal impairment but less so than many of functional profiles derived from gut microbiota, with the CAZyme genes being the top performing model to accurately predict early stage of diseases. In addition, co-occurrence analyses revealed coordinated host-microbe relationships in CKD. Specifically, the highest fractions of significant correlations were identified with circulating metabolites by several taxonomic and functional profiles of gut microbiome, while immunotype features were moderately associated with the abundance of microbiome-encoded metabolic pathways and serum levels of amino acids (e.g. B cell cluster-tryptophan and B cell cluster-tryptophan metabolism).

CONCLUSION: Overall, our multi-omics integration revealed several signatures of systems-level gut microbiome in robust associations with host-microbe co-metabolites and renal function, which may be of etiological and diagnostic implications in CKD.}, } @article {pmid38244164, year = {2024}, author = {Jirasansawat, K and Chiemchaisri, W and Chiemchaisri, C}, title = {Enhancement of sulfide removal and sulfur recovery in piggery wastewater via lighting-anaerobic digestion with bioaugmentation of phototrophic green sulfur bacteria.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38244164}, issn = {1614-7499}, abstract = {Anaerobic pig wastewater treatment commonly generates high sulfide concentrations in the treated wastewater. This study aims to apply phototrophic green sulfur bacteria (PGB) to promote sulfide removal in lighting-anaerobic digestion (lighting-AD) treating pig wastewater. Initially, batch AD tests of pig wastewater with/without PGB addition were carried out under dark (D) and light (L) conditions. The results showed that the lighting-AD with PGB gave a higher growth rate of PGB (0.056 h[-1]) and the highest COD/sulfide removals as compared to the dark-AD with PGB and lighting-AD solely. More experiments under various light intensities were performed in order to find an optimal intensity for PGB growth concurrently with metagenomic changes concerning treatment performance. It appeared that sulfide removal rates had increased as increasing light intensity up to 473 lx by giving the highest rate of 12.5 mg L[-1] d[-1] with the highest sulfur element content in the biomass. Contrastingly, many PGB species disappeared at 1350 lx exposure subsequently sharply decreasing the rate of sulfide removal. In sum, the application of low light intensities of 400-500 lx with bioaugmented PGB could promote PGB growth and activity in sulfide removal in pig wastewater in the lighting of the AD process.}, } @article {pmid38243750, year = {2024}, author = {Cerk, K and Ugalde-Salas, P and Nedjad, CG and Lecomte, M and Muller, C and Sherman, DJ and Hildebrand, F and Labarthe, S and Frioux, C}, title = {Community-scale models of microbiomes: Articulating metabolic modelling and metagenome sequencing.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {e14396}, doi = {10.1111/1751-7915.14396}, pmid = {38243750}, issn = {1751-7915}, support = {BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; }, abstract = {Building models is essential for understanding the functions and dynamics of microbial communities. Metabolic models built on genome-scale metabolic network reconstructions (GENREs) are especially relevant as a means to decipher the complex interactions occurring among species. Model reconstruction increasingly relies on metagenomics, which permits direct characterisation of naturally occurring communities that may contain organisms that cannot be isolated or cultured. In this review, we provide an overview of the field of metabolic modelling and its increasing reliance on and synergy with metagenomics and bioinformatics. We survey the means of assigning functions and reconstructing metabolic networks from (meta-)genomes, and present the variety and mathematical fundamentals of metabolic models that foster the understanding of microbial dynamics. We emphasise the characterisation of interactions and the scaling of model construction to large communities, two important bottlenecks in the applicability of these models. We give an overview of the current state of the art in metagenome sequencing and bioinformatics analysis, focusing on the reconstruction of genomes in microbial communities. Metagenomics benefits tremendously from third-generation sequencing, and we discuss the opportunities of long-read sequencing, strain-level characterisation and eukaryotic metagenomics. We aim at providing algorithmic and mathematical support, together with tool and application resources, that permit bridging the gap between metagenomics and metabolic modelling.}, } @article {pmid38243343, year = {2024}, author = {Hu, M and Lin, X and Sun, T and Shao, X and Huang, X and Du, W and Guo, M and Zhu, X and Zhou, Y and Tong, T and Guo, F and Han, T and Wu, X and Shi, Y and Xiao, X and Zhang, Y and Hong, J and Chen, H}, title = {Gut microbiome for predicting immune checkpoint blockade-associated adverse events.}, journal = {Genome medicine}, volume = {16}, number = {1}, pages = {16}, pmid = {38243343}, issn = {1756-994X}, support = {82073115//National Natural Science Foundation of China/ ; 82002487//National Natural Science Foundation of China/ ; 81973346//National Natural Science Foundation of China/ ; 2022YFE0125300//Key Technologies Research and Development Program/ ; 2019M660142//China Postdoctoral Science Foundation/ ; }, abstract = {BACKGROUND: The impact of the gut microbiome on the initiation and intensity of immune-related adverse events (irAEs) prompted by immune checkpoint inhibitors (ICIs) is widely acknowledged. Nevertheless, there is inconsistency in the gut microbial associations with irAEs reported across various studies.

METHODS: We performed a comprehensive analysis leveraging a dataset that included published microbiome data (n = 317) and in-house generated data from 16S rRNA and shotgun metagenome samples of irAEs (n = 115). We utilized a machine learning-based approach, specifically the Random Forest (RF) algorithm, to construct a microbiome-based classifier capable of distinguishing between non-irAEs and irAEs. Additionally, we conducted a comprehensive analysis, integrating transcriptome and metagenome profiling, to explore potential underlying mechanisms.

RESULTS: We identified specific microbial species capable of distinguishing between patients experiencing irAEs and non-irAEs. The RF classifier, developed using 14 microbial features, demonstrated robust discriminatory power between non-irAEs and irAEs (AUC = 0.88). Moreover, the predictive score from our classifier exhibited significant discriminative capability for identifying non-irAEs in two independent cohorts. Our functional analysis revealed that the altered microbiome in non-irAEs was characterized by an increased menaquinone biosynthesis, accompanied by elevated expression of rate-limiting enzymes menH and menC. Targeted metabolomics analysis further highlighted a notably higher abundance of menaquinone in the serum of patients who did not develop irAEs compared to the irAEs group.

CONCLUSIONS: Our study underscores the potential of microbial biomarkers for predicting the onset of irAEs and highlights menaquinone, a metabolite derived from the microbiome community, as a possible selective therapeutic agent for modulating the occurrence of irAEs.}, } @article {pmid38243335, year = {2024}, author = {Han, Y and Zeng, X and Hua, L and Quan, X and Chen, Y and Zhou, M and Chuang, Y and Li, Y and Wang, S and Shen, X and Wei, L and Yuan, Z and Zhao, Y}, title = {The fusion of multi-omics profile and multimodal EEG data contributes to the personalized diagnostic strategy for neurocognitive disorders.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {12}, pmid = {38243335}, issn = {2049-2618}, support = {0106/2019/A2//Science and Technology Development Fund, Macau SAR/ ; MYRG-CRG2022-00011-ICMS//University of Macau/ ; }, abstract = {BACKGROUND: The increasing prevalence of neurocognitive disorders (NCDs) in the aging population worldwide has become a significant concern due to subjectivity of evaluations and the lack of precise diagnostic methods and specific indicators. Developing personalized diagnostic strategies for NCDs has therefore become a priority.

RESULTS: Multimodal electroencephalography (EEG) data of a matched cohort of normal aging (NA) and NCDs seniors were recorded, and their faecal samples and urine exosomes were collected to identify multi-omics signatures and metabolic pathways in NCDs by integrating metagenomics, proteomics, and metabolomics analysis. Additionally, experimental verification of multi-omics signatures was carried out in aged mice using faecal microbiota transplantation (FMT). We found that NCDs seniors had low EEG power spectral density and identified specific microbiota, including Ruminococcus gnavus, Enterocloster bolteae, Lachnoclostridium sp. YL 32, and metabolites, including L-tryptophan, L-glutamic acid, gamma-aminobutyric acid (GABA), and fatty acid esters of hydroxy fatty acids (FAHFAs), as well as disturbed biosynthesis of aromatic amino acids and TCA cycle dysfunction, validated in aged mice. Finally, we employed a support vector machine (SVM) algorithm to construct a machine learning model to classify NA and NCDs groups based on the fusion of EEG data and multi-omics profiles and the model demonstrated 92.69% accuracy in classifying NA and NCDs groups.

CONCLUSIONS: Our study highlights the potential of multi-omics profiling and EEG data fusion in personalized diagnosis of NCDs, with the potential to improve diagnostic precision and provide insights into the underlying mechanisms of NCDs. Video Abstract.}, } @article {pmid38243314, year = {2024}, author = {Yang, HT and Jiang, ZH and Yang, Y and Wu, TT and Zheng, YY and Ma, YT and Xie, X}, title = {Faecalibacterium prausnitzii as a potential Antiatherosclerotic microbe.}, journal = {Cell communication and signaling : CCS}, volume = {22}, number = {1}, pages = {54}, pmid = {38243314}, issn = {1478-811X}, abstract = {BACKGROUND: The gut microbiota plays a crucial role in coronary artery disease (CAD) development, but limited attention has been given to the role of the microbiota in preventing this disease. This study aimed to identify key biomarkers using metagenomics and untargeted metabolomics and verify their associations with atherosclerosis.

METHODS: A total of 371 participants, including individuals with various CAD types and CAD-free controls, were enrolled. Subsequently, significant markers were identified in the stool samples through gut metagenomic sequencing and untargeted metabolomics. In vivo and in vitro experiments were performed to investigate the mechanisms underlying the association between these markers and atherosclerosis.

RESULTS: Faecal omics sequencing revealed that individuals with a substantial presence of Faecalibacterium prausnitzii had the lowest incidence of CAD across diverse CAD groups and control subjects. A random forest model confirmed the significant relationship between F. prausnitzii and CAD incidence. Notably, F. prausnitzii emerged as a robust, independent CAD predictor. Furthermore, our findings indicated the potential of the gut microbiota and gut metabolites to predict CAD occurrence and progression, potentially impacting amino acid and vitamin metabolism. F. prausnitzii mitigated inflammation and exhibited an antiatherosclerotic effect on ApoE[-/-] mice after gavage. This effect was attributed to reduced intestinal LPS synthesis and reinforced mechanical and mucosal barriers, leading to decreased plasma LPS levels and an antiatherosclerotic outcome.

CONCLUSIONS: Sequencing of the samples revealed a previously unknown link between specific gut microbiota and atherosclerosis. Treatment with F. prausnitzii may help prevent CAD by inhibiting atherosclerosis.}, } @article {pmid38243297, year = {2024}, author = {Garcia-Fernandez, H and Arenas-de Larriva, AP and Lopez-Moreno, J and Gutierrez-Mariscal, FM and Romero-Cabrera, JL and Molina-Abril, H and Torres-Peña, JD and Rodriguez-Cano, D and Malagon, MM and Ordovas, JM and Delgado-Lista, J and Perez-Martinez, P and Lopez-Miranda, J and Camargo, A}, title = {Sex-specific differences in intestinal microbiota associated with cardiovascular diseases.}, journal = {Biology of sex differences}, volume = {15}, number = {1}, pages = {7}, pmid = {38243297}, issn = {2042-6410}, support = {Cordioprev-CEAS, 1/2016//the Fundacion Patrimonio Comunal Olivarero/ ; AGL2015-67896-P//Secretaría de Estado de Investigación, Desarrollo e Innovación/ ; AGL2012/39615//Ministerio de Ciencia e Innovación/ ; PID2019-104362RB-Ioo//Ministerio de Ciencia e Innovación/ ; PIE14/00005//Instituto de Salud Carlos III/ ; PIE14/00031//Instituto de Salud Carlos III/ ; CP14/00114//Instituto de Salud Carlos III/ ; DTS19/00007//Instituto de Salud Carlos III/ ; PI22/00925//Instituto de Salud Carlos III/ ; CPII19/00007//Instituto de Salud Carlos III/ ; PI-0055-2021//Consejería de Salud y Familias, Junta de Andalucía/ ; C1-0001-2022//Servicio Andaluz de Salud/ ; }, abstract = {BACKGROUND: Cardiovascular diseases (CVD), including coronary heart disease (CHD), display a higher prevalence in men than women. This study aims to evaluate the variations in the intestinal microbiota between men and women afflicted with CHD and delineate these against a non-CVD control group for each sex.

METHODS: Our research was conducted in the framework of the CORDIOPREV study, a clinical trial which involved 837 men and 165 women with CHD. We contrasted our findings with a reference group of 375 individuals (270 men, 105 women) without CVD. The intestinal microbiota was examined through 16S metagenomics on the Illumina MiSeq platform and the data processed with Quiime2 software.

RESULTS: Our results showed a sex-specific variation (beta diversity) in the intestinal microbiota, while alpha-biodiversity remained consistent across both sexes. Linear discriminant analysis effect size (LEfSe) analysis revealed sex-centric alterations in the intestinal microbiota linked to CVD. Moreover, using random forest (RF) methodology, we identified seven bacterial taxa-g_UBA1819 (Ruminococcaceae), g_Bilophila, g_Subdoligranulum, g_Phascolarctobacterium, f_Barnesiellaceae, g_Ruminococcus, and an unknown genus from the Ruminococcaceae family (Ruminococcaceae incertae sedis)-as key discriminators between men and women diagnosed with CHD. The same taxa also emerged as critical discriminators between CHD-afflicted and non-CVD individuals, when analyzed separately by sex.

CONCLUSION: Our findings suggest a sex-specific dysbiosis in the intestinal microbiota linked to CHD, potentially contributing to the sex disparity observed in CVD incidence. Trial registration Clinical Trials.gov.Identifier NCT00924937.}, } @article {pmid38243162, year = {2024}, author = {Jin, Y and Lan, W and Chen, X and Liu, W and Luo, W and Chen, S}, title = {A rare case of anti-DPPX encephalitis combined with neuroleptospirosis.}, journal = {BMC neurology}, volume = {24}, number = {1}, pages = {34}, pmid = {38243162}, issn = {1471-2377}, abstract = {BACKGROUND: Neuroleptospirosis and anti-dipeptidyl-peptidase-like protein 6 (DPPX) encephalitis are both very rare and have only been reported in the form of respective case reports. There are no reports of anti-DPPX encephalitis combined with neuroleptospirosis in the literature. We reported the first case of neuroleptospirosis combined with elevated DPPX antibodies in serum and cerebrospinal fluid (CSF).

CASE PRESENTATION: A previously healthy 53-year-old Chinese male farmer with a history of drinking raw stream water and flood sewage exposure was brought to the hospital due to an acute onset of neuropsychiatric symptoms. No fever or meningeal irritation signs were detected on physical examination. Routine laboratory investigations, including infection indicators, leukocyte and protein in CSF, electroencephalogram and gadolinium-enhanced magnetic resonance imaging of the brain, all revealed normal. While metagenomic next-generation sequencing (mNGS) identified the DNA genome of Leptospira interrogans in the CSF. Anti-DPPX antibody was detected both in blood and in CSF. A diagnosis of neuroleptospirosis combined with autoimmune encephalitis associated with DPPX-Ab was eventually made. He resolved completely after adequate amount of penicillin combined with immunotherapy.

CONCLUSION: We highlight that in patients with acute or subacute behavioral changes, even in the absence of fever, if the most recent freshwater exposure is clear, physicians should pay attention to leptospirosis. Due to the low sensitivity of routine microscopy, culture, polymerase chain reaction and antibody testing, mNGS may have more advantages in diagnosing neuroleptospirosis. As autoimmune encephalitis can be triggered by various infections, neuroleptospirosis may be one of the causes of autoimmune encephalitis. Since neuronal antibody measurements themselves are not that common in neuroleptospirosis, future studies are needed to determine whether the detection of anti-DPPX antibodies is a rare event in leptospirosis. Early identification of autoimmune encephalitis and timely administration of immunotherapy may lead to a better outcome.}, } @article {pmid38242997, year = {2024}, author = {Abe, S and Masuda, A and Matsumoto, T and Inoue, J and Toyama, H and Sakai, A and Kobayashi, T and Tanaka, T and Tsujimae, M and Yamakawa, K and Gonda, M and Masuda, S and Uemura, H and Kohashi, S and Inomata, N and Nagao, K and Harada, Y and Miki, M and Irie, Y and Juri, N and Ko, T and Yokotani, Y and Oka, Y and Ota, S and Kanzawa, M and Itoh, T and Imai, T and Fukumoto, T and Hara, E and Kodama, Y}, title = {Impact of intratumoral microbiome on tumor immunity and prognosis in human pancreatic ductal adenocarcinoma.}, journal = {Journal of gastroenterology}, volume = {}, number = {}, pages = {}, pmid = {38242997}, issn = {1435-5922}, abstract = {BACKGROUND: Recent evidence suggests that the presence of microbiome within human pancreatic ductal adenocarcinoma (PDAC) tissue potentially influences cancer progression and prognosis. However, the significance of tumor-resident microbiome remains unclear. We aimed to elucidate the impact of intratumoral bacteria on the pathophysiology and prognosis of human PDAC.

METHODS: The presence of intratumoral bacteria was assessed in 162 surgically resected PDACs using quantitative polymerase chain reaction (qPCR) and in situ hybridization (ISH) targeting 16S rRNA. The intratumoral microbiome was explored by 16S metagenome sequencing using DNA extracted from formalin-fixed paraffin-embedded tissues. The profile of intratumoral bacteria was compared with clinical information, pathological findings including tumor-infiltrating T cells, tumor-associated macrophage, fibrosis, and alterations in four main driver genes (KRAS, TP53, CDKN2A/p16, SMAD4) in tumor genomes.

RESULTS: The presence of intratumoral bacteria was confirmed in 52 tumors (32%) using both qPCR and ISH. The 16S metagenome sequencing revealed characteristic bacterial profiles within these tumors, including phyla such as Proteobacteria and Firmicutes. Comparison of bacterial profiles between cases with good and poor prognosis revealed a significant positive correlation between a shorter survival time and the presence of anaerobic bacteria such as Bacteroides, Lactobacillus, and Peptoniphilus. The abundance of these bacteria was correlated with a decrease in the number of tumor-infiltrating T cells positive for CD4, CD8, and CD45RO.

CONCLUSIONS: Intratumoral infection of anaerobic bacteria such as Bacteroides, Lactobacillus, and Peptoniphilus is correlated with the suppressed anti-PDAC immunity and poor prognosis.}, } @article {pmid38242941, year = {2024}, author = {Kim, G and Park, C and Yoon, YK and Park, D and Lee, JE and Lee, D and Sun, P and Park, S and Yun, C and Kang, DH and Chung, C}, title = {Prediction of lung cancer using novel biomarkers based on microbiome profiling of bronchoalveolar lavage fluid.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {1691}, pmid = {38242941}, issn = {2045-2322}, support = {NRF-2022R1C1C1007301//The Basic Science Research Program of the National Research Foundation of Korea (NRF), funded by the Ministry of Science and Technology/ ; HR22C1734//The Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea/ ; HR20C0025//The Korea Health Technology R&D Project through the Korea Health Industry Development Institute (KHIDI), funded by the Ministry of Health & Welfare, Republic of Korea/ ; }, abstract = {There is an unmet need for biomarkers for the diagnosis of lung cancer and decision criteria for lung biopsy. We comparatively investigated the lung microbiomes of patients with lung cancer and benign lung diseases. Patients who underwent bronchoscopy at Chungnam National University Hospital between June 2021 and June 2022 were enrolled. Bronchoalveolar lavage fluid (BALF) was collected from 24 patients each with lung cancer and benign lung diseases. The samples were analyzed using 16S rRNA-based metagenomic sequencing. We found that alpha diversity and the beta diversity distribution (P = 0.001) differed significantly between patients with benign lung diseases and those with lung cancer. Firmicutes was the most abundant phylum in patients with lung cancer (33.39% ± 17.439), whereas Bacteroidota was the most abundant phylum in patients with benign lung disease (31.132% ± 22.505), respectively. In differential abundance analysis, the most differentially abundant microbiota taxon was unclassified_SAR202_clade, belonging to the phylum Chloroflexi. The established prediction model distinguished patients with benign lung disease from those with lung cancer with a high accuracy (micro area under the curve [AUC] = 0.98 and macro AUC = 0.99). The BALF microbiome may be a novel biomarker for the detection of lung cancer.}, } @article {pmid38242453, year = {2024}, author = {Liang, X and Wen, X and Yang, H and Lu, H and Wang, A and Liu, S and Li, Q}, title = {Incorporating microbial inoculants to reduce nitrogen loss during sludge composting by suppressing denitrification and promoting ammonia assimilation.}, journal = {The Science of the total environment}, volume = {915}, number = {}, pages = {170000}, doi = {10.1016/j.scitotenv.2024.170000}, pmid = {38242453}, issn = {1879-1026}, abstract = {To address the challenge of increasing nitrogen retention in compost, this study investigated the effects of microbial communities on denitrification and ammonia assimilation during sludge composting by inoculating microbial inoculants. The results showed that the retention rates of total Kjeldahl nitrogen (TKN) and humic acid (HA) in MIs group (with microbial inoculants) were 4.94 % and 18.52 % higher than those in the control group (CK), respectively. Metagenomic analysis showed that Actinobacteria and Proteobacteria were identified as main microorganisms contributing to denitrification and ammonia assimilation. The addition of microbial agents altered the structure of the microbial community, which in turn stimulated the expression of functional genes. During cooling period, the ammonia assimilation genes glnA, gltB and gltD in MIs were 15.98 %, 24.84 % and 32.88 % higher than those in CK, respectively. Canonical correspondence analysis revealed a positive correlation between the dominant bacterial genera from the cooling stage to the maturity stage and the levels of NO3[-]-N, NH4[+]-N, HA, and TKN contents. NH4[+]-N was positively correlated with HA, indicating NH4[+]-N might be incorporated into HA. Heat map and network analyses revealed NH4[+]-N as a key factor affecting functional genes of denitrification and ammonia assimilation, with Nitrospira identified as the core bacteria in the microbial network. Therefore, the addition of microbial agents could increase nitrogen retention and improve compost product quality.}, } @article {pmid38242249, year = {2024}, author = {Hussain, A and Patwekar, U and Mongad, DS and Nimonkar, Y and Mundhe, S and Paul, D and Prakash, O and Shouche, YS}, title = {Functional antagonism and insights into the biosynthetic potential of human gut-derived microbes.}, journal = {International journal of antimicrobial agents}, volume = {}, number = {}, pages = {107091}, doi = {10.1016/j.ijantimicag.2024.107091}, pmid = {38242249}, issn = {1872-7913}, abstract = {The specialized small molecules encoded by commensal microbes mediate distinct functional interactions. However, the landscape of antagonistic interactions mediated by specialized strains and their small molecules broadly remains. Herein, to evaluate antimicrobial interactions as a defensive contributor to gain new insights into structure-related functions, we elucidated the antagonistic landscape within a collection of 330 human gut-derived commensal microbial strains. The potential antagonistic gut-derived strains displayed strain-specific selective inhibition, in contrast to common antimicrobial drugs that typically wipe out broad range of species, usually found in environmental microbes. Genome sequencing of representative gut strains revealed the presence of significant biosynthetic gene clusters (BGCs) encoding compound families that contribute to antagonistic activities, and are important in host defence or maintaining gut homeostasis. Subsets of these BGCs were abundantly found in metagenomic sequencing data from healthy individuals. Furthermore, the cell culture secretome of these strains revealed potential biomarkers linked to hallmark pathways. Together, these microorganisms exhibit biosynthetic novelty and represent a source of biologically significant natural products that are essential in the development of new agents for combating infectious diseases to cut the usage of broad-spectrum antibiotics and combat antimicrobial resistance.}, } @article {pmid38242018, year = {2024}, author = {Liang, H and Huang, J and Tao, Y and Klümper, U and Berendonk, TU and Zhou, K and Xia, Y and Yang, Y and Yu, Y and Yu, K and Lin, L and Li, X and Li, B}, title = {Investigating the antibiotic resistance genes and their potential risks in the megacity water environment: A case study of Shenzhen Bay Basin, China.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133536}, doi = {10.1016/j.jhazmat.2024.133536}, pmid = {38242018}, issn = {1873-3336}, abstract = {Antibiotic resistance genes (ARGs) constitute emerging pollutants and pose serious risks to public health. Anthropogenic activities are recognized as the main driver of ARG dissemination in coastal regions. However, the distribution and dissemination of ARGs in Shenzhen Bay Basin, a typical megacity water environment, have been poorly investigated. Here, we comprehensively profiled ARGs in Shenzhen Bay Basin using metagenomic approaches, and estimated their associated health risks. ARG profiles varied greatly among different sampling locations with total abundance ranging from 2.79 × 10[-2] (Shenzhen Bay sediment) to 1.04 (hospital sewage) copies per 16S rRNA gene copy, and 45.4% of them were located on plasmid-like sequences. Sewage treatment plants effluent and the corresponding tributary rivers were identified as the main sources of ARG contamination in Shenzhen Bay. Mobilizable plasmids and complete integrons carrying various ARGs probably participated in the dissemination of ARGs in Shenzhen Bay Basin. Additionally, 19 subtypes were assigned as high-risk ARGs (Rank I), and numerous ARGs were identified in potential human-associated pathogens, such as Burkholderiaceae, Rhodocyclaceae, Vibrionaceae, Pseudomonadaceae, and Aeromonadaceae. Overall, Shenzhen Bay represented a higher level of ARG risk than the ocean environment based on quantitative risk assessment. This study deepened our understanding of the ARGs and the associated risks in the megacity water environment.}, } @article {pmid38241573, year = {2024}, author = {Zheng, C and Ye, J and Song, M and Guo, Y and Gao, W and Hao, J and Feng, Z and Zhang, L}, title = {The second cutaneous anthrax infection diagnosed by metagenomic next-generation sequencing: A case report.}, journal = {Medicine}, volume = {103}, number = {3}, pages = {e36921}, doi = {10.1097/MD.0000000000036921}, pmid = {38241573}, issn = {1536-5964}, abstract = {RATIONALE: Anthrax is a severe zoonotic infectious disease caused by Bacillus anthracis. Most reported cases were traditionally diagnosed through culture and microscopy. We reported here the second case of cutaneous anthrax diagnosed by metagenomic next-generation sequencing (mNGS).

PATIENT CONCERNS: A 63-year-old man had a history of contact with an unwell sheep, developing local redness and swelling on wrist. The dorsal side of the left hand and forearm, with tension blisters on the back of the left.

DIAGNOSIS: B anthracis was detected from culturing and mNGS of tension blisters.

INTERVENTIONS: On the second day of admission, the patient was administered 3.2 million units of penicillin every 6 hours, and isolated and closely observed.

OUTCOMES: The patient improves and is discharged.

LESSONS: Traditional bacterial cultures are time-consuming, while mNGS offers the advantage of accurate, quick, high-throughput, unbiased sequencing of all genetic material in a sample, which is a good technical tool for assisting in the diagnosis of rare pathogen infections.}, } @article {pmid38241320, year = {2024}, author = {Mario-Vasquez, JE and Bagal, UR and Lowe, E and Morgulis, A and Phan, J and Sexton, DJ and Shiryev, S and Slatkevičius, R and Welsh, R and Litvintseva, AP and Blumberg, M and Agarwala, R and Chow, NA}, title = {Finding Candida auris in public metagenomic repositories.}, journal = {PloS one}, volume = {19}, number = {1}, pages = {e0291406}, doi = {10.1371/journal.pone.0291406}, pmid = {38241320}, issn = {1932-6203}, abstract = {Candida auris is a newly emerged multidrug-resistant fungus capable of causing invasive infections with high mortality. Despite intense efforts to understand how this pathogen rapidly emerged and spread worldwide, its environmental reservoirs are poorly understood. Here, we present a collaborative effort between the U.S. Centers for Disease Control and Prevention, the National Center for Biotechnology Information, and GridRepublic (a volunteer computing platform) to identify C. auris sequences in publicly available metagenomic datasets. We developed the MetaNISH pipeline that uses SRPRISM to align sequences to a set of reference genomes and computes a score for each reference genome. We used MetaNISH to scan ~300,000 SRA metagenomic runs from 2010 onwards and identified five datasets containing C. auris reads. Finally, GridRepublic has implemented a prospective C. auris molecular monitoring system using MetaNISH and volunteer computing.}, } @article {pmid38240981, year = {2024}, author = {Marini, E and De Bernardi, A and Tagliabue, F and Casucci, C and Tiano, L and Marcheggiani, F and Vaccari, F and Taskin, E and Puglisi, E and Brunetti, G and Vischetti, C}, title = {Copper toxicity on Eisenia fetida in a vineyard soil: a combined study with standard tests, genotoxicity assessment and gut metagenomic analysis.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38240981}, issn = {1614-7499}, support = {ID10852//CARIVERONA FOUNDATION/ ; SIME 2019.0423//CARIVERONA FOUNDATION/ ; }, abstract = {Copper (Cu) toxicity is a pressing concern for several soils, especially in organic viticulture. The objective of this work was to assess Cu toxicity on the non-target organism Eisenia fetida, employing both traditional and novel tools for early identification of Cu-induced damages. In addition to traditional tests like avoidance and reproductive toxicity experiments, other tests such as the single cell gel electrophoresis (SCGE) and gut microbiome analysis were evaluated to identify early and more sensitive pollution biomarkers. Four sub-lethal Cu concentrations were studied, and the results showed strong dose-dependent responses by the earthworm avoidance test and the exceeding of habitat threshold limit at the higher Cu doses. An inverse proportionality was observed between reproductive output and soil Cu concentration. Bioaccumulation was not detected in earthworms; soil concentrations of potentially bioavailable Cu were not affected by E. fetida presence or by time. On the contrary, the SCGE test revealed dose-dependent genotoxicity for the 'tail length' parameter already at the second day of Cu exposition. Gut microbiome analysis a modulation of microbial composition, with the most aboundant families being Pectobateriaceae, Comamonadaceae and Microscillaceae. Bacillaceae increased over time and showed adaptability to copper up to 165 mg/kg, while at the highest dose even the sensitive Acetobacteriaceae family was affected. The research provided new insights into the ecotoxicity of Cu sub-lethal doses highlighting both alterations at earthworms' cellular level and changes in their gut microbiota.}, } @article {pmid38240649, year = {2024}, author = {Martínez-Ugalde, E and Ávila-Akerberg, V and González Martínez, TM and Rebollar, EA}, title = {Gene functions of the Ambystoma altamirani skin microbiome vary across space and time but potential antifungal genes are widespread and prevalent.}, journal = {Microbial genomics}, volume = {10}, number = {1}, pages = {}, doi = {10.1099/mgen.0.001181}, pmid = {38240649}, issn = {2057-5858}, abstract = {Amphibian skin microbiomes can play a critical role in host survival against emerging diseases by protecting their host against pathogens. While a plethora of biotic and abiotic factors have been shown to influence the taxonomic diversity of amphibian skin microbiomes it remains unclear whether functional genomic diversity varies in response to temporal and environmental factors. Here we applied a metagenomic approach to evaluate whether seasonality, distinct elevations/sites, and pathogen presence influenced the functional genomic diversity of the A. altamirani skin microbiome. We obtained a gene catalogue of 92 107 nonredundant annotated genes and a set of 50 unique metagenome assembled genomes (MAGs). Our analysis showed that genes linked to general and potential antifungal traits significantly differed across seasons and sampling locations at different elevations. Moreover, we found that the functional genomic diversity of A. altamirani skin microbiome differed between B. dendrobatidis infected and not infected axolotls only during winter, suggesting an interaction between seasonality and pathogen infection. In addition, we identified the presence of genes and biosynthetic gene clusters (BGCs) linked to potential antifungal functions such as biofilm formation, quorum sensing, secretion systems, secondary metabolite biosynthesis, and chitin degradation. Interestingly genes linked to these potential antifungal traits were mainly identified in Burkholderiales and Chitinophagales MAGs. Overall, our results identified functional traits linked to potential antifungal functions in the A. altamirani skin microbiome regardless of variation in the functional diversity across seasons, elevations/sites, and pathogen presence. Our findings suggest that potential antifungal traits found in Burkholderiales and Chitinophagales taxa could be related to the capacity of A. altamirani to survive in the presence of Bd, although further experimental analyses are required to test this hypothesis.}, } @article {pmid38240642, year = {2024}, author = {Mirza, JD and de Oliveira Guimarães, L and Wilkinson, S and Rocha, EC and Bertanhe, M and Helfstein, VC and de-Deus, JT and Claro, IM and Cumley, N and Quick, J and Faria, NR and Sabino, EC and Kirchgatter, K and Loman, NJ}, title = {Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosquitoes.}, journal = {Microbial genomics}, volume = {10}, number = {1}, pages = {}, doi = {10.1099/mgen.0.001184}, pmid = {38240642}, issn = {2057-5858}, abstract = {The risk to human health from mosquito-borne viruses such as dengue, chikungunya and yellow fever is increasing due to increased human expansion, deforestation and climate change. To anticipate and predict the spread and transmission of mosquito-borne viruses, a better understanding of the transmission cycle in mosquito populations is needed. We present a pathogen-agnostic combined sequencing protocol for identifying vectors, viral pathogens and their hosts or reservoirs using portable Oxford Nanopore sequencing. Using mosquitoes collected in São Paulo, Brazil, we extracted RNA for virus identification and DNA for blood meal and mosquito identification. Mosquitoes and blood meals were identified by comparing cytochrome c oxidase I (COI) sequences against a curated Barcode of Life Data System (BOLD). Viruses were identified using the SMART-9N protocol, which allows amplified DNA to be prepared with native barcoding for nanopore sequencing. Kraken 2 was employed to detect viral pathogens and Minimap2 and BOLD identified the contents of the blood meal. Due to the high similarity of some species, mosquito identification was conducted using blast after generation of consensus COI sequences using RACON polishing. This protocol can simultaneously uncover viral diversity, mosquito species and mosquito feeding habits. It also has the potential to increase understanding of mosquito genetic diversity and transmission dynamics of zoonotic mosquito-borne viruses.}, } @article {pmid38240578, year = {2024}, author = {Chen, J and Sun, C and Dong, Y and Jin, M and Lai, S and Jia, L and Zhao, X and Wang, H and Gao, NL and Bork, P and Liu, Z and Chen, WH and Zhao, XM}, title = {Efficient Recovery of Complete Gut Viral Genomes by Combined Short- and Long-Read Sequencing.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {}, number = {}, pages = {e2305818}, doi = {10.1002/advs.202305818}, pmid = {38240578}, issn = {2198-3844}, support = {T2225015//National Natural Science Foundation of China/ ; 61932008//National Natural Science Foundation of China/ ; 32070660//National Natural Science Foundation of China/ ; 31770132//National Natural Science Foundation of China/ ; 81873969//National Natural Science Foundation of China/ ; 82161138017//NNSF-VR Sino-Swedish Joint Research Programme/ ; 2020YFA0712403//National Key Research and Development Program of China/ ; 2019YFA0905600//National Key Research and Development Program of China/ ; 2018SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; 2021YFF0703703//Shanghai Municipal Science and Technology Major Project/ ; }, abstract = {Current metagenome assembled human gut phage catalogs contained mostly fragmented genomes. Here, comprehensive gut virome detection procedure is developed involving virus-like particle (VLP) enrichment from ≈500 g feces and combined sequencing of short- and long-read. Applied to 135 samples, a Chinese Gut Virome Catalog (CHGV) is assembled consisting of 21,499 non-redundant viral operational taxonomic units (vOTUs) that are significantly longer than those obtained by short-read sequencing and contained ≈35% (7675) complete genomes, which is ≈nine times more than those in the Gut Virome Database (GVD, ≈4%, 1,443). Interestingly, the majority (≈60%, 13,356) of the CHGV vOTUs are obtained by either long-read or hybrid assemblies, with little overlap with those assembled from only the short-read data. With this dataset, vast diversity of the gut virome is elucidated, including the identification of 32% (6,962) novel vOTUs compare to public gut virome databases, dozens of phages that are more prevalent than the crAssphages and/or Gubaphages, and several viral clades that are more diverse than the two. Finally, the functional capacities are also characterized of the CHGV encoded proteins and constructed a viral-host interaction network to facilitate future research and applications.}, } @article {pmid38240472, year = {2024}, author = {Cissell, EC and McCoy, SJ}, title = {Convergent photophysiology and prokaryotic assemblage structure in epilithic cyanobacterial tufts and algal turf communities.}, journal = {Journal of phycology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jpy.13424}, pmid = {38240472}, issn = {1529-8817}, support = {074012-520-044116//National Science Foundation/ ; POR_2020_03//Florida "Protect Our Reefs" Grants Program/ ; }, abstract = {As global change spurs shifts in benthic community composition on coral reefs globally, a better understanding of the defining taxonomic and functional features that differentiate proliferating benthic taxa is needed to predict functional trajectories of reef degradation better. This is especially critical for algal groups, which feature dramatically on changing reefs. Limited attention has been given to characterizing the features that differentiate tufting epilithic cyanobacterial communities from ubiquitous turf algal assemblages. Here, we integrated an in situ assessment of photosynthetic yield with metabarcoding and shotgun metagenomic sequencing to explore photophysiology and prokaryotic assemblage structure within epilithic tufting benthic cyanobacterial communities and epilithic algal turf communities. Significant differences were not detected in the average quantum yield. However, variability in yield was significantly higher in cyanobacterial tufts. Neither prokaryotic assemblage diversity nor structure significantly differed between these functional groups. The sampled cyanobacterial tufts, predominantly built by Okeania sp., were co-dominated by members of the Proteobacteria, Firmicutes, and Bacteroidota, as were turf algal communities. Few detected ASVs were significantly differentially abundant between functional groups and consisted exclusively of taxa belonging to the phyla Proteobacteria and Firmicutes. Assessment of the distribution of recovered cyanobacterial amplicons demonstrated that alongside sample-specific cyanobacterial diversification, the dominant cyanobacterial members were conserved across tufting cyanobacterial and turf algal communities. Overall, these data suggest a convergence in taxonomic identity and mean photosynthetic potential between tufting epilithic cyanobacterial communities and algal turf communities, with numerous implications for consumer-resource dynamics on future reefs and trajectories of reef functional ecology.}, } @article {pmid38240324, year = {2024}, author = {Onoja, BA and Oguzie, JU and George, UE and Asoh, KE and Ajayi, P and Omofaye, TF and Igeleke, IO and Eromon, P and Harouna, S and Parker, E and Adeniji, AJ and Happi, CT}, title = {Whole Genome Sequencing Unravels Cryptic Circulation of Divergent Dengue Virus Lineages in the Rainforest Region of Nigeria.}, journal = {Emerging microbes & infections}, volume = {}, number = {}, pages = {2307511}, doi = {10.1080/22221751.2024.2307511}, pmid = {38240324}, issn = {2222-1751}, abstract = {AbstractDengue is often misclassified and underreported in Africa due to inaccurate differential diagnoses of nonspecific febrile illnesses such as malaria, sparsity of diagnostic testing and poor clinical and genomic surveillance. There are limited reports on the seroprevalence and genetic diversity of dengue virus (DENV) in humans and vectors in Nigeria. In this study, we investigated the epidemiology and genetic diversity of dengue in the rainforest region of Nigeria. We screened 515 febrile patients who tested negative for malaria and typhoid fever in three hospitals in Oyo and Ekiti States in southern Nigeria with a combination of anti-dengue IgG/IgM/NS1 rapid test kits and metagenomic sequencing. We found that approximately 28% of screened patients had previous DENV exposure, with the highest prevalence in persons over sixty. Approximately 8% of the patients showed evidence of recent or current infection, and 2.7% had acute infection. Following sequencing of sixty samples, we assembled twenty DENV-1 genomes (3 complete and 17 partial). We found that all assembled genomes belonged to DENV-1 genotype III. Our phylogenetic analyses showed evidence of prolonged cryptic circulation of divergent DENV lineages in Oyo state. We were unable to resolve the source of DENV in Nigeria owing to limited sequencing data from the region. However, our sequences clustered closely with sequences in Tanzania and sequences reported in Chinese with travel history to Tanzania in 2019. This may reflect the wider unsampled bidirectional transmission of DENV-1 in Africa, which strongly emphasizes the importance of genomic surveillance in monitoring ongoing DENV transmission in Africa.}, } @article {pmid38239028, year = {2023}, author = {Dominguez-Lafage, C and Laganà, M and Gesbert, F and Marin-Esteban, V and Schlecht-Louf, G and Bachelerie, F and Deback, C}, title = {[The cutaneous virome: from virology to personalized medicine].}, journal = {Virologie (Montrouge, France)}, volume = {27}, number = {6}, pages = {333-354}, doi = {10.1684/vir.2023.1028}, pmid = {38239028}, issn = {1267-8694}, abstract = {The virome of the skin, defined as all viruses detected in the skin, represents a significant part of the microbiota. A much more recent discovery than the bacterial flora, the existence of the cutaneous virome has been revealed by recent metagenomic studies. The normal human skin virome is dominated by bacteriophages, Papillomaviridae, whose genomic diversity has proved extraordinary, and Polyomaviridae. Many yet unknown viral genomes within this virome await identification. The composition of the virome of the skin has been shown to be strictly individual and relatively stable over time, resulting from adaptation to everyone's genetics, lifestyle and mechanisms of immunological tolerance finely selected over the course of evolution. Yet little studied, the virome of the skin and all its interactions with other microbiota and the host are attracting growing interest. Indeed, constitutional or acquired alterations in the homeostasis between the commensal virome and the skin, ranging from sub-clinical viral dysbiosis to severe transformation of keratinocytes or adnexal cells, have been observed. These recent observations are stimulating the search for innovative solutions aimed at measuring or even modulating its pathological expression, with a view to personalized medicine.}, } @article {pmid38238719, year = {2024}, author = {He, S and Xiong, Y and Tu, T and Feng, J and Fu, Y and Hu, X and Wang, N and Li, D}, title = {Diagnostic performance of metagenomic next-generation sequencing for the detection of pathogens in cerebrospinal fluid in pediatric patients with central nervous system infection: a systematic review and meta-analysis.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {103}, pmid = {38238719}, issn = {1471-2334}, abstract = {BACKGROUND: Detecting pathogens in pediatric central nervous system infection (CNSI) is still a major challenge in medicine. In addition to conventional diagnostic patterns, metagenomic next-generation sequencing (mNGS) shows great potential in pathogen detection. Therefore, we systematically evaluated the diagnostic performance of mNGS in cerebrospinal fluid (CSF) in pediatric patients with CNSI.

METHODS: Related literature was searched in the Web of Science, PubMed, Embase, and Cochrane Library. We screened the literature and extracted the data according to the selection criteria. The quality of included studies was assessed by the Quality Assessment of Diagnostic Accuracy Studies-2 (QUADAS-2) tool and the certainty of the evidence was measured by the Grading of Recommendations, Assessment, Development, and Evaluations (GRADE) score system. Then, the pooled sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odd's ratio (DOR), and area under the curve (AUC) of the summary receiver operating characteristic curve (sROC) were estimated in Stata Software and MetaDisc. Subgroup analyses were performed to investigate the potential factors that influence the diagnostic performance.

RESULTS: A total of 10 studies were included in the meta-analysis. The combined sensitivity was 0.68 (95% confidence interval [CI]: 0.59 to 0.76, I[2] = 66.77%, p < 0.001), and the combined specificity was 0.89 (95% CI: 0.80 to 0.95, I[2] = 83.37%, p < 0.001). The AUC of sROC was 0.85 (95% CI, 0.81 to 0.87). The quality level of evidence elevated by the GRADE score system was low.

CONCLUSIONS: Current evidence shows that mNGS presents a good diagnostic performance in pediatric CNSI. Due to the limited quality and quantity of the included studies, more high-quality studies are needed to verify the above conclusion.}, } @article {pmid38238650, year = {2024}, author = {Terlouw, D and Boot, A and Ducarmon, QR and Nooij, S and Suerink, M and van Leerdam, ME and van Egmond, D and Tops, CM and Zwittink, RD and Ruano, D and Langers, AMJ and Nielsen, M and van Wezel, T and Morreau, H}, title = {Enrichment of colibactin-associated mutational signatures in unexplained colorectal polyposis patients.}, journal = {BMC cancer}, volume = {24}, number = {1}, pages = {104}, pmid = {38238650}, issn = {1471-2407}, support = {11292//KWF Kankerbestrijding/ ; }, abstract = {BACKGROUND: Colibactin, a genotoxin produced by polyketide synthase harboring (pks[+]) bacteria, induces double-strand breaks and chromosome aberrations. Consequently, enrichment of pks[+]Escherichia coli in colorectal cancer and polyposis suggests a possible carcinogenic effect in the large intestine. Additionally, specific colibactin-associated mutational signatures; SBS88 and ID18 in the Catalogue of Somatic Mutations in Cancer database, are detected in colorectal carcinomas. Previous research showed that a recurrent APC splice variant perfectly fits SBS88.

METHODS: In this study, we explore the presence of colibactin-associated signatures and fecal pks in an unexplained polyposis cohort. Somatic targeted Next-Generation Sequencing (NGS) was performed for 379 patients. Additionally, for a subset of 29 patients, metagenomics was performed on feces and mutational signature analyses using Whole-Genome Sequencing (WGS) on Formalin-Fixed Paraffin Embedded (FFPE) colorectal tissue blocks.

RESULTS: NGS showed somatic APC variants fitting SBS88 or ID18 in at least one colorectal adenoma or carcinoma in 29% of patients. Fecal metagenomic analyses revealed enriched presence of pks genes in patients with somatic variants fitting colibactin-associated signatures compared to patients without variants fitting colibactin-associated signatures. Also, mutational signature analyses showed enrichment of SBS88 and ID18 in patients with variants fitting these signatures in NGS compared to patients without.

CONCLUSIONS: These findings further support colibactins ability to mutagenize colorectal mucosa and contribute to the development of colorectal adenomas and carcinomas explaining a relevant part of patients with unexplained polyposis.}, } @article {pmid38238372, year = {2024}, author = {Kırdök, E and Kashuba, N and Damlien, H and Manninen, MA and Nordqvist, B and Kjellström, A and Jakobsson, M and Lindberg, AM and Storå, J and Persson, P and Andersson, B and Aravena, A and Götherström, A}, title = {Metagenomic analysis of Mesolithic chewed pitch reveals poor oral health among stone age individuals.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22125}, pmid = {38238372}, issn = {2045-2322}, support = {2019-3-AP3-3729//Mersin University BAP project/ ; The Research Council of Norway project no. 231305//Pioneers of NW Europe/ ; The Research Council of Norway project no. 231305//Pioneers of NW Europe/ ; The Research Council of Norway project no. 231305//Pioneers of NW Europe/ ; The Research Council of Norway project no. 231305//Pioneers of NW Europe/ ; project no. 2019-00849//The Swedish Research Council/ ; }, abstract = {Prehistoric chewed pitch has proven to be a useful source of ancient DNA, both from humans and their microbiomes. Here we present the metagenomic analysis of three pieces of chewed pitch from Huseby Klev, Sweden, that were dated to 9,890-9,540 before present. The metagenomic profile exposes a Mesolithic oral microbiome that includes opportunistic oral pathogens. We compared the data with healthy and dysbiotic microbiome datasets and we identified increased abundance of periodontitis-associated microbes. In addition, trained machine learning models predicted dysbiosis with 70-80% probability. Moreover, we identified DNA sequences from eukaryotic species such as red fox, hazelnut, red deer and apple. Our results indicate a case of poor oral health during the Scandinavian Mesolithic, and show that pitch pieces have the potential to provide information on material use, diet and oral health.}, } @article {pmid38238332, year = {2024}, author = {Wang, X and Zain Ul Arifeen, M and Hou, S and Zheng, Q}, title = {Depth-dependent microbial metagenomes sampled in the northeastern Indian Ocean.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {88}, pmid = {38238332}, issn = {2052-4463}, support = {42276163//National Natural Science Foundation of China (National Science Foundation of China)/ ; 92251306//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42222604//National Natural Science Foundation of China (National Science Foundation of China)/ ; JCYJ20220530115401003//Shenzhen Science and Technology Innovation Commission/ ; }, abstract = {The northeastern Indian Ocean exhibits distinct hydrographic characteristics influenced by various local and remote forces. Variations in these driving factors may alter the physiochemical properties of seawater, such as dissolved oxygen levels, and affect the diversity and function of microbial communities. How the microbial communities change across water depths spanning a dissolved oxygen gradient has not been well understood. Here we employed both 16S rDNA amplicon and metagenomic sequencing approaches to study the microbial communities collected from different water depths along the E87 transect in the northeastern Indian Ocean. Samples were collected from the surface, Deep Chlorophyll Maximum (DCM), Oxygen Minimum Zone (OMZ), and bathypelagic layers. Proteobacteria were prevalent throughout the water columns, while Thermoproteota were found to be abundant in the aphotic layers. A total of 675 non-redundant metagenome-assembled genomes (MAGs) were constructed, spanning 21 bacterial and 5 archaeal phyla. The community structure and genomic information provided by this dataset offer valuable resources for the analysis of microbial biogeography and metabolism in the northeastern Indian Ocean.}, } @article {pmid38237912, year = {2024}, author = {, and , and , }, title = {[Expert consensus on clinical localization detection standards for metagenomic next generation sequencing of pathogens].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {58}, number = {}, pages = {1-12}, doi = {10.3760/cma.j.cn112150-20230720-00019}, pmid = {38237912}, issn = {0253-9624}, abstract = {Infectious diseases seriously endanger human health. Rapid and accurate detection of pathogens is the key to effective treatment and precise prevention and control of infectious diseases. Traditional pathogen testing techniques cover a limited variety of microorganisms, making it difficult to meet clinical needs. Metagenomic Next Generation Sequencing (mNGS) theoretically can simultaneously detect all known gene sequences of pathogens, greatly improving the clinical capacity of diagnosing and treating patients with severe, complicated, rare, and emerging pathogen infections. In the context of individualized health needs, the self-built testing of new technologies in laboratories can continuously improve the level of clinical diagnosis and treatment. Due to the high starting point of research and development and the complex operation process of the mNGS technology platform, this study reaches a consensus on the experimental procedure, assay validation, quality control, and report review of the mNGS-LDT in the fields of clinical testing, infection, critical care, and in vitro diagnosis to ensure the appropriate application of the technology and guarantee patient safety and proposes standardized requirements and suggestions.}, } @article {pmid38237784, year = {2024}, author = {Zhou, N and Guo, H and Zhang, Z and Wang, H}, title = {The discrepant metabolic pathways of PAHs by facultative anaerobic bacteria under aerobic and nitrate-reducing conditions.}, journal = {Chemosphere}, volume = {}, number = {}, pages = {141230}, doi = {10.1016/j.chemosphere.2024.141230}, pmid = {38237784}, issn = {1879-1298}, abstract = {Studies regarding the facultative anaerobic biodegradation of polycyclic aromatic hydrocarbons (PAHs) were still in the initial stage. In this study, a facultative anaerobe which was identified as Bacillus Firmus and named as PheN7 was firstly isolated from the mixed petroleum-polluted soil samples using phenanthrene and nitrate as the solo carbon resource and electron acceptor under anaerobic condition. The degradation rates of PheN7 towards phenanthrene were detected as 33.17 μM/d, 13.81 μM/d and 7.11 μM/d at the initial phenanthrene concentration of 250.17 μM with oxygen, nitrate and sulfate as the electron acceptor, respectively. The metabolic pathways toward phenanthrene by PheN7 were deduced combining the metagenome analysis of PheN7 and intermediate metabolites of phenanthrene under aerobic and nitrate-reducing conditions. Dioxygenation and carboxylation were inferred as the initial activation reactions of phenanthrene degradation in these two pathways. This study highlighted the significance of facultative anaerobic bacteria in natural PAHs biodegradation, revealing the discrepant metabolic fates of PAHs by one solo bacteria under aerobic and anaerobic environments.}, } @article {pmid38237397, year = {2024}, author = {Yu, Z and Wang, Q and Pinilla-Redondo, R and Madsen, JS and Clasen, KAD and Ananbeh, H and Olesen, AK and Gong, Z and Yang, N and Dechesne, A and Smets, B and Nesme, J and Sørensen, SJ}, title = {Horizontal transmission of a multidrug-resistant IncN plasmid isolated from urban wastewater.}, journal = {Ecotoxicology and environmental safety}, volume = {271}, number = {}, pages = {115971}, doi = {10.1016/j.ecoenv.2024.115971}, pmid = {38237397}, issn = {1090-2414}, abstract = {Wastewater treatment plants (WWTPs) are considered reservoirs of antibiotic resistance genes (ARGs). Given that plasmid-mediated horizontal gene transfer plays a critical role in disseminating ARGs in the environment, it is important to inspect the transfer potential of transmissible plasmids to have a better understanding of whether these mobile ARGs can be hosted by opportunistic pathogens and should be included in One Health's considerations. In this study, we used a fluorescent-reporter-gene based exogenous isolation approach to capture extended-spectrum beta-lactamases encoding mobile determinants from sewer microbiome samples that enter an urban water system (UWS) in Denmark. After screening and sequencing, we isolated a ∼73 Kbp IncN plasmid (pDK_DARWIN) that harboured and expressed multiple ARGs. Using a dual fluorescent reporter gene system, we showed that this plasmid can transfer into resident urban water communities. We demonstrated the transfer of pDK_DARWIN to microbiome members of both the sewer (in the upstream UWS compartment) and wastewater treatment (in the downstream UWS compartment) microbiomes. Sequence similarity search across curated plasmid repositories revealed that pDK_DARWIN derives from an IncN backbone harboured by environmental and nosocomial Enterobacterial isolates. Furthermore, we searched for pDK_DARWIN sequence matches in UWS metagenomes from three countries, revealing that this plasmid can be detected in all of them, with a higher relative abundance in hospital sewers compared to residential sewers. Overall, this study demonstrates that this IncN plasmid is prevalent across Europe and an efficient vector capable of disseminating multiple ARGs in the urban water systems.}, } @article {pmid38237031, year = {2024}, author = {Khan, R and Di Gesù, CM and Lee, J and McCullough, LD}, title = {The contribution of age-related changes in the gut-brain axis to neurological disorders.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2302801}, doi = {10.1080/19490976.2024.2302801}, pmid = {38237031}, issn = {1949-0984}, abstract = {Trillions of microbes live symbiotically in the host, specifically in mucosal tissues such as the gut. Recent advances in metagenomics and metabolomics have revealed that the gut microbiota plays a critical role in the regulation of host immunity and metabolism, communicating through bidirectional interactions in the microbiota-gut-brain axis (MGBA). The gut microbiota regulates both gut and systemic immunity and contributes to the neurodevelopment and behaviors of the host. With aging, the composition of the microbiota changes, and emerging studies have linked these shifts in microbial populations to age-related neurological diseases (NDs). Preclinical studies have demonstrated that gut microbiota-targeted therapies can improve behavioral outcomes in the host by modulating microbial, metabolomic, and immunological profiles. In this review, we discuss the pathways of brain-to-gut or gut-to-brain signaling and summarize the role of gut microbiota and microbial metabolites across the lifespan and in disease. We highlight recent studies investigating 1) microbial changes with aging; 2) how aging of the maternal microbiome can affect offspring health; and 3) the contribution of the microbiome to both chronic age-related diseases (e.g., Parkinson's disease, Alzheimer's disease and cerebral amyloidosis), and acute brain injury, including ischemic stroke and traumatic brain injury.}, } @article {pmid38236043, year = {2024}, author = {Narrowe, AB and Liu, L and Lemons, JMS and Firrman, JA and Mahalak, KK and Deyaert, S and Baudot, A and Van den Abbeele, P}, title = {Metagenomes and metagenome-assembled genomes from ex vivo fecal incubations of six unique donors.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0086223}, doi = {10.1128/mra.00862-23}, pmid = {38236043}, issn = {2576-098X}, abstract = {We present a donor-specific collection of 78 metagenomes (13/donor) and 143 metagenome-assembled genomes (MAGs), representing the gut microbiomes of six healthy adult human donors. In addition to adding to the catalog of publicly available human gut MAGs, this resource permits a genome-resolved look into microbial co-occurrence across six individuals.}, } @article {pmid38235435, year = {2023}, author = {Muralidharan, HS and Fox, NY and Pop, M}, title = {The impact of transitive annotation on the training of taxonomic classifiers.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1240957}, pmid = {38235435}, issn = {1664-302X}, abstract = {INTRODUCTION: A common task in the analysis of microbial communities involves assigning taxonomic labels to the sequences derived from organisms found in the communities. Frequently, such labels are assigned using machine learning algorithms that are trained to recognize individual taxonomic groups based on training data sets that comprise sequences with known taxonomic labels. Ideally, the training data should rely on labels that are experimentally verified-formal taxonomic labels require knowledge of physical and biochemical properties of organisms that cannot be directly inferred from sequence alone. However, the labels associated with sequences in biological databases are most commonly computational predictions which themselves may rely on computationally-generated data-a process commonly referred to as "transitive annotation."

METHODS: In this manuscript we explore the implications of training a machine learning classifier (the Ribosomal Database Project's Bayesian classifier in our case) on data that itself has been computationally generated. We generate new training examples based on 16S rRNA data from a metagenomic experiment, and evaluate the extent to which the taxonomic labels predicted by the classifier change after re-training.

RESULTS: We demonstrate that even a few computationally-generated training data points can significantly skew the output of the classifier to the point where entire regions of the taxonomic space can be disturbed.

DISCUSSION AND CONCLUSIONS: We conclude with a discussion of key factors that affect the resilience of classifiers to transitively-annotated training data, and propose best practices to avoid the artifacts described in our paper.}, } @article {pmid38235358, year = {2024}, author = {Huang, HY and Li, FR and Zhang, YF and Lau, HC and Hsueh, CY and Zhou, L and Zhang, M}, title = {Metagenomic shotgun sequencing reveals the enrichment of Salmonella and Mycobacterium in larynx due to prolonged ethanol exposure.}, journal = {Computational and structural biotechnology journal}, volume = {23}, number = {}, pages = {396-405}, pmid = {38235358}, issn = {2001-0370}, abstract = {UNLABELLED: The exposure of ethanol increases the risk of head and neck inflammation and tumor progression. However, limited studies have investigated the composition and functionality of laryngeal microbiota under ethanol exposure. We established an ethanol-exposed mouse model to investigate the changes in composition and function of laryngeal microbiota using Metagenomic shotgun sequencing. In the middle and late stages of the experiment, the laryngeal microbiota of mice exposed to ethanol exhibited obvious distinguished from that of the control group on principal-coordinate analysis (PCoA) plots. Among the highly abundant species, Salmonella enterica and Mycobacterium marinum were likely to be most impacted. Our findings indicated that the exposure to ethanol significantly increased their abundance in larynxes in mice of the same age, which has been confirmed through FISH experiments. Among the species-related functions and genes, metabolism is most severely affected by ethanol. The difference was most obvious in the second month of the experiment, which may be alleviated later because the animal established tolerance. Notable enrichments concerning energy, amino acid, and carbohydrate metabolic pathways occurred during the second month under ethanol exposure. Finally, based on the correlation between species and functional variations, a network was established to investigate relationships among microbiota, functional pathways, and related genes affected by ethanol. Our data first demonstrated the continuous changes of abundance, function and their interrelationship of laryngeal microbiota under ethanol exposure by Metagenomic shotgun sequencing.

IMPORTANCE: Ethanol may participate in the inflammation and tumor progression by affecting the composition of the laryngeal microbiota. Here, we applied the metagenomic shotgun sequencing instead of 16 S rRNA sequencing method to identify the laryngeal microbiota under ethanol exposure. Salmonella enterica and Mycobacterium marinum are two dominant species that may play a role in the reconstruction of the laryngeal microenvironment, as their local abundance increases following exposure to ethanol. The metabolic function is most evidently impacted, and several potential metabolic pathways could be associated with alterations in microbiota composition. These findings could help us better understand the impact of prolonged ethanol exposure on the microbial composition and functionality in the larynx.}, } @article {pmid38234354, year = {2024}, author = {Huang, C and Liu, M and Gu, B and Yuan, C and Wang, Y and Cai, T and Gao, J and Yin, J and Yu, S and Zhou, M}, title = {Chlamydia psittaci causing severe pneumonia with an initial complaint of massive watery sputum: a case report.}, journal = {AME case reports}, volume = {8}, number = {}, pages = {27}, pmid = {38234354}, issn = {2523-1995}, abstract = {BACKGROUND: With the widespread application of metagenomic next-generation sequencing (mNGS) in pathogen detection, the reports of severe Chlamydia psittaci (C. psittaci) pneumonia are increasing. It is essential to determine the best management of severe C. psittaci pneumonia.

CASE DESCRIPTION: This report describes a 51-year-old male patient who presented with symptoms of expectoration, relative bradycardia, and dyspnea. Lung computed tomography (CT) on day 1 (D1) showed consolidation of the left lower lobe. He was intubated and transferred to the intensive care unit (ICU). The symptoms of high fever and progressive dyspnea [the lowest level of arterial partial pressure of oxygen/fractional inspired oxygen (PaO2/FiO2): 52 mmHg] persisted on D3. Meanwhile, he produced a large volume of golden-yellow, watery sputum, due to which endotracheal suction was repeatedly performed to maintain patency of the airway. The repeat radiography showed extensive deterioration of diffuse exudation in bilateral lobes. An early treatment with methylprednisolone was initiated on D3, after which the watery sputum decreased and turned viscous. The mNGS of the bronchoalveolar lavage fluid (BALF) identified C. psittaci on D7, and combined targeted antimicrobial therapy (azithromycin and doxycycline) was subsequently initiated. After 1 week of treatment, the patient was extubated on D14. He was transferred to the respiratory department on D17 and discharged on D25 with oral medications (azithromycin and doxycycline for 2 weeks). The repeat chest CT on D68 showed that the bilateral exudation and left lower lobe consolidation had almost disappeared, without pleural effusion.

CONCLUSIONS: In severe C. psittaci pneumonia, although the presentations differ, the rapid pathogen identification through BALF mNGS may facilitate the early use of effective antibiotics. Timely and comprehensive treatment is important for improving outcomes in severe C. psittaci pneumonia.}, } @article {pmid38233085, year = {2024}, author = {Nie, MT and Wang, PQ and Shi, PM and Hong, XL and Zhang, X and Xiang, B and Zhang, M and Xie, WF}, title = {Rifaximin treatment shapes a unique metagenome-metabolism network in patients with decompensated cirrhosis.}, journal = {Journal of gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jgh.16484}, pmid = {38233085}, issn = {1440-1746}, support = {82030021//National Natural Science Foundation of China/ ; SHDC12016103//New Cutting-edge Technology Joint Research Project of Shanghai Shenkang Center/ ; 202140335//The Scientific Research Project of Shanghai Municipal Health Commission/ ; }, abstract = {BACKGROUND: Patients with decompensated cirrhosis face poor prognosis and increased mortality risk. Rifaximin, a non-absorbable antibiotic, has been shown to have beneficial effects in preventing complications and improving survival in these patients. However, the underlying mechanisms of rifaximin's effects remain unclear.

METHODS: We obtained fecal samples from decompensated cirrhotic patients undergoing rifaximin treatment and controls, both at baseline and after 6 months of treatment. Shotgun metagenome sequencing profiled the gut microbiome, and untargeted metabolomics analyzed fecal metabolites. Linear discriminant and partial least squares discrimination analyses were used to identify differing species and metabolites between rifaximin-treated patients and controls.

RESULTS: Forty-two patients were enrolled and divided into two groups (26 patients in the rifaximin group and 16 patients in the control group). The gut microbiome's beta diversity changed in the rifaximin group but remained unaffected in the control group. We observed 44 species with reduced abundance in the rifaximin group, including Streptococcus_salivarius, Streptococcus_vestibularis, Haemophilus_parainfluenzae, etc. compared to only four in the control group. Additionally, six species were enriched in the rifaximin group, including Eubacterium_sp._CAG:248, Prevotella_sp._CAG:604, etc., and 14 in the control group. Furthermore, rifaximin modulated different microbial functions compared to the control. Seventeen microbiome-related metabolites were altered due to rifaximin, while six were altered in the control group.

CONCLUSION: Our study revealed distinct microbiome-metabolite networks regulated by rifaximin intervention in patients with decompensated cirrhosis. These findings suggest that targeting these specific metabolites or related bacteria might be a potential therapeutic strategy for decompensated cirrhosis.}, } @article {pmid38232682, year = {2023}, author = {Sandby, K and Magkos, F and Chabanova, E and Petersen, ET and Krarup, T and Bertram, HC and Kristiansen, K and Geiker, NRW}, title = {The effect of dairy products on liver fat and metabolic risk markers in males with abdominal obesity - a four-arm randomized controlled trial.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {43}, number = {2}, pages = {534-542}, doi = {10.1016/j.clnu.2023.12.018}, pmid = {38232682}, issn = {1532-1983}, abstract = {BACKGROUND & AIMS: In recent years, epidemiological studies have reported links between the consumption of fermented dairy products, such as yogurt, and health; however, evidence from human intervention trials is scarce and inconsistent. We aimed to investigate the effect of consumption of four different types of dairy products (two fermented and two non-fermented) on liver fat (primary outcome) and metabolic risk markers in males with abdominal obesity.

METHODS: In this parallel randomized controlled trial with four arms, 100 males aged 30-70 years, with body mass index 28.0-45.0 kg/m[2], and waist circumference ≥102 cm underwent a 16-weeks intervention where they were instructed to consume 400 g/day of either milk, yogurt, heat-treated yogurt, or acidified milk as part of their habitual diet. Liver fat was measured by magnetic resonance imaging.

RESULTS: In the complete case analyses (n = 80), no effects of the intervention or differences between groups were detected in anthropometry or body composition including liver fat. Moreover, no effects were detected in inflammatory markers. Main effects of time were detected in blood pressure (decrease; P < 0.001), insulin (decrease; P < 0.001), C-peptide (decrease; P = 0.040), homeostatic model assessment for insulin resistance (decrease; P < 0.001), total cholesterol (decrease; P = 0.016), low-density lipoprotein (decrease; P = 0.033), high-density lipoprotein (decrease; P = 0.006), and alanine transaminase (decrease; P = 0.019). Interactions between group and time failed to reach significance.

CONCLUSIONS: In conclusion, findings from our study do not confirm that fermented yogurt products are superior in reducing liver fat or improving metabolic risk markers compared to non-fermented milk products. In fact, all intervention products (both fermented yogurt products and non-fermented milk products) did not affect liver fat and caused largely similar modest favorable changes in some metabolic risk markers. The study was registered at www.

CLINICALTRIALS: gov (# NCT04755530).}, } @article {pmid38233815, year = {2024}, author = {Song, L and Feng, Z and Zhou, Q and Wu, X and Zhang, L and Sun, Y and Li, R and Chen, H and Yang, F and Yu, Y}, title = {Metagenomic analysis of healthy and diseased peri-implant microbiome under different periodontal conditions: a cross-sectional study.}, journal = {BMC oral health}, volume = {24}, number = {1}, pages = {105}, pmid = {38233815}, issn = {1472-6831}, support = {2020MZYS08//high-level professional physician training program of Minhang District/ ; 201940382//Shanghai Municipal Planning Commission of Science and Research Fund/ ; 82170990//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Peri-implantitis is a polybacterial infection that can lead to the failure of dental implant rehabilitation. This study aimed to profile the microbiome of the peri-implant plaque and estimate the effect of periodontitis on it among 40 Chinese participants with dental implant prostheses and presenting with varying peri-implant and periodontal health states.

METHODS: Submucosal plaque samples were collected from four distinct clinical categories based on both their implant and periodontal health status at sampling point. Clinical examinations of dental implant and remaining teeth were carried out. Metagenomic analysis was then performed.

RESULTS: The microbiome of the peri-implantitis sites differed from that of healthy implant sites, both taxonomically and functionally. Moreover, the predominant species in peri-implantitis sites were slightly affected by the presence of periodontitis. T. forsythia, P. gingivalis, T. denticola, and P. endodontalis were consistently associated with peri-implantitis and inflammatory clinical parameters regardless of the presence of periodontitis. Prevotella spp. and P. endodontalis showed significant differences in the peri-implantitis cohorts under different periodontal conditions. The most distinguishing function between diseased and healthy implants is related to flagellar assembly, which plays an important role in epithelial cell invasion.

CONCLUSIONS: The composition of the peri-implant microbiome varied in the diseased and healthy states of implants and is affected by individual periodontal conditions. Based on their correlations with clinical parameters, certain species are associated with disease and healthy implants. Flagellar assembly may play a vital role in the process of peri-implantitis.}, } @article {pmid38233647, year = {2024}, author = {Liu, C and Du, MX and Xie, LS and Wang, WZ and Chen, BS and Yun, CY and Sun, XW and Luo, X and Jiang, Y and Wang, K and Jiang, MZ and Qiao, SS and Sun, M and Cui, BJ and Huang, HJ and Qu, SP and Li, CK and Wu, D and Wang, LS and Jiang, C and Liu, HW and Liu, SJ}, title = {Gut commensal Christensenella minuta modulates host metabolism via acylated secondary bile acids.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {38233647}, issn = {2058-5276}, abstract = {A strong correlation between gut microbes and host health has been observed in numerous gut metagenomic cohort studies. However, the underlying mechanisms governing host-microbe interactions in the gut remain largely unknown. Here we report that the gut commensal Christensenella minuta modulates host metabolism by generating a previously undescribed class of secondary bile acids with 3-O-acylation substitution that inhibit the intestinal farnesoid X receptor. Administration of C. minuta alleviated features of metabolic disease in high fat diet-induced obese mice associated with a significant increase in these acylated bile acids, which we refer to as 3-O-acyl-cholic acids. Specific knockout of intestinal farnesoid X receptor in mice counteracted the beneficial effects observed in their wild-type counterparts. Finally, we showed that 3-O-acyl-CAs were prevalent in healthy humans but significantly depleted in patients with type 2 diabetes. Our findings indicate a role for C. minuta and acylated bile acids in metabolic diseases.}, } @article {pmid38233502, year = {2024}, author = {Chopra, A and Franco-Duarte, R and Rajagopal, A and Choowong, P and Soares, P and Rito, T and Eberhard, J and Jayasinghe, TN}, title = {Exploring the presence of oral bacteria in non-oral sites of patients with cardiovascular diseases using whole metagenomic data.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {1476}, pmid = {38233502}, issn = {2045-2322}, support = {2022.00340.CEECIND//Fundação para a Ciência e a Tecnologia/ ; "Contrato-Programa" UIDB/04050/2020//Fundação para a Ciência e a Tecnologia/ ; }, abstract = {Cardiovascular diseases (CVDs) encompass various conditions affecting the heart and its blood vessels and are often linked with oral microbes. Our data analysis aimed to identify oral bacteria from other non-oral sites (i.e., gut, arterial plaque and cultured blood) that could be linked with CVDs. Taxonomic profiling identified bacteria to the species level and compared with the Human Oral Microbiome Database (HOMD). The oral bacteria in the gut, cultured blood and arterial plaque samples were catalogued, with their average frequency calculated for each sample. Additionally, data were filtered by comparison with the Human Microbiome Project (HMP) database. We identified 17,243 microbial species, of which 410 were present in the HOMD database and further denominated as "oral", and were found in at least one gut sample, but only 221 and 169 species were identified in the cultured blood and plaque samples, respectively. Of the 410 species, 153 were present solely in oral-associated environments after comparison with the HMP database, irrespective of their presence in other body sites. Our results suggest a potential connection between the presence of specific species of oral bacterial and occurrence of CVDs. Detecting these oral bacterial species in non-oral sites of patients with CVDs could help uncover the link between oral health and general health, including cardiovascular conditions via bacterial translocation.}, } @article {pmid38233447, year = {2024}, author = {Valencia, EM and Maki, KA and Dootz, JN and Barb, JJ}, title = {Mock community taxonomic classification performance of publicly available shotgun metagenomics pipelines.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {81}, pmid = {38233447}, issn = {2052-4463}, abstract = {Shotgun metagenomic sequencing comprehensively samples the DNA of a microbial sample. Choosing the best bioinformatics processing package can be daunting due to the wide variety of tools available. Here, we assessed publicly available shotgun metagenomics processing packages/pipelines including bioBakery, Just a Microbiology System (JAMS), Whole metaGenome Sequence Assembly V2 (WGSA2), and Woltka using 19 publicly available mock community samples and a set of five constructed pathogenic gut microbiome samples. Also included is a workflow for labelling bacterial scientific names with NCBI taxonomy identifiers for better resolution in assessing results. The Aitchison distance, a sensitivity metric, and total False Positive Relative Abundance were used for accuracy assessments for all pipelines and mock samples. Overall, bioBakery4 performed the best with most of the accuracy metrics, while JAMS and WGSA2, had the highest sensitivities. Furthermore, bioBakery is commonly used and only requires a basic knowledge of command line usage. This work provides an unbiased assessment of shotgun metagenomics packages and presents results assessing the performance of the packages using mock community sequence data.}, } @article {pmid38233391, year = {2024}, author = {Wang, Z and You, R and Han, H and Liu, W and Sun, F and Zhu, S}, title = {Effective binning of metagenomic contigs using contrastive multi-view representation learning.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {585}, pmid = {38233391}, issn = {2041-1723}, support = {62272105//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2023M730650//China Postdoctoral Science Foundation/ ; }, abstract = {Contig binning plays a crucial role in metagenomic data analysis by grouping contigs from the same or closely related genomes. However, existing binning methods face challenges in practical applications due to the diversity of data types and the difficulties in efficiently integrating heterogeneous information. Here, we introduce COMEBin, a binning method based on contrastive multi-view representation learning. COMEBin utilizes data augmentation to generate multiple fragments (views) of each contig and obtains high-quality embeddings of heterogeneous features (sequence coverage and k-mer distribution) through contrastive learning. Experimental results on multiple simulated and real datasets demonstrate that COMEBin outperforms state-of-the-art binning methods, particularly in recovering near-complete genomes from real environmental samples. COMEBin outperforms other binning methods remarkably when integrated into metagenomic analysis pipelines, including the recovery of potentially pathogenic antibiotic-resistant bacteria (PARB) and moderate or higher quality bins containing potential biosynthetic gene clusters (BGCs).}, } @article {pmid38231673, year = {2024}, author = {Sung, C and Park, CG and Maienschein-Cline, M and Chlipala, G and Green, S and Doorenbos, A and Fink, A and Bronas, U and Lockwood, M}, title = {Associations Between Gut Microbial Features and Sickness Symptoms in Kidney Transplant Recipients.}, journal = {Biological research for nursing}, volume = {}, number = {}, pages = {10998004241227560}, doi = {10.1177/10998004241227560}, pmid = {38231673}, issn = {1552-4175}, abstract = {PURPOSE: The study investigated the relationship of gut microbiome features and sickness symptoms in kidney transplant recipients.

METHODS: Employing a prospective, longitudinal design, we collected data from 19 participants who had undergone living-donor kidney transplant at three timepoints (pre-transplant and 1 week and 3 months post-transplant). Sickness symptom data and fecal specimens were collected at each timepoint. Participants were grouped either as high or low sickness symptom severity at baseline. Shotgun metagenomics sequencing characterized gut microbial structure and functional gene content. Fecal microbial features, including alpha (evenness and richness within samples) and beta (dissimilarities between samples) diversity and relative abundances, were analyzed using R statistical packages. Cross-sectional and longitudinal analyses examined relationships between gut microbial features and sickness symptoms.

RESULTS: Although our exploratory findings revealed no significant differences in alpha and beta diversity between groups, the high-severity group showed lower microbial richness and evenness than the low-severity group. The high-severity group had enriched relative abundance of bacteria from the genera Citrobacter and Enterobacter and reduced relative abundance of bacteria from the genus Akkermansia across timepoints. No functional genes differed significantly between groups or timepoints.

CONCLUSIONS: Kidney transplant recipients with high symptom burden displayed increased putative proinflammatory bacteria and decreased beneficial bacteria. This study provides an effect size that future large cohort studies can employ to confirm associations between gut microbial features and sickness symptom experiences in the kidney transplant population. The study findings also have implications for future interventional studies aiming to alleviate the sickness symptom burden in this population.}, } @article {pmid38231565, year = {2024}, author = {Decadt, H and Vermote, L and Díaz-Muñoz, C and Weckx, S and De Vuyst, L}, title = {Decarboxylase activity of the non-starter lactic acid bacterium Loigolactobacillus rennini gives crack defects in Gouda cheese through the production of γ-aminobutyric acid.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0165523}, doi = {10.1128/aem.01655-23}, pmid = {38231565}, issn = {1098-5336}, abstract = {Crack defects in Gouda cheeses are still poorly understood, although they can lead to major economic losses in cheese companies. In this study, the bacterial cause of a crack defect in Gouda cheeses was identified, and the pathways involved in the crack formation were unraveled. Moreover, possible contamination sources were identified. The brine bath might be a major source of bacteria with the potential to deteriorate cheese quality, which suggests that cheese producers should regularly investigate the quality and microbial composition of their brines. This study illustrated how a multiphasic approach can understand and mitigate problems in a cheese company.}, } @article {pmid38231265, year = {2024}, author = {Yu, SJ and Morris, A and Kayal, A and Milošević, I and Van, TTH and Bajagai, YS and Stanley, D}, title = {Pioneering gut health improvements in piglets with phytogenic feed additives.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {142}, pmid = {38231265}, issn = {1432-0614}, abstract = {This research investigates the effects of phytogenic feed additives (PFAs) on the growth performance, gut microbial community, and microbial metabolic functions in weaned piglets via a combined 16S rRNA gene amplicon and shotgun metagenomics approach. A controlled trial was conducted using 200 pigs to highlight the significant influence of PFAs on gut microbiota dynamics. Notably, the treatment group revealed an increased gut microbiota diversity, as measured with the Shannon and Simpson indices. The increase in diversity is accompanied by an increase in beneficial bacterial taxa, such as Roseburia, Faecalibacterium, and Prevotella, and a decline in potential pathogens like Clostridium sensu stricto 1 and Campylobacter. Shotgun sequencing at the species level confirmed these findings. This modification in microbial profile was coupled with an altered profile of microbial metabolic pathways, suggesting a reconfiguration of microbial function under PFA influence. Significant shifts in overall microbial community structure by week 8 demonstrate PFA treatment's temporal impact. Histomorphological examination unveiled improved gut structure in PFA-treated piglets. The results of this study indicate that the use of PFAs as dietary supplements can be an effective strategy, augmenting gut microbiota diversity, reshaping microbial function, enhancing gut structure, and optimising intestinal health of weaned piglets providing valuable implications for swine production. KEY POINTS: • PFAs significantly diversify the gut microbiota in weaned piglets, aiding balance. • Changes in gut structure due to PFAs indicate improved resistance to weaning stress. • PFAs show potential to ease weaning stress, offering a substitute for antibiotics in piglet diets.}, } @article {pmid38231130, year = {2024}, author = {Wang, Z and Kasper, A and Amador, AM and Hernandez, Y and Ternei, M and Takahashi, M and Bhattacharjee, A and Kan, J and Brady, S}, title = {Tapcin, an in vivo active dual topoisomerase I/II inhibitor discovered by syn-BNP coupled metagenomics.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {}, number = {}, pages = {e202317187}, doi = {10.1002/anie.202317187}, pmid = {38231130}, issn = {1521-3773}, abstract = {DNA topoisomerases are attractive targets for anticancer agents. Dual topoisomerase I/II inhibitors are particularly appealing due to their reduced rates of resistance. A number of therapeutically relevant topoisomerase inhibitors are bacterial natural products. Mining the untapped chemical diversity encoded by soil microbiomes presents an opportunity to identify additional natural topoisomerase inhibitors. Here we couple metagenome mining, bioinformatic structure prediction algorithms, and chemical synthesis to produce the dual topoisomerase inhibitor tapcin. Tapcin is a mixed p-aminobenzoic acid (PABA)-thiazole with a rare tri-thiazole substructure and picomolar antiproliferative activity. Tapcin reduced colorectal adenocarcinoma HT-29 cell proliferation and tumor volume in mouse hollow fiber and xenograft models, respectively. In both studies it showed similar activity to the clinically used topoisomerase I inhibitor irinotecan. The study suggests that the interrogation of soil microbiomes using synthetic bioinformatic natural product methods has the potential to be a rewarding strategy for identifying potent, biomedically relevant, antiproliferative agents.}, } @article {pmid38230938, year = {2024}, author = {Marinos, G and Hamerich, IK and Debray, R and Obeng, N and Petersen, C and Taubenheim, J and Zimmermann, J and Blackburn, D and Samuel, BS and Dierking, K and Franke, A and Laudes, M and Waschina, S and Schulenburg, H and Kaleta, C}, title = {Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0114423}, doi = {10.1128/spectrum.01144-23}, pmid = {38230938}, issn = {2165-0497}, abstract = {While various mechanisms through which the microbiome influences disease processes in the host have been identified, there are still only few approaches that allow for targeted manipulation of microbiome composition as a first step toward microbiome-based therapies. Here, we propose the concept of precision prebiotics that allow to boost the abundance of already resident health-beneficial microbial species in a microbiome. We present a constraint-based modeling pipeline to predict precision prebiotics for a minimal microbial community in the worm Caenorhabditis elegans comprising the host-beneficial Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71 with the aim to boost the growth of MYb11. Experimentally testing four of the predicted precision prebiotics, we confirm that they are specifically able to increase the abundance of MYb11 in vitro and in vivo. These results demonstrate that constraint-based modeling could be an important tool for the development of targeted microbiome-based therapies against human diseases.}, } @article {pmid38230927, year = {2024}, author = {Wang, Q and Wang, B-Y and Pratap, S and Xie, H}, title = {Oral microbiome associated with differential ratios of Porphyromonas gingivalis and Streptococcus cristatus.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0348223}, doi = {10.1128/spectrum.03482-23}, pmid = {38230927}, issn = {2165-0497}, abstract = {Periodontitis, one of the most common chronic diseases, is linked to several systemic diseases, such as cardiovascular disease and diabetes. Although Porphyromonas gingivalis is a keystone pathogen that causes periodontitis, its levels, interactions with accessory bacteria and pathobionts in the oral microbiome, and its association with the pathogenic potential of the microbial communities are still not well understood. In this study, we revealed the role of Streptococcus cristatus and the ratios of S. cristatus and P. gingivalis in modulating the oral microbiome to facilitate a deeper understanding of periodontitis and its progression. The study has important clinical implications as it laid a foundation for developing novel non-antibiotic therapies against P. gingivalis and improving the efficiency of periodontal treatments.}, } @article {pmid38230911, year = {2024}, author = {Eiamsam-Ang, T and Tadee, P and Buddhasiri, S and Chuammitri, P and Kittiwan, N and Pascoe, B and Patchanee, P}, title = {Commercial farmed swine harbour a variety of pathogenic bacteria and antimicrobial resistance genes.}, journal = {Journal of medical microbiology}, volume = {73}, number = {1}, pages = {}, doi = {10.1099/jmm.0.001787}, pmid = {38230911}, issn = {1473-5644}, abstract = {Introduction. The northern region of Thailand serves as a crucial area for swine production, contributing to the Thai community food supply. Previous studies have highlighted the presence of foodborne bacterial pathogens originating from swine farms in this region, posing a threat to both human and animal health.Gap statement. Multiple swine bacterial pathogens have been studied at a species level, but the distribution and co-occurrence of bacterial pathogens in agricultural swine has not been well established.Aim. Our study employed the intestinal scraping technique to directly examine the bacterial micro-organisms interacting with the swine host.Methodology. We used shotgun metagenomic sequencing to analyse the bacterial pathogens inhabiting the caecal microbiome of swine from five commercial farms in northern Thailand.Results. A variety of pathogenic and opportunistic bacteria were identified, including Escherichia coli, Clostridium botulinum, Staphylococcus aureus and the Corynebacterium genus. From a One Health perspective, these species are important foodborne and opportunistic pathogens in both humans and agricultural animals, making swine a critical pathogen reservoir that can cause illness in humans, especially farm workers. Additionally, the swine caecal microbiome contains commensal bacteria such as Bifidobacterium, Lactobacillus and Faecalibacterium, which are associated with normal physiology and feed utilization in healthy swine. Antimicrobial resistance genes were also detected in all samples, specifically conferring resistance to tetracycline and aminoglycosides, which have historically been used extensively in swine farming.Conclusion. The findings further support the need for improved sanitation standards in swine farms, and additional monitoring of agricultural animals and farm workers to reduce contamination and improved produce safety for human consumption.}, } @article {pmid38230604, year = {2024}, author = {Saadatzadeh, T and Angarone, M and Stosor, V}, title = {Pneumocystis jirovecii in solid organ transplant recipients: updates in epidemiology, diagnosis, treatment, and prevention.}, journal = {Current opinion in infectious diseases}, volume = {}, number = {}, pages = {}, pmid = {38230604}, issn = {1473-6527}, abstract = {PURPOSE OF REVIEW: This review highlights the epidemiology of Pneumocystis jirovecii pneumonia in solid organ transplant recipients, advancements in the diagnostic landscape, and updates in treatment and prevention.

RECENT FINDINGS: The increasing use of immune-depleting agents in the context of solid organ transplantation has given rise to P. jirovecii pneumonia in this population. The use of prophylaxis has dramatically reduced risk of infection; however, late-onset infections occur after cessation of prophylaxis and in the setting of lymphopenia, advancing patient age, acute allograft rejection, and cytomegalovirus infection. Diagnosis requires respiratory specimens, with PCR detection of Pneumocystis replacing traditional staining methods. Quantitative PCR may be a useful adjunct to differentiate between infection and colonization. Metagenomic next-generation sequencing is gaining attention as a noninvasive diagnostic tool. Trimethoprim-sulfamethoxazole remains the drug of choice for treatment and prevention of Pneumocystis pneumonia. Novel antifungal agents are under investigation.

SUMMARY: P. jirovecii is a fungal opportunistic pathogen that remains a cause of significant morbidity and mortality in solid organ transplant recipients. Early detection and timely treatment remain the pillars of management.}, } @article {pmid38230544, year = {2024}, author = {Sudagidan, M and Yegin, Z and Mamatova, Z and Yurt, MNZ and Tasbasi, BB and Acar, EE and Ucak, S and Süleymanoğlu, AA and Aydin, A and Ozalp, VC}, title = {A metagenomic survey of bacterial communities from kurut: The fermented cow milk in Kyrgyzstan.}, journal = {Chemistry & biodiversity}, volume = {}, number = {}, pages = {e202301374}, doi = {10.1002/cbdv.202301374}, pmid = {38230544}, issn = {1612-1880}, abstract = {Kurut is a traditional dry dairy product mostly consumed in Central Asia. In this study, the distribution of the dominant bacteria present in kurut samples (n=84) originated from seven (Chuy, Issyk-Kul, Talas, Naryn, Jalal-Abad, Osh, and Batken) regions in Kyrgyzstan were analyzed with Illumina iSeq100 platform. The dominant phylum detected was Firmicutes followed by Proteobacteria, Actinobacteria, Cyanobacteria/Chloroplast, and Tenericutes. The most abundant family detected was Lactobacillaceae followed by Streptococcaceae, Enterococcaceae, Chloroplast, and Leuconostocaceae. At the genus level, Lactobacillus was the predominant one in samples and Streptococcus, Enterococcus, Lactococcus, and Streptophyta followed this. Further comprehensive characterization analyses in kurut samples may have potential applications both in industrial starter culture developments and also future therapeutic approaches based on potential strains with probiotic properties.}, } @article {pmid38230053, year = {2024}, author = {International, BR}, title = {Retracted: Gut Microbiota Profiles in Dairy Cattle from Highland and Coastal Regions Using Shotgun Metagenomic Approach.}, journal = {BioMed research international}, volume = {2024}, number = {}, pages = {9797325}, pmid = {38230053}, issn = {2314-6141}, abstract = {[This retracts the article DOI: 10.1155/2022/3659052.].}, } @article {pmid38229852, year = {2024}, author = {Jang, YJ and Moon, JS and Kim, JE and Kim, D and Choi, HS and Oh, I}, title = {Blending Three Probiotics Alleviates Loperamide-Induced Constipation in Sprague-Dawley (SD)-Rats.}, journal = {Food science of animal resources}, volume = {44}, number = {1}, pages = {119-131}, pmid = {38229852}, issn = {2636-0780}, abstract = {BIOVITA 3 bacterial species (BIOVITA 3), a probiotic blend powder containing Clostridium butyricum IDCC 1301, Weizmannia coagulans IDCC 1201 and Bacillus subtilis IDCC 1101, has been used as a food ingredient for gut health. However, its efficacy in improving constipation has not been reported. Therefore, we aimed to investigate the functional effects of oral administration of BIOVITA 3 as well as its component strains alone (at 1.0×10[9] CFU/day) in Sprague-Dawley (SD) rats with loperamide-induced constipation. The study included fecal analysis, gastrointestinal transit ratio, histopathological analysis, short chain fatty acids (SCFAs), and metagenome analysis. As results, the BIOVITA 3 group showed significant improvements in fecal number, water content, gastrointestinal transit ratio, and thickening of the mucosal layer. In the SCFAs analysis, all probiotic-treated groups showed an increase in total SCFAs compared to the loperamide-constipated group. Changes in microbial abundance and the diversity index of three groups (normal, constipated, and BIOVITA 3) were also defined. Of these, the BIOVITA 3 showed a significant improvement in loperamide-constipated SD-rats. This study suggests the possibility that BIOVITA 3 can be applied as an ingredient in functional foods to relieve constipation.}, } @article {pmid38229335, year = {2024}, author = {Venkatachalam, S and Jabir, T and Vipindas, PV and Krishnan, KP}, title = {Ecological significance of Candidatus ARS69 and Gemmatimonadota in the Arctic glacier foreland ecosystems.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {128}, pmid = {38229335}, issn = {1432-0614}, abstract = {The Gemmatimonadota phylum has been widely detected in diverse natural environments, yet their specific ecological roles in many habitats remain poorly investigated. Similarly, the Candidatus ARS69 phylum has been identified only in a few habitats, and literature on their metabolic functions is relatively scarce. In the present study, we investigated the ecological significance of phyla Ca. ARS69 and Gemmatimonadota in the Arctic glacier foreland (GF) ecosystems through genome-resolved metagenomics. We have reconstructed the first high-quality metagenome-assembled genome (MAG) belonging to Ca. ARS69 and 12 other MAGs belonging to phylum Gemmatimonadota from the three different Arctic GF samples. We further elucidated these two groups phylogenetic lineage and their metabolic function through phylogenomic and pangenomic analysis. The analysis showed that all the reconstructed MAGs potentially belonged to novel species. The MAGs belonged to Ca. ARS69 consist about 8296 gene clusters, of which only about 8% of single-copy core genes (n = 980) were shared among them. The study also revealed the potential ecological role of Ca. ARS69 is associated with carbon fixation, denitrification, sulfite oxidation, and reduction biochemical processes in the GF ecosystems. Similarly, the study demonstrates the widespread distribution of different classes of Gemmatimonadota across wide ranges of ecosystems and their metabolic functions, including in the polar region. KEY POINTS: • Glacier foreland ecosystems act as a natural laboratory to study microbial community structure. • We have reconstructed 13 metagenome-assembled genomes from the soil samples. • All the reconstructed MAGs belonged to novel species with different metabolic processes. • Ca. ARS69 and Gemmatimonadota MAGs were found to participate in carbon fixation and denitrification processes.}, } @article {pmid38229333, year = {2024}, author = {Sharma, P and Mahongnao, S and Ahamad, A and Gupta, R and Goel, A and Kumar, N and Nanda, S}, title = {16S rRNA metagenomic profiling of red amaranth grown organically with different composts and soils.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {129}, pmid = {38229333}, issn = {1432-0614}, abstract = {In recent years organic food is gaining popularity as it is believed to promote better human health and improve soil sustainability, but there are apprehensions about pathogens in organic produces. This study was designed to understand the effect of different composts and soils on the status of the microbiome present in organically grown leafy vegetables. 16S rRNA metagenomic profiling of the leaves was done, and data were analyzed. It was found that by adding composts, the OTU of the microbiome in the organic produce was higher than in the conventional produce. The beneficial genera identified across the samples included plant growth promoters (Achromobacter, Paenibacillus, Pseudomonas, Sphingobacterium) and probiotics (Lactobacillus), which were higher in the organic produce. Some pathogenic genera, viz., plant pathogenic bacteria (Cellvibrio, Georgenia) and human pathogenic bacteria (Corynebacterium, Acinetobacter, Streptococcus, Streptomyces) were also found but with relatively low counts in the organic produce. Thus, the present study highlights that organic produce has lesser pathogen contamination than the conventional produce. KEY POINTS: • 16S rRNA metagenomics profiling done for organic red amaranth cultivar • Microbial richness varied with respect to the soil and compost type used • The ratio of beneficial to pathogenic genera improves with the addition of compost.}, } @article {pmid38229330, year = {2024}, author = {Zhang, Z and Bao, C and Li, Z and He, C and Jin, W and Li, C and Chen, Y}, title = {Integrated omics analysis reveals the alteration of gut microbiota and fecal metabolites in Cervus elaphus kansuensis.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {125}, pmid = {38229330}, issn = {1432-0614}, support = {2021-JS-02//Science and Technology Innovation Project of Three RiverSource First-class Discipline, College of Eco-Environment Engineering, Qinghai University/ ; 2021-BS-093//Doctoral Scientific Research Start-up Foundation of Qinghai University/ ; }, abstract = {The gut microbiota is the largest and most complex microecosystem in animals. It is influenced by the host's dietary habits and living environment, and its composition and diversity play irreplaceable roles in animal nutrient metabolism, immunity, and adaptation to the environment. Although the gut microbiota of red deer has been studied, the composition and function of the gut microbiota in Gansu red deer (Cervus elaphus kansuensis), an endemic subspecies of red deer in China, has not been reported. In this study, the composition and diversity of the gut microbiome and fecal metabolomics of C. elaphus kansuensis were identified and compared for the first time by using 16S rDNA sequencing, metagenomic sequencing, and LC-MS/MS. There were significant differences in gut microbiota structure and diversity between wild and farmed C. elaphus kansuensis. The 16S rDNA sequencing results showed that the genus UCRD-005 was dominant in both captive red deer (CRD) and wild red deer (WRD). Metagenomic sequencing showed similar results to those of 16S rDNA sequencing for gut microbiota in CRD and WRD at the phylum and genus levels. 16S rDNA and metagenomics sequencing data suggested that Bacteroides and Bacillus might serve as marker genera for CRD and WRD, respectively. Fecal metabolomics results showed that 520 metabolites with significant differences were detected between CRD and WRD and most differential metabolites were involved in lipid metabolism. The results suggested that large differences in gut microbiota composition and fecal metabolites between CRD and WRD, indicating that different dietary habits and living environments over time have led to the development of stable gut microbiome characteristics for CRD and WRD to meet their respective survival and reproduction needs. KEY POINTS: • Environment and food affected the gut microbiota and fecal metabolites in red deer • Genera Bacteroides and Bacillus may play important roles in CRD and WRD, respectively • Flavonoids and ascorbic acid in fecal metabolites may influence health of red deer.}, } @article {pmid38229327, year = {2024}, author = {Liu, K and Wang, M and Zhang, Y and Fang, C and Zhang, R and Fang, L and Sun, J and Liu, Y and Liao, X}, title = {Distribution of antibiotic resistance genes and their pathogen hosts in duck farm environments in south-east coastal China.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {136}, pmid = {38229327}, issn = {1432-0614}, support = {31730097//National Natural Science Foundation of China/ ; 32121004//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 2019BT02N054//Local Innovative and Research Teams Project of Guangdong Pearl River Talents Program/ ; }, abstract = {Livestock farms are major reservoirs of antibiotic resistance genes (ARGs) that are discharged into the environment. However, the abundance, diversity, and transmission of ARGs in duck farms and its impact on surrounding environments remain to be further explored. Therefore, the characteristics of ARGs and their bacterial hosts from duck farms and surrounding environment were investigated by using metagenomic sequencing. Eighteen ARG types which consist of 823 subtypes were identified and the majority conferred resistance to multidrug, tetracyclines, aminoglycosides, chloramphenicols, MLS, and sulfonamides. The floR gene was the most abundant subtype, followed by sul1, tetM, sul2, and tetL. ARG abundance in fecal sample was significantly higher than soil and water sample. Our results also lead to a hypothesis that Shandong province have been the most contaminated by ARGs from duck farm compared with other four provinces. PcoA results showed that the composition of ARG subtypes in water and soil samples was similar, but there were significant differences between water and feces samples. However, the composition of ARG subtypes were similar between samples from five provinces. Bacterial hosts of ARG subtypes were taxonomically assigned to eight phyla that were dominated by the Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria. In addition, some human bacterial pathogens could be enriched in duck feces, including Enterococcus faecium, Acinetobacter baumannii, and Staphylococcus aureus, and even serve as the carrier of ARGs. The combined results indicate that a comprehensive overview of the diversity and abundance of ARGs, and strong association between ARGs and bacterial community shift proposed, and benefit effective measures to improve safety of antibiotics use in livestock and poultry farming. KEY POINTS: • ARG distribution was widespread in the duck farms and surroundings environment • ARG abundance on the duck farms was significantly higher than in soil and water • Human bacterial pathogens may serve as the vectors for ARGs.}, } @article {pmid38229296, year = {2024}, author = {Telek, A and Molnár, Z and Takács, K and Varga, B and Grolmusz, V and Tasnádi, G and Vértessy, BG}, title = {Discovery and biocatalytic characterization of opine dehydrogenases by metagenome mining.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {101}, pmid = {38229296}, issn = {1432-0614}, support = {K119493//National Research, Development and Innovation Office/ ; K135231//National Research, Development and Innovation Office/ ; VEKOP-2.3.2-16-2017-00013//National Research, Development and Innovation Office/ ; NKP-2018-1.2.1-NKP-2018-00005//National Research, Development and Innovation Office/ ; TKP2021-EGA-02//National Research, Development and Innovation Office/ ; ÚNKP-22-4-II-BME-158//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-000 15//National Research, Development and Innovation Office/ ; C1580174//Nemzeti Kutatási, Fejlesztési és Innovaciós Alap/ ; ELTE TKP 2021-NKTA-62//Nemzeti Kutatási, Fejlesztési és Innovaciós Alap/ ; 2022-1.2.2-TÉT-IPARI-UZ-2022-00003//Nemzeti Kutatási, Fejlesztési és Innovaciós Alap/ ; }, abstract = {Enzymatic processes play an increasing role in synthetic organic chemistry which requires the access to a broad and diverse set of enzymes. Metagenome mining is a valuable and efficient way to discover novel enzymes with unique properties for biotechnological applications. Here, we report the discovery and biocatalytic characterization of six novel metagenomic opine dehydrogenases from a hot spring environment (mODHs) (EC 1.5.1.X). These enzymes catalyze the asymmetric reductive amination between an amino acid and a keto acid resulting in opines which have defined biochemical roles and represent promising building blocks for pharmaceutical applications. The newly identified enzymes exhibit unique substrate specificity and higher thermostability compared to known examples. The feature that they preferably utilize negatively charged polar amino acids is so far unprecedented for opine dehydrogenases. We have identified two spatially correlated positions in their active sites that govern this substrate specificity and demonstrated a switch of substrate preference by site-directed mutagenesis. While they still suffer from a relatively narrow substrate scope, their enhanced thermostability and the orthogonality of their substrate preference make them a valuable addition to the toolbox of enzymes for reductive aminations. Importantly, enzymatic reductive aminations with highly polar amines are very rare in the literature. Thus, the preparative-scale enzymatic production, purification, and characterization of three highly functionalized chiral secondary amines lend a special significance to our work in filling this gap. KEY POINTS: • Six new opine dehydrogenases have been discovered from a hot spring metagenome • The newly identified enzymes display a unique substrate scope • Substrate specificity is governed by two correlated active-site residues.}, } @article {pmid38226964, year = {2024}, author = {Wang, Y and Xu, J and Ben Abid, F and Salah, H and Sundararaju, S and Al Ismail, K and Wang, K and Sara Matthew, L and Taj-Aldeen, S and Ibrahim, EB and Tang, P and Perez-Lopez, A and Tsui, CKM}, title = {Population genomic analyses reveal high diversity, recombination and nosocomial transmission among Candida glabrata (Nakaseomyces glabrata) isolates causing invasive infections.}, journal = {Microbial genomics}, volume = {10}, number = {1}, pages = {}, doi = {10.1099/mgen.0.001179}, pmid = {38226964}, issn = {2057-5858}, mesh = {Humans ; *Candida glabrata/genetics ; *Cross Infection/epidemiology ; Genome-Wide Association Study ; Metagenomics ; Genomics ; Recombination, Genetic ; }, abstract = {Candida glabrata is a commensal yeast of the gastrointestinal tract and skin of humans. However, it causes opportunistic infections in immunocompromised patients, and is the second most common Candida pathogen causing bloodstream infections. Although there are many studies on the epidemiology of C. glabrata infections, the fine- and large-scale geographical nature of C. glabrata remain incompletely understood. Here we investigated both the fine- and large-scale population structure of C. glabrata through genome sequencing of 80 clinical isolates obtained from six tertiary hospitals in Qatar and by comparing with global collections. Our fine-scale analyses revealed high genetic diversity within the Qatari population of C. glabrata and identified signatures of recombination, inbreeding and clonal expansion within and between hospitals, including evidence for nosocomial transmission among coronavirus disease 2019 (COVID-19) patients. In addition to signatures of recombination at the population level, both MATa and MATα alleles were detected in most hospitals, indicating the potential for sexual reproduction in clinical environments. Comparisons with global samples showed that the Qatari C. glabrata population was very similar to those from other parts of the world, consistent with the significant role of recent anthropogenic activities in shaping its population structure. Genome-wide association studies identified both known and novel genomic variants associated with reduced susceptibilities to fluconazole, 5-flucytosine and echinocandins. Together, our genomic analyses revealed the diversity, transmission patterns and antifungal drug resistance mechanisms of C. glabrata in Qatar as well as the relationships between Qatari isolates and those from other parts of the world.}, } @article {pmid38228164, year = {2024}, author = {Aerts, R and Feys, S and Mercier, T and Lagrou, K}, title = {Microbiological Diagnosis of Pulmonary Aspergillus Infections.}, journal = {Seminars in respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1055/s-0043-1776777}, pmid = {38228164}, issn = {1098-9048}, abstract = {As microbiological tests play an important role in our diagnostic algorithms and clinical approach towards patients at-risk for pulmonary aspergillosis, a good knowledge of the diagnostic possibilities and especially their limitations is extremely important. In this review, we aim to reflect critically on the available microbiological diagnostic modalities for diagnosis of pulmonary aspergillosis and formulate some future prospects. Timely start of adequate antifungal treatment leads to a better patient outcome, but overuse of antifungals should be avoided. Current diagnostic possibilities are expanding, and are mainly driven by enzyme immunoassays and lateral flow device tests for the detection of Aspergillus antigens. Most of these tests are directed towards similar antigens, but new antibodies towards different targets are under development. For chronic forms of pulmonary aspergillosis, anti-Aspergillus IgG antibodies and precipitins remain the cornerstone. More studies on the possibilities and limitations of molecular testing including targeting resistance markers are ongoing. Also, metagenomic next-generation sequencing is expanding our future possibilities. It remains important to combine different test results and interpret them in the appropriate clinical context to improve performance. Test performances may differ according to the patient population and test results may be influenced by timing, the tested matrix, and prophylactic and empiric antifungal therapy. Despite the increasing armamentarium, a simple blood or urine test for the diagnosis of aspergillosis in all patient populations at-risk is still lacking. Research on diagnostic tools is broadening from a pathogen focus on biomarkers related to the patient and its immune system.}, } @article {pmid38228159, year = {2024}, author = {Nenciarini, S and Renzi, S and di Paola, M and Meriggi, N and Cavalieri, D}, title = {Ascomycetes yeasts: The hidden part of human microbiome.}, journal = {WIREs mechanisms of disease}, volume = {}, number = {}, pages = {e1641}, doi = {10.1002/wsbm.1641}, pmid = {38228159}, issn = {2692-9368}, support = {G84I18000160002//Regione Toscana/ ; 36954/7303/18//Ministero delle Politiche Agricole Alimentari e Forestali/ ; 529051018//Joint Programming Initiative A healthy diet for a healthy life/ ; JTC-2017-7//Joint Programming Initiative A healthy diet for a healthy life/ ; }, abstract = {The fungal component of the microbiota, the mycobiota, has been neglected for a long time due to its poor richness compared to bacteria. Limitations in fungal detection and taxonomic identification arise from using metagenomic approaches, often borrowed from bacteriome analyses. However, the relatively recent discoveries of the ability of fungi to modulate the host immune response and their involvement in human diseases have made mycobiota a fundamental component of the microbial communities inhabiting the human host, deserving some consideration in host-microbe interaction studies and in metagenomics. Here, we reviewed recent data on the identification of yeasts of the Ascomycota phylum across human body districts, focusing on the most representative genera, that is, Saccharomyces and Candida. Then, we explored the key factors involved in shaping the human mycobiota across the lifespan, ranging from host genetics to environment, diet, and lifestyle habits. Finally, we discussed the strengths and weaknesses of culture-dependent and independent methods for mycobiota characterization. Overall, there is still room for some improvements, especially regarding fungal-specific methodological approaches and bioinformatics challenges, which are still critical steps in mycobiota analysis, and to advance our knowledge on the role of the gut mycobiota in human health and disease. This article is categorized under: Immune System Diseases > Genetics/Genomics/Epigenetics Immune System Diseases > Environmental Factors Infectious Diseases > Environmental Factors.}, } @article {pmid38229068, year = {2024}, author = {Xu, M and Li, Y and Shi, Y and Liu, H and Tong, X and Ma, L and Gao, J and Du, Q and Du, H and Liu, D and Lu, X and Yan, Y}, title = {Molecular epidemiology of Mycoplasma pneumoniae pneumonia in children, Wuhan, 2020-2022.}, journal = {BMC microbiology}, volume = {24}, number = {1}, pages = {23}, pmid = {38229068}, issn = {1471-2180}, support = {20220208010567//Knowledge innovation project of Wuhan Science and Technology/ ; 20220208010567//Knowledge innovation project of Wuhan Science and Technology/ ; 20220208010567//Knowledge innovation project of Wuhan Science and Technology/ ; 20220208010567//Knowledge innovation project of Wuhan Science and Technology/ ; WJ2021M262//Health Commission of Hubei Province/ ; WJ2021M262//Health Commission of Hubei Province/ ; WJ2021M262//Health Commission of Hubei Province/ ; WJ2021M262//Health Commission of Hubei Province/ ; 2021CFA012//Natural Science Fund of Hubei Province/ ; 2021CFA012//Natural Science Fund of Hubei Province/ ; 2021CFA012//Natural Science Fund of Hubei Province/ ; 2021CFA012//Natural Science Fund of Hubei Province/ ; 2021CFA012//Natural Science Fund of Hubei Province/ ; 31970548//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Mycoplasma pneumoniae (M. pneumoniae) is an important pathogen of community-acquired pneumonia in children. The factors contributing to the severity of illness caused by M. pneumoniae infection are still under investigation. We aimed to evaluate the sensitivity of common M. pneumoniae detection methods, as well as to analyze the clinical manifestations, genotypes, macrolide resistance, respiratory microenvironment, and their relationship with the severity of illness in children with M. pneumoniae pneumonia in Wuhan.

RESULTS: Among 1,259 clinical samples, 461 samples were positive for M. pneumoniae via quantitative polymerase chain reaction (qPCR). Furthermore, we found that while serological testing is not highly sensitive in detecting M. pneumoniae infection, but it may serve as an indicator for predicting severe cases. We successfully identified the adhesin P1 (P1) genotypes of 127 samples based on metagenomic and Sanger sequencing, with P1-type 1 (113/127, 88.98%) being the dominant genotype. No significant difference in pathogenicity was observed among different genotypes. The macrolide resistance rate of M. pneumoniae isolates was 96% (48/50) and all mutations were A2063G in domain V of 23S rRNA gene. There was no significant difference between the upper respiratory microbiome of patients with mild and severe symptoms.

CONCLUSIONS: During the period of this study, the main circulating M. pneumoniae was P1-type 1, with a resistance rate of 96%. Key findings include the efficacy of qPCR in detecting M. pneumoniae, the potential of IgM titers exceeding 1:160 as indicators for illness severity, and the lack of a direct correlation between disease severity and genotypic characteristics or respiratory microenvironment. This study is the first to characterize the epidemic and genomic features of M. pneumoniae in Wuhan after the COVID-19 outbreak in 2020, which provides a scientific data basis for monitoring and infection prevention and control of M. pneumoniae in the post-pandemic era.}, } @article {pmid38229026, year = {2024}, author = {Wang, X and Li, S and Zhu, M and Qiu, Y and Hui, Y and Li, Y and Zhan, Y and Wang, Y and Ye, F and Li, Z}, title = {Pulmonary cryptococcosis complicated with pulmonary aspergillosis: a series of studies and a literature review.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {92}, pmid = {38229026}, issn = {1471-2334}, support = {82270007//National Natural Science Foundation of China/ ; 202201020537//Guangzhou Science and Technology Bureau/ ; SKLRD-OP-202102//Independent project of State Key Laboratory of Respiratory Diseases/ ; }, abstract = {BACKGROUND/OBJECTIVE: With the development of society, pulmonary fungal diseases, represented by pulmonary aspergillosis and pulmonary cryptococcosis, have become increasingly common. However, there is a lack of clear understanding regarding coinfection by these two types of fungi in immunocompetent individuals.

METHODS: A retrospective study from 2014 to 2022 and a systematic literature review of original articles published in English were performed. Patients with pulmonary cryptococcosis complicated with pulmonary aspergillosis including 5 in the retrospective study and 6 in the systematic literature review.

RESULT: The diagnosis of concurrent pulmonary cryptococcosis and pulmonary aspergillosis in patients was confirmed through repeated biopsies or surgical resection. Pulmonary cryptococcosis is often diagnosed initially (6/11, 55%), while the diagnosis of pulmonary aspergillosis is established when the lesions become fixed or enlarged during treatment. Transbronchial lung biopsy (3/11, 27%), thoracoscopic lung biopsy (2/11, 18%), and percutaneous aspiration biopsy of the lung (1/11, 9%) were the main methods to confirm concurrent infection. Most patients were treated with voriconazole, resulting in a cure for the coinfection (6/11, 55%).

CONCLUSION: Pulmonary cryptococcosis complicated with pulmonary Aspergillus is an easily neglected mixed fungal infection. During the treatment of lesion enlargement in clinical cryptococcus, we need to watch out for Aspergillus infection.}, } @article {pmid38228744, year = {2024}, author = {Adeniyi-Ipadeola, GO and Hoffman, KL and Yang, H and Javornik Cregeen, SJ and Preidis, GA and Ramani, S and Hair, AB}, title = {Human milk cream alters intestinal microbiome of preterm infants: a prospective cohort study.}, journal = {Pediatric research}, volume = {}, number = {}, pages = {}, pmid = {38228744}, issn = {1530-0447}, abstract = {BACKGROUND: In very low birth weight (VLBW) infants, human milk cream added to standard human milk fortification is used to improve growth. This study aimed to evaluate the impact of cream supplement on the intestinal microbiome of VLBW infants.

METHODS: Whole genome shotgun sequencing was performed on stool (n = 57) collected from a cohort of 23 infants weighing 500-1250 grams (control = 12, cream = 11). Both groups received an exclusive human milk diet (mother's own milk, donor human milk, and donor human milk-derived fortifier) with the cream group receiving an additional 2 kcal/oz cream at 100 mL/kg/day of fortified feeds and then 4 kcal/oz if poor growth.

RESULTS: While there were no significant differences in alpha diversity, infants receiving cream significantly differed from infants in the control group in beta diversity. Cream group samples had significantly higher prevalence of Proteobacteria and significantly lower Firmicutes compared to control group. Klebsiella species dominated the microbiota of cream-exposed infants, along with bacterial pathways involved in lipid metabolism and metabolism of cofactors and amino acids.

CONCLUSIONS: Cream supplementation significantly altered composition of the intestinal microbiome of VLBW infants to favor increased prevalence of Proteobacteria and functional gene content associated with these bacteria.

IMPACT: We report changes to the intestinal microbiome associated with administration of human milk cream; a novel supplement used to improve growth rates of preterm very low birth weight infants. Since little is known about the impact of cream on intestinal microbiota composition of very low birth weight infants, our study provides valuable insight on the effects of diet on the microbiome of this population. Dietary supplements administered to preterm infants in neonatal intensive care units have the potential to influence the intestinal microbiome composition which may affect overall health status of the infant.}, } @article {pmid38228614, year = {2024}, author = {Rashidi, A and Gem, H and McLean, JS and Kerns, K and Dean, DR and Dey, N and Minot, S}, title = {Multi-cohort shotgun metagenomic analysis of oral and gut microbiota overlap in healthy adults.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {75}, pmid = {38228614}, issn = {2052-4463}, abstract = {The multitude of barriers between the mouth and colon may eliminate swallowed oral bacteria. Ascertaining the presence of the same bacteria in the mouth and colon is methodologically challenging partly because 16S rRNA gene sequencing - the most commonly used method to characterize the human microbiota - has low confidence in taxonomic assignments deeper than genus for most bacteria. As different species of the same genus can have low-level variation across the same 16S rRNA gene region, shotgun sequencing is needed to identify a true overlap. We analyzed a curated, multi-cohort, shotgun metagenomic database with species-level taxonomy and clade-specific marker genes to fill this knowledge gap. Using 500 paired fecal/oral (4 oral sites) samples from 4 healthy adult cohorts, we found a minute overlap between the two niches. Comparing marker genes between paired oral and fecal samples with species-level overlap, the pattern of overlap in only 7 individuals was consistent with same-strain colonization. These findings argue against ectopic colonization of oral bacteria in the distal gut in healthy adults.}, } @article {pmid38228587, year = {2024}, author = {Viver, T and Conrad, RE and Rodriguez-R, LM and Ramírez, AS and Venter, SN and Rocha-Cárdenas, J and Llabrés, M and Amann, R and Konstantinidis, KT and Rossello-Mora, R}, title = {Towards estimating the number of strains that make up a natural bacterial population.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {544}, pmid = {38228587}, issn = {2041-1723}, support = {1831582//National Science Foundation (NSF)/ ; 2129823//National Science Foundation (NSF)/ ; PGC2018-096956-B-C41//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/ ; PID2021-126114NB-C42//Ministerio de Economía y Competitividad (Ministry of Economy and Competitiveness)/ ; }, abstract = {What a strain is and how many strains make up a natural bacterial population remain elusive concepts despite their apparent importance for assessing the role of intra-population diversity in disease emergence or response to environmental perturbations. To advance these concepts, we sequenced 138 randomly selected Salinibacter ruber isolates from two solar salterns and assessed these genomes against companion short-read metagenomes from the same samples. The distribution of genome-aggregate average nucleotide identity (ANI) values among these isolates revealed a bimodal distribution, with four-fold lower occurrence of values between 99.2% and 99.8% relative to ANI >99.8% or <99.2%, revealing a natural "gap" in the sequence space within species. Accordingly, we used this ANI gap to define genomovars and a higher ANI value of >99.99% and shared gene-content >99.0% to define strains. Using these thresholds and extrapolating from how many metagenomic reads each genomovar uniquely recruited, we estimated that -although our 138 isolates represented about 80% of the Sal. ruber population- the total population in one saltern pond is composed of 5,500 to 11,000 genomovars, the great majority of which appear to be rare in-situ. These data also revealed that the most frequently recovered isolate in lab media was often not the most abundant genomovar in-situ, suggesting that cultivation biases are significant, even in cases that cultivation procedures are thought to be robust. The methodology and ANI thresholds outlined here should represent a useful guide for future microdiversity surveys of additional microbial species.}, } @article {pmid38228585, year = {2024}, author = {Risely, A and Newbury, A and Stalder, T and Simmons, BI and Top, EM and Buckling, A and Sanders, D}, title = {Host- plasmid network structure in wastewater is linked to antimicrobial resistance genes.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {555}, pmid = {38228585}, issn = {2041-1723}, support = {BB/X010473/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, abstract = {As mobile genetic elements, plasmids are central for our understanding of antimicrobial resistance spread in microbial communities. Plasmids can have varying fitness effects on their host bacteria, which will markedly impact their role as antimicrobial resistance vectors. Using a plasmid population model, we first show that beneficial plasmids interact with a higher number of hosts than costly plasmids when embedded in a community with multiple hosts and plasmids. We then analyse the network of a natural host-plasmid wastewater community from a Hi-C metagenomics dataset. As predicted by the model, we find that antimicrobial resistance encoding plasmids, which are likely to have positive fitness effects on their hosts in wastewater, interact with more bacterial taxa than non-antimicrobial resistance plasmids and are disproportionally important for connecting the entire network compared to non- antimicrobial resistance plasmids. This highlights the role of antimicrobials in restructuring host-plasmid networks by increasing the benefits of antimicrobial resistance carrying plasmids, which can have consequences for the spread of antimicrobial resistance genes through microbial networks. Furthermore, that antimicrobial resistance encoding plasmids are associated with a broader range of hosts implies that they will be more robust to turnover of bacterial strains.}, } @article {pmid38228558, year = {2024}, author = {Zhao, CL and Liu, K and Zhou, YZ}, title = {[The clinical application of targeted next-generation sequencing and metagenomics next-generation sequencing in pathogenic microorganism detection].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {58}, number = {1}, pages = {114-121}, doi = {10.3760/cma.j.cn112150-20230201-00072}, pmid = {38228558}, issn = {0253-9624}, support = {2022YFC2406804//National Key Research and Development Project of China/ ; }, abstract = {Infectious diseases seriously threaten human health. The early detection of the causative organism and antibiotic resistance genes of infection remains a major clinical challenge. Next-generation sequencing has been widely used in diagnosing infectious diseases. Cheaper and faster targeted next-generation sequencing technology is progressively being used in clinical practice. However, the awareness among clinicians about the clinical utility of this technology is limited. The article presents the theoretical background, advantages and disadvantages, clinical applications of targeted next-generation sequencing, and its contrasts with metagenomics next-generation sequencing. It provides a reference for clinicians to select laboratory methods for identifying pathogens in clinical practice.}, } @article {pmid38228000, year = {2024}, author = {Ma, J and Sun, H and Li, B and Wu, B and Zhang, X and Ye, L}, title = {Horizontal transfer potential of antibiotic resistance genes in wastewater treatment plants unraveled by microfluidic-based mini-metagenomics.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133493}, doi = {10.1016/j.jhazmat.2024.133493}, pmid = {38228000}, issn = {1873-3336}, abstract = {Wastewater treatment plants (WWTPs) are known to harbor antibiotic resistance genes (ARGs), which can potentially spread to the environment and human populations. However, the extent and mechanisms of ARG transfer in WWTPs are not well understood due to the high microbial diversity and limitations of molecular techniques. In this study, we used a microfluidic-based mini-metagenomics approach to investigate the transfer potential and mechanisms of ARGs in activated sludge from WWTPs. Our results show that while diverse ARGs are present in activated sludge, only a few highly similar ARGs are observed across different taxa, indicating limited transfer potential. We identified two ARGs, ermF and tla-1, which occur in a variety of bacterial taxa and may have high transfer potential facilitated by mobile genetic elements. Interestingly, genes that are highly similar to the sequences of these two ARGs, as identified in this study, display varying patterns of abundance across geographic regions. Genes similar to ermF found are widely found in Asia and the Americas, while genes resembling tla-1 are primarily detected in Asia. Genes similar to both genes are barely detected in European WWTPs. These findings shed light on the limited horizontal transfer potential of ARGs in WWTPs and highlight the importance of monitoring specific ARGs in different regions to mitigate the spread of antibiotic resistance.}, } @article {pmid38227799, year = {2024}, author = {Kai, N and Qingsong, C and Kejia, M and Weiwei, L and Xing, W and Xuejie, C and Lixia, C and Minzi, D and Yuanyuan, Y and Xiaoyan, W}, title = {An Inflammatory Bowel Diseases Integrated Resources Portal (IBDIRP).}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, doi = {10.1093/database/baad097}, pmid = {38227799}, issn = {1758-0463}, support = {82300636//National Natural Science Foundation of China/ ; 2023JJ40898//Young Hunan Natural Science Foundation (HNSF)/ ; 82300636//National Natural Science Foundation of China/ ; 2023JJ40898//Young Hunan Natural Science Foundation (HNSF)/ ; }, abstract = {IBD, including ulcerative colitis and Crohn's disease, is a chronic and debilitating gastrointestinal disorder that affects millions of people worldwide. Research on IBD has generated massive amounts of data, including literature, metagenomics, metabolomics, bioresources and databases. We aim to create an IBD Integrated Resources Portal (IBDIRP) that provides the most comprehensive resources for IBD. An integrated platform was developed that provides information on different aspects of IBD research resources, such as single-nucleotide polymorphisms (SNPs), genes, transcriptome, microbiota, metabolomics, single cells and other resources. Valuable and comprehensive IBD-related data were collected from PubMed, Google, GMrepo, gutMega, gutMDisorder, Single Cell Portal and other sources. Then, the data were systematically sorted, and these resources were manually curated. We systematically sorted and cataloged more than 320 unique risk SNPs associated with IBD in the SNP section. We presented over 289 IBD-related genes based on the database collection in the gene section. We also obtained 153 manually curated IBD transcriptomics data, including 12 388 samples, on the Gene Expression Omnibus database. The sorted IBD-related microbiota data from three primary microbiome databases (GMrepo, gutMega and gutMDisorder) were available for download. We selected 23 149 IBD-related taxonomic records from these databases. Additionally, we collected 24 IBD metabolomics studies with 2896 participants in the metabolomics section. We introduced two interactive single-cell data plug-in units that provided data visualization based on cells and genes. Finally, we listed 18 significant IBD web resources, such as the official European Crohn's and Colitis Organisation and International Organization for the Study of IBD websites, IBD scoring tools, IBD genetic and multi-omics resources, IBD biobanks and other useful research resources. The IBDIRP website is the first integrated resource for global IBD researchers. This portal will help researchers by providing comprehensive knowledge and enabling them to reinforce the multidimensional impression of IBD. The IBDIRP website is accessible via www.ibdirp.com Database URL: www.ibdirp.com.}, } @article {pmid38227477, year = {2024}, author = {Sun, X and Feng, S and Qin, B and Ye, J and Xie, L and Gui, J and Sang, M}, title = {Integrated multi-omics profiling highlights the benefits of resveratrol hydroxypropyl-β-cyclodextrin inclusion complex for A53T transgenic mice through the microbiota-gut-brain axis.}, journal = {Food & function}, volume = {}, number = {}, pages = {}, doi = {10.1039/d3fo03667g}, pmid = {38227477}, issn = {2042-650X}, abstract = {Parkinson's disease (PD) is a neurological disorder characterized by motor and gastrointestinal dysfunctions. Resveratrol is a potent antioxidant and anti-inflammatory phytoalexin known for its health-promoting benefits. However, little is known about its potential in treating PD by modulating the microbial gut-brain axis, and its clinical application has been limited due to poor water solubility, rapid metabolism, and limited systemic bioavailability. Our study aimed to evaluate the therapeutic potential of RHSD, a resveratrol-cyclodextrin inclusion complex, in treating PD through the gut-brain axis in human SNCA-transgenic (A53T) mice PD models. Building on our previous study, we prepared RHSD and compared its efficacy with uncoated resveratrol for PD treatment. The study results demonstrated that RHSD exhibited several advantages in improving motor function, alleviating cognitive impairment, restoring intestinal barrier function, and inhibiting neuropathy. Subsequently, a series of analyses, including fecal microbiota metagenomic sequencing, non-target metabolic assays, host transcriptome sequencing, and integrative analysis were performed to reveal the potential therapeutic pathways of RHSD in A53T mice. The metagenomic sequencing results indicated a significant increase in the levels of Lactobacillus murinus, Lactobacillus reuteri, Enterorhabduscaecimuris, Lactobacillus taiwanensis, and Lactobacillus animals following RHSD administration. Furthermore, metabolomics profiling showed that the levels of gut microbiome metabolites were reversed after RHSD treatment, and differential metabolites were significantly correlated with motor function and intestinal function in PD mice. The integrated analysis of microbial metabolites and host transcriptomics suggested that abnormal amino acid metabolism, mitochondrial dysfunction, oxidative stress, and neuroinflammation in the PD model were associated with the diffusion of abnormal metabolites. This study illustrates the profound impact of RHSD administration on rectifying gut microbiota dysbiosis and improving the A53T mouse model. Notably, we observed significant alterations in the proliferation and metabolism of multiple probiotic strains of Lactobacillus. Furthermore, our research supports the hypothesis that microbiota-related metabolites may regulate the transcription of host genes, including dopamine receptors and calcium stabilization. Consequently, our findings underscore the potential of RHSD as a promising therapeutic candidate for the treatment of PD through the modulation of several signaling pathways within the microbiota-gut-brain axis.}, } @article {pmid38226809, year = {2024}, author = {Sievers, BL and Siegers, JY and Cadènes, JM and Hyder, S and Sparaciari, FE and Claes, F and Firth, C and Horwood, PF and Karlsson, EA}, title = {"Smart markets": harnessing the potential of new technologies for endemic and emerging infectious disease surveillance in traditional food markets.}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0168323}, doi = {10.1128/jvi.01683-23}, pmid = {38226809}, issn = {1098-5514}, abstract = {Fast detection and rapid intervention are crucial to mitigate risks of pathogen emergence, spillover and spread-every second counts. However, comprehensive, active, longitudinal surveillance systems at high-risk interfaces that provide real-time data for action remain lacking. This paper proposes "smart market" systems harnessing cutting-edge tools and a range of sampling techniques, including wastewater and air collection, multiplex assays, and metagenomic sequencing. Coupled with robust response pathways, these systems could better enable Early Warning and bolster prevention efforts.}, } @article {pmid37987757, year = {2024}, author = {Engevik, KA and Scribano, FJ and Gebert, JT and Perry, JL and Crawford, SE and Hyser, JM}, title = {Distribution of P2Y and P2X purinergic receptor expression within the intestine.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {326}, number = {2}, pages = {G107-G119}, doi = {10.1152/ajpgi.00108.2023}, pmid = {37987757}, issn = {1522-1547}, support = {F30 DK131828/DK/NIDDK NIH HHS/United States ; }, abstract = {Nucleotides are potent extracellular signaling molecules during homeostasis, infection, and injury due to their ability to activate purinergic receptors. The nucleotide ATP activates P2X receptors (P2RXs), whereas the nucleotides ADP, ATP, UTP, and UDP-glucose selectively activate different P2Y receptors (P2RYs). Several studies have established crucial roles for P2 receptors during intestinal inflammatory and infectious diseases, yet the most extensive characterization of purinergic signaling has focused on immune cells and the central and enteric nervous systems. As epithelial cells serve as the first barrier against irritants and infection, we hypothesized that the gut epithelium may express multiple purinergic receptors that respond to extracellular nucleotide signals. Using the Human Protein Atlas and Gut Cell Survey, we queried single-cell RNA sequencing (RNAseq) data for the P2 purinergic receptors in the small and large intestines. In silico analysis reveals robust mRNA expression of P2RY1, P2RY2, P2RY11, and P2RX4 throughout the gastrointestinal tract. Human intestinal organoids exhibited a similar expression pattern with a prominent expression of P2RY1, P2RY2, and P2RX4, but this purinergic receptor repertoire was not conserved in T84, Caco2, and HT29 intestinal epithelial cell lines. Finally, P2YR1 and P2YR2 agonists elicited robust calcium responses in human intestinal organoids, but calcium responses were weaker or absent in the cell lines. These findings suggest that the gastrointestinal epithelia respond to extracellular purinergic signaling via P2RY1, P2RY2, P2RY11, and P2RX4 receptors and highlight the benefit of using intestinal organoids as a model of intestinal purinergic signaling.NEW & NOTEWORTHY Several studies have revealed crucial roles for P2 receptors during inflammatory and infectious diseases, however, these have largely been demonstrated in immune cells and the enteric nervous system. Although epithelial cells serve as the first barrier against infection and inflammation, the role of purinergic signaling within the gastrointestinal tract remains largely unknown. This work expands our knowledge of purinergic receptor distribution and relative expression along the intestine.}, } @article {pmid38226032, year = {2024}, author = {Gallardo, FJF and Hernández Flores, JL and Aguirre, SA and López, MÁR and Gómez, JLA and Saldaña Gutierrez, C and Gutiérrez, MCG and Morales, JAR and Guillén, JC}, title = {Metagenome-assembled bacterial genomes recovered from the datasets of Spodoptera frugiperda (Smith) (Lepidoptera: Noctuidae).}, journal = {Data in brief}, volume = {52}, number = {}, pages = {109989}, doi = {10.1016/j.dib.2023.109989}, pmid = {38226032}, issn = {2352-3409}, abstract = {Spodoptera frugiperda (Smith) (Lepidoptera: Noctuidae), also known as the fall armyworm, is an economically important and widespread polyphagous pest. Microorganisms associated to this insect during life cycle play important ecological roles. We report 3 metagenome-assembled bacterial genomes reconstructed from a metagenome dataset obtained from S. frugiperda larvae F3 3rd-instar reared using artificial diet under laboratory conditions. Genome data for Enterococcus casseliflavus indicated a genome length of 3,659,8333 bp and GC content of 42.54%. Genome data for E. mundtii indicated a genome length of 2,921,701 bp and GC content of 38.37%. Finally, genome data for Lactiplantibacillus plantarum indicated a genome length of 3,298,601 bp, GC content of 44.31%. Genome analysis allowed us to identify genus-specific protein families (PLFams), transporters and antibiotic resistance-related genes among others. DNA sequences were deposited in National Center for Biotechnology Information (https://www.ncbi.nlm.nih.gov/) as Bioproject accession PRJNA899064.}, } @article {pmid38225663, year = {2024}, author = {Saleem, F and Li, E and Edge, TA and Tran, KL and Schellhorn, HE}, title = {Identification of potential microbial risk factors associated with fecal indicator exceedances at recreational beaches.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {4}, pmid = {38225663}, issn = {2524-6372}, support = {ALLRP-554507-2020//Nautral Sciences and Engineering Council of Canada/ ; ALLRP-554507-2020//Nautral Sciences and Engineering Council of Canada/ ; ALLRP-554507-2020//Nautral Sciences and Engineering Council of Canada/ ; ALLRP-554507-2020//Nautral Sciences and Engineering Council of Canada/ ; ALLRP-554507-2020//Nautral Sciences and Engineering Council of Canada/ ; }, abstract = {BACKGROUND: Fecal bacterial densities are proxy indicators of beach water quality, and beach posting decisions are made based on Beach Action Value (BAV) exceedances for a beach. However, these traditional beach monitoring methods do not reflect the full extent of microbial water quality changes associated with BAV exceedances at recreational beaches (including harmful cyanobacteria). This proof of concept study evaluates the potential of metagenomics for comprehensively assessing bacterial community changes associated with BAV exceedances compared to non-exceedances for two urban beaches and their adjacent river water sources.

RESULTS: Compared to non-exceedance samples, BAV exceedance samples exhibited higher alpha diversity (diversity within the sample) that could be further differentiated into separate clusters (Beta-diversity). For Beach A, Cyanobacterial sequences (resolved as Microcystis and Pseudanabaena at genus level) were significantly more abundant in BAV non-exceedance samples. qPCR validation supported the Cyanobacterial abundance results from metagenomic analysis and also identified saxitoxin genes in 50% of the non-exceedance samples. Microcystis sp and saxitoxin gene sequences were more abundant on non-exceedance beach days (when fecal indicator data indicated the beach should be open for water recreational purposes). For BAV exceedance days, Fibrobacteres, Pseudomonas, Acinetobacter, and Clostridium sequences were significantly more abundant (and positively correlated with fecal indicator densities) for Beach A. For Beach B, Spirochaetes (resolved as Leptospira on genus level) Burkholderia and Vibrio sequences were significantly more abundant in BAV exceedance samples. Similar bacterial diversity and abundance trends were observed for river water sources compared to their associated beaches. Antibiotic Resistance Genes (ARGs) were also consistently detected at both beaches. However, we did not observe a significant difference or correlation in ARGs abundance between BAV exceedance and non-exceedance samples.

CONCLUSION: This study provides a more comprehensive analysis of bacterial community changes associated with BAV exceedances for recreational freshwater beaches. While there were increases in bacterial diversity and some taxa of potential human health concern associated with increased fecal indicator densities and BAV exceedances (e.g. Pseudomonas), metagenomics analyses also identified other taxa of potential human health concern (e.g. Microcystis) associated with lower fecal indicator densities and BAV non-exceedances days. This study can help develop more targeted beach monitoring strategies and beach-specific risk management approaches.}, } @article {pmid38225378, year = {2024}, author = {Minor, NR and Ramuta, MD and Stauss, MR and Harwood, OE and Brakefield, SF and Alberts, A and Vuyk, WC and Bobholz, MJ and Rosinski, JR and Wolf, S and Lund, M and Mussa, M and Beversdorf, LJ and Aliota, MT and O'Connor, SL and O'Connor, DH}, title = {Author Correction: Metagenomic sequencing detects human respiratory and enteric viruses in air samples collected from congregate settings.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {1316}, doi = {10.1038/s41598-024-51814-0}, pmid = {38225378}, issn = {2045-2322}, } @article {pmid38225124, year = {2024}, author = {Chang, H and Gu, C and Wang, M and Chang, Z and Zhou, J and Yue, M and Chen, J and Qin, X and Feng, Z}, title = {Integrating shotgun metagenomics and metabolomics to elucidate the dynamics of microbial communities and metabolites in fine flavor cocoa fermentation in Hainan.}, journal = {Food research international (Ottawa, Ont.)}, volume = {177}, number = {}, pages = {113849}, doi = {10.1016/j.foodres.2023.113849}, pmid = {38225124}, issn = {1873-7145}, abstract = {The aim of this study was to investigate the dynamic profile of microorganisms and metabolites in Hainan Trinitario cocoa during a six-day spontaneous box fermentation process. Shotgun metagenomic and metabolomic approaches were employed for this investigation. The potential metabolic functions of microorganisms in cocoa fermentation were revealed through a joint analysis of microbes, functional genes, and metabolites. During the anaerobic fermentation phase, Hanseniaspora emerged as the most prevalent yeast genus, implicated in pectin decomposition and potentially involved in glycolysis and starch and sucrose metabolism. Tatumella, possessing potential for pyruvate kinase, and Fructobacillus with a preference for fructose, constituted the primary bacteria during the pre-turning fermentation stage. Upon the introduction of oxygen into the fermentation mass, acetic acid bacteria ascended to dominant within the microflora. The exponential proliferation of Acetobacter resulted in a decline in taxonomic richness and abundance. Moreover, the identification of novel species within the Komagataeibacter genus suggests that Hainan cocoa may serve as a valuable reservoir for the discovery of unique cocoa fermentation bacteria. The KEGG annotation of metabolites and enzymes also highlighted the significant involvement of phenylalanine metabolism in cocoa fermentation. This research will offer a new perspective for the selection of starter strains and the formulation of mixed starter cultures.}, } @article {pmid38225117, year = {2024}, author = {Xiang, Y and Zhou, B and Jiang, C and Tang, Z and Liu, P and Ding, W and Lin, H and Tang, J}, title = {Revealing the formation mechanisms of key flavors in fermented broad bean paste.}, journal = {Food research international (Ottawa, Ont.)}, volume = {177}, number = {}, pages = {113880}, doi = {10.1016/j.foodres.2023.113880}, pmid = {38225117}, issn = {1873-7145}, abstract = {Pixian Douban (PXDB) is a popular Chinese condiment for its distinctive flavor. Broad bean fermentation (Meju) is the most important process in the formation of flavor substances. Key flavors were analyzed qualitatively and quantitatively, and metagenomic technology was applied to study the microbial diversity during broad bean fermentation. In addition, the main metabolic pathways of key flavors were explored. Results indicated that Staphylococcus_gallinarum was the main microorganism in the microbial community, accounting for 39.13%, followed by Lactobacillus_agilis, accounting for 13.76%. Aspergillus_flavus was the fungus with the highest species abundance, accounting for 3.02%. The KEGG Pathway enrichment analysis showed that carbohydrate metabolism and amino acid metabolism were the main metabolic pathways. Glycoside hydrolase and glycosyltransferase genes were the most abundant, accounting for more than 70% of the total number of active enzyme genes. A total of 113 enzymes related to key flavors and 39 microorganisms corresponding to enzymes were annotated. And Staphylococcus_gallinarum, Lactobacillus_agilis, Weissella_confusa, Pediococcus_acidilactici, Staphylococcus_kloosii, Aspergillus_oryzae, and Aspergillus_flavus played a key role in the metabolic pathway. This study reveals the formation mechanism of key flavors in fermented broad bean, it is important for guiding the industrial production of PXDB and improving product quality.}, } @article {pmid38225054, year = {2024}, author = {Chen, K and Yang, J and Guo, X and Han, W and Wang, H and Zeng, X and Wang, Z and Yuan, Y and Yue, T}, title = {Microflora structure and functional capacity in Tibetan kefir grains and selenium-enriched Tibetan kefir grains: A metagenomic analysis.}, journal = {Food microbiology}, volume = {119}, number = {}, pages = {104454}, doi = {10.1016/j.fm.2023.104454}, pmid = {38225054}, issn = {1095-9998}, abstract = {Tibetan kefir grains (TKGs) are a complex protein-lipid-polysaccharide matrix composed of various microorganisms. Microorganisms have the benefit of being effective, secure, and controllable when used for selenium enrichment. In this study, selenium-enriched Tibetan kefir grains (Se-TKGs) were made, and the microbiology composition was analyzed through a metagenomic analysis, to explore the influence of selenium enrichment. The microbial composition of TKGs and Se-TKGs, as well as the probiotic species, quorum sensing system (QS) and functional genes were compared and evaluated. Lactobacillus kefiranofaciens was the most abundant microbial species in both communities. Compared with TKGs, Se-TKGs had a much higher relative abundance of acetic acid bacteria. Lactobacillus helveticus was the most common probiotic species both in TKGs and Se-TKGs. Probiotics with antibacterial and anti-inflammatory properties were more abundant in Se-TKGs. QS analysis revealed that Se-TKGs contained more QS system-associated genes than TKGs. Moreover, Kyoto Encyclopedia of Genes and Genomes analysis revealed that the pathway for human disease ko01501 had the greatest relative abundance in both TKGs and Se-TKGs. Compared with TKGs, Se-TKGs demonstrated a greater relative abundance of different drug resistance-related metabolic pathways. Additionally, linear discriminant analysis effect size was used to examine the biomarkers responsible for the difference between the two groups. In this study, we focused on the microbiological structure of TKGs and Se-TKGs, with the aim of establishing a foundation for a more thorough investigation of Se-TKGs and providing a basis for exploring potential future use.}, } @article {pmid38225038, year = {2024}, author = {Almeida, OGG and Pereira, MG and Bighetti-Trevisan, RL and Santos, ES and De Campos, EG and Felis, GE and Guimarães, LHS and Polizeli, MLTM and De Martinis, BS and De Martinis, ECP}, title = {Investigating luxS gene expression in lactobacilli along lab-scale cocoa fermentations.}, journal = {Food microbiology}, volume = {119}, number = {}, pages = {104429}, doi = {10.1016/j.fm.2023.104429}, pmid = {38225038}, issn = {1095-9998}, abstract = {Previous metagenomic analyses have suggested that lactobacilli present potential for Quorum Sensing (QS) in cocoa fermentation, and in the present research, laboratory scale fermentations were carried out to monitor the expression of luxS, a universal marker of QS. For that, 96 h-fermentations were studied, as follows: F0 (non inoculated control), F1 (inoculated with yeasts, lactic acid bacteria, and acetic acid bacteria), F2 (inoculated with yeasts and acetic acid bacteria), F3 (inoculated with yeasts only). The parameters evaluated were: plate counting, quantification of key enzymes and analysis of volatile organic compounds associated with key sensory descriptors, using headspace gas chromatography-mass spectrometry (GC-MS). Furthermore, QS was estimated by the quantification of the expression of luxS genes by Reverse Transcriptase Real-Time PCR. The results demonstrated that microbial succession occurred in pilot scale fermentations, but no statistical differences for microbial enumeration and α-diversity index were observed among experiments and control. Moreover, it was not possible to make conclusive correlations of enzymatic profile and fermenting microbiota, likely due to the intrinsic activity of plant hydrolases. Regarding to the expression of luxS genes, in Lactiplantibacillus plantarum they were active along the fermentation, but for Limosilactobacillus fermentum, luxS was expressed only at early and middle phases. Correlation analysis of luxS expression and production of volatile metabolites evidenced a possible negative association of Lp. Plantarum with fermentation quality. In conclusion, these data corroborate former shotgun metagenomic analysis by demonstrating the expression of luxS by lactobacilli in pilot scale cocoa fermentation and evidence Lp. Plantarum is the main lactic acid bacteria related to its expression.}, } @article {pmid38224956, year = {2024}, author = {Behr, JH and Kuhl-Nagel, T and Sommermann, L and Moradtalab, N and Chowdhury, SP and Schloter, M and Windisch, S and Schellenberg, I and Maccario, L and Sörensen, SJ and Rothballer, M and Geistlinger, J and Smalla, K and Ludewig, U and Neumann, G and Grosch, R and Babin, D}, title = {Long-term conservation tillage with reduced nitrogen fertilization intensity can improve winter wheat health via positive plant-microorganism feedback in the rhizosphere.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiae003}, pmid = {38224956}, issn = {1574-6941}, abstract = {Microbiome-based solutions are regarded key for sustainable agroecosystems. However, it is unclear how agricultural practices affect the rhizosphere microbiome, plant-microorganism interactions and crop performance under field conditions. Therefore, we installed root observation windows in a winter wheat field cultivated either under long-term mouldboard plough (MP) or cultivator tillage (CT). Each tillage practice was also compared at two nitrogen (N) fertilization intensities, intensive (recommended N-supply with pesticides/growth regulators) or extensive (reduced N-supply, no fungicides/growth regulators). Shoot biomass, root exudates, leaf metabolites and gene expression were analyzed together with the rhizosphere microbiome (bacterial/archaeal 16S rRNA gene, fungal ITS amplicon and shotgun metagenome sequencing) shortly before flowering. Compared to MP, the rhizosphere of CT winter wheat contained more primary and secondary metabolites, especially benzoxazinoid derivatives. Potential copiotrophic and plant-beneficial taxa (e.g. Bacillus, Devosia, Trichoderma) as well as functional genes (e.g. siderophore production, trehalose synthase, ACC deaminase) were enriched in the CT rhizosphere, suggesting that tillage affected belowground plant-microorganism interactions. In addition, physiological stress markers were suppressed in CT winter wheat compared to MP. In summary, tillage practice was a major driver of crop performance, root deposits and rhizosphere microbiome interactions, while the N-fertilization intensity was also relevant, but less important.}, } @article {pmid38224719, year = {2023}, author = {Kim, D and Jeon, J and Kim, M and Jeong, J and Heo, YM and Lee, DG and Yon, DK and Han, K}, title = {Comparison of microbial molecular diagnosis efficiency within unstable template metagenomic DNA samples between qRT-PCR and chip-based digital PCR platforms.}, journal = {Genomics & informatics}, volume = {21}, number = {4}, pages = {e52}, doi = {10.5808/gi.23068}, pmid = {38224719}, issn = {1598-866X}, support = {2019R1A6C1010033//Ministry of Education/ ; }, abstract = {Accurate and efficient microbial diagnosis is crucial for effective molecular diagnostics, especially in the field of human healthcare. The gold standard equipment widely employed for detecting specific microorganisms in molecular diagnosis is quantitative real-time polymerase chain reaction (qRT-PCR). However, its limitations in low metagenomic DNA yield samples necessitate exploring alternative approaches. Digital PCR, by quantifying the number of copies of the target sequence, provides absolute quantification results for the bacterial strain. In this study, we compared the diagnostic efficiency of qRT-PCR and digital PCR in detecting a particular bacterial strain (Staphylococcus aureus), focusing on skin-derived DNA samples. Experimentally, specific primer for S. aureus were designed at transcription elongation factor (greA) gene and the target amplicon were cloned and sequenced to validate efficiency of specificity to the greA gene of S. aureus. To quantify the absolute amount of microorganisms present on the skin, the variable region 5 (V5) of the 16S rRNA gene was used, and primers for S. aureus identification were used to relative their amount in the subject's skin. The findings demonstrate the absolute convenience and efficiency of digital PCR in microbial diagnostics. We suggest that the high sensitivity and precise quantification provided by digital PCR could be a promising tool for detecting specific microorganisms, especially in skin-derived DNA samples with low metagenomic DNA yields, and that further research and implementation is needed to improve medical practice and diagnosis.}, } @article {pmid38224716, year = {2023}, author = {Kumar, A and Robertsen, EM and Willassen, NP and Fu, J and Hjerde, E}, title = {Comparative analysis of HiSeq3000 and BGISEQ-500 sequencing platform over whole genome sequencing metagenomics data.}, journal = {Genomics & informatics}, volume = {21}, number = {4}, pages = {e49}, doi = {10.5808/gi.23072}, pmid = {38224716}, issn = {1598-866X}, abstract = {Recent advances in sequencing technologies and platforms have enabled to generate metagenomics sequences using different sequencing platforms. In this study, we analyzed and compared shotgun metagenomic sequences generated by HiSeq3000 and BGISEQ-500 platforms from 12 sediment samples collected across the Norwegian coast. Metagenomics DNA sequences were normalized to an equal number of bases for both platforms and further evaluated by using different taxonomic classifiers, reference databases, and assemblers. Normalized BGISEQ-500 sequences retained more reads and base counts after preprocessing, while a slightly higher fraction of HiSeq3000 sequences were taxonomically classified. Kaiju classified a higher percentage of reads relative to Kraken2 for both platforms, and comparison of reference database for taxonomic classification showed that MAR database outperformed RefSeq. Assembly using MEGAHIT produced longer assemblies and higher total contigs count in majority of HiSeq3000 samples than using metaSPAdes, but the assembly statistics notably improved with unprocessed or normalized reads. Our results indicate that both platforms perform comparably in terms of the percentage of taxonomically classified reads and assembled contig statistics for metagenomics samples. This study provides valuable insights for researchers in selecting an appropriate sequencing platform and bioinformatics pipeline for their metagenomics studies.}, } @article {pmid38223708, year = {2024}, author = {Qu, H and Wang, Y and Diao, H and Ren, G and Wang, Z and Shang, J and Shangguan, L and Wang, H}, title = {Clinical characteristics of 15 patients with listeria meningitis in adult.}, journal = {Heliyon}, volume = {10}, number = {1}, pages = {e23755}, pmid = {38223708}, issn = {2405-8440}, abstract = {OBJECTIVE: To report and analyze the clinical characteristics of 15 patients with Listeria meningitis in adult.

METHODS: We reviewed the medical records of 15 patients with Listeria meningitis who were admitted to Shanxi Bethune Hospital between January 2017 and January 2023.

RESULTS: The clinical manifestations was primarily characterized by fever， altered mental status, headache, neck stiffness, and vomiting. Blood or cerebrospinal fluid (CSF) cultures were performed in 15 cases, and pathogens were detected in 11 of them. Metagenomic next-generation sequencing (mNGS) detected pathogens in 10 cases, with four being negative by conventional methods and six being positive through traditional tests. The laboratory blood results presented leukocytosis. The CSF analysis upon admission showed elevated levels of white blood cells and proteins, as well as decreased chloride and glucose concentration. The brain computed tomography (CT) revealed ventricular enlargement in 3 patients. The brain magnetic resonance imaging (MRI) showed abnormalities in multiple areas of the brain. Despite 3 patients with decompensated hydrocephalus underwent lateral ventricle puncture and drainage，their neurological deterioration were increasingly deteriorating.7 patients were treated by mechanical ventilation due to respiratory insufficiency. After 3 months, there were 9 cases with excellent outcomes（modified Rankin Scale score of 0-2）,2 cases with favorable outcomes（score of 3-5）, and 4 deaths（score of 6）.

CONCLUSIONS: This thesis found that the detection rate of Listeria monocytogenes has been on a rise over the past six years in our department, ranking second only to Streptococcus pneumoniae. Additionally, the detection rate achieved by mNGS surpasses that of other conventional methods. Among the patient cohort, 11 had underlying diseases such as systemic lupus erythematosus, tuberculosis, diabetes mellitus, pituitary neoplasms, leukemia and other related illnesses. Once listeriosis is early identified, the adequate antibiotic therapy should be promptly introduced in the course of empirical treatment.}, } @article {pmid38223562, year = {2024}, author = {Huang, MQ and Zheng, TT and Wang, XR and Xiang, F}, title = {The Clinical Value of Metagenomic Next-Generation Sequencing in Pneumocystis jirovecii Pneumonia.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {69-80}, pmid = {38223562}, issn = {1178-6973}, abstract = {BACKGROUND: The incidence of Pneumocystis jirovecii pneumonia (PJP) is increasing.

METHODS: 108 patients were analysed retrospectively at the Wuhan Union Hospital. The patients were classified into the PJP group or the P. jirovecii colonisation (PJC) group based on clinical diagnosis. Clinical data included demographics, laboratory examinations, treatment, and outcomes.

RESULTS: A notable difference in the fungal load was seen between two groups, with median reads of 3215.79 vs. 5.61 in two groups, respectively (P<0.001). The optimal threshold value for discriminating P. jirovecii infection between colonisation for mNGS was six, and serum (1,3)-β-D-glucan (BDG) was 47.6 pg/mL. Besides, the positive detection rate of mNGS for co-pathogens in PJP patients was significantly higher than that of culture (88.16% vs. 22.37%, P<0.0001). Epstein-Barr virus and cytomegalovirus were the most common pathogens of co-infection in PJP patients. The antibiotic therapy in PJP patients was adjusted according to the mNGS results, of which seventeen (22.37%) were downgraded, 38 (50.0%) patients were upgraded, and 21 (27.63%) were unchanged. And almost all patients showed significant improvement in C-reactive protein.

CONCLUSION: mNGS is a promising and valuable technique with good performance for differentiating P. jirovecii infection and colonisation, the detection of pathogens, and antibiotic treatment.}, } @article {pmid38223561, year = {2024}, author = {Wang, J and Dong, S and Fang, M and Fan, Z and Xu, Y}, title = {Omadacycline for the Treatment of Severe Chlamydia psittaci Pneumonia Complicated with Guillain-Barre Syndrome.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {81-87}, pmid = {38223561}, issn = {1178-6973}, abstract = {BACKGROUND: Chlamydia psittaci (C. psittaci) is a pathogen that is seldom implicated in community-acquired pneumonia and is rarely linked to severe pneumonia. Reports of severe C. psittaci pneumonia accompanied by Guillain-Barre syndrome (GBS) are scarce. Tetracyclines are the preferred therapeutic approach for psittacosis. Omadacycline, a novel tetracycline, demonstrates strong antibacterial efficacy against typical bacteria and atypical pathogens, including C. psittaci. However, its application in the treatment of psittacosis pneumonia remains constrained.

CASE PRESENTATION: A 77-year-old female patient was admitted to the hospital presenting with symptoms of fever, low back pain, and headache. The diagnosis of C. psittaci was established through the utilization of metagenomic next-generation sequencing (mNGS). Initial administration of moxifloxacin, meropenem, piperacillin-tazobactam, and doxycycline proved to be ineffective. Subsequent omadacycline leaded to the successful resolution of fever and dyspnea. However, after the endotracheal tube was removed, the patient experienced a rapid decline in symmetrical limb strength, leading to a diagnosis of GBS based on clinical manifestations, cerebrospinal fluid analysis, and electromyography. Following a 5-day course of immunoglobulin therapy and nutritional nerve treatment, the patient's condition ameliorated, culminating in an uncomplicated discharge.

CONCLUSION: This case provides evidence supporting the potential use of omadacycline as a therapeutic option for the treatment of severe C. psittaci pneumonia. The utilization of mNGS technology is of paramount importance in the prompt identification of uncommon pathogens, including C. psittaci. Nevertheless, the occurrence of GBS should be taken into consideration when C. psittaci pneumonia is accompanied by symmetrical limb weakness. These findings have important implications for the diagnosis, treatment, and management of patients with C. psittaci pneumonia.}, } @article {pmid38222109, year = {2024}, author = {Gross, K and Santiago, M and Krieger, JM and Hagele, AM and Zielinska, K and Scheiman, J and Jäger, R and Kostic, A and Kerksick, CM}, title = {Impact of probiotic Veillonella atypica FB0054 supplementation on anaerobic capacity and lactate.}, journal = {iScience}, volume = {27}, number = {1}, pages = {108643}, pmid = {38222109}, issn = {2589-0042}, abstract = {Seven healthy, physically active men (n = 3) and women (n = 4) (30.7 ± 7.5 years, 172.7 ± 8.7 cm, 70.4 ± 11.6 kg, 23.6 ± 4.1 kg/m[2], 49.2 ± 8.4 mL/kg/min) supplemented for 14 days with a placebo (PLA) or 1 × 10[10] CFU doses of the probiotic Veillonella atypica FB0054 (FitBiomics, New York, NY). Participants had safety panels, hemodynamics, lactate, and anaerobic capacity assessed. Stool samples were collected to evaluate for metagenomic and metabolomic changes. Exhaustion times were not different between groups, whereas anaerobic capacity tended to shorten with PLA (61.14 ± 72.04 s; 95% CI: -5.49, 127.77 s, p = 0.066) with no change with VA (13.29 ± 100.13 s, 95% CI: -79.32, 105.89 s, p = 0.738). No changes in lactate, hemodynamics, or bacterial community changes were observed, whereas 14 metabolites exhibited differential expression patterns with VA supplementation. In conclusion, VA maintained exercise performance that tended to decline in PLA. Supplementation was well tolerated with no changes in safety markers or reported adverse events.}, } @article {pmid38221981, year = {2024}, author = {Hill, JA and Park, SY and Gajurel, K and Taplitz, R}, title = {A Systematic Literature Review to Identify Diagnostic Gaps in Managing Immunocompromised Patients With Cancer and Suspected Infection.}, journal = {Open forum infectious diseases}, volume = {11}, number = {1}, pages = {ofad616}, pmid = {38221981}, issn = {2328-8957}, abstract = {Patients with cancer are increasingly vulnerable to infections, which may be more severe than in the general population. Improvements in rapid and timely diagnosis to optimize management are needed. We conducted a systematic literature review to determine the unmet need in diagnosing acute infections in immunocompromised patients with cancer and identified 50 eligible studies from 5188 records between 1 January 2012 and 23 June 2022. There was considerable heterogeneity in study designs and parameters, laboratory methods and definitions, and assessed outcomes, with limited evaluation of diagnostic impact on clinical outcomes. Culture remains the primary diagnostic strategy. Fewer studies employing molecular technologies exist, but emerging literature suggests that pathogen-agnostic molecular tests may add to the diagnostic armamentarium. Well-designed clinical studies using standardized methodologies are needed to better evaluate performance characteristics and clinical and economic impacts of emerging diagnostic techniques to improve patient outcomes.}, } @article {pmid38221930, year = {2024}, author = {Zhang, J and Zhou, Y and Zhong, Z and Lv, Y and Yang, X and Liu, X}, title = {Identification of mixed anaerobic infections after inguinal hernia repair based on metagenomic next-generation sequencing: A case report.}, journal = {Open medicine (Warsaw, Poland)}, volume = {19}, number = {1}, pages = {20230887}, pmid = {38221930}, issn = {2391-5463}, abstract = {Infection following inguinal hernia repair (IHR) is uncommon. Rational use of antibiotics can significantly improve the prognosis of patients. However, accurately identifying the pathogen involved is usually challenging. This case report describes a patient who developed intermittent fever after undergoing open preperitoneal tension-free repair of a bilateral inguinal hernia. The scrotal fluid specimen was cultured and subjected to metagenomic next-generation sequencing (mNGS). Culture revealed the presence of Enterococcus faecalis (a facultative anaerobe). However, mNGS detected E. faecalis along with multiple anaerobic bacteria including Bacteroides thetaiotaomicron, Parabacteroides distasonis, and Levyella massiliensis. The patient was finally diagnosed with a mixed infection of E. faecalis and multiple anaerobes, and his condition was effectively controlled after timely adjustment of the antibiotic regimen. Treating postoperative infections with multiple concurrent conditions can be challenging. mNGS is valuable for the accurate diagnosis and treatment of infections, as it not only can further verify the culture results, but also assist clinicians in ruling out pulmonary infection caused by hematogenous dissemination after IHR in patients.}, } @article {pmid38221534, year = {2024}, author = {Hu, T and Chen, J and Lin, X and He, W and Liang, H and Wang, M and Li, W and Wu, Z and Han, M and Jin, X and Kristiansen, K and Xiao, L and Zou, Y}, title = {Comparison of the DNBSEQ platform and Illumina HiSeq 2000 for bacterial genome assembly.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {1292}, pmid = {38221534}, issn = {2045-2322}, support = {XMHT20220104017//Shenzhen Municipal Government of China/ ; 32100009//National Natural Science Foundation of China/ ; 2019B020230001//Natural Science Foundation of Guangdong Province/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; *Genome, Bacterial ; *DNA ; High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics ; }, abstract = {The Illumina HiSeq platform has been a commonly used option for bacterial genome sequencing. Now the BGI DNA nanoball (DNB) nanoarrays platform may provide an alternative platform for sequencing of bacterial genomes. To explore the impact of sequencing platforms on bacterial genome assembly, quality assessment, sequence alignment, functional annotation, mutation detection, and metagenome mapping, we compared genome assemblies based on sequencing of cultured bacterial species using the HiSeq 2000 and BGISEQ-500 platforms. In addition, simulated reads were used to evaluate the impact of insert size on genome assembly. Genome assemblies based on BGISEQ-500 sequencing exhibited higher completeness and fewer N bases in high GC genomes, whereas HiSeq 2000 assemblies exhibited higher N50. The majority of assembly assessment parameters, sequences of 16S rRNA genes and genomes, numbers of single nucleotide variants (SNV), and mapping to metagenome data did not differ significantly between platforms. More insertions were detected in HiSeq 2000 genome assemblies, whereas more deletions were detected in BGISEQ-500 genome assemblies. Insert size had no significant impact on genome assembly. Taken together, our results suggest that DNBSEQ platforms would be a valid substitute for HiSeq 2000 for bacterial genome sequencing.}, } @article {pmid38220540, year = {2024}, author = {Russo, AE and Memon, A and Ahmed, S}, title = {Bladder Cancer and the Urinary Microbiome-New Insights and Future Directions: A Review.}, journal = {Clinical genitourinary cancer}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.clgc.2023.12.015}, pmid = {38220540}, issn = {1938-0682}, abstract = {The presence of a microbiome in the urinary system has been established through recent advancements in technology and investigation of microbial communities in the human body. The study of the taxonomic and genomic ecology of microbial communities has been greatly improved by the use of metagenomics. The research in this area has expanded our understanding of microbial ecosystems and shows that the urinary tract contains over 100 species from over 50 genera, with Lactobacillus, Gardnerella, and Streptococcus being the most common. Previous studies have suggested that the microbiota in the urinary tract may play a role in carcinogenesis by causing chronic inflammation and genotoxicity, but more research is needed to reach a definite conclusion. This is a narrative review. We conducted a search for relevant publications by using the databases Medline/PubMed and Google Scholar. The search was based on keywords such as "urinary microbiome," "bladder cancer," "carcinogenesis," "urothelial carcinoma," and "next-generation sequencing." The retrieved publications were then reviewed to study the contribution of the urinary microbiome in the development of bladder cancer. The results have been categorized into four sections to enhance understanding of the urinary microbiome and to highlight its role in the emergence of bladder cancer through alterations in the immune response that involve T-cells and antibodies. The immune system and microbiome play crucial roles in maintaining health and preventing disease. Manipulating the immune system is a key aspect of various cancer treatments, and certain gut bacteria have been linked to positive responses to immunotherapies. However, the impact of these treatments on the urinary microbiome, and how diet and lifestyle affect it, are not well understood. Research in this area could have significant implications for improving bladder cancer treatment and patient outcomes.}, } @article {pmid38220146, year = {2024}, author = {Pan, SY and Zhou, CB and Deng, JW and Zhou, YL and Liu, ZH and Fang, JY}, title = {The effects of pks[+] Escherichia coli and bile acid in colorectal tumorigenesis among people with cholelithiasis or cholecystectomy.}, journal = {Journal of gastroenterology and hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/jgh.16462}, pmid = {38220146}, issn = {1440-1746}, support = {2016YFC0906002//National Key R&D Program of China/ ; 2020YFA0509200//National Key R&D Program of China/ ; 31970718//National Natural Science Foundation of China/ ; 81830081//National Natural Science Foundation of China/ ; 81972203//National Natural Science Foundation of China/ ; 82070570//National Natural Science Foundation of China/ ; 82203224//National Natural Science Foundation of China/ ; 2019CXJQ02//Shanghai Municipal Health Commission, Collaborative Innovation Cluster Project/ ; 21YF1425600//Shanghai Sailing Program/ ; 2022M712124//China Postdoctoral Science Foundation/ ; }, abstract = {BACKGROUND AND AIM: Patients with cholelithiasis (CL) or cholecystectomy (CE) would have more chances of getting colorectal adenoma (CRA) or cancer (CRC). We aimed to figure out the effects of gut microbiota and bile acid on colorectal neoplasm in CL and CE patients.

METHODS: This was a retrospective observational study that recruited 514 volunteers, including 199 people with normal gallbladders (normal), 152 CL, and 163 CE patients. Discovery cohort was established to explore the difference in gut microbiota through 16S rRNA and metagenomics sequencing. Validation cohort aimed to verify the results through quantitative polymerase chain reaction (qPCR).

RESULTS: Significant enrichment of Escherichia coli was found in patients with cholelithiasis or cholecystectomy both in the discovery cohort (16S rRNA sequencing, PNormal-CL  = 0.013, PNormal-CE  = 0.042; metagenomics sequencing, PNormal-CE  = 0.026) and validation cohort (PNormal-CL  < 0.0001, PNormal-CE  < 0.0001). Pks[+] E. coli was found enriched in CL and CE patients through qPCR (in discovery cohort: PNormal-CE  = 0.018; in validation cohort: PNormal-CL  < 0.0001, PNormal-CE  < 0.0001). The differences in bile acid metabolism were found both through Tax4Fun analysis of 16S rRNA sequencing (Ko00120, primary bile acid biosynthesis, PNormal-CE  = 0.014; Ko00121, secondary bile acid biosynthesis, PNormal-CE  = 0.010) and through metagenomics sequencing (map 00121, PNormal-CE  = 0.026). The elevation of serum total bile acid of CE patients was also found in validation cohort (PNormal-CE  < 0.0001). The level of serum total bile acid was associated with the relative abundance of pks[+] E. coli (r = 0.1895, P = 0.0012).

CONCLUSIONS: E. coli, especially pks[+] species, was enriched in CL and CE patients. Pks[+] E. coli and bile acid metabolism were found associated with CRA and CRC in people after cholecystectomy.}, } @article {pmid38219994, year = {2024}, author = {Koloti, LE and Nkuna, R and Matambo, TS}, title = {Impact of current anthropogenic activities on Blesbokspruit wetland microbiome and functions.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170010}, doi = {10.1016/j.scitotenv.2024.170010}, pmid = {38219994}, issn = {1879-1026}, abstract = {Till present, natural wetlands have been continuously subjected to intensive pollution stress in recent years, mainly because of the rapidly growing industrialization and urbanization that are associated with a myriad of anthropogenic activities and land use practices. These man-made sources of pollution change the chemical properties of the natural wetlands, which in turn alter their microbial ecological biodiversity and functions. For the first time, the impact of the current anthropogenic activities and land use practices on the Blesbokspruit wetland chemical status and their consequential effect on the microbial structure and functions were investigated. Sites of high pollution intensity were identified using geographic information systems mapping (GISMapping) and the wetland microbiome and functional profile were studied through the use of high throughput shotgun metagenomics sequencing analysis. The predominant phyla that stemmed along the Blesbokspruit wetland were found to be Proteobacteria which was more dominant in water (93 %) than in the sediments (89 %), followed by firmicutes which was more abundant in sediments (9 %) than in water (6 %), and Bacteroidetes were relatively low in abundance within both the sediments (2 %) and the overlying water (1 %). The genera Klebsiella (70.4 %-28.2 %), Citrobacter (52.0 %-30.6 %), Escherichia (51.0 %-8.4 %), and Lynsinibacillus (9.3 %-1.5 %) were observed in most water and sediment samples. Within the six polluted sites, Site 2 was found to be the most highly polluted site in the Blesbokspruit wetland with very high COD (900 mg/L), TOC (11.60 mg/L), NO3[-] (39.74 mg/L), NO2[-] (12.64 mg/L), PO4[3] (4.14 mg/L), Fl[-] (143.88 mg/L), Cl[-] (145.95 mg/L) concentrations recorded in the water and high levels of TOC (0.37 mg/L), TC (6.92 %), TN (1.82 %), TS (0.53 %) in sediments. The microbial community structure and functions were found to be strongly influenced by the high organic content from the intense agricultural activities and sewage spillages and heavy metals from the mining activities nearby.}, } @article {pmid38219969, year = {2024}, author = {Keeney, JG and Gulzar, N and Baker, JB and Klempir, O and Hannigan, GD and Bitton, DA and Maritz, JM and King, CHS and Patel, JA and Duncan, P and Mazumder, R}, title = {Communicating computational workflows in a regulatory environment.}, journal = {Drug discovery today}, volume = {}, number = {}, pages = {103884}, doi = {10.1016/j.drudis.2024.103884}, pmid = {38219969}, issn = {1878-5832}, abstract = {The volume of nucleic acid sequence data has exploded recently, amplifying the challenge of transforming data into meaningful information. Processing data can require an increasingly complex ecosystem of customized tools, which increases difficulty in communicating analyses in an understandable way yet is of sufficient detail to enable informed decisions or repeats. This can be of particular interest to institutions and companies communicating computations in a regulatory environment. BioCompute Objects (BCOs; an instance of pipeline documentation that conforms to the IEEE 2791-2020 standard) were developed as a standardized mechanism for analysis reporting. A suite of BCOs is presented, representing interconnected elements of a computation modeled after those that might be found in a regulatory submission but are shared publicly - in this case a pipeline designed to identify viral contaminants in biological manufacturing, such as for vaccines. Teaser: Realistic examples of a substantially improved vehicle for documentation and reporting of computational workflows in a regulatory environment.}, } @article {pmid38219925, year = {2024}, author = {Zheng, X and Xie, J and Chen, W and Liu, M and Xie, L}, title = {Boosting anaerobic digestion of long chain fatty acid with microbial electrolysis cell combining metal organic framework as cathode: Biofilm construction and metabolic pathways.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {130284}, doi = {10.1016/j.biortech.2023.130284}, pmid = {38219925}, issn = {1873-2976}, abstract = {The role of metal organic framework (MOF) modified cathode in promoting long chain fatty acid (LCFA) methanation was identified in microbial electrolysis cell coupled anaerobic digestion (MEC-AD) system. The maximum methane production rate of MEC-AD-MOF achieved 49.8 ± 3.4 mL/d, which increased by 41 % compared to MEC-AD-C. The analysis of bio-cathode biofilm revealed that microbial activity, distribution, population, and protein secretion prompted by MOF cathode, which in turn led to an acceleration of electron transfer between the cathode and microbes. Specifically, the relative abundance of acetate-oxidizing bacterium (Mesotoga) in MEC-AD-MOF was 1.5-3.6 times higher than that in MEC-AD-C, with a co-metabolized enrichment of Methanobacterium. Moreover, MOF cathode reinforced LCFA methanation by raising the relative abundance of genes coded key enzymes involved in CO2-reducing pathway, and elevating the tolerance of microbes to LCFA inhibition. These results indicate that MOF can enhance biofilm construction in MEC-AD, thereby improving the treatment performance of lipid wastewater.}, } @article {pmid38219924, year = {2024}, author = {Zhou, Q and Mi, K and Ma, W and Feng, F and Huo, M and Sun, Y and Huang, L}, title = {Metagenomic analysis reveals impact of acyl homoserine endolipid-like signaling molecules on the aqueous sediment resistome under florfenicol stress.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {130318}, doi = {10.1016/j.biortech.2024.130318}, pmid = {38219924}, issn = {1873-2976}, abstract = {Quorum sensing potentially helps microorganisms adapt to antibiotic stress encountered in the environment. This experiment investigated the effect of acyl homoserine endolipid-like signaling molecules on microbial antibiotic resistance gene structures in aqueous sediments under florfenicol stress. Additional acyl homoserine endolipid-like signaling molecules (AHLs) alter the structure of multidrug resistance genes in florfenicol-stressed sediments, particularly the multidrug resistance efflux pump gene family. Prophages and integrative and conjugative elements (ICEs) determined the resistance genes structure, and pathways related to mobile genetic elements (MGEs) transfer may play an essential role in this process. The practical application of AHLs to regulate quorum sensing systems may alter bacterial stress responses to environmental florfenicol residues, thereby reducing the development of antibiotic resistance in the environment.}, } @article {pmid38219691, year = {2024}, author = {Xie, X and Yan, L and Sun, S and Pi, K and Shi, J and Wang, Y}, title = {Arsenic biogeochemical cycling association with basin-scale dynamics of microbial functionality and organic matter molecular composition.}, journal = {Water research}, volume = {251}, number = {}, pages = {121117}, doi = {10.1016/j.watres.2024.121117}, pmid = {38219691}, issn = {1879-2448}, abstract = {Geogenic arsenic (As)-contaminated groundwater is a sustaining global health concern that is tightly constrained by multiple interrelated biogeochemical processes. However, a complete spectrum of the biogeochemical network of high-As groundwater remains to be established, concurrently neglecting systematic zonation of groundwater biogeochemistry on the regional scale. We uncovered the geomicrobial interaction network governing As biogeochemical pathways by merging in-field hydrogeochemical monitoring, metagenomic analyses, and ultrahigh resolution mass spectrometry (FT-ICR MS) characterization of dissolved organic matter. In oxidizing to weakly reducing environments, the nitrate-reduction and sulfate-reduction encoding genes (narGHI, sat) inhibited the dissolution of As-bearing iron minerals, leading to lower As levels in groundwater. In settings from weakly to moderately reducing, high abundances of sulfate-reduction and iron-transport encoding genes boosted iron mineral dissolution and consequent As release. As it evolved to strongly reducing stage, elevated abundance of methane cycle-related genes (fae, fwd, fmd) further enhanced As mobilization in part by triggering the formation of gaseous methylarsenic. During redox cycling of N, S, Fe, C and As in groundwater, As migration to groundwater and immobilization in mineral particles are geochemically constrained by basin-scale dynamics of microbial functionality and DOM molecular composition. The study constructs a theoretical model to summarize new perspectives on the biogeochemical network of As cycling.}, } @article {pmid38219578, year = {2024}, author = {He, L and Yang, SS and Ding, J and Chen, CX and Yang, F and He, ZL and Pang, JW and Peng, BY and Zhang, Y and Xing, DF and Ren, NQ and Wu, WM}, title = {Biodegradation of polyethylene terephthalate by Tenebrio molitor: Insights for polymer chain size, gut metabolome and host genes.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133446}, doi = {10.1016/j.jhazmat.2024.133446}, pmid = {38219578}, issn = {1873-3336}, abstract = {Polyethylene terephthalate (PET or polyester) is a commonly used plastic and also contributes to the majority of plastic wastes. Mealworms (Tenebrio molitor larvae) are capable of biodegrading major plastic polymers but their degrading ability for PET has not been characterized based on polymer chain size molecular size, gut microbiome, metabolome and transcriptome. We verified biodegradation of commercial PET by T. molitor larvae in a previous report. Here, we reported that biodegradation of commercial PET (Mw 29.43 kDa) was further confirmed by using the δ[13]C signature as an indication of bioreaction, which was increased from - 27.50‰ to - 26.05‰. Under antibiotic suppression of gut microbes, the PET was still depolymerized, indicating that the host digestive enzymes could degrade PET independently. Biodegradation of high purity PET with low, medium, and high molecular weights (MW), i.e., Mw values of 1.10, 27.10, and 63.50 kDa with crystallinity 53.66%, 33.43%, and 4.25%, respectively, showed a mass reduction of > 95%, 86%, and 74% via broad depolymerization. Microbiome analyses indicated that PET diets shifted gut microbiota to three distinct structures, depending on the low, medium, and high MW. Metagenome sequencing, transcriptomic, and metabolic analyses indicated symbiotic biodegradation of PET by the host and gut microbiota. After PET was fed, the host's genes encoding degradation enzymes were upregulated, including genes encoding oxidizing, hydrolyzing, and non-specific CYP450 enzymes. Gut bacterial genes for biodegrading intermediates and nitrogen fixation also upregulated. The multiple-functional metabolic pathways for PET biodegradation ensured rapid biodegradation resulting in a half-life of PET less than 4 h with less negative impact by PET MW and crystallinity.}, } @article {pmid38218544, year = {2024}, author = {Ren, Z and Zhang, C and Li, X and Luo, W}, title = {Thermokarst lakes are hotspots of antibiotic resistance genes in permafrost regions on the Qinghai-Tibet Plateau.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {344}, number = {}, pages = {123334}, doi = {10.1016/j.envpol.2024.123334}, pmid = {38218544}, issn = {1873-6424}, abstract = {Antibiotic resistance genes (ARGs) are natural products and emerging pollutants in remote environments, including permafrost regions that are rapidly thawing due to climate warming. We investigated the role of thermokarst lakes (including sediment and water) in reserving ARGs compared to permafrost soils across the permafrost regions on the Qinghai-Tibet Plateau. As intrinsically connected distinct environments, permafrost soil, lake sediment, and lake water harbored 1239 ARGs in total, while a considerable number of same ARGs (683 out of 1239) concurrently presented in all these environments. Soil and sediment had a higher number of ARGs than water. Multidrug resistance genes were the most diverse and abundant in all three environments, where cls, ropB, mdfA, fabI, and macB were the top five most abundant ARGs while with different orders. Soil and sediment had similar ARG profiles, and the alpha and beta diversity of ARGs in sediment were positively correlated with that in soil. The beta diversity of ARG profiles between sediment and soil was highly contributed by turnover component (89%). However, turnover and nestedness components were almost equality contributed (46%-54%) to the beta diversity of ARG profiles between soil and water as well as between sediment and water. The results suggested that thermokarst lake sediments might inherit the ARGs in permafrost soils. Water ARGs are the subset of soil ARGs and sediment ARGs to a certain degree with species turnover playing a significant role. When accounting the ARGs in sediment and water together, thermokarst lakes had a significantly higher number of ARGs than permafrost soils, suggesting that thermokarst lakes act as the hotspots of ARGs in permafrost regions. These findings are disturbing especially due to the fact that tremendous number of thermokarst lakes are forming under accelerating climate change.}, } @article {pmid38218523, year = {2024}, author = {Kumar, N and Shukla, P}, title = {Microalgal multiomics-based approaches in bioremediation of hazardous contaminants.}, journal = {Environmental research}, volume = {}, number = {}, pages = {118135}, doi = {10.1016/j.envres.2024.118135}, pmid = {38218523}, issn = {1096-0953}, abstract = {The enhanced industrial growth and higher living standards owing to the incessant population growth have caused heightened production of various chemicals in different manufacturing sectors globally, resulting in pollution of aquatic systems and soil with hazardous chemical contaminants. The bioremediation of such hazardous pollutants through microalgal processes is a viable and sustainable approach. Accomplishing microalgal-based bioremediation of polluted wastewater requires a comprehensive understanding of microalgal metabolic and physiological dynamics. Microalgae-bacterial consortia have emerged as a sustainable agent for synergistic bioremediation and metabolite production. Effective bioremediation involves proper consortium functioning and dynamics. The present review highlights the mechanistic processes employed through microalgae in reducing contaminants present in wastewater. It discusses the multi-omics approaches and their advantages in understanding the biological processes, monitoring, and dynamics among the partners in consortium through metagenomics. Transcriptomics, proteomics, and metabolomics enable an understanding of microalgal cell response toward the contaminants in the wastewater. Finally, the challenges and future research endeavors are summarised to provide an outlook on microalgae-based bioremediation.}, } @article {pmid38218496, year = {2024}, author = {Wu, X and Kong, L and Feng, Y and Zheng, R and Zhou, J and Sun, J and Liu, S}, title = {Communication mediated interaction between bacteria and microalgae advances photogranulation.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {169975}, doi = {10.1016/j.scitotenv.2024.169975}, pmid = {38218496}, issn = {1879-1026}, abstract = {Recently, photogranules composed of bacteria and microalgae for carbon-negative nitrogen removal receive extensive attention worldwide, yet which type of bacteria is helpful for rapid formation of photogranules and whether they depend on signaling communication remain elusive. Varied signaling communication was analyzed using metagenomic method among bacteria and microalgae in via of two types of experimentally verified signaling molecule from bacteria to microalgae, which include indole-3-acetic acid (IAA) and N-acyl homoserine lactones (AHLs) during the operation of photo-bioreactors. Signaling communication is helpful for the adaptability of bacteria to survive with algae. Compared with non-signaling bacteria, signaling bacteria more easily adapt to the varied conditions, evidenced by the increased abundance in the operated reactors. Signaling bacteria are easier to enter the phycosphere, and they dominate the interactions between bacteria and algae rather than non-signaling bacteria. The co-abundance groups (CAGs) with signaling bacteria possess higher abundance than that without signaling bacteria (22.27 % and 6.67 %). Importantly, signaling bacteria accessibly interact with microalgae, which possess higher degree centralities and 32.50 % of them are keystone nodes in the network, in contrast to only 18.66 % of non-signaling bacteria. Thauera carrying both IAA and AHLs synthase genes are highly enriched and positively correlated with nitrogen removal rate. Our work not only highlights the essential roles of signaling communication between microalgae and bacteria in the development of photogranules, but also enriches our understanding of microbial sociobiology.}, } @article {pmid38218484, year = {2024}, author = {Wang, Z and Wang, L and Li, Y and Zou, Y and Hou, X and Wang, L}, title = {How redox gradient potentially influences nitrate reduction coupled with sulfur cycling: A new insight into nitrogen cycling in the hyporheic zone of effluent-dominated rivers.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {170070}, doi = {10.1016/j.scitotenv.2024.170070}, pmid = {38218484}, issn = {1879-1026}, abstract = {The coupled N and S cycling in variable redox gradients in the hyporheic zone (HZ) of the rivers receiving effluents from wastewater treatment plants is unclear. Using two representative effluent-dominated rivers as model systems, a metagenome approach was employed to explore the spatiotemporal redox zonation of the HZ and the N/S cycling processes within the system. The results manifested that nitrate reduction represented the fundamental nitrogen pathway in the HZ. Interestingly, DNRA coupled with sulfur reduction, and denitrification coupled with sulfur oxidation were respectively abundant in the oxic and anoxic zone. Lower nitrate concentration (0-2.72 mg-N/L) and more abundant genes involved in denitrification (napB, NarGHI) and sulfur oxidation (sseA, glpE) were detected in the anoxic zone. Contrarily, the nitrate concentration (0.07-4.87 mg-N/L) and the abundance of genes involved in sulfur reduction (ttrB, sudA) and DNRA (nirBD) were observed more abundant in the oxic zone. Therefore, the results verified the oxygen-limited condition did not suppress but rather facilitated the denitrification process in the presence of active S cycling. The high relative abundances of nosZ gene encoding sequence (3-5 % relative to all nitrogen-cycling processes) in both the effluent-discharging area and downstream area highly confirmed that HZ was capable of alleviating the N2O emission in the region. The functional keystone taxa were revealed through co-occurrence network analysis. The structural equation model shows that the genes of N/S cycling were positively impacted by functional keystone taxa, especially the N cycling genes. Functional keystone taxa were proven driven by the redox gradient, demonstrating their positive roles in mediating N/S cycling processes. The promoting effect on nitrate reduction coupled with sulfur cycling was clarified when redox conditions oscillated, providing a new perspective on mitigating nitrogen pollution and greenhouse gas emissions in effluent-receiving rivers.}, } @article {pmid38218318, year = {2024}, author = {Shen, X and Tilves, C and Kim, H and Tanaka, T and Spira, AP and Chia, CW and Talegawkar, SA and Ferrucci, L and Mueller, NT}, title = {Plant-Based Diets and the Gut Microbiome: Findings from the Baltimore Longitudinal Study of Aging.}, journal = {The American journal of clinical nutrition}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajcnut.2024.01.006}, pmid = {38218318}, issn = {1938-3207}, abstract = {BACKGROUND: Mounting evidence indicates that while some plant-based diets are healthful, others are not. Changes in the gut microbiome and microbial metabolites, such as trimethylamine N-oxide (TMAO), may explain differential health effects of plant-based diets. However, human data is sparse on whether qualitatively distinct types of plant-based diets differentially affect gut microbiome diversity and composition, particularly at the species level.

OBJECTIVES: We aimed to examine cross-sectional associations of different plant-based indices with adult gut microbiome diversity, composition, and the microbial metabolite TMAO.

METHODS: We studied 705 adults in the Baltimore Longitudinal Study of Aging with data for diet, fecal microbiome (shotgun metagenomic sequencing), and key covariates. We derived healthful and unhealthful plant-based diet indices (hPDI and uPDI, respectively) using data from food-frequency questionnaires. We examined plant-based diet indices with microbiome alpha diversity (richness and evenness measures), beta diversity (Bray-Curtis and Unifrac measures), composition (species level), and plasma TMAO. We used regression models to determine associations before and after adjustment for age, sex, education, physical activity, smoking status, BMI, and total energy intake.

RESULTS: The analytic sample (mean age 71.0y, SD=12.8y) comprised 55.6% female and 32.5% non-Hispanic White participants. hPDI was positively and uPDI negatively associated with microbiome alpha diversity, driven by microbial evenness (Pielou P < 0.05). hPDI was also positively associated with relative abundance of three polysaccharide-degrading bacterial species (Faecalibacterium prausnitzii, Eubacterium eligens, and Bacteroides thetaiotaomicron) and inversely associated with six species (Blautia hydrogenotrophica, Dorea sp CAG 317, Eisenbergiella massiliensis, Sellimonas intestinalis, and Blautia wexlerae, and Alistipes Shahii). Furthermore, hPDI was inversely associated with TMAO. Associations did not differ by age, sex, or race.

CONCLUSIONS: Greater adherence to a healthful plant-based diet was associated with microbiome features that have been linked to positive health; adherence to an unhealthful plant-based diet had opposing or null associations with these features.}, } @article {pmid38218033, year = {2024}, author = {Liu, Y and Zhao, N and Dai, S and He, R and Zhang, Y}, title = {Metagenomic insights into phenanthrene biodegradation in electrical field-governed biofilms for groundwater bioremediation.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133477}, doi = {10.1016/j.jhazmat.2024.133477}, pmid = {38218033}, issn = {1873-3336}, abstract = {Electrical fields (EFs)-assisted in-situ bioremediation of petroleum-contaminated groundwater, such as polycyclic aromatic hydrocarbons, has drawn increasing attention. However, the long-term stability, the EFs influence, and metabolic pathways are still poorly understood, hindering the further development of robust technology design. Herein, a series of EFs was applied to the phenanthrene-contaminated groundwater, and the corresponding system performance was investigated. The highest removal capacity of phenanthrene (phe) (7.63 g/(m[3]·d)) was achieved with EF_0.8 V biofilm at a hydrolytic retention time of 0.5 d. All the biofilms with four EFs exhibited a high removal efficiency of phe over 80% during a 100-d continuous-flow operation. Intermediates analysis revealed the main pathways of phe degradation: phthalate and salicylate via hydroxylation, methylation, carboxylation, and ring cleavage steps. Synergistic effects between phe-degraders (Dechloromonas), fermentative bacteria (Delftia), and electroactive microorganisms (Geobacter) were the main contributors to the complete phe mineralization. Genes encoding various proteins of methyl-accepting (mcp), response regulator (cheABDRY), and type IV pilus (pilABCMQV) were dominant, revealing the importance of cell motility and extracellular electron transfer. Metagenomics analysis unveiled phe-degrading genes, including ring reduction enzymes (bamBCDE), carboxylase of aromatics (ubiD), and methyltransferase protein (ubiE, pcm). These findings offered a molecular understanding of refractory organics' decompositions in EFs-governed biotechnology.}, } @article {pmid38217947, year = {2024}, author = {Duan, R and Lyu, D and Qin, S and Liang, J and Gu, W and Duan, Q and Wu, W and Tang, D and Han, H and Zheng, X and Xi, J and Bukai, A and Lu, X and Zhang, P and Zhang, D and Xiao, M and Jing, H and Wang, X}, title = {Pasteurella multocida strains of a novel capsular serotype and lethal to Marmota himalayana on Qinghai-Tibet plateau in China.}, journal = {International journal of medical microbiology : IJMM}, volume = {314}, number = {}, pages = {151597}, doi = {10.1016/j.ijmm.2024.151597}, pmid = {38217947}, issn = {1618-0607}, abstract = {Pasteurella multocida is a zoonotic pathogen causing serious diseases in humans and animals. Here, we report P. multocida from wildlife on China's Qinghai-Tibet plateau with a novel capsular serotype, forming a single branch on the core-genome phylogenetic tree: four strains isolated from dead Himalayan marmot (Marmota himalayana) and one genome assembled from metagenomic sequencing of a dead Woolly hare (Lepus oiostolus). Four of the strains were identified as subspecies multocida and one was septica. The mouse model showed that the challenge strain killed mice within 24 h at an infectious dose of less than 300 bacteria. The short disease course is comparable to septicemic plague: the host has died before more severe pathological changes could take place. Though pathological changes were relatively mild, cytokine storm was obvious with a significant rise of IL-12p70, IL-6, TNF-αand IL-10 (P < 0.05). Our findings suggested P. multocida is a lethal pathogen for wildlife on Qinghai-Tibet plateau, in addition to Yersinia pestis. Individuals residing within the M. himalayana plague focus are at risk for P. multocida infection, and public health warnings are necessitated.}, } @article {pmid38217902, year = {2024}, author = {Dong, B and Lu, J and Liu, Y and Zhang, R and Xing, B}, title = {A multi-omics approach to unravelling the coupling mechanism of nitrogen metabolism and phenanthrene biodegradation in soil amended with biochar.}, journal = {Environment international}, volume = {183}, number = {}, pages = {108435}, doi = {10.1016/j.envint.2024.108435}, pmid = {38217902}, issn = {1873-6750}, abstract = {The presence of polycyclic aromatic hydrocarbons (PAHs) in soil negatively affects the environment and the degradation of these contaminants is influenced by nitrogen metabolism. However, the mechanisms underlying the interrelationships between the functional genes involved in nitrogen metabolism and phenanthrene (PHE) biodegradation, as well as the effects of biochar on these mechanisms, require further study. Therefore, this study utilised metabolomic and metagenomic analysis to investigate primary nitrogen processes, associated functional soil enzymes and functional genes, and differential soil metabolites in PHE-contaminated soil with and without biochar amendment over a 45-day incubation period. Results showed that dissimilatory nitrate reduction to ammonium (DNRA) and denitrification were the dominant nitrogen metabolism processes in PHE-contaminated soil. The addition of biochar enhanced nitrogen modules, exhibiting discernible temporal fluctuations in denitrification and DNRA proportions. Co-occurrence networks and correlation heatmap analysis revealed potential interactions among functional genes and enzymes responsible for PHE biodegradation and nitrogen metabolism. Notably, enzymes associated with denitrification and DNRA displayed significant positive correlation with enzymes involved in downstream phenanthrene degradation. Of particular interest was stronger correlation observed with the addition of biochar. However, biochar amendment inhibited the 9-phenanthrol degradation pathway, resulting in elevated levels of glutathione (GSH) in response to environmental stress. These findings provide new insights into the interactions between nitrogen metabolism and PHE biodegradation in soil and highlight the dual effects of biochar on these processes.}, } @article {pmid38217803, year = {2024}, author = {Chernitsyna, SM and Elovskaya, IS and Bukin, SV and Bukin, YS and Pogodaeva, TV and Kwon, DA and Zemskaya, TI}, title = {Genomic and morphological characterization of a new Thiothrix species from a sulfide hot spring of the Zmeinaya bay (Northern Baikal, Russia).}, journal = {Antonie van Leeuwenhoek}, volume = {117}, number = {1}, pages = {23}, pmid = {38217803}, issn = {1572-9699}, support = {22-14-00084//Russian Science Foundation/ ; }, mesh = {*Thiothrix/genetics/metabolism ; *Hot Springs/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Bays ; Russia ; Bacteria/genetics ; Lakes/microbiology ; Water ; Sulfides/metabolism ; Genomics ; DNA ; }, abstract = {A survey for bacteria of the genus Thiothrix indicated that they inhabited the area where the water of the Zmeiny geothermal spring (northern basin of Lake Baikal, Russia) mixed with the lake water. In the coastal zone of the lake oxygen (8.25 g/L) and hydrogen sulfide (up to 1 mg/L) were simultaneously present at sites of massive growth of these particular Thiothrix bacteria. Based on the analysis of the morphological characteristics and sequence of individual genes (16S rRNA, rpoB and tilS), we could not attribute the Thiothrix from Lake Baikal to any of the known species of this genus. To determine metabolic capabilities and phylogenetic position of the Thiothrix sp. from Lake Baikal, we analyzed their whole genome. Like all members of this genus, the bacteria from Lake Baikal were capable of organo-heterotrophic, chemolithoheterotrophic, and chemolithoautotrophic growth and differed from its closest relatives in the spectrum of nitrogen and sulfur cycle genes as well as in the indices of average nucleotide identity (ANI < 75-94%), amino acid identity (AAI < 94%) and in silico DNA-DNA hybridization (dDDH < 17-57%), which were below the boundary of interspecies differences, allowing us to identify them as novel candidate species.}, } @article {pmid38217470, year = {2024}, author = {Patangia, DV and Grimaud, G and Wang, S and Ross, RP and Stanton, C}, title = {Influence of age, socioeconomic status, and location on the infant gut resistome across populations.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2297837}, doi = {10.1080/19490976.2023.2297837}, pmid = {38217470}, issn = {1949-0984}, mesh = {Infant ; Humans ; Aged ; *Genes, Bacterial ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Escherichia/genetics ; Social Class ; }, abstract = {Antibiotic resistance is a growing global concern, with many ecological niches showing a high abundance of antibiotic resistance genes (ARGs), including the human gut. With increasing indications of ARGs in infants, this study aims to investigate the gut resistome profile during early life at a wider geographic level. To achieve this objective, we utilized stool samples data from 26 studies involving subjects aged up to 3 years from different geographical locations. The 32,277 Metagenome Assembled Genomes (MAGs) previously generated from shotgun sequencing reads from these studies were used for resistome analysis using RGI with the CARD database. This analysis showed that the distribution of ARGs across the countries in our study differed in alpha diversity and compositionally. In particular, the abundance of ARGs was found to vary by socioeconomic status and healthcare access and quality (HAQ) index. Surprisingly, countries having lower socioeconomic status and HAQ indices showed lower ARG abundance, which was contradictory to previous reports. Gram-negative genera, including Escherichia, Enterobacter, Citrobacter, and Klebsiella harbored a particularly rich set of ARGs, which included antibiotics that belong to the Reserve, Access or Watch category, such as glycopeptides, fluoroquinolones, sulfonamides, macrolides, and tetracyclines. We showed that ARG abundance exponentially decreased with time during the first 3 years of life. Many highly ARG-abundant species including Escherichia, Klebsiella, Citrobacter species that we observed are well-known pathobionts found in the infant gut in early life. High abundance of these species and a diverse range of ARGs in their genomes point toward the infant gut, acting as an ARG reservoir. This is a concern and further studies are needed to examine the causal effect and its consequences on long-term health.}, } @article {pmid38217406, year = {2024}, author = {Shen, Y and Li, Y and Wu, T and Dong, Q and Deng, Q and Liu, L and Guo, Y and Cao, Y and Li, Q and Shi, J and Zou, H and Jiao, Y and Ding, L and Li, J and Gao, Y and Hu, S and Wang, Y and Chen, L}, title = {Early microbial intervention reshapes phenotypes of newborn Bos taurus through metabolic regulations.}, journal = {GigaScience}, volume = {13}, number = {}, pages = {}, pmid = {38217406}, issn = {2047-217X}, support = {//High-Performance Computing Centre of Nanjing Medical University/ ; 32302756//National Natural Science Foundation of China/ ; CARS36//The Earmarked Fund/ ; HBCT2023180207//Hebei Dairy Cattle Innovation Team of Modern Agro-industry Technology Research System/ ; 6012018//The Top Talent Project of Hebei Province/ ; 1090064//Precision Animal Husbandry Discipline Group Construction Project of Hebei Agricultural University/ ; C2022204248//Natural Science Foundation of Hebei Province/ ; BK20220709//Natural Science Foundation of Jiangsu/ ; CMCM202204//Nanjing Medical University, Changzhou Medical Centre Grant/ ; 303073572NC21//Nanjing Medical University/ ; }, mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome ; Metagenome ; Metabolomics ; Phenotype ; }, abstract = {BACKGROUND: The rumen of neonatal calves has limited functionality, and establishing intestinal microbiota may play a crucial role in their health and performance. Thus, we aim to explore the temporal colonization of the gut microbiome and the benefits of early microbial transplantation (MT) in newborn calves.

RESULTS: We followed 36 newborn calves for 2 months and found that the composition and ecological interactions of their gut microbiomes likely reached maturity 1 month after birth. Temporal changes in the gut microbiome of newborn calves are widely associated with changes in their physiological statuses, such as growth and fiber digestion. Importantly, we observed that MT reshapes the gut microbiome of newborns by altering the abundance and interaction of Bacteroides species, as well as amino acid pathways, such as arginine biosynthesis. Two-year follow-up of those calves further showed that MT improves their later milk production. Notably, MT improves fiber digestion and antioxidant capacity of newborns while reducing diarrhea. MT also contributes to significant changes in the metabolomic landscape, and with putative causal mediation analysis, we suggest that altered gut microbial composition in newborns may influence physiological status through microbial-derived metabolites.

CONCLUSIONS: Our study provides a metagenomic and metabolomic atlas of the temporal development of the gut microbiome in newborn calves. MT can alter the gut microbiome of newborns, leading to improved physiological status and later milk production. The data may help develop strategies to manipulate the gut microbiota during early life, which may be relevant to the health and production of newborn calves.}, } @article {pmid38216924, year = {2024}, author = {Steinke, K and Pamp, SJ and Munk, P}, title = {MAGICIAN: MAG simulation for investigating criteria for bioinformatic analysis.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {55}, pmid = {38216924}, issn = {1471-2164}, mesh = {*Metagenome ; Computer Simulation ; *Microbiota/genetics ; Metagenomics/methods ; Computational Biology ; }, abstract = {BACKGROUND: The possibility of recovering metagenome-assembled genomes (MAGs) from sequence reads allows for further insights into microbial communities and their members, possibly even analyzing such sequences with tools designed for single-isolate genomes. As result quality depends on sequence quality, performance of tools for single-isolate genomes on MAGs should be tested beforehand. Bioinformatics can be leveraged to quickly create varied synthetic test sets with known composition for this purpose.

RESULTS: We present MAGICIAN, a flexible, user-friendly pipeline for the simulation of MAGs. MAGICIAN combines a synthetic metagenome simulator with a metagenomic assembly and binning pipeline to simulate MAGs based on user-supplied input genomes, allowing users to test performance of tools on MAGs while having a ground truth to compare results to. Using MAGICIAN, we found that even very slight (1%) changes in depth of coverage can drastically affect whether a genome can be recovered. We also demonstrate the use of simulated MAGs by evaluating the suitability of such genomes obtained with MAGICIAN's current default pipeline for analysis with the antimicrobial resistance gene identification tool ResFinder.

CONCLUSIONS: Using MAGICIAN, it is possible to simulate MAGs which, while generally high in quality, reflect issues encountered with real-world data, thus providing realistic best-case data. Evaluating the results of ResFinder analysis of these genomes revealed a risk for plausible-looking false positives, which underlines the need for pipeline validation so that researchers are aware of the potential issues when interpreting real-world data. Furthermore, the effects of fluctuations in depth of coverage on genome recovery in our simulated "random sequencing" warrant further investigation and indicate random subsampling of reads may affect discovery of more genomes.}, } @article {pmid38216798, year = {2024}, author = {Saiyam, D and Dubey, A and Malla, MA and Kumar, A}, title = {Lipopeptides from Bacillus: unveiling biotechnological prospects-sources, properties, and diverse applications.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {38216798}, issn = {1678-4405}, support = {CRG/2021/003696//Department of Science and Technology, SERB-CRG, New Delhi, India/ ; }, abstract = {Bacillus sp. has proven to be a goldmine of diverse bioactive lipopeptides, finding wide-range of industrial applications. This review highlights the importance of three major families of lipopeptides (iturin, fengycin, and surfactin) produced by Bacillus sp. and their diverse activities against plant pathogens. This review also emphasizes the role of non-ribosomal peptide synthetases (NRPS) as significant enzymes responsible for synthesizing these lipopeptides, contributing to their peptide diversity. Literature showed that these lipopeptides exhibit potent antifungal activity against various plant pathogens and highlight their specific mechanisms, such as siderophore activity, pore-forming properties, biofilm inhibition, and dislodging activity. The novelty of this review comes from its comprehensive coverage of Bacillus sp. lipopeptides, their production, classification, mechanisms of action, and potential applications in plant protection. It also emphasizes the importance of ongoing research for developing new and enhanced antimicrobial agents. Furthermore, this review article highlights the need for future research to improve the production efficiency of these lipopeptides for commercial applications. It recognizes the potential for these lipopeptides to expand the field of biological pest management for both existing and emerging plant diseases.}, } @article {pmid38216505, year = {2024}, author = {Wang, QS and Cheng, B and Liu, Y and Deng, J and Xu, Y and Sun, CH and Yuan, LY and Zuo, J and Si, F and Gao, LJ}, title = {[Analysis of Bacterial Communities and Antibiotic Resistance Genes in the Aquaculture Area of Changli County].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {45}, number = {1}, pages = {567-575}, doi = {10.13227/j.hjkx.202301039}, pmid = {38216505}, issn = {0250-3301}, mesh = {Animals ; *Anti-Bacterial Agents/analysis ; *Bacteria/genetics ; Genes, Bacterial ; Aquaculture ; Drug Resistance, Microbial/genetics ; Fishes/genetics ; RNA, Ribosomal, 16S ; }, abstract = {In order to understand the distribution of microorganisms and various antibiotic resistance genes in the aquaculture area of Changli County, Qinhuangdao, high-throughput sequencing technology was used in this study. We utilized 16S rDNA gene sequencing and metagenome sequencing methods to analyze the seawater, sediment, and gut contents of the local fish Synechogobius hasta in the aquaculture area in spring. The results showed that Proteobacteria, Firmicutes, and Bacteroidota were the dominant bacteria in seawater; and Proteobacteria, Crenarchaeota, Acidobacter, and Actinobaciota were rich in the sediment; whereas Proteobacteria, Cyanobacteria, Firmicutes, and Bacteroidota were in relatively high abundance in fish gut contents. The microbial diversity of sediment samples was the most abundant, followed by seawater samples, and the microbial diversity of fish intestinal contents was the lowest. Moreover, the microbial diversity of similar samples was relatively similar, and the microbial diversity of different types of samples was quite different. For samples at different sites, there were significant differences between seawater samples at each site, and there were small differences between sediment samples at each site, and some sediment sample groups did not have significant differences in microbial composition. In all sample groups, five β-lactam antibiotic resistance genes (blaOXA-325, cepS, blaCARB-20, blaOXA-55, and blaTRU-1) and four aminoglycoside antibiotic resistance genes[aac(6')-IIb, amrA, aac(6')-Ie-aph(2″)-Ia, and aph(3')-Vc] were detected. There was also a certain correlation between antibiotic resistance genes and microbial communities.}, } @article {pmid38216107, year = {2024}, author = {Elmallawany, MA and Ldelkl, AA and Lu Eleinen, KG and Nadar, AH and El-Adawy, AI and El-Dardiry, MA and Ldel-Hafez, YN and Kotb, AA and Saif, ATS and Shaheen, HAA and Sayed, A and Samir, O and Alatyar, AA and Sheble, MA and Elnakib, M and Badr, MS and Nahnoush, RK}, title = {Metagenomic analysis of the ocular toxoplasmosis in children uveitis from Fayoum governorate, Egypt.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {}, number = {}, pages = {105551}, doi = {10.1016/j.meegid.2024.105551}, pmid = {38216107}, issn = {1567-7257}, abstract = {Granulomatous anterior uveitis with single or numerous gelatinous nodules was found in children living in rural Egypt. All ocular diseases were originally thought to be water-born and related to digenic flukes. The current study sought to learn more about the causes of anterior granulomatous uveitis in Egyptian youngsters who used to swim in rural water canals. 50 children with eye lesions that had not responded to medical treatment were recruited. Four samples were surgically extracted and examined using real-time PCR, transmission electron microscopy (TEM), and shotgun metagenomic sequencing (SMS). Toxoplasma gondii was detected free within the syncytium's distal section, while the proximal part exhibited active synthesis of a presumably extra-polymeric material, possibly released by the microbial population. Toxoplasma gondii was found in 30 samples. Serologically, distinct anti-Toxoplasma antibodies were not found in 91.6% of patients. SMS showed that the T. gondii ME 49 strain had the greatest percentage (29-25%) in all samples within an Acinetobacter-containing microbial community. These findings suggested that these bacteria entered the body via the exterior route rather than the circulatory route. The lack of genetic evidence for subsequent parasite stages invalidates the prior findings about the assumed trematode stage.}, } @article {pmid38215846, year = {2024}, author = {Zheng, Y and Su, Z and Liu, D and Huang, B and Mu, Q and Li, Y and Wen, D}, title = {Metagenomics reveals the influence of small microplastics on microbial communities in coastal sediments.}, journal = {The Science of the total environment}, volume = {914}, number = {}, pages = {169982}, doi = {10.1016/j.scitotenv.2024.169982}, pmid = {38215846}, issn = {1879-1026}, abstract = {The ecological impact of microplastics (MPs) in coastal environments has been widely studied. However, the influence of small microplastics in the actual environment is often overlooked due to measurement challenges. In this study, Hangzhou Bay (HZB), China, was selected as our study area. High-throughput metagenomic sequencing and micro-Raman spectrometry were employed to analyze the microbial communities and microplastics of coastal sediment samples, respectively. We aimed to explore the ecological impact of MPs with small sizes (≤ 100 μm) in real coastal sediment environments. Our results revealed that as microplastic size decreased, the environmental behavior of MPs underwent alterations. In the coastal sediments, no significant correlations were observed between the detected MPs and the whole microbial communities, but small MPs posed potential hazards to eukaryotic communities. Moreover, these small MPs were more prone to microbial degradation and significantly affected carbon metabolism in the habitat. This study is the first to reveal the comprehensive impact of small MPs on microbial communities in a real coastal sediment environment.}, } @article {pmid38215740, year = {2024}, author = {Schirmer, M and Stražar, M and Avila-Pacheco, J and Rojas-Tapias, DF and Brown, EM and Temple, E and Deik, A and Bullock, K and Jeanfavre, S and Pierce, K and Jin, S and Invernizzi, R and Pust, MM and Costliow, Z and Mack, DR and Griffiths, AM and Walters, T and Boyle, BM and Kugathasan, S and Vlamakis, H and Hyams, J and Denson, L and Clish, CB and Xavier, RJ}, title = {Linking microbial genes to plasma and stool metabolites uncovers host-microbial interactions underlying ulcerative colitis disease course.}, journal = {Cell host & microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.chom.2023.12.013}, pmid = {38215740}, issn = {1934-6069}, abstract = {Understanding the role of the microbiome in inflammatory diseases requires the identification of microbial effector molecules. We established an approach to link disease-associated microbes to microbial metabolites by integrating paired metagenomics, stool and plasma metabolomics, and culturomics. We identified host-microbial interactions correlated with disease activity, inflammation, and the clinical course of ulcerative colitis (UC) in the Predicting Response to Standardized Colitis Therapy (PROTECT) pediatric inception cohort. In severe disease, metabolite changes included increased dipeptides and tauro-conjugated bile acids (BAs) and decreased amino-acid-conjugated BAs in stool, whereas in plasma polyamines (N-acetylputrescine and N1-acetylspermidine) increased. Using patient samples and Veillonella parvula as a model, we uncovered nitrate- and lactate-dependent metabolic pathways, experimentally linking V. parvula expansion to immunomodulatory tryptophan metabolite production. Additionally, V. parvula metabolizes immunosuppressive thiopurine drugs through xdhA xanthine dehydrogenase, potentially impairing the therapeutic response. Our findings demonstrate that the microbiome contributes to disease-associated metabolite changes, underscoring the importance of these interactions in disease pathology and treatment.}, } @article {pmid38215690, year = {2024}, author = {Zeng, W and Wu, J and Xie, H and Xu, H and Liang, D and He, Q and Yang, X and Liu, C and Gong, J and Zhang, Q and Luo, Z and Chen, Y and He, Z and Lan, P}, title = {Enteral nutrition promotes the remission of colitis by gut bacteria-mediated histidine biosynthesis.}, journal = {EBioMedicine}, volume = {100}, number = {}, pages = {104959}, doi = {10.1016/j.ebiom.2023.104959}, pmid = {38215690}, issn = {2352-3964}, abstract = {BACKGROUND: Exclusive enteral nutrition (EEN) is an important alternative strategy for patients with Crohn's disease (CD), and during this process, microbiota alterations have been observed. However, the underlying mechanisms by which EEN reduces intestinal inflammation are currently unclear.

METHODS: The therapeutic potential of enteral nutrition (EN) was assessed using various mouse models. Fecal full-length 16S rDNA sequencing analysis and several CD metagenome datasets were used to identify the candidate therapeutic bacteria Faecalibaculum rodentium (F. rodentium). Whole genome sequencing of F. rodentium and widely-targeted metabolome analysis of the supernatant showed that EN-induced F. rodentium accumulation protected against colitis via histidine biosynthesis.

FINDINGS: The therapeutic potential of EN therapy was observed in both dextran sulfate sodium (DSS)-induced colitis and Il10[-/-] spontaneous colitis mouse models. Accumulation of F. rodentium after EN therapy was determined using full-length 16S rDNA sequencing and verified with several metagenome datasets from patients with CD. Colonization of an isolated F. rodentium could reduce colitis in Il10[-/-] mice. Significant histidine enrichment was observed in the F. rodentium culture supernatant, and a series of histidine biosynthesis genes were observed in the F. rodentium genome. Engineered Escherichia coli Nissle 1917 (EcN), encoding the heterologous hisG of F. rodentium (EcN-hisG), which was a key driver of histidine biosynthesis in F. rodentium, was found to protect against colitis.

INTERPRETATION: This study suggests that EN-induced F. rodentium accumulation protects against colitis in mice via gut bacteria-mediated histidine biosynthesis.

FUNDING: A full list of funding bodies can be found in the Acknowledgements section.}, } @article {pmid38215548, year = {2024}, author = {Ottinger, S and Robertson, CM and Branthoover, H and Patras, KA}, title = {The human vaginal microbiota: from clinical medicine to models to mechanisms.}, journal = {Current opinion in microbiology}, volume = {77}, number = {}, pages = {102422}, doi = {10.1016/j.mib.2023.102422}, pmid = {38215548}, issn = {1879-0364}, abstract = {The composition of the vaginal microbiota is linked to numerous reproductive health problems, including increased susceptibility to infection, pregnancy complications, and impaired vaginal tissue repair; however, the mechanisms contributing to these adverse outcomes are not yet fully defined. In this review, we highlight recent clinical advancements associating vaginal microbiome composition and function with health outcomes. Subsequently, we provide a summary of emerging models employed to identify microbe-microbe interactions contributing to vaginal health, including metagenomic sequencing, multi-omics approaches, and advances in vaginal microbiota cultivation. Last, we review new in vitro, ex vivo, and in vivo models, such as organoids and humanized microbiota murine models, used to define and mechanistically explore host-microbe interactions at the vaginal mucosa.}, } @article {pmid38214875, year = {2024}, author = {de Paula, RS and E Souza, CC and Gonçalves, CAX and de Holanda Moura, MV and Guañabens, ACP and Andrade, GR and Nascimento, AMA and Cardoso, AV and de Paula Reis, M and Jorge, EC}, title = {Diversity and distribution of iron-oxidising bacteria belonging to Gallionellaceae in different sites of a hydroelectric power plant.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {}, number = {}, pages = {}, pmid = {38214875}, issn = {1678-4405}, support = {GT-604//Companhia Energética de Minas Gerais/ ; }, abstract = {Iron (Fe) is the fourth most abundant element on the planet, and iron-oxidising bacteria (FeOB) play an important role in the biogeochemical cycle of this metal in nature. FeOB stands out as Fe oxidisers in microaerophilic environments, and new members of this group have been increasingly discussed in the literature, even though their isolation can still be challenging. Among these bacteria is the Gallionellaceae family, mainly composed of neutrophilic FeOB, highlighting Gallionella ferruginea, and nitrite-oxidiser genera. In the previous metagenomic study of the biofilm and sediments of the cooling system from the Irapé hydroelectric power plant (HPP-Irapé), 5% of the total bacteria sequences were related to Gallionellaceae, being 99% unclassified at genus level. Thus, in the present study, a phylogenetic tree based on this family was constructed, in order to search for shared and unique Gallionellaceae signatures in a deep phylogenetic level affiliation and correlated them with geomorphologic characteristics. The results revealed that Gallionella and Ferrigenium were ubiquitous reflecting their ability to adapt to various locations in the power plant. The cave was considered a hotspot for neutrophilic FeOB since it harboured most of the Gallionellaceae diversity. Microscopic biosignatures were detected only in the CS1 sample, which presented abundance of the stalk-forming Ferriphaselus and of the sheath-forming Crenothrix. Further studies are required to provide more detailed insights on Gallionellaceae distribution and diversity patterns in hydroelectric power plants, particularly its biotechnological potential in this industry.}, } @article {pmid38214730, year = {2024}, author = {Onwusereaka, CO and Jalaludin, J and Oluchi, SE and Poh Choo, VC}, title = {New generation sequencing: molecular approaches for the detection and monitoring of bioaerosols in an indoor environment: a systematic review.}, journal = {Reviews on environmental health}, volume = {}, number = {}, pages = {}, pmid = {38214730}, issn = {2191-0308}, abstract = {INTRODUCTION: The exposure of occupants to indoor air pollutants has increased in recent decades. The aim of this review is to discuss an overview of new approaches that are used to study fungal aerosols. Thus, this motivation was to compensate the gaps caused by the use of only traditional approaches in the study of fungal exposure.

CONTENT: The search involved various databases such as; Science Direct, PubMed, SAGE, Springer Link, EBCOHOST, MEDLINE, CINAHL, Cochrane library, Web of Science and Wiley Online Library. It was limited to full text research articles that reported the use of non-viable method in assessing bioaerosol, written in English Language, full text publications and published from year 2015-2022.

SUMMARY AND OUTLOOK: A total of 15 articles met the inclusion criteria and was included in this review. The use of next-generation sequencing, which is more commonly referred to as high-throughput sequencing (HTS) or molecular methods in microbial studies is based on the detection of genetic material of organisms present in a given sample. Applying these methods to different environments permitted the identification of the microorganisms present, and a better comprehension of the environmental impacts and ecological roles of microbial communities. Based on the reviewed articles, there is evidence that dust samples harbour a high diversity of human-associated bacteria and fungi. Molecular methods such as next generation sequencing are reliable tools for identifying and tracking the bacterial and fungal diversity in dust samples using 18S metagenomics approach.}, } @article {pmid38214674, year = {2024}, author = {Zhang, H and Zhang, H and Du, H and Yu, X and Xu, Y}, title = {The insights into the phage communities of fermented foods in the age of viral metagenomics.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/10408398.2023.2299323}, pmid = {38214674}, issn = {1549-7852}, abstract = {Phages play a critical role in the assembly and regulation of fermented food microbiome through lysis and lysogenic lifestyle, which in turn affects the yield and quality of fermented foods. Therefore, it is important to investigate and characterize the diversity and function of phages under complex microbial communities and nutrient substrate conditions to provide novel insights into the regulation of traditional spontaneous fermentation. Viral metagenomics has gradually garnered increasing attention in fermented food research to elucidate phage functions and characterize the interactions between phages and the microbial community. Advances in this technology have uncovered a wide range of phages associated with the production of traditional fermented foods and beverages. This paper reviews the common methods of viral metagenomics applied in fermented food research, and summarizes the ecological functions of phages in traditional fermented foods. In the future, combining viral metagenomics with culturable methods and metagenomics will broaden the scope of research on fermented food systems, revealing the complex role of phages and intricate phage-bacterium interactions.}, } @article {pmid38213715, year = {2024}, author = {Shimizu, K and Hirata, H and Tokuhira, N and Motooka, D and Nakamura, S and Ueda, A and Tachino, J and Koide, M and Uchiyama, A and Ogura, H and Oda, J}, title = {Dysbiosis of gut microbiota in patients with severe COVID-19.}, journal = {Acute medicine & surgery}, volume = {11}, number = {1}, pages = {e923}, pmid = {38213715}, issn = {2052-8817}, abstract = {AIM: Altered gut microbiota has been proposed as one of the causes of exacerbation of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2/COVID-19) from the perspective of the gut-lung axis. We aimed to evaluate gut microbiota in mechanically ventilated patients with COVID-19 prior to using antibiotics.

METHODS: We retrospectively selected for enrollment COVID-19 patients who required mechanical ventilation on admission but who had not used antibiotics before admission to observe the influence of SARS-Cov-2 on gut microbiota. Fecal samples were collected serially on admission and were evaluated by 16S rRNA gene deep sequencing.

RESULTS: The phylum of Bacteroidetes decreased, and those of Firmicutes and Actinobacteria increased in COVID-19 patients compared with those in healthy controls (p < 0.001). The main commensals of Bacteroides, Faecalibacterium, and Blautia at the genus level were significantly decreased in the COVID-19 patients, and opportunistic bacteria including Corynebacterium, Anaerococcus, Finegoldia Peptoniphilus, Actinomyces, and Enterococcus were increased (p < 0.001). α-Diversity and β-diversity in COVID-19 patients significantly changed compared with those in the healthy controls.

CONCLUSION: The commensal gut microbiota were altered, and opportunistic bacteria increased in patients with severe COVID-19 who required mechanical ventilation on admission.}, } @article {pmid38213395, year = {2024}, author = {Khan, T and Song, W and Nappi, J and Marzinelli, EM and Egan, S and Thomas, T}, title = {Functional guilds and drivers of diversity in seaweed-associated bacteria.}, journal = {FEMS microbes}, volume = {5}, number = {}, pages = {xtad023}, pmid = {38213395}, issn = {2633-6685}, abstract = {Comparisons of functional and taxonomic profiles from bacterial communities in different habitats have suggested the existence of functional guilds composed of taxonomically or phylogenetically distinct members. Such guild membership is, however, rarely defined and the factors that drive functional diversity in bacteria remain poorly understood. We used seaweed-associated bacteria as a model to shed light on these important aspects of community ecology. Using a large dataset of over 1300 metagenome-assembled genomes from 13 seaweed species we found substantial overlap in the functionality of bacteria coming from distinct taxa, thus supporting the existence of functional guilds. This functional equivalence between different taxa was particularly pronounced when only functions involved in carbohydrate degradation were considered. We further found that bacterial taxonomy is the dominant driver of functional differences between bacteria and that seaweed species or seaweed type (i.e. brown, red and green) had relatively stronger impacts on genome functionality for carbohydrate-degradation functions when compared to all other cellular functions. This study provides new insight into the factors underpinning the functional diversity of bacteria and contributes to our understanding how community function is generated from individual members.}, } @article {pmid38212694, year = {2024}, author = {Marić, J and Križanović, K and Riondet, S and Nagarajan, N and Šikić, M}, title = {Comparative analysis of metagenomic classifiers for long-read sequencing datasets.}, journal = {BMC bioinformatics}, volume = {25}, number = {1}, pages = {15}, pmid = {38212694}, issn = {1471-2105}, support = {KK.01.1.1.01.0009//European Regional Development Fund/ ; HRZZ-IP-2018-01-5886//Croatian Science Fundation/ ; MOH-000649-01//National Medical Research Council, Singapore/ ; }, mesh = {Sequence Analysis, DNA ; *High-Throughput Nucleotide Sequencing ; *Metagenome ; Metagenomics ; Databases, Protein ; Nucleotides ; }, abstract = {BACKGROUND: Long reads have gained popularity in the analysis of metagenomics data. Therefore, we comprehensively assessed metagenomics classification tools on the species taxonomic level. We analysed kmer-based tools, mapping-based tools and two general-purpose long reads mappers. We evaluated more than 20 pipelines which use either nucleotide or protein databases and selected 13 for an extensive benchmark. We prepared seven synthetic datasets to test various scenarios, including the presence of a host, unknown species and related species. Moreover, we used available sequencing data from three well-defined mock communities, including a dataset with abundance varying from 0.0001 to 20% and six real gut microbiomes.

RESULTS: General-purpose mappers Minimap2 and Ram achieved similar or better accuracy on most testing metrics than best-performing classification tools. They were up to ten times slower than the fastest kmer-based tools requiring up to four times less RAM. All tested tools were prone to report organisms not present in datasets, except CLARK-S, and they underperformed in the case of the high presence of the host's genetic material. Tools which use a protein database performed worse than those based on a nucleotide database. Longer read lengths made classification easier, but due to the difference in read length distributions among species, the usage of only the longest reads reduced the accuracy. The comparison of real gut microbiome datasets shows a similar abundance profiles for the same type of tools but discordance in the number of reported organisms and abundances between types. Most assessments showed the influence of database completeness on the reports.

CONCLUSION: The findings indicate that kmer-based tools are well-suited for rapid analysis of long reads data. However, when heightened accuracy is essential, mappers demonstrate slightly superior performance, albeit at a considerably slower pace. Nevertheless, a combination of diverse categories of tools and databases will likely be necessary to analyse complex samples. Discrepancies observed among tools when applied to real gut datasets, as well as a reduced performance in cases where unknown species or a significant proportion of the host genome is present in the sample, highlight the need for continuous improvement of existing tools. Additionally, regular updates and curation of databases are important to ensure their effectiveness.}, } @article {pmid38212658, year = {2024}, author = {Ning, D and Wang, Y and Fan, Y and Wang, J and Van Nostrand, JD and Wu, L and Zhang, P and Curtis, DJ and Tian, R and Lui, L and Hazen, TC and Alm, EJ and Fields, MW and Poole, F and Adams, MWW and Chakraborty, R and Stahl, DA and Adams, PD and Arkin, AP and He, Z and Zhou, J}, title = {Environmental stress mediates groundwater microbial community assembly.}, journal = {Nature microbiology}, volume = {}, number = {}, pages = {}, pmid = {38212658}, issn = {2058-5276}, support = {DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; DE-AC02-05CH11231//DOE | SC | Biological and Environmental Research (BER)/ ; EF-2025558//National Science Foundation (NSF)/ ; DEB-2129235//National Science Foundation (NSF)/ ; EF-2025558//National Science Foundation (NSF)/ ; DEB-2129235//National Science Foundation (NSF)/ ; EF-2025558//National Science Foundation (NSF)/ ; }, abstract = {Community assembly describes how different ecological processes shape microbial community composition and structure. How environmental factors impact community assembly remains elusive. Here we sampled microbial communities and >200 biogeochemical variables in groundwater at the Oak Ridge Field Research Center, a former nuclear waste disposal site, and developed a theoretical framework to conceptualize the relationships between community assembly processes and environmental stresses. We found that stochastic assembly processes were critical (>60% on average) in shaping community structure, but their relative importance decreased as stress increased. Dispersal limitation and 'drift' related to random birth and death had negative correlations with stresses, whereas the selection processes leading to dissimilar communities increased with stresses, primarily related to pH, cobalt and molybdenum. Assembly mechanisms also varied greatly among different phylogenetic groups. Our findings highlight the importance of microbial dispersal limitation and environmental heterogeneity in ecosystem restoration and management.}, } @article {pmid38212429, year = {2024}, author = {Cheng, S and Cui, H and Zhang, J and Wang, Q and Duan, Z}, title = {Probiotic potential of Lacticaseibacillus rhamnosus VHProbi M15 on sucralfate-induced constipation in mice.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {1131}, pmid = {38212429}, issn = {2045-2322}, support = {Grant No. tscy20180317//Mountain Tai New Strategy Industry Leader Program/ ; }, mesh = {Mice ; Animals ; *Lacticaseibacillus rhamnosus ; Sucralfate/adverse effects ; RNA, Ribosomal, 16S ; Constipation/chemically induced/drug therapy ; *Probiotics/pharmacology/therapeutic use ; Phenolphthaleins/adverse effects ; Substance P/*analogs & derivatives ; Galanin/*analogs & derivatives ; }, abstract = {The main objective of this study was to investigate the potential probiotic properties of Lacticaseibacillus rhamnosus VHProbi®M15 (M15). This study examined the effects of M15 on sucralfate-induced constipation in a mouse model. The BALB/c mice were randomly divided into four groups: the normal group (NOR) was without any treatment, while the constipation (CON), phenolphthalein (PHE), and probiotic (PRO) treatment groups were fed with sucralfate until the appearance of constipation symptoms. Afterward, the NOR and CON groups were given 1 ml saline orally every day until the end of the experiment; the PHE and PRO groups were given phenolphthalein or M15 suspension in 1 ml orally, respectively. Compared with the CON group, the fecal water content and intestinal peristalsis improved in the PRO group. Here, intake of M15 effectively attenuated sucralfate-induced constipation, recuperated colonic epithelial integrity, and increased serum levels of gastrointestinal excitatory neurotransmitters (motilin, gastrin, substance P). Analysis of the intestinal microbiota of mice by 16S rRNA metagenomic revealed an increase in the relative abundance of Bacteroides and a decrease in Sclerotinia, Verrucosa and Proteus in the PRO group. Compared with the CON group, the constipation-induced intestinal microecological changes were partially recovered in the PHE and PRO groups. These results demonstrate that M15 enhanced gastrointestinal transit and alleviated in mice with sucralfate-induced constipation.}, } @article {pmid38212383, year = {2024}, author = {Haytham, H and Kamel, C and Wafa, D and Salma, F and Naima, BM and George, T and Ameur, C and Msaad Guerfali, M}, title = {Probiotic consortium modulating the gut microbiota composition and function of sterile Mediterranean fruit flies.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {1058}, pmid = {38212383}, issn = {2045-2322}, support = {PRFD6P2/2019//Ministère de l'Enseignement Supérieur et de la Recherche Scientifique, Tunisie/ ; }, mesh = {Male ; Animals ; *Ceratitis capitata/physiology ; *Gastrointestinal Microbiome ; Enterobacter/physiology ; Reproduction ; Larva/physiology ; *Probiotics ; Pest Control, Biological/methods ; }, abstract = {The sterile insect technique (SIT) remains a successful approach in managing pest insects. However, the long-term mass rearing and sterilizing radiation associated with SIT have been observed to induce physiological and ecological fitness decline in target insects. This decline may be attributed to various factors, including commensal microbiota dysbiosis, selection procedures, loss of heterozygosity, and other complex interactions.. There is evidence that the bacterial symbiont of insects may play critical roles in digestion, development, reproduction, and behavior. Probiotics are an increasingly common approach for restoring the intestinal microbiota structure and fitness parameters of sterile insects, particularly in the Vienna 8 genetic sexing strain (V8-GSS) of the Mediterranean fruit fly (medfly), Ceratitis capitata. Here, we explore the influence of the previously isolated bacterial strain, Lactococcus lactis, Enterobacter sp., and Klebsiella oxytoca, administration as probiotic consortia (LEK-PC) to the larvae and/or adult diet over the course of 20 rearing generations on fitness parameters. The experiment was carried out in four colonies: a control colony (C), one to which probiotics were not added, one to which probiotics were added to the larval medium (L+), one to which probiotics were added to the adult medium (A+), and one to which probiotics were added to both the larval and adult mediums (AL+). Emergence, flight ability, survival under stress conditions, and mating competitiveness, were all significantly improved by the LEK-PC treatment independently of the administration stage. The intestinal microbiota structure of various medfly V8-GSS colonies also underwent a significant shift, despite the fact that the core microbial community was unaffected by the LEK-PC administration stage, according to 16S metagenomics sequencing. Comparison of the metabolic function prediction and associated carbohydrate enzymes among colonies treated with "LEK-PC" showed an enrichment of metabolic functions related to carbohydrates, amino acids, cofactors, and vitamins metabolism, as well as, glycoside hydrolase enzymes in the AL+ colony compared to the control. This study enriches the knowledge regarding the benefits of probiotic treatment to modulate and restore the intestinal microbiota of C. capitata sterile males for a better effectiveness of the SIT.}, } @article {pmid38211536, year = {2023}, author = {Díaz-García, L and Chuvochina, M and Feuerriegel, G and Bunk, B and Spröer, C and Streit, WR and Rodriguez-R, LM and Overmann, J and Jiménez, DJ}, title = {Andean soil-derived lignocellulolytic bacterial consortium as a source of novel taxa and putative plastic-active enzymes.}, journal = {Systematic and applied microbiology}, volume = {47}, number = {1}, pages = {126485}, doi = {10.1016/j.syapm.2023.126485}, pmid = {38211536}, issn = {1618-0984}, abstract = {An easy and straightforward way to engineer microbial environmental communities is by setting up liquid enrichment cultures containing a specific substrate as the sole source of carbon. Here, we analyzed twenty single-contig high-quality metagenome-assembled genomes (MAGs) retrieved from a microbial consortium (T6) that was selected by the dilution-to-stimulation approach using Andean soil as inoculum and lignocellulose as a selection pressure. Based on genomic metrics (e.g., average nucleotide and amino acid identities) and phylogenomic analyses, 15 out of 20 MAGs were found to represent novel bacterial species, with one of those (MAG_26) belonging to a novel genus closely related to Caenibius spp. (Sphingomonadaceae). Following the rules and requirements of the SeqCode, we propose the name Andeanibacterium colombiense gen. nov., sp. nov. for this taxon. A subsequent functional annotation of all MAGs revealed that MAG_7 (Pseudobacter hemicellulosilyticus sp. nov.) contains 20, 19 and 16 predicted genes from carbohydrate-active enzymes families GH43, GH2 and GH92, respectively. Its lignocellulolytic gene profile resembles that of MAG_2 (the most abundant member) and MAG_3858, both of which belong to the Sphingobacteriaceae family. Using a database that contains experimentally verified plastic-active enzymes (PAZymes), twenty-seven putative bacterial polyethylene terephthalate (PET)-active enzymes (i.e., alpha/beta-fold hydrolases) were detected in all MAGs. A maximum of five putative PETases were found in MAG_3858, and two PETases were found to be encoded by A. colombiense. In conclusion, we demonstrate that lignocellulose-enriched liquid cultures coupled with genome-resolved metagenomics are suitable approaches to unveil the hidden bacterial diversity and its polymer-degrading potential in Andean soil ecosystems.}, } @article {pmid38211474, year = {2023}, author = {Xie, Y and Su, J and Shao, K and Hu, T and Ming, H and Shi, T and Wang, W and Fan, J}, title = {Long-term response of the microbial community to the degradation of DOC released from Undaria pinnatifida.}, journal = {Marine environmental research}, volume = {194}, number = {}, pages = {106313}, doi = {10.1016/j.marenvres.2023.106313}, pmid = {38211474}, issn = {1879-0291}, abstract = {With the aim to study the mechanism underlying the macroalgal carbon sequestration driven by microbes, we investigated the microbial community using metagenomics methods and its long-term degradation of dissolved organic carbon (DOC) derived from Undaria pinnatifida. It was observed that after removing U. pinnatifida, the concentration of the DOC decreased significantly (p < 0.05) within 4 days. Over a period of 120 days of degradation, the concentration of remaining DOC (26%) remained stable. The succession of microbial community corresponded to the three stages of DOC concentration variation. Moreover, the structure of microbes community and its metabolic function exhibited evident patterns of succession. The concentration of DOC was correlated negatively with the abundances of Planctomycetaceae (p < 0.01), and was correlated positively with the abundances of Roseobacteraceae and Rhodobacteraceae (p < 0.01). In addition, the metabolic pathways related to "Glycolysis/Gluconeogenesis", "Alanine, aspartate, and glutamate metabolism", "Citrate cycle (TCA cycle)" and "Tryptophan metabolism" was significantly correlated with the variations in DOC concentration (p < 0.05). These findings indicate that the variation in the DOC concentration was closely linked to the succession of Planctomycetaceae, Roseobacteraceae, Rhodobacteraceae, and the degradation of DOC derived from U. pinnatifida appeared to be influenced by metabolic functions.}, } @article {pmid38206964, year = {2024}, author = {Ghafari, M and Sõmera, M and Sarmiento, C and Niehl, A and Hébrard, E and Tsoleridis, T and Ball, J and Moury, B and Lemey, P and Katzourakis, A and Fargette, D}, title = {Revisiting the origins of the Sobemovirus genus: A case for ancient origins of plant viruses.}, journal = {PLoS pathogens}, volume = {20}, number = {1}, pages = {e1011911}, doi = {10.1371/journal.ppat.1011911}, pmid = {38206964}, issn = {1553-7374}, abstract = {The discrepancy between short- and long-term rate estimates, known as the time-dependent rate phenomenon (TDRP), poses a challenge to extrapolating evolutionary rates over time and reconstructing evolutionary history of viruses. The TDRP reveals a decline in evolutionary rate estimates with the measurement timescale, explained empirically by a power-law rate decay, notably observed in animal and human viruses. A mechanistic evolutionary model, the Prisoner of War (PoW) model, has been proposed to address TDRP in viruses. Although TDRP has been studied in animal viruses, its impact on plant virus evolutionary history remains largely unexplored. Here, we investigated the consequences of TDRP in plant viruses by applying the PoW model to reconstruct the evolutionary history of sobemoviruses, plant pathogens with significant importance due to their impact on agriculture and plant health. Our analysis showed that the Sobemovirus genus dates back over four million years, indicating an ancient origin. We found evidence that supports deep host jumps to Poaceae, Fabaceae, and Solanaceae occurring between tens to hundreds of thousand years ago, followed by specialization. Remarkably, the TDRP-corrected evolutionary history of sobemoviruses was extended far beyond previous estimates that had suggested their emergence nearly 9,000 years ago, a time coinciding with the Neolithic period in the Near East. By incorporating sequences collected through metagenomic analyses, the resulting phylogenetic tree showcases increased genetic diversity, reflecting a deep history of sobemovirus species. We identified major radiation events beginning between 4,600 to 2,000 years ago, which aligns with the Neolithic period in various regions, suggesting a period of rapid diversification from then to the present. Our findings make a case for the possibility of deep evolutionary origins of plant viruses.}, } @article {pmid38206690, year = {2023}, author = {Huang, Y and Xia, L and Shen, W and Fu, T}, title = {A case report: Infection-related glomerulonephritis and mantle cell lymphoma due to mycobacterium avium complex infection.}, journal = {Medicine}, volume = {102}, number = {52}, pages = {e35620}, pmid = {38206690}, issn = {1536-5964}, mesh = {Male ; Humans ; Adult ; Aged ; Mycobacterium avium Complex ; *Mycobacterium avium-intracellulare Infection/complications/diagnosis/drug therapy ; *Lymphoma, Mantle-Cell ; *Glomerulonephritis/etiology ; *Peritonitis/microbiology ; }, abstract = {RATIONALE: Mycobacterium avium complex (MAC) infection is common in lung, liver and skin. However, MAC presenting with peritonitis is uncommon and is particularly rare in immunocompetent patients. We report a case of infection-associated glomerulonephritis and mantle cell lymphoma caused by peritonitis due to MAC.

PATIENT CONCERNS: We report a case of a 73-year-old elderly man with fever and abdominal pain for 2 days and gradually developed anuria, ascites, and abdominal lymphadenopathy.

DIAGNOSES: The initial diagnosis was peritonitis and acute renal failure. There was no significant relief of symptoms after empirical anti-infective therapy and hemodialysis. infection-associated glomerulonephritis, mantle cell lymphoma, and peritonitis due to MAC were diagnosed by renal biopsy, abdominal lymph node biopsy, and metagenomics next-generation sequencing.

INTERVENTIONS: The patient received empirical antibiotic therapy, hemodialysis, and anti-MAC therapy.

OUTCOMES: Unfortunately, the patient eventually died of septic shock after the 21st day of admissiom.

LESSONS: Early diagnosis of MAC infection is essential. When the cause of fever is unknown, metagenomics next-generation sequencing can be considered.}, } @article {pmid38206097, year = {2024}, author = {Dineen, RL and Bottacini, F and O'Connell-Motherway, M and van Sinderen, D}, title = {Transcriptional landscape of the pMP7017 megaplasmid and its impact on the Bifidobacterium breve UCC2003 transcriptome.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {e14405}, doi = {10.1111/1751-7915.14405}, pmid = {38206097}, issn = {1751-7915}, support = {SFI 12/RC/2273/SFI_/Science Foundation Ireland/Ireland ; }, abstract = {The 190 kb megaplasmid pMP7017 of Bifidobacterium breve JCM7017 represents the first conjugative and largest plasmid characterised within this genus to date. In the current study, we adopted an integrated approach combining transcriptomics, whole genome comparative analysis and metagenomic data mining to understand the biology of pMP7017 and related megaplasmids, and to assess the impact of plasmid-carriage on the host strain. The data generated revealed variations within basic features of promoter elements which correlate with a high level of transcription on the plasmid and highlight the transcriptional activity of genes encoding both offensive and defensive adaptations, including a Type IIL restriction-modification system, an anti-restriction system and four Type II toxin-antitoxin systems. Furthermore, a highly transcribed tmRNA, which likely provides translational support to the host strain, was identified, making pMP7017 the first plasmid of the Bifidobacterium genus and the smallest plasmid known to express a tmRNA. Analyses of synteny and variability among pMP7017 and related plasmids indicate substantial diversity in gene organisation and accessory gene cargo highlighting diverse (co-)evolution and potential host-specific rearrangements and adaptations. Systematic analysis of the codon usage profile of transcriptionally active pMP7017-encoded genes suggests that pMP7017 originated from (sub)species of Bifidobacterium longum. Furthermore, mining of metagenomic data suggests the presence of pMP7017-homologues in ~10% of microbiome samples, mostly infants and/or mothers from various geographical locations. Comparative transcriptome analysis of the B. breve UCC2003 chromosome in the presence or absence of pMP7017 revealed differential expression of genes representing 8% of the total gene pool. Genes involved in genetic information processing were exclusively upregulated, while altered expression of genes involved in biofilm production and polysaccharide biosynthesis was also observed.}, } @article {pmid38206014, year = {2024}, author = {Nothias, L-F and Schmid, R and Garlet, A and Cameron, H and Leoty-Okombi, S and André-Frei, V and Fuchs, R and Dorrestein, PC and Ternes, P}, title = {Functional metabolomics of the human scalp: a metabolic niche for Staphylococcus epidermidis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0035623}, doi = {10.1128/msystems.00356-23}, pmid = {38206014}, issn = {2379-5077}, abstract = {Systems biology research on host-associated microbiota focuses on two fundamental questions: which microbes are present and how do they interact with each other, their host, and the broader host environment? Metagenomics provides us with a direct answer to the first part of the question: it unveils the microbial inhabitants, e.g., on our skin, and can provide insight into their functional potential. Yet, it falls short in revealing their active role. Metabolomics shows us the chemical composition of the environment in which microbes thrive and the transformation products they produce. In particular, untargeted metabolomics has the potential to observe a diverse set of metabolites and is thus an ideal complement to metagenomics. However, this potential often remains underexplored due to the low annotation rates in MS-based metabolomics and the necessity for multiple experimental chromatographic and mass spectrometric conditions. Beyond detection, prospecting metabolites' functional role in the host/microbiome metabolome requires identifying the biological processes and entities involved in their production and biotransformations. In the present study of the human scalp, we developed a strategy to achieve comprehensive structural and functional annotation of the metabolites in the human scalp environment, thus diving one step deeper into the interpretation of "omics" data. Leveraging a collection of openly accessible software tools and integrating microbiome data as a source of functional metabolite annotations, we finally identified the specific metabolic niche of Staphylococcus epidermidis, one of the key players of the human skin microbiome.}, } @article {pmid38205047, year = {2023}, author = {Ugyen, U and Singanusong, R and Phinyo, M and Changtor, P and Chaijamrus, S and Thongsook, T}, title = {Extraction of Heat-Stabilised Defatted Rice Bran Protein by Solid-State Fermentation Using Heterofermentative Microbes from Traditional Asian Starters.}, journal = {Food technology and biotechnology}, volume = {61}, number = {4}, pages = {523-535}, pmid = {38205047}, issn = {1330-9862}, abstract = {RESEARCH BACKGROUND: Heat-stabilised defatted rice bran (HSDRB) is a primary by-product of rice bran oil extraction industry and a nutritious source of protein. However, despite the unique nutritional profile of rice bran protein, the protein-rich by-product, HSDRB is underutilised as a low-value animal feed. Research on protein extraction from HSDRB by enzymatic hydrolysis has attracted the attention of numerous scientists. However, a cost-effective extraction method is required to mitigate the high costs associated with the use of enzymes. Therefore, we have presented an alternative economical and natural approach for protein extraction from HSDRB by solid-state fermentation (SSF) with heterofermentative microbes.

EXPERIMENTAL APPROACH: SSF of HSDRB with two types of traditional Asian fermentation starters, namely loog-pang and koji, were evaluated for enzyme production and their efficacy in extracting proteins from HSDRB. For this purpose, HSDRB fermentation was carried out for 0, 12, 24, 48, 72 and 96 h followed by 24-hour hydrolysis to evaluate the extracted rice bran protein. In addition, microbiome diversity in the fermentation starters was also determined by metagenomic sequencing of 16S rRNA and internal transcribed spacer to identify bacteria and fungi, respectively.

RESULTS AND CONCLUSIONS: The microbial community in the fermentation starters showed the dominance of lactic acid bacteria (LAB) such as Bacillus subtilis in loog-pang and Streptococcus lutetiensis, Bacillus pumilus, Lactococcus cremoris, Lactococcus garvieae and Pediococcus pentosaceus in koji, while yeast species Saccharomycopsis fibuligera and Saccharomyces cerevisiae dominated the fungal diversity in loog-pang and koji starters, respectively. The results suggest that loog-pang and koji can produce cellulase, neutral and acid proteases during fermentation. Despite the discrepancy in their microbial diversity and the enzyme activity during SSF, both starters could effectively increase protein extraction from HSDRB. A positive relationship between the SSF duration and extracted protein was observed. During SSF with loog-pang and koji after 72 h followed by 24-hour hydrolysis, 65.66 and 66.67 % protein was extracted from HSDRB, respectively. The amino acid analysis of the protein hydrolysate produced by the non-fermented and fermented methods showed no difference and had an abundance of glutamic and aspartic acids, leucine, arginine, alanine and glycine amino acids, which accounted for approx. 58 % of the total amino acids.

Loog-pang and koji (traditional Thai and Japanese fermentation starters, respectively) were found to be effective in extracting proteins from HSDRB by SSF although they are inexpensive microbial enzyme sources. Future research aimed at scaling up HSDRB protein extraction for usage in industrial applications can draw on our results.}, } @article {pmid38204360, year = {2024}, author = {Kiran, A and Hanachi, M and Alsayed, N and Fassatoui, M and Oduaran, OH and Allali, I and Maslamoney, S and Meintjes, A and Zass, L and Rocha, JD and Kefi, R and Benkahla, A and Ghedira, K and Panji, S and Mulder, N and Fadlelmola, FM and Souiai, O}, title = {The African Human Microbiome Portal: a public web portal of curated metagenomic metadata.}, journal = {Database : the journal of biological databases and curation}, volume = {2024}, number = {}, pages = {}, pmid = {38204360}, issn = {1758-0463}, support = {H3ABioNet U24HG006941//The National Human Genome Research Institute of the National Institutes of Health/ ; H3ABioNet U24HG006941//The National Human Genome Research Institute of the National Institutes of Health/ ; }, mesh = {Humans ; *Metadata ; Metagenome ; Databases, Factual ; Metagenomics ; *Microbiota/genetics ; }, abstract = {There is growing evidence that comprehensive and harmonized metadata are fundamental for effective public data reusability. However, it is often challenging to extract accurate metadata from public repositories. Of particular concern is the metagenomic data related to African individuals, which often omit important information about the particular features of these populations. As part of a collaborative consortium, H3ABioNet, we created a web portal, namely the African Human Microbiome Portal (AHMP), exclusively dedicated to metadata related to African human microbiome samples. Metadata were collected from various public repositories prior to cleaning, curation and harmonization according to a pre-established guideline and using ontology terms. These metadata sets can be accessed at https://microbiome.h3abionet.org/. This web portal is open access and offers an interactive visualization of 14 889 records from 70 bioprojects associated with 72 peer reviewed research articles. It also offers the ability to download harmonized metadata according to the user's applied filters. The AHMP thereby supports metadata search and retrieve operations, facilitating, thus, access to relevant studies linked to the African Human microbiome. Database URL: https://microbiome.h3abionet.org/.}, } @article {pmid38204131, year = {2024}, author = {Adjeroud, M and Kecha, M and Escuder-Rodríguez, JJ and Becerra, M and González-Siso, MI}, title = {AMWEst, a new thermostable and detergent-tolerant esterase retrieved from the Albian aquifer.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {1-17}, pmid = {38204131}, issn = {1432-0614}, support = {01N01UN060120190002//Algerian Ministry of Higher Education/ ; ED431C2020-08//Xunta de Galicia/ ; }, mesh = {*Esterases/genetics ; *Detergents ; Saccharomyces cerevisiae/genetics ; Amino Acids ; Carbon ; }, abstract = {A fosmid library was constructed with the metagenomic DNA from the high-temperature sediment-rich water of the Albian aquifer (Algeria). Functional screening of this library was subsequently done looking for genes encoding lipolytic enzymes. We identified a novel gene named AMWEst (1209 base pairs) encoding a protein of 402 amino acids with a predicted molecular weight of 43.44 kDa and conferring esterase activity. AMWEst was successfully overexpressed in the yeast mesophilic host Saccharomyces cerevisiae, and the expression system used proved to be efficient and produced sufficient activity for its biochemical characterization. Multiple sequence alignment indicated that AMWEst contained a conserved pentapeptide motif (Gly120-His121-Ser122-Gln123-Gly124). The optimum pH and temperature of the recombinant esterase AMWEst were 8 and 80 °C, respectively. Additionally, AMWEst showed higher activity towards short carbon substrates and showed maximum activity for p-nitrophenyl hexanoate (C6). Notably, AMWEst has a remarkable thermostability, and the enzyme retains almost maximum activity at 70 °C after incubation for 1 h. Moreover, enzyme activity was enhanced by high concentrations of SDS and Triton X-100 detergents. KEY POINTS: • A novel thermostable esterase has been retrieved through functional metagenomics • The esterase is detergent-tolerant, which is attractive for some applications • The esterase can be expressed in a yeast mesophilic host to enhance its yield.}, } @article {pmid38203738, year = {2024}, author = {Brīvība, M and Silamiķele, L and Birzniece, L and Ansone, L and Megnis, K and Silamiķelis, I and Pelcmane, L and Borisova, D and Rozenberga, M and Jagare, L and Elbere, I and Kloviņš, J}, title = {Gut Microbiome Composition and Dynamics in Hospitalized COVID-19 Patients and Patients with Post-Acute COVID-19 Syndrome.}, journal = {International journal of molecular sciences}, volume = {25}, number = {1}, pages = {}, pmid = {38203738}, issn = {1422-0067}, support = {1.1.1.1/21/A/029//European Regional Development Fund/ ; }, mesh = {Humans ; *COVID-19 ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Post-Acute COVID-19 Syndrome ; Patients ; Clostridiales ; }, abstract = {The gut microbiome plays a pivotal role in the modulation of host responses during viral infections, and recent studies have underscored its significance in the context of coronavirus disease 2019 (COVID-19). We aimed to investigate the dynamics and compositional changes in the gut microbiome of COVID-19 patients, addressing both the acute phase and the recovery process, with a particular focus on the emergence of post-COVID-19 conditions. Involving 146 COVID-19 patients and 110 healthy controls, this study employed a shotgun metagenomics approach for cross-sectional and longitudinal analyses with one- and three-month follow-ups. We observed a decline in taxonomic diversity among hospitalized COVID-19 patients compared to healthy controls, while a subsequent increase in alpha diversity was shown during the recovery process. A notable contribution of Enterococcus faecium was identified in the acute phase of the infection, accompanied by an increasing abundance of butyrate-producing bacteria (e.g., Roseburia, Lachnospiraceae_unclassified) during the recovery period. We highlighted a protective role of the Prevotella genus in the long-term recovery process and suggested a potential significance of population-specificity in the early gut microbiome markers of post-acute COVID-19 syndrome. Our study represents distinctive gut microbiome signatures in COVID-19, with potential diagnostic and prognostic implications, pinpointing potential modulators of the disease progression.}, } @article {pmid38203712, year = {2023}, author = {Jean Wilson, E and Sirpu Natesh, N and Ghadermazi, P and Pothuraju, R and Prajapati, DR and Pandey, S and Kaifi, JT and Dodam, JR and Bryan, JN and Lorson, CL and Watrelot, AA and Foster, JM and Mansell, TJ and Joshua Chan, SH and Batra, SK and Subbiah, J and Rachagani, S}, title = {Red Cabbage Juice-Mediated Gut Microbiota Modulation Improves Intestinal Epithelial Homeostasis and Ameliorates Colitis.}, journal = {International journal of molecular sciences}, volume = {25}, number = {1}, pages = {}, pmid = {38203712}, issn = {1422-0067}, support = {R01 CA247763/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Mice ; Mice, Inbred C57BL ; *Gastrointestinal Microbiome ; *Colitis/chemically induced ; *Inflammatory Bowel Diseases ; Homeostasis ; }, abstract = {Gut microbiota plays a crucial role in inflammatory bowel diseases (IBD) and can potentially prevent IBD through microbial-derived metabolites, making it a promising therapeutic avenue. Recent evidence suggests that despite an unclear underlying mechanism, red cabbage juice (RCJ) alleviates Dextran Sodium Sulfate (DSS)-induced colitis in mice. Thus, the study aims to unravel the molecular mechanism by which RCJ modulates the gut microbiota to alleviate DSS-induced colitis in mice. Using C57BL/6J mice, we evaluated RCJ's protective role in DSS-induced colitis through two cycles of 3% DSS. Mice were daily gavaged with PBS or RCJ until the endpoint, and gut microbiota composition was analyzed via shotgun metagenomics. RCJ treatment significantly improved body weight (p ≤ 0.001), survival in mice (p < 0.001) and reduced disease activity index (DAI) scores. Further, RCJ improved colonic barrier integrity by enhancing the expression of protective colonic mucins (p < 0.001) and tight junction proteins (p ≤ 0.01) in RCJ + DSS-treated mice compared to the DSS group. Shotgun metagenomic analysis revealed an enrichment of short-chain fatty acids (SCFAs)-producing bacteria (p < 0.05), leading to increased Peroxisome Proliferator-Activated Receptor Gamma (PPAR-γ) activation (p ≤ 0.001). This, in turn, resulted in repression of the nuclear factor κB (NFκB) signaling pathway, causing decreased production of inflammatory cytokines and chemokines. Our study demonstrates colitis remission in a DSS-induced mouse model, showcasing RCJ as a potential modulator for gut microbiota and metabolites, with promising implications for IBD prevention and treatment.}, } @article {pmid38202388, year = {2023}, author = {Park, JW and Braswell, WE and Kunta, M}, title = {Co-Occurrence Analysis of Citrus Root Bacterial Microbiota under Citrus Greening Disease.}, journal = {Plants (Basel, Switzerland)}, volume = {13}, number = {1}, pages = {}, pmid = {38202388}, issn = {2223-7747}, support = {USDA APHIS Agmt. AP20PPQS&T00C114 and AP22PPQS&T00C127.//Plant Pest and Disease Management and Disaster Prevention Program (PPDMDPP), USDA APHIS Plant Protection Act (PPA) Section 7721/ ; }, abstract = {Candidatus Liberibacter asiaticus (CLas) is associated with Citrus Huanglongbing (HLB), a devastating disease in the US. Previously, we conducted a two-year-long monthly HLB survey by quantitative real-time PCR using root DNA fractions prepared from 112 field grapefruit trees grafted on sour orange rootstock. Approximately 10% of the trees remained CLas-free during the entire survey period. This study conducted 16S metagenomics using the time-series root DNA fractions, monthly prepared during twenty-four consecutive months, followed by microbial co-occurrence network analysis to investigate the microbial factors contributing to the CLas-free phenotype of the aforementioned trees. Based on the HLB status and the time when the trees were first diagnosed as CLas-positive during the survey, the samples were divided into four groups, Stage H (healthy), Stage I (early), II (mid), and III (late) samples. The 16S metagenomics data using Silva 16S database v132 revealed that HLB compromised the diversity of rhizosphere microbiota. At the phylum level, Actinobacteria and Proteobacteria were the predominant bacterial phyla, comprising >93% of total bacterial phyla, irrespective of HLB status. In addition, a temporal change in the rhizosphere microbe population was observed during a two-year-long survey, from which we confirmed that some bacterial families differently responded to HLB disease status. The clustering of the bacterial co-occurrence network data revealed the presence of a subnetwork composed of Streptomycetaceae and bacterial families with plant growth-promoting activity in Stage H and III samples. These data implicated that the Streptomycetaceae subnetwork may act as a functional unit against HLB.}, } @article {pmid38200851, year = {2023}, author = {Tang, L and Lei, X and Ouyang, K and Wang, L and Qiu, Q and Li, Y and Zang, Y and Liu, C and Zhao, X}, title = {A Glycosyl Hydrolase 30 Family Xylanase from the Rumen Metagenome and Its Effects on In Vitro Ruminal Fermentation of Wheat Straw.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {1}, pages = {}, pmid = {38200851}, issn = {2076-2615}, support = {20221ZDF03017//Central Leading Local Science and Technology Development Special Project/ ; 20224ACB205007//Natural Science Foundation of Jiangxi Province/ ; 20232BBF60009//Key Research and Development Program of Jiangxi Province/ ; }, abstract = {The challenge of wheat straw as a ruminant feed is its low ruminal digestibility. This study investigated the impact of a xylanase called RuXyn, derived from the rumen metagenome of beef cattle, on the in vitro ruminal fermentation of wheat straw. RuXyn encoded 505 amino acids and was categorized within subfamily 8 of the glycosyl hydrolase 30 family. RuXyn was heterologously expressed in Escherichia coli and displayed its highest level of activity at pH 6.0 and 40 °C. RuXyn primarily hydrolyzed xylan, while it did not show any noticeable activity towards other substrates, including carboxymethylcellulose and Avicel. At concentrations of 5 mM, Mn[2+] and dithiothreitol significantly enhanced RuXyn's activity by 73% and 20%, respectively. RuXyn's activity was almost or completely inactivated in the presence of Cu[2+], even at low concentrations. The main hydrolysis products of corncob xylan by RuXyn were xylopentose, xylotriose, and xylotetraose. RuXyn hydrolyzed wheat straw and rice straw more effectively than it did other agricultural by-products. A remarkable synergistic effect was observed between RuXyn and a cellulase cocktail on wheat straw hydrolysis. Supplementation with RuXyn increased dry matter digestibility; acetate, propionate, valerate, and total volatile fatty acid yields; NH3-N concentration, and total bacterial number during in vitro fermentation of wheat straw relative to the control. RuXyn's inactivity at 60 °C and 70 °C was remedied by mutating proline 151 to phenylalanine and aspartic acid 204 to leucine, boosting activity to 20.3% and 21.8% of the maximum activity at the respective temperatures. As an exogenous enzyme preparation, RuXyn exhibits considerable potential to improve ruminal digestion and the utilization of wheat straw in ruminants. As far as we know, this is the first study on a GH30 xylanase promoting the ruminal fermentation of agricultural straws. The findings demonstrate that the utilization of RuXyn can significantly enhance the ruminal digestibility of wheat straw by approximately 10 percentage points. This outcome signifies the emergence of a novel and highly efficient enzyme preparation that holds promise for the effective utilization of wheat straw, a by-product of crop production, in ruminants.}, } @article {pmid38200786, year = {2023}, author = {Lou, C and Chen, Z and Bai, Y and Chai, T and Guan, Y and Wu, B}, title = {Exploring the Microbial Community Structure in the Chicken House Environment by Metagenomic Analysis.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {1}, pages = {}, pmid = {38200786}, issn = {2076-2615}, support = {32102752//National Natural Science Foundation of China Youth Science Foundation/ ; }, abstract = {The environmental conditions of chicken houses play an important role in the growth and development of these animals. The chicken house is an essential place for the formation of microbial aerosols. Microbial aerosol pollution and transmission can affect human and animal health. In this work, we continuously monitored fine particulate matter (PM2.5) in the chicken house environment for four weeks and studied the microbial community structure in the aerosols of the chicken house environment through metagenomic sequencing. Our results found that bacteria, fungi, viruses, and archaea were the main components of PM2.5 in the chicken house environment, accounting for 89.80%, 1.08%, 2.06%, and 0.49%, respectively. Conditional pathogens are a type of bacteria that poses significant harm to animals themselves and to farm workers. We screened ten common conditional pathogens and found that Staphylococcus had the highest relative abundance, while Clostridium contained the most microbial species, up to 456. Basidiomycetes and Ascomycota in fungi showed dramatic changes in relative abundance, and other indexes showed no significant difference. Virulence factors (VF) are also a class of molecules produced by pathogenic microbes that can cause host diseases. The top five virulence factors were found in four groups: FbpABC, HitABC, colibactin, acinetobactin, and capsule, many of which are used for the iron uptake system. In the PM2.5 samples, eight avian viruses were the most significant discoveries, namely Fowl aviadovirus E, Fowl aviadovirus D, Avian leukosis virus, Avian endogenous retrovirus EAV-HP, Avian dependent parvovirus 1, Fowl adenovus, Fowl aviadovirus B, and Avian sarcoma virus. The above results significantly improve our understanding of the microbial composition of PM2.5 in chicken houses, filling a gap on virus composition; they also indicate a potential threat to poultry and to human health. This work provides an important theoretical basis for animal house environmental monitoring and protection.}, } @article {pmid38200759, year = {2023}, author = {Yan, D and Li, G and Zhang, H and Xue, Q and Zhou, C and Jiang, Y and Yin, J and Wang, Z and Zhao, W and Han, W}, title = {Metagenomic Sequencing Revealed Differences in the Composition of Cecal Microbes in Different Breeds of Chickens.}, journal = {Animals : an open access journal from MDPI}, volume = {14}, number = {1}, pages = {}, pmid = {38200759}, issn = {2076-2615}, support = {2021YFD1200803//National Key Research and Development Program of China/ ; JBGS〔2021〕029//"JBGS" Project of Seed Industry Revitalization in Jiangsu Province/ ; }, abstract = {Intestinal microorganisms are closely related to the health, development, and production performance of animals and can also provide basic information for us to fully understand and explore the germplasm characteristics and traits of local chicken breeds. In this experiment, we used five local Chinese chicken breeds as research materials; metagenomic sequencing technology was used to explore the differences in the composition of intestinal microorganisms in different breeds, and it was found that each local chicken breed had unique unigenes, of which Silkies had the most, with a total of 12,948. GO and KEGG analyses found that the biological processes most enriched by differential functional genes include genetic coding, macromolecular transport, protein synthesis, and molecular functions such as glycoprotein binding, protein hydrolysis, etc. Each breed is enriched with specific pathways, such as Anyi tile-like gray chickens, which are enriched with pathways related to disease resistance, while Gamecocks' enrichment is related to amino acid metabolism. Random Forest and LEfSe analyses revealed specific species of intestinal microorganisms in the cecum of different breeds, such as Exiguobacterium, which is associated with melanin deposition in Silkies. Therefore, we infer that gut microorganisms are closely related to the formation of chicken breed characteristics, and the results of this experiment can provide a theoretical basis for the discovery of high-quality traits and the improvement of feeding conditions in the future.}, } @article {pmid38200389, year = {2024}, author = {Ariaeenejad, S and Gharechahi, J and Foroozandeh Shahraki, M and Fallah Atanaki, F and Han, JL and Ding, XZ and Hildebrand, F and Bahram, M and Kavousi, K and Hosseini Salekdeh, G}, title = {Precision enzyme discovery through targeted mining of metagenomic data.}, journal = {Natural products and bioprospecting}, volume = {14}, number = {1}, pages = {7}, pmid = {38200389}, issn = {2192-2195}, abstract = {Metagenomics has opened new avenues for exploring the genetic potential of uncultured microorganisms, which may serve as promising sources of enzymes and natural products for industrial applications. Identifying enzymes with improved catalytic properties from the vast amount of available metagenomic data poses a significant challenge that demands the development of novel computational and functional screening tools. The catalytic properties of all enzymes are primarily dictated by their structures, which are predominantly determined by their amino acid sequences. However, this aspect has not been fully considered in the enzyme bioprospecting processes. With the accumulating number of available enzyme sequences and the increasing demand for discovering novel biocatalysts, structural and functional modeling can be employed to identify potential enzymes with novel catalytic properties. Recent efforts to discover new polysaccharide-degrading enzymes from rumen metagenome data using homology-based searches and machine learning-based models have shown significant promise. Here, we will explore various computational approaches that can be employed to screen and shortlist metagenome-derived enzymes as potential biocatalyst candidates, in conjunction with the wet lab analytical methods traditionally used for enzyme characterization.}, } @article {pmid38200295, year = {2024}, author = {Allentoft, ME and Sikora, M and Refoyo-Martínez, A and Irving-Pease, EK and Fischer, A and Barrie, W and Ingason, A and Stenderup, J and Sjögren, KG and Pearson, A and Sousa da Mota, B and Schulz Paulsson, B and Halgren, A and Macleod, R and Jørkov, MLS and Demeter, F and Sørensen, L and Nielsen, PO and Henriksen, RA and Vimala, T and McColl, H and Margaryan, A and Ilardo, M and Vaughn, A and Fischer Mortensen, M and Nielsen, AB and Ulfeldt Hede, M and Johannsen, NN and Rasmussen, P and Vinner, L and Renaud, G and Stern, A and Jensen, TZT and Scorrano, G and Schroeder, H and Lysdahl, P and Ramsøe, AD and Skorobogatov, A and Schork, AJ and Rosengren, A and Ruter, A and Outram, A and Timoshenko, AA and Buzhilova, A and Coppa, A and Zubova, A and Silva, AM and Hansen, AJ and Gromov, A and Logvin, A and Gotfredsen, AB and Henning Nielsen, B and González-Rabanal, B and Lalueza-Fox, C and McKenzie, CJ and Gaunitz, C and Blasco, C and Liesau, C and Martinez-Labarga, C and Pozdnyakov, DV and Cuenca-Solana, D and Lordkipanidze, DO and En'shin, D and Salazar-García, DC and Price, TD and Borić, D and Kostyleva, E and Veselovskaya, EV and Usmanova, ER and Cappellini, E and Brinch Petersen, E and Kannegaard, E and Radina, F and Eylem Yediay, F and Duday, H and Gutiérrez-Zugasti, I and Merts, I and Potekhina, I and Shevnina, I and Altinkaya, I and Guilaine, J and Hansen, J and Aura Tortosa, JE and Zilhão, J and Vega, J and Buck Pedersen, K and Tunia, K and Zhao, L and Mylnikova, LN and Larsson, L and Metz, L and Yepiskoposyan, L and Pedersen, L and Sarti, L and Orlando, L and Slimak, L and Klassen, L and Blank, M and González-Morales, M and Silvestrini, M and Vretemark, M and Nesterova, MS and Rykun, M and Rolfo, MF and Szmyt, M and Przybyła, M and Calattini, M and Sablin, M and Dobisíková, M and Meldgaard, M and Johansen, M and Berezina, N and Card, N and Saveliev, NA and Poshekhonova, O and Rickards, O and Lozovskaya, OV and Gábor, O and Uldum, OC and Aurino, P and Kosintsev, P and Courtaud, P and Ríos, P and Mortensen, P and Lotz, P and Persson, P and Bangsgaard, P and de Barros Damgaard, P and Vang Petersen, P and Martinez, PP and Włodarczak, P and Smolyaninov, RV and Maring, R and Menduiña, R and Badalyan, R and Iversen, R and Turin, R and Vasilyev, S and Wåhlin, S and Borutskaya, S and Skochina, S and Sørensen, SA and Andersen, SH and Jørgensen, T and Serikov, YB and Molodin, VI and Smrcka, V and Merts, V and Appadurai, V and Moiseyev, V and Magnusson, Y and Kjær, KH and Lynnerup, N and Lawson, DJ and Sudmant, PH and Rasmussen, S and Korneliussen, TS and Durbin, R and Nielsen, R and Delaneau, O and Werge, T and Racimo, F and Kristiansen, K and Willerslev, E}, title = {Population genomics of post-glacial western Eurasia.}, journal = {Nature}, volume = {625}, number = {7994}, pages = {301-311}, pmid = {38200295}, issn = {1476-4687}, support = {U19 AG023122/AG/NIA NIH HHS/United States ; R35 GM142916/GM/NIGMS NIH HHS/United States ; UH2 AG064706/AG/NIA NIH HHS/United States ; U24 AG051129/AG/NIA NIH HHS/United States ; R01 GM138634/GM/NIGMS NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Agriculture/history ; Asia, Western ; Black Sea ; Diploidy ; Europe/ethnology ; *Genetics, Population ; *Genome, Human ; Genotype ; History, Ancient ; *Human Migration/history ; Hunting/history ; *Metagenomics ; Ice Cover ; }, abstract = {Western Eurasia witnessed several large-scale human migrations during the Holocene[1-5]. Here, to investigate the cross-continental effects of these migrations, we shotgun-sequenced 317 genomes-mainly from the Mesolithic and Neolithic periods-from across northern and western Eurasia. These were imputed alongside published data to obtain diploid genotypes from more than 1,600 ancient humans. Our analyses revealed a 'great divide' genomic boundary extending from the Black Sea to the Baltic. Mesolithic hunter-gatherers were highly genetically differentiated east and west of this zone, and the effect of the neolithization was equally disparate. Large-scale ancestry shifts occurred in the west as farming was introduced, including near-total replacement of hunter-gatherers in many areas, whereas no substantial ancestry shifts happened east of the zone during the same period. Similarly, relatedness decreased in the west from the Neolithic transition onwards, whereas, east of the Urals, relatedness remained high until around 4,000 BP, consistent with the persistence of localized groups of hunter-gatherers. The boundary dissolved when Yamnaya-related ancestry spread across western Eurasia around 5,000 BP, resulting in a second major turnover that reached most parts of Europe within a 1,000-year span. The genetic origin and fate of the Yamnaya have remained elusive, but we show that hunter-gatherers from the Middle Don region contributed ancestry to them. Yamnaya groups later admixed with individuals associated with the Globular Amphora culture before expanding into Europe. Similar turnovers occurred in western Siberia, where we report new genomic data from a 'Neolithic steppe' cline spanning the Siberian forest steppe to Lake Baikal. These prehistoric migrations had profound and lasting effects on the genetic diversity of Eurasian populations.}, } @article {pmid38200287, year = {2024}, author = {Malacrinò, A and Böttner, L and Nouere, S and Huber, M and Schäfer, M and Xu, S}, title = {Induced responses contribute to rapid adaptation of Spirodela polyrhiza to herbivory by Lymnaea stagnalis.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {81}, pmid = {38200287}, issn = {2399-3642}, support = {422213951//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 438887884//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 435681637//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; P400PB_186770//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; }, mesh = {Animals ; *Lymnaea ; Herbivory ; *Araceae ; Adaptation, Physiological ; Biological Assay ; }, abstract = {Herbivory-induced responses in plants are typical examples of phenotypic plasticity, and their evolution is thought to be driven by herbivory. However, direct evidence of the role of induced responses in plant adaptive evolution to herbivores is scarce. Here, we experimentally evolve populations of an aquatic plant (Spirodela polyrhiza, giant duckweed) and its native herbivore (Lymnaea stagnalis, freshwater snail), testing whether herbivory drives rapid adaptive evolution in plant populations using a combination of bioassays, pool-sequencing, metabolite analyses, and amplicon metagenomics. We show that snail herbivory drove rapid phenotypic changes, increased herbivory resistance, and altered genotype frequencies in the plant populations. Additional bioassays suggest that evolutionary changes of induced responses contributed to the rapid increase of plant resistance to herbivory. This study provides direct evidence that herbivory-induced responses in plants can be subjected to selection and have an adaptive role by increasing resistance to herbivores.}, } @article {pmid38199973, year = {2024}, author = {Tong, CH and Huo, ZP and Diao, L and Xiao, DY and Zhao, RN and Zeng, ZL and Xiong, WG}, title = {Core and variable antimicrobial resistance genes in the gut microbiomes of Chinese and European pigs.}, journal = {Zoological research}, volume = {45}, number = {1}, pages = {189-200}, doi = {10.24272/j.issn.2095-8137.2023.012}, pmid = {38199973}, issn = {2095-8137}, mesh = {Humans ; Animals ; Swine ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/pharmacology ; Manure ; Drug Resistance, Bacterial/genetics ; *Anti-Infective Agents ; }, abstract = {Monitoring the prevalence of antimicrobial resistance genes (ARGs) is vital for addressing the global crisis of antibiotic-resistant bacterial infections. Despite its importance, the characterization of ARGs and microbiome structures, as well as the identification of indicators for routine ARG monitoring in pig farms, are still lacking, particularly concerning variations in antimicrobial exposure in different countries or regions. Here, metagenomics and random forest machine learning were used to elucidate the ARG profiles, microbiome structures, and ARG contamination indicators in pig manure under different antimicrobial pressures between China and Europe. Results showed that Chinese pigs exposed to high-level antimicrobials exhibited higher total and plasmid-mediated ARG abundances compared to those in European pigs (P<0.05). ANT(6)-Ib, APH(3')-IIIa, and tet(40) were identified as shared core ARGs between the two pig populations. Furthermore, the core ARGs identified in pig populations were correlated with those found in human populations within the same geographical regions. Lactobacillus and Prevotella were identified as the dominant genera in the core microbiomes of Chinese and European pigs, respectively. Forty ARG markers and 43 biomarkers were able to differentiate between the Chinese and European pig manure samples with accuracies of 100% and 98.7%, respectively. Indicators for assessing ARG contamination in Chinese and European pigs also achieved high accuracy (r=0.72-0.88). Escherichia flexneri in both Chinese and European pig populations carried between 21 and 37 ARGs. The results of this study emphasize the importance of global collaboration in reducing antimicrobial resistance risk and provide validated indicators for evaluating the risk of ARG contamination in pig farms.}, } @article {pmid38199682, year = {2024}, author = {Pafčo, B and Nosková, E and Ilík, V and Anettová, L and Červená, B and Kreisinger, J and Pšenková, I and Václavek, P and Vyhlídalová, T and Ježková, J and Malát, K and Mihalca, AD and Modrý, D}, title = {First insight into strongylid nematode diversity and anthelmintic treatment effectiveness in beef cattle in the Czech Republic explored by HTS metagenomics.}, journal = {Veterinary parasitology, regional studies and reports}, volume = {47}, number = {}, pages = {100961}, doi = {10.1016/j.vprsr.2023.100961}, pmid = {38199682}, issn = {2405-9390}, mesh = {Cattle ; Animals ; Czech Republic ; Pilot Projects ; *Anthelmintics/therapeutic use ; Treatment Outcome ; *Haemonchus ; *Trichostrongyloidea/genetics ; Ostertagia ; }, abstract = {Parasitic diseases and mitigation of their effects play an important role in the health management of grazing livestock worldwide, with gastrointestinal strongylid nematodes being of prominent importance. These helminths typically occur in complex communities, often composed of species from numerous strongylid genera. Detecting the full diversity of strongylid species in non-invasively collected faecal samples is nearly impossible using conventional methods. In contrast, high-throughput amplicon sequencing (HTS) can effectively identify co-occurring species. During the four-year project, we collected and analysed faecal samples from beef cattle on >120 farms throughout the Czech Republic. Strongylids were the predominant nematodes, detected in 56% of the samples, but at a low level of infection. The apparent limitations in identifying strongylid taxa prompted this pilot study on a representative group of samples testing positive for strongylids using ITS-2 metabarcoding. The most widespread genera parasitizing Czech cattle were Ostertagia (O. ostertagi) and Oesophagostomum spp., followed by Trichostrongylus and Cooperia, while Bunostomum, Nematodirus and Chabertia were present only in a minority. As comparative material, 21 samples of cattle from the Danube Delta in Romania were used, which, in contrast, were dominated by Haemonchus placei. Finally, the effect of ivermectin treatment was tested at two Czech farms. After treatment with the anthelmintic, there was a shift in the strongylid communities, with a dominance of Cooperia and Ostertagia.}, } @article {pmid38199475, year = {2024}, author = {Hong, W and Mei, H and Shi, X and Lin, X and Wang, S and Ni, R and Wang, Y and Song, L}, title = {Viral community distribution, assembly mechanism, and associated hosts in an industrial park wastewater treatment plant.}, journal = {Environmental research}, volume = {}, number = {}, pages = {118156}, doi = {10.1016/j.envres.2024.118156}, pmid = {38199475}, issn = {1096-0953}, abstract = {Viruses manipulate bacterial community composition and impact wastewater treatment efficiency. Some viruses pose threats to the environment and human populations through infection. Improving the efficiency of wastewater treatment and ensuring the health of the effluent and receptor pools requires an understanding of how viral communities assemble and interact with hosts in wastewater treatment plants (WWTPs). We used metagenomic analysis to study the distribution, assembly mechanism, and sensitive hosts for the viral communities in raw water, anaerobic tanks, and returned activated sludge units of a large-scale industrial park WWTP. Uroviricota (53.42% ± 0.14%) and Nucleocytoviricota (26.1% ± 0.19%) were dominant in all units. Viral community composition significantly differed between units, as measured by β diversity (P = 0.005). Compared to raw water, the relative viral abundance decreased by 29.8% in the anaerobic tank but increased by 9.9% in the activated sludge. Viral community assembly in raw water and anaerobic tanks was predominantly driven by deterministic processes (MST <0.5) versus stochastic processes (MST >0.5) in the activated sludge, indicating that differences in diffusion limits may fundamentally alter the assembly mechanisms of viral communities between the solid and liquid-phase environments. Acidobacteria was identified as the sensitive host contributing to viral abundance, exhibiting strong interactions and a mutual dependence (degree = 59). These results demonstrate the occurrence and prevalence of viruses in WWTPs, their different assembly mechanism, and sensitive hosts. These observations require further study of the mechanisms of viral community succession, ecological function, and roles in the successive wastewater treatment units.}, } @article {pmid38199380, year = {2024}, author = {Wang, X and Li, J and Zheng, J and Zhao, L and Ruan, C and Zhang, D and Pan, X}, title = {Polysaccharide preferred minority-dominant community assembly and exoenzyme enrichment in transparent exopolymer particles: Implication for global carbon cycle in water.}, journal = {The Science of the total environment}, volume = {914}, number = {}, pages = {169976}, doi = {10.1016/j.scitotenv.2024.169976}, pmid = {38199380}, issn = {1879-1026}, abstract = {The ubiquitous transparent exopolymer particles (TEPs) are an important organic carbon pool and an ideal microhabitat for bacteria in aquatic environments. They play a crucial role in the global carbon cycle. Organic matter transformation and carbon turnover in TEPs strongly depend on the assembly of their associated bacterial communities and enzyme activity. However, the mechanisms of bacterial community assembly and their potential effects on the organic carbon cycle in TEPs are still unclear. In this study, we comparatively explored the community assembly of TEP-associated bacteria and bacterioplankton from surface freshwater using metagenomics. It was found that the bacterial community assembly in TEPs followed a minority-dominant rule and was governed by homogeneous selection. Pseudomonadota and Actinomycetota, which are responsible for polysaccharide degradation, serve as taxon-specific biomarkers among the abundant and diverse bacteria in TEPs. The network of TEP-associated bacteria displayed stronger robustness than that of bacterioplankton. Bin 76 (majorly Acinetobacter) was the overwhelmingly dominant taxa in TEPs, whereas there was no clearly dominant taxa in TEP-free water. Exoenzyme analysis showed that 64 out of 71 identified polysaccharide hydrolases were markedly linked with the dominant bin 76 in TEPs, while no such linkage was observed for bacterioplankton. Generally, Acinetobacter, which is capable of utilizing polysaccharides, is preferred to be assembled in TEPs together with high polysaccharide hydrolase activity. This may significantly accelerate the turnover of organic carbon in the giant global TEP pool. These findings are important for a deep understanding of the carbon cycle in water.}, } @article {pmid38198973, year = {2024}, author = {Xia, Z and Ng, HY and Xu, D and Bae, S}, title = {Lumen air pressure regulated multifunctional microbiotas in membrane-aerated biofilm reactors for simultaneous nitrogen removal and antibiotic elimination from aquaculture wastewater.}, journal = {Water research}, volume = {251}, number = {}, pages = {121102}, doi = {10.1016/j.watres.2024.121102}, pmid = {38198973}, issn = {1879-2448}, abstract = {In this study, two membrane-aerated biofilm reactors (MABRs) were constructed: one solely utilizing biofilm and another hybrid MABR (HMABR) incorporating both suspended-sludge and biofilm to treat low C/N aquaculture wastewater under varying lumen air pressure (LAP). Both HMABR and MABR demonstrated superior nitrogen removal than conventional aeration reactors. Reducing LAP from 10 kPa to 2 kPa could enhance denitrification processes without severely compromising nitrification, resulting in an increase in total inorganic nitrogen (TIN) removal from 50.2±3.1 % to 71.6±1.0 %. The HMABR exhibited better denitrification efficacy than MABR, underscoring its potential for advanced nitrogen removal applications. A decline in LAP led to decreased extracellular polymeric substance (EPS) production, which could potentially augment reactor performance by minimizing mass transfer resistance while maintaining microbial matrix stability and function. Gene-centric metagenomics analysis revealed decreasing LAP impacted nitrogen metabolic potentials and electron flow pathways. The enrichment of napAB at higher LAP and the presence of complete ammonia oxidation (Comammox) Nitrospira at lower LAP indicated aerobic denitrification and Comammox processes in nitrogen removal. Multifunctional microbial communities developed under LAP regulation, diversifying the mechanisms for simultaneous nitrification-denitrification. Increased denitrifying gene pool (narGHI, nirK, norB) and enzymatic activity at a low LAP can amplify denitrification by promoting denitrifying genes and electron flow towards denitrifying enzymes. Sulfamethoxazole (SMX) was simultaneously removed with efficiency up to 80.2 ± 3.7 %, mainly via biodegradation, while antibiotic resistome and mobilome were propagated. Collectively, these findings could improve our understanding of nitrogen and antibiotic removal mechanisms under LAP regulation, offering valuable insights for the effective design and operation of MABR systems in aquaculture wastewater treatment.}, } @article {pmid38198972, year = {2024}, author = {Du, J and Tian, C and Xiao, J and Liu, Y and Zhang, F and Gao, X and Xing, B and Zhao, Y}, title = {Co-fermentation of titanium-flocculated-sludge with food waste towards simultaneous water purification and resource recovery.}, journal = {Water research}, volume = {251}, number = {}, pages = {121110}, doi = {10.1016/j.watres.2024.121110}, pmid = {38198972}, issn = {1879-2448}, abstract = {Recovery of resources from domestic sewage and food waste has always been an international-thorny problem. Titanium-based flocculation can achieve high-efficient destabilization, quick concentration and separation of organic matter from sewage to sludge. This study proposed co-fermentation of the titanium-flocculated sludge (Ti-loaded sludge) and food waste towards resource recovery by converting organic matter to value-added volatile fatty acids (VFAs) and inorganic matter to struvite and TiO2 nanoparticles. When Ti-loaded sludge and food waste were co-fermented at a mass ratio of 3:1, the VFAs yield reached 3725.2 mg-COD/L (VFAs/SCOD 91.0%), which was more than 4 times higher than the case of the sludge alone. The 48-day semicontinuous co-fermentation demonstrated stable long-term operation, yielding VFAs at 2529.0 mg-COD/L (VFAs/SCOD 89.8%) and achieving a high CODVFAs/NNH4 of 58.9. Food waste provided sufficient organic substrate, enriching plenty of acid-producing fermentation bacteria (such as Prevotella 7 about 21.0% and Bacteroides about 9.4%). Moreover, metagenomic sequencing analysis evidenced the significant increase of the relative gene abundance corresponding to enzymes in pathways, such as extracellular hydrolysis, substrates metabolism, and VFAs biosynthesis. After fermentation, the precious element P (≥ 99.0%) and extra-added element Ti (≥99.0%) retained in fermented residues, without releasing to VFAs supernatant, which facilitated the direct re-use of VFAs as resource. Through simple and commonly used calcination and acid leaching methodologies, 80.9% of element P and 82.1% of element Ti could be successfully recovered as struvite and TiO2 nanoparticles, respectively. This research provides a strategy for the co-utilization of domestic sludge and food waste, which can realize both reduction of sludge and recovery of resources.}, } @article {pmid38198862, year = {2024}, author = {Li, K and Xu, L and Bai, X and Zhang, G and Zhang, M and Huang, Y}, title = {Potential environmental risks of field bio/non-degradable microplastic from mulching residues in farmland: Evidence from metagenomic analysis of plastisphere.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133428}, doi = {10.1016/j.jhazmat.2024.133428}, pmid = {38198862}, issn = {1873-3336}, abstract = {The plastisphere may act as reservoir of antibiotic resistome, accelerating global antimicrobial resistance dissemination. However, the environmental risks in the plastisphere of field microplastics (MPs) in farmland remain largely unknown. Here, antibiotic resistance genes (ARGs) and virulence factors (VFs) on polyethylene microplastics (PE-MPs) and polybutylene adipate terephthalate and polylactic acid microplastics (PBAT/PLA-MPs) from residues were investigated using metagenomic analysis. The results suggested that the profiles of ARG and VF in the plastisphere of PBAT/PLA-MPs had greater number of detected genes with statistically higher values of diversity and abundance than soil and PE-MP. Procrustes analysis indicated a good fitting correlation between ARG/VF profiles and bacterial community composition. Actinobacteria was the major host for tetracycline and glycopeptide resistance genes in the soil and PE-MP plastisphere, whereas the primary host for multidrug resistance genes changed to Proteobacteria in PBAT/PLA-MP plastisphere. Besides, three human pathogens, Sphingomonas paucimobilis, Lactobacillus plantarum and Pseudomonas aeruginosa were identified in the plastisphere. The PE-MP plastisphere exhibited a higher transfer potential of ARGs than PBAT/PLA-MP plastisphere. This work enhances our knowledge of potential environmental risks posed by microplastic in farmland and provides valuable insights for risk assessment and management of agricultural mulching applications.}, } @article {pmid38197778, year = {2024}, author = {He, J and Zhang, B and Yan, W and Lai, Y and Tang, Y and Han, Y and Liu, J}, title = {Deciphering Vanadium Speciation in Smelting Ash and Adaptive Responses of Soil Microorganisms.}, journal = {ACS nano}, volume = {}, number = {}, pages = {}, doi = {10.1021/acsnano.3c11204}, pmid = {38197778}, issn = {1936-086X}, abstract = {Abundant smelting ash is discharged during pyrometallurgical vanadium (V) production. However, its associated V speciation and resultant ecological impact have remained elusive. In this study, V speciation in smelting ash and its influence on the metabolism of soil microorganisms were investigated. Smelting ashes from V smelters contained abundant V (19.6-115.9 mg/g). V(V) was the dominant species for soluble V, while solid V primarily existed in bioavailable forms. Previously unrevealed V nanoparticles (V-NPs) were prevalently detected, with a peak concentration of 1.3 × 10[13] particles/g, a minimal size of 136.0 ± 0.6 nm, and primary constituents comprising FeVO4, VO2, and V2O5. Incubation experiments implied that smelting ash reshaped the soil microbial community. Metagenomic binning, gene transcription, and component quantification revealed that Microbacterium sp. and Tabrizicola sp. secreted extracellular polymeric substances through epsB and yhxB gene regulation for V-NPs aggregation to alleviate toxicity under aerobic operations. The V K-edge X-ray absorption near-edge structure (XANES) spectra suggested that VO2 NPs were oxidized to V2O5 NPs. In the anaerobic case, Comamonas sp. and Achromobacter sp. reduced V(V) to V(IV) for detoxification regulated by the napA gene. This study provides a deep understanding of the V speciation in smelting ash and microbial responses, inspiring promising bioremediation strategies to reduce its negative environmental impacts.}, } @article {pmid38197744, year = {2024}, author = {Vigneron, A and Guyoneaud, R and Goñi-Urriza, M}, title = {Genome-Centric Metatranscriptomics Reveals Multiple Co-occurring Routes for Hydrocarbon Degradation in Chronically Contaminated Marine Microbial Mats.}, journal = {Environmental science & technology}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.est.3c08386}, pmid = {38197744}, issn = {1520-5851}, abstract = {Long-term hydrocarbon pollution is a devious threat to aquatic and marine ecosystems. However, microbial responses to chronic pollution remain poorly understood. Combining genome-centric metagenomic and metatranscriptomic analyses of microbial mat samples that experienced chronic hydrocarbon pollution for more than 80 years, we analyzed the transcriptomic activity of alkane and aromatic hydrocarbon degradation pathways at the population level. Consistent with the fluctuating and stratified redox conditions of the habitat, both aerobic and anaerobic hydrocarbon degradation pathways were expressed by taxonomically and metabolically contrasted lineages including members of Bacteroidiales, Desulfobacteraceae, Pseudomonadales; Alcanivoraceae and Halieaceae populations with (photo)-heterotrophic, sulfur- and organohalide-based metabolisms, providing evidence for the co-occurrence and activity of aerobic and anaerobic hydrocarbon degradation pathways in shallow marine microbial mats. In addition, our results suggest that aerobic alkane degradation in long-term pollution involved bacterial families that are naturally widely distributed in marine habitats, but hydrocarbon concentration and composition were found to be a strong structuring factor of their intrafamily diversity and transcriptomic activities.}, } @article {pmid38197657, year = {2024}, author = {You, Y and Wang, L and Liu, X and Wang, X and Jiang, L and Ding, C and Wang, W and Zhang, D and Zhao, X}, title = {Interspecific plant interaction structures the microbiomes of poplar-soil interface to alter nutrient cycling and utilization.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0336823}, doi = {10.1128/spectrum.03368-23}, pmid = {38197657}, issn = {2165-0497}, abstract = {Poplar has the characteristics of wide distribution, strong adaptability, and fast growth, which is an ideal tree species for timber forest. In this study, metagenomics and elemental analysis were used to comprehensively reveal the effects of interspecific plant interactions on microbial communities and functions in different ecological niches. It can provide a theoretical basis for the development and application of the precise management model in poplar.}, } @article {pmid38196273, year = {2024}, author = {Xu, J and Xia, Q and Wu, T and Shao, Y and Wang, Y and Jin, N and Tian, P and Wu, L and Lu, X}, title = {Prophylactic treatment with Bacteroides uniformis and Bifidobacterium bifidum counteracts hepatic NK cell immune tolerance in nonalcoholic steatohepatitis induced by high fat diet.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2302065}, doi = {10.1080/19490976.2024.2302065}, pmid = {38196273}, issn = {1949-0984}, mesh = {Humans ; Animals ; Mice ; *Non-alcoholic Fatty Liver Disease/etiology/prevention & control ; Diet, High-Fat/adverse effects ; *Bifidobacterium bifidum ; Proteomics ; *Gastrointestinal Microbiome ; Killer Cells, Natural ; Immune Tolerance ; }, abstract = {Hepatic immunity is one of the driving forces for the development of nonalcoholic steatohepatitis (NASH), and targeting gut microbiota is believed to affect the hepatic immune constitution. Here, we aimed to investigate the hepatic immunological state in NASH, with a specific emphasis on natural killer (NK) cells. In addition, we aimed to identify the contributing species that target hepatic immunity to provide new directions and support the feasibility of immunotherapy for NASH. A possible NASH population was determined by combination of long-term severe fatty liver, metabolic disorders and increased serum CK18 to detect serum immune factors and gut microbiota. NASH was induced in mice fed a high-fat diet to verify the prophylactic effect of the functional species on the immunopathology and development of NASH. Hepatic immunologic state was examined, and the effector functions of NK cells were detected. Hepatic transcriptome, proteomic, and fecal metagenome were performed. We observed a statistical increase in serum IL-10 (p < 0.001) and non-statistical decrease in interferon-γ and IL-6 in NASH population, hinting at the possibility of immune tolerance. Fecal Bacteroides uniformis and Bifidobacterium bifidum were abundant in healthy population but depleted in NASH patients. In NASH mice, hepatic CD8+T cells, macrophages, and dendritic cells were increased (p < 0.01), and NK cells were inhibited, which were identified with decreased granzyme B (p < 0.05). Bacteroides uniformis and Bifidobacterium bifidum improved hepatic pathological and metabolic cues, increased hepatic NK cells and reduced macrophages (p < 0.05). Bacteroides uniformis also restored hepatic NK cell function, which was identified as increased CD107a (p < 0.05). Transcriptional and translational profiling revealed that the functional species might restore the function of hepatic NK cells through multiple pathways, such as reduction of inhibitory molecules in NK cells. Bacteroides uniformis and Bifidobacterium bifidum are novel prophylactics for NASH that restore the impaired function of hepatic NK cells.}, } @article {pmid38196163, year = {2024}, author = {Hu, P and Henry, J and Tiesman, JP and Parlov, M and Bacon, R and Charbonneau, D and Venkataraman, A and Locker, KCS and Krigbaum, H and Schwartz, J}, title = {Scalp microbiome composition changes and pathway evaluations due to effective treatment with Piroctone Olamine shampoo.}, journal = {International journal of cosmetic science}, volume = {}, number = {}, pages = {}, doi = {10.1111/ics.12933}, pmid = {38196163}, issn = {1468-2494}, support = {//Procter & Gamble Company/ ; }, abstract = {OBJECTIVE: To characterize the scalp microbial composition, function, and connection to dandruff severity using a metagenomics approach and to understand the impact of a Piroctone Olamine containing anti-dandruff shampoo on the scalp microbiome.

METHODS: Shotgun metagenomics was used to characterize the composition of the scalp microbiomes from 94 subjects with and without clinically defined dandruff. Furthermore, the microbiome of the scalps of 100 dandruff sufferers before and after 3 weeks of treatment with either control or anti-dandruff shampoo containing 0.5% Piroctone Olamine (PO) was characterized and compared to identify microorganisms associated with the dandruff condition and the associated pathways and processes that may contribute to PO's effect on scalp microbiome.

RESULTS: A higher relative abundance of Malassezia restricta and Staphylococcus capitis and a lower abundance of Cutibacterium acnes were associated with the dandruff scalps relative to the no-dandruff scalps. A 3-week PO shampoo treatment reduced the relative abundance of Malassezia species and Staphylococcus capitis and increased the relative abundance of Cutibacterium acnes. This change to the scalp microbiome composition is consistent with a return to a healthy no-dandruff microbiome and improved clinical signs and symptoms as measured by adherent scalp flaking score (ASFS) compared with the control shampoo. Functional genomics analysis showed that the PO shampoo treatment reduced oxidative stress-associated genes and decreased the abundance of protease, urease, and lipase genes. These changes correlated positively to improvements in dandruff severity. PO treatment favourably shifted scalp microbiomes in dandruff subjects toward the no-dandruff state.

CONCLUSION: Our results suggest that part of the aetiology of dandruff can be attributed to dysbiosis of the scalp microbiome. PO treatment can restore a healthier microbiome, reducing oxidative stress and promoting better scalp health.}, } @article {pmid38196020, year = {2024}, author = {Yu, M and Liu, J and Chen, J and Lin, C and Deng, S and Wu, M}, title = {Metagenomic and metabolomic profiling of dried shrimp (Litopenaeus vannamei) prepared by a procedure traditional to the south China coastal area.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {38196020}, issn = {1618-1905}, support = {2021KCXTD081//Guangdong University Innovation Team Project/ ; 2021KCXTD081//Guangdong University Innovation Team Project/ ; 2021KCXTD081//Guangdong University Innovation Team Project/ ; 2021KCXTD081//Guangdong University Innovation Team Project/ ; 2021KCXTD081//Guangdong University Innovation Team Project/ ; 2021KCXTD081//Guangdong University Innovation Team Project/ ; 2019GKTSCX120//the Innovation Projects of Colleges and Universities in Guangdong Province/ ; 2019GKTSCX120//the Innovation Projects of Colleges and Universities in Guangdong Province/ ; 2019GKTSCX120//the Innovation Projects of Colleges and Universities in Guangdong Province/ ; 2019GKTSCX120//the Innovation Projects of Colleges and Universities in Guangdong Province/ ; 2019GKTSCX120//the Innovation Projects of Colleges and Universities in Guangdong Province/ ; 2019GKTSCX120//the Innovation Projects of Colleges and Universities in Guangdong Province/ ; KY201902, KY201903//Foundation of Foshan Polytechnic/ ; KY201902, KY201903//Foundation of Foshan Polytechnic/ ; KY201902, KY201903//Foundation of Foshan Polytechnic/ ; KY201902, KY201903//Foundation of Foshan Polytechnic/ ; KY201902, KY201903//Foundation of Foshan Polytechnic/ ; KY201902, KY201903//Foundation of Foshan Polytechnic/ ; 2020A1515110332//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2020A1515110332//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2020A1515110332//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2020A1515110332//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2020A1515110332//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2020A1515110332//Basic and Applied Basic Research Foundation of Guangdong Province/ ; }, abstract = {Sun-drying is a traditional process for preparing dried shrimp in coastal area of South China, but its impacts on nutrition and the formation of flavor-contributory substances in dried shrimp remain largely unknown. This study aimed to examine the effects of the production process on the microbiota and metabolites in dried shrimp. 16S rDNA amplicon sequencing was employed to identify 170 operational taxonomic units (OTUs), with Vibrio, Photobacterium, and Shewanella emerging as the primary pathogenic bacteria in shrimp samples. Lactococcus lactis was identified as the principal potential beneficial microorganism to accrue during the dried shrimp production process and found to contribute significantly to the development of desirable shrimp flavors. LC-MS-based analyses of dried shrimp sample metabolomes revealed a notable increase in compounds associated with unsaturated fatty acid biosynthesis, arachidonic acid metabolism, amino acid biosynthesis, and flavonoid and flavanol biosynthesis throughout the drying process. Subsequent exploration of the relationship between metabolites and bacterial communities highlighted the predominant coexistence of Bifidobacterium, Clostridium, and Photobacterium contributing heterocyclic compounds and metabolites of organic acids and their derivatives. Conversely, Arthrobacter and Staphylococcus were found to inhibit each other, primarily in the presence of heterocyclic compounds. This comprehensive investigation provides valuable insights into the dynamic changes in the microbiota and metabolites of dried shrimps spanning different drying periods, which we expect to contribute to enhancing production techniques and safety measures for dried shrimp processing.}, } @article {pmid38195681, year = {2024}, author = {Tapilatu, Y and Fauzan, I and Pradipta, A and Kusuma, AB}, title = {A first report on prokaryotic diversity in northwestern Arafura deep-sea sediments, Indonesia.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {895}, pmid = {38195681}, issn = {2045-2322}, mesh = {Indonesia ; RNA, Ribosomal, 16S/genetics ; *Prokaryotic Cells ; Archaea/genetics ; *Microbiota ; }, abstract = {Indonesia's deep-sea microbial communities remain poorly understood, prompting the need for comprehensive investigations. This study aimed to assess the bacterial and archaeal diversities in northwestern Arafura deep-sea sediments, spanning depths of 100 to 1,457 m using a 16S rRNA based-metagenomic sequencing approach, without technical and biological replicates. Principal component analyses based on the Bray-Curtis dissimilarity index indicated that most of the bacterial and archaeal communities were habitat-specific and influenced by depth. The most prevalent known bacterial phylotypes were detected from all samples belonging to the phylum of Desulfobacteriota, Pseudomonadota, and Firmicutes. In addition, the samples also harbored diverse members of the Archaea domain, including Crenarchaeota, Nanoarchaeota and Haloarchaeota. Notably, the sequencing data revealed the significant presence of rare prokaryotic taxa, including uncultured counterparts with less than 1% abundance. The findings suggest that novel and rare prokaryotic taxa are abundant in northwestern Arafura deep-sea ecosystem, offering unique opportunities for further bioprospecting and functional ecology studies.}, } @article {pmid38195441, year = {2024}, author = {Rádai, Z and Váradi, A and Takács, P and Nagy, NA and Schmitt, N and Prépost, E and Kardos, G and Laczkó, L}, title = {An overlooked phenomenon: complex interactions of potential error sources on the quality of bacterial de novo genome assemblies.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {45}, pmid = {38195441}, issn = {1471-2164}, support = {GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; GINOP-2.3.4-15-2020-00008//European Regional Development Fund/ ; }, mesh = {*Research Design ; *Genome, Bacterial ; Benchmarking ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Parameters adversely affecting the contiguity and accuracy of the assemblies from Illumina next-generation sequencing (NGS) are well described. However, past studies generally focused on their additive effects, overlooking their potential interactions possibly exacerbating one another's effects in a multiplicative manner. To investigate whether or not they act interactively on de novo genome assembly quality, we simulated sequencing data for 13 bacterial reference genomes, with varying levels of error rate, sequencing depth, PCR and optical duplicate ratios.

RESULTS: We assessed the quality of assemblies from the simulated sequencing data with a number of contiguity and accuracy metrics, which we used to quantify both additive and multiplicative effects of the four parameters. We found that the tested parameters are engaged in complex interactions, exerting multiplicative, rather than additive, effects on assembly quality. Also, the ratio of non-repeated regions and GC% of the original genomes can shape how the four parameters affect assembly quality.

CONCLUSIONS: We provide a framework for consideration in future studies using de novo genome assembly of bacterial genomes, e.g. in choosing the optimal sequencing depth, balancing between its positive effect on contiguity and negative effect on accuracy due to its interaction with error rate. Furthermore, the properties of the genomes to be sequenced also should be taken into account, as they might influence the effects of error sources themselves.}, } @article {pmid38194857, year = {2024}, author = {Zheng, X and Jiang, J and Wang, C and Hua, Y and Huang, H and Xu, Y and Wei, P and Tao, J and Cao, P and Kang, Z and Li, X and Gao, Q and Chen, Q}, title = {NRAMP6c plays a key role in plant cadmium accumulation and resistance in tobacco (Nicotiana tabacum L.).}, journal = {Ecotoxicology and environmental safety}, volume = {271}, number = {}, pages = {115885}, doi = {10.1016/j.ecoenv.2023.115885}, pmid = {38194857}, issn = {1090-2414}, abstract = {Tobacco plants (Nicotiana tabacum L.) exhibit considerable potential for phytoremediation of soil cadmium (Cd) pollutants, owing to their substantial biomass and efficient metal accumulation capabilities. The reduction of Cd accumulation in tobacco holds promise for minimizing Cd intake in individuals exposed to cigar smoking. NRAMP transporters are pivotal in the processes of Cd accumulation and resistance in plants; however, limited research has explored the functions of NRAMPs in tobacco plants. In this investigation, we focused on NtNRAMP6c, one of the three homologs of NRAMP6 in tobacco. We observed a robust induction of NtNRAMP6c expression in response to both Cd toxicity and iron (Fe) deficiency, with the highest expression levels detected in the roots. Subsequent subcellular localization and heterologous expression analyses disclosed that NtNRAMP6c functions as a plasma membrane-localized Cd transporter. Moreover, its overexpression significantly heightened the sensitivity of yeast cells to Cd toxicity. Through CRISPR-Cas9-mediated knockout of NtNRAMP6c, we achieved a reduction in Cd accumulation and an enhancement in Cd resistance in tobacco plants. Comparative transcriptomic analysis unveiled substantial alterations in the transcriptional profiles of genes associated with metal ion transport, photosynthesis, and macromolecule catabolism upon NtNRAMP6c knockout. Furthermore, our study employed plant metabolomics and rhizosphere metagenomics to demonstrate that NtNRAMP6c knockout led to changes in phytohormone homeostasis, as well as shifts in the composition and abundance of microbial communities. These findings bear significant biological implications for the utilization of tobacco in phytoremediation strategies targeting Cd pollutants in contaminated soils, and concurrently, in mitigating Cd accumulation in tobacco production destined for cigar consumption.}, } @article {pmid38194811, year = {2024}, author = {Tang, J and Zhao, H and Li, K and Zhou, H and Chen, Q and Wang, H and Li, S and Xu, J and Sun, Y and Chang, X}, title = {Intestinal microbiota promoted NiONPs-induced liver fibrosis via effecting serum metabolism.}, journal = {Ecotoxicology and environmental safety}, volume = {270}, number = {}, pages = {115943}, doi = {10.1016/j.ecoenv.2024.115943}, pmid = {38194811}, issn = {1090-2414}, abstract = {Nickel oxide nanoparticles (NiONPs) are toxic heavy metal compounds that induce liver fibrosis and metabolic disorders. Current research shows that the intestinal microbiota regulates liver metabolism through the gut-liver axis. However, it is unclear whether NiONPs affect the intestinal microbiota and the relationship between microbiota and liver metabolic disorders. Therefore, in this study, we established liver fibrosis model by administering 0.015, 0.06 and 0.24 mg/mL NiONPs through tracheal instillation twice a week for 9 weeks in rats, then we collected serum and fecal sample for whole metabolomics and metagenomic sequencing. As the result of sequencing, we screened out seven metabolites (beta-D-glucuronide, methylmalonic acid, linoleic acid, phosphotidylcholine, lysophosphatidylinositol, docosapentaenoic acid and progesterone) that related to functional alterations (p < 0.05), and obtained a decrease of probiotics abundances (p < 0.05) as well as a variation of the microbiota enzyme activity (p < 0.05), indicating that NiONPs inhibited the proliferation of probiotics. As the result of correlation analysis, we found a positive correlation between differential metabolites and probiotics, such as lysophosphatidylinositol was positively correlated with Desulfuribacillus, Jeotgallibacillus and Rummeliibacillus (p < 0.05). We also found that differential metabolites had correlations with differential proteins and enzymes of intestinal microbiota, such as glucarate dehydratase, dihydroorotate dehydrogenase and acetyl-CoA carboxylase (p < 0.05). Finally, we screened six metabolic pathways with both differential intestinal microbiota enzymes and metabolites were involved, such as pentose and glucuronate interconversions, and linoleic acid metabolism. In vitro experiments showed that NiONPs increased the transcriptional expression of Col1A1 in LX-2 cells, while reducing the mRNA expression of serine/threonine activators, acetyl coenzyme carboxylase, and lysophosphatidylinositol synthase, and short chain fatty acid sodium butyrate can alleviate these variation trends. The results proved that the intestinal microbiota enzyme systems were associated with serum metabolites, suggesting that the disturbance of intestinal microbiota and reduction of probiotics promoted the occurrence and development of NiONPs-induced liver fibrosis by affecting metabolic pathways.}, } @article {pmid38194448, year = {2024}, author = {Bradshaw, AJ and Ramírez-Cruz, V and Awan, AR and Furci, G and Guzmán-Dávalos, L and Dentinger, BTM}, title = {Phylogenomics of the psychoactive mushroom genus Psilocybe and evolution of the psilocybin biosynthetic gene cluster.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {121}, number = {3}, pages = {e2311245121}, doi = {10.1073/pnas.2311245121}, pmid = {38194448}, issn = {1091-6490}, support = {DEB #2114785//National Science Foundation (NSF)/ ; }, mesh = {*Psilocybe/genetics ; *Agaricales/genetics ; Phylogeny ; Psilocybin/genetics ; Multigene Family/genetics ; }, abstract = {Psychoactive mushrooms in the genus Psilocybe have immense cultural value and have been used for centuries in Mesoamerica. Despite the recent surge of interest in these mushrooms due to the psychotherapeutic potential of their natural alkaloid psilocybin, their phylogeny and taxonomy remain substantially incomplete. Moreover, the recent elucidation of the psilocybin biosynthetic gene cluster is known for only five of ~165 species of Psilocybe, four of which belong to only one of two major clades. We set out to improve the phylogeny of Psilocybe using shotgun sequencing of fungarium specimens, from which we obtained 71 metagenomes including from 23 types, and conducting phylogenomic analysis of 2,983 single-copy gene families to generate a fully supported phylogeny. Molecular clock analysis suggests the stem lineage of Psilocybe arose ~67 mya and diversified ~56 mya. We also show that psilocybin biosynthesis first arose in Psilocybe, with 4 to 5 possible horizontal transfers to other mushrooms between 40 and 9 mya. Moreover, predicted orthologs of the psilocybin biosynthetic genes revealed two distinct gene orders within the biosynthetic gene cluster that corresponds to a deep split within the genus, possibly a signature of two independent acquisitions of the cluster within Psilocybe.}, } @article {pmid38194349, year = {2024}, author = {Chaudhury, R and Chakraborty, A and Rahaman, F and Sarkar, T and Dey, S and Das, M}, title = {Mycorrhization in trees: ecology, physiology, emerging technologies and beyond.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {}, number = {}, pages = {}, doi = {10.1111/plb.13613}, pmid = {38194349}, issn = {1438-8677}, support = {BT/INF/22/SP45088/2022//Department of Biotechnology, Ministry of Science and Technology, India/ ; 38(1493)/19/EMR-II//Council of Scientific and Industrial Research, India/ ; }, abstract = {Mycorrhization has been an integral part of plants since colonization by the early land plants. Over decades, substantial research has highlighted its potential role in improving nutritional efficiency and growth, development and survival of crop plants. However, the focus of this review is trees. Evidence have been provided to explain ecological and physiological significance of mycorrhization in trees. Advances in recent technologies (e.g., metagenomics, artificial intelligence, machine learning, agricultural drones) may open new windows to apply this knowledge in promoting tree growth in forest ecosystems. Dual mycorrhization relationships in trees and even triple relationships among trees, mycorrhizal fungi and bacteria offer an interesting physiological system to understand how plants interact with other organisms for better survival. Besides, studies indicate additional roles of mycorrhization in learning, memorizing and communication between host trees through a common mycorrhizal network (CMN). Recent observations in trees suggest that mycorrhization may even promote tolerance to multiple abiotic (e.g., drought, salt, heavy metal stress) and biotic (e.g. fungi) stresses. Due to the extent of physiological reliance, local adaptation of trees is heavily impacted by the mycorrhizal community. This knowledge opens the possibility of a non-GMO avenue to promote tree growth and development. Indeed, mycorrhization could impact growth of trees in nurserys and subsequent survival of the inoculated trees in field conditions. Future studies might integrate hyperspectral imaging and drone technologies to identify tree communities that are deficient in nitrogen and spray mycorrhizal spore formulations on them.}, } @article {pmid38194263, year = {2024}, author = {Ramos, PIP and Marcilio, I and Bento, AI and Penna, GO and de Oliveira, JF and Khouri, R and Andrade, RFS and Carreiro, RP and Oliveira, VA and Galvão, LAC and Landau, L and Barreto, ML and van der Horst, K and Barral-Netto, M and , }, title = {Combining Digital and Molecular Approaches Using Health and Alternate Data Sources in a Next-Generation Surveillance System for Anticipating Outbreaks of Pandemic Potential.}, journal = {JMIR public health and surveillance}, volume = {10}, number = {}, pages = {e47673}, doi = {10.2196/47673}, pmid = {38194263}, issn = {2369-2960}, mesh = {Humans ; *Artificial Intelligence ; *Influenza A Virus, H1N1 Subtype/genetics ; Chromosome Mapping ; Data Science ; Disease Outbreaks/prevention & control ; }, abstract = {Globally, millions of lives are impacted every year by infectious diseases outbreaks. Comprehensive and innovative surveillance strategies aiming at early alert and timely containment of emerging and reemerging pathogens are a pressing priority. Shortcomings and delays in current pathogen surveillance practices further disturbed informing responses, interventions, and mitigation of recent pandemics, including H1N1 influenza and SARS-CoV-2. We present the design principles of the architecture for an early-alert surveillance system that leverages the vast available data landscape, including syndromic data from primary health care, drug sales, and rumors from the lay media and social media to identify areas with an increased number of cases of respiratory disease. In these potentially affected areas, an intensive and fast sample collection and advanced high-throughput genome sequencing analyses would inform on circulating known or novel pathogens by metagenomics-enabled pathogen characterization. Concurrently, the integration of bioclimatic and socioeconomic data, as well as transportation and mobility network data, into a data analytics platform, coupled with advanced mathematical modeling using artificial intelligence or machine learning, will enable more accurate estimation of outbreak spread risk. Such an approach aims to readily identify and characterize regions in the early stages of an outbreak development, as well as model risk and patterns of spread, informing targeted mitigation and control measures. A fully operational system must integrate diverse and robust data streams to translate data into actionable intelligence and actions, ultimately paving the way toward constructing next-generation surveillance systems.}, } @article {pmid38193687, year = {2024}, author = {Zhao, L and Yang, X and Liang, Y and Zhang, Z and Ding, Y and Wang, Y and Chen, B and Wu, J and Jin, C and Zhao, G and Li, Z and Zhang, L}, title = {Temporal development and potential interactions between the gut microbiome and resistome in early childhood.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0317723}, doi = {10.1128/spectrum.03177-23}, pmid = {38193687}, issn = {2165-0497}, abstract = {In recent years, the irrational or inappropriate use of antibiotics, an important life-saving medical intervention, has led to the emergence and increase of drug-resistant and even multidrug-resistant bacteria. It remains unclear how antibiotic exposure affects various developmental stages of early childhood and how gut core microbes under antibiotic exposure affect the structural composition of the gut resistome. In this study, we focused on early antibiotic exposure and analyzed these questions in detail using samples from infants at various developmental stages. The significance of our research is to elucidate the impact of early antibiotic exposure on the dynamic patterns of the gut resistome in children and to provide new insights for early-life studies.}, } @article {pmid38193672, year = {2024}, author = {Yu, Y and Zhang, Q and Kang, J and Xu, N and Zhang, Z and Deng, Y and Gillings, M and Lu, T and Qian, H}, title = {Effects of organic fertilizers on plant growth and the rhizosphere microbiome.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0171923}, doi = {10.1128/aem.01719-23}, pmid = {38193672}, issn = {1098-5336}, abstract = {This study provides valuable guidance for use of organic fertilizers in agricultural production from the perspective of the microbiome and ecological risk.}, } @article {pmid38193195, year = {2024}, author = {Abdulnour-Nakhoul, SM and Kolls, JK and Flemington, EK and Ungerleider, NA and Nakhoul, HN and Song, K and Nakhoul, NL}, title = {Alterations in gene expression and microbiome composition upon calcium sensing receptor deletion in the mouse esophagus.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {}, number = {}, pages = {}, doi = {10.1152/ajpgi.00066.2023}, pmid = {38193195}, issn = {1522-1547}, support = {U54 GM104940/GM/NIGMS NIH HHS/United States ; }, abstract = {The calcium sensing receptor (CaSR), a G-protein-coupled receptor, regulates Ca[2+] concentration in plasma by regulating parathyroid hormone secretion. In other tissues, it is reported to play roles in cellular differentiation and migration, and in secretion and absorption. We reported previously that CaSR can be conditionally deleted in the mouse esophagus. This conditional knock-out (KO) model showed significant reduction in levels of adherens and tight junction proteins and had marked build-up of bacteria on the luminal esophageal surface. To further examine the role of CaSR, we used RNA sequencing to determine gene expression profiles in esophageal epithelia of control and conditional KO mice ([Eso]CaSR[-/-]). RNA Seq data indicated upregulation of gene sets involved in DNA replication and cell cycle in [Eso]CaSR[-/-]. This is accompanied by downregulation of gene sets involved in the innate immune response and in protein homeostasis including peptide elongation and protein trafficking. Ingenuity Pathway Analysis (IPA) demonstrated that these genes are mapped to important biological networks including Calcium and RhoA signaling pathways. To further explore the bacterial buildup in [Eso]CaSR[-/-] esophageal tissue, 16S sequencing of the mucosal-associated bacterial microbiome was performed. Three bacterial species, g_Rodentibacter, s_Rodentibacter_unclassified, and s_Lactobacillus_hilgardi were significantly increased in [Eso]CaSR[-/-]. Furthermore, metagenomic analysis of 16S sequences indicated that pathways related to oxidative phosphorylation and metabolism were downregulated in [Eso]CaSR[-/-] tissues. These data demonstrate that CaSR impacts major pathways of cell proliferation, differentiation, cell cycle and innate immune response in esophageal epithelium. The disruption of these pathways causes inflammation and significant modifications of the microbiome.}, } @article {pmid38192762, year = {2024}, author = {Xi, M and Cui, S and Zhong, YL and Liu, L and Zhang, Y and Zhu, SY and He, CL and Xiong, F}, title = {Meningitis in neonate caused by Mycoplasma hominis: A case report.}, journal = {Heliyon}, volume = {10}, number = {1}, pages = {e23489}, pmid = {38192762}, issn = {2405-8440}, abstract = {BACKGROUND: Mycoplasma hominis (M. hominis) commonly colonizes the genitourinary tract of adult women and may result in neonatal meningitis through vertical transmission. Although there are few case reports, if the treatment is not conducted timely, the disease progresses rapidly, which may lead to serious complications and a poor prognosis.

CASE PRESENTATION: In the present study, a 10-day-old full-term neonate who presented with fever as the initial symptom and was eventually diagnosed with meningitis caused by M. hominis was reported. In the present case, the pathogen was not detected during the initial routine investigations, and the therapeutic effects of empiric antibiotic therapy were poor. Metagenomic next-generation sequencing (mNGS) in the cerebrospinal fluid (CSF) was conducted with the detection of M. hominis, and the antibiotics were adjusted to moxifloxacin combined with doxycycline. The clinical symptoms of the pediatric patient disappeared with an improvement in related laboratory results.

CONCLUSION: It was difficult to detect M. hominis by routine bacterial culture. Therefore, M. hominis infection should be checked for in children with meningitis who had a negative result in CSF culture and poor therapeutic effects of empirical medication. mNGS in CSF should be conducted as soon as possible, and sensitive antibiotics should be administered in time to reduce the incidence of complications and improve the prognosis.}, } @article {pmid38192720, year = {2023}, author = {Wang, S and Wang, H and Jiang, Q and Dai, J and Dai, W and Kang, X and Xu, T and Zheng, X and Fu, A and Xing, Z and Chen, Y and He, Z and Lu, L and Gu, L}, title = {Supplementation of dietary areca nut extract modulates the growth performance, cecal microbiota composition, and immune function in Wenchang chickens.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1278312}, pmid = {38192720}, issn = {2297-1769}, abstract = {INTRODUCTION: The study was aimed at evaluating the effects of areca nut extract (ANE) on the growth performance, cecal microbiota, and immunity of Wenchang chickens.

METHODS: For this study, 42-day-old healthy Wenchang chickens (n = 450) with similar body weight were chosen. The animals were randomly divided into five groups, with six replicates per group and 15 chickens per replicate. One group was fed a basal diet (control; CCK). The remaining four groups were fed a basal diet supplemented with varying ANE concentrations: 0.038, 0.063, 0.100, and 0.151 g/kg, with the groups denoted as CNT1, CNT2, CNT3, and CNT4, respectively. The feeding experiment lasted 35 days. The ligated cecum segments of the control and experimental groups were collected for metabolomic and metagenomic analysis, while the bone marrow samples were extracted for tandem mass tag (TMT)-based proteomic analysis.

RESULTS: All the experimental groups exhibited significantly higher average daily gain (ADG) and significantly lower feed-to-weight (F/G) ratios than CCK. Metabolomic screening of the cecum contents revealed the presence of 544 differential metabolites, including several gut health-related metabolites, such as xanthine, hydroxy hypoxanthine, 2,5-dimethylhydrazine, ganoderic acid, and 2-aminohexanoic acid. Metagenomic analysis of the cecum contents showed an upregulation in the abundance of Prevotella spp. in the experimental groups. However, we observed no significant differences in the abundances of other cecal microbes at phylum and genus levels. Furthermore, we observed significant associations between Prevotella spp. and the differentially abundant metabolites, such as cherubins, thiaburimamide, and 3,4-dihydroxy-L-phenylalanine, (r)-mevalonate, 5-O-methylalloptaeroxylin, nalidixic acid, and deoxyloganin (p < 0.05). Proteomic analysis revealed that the differentially expressed proteins (such as interferon-induced protein with tetratricopeptide repeats 5 (IFIT5), MHC-BF1, and death domain-associated protein (Daxx)) in the bone marrow of the chickens were primarily enriched in the immune network for IgA production and B cell receptor signaling pathway.

CONCLUSION: In conclusion, dietary ANE supplementation was found to enhance metabolic activity and energy utilization, improve growth performance, modulate cecal microbiota, and strengthen the immunity of Wenchang chickens.}, } @article {pmid38192694, year = {2023}, author = {Zhou, W and Shi, W and Soltis, PS and Soltis, DE and Xiang, QJ}, title = {Foliar endophyte diversity in Eastern Asian-Eastern North American disjunct tree species - influences of host identity, environment, phylogeny, and geographic isolation.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1274746}, pmid = {38192694}, issn = {1664-462X}, abstract = {INTRODUCTION: The well-known eastern Asian (EA) and eastern North American (ENA) floristic disjunction provides a unique system for biogeographic and evolutionary studies. Despite considerable interest in the disjunction, few studies have investigated the patterns and their underlying drivers of allopatric divergence in sister species or lineages isolated in the two areas. Endophyte diversity and assembly in disjunct sister taxa, as an ecological trait, may have played an important role in the processes of allopatric evolution, but no studies have examined endophytes in these lineages. Here we compared foliar endophytic fungi and bacteria-archaea (FEF and FEB) in 17 EA-ENA disjunct species or clade pairs from genera representing conifers and 10 orders of five major groups of angiosperms and 23 species of Cornus from EA and North America.

METHODS: Metagenomic sequencing of fungal ITS and bacterial-archaeal 16S rDNA was used to capture the foliar endophytic communities. Alpha and beta diversity of fungi and bacteria were compared at multiple scales and dimensions to gain insights into the relative roles of historical geographic isolation, host identity, phylogeny, and environment from samples at different sites in shaping endophytic diversity patterns.

RESULTS: We found that beta diversity of endophytes varied greatly among plant individuals within species and between species among genera at the same sampling site, and among three sampling sites, but little variation between region-of-origin of all plant species (EA vs ENA) and between EA-ENA disjunct counterparts within genera. Various numbers of indicator fungal species differing in abundance were identified for each plant genus and Cornus species. An overall significant correlation between endophyte community dissimilarity and phylogenetic distance of plants was detected among the disjunct genera but not among species of Cornus. However, significant correlations between beta diversities at different taxonomic scales of endophytes and phylogenetic distances of Cornus species were observed.

DISCUSSION: Our results suggest important roles of host identity and environment (sampling sites), and a likely minor role of phylogenetic divergence and historical biogeographic isolation in shaping the pattern of foliar endophyte diversity and assembly in the EA-ENA disjunct genera and Cornus. The results lead to a hypothesis that the sister taxa in EA and ENA likely differ in FEF and FEB when growing in native habitats due to differences in local environments, which may potentially drive allopatric divergence of the functional features of species.}, } @article {pmid38192400, year = {2023}, author = {Liu, Y and Xu, Y and Xu, X and Chen, X and Chen, H and Zhang, J and Ma, J and Zhang, W and Zhang, R and Chen, J}, title = {Metagenomic identification of pathogens and antimicrobial-resistant genes in bacterial positive blood cultures by nanopore sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1283094}, pmid = {38192400}, issn = {2235-2988}, mesh = {Humans ; *Nanopore Sequencing ; Blood Culture ; Microbial Sensitivity Tests ; *Mycobacterium tuberculosis ; *Anti-Infective Agents ; *Sepsis ; Escherichia coli ; }, abstract = {Nanopore sequencing workflows have attracted increasing attention owing to their fast, real-time, and convenient portability. Positive blood culture samples were collected from patients with bacterial bloodstream infection and tested by nanopore sequencing. This study compared the sequencing results for pathogen taxonomic profiling and antimicrobial resistance genes to those of species identification and phenotypic drug susceptibility using traditional microbiology testing. A total of 37 bacterial positive blood culture results of strain genotyping by nanopore sequencing were consistent with those of mass spectrometry. Among them, one mixed infection of bacteria and fungi was identified using nanopore sequencing and confirmatory quantitative polymerase chain reaction. The amount of sequencing data was 21.89 ± 8.46 MB for species identification, and 1.0 MB microbial strain data enabled accurate determination. Data volumes greater than or equal to 94.6 MB nearly covered all the antimicrobial resistance genes of the bacteria in our study. In addition, the results of the antimicrobial resistance genes were compared with those of phenotypic drug susceptibility testing for Escherichia coli, Klebsiella pneumoniae, and Staphylococcus aureus. Therefore, the nanopore sequencing platform for rapid identification of causing pathogens and relevant antimicrobial resistance genes complementary to conventional blood culture outcomes may optimize antimicrobial stewardship management for patients with bacterial bloodstream infection.}, } @article {pmid38192332, year = {2024}, author = {Xie, M and Liu, J and Zheng, J and Wang, J and Han, D}, title = {Lemierre Syndrome: Report of a Case with an Innovative Diagnostic Method and Literature Review.}, journal = {Infection and drug resistance}, volume = {17}, number = {}, pages = {1-10}, pmid = {38192332}, issn = {1178-6973}, abstract = {OBJECTIVE: To understand the clinical features, diagnosis and treatment of Lemierre syndrome (LS), a high-risk and low-prevalence infectious disease.

METHODS: We present the severe LS case that was diagnosed using metagenomic next-generation sequencing (mNGS) in our hospital, and systematically summarized the diagnosis and treatment strategies of patients that reported LS from 2006 to 2022.

RESULTS: The 24-year-old patient in our hospital suffered from cranial nerve paralysis, a neurological complication rarely seen in LS cases. The causative agent (Fusobacterium necrophorum, Fn) of this patient was only detected by mNGS tests, and the reads number of Fn detected by plasma mNGS tests was decrease as the patients gradually improved, indicating plasma mNGS is valuable in monitoring treatment efficacy. Although most of the cases retrieved from the literature showed typical symptoms, such as a history of sore throat, septic emboli, and internal jugular vein thrombosis, clinical manifestations were still relatively heterogeneous (eg, diversity of predisposing factors and pathogens, differences in pulmonary imaging features).

CONCLUSION: We summarized the clinical presentation, diagnosis, treatment, and regression of 17 symptomatic cases reported LS to provide clinicians with knowledge about this rare but fatal disease. mNGS assays should be considered as early as possible to identify the responsible pathogens for acute and critically ill patients with suspected infections in order to implement accurate and effective treatment.}, } @article {pmid38192240, year = {2024}, author = {Skoog, EJ and Bosak, T}, title = {Predicted metabolic roles and stress responses provide insights into candidate phyla Hydrogenedentota and Sumerlaeota as members of the rare biosphere in biofilms from various environments.}, journal = {Environmental microbiology reports}, volume = {}, number = {}, pages = {}, doi = {10.1111/1758-2229.13228}, pmid = {38192240}, issn = {1758-2229}, support = {327126//Simons Foundation/ ; 344707//Simons Foundation/ ; }, abstract = {Pustular mats from Shark Bay, Western Australia, host complex microbial communities bound within an organic matrix. These mats harbour many poorly characterized organisms with low relative abundances (<1%), such as candidate phyla Hydrogenedentota and Sumerlaeota. Here, we aim to constrain the metabolism and physiology of these candidate phyla by analyzing two representative metagenome-assembled genomes (MAGs) from a pustular mat. Metabolic reconstructions of these MAGs suggest facultatively anaerobic, chemoorganotrophic lifestyles of both organisms and predict that both MAGs can metabolize a diversity of carbohydrate substrates. Ca. Sumerlaeota possesses genes involved in degrading chitin, cellulose and other polysaccharides, while Ca. Hydrogenedentota can metabolize cellulose derivatives in addition to glycerol, fatty acids and phosphonates. Both Ca. phyla can respond to nitrosative stress and participate in nitrogen metabolism. Metabolic comparisons of MAGs from Shark Bay and those from various polyextreme environments (i.e., hot springs, hydrothermal vents, subsurface waters, anaerobic digesters, etc.) reveal similar metabolic capabilities and adaptations to hypersalinity, oxidative stress, antibiotics, UV radiation, nitrosative stress, heavy metal toxicity and life in surface-attached communities. These adaptations and capabilities may account for the widespread nature of these organisms and their contributions to biofilm communities in a range of extreme surface and subsurface environments.}, } @article {pmid38191834, year = {2024}, author = {Ashiqueali, SA and Chaudhari, D and Zhu, X and Noureddine, S and Siddiqi, S and Garcia, DN and Gostynska, A and Stawny, M and Rubis, B and Zanini, BM and Mansoor, MAM and Schneider, A and Naser, SA and Yadav, H and Masternak, MM}, title = {Fisetin modulates the gut microbiota alongside biomarkers of senescence and inflammation in a DSS-induced murine model of colitis.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {38191834}, issn = {2509-2723}, support = {R56 AG074499/GF/NIH HHS/United States ; }, abstract = {Colitis, a subtype of inflammatory bowel disease (IBD), is a multifactorial disorder characterized by chronic inflammation of the colon. Among various experimental models used in the study of IBD, the chemical colitogenic dextran sulfate sodium (DSS) is most commonly employed to induce colitis in vivo. In the search for new therapeutic strategies, Fisetin, a flavonoid found in many fruits and vegetables, has recently garnered attention for its senolytic properties. Female mice were administered 2.5% DSS in sterile drinking water and were subsequently treated with Fisetin or vehicle by oral gavage. DSS significantly upregulated beta-galactosidase activity in colonic proteins, while Fisetin remarkably inhibited its activity to baseline levels. Particularly, qPCR revealed that the senescence and inflammation markers Vimentin and Ptgs2 were elevated by DSS exposure with Fisetin treatment inhibiting the expression of p53, Bcl2, Cxcl1, and Mcp1, indicating that the treatment reduced senescent cell burden in the DSS targeted intestine. Alongside, senescence and inflammation associated miRNAs miR-149-5p, miR-96-5p, miR-34a-5p, and miR-30e-5p were significantly inhibited by DSS exposure and restored by Fisetin treatment, revealing novel targets for the treatment of IBDs. Metagenomics was implemented to assess impacts on the microbiota, with DSS increasing the prevalence of bacteria in the phyla Bacteroidetes. Meanwhile, Fisetin restored gut health through increased abundance of Akkermansia muciniphila, which is negatively correlated with senescence and inflammation. Our study suggests that Fisetin mitigates DSS-induced colitis by targeting senescence and inflammation and restoring beneficial bacteria in the gut indicating its potential as a therapeutic intervention for IBDs.}, } @article {pmid38191433, year = {2024}, author = {Zhang, RY and Wang, YR and Liu, RL and Rhee, SK and Zhao, GP and Quan, ZX}, title = {Metagenomic characterization of a novel non-ammonia-oxidizing Thaumarchaeota from hadal sediment.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {7}, pmid = {38191433}, issn = {2049-2618}, support = {2021R1A2C3004015//National Research Foundation of Korea/ ; 2018YFC0310600//the National Key R&D Program of China/ ; 31870109, 31811540398//the National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Metagenome/genetics ; *Ammonia ; Ecosystem ; Metagenomics ; Archaea/genetics ; }, abstract = {BACKGROUND: The hadal sediment, found at an ocean depth of more than 6000 m, is geographically isolated and under extremely high hydrostatic pressure, resulting in a unique ecosystem. Thaumarchaeota are ubiquitous marine microorganisms predominantly present in hadal environments. While there have been several studies on Thaumarchaeota there, most of them have primarily focused on ammonia-oxidizing archaea (AOA). However, systematic metagenomic research specifically targeting heterotrophic non-AOA Thaumarchaeota is lacking.

RESULTS: In this study, we explored the metagenomes of Challenger Deep hadal sediment, focusing on the Thaumarchaeota. Functional analysis of sequence reads revealed the potential contribution of Thaumarchaeota to recalcitrant dissolved organic matter degradation. Metagenome assembly binned one new group of hadal sediment-specific and ubiquitously distributed non-AOA Thaumarchaeota, named Group-3.unk. Pathway reconstruction of this new type of Thaumarchaeota also supports heterotrophic characteristics of Group-3.unk, along with ABC transporters for the uptake of amino acids and carbohydrates and catabolic utilization of these substrates. This new clade of Thaumarchaeota also contains aerobic oxidation of carbon monoxide-related genes. Complete glyoxylate cycle is a distinctive feature of this clade in supplying intermediates of anabolic pathways. The pan-genomic and metabolic analyses of metagenome-assembled genomes belonging to Group-3.unk Thaumarchaeota have highlighted distinctions, including the dihydroxy phthalate decarboxylase gene associated with the degradation of aromatic compounds and the absence of genes related to the synthesis of some types of vitamins compared to AOA. Notably, Group-3.unk shares a common feature with deep ocean AOA, characterized by their high hydrostatic pressure resistance, potentially associated with the presence of V-type ATP and di-myo-inositol phosphate syntheses-related genes. The enrichment of organic matter in hadal sediments might be attributed to the high recruitment of sequence reads of the Group-3.unk clade of heterotrophic Thaumarchaeota in the trench sediment. Evolutionary and genetic dynamic analyses suggest that Group-3 non-AOA consists of mesophilic Thaumarchaeota organisms. These results indicate a potential role in the transition from non-AOA to AOA Thaumarchaeota and from thermophilic to mesophilic Thaumarchaeota, shedding light on recent evolutionary pathways.

CONCLUSIONS: One novel clade of heterotrophic non-AOA Thaumarchaeota was identified through metagenome analysis of sediments from Challenger Deep. Our study provides insight into the ecology and genomic characteristics of the new sub-group of heterotrophic non-AOA Thaumarchaeota, thereby extending the knowledge of the evolution of Thaumarchaeota. Video Abstract.}, } @article {pmid38190922, year = {2024}, author = {Liu, B and Zheng, Y and Wang, X and Qi, L and Zhou, J and An, Z and Wu, L and Chen, F and Lin, Z and Yin, G and Dong, H and Li, X and Liang, X and Han, P and Liu, M and Hou, L}, title = {Active dark carbon fixation evidenced by [14]C isotope assimilation and metagenomic data across the estuarine-coastal continuum.}, journal = {The Science of the total environment}, volume = {914}, number = {}, pages = {169833}, doi = {10.1016/j.scitotenv.2023.169833}, pmid = {38190922}, issn = {1879-1026}, abstract = {Estuaries, as important land-ocean transitional zones across the Earth's surface, are hotspots of microbially driven dark carbon fixation (DCF), yet understanding of DCF process remains limited across the estuarine-coastal continuum. This study explored DCF activities and associated chemoautotrophs along the estuarine and coastal environmental gradients, using radiocarbon labelling and molecular techniques. Significantly higher DCF rates were observed at middle- and high-salinity regions (0.65-2.31 and 0.66-2.82 mmol C m[-2] d[-1], respectively), compared to low-salinity zone (0.07-0.19 mmol C m[-2] d[-1]). Metagenomic analysis revealed relatively stable DCF pathways along the estuarine-coastal continuum, primarily dominated by Calvin-Benson-Bassham (CBB) cycle and Wood-Ljungdahl (WL) pathway. Nevertheless, chemoautotrophic communities driving DCF exhibited significant spatial variations. It is worth noting that although CBB cycle played an important role in DCF in estuarine sediments, WL pathway might play a more significant role, which has not been previously recognized. Overall, this study highlights that DCF activities coincide with the genetic potential of chemoautotrophy and the availability of reductive substrates across the estuarine-coastal continuum, and provides an important scientific basis for accurate quantitative assessment of global estuarine carbon sink.}, } @article {pmid38190719, year = {2024}, author = {Neyton, LPA and Sinha, P and Sarma, A and Mick, E and Kalantar, K and Chen, S and Wu, N and Delucchi, K and Zhuo, H and Bos, LDJ and Jauregui, A and Gomez, A and Hendrickson, CM and Kangelaris, KN and Leligdowicz, A and Liu, KD and Matthay, MA and Langelier, CR and Calfee, CS}, title = {Host and Microbe Blood Metagenomics Reveals Key Pathways Characterizing Critical Illness Phenotypes.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1164/rccm.202308-1328OC}, pmid = {38190719}, issn = {1535-4970}, abstract = {RATIONALE: Two molecular phenotypes of sepsis and acute respiratory distress syndrome, termed hyperinflammatory and hypoinflammatory, have been consistently identified by latent class analysis in numerous cohorts, with widely divergent clinical outcomes and differential responses to some treatments; however, the key biological differences between these phenotypes remain poorly understood.

OBJECTIVES: We used host and microbe metagenomic sequencing data from blood to deepen our understanding of biological differences between latent class analysis-derived phenotypes and to assess concordance between the latent class analysis-derived phenotypes and phenotypes reported by other investigative groups (e.g., SRS1-2, MARS1-4, reactive/uninflamed).

METHODS: We analyzed data from 113 hypoinflammatory and 76 hyperinflammatory sepsis patients enrolled in a two-hospital prospective cohort study. Molecular phenotypes had been previously assigned using latent class analysis.

MEASUREMENTS AND MAIN RESULTS: The hyperinflammatory and hypoinflammatory phenotypes of sepsis had distinct gene expression signatures, with 5,755 genes (31%) differentially expressed. The hyperinflammatory phenotype was associated with elevated expression of innate immune response genes, while the hypoinflammatory phenotype was associated with elevated expression of adaptive immune response genes, and notably, T-cell response genes. Plasma metagenomic analysis identified differences in prevalence of bacteremia, bacterial DNA abundance and composition between the phenotypes, with an increased presence and abundance of Enterobacteriaceae in the hyperinflammatory phenotype. Significant overlap was observed between these phenotypes and previously identified transcriptional subtypes of acute respiratory distress syndrome (reactive/uninflamed) and sepsis (SRS1-2). Analysis of data from the VANISH trial indicated that corticosteroids might have a detrimental effect in hypoinflammatory patients.

CONCLUSIONS: The hyperinflammatory and hypoinflammatory phenotypes have distinct transcriptional and metagenomic features that could be leveraged for precision treatment strategies.}, } @article {pmid38190489, year = {2023}, author = {Lv, Q and Cao, Y and Wang, J and Meng, L and Wang, G}, title = {Metagenomic Next-generation Sequencing May be a Tool for Timely Diagnosis of Seronegative and Primary Toxoplasma Infection After Allogeneic Hematopoietic Stem Cell Transplantation: A Case Report and Literature Review.}, journal = {The Pediatric infectious disease journal}, volume = {}, number = {}, pages = {}, doi = {10.1097/INF.0000000000004170}, pmid = {38190489}, issn = {1532-0987}, abstract = {We report a case of Toxoplasma gondii (T. gondii) antibody seronegativity in a 14-year-old boy with a primary infection of T. gondii after allogeneic hematopoietic stem cell transplantation for acute T-cell lymphoblastic leukemia who was rapidly diagnosed through metagenomic next-generation sequencing of peripheral blood as well as clinical manifestations. He was successfully cured with timely administration of trimethoprim-sulfamethoxazole due to early diagnosis.}, } @article {pmid38189540, year = {2023}, author = {Lin, Y and Zhang, Y and Sun, H and Jiang, H and Zhao, X and Teng, X and Lin, J and Shu, B and Sun, H and Liao, Y and Zhou, J}, title = {NanoDeep: a deep learning framework for nanopore adaptive sampling on microbial sequencing.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {1}, pages = {}, pmid = {38189540}, issn = {1477-4054}, support = {31900447//National Natural Science Foundation of China/ ; 2019RC06//Startup Foundation of Dermatology Hospital, Southern Medical University/ ; //State Key Development Program/ ; 2021YFC2302200//Ministry of Science and Technology of China/ ; HR202108//Hua Run fund of Joint Laboratory of Dermatology Hospital, Southern Medical University and China Resources Sanjiu Medical & Pharmaceutical/ ; }, mesh = {Humans ; *Deep Learning ; *Nanopores ; *Nanopore Sequencing ; Gene Library ; Genome, Bacterial ; }, abstract = {Nanopore sequencers can enrich or deplete the targeted DNA molecules in a library by reversing the voltage across individual nanopores. However, it requires substantial computational resources to achieve rapid operations in parallel at read-time sequencing. We present a deep learning framework, NanoDeep, to overcome these limitations by incorporating convolutional neural network and squeeze and excitation. We first showed that the raw squiggle derived from native DNA sequences determines the origin of microbial and human genomes. Then, we demonstrated that NanoDeep successfully classified bacterial reads from the pooled library with human sequence and showed enrichment for bacterial sequence compared with routine nanopore sequencing setting. Further, we showed that NanoDeep improves the sequencing efficiency and preserves the fidelity of bacterial genomes in the mock sample. In addition, NanoDeep performs well in the enrichment of metagenome sequences of gut samples, showing its potential applications in the enrichment of unknown microbiota. Our toolkit is available at https://github.com/lysovosyl/NanoDeep.}, } @article {pmid38189294, year = {2024}, author = {Zhang, J and Shi, M and Zhao, C and Liang, G and Li, C and Ge, X and Pei, C and Kong, Y and Li, D and Yang, W and Cao, B and Fu, L and Yan, Y and Wu, J and Zhou, J and Fang, Y and Meng, X and Li, Y and Wang, L}, title = {Role of intestinal flora in the development of nonalcoholic fatty liver disease in children.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0100623}, doi = {10.1128/spectrum.01006-23}, pmid = {38189294}, issn = {2165-0497}, abstract = {This study aims to characterize the gut microbiota in Chinese children with nonalcoholic fatty liver disease (NAFLD) through 16S rRNA and metagenomic sequencing. The results highlight the association between fecal microbiota and NAFLD in Chinese children, demonstrating distinct characteristics compared to adults and children from other countries. Based on the sequencing data from our cohort's fecal samples, we propose a microbiota model with a high area under the curve for distinguishing between NAFLD and healthy individuals. Furthermore, our follow-up study reveals that changes in the relative abundance of microbial biomarkers in this model are consistent with variations in patients' body mass index. These findings suggest the potential utility of the microbiota model and microbial biomarkers for diagnosing and treating NAFLD in children.}, } @article {pmid38189173, year = {2024}, author = {Biderre-Petit, C and Courtine, D and Hennequin, C and Galand, PE and Bertilsson, S and Debroas, D and Monjot, A and Lepère, C and Divne, AM and Hochart, C}, title = {A pan-genomic approach reveals novel Sulfurimonas clade in the ferruginous meromictic Lake Pavin.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e13923}, doi = {10.1111/1755-0998.13923}, pmid = {38189173}, issn = {1755-0998}, abstract = {The permanently anoxic waters in meromictic lakes create suitable niches for the growth of bacteria using sulphur metabolisms like sulphur oxidation. In Lake Pavin, the anoxic water mass hosts an active cryptic sulphur cycle that interacts narrowly with iron cycling, however the metabolisms of the microorganisms involved are poorly known. Here we combined metagenomics, single-cell genomics, and pan-genomics to further expand our understanding of the bacteria and the corresponding metabolisms involved in sulphur oxidation in this ferruginous sulphide- and sulphate-poor meromictic lake. We highlighted two new species within the genus Sulfurimonas that belong to a novel clade of chemotrophic sulphur oxidisers exclusive to freshwaters. We moreover conclude that this genus holds a key-role not only in limiting sulphide accumulation in the upper part of the anoxic layer but also constraining carbon, phosphate and iron cycling.}, } @article {pmid38188910, year = {2023}, author = {Shi, X and Qiu, S and Ji, L and Lu, H and Wu, S and Chen, Q and Zou, X and Hu, Q and Feng, T and Chen, S and Cui, W and Xu, S and Jiang, M and Cai, R and Geng, Y and Bai, Q and Huang, D and Liu, P}, title = {Pathogenetic characterization of a Micrococcus luteus strain isolated from an infant.}, journal = {Frontiers in pediatrics}, volume = {11}, number = {}, pages = {1303040}, pmid = {38188910}, issn = {2296-2360}, abstract = {PURPOSE: To explore the clinical characteristics of Micrococcus luteus bloodstream infection in an infant and characterize the phenotype and genotype of the isolated strains, as well as seek suitable infection models for assessing virulence.

METHODS: Clinical data was collected from an infant patient diagnosed with M. luteus bloodstream infection. Metagenomic sequencing was performed on the isolated blood sample. The strain was isolated and underwent mass spectrometry, biochemical tests, antibiotic susceptibility assays, and whole-genome sequencing. The Galleria mellonella infection model was used to assess M. luteus virulence.

RESULTS: Patient responded poorly to cephalosporins, but recovered after Linezolid treatment. Metagenomic sequencing identified M. luteus as the predominant species in the sample, confirming infection. They were identified as M. luteus with a high confidence level of 98.99% using mass spectrometry. The strain showed positive results for Catalase, Oxidase, and Urea tests, and negative results for Mannose, Xylose, Lactose, Mannitol, Arginine, and Galactose tests, consistent with the biochemical profile of M. luteus reference standards. M. luteus susceptibility to 15 antibiotics was demonstrated and no resistance genes were detected. Predicted virulence genes, including clpB, were associated with metabolic pathways and the type VI secretion system. The infection model demonstrated dose-dependent survival rates.

CONCLUSION: The infant likely developed a bloodstream infection with M. luteus due to compromised immunity. Although the isolated strain is sensitive to cephalosporin antibiotics and has low pathogenicity in infection models, clinical treatment with cephalosporins was ineffective. Linezolid proved to be effective, providing valuable guidance for future clinical management of such rare infections.}, } @article {pmid38188631, year = {2023}, author = {Qian, M and Li, C and Zhang, M and Zhan, Y and Zhu, B and Wang, L and Shen, Q and Yue, L and Chen, H and Cheng, Y}, title = {Blood metagenomics next-generation sequencing has advantages in detecting difficult-to-cultivate pathogens, and mixed infections: results from a real-world cohort.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1268281}, pmid = {38188631}, issn = {2235-2988}, mesh = {Humans ; *Coinfection ; High-Throughput Nucleotide Sequencing ; Intensive Care Units ; Metagenomics ; }, abstract = {BACKGROUND: Blood is a common sample source for metagenomics next-generation sequencing (mNGS) in clinical practice. In this study, we aimed to detect the diagnostic value of blood mNGS in a large real-world cohorts.

METHODS: Blood mNGS results of 1,046 cases were collected and analyzed along with other laboratory tests. The capabilities and accuracy of blood mNGS were compared with other conventional approaches.

RESULTS: Both the surgical department and the intensive care unit had a positive rate of over 80% in blood mNGS. The positive rate of mNGS was consistent with clinical manifestations. Among the 739 positive samples, 532 were detected as mixed infections. Compared to pathogen cultures, the negative predictive value of blood mNGS for bacteria and fungi detection was 98.9% [95%CI, 96.9%-100%], with an accuracy rate of 89.39%. When compared with polymer chain reaction, the consistency rates of blood mNGS for virus identification were remarkably high.

CONCLUSIONS: Blood mNGS have significant advantages in detecting difficult-to-cultivate bacteria or fungi, viruses, and mixed infections, which benefits patients of surgery department the most. Samples other than blood are recommended for mNGS test if a specific infection is suspected. The reporting threshold and reporting criteria of blood mNGS need to be optimized.}, } @article {pmid38188628, year = {2023}, author = {Liu, Y and Wen, Z and Fang, Y and Wang, T and Wu, F and Zhang, H and Chen, D and Liu, J}, title = {Herpesvirus reactivation in respiratory tract is associated with increased mortality of severe pneumonia patients and their respiratory microbiome dysbiosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1294142}, pmid = {38188628}, issn = {2235-2988}, mesh = {Humans ; Dysbiosis ; Retrospective Studies ; Respiratory System ; *Pneumonia ; *Herpesviridae/genetics ; *Herpesvirus 1, Human ; Herpesvirus 2, Human ; Herpesvirus 4, Human ; *Microbiota ; }, abstract = {Severe pneumonia (SP) is a respiratory tract disease that seriously threatens human health. The herpesvirus detected in patients, especially with severe and immunodeficient diseases, is gradually attracting the attention of clinical doctors. However, little is known about the effect of herpesvirus on the prognosis of SP patients and the pulmonary microbial community. Here, we retrospectively analyzed respiratory samples from 45 SP patients detected by metagenomic next-generation sequencing (mNGS). A total of five types of herpesviruses were detected, with Human alphaherpesvirus 1 (HHV-1) in 19 patients, Human betaherpesvirus 5 (CMV) in 7 patients, Human betaherpesvirus 7 (HHV-7) in 6 patients, Human alphaherpesvirus 2 (HHV-2) in 5 patients, and Human gammaherpesvirus 4 (EBV) in 4 patients. Further analysis showed that the mortality of the herpesvirus-positive group was significantly higher than that of the negative group. The results also showed that HHV-1 was significantly associated with the prognosis of SP patients, while the other herpesviruses did not have a significant difference in patient mortality. A comparison of the microbial community characteristics of SP patients showed a significant difference in beta-diversity between herpesvirus-positive and negative groups. Species difference analysis showed that the herpesvirus-positive group was related to more conditional pathogens, such as Pneumocystis jirovecii and Burkholderia cepacia. In summary, our results suggest that the presence of herpesvirus is associated with the mortality of SP patients. Furthermore, enrichment of conditional pathogens in the respiratory tract of herpesvirus-positive SP patients may be a potential reason for the increased mortality.}, } @article {pmid38188627, year = {2023}, author = {Shi, Y and Peng, JM and Hu, XY and Yang, QW and Wang, Y}, title = {Metagenomic next-generation sequencing for detecting Aspergillosis pneumonia in immunocompromised patients: a retrospective study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1209724}, pmid = {38188627}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *Aspergillosis ; *Invasive Pulmonary Aspergillosis/diagnosis ; High-Throughput Nucleotide Sequencing ; Immunocompromised Host ; }, abstract = {PURPOSE: The identification of Aspergillus by metagenomic next-generation sequencing (mNGS) remains a challenging task due to the difficulty of nucleic acid extraction. The objective of this study was to determine whether mNGS could provide an accurate and efficient method for detecting invasive pulmonary aspergillosis (IPA) in immunocompromised patients (ICP).

METHODS: A total of 133 ICP admitted to the ICU between January 2020 and September 2022 were enrolled in the study, of which 46 were diagnosed with IPA and 87 were non-IPA cases. The bronchoalveolar lavage fluid (BALF) was analyzed for the presence of Aspergillosis and other co-pathogens using mNGS, and its diagnostic performance was compared to conventional microbial tests (CMTs) that included smear, cultures, serum and BALF galactomannan (GM) test. Clinical composite diagnosis was used as the reference standard.

RESULTS: mNGS had a sensitivity, specificity, and accuracy of 82.6%, 97.7%, and 92.5%, respectively, in diagnosing IPA. These findings were comparable to those of the combination of multiple CMTs. Interestingly, the sensitivity of mNGS was superior to that of any single CMT method, as demonstrated by comparisons with smears (8.7%, P < 0.001), culture (39.1%, P < 0.001), serum GM (23.9%, P < 0.001) and BALF GM (69.6%, P = 0.031). mNGS was capable of accurately distinguish strains of Aspergillus genus, with a consistency of 77.8% with culture. Furthermore, mNGS also identified A. fumigatus, A. flavus, A. terrestris, A. oryzae and Mucor spp. in culture-negative cases. The sequencing reads of Aspergillus by mNGS exhibited extensive variation, ranging from 11 to1702. A positive correlation was observed between the optical density index of BALF GM and unique reads by mNGS (r = 0.607, P = 0.001) in BALF-GM positive patients. Notably, mNGS was able to diagnose 35 out of 37 cases with mixed infection, with P. jirovecii and cytomegalovirus being the most common co-pathogens.

CONCLUSIONS: mNGS presents a feasible and remarkably sensitive approach for detecting Aspergillus in ICP, thereby serving as a valuable adjunctive tool to CMT. Furthermore, mNGS's ability to accurately identify fungal species and co-pathogens can assist in guiding appropriate antimicrobial therapy.}, } @article {pmid38188585, year = {2023}, author = {Xu, J and Wang, L and Lv, W and Song, X and Nie, Y and Wu, XL}, title = {Metabolic profiling of petroleum-degrading microbial communities incubated under high-pressure conditions.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1305731}, pmid = {38188585}, issn = {1664-302X}, abstract = {While pressure is a significant characteristic of petroleum reservoirs, it is often overlooked in laboratory studies. To clarify the composition and metabolic properties of microbial communities under high-pressure conditions, we established methanogenic and sulfate-reducing enrichment cultures under high-pressure conditions using production water from the Jilin Oilfield in China. We utilized a metagenomics approach to analyze the microbial community after a 90-day incubation period. Under methanogenic conditions, Firmicutes, Deferribacteres, Ignavibacteriae, Thermotogae, and Nitrospirae, in association with the hydrogenotrophic methanogen Archaeoglobaceae and acetoclastic Methanosaeta, were highly represented. Genomes for Ca. Odinarchaeota and the hydrogen-dependent methylotrophic Ca. Methanosuratus were also recovered from the methanogenic culture. The sulfate-reducing community was dominated by Firmicutes, Thermotogae, Nitrospirae, Archaeoglobus, and several candidate taxa including Ca. Bipolaricaulota, Ca. Aminicenantes, and Candidate division WOR-3. These candidate taxa were key pantothenate producers for other community members. The study expands present knowledge of the metabolic roles of petroleum-degrading microbial communities under high-pressure conditions. Our results also indicate that microbial community interactions were shaped by syntrophic metabolism and the exchange of amino acids and cofactors among members. Furthermore, incubation under in situ pressure conditions has the potential to reveal the roles of microbial dark matter.}, } @article {pmid38188580, year = {2023}, author = {Wu, D and Yin, C and Fan, Y and Chi, H and Liu, Z and Jin, G}, title = {Effect of forest planting patterns on the formation of soil organic carbon during litter lignocellulose degradation from a microbial perspective.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1327481}, pmid = {38188580}, issn = {1664-302X}, abstract = {Litter decomposition is an important source of soil organic carbon, and it plays a key role in maintaining the stability of forest ecosystems. The microbial mechanism of soil organic carbon (SOC) formation in different urban forest planting patterns during litter lignocellulose degradation is still unclear. The key genes, microbes, and metabolites in the process of lignocellulose degradation and SOC formation were determined by metagenomics and metabolomics in different litter decomposition layers and soil layers in different urban forest planting patterns, including three types of broadleaf forests (BP forests), three types of coniferous forests (CP forests), and two types of mixed coniferous and broadleaf forests (MCBP forests). The results indicated that the cellulose, hemicellulose, and lignin concentrations from the undecomposed layer to the totally decomposed layer decreased by 70.07, 86.83, and 73.04% for CP litter; 74.30, 93.80, and 77.55% for BP litter; and 62.51, 48.58, and 90.61% for MCBP litter, respectively. The soil organic carbon of the BP forests and MCBP forests was higher than that of the CP forests by 38.06 and 94.43% for the 0-10 cm soil layer and by 38.55 and 20.87% for the 10-20 cm soil layer, respectively. Additionally, the gene abundances of glycoside hydrolases (GHs) and polysaccharide lyases (PLs) in the BP forests were higher than those in the MCBP forests and CP forests. Amino acid metabolism, sugar metabolism, TCA metabolism, and cAMP signaling metabolism were mainly between the CP forests and BP forests, while the TCA cycle, pyruvate metabolism, phenylalanine metabolism, and tyrosine metabolism were mainly between the BP forests and MCBP forests during litter decomposition. Additionally, ammonia nitrogen and hemicellulose were key factors driving SOC formation in the CP forests, while ammonia nitrogen, hemicellulose, and lignocellulose-degrading genes were key factors driving SOC formation in the BP forests. For the MCBP forests, cellulose, pH, ammonia nitrogen, and lignin were key factors driving SOC formation. Our findings revealed that the BP forests and MCBP forests had stronger lignocellulose degradation performance in the formation of SOC. This study provided a theoretical basis for the flow and transformation of nutrients in different urban forest management patterns.}, } @article {pmid38188577, year = {2023}, author = {He, Y and Cui, W and Fang, T and Zhang, Z and Zeng, M}, title = {Metabolites of the gut microbiota may serve as precise diagnostic markers for sarcopenia in the elderly.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1301805}, pmid = {38188577}, issn = {1664-302X}, abstract = {Sarcopenia, a disease recognized by the World Health Organization, has posed a great challenge to the world in the current aging society. The vital role of the gut microbiome through the gut-muscle axis in sarcopenia is increasingly recognized. However, the working mechanisms by which the gut microbiota functions have not been fully explored in the multi-omics field. Here, we designed a cross-sectional study that recruited patients (n = 32) with sarcopenia and healthy old adults (n = 31). Diagnosis of sarcopenia was based on the Asian Working Group for Sarcopenia (AWGS) in 2019 criteria. Muscle mass was represented by appendicular skeletal muscle mass measured by using direct segmental multi-frequency bioelectrical impedance and muscle strength was evaluated using the handgrip strength. The Short Physical Performance Battery, the 5-time Chair Stand Test, and the 4-metre Walk Test were used to assess physical performance. Shotgun metagenomic sequencing was used to profile the gut microbiome in order to identify its construction and function. Metabolome based on untargeted metabolomics was applied to describe the features and structure of fecal metabolites. In clinical indexes including triglycerides and high-density lipoprotein cholesterol, we noted a significant decrease in triglycerides (TG) and a significant increase in high-density lipoprotein cholesterol (HDL-C) in patients with sarcopenia. Appendicular skeletal muscle mass of patients with sarcopenia was lower than the health group. Based on intestinal metagenomic and fecal metabolomic profiles, we found that the gut microbiome and metabolome were disturbed in patients with sarcopenia, with significant decreases in bacteria such as Bifidobacterium longum, Bifidobacterium pseudocatenulatum, and Bifidobacterium adolescentis, as well as metabolites such as shikimic acid. Also, we plotted supervised classification models at the species level of gut bacteria (AUC = 70.83-88.33) and metabolites (AUC = 92.23-98.33) based on machine learning, respectively. Based on the gut-muscle axis network, a potential mechanism is proposed along the gut microbiome - key metabolites - clinical index, that Phascolarctobacterium faecium affects appendicular skeletal muscle mass, calf circumference, handgrip strength, and BMI via Shikimic acid metabolites. This study elucidates the potential mechanisms by which the gut microbiome influences the progress of sarcopenia through metabolites and provides a meaningful theoretical foundation for reference in the diagnosis and treatment of sarcopenia.}, } @article {pmid38188576, year = {2023}, author = {Ma, X and Wang, W and Cai, L and Xiao, M and He, F and Liu, Z and Chen, D and Wang, Y and Shen, L and Gu, Y}, title = {Analysis of the microbial diversity in takin (Budorcas taxicolor) feces.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1303085}, pmid = {38188576}, issn = {1664-302X}, abstract = {INTRODUCTION: The intestinal tract of animals is a complex and dynamic microecosystem that is inextricably linked to the health of the host organism. Takin (Budorcas taxicolor) is a threatened species, and its gut microbiome is poorly understood. Therefore, this study aimed to analyze the microbial community structure and potential pathogens of takin.

METHODS: Takin fecal samples were collected from five sites in a nature reserve to ensure the uniformity of sample collection, determine the effects of different geographical locations on gut microbes, and analyze the differences in microbial communities between sites. Subsequently, high-throughput 16S rDNA gene sequencing was performed to analyze the microbial diversity and potential pathogens in the gut; the findings were verified by isolating and culturing bacteria and metagenomic sequencing.

RESULTS AND DISCUSSION: The takin gut microflora consisted mainly of four phyla: Firmicutes (69.72%), Bacteroidota (13.55%), Proteobacteria (9.02%), and Verrucomicrobiota (3.77%), representing 96.07% of all microorganisms. The main genera were UCG-005 (20.25%), UCG-010_unclassified (12.35%), Firmicus_unclassified (4.03%), and Rumino coccsea_unclassified (3.49%), while the main species were assigned to Bacteria_unclassified. Potential pathogens were also detected, which could be used as a reference for the protection of takin. Pseudomonas presented the highest abundance at Shuichiping and may represent the main pathogen responsible for the death of takin at the site. This study provides an important reference for investigating the composition of the bacterial community in the intestine of takin.}, } @article {pmid38188569, year = {2023}, author = {Liu, S and Wang, Z and Wang, Z and Wu, Q and Zhou, J and Wang, R and Han, J and Su, X}, title = {Comparison of the gut microbiota and metabolism in different regions of Red Swamp Crayfish (Procambarus clarkii).}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1289634}, pmid = {38188569}, issn = {1664-302X}, abstract = {BACKGROUND: The gut microbiota is very important for maintaining the homeostasis and health of crustaceans. Many factors affect the gut microbiota of crustaceans, one of which is temperature. However, it is currently unclear how temperature affects the gut microbiota and metabolites of Procambarus clarkii.

METHODS: Using metagenomic sequencing and gas chromatography-mass spectrometry (GC-MS) techniques, the gut microbiota and metabolites of P. clarkii from Hubei (HB), Jiangsu (JS), Shandong (SD), and Zhejiang (ZJ) in China were investigated.

RESULTS: Under the impact of temperature, the gut microbiota and metabolites of P. clarkii exhibit a specific trend of change. The primary pathogenic bacteria affecting P. clarkii are Citrobacter, Enterobacterium, and Aeromonas, which are affected by temperature. Two metabolites, namely, sugars and amino acids, are regulated by temperature.

IMPLICATION: This study demonstrated that the gut microbiota and gut metabolites of P. clarkii were considerably affected by temperature. It provides a theoretical basis for the systematic study of P. clarkii and provides a basis for a healthy culture of P. clarkii.}, } @article {pmid38188564, year = {2023}, author = {Tan, G and Qi, S and Wang, Y and Li, X and Li, X and Li, M and Li, L and Zhao, L and Hu, M}, title = {Uncovering differences in the composition and function of phage communities and phage-bacterium interactions in raw soy sauce.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1328158}, pmid = {38188564}, issn = {1664-302X}, abstract = {INTRODUCTION: Although the composition and succession of microbial communities in soy sauce fermentation have been well-characterized, the understanding of phage communities in soy sauce remains limited.

METHODS: This study determined the diversity, taxonomic composition, and predicted function of phage communities and the phage-host interactions in two types of raw soy sauce (Cantonese-type fermentation, NJ; Japanese-type fermentation, PJ) using shotgun metagenomics.

RESULTS AND DISCUSSION: These two raw soy sauces showed differences in phage composition (121 viral operational taxonomic units (vOTUs) in NJ and 387 vOTUs in PJ), with a higher abundance of the family Siphoviridae (58.50%) in the NJ phage community and a higher abundance of Myoviridae (33.01%) in PJ. Auxiliary metabolic functional annotation analyses showed that phages in the raw soy sauces mostly encoded genes with unknown functions (accounting for 66.33% of COG profiles), but the NJ sample contained genes mostly annotated to conventional functions related to carbohydrate metabolism (0.74%) and lipid metabolism (0.84%), while the PJ sample presented a higher level of amino acid metabolism functions (0.12%). Thirty auxiliary metabolism genes (AMGs) were identified in phage genomes, which were associated with carbohydrate utilization, cysteine and methionine metabolism, and aspartic acid biosynthesis for the host. To identify phage-host interactions, 30 host genomes (affiliated with 22 genera) were also recruited from the metagenomic dataset. The phage-host interaction analysis revealed a wide range of phage hosts, for which a total of 57 phage contigs were associated with 17 host genomes, with Shewanella fodinae and Weissella cibaria infected by the most phages. This study provides a comprehensive understanding of the phage community composition, auxiliary metabolic functions, and interactions with hosts in two different types of raw soy sauce.}, } @article {pmid38188309, year = {2024}, author = {Chauhan, G and Arya, M and Kumar, V and Verma, D and Sharma, M}, title = {An improved protocol for metagenomic DNA isolation from low microbial biomass alkaline hot-spring sediments and soil samples.}, journal = {3 Biotech}, volume = {14}, number = {1}, pages = {34}, pmid = {38188309}, issn = {2190-572X}, abstract = {High-quality, humic-acid-free pure DNA is a prerequisite for functional and sequence-based approaches of metagenomics. In the present investigation, an improved extraction buffer was developed by making a combination of powdered activated charcoal (2%; w/v), polyvinyl poly pyrrolidone (2%; w/v), and CaCl2 (2%; w/v). This trio significantly improved the purity and yield of the metagenomic DNA from the hot spring's hot and alkaline soil. The quality of extracted metagenomic DNA was successfully validated by PCR amplification and restriction enzymes. Besides, the thermophilic amylase encoding genes were also retrieved from these soil DNA samples. Extreme habitats I harbour low microbial biomass and, therefore, demand in-situ lysis of the microbial cells to access their genomes. The protocol can potentially extract DNA from geothermal spring habitats where the count of microbial cells is low.}, } @article {pmid38188174, year = {2024}, author = {Kerkvliet, JJ and Bossers, A and Kers, JG and Meneses, R and Willems, R and Schürch, AC}, title = {Metagenomic assembly is the main bottleneck in the identification of mobile genetic elements.}, journal = {PeerJ}, volume = {12}, number = {}, pages = {e16695}, pmid = {38188174}, issn = {2167-8359}, mesh = {*Metagenome/genetics ; DNA Transposable Elements/genetics ; Ecosystem ; Algorithms ; *Bacteriophages/genetics ; }, abstract = {Antimicrobial resistance genes (ARG) are commonly found on acquired mobile genetic elements (MGEs) such as plasmids or transposons. Understanding the spread of resistance genes associated with mobile elements (mARGs) across different hosts and environments requires linking ARGs to the existing mobile reservoir within bacterial communities. However, reconstructing mARGs in metagenomic data from diverse ecosystems poses computational challenges, including genome fragment reconstruction (assembly), high-throughput annotation of MGEs, and identification of their association with ARGs. Recently, several bioinformatics tools have been developed to identify assembled fragments of plasmids, phages, and insertion sequence (IS) elements in metagenomic data. These methods can help in understanding the dissemination of mARGs. To streamline the process of identifying mARGs in multiple samples, we combined these tools in an automated high-throughput open-source pipeline, MetaMobilePicker, that identifies ARGs associated with plasmids, IS elements and phages, starting from short metagenomic sequencing reads. This pipeline was used to identify these three elements on a simplified simulated metagenome dataset, comprising whole genome sequences from seven clinically relevant bacterial species containing 55 ARGs, nine plasmids and five phages. The results demonstrated moderate precision for the identification of plasmids (0.57) and phages (0.71), and moderate sensitivity of identification of IS elements (0.58) and ARGs (0.70). In this study, we aim to assess the main causes of this moderate performance of the MGE prediction tools in a comprehensive manner. We conducted a systematic benchmark, considering metagenomic read coverage, contig length cutoffs and investigating the performance of the classification algorithms. Our analysis revealed that the metagenomic assembly process is the primary bottleneck when linking ARGs to identified MGEs in short-read metagenomics sequencing experiments rather than ARGs and MGEs identification by the different tools.}, } @article {pmid38187747, year = {2023}, author = {Cook, R and Telatin, A and Bouras, G and Camargo, AP and Larralde, M and Edwards, RA and Adriaenssens, EM}, title = {Predicting stop codon reassignment improves functional annotation of bacteriophages.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38187747}, support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; }, abstract = {The majority of bacteriophage diversity remains uncharacterised, and new intriguing mechanisms of their biology are being continually described. Members of some phage lineages, such as the Crassvirales, repurpose stop codons to encode an amino acid by using alternate genetic codes. Here, we investigated the prevalence of stop codon reassignment in phage genomes and subsequent impacts on functional annotation. We predicted 76 genomes within INPHARED and 712 vOTUs from the Unified Human Gut Virome catalogue (UHGV) that repurpose a stop codon to encode an amino acid. We re-annotated these sequences with modified versions of Pharokka and Prokka, called Pharokka-gv and Prokka-gv, to automatically predict stop codon reassignment prior to annotation. Both tools significantly improved the quality of annotations, with Pharokka-gv performing best. For sequences predicted to repurpose TAG to glutamine (translation table 15), Pharokka-gv increased the median gene length (median of per genome medians) from 287 to 481 bp for UHGV sequences (67.8% increase) and from 318 to 550 bp for INPHARED sequences (72.9% increase). The re-annotation increased mean coding density from 66.8% to 90.0%, and from 69.0% to 89.8% for UHGV and INPHARED sequences. Furthermore, the proportion of genes that could be assigned functional annotation increased, including an increase in the number of major capsid proteins that could be identified. We propose that automatic prediction of stop codon reassignment before annotation is beneficial to downstream viral genomic and metagenomic analyses.}, } @article {pmid38187087, year = {2024}, author = {Ortiz-Velez, A and Kelley, ST}, title = {Data-driven mathematical and visualization approaches for removing rare features for Compositional Data Analysis (CoDA).}, journal = {NAR genomics and bioinformatics}, volume = {6}, number = {1}, pages = {lqad110}, pmid = {38187087}, issn = {2631-9268}, abstract = {Sparse feature tables, in which many features are present in very few samples, are common in big biological data (e.g. metagenomics). Ignoring issues of zero-laden datasets can result in biased statistical estimates and decreased power in downstream analyses. Zeros are also a particular issue for compositional data analysis using log-ratios since the log of zero is undefined. Researchers typically deal with this issue by removing low frequency features, but the thresholds for removal differ markedly between studies with little or no justification. Here, we present CurvCut, an unsupervised data-driven approach with human confirmation for rare-feature removal. CurvCut implements two distinct approaches for determining natural breaks in the feature distributions: a method based on curvature analysis borrowed from thermodynamics and the Fisher-Jenks statistical method. Our results show that CurvCut rapidly identifies data-specific breaks in these distributions that can be used as cutoff points for low-frequency feature removal that maximizes feature retention. We show that CurvCut works across different biological data types and rapidly generates clear visual results that allow researchers to confirm and apply feature removal cutoffs to individual datasets.}, } @article {pmid38187015, year = {2024}, author = {Liu, L and Sun, Y and Du, S and Li, Y and Wang, J}, title = {Nanoplastics promote the dissemination of antibiotic resistance genes and diversify their bacterial hosts in soil.}, journal = {Eco-Environment & Health (Online)}, volume = {3}, number = {1}, pages = {1-10}, pmid = {38187015}, issn = {2772-9850}, abstract = {The wide application of plastics has led to the ubiquitous presence of nanoplastics and microplastics in terrestrial environments. However, few studies have focused on the mechanism underlying the effects of plastic particles on soil microbiomes and resistomes, especially the differences between nanoplastics and microplastics. This study investigated the microbiome and resistome in soil exposed to polystyrene microplastics (mPS) or nanoplastics (nPS) through 16S rRNA and shotgun metagenomic sequencing. Distinct microbial communities were observed between mPS and nPS exposure groups, and nPS exposure significantly changed the bacterial composition even at the lowest amended rate (0.01%, w/w). The abundance of antibiotic resistance genes (ARGs) in nPS exposure (1%) was 0.26 copies per cell, significantly higher than that in control (0.21 copies per cell) and mPS exposure groups (0.21 copies per cell). It was observed that nanoplastics, bacterial community, and mobile genetic elements (MGEs) directly affected the ARG abundance in nPS exposure groups, while in mPS exposure groups, only MGEs directly induced the change of ARGs. Streptomyces was the predominant host for multidrug in the control and mPS exposure, whereas the primary host was changed to Bacillus in nPS exposure. Additionally, exposure to nPS induced several bacterial hosts to exhibit possible multi-antibiotic resistance characteristics. Our results indicated that the effects of plastic particles on the soil microbial community were size-dependent, and nano-sized plastic particles exhibited more substantial impacts. Both microplastics and nanoplastics promoted ARG transfer and diversified their bacterial hosts. These findings bear implications for the regulation of plastic waste and ARGs.}, } @article {pmid38186742, year = {2024}, author = {Babalola, OO and Enagbonma, BJ}, title = {Dataset of amplicon metagenomic assessment of barley rhizosphere bacteria under different fertilization regimes.}, journal = {Data in brief}, volume = {52}, number = {}, pages = {109920}, pmid = {38186742}, issn = {2352-3409}, abstract = {The metagenomic dataset profiled in this research is built on bacterial 16S rRNA gene amplicon of DNA mined from barley rhizosphere under chemical (CB) and organic (OB) fertilization. Amplicon-based sequencing was prepared by the Illumina platform, and the raw sequence dataset was examined using Metagenomic Rast Server (MG-RAST). The metagenome comprised sixteen samples that include CB1 (494,583 bp), CB2 (586,532 bp), CB3 (706,685 bp), CB4 (574,606 bp), CB5 (395,460 bp), CB6 (520,822 bp), CB7 (511,729 bp), CB8 (548,074 bp), OB1 (642,794 bp), OB2 (513,767 bp), OB3 (461,293 bp), OB4 (498,241 bp), OB5 (689,497 bp), OB6 (423,436 bp), OB7 (478,657 bp) and OB8 (279,186 bp). Information from the metagenome sequences is accessible under the bioproject numbers PRJNA827679 (CB1), PRJNA827686 (CB2), PRJNA827693 (CB3), PRJNA827699 (CB4), PRJNA827706 (CB5), PRJNA827761 (CB6), PRJNA827780 (CB7), PRJNA827786 (CB8), PRJNA826806 (OB1), PRJNA826824 (OB2), PRJNA826834 (OB3), PRJNA826841 (OB4), PRJNA826853 (OB5), PRJNA827254 (OB6), PRJNA827256 (OB7), and PRJNA827257 (OB8) at NCBI. Actinobacteria dominated the soil samples at the phylum level.}, } @article {pmid38186741, year = {2024}, author = {Dusengemungu, L and Gwanama, C and Mubemba, B}, title = {Data on fungal abundance and diversity in copper and cobalt contaminated tailing soils in Kitwe, Zambia.}, journal = {Data in brief}, volume = {52}, number = {}, pages = {109951}, pmid = {38186741}, issn = {2352-3409}, abstract = {Mining activities in the Zambian Copperbelt Province have led to the release of heavy metal-containing waste, causing contamination in nearby areas. Despite this environmental challenge, limited knowledge exists regarding the mycobiota in copper mine sites. This study investigates fungal community structure in copper(Cu) and cobalt (Co) contaminated soils around decommisioned dams in Kitwe. Metagenomic analysis of the ITSF1 gene amplicons was used for the purpose. The composition of soil fungal communities was characterized, and the findings revealed significant insights. At the phylum level, Basidiomycota dominated the fungal profiles in the tailings (64.59%), followed by Ascomycota (21.30%), Glomeromycota (4.53%), and Rozellomycota (0.0275%). Several fungal genera, including Vanrija, Paraconiothyrium, Toxicladosporium, Neocosmospora, Septoglomus, and Fusarium, were more abundant in contaminated tailings soils, suggesting their potential in leaching, absorbing, and transforming heavy metals. In contrast, the reference soil at Mwekera National Forest exhibited different dominance patterns with four fungal phyla identified, with Basidiomycota and Ascomycota dominating most samples. Glomeromycota, known for forming arbuscular mycorrhizae with plants, were found in contaminated soils, while Rozellomycota, which can serve ecological roles in various ecosystems, were also present. Notable fungal species such as Aspergillus, Penicillium, Fusarium, and Oidiodendron demonstrated resilience to Cu and Co, the primary contaminants in the Copperbelt.}, } @article {pmid38186739, year = {2024}, author = {Rahayu, T and Tyastuti, EM and Ambarwati, A and Agustina, L and Setiyadi, NA and Jamil, N and Sidiq, Y}, title = {Metagenomic data of bacterial 16S rRNA in the cemetery soil samples in Surakarta City, Indonesia.}, journal = {Data in brief}, volume = {52}, number = {}, pages = {109963}, pmid = {38186739}, issn = {2352-3409}, abstract = {Cemetery soils most likely contain degradative bacteria which possibly have beneficial potencies. However, the bacterial exploration in these potencies is still limitedly conducted in Indonesia. The raw sequence data of total bacteria in the cemetery soils through metagenomic analysis have been revealed. The data were obtained by collecting soil samples from six spots of two major Cemetery areas, which were Pracimaloyo (P) and Bonoloyo (B), in Surakarta City, Central Java, Indonesia. The six sample spots consisted of two samples from P area with respectively 20 cm and 140 cm depths and four samples of each two samples from B area with 20 and 40 cm depths. The total DNA was subsequently extracted from the collected soils using ZymoBIOMICS DNA Miniprep Kit. The total DNA then was amplified using a couple of 16S rRNA primers through Illumina HiSeq 2500 PE250 (Novogen, Korea) environment system. The raw sequence data has been submitted to the National Center for Biotechnology Information (NCBI) with project ID PRJNA997385. The archived sequence can be accessed in the NCBI website with the following URLs https://www.ncbi.nlm.nih.gov/sra/PRJNA997385. A brief analysis of the sequence data showed that the most common phyla in 20 cm-depths were Proteobacteria (29.5%), Actinobacteria (21.6%), and Firmicutes (19.2%), while Actinobacteria were the most found in 140 cm-depths with 34.2% followed by Proteobacteria (21.9%) and Firmicutes (16.6%). This data would be the first report of total bacterial sequence from cemetery soils in Indonesia.}, } @article {pmid38186256, year = {2023}, author = {Qi, W and Xue, MY and Jia, MH and Zhang, S and Yan, Q and Sun, HZ}, title = {- Invited Review - Understanding the functionality of the rumen microbiota: searching for better opportunities for rumen microbial manipulation.}, journal = {Animal bioscience}, volume = {}, number = {}, pages = {}, doi = {10.5713/ab.23.0308}, pmid = {38186256}, issn = {2765-0189}, abstract = {The rumen microbiota plays a central role in the digestive process of ruminants. Its remarkable ability to break down complex plant fibers and proteins, converting them into essential organic compounds that provide animals with energy and nutrition. Research on rumen microbiota not only contributes to improving animal production performance and enhancing feed utilization efficiency but also holds the potential to reduce methane emission and environment impact. Nevertheless, studies on rumen microbiota face numerous challenges, including complexity, difficulties in cultivation, and obstacles in functional analysis. This review provides an overview of microbial species involved in the degradation of macromolecules, the fermentation processes, and methane production in the rumen, all based on cultivation methods. Additionally, the review introduces the applications, advantages, and limitations of emerging omics technologies such as metagenomics, metatranscriptomics, metaproteomics, and metabolomics, in investigating the functionality of rumen microbiota. Finally, the article offers a forward-looking perspective on the new horizons and technologies in the field of rumen microbiota functional research. These emerging technologies, with continuous refinement and mutual complementation, have deepened our understanding of rumen microbiota functionality, thereby enabling effective manipulation of the rumen microbial community.}, } @article {pmid38186252, year = {2023}, author = {Mizoguchi, Y and Guan, LL}, title = {- Invited Review - Translational gut microbiome research for strategies to improve beef cattle production sustainability and meat quality.}, journal = {Animal bioscience}, volume = {}, number = {}, pages = {}, doi = {10.5713/ab.23.0387}, pmid = {38186252}, issn = {2765-0189}, abstract = {Advanced and innovative breeding and management of meat-producing animals are needed to address the global food security and sustainability challenges. Beef production is an important industry for securing animal protein resources in the world and meat quality significantly contributes to the economic values and human needs. Improvement of cattle feed efficiency has become an urgent task as it can lower the environmental burden of methane gas emissions and the reduce the consumption of human edible cereal grains. Cattle depend on their symbiotic microbiome and its activity in the rumen and gut to maintain growth and health. Recent developments in high-throughput omics analysis (metagenome, metatranscriptome, metabolome, metaproteome and so on) have made it possible to comprehensively analyze microbiome, hosts and their interactions and to define their roles in affecting cattle biology. In this review, we focus on the relationships among gut microbiome and beef meat quality, feed efficiency, methane emission as well as host genetics in beef cattle, aiming to determine the current knowledge gaps for the development of the strategies to improve the sustainability of beef production.}, } @article {pmid38185909, year = {2024}, author = {Niu, C and Lv, W and Zhu, X and Dong, Z and Yuan, K and Jin, Q and Zhang, P and Li, P and Mao, M and Dong, T and Chen, Z and Luo, J and Hou, L and Zhang, C and Hao, K and Chen, S and Huang, Z}, title = {Intestinal Translocation of Live Porphyromonas gingivalis Drives Insulin Resistance.}, journal = {Journal of dental research}, volume = {}, number = {}, pages = {220345231214195}, doi = {10.1177/00220345231214195}, pmid = {38185909}, issn = {1544-0591}, abstract = {Periodontitis has been emphasized as a risk factor of insulin resistance-related systemic diseases. Accumulating evidence has suggested a possible "oral-gut axis" linking oral infection and extraoral diseases, but it remains unclear whether periodontal pathogens can survive the barriers of the digestive tract and how they play their pathogenic roles. The present study established a periodontitis mouse model through oral ligature plus Porphyromonas gingivalis inoculation and demonstrated that periodontitis aggravated diet-induced obesity and insulin resistance, while also causing P. gingivalis enrichment in the intestine. Metabolic labeling strategy validated that P. gingivalis could translocate to the gastrointestinal tract in a viable state. Oral administration of living P. gingivalis elicited insulin resistance, while administration of pasteurized P. gingivalis had no such effect. Combination analysis of metagenome sequencing and nontargeted metabolomics suggested that the tryptophan metabolism pathway, specifically indole and its derivatives, was involved in the pathogenesis of insulin resistance caused by oral administration of living P. gingivalis. Moreover, liquid chromatography-high-resolution mass spectrometry analysis confirmed that the aryl hydrocarbon receptor (AhR) ligands, mainly indole acetic acid, tryptamine, and indole-3-aldehyde, were reduced in diet-induced obese mice with periodontitis, leading to inactivation of AhR signaling. Supplementation with Ficz (6-formylindolo (3,2-b) carbazole), an AhR agonist, alleviated periodontitis-associated insulin resistance, in which the restoration of gut barrier function might play an important role. Collectively, these findings reveal that the oral-gut translocation of viable P. gingivalis works as a fuel linking periodontitis and insulin resistance, in which reduction of AhR ligands and inactivation of AhR signaling are involved. This study provides novel insight into the role of the oral-gut axis in the pathogenesis of periodontitis-associated comorbidities.}, } @article {pmid38185596, year = {2024}, author = {De Coninck, L and Matthijnssens, J}, title = {The mosquito core virome: beyond the buzz.}, journal = {Trends in parasitology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pt.2023.12.012}, pmid = {38185596}, issn = {1471-5007}, } @article {pmid38185288, year = {2024}, author = {Luan, Z and Fu, S and Qi, S and Li, C and Chen, J and Zhao, Y and Zhang, H and Wu, J and Zhao, Z and Zhang, J and Chen, Y and Zhang, W and Jing, Y and Wang, S and Sun, G}, title = {A metagenomics study reveals the gut microbiome as a sex-specific modulator of healthy aging in Hainan centenarians.}, journal = {Experimental gerontology}, volume = {186}, number = {}, pages = {112356}, doi = {10.1016/j.exger.2023.112356}, pmid = {38185288}, issn = {1873-6815}, abstract = {BACKGROUND: Sex differences in health status and life expectancy are widely accepted to exist. The mechanisms underlying it are still poorly understood. In this study, we aimed to clarify the influences and contributions of sex on the gut microbiome in healthy centenarians and to explore the different roles played by the gut microbiome in healthy aging between the sexes.

RESULTS: Taking covariates of different dimensions into account (social demographics, anthropometry, the activities of daily living, dietary structure, mental state, blood tests, lifestyle and disease history), our data showed that sex was one of the most significant covariates affecting the gut microbiome of healthy centenarians at both the species and Kyoto Encyclopedia of Genes and Genomes Orthology (KO) levels. The beta diversity between the sexes were significantly different (Adonis test: p = 0.011, R[2] = 0.031), and the male centenarians had a greater alpha diversity than the females (Simpson and Shannon test: P<0.05). At the species level, we identified 31 species enriched in males and 7 species enriched in females. The composition and function patterns of the microbiome varied between the sexes. Further functional analysis showed that males' gut microbiome exhibited greater resistance to oxidative stress compared to females. In contrast to men, the species associated with healthy aging dominated among healthy female centenarians, while the species associated with unhealthy aging were relatively rare.

CONCLUSIONS: The present study reveals that the gut microbiome structure and resistance to oxidative stress in healthy centenarians differ between the sexes and provides new insights into the possible sex-specific role of the gut microbiome in healthy aging.}, } @article {pmid38185173, year = {2024}, author = {Yu, T and Chen, X and Zeng, XC and Wang, Y}, title = {Biological oxidation of Sb(III) and As(III) by a novel bacterium with Sb(III) oxidase rather than As(III) oxidase under anaerobic and aerobic conditions.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {169893}, doi = {10.1016/j.scitotenv.2024.169893}, pmid = {38185173}, issn = {1879-1026}, abstract = {Sb and As are chemically similar, but the sequences and structures of Sb(III) and As(III) oxidase are totally distinct. It is thus interesting to explore whether Sb(III) oxidase oxidizes As(III), and if so, how microbial oxidations of Sb(III) and As(III) influence one another. Previous investigations have yielded ambiguous or even erroneous conclusions. This study aimed to clarify this issue. Firstly, metagenomic analysis reveals that Sb(III)-oxidizing prokaryotes (SOPs) with the Sb(III) oxidase gene, but lacking the As(III) oxidase gene are predominant in SOP community. Despite this, SOPs exhibit comparable Sb(III) and As(III)-oxidizing activities in both aerobic and anaerobic conditions, indicating that at the microbial community level, Sb(III) oxidase can oxidize As(III). Secondly, we isolated a representative cultivable SOP, Ralstonia sp. SbOX with Sb(III) oxidase gene but without As(III) oxidase gene from the soils. Genomic analysis of SbOX reveals that this SOP strain has a complete Sb(III) oxidase (AnoA) gene, but lacks As(III) oxidase (AioAB and ArxAB) genes. It is interesting to discover that, besides its Sb(III) oxidation activities, SbOX also exhibits significant capabilities in oxidizing As(III) under both aerobic and anaerobic conditions. Moreover, under aerobic conditions and in the presence of both Sb(III) and As(III), SbOX exhibited a preference for oxidizing Sb(III). Only after the complete oxidation of Sb(III) did SbOX initiate rapid oxidation of As(III). In contrast, under anaerobic conditions and in the presence of both Sb(III) and As(III), Sb(III) oxidation notably inhibited the As(III) oxidation pathway in SbOX, while As(III) exhibited minimal effects on the Sb(III) oxidation. These findings suggest that SOPs can oxidize As(III) under both aerobic and anaerobic conditions, with SOPs showing a high preference for Sb(III) oxidation over As(III) oxidation in the presence of both Sb(III) and As(III). This unveils a new mechanism of interaction within the Sb and As biogeochemical cycles.}, } @article {pmid38185167, year = {2024}, author = {Guo, B and Li, G and Xu, H and Fang, Y and Gao, Z and Zhao, Y and Zhang, J}, title = {Enhanced denitrification performance in iron-carbon wetlands through biomass addition: Impact on nitrate and ammonia transformation.}, journal = {The Science of the total environment}, volume = {914}, number = {}, pages = {169913}, doi = {10.1016/j.scitotenv.2024.169913}, pmid = {38185167}, issn = {1879-1026}, abstract = {This study investigated the influence of biomass addition on the denitrification performance of iron-carbon wetlands. During long-time operation, the effluent NO3[-]-N concentration of CW-BFe was observed to be the lowest, registering at 0.418 ± 0.167 mg/L, outperforming that of CW-Fe, which recorded 1.467 ± 0.467 mg/L. However, the effluent NH4[+]-N for CW-BFe increased to 1.465 ± 0.121 mg/L, surpassing CW-Fe's 0.889 ± 0.224 mg/L. Within a typical cycle, when establishing first-order reaction kinetics based on NO3[-]-N concentrations, the introduction of biomass was found to amplify the kinetic constants across various stages in the iron-carbon wetland, ranging between 2.4 and 5.4 times that of CW-Fe. A metagenomic analysis indicated that biomass augments the reduction of NO3[-]-N and NO2[-]-N nitrogen and significantly bolsters the dissimilation nitrate reduction to ammonia pathway. Conversely, it impedes the reduction of N2O, leading to a heightened proportion of 2.715 % in CW-BFe's nitrogen mass balance, a stark contrast to CW-Fe's 0.379 %.}, } @article {pmid38184913, year = {2024}, author = {Chen, X and Sheng, Y and Wang, G and Zhou, P and Liao, F and Mao, H and Zhang, H and Qiao, Z and Wei, Y}, title = {Spatiotemporal successions of N, S, C, Fe, and As cycling genes in groundwater of a wetland ecosystem: Enhanced heterogeneity in wet season.}, journal = {Water research}, volume = {251}, number = {}, pages = {121105}, doi = {10.1016/j.watres.2024.121105}, pmid = {38184913}, issn = {1879-2448}, abstract = {Microorganisms in wetland groundwater play an essential role in driving global biogeochemical cycles. However, largely due to the dynamics of spatiotemporal surface water-groundwater interaction, the spatiotemporal successions of biogeochemical cycling in wetland groundwater remain poorly delineated. Herein, we investigated the seasonal coevolution of hydrogeochemical variables and microbial functional genes involved in nitrogen, carbon, sulfur, iron, and arsenic cycling in groundwater within a typical wetland, located in Poyang Lake Plain, China. During the dry season, the microbial potentials for dissimilatory nitrate reduction to ammonium and ammonification were dominant, whereas the higher potentials for nitrogen fixation, denitrification, methane metabolism, and carbon fixation were identified in the wet season. A likely biogeochemical hotspot was identified in the area located in the low permeable aquifer near the lake, characterized by reducing conditions and elevated levels of Fe[2+] (6.65-17.1 mg/L), NH4[+] (0.57-3.98 mg/L), total organic carbon (1.02-1.99 mg/L), and functional genes. In contrast to dry season, higher dissimilarities of functional gene distribution were observed in the wet season. Multivariable statistics further indicated that the connection between the functional gene compositions and hydrogeochemical variables becomes less pronounced as the seasons transition from dry to wet. Despite this transition, Fe[2+] remained the dominant driving force on gene distribution during both seasons. Gene-based co-occurrence network displayed reduced interconnectivity among coupled C-N-Fe-S cycles from the dry to the wet season, underpinning a less complex and more destabilizing occurrence pattern. The rising groundwater level may have contributed to a reduction in the stability of functional microbial communities, consequently impacting ecological functions. Our findings shed light on microbial-driven seasonal biogeochemical cycling in wetland groundwater.}, } @article {pmid38183799, year = {2023}, author = {Liu, H and Jiao, P and Guan, L and Wang, C and Zhang, XX and Ma, L}, title = {Functional traits and health implications of the global household drinking-water microbiome retrieved using an integrative genome-centric approach.}, journal = {Water research}, volume = {250}, number = {}, pages = {121094}, doi = {10.1016/j.watres.2023.121094}, pmid = {38183799}, issn = {1879-2448}, abstract = {The biological safety of drinking water plays a crucial role in public health protection. However, research on the drinking water microbiome remains in its infancy, especially little is known about the potentially pathogenic bacteria in and functional characteristics of the microbiome in household tap water that people are directly exposed to. In this study, we used a genomic-centric approach to construct a genetic catalogue of the drinking water microbiome by analysing 116 metagenomic datasets of household tap water worldwide, spanning nine countries/regions on five continents. We reconstructed 859 high-quality metagenome-assembled genomes (MAGs) spanning 27 bacterial and 2 archaeal phyla, and found that the core MAGs belonging to the phylum Proteobacteria encoded the highest metabolic functional diversity of the 33 key complete metabolic modules. In particular, we found that two core MAGs of Brevibacillus and Methylomona encoded genes for methane metabolism, which may support the growth of heterotrophic organisms observed in the oligotrophic ecosystem. Four MAGs of complete ammonia oxidation (comammox) Nitrospira were identified and functional metabolic analysis suggested these may enable mixotrophic growth and encode genes for reactive oxygen stress defence and arsenite reduction that could aid survival in the environment of oligotrophic drinking water systems. Four MAGs were annotated as potentially pathogenic bacteria (PPB) and thus represented a possible public health concern. They belonged to the genera Acinetobacter (n = 3) and Mycobacterium (n = 1), with a total relative abundance of 1.06 % in all samples. The genomes of PPB A. junii and A. ursingii were discovered to contain antibiotic resistance genes and mobile genetic elements that could contribute to antimicrobial dissemination in drinking water. Further network analysis suggested that symbiotic microbes which support the growth of pathogenic bacteria can be targets for future surveillance and removal.}, } @article {pmid38183548, year = {2024}, author = {Parekh, D and Vaidh, S and Ailani, R and Banerjee, S and Vishwakarma, GS}, title = {Investigation of biochemical, enzymatic, and metagenomic profiles of garbage enzymes and its application in dumping site leachate treatment.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38183548}, issn = {1614-7499}, support = {GSBTM L1Y5SU//GUJARAT STATE BIOTECHNOLOGY MISSION/ ; DST/TMD(EWO)OWUIS-2018/RS-20G//DEPARTMENT OF SCIENCE AND TECHNOLOGY/ ; }, abstract = {The current article focuses on the preparation and characterization of garbage enzyme (GE) and explores its applications in treating leachate. GE is prepared from fruit and vegetable wastes and characterized via analysis of metabolites, carbohydrates, proteins, antioxidants, and enzymatic activities. This study extends our understanding of GE by reporting the presence of various metabolites. Moreover, a metagenomic analysis of GE is presented, shedding light on the microbial diversity. Firmicutes emerged as the dominant phylum, surpassing other phyla, including Proteobacteria and Actinobacteria. When exploring the potential for leachate treatment, the results indicate that vegetable GE shows 68% reduction in COD (chemical oxygen demand) and 39% reduction in ammoniacal nitrogen. Similarly, non-citrus GE also showed 64% reduction in COD and a 37% reduction in ammoniacal nitrogen, followed by citrus GE with a 33% reduction in COD and a 34% reduction in ammoniacal nitrogen compared to the control.}, } @article {pmid38183371, year = {2024}, author = {Yi, S and Zhu, Z and Li, F and Zhu, L and Wu, C and Ge, F and Ji, X and Tian, J}, title = {Metagenomic and proteomic insights into the self-adaptive cell surface hydrophobicity of Sphingomonas sp. strain PAH02 reducing the migration of cadmium-phenanthrene co-pollutant in rice.}, journal = {Environmental microbiology}, volume = {}, number = {}, pages = {e16577}, doi = {10.1111/1462-2920.16577}, pmid = {38183371}, issn = {1462-2920}, support = {22176161//National Natural Science Foundation of China/ ; 2021JJ30655//Natural Science Foundation of Hunan Province/ ; CX20230554//Postgraduate Scientific Research Innovation Project of Hunan Province/ ; CX20220599//Postgraduate Scientific Research Innovation Project of Hunan Province/ ; U21A20293//National Natural Science Foundation of China-Hunan Joint Fund/ ; }, abstract = {Cell surface hydrophobicity (CSH) dominates the interactions between rhizobacteria and pollutants at the soil-water interface, which is critical for understanding the dissipation of pollutants in the rhizosphere microzone of rice. Herein, we explored the effects of self-adaptive CSH of Sphingomonas sp. strain PAH02 on the translocation and biotransformation behaviour of cadmium-phenanthrene (Cd-Phe) co-pollutant in rice and rhizosphere microbiome. We evidenced that strain PAH02 reduced the adsorption of Cd-Phe co-pollutant on the rice root surface while enhancing the degradation of Phe and adsorption of Cd via its self-adaptive CSH in the hydroponic experiment. The significant upregulation of key protein expression levels such as MerR, ARHDs and enoyl-CoA hydratase/isomerase, ensures self-adaptive CSH to cope with the stress of Cd-Phe co-pollutant. Consistently, the bioaugmentation of strain PAH02 promoted the formation of core microbiota in the rhizosphere soil of rice (Oryza sativa L.), such as Bradyrhizobium and Streptomyces and induced gene enrichment of CusA and PobA that are strongly associated with pollutant transformation. Consequently, the contents of Cd and Phe in rice grains at maturity decreased by 17.2% ± 0.2% and 65.7% ± 0.3%, respectively, after the bioaugmentation of strain PAH02. These findings present new opportunities for the implementation of rhizosphere bioremediation strategies of co-contaminants in paddy fields.}, } @article {pmid38182885, year = {2024}, author = {Zhu, X and Xu, P and Zhu, R and Gao, W and Yin, W and Lan, P and Zhu, L and Jiao, N}, title = {Multi-kingdom microbial signatures in excess body weight colorectal cancer based on global metagenomic analysis.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {24}, pmid = {38182885}, issn = {2399-3642}, support = {82000536//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; Metagenome ; Arginine ; *Gastrointestinal Microbiome/genetics ; Weight Gain ; *Colorectal Neoplasms/diagnosis/genetics ; }, abstract = {Excess body weight (EBW) increases the risk of colorectal cancer (CRC) and is linked to lower colonoscopy compliance. Here, we extensively analyzed 981 metagenome samples from multiple cohorts to pinpoint the specific microbial signatures and their potential capability distinguishing EBW patients with CRC. The gut microbiome displayed considerable variations between EBW and lean CRC. We identify 44 and 37 distinct multi-kingdom microbial species differentiating CRC and controls in EBW and lean populations, respectively. Unique bacterial-fungal associations are also observed between EBW-CRC and lean-CRC. Our analysis revealed specific microbial functions in EBW-CRC, including D-Arginine and D-ornithine metabolism, and lipopolysaccharide biosynthesis. The best-performing classifier for EBW-CRC, comprising 12 bacterial and three fungal species, achieved an AUROC of 0.90, which was robustly validated across three independent cohorts (AUROC = 0.96, 0.94, and 0.80). Pathogenic microbial species, Anaerobutyricum hallii, Clostridioides difficile and Fusobacterium nucleatum, are EBW-CRC specific signatures. This work unearths the specific multi-kingdom microbial signatures for EBW-CRC and lean CRC, which may contribute to precision diagnosis and treatment of CRC.}, } @article {pmid38182877, year = {2024}, author = {Jin, Z and Cao, Y and Wen, Q and Zhang, H and Fang, Z and Zhao, Q and Xi, Y and Luo, Z and Jiang, H and Zhang, Z and Hang, J}, title = {Dapagliflozin ameliorates diabetes-induced spermatogenic dysfunction by modulating the adenosine metabolism along the gut microbiota-testis axis.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {641}, pmid = {38182877}, issn = {2045-2322}, support = {82101676//National Natural Science Foundation of China/ ; 82271630//National Natural Science Foundation of China/ ; 82071698//National Natural Science Foundation of China/ ; 82071658//National Natural Science Foundation of China/ ; 2022M710259//China Postdoctoral Science Foundation/ ; 2021YFC2700203//National Key Research and Development Program of China/ ; 2022YFC2702904//National Key Research and Development Program of China/ ; 7222208//Natural Science Foundation of Beijing Municipality/ ; 20220484160//Beijing Nova Program/ ; BYSYZD2023033//Key Clinical Projects of Peking University Third Hospital/ ; }, mesh = {Male ; Animals ; Mice ; Humans ; Testis ; *Gastrointestinal Microbiome ; Semen ; Sperm Motility ; Spermatogenesis ; Adenosine ; *Infertility, Male/drug therapy/etiology ; *Diabetes Mellitus ; }, abstract = {Male infertility is one of the most common complications of diabetes mellitus (DM). Dapagliflozin is widely used to manage the type II DM. This study aimed to assess the dapagliflozin's effects on the spermatogenesis by administering either dapagliflozin (Dapa) or vehicle (db) to male db/db mice, and using littermate male db/m mice as the control (Con). We further performed the integrative analyses of the cecal shotgun metagenomics, cecal/plasmatic/testicular metabolomics, and testicular proteomics. We found that dapagliflozin treatment significantly alleviated the diabetes-induced spermatogenic dysfunction by improving sperm quality, including the sperm concentration and sperm motility. The overall microbial composition was reshaped in Dapa mice and 13 species (such as Lachnospiraceae bacterium 3-1) were regarded as potential beneficial bacteria. Metabolites exhibited modified profiles, in which adenosine, cAMP, and 2'-deoxyinosine being notably altered in the cecum, plasma, and testis, respectively. Testicular protein expression patterns were similar between the Dapa and Con mice. In vivo results indicated that when compared with db group, dapagliflozin treatment alleviated apoptosis and oxidative stress in testis tissues by down-regulating 2'-deoxyinosine. This was further validated by in vitro experiments using GC-2 cells. Our findings support the potential use of dapagliflozin to prevent the diabetes-induced impaired sperm quality and to treat diabetic male infertility.}, } @article {pmid38182754, year = {2024}, author = {Rhoades, NS and Cinco, IR and Hendrickson, SM and Prongay, K and Haertel, AJ and Flores, GE and Slifka, MK and Messaoudi, I}, title = {Infant diarrheal disease in rhesus macaques impedes microbiome maturation and is linked to uncultured Campylobacter species.}, journal = {Communications biology}, volume = {7}, number = {1}, pages = {37}, pmid = {38182754}, issn = {2399-3642}, support = {OPP1149233//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; }, mesh = {Child ; Infant ; Animals ; Humans ; Macaca mulatta ; *Campylobacter/genetics ; *Microbiota ; Metagenome ; Diarrhea ; }, abstract = {Diarrheal diseases remain one of the leading causes of death for children under 5 globally, disproportionately impacting those living in low- and middle-income countries (LMIC). Campylobacter spp., a zoonotic pathogen, is one of the leading causes of food-borne infection in humans. Yet to be cultured Campylobacter spp. contribute to the total burden in diarrheal disease in children living in LMIC thus hampering interventions. We performed microbiome profiling and metagenomic genome assembly on samples collected from over 100 infant rhesus macaques longitudinally and during cases of clinical diarrhea within the first year of life. Acute diarrhea was associated with long-lasting taxonomic and functional shifts of the infant gut microbiome indicative of microbiome immaturity. We constructed 36 Campylobacter metagenomic assembled genomes (MAGs), many of which fell within 4 yet to be cultured species. Finally, we compared the uncultured Campylobacter MAGs assembled from infant macaques with publicly available human metagenomes to show that these uncultured species are also found in human fecal samples from LMIC. These data highlight the importance of unculturable Campylobacter spp. as an important target for reducing disease burden in LMIC children.}, } @article {pmid38182626, year = {2024}, author = {Rühlemann, MC and Bang, C and Gogarten, JF and Hermes, BM and Groussin, M and Waschina, S and Poyet, M and Ulrich, M and Akoua-Koffi, C and Deschner, T and Muyembe-Tamfum, JJ and Robbins, MM and Surbeck, M and Wittig, RM and Zuberbühler, K and Baines, JF and Leendertz, FH and Franke, A}, title = {Functional host-specific adaptation of the intestinal microbiome in hominids.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {326}, pmid = {38182626}, issn = {2041-1723}, support = {261376515//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 244372499//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 261376515//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 390884018//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Animals ; *Hominidae ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Pan troglodytes ; Pan paniscus ; }, abstract = {Fine-scale knowledge of the changes in composition and function of the human gut microbiome compared that of our closest relatives is critical for understanding the evolutionary processes underlying its developmental trajectory. To infer taxonomic and functional changes in the gut microbiome across hominids at different timescales, we perform high-resolution metagenomic-based analyzes of the fecal microbiome from over two hundred samples including diverse human populations, as well as wild-living chimpanzees, bonobos, and gorillas. We find human-associated taxa depleted within non-human apes and patterns of host-specific gut microbiota, suggesting the widespread acquisition of novel microbial clades along the evolutionary divergence of hosts. In contrast, we reveal multiple lines of evidence for a pervasive loss of diversity in human populations in correlation with a high Human Development Index, including evolutionarily conserved clades. Similarly, patterns of co-phylogeny between microbes and hosts are found to be disrupted in humans. Together with identifying individual microbial taxa and functional adaptations that correlate to host phylogeny, these findings offer insights into specific candidates playing a role in the diverging trajectories of the gut microbiome of hominids. We find that repeated horizontal gene transfer and gene loss, as well as the adaptation to transient microaerobic conditions appear to have played a role in the evolution of the human gut microbiome.}, } @article {pmid38181963, year = {2024}, author = {Li, X and Tang, X and Chen, M and Wang, S and Tong, C and Xu, J and Xie, G and Ma, B and Zou, Y and Wang, Y and Wen, X and Wu, Y}, title = {Intramuscular therapeutic doses of enrofloxacin affect microbial community structure but not the relative abundance of fluoroquinolones resistance genes in swine manure.}, journal = {The Science of the total environment}, volume = {913}, number = {}, pages = {169794}, doi = {10.1016/j.scitotenv.2023.169794}, pmid = {38181963}, issn = {1879-1026}, abstract = {Livestock manure is a major source of veterinary antibiotics and antibiotic resistance genes (ARGs). Elucidation of the residual characteristics of ARGs in livestock manure following the administration of veterinary antibiotics is critical to assess their ecotoxicological effects and environmental contamination risks. Here, we investigated the effects of enrofloxacin (ENR), a fluoroquinolone antibiotic commonly used as a therapeutic drug in animal husbandry, on the characteristics of ARGs, mobile genetic elements, and microbial community structure in swine manure following its intramuscular administration for 3 days and a withdrawal period of 10 days. The results revealed the highest concentrations of ENR and ciprofloxacin (CIP) in swine manure at the end of the administration period, ENR concentrations in swine manure in groups L and H were 88.67 ± 45.46 and 219.75 ± 88.05 mg/kg DM, respectively. Approximately 15 fluoroquinolone resistance genes (FRGs) and 48 fluoroquinolone-related multidrug resistance genes (F-MRGs) were detected in swine manure; the relative abundance of the F-MRGs was considerably higher than that of the FRGs. On day 3, the relative abundance of qacA was significantly higher in group H than in group CK, and no significant differences in the relative abundance of other FRGs, F-MRGs, or MGEs were observed between the three groups on day 3 and day 13. The microbial community structure in swine manure was significantly altered on day 3, and the altered community structure was restored on day 13. The FRGs and F-MRGs with the highest relative abundance were qacA and adeF, respectively, and Clostridium and Lactobacillus were the dominant bacterial genera carrying these genes in swine manure. In summary, a single treatment of intramuscular ENR transiently increased antibiotic concentrations and altered the microbial community structure in swine manure; however, this treatment did not significantly affect the abundance of FRGs and F-MRGs.}, } @article {pmid38181946, year = {2024}, author = {Chen, L and Huang, F and Lu, A and Liu, F and Guan, X and Wang, J}, title = {Critical role of multiple antibiotics on the denitrification rate in groundwater: Field investigative proof.}, journal = {The Science of the total environment}, volume = {914}, number = {}, pages = {169785}, doi = {10.1016/j.scitotenv.2023.169785}, pmid = {38181946}, issn = {1879-1026}, abstract = {The impact of antibiotics on denitrification has emerged as a significant topic; however, there is a dearth of mechanistic understanding regarding the effects of multiple antibiotics at the ng/L level on denitrification in groundwater. This study conducted five field samplings between March 2019 and July 2021 at two representative monitoring wells. The investigation utilized metagenomic sequencing to unveil the antibiotic mechanisms influencing denitrification. Results revealed the detection of 16 out of 64 antibiotics, with a maximum detection frequency and total concentration of 100 % and 187 ng/L, respectively. Additionally, both nitrate and total antibiotic concentrations exhibited a gradual decrease along the groundwater flow direction. Metagenomic evidence indicated that denitrification served as the dominant biogeochemical process controlling nitrate attenuation in groundwater. However, the denitrification capacity experienced significant inhibition in the presence of multiple antibiotics at the ng/L level. This inhibition was attributed to decreases in the relative abundance of dominant denitrifying bacteria (Candidatus_Scalindua, Herminiimonas and unclassified_p_Planctomycetes) and denitrifying functional genes (narGH, nirKS and norB), signifying the pressure exerted by antibiotics on denitrifying bacteria. The variation in antibiotic concentration (∆Cantibiotics) indicated a change in antibiotic pressure on denitrifying bacteria. A larger ∆Cantibiotics corresponded to a greater rebound in the relative abundance of denitrifying functional genes, resulting in a faster denitrification rate (Kdenitrification). Field observations further demonstrated a positive correlation between Kdenitrification and ∆Cantibiotics. Comparatively, a higher Kdenitrification observed at higher ∆Cantibiotics was primarily due to the enrichment of more nondominant denitrifying bacteria carrying key denitrifying functional genes. In conclusion, this study underscores that multiple antibiotics at the ng/L level in groundwater inhibited denitrification, and the degree of inhibition was closely related to ∆Cantibiotics.}, } @article {pmid38181823, year = {2024}, author = {Zheng, C and Wang, L and Zou, T and Lian, S and Luo, J and Lu, Y and Hao, H and Xu, Y and Xiang, Y and Zhang, X and Xu, G and Zou, X and Jiang, R}, title = {Ileitis promotes MASLD progression via bile acid modulation and enhanced TGR5 signaling in ileal CD8+ T cells.}, journal = {Journal of hepatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhep.2023.12.024}, pmid = {38181823}, issn = {1600-0641}, abstract = {BACKGROUND: Clinical evidence substantiates a link between inflammatory bowel disease (IBD), particularly Crohn's disease (CD), and metabolic dysfunction associated steatotic liver disease (MASLD). This study aims to explore the underlying molecular mechanisms responsible for this association.

METHODS: MASLD was induced by administering high-fat and western diets, while IBD was induced using dextran sulfate sodium salt (DSS) and the Il10 KO mice model. The investigation into the role of secondary bile acids (SBA) in ileitis involved employing metagenomic sequencing, conducting metabolomics detection, performing fecal bacterial transplantation, and constructing CD8[+] T cell specific gene knockout mice.

RESULTS: In MASLD+DSS and Il10 KO MASLD mice, we observed ileitis characterized by T cell infiltration and activation in the terminal ileum. This condition resulted in decreased bile acid levels in the portal vein and liver, inhibited hepatic Farnesol X receptor (FXR) activation, and exacerbated MASLD. Metagenomic and metabolomic analysis of ileum contents revealed increased Clostridium proliferation and elevated SBA levels in MASLD-associated ileitis. Experiments using germ-free mice and fecal microbiota transplantation suggested an association between SBA and MASLD-related ileitis. In vitro, SBA promoted CD8[+] T cell activation via the TGR5, mTOR, and Oxidative Phosphorylation (OXPHOS) pathways. In vivo, TGR5 knockout in CD8[+] T cells effectively alleviated ileitis and worsened the MASLD phenotype. Clinical data further supported these findings, demonstrating a positive correlation ileitis and MASLD.

CONCLUSION: MASLD-induced changes in intestinal flora result in elevated levels of SBA in the ileum. In the presence of compromised intestinal barrier, this leads to severe CD8[+] T cell-mediated ileitis through the TGR5/mTOR/OXPHOS signaling pathway. Ileitis-induced tissue damage impairs enterohepatic circulation, inhibits hepatic FXR activation, and exacerbates the MASLD phenotype.

IMPACT AND IMPLICATIONS: Our study provides a comprehensive investigation of the interplay and underlying mechanisms connecting ileitis and MASLD. SBA produced by intestinal bacteria, as the critical link between MASLD and ileitis. This compound exerts its influence by disrupting liver lipid metabolism through the promotion of CD8[+] T cell-mediated ileitis. In future endeavors to prevent and treat MASLD, it is essential to thoroughly account for the impact of the intestinal tract, especially the ileum, on liver function via the enterohepatic circulation.}, } @article {pmid38180652, year = {2024}, author = {Ben Abdallah, M and Chamkha, M and Karray, F and Sayadi, S}, title = {Microbial diversity in polyextreme salt flats and their potential applications.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38180652}, issn = {1614-7499}, abstract = {Recent geological, hydrochemical, and mineralogical studies performed on hypersaline salt flats have given insights into similar geo-morphologic features on Mars. These salt-encrusted depressions are widely spread across the Earth, where they are characterized by high salt concentrations, intense UV radiation, high evaporation, and low precipitation. Their surfaces are completely dry in summer; intermittent flooding occurs in winter turning them into transitory hypersaline lakes. Thanks to new approaches such as culture-dependent, culture-independent, and metagenomic-based methods, it is important to study microbial life under polyextreme conditions and understand what lives in these dynamic ecosystems and how they function. Regarding these particular features, new halophilic microorganisms have been isolated from some salt flats and identified as excellent producers of primary and secondary metabolites and granules such as halocins, enzymes, carotenoids, polyhydroxyalkanoates, and exopolysaccharides. Additionally, halophilic microorganisms are implemented in heavy metal bioremediation and hypersaline wastewater treatment. As a result, there is a growing interest in the distribution of halophilic microorganisms around the world that can be looked upon as good models to develop sustainable biotechnological processes for all fields. This review provides insights into diversity, ecology, metabolism, and genomics of halophiles in hypersaline salt flats worldwide as well as their potential uses in biotechnology.}, } @article {pmid38180447, year = {2024}, author = {Wu, E and Yang, Y and Zhao, J and Zheng, J and Wang, X and Shen, C and Qiao, L}, title = {High-Abundance Protein-Guided Hybrid Spectral Library for Data-Independent Acquisition Metaproteomics.}, journal = {Analytical chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.analchem.3c03255}, pmid = {38180447}, issn = {1520-6882}, abstract = {Metaproteomics offers a direct avenue to identify microbial proteins in microbiota, enabling the compositional and functional characterization of microbiota. Due to the complexity and heterogeneity of microbial communities, in-depth and accurate metaproteomics faces tremendous limitations. One challenge in metaproteomics is the construction of a suitable protein sequence database to interpret the highly complex metaproteomic data, especially in the absence of metagenomic sequencing data. Herein, we present a high-abundance protein-guided hybrid spectral library strategy for in-depth data independent acquisition (DIA) metaproteomic analysis (HAPs-hyblibDIA). A dedicated high-abundance protein database of gut microbial species is constructed and used to mine the taxonomic information on microbiota samples. Then, a sample-specific protein sequence database is built based on the taxonomic information using Uniprot protein sequence for subsequent analysis of the DIA data using hybrid spectral library-based DIA analysis. We evaluated the accuracy and sensitivity of the method using synthetic microbial community samples and human gut microbiome samples. It was demonstrated that the strategy can successfully identify taxonomic compositions of microbiota samples and that the peptides identified by HAPs-hyblibDIA overlapped greatly with the peptides identified using a metagenomic sequencing-derived database. At the peptide and species level, our results can serve as a complement to the results obtained using a metagenomic sequencing-derived database. Furthermore, we validated the applicability of the HAPs-hyblibDIA strategy in a cohort of human gut microbiota samples of colorectal cancer patients and controls, highlighting its usability in biomedical research.}, } @article {pmid38179742, year = {2023}, author = {Yuan, Z and Liu, F and Zeng, ZH and Pan, H}, title = {Community Structure and Diversity of Rhizosphere Soil and Endophytic Bacteria during the Period of Growth of Moso Bamboo Shoots.}, journal = {Frontiers in bioscience (Landmark edition)}, volume = {28}, number = {12}, pages = {329}, doi = {10.31083/j.fbl2812329}, pmid = {38179742}, issn = {2768-6698}, support = {2021FKJ07//Forestry Science and Technology Project of Fujian Province/ ; }, mesh = {Humans ; *Soil ; Rhizosphere ; Poaceae/microbiology ; *Cyanobacteria ; }, abstract = {BACKGROUND: The purpose of this study was to elucidate the community structure of rhizosphere soil bacteria and endophytic bacteria during the growth of moso bamboo (Phyllostachys edulis) shoots.

METHODS: This study collected the rhizospheric soil samples, tissue samples of rhizome roots, shoot buds, winter bamboo shoots, spring bamboo shoots, and samples of forest soil. Their metagenomic DNA was extracted, and the bacterial community structure and diversity characteristics were compared and analyzed using high-throughput sequencing technology.

RESULTS: These samples enabled the identification of 32 phyla, 52 classes, 121 orders, 251 families, and 593 genera of bacteria. The phyla primarily included Proteobacteria, Acidobacteria, and Cyanobacteria among others. Proteobacteria was the dominant phylum in the samples of bamboo shoots and rhizome roots, whereas Acidobacteria was dominant in the rhizosphere and forest soil samples. The predominant genera of the rhizome root samples were Acidothermus, Bradyrhizobium and Acidobacterium, and the predominant genera of the soil samples were Acidothermus and Acidobacterium.

CONCLUSIONS: This study preliminarily revealed the regularity between the growth and development of bamboo shoots and the changes in the community structure of rhizosphere soil and endophytic bacteria, which provides insights into the relationship between growth and the bacterial community structure in different stages of bamboo shoots.}, } @article {pmid38179476, year = {2023}, author = {Wang, Z and Peng, D and Fu, C and Luo, X and Guo, S and Li, L and Yin, H}, title = {Pan-metagenome reveals the abiotic stress resistome of cigar tobacco phyllosphere microbiome.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1248476}, pmid = {38179476}, issn = {1664-462X}, abstract = {The important role of microbial associations in mediating plant protection and responses to abiotic stresses has been widely recognized. However, there have been limited studies on the functional profile of the phyllosphere microbiota from tobacco (Nicotiana tabacum), hindering our understanding of the mechanisms underlying stress resilience in this representative and easy-to-cultivate model species from the solanaceous family. To address this knowledge gap, our study employed shotgun metagenomic sequencing for the first time to analyze the genetic catalog and identify putative plant growth promoting bacteria (PGPB) candidates that confer abiotic stress resilience throughout the growth period of cigar tobacco in the phyllosphere. We identified abundant genes from specific bacterial lineages, particularly Pseudomonas, within the cigar tobacco phyllospheric microbiome. These genes were found to confer resilience against a wide range of stressors, including osmotic and drought stress, heavy metal toxicity, temperature perturbation, organic pollutants, oxidative stress, and UV light damage. In addition, we conducted a virome mining analysis on the metagenome to explore the potential roles of viruses in driving microbial adaptation to environmental stresses. Our results identified a total of 3,320 scaffolds predicted to be viral from the cigar tobacco phyllosphere metagenome, with various phages infecting Pseudomonas, Burkholderia, Enterobacteria, Ralstonia, and related viruses. Within the virome, we also annotated genes associated with abiotic stress resilience, such as alkaline phosphatase D (phoD) for nutrient solubilization and glutamate-5-semialdehyde dehydrogenase (proA) for osmolyte synthesis. These findings shed light on the unexplored roles of viruses in facilitating and transferring abiotic stress resilience in the phyllospheric microbiome through beneficial interactions with their hosts. The findings from this study have important implications for agricultural practices, as they offer potential strategies for harnessing the capabilities of the phyllosphere microbiome to enhance stress tolerance in crop plants.}, } @article {pmid38179451, year = {2023}, author = {Huang, YY and Lv, ZH and Zheng, HZ and Zhu, Q and Liu, MT and Sang, P and Wang, F and Zhu, D and Xian, WD and Yin, YR}, title = {Characterization of a thermophilic and glucose-tolerant GH1 β-glucosidase from hot springs and its prospective application in corn stover degradation.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1286682}, pmid = {38179451}, issn = {1664-302X}, abstract = {INTRODUCTION: β-Glucosidase serves as the pivotal rate-limiting enzyme in the cellulose degradation process, facilitating the hydrolysis of cellobiose and cellooligosaccharides into glucose. However, the widespread application of numerous β-glucosidases is hindered by their limited thermostability and low glucose tolerance, particularly in elevated-temperature and high-glucose environments.

METHODS: This study presents an analysis of a β-glucosidase gene belonging to the GH1 family, denoted lqbg8, which was isolated from the metagenomic repository of Hehua hot spring located in Tengchong, China. Subsequently, the gene was cloned and heterologously expressed in Escherichia coli BL21(DE3). Post expression, the recombinant β-glucosidase (LQBG8) underwent purification through a Ni affinity chromatography column, thereby enabling the in-depth exploration of its enzymatic properties.

RESULTS: LQBG8 had an optimal temperature of 70°C and an optimum pH of 5.6. LQBG8 retained 100 and 70% of its maximum activity after 2-h incubation periods at 65°C and 70°C, respectively. Moreover, even following exposure to pH ranges of 3.0-10.0 for 24 h, LQBG8 retained approximately 80% of its initial activity. Notably, the enzymatic prowess of LQBG8 remained substantial at glucose concentrations of up to 3 M, with a retention of over 60% relative activity. The kinetic parameters of LQBG8 were characterized using cellobiose as substrate, with Km and Vmax values of 28 ± 1.9 mg/mL and 55 ± 3.2 μmol/min/mg, respectively. Furthermore, the introduction of LQBG8 (at a concentration of 0.03 mg/mL) into a conventional cellulase reaction system led to an impressive 43.7% augmentation in glucose yield from corn stover over a 24-h period. Molecular dynamics simulations offered valuable insights into LQBG8's thermophilic nature, attributing its robust stability to reduced fluctuations, conformational changes, and heightened structural rigidity in comparison to mesophilic β-glucosidases.

DISCUSSION: In summation, its thermophilic, thermostable, and glucose-tolerant attributes, render LQBG8 ripe for potential applications across diverse domains encompassing food, feed, and the production of lignocellulosic ethanol.}, } @article {pmid38179449, year = {2023}, author = {Takeda-Nishikawa, K and Palanichamy, R and Miyazato, N and Suzuki, T}, title = {What samples are suitable for monitoring antimicrobial-resistant genes? Using NGS technology, a comparison between eDNA and mrDNA analysis from environmental water.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {954783}, pmid = {38179449}, issn = {1664-302X}, abstract = {INTRODUCTION: The rise in antimicrobial resistance (AMR) that is affecting humans, animals, and the environment, compromises the human immune system and represents a significant threat to public health. Regarding the impact on water sanitation, the risk that antimicrobial-resistant genes (ARGs) and antimicrobial-resistant bacteria in surface water in cities pose to human health remains unclear. To determine the prevalence of AMR in environmental surface water in Japan, we used DNA sequencing techniques on environmental water DNA (eDNA) and the DNA of multidrug-resistant bacteria (mrDNA).

METHODS: The eDNA was extracted from four surface water samples obtained from the Tokyo area and subjected to high- throughput next-generation DNA sequencing using Illumina-derived shotgun metagenome analysis. The sequence data were analyzed using the AmrPlusPlus pipeline and the MEGARes database. Multidrug-resistant bacteria were isolated using a culture-based method from water samples and were screened by antimicrobial susceptibility testing (for tetracycline, ampicillin-sulbactam, amikacin, levofloxacin, imipenem, and clarithromycin). Of the 284 isolates, 22 were identified as multidrug-resistant bacteria. The mrDNA was sequenced using the Oxford nanopore MinION system and analyzed by NanoARG, a web service for detecting and contextualizing ARGs.

RESULTS AND DISCUSSION: The results from eDNA and mrDNA revealed that ARGs encoding beta-lactams and multidrug resistance, including multidrug efflux pump genes, were frequently detected in surface water samples. However, mrDNA also revealed many sequence reads from multidrug-resistant bacteria, as well as nonspecific ARGs, whereas eDNA revealed specific ARGs such as pathogenic OXA-type and New Delhi metallo (NDM)-beta-lactamase ARGs.

CONCLUSION: To estimate potential AMR pollution, our findings suggested that eDNA is preferable for detecting pathogen ARGs.}, } @article {pmid38179448, year = {2023}, author = {Khan, S and Banerjee, G and Setua, S and Jones, DH and Chauhan, BV and Dhasmana, A and Banerjee, P and Yallapu, MM and Behrman, S and Chauhan, SC}, title = {Metagenomic analysis unveils the microbial landscape of pancreatic tumors.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1275374}, pmid = {38179448}, issn = {1664-302X}, abstract = {The composition of resident microbes in the human body is linked to various diseases and their treatment outcomes. Although studies have identified pancreatic ductal adenocarcinoma (PDAC)-associated bacterial communities in the oral and gut samples, herein, we hypothesize that the prevalence of microbiota in pancreatic tumor tissues is different as compared with their matched adjacent, histologically normal appearing tissues, and these microbial molecular signatures can be highly useful for PDAC diagnosis/prognosis. In this study, we performed comparative profiling of bacterial populations in pancreatic tumors and their respective adjacent normal tissues using 16S rRNA-based metagenomics analysis. This study revealed a higher abundance of Proteobacteria and Actinomycetota in tumor tissues compared with adjacent normal tissues. Interestingly, the linear discriminant analysis (LDA) scores unambiguously revealed an enrichment of Delftia in tumor tissues, whereas Sphingomonas, Streptococcus, and Citrobacter exhibited a depletion in tumor tissues. Furthermore, we analyzed the microbial composition between different groups of patients with different tumor differentiation stages. The bacterial genera, Delftia and Staphylococcus, were very high at the G1 stages (well differentiated) compared with G2 (well to moderate/moderately differentiated) and G3/G4 (poorly differentiated) stages. However, the abundance of Actinobacter and Cloacibacterium was found to be very high in G2 and G3, respectively. Additionally, we evaluated the correlation of programmed death-ligand (PDL1) expression with the abundance of bacterial genera in tumor lesions. Our results indicated that three genera such as Streptomyces, Cutibacterium, and Delftia have a positive correlation with PD-L1 expression. Collectively, these findings demonstrate that PDAC lesions harbor relatively different microbiota compared with their normal tumor adjacent tissues, and this information may be helpful for the diagnosis and prognosis of PADC patients.}, } @article {pmid38179444, year = {2023}, author = {Khalaf, EM and Shrestha, A and Reid, M and McFadyen, BJ and Raizada, MN}, title = {Conservation and diversity of the pollen microbiome of Pan-American maize using PacBio and MiSeq.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1276241}, pmid = {38179444}, issn = {1664-302X}, abstract = {Pollen is a vector for diversification, fitness-selection, and transmission of plant genetic material. The extent to which the pollen microbiome may contribute to host diversification is largely unknown, because pollen microbiome diversity within a plant species has not been reported, and studies have been limited to conventional short-read 16S rRNA gene sequencing (e.g., V4-MiSeq) which suffers from poor taxonomic resolution. Here we report the pollen microbiomes of 16 primitive and traditional accessions of maize (corn) selected by indigenous peoples across the Americas, along with the modern U.S. inbred B73. The maize pollen microbiome has not previously been reported. The pollen microbiomes were identified using full-length (FL) 16S rRNA gene PacBio SMRT sequencing compared to V4-MiSeq. The Pan-American maize pollen microbiome encompasses 765 taxa spanning 39 genera and 46 species, including known plant growth promoters, insect-obligates, plant pathogens, nitrogen-fixers and biocontrol agents. Eleven genera and 13 species composed the core microbiome. Of 765 taxa, 63% belonged to only four genera: 28% were Pantoea, 15% were Lactococcus, 11% were Pseudomonas, and 10% were Erwinia. Interestingly, of the 215 Pantoea taxa, 180 belonged to a single species, P. ananatis. Surprisingly, the diversity within P. ananatis ranged nearly 10-fold amongst the maize accessions analyzed (those with ≥3 replicates), despite being grown in a common field. The highest diversity within P. ananatis occurred in accessions that originated near the center of diversity of domesticated maize, with reduced diversity associated with the north-south migration of maize. This sub-species diversity was revealed by FL-PacBio but missed by V4-MiSeq. V4-MiSeq also mis-identified some dominant genera captured by FL-PacBio. The study, though limited to a single season and common field, provides initial evidence that pollen microbiomes reflect evolutionary and migratory relationships of their host plants.}, } @article {pmid38179421, year = {2023}, author = {Magnan, C and Lancry, T and Salipante, F and Trusson, R and Dunyach-Remy, C and Roger, C and Lefrant, JY and Massanet, P and Lavigne, JP}, title = {Role of gut microbiota and bacterial translocation in acute intestinal injury and mortality in patients admitted in ICU for septic shock.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1330900}, pmid = {38179421}, issn = {2235-2988}, mesh = {Adult ; Female ; Humans ; *Shock, Septic ; *Gastrointestinal Microbiome ; Bacterial Translocation ; Lactation ; Intensive Care Units ; Hospitalization ; Bacteria/genetics ; }, abstract = {INTRODUCTION: Sepsis is a life-threatening organ dysfunction with high mortality rate. The gut origin hypothesis of multiple organ dysfunction syndrome relates to loss of gut barrier function and the ensuing bacterial translocation. The aim of this study was to describe the evolution of gut microbiota in a cohort of septic shock patients over seven days and the potential link between gut microbiota and bacterial translocation.

METHODS: Sixty consecutive adult patients hospitalized for septic shock in intensive care units (ICU) were prospectively enrolled. Non-inclusion criteria included patients with recent or scheduled digestive surgery, having taken laxatives, pre- or probiotic in the previous seven days, a progressive digestive neoplasia, digestive lymphoma, chronic inflammatory bowel disease, moribund patient, and pregnant and lactating patients. The primary objective was to evaluate the evolution of bacterial diversity and richness of gut microbiota during seven days in septic shock. Epidemiological, clinical and biological data were gathered over seven days. Gut microbiota was analyzed through a metagenomic approach. 100 healthy controls were selected among healthy blood donors for reference basal 16S rDNA values.

RESULTS: Significantly lower bacterial diversity and richness was observed in gut microbiota of patients at Day 7 compared with Day 0 (p<0.01). SOFA score at Day 0, Acute Gastrointestinal Injury (AGI) local grade, septic shock origin and bacterial translocation had an impact on alpha diversity. A large increase in Enterococcus genus was observed at Day 7 with a decrease in Enterobacterales, Clostridiales, Bifidobacterium and other butyrate-producing bacteria.

DISCUSSION: This study shows the importance of bacterial translocation during AGI in septic shock patients. This bacterial translocation decreases during hospitalization in ICUs in parallel to the decrease of microbiota diversity. This work highlights the role of gut microbiota and bacterial translocation during septic shock.}, } @article {pmid38179151, year = {2024}, author = {Fraiture, MA and Gobbo, A and Guillitte, C and Marchesi, U and Verginelli, D and De Greve, J and D'aes, J and Vanneste, K and Papazova, N and Roosens, NHC}, title = {Pilot market surveillance of GMM contaminations in alpha-amylase food enzyme products: A detection strategy strengthened by a newly developed qPCR method targeting a GM Bacillus licheniformis producing alpha-amylase.}, journal = {Food chemistry. Molecular sciences}, volume = {8}, number = {}, pages = {100186}, pmid = {38179151}, issn = {2666-5662}, abstract = {Using high-throughput metagenomics on commercial microbial fermentation products, DNA from a new unauthorized genetically modified microorganism (GMM), namely the GM B. licheniformis strain producing alpha-amylase (GMM alpha-amylase2), was recently discovered and characterized. On this basis, a new qPCR method targeting an unnatural association of sequences specific to the GMM alpha-amylase2 strain was designed and developed in this study, allowing to strengthen the current GMM detection strategy. The performance of the newly developed qPCR method was assessed for its specificity and sensitivity to comply with the minimum performance requirements established by the European Network of GMO Laboratories for GMO analysis. Moreover, the transferability of the in house validated qPCR method was demonstrated. Finally, its applicability was confirmed by a pilot market surveillance of GMM contaminations conducted for the first time on 40 alpha-amylase food enzyme products labelled as containing alpha-amylase. This pilot market surveillance allowed also to highlight numerous contaminations with GMM alpha-amylase2, including frequent cross-contaminations with other GMM strains previously characterized. In addition, the presence of full-length AMR genes, raising health concerns, was also reported.}, } @article {pmid38178148, year = {2024}, author = {Koller, EJ and Wood, CA and Lai, Z and Borgenheimer, E and Hoffman, KL and Jankowsky, JL}, title = {Doxycycline for transgene control disrupts gut microbiome diversity without compromising acute neuroinflammatory response.}, journal = {Journal of neuroinflammation}, volume = {21}, number = {1}, pages = {11}, pmid = {38178148}, issn = {1742-2094}, support = {F31 AG067676-01A1/NH/NIH HHS/United States ; P30 ES030285/NH/NIH HHS/United States ; RF1 AG058188/NH/NIH HHS/United States ; }, mesh = {Mice ; Animals ; *Doxycycline/pharmacology ; Mice, Transgenic ; *Gastrointestinal Microbiome ; Lipopolysaccharides ; Tetracycline/pharmacology ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Trans-Activators/genetics ; Inflammation ; Transgenes ; }, abstract = {The tetracycline transactivator (tTA) system provides controllable transgene expression through oral administration of the broad-spectrum antibiotic doxycycline. Antibiotic treatment for transgene control in mouse models of disease might have undesirable systemic effects resulting from changes in the gut microbiome. Here we assessed the impact of doxycycline on gut microbiome diversity in a tTA-controlled model of Alzheimer's disease and then examined neuroimmune effects of these microbiome alterations following acute LPS challenge. We show that doxycycline decreased microbiome diversity in both transgenic and wild-type mice and that these changes persisted long after drug withdrawal. Despite the change in microbiome composition, doxycycline treatment had minimal effect on basal transcriptional signatures of inflammation the brain or on the neuroimmune response to LPS challenge. Our findings suggest that central neuroimmune responses may be less affected by doxycycline at doses needed for transgene control than by antibiotic cocktails at doses used for experimental microbiome disruption.}, } @article {pmid38177994, year = {2024}, author = {Albuquerque, NK and Silva, SP and Aragão, CF and Cunha, TCAS and Paiva, FAS and Coelho, TFSB and Cruz, ACR}, title = {Virome analysis of Desmodus rotundus tissue samples from the Amazon region.}, journal = {BMC genomics}, volume = {25}, number = {1}, pages = {34}, pmid = {38177994}, issn = {1471-2164}, support = {314522/2021-02//Coordination for the Improvement of Higher Education Personnel (CAPES)/ ; 314522/2021-02//Coordination for the Improvement of Higher Education Personnel (CAPES)/ ; }, mesh = {Animals ; *Bacteriophages ; *Chiroptera/virology ; Ecology ; Phylogeny ; Virome/genetics ; *Viruses/genetics ; }, abstract = {BACKGROUND: Bats are renowned for harboring a high viral diversity, their characteristics contribute to emerging infectious diseases. However, environmental and anthropic factors also play a significant role in the emergence of zoonotic viruses. Metagenomic is an important tool for investigating the virome of bats and discovering new viruses.

RESULTS: Twenty-four families of virus were detected in lung samples by sequencing and bioinfomatic analysis, the largest amount of reads was focused on the Retroviridae and contigs assembled to Desmodus rotundus endogenous retrovirus, which was feasible to acquire complete sequences. The reads were also abundant for phages.

CONCLUSION: This lung virome of D. rotundus contributes valuable information regarding the viral diversity found in bats, which is useful for understanding the drivers of viral cycles and their ecology in this species. The identification and taxonomic categorization of viruses hosted by bats carry epidemiological significance due to the potential for viral adaptation to other animals and humans, which can have severe repercussions for public health. Furthermore, the characterization of endogenized viruses helps to understanding the host genome and the evolution of the species.}, } @article {pmid38177508, year = {2024}, author = {Cao, L and Kong, Y and Fan, Y and Ni, M and Tourancheau, A and Ksiezarek, M and Mead, EA and Koo, T and Gitman, M and Zhang, XS and Fang, G}, title = {mEnrich-seq: methylation-guided enrichment sequencing of bacterial taxa of interest from microbiome.}, journal = {Nature methods}, volume = {}, number = {}, pages = {}, pmid = {38177508}, issn = {1548-7105}, support = {R35 GM139655/GM/NIGMS NIH HHS/United States ; }, abstract = {Metagenomics has enabled the comprehensive study of microbiomes. However, many applications would benefit from a method that sequences specific bacterial taxa of interest, but not most background taxa. We developed mEnrich-seq (in which 'm' stands for methylation and seq for sequencing) for enriching taxa of interest from metagenomic DNA before sequencing. The core idea is to exploit the self versus nonself differentiation by natural bacterial DNA methylation and rationally choose methylation-sensitive restriction enzymes, individually or in combination, to deplete host and background taxa while enriching targeted taxa. This idea is integrated with library preparation procedures and applied in several applications to enrich (up to 117-fold) pathogenic or beneficial bacteria from human urine and fecal samples, including species that are hard to culture or of low abundance. We assessed 4,601 bacterial strains with mapped methylomes so far and showed broad applicability of mEnrich-seq. mEnrich-seq provides microbiome researchers with a versatile and cost-effective approach for selective sequencing of diverse taxa of interest.}, } @article {pmid38177492, year = {2023}, author = {Shen, J and Yu, Q and Chen, S and Tan, Q and Li, J and Li, Y}, title = {Unbiased organism-agnostic and highly sensitive signal peptide predictor with deep protein language model.}, journal = {Nature computational science}, volume = {}, number = {}, pages = {}, pmid = {38177492}, issn = {2662-8457}, support = {GHP/065/21SZ//Innovation and Technology Commission (ITF)/ ; }, abstract = {Signal peptides (SPs) are essential to target and transfer transmembrane and secreted proteins to the correct positions. Many existing computational tools for predicting SPs disregard the extreme data imbalance problem and rely on additional group information of proteins. Here we introduce Unbiased Organism-agnostic Signal Peptide Network (USPNet), an SP classification and cleavage-site prediction deep learning method. Extensive experimental results show that USPNet substantially outperforms previous methods on classification performance by 10%. An SP-discovering pipeline with USPNet is designed to explore unprecedented SPs from metagenomic data. It reveals 347 SP candidates, with the lowest sequence identity between our candidates and the closest SP in the training dataset at only 13%. In addition, the template modeling scores between candidates and SPs in the training set are mostly above 0.8. The results showcase that USPNet has learnt the SP structure with raw amino acid sequences and the large protein language model, thereby enabling the discovery of unknown SPs.}, } @article {pmid38177233, year = {2024}, author = {Kwak, H and Lee, D and Kim, Y and Park, J and Yeum, H and Kim, D and Dong, YW and Nakano, T and Jeong, C and Park, JK}, title = {Genome assembly and population genomic data of a pulmonate snail Ellobium chinense.}, journal = {Scientific data}, volume = {11}, number = {1}, pages = {31}, pmid = {38177233}, issn = {2052-4463}, support = {2015R1A4A1041997, 2020R1A2C2005393//National Research Foundation of Korea (NRF)/ ; the management of Marine Fishery Bio-resources Center (2023)//National Marine Biodiversity Institute of Korea (Marine Biodiversity institute of Korea)/ ; }, mesh = {Animals ; Ecosystem ; *Genome ; Genomics ; *Metagenomics ; *Snails/genetics ; }, abstract = {Ellobium chinense is an airbreathing, pulmonate gastropod species that inhabits saltmarshes in estuaries of the northwestern Pacific. Due to a rapid population decline and their unique ecological niche in estuarine ecosystems, this species has attracted special attention regarding their conservation and the genomic basis of adaptation to frequently changing environments. Here we report a draft genome assembly of E. chinense with a total size of 949.470 Mb and a scaffold N50 of 1.465 Mb. Comparative genomic analysis revealed that the GO terms enriched among four gastropod species are related to signal transduction involved in maintaining electrochemical gradients across the cell membrane. Population genomic analysis using the MSMC model for 14 re-sequenced individuals revealed a drastic decline in Korean and Japanese populations during the last glacial period, while the southern Chinese population retained a much larger effective population size (Ne). These contrasting demographic changes might be attributed to multiple environmental factors during the glacial-interglacial cycles. This study provides valuable genomic resources for understanding adaptation and historical demographic responses to climate change.}, } @article {pmid38176300, year = {2024}, author = {Li, X and Li, D and Han, D}, title = {Rapid diagnosis of Aspergillus fumigatus endocarditis using mNGS assay: A case report and review of the literature.}, journal = {Diagnostic microbiology and infectious disease}, volume = {108}, number = {3}, pages = {116171}, doi = {10.1016/j.diagmicrobio.2023.116171}, pmid = {38176300}, issn = {1879-0070}, abstract = {Fungal endocarditis is caused mainly by Candida albicans and Aspergillus spp. and was first reported in the 1950s. Natural-valve endocarditis caused by Aspergillus is relatively uncommon. In this case, a 56-year-old male patient was admitted to the hospital on account of a cough accompanied by chills and fever and ineffective self-medication. Infective endocarditis was initially suspected based on echocardiography (indicating right atrial growth) and clinical manifestations. However, routine pathogen detections were always negative. The patient's condition was identified as Aspergillus fumigatus endocarditis (AFE) and was treated with targeted therapy, considering the detection of significant AFE sequences in the blood through metagenomic next-generation sequencing (mNGS). On this basis, the paper further summarizes the clinical manifestations, diagnosis, treatments, and outcomes of AFE endocarditis cases reported in recent years, aiming to provide a reference to better understand this rare infective disease and guide medical practitioners in choosing the right diagnostic and therapeutic strategy.}, } @article {pmid38176299, year = {2023}, author = {Guan, Y and Ma, X and Sun, X and Zhang, H}, title = {Metagenomic next-generation sequencing on bronchoalveolar lavage fluid to contribute to diagnosis of subclinical pulmonary tuberculosis with scarce sputum and negative smear in a patient mimicking adult- onset still's disease: A case report.}, journal = {Diagnostic microbiology and infectious disease}, volume = {108}, number = {3}, pages = {116165}, doi = {10.1016/j.diagmicrobio.2023.116165}, pmid = {38176299}, issn = {1879-0070}, abstract = {Extremely high serum ferritin, which is regarded as a marker of adult-onset still's disease (AOSD), has been rarely observed in patients with TB. We report a case of TB diagnose by metagenomic next-generation sequencing(mNGS) who presented with clinical criteria of AOSD and extreme hyperferritinemia, which posed a diagnostic confusion. TB presenting with major clinical criteria of AOSD should be notable. Since TB remains a potentially curable disease, an awareness of its' protean manifestations is essential. A typical or even normal outcomes of clinical, microbiochemical, and radiologic evaluation should not be overlooked and dedicated diagnostic work-up should be performed for TB diagnosis. For equivocal cases, mNGS could be helpful.}, } @article {pmid38175233, year = {2024}, author = {Wu, S and Xu, G and Su, Y and Huang, H and Xu, X and Zhang, Y and Tian, J and Zhang, W and Zhang, Z and Liu, B}, title = {Mining and rational design of psychrophilic catalases using metagenomics and deep learning models.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {1-10}, pmid = {38175233}, issn = {1432-0614}, support = {2021YFA0910602//National Key Research and Development Program of China/ ; 2022YFA0912301//National Key Research and Development Program of China/ ; CAAS-ZDRW202305//Agricultural Science and Technology Innovation Program/ ; CARS-41//the China Agriculture Research System of MOF and MARA/ ; }, mesh = {Catalase/genetics ; *Deep Learning ; Amino Acid Sequence ; Amino Acids ; Soil ; }, abstract = {A complete catalase-encoding gene, designated soiCat1, was obtained from soil samples via metagenomic sequencing, assembly, and gene prediction. soiCat1 showed 73% identity to a catalase-encoding gene of Mucilaginibacter rubeus strain P1, and the amino acid sequence of soiCAT1 showed 99% similarity to the catalase of a psychrophilic bacterium, Pedobacter cryoconitis. soiCAT1 was identified as a psychrophilic enzyme due to the low optimum temperature predicted by the deep learning model Preoptem, which was subsequently validated through analysis of enzymatic properties. Experimental results showed that soiCAT1 has a very narrow range of optimum temperature, with maximal specific activity occurring at the lowest test temperature (4 °C) and decreasing with increasing reaction temperature from 4 to 50 °C. To rationally design soiCAT1 with an improved temperature range, soiCAT1 was engineered through site-directed mutagenesis based on molecular evolution data analyzed through position-specific amino acid possibility calculation. Compared with the wild type, one mutant, soiCAT1[S205K], exhibited an extended range of optimum temperature ranging from 4 to 20 °C. The strategies used in this study may shed light on the mining of genes of interest and rational design of desirable proteins. KEY POINTS: • Numerous putative catalases were mined from soil samples via metagenomics. • A complete sequence encoding a psychrophilic catalase was obtained. • A mutant psychrophilic catalase with an extended range of optimum temperature was engineered through site-directed mutagenesis.}, } @article {pmid38174949, year = {2024}, author = {, }, title = {Retraction for Amrane et al., "Clostridium scindens Is Present in the Gut Microbiota during Clostridium difficile Infection: a Metagenomic and Culturomic Analysis".}, journal = {Journal of clinical microbiology}, volume = {}, number = {}, pages = {e0150723}, doi = {10.1128/jcm.01507-23}, pmid = {38174949}, issn = {1098-660X}, } @article {pmid38173792, year = {2023}, author = {Zhou, J and Wu, X and Xiang, T and Liu, F and Gao, H and Tong, L and Yan, B and Li, Z and Zhang, C and Wang, L and Ou, L and Li, Z and Wang, W and Yang, T and Li, F and Ma, H and Zhao, X and Mi, N and Yu, Z and Lan, C and Wang, Q and Li, H and Wang, L and Wang, X and Li, Y and Zeng, Q}, title = {Dynamical alterations of brain function and gut microbiome in weight loss.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1269548}, pmid = {38173792}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; Caloric Restriction/methods ; Escherichia coli ; Obesity ; Weight Loss ; }, abstract = {OBJECTIVE: Intermittent energy restriction (IER) is an effective weight loss strategy. However, little is known about the dynamic effects of IER on the brain-gut-microbiome axis.

METHODS: In this study, a total of 25 obese individuals successfully lost weight after a 2-month IER intervention. FMRI was used to determine the activity of brain regions. Metagenomic sequencing was performed to identify differentially abundant gut microbes and pathways in from fecal samples.

RESULTS: Our results showed that IER longitudinally reduced the activity of obese-related brain regions at different timepoints, including the inferior frontal orbital gyrus in the cognitive control circuit, the putamen in the emotion and learning circuit, and the anterior cingulate cortex in the sensory circuit. IER longitudinally reduced E. coli abundance across multiple timepoints while elevating the abundance of obesity-related Faecalibacterium prausnitzii, Parabacteroides distasonis, and Bacterokles uniformis. Correlation analysis revealed longitudinally correlations between gut bacteria abundance alterations and brain activity changes.

CONCLUSIONS: There was dynamical alteration of BGM axis (the communication of E. coli with specific brain regions) during the weight loss under the IER.}, } @article {pmid38173160, year = {2024}, author = {Chang, YH and Choi, YJ and Shin, CM and Moon, JS and Kim, TY and Yoon, H and Park, YS and Kim, N and Lee, DH}, title = {Efficacy of Quadruple-coated Probiotics in Patients With Irritable Bowel Syndrome: A Randomized, Double-blind, Placebo-controlled, Parallel-group Study.}, journal = {Journal of neurogastroenterology and motility}, volume = {30}, number = {1}, pages = {73-86}, doi = {10.5056/jnm23036}, pmid = {38173160}, issn = {2093-0879}, abstract = {BACKGROUND/AIMS: To evaluate the efficacy of quadruple-coated probiotics (gQlab) in patients with irritable bowel syndrome (IBS), focusing on sex differences and IBS subtypes.

METHODS: One hundred and nine Rome III-diagnosed IBS patients were randomized into either a gQlab or placebo group and received either gQlab or a placebo for 4 weeks. Participants replied to questionnaires assessing compliance, symptoms, and safety. Fecal samples were collected at 0 and 4 weeks to measure the probiotic levels using real-time quantitative polymerase chain reaction (qPCR) and to perform metagenomic analysis via 16S ribosomal DNA sequencing. The primary endpoint was the change in the overall IBS symptoms after 4 weeks of treatment.

RESULTS: Ninety-two subjects (47 and 45 in the gQlab and placebo groups, respectively) completed the study protocol. At week 4, there was a higher relief of the overall IBS symptoms in the gQlab group (P = 0.005). The overall IBS symptom improvement was statistically significant (P = 0.017) in female patients of the gQlab group compared with the placebo group. Among the IBS subtypes, constipation-predominant IBS patients showed significant relief of the overall IBS symptoms (P = 0.002). At week 4, the fecal microbiome profiles between the 2 groups did not differ, but the qPCR levels of Lactobacillus plantarum, Lactobacillus acidophilus, Lactobacillus helveticus, Bifidobacterium longum, and Bifidobacterium breve were increased in the gQlab group (P < 0.05 by repeated measures ANOVA).

CONCLUSIONS: gQlab administration can improve the overall IBS symptoms, especially in female and constipation-predominant IBS patients. Further research is necessary to clarify the pathophysiology behind sex-related treatment responses in IBS patients.}, } @article {pmid38172958, year = {2024}, author = {Tsola, SL and Zhu, Y and Chen, Y and Sanders, IA and Economou, CK and Brüchert, V and Eyice, Ö}, title = {Methanolobus use unspecific methyltransferases to produce methane from dimethylsulphide in Baltic Sea sediments.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {3}, pmid = {38172958}, issn = {2049-2618}, support = {PhD Scholarship//Queen Mary University of London/ ; NE/S007725/1//Natural Environment Research Council/ ; 10.46936/10.25585/60001216//Joint Genome Institute/ ; }, mesh = {*Methane/metabolism ; Methanosarcinaceae/genetics/metabolism ; Methyltransferases/genetics/metabolism ; *Greenhouse Gases ; Geologic Sediments ; Sulfates/metabolism ; }, abstract = {BACKGROUND: In anoxic coastal and marine sediments, degradation of methylated compounds is the major route to the production of methane, a powerful greenhouse gas. Dimethylsulphide (DMS) is the most abundant biogenic organic sulphur compound in the environment and an abundant methylated compound leading to methane production in anoxic sediments. However, understanding of the microbial diversity driving DMS-dependent methanogenesis is limited, and the metabolic pathways underlying this process in the environment remain unexplored. To address this, we used anoxic incubations, amplicon sequencing, genome-centric metagenomics and metatranscriptomics of brackish sediments collected along the depth profile of the Baltic Sea with varying sulphate concentrations.

RESULTS: We identified Methanolobus as the dominant methylotrophic methanogens in all our DMS-amended sediment incubations (61-99%) regardless of their sulphate concentrations. We also showed that the mtt and mta genes (trimethylamine- and methanol-methyltransferases) from Methanolobus were highly expressed when the sediment samples were incubated with DMS. Furthermore, we did not find mtsA and mtsB (methylsulphide-methyltransferases) in metatranscriptomes, metagenomes or in the Methanolobus MAGs, whilst mtsD and mtsF were found 2-3 orders of magnitude lower in selected samples.

CONCLUSIONS: Our study demonstrated that the Methanolobus genus is likely the key player in anaerobic DMS degradation in brackish Baltic Sea sediments. This is also the first study analysing the metabolic pathways of anaerobic DMS degradation in the environment and showing that methylotrophic methane production from DMS may not require a substrate-specific methyltransferase as was previously accepted. This highlights the versatility of the key enzymes in methane production in anoxic sediments, which would have significant implications for the global greenhouse gas budget and the methane cycle. Video Abstract.}, } @article {pmid38172637, year = {2024}, author = {Zhernakova, DV and Wang, D and Liu, L and Andreu-Sánchez, S and Zhang, Y and Ruiz-Moreno, AJ and Peng, H and Plomp, N and Del Castillo-Izquierdo, Á and Gacesa, R and Lopera-Maya, EA and Temba, GS and Kullaya, VI and van Leeuwen, SS and , and Xavier, RJ and de Mast, Q and Joosten, LAB and Riksen, NP and Rutten, JHW and Netea, MG and Sanna, S and Wijmenga, C and Weersma, RK and Zhernakova, A and Harmsen, HJM and Fu, J}, title = {Host genetic regulation of human gut microbial structural variation.}, journal = {Nature}, volume = {}, number = {}, pages = {}, pmid = {38172637}, issn = {1476-4687}, abstract = {Although the impact of host genetics on gut microbial diversity and the abundance of specific taxa is well established[1-6], little is known about how host genetics regulates the genetic diversity of gut microorganisms. Here we conducted a meta-analysis of associations between human genetic variation and gut microbial structural variation in 9,015 individuals from four Dutch cohorts. Strikingly, the presence rate of a structural variation segment in Faecalibacterium prausnitzii that harbours an N-acetylgalactosamine (GalNAc) utilization gene cluster is higher in individuals who secrete the type A oligosaccharide antigen terminating in GalNAc, a feature that is jointly determined by human ABO and FUT2 genotypes, and we could replicate this association in a Tanzanian cohort. In vitro experiments demonstrated that GalNAc can be used as the sole carbohydrate source for F. prausnitzii strains that carry the GalNAc-metabolizing pathway. Further in silico and in vitro studies demonstrated that other ABO-associated species can also utilize GalNAc, particularly Collinsella aerofaciens. The GalNAc utilization genes are also associated with the host's cardiometabolic health, particularly in individuals with mucosal A-antigen. Together, the findings of our study demonstrate that genetic associations across the human genome and bacterial metagenome can provide functional insights into the reciprocal host-microbiome relationship.}, } @article {pmid38172624, year = {2024}, author = {Hall, B and Levy, S and Dufault-Thompson, K and Arp, G and Zhong, A and Ndjite, GM and Weiss, A and Braccia, D and Jenkins, C and Grant, MR and Abeysinghe, S and Yang, Y and Jermain, MD and Wu, CH and Ma, B and Jiang, X}, title = {BilR is a gut microbial enzyme that reduces bilirubin to urobilinogen.}, journal = {Nature microbiology}, volume = {9}, number = {1}, pages = {173-184}, pmid = {38172624}, issn = {2058-5276}, support = {U54 DK110858/DK/NIDDK NIH HHS/United States ; }, mesh = {Infant, Newborn ; Adult ; Humans ; *Bilirubin/metabolism ; Urobilinogen/metabolism ; *Gastrointestinal Microbiome ; Liver/metabolism ; Bacteria/genetics/metabolism ; }, abstract = {Metabolism of haem by-products such as bilirubin by humans and their gut microbiota is essential to human health, as excess serum bilirubin can cause jaundice and even neurological damage. The bacterial enzymes that reduce bilirubin to urobilinogen, a key step in this pathway, have remained unidentified. Here we used biochemical analyses and comparative genomics to identify BilR as a gut-microbiota-derived bilirubin reductase that reduces bilirubin to urobilinogen. We delineated the BilR sequences from similar reductases through the identification of key residues critical for bilirubin reduction and found that BilR is predominantly encoded by Firmicutes species. Analysis of human gut metagenomes revealed that BilR is nearly ubiquitous in healthy adults, but prevalence is decreased in neonates and individuals with inflammatory bowel disease. This discovery sheds light on the role of the gut microbiome in bilirubin metabolism and highlights the significance of the gut-liver axis in maintaining bilirubin homeostasis.}, } @article {pmid38172612, year = {2024}, author = {Rubas, NC and Peres, R and Kunihiro, BP and Allan, NP and Phankitnirundorn, K and Wells, RK and McCraken, TA and Lee, RH and Umeda, L and Conching, A and Juarez, R and Maunakea, AK}, title = {HMGB1 mediates microbiome-immune axis dysregulation underlying reduced neutralization capacity in obesity-related post-acute sequelae of SARS-CoV-2.}, journal = {Scientific reports}, volume = {14}, number = {1}, pages = {355}, pmid = {38172612}, issn = {2045-2322}, support = {20HCF-101573//Hawaii Community Foundation/ ; W911NF21P0025//U.S. Army/ ; 2036240//National Science Foundation/ ; }, mesh = {Humans ; *COVID-19/complications ; Disease Progression ; *HMGB1 Protein/genetics ; Longitudinal Studies ; *Microbiota ; Obesity/complications ; Post-Acute COVID-19 Syndrome ; SARS-CoV-2 ; }, abstract = {While obesity is a risk factor for post-acute sequelae of SARS-CoV-2 infection (PASC, "long-COVID"), the mechanism(s) underlying this phenomenon remains poorly understood. To address this gap in knowledge, we performed a 6-week longitudinal study to examine immune activity and gut microbiome dysbiosis in post-acute stage patients recovering from SARS-CoV-2 infection. Self-reported symptom frequencies and blood samples were collected weekly, with plasma assessed by ELISA and Luminex for multiple biomarkers and immune cell profiling. DNA from stool samples were collected at the early stage of recovery for baseline assessments of gut microbial composition and diversity using 16S-based metagenomic sequencing. Multiple regression analyses revealed obesity-related PASC linked to a sustained proinflammatory immune profile and reduced adaptive immunity, corresponding with reduced gut microbial diversity. In particular, enhanced signaling of the high mobility group box 1 (HMGB1) protein was found to associate with this dysregulation, with its upregulated levels in plasma associated with significantly impaired viral neutralization that was exacerbated with obesity. These findings implicate HMGB1 as a candidate biomarker of PASC, with potential applications for risk assessment and targeted therapies.}, } @article {pmid38172339, year = {2024}, author = {Thiele Orberg, E and Meedt, E and Hiergeist, A and Xue, J and Heinrich, P and Ru, J and Ghimire, S and Miltiadous, O and Lindner, S and Tiefgraber, M and Göldel, S and Eismann, T and Schwarz, A and Göttert, S and Jarosch, S and Steiger, K and Schulz, C and Gigl, M and Fischer, JC and Janssen, KP and Quante, M and Heidegger, S and Herhaus, P and Verbeek, M and Ruland, J and van den Brink, MRM and Weber, D and Edinger, M and Wolff, D and Busch, DH and Kleigrewe, K and Herr, W and Bassermann, F and Gessner, A and Deng, L and Holler, E and Poeck, H}, title = {Bacteria and bacteriophage consortia are associated with protective intestinal metabolites in patients receiving stem cell transplantation.}, journal = {Nature cancer}, volume = {}, number = {}, pages = {}, pmid = {38172339}, issn = {2662-1347}, support = {395357507//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 395357507//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 360372040//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; BA 2851/6-1, 360372040//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 395357507//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DE 2360/6-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; DE 2360/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 464797012//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 324392634, 395357507//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 360372040, 395357507, 324392634//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; R01-HL123340, R01-HL147584//U.S. Department of Health & Human Services | NIH | National Heart, Lung, and Blood Institute (NHLBI)/ ; DJCLS 01 GvHD/2016//Jos& Carreras Leuk&mie-Stiftung (Deutsche Jos& Carreras Leuk&mie-Stiftung)/ ; 70114547//Deutsche Krebshilfe (German Cancer Aid)/ ; 2021.040.1//Wilhelm Sander-Stiftung (Wilhelm Sander Foundation)/ ; }, abstract = {The microbiome is a predictor of clinical outcome in patients receiving allogeneic hematopoietic stem cell transplantation (allo-SCT). Microbiota-derived metabolites can modulate these outcomes. How bacteria, fungi and viruses contribute to the production of intestinal metabolites is still unclear. We combined amplicon sequencing, viral metagenomics and targeted metabolomics from stool samples of patients receiving allo-SCT (n = 78) and uncovered a microbiome signature of Lachnospiraceae and Oscillospiraceae and their associated bacteriophages, correlating with the production of immunomodulatory metabolites (IMMs). Moreover, we established the IMM risk index (IMM-RI), which was associated with improved survival and reduced relapse. A high abundance of short-chain fatty acid-biosynthesis pathways, specifically butyric acid via butyryl-coenzyme A (CoA):acetate CoA-transferase (BCoAT, which catalyzes EC 2.8.3.8) was detected in IMM-RI low-risk patients, and virome genome assembly identified two bacteriophages encoding BCoAT as an auxiliary metabolic gene. In conclusion, our study identifies a microbiome signature associated with protective IMMs and provides a rationale for considering metabolite-producing consortia and metabolite formulations as microbiome-based therapies.}, } @article {pmid38172093, year = {2024}, author = {Zhang, Q and Li, G and Zhao, W and Wang, X and He, J and Zhou, L and Zhang, X and An, P and Liu, Y and Zhang, C and Zhang, Y and Liu, S and Zhao, L and Liu, R and Li, Y and Jiang, W and Wang, X and Wang, Q and Fang, B and Zhao, Y and Ren, Y and Niu, X and Li, D and Shi, S and Hung, WL and Wang, R and Liu, X and Ren, F}, title = {Efficacy of Bifidobacterium animalis subsp. lactis BL-99 in the treatment of functional dyspepsia: a randomized placebo-controlled clinical trial.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {227}, pmid = {38172093}, issn = {2041-1723}, mesh = {Humans ; *Bifidobacterium animalis ; *Dyspepsia/therapy ; *Probiotics/therapeutic use ; Feces/microbiology ; Double-Blind Method ; }, abstract = {Current treatment for functional dyspepsia (FD) has limited and unsustainable efficacy. Probiotics have the sustainable potential to alleviate FD. This randomized controlled clinical trial (Chinese Clinical Trial Registry, ChiCTR2000041430) assigned 200 FD patients to receive placebo, positive-drug (rabeprazole), or Bifidobacterium animalis subsp. lactis BL-99 (BL-99; low, high doses) for 8-week. The primary outcome was the clinical response rate (CRR) of FD score after 8-week treatment. The secondary outcomes were CRR of FD score at other periods, and PDS, EPS, serum indicators, fecal microbiota and metabolites. The CRR in FD score for the BL-99_high group [45 (90.0%)] was significantly higher than that for placebo [29 (58.0%), p = 0.001], BL-99_low [37 (74.0%), p = 0.044] and positive_control [35 (70.0%), p = 0.017] groups after 8-week treatment. This effect was sustained until 2-week after treatment but disappeared 8-week after treatment. Further metagenomic and metabolomics revealed that BL-99 promoted the accumulation of SCFA-producing microbiota and the increase of SCFA levels in stool and serum, which may account for the increase of serum gastrin level. This study supports the potential use of BL-99 for the treatment of FD.}, } @article {pmid38171496, year = {2024}, author = {Linz, AM and Anderson, JL and Meece, JK}, title = {Detection of Blastomyces gilchristii via metagenomic sequencing in outbreak-associated soils.}, journal = {Medical mycology}, volume = {}, number = {}, pages = {}, doi = {10.1093/mmy/myad140}, pmid = {38171496}, issn = {1460-2709}, abstract = {Cases of Blastomycosis, a serious fungal disease globally rare but endemic to North America, can appear both sporadically and in outbreaks. Tracing these outbreaks to their environment has traditionally used culturing and polymerase chain reaction (PCR). Here, we present our method for metagenomic detection of Blastomyces in a 2015 outbreak soil sample from central Wisconsin. By sequencing this sample to multiple depths, we simulated the minimum required depth to detect Blastomyces in this outbreak. Our methods and recommendations can be used to identify the sources of blastomycosis during outbreaks and to learn about the ecology of Blastomyces.}, } @article {pmid38171202, year = {2023}, author = {Jia, B and Wan, J and Liu, H and Yan, B and Zhang, L and Su, X}, title = {DIET-like and MIET-like mutualism of S. oneidensis MR-1 and metal-reducing function microflora boosts Cr(VI) reduction.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133401}, doi = {10.1016/j.jhazmat.2023.133401}, pmid = {38171202}, issn = {1873-3336}, abstract = {Microbial treatment of Cr(VI) is an environmentally friendly and low-cost approach. However, the mechanism of mutualism and the role of interspecies electron transfer in Cr(VI) reducing microflora are unclear. Herein, we constructed an intersymbiotic microbial association flora to augment interspecies electron transfer via functionalizing electroactive Shewanella oneidensis MR-1 with metal-reducing microflora, and thus the efficiency of Cr(VI) reduction. The findings suggest that the metal-reducing active microflora could converts glucose into lactic acid and riboflavin for S. oneidensis MR-1 to act as a carbon source and electron mediator. Thus, when adding initial 25 mg/L Cr (VI), this microflora exhibited an outstanding Cr (VI) removal efficiency (100%) at 12 h and elevated Cr (III) immobilization efficiency (80%) at 60 h with the assistance of 25 mg/L Cu(II). A series of electrochemical experiments proved this remarkable removal efficiency were ascribed to the improved interspecies electron transfer efficiency through direct interspecies electron transfer and riboflavin through mediated interspecies electron transfer. Furthermore, the metagenomic analysis revealed the expression level of the electron transport pathway was promoted. Intriguing high abundance of genes participating in the bio-reduction and biotransformation of Cr(VI) was also observed in functional microflora. These outcomes give a novel strategy for enhancing the reduction and fixation of harmful heavy metals by coculturing function microflora with electrogenic microorganisms.}, } @article {pmid38171069, year = {2023}, author = {Liu, Y and Gao, J and Nie, Z and Wang, J and Sun, Y and Xu, G}, title = {Integration of metagenome and metabolome analysis reveals the correlation of gut microbiota, oxidative stress, and inflammation in Coilia nasus under air exposure stress and salinity mitigation.}, journal = {Comparative biochemistry and physiology. Part D, Genomics & proteomics}, volume = {49}, number = {}, pages = {101175}, doi = {10.1016/j.cbd.2023.101175}, pmid = {38171069}, issn = {1878-0407}, abstract = {Due to the strong response to air exposure, high mortality was occurred in Coilia nasus. Previous studies reported that 10 ‰ NaCl could significantly reduce mortality in C. nasus under air exposure. To investigate the mechanisms that 10 ‰ NaCl can alleviate stress, community structure and metabolism of the intestinal flora of C. nasus were detected via metagenome and metabolome. In this study, C. nasus were divided into control group (C), air exposure group without 10 ‰ NaCl (AE), and air exposure group with 10 ‰ NaCl (AES). After air exposure stress and salinity mitigation, the mortality, intestinal microorganisms, metabolites, and physiological biomarkers were analyzed. The results showed that the mortality rate of C. nasus was reduced after salinity reduction; the antioxidant capacity was elevated compared to the AE group; and anti-inflammatory capacity was increased in the AES group compared to the AE group. Metagenomic sequencing results showed that the levels of harmful bacteria (E. coli, Aeromonas) in the Candida nasus gut increased after air exposure; beneficial bacteria (Actinobacteria, Corynebacteria) in the C. nasus gut increased after salinity reduction. Metabolomics analyses showed that AE decreased the expression of beneficial metabolites and increased the expression of harmful metabolites; AES increased beneficial metabolites and decreased harmful metabolites. Correlation analysis showed that in the AE group, beneficial metabolites were negatively correlated with oxidative stress and inflammatory response, while harmful metabolites were positively correlated with oxidative stress and inflammatory response, and were associated with bacterial communities such as Gillisia, Alkalitalia, Avipoxvirus, etc.; the correlation of metabolites with oxidative stress and inflammatory response was opposite to that of AE in the case of AES, and was associated with Lentilactobacillus, Cyanobacterium, and other bacterial communities. Air exposure caused damage to Candida rhinoceros and 10 ‰ salinity was beneficial in alleviating C. nasus stress. These results will provide new insights into methods and mechanisms to mitigate stress in fish.}, } @article {pmid38170981, year = {2024}, author = {Real, MVF and Colvin, MS and Sheehan, MJ and Moeller, AH}, title = {Major urinary protein (Mup) gene family deletion drives sex-specific alterations in the house-mouse gut microbiota.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0356623}, doi = {10.1128/spectrum.03566-23}, pmid = {38170981}, issn = {2165-0497}, abstract = {The community of microorganisms that inhabits the gastrointestinal tract can have profound effects on host phenotypes. The gut microbiota is in turn shaped by host genes, including those involved with host metabolism. In adult male house mice, expression of the major urinary protein (Mup) gene cluster represents a substantial energy investment, and deletion of the Mup gene family leads to fat accumulation and weight gain in males. We show that deleting Mup genes also alters the gut microbiota of male, but not female, mice in terms of both taxonomic and functional compositions. Male mice without Mup genes harbored fewer gut bacterial families and reduced abundance of a species of Ruminococcaceae, a family that has been previously shown to reduce obesity risk. Studying the impact of the Mup gene family on the gut microbiota has the potential to reveal the ways in which these genes affect host phenotypes.}, } @article {pmid38170974, year = {2024}, author = {Jitsuno, K and Hoshino, T and Nishikawa, Y and Kogawa, M and Mineta, K and Strasser, M and Ikehara, K and Everest, J and Maeda, L and Inagaki, F and Takeyama, H and , }, title = {Comparative single-cell genomics of Atribacterota JS1 in the Japan Trench hadal sedimentary biosphere.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0033723}, doi = {10.1128/msphere.00337-23}, pmid = {38170974}, issn = {2379-5042}, abstract = {The Japan Trench represents tectonically active hadal environments associated with Pacific plate subduction beneath the northeastern Japan arc. This study, for the first time, documented a large-scale single-cell and metagenomic survey along an approximately 500 km transect of the Japan Trench, obtaining high-quality genomic information on hadal sedimentary microbial communities. Single-cell genomics revealed the predominance of diverse JS1 lineages not recoverable through conventional metagenomic binning. Their metabolic potential includes genes related to the degradation of organic matter, which contributes to methanogenesis in the deeper layers. Our findings enhance understanding of sedimentary microbial communities at water depths exceeding 7,000 m and provide new insights into the ecological role of biogeochemical carbon cycling in the hadal sedimentary biosphere.}, } @article {pmid38170354, year = {2024}, author = {Xing, M and Zhao, R and Yang, G and Li, Z and Sun, Y and Xue, Z}, title = {Elimination of antibiotic-resistant bacteria and resistance genes by earthworms during vermifiltration treatment of excess sludge.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38170354}, issn = {1614-7499}, support = {0400219423//Tongji University/ ; 19DZ1204304//Science and Technology Commission of Shanghai Municipality/ ; }, abstract = {Vermifiltration (VF) and a conventional biofilter (BF, no earthworm) were investigated by metagenomics to evaluate the removal rates of antibiotic-resistant bacteria (ARB), antibiotic resistance genes (ARGs), and class 1 integron-integrase (intI1), as well as the impact mechanism in combination with the microbial community. According to the findings of qPCR and metagenomics, the VF facilitated greater removal rates of ARGs (78.83% ± 17.37%) and ARB (48.23% ± 2.69%) than the BF (56.33% ± 14.93%, 20.21% ± 6.27%). Compared to the control, the higher biological activity of the VF induced an increase of over 60% in the inhibitory effect of earthworm coelomic fluid on ARB. The removal rates of ARGs by earthworm guts also reached over 22%. In addition, earthworms enhanced the decomposition of refractory organics, toxic, and harmful organics, which led to a lower selective pressure on ARGs and ARB. It provides a strategy for reducing resistant pollution in sewage treatment plants and recognizing the harmless stability of sludge.}, } @article {pmid38170239, year = {2024}, author = {Kachor, A and Tistechok, S and Rebets, Y and Fedorenko, V and Gromyko, O}, title = {Bacterial community and culturable actinomycetes of Phyllostachys viridiglaucescens rhizosphere.}, journal = {Antonie van Leeuwenhoek}, volume = {117}, number = {1}, pages = {9}, pmid = {38170239}, issn = {1572-9699}, support = {Н/309-2003//Ministry of Education and Science of Ukraine/ ; Н/309-2003//Ministry of Education and Science of Ukraine/ ; Н/309-2003//Ministry of Education and Science of Ukraine/ ; Н/309-2003//Ministry of Education and Science of Ukraine/ ; }, mesh = {*Actinobacteria ; Actinomyces/genetics ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; *Actinomycetales/genetics ; *Streptomyces ; Poaceae ; Soil Microbiology ; }, abstract = {During the course of development plants form tight interactions with microorganisms inhabiting their root zone. In turn, rhizosphere bacteria, in particular members of the phylum Actinomycetota, positively influence the host plant by increasing access to essential nutrients and controlling the pathogenic microorganism's population. Herein, we report the characterisation of the rhizosphere associated actinobacteria community of Phyllostachys viridiglaucescens growing in the Nikitsky Botanical Garden (Crimean Peninsula, Ukraine). The overall composition of the bacterial community was elucidated by 16S rRNA gene amplicon sequencing followed by isolation of culturable microorganisms with the focus on actinomycetes. The metagenomic approach revealed that the representatives of phylum Actinomycetota (57.1%), Pseudomonadota (20.0%), and Acidobacteriota (12.2%) were dominating in the studied microbiome with Ilumatobacter (phylum Actinomycetota) (13.1%) being the dominant genus. Furthermore, a total of 159 actinomycete isolates, belonging to eight genera of Streptomyces, Micromonospora, Nonomuraea, Arthrobacter, Actinomadura, Kribbella, Cellulosimicrobium, and Mumia, were recovered from P. viridiglaucescens rhizosphere. The isolated species were tested for antimicrobial activity. 64% of isolates were active against at least one bacterial test-culture and 7.5% against fungal test culture. In overall, the rhizosphere bacterial communities act as a great source of actinobacterial diversity with the high potential for production of new bioactive compounds.}, } @article {pmid38169331, year = {2024}, author = {Campbell, E and Hesser, LA and Berni Canani, R and Carucci, L and Paparo, L and Patry, RT and Nagler, CR}, title = {A Lipopolysaccharide-Enriched Cow's Milk Allergy Microbiome Promotes a TLR4-Dependent Proinflammatory Intestinal Immune Response.}, journal = {Journal of immunology (Baltimore, Md. : 1950)}, volume = {}, number = {}, pages = {}, doi = {10.4049/jimmunol.2300518}, pmid = {38169331}, issn = {1550-6606}, support = {AI146099//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; }, abstract = {We have previously reported that the gut microbiota of healthy infants harbors allergy-protective bacteria taxa that are depleted in infants with cow's milk allergy (CMA). Few reports have investigated the role of the gut microbiota in promoting allergic responses. In this study we selected a CMA-associated microbiota with increased abundance of Gram-negative bacteria for analysis of its proinflammatory potential. LPS is the major component of the outer membrane of Gram-negative bacteria. Colonization of mice with a global or conditional mutation of the LPS receptor TLR4 with this CMA microbiota induced expression of serum amyloid A1 (Saa1) and other Th17-, B cell-, and Th2-associated genes in the ileal epithelium in a TLR4-dependent manner. In agreement with the gene expression data, mice colonized with the CMA microbiota have expanded populations of Th17 and regulatory T cells and elevated concentrations of fecal IgA. Importantly, we used both antibiotic-treated specific pathogen-free and germ-free rederived mice with a conditional mutation of TLR4 in the CD11c+ compartment to demonstrate that the induction of proinflammatory genes, fecal IgA, and Th17 cells is dependent on TLR4 signaling. Furthermore, metagenomic sequencing revealed that the CMA microbiota has an increased abundance of LPS biosynthesis genes. Taken together, our results show that a microbiota displaying a higher abundance of LPS genes is associated with TLR4-dependent proinflammatory gene expression and a mixed type 2/type 3 response in mice, which may be characteristic of a subset of infants with CMA.}, } @article {pmid38169204, year = {2023}, author = {Duster, N and Ramchandar, N and Foley, J and Farnaes, L and Coufal, NG}, title = {Application of cell-free plasma next-generation sequencing technology in the diagnosis and management of pediatric meningitis.}, journal = {Journal of microbiological methods}, volume = {217-218}, number = {}, pages = {106887}, doi = {10.1016/j.mimet.2023.106887}, pmid = {38169204}, issn = {1872-8359}, abstract = {This retrospective study evaluates the clinical utility of CFPNGS in the diagnosis and management of pediatric meningitis. CFPNGS identified a causative pathogen in 36% of 28 subjects, compared to 50% for diverse conventional testing (57% combined). CFPNGS may be considered as an adjunct to standard testing.}, } @article {pmid38169199, year = {2023}, author = {Liao, Y and Li, S and Ji, G}, title = {Graphene oxide stimulated low-temperature denitrification activity of microbial communities in lake sediments by enhancing anabolism and inhibiting cellular respiration.}, journal = {Chemosphere}, volume = {350}, number = {}, pages = {141090}, doi = {10.1016/j.chemosphere.2023.141090}, pmid = {38169199}, issn = {1879-1298}, abstract = {Nitrate pollution in fresh water is becoming increasingly serious. In this study, the effects of temperature and graphene oxide materials on the potential functions of denitrification communities in lake sediments were investigated by metagenome. The addition of graphene oxide significantly affected the abundance of denitrification genes such as Nap, Nos, and enhanced the contribution of Pseudomonas, making low temperature and material addition conducive to the denitrification process. Module network implied that low temperature increased the centrality of denitrification in community functions. At low temperatures, graphene oxide enhanced community anabolism by stimulation organic carbon consumption and regulating the gene abundance in the citric acid cycle and the semi-phosphorylation Entner-Doudoroff, thus possibly stimulating extracellular polymeric substances (EPS) synthesis and secretion. In addition, graphene oxide may also regulate the transfer of reducing electrons from NADH to denitrifying enzymes by affecting the gene abundances of complex I and complex IV.}, } @article {pmid38168989, year = {2024}, author = {Benoit, G and Raguideau, S and James, R and Phillippy, AM and Chikhi, R and Quince, C}, title = {High-quality metagenome assembly from long accurate reads with metaMDBG.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {38168989}, issn = {1546-1696}, support = {NE/T013230/1//RCUK | Natural Environment Research Council (NERC)/ ; MR/S037195/1//RCUK | Medical Research Council (MRC)/ ; BB/CSP1720/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BS/E/T/000PR9818//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BBS/E/T/000PR9817//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; BB/N023285/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; 956229//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, abstract = {We introduce metaMDBG, a metagenomics assembler for PacBio HiFi reads. MetaMDBG combines a de Bruijn graph assembly in a minimizer space with an iterative assembly over sequences of minimizers to address variations in genome coverage depth and an abundance-based filtering strategy to simplify strain complexity. For complex communities, we obtained up to twice as many high-quality circularized prokaryotic metagenome-assembled genomes as existing methods and had better recovery of viruses and plasmids.}, } @article {pmid38168439, year = {2023}, author = {Minot, SS and Mayer-Blackwell, K and Fiore-Gartland, A and Johnson, A and Self, S and Bhatti, P and Yao, L and Liu, L and Sun, X and Jinfa, Y and Kublin, J}, title = {Strain-level characterization of health-associated bacterial consortia that colonize the human gut during infancy.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {38168439}, support = {R01 AI127100/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: The human gut microbiome develops rapidly during infancy, a key window of development coinciding with maturation of the adaptive immune system. However, little is known of the microbiome growth dynamics over the first few months of life and whether there are any generalizable patterns across human populations. We performed metagenomic sequencing on stool samples (n=94) from a cohort of infants (n=15) at monthly intervals in the first six months of life, augmenting our dataset with seven published studies for a total of 4,441 metagenomes from 1,162 infants.

RESULTS: Strain-level de novo analysis was used to identify 592 of the most abundant organisms in the infant gut microbiome. Previously unrecognized consortia were identified which exhibited highly correlated abundances across samples and were composed of diverse species spanning multiple genera. Analysis of a cohort of infants with cystic fibrosis identified one such novel consortium of diverse Enterobacterales which was positively correlated with weight gain. While all studies showed an increased community stability during the first year of life, microbial dynamics varied widely in the first few months of life, both by study and by individual.

CONCLUSION: By augmenting published metagenomic datasets with data from a newly established cohort we were able to identify novel groups of organisms that are correlated with measures of robust human development. We hypothesize that the presence of these groups may impact human health in aggregate in ways that individual species may not in isolation.}, } @article {pmid38168399, year = {2023}, author = {Yu, Y and Xu, F and Zhao, W and Thoma, C and Che, S and Richman, JE and Jin, B and Zhu, Y and Xing, Y and Wackett, L and Men, Y}, title = {Electron-bifurcation and fluoride efflux systems in Acetobacterium spp. drive defluorination of perfluorinated unsaturated carboxylic acids.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.12.13.568471}, pmid = {38168399}, abstract = {Enzymatic cleavage of C-F bonds in per- and polyfluoroalkyl substances (PFAS) is largely unknown but avidly sought to promote systems biology for PFAS bioremediation. Here, we report the reductive defluorination of α, β-unsaturated per- and polyfluorocarboxylic acids by Acetobacterium spp. Two critical molecular features in Acetobacterium species enabling reductive defluorination are (i) a functional fluoride efflux transporter (CrcB) and (ii) an electron-bifurcating caffeate reduction pathway (CarABCDE). The fluoride transporter was required for detoxification of released fluoride. Car enzymes were implicated in defluorination by the following evidence: (i) only Acetobacterium spp. with car genes catalyzed defluorination; (ii) caffeate and PFAS competed in vivo ; (iii) models from the X-ray structure of the electron-bifurcating reductase (CarC) positioned the PFAS substrate optimally for reductive defluorination; (iv) products identified by [19] F-NMR and high-resolution mass spectrometry were consistent with the model. Defluorination biomarkers identified here were found in wastewater treatment plant metagenomes on six continents.}, } @article {pmid38168274, year = {2023}, author = {Liu, R and Wang, Y and Cheng, D}, title = {Micro-DeMix: A mixture beta-multinomial model for investigating the fecal microbiome compositions.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38168274}, support = {R01 GM145772/GM/NIGMS NIH HHS/United States ; }, abstract = {Extensive research has uncovered the involvement of the human gut microbiome in various facets of human health, including metabolism, nutrition, physiology, and immune function. Researchers often study fecal microbiota as a proxy for understanding the gut microbiome. However, it has been demonstrated that this approach may not suffice to yield a comprehensive understanding of the entire gut microbial community. Emerging research is revealing the heterogeneity of the gut microbiome across different gastrointestinal (GI) locations in both composition and functions. While spatial metagenomics approach has been developed to address these variations in mice, limitations arise when applying it to human-subject research, primarily due to its invasive nature. With these restrictions, we introduce Micro-DeMix, a mixture beta-multinomial model that decomposes the fecal microbiome at compositional level to understand the heterogeneity of the gut microbiome across various GI locations and extract meaningful insights about the biodiversity of the gut microbiome. Moreover, Micro-DeMix facilitates the discovery of differentially abundant microbes between GI regions through a hypothesis testing framework. We utilize the Inflammatory Bowel Disease (IBD) data from the NIH Integrative Human Microbiome Project to demonstrate the effectiveness and efficiency of the proposed Micro-DeMix.}, } @article {pmid38168205, year = {2023}, author = {Commichaux, S and Luan, T and Muralidharan, HS and Pop, M}, title = {Database size positively correlates with the loss of species-level taxonomic resolution for the 16S rRNA and other prokaryotic marker genes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.12.13.571439}, pmid = {38168205}, abstract = {UNLABELLED: For decades, the 16S rRNA gene has been used to taxonomically classify prokaryotic species and to taxonomically profile microbial communities. The 16S rRNA gene has been criticized for being too conserved to differentiate between distinct species. We argue that the inability to differentiate between species is not a unique feature of the 16S rRNA gene. Rather, we observe the gradual loss of species-level resolution for other marker genes as the number of gene sequences increases in reference databases. We demonstrate this effect through the analysis of three commonly used databases of nearly-universal prokaryotic marker genes: the SILVA 16S rRNA gene database, the Genome Taxonomy Database (GTDB), and a set of 40 taxonomically-informative single-copy genes. Our results reflect a more fundamental property of the taxonomies themselves and have broad implications for bioinformatic analyses beyond taxonomic classification. Effective solutions for fine-level taxonomic classification require a more precise, and operationally-relevant, definition of the taxonomic labels being sought, and the use of combinations of genomic markers in the classification process.

IMPORTANCE: The use of reference databases for assigning taxonomic labels to genomic and metagenomic sequences is a fundamental bioinformatic task in the characterization of microbial communities. The increasing accessibility of high throughput sequencing has led to a rapid increase in the size and number of sequences in databases. This has been beneficial for improving our understanding of the global microbial genetic diversity. However, there is evidence that as the microbial diversity is more densely sampled, increasingly longer genomic segments are needed to differentiate between distinct species. The scientific community needs to be aware of this issue and needs to develop methods that better account for it when assigning taxonomic labels to metagenomic sequences from microbial communities.}, } @article {pmid38168034, year = {2024}, author = {Zhu, L and Jian, X and Zhou, B and Liu, R and Muñoz, M and Sun, W and Xie, L and Chen, X and Peng, C and Maurer, M and Li, J}, title = {Gut microbiota facilitate chronic spontaneous urticaria.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {112}, pmid = {38168034}, issn = {2041-1723}, support = {81974476//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82173424//National Natural Science Foundation of China (National Science Foundation of China)/ ; 82073458//National Natural Science Foundation of China (National Science Foundation of China)/ ; 81830096//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; Mice ; Animals ; *Gastrointestinal Microbiome ; Lipopolysaccharides/pharmacology ; Fatty Acids, Volatile/metabolism ; *Chronic Urticaria ; *Dermatitis ; Inflammation ; Dysbiosis/microbiology ; }, abstract = {Chronic spontaneous urticaria (CSU) comes with gut dysbiosis, but its relevance remains elusive. Here we use metagenomics sequencing and short-chain fatty acids metabolomics and assess the effects of human CSU fecal microbial transplantation, Klebsiella pneumoniae, Roseburia hominis, and metabolites in vivo. CSU gut microbiota displays low diversity and short-chain fatty acids production, but high gut Klebsiella pneumoniae levels, negatively correlates with blood short-chain fatty acids levels and links to high disease activity. Blood lipopolysaccharide levels are elevated, link to rapid disease relapse, and high gut levels of conditional pathogenic bacteria. CSU microbiome transfer and Klebsiella pneumoniae transplantation facilitate IgE-mediated mast cell(MC)-driven skin inflammatory responses and increase intestinal permeability and blood lipopolysaccharide accumulation in recipient mice. Transplantation of Roseburia hominis and caproate administration protect recipient mice from MC-driven skin inflammation. Here, we show gut microbiome alterations, in CSU, may reduce short-chain fatty acids and increase lipopolysaccharide levels, respectively, and facilitate MC-driven skin inflammation.}, } @article {pmid38167814, year = {2024}, author = {Power, JF and Carere, CR and Welford, HE and Hudson, DT and Lee, KC and Moreau, JW and Ettema, TJG and Reysenbach, AL and Lee, CK and Colman, DR and Boyd, ES and Morgan, XC and McDonald, IR and Craig Cary, S and Stott, MB}, title = {A genus in the bacterial phylum Aquificota appears to be endemic to Aotearoa-New Zealand.}, journal = {Nature communications}, volume = {15}, number = {1}, pages = {179}, pmid = {38167814}, issn = {2041-1723}, support = {C05X1203//Ministry of Business, Innovation and Employment (MBIE)/ ; 80NSSC19M0150//National Aeronautics and Space Administration (NASA)/ ; }, mesh = {New Zealand ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Microbiota ; Metagenome ; }, abstract = {Allopatric speciation has been difficult to examine among microorganisms, with prior reports of endemism restricted to sub-genus level taxa. Previous microbial community analysis via 16S rRNA gene sequencing of 925 geothermal springs from the Taupō Volcanic Zone (TVZ), Aotearoa-New Zealand, revealed widespread distribution and abundance of a single bacterial genus across 686 of these ecosystems (pH 1.2-9.6 and 17.4-99.8 °C). Here, we present evidence to suggest that this genus, Venenivibrio (phylum Aquificota), is endemic to Aotearoa-New Zealand. A specific environmental niche that increases habitat isolation was identified, with maximal read abundance of Venenivibrio occurring at pH 4-6, 50-70 °C, and low oxidation-reduction potentials. This was further highlighted by genomic and culture-based analyses of the only characterised species for the genus, Venenivibrio stagnispumantis CP.B2[T], which confirmed a chemolithoautotrophic metabolism dependent on hydrogen oxidation. While similarity between Venenivibrio populations illustrated that dispersal is not limited across the TVZ, extensive amplicon, metagenomic, and phylogenomic analyses of global microbial communities from DNA sequence databases indicates Venenivibrio is geographically restricted to the Aotearoa-New Zealand archipelago. We conclude that geographic isolation, complemented by physicochemical constraints, has resulted in the establishment of an endemic bacterial genus.}, } @article {pmid38167775, year = {2024}, author = {Vinh Dong, H and Saleh, T and Kaur, I and Yang, S}, title = {Elucidating the Clinical Interpretation and Impact of a Positive Plasma Cell-Free DNA Metagenomics Test Result-A Single Center Retrospective Study.}, journal = {The journal of applied laboratory medicine}, volume = {9}, number = {1}, pages = {14-27}, doi = {10.1093/jalm/jfad083}, pmid = {38167775}, issn = {2576-9456}, mesh = {Humans ; Retrospective Studies ; *Communicable Diseases/diagnosis/genetics ; Bacteria/genetics ; Metagenome ; *Cell-Free Nucleic Acids ; }, abstract = {BACKGROUND: The Karius Test (KT), a cell-free DNA metagenomic next-generation sequencing assay, has potential to improve diagnostic evaluation of infectious diseases. Published data describing clinical impact of positive KT results are limited. We attempt to elucidate the clinical interpretation and impact of positive KT results based on types and patterns of detected pathogens and patient characteristics.

METHODS: All positive KT results from a single institution in 2022 were screened. Patients with results that met predefined categories were included for review by a panel of 3 infectious diseases physicians and one clinical microbiologist. Predefined categories included reports with fungal, parasitic, notable bacterial, notable viral pathogens, or polybacterial results (≥3 bacteria). Polybacterial results were further classified into patterns of microbiome detected. Clinical impact and its correlation with result or patient characteristics were explored.

RESULTS: Ninety-two patients met the inclusion criteria, most were immunocompromised (73%). Positive KT results that met predefined categories had the following clinical impact: positive in 30.4%, negative in 2.2%, and none in 65.2%. Polybacterial results, especially interpreted as oral flora had lowest clinical impact (7.1% and 0.0%, respectively), while detection of parasites or notable bacterial pathogens had the highest clinical impact (100% and 77.8%, respectively). There was no correlation between patient characteristics and clinical impact.

CONCLUSIONS: Among a cohort of largely immunocompromised patients, we were able to demonstrate clinical impact of specific KT result types and patterns but did not find correlation between patient characteristics and clinical impact. Our results should be confirmed in future larger cohorts.}, } @article {pmid38167654, year = {2024}, author = {Zheng, W and Wuyun, Q and Li, Y and Zhang, C and Freddolino, PL and Zhang, Y}, title = {Improving deep learning protein monomer and complex structure prediction using DeepMSA2 with huge metagenomics data.}, journal = {Nature methods}, volume = {}, number = {}, pages = {}, pmid = {38167654}, issn = {1548-7105}, support = {GM136422//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; S10OD026825//U.S. Department of Health & Human Services | NIH | National Institute of General Medical Sciences (NIGMS)/ ; AI134678//Division of Intramural Research, National Institute of Allergy and Infectious Diseases (Division of Intramural Research of the NIAID)/ ; IIS1901191//National Science Foundation (NSF)/ ; MTM2025426//National Science Foundation (NSF)/ ; }, abstract = {Leveraging iterative alignment search through genomic and metagenome sequence databases, we report the DeepMSA2 pipeline for uniform protein single- and multichain multiple-sequence alignment (MSA) construction. Large-scale benchmarks show that DeepMSA2 MSAs can remarkably increase the accuracy of protein tertiary and quaternary structure predictions compared with current state-of-the-art methods. An integrated pipeline with DeepMSA2 participated in the most recent CASP15 experiment and created complex structural models with considerably higher quality than the AlphaFold2-Multimer server (v.2.2.0). Detailed data analyses show that the major advantage of DeepMSA2 lies in its balanced alignment search and effective model selection, and in the power of integrating huge metagenomics databases. These results demonstrate a new avenue to improve deep learning protein structure prediction through advanced MSA construction and provide additional evidence that optimization of input information to deep learning-based structure prediction methods must be considered with as much care as the design of the predictor itself.}, } @article {pmid38167520, year = {2024}, author = {Centurion, VB and Rossi, A and Orellana, E and Ghiotto, G and Kakuk, B and Morlino, MS and Basile, A and Zampieri, G and Treu, L and Campanaro, S}, title = {A unified compendium of prokaryotic and viral genomes from over 300 anaerobic digestion microbiomes.}, journal = {Environmental microbiome}, volume = {19}, number = {1}, pages = {1}, pmid = {38167520}, issn = {2524-6372}, support = {ALT 739-2022//EMBO Postdoctoral fellowship/ ; ex D.M.738 dd 08/08/2019 Consorzio Interuniversitario per le Biotecnologie//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; }, abstract = {BACKGROUND: The anaerobic digestion process degrades organic matter into simpler compounds and occurs in strictly anaerobic and microaerophilic environments. The process is carried out by a diverse community of microorganisms where each species has a unique role and it has relevant biotechnological applications since it is used for biogas production. Some aspects of the microbiome, including its interaction with phages, remains still unclear: a better comprehension of the community composition and role of each species is crucial for a cured understanding of the carbon cycle in anaerobic systems and improving biogas production.

RESULTS: The primary objective of this study was to expand our understanding on the anaerobic digestion microbiome by jointly analyzing its prokaryotic and viral components. By integrating 192 additional datasets into a previous metagenomic database, the binning process generated 11,831 metagenome-assembled genomes from 314 metagenome samples published between 2014 and 2022, belonging to 4,568 non-redundant species based on ANI calculation and quality verification. CRISPR analysis on these genomes identified 76 archaeal genomes with active phage interactions. Moreover, single-nucleotide variants further pointed to archaea as the most critical members of the community. Among the MAGs, two methanogenic archaea, Methanothrix sp. 43zhSC_152 and Methanoculleus sp. 52maCN_3230, had the highest number of SNVs, with the latter having almost double the density of most other MAGs.

CONCLUSIONS: This study offers a more comprehensive understanding of microbial community structures that thrive at different temperatures. The findings revealed that the fraction of archaeal species characterized at the genome level and reported in public databases is higher than that of bacteria, although still quite limited. The identification of shared spacers between phages and microbes implies a history of phage-bacterial interactions, and specifically lysogenic infections. A significant number of SNVs were identified, primarily comprising synonymous and nonsynonymous variants. Together, the findings indicate that methanogenic archaea are subject to intense selective pressure and suggest that genomic variants play a critical role in the anaerobic digestion process. Overall, this study provides a more balanced and diverse representation of the anaerobic digestion microbiota in terms of geographic location, temperature range and feedstock utilization.}, } @article {pmid38167330, year = {2024}, author = {Li, M and Liang, H and Yang, H and Ding, Q and Xia, R and Chen, J and Zhou, W and Yang, Y and Zhang, Z and Yao, Y and Ran, C and Zhou, Z}, title = {Deciphering the gut microbiome of grass carp through multi-omics approach.}, journal = {Microbiome}, volume = {12}, number = {1}, pages = {2}, pmid = {38167330}, issn = {2049-2618}, support = {31925038//National Natural Science Foundation of China/ ; 31925038//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Carps ; Multiomics ; *Microbiota ; Proteobacteria/genetics ; Fusobacteria/genetics ; Bacteroidetes/genetics ; Firmicutes/genetics ; Fusobacterium/genetics ; RNA, Ribosomal, 16S/genetics ; Mammals/genetics ; }, abstract = {BACKGROUND: Aquaculture plays an important role in global protein supplies and food security. The ban on antibiotics as feed additive proposes urgent need to develop alternatives. Gut microbiota plays important roles in the metabolism and immunity of fish and has the potential to give rise to novel solutions for challenges confronted by fish culture. However, our understanding of fish gut microbiome is still lacking.

RESULTS: We identified 575,856 non-redundant genes by metagenomic sequencing of the intestinal content samples of grass carp. Taxonomic and functional annotation of the gene catalogue revealed specificity of the gut microbiome of grass carp compared with mammals. Co-occurrence analysis indicated exclusive relations between the genera belonging to Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes, suggesting two independent ecological groups of the microbiota. The association pattern of Proteobacteria with the gene expression modules of fish gut and the liver was consistently opposite to that of Fusobacteria, Firmicutes, and Bacteroidetes, implying differential functionality of Proteobacteria and Fusobacteria/Firmicutes/Bacteroidetes. Therefore, the two ecological groups were considered as two functional groups, i.e., Functional Group 1: Proteobacteria and Functional Group 2: Fusobacteria/Firmicutes/Bacteroidetes. Further analysis revealed that the two functional groups differ in genetic capacity for carbohydrate utilization, virulence factors, and antibiotic resistance. Finally, we proposed that the ratio of "Functional Group 2/Functional Group 1" can be used as a biomarker that efficiently reflects the structural and functional characteristics of the microbiota of grass carp.

CONCLUSIONS: The gene catalogue is an important resource for investigating the gut microbiome of grass carp. Multi-omics analysis provides insights into functional implications of the main phyla that comprise the fish microbiota and shed lights on targets for microbiota regulation. Video Abstract.}, } @article {pmid38166809, year = {2024}, author = {Baomo, L and Guofen, Z and Jie, D and Liu, X and Shuru, C and Jing, L}, title = {Disseminated cryptococcosis in a patient with idiopathic CD4 + T lymphocytopenia presenting as prostate and adrenal nodules: diagnosis from pathology and mNGS, a case report.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {26}, pmid = {38166809}, issn = {1471-2334}, support = {2021A1515110133//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 82170612//National Natural Science Foundation of China/ ; 2023B01J1007//Guangzhou Municipal Science and Technology Program key projects/ ; Z-2018-35-2003//China International Medical Exchange Foundation for Young and middle-aged medical Research Foundation/ ; }, mesh = {Male ; Humans ; Middle Aged ; Prostate ; *Cryptococcosis/complications/diagnosis ; *T-Lymphocytopenia, Idiopathic CD4-Positive/complications/diagnosis ; *Cryptococcus neoformans ; *Meningoencephalitis ; }, abstract = {Disseminated Cryptococcosis infection typically occurs in immunocompromised patients, often manifested as pneumonia or meningoencephalitis. Cases with involvement of either prostate or adrenal glands are less frequent. We describe a case of an immunocompromised 62-year-old man with new-found Idiopathic CD4 + T lymphocytopenia who presented with urinary irritation symptoms followed by headache. The patient was finally diagnosed as disseminated cryptococcosis of prostate, adrenal gland involvement with the help of combining histopathology of formalin-fixed, paraffin-embedded tissue with metagenomic next-generation sequencing technique to identify C neoformans sensu stricto in prostate, adrenal gland tissues. Clinicians should be aware of atypical presentations of cryptococcal disease. In this case of cryptococcosis in immunocompromised patients, we find that cryptococcosis can affect varied organs simultaneously and should be considered in the differential of infectious diseases. And mNGS technology helps to confirm the diagnosis.}, } @article {pmid38166638, year = {2024}, author = {Cui, M and Sun, W and Xue, Y and Yang, J and Xu, T}, title = {Hepatitis E virus and Klebsiella pneumoniae co-infection detected by metagenomics next-generation sequencing in a patient with central nervous system and bloodstream Infection: a case report.}, journal = {BMC infectious diseases}, volume = {24}, number = {1}, pages = {33}, pmid = {38166638}, issn = {1471-2334}, mesh = {Male ; Humans ; Aged ; Klebsiella pneumoniae/genetics ; *Hepatitis E virus/genetics ; *Coinfection/diagnosis ; Central Nervous System ; *Sepsis ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Hepatitis E virus (HEV) is the most common cause of acute viral hepatitis worldwide with major prevalence in the developing countries and can cause extrahepatic disease including the nervous system. Central nervous system infections caused by HEV are rare and caused by HEV together with other bacteria are even rarer.

CASE PRESENTATION: A 68-year-old man was admitted to the hospital due to a headache lasting for 6 days and a fever for 3 days. Lab tests showed significantly raised indicators of inflammation, cloudy cerebrospinal fluid, and liver dysfunction. Hepatitis E virus and Klebsiella pneumoniae were identified in the blood and cerebrospinal fluid using metagenomic next-generation sequencing. The patient received meropenem injection to treat K. pneumoniae infection, isoglycoside magnesium oxalate injection and polyene phosphatidylcholine injection for liver protection. After ten days of treatment, the patient improved and was discharged from the hospital.

CONCLUSION: Metagenomic next-generation sequencing, which can detect various types of microorganisms, is powerful for identifying complicated infections.}, } @article {pmid38166547, year = {2024}, author = {Zhang, Y and Hu, H and Xu, Y and Chen, Y and Liu, B and Chen, J and Nie, W and Zhong, S and Ma, J and Liu, C}, title = {Venous-arterial extracorporeal membrane oxygenation for psittacosis pneumonia complicated with cardiogenic shock: case report and literature review.}, journal = {BMC cardiovascular disorders}, volume = {24}, number = {1}, pages = {6}, pmid = {38166547}, issn = {1471-2261}, mesh = {Male ; Humans ; Aged ; Shock, Cardiogenic/diagnosis/etiology/therapy ; *Extracorporeal Membrane Oxygenation/adverse effects ; *Psittacosis/complications ; *Heart Failure/complications ; *Shock ; *Cardiomyopathies/complications ; *Pneumonia/complications/diagnosis/therapy ; *Cardiomyopathy, Dilated/complications ; }, abstract = {INTRODUCTION: Dilated cardiomyopathy (DCM) is characterized by the enlargement of the left ventricle or biventricular, accompanied by myocardial systolic dysfunction. Chlamydia psittacosis (CP) is a zoonotic pathogen, which can cause severe pneumonia, respiratory failure, and acute organ dysfunction. The deterioration of DCM caused by CP infection is extremely rare, and few cases of successful management were reported.

CASE PRESENTATION: We reported a 67-year-old male patient with DCM and chronic heart failure. Who was admitted to ICU with severe pneumonia, acute hypoxemic respiratory failure, acute decompensated heart failure, arrhythmia, and cardiogenic shock. Mechanical ventilation (MV) and venous-arterial extracorporeal membrane oxygenation (VA-ECMO) were established for respiratory and circulatory support. Broncho alveolar lavage fluid(BALF)was collected for culture and metagenomics next-generation sequencing (mNGS) test. Repeated mNGS tests indicated the high possibility of CP pneumonia, thereafter, moxifloxacin and doxycycline were prescribed. After targeted antibiotics and organ support treatment, pneumonia, respiratory and circulatory failure were gradually resolved, patient was successfully weaned from MV and VA-ECMO. Finally, the patient was recovered and discharged alive.

CONCLUSIONS: Severe respiratory and circulatory failure caused by CP infection in DCM patients is a rare life-threatening clinical condition. Early accurate diagnosis, targeted antibiotic therapy, coupled with extracorporeal life support posed positive impact on the patient's disease course and outcome.}, } @article {pmid38164400, year = {2023}, author = {Wang, S and Chen, X and Li, W and Gong, W and Wang, Z and Cao, W}, title = {Grazing exclusion alters soil methane flux and methanotrophic and methanogenic communities in alpine meadows on the Qinghai-Tibet Plateau.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1293720}, pmid = {38164400}, issn = {1664-302X}, abstract = {Grazing exclusion (GE) is an effective measure for restoring degraded grassland ecosystems. However, the effect of GE on methane (CH4) uptake and production remains unclear in dominant bacterial taxa, main metabolic pathways, and drivers of these pathways. This study aimed to determine CH4 flux in alpine meadow soil using the chamber method. The in situ composition of soil aerobic CH4-oxidizing bacteria (MOB) and CH4-producing archaea (MPA) as well as the relative abundance of their functional genes were analyzed in grazed and nongrazed (6 years) alpine meadows using metagenomic methods. The results revealed that CH4 fluxes in grazed and nongrazed plots were -34.10 and -22.82 μg‧m[-2]‧h[-1], respectively. Overall, 23 and 10 species of Types I and II MOB were identified, respectively. Type II MOB comprised the dominant bacteria involved in CH4 uptake, with Methylocystis constituting the dominant taxa. With regard to MPA, 12 species were identified in grazed meadows and 3 in nongrazed meadows, with Methanobrevibacter constituting the dominant taxa. GE decreased the diversity of MPA but increased the relative abundance of dominated species Methanobrevibacter millerae from 1.47 to 4.69%. The proportions of type I MOB, type II MOB, and MPA that were considerably affected by vegetation and soil factors were 68.42, 21.05, and 10.53%, respectively. Furthermore, the structural equation models revealed that soil factors (available phosphorus, bulk density, and moisture) significantly affected CH4 flux more than vegetation factors (grass species number, grass aboveground biomass, grass root biomass, and litter biomass). CH4 flux was mainly regulated by serine and acetate pathways. The serine pathway was driven by soil factors (0.84, p < 0.001), whereas the acetate pathway was mainly driven by vegetation (-0.39, p < 0.05) and soil factors (0.25, p < 0.05). In conclusion, our findings revealed that alpine meadow soil is a CH4 sink. However, GE reduces the CH4 sink potential by altering vegetation structure and soil properties, especially soil physical properties.}, } @article {pmid38165520, year = {2024}, author = {Kipgen, L and Singha, NA and Lyngdoh, WJ and Nongdhar, J and Singh, AK}, title = {Degradation and metagenomic analysis of 4-chlorophenol utilizing multiple metal tolerant bacterial consortium.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {2}, pages = {56}, pmid = {38165520}, issn = {1573-0972}, mesh = {Humans ; *Metagenome ; Metals ; *Chlorophenols ; Carbon ; }, abstract = {Chlorophenols are persistent environmental pollutants used in synthesizing dyes, drugs, pesticides, and other industrial products. The chlorophenols released from these processes seriously threaten the environment and human health. The present study describes 4-chlorophenol (4-CP) degradation activity and metagenome structure of a bacterial consortium enriched in a 4-CP-containing medium. The consortium utilized 4-CP as a single carbon source at a wide pH range, temperature, and in the presence of heavy metals. The immobilized consortium retained its degradation capacity for an extended period. The 4-aminoantipyrine colorimetric analysis revealed complete mineralization of 4-CP up to 200 mg/L concentration and followed the zero-order kinetics. The addition of glycerol and yeast extract enhanced the degradation efficiency. The consortium showed both ortho- and meta-cleavage activity of catechol dioxygenase. Whole genome sequence (WGS) analysis revealed the microbial compositions and functional genes related to xenobiotic degradation pathways. The identified genes were mapped on the KEGG database to construct the 4-CP degradation pathway. The results exhibited the high potential of the consortium for bioremediation of 4-CP contaminated sites. To our knowledge, this is the first report on WGS analysis of a 4-CP degrading bacterial consortium.}, } @article {pmid38165420, year = {2024}, author = {Erhardt, R and Steels, E and Harnett, JE and Taing, MW and Steadman, KJ}, title = {Effects of a prebiotic formulation on the composition of the faecal microbiota of people with functional constipation.}, journal = {European journal of nutrition}, volume = {}, number = {}, pages = {}, pmid = {38165420}, issn = {1436-6215}, abstract = {PURPOSE: Prebiotics are defined as substances which selectively promote beneficial gut microbes leading to a health benefit for the host. Limited trials have been carried out investigating their effect on the microbiota composition of individuals afflicted by functional constipation with equivocal outcomes. In a 21-day randomised, controlled clinical trial involving 61 adults with functional constipation, a prebiotic formulation with partially hydrolysed guar gum and acacia gum as its main ingredients, significantly increased complete spontaneous bowel motions in the treatment group. This follow-up exploratory analysis investigated whether the prebiotic was associated with changes to the composition, richness, and diversity of the faecal microbiota.

METHODS: Participants provided a faecal specimen at baseline and on day 21 of the intervention period. Whole genome metagenomic shotgun sequencing comprehensively assessed taxonomic and functional composition of the microbiota.

RESULTS: Linear mixed effects regression models adjusted for potential confounders showed a significant reduction in species richness of 28.15 species (95% CI - 49.86, - 6.43) and Shannon diversity of 0.29 units (95% CI - 0.56, - 0.02) over the trial period in the prebiotic group. These changes were not observed in the control group, and functional composition was unchanged in both groups.

CONCLUSION: In adults with functional constipation, the intake of a prebiotic formulation was associated with a decline of species richness and Shannon diversity. Further research regarding the associations between prebiotics and the composition and function of the gut microbiota is warranted.}, } @article {pmid38163713, year = {2024}, author = {Huang, Y and Li, D and Mu, Y and Zhu, Z and Wu, Y and Qi, Q and Mu, Y and Su, W}, title = {Exploring the heterogeneity of community and function and correspondence of "species-enzymes" among three types of Daqu with different fermentation peak-temperature via high-throughput sequencing and metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {176}, number = {}, pages = {113805}, doi = {10.1016/j.foodres.2023.113805}, pmid = {38163713}, issn = {1873-7145}, mesh = {Fermentation ; *Alcoholic Beverages/microbiology ; Temperature ; *Bacteria/genetics/metabolism ; High-Throughput Nucleotide Sequencing ; }, abstract = {The enzyme activity of Daqu is an important prerequisite for defining it as a Baijiu starter. However, little is known about the functional species related to enzymes in different types of Daqu at the metagenomic level. Therefore, we analyzed the differences in enzymatic properties, microbial composition and metabolic function of three types of Daqu, namely high-, medium- and low-temperature Daqus (HTD, MTD and LTD), by combining chemical feature and multi-dimensional sequencing. The results showed that both liquefaction, saccharification, fermentation and esterification powers were remarkably weaker in HTD compared to MTD and LTD. Totally, 30 bacterial and 5 fungal phyla were identified and significant differences in community structures were also observed among samples, with Brevibacterium/Microascus, Pseudomonas, and Lactobacillus/Saccharomycopsis identified as biomarkers for HTD, MTD and LTD, respectively. Additionally, the importance of deterministic assembly in bacterial communities was proportional to the fermentation peak-temperature, while stochastic assembly dominated in fungal ones. Metagenomics analysis indicated eukaryota (>80 %, mainly Ascomycota) predominated in HTD and MTD while bacteria (54.3 %, mainly Actinobacteriota) were more abundant in LTD. However, the functional profiles and pathways of MTD and LTD were more similar, and the synthesis and metabolism of carbohydrates and amino acids were the crucial biological functions of all samples. Finally, the relationship between species and enzymes in different samples was constructed and the functional species in LTD and MTD were more diverse than HTD, which elucidated the functional species associated with enzyme activity in each type of Daqu. These results will greatly enrich our understanding of the core functional species in three typical Daqu, which provide available information for rational regulation of Daqu quality and the Baijiu fermentation.}, } @article {pmid38163547, year = {2023}, author = {Tiwari, A and Krolicka, A and Tran, TT and Räisänen, K and Ásmundsdóttir, ÁM and Wikmark, OG and Lood, R and Pitkänen, T}, title = {Antibiotic resistance monitoring in wastewater in the Nordic countries: A systematic review.}, journal = {Environmental research}, volume = {246}, number = {}, pages = {118052}, doi = {10.1016/j.envres.2023.118052}, pmid = {38163547}, issn = {1096-0953}, abstract = {The Nordic countries (Denmark, Finland, Iceland, Norway, and Sweden) have effectively kept lower antibiotic-resistant bacterial (ARB) pathogen rates than many other countries. However, in recent years, these five countries have encountered a rise in ARB cases and challenges in treating infections due to the growing prevalence of ARB pathogens. Wastewater-based surveillance (WBS) is a valuable supplement to clinical methods for ARB surveillance, but there is a lack of comprehensive understanding of WBS application for ARB in the Nordic countries. This review aims to compile the latest state-of-the-art developments in WBS for ARB monitoring in the Nordic countries and compare them with clinical surveillance practices. After reviewing 1480 papers from the primary search, 54 were found relevant, and 15 additional WBS-related papers were included. Among 69 studies analyzed, 42 dedicated clinical epidemiology, while 27 focused on wastewater monitoring. The PRISMA review of the literature revealed that Nordic countries focus on four major WBS objectives of ARB: assessing ARB in the human population, identifying ARB evading wastewater treatment, quantifying removal rates, and evaluating potential ARB evolution during the treatment process. In both clinical and wastewater contexts, the most studied targets were pathogens producing carbapenemase and extended-spectrum beta-lactamase (ESBL), primarily Escherichia coli and Klebsiella spp. However, vancomycin-resistant Enterococcus (VRE) and methicillin-resistant Staphylococcus aureus (MRSA) have received more attention in clinical epidemiology than in wastewater studies, probably due to their lower detection rates in wastewater. Clinical surveillance has mostly used culturing, antibiotic susceptibility testing, and genotyping, but WBS employed PCR-based and metagenomics alongside culture-based techniques. Imported cases resulting from international travel and hospitalization abroad appear to have frequently contributed to the rise in ARB pathogen cases in these countries. The many similarities between the Nordic countries (e.g., knowledge exchange practices, antibiotic usage patterns, and the current ARB landscape) could facilitate collaborative efforts in developing and implementing WBS for ARB in population-level screening.}, } @article {pmid38163545, year = {2023}, author = {Yang, S and Deng, W and Li, G and Jin, L and Huang, Y and He, Y and Wu, D and Li, D and Zhang, A and Liu, C and Li, C and Zhang, H and Xu, H and Penttinen, P and Zhao, K and Zou, L}, title = {Reference gene catalog and metagenome-assembled genomes from the gut microbiome reveal the microbial composition, antibiotic resistome, and adaptability of a lignocellulose diet in the giant panda.}, journal = {Environmental research}, volume = {245}, number = {}, pages = {118090}, doi = {10.1016/j.envres.2023.118090}, pmid = {38163545}, issn = {1096-0953}, abstract = {The giant panda, a strict herbivore that feeds on bamboo, still retains a typical carnivorous digestive system. Reference catalogs of microbial genes and genomes are lacking, largely limiting the antibiotic resistome and functional exploration of the giant panda gut microbiome. Here, we integrated 177 fecal metagenomes of captive and wild giant pandas to construct a giant panda integrated gene catalog (GPIGC) comprised of approximately 4.5 million non-redundant genes and reconstruct 393 metagenome-assembled genomes (MAGs). Taxonomic and functional characterization of genes revealed that the captivity of the giant panda significantly changed the core microbial composition and the distribution of microbial genes. Higher abundance and prevalence of antibiotic resistance genes (ARGs) were detected in the guts of captive giant pandas, and ARG distribution was influenced by geography, for both captive and wild individuals. Escherichia, as the prevalent genus in the guts of captive giant pandas, was the main carrier of ARGs, meaning there is a high risk of ARG transmission by Escherichia. We also found that multiple mcr gene variants, conferring plasmid-mediated mobile colistin resistance, were widespread in the guts of captive and wild giant pandas. There were low proportions of carbohydrate-active enzyme (CAZyme) genes in GPIGC and MAGs compared with several omnivorous and herbivorous mammals. Many members of Clostridium MAGs were significantly enriched in the guts of adult, old and wild giant pandas. The genomes of isolates and MAGs of Clostridiaceae harbored key genes or enzymes in complete pathways for degrading lignocellulose and producing short-chain fatty acids (SCFAs), indicating the potential of these bacteria to utilize the low-nutrient bamboo diet. Overall, our data presented an exhaustive reference gene catalog and MAGs in giant panda gut and provided a comprehensive understanding of the antibiotic resistome and microbial adaptability for a high-lignocellulose diet.}, } @article {pmid38163476, year = {2023}, author = {Hameleers, L and Pijning, T and Gray, BB and Fauré, R and Jurak, E}, title = {Novel β-galactosidase activity and first crystal structure of Glycoside Hydrolase family 154.}, journal = {New biotechnology}, volume = {80}, number = {}, pages = {1-11}, doi = {10.1016/j.nbt.2023.12.011}, pmid = {38163476}, issn = {1876-4347}, abstract = {Polysaccharide Utilization Loci (PULs) are physically linked gene clusters conserved in the Gram-negative phylum of Bacteroidota and are valuable sources for Carbohydrate Active enZyme (CAZyme) discovery. This study focuses on BD-β-Gal, an enzyme encoded in a metagenomic PUL and member of the Glycoside Hydrolase family 154 (GH154). BD-β-Gal showed exo-β-galactosidase activity with regiopreference for hydrolyzing β-d-(1,6) glycosidic linkages. Notably, it exhibited a preference for d-glucopyranosyl (d-Glcp) over d-galactopyranosyl (d-Galp) and d-fructofuranosyl (d-Fruf) at the reducing end of the investigated disaccharides. In addition, we determined the high resolution crystal structure of BD-β-Gal, thus providing the first structural characterization of a GH154 enzyme. Surprisingly, this revealed an (α/α)6 topology, which has not been observed before for β-galactosidases. BD-β-Gal displayed low structural homology with characterized CAZymes, but conservation analysis suggested that the active site was located in a central cavity, with conserved E73, R252, and D253 as putative catalytic residues. Interestingly, BD-β-Gal has a tetrameric structure and a flexible loop from a neighboring protomer may contribute to its reaction specificity. Finally, we showed that the founding member of GH154, BT3677 from Bacteroides thetaiotaomicron, described as β-glucuronidase, displayed exo-β-galactosidase activity like BD-β-Gal but lacked a tetrameric structure.}, } @article {pmid38163076, year = {2023}, author = {Conteville, LC and da Silva, JV and Andrade, BGN and Cardoso, TF and Bruscadin, JJ and de Oliveira, PSN and Mourão, GB and Coutinho, LL and Palhares, JCP and Berndt, A and de Medeiros, SR and Regitano, LCA}, title = {Rumen and fecal microbiomes are related to diet and production traits in Bos indicus beef cattle.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1282851}, pmid = {38163076}, issn = {1664-302X}, abstract = {BACKGROUND: Ruminants harbor a complex microbial community within their gastrointestinal tract, which plays major roles in their health and physiology. Brazil is one of the largest producers of beef in the world and more than 90% of the beef cattle herds are composed of pure and crossbred Nelore (Bos indicus). Despite its importance to the Brazilian economy and human feeding, few studies have characterized the Nelore microbiome. Therefore, using shotgun metagenomics, we investigated the impact of diet on the composition and functionality of the Nelore microbiome, and explored the associations between specific microbial taxa and their functionality with feed efficiency and methane emission.

RESULTS: The ruminal microbiome exhibited significantly higher microbial diversity, distinctive taxonomic profile and variations in microbial functionality compared to the fecal microbiome, highlighting the distinct contributions of the microbiomes of these environments. Animals subjected to different dietary treatments exhibited significant differences in their microbiomes' archaeal diversity and in the abundance of 89 genera, as well as in the functions associated with the metabolism of components of each diet. Moreover, depending on the diet, feed-efficient animals and low methane emitters displayed higher microbial diversity in their fecal microbiome. Multiple genera were associated with an increase or decrease of the phenotypes. Upon analyzing the functions attributed to these taxa, we observed significant differences on the ruminal taxa associated with feed efficient and inefficient cattle. The ruminal taxa that characterized feed efficient cattle stood out for having significantly more functions related to carbohydrate metabolism, such as monosaccharides, di-/oligosaccharides and amino acids. The taxa associated with methane emission had functions associated with methanogenesis and the production of substrates that may influence methane production, such as hydrogen and formate.

CONCLUSION: Our findings highlight the significant role of diet in shaping Nelore microbiomes and how its composition and functionality may affect production traits such as feed efficiency and methane emission. These insights provide valuable support for the implementation of novel feeding and biotechnological strategies.}, } @article {pmid38163074, year = {2023}, author = {Huang, Y and Hu, H and Yue, E and Ying, W and Niu, T and Yan, J and Lu, Q and Ruan, S}, title = {Role of plant metabolites in the formation of bacterial communities in the rhizosphere of Tetrastigma hemsleyanum.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1292896}, pmid = {38163074}, issn = {1664-302X}, abstract = {Tetrastigma hemsleyanum Diels et Gilg, commonly known as Sanyeqing (SYQ), is an important traditional Chinese medicine. The content of bioactive constituents varies in different cultivars of SYQ. In the plant growth related researches, rhizosphere microbiome has gained significant attention. However, the role of bacterial communities in the accumulation of metabolites in plants have not been investigated. Herein, the composition of bacterial communities in the rhizosphere soils and the metabolites profile of different SYQ cultivars' roots were analyzed. It was found that the composition of microbial communities varied in the rhizosphere soils of different SYQ cultivars. The high abundance of Actinomadura, Streptomyces and other bacteria was found to be associated with the metabolites profile of SYQ roots. The findings suggest that the upregulation of rutin and hesperetin may contribute to the high bioactive constituent in SYQ roots. These results provide better understanding of the metabolite accumulation pattern in SYQ, and also provide a solution for enhancing the quality of SYQ by application of suitable microbial consortia.}, } @article {pmid38163067, year = {2023}, author = {Pelevina, A and Gruzdev, E and Berestovskaya, Y and Dorofeev, A and Nikolaev, Y and Kallistova, A and Beletsky, A and Ravin, N and Pimenov, N and Mardanov, A}, title = {New insight into the granule formation in the reactor for enhanced biological phosphorus removal.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1297694}, pmid = {38163067}, issn = {1664-302X}, abstract = {While granulated activated sludge exhibits high productivity, the processes of granule formation are incompletely studied. The processes of granule formation and succession of communities were investigated in a laboratory sequencing batch reactor (SBR) under conditions for enhanced biological phosphorus removal (EBPR) using microbiological and molecular techniques. Active consumption of acetate, primarily by the phosphate-accumulating organisms (PAO), commenced at day 150 of cultivation. This was indicated by the high ratio of molar P-released/acetate uptake (0.73-0.77 P-mol/C-mol), characteristic of PAO. During this period, two types of granule-like aggregates formed spontaneously out of the activated sludge flocs. The aggregates differed in morphology and microbial taxonomic composition. While both aggregate types contained phosphorus-enriched bacterial cells, PAO prevailed in those of morphotype I, and glycogen-accumulating organisms (GAOs) were predominant in the aggregates of morphotype II. After 250 days, the elimination of the morphotype II aggregates from the reactor was observed. The subsequent selection of the community was associated with the development of the morphotype I aggregates, in which the relative abundance of PAO increased significantly, resulting in higher efficiency of phosphorus removal. Metagenomic analysis revealed a predominance of the organisms closely related to Candidatus Accumulibacter IС and IIС and of Ca. Accumulibacter IIB among the PAO. Based on the content of the genes of the key metabolic pathways, the genomes of potential PAO belonging to the genera Amaricoccus, Azonexus, Thauera, Zoogloea, Pinisolibacter, and Siculibacillus were selected. The patterns of physicochemical processes and the microbiome structure associated with granule formation and succession of the microbial communities were revealed.}, } @article {pmid38163063, year = {2023}, author = {Diallo, K and Missa, KF and Tuo, JK and Amoikon, TLS and Bla, BK and Bonfoh, B}, title = {Narrative review of application of metagenomic approaches to study the link between oropharyngeal microbiome and infectious diseases.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1292526}, pmid = {38163063}, issn = {1664-302X}, abstract = {CONTEXT: Viral and bacterial infections are major causes of morbidity and mortality worldwide. The oropharyngeal microbiome could play an important role in preventing invasion of viral and bacterial pathogens by modulating its content and the host's innate immune response. Next Generation Sequencing (NGS) technologies now enable in-depth study of the genomes of microbial communities. The objective of this review is to highlight how metagenomics has contributed to establish links between changes in the oropharyngeal microbiome and emergence of bacterial and viral diseases.

METHOD: Two search engines, PubMed and Google scholar were used with filters to focus searches on peer-reviewed original articles published between January 2010 and September 2022. Different keywords were used and only articles with metagenomic approaches were included.

RESULTS: This review shows that there were few articles studying the link between oropharyngeal microbiome and infectious diseases. Studies on viruses using metagenomic techniques have been growing exponentially in recent years due to the Covid-19 pandemic. This review shows that most studies still focus on the basic identification of microorganisms in different disease states and multiple microorganisms (Alloprevotella, Prevotella, Bacteroides, Haemophilus, Streptococcus, Klebsiella sp., Acinetobacter sp…), have been associated with development of infections such as childhood wheezing, influenza, Covid-19, pneumonia, meningitis, and tuberculosis.

CONCLUSION: The oropharyngeal microbiome, despite its importance, remains poorly studied. A limited number of articles were identified but this number has increased exponentially since 2020 due to research conducted on Covid-19. These studies have shown that metagenomic has contributed to the unbiased identification of bacteria that could be used as biomarkers of various diseases and that further research is now needed to capitalize on those findings for human health benefit.}, } @article {pmid38162520, year = {2023}, author = {Capeding, MRZ and Phee, LCM and Ming, C and Noti, M and Vidal, K and Le Carrou, G and Frézal, A and Moll, JM and Vogt, JK and Myers, PN and Nielsen, BH and Boulangé, CL and Samuel, TM and Berger, B and Cercamondi, CI}, title = {Safety, efficacy, and impact on gut microbial ecology of a Bifidobacterium longum subspecies infantis LMG11588 supplementation in healthy term infants: a randomized, double-blind, controlled trial in the Philippines.}, journal = {Frontiers in nutrition}, volume = {10}, number = {}, pages = {1319873}, pmid = {38162520}, issn = {2296-861X}, abstract = {INTRODUCTION: Bifidobacterium longum subspecies infantis (B. infantis) may play a key role in infant gut development. This trial evaluated safety, tolerability, and efficacy of B. infantis LMG11588 supplementation.

METHODS: This randomized, placebo-controlled, double-blind study conducted in the Philippines included healthy breastfed and/or formula-fed infants (14-21 days old) randomized for 8 weeks to a control group (CG; n = 77), or any of two B. infantis experimental groups (EGs): low (Lo-EG; 1*10[8] CFU/day; n = 75) or high dose (Hi-EG; 1.8*10[10] CFU/day; n = 76). Primary endpoint was weight gain; secondary endpoints included stooling patterns, gastrointestinal symptoms, adverse events, fecal microbiome, biomarkers, pH, and organic acids.

RESULTS: Non-inferiority in weight gain was demonstrated for Hi-EG and Lo-EG vs. CG. Overall, probiotic supplementation promoted mushy-soft stools, fewer regurgitation episodes, and increased fecal acetate production, which was more pronounced in the exclusively breastfed infants (EBF) and positively correlated with B. infantis abundance. In EBF, fecal pro-inflammatory cytokines (IL-1 beta, IL-8) were reduced. Strain-level metagenomic analysis allowed attributing the increased abundance of B. infantis in EGs versus CG, to LMG11588 probiotic colonization. Colonization by autochthonous B. infantis strains was similar between groups.

DISCUSSION: B. infantis LMG11588 supplementation was associated with normal infant growth, was safe and well-tolerated and promoted a Bifidobacterium-rich microbiota driven by B. infantis LMG11588 colonization without disturbing the natural dispersal of autochthonous B. infantis strains. In EBF, supplementation stimulated microbial metabolic activity and beneficially modulated enteric inflammation.}, } @article {pmid38160549, year = {2024}, author = {Wang, Y and Wang, B and Chen, J and Sun, L and Hou, Y and Wang, Y and Wang, J and Gan, J and Barmukh, R and Li, S and Fan, Z and Bao, P and Cao, B and Cai, C and Jing, X and Singh, BK and Varshney, RK and Zhao, H}, title = {Dynamics of rhizosphere microbial structure and function associated with the biennial bearing of moso bamboo.}, journal = {Journal of environmental management}, volume = {351}, number = {}, pages = {119977}, doi = {10.1016/j.jenvman.2023.119977}, pmid = {38160549}, issn = {1095-8630}, mesh = {*Rhizosphere ; RNA, Ribosomal, 16S/genetics ; *Poaceae ; Forests ; Soil/chemistry ; }, abstract = {Moso bamboo (Phyllostachys edulis) is a valuable nontimber forestry product with a biennial cycle, producing abundant bamboo shoots within one year (on-year) and few shoots within the following year (off-year). Moso bamboo plants undergo clonal reproduction, resulting in similar genetic backgrounds. However, the number of moso bamboo shoots produced each year varies. Despite this variation, the impact of soil nutrients and the root microbiome on the biennial bearing of moso bamboo is poorly understood. We collected 139 soil samples and determined 14 major physicochemical properties of the rhizosphere, rhizoplane, and bulk soil in different seasons (i.e., the growing and deciduous seasons) and different years (i.e., on- and off-years). Based on 16S rRNA and metagenomic sequencing, major variations were found in the rhizospheric microbial composition during different seasons and years in the moso bamboo forest. Environmental driver analysis revealed that essential nutrients (i.e., SOC, TOC, TN, P, and NH4[+]) were the main drivers of the soil microbial community composition and were correlated with the on- and off-year cycles. Moreover, 19 MAGs were identified as important biomarkers that could distinguish on- and off-years. We found that both season and year influenced both the microbial community structure and functional pathways through the biosynthesis of nutrients that potentially interact with the moso bamboo growth rhythm, especially the on-year root-associated microbiome, which had a greater abundance of specific nutrients such as gibberellins and vitamin B6. This work provides a dynamic perspective of the differential responses of various on- and off-year microbial communities and enhances our understanding of bamboo soil microbiome biodiversity and stability.}, } @article {pmid38160303, year = {2024}, author = {Sapoval, N and Tanevski, M and Treangen, TJ}, title = {KombOver: Efficient k-core and K-truss based characterization of perturbations within the human gut microbiome.}, journal = {Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing}, volume = {29}, number = {}, pages = {506-520}, pmid = {38160303}, issn = {2335-6936}, support = {P01 AI152999/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; DNA Copy Number Variations ; Computational Biology ; *Microbiota/genetics ; Metagenome ; Metagenomics/methods ; }, abstract = {The microbes present in the human gastrointestinal tract are regularly linked to human health and disease outcomes. Thanks to technological and methodological advances in recent years, metagenomic sequencing data, and computational methods designed to analyze metagenomic data, have contributed to improved understanding of the link between the human gut microbiome and disease. However, while numerous methods have been recently developed to extract quantitative and qualitative results from host-associated microbiome data, improved computational tools are still needed to track microbiome dynamics with short-read sequencing data. Previously we have proposed KOMB as a de novo tool for identifying copy number variations in metagenomes for characterizing microbial genome dynamics in response to perturbations. In this work, we present KombOver (KO), which includes four key contributions with respect to our previous work: (i) it scales to large microbiome study cohorts, (ii) it includes both k-core and K-truss based analysis, (iii) we provide the foundation of a theoretical understanding of the relation between various graph-based metagenome representations, and (iv) we provide an improved user experience with easier-to-run code and more descriptive outputs/results. To highlight the aforementioned benefits, we applied KO to nearly 1000 human microbiome samples, requiring less than 10 minutes and 10 GB RAM per sample to process these data. Furthermore, we highlight how graph-based approaches such as k-core and K-truss can be informative for pinpointing microbial community dynamics within a myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) cohort. KO is open source and available for download/use at: https://github.com/treangenlab/komb.}, } @article {pmid38159771, year = {2023}, author = {Xiao, R and Hu, Y and Wang, Y and Li, J and Guo, C and Bai, J and Zhang, L and Zhang, K and Jorquera, MA and Acuña, JJ and Pan, W}, title = {Pathogen profile of Baiyangdian Lake sediments using metagenomic analysis and their correlation with environmental factors.}, journal = {The Science of the total environment}, volume = {913}, number = {}, pages = {169628}, doi = {10.1016/j.scitotenv.2023.169628}, pmid = {38159771}, issn = {1879-1026}, abstract = {Increasing concerns about public health and safety after covid-19 have raised pathogen studies, especially in aquatic environments. However, the extent to how different location and human activities affect geographic occurrence and distribution of pathogens in response to agricultural pollution, boat tourism disturbances and municipal wastewater inflow in a degraded lake remains unclear. Since the surrounding residents depend on the lake for their livelihood, understanding the pathogens reserved in lake sediment and the regulation possibility by environmental factors are challenges with far-reaching significance. Results showed that 187 pathogens were concurrently shared by the nine sediment samples, with Salmonella enterica and Pseudomonas aeruginosa being the most abundant. The similar composition of the pathogens suggests that lake sediment may act as reservoirs of generalist pathogens which may pose infection risk to a wide range of host species. Of the four virulence factors (VFs) types analyzed, offensive VFs were dominant (>46 % on average) in all samples, with dominant subtypes including adherence, secretion systems and toxins. Notably, the lake sediments under the impact of agricultural use (g1) showed significantly higher diversity and abundance of pathogen species and VFs than those under the impact of boat tourism (g2) and/or municipal wastewater inflow with reed marshes filtration (g3). From the co-occurrence networks, pathogens and pesticides, aggregate fractions, EC, pH, phosphatase have strong correlations. Strong positive correlations between pathogens and diazinon in g1 and ppDDT in g2 and g3 suggest higher pesticide-pathogen co-exposure risk. These findings highlight the need to explore pathogen - environmental factor interaction mechanisms in the human-impacted water environments where the control of pathogen invasion by environmental factors may accessible.}, } @article {pmid38159125, year = {2023}, author = {Hao, Z and Wang, Q and Wang, J and Deng, Y and Yan, Z and Tian, L and Jiang, H}, title = {Water Level Fluctuations Modulate the Microbiomes Involved in Biogeochemical Cycling in Floodplains.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {24}, pmid = {38159125}, issn = {1432-184X}, support = {51839011//National Natural Science Foundation of China/ ; }, mesh = {*Water ; Nitrates ; *Microbiota/genetics ; Metagenome ; Nitrogen/metabolism ; }, abstract = {Drastic changes in hydrological conditions within floodplain ecosystems create distinct microbial habitats. However, there remains a lack of exploration regarding the variations in microbial function potentials across the flooding and drought seasons. In this study, metagenomics and environmental analyses were employed in floodplains that experience hydrological variations across four seasons. Analysis of functional gene composition, encompassing nitrogen, carbon, and sulfur metabolisms, revealed apparent differences between the flooding and drought seasons. The primary environmental drivers identified were water level, overlying water depth, submergence time, and temperature. Specific modules, e.g., the hydrolysis of β-1,4-glucosidic bond, denitrification, and dissimilatory/assimilatory nitrate reduction to ammonium, exhibited higher relative abundance in summer compared to winter. It is suggested that cellulose degradation was potentially coupled with nitrate reduction during the flooding season. Phylogenomic analysis of metagenome-assembled genomes (MAGs) unveiled that the Desulfobacterota lineage possessed abundant nitrogen metabolism genes supported by pathway reconstruction. Variation of relative abundance implied its environmental adaptability to both the wet and dry seasons. Furthermore, a novel order was found within Methylomirabilota, containing nitrogen reduction genes in the MAG. Overall, this study highlights the crucial role of hydrological factors in modulating microbial functional diversity and generating genomes with abundant nitrogen metabolism potentials.}, } @article {pmid38159115, year = {2024}, author = {Li, H and Chen, S and Wang, M and Shi, S and Zhao, W and Xiong, G and Zhou, J and Qu, J}, title = {Phosphate solubilization and plant growth properties are promoted by a lactic acid bacterium in calcareous soil.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {1-14}, pmid = {38159115}, issn = {1432-0614}, mesh = {*Phosphates/metabolism ; Soil/chemistry ; *Lactobacillales/metabolism ; Phosphorus/metabolism ; Seedlings ; Lactic Acid ; Soil Microbiology ; }, abstract = {On the basis of good phosphate solubilization ability of a lactic acid bacteria (LAB) strain Limosilactobacillus sp. LF-17, bacterial agent was prepared and applied to calcareous soil to solubilize phosphate and promote the growth of maize seedlings in this study. A pot experiment showed that the plant growth indicators, phosphorus content, and related enzyme activity of the maize rhizospheric soils in the LF treatment (treated with LAB) were the highest compared with those of the JP treatment (treated with phosphate solubilizing bacteria, PSB) and the blank control (CK). The types of organic acids in maize rhizospheric soil were determined through LC-MS, and 12 acids were detected in all the treatments. The abundant microbes belonged to the genera of Lysobacter, Massilia, Methylbacillus, Brevundimonas, and Limosilactobacillus, and they were beneficial to dissolving phosphate or secreting growth-promoting phytohormones, which were obviously higher in the LF and JP treatments than in CK as analyzed by high-throughput metagenomic sequencing methods. In addition, the abundance values of several enzymes, Kyoto Encyclopedia of Genes and Genomes (KEGG) orthology, and Carbohydrate-Active Enzymes (CAZys), which were related to substrate assimilation and metabolism, were the highest in the LF treatment. Therefore, aside from phosphate-solubilizing microorganisms, LAB can be used as environmentally friendly crop growth promoters in agriculture and provide another viable option for microbial fertilizers. KEY POINTS: • The inoculation of LAB strain effectively promoted the growth and chlorophyll synthesis of maize seedlings. • The inoculation of LAB strain significantly increased the TP content of maize seedlings and the AP concentration of the rhizosphere soil. • The inoculation of LAB strain increased the abundances of the dominant beneficial functional microbes in the rhizosphere soil.}, } @article {pmid38159114, year = {2024}, author = {Liu, F and Yang, J and Zhang, Y and Yang, S and Zhang, Y and Chen, Y and Shao, Y and Gao, D and Yuan, Z and Zhang, Y}, title = {Mulches assist degraded soil recovery via stimulating biogeochemical cycling: metagenomic analysis.}, journal = {Applied microbiology and biotechnology}, volume = {108}, number = {1}, pages = {1-13}, pmid = {38159114}, issn = {1432-0614}, mesh = {*Soil/chemistry ; *Carbon ; Soil Microbiology ; Nitrogen ; Phosphorus ; }, abstract = {Soil degradation of urban greening has caused soil fertility loss and soil organic carbon depletion. Organic mulches are made from natural origin materials, and represent a cost-effective and environment-friendly remediation method for urban greening. To reveal the effects of organic mulch on soil physicochemical characteristics and fertility, we selected a site that was covered with organic mulch for 6 years and a nearby lawn-covered site. The results showed that soil organic matter, total nitrogen, and available phosphorus levels were improved, especially at a depth of 0-20 cm. The activities of cellulase, invertase, and dehydrogenase in soil covered with organic mulch were 17.46%, 78.98%, and 283.19% higher than those under lawn, respectively. The marker genes of fermentation, aerobic respiration, methanogenesis, and methane oxidation were also enriched in the soil under organic mulch. Nitrogen cycling was generally repressed by the organic mulch, but the assimilatory nitrate and nitrite reduction processes were enhanced. The activity of alkaline phosphatase was 12.63% higher in the mulch-covered soil, and functional genes involved in phosphorus cycling were also enriched. This study presents a comprehensive investigation of the influence of organic mulch on soil microbes and provides a deeper insight into the recovery strategy for soil degradation following urban greening. KEY POINTS: • Long-term cover with organic mulches assists soil recovery from degradation • Soil physical and chemical properties were changed by organic mulches • Organic mulches enhanced genes involved in microbially mediated C and P cycling • Soil organic matter was derived from decomposition of organic mulch and carbon fixation • N cycling was repressed by mulches, except for assimilatory NO2[-] and NO3[-] reductions.}, } @article {pmid38158480, year = {2023}, author = {Biswas, S and Foysal, MJ and Mannan, A and Sharifuzzaman, SM and Tanzina, AY and Tanni, AA and Sharmen, F and Hossain, MM and Chowdhury, MSN and Tay, AC and Islam, SMR}, title = {Microbiome pattern and diversity of an anadromous fish, hilsa shad (Tenualosa ilisha).}, journal = {Molecular biology reports}, volume = {51}, number = {1}, pages = {38}, pmid = {38158480}, issn = {1573-4978}, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Fishes/genetics ; Fresh Water ; Bacteria/genetics ; *Microbiota/genetics ; Water ; }, abstract = {BACKGROUND: The host-microbe interactions are complex, dynamic and context-dependent. In this regard, migratory fish species like hilsa shad (Tenualosa ilisha), which migrates from seawater to freshwater for spawning, provides a unique system for investigating the microbiome under an additional change in fish's habitat. This work was undertaken to detect taxonomic variation of microbiome and their function in the migration of hilsa.

METHODS AND RESULTS: The study employed 16S rRNA amplicon-based metagenomic analysis to scrutinize bacterial diversity in hilsa gut, skin mucus and water. Thus, a total of 284 operational taxonomic units (OTUs), 9 phyla, 35 orders and 121 genera were identified in all samples. More than 60% of the identified bacteria were Proteobacteria with modest abundance (> 5%) of Firmicutes, Bacteroidetes and Actinobacteria. Leucobacter in gut and Serratia in skin mucus were the core bacterial genera, while Acinetobacter, Pseudomonas and Psychrobacter exhibited differential compositions in gut, skin mucus and water.

CONCLUSIONS: Representative fresh-, brackish- and seawater samples of hilsa habitats were primarily composed of Vibrio, Serratia and Psychrobacter, and their diversity in seawater was significantly higher (P < 0.05) than freshwater. Overall, salinity and water microbiota had an influence on the microbial composition of hilsa shad, contributing to host metabolism and adaptation processes. This pioneer exploration of hilsa gut and skin mucus bacteria across habitats will advance our insights into microbiome assembly in migratory fish populations.}, } @article {pmid38158469, year = {2023}, author = {Uwaremwe, C and Bao, W and Daoura, BG and Mishra, S and Zhang, X and Shen, L and Xia, S and Yang, X}, title = {Shift in the rhizosphere soil fungal community associated with root rot infection of Plukenetia volubilis Linneo caused by Fusarium and Rhizopus species.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {38158469}, issn = {1618-1905}, abstract = {BACKGROUND: Plukenetia volubilis Linneo is an oleaginous plant belonging to the family Euphorbiaceae. Due to its seeds containing a high content of edible oil and rich in vitamins, P. volubilis is cultivated as an economical plant worldwide. However, the cultivation and growth of P. volubilis is challenged by phytopathogen invasion leading to production loss.

METHODS: In the current study, we tested the pathogenicity of fungal pathogens isolated from root rot infected P. volubilis plant tissues by inoculating them into healthy P. volubilis seedlings. Metagenomic sequencing was used to assess the shift in the fungal community of P. volubilis rhizosphere soil after root rot infection.

RESULTS: Four Fusarium isolates and two Rhizopus isolates were found to be root rot causative agents of P. volubilis as they induced typical root rot symptoms in healthy seedlings. The metagenomic sequencing data showed that root rot infection altered the rhizosphere fungal community. In root rot infected soil, the richness and diversity indices increased or decreased depending on pathogens. The four most abundant phyla across all samples were Ascomycota, Glomeromycota, Basidiomycota, and Mortierellomycota. In infected soil, the relative abundance of each phylum increased or decreased depending on the pathogen and functional taxonomic classification.

CONCLUSIONS: Based on our results, we concluded that Fusarium and Rhizopus species cause root rot infection of P. volubilis. In root rot infected P. volubilis, the shift in the rhizosphere fungal community was pathogen-dependent. These findings may serve as a key point for a future study on the biocontrol of root rot of P. volubilis.}, } @article {pmid38158101, year = {2024}, author = {Yu, L and Hu, X and Xu, R and Zhao, Y and Xiong, L and Ai, J and Wang, X and Chen, X and Ba, Y and Xing, Z and Guo, C and Mi, S and Wu, X}, title = {Piperine promotes PI3K/AKT/mTOR-mediated gut-brain autophagy to degrade α-Synuclein in Parkinson's disease rats.}, journal = {Journal of ethnopharmacology}, volume = {322}, number = {}, pages = {117628}, doi = {10.1016/j.jep.2023.117628}, pmid = {38158101}, issn = {1872-7573}, mesh = {Rats ; Humans ; Animals ; *Parkinson Disease/drug therapy ; alpha-Synuclein/metabolism ; Proto-Oncogene Proteins c-akt/metabolism ; Phosphatidylinositol 3-Kinases/metabolism ; Oxidopamine ; Tandem Mass Spectrometry ; *Neuroblastoma ; *Alkaloids/pharmacology/therapeutic use ; TOR Serine-Threonine Kinases/metabolism ; Brain/metabolism ; Autophagy ; *Piperidines ; *Benzodioxoles ; *Polyunsaturated Alkamides ; }, abstract = {Piper longum L., a medicinal and food homologous herb, has a traditional history of use in treating gastrointestinal and neurological disorders. Piperine (PIP) the main alkaloid of P. longum, exists neuroprotective effects on various animal models of Parkinson's disease (PD). Nevertheless, the underlying mechanism, particularly the role of PIP in promoting gut-brain autophagy for α-Synuclein (α-Syn) degradation in PD, remains incompletely understood.

AIM OF THE STUDY: To explore the role of PIP in regulating the gut-brain autophagy signaling pathway to reduce α-Syn levels in both the colon and substantia nigra (SN) of PD model rats.

MATERIALS AND METHODS: Behavioral experiments were conducted to assess the impact of PIP on 6-hydroxydopamine (6-OHDA)-induced PD rats. The intestinal microbiome composition and intestinal metabolites were analyzed by metagenomics and GC-MS/MS. The auto-phagosomes were visualized by transmission electron microscopy. Immunohistochemistry, immunofluorescence, and western blotting were performed to assess the levels of tyrosine hydroxylase (TH), α-Syn, LC3II/LC3I, p62, and the PI3K/AKT/mTOR pathway in both the SN and colon of the rats. The pathway-related inhibitor and agonist were used to verify the autophagy mechanism in the SH-SY5Y cells overexpressing A53T mutant α-Syn (A53T-α-Syn).

RESULTS: PIP improved autonomic movement and gastrointestinal dysfunctions, reduced α-Syn aggregation and attenuated the loss of dopaminergic neurons in 6-OHDA-induced PD rats. After oral administration of PIP, the radio of LC3II/LC3I increased and the expression of p62 was degraded, as well as the phosphorylation levels of PI3K, AKT and mTOR decreased in the SN and colon of rats. The effect of PIP on reducing A53T-α-Syn through the activation of the PI3K/AKT/mTOR-mediated autophagy pathway was further confirmed in A53T-α-Syn transgenic SH-SY5Y cells. This effect could be inhibited by the autophagy inhibitor bafilomycin A1 and the PI3K agonist 740 Y-P.

CONCLUSIONS: Our findings suggested that PIP could protect neurons by activating autophagy to degrade α-Syn in the SN and colon, which were related to the suppression of PIP on the activation of PI3K/AKT/mTOR signaling pathway.}, } @article {pmid38158092, year = {2023}, author = {DeCola, AC and Toppen, LC and Brown, KP and Dadkhah, A and Rizzo, DM and Ziels, RM and Scarborough, MJ}, title = {Microbiome assembly and stability during start-up of a full-scale, two-phase anaerobic digester fed cow manure and mixed organic feedstocks.}, journal = {Bioresource technology}, volume = {394}, number = {}, pages = {130247}, doi = {10.1016/j.biortech.2023.130247}, pmid = {38158092}, issn = {1873-2976}, abstract = {Carbon transformations during anaerobic digestion are mediated by complex microbiomes, but their assembly is poorly understood, especially in full-scale digesters. Gene-centric metagenomics combining functional and taxonomic classification was performed for an on-farm digester during start-up. Cow manure and organic waste pre-treated in a hydrolysis tank were fed to the methane-producing digester and the volatile solids loading rate was slowly increased from 0 to 3.5 kg volatile solids m[-3] d[-1] over one year. The microbial community in the anaerobic digester exhibited a high ratio of archaea, which were dominated by hydrogenotrophic methanogens. Bacteria in the anaerobic digester had a high abundance of genes for ferredoxin cycling, H2 generation, and more metabolically complex fermentations than in the hydrolysis tank. In total, the results show that a functionally stable microbiome was achieved quickly during start-up and that the microbiome created in the low-pH hydrolysis tank did not persist in the downstream anaerobic digester.}, } @article {pmid38157957, year = {2023}, author = {Jiang, X and Li, Z and Lin, K and Zhao, Y and Su, L and Wu, T and Zhou, T}, title = {Enhancement of anaerobic digestion from food waste via inert substances based on metagenomic analysis: Oxidative phosphorylation and metabolism.}, journal = {Environmental research}, volume = {246}, number = {}, pages = {118033}, doi = {10.1016/j.envres.2023.118033}, pmid = {38157957}, issn = {1096-0953}, abstract = {The application of anaerobic digestion (AD) in the treatment of food waste (FW) has become widespread. However, the presence of inert substances, such as bones, ceramics, and shells, within FW introduces a degree of uncertainty into the AD process. To clarify this intricate issue, this study conducted an in-depth investigation into the influence of inert substances on AD. The results revealed that when inert substances were present at a concentration of 0.08 g/g VSS, methane productivity in the AD process was significantly augmented by 86%. Subsequent investigations suggested that this positive effect was primarily evident in various biochemical processes, including solubilization, hydrolysis acidification, methanogenesis, and the accumulation of extracellular polymeric substances. Metagenomic analysis showed that inert substances enhance the relative abundance of hydrolytic bacteria and have a pronounced impact on the relative abundance of hydrogenotrophic methanogens (Methanosarcina) and acetotrophic methanogens (Methanobacterium). Additionally, inert substances significantly increased the relative abundance of functional genes in oxidative phosphorylation, a pivotal pathway for ATP synthesis. Furthermore, inert substances had a substantial effect on the functional genes related to the metabolic pathways associated with methanogenesis (both hydrogenotrophic and acetotrophic). This comprehensive study shed light on the substantial impact of inert substances on the AD of food waste, contributing to an enhanced understanding of the underlying mechanisms of anaerobic fermentation.}, } @article {pmid38157865, year = {2024}, author = {Chandra, V and Li, L and Le Roux, O and Zhang, Y and Howell, RM and Rupani, DN and Baydogan, S and Miller, HD and Riquelme, E and Petrosino, J and Kim, MP and Bhat, KPL and White, JR and Kolls, JK and Pylayeva-Gupta, Y and McAllister, F}, title = {Gut epithelial Interleukin-17 receptor A signaling can modulate distant tumors growth through microbial regulation.}, journal = {Cancer cell}, volume = {42}, number = {1}, pages = {85-100.e6}, doi = {10.1016/j.ccell.2023.12.006}, pmid = {38157865}, issn = {1878-3686}, mesh = {Mice ; Animals ; Humans ; *Interleukin-17 ; Receptors, Interleukin-17/genetics ; Mice, Knockout ; Signal Transduction ; *Pancreatic Neoplasms/pathology ; }, abstract = {Microbes influence cancer initiation, progression and therapy responsiveness. IL-17 signaling contributes to gut barrier immunity by regulating microbes but also drives tumor growth. A knowledge gap remains regarding the influence of enteric IL-17-IL-17RA signaling and their microbial regulation on the behavior of distant tumors. We demonstrate that gut dysbiosis induced by systemic or gut epithelial deletion of IL-17RA induces growth of pancreatic and brain tumors due to excessive development of Th17, primary source of IL-17 in human and mouse pancreatic ductal adenocarcinoma, as well as B cells that circulate to distant tumors. Microbial dependent IL-17 signaling increases DUOX2 signaling in tumor cells. Inefficacy of pharmacological inhibition of IL-17RA is overcome with targeted microbial ablation that blocks the compensatory loop. These findings demonstrate the complexities of IL-17-IL-17RA signaling in different compartments and the relevance for accounting for its homeostatic host defense function during cancer therapy.}, } @article {pmid38157791, year = {2023}, author = {Qu, L and Chai, T and Guo, Z and Zhang, Z and Huang, Z and Li, N}, title = {Studies on the airborne bacterial communities and antimicrobial resistance genes in duck houses based on metagenome and PCR analysis.}, journal = {Poultry science}, volume = {103}, number = {2}, pages = {103365}, doi = {10.1016/j.psj.2023.103365}, pmid = {38157791}, issn = {1525-3171}, abstract = {The threat of antimicrobial resistance (AMR) is on the rise globally, especially with the development of animal husbandry and the increased demand for antibiotics. Livestock and poultry farms, as key sites for prevalence of antibiotic-resistant bacteria (ARB), can spread antimicrobial resistance genes (ARGs) through microbial aerosols and affect public health. In this study, total suspended particulate matter (TSP) and airborne culturable microorganisms were collected from duck houses in Tai'an, Shandong Province, and the bacterial communities and airborne ARGs were analyzed using metagenomics and PCR methods. The results showed that the bacterial communities in the air of duck houses were mainly Actinobacteria, Firmicutes, Proteobactria, Chlamydia, and Bcateroidetes at the phylum level. At the genus level, the air was dominated by Corynebacterium, Jeotgalicoccus, Staphylococcus, Brevibacterium, and Megacoccus, and contained some pathogenic bacteria such as Staphylococcus aureus, Corynebacterium diphtheriae, Klebsiella oxytoca, Acinetobacter baumannii, and Pseudomonas aeruginosa, which were also potential hosts for ARGs. The airborne ARGs were mainly macrolides (10.97%), penicillins (10.73%), cephalosporins (8.91%), streptozotocin (8.91%), and aminoglycosides (8.02%). PCR detected 27 ARGs in airborne culturable microorganisms, and comparative analysis between PCR and the metagenomic data revealed that a total of 9 ARGs were found to the same, including macrolides ErmA, ErmF, tetracyclines tetG, tetX, methicarbamazepines dfrA12, dfrA15, aminoglycosides APH3-VI, ANT2-Ⅰ, and sulfonamides sul2. Moreover, inhalation exposure modeling showed that the workers in duck houses inhaled higher concentrations of ARB, human pathogenic bacteria (HPB) and human pathogenic antibiotic-resistant bacteria (HPARB) than hospital workers. These results provide new insights into airborne microorganisms and ARGs in animal farms and lay the foundation for further study.}, } @article {pmid38157274, year = {2023}, author = {Zhang, M and Shi, Z and Wu, C and Yang, F and Su, T and Jing, X and Shi, J and Ren, H and Jiang, L and Jiang, Y and Zhang, C and Zhou, W and Zhou, Y and Wu, K and Zheng, S and Zhong, X and Wu, L and Gu, W and Hong, J and Wang, J and Ning, G and Liu, R and Zhong, H and Zhou, W and Wang, W}, title = {Cushing's Syndrome is associated with Gut Microbial Dysbiosis and Cortisol-Degrading Bacteria.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {}, number = {}, pages = {}, doi = {10.1210/clinem/dgad766}, pmid = {38157274}, issn = {1945-7197}, abstract = {CONTEXT: Cushing's Syndrome (CS) is a severe endocrine disease characterized by excessive secretion of cortisol with multiple metabolic disorders. While gut dysbiosis plays a vital role in metabolic disorders, the role of gut microbiota in CS remains unclear.

OBJECTIVE: The objective of this work is to examine the alteration of gut microbiota in patients with CS.

METHODS: We performed shotgun metagenomic sequencing of fecal samples from 78 patients with CS and 78 healthy controls matched for age and body mass index. Furthermore, we verify the cortisol-degradation capacity of Ruminococcus gnavus in vitro and identify the potential metabolite by LC-MC/MS.

RESULTS: We observed significant differences in microbial composition between CS and controls in both sexes, with CS showing reduced Bacteroidetes (Bacteroides vulgatus) and elevated Firmicutes (Erysipelotrichaceae_bacterium_6_1_45) and Proteobacteria (Enterobacter cloacae). Despite distinct causes of hypercortisolism in ACTH-dependent and ACTH-independent CS, we found no significant differences in metabolic profiles or gut microbiota between the two subgroups. Furthermore, we identified a group of gut species, including R. gnavus, were positively correlated with cortisol levels in CS. These bacteria were found to harbor cortisol-degrading desAB genes and were consistently enriched in CS. Moreover, we demonstrated the efficient capacity of R. gnavus to degrade cortisol to 11-oxygenated androgens in vitro.

CONCLUSIONS: This study provides evidence of gut microbial dysbiosis in patients with CS and identifies a group of CS-enriched bacteria capable of degrading cortisol. These findings highlight the potential role of gut microbiota in regulating host steroid hormone levels, and consequently host health.}, } @article {pmid38157124, year = {2023}, author = {Singh, CK and Sodhi, KK and Singh, DK}, title = {Understanding the bacterial community structure associated with the Eichhornia crassipes rootzone.}, journal = {Molecular biology reports}, volume = {51}, number = {1}, pages = {35}, pmid = {38157124}, issn = {1573-4978}, mesh = {Humans ; *Eichhornia ; Ecosystem ; Anti-Bacterial Agents/metabolism ; Ciprofloxacin ; Fluoroquinolones ; Bacteria/genetics ; }, abstract = {BACKGROUND: Plant microbiome acts as an interface between plants and their environment, aiding in the functioning of the ecosystem, such as protection against abiotic and biotic stress along with improving nutrient uptake. The rhizosphere is an essential interface for the interaction between plants and microbes and plays a substantial part in the removal as well as uptake of heavy metals and antibiotics from contaminated locations. Eichhornia crassipes is a promising plant that contains a rich community of microbes in its rhizosphere. Microorganism's association with plants embodies a crucial pathway via which humans can also be exposed to antibiotic-resistant genes and bacteria.

METHODS AND RESULTS: In our earlier study enhanced removal of ciprofloxacin was observed by plant growth-promoting Microbacterium sp. WHC1 in the presence of E. crassipes root exudates. Therefore, the V3-V4, hypervariable region of the 16 S rRNA gene was studied to assess the bacterial diversity and functional profiles of the microbiota associated with plant roots. Using the QIIME software program, 16 S rRNA data from the Next Generation Sequencing (NGS) platform was examined. Alpha diversity including Chao1, Observed Shannon, and Simpson index denote significantly higher bacterial diversity. Proteobacteria (79%) was the most abundant phylum which was present in the root samples followed by Firmicutes (8%) and Cyanobacteria (8%). Sulfuricurvum (36%) is the most abundant genus belonging to the family Helicobacteraceae and the species kujiense in the genus Sulfuricurvum is the most abundant species present in the root sample. Also, the bacterial communities in the rhizoplane of Eichhornia crassipes harbor the genes conferring resistance to beta-lactams, tetracycline, fluoroquinolones, and penams.

CONCLUSION: Metagenomic studies on the E. crassipes microbiome showed that the bacterial communities constituting the root exudates of the Eichhornia aid them to survive in a polluted environment.}, } @article {pmid38156313, year = {2023}, author = {Han, J and Zhang, B and Zhang, Y and Yin, T and Cui, Y and Liu, J and Yang, Y and Song, H and Shang, D}, title = {Gut microbiome: decision-makers in the microenvironment of colorectal cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1299977}, pmid = {38156313}, issn = {2235-2988}, mesh = {Humans ; *Colorectal Neoplasms/etiology ; *Gastrointestinal Microbiome ; Bacteria/genetics ; Carcinogenesis ; Decision Making ; Tumor Microenvironment ; }, abstract = {Colorectal cancer (CRC) is a common malignancy of the gastrointestinal tract, accounting for the second most common cause of gastrointestinal tumors. As one of the intestinal barriers, gut bacteria form biofilm, participate in intestinal work, and form the living environment of intestinal cells. Metagenomic next-generation sequencing (mNGS) of the gut bacteria in a large number of CRC patients has been established, enabling specific microbial signatures to be associated with colorectal adenomato-carcinoma. Gut bacteria are involved in both benign precursor lesions (polyps), in situ growth and metastasis of CRC. Therefore, the term tumorigenic bacteria was proposed in 2018, such as Escherichia coli, Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, etc. Meanwhile, bacteria toxins (such as cytolethal distending toxin (CDT), Colibactin (Clb), B. fragilis toxin) affect the tumor microenvironment and promote cancer occurrence and tumor immune escape. It is important to note that there are differences in the bacteria of different types of CRC. In this paper, the role of tumorigenic bacteria in the polyp-cancer transformation and the effects of their secreted toxins on the tumor microenvironment will be discussed, thereby further exploring new ideas for the prevention and treatment of CRC.}, } @article {pmid38156301, year = {2023}, author = {Wani, AK and Ahmad, S and Américo-Pinheiro, JHP and Tizro, N and Singh, R}, title = {Building the taxonomic profile of the Riniaie Marwah hot spring of Kishtwar in Jammu and Kashmir: the first high-throughput sequencing-based metagenome study.}, journal = {Iranian journal of microbiology}, volume = {15}, number = {6}, pages = {723-733}, pmid = {38156301}, issn = {2008-3289}, abstract = {BACKGROUND AND OBJECTIVES: Rinaie Marwah hot spring Kishtwar (RMHSK) is one of the geothermal springs located at 33°51'51″N 75°32'07″E with an elevation of 2134 meters above sea level in Jammu and Kashmir, India. We aimed to study the microbial diversity of this geothermal spring using metagenomics.

MATERIALS AND METHODS: In the present study, physiochemical parameters including temperature (65-75°C), pH (6. 9-8. 8), hardness (250 ppm), and mineral content was measured along with the microbial diversity using Illumina MiSeq metagenome-based 16s amplicon sequencing (V3-V4). The sequence reads were classified taxonomically into 31 phyla, 71 classes, 152 orders, 256 families, 410 genus, and 665 species. QIIME 2 (Quantitative Insights into Microbial Ecology), an extensible, powerful, and decentralized analytical tool, was used for taxonomic analysis.

RESULTS: Bacteroidota (32. 57%) was the dominant phylum, Bacteroidia (32. 51%) the dominant class, Bacteroidales (16. 6%) the dominant order, and Lentimicrobiaceae (14. 23%) was the dominant family per the abundance analysis. Shannon (2. 28) and Chao 1 (87. 0) diversity indices support the existence of higher microbial diversity in RMHSK (50717 OTUs).

CONCLUSION: The microbial diversity of RMHSK is reported for the first time through a metagenomic study. Identification of microorganisms with characteristics that are relevant to industries.}, } @article {pmid38156010, year = {2023}, author = {Huang, H and Pang, X and Que, T and Chen, P and Li, S and Wu, A and He, M and Qiu, H and Hu, Y}, title = {Antibiotic resistance profiles of gut microbiota across various primate species in Guangxi.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1309709}, pmid = {38156010}, issn = {1664-302X}, abstract = {INTRODUCTION: Understanding the gut microbiota and antibiotic resistance gene (ARG) profiles in non-human primates (NHPs) is crucial for evaluating their potential impact on human health and the environment.

METHODS: In this study, we performed metagenomic analysis of 203 primate fecal samples, including nine NHP species and humans, to comprehensively characterize their gut microbiota and ARGs.

RESULTS: Our study reveals the prevailing phyla in primates as Firmicutes, Bacteroidetes, Euryarchaeota, and Proteobacteria. The captive NHPs exhibited higher ARG abundance compared to their wild counterparts, with tetracycline and beta-lactam resistance genes prevailing. Notably, ARG subtypes in Trachypithecus leucocephalus (T. leucocephalus) residing in karst limestone habitats displayed a more dispersed distribution compared to other species. Interestingly, ARG profiles of NHPs clustered based on geographic location and captivity status. Co-occurrence network analysis revealed intricate correlations between ARG subtypes and bacterial taxa. Procrustes analysis unveiled a significant correlation between ARGs and microbial phylogenetic community structure. Taxonomic composition analysis further highlighted differences in microbial abundance among NHPs and humans.

DISCUSSION: Our study underscores the impact of lifestyle and geographical location on NHP gut microbiota and ARGs, providing essential insights into the potential risks posed by NHPs to antibiotic resistance dissemination. This comprehensive analysis enhances our understanding of the interplay between NHPs and the gut resistome, offering a critical reference for future research on antibiotic resistance and host-microbe interactions.}, } @article {pmid38156003, year = {2023}, author = {Mukhopadhyay, M and Mukherjee, A and Ganguli, S and Chakraborti, A and Roy, S and Choudhury, SS and Subramaniyan, V and Kumarasamy, V and Sayed, AA and El-Demerdash, FM and Almutairi, MH and Şuţan, A and Dhara, B and Mitra, AK}, title = {Marvels of Bacilli in soil amendment for plant-growth promotion toward sustainable development having futuristic socio-economic implications.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1293302}, pmid = {38156003}, issn = {1664-302X}, abstract = {Microorganisms are integral components of ecosystems, exerting profound impacts on various facets of human life. The recent United Nations General Assembly (UNGA) Science Summit emphasized the critical importance of comprehending the microbial world to address global challenges, aligning with the United Nations Sustainable Development Goals (SDGs). In agriculture, microbes are pivotal contributors to food production, sustainable energy, and environmental bioremediation. However, decades of agricultural intensification have boosted crop yields at the expense of soil health and microbial diversity, jeopardizing global food security. To address this issue, a study in West Bengal, India, explored the potential of a novel multi-strain consortium of plant growth promoting (PGP) Bacillus spp. for soil bioaugmentation. These strains were sourced from the soil's native microbial flora, offering a sustainable approach. In this work, a composite inoculum of Bacillus zhangzhouensis MMAM, Bacillus cereus MMAM3), and Bacillus subtilis MMAM2 were introduced into an over-exploited agricultural soil and implications on the improvement of vegetative growth and yield related traits of Gylcine max (L) Meril. plants were evaluated, growing them as model plant, in pot trial condition. The study's findings demonstrated significant improvements in plant growth and soil microbial diversity when using the bacterial consortium in conjunction with vermicompost. Metagenomic analyses revealed increased abundance of many functional genera and metabolic pathways in consortium-inoculated soil, indicating enhanced soil biological health. This innovative bioaugmentation strategy to upgrade the over-used agricultural soil through introduction of residual PGP bacterial members as consortia, presents a promising path forward for sustainable agriculture. The rejuvenated patches of over-used land can be used by the small and marginal farmers for cultivation of resilient crops like soybean. Recognizing the significance of multi-strain PGP bacterial consortia as potential bioinoculants, such technology can bolster food security, enhance agricultural productivity, and mitigate the adverse effects of past agricultural activities.}, } @article {pmid38156566, year = {2023}, author = {Roev, GV and Borisova, NI and Chistyakova, NV and Vyhodtseva, AV and Akimkin, VG and Khafizov, KF}, title = {Bastroviruses (Astroviridae): genetic diversity and potential impact on human and animal health.}, journal = {Voprosy virusologii}, volume = {68}, number = {6}, pages = {505-512}, doi = {10.36233/0507-4088-192}, pmid = {38156566}, issn = {2411-2097}, mesh = {Animals ; Humans ; *Astroviridae/genetics ; *Astroviridae Infections ; Phylogeny ; *Chiroptera/genetics ; Genetic Variation ; }, abstract = {INTRODUCTION: Bastroviruses were discovered in the Netherlands in 2016 in human stool samples and show partial genetic similarities to astroviruses and hepatitis E viruses. Their association with disease onset has not yet been established.

MATERIALS AND METHODS: Metagenomic sequencing of fecal samples of Nyctalus noctula bats collected in the Russian Federation in 2023 was performed. Two almost complete genomes of bastroviruses were assembled. The zoonotic potential of these viruses was assessed using machine learning methods, their recombination was studied, and phylogenetic trees were constructed.

RESULTS: A nearly complete bastrovirus genome was de novo assembled in one of the samples, and it was used to assemble another genome in another sample. The zoonotic potential of the virus from one of these samples was estimated as high. The existence of recombination between structural and non-structural polyproteins was demonstrated.

CONCLUSION: Two bastrovirus genomes were assembled, phylogenetic and recombination analyses were performed, and the zoonotic potential was evaluated.}, } @article {pmid38155006, year = {2023}, author = {Jiang, Q and Zhang, J and Zhou, G}, title = {Oral Malassezia infection co-occurring with tinea versicolor: Metagenomic sequencing of the saliva.}, journal = {Oral surgery, oral medicine, oral pathology and oral radiology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.oooo.2023.10.009}, pmid = {38155006}, issn = {2212-4411}, abstract = {Malassezia is a lipid-dependent cutaneous symbiotic fungal genus associated with tinea versicolor. Here, we first present a rare case of a young tinea versicolor patient with oral manifestations presenting as white strips, patches, and pigmentation. The patient had a family history of tinea versicolor and a habit of frequent intake of cream. Histopathologic features and periodic acid-schiff staining of oral lesion indicated oral infection with round budding yeasts with short hyphae. Saliva metagenomic sequencing identified Malassezia and demonstrated the upregulated amount, diversity and activity of inflammatory bacteria. The clinical manifestations of oral Malassezia infection and changes in bacterial communities shed light on the pathogenic role of Malassezia in oral mucosa. In conclusion, we report the first oral Malassezia infection, which broadens the pathogenic cognitive scope of Malassezia and highlights the value of molecular techniques in the diagnostic process.}, } @article {pmid38154733, year = {2023}, author = {Liu, W and Sun, C and Ren, Z and Hao, S and Chen, Z and Li, T and Wen, X}, title = {Long-term occurrence, resistance risk and chaotic characteristics of antibiotic resistance genes in sludge anaerobic digestion system.}, journal = {Bioresource technology}, volume = {394}, number = {}, pages = {130267}, doi = {10.1016/j.biortech.2023.130267}, pmid = {38154733}, issn = {1873-2976}, abstract = {The long-term occurrence, dynamics and risk of antibiotic resistance genes (ARGs) in anaerobic digestion (AD) of excess sludge (ES) are not fully understood. Therefore, 13-month metagenomic monitoring was carried out in a full-scale AD plant. The highest ARG abundance and risk scores were observed in spring. AD achieved a 35 % removal rate for the total ARG abundance, but the risk score of AD sludge was not always lower than ES samples, because of the higher proportion of Rank I ARGs in AD sludge. ARGs showed less obvious patterns under linear models compared with microbial community, implying their chaotic dynamics, which was further confirmed by nonlinearity tests. Empirical dynamic modeling performed better than the autoregressive integrated moving average model for ARG dynamics, especially for those with simple and nonlinear dynamics. This study highlighted spring for its higher ARG abundance and risk, and recommended nonlinear models for revealing the dynamics of ARGs.}, } @article {pmid38154626, year = {2023}, author = {Mthethwa-Hlongwa, NP and Amoah, ID and Gomez, A and Davison, S and Reddy, P and Bux, F and Kumari, S}, title = {Profiling pathogenic protozoan and their functional pathways in wastewater using 18S rRNA and shotgun metagenomics.}, journal = {The Science of the total environment}, volume = {}, number = {}, pages = {169602}, doi = {10.1016/j.scitotenv.2023.169602}, pmid = {38154626}, issn = {1879-1026}, abstract = {Despite extensive research, little is known about the composition of eukaryotic protists in environmental samples. This is due to low parasite concentrations, the complexity of parasite diversity, and a lack of suitable reference databases and standardized protocols. To bridge this knowledge gap, this study used 18S rRNA short amplicon and shotgun metagenomic sequencing approaches to profile protozoan microbial communities as well as their functional pathways in treated and untreated wastewater samples collected from different regions of South Africa. Results demonstrated that protozoan diversity (Shannon index P-value = 0.03) and taxonomic composition (PERMANOVA, P-value = 0.02) was mainly driven by the type of wastewater samples (treated & untreated) and geographic location. However, these WWTPs were also found to contain a core community of protozoan parasites. The untreated wastewater samples revealed a predominant presence of free-living, parasitic, and potentially pathogenic protists typically found in humans and animals, ranging from Alveolata (27 %) phylum (Apicomplexa and Ciliophora) to Excavata (3.88 %) (Discoba and Parasalia) and Amoebozoa (2.84 %) (Entamoeba and Acanthamoeba). Shotgun metagenomics analyses in a subset of the untreated wastewater samples confirmed the presence of public health-importance protozoa, including Cryptosporidium species (3.48 %), Entamoeba hystolitica (6.58 %), Blastocystis hominis (2.91 %), Naegleria gruberi (2.37 %), Toxoplasma gondii (1.98 %), Cyclospora cayetanensis (1.30 %), and Giardia intestinalis (0.31 %). Virulent gene families linked to pathogenic protozoa, such as serine/threonine protein phosphatase and mucin-desulfating sulfatase were identified. Additionally, enriched pathways included thiamine diphosphate biosynthesis III, heme biosynthesis, Methylerythritol 4-Phosphate Pathway, methyl erythritol phosphate (MEP), and pentose phosphate pathways. These findings suggest that protozoan pathogens may possess metabolic and growth potential within WWTPs, posing a severe risk of transmission to humans and animals if inadequately disinfected before release. This study provides a baseline for the future investigation of diverse protozoal communities in wastewater, which are of public health importance.}, } @article {pmid38154252, year = {2024}, author = {Galli, BD and Nikoloudaki, O and Granehäll, L and Carafa, I and Pozza, M and De Marchi, M and Gobbetti, M and Di Cagno, R}, title = {Comparative analysis of microbial succession and proteolysis focusing on amino acid pathways in Asiago-PDO cheese from two dairies.}, journal = {International journal of food microbiology}, volume = {411}, number = {}, pages = {110548}, doi = {10.1016/j.ijfoodmicro.2023.110548}, pmid = {38154252}, issn = {1879-3460}, mesh = {Animals ; Proteolysis ; Amino Acids/metabolism ; *Cheese/microbiology ; *Lactobacillales/metabolism ; Milk/microbiology ; }, abstract = {In this study, a comprehensive and comparative analysis was conducted on Italian Asiago-PDO cheese obtained from two different dairies named Dairy I and Dairy II using industrial and natural fermented milk, respectively. The analysis encompassed the evaluation of chemical composition, the succession of the microbiota during manufacture and ripening, and proteolysis mainly focusing on free individual amino acid (FAA) profiles. A metagenomic approach was used to investigate the cheese microbiome functionality. Differences in gross chemical composition were more evident during ripening, with Dairy II showing higher variability within batches. The microbiota varied significantly between the two dairies and ripening stages. The choice of starter culture shaped the microbiota during production and affected the microbial diversity of non-starter lactic acid bacteria (NSLAB) originated from the raw milk during ripening. Peptide chromatographic profiles and FAA concentrations increased as ripening progressed, with Dairy I showing higher production of FAA. Functional analysis of the metagenomes linked species to specific amino acid metabolism/catabolism pathways. The amino acid metabolism pathways, particularly those related to aromatic amino acids, lysine, and branched-chain amino acids, were affected by the presence of specific NSLAB species, which differed between the two dairies. The results obtained in this study reveal the impact of starter culture on peculiar cheese microbiota assemblies, which selectively targets amino acid pathways, providing insights into the potential flavor and aroma characteristics of Asiago-PDO cheese.}, } @article {pmid38154222, year = {2024}, author = {Chen, J and Liu, K and Liu, Y}, title = {Synergistic molecular mechanism of degradation in dye wastewater by Rhodopseudomonas palustris intimately coupled carbon nanotube - Silver modified titanium dioxide photocatalytic composite with sodium alginate.}, journal = {Journal of environmental management}, volume = {351}, number = {}, pages = {119913}, doi = {10.1016/j.jenvman.2023.119913}, pmid = {38154222}, issn = {1095-8630}, mesh = {*Wastewater ; Silver ; *Nanotubes, Carbon ; Coloring Agents/metabolism ; Titanium ; Biodegradation, Environmental ; Azo Compounds ; Catalysis ; *Rhodopseudomonas ; }, abstract = {The intimately coupled photocatalysis and biodegradation (ICPB), which combined the advantages of high oxidation capacity of photocatalysis and high mineralization rate of biodegradation, has demonstrated excellent removal performance in the degradation of azo dyes with highly toxic, refractory, mutagenic and carcinogenic. In order to explore the metagenomics mechanism of the ICPB system, a novel ICPB was prepared by coupling Rhodopseudomonas palustris (R. Palustris), carbon nanotube - silver modified titanium dioxide photocatalytic composite (CNT-Ag -TiO2, CAT) and sodium alginate (SA) (R. palustris/CAT@SA, R-CAT). Metagenomics sequencing was used to investigate the molecular mechanism of adaptation and degradation of dyes by photosynthetic microorganisms and the adaptive and synergistic interaction between photosynthetic microorganisms and photocatalyst. Experiments on the adaptability and degradability of photosynthetic microorganisms have proved that low concentration azo dyes could be utilized as carbon sources for growth of photosynthetic microorganisms. Metagenomics sequencing revealed that R. palustris was the main degrading bacterium in photosynthetic microorganisms and the functional genes related to carbohydrate metabolism, biological regulation and catalytic activity were abundant. It was found that the addition of photocatalyst significantly up-regulated the functional genes related to the catabolic process, electron transport, oxidoreductase activity and superoxide metabolism of organic matter in the photosynthetic microorganisms. Moreover, many key gene such as alpha-amylase, 1-acyl-sn-glycerol-3-phosphate acyltransferase, aldehyde dehydrogenase enrichment in microbial basal metabolism, such as enoyl-CoA hydratase, malate dehydrogenase, glutathione S-transferase enrichment in degrading azo dyes and electron transport, and many key gene such as undecaprenyl-diphosphatase, carbon storage regulator, DNA ligase enrichment in response to dyes and photocatalysts were discovered. These findings would contribute to a comprehensive understanding of the mechanism of degradation of dye wastewater by ICPB system, a series of genes was produced to adapt to environmental changes, and played synergistic role in terms of intermediate product degradation and electron transfer for degrading azo dyes. The photosynthetic microorganisms might be a promising microorganism for constructing ICPB system.}, } @article {pmid38153974, year = {2023}, author = {Ai, L and Wang, W and Li, Y}, title = {Letter to the Editor: Diagnosis of Aspergillus flavus-Induced Pneumonia Through Metagenomic Next-Generation Sequencing: A Case Report.}, journal = {Surgical infections}, volume = {}, number = {}, pages = {}, doi = {10.1089/sur.2023.314}, pmid = {38153974}, issn = {1557-8674}, } @article {pmid38153618, year = {2023}, author = {Xiong, L and Li, Y and Zeng, K and Wei, Y and Li, H and Ji, X}, title = {Revealing viral diversity in the Napahai plateau wetland based on metagenomics.}, journal = {Antonie van Leeuwenhoek}, volume = {117}, number = {1}, pages = {3}, pmid = {38153618}, issn = {1572-9699}, support = {32160294, 42267059//National Natural Science Foundation of China/ ; }, mesh = {*Wetlands ; Ecosystem ; Phylogeny ; China ; *Bacteriophages ; }, abstract = {We focused on exploring the diversity of viruses in the Napahai plateau wetland, a unique ecosystem located in Yunnan, China. While viruses in marine environments have been extensively studied for their influence on microbial metabolism and biogeochemical cycles, little is known about their composition and function in plateau wetlands. Metagenomic analysis was employed to investigate the viral diversity and biogeochemical impacts in the Napahai wetland. It revealed that the Caudoviricetes and Malgrandaviricetes class level was the most abundant viral category based on phylogenetic analysis. Additionally, a gene-sharing network highlighted the presence of numerous unexplored viruses and demonstrated their unique characteristics and significant variation within the viral community of the Napahai wetland. Furthermore, the study identified the auxiliary metabolic genes (AMGs). AMGs provide phages with additional functions, such as protection against host degradation and involvement in metabolic pathways, such as the pentose phosphate pathway and DNA biosynthesis. The viruses in the Napahai wetland were found to influence carbon, nitrogen, sulfur, and amino acid metabolism, indirectly contributing to biogeochemical cycling through these AMGs. Overall, the research sheds light on the diverse and unique viral communities in the Napahai plateau wetland and emphasizes the significant roles of viruses in microbial ecology. The findings contribute to a deeper understanding of the characteristics and ecological functions of viral communities in plateau wetland ecosystems.}, } @article {pmid38153158, year = {2023}, author = {Littleford-Colquhoun, B and Kartzinel, TR}, title = {A CRISPR-based strategy for targeted sequencing in biodiversity science.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {e13920}, doi = {10.1111/1755-0998.13920}, pmid = {38153158}, issn = {1755-0998}, support = {//Institute at Brown for Environment and Society seed award/ ; NSF DEB-2046797//National Science Foundation/ ; }, abstract = {Many applications in molecular ecology require the ability to match specific DNA sequences from single- or mixed-species samples with a diagnostic reference library. Widely used methods for DNA barcoding and metabarcoding employ PCR and amplicon sequencing to identify taxa based on target sequences, but the target-specific enrichment capabilities of CRISPR-Cas systems may offer advantages in some applications. We identified 54,837 CRISPR-Cas guide RNAs that may be useful for enriching chloroplast DNA across phylogenetically diverse plant species. We tested a subset of 17 guide RNAs in vitro to enrich plant DNA strands ranging in size from diagnostic DNA barcodes of 1,428 bp to entire chloroplast genomes of 121,284 bp. We used an Oxford Nanopore sequencer to evaluate sequencing success based on both single- and mixed-species samples, which yielded mean chloroplast sequence lengths of 2,530-11,367 bp, depending on the experiment. In comparison to mixed-species experiments, single-species experiments yielded more on-target sequence reads and greater mean pairwise identity between contigs and the plant species' reference genomes. But nevertheless, these mixed-species experiments yielded sufficient data to provide ≥48-fold increase in sequence length and better estimates of relative abundance for a commercially prepared mixture of plant species compared to DNA metabarcoding based on the chloroplast trnL-P6 marker. Prior work developed CRISPR-based enrichment protocols for long-read sequencing and our experiments pioneered its use for plant DNA barcoding and chloroplast assemblies that may have advantages over workflows that require PCR and short-read sequencing. Future work would benefit from continuing to develop in vitro and in silico methods for CRISPR-based analyses of mixed-species samples, especially when the appropriate reference genomes for contig assembly cannot be known a priori.}, } @article {pmid38153067, year = {2023}, author = {Long, W and Li, M and Gao, Y and Zhang, Y and Yuan, X and Ye, H and Huang, H and Liang, W and Zhang, R and Du, G}, title = {Microbial community, pathogenic bacteria and high-risk anti-biotic resistance genes at two tropical coastal beaches adjacent to villages in Hainan, China.}, journal = {Annals of agricultural and environmental medicine : AAEM}, volume = {30}, number = {4}, pages = {645-653}, doi = {10.26444/aaem/176090}, pmid = {38153067}, issn = {1898-2263}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Water Microbiology ; Bacteria/genetics ; Anti-Bacterial Agents ; *Microbiota ; }, abstract = {OBJECTIVE: The aim of the study was to explore the correlation between characteristics of microbial community, pathogenic bacteria and high-risk antibiotic-resistant genes, between coastal beaches and a multi-warm-blooded host, as well as to determine potential species biomarkers for faecal source contamination on tropical coastal beaches in China.

MATERIAL AND METHODS: The 'One-Health' approach was used in a microbiological study of beaches and warm-blooded hosts. The microbial.community was analyzed using 16S rRNA gene amplicons and shotgun metagenomics on Illumina NovaSeq.

RESULTS: The Chao, Simpson, Shannon, and ACE indices of non-salt beach were greater than those of salt beaches at the genus and OTU levels (P < 0.001). Bacteroidota, Halanaerobiaeota, Cyanobacteria, and Firmicutes were abundant on salt beaches (P<0.01). Human-sourced microorganisms were more abundant on salt beaches, which accounted for 0.57%. Faecalibacterium prausnitzii and Eubacterium hallii were considered as reliable indicators for the contamination of human faeces. High-risk carbapenem-resistant Klebsiella pneumoniae and the genotypes KPC-14 and KPC-24 were observed on salt beaches. Tet(X3)/tet(X4) genes and four types of MCR genes co-occurred on beaches and humans; MCR9.1 accounted for the majority. Tet(X4) found among Cyanobacteria. Although rarely reported at Chinese beaches, pathogens, such as Vibrio vulnificus, Legionella pneumophila, and Helicobacter pylori, were observed.

CONCLUSIONS: The low microbial community diversity, however, did not indicate a reduced risk. The transfer of high-risk ARGs to extreme coastal environments should be given sufficient attention.}, } @article {pmid38152703, year = {2023}, author = {Zhou, Z and Martin, C and Kosmopoulos, JC and Anantharaman, K}, title = {ViWrap: A modular pipeline to identify, bin, classify, and predict viral-host relationships for viruses from metagenomes.}, journal = {iMeta}, volume = {2}, number = {3}, pages = {}, pmid = {38152703}, issn = {2770-596X}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; }, abstract = {Viruses are increasingly being recognized as important components of human and environmental microbiomes. However, viruses in microbiomes remain difficult to study because of the difficulty in culturing them and the lack of sufficient model systems. As a result, computational methods for identifying and analyzing uncultivated viral genomes from metagenomes have attracted significant attention. Such bioinformatics approaches facilitate the screening of viruses from enormous sequencing datasets originating from various environments. Though many tools and databases have been developed for advancing the study of viruses from metagenomes, there is a lack of integrated tools enabling a comprehensive workflow and analyses platform encompassing all the diverse segments of virus studies. Here, we developed ViWrap, a modular pipeline written in Python. ViWrap combines the power of multiple tools into a single platform to enable various steps of virus analysis, including identification, annotation, genome binning, species- and genus-level clustering, assignment of taxonomy, prediction of hosts, characterization of genome quality, comprehensive summaries, and intuitive visualization of results. Overall, ViWrap enables a standardized and reproducible pipeline for both extensive and stringent characterization of viruses from metagenomes, viromes, and microbial genomes. Our approach has flexibility in using various options for diverse applications and scenarios, and its modular structure can be easily amended with additional functions as necessary. ViWrap is designed to be easily and widely used to study viruses in human and environmental systems. ViWrap is publicly available via GitHub (https://github.com/AnantharamanLab/ViWrap). A detailed description of the software, its usage, and interpretation of results can be found on the website.}, } @article {pmid38151716, year = {2024}, author = {Fritz, P and Fritz, R and Bóday, P and Bóday, Á and Bató, E and Kesserű, P and Oláh, C}, title = {Gut microbiome composition: link between sports performance and protein absorption?.}, journal = {Journal of the International Society of Sports Nutrition}, volume = {21}, number = {1}, pages = {2297992}, pmid = {38151716}, issn = {1550-2783}, mesh = {Humans ; *Gastrointestinal Microbiome ; Dietary Supplements ; *Athletic Performance ; *Probiotics ; Anthropometry ; Body Composition ; }, abstract = {BACKGROUND: Sufficient protein intake is essential for adequate physical condition and athletic performance. However, numerous factors can influence the absorption of consumed protein, including timing, type of protein intake, and gut microbiota. In the present study, elite male water polo players consumed a plant-based, vegan protein supplement with (n = 10) or without (n = 10) pre- and probiotics daily during the 31-day study period.

METHODS: We determined the anthropometric characteristics and body composition, dietary habits, gut microbiota composition, and blood parameters of the players at the beginning and at the end of the study. Body composition parameters were analyzed using the InBody 970 bioimpedance analyzer. Gut microbiome composition was determined from stool samples by metagenome sequencing. Paired and unpaired t-tests were used to determine differences between body composition and blood parameters within the groups and between the two groups at the two different sampling times. The Wilcoxon test was used to determine the change in bacterial composition during the study. Correlations between changes in body composition, blood parameters, and taxonomic groups were analyzed using a linear correlation calculation.

RESULTS: Skeletal muscle mass (p < 0.001), body cell mass (p = 0.002), arm circumference (p = 0.003), and protein mass (p < 0.001) increased, while body fat mass (p = 0.004) decreased significantly in the intervention group which consumed pre- and probiotics in addition to protein supplement. Activated acetate (reductive TCA cycle I) and propionate (pyruvate fermentation to propanoate I) pathways correlated positively with increased skeletal muscle mass (p < 0.01 and p < 0.05), and the relative abundance of butyrate-producing species showed a significant positive correlation with changes in body fat mass in the intervention group (p < 0.05). These correlations were not observed in the control group without the intake of pre- and probiotics.

CONCLUSIONS: The composition of the gut microbiota may influence protein absorption and therefore body composition and consequently physical condition and sports performance.}, } @article {pmid38151208, year = {2023}, author = {Wei, L and Zheng, J and Han, Y and Xu, X and Li, M and Zhu, L}, title = {Insights into the roles of biochar pores toward alleviating antibiotic resistance genes accumulation in biofiltration systems.}, journal = {Bioresource technology}, volume = {394}, number = {}, pages = {130257}, doi = {10.1016/j.biortech.2023.130257}, pmid = {38151208}, issn = {1873-2976}, abstract = {Biofiltration systems would harbor and spread various antibiotic resistance genes (ARGs) when treating antibiotic micro-pollution, constituting a potential ecological risk. This study aimed to investigate the effects of biochar pores on ARG emergence and related microbial response mechanisms in bench-scale biofiltration systems. Results showed that biochar pores effectively reduced the absolute copies of the corresponding ARGs sul1 and sul2 by 54.1% by lowering the sorbed-SMX's bioavailability compared to non-porous anthracite. An investigation of antimicrobial resistomes revealed a considerable decrease in the abundance and diversity of ARGs and mobile gene elements. Metagenomic and metaproteomic analysis demonstrated that biochar pores induced the changeover of microbial defense strategy against SMX from blocking SMX uptake by EPS absorbing to SMX biotransformation. Microbial SOS response, antibiotic efflux pump, EPS secretion, and biofilm formation were decreased. Functions related to SMX biotransformation, such as sadABC-mediated transformation, xenobiotics degradation, and metabolism, were significantly promoted.}, } @article {pmid38150911, year = {2023}, author = {Polsomboon Nelson, S and Ergunay, K and Bourke, BP and Reinbold-Wasson, DD and Caicedo-Quiroga, L and Kirkitadze, G and Chunashvili, T and Tucker, CL and Linton, YM}, title = {Nanopore-based metagenomics reveal a new Rickettsia in Europe.}, journal = {Ticks and tick-borne diseases}, volume = {15}, number = {2}, pages = {102305}, doi = {10.1016/j.ttbdis.2023.102305}, pmid = {38150911}, issn = {1877-9603}, abstract = {Accurate identification of tick-borne bacteria, including those associated with rickettsioses, pose significant challenges due to the polymicrobial and polyvectoral nature of the infections. We aimed to carry out a comparative evaluation of a non-targeted metagenomic approach by nanopore sequencing (NS) and commonly used PCR assays amplifying Rickettsia genes in field-collected ticks. The study included a total of 310 ticks, originating from Poland (44.2 %) and Bulgaria (55.8 %). Samples comprised 7 species, the majority of which were Ixodes ricinus (62.9 %), followed by Dermacentor reticulatus (21.2 %). Screening was carried out in 55 pools, using total nucleic acid extractions from individual ticks. NS and ompA/gltA PCRs identified Rickettsia species in 47.3 % and 54.5 % of the pools, respectively. The most frequently detected species were Rickettsia asiatica (27.2 %) and Rickettsia raoultii (21.8 %), followed by Rickettsia monacensis (3.6 %), Rickettsia helvetica (1.8 %), Rickettsia massiliae (1.8 %) and Rickettsia tillamookensis (1.8 %). Phylogeny construction on mutS, uvrD, argS and virB4 sequences and a follow-up deep sequencing further supported R. asiatica identification, documented in Europe for the first time. NS further enabled detection of Anaplasma phagocytophilum (9.1 %), Coxiella burnetii (5.4 %) and Neoehrlichia mikurensis (1.8 %), as well as various endosymbionts of Rickettsia and Coxiella. Co-detection of multiple rickettsial and non-rickettsial bacteria were observed in 16.4 % of the pools with chromosome and plasmid-based contigs. In conclusion, non-targeted metagenomic sequencing was documented as a robust strategy capable of providing a broader view of the tick-borne bacterial pathogen spectrum.}, } @article {pmid38150226, year = {2023}, author = {Li, S and Fan, Y and Han, J and Liu, F and Ding, Y and Li, X and Yu, E and Wang, S and Wang, F and Wang, C}, title = {Foodborne Pathogen and Microbial Community Differences in Fresh Processing Tomatoes in Xinjiang, China.}, journal = {Foodborne pathogens and disease}, volume = {}, number = {}, pages = {}, doi = {10.1089/fpd.2023.0014}, pmid = {38150226}, issn = {1556-7125}, abstract = {The microbes on fresh processing tomatoes correlate closely with diseases, preservation, and quality control. Investigation of the microbial communities on processing tomatoes from different production regions may help define microbial specificity, inform disease prevention methods, and improve quality. In this study, surface microbes on processing tomatoes from 10 samples in two primary production areas of southern and northern Xinjiang were investigated by sequencing fungal internal transcribed spacer and bacterial 16S rRNA hypervariable sequences. A total of 133 different fungal and bacterial taxonomies were obtained from processing tomatoes in the two regions, of which 63 genera were predominant. Bacterial and fungal communities differed significantly between southern and northern Xinjiang, and fungal diversity was higher in southern Xinjiang. Alternaria and Cladosporium on processing tomatoes in southern Xinjiang were associated with plant pathogenic risk. The plant pathogenic fungi of processing tomatoes in northern Xinjiang were more abundant in Alternaria and Fusarium. The abundance of Alternaria on processing tomatoes was higher in four regions of northern Xinjiang, indicating that there is a greater risk of plant pathogenicity in these areas. Processing tomatoes in northern and southern Xinjiang contained bacterial genera identified as gut microbes, such as Pantoea, Erwinia, Enterobacter, Enterococcus, and Serratia, indicating the potential risk of contamination of processing tomatoes with foodborne pathogens. This study highlighted the microbial specificity of processing tomatoes in two tomato production regions, providing a basis for further investigation and screening for foodborne pathogenic microorganisms.}, } @article {pmid38150074, year = {2023}, author = {Kara, K and Pirci, G}, title = {Immunity, rumen metagenomics, ruminal variables, and growth performance of calves fed milk with sage (Salvia officinalis) essential oil.}, journal = {Tropical animal health and production}, volume = {56}, number = {1}, pages = {27}, doi = {10.1007/s11250-023-03831-w}, pmid = {38150074}, issn = {1573-7438}, support = {TDK-2022-11515//Bilimsel Araştırma Projeleri, Erciyes Üniversitesi/ ; }, mesh = {Animals ; Cattle ; *Milk ; *Salvia officinalis ; Interleukin-6 ; Rumen ; Tumor Necrosis Factor-alpha ; Butyric Acid ; Immunoglobulin E ; Immunoglobulin G ; Immunoglobulin M ; }, abstract = {The study aimed to determine the effect of sage (Salvia officinalis) essential oil (EO) to the drinking milk until the weaning stage of Holstein calves on the growth performance, body measurements, ruminal fermentation, rumen metagenomic profile, proinflammatory cytokines [interleukin-6 (IL-6), tumor necrosis factor (TNF-α), and IL-1β], immune globulins (IgG, IgM, and IgE), and acute phase proteins (serum amyloid-A, SAA). In the study, 24 Holstein calves were divided into three groups as 0 μL (SAG0; control group), 100 μL (SAG100), or 200 μL (SAG200) of sage EO to the milk per calf per day. The addition of sage EO to the milk linearly increased the live weight, feed intake, and daily body weight gain (P < 0.05). The addition of sage EO to the milk in calves linearly increased serum IgG titter dose dependently (P < 0.05), but serum IgM and IgE titters did not change (P > 0.05). The concentrations of serum TNF-α, IL-1β, and IL-6 in the weaned calves linearly decreased by the sage aromatic oil addition to the milk (P < 0.05). The serum SAA concentrations of calves did not differ among the control and treatment groups (P > 0.05). Probiotic Bifidobacterium and Acidaminococcus genus in calf rumen fluid can increase by sage EO addition to milk. The relative abundance of genus Prevotella, Prevotellaceae_NK3B31_group, and Prevotella_9 increase with sage EO. The ruminal ammonia-nitrogen (NH3-N) concentration and total short chain fatty acid (T-SCFA) molarity decreased by sage EO addition to the drinking milk (P < 0.05). The molarities of iso butyric (IBA) and iso valeric acids (IVA) in rumen fluid of the weaned calves linearly reduced by the increasing sage EO dose to the milk (P < 0.05). The butyric acid (BA) and iso caproic acid (ICA) molarities in rumen fluid did not change by the sage EO addition (P > 0.05). Consequently, it has been observed that sage EO addition to the milk of calves positively affected the immune system variables and performance parameters. Sage EO addition of calves before weaning may support the immune system in the eventual immunosuppression at the weaning stage.}, } @article {pmid38149413, year = {2023}, author = {Lawrence, K and Fibert, P and Hobbs, J and Myrissa, K and Toribio-Mateas, MA and Quadt, F and Cotter, PD and Gregory, AM}, title = {Randomised controlled trial of the effects of kefir on behaviour, sleep and the microbiome in children with ADHD: a study protocol.}, journal = {BMJ open}, volume = {13}, number = {12}, pages = {e071063}, pmid = {38149413}, issn = {2044-6055}, mesh = {Child ; Humans ; *Attention Deficit Disorder with Hyperactivity/therapy/complications ; *Gastrointestinal Microbiome ; *Kefir ; Randomized Controlled Trials as Topic ; Sleep ; Adolescent ; }, abstract = {INTRODUCTION: Current interventions for children with attention-deficit/hyperactivity disorder (ADHD) are primarily medication, behavioural therapy and parent training. However, research suggests dietary manipulations may provide therapeutic benefit for some. There is accumulating evidence that the gut microbiome may be atypical in ADHD, and therefore, manipulating gut bacteria in such individuals may help alleviate some of the symptoms of this condition. The aim of this study is to explore the effects of supplementation with kefir (a fermented dairy drink) on ADHD symptomatology, sleep, attention and the gut microbiome in children diagnosed with ADHD.

METHODS AND ANALYSIS: A 6-week randomised, double-blind, placebo-controlled trial in 70 children aged 8-13 years diagnosed with ADHD. Participants will be recruited throughout the UK, through support groups, community groups, schools, social media and word of mouth. Children will be randomised to consume daily either dairy kefir or a placebo dairy drink for 6 weeks. The primary outcome, ADHD symptomatology, will be measured by The Strengths and Weakness of ADHD-symptoms and Normal-behaviour scale. Secondary outcomes will include gut microbiota composition (using shotgun metagenomic microbiome sequencing), gut symptomatology (The Gastrointestinal Severity Index questionnaire), sleep (using 7-day actigraphy recordings, The Child's Sleep Habits Questionnaire and Sleep Self Report questionnaire), inattention and impulsivity (with a computerised Go/NoGo test). Assessments will be conducted prior to the intervention and at the end of the intervention. Interaction between time (preintervention/postintervention) and group (probiotic/placebo) is to be analysed using a Mixed Model Analysis of Variances.

ETHICS AND DISSEMINATION: Ethical approval for the study was granted by St Mary's University Ethics Committee. Results will be disseminated through peer-reviewed publications, presentations to the scientific community and support groups.

TRIAL REGISTRATION NUMBER: NCT05155696.}, } @article {pmid38149278, year = {2023}, author = {Jaarsma, AH and Zervas, A and Sipes, K and Campuzano Jiménez, F and Smith, AC and Svendsen, LV and Thøgersen, MS and Stougaard, P and Benning, LG and Tranter, M and Anesio, AM}, title = {The undiscovered biosynthetic potential of the Greenland Ice Sheet microbiome.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1285791}, pmid = {38149278}, issn = {1664-302X}, abstract = {The Greenland Ice Sheet is a biome which is mainly microbially driven. Several different niches can be found within the glacial biome for those microbes able to withstand the harsh conditions, e.g., low temperatures, low nutrient conditions, high UV radiation in summer, and contrasting long and dark winters. Eukaryotic algae can form blooms during the summer on the ice surface, interacting with communities of bacteria, fungi, and viruses. Cryoconite holes and snow are also habitats with their own microbial community. Nevertheless, the microbiome of supraglacial habitats remains poorly studied, leading to a lack of representative genomes from these environments. Under-investigated extremophiles, like those living on the Greenland Ice Sheet, may provide an untapped reservoir of chemical diversity that is yet to be discovered. In this study, an inventory of the biosynthetic potential of these organisms is made, through cataloging the presence of biosynthetic gene clusters in their genomes. There were 133 high-quality metagenome-assembled genomes (MAGs) and 28 whole genomes of bacteria obtained from samples of the ice sheet surface, cryoconite, biofilm, and snow using culturing-dependent and -independent approaches. AntiSMASH and BiG-SCAPE were used to mine these genomes and subsequently analyze the resulting predicted gene clusters. Extensive sets of predicted Biosynthetic Gene Clusters (BGCs) were collected from the genome collection, with limited overlap between isolates and MAGs. Additionally, little overlap was found in the biosynthetic potential among different environments, suggesting specialization of organisms in specific habitats. The median number of BGCs per genome was significantly higher for the isolates compared to the MAGs. The most talented producers were found among Proteobacteria. We found evidence for the capacity of these microbes to produce antimicrobials, carotenoid pigments, siderophores, and osmoprotectants, indicating potential survival mechanisms to cope with extreme conditions. The majority of identified BGCs, including those in the most prevalent gene cluster families, have unknown functions, presenting a substantial potential for bioprospecting. This study underscores the diverse biosynthetic potential in Greenland Ice Sheet genomes, revealing insights into survival strategies and highlighting the need for further exploration and characterization of these untapped resources.}, } @article {pmid38149271, year = {2023}, author = {Wang, XP and Shan, RY and Li, ZL and Kong, XR and Hou, RT and Wu, HN and Chen, CS}, title = {Metabolic improvements of novel microbial fermentation on black tea by Eurotium cristatum.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1287802}, pmid = {38149271}, issn = {1664-302X}, abstract = {Due to its traditional fermentation, there are obvious limits on the quality improvements in black tea. However, microbial fermentation can provide an abundance of metabolites and improve the flavor of tea. The "golden flower" fungi are widely used in the microbial fermentation of tea and has unique uses in healthcare. To further explore the improvements in black tea quality achieved via microbial fermentation, we used widely targeted metabolomics and metagenomics analyses to investigate the changes in and effects of metabolites and other microorganisms during the interaction between the "golden flower" fungi and black tea. Five key flavor metabolites were detected, the levels of catechin, epigallocatechin gallate, (-)-epicatechin gallate were decreased by different degrees after the inoculation of the "golden flower" fungus, whereas the levels of caffeine and (+)-gallocatechin increased. Botryosphaeriaceae, Botryosphaeriales, Dothideomycetes, Aspergillaceae, Trichocomaceae, and Lecanoromycetes play a positive role in the black tea fermentation process after inoculation with the "golden flower" fungi. D-Ribose can prevent hypoxia-induced apoptosis in cardiac cells, and it shows a strong correlation with Botryosphaeriaceae and Botryosphaeriales. The interaction between microorganisms and metabolites is manifested in tryptophan metabolism, starch and sucrose metabolism, and amino sugar and nucleotide sugar metabolism. In conclusion, the changes in metabolites observed during the fermentation of black tea by "golden flower" fungi are beneficial to human health. This conclusion extends the knowledge of the interaction between the "golden flower" fungi and black tea, and it provides important information for improving the quality of black tea.}, } @article {pmid38148812, year = {2024}, author = {Guo, Q and Xiao, Y and Zhang, S}, title = {Metagenomic next generation sequencing of bronchoalveolar lavage samples for the diagnosis of lower respiratory tract infections: A systematic review and meta-analysis.}, journal = {Heliyon}, volume = {10}, number = {1}, pages = {e23188}, pmid = {38148812}, issn = {2405-8440}, abstract = {BACKGROUND: Lower respiratory tract infections (LRTI)are known to be diagnosed late or inaccurately. This has fueled the unscrupulous use of antibiotics, as they are often used empirically and clinically, leading to antibiotic abuse and multidrug resistance in patients. Metagenomic next-generation sequencing (mNGS), now widely used in clinical studies, could be a potential intervention to revolutionize microbiology by rapidly identifying unknown species.

METHODS: This review and meta-analysis were conducted on eligible studies with respect to metagenomic sequencing on clinical LRTI diagnostics up to May 01, 2022. QUADAS-2 was employed to assess the methodological bias as well as applicability. After that, a meta-analysis was conducted to analyze the accuracy of mNGS, compared with the composite reference standard (CRS), among the enrolled studies.

RESULTS: This work collected 1248 samples in 13/21 qualified articles to factor in the accuracy of the diagnostic test. Typically, methods like molecular testing, culture, composite measures, and clinical decision-making were adopted as the reference criteria. With regard to Bronchoalveolar Lavage Samples, their sensitivity was 89% (82-93%) while their specificity was 90% (66-98%), with obvious heterogeneities in these two factors as demonstrated by different studies. The summary receiver operating characteristic (SROC) curve was plotted for mNGS as a function of LRTI, and the area under the curve (AUC) was 0.94. A Funnel plot with a p-value greater than 0.05 indicated the absence of publication bias. Positive and negative likelihood ratios (PLR and NLR) were >10 and > 0.1, respectively. In this pre-test probability-post-probability-likelihood ratio relationship graph, the values were Prior prob (%) = 20, Post-prob-Pos (%) = 77 and Post-prob-Neg (%) = 4.

CONCLUSION: The AUC value of SROC suggested a high accuracy of mNGS in diagnosis, with no publication bias and high reliability. The application of mNGS exhibits notable diagnostic efficacy in discerning pathogens present in bronchoalveolar lavage fluid (BALF) among patients afflicted with LRTI. However, mNGS is more meaningful for the definitive diagnosis of the disease rather than the exclusion of the disease. This post-test probability is significantly higher than the pre-test probability.}, } @article {pmid38148807, year = {2024}, author = {Fan, W and Fu, Q and Yu, Y}, title = {Pulmonary strongyloidiasis and hyperinfection in a Patient with idiopathic inflammatory myopathy：A case report.}, journal = {Heliyon}, volume = {10}, number = {1}, pages = {e23484}, pmid = {38148807}, issn = {2405-8440}, abstract = {Pulmonary strongyloidiasis is a rare infection in patients with autoimmune diseases, and immunosuppression can lead to the development of hyperinfection syndrome with a high mortality rate. We present a case of a 78-year-old male with previous idiopathic inflammatory myopathy (IIM) with interstitial lung disease. He developed hyperinfection syndrome and respiratory failure, and diagnostic metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) confirmed the presence of Strongyloides stercoralis. After treatment with ivermectin, the patient's symptoms improved. Therefore, adequate screening and prophylactic treatment are needed for people at risk of immunosuppression, which can reduce the occurrence of the devastating S. stercoralis hyperinfection syndrome. It also highlights mNGS as a highly accurate test for the detection of difficult to atypical pathogens.}, } @article {pmid38148773, year = {2023}, author = {Guo, Y and Li, X and Xiao, Q and Yang, J and Tao, R and Xu, L and Zhu, B}, title = {Mycobacterium colombiense Pneumonia in HIV-Infected Patients: Three Case Reports and a Literature Review.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {7767-7773}, pmid = {38148773}, issn = {1178-6973}, abstract = {BACKGROUND: Mycobacterium colombiense pneumonia in HIV-infected patients is relatively unusual but is associated with a high mortality rate, as well as high rates of misdiagnosis and delayed diagnosis. Clinical metagenome next-generation sequencing (mNGS) may have potential for its accurate and timely diagnosis.

CASE PRESENTATION: We retrospectively reviewed the medical records of three HIV-infected patients who presented with M. colombiense pneumonia in Zhejiang Province between January 2019 and December 2020. No specific clinical presentations or radiological manifestations were found in any of the patients. The detection of M. colombiense is 28-55 days earlier using mNGS on bronchoalveolar lavage fluid (BALF) compared to traditional culture methods. A combined treatment of rifabutin, clarithromycin, or azithromycin, and ethambutol did not provide timely relief of symptoms in these three patients. In the early stage of treatment, moxifloxacin and linezolid were used for several weeks. The average course of treatment for all three patients was close to 17 months.

CONCLUSION: We recommend early BALF mNGS for fast and accurate diagnosis of M. colombiense pneumonia in HIV-infected patients with low CD4 counts and long duration of symptoms. Further, moxifloxacin and linezolid may be beneficial in the early stage of treatment.}, } @article {pmid38148496, year = {2024}, author = {Wang, HT and Gan, QY and Li, G and Zhu, D}, title = {Effects of Zinc Thiazole and Oxytetracycline on the Microbial Metabolism, Antibiotic Resistance, and Virulence Factor Genes of Soil, Earthworm Gut, and Phyllosphere.}, journal = {Environmental science & technology}, volume = {58}, number = {1}, pages = {160-170}, doi = {10.1021/acs.est.3c06513}, pmid = {38148496}, issn = {1520-5851}, mesh = {Animals ; *Oxytetracycline/pharmacology ; *Oligochaeta/genetics ; Genes, Bacterial ; Zinc ; Soil ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Soil Microbiology ; }, abstract = {Pesticides and antibiotics are believed to increase the incidence of antibiotic resistance genes (ARGs) and virulence factor genes (VFGs), constituting a serious threat to global health. However, the impact of this combined pollution on the microbiome and that of the related ARGs and VFGs on soil-plant-animal systems remain unknown. In this study, a 60-day microcosm experiment was conducted to reveal the effects of zinc thiazole (ZT) and oxytetracycline (OTC) on microbial communities, antibiotic resistomes, and virulence factors in soil, earthworm gut, and phyllosphere samples using metagenomics. ZT exposure perturbed microbial communities and nutrient metabolism and increased the abundance of ARGs and VFGs in the gut. Combined exposure changed the profiles of ARGs and VFGs by decreasing microbial diversity in the phyllosphere. Host-tracking analysis identified some genera, such as Citrobacter and Aeromonas, as frequent hosts of ARGs and VFGs in the gut. Notably, some co-occurrence patterns of ARGs and MGEs were observed on the metagenome-assembled contigs. More importantly, ZT markedly increased the abundance of potentially drug-resistant pathogens Acinetobacter soli and Acinetobacter junii in the phyllosphere. Overall, this study expands our current understanding of the spread of ARGs and VFGs in soil-plant-animal systems under pollutant-induced stress and the associated health risks.}, } @article {pmid38147943, year = {2024}, author = {Ma, X and Qiu, Y and Mao, M and Lu, B and Zhao, H and Pang, Z and Li, S}, title = {PuRenDan alleviates type 2 diabetes mellitus symptoms by modulating the gut microbiota and its metabolites.}, journal = {Journal of ethnopharmacology}, volume = {322}, number = {}, pages = {117627}, doi = {10.1016/j.jep.2023.117627}, pmid = {38147943}, issn = {1872-7573}, mesh = {Rats ; Animals ; *Diabetes Mellitus, Type 2/metabolism ; Rats, Sprague-Dawley ; *Gastrointestinal Microbiome ; Blood Glucose ; Bacteria ; *Insulin Resistance ; Biomarkers ; }, abstract = {PuRenDan (PRD) is a traditional Chinese medicine formula comprising five herbs that have been traditionally used to treat type 2 diabetes mellitus (T2DM). While PRD has been shown to be effective in treating T2DM in clinical and animal studies, the mechanisms by which it works on the gut microbiome and metabolites related to T2DM are not well understood.

AIM OF THE STUDY: The objective of this study was to partially elucidate the mechanism of PRD in treating T2DM through analyses of the gut microbiota metagenome and metabolome.

MATERIALS AND METHODS: Sprague-Dawley rats were fed high-fat diets (HFDs) and injected with low-dose streptozotocin (STZ) to replicate T2DM models. Then the therapeutic effects of PRD were evaluated by measuring clinical markers such as blood glucose, insulin resistance (IR), lipid metabolism biomarkers (total cholesterol, low-density lipoprotein, non-esterified fatty acids, and triglycerides), and inflammatory factors (tumor necrosis factor alpha, interleukin-6 [IL-6], interferon gamma, and IL-1β). Colon contents were collected, and metagenomics, combined with ultra-high-performance liquid chromatography quadrupole time-of-flight mass spectrometry metabolic profiling, was performed to evaluate the effects of T2DM and PRD on gut microbiota and its metabolites in rats. Spearman analysis was used to calculate the correlation coefficient among different microbiota, clinical indices, and metabolites.

RESULTS: PRD exhibited significant improvement in blood glucose and IR, and reduced serum levels of lipid metabolism biomarkers and inflammatory factors. Moreover, the diversity and abundance of gut microbiota undergo significant changes in rats with T2DM that PRD was able to reverse. The gut microbiota associated with T2DM including Rickettsiaceae bacterium 4572_127, Psychrobacter pasteurii, Parabacteroides sp. CAG409, and Paludibacter propionicigenes were identified. The gut microbiota most closely related to PRD were Prevotella sp. 10(H), Parabacteroides sp. SN4, Flavobacteriales bacterium, Bacteroides massiliensis, Alistipes indistinctus, and Ruminococcus flavefaciens. Additionally, PRD regulated the levels of gut microbiota metabolites including pantothenic acid, 1-Methylhistamine, and 1-Methylhistidine; these affected metabolites were involved in pantothenate and coenzyme A biosynthesis, histidine metabolism, and secondary bile acid biosynthesis. Correlation analysis illustrated a close relationship among gut microbiota, its metabolites, and T2DM-related indexes.

CONCLUSION: Our study provides insights into the gut microbiota and its metabolites of PRD therapy for T2DM. It clarifies the role of gut microbiota and the metabolites in the pathogenesis of T2DM, highlighting the potential of PRD for the treatment of this disease.}, } @article {pmid38147751, year = {2023}, author = {Xu, JY and Ding, J and Du, S and Zhu, D}, title = {Tire particles and its leachates: Impact on antibiotic resistance genes in coastal sediments.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133333}, doi = {10.1016/j.jhazmat.2023.133333}, pmid = {38147751}, issn = {1873-3336}, abstract = {Tire particles (TPs), a significant group of microplastics, can be discharged into the coastal environments in various ways. However, our understanding of how TPs impact the antibiotic resistance and pathogenic risks of microorganisms in coastal sediments remains limited. In this study, we used metagenomics to investigate how TPs and their leachates could affect the prevalence of antibiotic resistance genes (ARGs), virulence factor genes (VFGs), and their potential risks to the living creatures such as soil invertebrates and microorganisms in the coastal sediments. We discovered that TP addition significantly increased the abundance and diversity of ARGs and VFGs in coastal sediments, with raw TPs displayed higher impacts than TP leachates and TPs after leaching on ARGs and VFGs. With increasing TP exposure concentrations, the co-occurrence frequency of ARGs and mobile genetic elements (MGEs) in the same contig also increased, suggesting that TPs could enhance the dispersal risk of ARGs. Our metagenome-based binning analysis further revealed that exposure to TPs increased the abundance of potentially pathogenic antibiotic-resistant bacteria (PARB). In addition, chemical additives of TP leachates (e.g., Zn and N-cyclohexylformamide) significantly affected the changes of ARGs in the pore water. In summary, our study provides novel insights into the adverse effects of TP pollutions on aggravating the dissemination and pathogenic risks of ARGs and PARB in the coastal environment.}, } @article {pmid38147199, year = {2023}, author = {Liu, L and Ji, T and Chen, R and Fan, L and Dai, J and Qiu, Y}, title = {High prevalence of pneumocystis pneumonia in interstitial lung disease: a retrospective study.}, journal = {Infection}, volume = {}, number = {}, pages = {}, pmid = {38147199}, issn = {1439-0973}, abstract = {BACKGROUND: Interstitial lung disease (ILD) is a new risk category for pneumocystis pneumonia (PCP) with a high mortality rate. The definite diagnostic criteria of PCP in ILD patients have not been established until now. The aims of this study were to identify potential risk factors of PCP in patients with ILD, and to evaluate the performance of metagenomic next-generation sequencing (mNGS), CD4 + T cell count, (1-3)-β-D-Glucan (BG) and lactate dehydrogenase (LDH) in the diagnosis of PCP in ILD patients.

METHODS: This is a retrospective, single-center, case-control study. ILD patients who underwent mNGS from December 2018 to December 2022 were included in the study. Based on the diagnosis criteria of PCP, these patients were divided into PCP-ILD and non-PCP-ILD groups. The potential risk factors for PCP occurrence in ILD patients were analysed via logistic regression. The diagnostic efficacy of mNGS was compared with serological biomarkers.

RESULTS: 92 patients with ILD were enrolled, 31 of which had a definite PCP and were assigned to the PCP-ILD group while 61 were to the non-PCP-ILD group. The infection rate of PJ in ILD patients was 33.7% (31/92). The history of glucocorticoid therapy, CD4 + T cell count, BG level and traction bronchiectasis on HRCT were associated with PCP occurrence in ILD patients. LDH level did not reach statistical significance in the logistic regression analysis. mNGS was confirmed as the most accurate test for PCP diagnosis in ILD patients.

CONCLUSION: ILD is a new risk group of PCP with high PCP prevalence. Clinicians should pay close attention to the occurrence of PCP in ILD patients who possess the risk factors of previous glucocorticoid therapy, decreased CD4 + T cell count, increased BG level and absence of traction bronchiectasis on HRCT. mNGS showed the most excellent performance for PCP diagnosis in ILD patients. Peripheral blood CD4 + T cell count and BG level are alternative diagnostic methods for PCP in ILD patients. However, the diagnostic value of serum LDH level was limited in ILD patients.}, } @article {pmid38147149, year = {2023}, author = {Zou, Y and Ro, KS and Jiang, C and Yin, D and Zhao, L and Zhang, D and Du, L and Xie, J}, title = {The anti-hyperuricemic and gut microbiota regulatory effects of a novel purine assimilatory strain, Lactiplantibacillus plantarum X7022.}, journal = {European journal of nutrition}, volume = {}, number = {}, pages = {}, pmid = {38147149}, issn = {1436-6215}, support = {No. 2021YFC2100300//National Key Research and Development Program of China/ ; No. 2020YFA0907800//National Key Research and Development Program of China/ ; No. 21ZR1416200//Natural Science Foundation of Shanghai Municipality/ ; }, abstract = {PURPOSE: Probiotics have been reported to effectively alleviate hyperuricemia and regulate the gut microbiota. The aim of this work was to study the in vivo anti-hyperuricemic properties and the mechanism of a novel strain, Lactiplantibacillus plantarum X7022.

METHODS: Purine content and mRNA expression of purine assimilation related enzymes were determined by HPLC and qPCR, respectively. Hyperuricemic mice were induced by potassium oxonate and hypoxanthine. Uric acid (UA), blood urea nitrogen, creatinine and renal inflammation were examined by kits. The expression of renal UA transporters was subjected to western blotting. Kidney tissues were sectioned for histological analysis. The fecal short-chain fatty acids (SCFAs) were determined by HPLC, and gut microbiota was investigated using the 16S rDNA metagenomic sequencing.

RESULTS: L. plantarum X7022 possesses a complete purine assimilation pathway and can exhaust xanthine, guanine, and adenine by 82.1%, 33.1%, and 12.6%, respectively. The strain exhibited gastrointestinal viability as 44% at the dose of 10[9] CFU/mL in mice. After four-week administration of the strain, a significant decrease of 35.5% in the serum UA level in hyperuricemic mice was achieved. The diminished contents of fecal propionate and butyrate were dramatically boosted. The treatment also alleviated renal inflammation and restored renal damage. The above physiological changes may due to the inhibited xanthine oxidase (XO) activity, as well as the expressional regulation of UA transporters (GLUT9, URAT1 and OAT1) to the normal level. Notably, gut microbiota dysbiosis in hyperuricemic mice was improved with the inflammation and hyperuricemia related flora depressed, and SCFAs production related flora promoted.

CONCLUSION: The strain is a promising probiotic strain for ameliorating hyperuricemia.}, } @article {pmid38146344, year = {2023}, author = {Chen, W and Zeng, Y and Liu, H and Sun, D and Liu, X and Xu, H and Wu, H and Qiu, B and Dang, Y}, title = {Granular activated carbon enhances volatile fatty acid production in the anaerobic fermentation of garden wastes.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {11}, number = {}, pages = {1330293}, pmid = {38146344}, issn = {2296-4185}, abstract = {Garden waste, one type of lignocellulosic biomass, holds significant potential for the production of volatile fatty acids (VFAs) through anaerobic fermentation. However, the hydrolysis efficiency of garden waste is limited by the inherent recalcitrance, which further influences VFA production. Granular activated carbon (GAC) could promote hydrolysis and acidogenesis efficiency during anaerobic fermentation. This study developed a strategy to use GAC to enhance the anaerobic fermentation of garden waste without any complex pretreatments and extra enzymes. The results showed that GAC addition could improve VFA production, especially acetate, and reach the maximum total VFA yield of 191.55 mg/g VSadded, which increased by 27.35% compared to the control group. The highest VFA/sCOD value of 70.01% was attained in the GAC-amended group, whereas the control group only reached 49.35%, indicating a better hydrolysis and acidogenesis capacity attributed to the addition of GAC. Microbial community results revealed that GAC addition promoted the enrichment of Caproiciproducens and Clostridium, which are crucial for anaerobic VFA production. In addition, only the GAC-amended group showed the presence of Sphaerochaeta and Oscillibacter genera, which are associated with electron transfer processes. Metagenomics analysis indicated that GAC addition improved the abundance of glycoside hydrolases (GHs) and key functional enzymes related to hydrolysis and acidogenesis. Furthermore, the assessment of major genera influencing functional genes in both groups indicated that Sphaerochaeta, Clostridium, and Caproicibacter were the primary contributors to upregulated genes. These findings underscored the significance of employing GAC to enhance the anaerobic fermentation of garden waste, offering a promising approach for sustainable biomass conversion and VFA production.}, } @article {pmid38146029, year = {2023}, author = {Johnson, J and Jain, KR and Patel, A and Parmar, N and Joshi, C and Madamwar, D}, title = {Chronic industrial perturbation and seasonal change induces shift in the bacterial community from gammaproteobacteria to betaproteobacteria having catabolic potential for aromatic compounds at Amlakhadi canal.}, journal = {World journal of microbiology & biotechnology}, volume = {40}, number = {2}, pages = {52}, pmid = {38146029}, issn = {1573-0972}, support = {BT/1/CEIB/09/V/05//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {Humans ; *Gammaproteobacteria/genetics ; *Betaproteobacteria/genetics/metabolism ; Seasons ; Bacteria/metabolism ; *Microbiota/genetics ; Organic Chemicals/metabolism ; }, abstract = {Escalating proportions of industrially contaminated sites are one of the major catastrophes faced at the present time due to the industrial revolution. The difficulties associated with culturing the microbes, has been circumvent by the direct use of metagenomic analysis of various complex niches. In this study, a metagenomic approach using next generation sequencing technologies was applied to exemplify the taxonomic abundance and metabolic potential of the microbial community residing in Amlakhadi canal, Ankleshwar at two different seasons. All the metagenomes revealed a predominance of Proteobacteria phylum. However, difference was observed within class level where Gammaproteobacteria was relatively high in polluted metagenome in Summer while in Monsoon the abundance shifted to Betaproteobacteria. Similarly, significant statistical differences were obtained while comparing the genera amongst contaminated sites where Serratia, Achromobacter, Stenotrophomonas and Pseudomonas were abundant in summer season and the dominance changed to Thiobacillus, Thauera, Acidovorax, Nitrosomonas, Sulfuricurvum, Novosphingobium, Hyphomonas and Geobacter in monsoon. Further upon functional characterization, the microbiomes revealed the diverse survival mechanisms, in response to the prevailing ecological conditions (such as degradation of aromatic compounds, heavy metal resistance, oxidative stress responses and multidrug resistance efflux pumps, etc.). The results have important implications in understanding and predicting the impacts of human-induced activities on microbial communities inhabiting natural niche and their responses in coping with the fluctuating pollution load.}, } @article {pmid38145852, year = {2023}, author = {Zhang, F and Guo, L and Shi, J and Jiang, H and Zhou, F and Zhou, Y and Lv, B and Xu, M}, title = {Choline metabolism in regulating inflammatory bowel disease-linked anxiety disorders: A multi-omics exploration of the gut-brain axis.}, journal = {Neurobiology of disease}, volume = {191}, number = {}, pages = {106390}, doi = {10.1016/j.nbd.2023.106390}, pmid = {38145852}, issn = {1095-953X}, abstract = {Anxiety and depression caused by inflammatory bowel disease (IBD) negatively affect the mental health of patients. Emerging studies have demonstrated that the gut-brain axis (GBA) mediates IBD-induced mood disorders, but the underlying mechanisms of these findings remain unknown. Therefore, it's vital to conduct comprehensive research on the GBA in IBD. Multi-omics studies can provide an understanding of the pathological mechanisms of the GBA in the development of IBD, helping to uncover the mechanisms underlying the onset and progression of the disease. Thus, we analyzed the prefrontal cortex (PFC) of Dextran Sulfate Sodium Salt (DSS)-induced IBD mice using transcriptomics and metabolomics. We observed increased mRNA related to acetylcholine synthesis and secretion, along with decreased phosphatidylcholine (PC) levels in the PFC of DSS group compared to the control group. Fecal metagenomics also revealed abnormalities in the microbiome and lipid metabolism in the DSS group. Since both acetylcholine and PC are choline metabolites, we posited that the DSS group may experience choline deficiency and choline metabolism disorders. Subsequently, when we supplemented CDP-choline, IBD mice exhibited improvements, including decreased anxiety-like behaviors, reduced PC degradation, and increased acetylcholine synthesis in the PFC. In addition, administration of CDP-choline can restore imbalances in the gut microbiome and disruptions in lipid metabolism caused by DSS treatment. This study provides compelling evidence to suggest that choline metabolism plays a crucial role in the development and treatment of mood disorders in IBD. Choline and its metabolites appear to have a significant role in maintaining the stability of the GBA.}, } @article {pmid38145816, year = {2023}, author = {G, R and K, C and Aranega-Bou, P and A, R and G, M and Kl, H and S, H and As, W and N, S}, title = {A workflow for the detection of antibiotic residues, measurement of water chemistry and preservation of hospital sink drain samples for metagenomic sequencing.}, journal = {The Journal of hospital infection}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jhin.2023.11.021}, pmid = {38145816}, issn = {1532-2939}, abstract = {BACKGROUND: Hospital sinks are environmental reservoirs that harbour healthcare-associated (HCA) pathogens. Selective pressures in sink environments, such as antibiotic residues, nutrient waste and hardness ions, may promote antibiotic resistance gene (ARG) exchange between bacteria. However, cheap and accurate sampling methods to characterise these factors are lacking.

AIM: To validate a workflow to detect antibiotic residues and evaluate water chemistry using dipsticks. Secondarily, to validate boric acid to preserve the taxonomic and ARG ("resistome") composition of sink trap samples for metagenomic sequencing.

METHODS: Antibiotic residue dipsticks were validated against serial dilutions of ampicillin, doxycycline, sulfamethoxazole and ciprofloxacin, and water chemistry dipsticks against serial dilutions of chemical calibration standards. Sink trap aspirates were used for a "real-world" pilot evaluation of dipsticks. To assess boric acid as a preservative of microbial diversity, the impact of incubation with and without boric acid at ∼22°C on metagenomic sequencing outputs was evaluated at Day 2 and Day 5 compared with baseline (Day 0).

FINDINGS: The limits of detection for each antibiotic were: 3μg/L (ampicillin), 10μg/L (doxycycline), 20μg/L (sulfamethoxazole) and 8μg/L (ciprofloxacin). The best performing water chemistry dipstick correctly characterised 34/40 (85%) standards in a concentration-dependent manner. One trap sample tested positive for the presence of tetracyclines and sulfonamides. Taxonomic and resistome composition were largely maintained after storage with boric acid at ∼22°C for up to five days.

CONCLUSIONS: Dipsticks can be used to detect antibiotic residues and characterise water chemistry in sink trap samples. Boric acid was an effective preservative of trap sample composition, representing a low-cost alternative to cold-chain transport.}, } @article {pmid38145758, year = {2024}, author = {Wu, J and Hu, Q and Rao, X and Zhao, H and Tang, H and Wang, Y}, title = {Gut microbiome and metabolic profiles of mouse model for MeCP2 duplication syndrome.}, journal = {Brain research bulletin}, volume = {206}, number = {}, pages = {110862}, doi = {10.1016/j.brainresbull.2023.110862}, pmid = {38145758}, issn = {1873-2747}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Mice, Transgenic ; Disease Models, Animal ; Metabolome ; Neurotransmitter Agents ; *Mental Retardation, X-Linked ; }, abstract = {The extra copy of the methyl-CpG-binding protein 2 (MeCp2) gene causes MeCP2 duplication syndrome (MDS), a neurodevelopmental disorder characterized by intellectual disability and autistic phenotypes. However, the disturbed microbiome and metabolic profiling underlying the autistic-like behavioral deficits of MDS are rarely investigated. Here we aimed to understand the contributions of microbiome disruption and associated metabolic alterations, especially the disturbed neurotransmitters in MDS employing a transgenic mouse model with MeCP2 overexpression. We analyzed metabolic profiles of plasma, urine, and cecum content and microbiome profiles by both 16 s RNA and shotgun metagenomics sequence technology. We found the decreased levels of Firmicutes and increased levels of Bacteroides in the single MeCP2 gene mutation autism-like mouse model, demonstrating the importance of the host genome in a selection of microbiome, leading to the heterogeneity characteristics of microbiome in MDS. Furthermore, the changed levels of several neurotransmitters (such as dopamine, taurine, and glutamate) implied the excitatory-inhibitory imbalance caused by the single gene mutation. Concurrently, a range of microbial metabolisms of aromatic amino acids (such as tryptophan and phenylalanine) were identified in different biological matrices obtained from MeCP2 transgenic mice. Our investigation revealed the importance of genetic variation in accounting for the differences in microbiomes and confirmed the bidirectional regulatory axis of microbiota-gut-brain in studying the role of microbiome on MDS, which could be useful in deeply understanding the microbiome-based treatment in this autistic-like disease.}, } @article {pmid38145697, year = {2023}, author = {Merker Breyer, G and De Carli, S and Rocha Jacques Da Silva, ME and Dias, ME and Muterle Varela, AP and Bertoni Mann, M and Frazzon, J and Quoos Mayer, F and Góes Neto, A and Maboni Siqueira, F}, title = {Alternative amplicon-PCR protocol for maximizing bacterial and fungal sequencing in low-biomass samples.}, journal = {Analytical biochemistry}, volume = {687}, number = {}, pages = {115449}, doi = {10.1016/j.ab.2023.115449}, pmid = {38145697}, issn = {1096-0309}, abstract = {Determining bacterial and fungal communities from low-biomass samples remains a challenge for high-throughput sequencing. Due to the low microbial load and host contamination, some sites, including the female upper reproductive tract and the lower respiratory tract, were even considered sterile until recent years. Despite efforts to improve sampling and DNA isolation protocols, some samples provide insufficient microbial DNA input for library preparation and sequencing. Herein, we propose an alternative amplicon-PCR protocol to be used in bacterial and fungal sequencing in low-biomass samples, targeting 16S-rDNA and the internal transcribed spacer region (ITS), respectively. Similar to a nested-PCR, we performed two sequential PCR reactions to maximise the target amplicon. We compared metagenomic results from the original Illumina protocol (Protocol 1 - P1) and the alternative one (Protocol 2 - P2), using a mock community and clinical samples with different microbial loads. Our findings showed no significant differences in data generated by P1 and P2, indicating that the second amplification round does not bias the microbiota diversity rates. Thus, the alternative protocol can be applied for low-biomass samples when the original protocol results in spurious output, preventing library preparation and sequencing.}, } @article {pmid38145402, year = {2023}, author = {Zimmermann, P and Pittet, LF and Jakob, W and Messina, NL and Falquet, L and Curtis, N}, title = {The Effect of Bacille Calmette-Guérin Vaccination on the Composition of the Intestinal Microbiome in Neonates From the MIS BAIR Trial.}, journal = {The Pediatric infectious disease journal}, volume = {}, number = {}, pages = {}, pmid = {38145402}, issn = {1532-0987}, support = {grants GNT1051228 and GNT1099680//Institut National de la Santé et de la Recherche Médicale/ ; }, abstract = {INTRODUCTION: The early-life intestinal microbiome plays an important role in the development and regulation of the immune system. It is unknown whether the administration of vaccines influences the composition of the intestinal microbiome.

OBJECTIVE: To investigate whether Bacille Calmette-Guérin (BCG) vaccine given in the first few days of life influences the abundance of bacterial taxa and metabolic pathways in the intestinal microbiome at 1 week of age.

METHODS: Healthy, term-born neonates were randomized at birth to receive BCG or no vaccine within the first few days of life. Stool samples were collected at 1 week of age from 335 neonates and analyzed using shotgun metagenomic sequencing and functional analyses.

RESULTS: The composition of the intestinal microbiome was different between neonates born by cesarean section (CS) and those born vaginally. Differences in the composition between BCG-vaccinated and BCG-naïve neonates were only minimal. CS-born BCG-vaccinated neonates had a higher abundance of Staphylococcus lugdunensis compared with CS-born BCG-naïve neonates. The latter had a higher abundance of Streptococcus infantis and Trabulsiella guamensis. Vaginally-born BCG-vaccinated neonates had a higher abundance of Clostridiaceae and Streptococcus parasanguinis compared with vaginally-born BCG-naïve neonates, and a lower abundance of Veillonella atypica and Butyricimonas faecalis. Metabolic pathways that were differently abundant between BCG-vaccinated and BCG-naïve neonates were mainly those involved in sugar degradation and nucleotide/nucleoside biosynthesis.

CONCLUSION: BCG given in the first few days of life has little effect on the composition of the intestinal microbiome at 1 week of age but does influence the abundance of certain metabolic pathways.}, } @article {pmid38145055, year = {2023}, author = {Zhou, DT and Mudhluli, TE and Hall, LJ and Manasa, J and Munyati, S}, title = {A Scoping Review of Gut Microbiome and Bifidobacterium Research in Zimbabwe: Implications for Future Studies.}, journal = {Pediatric health, medicine and therapeutics}, volume = {14}, number = {}, pages = {483-496}, pmid = {38145055}, issn = {1179-9927}, abstract = {BACKGROUND: Gut microbiota play a key role in host health, with certain Bifidobacterium strains critical for immune development. The healthy gut of breastfed infants is dominated by these pioneer microbes, especially the strains that feed on human milk oligosaccharides.

OBJECTIVE: This is a scoping review of gut microbiome research from Zimbabwe. It focuses on distribution and dynamic changes of bifidobacteria, and milk components that promote growth of microbes in infants, together with the distribution of associated gut microbes in adults.

DESIGN: Online databases were searched for publications from 2000 to 2023.

RESULTS AND ANALYSIS: Fourteen publications on microbiota of infants and adults were included in this scoping review. Most were cross-sectional, while three were clinical trials/cohort protocols. Publications focused on pediatrics (78.5%), pregnant women (14.3%), and men (7.2%). Zimbabwe has a high burden of HIV; hence 35.7% of study populations were delineated by HIV status. The laboratory methods used included shotgun metagenomics (62%) or 16S rRNA gene amplicon sequencing. Almost 85% of the studies focused on total microbiome profiles and rarely reported the distribution of different Bifidobacterium species and variants. None of the papers studied human breast milk composition. There were reports of reduced abundance of beneficial genera in pregnant women, children, and adolescents living with HIV. Additionally, gut microbiota was reported to be poorly predictive of child growth and vaccine response, though this was not conclusive.

CONCLUSION: There are few studies that characterize the gut microbiome by Zimbabwe-based researchers. However, studies on strain level diversity of Bifidobacterium and other key microbes, and their role in health during and beyond infancy, lag behind in Zimbabwe and other low- and middle-income countries. Such cohorts are needed to inform future mechanistic studies and downstream translational work such as next-generation probiotics and prebiotics.}, } @article {pmid38145053, year = {2023}, author = {Hao, J and Li, W and Wang, Y and Zhao, J and Chen, Y}, title = {Clinical utility of metagenomic next-generation sequencing in pathogen detection for lower respiratory tract infections and impact on clinical outcomes in southernmost China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1271952}, pmid = {38145053}, issn = {2235-2988}, mesh = {Humans ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Antimicrobial Stewardship ; China ; Haemophilus influenzae ; Metagenomics ; *Respiratory Tract Infections/diagnosis ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Today, metagenomic next-generation sequencing (mNGS) has emerged as a diagnostic tool for infections. However, since Hainan has a complicated pathogen spectrum, the diagnostic value and impact on patient outcomes of mNGS in Hainan are to be explored.

METHODS: From April 2020 to October 2021, 266 suspected lower respiratory tract infections (LRTIs) patients in Hainan were enrolled, and specimens were collected before antibiotic treatment. Bronchoalveolar lavage fluid (BALF) samples were subjected to mNGS and culture to compare the diagnostic performance. Other conventional microbiological tests (CMT) were also performed. Patients' treatments and clinical outcomes were recorded, and the antibiotic resistance genes (ARGs) were detected via mNGS workflow.

RESULTS: The positive rate of mNGS outperformed that of culture (87.55% vs. 39.30%, p<0.001) and CMT (87.12% vs. 52.65%, p<0.001). Specifically, mNGS detected more P. aeruginosa (12.03% vs 9.02%, p<0.05), H. influenzae (9.77% vs 2.26%, p<0.001), Aspergillus fumigatus (3.00% vs 0.75%, p<0.05), Candida albicans (26.32% vs 7.52%, p<0.001) and uncommon pathogens. It also demonstrated great diagnostic advantages in Mycobacterium tuberculosis with 80% sensitivity and 97.4% specificity. Over half of the patients (147, 55.26%) had modified empirical treatment according to mNGS results and 89.12% of them responded well. For three deaths with modified treatment, multiple drug resistance was predicted by mNGS and confirmed by antibiotic susceptibility test.

CONCLUSIONS: The application of mNGS can benefit clinics in pathogen identification and antimicrobial treatment stewardship. Physicians should be alert to some emerging uncommon pathogens, including Chlamydia Psittaci, Nocardia otitidiscaviarum, and rare NTM.}, } @article {pmid38145049, year = {2023}, author = {Lemons, JMS and Narrowe, AB and Liu, L and Firrman, J and Mahalak, KK and Van den Abbeele, P and Baudot, A and Deyaert, S and Li, Y and Yu, LL}, title = {Impact of Baizhu, Daqingye, and Hehuanhua extracts on the human gut microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1298392}, pmid = {38145049}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Drugs, Chinese Herbal/pharmacology/chemistry ; Medicine, Chinese Traditional ; }, abstract = {INTRODUCTION: In traditional Chinese medicine, the rhizome of Atractylodes macrocephala (Baizhu), the leaves of Isatis indigotica (Daqingye), and the flowers of Albizia julibrissin (Hehuanhua) have been used to treat gastrointestinal illnesses, epidemics, and mental health issues. Modern researchers are now exploring the underlying mechanisms responsible for their efficacy. Previous studies often focused on the impact of purified chemicals or mixed extracts from these plants on cells in tissue culture or in rodent models.

METHODS: As modulation of the human gut microbiome has been linked to host health status both within the gastrointestinal tract and in distant tissues, the effects of lipid-free ethanol extracts of Baizhu, Daqingye, and Hehuanhua on the human adult gut microbiome were assessed using Systemic Intestinal Fermentation Research (SIFR[®]) technology (n=6).

RESULTS AND DISCUSSION: Baizhu and Daqingye extracts similarly impacted microbial community structure and function, with the extent of effects being more pronounced for Baizhu. These effects included decreases in the Bacteroidetes phylum and increases in health-related Bifidobacterium spp. and short chain fatty acids which may contribute to Baizhu's efficacy against gastrointestinal ailments. The changes upon Hehuanhua treatment were larger and included increases in multiple bacterial species, including Agathobaculum butyriciproducens, Adlercreutzia equolifaciens, and Gordonibacter pamelaeae, known to produce secondary metabolites beneficial to mental health. In addition, many of the changes induced by Hehuanhua correlated with a rise in Enterobacteriaceae spp., which may make the tested dose of this herb contraindicated for some individuals. Overall, there is some evidence to suggest that the palliative effect of these herbs may be mediated, in part, by their impact on the gut microbiome, but more research is needed to elucidate the exact mechanisms.}, } @article {pmid38144226, year = {2023}, author = {Chen, SX and Lin, R and Shi, JL and Lin, W and Yu, XF and Chen, JY}, title = {Pathogenic Profile Characteristics and Clinical Risk Factor Analysis of Patients Who Died from Sepsis Combined with Pulmonary Infection by Metagenomic Next-Generation Sequencing.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {7695-7705}, pmid = {38144226}, issn = {1178-6973}, abstract = {INTRODUCTION: Sepsis is one of the major diseases that seriously threatens human health, and its incidence and in-hospital morbidity and mortality rates remain high. Applying metagenomic next-generation sequencing (mNGS) technology to analyze the differences in pathogenic profiles and clinical factors in patients surviving and dying from sepsis combined with pulmonary infections provides diagnostic value and application for clinical purposes.

METHODS: Sixty-three BALF samples from patients with sepsis combined with pulmonary infection from Fuqing Hospital Affiliated to Fujian Medical University were collected, and all of them were tested by simultaneous mNGS and conventional microbial combined test (CMT) to compare the pathogenic profiles and clinical indices of patients who survived and died of sepsis combined with pulmonary infection and to further compare the diagnostic differences between mNGS and CMT in patients who survived and died of sepsis combined with pulmonary infection. We analyzed the diagnostic value of mNGS for sepsis combined with pulmonary infection.

RESULTS: A total of 141 strains of pathogens were isolated from 63 samples of patients with sepsis combined with pneumonia at suspected infection sites, Klebsiella pneumoniae, Acinetobacter baumannii, and Stenotrophomonas maltophilia are predominant, and higher ApacheII, LAC, P and PT are all risk factors affecting the death of septic patients.

CONCLUSION: Applying the mNGS method to patients with sepsis combined with pneumonia can improve the positive detection rate of pathogenic microorganisms and focus on death-related risk factors such as pathogenic bacteria species as well as clinical laboratory indices, which can guide clinicians to take appropriate measures to treat patients with sepsis and reduce the occurrence of death.}, } @article {pmid38144203, year = {2023}, author = {Hu, M and Liu, L}, title = {Choline regulation of triglycerides synthesis through ubiquintination pathway in MAC-T cells.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16611}, pmid = {38144203}, issn = {2167-8359}, mesh = {Female ; Animals ; Cattle ; *Milk/metabolism ; *T-Lymphocytes/metabolism ; Lipogenesis ; Ubiquitination ; Triglycerides/metabolism ; }, abstract = {This study aims to investigate the regulatory mechanism of choline (CH) on triglyceride (TG) synthesis in cows, with a specific focus on its potential association with high milk fat percentage in the gut of the Zhongdian yak. By employing combined metagenomics and metabolomics analysis, we establish a correlation between CH and milk fat production in yaks. Bovine mammary epithelial cells (MAC-T) were exposed to varying CH concentrations, and after 24 h, we analyzed the expression levels of key proteins (membrane glycoprotein CD36 (CD36); adipose differentiation-related protein (ADFP); and ubiquintin (UB)), cellular TG content, lipid droplets, and cell vitality. Additionally, we evaluated the genes potentially related to the CH-mediated regulation of TG synthesis using real-time qPCR. CH at 200 μM significantly up-regulated CD36, ADFP, UB, and TG content. Pathway analysis reveals the involvement of the ubiquitination pathway in CH-mediated regulation of TG synthesis. These findings shed light on the role of CH in controlling TG synthesis in MAC-T cells and suggest its potential as a feed additive for cattle, offering possibilities to enhance milk fat production efficiency and economic outcomes in the dairy industry.}, } @article {pmid38143861, year = {2023}, author = {Gastineau, R and Harðardóttir, S and Guilmette, C and Lemieux, C and Turmel, M and Otis, C and Boyle, B and Levesque, RC and Gauthier, J and Potvin, M and Lovejoy, C}, title = {Mitochondrial genome sequence of the protist Ancyromonas sigmoides Kent, 1881 (Ancyromonadida) from the Sugluk Inlet, Hudson Strait, Nunavik, Québec.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1275665}, pmid = {38143861}, issn = {1664-302X}, abstract = {INTRODUCTION: There is little information on evolutionarily ancient eukaryotes, which are often referred to as basal eukaryotes, in Arctic waters. Despite earlier studies being conducted in the Russian White Sea, only few have been reported.

METHODS: Following a shotgun sequence survey of diatom cultures from Sugluk Inlet off the Hudson Strait in Northern Québec, we obtained the complete mitochondrial genome and the operon of nuclear ribosomal RNA genes from a strain that matches that of Ancyromonas sigmoides (Kent, 1881).

RESULTS: The sequence of the mitogenome retrieved was 41,889 bp in length and encoded 38 protein-coding genes, 5 non-conserved open-reading frames, and 2 rRNA and 24 tRNA genes. The mitogenome has retained sdh2 and sdh3, two genes of the succinate dehydrogenase complex, which are sometimes found among basal eukaryotes but seemingly missing among the Malawimonadidae, a lineage sister to Ancyromonadida in some phylogenies. The phylogeny inferred from the 18S rRNA gene associated A. sigmoides from Sugluk Inlet with several other strains originating from the Arctic. The study also unveiled the presence of a metagenomic sequence ascribed to bacteria in GenBank, but it was clearly a mitochondrial genome with a gene content highly similar to that of A. sigmoides, including the non-conserved open-reading frames.

DISCUSSION: After re-annotation, a phylogeny was inferred from mitochondrial protein sequences, and it strongly associated A. sigmoides with the misidentified organism, with the two being possibly conspecific or sibling species as they are more similar to one another than to species of the genus Malawimonas. Overall our phylogeny showed that the ice associated ancryomonads were clearly distinct from more southerly strains.}, } @article {pmid38143446, year = {2023}, author = {Boualam, MA and Corbara, AG and Aboudharam, G and Istria, D and Signoli, M and Costedoat, C and Drancourt, M and Pradines, B}, title = {The millennial dynamics of malaria in the mediterranean basin: documenting Plasmodium spp. on the medieval island of Corsica.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1265964}, pmid = {38143446}, issn = {2296-858X}, abstract = {INTRODUCTION: The lack of well-preserved material upon which to base the paleo-microbiological detection of Plasmodium parasites has prevented extensive documentation of past outbreaks of malaria in Europe. By trapping intact erythrocytes at the time of death, dental pulp has been shown to be a suitable tissue for documenting ancient intraerythrocytic pathogens such as Plasmodium parasites.

METHODS: Total DNA and proteins extracted from 23 dental pulp specimens collected from individuals exhumed from the 9th to 13th century archaeological site in Mariana, Corsica, were analyzed using open-mind paleo-auto-immunohistochemistry and direct metagenomics, Plasmodium-targeting immunochromatography assays. All experiments incorporated appropriate negative controls.

RESULTS: Paleo-auto-immunohistochemistry revealed the presence of parasites Plasmodium spp. in the dental pulp of nine teeth. A further immunochromatography assay identified the presence of at least one Plasmodium antigen in nine individuals. The nine teeth, for which the PfHRP-2 antigen specific of P. falciparum was detected, were also positive using paleo-autoimmunohistochemistry and metagenomics.

CONCLUSION: Dental pulp erythrocytes proved to be suitable for the direct paleomicrobiology documentation of malaria in nine individuals buried in medieval Corsica, in agreement with historical data. This provides additional information on the millennial dynamics of Plasmodium spp. in the Mediterranean basin.}, } @article {pmid38142991, year = {2023}, author = {Sun, F and Yang, H and Zhang, X and Tan, F and Wang, G and Shi, Q}, title = {Metagenomic and metabolomic analysis of the effect of bleaching on unsaturated fatty acid synthesis pathways in coral symbionts.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169487}, doi = {10.1016/j.scitotenv.2023.169487}, pmid = {38142991}, issn = {1879-1026}, abstract = {Unsaturated fatty acids (UFAs) are known to play a vital role in regulating stress resistance and metabolism in corals. Nevertheless, a comprehensive understanding of the microbial and functional composition of the UFA synthesis pathway (UFASP) remains lacking. This study employed metagenome and metabolome to investigate the microbial community, function, and metabolic response of UFASP in reef-building corals inhabiting the Nansha Islands. Our findings revealed significantly higher diversity for the UFASP microbe in bleached corals compared to unbleached corals. Furthermore, principal coordinates analysis (PCoA) and taxonomy assessments exhibited notable distinctions in the microbe between the two coral states. Notably, the dominant microorganisms involved in UFASP were Dinophyceae, Sordariomycetes, Ulvophyceae, and Chlorophyceae. Bleaching resulted in a considerable increase in fungal abundance within coral symbionts. A total of 12 KEGG Orthology (KO) were identified in UFASP, with PCoA analysis indicating significant differences in their abundance between bleached and unbleached corals. UFASP's beta-Oxidation module exhibited reduced abundance in bleached corals. Contribution analysis highlighted the participation of Symbiodiniaceae, Ascomycota, Chlorophyta, Proteobacteria, and Actinobacteria in UFASP. Notably, Symbiodiniaceae and Ascomycota were the major contributors to two UFASP modules, with the latter displaying greater involvement in bleached corals. Furthermore, significant differences in n3 and n6-family metabolites were observed between bleached and unbleached corals. Notably, bleaching induced a reduction in metabolites of Symbiodiniaceae, while an increase in the multiple UFAs abundance was detected in bleached corals. These findings suggest that bleaching-induced alterations coral symbionts composition directly impact the functionality of UFASP, ultimately affecting the corals' capacity to adapt to stress.}, } @article {pmid38142507, year = {2023}, author = {Lu, Z and Cai, Q and Lai, S and Chen, N and Huang, L and Liu, Y and Lei, L and Gan, S and Zhang, L and Paerl, HW and Wang, F}, title = {Coupling of cylindrospermopsin and pho-harboring Verrucomicrobia supports the formation of Raphidiopsis blooms in low-phosphorus waters.}, journal = {Water research}, volume = {250}, number = {}, pages = {121010}, doi = {10.1016/j.watres.2023.121010}, pmid = {38142507}, issn = {1879-2448}, abstract = {Cylindrospermopsin (CYN) can induce phytoplankton community to secrete alkaline phosphatase (ALP), which is one of the important strategies for the bloom-forming cyanobacterium Raphidiopsis to thrive in extremely low-phosphorus (P) waters. However, how bacterioplankton community, another major contributor to ALPs in waters, couples to Raphidiopsis through CYN, and the role of this coupling in supporting the dominance of Raphidiopsis in nature remain largely unknown. Here, we conducted microcosm experiments to address this knowledge gap, using a combination of differential filtration-based and metagenomics-based methods to identify the sources of ALPs. We found that, compared with algal-derived ALPs, bacteria-derived ALPs exhibited a more pronounced and sensitive response to CYN. This response to CYN was enhanced under low-P conditions. Interestingly, we found that Verrucomicrobia made the largest contribution to the total abundance of pho genes, which encode ALPs. Having high gene abundance of the CYN-sensing PI3K-AKT signaling pathway, Verrucomicrobia's proportion increased with higher concentrations of CYN under low-P conditions, thereby explaining the observed increase in pho gene abundance. Compared with other cyanobacterial genera, Raphidiopsis had a higher abundance of the pst gene. This suggests that Raphidiopsis exhibited a greater capacity to uptake the inorganic P generated by ALPs secreted by other organisms. Overall, our results reveal the mechanism of CYN-induced ALP secretion and its impact on planktonic P-cycling, and provide valuable insights into the role of CYN in supporting the formation of Raphidiopsis blooms.}, } @article {pmid38141936, year = {2024}, author = {Chen, M and Cai, Y and Wang, L and Jiang, Y and Qian, J and Qin, J and Xu, J and Li, J and Yu, S and Shen, B}, title = {Metagenomic next-generation sequencing testing from the perspective of clinical benefits.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {553}, number = {}, pages = {117730}, doi = {10.1016/j.cca.2023.117730}, pmid = {38141936}, issn = {1873-3492}, mesh = {Humans ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; Sensitivity and Specificity ; }, abstract = {BACKGROUND AND AIMS: Metagenomic next-generation sequencing (mNGS) provided promising supports to rapid pathogen diagnosis. However, summary of scientific application strategy based on clinical practice study is still necessary for enhancing clinical benefits.

MATERIALS AND METHODS: We conducted a retrospective analysis of 775 samples from patients with suspected infectious diseases (IDs). Based on final diagnosis, diagnostic performance, clinical relevance and clinical impact of mNGS among various clinical settings were assessed, and influencing factors were deeply explored.

RESULTS: 84.26 % tests were clinically relevant; sample, but not sequencing, was the influencing factor. 40.77 % tests contributed to positive clinical impact, while 0.13 % and 59.10 % to negative and no impact respectively. mNGS utility in patients with IDs, definite infection site, BALF and CSF contributed to higher positive impacts. Days of empirical treatment before sampling ≤ 5 in ICU and ≤ 2 or between 11 and 20 in non-ICU, and reporting in 2 days brought about higher clinical benefit rates. Characteristic pathogen spectrum between ICU and non-ICU cases were revealed.

CONCLUSIONS: Our findings highlighted clinical benefits from mNGS varied among different clinical settings, and elucidated choices on patients, samples, sampling and reporting time were four key factors. Rational strategy should be concerned to promote scientific application of mNGS and better improve clinical value.}, } @article {pmid38141330, year = {2023}, author = {Mo, H and Chen, X and Tang, M and Qu, Y and Li, Z and Liu, W and Yang, C and Chen, Y and Sun, J and Yang, H and Du, G}, title = {Expression of a thermostable glucose-stimulated β-glucosidase from a hot-spring metagenome and its promising application to produce gardenia blue.}, journal = {Bioorganic chemistry}, volume = {143}, number = {}, pages = {107036}, doi = {10.1016/j.bioorg.2023.107036}, pmid = {38141330}, issn = {1090-2120}, abstract = {This study reports a thermostable glucose-stimulated β-glucosidase, BglY442, from hot-spring metagenomic data that was cloned and expressed in Escherichia coli BL21 (DE3). The molecular mass of recombinant BglY442 was 69.9 kDa and was used in the production of gardenia blue. The recombinant BglY442 showed its maximum activity at pH 6.0 and 75 °C, maintained 50 % activity at 70 °C for 36 h, presented over 90 % activity in a broad pH range and a wide range of pH stability. Moreover, BglY442 exhibited excellent tolerance toward methanol and ethanol. The specific activity of BglY442 was 235 U/mg at pH 6.0 and 75 °C with 10 mM pNPG as substrate. BglY442 activity increased by over fourfold with 2 M glucose or xylose. Specifically, the enzyme kinetics of BglY442 seem to be non-Michaelis-Menten kinetics or atypical kinetics because the Michaelis-Menten saturation kinetics were not observed with pNPG, oNPG or geniposide as substrates. Under optimum conditions, geniposide was dehydrated by BglY442 and reacted with nine amino acids respectively by the one-pot method. Only the Arg or Met derived pigments showed bright blue, and these two pigments had similar ultraviolet absorption spectra. The OD590 nm of GB was detected to be 1.06 after 24 h with the addition of Arg and 1.61 after 36 h with the addition of Met. The intermediate was elucidated and identified as ginipin. Molecular docking analysis indicated that the enzyme had a similar catalytic mechanism to the reported GH1 Bgls. BglY442 exhibited potential for gardenia blue production by the one-pot method. With outstanding thermostability and glucose tolerance, BglY442 should be considered a potential β-glucosidase in biotechnology applications.}, } @article {pmid38141256, year = {2023}, author = {Hassan-Zahraee, M and Ye, Z and Xi, L and Dushin, E and Lee, J and Romatowski, J and Leszczyszyn, J and Danese, S and Sandborn, WJ and Banfield, C and Gale, JD and Peeva, E and Longman, RS and Hyde, CL and Hung, KE}, title = {Baseline serum and stool microbiome biomarkers predict clinical efficacy and tissue molecular response after ritlecitinib induction therapy in ulcerative colitis.}, journal = {Journal of Crohn's & colitis}, volume = {}, number = {}, pages = {}, doi = {10.1093/ecco-jcc/jjad213}, pmid = {38141256}, issn = {1876-4479}, abstract = {BACKGROUND AND AIMS: Ritlecitinib, an oral JAK3/TEC family kinase inhibitor, was well- tolerated and efficacious in the phase 2b VIBRATO study in participants with moderate-to-severe ulcerative colitis (UC). The aim of this study was to identify baseline serum and microbiome markers that predict subsequent clinical efficacy and to develop noninvasive serum signatures as potential real-time noninvasive surrogates of clinical efficacy after ritlecitinib.

METHODS: Tissue and peripheral blood proteomics, transcriptomics, and fecal metagenomics were performed on samples before and after 8-week oral ritlecitinib induction therapy (20 mg, 70 mg, 200 mg, or placebo once daily, N=39, 41, 33, and 18, respectively). Linear mixed models were used to identify baseline and longitudinal protein markers associated with efficacy. The combined predictivity of these proteins was evaluated using a logistic model with permuted efficacy data. Differential expression of fecal metagenomic was used to differentiate responders and nonresponders.

RESULTS: Peripheral blood serum proteomics identified 4 baseline serum markers (LTA, CCL21, HLA-E, MEGF10) predictive of modified clinical remission (MR), endoscopic improvement (EI), histologic remission (HR), and integrative score of tissue molecular improvement. In responders, 37 serum proteins significantly changed at Week 8 compared with baseline (FDR<0.05); of these, changes in 4 (IL4R, TNFRSF4, SPINK4, and LAIR-1) predicted concurrent EI and HR responses. Fecal metagenomics analysis revealed baseline and treatment response signatures that correlated with EI, MR, and tissue molecular improvement.

CONCLUSIONS: Blood and microbiome biomarkers stratify endoscopic, histologic, and tissue molecular response to ritlecitinib, which may help guide future precision medicine approaches to UC treatment.}, } @article {pmid38140571, year = {2023}, author = {Kallies, R and Hu, D and Abdulkadir, N and Schloter, M and Rocha, U}, title = {Identification of Huge Phages from Wastewater Metagenomes.}, journal = {Viruses}, volume = {15}, number = {12}, pages = {}, pmid = {38140571}, issn = {1999-4915}, support = {460129525//Deutsche Forschungsgemeinschaft/ ; VH-NH-1248 Micro 'BigData'//Helmholtz Association of German Research Centres/ ; }, mesh = {*Bacteriophages/genetics ; Metagenome ; Wastewater ; Phylogeny ; Genome, Viral ; }, abstract = {Huge phages have genomes larger than 200 kilobases, which are particularly interesting for their genetic inventory and evolution. We screened 165 wastewater metagenomes for the presence of viral sequences. After identifying over 600 potential huge phage genomes, we reduced the dataset using manual curation by excluding viral contigs that did not contain viral protein-coding genes or consisted of concatemers of several small phage genomes. This dataset showed seven fully annotated huge phage genomes. The phages grouped into distinct phylogenetic clades, likely forming new genera and families. A phylogenomic analysis between our huge phages and phages with smaller genomes, i.e., less than 200 kb, supported the hypothesis that huge phages have undergone convergent evolution. The genomes contained typical phage protein-coding genes, sequential gene cassettes for metabolic pathways, and complete inventories of tRNA genes covering all standard and rare amino acids. Our study showed a pipeline for huge phage analyses that may lead to new enzymes for therapeutic or biotechnological applications.}, } @article {pmid38140296, year = {2023}, author = {Chan, HHY and Siu, PLK and Choy, CT and Chan, UK and Zhou, J and Wong, CH and Lee, YW and Chan, HW and Tsui, JCC and Loo, SKF and Tsui, SKW}, title = {Novel Multi-Strain E3 Probiotic Formulation Improved Mental Health Symptoms and Sleep Quality in Hong Kong Chinese.}, journal = {Nutrients}, volume = {15}, number = {24}, pages = {}, pmid = {38140296}, issn = {2072-6643}, support = {NA//Hong Kong Society of Gut Microbiome (HKSGM)/ ; }, mesh = {Humans ; *Sleep Quality ; Mental Health ; RNA, Ribosomal, 16S/genetics ; Hong Kong ; *Probiotics/therapeutic use ; }, abstract = {Mental health issues have emerged as a significant concern in public health, given their association with physical and psychological comorbidities and the resultant socioeconomic burdens. Recent studies have highlighted the interplay between gut microbes and brain functions through the gut-brain axis. To investigate this further, we conducted a targeted 16S rRNA sequencing and comprehensive bioinformatic analysis among Southern Chinese individuals to explore the role of the gut microbiome in depression, anxiety, and sleep disturbance. We analyzed the differences in the gut microbiome profile of 68 participants with sleep disturbance and mood symptoms before and after an 8-week course of a novel oral E3 multi-strain probiotics formula. The results revealed a significant improvement in subjective sleep quality (PSQI: mean 8.79 at baseline vs. 7.10 at week 8, p < 0.001), depressive symptoms (PHQ9: mean 6.17 at baseline vs. 4.76 at week 8, p < 0.001), and anxious symptoms (GAD7: mean 4.90 at baseline vs. 3.76 at week 8, p < 0.001). Additionally, there were notable differences in beta diversity (weighted UniFrac; p = 0.045) and increased Firmicutes/Bacteroidetes (F/B) ratio (p = 4 × 10[-4]) were observed in the gut microbiome analysis. Furthermore, the relative abundance of Bifidobacterium bifidum (p < 0.001), Lactobacillus acidophilus (p < 0.001), Lactobacillus helveticus (p < 0.001) and Lactobacillus plantarum (p < 0.001) were significantly increased after the 8-week probiotic supplementation. Our study suggests that the gut microbial landscape varies between responders and non-responders at multiple levels, including genera, species, functional, and network interaction. Notably, the use of probiotics in populations with depressive or anxious symptoms and poor sleeping quality remodeled the gut microbiome and demonstrated improved mood and sleep quality.}, } @article {pmid38140133, year = {2023}, author = {Machado, ACHR and Marinheiro, LJ and Benson, HAE and Grice, JE and Martins, TDS and Lan, A and Lopes, PS and Andreo-Filho, N and Leite-Silva, VR}, title = {A Novel Handrub Tablet Loaded with Pre- and Post-Biotic Solid Lipid Nanoparticles Combining Virucidal Activity and Maintenance of the Skin Barrier and Microbiome.}, journal = {Pharmaceutics}, volume = {15}, number = {12}, pages = {}, pmid = {38140133}, issn = {1999-4923}, support = {UNIFESP Process Nº 23089.125507 / 2020-08, Project Code PFSP-2101.0005//Embrapii - Empresa Brasileira de Pesquisa e Inovação Industrial/ ; }, abstract = {OBJECTIVE: This study aimed to develop a holobiont tablet with rapid dispersibility to provide regulation of the microbiota, virucidal activity, and skin barrier protection.

METHODS: A 2[3] factorial experiment was planned to define the best formulation for the development of the base tablet, using average weight, hardness, dimensions, swelling rate, and disintegration time as parameters to be analyzed. To produce holobiont tablets, the chosen base formulation was fabricated by direct compression of prebiotics, postbiotics, and excipients. The tablets also incorporated solid lipid nanoparticles containing postbiotics that were obtained by high-pressure homogenization and freeze-drying. The in vitro virucidal activity against alpha-coronavirus particles (CCoV-VR809) was determined in VERO cell culture. In vitro analysis, using monolayer cells and human equivalent skin, was performed by rRTq-PCR to determine the expression of interleukins 1, 6, 8, and 17, aquaporin-3, involucrin, filaggrin, FoxO3, and SIRT-1. Antioxidant activity and collagen-1 synthesis were also performed in fibroblast cells. Metagenomic analysis of the skin microbiome was determined in vivo before and after application of the holobiont tablet, during one week of continuous use, and compared to the use of alcohol gel. Samples were analyzed by sequencing the V3-V4 region of the 16S rRNA gene.

RESULTS: A handrub tablet with rapid dispersibility was developed for topical use and rinse off. After being defined as safe, the virucidal activity was found to be equal to or greater than that of 70% alcohol, with a reduction in interleukins and maintenance or improvement of skin barrier gene markers, in addition to the reestablishment of the skin microbiota after use.

CONCLUSIONS: The holobiont tablets were able to improve the genetic markers related to the skin barrier and also its microbiota, thereby being more favorable for use as a hand sanitizer than 70% alcohol.}, } @article {pmid38140087, year = {2023}, author = {Yu, T and Xing, Y and Gao, Q and Wang, D and Chen, H and Wang, H and Zhang, Y}, title = {Ginkgo biloba Extract Drives Gut Flora and Microbial Metabolism Variation in a Mouse Model of Alzheimer's Disease.}, journal = {Pharmaceutics}, volume = {15}, number = {12}, pages = {}, pmid = {38140087}, issn = {1999-4923}, support = {81973297，82003719, 82204374, and 81872841//National Natural Science Foundation of China/ ; 19JC1413100//Key Project of Shanghai Science and Technology Commission/ ; ZH2018ZDA23//Research Foundation of Translational Medicine of Shanghai Jiao Tong University/ ; zyyzdxk-2023070//NATCM's Project of High-level Construction of Key TCM Disciplines/ ; }, abstract = {Alzheimer's disease (AD) is a complex neurodegenerative disease. Numerous investigations have demonstrated that medications that regulate the "brain-gut" axis can ameliorate disease symptoms of AD. Studies have shown that Ginkgo biloba extract (EGb) is involved in intestinal metabolism to meet the goal of illness treatment. EGb is currently utilized extensively in the clinical prevention and treatment of cardiovascular and cerebrovascular diseases. However, the regulatory effect of EGb on intestinal flora and its metabolites in AD pathology remains largely speculative. In this study, the Morris water maze test showed a significant improvement of spatial memory in the AD mouse model (APP/PS1 mice) after EGb treatment. We next confirmed the positive effects of EGb on the gut flora and metabolites of APP/PS1 mice and further showed that EGb treatment reshaped the disturbed gut microbiome, in particular by reducing the Firmicutes/Bacteroides ratio and increasing the abundance of Bacteroidetes, Uroviricota, Streptophyta, and Spirochaetes. Meanwhile, a non-targeted metabolomics analysis showed that EGb treatment significantly reversed the dysfunction of the microbial metabolic phenotype by altering Limosilactobacillus and Parvibacte, with 300 differential metabolites modulated (131 up-regulated, 169 down-regulated). Our findings highlight the significant regulatory impact of EGb on intestinal microflora and microbial metabolism in AD mice models and provide a potential therapeutic strategy for AD.}, } @article {pmid38139456, year = {2023}, author = {Mathieu, E and Léjard, V and Ezzine, C and Govindin, P and Morat, A and Giat, M and Lapaque, N and Doré, J and Blottière, HM}, title = {An Insight into Functional Metagenomics: A High-Throughput Approach to Decipher Food-Microbiota-Host Interactions in the Human Gut.}, journal = {International journal of molecular sciences}, volume = {24}, number = {24}, pages = {}, pmid = {38139456}, issn = {1422-0067}, support = {ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; }, mesh = {Humans ; Host Microbial Interactions ; *Microbiota ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Metagenome ; }, abstract = {Our understanding of the symbiotic relationship between the microbiota and its host has constantly evolved since our understanding that the "self" was not only defined by our genetic patrimony but also by the genomes of bugs living in us. The first culture-based methods highlighted the important functions of the microbiota. However, these methods had strong limitations and did not allow for a full understanding of the complex relationships that occur at the interface between the microbiota and the host. The recent development of metagenomic approaches has been a groundbreaking step towards this understanding. Its use has provided new insights and perspectives. In the present chapter, we will describe the advances of functional metagenomics to decipher food-microbiota and host-microbiota interactions. This powerful high-throughput approach allows for the assessment of the microbiota as a whole (including non-cultured bacteria) and enabled the discovery of new signaling pathways and functions involved in the crosstalk between food, the gut microbiota and its host. We will present the pipeline and highlight the most important studies that helped to develop the field. To conclude, we will emphasize the most recent developments and hot topics in functional metagenomics.}, } @article {pmid38139262, year = {2023}, author = {Tao, Q and Liu, XW and Zhang, ZD and Ma, N and Lu, XR and Ge, WB and Li, JY and Yang, YJ}, title = {Protective Effect and Mechanism of Aspirin Eugenol Ester on Lipopolysaccharide-Induced Intestinal Barrier Injury.}, journal = {International journal of molecular sciences}, volume = {24}, number = {24}, pages = {}, pmid = {38139262}, issn = {1422-0067}, support = {32273069//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Rats ; Animals ; *Lipopolysaccharides/pharmacology ; Caco-2 Cells ; Aspirin/pharmacology/metabolism ; Intestinal Mucosa/metabolism ; Inflammation/metabolism ; Eugenol/pharmacology/metabolism ; *Intestinal Diseases/metabolism ; }, abstract = {Intestinal inflammation is a complex and recurrent inflammatory disease. Pharmacological and pharmacodynamic experiments showed that aspirin eugenol ester (AEE) has good anti-inflammatory, antipyretic, and analgesic effects. However, the role of AEE in regulating intestinal inflammation has not been explored. This study aimed to investigate whether AEE could have a protective effect on LPS-induced intestinal inflammation and thus help to alleviate the damage to the intestinal barrier. This was assessed with an inflammation model in Caco-2 cells and in rats induced with LPS. The expression of inflammatory mediators, intestinal epithelial barrier-related proteins, and redox-related signals was analyzed using an enzyme-linked immunosorbent assay (ELISA), Western blotting, immunofluorescence staining, and RT-qPCR. Intestinal damage was assessed by histopathological examination. Changes in rat gut microbiota and their functions were detected by the gut microbial metagenome. AEE significantly reduced LPS-induced pro-inflammatory cytokine levels (p < 0.05) and oxidative stress levels in Caco-2 cells and rats. Compared with the LPS group, AEE could increase the relative expression of Occludin, Claudin-1, and zonula occludens-1 (ZO-1) and decrease the relative expression of kappa-B (NF-κB) and matrix metalloproteinase-9. AEE could significantly improve weight loss, diarrhea, reduced intestinal muscle thickness, and intestinal villi damage in rats. Metagenome results showed that AEE could regulate the homeostasis of the gut flora and alter the relative abundance of Firmicutes and Bacteroidetes. Flora enrichment analysis indicated that the regulation of gut flora with AEE may be related to the regulation of glucose metabolism and energy metabolism. AEE could have positive effects on intestinal inflammation-related diseases.}, } @article {pmid38139153, year = {2023}, author = {Baykov, IK and Tikunov, AY and Babkin, IV and Fedorets, VA and Zhirakovskaia, EV and Tikunova, NV}, title = {Tentaclins-A Novel Family of Phage Receptor-Binding Proteins That Can Be Hypermutated by DGR Systems.}, journal = {International journal of molecular sciences}, volume = {24}, number = {24}, pages = {}, pmid = {38139153}, issn = {1422-0067}, support = {21-14-00360//Russian Science Foundation/ ; FWUR-2023-0003//Ministry of Science and Higher Education/ ; }, mesh = {Humans ; *Bacteriophage Receptors/genetics ; Carrier Proteins/genetics ; Proteins/genetics ; *Bacteriophages/genetics ; Prophages/genetics ; Bacteria/genetics ; Retroelements ; }, abstract = {Diversity-generating retroelements (DGRs) are prokaryotic systems providing rapid modification and adaptation of target proteins. In phages, the main targets of DGRs are receptor-binding proteins that are usually parts of tail structures and the variability of such host-recognizing structures enables phage adaptation to changes on the bacterial host surface. Sometimes, more than one target gene containing a hypermutated variable repeat (VR) can be found in phage DGRs. The role of mutagenesis of two functionally different genes is unclear. In this study, several phage genomes that contain DGRs with two target genes were found in the gut virome of healthy volunteers. Bioinformatics analysis of these genes indicated that they encode proteins with different topology; however, both proteins contain the C-type lectin (C-lec) domain with a hypermutated beta-hairpin on its surface. One of the target proteins belongs to a new family of proteins with a specific topology: N-terminal C-lec domain followed by one or more immunoglobulin domains. Proteins from the new family were named tentaclins after TENTACLe + proteIN. The genes encoding such proteins were found in the genomes of prophages and phages from the gut metagenomes. We hypothesized that tentaclins are involved in binding either to bacterial receptors or intestinal/immune cells.}, } @article {pmid38139130, year = {2023}, author = {Popov, IV and Popov, IV and Krikunova, AA and Lipilkina, TA and Derezina, TN and Chikindas, ML and Venema, K and Ermakov, AM}, title = {Gut Microbiota Composition of Insectivorous Synanthropic and Fructivorous Zoo Bats: A Direct Metagenomic Comparison.}, journal = {International journal of molecular sciences}, volume = {24}, number = {24}, pages = {}, pmid = {38139130}, issn = {1422-0067}, support = {23-14-00316//Russian Science Foundation/ ; Agreement 075-10-2021-093, Project [IMB-2102]//Ministry of Science and Higher Education of the Russian Federation/ ; //K.V. was supported by the Dutch Province of Limburg with a grant to the Centre for Healthy Eating & Food Innovation (HEFI) of Maastricht University-campus Venlo/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Chiroptera ; RNA, Ribosomal, 16S/genetics ; Metagenome ; Bacteria/genetics ; }, abstract = {Bats are natural reservoirs for many emerging viral diseases. That is why their virome is widely studied. But at the same time, studies of their bacterial gut microbiota are limited, creating a degree of uncertainty about the role of bats in global microbial ecology. In this study, we analyzed gut microbiota of insectivorous Nyctalus noctula and Vespertilio murinus from rehabilitation centers from Rostov-on-Don and Moscow, respectively, and fructivorous Carollia perspicillata from the Moscow Zoo based on V3-V4 16S rRNA metagenomic sequencing. We revealed that microbial diversity significantly differs between the insectivorous and fructivorous species studied, while the differences between N. noctula and V. murinus are less pronounced, which shows that bats' gut microbiota is not strictly species-specific and depends more on diet type. In the gut microbiota of synanthropic bats, we observed bacteria that are important for public health and animal welfare such as Bacteroides, Enterobacter, Clostridiaceae, Enterococcus, Ureaplasma, Faecalibacterium, and Helicobacter, as well as some lactic acid bacteria such as Pediococcus, Lactobacillus, Lactococcus, and Weisella. All these bacteria, except for Bacteroides and Weisella, were significantly less abundant in C. perspicillata. This study provides a direct metagenomic comparison of synanthropic insectivorous and zoo fructivorous bats, suggesting future directions for studying these animals' role in microbial ecology.}, } @article {pmid38139096, year = {2023}, author = {Hsieh, SY and Savva, GM and Telatin, A and Tiwari, SK and Tariq, MA and Newberry, F and Seton, KA and Booth, C and Bansal, AS and Wileman, T and Adriaenssens, EM and Carding, SR}, title = {Investigating the Human Intestinal DNA Virome and Predicting Disease-Associated Virus-Host Interactions in Severe Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS).}, journal = {International journal of molecular sciences}, volume = {24}, number = {24}, pages = {}, pmid = {38139096}, issn = {1422-0067}, support = {BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *Fatigue Syndrome, Chronic ; Virome ; Host Microbial Interactions ; DNA ; }, abstract = {Understanding how the human virome, and which of its constituents, contributes to health or disease states is reliant on obtaining comprehensive virome profiles. By combining DNA viromes from isolated virus-like particles (VLPs) and whole metagenomes from the same faecal sample of a small cohort of healthy individuals and patients with severe myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS), we have obtained a more inclusive profile of the human intestinal DNA virome. Key features are the identification of a core virome comprising tailed phages of the class Caudoviricetes, and a greater diversity of DNA viruses including extracellular phages and integrated prophages. Using an in silico approach, we predicted interactions between members of the Anaerotruncus genus and unique viruses present in ME/CFS microbiomes. This study therefore provides a framework and rationale for studies of larger cohorts of patients to further investigate disease-associated interactions between the intestinal virome and the bacteriome.}, } @article {pmid38138126, year = {2023}, author = {Lee, C and Zaheer, R and Munns, K and Holman, DB and Van Domselaar, G and Zovoilis, A and McAllister, TA}, title = {Effect of Antimicrobial Use in Conventional Versus Natural Cattle Feedlots on the Microbiome and Resistome.}, journal = {Microorganisms}, volume = {11}, number = {12}, pages = {}, pmid = {38138126}, issn = {2076-2607}, support = {//Genomics Research and Development Initiative (GRDI) of the Government of Canada/ ; //Major Innovation Fund of the Government of Alberta in conjunction with the University of Calgary AMR One Health Consortium/ ; }, abstract = {Antimicrobial use (AMU) in the livestock industry has been associated with increased levels of antimicrobial resistance. Recently, there has been an increase in the number of "natural" feedlots in the beef cattle sector that raise cattle without antibiotics. Shotgun metagenomics was employed to characterize the impact of AMU in feedlot cattle on the microbiome, resistome, and mobilome. Sequenced fecal samples identified a decline (q < 0.01) in the genera Methanobrevibacter and Treponema in the microbiome of naturally vs. conventionally raised feedlot cattle, but this difference was not (q > 0.05) observed in catch basin samples. No differences (q > 0.05) were found in the class-level resistome between feedlot practices. In fecal samples, decreases from conventional to natural (q < 0.05) were noted in reads for the antimicrobial-resistant genes (ARGs) mefA, tet40, tetO, tetQ, and tetW. Plasmid-associated ARGs were more common in feces from conventional than natural feedlot cattle. Interestingly, more chromosomal- than plasmid-associated macrolide resistance genes were observed in both natural and conventional feedlots, suggesting that they were more stably conserved than the predominately plasmid-associated tetracycline resistance genes. This study suggests that generationally selected resistomes through decades of AMU persist even after AMU ceases in natural production systems.}, } @article {pmid38138036, year = {2023}, author = {Goletic, S and Goletic, T and Omeragic, J and Supic, J and Kapo, N and Nicevic, M and Skapur, V and Rukavina, D and Maksimovic, Z and Softic, A and Alic, A}, title = {Metagenomic Sequencing of Lloviu Virus from Dead Schreiber's Bats in Bosnia and Herzegovina.}, journal = {Microorganisms}, volume = {11}, number = {12}, pages = {}, pmid = {38138036}, issn = {2076-2607}, abstract = {Bats are a natural host for a number of viruses, many of which are zoonotic and thus present a threat to human health. RNA viruses of the family Filoviridae, many of which cause disease in humans, have been associated with specific bat hosts. Lloviu virus is a Filovirus which has been connected to mass mortality events in Miniopterus schreibersii colonies in Spain and Hungary, and some studies have indicated its immense zoonotic potential. A die-off has been recorded among Miniopterus schreibersii in eastern Bosnia and Herzegovina for the first time, prompting the investigation to determine the causative agent. Bat carcasses were collected and subjected to pathological examination, after which the lung samples with notable histopathological changes, lung samples with no changes and guano were analyzed using metagenomic sequencing and RT-PCR. A partial Lloviu virus genome was sequenced from lung samples with histopathological changes and found to be closely related to Hungarian and Italian virus sequences. Further accumulation of mutations on the GP gene, coding the glycoprotein responsible for cell tropism and host preference, enhances the need for further characterization and monitoring of this virus to prevent spillover events and protect human health.}, } @article {pmid38136990, year = {2023}, author = {Skoog, EJ and Fournier, GP and Bosak, T}, title = {Assessing the Influence of HGT on the Evolution of Stress Responses in Microbial Communities from Shark Bay, Western Australia.}, journal = {Genes}, volume = {14}, number = {12}, pages = {}, pmid = {38136990}, issn = {2073-4425}, support = {327126//Simons Foundation/ ; 344707//Simons Foundation/ ; }, mesh = {Western Australia ; *Bays ; Gene Transfer, Horizontal ; *Microbiota ; Metagenome ; }, abstract = {Pustular microbial mats in Shark Bay, Western Australia, are modern analogs of microbial systems that colonized peritidal environments before the evolution of complex life. To understand how these microbial communities evolved to grow and metabolize in the presence of various environmental stresses, the horizontal gene transfer (HGT) detection tool, MetaCHIP, was used to identify the horizontal transfer of genes related to stress response in 83 metagenome-assembled genomes from a Shark Bay pustular mat. Subsequently, maximum-likelihood phylogenies were constructed using these genes and their most closely related homologs from other environments in order to determine the likelihood of these HGT events occurring within the pustular mat. Phylogenies of several stress-related genes-including those involved in response to osmotic stress, oxidative stress and arsenic toxicity-indicate a potentially long history of HGT events and are consistent with these transfers occurring outside of modern pustular mats. The phylogeny of a particular osmoprotectant transport gene reveals relatively recent adaptations and suggests interactions between Planctomycetota and Myxococcota within these pustular mats. Overall, HGT phylogenies support a potentially broad distribution in the relative timing of the HGT events of stress-related genes and demonstrate ongoing microbial adaptations and evolution in these pustular mat communities.}, } @article {pmid38136875, year = {2023}, author = {Han, X and Xia, Z}, title = {Application of Host-Depleted Nanopore Metagenomic Sequencing in the Clinical Detection of Pathogens in Pigs and Cats.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {24}, pages = {}, pmid = {38136875}, issn = {2076-2615}, abstract = {Metagenomic sequencing is a valuable tool for non-specifically detecting various microorganisms in samples, offering unique advantages for detecting emerging pathogens, fastidious or uncultivable pathogens, and mixed infections. It has recently been applied to clinically detect pathogenic microorganisms in animals; however, the high proportion of host genes, expensive sequencing equipment, and the complexity of sequencing and data analysis methods have limited its clinical utility. In this study, a combination of tissue homogenization and nuclease digestion was employed to remove host genes from pig and cat samples; DNA and RNA were then extracted and subjected to nonselective PCR amplification to simultaneously detect DNA and RNA pathogen genomes using R9.4.1 or R10.4.1 flow cells on the MinION platform. Real-time pathogen detection was conducted using EPI2M WIMP, and viral genome assembly was performed using NanoFilt, minimap2, samtools, and ivar. Pathogens in five clinical samples (serum, nasopharyngeal swab, feces, or ascites) from cats and four clinical samples (lung or small intestine tissue) from pigs were examined by metagenomic sequencing, and the results were consistent with those obtained by PCR and bacterial culture. Additionally, we detected four viruses and three bacteria that may be associated with diseases. A comparison of results before and after host gene removal in three samples showed a 9-50% reduction in host genes. We also compared the assembly efficiency of six virus genomes and found that data volumes ranging from 3.3 to 98.3 MB were sufficient to assemble >90% of the viral genomes. In summary, this study utilized optimized nanopore metagenomic sequencing and analysis methods to reduce host genes, decrease the required data volume for sequencing analysis, and enable real-time detection to determine when to stop sequencing. The streamlined sequencing and analysis process overcomes barriers to the veterinary clinical application of metagenomic sequencing and provides a reference for clinical implementation.}, } @article {pmid38136849, year = {2023}, author = {Shao, Y and Wu, X and Yu, Z and Li, M and Sheng, T and Wang, Z and Tu, J and Song, X and Qi, K}, title = {Gut Microbiome Analysis and Screening of Lactic Acid Bacteria with Probiotic Potential in Anhui Swine.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {24}, pages = {}, pmid = {38136849}, issn = {2076-2615}, support = {32372955//The National Natural Science Foundation of China/ ; 32202891//The National Science Fund for Distinguished Young Scholars of China/ ; }, abstract = {With the widespread promotion of the green feeding concept of "substitution and resistance", there is a pressing need for alternative products in feed and breeding industries. Employing lactic acid bacteria represents one of the most promising antimicrobial strategies to combat infections caused by pathogenic bacteria. As such, we analyzed the intestinal tract of Anhui local pig breeds, including LiuBai Pig, YueHei Pig, and HuoShou Pig, to determine the composition and diversity of intestinal microbiota using 16S rRNA. Further, the functionality of the pigs' intestinal microbiota was studied through metagenomic sequencing. This study revealed that lactic acid bacteria were the primary contributors to the functional composition, as determined through a species functional contribution analysis. More specifically, the functional contribution of lactic acid bacteria in the HuoShou Pig group was higher than that of the LiuBai Pig and YueHei Pig. Subsequently, the intestinal contents of the HuoShou Pig group were selected for the screening of the dominant lactic acid bacteria strains. Out of eight strains of lactic acid bacteria, the acid-production capacity, growth curve, and tolerance to a simulated intestinal environment were assessed. Additional assessments included surface hydrophobicity, the self-aggregation capability, co-agglutination of lactic acid bacteria with pathogenic bacteria, and an in vitro bacteriostatic activity assay. Lactobacillus johnsonii L5 and Lactobacillus reuteri L8 were identified as having a strong overall performance. These findings serve as a theoretical basis for the further development of pig-derived probiotics, thereby promoting the application of lactic acid bacteria to livestock production.}, } @article {pmid38136769, year = {2023}, author = {Rout, AK and Tripathy, PS and Dixit, S and Behera, DU and Behera, B and Das, BK and Behera, BK}, title = {Unveiling the Microbiome Landscape: A Metagenomic Study of Bacterial Diversity, Antibiotic Resistance, and Virulence Factors in the Sediments of the River Ganga, India.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {38136769}, issn = {2079-6382}, abstract = {The global rise in antibiotic resistance, fueled by indiscriminate antibiotic usage in medicine, aquaculture, agriculture, and the food industry, presents a significant public health challenge. Urban wastewater and sewage treatment plants have become key sources of antibiotic resistance proliferation. The present study focuses on the river Ganges in India, which is heavily impacted by human activities and serves as a potential hotspot for the spread of antibiotic resistance. We conducted a metagenomic analysis of sediment samples from six distinct locations along the river to assess the prevalence and diversity of antibiotic resistance genes (ARGs) within the microbial ecosystem. The metagenomic analysis revealed the predominance of Proteobacteria across regions of the river Ganges. The antimicrobial resistance (AMR) genes and virulence factors were determined by various databases. In addition to this, KEGG and COG analysis revealed important pathways related to AMR. The outcomes highlight noticeable regional differences in the prevalence of AMR genes. The findings suggest that enhancing health and sanitation infrastructure could play a crucial role in mitigating the global impact of AMR. This research contributes vital insights into the environmental aspects of antibiotic resistance, highlighting the importance of targeted public health interventions in the fight against AMR.}, } @article {pmid38136762, year = {2023}, author = {Kerek, Á and Török, B and Laczkó, L and Kardos, G and Bányai, K and Somogyi, Z and Kaszab, E and Bali, K and Jerzsele, Á}, title = {In Vitro Microevolution and Co-Selection Assessment of Florfenicol Impact on Escherichia coli Resistance Development.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {38136762}, issn = {2079-6382}, support = {ÚNKP-20- 3-I-ÁTE-1//National Research, Development and Innovation Office/ ; ÚNKP- 21-2-I-ÁTE-3//National Research, Development and Innovation Office/ ; RRF-2.3.1-21-2022-00001//National Research, Development and Innovation Office/ ; }, abstract = {The issue of antimicrobial resistance is becoming an increasingly serious challenge in both human and veterinary medicine. Prudent antimicrobial use in veterinary medicine is warranted and supported by international guidelines, with the Antimicrobial Advice Ad Hoc Expert Group (AMEG) placing particular emphasis on the critically important group B antimicrobials. These antimicrobials are commonly employed, especially in the poultry and swine industry. The impact of florfenicol, a veterinary antibiotic, was studied on the resistance development of Escherichia coli. The aim of the study was to investigate the effect of the use of florfenicol on the development of phenotypic and genomic resistances, not only to the drug itself but also to other drugs. The minimum inhibitory concentrations (MICs) of the antibiotics were investigated at 1×, 10×, 100× and 1000× concentrations using the adapted Microbial Evolution and Growth Arena (MEGA-plate) method. The results demonstrate that florfenicol can select for resistance to fluoroquinolone antibiotics (167× MIC value increase) and cephalosporins (67× MIC value increase). A total of 44 antimicrobial resistance genes were identified, the majority of which were consistent across the samples. Chromosomal point mutations, including alterations in resistance-associated and regulatory genes (acrB, acrR, emrR and robA), are thought to trigger multiple drug efflux pump activations, leading to phenotypically increased resistance. The study underscores the impact of florfenicol and its role in the development of antimicrobial resistance, particularly concerning fluoroquinolone antibiotics and cephalosporins. This study is the first to report florfenicol's dose-dependent enhancement of other antibiotics' MICs, linked to mutations in SOS-box genes (mdtABC-tolC, emrAB-tolC and acrAB-tolC) and increased multidrug efflux pump genes. Mutations in the regulatory genes acrR, emrR and rpbA support the possibility of increased gene expression. The results are crucial for understanding antimicrobial resistance and its development, highlighting the promising potential of in vitro evolutionary and coselection studies for future research.}, } @article {pmid38136731, year = {2023}, author = {Balcha, ES and Gómez, F and Gemeda, MT and Bekele, FB and Abera, S and Cavalazzi, B and Woldesemayat, AA}, title = {Shotgun Metagenomics-Guided Prediction Reveals the Metal Tolerance and Antibiotic Resistance of Microbes in Poly-Extreme Environments in the Danakil Depression, Afar Region.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {38136731}, issn = {2079-6382}, abstract = {The occurrence and spread of antibiotic resistance genes (ARGs) in environmental microorganisms, particularly in poly-extremophilic bacteria, remain underexplored and have received limited attention. This study aims to investigate the prevalence of ARGs and metal resistance genes (MRGs) in shotgun metagenome sequences obtained from water and salt crust samples collected from Lake Afdera and the Assale salt plain in the Danakil Depression, northern Ethiopia. Potential ARGs were characterized by the comprehensive antibiotic research database (CARD), while MRGs were identified by using BacMetScan V.1.0. A total of 81 ARGs and 39 MRGs were identified at the sampling sites. We found a copA resistance gene for copper and the β-lactam encoding resistance genes were the most abundant the MRG and ARG in the study area. The abundance of MRGs is positively correlated with mercury (Hg) concentration, highlighting the importance of Hg in the selection of MRGs. Significant correlations also exist between heavy metals, Zn and Cd, and ARGs, which suggests that MRGs and ARGs can be co-selected in the environment contaminated by heavy metals. A network analysis revealed that MRGs formed a complex network with ARGs, primarily associated with β-lactams, aminoglycosides, and tetracyclines. This suggests potential co-selection mechanisms, posing concerns for both public health and ecological balance.}, } @article {pmid38136701, year = {2023}, author = {Sardzikova, S and Andrijkova, K and Svec, P and Beke, G and Klucar, L and Minarik, G and Bielik, V and Kolenova, A and Soltys, K}, title = {High Diversity but Monodominance of Multidrug-Resistant Bacteria in Immunocompromised Pediatric Patients with Acute Lymphoblastic Leukemia Developing GVHD Are Not Associated with Changes in Gut Mycobiome.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {38136701}, issn = {2079-6382}, support = {APVV-17-0099//Slovak Research and Development Agency/ ; }, abstract = {Graft-versus-host disease (GvHD) is a severe complication after hematopoietic stem cell transplantation (HSCT). Our study focused on identifying multidrug-resistant (MDR) gut bacteria associated with GvHD-prone guts and association with gut microbiota (GM) diversity, bacteriome, and mycobiome composition in post-HSCT patients. We examined 11 pediatric patients with acute lymphoblastic leukemia (ALL), including six with GvHD, within three time points: seven days pre-HSCT, seven days post-, and 28 days post-HSCT. The gut microbiome and its resistome were investigated using metagenomic sequencing, taxonomically classified with Kraken2, and statistically evaluated for significance using appropriate tests. We observed an increase in the abundance of MDR bacteria, mainly Enterococcus faecium strains carrying msr(C), erm(T), aac(6')-li, dfrG, and ant(6)-la genes, in GvHD patients one week post-HSCT. Conversely, non-GvHD patients had more MDR beneficial bacteria pre-HSCT, promoting immunosurveillance, with resistance genes increasing one-month post-HSCT. MDR beneficial bacteria included the anti-inflammatory Bacteroides fragilis, Ruminococcus gnavus, and Turicibacter, while most MDR bacteria represented the dominant species of GM. Changes in the gut mycobiome were not associated with MDR bacterial monodominance or GvHD. Significant α-diversity decline (Shannon index) one week and one month post-HSCT in GvHD patients (p < 0.05) was accompanied by increased Pseudomonadota and decreased Bacteroidota post-HSCT. Our findings suggest that MDR commensal gut bacteria may preserve diversity and enhance immunosurveillance, potentially preventing GvHD in pediatric ALL patients undergoing HSCT. This observation has therapeutic implications.}, } @article {pmid38135695, year = {2023}, author = {Trouche, B and Schauberger, C and Bouderka, F and Auguet, JC and Belser, C and Poulain, J and Thamdrup, B and Wincker, P and Arnaud-Haond, S and Glud, RN and Maignien, L}, title = {Distribution and genomic variation of ammonia-oxidizing archaea in abyssal and hadal surface sediments.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {133}, pmid = {38135695}, issn = {2730-6151}, abstract = {Ammonia-oxidizing archaea of the phylum Thaumarchaeota play a central role in the biogeochemical cycling of nitrogen in benthic sediments, at the interface between pelagic and subsurface ecosystems. However, our understanding of their niche separation and of the processes controlling their population structure in hadal and abyssal surface sediments is still limited. Here, we reconstructed 47 AOA metagenome-assembled genomes (MAGs) from surface sediments of the Atacama and Kermadec trench systems. They formed deep-sea-specific groups within the family Nitrosopumilaceae and were assigned to six amoA gene-based clades. MAGs from different clades had distinct distribution patterns along oxygen-ammonium counter gradients in surface sediments. At the species level, MAGs thus seemed to form different ecotypes and follow deterministic niche-based distributions. In contrast, intraspecific population structure, defined by patterns of Single Nucleotide Variants (SNV), seemed to reflect more complex contributions of both deterministic and stochastic processes. Firstly, the bathymetric range had a strong effect on population structure, with distinct populations in abyssal plains and hadal trenches. Then, hadal populations were clearly separated by trench system, suggesting a strong isolation-by-topography effect, whereas abyssal populations were rather controlled by sediment depth or geographic distances, depending on the clade considered. Interestingly, genetic variability between samples was lowest in sediment layers where the mean MAG coverage was highest, highlighting the importance of selective pressure linked with each AOA clade's ecological niche. Overall, our results show that deep-sea AOA genome distributions seem to follow both deterministic and stochastic processes, depending on the genomic variability scale considered.}, } @article {pmid38135681, year = {2023}, author = {Li, X and Brejnrod, A and Thorsen, J and Zachariasen, T and Trivedi, U and Russel, J and Vestergaard, GA and Stokholm, J and Rasmussen, MA and Sørensen, SJ}, title = {Differential responses of the gut microbiome and resistome to antibiotic exposures in infants and adults.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {8526}, pmid = {38135681}, issn = {2041-1723}, support = {NNF19OC0057934598//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; NNF17OC0025014//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; 300489//Norges Forskningsråd (Research Council of Norway)/ ; }, mesh = {Infant ; Young Adult ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/genetics ; Escherichia coli/genetics ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; }, abstract = {Despite their crucial importance for human health, there is still relatively limited knowledge on how the gut resistome changes or responds to antibiotic treatment across ages, especially in the latter case. Here, we use fecal metagenomic data from 662 Danish infants and 217 young adults to fill this gap. The gut resistomes are characterized by a bimodal distribution driven by E. coli composition. The typical profile of the gut resistome differs significantly between adults and infants, with the latter distinguished by higher gene and plasmid abundances. However, the predominant antibiotic resistance genes (ARGs) are the same. Antibiotic treatment reduces bacterial diversity and increased ARG and plasmid abundances in both cohorts, especially core ARGs. The effects of antibiotic treatments on the gut microbiome last longer in adults than in infants, and different antibiotics are associated with distinct impacts. Overall, this study broadens our current understanding of gut resistome dynamics and the impact of antibiotic treatment across age groups.}, } @article {pmid38135391, year = {2024}, author = {Chen, K and Liang, J and Wang, Y and Tao, Y and Lu, Y and Wang, A}, title = {A global perspective on microbial risk factors in effluents of wastewater treatment plants.}, journal = {Journal of environmental sciences (China)}, volume = {138}, number = {}, pages = {227-235}, doi = {10.1016/j.jes.2023.04.012}, pmid = {38135391}, issn = {1001-0742}, mesh = {*Wastewater ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Risk Factors ; *Water Purification ; Escherichia coli ; }, abstract = {Effective monitoring and management of microbial risk factors in wastewater treatment plants (WWTPs) effluents require a comprehensive investigation of these risks. A global survey on microbial risk factors in WWTP effluents could reveal important insights into their risk features. This study aims to explore the abundance and types of antibiotic resistance genes (ARGs), virulence factor genes (VFGs), the vector of ARG/VFG, and dominant pathogens in global WWTP effluents. We collected 113 metagenomes of WWTP effluents from the Sequence Read Archive of the National Center for Biotechnology Information and characterized the microbial risk factors. Our results showed that multidrug resistance was the dominant ARG type, while offensive virulence factors were the most abundant type of VFGs. The most dominant types of ARGs in the vector of plasmid and phage were both aminoglycoside resistance, which is concerning as aminoglycosides are often a last resort for treating multi-resistant infections. Acinetobacter baumannii was the most dominant pathogen, rather than Escherichia coli, and a weak negative correlation between Escherichia coli and two other dominant pathogens (Acinetobacter baumannii and Bacteroides uniformis) suggests that using Escherichia coli as a biological indicator for all pathogens in WWTP effluents may not be appropriate. The Getah virus was the most dominant virus found in global WWTP effluents. Our study presents a comprehensive global-scale investigation of microbial risk factors in WWTP effluents, providing valuable insights into the potential risks associated with WWTP effluents and contributing to the monitoring and control of these risks.}, } @article {pmid38135265, year = {2024}, author = {Medina, JE and Castañeda, S and Páez-Triana, L and Camargo, M and Garcia-Corredor, DJ and Gómez, M and Luna, N and Ramírez, AL and Pulido-Medellín, M and Muñoz, M and Ramírez, JD}, title = {High prevalence of Enterovirus E, Bovine Kobuvirus, and Astrovirus revealed by viral metagenomics in fecal samples from cattle in Central Colombia.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {117}, number = {}, pages = {105543}, doi = {10.1016/j.meegid.2023.105543}, pmid = {38135265}, issn = {1567-7257}, mesh = {Humans ; Animals ; Cattle ; Phylogeny ; Prevalence ; Colombia/epidemiology ; *Viruses ; *Astroviridae/genetics ; Feces ; Metagenomics ; *Enterovirus ; *Kobuvirus ; }, abstract = {Livestock plays a crucial role in ensuring food security and driving the global economy. However, viral infections can have far-reaching consequences beyond economic productivity, affecting the health of cattle, as well as posing risks to human health and other animals. Identifying viruses present in fecal samples, a primary route of pathogen transmission, is essential for developing effective prevention, control, and surveillance strategies. Viral metagenomic approaches offer a broader perspective and hold great potential for detecting previously unknown viruses or uncovering previously undescribed agents. Ubaté Province is Colombia's dairy capital and a key center for livestock production in the country. Therefore, the purpose of this study was to characterize viral communities in fecal samples from cattle in this region. A total of 42 samples were collected from three municipalities in Ubaté Province, located in central Colombia, using a convenient non-probabilistic sampling method. We utilized metagenomic sequencing with Oxford Nanopore Technologies (ONT), combined with diversity and phylogenetic analysis. The findings revealed a consistent and stable viral composition across the municipalities, primarily comprising members of the Picornaviridae family. At the species level, the most frequent viruses were Enterovirus E (EVE) and Bovine Astrovirus (BoAstV). Significantly, this study reported, for the first time in Colombia, the presence of viruses with veterinary importance occurring at notable frequencies: EVE (59%), Bovine Kobuvirus (BKV) (52%), and BoAstV (19%). Additionally, the study confirmed the existence of Circular replicase-encoding single-stranded (CRESS) Virus in animal feces. These sequences were phylogenetically grouped with samples obtained from Asia and Latin America, underscoring the importance of having adequate representation across the continent. The virome of bovine feces in Ubaté Province is characterized by the predominance of potentially pathogenic viruses such as BoAstV and EVE that have been reported with substantial frequency and quantities. Several of these viruses were identified in Colombia for the first time. This study showcases the utility of using metagenomic sequencing techniques in epidemiological surveillance. It also paves the way for further research on the influence of these agents on bovine health and their frecuency across the country.}, } @article {pmid38135052, year = {2023}, author = {Vermeersch, AS and Ali, M and Gansemans, Y and Van Nieuwerburgh, F and Ducatelle, R and Geldhof, P and Deforce, D and Callens, J and Opsomer, G}, title = {An in-depth investigation of the microbiota and its virulence factors associated 11 with severe udder cleft dermatitis lesions.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2023-24180}, pmid = {38135052}, issn = {1525-3198}, abstract = {Udder cleft dermatitis (UCD) is a skin condition affecting the anterior parts of the udder in dairy cattle. In the present study, we aimed to shed light on the microbiota in severe UCD lesions versus healthy udder skin by putting forward a taxonomic and functional profile based on a virulence factor analysis. Through shotgun metagenomic sequencing, we found a high proportion of bacteria besides a low abundance of archaea. A distinct clustering of healthy udder skin versus UCD lesion samples was shown by applying principal component analysis and (sparse) partial least squares ((s)PLS) analysis on the metagenomic data. Proteobacteria, Bacillota and Actinomycetota were among the most abundant phyla in healthy udder skin samples. In UCD samples, Bacteroidota was the most abundant phylum. At genus level, Bifidobacterium spp. had the highest relative abundance in healthy skin samples, while Porphyromonas spp. and Corynebacterium spp. had the highest relative abundance in UCD samples. In the differential abundance analysis, Porphyromonas spp. and Bacteroides spp. were significantly differentially abundant in UCD samples whereas Bifidobacterium spp., Staphylococcus sp. AntiMn-1 and Staphylococcus equorum were more commonly found in healthy samples. Moreover, the abundance of several treponeme phylotypes was significantly higher in lesion samples. The streptococcal cysteine protease speB was among the most abundant virulence factors present in severe UCD lesions while a plethora of virulence factors such as the antitoxin relB were downregulated, possibly contributing to creating the ideal wound climate for the dysbiotic community. Network analysis showed healthy lesion samples had a large network of, especially positive, correlations between the abundances of beneficial species such as Aerococcus urinaeequi and Bifidobacterium angulatum, indicating that the healthy skin microbiome forms an active protective bacterial network which is disrupted in case of UCD. In UCD samples, a smaller microbial network mainly consisting of positive correlations between the abundances of Bacteroides fragilis and anaerobic Bacteroidota was exposed. Moreover, a high correlation between the taxonomic data and virulence factors was revealed, concurrently with 2 separate networks of microbes and virulence factors. One network, matching with the taxonomic findings in the healthy udder skin samples, showcased a community of harmless and/or beneficial bacteria such as Bifidobacterium spp. and Butyrivibrio proteoclasticus associated with hcnB, hcnC, relB, glyoxalase and cupin 2. The other network, corresponding with UCD samples, consisted of pathogenic or facultative pathogenic and mainly anaerobic bacteria such as Treponema spp., Mycoplasmopsis spp., and bovine gammaherpesvirus 4, that correlated with virulence factors SpvB, fhaB and haemagglutination activity domain associated factor. Our results point toward a dysbiotic community with a significant decrease in diversity and evenness, with a loss of normal skin inhabitants and innocuous and/or useful species making way for predominantly anaerobic, facultative pathogens. The shift in the abundance of virulence factors such as fhaB and SpvB could play a role in the manifestation of a local micro-environment favorable to the microbiome associated with udder skin lesions. Lastly, the presence of specific networks between microbial species, and between microbes and virulence factors was shown.}, } @article {pmid38134685, year = {2023}, author = {Huang, JN and Xu, L and Wen, B and Gao, JZ and Chen, ZZ}, title = {Reshaping the plastisphere upon deposition: Promote N2O production through affecting sediment microbial communities in aquaculture pond.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133290}, doi = {10.1016/j.jhazmat.2023.133290}, pmid = {38134685}, issn = {1873-3336}, abstract = {Microplastics (MPs) could provide vector for microorganisms to form biofilm (plastisphere), but the shaping process of MPs biofilm and its effects on the structure and function of sedimentary microbial communities especially in aquaculture environments are not reported. For this, we incubated MPs biofilm in situ in an aquaculture pond and established a sediment microcosm with plastisphere. We found that the formation of MPs biofilm in surface water was basically stable after 30 d incubation, but the biofilm communities were reshaped after deposition for another 30 d, because they were more similar to plastisphere communities incubated directly within sediment but not surface water. Moreover, microbial communities of MPs-contaminated sediment were altered, which was mainly driven by the biofilm communities present on MPs, because they but not sediment communities in proximity to MPs had a more pronounced separation from the control sediment communities. In the presence of MPs, increased sediment nitrification, denitrification and N2O production rates were observed. The K00371 (NO2[-]⇋NO3[-]) pathway and elevated abundance of nxrB and narH genes were screened by metagenomic analysis. Based on structural equation model, two key bacteria (Alphaproteobacteria bacterium and Rhodobacteraceae bacterium) associated with N2O production were further identified. Overall, the settling of MPs could reshape the original biofilm and promote N2O production by selectively elevating sedimental microorganisms and functional genes in aquaculture pond.}, } @article {pmid38134579, year = {2024}, author = {Cardin, M and Cardazzo, B and Coton, M and Carraro, L and Lucchini, R and Novelli, E and Coton, E and Mounier, J}, title = {Ecological diversity and associated volatilome of typical mountain Caciotta cheese from Italy.}, journal = {International journal of food microbiology}, volume = {411}, number = {}, pages = {110523}, doi = {10.1016/j.ijfoodmicro.2023.110523}, pmid = {38134579}, issn = {1879-3460}, mesh = {Animals ; *Cheese/microbiology ; Bacteria ; *Lactobacillus delbrueckii ; Temperature ; Italy ; Milk/microbiology ; }, abstract = {Traditional products are particularly appreciated by consumers and among these products, cheese is a major contributor to the Italian mountainous area economics. In this study, shotgun metagenomics and volatilomics were used to understand the biotic and abiotic factors contributing to mountain Caciotta cheese typicity and diversity. Results showed that the origin of cheese played a significant role; however, curd cooking temperature, pH, salt concentration and water activity also had an impact. Viral communities exhibited higher biodiversity and discriminated cheese origins in terms of production farms. Among the most dominant bacteria, Streptococcus thermophilus showed higher intraspecific diversity and closer relationship to production farm when compared to Lactobacillus delbrueckii. However, despite a few cases in which the starter culture was phylogenetically separated from the most dominant strains sequenced in the cheese, starter cultures and dominant cheese strains clustered together suggesting substantial starter colonization in mountain Caciotta cheese. The Caciotta cheese volatilome contained prominent levels of alcohols and ketones, accompanied by lower proportions of terpenes. Volatile profile not only demonstrated a noticeable association with production farm but also significant differences in the relative abundances of enzymes connected to flavor development. Moreover, correlations of different non-homologous isofunctional enzymes highlighted specific contributions to the typical flavor of mountain Caciotta cheese. Overall, this study provides a deeper understanding of the factors shaping typical mountain Caciotta cheese, and the potential of metagenomics for characterizing and potentially authenticating food products.}, } @article {pmid38133826, year = {2023}, author = {Odisi, EJ and de Freitas, RC and do Amaral, DS and da Silva, SB and da Silva, MAC and de Oliveira Sant Ana, W and de Souza Lima, AO and Rörig, LR}, title = {Metataxonomy of acid mine drainage microbiomes from the Santa Catarina Carboniferous Basin (Southern Brazil).}, journal = {Extremophiles : life under extreme conditions}, volume = {28}, number = {1}, pages = {8}, pmid = {38133826}, issn = {1433-4909}, support = {FAPESC-2021TR000671//Fundação de Amparo à Pesquisa e Inovação do Estado de Santa Catarina/ ; DS 88882.438331/2019-01//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, mesh = {Brazil ; *Bacteria/genetics ; *Microbiota ; Rivers/microbiology ; Fungi ; Water ; }, abstract = {Mining activities generate large quantities of wastes that significantly alter the biogeochemistry and ecological structure of entire river basins. Microbial communities that develop in these areas present a variety of survival and adaptation mechanisms. Knowing this diversity at the molecular level is strategic both for understanding adaptive processes and for identifying genomes with potential use in bioremediation and bioprospecting. In this work, prokaryotic and eukaryotic communities were evaluated by meta-taxonomics (16S and 18S amplicons) in sediments and water bodies impacted by acid mine drainage in an important coal mining area in southern Brazil. Five sampling stations were defined on a gradient of impacts (pH 2.7-4.25). Taxon diversity was directly proportional to pH, being greater in sediments than in water. The dominant prokaryotic phyla in the samples were Proteobacteria, Actinobacteria, Acidobacteria, OD1, Nitrospirae, and Euryarchaeota, and among the eukaryotes, algae (Ochrophyta, Chlorophyta, Cryptophyceae), fungi (Basidiomycota, Ascomycota, and Cryptomycota), and protists (Ciliophora, Heterolobosea, Cercozoa). The prokaryotic genera Leptospirillum, Acidithiobacillus, Acidiphilium, Thiomonas, Thermogymnomonas, and Acidobacterium, and the eukaryotic genera Pterocystis and Poteriospumella were associated with more acidic conditions and higher metal concentrations, while the prokaryotic genera Sediminibacterium, Gallionella Geothrix, and Geobacter were more abundant in transitional environments.}, } @article {pmid38133388, year = {2023}, author = {Jiang, C and Almuhtaram, H and McKie, MJ and Andrews, RC}, title = {Assessment of Biofilm Growth on Microplastics in Freshwaters Using a Passive Flow-Through System.}, journal = {Toxics}, volume = {11}, number = {12}, pages = {}, pmid = {38133388}, issn = {2305-6304}, support = {Industrial Research Chair in Drinking Water Treatment//Natural Sciences and Engineering Research Council/ ; GCXE21S054//Environment and Climate Change Canada/ ; }, abstract = {Biofilms that colonize on the surface of microplastics (MPs) in freshwaters may pose a potential health risk. This study examined factors that influence MP-associated biofilm growth, including polymer type, degree of weathering, and source water quality. Weathered MPs produced in-lab were employed in biofilm trials conducted on site using a passive flow-through system with raw water at drinking water treatment facility intakes. Adenosine triphosphate (ATP) was used to quantify biofilm abundance; biofilm composition was assessed via metagenomic sequencing. Biofilm growth was observed on all polymer types examined and most prevalent on polyvinyl chloride (PVC), where ATP levels were 6 to 12 times higher when compared to other polymers. Pathogen-containing species including Salmonella enterica and Escherichia coli were present on all polymers with relative abundance up to 13.7%. S. enterica was selectively enriched on weathered MPs in specific water matrices. These findings support the need to research the potential accumulation of pathogenic organisms on microplastic surfaces.}, } @article {pmid38133341, year = {2023}, author = {Zell, R and Groth, M and Selinka, L and Selinka, HC}, title = {Exploring the Diversity of Plant-Associated Viruses and Related Viruses in Riverine Freshwater Samples Collected in Berlin, Germany.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {38133341}, issn = {2076-0817}, abstract = {Plant-infecting RNA viruses from 30 families and floating genera, as well as a great number of uncultured as yet-unclassified plant-associated viruses have been described. Even so, the plant RNA virosphere is still underexplored. RNA extracted from enriched virus particles of 50 L water samples from the Teltow Canal and the Havel River in Berlin, Germany, was sequenced using Illumina next-generation sequencing. Sequences were searched for plant viruses with BLAST and DIAMOND. Phylogenetic analyses were conducted with IQ-TREE 2. Altogether, 647 virus sequences greater than 1 kb were detected and further analyzed. These data revealed the presence of accepted and novel viruses related to Albetovirus, Alphaflexiviridae, Aspiviridae, Bromoviridae, Endornaviridae, Partitiviridae, Potyviridae, Solemoviridae, Tombusviridae and Virgaviridae. The vast majority of the sequences were novel and could not be taxonomically assigned. Several tombus- and endorna-like viruses make use of alternative translation tables that suggest unicellular green algae, ciliates, or diplomonades as their hosts. The identification of 27 albeto-like satellite viruses increases available sequence data five-fold. Sixteen new poty-like viruses align with other poty-like viruses in a link that combines the Astroviridae and Potyviridae families. Further, the identification of viruses with peptidase A6-like and peptidase A21-like capsid proteins suggests horizontal gene transfer in the evolution of these viruses.}, } @article {pmid38133241, year = {2023}, author = {Afonso, CL and Afonso, AM}, title = {Next-Generation Sequencing for the Detection of Microbial Agents in Avian Clinical Samples.}, journal = {Veterinary sciences}, volume = {10}, number = {12}, pages = {}, pmid = {38133241}, issn = {2306-7381}, abstract = {Direct-targeted next-generation sequencing (tNGS), with its undoubtedly superior diagnostic capacity over real-time PCR (RT-PCR), and direct-non-targeted NGS (ntNGS), with its higher capacity to identify and characterize multiple agents, are both likely to become diagnostic methods of choice in the future. tNGS is a rapid and sensitive method for precise characterization of suspected agents. ntNGS, also known as agnostic diagnosis, does not require a hypothesis and has been used to identify unsuspected infections in clinical samples. Implemented in the form of multiplexed total DNA metagenomics or as total RNA sequencing, the approach produces comprehensive and actionable reports that allow semi-quantitative identification of most of the agents present in respiratory, cloacal, and tissue samples. The diagnostic benefits of the use of direct tNGS and ntNGS are high specificity, compatibility with different types of clinical samples (fresh, frozen, FTA cards, and paraffin-embedded), production of nearly complete infection profiles (viruses, bacteria, fungus, and parasites), production of "semi-quantitative" information, direct agent genotyping, and infectious agent mutational information. The achievements of NGS in terms of diagnosing poultry problems are described here, along with future applications. Multiplexing, development of standard operating procedures, robotics, sequencing kits, automated bioinformatics, cloud computing, and artificial intelligence (AI) are disciplines converging toward the use of this technology for active surveillance in poultry farms. Other advances in human and veterinary NGS sequencing are likely to be adaptable to avian species in the future.}, } @article {pmid38133230, year = {2023}, author = {Lima, J and Ingabire, W and Roehe, R and Dewhurst, RJ}, title = {Estimating Microbial Protein Synthesis in the Rumen-Can 'Omics' Methods Provide New Insights into a Long-Standing Question?.}, journal = {Veterinary sciences}, volume = {10}, number = {12}, pages = {}, pmid = {38133230}, issn = {2306-7381}, support = {61110068//Agriculture and Horticulture Development Board/ ; }, abstract = {Rumen microbial protein synthesis (MPS) provides at least half of the amino acids for the synthesis of milk and meat protein in ruminants. As such, it is fundamental to global food protein security. Estimating microbial protein is central to diet formulation, maximising nitrogen (N)-use efficiency and reducing N losses to the environment. Whilst factors influencing MPS are well established in vitro, techniques for in vivo estimates, including older techniques with cannulated animals and the more recent technique based on urinary purine derivative (UPD) excretion, are subject to large experimental errors. Consequently, models of MPS used in protein rationing are imprecise, resulting in wasted feed protein and unnecessary N losses to the environment. Newer 'omics' techniques are used to characterise microbial communities, their genes and resultant proteins and metabolites. An analysis of microbial communities and genes has recently been used successfully to model complex rumen-related traits, including feed conversion efficiency and methane emissions. Since microbial proteins are more directly related to microbial genes, we expect a strong relationship between rumen metataxonomics/metagenomics and MPS. The main aims of this review are to gauge the understanding of factors affecting MPS, including the use of the UPD technique, and explore whether omics-focused studies could improve the predictability of MPS, with a focus on beef cattle.}, } @article {pmid38133228, year = {2023}, author = {Popov, IV and Einhardt Manzke, N and Sost, MM and Verhoeven, J and Verbruggen, S and Chebotareva, IP and Ermakov, AM and Venema, K}, title = {Modulation of Swine Gut Microbiota by Phytogenic Blends and High Concentrations of Casein in a Validated Swine Large Intestinal In Vitro Model.}, journal = {Veterinary sciences}, volume = {10}, number = {12}, pages = {}, pmid = {38133228}, issn = {2306-7381}, support = {//This research was funded by AHC and has been made possible with the support of the Dutch Province of Limburg with a grant to the Centre for Healthy Eating & Food Innovation (HEFI) of Maastricht University-campus Venlo/ ; }, abstract = {Phytogenic feed additives are gaining popularity in livestock as a replacement for antibiotic growth promotors. Some phytogenic blends (PB) positively affect the production performance, inhibit pathogens within the gut microbiota, and improve the overall health of farm animals. In this study, a swine large intestine in vitro model was used to evaluate the effect of two PBs, alone or in combination with casein, on swine gut microbiota. As a result, the combination of casein with PB1 had the most beneficial effects on swine gut microbiota, as it increased the relative abundance of some commensal bacteria and two genera (Lactobacillus and Oscillospiraceae UCG-002), which are associated with greater production performance in pigs. At the same time, supplementation with PBs did not lead to an increase in opportunistic pathogens, indicating their safety for pigs. Both PBs showed fewer changes in swine gut microbiota compared to interventions with added casein. In contrast, casein supplementation significantly increased beta diversity and the relative abundance of commensal as well as potentially beneficial bacteria. In conclusion, the combination of casein with PBs, in particular PB1, had the most beneficial effects among the studied supplements in vitro, with respect to microbiota modulation and metabolite production, although this data should be proven in further in vivo studies.}, } @article {pmid38132731, year = {2023}, author = {Alleyne, A and Mason, S and Vallès, Y}, title = {Characterization of the Cassava Mycobiome in Symptomatic Leaf Tissues Displaying Cassava Superelongation Disease.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {12}, pages = {}, pmid = {38132731}, issn = {2309-608X}, abstract = {Superelongation disease (SED) is a fungal disease that affects cassava in the Caribbean. The symptoms include the appearance of dry necrotic spots and lesions on the leaves, which may severely affect the plant yield. However, the primary causal pathogen is difficult to culture and isolate in the lab because of its slow growth and potential contamination from faster-growing organisms. In addition, the leaf symptoms can be confused with those caused by other pathogens that produce similar necrotic spots and scab-like lesions. There is also little or no information on the contribution of endophytes, if any, to disease symptoms in cassava, a plant where the disease is prevalent. Therefore, this study aimed to characterize the fungal communities in cassava associated with SED symptoms by analyzing gross fungal morphology and performing metagenomics profiling. First, several individual pathogenic fungi were isolated and cultured from diseased cassava leaf tissues from seven locations in Barbados (BB). Both culture isolation and molecular community analyses showed the presence of several other fungi in the disease microenvironment of symptomatic cassava leaves. These included Fusarium, Colletotrichum, and Alternaria species and the suspected species Elsinoë brasiliensis synonym Sphaceloma manihoticola. Additionally, a community analysis using ITS2 amplicon sequencing of 21 symptomatic leaf tissues from BB, St. Vincent and the Grenadines (SVG), Trinidad and Tobago (TT), and Jamaica (JA) revealed that the disease symptoms of superelongation may also result from the interactions of fungal communities in the mycobiome, including Elsinoë species and other fungi such as Colletotrichum, Cercospora, Alternaria, and Fusarium. Therefore, we suggest that examining the pathobiome concept in SED in the future is necessary.}, } @article {pmid38132570, year = {2023}, author = {Ma, Y and Wu, N and Zhang, T and Li, Y and Cao, L and Zhang, P and Zhang, Z and Zhu, T and Zhang, C}, title = {The microbiome, resistome, and their co-evolution in sewage at a hospital for infectious diseases in Shanghai, China.}, journal = {Microbiology spectrum}, volume = {}, number = {}, pages = {e0390023}, doi = {10.1128/spectrum.03900-23}, pmid = {38132570}, issn = {2165-0497}, abstract = {Environmental antibiotic resistance genes (ARGs) play a critical role in the emergence and spread of antimicrobial resistance, which poses a global health threat. Wastewater from healthcare facilities serves as a significant reservoir for ARGs. Here, we characterized the microbial community along with the resistome (comprising all antibiotic resistance genes) in wastewater from a specialized hospital for infectious diseases in Shanghai. Potential pathogenic bacteria (e.g., Escherichia coli, Pseudomonas aeruginosa, Klebsiella pneumoniae, Enterococcus B faecium) were frequently detected in hospital wastewater and carried multiple ARGs. A complex link between microbiome and resistome was observed in the wastewater of this hospital. The monitoring of ARGs and antibiotic-resistant bacteria (ARB) in hospital wastewater might be of great significance for preventing the spread of ARB.}, } @article {pmid38130927, year = {2023}, author = {LoTempio, J and Delot, E and Vilain, E}, title = {Benchmarking long-read genome sequence alignment tools for human genomics applications.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16515}, pmid = {38130927}, issn = {2167-8359}, mesh = {Humans ; Sequence Analysis, DNA/methods ; *Genome, Human/genetics ; *Benchmarking ; Sequence Alignment ; Genomics/methods ; }, abstract = {BACKGROUND: The utility of long-read genome sequencing platforms has been shown in many fields including whole genome assembly, metagenomics, and amplicon sequencing. Less clear is the applicability of long reads to reference-guided human genomics, which is the foundation of genomic medicine. Here, we benchmark available platform-agnostic alignment tools on datasets from nanopore and single-molecule real-time platforms to understand their suitability in producing a genome representation.

RESULTS: For this study, we leveraged publicly-available data from sample NA12878 generated on Oxford Nanopore and sample NA24385 on Pacific Biosciences platforms. We employed state of the art sequence alignment tools including GraphMap2, long-read aligner (LRA), Minimap2, CoNvex Gap-cost alignMents for Long Reads (NGMLR), and Winnowmap2. Minimap2 and Winnowmap2 were computationally lightweight enough for use at scale, while GraphMap2 was not. NGMLR took a long time and required many resources, but produced alignments each time. LRA was fast, but only worked on Pacific Biosciences data. Each tool widely disagreed on which reads to leave unaligned, affecting the end genome coverage and the number of discoverable breakpoints. No alignment tool independently resolved all large structural variants (1,001-100,000 base pairs) present in the Database of Genome Variants (DGV) for sample NA12878 or the truthset for NA24385.

CONCLUSIONS: These results suggest a combined approach is needed for LRS alignments for human genomics. Specifically, leveraging alignments from three tools will be more effective in generating a complete picture of genomic variability. It should be best practice to use an analysis pipeline that generates alignments with both Minimap2 and Winnowmap2 as they are lightweight and yield different views of the genome. Depending on the question at hand, the data available, and the time constraints, NGMLR and LRA are good options for a third tool. If computational resources and time are not a factor for a given case or experiment, NGMLR will provide another view, and another chance to resolve a case. LRA, while fast, did not work on the nanopore data for our cluster, but PacBio results were promising in that those computations completed faster than Minimap2. Due to its significant burden on computational resources and slow run time, Graphmap2 is not an ideal tool for exploration of a whole human genome generated on a long-read sequencing platform.}, } @article {pmid38130728, year = {2023}, author = {Zha, X and Su, S and Wu, D and Zhang, P and Wei, Y and Fan, S and Huang, Q and Peng, X}, title = {The impact of gut microbiota changes on the intestinal mucus barrier in burned mice: a study using 16S rRNA and metagenomic sequencing.}, journal = {Burns & trauma}, volume = {11}, number = {}, pages = {tkad056}, pmid = {38130728}, issn = {2321-3868}, abstract = {BACKGROUND: The gut microbiota is a complex ecosystem that plays a critical role in human health and disease. However, the relationship between gut microbiota and intestinal damage caused by burns is not well understood. The intestinal mucus layer is crucial for maintaining intestinal homeostasis and providing a physiological barrier against bacterial invasion. This study aims to investigate the impact of gut microbiota on the synthesis and degradation of intestinal mucus after burns and explore potential therapeutic targets for burn injury.

METHODS: A modified histopathological grading system was employed to investigate the effects of burn injury on colon tissue and the intestinal mucus barrier in mice. Subsequently, 16S ribosomal RNA sequencing was used to analyze alterations in the gut microbiota at days 1-10 post-burn. Based on this, metagenomic sequencing was conducted on samples collected at days 1, 5 and 10 to investigate changes in mucus-related microbiota and explore potential underlying mechanisms.

RESULTS: Our findings showed that the mucus barrier was disrupted and that bacterial translocation occurred on day 3 following burn injury in mice. Moreover, the gut microbiota in mice was significantly disrupted from days 1 to 3 following burn injury, but gradually recovered to normal as the disease progressed. Specifically, there was a marked increase in the abundance of symbiotic and pathogenic bacteria associated with mucin degradation on day 1 after burns, but the abundance returned to normal on day 5. Conversely, the abundance of probiotic bacteria associated with mucin synthesis changed in the opposite direction. Further analysis revealed that after a burn injury, bacteria capable of degrading mucus may utilize glycoside hydrolases, flagella and internalins to break down the mucus layer, while bacteria that synthesize mucus may help restore the mucus layer by promoting the production of short-chain fatty acids.

CONCLUSIONS: Burn injury leads to disruption of colonic mucus barrier and dysbiosis of gut microbiota. Some commensal and pathogenic bacteria may participate in mucin degradation via glycoside hydrolases, flagella, internalins, etc. Probiotics may provide short-chain fatty acids (particularly butyrate) as an energy source for stressed intestinal epithelial cells, promote mucin synthesis and accelerate repair of mucus layer.}, } @article {pmid38130711, year = {2023}, author = {}, title = {Correction to "Shotgun metagenomics of soil invertebrate communities reflects taxonomy, biomass, and reference genome properties".}, journal = {Ecology and evolution}, volume = {13}, number = {12}, pages = {e10779}, doi = {10.1002/ece3.10779}, pmid = {38130711}, issn = {2045-7758}, abstract = {[This corrects the article DOI: 10.1002/ece3.8991.].}, } @article {pmid38130518, year = {2023}, author = {Goren, LR and Adeyi, O and Thielen, BK}, title = {Possible Donor-Derived Infection in a Pediatric Liver Transplant Patient With Granulomatous Hepatitis.}, journal = {Cureus}, volume = {15}, number = {11}, pages = {e49136}, pmid = {38130518}, issn = {2168-8184}, abstract = {Pediatric liver transplant recipients are a high-risk group for the development of adenovirus hepatitis and other manifestations of disseminated adenoviral disease. The risk is greatest during periods of increased immunosuppression, including immediately post-transplantation and following treatment for rejection. Manifestations of adenovirus hepatitis are heterogeneous with a wide spectrum of clinical severity, ranging from mild, focal disease to fulminant liver failure. Here we report a case of liver transplantation-associated adenovirus hepatitis presenting with fever and multifocal liver lesions. The diagnosis was not clinically suspected due to atypical imaging findings and pathology. Non-targeted metagenomic sequencing of plasma cell-free DNA facilitated and expedited the diagnosis. Confirmatory conventional testing was obtained, allowing for appropriate initiation of targeted treatment in this patient.}, } @article {pmid38130486, year = {2023}, author = {Song, W and Wang, Y and Peng, B and Yang, L and Gao, J and Xiao, C}, title = {Structure and function of microbiomes in the rhizosphere and endosphere response to temperature and precipitation variation in Inner Mongolia steppes.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1297399}, pmid = {38130486}, issn = {1664-462X}, abstract = {INTRODUCTION: Owing to challenges in the study of complex rhizosphere and endophytic microbial communities, the composition and function of such microbial communities in steppe ecosystems remain elusive. Here, we studied the microbial communities of the rhizosphere and endophytic microbes of the dominant plant species across the Inner Mongolian steppes using metagenomic sequencing and investigated their relationships with changes in mean annual temperature (MAT) and mean annual precipitation (MAP).

METHODS: Metagenomic sequencing based on Illumina high-throughput sequencing, using the paired end method to construct a small fragment library for sequencing.

RESULTS: Adaptation of root systems to the environment affected the composition and function of rhizosphere and endophytic microbial communities. However, these communities exhibited distinct community assembly and environmental adaptation patterns. Both rhizosphere and endophytic microbial communities can be divided into two unrelated systems based on their ecological niches. The composition and function of the rhizosphere microbial communities were mainly influenced by MAT, while those of the endophytic microbial communities were mainly influenced by MAP. MAT affected the growth, reproduction, and lipid decomposition of rhizosphere microorganisms, whereas MAP affected reverse transcription and cell wall/membrane/envelope biogenic functions of endophytic microorganisms.

CONCLUSION: Our findings reveal the composition and function of the rhizosphere and endophytic microbial communities in response to changes in MAP and MAT, which has important implications for future biogeography and climate change research.}, } @article {pmid38130425, year = {2024}, author = {Agarwal, J and Pandey, P and Saxena, SK and Kumar, S}, title = {Comparative analysis of salivary microbiota in diabetic and non-diabetic individuals of North India using metagenomics.}, journal = {Journal of oral biology and craniofacial research}, volume = {14}, number = {1}, pages = {22-26}, pmid = {38130425}, issn = {2212-4268}, abstract = {BACKGROUND: Saliva, an oral secretion is considered an essential biological modulator involved in maintaining oral homeostasis. Increased glucose levels in diabetic patients' saliva may have an impact on diversity of microbes. Comparing the salivary microflora of diabetic and non-diabetic cohorts will help in diagnosis and risk assessment of oral health complications. This will provide greater knowledge about the contribution of oral microbes to the development of oral illnesses. The association between salivary microbiota and diabetic state is less explored in the North Indian population, hence current observational study was performed to analyze the salivary microflora of diabetic and non-diabetic individuals using metagenomic analysis.

MATERIALS AND METHODS: This single-center non-randomized observational trial was conducted in Uttar Pradesh, India. Participants were enrolled into either diabetic (n = 68) or non-diabetic groups (n = 68) based on their diabetes status. Following saliva collection, DNA was extracted and metagenomic sequencing was performed.

RESULTS: Phylum Bacteroidetes and Fusobacteria were significantly abundant in diabetic individuals (p < 0.0001), while Proteobacteria was significantly higher among non-diabetic individuals (p < 0.0001). No statistical difference in phylum Actinobacteria and Firmicutes among diabetics and non-diabetics. Veillonella, Prevotella, Porphyromonas, Leptotrichia, Lactobacillus, and Streptococcus were greater in diabetics whereas the abundance of Capnocytophaga and Neisseria was more among non-diabetics (p < 0.05).

CONCLUSIONS: The genera Veillonella, Prevotella, Porphyromonas, Leptotrichia, Lactobacillus, and Streptococcus were comparatively over the odds with the diabetics in India. The association between microbiota in diabetic population and risk related to increase in occurrence of caries, gingivitis, and periodontitis in diabetic population prevalence should be investigated.}, } @article {pmid38129922, year = {2023}, author = {Monira, S and Barman, I and Jubyda, FT and Ali, SI and Islam, A and Rahman, KMZ and Rashid, MU and Johura, FT and Sultana, M and Zohura, F and Bhuyian, SI and Parvin, T and Sack, D and Ahmed, T and Saif-Ur-Rahman, KM and Hossain, M and Watanabe, H and George, CM and Alam, M}, title = {Gut microbiota shifts favorably with delivery of handwashing with soap and water treatment intervention in a prospective cohort (CHoBI7 trial).}, journal = {Journal of health, population, and nutrition}, volume = {42}, number = {1}, pages = {146}, pmid = {38129922}, issn = {2072-1315}, mesh = {Humans ; *Cholera/prevention & control ; Soaps ; Hand Disinfection/methods ; *Gastrointestinal Microbiome ; Prospective Studies ; Bangladesh ; *Water Purification/methods ; }, abstract = {BACKGROUND: Cholera can result in the expulsion of important microbiota from the gut and result in death if left untreated. The disease transmits mainly via drinking water carrying Vibrio cholerae; and household contacts (HHC) of cholera patients are at elevated risk during the first week of infection. The gut microbiota profiles of HHC-children of cholera patients at Dhaka city slums were investigated before (day 0) and after (day 8) delivery of chlorinated water as part of the major study 'CHoBI7 trial (cholera-hospital-based intervention for 7 days)'.

RESULT: Results of sequencing and analysis of bacterial community DNA revealed the predominance of two bacterial phyla: Bacteroidetes and Firmicutes at day 0 with a relative abundance of 62 ± 6 (mean ± SEM%) and 32 ± 7, respectively. The pattern reversed at day 8 with a decreased relative abundance of Bacteroidetes (39 ± 12; p = 0.034) and an increased abundance of Firmicutes (49 ± 12; p = 0.057). Of 65 bacterial families confirmed at day 0, six belonging to Proteobacteria including Vibrionaceae disappeared at day 8. Interestingly, the relative abundance of four Firmicutes families-Lachnospiraceae, Bifidobacteriaceae, Clostridiaceae, and Ruminococcaceae was increased in all five study children at day 8.

CONCLUSION: The observed exclusion of pathogenic Proteobacteria and enhancement of beneficial Firmicutes in the gut of children delivered with chlorinated water as part of WASH intervention reflect a great promise of the CHoBI7 program in preventing cholera and improving child health.}, } @article {pmid38129781, year = {2023}, author = {Luo, Y and Hu, W and Wu, L and Duan, S and Zhong, X}, title = {Klebsiella pneumoniae invasive syndrome with liver, lung, and brain abscesses complicated with pulmonary fungal infection: a case report and review of the literature.}, journal = {International journal of emergency medicine}, volume = {16}, number = {1}, pages = {92}, pmid = {38129781}, issn = {1865-1372}, abstract = {BACKGROUND: Klebsiella pneumoniae invasion syndrome (KPIS) is a severe multi-site infection that is usually caused by hypervirulent Klebsiella pneumoniae. The bacteria are relatively common in Asian diabetics and can cause organ abscesses or sepsis. When patients develop intracranial infection, the prognosis is poor. After anti-infective treatment, the Klebsiella pneumoniae-induced liver and lung abscesses and pulmonary fungal infection were relieved, but the brain abscesses worsened. Such complex and severe infection cases are rarely reported. Early identification of intracranial infection, selection of antibiotics with high concentrations in cerebrospinal fluid, and active treatment of complications such as diabetes and fungal infection are of great significance for the prognosis of patients.

CASE PRESENTATION: A 71-year-old patient diagnosed with liver abscess in another hospital was transferred to our hospital due to a worsening condition. On day 1 (day of admission), the patient was given invasive mechanical ventilation, continuous renal replacement therapy combined with endotoxin adsorption, antimicrobial treatment with imipenem-cilastatin, and percutaneous catheter drainage for liver abscess. Metagenomic next-generation sequencing in bronchoalveolar lavage fluid indicated Klebsiella pneumoniae (K. pneumoniae), Candida albicans, and Aspergillus flavus complex, and no viruses were detected. Blood and pus cultures revealed K. pneumoniae that was sensitive to piperacillin/tazobactam. The anti-infection therapy was adjusted to piperacillin/tazobactam combined with voriconazole. On day 14, a head computed tomography (CT) scan showed no significant changes, and a chest CT scan showed absorption of multiple abscesses in both lungs. The patient was still unconscious. After the endotracheal tube was removed, cranial magnetic resonance imaging (MRI) showed multiple brain abscesses. Finally, his family gave up, and the patient was discharged and died in a local hospital.

CONCLUSION: In cases of K. pneumoniae infection, the possibility of intracranial, liver, lung, or other site infections should be considered, and physicians should be vigilant for the occurrence of KPIS. For patients suspected of developing an intracranial infection, cerebrospinal fluid should be tested and cultured as soon as possible, a head MRI should be performed, and antibiotics with high distribution in cerebrospinal fluid should be used early. When patients are complicated with diabetes, in addition to glycemic control, vigilance for concurrent fungal infections is also needed.}, } @article {pmid38129103, year = {2023}, author = {Ammer-Herrmenau, C and Antweiler, KL and Asendorf, T and Beyer, G and Buchholz, SM and Cameron, S and Capurso, G and Damm, M and Dang, L and Frost, F and Gomes, A and Hamm, J and Henker, R and Hoffmeister, A and Meinhardt, C and Nawacki, L and Nunes, V and Panyko, A and Pardo, C and Phillip, V and Pukitis, A and Rasch, S and Riekstina, D and Rinja, E and Ruiz-Rebollo, ML and Sirtl, S and Weingarten, M and Sandru, V and Woitalla, J and Ellenrieder, V and Neesse, A}, title = {Gut microbiota predicts severity and reveals novel metabolic signatures in acute pancreatitis.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2023-330987}, pmid = {38129103}, issn = {1468-3288}, abstract = {OBJECTIVE: Early disease prediction is challenging in acute pancreatitis (AP). Here, we prospectively investigate whether the microbiome predicts severity of AP (Pancreatitis-Microbiome As Predictor of Severity; P-MAPS) early at hospital admission.

DESIGN: Buccal and rectal microbial swabs were collected from 424 patients with AP within 72 hours of hospital admission in 15 European centres. All samples were sequenced by full-length 16S rRNA and metagenomic sequencing using Oxford Nanopore Technologies. Primary endpoint was the association of the orointestinal microbiome with the revised Atlanta classification (RAC). Secondary endpoints were mortality, length of hospital stay and severity (organ failure >48 hours and/or occurrence of pancreatic collections requiring intervention) as post hoc analysis. Multivariate analysis was conducted from normalised microbial and corresponding clinical data to build classifiers for predicting severity. For functional profiling, gene set enrichment analysis (GSEA) was performed and normalised enrichment scores calculated.

RESULTS: After data processing, 411 buccal and 391 rectal samples were analysed. The intestinal microbiome significantly differed for the RAC (Bray-Curtis, p value=0.009), mortality (Bray-Curtis, p value 0.006), length of hospital stay (Bray-Curtis, p=0.009) and severity (Bray-Curtis, p value=0.008). A classifier for severity with 16 different species and systemic inflammatory response syndrome achieved an area under the receiving operating characteristic (AUROC) of 85%, a positive predictive value of 67% and a negative predictive value of 94% outperforming established severity scores. GSEA revealed functional pathway units suggesting elevated short-chain fatty acid (SCFA) production in severe AP.

CONCLUSIONS: The orointestinal microbiome predicts clinical hallmark features of AP, and SCFAs may be used for future diagnostic and therapeutic concepts.

TRIAL REGISTRATION NUMBER: NCT04777812.}, } @article {pmid38129066, year = {2024}, author = {Sequino, G and Valentino, V and Esposito, A and Volpe, S and Torrieri, E and De Filippis, F and Ercolini, D}, title = {Microbiome dynamics, antibiotic resistance gene patterns and spoilage-associated genomic potential in fresh anchovies stored in different conditions.}, journal = {Food research international (Ottawa, Ont.)}, volume = {175}, number = {}, pages = {113788}, doi = {10.1016/j.foodres.2023.113788}, pmid = {38129066}, issn = {1873-7145}, mesh = {Animals ; *Food Packaging ; Anti-Bacterial Agents/pharmacology ; Food Microbiology ; Food Preservation ; Genomics ; *Microbiota/genetics ; }, abstract = {Fresh fish is a highly perishable product and is easily spoiled by microbiological activity and chemical oxidation of lipids. However, microbial spoilage is the main factor linked with the rapid fish sensorial degradation due to the action of specific spoilage organisms (SSOs) that have the ability to dominate over other microorganisms and produce metabolites responsible for off-flavours. We explored the microbial dynamics in fresh anchovies stored in different packaging (air, modified atmosphere, under vacuum) and temperatures (0, 4 and 10 °C) using shotgun metagenomics, highlighting the selection of different microbial species according to the packaging type. Indeed, Pseudoalteromonas nigrifaciens, Psychrobacter cryohalolentis and Ps. immobilis, Pseudomonas deceptionensis and Vibrio splendidus have been identified as the main SSOs in aerobically stored anchovies, while Shewanella baltica, Photobacterium iliopiscarium, Ps. cryohalolentis and Ps. immobilis prevailed in VP and MAP. In addition, we identified the presence of spoilage-associated genes, leading to the potential production of biogenic amines and different off-flavors (H2S, TMA). In particular, the abundance of microbial genes leading to BA biosynthesis increased at higher storage temperature, while those related to H2S and TMA production were enriched in aerobically and VP packed anchovies, suggesting that MAP could be an effective strategy in delaying the production of these compounds. Finally, we provided evidence of the presence of a wide range of antibiotic resistance genes conferring resistance to different classes of antibiotic (β-lactams, tetracyclines, polymyxins, trimethoprims and phenicols) and highlighted that storage at higher temperature (4 and 10 °C) boosted the abundance of ARG-carrying taxa, especially in aerobically and MAP packed fish.}, } @article {pmid38129049, year = {2024}, author = {Li, L and Li, N and Fu, J and Liu, J and Ping Wen, X and Cao, H and Xu, H and Zhang, Y and Cao, R}, title = {Synthesis of an autochthonous microbial community by analyzing the core microorganisms responsible for the critical flavor of bran vinegar.}, journal = {Food research international (Ottawa, Ont.)}, volume = {175}, number = {}, pages = {113742}, doi = {10.1016/j.foodres.2023.113742}, pmid = {38129049}, issn = {1873-7145}, mesh = {*Acetic Acid/metabolism ; *Microbiota ; Fermentation ; Amino Acids/metabolism ; Metagenomics ; }, abstract = {Traditional bran vinegar brewing unfolds through natural fermentation, a process driven by spontaneous microbial activity. The unique metabolic activities of various microorganisms lead to distinct flavors and qualities in each batch of vinegar, making it challenging to consistently achieve the desired characteristic flavor compounds. Therefore, identifying the critical microbial species responsible for flavor production and designing starter cultures with improved fermentation efficiency and characteristic flavors are effective methods to address this discrepancy. In this study, 11 core functional microbial species affecting the fermentation flavor of Sichuan shai vinegar (Cupei were placed outside solarization and night-dew for more than one year, and vinegar was the liquid leached from Cupei) (SSV), were revealed by combining PacBio full-length diversity sequencing based on previous metagenomics. The effects of environmental factors and microbial interactions on the growth of 11 microorganisms during fermentation were verified using fermentation experiments. Ultimately, the microbial community was strategically synthesized using a 'top-down' approach, successfully replicating the distinctive flavor profile of Sichuan shai vinegar (SSV). The results showed that the interaction between microorganisms and environmental factors affected microorganism growth. Compared with traditional fermentation, the synthetic microbial community's vinegar-fermented grains (Cupei) can reproduce the key flavor of SSV and is conducive to the production of amino acids. In this study, the key flavor of SSV was reproduced through rational design of the synthetic microbial community. This achievement holds profound significance for the broader application of microbiome assembly strategies in the realm of fermented foods.}, } @article {pmid38128385, year = {2023}, author = {Song, J and Chen, Y and Mi, H and Xu, R and Zhang, W and Wang, C and Rensing, C and Wang, Y}, title = {Prevalence of antibiotic and metal resistance genes in phytoremediated cadmium and zinc contaminated soil assisted by chitosan and Trichoderma harzianum.}, journal = {Environment international}, volume = {183}, number = {}, pages = {108394}, doi = {10.1016/j.envint.2023.108394}, pmid = {38128385}, issn = {1873-6750}, abstract = {Heavy metal in soil have been shown to be toxic with high concentrations and acts as selective pressure on both bacterial metal and antibiotic resistance determinants, posing a serious risk to public health. In cadmium (Cd) and zinc (Zn) contaminated soil, chitosan (Chi) and Trichoderma harzianum (Tri) were applied alone and in combination to assist phytoremediation by Amaranthus hypochondriacus L. Prevalence of antibiotic and metal resistance genes (ARGs and MRGs) in the soil was also evaluated using metagenomic approach. Results indicated that the phytoremediation of Cd and Zn contaminated soil was promoted by Chi, and Tri further reinforced this effect, along with the increased availability of Cd and Zn in soil. Meanwhile, combination of Chi and Tri enhanced the prevalence of ARGs (e.g., multidrug and β-lactam resistance genes) and maintained a high level of MRGs (e.g., chromium, copper) in soil. Soil available Zn and Cd fractions were the main factors contributing to ARGs profile by co-selection, while boosted bacterial hosts (e.g., Mitsuaria, Solirubrobacter, Ramlibacter) contributed to prevalence of most MRGs (e.g., Cd). These findings indicate the potential risk of ARGs and MRGs propagation in phytoremediation of metal contaminated soils assisted by organic and biological agents.}, } @article {pmid38128305, year = {2023}, author = {Heyer, R and Hellwig, P and Maus, I and Walke, D and Schlüter, A and Hassa, J and Sczyrba, A and Tubbesing, T and Klocke, M and Mächtig, T and Schallert, K and Seick, I and Reichl, U and Benndorf, D}, title = {Breakdown of hardly degradable carbohydrates (lignocellulose) in a two-stage anaerobic digestion plant is favored in the main fermenter.}, journal = {Water research}, volume = {250}, number = {}, pages = {121020}, doi = {10.1016/j.watres.2023.121020}, pmid = {38128305}, issn = {1879-2448}, abstract = {The yield and productivity of biogas plants depend on the degradation performance of their microbiomes. The spatial separation of the anaerobic digestion (AD) process into a separate hydrolysis and a main fermenter should improve cultivation conditions of the microorganisms involved in the degradation of complex substrates like lignocellulosic biomass (LCB) and, thus, the performance of anaerobic digesters. However, relatively little is known about such two-stage processes. Here, we investigated the process performance of a two-stage agricultural AD over one year, focusing on chemical and technical process parameters and metagenome-centric metaproteomics. Technical and chemical parameters indicated stable operation of the main fermenter but varying conditions for the open hydrolysis fermenter. Matching this, the microbiome in the hydrolysis fermenter has a higher dynamic than in the main fermenter. Metaproteomics-based microbiome analysis revealed a partial separation between early and common steps in carbohydrate degradation and primary fermentation in the hydrolysis fermenter but complex carbohydrate degradation, secondary fermentation, and methanogenesis in the main fermenter. Detailed metagenomics and metaproteomics characterization of the single metagenome-assembled genomes showed that the species focus on specific substrate niches and do not utilize their full genetic potential to degrade, for example, LCB. Overall, it seems that a separation of AD in a hydrolysis and a main fermenter does not improve the cleavage of complex substrates but significantly improves the overall process performance. In contrast, the remaining methanogenic activity in the hydrolysis fermenter may cause methane losses.}, } @article {pmid38128304, year = {2023}, author = {Páez-Watson, T and van Loosdrecht, MCM and Wahl, SA}, title = {From metagenomes to metabolism: Systematically assessing the metabolic flux feasibilities for "Candidatus Accumulibacter" species during anaerobic substrate uptake.}, journal = {Water research}, volume = {250}, number = {}, pages = {121028}, doi = {10.1016/j.watres.2023.121028}, pmid = {38128304}, issn = {1879-2448}, abstract = {With the rapid growing availability of metagenome assembled genomes (MAGs) and associated metabolic models, the identification of metabolic potential in individual community members has become possible. However, the field still lacks an unbiassed systematic evaluation of the generated metagenomic information to uncover not only metabolic potential, but also feasibilities of these models under specific environmental conditions. In this study, we present a systematic analysis of the metabolic potential in species of "Candidatus Accumulibacter", a group of polyphosphate-accumulating organisms (PAOs). We constructed a metabolic model of the central carbon metabolism and compared the metabolic potential among available MAGs for "Ca. Accumulibacter" species. By combining Elementary Flux Modes Analysis (EFMA) with max-min driving force (MDF) optimization, we obtained all possible flux distributions of the metabolic network and calculated their individual thermodynamic feasibility. Our findings reveal significant variations in the metabolic potential among "Ca. Accumulibacter" MAGs, particularly in the presence of anaplerotic reactions. EFMA revealed 700 unique flux distributions in the complete metabolic model that enable the anaerobic uptake of acetate and its conversion into polyhydroxyalkanoates (PHAs), a well-known phenotype of "Ca. Accumulibacter". However, thermodynamic constraints narrowed down this solution space to 146 models that were stoichiometrically and thermodynamically feasible (MDF > 0 kJ/mol), of which only 8 were strongly feasible (MDF > 7 kJ/mol). Notably, several novel flux distributions for the metabolic model were identified, suggesting putative, yet unreported, functions within the PAO communities. Overall, this work provides valuable insights into the metabolic variability among "Ca. Accumulibacter" species and redefines the anaerobic metabolic potential in the context of phosphate removal. More generally, the integrated workflow presented in this paper can be applied to any metabolic model obtained from a MAG generated from microbial communities to objectively narrow the expected phenotypes from community members.}, } @article {pmid38127978, year = {2023}, author = {Liuu, S and Nepelska, M and Pfister, H and Gamelas Magalhaes, J and Chevalier, G and Strozzi, F and Billerey, C and Maresca, M and Nicoletti, C and Di Pasquale, E and Pechard, C and Bardouillet, L and Girardin, SE and Boneca, IG and Doré, J and Blottière, HM and Bonny, C and Chene, L and Cultrone, A}, title = {Identification of a muropeptide precursor transporter from gut microbiota and its role in preventing intestinal inflammation.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {52}, pages = {e2306863120}, pmid = {38127978}, issn = {1091-6490}, support = {FP7/2007-2013//European community's Seventh Framework Programme/ ; FP7/2007-2013//European community's Seventh framework Programme/ ; }, mesh = {Humans ; Mice ; Animals ; *Gastrointestinal Microbiome ; Peptidoglycan/metabolism ; Intestines/pathology ; Inflammation/metabolism ; Membrane Transport Proteins/metabolism ; Anti-Inflammatory Agents/metabolism ; Dextran Sulfate ; *Colitis/metabolism ; Disease Models, Animal ; Colon/metabolism ; Mice, Inbred C57BL ; }, abstract = {The gut microbiota is a considerable source of biologically active compounds that can promote intestinal homeostasis and improve immune responses. Here, we used large expression libraries of cloned metagenomic DNA to identify compounds able to sustain an anti-inflammatory reaction on host cells. Starting with a screen for NF-κB activation, we have identified overlapping clones harbouring a heterodimeric ATP-binding cassette (ABC)-transporter from a Firmicutes. Extensive purification of the clone's supernatant demonstrates that the ABC-transporter allows for the efficient extracellular accumulation of three muropeptide precursor, with anti-inflammatory properties. They induce IL-10 secretion from human monocyte-derived dendritic cells and proved effective in reducing AIEC LF82 epithelial damage and IL-8 secretion in human intestinal resections. In addition, treatment with supernatants containing the muropeptide precursor reduces body weight loss and improves histological parameters in Dextran Sulfate Sodium (DSS)-treated mice. Until now, the source of peptidoglycan fragments was shown to come from the natural turnover of the peptidoglycan layer by endogenous peptidoglycan hydrolases. This is a report showing an ABC-transporter as a natural source of secreted muropeptide precursor and as an indirect player in epithelial barrier strengthening. The mechanism described here might represent an important component of the host immune homeostasis.}, } @article {pmid38127927, year = {2023}, author = {Castellot, A and Camacho, J and Fernández-García, MD and Tarragó, D}, title = {Shotgun metagenomics to investigate unknown viral etiologies of pediatric meningoencephalitis.}, journal = {PloS one}, volume = {18}, number = {12}, pages = {e0296036}, pmid = {38127927}, issn = {1932-6203}, mesh = {Humans ; Child ; Retrospective Studies ; *Meningoencephalitis/diagnosis ; *Viruses/genetics ; *Virus Diseases/complications/diagnosis ; Inflammation ; Herpesvirus 3, Human ; Metagenomics/methods ; }, abstract = {INTRODUCTION: Meningoencephalitis in children poses a diagnostic challenge, as etiology remains unknown for most of patients. Viral metagenomics by shotgun sequencing represents a powerful tool for investigating unknown viral infections related to these cases.

PATIENTS AND METHODS: In a two-year, reference-centre, retrospective study, we investigated the usefulness of viral metagenomics of cerebrospinal fluid (CSF) for the diagnosis of viral infectious meningoencephalitis in forty seven pediatric patients, forty of them previously tested negative with a routine neurologic panel of viral targets that included herpesvirus 1-3 and enterovirus. We enhanced the detection by targeting viral sequences by hybrid capture. Raw sequence data was analysed using three bioinformatics pipelines.

RESULTS: Out of forty remaining children with meningoencephalitis of unknown viral etiology, a significant detection of viral nucleic acid by shotgun sequencing was found in twenty one, which was confirmed in ten of them by specific PCR: seven human endogenous retrovirus K113 (HER K113), one parechovirus 3, one human herpesvirus 5 (HHV5); one enterovirus B (Echovirus 9). The remaining eleven CSF were not confirmed by PCR: three rotavirus, one human herpesvirus 7 (HHV7), one influenza A, one mastadenovirus C, one sindbis virus, one torque teno virus, one human immunodeficiency virus 1 (HIV-1), one human alphaherpesvirus 3 (HHV3), one human alphaherpesvirus 2 (HHV2).

CONCLUSIONS: Underutilization of currently available meningitis-encephalitis diagnostic techniques such as BioFire® FilmArray® is the main cause of undiagnosed cases of meningoencephalitis. However, in this study we detected uncommon viruses that should be considered, including virus, rotavirus, sindbis virus, influenza A virus and HHV7. No other viral sequences that could be readily linked to CNS inflammation were detected. Some findings may stem from reagent or sample contamination, as seen with papillomavirus; for others, the clinical relevance of the virus remains uncertain and should be substantiated by further studies, as is the case with endogenous retrovirus K113 virus. Online bioinformatics pipeline CZID represents a valuable tool for analysing shotgun sequencing data in cases of neurological conditions with unknown etiology. Altogether, this study highlights the potential of shotgun sequencing in identifying previously unknown viral neuropathogens and sheds light on the interpretation issues related to its application in clinical microbiology.}, } @article {pmid38127234, year = {2023}, author = {Herrera-Calderon, AC and Leal, L and Suárez-Bautista, JD and Manotas-Viloria, HS and Muñoz-García, A and Franco, D and Arenas, NE and Vanegas, J}, title = {Metagenomic and genomic analysis of heavy metal-tolerant and -resistant bacteria in resource islands in a semi-arid zone of the Colombian Caribbean.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38127234}, issn = {1614-7499}, abstract = {Bacteria from resource islands can adapt to different extreme conditions in semi-arid regions. We aimed to determine the potential resistance and tolerance to heavy metals from the bacterial community under the canopy of three resource islands in a semi-arid zone of the Colombian Caribbean. Total DNA was extracted from soil and through a metagenomics approach, we identified genes related to heavy metal tolerance and resistance under the influence of drought and humidity conditions, as well as the presence or absence of vegetation. We characterized the genomes of bacterial isolates cultivated in the presence of four heavy metals. The abundances of genes related to heavy metal resistance and tolerance were favored by soil moisture and the presence of vegetation. We observed a high abundance of resistance genes (60.4%) for Cu, Zn, and Ni, while 39.6% represented tolerance. These genes positively correlated with clay and silt content, and negatively correlated with sand content. Resistance and tolerance were associated with detoxification mechanisms involving oxidoreductase enzymes, metalloproteases, and hydrolases, as well as transmembrane proteins involved in metal transport such as efflux pumps and ion transmembrane transporters. The Bacillus velezensis C3-3 and Cytobacillus gottheilii T106 isolates showed resistance to 5 mM of Cd, Co, Mn, and Ni through detoxification genes associated with ABC pumps, metal transport proteins, ion antiporter proteins, and import systems, among others. Overall, these findings highlight the potential of bacteria from resource islands in bioremediation processes of soils contaminated with heavy metals.}, } @article {pmid38127231, year = {2023}, author = {Brzeszcz, J and Steliga, T and Ryszka, P and Kaszycki, P and Kapusta, P}, title = {Bacteria degrading both n-alkanes and aromatic hydrocarbons are prevalent in soils.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38127231}, issn = {1614-7499}, support = {UMO-2012/07/N/NZ9/00920//Narodowe Centrum Nauki/ ; }, abstract = {This study was undertaken to determine the distribution of soil bacteria capable of utilizing both n-alkanes and aromatic hydrocarbons. These microorganisms have not been comprehensively investigated so far. Ten contaminated (4046-43,861 mg of total petroleum hydrocarbons (TPH) kg[-1] of dry weight of soil) and five unpolluted (320-2754 mg TPH kg[-1] of dry weight of soil) soil samples from temperate, arid, and Alpine soils were subjected to isolation of degraders with extended preferences and shotgun metagenomic sequencing (selected samples). The applied approach allowed to reveal that (a) these bacteria can be isolated from pristine and polluted soils, and (b) the distribution of alkane monooxygenase (alkB) and aromatic ring hydroxylating dioxygenases (ARHDs) encoding genes is not associated with the contamination presence. Some alkB and ARHD genes shared the same taxonomic affiliation; they were most often linked with the Rhodococcus, Pseudomonas, and Mycolicibacterium genera. Moreover, these taxa together with the Paeniglutamicibacter genus constituted the most numerous groups among 132 culturable strains growing in the presence of both n-alkanes and aromatic hydrocarbons. All those results indicate (a) the prevalence of the hydrocarbon degraders with extended preferences and (b) the potential of uncontaminated soil as a source of hydrocarbon degraders applied for bioremediation purposes.}, } @article {pmid38127093, year = {2023}, author = {Brown, EL and Essigmann, HT and Hoffman, KL and Petrosino, J and Jun, G and Brown, SA and Aguilar, D and Hanis, CL}, title = {C-Reactive Protein Levels Correlate with Measures of Dysglycemia and Gut Microbiome Profiles.}, journal = {Current microbiology}, volume = {81}, number = {1}, pages = {45}, pmid = {38127093}, issn = {1432-0991}, support = {R01 DK116378/DK/NIDDK NIH HHS/United States ; R01DK109920/NH/NIH HHS/United States ; R01DK116378/NH/NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; C-Reactive Protein ; *Diabetes Mellitus, Type 2 ; *Microbiota ; Inflammation ; }, abstract = {C-reactive protein (CRP) is a commonly used marker of low-grade inflammation as well as a marker of acute infection. CRP levels are elevated in those with diabetes and increased CRP concentrations are a risk factor for developing type 2 diabetes. Gut microbiome effects on metabolism and immune responses can impact chronic inflammation, including affecting CRP levels, that in turn can lead to the development and maintenance of dysglycemia. Using a high-sensitivity C-reactive protein (hsCRP) assay capable of detecting subtle changes in C-reactive protein, we show that higher hsCRP levels specifically correlate with worsening glycemia, reduced microbial richness and evenness, and with a reduction in the Firmicutes/Bacteroidota ratio. These data demonstrate a pivotal role for CRP not only in the context of worsening glycemia and changes to the gut microbiota, but also highlight CRP as a potential target for mitigating type 2 diabetes progression or as a therapeutic target that could be manipulated through the microbiome. Understanding these processes will provide insights into the etiology of type 2 diabetes in addition to opening doors leading to possible novel diagnostic strategies and therapeutics.}, } @article {pmid38126779, year = {2023}, author = {Ahmed, N and Joglekar, P and Deming, C and , and Lemon, KP and Kong, HH and Segre, JA and Conlan, S}, title = {Genomic characterization of the C. tuberculostearicum species complex, a prominent member of the human skin microbiome.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0063223}, doi = {10.1128/msystems.00632-23}, pmid = {38126779}, issn = {2379-5077}, support = {R35 GM141806/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Corynebacterium Infections/microbiology ; Genomics ; Whole Genome Sequencing ; *Microbiota/genetics ; }, abstract = {Amplicon sequencing data combined with isolate whole genome sequencing have expanded our understanding of Corynebacterium on the skin. Healthy human skin is colonized by a diverse collection of Corynebacterium species, but Corynebacterium tuberculostearicum predominates on many skin sites. Our work supports the emerging idea that C. tuberculostearicum is a species complex encompassing several distinct species. We produced a collection of genomes that help define this complex, including a potentially new species we term Corynebacterium hallux based on a preference for sites on the feet, whole-genome average nucleotide identity, pangenomic analysis, and growth in skin-like media. This isolate collection and high-quality genome resource set the stage for developing engineered strains for both basic and translational clinical studies.}, } @article {pmid38126755, year = {2023}, author = {Nesbø, CL and Fitamo, TM and Lee, H and Edwards, EA}, title = {Metagenomes and metagenome-assembled genomes from a sequentially fed anaerobic digester treating solid organic municipal waste.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0091923}, doi = {10.1128/mra.00919-23}, pmid = {38126755}, issn = {2576-098X}, abstract = {We present a data set of four metagenomes and 281 metagenome-assembled genomes describing the microbial community of a laboratory-scale high solids anaerobic digester. Our objective was to obtain information on the coding potential of the microbial community and draft genomes of the most abundant organisms in the digester.}, } @article {pmid38126754, year = {2023}, author = {Tannock, GW}, title = {Understanding the gut microbiota by considering human evolution: a story of fire, cereals, cooking, molecular ingenuity, and functional cooperation.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {}, number = {}, pages = {e0012722}, doi = {10.1128/mmbr.00127-22}, pmid = {38126754}, issn = {1098-5557}, abstract = {SUMMARYThe microbial community inhabiting the human colon, referred to as the gut microbiota, is mostly composed of bacterial species that, through extensive metabolic networking, degrade and ferment components of food and human secretions. The taxonomic composition of the microbiota has been extensively investigated in metagenomic studies that have also revealed details of molecular processes by which common components of the human diet are metabolized by specific members of the microbiota. Most studies of the gut microbiota aim to detect deviations in microbiota composition in patients relative to controls in the hope of showing that some diseases and conditions are due to or exacerbated by alterations to the gut microbiota. The aim of this review is to consider the gut microbiota in relation to the evolution of Homo sapiens which was heavily influenced by the consumption of a nutrient-dense non-arboreal diet, limited gut storage capacity, and acquisition of skills relating to mastering fire, cooking, and cultivation of cereal crops. The review delves into the past to gain an appreciation of what is important in the present. A holistic view of "healthy" microbiota function is proposed based on the evolutionary pathway shared by humans and gut microbes.}, } @article {pmid38126212, year = {2023}, author = {Li, Y and Yu, H and Xiong, L and Zeng, K and Wei, Y and Li, H and Ji, X}, title = {Diversity and function of viral AMGs associated with DNA biosynthesis in the Napahai plateau wetland.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-15}, doi = {10.1080/09593330.2023.2296531}, pmid = {38126212}, issn = {1479-487X}, abstract = {Viruses play an important role in microbial community structure and biodiversity by lysing host cells, and can also affect host metabolic pathways by expressing auxiliary metabolic genes (AMGs). As a unique low-latitude, high-altitude seasonal plateau wetland in China, Napahai has high research value. However, studies on the genetic diversity of AMGs and viruses associated with DNA biosynthesis have not been reported. Based on metagenomics, with the phylogenetic tree, PCoA, and α diversity analysis, we found that three DNA biosynthesis-related viral AMGs (cobS, mazG, and purM) in the Napahai plateau wetland were rich in genetic diversity, uniqueness, and differences compared with other habitats and host sources. Through the KEGG metabolic pathway and metabolic flow analysis of Pseudomonas mandelii (SW-3) and phage (VSW-3), the AMGs (cobS, mazG, and purM) genes of the three related viruses involved in DNA biosynthesis were upregulated and their expression increased significantly. In general, we systematically described the genetic diversity of AMGs associated with DNA biosynthesis in plateau wetland ecosystems and clarified the contribution of viral AMGs in the Napahai plateau wetland to DNA biosynthesis, as well as the changes of metabolites and genes. It further expands the understanding of phage-host interactions, which is of great significance for further revealing the role of viral AMGs in the biological evolution and biogeochemical cycle of wetland ecosystems.}, } @article {pmid38126017, year = {2023}, author = {Gätjens-Boniche, O and Jiménez-Madrigal, JP and Whetten, RW and Valenzuela-Diaz, S and Alemán-Gutiérrez, A and Hanson, PE and Pinto-Tomás, AA}, title = {Microbiome and plant cell transformation trigger insect gall induction in cassava.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1237966}, pmid = {38126017}, issn = {1664-462X}, abstract = {Several specialised insects can manipulate normal plant development to induce a highly organised structure known as a gall, which represents one of the most complex interactions between insects and plants. Thus far, the mechanism for insect-induced plant galls has remained elusive. To study the induction mechanism of insect galls, we selected the gall induced by Iatrophobia brasiliensis (Diptera: Cecidomyiidae) in cassava (Euphorbiaceae: Manihot esculenta Crantz) as our model. PCR-based molecular markers and deep metagenomic sequencing data were employed to analyse the gall microbiome and to test the hypothesis that gall cells are genetically transformed by insect vectored bacteria. A shotgun sequencing discrimination approach was implemented to selectively discriminate between foreign DNA and the reference host plant genome. Several known candidate insertion sequences were identified, the most significant being DNA sequences found in bacterial genes related to the transcription regulatory factor CadR, cadmium-transporting ATPase encoded by the cadA gene, nitrate transport permease protein (nrtB gene), and arsenical pump ATPase (arsA gene). In addition, a DNA fragment associated with ubiquitin-like gene E2 was identified as a potential accessory genetic element involved in gall induction mechanism. Furthermore, our results suggest that the increased quality and rapid development of gall tissue are mostly driven by microbiome enrichment and the acquisition of critical endophytes. An initial gall-like structure was experimentally obtained in M. esculenta cultured tissues through inoculation assays using a Rhodococcus bacterial strain that originated from the inducing insect, which we related to the gall induction process. We provide evidence that the modification of the endophytic microbiome and the genetic transformation of plant cells in M. esculenta are two essential requirements for insect-induced gall formation. Based on these findings and having observed the same potential DNA marker in galls from other plant species (ubiquitin-like gene E2), we speculate that bacterially mediated genetic transformation of plant cells may represent a more widespread gall induction mechanism found in nature.}, } @article {pmid38126014, year = {2023}, author = {Wang, Y and Lin, S and Li, J and Jia, X and Hu, M and Cai, Y and Cheng, P and Li, M and Chen, Y and Lin, W and Wang, H and Wu, Z}, title = {Metagenomics-based exploration of key soil microorganisms contributing to continuously planted Casuarina equisetifolia growth inhibition and their interactions with soil nutrient transformation.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1324184}, pmid = {38126014}, issn = {1664-462X}, abstract = {Casuarina equisetifolia (C. equisetifolia) is an economically important forest tree species, often cultivated in continuous monoculture as a coastal protection forest. Continuous planting has gradually affected growth and severely restricted the sustainable development of the C. equisetifolia industry. In this study, we analyzed the effects of continuous planting on C. equisetifolia growth and explored the rhizosphere soil microecological mechanism from a metagenomic perspective. The results showed that continuous planting resulted in dwarfing, shorter root length, and reduced C. equisetifolia seedling root system. Metagenomics analysis showed that 10 key characteristic microorganisms, mainly Actinoallomurus, Actinomadura, and Mycobacterium, were responsible for continuously planted C. equisetifolia trees. Quantitative analysis showed that the number of microorganisms in these three genera decreased significantly with the increase of continuous planting. Gene function analysis showed that continuous planting led to the weakening of the environmental information processing-signal transduction ability of soil characteristic microorganisms, and the decrease of C. equisetifolia trees against stress. Reduced capacity for metabolism, genetic information processing-replication and repair resulted in reduced microbial propagation and reduced microbial quantity in the rhizosphere soil of C. equisetifolia trees. Secondly, amino acid metabolism, carbohydrate metabolism, glycan biosynthesis and metabolism, lipid metabolism, metabolism of cofactors and vitamins were all significantly reduced, resulting in a decrease in the ability of the soil to synthesize and metabolize carbon and nitrogen. These reduced capacities further led to reduced soil microbial quantity, microbial carbon and nitrogen, microbial respiration intensity, reduced soil enzyme nutrient cycling and resistance-related enzyme activities, a significant reduction in available nutrient content of rhizosphere soils, a reduction in the ion exchange capacity, and an impediment to C. equisetifolia growth. This study provides an important basis for the management of continuously planted C. equisetifolia plantations.}, } @article {pmid38125907, year = {2023}, author = {Deng, Y and Zhu, C and Jiang, R and Yu, C and Zhao, J and Jiang, X and Wen, J}, title = {Salivary signatures of oral-brain communication in sleep bruxers.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1321855}, pmid = {38125907}, issn = {2235-2988}, mesh = {Humans ; *Sleep Bruxism/complications/diagnosis ; Sleep ; Brain/metabolism ; Risk Factors ; }, abstract = {INTRODUCTION: Microbiota and their interaction with hosts have been of great interest in brain research in recent years. However, the role of oral microbiota in mental illness and the underlying mechanism of oral-brain communication remains elusive. Sleep bruxism (SB) is an oral parafunctional activity related to the nervous system and is considered a risk factor for harmful clinical consequences and severe systemic conditions. Exploring the connection between oral microbiota and sleep bruxism may deepen our understanding of the complex relationship between oral-brain axis and provide insights for treatment.

METHODS: In this study, salivary samples were collected from 22 individuals with SB and 21 healthy controls, and metagenomics with metabolomics was performed. Nonparametric Wilcoxon test were applied for the statistical analysis between the two groups. Microbial dysbiosis and altered oral metabolites were found in the SB individuals.

RESULTS: The characteristic metabolite N-acetylglucosamine (GlcNAc) (VIP=8.4823, P<0.05) was correlated to a statistically lower Streptococcus mitis level in SB individuals. Salivary IFN-g level and IFN-g/IL-4 ratio were detected with significant changes in a chip assay. Amino acid metabolism pathways were upregulated, and the pathway with the largest number of differentially expressed genes is related to amino-tRNA charging pathway, while the most significantly enriched pathway is related to arginine biosynthesis. Neurotransmitter-associated pathways with glutamatergic and GABAergic synapses and cardiovascular system-related pathways were enriched in the SB group.

DISCUSSION: These results indicate a possible neuroimmune regulatory network of oral-brain communication in SB, which helps explain the mechanism of the oral microbiome with the host in sleep bruxers and provides a reference for early clinical and therapeutic intervention to improve the diagnosis and treatment of SB and similar diseases.}, } @article {pmid38125540, year = {2023}, author = {Dhivahar, J and Parthasarathy, A and Krishnan, K and Kovi, BS and Pandian, GN}, title = {Bat-associated microbes: Opportunities and perils, an overview.}, journal = {Heliyon}, volume = {9}, number = {12}, pages = {e22351}, pmid = {38125540}, issn = {2405-8440}, abstract = {The potential biotechnological uses of bat-associated bacteria are discussed briefly, indicating avenues for biotechnological applications of bat-associated microbes. The uniqueness of bats in terms of their lifestyle, genomes and molecular immunology may predispose bats to act as disease reservoirs. Molecular phylogenetic analysis has shown several instances of bats harbouring the ancestral lineages of bacterial (Bartonella), protozoal (Plasmodium, Trypanosoma cruzi) and viral (SARS-CoV2) pathogens infecting humans. Along with the transmission of viruses from bats, we also discuss the potential roles of bat-associated bacteria, fungi, and protozoan parasites in emerging diseases. Current evidence suggests that environmental changes and interactions between wildlife, livestock, and humans contribute to the spill-over of infectious agents from bats to other hosts. Domestic animals including livestock may act as intermediate amplifying hosts for bat-origin pathogens to transmit to humans. An increasing number of studies investigating bat pathogen diversity and infection dynamics have been published. However, whether or how these infectious agents are transmitted both within bat populations and to other hosts, including humans, often remains unknown. Metagenomic approaches are uncovering the dynamics and distribution of potential pathogens in bat microbiomes, which might improve the understanding of disease emergence and transmission. Here, we summarize the current knowledge on bat zoonoses of public health concern and flag the gaps in the knowledge to enable further research and allocation of resources for tackling future outbreaks.}, } @article {pmid38125306, year = {2023}, author = {Cui, C and Jiang, M and Zhang, C and Zhang, N and Jin, FJ and Li, T and Lee, HG and Jin, L}, title = {Assembly strategies for rubber-degrading microbial consortia based on omics tools.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {11}, number = {}, pages = {1326395}, pmid = {38125306}, issn = {2296-4185}, abstract = {Numerous microorganisms, including bacteria and fungus, have been identified as capable of degrading rubber. Rubber biodegradation is still understudied due to its high stability and the lack of well-defined pathways and efficient enzymes involved in microorganism metabolism. However, rubber products manufacture and usage cause substantial environmental issues, and present physical-chemical methods involve dangerous chemical solvents, massive energy, and trash with health hazards. Eco-friendly solutions are required in this context, and biotechnological rubber treatment offers considerable promise. The structural and functional enzymes involved in poly (cis-1,4-isoprene) rubber and their cleavage mechanisms have been extensively studied. Similarly, novel bacterial strains capable of degrading polymers have been investigated. In contrast, relatively few studies have been conducted to establish natural rubber (NR) degrading bacterial consortia based on metagenomics, considering process optimization, cost effective approaches and larger scale experiments seeking practical and realistic applications. In light of the obstacles encountered during the constructing NR-degrading consortia, this study proposes the utilization of multi-omics tools to discern the underlying mechanisms and metabolites of rubber degradation, as well as associated enzymes and effective synthesized microbial consortia. In addition, the utilization of omics tool-based methods is suggested as a primary research direction for the development of synthesized microbial consortia in the future.}, } @article {pmid38124733, year = {2023}, author = {Jiang, D and Goswami, R and Dennis, M and Heimsath, H and Kozlowski, PA and Ardeshir, A and Van Rompay, KKA and De Paris, K and Permar, SR and Surana, NK}, title = {Sutterella and its metabolic pathways positively correlate with vaccine-elicited antibody responses in infant rhesus macaques.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1283343}, pmid = {38124733}, issn = {1664-3224}, support = {P01 AI117915/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Animals ; Antibody Formation ; Macaca mulatta ; RNA, Ribosomal, 16S/genetics ; *Vaccines ; *HIV Infections ; Metabolic Networks and Pathways ; Bile Acids and Salts ; Fatty Acids, Volatile ; }, abstract = {INTRODUCTION: It is becoming clearer that the microbiota helps drive responses to vaccines; however, little is known about the underlying mechanism. In this study, we aimed to identify microbial features that are associated with vaccine immunogenicity in infant rhesus macaques.

METHODS: We analyzed 16S rRNA gene sequencing data of 215 fecal samples collected at multiple timepoints from 64 nursery-reared infant macaques that received various HIV vaccine regimens. PERMANOVA tests were performed to determine factors affecting composition of the gut microbiota throughout the first eight months of life in these monkeys. We used DESeq2 to identify differentially abundant bacterial taxa, PICRUSt2 to impute metagenomic information, and mass spectrophotometry to determine levels of fecal short-chain fatty acids and bile acids.

RESULTS: Composition of the early-life gut microbial communities in nursery-reared rhesus macaques from the same animal care facility was driven by age, birth year, and vaccination status. We identified a Sutterella and a Rodentibacter species that positively correlated with vaccine-elicited antibody responses, with the Sutterella species exhibiting more robust findings. Analysis of Sutterella-related metagenomic data revealed five metabolic pathways that significantly correlated with improved antibody responses following HIV vaccination. Given these pathways have been associated with short-chain fatty acids and bile acids, we quantified the fecal concentration of these metabolites and found several that correlated with higher levels of HIV immunogen-elicited plasma IgG.

DISCUSSION: Our findings highlight an intricate bidirectional relationship between the microbiota and vaccines, where multiple aspects of the vaccination regimen modulate the microbiota and specific microbial features facilitate vaccine responses. An improved understanding of this microbiota-vaccine interplay will help develop more effective vaccines, particularly those that are tailored for early life.}, } @article {pmid38124452, year = {2023}, author = {Velarde-Garcéz, DA and Mata, VA and Beja, P and da Silva, LP}, title = {DNA metabarcoding, diversity partitioning and null models reveal mechanisms of seasonal trophic specialization in a Mediterranean warbler.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {e17245}, doi = {10.1111/mec.17245}, pmid = {38124452}, issn = {1365-294X}, support = {//EDP Biodiversity Chair/ ; //ERA Chair in Environmental Metagenomics/ ; POCI-01-0145-FEDER-022127//Portuguese E-Infrastructure for Information and Research on Biodiversity/ ; 857251//Teaming Project Biopolis/ ; 668981//Teaming Project Biopolis/ ; 2020.02547.CEECIND//Fundação para a Ciência e Tecnologia/ ; CEECIND/02064/2017//Fundação para a Ciência e Tecnologia/ ; }, abstract = {Optimal Foraging Theory (OFT) predicts that a population's trophic niche expansion should occur in periods of food scarcity as individuals begin to opportunistically exploit sub-optimal food items. However, the Niche Variation Hypothesis (NVH) posits that niche widening may result from increased among-individual differentiation due to food partitioning to avoid competition. We tested these hypotheses through a DNA metabarcoding study of the Sardinian Warbler (Curruca melanocephala) diet over a year. We used null models and the decomposition of beta diversity on among-individual dietary differentiation to infer the mechanisms driving the population's niche variation. Warblers fed frequently on berries, with a peak in late summer and, to a lesser extent, in autumn. Their diet also included a wide range of arthropods, with their prevalence varying among seasons. Consistent with OFT, the population's niche width was narrower in spring/summer when the population was strongly specialized in berries. In winter, the population's niche expanded, possibly reflecting seasonal declines in food abundance. As predicted by NVH, among-individual differentiation tended to be higher in winter, but this was mainly due to increased differences in dietary richness rather than to the partitioning of resources. Overall, our results suggest that within-individual niche does not increase in lean periods, and instead, individuals adopt either a more opportunistic or more specialized foraging strategy. Increased competition in periods of scarcity may help explain such patterns, but instead of showing increased food partitioning as expected from NVH, it may reflect OFT mechanisms on individuals with differential competitive ability to access better food resources.}, } @article {pmid38123635, year = {2023}, author = {Park, J and Lee, KE and Choi, DH and Kim, YK and Lee, WH and Kim, MS and Sung, HWJ and Chang, JW and Park, YS}, title = {The association of tonsillar microbiota with biochemical indices based on obesity and tonsillar hypertrophy in children.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22716}, pmid = {38123635}, issn = {2045-2322}, support = {2021R1C1C1014142//National Research Foundation of Korea/ ; 2020R1A2C1101340//National Research Foundation of Korea/ ; 1711138229//Korea Medical Device Development Fund/ ; }, mesh = {Humans ; Child ; Palatine Tonsil ; *Pediatric Obesity/complications ; RNA, Ribosomal, 16S/genetics ; Hypertrophy/complications ; *Microbiota ; }, abstract = {The correlation between tonsil microbiome and tonsillar hypertrophy has not been well established. Given that oral dysbiosis is related to several metabolic diseases and that tonsillar hypertrophy leads to disordered breathing during sleep and obesity in children, it is necessary to investigate the relationship between the oral microbiome and tonsillar hypertrophy. After 16S rRNA amplicon sequencing of tonsillectomy samples, we evaluated the correlation between the tonsil microbiome and biochemical blood indices in pediatric patients who underwent tonsillectomy. Groups are classified into two categories: based on BMI, and grades 2, 3, and 4 based on tonsil size. Children with obesity and tonsillar hypertrophy have similar microbiome compositions and induce comparable changes in microbiome abundance and composition, confirming the association from a metagenomic perspective. In addition, obesity and tonsillar hypertrophy demonstrated a strong correlation with the Proteobacteria to Firmicutes (P/F) ratio, and among various biochemical indicators, alanine aminotransferase (ALT) levels increase with obesity and tonsillar hypertrophy, indicating a possible association of tonsil microbiome and liver metabolism. These novel findings demonstrate the significance of the tonsil microbiome and suggest the need for tonsil regulation, particularly during childhood.}, } @article {pmid38123079, year = {2023}, author = {Fu, Q and Qiu, Y and Zhao, J and Li, J and Xie, S and Liao, Q and Fu, X and Huang, Y and Yao, Z and Dai, Z and Qiu, Y and Yang, Y and Li, F and Chen, H}, title = {Monotonic trends of soil microbiomes, metagenomic and metabolomic functioning across ecosystems along water gradients in the Altai region, northwestern China.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169351}, doi = {10.1016/j.scitotenv.2023.169351}, pmid = {38123079}, issn = {1879-1026}, abstract = {To investigate microbial communities and their contributions to carbon and nutrient cycling along water gradients can enhance our comprehension of climate change impacts on ecosystem services. Thus, we conducted an assessment of microbial communities, metagenomic functions, and metabolomic profiles within four ecosystems, i.e., desert grassland (DG), shrub-steppe (SS), forest (FO), and marsh (MA) in the Altai region of Xinjiang, China. Our results showed that soil total carbon (TC), total nitrogen, NH4[+], and NO3[-] increased, but pH decreased with soil water gradients. Microbial abundances and richness also increased with soil moisture except the abundances of fungi and protists being lowest in MA. A shift in microbial community composition is evident along the soil moisture gradient, with Proteobacteria, Basidiomycota, and Evosea proliferating but a decline in Actinobacteria and Cercozoa. The β-diversity of microbiomes, metagenomic, and metabolomic functioning were correlated with soil moisture gradients and have significant associations with specific soil factors of TC, NH4[+], and pH. Metagenomic functions associated with carbohydrate and DNA metabolisms, as well as phages, prophages, TE, plasmids functions diminished with moisture, whereas the genes involved in nitrogen and potassium metabolism, along with certain biological interactions and environmental information processing functions, demonstrated an augmentation. Additionally, MA harbored the most abundant metabolomics dominated by lipids and lipid-like molecules and organic oxygen compounds, except certain metabolites showing decline trends along water gradients, such as N'-Hydroxymethylnorcotinine and 5-Hydroxyenterolactone. Thus, our study suggests that future ecosystem succession facilitated by changes in rainfall patterns will significantly alter soil microbial taxa, functional potential, and metabolite fractions.}, } @article {pmid38123024, year = {2023}, author = {So, SY and Badu, S and Wu, Q and Yalcinkaya, N and Mirabile, Y and Castaneda, R and Musaad, S and Heitkemper, M and Savidge, TC and Shulman, RJ}, title = {Sex-dependent efficacy of dietary fiber in pediatric functional abdominal pain.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2023.12.011}, pmid = {38123024}, issn = {1528-0012}, abstract = {BACKGROUND AND AIMS: Functional abdominal pain disorders (FAPDs) are more prevalent in females. Dietary fiber may alleviate FAPDs symptoms; however, whether this effect is sex-dependent remains unclear. We investigated the sex-dependency of dietary fiber benefit on abdominal pain in children with FAPDs and explored the potential involvement of the gut microbiome.

METHODS: In two cross-sectional cohorts of children with FAPDs (n=209) and healthy controls (HC; n=105), we correlated dietary fiber intake with abdominal pain symptoms after stratifying by sex. We also performed sex-stratified and sex-interaction analysis on data from a double-blind trial in children with irritable bowel syndrome (IBS) randomized to psyllium fiber (n=39) or placebo (n=49) for six weeks. Shotgun metagenomics was used to investigate gut microbiome community changes potentially linking dietary fiber intake with abdominal pain.

RESULTS: In the cross-sectional cohorts, fiber intake inversely correlated with pain symptoms in boys (pain episodes: r= -0.24, P=0.005; pain days: r= -0.24, P=0.004) but not in girls. Similarly, in the randomized trial, psyllium fiber reduced the number of pain episodes in boys (P=.012), but not in girls. Generalized linear regression models confirmed that boys treated with psyllium fiber had greater reduction in pain episodes than girls (P=.007 for fiber x sex x time interaction). Age, sexual development, IBS subtype, stool form and microbiome composition were not significant determinants in the dietary fiber effects on pain reduction.

CONCLUSIONS: Dietary fiber preferentially reduces abdominal pain frequency in boys, highlighting the importance of considering sex in future dietary intervention studies for FAPDs. ClincialTrials.gov number, NCT00526903.}, } @article {pmid38123012, year = {2024}, author = {Li, H and Yang, Y and Yang, Y and Zhai, C and Yao, J and Liao, W and Wang, Y and Wang, J and Cao, C and Darwish, HW and Wu, W and Li, W and Ge, B and Ma, Y and Wu, H and Wu, W and Zhai, F}, title = {Multiomics was used to clarify the mechanism by which air pollutants affect chronic obstructive pulmonary disease: A human cohort study.}, journal = {Toxicology}, volume = {501}, number = {}, pages = {153709}, doi = {10.1016/j.tox.2023.153709}, pmid = {38123012}, issn = {1879-3185}, mesh = {Humans ; *Air Pollutants/toxicity/analysis ; Cohort Studies ; Multiomics ; *Pulmonary Disease, Chronic Obstructive ; Biomarkers/analysis ; Particulate Matter/toxicity ; }, abstract = {Exposure to air pollutants has been associated with various adverse health outcomes, including chronic obstructive pulmonary disease (COPD). However, the precise underlying mechanism by which air pollution impacts COPD through remains insufficiently understood. To elucidated the molecular mechanism by which air pollutant exposure contributes to alterations in the gut microbiome and metabolism in AECOPD patients, we employed metagenomics and untargeted metabolomics to analyse the gut microbial, faecal, and serum metabolites. The correlations among air pollutants, gut microbes, serum metabolites, and blood biochemical markers were assessed using generalised additive mixed models and Spearman correlation analysis. The findings revealed that for every 10 μg/m[3] increase in PM2.5 concentration, the α-diversity of the gut flora decreased by 2.16% (95% CI: 1.80%-2.53%). We found seven microorganisms that were significantly associated with air pollutants, of which Enterococcus faecium, Bacteroides fragilis, Ruthenibacterium lactatiformans, and Subdoligranulum sp.4_3_54A2FAA were primarily associated with glycolysis. We identified 13 serum metabolites and 17 faecal metabolites significantly linked to air pollutants. Seven of these metabolites, which were strongly associated with air pollutants and blood biochemical indices, were found in both serum and faecal samples. Some of these metabolites, such as 2,5-furandicarboxylic acid, C-8C1P and melatonin, were closely associated with disturbances in lipid and fatty acid metabolism in AECOPD patients. These findings underscore the impact of air pollutants on overall metabolism based on influencing gut microbes and metabolites in AECOPD patients. Moreover, these altered biomarkers establish the biologic connection between air pollutant exposure and AECOPD outcomes.The identification of pertinent biomarkers provides valuable insights for the development of precision COPD prevention strategies.}, } @article {pmid38118419, year = {2023}, author = {Quesada-Vázquez, S and Castells-Nobau, A and Latorre, J and Oliveras-Cañellas, N and Puig-Parnau, I and Tejera, N and Tobajas, Y and Baudin, J and Hildebrand, F and Beraza, N and Burcelin, R and Martinez-Gili, L and Chilloux, J and Dumas, ME and Federici, M and Hoyles, L and Caimari, A and Del Bas, JM and Escoté, X and Fernández-Real, JM and Mayneris-Perxachs, J}, title = {Potential therapeutic implications of histidine catabolism by the gut microbiota in NAFLD patients with morbid obesity.}, journal = {Cell reports. Medicine}, volume = {4}, number = {12}, pages = {101341}, pmid = {38118419}, issn = {2666-3791}, mesh = {Humans ; Mice ; Rats ; Animals ; *Non-alcoholic Fatty Liver Disease/drug therapy ; Histidine/therapeutic use ; *Obesity, Morbid ; *Gastrointestinal Microbiome/physiology ; Diet, High-Fat ; }, abstract = {The gut microbiota contributes to the pathophysiology of non-alcoholic fatty liver disease (NAFLD). Histidine is a key energy source for the microbiota, scavenging it from the host. Its role in NAFLD is poorly known. Plasma metabolomics, liver transcriptomics, and fecal metagenomics were performed in three human cohorts coupled with hepatocyte, rodent, and Drosophila models. Machine learning analyses identified plasma histidine as being strongly inversely associated with steatosis and linked to a hepatic transcriptomic signature involved in insulin signaling, inflammation, and trace amine-associated receptor 1. Circulating histidine was inversely associated with Proteobacteria and positively with bacteria lacking the histidine utilization (Hut) system. Histidine supplementation improved NAFLD in different animal models (diet-induced NAFLD in mouse and flies, ob/ob mouse, and ovariectomized rats) and reduced de novo lipogenesis. Fecal microbiota transplantation (FMT) from low-histidine donors and mono-colonization of germ-free flies with Enterobacter cloacae increased triglyceride accumulation and reduced histidine content. The interplay among microbiota, histidine catabolism, and NAFLD opens therapeutic opportunities.}, } @article {pmid38118357, year = {2024}, author = {Zheng, J and Reed, E and Maounounen-Laasri, A and Deng, X and Wang, SS and Ramachandran, P and Ferreira, C and Bell, R and Brown, EW and Hammack, TS and Wang, H}, title = {Evaluation of universal preenrichment broth and comparison of rapid molecular methods for the detection of Salmonella from spent sprout irrigation water (SSIW).}, journal = {International journal of food microbiology}, volume = {411}, number = {}, pages = {110527}, doi = {10.1016/j.ijfoodmicro.2023.110527}, pmid = {38118357}, issn = {1879-3460}, mesh = {Culture Media/analysis ; *Food Microbiology ; Salmonella/genetics ; *Salmonella enterica ; Food Contamination/analysis ; }, abstract = {Sprouts and spent sprout irrigation water (SSIW) present unique challenges for the development of a Salmonella detection method in food matrices. This study aimed to compare universal preenrichment broth (UPB) and lactose broth (LB) as preenrichment media for cultural and rapid screening methods and to compare their abilities to recover Salmonella in SSIW samples from different sprout varieties (i.e., alfalfa, broccoli, and mung bean sprouts). The associated co-enriched microbiota with different sprout varieties using different preenrichment media were also examined using a quasi-metagenomic approach. The performance of media and detection methods was compared using the relative level of detection (RLOD) value, as recommended by ISO 16140-2:2016. The level of detection (LOD) for Salmonella culture method with UPB was similar to that with LB in low aerobic plate count (APC) background samples (the relative LOD, i.e., RLOD, was nearly 1 after adjusting for the effects of SSIW variety and serovar), but significantly lower than that with LB in high APC background samples (RLOD = 0.32). The LOD for Salmonella with selected rapid methods was comparable to each other (RLOD from 0.97 to 1.50) and to the culture method (RLOD from 0.69 to 1.03), and no significant difference was detected between preenrichment broths in low APC background samples with RLOD values between 0.76 and 1.04. In samples with a high APC background, however, a drastic difference in LOD was observed between methods and between preenrichment broths for each method. The RLOD ranged from 0.03 to 0.32 when UPB was compared to LB as preenrichment broth. The composition and relative abundance (RA) of co-enriched microbiota was affected by multiple factors including food matrices, preenrichment media and Salmonella contamination. Altogether, this study validated UPB as a better preenrichment broth than LB for the detection of Salmonella enterica from SSIW. This study also suggested UPB may also be an optimal preenrichment medium for rapid screening methods when APC level is high. The observation of potential exclusion of Salmonella in preenrichment through the overgrowth of competitive microflora from the quasi-metagenomic study provided novel information that may be used to further optimize preenrichment formulations.}, } @article {pmid38118251, year = {2023}, author = {Zheng, CW and Lai, YS and Luo, YH and Cai, Y and Wu, W and Rittmann, BE}, title = {A two-stage design enhanced biodegradation of high concentrations of a C16-alkyl quaternary ammonium compound in oxygen-based membrane biofilm reactors.}, journal = {Water research}, volume = {250}, number = {}, pages = {120963}, doi = {10.1016/j.watres.2023.120963}, pmid = {38118251}, issn = {1879-2448}, abstract = {Quaternary ammonia compounds (QAC), such as hexadecyltrimethyl-ammonium (CTAB), are widely used as disinfectants and in personal-care products. Their use as disinfectants grew during the SARS-CoV-2 (COVID-19) pandemic, leading to increased loads to wastewater treatment systems and the environment. Though low concentrations of CTAB are biodegradable, high concentrations are toxic to bacteria. Sufficient O2 delivery is a key to achieve high CTAB removal, and the O2-based Membrane Biofilm Reactor (O2-MBfR) is a proven means to biodegrade CTAB in a bubble-free, non-foaming manner. A strategy for achieving complete biodegradation of high-concentrations of CTAB is a two-stage O2-MBfR, in which partial CTAB removal in the Lead reactor relieves inhibition in the Lag reactor. Here, more than 98 % removal of 728 mg/L CTAB could be achieved in the two-stage MBfR, and the CTAB-removal rate was 70 % higher than for a one-stage MBfR with the same O2-delivery capacity. CTAB exposure shifted the bacterial community toward Pseudomonas and Stenotrophomonas as the dominant genera. In particular, P. alcaligenes and P. aeruginosa were enriched in the Lag reactor, as they were capable of biodegrading the metabolites of initial CTAB monooxygenation. Metagenomic analysis also revealed that the Lag reactor was enriched in genes for CTAB and metabolite oxygenation, due to reduced CTAB inhibition.}, } @article {pmid38118139, year = {2023}, author = {Obayori, OS and Adesina, OD and Salam, LB and Ashade, AO and Nwaokorie, FO}, title = {Depletion of hydrocarbons and concomitant shift in bacterial community structure of a diesel-spiked tropical agricultural soil.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-16}, doi = {10.1080/09593330.2023.2291421}, pmid = {38118139}, issn = {1479-487X}, abstract = {Bacterial community of a diesel-spiked agricultural soil was monitored over a 42-day period using the metagenomic approach in order to gain insight into key phylotypes impacted by diesel contamination and be able to predict end point of bioattenuation. Soil physico-chemical parameters showed significant differences (P < 0.05) between the Polluted Soil (PS) and the Unpolluted control (US)across time points. After 21 days, the diesel content decreased by 27.39%, and at the end of 42 days, by 57.11%. Aromatics such as benzene, anthanthrene, propylbenzene, phenanthrenequinone, anthraquinone, and phenanthridine were degraded to non-detected levels within 42 days, while some medium range alkanes and polyaromatics such as acenaphthylene, naphthalene, and anthracene showed significant levels of degradation. After 21 days (LASTD21), there was a massive enrichment of the phylum Proteobacteria (72.94%), a slight decrease in the abundance of phylum Actinobacteriota (12.74%), and > 500% decrease in the abundance of the phylum Acidobacteriodota (5.26%). Day 42 (LASTD42) saw establishment of the dominance of the Proteobacteria (34.95%), Actinobacteriota, (21.71%), and Firmicutes (32.14%), and decimation of phyla such as Gemmatimonadota, Planctomycetota, and Verrucromicrobiota which play important roles in the cycling of elements and soil health. Principal component analysis showed that in PS moisture contents, phosphorus, nitrogen, organic carbon, had greater impacts on the community structure in LASTD21, while acidity, potassium, sodium, calcium and magnesium impacted the control sample. Recovery time of the soil based on the residual hydrocarbons at Day 42 was estimated to be 229.112 d. Thus, additional biostimulation may be required to achieve cleanup within one growing season.}, } @article {pmid38118133, year = {2024}, author = {Bao, Y and Ruan, Y and Wu, J and Wang, WX and Leung, KMY and Lee, PKH}, title = {Metagenomics-Based Microbial Ecological Community Threshold and Indicators of Anthropogenic Disturbances in Estuarine Sediments.}, journal = {Environmental science & technology}, volume = {58}, number = {1}, pages = {780-794}, doi = {10.1021/acs.est.3c08076}, pmid = {38118133}, issn = {1520-5851}, mesh = {Humans ; *Ecosystem ; Anthropogenic Effects ; Geologic Sediments/analysis ; Biota ; Rivers ; *Microbiota ; Estuaries ; Environmental Monitoring ; }, abstract = {Assessing the impacts of cumulative anthropogenic disturbances on estuarine ecosystem health is challenging. Using spatially distributed sediments from the Pearl River Estuary (PRE) in southern China, which are significantly influenced by anthropogenic activities, we demonstrated that metagenomics-based surveillance of benthic microbial communities is a robust approach to assess anthropogenic impacts on estuarine benthic ecosystems. Correlational and threshold analyses between microbial compositions and environmental conditions indicated that anthropogenic disturbances in the PRE sediments drove the taxonomic and functional variations in the benthic microbial communities. An ecological community threshold of anthropogenic disturbances was identified, which delineated the PRE sediments into two groups (H and L) with distinct taxa and functional traits. Group H, located nearshore and subjected to a higher level of anthropogenic disturbances, was enriched with pollutant degraders, putative human pathogens, fecal pollution indicators, and functional traits related to stress tolerance. In contrast, Group L, located offshore and subjected to a lower level of anthropogenic disturbances, was enriched with halotolerant and oligotrophic taxa and functional traits related to growth and resource acquisition. The machine learning random forest model identified a number of taxonomic and functional indicators that could differentiate PRE sediments between Groups H and L. The identified ecological community threshold and microbial indicators highlight the utility of metagenomics-based microbial surveillance in assessing the adverse impacts of anthropogenic disturbances in estuarine sediments, which can assist environmental management to better protect ecosystem health.}, } @article {pmid38117560, year = {2024}, author = {Wu, X and Zhang, T and Zhang, T and Park, S}, title = {The impact of gut microbiome enterotypes on ulcerative colitis: identifying key bacterial species and revealing species co-occurrence networks using machine learning.}, journal = {Gut microbes}, volume = {16}, number = {1}, pages = {2292254}, pmid = {38117560}, issn = {1949-0984}, mesh = {Humans ; *Colitis, Ulcerative ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Clostridioides difficile ; Bacteria/genetics ; Bacteroidaceae ; Machine Learning ; }, abstract = {Ulcerative colitis (UC) is a chronic inflammatory intestinal disease affecting the colon and rectum, with its pathogenesis attributed to genetic background, environmental factors, and gut microbes. This study aimed to investigate the role of enterotypes in UC by conducting a hierarchical analysis, determining differential bacteria using machine learning, and performing Species Co-occurrence Network (SCN) analysis. Fecal bacterial data were collected from UC patients, and a 16S rRNA metagenomic analysis was performed using the QIIME2 bioinformatics pipeline. Enterotype clustering was conducted at the family level, and deep neural network (DNN) classification models were trained for UC and healthy controls (HC) in each enterotype. Results from eleven 16S rRNA gut microbiome datasets revealed three enterotypes: Bacteroidaceae (ET-B), Lachnospiraceae (ET-L), and Clostridiaceae (ET-C). Ruminococcus (R. gnavus) abundance was significantly higher in UC subjects with ET-B and ET-C than in those with ET-L. R. gnavus also showed a positive correlation with Clostridia in UC SCN for ET-B and ET-C subjects, with a higher correlation in ET-C subjects. Conversely, Odoribacter (O.) splanchnicus and Bacteroides (B.) uniformis exhibited a positive correlation with tryptophan metabolism and AMP-activated protein kinase (AMPK) signaling pathways, while R. gnavus showed a negative correlation. In vitro co-culture experiments with Clostridium (C.) difficile demonstrated that fecal microbiota from ET-B subjects had a higher abundance of C. difficile than ET-L subjects. In conclusion, the ET-B enterotype predisposes individuals to UC, with R. gnavus as a potential risk factor and O. splanchnicus and B. uniformis as protective bacteria, and those with UC may have ultimately become ET-C.}, } @article {pmid38117091, year = {2023}, author = {Bommana, S and Hu, Y-J and Kama, M and Wang, R and Kodimerla, R and Jijakli, K and Read, TD and Dean, D}, title = {Unique microbial diversity, community composition, and networks among Pacific Islander endocervical and vaginal microbiomes with and without Chlamydia trachomatis infection in Fiji.}, journal = {mBio}, volume = {}, number = {}, pages = {e0306323}, doi = {10.1128/mbio.03063-23}, pmid = {38117091}, issn = {2150-7511}, support = {R01 AI151075/AI/NIAID NIH HHS/United States ; }, abstract = {Chlamydia trachomatis (Ct) is the most common sexually transmitted bacterium globally. Endocervical and vaginal microbiome interactions are rarely examined within the context of Ct or among vulnerable populations. We evaluated 258 vaginal and 92 paired endocervical samples from Fijian women using metagenomic shotgun sequencing. Over 37% of the microbiomes could not be classified into sub-community state types (subCSTs). We, therefore, developed subCSTs IV-D0, IV-D1, IV-D2, and IV-E-dominated primarily by Gardnerella vaginalis-to improve classification. Among paired microbiomes, the endocervix had a significantly higher alpha diversity and, independently, higher diversity for high-risk human papilloma virus (HPV) genotypes compared to low-risk and no HPV. Ct-infected endocervical networks had smaller clusters without interactions with potentially beneficial Lactobacillus spp. Overall, these data suggest that G. vaginalis may generate polymicrobial biofilms that predispose to and/or promote Ct and possibly HPV persistence and pathogenicity. Our findings expand on the existing repertoire of endocervical and vaginal microbiomes and fill in knowledge gaps regarding Pacific Islanders.}, } @article {pmid38117057, year = {2023}, author = {Romanis, CS and Timms, VJ and Nebauer, DJ and Crosbie, ND and Neilan, BA}, title = {Microbiome analysis reveals Microcystis blooms endogenously seeded from benthos within wastewater maturation ponds.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0158523}, doi = {10.1128/aem.01585-23}, pmid = {38117057}, issn = {1098-5336}, abstract = {Cyanobacterial blooms are prevalent to wastewater treatment facilities owing to the stable, eutrophic conditions. Cyanobacterial proliferations can disrupt operational procedures through the blocking of filtration apparatus or altering the wastewater treatment plant (WWTP) microbiome, reducing treatment efficiency. Conventional wastewater treatment often results in the lysis of cyanobacterial cells and the release of intracellular toxins which pose a health risk to end users. This research identifies a potential seeding source of recurrent toxigenic cyanobacterial blooms within wastewater treatment facilities. Our results demonstrate the capacity of Microcystis to transition between the sediments and surface waters (SWs) of wastewater treatment ponds enabling water utilities to develop adequate monitoring and management strategies. Further, we developed a novel model to demonstrate benthic recruitment of toxigenic Microcystis under laboratory conditions facilitating future research into the genetic mechanisms behind bloom development.}, } @article {pmid38116701, year = {2023}, author = {Ojo, AO and Castillo, J and Cason, ED and Valverde, A}, title = {Biodegradation of chloroethene compounds under microoxic conditions.}, journal = {Biotechnology and bioengineering}, volume = {}, number = {}, pages = {}, doi = {10.1002/bit.28630}, pmid = {38116701}, issn = {1097-0290}, abstract = {The biodegradation of chloroethene compounds under oxic and anoxic conditions is well established. However, the biological reactions that take place under microoxic conditions are unknown. Here, we report the biostimulated (BIOST: addition of lactate) and natural attenuated (NAT) degradation of chloroethene compounds under microoxic conditions by bacterial communities from chloroethene compounds-contaminated groundwater. The degradation of tetrachloroethene was significantly higher in NAT (15.14% on average) than in BIOST (10.13% on average) conditions at the end of the experiment (90 days). Sporomusa, Paracoccus, Sedimentibacter, Pseudomonas, and Desulfosporosinus were overrepresented in NAT and BIOST compared to the source groundwater. The NAT metagenome contains phenol hydrolase P1 oxygenase (dmpL), catechol-1,2-dioxygenase (catA), catechol-2,3-dioxygenases (dmpB, todE, and xylE) genes, which could be involved in the cometabolic degradation of chloroethene compounds; and chlorate reductase (clrA), that could be associated with partial reductive dechlorination of chloroethene compounds. Our data provide a better understanding of the bacterial communities, genes, and pathways potentially implicated in the reductive and cometabolic degradation of chloroethene compounds under microoxic conditions.}, } @article {pmid38116510, year = {2023}, author = {Krasnikov, N and Yuzhakov, A}, title = {Interspecies recombination in NSP3 gene in the first porcine rotavirus H in Russia identified using nanopore-based metagenomic sequencing.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1302531}, pmid = {38116510}, issn = {2297-1769}, abstract = {During the last decade, porcine rotavirus H was detected in the USA, Asian regions, South Africa, Brazil, and a couple of European countries. In the presented study, the virus was identified in piglets on a farrow-to-finish farm in Russia during metagenomic surveillance. Currently, it is the first identification of this species in the country. As a diagnostic method, nanopore-based metagenomic sequencing was applied. The obtained nanopore reads allowed for the assembly of 10 genome segments out of 11. The phylogenetic analysis revealed the virus belonged to the porcine cluster and had GX-P3-I3-R3-C3-M8-A7-N1-T5-E3-H3 genome constellation. Moreover, three potential new genotype groups for VP3, NSP1, and NSP3 genes were determined. Additionally, a recombination between RVH and RVC in the NSP3 gene was detected. The study provides significant information about a novel RVH strain.}, } @article {pmid38116074, year = {2024}, author = {Sheng, Y and Wang, J and Gao, Y and Peng, Y and Li, X and Huang, W and Zhou, H and Liu, R and Zhang, W}, title = {Combined analysis of cross-population healthy adult human microbiome reveals consistent differences in gut microbial characteristics between Western and non-Western countries.}, journal = {Computational and structural biotechnology journal}, volume = {23}, number = {}, pages = {87-95}, pmid = {38116074}, issn = {2001-0370}, abstract = {Despite extensive research on the gut microbiome of healthy individuals from a single country, there are still a limited number of population-level comparative studies. Moreover, the sequencing approach used in most related studies involves 16 S ribosomal RNA (rRNA) sequencing with a limited resolution, which cannot provide detailed functional profiles. In the present study, we applied a combined analysis approach to analyze whole metagenomic shotgun sequencing data from 2035 healthy adult samples from six countries across four continents. Analysis of core species revealed that 13 species were present in more than 90 % of all investigated individuals, the majority of which produced short-chain fatty acids (SCFA)-producing bacteria. Our analysis revealed consistently significant differences in gut microbial species and pathways between Western and non-Western countries, such as Escherichia coli and the relation of MetaCyc pathways to the TCA cycle. Specific changes in microbial species and pathways are potentially related to lifestyle and diet. Furthermore, we identified several noteworthy microbial species and pathways that exhibit distinct characteristics specific to China. Interestingly, we observed that China (CHN) was more similar to the United States (USA) and United Kingdom (GBR) in terms of the taxonomic and functional composition of the gut microbiome than India (IND) and Madagascar (MDG), which were more similar to the China (CHN) diet. The current study identified consistent microbial features associated with population and geography, which will inspire further clinical translations that consider paying attention to differences in microbiota backgrounds and confounding factors.}, } @article {pmid38115299, year = {2023}, author = {Lu, D and Li, C and Zhong, Z and Abudouaini, M and Amar, A and Wu, H and Wei, X}, title = {Changes in the airway microbiome in patients with bronchiectasis.}, journal = {Medicine}, volume = {102}, number = {50}, pages = {e36519}, pmid = {38115299}, issn = {1536-5964}, mesh = {Humans ; Adult ; Middle Aged ; Aged ; Prospective Studies ; Quality of Life ; *Bronchiectasis ; *Microbiota/genetics ; Respiratory System ; Anti-Bacterial Agents ; High-Throughput Nucleotide Sequencing ; Sensitivity and Specificity ; }, abstract = {This study used metagenomic next-generation sequencing (mNGS) technology to explore the changes of the microbial characteristics in the lower respiratory tract in patients with acute exacerbations of bronchiectasis (noncystic fibrosis) to guide clinical treatment and improve patients' quality of life and prognosis. This prospective study included 54 patients with acute exacerbation and 46 clinically stable patients admitted to the Respiratory and Critical Care Medicine Center of the People's Hospital of Xinjiang Uygur Autonomous Region from January 2020 to July 2022. Sputum was subjected to routine microbiological tests, and bronchoalveolar lavage fluid (BALF) samples were subjected to microbiological tests and mNGS of BALF before empirical antibiotic therapy. Serum inflammatory markers (white blood cell count, interleukin-6, procalcitonin, and C-reactive protein) were measured. In addition, we evaluated the pathogen of mNGS and compared the airway microbiome composition of patients with acute exacerbation and control patients. The mean age of our cohort was 56 ± 15.2 years. Eighty-nine patients had positive results by mNGS. There was a significant difference in the detection of viruses between the groups (χ2 = 6.954, P < .01). The fungal species Candida albicans, Pneumocystis jirovecii, and Aspergillus fumigatus were significantly more common in patients with acute exacerbations (χ2 = 5.98, P = .014). The bacterial species Acinetobacter baumannii, Mycobacterium tuberculosis, Haemophilus influenzae, Haemophilus parahaemolyticus, Abiotrophia defectiva, and Micromonas micros were significantly more prevalent in patients with acute exacerbations (χ2 = 4.065, P = .044). The most common bacterial species isolated from the sputum and BALF samples of patients with acute exacerbation was A. baumannii. Chlamydia psittaci was found in 4 patients. In addition, of 77 patients with negative sputum culture, 66 had positive results by mNGS, demonstrating the increased sensitivity and accuracy of mNGS. Patients with acute exacerbation of bronchiectasis tend to have mixed infections in the lower respiratory tract. The frequency of viruses, fungi, and Mycoplasma was higher in these patients. Our findings suggest that mNGS could be used to identify pathogenic microorganisms in these patients, increasing the effectiveness of antibiotic therapy.}, } @article {pmid38115159, year = {2023}, author = {Liu, M and Zhang, J and Zhou, Y and Xiong, S and Zhou, M and Wu, L and Liu, Q and Chen, Z and Jiang, H and Yang, J and Liu, Y and Wang, Y and Chen, C and Huang, L}, title = {Gut microbiota affects the estrus return of sows by regulating the metabolism of sex steroid hormones.}, journal = {Journal of animal science and biotechnology}, volume = {14}, number = {1}, pages = {155}, pmid = {38115159}, issn = {1674-9782}, support = {2022YFA1304204//National Key R&D Program of China/ ; 31772579//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Sex hormones play important roles in the estrus return of post-weaning sows. Previous studies have demonstrated a complex and bi-directional regulation between sex hormones and gut microbiota. However, the extent to which the gut microbiota affects estrus return of post-weaning sows is largely unknown.

RESULTS: In this study, we first screened 207 fecal samples from well-phenotyped sows by 16S rRNA gene sequencing and identified significant associations between microbes and estrus return of post-weaning sows. Using metagenomic sequencing data from 85 fecal samples, we identified 37 bacterial species that were significantly associated with estrus return. Normally returning sows were characterized by increased abundances of L. reuteri and P. copri and decreased abundances of B. fragilis, S. suis, and B. pseudolongum. The changes in gut microbial composition significantly altered the functional capacity of steroid hormone biosynthesis in the gut microbiome. The results were confirmed in a validation cohort. Significant changes in sex steroid hormones and related compounds were found between normal and non-return sows via metabolome analysis. An integrated analysis of differential bacterial species, metagenome, and fecal metabolome provided evidence that normal return-associated bacterial species L. reuteri and Prevotella spp. participated in the degradation of pregnenolone, progesterone, and testosterone, thereby promoting estrogen biosynthesis. Furthermore, the microbial metabolites related to sow energy and nutrient supply or metabolic disorders also showed relationships with sow estrus return.

CONCLUSIONS: An integrated analysis of differentially abundant bacterial species, metagenome, and fecal metabolome revealed the involvement of L. reuteri and Prevotella spp. in sow estrus return. These findings provide deep insight into the role of gut microbiota in the estrus return of post-weaning sows and the complex cross-talk between gut microbiota and sex hormones, suggesting that the manipulation of the gut microbiota could be an effective strategy to improve sow estrus return after weaning.}, } @article {pmid38115019, year = {2023}, author = {Liu, X and Liu, D and Tan, C and Feng, W}, title = {Gut microbiome-based machine learning for diagnostic prediction of liver fibrosis and cirrhosis: a systematic review and meta-analysis.}, journal = {BMC medical informatics and decision making}, volume = {23}, number = {1}, pages = {294}, pmid = {38115019}, issn = {1472-6947}, mesh = {Humans ; *Gastrointestinal Microbiome ; Liver Cirrhosis/diagnosis/pathology ; Fibrosis ; Machine Learning ; }, abstract = {BACKGROUND: Invasive detection methods such as liver biopsy are currently the gold standard for diagnosing liver cirrhosis and can be used to determine the degree of liver fibrosis and cirrhosis. In contrast, non-invasive diagnostic methods, such as ultrasonography, elastography, and clinical prediction scores, can prevent patients from invasiveness-related discomfort and risks and are often chosen as alternative or supplementary diagnostic methods for liver fibrosis or cirrhosis. However, these non-invasive methods cannot specify the pathological grading and early diagnosis of the lesions. Recent studies have revealed that gut microbiome-based machine learning can be utilized as a non-invasive diagnostic technique for liver cirrhosis or fibrosis, but there is no evidence-based support. Therefore, this study conducted a systematic review and meta-analysis for the first time to investigate the accuracy of machine learning based on the gut microbiota in the prediction of liver fibrosis and cirrhosis.

METHODS: A comprehensive and systematic search of publications published before April 2th, 2023 in PubMed, Cochrane Library, Embase, and Web of Science was conducted for relevant studies on the application of gut microbiome-based metagenomic sequencing modeling technology to the diagnostic prediction of liver cirrhosis or fibrosis. A bivariate mixed-effects model and Stata software 15.0 were adopted for the meta-analysis.

RESULTS: Ten studies were included in the present study, involving 11 prediction trials and 838 participants, 403 of whom were fibrotic and cirrhotic patients. Meta-analysis showed the pooled sensitivity (SEN) = 0.81 [0.75, 0.85], specificity (SEP) = 0.85 [0.77, 0.91], positive likelihood ratio (PLR) = 5.5 [3.6, 8.7], negative likelihood ratio (NLR) = 0.23 [0.18, 0.29], diagnostic odds ratio (DOR) = 24 [14, 41], and area under curve (AUC) = 0.86 [0.83-0.89]. The results demonstrated that machine learning methods had excellent potential to analyze gut microbiome data and could effectively predict liver cirrhosis or fibrosis. Machine learning provides a powerful tool for non-invasive prediction and diagnosis of liver cirrhosis or liver fibrosis, with broad clinical application prospects. However, these results need to be interpreted with caution due to limited clinical data.

CONCLUSION: Gut microbiome-based machine learning can be utilized as a practical, non-invasive technique for the diagnostic prediction of liver cirrhosis or fibrosis. However, most of the included studies applied the random forest algorithm in modeling, so a diversified prediction system based on microorganisms is needed to improve the non-invasive detection of liver cirrhosis or fibrosis.}, } @article {pmid38115005, year = {2023}, author = {Lan, Q and Zhang, C and Hua, H and Hu, X}, title = {Compositional and functional changes in the salivary microbiota related to oral leukoplakia and oral squamous cell carcinoma: a case control study.}, journal = {BMC oral health}, volume = {23}, number = {1}, pages = {1021}, pmid = {38115005}, issn = {1472-6831}, support = {PKUSSNMP-201907//the 2021 National Program for Multidisciplinary Cooperative Treatment on Major Diseases/ ; PKUSSNMP-202109//the 2022 National Program for Multidisciplinary Cooperative Treatment on Major Diseases/ ; PKUSS20170104//Young People Fund of Peking University School and Hospital of Stomatology/ ; PKUSSNCT-23B11//Program for New Clinical Techniques and Therapies of Peking University School and Hospital of Stomatology/ ; }, mesh = {Humans ; *Mouth Neoplasms/pathology ; Squamous Cell Carcinoma of Head and Neck ; *Carcinoma, Squamous Cell/pathology ; Case-Control Studies ; Cysteine ; Leukoplakia, Oral ; Carcinogenesis ; *Microbiota ; *Head and Neck Neoplasms ; Methionine ; }, abstract = {BACKGROUND: Oral squamous cell carcinoma (OSCC) is one of the most common malignant tumours with increasing incidence, and oral leukoplakia (OLK) has a strong tendency to undergo malignant transformation. The oral microbiota may influence oral cancer progression, but the salivary bacterial composition and functional changes in OSCC and OLK have not been comprehensively elucidated. Therefore, we compared salivary bacteria in OLK and OSCC patients with healthy controls (HC).

METHODS: Metagenomic sequencing was used to compare the bacterial composition and functional changes of 18 OSCC patients, 21 OLK patients and 21 HC. Spearman correlation was used to identify possible associations between functions and bacteria.

RESULTS: Gemella was the most differentially enriched genus in OSCC. At the species level, Streptococcus sp. NPS 308, Streptococcus agalactiae, Gemella haemolysans and Gemella morbillorum were slightly increased in OLK and OSCC. Kyoto Encyclopedia of Genes and Genomes (KEGG) results showed that OSCC was mainly associated with metabolism functions, including lipid metabolism, carbohydrate metabolism and glycan biosynthesis and metabolism. The synthesis and degradation of ketone bodies, cysteine and methionine metabolism and glycerolipid metabolism differed significantly among the three groups, and were highest in OSCC and lowest in HC. And G. haemolysans was significantly associated with these selected metabolic pathways.

CONCLUSIONS: Metagenomic analysis revealed significant differences in the salivary microbiota among OSCC, OLK and HC. Thus, salivary microbiota composition and functional changes may be associated with OSCC progression. Metabolism of nonessential amino acids such as cysteine and methionine in bacteria may play an important role in oral oncogenesis, and more studies of the mechanism between metabolisms of bacteria and oral oncogenesis are needed in the future.}, } @article {pmid38114947, year = {2023}, author = {Trapella, G and Cinti, N and Parma, L and De Marco, A and Dell'Acqua, AN and Turroni, S and Rampelli, S and Scicchitano, D and Iuffrida, L and Bonaldo, A and Franzellitti, S and Candela, M and Palladino, G}, title = {Microbiome variation at the clam-sediment interface may explain changes in local productivity of Chamelea gallina in the North Adriatic sea.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {402}, pmid = {38114947}, issn = {1471-2180}, support = {818290//"Controlling Microbiomes Circulations for Better Food Systems", European Union's Horizon 2020/ ; }, mesh = {Animals ; *Bivalvia ; Seafood ; }, abstract = {BACKGROUND: The clam Chamelea gallina is an ecologically and economically important marine species in the Northwestern Adriatic Sea, which currently suffers from occasional, and still unexplained, widespread mortality events. In order to provide some glimpses in this direction, this study explores the connections between microbiome variations at the clam-sediment interface and the nutritional status of clams collected at four Italian production sites along the Emilia Romagna coast, with different mortality incidence, higher in the Northern sites and lower in the Southern sites.

RESULTS: According to our findings, each production site showed a peculiar microbiome arrangement at the clam-sediment interface, with features that clearly differentiate the Northern and Southern sites, with the latter also being associated with a better nutritional status of the animal. Interestingly, the C. gallina digestive gland microbiome from the Southern sites was enriched in some health-promoting microbiome components, capable of supplying the host with essential nutrients and defensive molecules. Furthermore, in experiments conducted under controlled conditions in aquaria, we provided preliminary evidence of the prebiotic action of sediments from the Southern sites, allowing to boost the acquisition of previously identified health-promoting components of the digestive gland microbiome by clams from the Northern sites.

CONCLUSIONS: Taken together, our findings may help define innovative microbiome-based management strategies for the preservation of the productivity of C. gallina clams in the Adriatic Sea, through the identification and maintenance of a probiotic niche at the animal-sediment interface.}, } @article {pmid38114770, year = {2023}, author = {Toh, SI and Elaine Keisha, J and Wang, YL and Pan, YC and Jhu, YH and Hsiao, PY and Liao, WT and Chen, PY and Ko, TM and Chang, CY}, title = {Discovery and characterization of genes conferring natural resistance to the antituberculosis antibiotic capreomycin.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {1282}, pmid = {38114770}, issn = {2399-3642}, support = {111-2113-M-002-025//Ministry of Science and Technology, Taiwan (Ministry of Science and Technology of Taiwan)/ ; }, mesh = {*Capreomycin/pharmacology ; *Anti-Bacterial Agents/pharmacology/metabolism ; Bacteria/genetics ; Genes, Bacterial ; Immunity, Innate ; }, abstract = {Metagenomic-based studies have predicted an extraordinary number of potential antibiotic-resistance genes (ARGs). These ARGs are hidden in various environmental bacteria and may become a latent crisis for antibiotic therapy via horizontal gene transfer. In this study, we focus on a resistance gene cph, which encodes a phosphotransferase (Cph) that confers resistance to the antituberculosis drug capreomycin (CMN). Sequence Similarity Network (SSN) analysis classified 353 Cph homologues into five major clusters, where the proteins in cluster I were found in a broad range of actinobacteria. We examine the function and antibiotics targeted by three putative resistance proteins in cluster I via biochemical and protein structural analysis. Our findings reveal that these three proteins in cluster I confer resistance to CMN, highlighting an important aspect of CMN resistance within this gene family. This study contributes towards understanding the sequence-structure-function relationships of the phosphorylation resistance genes that confer resistance to CMN.}, } @article {pmid38114587, year = {2023}, author = {Roume, H and Mondot, S and Saliou, A and Le Fresne-Languille, S and Doré, J}, title = {Multicenter evaluation of gut microbiome profiling by next-generation sequencing reveals major biases in partial-length metabarcoding approach.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22593}, pmid = {38114587}, issn = {2045-2322}, support = {2017-AdG No. 788191/ERC_/European Research Council/International ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Reproducibility of Results ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; DNA, Bacterial/genetics/analysis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Next-generation sequencing workflows, using either metabarcoding or metagenomic approaches, have massively contributed to expanding knowledge of the human gut microbiota, but methodological bias compromises reproducibility across studies. Where these biases have been quantified within several comparative analyses on their own, none have measured inter-laboratory reproducibility using similar DNA material. Here, we designed a multicenter study involving seven participating laboratories dedicated to partial- (P1 to P5), full-length (P6) metabarcoding, or metagenomic profiling (MGP) using DNA from a mock microbial community or extracted from 10 fecal samples collected at two time points from five donors. Fecal material was collected, and the DNA was extracted according to the IHMS protocols. The mock and isolated DNA were then provided to the participating laboratories for sequencing. Following sequencing analysis according to the laboratories' routine pipelines, relative taxonomic-count tables defined at the genus level were provided and analyzed. Large variations in alpha-diversity between laboratories, uncorrelated with sequencing depth, were detected among the profiles. Half of the genera identified by P1 were unique to this partner and two-thirds of the genera identified by MGP were not detected by P3. Analysis of beta-diversity revealed lower inter-individual variance than inter-laboratory variances. The taxonomic profiles of P5 and P6 were more similar to those of MGP than those obtained by P1, P2, P3, and P4. Reanalysis of the raw sequences obtained by partial-length metabarcoding profiling, using a single bioinformatic pipeline, harmonized the description of the bacterial profiles, which were more similar to each other, except for P3, and closer to the profiles obtained by MGP. This study highlights the major impact of the bioinformatics pipeline, and primarily the database used for taxonomic annotation. Laboratories need to benchmark and optimize their bioinformatic pipelines using standards to monitor their effectiveness in accurately detecting taxa present in gut microbiota.}, } @article {pmid38114556, year = {2023}, author = {Sobolewska, E and Borowski, S and Nowicka-Krawczyk, P and Jurczak, T}, title = {Growth of microalgae and cyanobacteria consortium in a photobioreactor treating liquid anaerobic digestate from vegetable waste.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22651}, pmid = {38114556}, issn = {2045-2322}, mesh = {Photobioreactors ; Waste Disposal, Fluid/methods ; *Microalgae ; Vegetables ; Anaerobiosis ; *Cyanobacteria ; Nitrogen ; *Chlorophyceae ; Biomass ; }, abstract = {This research examines the biological treatment of undiluted vegetable waste digestate conducted in a bubble column photobioreactor. Initially, the bioreactor containing 3N-BBM medium was inoculated with Microglena sp., Tetradesmus obliquus, and Desmodesmus subspicatus mixture with a density of 1.0 × 10[4] cells/mL and the consortium was cultivated for 30 days. Then, the bioreactor was semi-continuously fed with liquid digestate with hydraulic retention time (HRT) of 30 days, and the treatment process was continued for the next 15 weeks. The change in the microalgal and cyanobacterial species domination was measured in regular intervals using cell counting with droplet method on a microscope slide. At the end of the experiment, Desmonostoc sp. cyanobacteria (identified with 16S ribosomal RNA genetical analysis) as well as Tetradesmus obliquus green algae along with Rhodanobacteraceae and Planococcaceae bacteria (determined with V3-V4 16sRNA metagenomic studies) dominated the microbial community in the photobioreactor. The experiment demonstrated high treatment efficiency, since nitrogen and soluble COD were removed by 89.3 ± 0.5% and 91.2 ± 1.6%, respectively, whereas for phosphates, 72.8 ± 2.1% removal rate was achieved.}, } @article {pmid38114447, year = {2024}, author = {Bucci, L and Ghiotto, G and Zampieri, G and Raga, R and Favaro, L and Treu, L and Campanaro, S}, title = {Adaptation of Anaerobic Digestion Microbial Communities to High Ammonium Levels: Insights from Strain-Resolved Metagenomics.}, journal = {Environmental science & technology}, volume = {58}, number = {1}, pages = {580-590}, pmid = {38114447}, issn = {1520-5851}, mesh = {Anaerobiosis ; Bioreactors/microbiology ; Bacteria/genetics/metabolism ; *Microbiota ; Metagenomics ; Ammonia/metabolism ; *Ammonium Compounds/metabolism ; Methane ; }, abstract = {Ammonia release from proteinaceous feedstocks represents the main inhibitor of the anaerobic digestion (AD) process, which can result in a decreased biomethane yield or even complete failure of the process. The present study focused on the adaptation of mesophilic AD communities to a stepwise increase in the concentration of ammonium chloride in synthetic medium with casein used as the carbon source. An adaptation process occurring over more than 20 months allowed batch reactors to reach up to 20 g of NH4[+] N/L without collapsing in acidification nor ceasing methane production. To decipher the microbial dynamics occurring during the adaptation and determine the genes mostly exposed to selective pressure, a combination of biochemical and metagenomics analyses was performed, reconstructing the strains of key species and tracking them over time. Subsequently, the adaptive metabolic mechanisms were delineated by following the single nucleotide variants (SNVs) characterizing the strains and prioritizing the associated genes according to their function. An in-depth exploration of the archaeon Methanoculleus bourgensis vb3066 and the putative syntrophic acetate-oxidizing bacteria Acetomicrobium sp. ma133 identified positively selected SNVs on genes involved in stress adaptation. The intraspecies diversity with multiple coexisting strains in a temporal succession pattern allows us to detect the presence of an additional level of diversity within the microbial community beyond the species level.}, } @article {pmid38114436, year = {2024}, author = {Wang, HY and Liu, LX and Chen, XY and Zhang, YD and Li, WX and Li, WW and Wang, L and Mo, XL and Wei, H and Ji, P and Xie, P}, title = {Comprehensive analysis of the gut microbiome and post-translational modifications elucidates the route involved in microbiota-host interactions.}, journal = {Zoological research}, volume = {45}, number = {1}, pages = {95-107}, doi = {10.24272/j.issn.2095-8137.2023.008}, pmid = {38114436}, issn = {2095-8137}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Lysine/metabolism ; Host Microbial Interactions ; Proteomics/methods ; Protein Processing, Post-Translational ; }, abstract = {The gut microbiome interacts with the host to maintain body homeostasis, with gut microbial dysbiosis implicated in many diseases. However, the underlying mechanisms of gut microbe regulation of host behavior and brain functions remain unclear. This study aimed to elucidate the influence of gut microbiota on brain functions via post-translational modification mechanisms in the presence or absence of bacteria without any stimulation. We conducted succinylome analysis of hippocampal proteins in germ-free (GF) and specific pathogen-free (SPF) mice and metagenomic analysis of feces from SPF mice. These results were integrated with previously reported hippocampal acetylome and phosphorylome data from the same batch of mice. Subsequent bioinformatics analyses revealed 584 succinylation sites on 455 proteins, including 54 up-regulated succinylation sites on 91 proteins and 99 down-regulated sites on 51 proteins in the GF mice compared to the SPF mice. We constructed a panoramic map of gut microbiota-regulated succinylation, acetylation, and phosphorylation, and identified cross-talk and relative independence between the different types of post-translational modifications in modulating complicated intracellular pathways. Pearson correlation analysis indicated that 13 taxa, predominantly belonging to the Bacteroidetes phylum, were correlated with the biological functions of post-translational modifications. Positive correlations between these taxa and succinylation and negative correlations between these taxa and acetylation were identified in the modulation of intracellular pathways. This study highlights the hippocampal physiological changes induced by the absence of gut microbiota, and proteomic quantification of succinylation, phosphorylation, and acetylation, contributing to our understanding of the role of the gut microbiome in brain function and behavioral phenotypes.}, } @article {pmid38114197, year = {2023}, author = {Jiang, T and Liu, K and Li, J and Zhang, Y and Zhang, W and Doherty, M and Yang, Z and Yang, T and Yang, Y and Weng, Q and Luo, X and Xie, H and Li, C and Ai, K and Wei, J and Lei, G and Zeng, C}, title = {Gut-joint axis in knee synovitis: gut fungal dysbiosis and altered fungi-bacteria correlation network identified in a community-based study.}, journal = {RMD open}, volume = {9}, number = {4}, pages = {}, pmid = {38114197}, issn = {2056-5933}, mesh = {Humans ; Female ; Middle Aged ; *Dysbiosis/microbiology ; Cross-Sectional Studies ; *Synovitis/pathology ; Fungi ; Bacteria/genetics ; }, abstract = {OBJECTIVES: Knee synovitis is a highly prevalent and potentially curable condition for knee pain; however, its pathogenesis remains unclear. We sought to assess the associations of the gut fungal microbiota and the fungi-bacteria correlation network with knee synovitis.

METHODS: Participants were derived from a community-based cross-sectional study. We performed an ultrasound examination of both knees. A knee was defined as having synovitis if its synovium was ≥4 mm and/or Power Doppler (PD) signal was within the knee synovium area (PD synovitis). We collected faecal specimens from each participant and assessed gut fungal and bacterial microbiota using internal transcribed spacer 2 and shotgun metagenomic sequencing. We examined the relation of α-diversity, β-diversity, the relative abundance of taxa and the interkingdom correlations to knee synovitis.

RESULTS: Among 977 participants (mean age: 63.2 years; women: 58.8%), 191 (19.5%) had knee synovitis. β-diversity of the gut fungal microbiota, but not α-diversity, was significantly associated with prevalent knee synovitis. The fungal genus Schizophyllum was inversely correlated with the prevalence and activity (ie, control, synovitis without PD signal and PD synovitis) of knee synovitis. Compared with those without synovitis, the fungi-bacteria correlation network in patients with knee synovitis was smaller (nodes: 93 vs 153; edges: 107 vs 244), and the average number of neighbours was fewer (2.3 vs 3.2).

CONCLUSION: Alterations of gut fungal microbiota and the fungi-bacteria correlation network are associated with knee synovitis. These novel findings may help understand the mechanisms of the gut-joint axis in knee synovitis and suggest potential targets for future treatment.}, } @article {pmid38113887, year = {2024}, author = {Zhu, Y and Jian, X and Chen, S and An, G and Jiang, D and Yang, Q and Zhang, J and Hu, J and Qiu, Y and Feng, X and Guo, J and Chen, X and Li, Z and Zhou, R and Hu, C and He, N and Shi, F and Huang, S and Liu, H and Li, X and Xie, L and Zhu, Y and Zhao, L and Jiang, Y and Li, J and Wang, J and Qiu, L and Chen, X and Jia, W and He, Y and Zhou, W}, title = {Targeting gut microbial nitrogen recycling and cellular uptake of ammonium to improve bortezomib resistance in multiple myeloma.}, journal = {Cell metabolism}, volume = {36}, number = {1}, pages = {159-175.e8}, doi = {10.1016/j.cmet.2023.11.019}, pmid = {38113887}, issn = {1932-7420}, mesh = {Humans ; Bortezomib/pharmacology/therapeutic use/metabolism ; *Multiple Myeloma/drug therapy/metabolism ; *Gastrointestinal Microbiome ; Cell Line, Tumor ; Membrane Proteins/metabolism ; NIMA-Related Kinases/metabolism/therapeutic use ; Solute Carrier Family 12, Member 2/pharmacology ; }, abstract = {The gut microbiome has been found to play a crucial role in the treatment of multiple myeloma (MM), which is still considered incurable due to drug resistance. In previous studies, we demonstrated that intestinal nitrogen-recycling bacteria are enriched in patients with MM. However, their role in MM relapse remains unclear. This study highlights the specific enrichment of Citrobacter freundii (C. freundii) in patients with relapsed MM. Through fecal microbial transplantation experiments, we demonstrate that C. freundii plays a critical role in inducing drug resistance in MM by increasing levels of circulating ammonium. The ammonium enters MM cells through the transmembrane channel protein SLC12A2, promoting chromosomal instability and drug resistance by stabilizing the NEK2 protein. We show that furosemide sodium, a loop diuretic, downregulates SLC12A2, thereby inhibiting ammonium uptake by MM cells and improving progression-free survival and curative effect scores. These findings provide new therapeutic targets and strategies for the intervention of MM progression and drug resistance.}, } @article {pmid38113745, year = {2023}, author = {Gou, Y and Song, Y and Li, P and Wei, W and Luo, N and Wang, H}, title = {Study on the accelerated biodegradation of PAHs in subsurface soil via coupled low-temperature thermally treatment and electron acceptor stimulation based on metagenomic sequencing.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133265}, doi = {10.1016/j.jhazmat.2023.133265}, pmid = {38113745}, issn = {1873-3336}, abstract = {In situ anoxic bioremediation is a sustainable technology to remediate PAHs contaminated soils. However, the limited degradation rate of PAHs under anoxic conditions has become the primary bottleneck hindering the application of this technology. In this study, coupled low-temperature thermally treatment (<50 °C) and EA biostimulation was used to enhance PAH removal. Anoxic biodegradation of PAHs in soil was explored in microcosms in the absence and presence of added EAs at 3 temperatures (15 °C, 30 °C, and 45 °C). The influence of temperature, EA, and their interaction on the removal of PAHs were identified. A PAH degradation model based on PLSR analysis identified the importance and the positive/negative role of parameters on PAH removal. Soil archaeal and bacterial communities showed similar succession patterns, the impact of temperature was greater than that of EA. Soil microbial community and function were more influenced by temperature than EAs. Close and frequent interactions were observed among soil bacteria, archaea, PAH-degrading genes and methanogenic genes. A total of 15 bacterial OTUs, 1 PAH-degrading gene and 2 methanogenic genes were identified as keystones in the network. Coupled low-temperature thermally treatment and EA stimulation resulted in higher PAH removal efficiencies than EA stimulation alone and low-temperature thermally treatment alone.}, } @article {pmid38113233, year = {2023}, author = {Troth, TD and McInnes, RS and Dunn, SJ and Mirza, J and Whittaker, AH and Goodchild, SA and Loman, NJ and Harding, SV and van Schaik, W}, title = {Differences in the gut microbiota between Gurkhas and soldiers of British origin.}, journal = {PloS one}, volume = {18}, number = {12}, pages = {e0292645}, pmid = {38113233}, issn = {1932-6203}, mesh = {Humans ; *Gastrointestinal Microbiome ; White People ; Asian People ; *Military Personnel ; Metagenome ; }, abstract = {Previous work indicated that the incidence of travellers' diarrhoea (TD) is higher in soldiers of British origin, when compared to soldiers of Nepalese descent (Gurkhas). We hypothesise that the composition of the gut microbiota may be a contributing factor in the risk of developing TD in soldiers of British origin. This study aimed to characterise the gut microbial composition of Gurkha and non-Gurkha soldiers of the British Army. Recruitment of 38 soldiers (n = 22 Gurkhas, n = 16 non-Gurkhas) and subsequent stool collection, enabled shotgun metagenomic sequencing-based analysis of the gut microbiota. The microbiota of Gurkhas had significantly (P < 0.05) lower diversity, for both Shannon and Simpson diversity indices, using species level markers than the gut microbiota of non-Gurkha soldiers. Non-metric Multidimensional Scaling (NMDS) of the Bray-Curtis distance matrix revealed a significant difference in the composition of the gut microbiota between Gurkhas and non-Gurkha soldiers, at both the species level (P = 0.0178) and the genus level (P = 0.0483). We found three genera and eight species that were significantly enriched in the non-Gurkha group and one genus (Haemophilus) and one species (Haemophilus parainfluenzae) which were enriched in the Gurkha group. The difference in the microbiota composition between Gurkha soldiers and soldiers of British origin may contribute to higher colonization resistance against diarrhoeal pathogens in the former group. Our findings may enable further studies into interventions that modulate the gut microbiota of soldiers to prevent TD during deployment.}, } @article {pmid38112856, year = {2023}, author = {Kannan, P and Verma, I and Banerjee, B and Saleena, LM}, title = {Unveiling bacterial consortium for xenobiotic biodegradation from Pichavaram mangrove forest soil: a metagenomic approach.}, journal = {Archives of microbiology}, volume = {206}, number = {1}, pages = {27}, pmid = {38112856}, issn = {1432-072X}, mesh = {*Wetlands ; *Xenobiotics/metabolism ; Soil/chemistry ; Furaldehyde ; Bacteria/genetics/metabolism ; Microbial Consortia/genetics ; Soil Microbiology ; Biodegradation, Environmental ; Steroids/metabolism ; }, abstract = {Pichavaram mangrove forest was established as a wetland of International Importance by Article 2.1 in April 2022 by the Ministry of Environment, Forest and Climate Change, India. Even though it is a conserved site, xenobiotic agrochemical leaching on the forest land during monsoon is inevitable. These threaten the microbial diversity in the environment. Xenobiotic degradation is achieved using bacterial consortia already acclimatised to this environment. This study aims to identify the indigenous microbial consortia able to degrade xenobiotic compounds such as fluorobenzoate, furfural, and steroids. Pichavaram mangrove metagenomic dataset was obtained by shotgun sequencing of soil DNA and processed using the automated tool SqueezeMeta. Further, the DIAMOND database provided the taxonomical classification of the microbes in each contig. With reference to the KEGG database, the selected xenobiotic degradation pathways were confirmed in the dataset. Of 1,253,029 total contigs, 1332, 72 and 1262 were involved in fluorobenzoate, furfural and steroid degradation, respectively. This study identified that microbial consortia comprising Marinobacter, Methyloceanibacter and Vibrio natriegens/Gramella sp. can degrade fluorobenzoate. While Afipia, Nitrosopumilus sp., and Phototrophicus methaneseepsis favour the degradation of furfural compound. The steroid degradation pathway possessed a plethora of bacteria belonging to the phylum Proteobacteria.}, } @article {pmid38112482, year = {2023}, author = {Perry, JL and Scribano, FJ and Gebert, JT and Engevik, KA and Ellis, JM and Hyser, JM}, title = {Host IP3R channels are dispensable for rotavirus Ca[2+] signaling but critical for intercellular Ca[2+] waves that prime uninfected cells for rapid virus spread.}, journal = {mBio}, volume = {}, number = {}, pages = {e0214523}, doi = {10.1128/mbio.02145-23}, pmid = {38112482}, issn = {2150-7511}, abstract = {Many viruses exploit host Ca[2+] signaling to facilitate their replication; however, little is known about how Ca[2+] signals from different host and viral channels contribute to the overall dysregulation of Ca[2+] signaling or promote virus replication. Using cells lacking IP3R, a host ER Ca[2+] channel, we delineated intracellular Ca[2+] signals within virus-infected cells and intercellular Ca[2+] waves (ICWs), which increased Ca[2+] signaling in neighboring, uninfected cells. In infected cells, IP3R was dispensable for rotavirus-induced Ca[2+] signaling and replication, suggesting the rotavirus NSP4 viroporin supplies these signals. However, IP3R-mediated ICWs increase rotavirus replication kinetics and spread, indicating that the Ca[2+] signals from the ICWs may prime nearby uninfected cells to better support virus replication upon eventual infection. This "pre-emptive priming" of uninfected cells by exploiting host intercellular pathways in the vicinity of virus-infected cells represents a novel mechanism for viral reprogramming of the host to gain a replication advantage.}, } @article {pmid38112479, year = {2023}, author = {Shi, X and Wei, W and Wu, L and Huang, Y and Ni, B-J}, title = {Biosynthesis mechanisms of medium-chain carboxylic acids and alcohols in anaerobic microalgae fermentation regulated by pH conditions.}, journal = {Applied and environmental microbiology}, volume = {}, number = {}, pages = {e0125023}, doi = {10.1128/aem.01250-23}, pmid = {38112479}, issn = {1098-5336}, abstract = {Carboxylate platforms encompass a biosynthesis process involving a mixed and undefined culture, enabling the conversion of microalgae, rich in carbohydrates and protein, into valuable fuels and mitigating the risks associated with algae blooms. However, there is little known about the effects of pH on the metabolic pathways of chain elongation and alcohol production in anaerobic microalgae fermentation. Moreover, convoluted and interdependent microbial interactions encumber efforts to characterize how organics and electrons flow among microbiome members. In this work, we compared metabolic differences among three different pH levels (5, 7, and 10) in anaerobic microalgae fermentation. In addition, genome-centric metagenomic analysis was conducted to reveal the microbial interaction for medium-chain carboxylic acid and alcohol production.}, } @article {pmid38112280, year = {2023}, author = {Yuan, D and Shen, L and Qin, BE and Xu, X and Su, Z and Liu, J and Xia, H and Peng, F and Jiang, Y}, title = {Central nervous system nocardiosis diagnosed by metagenomic next-generation sequencing: A case series and literature review.}, journal = {Advances in clinical and experimental medicine : official organ Wroclaw Medical University}, volume = {32}, number = {12}, pages = {1453-1463}, doi = {10.17219/acem/175818}, pmid = {38112280}, issn = {1899-5276}, mesh = {Humans ; Retrospective Studies ; *Nocardia Infections/diagnosis/drug therapy/microbiology ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; *Nocardia/genetics ; Anti-Bacterial Agents/therapeutic use ; Brain/diagnostic imaging ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Central nervous system (CNS) nocardiosis is a rare suppurative disease caused by the genus Nocardia. It is found most frequently in immunocompromised individuals.

OBJECTIVES: In this study, we retrospectively reviewed the clinical presentations, laboratory examination, therapy and outcomes of 9 patients with CNS nocardiosis diagnosed using metagenomic next-generation sequencing (mNGS) in our hospital.

MATERIAL AND METHODS: We reviewed 9 patients with confirmed diagnosis of CNS Nocardia infection from January 2017 to December 2021 in the Department of Neurology at The Third Affiliated Hospital, Sun Yat-sen University (Guangzhou, China). In addition, we searched literature related to CNS Nocardia infection on PubMed and included all case reports with proven CNS nocardiosis since 2016.

RESULTS: The metagenomic next-generation sequencing (mNGS) of CSF can be used for the rapid diagnosis of nocardiosis in CNS and N. farcinica are the most commonly isolated species. Underlying autoimmune diseases, immunosuppressive agents including corticosteroids and organ transplantation are predisposing factors of developing CNS nocardiosis. Single or multiple hyper-enhanced ring lesions indicative of cerebral abscesses are commonly presented in brain imaging. Trimethoprim-sulfamethoxazole (TMP-SMX) is used as the primary agent for the antibacterial therapy and in combination with other antibacterial agents.

CONCLUSION: Our study demonstrated that mNGS of CSF can be conducted for definitive and rapid diagnosis for CNS nocardiosis.}, } @article {pmid38112274, year = {2024}, author = {Gaspari, M and Ghiotto, G and Centurion, VB and Kotsopoulos, T and Santinello, D and Campanaro, S and Treu, L and Kougias, PG}, title = {Decoding Microbial Responses to Ammonia Shock Loads in Biogas Reactors through Metagenomics and Metatranscriptomics.}, journal = {Environmental science & technology}, volume = {58}, number = {1}, pages = {591-602}, pmid = {38112274}, issn = {1520-5851}, mesh = {*Ammonia/metabolism/pharmacology ; Biofuels ; Bioreactors ; *Microbiota ; Metagenome ; Anaerobiosis ; Methane ; Metagenomics ; }, abstract = {The presence of elevated ammonia levels is widely recognized as a significant contributor to process inhibition in biogas production, posing a common challenge for biogas plant operators. The present study employed a combination of biochemical, genome-centric metagenomic and metatranscriptomic data to investigate the response of the biogas microbiome to two shock loads induced by single pulses of elevated ammonia concentrations (i.e., 1.5 g NH4[+]/LR and 5 g NH4[+]/LR). The analysis revealed a microbial community of high complexity consisting of 364 Metagenome Assembled Genomes (MAGs). The hydrogenotrophic pathway was the primary route for methane production during the entire experiment, confirming its efficiency even at high ammonia concentrations. Additionally, metatranscriptomic analysis uncovered a metabolic shift in the methanogens Methanothrix sp. MA6 and Methanosarcina flavescens MX5, which switched their metabolism from the acetoclastic to the CO2 reduction route during the second shock. Furthermore, multiple genes associated with mechanisms for maintaining osmotic balance in the cell were upregulated, emphasizing the critical role of osmoprotection in the rapid response to the presence of ammonia. Finally, this study offers insights into the transcriptional response of an anaerobic digestion community, specifically focusing on the mechanisms involved in recovering from ammonia-induced stress.}, } @article {pmid38112143, year = {2023}, author = {Feng, RG and Zhou, LY and Dou, R and Zhou, XY and Wang, LR and Han, LH and Wang, YM}, title = {[Application of metagenomic next-generation sequencing of bronchoalveolar lavage fluid in the diagnosis and treatment of refractory pneumonia in children].}, journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics}, volume = {25}, number = {12}, pages = {1253-1258}, pmid = {38112143}, issn = {1008-8830}, mesh = {Humans ; Child ; Bronchoalveolar Lavage Fluid ; Retrospective Studies ; *Pneumonia/diagnosis/therapy ; High-Throughput Nucleotide Sequencing ; Bronchoscopy ; Sensitivity and Specificity ; }, abstract = {OBJECTIVES: To investigate the clinical application of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in the etiological diagnosis and treatment of refractory pneumonia (RTP) in children.

METHODS: A retrospective analysis was performed on 160 children with RTP who were admitted to the Department of Pediatric Internal Medicine, Maternal and Child Health Hospital of Inner Mongolia Autonomous Region, from January 2020 to March 2023. According to whether mNGS was performed, they were divided into two groups: mNGS (n=80) and traditional testing (n=80). All children received the tests of inflammatory markers and pathogen tests after admission. Traditional pathogenicity tests included microbial culture (sputum specimen collected by suction tube), nucleic acid detection of respiratory pathogens, and serological test (mycoplasma, tuberculosis, and fungi). For the mNGS group, BALF specimens were collected after bronchoscopy and were sent to the laboratory for mNGS and microbial culture. The two groups were analyzed and compared in terms of the detection of pathogens and treatment.

RESULTS: Compared with the traditional testing group, the mNGS group had a significantly higher detection rate of pathogens (92% vs 58%, P<0.05), with more types of pathogens and a higher diagnostic rate of mixed infections. Compared with the traditional testing group, the mNGS group had a significantly higher treatment response rate and a significantly lower incidence rate of complications during hospitalization (P<0.05). Treatment was adjusted for 68 children in the mNGS group according to the results of mNGS, with a treatment response rate of 96% (65/68) after adjustment.

CONCLUSIONS: Compared with traditional pathogen tests, BALF mNGS can significantly improve the detection rate of pathogens and find some rare pathogens. In clinical practice, when encountering bottlenecks during the diagnosis and treatment of children with RTP, it is advisable to promptly perform the mNGS to identify the pathogens.}, } @article {pmid38112024, year = {2023}, author = {Gao, H and Fang, B and Sun, Z and Du, X and Guo, H and Zhao, L and Zhang, M}, title = {Effect of Human Milk Oligosaccharides on Learning and Memory in Mice with Alzheimer's Disease.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.3c05949}, pmid = {38112024}, issn = {1520-5118}, abstract = {Alzheimer's disease (AD) is distinguished by cognitive dysfunction and neuroinflammation in the brain. 2'-Fucosyllactose (2'-FL) is a major human milk oligosaccharide (HMO) that is abundantly present in breast milk and has been demonstrated to exhibit immunomodulatory effects. However, the role of 2'-FL and HMO in gut microbiota modulation in relation to AD remains insufficiently investigated. This study aimed to elucidate the preventive effect of the 2'-FL and HMO impact of AD and the relevant mechanism involved. Here, the behavioral results showed that 2'-FL and HMO intervention decreased the expression of Tau phosphorylation and amyloid-β (Aβ), inhibited neuroinflammation, and restored cognitive impairment in AD mice. The metagenomic analysis proved that 2'-FL and HMO intervention restored the dysbiosis of the gut microbiota in AD. Notably, 2'-FL and HMO intervention significantly enhanced the relative abundance of Clostridium and Akkermansia. The metabolomics results showed that 2'-FL and HMO enhanced the oleoyl-l-carnitine metabolism as potential drivers. More importantly, the levels of oleoyl-l-carnitine were positively correlated with the abundances of Clostridium and Akkermansia. These results indicated that 2'-FL and HMO had therapeutic potential to prevent AD-induced cognitive impairment, which is of great significance for the treatment of AD.}, } @article {pmid38111685, year = {2023}, author = {Segura, J and Rose, Y and Bi, C and Duarte, J and Burley, SK and Bittrich, S}, title = {RCSB Protein Data Bank: visualizing groups of experimentally determined PDB structures alongside computed structure models of proteins.}, journal = {Frontiers in bioinformatics}, volume = {3}, number = {}, pages = {1311287}, pmid = {38111685}, issn = {2673-7647}, abstract = {Recent advances in Artificial Intelligence and Machine Learning (e.g., AlphaFold, RosettaFold, and ESMFold) enable prediction of three-dimensional (3D) protein structures from amino acid sequences alone at accuracies comparable to lower-resolution experimental methods. These tools have been employed to predict structures across entire proteomes and the results of large-scale metagenomic sequence studies, yielding an exponential increase in available biomolecular 3D structural information. Given the enormous volume of this newly computed biostructure data, there is an urgent need for robust tools to manage, search, cluster, and visualize large collections of structures. Equally important is the capability to efficiently summarize and visualize metadata, biological/biochemical annotations, and structural features, particularly when working with vast numbers of protein structures of both experimental origin from the Protein Data Bank (PDB) and computationally-predicted models. Moreover, researchers require advanced visualization techniques that support interactive exploration of multiple sequences and structural alignments. This paper introduces a suite of tools provided on the RCSB PDB research-focused web portal RCSB. org, tailor-made for efficient management, search, organization, and visualization of this burgeoning corpus of 3D macromolecular structure data.}, } @article {pmid38111066, year = {2023}, author = {Ch'ng, L and Low, DHW and Borthwick, SA and Zhang, R and Ong, ZA and Su, YCF and Hitch, AT and Smith, GJD and Mendenhall, IH}, title = {Evolution and ecology of Jeilongvirus among wild rodents and shrews in Singapore.}, journal = {One health outlook}, volume = {5}, number = {1}, pages = {19}, pmid = {38111066}, issn = {2524-4655}, support = {Duke-NUS Signature Research Programme//Ministry of Health -Singapore/ ; }, abstract = {BACKGROUND: Jeilongvirus was proposed as a new genus within the Paramyxoviridae in 2018. The advancement in metagenomic approaches has encouraged multiple reports of Jeilongvirus detection following the initial species discovery, enriching species diversity and host range within the genus. However, Jeilongvirus remains understudied in Singapore, where interfaces between humans and small mammals are plentiful.

METHODS: Here, we utilized metagenomic sequencing for the exploration of viral diversity in small mammal tissues. Upon discovery of Jeilongvirus, molecular screening and full genome sequencing was conducted, with the data used to conduct statistical modelling and phylogenetic analysis.

RESULTS: We report the presence of Jeilongvirus in four species of Singapore wild small mammals, detected in their spleen and kidney. We show that full genomes of three Singapore Jeilongvirus encode for eight ORFs including the small hydrophobic and transmembrane proteins. All generated genomes cluster phylogenetically within the small mammal subclade, but share low genetic similarity with representative Jeilongvirus species. Statistical modelling showed no spatial or temporal patterns and differences among species, life history traits and habitat types.

CONCLUSIONS: This study serves as a basis for understanding dynamics between Jeilongvirus and small mammal hosts in Singapore by displaying the virus generalist nature. In addition, the initial detection can help to invoke improved routine surveillance and detection of circulating pathogens in synanthropic hosts.}, } @article {pmid38110543, year = {2023}, author = {Leiva, AM and Pardo, JM and Arinaitwe, W and Newby, J and Vongphachanh, P and Chittarath, K and Oeurn, S and Thi Hang, L and Gil-Ordóñez, A and Rodriguez, R and Cuellar, WJ}, title = {Ceratobasidium sp. is associated with cassava witches' broom disease, a re-emerging threat to cassava cultivation in Southeast Asia.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22500}, pmid = {38110543}, issn = {2045-2322}, mesh = {Phytoplasma Disease ; *Manihot ; Plant Diseases/microbiology ; *Phytoplasma ; Fungi ; *Cacao/microbiology ; }, abstract = {Cassava witches' broom disease (CWBD) is a devastating disease of cassava in Southeast Asia (SEA), of unknown etiology. Affected plants show reduced internodal length, proliferation of leaves and weakening of stems. This results in poor germination of infected stem cuttings (i.e., planting material) and significant reductions in fresh root yields and starch content, causing economic losses for farmers and processors. Using a metagenomic approach, we identified a fungus belonging to the Ceratobasidium genus, sharing more than 98.3-99.7% nucleotide identity at the Internal Transcribed Spacer (ITS), with Ceratobasidium theobromae a pathogen causing similar symptoms in cacao. Microscopy analysis confirmed the identity of the fungus and specific designed PCR tests readily showed (1) Ceratobasidium sp. of cassava is strongly associated with CWBD symptoms, (2) the fungus is present in diseased samples collected since the first recorded CWBD outbreaks in SEA and (3) the fungus is transmissible by grafting. No phytoplasma sequences were detected in diseased plants. Current disease management efforts include adjustment of quarantine protocols and guarantee the production and distribution of Ceratobasidium-free planting material. Implications of related Ceratobasidium fungi, infecting cassava, and cacao in SEA and in other potential risk areas are discussed.}, } @article {pmid38110487, year = {2023}, author = {Clagnan, E and Cucina, M and De Nisi, P and Dell'Orto, M and D'Imporzano, G and Kron-Morelli, R and Llenas-Argelaguet, L and Adani, F}, title = {Effects of the application of microbiologically activated bio-based fertilizers derived from manures on tomato plants and their rhizospheric communities.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22478}, pmid = {38110487}, issn = {2045-2322}, support = {862849//Horizon 2020 Framework Programme/ ; 862849//Horizon 2020 Framework Programme/ ; 862849//Horizon 2020 Framework Programme/ ; 862849//Horizon 2020 Framework Programme/ ; 862849//Horizon 2020 Framework Programme/ ; 862849//Horizon 2020 Framework Programme/ ; 862849//Horizon 2020 Framework Programme/ ; 862849//Horizon 2020 Framework Programme/ ; }, mesh = {Animals ; Fertilizers ; *Solanum lycopersicum ; Manure ; Agriculture ; *Trichoderma ; Soil ; }, abstract = {Bio-based fertilizers (BBFs) recovered from animal manure are promising products to optimise resources recovery and generate high agricultural yields. However, their fertilization value may be limited and it is necessary to enrich BBFs with microbial consortia to enhance their fertilization value. Three specific microbial consortia were developed according to the characteristics of three different BBFs produced from manure (bio-dried solid fraction, solid fraction of digestate and biochar) to enhance plant growth and product quality. A greenhouse pot experiment was carried out with tomato plants grown with microbiologically activated BBFs applied either as N-organic fertilizers or as an organic amendment. A next generation sequencing analysis was used to characterise the development of each rhizospheric community. All the activated BBFs gave enhanced tomato yields (fresh and dry weight) compared with the non-activated treatments and similar to, or higher than, chemical fertilization. Concerning the tomato fruits' organoleptic quality, lycopene and carotenoids concentrations were improved by biological activation. Metagenomic analysis points at Trichoderma as the main driver of the positive effects, with the effects of added bacteria being negligible or limited at the early stages after fertilization. In the context of the circular economy, the activated BBFs could be used to replace synthetic fertilisers, reducing costs and environmental burdens and increasing production.}, } @article {pmid38109983, year = {2023}, author = {He, Y and Zuo, Y and Che, Y and Chen, J}, title = {Metagenomic capture sequencing helped diagnose a case of atypical scrub typhus in man misdiagnosed as acute osteomyelitis.}, journal = {Travel medicine and infectious disease}, volume = {57}, number = {}, pages = {102682}, doi = {10.1016/j.tmaid.2023.102682}, pmid = {38109983}, issn = {1873-0442}, } @article {pmid38109978, year = {2023}, author = {Xiang, P and Ma, P and He, Q and Song, Z and Miao, Z}, title = {Enhanced removal of phenol and chemical oxygen demand from coking wastewater using micro and nano bubbles: Microbial community and metabolic pathways.}, journal = {Bioresource technology}, volume = {394}, number = {}, pages = {130207}, doi = {10.1016/j.biortech.2023.130207}, pmid = {38109978}, issn = {1873-2976}, abstract = {The treatment of coking wastewater with high phenol concentrations has been a challenge for conventional biological treatment technology. In this short communication, phenol-degrading bacteria domesticated by micro and nano bubbles (MNBs) water are used to treat the high- concentration phenol in an MNBs aeration reactor (MNB-AR). The results show that the MNB-AR can greatly improve the removal of phenol and chemical oxygen demand (COD). At a phenol concentration of 1000 mg L[-1], the phenol and COD removal rates in the MNB-AR are 55 % and 39 % higher than in the conventional bubble aeration reactor respectively. MNB-AR performs more stably and reaches a higher phenol tolerance under fluctuating high-phenol-concentration loadings. Metagenomic analysis shows that MNBs promote the growth and metabolism of aerobic microorganisms related to phenol degradation, and enhance gene abundance related to carbon metabolism. MNBs aeration combined with microorganisms is an efficient solution for treating coking wastewater.}, } @article {pmid38109977, year = {2023}, author = {Xu, J and Shi, Z and Xu, L and Zheng, X and Zong, Y and Luo, G and Zhang, C and Liu, M and Xie, L}, title = {Recovery capability of anaerobic digestion from ammonia stress: Metabolic activity, energy generation, and genome-centric metagenomics.}, journal = {Bioresource technology}, volume = {394}, number = {}, pages = {130203}, doi = {10.1016/j.biortech.2023.130203}, pmid = {38109977}, issn = {1873-2976}, abstract = {Excessive ammonia stresses anaerobic digestion (AD) significantly. Although there has been progress in understanding AD under ammonia exposure, investigations on AD liberated from ammonia exposure are limited. Here, the recovery capability of AD from ammonia stress was evaluated, by examining specific methanogenic activity, energy-conserving capability, microbial community succession, and metabolic pathway reconstruction. The findings demonstrated that ammonia stress relief resulted in < 50% methane recovery, with propionate conversion identified as the critical impediment to AD reactivation. Energy generation could not recovered either. Efforts to mitigate ammonia stress failed to restore acetoclastic methanogens, e.g., Methanothrix soehngenii, and proved futile in awakening propionate oxidizers, e.g., Desulfobulbus. Interestingly, a symbiotic metabolism emerged, prevailing in stress-relieved AD due to its energy-conserving advantage. This study underscores the importance of targeted interventions, including stimulating acetoclastic methanogenesis, propionate oxidation, and energy generation, as priorities for AD recovery following ammonia stress, rather than focusing solely on ammonia level management.}, } @article {pmid38109938, year = {2023}, author = {Rodríguez Del Río, Á and Giner-Lamia, J and Cantalapiedra, CP and Botas, J and Deng, Z and Hernández-Plaza, A and Munar-Palmer, M and Santamaría-Hernando, S and Rodríguez-Herva, JJ and Ruscheweyh, HJ and Paoli, L and Schmidt, TSB and Sunagawa, S and Bork, P and López-Solanilla, E and Coelho, LP and Huerta-Cepas, J}, title = {Functional and evolutionary significance of unknown genes from uncultivated taxa.}, journal = {Nature}, volume = {}, number = {}, pages = {}, doi = {10.1038/s41586-023-06955-z}, pmid = {38109938}, issn = {1476-4687}, abstract = {Many of Earth's microbes remain uncultured and under-studied, limiting our understanding of the functional and evolutionary aspects of their genetic material, which remain largely overlooked in most metagenomic studies[1]. Here, we analyzed 149,842 environmental genomes from multiple habitats[2-6] and compiled a curated catalog of 404,085 functionally and evolutionarily significant novel (FESNov) gene families exclusive to uncultivated prokaryotic taxa. All FESNov families span multiple species, exhibit strong signals of purifying selection, and qualify as new orthologous groups, thus nearly tripling the number of bacterial and archaeal gene families described to date. The FESNov catalog is enriched in clade-specific traits, including 1,034 novel families that can distinguish entire uncultivated phyla, classes, and orders, likely representing synapomorphies that facilitated their evolutionary divergence. Using genomic context analysis and structural alignments, we predicted functional associations for 32.4% of FESNov families, including 4,349 high-confidence associations with important biological processes. These predictions provide a valuable hypothesis-driven framework, which we employed to experimentally validate a new gene family involved in cell motility and a novel set of antimicrobial peptides. We also demonstrate that the relative abundance profiles of novel families can discriminate between environments and clinical conditions, leading to the discovery of potentially new biomarkers associated with colorectal cancer. We expect this work to enhance future metagenomics studies and expand our knowledge of the genetic repertory of uncultivated organisms.}, } @article {pmid38108689, year = {2023}, author = {Zhang, JY and Xiao, J and Xie, B and Barba, H and Boachie-Mensah, M and Shah, RN and Nadeem, U and Spedale, M and Dylla, N and Lin, H and Sidebottom, AM and D'Souza, M and Theriault, B and Sulakhe, D and Chang, EB and Skondra, D}, title = {Oral Metformin Inhibits Choroidal Neovascularization by Modulating the Gut-Retina Axis.}, journal = {Investigative ophthalmology & visual science}, volume = {64}, number = {15}, pages = {21}, pmid = {38108689}, issn = {1552-5783}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; }, mesh = {Male ; Female ; Animals ; Mice ; Angiogenesis Inhibitors ; RNA, Ribosomal, 16S ; Vascular Endothelial Growth Factor A ; Visual Acuity ; *Wet Macular Degeneration ; Retina ; *Choroidal Neovascularization/prevention & control ; }, abstract = {PURPOSE: Emerging data indicate that metformin may prevent the development of age-related macular degeneration (AMD). Whereas the underlying mechanisms of metformin's anti-aging properties remain undetermined, one proposed avenue is the gut microbiome. Using the laser-induced choroidal neovascularization (CNV) model, we investigate the effects of oral metformin on CNV, retinal pigment epithelium (RPE)/choroid transcriptome, and gut microbiota.

METHODS: Specific pathogen free (SPF) male mice were treated via daily oral gavage of metformin 300 mg/kg or vehicle. Male mice were selected to minimize sex-specific differences to laser induction and response to metformin. Laser-induced CNV size and macrophage/microglial infiltration were assessed by isolectin and Iba1 immunostaining. High-throughput RNA-seq of the RPE/choroid was performed using Illumina. Fecal pellets were analyzed for gut microbiota composition/pathways with 16S rRNA sequencing/shotgun metagenomics, as well as microbial-derived metabolites, including small-chain fatty acids and bile acids. Investigation was repeated in metformin-treated germ-free (GF) mice and antibiotic-treated/GF mice receiving fecal microbiota transplantation (FMT) from metformin-treated SPF mice.

RESULTS: Metformin treatment reduced CNV size (P < 0.01) and decreased Iba1+ macrophage/microglial infiltration (P < 0.005). One hundred forty-five differentially expressed genes were identified in the metformin-treated group (P < 0.05) with a downregulation in pro-angiogenic genes Tie1, Pgf, and Gata2. Furthermore, metformin altered the gut microbiome in favor of Bifidobacterium and Akkermansia, with a significant increase in fecal levels of butyrate, succinate, and cholic acid. Metformin did not suppress CNV in GF mice but colonization of microbiome-depleted mice with metformin-derived FMT suppressed CNV.

CONCLUSIONS: These data suggest that oral metformin suppresses CNV, the hallmark lesion of advanced neovascular AMD, via gut microbiome modulation.}, } @article {pmid38108654, year = {2023}, author = {Miao, Z and Chen, L and Zhang, Y and Zhang, J and Zhang, H}, title = {Bifidobacterium animalis subsp. lactis Probio-M8 alleviates abnormal behavior and regulates gut microbiota in a mouse model suffering from autism.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0101323}, doi = {10.1128/msystems.01013-23}, pmid = {38108654}, issn = {2379-5077}, abstract = {Individuals with autism often exhibit symptoms of social invariance, obsessive-compulsive tendencies, and repetitive behaviors. However, early intervention and treatment can be effective in improving social skills and mitigating autism symptoms, including behaviors related to irritability. Although taking medication for autism may lead to side effects such as weight gain, probiotics can be an ideal intervention for alleviating these symptoms. In this study, we investigated the effects of Probio-M8 intervention on the behavior of autistic mice using an open-field test, a three-chamber sociability test, and a novel object recognition test. Metagenomic analysis revealed differences in gut microbiota diversity among groups, predicted changes in metabolite levels, and functionally annotated CAZy. Additionally, we analyzed serum neurotransmitter levels and found that probiotics were beneficial in mitigating neurotransmitter imbalances in mice with autism.}, } @article {pmid38108401, year = {2023}, author = {Liu, L and Ito, T and Li, B and Tani, H and Okuzaki, D and Motooka, D and Miyazaki, H and Ogino, T and Nakamura, S and Takeda, K and Kayama, H}, title = {The UDP-glucose/P2Y14 receptor axis promotes eosinophil-dependent large intestinal inflammation.}, journal = {International immunology}, volume = {}, number = {}, pages = {}, doi = {10.1093/intimm/dxad050}, pmid = {38108401}, issn = {1460-2377}, abstract = {Ulcerative colitis (UC) is a chronic disorder of the large intestine with inflammation and ulceration. The incidence and prevalence of UC have been rapidly increasing worldwide, but its etiology remains unknown. In patients with UC, the accumulation of eosinophils in the large intestinal mucosa is associated with increased disease activity. However, the molecular mechanism underlying the promotion of intestinal eosinophilia in patients with UC remains poorly understood. Here, we show that uridine diphosphate (UDP)-glucose mediates the eosinophil-dependent promotion of colonic inflammation via the purinergic receptor P2Y14. The expression of P2RY14 mRNA was upregulated in the large intestinal mucosa of patients with UC. The P2Y14 receptor ligand UDP-glucose was increased in the large intestinal tissue of mice administered dextran sodium sulfate (DSS). In addition, P2ry14 deficiency and P2Y14 receptor blockade mitigated DSS-induced colitis. Among the large intestinal immune cells and epithelial cells, eosinophils highly expressed P2ry14 mRNA. P2ry14-/- mice transplanted with wild-type bone marrow eosinophils developed more severe DSS-induced colitis compared with P2ry14-/- mice that received P2ry14-deficient eosinophils. UDP-glucose prolonged the lifespan of eosinophils and promoted gene transcription in the cells through P2Y14 receptor-mediated activation of ERK1/2 signaling. Thus, the UDP-glucose/P2Y14 receptor axis aggravates large intestinal inflammation by accelerating the accumulation and activation of eosinophils.}, } @article {pmid38108377, year = {2023}, author = {Goppold, A and Conradie, L and Almeida, OGG and De Martinis, ECP and Oguntoyinbo, FA}, title = {Profiling the Bacterial Community of Fermenting Traminette Grapes during Wine Production using Metagenomic Amplicon Sequencing.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {202}, pages = {}, doi = {10.3791/65598}, pmid = {38108377}, issn = {1940-087X}, mesh = {*Vitis ; *Wine ; Bacteria/genetics ; Metagenome ; Proteobacteria ; }, abstract = {Advances in sequencing technology and the relatively easy access to the use of bioinformatics tools to profile microbial community structures have facilitated a better understanding of both culturable and non-culturable microbes in grapes and wine. During industrial fermentation, microbes, known and unknown, are often responsible for product development and off-flavor. Therefore, profiling the bacteria from grape to wine can enable an easy understanding of in situ microbial dynamics. In this study, the bacteria of Traminette grapes must undergoing fermentation, and the final wine were subjected to DNA extraction that yielded 15 ng/µL to 87 ng/µL. The 16S amplicon of the hypervariable region of the V4 region was sequenced, relatively abundant bacteria consisting of phyla Proteobacteria, Actinobacteriota, Firmicutes, Bacteroidota, Fusobacteriota and followed by the Verrucomicrobiota, Halobacterota, Desulfobacterota, Myxococcota, and Acidobacteriota. A Venn diagram analysis of the shared unique operational taxonomic units (OTU) revealed that 15 bacteria phyla were common to both grape must, fermenting stage, and final wine. Phyla that were not previously reported were detected using the 16S amplicon sequencing, as well as genera such as Enterobacteriaceae and Lactobacillaceae. Variation in the organic nutrient use in wine and its impact on bacteria was tested; Traminette R tank containing Fermaid O and Traminette L stimulated with Stimula Sauvignon blanc + Fermaid O. Alpha diversity using the Kruskal-Wallis test determined the degree of evenness. The beta diversity indicated a shift in the bacteria at the fermentation stage for the two treatments, and the final wine bacteria looked similar. The study confirmed that 16S amplicon sequencing can be used to monitor bacteria changes during wine production to support quality and better utilization of grape bacteria during wine production.}, } @article {pmid38108273, year = {2023}, author = {Zhang, S-h and Jia, X-y and Wu, Q and Jin, J and Xu, L-s and Yang, L and Han, J-g and Zhou, Q-h}, title = {The involvement of the gut microbiota in postoperative cognitive dysfunction based on integrated metagenomic and metabolomics analysis.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0310423}, pmid = {38108273}, issn = {2165-0497}, mesh = {Aged ; Humans ; Animals ; Mice ; *Postoperative Cognitive Complications ; *Gastrointestinal Microbiome ; Metabolomics ; *Cognitive Dysfunction ; Bacteroides ; }, abstract = {As the population ages and medical technology advances, anesthesia procedures for elderly patients are becoming more common, leading to an increased prevalence of postoperative cognitive dysfunction. However, the etiology and correlation between the gut microbiota and cognitive dysfunction are poorly understood, and research in this area is limited. In this study, mice with postoperative cognitive dysfunction were found to have reduced levels of fatty acid production and anti-inflammatory flora in the gut, and Bacteroides was associated with increased depression, leading to cognitive dysfunction and depression. Furthermore, more specific microbial species were identified in the disease model, suggesting that modulation of host metabolism through gut microbes may be a potential avenue for preventing postoperative cognitive dysfunction.}, } @article {pmid38107432, year = {2023}, author = {Kuang, J and Luo, Z and Zhou, F}, title = {Acute Pulmonary Actinomycosis Induced by Immunotherapy and Chemotherapy Used for SCLC Treatment: A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {7575-7580}, pmid = {38107432}, issn = {1178-6973}, abstract = {A 66-year-old male patient diagnosed with small-cell lung cancer received chemotherapy and immunotherapy, resulting in successful tumor control. However, the patient subsequently experienced a fever and rapid progression of the pulmonary cavity. Despite sampling bronchoscopic bronchoalveolar lavage fluid for targeted next-generation sequencing (tNGS), the cause remained unidentified. Adding bronchoalveolar lavage fluid to sense metagenomic next-generation sequencing (mNGS) confirmed the infection caused by actinomycetes. The patient's condition improved after active anti-infection treatment. This case was further analyzed and discussed through a comprehensive literature review, focusing on molecular microbiological diagnosis and treatment processes. The points outlined were as follows: the advancement of molecular microbiology has gradually reduced the challenges associated with diagnosing rare infectious diseases such as pulmonary actinomycosis. Additionally, in immunodeficient individuals, certain infectious diseases with a chronic course may exhibit acute and aggressive characteristics, which is of concern to all colleagues. Currently, tNGS and mNGS are widely employed in clinical settings as practical tools for diagnosing infectious diseases. Notably, these two methods are not substitutes for each other but complement each other.}, } @article {pmid38107430, year = {2023}, author = {Cheng, H and Wu, H and Tan, N and Liu, Z and Wang, N and Chen, N and Li, C}, title = {Diagnostic Efficacy of Metagenomic Next-Generation Sequencing in Patients with Spinal Infections: A Retrospective Study.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {7613-7620}, pmid = {38107430}, issn = {1178-6973}, abstract = {PURPOSE: Early diagnosis of spinal infections remains challenging, and emerging metagenomic next-generation sequencing (mNGS) technology holds promise in addressing this issue. The aim of this study is to investigate the diagnostic efficacy of mNGS in spinal infections.

PATIENTS AND METHODS: A total of 78 cases with suspected spinal infections were enrolled in this study, all of whom underwent laboratory, histopathological and mNGS examinations upon admission. Lesion samples were obtained by surgical or C-arm-guided puncture. Sensitivity, specificity, positive predictive value and negative predictive value of culture and mNGS were calculated for statistical analysis.

RESULTS: With histopathological results as the reference, the included 78 patients were categorized into 50 cases in the spinal infection group and 28 cases in the aseptic group. The sensitivity (84%) and negative predictive value (77.14%) of mNGS were significantly higher than those of culture (32% and 44.26%, respectively), whereas no significant differences were observed in terms of specificity and positive predictive value. In the subgroup analysis for Mycobacterium tuberculosis, the sensitivity of mNGS (90.91%) and T-spot (90.91%) was significantly higher than that of culture (0). Additionally, mNGS demonstrated markedly higher specificity (100%) compared to T-spot (85.07%).

CONCLUSION: This study underscores the substantial advantages of mNGS in terms of diagnostic accuracy and bacterial coverage for spinal infections. The findings provide compelling clinical evidence that supports the enhanced diagnostic efficacy of mNGS.}, } @article {pmid38106477, year = {2023}, author = {Zhang, D and Yu, F and Han, D and Chen, W and Yuan, L and Xie, M and Zheng, J and Wang, J and Lou, B and Zheng, S and Chen, Y}, title = {ddPCR provides a sensitive test compared with GeneXpert MTB/RIF and mNGS for suspected Mycobacterium tuberculosis infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1216339}, pmid = {38106477}, issn = {2235-2988}, mesh = {Humans ; *Tuberculosis, Pulmonary/diagnosis ; Rifampin ; *Mycobacterium tuberculosis/genetics ; *Antibiotics, Antitubercular/therapeutic use ; Sensitivity and Specificity ; *Tuberculosis/microbiology ; High-Throughput Nucleotide Sequencing ; }, abstract = {INTRODUCTION: The Metagenomics next-generation sequencing (mNGS) and GeneXpert MTB/RIF assay (Xpert) exhibited a sensitivity for tuberculosis (TB) diagnostic performance. Research that directly compared the clinical performance of ddPCR analysis, mNGS, and Xpert in mycobacterium tuberculosis complex (MTB) infection has not been conducted.

METHODS: The study aimed to evaluate the diagnostic performance of ddPCR compared to mNGS and Xpert for the detection of MTB in multiple types of clinical samples. The final clinical diagnosis was used as the reference standard.

RESULTS: Out of 236 patients with suspected active TB infection, 217 underwent synchronous testing for tuberculosis using ddPCR, Xpert, and mNGS on direct clinical samples. During follow-up, 100 out of 217 participants were diagnosed with MTB infection. Compared to the clinical final diagnosis, ddPCR produced the highest sensitivity of 99% compared with mNGS (86%) and Xpert (64%) for all active MTB cases.

DISCUSSION: Twenty-two Xpert-negative samples were positive in mNGS tests, which confirmed the clinical diagnosis results from ddPCR and clinical manifestation, radiologic findings. Thirteen mNGS-negative samples were positive in ddPCR assays, which confirmed the clinical final diagnosis.ddPCR provides a higher sensitive compared to Xpert and mNGS for MTB diagnosis, as defined by the high concordance between ddPCR assay and clinical final diagnosis.}, } @article {pmid38106471, year = {2023}, author = {Wang, L and Liu, N and Zhang, L and Cui, L and Zhu, M and Li, Z and Wang, P and Wang, Z}, title = {Performance of next-generation sequencing for diagnosis of blood infections by Klebsiella pneumoniae.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1278482}, pmid = {38106471}, issn = {2235-2988}, mesh = {Humans ; *Klebsiella pneumoniae/genetics ; Retrospective Studies ; *Sepsis ; Blood Culture ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {OBJECTIVE: Klebsiella pneumoniae (Kp) bloodstream infections (BSI) can be a life-threatening opportunistic infection. We aimed to evaluate the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) for Kp BSI.

METHODS: We retrospectively analyzed 72 patients suspected with bloodstream infection and mNGS Kp positive in peripheral blood, who were hospitalized in our hospital from January 2022 to January 2023. Clinical data and laboratory parameters were collected. All patients had blood drawn and other samples for blood mNGS, blood cultures (BC) and other cultures (OC). The accuracy of mNGS results was analyzed according to infection site, clinical indicators, therapeutic effect and routine culture results. The detection of pathogenic microorganisms by blood mNGS and routine culture was compared.

RESULTS: Among 72 infection patients, 29 cases (40.28%) were BC positive, 43 cases (59.72%) were other culture (OC) positive, 16 cases (22.22%) were both BC and OC positive, 56 cases were positive for both mNGS and routine culture. Among the 56 double-positive cases, mNGS and conventional cultures were completely consistent in 27 cases, partially consistent in 15 cases, and completely inconsistent in 14 cases. Using the clinical diagnosis as the reference standard, There were 51 cases consistent with the results of mNGS with Kp BSI, the clinical consistency was 70.83% (51/72). The coincidence rate of mNGS and clinical diagnosis was higher than that of BC (54.17%, 39/72), indicating a statistically significant difference between the two methods (P<0.01).

CONCLUSIONS: Current evidence indicates that mNGS exhibits excellent accuracy for the diagnosis of Kp BSI. Although it cannot replace blood culture detection technology, it can be used as a supplement to provide stronger diagnostic capabilities for BSI and optimize treatment.}, } @article {pmid38104842, year = {2023}, author = {Zhu, L and Li, W and Huang, C and Tian, Y and Xi, B}, title = {Functional redundancy is the key mechanism used by microorganisms for nitrogen and sulfur metabolism during manure composting.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169389}, doi = {10.1016/j.scitotenv.2023.169389}, pmid = {38104842}, issn = {1879-1026}, abstract = {The microbial ecological functions associated with the nitrogen and sulfur cycles during composting have not been thoroughly elucidated. Using metagenomic sequencing, the microbial mechanisms underlying the nitrogen and sulfur metabolism during livestock and poultry manure composting were investigated in this study. The findings demonstrate that functional redundancy among microorganisms is a crucial factor for the nitrogen and sulfur cycling during livestock and poultry manure composting. Processes such as organic sulfur synthesis, assimilatory sulfate reduction, ammonia assimilation, and denitrification were found to be prevalent. Additionally, there was a certain degree of conservation in nitrogen and sulfur conversion functions among microorganisms at the phylum level. All high-quality metagenomic assembly genomes (MAGs) possessed carbon fixation potential, with 86.3 % of MAGs containing both nitrogen and sulfur conversion genes. Except for bin30, other MAGs encoding sulfur oxidation enzymes were found to be associated with at least one denitrification gene. This suggests a potential interplay between nitrogen and sulfur metabolism among microorganisms. 45, 19, 1, 31, 1, and 2 MAGs could completely regulate organic sulfur synthesis, assimilatory sulfate reduction, thiosulfate oxidation to sulfate, glutamine synthase-glutamate synthase pathway (GS-GOGAT), denitrification, and dissimilatory nitrate reduction, respectively by encoding the required enzymes. TN and pH were the key factors driving the functional redundancy in nitrogen and sulfur microbial community.}, } @article {pmid38104836, year = {2023}, author = {Gan, X and Hu, H and Fu, Q and Zhu, J}, title = {Nitrate reduction coupling with As(III) oxidation in neutral As-contaminated paddy soil preserves nitrogen, reduces N2O emissions and alleviates As toxicity.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169360}, doi = {10.1016/j.scitotenv.2023.169360}, pmid = {38104836}, issn = {1879-1026}, abstract = {In arsenic (As)-contaminated paddy soil, microbial-driven nitrate (NO3[-]) reduction coupled with arsenite (As(III)) oxidation can reduce As toxicity, but the whereabouts of NO3[-] remain unclear. In this study, the experiments were established using selective streptomycin (STP) and cyclohexylamine to inhibit bacterial and fungal functional responses, respectively, and metagenomic sequencing techniques were used to explain the biological mechanisms of NO3[-] reduction coupled with As(III) oxidation in neutral As-contaminated paddy soil. The results indicated that fungal denitrification resulted in stronger nitrous oxide (N2O) emissions (321.6 μg kg[-1]) than bacterial denitrification (175.9 μg kg[-1]) in neutral As-contaminated paddy soil, but NO3[-] reduction coupled with As(III) oxidation reduced the N2O emissions. Only adding STP led to ammonium (NH4[+]) generation (17.7 mg kg[-1]), and simultaneously more NH4[+] appeared in NO3[-] reduction coupled with As(III) oxidation; this may be because it improved the electron transfer efficiency by 18.2 %. Achromobacter was involved in denitrification coupled with As(III) oxidation. Burkholderiales was responsible for NO3[-] reduction to NH4[+] coupled with As(III) oxidation. This study provided a theoretical basis for NO3[-] reduction coupled with As(III) oxidation reducing N2O emissions, promoting the reduction of NO3[-] to NH4[+], and reducing As toxicity in paddy soil.}, } @article {pmid38104834, year = {2023}, author = {Ye, Y and Peng, C and Zhu, D and Yang, R and Deng, L and Wang, T and Tang, Y and Lu, L}, title = {Identification of sulfamethazine degraders in swine farm-impacted river and farmland: A comparative study of aerobic and anaerobic environments.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169299}, doi = {10.1016/j.scitotenv.2023.169299}, pmid = {38104834}, issn = {1879-1026}, abstract = {Sulfonamides (SAs) are extensively used antibiotics in the prevention and treatment of animal diseases, leading to significant SAs pollution in surrounding environments. Microbial degradation has been proposed as a crucial mechanism for removing SAs, but the taxonomic identification of microbial functional guilds responsible for SAs degradation in nature remain largely unexplored. Here, we employed [13]C-sulfamethazine (SMZ)-based DNA-stable isotope probing (SIP) and metagenomic sequencing to investigate SMZ degraders in three distinct swine farm wastewater-receiving environments within an agricultural ecosystem. These environments include the aerobic riparian wetland soil, agricultural soil, and anaerobic river sediment. SMZ mineralization activities exhibited significant variation, with the highest rate observed in aerobic riparian wetland soil. SMZ had a substantial impact on the microbial community compositions across all samples. DNA-SIP analysis demonstrated that Thiobacillus, Auicella, Sphingomonas, and Rhodobacter were dominant active SMZ degraders in the wetland soil, whereas Ellin6067, Ilumatobacter, Dongia, and Steroidobacter predominated in the agricultural soil. The genus MND1 and family Vicinamibacteraceae were identified as SMZ degrader in both soils. In contrast, anaerobic SMZ degradation in the river sediment was mainly performed by genera Microvirga, Flavobacterium, Dechlorobacter, Atopostipes, and families Nocardioidaceae, Micrococcaceae, Anaerolineaceae. Metagenomic analysis of [13]C-DNA identified key SAs degradation genes (sadA and sadC), and various of dioxygenases, and aromatic hydrocarbon degradation-related functional genes, indicating their involvement in degradation of SMZ and its intermediate products. These findings highlight the variations of indigenous SAs oxidizers in complex natural habitats and emphasize the consideration of applying these naturally active degraders in future antibiotic bioremediation.}, } @article {pmid38104736, year = {2024}, author = {Bakhti, A and Moghimi, H and Bozorg, A and Stankovic, S and Manafi, Z and Schippers, A}, title = {Comparison of bioleaching of a sulfidic copper ore (chalcopyrite) in column percolators and in stirred-tank bioreactors including microbial community analysis.}, journal = {Chemosphere}, volume = {349}, number = {}, pages = {140945}, doi = {10.1016/j.chemosphere.2023.140945}, pmid = {38104736}, issn = {1879-1298}, mesh = {*Copper ; RNA, Ribosomal, 16S/genetics ; Sodium Chloride ; Bioreactors/microbiology ; Iron ; Sulfur ; Sulfides ; *Microbiota ; }, abstract = {Chalcopyrite is the most abundant Cu-sulfide and economically the most important copper mineral in the world. It is known to be recalcitrant in hydrometallurgical processing and therefore chalcopyrite bioleaching has been thoroughly studied for improvement of processing. In this study, the microbial diversity in 22 samples from the Sarcheshmeh copper mine in Iran was investigated via 16S rRNA gene sequencing. In total, 1063 species were recognized after metagenomic analysis including the ferrous iron- and sulfur-oxidizing acidophilic genera Acidithiobacillus, Leptospirillum, Sulfobacillus and Ferroplasma. Mesophilic as well as moderately thermophilic acidophilic ferrous iron- and sulfur-oxidizing microorganisms were enriched from these samples and bioleaching was studied in shake flask experiments using a chalcopyrite-containing ore sample from the same mine. These enrichment cultures were further used as inoculum for bioleaching experiments in percolation columns for simulating heap bioleaching. Addition of 100 mM NaCl to the bioleaching medium was assessed to improve the dissolution rate of chalcopyrite. For comparison, bioleaching in stirred tank reactors with a defined microbial consortium was carried out as well. While just maximal 32% copper could be extracted in the flask bioleaching experiments, 73% and 76% of copper recovery was recorded after 30 and 10 days bioleaching in columns and bioreactors, respectively. Based on the results, both, the application of moderately thermophilic acidophilic bacteria in stirred tank bioreactors, and natural enrichment cultures of mesoacidophiles, with addition of 100 mM NaCl in column percolators with agglomerated ore allowed for a robust chalcopyrite dissolution and copper recovery from Sarcheshmeh copper ore via bioleaching.}, } @article {pmid38104504, year = {2023}, author = {Valles-Colomer, M and Manghi, P and Cumbo, F and Masetti, G and Armanini, F and Asnicar, F and Blanco-Miguez, A and Pinto, F and Punčochář, M and Garaventa, A and Amoroso, L and Ponzoni, M and Corrias, MV and Segata, N}, title = {Neuroblastoma is associated with alterations in gut microbiome composition subsequent to maternal microbial seeding.}, journal = {EBioMedicine}, volume = {99}, number = {}, pages = {104917}, pmid = {38104504}, issn = {2352-3964}, abstract = {BACKGROUND: Neuroblastoma is the most frequent extracranial solid tumour in children, accounting for ∼15% of deaths due to cancer in childhood. The most common clinical presentation are abdominal tumours. An altered gut microbiome composition has been linked to multiple cancer types, and reported in murine models of neuroblastoma. Whether children with neuroblastoma display alterations in gut microbiome composition remains unexplored.

METHODS: We assessed gut microbiome composition by shotgun metagenomic profiling in an observational cross-sectional study on 288 individuals, consisting of patients with a diagnosis of neuroblastoma at disease onset (N = 63), healthy controls matching the patients on the main covariates of microbiome composition (N = 94), healthy siblings of the patients (N = 13), mothers of patients (N = 59), and mothers of the controls (N = 59). We examined taxonomic and functional microbiome composition and mother-infant strain transmission patterns.

FINDINGS: Patients with neuroblastoma displayed alterations in gut microbiome composition characterised by reduced microbiome richness, decreased relative abundances of 18 species (including Phocaeicola dorei and Bifidobacterium bifidum), enriched protein fermentation and reduced carbohydrate fermentation potential. Using machine learning, we could successfully discriminate patients from controls (AUC = 82%). Healthy siblings did not display such alterations but resembled the healthy control group. No significant differences in maternal microbiome composition nor mother-to-offspring transmission were detected.

INTERPRETATION: Patients with neuroblastoma display alterations in taxonomic and functional gut microbiome composition, which cannot be traced to differential maternal seeding. Follow-up research should include investigating potential causal links.

FUNDING: Italian Ministry of Health Ricerca Corrente and Ricerca Finalizzata 5 per mille (to MPonzoni); Fondazione Italiana Neuroblastoma (to MPonzoni); European Research Council (ERC-StG project MetaPG-716575 and ERC-CoG microTOUCH-101045015 to NS); the European H2020 program ONCOBIOME-825410 project (to NS); the National Cancer Institute of the National Institutes of Health 1U01CA230551 (to NS); the Premio Internazionale Lombardia e Ricerca 2019 (to NS); the MIUR Progetti di Ricerca di Rilevante Interesse Nazionale (PRIN) Bando 2017 Grant 2017J3E2W2 (to NS); EMBO ALTF 593-2020 and Knowledge Generation Project from the Spanish Ministry of Science and Innovation (PID2022-139328OA-I00) (to MV-C).}, } @article {pmid38104411, year = {2023}, author = {Jan, TR and Lin, CS and Yang, WY}, title = {Differential cytokine profiling and microbial species involved in cecal microbiota modulations in SPF chicks immunized with a dual vaccine against Salmonella Typhimurium infection.}, journal = {Poultry science}, volume = {103}, number = {2}, pages = {103334}, pmid = {38104411}, issn = {1525-3171}, abstract = {Salmonella Typhimurium (ST) infection in laying hens is a significant threat to public health and food safety. Host resistance against enteric pathogen invasion primarily relies on immunity and gut barrier integrity. This study applied the ST infection model and a dual live vaccine containing Salmonella Enteritidis (SE) strain Sm24/Rif12/Ssq and ST strain Nal2/Rif9/Rtt to investigate the cellular cytokine expression profiles and the differential community structure in the cecal microbiota of specific-pathogen-free (SPF) chicks and field-raised layers. The results showed that ST challenge significantly upregulated expressions of IL-1β in SPF chicks. Vaccination, on the other hand, led to an elevation in IFNγ expression and restrained IL-1β levels. In the group where vaccination preceded the ST challenge (S.STvc), heightened expressions of IL-1β, IL-6, IL-10, and IL-12β were observed, indicating active involvement of both humoral and cell-mediated immunity in the defense against ST. Regarding the cecal microbiota, the vaccine did not affect alpha diversity nor induce a significant shift in the microbial community. Conversely, ST infection significantly affected the alpha and beta diversity in the cecal microbiota, reducing beneficial commensal genera, such as Blautia and Subdoligranulum. MetagenomeSeq analysis reveals a significant increase in the relative abundance of Faecalibacterium prausnitzii in the groups (S.STvc and STvc) exhibiting protection against ST infection. LEfSe further demonstrated Faecalibacterium prausnitzii as the prominent biomarker within the cecal microbiota of SPF chicks and field layers demonstrating protection. Another biomarker identified in the S.STvc group, Eubacterium coprostanoligenes, displayed an antagonistic relationship with Faecalibacterium prausnitzii, suggesting the limited biological significance of the former in reducing cloacal shedding and tissue invasion. In conclusion, the application of AviPro Salmonella DUO vaccine stimulates host immunity and modulates cecal microbiota to defend against ST infection. Among the microbial modulations observed in SPF chicks and field layers with protection, Faecalibacterium prausnitzii emerges as a significant species in the ceca. Further research is warranted to elucidate its role in protecting layers against ST infection.}, } @article {pmid38104165, year = {2023}, author = {Dash, NR and Al Bataineh, MT and Alili, R and Al Safar, H and Alkhayyal, N and Prifti, E and Zucker, JD and Belda, E and Clément, K}, title = {Functional alterations and predictive capacity of gut microbiome in type 2 diabetes.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22386}, pmid = {38104165}, issn = {2045-2322}, support = {17CVD01//Sorbonne Université/ ; }, mesh = {Humans ; *Diabetes Mellitus, Type 2/metabolism ; *Gastrointestinal Microbiome/genetics ; Firmicutes ; Metagenome ; *Diabetic Cardiomyopathies ; }, abstract = {The gut microbiome plays a significant role in the development of Type 2 Diabetes Mellitus (T2DM), but the functional mechanisms behind this association merit deeper investigation. Here, we used the nanopore sequencing technology for metagenomic analyses to compare the gut microbiome of individuals with T2DM from the United Arab Emirates (n = 40) with that of control (n = 44). DMM enterotyping of the cohort resulted concordantly with previous results, in three dominant groups Bacteroides (K1), Firmicutes (K2), and Prevotella (K3) lineages. The diversity analysis revealed a high level of diversity in the Firmicutes group (K2) both in terms of species richness and evenness (Wilcoxon rank-sum test, p value < 0.05 vs. K1 and K3 groups), consistent with the Ruminococcus enterotype described in Western populations. Additionally, functional enrichment analyses of KEGG modules showed significant differences in abundance between individuals with T2DM and controls (FDR < 0.05). These differences include modules associated with the degradation of amino acids, such as arginine, the degradation of urea as well as those associated with homoacetogenesis. Prediction analysis with the Predomics approach suggested potential biomarkers for T2DM, including a balance between a depletion of Enterococcus faecium and Blautia lineages with an enrichment of Absiella spp or Eubacterium limosum in T2DM individuals, highlighting the potential of metagenomic analysis in predicting predisposition to diabetic cardiomyopathy in T2DM patients.}, } @article {pmid38103344, year = {2023}, author = {Saibu, S and Uhanie Perera, I and Suzuki, S and Rodó, X and Fujiyoshi, S and Maruyama, F}, title = {Resistomes in freshwater bioaerosols and their impact on drinking and recreational water safety: A perspective.}, journal = {Environment international}, volume = {183}, number = {}, pages = {108377}, doi = {10.1016/j.envint.2023.108377}, pmid = {38103344}, issn = {1873-6750}, abstract = {Antibiotic resistance genes (ARGs) are widespread environmental pollutants of biological origin that pose a significant threat to human, animal, and plant health, as well as to ecosystems. ARGs are found in soil, water, air, and waste, and several pathways for global dissemination in the environment have been described. However, studies on airborne ARG transport through atmospheric particles are limited. The ARGs in microorganisms inhabiting an environment are referred to as the "resistome". A global search was conducted of air-resistome studies by retrieving bioaerosol ARG-related papers published in the last 30 years from PubMed. We found that there is no dedicated methodology for isolating ARGs in bioaerosols; instead, conventional methods for microbial culture and metagenomic analysis are used in combination with standard aerosol sampling techniques. There is a dearth of information on the bioaerosol resistomes of freshwater environments and their impact on freshwater sources used for drinking and recreational activities. More studies of aerobiome freshwater environments are needed to ensure the safe use of water and sanitation. In this review we outline and synthesize the few studies that address the freshwater air microbiome (from tap water, bathroom showers, rivers, lakes, and swimming pools) and their resistomes, as well as the likely impacts on drinking and recreational waters. We also discuss current knowledge gaps for the freshwater airborne resistome. This review will stimulate new investigations of the atmospheric microbiome, particularly in areas where both air and water quality are of public health concern.}, } @article {pmid38103297, year = {2023}, author = {Wang, W and Luo, T and Zhao, Y and Yang, X and Wang, D and Yang, G and Jin, Y}, title = {Antibiotic resistance gene distribution in Shine Muscat grapes and health risk assessment of streptomycin residues in mice.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133254}, doi = {10.1016/j.jhazmat.2023.133254}, pmid = {38103297}, issn = {1873-3336}, abstract = {Antibiotic residues and antibiotic resistance genes (ARGs) in fruits and vegetables pose public health risks via the food chain, attracting increased attention. Antibiotics such as streptomycin, used directly on seedless grapes or introduced into vineyard soil through organic fertilizers. However, extensive data supporting the risk assessment of antibiotic residues and resistance in these produce remains lacking. Utilizing metagenomic sequencing, we characterized Shine Muscat grape antibiotic resistome and mobile genetic elements (MGEs). Abundant MGEs and ARGs were found in grapes, with 174 ARGs on the grape surface and 32 in the fruit. Furthermore, our data indicated that soil is not the primary source of these MGEs and ARGs. Escherichia was identified as an essential carrier and potential transmitter of ARGs. In our previous study, streptomycin residue was identified in grapes. Further short-term exposure experiments in mice revealed no severe physiological or histological damage at several environment-related concentrations. However, with increased exposure, some ARGs levels in mouse gut microbes increased, indicating a potential threat to animal health. Overall, this study provides comprehensive insights into the resistance genome and potential hosts in grapes, supporting the risk assessment of antibiotic resistance in fruits and vegetables.}, } @article {pmid38102689, year = {2023}, author = {Wang, D and Li, J and Su, L and Shen, W and Feng, K and Peng, X and Wang, Z and Zhao, B and Zhang, Z and Zhang, Z and Yergeau, É and Deng, Y}, title = {Phylogenetic diversity of functional genes in deep-sea cold seeps: a novel perspective on metagenomics.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {276}, pmid = {38102689}, issn = {2049-2618}, support = {No. 2019YFC1905001//National Key Research and Development Program of China/ ; 42277104//National Natural Science Foundation of China/ ; Grant No. kf2021003//Open Project of Key Laboratory of Environmental Biotechnology, CAS/ ; }, mesh = {*Geologic Sediments ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Methane/metabolism ; *Microbiota ; }, abstract = {BACKGROUND: Leakages of cold, methane-rich fluids from subsurface reservoirs to the sea floor are termed cold seeps. Recent exploration of the deep sea has shed new light on the microbial communities in cold seeps. However, conventional metagenomic methods largely rely on reference databases and neglect the phylogeny of functional genes.

RESULTS: In this study, we developed the REMIRGE program to retrieve the full-length functional genes from shotgun metagenomic reads and fully explored the phylogenetic diversity in cold seep sediments. The abundance and diversity of functional genes involved in the methane, sulfur, and nitrogen cycles differed in the non-seep site and five cold seep sites. In one Haima cold seep site, the divergence of functional groups was observed at the centimeter scale of sediment depths, with the surface layer potentially acting as a reservoir of microbial species and functions. Additionally, positive correlations were found between specific gene sequence clusters of relevant genes, indicating coupling occurred within specific functional groups.

CONCLUSION: REMIRGE revealed divergent phylogenetic diversity of functional groups and functional pathway preferences in a deep-sea cold seep at finer scales, which could not be detected by conventional methods. Our work highlights that phylogenetic information is conducive to more comprehensive functional profiles, and REMIRGE has the potential to uncover more new insights from shotgun metagenomic data. Video Abstract.}, } @article {pmid38101649, year = {2023}, author = {Hu, J and Wan, K and Deng, X and Liu, X and Fang, Y and Zhou, F and Yu, J and Chi, R and Xiao, C}, title = {Metagenomic analysis revealed the evolution of microbial communities, metabolic pathways, and functional genes in the heterotrophic nitrification-aerobic denitrification process under La[3+] stress.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169243}, doi = {10.1016/j.scitotenv.2023.169243}, pmid = {38101649}, issn = {1879-1026}, abstract = {Trivalent lanthanum (La[3+]) exists widely in ammonia nitrogen (NH4[+]-N) tailing water from ionic rare earth mines; however, its effect on heterotrophic nitrification-aerobic denitrification (HN-AD) is unknown, thereby limiting the application of the HN-AD process in this field. In this study, we conducted an HN-AD process using a sequencing batch reactor (5 L) that was continuously operated to directly treat acidic (NH4)2SO4 wastewater (influent NH4[+]-N concentration of approximately 110 mg/L and influent pH of 5) containing different La[3+] concentrations (0-100 mg/L). The NH4[+]-N removal efficiency of the reactor reached 98.25 % at a La[3+] concentration of 100 mg/L. The reactor was in a neutral-to-alkaline environment, which favored La[3+] precipitation and complexation. Metagenomic analysis revealed that the relative abundance of Thauera in the reactor remained high (88.62-92.27 %) under La[3+] stress. The relative abundances of Pannonobacter and Hyphomonas significantly increased, whereas that of Azoarcus significantly decreased. Metabolic functions in the reactor were mainly contributed by Thauera, and the abundance of metabolic functions under low La[3+] stress (≤5 mg/L) significantly differed from that under high La[3+] stress (≥10 mg/L). The relative abundance of ammonia assimilation-related genes in the reactor was high and significantly correlated with ammonia removal. However, traditional ammonia oxidation genes were not annotated, and unknown ammonia oxidation pathways may have been present in the reactor. Moreover, La[3+] stimulated amino acid biosynthesis and translocation, the citrate cycle, sulfur metabolism, and oxidative phosphorylation and promoted the overproduction of extracellular polymeric substances, which underwent complexation and adsorbed La[3+] to reduce its toxicity. Our results showed that the HN-AD process had a strong tolerance to La[3+], stable NH4[+]-N removal efficiency, the potential to recover La[3+], and considerable application prospects in treating NH4[+]-N tailing water from ionic rare earth mines.}, } @article {pmid38101529, year = {2023}, author = {Sun, Y and Zhang, Y and Ma, Y and Xin, R and Li, X and Niu, Z}, title = {Exploring the potential of a new marine bacterium associated with plastisphere to metabolize dibutyl phthalate and bis(2-ethylhexyl) phthalate by enrichment cultures combined with multi-omics analysis.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {342}, number = {}, pages = {123146}, doi = {10.1016/j.envpol.2023.123146}, pmid = {38101529}, issn = {1873-6424}, abstract = {Phthalic acid esters (PAEs) plasticizers are virulent endocrine disruptors that are mixed into plastics while fabricating and can filter out once they release into the surrounding environments. Plastic surfaces serve as new habitats for microorganisms, referred to as 'plastisphere'. Previous metagenomic investigations of the 'plastisphere' indicated that marine plastic surfaces may harbor microbes that degrade PAEs plasticizers. To our knowledge, the potential of microorganisms in the marine 'plastisphere' to metabolize PAEs is poorly understood. In this study, by screening the natural microbial community on plastic debris that had been deployed in situ for up to 20 months, a novel marine bacterium, Microbacterium esteraromaticum DEHP-1, was successfully isolated, which could degrade and mineralize 10-200 mg/L dibutyl phthalate (DBP) and bis(2-ethylhexyl) phthalate (DEHP). According to the results of gas chromatography-mass spectrometry (GC-MS) and whole genome mining of strain DEHP-1, we found that strain DEHP-1 may metabolize DBP by successive removal of the ester side chain by esterase 2518 to produce mono-butyl phthalate (MBP) and phthalic acid (PA), whereas the degradation of DEHP may take place by the direct action of monooxygenase 0132 on the fatty acid side chain of the DEHP molecule to produce di-n-hexyl phthalate (DnHP) and DBP, and then the subsequent hydrolysis of DBP by de-esterification to PA and finally into the tricarboxylic acid (TCA) cycle. Non-targeted metabolomics results showed that intracellular degradation of PAEs did not happen. However, exposure to PAEs was found to significantly affect pathways such as arginine and proline, riboflavin, glutathione and lysine degradation. Therefore, the intracellular metabolic behavior of strain DEHP-1 exposed to PAEs was proposed for the first time. This study sheds light on the metabolic capacity and strategies of bacteria in the marine 'plastisphere' to effectively degrade PAEs and highlights the importance of marine microbes in mitigating plastic poisonousness.}, } @article {pmid38101104, year = {2023}, author = {Bhattacharjee, AS and Phan, D and Zheng, C and Ashworth, D and Schmidt, M and Men, Y and Ferreira, JFS and Muir, G and Hasan, NA and Ibekwe, AM}, title = {Dissemination of antibiotic resistance genes through soil-plant-earthworm continuum in the food production environment.}, journal = {Environment international}, volume = {183}, number = {}, pages = {108374}, doi = {10.1016/j.envint.2023.108374}, pmid = {38101104}, issn = {1873-6750}, abstract = {Treated municipal wastewater (TMW) can provide a reliable source of irrigation water for crops, which is especially important in arid areas where water resources are limited or prone to drought. Nonetheless, TMW may contain residual antibiotics, potentially exposing the crops to these substances. The goal of this study was to investigate the dissemination of antibiotics resistance genes (ARGs) in the soil-plant-earthworm continuum after irrigation of spinach and radish plants with TMW containing trimethoprim, sulfamethoxazole, and sulfapyridine in a greenhouse experiment, followed by feeding of earthworms with harvested plant materials. Our results showed that antibiotic resistance genes (ARGs) were enriched in the soil-plant-earthworm microbiomes irrigated with TMW and TMW spiked with higher concentrations of antibiotics. The number of ARGs and antibiotic-resistant bacteria (ARB) enrichment varied with plant type, with spinach harboring a significantly higher amount of ARGs and ARB compared to radish. Our data showed that bulk and rhizosphere soils of spinach and radish plants irrigated with MilliQ water, TMW, TMW10, or TMW100 had significant differences in bacterial community (p < 0.001), ARG (p < 0.001), and virulence factor gene (VFG) (p < 0.001) diversities. The abundance of ARGs significantly decreased from bulk soil to rhizosphere to phyllosphere and endosphere. Using metagenome assembled genomes (MAGs), we recovered many bacterial MAGs and a near complete genome (>90 %) of bacterial MAG of genus Leclercia adecarboxylata B from the fecal microbiome of earthworm that was fed harvested radish tubers and spinach leaves grown on TMW10 irrigated waters, and this bacterium has been shown to be an emerging pathogen causing infection in immunocompromised patients that may lead to health complications and death. Therefore, crops irrigated with TMW containing residual antibiotics and ARGs may lead to increased incidences of enrichment of ARB in the soil-plant-earthworm continuum.}, } @article {pmid38101077, year = {2024}, author = {Li, Q and Wang, Z and Jiang, J and He, B and He, S and Tu, C and Guo, Y and Gong, W}, title = {Outbreak of piglet diarrhea associated with a new reassortant porcine rotavirus B.}, journal = {Veterinary microbiology}, volume = {288}, number = {}, pages = {109947}, doi = {10.1016/j.vetmic.2023.109947}, pmid = {38101077}, issn = {1873-2542}, mesh = {Animals ; Swine ; *Rotavirus/genetics ; *Rotavirus Infections/epidemiology/veterinary ; Genome, Viral ; Phylogeny ; Diarrhea/epidemiology/veterinary ; Nucleotides ; Genotype ; *Swine Diseases ; }, abstract = {Rotavirus B (RVB) is a causative agent leading to acute viral gastroenteritis diarrhea in both children and young animals, and has been commonly detected in piglets. In order to determine the causative agent of diarrheal outbreak occurring in December 2022 in piglets from a pig herd in Luoyang, Henan province of China, four common viral pathogens causing piglet diarrhea-three coronaviruses and rotavirus A (RVA) were first tested and found negative, therefore metagenomic sequencing was performed to explore other potential pathogens in the diarrheal samples. Unexpectedly, the most abundant viral reads mapped to RVB, and were de novo assembled to complete 11 viral gene segments. Sequence comparisons revealed that 5 gene segments encoding VP1, VP2, VP3, NSP3 and NSP4 of RVB strain designated as HNLY-2022 are most closely related to RVB strains derived from herbivores with low nucleotide similarities of 65.7-75.3%, and the remaining segments were relatively close to porcine RVB strains with the VP4 gene segment showing very low nucleotide identity (65.0%) with reference strains, indicating HNLY-2022 is a new reassortant RVB strain. Based on the previously proposed genotype classification criterion, the genotype constellation of RVB strain HNLY-2022 is G6-P[6]-I4-R6-C6-M6-A7-N5-T7-E5-H4 with more than half of the genotypes (P[6], R6, C6, M6, T7 and E5) newly reported. Therefore, the new reassortant RVB strain is the likely causative agent for the diarrheal outbreak of piglets occurred in China and more epidemiological studies should be conducted to monitor the spread of this newly identified porcine RVB strain.}, } @article {pmid38101011, year = {2023}, author = {Rincón-Tomás, B and Lanzén, A and Sánchez, P and Estupiñán, M and Sanz-Sáez, I and Bilbao, ME and Rojo, D and Mendibil, I and Pérez-Cruz, C and Ferri, M and Capo, E and Abad-Recio, IL and Amouroux, D and Bertilsson, S and Sánchez, O and Acinas, SG and Alonso-Sáez, L}, title = {Revisiting the mercury cycle in marine sediments: A potential multifaceted role for Desulfobacterota.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133120}, doi = {10.1016/j.jhazmat.2023.133120}, pmid = {38101011}, issn = {1873-3336}, abstract = {Marine sediments impacted by urban and industrial pollutants are typically exposed to reducing conditions and represent major reservoirs of toxic mercury species. Mercury methylation mediated by anaerobic microorganisms is favored under such conditions, yet little is known about potential microbial mechanisms for mercury detoxification. We used culture-independent (metagenomics, metabarcoding) and culture-dependent approaches in anoxic marine sediments to identify microbial indicators of mercury pollution and analyze the distribution of genes involved in mercury reduction (merA) and demethylation (merB). While none of the isolates featured merB genes, 52 isolates, predominantly affiliated with Gammaproteobacteria, were merA positive. In contrast, merA genes detected in metagenomes were assigned to different phyla, including Desulfobacterota, Actinomycetota, Gemmatimonadota, Nitrospirota, and Pseudomonadota. This indicates a widespread capacity for mercury reduction in anoxic sediment microbiomes. Notably, merA genes were predominately identified in Desulfobacterota, a phylum previously associated only with mercury methylation. Marker genes involved in the latter process (hgcAB) were also mainly assigned to Desulfobacterota, implying a potential central and multifaceted role of this phylum in the mercury cycle. Network analysis revealed that Desulfobacterota were associated with anaerobic fermenters, methanogens and sulfur-oxidizers, indicating potential interactions between key players of the carbon, sulfur and mercury cycling in anoxic marine sediments.}, } @article {pmid38100390, year = {2024}, author = {Du, SB and Zhou, HH and Xue, ZP and Gao, S and Li, J and Meng, Y and Zhao, YJ and Wang, PF and Li, N and Bai, JX and Bai, JQ and Wang, XP}, title = {Metagenomic sequencing revealed the regulative effect of Danshen and Honghua herb pair on the gut microbiota in rats with myocardial ischemia injury.}, journal = {FEMS microbiology letters}, volume = {371}, number = {}, pages = {}, doi = {10.1093/femsle/fnad133}, pmid = {38100390}, issn = {1574-6968}, support = {81974544//National Natural Science Foundation of China/ ; }, mesh = {Rats ; Animals ; *Salvia miltiorrhiza/chemistry ; *Gastrointestinal Microbiome ; *Myocardial Ischemia/drug therapy/metabolism/pathology ; *Carthamus tinctorius ; Isoproterenol/therapeutic use ; }, abstract = {In recent years, more and more evidence has shown that the disorder of gut microbiota (GM) is closely correlated with myocardial ischemia (MI). Even though the Danshen and Honghua herb pair (DHHP) is widely used in treating cardiovascular disease in China and exhibits obvious clinical efficacy on MI, the anti-MI mechanism of DHHP remains and needs to be explored in depth. Thus, in this study, we investigated whether the amelioration effect and molecular mechanism of DHHP on MI were related to regulating GM through pharmacodynamics evaluation and metagenomic sequencing. Histopathological testing results showed that DHHP treatment could alleviate the pathological changes of myocardial tissue in the acute MI (AMI) rats induced by isoproterenol (ISO), especially structural disorder, irregular distribution, and enlargement of the myocardial space. These pathological changes were all alleviated to some extent by DHHP treatment. Biochemical analysis results suggested that compared with the control group, the serum levels of AST, CTn-I, CK-MB, and TNF-α in model group rats were notably decreased, and the CAT and SOD levels in serum were markedly increased. These abnormal trends were significantly reversed by DHHP treatment. Furthermore, metagenomic sequencing analysis results indicated that DHHP could improve disorders in the composition and function of GM in AMI rats, mainly reflected in increasing diversity and richness, and obviously enhancing the abundance of Bacteroides fluxus, B. uniformis, B. stercoris, Roseburia hominis, Schaedlerella arabinosiphila, and R. intestinalis, and reducing the abundance of Enterococcus avium and E. canintestini, which were associated with purine metabolism, tyrosine metabolism, cyanoamino acid metabolism, and glutathione metabolism. In conclusion, DHHP may attenuate ISO-induced MI by regulating the structure, composition, and function of GM, thus contributing to further our understanding of the anti-MI mechanisms of DHHP and providing new therapeutic ideas and diagnostic targets for the clinical studies of MI.}, } @article {pmid38099742, year = {2023}, author = {Fu, Y and Sun, H and Luo, Y and Zhang, W and Cai, Z and Li, Y and Luan, L and Ning, Q and Shi, Q and Liang, Y and Liang, C and Tang, C and Li, Y and Zhang, H and Xie, Z and Chen, L and Xu, J and Kuzyakov, Y}, title = {Deciphering Biotic and Abiotic Mechanisms Underlying Straw Decomposition and Soil Organic Carbon Priming in Agriculture Soils Receiving Long-Term Fertilizers.}, journal = {Journal of agricultural and food chemistry}, volume = {71}, number = {51}, pages = {20549-20562}, doi = {10.1021/acs.jafc.3c03209}, pmid = {38099742}, issn = {1520-5118}, mesh = {*Soil/chemistry ; *Carbon/chemistry ; Fertilizers/analysis ; Ecosystem ; Agriculture ; Soil Microbiology ; }, abstract = {Straw-related carbon (C) dynamics are central for C accrual in agro-ecosystems and should be assessed by investigating their decomposition and soil organic carbon (SOC) priming effects. Our understanding of biotic and abiotic mechanisms underpinning these two C processes, however, is still not sufficiently profound. Soils that had received organic and mineral fertilizers for 26 years were sampled for a 28 day incubation experiment to assess [13]C-labeled straw decomposition and SOC priming effects. On the basis of analyzing physicochemical properties, fungal taxonomic (MiSeq sequencing) and functional (metagenomics) guilds, we quantified the contributions of biotic and abiotic attributes to straw decomposition and SOC priming. Here, we propose two distinct mechanisms underlying straw decomposition and SOC priming in agriculture soils: (i) accelerated straw mineralization in manure-treated soils was mainly driven by biotic forces, while (ii) larger SOC priming in NPK-amended soils was through abiotic regulation.}, } @article {pmid38099689, year = {2023}, author = {Han, N and Peng, X and Zhang, T and Qiang, Y and Li, X and Zhang, W}, title = {Rapid turnover and short-term blooms of Escherichia coli in the human gut.}, journal = {Journal of bacteriology}, volume = {}, number = {}, pages = {e0023923}, doi = {10.1128/jb.00239-23}, pmid = {38099689}, issn = {1098-5530}, abstract = {Escherichia coli (E. coli) is a microorganism closely linked to human health, and its presence in the human gut has been a topic of debate. Our study, using whole-genome shotgun metagenomic sequencing, revealed that E. coli exists at a low abundance in the human body, with occasional short-term bursts leading to temporary increases. Strain and genome variations were observed within fecal samples from the same individuals at different time points, suggesting transient rather than permanent residence of E. coli in the gut. The rapid turnover rate and short-term blooms of E. coli can establish latent infections while also posing a risk of introducing pathogenic strains. These findings enhance our understanding of the relationship between E. coli, the gut microbiota, and human health.}, } @article {pmid38099660, year = {2023}, author = {Shifflett, SA and Ferreira, FC and González, J and Toledo, A and Fonseca, DM and Ellis, VA}, title = {Diversity and host specificity of Borrelia burgdorferi's outer surface protein C (ospC) alleles in synanthropic mammals, with a notable ospC allele U absence from mixed infections.}, journal = {Infection and immunity}, volume = {}, number = {}, pages = {e0024423}, doi = {10.1128/iai.00244-23}, pmid = {38099660}, issn = {1098-5522}, abstract = {Interactions among pathogen genotypes that vary in host specificity may affect overall transmission dynamics in multi-host systems. Borrelia burgdorferi, a bacterium that causes Lyme disease, is typically transmitted among wildlife by Ixodes ticks. Despite the existence of many alleles of B. burgdorferi's sensu stricto outer surface protein C (ospC) gene, most human infections are caused by a small number of ospC alleles ["human infectious alleles" (HIAs)], suggesting variation in host specificity associated with ospC. To characterize the wildlife host association of B. burgdorferi's ospC alleles, we used metagenomics to sequence ospC alleles from 68 infected individuals belonging to eight mammalian species trapped at three sites in suburban New Brunswick, New Jersey (USA). We found that multiple allele ("mixed") infections were common. HIAs were most common in mice (Peromyscus spp.) and only one HIA was detected at a site where mice were rarely captured. ospC allele U was exclusively found in chipmunks (Tamias striatus), and although a significant number of different alleles were observed in chipmunks, including HIAs, allele U never co-occurred with other alleles in mixed infections. Our results suggest that allele U may be excluding other alleles, thereby reducing the capacity of chipmunks to act as reservoirs for HIAs.}, } @article {pmid38099503, year = {2023}, author = {Govindarajan, V and Chandar, J and Nath, A and Shah, AH}, title = {Metagenome analyses identify human endogenous retrovirus-K113 (HML-2) subtype in glioblastoma. Reply.}, journal = {The Journal of clinical investigation}, volume = {133}, number = {24}, pages = {}, pmid = {38099503}, issn = {1558-8238}, mesh = {Humans ; *Endogenous Retroviruses/genetics ; *Glioblastoma/genetics ; Metagenome ; }, } @article {pmid38099502, year = {2023}, author = {Macamo, A and Beckervordersandforth, J and Zur Hausen, A}, title = {Metagenome analyses identify human endogenous retrovirus-K113 (HML-2) subtype in glioblastoma.}, journal = {The Journal of clinical investigation}, volume = {133}, number = {24}, pages = {}, pmid = {38099502}, issn = {1558-8238}, mesh = {Humans ; *Endogenous Retroviruses/genetics ; *Glioblastoma/genetics ; Metagenome ; }, } @article {pmid38098672, year = {2023}, author = {Jeong, J and Song, H and Kim, WH and Chae, M and Lee, JY and Kwon, YK and Cho, S}, title = {Tracking the contamination sources of microbial population and characterizing Listeria monocytogenes in a chicken slaughterhouse by using culture-dependent and -independent methods.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1282961}, pmid = {38098672}, issn = {1664-302X}, abstract = {Listeria monocytogenes is the etiologic agent of listeriosis, a foodborne disease that poses a threat to public health globally. Chicken meat exhibits heightened susceptibility to L. monocytogenes contamination during butchery. The persistence of this pathogen in the slaughterhouse environment enables recurring contamination of meat products. This study aimed at identifying the sources and transmission routes of L. monocytogenes contamination within an abattoir where it was consistently detected for three consecutive years (2019-2021). Furthermore, the environmental factors aiding contamination along chicken processing lines were determined by surveying the microbiome within the facility. Samples collected in 2019 to 2021 were subjected to culture-dependent analysis to assess the prevalence, serotypes, and multi-locus sequence typing (MLST) of L. monocytogenes. Additionally, the specimens collected in 2021 underwent culture-independent analysis via real-time quantitative polymerase chain reaction (qPCR) and 16S rRNA gene amplicon sequencing to identify the contamination sources and characterize the entire microbial community within the slaughterhouse. L. monocytogenes was isolated only from the clean zone, where the final slaughtering stage occurs. Most strains isolated from the final carcasses showed the same genetic cluster as the isolate in the chilling water and were assigned to MLST profile ST3. Culture-independent qPCR confirmed L. monocytogenes contamination in all samples, excluding post-scalding carcasses, prewashed post-evisceration carcasses, and the bleeding areas. Consequently, qPCR enabled more comprehensive identification of L. monocytogenes contamination points than culture-dependent approaches. Moreover, 16S rRNA gene amplicon sequencing demonstrated that psychro-tolerant and spoilage-related bacteria with L. monocytogenes-like attributes exhibited enhanced viability in the clean zone and immersion-chilling water. Metagenomics-based source tracking analysis further revealed that the shackles and chilling waters represent predominant sources of cross-contamination between different slaughterhouse zones, whereas the grading and packaging workstations and chilling water in the clean zone were deemed crucial sources affecting final carcass contamination. Collectively, these findings demonstrate through culture-dependent and -independent methods that L. monocytogenes spreads along the slaughter line, contaminating the slaughterhouse. Moreover, by investigating changes in microbial community and bacterial flow along the slaughter line within the facility, the sources influencing carcass contamination can be effectively traced.}, } @article {pmid38098661, year = {2023}, author = {Wang, M and Zhao, K and Li, X and Xie, BB}, title = {Insights into the composition and assembly mechanism of microbial communities on intertidal microsand grains.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1308767}, pmid = {38098661}, issn = {1664-302X}, abstract = {INTRODUCTION: Marine microorganisms are essential in marine ecosystems and have always been of interest. Currently, most marine microbial communities are studied at the bulk scale (millimeters to centimeters), and the composition, function and underlying assembly mechanism of microbial communities at the microscale (sub-100 micrometers) are unclear.

METHODS: The microbial communities on microsand grains (40-100 µm, n = 150) from marine sediment were investigated and compared with those on macrosand grains (400-1000 µm, n = 60) and bulk sediments (n = 5) using amplicon sequencing technology.

RESULTS: The results revealed a significant difference between microsand grains and macrosand grains. Microsand grains had lower numbers of operational taxonomic units (OTUs(97%)) and predicted functional genes than macrosand grains and bulk-scale samples. Microsand grains also showed greater intersample differences in the community composition and predicted functional genes than macrosand grains, suggesting a high level of heterogeneity of microbial communities at the microscale. Analyses based on ecological models indicated that stochastic processes dominated the assembly of microbial communities on sand grains. Consistently, cooccurrence network analyses showed that most microbial cooccurrence associations on sand grains were highly unstable. Metagenomic sequencing and further genome-scale metabolic modeling revealed that only a small number (1.3%) of microbe pairs showed high cooperative potential.

DISCUSSION: This study explored the microbial community of marine sediments at the sub-100 µm scale, broadening the knowledge of the structure and assembly mechanism of marine microbial communities.}, } @article {pmid38098653, year = {2023}, author = {Fourie, A and Venter, SN and Slippers, B and Fourie, G}, title = {Pantoea bathycoeliae sp. nov and Sodalis sp. are core gut microbiome symbionts of the two-spotted stink bug.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1284397}, pmid = {38098653}, issn = {1664-302X}, abstract = {Stink bug species (Pentatomoidea superfamily) have developed an interdependence with obligate bacterial gut symbionts in specialized midgut crypts (M4 sub-region). Species of the Enterobacteriaceae family (predominantly Pantoea) are vertically transferred to their offspring and provide nutrients that cannot be obtained from plant sap food sources. However, the bacteria in the other gut compartments of stink bugs have rarely been investigated. The two-spotted stink bug, Bathycoelia distincta, is a serious pest of macadamias in South Africa. Nothing is currently known regarding its gut microbiome or how symbionts are transferred between insect generations. In this study, the consistency of B. distincta gut bacteria across geographic locations and life stages was determined with 16S rRNA metabarcoding, considering both the M4 and other gut compartments. A novel Pantoea species was found to be the primary M4 gut symbiont and is vertically transferred to the offspring. The other gut compartments had a low bacterial diversity and genera varied between stink bug populations but a Sodalis species was prominent in all populations. Sequence data of the M4 compartment were used to produce high-quality metagenome-assembled genomes (MAGs) for the Pantoea and Sodalis species. Functional analyses suggested a similar role in nutrient provision for the host, yet also unique metabolites produced by each species. The Sodalis sp. also had additional traits, such as secretion systems, that likely allowed it to establish itself in the host. The Pantoea species was described as Pantoea bathycoeliae sp. nov based on the rules of the SeqCode.}, } @article {pmid38098424, year = {2023}, author = {Wang, XJ and Jiang, MT and Li, S and Ni, HW and Sun, B and Liang, YT}, title = {[Functional Genomics Analysis of Nitrogen and Phosphorus Transformation in Maize Rhizosphere Microorganisms].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {44}, number = {12}, pages = {7014-7023}, doi = {10.13227/j.hjkx.202211317}, pmid = {38098424}, issn = {0250-3301}, mesh = {*Rhizosphere ; *Zea mays/metabolism ; Phosphorus/metabolism ; Nitrogen/analysis ; Soil ; Genomics ; Soil Microbiology ; Fertilizers/analysis ; }, abstract = {Fertilizer reduction and efficiency improvement is an important basis for ensuring the safety of the agricultural ecological environment. Microorganisms are the key driving force for regulating the soil nitrogen and phosphorus cycle. Studying the nitrogen and phosphorus transformation function of rhizosphere microorganisms can provide a microbiological regulation approach for further improving the use efficiency of soil nitrogen and phosphorus. Based on the field micro-plot experiments of three typical farmland soils(phaeozem, cambisol, and acrisol), metagenomic sequencing technology was used to study the differences in functional genes and regulatory factors of maize rhizosphere microorganisms during soil nitrogen and phosphorus transformation. The results showed that the functional diversity of maize rhizosphere microorganisms was affected by soil type. The functional diversity of rhizosphere microorganisms in phaeozem and cambisol was mainly affected by water content and nutrient content, and that in acrisol was affected by total phosphorus(TP) and available phosphorus(AP). For soil nitrogen transformation, the gene abundance of related enzymes in the pathway of nitrogen transformation was the highest in the urease gene(ureC) and glucose dehydrogenase gene(gdh), which were 7.25×10[-5]-12.88×10[-5] and 4.47×10[-5]-7.49×10[-5], respectively. The total abundance of assimilatory nitrate reduction functional genes in acrisol was higher than that in phaeozem and cambisol, and the total abundance of functional genes related to other processes was the highest in cambisol. The abundance of functional genes encoding enzymes related to nitrogen metabolism was mainly driven by soil bacterial richness, total potassium(TK), and TP. For soil phosphorus transformation, the number of alkaline phosphatase genes(phoD) catalyzing organic phosphorus mineralization was 1093, and the number of acid phosphatase genes(PHO) was 42. The abundance of phoD was two orders of magnitude higher than that of PHO. In addition, fertilization had no significant effect on the abundance of phoD and PHO in the same soil type. Random forest analysis showed that the abundances of phoD and PHO were significantly affected by soil moisture, organic matter(OM), and total nitrogen(TN), but AP content had the greatest impact on PHO abundance. These results clarified the nitrogen and phosphorus transformation characteristics of maize rhizosphere microorganisms at the functional genomic level and enriched the molecular biological mechanism of the microbial nitrogen and phosphorus transformation function.}, } @article {pmid38098420, year = {2023}, author = {Duan, LY and Zhang, Y and Ren, XM and Li, YY and Zhang, YJ and Zhang, H and Han, H and Chen, ZJ}, title = {[Effects of Combined Pollution of Microplastics and Cadmium on Microbial Community Structure and Function of Pennisetum hydridum Rhizosphere Soil].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {44}, number = {12}, pages = {6973-6981}, doi = {10.13227/j.hjkx.202212135}, pmid = {38098420}, issn = {0250-3301}, mesh = {Cadmium/analysis ; Microplastics/analysis ; Soil/chemistry ; *Pennisetum/metabolism ; Plastics ; Rhizosphere ; *Metals, Heavy/analysis ; *Microbiota ; Bacteria/metabolism ; Amino Acids ; *Soil Pollutants/analysis ; }, abstract = {The combined pollution of microplastics and heavy metals can potentially interact. This may have an important impact on the growth and development of plants and the rhizosphere microbial community and function. In this study, the effects of heavy metal cadmium combined with different types of microplastics(PE and PS), different particle sizes(13 μm and 550 μm), and different concentrations(0.1% and 1%) on Pennisetum hydridum growth were studied under pot conditions. The results showed that the effects of the combined pollution of MPs and Cd on plant dry weight and Cd accumulation varied with different types, concentrations, and particle sizes of MPs, and the combined pollution stress increased, whereas the Cd content and Cd accumulation decreased. Metagenomic analysis showed that the combined contamination of MPs and Cd could change the composition of the bacterial community and reduce bacterial diversity, among which the ACE index and Chao1 index in the 550 μm 0.1% PE+Cd treatment group were the most significant. Metagenomic analysis of microbial species function showed that the main functional groups were metabolism, amino acid transport and metabolism, energy generation and conversion, and signal transduction mechanisms. Compared with that under single Cd pollution, the addition of MPs could change the gene abundance of functional groups such as metabolism, amino acid transport and metabolism, and energy generation and conversion, and the effects of different MPs types, concentrations, and particle sizes varied. In this study, metagenomics and amplification sequencing were used to analyze the effects of the combined pollution of MPs and Cd on the bacterial community and function in P. hydridum in order to provide basic data and scientific basis for the ecotoxicological effects of the combined heavy metal pollution of MPs and its biological remediation.}, } @article {pmid38098148, year = {2023}, author = {Duan, Y and Wang, T and Zhang, P and Zhao, X and Jiang, J and Ma, Y and Zhu, X and Fang, W}, title = {The effect of intercropping leguminous green manure on theanine accumulation in the tea plant: A metagenomic analysis.}, journal = {Plant, cell & environment}, volume = {}, number = {}, pages = {}, doi = {10.1111/pce.14784}, pmid = {38098148}, issn = {1365-3040}, support = {31972460//National Natural Science Foundation of China/ ; 32160729//National Natural Science Foundation of China/ ; (CARS-19)//China Agriculture Research System of MOF and MARA/ ; ZK[2021]154//Science and Technology Support Project of Guizhou Province/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; 2022ZB340//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; }, abstract = {Intercropping is a widely recognised technique that contributes to agricultural sustainability. While intercropping leguminous green manure offers advantages for soil health and tea plants growth, the impact on the accumulation of theanine and soil nitrogen cycle are largely unknown. The levels of theanine, epigallocatechin gallate and soluble sugar in tea leaves increased by 52.87% and 40.98%, 22.80% and 6.17%, 22.22% and 29.04% in intercropping with soybean-Chinese milk vetch rotation and soybean alone, respectively. Additionally, intercropping significantly increased soil amino acidnitrogen content, enhanced extracellular enzyme activities, particularly β-glucosidase and N-acetyl-glucosaminidase, as well as soil multifunctionality. Metagenomics analysis revealed that intercropping positively influenced the relative abundances of several potentially beneficial microorganisms, including Burkholderia, Mycolicibacterium and Paraburkholderia. Intercropping resulted in lower expression levels of nitrification genes, reducing soil mineral nitrogen loss and N2 O emissions. The expression of nrfA/H significantly increased in intercropping with soybean-Chinese milk vetch rotation. Structural equation model analysis demonstrated that the accumulation of theanine in tea leaves was directly influenced by the number of intercropping leguminous green manure species, soil ammonium nitrogen and amino acid nitrogen. In summary, the intercropping strategy, particularly intercropping with soybean-Chinese milk vetch rotation, could be a novel way for theanine accumulation.}, } @article {pmid38098063, year = {2023}, author = {Xie, Z and Canalda-Baltrons, A and d'Enfert, C and Manichanh, C}, title = {Shotgun metagenomics reveals interkingdom association between intestinal bacteria and fungi involving competition for nutrients.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {275}, pmid = {38098063}, issn = {2049-2618}, support = {812969//Marie Sklodowska-Curie Action/ ; 812969//Marie Sklodowska-Curie Action/ ; 812969//Marie Sklodowska-Curie Action/ ; }, mesh = {Humans ; Fungi/genetics ; *Microbiota ; *Mycobiome/genetics ; Bacteria/genetics ; Metagenomics/methods ; Nutrients ; }, abstract = {BACKGROUND: The accuracy of internal-transcribed-spacer (ITS) and shotgun metagenomics has not been robustly evaluated, and the effect of diet on the composition and function of the bacterial and fungal gut microbiome in a longitudinal setting has been poorly investigated. Here we compared two approaches to study the fungal community (ITS and shotgun metagenomics), proposed an enrichment protocol to perform a reliable mycobiome analysis using a comprehensive in-house fungal database, and correlated dietary data with both bacterial and fungal communities.

RESULTS: We found that shotgun DNA sequencing after a new enrichment protocol combined with the most comprehensive and novel fungal databases provided a cost-effective approach to perform gut mycobiome profiling at the species level and to integrate bacterial and fungal community analyses in fecal samples. The mycobiome was significantly more variable than the bacterial community at the compositional and functional levels. Notably, we showed that microbial diversity, composition, and functions were associated with habitual diet composition instead of driven by global dietary changes. Our study indicates a potential competitive inter-kingdom interaction between bacteria and fungi for food foraging.

CONCLUSION: Together, our present work proposes an efficient workflow to study the human gut microbiome integrating robustly fungal, bacterial, and dietary data. These findings will further advance our knowledge of the interaction between gut bacteria and fungi and pave the way for future investigations in human mycobiome. Video Abstract.}, } @article {pmid38097625, year = {2023}, author = {Chen, SJ and Wu, YJ and Chen, CC and Wu, YW and Liou, JM and Wu, MS and Kuo, CH and Lin, CH}, title = {Plasma metabolites of aromatic amino acids associate with clinical severity and gut microbiota of Parkinson's disease.}, journal = {NPJ Parkinson's disease}, volume = {9}, number = {1}, pages = {165}, pmid = {38097625}, issn = {2373-8057}, support = {NTU-110-A-CC-5400-64841//National Taiwan University (NTU)/ ; NTU-110-A-CC-5400-64841//National Taiwan University (NTU)/ ; NHRI-EX112-11136NI//National Health Research Institutes (NHRI)/ ; }, abstract = {Gut microbial proteolytic metabolism has been reportedly altered in Parkinson's disease (PD). However, the circulating aromatic amino acids (AAA) described in PD are inconsistent. Here we aimed to investigate plasma AAA profiles in a large cohort of PD patients, and examine their correlations with clinical severity and gut microbiota changes. We enrolled 500 participants including 250 PD patients and 250 neurologically normal controls. Plasma metabolites were measured using liquid chromatography mass spectrometry. Faecal samples were newly collected from 154 PD patients for microbiota shotgun metagenomic sequencing combined with data derived from 96 PD patients reported before. Data were collected regarding diet, medications, and motor and non-motor symptoms of PD. Compared to controls, PD patients had higher plasma AAA levels, including phenylacetylglutamine (PAGln), p-cresol sulfate (Pcs), p-cresol glucuronide (Pcg), and indoxyl sulfate (IS). Multivariable linear regression analyses, with adjustment for age, sex, and medications, revealed that the plasma levels of PAGln (coefficient 4.49, 95% CI 0.40-8.58, P = 0.032) and Pcg (coefficient 1.79, 95% CI 0.07-3.52, P = 0.042) positively correlated with motor symptom severity but not cognitive function. After correcting for abovementioned potential confounders, these AAA metabolites were also associated with the occurrence of constipation in PD patients (all P < 0.05). Furthermore, plasma levels of AAA metabolites were correlated with the abundance of specific gut microbiota species, including Bacteroides sp. CF01-10NS, Bacteroides vulgatus, and Clostridium sp. AF50-3. In conclusion, elevated plasma AAA metabolite levels correlated with disease characteristics in PD, suggesting that upregulated proteolytic metabolism may contribute to the pathophysiology of PD.}, } @article {pmid38097581, year = {2023}, author = {Lopez-Simon, J and Vila-Nistal, M and Rosenova, A and De Corte, D and Baltar, F and Martinez-Garcia, M}, title = {Viruses under the Antarctic Ice Shelf are active and potentially involved in global nutrient cycles.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {8295}, pmid = {38097581}, issn = {2041-1723}, mesh = {*Ecosystem ; Antarctic Regions ; Archaea ; *Viruses/genetics ; Sulfur ; Ice Cover ; }, abstract = {Viruses play an important role in the marine ecosystem. However, our comprehension of viruses inhabiting the dark ocean, and in particular, under the Antarctic Ice Shelves, remains limited. Here, we mine single-cell genomic, transcriptomic, and metagenomic data to uncover the viral diversity, biogeography, activity, and their role as metabolic facilitators of microbes beneath the Ross Ice Shelf. This is the largest Antarctic ice shelf with a major impact on global carbon cycle. The viral community found in the cavity under the ice shelf mainly comprises endemic viruses adapted to polar and mesopelagic environments. The low abundance of genes related to lysogenic lifestyle (<3%) does not support a predominance of the Piggyback-the-Winner hypothesis, consistent with a low-productivity habitat. Our results indicate a viral community actively infecting key ammonium and sulfur-oxidizing chemolithoautotrophs (e.g. Nitrosopumilus spp, Thioglobus spp.), supporting a "kill-the-winner" dynamic. Based on genome analysis, these viruses carry specific auxiliary metabolic genes potentially involved in nitrogen, sulfur, and phosphorus acquisition. Altogether, the viruses under Antarctic ice shelves are putatively involved in programming the metabolism of ecologically relevant microbes that maintain primary production in these chemosynthetically-driven ecosystems, which have a major role in global nutrient cycles.}, } @article {pmid38097035, year = {2023}, author = {Zhang, JS and Huang, S and Chen, Z and Chu, CH and Takahashi, N and Yu, OY}, title = {Application of omics technologies in cariology research: A critical review with bibliometric analysis.}, journal = {Journal of dentistry}, volume = {141}, number = {}, pages = {104801}, doi = {10.1016/j.jdent.2023.104801}, pmid = {38097035}, issn = {1879-176X}, abstract = {OBJECTIVES: To review the application of omics technologies in the field of cariology research and provide critical insights into the emerging opportunities and challenges.

DATA & SOURCES: Publications on the application of omics technologies in cariology research up to December 2022 were sourced from online databases, including PubMed, Web of Science and Scopus. Two independent reviewers assessed the relevance of the publications to the objective of this review.

STUDY SELECTION: Studies that employed omics technologies to investigate dental caries were selected from the initial pool of identified publications. A total of 922 publications with one or more omics technologies adopted were included for comprehensive bibliographic analysis. (Meta)genomics (676/922, 73 %) is the predominant omics technology applied for cariology research in the included studies. Other applied omics technologies are metabolomics (108/922, 12 %), proteomics (105/922, 11 %), and transcriptomics (76/922, 8 %).

CONCLUSION: This study identified an emerging trend in the application of multiple omics technologies in cariology research. Omics technologies possess significant potential in developing strategies for the detection, staging evaluation, risk assessment, prevention, and management of dental caries. Despite the numerous challenges that lie ahead, the integration of multi-omics data obtained from individual biological samples, in conjunction with artificial intelligence technology, may offer potential avenues for further exploration in caries research.

CLINICAL SIGNIFICANCE: This review presented a comprehensive overview of the application of omics technologies in cariology research and discussed the advantages and challenges of using these methods to detect, assess, predict, prevent, and treat dental caries. It contributes to steering research for improved understanding of dental caries and advancing clinical translation of cariology research outcomes.}, } @article {pmid38096814, year = {2024}, author = {Lou, YC and Chen, L and Borges, AL and West-Roberts, J and Firek, BA and Morowitz, MJ and Banfield, JF}, title = {Infant gut DNA bacteriophage strain persistence during the first 3 years of life.}, journal = {Cell host & microbe}, volume = {32}, number = {1}, pages = {35-47.e6}, doi = {10.1016/j.chom.2023.11.015}, pmid = {38096814}, issn = {1934-6069}, mesh = {Infant ; Female ; Adult ; Humans ; Infant, Newborn ; Child, Preschool ; *Bacteriophages/genetics ; Codon, Terminator ; Infant, Premature ; *Gastrointestinal Microbiome/genetics ; DNA ; }, abstract = {Bacteriophages are key components of gut microbiomes, yet the phage colonization process in the infant gut remains uncertain. Here, we establish a large phage sequence database and use strain-resolved analyses to investigate DNA phage succession in infants throughout the first 3 years of life. Analysis of 819 fecal metagenomes collected from 28 full-term and 24 preterm infants and their mothers revealed that early-life phageome richness increases over time and reaches adult-like complexity by age 3. Approximately 9% of early phage colonizers, which are mostly maternally transmitted and infect Bacteroides, persist for 3 years and are more prevalent in full-term than in preterm infants. Although rare, phages with stop codon reassignment are more likely to persist than non-recoded phages and generally display an increase in in-frame reassigned stop codons over 3 years. Overall, maternal seeding, stop codon reassignment, host CRISPR-Cas locus prevalence, and diverse phage populations contribute to stable viral colonization.}, } @article {pmid38096729, year = {2024}, author = {Xin, Y and Liu, L and Yang, XR and Yang, LY and Guang, SB and Zheng, YM and Zhao, QB}, title = {Adaptive shifts in plant traits associated with nitrogen removal driven by phytoremediation strategies in subtropical river restoration.}, journal = {Water research}, volume = {249}, number = {}, pages = {121008}, doi = {10.1016/j.watres.2023.121008}, pmid = {38096729}, issn = {1879-2448}, mesh = {*Nitrates ; Ecosystem ; Biodegradation, Environmental ; Rivers ; Nitrogen/metabolism ; Denitrification ; *Ammonium Compounds ; }, abstract = {Phytoremediation, which is commonly carried out through hydroponics and substrate-based strategies, is essential for the effectiveness of nature-based engineered solutions aimed at addressing excess nitrogen in aquatic ecosystems. However, the performance and mechanisms of plants involving nitrogen removal between different strategies need to be deeply understood. Here, this study employed in-situ cultivation coupled with static nitrogen tracing experiments to elucidate the influence of both strategies on plant traits associated with nitrogen removal. The results indicated that removal efficiencies in plants with substrate-based strategies for ammonium nitrogen and nitrate nitrogen were 30.51-71.11 % and 16.82-99.95 %, respectively, which were significantly higher than those with hydroponics strategies (25.98-58.18 % and 7.29-79.19 %, respectively). Similarly, the plant nitrogen uptake rates in the substrate-based strategy also generally showed higher levels compared to hydroponics strategies (P < 0.05). Meanwhile, the microorganisms-mediated nitrous oxide emission rates in the substrate-based strategy during summer (unamended: 0.00-0.58 μg/g/d; potential: 3.35-7.65 μg/g/d) were obviously lower than those in the hydroponics strategy (unamended: 2.23-11.70 μg/g/d; potential: 9.72-43.09 μg/g/d) (P < 0.05). Notably, analysis of similarity tests indicated that the influences of strategy on the above parameters generally surpass the effects attributable to interspecies plant differences, particularly during summer (R > 0, P < 0.05). Based on statistical and metagenomic analyses, this study revealed that these differences were driven by the stabilizing influence of substrate-based strategy on plant roots and enhancing synergistic interplay among biochemical factors within plant-root systems. Even so, phytoremediation strategies did not significantly alter the characteristics of plants with regards to their tendency towards ammonium nitrogen uptake (up to 87.68 %) and dissimilatory nitrate reduction to ammonium as primary biological pathway for nitrogen transformation which accounted for 53.66-96.47 % nitrate removal. In summary, this study suggested that the substrate-based strategy should be a more effective strategy for enhancing the nitrogen removal ability of plants in subtropical river restoration practices.}, } @article {pmid38095826, year = {2023}, author = {Kondo, M and Torisu, T and Nagasue, T and Shibata, H and Umeno, J and Kawasaki, K and Fujioka, S and Matsuno, Y and Moriyama, T and Kitazono, T}, title = {Duodenal microbiome in chronic kidney disease.}, journal = {Clinical and experimental nephrology}, volume = {}, number = {}, pages = {}, pmid = {38095826}, issn = {1437-7799}, support = {JP21K06783//Japan Society for the Promotion of Science/ ; }, abstract = {BACKGROUND: The intestinal microbiome is involved in the pathogenesis of chronic kidney disease (CKD). Despite its importance, the microbiome of the small intestinal mucosa has been little studied due to sampling difficulties, and previous studies have mainly focused on fecal sources for microbiome studies. We aimed to characterize the small intestinal microbiome of CKD patients by studying the microbiome collected from duodenal and fecal samples of CKD patients and healthy controls.

METHODS: Overall, 28 stage 5 CKD patients and 21 healthy participants were enrolled. Mucosal samples were collected from the deep duodenum during esophagogastroduodenoscopy and fecal samples were also collected. The 16S ribosomal RNA gene sequencing using Qiime2 was used to investigate and compare the microbial structure and metagenomic function of the duodenal and fecal microbiomes.

RESULTS: The duodenal flora of CKD patients had decreased alpha diversity compared with the control group. On the basis of taxonomic composition, Veillonella and Prevotella were significantly reduced in the duodenal flora of CKD patients. The tyrosine and tryptophan metabolic pathways were enhanced in the urea toxin-related metabolic pathways based on the Kyoto Encyclopedia of Genes and Genomes database.

CONCLUSION: The small intestinal microbiome in CKD patients is significantly altered, indicating that increased intestinal permeability and production of uremic toxin may occur in the upper small intestine of CKD patients.}, } @article {pmid38095693, year = {2023}, author = {Abou Chacra, L and Benatmane, A and Iwaza, R and Ly, C and Alibar, S and Armstrong, N and Mediannikov, O and Bretelle, F and Fenollar, F}, title = {Culturomics reveals a hidden world of vaginal microbiota with the isolation of 206 bacteria from a single vaginal sample.}, journal = {Archives of microbiology}, volume = {206}, number = {1}, pages = {20}, pmid = {38095693}, issn = {1432-072X}, support = {ANR-10-IAHU-03//Agence Nationale de la Recherche/ ; ANR-10-IAHU-03//Agence Nationale de la Recherche/ ; ANR-10-IAHU-03//Agence Nationale de la Recherche/ ; ANR-10-IAHU-03//Agence Nationale de la Recherche/ ; ANR-10-IAHU-03//Agence Nationale de la Recherche/ ; ANR-10-IAHU-03//Agence Nationale de la Recherche/ ; ANR-10-IAHU-03//Agence Nationale de la Recherche/ ; ANR-10-IAHU-03//Agence Nationale de la Recherche/ ; ANR-10-IAHU-03//Agence Nationale de la Recherche/ ; }, mesh = {Humans ; Female ; *Bacteria/genetics ; *Microbiota/genetics ; Firmicutes/genetics ; Vagina/microbiology ; Bacteroidetes ; }, abstract = {The composition of the vaginal microbiota is known to be influenced by various factors and to be associated with several disorders affecting women's health. Although metagenomics is currently a widely used method for studying the human microbiota, it has certain limitations, such as a lack of information on bacterial viability. It is therefore important to use culture-based methods such as culturomics. Here, we used 35 different culture conditions to comprehensively characterize the vaginal bacterial diversity of a single woman's flora. A total of 206 bacterial species, belonging to six phyla (for a little more than half to Firmicutes, followed mainly by Actinobacteria, Bacteroidetes, and Proteobacteria) and 45 families, and 2 fungal species were cultivated. While several species of lactobacilli have been isolated, a wide variety of other bacteria were also separated, including 65 never reported before in vaginal flora, including a new bacterial species, Porphyromonas vaginalis sp. nov. Extensive culture-based methods are essential to establish a comprehensive, evidence-based repertoire of bacterial viability. If combined with molecular methods, they can provide a much more thorough understanding of the vaginal microbiota and fulfil the unknown part of metagenomic studies.}, } @article {pmid38095471, year = {2024}, author = {Lu, Y and Zhang, Y and Lou, Z and He, X and Zhang, Q and Zhang, Q and Zhao, S and Chen, H and Zhu, H and Song, Z and Zhang, R and Ma, C and Liu, D}, title = {Metagenomic next-generation sequencing of cell-free DNA for the identification of viruses causing central nervous system infections.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0226423}, pmid = {38095471}, issn = {2165-0497}, support = {No.YX202205//Wisdom Accumulation and Talent Cultivation Project of the Third xiangya hospital of Central South University/ ; }, mesh = {Humans ; *Cell-Free Nucleic Acids/genetics ; Retrospective Studies ; *Central Nervous System Infections/diagnosis ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Viruses/genetics ; DNA ; *Virus Diseases/diagnosis ; }, abstract = {This study provides significant new data on the application of metagenomic next-generation sequencing (mNGS) to clinical diagnostics of central nervous system (CNS) viral infections, which can have high mortality rates and severe sequelae. Conventional diagnostic procedures for identifying viruses can be inefficient and rely on preconceived assumptions about the pathogen, making mNGS an appealing alternative. However, the effectiveness of mNGS is affected by the presence of human DNA contamination, which can be minimized by using cell-free DNA (cfDNA) instead of whole-cell DNA (wcDNA). This multi-center retrospective study of patients with suspected viral CNS infection found that mNGS using cfDNA had a significantly lower proportion of human DNA and higher sensitivity for detecting viruses than mNGS using wcDNA. Herpesviruses, particularly VZV, were found to be the most common DNA viruses in these patients. Overall, mNGS using cfDNA is a promising complementary diagnostic method for detecting CNS viral infections.}, } @article {pmid38095467, year = {2024}, author = {Wang, W and Yao, Y and Li, X and Zhang, S and Zeng, Z and Zhou, H and Yang, Q}, title = {Clinical impact of metagenomic next-generation sequencing of peripheral blood for the diagnosis of invasive mucormycosis: a single-center retrospective study.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0355323}, pmid = {38095467}, issn = {2165-0497}, support = {2023C03068//Key Research and Development Program of Zhejiang Province (Key R&D plan of Zhejiang Province)/ ; 2022YFC2504502//Ministry of Science and Technology of the People's Republic of China (MOST)/ ; 81971897, 82272338//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Humans ; *Mucormycosis/diagnosis ; Retrospective Studies ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics ; }, abstract = {Given the high fatality rates, prompt and accurate identification of the fungal culprit is crucial, emphasizing the need for invasive mucormycosis. Unfortunately, mucormycosis lacks definitive biomarkers, depending primarily on smears, cultures, or pathology, all necessitating invasive specimen collection from the infection site. However, obtaining valid specimens early in critically ill patients poses substantial risks and challenges. Whether peripheral blood metagenomic next-generation sequencing (mNGS) can enhance early mucormycosis diagnosis, especially when direct specimen collection from the infection site is challenging, is warranted. This is a large-scale clinical study conducted to evaluate the utility and clinical impact of mNGS of peripheral blood for the diagnosis of invasive mucormycosis. We believe our study provided both novelty in translational medicine and a great value for the medical community to understand the strengths and limitations of mNGS of peripheral blood as a new diagnostic tool for the diagnosis and management of invasive mucormycosis.}, } @article {pmid38095449, year = {2023}, author = {Arehart, CH and Sterrett, JD and Garris, RL and Quispe-Pilco, RE and Gignoux, CR and Evans, LM and Stanislawski, MA}, title = {Poly-omic risk scores predict inflammatory bowel disease diagnosis.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0067723}, doi = {10.1128/msystems.00677-23}, pmid = {38095449}, issn = {2379-5077}, support = {K01 HL157658/HL/NHLBI NIH HHS/United States ; }, abstract = {Complex traits are characterized by many biological and environmental factors, such that multi-omic data sets are well-positioned to help us understand their underlying etiologies. We applied a prediction framework across multiple omics (metagenomics, metatranscriptomics, metabolomics, and viromics) from the gut ecosystem to predict inflammatory bowel disease (IBD) diagnosis. The predicted scores from our models highlighted key features and allowed us to compare the relative utility of each omic data set in single-omic versus multi-omic models. Our results emphasized the importance of metabolomics and viromics over metagenomics and metatranscriptomics for predicting IBD status. The greater predictive capability of metabolomics and viromics is likely because these omics serve as markers of lifestyle factors such as diet. This study provides a modeling framework for multi-omic data, and our results show the utility of combining multiple omic data types to disentangle complex disease etiologies and biological signatures.}, } @article {pmid38095429, year = {2023}, author = {Bogri, A and Jensen, EEB and Borchert, AV and Brinch, C and Otani, S and Aarestrup, FM}, title = {Transmission of antimicrobial resistance in the gut microbiome of gregarious cockroaches: the importance of interaction between antibiotic exposed and non-exposed populations.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0101823}, doi = {10.1128/msystems.01018-23}, pmid = {38095429}, issn = {2379-5077}, abstract = {Antimicrobial resistance is a rising threat to human and animal health. The spread of resistance through the transmission of the symbiotic gut microbiome is of concern and has been explored in theoretical modeling studies. In this study, we employ gregarious insect populations to examine the emergence and transmission of antimicrobial resistance in vivo and validate modeling hypotheses. We find that antimicrobial treatment increases the levels of resistance in treated populations. Most importantly, we show that resistance increased in untreated populations after interacting with the treated ones. The level of resistance transmission was affected by the magnitude and frequency of population mixing. Our results highlight the importance of microbial transmission in the spread of antimicrobial resistance.}, } @article {pmid38095414, year = {2023}, author = {Gómez, M and Martínez, D and Páez-Triana, L and Luna, N and Ramírez, A and Medina, J and Cruz-Saavedra, L and Hernández, C and Castañeda, S and Bohórquez Melo, R and Suarez, LA and Palma-Cuero, M and Murcia, LM and González Páez, L and Estrada Bustos, L and Medina, MA and Ariza Campo, K and Padilla, HD and Zamora Flórez, A and De Las Salas, JL and Muñoz, M and Ramírez, JD}, title = {Influence of dengue virus serotypes on the abundance of Aedes aegypti insect-specific viruses (ISVs).}, journal = {Journal of virology}, volume = {}, number = {}, pages = {e0150723}, doi = {10.1128/jvi.01507-23}, pmid = {38095414}, issn = {1098-5514}, abstract = {In this study, we employed a metagenomic approach to characterize the virome of Aedes aegypti mosquitoes, with and without natural DENV infection, in several regions of Colombia. Our findings indicate that the mosquito virome is predominantly composed of insect-specific viruses (ISVs) and that infection with different DENV serotypes (DENV-1 and DENV-2) could lead to alterations in the relative abundance of viral families and species constituting the core virome in Aedes spp. The study also sheds light on the identification of the genome and evolutionary relationships of the Phasi Charoen-like phasivirus in Ae. aegypti in Colombia, a widespread ISV in areas with high DENV incidence.}, } @article {pmid38094744, year = {2023}, author = {Wang, ZY and Li, LL and Cao, XL and Li, P and Du, J and Zou, MJ and Wang, LL}, title = {Clinical application of amplification-based versus amplification-free metagenomic next-generation sequencing test in infectious diseases.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1138174}, pmid = {38094744}, issn = {2235-2988}, mesh = {Humans ; *Communicable Diseases/diagnosis ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents ; Metagenome ; Metagenomics ; DNA ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Recently, metagenomic next-generation sequencing (mNGS) has been used in the diagnosis of infectious diseases (IDs) as an emerging and powerful tool. However, whether the complicated methodological variation in mNGS detections makes a difference in their clinical performance is still unknown. Here we conducted a method study on the clinical application of mNGS tests in the DNA detection of IDs.

METHODS: We analyzed the effect of several potential factors in the whole process of mNGS for DNA detection on microorganism identification in 98 samples of suspected ID patients by amplification-based mNGS. The amplification-based and amplification-free mNGS tests were successfully performed in 41 samples. Then we compared the clinical application of the two mNGS methods in the DNA detection of IDs.

RESULTS: We found that a higher concentration of extracted nucleic acid was more conducive to detecting microorganisms. Other potential factors, such as read depth and proportion of human reads, might not be attributed to microorganism identification. The concordance rate of amplification-based and amplification-free mNGS results was 80.5% (33/41) in the patients with suspected IDs. Amplification-based mNGS showed approximately 16.7% higher sensitivity than amplification-free mNGS. However, 4 cases with causative pathogens only detected by amplification-based mNGS were finally proved false-positive. In addition, empirical antibiotic treatments were adjusted in 18 patients following mNGS testing with unexpected pathogens.

CONCLUSIONS: Amplification-based and amplification-free mNGS tests showed their specific advantages and disadvantages in the diagnosis of IDs. The clinical application of mNGS still needs more exploration from a methodological perspective. With advanced technology and standardized procedure, mNGS will play a promising role in the diagnosis of IDs and help guide the use of antibiotics.}, } @article {pmid38094659, year = {2023}, author = {Li, GS and Guo, HQ}, title = {Misdiagnosis of pneumorrhagia leptospirosis as common CAP: A case report and literature review.}, journal = {Respiratory medicine case reports}, volume = {46}, number = {}, pages = {101954}, pmid = {38094659}, issn = {2213-0071}, abstract = {BACKGROUND: The incidence of critical leptospirosis manifested as massive pulmonary hemorrhage has been significantly reduced, which has been rarely reported in recent years, while the mortality rate is extremely high once it occurs.

CASE PRESENTATION: A 54-year-old man with no HIV infection was admitted to the local county hospital due to high-grade continuous fever lasting four days (38.5-40.5C), upper limb and shoulder-back muscle pain, and general fatigue. The chest CT (Aug 26, 2021) showed "multiple patchy, cloudy, and fuzzy shadows in both lungs, mainly under the pleura of the upper and lower lobes of both lungs; some lymph nodes in the mediastinum are enlarged". Despite being diagnosed with "common community-acquired pneumonia" and starting injectable levofloxacin, the symptoms worsened, and massive hemoptysis occurred. However, after being transferred to our hospital, the patient was diagnosed with the "pulmonary hemorrhage type of leptospirosis" through comprehensive dynamic analysis. The patient recovered very well after undergoing "penicillin 3MIU q6h" alone for two weeks to fight the infection.

CONCLUSIONS: Leptospirosis has a high mortality rate when it becomes critical or severe. Diagnosis typically relies on factors such as epidemiology, clinical symptoms, and pathogenetic testing. Metagenomic next-generation sequencing (mNGS) is more effective in sensitivity and speed than traditional detection methods, making it an excellent option for diagnosing challenging and severe infections in emergencies. Additionally, when experiencing sudden coughing up of blood, it's important to consider the possibility of pulmonary hemorrhage as a type of leptospirosis.}, } @article {pmid38094635, year = {2023}, author = {Pagan, L and Huisman, BW and van der Wurff, M and Naafs, RGC and Schuren, FHJ and Sanders, IMJG and Smits, WK and Zwittink, RD and Burggraaf, J and Rissmann, R and Piek, JMJ and Henderickx, JGE and van Poelgeest, MIE}, title = {The vulvar microbiome in lichen sclerosus and high-grade intraepithelial lesions.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1264768}, pmid = {38094635}, issn = {1664-302X}, abstract = {BACKGROUND: The role of the vulvar microbiome in the development of (pre)malignant vulvar disease is scarcely investigated. The aim of this exploratory study was to analyze vulvar microbiome composition in lichen sclerosus (LS) and vulvar high-grade squamous intraepithelial lesions (HSIL) compared to healthy controls.

METHODS: Women with vulvar lichen sclerosus (n = 10), HSIL (n = 5) and healthy controls (n = 10) were included. Swabs were collected from the vulva, vagina and anal region for microbiome characterization by metagenomic shotgun sequencing. Both lesional and non-lesional sites were examined. Biophysical assessments included trans-epidermal water loss for evaluation of the vulvar skin barrier function and vulvar and vaginal pH measurements.

RESULTS: Healthy vulvar skin resembled vaginal, anal and skin-like microbiome composition, including the genera Prevotella, Lactobacillus, Gardnerella, Staphylococcus, Cutibacterium, and Corynebacterium. Significant differences were observed in diversity between vulvar skin of healthy controls and LS patients. Compared to the healthy vulvar skin, vulvar microbiome composition of both LS and vulvar HSIL patients was characterized by significantly higher proportions of, respectively, Papillomaviridae (p = 0.045) and Alphapapillomavirus (p = 0.002). In contrast, the Prevotella genus (p = 0.031) and Bacteroidales orders (p = 0.038) were significantly less abundant in LS, as was the Actinobacteria class (p = 0.040) in vulvar HSIL. While bacteria and viruses were most abundant, fungal and archaeal taxa were scarcely observed. Trans-epidermal water loss was higher in vulvar HSIL compared to healthy vulvar skin (p = 0.043).

CONCLUSION: This study is the first to examine the vulvar microbiome through metagenomic shotgun sequencing in LS and HSIL patients. Diseased vulvar skin presents a distinct signature compared to healthy vulvar skin with respect to bacterial and viral fractions of the microbiome. Key findings include the presence of papillomaviruses in LS as well as in vulvar HSIL, although LS is generally considered an HPV-independent risk factor for vulvar dysplasia. This exploratory study provides clues to the etiology of vulvar premalignancies and may act as a steppingstone for expanding the knowledge on potential drivers of disease progression.}, } @article {pmid38094621, year = {2023}, author = {Li, SQ and Shen, Y and Zhang, J and Weng, CZ and Wu, SD and Jiang, W}, title = {Immune modulation of gut microbiota and its metabolites in chronic hepatitis B.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1285556}, pmid = {38094621}, issn = {1664-302X}, abstract = {The gut microbiota is a diverse ecosystem consisting of 100 trillion microbiomes. The interaction between the host's gut and distal organs profoundly impacts various functions such as metabolism, immunity, neurology, and nutrition within the human body. The liver, as the primary immune organ, plays a crucial role in maintaining immune homeostasis by receiving a significant influx of gut-derived components and toxins. Perturbations in gut microbiota homeostasis have been linked to a range of liver diseases. The advancements in sequencing technologies, such as 16S rRNA and metagenomics, have opened up new avenues for comprehending the intricate physiological interplay between the liver and the intestine. Metabolites produced by the gut microbiota function as signaling molecules and substrates, influencing both pathological and physiological processes. Establishing a comprehensive host-bacterium-metabolism axis holds tremendous potential for investigating the mechanisms underlying liver diseases. In this review, we have provided a summary of the detrimental effects of the gut-liver axis in chronic liver diseases, primarily focusing on hepatitis B virus-related chronic liver diseases. Moreover, we have explored the potential mechanisms through which the gut microbiota and its derivatives interact with liver immunity, with implications for future clinical therapies.}, } @article {pmid38093327, year = {2023}, author = {Zhong, HJ and Wang, SQ and Zhang, RX and Zhuang, YP and Li, L and Yi, SZ and Li, Y and Wu, L and Ding, Y and Zhang, J and Xie, X and He, XX and Wu, Q}, title = {Supplementation with high-GABA-producing Lactobacillus plantarum L5 ameliorates essential tremor triggered by decreased gut bacteria-derived GABA.}, journal = {Translational neurodegeneration}, volume = {12}, number = {1}, pages = {58}, pmid = {38093327}, issn = {2047-9158}, support = {2022B1111070006//Guangdong Science and Technology Department/ ; 2019QN01N107//Guangdong Science and Technology Department/ ; 2022GDASZH-2022020402-01//Guangdong Academy of Sciences/ ; }, mesh = {Humans ; Mice ; Animals ; *Lactobacillus plantarum/genetics ; *Essential Tremor ; Tremor ; Bacteria ; gamma-Aminobutyric Acid ; Dietary Supplements ; Mammals ; }, abstract = {BACKGROUND: The γ-aminobutyric acid (GABA) hypothesis posits a role of GABA deficiency in the central nervous system in the pathogenesis and progression of essential tremor (ET). However, the specific causative factor for GABA deficiency is not clear. The gut microbiota in mammals has recently been considered as a significant source of GABA. Furthermore, the GABA-based signals originating from the intestine can be transmitted to the brain through the "enteric nervous system-vagus nerve-brain" axis. However, the plausible contribution of gut microbiota to ET seems inspiring but remains obscure.

METHODS: Fecal samples from patients with ET and healthy controls were examined by metagenomic sequencing to compare the composition of gut microbiota and the expression of genes involved in GABA biosynthesis. The impact of gut microbiota on ET was explored through transplantation of fecal microbiota from patients with ET into the murine ET model. Lactic acid bacteria producing high amounts of GABA were identified through whole-genome sequencing and ultra-performance liquid chromatography-tandem mass spectrometry. Subsequently, mice were treated with the high-GABA-producing strain Lactobacillus plantarum L5. Tremor severity, behavioral tests, pro-inflammatory cytokines, GABA concentration, and gut microbiota composition were examined in these mice.

RESULTS: The gut microbiota of patients with ET demonstrated an impaired GABA-producing capacity and a reduced fecal GABA concentration. Transplantation of the gut microbiota from patients with ET induced an extension of tremor duration and impaired mobility in the murine model of ET. L5 exhibited an augmented GABA-producing capacity, with the De Man-Rogosa-Sharpe culture broth containing 262 mg/l of GABA. In addition, administration of L5 significantly decreased the tremor severity and enhanced the movement capability and grasping ability of ET mice. In vivo mechanistic experiments indicated that L5 reshaped the gut microbial composition, supplemented the mucosa-associated microbiota with GABA-producing capacity, increased the GABA concentrations in the cerebellum, and diminished inflammation in the central nervous system.

CONCLUSIONS: These findings highlight that deficiency of GABA-producing gut microbes plays an essential role in the pathogenesis of ET and that L5 is a promising candidate for treating ET.}, } @article {pmid38093016, year = {2024}, author = {Hibberd, MC and Webber, DM and Rodionov, DA and Henrissat, S and Chen, RY and Zhou, C and Lynn, HM and Wang, Y and Chang, HW and Lee, EM and Lelwala-Guruge, J and Kazanov, MD and Arzamasov, AA and Leyn, SA and Lombard, V and Terrapon, N and Henrissat, B and Castillo, JJ and Couture, G and Bacalzo, NP and Chen, Y and Lebrilla, CB and Mostafa, I and Das, S and Mahfuz, M and Barratt, MJ and Osterman, AL and Ahmed, T and Gordon, JI}, title = {Bioactive glycans in a microbiome-directed food for children with malnutrition.}, journal = {Nature}, volume = {625}, number = {7993}, pages = {157-165}, pmid = {38093016}, issn = {1476-4687}, support = {R01 DK030292/DK/NIDDK NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; }, mesh = {Child ; Humans ; Infant ; *Malnutrition ; Bacteria/genetics ; Body Weight/genetics ; Polysaccharides/metabolism ; *Gastrointestinal Microbiome/physiology ; Metagenome ; }, abstract = {Evidence is accumulating that perturbed postnatal development of the gut microbiome contributes to childhood malnutrition[1-4]. Here we analyse biospecimens from a randomized, controlled trial of a microbiome-directed complementary food (MDCF-2) that produced superior rates of weight gain compared with a calorically more dense conventional ready-to-use supplementary food in 12-18-month-old Bangladeshi children with moderate acute malnutrition[4]. We reconstructed 1,000 bacterial genomes (metagenome-assembled genomes (MAGs)) from the faecal microbiomes of trial participants, identified 75 MAGs of which the abundances were positively associated with ponderal growth (change in weight-for-length Z score (WLZ)), characterized changes in MAG gene expression as a function of treatment type and WLZ response, and quantified carbohydrate structures in MDCF-2 and faeces. The results reveal that two Prevotella copri MAGs that are positively associated with WLZ are the principal contributors to MDCF-2-induced expression of metabolic pathways involved in utilizing the component glycans of MDCF-2. The predicted specificities of carbohydrate-active enzymes expressed by their polysaccharide-utilization loci are correlated with (1) the in vitro growth of Bangladeshi P. copri strains, possessing varying degrees of polysaccharide-utilization loci and genomic conservation with these MAGs, in defined medium containing different purified glycans representative of those in MDCF-2, and (2) the levels of faecal carbohydrate structures in the trial participants. These associations suggest that identifying bioactive glycan structures in MDCFs metabolized by growth-associated bacterial taxa will help to guide recommendations about their use in children with acute malnutrition and enable the development of additional formulations.}, } @article {pmid38092853, year = {2023}, author = {Demkina, A and Slonova, D and Mamontov, V and Konovalova, O and Yurikova, D and Rogozhin, V and Belova, V and Korostin, D and Sutormin, D and Severinov, K and Isaev, A}, title = {Benchmarking DNA isolation methods for marine metagenomics.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22138}, pmid = {38092853}, issn = {2045-2322}, support = {075-10-2021-114//Ministry of Science and Higher Education of the Russian Federation/ ; 22-14-00004//Russian Scientific Foundation/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Benchmarking ; Reproducibility of Results ; *DNA/genetics ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; DNA, Bacterial/genetics ; }, abstract = {Metagenomics is a powerful tool to study marine microbial communities. However, obtaining high-quality environmental DNA suitable for downstream sequencing applications is a challenging task. The quality and quantity of isolated DNA heavily depend on the choice of purification procedure and the type of sample. Selection of an appropriate DNA isolation method for a new type of material often entails a lengthy trial and error process. Further, each DNA purification approach introduces biases and thus affects the composition of the studied community. To account for these problems and biases, we systematically investigated efficiency of DNA purification from three types of samples (water, sea sediment, and digestive tract of a model invertebrate Magallana gigas) with eight commercially available DNA isolation kits. For each kit-sample combination we measured the quantity of purified DNA, extent of DNA fragmentation, the presence of PCR-inhibiting contaminants, admixture of eukaryotic DNA, alpha-diversity, and reproducibility of the resulting community composition based on 16S rRNA amplicons sequencing. Additionally, we determined a "kitome", e.g., a set of contaminating taxa inherent for each type of purification kit used. The resulting matrix of evaluated parameters allows one to select the best DNA purification procedure for a given type of sample.}, } @article {pmid38092264, year = {2024}, author = {Vitória Minzoni de Souza Iacia, M and Eduarda Ferraz Mendes, M and Cristiny de Oliveira Vieira, K and Cristine Marques Ruiz, G and José Leopoldo Constantino, C and da Silva Martin, C and Eloizo Job, A and Alborghetti Nai, G and Kretli Winkelstroter Eller, L}, title = {Evaluation of curcumin nanoemulsion effect to prevent intestinal damage.}, journal = {International journal of pharmaceutics}, volume = {650}, number = {}, pages = {123683}, doi = {10.1016/j.ijpharm.2023.123683}, pmid = {38092264}, issn = {1873-3476}, mesh = {Mice ; Male ; Animals ; *Curcumin ; Emulsions/chemistry ; Mice, Inbred C57BL ; Microscopy, Electron, Scanning ; Inflammation ; }, abstract = {Curcumin has gained great prominence for the prevention and treatment of inflammatory bowel disease. However, studies have reported the low bioavailability of orally administered curcumin. This work aimed to evaluate the characteristics, stability and effects of a curcumin-carrying nanoemulsion in preventing intestinal damage induced by indomethacin. Nanoemulsions containing curcumin were prepared by spontaneous emulsification method and it was characterized by dynamic light scattering (DLS), zeta potential and the morphology was evaluated by scanning electron microscopy (SEM). Its stability was tested under different conditions of pH, temperature at 0, 7, 14, 21 and 28 days. In animal experimentation, 36 male mice of the Mus musculus lineage (C57BL/6) were used. The intestinal inflammation was evaluated based on macroscopic, histopathological and metagenomic analysis. It was found a stable nanoemulsion with a size of 409.8 nm, polydispersion index (PDI) of 0.132 and zeta potential of -18.8 mV. However, these lost charge in pH2, showing instability in acidic media (p < 0.05). In animal experiments, the nanoemulsion did not significantly improve intestinal inflammation. However, the group treated with curcumin nanoemulsion showed a higher relative abundance of the genus Lactobacillus (p < 0.05). In conclusion, the curcumin nanoemulsion was relevant in the modulation of the intestinal microbiota.}, } @article {pmid38092236, year = {2023}, author = {Guo, C and Lin, S and Lyu, T and Ma, Y and Dong, R and Liu, S}, title = {Effect of reactor operation modes on mitigating antibiotic resistance genes (ARGs) and methane production from hydrothermally-pretreated pig manure.}, journal = {Environmental research}, volume = {244}, number = {}, pages = {117894}, doi = {10.1016/j.envres.2023.117894}, pmid = {38092236}, issn = {1096-0953}, abstract = {Numerous efforts have been made to enhance the performance of anaerobic digestion (AD) for accelerating renewable energy generation, however, it remains unclear whether the intensified measures could enhance the proliferation and transmissions of antibiotic resistance genes (ARGs) in the system. This study assessed the impact of an innovative pig manure AD process, which includes hydrothermal pretreatment (HTP) and a two-stage configuration with separated acidogenic and methanogenic phases, on biomethane (CH4) production and ARGs dynamics. Results showed that HTP significantly increase CH4 production from 0.65 to 0.75 L/L/d in conventional single-stage AD to 0.82 and 0.91 L/L/d in two-stage AD. This improvement correlated with a rise in the relative abundance of Methanosarcina, a key methanogenesis microorganism. In the two-stage AD, the methanogenic stage offered an ideal environment for methanogens growth, resulting in substantially faster and higher CH4 production by about 10% compared to single-stage AD. Overall, the combined use of HTP and the two-stage AD configuration enhanced CH4 production by 40% compared to traditional single-stage AD. The abundance and diversity of ARGs were significantly reduced in the acidogenic reactors after HTP. However, the ARGs levels increased by about two times in the following methanogenesis stage and reached similar or higher levels than in single stage AD. The erm(F), erm(G), ant(6)-Ia, tet(W), mef(A) and erm(B) were the six main ARGs with significant differences in relative abundances in various treatments. The two-stage AD mode could better remove sul2, but it also had a rebound which elevated the risk of ARGs to the environment and human health. Network analysis identified pH and TVFAs as critical factors driving microbial communities and ARG proliferation in the new AD process. With the results, this study offers valuable insights into the trade-offs between AD performance enhancement and ARG-related risks, pinpointing essential areas for future research and practical improvements.}, } @article {pmid38091707, year = {2024}, author = {Zang, X and Wu, JL and Zeng, XD and Liu, J and Guo, HM and Chen, JM}, title = {Native mitral valve fungal endocarditis caused by Aspergillus fumigatus: A case report.}, journal = {International journal of surgery case reports}, volume = {114}, number = {}, pages = {109128}, pmid = {38091707}, issn = {2210-2612}, abstract = {INTRODUCTION: Aspergillus endocarditis is a rare fungal infection associated with a poor prognosis. Most cases of Aspergillus endocarditis involve prosthetic valves, with native valve involvement being rarely reported.

CASE PRESENTATION: A 53-year-old asian female patient presented with fever, chills, dyspnea, generalized fatigue, and significant weight loss one month after undergoing left lower lobectomy for a pulmonary abscess. Echocardiogram showed a large mobile vegetation with a broad base on the anterior leaflet of the mitral valve, resembling atrial myxoma. Despite negative blood cultures, circulating DNA of Aspergillus fumigatus was detected by metagenome Next Generation Sequencing, prompting the initiation of empiric antifungal therapy with voriconazole. Emergency surgery, involving thorough debridement and mitral valve replacement, was successfully performed. Indefinite fungal suppression therapy with oral voriconazole is continued to mitigate the risk of recurrence. The patient survived with no signs of Aspergillus disease recurrence for four years.

CLINICAL DISCUSSION: Diagnosis of Aspergillus endocarditis requires a high index of suspicion and is often delayed due to consistently negative results from blood cultures. Non-culture-based methods, particularly metagenome Next-Generation Sequencing, play a crucial role in early diagnosis and therapeutic decision-making. Surgical debridement and valve replacement are imperative for survival in cases of Aspergillus endocarditis. Voriconazole should be considered the primary fungicidal agent for its treatment. Moreover, lifelong fungal suppression therapy is strongly recommended for all survivors to ensure long-term survival and minimize the risk of recurrence.

CONCLUSION: Despite grim prognosis associated with Aspergillus endocarditis, patients can attain long-term survival through meticulous surgical debridement and lifelong antifungal therapy.}, } @article {pmid38091183, year = {2023}, author = {Cardia Caserta, L and Mansano do Nascimento, G and Joshi, LR and Mausbach Simão, R and Miller, ME and Nunes Felippe, PA and Diel, DG and Weis Arns, C}, title = {Bacterial and Viral Diversity of Didelphid Opossums from Brazil.}, journal = {EcoHealth}, volume = {}, number = {}, pages = {}, pmid = {38091183}, issn = {1612-9210}, support = {870370/1997-9//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 2014/50696-4//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {Marsupials belonging to the Didelphis genus are widely distributed in the American Continent, and Didelphis albiventris and Didelphis aurita, are common in all of their areas of distribution in Brazil. Here we describe the bacterial and viral diversity of samples from opossums captured in three forest fragments in the State of São Paulo, Brazil. Microbiomes from the same body site were more similar across species and sampling sites while oral swabs presented higher bacterial diversity than rectal swabs. We also identified sequences related to bacterial species involved in zoonotic diseases. The detection of pathogens in such abundant mammal species warns for the possibility of emergence in other species.}, } @article {pmid38091182, year = {2023}, author = {Okoh, GR and Ariel, E and Whitmore, D and Horwood, PF}, title = {Metagenomic and Molecular Detection of Novel Fecal Viruses in Free-Ranging Agile Wallabies.}, journal = {EcoHealth}, volume = {}, number = {}, pages = {}, pmid = {38091182}, issn = {1612-9210}, abstract = {The agile wallaby (Notamacropus agilis) is one of the most abundant marsupial species in northern Queensland and a competent host for the zoonotic Ross River virus. Despite their increased proximity and interactions with humans, little is known about the viruses carried by these animals, and whether any are of conservation or zoonotic importance. Metagenomics and molecular techniques were used in a complementary manner to identify and characterize novel viruses in the fecal samples of free-ranging agile wallabies. We detected a variety of novel marsupial-related viral species including agile wallaby atadenovirus 1, agile wallaby chaphamaparvovirus 1-2, agile wallaby polyomavirus 1-2, agile wallaby associated picobirnavirus 1-9, and a known macropod gammaherpesvirus 3. Phylogenetic analyses indicate that most of these novel viruses would have co-evolved with their hosts (agile wallabies). Additionally, non-marsupial viruses that infect bacteria (phages), plants, insects, and other eukaryotes were identified. This study highlighted the utility of non-invasive sampling as well as the integration of broad-based molecular assays (consensus PCR and next generation sequencing) for monitoring the emergence of potential pathogenic viruses in wildlife species. Furthermore, the novel marsupial viruses identified in this study will enrich the diversity of knowledge about marsupial viruses, and may be useful for developing diagnostics and vaccines.}, } @article {pmid38090133, year = {2024}, author = {Sheikh, A and Mohamed Ibrahim, HI and Almathen, F and Alfattah, M and Khalifa, A}, title = {Beneficial probiotic bacteria prevalence in different lactating dromedary camel milk of Saudi Arabia.}, journal = {Saudi journal of biological sciences}, volume = {31}, number = {1}, pages = {103879}, pmid = {38090133}, issn = {1319-562X}, abstract = {Dromedary camel or Arabian camel (Camelus dromedarius) has great economic importance due to its milk and byproducts. Its milk has high nutrition along with healthy bacteria such as Lactic acid bacteria helpful in the fermentation process. The aim was to compare the probiotic bacteria from one week of lactating camel milk vs one year lactating camel milk to differentiate the potential probiotics. This study analyzed the microbiomes of one year lactating raw camel milk M1, M2 (A) (n = 10) and one week of lactating camel milk M3, M4 (B) (n = 10) through metagenomic analysis of 16S rRNA. In total, 276 species were found in two groups (A and B) and they shared 55 genes. Group B showed a higher number of species (2 2 0) than group A (56). The statistical data on functional annotations such as Card, COG, NOG and Swiss-prot revealed at least one or more contributions from this study sample database. The phylum Proteobacteria contributed largely up to 75 % in group B. In contrast, Ascomycota and Verrucomicrobia existed in higher quantity in group A than in group B and Firmicutes were slightly higher in group A than in group B. Actinobacteria were higher in group B whereas Bacteroidetes dominated in group A than group B. The potential probiotic bacteria found in camel milk including Enterococcus faecalis, Enterococcus faecium, Propionibacterium, Streptococcus thermophilus, Solibacillus silvestris and Akkermansia muciniphila. Despite the probiotic bacteria some pathogenic microbes also resided in the studied samples, hence it is strongly recommended proper sterilization before consumption. This proposed research is to get an efficient microbial consortium of beneficial bacteria and their functional roles.}, } @article {pmid38089958, year = {2023}, author = {Li, X and Chen, C and Tong, L and Gao, Q and Chen, W and Zhou, G and Tong, Z and Wang, W}, title = {The Challenging Path to Diagnosing Extraintestinal Amoebiasis: A Case Report of an HIV-Infected Patient.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {7569-7574}, pmid = {38089958}, issn = {1178-6973}, abstract = {BACKGROUND: Amoebiasis, an infectious disease caused by the parasitic protozoan E. histolytica, is easily misdiagnosed due to its declining incidence and atypical symptoms.

CASE PRESENTATION: A 31-year-old male presented to the hospital with dyspnea and inability to lie flat. Imaging studies indicated a large amount of pleural effusion on the right side and multiple huge cysts in the liver. The patient underwent liver tumor resection surgery at another hospital due to suspected malignancy, but no evidence of relevant malignant tumors was found in the pathological examination. Subsequently, we performed metagenomic next-generation sequencing on the liver drainage fluid and obtained liver pathology slides from the hospital where the surgery was performed at that time. Both of them confirmed the diagnosis of amoebic infection. Empirical treatment with metronidazole was initiated before the diagnosis was confirmed, along with symptomatic treatments such as thoracic drainage and liver drainage. Eventually, the patient's condition improved and he was discharged smoothly.

CONCLUSION: In order to avoid misdiagnosis of amoebiasis, thoroughly inquiring about the patient's medical history, shifting perspectives and continuing investigating are necessary when one diagnostic approach proves ineffective. Besides, interdisciplinary collaboration and persistent efforts are crucial for accurate diagnosis.}, } @article {pmid38089957, year = {2023}, author = {Zhuang, S and Yu, X and Zhang, Y and Chen, X}, title = {A Case of Adult Epstein-Barr Virus-Associated Pneumonia with Multiple Cavitary Pulmonary Lesions Confirmed by Lung Biopsy mNGS: A Case Report.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {7507-7513}, pmid = {38089957}, issn = {1178-6973}, abstract = {BACKGROUND: EBV pneumonia with multiple cavitary pulmonary lesions is clinically rare. We analyzed the clinical characteristics, diagnosis and treatment, with an aim to enhance clinicians' awareness of this disease and reduce misdiagnosis and missed diagnoses.

CASE PRESENTATION: This paper presents A 59-year-old male patient's initial symptoms included fever, cough, sputum, and asthma. The pulmonary CT imaging demonstrated multiple patchy and ground glass consolidation in both lungs, partial cavitary formation, and subpleural mesh lattice changes in the lower lobe of both lungs. Further analysis, including bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) and CT-guided percutaneous lung biopsy mNGS, supported the diagnosis of EBV pneumonia. The patient was treated with acyclovir antiviral therapy for a week, resulting in symptom relief. Follow-up lung CT scans indicated interval reduction of inflammatory lesions, cavities, and interstitial changes. As the patient's condition improved significantly and he was discharged from hospital. The treatment was continued with oral acyclovir for 12 days. Subsequent outpatient follow-up CT performed 12 days after discharge revealed further improvement of the inflammatory lesions, as well as a reduction in cavitary and interstitial changes.

CONCLUSION: The clinical imaging findings in the presented case were highly distinctive and have not been documented in either domestic or international literature. This uniqueness could have potentially contributed to misdiagnosis or overlooked diagnosis. mNGS of percutaneous lung puncture tissue is valuable for the diagnosis of infection with rare lung pathogens.}, } @article {pmid38089944, year = {2023}, author = {Andreescu, M}, title = {Molecular Insights Into the Role of Gut Microbiota in Antibiotic Therapy Selection and Resistance Mitigation.}, journal = {Cureus}, volume = {15}, number = {12}, pages = {e50318}, pmid = {38089944}, issn = {2168-8184}, abstract = {Antibiotic therapy is a cornerstone of modern medicine, yet the development of antibiotic resistance threatens to render these therapies ineffective. The gut microbiota, a complex ecosystem of microorganisms residing in the gastrointestinal tract, plays a critical role in modulating antibiotic efficacy and resistance. This review delves into the intricate relationship between gut microbiota, antibiotic therapy, and resistance and discusses the potential applications of gut microbiota research in guiding personalized antibiotic therapy and resistance mitigation strategies. Recent advancements in metagenomics, metatranscriptomics, and metabolomics have demonstrated the potential for tailored antibiotic regimens that minimize collateral damage to commensal bacteria and reduce the risk of resistance. Adjuvant therapies, such as probiotics, prebiotics, and synbiotics, have shown promise in restoring gut microbial balance and mitigating the adverse effects of antibiotic therapy. We address the challenges associated with this emerging field, including the need for standardized methodologies, ethical considerations, and interdisciplinary collaboration. With continued interdisciplinary collaboration and the implementation of standardized methodologies, gut microbiota research can contribute to the global fight against antibiotic resistance and improve patient outcomes.}, } @article {pmid38089819, year = {2023}, author = {Huang, F and Wang, H and Qiao, R and Peng, Q and Zhao, C and Miao, L}, title = {Diagnostic accuracy and microbial profiles of tuberculous pleurisy: a comparative study of metagenomic next generation sequencing and GeneXpert Mycobacterium tuberculosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1243441}, pmid = {38089819}, issn = {2235-2988}, mesh = {Humans ; *Mycobacterium tuberculosis/genetics ; *Tuberculosis, Pleural/diagnosis/microbiology ; High-Throughput Nucleotide Sequencing ; Sensitivity and Specificity ; *Pleural Effusion ; }, abstract = {INTRODUCTION: There is a clinical challenge in diagnosing tuberculous pleurisy accurately and promptly, highlighting the urgent need for a rapid and sensitive diagnostic method. This study aimed to evaluate the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) and GeneXpert Mycobacterium tuberculosis (MTB) for identifying tuberculous pleurisy and analyzing the microbial profiles of both tuberculous and non-tuberculous pleural effusions.

METHODS: The study enrolled 31 patients with suspected tuberculous pleurisy, of which 15 were confirmed to have tuberculous pleurisy and subsequently allocated to the tuberculous pleurisy group (TP group), while the remaining 16 individuals were assigned to the non-tuberculous pleurisy group (NTP group). mNGS and GeneXpert MTB were performed on pleural effusion samples, and the diagnostic accuracy of both tests was compared. We employed established formulas to compute crucial indicators, including sensitivity, specificity, missed diagnosis rate, misdiagnosed rate, positive predictive value (PPV), and negative predictive value (NPV).

RESULTS: The results showed that both tests had high specificity (100%) and positive predictive value (100%) for detecting tuberculous pleurisy, along with comparable sensitivity (46.67% for mNGS and 40.0% for GeneXpert MTB). Further analysis of the combined efficacy of mNGS and GeneXpert MTB showed that the combined test had a sensitivity of 66.67% and a specificity of 100%. mNGS analysis revealed that MTB was detected in 7 out of 15 patients with tuberculous pleural effusions, while non-tuberculous pleural effusions were associated with a diverse range of microbial genera and species. The most frequently detected genera at the microbial genus level in the NTP group were Microbacterium spp. (6/16), Prevotella spp. (5/16), and Campylobacter spp. (5/16).

DISCUSSION: These findings suggest that mNGS and GeneXpert MTB are useful diagnostic tools for identifying patients with tuberculous pleurisy, and mNGS can provide valuable insights into the microbial profiles of both tuberculous and non-tuberculous pleural effusions.}, } @article {pmid38089712, year = {2023}, author = {Huang, J and Weng, H and Ye, L and Jiang, M and Li, Y and Li, H}, title = {Clinical Application and Evaluation of Metagenomic Next-Generation Sequencing for Lower Respiratory Tract Infections and Human Tumor Screening.}, journal = {International journal of general medicine}, volume = {16}, number = {}, pages = {5763-5777}, pmid = {38089712}, issn = {1178-7074}, abstract = {BACKGROUND: To evaluate the clinical value of metagenomic next-generation sequencing (mNGS) in screening of lower respiratory tract infections (LRTIs) and human tumors.

METHODS: Human samples included bronchoalveolar lavage fluid (BALF), sputum, lung biopsy tissue, and peripheral blood from 188 patients who were admitted to our hospital between January 2020 and September 2022 were analyzed using mNGS for simultaneous pathogen and chromosome copy number variation (CNV) detection. Traditional microbial culture and comprehensive microbial test (CMT) were also conducted. The diagnostic efficiencies of the three methods (mNGS, traditional culture, and CMT groups) were compared.

RESULTS: Among the 188 patients, 149 (79.3%) were in the LRTIs group and 39 (20.7%) were in the non-LRTIs group. The diagnostic sensitivity and accuracy of the mNGS group were higher than those of the traditional culture and CMT groups (P < 0.001; P < 0.001; P < 0.001; P < 0.001), and the specificity was higher than that of the CMT group (P = 0.039) but lower than that of the traditional culture group (P = 0.006). The positive predictive values of the mNGS and traditional culture groups were higher than that of the CMT group (P = 0.004; P = 0.011). The negative predictive value of the mNGS group was higher than that of the CMT group (P = 0.003). In addition, all samples were subjected to simultaneous chromosome CNV detection, and 8% (15/188) were positive for CNV. Of the 15 patients, 10 were initially misdiagnosed as non-neoplastic diseases, with a misdiagnosis rate of 66.7% (10/15). The BALF CNV test was performed on 13 patients diagnosed with primary or metastatic lung cancer, with a positivity rate of 38.5%.

CONCLUSION: The sensitivity and accuracy of pathogen diagnosis using mNGS were better than those of traditional culture and CMT. CNV detection is an important auxiliary diagnostic tool for cancer, particularly for screening occult tumors.}, } @article {pmid38089151, year = {2024}, author = {Abdullah, A and Nurhayati, T and Dwiyanti, FG and Sauqi, SDA}, title = {Sampling technique to pool genetic materials of microorganism communities in blue-swimming crab processing plant industry.}, journal = {MethodsX}, volume = {12}, number = {}, pages = {102503}, pmid = {38089151}, issn = {2215-0161}, abstract = {The crab and seafood processing industry must fulfill standard requirements for sanitation, hygiene, and good manufacturing methods to ensure the safety of the products and free from foodborne bacteria. However, equipment and processing unit surfaces are challenging to clean optimally, which can cause persistent bacteria to emerge. Eliminating persistent bacteria is the latest challenge in the fish processing industry for optimal disinfection, preventing cross-contamination, and controlling foodborne outbreaks. Microbiological testing in industry has been limited to selective culture-media techniques; thus, a rapid, sensitive, accurate, and routine applicable analytical method is urgently needed. The significant reduction in the costs of high-throughput sequencing technologies supports the possibility of routine applications in the industry. This study aimed to determine the profile of the microbial community on the surface of the production room and blue-swimming crab processing unit equipment using short-read metagenomic techniques. The analysis included the stages of sampling, bacterial incubation, bacterial DNA isolation, sequencing, and bioinformatics analysis. The first important step to increase the possibility of routine adoption in the seafood industry is to reduce the cost, complexity, and time required to complete the analysis. Therefore, in this protocol, we generate a scalable, flexible, cost-effective, and auditable workflow.•Collection of bacterial samples by swabbing the surface of the equipment using a sterile cotton swab and sterile cloth, which is easy to apply and follow in the blue-swimming crab processing plant industry.•Effective and efficient sample-pooling is an important step in identifying bacterial communities by metagenomic analysis.}, } @article {pmid38088974, year = {2023}, author = {Sood, U and Pandey, J and Patel, SKS and Verma, H}, title = {Editorial: Omics techniques in deciphering environmental, industrial and therapeutic applications of microbes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1327368}, doi = {10.3389/fmicb.2023.1327368}, pmid = {38088974}, issn = {1664-302X}, } @article {pmid38088971, year = {2023}, author = {Miklós, M and Cseri, K and Laczkó, L and Kardos, G and Fraune, S and Tökölyi, J}, title = {Environmental bacteria increase population growth of hydra at low temperature.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1294771}, pmid = {38088971}, issn = {1664-302X}, abstract = {Multicellular organisms engage in complex ecological interactions with microorganisms, some of which are harmful to the host's health and fitness (e.g., pathogens or toxin-producing environmental microbiota), while others are either beneficial or have a neutral impact (as seen in components of host-associated microbiota). Although environmental microorganisms are generally considered to have no significant impact on animal fitness, there is evidence suggesting that exposure to these microbes might be required for proper immune maturation and research in vertebrates has shown that developing in a sterile environment detrimentally impacts health later in life. However, it remains uncertain whether such beneficial effects of environmental microorganisms are present in invertebrates that lack an adaptive immune system. In the present study, we conducted an experiment with field-collected Hydra oligactis, a cold-adapted freshwater cnidarian. We cultured these organisms in normal and autoclaved lake water at two distinct temperatures: 8°C and 12°C. Our findings indicated that polyps maintained in sterilized lake water displayed reduced population growth that depended on temperature, such that the effect was only present on 8°C. To better understand the dynamics of microbial communities both inhabiting polyps and their surrounding environment we conducted 16S sequencing before and after treatment, analyzing samples from both the polyps and the water. As a result of culturing in autoclaved lake water, the polyps showed a slightly altered microbiota composition, with some microbial lineages showing significant reduction in abundance, while only a few displayed increased abundances. The autoclaved lake water was recolonized, likely from the surface of hydra polyps, by a complex albeit different community of bacteria, some of which (such as Pseudomonas, Flavobacteriaceae) might be pathogenic to hydra. The abundance of the intracellular symbiont Polynucleobacter was positively related to hydra population size. These findings indicate that at low temperature environmental microbiota can enhance population growth rate in hydra, suggesting that environmental microorganisms can provide benefits to animals even in the absence of an adaptive immune system.}, } @article {pmid38088959, year = {2023}, author = {Deng, H and Yu, Y and Sha, Q and Sun, W and Liang, L and Ren, F and Ji, H and Shen, X and Fan, X}, title = {Construction of antibiotic-induced depression mice model and the function of intestinal microbiota.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1093486}, pmid = {38088959}, issn = {1664-302X}, abstract = {Many research studies focus on intestinal microbiota-related depression induced by the usage of antibiotics, but the use of antibiotics is fairly different. To construct an effective antibiotic-induced depression mice model and explore the effect of intestinal microbiota in antibiotic-induced depression, we used several kinds of antibiotic mixtures to induce mice depression and used depression-related behavioral tests and neurobiological factors to evaluate the construction of the antibiotic-induced depression mice model. SPSS statistical software was used to analyze the above data, and the optimal model was selected according to the stability of the results and the simplicity of the modeling methods. Metagenomic analysis and fecal microbiota transplantation (FMT) of intestinal microbiota from antibiotic-induced depression mice were performed to analyze the effect of intestinal microbiota. The results showed that antibiotic mixture A (1.25 μg/mL natamycin, 5 mg/mL neomycin sulfate, and 5 mg/mL bacitracin), antibiotic mixture B (24 mg/mL bacitracin, 24 mg/mL neomycin sulfate, 9.6 mg/mL ampicillin, 4.8 mg/mL meropenem, and 1.47 mg/mL vancomycin), and antibiotic solution D (only containing 5 mg/mL neomycin sulfate) could induce depression-like behavior in mice. By using these antibiotics, the concentrations of norepinephrine (NE), 5-hydroxytryptamine (5-HT), and brain-derived neurotrophic factor (BDNF) in mice hippocampus and prefrontal cortex tissues were significantly decreased. All the above results were consistent with those of chronic unpredictable mild stress (CUMS) depression mice. The FMT results showed that fecal microbiota from antibiotic-induced depressed mice transplanted into normal mice (8 weeks-old male C57BL/6J SPF mice) also could induce depression-like behavior and cause similar changes in neurobiological factors. Metagenomic analysis showed that the community structure of microbiota in the intestinal tract of antibiotic-induced depression mice was significantly different from that in control mice, the intestinal microbiota species diversity in antibiotic-induced depression mice was lower, the lipoic acid metabolism pathway was significantly activated, and the abundance of functional gene lipA was explicitly increased. Quantitative real-time PCR (qPCR) further verified the abundance of enriched bacteria in the intestinal microbiota of antibiotic-induced depression mice. In summary, the specific antibiotic mixtures can induce depression by causing changes in intestinal microbiota in mice. Antibiotic-induced depressed mice show differences in intestinal microbiota abundance, high enrichment of the unique metabolic pathway, and the functional gene.}, } @article {pmid38087304, year = {2023}, author = {Kaur, S and Sharma, P and Mayer, MJ and Neuert, S and Narbad, A and Kaur, S}, title = {Beneficial effects of GABA-producing potential probiotic Limosilactobacillus fermentum L18 of human origin on intestinal permeability and human gut microbiota.}, journal = {Microbial cell factories}, volume = {22}, number = {1}, pages = {256}, pmid = {38087304}, issn = {1475-2859}, support = {42-478/2013 SR//University Grants Commission (UGC), New Delhi, India/ ; Institute Strategic Programmes Gut Microbes and Health (BB/R012490/1 Theme 3 BBS/E/F/000PR10356)//UK Biotechnology and Biological Sciences Research Council (BBSRC)/ ; Institute Strategic Programmes Gut Microbes and Health (BB/R012490/1 Theme 3 BBS/E/F/000PR10356)//UK Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Humans ; *Limosilactobacillus fermentum ; Caco-2 Cells ; Lipopolysaccharides ; *Gastrointestinal Microbiome ; Intestinal Barrier Function ; Bacteria/metabolism ; *Probiotics/therapeutic use ; }, abstract = {BACKGROUND: Gamma-aminobutyric acid (GABA) is a non-protein amino acid with neuroinhibitory, antidiabetic, and antihypertensive properties and is used as a drug for treating anxiety and depression. Some strains of lactobacilli are known to produce GABA and strengthen the gut barrier function which play an important role in ameliorating the effects caused by the pathogen on the gut barrier. The probiotic bacteria are also known to modulate the human fecal microbiota, however, the role of GABA-producing strains on the gut epithelium permeability and gut microbiota is not known.

RESULTS: In this study, we report the production of high levels of GABA by potential probiotic bacterium Limosilactobacillus fermentum L18 for the first time. The kinetics of the production of GABA by L18 showed that the maximum production of GABA in the culture supernatant (CS) occurred at 24 h, whereas in fermented milk it took 48 h of fermentation. The effect of L18 on the restoration of lipopolysaccharide (LPS)-disrupted intestinal cell membrane permeability in Caco-2 monolayers showed that it significantly restored the transepithelial electrical resistance (TEER) values, by significantly increasing the levels of junction proteins, occludin and E-cadherin in L18 and LPS-treated Caco-2 cells as compared to only LPS-treated cells. The effect of GABA-secreting L18 on the metataxonome of human stool samples from healthy individuals was investigated by a batch fermentor that mimics the conditions of the human colon. Although, no differences were observed in the α and β diversities of the L18-treated and untreated samples at 24 h, the relative abundances of bacterial families Lactobacillaceae and Bifidobacteriaceae increased in the L18-treated group, but both decreased in the untreated groups. On the other hand, the relative abundance of Enterobacteriaceae decreased in the L18 samples but it increased in the untreated samples.

CONCLUSION: These results indicate that Li. fermentum L18 is a promising GABA-secreting strain that strengthens the gut epithelial barrier by increasing junction protein concentrations and positively modulating the gut microbiota. It has the potential to be used as a psychobiotic or for the production of functional foods for the management of anxiety-related illnesses.}, } @article {pmid38087204, year = {2023}, author = {Mouratidis, I and Chantzi, N and Khan, U and Konnaris, MA and Chan, CSY and Mareboina, M and Moeckel, C and Georgakopoulos-Soares, I}, title = {Frequentmers - a novel way to look at metagenomic next generation sequencing data and an application in detecting liver cirrhosis.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {768}, pmid = {38087204}, issn = {1471-2164}, support = {T32 GM067547/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Liver Cirrhosis/diagnosis/genetics ; Health Status ; Metagenome ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {Early detection of human disease is associated with improved clinical outcomes. However, many diseases are often detected at an advanced, symptomatic stage where patients are past efficacious treatment periods and can result in less favorable outcomes. Therefore, methods that can accurately detect human disease at a presymptomatic stage are urgently needed. Here, we introduce "frequentmers"; short sequences that are specific and recurrently observed in either patient or healthy control samples, but not in both. We showcase the utility of frequentmers for the detection of liver cirrhosis using metagenomic Next Generation Sequencing data from stool samples of patients and controls. We develop classification models for the detection of liver cirrhosis and achieve an AUC score of 0.91 using ten-fold cross-validation. A small subset of 200 frequentmers can achieve comparable results in detecting liver cirrhosis. Finally, we identify the microbial organisms in liver cirrhosis samples, which are associated with the most predictive frequentmer biomarkers.}, } @article {pmid38086977, year = {2023}, author = {Ryu, SW and Moon, JC and Oh, BS and Yu, SY and Bak, JE and Heo, ES and Jeong, JH and Lee, JH}, title = {Anti-obesity activity of human gut microbiota Bacteroides stercoris KGMB02265.}, journal = {Archives of microbiology}, volume = {206}, number = {1}, pages = {19}, pmid = {38086977}, issn = {1432-072X}, support = {NRF-2016M3A9F3947962 and NRF-2019M3A9F3065226//Bio & Medical Technology Development program of the National Research Foundation of Korea/ ; KGM5232322//Korea Research Institute of Bioscience & Biotechnology (KRIBB) Research initiative program/ ; }, mesh = {Humans ; Mice ; Animals ; *Diabetes Mellitus, Type 2/complications ; *Gastrointestinal Microbiome ; Obesity ; Bacteroides/genetics ; Mice, Inbred C57BL ; }, abstract = {Obesity is a global health threat that causes various complications such as type 2 diabetes and nonalcoholic fatty liver disease. Gut microbiota is closely related to obesity. In particular, a higher Firmicutes to Bacteroidetes ratio has been reported as a biomarker of obesity, suggesting that the phylum Bacteroidetes may play a role in inhibiting obesity. Indeed, the genus Bacteroides was enriched in the healthy subjects based on metagenome analysis. In this study, we determined the effects of Bacteroides stercoris KGMB02265, a species belonging to the phylum Bacteroidetes, on obesity both in vitro and in vivo. The cell-free supernatant of B. stercoris KGMB02265 inhibited lipid accumulation in 3T3-L1 preadipocytes, in which the expression of adipogenic marker genes was repressed. In vivo study showed that the oral administration of B. stercoris KGMB02265 substantially reduced body weight and fat weight in high-fat diet induced obesity in mice. Furthermore, obese mice orally administered with B. stercoris KGMB02265 restored glucose sensitivity and reduced leptin and triglyceride levels. Taken together, our study reveals that B. stercoris KGMB02265 has anti-obesity activity and suggests that it may be a promising candidate for treating obesity.}, } @article {pmid38086912, year = {2023}, author = {Satari, L and Torrent, D and Ortega-Legarreta, A and Latorre-Pérez, A and Pascual, J and Porcar, M and Iglesias, A}, title = {A laboratory ice machine as a cold oligotrophic artificial microbial niche for biodiscovery.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22089}, pmid = {38086912}, issn = {2045-2322}, support = {820699//European CSA on biological standardization BIOROBOOST/ ; ID101000470//European Union's Horizon 2020 research and innovation program/ ; DI-17-09613//Ministerio de Ciencia, Innovación y Universidades/ ; RTI2018-095584-B-C41-42-43-44//Spanish Government/ ; BIO2015-66960-C3-1-R//Helios project/ ; PCI2019-111845-2//Programación Conjunta Internacional 2019, AEI/ ; }, mesh = {*Ice ; RNA, Ribosomal, 16S/genetics/metabolism ; *Extracellular Polymeric Substance Matrix ; Bacteria ; Metagenome ; }, abstract = {Microorganisms are ubiquitously distributed in nature and usually appear as biofilms attached to a variety of surfaces. Here, we report the development of a thick biofilm in the drain pipe of several standard laboratory ice machines, and we describe and characterise, through culture-dependent and -independent techniques, the composition of this oligotrophic microbial community. By using culturomics, 25 different microbial strains were isolated and taxonomically identified. The 16S rRNA high-throughput sequencing analysis revealed that Bacteroidota and Proteobacteria were the most abundant bacterial phyla in the sample, followed by Acidobacteriota and Planctomycetota, while ITS high-throughput sequencing uncovered the fungal community was clearly dominated by the presence of a yet-unidentified genus from the Didymellaceae family. Alpha and beta diversity comparisons of the ice machine microbial community against that of other similar cold oligotrophic and/or artificial environments revealed a low similarity between samples, highlighting the ice machine could be considered a cold and oligotrophic niche with a unique selective pressure for colonisation of particular microorganisms. The recovery and analysis of high-quality metagenome-assembled genomes (MAGs) yielded a strikingly high rate of new species. The functional profiling of the metagenome sequences uncovered the presence of proteins involved in extracellular polymeric substance (EPS) and fimbriae biosynthesis and also allowed us to detect the key proteins involved in the cold adaptation mechanisms and oligotrophic metabolic pathways. The metabolic functions in the recovered MAGs confirmed that all MAGs have the genes involved in psychrophilic protein biosynthesis. In addition, the highest number of genes for EPS biosynthesis was presented in MAGs associated with the genus Sphingomonas, which was also recovered by culture-based method. Further, the MAGs with the highest potential gene number for oligotrophic protein production were closely affiliated with the genera Chryseoglobus and Mycobacterium. Our results reveal the surprising potential of a cold oligotrophic microecosystem within a machine as a source of new microbial taxa and provide the scientific community with clues about which microorganisms are able to colonise this ecological niche and what physiological mechanisms they develop. These results pave the way to understand how and why certain microorganisms can colonise similar anthropogenic environments.}, } @article {pmid38086841, year = {2023}, author = {Gómez, M and Martínez, D and Páez-Triana, L and Luna, N and De Las Salas, JL and Hernández, C and Flórez, AZ and Muñoz, M and Ramírez, JD}, title = {Characterizing viral species in mosquitoes (Culicidae) in the Colombian Orinoco: insights from a preliminary metagenomic study.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {22081}, pmid = {38086841}, issn = {2045-2322}, support = {Internal funds//Universidad del Rosario,Colombia/ ; }, mesh = {Animals ; Humans ; *Culicidae ; Colombia ; *Aedes ; Ecosystem ; *Culex ; *Arboviruses/genetics ; *Viruses ; *Insect Viruses ; }, abstract = {Mosquitoes (Diptera: Culicidae) are primary vectors of arthropod-borne viruses (arboviruses) that pose significant public health threats. Recent advances in sequencing technology emphasize the importance of understanding the arboviruses and insect-specific viruses (ISVs) hosted by mosquitoes, collectively called the "virome". Colombia, a tropical country with favorable conditions for the development and adaptation of multiple species of Culicidae, offers a favorable scenario for the transmission of epidemiologically important arboviruses. However, entomovirological surveillance studies are scarce in rural areas of the country, where humans, mosquitoes, and animals (both domestic and wild) coexist, leading to a higher risk of transmission of zoonotic diseases to humans. Thus, our study aimed to perform a preliminary metagenomic analysis of the mosquitoes of special relevance to public health belonging to the genera Ochlerotatus, Culex, Limatus, Mansonia, Psorophora, and Sabethes, within a rural savanna ecosystem in the Colombian Orinoco. We employed third-generation sequencing technology (Oxford Nanopore Technologies; ONT) to describe the virome of mosquitoes samples. Our results revealed that the virome was primarily shaped by insect-specific viruses (ISVs), with the Iflaviridae family being the most prevalent across all mosquito samples. Furthermore, we identified a group of ISVs that were common in all mosquito species tested, displaying the highest relative abundance concerning other groups of viruses. Notably, Hanko iflavirus-1 was especially prevalent in Culex eknomios (88.4%) and Ochlerotatus serratus (88.0%). Additionally, other ISVs, such as Guadalupe mosquito virus (GMV), Hubei mosquito virus1 (HMV1), Uxmal virus, Tanay virus, Cordoba virus, and Castlerea virus (all belonging to the Negevirus genus), were found as common viral species among the mosquitoes, although in lower proportions. These initial findings contribute to our understanding of ISVs within mosquito vectors of the Culicidae family in the Eastern Plains of Colombia. We recommend that future research explore deeper into ISV species shared among diverse vector species, and their potential interactions with arboviruses. In addition, we also showed the need for a thorough exploration of the influence of local rural habitat conditions on the shape of the virome in mosquito vectors.}, } @article {pmid38086813, year = {2023}, author = {Saghaï, A and Pold, G and Jones, CM and Hallin, S}, title = {Phyloecology of nitrate ammonifiers and their importance relative to denitrifiers in global terrestrial biomes.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {8249}, pmid = {38086813}, issn = {2041-1723}, support = {2019-00392//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/ ; }, mesh = {*Nitrates/pharmacology ; *Bacteria/genetics ; Nitrite Reductases/genetics/pharmacology ; Soil ; Ecosystem ; Nitrogen/pharmacology ; Denitrification ; Soil Microbiology ; }, abstract = {Nitrate ammonification is important for soil nitrogen retention. However, the ecology of ammonifiers and their prevalence compared with denitrifiers, being competitors for nitrate, are overlooked. Here, we screen 1 million genomes for nrfA and onr, encoding ammonifier nitrite reductases. About 40% of ammonifier assemblies carry at least one denitrification gene and show higher potential for nitrous oxide production than consumption. We then use a phylogeny-based approach to recruit gene fragments of nrfA, onr and denitrification nitrite reductase genes (nirK, nirS) in 1861 global terrestrial metagenomes. nrfA outnumbers the nearly negligible onr counts in all biomes, but denitrification genes dominate, except in tundra. Random forest modelling teases apart the influence of the soil C/N on nrfA-ammonifier vs denitrifier abundance, showing an effect of nitrate rather than carbon content. This study demonstrates the multiple roles nitrate ammonifiers play in nitrogen cycling and identifies factors ultimately controlling the fate of soil nitrate.}, } @article {pmid38086476, year = {2023}, author = {Zhang, M and Zhao, B and Yan, Y and Cheng, Z and Li, Z and Han, L and Sun, Y and Zheng, Y and Xia, Y}, title = {Comamonas-dominant microbial community in carbon poor aquitard sediments revealed by metagenomic-based growth rate investigation.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169203}, doi = {10.1016/j.scitotenv.2023.169203}, pmid = {38086476}, issn = {1879-1026}, abstract = {The microbiological ecology of a low-nutrient shallow aquifer with high arsenic content in the Yinchuan Plain was investigated in this study. Amplicon sequencing data from five samples (depths: 1.5 m, 3.5 m, 11.2 m, 19.3 m, and 25.5 m) revealed diverse and adaptable microbial community. Among the microbial community, Comamonas was the most prominent, accounting for 10.52 % of the total. This genus displayed high growth rates, with a maximum growth rate of 12.06 d[-1] and a corresponding doubling time of 1.38 days, as determined through an analysis of codon usage bias. Functional annotation of Metagenome-Assembled Genomes (MAGs) for samples at 1.5 m and 11.2 m depths revealed Comamonas' metabolic versatility, including various carbon pathways, assimilative sulfate reduction (ASR), and dissimilatory reduction to ammonium (DNRA). The TPM (Transcripts Per Kilobase of exon model per Million mapped reads) of MAGs at 11.2 m sample was 15.7 and 12.3. The presence of arsenic resistance genes in Comamonas aligns with sediment arsenic levels (65.8 mg/kg for 1.5 m depth, 32.8 mg/kg for 11.2 m depth). This study highlights the role of Comamonas as a 'generalist' bacteria in challenging oligotrophic sediments, emphasizing the significance of such organisms in community stability and ecological functions. ENVIRONMENTAL IMPLICATION: Low-biomass limits the microbial activity and biogeochemical study in oligotrophic environments, which is the typical condition for underground aquatic ecosystems. Facilitated by growth rate estimation, our research focuses on active functional microorganisms and their biogeochemical metabolic in oligotrophic aquifer sediments, revealing their impact on the environment and response to arsenic threats. Findings illuminate the metabolic advantage of a 'generalist life-style' in carbon-scarce environments and contribute to a broader understanding of bacterial ecosystems and environmental impacts in oligotrophic aquifer sediments worldwide.}, } @article {pmid38086007, year = {2024}, author = {Wang, Y and Sharma, A and Weber, KM and Topper, E and Appleton, AA and Gustafson, D and Clish, CB and Kaplan, RC and Burk, RD and Qi, Q and Peters, BA}, title = {The menopause-related gut microbiome: associations with metabolomics, inflammatory protein markers, and cardiometabolic health in women with HIV.}, journal = {Menopause (New York, N.Y.)}, volume = {31}, number = {1}, pages = {52-64}, pmid = {38086007}, issn = {1530-0374}, support = {R01 HL140976/HL/NHLBI NIH HHS/United States ; U01 HL146202/HL/NHLBI NIH HHS/United States ; }, mesh = {Female ; Humans ; Male ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; Menopause ; *HIV Infections/complications ; *Cardiovascular Diseases ; }, abstract = {OBJECTIVE: This study aimed to identify menopause-related gut microbial features, as well as their related metabolites and inflammatory protein markers, and link with cardiometabolic risk factors in women with and without HIV.

METHODS: In the Women's Interagency HIV Study, we performed shotgun metagenomic sequencing on 696 stool samples from 446 participants (67% women with HIV), and quantified plasma metabolomics and serum proteomics in a subset (~86%). We examined the associations of menopause (postmenopausal vs premenopausal) with gut microbial features in a cross-sectional repeated-measures design and further evaluated those features in relation to metabolites, proteins, and cardiometabolic risk factors.

RESULTS: Different overall gut microbial composition was observed by menopausal status in women with HIV only. We identified a range of gut microbial features that differed between postmenopausal and premenopausal women with HIV (but none in women without HIV), including abundance of 32 species and functional potentials involving 24 enzymatic reactions and lower β-glucuronidase bacterial gene ortholog. Specifically, highly abundant species Faecalibacterium prausnitzii , Bacteroides species CAG:98 , and Bifidobacterium adolescentis were depleted in postmenopausal versus premenopausal women with HIV. Menopause-depleted species (mainly Clostridia) in women with HIV were positively associated with several glycerophospholipids, while negatively associated with imidazolepropionic acid and fibroblast growth factor 21. Mediation analysis suggested that menopause may decrease plasma phosphatidylcholine plasmalogen C36:1 and C36:2 levels via reducing abundance of species F. prausnitzii and Acetanaerobacterium elongatum in women with HIV. Furthermore, waist-to-hip ratio was associated with menopause-related microbes, metabolites, and fibroblast growth factor 21 in women with HIV.

CONCLUSIONS: Menopause was associated with a differential gut microbiome in women with HIV, related to metabolite and protein profiles that potentially contribute to elevated cardiometabolic risk.}, } @article {pmid38085930, year = {2023}, author = {Alsanea, A and Bounaga, A and Danouche, M and Lyamlouli, K and Zeroual, Y and Boulif, R and Zhou, C and Rittmann, B}, title = {Optimizing Autotrophic Sulfide Oxidation in the Oxygen-Based Membrane Biofilm Reactor to Recover Elemental Sulfur.}, journal = {Environmental science & technology}, volume = {57}, number = {51}, pages = {21736-21743}, doi = {10.1021/acs.est.3c05785}, pmid = {38085930}, issn = {1520-5851}, mesh = {*Oxygen ; *Bioreactors ; Oxidation-Reduction ; Sulfur ; Biofilms ; Sulfides ; Denitrification ; }, abstract = {Biological sulfide oxidation is an efficient means to recover elemental sulfur (S[0]) as a valuable resource from sulfide-bearing wastewater. This work evaluated the autotrophic sulfide oxidation to S[0] in the O2-based membrane biofilm reactor (O2-MBfR). High recovery of S[0] (80-90% of influent S) and high sulfide oxidation (∼100%) were simultaneously achieved when the ratio of O2-delivery capacity to sulfide-to S[0] surface loading (SL) (O2/S[2-] → S[0] ratio) was around 1.5 (g O2/m[2]-day/g O2/m[2]-day). On average, most of the produced S[0] was recovered in the MBfR effluent, although the biofilm could be a source or sink for S[0]. Shallow metagenomic analysis of the biofilm showed that the top sulfide-oxidizing genera present in all stages were Thauera, Thiomonas, Thauera_A, and Pseudomonas. Thiomonas or Pseudomonas was the most important genus in stages that produced almost only S[0] (i.e., the O2/S[2-] → S[0] ratio around 1.5 g of the O2/m[2]-day/g O2/m[2]-day). With a lower sulfide SL, the S[0]-producing genes were sqr and fccAB in Thiomonas. With a higher sulfide SL, the S[0]-producing genes were in the soxABDXYZ system in Pseudomonas. Thus, the biofilm community of the O2-MBfR adapted to different sulfide-to-S[0] SLs and corresponding O2-delivery capacities. The results illustrate the potential for S[0] recovery using the O2-MBfR.}, } @article {pmid38085234, year = {2023}, author = {Liao, H and Shang, J and Sun, Y}, title = {GDmicro: classifying host disease status with GCN and deep adaptation network based on the human gut microbiome data.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {12}, pages = {}, pmid = {38085234}, issn = {1367-4811}, support = {9678241//City University of Hong Kong/ ; //Hong Kong Innovation and Technology Commission/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Metagenome ; *Inflammatory Bowel Diseases ; Biomarkers ; }, abstract = {MOTIVATION: With advances in metagenomic sequencing technologies, there are accumulating studies revealing the associations between the human gut microbiome and some human diseases. These associations shed light on using gut microbiome data to distinguish case and control samples of a specific disease, which is also called host disease status classification. Importantly, using learning-based models to distinguish the disease and control samples is expected to identify important biomarkers more accurately than abundance-based statistical analysis. However, available tools have not fully addressed two challenges associated with this task: limited labeled microbiome data and decreased accuracy in cross-studies. The confounding factors, such as the diet, technical biases in sample collection/sequencing across different studies/cohorts often jeopardize the generalization of the learning model.

RESULTS: To address these challenges, we develop a new tool GDmicro, which combines semi-supervised learning and domain adaptation to achieve a more generalized model using limited labeled samples. We evaluated GDmicro on human gut microbiome data from 11 cohorts covering 5 different diseases. The results show that GDmicro has better performance and robustness than state-of-the-art tools. In particular, it improves the AUC from 0.783 to 0.949 in identifying inflammatory bowel disease. Furthermore, GDmicro can identify potential biomarkers with greater accuracy than abundance-based statistical analysis methods. It also reveals the contribution of these biomarkers to the host's disease status.

https://github.com/liaoherui/GDmicro.}, } @article {pmid38084973, year = {2024}, author = {Thorn, AV and Aarestrup, FM and Munk, P}, title = {Flankophile: a bioinformatic pipeline for prokaryotic genomic synteny analysis.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0241323}, pmid = {38084973}, issn = {2165-0497}, support = {NNF16OC0021856//Novo Nordisk Foundation/ ; 874735//European Union's Horizon 2020 research and innovation programme/ ; }, mesh = {Humans ; Synteny ; *Genomics ; *Computational Biology ; Genome ; Prokaryotic Cells ; }, abstract = {The Flankophile pipeline enables the analysis and visualization of flanking regions of prokaryotic sequences of interest on large data sets in one step and in a consistent manner. A specific tool for flanking region analysis with automated visualization has not been developed before, and Flankophile will make flanking region analysis easier and accessible to more people. Flankophile will be especially useful in the field of genomic epidemiology of acquired antimicrobial resistance genes. Here, information from flanking region sequences can be instrumental in rejecting or supporting the possibility of a recent common source of the same resistance gene found in different samples.}, } @article {pmid38084800, year = {2023}, author = {Song, J and Lin, S and Zhu, L and Lin, Y and An, W and Zhang, J and Wang, H and Yang, Z and Liao, Y and Xu, Y and Li, Q}, title = {Direct identification of pathogens via microbial cellular DNA in whole blood by MeltArray.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.14380}, pmid = {38084800}, issn = {1751-7915}, support = {2021YFC1200200//National Key Research and Development Program of China/ ; 2021Y4001//The Industry-University-Research Joint Innovation Project of Fujian Universities/ ; 2022CXY0113//Xiamen Industry-University-Research Project Subsidy Project/ ; 3502Z20231025//Xiamen Major Science and Technology Project/ ; }, abstract = {Rapid identification of pathogens is critical for early and appropriate treatment of bloodstream infections. The various culture-independent assays that have been developed often have long turnaround times, low sensitivity and narrow pathogen coverage. Here, we propose a new multiplex PCR assay, MeltArray, which uses intact microbial cells as the source of genomic DNA (gDNA). The successive steps of the MeltArray assay, including selective lysis of human cells, microbial cell sedimentation, microbial cellular DNA extraction, target-specific pre-amplification and multiplex PCR detection, allowed the detection of 35 major bloodstream infectious pathogens in whole blood within 5.5 h. The limits of detection varied depending on the pathogen and ranged from 1 to 5 CFU/mL. Of 443 blood culture samples, including 373 positive blood culture samples and 70 negative blood culture samples, the MeltArray assay showed a sensitivity of 93.8% (350/373, 95% confidence interval [CI] = 90.7%-96.0%), specificity of 98.6% (69/70, 95% CI = 91.2%-99.9%), positive predictive value of 99.7% (95% CI = 98.1%-99.9%), and negative predictive value of 75.0% (95% CI = 64.7%-83.2%). The MeltArray detection results of 16 samples differed from MALDI-TOF and were confirmed by Sanger sequencing. Further testing of 110 whole blood samples from patients with suspected bloodstream infections using blood culture results revealed that the MeltArray assay had a clinical sensitivity of 100% (9/9, 95% CI = 62.8%-100.0%), clinical specificity of 74.5% (70/94, 95% CI = 64.2%-82.7%), positive predictive value of 27.3% (95% CI = 13.9%-45.8%), and negative predictive value of 100.0% (95% CI = 93.5%-100.0%). Compared with metagenomic next-generation sequencing, the MeltArray assay displayed a positive agreement of 85.7% (6/7, 95% CI = 42.0%-99.2%) and negative agreement of 100.0% (4/4, 95% CI = 39.6%-100.0%). We conclude that the MeltArray assay can be used as a rapid and reliable tool for direct identification of pathogens in bloodstream infections.}, } @article {pmid38084697, year = {2023}, author = {Fu, C and Wen, R and Zhou, J and Hu, J and Liu, X}, title = {A Case of Fetal Familial Hemophagocytic Lymphohistiocytosis Type 5 caused by STXBP2 Gene Mutation.}, journal = {Clinical laboratory}, volume = {69}, number = {12}, pages = {}, doi = {10.7754/Clin.Lab.2023.230648}, pmid = {38084697}, issn = {1433-6510}, mesh = {Infant, Newborn ; Humans ; *Lymphohistiocytosis, Hemophagocytic/diagnosis/genetics ; Homozygote ; Sequence Deletion ; Mutation ; Munc18 Proteins/genetics ; }, abstract = {BACKGROUND: Familial hemophagocytic lymphohistiocytosis type 5 (FHL-5) is a rare hyper-inflammatory syndrome caused by mutations in STXBP2. Most cases present at 2 - 6 months of age, and FHL-5 is extremely rare in neonates.

METHODS: Appropriate laboratory tests, abdominal ultrasonography and whole exome sequencing were carried out. Respiratory support, antibiotics, and transfusion of blood products were done.

RESULTS: Laboratory tests revealed metabolic acidosis, thrombocytopenia, mild anemia, and low fibrinogen level. Blood culture, metagenomics, and TORCH screening were negative. Liver and spleen enlargements were confirmed by abdominal ultrasonography. Whole exome sequencing identified a homozygous mutation in STXBP2 c. 1432del G (p. V478Sfs*5). The heterozygous STXBP2 mutation was identified in the paternal grandfather, maternal grandfather, and parents.

CONCLUSIONS: Here we report a case with a novel homozygous deletion in exon 16 of STXBP2, which caused the earliest reported case of FHL-5 in a neonate. Our results identify a new pathogenic variant for the early identification and clinical consultation of FHL-5.}, } @article {pmid38082336, year = {2023}, author = {Ekhlas, D and Cobo Díaz, JF and Cabrera-Rubio, R and Alexa, E and Ortiz Sanjuán, JM and Garcia Manzanilla, E and Crispie, F and Cotter, PD and Leonard, FC and Argüello, H and Burgess, CM}, title = {Metagenomic comparison of the faecal and environmental resistome on Irish commercial pig farms with and without zinc oxide and antimicrobial usage.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {62}, pmid = {38082336}, issn = {2524-4671}, support = {2018027//Teagasc/ ; }, abstract = {BACKGROUND: Antimicrobials and heavy metals such as zinc oxide (ZnO) have been commonly used on Irish commercial pig farms for a 2-week period post-weaning to help prevent infection. In 2022, the prophylactic use of antimicrobials and ZnO was banned within the European Union due to concerns associated with the emergence of antimicrobial resistance (AMR) and contamination of the environment with heavy metals. In this study, faecal and environmental samples were taken from piglets during the weaning period from ten commercial farms, of which five farms used antimicrobial or ZnO prophylaxis (AB-ZnO farms) and five which had not used antimicrobials or ZnO for the previous 3 years (AB-ZnO free farms). A total of 50 samples were compared using a metagenomic approach.

RESULTS: The results of this study showed some significant differences between AB-ZnO and AB-ZnO free farms and suggested positive selection for AMR under antimicrobial and ZnO treatment. Moreover, strong differences between environmental and faecal samples on farms were observed, suggesting that the microbiome and its associated mobile genetic elements may play a key role in the composition of the resistome. Additionally, the age of piglets affected the resistome composition, potentially associated with changes in the microbiome post-weaning.

CONCLUSIONS: Overall, our study showed few differences in the resistome of the pig and its environment when comparing AB-ZnO farms with AB-ZnO free farms. These results suggest that although 3 years of removal of in-feed antimicrobial and ZnO may allow a reduction of AMR prevalence on AB-ZnO farms, more time, repeated sampling and a greater understanding of factors impacting AMR prevalence will be required to ensure significant and persistent change in on-farm AMR.}, } @article {pmid38082149, year = {2024}, author = {Jiang, K and Li, W and Tong, M and Xu, J and Chen, Z and Yang, Y and Zang, Y and Jiao, X and Liu, C and Lim, B and Jiang, X and Wang, J and Wu, D and Wang, M and Liu, SJ and Shao, F and Gao, X}, title = {Bacteroides fragilis ubiquitin homologue drives intraspecies bacterial competition in the gut microbiome.}, journal = {Nature microbiology}, volume = {9}, number = {1}, pages = {70-84}, pmid = {38082149}, issn = {2058-5276}, support = {32122007//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Humans ; Animals ; Mice ; Bacteroides fragilis/genetics ; *Gastrointestinal Microbiome ; Ubiquitin/metabolism ; Bacteria/metabolism ; *Bacterial Infections ; Peptidylprolyl Isomerase/metabolism ; }, abstract = {Interbacterial antagonism and associated defensive strategies are both essential during bacterial competition. The human gut symbiont Bacteroides fragilis secretes a ubiquitin homologue (BfUbb) that is toxic to a subset of B. fragilis strains in vitro. In the present study, we demonstrate that BfUbb lyses certain B. fragilis strains by non-covalently binding and inactivating an essential peptidyl-prolyl isomerase (PPIase). BfUbb-sensitivity profiling of B. fragilis strains revealed a key tyrosine residue (Tyr119) in the PPIase and strains that encode a glutamic acid residue at Tyr119 are resistant to BfUbb. Crystal structural analysis and functional studies of BfUbb and the BfUbb-PPIase complex uncover a unique disulfide bond at the carboxy terminus of BfUbb to mediate the interaction with Tyr119 of the PPIase. In vitro coculture assays and mouse studies show that BfUbb confers a competitive advantage for encoding strains and this is further supported by human gut metagenome analyses. Our findings reveal a previously undescribed mechanism of bacterial intraspecies competition.}, } @article {pmid38082111, year = {2023}, author = {Bellas, CM and Campbell, K and Tranter, M and Sánchez-Baracaldo, P}, title = {Nitrogen and sulfur metabolisms encoded in prokaryotic communities associated with sea ice algae.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {131}, pmid = {38082111}, issn = {2730-6151}, support = {FWF P-34620//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; NE/R012849/1; 03F0810A//RCUK | Natural Environment Research Council (NERC)/ ; 325405//Norges Forskningsråd (Research Council of Norway)/ ; }, abstract = {Sea ice habitats harbour seasonally abundant microalgal communities, which can be highly productive in the spring when the availability of light increases. An active, bloom-associated prokaryotic community relies on these microalgae for their organic carbon requirements, however an analysis of the encoded metabolic pathways within them is lacking. Hence, our understanding of biogeochemical cycling within sea ice remains incomplete. Here, we generated metagenomic assembled genomes from the bottom of first-year sea ice in northwestern Hudson Bay, during a spring diatom bloom. We show that the prokaryotic community had the metabolic potential to degrade algal derived dimethylsulphoniopropionate and oxidise sulfur. Facultative anaerobic metabolisms, specifically, dissimilatory nitrate reduction and denitrification were also prevalent here, suggesting some sea ice prokaryotes are metabolically capable of adapting to fluctuating oxygen levels during algal bloom conditions. Such denitrification could be an important loss of fixed-N2 in the changing Arctic marine system.}, } @article {pmid38081548, year = {2023}, author = {Wan, S and Zhou, A and Chen, R and Fang, S and Lu, J and Lv, N and Wang, C and Gao, J and Li, J and Wu, W}, title = {Metagenomics Next-Generation Sequencing (mNGS) Reveals Emerging Infection Induced by Klebsiella pneumoniae.}, journal = {International journal of antimicrobial agents}, volume = {63}, number = {2}, pages = {107056}, doi = {10.1016/j.ijantimicag.2023.107056}, pmid = {38081548}, issn = {1872-7913}, abstract = {OBJECTIVES: The increasing emergence of hypervirulent Klebsiella pneumoniae (hv-Kp) and carbapenem-resistant K. pneumoniae (CR-Kp) is a serious and substantial public health problem. The use of the last resort antimicrobials, tigecycline and polymyxin to combat infections is complicated by the expanding repertoire of newly-identified CR-hvKp. The transmission and co-occurrence of the corresponding antimicrobial resistance and virulence determinants are largely unknown. The aim of this study was to investigate the dissemination and dynamics of CR-Kp and its antibiotic resistance in a hospitalised patient.

METHODS: Metagenomic next-generation sequencing (mNGS) was conducted for different specimens collected from an elderly male hospitalised patient. CR-Kp strains were examined using antibiotic susceptibility and string testing. Antimicrobial and virulence genes were annotated using whole-genome sequencing (WGS).

RESULTS: A clinical case of a patient infected with a variety of CR-Kp isolates was reported. The co-occurrence of KPC-2 and NDM-1 in the patient was revealed. The CR-Kp isolates, such as BALF2, and Sputum T1 and T3, were classified into ST11 and ST147, respectively. The genetic signature (iuc operon) of hypervirulence was identified in strain T1, although string testing indicated its intermediate virulence.

CONCLUSIONS: In this study, multiple infections of CR-Kp isolates were revealed by mNGS, and their dissemination was attributed to plasmid variations, mgrB inactivation and integrative conjugative elements (ICEs). Furthermore, the finding indicated one likely convergence to form CR-hvKp, different from acquisition of carbapenem-resistance determinants in hvKp. A combination of mNGS and WGS is beneficial for clinical diagnosis and anti-infection therapy, and facilitates a better understanding of genetic variants conferring antimicrobial and virulence properties.}, } @article {pmid38081470, year = {2023}, author = {Cai, R and Li, R and Cao, X and Xu, C}, title = {Available sulfur and phosphorus transformation mechanism and functional microorganisms during sheep manure composting on Qinghai-Tibet Plateau under two moisture contents.}, journal = {Bioresource technology}, volume = {394}, number = {}, pages = {130191}, doi = {10.1016/j.biortech.2023.130191}, pmid = {38081470}, issn = {1873-2976}, abstract = {Understanding the mechanisms of sulfur and phosphorus transformation during composting is important for improving compost fertility. This study aims to investigate the microbial mechanism of available sulfur and phosphorus transformation during sheep manure composting under different moisture contents (45%: M45 and 60%: M60) on the Qinghai-Tibet Plateau using metagenomics technology. The results showed that the final available sulfur and phosphorus contents of M45 were 11% and 13% higher than those of M60, respectively. M45 enhanced sulfur oxidation, sulfate reduction, and thiosulfate disproportionation. These steps were significantly positively correlated with available sulfur, and Pseudomonas, Thermobifida, Luteimonas, Brevibacterium, Planifilum, and Xinfangfangia were the main participants. Available phosphorus was significantly positively correlated with polyphosphate degradation and inorganic P solubilization, and the main participants in these steps were Luteimonas, Brachybacterium, Corynebacterium, Jeotgalicoccus, Microbacterium, Streptomyces, and Pseudoxanthomonas. These findings reveal the microbial mechanisms of available and phosphorus transformation during composting at two moisture contents.}, } @article {pmid38079031, year = {2023}, author = {He, F and Jin, X and Sun, K and Zhao, L and Yang, W and Zhang, X and Dong, X and Zhao, Y and Pan, L and Bao, N and Sun, H}, title = {Bacillus subtilis JATP-3 Improves Nitrogen Metabolism by Regulating Intestinal Flora and AKG in Weaned Piglets.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {38079031}, issn = {1867-1314}, support = {20210101019JC//Natural Science Foundation of Jilin Province/ ; }, abstract = {Recently, it has been reported that oral probiotics improve the apparent digestibility of nitrogen in weaned piglets; however, the underlying mechanism is unclear. A total of 12 crossbred piglets (Yorkshire × Landrace; 28 days old) were randomly divided into two groups. The control (Con) group was fed with a basic diet + Luria-Bertani (LB; sterile; 10 mL), whereas the subject (Sub) group was fed with a basic diet + B. subtilis JATP-3 (1 × 10[9] CFU/mL; 10 mL). The results showed that feeding B. subtilis JATP-3 increased the final body weight and nitrogen deposition rate of weaned piglets (P < 0.05); while the daily weight gain showed an upward trend (P < 0.1). The abundance of Pedicoccus, Collinella, Turiciator, Veillonella, Clostridium, and Escherichia were significantly increased in the jejunum (P < 0.05). The abundance of Olsenella and Pediococcus were significantly increased in the ileum (P < 0.05). The metabolomics analysis showed that the levels of l-lactic acid and Alpha-ketoglutaric acid (AKG) in portal vein plasma were significantly increased (P < 0.05). In addition, the content of AKG in muscle and liver increased significantly (P < 0.01). The metagenomics analysis showed that Veillonella encoded the functional genes of 2-oxoglutarate synthase and promoted AKG production. The protein expression of eIF4E-binding protein 1 (4EBP1) phosphorylated in the skeletal muscle increased (P < 0.05). In summary, B. subtilis JATP-3 promotes dietary nitrogen metabolism and skeletal muscle synthesis by modulating the intestinal microbiota and its metabolites, in which AKG may be one of the main mediators of the therapeutic effects of B. subtilis JATP-3.}, } @article {pmid38078817, year = {2023}, author = {Xu, C and Huang, J and Gao, Y and Zhao, W and Shen, Y and Luo, F and Yu, G and Zhu, F and Ni, Y}, title = {OBMeta: a comprehensive web server to analyze and validate gut microbial features and biomarkers for obesity-associated metabolic diseases.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {12}, pages = {}, doi = {10.1093/bioinformatics/btad715}, pmid = {38078817}, issn = {1367-4811}, support = {2021YFC2701904//National Key Research and Development Program of China/ ; 82170583//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/complications ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2/diagnosis ; Obesity/diagnosis/complications/metabolism ; *Metabolic Diseases/diagnosis/complications ; Biomarkers ; }, abstract = {MOTIVATION: Gut dysbiosis is closely associated with obesity and related metabolic diseases including type 2 diabetes (T2D) and nonalcoholic fatty liver disease (NAFLD). The gut microbial features and biomarkers have been increasingly investigated in many studies, which require further validation due to the limited sample size and various confounding factors that may affect microbial compositions in a single study. So far, it lacks a comprehensive bioinformatics pipeline providing automated statistical analysis and integrating multiple independent studies for cross-validation simultaneously.

RESULTS: OBMeta aims to streamline the standard metagenomics data analysis from diversity analysis, comparative analysis, and functional analysis to co-abundance network analysis. In addition, a curated database has been established with a total of 90 public research projects, covering three different phenotypes (Obesity, T2D, and NAFLD) and more than five different intervention strategies (exercise, diet, probiotics, medication, and surgery). With OBMeta, users can not only analyze their research projects but also search and match public datasets for cross-validation. Moreover, OBMeta provides cross-phenotype and cross-intervention-based advanced validation that maximally supports preliminary findings from an individual study. To summarize, OBMeta is a comprehensive web server to analyze and validate gut microbial features and biomarkers for obesity-associated metabolic diseases.

OBMeta is freely available at: http://obmeta.met-bioinformatics.cn/.}, } @article {pmid38078780, year = {2023}, author = {Li, Y and Yu, H and Xiong, L and Wei, Y and Li, H and Ji, X}, title = {Viral AMGs-driven pentose phosphate pathway in natural wetland.}, journal = {Journal of basic microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1002/jobm.202300569}, pmid = {38078780}, issn = {1521-4028}, support = {YNWR-QNBJ-2019-202//Young Talents Support Program of Yunnan Province/ ; YNWR-QNBJ-2019-202//Young Talents Support Program of Yunnan Province/ ; 32160294//National Natural Science Foundation of China/ ; }, abstract = {Viruses exist anywhere on earth where there is life, and among them, virus-encoded auxiliary metabolic genes (AMGs) can maintain ecosystem balance and play a major role in the global ecosystem. Although the function of AMGs has been widely reported, the genetic diversity of AMGs in natural ecosystems is still poorly understood. Exploring the genetic diversity of viral community-wide AMGs is essential to gain insight into the complex interactions between viruses and hosts. In this article, we studied the phylogenetic tree, principal co-ordinates analysis (PCoA), α diversity, and metabolic pathways of viral auxiliary metabolism genes involved in the pentose phosphate pathway (PPP) through metagenomics, and the changes of metabolites and genes of host bacteria were further studied by using Pseudomonas mandelii SW-3 and its lytic phage based on metabolic flow and AMGs expression. We found that the viral AMGs in the Napahai plateau wetland were created by a combination of various external forces, which contributed to the rich genetic diversity, uniqueness, and differences of the virus, which promoted the reproduction of offspring and better adaptation to the environment. Overall, this study systematically describes the genetic diversity of AMGs associated with the PPP in plateau wetland ecosystems and further expands the understanding of phage-host unique interactions.}, } @article {pmid38078749, year = {2023}, author = {Park, H and Joachimiak, MP and Jungbluth, SP and Yang, Z and Riehl, WJ and Canon, RS and Arkin, AP and Dehal, PS}, title = {A bacterial sensor taxonomy across earth ecosystems for machine learning applications.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0002623}, doi = {10.1128/msystems.00026-23}, pmid = {38078749}, issn = {2379-5077}, abstract = {Microbes infect, colonize, and proliferate due to their ability to sense and respond quickly to their surroundings. In this research, we extract the sensory proteins from a diverse range of environmental, engineered, and host-associated metagenomes. We trained machine learning classifiers using sensors as features such that it is possible to predict the ecosystem for a metagenome from its sensor profile. We use the optimized model's feature importance to identify the most impactful and predictive sensors in different environments. We next use the sensor profile from human gut metagenomes to classify their disease states and explore which sensors can explain differences between diseases. The sensors most predictive of environmental labels here, most of which correspond to uncharacterized proteins, are a useful starting point for the discovery of important environment signals and the development of possible diagnostic interventions.}, } @article {pmid38078115, year = {2023}, author = {Liu, J and Jiang, H and Huang, Y and Zhong, L and Xu, Q and Yang, Q and Liu, S and Wei, X and Liang, Y and Chai, S}, title = {Combined analysis of metagenome and transcriptome revealed the adaptive mechanism of different golden Camellia species in karst regions.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1180472}, pmid = {38078115}, issn = {1664-462X}, abstract = {Camellia sect. Chrysantha is an important rare and protected plant species. Some golden Camellia species grow in karst soil while others grow in acidic soil. In order to study the adaptation mechanism of golden Camellia to the karst environment, four species of golden Camellia growing in the karst soil (Camellia pubipetala, Camellia perpetua, Camellia grandis, and Camellia limonia) and four species growing in the acidic soil (Camellia nitidissima, Camellia euphlebia, Camellia tunghinensis, and Camellia parvipetala) were selected for this study. Combining the metagenome and transcriptome, the structure and function of the rhizosphere microbial communities and the gene expression in roots of golden Camellia were analyzed. The results showed that the rhizosphere microbial communities in different golden Camellia were significantly different in abundance of Acidobacteria, Actinobacteria, Candidatus_Rokubacteria, Nitrospirae, Planctomycetes, and Candidatus_Tectomicrobia. The proportion of Candidatus_Rokubacteria was significantly higher in the rhizosphere soil of four species of golden Camellia grown in karst areas, compared to C. nitidissima, C. euphlebia, and C. tunghinensis. The linear discriminant analysis Effect Size showed that C. parvipetala was similar to karst species in the enrichment of ABC transporters and quorum sensing. During the transcriptome analysis, numerous upregulated genes in four karst species, including CYP81E, CHS, F3H, C12RT1, NAS, and CAD, were found to be enriched in the secondary metabolite synthesis pathway in the KEGG library, when compared to C. tunghinensis. This study provides information for plant adaptation mechanisms on the rhizosphere soil microbial composition and gene expression in secondary metabolic pathways to karst habitats and its distribution in karst areas.}, } @article {pmid38078081, year = {2023}, author = {Lucchetta, M and Romano, A and Alzate Zuluaga, MY and Fornasier, F and Monterisi, S and Pii, Y and Marcuzzo, P and Lovat, L and Gaiotti, F}, title = {Compost application boosts soil restoration in highly disturbed hillslope vineyard.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1289288}, pmid = {38078081}, issn = {1664-462X}, abstract = {A field trial was carried out to investigate the effects of compost application on a young Cabernet sauvignon vineyard located in a hilly area in the North-East of Italy and subjected to land terracing before plantation. The use of a compost based on manure, pruning residues and pomace at a rate of 65 t ha[-1] was compared to the mineral fertilization regime recommended for the vineyards in the area (NPK: 80, 50, 200 kg ha[-1]). A multi-factorial approach that considered soil chemical properties, microbial community structure and function, vine nutritional and vegetative indexes, yield and quality parameters was applied in the attempt of depict interrelated effects of compost on all these factors. Results of this study show that the application of compost for three consequent years greatly increased soil organic matter content and improved the mineral nutrient availability in the soil. Soil biological fertility showed a slow but significant response to compost addition as from the second year of treatment microbial growth and enzyme activity were increased compared to those of the inorganic fertilization, with special regard to enzymes involved in P cycle. A shift in the soil microbial community structure was also observed in compost-treated soil, with higher presence of copiotrophic bacteria, indicators of soil quality, and phosphorus solubilizing bacteria. A decrease of pathogenic fungal strains was also observed. Organic fertilization increased plant nutrient uptake and vegetative growth compared to those observed in chemically fertilized vines. A trend toward increased yield and improvements for some grape quality parameters such as acidity and pH were observed in the first year of production. These results provide evidence that compost can boost soil fertility restoration in vineyard disturbed by land terracing, allowing for agronomic performances comparable or even improved than those of chemically fertilized vines.}, } @article {pmid38077024, year = {2023}, author = {Ma, K and Thairu, MW and Sankaran, K}, title = {MolPad: An R-Shiny Package for Cluster Co-Expression Analysis in Longitudinal Microbiomics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.11.29.569321}, pmid = {38077024}, abstract = {The R-Shiny package MolPad provides an interactive dashboard for understanding the dynamics of longitudinal molecular co-expression in microbiomics. The main idea for addressing the issue is first to use a network to overview major patterns among their predictive relationships and then zoom into specific clusters of interest. It is designed with a focus-plus-context analysis strategy and automatically generates links to online curated annotations. The dashboard consists of a cluster-level network, a bar plot of taxonomic composition, a line plot of data modalities, and a table for each pathway. Further, the package includes functions that handle the data processing for creating the dashboard. This makes it beginner-friendly for users with less R programming experience. We illustrate these methods with a case study on a longitudinal metagenomics analysis of the cheese microbiome.}, } @article {pmid38076970, year = {2023}, author = {Ismail, HM and Perera, D and Mandal, R and DiMeglio, LA and Evans-Molina, C and Hannon, T and Petrosino, J and Javornick CreGreen, S and Schmidt, NW}, title = {Gut microbial changes associated with obesity in youth with type 1 diabetes.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.12.01.23299251}, pmid = {38076970}, abstract = {UNLABELLED: Obesity is increasingly prevalent in type 1 diabetes (T1D) and is associated with management problems and higher risk for diabetes complications. Gut microbiome changes have been described separately in each of T1D and obesity, however, it is unknown to what extent gut microbiome changes are seen when obesity and T1D concomitantly occur.

OBJECTIVE: To describe the gut microbiome and microbial metabolite changes associated with obesity in T1D. We hypothesized significant gut microbial and metabolite differences between T1D youth who are lean (BMI: 5-<85%) vs. those with obesity (BMI: ≥95%).

METHODS: We analyzed stool samples for gut microbial (using metagenomic shotgun sequencing) and short-chain fatty acid (SCFA) metabolite differences in lean (n=27) and obese (n=21) T1D youth. The mean±SD age was 15.3±2.2yrs, A1c 7.8±1.3%, diabetes duration 5.1±4.4yrs, 42.0% females, and 94.0% were White. Linear discriminant analysis (LDA) effect size (LEfSe) was used to identify taxa that best discriminated between the BMI groups.

RESULTS: Bacterial community composition showed differences in species type (β-diversity) by BMI group (p=0.013). At the genus level, there was a higher ratio of Prevotella to Bacteroides in the obese group (p=0.0058). LEfSe analysis showed a differential distribution of significantly abundant taxa in either the lean or obese groups, including increased relative abundance of Prevotella copri , among other taxa in the obese group. Functional profiling showed that pathways associated with decreased insulin sensitivity were upregulated in the obese group. Stool SCFAs (acetate, propionate and butyrate) were higher in the obese compared to the lean group (p<0.05 for all).

CONCLUSIONS: Our findings identify gut microbiome, microbial metabolite and functional pathways differences associated with obesity in T1D. These findings could be helpful in identifying gut microbiome targeted therapies to manage obesity in T1D.}, } @article {pmid38076955, year = {2023}, author = {Oliver, A and Podell, S and Kelly, LW and Sparagon, WJ and Plominsky, AM and Nelson, RS and Laurens, LML and Augyte, S and Sims, NA and Nelson, CE and Allen, EE}, title = {Enrichable consortia of microbial symbionts degrade macroalgal polysaccharides in Kyphosus fish.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38076955}, support = {R01 ES030316/ES/NIEHS NIH HHS/United States ; S10 OD026929/OD/NIH HHS/United States ; }, abstract = {Coastal herbivorous fishes consume macroalgae, which is then degraded by microbes along their digestive tract. However, there is scarce foundational genomic work on the microbiota that perform this degradation. This study explores the potential of Kyphosus gastrointestinal microbial symbionts to collaboratively degrade and ferment polysaccharides from red, green, and brown macroalgae through in silico study of carbohydrate-active enzyme and sulfatase sequences. Recovery of metagenome-assembled genomes (MAGs) reveals differences in enzymatic capabilities between the major microbial taxa in Kyphosus guts. The most versatile of the recovered MAGs were from the Bacteroidota phylum, whose MAGs house enzymes able to decompose a variety of algal polysaccharides. Unique enzymes and predicted degradative capacities of genomes from the Bacillota (genus Vallitalea) and Verrucomicrobiota (order Kiritimatiellales) suggest the potential for microbial transfer between marine sediment and Kyphosus digestive tracts. Few genomes contain the required enzymes to fully degrade any complex sulfated algal polysaccharide alone. The distribution of suitable enzymes between MAGs originating from different taxa, along with the widespread detection of signal peptides in candidate enzymes, is consistent with cooperative extracellular degradation of these carbohydrates. This study leverages genomic evidence to reveal an untapped diversity at the enzyme and strain level among Kyphosus symbionts and their contributions to macroalgae decomposition. Bioreactor enrichments provide a genomic foundation for degradative and fermentative processes central to translating the knowledge gained from this system to the aquaculture and bioenergy sectors.}, } @article {pmid38076927, year = {2023}, author = {Schaible, GA and Jay, ZJ and Cliff, J and Schulz, F and Gauvin, C and Goudeau, D and Malmstrom, RR and Emil Ruff, S and Edgcomb, V and Hatzenpichler, R}, title = {Multicellular magnetotactic bacterial consortia are metabolically differentiated and not clonal.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38076927}, support = {P30 GM140963/GM/NIGMS NIH HHS/United States ; }, abstract = {Consortia of multicellular magnetotactic bacteria (MMB) are currently the only known example of bacteria without a unicellular stage in their life cycle. Because of their recalcitrance to cultivation, most previous studies of MMB have been limited to microscopic observations. To study the biology of these unique organisms in more detail, we use multiple culture-independent approaches to analyze the genomics and physiology of MMB consortia at single cell resolution. We separately sequenced the metagenomes of 22 individual MMB consortia, representing eight new species, and quantified the genetic diversity within each MMB consortium. This revealed that, counter to conventional views, cells within MMB consortia are not clonal. Single consortia metagenomes were then used to reconstruct the species-specific metabolic potential and infer the physiological capabilities of MMB. To validate genomic predictions, we performed stable isotope probing (SIP) experiments and interrogated MMB consortia using fluorescence in situ hybridization (FISH) combined with nano-scale secondary ion mass spectrometry (NanoSIMS). By coupling FISH with bioorthogonal non-canonical amino acid tagging (BONCAT) we explored their in situ activity as well as variation of protein synthesis within cells. We demonstrate that MMB consortia are mixotrophic sulfate reducers and that they exhibit metabolic differentiation between individual cells, suggesting that MMB consortia are more complex than previously thought. These findings expand our understanding of MMB diversity, ecology, genomics, and physiology, as well as offer insights into the mechanisms underpinning the multicellular nature of their unique lifestyle.}, } @article {pmid38076824, year = {2023}, author = {Schweickart, A and Batra, R and Neth, BJ and Martino, C and Shenhav, L and Zhang, AR and Shi, P and Karu, N and Huynh, K and Meikle, PJ and Schimmel, L and Dilmore, AH and Blennow, K and Zetterberg, H and Blach, C and Dorrestein, PC and Knight, R and , and Craft, S and Kaddurah-Daouk, R and Krumsiek, J}, title = {A Modified Mediterranean Ketogenic Diet mitigates modifiable risk factors of Alzheimer's Disease: a serum and CSF-based metabolic analysis.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {38076824}, support = {R01 AG046171/AG/NIA NIH HHS/United States ; R01 AG069901/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; P30 AG049638/AG/NIA NIH HHS/United States ; UL1 TR001420/TR/NCATS NIH HHS/United States ; RF1 AG059093/AG/NIA NIH HHS/United States ; U01 AG061359/AG/NIA NIH HHS/United States ; RF1 AG057452/AG/NIA NIH HHS/United States ; RF1 AG058942/AG/NIA NIH HHS/United States ; RF1 AG051550/AG/NIA NIH HHS/United States ; }, abstract = {Alzheimer's disease (AD) is influenced by a variety of modifiable risk factors, including a person's dietary habits. While the ketogenic diet (KD) holds promise in reducing metabolic risks and potentially affecting AD progression, only a few studies have explored KD's metabolic impact, especially on blood and cerebrospinal fluid (CSF). Our study involved participants at risk for AD, either cognitively normal or with mild cognitive impairment. The participants consumed both a modified Mediterranean-ketogenic diet (MMKD) and the American Heart Association diet (AHAD) for 6 weeks each, separated by a 6-week washout period. We employed nuclear magnetic resonance (NMR)-based metabolomics to profile serum and CSF and metagenomics profiling on fecal samples. While the AHAD induced no notable metabolic changes, MMKD led to significant alterations in both serum and CSF. These changes included improved modifiable risk factors, like increased HDL-C and reduced BMI, reversed serum metabolic disturbances linked to AD such as a microbiome-mediated increase in valine levels, and a reduction in systemic inflammation. Additionally, the MMKD was linked to increased amino acid levels in the CSF, a breakdown of branched-chain amino acids (BCAAs), and decreased valine levels. Importantly, we observed a strong correlation between metabolic changes in the CSF and serum, suggesting a systemic regulation of metabolism. Our findings highlight that MMKD can improve AD-related risk factors, reverse some metabolic disturbances associated with AD, and align metabolic changes across the blood-CSF barrier.}, } @article {pmid38076477, year = {2024}, author = {Emami-Khoyi, A}, title = {Reconstruction of the complete mitogenomes of predator and prey from a faecal metagenomic dataset.}, journal = {Data in brief}, volume = {52}, number = {}, pages = {109830}, pmid = {38076477}, issn = {2352-3409}, abstract = {The application of faecal DNA in genetic studies of wild populations minimises disturbances to their normal behaviours and body integrity. Here, I present an analysis of a metagenomic dataset generated from the faecal DNA of several specimens of the estuarine pipefish, Syngnathus watermeyeri, to simultaneously assemble the mitogenomes of the predator and its main prey species, the copepod Pseudodiaptomus hessei. The mitogenomes of the pipefish and the copepod were successfully reconstructed using a combination of short seed extension and denovo metagenomic assembly. Nucleotide blast searches of the circular contigs, mitogenome annotations, and Bayesian phylogenetic analyses confirm the completeness and correct taxonomic placements of the two mitogenomes. In addition, heteroplasmy detection and Pool-Seq variant calling quantified the level of genetic diversity in the sequences that formed these assemblies. These can be used as a first step to non-invasively survey genetic diversity in these populations.}, } @article {pmid38076456, year = {2023}, author = {Zhou, X and Wu, X and Chen, Z and Cui, X and Cai, Y and Liu, Y and Weng, B and Zhan, Q and Huang, L}, title = {Risk factors and the value of microbiological examinations of COVID-19 associated pulmonary aspergillosis in critically ill patients in intensive care unit: the appropriate microbiological examinations are crucial for the timely diagnosis of CAPA.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1287496}, pmid = {38076456}, issn = {2235-2988}, mesh = {Humans ; *Invasive Pulmonary Aspergillosis/diagnosis ; *COVID-19/diagnosis/complications ; Critical Illness ; Prospective Studies ; *Influenza, Human/complications ; Sensitivity and Specificity ; *Pulmonary Aspergillosis/diagnosis/complications ; Intensive Care Units ; Risk Factors ; Bronchoalveolar Lavage Fluid/microbiology ; COVID-19 Testing ; }, abstract = {INTRODUCTION: During the Omicron pandemic in China, a significant proportion of patients with Coronavirus Disease 2019 (COVID-19) associated pulmonary aspergillosis (CAPA) necessitated admission to intensive care unit (ICU) and experienced a high mortality. To explore the clinical risk factors and the application/indication of microbiological examinations of CAPA in ICU for timely diagnosis are very important.

METHODS: This prospective study included patients with COVID-19 admitted to ICU between December 1, 2022, and February 28, 2023. The clinical data of influenza-associated pulmonary aspergillosis (IAPA) patients from the past five consecutive influenza seasons (November 1, 2017, to March 31, 2022) were collected for comparison. The types of specimens and methods used for microbiological examinations were also recorded to explore the efficacy in early diagnosis.

RESULTS: Among 123 COVID-19 patients, 36 (29.3%) were diagnosed with probable CAPA. CAPA patients were more immunosuppressed, in more serious condition, required more advanced respiratory support and had more other organ comorbidities. Solid organ transplantation, APACHEII score ≥20 points, 5 points ≤SOFA score <10 points were independent risk factors for CAPA. Qualified lower respiratory tract specimens were obtained from all patients, and 84/123 (68.3%) patients underwent bronchoscopy to obtain bronchoalveolar lavage fluid (BALF) specimens. All patients' lower respiratory tract specimens underwent fungal smear and culture; 79/123 (64.2%) and 69/123 (56.1%) patients underwent BALF galactomannan (GM) and serum GM detection, respectively; metagenomic next-generation sequencing (mNGS) of the BALF was performed in 62/123 (50.4%) patients. BALF GM had the highest diagnostic sensitivity (84.9%), the area under the curve of the mNGS were the highest (0.812).

CONCLUSION: The incidence of CAPA was extremely high in patients admitted to the ICU. CAPA diagnosis mainly depends on microbiological evidence owing to non-specific clinical manifestations, routine laboratory examinations, and CT findings. The bronchoscopy should be performed and the BALF should be obtained as soon as possible. BALF GM are the most suitable microbiological examinations for the diagnosis of CAPA. Due to the timely and accuracy result of mNGS, it could assist in early diagnosis and might be an option in critically ill CAPA patients.}, } @article {pmid38076410, year = {2023}, author = {Oghuan, J and Chavarria, C and Vanderwal, SR and Gitter, A and Ojaruega, AA and Monserrat, C and Bauer, CX and Brown, EL and Cregeen, SJ and Deegan, J and Hanson, BM and Tisza, M and Ocaranza, HI and Balliew, J and Maresso, AW and Rios, J and Boerwinkle, E and Mena, KD and Wu, F}, title = {Wastewater analysis of Mpox virus in a city with low prevalence of Mpox disease: an environmental surveillance study.}, journal = {Lancet regional health. Americas}, volume = {28}, number = {}, pages = {100639}, pmid = {38076410}, issn = {2667-193X}, abstract = {BACKGROUND: Tracking infectious diseases at the community level is challenging due to asymptomatic infections and the logistical complexities of mass surveillance. Wastewater surveillance has emerged as a valuable tool for monitoring infectious disease agents including SARS-CoV-2 and Mpox virus. However, detecting the Mpox virus in wastewater is particularly challenging due to its relatively low prevalence in the community. In this study, we aim to characterize three molecular assays for detecting and tracking the Mpox virus in wastewater from El Paso, Texas, during February and March 2023.

METHODS: In this study, a combined approach utilizing three real-time PCR assays targeting the C22L, F3L, and F8L genes and sequencing was employed to detect and track the Mpox virus in wastewater samples. The samples were collected from four sewersheds in the City of El Paso, Texas, during February and March 2023. Wastewater data was compared with reported clinical case data in the city.

FINDINGS: Mpox virus DNA was detected in wastewater from all the four sewersheds, whereas only one Mpox case was reported during the sampling period. Positive signals were still observed in multiple sewersheds after the Mpox case was identified. Higher viral concentrations were found in the pellet than in the supernatant of wastewater. Notably, an increasing trend in viral concentration was observed approximately 1-2 weeks before the reporting of the Mpox case. Further sequencing and epidemiological analysis provided supporting evidence for unreported Mpox infections in the city.

INTERPRETATION: Our analysis suggests that the Mpox cases in the community is underestimated. The findings emphasize the value of wastewater surveillance as a public health tool for monitoring infectious diseases even in low-prevalence areas, and the need for heightened vigilance to mitigate the spread of Mpox disease for safeguarding global health.

FUNDING: Center of Infectious Diseases at UTHealth, the University of Texas System, and the Texas Epidemic Public Health Institute. The content of this paper is solely the responsibility of the authors and does not necessarily represent the official views of these funding organizations.}, } @article {pmid38076254, year = {2023}, author = {Bu, C and Lei, S and Chen, L and Xie, Y and Zheng, G and Hua, L}, title = {Case report: Fatal Legionella infection diagnosed via by metagenomic next-generation sequencing in a patient with chronic myeloid leukemia.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1266895}, pmid = {38076254}, issn = {2296-858X}, abstract = {Legionella is an aerobic, gram-negative, intracellular pathogen and is an important cause of community-acquired pneumonia. Legionella pneumophila is the most common causative agent of Legionella pneumonia. Clinical diagnosis of Legionella pneumonia is challenging due to the lack of specific clinical manifestations and the low positive rates of conventional pathogen detection methods. In this study, we report a case of a patient with chronic myeloid leukemia who developed rigors and high fever after chemotherapy and immunotherapy. Chest computed tomography revealed consolidation in the left lower lobe of the lung and ground-glass opacities in both lower lobes. Multiple blood cultures showed Escherichia coli, Staphylococcus aureus, Bacillus licheniformis, and positive results in the β-D-glucan test (G test). The patient was treated with various sensitive antimicrobial agents, including meropenem plus fluconazole, meropenem plus carpofungin, and vancomycin. Unfortunately, the patient's condition gradually worsened and eventually resulted in death. On the following day of death, metagenomic next-generation sequencing (mNGS) of 1whole blood revealed L. pneumophila pneumonia with concurrent bloodstream infection (blood mNGS reads 114,302). These findings suggest that when conventional empirical antimicrobial therapy proves ineffective for critically ill patients with pneumonia, the possibility of combined Legionella infection must be considered, and mNGS can provide a diagnostic tool in such cases.}, } @article {pmid38075934, year = {2023}, author = {Hempel, CA and Buchner, D and Mack, L and Brasseur, MV and Tulpan, D and Leese, F and Steinke, D}, title = {Predicting environmental stressor levels with machine learning: a comparison between amplicon sequencing, metagenomics, and total RNA sequencing based on taxonomically assigned data.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1217750}, pmid = {38075934}, issn = {1664-302X}, abstract = {INTRODUCTION: Microbes are increasingly (re)considered for environmental assessments because they are powerful indicators for the health of ecosystems. The complexity of microbial communities necessitates powerful novel tools to derive conclusions for environmental decision-makers, and machine learning is a promising option in that context. While amplicon sequencing is typically applied to assess microbial communities, metagenomics and total RNA sequencing (herein summarized as omics-based methods) can provide a more holistic picture of microbial biodiversity at sufficient sequencing depths. Despite this advantage, amplicon sequencing and omics-based methods have not yet been compared for taxonomy-based environmental assessments with machine learning.

METHODS: In this study, we applied 16S and ITS-2 sequencing, metagenomics, and total RNA sequencing to samples from a stream mesocosm experiment that investigated the impacts of two aquatic stressors, insecticide and increased fine sediment deposition, on stream biodiversity. We processed the data using similarity clustering and denoising (only applicable to amplicon sequencing) as well as multiple taxonomic levels, data types, feature selection, and machine learning algorithms and evaluated the stressor prediction performance of each generated model for a total of 1,536 evaluated combinations of taxonomic datasets and data-processing methods.

RESULTS: Sequencing and data-processing methods had a substantial impact on stressor prediction. While omics-based methods detected a higher diversity of taxa than amplicon sequencing, 16S sequencing outperformed all other sequencing methods in terms of stressor prediction based on the Matthews Correlation Coefficient. However, even the highest observed performance for 16S sequencing was still only moderate. Omics-based methods performed poorly overall, but this was likely due to insufficient sequencing depth. Data types had no impact on performance while feature selection significantly improved performance for omics-based methods but not for amplicon sequencing.

DISCUSSION: We conclude that amplicon sequencing might be a better candidate for machine-learning-based environmental stressor prediction than omics-based methods, but the latter require further research at higher sequencing depths to confirm this conclusion. More sampling could improve stressor prediction performance, and while this was not possible in the context of our study, thousands of sampling sites are monitored for routine environmental assessments, providing an ideal framework to further refine the approach for possible implementation in environmental diagnostics.}, } @article {pmid38075911, year = {2023}, author = {Bakir-Gungor, B and Temiz, M and Jabeer, A and Wu, D and Yousef, M}, title = {microBiomeGSM: the identification of taxonomic biomarkers from metagenomic data using grouping, scoring and modeling (G-S-M) approach.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1264941}, pmid = {38075911}, issn = {1664-302X}, abstract = {Numerous biological environments have been characterized with the advent of metagenomic sequencing using next generation sequencing which lays out the relative abundance values of microbial taxa. Modeling the human microbiome using machine learning models has the potential to identify microbial biomarkers and aid in the diagnosis of a variety of diseases such as inflammatory bowel disease, diabetes, colorectal cancer, and many others. The goal of this study is to develop an effective classification model for the analysis of metagenomic datasets associated with different diseases. In this way, we aim to identify taxonomic biomarkers associated with these diseases and facilitate disease diagnosis. The microBiomeGSM tool presented in this work incorporates the pre-existing taxonomy information into a machine learning approach and challenges to solve the classification problem in metagenomics disease-associated datasets. Based on the G-S-M (Grouping-Scoring-Modeling) approach, species level information is used as features and classified by relating their taxonomic features at different levels, including genus, family, and order. Using four different disease associated metagenomics datasets, the performance of microBiomeGSM is comparatively evaluated with other feature selection methods such as Fast Correlation Based Filter (FCBF), Select K Best (SKB), Extreme Gradient Boosting (XGB), Conditional Mutual Information Maximization (CMIM), Maximum Likelihood and Minimum Redundancy (MRMR) and Information Gain (IG), also with other classifiers such as AdaBoost, Decision Tree, LogitBoost and Random Forest. microBiomeGSM achieved the highest results with an Area under the curve (AUC) value of 0.98% at the order taxonomic level for IBDMD dataset. Another significant output of microBiomeGSM is the list of taxonomic groups that are identified as important for the disease under study and the names of the species within these groups. The association between the detected species and the disease under investigation is confirmed by previous studies in the literature. The microBiomeGSM tool and other supplementary files are publicly available at: https://github.com/malikyousef/microBiomeGSM.}, } @article {pmid38075901, year = {2023}, author = {Li, Y and Zhang, Y and Luo, X and Meng, Y and Zhong, Z and Zheng, H and Yang, Y}, title = {The fecal microbiota from children with autism impact gut metabolism and learning and memory abilities of honeybees.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1278162}, pmid = {38075901}, issn = {1664-302X}, abstract = {Autism spectrum disorder (ASD) is a set of neurodevelopmental disorders, with an increasing incidence. Gastrointestinal symptoms are common comorbidities of ASD. The gut microbiota composition of children with autism is distinct from that of typical developmental (TD) children, suggesting that the gut microbiota probably influences on hosts via the microbiota-gut-brain axis. However, the relationship between intestinal dysbiosis and host brain function remains unclear. In this study, we creatively developed a honeybee model and investigated the potential effects of fecal microbiota on hosts. Fecal microbiota from children with autism and TD children were transplanted into microbiota-free honeybees (Apis mellifera), resulting in induced ASD-fecal microbiota transplantation (FMT) honeybees (A-BEE group) and TD-FMT honeybees (T-BEE group), respectively. We found that cognitive abilities of honeybees in the A-BEE group were significantly impaired in olfactory proboscis extension response conditioning. Metagenomics was used to evaluate fecal microbiota colonization, revealing several differential species responsible for altered tryptophan metabolism and taurine metabolism within the bee gut, including Bacteroides dorei, Bacteroides fragilis, Lactobacillus gasseri, and Lactobacillus paragasseri. Furthermore, fecal microbiota from children with autism downregulated brain genes involved in neural signaling and synaptic transmission within honeybees. Notably, differentially spliced genes observed within brains of honeybees from the A-BEE group largely overlapped with those identified in human diagnosed with autism via SFARI and SPARK gene sets. These differentially spliced genes were also enriched within pathways related to neural synaptic transmission. Our findings provide novel insights into the pivotal role of the human gut microbiota, which may contribute to neurological processes in honeybees. Additionally, we present a few research sources on gut-brain connections in ASD.}, } @article {pmid38075858, year = {2023}, author = {Marcos-Zambrano, LJ and López-Molina, VM and Bakir-Gungor, B and Frohme, M and Karaduzovic-Hadziabdic, K and Klammsteiner, T and Ibrahimi, E and Lahti, L and Loncar-Turukalo, T and Dhamo, X and Simeon, A and Nechyporenko, A and Pio, G and Przymus, P and Sampri, A and Trajkovik, V and Lacruz-Pleguezuelos, B and Aasmets, O and Araujo, R and Anagnostopoulos, I and Aydemir, Ö and Berland, M and Calle, ML and Ceci, M and Duman, H and Gündoğdu, A and Havulinna, AS and Kaka Bra, KHN and Kalluci, E and Karav, S and Lode, D and Lopes, MB and May, P and Nap, B and Nedyalkova, M and Paciência, I and Pasic, L and Pujolassos, M and Shigdel, R and Susín, A and Thiele, I and Truică, CO and Wilmes, P and Yilmaz, E and Yousef, M and Claesson, MJ and Truu, J and Carrillo de Santa Pau, E}, title = {A toolbox of machine learning software to support microbiome analysis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1250806}, pmid = {38075858}, issn = {1664-302X}, abstract = {The human microbiome has become an area of intense research due to its potential impact on human health. However, the analysis and interpretation of this data have proven to be challenging due to its complexity and high dimensionality. Machine learning (ML) algorithms can process vast amounts of data to uncover informative patterns and relationships within the data, even with limited prior knowledge. Therefore, there has been a rapid growth in the development of software specifically designed for the analysis and interpretation of microbiome data using ML techniques. These software incorporate a wide range of ML algorithms for clustering, classification, regression, or feature selection, to identify microbial patterns and relationships within the data and generate predictive models. This rapid development with a constant need for new developments and integration of new features require efforts into compile, catalog and classify these tools to create infrastructures and services with easy, transparent, and trustable standards. Here we review the state-of-the-art for ML tools applied in human microbiome studies, performed as part of the COST Action ML4Microbiome activities. This scoping review focuses on ML based software and framework resources currently available for the analysis of microbiome data in humans. The aim is to support microbiologists and biomedical scientists to go deeper into specialized resources that integrate ML techniques and facilitate future benchmarking to create standards for the analysis of microbiome data. The software resources are organized based on the type of analysis they were developed for and the ML techniques they implement. A description of each software with examples of usage is provided including comments about pitfalls and lacks in the usage of software based on ML methods in relation to microbiome data that need to be considered by developers and users. This review represents an extensive compilation to date, offering valuable insights and guidance for researchers interested in leveraging ML approaches for microbiome analysis.}, } @article {pmid38075439, year = {2023}, author = {Lee, JY}, title = {The Principles and Applications of High-Throughput Sequencing Technologies.}, journal = {Development & reproduction}, volume = {27}, number = {1}, pages = {9-24}, pmid = {38075439}, issn = {2465-9525}, abstract = {The advancement in high-throughput sequencing (HTS) technology has revolutionized the field of biology, including genomics, epigenomics, transcriptomics, and metagenomics. This technology has become a crucial tool in many areas of research, allowing scientists to generate vast amounts of genetic data at a much faster pace than traditional methods. With this increased speed and scale of data generation, researchers can now address critical questions and gain new insights into the inner workings of living organisms, as well as the underlying causes of various diseases. Although the first HTS technology have been introduced about two decades ago, it can still be challenging for those new to the field to understand and use effectively. This review aims to provide a comprehensive overview of commonly used HTS technologies these days and their applications in terms of genome sequencing, transcriptome, DNA methylation, DNA-protein interaction, chromatin accessibility, three-dimensional genome organization, and microbiome.}, } @article {pmid38075017, year = {2023}, author = {Flurin, L and Fisher, CR and Wolf, MJ and Pritt, BS and DeSimone, DC and Patel, R}, title = {Comparison of Blood-Based Shotgun and Targeted Metagenomic Sequencing for Microbiological Diagnosis of Infective Endocarditis.}, journal = {Open forum infectious diseases}, volume = {10}, number = {12}, pages = {ofad546}, pmid = {38075017}, issn = {2328-8957}, abstract = {BACKGROUND: Shotgun and targeted metagenomic sequencing have been shown in separate studies to be potentially useful for culture-free pathogen identification in blood and/or plasma of patients with infective endocarditis (IE). However, the 2 approaches have not been directly compared. The aim of this study was to compare shotgun metagenomic sequencing with targeted metagenomic sequencing (tMGS) for organism identification in blood or plasma of patients with IE.

METHODS: Patients with possible or definite IE were prospectively enrolled from October 2020 to July 2021. Shotgun metagenomic sequencing was performed with the Karius test, which uses microbial cell-free DNA (mcfDNA) sequencing to detect, identify, and quantitate DNA-based pathogens in plasma. tMGS was performed using a 16S ribosomal RNA (rRNA) polymerase chain reaction assay targeting the V1 to V3 regions of the 16S rRNA gene. Results were compared using the McNemar test of paired proportions.

RESULTS: Samples from 34 patients were investigated. The Karius test was positive in 24/34 (71%), including 3/6 (50%) with blood culture-negative endocarditis (BCNE), which was not significantly different from the positivity rate of tMGS (P = .41). Results of the Karius test were concordant with tMGS in 75% of cases. The Karius test detected 2 cases of methicillin-resistant Staphylococcus aureus among the 7 S. aureus detections, in accordance with results of phenotypic susceptibility testing. The combination of blood cultures, the Karius test, and tMGS found a potential causative pathogen in 33/34 (97%), including 5/6 with BCNE.

CONCLUSIONS: The Karius test and tMGS yielded comparable detection rates; however, beyond organism identification, the Karius test generated potentially useful antibiotic resistance data.}, } @article {pmid38073689, year = {2023}, author = {Qi, DD and Zhuang, Y and Chen, Y and Guo, JJ and Zhang, Z and Gu, Y}, title = {Interstitial pneumonia combined with nocardia cyriacigeorgica infection: A case report.}, journal = {World journal of clinical cases}, volume = {11}, number = {32}, pages = {7920-7925}, pmid = {38073689}, issn = {2307-8960}, abstract = {BACKGROUND: Nocardia infection is a relatively uncommon disease, with no reports among patients with interstitial pneumonia. Due to its atypical clinical symptoms and chest computed tomography (CT) findings and the frequent yielding of negative results by conventional cultures, it poses challenges for timely diagnosis and treatment.

CASE SUMMARY: A 63-year-old female patient presented to our hospital in July 2022 with a 3-mo history of intermittent cough and poor appetite, accompanied by a 2-wk long duration of headaches. She had a previous medical history of interstitial pneumonia and was on oral prednisone and cyclosporine. Chest CT revealed the presence of newly developed round nodules. The diagnosis of Nocardia cyriacigeorgica infection was confirmed through metagenomic next-generation sequencing (mNGS) performed on bronchoalveolar lavage fluid. Targeted anti-infection therapy was initiated, resulting in symptom improvement and radiological resolution, further validating the mNGS results.

CONCLUSION: Nocardia cyriacigeorgica infection is a clinically rare condition that is primarily observed in immunocompromised patients. Its clinical and radiological manifestations lack specificity, but mNGS can aid in rapidly obtaining pathogenic information. Early initiation of targeted antimicrobial therapy based on mNGS results can improve patient prognosis.}, } @article {pmid38073622, year = {2023}, author = {Del Amo, LL and Durán-González, E and Ramírez-Tejero, JA and Martínez-Lara, A and Cotán, D}, title = {Study protocol for FIBROKIT: a new tool for fibromyalgia diagnosis and patient follow-up.}, journal = {Frontiers in neurology}, volume = {14}, number = {}, pages = {1286539}, pmid = {38073622}, issn = {1664-2295}, abstract = {Fibromyalgia (FM) is a complex disease that is characterized by chronic musculoskeletal pain and has great economic impact. FM prevalence is about 2% to 4% worldwide, affecting mainly middle-aged women, and its complex pathophysiology complicates diagnosis, treatment and the findings of solid biomarkers. Previous studies have suggested an association between the disease and oxidative stress, mitochondrial metabolism, intestinal microbiota and inflammation, providing sufficient data to support the multifactorial origin of FM. Hence, the objective of this randomized, prospective, low-interventional, double-blinded and placebo-controlled clinical trial is the development of a specific panel of FM biomarkers and the evaluation of their response to a six-month nutritional intervention based on the Mediterranean diet supplemented with extra virgin olive oil (EVOO). For this purpose, the experimental design implies the recruitment of a large cohort of female Spanish patients. Middle-aged women who meet the diagnostic criteria for FM according to the American College of Rheumatology (ACR) will be eligible, along with age-matched healthy women. Both groups will be randomly divided into placebo (olive oil, OO) and treatment groups (extra virgin olive oil, EVOO), and will provide samples at the beginning (T0), after 3 months of nutritional intervention (T1), at the end of the nutritional intervention in 6 months (T2), and 6 months after the end of nutritional intervention (TF), being enrolled for 1 year. Data will be collected through health questionnaires, and whole blood and stool samples will be taken and analyzed. Blood will be used for western-blotting and proteomic analysis of mitochondrial homeostasis and plasma proteome, while stool will undergo metagenomic analysis, respectively. This study represents the first low-interventional investigation with more than 200 participants focused on exploring the association of oxidative stress, mitochondrial metabolism, intestinal microbiota and related pathways with a nutritional intervention in the context of FM. As a result, the outcomes of this study will significantly contribute to the development of a comprehensive and robust panel of diagnostic biomarkers, and will shed some light on their modulation with non-pharmacological therapies such as nutrition. Clinical trial registration: https://clinicaltrials.gov/study/NCT05921409, identifier: NCT05921409.}, } @article {pmid38073524, year = {2023}, author = {Gao, H and He, C and Xin, S and Hua, R and Du, Y and Wang, B and Gong, F and Yu, X and Pan, L and Liang, C and Gao, L and Shang, H and Xu, JD}, title = {Rhubarb extract rebuilding the mucus homeostasis and regulating mucin-associated flora to relieve constipation.}, journal = {Experimental biology and medicine (Maywood, N.J.)}, volume = {}, number = {}, pages = {15353702231211859}, doi = {10.1177/15353702231211859}, pmid = {38073524}, issn = {1535-3699}, abstract = {In clinical trials, rhubarb extract (Rb) was demonstrated to efficiently alleviate constipation. We would like to find out the underlying mechanism of rhubarb relieving constipation. However, there are few studies on the effects of rhubarb on colonic mucus secretion and constipation. The aim of this study was to investigate the effects of rhubarb on colonic mucus secretion and its underlying mechanism. The mice were randomly divided into four groups. Group I was the control group and Group II was the rhubarb control group, with Rb (24 g/kg body weight [b.w.]) administered through intragastric administration for three days. Group III mice were given diphenoxylate (20 mg/kg b.w.) for five days via gavage to induce constipation. Group IV received diphenoxylate lasting five days before undergoing Rb administration for three days. The condition of the colon was evaluated using an endoscope. Particularly, the diameter of blood vessels in the colonic mucosa expanded considerably in constipation mice along with diminishing mucus output, which was in line with the observation via scanning electron microscope (SEM) and transmission electron microscope (TEM). We also performed metagenomic analysis to reveal the microbiome related to mucin gene expression level referring to mucin secretion. In conclusion, Rb relieves constipation by rebuilding mucus homeostasis and regulating the microbiome.}, } @article {pmid38073164, year = {2023}, author = {Sankar, J and Thakral, V and Bharadwaj, K and Agarwal, S and Kabra, SK and Lodha, R and Rathore, S}, title = {The Microbiome and Metabolome of the Gut of Children with Sepsis and Septic Shock.}, journal = {Journal of intensive care medicine}, volume = {}, number = {}, pages = {8850666231216361}, doi = {10.1177/08850666231216361}, pmid = {38073164}, issn = {1525-1489}, abstract = {BACKGROUND: There is limited understanding of alteration of gut microbiota and metabolome in children with sepsis/septic shock.

METHODS: In this prospective observational study carried out in a pediatric intensive care unit of a tertiary care center from 2020 to 2022, patients aged <17 years with sepsis/septic shock and healthy children (HC) were enrolled. We characterized the gut bacterial compositions by metagenome sequencing and metabolomes by untargeted gas chromatography-mass spectrometry. The primary outcome was to compare the gut microbiota and metabolome of children with sepsis/septic shock with that of HC. The Firmicutes/Bacteroidetes (F/B) ratio was compared between children with sepsis/septic shock and HC. Key secondary outcomes were to evaluate association of factors associated with a low F/B ratio in children with sepsis/septic shock.

RESULTS: A total of 40 children (63% boys) (15 children with sepsis and septic shock and 10 healthy children) with a median (IQR) age of 5.5 (1.5, 10) years were enrolled. In the fecal microbiota, the α-diversity index including Shannon and Simpson indices of the sepsis/septic shock groups was significantly lower than that of the HC. The samples lacked beneficial Bifidobacterium spp. and were dominated by Bacteroides, Enterobacteriaceae, and Enterococcaceae. There was reduction in short-chain fatty acids (SCFAs) in patients with sepsis/septic shock as compared to healthy children. A lower F/B ratio (≤1.57) of the gut microbiota discriminated well between children with sepsis/septic shock and HC. Factors associated with lower F/B ratio were male gender, clinical GI dysfunction, elevated inflammatory markers, and higher organ failure scores.

CONCLUSION: There were significant alterations in the gut microbiota and metabolome in children with sepsis/septic shock as compared to healthy children. Larger study is needed to confirm these exploratory findings and develop potential therapeutic targets that will improve outcomes in children with sepsis/septic shock.}, } @article {pmid38072301, year = {2024}, author = {Zeng, X and Liang, Y and Wang, H and Chen, J and Xu, Y and Ou, Q and Yin, J and Zhuang, J and Xiong, W and Tang, L and Li, X and Tong, G and Lei, L and Jian, X}, title = {Detection of pathogens from venous or arterial blood of patients with left-sided infective endocarditis by metagenomic next-generation sequencing: A prospective study.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {552}, number = {}, pages = {117698}, doi = {10.1016/j.cca.2023.117698}, pmid = {38072301}, issn = {1873-3492}, mesh = {Humans ; Prospective Studies ; *Veins ; *Endocarditis/diagnosis ; Leukocytes ; High-Throughput Nucleotide Sequencing ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Infective endocarditis is a life-threatening uncommon infectious disease, and we aimed to explore the clinical utility of venous or arterial blood-based metagenomic next-generation sequencing (mNGS) approaches to diagnose left-sided infective endocarditis (LSIE).

METHODS: We prospectively studied 79 LSIE patients who received valvular surgery in our hospital. Results of blood culture, valve culture, venous blood-based mNGS, arterial blood-based mNGS, venous blood-based mNGS plus blood culture, and arterial blood-based mNGS plus blood culture were evaluated and compared.

RESULTS: Both venous blood- and arterial blood-based mNGS methods displayed significantly higher positive detection rates than blood culture and valve culture (43.0 %, 49.4 % vs. 32.9 %, 19.0 %; P < 0.001). Strikingly, when combining blood-based mNGS and blood culture, the positive rate could be further improved to more than 60 %. Moreover, we found mNGS LSIE detection was closely associated with preoperative leukocyte (P = 0.027), neutrophil value (P = 0.018), vegetation ≥ 14 mm (P = 0.043), and vegetations in aortic valve (P = 0.048). In addition, we discovered that blood-based mNGS had a superir capacity over blood culture to detect gram-negative bacteria, fungi, Bartonella Quintana, and mixed infections than blood culture.

CONCLUSION: This study indicates that venous blood- and arterial blood-based mNGS displayed high positive rate in the rapid detection of pathogens in high-risk LSIE patients.}, } @article {pmid38072280, year = {2023}, author = {Zhang, R and Gong, C and Li, J and Zhuang, H and Lan, L and Zhou, L and Shan, S and Wang, Y}, title = {Tracing the transfer characteristics of antibiotic resistance genes from swine manure to biogas residue and then to soil.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169181}, doi = {10.1016/j.scitotenv.2023.169181}, pmid = {38072280}, issn = {1879-1026}, abstract = {Based on laboratory simulation experiments and metagenomic analysis, this study tracked the transmission of antibiotic resistance genes (ARGs) from swine manure (SM) to biogas residue and then to soil (biogas residue as organic fertilizer (OF) application). ARGs were abundant in SM and they were assigned to 11 categories of antibiotics. Among the 383 ARG subtypes in SM, 43 % ARG subtypes were absent after anaerobic digestion (AD), which avoided the transfer of these ARGs from SM to soil. Furthermore, 9 % of the ARG subtypes in SM were introduced into soil after amendment with OF. Moreover, 43 % of the ARG subtypes in SM were present in OF and soil, and their abundances increased slightly in the soil amended with OF. The bacterial community in the soil treated with OF was restored to its original state within 60 to 90 days, probably because the abundances of ARGs were elevated but not significantly in the soil. Network analysis identified 31 potential co-host bacteria of ARGs based on the relationships between the bacteria community members, where they mainly belonged to Firmicutes, followed by Bacteroidetes, Actinobacteria, and Proteobacteria. This study provides a basis for objectively evaluating pollution by ARGs in livestock manure for agricultural use.}, } @article {pmid38072228, year = {2024}, author = {Zhang, J and Shi, B and Lu, S and Wang, S and Ren, X and Liu, R and Dong, H and Li, K and Fouad, D and Ataya, FS and Mansoor, MK and Qamar, H and Wu, Q}, title = {Metagenomic analysis for exploring the potential of Lactobacillus yoelii FYL1 to mitigate bacterial diarrhea and changes in the gut microbiota of juvenile yaks.}, journal = {Microbial pathogenesis}, volume = {186}, number = {}, pages = {106496}, doi = {10.1016/j.micpath.2023.106496}, pmid = {38072228}, issn = {1096-1208}, mesh = {Cattle ; Animals ; Lactobacillus ; *Gastrointestinal Microbiome ; Escherichia coli ; Diarrhea/veterinary/microbiology ; Bacteria ; *Dysentery ; *Bacterial Infections ; }, abstract = {Diarrhea in calves is a common disease that results in poor nutrient absorption, poor growth and early death which leads to productivity and economic losses. Therefore, it is important to explore the methods to reduce diarrhea in yak's calves. Efficacy of lactic acid bacteria (LAB) for improvement of bacterial diarrhea is well recognized. For this purpose, two different doses (10[7] CFU, 10[11] CFU) of Lactobacillus yoelii FYL1 isolated from yaks were fed to juvenile yaks exposed to E. coli O78. After a trial period of ten days fresh feces and intestinal contents of the experimental yaks were collected and metagenomics sequencing was performed. It was found that feeding a high dose of Lactobacillus yoelii FYL1 decreased abundance of phylum Firmicutes in the E. coli O78 infected group whereas, it was high in animals fed low dose of Lactobacillu yoelii FYL1. Results also revealed that counts of bacteria from the family Oscillospiraceae, genus Synergistes and Megasphaera were higher in control group whereas, order Bifidobacteriales and family Bifidobacteriaceae were higher in infected group. It was observed that bacterial counts for Pseudoruminococcus were significantly (P < 0.05) higher in animals of group that were given high dose of Lactobacillus yoelii FYL1 (HLAB). Compared to infected group multiple beneficial bacterial genera such as Deinococus and Clostridium were found higher in the animals that were given a low dose of Lactobacillus yoelii FYL1 (LLAB). The abundance of pathogenic bacterial genera that included Parascardovia, Bacteroides and Methanobrevibacter was decreased (P < 0.05) in the lower dose treated group. The results of functional analysis revealed that animals of LLAB had a higher metabolism of terpenoids and polyketides compared to animals of infected group. Virus annotation also presented a significant inhibitory effect of LLAB on some viruses (P < 0.05). It was concluded that L. yoelii FYL1 had an improved effect on gut microbiota of young yaks infected with E. coli O78. This experiment contributes to establish the positive effects of LAB supplementation while treating diarrhea.}, } @article {pmid38072100, year = {2023}, author = {Chakraborty, S and Ghosh, S and Banerjee, S and Kumar, S and Bhattacharyya, P}, title = {Elucidating the synergistic effect of acidity and metalloid poisoning on the microbiome through metagenomics and machine learning approaches.}, journal = {Environmental research}, volume = {243}, number = {}, pages = {117885}, doi = {10.1016/j.envres.2023.117885}, pmid = {38072100}, issn = {1096-0953}, abstract = {The abundance and diversity of the microflora in a complex environment such as soil is everchanging. Mica mining has led to metalloid poisoning and changes in soil biogeochemistry affecting the overall produce and leading to toxic dietary exposure. The study focuses on two prominent stressors acidity and arsenic, in mining-contaminated agricultural locations. Soil samples were collected from agricultural fields at a distance of 50 m (zone 1) and 500 m (zone 2) from active mines. Mean arsenic concentration was higher in zone 1 and pH was lower. Geostatistical and self-organizing maps were employed to report that the pattern of localization of soil acidity and arsenic content is similar indicating a causal relationship. Cluster and principal component analysis were further used to materialize a negative effect of soil acidity fractions and arsenic labile pool on soil enzymatic activity (fluorescein diacetate, dehydrogenase, β-1,4-glucosidase, phosphatase, and urease), respiration and Microbial biomass carbon. Soil metagenomic analysis revealed significant differences in the abundance of microbial populations with zone 1 (contaminated zone) having lower alpha and beta diversity. Finally, the efficacy of several machine-learning tools was tested using Taylor diagrams and an effort was made to select a potent algorithm to predict the causal stressors responsible for depreciating soil microbial health. Random Forrest had superior predictive power based on numerical evidence and was therefore chosen as the best-fitted model. The aforementioned insights into soil microbial health and sustenance in stressed conditions can be beneficial for predicting remedial strategies and practicing sustainable agriculture.}, } @article {pmid38071920, year = {2024}, author = {Yang, T and Wang, X and Jiang, L and Hui, X and Bi, X and Zheng, X and Jiang, B and Wang, X}, title = {Mobility, bacterial hosts, and risks of antibiotic resistome in submicron bioaerosols from a full-scale wastewater treatment plant.}, journal = {Journal of environmental management}, volume = {351}, number = {}, pages = {119771}, doi = {10.1016/j.jenvman.2023.119771}, pmid = {38071920}, issn = {1095-8630}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Bacteria/genetics ; Wastewater ; *Water Purification ; }, abstract = {Antibiotic resistome could be loaded by bioaerosols and escape from wastewater or sludge to atmosphere environments. However, until recently, their profile, mobility, bacterial hosts, and risks in submicron bioaerosols (PM1.0) remain unclear. Here, metagenomic sequencing and assembly were employed to conduct an investigation of antibiotic resistome associated with PM1.0 within and around a full-scale wastewater treatment plant (WWTP). More subtypes of antibiotic resistant genes (ARGs) with higher total abundance were found along the upwind-downwind-WWTP transect. ARGs in WWTP-PM1.0 were mainly mediated by plasmids and transposases were the most prevalent mobile genetic elements (MGEs) co-occurring with ARGs. A contig-based analysis indicated that very small proportions (15.32%-19.74%) of ARGs in WWTP-PM1.0 were flanked by MGEs. Proteobacteria was the most dominant host of ARGs. A total of 28 kinds of potential pathogens, such as Pseudomonas aeruginosa and Escherichia coli, carried multiple ARG types. Compared to upwind, WWTP and corresponding downwind were characterized by higher PM1.0 resistome risk. This study emphasizes the vital role of WWTPs in discharging PM1.0-loaded ARGs and antibiotic resistant pathogens to air, and indicates the need for active safeguard procedures, such as that employees wear masks and work clothes, covering the main emission sites, and collecting and destroying of bioaerosols.}, } @article {pmid38071833, year = {2024}, author = {Afridi, MS and Kumar, A and Javed, MA and Dubey, A and de Medeiros, FHV and Santoyo, G}, title = {Harnessing root exudates for plant microbiome engineering and stress resistance in plants.}, journal = {Microbiological research}, volume = {279}, number = {}, pages = {127564}, doi = {10.1016/j.micres.2023.127564}, pmid = {38071833}, issn = {1618-0623}, mesh = {*Plant Roots/microbiology ; *Microbiota/physiology ; Exudates and Transudates/metabolism ; Plant Exudates/metabolism ; Quorum Sensing ; Plants/microbiology ; Rhizosphere ; Soil Microbiology ; }, abstract = {A wide range of abiotic and biotic stresses adversely affect plant's growth and production. Under stress, one of the main responses of plants is the modulation of exudates excreted in the rhizosphere, which consequently leads to alterations in the resident microbiota. Thus, the exudates discharged into the rhizospheric environment play a preponderant role in the association and formation of plant-microbe interactions. In this review, we aimed to provide a synthesis of the latest and most pertinent literature on the diverse biochemical and structural compositions of plant root exudates. Also, this work investigates into their multifaceted role in microbial nutrition and intricate signaling processes within the rhizosphere, which includes quorum-sensing molecules. Specifically, it explores the contributions of low molecular weight compounds, such as carbohydrates, phenolics, organic acids, amino acids, and secondary metabolites, as well as the significance of high molecular weight compounds, including proteins and polysaccharides. It also discusses the state-of-the-art omics strategies that unveil the vital role of root exudates in plant-microbiome interactions, including defense against pathogens like nematodes and fungi. We propose multiple challenges and perspectives, including exploiting plant root exudates for host-mediated microbiome engineering. In this discourse, root exudates and their derived interactions with the rhizospheric microbiota should receive greater attention due to their positive influence on plant health and stress mitigation.}, } @article {pmid38071777, year = {2023}, author = {Hu, Y and Wei, J and Yuan, Y and Wei, H and Zhou, Y and Xiao, N and Xiong, J and Ren, Z and Peng, J and Cui, C and Zhou, Z}, title = {Intervention effects of fructooligosaccharide and astragalus polysaccharide, as typical antibiotic alternatives, on antibiotic resistance genes in feces of layer breeding: advantages and defects.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133172}, doi = {10.1016/j.jhazmat.2023.133172}, pmid = {38071777}, issn = {1873-3336}, abstract = {Although antibiotic alternatives are widely used in livestock and poultry breeding industry after in-feed antibiotics ban, their intervention effects on antibiotic resistance genes (ARGs) in these food animals' feces remain poorly understood. Here effects of fructooligosaccharide (FOS) and astragalus polysaccharide (APS), as typical antibiotic alternatives in China, on ARGs in layer feces were estimated by performing metagenomic sequencings and fluorescence quantitative PCR. Fructooligosaccharide significantly reduced sum abundance of ARGs and mobile genetic elements (MGEs) by increasing Lactobacillus clones and reducing Escherichia clones which had relatively higher abundances of ARG subtypes and MGE subtypes in layer feces. However, at least parts of core ARGs and MGEs categories were not reduced by FOS, such as aminoglycosides- and tetracyclines-resistant genes, Tn916, Integrase, and so on. MGEs and microbiome, especially Escherichia genus and Lactobacillus genus, were the key factors affecting ARGs' sum abundance. MGEs had a higher correlation coefficient with ARGs' sum abundance than Escherichia genus and Lactobacillus genus. These findings firstly reveal the defects of antibiotic alternatives in controlling bacterial resistance in livestock and poultry breeding after in-feed antibiotics ban, and more strategies are needed to control pollutions and risks of core ARGs and MGEs in food animals' feces under a special environment.}, } @article {pmid38071676, year = {2023}, author = {Cullom, A and Spencer, MS and Williams, MD and Falkinham, JO and Brown, C and Edwards, MA and Pruden, A}, title = {Premise Plumbing Pipe Materials and In-Building Disinfectants Shape the Potential for Proliferation of Pathogens and Antibiotic Resistance Genes.}, journal = {Environmental science & technology}, volume = {57}, number = {50}, pages = {21382-21394}, doi = {10.1021/acs.est.3c05905}, pmid = {38071676}, issn = {1520-5851}, mesh = {Sanitary Engineering ; *Disinfectants/pharmacology ; Water Supply ; Anti-Bacterial Agents/pharmacology ; Copper ; Cell Proliferation ; *Drinking Water ; }, abstract = {In-building disinfectants are commonly applied to control the growth of pathogens in plumbing, particularly in facilities such as hospitals that house vulnerable populations. However, their application has not been well optimized, especially with respect to interactive effects with pipe materials and potential unintended effects, such as enrichment of antibiotic resistance genes (ARGs) across the microbial community. Here, we used triplicate convectively mixed pipe reactors consisting of three pipe materials (PVC, copper, and iron) for replicated simulation of the distal reaches of premise plumbing and evaluated the effects of incrementally increased doses of chlorine, chloramine, chlorine dioxide, and copper-silver disinfectants. We used shotgun metagenomic sequencing to characterize the resulting succession of the corresponding microbiomes over the course of 37 weeks. We found that both disinfectants and pipe material affected ARG and microbial community taxonomic composition both independently and interactively. Water quality and total bacterial numbers were not found to be predictive of pathogenic species markers. One result of particular concern was the tendency of disinfectants, especially monochloramine, to enrich ARGs. Metagenome assembly indicated that many ARGs were enriched specifically among the pathogenic species. Functional gene analysis was indicative of a response of the microbes to oxidative stress, which is known to co/cross-select for antibiotic resistance. These findings emphasize the need for a holistic evaluation of pathogen control strategies for plumbing.}, } @article {pmid38071398, year = {2023}, author = {Priest, T and Vidal-Melgosa, S and Hehemann, JH and Amann, R and Fuchs, BM}, title = {Carbohydrates and carbohydrate degradation gene abundance and transcription in Atlantic waters of the Arctic.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {130}, pmid = {38071398}, issn = {2730-6151}, support = {HE 7217/5-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Carbohydrates are chemically and structurally diverse, represent a substantial fraction of marine organic matter and are key substrates for heterotrophic microbes. Studies on carbohydrate utilisation by marine microbes have been centred on phytoplankton blooms in temperate regions, while far less is known from high-latitude waters and during later seasonal stages. Here, we combine glycan microarrays and analytical chromatography with metagenomics and metatranscriptomics to show the spatial heterogeneity in glycan distribution and potential carbohydrate utilisation by microbes in Atlantic waters of the Arctic. The composition and abundance of monomers and glycan structures in POM varied with location and depth. Complex fucose-containing sulfated polysaccharides, known to accumulate in the ocean, were consistently detected, while the more labile β-1,3-glucan exhibited a patchy distribution. Through 'omics analysis, we identify variations in the abundance and transcription of carbohydrate degradation-related genes across samples at the community and population level. The populations contributing the most to transcription were taxonomically related to those known as primary responders and key carbohydrate degraders in temperate ecosystems, such as NS4 Marine Group and Formosa. The unique transcription profiles for these populations suggest distinct substrate utilisation potentials, with predicted glycan targets corresponding to those structurally identified in POM from the same sampling sites. By combining cutting-edge technologies and protocols, we provide insights into the carbohydrate component of the carbon cycle in the Arctic during late summer and present a high-quality dataset that will be of great value for future comparative analyses.}, } @article {pmid38071295, year = {2023}, author = {Yang, J and Wang, J and Liu, Z and Chen, J and Jiang, J and Zhao, M and Gong, D}, title = {Ligilactobacillus Salivarius improve body growth and anti-oxidation capacity of broiler chickens via regulation of the microbiota-gut-brain axis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {395}, pmid = {38071295}, issn = {1471-2180}, support = {AGBMD202205//Jiangsu Key Laboratory of Animal genetic Breeding and Molecular Design/ ; NY2023016//Major Scientific and Technological Innovation Project of Zhenjiang city/ ; NY2023016//Major Scientific and Technological Innovation Project of Zhenjiang city/ ; [JBGS[2021]027; JBGS[2021]105]//JBGS" Project of Seed Industry Revitalization in Jiangsu Province/ ; [JBGS[2021]027; JBGS[2021]105]//JBGS" Project of Seed Industry Revitalization in Jiangsu Province/ ; }, mesh = {Animals ; *Ligilactobacillus salivarius ; Chickens ; Brain-Gut Axis ; Animal Feed/analysis ; *Probiotics/pharmacology ; Bacteria ; Peptides/metabolism ; }, abstract = {Certain strains of probiotic bacteria can secret functional substances namely digestive enzymes and functional peptides to regulate physiological conditions such as digestion and anti-oxidation, which are often incorporated in industrial broiler chick production. However, few studies have detailed the action mechanisms and effects of these bacteria on regulating growth and anti-oxidation levels in broiler chickens. Ligilactobacillus salivarius is a strain of probiotic bacteria used as dietary supplement. In the present study, Ligilactobacillus salivarius was evaluated for its secreted digestive enzymes in vitro. To detailed evaluate the action mechanisms and effects of gastrointestinal tract (GIT) microbiota on alleviating anti-oxidation levels of broiler chickens through the gut-brain axis. Ligilactobacillus salivarius was cultured and supplemented in the food of broilers to evaluate the probiotic effect on growth and anti-oxidation by modulation of gut microbial composition and its functional metabolites using metagenomic and metabolomic assays. Biochemical results showed that Ligilactobacillus salivarius secreted digestive enzymes: protease, lipase, and amylase. Broiler chickens with Ligilactobacillus salivarius supplemented for 42 days, showed increased body weights, a reduced oxidative status, decreased malondialdehyde levels, and improved activities rates of total superoxide dismutase, glutathione peroxidase IIand IV improved. The microbial composition of caecum was more abundant than those broiler without probiotics supplementation, owing 400 of total number (489) of bacterial operational taxonomic units (OTU). The genera of Lactobacillus, Megamonas, Ruminoccoccaceae, Ruminococcus, Alistipes and Helicobacter shared the dominant proportion of Candidatus _Arthromitus compared with the control chickens. These functional bacteria genera assisted in the transportation and digestion of amino acids, carbohydrates, and ions, synthesis of cellular membranes, and anti-oxidation. Uncultured_organism_g_ Anaerosporobacter, Lactobacillus salivarius, uncultured_bacterium_g_ Ruminococcaceae_UCG-014, uncultured_bacterium_g_ Peptococcus were strongly and positively correlated with body growth performance and anti-oxidation. A metabonomic assay suggested that the secreted of gamma-aminobutyric acid and monobactam was metabolized according to the Kyoto Encyclopedia of Genes and Genomes analysis. In conclusion, Ligilactobacillus salivarius optimized microbial composition of the caecum and secreted functional peptides through gut-brain axis to improve the body growth and antioxidation of broiler chicken.}, } @article {pmid38071207, year = {2023}, author = {Ristinmaa, AS and Tafur Rangel, A and Idström, A and Valenzuela, S and Kerkhoven, EJ and Pope, PB and Hasani, M and Larsbrink, J}, title = {Resin acids play key roles in shaping microbial communities during degradation of spruce bark.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {8171}, pmid = {38071207}, issn = {2041-1723}, support = {46559-1//Energimyndigheten (Swedish Energy Agency)/ ; 46559-1//Vetenskapsrådet (Swedish Research Council)/ ; CTS 21:1424//Carl Tryggers Stiftelse för Vetenskaplig Forskning (Carl Trygger Foundation)/ ; NNF20CC0035580//Novo Nordisk Fonden (Novo Nordisk Foundation)/ ; }, mesh = {Plant Bark ; *Picea ; *Microbiota ; Metagenome ; Bacteria/genetics ; }, abstract = {The bark is the outermost defense of trees against microbial attack, largely thanks to toxicity and prevalence of extractive compounds. Nevertheless, bark decomposes in nature, though by which species and mechanisms remains unknown. Here, we have followed the development of microbial enrichments growing on spruce bark over six months, by monitoring both chemical changes in the material and performing community and metagenomic analyses. Carbohydrate metabolism was unexpectedly limited, and instead a key activity was metabolism of extractives. Resin acid degradation was principally linked to community diversification with specific bacteria revealed to dominate the process. Metagenome-guided isolation facilitated the recovery of the dominant enrichment strain in pure culture, which represents a new species (Pseudomonas abieticivorans sp. nov.), that can grow on resin acids as a sole carbon source. Our results illuminate key stages in degradation of an abundant renewable resource, and how defensive extractive compounds have major roles in shaping microbiomes.}, } @article {pmid38070873, year = {2023}, author = {Wu, C and A, R and Ye, S and Ye, F and Huo, W and Lu, R and Tang, Y and Yang, J and Meng, X and Tang, Y and Chen, S and Zhao, L and Huang, B and Zhang, Z and Chen, Y and Li, D and Wang, W and Shan, KJ and Lu, J and Tan, W}, title = {Rapid identification of full-length genome and tracing variations of monkeypox virus in clinical specimens based on mNGS and amplicon sequencing.}, journal = {Virologica Sinica}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.virs.2023.12.002}, pmid = {38070873}, issn = {1995-820X}, abstract = {The monkeypox virus (MPXV) has triggered a current outbreak globally. Genome sequencing of MPXV and rapid tracing of genetic variants will benefit disease diagnosis and control. It is a significant challenge but necessary to optimize the strategy and application of rapid full-length genome identification and to track variations of MPXV in clinical specimens with low viral loads, as it is one of the DNA viruses with the largest genome and the most AT-biased, and has a significant number of tandem repeats. Here we evaluated the performance of metagenomic and amplicon sequencing techniques, and three sequencing platforms in MPXV genome sequencing based on multiple clinical specimens of five mpox cases in Chinese mainland. We rapidly identified the full-length genome of MPXV with the assembly of accurate tandem repeats in multiple clinical specimens. Amplicon sequencing enables cost-effective and rapid sequencing of clinical specimens to obtain high-quality MPXV genomes. Third-generation sequencing facilitates the assembly of the terminal tandem repeat regions in the monkeypox virus genome and corrects a common misassembly in published sequences. Besides, several intra-host single nucleotide variations were identified in the first imported mpox case. This study offers an evaluation of various strategies aimed at identifying the complete genome of MPXV in clinical specimens. The findings of this study will significantly enhance the surveillance of MPXV.}, } @article {pmid38070858, year = {2023}, author = {Wang, Y and Cai, J and Chen, X and Guo, B and Liu, J and Qiu, G and Li, H}, title = {The connection between the antibiotic resistome and nitrogen-cycling microorganisms in paddy soil is enhanced by application of chemical and plant-derived organic fertilizers.}, journal = {Environmental research}, volume = {243}, number = {}, pages = {117880}, doi = {10.1016/j.envres.2023.117880}, pmid = {38070858}, issn = {1096-0953}, abstract = {Antibiotic resistant genes (ARGs) present significant risks to environments and public health. In particular, there is increasing awareness of the role of soil nitrogen in ARG dissemination. Here, we investigated the connections between antibiotic resistome and nitrogen-cycling microbes in paddy soil by performing five-year field experiments with the treatments of no nitrogen fertilization (CK), reduced chemical nitrogen fertilization (LN), conventional chemical nitrogen fertilization (CN) and plant-derived organic nitrogen fertilization (ON). Compared with CK treatment, CN and ON treatments significantly increased soil NH4[+] and TN concentrations by 25.4%-56.5% and 10.4%-20.1%, respectively. Redundancy analysis revealed significantly positive correlation of NH4[+] with most ARGs, including tetA, macB and barA. Correspondingly, CN and ON treatments enhanced ARG abundances by 21.9%-23.2%. Moreover, CN and ON treatments promoted nitrate/nitrite-reducing bacteria and linked the corresponding N-cycling functional genes (narG, narH, nirK and nrfA) with most ARGs. Metagenomic binning was performed and identified Gemmatimonadaceae, Caulobacteraceae, Ilumatobacteraceae and Anaerolineaceae as hosts for both ARGs and nitrate/nitrite reduction genes that were enriched by CN and ON treatments. Soil resistome risk score analysis indicated that, although there was increased relation of ARG to nitrogen-cycling microorganisms with nitrogen fertilizer application, the environmental risk of ARGs was not increased due to the lower distribution of ARGs in pathogens. This study contributed to a deeper understanding of the role of soil nitrogen in shaping ARG profiles and controlling soil resistome risk.}, } @article {pmid38070726, year = {2023}, author = {Lousada, MB and Edelkamp, J and Lachnit, T and Fehrholz, M and Pastar, I and Jimenez, F and Erdmann, H and Bosch, TCG and Paus, R}, title = {Spatial distribution and functional impact of human scalp hair follicle microbiota.}, journal = {The Journal of investigative dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jid.2023.11.006}, pmid = {38070726}, issn = {1523-1747}, abstract = {Human hair follicles (HFs) constitute a unique microbiota habitat that differs substantially from the skin surface. Traditional HF sampling methods fail to eliminate skin microbial contaminants or assess the HF microbiota incompletely, while microbiota functions in human HF physiology remain ill-explored. Therefore, we used laser-capture microdissection, metagenomic shotgun sequencing, and FISH to characterize the human scalp HF microbiota in defined anatomical compartments. This revealed significant compartment-, tissue lineage- and donor age-dependent variations in microbiota composition. Greatest abundance variations between HF compartments were observed for viruses, archaea, Staphylococcus epidermidis, Cutibacterium acnes and Malassezia restricta, with the latter two being surprisingly higher in the HF mesenchyme, and the most abundant viable HF epithelium colonizers (tested by propidium monoazide assay). Transfection of organ-cultured human scalp HFs with S. epidermidis-specific lytic bacteriophages ex vivo downregulated transcription of genes known to regulate HF growth and development, metabolism and melanogenesis, suggesting that selected microbial products can modulate HF functions. Indeed, treatment with butyrate, a bacterial metabolite of S. epidermidis amongst other HF microbiota, delayed catagen, promoted autophagy, mitochondrial activity, gp100, and dermcidin expression ex vivo. Thus, human HF microbiota show variations in spatial abundance and exert important modulatory effects on their host, inviting therapeutic targeting.}, } @article {pmid38070671, year = {2023}, author = {Majumder, S and Kiritkumar Makwana, R and Shetty, V and Mukherjee, S and Narayan, P}, title = {Cardiovascular diseases and the heart-gut cross talk.}, journal = {Indian heart journal}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ihj.2023.12.003}, pmid = {38070671}, issn = {2213-3763}, abstract = {The purpose of this narrative review is to provide a comprehensive overview of current research on heart-gut cross talk and its implications for cardiovascular disease. To uncover relevant preclinical and clinical research examining heart-gut cross talk, a thorough literature search was undertaken utilising electronic databases. The chosen publications were critically examined, and major findings were synthesised to offer a thorough perspective on the subject. We want to synthesise the most recent study findings, explain the underlying mechanisms, and provide potential treatment techniques. By exploring bidirectional connection between the heart and the gut, we shed light on novel future options for the prevention and treatment of cardiovascular diseases. The heart-gut cross talk is an exciting field of study with implications for cardiovascular disease. Understanding the complex connection between the heart and the gastrointestinal tract may lead to the development of novel therapeutic targets and therapies for the prevention and management of cardiovascular diseases. Future research should concentrate on identifying the specific processes driving this crosstalk as well as assessing the efficacy of therapies targeting the gut microbiota and the gut-brain axis in improving cardiovascular outcomes.}, } @article {pmid38070547, year = {2023}, author = {Li, X and Zhu, L and Zhang, SY and Li, J and Lin, D and Wang, M}, title = {Characterization of microbial contamination in agricultural soil: A public health perspective.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169139}, doi = {10.1016/j.scitotenv.2023.169139}, pmid = {38070547}, issn = {1879-1026}, abstract = {Soil is widely recognized as a reservoir of microbial contaminants including antibiotic resistance genes (ARGs) and human bacterial pathogens (HBPs), which are major public health concerns. Although the risks associated with soil safety in different soil habitats have been studied, the results are not comprehensive. In this study, dryland soils used for vegetable, corn, and soybean planting, and submerged soils used for rice planting and crab farming were collected and subjected to metagenomic sequencing to characterize HBPs, ARGs, and virulence factor genes (VFGs). The results showed that submerged soils had a higher abundance of HBP than dryland soils. In addition, the submerged soil microbiome acquired significantly higher levels of high-risk ARGs than the dryland soil microbiome and these ARGs were mainly assigned to bacA, sul1, and aadA genes submerged. Network analysis revealed that 11 HBPs, including Yersinia enterocolitica, Vibrio cholerae, Escherichia coli, and Leptospira interrogans, were high-risk because of their close association with ARGs, VFGs, and mobile genetic elements (MGEs). Procrustes and network analyses showed that HBPs and ARGs were more closely linked in submerged soil. This study confirms that submerged field has higher ecological environment risk and human health risk than dryland soil.}, } @article {pmid38070437, year = {2023}, author = {Wang, JF and Huang, JW and Cai, ZX and Li, QS and Sun, YY and Zhou, HZ and Zhu, H and Song, XS and Wu, HM}, title = {Differential Nitrous oxide emission and microbiota succession in constructed wetlands induced by nitrogen forms.}, journal = {Environment international}, volume = {183}, number = {}, pages = {108369}, doi = {10.1016/j.envint.2023.108369}, pmid = {38070437}, issn = {1873-6750}, abstract = {Nitrous oxide (N2O) emission during the sewage treatment process is a serious environmental issue that requires attention. However, the N2O emission in constructed wetlands (CWs) as affected by different nitrogen forms in influents remain largely unknown. This study investigated the N2O emission profiles driven by microorganisms in CWs when exposed to two typical nitrogen sources (NH4[+]-N or NO3[-]-N) along with different carbon source supply (COD/N ratios: 3, 6, and 9). The results showed that CWs receiving NO3[-]-N caused a slight increase in total nitrogen removal (by up to 11.8 %). This increase was accomplished by an enrichment of key bacteria groups, including denitrifiers, dissimilatory nitrate reducers, and assimilatory nitrate reducers, which enhanced the stability of microbial interaction. Additionally, it led to a greater abundance of denitrification genes (e.g., nirK, norB, norC, and nosZ) as inferred from the database. Consequently, this led to a gradual increase in N2O emission from 66.51 to 486.77 ug-N/(m[2]·h) as the COD/N ratio increased in CWs. Conversely, in CWs receiving NH4[+]-N, an increasing influent COD/N ratio had a negative impact on nitrogen biotransformation. This resulted in fluctuating trend of N2O emissions, which decreased initially, followed by an increase at later stage (with values of 122.87, 44.00, and 148.59 ug-N/(m[2]·h)). Furthermore, NH4[+]-N in the aquatic improved the nitrogen uptake by plants and promoted the production of more root exudates. As a result, it adjusted the nitrogen-transforming function, ultimately reducing N2O emissions in CWs. This study highlights the divergence in microbiota succession and nitrogen transformation in CWs induced by nitrogen form and COD/N ratio, contributing to a better understanding of the microbial mechanisms of N2O emission in CWs with NH4[+]-N or NO3[-]-N at different COD/N ratios.}, } @article {pmid38070426, year = {2024}, author = {Mukherjee, P and Sharma, RS and Rawat, D and Sharma, U and Karmakar, S and Yadav, A and Mishra, V}, title = {Microbial communities drive flux of acid orange 7 and crystal violet dyes in water-sediment system.}, journal = {Journal of environmental management}, volume = {351}, number = {}, pages = {119699}, doi = {10.1016/j.jenvman.2023.119699}, pmid = {38070426}, issn = {1095-8630}, mesh = {*Gentian Violet ; Coloring Agents/chemistry ; Azo Compounds/chemistry ; *Microbiota ; *Benzenesulfonates ; }, abstract = {Unchecked dye effluent discharge poses escalating environmental and economic concerns, especially in developing nations. While dyes are well-recognized water pollutants, the mechanisms of their environmental spread are least understood. Therefore, the present study examines the partitioning of Acid Orange 7 (AO7) and Crystal Violet (CV) dyes using water-sediment microcosms and reports that native microbes significantly affect AO7 decolorization and transfer. Both dyes transition from infused to pristine matrices, reaching equilibrium in a fortnight. While microbes influence CV partitioning, their role in decolorization is minimal, emphasizing their varied impact on the environmental fate of dyes. Metagenomic analyses reveal contrasting microbial composition between control and AO7-infused samples. Control water samples displayed a dominance of Proteobacteria (62%), Firmicutes (24%), and Bacteroidetes (9%). However, AO7 exposure led to Proteobacteria reducing to 57% and Bacteroidetes to 3%, with Firmicutes increasing to 34%. Sediment samples, primarily comprising Firmicutes (47%) and Proteobacteria (39%), shifted post-AO7 exposure: Proteobacteria increased to 53%, and Firmicutes dropped to 38%. At the genus level, water samples dominated by Niveispirillum (34%) declined after AO7 exposure, while Bacillus and Pseudomonas increased. Notably, Serratia and Sphingomonas, known for azo dye degradation, rose post-exposure, hinting at their role in AO7 decolorization. Conversely, sediment samples showed a decrease in the growth of Bacillus and an increase in that of Pseudomonas and Serratia. These findings emphasize the significant role of microbial communities in determining the environmental fate of dyes, providing insights on its environmental implications and management.}, } @article {pmid38070135, year = {2023}, author = {Lum, GR and Ha, SM and Olson, CA and Blencowe, M and Paramo, J and Reyes, B and Matsumoto, JH and Yang, X and Hsiao, EY}, title = {Ketogenic diet therapy for pediatric epilepsy is associated with alterations in the human gut microbiome that confer seizure resistance in mice.}, journal = {Cell reports}, volume = {42}, number = {12}, pages = {113521}, pmid = {38070135}, issn = {2211-1247}, support = {R01 NS115537/NS/NINDS NIH HHS/United States ; }, mesh = {Child ; Humans ; Animals ; Mice ; *Diet, Ketogenic ; *Gastrointestinal Microbiome ; *Epilepsy ; *Microbiota ; Ketone Bodies ; Disease Models, Animal ; Seizures ; }, abstract = {The gut microbiome modulates seizure susceptibility and the anti-seizure effects of the ketogenic diet (KD) in animal models, but whether these relationships translate to KD therapies for human epilepsy is unclear. We find that the clinical KD alters gut microbial function in children with refractory epilepsy. Colonizing mice with KD-associated microbes promotes seizure resistance relative to matched pre-treatment controls. Select metagenomic and metabolomic features, including those related to anaplerosis, fatty acid β-oxidation, and amino acid metabolism, are seen with human KD therapy and preserved upon microbiome transfer to mice. Mice colonized with KD-associated gut microbes exhibit altered hippocampal transcriptomes, including pathways related to ATP synthesis, glutathione metabolism, and oxidative phosphorylation, and are linked to susceptibility genes identified in human epilepsy. Our findings reveal key microbial functions that are altered by KD therapies for pediatric epilepsy and linked to microbiome-induced alterations in brain gene expression and seizure protection in mice.}, } @article {pmid38070037, year = {2023}, author = {Aziz, K and Gilbert, JA and Zaidi, AH}, title = {Genomic and Phenotypic Insight into the Probiotic Potential of Lactic Acid Bacterial spp. Associated with the Human Gut Mucosa.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {38070037}, issn = {1867-1314}, support = {SIG # S10 OD026929/NH/NIH HHS/United States ; }, abstract = {Commensal microbiome-based health support is gaining respect in the medical community and new human gut-associated Lactic Acid Bacteria (LAB) strains must be evaluated for their probiotic potential. Here we characterized the phenotype and genomes of human ileocecal mucosa-associated LAB strains using metagenomic sequencing and in vitro testing. The strains characterized belonged to the genus Enterococcus (Enterococcus lactis NPL1366, NPL1371, and Enterococcus mundtii NPL1379) and Lactobacillus (Lactobacillus paragasseri, NPL1369, NPL1370, and Lactiplantibacillus plantarum NPL1378). Genome annotation suggested bacterial adaptation to both human physiological and industrial manufacturing-related stressors. Genes for histidine kinases in enterococci and Na + /K + antiporters and F0F1 ATP synthases in Lactobacillus strains may support their tolerance to acid seen in vitro. The bile salt hydrolase (BSH) gene in Lp. plantarum and L. paragasseri may help explain their reported bile salt deconjugation and cholesterol-lowering behavior. Thioredoxin is the principal antioxidant system, and several oxidases and general stress-related proteins are found in lactobacilli, most notably in L. plantarum NPL1378. Multiple adhesion and biofilm-related genes were predicted in the LAB genomes. Adhesion and biofilm-related genes figured prominently in the genomes of enterococcal strains, especially E. lactis, corresponding to its biofilm formation capacity in vitro. Bacteriocin and secondary metabolite biosynthetic gene clusters in the sequenced genomes of E. lactis NPL1366 and Lp. plantarum NPL1378 may explain their in vitro pathogenic antagonism. Moreover, folate producing Lp. plantarum strain holds potential to be used in therapeutics or biofortification of food. All the strains were deemed safe through in vitro and in silico analysis. This basic genetic and phenotypic information supports their contention as probiotic adjuncts to conventional medical therapy.}, } @article {pmid38069903, year = {2024}, author = {Mirchandani, CD and Shultz, AJ and Thomas, GWC and Smith, SJ and Baylis, M and Arnold, B and Corbett-Detig, R and Enbody, E and Sackton, TB}, title = {A Fast, Reproducible, High-throughput Variant Calling Workflow for Population Genomics.}, journal = {Molecular biology and evolution}, volume = {41}, number = {1}, pages = {}, pmid = {38069903}, issn = {1537-1719}, mesh = {Animals ; *Software ; *Metagenomics ; Workflow ; Genomics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; }, abstract = {The increasing availability of genomic resequencing data sets and high-quality reference genomes across the tree of life present exciting opportunities for comparative population genomic studies. However, substantial challenges prevent the simple reuse of data across different studies and species, arising from variability in variant calling pipelines, data quality, and the need for computationally intensive reanalysis. Here, we present snpArcher, a flexible and highly efficient workflow designed for the analysis of genomic resequencing data in nonmodel organisms. snpArcher provides a standardized variant calling pipeline and includes modules for variant quality control, data visualization, variant filtering, and other downstream analyses. Implemented in Snakemake, snpArcher is user-friendly, reproducible, and designed to be compatible with high-performance computing clusters and cloud environments. To demonstrate the flexibility of this pipeline, we applied snpArcher to 26 public resequencing data sets from nonmammalian vertebrates. These variant data sets are hosted publicly to enable future comparative population genomic analyses. With its extensibility and the availability of public data sets, snpArcher will contribute to a broader understanding of genetic variation across species by facilitating the rapid use and reuse of large genomic data sets.}, } @article {pmid38069639, year = {2023}, author = {Jeong, DE and Sundrani, S and Hall, RN and Krupovic, M and Koonin, EV and Fire, AZ}, title = {DNA Polymerase Diversity Reveals Multiple Incursions of Polintons During Nematode Evolution.}, journal = {Molecular biology and evolution}, volume = {40}, number = {12}, pages = {}, pmid = {38069639}, issn = {1537-1719}, support = {R35GM130366/GM/NIGMS NIH HHS/United States ; /NH/NIH HHS/United States ; /LM/NLM NIH HHS/United States ; }, mesh = {Humans ; Animals ; Phylogeny ; DNA Transposable Elements ; DNA-Directed DNA Polymerase/genetics ; *Viruses/genetics ; *Nematoda/genetics ; }, abstract = {Polintons are double-stranded DNA, virus-like self-synthesizing transposons widely found in eukaryotic genomes. Recent metagenomic discoveries of Polinton-like viruses are consistent with the hypothesis that Polintons invade eukaryotic host genomes through infectious viral particles. Nematode genomes contain multiple copies of Polintons and provide an opportunity to explore the natural distribution and evolution of Polintons during this process. We performed an extensive search of Polintons across nematode genomes, identifying multiple full-length Polinton copies in several species. We provide evidence of both ancient Polinton integrations and recent mobility in strains of the same nematode species. In addition to the major nematode Polinton family, we identified a group of Polintons that are overall closely related to the major family but encode a distinct protein-primed DNA polymerase B (pPolB) that is related to homologs from a different group of Polintons present outside of the Nematoda. Phylogenetic analyses on the pPolBs support the evolutionary scenarios in which these extrinsic pPolBs that seem to derive from Polinton families present in oomycetes and molluscs replaced the canonical pPolB in subsets of Polintons found in terrestrial and marine nematodes, respectively, suggesting interphylum horizontal gene transfers. The pPolBs of the terrestrial nematode and oomycete Polintons share a unique feature, an insertion of an HNH nuclease domain, whereas the pPolBs in the marine nematode Polintons share an insertion of a VSR nuclease domain with marine mollusc pPolBs. We hypothesize that horizontal gene transfer occurs among Polintons from widely different but cohabiting hosts.}, } @article {pmid38069429, year = {2023}, author = {Gunitseva, N and Evteeva, M and Korzhenkov, A and Patrushev, M}, title = {A New RNA-Dependent Cas12g Nuclease.}, journal = {International journal of molecular sciences}, volume = {24}, number = {23}, pages = {}, pmid = {38069429}, issn = {1422-0067}, support = {agreement number 075-15-2021-1062//The study was supported by grants from the Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {*RNA/genetics ; *Gene Editing/methods ; CRISPR-Cas Systems ; Endonucleases/genetics/metabolism ; }, abstract = {The development of RNA-targeting CRISPR-Cas systems represents a major step forward in the field of gene editing and regulation. RNA editing presents a viable alternative to genome editing in certain scenarios as it offers a reversible and manageable approach, reducing the likelihood of runaway mutant variants. One of the most promising applications is in the treatment of genetic disorders caused by mutations in RNA molecules. In this study, we investigate a previously undescribed Cas12g nuclease which was found in metagenomes from promising thermophilic microbial communities during the expedition to the Republic of North Ossetia-Alania in 2020. The method outlined in this study can be applied to other Cas orthologs and variants, leading to a better understanding of the CRISPR-Cas system and its enzymatic activities. The cis-cleavage activity of the new type V-G Cas effector was indicated by in vitro RNA cleavage experiments. While CRISPR-Cas systems are known for their high specificity, there is still a risk of unintended cleavage of nontargeted RNA molecules. Ultimately, the search for new genome editing tools and the study of their properties will remove barriers to research in this area. With continued research and development, we may be able to unlock their full potential.}, } @article {pmid38069344, year = {2023}, author = {Butina, TV and Zemskaya, TI and Bondaryuk, AN and Petrushin, IS and Khanaev, IV and Nebesnykh, IA and Bukin, YS}, title = {Viral Diversity in Samples of Freshwater Gastropods Benedictia baicalensis (Caenogastropoda: Benedictiidae) Revealed by Total RNA-Sequencing.}, journal = {International journal of molecular sciences}, volume = {24}, number = {23}, pages = {}, pmid = {38069344}, issn = {1422-0067}, support = {22-24-01120//Russian Science Foundation/ ; }, mesh = {Animals ; *Gastropoda/genetics ; Ecosystem ; *Viruses/genetics ; Lakes ; *RNA Viruses/genetics ; Genome, Viral ; RNA ; Phylogeny ; }, abstract = {Previously, the main studies were focused on viruses that cause disease in commercial and farmed shellfish and cause damage to food enterprises (for example, Ostreavirusostreidmalaco1, Aurivirus haliotidmalaco1 and Aquabirnavirus tellinae). Advances in high-throughput sequencing technologies have extended the studies to natural populations of mollusks (and other invertebrates) as unexplored niches of viral diversity and possible sources of emerging diseases. These studies have revealed a huge diversity of mostly previously unknown viruses and filled gaps in the evolutionary history of viruses. In the present study, we estimated the viral diversity in samples of the Baikal endemic gastropod Benedictia baicalensis using metatranscriptomic analysis (total RNA-sequencing); we were able to identify a wide variety of RNA-containing viruses in four samples (pools) of mollusks collected at three stations of Lake Baikal. Most of the identified viral genomes (scaffolds) had only distant similarities to known viruses or (in most cases) to metagenome-assembled viral genomes from various natural samples (mollusks, crustaceans, insects and others) mainly from freshwater ecosystems. We were able to identify viruses similar to those previously identified in mollusks (in particular to the picornaviruses Biomphalaria virus 1 and Biomphalaria virus 3 from the freshwater gastropods); it is possible that picorna-like viruses (as well as a number of other identified viruses) are pathogenic for Baikal gastropods. Our results also suggested that Baikal mollusks, like other species, may bioaccumulate or serve as a reservoir for numerous viruses that infect a variety of organisms (including vertebrates).}, } @article {pmid38068802, year = {2023}, author = {Cordero-Varela, JA and Reyes-Corral, M and Lao-Pérez, M and Fernández-Santos, B and Montenegro-Elvira, F and Sempere, L and Ybot-González, P}, title = {Analysis of Gut Characteristics and Microbiota Changes with Maternal Supplementation in a Neural Tube Defect Mouse Model.}, journal = {Nutrients}, volume = {15}, number = {23}, pages = {}, pmid = {38068802}, issn = {2072-6643}, support = {DOC_01701//Consejería de Transformación Económica, Industria, Conocimiento y Universidades; Junta de Andalucía/ ; P20_01267//Consejería de Transformación Económica, Industria, Conocimiento y Universidades; Junta de Andalucía/ ; RH-0033-2020//Consejería de Salud y Bienestar Social; Junta de Andalucía/ ; C-0025-2018//Consejería de Salud y Bienestar Social; Junta de Andalucía/ ; EF- 0084-2016//Consejería de Salud y Bienestar Social; Junta de Andalucía/ ; 050561//Consejo Superior de Investigaciones Científicas; Ministerio de Ciencia e Innovación/ ; PI17/00693//Instituto de Salud Carlos III (ISCIII) and co-funded by the European Union/ ; PI20/00769//Instituto de Salud Carlos III (ISCIII) and co-funded by the European Union/ ; 202220/095//Consejo Superior de Investigaciones Científicas; Ministerio de Ciencia e Innovación/ ; }, mesh = {Female ; Pregnancy ; Mice ; Animals ; RNA, Ribosomal, 16S/genetics ; *Neural Tube Defects/prevention & control ; Folic Acid/pharmacology ; Dietary Supplements ; Inositol ; *Microbiota ; Disease Models, Animal ; }, abstract = {Adequate nutrient supply is crucial for the proper development of the embryo. Although nutrient supply is determined by maternal diet, the gut microbiota also influences nutrient availability. While currently there is no cure for neural tube defects (NTDs), their prevention is largely amenable to maternal folic acid and inositol supplementation. The gut microbiota also contributes to the production of these nutrients, which are absorbed by the host, but its role in this context remains largely unexplored. In this study, we performed a functional and morphological analysis of the intestinal tract of loop-tail mice (Vangl2 mutants), a mouse model of folate/inositol-resistant NTDs. In addition, we investigated the changes in gut microbiota using 16S rRNA gene sequencing regarding (1) the host genotype; (2) the sample source for metagenomics analysis; (3) the pregnancy status in the gestational window of neural tube closure; (4) folic acid and (5) D-chiro-inositol supplementation. We observed that Vangl2[+/Lp] mice showed no apparent changes in gastrointestinal transit time or fecal output, yet exhibited increased intestinal length and cecal weight and gut dysbiosis. Moreover, our results showed that the mice supplemented with folic acid and D-chiro-inositol had significant changes in their microbiota composition, which are changes that could have implications for nutrient absorption.}, } @article {pmid38068569, year = {2023}, author = {Kim, N and Lee, D and Lee, SB and Lim, GH and Kim, SW and Kim, TJ and Park, DS and Seo, YS}, title = {Understanding Burkholderia glumae BGR1 Virulence through the Application of Toxoflavin-Degrading Enzyme, TxeA.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {23}, pages = {}, pmid = {38068569}, issn = {2223-7747}, support = {2022R1A2C1003190//National Research Foundation of Korea/ ; 2022R1A4A5031503//Ministry of Education/ ; }, abstract = {Rice (Oryzae sativa cv. dongjin) is a cornerstone of global food security; however, Burkholderia glumae BGR1, which is responsible for bacterial panicle blight (BPB), threatens its productive output, with dire consequences for rice and other crops. BPB is primarily caused by toxoflavin, a potent phytotoxin that disrupts plant growth at various developmental stages. Therefore, understanding the mechanisms through which toxoflavin and BPB affect rice plants is critical. Toxoflavin biosynthesis in B. glumae BGR1 relies on the toxABCDE operon, with ToxA playing a central role. In response to this threat, our study explores a metagenome-derived toxoflavin-degrading enzyme, TxeA, as a potential defense mechanism against toxoflavin's destructive impact. TxeA-induced degradation of toxoflavin represents a potential strategy to mitigate crop damage. We introduce a groundbreaking approach: engineering transgenic rice plants to produce toxoflavin-degrading enzymes. These genetically modified plants, armed with TxeA, hold significant potential for combating toxoflavin-related crop losses. However, removal of toxoflavin, a major virulence factor in B. glumae BGR1, does not completely inhibit virulence. This innovative perspective offers a new shift from pathogen eradication to leveraging transgenic plants' power, offering a beacon of hope for crop protection and disease management. Our study offers insights into the intricate interplay between toxoflavin, BPB, and TxeA, providing a promising avenue to safeguard rice crops, ensure food security, and potentially enhance the resilience of various agricultural crops to B. glumae BGR1-induced diseases.}, } @article {pmid38066947, year = {2023}, author = {Lisjak, A and Correa Lopes, B and Pilla, R and Nemec, A and Suchodolski, JS and Tozon, N}, title = {A Comparison of the Oral Microbiota in Healthy Dogs and Dogs with Oral Tumors.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {23}, pages = {}, pmid = {38066947}, issn = {2076-2615}, support = {P3-0428, P4-0053, J4-2546//Slovenian Research Agency/ ; The microbiome research at the Gastrointestinal Laboratory at Texas A&M University is in part funded by Purina PetCare Research Excellence Fund//Purina PetCare Research Excellence Fund/ ; }, abstract = {The aim of this study was to further describe the oral microbiota of healthy dogs by DNA shotgun sequencing and compare those to dogs with oral tumors. Oral swabs (representative of all niches of the oral cavity) were collected from healthy dogs (n = 24) and from dogs with different oral tumors (n = 7). DNA was extracted from the swabs and shotgun metagenomic sequencing was performed. Only minor differences in microbiota composition were observed between the two groups. At the phylum level, the Bacteroidota, Proteobacteria, Actinobacteriota, Desulfobacterota and Firmicutes were most abundant in both groups. Observed Operational Taxonomic Units-OTUs (species richness) was significantly higher in the healthy patients, but there was no significant difference in the Shannon diversity index between the groups. No significant difference was found in beta diversity between the groups. The core oral microbiota consisted of 67 bacterial species that were identified in all 24 healthy dogs. Our study provides further insight into the composition of the oral microbiota of healthy dogs and in dogs with oral tumors.}, } @article {pmid38066630, year = {2023}, author = {Baud, GLC and Prasad, A and Ellegaard, KM and Engel, P}, title = {Turnover of strain-level diversity modulates functional traits in the honeybee gut microbiome between nurses and foragers.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {283}, pmid = {38066630}, issn = {1474-760X}, support = {714804//H2020 European Research Council/ ; 180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 179487//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; IZSTZ0_189496//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, mesh = {Humans ; Bees/genetics ; Animals ; *Gastrointestinal Microbiome/genetics ; Symbiosis/physiology ; *Microbiota ; Bacteria/genetics ; Metagenomics ; }, abstract = {BACKGROUND: Strain-level diversity is widespread among bacterial species and can expand the functional potential of natural microbial communities. However, to what extent communities undergo consistent shifts in strain composition in response to environmental/host changes is less well understood.

RESULTS: Here, we used shotgun metagenomics to compare the gut microbiota of two behavioral states of the Western honeybee (Apis mellifera), namely nurse and forager bees. While their gut microbiota is composed of the same bacterial species, we detect consistent changes in strain-level composition between nurses and foragers. Single nucleotide variant profiles of predominant bacterial species cluster by behavioral state. Moreover, we identify strain-specific gene content related to nutrient utilization, vitamin biosynthesis, and cell-cell interactions specifically associated with the two behavioral states.

CONCLUSIONS: Our findings show that strain-level diversity in host-associated communities can undergo consistent changes in response to host behavioral changes modulating the functional potential of the community.}, } @article {pmid38066544, year = {2023}, author = {Liang, Y and Dou, S and Zhao, G and Shen, J and Fu, G and Fu, L and Li, S and Cong, B and Dong, C}, title = {Prediction of BMI traits in the Chinese population based on the gut metagenome.}, journal = {Microbial cell factories}, volume = {22}, number = {1}, pages = {250}, pmid = {38066544}, issn = {1475-2859}, mesh = {Humans ; Metagenome ; Body Mass Index ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; Feces/microbiology ; China ; }, abstract = {BACKGROUND: Identifying individual characteristics based on trace evidence left at a crime scene is crucial in forensic identification. Microbial communities found in fecal traces have high individual specificity and could serve as potential markers for forensic characterization. Previous research has established that predicting body type based on the relative abundance of the gut microbiome is relatively accurate. However, the long-term stability and high individual specificity of the gut microbiome are closely linked to changes at the genome level of the microbiome. No studies have been conducted to deduce body shape from genetic traits. Therefore, in this study, the vital role of gut bacterial community characteristics and genetic traits in predicting body mass index (BMI) was investigated using gut metagenomic data from a healthy Chinese population.

RESULTS: Regarding the gut microbial community, the underweight group displayed increased α-diversity in comparison to the other BMI groups. There were significant differences in the relative abundances of 19 species among these three BMI groups. The BMI prediction model, based on the 31 most significant species, showed a goodness of fit (R[2]) of 0.56 and a mean absolute error (MAE) of 2.09 kg/m[2]. The overweight group exhibited significantly higher α-diversity than the other BMI groups at the level of gut microbial genes. Furthermore, there were significant variations observed in the single-nucleotide polymorphism (SNP) density of 732 contigs between these three BMI groups. The BMI prediction model, reliant on the 62 most contributing contigs, exhibited a model R[2] of 0.72 and an MAE of 1.56 kg/m[2]. The model predicting body type from 44 contigs correctly identified the body type of 93.55% of the study participants.

CONCLUSION: Based on metagenomic data from a healthy Chinese population, we demonstrated the potential of genetic traits of gut bacteria to predict an individual's BMI. The findings of this study suggest the effectiveness of a novel method for determining the body type of suspects in forensic applications using the genetic traits of the gut microbiome and holds great promise for forensic individual identification.}, } @article {pmid38066426, year = {2023}, author = {Ma, B and Gavzy, SJ and France, M and Song, Y and Lwin, HW and Kensiski, A and Saxena, V and Piao, W and Lakhan, R and Iyyathurai, J and Li, L and Paluskievicz, C and Wu, L and WillsonShirkey, M and Mongodin, EF and Mas, VR and Bromberg, JS}, title = {Rapid intestinal and systemic metabolic reprogramming in an immunosuppressed environment.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {394}, pmid = {38066426}, issn = {1471-2180}, support = {R01 HL148672/HL/NHLBI NIH HHS/United States ; T32 AI095190/AI/NIAID NIH HHS/United States ; R01HL148672/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Mice ; Immunosuppressive Agents/pharmacology ; Metabolome ; Metabolomics ; *Tacrolimus ; }, abstract = {Intrinsic metabolism shapes the immune environment associated with immune suppression and tolerance in settings such as organ transplantation and cancer. However, little is known about the metabolic activities in an immunosuppressive environment. In this study, we employed metagenomic, metabolomic, and immunological approaches to profile the early effects of the immunosuppressant drug tacrolimus, antibiotics, or both in gut lumen and circulation using a murine model. Tacrolimus induced rapid and profound alterations in metabolic activities within two days of treatment, prior to alterations in gut microbiota composition and structure. The metabolic profile and gut microbiome after seven days of treatment was distinct from that after two days of treatment, indicating continuous drug effects on both gut microbial ecosystem and host metabolism. The most affected taxonomic groups are Clostriales and Verrucomicrobiae (i.e., Akkermansia muciniphila), and the most affected metabolic pathways included a group of interconnected amino acids, bile acid conjugation, glucose homeostasis, and energy production. Highly correlated metabolic changes were observed between lumen and serum metabolism, supporting their significant interactions. Despite a small sample size, this study explored the largely uncharacterized microbial and metabolic events in an immunosuppressed environment and demonstrated that early changes in metabolic activities can have significant implications that may serve as antecedent biomarkers of immune activation or quiescence. To understand the intricate relationships among gut microbiome, metabolic activities, and immune cells in an immune suppressed environment is a prerequisite for developing strategies to monitor and optimize alloimmune responses that determine transplant outcomes.}, } @article {pmid38066275, year = {2023}, author = {Kosma, EB and Manav-Demir, N and Civelek-Yoruklu, H and Ozkaya, B}, title = {Enrichment, characterization, and sand consolidation application of urease active calcite-producing bacteria.}, journal = {Environmental science and pollution research international}, volume = {}, number = {}, pages = {}, pmid = {38066275}, issn = {1614-7499}, support = {YTÜ BAP FBA-2021-4517//Yildiz Teknik Üniversitesi/ ; }, abstract = {Minerals such as calcium carbonate, which is prevalent in marble and limestone, are present naturally in rocks. Both physicochemical processes and microbial processes can result in the creation of calcium carbonate in nature, as is well documented. In this study, microbiologically induced calcite precipitation potential of three different Travertine-type water sources (Pamukkale Travertine Spring (PTS), Pamukkale Travertine Terraces (PTT), and Red Travertine of Karahayit (RTK)) using three different incubation media (NB, NB3, and ATCC1832) were investigated. After enrichment with ATCC1832 media, urease assays were positive for all of the microbial sources. The PTS and PTT were cultured with ATCC1832 medium for 48 h, which showed the best results for urease activity and microbial growth among other samples. Metagenome analyses indicated that PTT enriched with ATCC1832 media contains > 99% Firmicutes, while PTS enriched with ATCC1832 contains > 99% Proteobacteria at the Phylum level. Results from SEM-EDX and XRD analysis revealed that calcite and/or vaterite were the minerals that emerged from the mineralization of the PTS and PTT during incubation. The type of calcium carbonate crystals tended to change from one form to another when the incubation period extends from 72 to 120 h. Both the PTS and the PTT were able to precipitate calcite within the sand column. However, the bacteria from the PTT (26% CaCO3) outperformed those from the PTS (18% CaCO3) in terms of calcium carbonate deposition on the 21st day of incubation.}, } @article {pmid38066117, year = {2023}, author = {Likar, M and Grašič, M and Stres, B and Regvar, M and Gaberščik, A}, title = {Metagenomics reveals effects of fluctuating water conditions on functional pathways in plant litter microbial community.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {21741}, pmid = {38066117}, issn = {2045-2322}, support = {P1-0212//Javna Agencija za Raziskovalno Dejavnost RS/ ; P1-0212//Javna Agencija za Raziskovalno Dejavnost RS/ ; P1-0212//Javna Agencija za Raziskovalno Dejavnost RS/ ; P1-0212//Javna Agencija za Raziskovalno Dejavnost RS/ ; }, mesh = {*Soil Microbiology ; Plant Leaves/metabolism ; Ecosystem ; *Microbiota/physiology ; Plants ; Poaceae ; Soil ; }, abstract = {Climate change modifies environmental conditions, resulting in altered precipitation patterns, moisture availability and nutrient distribution for microbial communities. Changes in water availability are projected to affect a range of ecological processes, including the decomposition of plant litter and carbon cycling. However, a detailed understanding of microbial stress response to drought/flooding is missing. In this study, an intermittent lake is taken up as a model for changes in water availability and how they affect the functional pathways in microbial communities of the decomposing Phragmites australis litter. The results show that most enriched functions in both habitats belonged to the classes of Carbohydrates and Clustering-based subsystems (terms with unknown function) from SEED subsystems classification. We confirmed that changes in water availability resulted in altered functional makeup of microbial communities. Our results indicate that microbial communities under more frequent water stress (due to fluctuating conditions) could sustain an additional metabolic cost due to the production or uptake of compatible solutes to maintain cellular osmotic balance. Nevertheless, although prolonged submergence seemed to have a negative impact on several functional traits in the fungal community, the decomposition rate was not affected.}, } @article {pmid38065789, year = {2024}, author = {Koh, C and Saleh, MC}, title = {Translating mosquito viromes into vector management strategies.}, journal = {Trends in parasitology}, volume = {40}, number = {1}, pages = {10-20}, doi = {10.1016/j.pt.2023.11.002}, pmid = {38065789}, issn = {1471-5007}, mesh = {Animals ; Humans ; *Culicidae/genetics ; Virome ; Genome, Viral ; Mosquito Vectors ; *Viruses/genetics ; }, abstract = {Mosquitoes are best known for transmitting human and animal viruses. However, they also harbour mosquito-specific viruses (MSVs) as part of their microbiota. These are a group of viruses whose diversity and prevalence overshadow their medically relevant counterparts. Although metagenomics sequencing has remarkably accelerated the discovery of these viruses, what we know about them is often limited to sequence information, leaving much of their fundamental biology to be explored. Understanding the biology and ecology of MSVs can enlighten our knowledge of virus-virus interactions and lead to new innovations in the management of mosquito-borne viral diseases. We retrace the history of their discovery and discuss research milestones that would line the path from mosquito virome knowledge to vector management strategies.}, } @article {pmid38065767, year = {2023}, author = {Xu, CH and Chen, X and Zhu, GQ and Yi, HM and Chen, SL and Liu, T and Yu, YT and Zhang, QH and Jiang, EL and Feng, SZ}, title = {Diagnostic performance and clinical impacts of metagenomic sequencing after allogeneic hematopoietic stem cell transplantation.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jmii.2023.11.002}, pmid = {38065767}, issn = {1995-9133}, abstract = {BACKGROUND: Metagenomic Next-Generation Sequencing (mNGS) is a rapid, non-culture-based, high-throughput technique for pathogen diagnosis. Despite its numerous advantages, only a few studies have investigated its use in patients undergoing allogeneic hematopoietic stem cell transplantation (allo-HSCT).

METHODS: We conducted a retrospective analysis of 404 mNGS tests performed on 264 patients after allo-HSCT. The tests were divided into three groups (Phase A, B, C) based on the time spent hospitalized post-transplantation, and we evaluated the analytical performance of mNGS in comparison with conventional microbiological tests (CMT), while also analyzing its clinical utility for clinical impacts.

RESULTS: Metagenomic sequencing demonstrated a significantly higher rate of positive microbiological findings as compared to CMT (334/404 (82.7 %) vs. 159/404 (39.4 %), respectively, P < 0.001). The detection rates by both mNGS and CMT varied across the three-phase (mNGS: A-60/89 (67.4 %), B-147/158 (93.0 %), C-125/157 (79.6 %), respectively, P < 0.001; CMT: A-21/89 (23.6 %), B-79/158 (50.0 %), C-59/157 (37.6 %), respectively, P < 0.001). The infection sites and types of pathogens were also different across the three phases. Compared to non-GVHD cases, mNGS detected more Aspergillus spp. and Mucorales in GVHD patients (Aspergillus: 12/102 (11.8 %) vs. 8/158 (5.1 %), respectively, P = 0.048; Mucorales: 6/102 (5.9 %) vs. 2/158 (1.3 %), respectively, P = 0.035). Forty-five (181/404) percent of mNGS tests yielded a positive impact on the clinical diagnosis, while 24.3 % (98/404) of tests benefited the patients in antimicrobial treatment.

CONCLUSION: mNGS is an indispensable diagnostic tool in identifying pathogens and optimizing antibiotic therapy for hematological patients receiving allo-HSCT.}, } @article {pmid38065016, year = {2023}, author = {Liu, RT and Zhang, D and Li, S and Chen, Y and Wan, XX and Diao, ST and Weng, L and Peng, JM and Du, B}, title = {Comparison of different criteria of metagenomic next-generation sequencing for the diagnosis of invasive pulmonary aspergillosis in critically ill patients.}, journal = {Diagnostic microbiology and infectious disease}, volume = {108}, number = {2}, pages = {116135}, doi = {10.1016/j.diagmicrobio.2023.116135}, pmid = {38065016}, issn = {1879-0070}, abstract = {OBJECTIVE: To compare different criteria of Metagenomic Next-Generation Sequencing (mNGS) in bronchoalveolar lavage fluid (BALF) for diagnosing invasive pulmonary aspergillosis (IPA).

METHODS: We compared the diagnostic agreement and performances of six BALF mNGS-derived criteria (SDSMRN>1, SDSMRN≥3, SMRN≥10, SMRN≥50, RPM ratio≥10, and relative abundance of genus>30 %) in pneumonia patients.

RESULTS: A total of 115 patients were analyzed, with 28 identified with IPA. Diagnostic agreement among the six mNGS-derived criteria was moderate, with a Cohen's kappa of 0.577(P < 0.001). mNGS-derived criteria had low sensitivity ranging from 21.4 % to 57.1 % and high specificity from 88 % to 92 %. The optimal threshold of SDSMRN, SMRN, RPM ratio, and relative abundance of genus for diagnosing IPA were 5, 0.25, 8, and 20 %, respectively. Although using the optimal threshold, the sensitivity of mNGS is lower than 50 %.

CONCLUSIONS: All mNGS-derived criteria had low sensitivity for diagnosing IPA. A combination of mNGS and conventional mycological tests may be the best diagnostic strategy.}, } @article {pmid38064782, year = {2024}, author = {Ke, Y and Sun, W and Chen, Z and Zhu, Y and Chen, X and Yan, S and Li, Y and Xie, S}, title = {Effects of disinfectant type and dosage on biofilm's activity, viability, microbiome and antibiotic resistome in bench-scale drinking water distribution systems.}, journal = {Water research}, volume = {249}, number = {}, pages = {120958}, doi = {10.1016/j.watres.2023.120958}, pmid = {38064782}, issn = {1879-2448}, mesh = {*Disinfectants/pharmacology ; *Drinking Water/chemistry ; Chloramines/pharmacology ; Chlorine/pharmacology ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Bacteria/genetics ; Biofilms ; Adenosine Triphosphate ; *Water Purification ; }, abstract = {Drinking water distribution systems (DWDSs) are important for supplying high-quality water to consumers and disinfectant is widely used to control microbial regrowth in DWDSs. However, the disinfectant's influences on microbial community and antibiotic resistome in DWDS biofilms and the underlying mechanisms driving their dynamics remain elusive. The study investigated the effects of chlorine and chloramine disinfection on the microbiome and antibiotic resistome of biofilms in bench-scale DWDSs using metagenomics assembly. Additionally, the biofilm activity and viability were monitored based on adenosine triphosphate (ATP) and flow cytometer (FCM) staining. The results showed that both chlorine and chloramine disinfectants decreased biofilm ATP, although chloramine at a lower dosage (1 mg/L) could increase it. Chloramine caused a greater decrease in living cells than chlorine. Furthermore, the disinfectants significantly lowered the microbial community diversity and altered microbial community structure. Certain bacterial taxa were enriched, such as Mycobacterium, Sphingomonas, Sphingopyxis, Azospira, and Dechloromonas. Pseudomonas aeruginosa exhibited high resistance towards disinfectants. The disinfectants also decreased the complexity of microbial community networks. Some functional taxa (e.g., Nitrospira, Nitrobacter, Nitrosomonas) were identified as keystones in chloramine-treated DWDS microbial ecological networks. Stochasticity drove biofilm microbial community assembly, and disinfectants increased the contributions of stochastic processes. Chlorine had greater promotion effects on antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and ARG hosts than chloramine. The disinfectants also selected pathogens, such as Acinetobacter baumannii and Klebsiella pneumonia, and these pathogens also harbored ARGs and MGEs. Overall, this study provides new insights into the effects of disinfectants on biofilm microbiome and antibiotic resistome, highlighting the importance of monitoring and managing disinfection practices in DWDSs.}, } @article {pmid38064390, year = {2023}, author = {Liu, Z and Sun, C and Xiao, X and Zhou, L and Huang, Y and Shi, Y and Yin, X and Mao, Z and Zhang, Q}, title = {Application of metagenomic next-generation sequencing (mNGS) in diagnosing pneumonia of adults.}, journal = {Journal of infection in developing countries}, volume = {17}, number = {11}, pages = {1566-1573}, doi = {10.3855/jidc.18696}, pmid = {38064390}, issn = {1972-2680}, mesh = {Adult ; Humans ; *Epstein-Barr Virus Infections ; Herpesvirus 4, Human ; *Pneumonia/diagnosis ; High-Throughput Nucleotide Sequencing ; Streptococcus pneumoniae ; *Mycobacterium tuberculosis ; Sensitivity and Specificity ; }, abstract = {INTRODUCTION: Accurate identification of pathogens that cause pulmonary infections is essential for effective treatment and hastening recovery in adults diagnosed with pneumonia. At present, despite metagenomic next-generation sequencing (mNGS) technology has been widely used in clinical practice for pathogen identification, the clinical significance and necessity of detecting pathogen in bronchoalveolar lavage fluid (BALF) for pneumonia-stricken adults remain ambiguous.

METHODOLOGY: In this study, 80 patients suffering from pulmonary infection were enrolled, who were admitted to the Affiliated Changzhou Second People's Hospital of Nanjing Medical University between January 2020 and September 2022. The diagnostic performances of mNGS and conventional methods (CM) were systematically analyzed based on BALF samples, and we further investigated the influence of mNGS and CM in diagnosis modification and treatment.

RESULTS: We found a significantly higher positive rate for the mNGS method in contrast to CM. Bacteria were the most common pathogens, and Streptococcus pneumoniae was the most commonly identified pathogen. Candida albicans and Epstein-Barr virus were the most frequently identified fungus and virus. Atypical pathogens such as Mycobacterium tuberculosis, virus Nontuberculous mycobacteria, and Chlamydia psittaci were also identified. A total of 77 patients were identified with mixed infections by mNGS. As the disease progressed and recurrent antibiotic treatment persisted, significant dynamic changes in the clinical manifestation from the BALF samples could be found by mNGS.

CONCLUSIONS: This study underscores the efficacy of mNGS in detecting pathogens in BALF samples from patients suffering pulmonary infections. Compared with the CM, mNGS significantly enhanced the positive diagnosis ratio, particularly in diagnosing Mycobacterium tuberculosis, atypical pathogens, and viral or fungal infections.}, } @article {pmid38064275, year = {2023}, author = {Pan, D and Chen, P and Yang, G and Niu, R and Bai, Y and Cheng, K and Huang, G and Liu, T and Li, X and Li, F}, title = {Fe(II) Oxidation Shaped Functional Genes and Bacteria Involved in Denitrification and Dissimilatory Nitrate Reduction to Ammonium from Different Paddy Soils.}, journal = {Environmental science & technology}, volume = {57}, number = {50}, pages = {21156-21167}, doi = {10.1021/acs.est.3c06337}, pmid = {38064275}, issn = {1520-5851}, mesh = {*Nitrates/metabolism ; *Ammonium Compounds/metabolism ; Nitrites/metabolism ; Soil ; Denitrification ; Nitrogen Dioxide ; Bacteria/genetics/metabolism ; Oxidation-Reduction ; Ferrous Compounds/metabolism ; Nitrogen/metabolism ; }, abstract = {Microbial nitrate reduction can drive Fe(II) oxidation in anoxic environments, affecting the nitrous oxide emission and ammonium availability. The nitrate-reducing Fe(II) oxidation usually causes severe cell encrustation via chemodenitrification and potentially inhibits bacterial activity due to the blocking effect of secondary minerals. However, it remains unclear how Fe(II) oxidation and subsequent cell encrustation affect the functional genes and bacteria for denitrification and dissimilatory nitrate reduction to ammonium (DNRA). Here, bacteria were enriched from different paddy soils with and without Fe(II) under nitrate-reducing conditions. Fe(II) addition decelerated nitrate reduction and increased NO2[-] accumulation, due to the rapid Fe(II) oxidation and cell encrustation in the periplasm and on the cell surface. The N2O accumulation was lower in the treatment with Fe(II) and nitrate than that in the treatment with nitrate only, although the proportions of N2O and NH4[+] to the reduced NO3[-] were low (3.25% ∼ 6.51%) at the end of incubation regardless of Fe(II) addition. The dominant bacteria varied from soils under nitrate-reducing conditions, while Fe(II) addition shaped a similar microbial community, including Dechloromonas, Azospira, and Pseudomonas. Fe(II) addition increased the relative abundance of napAB, nirS, norBC, nosZ, and nirBD genes but decreased that of narG and nrfA, suggesting that Fe(II) oxidation favored denitrification in the periplasm and NO2[-]-to-NH4[+] reduction in the cytoplasm. Dechloromonas dominated the NO2[-]-to-N2O reduction, while Thauera mediated the periplasmic nitrate reduction and cytoplasmic NO2[-]-to-NH4[+] during Fe(II) oxidation. However, Thauera showed much lower abundance than the dominant genera, resulting in slow nitrate reduction and limited NH4[+] production. These findings provide new insights into the response of denitrification and DNRA bacteria to Fe(II) oxidation and cell encrustation in anoxic environments.}, } @article {pmid38063370, year = {2024}, author = {Tamames, J and Jiménez-Lalana, D and Redondo, Á and Martínez-García, S and de Los Rios, A}, title = {In situ metagenomics: A platform for rapid sequencing and analysis of metagenomes in less than one day.}, journal = {Molecular ecology resources}, volume = {24}, number = {2}, pages = {e13909}, doi = {10.1111/1755-0998.13909}, pmid = {38063370}, issn = {1755-0998}, mesh = {*Metagenome ; *Microbiota/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Spain ; }, abstract = {We present here a complete system for metagenomic analysis that allows performing the sequencing and analysis of a medium-size metagenome in less than one day. This unprecedented development was possible due to the conjunction of state-of-the-art experimental and computational advances: a portable laboratory suitable for DNA extraction and sequencing with nanopore technology; the powerful metagenomic analysis pipeline SqueezeMeta, capable to provide a complete analysis in a few hours and using scarce computational resources; and tools for the automatic inspection of the results via a graphical user interface, that can be coupled to a web server to allow remote visualization of data (SQMtools and SQMxplore). We have tested the feasibility of our approach in the sequencing of the microbiota associated to volcanic rocks in La Palma, Canary Islands. Also, we did a two-day sampling campaign of marine waters in which the results obtained on the first day guided the experimental design of the second day. We demonstrate that it is possible to generate metagenomic information in less than one day, making it feasible to obtain taxonomic and functional profiles fast and efficiently, even in field conditions. This capacity can be used in the further to perform real-time functional and taxonomic monitoring of microbial communities in remote areas.}, } @article {pmid38062990, year = {2023}, author = {Dunbar, A and Drigo, B and Djordjevic, SP and Donner, E and Hoye, BJ}, title = {Impacts of coprophagic foraging behaviour on the avian gut microbiome.}, journal = {Biological reviews of the Cambridge Philosophical Society}, volume = {}, number = {}, pages = {}, doi = {10.1111/brv.13036}, pmid = {38062990}, issn = {1469-185X}, support = {//University of South Australia's Science, Technology, Engineering, and Mathematics/ ; DE200100884//Australian Research Council/ ; }, abstract = {Avian gut microbial communities are complex and play a fundamental role in regulating biological functions within an individual. Although it is well established that diet can influence the structure and composition of the gut microbiota, foraging behaviour may also play a critical, yet unexplored role in shaping the composition, dynamics, and adaptive potential of avian gut microbiota. In this review, we examine the potential influence of coprophagic foraging behaviour on the establishment and adaptability of wild avian gut microbiomes. Coprophagy involves the ingestion of faeces, sourced from either self (autocoprophagy), conspecific animals (allocoprophagy), or heterospecific animals. Much like faecal transplant therapy, coprophagy may (i) support the establishment of the gut microbiota of young precocial species, (ii) directly and indirectly provide nutritional and energetic requirements, and (iii) represent a mechanism by which birds can rapidly adapt the microbiota to changing environments and diets. However, in certain contexts, coprophagy may also pose risks to wild birds, and their microbiomes, through increased exposure to chemical pollutants, pathogenic microbes, and antibiotic-resistant microbes, with deleterious effects on host health and performance. Given the potentially far-reaching consequences of coprophagy for avian microbiomes, and the dearth of literature directly investigating these links, we have developed a predictive framework for directing future research to understand better when and why wild birds engage in distinct types of coprophagy, and the consequences of this foraging behaviour. There is a need for comprehensive investigation into the influence of coprophagy on avian gut microbiotas and its effects on host health and performance throughout ontogeny and across a range of environmental perturbations. Future behavioural studies combined with metagenomic approaches are needed to provide insights into the function of this poorly understood behaviour.}, } @article {pmid38062325, year = {2023}, author = {Gwak, JH and Awala, SI and Kim, SJ and Lee, SH and Yang, EJ and Park, J and Jung, J and Rhee, SK}, title = {Transcriptomic Insights into Archaeal Nitrification in the Amundsen Sea Polynya, Antarctica.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {61}, number = {11}, pages = {967-980}, pmid = {38062325}, issn = {1976-3794}, support = {2020R1A6A1A06046235//Ministry of Education/ ; 2021R1A2C3004015//Ministry of Science and ICT, South Korea/ ; RS-2023-00213601//Ministry of Science and ICT, South Korea/ ; PJ01700703//Ministry of Rural Development Administration, South Korea/ ; PE23110//Korea Polar Research Institute/ ; }, mesh = {*Archaea/genetics/metabolism ; *Nitrification ; Antarctic Regions ; Ecosystem ; Ammonia/metabolism ; Oxidation-Reduction ; Gene Expression Profiling ; Phytoplankton ; Phylogeny ; }, abstract = {Antarctic polynyas have the highest Southern Ocean summer primary productivity, and due to anthropogenic climate change, these areas have formed faster recently. Ammonia-oxidizing archaea (AOA) are among the most ubiquitous and abundant microorganisms in the ocean and play a primary role in the global nitrogen cycle. We utilized metagenomics and metatranscriptomics to gain insights into the physiology and metabolism of AOA in polar oceans, which are associated with ecosystem functioning. A polar-specific ecotype of AOA, from the "Candidatus Nitrosomarinus"-like group, was observed to be dominant in the Amundsen Sea Polynya (ASP), West Antarctica, during a succession of summer phytoplankton blooms. AOA had the highest transcriptional activity among prokaryotes during the bloom decline phase (DC). Metatranscriptomic analysis of key genes involved in ammonia oxidation, carbon fixation, transport, and cell division indicated that this polar AOA ecotype was actively involved in nitrification in the bloom DC in the ASP. This study revealed the physiological and metabolic traits of this key polar-type AOA in response to phytoplankton blooms in the ASP and provided insights into AOA functions in polar oceans.}, } @article {pmid38061654, year = {2023}, author = {Han, Y and Teng, Y and Wang, X and Wen, D and Gao, P and Yan, D and Yang, N}, title = {Biodegradable PBAT microplastics adversely affect pakchoi (Brassica chinensis L.) growth and the rhizosphere ecology: Focusing on rhizosphere microbial community composition, element metabolic potential, and root exudates.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169048}, doi = {10.1016/j.scitotenv.2023.169048}, pmid = {38061654}, issn = {1879-1026}, abstract = {Biodegradable plastics (BPs) have gained increased attention as a promising solution to plastics pollution problem. However, BPs often exhibited limited in situ biodegradation in the soil environment, so they may also release microplastics (MPs) into soils just like conventional non-degradable plastics. Therefore, it is necessary to evaluate the impacts of biodegradable MPs (BMPs) on soil ecosystem. Here, we explored the effects of biodegradable poly(butylene adipate-co-terephthalate) (PBAT) MPs and conventional polyethylene (PE) MPs on soil-plant (pakchoi) system at three doses (0.02 %, 0.2 %, and 2 %, w/w). Results showed that PBAT MPs reduced plant growth in a dose-dependent pattern, while PE MPs exhibited no significant phytotoxicity. High-dose PBAT MPs negatively affected the rhizosphere soil nutrient availability, e.g., decreased available phosphorus and available potassium. Metagenomics analysis revealed that PBAT MPs caused more serious interference with the rhizosphere microbial community composition and function than PE MPs. In particular, compared with PE MPs, PBAT MPs induced greater changes in functional potential of carbon, nitrogen, phosphorus, and sulfur cycles, which may lead to alterations in soil biogeochemical processes and ecological functions. Moreover, untargeted metabolomics showed that PBAT MPs and PE MPs differentially affect plant root exudates. Mantel tests, correlation analysis, and partial least squares path model analysis showed that changes in plant growth and root exudates were significantly correlated with soil properties and rhizosphere microbiome driven by the MPs-rhizosphere interactions. This work improves our knowledge of how biodegradable and conventional non-degradable MPs affect plant growth and the rhizosphere ecology, highlighting that BMPs might pose greater threat to soil ecosystems than non-degradable MPs.}, } @article {pmid38061430, year = {2023}, author = {Liu, X and Fu, Z and Liu, TX and Liang, P}, title = {Effects of repeated afidopyropen treatment on the structure and function of the soil microbial community.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {342}, number = {}, pages = {123083}, doi = {10.1016/j.envpol.2023.123083}, pmid = {38061430}, issn = {1873-6424}, abstract = {Chemical insecticides are the most effective pest control agents. Afidopyropen is a novel insecticide used against sap-sucking insects, such as aphids. However, the effects of repeated afidopyropen application on the structure and function of soil microorganisms remain unknown. In this study, the changes in the enzyme activities, community structure and function, and relative abundance of antibiotic resistance ontology (ARO) of soil microorganisms were investigated during three repeated afidopyropen applications under laboratory conditions at the maximum recommended dosage (M1) and 10 times the M1 (M10). The neutral phosphatase (NPA) and catalase (CAT) activities in the soil were significantly suppressed after afidopyropen treatment. The Simpson diversity index (1/D) and Shannon-Wiener diversity index (H) also decreased in both the M1 and M10 afidopyropen-treated soils, indicating a remarkable decrease in soil microorganism diversity. The average well color development (AWCD) first increased and subsequently recovered to normal levels after the third application of the insecticide, suggesting that afidopyropen application could increase the metabolic activity of soil microorganisms. Metagenomic analysis showed that repeated afidopyropen application in both the M1 and M10 treatment groups altered the community structure of soil microorganisms, albeit in different ways. Furthermore, repeated afidopyropen application significantly increased the relative ARO abundance, especially in the M10 treatment, with the most dominant AROs being adeF, baeS, and IND-6. These findings reveal the effects of excessive afidopyropen application on soil microorganisms and lay an important foundation for the comprehensive evaluation of the impact of this insecticide on the environment.}, } @article {pmid38060843, year = {2023}, author = {Prins, FM and Collij, V and Groot, HE and Björk, JR and Swarte, JC and Andreu-Sánchez, S and Jansen, BH and Fu, J and Harmsen, HJM and Zhernakova, A and Lipsic, E and van der Harst, P and Weersma, RK and Gacesa, R}, title = {The gut microbiome across the cardiovascular risk spectrum.}, journal = {European journal of preventive cardiology}, volume = {}, number = {}, pages = {}, doi = {10.1093/eurjpc/zwad377}, pmid = {38060843}, issn = {2047-4881}, abstract = {AIMS: Despite treatment advancements, cardiovascular disease remains a leading cause of death worldwide. Identifying new targets is crucial for enhancing preventive and therapeutic strategies. The gut microbiome has been associated with coronary artery disease (CAD), however our understanding of specific changes during CAD development remains limited. We aimed to investigate microbiome changes in participants without clinically manifest CAD with different cardiovascular risk levels and in patients with ST-elevation myocardial infarction (STEMI).

METHODS: In this cross-sectional study, we characterized the gut microbiome using metagenomics of 411 faecal samples from individuals with low (n=130), intermediate (n=130) and high (n=125) cardiovascular risk based on the Framingham score, and STEMI patients (n=26). We analysed diversity, and differential abundance of species and functional pathways while accounting for confounders including medication and technical covariates.

RESULTS: Collinsella stercoris, Flavonifractor plautii and Ruthenibacterium lactatiformans showed increased abundances with cardiovascular risk, while Streptococcus thermophilus was negatively associated. Differential abundance analysis revealed eight species and 49 predicted metabolic pathways that were differently abundant among the groups. In the gut microbiome of STEMI patients, there was a depletion of pathways linked to vitamin, lipid and amino-acid biosynthesis.

CONCLUSION: We identified four microbial species showing a gradual trend in abundance from low-risk individuals to those with STEMI, and observed differential abundant species and pathways in STEMI patients compared to those without clinically manifest CAD. Further investigation is warranted to gain deeper understanding of their precise role in CAD progression and potential implications, with the ultimate goal of identifying novel therapeutic targets.}, } @article {pmid38060520, year = {2023}, author = {Paul, LJ and Ericsson, AC and Andrews, FM and McAdams, Z and Keowen, ML and St Blanc, MP and Banse, HE}, title = {Field study examining the mucosal microbiome in equine glandular gastric disease.}, journal = {PloS one}, volume = {18}, number = {12}, pages = {e0295697}, pmid = {38060520}, issn = {1932-6203}, mesh = {Horses ; Animals ; *Stomach Diseases/pathology ; Gastric Mucosa/pathology ; Risk Factors ; *Horse Diseases/pathology ; *Microbiota ; *Stomach Ulcer/pathology ; }, abstract = {Equine glandular gastric disease (EGGD) is a common disease among athletic horses that can negatively impact health and performance. The pathophysiology of this EGGD remains poorly understood. Previous studies using controlled populations of horses identified differences in the gastric glandular mucosal microbiome associated with disease. The objective of this study was to compare the gastric microbiome in horses with EGGD and those without across multiple barns and differing management practices. We hypothesized that alterations in the microbiome of the gastric glandular mucosa are associated with EGGD. A secondary objective was to perform a risk factor analysis for EGGD using the diet and management data collected. Microbial populations of biopsies from normal pyloric mucosa of horses without EGGD (control biopsies), normal pyloric mucosa of horses with EGGD (normal biopsies) and areas of glandular mucosal disruption in horses with EGGD (lesion biopsies) were compared. Lesion biopsies had a different microbial community structure than control biopsies. Control biopsies had a higher read count for the phylum Actinomycetota compared to lesion biopsies. Control biopsies also had an enrichment of the genera Staphylococcus and Lawsonella and the species Streptococcus salivarius. Lesion biopsies had an enrichment of the genera Lactobacillus and Actinobacillus and the species Lactobacillus equigenerosi. These results demonstrate differences in the gastric glandular microbiome between sites of disrupted mucosa in horses with EGGD compared to pyloric mucosa of horses without EGGD. Risk factor analysis indicated that exercise duration per week was a risk factor for EGGD.}, } @article {pmid38060130, year = {2024}, author = {Pecman, A and Mehle, N and Kutnjak, D}, title = {Detection of Plant Viruses Using Nanopore Sequencing Based Metagenomic Approach.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2732}, number = {}, pages = {251-264}, pmid = {38060130}, issn = {1940-6029}, mesh = {*Nanopore Sequencing ; Metagenome ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Plant Viruses/genetics ; }, abstract = {Nanopore sequencing has proven to be a useful tool for the generic detection of plant viruses, especially in laboratories working with small number of samples. In this chapter, we describe the steps prior to library preparation as well as the library preparation itself, which we found provides comparable results to Illumina sequencing.}, } @article {pmid38060126, year = {2024}, author = {Jaksa-Czotter, N and Nagyné Galbács, Z and Jahan, A and Demián, E and Várallyay, É}, title = {Viromes of Plants Determined by High-Throughput Sequencing of Virus-Derived siRNAs.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2732}, number = {}, pages = {179-198}, pmid = {38060126}, issn = {1940-6029}, mesh = {RNA, Small Interfering/genetics ; Virome ; RNA, Viral/analysis ; *Viruses/genetics ; RNA, Double-Stranded ; Plants/genetics ; *Virus Diseases ; High-Throughput Nucleotide Sequencing/methods ; Plant Diseases/genetics ; }, abstract = {Plants growing in open airfields can be infected by several viruses even as a multiple infection. Virus infection in crops can lead to a serious damage to the harvest. In addition, virus presence in grapevine, fruit trees, and tuberous vegetables, propagated vegetatively affects the phytosanitary status of the propagation material (both the rootstock and the variety) having profound effect on the lifetime and health of the new plantations. The fast evolution of sequencing techniques provides a new opportunity for metagenomics-based viral diagnostics. Small interfering (si) RNAs produced by the RNA silencing-based host immune system during viral infection can be sequenced by high-throughput techniques and analyzed for the presence of viruses, revealing the presence of all known viral pathogens in the sample and therefore opening new avenues in virus diagnostics. This method is based on Illumina sequencing and bioinformatics analysis of virus-derived siRNAs in the host. Here we describe a protocol for this challenging technique step by step with notes, to ensure success for every user.}, } @article {pmid38060124, year = {2024}, author = {Cebriá-Mendoza, M and Díaz, W and Sanjuán, R and Cuevas, JM}, title = {Optimized Recovery of Viral DNA and RNA from Blood Plasma for Viral Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2732}, number = {}, pages = {155-164}, pmid = {38060124}, issn = {1940-6029}, mesh = {Humans ; *DNA, Viral/genetics ; Ecosystem ; *Viruses/genetics ; RNA, Viral/genetics ; Metagenomics/methods ; Plasma ; Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Metagenomics is vastly improving our ability to discover new viruses, as well as their possible associations with disease. However, metagenomics has also changed our understanding of viruses in general. This is because we can find viruses in healthy hosts in the absence of disease, which changes the perspective of viruses as mere pathogens and offers a new perspective in which viruses function as important components of ecosystems. In concrete, human blood metagenomics has revealed the presence of different types of viruses in apparently healthy subjects. These viruses are human anelloviruses and, to a lower extent, human pegiviruses. Viral metagenomics' major challenge is the correct isolation of the viral nucleic acids from a specific sample. For the protocol to be successful, all steps must be carefully chosen, in particular those that optimize the recovery of viral nucleic acids. Here, we present a procedure that allows the recovery of both DNA and RNA viruses from plasma samples.}, } @article {pmid38060122, year = {2024}, author = {Lamy-Besnier, Q and Garneau, JR}, title = {Enrichment, Sequencing, and Identification of DNA Bacteriophages from Fecal Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2732}, number = {}, pages = {133-144}, pmid = {38060122}, issn = {1940-6029}, mesh = {*Bacteriophages/genetics ; Ecosystem ; DNA/genetics ; Feces ; *Viruses/genetics ; Metagenomics/methods ; }, abstract = {Research on individual viruses and phages, as well as viral populations (viromes), is greatly expanding. Phages and viromes are increasingly suspected to have numerous impacts on the ecosystem in which they reside by interacting directly or indirectly with the other organisms present in their environment. In particular, phage communities of the gut microbiota have been associated with a wide range of diseases. However, properly investigating intestinal viromes is still very challenging, both experimentally and analytically. This chapter proposes a simple and reproducible protocol to separate and enrich DNA phage particles from fecal samples, to sequence them, and finally obtain a basic but robust bioinformatic characterization and classification of the global bacteriophage community.}, } @article {pmid38060120, year = {2024}, author = {Guevara-Rivera, EA and Rodríguez-Negrete, EA and Lozano-Durán, R and Bejarano, ER and Torres-Calderón, AM and Arce-Leal, ÁP and Leyva-López, NE and Méndez-Lozano, J}, title = {From Metagenomics to Ecogenomics: NGS-Based Approaches for Discovery of New Circular DNA Single-Stranded Viral Species.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2732}, number = {}, pages = {103-117}, pmid = {38060120}, issn = {1940-6029}, mesh = {*DNA, Viral/genetics ; Phylogeny ; Plants/genetics ; *Begomovirus/genetics ; Genome, Viral ; Metagenomics/methods ; DNA, Plant ; DNA, Circular/genetics ; Plant Diseases ; }, abstract = {Viruses comprise the most abundant genetic material in the biosphere; however, global viral genomic population (virome) has been largely underestimated. Recently, high-throughput sequencing (HTS) has provided a powerful tool for the detection of known viruses and the discovery of novel viral species from environmental and individual samples using metagenomics and ecogenomics approaches, respectively. Viruses with circular DNA single-stranded (ssDNA) genomes belonging to the begomovirus genera (family Geminiviridae) constitute the largest group of emerging plant viruses worldwide. The knowledge of begomoviruses viromes is mostly restricted to crop plant systems; nevertheless, it has been described that noncultivated plants specifically at the interface between wild and cultivated plants are important reservoirs leading to viral evolution and the emergence of new diseases. Here we present a protocol that allows the identification and isolation of known and novel begomoviruses species infecting cultivated and noncultivated plant species. The method consists of circular viral molecules enrichment by rolling circle amplification (RCA) from begomovirus-positive total plant DNA, followed by NGS-based metagenomic sequencing. Subsequently, metagenomic reads are processed for taxonomic classification using Viromescan software and a customized Geminiviridae family database, and begomovirus-related reads are used for contigs assembly and annotation using Spades software and Blastn algorithm, respectively. Then, the obtained begomovirus-related signatures are used as templates for specific primers design and implemented for PCR-based ecogenomic identification of individual samples harboring the corresponding viral species. Lastly, full-length begomovirus genomes are obtained by RCA-based amplification from total plant DNA of selected individual samples, cloning, and viral molecular identity corroborated by Sanger sequencing. Conclusively, the identification and isolation of a novel monopartite begomovirus species native to the New World (NW) named Gallium leaf deformation virus (GLDV) is shown.}, } @article {pmid38060119, year = {2024}, author = {Ruiz-Padilla, A and Rodríguez-Romero, JL and Pacifico, D and Chiapello, M and Ayllón, MA}, title = {Determination of the Mycovirome of a Necrotrophic Fungus.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2732}, number = {}, pages = {83-101}, pmid = {38060119}, issn = {1940-6029}, mesh = {*Fungi/genetics ; *Plants/genetics ; Base Sequence ; RNA ; Botrytis/genetics ; Plant Diseases/microbiology ; }, abstract = {Next-generation sequencing (NGS) of total RNA has allowed the detection of novel viruses infecting different hosts, such as fungi, increasing our knowledge on virus horizontal transfer events among different hosts, virus diversity, and virus evolution. Here, we describe the detailed protocols for the isolation of the plant pathogenic fungus Botrytis cinerea, from grapevine plants showing symptoms of the mold gray disease, the culture and maintenance of the isolated B. cinerea strains, the extraction of total RNA from B. cinerea strains for NGS, the bioinformatics pipeline designed and followed to detect mycoviruses in the sequenced samples, and the validation of the in silico detected mycoviruses by different approaches.}, } @article {pmid38060118, year = {2024}, author = {Kambara, K and Shimura, H and Fujino, K and Masuta, C}, title = {Metagenomic Analyses of Viruses in the Orchid Mycorrhizal Interaction Using Improved Assemble Tools.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2732}, number = {}, pages = {67-81}, pmid = {38060118}, issn = {1940-6029}, mesh = {*Mycorrhizae/genetics ; Symbiosis/genetics ; Phylogeny ; *Orchidaceae/genetics/microbiology ; *Viruses/genetics ; }, abstract = {In nature, mycorrhizal association with soil-borne fungi is indispensable for orchid species. Compatible mycorrhizal fungi form endo-mycorrhizal structures in orchid cells, and the fungal structures are digested in orchid cells to be supplied to orchids as nutrition. Because orchid seeds lack the reserves for germination, they keep receiving nutrition through mycorrhizal formation from seed germination until nonphotosynthetic young seedlings develop leaves and become photoautotrophic. Seeds of all orchids germinate with the help of their own fungal partners, and therefore, specific partnership has been acquired in a long evolutionary history between orchids and fungi. Assuming that horizontal transmission of viruses may occur in such a close relationship, we are focusing on viruses that infect orchids and their mycorrhizal fungi. We prepared aseptically germinated orchid plants (i.e., fungi-free plants) together with pure-cultured fungal isolates and conducted transcriptome analyses (RNA-seq) by next-generation sequencing (NGS) approach. To reconstruct virus-related sequences that would have been present in the RNA sample of interest, de novo assembly process is required using short read sequences obtained from RNA-seq. In the previous version of our protocol (see Viral Metagenomics, first edition 2018), virus searches were conducted using contig sets constructed by a single assembler, but this time we devised a method to construct more reliable contigs using multiple assemblers and again reinvestigated that viruses could be detected. Because the virus detection efficiency and number of detected virus species clearly differed depending on the assembly pipeline and the number of the input data, multiple methods should be used to identify viral infection, if possible.}, } @article {pmid38060116, year = {2024}, author = {Moon, K and Cho, JC}, title = {Freshwater Viral Metagenome Analyses Targeting dsDNA Viruses.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2732}, number = {}, pages = {29-44}, pmid = {38060116}, issn = {1940-6029}, mesh = {*Metagenome ; Genome, Viral ; Metagenomics/methods ; Fresh Water ; *Viruses/genetics ; }, abstract = {Viral metagenomics is one of the most widely used approaches to study viral population genomics. With the recent development of bioinformatic tools, the number of molecular biological methods, programs, and software to analyze viral metagenome data have greatly increased. Here, we describe the basic analysis workflow along with bioinformatic tools that can be used to analyze viral metagenome data. Although this chapter assumes that the viral metagenome data are prepared from the freshwater samples and are subjected to dsDNA sequencing, the protocol can be applied and modified for other types of metagenome data collected from a variety of sources.}, } @article {pmid38060115, year = {2024}, author = {Rampelli, S and Turroni, S and Candela, M}, title = {From Whole Genome Shotgun Sequencing to Viral Community Profiling: The ViromeScan Tool.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2732}, number = {}, pages = {23-28}, pmid = {38060115}, issn = {1940-6029}, mesh = {*Software ; Ecosystem ; Whole Genome Sequencing/methods ; Metagenome ; *Viruses/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Genome, Viral ; }, abstract = {ViromeScan is an innovative metagenomic analysis tool that allows characterizing the taxonomy of viral communities from raw data of metagenomics sequencing, efficiently denoising samples from reads of other microorganisms. This means that users can use the same shotgun metagenomic sequencing data to fully characterize complex microbial ecosystems, including bacteria and viruses. Here we describe the analysis procedure with some examples, illustrating the processes computed by ViromeScan from raw data to the final output.}, } @article {pmid38060114, year = {2024}, author = {Zhou, Y and Wang, Y and Prangishvili, D and Krupovic, M}, title = {Exploring the Archaeal Virosphere by Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2732}, number = {}, pages = {1-22}, pmid = {38060114}, issn = {1940-6029}, mesh = {*Archaea ; Phylogeny ; Metagenomics/methods ; *Archaeal Viruses/genetics ; Genome, Archaeal ; }, abstract = {During the past decade, environmental research has demonstrated that archaea are abundant and widespread in nature and play important ecological roles at a global scale. Currently, however, the majority of archaeal lineages cannot be cultivated under laboratory conditions and are known exclusively or nearly exclusively through metagenomics. A similar trend extends to the archaeal virosphere, where isolated representatives are available for a handful of model archaeal virus-host systems. Viral metagenomics provides an alternative way to circumvent the limitations of culture-based virus discovery and offers insight into the diversity, distribution, and environmental impact of uncultured archaeal viruses. Presently, metagenomics approaches have been successfully applied to explore the viromes associated with various lineages of extremophilic and mesophilic archaea, including Asgard archaea (Asgardarchaeota), ANME-1 archaea (Methanophagales), thaumarchaea (Nitrososphaeria), altiarchaea (Altiarchaeota), and marine group II archaea (Poseidoniales). Here, we provide an overview of methods widely used in archaeal virus metagenomics, covering metavirome preparation, genome annotation, phylogenetic and phylogenomic analyses, and archaeal host assignment. We hope that this summary will contribute to further exploration and characterization of the enigmatic archaeal virome lurking in diverse environments.}, } @article {pmid38059755, year = {2023}, author = {Rosell-Díaz, M and Santos-González, E and Motger-Albertí, A and Ramió-Torrentà, L and Garre-Olmo, J and Pérez-Brocal, V and Moya, A and Jové, M and Pamplona, R and Puig, J and Ramos, R and Fernández-Real, JM and Mayneris-Perxachs, J}, title = {Gut microbiota links to serum ferritin and cognition.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2290318}, pmid = {38059755}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Tandem Mass Spectrometry ; Cognition ; Bacteria/genetics ; Metabolome ; Phenylalanine ; Iron ; Ferritins ; }, abstract = {Iron is required for the replication and growth of almost all bacterial species and in the production of myelin and neurotransmitters. Increasing clinical studies evidence that the gut microbiota plays a critical role in iron metabolism and cognition. However, the understanding of the complex iron-microbiome-cognition crosstalk remains elusive. In a recent study in the Aging Imageomics cohort (n = 1,030), we identified a positive association of serum ferritin (SF) with executive function (EF) as inferred from the semantic verbal fluency (SVF,) the total digit span (TDS) and the phonemic verbal fluency tests (PVF). Here, we explored the potential mechanisms by analyzing the gut microbiome and plasma metabolome using shotgun metagenomics and HPLC-ESI-MS/MS, respectively. Different bacterial species belonging to the Proteobacteria phylum (Klebsiella pneumoniae, Klebsiella michiganensis, Unclassified Escherichia) were negatively associated both with SF and executive function. At the functional level, an enrichment of microbial pathways involved in phenylalanine, arginine, and proline metabolism was identified. Consistently, phenylacetylglutamine, a metabolite derived from microbial catabolism of phenylalanine, was negatively associated with SF, EF, and semantic memory. Other metabolites such as ureidobutyric acid and 19,20-DiHDPA, a DHA-derived oxylipin, were also consistently and negatively associated with SF, EF, and semantic memory, while plasma eicosapentaenoic acid was positively associated. The associations of SF with cognition could be mediated by the gut microbiome through microbial-derived metabolites.}, } @article {pmid38059752, year = {2023}, author = {Dong, C and Guan, Q and Xu, W and Zhang, X and Jin, B and Yu, S and Xu, X and Xia, Y}, title = {Disentangling the age-related manner in the associations between gut microbiome and women's health: a multi-cohort microbiome study.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2290320}, pmid = {38059752}, issn = {1949-0984}, mesh = {Adolescent ; Humans ; Female ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2 ; *Inflammatory Bowel Diseases ; *Microbiota ; Women's Health ; *Atherosclerosis ; }, abstract = {Women's health encompasses life-course healthcare, and mounting evidence emphasizes the pivotal contribution of gut microbiota. Therefore, understanding the temporal dynamics of gut microbiota and how age influences disease-gut microbiota associations is essential for improving women's health. By analyzing metagenomic data from 3625 healthy women, we revealed significant effects of age on gut microbiota and age-dependent patterns in microbial features, such as relative abundance, Shannon index, and microbial network properties. Additionally, declining trends in the predictive accuracy of gut microbiota for age groups were shown using iterative sub-sampling based random forest (ISSRF) model. Age-specific species markers were also identified, many of which were shared across age groups. To investigate the influence of age on disease-gut microbiota associations, metagenomic data from 681 women with various disease conditions and 491 matched healthy controls were collected. A substantial proportion of species markers for inflammatory bowel disease (IBD), type 2 diabetes (T2D), atherosclerotic cardiovascular disease (ACVD), and impaired glucose tolerance (IGT) differed in relative abundance across age groups, and were also age-specific species markers. Besides, the microbiota-based probabilities of IBD and ACVD were positively correlated with age. Furthermore, the age specificity of disease-gut microbiota associations was explored using the ISSRF model. Associations between IBD and gut microbiota were age-specific, with reduced stability of disease species markers in childhood and adolescence, possibly due to decrease in the effect size between patients and controls. Our findings provided valuable insights into promoting healthy aging and developing personalized healthcare strategies for women.}, } @article {pmid38059641, year = {2024}, author = {Park, SY and Coufal, NG and Dominguez, SR and Farnaes, L and Messacar, K and Goldman, FD}, title = {Gaps in diagnosing suspected infection in immunocompromised children with cancer: A systematic review.}, journal = {Pediatric blood & cancer}, volume = {71}, number = {2}, pages = {e30794}, doi = {10.1002/pbc.30794}, pmid = {38059641}, issn = {1545-5017}, mesh = {Humans ; Child ; *Medical Oncology ; *Neoplasms/complications ; }, abstract = {While the survival of children with cancer has improved over time, infection remains a major morbidity and mortality risk. We conducted a systematic literature review to determine the unmet needs in diagnosing infection in immunocompromised children with cancer. The comprehensive search strategy followed the guidelines established by the Cochrane Handbook for Systematic Reviews of Interventions and the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) 2020 statement, and spanned multiple bibliographic databases and other public sources from January 1, 2012 to June 23, 2022. From 5188 records, 34 unique pediatric-focused studies met inclusion criteria. This review highlights the lack of published data on infectious disease testing in pediatric oncology patients, and the need for well-designed clinical impact and cost-effectiveness studies of both existing and novel diagnostic platforms. Such studies are necessary to optimize diagnostic and antimicrobial stewardship, leading to improvement in patient outcomes.}, } @article {pmid38059636, year = {2023}, author = {Goldman, AL and Fulk, EM and Momper, LM and Heider, C and Mulligan, J and Osburn, M and Masiello, CA and Silberg, JJ}, title = {Microbial sensor variation across biogeochemical conditions in the terrestrial deep subsurface.}, journal = {mSystems}, volume = {}, number = {}, pages = {e0096623}, doi = {10.1128/msystems.00966-23}, pmid = {38059636}, issn = {2379-5077}, abstract = {The ability to detect extracellular environmental conditions is a fundamental property of all life forms. Because microbial two-component sensor systems convert information about extracellular conditions into biochemical information that controls their behaviors, we evaluated how two-component sensor systems evolved within the deep Earth across multiple sites where abiotic and biotic properties vary. We show that these sensor systems remain abundant in microbial consortia at all subterranean sampling sites and observe correlations between sensor system abundances and abiotic (dissolved organic carbon variation) and biotic (consortia diversity) properties. These results suggest that multiple environmental properties may drive sensor protein evolution and highlight the need for further studies of metagenomic and geochemical data in parallel to understand the drivers of microbial sensor evolution.}, } @article {pmid38059479, year = {2023}, author = {Parry, RH and Slonchak, A and Campbell, LJ and Newton, ND and Debat, HJ and Gifford, RJ and Khromykh, AA}, title = {A novel tamanavirus (Flaviviridae) of the European common frog (Rana temporaria) from the UK.}, journal = {The Journal of general virology}, volume = {104}, number = {12}, pages = {}, pmid = {38059479}, issn = {1465-2099}, mesh = {Animals ; *Flaviviridae/genetics ; Rana temporaria/genetics ; Phylogeny ; RNA, Viral/genetics/chemistry ; *Flavivirus/genetics ; Polyproteins/genetics ; United Kingdom ; Genome, Viral ; }, abstract = {Flavivirids are small, enveloped, positive-sense RNA viruses from the family Flaviviridae with genomes of ~9-13 kb. Metatranscriptomic analyses of metazoan organisms have revealed a diversity of flavivirus-like or flavivirid viral sequences in fish and marine invertebrate groups. However, no flavivirus-like virus has been identified in amphibians. To remedy this, we investigated the virome of the European common frog (Rana temporaria) in the UK, utilizing high-throughput sequencing at six catch locations. De novo assembly revealed a coding-complete virus contig of a novel flavivirid ~11.2 kb in length. The virus encodes a single ORF of 3456 aa and 5' and 3' untranslated regions (UTRs) of 227 and 666 nt, respectively. We named this virus Rana tamanavirus (RaTV), as BLASTp analysis of the polyprotein showed the closest relationships to Tamana bat virus (TABV) and Cyclopterus lumpus virus from Pteronotus parnellii and Cyclopterus lumpus, respectively. Phylogenetic analysis of the RaTV polyprotein compared to Flavivirus and Flavivirus-like members indicated that RaTV was sufficiently divergent and basal to the vertebrate Tamanavirus clade. In addition to the Mitcham strain, partial but divergent RaTV, sharing 95.64-97.39 % pairwise nucleotide identity, were also obtained from the Poole and Deal samples, indicating that RaTV is widespread in UK frog samples. Bioinformatic analyses of predicted secondary structures in the 3'UTR of RaTV showed the presence of an exoribonuclease-resistant RNA (xrRNA) structure standard in flaviviruses and TABV. To examine this biochemically, we conducted an in vitro Xrn1 digestion assay showing that RaTV probably forms a functional Xrn1-resistant xrRNA.}, } @article {pmid38059467, year = {2023}, author = {Ren, CY and Zhao, HP}, title = {Synthetic Nuclease-Producing Microbiome Achieves Efficient Removal of Extracellular Antibiotic Resistance Genes from Wastewater Effluent.}, journal = {Environmental science & technology}, volume = {57}, number = {50}, pages = {21224-21234}, doi = {10.1021/acs.est.3c07974}, pmid = {38059467}, issn = {1520-5851}, mesh = {Humans ; *Anti-Bacterial Agents ; Wastewater ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; *Microbiota ; }, abstract = {Antibiotic resistance gene (ARG) transmission poses significant threats to human health. The effluent of wastewater treatment plants is demonstrated as a hotspot source of ARGs released into the environment. In this study, a synthetic microbiome containing nuclease-producing Deinococcus radiodurans was constructed to remove extracellular ARGs. Results of quantitative polymerase chain reaction (qPCR) showed significant reduction in plasmid RP4-associated ARGs (by more than 3 orders of magnitude) and reduction of indigenous ARG sul1 and mobile genetic element (MGE) intl1 (by more than 1 order of magnitude) in the synthetic microbiome compared to the control without D. radiodurans. Metagenomic analysis revealed a decrease in ARG and MGE diversity in extracellular DNA (eDNA) of the treated group. Notably, whereas eight antibiotic-resistant plasmids with mobility risk were detected in the control, only one was detected in the synthetic microbiome. The abundance of the nuclease encoding gene exeM, quantified by qPCR, indicated its enrichment in the synthetic microbiome, which ensures stable eDNA degradation even when D. radiodurans decreased. Moreover, intracellular ARGs and MGEs and pathogenic ARG hosts in the river receiving treated effluent were lower than those in the river receiving untreated effluent. Overall, this study presents a new approach for removing extracellular ARGs and further reducing the risk of ARG transmission in receiving rivers.}, } @article {pmid38059125, year = {2023}, author = {Zhang, T and Zhou, K and Wang, Y and Xu, J and Zheng, Q and Luo, T and Jiao, N}, title = {Genomic insights into the adaptation of Synechococcus to the coastal environment on Xiamen.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1292150}, pmid = {38059125}, issn = {1664-302X}, abstract = {Synechococcus are widely distributed in the global ocean, from the pelagic zone to coastal waters. However, little is known about Synechococcus in coastal seawater due to limitations in isolation and culture conditions. In this study, a combination of metagenomic sequencing technology, flow cytometry sorting, and multiple displacement amplification was used to investigate Synechococcus in the coastal seawater of Xiamen Island. The results revealed 18 clades of Synechococcus and diverse metabolic genes that appear to contribute to their adaptation to the coastal environment. Intriguingly, some metabolic genes related to the metabolism of carbohydrates, energy, nucleotides, and amino acids were found in 89 prophage regions that were detected in 16,258 Synechococcus sequences. The detected metabolic genes can enable prophages to contribute to the adaptation of Synechococcus hosts to the coastal marine environment. The detection of prophages also suggests that the cyanophages have infected Synechococcus. On the other hand, the identification of 773 genes associated with antiviral defense systems indicates that Synechococcus in Xiamen have evolved genetic traits in response to cyanophage infection. Studying the community diversity and functional genes of Synechococcus provides insights into their role in environmental adaptation and marine ecosystems.}, } @article {pmid38059001, year = {2024}, author = {Zhernova, DA and Pushkova, EN and Rozhmina, TA and Povkhova, LV and Novakovskiy, RO and Turba, AA and Borkhert, EV and Sigova, EA and Dvorianinova, EM and Krasnov, GS and Melnikova, NV and Dmitriev, AA}, title = {ITS and 16S rDNA metagenomic dataset of different soils from flax fields.}, journal = {Data in brief}, volume = {52}, number = {}, pages = {109827}, pmid = {38059001}, issn = {2352-3409}, abstract = {Flax (Linum usitatissimum L.), one of the important and versatile crops, is used for the production of oil and fiber. To obtain high and stable yields of flax products, L. usitatissimum varieties should be cultivated under optimal conditions, including the composition of the soil microbiome. We evaluated the diversity of microorganisms in soils under conditions unfavorable for flax cultivation (suboptimal acidity or herbicide treatment) or infected with causative agents of harmful flax diseases (Septoria linicola, Colletotrichum lini, Melampsora lini, or Fusarium oxysporum f. sp. lini). For this purpose, twenty-two sod-podzolic soil samples were collected from flax fields and their metagenomes were analyzed using the regions of 16S ribosomal RNA gene (16S rDNA) and internal transcribed spacers (ITS) of the ribosomal RNA genes, which are used in phylogenetic studies of bacteria and fungi. Amplicons were sequenced on the Illumina MiSeq platform (reads of 300 + 300 bp). On average, we obtained 8,400 reads for ITS and 43,300 reads for 16S rDNA per sample. For identification of microorganisms in the soil samples, the Illumina reads were processed using DADA2. The raw data are deposited in the Sequence Read Archive under the BioProject accession number PRJNA956957. Tables listing the microorganisms identified in the soil samples are available in this article. The obtained dataset can be used to analyze the fungal and bacterial composition of flax field soils and their relationship to environmental conditions, including suboptimal soil acidity and infection with fungal pathogens. In addition, it can help to understand the influence of herbicide treatment on the microbial diversity of flax fields. Another useful application of our data is the ability to assess the suitability of the soil microbiome for flax cultivation.}, } @article {pmid38058765, year = {2023}, author = {Ponsero, AJ and Miller, M and Hurwitz, BL}, title = {Comparison of k-mer-based de novo comparative metagenomic tools and approaches.}, journal = {Microbiome research reports}, volume = {2}, number = {4}, pages = {27}, pmid = {38058765}, issn = {2771-5965}, abstract = {Aim: Comparative metagenomic analysis requires measuring a pairwise similarity between metagenomes in the dataset. Reference-based methods that compute a beta-diversity distance between two metagenomes are highly dependent on the quality and completeness of the reference database, and their application on less studied microbiota can be challenging. On the other hand, de-novo comparative metagenomic methods only rely on the sequence composition of metagenomes to compare datasets. While each one of these approaches has its strengths and limitations, their comparison is currently limited. Methods: We developed sets of simulated short-reads metagenomes to (1) compare k-mer-based and taxonomy-based distances and evaluate the impact of technical and biological variables on these metrics and (2) evaluate the effect of k-mer sketching and filtering. We used a real-world metagenomic dataset to provide an overview of the currently available tools for de novo metagenomic comparative analysis. Results: Using simulated metagenomes of known composition and controlled error rate, we showed that k-mer-based distance metrics were well correlated to the taxonomic distance metric for quantitative Beta-diversity metrics, but the correlation was low for presence/absence distances. The community complexity in terms of taxa richness and the sequencing depth significantly affected the quality of the k-mer-based distances, while the impact of low amounts of sequence contamination and sequencing error was limited. Finally, we benchmarked currently available de-novo comparative metagenomic tools and compared their output on two datasets of fecal metagenomes and showed that most k-mer-based tools were able to recapitulate the data structure observed using taxonomic approaches. Conclusion: This study expands our understanding of the strength and limitations of k-mer-based de novo comparative metagenomic approaches and aims to provide concrete guidelines for researchers interested in applying these approaches to their metagenomic datasets.}, } @article {pmid38058764, year = {2023}, author = {Fabbrini, M and Scicchitano, D and Candela, M and Turroni, S and Rampelli, S}, title = {Connect the dots: sketching out microbiome interactions through networking approaches.}, journal = {Microbiome research reports}, volume = {2}, number = {4}, pages = {25}, pmid = {38058764}, issn = {2771-5965}, abstract = {Microbiome networking analysis has emerged as a powerful tool for studying the complex interactions among microorganisms in various ecological niches, including the human body and several environments. This analysis has been used extensively in both human and environmental studies, revealing key taxa and functional units peculiar to the ecosystem considered. In particular, it has been mainly used to investigate the effects of environmental stressors, such as pollution, climate change or therapies, on host-associated microbial communities and ecosystem function. In this review, we discuss the latest advances in microbiome networking analysis, including methods for constructing and analyzing microbiome networks, and provide a case study on how to use these tools. These analyses typically involve constructing a network that represents interactions among microbial taxa or functional units, such as genes or metabolic pathways. Such networks can be based on a variety of data sources, including 16S rRNA sequencing, metagenomic sequencing, and metabolomics data. Once constructed, these networks can be analyzed to identify key nodes or modules important for the stability and function of the microbiome. By providing insights into essential ecological features of microbial communities, microbiome networking analysis has the potential to transform our understanding of the microbial world and its impact on human health and the environment.}, } @article {pmid38058363, year = {2024}, author = {Vinothini, K and Nakkeeran, S and Saranya, N and Jothi, P and Prabu, G and Pavitra, K and Afzal, M}, title = {Metagenomic profiling of tomato rhizosphere delineates the diverse nature of uncultured microbes as influenced by Bacillus velezensis VB7 and Trichoderma koningiopsis TK towards the suppression of root-knot nematode under field conditions.}, journal = {3 Biotech}, volume = {14}, number = {1}, pages = {2}, pmid = {38058363}, issn = {2190-572X}, abstract = {UNLABELLED: The plant-parasitic Root Knot Nematodes (Meloidogyne spp.,) play a pivotal role to devastate vegetable crops across the globe. Considering the significance of plant-microbe interaction in the suppression of Root Knot Nematode, we investigated the diversity of microbiome associated with bioagents-treated and nematode-infected rhizosphere soil samples through metagenomics approach. The wide variety of organisms spread across different ecosystems showed the highest average abundance within each taxonomic level. In the rhizosphere, Proteobacteria, Firmicutes, and Actinobacteria were the dominant bacterial taxa, while Ascomycota, Basidiomycota, and Mucoromycota were prevalent among the fungal taxa. Regardless of the specific treatments, bacterial genera like Bacillus, Sphingomonas, and Pseudomonas were consistently found in high abundance. Shannon diversity index vividly ensured that, bacterial communities were maximum in B. velezensis VB7-treated soil (1.4-2.4), followed by Root Knot Nematode-associated soils (1.3-2.2), whereas richness was higher with Trichoderma konigiopsis TK drenched soils (1.3-2.0). The predominant occurrence of fungal genera such as Aspergillus Epicoccum, Choanephora, Alternaria and Thanatephorus habituate rhizosphere soils. Shannon index expressed the abundant richness of fungal species in treated samples (1.04-0.90). Further, refraction and species diversity curve also depicted a significant increase with maximum diversity of fungal species in B. velezensis VB7-treated soil than T. koningiopsis and nematode-infested soil. In field trial, bioagents-treated tomato plant (60% reduction of Meloidogyne incognita infection) had reduced gall index along with enhanced plant growth and increased fruit yield in comparison with the untreated plant. Hence, B. velezensis VB7 and T. koingiopsis can be well explored as an antinemic bioagents against RKN.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03851-1.}, } @article {pmid38057898, year = {2023}, author = {Jin, D and Le, J and Yang, Q and Cai, Q and Dai, H and Luo, L and Tong, J and Shu, W}, title = {Pneumocystis jirovecii with high probability detected in bronchoalveolar lavage fluid of chemotherapy-related interstitial pneumonia in patients with lymphoma using metagenomic next-generation sequencing technology.}, journal = {Infectious agents and cancer}, volume = {18}, number = {1}, pages = {80}, pmid = {38057898}, issn = {1750-9378}, abstract = {BACKGROUND: Previous studies achieved low microbial detection rates in lymphoma patients with interstitial pneumonia (IP) after chemotherapy. However, the metagenomic next-generation sequencing (mNGS) is a comprehensive approach that is expected to improve the pathogen identification rate. Thus far, reports on the use of mNGS in lymphoma patients with chemotherapy-related IP remain scarce. In this study, we summarized the microbial detection outcomes of lymphoma patients with chemotherapy-related IP through mNGS testing of bronchoalveolar lavage fluid (BALF).

METHODS: Fifteen lymphoma patients with chemotherapy-related IP were tested for traditional laboratory microbiology, along with the mNGS of BALF. Then, the results of mNGS and traditional laboratory microbiology were compared.

RESULTS: Of the 15 enrolled patients, 11 received rituximab and 8 were administered doxorubicin hydrochloride liposome. The overall microbial yield was 93.3% (14/15) for mNGS versus 13.3% (2/15) for traditional culture methods (P ≤ 0.05). The most frequently detected pathogens were Pneumocystis jirovecii (12/15, 80%), Cytomegalovirus (4/15, 26.7%), and Epstein-Barr virus (3/15, 20%). Mixed infections were detected in 10 cases. Five patients recovered after the treatment with antibiotics alone without glucocorticoids.

CONCLUSION: Our findings obtained through mNGS testing of BALF suggested a high microbial detection rate in lymphoma patients with IP after chemotherapy. Notably, there was an especially high detection rate of Pneumocystis jirovecii. The application of mNGS in patients with chemotherapy-related IP was more sensitive.}, } @article {pmid38057705, year = {2023}, author = {Yang, C and Hu, T and Xue, X and Su, X and Zhang, X and Fan, Y and Shen, X and Dong, X}, title = {Multi-omics analysis of fecal microbiota transplantation's impact on functional constipation and comorbid depression and anxiety.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {389}, pmid = {38057705}, issn = {1471-2180}, support = {202102130501015//Key R&D Program of Shanxi Province/ ; }, mesh = {Humans ; *Fecal Microbiota Transplantation ; Depression/therapy ; Multiomics ; Serotonin ; Constipation/therapy ; Feces/microbiology ; *Gastrointestinal Diseases ; Anxiety/therapy ; }, abstract = {BACKGROUND: Depression and anxiety are common comorbid diseases of constipation. Fecal microbiota transplantation (FMT) significantly relieves gastrointestinal-related symptoms, but its impact on psychiatric symptoms remains uncharted.

METHODS: We collected fecal and serum samples before and after FMT from 4 functional constipation patients with psychiatric symptoms and corresponding donor stool samples. We categorized the samples into two groups: before FMT (Fb) and after FMT (Fa). Parameters associated with constipation, depression, and anxiety symptoms were evaluated. Metagenomics and targeted neurotransmitter metabolomics were performed to investigate the gut microbiota and metabolites. 5-hydroxytryptamine (5-HT) biosynthesis was detected in patients' fecal supernatants exposed to the QGP-1 cell model in vitro.

RESULTS: Our study demonstrated that patient's constipation, depression, and anxiety were improved after FMT intervention. At the genus level, relative abundance of g_Bacteroides and g_Klebsiella decreased in the Fa group, while g_Lactobacillus, and g_Selenomonas content increased in the same group. These observations suggest a potential involvement of these genera in the pathogenesis of constipation with psychiatric symptoms. Metabolomics analysis showed that FMT intervention decreased serum 5-HT levels. Additionally, we found that species, including s_Klebsiella sp. 1_1_55, s_Odoribacter splanchnicus, and s_Ruminococcus gnavus CAG:126, were positively correlated with 5-HT levels. In contrast, s_Acetobacterium bakii, s_Enterococcus hermanniensis, s_Prevotella falsenii, s_Propionispira arboris, s_Schwartzia succinivorans, s_Selenomonas artemidis, and s_Selenomonas sp. FC4001 were negatively correlated with 5-HT levels. Furthermore, we observed that patients' fecal supernatants increased 5-HT biosynthesis in QGP-1 cells.

CONCLUSION: FMT can relieve patients' constipation, depression, and anxiety symptoms by reshaping gut microbiota. The 5-HT level was associated with an altered abundance of specific bacteria or metabolites. This study provides specific evidence for FMT intervention in constipation patients with psychiatric symptoms.}, } @article {pmid38057501, year = {2023}, author = {Yadav, P and Quattrone, A and Yang, Y and Owens, J and Kiat, R and Kuppusamy, T and Russo, SE and Weber, KA}, title = {Zea mays genotype influences microbial and viral rhizobiome community structure.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {129}, pmid = {38057501}, issn = {2730-6151}, support = {1557417//National Science Foundation (NSF)/ ; }, abstract = {Plant genotype is recognized to contribute to variations in microbial community structure in the rhizosphere, soil adherent to roots. However, the extent to which the viral community varies has remained poorly understood and has the potential to contribute to variation in soil microbial communities. Here we cultivated replicates of two Zea mays genotypes, parviglumis and B73, in a greenhouse and harvested the rhizobiome (rhizoplane and rhizosphere) to identify the abundance of cells and viruses as well as rhizobiome microbial and viral community using 16S rRNA gene amplicon sequencing and genome resolved metagenomics. Our results demonstrated that viruses exceeded microbial abundance in the rhizobiome of parviglumis and B73 with a significant variation in both the microbial and viral community between the two genotypes. Of the viral contigs identified only 4.5% (n = 7) of total viral contigs were shared between the two genotypes, demonstrating that plants even at the level of genotype can significantly alter the surrounding soil viral community. An auxiliary metabolic gene associated with glycoside hydrolase (GH5) degradation was identified in one viral metagenome-assembled genome (vOTU) identified in the B73 rhizobiome infecting Propionibacteriaceae (Actinobacteriota) further demonstrating the viral contribution in metabolic potential for carbohydrate degradation and carbon cycling in the rhizosphere. This variation demonstrates the potential of plant genotype to contribute to microbial and viral heterogeneity in soil systems and harbors genes capable of contributing to carbon cycling in the rhizosphere.}, } @article {pmid38056715, year = {2024}, author = {Maisto, M and Ranauda, MA and Zuzolo, D and Tartaglia, M and Postiglione, A and Prigioniero, A and Falzarano, A and Scarano, P and Castelvetro, V and Corti, A and Modugno, F and La Nasa, J and Biale, G and Sciarrillo, R and Guarino, C}, title = {Effects of microplastics on microbial community dynamics in sediments from the Volturno River ecosystem, Italy.}, journal = {Chemosphere}, volume = {349}, number = {}, pages = {140872}, doi = {10.1016/j.chemosphere.2023.140872}, pmid = {38056715}, issn = {1879-1298}, mesh = {Microplastics ; Plastics ; Ecosystem ; RNA, Ribosomal, 16S ; *Microbiota ; Polymers ; Italy ; Environmental Monitoring ; *Water Pollutants, Chemical ; Geologic Sediments ; }, abstract = {In this study, the sources, abundance, and ecological implications of microplastic (MP) pollution in Volturno, one of the main rivers in southern Italy, were explored by investigating the MP concentration levels in sediments collected along the watercourse. The samples were sieved through 5- and 2-mm sieves and treated with selective organic solvents. The polymer classes polystyrene (PS), polyethylene (PE), polypropylene (PP), polyethylene terephthalate (PET), polycarbonate (PC), nylon 6 (PA6), and nylon 6,6 (PA66) were quantified using pyrolysis-gas chromatography-mass spectrometry (Py-GC/MS) and high-performance liquid chromatography (HPLC). Furthermore, a 16S rRNA metagenomic analysis was performed using next-generation sequencing in Ion Torrent™ to explore the bacterial taxonomy and ecological dynamics of sediment samples. The MPs were detected in all samples collected from the study area. PP and PET were the most abundant and frequently detected polymer types in the analysed samples. The total MP concentration ranged from 1.05 to 14.55 ppm (parts per million), identifying two distinct data populations: high- and low-MP-contaminated sediments. According to the Polymer Hazard Index (PHI), MP pollution was categorised as hazard levels III and IV (corresponding to the danger category). Metagenomic data revealed that the presence of MPs significantly affected the abundance of bacterial taxa; Flavobacteraceae and Nocardiaceae, which are known to degrade polymeric substances, were present in high-MP-contaminated sediments. This study provides new insights into the ecological relevance of MP pollution and suggests that microorganisms may serve as biomarkers of MP pollution.}, } @article {pmid38056679, year = {2023}, author = {Li, H and Zhao, Z and Shi, M and Luo, B and Wang, G and Wang, X and Gu, J and Song, Z and Sun, Y and Zhang, L and Wang, J}, title = {Metagenomic binning analyses of swine manure composting reveal mechanism of nitrogen cycle amendment using kaolin.}, journal = {Bioresource technology}, volume = {393}, number = {}, pages = {130156}, doi = {10.1016/j.biortech.2023.130156}, pmid = {38056679}, issn = {1873-2976}, abstract = {The efficient control of nitrogen loss in composting and the enhancement of product quality have become prominent concerns in current research. The positive role of varying concentrations kaolin in reducing nitrogen loss during composting was revealed using metagenomic binning combined with reverse transcription quantitative polymerase chain reaction. The results indicated that the addition of 0.5 % kaolin significantly (P < 0.05) up-regulated the expression of nosZ and nifH on day 35, while concurrently reducing norB abundance, resulting in a reduction of NH3 and N2O emissions by 61.4 % and 17.5 %, respectively. Notably, this study represents the first investigation into the co-occurrence of nitrogen functional genes and heavy metal resistance genes within metagenomic assembly genomes during composting. Emerging evidence indicates that kaolin effectively impedes the binding of Cu/Zn to nirK and nosZ gene reductases through passivation. This study offers a novel approach to enhance compost quality and waste material utilization.}, } @article {pmid38056669, year = {2023}, author = {Xu, X and Wu, W and Li, X and Zhao, C and Qin, Y}, title = {Metagenomics coupled with thermodynamic analysis revealed a potential way to improve the nitrogen removal efficiency of the aerobic methane oxidation coupled to denitrification process under the hypoxic condition.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {168953}, doi = {10.1016/j.scitotenv.2023.168953}, pmid = {38056669}, issn = {1879-1026}, abstract = {Aerobic methane (CH4) oxidation coupled to denitrification (AME-D) is a promising wastewater treatment process for CH4 utilization and nitrogen removal. However, it is unclear which CH4-derived carbons are suitable for the AME-D process and how these organics are metabolized. In this study, metagenomics coupled with a thermodynamic model were used to explore the microorganisms and their metabolic mechanisms in an AME-D membrane biofilm reactor (MBfR) with high nitrogen removal efficiency. Results revealed that the aerobic methanotrophs of Methylomonas with the CH4-based fermentation potential were highly enriched and played an important role in CH4 conversion in the MBfR. Bacteria of Xanthomonadaceae, Methylophilaceae, Bacteroidetes, Rhodocyclaceae, Hyphomicrobium were the main denitrifiers. C1 compounds (methanol, formaldehyde and formate) and CH4-based fermentation products are promising cross-feeding intermediates of the AME-D. Specially, by means of integrating the CH4-based fermentation with denitrification, the minimum amount of CH4 required to remove per mole of nitrate can be further reduced to 1.25 mol-CH4 mol[-1]-NO3[-], even lower than that of methanol. Compared to the choice to secrete methanol, type I aerobic methanotrophs require a 15 % reduction in the amount of oxygen required to secrete fermentation metabolites, but a 72 % increase in the amount of CH4-C released. Based on this trade-off, optimizing oxygen supply strategies will help to construct engineered microbiomes focused on aerobic methanotrophs with CH4-based fermentation potential. This study gives an insight into C and N conversions in the AME-D process and highlights the role of CH4-based fermentation in improving the nitrogen removal efficiency of the AME-D process.}, } @article {pmid38056648, year = {2023}, author = {Scicchitano, D and Babbi, G and Palladino, G and Turroni, S and Mekonnen, YT and Laczny, C and Wilmes, P and Leekitcharoenphon, P and Castagnetti, A and D'Amico, F and Brigidi, P and Savojardo, C and Manfreda, G and Martelli, P and De Cesare, A and Aarestrup, FM and Candela, M and Rampelli, S}, title = {Routes of dispersion of antibiotic resistance genes from the poultry farm system.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169086}, doi = {10.1016/j.scitotenv.2023.169086}, pmid = {38056648}, issn = {1879-1026}, abstract = {Poultry farms are hotspots for the development and spread of antibiotic resistance genes (ARGs), due to high stocking densities and extensive use of antibiotics, posing a threat of spread and contagion to workers and the external environment. Here, we applied shotgun metagenome sequencing to characterize the gut microbiome and resistome of poultry, workers and their households - also including microbiomes from the internal and external farm environment - in three different farms in Italy during a complete rearing cycle. Our results highlighted a relevant overlap among the microbiomes of poultry, workers, and their families (gut and skin), with clinically relevant ARGs and associated mobile elements shared in both poultry and human samples. On a finer scale, the reconstruction of species-level genome bins (SGBs) allowed us to delineate the dynamics of microorganism and ARGs dispersion from farm systems. We found the associations with worker microbiomes representing the main route of ARGs dispersion from poultry to human populations. Collectively, our findings clearly demonstrate the urgent need to implement more effective procedures to counteract ARGs dispersion from poultry food systems and the relevance of metagenomics-based metacommunity approaches to monitor the ARGs dispersion process for the safety of the working environment on farms.}, } @article {pmid38056640, year = {2023}, author = {Zhu La, AT and Li, D and Cheng, Z and Wen, Q and Hu, D and Jin, X and Liu, D and Feng, Y and Guo, Y and Cheng, G and Hu, Y}, title = {Enzymatically prepared neoagarooligosaccharides improve gut health and function through promoting the production of spermidine by Faecalibacterium in chickens.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {169057}, doi = {10.1016/j.scitotenv.2023.169057}, pmid = {38056640}, issn = {1879-1026}, abstract = {Maintaining animal gut health through modulating the gut microbiota is a constant need when antibiotics are not used in animal feed during the food animal production process. Prebiotics is regarded as one of the most promising antibiotic alternatives for such purpose. As an attractive prebiotic, the role and mechanisms of neoagarooligosaccharides (NAOS) in promoting animal growth and gut health have not been elucidated. In this study, we first cloned and expressed marine bacterial β-agarase in yeast to optimize the NAOS preparation and then investigated the role and the underlying mechanisms of the prepared NAOS in improving chicken gut health and function. The marine bacterial β-agarase PDE13B was expressed in Pichia pastoris GS115 and generated even-numbered NAOS. Dietary the prepared NAOS promoted chicken growth and improved intestinal morphology, its barrier, and digestion capabilities, and absorption function. Metagenomic analysis indicated that NAOS modulated the chicken gut microbiota structure and function, and microbial interactions, and promoted the growth of spermidine-producing bacteria especially Faecalibacterium. Through integration of gut metagenome, gut content metabolome, and gut tissue transcriptome, we established connections among NAOS, gut microbes, spermidine, and chicken gut gene expression. The spermidine regulation of genes related to autophagy, immunity, and inflammation was further confirmed in chicken embryo intestinal epithelium cells. We also verified that NAOS can be utilized by Faecalibacterium prausnitzii to grow and produce spermidine in in vitro experiments. Collectively, we provide a systematic investigation of the role of NAOS in regulating gut health and demonstrate the microbial spermidine-mediated mechanism involved in prebiotic effects of NAOS, which lays foundation for future use of NAOS as a new antibiotic alternative in animal production.}, } @article {pmid38056093, year = {2023}, author = {Wang, M and Masoudi, A and Wang, C and Wu, C and Zhang, Z and Zhao, X and Liu, Y and Yu, Z and Liu, J}, title = {Impacts of net cages on pollutant accumulation and its consequence on antibiotic resistance genes (ARGs) dissemination in freshwater ecosystems: Insights for sustainable urban water management.}, journal = {Environment international}, volume = {183}, number = {}, pages = {108357}, doi = {10.1016/j.envint.2023.108357}, pmid = {38056093}, issn = {1873-6750}, abstract = {There has been increasing interest in the role of human activities in disseminating antibiotic-resistance genes (ARGs) in aquatic ecosystems. However, the influence of pollutant accumulation on anthropogenic pollutant-ARG synergistic actions is limited. This study explored the association of net cages with the propagation of anthropogenic pollutants and their consequences for influencing the enrichment of ARGs using high-throughput metagenomic sequencing. We showed that net cages could substantially impact the ecology of freshwater systems by enhancing i) ARG diversity and the tendency for ARG-horizontal gene transfer and ii) the overlap of mobile genetic elements (MGEs) with biocide-metal resistance genes (BMRGs) and ARGs. These findings suggested that the cotransfer of these three genetic determinants would be favored in net cage plots and that nonantibiotic factors such as metal(loid)s, particularly iron (Fe), displayed robust selective pressures on ARGs exerted by the net cage. The resistome risk scores of net cage sediments and biofilms were higher than those from off-net cage plots, indicating that the net cage-origin antibiotic resistome should be of great concern. The combination of deterministic and stochastic processes acting on bacterial communities could explain the higher ARG variations in cage plots (8.2%) than in off-cage plots (3.4%). Moreover, MGEs and pollutants together explained 43.3% of the total variation in ARG communities, which was higher than that of off-cage plots (8.8%), considering pollutants, environmental variables, MGEs, and assembly processes. These findings will inform the development of policies and guidelines to more effectively limit the spread of antimicrobial resistance and achieve the goal of sustainability in freshwater systems in urban areas.}, } @article {pmid38055755, year = {2023}, author = {Jaito, N and Kaewsawat, N and Phetlum, S and Uengwetwanit, T}, title = {Metagenomic discovery of lipases with predicted structural similarity to Candida antarctica lipase B.}, journal = {PloS one}, volume = {18}, number = {12}, pages = {e0295397}, pmid = {38055755}, issn = {1932-6203}, mesh = {*Enzymes, Immobilized/chemistry ; Fungal Proteins/genetics/chemistry ; *Lipase/genetics/chemistry ; Temperature ; Metagenomics ; }, abstract = {Here we employed sequence-based and structure-based screening for prospecting lipases that have structural homolog to Candida antarctica lipase B (CalB). CalB, a widely used biocatalyst, was used as structural template reference because of its enzymatic properties. Structural homolog could aid in the discovery of novel wild-type enzymes with desirable features and serve as a scaffold for further biocatalyst design. The available metagenomic data isolated from various environments was leveraged as a source for bioprospecting. We identified two bacteria lipases that showed high structural similarity to CalB with <40% sequence identity. Partial purification was conducted. In comparison to CalB, the enzymatic characteristics of two potential lipases were examined. A candidate exhibited optimal pH of 8 and temperature of 50°C similar to CalB. The second lipase candidate demonstrated an optimal pH of 8 and a higher optimal temperature of 55°C. Notably, this candidate sustained considerable activity at extreme conditions, maintaining high activity at 70°C or pH 9, contrasting with the diminished activity of CalB under similar conditions. Further comprehensive experimentation is warranted to uncover and exploit these novel enzymatic properties for practical biotechnological purposes.}, } @article {pmid38054950, year = {2023}, author = {Morton, L and Creppage, K and Rahman, N and Early, J and Hartman, L and Hydrick, A and Kasper, M}, title = {Challenges and Opportunities in Pathogen Agnostic Sequencing for Public Health Surveillance: Lessons Learned From the Global Emerging Infections Surveillance Program.}, journal = {Health security}, volume = {}, number = {}, pages = {}, doi = {10.1089/hs.2023.0068}, pmid = {38054950}, issn = {2326-5108}, } @article {pmid38054947, year = {2023}, author = {Knight, T and Sureka, S}, title = {A New Paradigm for Threat Agnostic Biodetection: Biological Intelligence (BIOINT).}, journal = {Health security}, volume = {}, number = {}, pages = {}, doi = {10.1089/hs.2023.0072}, pmid = {38054947}, issn = {2326-5108}, } @article {pmid38054740, year = {2023}, author = {Molina-Pardines, C and Haro-Moreno, JM and López-Pérez, M}, title = {Phosphate-related genomic islands as drivers of environmental adaptation in the streamlined marine alphaproteobacterial HIMB59.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0089823}, pmid = {38054740}, issn = {2379-5077}, support = {PID2020-118052GB-I00//Ministerio de Economía y Competitividad (MEC)/ ; PRE2021-098122//Ministerio de Economía y Competitividad (MEC)/ ; 2021/PER/00020//Ministerio de Universidades (MU)/ ; }, mesh = {Humans ; *Genome, Bacterial/genetics ; Seawater/microbiology ; Phosphates ; Genomic Islands/genetics ; *Alphaproteobacteria/genetics ; }, abstract = {These results shed light on the evolutionary strategies of microbes with streamlined genomes to adapt and survive in the oligotrophic conditions that dominate the surface waters of the global ocean. At the individual level, these microbes have been subjected to evolutionary constraints that have led to a more efficient use of nutrients, removing non-essential genes named as "streamlining theory." However, at the population level, they conserve a highly diverse gene pool in flexible genomic islands resulting in polyclonal populations on the same genomic background as an evolutionary response to environmental pressures. Localization of these islands at equivalent positions in the genome facilitates horizontal transfer between clonal lineages. This high level of environmental genomic heterogeneity could explain their cosmopolitan distribution. In the case of the order HIMB59 within the class Alphaproteobacteria, two factors exert evolutionary pressure and determine this intraspecific diversity: phages and the concentration of P in the environment.}, } @article {pmid38054728, year = {2023}, author = {Duarte, VdS and Porcellato, D}, title = {Host DNA depletion methods and genome-centric metagenomics of bovine hindmilk microbiome.}, journal = {mSphere}, volume = {}, number = {}, pages = {e0047023}, doi = {10.1128/msphere.00470-23}, pmid = {38054728}, issn = {2379-5042}, abstract = {Next-generation sequencing technologies have been widely used to gain new insights into the diversity of the microbial community of milk samples and dairy products for different purposes such as microbial safety, profiling of starter cultures, and host-microbiome interactions. Milk is a complex food matrix, and additionally, the presence of host nucleic acid sequences is considered a contaminant in untargeted high-throughput sequencing studies. Therefore, genomic-centric metagenomic studies of milk samples focusing on the health-disease status in dairy cattle are still scarce, which makes it difficult to evaluate the microbial ecophysiology of bovine hindmilk. This study provides an alternative method for genome-centric metagenome studies applied to hindmilk samples with high somatic cell content, which is indispensable to examining host-microbiome interactions in bovine mastitis.}, } @article {pmid38054020, year = {2023}, author = {Du, L and Dong, X and Song, J and Lei, T and Liu, X and Lan, Y and Liu, X and Wang, J and Yue, B and He, M and Fan, Z and Guo, T}, title = {Temporal and spatial differences in the vaginal microbiome of Chinese healthy women.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16438}, pmid = {38054020}, issn = {2167-8359}, mesh = {Female ; Humans ; *East Asian People ; Vagina/microbiology ; Lactobacillus ; Cervix Uteri/microbiology ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Up the reproductive tract, there are large differences in the composition of vaginal microbes. Throughout the menstrual cycle, the structure of the vaginal microbiome shifts. Few studies have examined both in combination. Our study was designed to explore trends in the microbiome of different parts of the vagina in healthy women over the menstrual cycle.

METHODS: We performed metagenomic sequencing to characterize the microbiome differences between the cervical orifice and mid-vagina throughout the menstrual cycle.

RESULTS: Our results showed the vaginal microbiome of healthy women in the cervical orifice and the mid-vagina was similar during the periovulatory and luteal phases, with Lactobacillus being the dominant bacteria. In the follicular phase, Acinetobacter was detected in the cervical orifice. From the follicular phase to the luteal phase, the community state types (all five community status types were defined as CSTs) in samples No. 10 and No. 11 changed from CST III to CST I. In addition, the composition of the vaginal microbiome in healthy women from different regions of China was significantly different. We also detected viruses including Human alphaherpesvirus 1 (HSV-1) during periovulatory phase.

CONCLUSION: This study is valuable for understanding whether the microbial composition of the vagina is consistent in different parts of the menstrual cycle.}, } @article {pmid38053854, year = {2023}, author = {Ju, C and Wang, L and Xu, P and Wang, X and Xiang, D and Xu, Y and Xu, X and Chen, R and He, J}, title = {Differentiation between lung allograft rejection and infection using donor-derived cell-free DNA and pathogen detection by metagenomic next-generation sequencing.}, journal = {Heliyon}, volume = {9}, number = {11}, pages = {e22274}, pmid = {38053854}, issn = {2405-8440}, abstract = {BACKGROUND: In lung transplant recipients (LTRs), the primary causes of mortality are rejection and infection, which often present similar symptoms, making differentiation challenging. This study aimed to explore the diagnostic efficacy of plasma donor-derived cell-free DNA (dd-cfDNA) in conjunction with metagenomic next-generation sequencing (mNGS) for pathogen detection in differentiation between lung allograft rejection and infection in LTRs experiencing new-onset pulmonary complications.

METHODS: We conducted a retrospective study on 188 LTRs who underwent lung or heart-lung transplantation at our institution from 2015 to 2021. The LTRs were categorized into three groups: stable, rejection, and infection. We measured plasma dd-cfDNA levels and utilized both mNGS and culture methods to identify pathogens in the bronchoalveolar lavage fluid (BALF).

RESULTS: The rejection group exhibited the highest levels of plasma dd-cfDNA (median 1.34 %, interquartile range [IQR] 1.06-2.19 %) compared to the infection group (median 0.72 %, IQR 0.62-1.07 %) and the stable group (median 0.69 %, IQR 0.58-0.78 %) (both p < 0.001). Within the infection group, a significantly higher level of dd-cfDNA was observed in the cytomegalovirus infection subgroup (p < 0.001), but not in the fungal (p > 0.05) or bacterial infection subgroups (p > 0.05), when compared to the stable group. Elevated dd-cfDNA levels, in combination with negative mNGS results, strongly indicated lung allograft rejection, with a positive predictive value and negative predictive value of 88.7 % and 99.2 %, respectively.

CONCLUSIONS: Plasma dd-cfDNA in combination with BALF pathogen detection by mNGS shows satisfactory accuracy in differentiating lung allograft rejection from infectious complications.}, } @article {pmid38053586, year = {2023}, author = {Lawrence, P and Padamsee, M and Lee, K and Lacap-Bugler, DC}, title = {Soil microbial functional gene dataset associated with Agathis australis.}, journal = {Data in brief}, volume = {51}, number = {}, pages = {109791}, pmid = {38053586}, issn = {2352-3409}, abstract = {Agathis australis (New Zealand kauri) is a significant and iconic native tree of Aotearoa New Zealand. Currently, Phytophthora agathidicida that causes kauri-dieback disease is killing kauri trees. Only 1% of the New Zealand virgin kauri forest remains [1,2]. Recent studies revealed that many soil-borne microorganisms had been found to systemically boost the defensive capacity of the trees by providing competition to pathogens for nutrient intake, thus preventing pathogen colonization and modulating plant immunity [3,4]. In addition, the root microbiome consists of an entire complex rhizosphere-associated microbes with their genetic elements and interactions that have influenced plant health. To date, very few studies have been conducted to investigate the microorganisms in the kauri soil and possible environmental drivers. To characterize the functional gene profile in relation to soil microbial diversity of the kauri trees at Auckland Botanic Gardens (ABG), Auckland, New Zealand the GeoChip 5.0 M (Glomics Inc. USA), a microarray-based metagenomics tool, was used. GeoChip 5.0 M comprises of 162,000 probes from 365,000 target genes (coding DNA sequence - CDS), which covers all taxonomic groups (archaea, bacteria, fungi, protists, algae, and viruses) [5]. The ABG has kauri trees that are approximately 20 years old, located in three distinct man-made environments: Native Forest, Kauri Grove, and Rose Garden. We selected two trees from the Native Forest and two from the Kauri Grove for our experiment. Soil samples were collected from the four cardinal points of each tree, at 10 cm depth. Pooled environmental DNA was sent to Glomics (USA) and the data were preprocessed using GeoChip data analysis pipeline described in http://www.ou.edu/ieg/tools/data-analysispipeline.html. Based on the GeoChip data generated from the soil samples, we have detected a total of 946 genes, 4342 taxa, 102 phyla, and 995 genera. The data presented here provide an overview of functional genes associated with kauri soil, which can serve as baseline for other kauri soil microbiome analysis at forest-scale studies. The raw data has been uploaded to Mendeley Data https://doi.org/10.17632/T22NNN385K.1.}, } @article {pmid38053553, year = {2023}, author = {Metze, F and Vollmers, J and Lenk, F and Kaster, AK}, title = {First shotgun metagenomics study of Juan de Fuca deep-sea sediments reveals distinct microbial communities above, within, between, and below sulfate methane transition zones.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1241810}, pmid = {38053553}, issn = {1664-302X}, abstract = {The marine deep subsurface is home to a vast microbial ecosystem, affecting biogeochemical cycles on a global scale. One of the better-studied deep biospheres is the Juan de Fuca (JdF) Ridge, where hydrothermal fluid introduces oxidants into the sediment from below, resulting in two sulfate methane transition zones (SMTZs). In this study, we present the first shotgun metagenomics study of unamplified DNA from sediment samples from different depths in this stratified environment. Bioinformatic analyses showed a shift from a heterotrophic, Chloroflexota-dominated community above the upper SMTZ to a chemolithoautotrophic Proteobacteria-dominated community below the secondary SMTZ. The reintroduction of sulfate likely enables respiration and boosts active cells that oxidize acetate, iron, and complex carbohydrates to degrade dead biomass in this low-abundance, low-diversity environment. In addition, analyses showed many proteins of unknown function as well as novel metagenome-assembled genomes (MAGs). The study provides new insights into microbial communities in this habitat, enabled by an improved DNA extraction protocol that allows a less biased view of taxonomic composition and metabolic activities, as well as uncovering novel taxa. Our approach presents the first successful attempt at unamplified shotgun sequencing samples from beyond 50 meters below the seafloor and opens new ways for capturing the true diversity and functional potential of deep-sea sediments.}, } @article {pmid38053549, year = {2023}, author = {Song, W and Li, H and Zhou, Y and Liu, X and Li, Y and Wang, M and Li, DD and Tu, Q}, title = {Discordant patterns between nitrogen-cycling functional traits and taxa in distant coastal sediments reveal important community assembly mechanisms.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1291242}, pmid = {38053549}, issn = {1664-302X}, abstract = {A central question in microbial ecology is how immense microbes are assembled in changing natural environments while executing critical ecosystem functions. Over the past decade, effort has been made to unravel the contribution of stochasticity and determinism to the compositional of microbial communities. However, most studies focus on microbial taxa, ignoring the importance of functional traits. By employing shotgun metagenomic sequencing and state-of-the-art bioinformatics approaches, this study comprehensively investigated the microbially mediated nitrogen (N) cycling processes in two geographically distant coastal locations. Both shotgun and 16S rRNA gene amplicon sequencing demonstrated significantly differed taxonomic compositions between the two sites. The relative abundance of major microbial phyla, such as Pseudomonadota, Thaumarchaeota, and Bacteroidota, significantly differed. In contrast, high homogeneity was observed for N-cycling functional traits. Statistical analyses suggested that N-cycling taxonomic groups were more related to geographic distance, whereas microbial functional traits were more influenced by environmental factors. Multiple community assembly models demonstrated that determinism strongly governed the microbial N-cycling functional traits, whereas their carrying taxonomic groups were highly stochastic. Such discordant patterns between N-cycling functional traits and taxa demonstrated an important mechanism in microbial ecology in which essential ecosystem functions are stably maintained despite geographic distance and stochastic community assembly.}, } @article {pmid38053531, year = {2023}, author = {Wang, Q and Hu, R and Zhu, Y and Zhu, W and Jiang, H}, title = {Case Report: The application of metagenomic next generation sequencing in diagnosing fungal malignant external otitis: a report of two cases.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1236414}, pmid = {38053531}, issn = {2235-2988}, mesh = {Humans ; *Otitis Externa/diagnosis ; High-Throughput Nucleotide Sequencing ; Antifungal Agents/therapeutic use ; Metagenome ; Metagenomics ; }, abstract = {BACKGROUND: Most of malignant external otitis (MEO) cases reported in the literature are attributed to Pseudomonas aeruginosa. Fungal infections in MEO are also likely but extremely rare. And conventional microbiology tests is difficult to diagnose.

CASE DESCRIPTION: Two patients were diagnosed with Fungal malignant external otitis (FMEO) due to Aspergillus by metagenomic Next-Generation Sequencing (mNGS) and recovered after comprehensive treatment including operation and voriconazole. The antifungal treatment was delayed due to repeated cultures of secretions being negative and pathological examination showed granulation tissue proliferation with extensive neutrophil infiltration.

CONCLUSION: mNGS might be helpful for patients suspected with FMEO, especially when conventional microbiology tests were negative.}, } @article {pmid38053159, year = {2023}, author = {Costa, LSAS and de Faria, MR and Chiaramonte, JB and Mendes, LW and Sepo, E and de Hollander, M and Fernandes, JMC and Carrión, VJ and Bettiol, W and Mauchline, TH and Raaijmakers, JM and Mendes, R}, title = {Repeated exposure of wheat to the fungal root pathogen Bipolaris sorokiniana modulates rhizosphere microbiome assembly and disease suppressiveness.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {85}, pmid = {38053159}, issn = {2524-6372}, support = {BB/N016246/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X010953/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: Disease suppressiveness of soils to fungal root pathogens is typically induced in the field by repeated infections of the host plant and concomitant changes in the taxonomic composition and functional traits of the rhizosphere microbiome. Here, we studied this remarkable phenomenon for Bipolaris sorokiniana in two wheat cultivars differing in resistance to this fungal root pathogen.

RESULTS: The results showed that repeated exposure of the susceptible wheat cultivar to the pathogen led to a significant reduction in disease severity after five successive growth cycles. Surprisingly, the resistant wheat cultivar, initially included as a control, showed the opposite pattern with an increase in disease severity after repeated pathogen exposure. Amplicon analyses revealed that the bacterial families Chitinophagaceae, Anaerolineaceae and Nitrosomonadaceae were associated with disease suppressiveness in the susceptible wheat cultivar; disease suppressiveness in the resistant wheat cultivar was also associated with Chitinophagaceae and a higher abundance of Comamonadaceae. Metagenome analysis led to the selection of 604 Biosynthetic Gene Clusters (BGCs), out of a total of 2,571 identified by AntiSMASH analysis, that were overrepresented when the soil entered the disease suppressive state. These BGCs are involved in the biosynthesis of terpenes, non-ribosomal peptides, polyketides, aryl polyenes and post-translationally modified peptides.

CONCLUSION: Combining taxonomic and functional profiling we identified key changes in the rhizosphere microbiome during disease suppression. This illustrates how the host plant relies on the rhizosphere microbiome as the first line of defense to fight soil-borne pathogens. Microbial taxa and functions identified here can be used in novel strategies to control soil-borne fungal pathogens.}, } @article {pmid38053032, year = {2023}, author = {Luo, H and Jiang, L and Chen, J and Wang, D and Kong, Y and Cao, G}, title = {Chlamydia psittaci Pneumonia in a patient with motor neuron disease: a case report.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {852}, pmid = {38053032}, issn = {1471-2334}, mesh = {Male ; Humans ; Aged ; *Chlamydophila psittaci ; *Psittacosis/complications/diagnosis/drug therapy ; *Pneumonia ; Bronchi ; *Motor Neuron Disease/complications/diagnosis ; Dyspnea ; }, abstract = {BACKGROUND: Motor neuron disease (MND) is a fatal neurodegenerative disorder that leads to progressive loss of motor neurons. Chlamydia psittaci (C. psittaci) is a rare etiology of community-acquired pneumonia characterized primarily by respiratory distress. We reported a case of C. psittaci pneumonia complicated with motor neuron disease (MND).

CASE PRESENTATION: A 74-year-old male was referred to the Shaoxing Second Hospital at January, 2022 complaining of fever and fatigue for 2 days. The patient was diagnosed of MND with flail arm syndrome 1 year ago. The metagenomic next-generation sequencing (mNGS) of sputum obtained through bedside fiberoptic bronchoscopy showed C. psittaci infection. Then doxycycline was administrated and bedside fiberoptic bronchoscopy was performed to assist with sputum excretion. Computed Tomography (CT) and fiberoptic bronchoscopy revealed a significant decrease in sputum production. On day 24 after admission, the patient was discharged with slight dyspnea, limited exercise tolerance. One month later after discharge, the patient reported normal respiratory function, and chest CT showed significant absorption of sputum.

CONCLUSIONS: The mNGS combined with bedside fiberoptic bronchoscopy could timely detect C. psittaci infection. Bedside fiberoptic bronchoscopy along with antibiotic therapy may be effective for C. psittaci treatment.}, } @article {pmid38052339, year = {2023}, author = {Tian, Y and Han, Z and Su, D and Luan, X and Yu, L and Tian, Z and Zhang, Y and Yang, M}, title = {Assessing impacts of municipal wastewater treatment plant upgrades on bacterial hazard contributions to the receiving urban river using SourceTracker.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {342}, number = {}, pages = {123075}, doi = {10.1016/j.envpol.2023.123075}, pmid = {38052339}, issn = {1873-6424}, abstract = {Upgrading municipal wastewater treatment plants (MWTPs) has been implemented in many megacities of China to reduce the discharges of nutrients and other pollutants and improve water quality of highly urbanized rivers. However, the contribution of MWTP discharge to bacterial hazards in the receiving rivers after upgrades has been largely unknown. In this study, high-throughput sequencing and shotgun metagenomics were applied to investigate the changes in the abundance, composition, potential risks, and contributions of bacteria and antibiotic resistance genes (ARGs) from effluent to receiving river after upgrading the third-largest MWTP in China with denitrification biofilters, ultrafiltration, ozonation, and disinfection processes. The annual loadings of total nitrogen and 27 types of pharmaceuticals were reduced by 42.4% ± 13.2% and 46.2% ± 15.4%, respectively. Bacterial biomass decreased from (3.58 ± 0.49) to (1.23 ± 0.27) × 10[7] 16S rRNA gene copies/mL, and identified biomarkers in effluent and downstream shifted due to the adopted processes. Opportunistic pathogen bacteria downstream were also reduced. Although the relative abundance of total ARGs in MWTP effluent increased from 1.10 ± 0.02 to 2.19 ± 0.03 copies/16S rRNA gene after upgrades, that of total and high-risk ARGs downstream showed no significant difference. More importantly, the Bayesian-based SourceTracker method provided valuable insight by revealing that the contributions of MWTP discharge to downstream bacteria (from 44.2% ± 1.5%-31.4% ± 0.9%) and ARGs (from 61.2% ± 5.3%-47.6% ± 4.1%) were significantly reduced following the upgrades, indicating upgrading MWTP showed integrated benefits to the bacterial hazards in the receiving river. This study provides useful information for better control of bacterial hazard risks and operational strategy for the improvement of the urban aquatic ecosystem.}, } @article {pmid38051927, year = {2023}, author = {O'Dwyer, DN and Kim, JS and Ma, SF and Ranjan, P and Das, P and Lipinski, JH and Metcalf, JD and Falkowski, NR and Yow, E and Anstrom, K and Dickson, RP and Huang, Y and Gilbert, JA and Martinez, FJ and Noth, I}, title = {Commensal Oral Microbiota, Disease Severity and Mortality in Fibrotic Lung Disease.}, journal = {American journal of respiratory and critical care medicine}, volume = {}, number = {}, pages = {}, doi = {10.1164/rccm.202308-1357OC}, pmid = {38051927}, issn = {1535-4970}, abstract = {RATIONALE: Oral microbiota associate with diseases of the mouth and serve as a source of lung microbiota. However, the role of oral microbiota in lung disease is unknown.

OBJECTIVES: To determine associations between oral microbiota and disease severity and death in idiopathic pulmonary fibrosis.

METHODS: We analyzed 16S rRNA gene and shotgun metagenomic sequencing data of buccal swabs from 511 patients with idiopathic pulmonary fibrosis in the multicenter CleanUP-IPF trial. Buccal swabs were collected from usual care, and antimicrobial cohorts. Microbiome data was correlated with measures of disease severity using principal component analysis and linear regression models. Associations between the buccal microbiome and mortality were determined using Cox additive models, Kaplan Meier analysis and Cox proportional hazards models.

MEASUREMENTS AND MAIN RESULTS: Greater buccal microbial diversity associated with lower forced vital capacity (FVC) at baseline [mean diff -3.60: 95% CI -5.92 to -1.29 percent predicted FVC per 1 unit increment]. The buccal proportion of Streptococcus correlated positively with FVC [mean diff 0.80: 95% CI 0.16-1.43 percent predicted per 10% increase] (n=490). Greater microbial diversity was associated with an increased risk of death [HR 1.73: 95% CI 1.03-2.90] while a greater proportion of Streptococcus was associated with a reduced risk of death [HR 0.85: 95% CI 0.73 to 0.99]. The Streptococcus genus was mainly comprised of Streptococcus mitis species.

CONCLUSIONS: Increasing buccal microbial diversity predicts disease severity and death in IPF. The oral commensal Streptococcus mitis spp associates with preserved lung function and improved survival.}, } @article {pmid38051631, year = {2024}, author = {Jo, J and Hu, C and Begum, K and Wang, W and Le, TM and Agyapong, S and Hanson, BM and Ayele, H and Lancaster, C and Jahangir Alam, M and Gonzales-Luna, AJ and Garey, KW}, title = {Fecal Pharmacokinetics and Gut Microbiome Effects of Oral Omadacycline Versus Vancomycin in Healthy Volunteers.}, journal = {The Journal of infectious diseases}, volume = {229}, number = {1}, pages = {273-281}, pmid = {38051631}, issn = {1537-6613}, support = {G0505124//Paratek Pharmaceuticals, Inc/ ; }, mesh = {Adult ; Humans ; Male ; Female ; Vancomycin/therapeutic use ; *Gastrointestinal Microbiome ; Healthy Volunteers ; Anti-Bacterial Agents/therapeutic use ; Tetracyclines/pharmacology/therapeutic use ; *Clostridium Infections/microbiology ; }, abstract = {BACKGROUND: Clostridioides difficile infection (CDI) is a common healthcare-associated infection with limited treatment options. Omadacycline, an aminomethylcycline tetracycline, has potent in vitro activity against C difficile and a low propensity to cause CDI in clinical trials. We aimed to assess fecal pharmacokinetics and gut microbiome effects of oral omadacycline compared to oral vancomycin in healthy adults.

METHODS: This was a phase 1, nonblinded, randomized clinical trial conducted in healthy volunteers aged 18-40 years. Subjects received a 10-day course of omadacycline or vancomycin. Stool samples were collected at baseline, daily during therapy, and at follow-up visits. Omadacycline and vancomycin stool concentrations were assessed, and microbiome changes were compared.

RESULTS: Sixteen healthy volunteers with a mean age of 26 (standard deviation [SD], 5) years were enrolled; 62.5% were male, and participants' mean body mass index was 23.5 (SD, 4.0) kg/m2. Omadacycline was well tolerated with no safety signal differences between the 2 antibiotics. A rapid initial increase in fecal concentrations of omadacycline was observed compared to vancomycin, with maximum concentrations achieved within 48 hours. A significant difference in alpha diversity was observed following therapy in both the omadacycline and vancomycin groups (P < .05). Bacterial abundance and beta diversity analysis showed differing microbiome changes in subjects who received omadacycline versus vancomycin.

CONCLUSIONS: Subjects given omadacycline had high fecal concentrations with a distinct microbiome profile compared to vancomycin.

CLINICAL TRIALS REGISTRATION: NCT06030219.}, } @article {pmid38051071, year = {2023}, author = {Verhoeven, MD and Nielsen, PH and Dueholm, MKD}, title = {Amplicon-guided isolation and cultivation of previously uncultured microbial species from activated sludge.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {12}, pages = {e0115123}, pmid = {38051071}, issn = {1098-5336}, support = {13351//Villum Fonden (Villum Foundation)/ ; //Nederlandse Organisatie voor Wetenschappelijk Onderzoek (NWO)/ ; NNF22OC0071498//Novo Nordisk Fonden (NNF)/ ; }, mesh = {*Sewage/microbiology ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; *Bacteria ; Wastewater ; }, abstract = {Biological wastewater treatment relies on complex microbial communities that assimilate nutrients and break down pollutants in the wastewater. Knowledge about the physiology and metabolism of bacteria in wastewater treatment plants (WWTPs) may therefore be used to improve the efficacy and economy of wastewater treatment. Our current knowledge is largely based on 16S rRNA gene amplicon profiling, fluorescence in situ hybridization studies, and predictions based on metagenome-assembled genomes. Bacterial isolates are often required to validate genome-based predictions as they allow researchers to analyze a specific species without interference from other bacteria and with simple bulk measurements. Unfortunately, there are currently very few pure cultures representing the microbes commonly found in WWTPs. To address this, we introduce an isolation strategy that takes advantage of state-of-the-art microbial profiling techniques to uncover suitable growth conditions for key WWTP microbes. We furthermore demonstrate that this information can be used to isolate key organisms representing global WWTPs.}, } @article {pmid38051048, year = {2024}, author = {Li, Y and Ma, J and Meng, J and Li, S and Zhang, Y and You, W and Sai, X and Yang, J and Zhang, S and Sun, W}, title = {Structural changes in the gut virome of patients with atherosclerotic cardiovascular disease.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0105023}, pmid = {38051048}, issn = {2165-0497}, support = {2180072120049//Beijing University of Chinese Medicine (BUCM)/ ; 81973849//MOST | National Natural Science Foundation of China (NSFC)/ ; }, mesh = {Humans ; Virome ; *Cardiovascular Diseases ; *Bacteriophages ; }, abstract = {Existing studies have found that there is a close relationship between human virome and numerous diseases, and diseases may affect the diversity and composition of the virome; at the same time, changes in the virome will in turn affect the onset and progression of the disease. However, the composition and functional capabilities of the gut virome associated with atherosclerotic cardiovascular disease (ACVD) have not been systematically investigated. To our knowledge, this is the first study investigating the gut virome in patients with ACVD. We characterized the structural changes in the gut virome of ACVD patients, which may facilitate additional mechanistic, diagnostic, and interventional studies of ACVD and related diseases.}, } @article {pmid38050281, year = {2023}, author = {Zhan, Z and Lin, X and Li, G and Zeng, J and Su, D and Liao, J and Shen, Q}, title = {Renal abscess complicating acute pyelonephritis in children: Two cases report and literature review.}, journal = {Medicine}, volume = {102}, number = {48}, pages = {e36355}, pmid = {38050281}, issn = {1536-5964}, mesh = {Child ; Humans ; Abscess/complications/diagnosis/drug therapy ; *Pyelonephritis/complications/diagnosis/drug therapy ; *Urinary Tract Infections/diagnosis ; *Kidney Diseases/complications ; Anti-Bacterial Agents/therapeutic use ; Escherichia coli ; Tomography, X-Ray Computed ; *Peritoneal Diseases/complications ; }, abstract = {RATIONALE: To describe the diagnostic and treatment approaches of renal abscesses complicated with acute pyelonephritis in children.

PATIENT CONCERNS: Two children presented with fever, vomiting, and abdominal pain with no typical manifestations, like frequent urination, urgency, dysuria, hematuria, foam urine, and lumbago. Renal abscess complicating acute pyelonephritis was diagnosed by B-ultrasound and computed tomography enhancement. Moreover, inflammatory markers were elevated significantly, but routine blood and urine cultures were repeatedly negative. The empirical anti-infection therapy had no obvious effect. A pathogenic diagnosis was confirmed in case two, and macro gene detection in blood and urine guided the follow-up treatment.

DIAGNOSES: Both children were diagnosed with acute gastroenteritis on admission, but renal abscess complicating acute pyelonephritis were diagnosed by imaging examination.

INTERVENTIONS: Both children were given anti-infection therapy of third-generation cephalosporin, which had no obvious effect. Routine blood and urine cultures were repeatedly negative. Case one was changed to piperacillin sodium tazobactam. We further carried out blood and urinary metagenomic next-generation sequencing detection for case two. Meanwhile, meropenem and linezolid anti-infection treatment was given. The results showed overlapping infection with Escherichia coli and Enterococcus faecalis. According to the genetic test results, amoxicillin clavulanate potassium combined with nitrofurantoin were prescribed after discharge.

OUTCOMES: Clinical symptoms of the 2 children disappeared, the infection was controlled, and imaging showed that renal abscess complicated with acute pyelonephritis disappeared.

LESSONS: The clinical spectrum of renal abscess complicating acute pyelonephritis is vague, with no specific manifestations, and can be easily misdiagnosed. B-ultrasound and computed tomography enhancement are helpful in making a definite diagnosis. Moreover, the sensitivity of routine culture is low, and metagenomic next-generation sequencing might be helpful to detect pathogenic microorganisms and guided treatment. Early treatment with broad-spectrum antibiotics might have favorable outcomes.}, } @article {pmid38050061, year = {2023}, author = {Zhu, J and Sun, C and Li, M and Hu, G and Zhao, XM and Chen, WH}, title = {Compared to histamine-2 receptor antagonist, proton pump inhibitor induces stronger oral-to-gut microbial transmission and gut microbiome alterations: a randomised controlled trial.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2023-330168}, pmid = {38050061}, issn = {1468-3288}, abstract = {OBJECTIVE: We aim to compare the effects of proton pump inhibitors (PPIs) and histamine-2 receptor antagonists (H2RAs) on the gut microbiota through longitudinal analysis.

DESIGN: Healthy volunteers were randomly assigned to receive either PPI (n=23) or H2RA (n=26) daily for seven consecutive days. We collected oral (saliva) and faecal samples before and after the intervention for metagenomic next-generation sequencing. We analysed intervention-induced alterations in the oral and gut microbiome including microbial abundance and growth rates, oral-to-gut transmissions, and compared differences between the PPI and H2RA groups.

RESULTS: Both interventions disrupted the gut microbiota, with PPIs demonstrating more pronounced effects. PPI usage led to a significantly higher extent of oral-to-gut transmission and promoted the growth of specific oral microbes in the gut. This led to a significant increase in both the number and total abundance of oral species present in the gut, including the identification of known disease-associated species like Fusobacterium nucleatum and Streptococcus anginosus. Overall, gut microbiome-based machine learning classifiers could accurately distinguish PPI from non-PPI users, achieving an area under the receiver operating characteristic curve (AUROC) of 0.924, in contrast to an AUROC of 0.509 for H2RA versus non-H2RA users.

CONCLUSION: Our study provides evidence that PPIs have a greater impact on the gut microbiome and oral-to-gut transmission than H2RAs, shedding light on the mechanism underlying the higher risk of certain diseases associated with prolonged PPI use.

TRIAL REGISTRATION NUMBER: ChiCTR2300072310.}, } @article {pmid38049915, year = {2023}, author = {Deng, W and Zhao, Z and Li, Y and Cao, R and Chen, M and Tang, K and Wang, D and Fan, W and Hu, A and Chen, G and Chen, CA and Zhang, Y}, title = {Strategies of chemolithoautotrophs adapting to high temperature and extremely acidic conditions in a shallow hydrothermal ecosystem.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {270}, pmid = {38049915}, issn = {2049-2618}, support = {42125603//National Natural Science Foundation of China/ ; 42125603//National Natural Science Foundation of China/ ; 42125603//National Natural Science Foundation of China/ ; 42125603//National Natural Science Foundation of China/ ; 42125603//National Natural Science Foundation of China/ ; 42125603//National Natural Science Foundation of China/ ; 42125603//National Natural Science Foundation of China/ ; 42125603//National Natural Science Foundation of China/ ; 42125603//National Natural Science Foundation of China/ ; 42125603//National Natural Science Foundation of China/ ; 42125603//National Natural Science Foundation of China/ ; 42125603//National Natural Science Foundation of China/ ; }, mesh = {Ecosystem ; Temperature ; Protons ; Carbon/metabolism ; *Epsilonproteobacteria ; DNA ; *Hydrothermal Vents/microbiology ; Phylogeny ; }, abstract = {BACKGROUND: Active hydrothermal vents create extreme conditions characterized by high temperatures, low pH levels, and elevated concentrations of heavy metals and other trace elements. These conditions support unique ecosystems where chemolithoautotrophs serve as primary producers. The steep temperature and pH gradients from the vent mouth to its periphery provide a wide range of microhabitats for these specialized microorganisms. However, their metabolic functions, adaptations in response to these gradients, and coping mechanisms under extreme conditions remain areas of limited knowledge. In this study, we conducted temperature gradient incubations of hydrothermal fluids from moderate (pH = 5.6) and extremely (pH = 2.2) acidic vents. Combining the DNA-stable isotope probing technique and subsequent metagenomics, we identified active chemolithoautotrophs under different temperature and pH conditions and analyzed their specific metabolic mechanisms.

RESULTS: We found that the carbon fixation activities of Nautiliales in vent fluids were significantly increased from 45 to 65 °C under moderately acidic condition, while their heat tolerance was reduced under extremely acidic conditions. In contrast, Campylobacterales actively fixed carbon under both moderately and extremely acidic conditions under 30 - 45 °C. Compared to Campylobacterales, Nautiliales were found to lack the Sox sulfur oxidation system and instead use NAD(H)-linked glutamate dehydrogenase to boost the reverse tricarboxylic acid (rTCA) cycle. Additionally, they exhibit a high genetic potential for high activity of cytochrome bd ubiquinol oxidase in oxygen respiration and hydrogen oxidation at high temperatures. In terms of high-temperature adaption, the rgy gene plays a critical role in Nautiliales by maintaining DNA stability at high temperature. Genes encoding proteins involved in proton export, including the membrane arm subunits of proton-pumping NADH: ubiquinone oxidoreductase, K[+] accumulation, selective transport of charged molecules, permease regulation, and formation of the permeability barrier of bacterial outer membranes, play essential roles in enabling Campylobacterales to adapt to extremely acidic conditions.

CONCLUSIONS: Our study provides in-depth insights into how high temperature and low pH impact the metabolic processes of energy and main elements in chemolithoautotrophs living in hydrothermal ecosystems, as well as the mechanisms they use to adapt to the extreme hydrothermal conditions. Video Abstract.}, } @article {pmid38049850, year = {2023}, author = {Sekiguchi, Y and Teramoto, K and Tourlousse, DM and Ohashi, A and Hamajima, M and Miura, D and Yamada, Y and Iwamoto, S and Tanaka, K}, title = {A large-scale genomically predicted protein mass database enables rapid and broad-spectrum identification of bacterial and archaeal isolates by mass spectrometry.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {257}, pmid = {38049850}, issn = {1474-760X}, support = {JP ae0121035h0002//Japan Agency for Medical Research and Development/ ; }, mesh = {Animals ; Mice ; *Archaea/genetics ; *Bacteria/genetics ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization/methods ; Databases, Factual ; }, abstract = {MALDI-TOF MS-based microbial identification relies on reference spectral libraries, which limits the screening of diverse isolates, including uncultured lineages. We present a new strategy for broad-spectrum identification of bacterial and archaeal isolates by MALDI-TOF MS using a large-scale database of protein masses predicted from nearly 200,000 publicly available genomes. We verify the ability of the database to identify microorganisms at the species level and below, achieving correct identification for > 90% of measured spectra. We further demonstrate its utility by identifying uncultured strains from mouse feces with metagenomics, allowing the identification of new strains by customizing the database with metagenome-assembled genomes.}, } @article {pmid38049781, year = {2023}, author = {Thapa, S and Zhou, S and O'Hair, J and Al Nasr, K and Ropelewski, A and Li, H}, title = {Exploring the microbial diversity and characterization of cellulase and hemicellulase genes in goat rumen: a metagenomic approach.}, journal = {BMC biotechnology}, volume = {23}, number = {1}, pages = {51}, pmid = {38049781}, issn = {1472-6750}, support = {2018-38821-27737//USDA-NIFA/ ; 2018-38821-27737//USDA-NIFA/ ; 2018-38821-27737//USDA-NIFA/ ; OCI 1053575//NSF/ ; }, mesh = {Animals ; *Cellulase/metabolism ; Metagenome ; Goats/genetics/metabolism/microbiology ; Rumen/metabolism/microbiology ; Escherichia coli/genetics ; Bacteria ; *Cellulases/genetics ; Cellulose ; }, abstract = {BACKGROUND: Goat rumen microbial communities are perceived as one of the most potential biochemical reservoirs of multi-functional enzymes, which are applicable to enhance wide array of bioprocesses such as the hydrolysis of cellulose and hemi-cellulose into fermentable sugar for biofuel and other value-added biochemical production. Even though, the limited understanding of rumen microbial genetic diversity and the absence of effective screening culture methods have impeded the full utilization of these potential enzymes. In this study, we applied culture independent metagenomics sequencing approach to isolate, and identify microbial communities in goat rumen, meanwhile, clone and functionally characterize novel cellulase and xylanase genes in goat rumen bacterial communities.

RESULTS: Bacterial DNA samples were extracted from goat rumen fluid. Three genomic libraries were sequenced using Illumina HiSeq 2000 for paired-end 100-bp (PE100) and Illumina HiSeq 2500 for paired-end 125-bp (PE125). A total of 435gb raw reads were generated. Taxonomic analysis using Graphlan revealed that Fibrobacter, Prevotella, and Ruminococcus are the most abundant genera of bacteria in goat rumen. SPAdes assembly and prodigal annotation were performed. The contigs were also annotated using the DOE-JGI pipeline. In total, 117,502 CAZymes, comprising endoglucanases, exoglucanases, beta-glucosidases, xylosidases, and xylanases, were detected in all three samples. Two genes with predicted cellulolytic/xylanolytic activities were cloned and expressed in E. coli BL21(DE3). The endoglucanases and xylanase enzymatic activities of the recombinant proteins were confirmed using substrate plate assay and dinitrosalicylic acid (DNS) analysis. The 3D structures of endoglucanase A and endo-1,4-beta xylanase was predicted using the Swiss Model. Based on the 3D structure analysis, the two enzymes isolated from goat's rumen metagenome are unique with only 56-59% similarities to those homologous proteins in protein data bank (PDB) meanwhile, the structures of the enzymes also displayed greater stability, and higher catalytic activity.

CONCLUSIONS: In summary, this study provided the database resources of bacterial metagenomes from goat's rumen fluid, including gene sequences with annotated functions and methods for gene isolation and over-expression of cellulolytic enzymes; and a wealth of genes in the metabolic pathways affecting food and nutrition of ruminant animals.}, } @article {pmid38049453, year = {2023}, author = {Minor, NR and Ramuta, MD and Stauss, MR and Harwood, OE and Brakefield, SF and Alberts, A and Vuyk, WC and Bobholz, MJ and Rosinski, JR and Wolf, S and Lund, M and Mussa, M and Beversdorf, LJ and Aliota, MT and O'Connor, SL and O'Connor, DH}, title = {Metagenomic sequencing detects human respiratory and enteric viruses in air samples collected from congregate settings.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {21398}, pmid = {38049453}, issn = {2045-2322}, support = {T32 AI055397/AI/NIAID NIH HHS/United States ; AAL4371/NH/NIH HHS/United States ; }, mesh = {Humans ; COVID-19 Testing ; Pandemics ; *COVID-19/epidemiology ; *RNA Viruses ; SARS-CoV-2/genetics ; *Enterovirus/genetics ; *Influenza A virus ; *Enterovirus Infections ; *Influenza, Human ; }, abstract = {Innovative methods for evaluating virus risk and spread, independent of test-seeking behavior, are needed to improve routine public health surveillance, outbreak response, and pandemic preparedness. Throughout the COVID-19 pandemic, environmental surveillance strategies, including wastewater andair sampling, have been used alongside widespread individual-based SARS-CoV-2 testing programs to provide population-level data. These environmental surveillance strategies have predominantly relied on pathogen-specific detection methods to monitor viruses through space and time. However, this provides a limited picture of the virome present in an environmental sample, leaving us blind to most circulating viruses. In this study, we explore whether pathogen-agnostic deep sequencing can expand the utility of air sampling to detect many human viruses. We show that sequence-independent single-primer amplification sequencing of nucleic acids from air samples can detect common and unexpected human respiratory and enteric viruses, including influenza virus type A and C, respiratory syncytial virus, human coronaviruses, rhinovirus, SARS-CoV-2, rotavirus, mamastrovirus, and astrovirus.}, } @article {pmid38049420, year = {2023}, author = {Yersin, S and Garneau, JR and Schneeberger, PHH and Osman, KA and Cercamondi, CI and Muhummed, AM and Tschopp, R and Zinsstag, J and Vonaesch, P}, title = {Gut microbiomes of agropastoral children from the Adadle region of Ethiopia reflect their unique dietary habits.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {21342}, pmid = {38049420}, issn = {2045-2322}, support = {180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; P3P3PA_177877//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 180575//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 7F-0057.01.02//Direktion für Entwicklung und Zusammenarbeit/ ; 7F-0057.01.02//Direktion für Entwicklung und Zusammenarbeit/ ; 7F-0057.01.02//Direktion für Entwicklung und Zusammenarbeit/ ; 7F-0057.01.02//Direktion für Entwicklung und Zusammenarbeit/ ; 7F-0057.01.02//Direktion für Entwicklung und Zusammenarbeit/ ; 2019-20//Nutricia Research Foundation/ ; 2019-20//Nutricia Research Foundation/ ; 2019-20//Nutricia Research Foundation/ ; 2020//Forschungsfonds der Universität Basel/ ; 2020//Forschungsfonds der Universität Basel/ ; 2020//Forschungsfonds der Universität Basel/ ; }, mesh = {Humans ; Child ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Ethiopia ; Bacteria/genetics ; Feces/microbiology ; Feeding Behavior ; }, abstract = {The composition and function of the intestinal microbiota are major determinants of human health and are strongly influenced by diet, antibiotic treatment, lifestyle and geography. Nevertheless, we currently have only little data on microbiomes of non-westernized communities. We assess the stool microbiota composition in 59 children aged 2-5 years from the Adadle district of Ethiopia, Somali Regional State. Here, milk and starch-rich food are predominant components of the local diet, where the inhabitants live a remote, traditional agropastoral lifestyle. Microbiota composition, function and the resistome were characterized by both 16S rRNA gene amplicon and shotgun metagenomic sequencing and compared to 1471 publicly available datasets from children living in traditional, transitional, and industrial communities with different subsistence strategies. Samples from the Adadle district are low in Bacteroidaceae, and Prevotellaceae, the main bacterial representatives in the feces of children living in industrialized and non-industrialized communities, respectively. In contrast, they had a higher relative abundance in Streptococcaceae, Bifidobacteriaceae and Erysipelatoclostridiaceae. Further, genes involved in degradation pathways of lactose, D-galactose and simple carbohydrates were enriched. Overall, our study revealed a unique composition of the fecal microbiota of these agropastoral children, highlighting the need to further characterize the fecal bacterial composition of human populations living different lifestyles.}, } @article {pmid38049144, year = {2023}, author = {Hamilton, TA and Joris, BR and Shrestha, A and Browne, TS and Rodrigue, S and Karas, BJ and Gloor, GB and Edgell, DR}, title = {De Novo Synthesis of a Conjugative System from Human Gut Metagenomic Data for Targeted Delivery of Cas9 Antimicrobials.}, journal = {ACS synthetic biology}, volume = {12}, number = {12}, pages = {3578-3590}, pmid = {38049144}, issn = {2161-5063}, mesh = {Humans ; *Escherichia coli/genetics ; CRISPR-Cas Systems/genetics ; RNA, Guide, CRISPR-Cas Systems ; Conjugation, Genetic/genetics ; Plasmids/genetics ; *Anti-Infective Agents ; }, abstract = {Metagenomic sequences represent an untapped source of genetic novelty, particularly for conjugative systems that could be used for plasmid-based delivery of Cas9-derived antimicrobial agents. However, unlocking the functional potential of conjugative systems purely from metagenomic sequences requires the identification of suitable candidate systems as starting scaffolds for de novo DNA synthesis. Here, we developed a bioinformatics approach that searches through the metagenomic "trash bin" for genes associated with conjugative systems present on contigs that are typically excluded from common metagenomic analysis pipelines. Using a human metagenomic gut data set representing 2805 taxonomically distinct units, we identified 1598 contigs containing conjugation genes with a differential distribution in human cohorts. We synthesized de novo an entire Citrobacter spp. conjugative system of 54 kb containing at least 47 genes and assembled it into a plasmid, pCitro. We found that pCitro conjugates from Escherichia coli to Citrobacter rodentium with a 30-fold higher frequency than to E. coli, and is compatible with Citrobacter resident plasmids. Mutations in the traV and traY conjugation components of pCitro inhibited conjugation. We showed that pCitro can be repurposed as an antimicrobial delivery agent by programming it with the TevCas9 nuclease and Citrobacter-specific sgRNAs to kill C. rodentium. Our study reveals a trove of uncharacterized conjugative systems in metagenomic data and describes an experimental framework to animate these large genetic systems as novel target-adapted delivery vectors for Cas9-based editing of bacterial genomes.}, } @article {pmid38048871, year = {2023}, author = {Lan, W and Liu, H and Weng, R and Zeng, Y and Lou, J and Xu, H and Yu, Y and Jiang, Y}, title = {Microbial community of municipal drinking water in Hangzhou using metagenomic sequencing.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {342}, number = {}, pages = {123066}, doi = {10.1016/j.envpol.2023.123066}, pmid = {38048871}, issn = {1873-6424}, abstract = {While traditional culture-dependent methods can effectively detect certain microorganisms, the comprehensive composition of the municipal drinking water (DW) microbiome, including bacteria, archaea, and viruses, remains unknown. Metagenomic sequencing has opened the door to accurately determine and analyze the entire microbial community of DW, providing a comprehensive understanding of DW species diversity, especially in the context of public health concerns during the COVID-19 era. In this study, we found that most of the culturable bacteria and some fecal indicator bacteria, such as Escherichia coli and Pseudomonas aeruginosa, were non-culturable using culture-dependent methods in all samples. However, metagenomic analysis showed that the predominant bacterial species in the DW samples belonged to the phyla Proteobacteria and Planctomycetes. Notably, the genus Methylobacterium was the most abundant in all water samples, followed by Sphingomonas, Gemmata, and Azospirilum. While low levels of virulence-associated factors, such as the Esx-5 type VII secretion system (T7SS) and DevR/S, were detected, only the erythromycin resistance gene erm(X), an rRNA methyltransferase, was identified at low abundance in one sample. Hosts corresponding to virulence and resistance genes were identified in some samples, including Mycobacterium spp. Archaeal DNA (Euryarchaeota, Crenarchaeota) was found in trace amounts in some DW samples. Viruses such as rotavirus, coxsackievirus, human enterovirus, and SARS-CoV-2 were negative in all DW samples using colloidal gold and real-time reverse transcription polymerase chain reaction (RT‒PCR) methods. However, DNA encoding a new order of reverse-transcribing viruses (Ortervirales) and Herpesvirales was found in some DW samples. The metabolic pathways of the entire microbial community involve cell‒cell communication and signal secretion, contributing to cooperation between different microbial populations in the water. This study provides insight into the microbial community and metabolic process of DW in Hangzhou, China, utilizing both culture-dependent methods and metagenomic sequencing combined with bioinformatics tools during the COVID-19 pandemic era.}, } @article {pmid38048804, year = {2023}, author = {Fourgeaud, J and Regnault, B and Ok, V and Da Rocha, N and Sitterlé, É and Mekouar, M and Faury, H and Milliancourt-Seels, C and Jagorel, F and Chrétien, D and Bigot, T and Troadec, É and Marques, I and Serris, A and Seilhean, D and Neven, B and Frange, P and Ferroni, A and Lecuit, M and Nassif, X and Lortholary, O and Leruez-Ville, M and Pérot, P and Eloit, M and Jamet, A}, title = {Performance of clinical metagenomics in France: a prospective observational study.}, journal = {The Lancet. Microbe}, volume = {}, number = {}, pages = {}, doi = {10.1016/S2666-5247(23)00244-6}, pmid = {38048804}, issn = {2666-5247}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) allows untargeted identification of a broad range of pathogens, including rare or novel microorganisms. Despite the recognition of mNGS as a valuable diagnostic tool for infections, the most relevant indications for this innovative strategy remain poorly defined. We aimed to assess the determinants of positivity and clinical utility of mNGS.

METHODS: In this observational study, we prospectively performed short-read shotgun metagenomics analysis as a second-line test (in cases of negative first-line test or when the symptoms were not fully explained by initial positive results) or as a first-line test in life-threatening situations requiring urgent non-targeted pathogen identification at the Necker-Enfants Malades Hospital (Paris, France). All sample types, clinical indications, and patient populations were included. Samples were accompanied by a mandatory form completed by the senior clinician or pathologist, on which the clinical level of suspected infection (defined as high or low) was indicated. We assessed the variables (gender, age, immune status, initial suspicion of infection, indication, and sample type) associated with mNGS pathogen detection using odds ratios (ORs) from multivariate logistic regression. Additional investigations were carried out using specific PCR or culture techniques, to confirm positive mNGS results, or when infectious suspicion was particularly high despite a negative mNGS result.

FINDINGS: Between Oct 29, 2019, and Nov 7, 2022, we analysed 742 samples collected from 523 patients. The initial suspicion of infection was either high (n=470, 63%) or low (n=272, 37%). Causative or possibly causative pathogens were detected in 117 (25%) samples from patients with high initial suspicion of infection, versus nine (3%) samples analysed to rule out infection (OR 9·1, 95% CI 4·6-20·4; p<0·0001). We showed that mNGS had higher odds of detecting a causative or possibly causative pathogenic virus on CNS biopsies than CSF samples (4·1, 1·7-10·7; p=0·0025) and in samples from immunodeficient compared with immunocompetent individuals (2·4, 1·4-4·1; p=0·0013). Concordance with conventional confirmatory tests results was 103 (97%) of 106, when mNGS detected causative or possibly causative pathogens. Altogether, among 231 samples investigated by both mNGS and subsequent specific tests, discordant results were found in 69 (30%) samples, of which 58 (84%) were mNGS positive and specific tests negative, and 11 (16%) mNGS negative and specific tests positive.

INTERPRETATION: Major determinants of pathogen detection by mNGS are immune status and initial level of suspicion of infection. These findings will contribute, along with future studies, to refining the positioning of mNGS in diagnostic and treatment decision-making algorithms.

FUNDING: Necker-Enfants Malades Hospital and Institut Pasteur.

TRANSLATION: For the French translation of the abstract see Supplementary Materials section.}, } @article {pmid38048079, year = {2023}, author = {Fu, P and Wu, Y and Zhang, Z and Qiu, Y and Wang, Y and Peng, Y}, title = {VIGA: a one-stop tool for eukaryotic virus identification and genome assembly from next-generation-sequencing data.}, journal = {Briefings in bioinformatics}, volume = {25}, number = {1}, pages = {}, pmid = {38048079}, issn = {1477-4054}, support = {32370700//National Natural Science Foundation of China/ ; 2022YFC2303802//National Key Plan for Scientific Research and Development of China/ ; }, mesh = {Humans ; High-Throughput Nucleotide Sequencing ; *Colitis, Ulcerative ; *Crohn Disease ; Genome, Viral ; Metagenome ; }, abstract = {Identification of viruses and further assembly of viral genomes from the next-generation-sequencing data are essential steps in virome studies. This study presented a one-stop tool named VIGA (available at https://github.com/viralInformatics/VIGA) for eukaryotic virus identification and genome assembly from NGS data. It was composed of four modules, namely, identification, taxonomic annotation, assembly and novel virus discovery, which integrated several third-party tools such as BLAST, Trinity, MetaCompass and RagTag. Evaluation on multiple simulated and real virome datasets showed that VIGA assembled more complete virus genomes than its competitors on both the metatranscriptomic and metagenomic data and performed well in assembling virus genomes at the strain level. Finally, VIGA was used to investigate the virome in metatranscriptomic data from the Human Microbiome Project and revealed different composition and positive rate of viromes in diseases of prediabetes, Crohn's disease and ulcerative colitis. Overall, VIGA would help much in identification and characterization of viromes, especially the known viruses, in future studies.}, } @article {pmid38047696, year = {2024}, author = {Klukowski, N and Eden, P and Uddin, MJ and Sarker, S}, title = {Virome of Australia's most endangered parrot in captivity evidenced of harboring hitherto unknown viruses.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0305223}, pmid = {38047696}, issn = {2165-0497}, mesh = {Animals ; *Parrots ; Virome ; *Viruses ; *Virus Diseases/epidemiology/veterinary ; Australia/epidemiology ; }, abstract = {The impact of circulating viruses on the critically endangered, orange-bellied parrot (OBP) population can be devastating. The OBP already faces numerous threats to its survival in the wild, including habitat loss, predation, and small population impacts. Conservation of the wild OBP population is heavily reliant on supplementation using OBPs from a managed captive breeding program. These birds may act as a source for introduction of a novel disease agent to the wild population that may affect survival and reproduction. It is, therefore, essential to monitor and assess the health of OBPs and take appropriate measures to prevent and control the spread of viral infections. This requires knowledge of the existing virome to identify novel and emerging viruses and support development of appropriate measures to manage associated risk. By monitoring and protecting these animals from emerging viral diseases, we can help ensure their ongoing survival and preserve the biodiversity of our planet.}, } @article {pmid38047654, year = {2023}, author = {Kwasiborski, A and Hourdel, V and Balière, C and Hoinard, D and Grassin, Q and Feher, M and De La Porte Des Vaux, C and Cresta, M and Vanhomwegen, J and Manuguerra, J-C and Batéjat, C and Caro, V}, title = {Direct metagenomic and amplicon-based Nanopore sequencing of French human monkeypox from clinical specimen.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0081123}, doi = {10.1128/MRA.00811-23}, pmid = {38047654}, issn = {2576-098X}, abstract = {We report the whole-genome sequence of monkeypox virus obtained using MinION technology (Oxford Nanopore Technologies) from a French clinical specimen during the 2022 epidemic. Amplicon-based sequencing and shotgun metagenomic approaches were directly applied to the sample.}, } @article {pmid38047395, year = {2023}, author = {Kane, Y and Tendu, A and Li, R and Chen, Y and Mastriani, E and Lan, J and Hughes, AC and Berthet, N and Wong, G}, title = {Viral diversity in wild and urban rodents of Yunnan Province, China.}, journal = {Emerging microbes & infections}, volume = {}, number = {}, pages = {2290842}, doi = {10.1080/22221751.2023.2290842}, pmid = {38047395}, issn = {2222-1751}, abstract = {Rodents represent over 40% of known mammal species and are found in various terrestrial habitats. They are significant reservoirs for zoonotic viruses, including harmful pathogens such as arenaviruses and hantaviruses, yet knowledge of their hosts and distributions is limited. Therefore, characterizing the virome profile in these animals is invaluable for outbreak preparedness, especially in potential hotspots of mammal diversity. This study included 681 organs from 124 rodents and one Chinese tree shrew collected from Yunnan Province, China, during 2020-2021. Metagenomic analysis revealed unique features of mammalian viruses in rodent organs across habitats with varying human disturbances. R. tanezumi in locations with high anthropogenic disturbance exhibited the highest mammal viral diversity, with spleen and lung samples showing the highest diversities for these viruses at the organ level. Mammal viral diversity for both commensal and non-commensal rats was identified to positively correlate with landscape disturbance. Some virus families were associated with particular organs or host species, suggesting tropism for these pathogens. Notably, known and novel viral species that are likely to infect humans were identified. R. tanezumi was identified as a reservoir and carrier for various zoonotic viruses, including porcine bocavirus, hantavirus, cardiovirus, and lyssavirus. These findings highlight the influence of rodent community composition and anthropogenic activities on diverse virome profiles, with R. tanezumi as an important reservoir for zoonotic viruses.}, } @article {pmid38047280, year = {2023}, author = {Ladeira, R and Tap, J and Derrien, M}, title = {Exploring Bifidobacterium species community and functional variations with human gut microbiome structure and health beyond infancy.}, journal = {Microbiome research reports}, volume = {2}, number = {2}, pages = {9}, pmid = {38047280}, issn = {2771-5965}, abstract = {Aim: The human gut Bifidobacterium community has been studied in detail in infants and following dietary interventions in adults. However, the variability of the distribution of Bifidobacterium species and intra-species functions have been little studied, particularly beyond infancy. Here, we explore the ecology of Bifidobacterium communities in a large public dataset of human gut metagenomes, mostly corresponding to adults. Methods: We selected 9.515 unique gut metagenomes from curatedMetagenomicData. Samples were partitioned by applying Dirichlet's multinomial mixture to Bifidobacterium species. A functional analysis was performed on > 2.000 human-associated Bifidobacterium metagenome-assembled genomes (MAGs) paired with participant gut microbiome and health features. Results: We identified several Bifidobacterium-based partitions in the human gut microbiome differing in terms of the presence and abundance of Bifidobacterium species. The partitions enriched in both B. longum and B. adolescentis were associated with gut microbiome diversity and a higher abundance of butyrate producers and were more prevalent in healthy individuals. B. bifidum MAGs harboring a set of genes potentially related to phages were more prevalent in partitions associated with a lower gut microbiome diversity and were genetically more closely related. Conclusion: This study expands our knowledge of the ecology and variability of the Bifidobacterium community, particularly in adults, and its specific association with the gut microbiota and health. Its findings may guide the rational selection of Bifidobacterium strains for gut microbiome complementation according to the individual's endogenous Bifidobacterium community. Our results also suggest that gut microbiome stratification for particular genera may be relevant for studies of variations of species and associations with the gut microbiome and health.}, } @article {pmid38047279, year = {2023}, author = {Candeliere, F and Musmeci, E and Amaretti, A and Sola, L and Raimondi, S and Rossi, M}, title = {Profiling of the intestinal community of Clostridia: taxonomy and evolutionary analysis.}, journal = {Microbiome research reports}, volume = {2}, number = {2}, pages = {13}, pmid = {38047279}, issn = {2771-5965}, abstract = {Aim: Clostridia are relevant commensals of the human gut due to their major presence and correlations to the host. In this study, we investigated intestinal Clostridia of 51 healthy subjects and reconstructed their taxonomy and phylogeny. The relatively small number of intestinal Clostridia allowed a systematic whole genome approach based on average amino acid identity (AAI) and core genome with the aim of revising the current classification into genera and determining evolutionary relationships. Methods: 51 healthy subjects' metagenomes were retrieved from public databases. After the dataset's validation through comparison with Human Microbiome Project (HMP) samples, the metagenomes were profiled using MetaPhlAn3 to identify the population ascribed to the class Clostridia. Intestinal Clostridia genomes were retrieved and subjected to AAI analysis and core genome identification. Phylogeny investigation was conducted with RAxML and Unweighted Pair Group Method with Arithmetic Mean (UPGMA) algorithms, and SplitsTree for split decomposition. Results: 225 out of 406 bacterial taxonomic units were ascribed to Bacillota [Firmicutes], among which 124 were assigned to the class Clostridia. 77 out of the 124 taxonomic units were referred to a species, altogether covering 87.7% of Clostridia abundance. According to the lowest AAI genus boundary set at 55%, 15 putative genera encompassing more than one species (G1 to G15) were identified, while 19 species did not cluster with any other one and each appeared to belong to a diverse genus. Phylogenetic investigations highlighted that most of the species clustered into three main evolutive clades. Conclusion: This study shed light on the species of Clostridia colonizing the gut of healthy adults and pinpointed several gaps in knowledge regarding the taxonomy and the phylogeny of Clostridia.}, } @article {pmid38047037, year = {2023}, author = {Yadav, BNS and Sharma, P and Maurya, S and Yadav, RK}, title = {Metagenomics and metatranscriptomics as potential driving forces for the exploration of diversity and functions of micro-eukaryotes in soil.}, journal = {3 Biotech}, volume = {13}, number = {12}, pages = {423}, pmid = {38047037}, issn = {2190-572X}, abstract = {Micro-eukaryotes are ubiquitous and play vital roles in diverse ecological systems, yet their diversity and functions are scarcely known. This may be due to the limitations of formerly used conventional culture-based methods. Metagenomics and metatranscriptomics are enabling to unravel the genomic, metabolic, and phylogenetic diversity of micro-eukaryotes inhabiting in different ecosystems in a more comprehensive manner. The in-depth study of structural and functional characteristics of micro-eukaryote community residing in soil is crucial for the complete understanding of this major ecosystem. This review provides a deep insight into the methodologies employed under these approaches to study soil micro-eukaryotic organisms. Furthermore, the review describes available computational tools, pipelines, and database sources and their manipulation for the analysis of sequence data of micro-eukaryotic origin. The challenges and limitations of these approaches are also discussed in detail. In addition, this review summarizes the key findings of metagenomic and metatranscriptomic studies on soil micro-eukaryotes. It also highlights the exploitation of these methods to study the structural as well as functional profiles of soil micro-eukaryotic community and to screen functional eukaryotic protein coding genes for biotechnological applications along with the future perspectives in the field.}, } @article {pmid38047031, year = {2023}, author = {Zhang, NN and Chen, XX and Liang, J and Zhao, C and Xiang, J and Luo, L and Wang, ET and Shi, F}, title = {Rhizocompartmental microbiomes of arrow bamboo (Fargesia nitida) and their relation to soil properties in Subalpine Coniferous Forests.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16488}, pmid = {38047031}, issn = {2167-8359}, mesh = {*Tracheophyta ; Soil ; beta-Fructofuranosidase ; Soil Microbiology ; *Microbiota/genetics ; Forests ; Bacteria/genetics ; Poaceae ; Plants ; Carbon ; Cellulose ; }, abstract = {Arrow bamboo (Fargesia nitida) is a pioneer plant in secondary forest succession in the Sichuan Province mountains. To comprehensively investigate the microbial communities and their functional variations in different rhizocompartments (root endosphere, rhizosphere, and root zone) of arrow bamboo (Fargesia nitida), a high-throughput metagenomic study was conducted in the present study. The results showed that the abundances of the dominant bacterial phyla Proteobacteria and Actinobacteria in the bamboo root endosphere were significantly lower than those in the rhizosphere and root zones. In contrast, the dominant fungal phyla, Ascomycota and Basidiomycota, showed the opposite tendency. Lower microbial diversity, different taxonomic composition and functional profiles, and a greater abundance of genes involved in nitrogen fixation (nifB), cellulose degradation (beta-glucosidase), and cellobiose transport (cellulose 1, 4-beta-cellobiosidase) were found in the bamboo root endosphere than in the other rhizocompartments. Greater soil total carbon, total nitrogen, NH4[+]-N, microbial biomass carbon, and greater activities of invertase and urease were found in the bamboo root zone than in the adjacent soil (spruce root zone). In contrast, the soil microbial community and functional profiles were similar. At the phylum level, invertase was significantly related to 31 microbial taxa, and the effect of NH4[+]-N on the microbial community composition was greater than that of NO3[-]-N. The soil physicochemical properties and enzyme activities were significantly correlated with microbial function. These results indicate that the root endosphere microbiomes of arrow bamboo were strongly selected by the host plant, which caused changes in the soil nutrient properties in the subalpine coniferous forest.}, } @article {pmid38046821, year = {2023}, author = {Mancabelli, L and Milani, C and Fontana, F and Liotto, N and Tabasso, C and Perrone, M and Lugli, GA and Tarracchini, C and Alessandri, G and Viappiani, A and Bernasconi, S and Roggero, P and Mosca, F and Turroni, F and Ventura, M}, title = {A pilot study to disentangle the infant gut microbiota composition and identification of bacteria correlates with high fat mass.}, journal = {Microbiome research reports}, volume = {2}, number = {3}, pages = {23}, pmid = {38046821}, issn = {2771-5965}, abstract = {Background: At birth, the human intestine is colonized by a complex community of microorganisms known as gut microbiota. These complex microbial communities that inhabit the gut microbiota are thought to play a key role in maintaining host physiological homeostasis. For this reason, correct colonization of the gastrointestinal tract in the early stages of life could be fundamental for human health. Furthermore, alterations of the infant microbiota are correlated with the development of human inflammatory diseases and disorders. In this context, the possible relationships between intestinal microbiota and body composition during infancy are of great interest. Methods: In this study, we have performed a pilot study based on 16S rRNA gene profiling and metagenomic approaches on repeatedly measured data on time involving a cohort of 41 Italian newborns, which is aimed to investigate the possible correlation between body fat mass percentage (FM%) and the infant gut microbiota composition. Results and conclusion: The taxonomical analysis of the stool microbiota of each infant included in the cohort allowed the identification of a specific correlation between intestinal bacteria, such as Bifidobacterium and Veillonella, and the increase in FM%. Moreover, the analysis of the infant microbiome's metabolic capabilities suggested that the intestinal microbiome functionally impacts the human host and its possible influence on host physiology.}, } @article {pmid38046639, year = {2023}, author = {Huang, J and Wang, Z and Chen, Z and Liang, H and Li, X and Li, B}, title = {Occurrence and Removal of Antibiotic Resistance in Nationwide Hospital Wastewater Deciphered by Metagenomics Approach - China, 2018-2022.}, journal = {China CDC weekly}, volume = {5}, number = {46}, pages = {1023-1028}, pmid = {38046639}, issn = {2096-7071}, abstract = {Hospital wastewater represents a significant conduit for the dissemination of antibiotic resistance genes (ARGs), including those that are of clinical importance. Yet, the variation in antibiotic resistance on a national level, which can be influenced by regional differences, has not been thoroughly elucidated.

WHAT IS ADDED BY THIS REPORT?: Uniform methodologies were employed to analyze data from various provincial-level administrative divisions in China, aiming to investigate the patterns of antibiotic resistance across these regions. This analysis illuminated the location preferences of clinically ARGs on plasmids. Additionally, our study uncovered regional variations in the presumed bacterial hosts of ARGs at the genus level.

This investigation has shed light on the nationwide prevalence of ARGs in hospital wastewater in China, uncovering the significant ecological and public health risks associated with the disposal of such effluents.}, } @article {pmid38046600, year = {2023}, author = {Tang, L and Zhan, L and Han, Y and Wang, Z and Dong, L and Zhang, Z}, title = {Microbial community assembly and functional profiles along the soil-root continuum of salt-tolerant Suaeda glauca and Suaeda salsa.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1301117}, pmid = {38046600}, issn = {1664-462X}, abstract = {Developing and planting salt-tolerant plants has become a promising way to utilize saline-alkali land resources and ensure food security. Root-associated microbes of salt-tolerant plants have been shown to promote plant growth and alleviate high salt stress, yet very little is known about the salt resistance mechanisms of core microbes in different niches. This study characterized the microbial community structures, assembly processes, and functional profiles in four root-related compartments of two salt-tolerant plants by amplicon and shotgun metagenomic sequencing. The results showed that both plants significantly altered the microbial community structure of saline soils, with greater microbial alpha diversity in the rhizosphere or rhizoplane compared with bulk soils. Stochastic process dominated the microbial assembly processes, and the impact was stronger in Suaeda salsa than in S. glauca, indicating that S. salsa may have stronger resistance abilities to changing soil properties. Keystone species, such as Pseudomonas in the endosphere of S. glauca and Sphingomonas in the endosphere of S. salsa, which may play key roles in helping plants alleviate salt stress, were identified by using microbial co-occurrence network analysis. Furthermore, the microbiomes in the rhizoplane soils had more abundant genes involved in promoting growth of plants and defending against salt stress than those in bulk soils, especially in salt-tolerant S. salsa. Moreover, microbes in the rhizoplane of S. salsa exhibited higher functional diversities, with notable enrichment of genes involved in carbon fixation, dissimilar nitrate reduction to ammonium, and sulfite oxidation. These findings revealed differences and similarities in the microbial community assembly, functional profiles and keystone species closely related to salt alleviation of the two salt-tolerant plants. Overall, our study provides new insights into the ecological functions and varied strategies of rhizosphere microbes in different plants under salt stress and highlights the potential use of keystone microbes for enhancing salt resistance of plants.}, } @article {pmid38046412, year = {2023}, author = {Xu, S and Lu, S and Gu, Y and Sun, H and Ma, M and Leng, Y and Liu, W}, title = {Metagenomic next-generation sequencing to investigate infectious keratitis by Corynespora cassiicola: a case report.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1285753}, pmid = {38046412}, issn = {2296-858X}, abstract = {In this report, the case of a 65-year-old immunosuppressed female who presented with recurring redness and irritation in her right eye for 2 months is described. Ocular examination revealed conjunctival congestion, feather-like greyish-white corneal deep stromal infiltrate, white, floccular material sprawling from the anterior chamber angle and hypopyon. The in vivo confocal microscopy (IVCM) instantly confirmed fungal keratitis, and empirical antifungal therapy was thus administered. The patient exhibited therapeutic penetrating keratoplasty, however, due to the progression of infection and the lack of identified pathogens. The fungal isolate was identified as Corynespora cassiicola by metagenomic next-generation sequencing (mNGS) of the host cornea. The patient responded well to intensive conservative therapy and subsequent surgical therapy. To our knowledge, this case represents the first case of C. cassiicola infection from China, highlighting the emergence of a rare fungus that causes keratitis. Furthermore, mNGS has the capability to facilitate prompt identification and timely management of challenging ocular infections that are difficult to diagnose.}, } @article {pmid38046237, year = {2023}, author = {Tian, C and Yan, H and Tang, P and Shi, J and Liang, M and Wan, Y and Li, W and Sun, X and Qin, C}, title = {Pelvic infection caused by periodontitis: A case report.}, journal = {Case reports in women's health}, volume = {40}, number = {}, pages = {e00563}, pmid = {38046237}, issn = {2214-9112}, abstract = {Oral bacteria in patients with periodontitis can disseminate into the bloodstream via broken oral epithelial cells, causing odontogenic maxillofacial infections, brain abscesses and endocarditis. However, pelvic infection caused by periodontitis is rare. The case of a 48-year-old woman with a long history of recurrent periodontal infections, who complained of abdominal distention and pain for 14 days after dental implantation, is reported here. Pelvic ultrasound and magnetic resonance imaging signaled multiple inflammatory encapsulated effusions in the posterior uterus, which were removed by laparoscopic surgery and tested with metagenomic next-generation sequencing (mNGS). Through mNGS, numerous oral pathogens, including Filifactor alocis, were identified in the pelvic effusions. The patient was subsequently diagnosed with a pelvic infection originating from periodontitis, and recovered after undergoing surgery and targeted antibacterial treatment. Thus, the possibility of extrabuccal complications in patients with a history of periodontitis or invasive oral procedures merits closer attention.}, } @article {pmid38046047, year = {2023}, author = {Jiang, X and Yan, J and Huang, H and Ai, L and Yu, X and Zhong, P and Chen, Y and Liang, Z and Qiu, W and Huang, H and Yan, W and Liang, Y and Chen, P and Wang, R}, title = {Development of novel parameters for pathogen identification in clinical metagenomic next-generation sequencing.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1266990}, pmid = {38046047}, issn = {1664-8021}, abstract = {Introduction: Metagenomic next-generation sequencing (mNGS) has emerged as a powerful tool for rapid pathogen identification in clinical practice. However, the parameters used to interpret mNGS data, such as read count, genus rank, and coverage, lack explicit performance evaluation. In this study, the developed indicators as well as novel parameters were assessed for their performance in bacterium detection. Methods: We developed several relevant parameters, including 10M normalized reads, double-discard reads, Genus Rank Ratio, King Genus Rank Ratio, Genus Rank Ratio*Genus Rank, and King Genus Rank Ratio*Genus Rank. These parameters, together with frequently used read indicators including raw reads, reads per million mapped reads (RPM), transcript per kilobase per million mapped reads (TPM), Genus Rank, and coverage were analyzed for their diagnostic efficiency in bronchoalveolar lavage fluid (BALF), a common source for detecting eight bacterium pathogens: Acinetobacter baumannii, Klebsiella pneumoniae, Streptococcus pneumoniae, Staphylococcus aureus, Hemophilus influenzae, Stenotrophomonas maltophilia, Pseudomonas aeruginosa, and Aspergillus fumigatus. Results: The results demonstrated that these indicators exhibited good diagnostic efficacy for the eight pathogens. The AUC values of all indicators were almost greater than 0.9, and the corresponding sensitivity and specificity values were almost greater than 0.8, excepted coverage. The negative predictive value of all indicators was greater than 0.9. The results showed that the use of double-discarded reads, Genus Rank Ratio*Genus Rank, and King Genus Rank Ratio*Genus Rank exhibited better diagnostic efficiency than that of raw reads, RPM, TPM, and in Genus Rank. These parameters can serve as a reference for interpreting mNGS data of BALF. Moreover, precision filters integrating our novel parameters were built to detect the eight bacterium pathogens in BALF samples through machine learning. Summary: In this study, we developed a set of novel parameters for pathogen identification in clinical mNGS based on reads and ranking. These parameters were found to be more effective in diagnosing pathogens than traditional approaches. The findings provide valuable insights for improving the interpretation of mNGS reports in clinical settings, specifically in BALF analysis.}, } @article {pmid38045609, year = {2023}, author = {Sabater, C and Iglesias-Gutiérrez, E and Ruiz, L and Margolles, A}, title = {Next-generation sequencing of the athletic gut microbiota: a systematic review.}, journal = {Microbiome research reports}, volume = {2}, number = {1}, pages = {5}, pmid = {38045609}, issn = {2771-5965}, abstract = {Aim: There is growing evidence that physical activity modulates gut microbiota composition through complex interactions between diet and microbial species. On the other hand, next-generation sequencing techniques include shotgun metagenomics and 16S amplicon sequencing. These methodologies allow a comprehensive characterisation of microbial communities of athletes from different disciplines as well as non-professional players and sedentary adults exposed to training. This systematic review summarises recent applications of next-generation sequencing to characterise the athletic gut microbiome. Methods: A systematic review of microbiome research was performed to determine the association of microbiota composition profiles with sports performance. Results: Bibliographic analysis revealed the importance of a novel research trend aiming at deciphering the associations between individual microbial species and sports performance. In addition, literature review highlighted the role of butyrate-producing bacteria such as Anaerostipes hadrus, Clostridium bolteae, Faecalibacterium prausnitzii, Roseburia hominis and unidentified species belonging to Clostridiales, Lachnospiraceae and Subdoligranulum species in gut health and sports performance across several disciplines. Interestingly, metabolic activities of Prevotella copri and Veillonella atypica involved in branched amino acid and lactate metabolism may contribute to reducing muscular fatigue. Other microbial metabolic pathways of interest involved in carbohydrate metabolism showed increased proportions in athletes´ metagenomes. Conclusion: Future research will aim at developing personalised nutrition interventions to modulate key species associated with certain components of exercise.}, } @article {pmid38045399, year = {2023}, author = {Olm, MR and Spencer, SP and Silva, EL and Sonnenburg, JL}, title = {Metagenomic Immunoglobulin Sequencing (MIG-Seq) Exposes Patterns of IgA Antibody Binding in the Healthy Human Gut Microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38045399}, support = {DP1 AT009892/AT/NCCIH NIH HHS/United States ; R01 DK085025/DK/NIDDK NIH HHS/United States ; T32 DK007056/DK/NIDDK NIH HHS/United States ; T32 AI007328/AI/NIAID NIH HHS/United States ; K08 DK134856/DK/NIDDK NIH HHS/United States ; S10 OD026929/OD/NIH HHS/United States ; S10 OD026831/OD/NIH HHS/United States ; F32 DK128865/DK/NIDDK NIH HHS/United States ; }, abstract = {IgA, the most highly produced human antibody, is continually secreted into the gut to shape the intestinal microbiota. Methodological limitations have critically hindered defining which microbial strains are targeted by IgA and why. Here, we develop a new technique, Metagenomic Immunoglobulin Sequencing (MIG-Seq), and use it to determine IgA coating levels for thousands of gut microbiome strains in healthy humans. We find that microbes associated with both health and disease have higher levels of coating, and that microbial genes are highly predictive of IgA binding levels, with mucus degradation genes especially correlated with high binding. We find a significant reduction in replication rates among microbes bound by IgA, and demonstrate that IgA binding is more correlated with host immune status than traditional microbial abundance measures. This study introduces a powerful technique for assessing strain-level IgA binding in human stool, paving the way for deeper understanding of IgA-based host microbe interactions.}, } @article {pmid38045253, year = {2023}, author = {Salamzade, R and Kalan, LR}, title = {skDER: microbial genome dereplication approaches for comparative and metagenomic applications.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38045253}, support = {R35 GM137828/GM/NIGMS NIH HHS/United States ; U19 AI142720/AI/NIAID NIH HHS/United States ; }, abstract = {skDER (https://github.com/raufs/skDER) combines recent advances to efficiently estimate average nucleotide identity (ANI) between thousands of microbial genomes by skani[1] with two low-memory methods for genomic dereplication. The first method implements a dynamic algorithm to determine a concise set of representative genomes. This approach is well-suited for selecting reference genomes to align metagenomic reads onto for tracking strain presence across related microbiome samples. This is because fewer representative genomes should alleviate the concern that reads belonging to the same strain get falsely partitioned across closely related genomes. The other method, which uses a greedy approach, is better suited for use in comparative genomics, where users might be overwhelmed with the high number of genomes available for certain taxa and aim to reduce redundancy and, therefore, computational requirements for downstream analytics. This method selects a larger number of representative genomes to comprehensively sample the pangenome space for the taxon of interest. To further aid usage for comparative genomics studies, skDER also features an option to automatically download genomes classified as a particular species or genus in the Genome Taxonomy Database[2-4] and we provide precomputed representative genomes for commonly studied bacterial taxa[5].}, } @article {pmid38045012, year = {2023}, author = {Medeot, DB and Nilson, A and Miazzo, RD and Grosso, V and Ferrari, W and Jofré, E and Soltermann, A and Peralta, MF}, title = {Stevia as a natural additive on gut health and cecal microbiota in broilers.}, journal = {Veterinary and animal science}, volume = {22}, number = {}, pages = {100322}, pmid = {38045012}, issn = {2451-943X}, abstract = {Stevia mash (SM), leaves of Stevia rebaudiana Bertoni plant, is an additive used in poultry that enhances growth and health. Objective: to determine the effect of 1 % SM on productive parameters, gut health, and the cecal microbiome in broilers between the first 15 and 21 days old. One hundred sixty male, 1-day-old broilers (48.5 ± 2.5 g) were divided into Control (C) without SM and Treated (T) with 1 % SM on diet, during 15/21 days. Each subgroup had eight broilers/five repetitions/treatment. At day 15 or 21, all broilers were dissected, Fabricius Bursa and Gut removed and processed for histomorphometry, followed by Villi Height/Crypt Deep (VH/CD) ratio. Conversion Index (CI) was determined. The V3-V4 region of 16S rRNA gene was amplified from DNA obtained from pooled cecal contents and sequenced on Illumina Miseq PE 2 × 250 platform. Sequence processing and taxonomic assignments were performed using the SHAMAN pipeline. Both T groups have better VH/CD Ratios than C groups (p ≤ 0.05). In guts, increased plasmatic and goblet cells number and thicker mucus layer were found in T15 and T21. All groups received SM showed early immunological maturity in Fabricius Bursa. IC was similar between all treatments. Faecalibacterium, Ruminococcus torques group, and Bacteroides were the major genera modulated by SM addition. At 15 and 21 days old, SM exerts a impact on diversity and evenness of the cecal microbiome. Conclusion: SM (1 %) produced early immunologic maturity on Fabricius Bursa, increased intestinal functionality, and modified the microbiota, increasing beneficial microbial genera and microbial diversity.}, } @article {pmid38044053, year = {2023}, author = {Wei, W and Cheng, LL and Jiang, Y}, title = {[A case of disseminated nocardiosis in a non-immunosuppressed host].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {46}, number = {12}, pages = {1245-1248}, doi = {10.3760/cma.j.cn112147-20230919-00168}, pmid = {38044053}, issn = {1001-0939}, mesh = {Humans ; *Nocardia Infections/diagnosis ; *Nocardia/genetics ; Immunocompromised Host ; *Neoplasms ; }, abstract = {Nocardia is an opportunistic pathogen that most commonly affects immunosuppressed hosts, while disseminated infections in healthy hosts are rare. In this paper, we described a case of disseminated Nocardia infection in a non-immunosuppressed host whose initial imaging was strikingly similar to systemic metastasis from a tumor. Since no tumor cells were found in any of the numerous biopsies taken, we considered infection by specific pathogens before metagenomic next-generation sequencing of a lumbar spine tissue biopsy finally confirmed the diagnosis of Nocardia infection. To help doctors better understand this condition and avoid misdiagnosis a, this article provided a summary of the clinical characteristics, diagnostic techniques, and therapeutic options for disseminated nocardiosis.}, } @article {pmid38043895, year = {2023}, author = {Li, Y and Li, R and Hou, J and Sun, X and Wang, Y and Li, L and Yang, F and Yao, Y and An, Y}, title = {Mobile genetic elements affect the dissemination of antibiotic resistance genes (ARGs) of clinical importance in the environment.}, journal = {Environmental research}, volume = {243}, number = {}, pages = {117801}, doi = {10.1016/j.envres.2023.117801}, pmid = {38043895}, issn = {1096-0953}, abstract = {The prevalence of antibiotic resistance genes (ARGs) in the environment is a quintessential One Health issue that threats both human and ecosystem health; however, the source and transmission of ARGs, especially clinically important ARGs (CLIARGs), in the environment have not yet been well studied. In the present study, shotgun metagenomic approaches were used to characterize the microbiome, resistome, and mobilome composition in human feces and six different environment sample types in South China. Overall, the resistome harbored 157 CLIARGs, with specific ARG hotspots (e.g., human feces, wastewater treatment plants, livestock manure and wastewater) excreting significantly higher abundance of CLIARGs compared with the natural environment. A redundancy analysis (RDA) was performed and revealed that the bacterial community compositions and mobile genetic elements (MGEs) explained 55.08% and 34.68% of the variations in ARG abundance, respectively, indicating that both bacterial community and MGEs are key contributors to the maintenance and dissemination of CLIARGs in the environment. The network analysis revealed non-random co-occurrence patterns between 200 bacterial genera and 147 CLIARGs, as well as between 135 MGEs and 123 CLIARGs. In addition to numerous co-shared CLIARGs among different sample types, the source tracking program based on the FEAST probabilistic model was used to estimate the relative contributions of the CLIARGs from potential sources to the natural environment. The source tracking analysis results delineated that mobilome, more than microbiome, contributed CLIARG transmission from those ARG hotspots into natural environment, and the MGEs in WWTPs seem to play the most significant role in the spread of CLIARGs to the natural environment (average contribution 32.9%-46.4%). Overall, this study demonstrated the distribution and dissemination of CLIARGs in the environment, and aimed to better inform strategies to control the spread of CLIARGs into the natural environment.}, } @article {pmid38043822, year = {2023}, author = {Liu, Q and He, W and Zhang, W and Wang, L and Tang, J}, title = {Metagenomic analysis reveals the microbial response to petroleum contamination in oilfield soils.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {168972}, doi = {10.1016/j.scitotenv.2023.168972}, pmid = {38043822}, issn = {1879-1026}, abstract = {The response of the microbes to total petroleum hydrocarbons (TPHs) in three types of oilfield soils was researched using metagenomic analysis. The ranges of TPH concentrations in the grassland, abandoned well, working well soils were 1.16 × 10[2]-3.50 × 10[2] mg/kg, 1.14 × 10[3]-1.62 × 10[4] mg/kg, and 5.57 × 10[3]-3.33 × 10[4] mg/kg, respectively. The highest concentration of n-alkanes and 16 PAHs were found in the working well soil of Shengli (SL) oilfield compared with those in Nanyang (NY) and Yanchang (YC) oilfields. The abandoned well soils showed a greater extent of petroleum biodegradation than the grassland and working well soils. Α-diversity indexes based on metagenomic taxonomy showed higher microbial diversity in grassland soils, whereas petroleum-degrading microbes Actinobacteria and Proteobacteria were more abundant in working and abandoned well soils. RDA demonstrated that low moisture content (MOI) in YC oilfield inhibited the accumulation of the petroleum-degrading microbes. Synergistic networks of functional genes and Spearman's correlation analysis showed that heavy petroleum contamination (over 2.10 × 10[4] mg/kg) negatively correlated with the abundance of the nitrogen fixation genes nifHK, however, in grassland soils, low petroleum content facilitated the accumulation of nitrogen fixation genes. A positive correlation was observed between the abundance of petroleum-degrading genes and denitrification genes (bphAa vs. nirD, todC vs. nirS, and nahB vs. nosZ), whereas a negative correlation was observed between alkB (alkane- degrading genes) and amo (ammonia oxidation), hao (nitrification). The ecotoxicity of petroleum contamination, coupled with petroleum hydrocarbons (PH) degradation competing with nitrifiers for ammonia inhibited ammonia oxidation and nitrification, whereas PH metabolism promoted the denitrification process. Moreover, positive correlations were observed between the abundance of amo gene and MOI, as well as between the abundance of the dissimilatory nitrate reduction gene nirA and clay content. Thus, improving the soil physicochemical properties is a promising approach for decreasing nitrogen loss and alleviating petroleum contamination in oilfield soils.}, } @article {pmid38043772, year = {2023}, author = {Shahar, S and Sant, KE and Allsing, N and Kelley, ST}, title = {Metagenomic analysis of microbial communities and antibiotic resistant genes in the Tijuana river, and potential sources.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {342}, number = {}, pages = {123067}, doi = {10.1016/j.envpol.2023.123067}, pmid = {38043772}, issn = {1873-6424}, abstract = {The Tijuana River is a transborder river that flows northwest across the border from Baja California in Mexico into Southern California before discharging into the Pacific Ocean. The river is frequently contaminated with raw sewage due to inadequate sanitary infrastructure in Tijuana. To assess the type and degree of microbial contamination, water samples were collected monthly from a near-border and an estuarine site from August 2020 until May 2021. A portion of each sample was used for epifluorescent microscopy and DNA was extracted directly from the rest for shotgun metagenomic sequencing. After sequence quality checking and processing, we used the rapid taxonomic identifier tool Kaiju to characterize the microbial diversity of the metagenomes and matched the sequences against the Comprehensive Antibiotic Resistance Database (CARD) to examine antimicrobial resistance genes (ARGs). Bacterial and viral-like particle (VLP) abundance was consistently higher in the near-border samples than in the estuarine samples, while alpha diversity (within sample biodiversity) was higher in estuarine samples. Beta-diversity analysis found clear compositional separation between samples from the two sites, and the near-border samples were more dissimilar to one another than were the estuarine sites. Near-border samples were dominated by fecal-associated bacteria and bacteria associated with sewage sludge, while estuarine sites were dominated by marine bacteria. ARGs were more abundant at the near-border site, but were also readily detectable in the estuarine samples, and the most abundant ARGs had multi-resistance to beta-lactam antibiotics. SourceTracker analysis identified human feces and sewage sludge to be the largest contributors to the near-border samples, while marine waters dominated estuarine samples except for two sewage overflow dates with high fecal contamination. Overall, our research determined human sewage microbes to be common in the Tijuana River, and the prevalence of ARGs confirms the importance of planned infrastructure treatment upgrades for environmental health.}, } @article {pmid38043766, year = {2023}, author = {Sabatino, R and Sbaffi, T and Corno, G and Cabello-Yeves, PJ and Di Cesare, A}, title = {The diversity of the antimicrobial resistome of lake Tanganyika increases with the water depth.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {342}, number = {}, pages = {123065}, doi = {10.1016/j.envpol.2023.123065}, pmid = {38043766}, issn = {1873-6424}, abstract = {The presence of antimicrobial resistance genes (ARGs) in the microbiome of freshwater communities is a consequence of thousands of years of evolution but also of the pressure exerted by anthropogenic activities, with potential negative impact on environmental and human health. In this study, we investigated the distribution of ARGs in Lake Tanganyika (LT)'s water column to define the resistome of this ancient lake. Additionally, we compared the resistome of LT with that of Lake Baikal (LB), the oldest known lake with different environmental characteristics and a lower anthropogenic pollution than LT. We found that richness and abundance of several antimicrobial resistance classes were higher in the deep water layers in both lakes. LT Kigoma region, known for its higher anthropogenic pollution, showed a greater richness and number of ARG positive MAGs compared to Mahale. Our results provide a comprehensive understanding of the antimicrobial resistome of LT and underscore its importance as reservoir of antimicrobial resistance. In particular, the deepest water layers of LT are the main repository of diverse ARGs, mirroring what was observed in LB and in other aquatic ecosystems. These findings suggest that the deep waters might play a crucial role in the preservation of ARGs in aquatic ecosystems.}, } @article {pmid38043346, year = {2024}, author = {Jia, S and Wang, S and Zhuang, Y and Gao, L and Zhang, X and Ye, L and Zhang, XX and Shi, P}, title = {Free-living lifestyle preferences drive the antibiotic resistance promotion during drinking water chlorination.}, journal = {Water research}, volume = {249}, number = {}, pages = {120922}, doi = {10.1016/j.watres.2023.120922}, pmid = {38043346}, issn = {1879-2448}, mesh = {*Genes, Bacterial ; *Drinking Water/microbiology ; Halogenation ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The risk associated with antibiotic resistance genes (ARGs) in size-fractionated bacterial community during drinking water chlorination remains unclear, and is of paramount importance for risk mitigation through process selection and optimization. This study employed metagenomic approaches to reveal the alterations of ARGs, their potential functions and hosts within the free-living and particle-associated fractions. The total relative abundance of ARGs, mobile genetic elements (MGEs), and virulence factor genes (VFGs) significantly increased in the free-living fraction after chlorination. The contribution of the free-living fraction to the ARG relative abundance rose from 16.40 ± 1.31 % to 93.62 ± 0.47 % after chlorination. Multidrug resistance genes (e.g. mexF and mexW) were major contributors, and their co-occurrence with MGEs in the free-living fraction was enhanced after chlorination. Considering multiple perspectives, including presence, mobility, and pathogenicity, chlorination led to a significant risk of the antibiotic resistome in the free-living fraction. Moreover, potential functions of ARGs, such as cell wall/membrane/envelope biogenesis, defense mechanisms, and transcription in the free-living fraction, were intensified following chlorination. Potential pathogens, including Pseudomonas aeruginosa, Pseudomonas alcaligenes, and Acinetobacter junii, were identified as the predominant hosts of multidrug resistance genes, with their increased abundances primarily contributing to the rise of the corresponding ARGs. Overall, alterations of hosts as well as enhancing mobility and biological functions could collectively aid the proliferation and spread of ARGs in the free-living fraction after chlorination. This study provides novel insights into antibiotic resistance evolution in size-fractionated bacteria community and offers a management strategy for microbiological safety in drinking water.}, } @article {pmid38042930, year = {2023}, author = {Tagirdzhanova, G and Scharnagl, K and Yan, X and Talbot, NJ}, title = {Genomic analysis of Coccomyxa viridis, a common low-abundance alga associated with lichen symbioses.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {21285}, pmid = {38042930}, issn = {2045-2322}, support = {BBS/E/J/000PR9798/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Lichens/genetics/microbiology ; Symbiosis/genetics ; *Ascomycota/genetics ; *Chlorophyta/genetics ; Genomics ; Phylogeny ; }, abstract = {Lichen symbiosis is centered around a relationship between a fungus and a photosynthetic microbe, usually a green alga. In addition to their main photosynthetic partner (the photobiont), lichen symbioses can contain additional algae present in low abundance. The biology of these algae and the way they interact with the rest of lichen symbionts remains largely unknown. Here we present the first genome sequence of a non-photobiont lichen-associated alga. Coccomyxa viridis was unexpectedly found in 12% of publicly available lichen metagenomes. With few exceptions, members of the Coccomyxa viridis clade occur in lichens as non-photobionts, potentially growing in thalli endophytically. The 45.7 Mbp genome of C. viridis was assembled into 18 near chromosome-level contigs, making it one of the most contiguous genomic assemblies for any lichen-associated algae. Comparing the C. viridis genome to its close relatives revealed the presence of traits associated with the lichen lifestyle. The genome of C. viridis provides a new resource for exploring the evolution of the lichen symbiosis, and how symbiotic lifestyles shaped evolution in green algae.}, } @article {pmid38042820, year = {2023}, author = {Swarte, JC and Knobbe, TJ and Björk, JR and Gacesa, R and Nieuwenhuis, LM and Zhang, S and Vila, AV and Kremer, D and Douwes, RM and Post, A and Quint, EE and Pol, RA and Jansen, BH and , and de Borst, MH and de Meijer, VE and Blokzijl, H and Berger, SP and Festen, EAM and Zhernakova, A and Fu, J and Harmsen, HJM and Bakker, SJL and Weersma, RK}, title = {Health-related quality of life is linked to the gut microbiome in kidney transplant recipients.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7968}, pmid = {38042820}, issn = {2041-1723}, mesh = {Humans ; Quality of Life ; *Gastrointestinal Microbiome/genetics ; *Kidney Transplantation/adverse effects ; Feces/microbiology ; Dysbiosis/microbiology ; }, abstract = {Kidney transplant recipients (KTR) have impaired health-related quality of life (HRQoL) and suffer from intestinal dysbiosis. Increasing evidence shows that gut health and HRQoL are tightly related in the general population. Here, we investigate the association between the gut microbiome and HRQoL in KTR, using metagenomic sequencing data from fecal samples collected from 507 KTR. Multiple bacterial species are associated with lower HRQoL, many of which have previously been associated with adverse health conditions. Gut microbiome distance to the general population is highest among KTR with an impaired physical HRQoL (R = -0.20, P = 2.3 × 10[-65]) and mental HRQoL (R = -0.14, P = 1.3 × 10[-3]). Physical and mental HRQoL explain a significant part of variance in the gut microbiome (R[2] = 0.58%, FDR = 5.43 × 10[-4] and R[2] = 0.37%, FDR = 1.38 × 10[-3], respectively). Additionally, multiple metabolic and neuroactive pathways (gut brain modules) are associated with lower HRQoL. While the observational design of our study does not allow us to analyze causality, we provide a comprehensive overview of the associations between the gut microbiome and HRQoL while controlling for confounders.}, } @article {pmid38042069, year = {2024}, author = {Zhao, Y and Yu, S and Tan, J and Wang, Y and Li, L and Zhao, H and Liu, M and Jiang, L}, title = {Bioconversion of citrus waste by long-term DMSO-cryopreserved rumen fluid to volatile fatty acids and biogas is feasible: A microbiome perspective.}, journal = {Journal of environmental management}, volume = {351}, number = {}, pages = {119693}, doi = {10.1016/j.jenvman.2023.119693}, pmid = {38042069}, issn = {1095-8630}, mesh = {Animals ; Dimethyl Sulfoxide/metabolism ; Biofuels ; Food ; Rumen/metabolism ; *Refuse Disposal ; Fatty Acids, Volatile/metabolism ; Fermentation ; *Microbiota ; Methane ; Diet ; Fatty Acids/metabolism ; Animal Feed/analysis ; }, abstract = {Preserving rumen fluid as the inoculum for anaerobic digestion of food waste is necessary when access to animal donors or slaughterhouses is limited. This study aims to compare two preservation methods relative to fresh ruminal inoculum: (1) cryoprotected with 5% dimethyl sulfoxide (DMSO) and stored at -20 °C and (2) frozen at -20 °C, both for 6 months. The fermentation activity of different inoculum was evaluated by rumen-based in vitro anaerobic fermentation tests (volatile fatty acids, biomass digestibility, and gas production). Citrus pomace was used as the substrate during a 96-h fermentation. The maximum volatile fatty acids, methane production, and citrus pomace digestibility from fresh rumen fluid were not significantly different from rumen fluid preserved with DMSO. Metagenome analysis revealed a significant difference in the rumen microbial composition and functions between fresh rumen fluid and frozen inoculum without DMSO. Storage of rumen fluid using -20 °C with DMSO demonstrated the less difference compared with fresh rumen fluid in microbial alpha diversity and taxa composition. The hierarchical clustering tree of CAZymes showed that DMSO cryoprotected fluid was clustered much closer to the fresh rumen fluid, showing more similarity in CAZyme profiles than frozen rumen fluid. The abundance of functional genes associated with carbohydrate metabolism and methane metabolism did not differ between fresh rumen fluid and the DMSO-20 °C, whereas the abundance of key functional genes significantly decreased in frozen rumen fluid. These findings suggest that using rumen liquid preserved using DMSO at -20 °C for 180 days is a feasible alternative to fresh rumen fluid. This would reduce the need for laboratories to maintain animal donors and/or reduce the frequency of collecting rumen fluid from slaughterhouses.}, } @article {pmid38042015, year = {2023}, author = {Ma, N and Zhao, Y and Tang, M and Xia, H and Li, D and Lu, G}, title = {Concurrent infection of Exophiala dermatitidis and Angiostrongylus cantonensis in central nervous system of a child with inherited CARD9 deficiency: A case report and literature review.}, journal = {Journal de mycologie medicale}, volume = {34}, number = {1}, pages = {101455}, doi = {10.1016/j.mycmed.2023.101455}, pmid = {38042015}, issn = {1773-0449}, abstract = {Exophiala dermatitidis is a relatively common environmental black yeast with a worldwide distribution that rarely causes fungal infection. Here, we report a case of a 6-year-old girl with central nervous system (CNS) encephalitis caused by E. dermatitidis and Angiostrongylus cantonensis. E. dermatitidis was identified by both cerebrospinal fluid culture and metagenomic next-generation sequencing (mNGS). Angiostrongylus cantonensis infection was confirmed by an enzyme linked immunosorbent assay (ELISA). Whole exome sequencing showed that this previously healthy girl carried a homozygous CARD9 mutation for c.820dupG (p.D274Gfs*61) that underlies invasive fungal and parasite infections. We chose glucocortieoid pulse therapy and anti-infective therapy based on the initial results of laboratory examination and cranial MRI images. With the aggravation of the disease and the evidence of the subsequent etiologic test, the combination of antifungal antiparasitic treatments (voriconazole, fluorocytosine and amphotericin B) were actively used. Unfortunately, the girl finally died due to severe systemic infection. mNGS performs a potential value for diagnosing rare CNS infections, and autosomal recessive CARD9 deficiency should be considered in patient with fatal invasive fungal infections.}, } @article {pmid38041547, year = {2024}, author = {Li, Y and Rao, G and Zhu, G and Cheng, C and Yuan, L and Li, C and Gao, J and Tang, J and Wang, Z and Li, W}, title = {Dysbiosis of lower respiratory tract microbiome are associated with proinflammatory states in non-small cell lung cancer patients.}, journal = {Thoracic cancer}, volume = {15}, number = {2}, pages = {111-121}, pmid = {38041547}, issn = {1759-7714}, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung ; *Lung Neoplasms/microbiology ; Dysbiosis/microbiology ; *Microbiota ; Lung ; Cytokines ; Tumor Microenvironment ; }, abstract = {BACKGROUND: The lung has a sophisticated microbiome, and respiratory illnesses are greatly influenced by the lung microbiota. Despite the fact that numerous studies have shown that lung cancer patients have a dysbiosis as compared to healthy people, more research is needed to explore the association between the microbiota dysbiosis and immune profile within the tumor microenvironment (TME).

METHODS: In this study, we performed metagenomic sequencing of tumor and normal tissues from 61 non-small cell lung cancer (NSCLC) patients and six patients with other lung diseases. In order to characterize the impact of the microbes in TME, the cytokine concentrations of 24 lung tumor and normal tissues were detected using a multiple cytokine panel.

RESULTS: Our results showed that tumors had lower microbiota diversity than the paired normal tissues, and the microbiota of NSCLC was enriched in Proteobacteria, Firmicutes, and Actinobacteria. In addition, proinflammatory cytokines such as IL-8, MIF, TNF- α, and so on, were significantly upregulated in tumor tissues.

CONCLUSION: We discovered a subset of bacteria linked to host inflammatory signaling pathways and, more precisely, to particular immune cells. We determined that lower airway microbiome dysbiosis may be linked to the disruption of the equilibrium of the immune system causing lung inflammation. The spread of lung cancer may be linked to specific bacteria.}, } @article {pmid38041127, year = {2023}, author = {Diaz, GR and Gaire, TN and Ferm, P and Case, L and Caixeta, LS and Goldsmith, TJ and Armstrong, J and Noyes, NR}, title = {Effect of castration timing and weaning strategy on the taxonomic and functional profile of ruminal bacteria and archaea of beef calves.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {61}, pmid = {38041127}, issn = {2524-4671}, support = {Grantee No. GNT-20212290//Fulbright Scholarship/ ; Contract No. 085-2020-FONDECYT//Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica from Peru/ ; MnDRIVE Graduate Student Professional Development award//MnDRIVE Global Food Ventures Program/ ; }, abstract = {BACKGROUND: Beef cattle experience several management challenges across their lifecycle. Castration and weaning, two major interventions in the early life of beef cattle, can have a substantial impact on animal performance. Despite the key role of the rumen microbiome on productive traits of beef cattle, the effect of castration timing and weaning strategy on this microbial community has not been formally described. We assessed the effect of four castration time windows (at birth, turnout, pre-weaning and weaning) and two weaning strategies (fence-line and truck transportation) on the rumen microbiome in a randomized controlled study with 32 male calves across 3 collection days (i.e., time points). Ruminal fluid samples were submitted to shotgun metagenomic sequencing and changes in the taxonomic (microbiota) and functional profile (metagenome) of the rumen microbiome were described.

RESULTS: Using a comprehensive yet stringent taxonomic classification approach, we identified 10,238 unique taxa classified under 40 bacterial and 7 archaeal phyla across all samples. Castration timing had a limited long-term impact on the rumen microbiota and was not associated with changes in alpha and beta diversity. The interaction of collection day and weaning strategy was associated with changes in the rumen microbiota, which experienced a significant decrease in alpha diversity and shifts in beta diversity within 48 h post-weaning, especially in calves abruptly weaned by truck transportation. Calves weaned using a fence-line weaning strategy had lower relative abundance of Bacteroides, Lachnospira, Fibrobacter and Ruminococcus genera compared to calves weaned by truck transportation. Some genes involved in the hydrogenotrophic methanogenesis pathway (fwdB and fwdF) had higher relative abundance in fence-line-weaned calves post-weaning. The antimicrobial resistance gene tetW consistently represented more than 50% of the resistome across time, weaning and castration groups, without significant changes in relative abundance.

CONCLUSIONS: Within the context of this study, castration timing had limited long-term effects on the rumen microbiota, while weaning strategy had short-term effects on the rumen microbiota and methane-associated metagenome, but not on the rumen resistome.}, } @article {pmid38041098, year = {2023}, author = {Kang, X and Xu, J and Luo, X and Schönhuth, A}, title = {Hybrid-hybrid correction of errors in long reads with HERO.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {275}, pmid = {38041098}, issn = {1474-760X}, support = {956229//HORIZON EUROPE European Research Council/ ; 872539//HORIZON EUROPE European Research Council/ ; }, mesh = {Sequence Analysis, DNA ; *Algorithms ; *High-Throughput Nucleotide Sequencing ; Benchmarking ; }, abstract = {Although generally superior, hybrid approaches for correcting errors in third-generation sequencing (TGS) reads, using next-generation sequencing (NGS) reads, mistake haplotype-specific variants for errors in polyploid and mixed samples. We suggest HERO, as the first "hybrid-hybrid" approach, to make use of both de Bruijn graphs and overlap graphs for optimal catering to the particular strengths of NGS and TGS reads. Extensive benchmarking experiments demonstrate that HERO improves indel and mismatch error rates by on average 65% (27[Formula: see text]95%) and 20% (4[Formula: see text]61%). Using HERO prior to genome assembly significantly improves the assemblies in the majority of the relevant categories.}, } @article {pmid38041056, year = {2023}, author = {Simon, SA and Schmidt, K and Griesdorn, L and Soares, AR and Bornemann, TLV and Probst, AJ}, title = {Dancing the Nanopore limbo - Nanopore metagenomics from small DNA quantities for bacterial genome reconstruction.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {727}, pmid = {38041056}, issn = {1471-2164}, mesh = {Sequence Analysis, DNA/methods ; *Nanopores ; *Dancing ; Metagenomics/methods ; Metagenome ; Genome, Bacterial ; DNA ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {BACKGROUND: While genome-resolved metagenomics has revolutionized our understanding of microbial and genetic diversity in environmental samples, assemblies of short-reads often result in incomplete and/or highly fragmented metagenome-assembled genomes (MAGs), hampering in-depth genomics. Although Nanopore sequencing has increasingly been used in microbial metagenomics as long reads greatly improve the assembly quality of MAGs, the recommended DNA quantity usually exceeds the recoverable amount of DNA of environmental samples. Here, we evaluated lower-than-recommended DNA quantities for Nanopore library preparation by determining sequencing quality, community composition, assembly quality and recovery of MAGs.

RESULTS: We generated 27 Nanopore metagenomes using the commercially available ZYMO mock community and varied the amount of input DNA from 1000 ng (the recommended minimum) down to 1 ng in eight steps. The quality of the generated reads remained stable across all input levels. The read mapping accuracy, which reflects how well the reads match a known reference genome, was consistently high across all libraries. The relative abundance of the species in the metagenomes was stable down to input levels of 50 ng. High-quality MAGs (> 95% completeness, ≤ 5% contamination) could be recovered from metagenomes down to 35 ng of input material. When combined with publicly available Illumina reads for the mock community, Nanopore reads from input quantities as low as 1 ng improved the quality of hybrid assemblies.

CONCLUSION: Our results show that the recommended DNA amount for Nanopore library preparation can be substantially reduced without any adverse effects to genome recovery and still bolster hybrid assemblies when combined with short-read data. We posit that the results presented herein will enable studies to improve genome recovery from low-biomass environments, enhancing microbiome understanding.}, } @article {pmid38040541, year = {2023}, author = {Zhang, X and Irajizad, E and Hoffman, KL and Fahrmann, JF and Li, F and Seo, YD and Browman, GJ and Dennison, JB and Vykoukal, J and Luna, PN and Siu, W and Wu, R and Murage, E and Ajami, NJ and McQuade, JL and Wargo, JA and Long, JP and Do, KA and Lampe, JW and Basen-Engquist, KM and Okhuysen, PC and Kopetz, S and Hanash, SM and Petrosino, JF and Scheet, P and Daniel, CR}, title = {Modulating a prebiotic food source influences inflammation and immune-regulating gut microbes and metabolites: insights from the BE GONE trial.}, journal = {EBioMedicine}, volume = {98}, number = {}, pages = {104873}, pmid = {38040541}, issn = {2352-3964}, mesh = {Humans ; *Prebiotics ; *Gastrointestinal Microbiome ; Proteomics ; Obesity/microbiology ; Inflammation ; }, abstract = {BACKGROUND: Accessible prebiotic foods hold strong potential to jointly target gut health and metabolic health in high-risk patients. The BE GONE trial targeted the gut microbiota of obese surveillance patients with a history of colorectal neoplasia through a straightforward bean intervention.

METHODS: This low-risk, non-invasive dietary intervention trial was conducted at MD Anderson Cancer Center (Houston, TX, USA). Following a 4-week equilibration, patients were randomized to continue their usual diet without beans (control) or to add a daily cup of study beans to their usual diet (intervention) with immediate crossover at 8-weeks. Stool and fasting blood were collected every 4 weeks to assess the primary outcome of intra and inter-individual changes in the gut microbiome and in circulating markers and metabolites within 8 weeks. This study was registered on ClinicalTrials.gov as NCT02843425, recruitment is complete and long-term follow-up continues.

FINDINGS: Of the 55 patients randomized by intervention sequence, 87% completed the 16-week trial, demonstrating an increase on-intervention in diversity [n = 48; linear mixed effect and 95% CI for inverse Simpson index: 0.16 (0.02, 0.30); p = 0.02] and shifts in multiple bacteria indicative of prebiotic efficacy, including increased Faecalibacterium, Eubacterium and Bifidobacterium (all p < 0.05). The circulating metabolome showed parallel shifts in nutrient and microbiome-derived metabolites, including increased pipecolic acid and decreased indole (all p < 0.002) that regressed upon returning to the usual diet. No significant changes were observed in circulating lipoproteins within 8 weeks; however, proteomic biomarkers of intestinal and systemic inflammatory response, fibroblast-growth factor-19 increased, and interleukin-10 receptor-α decreased (p = 0.01).

INTERPRETATION: These findings underscore the prebiotic and potential therapeutic role of beans to enhance the gut microbiome and to regulate host markers associated with metabolic obesity and colorectal cancer, while further emphasizing the need for consistent and sustainable dietary adjustments in high-risk patients.

FUNDING: This study was funded by the American Cancer Society.}, } @article {pmid38040311, year = {2023}, author = {Wang, YC and Lv, YH and Hu, XR and Lin, YT and Crittenden, JC and Wang, C}, title = {Microbial metabolic flexibility guarantees function resilience in response to starvation disturbance.}, journal = {Bioresource technology}, volume = {}, number = {}, pages = {130137}, doi = {10.1016/j.biortech.2023.130137}, pmid = {38040311}, issn = {1873-2976}, abstract = {Starvation disturbance due to nutrient limitation is a common problem in bioreactors. However, an understanding of how microbial systems respond to starvation remains in its infancy. Here the metabolic response mechanism of a biofilm community to starvation was investigated using a well-controlled gaseous toluene treatment biofilter through interruption of its operation. It was found that metabolic characteristics showed significant differences before and after starvation. The dominant carbon source utilization type shifted from amino acids and carboxylic acids to esters and carbohydrates after starvation, which is more conducive to improving energy production. Metagenomic sequencing analysis supported that the changes in the dominant metabolic substrate, enhanced metabolic stability, and flexibility in the mode of energy metabolism could be the main ways to guarantee functional resilience in ecosystems after starvation. The results highlight the microbial metabolic response to starvation, which would be beneficial to the understanding of functional resilience and bioreactor stability.}, } @article {pmid38040289, year = {2024}, author = {Mbow, FT and Akbari, A and Dopffel, N and Schneider, K and Mukherjee, S and Meckenstock, RU}, title = {Insights into the effects of anthropogenic activities on oil reservoir microbiome and metabolic potential.}, journal = {New biotechnology}, volume = {79}, number = {}, pages = {30-38}, doi = {10.1016/j.nbt.2023.11.004}, pmid = {38040289}, issn = {1876-4347}, mesh = {Humans ; Oil and Gas Fields ; Anthropogenic Effects ; Bacteria/metabolism ; *Microbiota ; Water ; *Disinfectants/metabolism ; }, abstract = {Microbial communities have long been observed in oil reservoirs, where the subsurface conditions are major drivers shaping their structure and functions. Furthermore, anthropogenic activities such as water flooding during oil production can affect microbial activities and community compositions in oil reservoirs through the injection of recycled produced water, often associated with biocides. However, it is still unclear to what extent the introduced chemicals and microbes influence the metabolic potential of the subsurface microbiome. Here we investigated an onshore oilfield in Germany (Field A) that undergoes secondary oil production along with biocide treatment to prevent souring and microbially induced corrosion (MIC). With the integrated approach of 16 S rRNA gene amplicon and shotgun metagenomic sequencing of water-oil samples from 4 production wells and 1 injection well, we found differences in microbial community structure and metabolic functions. In the injection water samples, amplicon sequence variants (ASVs) belonging to families such as Halanaerobiaceae, Ectothiorhodospiraceae, Hydrogenophilaceae, Halobacteroidaceae, Desulfohalobiaceae, and Methanosarcinaceae were dominant, while in the production water samples, ASVs of families such as Thermotogaceae, Nitrospiraceae, Petrotogaceae, Syntrophaceae, Methanobacteriaceae, and Thermoprotei were also dominant. The metagenomic analysis of the injection water sample revealed the presence of C1-metabolism, namely, genes involved in formaldehyde oxidation. Our analysis revealed that the microbial community structure of the production water samples diverged slightly from that of injection water samples. Additionally, a metabolic potential for oxidizing the applied biocide clearly occurred in the injection water samples indicating an adaptation and buildup of degradation capacity or resistance against the added biocide.}, } @article {pmid38039820, year = {2024}, author = {Jiang, C and Zhao, Z and Zhu, D and Pan, X and Yang, Y}, title = {Rare resistome rather than core resistome exhibited higher diversity and risk along the Yangtze River.}, journal = {Water research}, volume = {249}, number = {}, pages = {120911}, doi = {10.1016/j.watres.2023.120911}, pmid = {38039820}, issn = {1879-2448}, mesh = {*Genes, Bacterial ; *Rivers/microbiology ; Ecosystem ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {As important freshwater ecosystems, the occurrence and distribution of antibiotic resistance genes (ARGs) in rivers are relevant to public health. However, studies investigating ARGs of different environmental media in river ecosystems are limited. In this study, we analyzed the ARGs of microbes in free-living setting, particle-associated setting, sediment and bank soil of the Yangtze River using metagenomics. Twenty-six ARGs were found in all samples regardless of media (core resistome) with a diversity of 8.6 %-34.7 %, accounting for 22.7 %-89.2 % of the relative abundance of the overall ARGs. The core resistome of the Yangtze River was dominated by multidrug resistance genes consisting mainly of efflux pumps and bacitracin resistance genes. The rare resistome was dominated by multidrug, sulfonamide, and aminoglycoside resistance genes. The core resistome was more prevalent in chromosomes, implying that these ARGs with low diversity and high relative abundance may be intrinsic to microbes in the Yangtze River. The rare resistome was more prevalent in plasmids, suggesting these ARGs with high diversity and low relative abundance were acquired under environmental stresses and had transfer potential. Additionally, we found that core and rare resistome were mainly carried by specific bacteria. Noteworthily, twenty-two ARGs of high clinical concern were identified in rare resistome, especially aac(6')-I, sul1, and tetM, which were plasmid-borne and hosted by clinically relevant pathogens. Both core and rare resistome hosts showed the highest niche breadths in particle-associated setting compared to other media, and particle-associated setting could provide more stable and ideal conditions for resistome hosts to survive. This study elucidated the genetic locations of ARGs and the community assembly mechanisms of ARG hosts in freshwater environments.}, } @article {pmid38039804, year = {2024}, author = {Duan, B and Gan, M and Xu, Z and Chen, WX}, title = {Tonsil microbiome in pediatric patients with post tonsillectomy hemorrhage for tonsillar hypertrophy.}, journal = {International journal of pediatric otorhinolaryngology}, volume = {176}, number = {}, pages = {111788}, doi = {10.1016/j.ijporl.2023.111788}, pmid = {38039804}, issn = {1872-8464}, mesh = {Child ; Humans ; Palatine Tonsil/surgery/microbiology ; *Tonsillectomy/adverse effects ; Hemorrhage ; *Microbiota ; Hypertrophy ; Neisseria ; }, abstract = {OBJECTIVE: This study aimed to compare the tonsillar microbiota between post tonsillectomy patients with bleeding and without bleeding, and to investigate the potential role of tonsillar microbiota in the development of post-tonsillectomy hemorrhage (PTH).

METHODS: Nineteen tonsillar tissues from PTH patients and 21 tissues from control patients were collected. Metagenomic sequencing was used to compare the microbiota in PTH and control groups. Alpha diversity indices were used to compare the richness and evenness of the microbiota between the two groups. PCoA and NMDS analyses were used to evaluate beta diversity. LDA analysis was conducted to identify significantly abundant genera.

RESULTS: No significant difference in alpha diversity indices was found between PTH and control patients. The dominant bacteria in the tonsillar microbiota were Haemophilus, Streptococcus, and Fusobacterium. PCoA and NMDS analyses showed significant differences in beta diversity between PTH and control patients. PTH patients had a significantly higher relative abundance of Neisseria, Capnocytophaga, and Veillonella. Capnocytophaga was also identified as a significantly abundant genus by LDA analysis.

CONCLUSION: This study demonstrates that there is a difference in the tonsillar microbiota between PTH and control patients. The results suggest that Neisseria, Capnocytophaga, and Veillonella may be associated with the development of PTH. These findings provide new insights into the potential role of the tonsillar microbiota in the development of PTH, and may help to develop new strategies for preventing and treating this potentially life-threatening complication.}, } @article {pmid38038743, year = {2023}, author = {Fan, Y and Hou, Y and Li, Q and Dian, Z and Wang, B and Xia, X}, title = {RNA virus diversity in rodents.}, journal = {Archives of microbiology}, volume = {206}, number = {1}, pages = {9}, pmid = {38038743}, issn = {1432-072X}, support = {81960606//National Natural Science Foundation of China/ ; 202202AG050013//Yunnan Major Scientific and Technological Projects/ ; 202103AQ100001//Yunnan Key R&D Program/ ; 202101AS070028//Yunnan Province Basic Research Program Projects/ ; }, mesh = {Animals ; Humans ; Rodentia ; Zoonoses/epidemiology ; *Viruses/genetics ; *RNA Viruses/genetics ; Disease Outbreaks ; }, abstract = {Many zoonotic disease emergencies are associated with RNA viruses in rodents that substantially impact public health. With the widespread application of meta-genomics and meta-transcriptomics for virus discovery over the last decade, viral sequences deposited in public databases have expanded rapidly, and the number of novel viruses discovered in rodents has increased. As important reservoirs of zoonotic viruses, rodents have attracted increasing attention for the risk of potential spillover of rodent-borne viruses. However, knowledge of rodent viral diversity and the major factors contributing to the risk of zoonotic epidemic outbreaks remains limited. Therefore, this study analyzes the diversity and composition of rodent RNA viruses using virus records from the Database of Rodent-associated Viruses (DRodVir/ZOVER), which covers the published literatures and records in GenBank database, reviews the main rodent RNA virus-induced human infectious diseases, and discusses potential challenges in this field.}, } @article {pmid38038470, year = {2023}, author = {Rizzieri, YC and Lipari, A and Gunn, L and Li, F-W}, title = {Twelve new metagenome-assembled genomes from non-axenic culture of Griffithsia monilis (Rhodophyta).}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0072823}, doi = {10.1128/mra.00728-23}, pmid = {38038470}, issn = {2576-098X}, abstract = {We report 12 metagenome-assembled genomes from a non-axenic culture of the red alga Griffithsia monilis Harvey, some of which are distantly related to publicly available genomes.}, } @article {pmid38038451, year = {2024}, author = {Yang, L and Wang, K and Li, Y and Li, W and Liu, D}, title = {Joint application of metagenomic next-generation sequencing and histopathological examination for the diagnosis of pulmonary infectious disease.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0058623}, pmid = {38038451}, issn = {2165-0497}, support = {82173182//MOST | National Natural Science Foundation of China (NSFC)/ ; 2020YFS0572//Science and Technology Program of Sichuan, China/ ; }, mesh = {Humans ; *Communicable Diseases/diagnosis ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents ; Metagenome ; Metagenomics ; Lung ; }, abstract = {The diagnosis of some pulmonary infectious diseases and their pathogens is very difficult. A more precise diagnosis of pulmonary infectious diseases can help clinicians use proper antibiotics as well as reduce the development of drug-resistant bacteria. In this study, we performed both mNGS and pathology on lung puncture biopsy tissue from patients and found that combined mNGS and histopathology testing was significantly more effective than histopathology testing alone in detecting infectious diseases and identifying infectious diseases. In addition, the combined approach improves the detection rate of pathogenic microorganisms in infectious diseases and can be used to guide precision clinical treatment.}, } @article {pmid38038385, year = {2023}, author = {Li, CC and Hsu, WF and Chiang, PC and Kuo, MC and Wo, AM and Tseng, YJ}, title = {Characterization of markers, functional properties, and microbiome composition in human gut-derived bacterial extracellular vesicles.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2288200}, pmid = {38038385}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; Feces/microbiology ; Bacteria/genetics ; *Extracellular Vesicles ; RNA, Ribosomal, 16S/genetics ; DNA ; }, abstract = {Past studies have confirmed the etiologies of bacterial extracellular vesicles (BEVs) in various diseases, including inflammatory bowel disease (IBD) and colorectal cancer (CRC). This study aimed to investigate the characteristics of stool-derived bacterial extracellular vesicles (stBEVs) and discuss their association with stool bacteria. First, three culture models - gram-positive (G+)BcBEVs (from B.coagulans), gram-negative (G-)EcBEVs (from E.coli), and eukaryotic cell-derived EVs (EEV, from Colo205 cell line) - were used to benchmark various fractions of stEVs separated from optimized density gradient approach (DG). As such, WB, TEM, NTA, and functional assays, were utilized to analyze properties and distribution of EVs in cultured and stool samples. Stool samples from healthy individuals were interrogated using the approaches developed. Results demonstrated successful separation of most stBEVs (within DG fractions 8&9) from stEEVs (within DG fractions 5&6). Data also suggest the presence of stBEV DNA within vesicles after extraction of BEV DNA and DNase treatment. Metagenomic analysis from full-length (FL) region sequencing results confirmed significant differences between stool bacteria and stBEVs. Significantly, F8&9 and the pooled sample (F5-F9) exhibited a similar microbial composition, indicating that F8&9 were enriched in most stBEV species, primarily dominated by Firmicutes (89.6%). However, F5&6 and F7 still held low-density BEVs with a significantly higher proportion of Proteobacteria (20.5% and 40.7%, respectively) and Bacteroidetes (24% and 13.7%, respectively), considerably exceeding the proportions in stool and F8&9. Importantly, among five healthy individuals, significant variations were observed in the gut microbiota composition of their respective stBEVs, indicating the potential of stBEVs as a target for personalized medicine and research.}, } @article {pmid38037712, year = {2023}, author = {Gao, M and Xiong, C and Tsui, CKM and Cai, L}, title = {Pathogen invasion increases the abundance of predatory protists and their prey associations in the plant microbiome.}, journal = {Molecular ecology}, volume = {}, number = {}, pages = {}, doi = {10.1111/mec.17228}, pmid = {38037712}, issn = {1365-294X}, support = {32330002//National Natural Science Foundation of China/ ; }, abstract = {Soil and plant-associated protistan communities play a key role in shaping bacterial and fungal communities, primarily through their function as top-down predators. However, our understanding of how pathogen invasion influences these protistan communities and their relationships with bacterial and fungal communities remains limited. Here, we studied the protistan communities along the soil-plant continuum of healthy chilli peppers and those affected by Fusarium wilt disease (FWD), and integrated bacterial and fungal community data from our previous research. Our research showed that FWD was associated with a significant enrichment of phagotrophic protists in roots, and also increased the proportion and connectivity of these protists (especially Cercozoa and Ciliophora) in both intra- and inter-kingdom networks. Furthermore, the microbiome of diseased plants not only showed a higher relative abundance of functional genes related to bacterial anti-predator responses than healthy plants, but also contained a greater abundance of metagenome-assembled genomes with functional traits involved in this response. The increased microbial inter-kingdom associations between bacteria and protists, coupled with the notable bacterial anti-predator feedback in the microbiome of diseased plants, suggest that FWD may catalyse the associations between protists and their microbial prey. These findings highlight the potential role of predatory protists in influencing microbial assembly and functionality through top-down forces under pathogenic stress.}, } @article {pmid38037657, year = {2023}, author = {Cao, R and Dong, X and Zhao, Y and Yin, J}, title = {Effects of blister blight disease on endophytic microbial diversity and community structure in tea (Camellia sinensis) leaves.}, journal = {3 Biotech}, volume = {13}, number = {12}, pages = {421}, pmid = {38037657}, issn = {2190-572X}, abstract = {In this study, metagenomic sequencing technology was employed to analyze the ITS1 region sequence of the ITS rDNA gene of endophytic fungi and 16S sequence of endophytic bacteria in tea leaves with varying degrees of infection by tea blister blight disease as well as healthy tea leaves. Subsequently, a comparative analysis was conducted on the endophytic microbial diversity and the community structure in tea leaves. The findings of this investigation reveal a shift in the dominant endophytic fungal genera from Ascomycota to Basidiomycota as the disease progressed. Furthermore, a negative correlation was observed between Exobasidium and Talaromyce, with Talaromyce exhibiting potential as an antagonist against the disease. Meanwhile, our findings reveal that Proteobacteria, Firmicutes, and Actinobacteria were the three most abundant bacteria phyla in tea leaves. As the disease progressed, there was an increase in the relative abundance of Actinobacteria, while Variovorax, Sphingomonas, and Pseudomonas were found to have higher abundance in later stages. The diversity analysis results indicated that the endophytic microbial diversity and the community structure in tea leaves in the diseased group were lower than those in the healthy control group. In general, blister blight disease altered the community structure of endophytic microorganisms in tea leaves, resulting in a few species with high abundance. The study lays a foundation for investigating the pathogenic mechanism of tea blister disease and establishing a theoretical basis for controlling diseases in tea trees.}, } @article {pmid38036921, year = {2023}, author = {Gallardo-Becerra, L and Cervantes-Echeverría, M and Cornejo-Granados, F and Vazquez-Morado, LE and Ochoa-Leyva, A}, title = {Perspectives in Searching Antimicrobial Peptides (AMPs) Produced by the Microbiota.}, journal = {Microbial ecology}, volume = {87}, number = {1}, pages = {8}, pmid = {38036921}, issn = {1432-184X}, support = {Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnología/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnología/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnología/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnología/ ; Ciencia de Frontera-2019-263986//Consejo Nacional de Ciencia y Tecnología/ ; PAPIIT UNAM (IN219723)//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; PAPIIT UNAM (IN219723)//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; PAPIIT UNAM (IN219723)//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; PAPIIT UNAM (IN219723)//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; PAPIIT UNAM (IN219723)//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; }, mesh = {Humans ; *Antimicrobial Cationic Peptides/genetics/pharmacology ; Antimicrobial Peptides ; Bacteria/genetics ; *Microbiota/genetics ; Anti-Bacterial Agents ; }, abstract = {Changes in the structure and function of the microbiota are associated with various human diseases. These microbial changes can be mediated by antimicrobial peptides (AMPs), small peptides produced by the host and their microbiota, which play a crucial role in host-bacteria co-evolution. Thus, by studying AMPs produced by the microbiota (microbial AMPs), we can better understand the interactions between host and bacteria in microbiome homeostasis. Additionally, microbial AMPs are a new source of compounds against pathogenic and multi-resistant bacteria. Further, the growing accessibility to metagenomic and metatranscriptomic datasets presents an opportunity to discover new microbial AMPs. This review examines the structural properties of microbiota-derived AMPs, their molecular action mechanisms, genomic organization, and strategies for their identification in any microbiome data as well as experimental testing. Overall, we provided a comprehensive overview of this important topic from the microbial perspective.}, } @article {pmid38036528, year = {2023}, author = {Li, Z and Wang, J and Yue, H and Du, M and Jin, Y and Fan, J}, title = {Marine toxin domoic acid alters nitrogen cycling in sediments.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7873}, pmid = {38036528}, issn = {2041-1723}, support = {42177375//National Natural Science Foundation of China (National Science Foundation of China)/ ; 21876018//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Ecosystem ; *Geologic Sediments ; Nitrogen Cycle ; Nitrogen/analysis ; Denitrification ; }, abstract = {As a red tide algal toxin with intense neurotoxicity distributed worldwide, domoic acid (DA) has attracted increasing concerns. In this work, the integrative analysis of metagenome and metabolome are applied to investigate the impact of DA on nitrogen cycling in coastal sediments. Here we show that DA can act as a stressor to induce the variation of nitrogen (N) cycling by altering the abundance of functional genes and electron supply. Moreover, microecology theory revealed that DA can increase the role of deterministic assembly in microbial dynamic succession, resulting in the shift of niches and, ultimately, the alteration in N cycling. Notably, denitrification and Anammox, the important process for sediment N removal, are markedly limited by DA. Also, variation of N cycling implies the modification in cycles of other associated elements. Overall, DA is capable of ecosystem-level effects, which require further evaluation of its potential cascading effects.}, } @article {pmid38036425, year = {2023}, author = {Doolin, ML and Dearing, MD}, title = {Differential effects of two common antiparasitics on microbiota resilience.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiad547}, pmid = {38036425}, issn = {1537-6613}, abstract = {BACKGROUND: Parasitic infections challenge vertebrate health worldwide, and off-target effects of antiparasitic treatments may be an additional obstacle to recovery. However, there have been few investigations of the effects of antiparasitics on the gut microbiome in the absence of parasites.

METHODS: We investigated whether two common antiparasitics-albendazole and metronidazole-significantly alter the gut microbiome of parasite-free mice. We treated mice with albendazole or metronidazole daily for seven days and sampled the fecal microbiota immediately before and after treatment, and again after a two-week recovery period.

RESULTS: Albendazole did not immediately change the gut microbiota, while metronidazole decreased microbial richness by 8.5% and significantly changed community structure during treatment. The structural changes caused by metronidazole included depletion of the beneficial family Lachnospiraceae, and predictive metagenomic analysis revealed that these losses likely depressed microbiome metabolic function. Separately, we compared the fecal microbiotas of treatment groups after recovery, and there were minor differences in community structure between the albendazole, metronidazole, and sham-treated control groups.

CONCLUSIONS: These results suggest that a healthy microbiome is resilient after metronidazole-induced depletions of beneficial gut microbes and albendazole may cause slight, latent shifts in the microbiota but does not deplete healthy gut microbiota diversity.}, } @article {pmid38036118, year = {2023}, author = {Zhang, Y and Xu, Z and Chu, W and Zhang, J and Jin, W and Ye, C}, title = {Tracking the source of antibiotic resistome in the stormwater network drainage in the presence of sewage illicit connections.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {168989}, doi = {10.1016/j.scitotenv.2023.168989}, pmid = {38036118}, issn = {1879-1026}, abstract = {Stormwater pipes are illicitly connected with sewage in many countries, which means that sewage enters stormwater pipes and the drainage is discharged to surface water without any treatment. Sewage contains more pathogens and highly risky antibiotic resistance genes (ARGs) than surface runoff. Therefore, sewage may alter the microbial and ARG compositions in stormwater pipe drainage, which in turn leads to an increased risk of resistance in surface water. However, the effects of sewage on ARGs in the drainage of stormwater networks have not been systematically studied. This study characterized the microbial and ARG composition of several environmental compartments of a typical stormwater network and quantified their contributions to those in the drainage. This network transported ARGs and microorganisms from sewage, sediments in stormwater pipes, and surface runoff into the drainage and thus into the river. According to metagenomic analysis, multidrug resistance genes were most abundant in all samples and the numbers and relative abundance of ARGs in the drainage collected during wet weather were comparable to that of sewage. The results of SourceTracker showed that the relative contribution of sewage was double that of rainwater and surface runoff in the drainage during wet weather for both microorganisms and ARGs. Desulfovibrio, Azoarcus, and Sulfuritalea were connected with the greatest number of ARGs and were most abundant in the sediments of stormwater pipes. Furthermore, stochastic processes were found to dominate ARG and microbial assembly, as the effects of high hydrodynamic intensity outweighed the effects of environmental filtration and species interactions. The findings of this study can increase our understanding of ARGs in stormwater pipe drainage, a crucial medium linking ARGs in sewage to environmental ARGs.}, } @article {pmid38035860, year = {2024}, author = {Nannan, M and Wenjun, W and Ran, Z and Yongsheng, S and Rongyan, Z and Hui, C and Sumin, Z and Hui, X}, title = {Population genomics reveals that a missense mutation in EDNRB2 contributes to white plumage color in pigeons.}, journal = {Poultry science}, volume = {103}, number = {1}, pages = {103225}, pmid = {38035860}, issn = {1525-3171}, mesh = {Animals ; *Columbidae/genetics ; *Mutation, Missense ; Metagenomics ; Pigmentation/genetics ; Chickens/genetics ; Feathers ; Color ; }, abstract = {Plumage color is an important economic trait for breed feature identification and consumer's requirements in pigeons. The domestic pigeon has multiple types of plumage color, thereby providing a unique opportunity to identify the genetic basis of plumage coloration. White feather color is common for meat and medicinal use. To investigate the genetic variation associated with white plumage color in pigeons, we use genome resequencing and population genomics to identify the genomic regions with strong selective signature between pigeons with brown and white plumage color. Meanwhile, we obtained some candidate genes with melanin or melanosome biosynthesis in selected regions. Finally, we identified a missense mutation p.E256K in the EDNRB2 completely associated with white plumage color. These findings provide a basis for genetic variation in pigeons with plumage color phenotype.}, } @article {pmid38035404, year = {2024}, author = {Lindner, BG and Gerhardt, K and Feistel, DJ and Rodriguez-R, LM and Hatt, JK and Konstantinidis, KT}, title = {A user's guide to the bioinformatic analysis of shotgun metagenomic sequence data for bacterial pathogen detection.}, journal = {International journal of food microbiology}, volume = {410}, number = {}, pages = {110488}, doi = {10.1016/j.ijfoodmicro.2023.110488}, pmid = {38035404}, issn = {1879-3460}, mesh = {*Metagenome ; *Microbiota/genetics ; Metagenomics/methods ; Computational Biology ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; }, abstract = {Metagenomics, i.e., shotgun sequencing of the total microbial community DNA from a sample, has become a mature technique but its application to pathogen detection in clinical, environmental, and food samples is far from common or standardized. In this review, we summarize ongoing developments in metagenomic sequence analysis that facilitate its wider application to pathogen detection. We examine theoretical frameworks for estimating the limit of detection for a particular level of sequencing effort, current approaches for achieving species and strain analytical resolution, and discuss some relevant modern tools for these tasks. While these recent advances are significant and establish metagenomics as a powerful tool to provide insights not easily attained by culture-based approaches, metagenomics is unlikely to emerge as a widespread, routine monitoring tool in the near future due to its inherently high detection limits, cost, and inability to easily distinguish between viable and non-viable cells. Instead, metagenomics seems best poised for applications involving special circumstances otherwise challenging for culture-based and molecular (e.g., PCR-based) approaches such as the de novo detection of novel pathogens, cases of co-infection by more than one pathogen, and situations where it is important to assess the genomic composition of the pathogenic population(s) and/or its impact on the indigenous microbiome.}, } @article {pmid38035329, year = {2023}, author = {Mbaye, B and Magdy Wasfy, R and Borentain, P and Tidjani Alou, M and Mottola, G and Bossi, V and Caputo, A and Gerolami, R and Million, M}, title = {Increased fecal ethanol and enriched ethanol-producing gut bacteria Limosilactobacillus fermentum, Enterocloster bolteae, Mediterraneibacter gnavus and Streptococcus mutans in nonalcoholic steatohepatitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1279354}, pmid = {38035329}, issn = {2235-2988}, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/etiology ; Ethanol ; Streptococcus mutans/genetics ; *Limosilactobacillus fermentum ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Glucose ; Cholesterol ; }, abstract = {BACKGROUND: Non-alcoholic steatohepatitis (NASH) has become a major public health issue as one of the leading causes of liver disease and transplantation worldwide. The instrumental role of the gut microbiota is emerging but still under investigation. Endogenous ethanol (EtOH) production by gut bacteria and yeasts is an emerging putative mechanism. Microbial metagenomics and culture studies targeting enterobacteria or yeasts have been reported, but no culturomics studies have been conducted so far.

AIM: To assess fecal EtOH and other biochemical parameters, characterize NASH-associated dysbiosis and identify EtOH-producing gut microbes associated with the disease, fecal samples from 41 NASH patients and 24 controls were analyzed. High-performance liquid chromatography (HPLC) was used for EtOH, glucose, total proteins, triglyceride and total cholesterol. Viable bacteria were assessed with microbial culturomics. Microbial genetic material was assessed using 16S metagenomics targeting the hypervariable V3V4 region.

RESULTS: Fecal EtOH and glucose was elevated in the stools of NASH patients (p < 0.05) but not triglyceride, total cholesterol or proteins. In culturomics, EtOH-producing Enterocloster bolteae and Limosilactobacillus fermentum were enriched in NASH. V3V4 16S rRNA amplicon sequencing confirmed the enrichment in EtOH-producing bacteria including L. fermentum, Mediterraneibacter gnavus and Streptococcus mutans, species previously associated with NASH and other dysbiosis-associated diseases. Strikingly, E. bolteae was identified only by culturomics. The well-known Lacticaseibacillus casei was identified in controls but never isolated in patients with NASH (p < 0.05).

CONCLUSION: Elevated fecal EtOH and glucose is a feature of NASH. Several different EtOH-producing gut bacteria may play an instrumental role in the disease. Culturomics and metagenomics, two complementary methods, will be critical to identify EtOH-producing bacteria for future diagnostic markers and therapeutic targets for NASH. Suppression of EtOH-producing gut microbes and L. casei administration are options to be tested in NASH treatment.}, } @article {pmid38035326, year = {2023}, author = {Li, X and Wang, C and Guo, Z and Xiao, T and Ji, Y and Ma, Y and Li, M and Xia, J and Liu, X}, title = {Enhancing Vibrio vulnificus infection diagnosis for negative culture patients with metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1210919}, pmid = {38035326}, issn = {2235-2988}, mesh = {Animals ; Humans ; Retrospective Studies ; *Vibrio Infections/diagnosis/epidemiology ; *Vibrio vulnificus/genetics ; Anti-Bacterial Agents/therapeutic use ; High-Throughput Nucleotide Sequencing ; }, abstract = {OBJECTIVE: To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) in Vibrio vulnificus (V. vulnificus) infection.

METHODS: A retrospective analysis of patients with V. vulnificus infection at the Fifth Affiliated Hospital of Sun Yat-Sen University from January 1, 2020 to April 23, 2023 was conducted. 14 enrolled patients were diagnosed by culture or mNGS. The corresponding medical records were reviewed, and the clinical data analyzed included demographics, epidemiology laboratory findings, physical examination, symptoms at presentation, antibiotic and surgical treatment, and outcome.

RESULTS: In this study, 78.6% (11/14) patients had a history of marine trauma (including fish stab, shrimp stab, crab splints and fish hook wounds), 7.1% (1/14) had eaten seafood, and the remaining 14.3% (2/14) had no definite cause. Isolation of V. vulnificus from clinical samples including blood, tissue, fester and secreta. 9 cases were positive for culture, 5 cases were detected synchronously by mNGS and got positive for V. vulnificus. 85.7% (12/14) cases accepted surgical treatment, with 1 patient suffering finger amputated. 14 enrolled patients received appropriate antibiotic therapy, and all of them had recovered and discharged. 9 strains V. vulnificus isolated in this study were sensitive to most beta-lactam antibiotics, aminoglycosides, quinolones, etc.

CONCLUSION: Vibrio vulnificus infection is a common water-exposed disease in Zhuhai, which requires identification of a number of pathogens. Of severe infections with unknown pathogen, mNGS can be used simultaneously, and the potential to detect multiple pathogens is of great help in guiding treatment.}, } @article {pmid38034874, year = {2023}, author = {Ramanauskas, K and Igić, B}, title = {kakapo: easy extraction and annotation of genes from raw RNA-seq reads.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16456}, pmid = {38034874}, issn = {2167-8359}, mesh = {Humans ; RNA-Seq ; Phylogeny ; *Transcriptome/genetics ; *Databases, Nucleic Acid ; }, abstract = {kakapo (kākāpō) is a Python-based pipeline that allows users to extract and assemble one or more specified genes or gene families. It flexibly uses original RNA-seq read or GenBank SRA accession inputs without performing global assembly of entire transcriptomes or metatranscriptomes. The pipeline identifies open reading frames in the assembled gene transcripts and annotates them. It optionally filters raw reads for ribosomal, plastid, and mitochondrial reads, or reads belonging to non-target organisms (e.g., viral, bacterial, human). kakapo can be employed for targeted assembly, to extract arbitrary loci, such as those commonly used for phylogenetic inference in systematics or candidate genes and gene families in phylogenomic and metagenomic studies. We provide example applications and discuss how its use can offset the declining value of GenBank's single-gene databases and help assemble datasets for a variety of phylogenetic analyses.}, } @article {pmid38034829, year = {2023}, author = {Monleón-Getino, A and Pujol-Muncunill, G and Méndez Viera, J and Álvarez Carnero, L and Sanseverino, W and Paytuví-Gallart, A and Martín de Carpí, J}, title = {A pilot study of the use of the oral and faecal microbiota for the diagnosis of ulcerative colitis and Crohn's disease in a paediatric population.}, journal = {Frontiers in pediatrics}, volume = {11}, number = {}, pages = {1220976}, pmid = {38034829}, issn = {2296-2360}, abstract = {Crohn's disease (CD) and ulcerative colitis (UC) are chronic inflammatory bowel diseases (IBD) that affect the gastrointestinal tract. Changes in the microbiome and its interaction with the immune system are thought to play a key role in their development. The aim of this study was to determine whether metagenomic analysis is a feasible non-invasive diagnostic tool for IBD in paediatric patients. A pilot study of oral and faecal microbiota was proposed with 36 paediatric patients divided in three cohorts [12 with CD, 12 with UC and 12 healthy controls (HC)] with 6 months of follow-up. Finally, 30 participants were included: 13 with CD, 11 with UC and 8 HC (6 dropped out during follow-up). Despite the small size of the study population, a differential pattern of microbial biodiversity was observed between IBD patients and the control group. Twenty-one bacterial species were selected in function of their discriminant accuracy, forming three sets of potential markers of IBD. Although IBD diagnosis requires comprehensive medical evaluation, the findings of this study show that faecal metagenomics or a reduced set of bacterial markers could be useful as a non-invasive tool for an easier and earlier diagnosis.}, } @article {pmid38034805, year = {2023}, author = {Kaenying, W and Tagami, T and Suwan, E and Pitsanuwong, C and Chomngam, S and Okuyama, M and Kongsaeree, P and Kimura, A and Kongsaeree, PT}, title = {Structural and mutational analysis of glycoside hydrolase family 1 Br2 β-glucosidase derived from bovine rumen metagenome.}, journal = {Heliyon}, volume = {9}, number = {11}, pages = {e21923}, pmid = {38034805}, issn = {2405-8440}, abstract = {Ruminant animals rely on the activities of β-glucosidases from residential microbes to convert feed fibers into glucose for further metabolic uses. In this report, we determined the structures of Br2, which is a glycoside hydrolase family 1 β-glucosidase from the bovine rumen metagenome. Br2 folds into a classical (β/α)8-TIM barrel domain but displays unique structural features at loop β5→α5 and α-helix 5, resulting in different positive subsites from those of other GH1 enzymes. Br2 exhibited the highest specificity toward laminaritriose, suggesting its involvement in β-glucan hydrolysis in digested feed. We then substituted the residues at subsites +1 and + 2 of Br2 with those of Halothermothrix orenii β-glucosidase. The C170E and C221T mutations provided favorable interactions with glucooligosaccharide substrates at subsite +2, while the A219N mutation probably improved the substrate preference for cellobiose and gentiobiose relative to laminaribiose at subsite +1. The N407Y mutation increased the affinity toward cellooligosaccharides. These results give further insights into the molecular determinants responsible for substrate specificity in GH1 β-glucosidases and may provide a basis for future enzyme engineering applications.}, } @article {pmid38034579, year = {2023}, author = {Li, L and Hu, Z and Tan, G and Fan, J and Chen, Y and Xiao, Y and Wu, S and Zhi, Q and Liu, T and Yin, H and Tang, Q}, title = {Enhancing plant growth in biofertilizer-amended soil through nitrogen-transforming microbial communities.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1259853}, pmid = {38034579}, issn = {1664-462X}, abstract = {Biofertilizers have immense potential for enhancing agricultural productivity. However, there is still a need for clarification regarding the specific mechanisms through which these biofertilizers improve soil properties and stimulate plant growth. In this research, a bacterial agent was utilized to enhance plant growth and investigate the microbial modulation mechanism of soil nutrient turnover using metagenomic technology. The results demonstrated a significant increase in soil fast-acting nitrogen (by 46.7%) and fast-acting phosphorus (by 88.6%) upon application of the bacterial agent. This finding suggests that stimulated soil microbes contribute to enhanced nutrient transformation, ultimately leading to improved plant growth. Furthermore, the application of the bacterial agent had a notable impact on the accumulation of key genes involved in nitrogen cycling. Notably, it enhanced nitrification genes (amo, hao, and nar), while denitrification genes (nir and nor) showed a slight decrease. This indicates that ammonium oxidation may be the primary pathway for increasing fast-acting nitrogen in soils. Additionally, the bacterial agent influenced the composition and functional structure of the soil microbial community. Moreover, the metagenome-assembled genomes (MAGs) obtained from the soil microbial communities exhibited complementary metabolic processes, suggesting mutual nutrient exchange. These MAGs contained widely distributed and highly abundant genes encoding plant growth promotion (PGP) traits. These findings emphasize how soil microbial communities can enhance vegetation growth by increasing nutrient availability and regulating plant hormone production. This effect can be further enhanced by introducing inoculated microbial agents. In conclusion, this study provides novel insights into the mechanisms underlying the beneficial effects of biofertilizers on soil properties and plant growth. The significant increase in nutrient availability, modulation of key genes involved in nitrogen cycling, and the presence of MAGs encoding PGP traits highlight the potential of biofertilizers to improve agricultural practices. These findings have important implications for enhancing agricultural sustainability and productivity, with positive societal and environmental impacts.}, } @article {pmid38034573, year = {2023}, author = {Qi, H and Yu, F and Lü, S and Damaris, RN and Dong, G and Yang, P}, title = {Exploring domestication pattern in lotus: insights from dispensable genome assembly.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1294033}, pmid = {38034573}, issn = {1664-462X}, abstract = {Lotus (Nelumbo nucifera Gaertn.), an important aquatic plant in horticulture and ecosystems, has been cultivated for more than 7000 years and domesticated into three different subgroups: flower lotus, rhizome lotus, and seed lotus. To explore the domesticated regions of each subgroup, re-sequencing data of 371 lotus accessions collected from the public database were aligned to the genome of 'China-Antique (CA)'. Unmapped reads were used to build the dispensable genome of each subgroup using a metagenome-like assembly strategy. More than 27 Mb of the dispensable genome in these three subgroups and the wild group was assembled, of which 11,761 genes were annotated. Some of the contigs in the dispensable genome were similar to the genomic segments of other lotus accessions other than 'CA'. The annotated genes in each subgroup played essential roles in specific developmental processes. Dissection of selective signals in three cultivated subgroups also demonstrated that subgroup-specific metabolic pathways, such as the brassinosteroids metabolism enrichment in FL, associated with these selected genes in each subgroup and the contigs in dispensable genome nearly located in the domesticated regions of each subgroup, respectively. Our data presented a valuable resource for facilitating lotus genomic studies, complemented the helpful information to the reference genome, and shed light on the selective signals of domesticated subgroups.}, } @article {pmid38033594, year = {2023}, author = {Fujita, H and Ushio, M and Suzuki, K and Abe, MS and Yamamichi, M and Okazaki, Y and Canarini, A and Hayashi, I and Fukushima, K and Fukuda, S and Kiers, ET and Toju, H}, title = {Metagenomic analysis of ecological niche overlap and community collapse in microbiome dynamics.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1261137}, pmid = {38033594}, issn = {1664-302X}, abstract = {Species utilizing the same resources often fail to coexist for extended periods of time. Such competitive exclusion mechanisms potentially underly microbiome dynamics, causing breakdowns of communities composed of species with similar genetic backgrounds of resource utilization. Although genes responsible for competitive exclusion among a small number of species have been investigated in pioneering studies, it remains a major challenge to integrate genomics and ecology for understanding stable coexistence in species-rich communities. Here, we examine whether community-scale analyses of functional gene redundancy can provide a useful platform for interpreting and predicting collapse of bacterial communities. Through 110-day time-series of experimental microbiome dynamics, we analyzed the metagenome-assembled genomes of co-occurring bacterial species. We then inferred ecological niche space based on the multivariate analysis of the genome compositions. The analysis allowed us to evaluate potential shifts in the level of niche overlap between species through time. We hypothesized that community-scale pressure of competitive exclusion could be evaluated by quantifying overlap of genetically determined resource-use profiles (metabolic pathway profiles) among coexisting species. We found that the degree of community compositional changes observed in the experimental microbiome was correlated with the magnitude of gene-repertoire overlaps among bacterial species, although the causation between the two variables deserves future extensive research. The metagenome-based analysis of genetic potential for competitive exclusion will help us forecast major events in microbiome dynamics such as sudden community collapse (i.e., dysbiosis).}, } @article {pmid38033588, year = {2023}, author = {Wu, X and Xu, J and Li, J and Deng, M and Shen, Z and Nie, K and Luo, W and Zhang, C and Ma, K and Chen, X and Wang, X}, title = {Bacteroides vulgatus alleviates dextran sodium sulfate-induced colitis and depression-like behaviour by facilitating gut-brain axis balance.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1287271}, pmid = {38033588}, issn = {1664-302X}, abstract = {BACKGROUND: Patients with inflammatory bowel disease (IBD) have a higher prevalence of depression. Gut microbiota dysbiosis plays an important role in IBD and depression. However, few studies have explored the characteristic microbiota of patients with IBD and depression (IBDD), or their role in IBDD.

METHODS: We performed deep metagenomic sequencing and 16S rDNA quantitative PCR to characterise the gut microbial communities of patients with IBDD and patients with IBD without depression (IBDND). We then assessed the effect of the microbiota on colitis and depression in mouse models of dextran sulfate sodium salt (DSS)-induced colitis and lipopolysaccharide (LPS)-induced depression. Furthermore, liquid chromatography-tandem mass spectrometry was used to analyse the microbiota-derived metabolites involved in gut-brain communication. Evans Blue tracer dye was used to assess blood-brain barrier (BBB) permeability.

RESULTS: Our results showed that the faecal abundance of Bacteroides vulgatus (B. vulgatus) was lower in patients with IBDD than in those with IBDND. In the DSS-induced colitis mouse model, the B. vulgatus group showed a significantly lower disease activity index score, lesser weight loss, and longer colon length than the DSS group. Moreover, B. vulgatus relieved depression-like behaviour in the DSS-induced colitis mouse model and in the LPS-induced depression mouse model. Furthermore, the key metabolite of B. vulgatus was p-hydroxyphenylacetic acid (4-HPAA), which was found to relieve intestinal inflammation and alleviate depression-like behaviours in mouse models. By increasing the expression of the tight junction protein claudin-5 in the vascular endothelium of the BBB, B. vulgatus and 4-HPAA play critical roles in gut-brain communication.

CONCLUSION: B. vulgatus and B. vulgatus-derived 4-HPAA ameliorated intestinal inflammation and relieved depressive symptoms through the gut-brain axis. Thus, administration of B. vulgatus or 4-HPAA supplementation is a promising therapeutic strategy for treating IBD, particularly IBDD.}, } @article {pmid38033571, year = {2023}, author = {Sun, Y and Yu, Y and Wu, A and Zhang, C and Liu, X and Qian, C and Li, J and Ran, J}, title = {The composition and function of the gut microbiota of Francois' langurs (Trachypithecus francoisi) depend on the environment and diet.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1269492}, pmid = {38033571}, issn = {1664-302X}, abstract = {The microbiota is essential for the extraction of energy and nutrition from plant-based diets and may have facilitated primate adaptation to new dietary niches in response to rapid environmental shifts. In this study, metagenomic sequencing technology was used to analyze the compositional structure and functional differences of the gut microbial community of Francois' langurs (Trachypithecus francoisi) under different environmental and dietary conditions. The results showed that in terms of the composition of the gut microbial community, there were significant differences among the gut microbiota of Francois' langurs (anthropogenic disturbed populations, wild populations, and captive populations) under different environmental and dietary conditions. The microbial communities with the highest abundance in Francois' langurs were Firmicutes and Bacteroidetes. Firmicutes was the most abundant phylum in anthropogenic disturbed Francois' langurs and the least abundant in captive Francois' langurs. The abundance of Bacteroidetes was highest in captive Francois' langurs. In the analysis and comparison of alpha diversity, the diversity of the gut microbiota of Francois' langurs affected by anthropogenic disturbance was the highest. The significant differences in gut microbiota between Francois' langurs in different environments and different diets were further supported by principal coordinate analysis (PCoA), with the disturbance group having a gut microbiota more similar to the wild group. Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotation analysis indicated a high abundance of functional genes involved in carbohydrate metabolism, amino acid metabolism, replication and repair, cofactor and vitamin metabolism, and other amino acid metabolism pathways. Additionally, the functional genes involved in carbohydrate metabolism pathways were significantly enriched in the gut microbial community of Francois' langurs that were anthropogenic disturbed and captive. The gut microbiota of the Francois' langurs exhibited potential plasticity for dietary flexibility, and long-term food availability in captive populations leads to changes in gut microbiota composition and function. This study explored the composition and function of the gut microbiota of Francois' langurs and provided a scientific basis for understanding the physiological and health status of Francois' langurs, effectively protecting the population of wild Francois' langurs and reintroducing captive Francois' langurs into the wild.}, } @article {pmid38033562, year = {2023}, author = {Farmer, M and Rajasabhai, R and Tarpeh, W and Tyo, K and Wells, G}, title = {Meta-omic profiling reveals ubiquity of genes encoding for the nitrogen-rich biopolymer cyanophycin in activated sludge microbiomes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1287491}, pmid = {38033562}, issn = {1664-302X}, abstract = {Recovering nitrogen (N) from municipal wastewater is a promising approach to prevent nutrient pollution, reduce energy use, and transition toward a circular N bioeconomy, but remains a technologically challenging endeavor. Existing N recovery techniques are optimized for high-strength, low-volume wastewater. Therefore, developing methods to concentrate dilute N from mainstream wastewater will bridge the gap between existing technologies and practical implementation. The N-rich biopolymer cyanophycin is a promising candidate for N bioconcentration due to its pH-tunable solubility characteristics and potential for high levels of accumulation. However, the cyanophycin synthesis pathway is poorly explored in engineered microbiomes. In this study, we analyzed over 3,700 publicly available metagenome assembled genomes (MAGs) and found that the cyanophycin synthesis gene cphA was ubiquitous across common activated sludge bacteria. We found that cphA was present in common phosphorus accumulating organisms (PAO) Ca. 'Accumulibacter' and Tetrasphaera, suggesting potential for simultaneous N and P bioconcentration in the same organisms. Using metatranscriptomic data, we confirmed the expression of cphA in lab-scale bioreactors enriched with PAO. Our findings suggest that cyanophycin synthesis is a ubiquitous metabolic activity in activated sludge microbiomes. The possibility of combined N and P bioconcentration could lower barriers to entry for N recovery, since P concentration by PAO is already a widespread biotechnology in municipal wastewater treatment. We anticipate this work to be a starting point for future evaluations of combined N and P bioaccumulation, with the ultimate goal of advancing widespread adoption of N recovery from municipal wastewater.}, } @article {pmid38033561, year = {2023}, author = {Protasov, E and Nonoh, JO and Kästle Silva, JM and Mies, US and Hervé, V and Dietrich, C and Lang, K and Mikulski, L and Platt, K and Poehlein, A and Köhler-Ramm, T and Miambi, E and Boga, HI and Feldewert, C and Ngugi, DK and Plarre, R and Sillam-Dussès, D and Šobotník, J and Daniel, R and Brune, A}, title = {Diversity and taxonomic revision of methanogens and other archaea in the intestinal tract of terrestrial arthropods.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1281628}, pmid = {38033561}, issn = {1664-302X}, abstract = {Methane emission by terrestrial invertebrates is restricted to millipedes, termites, cockroaches, and scarab beetles. The arthropod-associated archaea known to date belong to the orders Methanobacteriales, Methanomassiliicoccales, Methanomicrobiales, and Methanosarcinales, and in a few cases also to non-methanogenic Nitrososphaerales and Bathyarchaeales. However, all major host groups are severely undersampled, and the taxonomy of existing lineages is not well developed. Full-length 16S rRNA gene sequences and genomes of arthropod-associated archaea are scarce, reference databases lack resolution, and the names of many taxa are either not validly published or under-classified and require revision. Here, we investigated the diversity of archaea in a wide range of methane-emitting arthropods, combining phylogenomic analysis of isolates and metagenome-assembled genomes (MAGs) with amplicon sequencing of full-length 16S rRNA genes. Our results allowed us to describe numerous new species in hitherto undescribed taxa among the orders Methanobacteriales (Methanacia, Methanarmilla, Methanobaculum, Methanobinarius, Methanocatella, Methanoflexus, Methanorudis, and Methanovirga, all gen. nova), Methanomicrobiales (Methanofilum and Methanorbis, both gen. nova), Methanosarcinales (Methanofrustulum and Methanolapillus, both gen. nova), Methanomassiliicoccales (Methanomethylophilaceae fam. nov., Methanarcanum, Methanogranum, Methanomethylophilus, Methanomicula, Methanoplasma, Methanoprimaticola, all gen. nova), and the new family Bathycorpusculaceae (Bathycorpusculum gen. nov.). Reclassification of amplicon libraries from this and previous studies using this new taxonomic framework revealed that arthropods harbor only CO2 and methyl-reducing hydrogenotrophic methanogens. Numerous genus-level lineages appear to be present exclusively in arthropods, suggesting long evolutionary trajectories with their termite, cockroach, and millipede hosts, and a radiation into various microhabitats and ecological niches provided by their digestive tracts (e.g., hindgut compartments, gut wall, or anaerobic protists). The distribution patterns among the different host groups are often complex, indicating a mixed mode of transmission and a parallel evolution of invertebrate and vertebrate-associated lineages.}, } @article {pmid38032574, year = {2023}, author = {Dennis, J and Massey, C and Muisyo, T and Moraru, G and Akande, M}, title = {Use of Metagenomic Next-Generation Sequencing in the Identification of Pneumocystis Jiroveci Pneumonia in a Previously Healthy Infant Diagnosed With X-Linked Hyper-IgM Syndrome.}, journal = {Journal of pediatric health care : official publication of National Association of Pediatric Nurse Associates & Practitioners}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.pedhc.2023.09.009}, pmid = {38032574}, issn = {1532-656X}, abstract = {This case describes a four-month-old male who was admitted to the pediatric intensive care unit for acute respiratory failure in the setting of a co-infection requiring increased ventilatory support. Immunodeficiency workup demonstrated poor vaccination response and low immunoglobulin titers. mNGS via Karius® test was positive for Pneumocystis jiroveci (PJP), Parvovirus, and Bocavirus. The patient was successfully treated with trimethoprim-sulfamethoxazole and prednisone. Genetic workup via Invitae panel confirmed that the patient had X-linked Hyper-IgM Syndrome. Use of mNGS can help with early identification of pathogens that conventional testing does not detect, even in patients not already identified as immunocompromised.}, } @article {pmid38032216, year = {2023}, author = {Peoples, LM and Dore, JE and Bilbrey, EM and Vick-Majors, TJ and Ranieri, JR and Evans, KA and Ross, AM and Devlin, SP and Church, MJ}, title = {Oxic methane production from methylphosphonate in a large oligotrophic lake: limitation by substrate and organic carbon supply.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {12}, pages = {e0109723}, pmid = {38032216}, issn = {1098-5336}, support = {1951002, 1950963//National Science Foundation (NSF)/ ; }, mesh = {*Lakes ; *Carbon ; Organophosphorus Compounds/metabolism ; Methane/metabolism ; }, abstract = {Methane is an important greenhouse gas that is typically produced under anoxic conditions. We show that methane is supersaturated in a large oligotrophic lake despite the presence of oxygen. Metagenomic sequencing indicates that diverse, widespread microorganisms may contribute to the oxic production of methane through the cleavage of methylphosphonate. We experimentally demonstrate that these organisms, especially members of the genus Acidovorax, can produce methane through this process. However, appreciable rates of methane production only occurred when both methylphosphonate and labile sources of carbon were added, indicating that this process may be limited to specific niches and may not be completely responsible for methane concentrations in Flathead Lake. This work adds to our understanding of methane dynamics by describing the organisms and the rates at which they can produce methane through an oxic pathway in a representative oligotrophic lake.}, } @article {pmid38032210, year = {2023}, author = {Kocurek, B and Behling, S and Martin, G and Ramachandran, P and Reed, E and Grim, C and Mammel, M and Zheng, J and Franklin, A and Garland, J and Tadesse, DA and Sharma, M and Tyson, GH and Kabera, C and Tate, H and McDermott, PF and Strain, E and Ottesen, A}, title = {Metagenomic survey of antimicrobial resistance (AMR) in Maryland surface waters differentiated by high and low human impact.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0047723}, doi = {10.1128/MRA.00477-23}, pmid = {38032210}, issn = {2576-098X}, abstract = {Here, we examine surface waters as a modality to better understand baseline antimicrobial resistance (AMR) across the environment to supplement existing AMR monitoring in pathogens associated with humans, foods, and animals. Data from metagenomic and quasimetagenomic (shotgun sequenced enrichments) are used to describe AMR in Maryland surface waters from high and low human impact classifications.}, } @article {pmid38032184, year = {2023}, author = {Muscatt, G and Cook, R and Millard, A and Bending, GD and Jameson, E}, title = {Viral metagenomics reveals diverse virus-host interactions throughout the soil depth profile.}, journal = {mBio}, volume = {14}, number = {6}, pages = {e0224623}, pmid = {38032184}, issn = {2150-7511}, abstract = {Soil viruses can moderate the roles that their host microbes play in global carbon cycling. However, given that most studies investigate the surface layer (i.e., top 20 cm) of soil, the extent to which this occurs in subsurface soil (i.e., below 20 cm) is unknown. Here, we leveraged public sequencing data to investigate the interactions between viruses and their hosts at soil depth intervals, down to 115 cm. While most viruses were detected throughout the soil depth profile, their adaptation to host microbes varied. Nonetheless, we uncovered evidence for the potential of soil viruses to encourage their hosts to recycle plant-derived carbon in both surface and subsurface soils. This work reasons that our understanding of soil viral functions requires us to continue to dig deeper and compare viruses existing throughout soil ecosystems.}, } @article {pmid38031968, year = {2023}, author = {Beauvais, M and Schatt, P and Montiel, L and Logares, R and Galand, PE and Bouget, FY}, title = {Functional redundancy of seasonal vitamin B12 biosynthesis pathways in coastal marine microbial communities.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {3753-3770}, doi = {10.1111/1462-2920.16545}, pmid = {38031968}, issn = {1462-2920}, support = {//Agence Nationale de la Recherche (ANR)/ ; }, mesh = {*Vitamin B 12/metabolism ; Seasons ; Archaea/genetics/metabolism ; *Microbiota ; Vitamins/metabolism ; }, abstract = {Vitamin B12 (cobalamin) is a major cofactor required by most marine microbes, but only produced by a few prokaryotes in the ocean, which is globally B12 -depleted. Despite the ecological importance of B12 , the seasonality of B12 metabolisms and the organisms involved in its synthesis in the ocean remain poorly known. Here we use metagenomics to assess the monthly dynamics of B12 -related pathways and the functional diversity of associated microbial communities in the coastal NW Mediterranean Sea over 7 years. We show that genes related to potential B12 metabolisms were characterized by an annual succession of different organisms carrying distinct production pathways. During the most productive winter months, archaea (Nitrosopumilus and Nitrosopelagicus) were the main contributors to B12 synthesis potential through the anaerobic pathway (cbi genes). In turn, Alphaproteobacteria (HIMB11, UBA8309, Puniceispirillum) contributed to B12 synthesis potential in spring and summer through the aerobic pathway (cob genes). Cyanobacteria could produce pseudo-cobalamin from spring to autumn. Finally, we show that during years with environmental perturbations, the organisms usually carrying B12 synthesis genes were replaced by others having the same gene, thus maintaining the potential for B12 production. Such ecological insurance could contribute to the long-term functional resilience of marine microbial communities exposed to contrasting inter-annual environmental conditions.}, } @article {pmid38031397, year = {2023}, author = {Nie, S and Zhang, Q and Chen, R and Lin, L and Li, Z and Sun, Y and Huang, J and Feng, Z and Cao, X and Ye, K and Tang, L and Zhou, J and Cai, G and Chen, X}, title = {Rapid detection of pathogens of peritoneal dialysis-related peritonitis, especially in patients who have taken antibiotics, using metagenomic next-generation sequencing: a pilot study.}, journal = {Renal failure}, volume = {45}, number = {2}, pages = {2284229}, doi = {10.1080/0886022X.2023.2284229}, pmid = {38031397}, issn = {1525-6049}, mesh = {Humans ; Pilot Projects ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/therapeutic use ; *Peritoneal Dialysis/adverse effects ; *Peritonitis/diagnosis/etiology ; Sensitivity and Specificity ; }, abstract = {INTRODUCTION: Peritoneal dialysis (PD)-related peritonitis is a serious complication of PD. Improving the diagnostic rate of peritonitis pathogens may substantially benefit peritonitis patients.

METHODS: The study was conducted in the People's Liberation Army (PLA) General Hospital from 1 June 2021 to 31 May 2022. Information about peritonitis, culture and metagenomic next-generation sequencing (mNGS) results and so on were collected. Patients were divided into antibiotic-use and antibiotic-free groups. The culture and mNGS results were compared using the paired χ2 test.

RESULTS: Data from 26 patients with peritonitis were collected. 50% of the patients had used antibiotics before samples were obtained (antibiotic-use group). The positivity rate using culture was 92.3% (12 cases) in the antibiotic-free group and 38.5% (5 cases) in the antibiotic-use group (p = 0.011). However, the positivity rate using mNGS was 92.3% (12 cases) regardless of whether antibiotics were used (p = 1.000). After revising the mNGS results, the positivity rate was 84.6% (11 cases) in both groups (p = 1.000). A significant difference between culture and mNGS results of all groups was observed (p = 0.039). The difference no matter between culture and mNGS (p = 0.016) or between culture and modified mNGS (p = 0.031) of the antibiotic-use group was observed.

CONCLUSION: For patients with PD-related peritonitis who previously received antibiotics, mNGS is suggested. For other patients, mNGS testing can be performed, but the results should be interpreted with caution. Much more research should be done to identify a powerful and ideal tool to detect pathogens underlying PD-related peritonitis.}, } @article {pmid38031339, year = {2023}, author = {Kamenova, S and de Muinck, EJ and Veiberg, V and Utsi, TA and Steyaert, SMJG and Albon, SD and Loe, LE and Trosvik, P}, title = {Gut microbiome biogeography in reindeer supersedes millennia of ecological and evolutionary separation.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {12}, pages = {}, pmid = {38031339}, issn = {1574-6941}, support = {//Horizon 2020/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; *Reindeer/genetics ; RNA, Ribosomal, 16S/genetics ; Gastrointestinal Tract ; Metagenome ; }, abstract = {Ruminants are dependent on their gut microbiomes for nutrient extraction from plant diets. However, knowledge about the composition, diversity, function, and spatial structure of gut microbiomes, especially in wild ruminants, is limited, largely because analysis has been restricted to faeces or the rumen. In two geographically separated reindeer subspecies, 16S rRNA gene amplicon sequencing revealed strong spatial structuring, and pronounced differences in microbial diversity of at least 33 phyla across the stomach, small intestine, and large intestine (including faeces). The main structural feature was the Bacteroidota to Firmicutes ratio, which declined from the stomach to the large intestine, likely reflecting functional adaptation. Metagenome shotgun sequencing also revealed highly significant structuring in the relative occurrence of carbohydrate-active enzymes (CAZymes). CAZymes were enriched in the rumen relative to the small and large intestines. Interestingly, taxonomic diversity was highest in the large intestine, suggesting an important and understudied role for this organ. Despite the two study populations being separated by an ocean and six millennia of evolutionary history, gut microbiome structuring was remarkably consistent. Our study suggests a strong selection for gut microbiome biogeography along the gastrointestinal tract in reindeer subspecies.}, } @article {pmid38031142, year = {2023}, author = {Holm, JB and France, MT and Gajer, P and Ma, B and Brotman, RM and Shardell, M and Forney, L and Ravel, J}, title = {Integrating compositional and functional content to describe vaginal microbiomes in health and disease.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {259}, pmid = {38031142}, issn = {2049-2618}, support = {R01 NR015495/NR/NINR NIH HHS/United States ; U19 AI084044/AI/NIAID NIH HHS/United States ; R01-NR015495/NR/NINR NIH HHS/United States ; }, mesh = {Female ; Humans ; Vagina/microbiology ; *Vaginosis, Bacterial/microbiology ; Bacteria/genetics ; Gardnerella vaginalis/genetics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: A Lactobacillus-dominated vaginal microbiome provides the first line of defense against adverse genital tract health outcomes. However, there is limited understanding of the mechanisms by which the vaginal microbiome modulates protection, as prior work mostly described its composition through morphologic assessment and marker gene sequencing methods that do not capture functional information. To address this gap, we developed metagenomic community state types (mgCSTs) which use metagenomic sequences to describe and define vaginal microbiomes based on both composition and functional potential.

RESULTS: MgCSTs are categories of microbiomes classified using taxonomy and the functional potential encoded in their metagenomes. MgCSTs reflect unique combinations of metagenomic subspecies (mgSs), which are assemblages of bacterial strains of the same species, within a microbiome. We demonstrate that mgCSTs are associated with demographics such as age and race, as well as vaginal pH and Gram stain assessment of vaginal smears. Importantly, these associations varied between mgCSTs predominated by the same bacterial species. A subset of mgCSTs, including three of the six predominated by Gardnerella vaginalis mgSs, as well as mgSs of L. iners, were associated with a greater likelihood of bacterial vaginosis diagnosed by Amsel clinical criteria. This L. iners mgSs, among other functional features, encoded enhanced genetic capabilities for epithelial cell attachment that could facilitate cytotoxin-mediated cell lysis. Finally, we report a mgSs and mgCST classifier for which source code is provided and may be adapted for use by the microbiome research community.

CONCLUSIONS: MgCSTs are a novel and easily implemented approach to reduce the dimension of complex metagenomic datasets while maintaining their functional uniqueness. MgCSTs enable the investigation of multiple strains of the same species and the functional diversity in that species. Future investigations of functional diversity may be key to unraveling the pathways by which the vaginal microbiome modulates the protection of the genital tract. Importantly, our findings support the hypothesis that functional differences between vaginal microbiomes, including those that may look compositionally similar, are critical considerations in vaginal health. Ultimately, mgCSTs may lead to novel hypotheses concerning the role of the vaginal microbiome in promoting health and disease, and identify targets for novel prognostic, diagnostic, and therapeutic strategies to improve women's genital health. Video Abstract.}, } @article {pmid38031135, year = {2023}, author = {Sun, X and Zhang, Q and Shan, H and Cao, Z and Huang, J}, title = {Genome characteristics of atypical porcine pestivirus from abortion cases in Shandong Province, China.}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {282}, pmid = {38031135}, issn = {1743-422X}, support = {SDAIT-08-07//the Shandong Province Modern Agricultural Industry Technology System/ ; 2017YFD0500603//the China National Key R&D Program during the 13th Five-year Plan Period/ ; }, mesh = {Animals ; Swine ; Female ; *Pestivirus Infections/epidemiology/veterinary ; Phylogeny ; Genome, Viral ; *Swine Diseases/epidemiology/genetics ; *Pestivirus/genetics ; China/epidemiology ; Polyproteins/genetics ; }, abstract = {BACKGROUND: Atypical porcine pestivirus (APPV) is a novel, highly variable porcine pestivirus. Previous reports have suggested that the virus is associated with congenital tremor (CT) type A-II in piglets, and little information is available about the correlation between the virus and sow abortion, or on coinfection with other viruses. In China, reported APPV strains were mainly isolated from South China and Central China, and data about the APPV genome from northern China are relatively scarce.

METHODS: Eleven umbilical cords, one placenta, and one aborted piglet, were collected from aborted sows of the same farm in Shandong Province of northern China. Nucleic acids were extracted from the above samples, and subsequently pooled for viral metagenomics sequencing and bioinformatics analysis. The viral coexistence status and complete genome characteristics of APPV in Shandong Province were determined.

RESULTS: In abortion cases, APPV was present with Getah virus, porcine picobirnavirus, porcine kobuvirus, porcine sapovirus, Po-Circo-like virus, porcine serum-associated circular virus, porcine bocavirus 1, porcine parvovirus 1, porcine parvovirus 3 and porcine circovirus 3, etc. The first complete genome sequence(11,556 nt) of APPV in Shandong Province of northern China, was obtained using viral metagenomics and designated APPV-SDHY-2022. Comparison with Chinese reference strains revealed that the polyprotein of APPV-SDHY-2022 shared 82.6-84.2%, 93.2-93.6%, and 80.7-85% nucleotide identity and 91.4-92.4%, 96.4-97.7%, and 90.6-92.2% amino acid identity with those of the Clade I, Clade II and Clade III strains, respectively. Phylogenetic analysis based on the complete polyprotein CDS and NS5A sequences concluded that APPV-SDHY-2022 belongs to Clade II. Analysis of the NS5A nucleotide sequences revealed homology of greater than 94.6% for the same isoform, 84.7-94.5% for different isoforms of the same clade and 76.8-81.1% for different clades. Therefore, Clade II was further divided into three subclades, and APPV-SDHY-2022 belonged to subclade 2.3. Members of Clade II have 20 unique amino acids in individual proteins, distinguishing them from Clade I and Clade III members. The E2 protein showed the greatest diversity of putative N-glycosylation sites with 9 patterns, and APPV-SDHY-2022 along with other Chinese APPV strains shared the conserved B-cell conformational epitope residues 39E, 70R, 173R, 190K and 191N of the E2 protein.

CONCLUSIONS: We reported viral coexistence and the first complete genome sequence of APPV from abortion cases and from Shandong Province. The new APPV isolate belongs to an independent branch of Clade II. Our results increase the molecular and epidemiological understanding of APPV in China.}, } @article {pmid38031016, year = {2023}, author = {Li, P and Jiang, J and Li, Y and Lan, Y and Yang, F and Wang, J and Xie, Y and Xiong, F and Wu, J and Liu, H and Fan, Z}, title = {Metagenomic analysis reveals distinct changes in the gut microbiome of obese Chinese children.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {721}, pmid = {38031016}, issn = {1471-2164}, support = {No. 2023YFS0034 and 2020YFS0109//the Science and Technology Bureau of Sichuan Province/ ; No. KL119//the Clinical Discipline Development Fund of West China Second Hospital, Sichuan University/ ; SCU2022D022//the Fundamental Research Funds for the Central Universities/ ; }, mesh = {Humans ; Child ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Pediatric Obesity/genetics ; East Asian People ; Overweight ; Feces/microbiology ; }, abstract = {BACKGROUND: The prevalence of obese children in China is increasing, which poses a great challenge to public health. Gut microbes play an important role in human gut health, and changes in gut status are closely related to obesity. However, how gut microbes contribute to obesity in children remains unclear. In our study, we performed shotgun metagenomic sequencing of feces from 23 obese children, 8 overweight children and 22 control children in Chengdu, Sichuan, China.

RESULTS: We observed a distinct difference in the gut microbiome of obese children and that of controls. Compared with the controls, bacterial pathogen Campylobacter rectus was significantly more abundant in obese children. In addition, functional annotation of microbial genes revealed that there might be gut inflammation in obese children. The guts of overweight children might belong to the transition state between obese and control children due to a gradient in relative abundance of differentially abundant species. Finally, we compared the gut metagenomes of obese Chinese children and obese Mexican children and found that Trichuris trichiura was significantly more abundant in the guts of obese Mexican children.

CONCLUSIONS: Our results contribute to understanding the changes in the species and function of intestinal microbes in obese Chinese children.}, } @article {pmid38030652, year = {2023}, author = {Bacci, G and Meriggi, N and Cheng, CLY and Ng, KH and Iannucci, A and Mengoni, A and Cavalieri, D and Cannicci, S and Fratini, S}, title = {Species-specific gill's microbiome of eight crab species with different breathing adaptations.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {21033}, pmid = {38030652}, issn = {2045-2322}, support = {207080320.088562.26020.430.01//Hong Kong Government/ ; 260008686.088562.26000.400.01//TUYF Charitable Trust funds, Hong Kong/ ; CN00000033//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; }, mesh = {Humans ; Animals ; *Brachyura/physiology ; Gills/metabolism ; Respiration ; Respiratory Rate ; *Microbiota ; }, abstract = {Transitions to physically different environments, such as the water-to-land transition, proved to be the main drivers of relevant evolutionary events. Brachyuran crabs evolved remarkable morphological, behavioral, and physiological adaptations to terrestrial life. Terrestrial species evolved new respiratory structures devoted to replace or support the gills, a multifunctional organ devoted to gas exchanges, ion-regulation and nitrogen excretion. It was hypothesized that microorganisms associated with respiratory apparatus could have facilitated the processes of osmoregulation, respiration, and elimination of metabolites along this evolutionary transition. To test if crab species with different breathing adaptations may host similar microbial communities on their gills, we performed a comparative targeted-metagenomic analysis, selecting two marine and six terrestrial crabs belonging to different families and characterised by different breathing adaptations. We analysed anterior and posterior gills separately according to their different and specific roles. Regardless of their terrestrial or marine adaptations, microbial assemblages were strongly species-specific indicating a non-random association between the host and its microbiome. Significant differences were found in only two terrestrial species when considering posterior vs. anterior gills, without any association with species-specific respiratory adaptations. Our results suggest that all the selected species are strongly adapted to the ecological niche and specific micro-habitat they colonise.}, } @article {pmid38030613, year = {2023}, author = {Chen, B and Ramazzotti, D and Heide, T and Spiteri, I and Fernandez-Mateos, J and James, C and Magnani, L and Graham, TA and Sottoriva, A}, title = {Contribution of pks[+] E. coli mutations to colorectal carcinogenesis.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7827}, pmid = {38030613}, issn = {2041-1723}, support = {202778/B/16/Z//Wellcome Trust (Wellcome)/ ; }, mesh = {Humans ; Escherichia coli/genetics ; *Colorectal Neoplasms/genetics/pathology ; Mutation ; Carcinogenesis/genetics ; *Colonic Neoplasms ; }, abstract = {The dominant mutational signature in colorectal cancer genomes is C > T deamination (COSMIC Signature 1) and, in a small subgroup, mismatch repair signature (COSMIC signatures 6 and 44). Mutations in common colorectal cancer driver genes are often not consistent with those signatures. Here we perform whole-genome sequencing of normal colon crypts from cancer patients, matched to a previous multi-omic tumour dataset. We analyse normal crypts that were distant vs adjacent to the cancer. In contrast to healthy individuals, normal crypts of colon cancer patients have a high incidence of pks + (polyketide synthases) E.coli (Escherichia coli) mutational and indel signatures, and this is confirmed by metagenomics. These signatures are compatible with many clonal driver mutations detected in the corresponding cancer samples, including in chromatin modifier genes, supporting their role in early tumourigenesis. These results provide evidence that pks + E.coli is a potential driver of carcinogenesis in the human gut.}, } @article {pmid38029295, year = {2024}, author = {Lydon, E and Langelier, CR}, title = {Respiratory Metagenomics: Ready for Prime Time?.}, journal = {American journal of respiratory and critical care medicine}, volume = {209}, number = {2}, pages = {124-126}, doi = {10.1164/rccm.202311-2039ED}, pmid = {38029295}, issn = {1535-4970}, mesh = {Humans ; *Respiratory Tract Infections ; Metagenomics ; Intensive Care Units ; }, } @article {pmid38029249, year = {2023}, author = {Zhu, N and Zhou, D and Xiong, W and Zhang, X and Li, S}, title = {Performance of mNGS in bronchoalveolar lavage fluid for the diagnosis of invasive pulmonary aspergillosis in non-neutropenic patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1271853}, pmid = {38029249}, issn = {2235-2988}, mesh = {Humans ; *Invasive Pulmonary Aspergillosis/diagnosis ; Bronchoalveolar Lavage Fluid/microbiology ; Sensitivity and Specificity ; Lung ; High-Throughput Nucleotide Sequencing ; Retrospective Studies ; }, abstract = {The diagnosis of invasive pulmonary aspergillosis (IPA) diseases in non-neutropenic patients remains challenging. It is essential to develop optimal non-invasive or minimally invasive detection methods for the rapid and reliable diagnosis of IPA. Metagenomic next-generation sequencing (mNGS) in bronchoalveolar lavage fluid (BALF) can be a valuable tool for identifying the microorganism. Our study aims to evaluate the performance of mNGS in BALF in suspected IPA patients and compare it with other detection tests, including serum/BALF galactomannan antigen (GM) and traditional microbiological tests (BALF fungal culture and smear and lung biopsy histopathology). Ninety-four patients with suspicion of IPA were finally enrolled in our study. Thirty-nine patients were diagnosed with IPA, and 55 patients were non-IPA. There was significance between the IPA and non-IPA groups, such as BALF GM (P < 0.001), history of glucocorticoid use (P = 0.004), and pulmonary comorbidities (P = 0.002), as well as no significance of the other demographic data including age, sex, BMI, history of cigarette, blood GM assay, T-SPOT.TB, and NEUT#/LYMPH#. The sensitivity of the BALF mNGS was 92.31%, which was higher than that of the traditional tests or the GM assays. The specificity of BALF mNGS was 92.73%, which was relatively similar to that of the traditional tests. The AUC of BALF mNGS was 0.925, which presented an excellent performance compared with other traditional tests or GM assays. Our study demonstrated the important role of BALF detection by the mNGS platform for pathogen identification in IPA patients with non-neutropenic states, which may provide an optimal way to diagnose suspected IPA disease.}, } @article {pmid38029219, year = {2023}, author = {Wang, T and Liu, J and Luo, Y and Yu, B and Kong, X and Zheng, P and Huang, Z and Mao, X and Yu, J and Luo, J and Yan, H and He, J}, title = {Corrigendum: Combined effects of host genetics and diet on porcine intestinal fungi and their pathogenic genes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1319760}, doi = {10.3389/fmicb.2023.1319760}, pmid = {38029219}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2023.1192288.].}, } @article {pmid38029212, year = {2023}, author = {Tsiola, A and Michoud, G and Daffonchio, D and Fodelianakis, S and Giannakourou, A and Malliarakis, D and Pavlidou, A and Pitta, E and Psarra, S and Santi, I and Zeri, C and Pitta, P}, title = {Depth-driven patterns in lytic viral diversity, auxiliary metabolic gene content, and productivity in offshore oligotrophic waters.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1271535}, pmid = {38029212}, issn = {1664-302X}, abstract = {INTRODUCTION: Marine viruses regulate microbial population dynamics and biogeochemical cycling in the oceans. The ability of viruses to manipulate hosts' metabolism through the expression of viral auxiliary metabolic genes (AMGs) was recently highlighted, having important implications in energy production and flow in various aquatic environments. Up to now, the presence and diversity of viral AMGs is studied using -omics data, and rarely using quantitative measures of viral activity alongside.

METHODS: In the present study, four depth layers (5, 50, 75, and 1,000 m) with discrete hydrographic features were sampled in the Eastern Mediterranean Sea; we studied lytic viral community composition and AMG content through metagenomics, and lytic production rates through the viral reduction approach in the ultra-oligotrophic Levantine basin where knowledge regarding viral actions is rather limited.

RESULTS AND DISCUSSION: Our results demonstrate depth-dependent patterns in viral diversity and AMG content, related to differences in temperature, nutrients availability, and host bacterial productivity and abundance. Although lytic viral production rates were similar along the water column, the virus-to-bacteria ratio was higher and the particular set of AMGs was more diverse in the bathypelagic (1,000 m) than the shallow epipelagic (5, 50, and 75 m) layers, revealing that the quantitative effect of viruses on their hosts may be the same along the water column through the intervention of different AMGs. In the resource- and energy-limited bathypelagic waters of the Eastern Mediterranean, the detected AMGs could divert hosts' metabolism toward energy production, through a boost in gluconeogenesis, fatty-acid and glycan biosynthesis and metabolism, and sulfur relay. Near the deep-chlorophyll maximum depth, an exceptionally high percentage of AMGs related to photosynthesis was noticed. Taken together our findings suggest that the roles of viruses in the deep sea might be even more important than previously thought as they seem to orchestrate energy acquisition and microbial community dynamics, and thus, biogeochemical turnover in the oceans.}, } @article {pmid38029196, year = {2023}, author = {Malik, PK and Trivedi, S and Kolte, AP and Mohapatra, A and Biswas, S and Bhattar, AVK and Bhatta, R and Rahman, H}, title = {Comparative analysis of rumen metagenome, metatranscriptome, fermentation and methane yield in cattle and buffaloes fed on the same diet.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1266025}, pmid = {38029196}, issn = {1664-302X}, abstract = {A study to compare the rumen microbial community composition, functional potential of the microbiota, methane (CH4) yield, and rumen fermentation was conducted in adult male cattle and buffaloes fed on the same diet. A total of 41 phyla, 169 orders, 374 families, and 1,376 microbial genera were identified in the study. Bacteroidetes and Firmicutes were the two most dominant bacterial phyla in both cattle and buffaloes. However, there was no difference in the abundance of Bacteroidetes and Firmicutes in the rumen metagenome of cattle and buffaloes. Based on the abundance, the Proteobacteria was the 3rd largest phylum in the metagenome, constituting 18-20% in both host species. Euryarchaeota was the most abundant phylum of the methanogens, whereas Methanobacteriales and Methanobrevibacter were the most abundant orders and genera in both species. The methanogen abundances were not different between the two host species. Like the metagenome, the difference between the compositional and functional abundances (metagenome vs. metatranscriptome) of the Bacteroidetes and Firmicutes was not significant, whereas the proteobacteria were functionally less active than their metagenomic composition. Contrary to the metagenome, the Euryarchaeota was the 3rd most functional phylum in the rumen and constituted ~15% of the metatranscriptome. Methanobacteriales were the most functional methanogens, accounting for more than 2/3rd of the total archaeal functionality. These results indicated that the methanogens from Euryarchaeota were functionally more active as compared to their compositional abundance. The CH4 yield (g/kg DMI), CH4 emission (g/kg DDM), dry matter (DM) intake, and rumen fermentation did not vary between the two host species. Overall, the study established a substantial difference between the compositional abundances and metabolic functionality of the rumen microbiota; however, feeding cattle and buffaloes on the same diet resulted in similar microbiota composition, metabolic functionality, and CH4 yield. Further studies are warranted to investigate the effect of different diets and environments on the composition and metabolic functionality of the rumen microbiota.}, } @article {pmid38029184, year = {2023}, author = {Ye, L and Zhang, B and Zhang, L and Yang, X and Tan, W and Zhang, X and Li, X}, title = {Pathogenic invasive microbes Trichoderma pleuroticola transform bacterial and fungal community diversity in Auricularia cornea crop production system.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1263982}, pmid = {38029184}, issn = {1664-302X}, abstract = {Pathogenic invasion of Trichoderma pleuroticola profoundly altered microflora in the Auricularia cornea crop production system, impacting diversity and composition in both artificial bed-log and fruiting bodies. A more complex ecological network between the diseased and healthy bodies. Researchers still have poor knowledge about how the important agricultural relationship between the composition of the microbiome of the artificial bed-log and the fruiting bodies is infected by the pathogenic invasive microbes T. pleuroticola, but this knowledge is crucial if we want to use or improve it. Here, we investigated 8 groups (48 biological samples) across 5 growth stages of the A. cornea production system using metagenomic technology. Diseased and healthy fruiting bodies exhibited distinct microbial compositions, while core members in artificial bed-logs remained stable. Core microbiota analysis highlighted Pseudomonas and Pandoraea bacterial genera, as well as Sarocladium, Cephalotrichum, Aspergillus, and Mortierella fungal genera as biomarker species after the bodies were treated with the pathogenic invasive microbes T. pleuroticola. In diseased bodies, these core members upregulated pathways including polymyxin resistance, L-arginine degradation II, superpathway of L-arginine and L-ornithine degradation, glucose degradation (oxidative), glucose and glucose-1-phosphate degradation, promoting fruit spoilage. Our data confirm that T. pleuroticola plays an important role in the early stages of disease development in the A. cornea crop generation system. The exposed volatile core microbiome may play an important role in accelerating T. pleuroticola-induced decay of fruiting bodies.}, } @article {pmid38029171, year = {2023}, author = {Barak, H and Fuchs, N and Liddor-Naim, M and Nir, I and Sivan, A and Kushmaro, A}, title = {Microbial dark matter sequences verification in amplicon sequencing and environmental metagenomics data.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1247119}, pmid = {38029171}, issn = {1664-302X}, abstract = {Although microorganisms constitute the most diverse and abundant life form on Earth, in many environments, the vast majority of them remain uncultured. As it is based on information gleaned mainly from cultivated microorganisms, our current body of knowledge regarding microbial life is partial and does not reflect actual microbial diversity. That diversity is hidden in the uncultured microbial majority, termed by microbiologists as "microbial dark matter" (MDM), a term borrowed from astrophysics. Metagenomic sequencing analysis techniques (both 16S rRNA gene and shotgun sequencing) compare gene sequences to reference databases, each of which represents only a small fraction of the existing microorganisms. Unaligned sequences lead to groups of "unknown microorganisms" that are usually ignored and rarefied from diversity analysis. To address this knowledge gap, we analyzed the 16S rRNA gene sequences of microbial communities from four different environments-a living organism, a desert environment, a natural aquatic environment, and a membrane bioreactor for wastewater treatment. From those datasets, we chose representative sequences of potentially unknown bacteria for additional examination as "microbial dark matter sequences" (MDMS). Sequence existence was validated by specific amplification and re-sequencing. These sequences were screened against databases and aligned to the Genome Taxonomy Database to build a comprehensive phylogenetic tree for additional sequence classification, revealing potentially new candidate phyla and other lineages. These putative MDMS were also screened against metagenome-assembled genomes from the explored environments for additional validation and for taxonomic and metabolic characterizations. This study shows the immense importance of MDMS in environmental metataxonomic analyses of 16S rRNA gene sequences and provides a simple and readily available methodology for the examination of MDM hidden behind amplicon sequencing results.}, } @article {pmid38029168, year = {2023}, author = {Xu, J and Kong, X and Li, J and Mao, H and Zhu, Y and Zhu, X and Xu, Y}, title = {Pediatric intensive care unit treatment alters the diversity and composition of the gut microbiota and antimicrobial resistance gene expression in critically ill children.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1237993}, pmid = {38029168}, issn = {1664-302X}, abstract = {INTRODUCTION: Common critical illnesses are a growing economic burden on healthcare worldwide. However, therapies targeting the gut microbiota for critical illnesses have not been developed on a large scale. This study aimed to investigate the changes in the characteristics of the gut microbiota in critically ill children after short-term pediatric intensive care unit (PICU) treatments.

METHODS: Anal swab samples were prospectively collected from March 2021 to March 2022 from children admitted to the PICU of Xinhua Hospital who received broad-spectrum antibiotics on days 1 (the D1 group) and 7 (the D7 group) of the PICU treatment. The structural and functional characteristics of the gut microbiota of critically ill children were explored using metagenomic next-generation sequencing (mNGS) technology, and a comparative analysis of samples from D1 and D7 was conducted.

RESULTS: After 7 days of PICU admission, a significant decrease was noted in the richness of the gut microbiota in critically ill children, while the bacterial diversity and the community structure between groups remained stable to some extent. The relative abundance of Bacilli and Lactobacillales was significantly higher, and that of Campylobacter hominis was significantly lower in the D7 group than in the D1 group. The random forest model revealed that Prevotella coporis and Enterobacter cloacae were bacterial biomarkers between groups. LEfSe revealed that two Gene Ontology entries, GO:0071555 (cell wall organization) and GO:005508 (transmembrane transport), changed significantly after the short-term treatment in the PICU. In addition, 30 KEGG pathways were mainly related to the activity of enzymes and proteins during the processes of metabolism, DNA catabolism and repair, and substance transport. Finally, 31 antimicrobial resistance genes had significantly different levels between the D7 and D1 groups. The top 10 up-regulated genes were Erm(A), ErmX, LptD, eptB, SAT-4, tetO, adeJ, adeF, APH(3')-IIIa, and tetM.

CONCLUSION: The composition, gene function, and resistance genes of gut microbiota of critically ill children can change significantly after short PICU treatments. Our findings provide a substantial basis for a better understanding of the structure and function of gut microbiota and their role in critical illnesses.}, } @article {pmid38029158, year = {2023}, author = {Arunrat, N and Sansupa, C and Sereenonchai, S and Hatano, R}, title = {Stability of soil bacteria in undisturbed soil and continuous maize cultivation in Northern Thailand.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1285445}, pmid = {38029158}, issn = {1664-302X}, abstract = {Rotational shifting cultivation (RSC) in Northern Thailand serves the dual purpose of ensuring food security and meeting economic goals through maize cultivation. However, the research question remains: Does the dynamics of soil bacterial communities differ between maize monoculture and RSC fields with continuous fallow throughout the season? Therefore, the objective of this study was to investigate and compare the variation of soil bacterial communities in maize monoculture and fallow RSC fields. A continuous 5-year fallow field (undisturbed soil; CF-5Y) and a continuous 5-year maize cultivation field (M-5Y) in Mae Chaem District, Chiang Mai Province, Northern Thailand, were selected due to their similarities in microclimate, topography, and the 5-year duration of different field activities. Over the span of a year, we collected soil samples from the surface layer (0-2 cm depth) at both sites. These collections occurred at 3-month intervals, starting from March 2022 (summer season) and followed by June (rainy season), September (rainy season), December (winter season), and March 2023 (summer season). Soil bacterial diversity and composition were analyzed using 16S rRNA gene-based metagenomic analysis. The results found that undisturbed soil over a 5-year period exhibited more stability in the richness and diversity of bacteria across seasons compared with M-5Y. Notably, fertilizer application and tillage practices in M-5Y can enhance both the diversity and richness of soil bacteria. In terms of bacterial abundance, Proteobacteria prevailed in CF-5Y, while Actinobacteria dominated in M-5Y. At the genus level, Candidatus Udaeobacter dominated during the summer and winter seasons in both CF-5Y and M-5Y sites. Interestingly, during the rainy season, the dominant genus shifted to Bacillus in both CF-5Y and M-5Y fields. The soil bacterial community in M-5Y was strongly influenced by organic matter (OM) and organic carbon (OC). In contrast, in CF-5Y, there was no correlation between soil properties and the soil bacterial community, likely due to the lower variation in soil properties across seasons. β-Glucosidase was the dominant enzyme in both CF-5Y and M-5Y sites, and it showed a positive correlation with OM and OC. Further studies should continue to investigate soil bacteria dynamics, considering the changes in land management practices.}, } @article {pmid38029096, year = {2023}, author = {Hu, Y and Zhang, K and Li, N and Wang, S}, title = {Composition, antibiotic resistance, and virulence analysis of microbiota in dormitory drain pipes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1272605}, pmid = {38029096}, issn = {1664-302X}, abstract = {INTRODUCTION: Dormitory washbasins can breed microorganisms that produce odorous gases, polluting the indoor environment.

METHODS: We utilized metagenome sequencing to analyze the microbiota of 40 samples from the drain pipes of dormitory washbasins. Our study aimed to investigate the microbial community structure, antibiotic resistance genes, and virulence factors, and to identify potential influencing factors such as gender, hometown, frequency of hand sanitizer usage, and number of dormitory residents.

RESULTS: The analysis revealed 12 phyla and 147 genera, with Proteobacteria and Actinobacteria being the dominant phyla, and Mycobacterium and Nakamurella being the dominant genera. We found that the factors influencing the microbial community structure of the dormitory washbasin drain pipe are complex. The investigated factors have a slight influence on the drain pipe microbial community, with gender exerting a discernible influence. The annotation results revealed the presence of various virulence factors, pathogenic toxins and antibiotic resistance genes, including 246 different toxin types and 30 different types of antibiotic resistance genes. In contrast to the observed differences in microbial composition among samples, the distribution of resistance genes shows relatively small changes among samples. Antibiotics should be a contributing factor in the overall increase of antibiotic resistance genes in drain pipes.

DISCUSSION: Overall, our study provides important insights into the community structure and function of microorganisms in dormitory drainage systems, and can guide efforts to prevent and control microbial pollution.}, } @article {pmid38029094, year = {2023}, author = {Semenov, M and Li, H and Luo, Y and Deng, Y and Kuzyakov, Y}, title = {Editorial: Microbial regulation of soil carbon cycling in terrestrial ecosystems.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1295624}, pmid = {38029094}, issn = {1664-302X}, } @article {pmid38029086, year = {2023}, author = {Yang, J and He, Y and Liao, X and Hu, J and Li, K}, title = {Does postoperative pulmonary infection correlate with intestinal flora following gastric cancer surgery? - a nested case-control study.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1267750}, pmid = {38029086}, issn = {1664-302X}, abstract = {INTRODUCTION: The primary objective of this study was to investigate the potential correlation between gut microbes and postoperative pulmonary infection in gastric cancer patients. Additionally, we aimed to deduce the mechanism of differential functional genes in disease progression to gain a better understanding of the underlying pathophysiology.

METHODS: A nested case-control study design was utilized to enroll patients with gastric cancer scheduled for surgery at West China Hospital of Sichuan University. Patients were categorized into two groups, namely, the pulmonary infection group and the control group, based on the development of postoperative pulmonary infection. Both groups were subjected to identical perioperative management protocols. Fecal samples were collected 24 h postoperatively and upon pulmonary infection diagnosis, along with matched controls. The collected samples were subjected to 16S rDNA and metagenomic analyses, and clinical data and blood samples were obtained for further analysis.

RESULTS: A total of 180 fecal specimens were collected from 30 patients in both the pulmonary infection and control groups for 16S rDNA analysis, and 3 fecal samples from each group were selected for metagenomic analysis. The study revealed significant alterations in the functional genes of the intestinal microbiome in patients with postoperative pulmonary infection in gastric cancer, primarily involving Klebsiella, Enterobacter, Ruminococcus, and Collinsella. During postoperative pulmonary infection, gut flora and inflammatory factors were found to be associated with the lipopolysaccharide synthesis pathway and short-chain fatty acid (SCFA) synthesis pathway.

DISCUSSION: The study identified enriched populations of Klebsiella, Escherella, and intestinal bacteria during pulmonary infection following gastric cancer surgery. These bacteria were found to regulate the lipopolysaccharide synthesis pathway, contributing to the initiation and progression of pulmonary infections. Inflammation modulation in patients with postoperative pulmonary infection may be mediated by short-chain fatty acids. The study also revealed that SCFA synthesis pathways were disrupted, affecting inflammation-related immunosuppression pathways. By controlling and maintaining intestinal barrier function, SCFAs may potentially reduce the occurrence of pulmonary infections after gastric cancer surgery. These findings suggest that targeting the gut microbiome and SCFA synthesis pathways may be a promising approach for preventing postoperative pulmonary infections in gastric cancer patients.}, } @article {pmid38028147, year = {2023}, author = {Edgar, R}, title = {Known phyla dominate the Tara Oceans RNA virome.}, journal = {Virus evolution}, volume = {9}, number = {2}, pages = {vead063}, pmid = {38028147}, issn = {2057-1577}, abstract = {A recent study proposed five new RNA virus phyla, two of which, 'Taraviricota' and 'Arctiviricota', were stated to be 'dominant in the oceans'. However, the study's assignments classify 28,353 putative RdRp-containing contigs to known phyla but only 886 (2.8%) to the five proposed new phyla combined. I re-mapped the reads to the contigs, finding that known phyla also account for a large majority (93.8%) of reads according to the study's classifications, and that contigs originally assigned to 'Arctiviricota' accounted for only a tiny fraction (0.01%) of reads from Arctic Ocean samples. Performing my own virus identification and classifications, I found that 99.95 per cent of reads could be assigned to known phyla. The most abundant species was Beihai picorna-like virus 34 (15% of reads), and the most abundant order-like cluster was classified as Picornavirales (45% of reads). Sequences in the claimed new phylum 'Pomiviricota' were placed inside a phylogenetic tree for established order Durnavirales with 100 per cent confidence. Moreover, two contigs assigned to the proposed phylum 'Taraviricota' were found to have high-identity alignments to dinoflagellate proteins, tentatively identifying this group of RdRp-like sequences as deriving from non-viral transcripts. Together, these results comprehensively contradict the claim that new phyla dominate the data.}, } @article {pmid38028014, year = {2023}, author = {Liu, W and Peng, L and Chen, L and Wan, J and Lou, S and Yang, T and Shen, Z}, title = {Skin microbial dysbiosis is a characteristic of systemic drug-related intertriginous and flexural exanthema-like lesions induced by EGFR inhibitor.}, journal = {Heliyon}, volume = {9}, number = {11}, pages = {e21690}, pmid = {38028014}, issn = {2405-8440}, abstract = {OBJECTIVES: To investigate the characteristics of the skin microbiome in severe afatinib-induced skin toxicity.

METHODS: Body site-matched skin surface samples were collected from the lesions on seven flexural sites of one lung cancer (Patient 1) with serious systemic drug-related intertriginous and flexural exanthema (SDRIFE)-like toxicity induced by EGFR-TKI and three healthy age/sex matched controls for whole metagenomics sequencing analysis. Lung cancer Patient 1 and Patient 2 were prescribed minocycline and followed up.

RESULTS: In SDRIFE-like toxicities induced by afatinib, lesion microbiota richness (ACE and Chao1 index: p < 0.001) and diversity (Shannon's and Simpson's diversity indices: p < 0.01) were reduced. Similarly, the beta diversity analysis (R = 1, p = 0.002 for ANOSIM) showed that the apparent difference in the microbiota composition was statistically significant. The microbial taxa composition in the patient showed an increased abundance of pathogenic bacteria and a decreased abundance of commensal bacteria. LEfSe analysis identified strong bacterial pathogenicity in the patient, while healthy controls exhibited enrichment in several pathways that are beneficial for skin commensal bacteria and skin physiology, including key amino acid metabolism, energy/lipid/glycan biosynthesis/metabolism, and cofactors/vitamins biosynthesis. Ultimately, the patients experienced significant improvement with minocycline.

CONCLUSION: Microbial dysbiosis is a characteristic of severe SDRIFE-like toxicity induced by afatinib.}, } @article {pmid38027571, year = {2023}, author = {Curini, V and Ancora, M and Jurisic, L and Di Lollo, V and Secondini, B and Mincarelli, LF and Caporale, M and Puglia, I and Di Gialleonardo, L and Mangone, I and Di Domenico, M and Di Pasquale, A and Lorusso, A and Marcacci, M and Cammà, C}, title = {Evaluation of next generation sequencing approaches for SARS-CoV-2.}, journal = {Heliyon}, volume = {9}, number = {11}, pages = {e21101}, pmid = {38027571}, issn = {2405-8440}, abstract = {Within public health control strategies for SARS-CoV-2, whole genome sequencing (WGS) is essential for tracking viral spread and monitoring the emergence of variants which may impair the effectiveness of vaccines, diagnostic methods, and therapeutics. In this manuscript different strategies for SARS-CoV-2 WGS including metagenomic shotgun (SG), library enrichment by myBaits® Expert Virus-SARS-CoV-2 (Arbor Biosciences), nCoV-2019 sequencing protocol, ampliseq approach by Swift Amplicon® SARS-CoV-2 Panel kit (Swift Biosciences), and Illumina COVIDSeq Test (Illumina Inc.), were evaluated in order to identify the best approach in terms of results, labour, and costs. The analysis revealed that Illumina COVIDSeq Test (Illumina Inc.) is the best choice for a cost-effective, time-consuming production of consensus sequences.}, } @article {pmid38027226, year = {2023}, author = {Tang, J and Han, Y and Pei, L and Gu, W and Qiu, R and Wang, S and Ma, Q and Gan, Y and Tang, M}, title = {Comparative analysis of the rhizosphere microbiome and medicinally active ingredients of Atractylodes lancea from different geographical origins.}, journal = {Open life sciences}, volume = {18}, number = {1}, pages = {20220769}, pmid = {38027226}, issn = {2391-5412}, abstract = {This study aimed to explore the important role of the rhizosphere microbiome in the quality of Atractylodes lancea (Thunb.) DC. (A. lancea). The rhizosphere microbial community of A. lancea at two sampling sites was studied using metagenomic technology. The results of α-diversity analysis showed that the rhizosphere microbial richness and diversity were higher in the Maoshan area. The higher abundance of core microorganisms of the rhizosphere, especially Penicillium and Streptomyces, in the Maoshan area compared with those in the Yingshan area might be an important factor affecting the yield of A. lancea. Redundancy analysis illustrated that the available phosphorus had a significant effect on the rhizosphere microbial community structure of A. lancea. We also showed that the plant-microbe and microbe-microbe interactions were closer in the Maoshan area than in the Yingshan area, and Streptomyces were the main contributors to the potential functional difference between the two regions. A. lancea in the Maoshan area had a high content of atractylodin and atractylon, which might be related to the enhanced abundance of Streptomyces, Candidatus-Solibacter, and Frankia. Taken together, this study provided theoretical insights into the interaction between medicinal plants and the rhizosphere microbiome and provides a valuable reference for studying beneficial microbes of A. lancea.}, } @article {pmid38026211, year = {2023}, author = {Ghaly, TM and Rajabal, V and Penesyan, A and Coleman, NV and Paulsen, IT and Gillings, MR and Tetu, SG}, title = {Functional enrichment of integrons: Facilitators of antimicrobial resistance and niche adaptation.}, journal = {iScience}, volume = {26}, number = {11}, pages = {108301}, pmid = {38026211}, issn = {2589-0042}, abstract = {Integrons are genetic elements, found among diverse bacteria and archaea, that capture and rearrange gene cassettes to rapidly generate genetic diversity and drive adaptation. Despite their broad taxonomic and geographic prevalence, and their role in microbial adaptation, the functions of gene cassettes remain poorly characterized. Here, using a combination of bioinformatic and experimental analyses, we examined the functional diversity of gene cassettes from different environments. We find that cassettes encode diverse antimicrobial resistance (AMR) determinants, including those conferring resistance to antibiotics currently in the developmental pipeline. Further, we find a subset of cassette functions is universally enriched relative to their broader metagenomes. These are largely involved in (a)biotic interactions, including AMR, phage defense, virulence, biodegradation, and stress tolerance. The remainder of functions are sample-specific, suggesting that they confer localised functions relevant to their microenvironment. Together, they comprise functional profiles different from bulk metagenomes, representing niche-adaptive components of the prokaryotic pangenome.}, } @article {pmid38026022, year = {2023}, author = {Tarnowski, MJ and Varliero, G and Scown, J and Phelps, E and Gorochowski, TE}, title = {Soil as a transdisciplinary research catalyst: from bioprospecting to biorespecting.}, journal = {Royal Society open science}, volume = {10}, number = {11}, pages = {230963}, pmid = {38026022}, issn = {2054-5703}, abstract = {The vast microbial biodiversity of soils is beginning to be observed and understood by applying modern DNA sequencing techniques. However, ensuring this potentially valuable information is used in a fair and equitable way remains a challenge. Here, we present a public engagement project that explores this topic through collaborative research of soil microbiomes at six urban locations using nanopore-based DNA sequencing. The project brought together researchers from the disciplines of synthetic biology, environmental humanities and microbial ecology, as well as school students aged 14-16 years old, to gain a broader understanding of views on the use of data from the environment. Discussions led to the transformation of 'bioprospecting', a metaphor with extractive connotations which is often used to frame environmental DNA sequencing studies, towards a more collaborative approach-'biorespecting'. This shift in terminology acknowledges that genetic information contained in soil arises as a result of entire ecosystems, including the people involved in its creation. Therefore, any use of sequence information should be accountable to the ecosystems from which it arose. As knowledge can arise from ecosystems and communities, science and technology should acknowledge this link and reciprocate with care and benefit-sharing to help improve the wellbeing of future generations.}, } @article {pmid38025767, year = {2023}, author = {Sun, H and Su, X and Liu, Y and Li, G and Du, Q}, title = {Roseburia intestinalis relieves intrahepatic cholestasis of pregnancy through bile acid/FXR-FGF15 in rats.}, journal = {iScience}, volume = {26}, number = {12}, pages = {108392}, pmid = {38025767}, issn = {2589-0042}, abstract = {Previous research has demonstrated significant differences in intestinal flora between pregnant women with intrahepatic cholestasis of pregnancy (ICP) and healthy pregnant women. The objective of our study is to identify the key bacteria involved in ICP rats and explore the underlying mechanism. We established an ICP rat model and collected rat feces for metagenomic sequencing and found that Roseburia intestinalis (R.I) is the key bacteria in ICP. Transplantation of R.I improved phenotypes associated with ICP through the bile acid/farnesoid X receptor-fibroblast growth factor 15 (FXR-FGF15) signaling pathway. We used the FXR antagonist Z-Guggulsterone (Z-Gu) to verify the key role of FXR in ICP and found that Z-Gu reversed the benefits of R.I on ICP rats. Our research highlights the important role of intestinal flora in the pathogenesis of ICP and provides a novel approach for its treatment.}, } @article {pmid38025758, year = {2023}, author = {Rodriguez Ruiz, A and Van Dam, AR}, title = {Metagenomic binning of PacBio HiFi data prior to assembly reveals a complete genome of Cosmopolites sordidus (Germar) (Coleopterea: Curculionidae, Dryophthorinae) the most damaging arthropod pest of bananas and plantains.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16276}, pmid = {38025758}, issn = {2167-8359}, mesh = {Animals ; *Weevils ; *Musa ; *Plantago ; *Arthropods ; Metagenome ; }, abstract = {PacBio HiFi sequencing was employed in combination with metagenomic binning to produce a high-quality reference genome of Cosmopolites sordidus. We compared k-mer and alignment reference based pre-binning and post-binning approaches to remove contamination. We were also interested to know if the post-binning approach had interspersed bacterial contamination within intragenic regions of Arthropoda binned contigs. Our analyses identified 3,433 genes that were composed with reads identified as of putative bacterial origins. The pre-binning approach yielded a C. sordidus genome of 1.07 Gb genome composed of 3,089 contigs with 98.6% and 97.1% complete and single copy genome and protein BUSCO scores respectively. In this article we demonstrate that in this case the pre-binning approach does not sacrifice assembly quality for more stringent metagenomic filtering. We also determine post-binning allows for increased intragenic contamination increased with increasing coverage, but the frequency of gene contamination increased with lower coverage. Future work should focus on developing reference free pre-binning approaches for HiFi reads produced from eukaryotic based metagenomic samples.}, } @article {pmid38025161, year = {2023}, author = {Chowdhary, A and Van Gelder, RN and Sundararajan, M}, title = {Methodologic Considerations for Studying the Ocular Surface Microbiome.}, journal = {Ophthalmology science}, volume = {3}, number = {4}, pages = {100408}, pmid = {38025161}, issn = {2666-9145}, abstract = {UNLABELLED: The ocular surface microbiome, unlike that of the skin or gut, has not been well characterized. Culture experiments historically suggested a nearly sterile ocular surface, but initial application of molecular methods such as 16S ribosomal RNA and high-throughput sequencing demonstrated a surprisingly rich ocular surface microbiome. However, a major limitation in studying such a low-biomass niche is the potential for artifactual results when amplification-based techniques such as ribosomal polymerase chain reaction and shotgun sequencing are used. It will be essential to establish standards across the field for sample collection, positive and negative controls, and limitation of contamination in both the laboratory setting and computational analysis. New developments in ocular microbiome research, including the generation of reference reagents and fluoroscopic imaging techniques, provide improved means to validate sequencing results and to visualize complex interactions between host cells and bacteria. Through more thorough characterization of the ocular surface microbiome, the connections between a dysregulated surface and ophthalmic disease may be better understood.

FINANCIAL DISCLOSURES: Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.}, } @article {pmid38024365, year = {2023}, author = {Chen, C and Wen, LF and Yang, LX and Li, J and Kan, QX and Xu, T and Liu, Z and Fu, JY and Cao, Y}, title = {Metagenomic and metaproteomic analyses of microbial amino acid metabolism during Cantonese soy sauce fermentation.}, journal = {Frontiers in nutrition}, volume = {10}, number = {}, pages = {1271648}, pmid = {38024365}, issn = {2296-861X}, abstract = {Cantonese soy sauce is an important type of traditional Chinese brewed soy sauce that was developed in southern China, mainly in Guangdong. Due to the long fermentation period and complex microbiota in Cantonese soy sauce, there are few reports on the microbial metaproteomics of Cantonese soy sauce. In this study, integrative metagenomic and metaproteomic analyzes were used to identify the changes in the dominant microbiota and amino acid synthesis-related enzymes and metabolism during Cantonese soy sauce fermentation. Metagenomic analysis revealed that Tetragenococcus halophilus, Weissella confusa, Weissella paramesenteroides, Enterobacter hormaechei, and Aspergillus oryzae were the dominant microbiota. Using the Top 15 dominant microbiota identified by metagenomics as the database, LTQ Orbitrap Velos Pro ETD mass spectrometry was used to obtain metaproteomic information about the microbes in the soy sauce, and the results indicated that the active enzymes involved in the metabolism of amino acids were secreted by microorganisms such as A. oryzae, T. halophilus, and Zygosaccharomyces rouxii. During the Cantonese soy sauce fermentation process. Among them, early fermentation (0-15d) was dominated by A. oryzae and T. halophilus, mid-term fermentation (60-90d) was dominated by Z. rouxii, A. oryzae, and T. halophilus, and late fermentation (90-120d) was dominated by A. oryzae, Z. rouxii, and T. halophilus. Kyoto Encyclopedia of Genes and Genomes analysis revealed that the main enzymes involved in the metabolism of umami amino acids were aspartate aminotransferase, citrate synthase, aconitase, and isocitrate dehydrogenase, which were produced by Z. rouxii and A. oryzae during early fermentation (0-15 d) and the middle fermentation stage (60-90 d). This study constructed a regulatory network of enzymes potentially involved in the metabolism of flavor amino acids, which provided a theoretical basis for studying the amino acid metabolism of Cantonese soy sauce.}, } @article {pmid38024253, year = {2023}, author = {Yi, B and Deng, Q and Guo, C and Li, X and Wu, Q and Zha, R and Wang, X and Lu, J}, title = {Evaluating the zoonotic potential of RNA viromes of rodents provides new insight into rodent-borne zoonotic pathogens in Guangdong, China.}, journal = {One health (Amsterdam, Netherlands)}, volume = {17}, number = {}, pages = {100631}, pmid = {38024253}, issn = {2352-7714}, abstract = {Emerging and re-emerging infectious diseases have been on the rise, with a significant proportion being zoonotic. Rodents, as the natural reservoirs of numerous diverse zoonotic viruses, pose a substantial threat to human health. To investigate the diversity of known and unknown viruses harbored by rodents in Guangdong (southern province of China), we conducted a comprehensive analysis of viral genomes through metagenomic sequencing of organs from 194 rodents. Our analysis yielded 2163 viral contigs that were assigned to 25 families known to infect a wide range of hosts, including vertebrates, invertebrates, amoebas, and plants. The viral compositions vary considerably among different organs, but not in rodent species. We also assessed and prioritized zoonotic potential of those detected viruses. Ninety-two viral species that are either known to infect vertebrates and invertebrates or only vertebrates were identified, among which 21 are considered high-risk to humans. The high-risk viruses included members of the Hantavirus, Picobirnaviruses, Astroviruses and Pestivirus. The phylogenetic trees of four zoonotic viruses revealed features of novel viral genomes that seem to fit evolutionarily into a zone of viruses that potentially pose a risk of transmission to humans. Recognizing that zoonotic diseases are a One Health issue, we approached the problem of identifying the zoonotic risk from rodent-transmitted disease in the Guangdong province by performing next-generation sequencing to look for potentially zoonotic viruses in these animals.}, } @article {pmid38023409, year = {2023}, author = {Du, J and Tao, Y and Yang, J and Cai, J and Zhou, H and Zhang, R and Hu, Y}, title = {Case Report: Metagenomic Next-Generation Sequencing Confirmed a Case of Spine Infection with Brucella melitensis in Non-Endemic Area.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {7219-7225}, pmid = {38023409}, issn = {1178-6973}, abstract = {Brucellosis is a zoonotic disease caused by Brucella spp., with the highest prevalence found in the northern cities of China. In this case report, we present an occurrence of spinal infection caused by B. melitensis in a 67-year-old man residing in a non-endemic area of southern China. The patient initially presented with chest and back pain, which was not accurately diagnosed and treated at a local hospital. Subsequently, due to worsening pain, he was admitted to our hospital. To determine the cause of the infection, we performed CT-guided aspiration biopsy and collected biopsy tissue for metagenomic next-generation sequencing (mNGS) on the second day of hospitalization. Imaging investigations revealed involvement of the thoracic vertebrae, specifically thoracic 4-7 with the main focus on 5-6, accompanied by stenosis of the intervertebral space. The mNGS results indicated that the spine infection was caused by B. melitensis. The patient's history as a shepherd and a positive Rose Bengal plate test (RBPT) further supported the diagnosis of brucella spondylitis. In order to alleviate pain and restore spinal function, the patient underwent posterior internal fixation of the thoracic spine. Treatment was initiated with cefoperazone/sulbactam, followed by doxycycline. Subsequently, the patient was switched to a combination therapy of rifampicin and doxycycline for a duration of six weeks. The patient responded well to treatment, and his condition remained stable. In conclusion, brucellosis is a common disease that can be easily misdiagnosed. This case report highlights the potential value of mNGS in early and rapid diagnosis. We believe that mNGS can serve as an effective tool to improve the diagnosis of spine infections caused by this pathogen.}, } @article {pmid38023405, year = {2023}, author = {Wang, J and Zhou, H and Dong, Z and Wang, J and Wang, R and Guan, Y}, title = {Diagnosis of Two Meningitis Cases Caused by Rickettsia Felis in China, with Metagenomic Next-Generation Sequencing: A Case Report.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {7239-7245}, pmid = {38023405}, issn = {1178-6973}, abstract = {BACKGROUND: Rickettsia felis is a kind of zoonotic pathogen. Rickettsia felis infections of the central nervous system are rare with only a few cases reported worldwide. The early diagnosis of R. felis is difficult due to its nonspecific clinical features and laboratory tests. Here, we report two meningitis cases caused by R. felis using metagenomic next-generation sequencing (mNGS).

METHODS: The clinical data of patients with meningitis who were diagnosed to have R. felis through cerebrospinal fluid culture, nuclear magnetic imaging, mNGS detection from January 2019 to December 2019 in The First Clinical Hospital of Shanxi Medical University, were retrospectively analyzed, and their clinical characteristics and disease regression findings were summarized.

CASE PRESENTATION: The first case was a female patient aged 23 years who was admitted to our hospital presenting with symptoms of headache, fever, and weakness in both lower limbs. Upon examination of spinal imaging, myelitis was diagnosed. However, routine examination and culture of cerebrospinal fluid did not identify the pathogen responsible. Subsequently, metagenomic second-generation sequencing (mNGS) revealed that the infection was caused by R. felis. The patient responded well to standard treatment and showed signs of recovery. The second case was a male patient aged 29 years who was admitted to our hospital with a headache and fever that had persisted for 4 days within a month. Routine examination and culture of the cerebrospinal fluid did not reveal any identifiable pathogens. However, metagenomic second-generation sequencing (mNGS) determined that the patient had a Rickettsial infection likely transmitted by a cat. The patient showed significant improvement after 14 days of doxycycline treatment. Tests for herpes simplex virus, cytomegalovirus, Epstein-Barr virus and tubercle bacillus nucleic acid in the CSF and blood were negative.Therefore mNGS of the cerebrospinal fluid was used, which identified the pathogen as R. felis. One case was diagnosed as subacute meningitis with immune-associated myelitis and the other as subacute meningitis.

CONCLUSION: mNGS of cerebrospinal fluid can be used as a fast and effective method to identify intracranial R. felis infections.}, } @article {pmid38023399, year = {2023}, author = {Li, X and Feng, Y and Li, D and Chen, L and Shen, M and Li, H and Li, S and Wu, X and Lu, L}, title = {Cerebral Abscess Infected by Nocardia gipuzkoensis.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {7247-7253}, pmid = {38023399}, issn = {1178-6973}, abstract = {PURPOSE: Nocardia gipuzkoensis is a novel species that solely identified in patients with pulmonary infections by far. Growing evidence showed the excellent performance of metagenomics next-generation sequencing (mNGS) on pathogenic identification, especially for new species. Here, we described the first case of an elderly female patient suddenly suffering from neurological disorders owing to N. gipuzkoensis infection. And linezolid could effectively treat N. gipuzkoensis infection.

PATIENTS AND METHODS: The results of imaging, laboratory cultures, and mNGS, as well as therapeutic process are shared.

RESULTS: An elderly female patient suddenly suffered from neurological disorders with dysphasia and right limb trembles under no obvious causes. Subsequently, she was diagnosed as intracranial space-occupying lesions by magnetic resonance imaging (MRI). The isolate from brain secretion was further identified as N. gipuzkoensis through mNGS. The targeted therapy with linezolid according to the antimicrobial susceptibility was used to treat cerebral abscess induced by N. gipuzkoensis. During the follow-up, no relapse was observed for the patient after surgery for 104 days.

CONCLUSION: Cerebral abscess induced by N. gipuzkoensis is rare disorder with high mortality. mNGS has been identified as a promising tool in pathogen diagnosis for timely therapy. Linezolid as one of the antimicrobial drugs could effectively treat N. gipuzkoensis infection and prevent adverse outcomes.}, } @article {pmid38022823, year = {2023}, author = {Shin, D and Kim, J and Lee, JH and Kim, JI and Oh, YM}, title = {Profiling of Microbial Landscape in Lung of Chronic Obstructive Pulmonary Disease Patients Using RNA Sequencing.}, journal = {International journal of chronic obstructive pulmonary disease}, volume = {18}, number = {}, pages = {2531-2542}, pmid = {38022823}, issn = {1178-2005}, mesh = {Humans ; *Pulmonary Disease, Chronic Obstructive/diagnosis/genetics/microbiology ; Reproducibility of Results ; Lung/microbiology ; Bacteria/genetics ; RNA ; Sequence Analysis, RNA ; }, abstract = {PURPOSE: The aim of the study was to use RNA sequencing (RNA-seq) data of lung from chronic obstructive pulmonary disease (COPD) patients to identify the bacteria that are most commonly detected. Additionally, the study sought to investigate the differences in these infections between normal lung tissues and those affected by COPD.

PATIENTS AND METHODS: We re-analyzed RNA-seq data of lung from 99 COPD patients and 93 non-COPD smokers to determine the extent to which the metagenomes differed between the two groups and to assess the reliability of the metagenomes. We used unmapped reads in the RNA-seq data that were not aligned to the human reference genome to identify more common infections in COPD patients.

RESULTS: We identified 18 bacteria that exhibited significant differences between the COPD and non-COPD smoker groups. Among these, Yersinia enterocolitica was found to be more than 30% more abundant in COPD. Additionally, we observed difference in detection rate based on smoking history. To ensure the accuracy of our findings and distinguish them from false positives, we double-check the metagenomic profile using Basic Local Alignment Search Tool (BLAST). We were able to identify and remove specific species that might have been misclassified as other species in Kraken2 but were actually Staphylococcus aureus, as identified by BLAST analysis.

CONCLUSION: This study highlighted the method of using unmapped reads, which were not typically used in sequencing data, to identify microorganisms present in patients with lung diseases such as COPD. This method expanded our understanding of the microbial landscape in COPD and provided insights into the potential role of microorganisms in disease development and progression.}, } @article {pmid38022583, year = {2023}, author = {Liu, X and van Beek, N and Cepic, A and Andreani, NA and Chung, CJ and Hermes, BM and Yilmaz, K and Benoit, S and Drenovska, K and Gerdes, S and Gläser, R and Goebeler, M and Günther, C and von Georg, A and Hammers, CM and Holtsche, MM and Hübner, F and Kiritsi, D and Schauer, F and Linnenmann, B and Huilaja, L and Tasanen-Määttä, K and Vassileva, S and Zillikens, D and Sadik, CD and Schmidt, E and Ibrahim, S and Baines, JF}, title = {The gut microbiome in bullous pemphigoid: implications of the gut-skin axis for disease susceptibility.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1212551}, pmid = {38022583}, issn = {1664-3224}, mesh = {Humans ; Aged ; *Gastrointestinal Microbiome/physiology ; *Pemphigoid, Bullous ; RNA, Ribosomal, 16S/genetics ; Disease Susceptibility ; Pilot Projects ; gamma-Aminobutyric Acid ; }, abstract = {Bullous pemphigoid (BP) is an autoimmune blistering disease that primarily affects the elderly. An altered skin microbiota in BP was recently revealed. Accumulating evidence points toward a link between the gut microbiota and skin diseases; however, the gut microbiota composition of BP patients remains largely underexplored, with only one pilot study to date, with a very limited sample size and no functional profiling of gut microbiota. To thoroughly investigate the composition and function of the gut microbiota in BP patients, and explore possible links between skin conditions and gut microbiota, we here investigated the gut microbiota of 66 patients (81.8% firstly diagnosed) suffering from BP and 66 age-, sex-, and study center-matched controls (CL) with non-inflammatory skin diseases (132 total participants), using 16S rRNA gene and shotgun sequencing data. Decreased alpha-diversity and an overall altered gut microbial community is observed in BP patients. Similar trends are observed in subclassifications of BP patients, including first diagnoses and relapsed cases. Furthermore, we observe a set of BP disease-associated gut microbial features, including reduced Faecalibacterium prausnitzii and greater abundance of pathways related to gamma-aminobutyric acid (GABA) metabolism in BP patients. Interestingly, F. prausnitzii is a well-known microbiomarker of inflammatory diseases, which has been reported to be reduced in the gut microbiome of atopic dermatitis and psoriasis patients. Moreover, GABA plays multiple roles in maintaining skin health, including the inhibition of itching by acting as a neurotransmitter, attenuating skin lesions by balancing Th1 and Th2 levels, and maintaining skin elasticity by increasing the expression of type I collagen. These findings thus suggest that gut microbiota alterations present in BP may play a role in the disease, and certain key microbes and functions may contribute to the link between gut dysbiosis and BP disease activity. Further studies to investigate the underlying mechanisms of the gut-skin interaction are thus clearly warranted, which could aid in the development of potential therapeutic interventions.}, } @article {pmid38020223, year = {2023}, author = {Elshafey, N and Mansour, MAI and Hamedo, HA and Elnosary, ME and Hagagy, N and Ahmed Al-Ghamdi, A and María Martínez-Espinosa, R}, title = {Phylogeny and functional diversity of halophilic microbial communities from a thalasso environment.}, journal = {Saudi journal of biological sciences}, volume = {30}, number = {12}, pages = {103841}, pmid = {38020223}, issn = {1319-562X}, abstract = {The El-Rawda solar saltern, located in North Sinai, Egypt, is formed through the process of water evaporation from the Bradawil lagoon. This evaporation leads to the precipitation of gypsum, halite minerals, and salt flats, which subsequently cover the southern and eastern areas of the lagoon. This study employed the shotgun metagenomic approach, the illumine platform, and bioinformatic tools to investigate the taxonomic composition and functional diversity of halophilic microbial communities in solar saltern. The metagenomic reads obtained from the brine sample exhibited a greater count compared to those from the sediment sample. Notably, the brine sample was primarily characterized by an abundance of archaea, while the sediment sample displayed a dominant abundance of bacteria. Both samples exhibited a relatively low abundance of eukaryotes, while viruses were only found in the brine sample. Furthermore, the comparative analysis of functional pathways showed many important processes related to central metabolism and protein processing in brine and sediment samples. In brief, this research makes a valuable contribution to the understanding of very halophilic ecosystems in Egypt, providing insights into their microbial biodiversity and functional processes.}, } @article {pmid38020222, year = {2023}, author = {Arakkal Thaiparambil, N and Radhakrishnan, V}, title = {Role of formulated bacterial consortia in biofortifying tomato fruits with nutrients: A nutritional, genomic and metagenomic analysis.}, journal = {Saudi journal of biological sciences}, volume = {30}, number = {12}, pages = {103851}, pmid = {38020222}, issn = {1319-562X}, abstract = {Nutrient deficiencies are a major problem that is prone to affect millions of people around the globe. Biofortification, a process of enriching nutrients in staple food crops is an effective method to tackle this malnutrition-associated disorder. Tomato (Solanum lycopersicum) is a globally consumed crop and therefore is a suitable candidate for biofortification. Many plant growth-promoting bacteria are reported to have the ability to enhance nutrient content in plants. In the present study, we have investigated the ability of two bacterial consortia (consortia-1 -co-culturing Lysinibacillus sp. strain VITKC-5 and Acinetobacter Sp. strain VITKC_6; and consortia-2 -co-culturing Lysinibacillus sp. strain VITKC-5 and Enterobacter sp. strain VITVLC-4) in the nutrient enrichment of tomato fruits. The results were then correlated with the elevated expression of nutrient transporter genes. Furthermore, the effect of these bacterial formulations on the indigenous microbiome has also been evaluated through metagenomic analysis. The application of bacterial formulations significantly improved the nutrient content when compared to the control (untreated) group. These findings advocate that PGPB-assisted biofortification has the potential to alleviate nutrient deficiency in humans.}, } @article {pmid38019198, year = {2023}, author = {Cavalcante, JVF and de Souza, ID and Morais, DAA and Dalmolin, RJS}, title = {Bridging the Gaps in Meta-Omic Analysis: Workflows and Reproducibility.}, journal = {Omics : a journal of integrative biology}, volume = {27}, number = {12}, pages = {547-549}, doi = {10.1089/omi.2023.0232}, pmid = {38019198}, issn = {1557-8100}, mesh = {Humans ; Workflow ; Reproducibility of Results ; *Software ; *Microbiota/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {The past few years have seen significant advances in the study of complex microbial communities associated with the evolution of sequencing technologies and increasing adoption of whole genome shotgun sequencing methods over the once more traditional Amplicon-based methods. Although these advances have broadened the horizon of meta-omic analyses in planetary health, human health, and ecology from simple sample composition studies to comprehensive taxonomic and metabolic profiles, there are still significant challenges in processing these data. First, there is a widespread lack of standardization in data processing, including software choices and the ease of installing and running attendant software. This can lead to several inconsistencies, making comparing results across studies and reproducing original results difficult. We argue that these drawbacks are especially evident in metatranscriptomic analysis, with most analyses relying on ad hoc scripts instead of pipelines implemented in workflow managers. Additional challenges rely on integrating meta-omic data, since methods have to consider the biases in the library preparation and sequencing methods and the technical noise that can arise from it. Here, we critically discuss the current limitations in metagenomics and metatranscriptomics methods with a view to catalyze future innovations in the field of Planetary Health, ecology, and allied fields of life sciences. We highlight possible solutions for these constraints to bring about more standardization, with ease of installation, high performance, and reproducibility as guiding principles.}, } @article {pmid38018980, year = {2024}, author = {Freeman, CN and Russell, JN and Yost, CK}, title = {Temporal metagenomic characterization of microbial community structure and nitrogen modification genes within an activated sludge bioreactor system.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0283223}, pmid = {38018980}, issn = {2165-0497}, mesh = {*Sewage ; Nitrogen ; *Microbiota/genetics ; Wastewater ; Bioreactors ; }, abstract = {Wastewater treatment plays an essential role in minimizing negative impacts on downstream aquatic environments. Microbial communities are known to play a vital role in the wastewater treatment process, particularly in the removal of nitrogen and phosphorus, which can be especially damaging to aquatic ecosystems. There is limited understanding of how these microbial communities may change in response to fluctuating temperatures or how seasonality may impact their ability to participate in the treatment process. The findings of this study indicate that the microbial communities of wastewater are relatively stable both compositionally and functionally across fluctuating temperatures.}, } @article {pmid38018967, year = {2023}, author = {Silva, SG and Nabhan Homsi, M and Keller-Costa, T and Rocha, U and Costa, R}, title = {Natural product biosynthetic potential reflects macroevolutionary diversification within a widely distributed bacterial taxon.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0064323}, pmid = {38018967}, issn = {2379-5077}, support = {PTDC/MAR-BIO/1547/2014, UIDB/04565/2020, UIDP/04565/2020, LA/P/0140/2020, 01/SAICT/2016 n{degree sign} 022153//MEC | Fundação para a Ciência e a Tecnologia (FCT)/ ; PD/BD/143029/2018//MEC | Fundação para a Ciência e a Tecnologia (FCT)/ ; CEECIND/00788/2017//MEC | Fundação para a Ciência e a Tecnologia (FCT)/ ; FEMS-GO-2019-511//Federation of European Microbiological Societies (FEMS)/ ; FA_05_2017_032//Direção-Geral de Política do Mar/ ; VH-NG-1248//Helmholtz-Zentrum für Umweltforschung (UFZ)/ ; 460129525//Deutsche Forschungsgemeinschaft (DFG)/ ; }, mesh = {*Biological Products/metabolism ; *Flavobacteriaceae/metabolism ; Secondary Metabolism ; Peptides/metabolism ; }, abstract = {This is the most comprehensive study performed thus far on the biosynthetic potential within the Flavobacteriaceae family. Our findings reveal intertwined taxonomic and natural product biosynthesis diversification within the family. We posit that the carbohydrate, peptide, and secondary metabolism triad synergistically shaped the evolution of this keystone bacterial taxon, acting as major forces underpinning the broad host range and opportunistic-to-pathogenic behavior encompassed by species in the family. This study further breaks new ground for future research on select Flavobacteriaceae spp. as reservoirs of novel drug leads.}, } @article {pmid38018965, year = {2023}, author = {Ottesen, A and Kocurek, B and Deaver, C and Chiesa, O and Cohen, R and Reed, E and Commichaux, S and Mammel, M and McDermott, P and Strain, E and Myers, M}, title = {Fecal microbiomes of laboratory beagles receiving antiparasitic formulations in an experimental setting.}, journal = {Microbiology resource announcements}, volume = {}, number = {}, pages = {e0086023}, doi = {10.1128/MRA.00860-23}, pmid = {38018965}, issn = {2576-098X}, abstract = {Here, we describe the fecal microbiome of laboratory beagles in a non-invasive experiment designed to contrast in vivo versus in vitro bioequivalence in response to antiparasitic drug administration. The experiment provided a unique opportunity to evaluate metagenomic profiles of canine feces before and after anti-parasitic drug exposure.}, } @article {pmid38017705, year = {2023}, author = {Delavy, M and Sertour, N and Patin, E and Le Chatelier, E and Cole, N and Dubois, F and Xie, Z and Saint-André, V and Manichanh, C and Walker, AW and Quintana-Murci, L and Duffy, D and d'Enfert, C and Bougnoux, ME and Consortium, MI}, title = {Unveiling Candida albicans intestinal carriage in healthy volunteers: the role of micro- and mycobiota, diet, host genetics and immune response.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2287618}, pmid = {38017705}, issn = {1949-0984}, mesh = {Humans ; *Candida albicans/physiology ; Genome-Wide Association Study ; *Gastrointestinal Microbiome/physiology ; Diet ; Immunity ; }, abstract = {Candida albicans is a commensal yeast present in the gut of most healthy individuals but with highly variable concentrations. However, little is known about the host factors that influence colonization densities. We investigated how microbiota, host lifestyle factors, and genetics could shape C. albicans intestinal carriage in 695 healthy individuals from the Milieu Intérieur cohort. C. albicans intestinal carriage was detected in 82.9% of the subjects using quantitative PCR. Using linear mixed models and multiway-ANOVA, we explored C. albicans intestinal levels with regard to gut microbiota composition and lifestyle factors including diet. By analyzing shotgun metagenomics data and C. albicans qPCR data, we showed that Intestinimonas butyriciproducens was the only gut microbiota species whose relative abundance was negatively correlated with C. albicans concentration. Diet is also linked to C. albicans growth, with eating between meals and a low-sodium diet being associated with higher C. albicans levels. Furthermore, by Genome-Wide Association Study, we identified 26 single nucleotide polymorphisms suggestively associated with C. albicans colonization. In addition, we found that the intestinal levels of C. albicans might influence the host immune response, specifically in response to fungal challenge. We analyzed the transcriptional levels of 546 immune genes and the concentration of 13 cytokines after whole blood stimulation with C. albicans cells and showed positive associations between the extent of C. albicans intestinal levels and NLRP3 expression, as well as secreted IL-2 and CXCL5 concentrations. Taken together, these findings open the way for potential new interventional strategies to curb C. albicans intestinal overgrowth.}, } @article {pmid38017389, year = {2023}, author = {Tsakmaklis, A and Farowski, F and Zenner, R and Lesker, TR and Strowig, T and Schlößer, H and Lehmann, J and von Bergwelt-Baildon, M and Mauch, C and Schlaak, M and Knuever, J and Schweinsberg, V and Heinzerling, LM and Vehreschild, MJGT}, title = {TIGIT[+] NK cells in combination with specific gut microbiota features predict response to checkpoint inhibitor therapy in melanoma patients.}, journal = {BMC cancer}, volume = {23}, number = {1}, pages = {1160}, pmid = {38017389}, issn = {1471-2407}, support = {70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; 70112696//Deutsche Krebshilfe/ ; }, mesh = {Humans ; *Melanoma/drug therapy ; *Gastrointestinal Microbiome ; *Skin Neoplasms/drug therapy ; Immune Checkpoint Inhibitors/pharmacology/therapeutic use ; Prospective Studies ; Killer Cells, Natural ; Receptors, Immunologic ; }, abstract = {BACKGROUND: Composition of the intestinal microbiota has been correlated to therapeutic efficacy of immune checkpoint inhibitors (ICI) in various cancer entities including melanoma. Prediction of the outcome of such therapy, however, is still unavailable. This prospective, non-interventional study was conducted in order to achieve an integrated assessment of the connection between a specific intestinal microbiota profile and antitumor immune response to immune checkpoint inhibitor therapy (anti-PD-1 and/or anti-CTLA-4) in melanoma patients.

METHODS: We assessed blood and stool samples of 29 cutaneous melanoma patients who received immune checkpoint inhibitor therapy. For functional and phenotypical immune analysis, 12-color flow cytometry and FluoroSpot assays were conducted. Gut microbiome was analyzed with shotgun metagenomics sequencing. To combine clinical, microbiome and immune variables, we applied the Random Forest algorithm.

RESULTS: A total of 29 patients was analyzed in this study, among whom 51.7% (n = 15) reached a durable clinical benefit. The Immune receptor TIGIT is significantly upregulated in T cells (p = 0.0139) and CD56[high] NK cells (p = 0.0037) of responders. Several bacterial taxa were associated with response (e.g. Ruminococcus torques) or failure (e.g. Barnesiella intestinihominis) to immune therapy. A combination of two microbiome features (Barnesiella intestinihominis and the Enterobacteriaceae family) and one immune feature (TIGIT[+] CD56[high] NK cells) was able to predict response to ICI already at baseline (AUC = 0.85; 95% CI: 0.841-0.853).

CONCLUSIONS: Our results reconfirm a link between intestinal microbiota and response to ICI therapy in melanoma patients and furthermore point to TIGIT as a promising target for future immunotherapies.}, } @article {pmid38017305, year = {2023}, author = {Singha, NA and Neihsial, R and Kipgen, L and Lyngdoh, WJ and Nongdhar, J and Chettri, B and Singh, P and Singh, AK}, title = {Taxonomic and Predictive Functional Profile of Hydrocarbonoclastic Bacterial Consortia Developed at Three Different Temperatures.}, journal = {Current microbiology}, volume = {81}, number = {1}, pages = {22}, pmid = {38017305}, issn = {1432-0991}, mesh = {Temperature ; RNA, Ribosomal, 16S/genetics/metabolism ; *Microbial Consortia/genetics ; Hydrocarbons/metabolism ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; *Petroleum/metabolism ; Bacteroidetes/genetics ; }, abstract = {Microbial community exhibit shift in composition in response to temperature variation. We report crude oil-degrading activity and high-throughput 16S rRNA gene sequencing (metagenome) profiles of four bacterial consortia enriched at three different temperatures in crude oil-amended Bushnell-Hass Medium from an oily sludge sediment. The consortia were referred to as O (4 ± 2 ℃ in 3% w/v crude oil), A (25 ± 2 ℃ in 1% w/v crude oil), H (25 ± 2 ℃ in 3% w/v crude oil), and X (45 ± 2 ℃ in 3% w/v crude oil). The hydrocarbon-degrading activity was highest for consortium A and H and lowest for consortium O. The metagenome profile revealed the predominance of Proteobacteria (62.12-1.25%) in each consortium, followed by Bacteroidota (18.94-37.77%) in the consortium O, A, and H. Contrarily, consortium X comprised 7.38% Actinomycetota, which was essentially low (< 0.09%) in other consortia, and only 0.41% Bacteroidota. The PICRUSt-based functional analysis predicted major functions associated with the metabolism and 5060 common KEGG Orthology (KOs). A total of 296 KOs were predicted exclusively in consortium X. Additionally, 247 KOs were predicted from xenobiotic biodegradation pathways. This study found that temperature had a stronger influence on the composition and function of the bacterial community than crude oil concentration.}, } @article {pmid38017092, year = {2023}, author = {Kim, J and Cho, Y and Lim, SK and Seo, MR and Sohn, JW and Kim, B and Rho, M and Pai, H}, title = {Comparative analyses of the faecal resistome against β-lactam and quinolone antibiotics in humans and livestock using metagenomic sequencing.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {20993}, pmid = {38017092}, issn = {2045-2322}, support = {2015R1C1A1A01055646//National Research Foundation of Korea/ ; 2017ER540702//Research of Korea Centers for Disease Control and Prevention/ ; }, mesh = {Humans ; Animals ; Swine ; Cattle ; *beta-Lactams/pharmacology ; Livestock/genetics ; Phylogeny ; Chickens/genetics ; Anti-Bacterial Agents/pharmacology ; Escherichia coli/genetics ; Plasmids/genetics ; beta-Lactamases/genetics ; *Quinolones/pharmacology ; }, abstract = {To assess the prevalence and abundance of antibiotic resistance genes in human and livestock gut microbiomes, 87 humans (healthy individuals and patients with Clostridioides difficile infection (CDI)) and 108 livestock (swine, cattle, and chickens) were enrolled. Gut microbiomes and fluoroquinolone-resistant Escherichia coli isolates were sequenced, and mobile genetic elements adjacent to the β-lactamase (bla) and transferable quinolone resistance (qnr) genes were compared using metagenomic contigs. Each group of humans and livestock exhibited distinctive microbiota and resistome compositions in the gut. Concerning the resistome of bla and qnr, the prevalence rates between chickens and patients with CDI were the most similar (R[2] = 0.46); blaTEM, blaOXA, blaCTX-M, and qnrS were highly prevalent in both groups. According to genomic and phylogenetic analyses, blaCTX-M and blaOXA expressed lineage specificity to either humans or livestock, while qnrS and blaTEM displayed a shared lineage between humans and livestock. A qnrS1 mobilome comprising five genes, including two recombinases, a transposase, and a plasmid gene, is commonly found in human and chicken gut microbiomes. Humans and chickens showed the most similar gut resistomes to β-lactams and quinolones. QnrS and blaTEM displayed especially strong co-occurrence between the guts of humans and livestock.}, } @article {pmid38017081, year = {2023}, author = {Li, C and Luan, Z and Zhao, Y and Chen, J and Yang, Y and Wang, C and Jing, Y and Qi, S and Li, Z and Guo, H and Xu, W and Zhao, B and Wu, C and Wang, S and Yang, Y and Sun, G}, title = {Author Correction: Deep insights into the gut microbial community of extreme longevity in south Chinese centenarians by ultra-deep metagenomics and large-scale culturomics.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {89}, doi = {10.1038/s41522-023-00456-7}, pmid = {38017081}, issn = {2055-5008}, } @article {pmid38016776, year = {2023}, author = {Peng, JY and Dai, HF and Huang, WX}, title = {[A case of acute fascioliasis diagnosed using metagenomic-next generation sequencing technology].}, journal = {Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology}, volume = {31}, number = {10}, pages = {1089-1091}, doi = {10.3760/cma.j.cn501113-20220126-00044}, pmid = {38016776}, issn = {1007-3418}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Fascioliasis/diagnosis ; Metagenomics ; }, } @article {pmid38016565, year = {2023}, author = {Zhu, K and Liu, J and Zhao, M and Fu, L and Du, Z and Meng, F and Gu, L and Liu, P and Liu, Y and Zhang, C and Zhang, X and Li, J}, title = {An intrusion and environmental effects of man-made silver nanoparticles in cold seeps.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {168890}, doi = {10.1016/j.scitotenv.2023.168890}, pmid = {38016565}, issn = {1879-1026}, abstract = {Silver nanoparticles (AgNPs) are among the most widely used metal-based engineered nanomaterials in biomedicine and nanotechnology, and account for >50 % of global nanomaterial consumer products. The increasing use of AgNPs potentially causes marine ecosystem changes; however, the environmental impacts of man-made AgNPs are still poorly studied. This study reports for the first time that man-made AgNPs intruded into cold seeps, which are important marine ecosystems where hydrogen sulfide, methane, and other hydrocarbon-rich fluid seepage occur. Using a combination of electron microscopy, geochemical and metagenomic analyses, we found that in the cold seeps with high AgNPs concentrations, the relative abundance of genes associated with anaerobic oxidation of methane (AOM) was lower, while those related to the sulfide oxidizing and sulfate reducing were higher. This suggests that AgNPs can stimulate the proliferation of sulfate-reducing and sulfide-oxidizing bacteria, likely due to the effects of activating repair mechanisms of the cells against the toxicant. A reaction of AgNPs with hydrogen sulfide to form silver sulfide could also effectively reduce the amount of available sulfate in local ecosystems, which is generally used as the AOM oxidant. These novel findings indicate that man-made AgNPs may be involved in the biogeochemical cycles of sulfur and carbon in nature, and their potential effects on the releasing of methane from the marine methane seeps should not be ignored in both scientific and environmental aspects.}, } @article {pmid38016543, year = {2023}, author = {Biswas, A and Chakraborty, S}, title = {Assessment of microbial population in integrated CW-MFC system and investigation of organics and fecal coliform removal pathway.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {168809}, doi = {10.1016/j.scitotenv.2023.168809}, pmid = {38016543}, issn = {1879-1026}, abstract = {The current study is focused on understanding the operational mechanism of an integrated constructed wetland-microbial fuel cell (CW-MFC) reactor emphasizing fecal coliform (FC) removal. Few studies are available in the literature investigating the inherent mechanisms of pathogen inactivation in a CW-MFC system. Raw domestic wastewater was treated in three vertical reactors, one planted constructed wetland (R1), one planted CW-MFC (R2), and one unplanted CW-MFC (R3). Spatial analysis of treated effluents showed a considerable amount of organics and fecal coliform removal at the vicinity of the anode in R2. Assessment of the microbial population inside all the reactors revealed that EABs (Firmicutes, Bacteroidetes, and Actinobacteria) were more abundant in R2 compared to R1 and R3. During the activity study, biomass obtained from R2 showed a maximum substrate utilization rate of 1.27 mg COD mgVSS[-1] d[-1]. Kinetic batch studies were carried out for FC removal in all the reactors, and the maximum first order FC removal rate was obtained at the anode of R2 as 2.13 d[-1] when operated in closed circuit mode. This value was much higher than the natural die-off rate of FCs in raw wastewater which was 1.16 d[-1]. Simultaneous bioelectricity monitoring inferred that voltage generation can be correlated to faster FC inactivation, which was probably due to EABs outcompeting other exogenous microbes in a preferable anaerobic environment with the presence of an anode. Reactor R2 was found to be functioning as a symbiotic bio-electrochemical mesocosm.}, } @article {pmid38016379, year = {2024}, author = {Kavita, and Om, H and Chand, U and Kushawaha, PK}, title = {Postbiotics: An alternative and innovative intervention for the therapy of inflammatory bowel disease.}, journal = {Microbiological research}, volume = {279}, number = {}, pages = {127550}, doi = {10.1016/j.micres.2023.127550}, pmid = {38016379}, issn = {1618-0623}, mesh = {Female ; Male ; Humans ; *Inflammatory Bowel Diseases/therapy/microbiology ; Intestines/microbiology ; *Microbiota ; Bacteria ; *Gastrointestinal Microbiome ; *Gastrointestinal Diseases ; *Probiotics/therapeutic use ; }, abstract = {Inflammatory Bowel Disease (IBD) is a persistent gastrointestinal (GI) tract inflammatory disease characterized by downregulated mucosal immune activities and a disrupted microbiota environment in the intestinal lumen. The involvement of bacterium postbiotics as mediators between the immune system and gut microbiome could be critical in determining why host-microbial relationships are disrupted in IBD. Postbiotics including Short-chain fatty acids (SCFAs), Organic acids, Proteins, Vitamins, Bacteriocins, and Tryptophan (Trp) are beneficial bioactive compounds formed via commensal microbiota in the gut environment during the fermentation process that can be used to improve consumer health. The use of metabolites or fragments from microorganisms can be a very attractive treatment and prevention technique in modern medicine. Postbiotics are essential in the immune system's development since they alter the barrier tightness, and the gut ecology and indirectly shape the microbiota's structure. As a result, postbiotics may be beneficial in treating or preventing various diseases, even some for which there is no effective causative medication. Postbiotics may be a promising tool for the treatment of IBD in individuals of all ages, genders, and even geographical locations. Direct distribution of postbiotics may provide a new frontier in microbiome-based therapy for IBD since it allows both the management of host homeostasis and the correction of the negative implications of dysbiosis. Further studies of the biological effects of these metabolites are expected to reveal innovative applications in medicine and beyond. This review attempts to explore the possible postbiotic-based interventions for the treatment of IBD.}, } @article {pmid38016315, year = {2023}, author = {Gao, FZ and He, LY and He, LX and Bai, H and Zhang, M and Chen, ZY and Qiao, LK and Liu, YS and Ying, GG}, title = {Swine farming shifted the gut antibiotic resistome of local people.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133082}, doi = {10.1016/j.jhazmat.2023.133082}, pmid = {38016315}, issn = {1873-3336}, abstract = {Antibiotic resistance genes (ARGs) are prevalent in the livestock environment, but little is known about impacts of animal farming on the gut antibiotic resistome of local people. Here we conducted metagenomic sequencing to investigate gut microbiome and resistome of residents in a swine farming village as well as environmental relevance by comparing with a nearby non-farming village. Results showed a shift of gut microbiome towards unhealthy status in the residents of swine farming village, with an increased abundance and diversity in pathogens and ARGs. The resistome composition in human guts was more similar with that in swine feces and air than that in soil and water. Mobile gene elements were closely associated with the prevalence of gut resistome. Some plasmid-borne ARGs were colocalized in similar genetic contexts in gut and environmental samples. Metagenomic binning obtained 47 ARGs-carrying families in human guts, and therein Enterobacteriaceae posed the highest threats in antibiotic resistance and virulence. Several ARGs-carrying families were shared by gut and environmental samples (mainly in swine feces and air), and the ARGs were evolutionarily conservative within genera. The findings highlight that swine farming can shape gut resistome of local people with close linkage to farm environmental exposures.}, } @article {pmid38016312, year = {2023}, author = {Zhang, S and Ye, X and Lin, X and Zeng, X and Meng, S and Luo, W and Yu, F and Peng, T and Huang, T and Li, J and Hu, Z}, title = {Novel insights into aerobic 17β-estradiol degradation by enriched microbial communities from mangrove sediments.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133045}, doi = {10.1016/j.jhazmat.2023.133045}, pmid = {38016312}, issn = {1873-3336}, abstract = {Various persistent organic pollutants (POPs) including estrogens are often enriched in mangrove regions. This research investigated the estrogens pollution levels in six mangroves located in the Southern China. The estrogen levels were found to be in the range of 5.3-24.9 ng/g dry weight, suggesting that these mangroves had been seriously contaminated. The bacterial communities under estrogen stress were further enriched by supplementing 17β-estradiol (E2) as the sole carbon source. The enriched bacterial communities showed an excellent E2 degradation capacity > 95 %. These communities were able to transform E2 into estrone (E1), 4-hydroxy-estrone, and keto-estrone, etc. 16 S rDNA sequencing and metagenomics analysis revealed that bacterial taxa Oleiagrimonas, Pseudomonas, Terrimonas, and Nitratireductor etc. were the main contributors to estrogen degradation. Moreover, the genes involved in E2 degradation were enriched in the microbial communities, including the genes encoding 17β-hydroxysteroid dehydrogenase, estrone 4-hydroxylase, etc. Finally, the analyses of functional genes and binning genomes demonstrated that E2 was degraded by bacterial communities via dehydrogenation into E1 by 17β-hydroxysteroid dehydrogenase. E1 was then catabolically converted to 3aα-H-4α(3'-propanoate)- 7aβ-methylhexahydro-1,5-indanedione via 4,5-seco pathway. Alternatively, E1 could also be hydroxylated to keto-estrone, followed by B-ring cleavage. This study provides novel insights into the biodegradation of E2 by the bacterial communities in estrogen-contaminated mangroves.}, } @article {pmid38016224, year = {2024}, author = {Ke, Y and Sun, W and Xue, Y and Zhu, Y and Yan, S and Xie, S}, title = {Effects of treatments and distribution on microbiome and antibiotic resistome from source to tap water in three Chinese geographical regions based on metagenome assembly.}, journal = {Water research}, volume = {249}, number = {}, pages = {120894}, doi = {10.1016/j.watres.2023.120894}, pmid = {38016224}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents/pharmacology ; Metagenome ; *Drinking Water/analysis ; Genes, Bacterial ; *Microbiota ; China ; }, abstract = {Antibiotic resistance genes (ARGs) represent emerging environmental pollutants that present health risks. Drinking water supply systems (DWSSs), including sources to tap water, play crucial roles in the dissemination and propagation of ARGs. However, there was a paucity of knowledge on the relative abundance, diversity, mobility, and pathogenic hosts of ARGs in DWSSs from source to tap. Therefore, the effects of treatments and distributions on the microbial community and ARGs from three geographical regions (downstream areas of the Yellow, Yangtze, and Pearl Rivers) were elucidated in the present study. Treatment processes lowered the complexity of the microbial community network, whereas transportation increased it. The assembly mechanisms of the microbial community and antibiotic resistome were primarily driven by stochastic processes. Distribution greatly increased the contribution of stochastic processes. Multidrug ARGs (for example, multidrug transporter and adeJ) and bacitracin ARG (bacA) were the primary mobile ARGs in drinking water, as identified by the metagenomic assembly. Achromobacter xylosoxidans, Acinetobacter calcoaceticus, and Acinetobacter junii harbored diverse multidrug ARGs and mobile genetic elements (MGEs) (recombinases, integrases, and transposases) as potential pathogens and were abundant in the disinfected water. Environmental factors, including pH, chlorine, latitude, longitude, and temperature, influenced the ARG abundance by directly regulating the MGEs and microbial community diversity. This study provides critical information on the fate, mobility, host pathogenicity, and driving factors of ARGs in drinking water, which is conducive to ARG risk assessment and management to provide high-quality drinking water to consumers.}, } @article {pmid38016054, year = {2023}, author = {Ilinskaya, ON and Gafarova, LF and Kurdy, W and Kolpakov, AI and Yakovleva, GY}, title = {[Microbiome of therapeutic muds used in Tatarstan].}, journal = {Voprosy kurortologii, fizioterapii, i lechebnoi fizicheskoi kultury}, volume = {100}, number = {5}, pages = {27-35}, doi = {10.17116/kurort202310005127}, pmid = {38016054}, issn = {0042-8787}, mesh = {Tatarstan ; *Microbiota ; Bacteria/genetics ; Sulfides ; Anti-Bacterial Agents ; }, abstract = {UNLABELLED: Therapeutic muds (peloids), which are widely used for body healing, improve metabolism and have antibacterial, anti-inflammatory and analgesic effects due to enrichment with necessary microelements and biological active substances. However, the microbiological component of these effects is not well studied.

OBJECTIVE: To characterize the microbiome of therapeutic muds, used in the Tatarstan Republic, by identifying spectrum of cultivated microorganisms, using molecular analysis of bacterial communities, and by determining their biodiversity and functional potential based on revealed genetic determinants.

MATERIAL AND METHODS: The study design of 5 peloids samples (local sapropels and peat deposits of swamp; 3 samples of Crimean sulfide muds) included three main techniques: isolation and taxonomic determination of cultivated microorganisms by time-of-flight mass-spectrometry; molecular analysis of peloids bacterial communities by 16S RNA high-throughput sequencing; identification of functional profiles of communities by their genetic determinant using Global Mapper tool on iVikodak platform.

RESULTS: Experimental studies have confirmed the safety of examined peloids, where non-pathogenic cultivated bacteria belonging mainly to Bacillus and Rhodococcus genera were dominant. Metagenomic analysis showed that Firmicutes, Proteobacteria and Actinobacteria were predominant in all samples in different ratios. It has been established, that there is both the internal biodiversity of each sample and difference between them. The functional profile of microbial communities was determined based on the identification of bacterial genes. It has been revealed that all communities have an ability to synthesize antibiotics, as well as to decompose dangerous xenobiotics - polyaromatic hydrocarbons, cyclic compounds, and dioxins.

CONCLUSION: Various microbial communities, which were identified in the therapeutic muds, contribute both to the clearance of toxicants in the peloids and to the antibacterial properties of the latter. The obtained priority results create a fundamental basis for the subsequent study of the role of peloids' microbiome of different origin in their healing action.}, } @article {pmid38015634, year = {2023}, author = {Gurczynski, SJ and Lipinski, JH and Strauss, J and Alam, S and Huffnagle, GB and Ranjan, P and Kennedy, LH and Moore, BB and O'Dwyer, DN}, title = {Horizontal transmission of gut microbiota attenuates mortality in lung fibrosis.}, journal = {JCI insight}, volume = {9}, number = {1}, pages = {}, doi = {10.1172/jci.insight.164572}, pmid = {38015634}, issn = {2379-3708}, mesh = {Mice ; Animals ; Humans ; *Gastrointestinal Microbiome/physiology ; *Pulmonary Fibrosis ; Mice, Inbred C57BL ; Lung ; *Microbiota/physiology ; }, abstract = {Pulmonary fibrosis is a chronic and often fatal disease. The pathogenesis is characterized by aberrant repair of lung parenchyma, resulting in loss of physiological homeostasis, respiratory failure, and death. The immune response in pulmonary fibrosis is dysregulated. The gut microbiome is a key regulator of immunity. The role of the gut microbiome in regulating the pulmonary immunity in lung fibrosis is poorly understood. Here, we determine the impact of gut microbiota on pulmonary fibrosis in substrains of C57BL/6 mice derived from different vendors (C57BL/6J and C57BL/6NCrl). We used germ-free models, fecal microbiota transplantation, and cohousing to transmit gut microbiota. Metagenomic studies of feces established keystone species between substrains. Pulmonary fibrosis was microbiota dependent in C57BL/6 mice. Gut microbiota were distinct by β diversity and α diversity. Mortality and lung fibrosis were attenuated in C57BL/6NCrl mice. Elevated CD4+IL-10+ T cells and lower IL-6 occurred in C57BL/6NCrl mice. Horizontal transmission of microbiota by cohousing attenuated mortality in C57BL/6J mice and promoted a transcriptionally altered pulmonary immunity. Temporal changes in lung and gut microbiota demonstrated that gut microbiota contributed largely to immunological phenotype. Key regulatory gut microbiota contributed to lung fibrosis, generating rationale for human studies.}, } @article {pmid38015339, year = {2023}, author = {Brar, B and Kumar, R and Sharma, D and Sharma, AK and Thakur, K and Mahajan, D and Kumar, R}, title = {Metagenomic analysis reveals diverse microbial community and potential functional roles in Baner rivulet, India.}, journal = {Journal, genetic engineering & biotechnology}, volume = {21}, number = {1}, pages = {147}, pmid = {38015339}, issn = {2090-5920}, abstract = {BACKGROUND: The health index of any population is directly correlated with the water quality, which in turn depends upon physicochemical characteristics and the microbiome of that aquatic source. For maintaining the water quality, knowledge of microbial diversity is a must. The present investigation attempts to evaluate the microflora of Baner. Metagenomics has been proven to be the technique for examining the genetic diversity of unculturable microbiota without using traditional culturing techniques. The microbial profile of Baner is analyzed using metagenomics for the first time to the best of our knowledge.

RESULTS: To explore the microbial diversity of Baner, metagenomics analysis from 3 different sites was done. Data analysis identified 29 phyla, 62 classes, 131 orders, 268 families, and 741 genera. Proteobacteria was found to be the most abundant phylum in all the sampling sites, with the highest abundance at S3 sampling site (94%). Bacteroidetes phylum was found to be second abundant in S1 and S2 site, whereas Actinobacteria was second dominant in sampling site S3. Enterobacteriaceae family was dominant in site S1, whereas Comamonadaceae and Pseudomonadaceae was abundant in sites S2 and S3 respectively. The Baner possesses an abundant bacterial profile that holds great promise for developing bioremediation tactics against a variety of harmful substances.

CONCLUSION: Baner river's metagenomic analysis offers the first insight into the microbial profile of this hilly stream. Proteobacteria was found to be the most abundant phylum in all the sampling sites indicating anthropogenic interference and sewage contamination. The highest abundance of proteobacteria at S3 reveals it to be the most polluted site, as it is the last sampling site downstream of the area under investigation, and falls after crossing the main city, so more human intervention and pollution were observed. Despite some pathogens, a rich profile of bacteria involved in bioremediation, xenobiotic degradation, and beneficial fish probiotics was observed, reflecting their potential applications for improving water quality and establishing a healthy aquaculture and fishery section.}, } @article {pmid38014976, year = {2024}, author = {Zhuang, Y and Guo, W and Cui, K and Tu, Y and Diao, Q and Zhang, N and Bi, Y and Ma, T}, title = {Altered microbiota, antimicrobial resistance genes, and functional enzyme profiles in the rumen of yak calves fed with milk replacer.}, journal = {Microbiology spectrum}, volume = {12}, number = {1}, pages = {e0131423}, doi = {10.1128/spectrum.01314-23}, pmid = {38014976}, issn = {2165-0497}, support = {2022YFA1304201//MOST | National Key Research and Development Program of China (NKPs)/ ; 32222081//MOST | National Natural Science Foundation of China (NSFC)/ ; Y2022QC10//Youth Innovation Program of CAAS/ ; CAAS-ASTIP-2017-FRI-04//CAAS | Agricultural Science and Technology Innovation Program (ASTIP)/ ; }, mesh = {Cattle ; Animals ; *Milk ; Anti-Bacterial Agents/pharmacology/metabolism ; Rumen/microbiology ; Drug Resistance, Bacterial/genetics ; Butyrates/pharmacology ; *Microbiota/genetics ; }, abstract = {Yaks, as ruminants inhabiting high-altitude environments, possess a distinct rumen microbiome and are resistant to extreme living conditions. This study investigated the microbiota, resistome, and functional gene profiles in the rumen of yaks fed milk or milk replacer (MR), providing insights into the regulation of the rumen microbiome and the intervention of antimicrobial resistance in yaks through dietary methods. The abundance of Prevotella members increased significantly in response to MR. Tetracycline resistance was the most predominant. The rumen of yaks contained multiple antimicrobial resistance genes (ARGs) originating from different bacteria, which could be driven by MR, and these ARGs displayed intricate and complex interactions. MR also induced changes in functional genes. The enzymes associated with fiber degradation and butyrate metabolism were activated and showed close correlations with Prevotella members and butyrate concentration. This study allows us to deeply understand the ruminal microbiome and ARGs of yaks and their relationship with rumen bacteria in response to different milk sources.}, } @article {pmid38014952, year = {2023}, author = {Meyer Cifuentes, IE and Degenhardt, J and Neumann-Schaal, M and Jehmlich, N and Ngugi, DK and Öztürk, B}, title = {Comparative biodegradation analysis of three compostable polyesters by a marine microbial community.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {12}, pages = {e0106023}, pmid = {38014952}, issn = {1098-5336}, support = {//BASF/ ; }, mesh = {Polyesters/metabolism ; Plastics/metabolism ; Polymers ; *Biodegradable Plastics/metabolism ; Biodegradation, Environmental ; *Microbiota ; }, abstract = {Biodegradable plastics can be used in applications where the end product cannot be efficiently recycled due to high levels of contaminations, e.g., food or soil. Some of these plastics have a dedicated end of life, such as composting, but their degradation in the marine environment is poorly understood. In this study we showed that marine microbial communities can degrade a range of biodegradable polymers with different physical and chemical properties and use these as a sole carbon source for growth. We have also provided insights into the degradation mechanisms using a combined metagenomic and metaproteomic approach. In addition, we have identified three new enzymes that are capable of degrading both aliphatic polymers and aliphatic-aromatic copolymers, which can be used for biotechnological applications.}, } @article {pmid38014300, year = {2023}, author = {Chen, L and Chen, A and Zhang, XD and Robles, MST and Han, HS and Xiao, Y and Xiao, G and Pipas, JM and Weitz, DA}, title = {High-sensitivity whole-genome recovery of single viral species in environmental samples.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38014300}, support = {R01 AI153156/AI/NIAID NIH HHS/United States ; }, abstract = {Characterizing unknown viruses is essential for understanding viral ecology and preparing against viral outbreaks. Recovering complete genome sequences from environmental samples remains computationally challenging using metagenomics, especially for low-abundance species with uneven coverage. This work presents a method for reliably recovering complete viral genomes from complex environmental samples. Individual genomes are encapsulated into droplets and amplified using multiple displacement amplification. A novel gene detection assay, which employs an RNA-based probe and an exonuclease, selectively identifies droplets containing the target viral genome. Labeled droplets are sorted using a microfluidic sorter, and genomes are extracted for sequencing. Validation experiments using a sewage sample spiked with two known viruses demonstrate the method's efficacy. We achieve 100% recovery of the spiked-in SV40 (Simian virus 40, 5243bp) genome sequence with uniform coverage distribution, and approximately 99.4% for the larger HAd5 genome (Human Adenovirus 5, 35938bp). Notably, genome recovery is achieved with as few as one sorted droplet, which enables the recovery of any desired genomes in complex environmental samples, regardless of their abundance. This method enables targeted characterizations of rare viral species and whole-genome amplification of single genomes for accessing the mutational profile in single virus genomes, contributing to an improved understanding of viral ecology.}, } @article {pmid38014294, year = {2023}, author = {Pereira, FC and Ge, X and Kristensen, JM and Kirkegaard, RH and Maritsch, K and Zhu, Y and Decorte, M and Hausmann, B and Berry, D and Wasmund, K and Schintlmeister, A and Boettcher, T and Cheng, JX and Wagner, M}, title = {The Parkinson's drug entacapone disrupts gut microbiome homeostasis via iron sequestration.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38014294}, support = {R01 AI141439/AI/NIAID NIH HHS/United States ; R35 GM136223/GM/NIGMS NIH HHS/United States ; S10 OD024993/OD/NIH HHS/United States ; }, abstract = {Increasing evidence shows that many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, much less is known about the mechanisms by which drugs target the microbiome and how drugs affect microbial function. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single-cell chemical imaging to investigate the impact of two widely prescribed nervous system-targeted drugs on the gut microbiome. Ex vivo supplementation of physiologically relevant concentrations of entacapone or loxapine succinate to faecal samples significantly impacted the abundance of up to one third of the microbial species present. Importantly, we demonstrate that the impact of these drugs on microbial metabolism is much more pronounced than their impact on abundances, with low concentrations of drugs reducing the activity, but not the abundance of key microbiome members like Bacteroides, Ruminococcus or Clostridium species. We further demonstrate that entacapone impacts the microbiome due to its ability to complex and deplete available iron, and that microbial growth can be rescued by replenishing levels of microbiota-accessible iron. Remarkably, entacapone-induced iron starvation selected for iron-scavenging organisms carrying antimicrobial resistance and virulence genes. Collectively, our study unveils the impact of two under-investigated drugs on whole microbiomes and identifies metal sequestration as a mechanism of drug-induced microbiome disturbance.}, } @article {pmid38014162, year = {2023}, author = {Subramanian, P and Romero-Soto, HN and Stern, DB and Maxwell, GL and Levy, S and Hourigan, SK}, title = {Delivery mode impacts gut bacteriophage colonization during infancy.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {38014162}, support = {K23 HD099240/HD/NICHD NIH HHS/United States ; }, abstract = {BACKGROUND: Cesarean section delivery is associated with altered early-life bacterial colonization and later adverse inflammatory and immune health outcomes. Although gut bacteriophages can alter gut microbiome composition and impact host immune responses, little is known about how delivery mode impacts bacteriophage colonization over time. To begin to address this we examined how delivery mode affected bacteriophage colonization over the first two years of life.

RESULTS: Shotgun metagenomic sequencing was conducted on 272 serial stool samples from 55 infants, collected at 1-2 days of life and 2, 6, 12 and 24 months. 33/55 (60%) infants were born by vaginal delivery. DNA viruses were identified, and by host inference, 94% of the viral sequences were found to be bacteriophages. Alpha diversity of the virome was increased in vaginally delivered infants compared to cesarean section delivered infants at 2 months (Shannon index, p=0.022). Beta diversity significantly differed by delivery mode at 2, 6, and 12 months when stratified by peripartum antibiotic use (Bray-Curtis dissimilarity, all p<0.05). Significant differentially abundant predicted bacteriophage hosts by delivery mode were seen at all time points. Moreover, there were differences in predicted bacteriophage functional gene abundances up to 24 months by delivery mode. Many of the functions considered to play a role in host response were increased in vaginal delivery.

CONCLUSIONS: Clear differences in bacteriophage composition and function were seen by delivery mode over the first two years of life. Given that phages are known to affect host immune response, our results suggest that future investigation into how delivery mode may lead to adverse inflammatory outcomes should not only include bacterial microbial colonization but also the potential role of bacteriophages and transkingdom interactions.}, } @article {pmid38014039, year = {2023}, author = {Ha, AD and Aylward, FO}, title = {Automated classification of giant virus genomes using a random forest model built on trademark protein families.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38014039}, support = {R35 GM147290/GM/NIGMS NIH HHS/United States ; }, abstract = {Viruses of the phylum Nucleocytoviricota, often referred to as "giant viruses," are prevalent in various environments around the globe and play significant roles in shaping eukaryotic diversity and activities in global ecosystems. Given the extensive phylogenetic diversity within this viral group and the highly complex composition of their genomes, taxonomic classification of giant viruses, particularly incomplete metagenome-assembled genomes (MAGs) can present a considerable challenge. Here we developed TIGTOG (Taxonomic Information of Giant viruses using Trademark Orthologous Groups), a machine learning-based approach to predict the taxonomic classification of novel giant virus MAGs based on profiles of protein family content. We applied a random forest algorithm to a training set of 1,531 quality-checked, phylogenetically diverse Nucleocytoviricota genomes using pre-selected sets of giant virus orthologous groups (GVOGs). The classification models were predictive of viral taxonomic assignments with a cross-validation accuracy of 99.6% to the order level and 97.3% to the family level. We found that no individual GVOGs or genome features significantly influenced the algorithm's performance or the models' predictions, indicating that classification predictions were based on a comprehensive genomic signature, which reduced the necessity of a fixed set of marker genes for taxonomic assigning purposes. Our classification models were validated with an independent test set of 823 giant virus genomes with varied genomic completeness and taxonomy and demonstrated an accuracy of 98.6% and 95.9% to the order and family level, respectively. Our results indicate that protein family profiles can be used to accurately classify large DNA viruses at different taxonomic levels and provide a fast and accurate method for the classification of giant viruses. This approach could easily be adapted to other viral groups.}, } @article {pmid38014029, year = {2023}, author = {Song, L and Langmead, B}, title = {Centrifuger: lossless compression of microbial genomes for efficient and accurate metagenomic sequence classification.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {38014029}, support = {P20 GM130454/GM/NIGMS NIH HHS/United States ; R01 HG011392/HG/NHGRI NIH HHS/United States ; R35 GM139602/GM/NIGMS NIH HHS/United States ; }, abstract = {Centrifuger is an efficient taxonomic classification method that compares sequencing reads against a microbial genome database. In Centrifuger, the Burrows-Wheeler transformed genome sequences are losslessly compressed using a novel scheme called run-block compression. Run-block compression achieves sublinear space complexity and is effective at compressing diverse microbial databases like RefSeq while supporting fast rank queries. Combining this compression method with other strategies for compacting the Ferragina-Manzini (FM) index, Centrifuger reduces the memory footprint by half compared to other FM-index-based approaches. Furthermore, the lossless compression and the unconstrained match length help Centrifuger achieve greater accuracy than competing methods at lower taxonomic levels.}, } @article {pmid38013098, year = {2023}, author = {Fang, GY and Liu, XQ and Jiang, YJ and Mu, XJ and Huang, BW}, title = {Horizontal gene transfer in activated sludge enhances microbial antimicrobial resistance and virulence.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {168908}, doi = {10.1016/j.scitotenv.2023.168908}, pmid = {38013098}, issn = {1879-1026}, abstract = {Activated sludge (AS) plays a vital role in removing organic pollutants and nutrients from wastewater. However, the risks posed by horizontal gene transfer (HGT) between bacteria in AS are still unclear. Here, a total of 478 high-quality non-redundant metagenome-assembled genomes (MAGs) were obtained. >50 % and 5 % of MAGs were involved in at least one HGT and recent HGT, respectively. Most of the transfers (82.4 %) of antimicrobial resistance genes (ARGs) occurred among the classes of Alphaproteobacteria and Gammaproteobacteria. The bacteria involved in the transfers of virulence factor genes (VFGs) mainly include Alphaproteobacteria (42.3 %), Bacteroidia (19.2 %), and Gammaproteobacteria (11.5 %). Moreover, the number of ARGs and VFGs in the classes of Alphaproteobacteria and Gammaproteobacteria was higher than that in other bacteria (P < 0.001). Mobile genetic elements were important contributors to ARGs and VFGs in AS bacteria. These results have implications for the management of antimicrobial resistance and virulence in activated sludge microorganisms.}, } @article {pmid38013035, year = {2023}, author = {Dong, W and Zhou, R and Li, X and Yan, H and Zheng, J and Peng, N and Zhao, S}, title = {Effect of simplified inoculum agent on performance and microbiome during cow manure-composting at industrial-scale.}, journal = {Bioresource technology}, volume = {393}, number = {}, pages = {130097}, doi = {10.1016/j.biortech.2023.130097}, pmid = {38013035}, issn = {1873-2976}, abstract = {A simplified inoculum agent, only comprising Bacillus subtilis and Aspergillus niger, was utilized for industrial-scale cow-manure composting to investigate its impact on composting performance and microbiome. Inoculants elevated the average and peak temperatures by up to 7 and 10 °C, respectively, during the thermophilic stage, reduced organic matter content, and raised germination index. Inoculation also extended the period of composting above 50 °C from 12 to 26 days. Sequencing unveiled significant shifts in microbial diversity, composition, and function. Aspergillus thrived during the mesophilic phase, potentially initiating composting, whereas Bacillus, Lysinibacillus, and Clostridium were enriched during the thermophilic stage. Metagenomic sequencing revealed an increased abundance of carbohydrate-active enzymes and glycometabolism-related genes responsible for lignocellulose degradation and heat generation after inoculation. These enriched microbes and functional genes contributed to organic matter degradation and temperature maintenance during thermophilic stage, expediting composting. This suggests the effectiveness of this simplified inoculum in industrial-level cow-manure composting.}, } @article {pmid38013027, year = {2024}, author = {Kishor, R and Verma, M and Saratale, GD and Romanholo Ferreira, LF and Kharat, AS and Chandra, R and Raj, A and Bharagava, RN}, title = {Treatment of industrial wastewaters by algae-bacterial consortium with Bio-H2 production: Recent updates, challenges and future prospects.}, journal = {Chemosphere}, volume = {349}, number = {}, pages = {140742}, doi = {10.1016/j.chemosphere.2023.140742}, pmid = {38013027}, issn = {1879-1298}, mesh = {Humans ; *Wastewater ; Bacteria ; Plants ; Fossil Fuels ; Biomass ; *Environmental Pollutants ; Water ; Biofuels ; }, abstract = {Currently, scarcity/security of clean water and energy resources are the most serious problems worldwide. Industries use large volume of ground water and a variety of chemicals to manufacture the products and discharge large volume of wastewater into environment, which causes severe impacts on environment and public health. Fossil fuels are considered as major energy resources for electricity and transportation sectors, which release large amount of CO2 and micro/macro pollutants, leading to cause the global warming and public health hazards. Therefore, algae-bacterial consortium (A-BC) may be eco-friendly, cost-effective and sustainable alternative way to treat the industrial wastewaters (IWWs) with Bio-H2 production. A-BC has potential to reduce the global warming and eutrophication. It also protects environment and public health as it converts toxic IWWs into non or less toxic (biomass). It also reduces 94%, 90% and 50% input costs of nutrients, freshwater and energy, respectively during IWWs treatment and Bio-H2 production. Most importantly, it produce sustainable alternative (Bio-H2) to replace use of fossil fuels and fill the world's energy demand in eco-friendly manner. Thus, this review paper provides a detailed knowledge on industrial wastewaters, their pollutants and toxic effects on water/soil/plant/humans and animals. It also provides an overview on A-BC, IWWs treatment, Bio-H2 production, fermentation process and its enhancement methods. Further, various molecular and analytical techniques are also discussed to characterize the A-BC structure, interactions, metabolites and Bio-H2 yield. The significance of A-BC, recent update, challenges and future prospects are also discussed.}, } @article {pmid38012968, year = {2023}, author = {Zhang, M and Xu, Y and Wang, J and Hu, J and Qi, S and Jiang, Z and Yang, S}, title = {Impact of biochar on the antibiotic resistome and associated microbial functions in rhizosphere and bulk soil in water-saving and flooding irrigated paddy fields.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {342}, number = {}, pages = {123026}, doi = {10.1016/j.envpol.2023.123026}, pmid = {38012968}, issn = {1873-6424}, abstract = {The addition of biochar in paddies under the condition of water-saving irrigation can simultaneously achieve soil improvement and water conservation, but little is known about the role of these two regulations in mediating the fate of antibiotic resistome in paddy soils. Here, metagenomic analysis was conducted to investigate the effects and intrinsic mechanisms of biochar application and irrigation patterns on propagation of antibiotic resistance genes (ARGs) in paddy soils. The addition of biochar in paddy soil resulted in a reduction of approximately 1.32%-8.01% in the total absolute abundance of ARGs and 0.60%-22.09% in the numbers of ARG subtype. Compared with flooding irrigation, the numbers of detected ARG subtype were reduced by 1.60%-22.90%, but the total absolute abundance of ARGs increased by 0.06%-5.79% in water-saving irrigation paddy soils. Moreover, the combined treatments of flooding irrigation and biochar could significantly reduce the abundance of ARGs in paddy soils. The incremental antibiotic resistance in soil induced by water-saving irrigation was likewise mitigated by the addition of biochar. Correlation analyses indicated that, the differences in soil physicochemical properties under biochar addition or irrigation treatments contributed to the corresponding changes in the abundance of ARGs. Moreover, the variations of microbial community diversity, multidrug efflux abundance and transport system-related genes in paddy soil were also important for mediating the corresponding differences in the abundance of ARGs under the conditions of biochar addition or irrigation treatments. The findings of this study demonstrated the effectiveness of biochar application in mitigating antibiotic resistance in paddy soils. However, it also highlighted a potential concern relating to the elevated antibiotic resistance associated with water-saving irrigation in paddy fields. Consequently, these results contribute to a deeper comprehension of the environmental risks posed by ARGs in paddy soils.}, } @article {pmid38012935, year = {2023}, author = {Jäger, HY and Atz Zanotelli, D and Maixner, F and Nicklisch, N and Alt, KW and Meller, H and Pap, I and Szikossy, I and Pálfi, G and Zink, AR}, title = {Hit or miss - A metagenomic evaluation of intra-bone variability of host pathogen load in tuberculosis-infected human remains.}, journal = {Tuberculosis (Edinburgh, Scotland)}, volume = {143S}, number = {}, pages = {102392}, doi = {10.1016/j.tube.2023.102392}, pmid = {38012935}, issn = {1873-281X}, mesh = {Humans ; *Mycobacterium tuberculosis/genetics ; Body Remains ; *Tuberculosis/microbiology ; Bone and Bones ; DNA ; DNA, Ancient ; }, abstract = {Many sampling protocols have been established to successfully retrieve human DNA from archaeological remains, however the systematic detection of ancient pathogens remains challenging. Here, we present a first assessment of the intra-bone variability of metagenomic composition in human skeletal remains and its effect on the sampling success for Mycobacterium tuberculosis (MTB) and human endogenous DNA. For this purpose, four bone samples from published peer-reviewed studies with PCR-based evidence for ancient MTB DNA were selected. Two bone samples of a Neolithic individual from Halberstadt, Germany and two ribs of two 18th-century Hungarian church mummies were sampled at multiple locations for equal amounts, followed by DNA extraction and library construction. Shotgun sequencing data was generated for taxonomic profiling as well as quantitative and qualitative evaluation of MTB and human endogenous DNA. Despite low variance in microbial diversity within and across samples, intra-bone variability of up to 36.45- and 62.88-fold for authentic ancient MTB and human reads, respectively, was detected. This study demonstrates the variable sampling success for MTB and human endogenous DNA within single skeletal samples despite relatively consistent microbial composition and highlights how a multisampling approach can facilitate the detection of hotspots with highly concentrated pathogen and human endogenous DNA.}, } @article {pmid38012750, year = {2023}, author = {Zhang, X and Miao, Q and Tang, B and Mijakovic, I and Ji, XJ and Qu, L and Wei, Y}, title = {Discovery of novel alkaline-tolerant xylanases from fecal microbiota of dairy cows.}, journal = {Biotechnology for biofuels and bioproducts}, volume = {16}, number = {1}, pages = {182}, pmid = {38012750}, issn = {2731-3654}, support = {32101003//the National Natural Science Foundation of China/ ; 32111530179//the National Natural Science Foundation of China/ ; NNF20CC0035580//the Novo Nordisk Foundation/ ; 212D007//Kaifeng City Science and Technology Development Projects/ ; }, abstract = {Xylo-oligosaccharides (XOS) are considered as a promising type of prebiotics that can be used in foods, feeds, and healthcare products. Xylanases play a key role in the production of XOS from xylan. In this study, we conducted a metagenomic analysis of the fecal microbiota from dairy cows fed with different types of fodders. Despite the diversity in their diets, the main phyla observed in all fecal microbiota were Firmicutes and Bacteroidetes. At the genus level, one group of dairy cows that were fed probiotic fermented herbal mixture-containing fodders displayed decreased abundance of Methanobrevibacter and increased growth of beneficial Akkermansia bacteria. Additionally, this group exhibited a high microbial richness and diversity. Through our analysis, we obtained a comprehensive dataset comprising over 280,000 carbohydrate-active enzyme genes. Among these, we identified a total of 163 potential xylanase genes and subsequently expressed 34 of them in Escherichia coli. Out of the 34 expressed genes, two alkaline xylanases with excellent temperature stability and pH tolerance were obtained. Notably, CDW-xyl-8 exhibited xylanase activity of 96.1 ± 7.5 U/mg protein, with an optimal working temperature of 55 ℃ and optimal pH of 8.0. CDW-xyl-16 displayed an activity of 427.3 ± 9.1 U/mg protein with an optimal pH of 8.5 and an optimal temperature at 40 ℃. Bioinformatic analyses and structural modeling suggest that CDW-xyl-8 belongs to GH10 family xylanase, and CDW-xyl-16 is a GH11 family xylanase. Both enzymes have the ability to hydrolyze beechwood xylan and produce XOS. In conclusion, this metagenomic study provides valuable insights into the fecal microbiota composition of dairy cows fed different fodder types, revealing main microbial groups and demonstrating the abundance of xylanases. Furthermore, the characterization of two novel xylanases highlights their potential application in XOS production.}, } @article {pmid38012564, year = {2023}, author = {Bian, W and Xie, Y and Shang, Y and Zhao, L and Yang, Z and Ma, X and He, Y and Yu, W and Xi, W and Yang, D and Wang, F and Chen, Y and Gong, P and Gao, Z}, title = {Relationship between clinical features and droplet digital PCR copy number in non-HIV patients with pneumocystis pneumonia.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {833}, pmid = {38012564}, issn = {1471-2334}, support = {N/A//the National and Provincial Key Clinical Specialty Capacity Building Project 2020 (Department of the Respiratory Medicine)/ ; N/A//the National and Provincial Key Clinical Specialty Capacity Building Project 2020 (Department of the Respiratory Medicine)/ ; N/A//the National and Provincial Key Clinical Specialty Capacity Building Project 2020 (Department of the Respiratory Medicine)/ ; N/A//the National and Provincial Key Clinical Specialty Capacity Building Project 2020 (Department of the Respiratory Medicine)/ ; N/A//the National and Provincial Key Clinical Specialty Capacity Building Project 2020 (Department of the Respiratory Medicine)/ ; N/A//the National and Provincial Key Clinical Specialty Capacity Building Project 2020 (Department of the Respiratory Medicine)/ ; N/A//the National and Provincial Key Clinical Specialty Capacity Building Project 2020 (Department of the Respiratory Medicine)/ ; N/A//the National and Provincial Key Clinical Specialty Capacity Building Project 2020 (Department of the Respiratory Medicine)/ ; N/A//the National and Provincial Key Clinical Specialty Capacity Building Project 2020 (Department of the Respiratory Medicine)/ ; N/A//the National and Provincial Key Clinical Specialty Capacity Building Project 2020 (Department of the Respiratory Medicine)/ ; N/A//the National and Provincial Key Clinical Specialty Capacity Building Project 2020 (Department of the Respiratory Medicine)/ ; N/A//the National and Provincial Key Clinical Specialty Capacity Building Project 2020 (Department of the Respiratory Medicine)/ ; N/A//the National and Provincial Key Clinical Specialty Capacity Building Project 2020 (Department of the Respiratory Medicine)/ ; N/A//the National and Provincial Key Clinical Specialty Capacity Building Project 2020 (Department of the Respiratory Medicine)/ ; N/A//Evaluation of droplet digital PCR for the detection of Pneumocystis jirovecii in alveolar lavage fluid and analysis of correlation between copy number and clinical characteristics/ ; N/A//Evaluation of droplet digital PCR for the detection of Pneumocystis jirovecii in alveolar lavage fluid and analysis of correlation between copy number and clinical characteristics/ ; N/A//Evaluation of droplet digital PCR for the detection of Pneumocystis jirovecii in alveolar lavage fluid and analysis of correlation between copy number and clinical characteristics/ ; N/A//Evaluation of droplet digital PCR for the detection of Pneumocystis jirovecii in alveolar lavage fluid and analysis of correlation between copy number and clinical characteristics/ ; N/A//Evaluation of droplet digital PCR for the detection of Pneumocystis jirovecii in alveolar lavage fluid and analysis of correlation between copy number and clinical characteristics/ ; N/A//Evaluation of droplet digital PCR for the detection of Pneumocystis jirovecii in alveolar lavage fluid and analysis of correlation between copy number and clinical characteristics/ ; N/A//Evaluation of droplet digital PCR for the detection of Pneumocystis jirovecii in alveolar lavage fluid and analysis of correlation between copy number and clinical characteristics/ ; N/A//Evaluation of droplet digital PCR for the detection of Pneumocystis jirovecii in alveolar lavage fluid and analysis of correlation between copy number and clinical characteristics/ ; N/A//Evaluation of droplet digital PCR for the detection of Pneumocystis jirovecii in alveolar lavage fluid and analysis of correlation between copy number and clinical characteristics/ ; N/A//Evaluation of droplet digital PCR for the detection of Pneumocystis jirovecii in alveolar lavage fluid and analysis of correlation between copy number and clinical characteristics/ ; N/A//Evaluation of droplet digital PCR for the detection of Pneumocystis jirovecii in alveolar lavage fluid and analysis of correlation between copy number and clinical characteristics/ ; N/A//Evaluation of droplet digital PCR for the detection of Pneumocystis jirovecii in alveolar lavage fluid and analysis of correlation between copy number and clinical characteristics/ ; N/A//Evaluation of droplet digital PCR for the detection of Pneumocystis jirovecii in alveolar lavage fluid and analysis of correlation between copy number and clinical characteristics/ ; N/A//Evaluation of droplet digital PCR for the detection of Pneumocystis jirovecii in alveolar lavage fluid and analysis of correlation between copy number and clinical characteristics/ ; }, mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis ; Retrospective Studies ; DNA Copy Number Variations ; Bronchoalveolar Lavage Fluid ; Polymerase Chain Reaction ; *Pneumocystis ; *Respiratory Distress Syndrome ; *Pneumocystis carinii/genetics ; }, abstract = {OBJECTIVE: Droplet digital PCR (ddPCR) is a novel assay to detect pneumocystis jjrovecii (Pj) which has been defined to be more sensitive than qPCR in recent studies. We aimed to explore whether clinical features of pneumocystis pneumonia (PCP) were associated with ddPCR copy numbers of Pj.

METHODS: A total of 48 PCP patients were retrospectively included. Pj detection was implemented by ddPCR assay within 4 h. Bronchoalveolar fluid (BALF) samples were collected from 48 patients with molecular diagnosis as PCP via metagenomic next generation sequencing (mNGS) or quantitative PCR detection. Univariate and multivariate logistic regression were performed to screen out possible indicators for the severity of PCP. The patients were divided into two groups according to ddPCR copy numbers, and their clinical features were further analyzed.

RESULTS: Pj loading was a pro rata increase with serum (1,3)-beta-D glucan, D-dimmer, neutrophil percentage, procalcitonin and BALF polymorphonuclear leucocyte percentage, while negative correlation with albumin, PaO2/FiO2, BALF cell count, and BALF lymphocyte percentage. D-dimmer and ddPCR copy number of Pj were independent indicators for moderate/severe PCP patients with PaO2/FiO2 lower than 300. We made a ROC analysis of ddPCR copy number of Pj for PaO2/FiO2 index and grouped the patients according to the cut-off value (2.75). The high copy numbers group was characterized by higher level of inflammatory markers. Compared to low copy number group, there was lower level of the total cell count while higher level of polymorphonuclear leucocyte percentage in BALF in the high copy numbers group. Different from patients with high copy numbers, those with high copy numbers had a tendency to develop more severe complications and required advanced respiratory support.

CONCLUSION: The scenarios of patients infected with high ddPCR copy numbers of Pj showed more adverse clinical conditions. Pj loading could reflect the severity of PCP to some extent.}, } @article {pmid38012208, year = {2023}, author = {Mara, P and Geller-McGrath, D and Edgcomb, V and Beaudoin, D and Morono, Y and Teske, A}, title = {Metagenomic profiles of archaea and bacteria within thermal and geochemical gradients of the Guaymas Basin deep subsurface.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7768}, pmid = {38012208}, issn = {2041-1723}, support = {OCE-2046799//National Science Foundation (NSF)/ ; OCE-1829903//National Science Foundation (NSF)/ ; OCE-2046799//National Science Foundation (NSF)/ ; OCE-1829903//National Science Foundation (NSF)/ ; OCE-1829903//National Science Foundation (NSF)/ ; OCE-2046799//National Science Foundation (NSF)/ ; OCE-1829903//National Science Foundation (NSF)/ ; JP19H00730//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JP23H00154//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {*Archaea/genetics ; Metagenome/genetics ; Geologic Sediments/chemistry ; Phylogeny ; Bacteria/genetics ; *Crenarchaeota ; RNA, Ribosomal, 16S ; }, abstract = {Previous studies of microbial communities in subseafloor sediments reported that microbial abundance and diversity decrease with sediment depth and age, and microbes dominating at depth tend to be a subset of the local seafloor community. However, the existence of geographically widespread, subsurface-adapted specialists is also possible. Here, we use metagenomic and metatranscriptomic analyses of the hydrothermally heated, sediment layers of Guaymas Basin (Gulf of California, Mexico) to examine the distribution and activity patterns of bacteria and archaea along thermal, geochemical and cell count gradients. We find that the composition and distribution of metagenome-assembled genomes (MAGs), dominated by numerous lineages of Chloroflexota and Thermoproteota, correlate with biogeochemical parameters as long as temperatures remain moderate, but downcore increasing temperatures beyond ca. 45 ºC override other factors. Consistently, MAG size and diversity decrease with increasing temperature, indicating a downcore winnowing of the subsurface biosphere. By contrast, specific archaeal MAGs within the Thermoproteota and Hadarchaeota increase in relative abundance and in recruitment of transcriptome reads towards deeper, hotter sediments, marking the transition towards a specialized deep, hot biosphere.}, } @article {pmid38011171, year = {2023}, author = {Tomita, S and Kuroda, K and Narihiro, T}, title = {A small step to discover candidate biological control agents from preexisting bioresources by using novel nonribosomal peptide synthetases hidden in activated sludge metagenomes.}, journal = {PloS one}, volume = {18}, number = {11}, pages = {e0294843}, pmid = {38011171}, issn = {1932-6203}, mesh = {*Metagenome ; *Sewage ; Biological Control Agents ; Polyketide Synthases/genetics ; Peptide Synthases/genetics ; }, abstract = {Biological control agents (BCAs), beneficial organisms that reduce the incidence or severity of plant disease, have been expected to be alternatives to replace chemical pesticides worldwide. To date, BCAs have been screened by culture-dependent methods from various environments. However, previously unknown BCA candidates may be buried and overlooked because this approach preferentially selects only easy-to-culture microbial lineages. To overcome this limitation, as a small-scale test case, we attempted to explore novel BCA candidates by employing the shotgun metagenomic information of the activated sludge (AS) microbiome, which is thought to contain unutilized biological resources. We first performed genome-resolved metagenomics for AS taken from a municipal sewage treatment plant and obtained 97 nonribosomal peptide synthetase (NRPS)/polyketide synthase (PKS)-related gene sequences from 43 metagenomic assembled bins, most of which were assigned to the phyla Proteobacteria and Myxococcota. Furthermore, these NRPS/PKS-related genes are predicted to be novel because they were genetically dissimilar to known NRPS/PKS gene clusters. Of these, the condensation domain of the syringomycin-related NRPS gene cluster was detected in Rhodoferax- and Rhodocyclaceae-related bins, and its homolog was found in previously reported AS metagenomes as well as the genomes of three strains available from the microbial culture collections, implying their potential BCA ability. Then, we tested the antimicrobial activity of these strains against phytopathogenic fungi to investigate the potential ability of BCA by in vitro cultivation and successfully confirmed the actual antifungal activity of three strains harboring a possibly novel NRPS gene cluster. Our findings provide a possible strategy for discovering novel BCAs buried in the environment using genome-resolved metagenomics.}, } @article {pmid38010882, year = {2024}, author = {Espada-Hinojosa, S and Karthäuser, C and Srivastava, A and Schuster, L and Winter, T and de Oliveira, AL and Schulz, F and Horn, M and Sievert, S and Bright, M}, title = {Comparative genomics of a vertically transmitted thiotrophic bacterial ectosymbiont and its close free-living relative.}, journal = {Molecular ecology resources}, volume = {24}, number = {1}, pages = {e13889}, doi = {10.1111/1755-0998.13889}, pmid = {38010882}, issn = {1755-0998}, support = {P 24565//Austrian Science Fund/ ; P 32197//Austrian Science Fund/ ; //WHOI Investment in Science Fund/ ; }, mesh = {Animals ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Bacteria ; *Genomics ; Symbiosis ; Sulfur/metabolism ; }, abstract = {Thiotrophic symbioses between sulphur-oxidizing bacteria and various unicellular and metazoan eukaryotes are widespread in reducing marine environments. The giant colonial ciliate Zoothamnium niveum, however, is the only host of thioautotrophic symbionts that has been cultivated along with its symbiont, the vertically transmitted ectosymbiont Candidatus Thiobius zoothamnicola (short Thiobius). Because theoretical predictions posit a smaller genome in vertically transmitted endosymbionts compared to free-living relatives, we investigated whether this is true also for an ectosymbiont. We used metagenomics to recover the high-quality draft genome of this bacterial symbiont. For comparison we have also sequenced a closely related free-living cultured but not formally described strain Milos ODIII6 (short ODIII6). We then performed comparative genomics to assess the functional capabilities at gene, metabolic pathway and trait level. 16S rRNA gene trees and average amino acid identity confirmed the close phylogenetic relationship of both bacteria. Indeed, Thiobius has about a third smaller genome than its free-living relative ODIII6, with reduced metabolic capabilities and fewer functional traits. The functional capabilities of Thiobius were a subset of those of the more versatile ODIII6, which possessed additional genes for oxygen, sulphur and hydrogen utilization and for the acquisition of phosphorus illustrating features that may be adaptive for the unstable environmental conditions at hydrothermal vents. In contrast, Thiobius possesses genes potentially enabling it to utilize lactate and acetate heterotrophically, compounds that may be provided as byproducts by the host. The present study illustrates the effect of strict host-dependence of a bacterial ectosymbiont on genome evolution and host adaptation.}, } @article {pmid38010871, year = {2023}, author = {Jinato, T and Sikaroodi, M and Fagan, A and Sterling, RK and Lee, H and Puri, P and Davis, BC and Fuchs, M and Gavis, E and Gillevet, PM and Bajaj, JS}, title = {Alterations in gut virome are associated with cognitive function and minimal hepatic encephalopathy cross-sectionally and longitudinally in cirrhosis.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2288168}, pmid = {38010871}, issn = {1949-0984}, support = {I01 CX001076/CX/CSRD VA/United States ; I01 CX002472/CX/CSRD VA/United States ; R01 AA029398/AA/NIAAA NIH HHS/United States ; }, mesh = {Humans ; *Hepatic Encephalopathy ; Virome ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Liver Cirrhosis/complications ; Fibrosis ; Cognition ; }, abstract = {Cognitive dysfunction due to minimal hepatic encephalopathy (MHE) adversely impacts patients with cirrhosis and more precise therapies are needed. Gut-brain axis changes are therapeutic targets, but prior studies have largely focused on bacterial changes. Our aim was to determine linkages between individual cognitive testing results and bacteria with the virome using a cross-sectional and longitudinal approach. We included cross-sectional (n = 138) and longitudinal analyses (n = 36) of patients with cirrhosis tested using three cognitive modalities, which were psychometric hepatic encephalopathy score (PHES), inhibitory control test (ICT), Stroop, and all three. Stool metagenomics with virome and bacteriome were analyzed studied cross-sectionally and in a subset followed for development/reversal of MHE repeated at 6 months (longitudinally only using PHES). Cross-sectional: We found no significant changes in α/β diversity in viruses or bacteria regardless of cognitive testing. Cognitively impaired patients were more likely to have higher relative abundance of bacteriophages linked with Streptococcus, Faecalibacterium, and Lactobacillus, which were distinct based on modality. These were also linked with cognition on correlation networks. Longitudinally, 27 patients remained stable while 9 changed their MHE status. Similar changes in phages that are linked with Streptococcus, Faecalibacterium, and Lactobacillus were seen. These phages can influence ammonia, lactate, and short-chain fatty acid generation, which are neuro-active. In conclusion, we found linkages between bacteriophages and cognitive function likely due to impact on bacteria that produce neuroactive metabolites cross-sectionally and longitudinally. These findings could help explore bacteriophages as options to influence treatment for MHE in cirrhosis.}, } @article {pmid38010636, year = {2023}, author = {Gladyshev, NS and Baram, DV and Gorbunova, AV and Krivolapov, YA}, title = {[Transcriptome analysis of tissue microbiota diversity in tumor and non-tumor lymph nodes].}, journal = {Arkhiv patologii}, volume = {85}, number = {6}, pages = {26-30}, doi = {10.17116/patol20238506126}, pmid = {38010636}, issn = {0004-1955}, mesh = {Humans ; *Lymphoma, Follicular/diagnosis/pathology ; Hyperplasia/pathology ; Lymph Nodes/pathology ; Gene Expression Profiling ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Metagenomic studies in recent years have demonstrated that all tissues of the human body studied by genomic and transcriptomic sequencing methods, both in pathological processes and in normality, contain fragments of DNA and RNA from a variety of microorganisms. The composition of tissue microbiota and its relationship with development of pathological changes are still poorly understood, despite increasing number of studies in this area every year. In this study, gene expression of the lymph node microbiome in reactive follicular hyperplasia and follicular lymphoma was investigated.

OBJECTIVE: To study expression of lymph node microbiome genes in reactive follicular hyperplasia and follicular lymphoma.

MATERIAL AND METHODS: The work included 38 biopsy samples of lymph nodes with follicular lymphoma of different cytological subtypes and 10 biopsy samples of lymph nodes with reactive follicular hyperplasia. Verification of diagnosis was carried out using standard histological, histochemical and immunohistochemical methods. Using sequencing method, the transcriptome was examined. Statistical analysis and data visualization were performed using the R programming language (version 4.2.1).

RESULTS: Tumor lymph nodes are characterized by large Simpson and Shannon alpha diversity values (p-value = 0.026465 and p-value = 0.007122, respectively). Two clusters were discovered, characterized by different levels of relative abundance of microorganisms.

CONCLUSION: It has been proven that diversity of microorganisms present in tumor tissue and their number are statistically significantly higher than corresponding indicators in the lymph nodes with follicular hyperplasia.}, } @article {pmid38010361, year = {2023}, author = {Nori, SRC and McGuire, TK and Lawton, EM and McAuliffe, FM and Sinderen, DV and Walsh, CJ and Cotter, PD and Feehily, C}, title = {Profiling of vaginal Lactobacillus jensenii isolated from preterm and full-term pregnancies reveals strain-specific factors relating to host interaction.}, journal = {Microbial genomics}, volume = {9}, number = {11}, pages = {}, pmid = {38010361}, issn = {2057-5858}, mesh = {Pregnancy ; Female ; Child ; Infant, Newborn ; Humans ; *Premature Birth/epidemiology/microbiology ; Lactobacillus ; Vagina/microbiology ; Bacteria ; }, abstract = {Each year, 15 million infants are born preterm (<37 weeks gestation), representing the leading cause of mortality for children under the age of five. Whilst there is no single cause, factors such as maternal genetics, environmental interactions, and the vaginal microbiome have been associated with an increased risk of preterm birth. Previous studies show that a vaginal microbiota dominated by Lactobacillus is, in contrast to communities containing a mixture of genera, associated with full-term birth. However, this binary principle does not fully consider more nuanced interactions between bacterial strains and the host. Here, through a combination of analyses involving genome-sequenced isolates and strain-resolved metagenomics, we identify that L. jensenii strains from preterm pregnancies are phylogenetically distinct from strains from full-term pregnancies. Detailed analysis reveals several genetic signatures that distinguish preterm birth strains, including genes predicted to be involved in cell wall synthesis, and lactate and acetate metabolism. Notably, we identify a distinct gene cluster involved in cell surface protein synthesis in our preterm strains, and profiling the prevalence of this gene cluster in publicly available genomes revealed it to be predominantly present in the preterm-associated clade. This study contributes to the ongoing search for molecular biomarkers linked to preterm birth and opens up new avenues for exploring strain-level variations and mechanisms that may contribute to preterm birth.}, } @article {pmid38010130, year = {2023}, author = {Zhou, Y and Wang, Y and Krupovic, M}, title = {ICTV Virus Taxonomy Profile: Aoguangviridae 2023.}, journal = {The Journal of general virology}, volume = {104}, number = {11}, pages = {}, pmid = {38010130}, issn = {1465-2099}, mesh = {*Virus Replication ; Genome, Viral ; *Viruses/genetics ; Virion/genetics ; Phylogeny ; }, abstract = {The family Aoguangviridae includes dsDNA viruses that have been associated with marine archaea. Currently, members of this virus family are known through metagenomics. Virions are predicted to consist of an icosahedral capsid and a helical tail, characteristic of members in the class Caudoviricetes. Aoguangviruses have some of the largest genomes among archaeal viruses and possess most of the components of the DNA replication machinery as well as auxiliary functions. The family Aoguangviridae includes the species Aobingvirus yangshanense. Many unclassified relatives of this virus group, referred to as 'magroviruses', have been discovered by metagenomics in globally distributed marine samples. This is a summary of the International Committee on Taxonomy of Viruses (ICTV) Report on the family Aoguangviridae, which is available at ictv.global/report/aoguangviridae.}, } @article {pmid38010080, year = {2023}, author = {Luoto, R and Pärtty, A and Vogt, JK and Rautava, S and Isolauri, E}, title = {Reversible aberrancies in gut microbiome of moderate and late preterm infants: results from a randomized, controlled trial.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2283913}, pmid = {38010080}, issn = {1949-0984}, mesh = {Infant ; Child ; Female ; Humans ; Infant, Newborn ; Infant, Premature ; *Gastrointestinal Microbiome/physiology ; *Probiotics ; Prebiotics ; Breast Feeding ; *Lacticaseibacillus rhamnosus ; }, abstract = {The aim of this study was to obtain insight into the composition and function of the deviant gut microbiome throughout infancy in children born moderately and late preterm and their response to microbiome modulation. We characterized the longitudinal development of the gut microbiome from birth to the age of 12 months by metagenomic sequencing in 43 moderate and late preterm children participating in a randomized, controlled trial (ClinicalTrials.gov/no.NCT00167700) assessing the impact of a probiotic (Lactobacillus rhamnosus GG, ATCC 53,103, currently Lacticaseibacillus rhamnosus GG) and a prebiotic (galacto-oligosaccharide and polydextrose mixture, 1:1) intervention as compared to a placebo administered from 3 to 60 days of life. In addition, 9 full-term, vaginally delivered, breast-fed infants, who remained healthy long-term were included as references. Significant differences in taxonomy, but not in functional potential, were found when comparing the gut microbiome composition of preterm and full-term infants during the first month of life. However, the gut microbiome of preterm infants resembled that of full-term infants by 6 months age. Probiotic and prebiotic treatments were found to mitigate the shift in the microbiome of preterm infants by accelerating Bifidobacteria-dominated gut microbiome in beta diversity analysis. This study provides intriguing information regarding the establishment of the gut microbiome in children born moderately and late preterm, representing the majority of children born preterm. Specific pro- and prebiotics may reverse the proinflammatory gut microbiome composition during the vulnerable period, when the microbiome is low in resilience and susceptible to environmental exposure and simultaneously promotes immunological and metabolic maturation.}, } @article {pmid38008898, year = {2023}, author = {Sun, H and Lei, L and Li, J and Niu, H and Yang, J and Chen, M}, title = {Clinical treatment of patients with scrub typhus-induced liver injury and intracranial infection.}, journal = {The Journal of international medical research}, volume = {51}, number = {11}, pages = {3000605231214503}, pmid = {38008898}, issn = {1473-2300}, mesh = {Humans ; *Scrub Typhus/complications/diagnosis/drug therapy ; *Chemical and Drug Induced Liver Injury, Chronic ; *Orientia tsutsugamushi ; }, abstract = {Scrub typhus is an infectious disease caused by Orientia tsutsugamushi, a bacterium within the family Rickettsiaceae. The clinical symptoms are usually acute and are characterized by fever, eschar formation or ulceration, local or generalized lymphadenopathy, and rash. Because of the extensive damage to small blood vessels throughout the body, scrub typhus can involve multiple systems and organs, causing damage to the respiratory, digestive, and nervous systems and inducing kidney and liver dysfunction. Death can occur in severe cases. We herein report two cases of scrub typhus with liver damage and intracranial infection. Among patients with scrub typhus, the risk of death is significantly higher in those who develop liver injury and intracranial infection. However, there are few reports on the treatment of patients with liver injury and intracranial infection caused by scrub typhus, and relevant treatment experience is thus lacking. Our clinical case report helps to fill the knowledge gap in this area.}, } @article {pmid38008755, year = {2023}, author = {Teng, M and Li, Y and Zhao, X and White, JC and Zhao, L and Sun, J and Zhu, W and Wu, F}, title = {Vitamin D modulation of brain-gut-virome disorder caused by polystyrene nanoplastics exposure in zebrafish (Danio rerio).}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {266}, pmid = {38008755}, issn = {2049-2618}, support = {42207335//National Natural Science Foundation of China/ ; 2022QNRC001//Young Elite Scientists Sponsorship Program by CAST/ ; 41925031//National Science Fund for Distinguished Young Scholars/ ; 2021YFC3201000//National Key Research and Development Program of China/ ; }, mesh = {Animals ; Polystyrenes/metabolism/toxicity ; Zebrafish ; Vitamin D/metabolism ; *Nanoparticles/metabolism/toxicity ; Microplastics/toxicity/metabolism ; Serotonin/metabolism ; Virome ; *Water Pollutants, Chemical/metabolism/toxicity ; Brain ; Cytochromes/metabolism ; }, abstract = {BACKGROUND: Many studies have investigated how nanoplastics (NPs) exposure mediates nerve and intestinal toxicity through a dysregulated brain-gut axis interaction, but there are few studies aimed at alleviating those effects. To determine whether and how vitamin D can impact that toxicity, fish were supplemented with a vitamin D-low diet and vitamin D-high diet.

RESULTS: Transmission electron microscopy (TEM) showed that polystyrene nanoplastics (PS-NPs) accumulated in zebrafish brain and intestine, resulting in brain blood-brain barrier basement membrane damage and the vacuolization of intestinal goblet cells and mitochondria. A high concentration of vitamin D reduced the accumulation of PS-NPs in zebrafish brain tissues by 20% and intestinal tissues by 58.8% and 52.2%, respectively, and alleviated the pathological damage induced by PS-NPs. Adequate vitamin D significantly increased the content of serotonin (5-HT) and reduced the anxiety-like behavior of zebrafish caused by PS-NPs exposure. Virus metagenome showed that PS-NPs exposure affected the composition and abundance of zebrafish intestinal viruses. Differentially expressed viruses in the vitamin D-low and vitamin D-high group affected the secretion of brain neurotransmitters in zebrafish. Virus AF191073 was negatively correlated with neurotransmitter 5-HT, whereas KT319643 was positively correlated with malondialdehyde (MDA) content and the expression of cytochrome 1a1 (cyp1a1) and cytochrome 1b1 (cyp1b1) in the intestine. This suggests that AF191073 and KT319643 may be key viruses that mediate the vitamin D reduction in neurotoxicity and immunotoxicity induced by PS-NPs.

CONCLUSION: Vitamin D can alleviate neurotoxicity and immunotoxicity induced by PS-NPs exposure by directionally altering the gut virome. These findings highlight the potential of vitamin D to alleviate the brain-gut-virome disorder caused by PS-NPs exposure and suggest potential therapeutic strategies to reduce the risk of NPs toxicity in aquaculture, that is, adding adequate vitamin D to diet. Video Abstract.}, } @article {pmid38008735, year = {2023}, author = {Xiao, X and Cui, Y and Lu, H and Wang, J and Yang, J and Liu, L and Liu, Z and Peng, X and Cao, H and Liu, X and Wei, X}, title = {Strontium ranelate enriched Ruminococcus albus in the gut microbiome of Sprague-Dawley rats with postmenopausal osteoporosis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {365}, pmid = {38008735}, issn = {1471-2180}, support = {2018QDJZR12//Cultivating Project for Young Scholar at Hubei University of Medicine/ ; 2015QDJZR06//Cultivating Project for Young Scholar at Hubei University of Medicine/ ; JC2022002//Innovation Research Program for Graduates of Basic Medical College, Hubei University of Medicine/ ; AD18281029//Guangxi Natural Science Foundation/ ; WJ2021M052//Hubei Provincial Health and Health Commission Funded Projects/ ; WJ2019Q025//Hubei Provincial Health and Health Commission Funded Projects/ ; }, mesh = {Humans ; Female ; Rats ; Animals ; Rats, Sprague-Dawley ; *Osteoporosis, Postmenopausal/drug therapy/metabolism ; *Gastrointestinal Microbiome ; Ruminococcus ; Lycopene/therapeutic use ; RNA, Ribosomal, 16S/genetics ; *Osteoporosis/drug therapy/metabolism ; }, abstract = {BACKGROUND: Gut microbiome is critical to our human health and is related to postmenopausal osteoporosis (PMO). Strontium ranelate (SrR) is an anti-osteoporosis oral drug that can promote osteoblast formation and inhibit osteoclast formation. However, the effect of SrR on gut microbiome has been rarely studied. Therefore, we investigated the effect of oral SrR on gut microbiome and metabolic profiles.

RESULTS: In this study, we used ovariectomized (OVX) Sprague-Dawley rats to construct a PMO model and applied oral SrR for 6 weeks. The relative abundance of intestinal microbiome was investigated by 16S rRNA metagenomic sequencing. Ultra-high-performance liquid chromatography-mass spectrometry (UHPLC-MS) was used to analyze changes in metabolites of intestinal contents. Results demonstrated that 6-week oral SrR alleviated osteoporosis and significantly changed the composition of the gut microbiome and metabolic profiles of OVX rats. Ruminococcus, Akkermansia and Oscillospira were significantly enriched in the gut of OVX rats after 6-week oral SrR. Especially, the species R. albus showed the greatest importance by a random forest classifier between OVX and OVX_Sr group. The enrichment of R. albus in the gut was positively correlated with bone mineral density and the accumulation of lycopene and glutaric acid, which also significantly elevated after oral SrR.

CONCLUSIONS: We discovered that oral SrR can improve bone health while stimulate the accumulation of gut microbe R. albus and metabolites (lycopene and glutaric acid). The results suggested possible connections between oral SrR and the gut-bone axis, which may provide new insight into the treatment/prevention of osteoporosis.}, } @article {pmid38008322, year = {2023}, author = {Hu, S and Xu, C and Xie, Y and Ma, L and Niu, Q and Han, G and Huang, J}, title = {Metagenomic insights into the diversity of 2,4-dichlorophenol degraders and the cooperation patterns in a bacterial consortium.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {168723}, doi = {10.1016/j.scitotenv.2023.168723}, pmid = {38008322}, issn = {1879-1026}, abstract = {2,4-Dichlorophenol, which is largely employed in herbicides and industrial production, is frequently detected in ecosystems and poses risks to human health and environmental safety. Microbial communities are thought to perform better than individual strains in the complete degradation of organic contaminants. However, the synergistic degradation mechanisms of the microbial consortia involved in 2,4-dichlorophenol degradation are still not widely understood. In this study, a bacterial consortium named DCP-2 that is capable of degrading 2,4-dichlorophenol was obtained. Metagenomic analysis, cultivation-dependent functional verification, and co-occurrence network analysis were combined to reveal the primary 2,4-dichlorophenol degraders and the cooperation patterns in the consortium DCP-2. Metagenomic analysis showed that Pseudomonas, Achromobacter, and Pigmentiphaga were the primary degraders for the complete degradation of 2,4-dichlorophenol. Thirty-nine phylogenetically diverse bacterial genera, such as Brucella, Acinetobacter, Aeromonas, Allochromatium and Bosea, were identified as keystone taxa for 2,4-dichlorophenol degradation by keystone taxa analysis of the co-occurrence networks. In addition, a stable synthetic consortium of isolates from DCP-2 was constructed, consisting of Pseudomonas sp. DD-13 and Brucella sp. FZ-1; this synthetic consortium showed superior degradation capability for 2,4-dichlorophenol in both mineral salt medium and wastewater compared with monoculture. The findings provide valuable insights into the practical bioremediation of 2,4-dichlorophenol-contaminated sites.}, } @article {pmid38008310, year = {2023}, author = {Yang, S and Hou, LJ and Dong, HP and Zhang, JW and Gao, DZ and Li, XF and Zheng, YL and Liang, X and Liu, M}, title = {Natural chalcopyrite mitigates nitrous oxide emissions in sediment from coastal wetlands.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {168766}, doi = {10.1016/j.scitotenv.2023.168766}, pmid = {38008310}, issn = {1879-1026}, abstract = {Coastal wetlands are one of the most important natural sources of nitrous oxide (N2O). Previous studies have shown that copper-containing chemicals are able to reduce N2O emissions from these ecosystems. However, these chemicals may harm organisms present in coastal waters and sediment, and disturb the ecological balance of these areas. Here, we first investigated the physiological characteristics and genetic potential of denitrifying bacteria isolated from coastal wetlands. Based on an isolated denitrifier carrying a complete denitrification pathway, we tested the effect of the natural mineral chalcopyrite on N2O production by the bacteria. The results demonstrated that chalcopyrite addition lowers N2O emissions from the bacteria while increasing its N2 production rate. Among the four denitrification genes of the isolate, only nosZ gene expression was significantly upregulated following the addition of 2 mg L[-1] chalcopyrite. Furthermore, chalcopyrite was applied to coastal wetland sediments. The N2O flux was significantly reduced in 50-100 mg L[-1] chalcopyrite-amended sets relative to the controls. Notably, the dissolved Cu concentration in chalcopyrite-amended sediment remained within the limit set by the National Sewage Treatment Discharge Standard. qPCR and metagenomic analysis revealed that the abundance of N2O-reducing bacteria with the nosZ or nirK + nosZ genotype increased significantly in the chalcopyrite-amended groups relative to the controls, suggesting their active involvement in the reduction of N2O emissions. Our findings offer valuable insights for the use of natural chalcopyrite in large-scale field applications to reduce N2O emissions.}, } @article {pmid38007896, year = {2024}, author = {Wu, C and Zhou, J and Pang, S and Yang, L and Lichtfouse, E and Liu, H and Xia, S and Rittmann, BE}, title = {Reduction and precipitation of chromium(VI) using a palladized membrane biofilm reactor.}, journal = {Water research}, volume = {249}, number = {}, pages = {120878}, doi = {10.1016/j.watres.2023.120878}, pmid = {38007896}, issn = {1879-2448}, mesh = {*Metal Nanoparticles ; Oxidation-Reduction ; Palladium ; Chromium ; Biofilms ; }, abstract = {H2-driven reduction of hexavalent chromium (Cr(VI)) using precious-metal catalysts is promising, but its implementation in water treatment has been restricted by poor H2-transfer efficiency and high catalyst loss. We investigated the reduction of Cr(VI) through hydrogenation catalyzed by elemental-palladium nanoparticles (PdNPs) generated in-situ within biofilm of a membrane biofilm reactor (MBfR), creating a Pd-MBfR. Experiments were conducted using a Pd-MBfR and a non-Pd MBfR. The Pd-MBfR achieved Cr(VI) (1000 μg L[-1]) reduction of >99 % and reduced the concentration of total Cr to below 50 μg L[-1], much lower than the total Cr concentration in the non-Pd MBfR effluent (290 μg L[-1]). The Pd-MBfR also had a lower concentration of dissolved organic compounds compared to the non-Pd MBfR, which minimized the formation of soluble organo-Cr(III) complexes and promoted precipitation of Cr(OH)3. Solid-state characterizations documented deposition of Cr(OH)3 as the product of Cr(VI) reduction in the Pd-MBfR. Metagenomic analyses revealed that the addition and reduction of Cr(VI) had minimal impact on the microbial community (dominated by Dechloromonas) and functional genes in the biofilm of the Pd-MBfR, since the PdNP-catalyzed reduction process was rapid. This study documented efficient Cr(VI) reduction and precipitation of Cr(OH)3 by the Pd-MBfR technology.}, } @article {pmid38007883, year = {2024}, author = {Geng, H and Xu, Y and Liu, R and Yang, D and Dai, X}, title = {Cation exchange resins enhance anaerobic digestion of sewage sludge: Roles in sequential recovery of hydrogen and methane.}, journal = {Water research}, volume = {248}, number = {}, pages = {120897}, doi = {10.1016/j.watres.2023.120897}, pmid = {38007883}, issn = {1879-2448}, mesh = {*Sewage/chemistry ; Anaerobiosis ; *Cation Exchange Resins ; Methane/metabolism ; Hydrogen ; Bacteria/metabolism ; Bioreactors/microbiology ; }, abstract = {The recovery of renewable bioenergy from anaerobic digestion (AD) of sludge is a promising method to alleviate the energy problem. Although methane can be effectively recovered through sludge pretreatment by cation exchange resin (CER), the simultaneous enhancement of hydrogen and methane generation from AD using CER has not been extensively investigated. Herein, the effect of CER on the sequential recovery of hydrogen and methane and the corresponding mechanisms were investigated. When CER is introduced, the maximum increases for the hydrogen and methane production are 104.7 % and 35.3 %, respectively, confirming the sequential enhancement effects of CER on the hydrogen and methane production. Analyses of the variations in the main biochemical components with and without the effect of CER demonstrate that CER promotes sludge organic solubilisation, hydrolysis, and acidification in both hydrogen- and methane-production stages. Moreover, investigations of variations in the solid-liquid interfacial thermodynamics and removal rates of main multivalent metals of sludge reveal that the ion exchange reactions between the CER and sludge in the hydrogen-production stage provide the direct driving force of effective contact between bacteria and organic particulates. Additionally, the residual effect of the CER during methane production reduces the energy barrier for mass transfer and provides a driving force for this transfer. Further analyses of the microbial community structure and metagenomics indicate that CER directly drives the enrichment of hydrogen-producing bacteria (+ 15.1 %) and key genes encoding enzymes in the hydrogen-production stage. Moreover, CER indirectly induces the enrichment of methane-producing anaerobes (e.g. Methanosaeta: + 16.7 %, Methanosarcina: + 316.5 %); enhances the bioconversion of different substrates into methyl-coenzyme M; and promotes the metabolism pathway of acetoclastic process and CO2 reduction in the methane-production stage. This study can provide valuable insights for simultaneously enhancing the production of hydrogen and methane from AD through sequential recovery.}, } @article {pmid38007474, year = {2023}, author = {Liu, Y and Brinkhoff, T and Berger, M and Poehlein, A and Voget, S and Paoli, L and Sunagawa, S and Amann, R and Simon, M}, title = {Metagenome-assembled genomes reveal greatly expanded taxonomic and functional diversification of the abundant marine Roseobacter RCA cluster.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {265}, pmid = {38007474}, issn = {2049-2618}, support = {TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; TRR51//Deutsche Forschungsgemeinschaft/ ; 205321_184955//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 205321_184955//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 51NF40_180575//National Center of Competence in Research Quantum Science and Technology/ ; }, mesh = {*Roseobacter/genetics ; Seawater/microbiology ; Metagenome ; Phylogeny ; Oceans and Seas ; Metagenomics ; }, abstract = {BACKGROUND: The RCA (Roseobacter clade affiliated) cluster belongs to the family Roseobacteracea and represents a major Roseobacter lineage in temperate to polar oceans. Despite its prevalence and abundance, only a few genomes and one described species, Planktomarina temperata, exist. To gain more insights into our limited understanding of this cluster and its taxonomic and functional diversity and biogeography, we screened metagenomic datasets from the global oceans and reconstructed metagenome-assembled genomes (MAG) affiliated to this cluster.

RESULTS: The total of 82 MAGs, plus five genomes of isolates, reveal an unexpected diversity and novel insights into the genomic features, the functional diversity, and greatly refined biogeographic patterns of the RCA cluster. This cluster is subdivided into three genera: Planktomarina, Pseudoplanktomarina, and the most deeply branching Candidatus Paraplanktomarina. Six of the eight Planktomarina species have larger genome sizes (2.44-3.12 Mbp) and higher G + C contents (46.36-53.70%) than the four Pseudoplanktomarina species (2.26-2.72 Mbp, 42.22-43.72 G + C%). Cand. Paraplanktomarina is represented only by one species with a genome size of 2.40 Mbp and a G + C content of 45.85%. Three novel species of the genera Planktomarina and Pseudoplanktomarina are validly described according to the SeqCode nomenclature for prokaryotic genomes. Aerobic anoxygenic photosynthesis (AAP) is encoded in three Planktomarina species. Unexpectedly, proteorhodopsin (PR) is encoded in the other Planktomarina and all Pseudoplanktomarina species, suggesting that this light-driven proton pump is the most important mode of acquiring complementary energy of the RCA cluster. The Pseudoplanktomarina species exhibit differences in functional traits compared to Planktomarina species and adaptations to more resource-limited conditions. An assessment of the global biogeography of the different species greatly expands the range of occurrence and shows that the different species exhibit distinct biogeographic patterns. They partially reflect the genomic features of the species.

CONCLUSIONS: Our detailed MAG-based analyses shed new light on the diversification, environmental adaptation, and global biogeography of a major lineage of pelagic bacteria. The taxonomic delineation and validation by the SeqCode nomenclature of prominent genera and species of the RCA cluster may be a promising way for a refined taxonomic identification of major prokaryotic lineages and sublineages in marine and other prokaryotic communities assessed by metagenomics approaches. Video Abstract.}, } @article {pmid38007438, year = {2023}, author = {Al, KF and Joris, BR and Daisley, BA and Chmiel, JA and Bjazevic, J and Reid, G and Gloor, GB and Denstedt, JD and Razvi, H and Burton, JP}, title = {Multi-site microbiota alteration is a hallmark of kidney stone formation.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {263}, pmid = {38007438}, issn = {2049-2618}, mesh = {Humans ; *Kidney Calculi ; *Microbiota/genetics ; Oxalates/metabolism ; Metagenome ; Bacteria ; }, abstract = {BACKGROUND: Inquiry of microbiota involvement in kidney stone disease (KSD) has largely focussed on potential oxalate handling abilities by gut bacteria and the increased association with antibiotic exposure. By systematically comparing the gut, urinary, and oral microbiota of 83 stone formers (SF) and 30 healthy controls (HC), we provide a unified assessment of the bacterial contribution to KSD.

RESULTS: Amplicon and shotgun metagenomic sequencing approaches were consistent in identifying multi-site microbiota disturbances in SF relative to HC. Biomarker taxa, reduced taxonomic and functional diversity, functional replacement of core bioenergetic pathways with virulence-associated gene markers, and community network collapse defined SF, but differences between cohorts did not extend to oxalate metabolism.

CONCLUSIONS: We conclude that multi-site microbiota alteration is a hallmark of SF, and KSD treatment should consider microbial functional restoration and the avoidance of aberrant modulators such as poor diet and antibiotics where applicable to prevent stone recurrence. Video Abstract.}, } @article {pmid38006912, year = {2024}, author = {Hu, X and Gu, H and Sun, X and Wang, Y and Liu, J and Yu, Z and Li, Y and Jin, J and Wang, G}, title = {Metagenomic exploration of microbial and enzymatic traits involved in microplastic biodegradation.}, journal = {Chemosphere}, volume = {348}, number = {}, pages = {140762}, doi = {10.1016/j.chemosphere.2023.140762}, pmid = {38006912}, issn = {1879-1298}, mesh = {*Microplastics ; *Plastics ; Polyethylene ; Carbohydrates ; Polyesters ; Soil ; }, abstract = {Agricultural mulch films are frequently applied to achieve high yield, resulting in large quantities of microplastic (MP) pollution in agroecosystem. However, studies focusing specifically on the diversity of MP-degrading enzymes and related microbial communities have yet to be conducted. Here, we established a soil microcosmic incubation with addition of 5% (w/w) conventional (low-density polyethylene (LDPE)) and biodegradable (blend of polylactic acid (PLA) and polybutylene adipate terephthalate (PBAT)) MPs for incubation 90 days. The DNA samples extracted from soils and plastisphere of MPs were examined by metagenomics and genome binning methods, specifically targeting carbohydrate-active enzymes (CAZymes) and plastic-degrading enzymes (PDZymes). The results revealed that plastisphere of MPs exhibited significantly distinct patterns of CAZymes and PDZymes from soils, and abundances of all examined exoenzymes were higher in plastisphere than those in soils. Plastisphere of LDPE-MPs selectively enriched proteases and alkane monooxygenase (alkB), and required families of carbohydrate-binding module (CBM) to increase the binding of CAZymes with MPs. Dissimilarly, diverse CAZymes with high abundances were observed in the plastisphere of PBAT-PLA MPs and esterases were important indicative PDZymes for PBAT-PLA degradation. The enriched exoenzymes in plastisphere of LDPE-MPs were mainly assigned to Actinobacteria while Proteobacteria with higher abundance in plastisphere of PBAT-PLA MPs containing most indicative exoenzymes. Moreover, a high-quality genome classified as Amycolatopsis japonica was reconstructed and found to contain one or more gene copies of indicative exoenzymes for polyethylene. Two novel genomes classified as Sphingomonas were selectively enriched in plastisphere of PBAT-PLA MPs and contained diverse genes encoding degrading exoenzymes. Taken together, our study highlighted the CAZymes and PDZymes can be exploited as potent microbial strategies for solving MPs pollution in croplands.}, } @article {pmid38006744, year = {2023}, author = {Elgart, M and Zhang, Y and Zhang, Y and Yu, B and Kim, Y and Zee, PC and Gellman, MD and Boerwinkle, E and Daviglus, ML and Cai, J and Redline, S and Burk, RD and Kaplan, R and Sofer, T}, title = {Anaerobic pathogens associated with OSA may contribute to pathophysiology via amino-acid depletion.}, journal = {EBioMedicine}, volume = {98}, number = {}, pages = {104891}, pmid = {38006744}, issn = {2352-3964}, mesh = {Humans ; *Amino Acids ; Anaerobiosis ; Cohort Studies ; Prospective Studies ; *Sleep Apnea, Obstructive/complications ; }, abstract = {BACKGROUND: The human microbiome is linked to multiple metabolic disorders such as obesity and diabetes. Obstructive sleep apnoea (OSA) is a common sleep disorder with several metabolic risk factors. We investigated the associations between the gut microbiome composition and function, and measures of OSA severity in participants from a prospective community-based cohort study: the Hispanic Community Health Study/Study of Latinos (HCHS/SOL).

METHODS: Bacterial-Wide Association Analysis (BWAS) of gut microbiome measured via metagenomics with OSA measures was performed adjusting for clinical, lifestyle and co-morbidities. This was followed by functional analysis of the OSA-enriched bacteria. We utilized additional metabolomic and transcriptomic associations to suggest possible mechanisms explaining the microbiome effects on OSA.

FINDINGS: Several uncommon anaerobic human pathogens were associated with OSA severity. These belong to the Lachnospira, Actinomyces, Kingella and Eubacterium genera. Functional analysis revealed enrichment in 49 processes including many anaerobic-related ones. Severe OSA was associated with the depletion of the amino acids glycine and glutamine in the blood, yet neither diet nor gene expression revealed any changes in the production or consumption of these amino acids.

INTERPRETATION: We show anaerobic bacterial communities to be a novel component of OSA pathophysiology. These are established in the oxygen-poor environments characteristic of OSA. We hypothesize that these bacteria deplete certain amino acids required for normal human homeostasis and muscle tone, contributing to OSA phenotypes. Future work should test this hypothesis as well as consider diagnostics via anaerobic bacteria detection and possible interventions via antibiotics and amino-acid supplementation.

FUNDING: Described in methods.}, } @article {pmid38006691, year = {2024}, author = {Hes, C and Desilets, A and Tonneau, M and El Ouarzadi, O and De Figueiredo Sousa, M and Bahig, H and Filion, É and Nguyen-Tan, PF and Christopoulos, A and Benlaïfaoui, M and Derosa, L and Alves Costa Silva, C and Ponce, M and Malo, J and Belkad, W and Charpentier, D and Aubin, F and Hamilou, Z and Jamal, R and Messaoudene, M and Soulières, D and Routy, B}, title = {Gut microbiome predicts gastrointestinal toxicity outcomes from chemoradiation therapy in patients with head and neck squamous cell carcinoma.}, journal = {Oral oncology}, volume = {148}, number = {}, pages = {106623}, doi = {10.1016/j.oraloncology.2023.106623}, pmid = {38006691}, issn = {1879-0593}, mesh = {Male ; Humans ; Female ; Squamous Cell Carcinoma of Head and Neck/complications ; *Head and Neck Neoplasms/complications ; *Mucositis/etiology ; Prospective Studies ; *Gastrointestinal Microbiome ; Chemoradiotherapy/adverse effects ; }, abstract = {OBJECTIVES: Chemoradiation (CRT) in patients with locally advanced head and neck squamous cell cancer (HNSCC) is associated with significant toxicities, including mucositis. The gut microbiome represents an emerging hallmark of cancer and a potentially important biomarker for CRT-related adverse events. This prospective study investigated the association between the gut microbiome composition and CRT-related toxicities in patients with HNSCC, including mucositis.

MATERIALS AND METHODS: Stool samples from patients diagnosed with locally advanced HNSCC were prospectively collected prior to CRT initiation and analyzed using shotgun metagenomic sequencing to evaluate gut microbiome composition at baseline. Concurrently, clinicopathologic data, survival outcomes and the incidence and grading of CRT-emergent adverse events were documented in all patients.

RESULTS: A total of 52 patients were included, of whom 47 had baseline stool samples available for metagenomic analysis. Median age was 62, 83 % patients were men and 54 % had stage III-IV disease. All patients developed CRT-induced mucositis, including 42 % with severe events (i.e. CTCAE v5.0 grade ≥ 3) and 25 % who required enteral feeding. With a median follow-up of 26.5 months, patients with severe mucositis had shorter overall survival (HR = 3.3, 95 %CI 1.0-10.6; p = 0.02) and numerically shorter progression-free survival (HR = 2.8, 95 %CI, 0.8-9.6; p = 0.09). The gut microbiome beta-diversity of patients with severe mucositis differed from patients with grades 1-2 mucositis (p = 0.04), with enrichment in Mediterraneibacter (Ruminococcus gnavus) and Clostridiaceae family members, including Hungatella hathewayi. Grade 1-2 mucositis was associated with enrichment in Eubacterium rectale, Alistipes putredinis and Ruminococcaceae family members. Similar bacterial profiles were observed in patients who required enteral feeding.

CONCLUSION: Patients who developed severe mucositis had decreased survival and enrichment in specific bacteria associated with mucosal inflammation. Interestingly, these same bacteria have been linked to immune checkpoint inhibitor resistance.}, } @article {pmid38006569, year = {2023}, author = {Aminu, S and Ascandari, A and Laamarti, M and Safdi, NEH and El Allali, A and Daoud, R}, title = {Exploring microbial worlds: a review of whole genome sequencing and its application in characterizing the microbial communities.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-25}, doi = {10.1080/1040841X.2023.2282447}, pmid = {38006569}, issn = {1549-7828}, abstract = {The classical microbiology techniques have inherent limitations in unraveling the complexity of microbial communities, necessitating the pivotal role of sequencing in studying the diversity of microbial communities. Whole genome sequencing (WGS) enables researchers to uncover the metabolic capabilities of the microbial community, providing valuable insights into the microbiome. Herein, we present an overview of the rapid advancements achieved thus far in the use of WGS in microbiome research. There was an upsurge in publications, particularly in 2021 and 2022 with the United States, China, and India leading the metagenomics research landscape. The Illumina platform has emerged as the widely adopted sequencing technology, whereas a significant focus of metagenomics has been on understanding the relationship between the gut microbiome and human health where distinct bacterial species have been linked to various diseases. Additionally, studies have explored the impact of human activities on microbial communities, including the potential spread of pathogenic bacteria and antimicrobial resistance genes in different ecosystems. Furthermore, WGS is used in investigating the microbiome of various animal species and plant tissues such as the rhizosphere microbiome. Overall, this review reflects the importance of WGS in metagenomics studies and underscores its remarkable power in illuminating the variety and intricacy of the microbiome in different environments.}, } @article {pmid38006557, year = {2024}, author = {Valerio, F and Twort, VG and Duplouy, A}, title = {Screening Host Genomic Data for Wolbachia Infections.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2739}, number = {}, pages = {251-274}, pmid = {38006557}, issn = {1940-6029}, mesh = {*Wolbachia/genetics ; Genome, Bacterial ; Genomics ; Base Sequence ; DNA, Bacterial/genetics ; Symbiosis/genetics ; }, abstract = {Less than a decade ago, the production of Wolbachia genomic assemblies was tedious, time-consuming, and expensive. The production of Wolbachia genomic DNA free of contamination from host DNA, as required for Wolbachia-targeted sequencing, was then only possible after the amplification and extraction of a large amount of clonal Wolbachia DNA. However, as an endosymbiotic bacterium, Wolbachia does not grow outside the host cell environment, and large-scale recovery of the bacteria required mass rearing of their host, preferably clones of a single individual to avoid strain genetic diversity, or amplification of cell cultures infected with a single Wolbachia strain. Bacterial DNA could be separated from host DNA based on genomic size. Nowadays, the production of full Wolbachia genomes does not require the physical isolation of the bacterial strains from their respective hosts, and the bacterium is often sequenced as a by-catch of host genomic projects. Here, we provide a step-by-step protocol to (1) identify whether host genome projects contain reads from associated Wolbachia and (2) isolate/retrieve the Wolbachia reads from the rest of the sequenced material. We hope this simple protocol will support many projects aiming at studying diverse Wolbachia genome assemblies.}, } @article {pmid38006548, year = {2024}, author = {Kaur, A and Brown, AMV}, title = {Detection and Analysis of Wolbachia in Plant-Parasitic Nematodes and Insights into Wolbachia Evolution.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2739}, number = {}, pages = {115-134}, pmid = {38006548}, issn = {1940-6029}, mesh = {Animals ; *Wolbachia/genetics ; *Nematoda/genetics ; Plants/parasitology ; Genomics ; Metagenomics ; }, abstract = {Since the discovery of Wolbachia in plant-parasitic nematodes (PPNs), there has been increased interest in this earliest branching clade that may hold important clues to early transitions in Wolbachia function in the Ecdysozoa. However, due to the specialized skills and equipment of nematology and the difficulty in culturing most PPNs, these PPN-type Wolbachia remain undersampled and poorly understood. To date, there are few established laboratory methods for working with PPN-type Wolbachia strains, and most research has relied on chance discovery and comparative genomics. Here, we address this challenge by providing detailed methods to assist researchers with more efficiently collecting PPNs and screen these communities, populations, or single nematodes with a newly developed PPN-type Wolbachia-specific PCR assay. We provide an overview of the typical yields and outcomes of these methods, to facilitate further targeted cultivation or experimental methods, and finally we provide a short introduction to some of the specific challenges and solutions in following through with comparative or population genomics on PPN-type Wolbachia strains.}, } @article {pmid38006423, year = {2023}, author = {Bhagchandani, T and Nikita, and Verma, A and Tandon, R}, title = {Exploring the Human Virome: Composition, Dynamics, and Implications for Health and Disease.}, journal = {Current microbiology}, volume = {81}, number = {1}, pages = {16}, pmid = {38006423}, issn = {1432-0991}, support = {(No. 61/06/2020/IMM/BMS)//Indian Council of Medical Research/ ; }, mesh = {Infant ; Humans ; Virome ; *Microbiota ; *Viruses/genetics ; *Bacteriophages/genetics ; Metagenome ; }, abstract = {Humans are colonized by large number of microorganisms-bacteria, fungi, and viruses. The overall genome of entire viruses that either lives on or inside the human body makes up the human virome and is indeed an essential fraction of the human metagenome. Humans are constantly exposed to viruses as they are ubiquitously present on earth. The human virobiota encompasses eukaryotic viruses, bacteriophages, retroviruses, and even giant viruses. With the advent of Next-generation sequencing (NGS) and ongoing development of numerous bioinformatic softwares, identification and taxonomic characterization of viruses have become easier. The viruses are abundantly present in humans; these can be pathogenic or commensal. The viral communities occupy various niches in the human body. The viruses start colonizing the infant gut soon after birth in a stepwise fashion and the viral composition diversify according to their feeding habits. Various factors such as diet, age, medications, etc. influence and shape the human virome. The viruses interact with the host immune system and these interactions have beneficial or detrimental effects on their host. The virome composition and abundance change during the course of disease and these alterations impact the immune system. Hence, the virome population in healthy and disease conditions influences the human host in numerous ways. This review presents an overview of assembly and composition of the human virome in healthy asymptomatic individuals, changes in the virome profiles, and host-virome interactions in various disease states.}, } @article {pmid38006234, year = {2023}, author = {Yadav, A and Ahlawat, S and Sharma, KK}, title = {Culturing the unculturables: strategies, challenges, and opportunities for gut microbiome study.}, journal = {Journal of applied microbiology}, volume = {134}, number = {12}, pages = {}, doi = {10.1093/jambio/lxad280}, pmid = {38006234}, issn = {1365-2672}, support = {5/4/8-1/2019-NCD-II//Indian Council of Medical Research/ ; }, mesh = {*Gastrointestinal Microbiome ; *Microbiota ; Metagenome ; Intestines ; Metagenomics/methods ; }, abstract = {Metagenome sequencing techniques revolutionized the field of gut microbiome study. However, it is equipped with experimental and computational biases, which affect the downstream analysis results. Also, live microbial strains are needed for a better understanding of host-microbial crosstalks and for designing next-generation treatment therapies based on probiotic strains and postbiotic molecules. Conventional culturing methodologies are insufficient to get the dark gut matter on the plate; therefore, there is an urgent need to propose novel culturing methods that can fill the limitations of metagenomics. The current work aims to provide a consolidated evaluation of the available methods for host-microbe interaction with an emphasis on in vitro culturing of gut microbes using organoids, gut on a chip, and gut bioreactor. Further, the knowledge of microbial crosstalk in the gut helps us to identify core microbiota, and key metabolites that will aid in designing culturing media and co-culturing systems for gut microbiome study. After the deeper mining of the current culturing methods, we recommend that 3D-printed intestinal cells in a multistage continuous flow reactor equipped with an extended organoid system might be a good practical choice for gut microbiota-based studies.}, } @article {pmid38006200, year = {2023}, author = {Houldcroft, CJ and Underdown, S}, title = {Infectious disease in the Pleistocene: Old friends or old foes?.}, journal = {American journal of biological anthropology}, volume = {182}, number = {4}, pages = {513-531}, doi = {10.1002/ajpa.24737}, pmid = {38006200}, issn = {2692-7691}, support = {//Oxford Brookes University/ ; }, mesh = {Animals ; Humans ; Friends ; *Hominidae ; *Communicable Diseases/epidemiology ; Genome ; DNA ; }, abstract = {The impact of endemic and epidemic disease on humans has traditionally been seen as a comparatively recent historical phenomenon associated with the Neolithisation of human groups, an increase in population size led by sedentarism, and increasing contact with domesticated animals as well as species occupying opportunistic symbiotic and ectosymbiotic relationships with humans. The orthodox approach is that Neolithisation created the conditions for increasing population size able to support a reservoir of infectious disease sufficient to act as selective pressure. This orthodoxy is the result of an overly simplistic reliance on skeletal data assuming that no skeletal lesions equated to a healthy individual, underpinned by the assumption that hunter-gatherer groups were inherently healthy while agricultural groups acted as infectious disease reservoirs. The work of van Blerkom, Am. J. Phys. Anthropol., vol. suppl 37 (2003), Wolfe et al., Nature, vol. 447 (2007) and Houldcroft and Underdown, Am. J. Phys. Anthropol., vol. 160, (2016) has changed this landscape by arguing that humans and pathogens have long been fellow travelers. The package of infectious diseases experienced by our ancient ancestors may not be as dissimilar to modern infectious diseases as was once believed. The importance of DNA, from ancient and modern sources, to the study of the antiquity of infectious disease, and its role as a selective pressure cannot be overstated. Here we consider evidence of ancient epidemic and endemic infectious diseases with inferences from modern and ancient human and hominin DNA, and from circulating and extinct pathogen genomes. We argue that the pandemics of the past are a vital tool to unlock the weapons needed to fight pandemics of the future.}, } @article {pmid38005845, year = {2023}, author = {Pérez-Rodríguez, FJ and Laubscher, F and Chudzinski, V and Kaiser, L and Cordey, S}, title = {Direct Dengue Virus Genome Sequencing from Antigen NS1 Rapid Diagnostic Tests: A Proof-of-Concept with the Standard Q Dengue Duo Assay.}, journal = {Viruses}, volume = {15}, number = {11}, pages = {}, pmid = {38005845}, issn = {1999-4915}, mesh = {Humans ; *Dengue/epidemiology ; *Dengue Virus ; Phylogeny ; Sensitivity and Specificity ; Viral Nonstructural Proteins/genetics ; Immunoglobulin M ; Genome, Viral ; Enzyme-Linked Immunosorbent Assay ; Antibodies, Viral ; }, abstract = {With nearly half of the world's population being at risk of infection, dengue virus represents a major global health issue. The use of dengue antigen rapid diagnostic tests (Ag-RDTs) represents an alternative to PCR methods for the diagnosis of acute infections since they display excellent sensitivities and specificities and can be performed outside the laboratory. The high genetic diversity of the dengue virus genome represents a challenge for vaccine development, and the progressive expansion of this virus into previously nonendemic regions justifies the implementation of a genomic surveillance program. In this proof-of-concept study, we show the feasibility of sequencing dengue virus genomes directly from positive Ag-RDT (Standard Q Dengue Duo Test assay, n = 7) cassettes stored up to 31 days at room temperature after testing. For 5 of the 7 samples, a high number of reads were obtained allowing phylogenetic analyses to be carried out to determine not only the serotypes (dengue 1, 2, 3 and 4 were detected) but also the genotypes. Furthermore, in one sample, our unbiased metagenomic next-generation sequencing approach made it possible to detect epizootic hemorrhagic disease virus sequences, an arthropod-transmitted virus in ruminants. To conclude, as such an approach requires no cold storage or freezing of samples, dengue Ag-RDTs represent a very pragmatic and robust alternative for the genomic surveillance of dengue virus.}, } @article {pmid38004830, year = {2023}, author = {Veloso, M and Waldisperg, A and Arros, P and Berríos-Pastén, C and Acosta, J and Colque, H and Varas, MA and Allende, ML and Orellana, LH and Marcoleta, AE}, title = {Diversity, Taxonomic Novelty, and Encoded Functions of Salar de Ascotán Microbiota, as Revealed by Metagenome-Assembled Genomes.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004830}, issn = {2076-2607}, support = {FONDECYT 1221193//Agencia Nacional de Investigación y Desarrollo/ ; Millenium Institute Center for Genome Regulation//Agencia Nacional de Investigación y Desarrollo/ ; }, abstract = {Salar de Ascotán is a high-altitude arsenic-rich salt flat exposed to high ultraviolet radiation in the Atacama Desert, Chile. It hosts unique endemic flora and fauna and is an essential habitat for migratory birds, making it an important site for conservation and protection. However, there is limited information on the resident microbiota's diversity, genomic features, metabolic potential, and molecular mechanisms that enable it to thrive in this extreme environment. We used long- and short-read metagenomics to investigate the microbial communities in Ascotán's water, sediment, and soil. Bacteria predominated, mainly Pseudomonadota, Acidobacteriota, and Bacteroidota, with a remarkable diversity of archaea in the soil. Following hybrid assembly, we recovered high-quality bacterial (101) and archaeal (6) metagenome-assembled genomes (MAGs), including representatives of two putative novel families of Patescibacteria and Pseudomonadota and two novel orders from the archaeal classes Halobacteriota and Thermoplasmata. We found different metabolic capabilities across distinct lineages and a widespread presence of genes related to stress response, DNA repair, and resistance to arsenic and other metals. These results highlight the remarkable diversity and taxonomic novelty of the Salar de Ascotán microbiota and its rich functional repertoire, making it able to resist different harsh conditions. The highly complete MAGs described here could serve future studies and bioprospection efforts focused on salt flat extremophiles, and contribute to enriching databases with microbial genome data from underrepresented regions of our planet.}, } @article {pmid38004813, year = {2023}, author = {Chauhan, RP and Fogel, R and Limson, J}, title = {Nanopore MinION Sequencing Generates a White Spot Syndrome Virus Genome from a Pooled Cloacal Swab Sample of Domestic Chickens in South Africa.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004813}, issn = {2076-2607}, support = {UID 95319//National Research Foundation/ ; Nano-Micro Manufacturing Facility//Department of Science and Innovation/ ; }, abstract = {White spot syndrome virus is a highly contagious pathogen affecting shrimp farming worldwide. The host range of this virus is primarily limited to crustaceans, such as shrimps, crabs, prawns, crayfish, and lobsters; however, several species of non-crustaceans, including aquatic insects, piscivorous birds, and molluscs may serve as the vectors for ecological dissemination. The present study was aimed at studying the faecal virome of domestic chickens (Gallus gallus domesticus) in Makhanda, Eastern Cape, South Africa. The cloacal swab specimens (n = 35) were collected from domestic chickens in December 2022. The cloacal swab specimens were pooled-each pool containing five cloacal swabs-for metagenomic analysis using a sequence-independent single-primer amplification protocol, followed by Nanopore MinION sequencing. While the metagenomic sequencing generated several contigs aligning with reference genomes of animal viruses, one striking observation was the presence of a White spot syndrome virus genome in one pool of cloacal swab specimens. The generated White spot syndrome virus genome was 273,795 bp in size with 88.5% genome coverage and shared 99.94% nucleotide sequence identity with a reference genome reported in China during 2018 (GenBank accession: NC_003225.3). The Neighbour-Joining tree grouped South African White spot syndrome virus genome with other White spot syndrome virus genomes reported from South East Asia. To our knowledge, this is the first report of a White spot syndrome virus genome generated from domestic chickens. The significance of White spot syndrome virus infection in domestic chickens is yet to be determined.}, } @article {pmid38004811, year = {2023}, author = {Danilova, OV and Oshkin, IY and Belova, SE and Miroshnikov, KK and Ivanova, AA and Dedysh, SN}, title = {One Step Closer to Enigmatic USCα Methanotrophs: Isolation of a Methylocapsa-like Bacterium from a Subarctic Soil.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004811}, issn = {2076-2607}, support = {21-14-00034//Russian Science Foundation/ ; }, abstract = {The scavenging of atmospheric trace gases has been recognized as one of the lifestyle-defining capabilities of microorganisms in terrestrial polar ecosystems. Several metagenome-assembled genomes of as-yet-uncultivated methanotrophic bacteria, which consume atmospheric CH4 in these ecosystems, have been retrieved in cultivation-independent studies. In this study, we isolated and characterized a representative of these methanotrophs, strain D3K7, from a subarctic soil of northern Russia. Strain D3K7 grows on methane and methanol in a wide range of temperatures, between 5 and 30 °C. Weak growth was also observed on acetate. The presence of acetate in the culture medium stimulated growth at low CH4 concentrations (~100 p.p.m.v.). The finished genome sequence of strain D3K7 is 4.15 Mb in size and contains about 3700 protein-encoding genes. According to the result of phylogenomic analysis, this bacterium forms a common clade with metagenome-assembled genomes obtained from the active layer of a permafrost thaw gradient in Stordalen Mire, Abisco, Sweden, and the mineral cryosol at Axel Heiberg Island in the Canadian High Arctic. This clade occupies a phylogenetic position in between characterized Methylocapsa methanotrophs and representatives of the as-yet-uncultivated upland soil cluster alpha (USCα). As shown by the global distribution analysis, D3K7-like methanotrophs are not restricted to polar habitats but inhabit peatlands and soils of various climatic zones.}, } @article {pmid38004759, year = {2023}, author = {Gomez-Ramirez, U and Nolasco-Romero, CG and Contreras-Rodríguez, A and Zuñiga, G and Mendoza-Elizalde, S and Prado-Galbarro, FJ and Pérez Aguilar, F and Pedraza Tinoco, JE and Valencia-Mayoral, P and Velázquez-Guadarrama, N}, title = {Dysbiosis by Eradication of Helicobacter pylori Infection Associated with Follicular Gastropathy and Pangastropathy.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004759}, issn = {2076-2607}, support = {HIM/2017/010 SSA 1305//Federal Resources of the Hospital Infanttil de México Federico Gómez/ ; }, abstract = {Dysbiosis plays an important role in the development of bacterial infections in the gastric mucosa, particularly Helicobacter pylori. The international guidelines for the treatment of H. pylori infections suggest standard triple therapy (STT). Nevertheless, because of the increasing resistance rates to clarithromycin, metronidazole has been widely considered in several countries. Unfortunately, the non-justified administration of antibiotics induces dysbiosis in the target organ. We characterized the gastric microbiota of patients diagnosed with follicular gastropathy and pangastropathy attributed to H. pylori infection, before and after the administration of STT with metronidazole. Dominant relative abundances of Cutibacterium were observed in pre-treatment patients, whereas H. pylori was observed at <11%, suggesting the multifactor property of the disease. The correlation of Cutibacterium acnes and H. pylori with gastric infectious diseases was also evaluated using quantitative real-time polymerase chain reaction. The dominance of C. acnes over H. pylori was observed in gastritis, gastropathies, and non-significant histological alterations. None of the microorganisms were detected in the intestinal metaplasia. Post-treatment alterations revealed an increase in the relative abundances of Staphylococcus, Pseudomonas, and Klebsiella. Non-H. pylori gastrointestinal bacteria can be associated with the initiation and development of gastric diseases, such as pathobiont C. acnes.}, } @article {pmid38004755, year = {2023}, author = {de Campos, GM and de La-Roque, DGL and Lima, ARJ and Zucherato, VS and de Carvalho, E and de Lima, LPO and de Queiroz Cattony Neto, P and Dos Santos, MM and Ciccozzi, M and Giovanetti, M and Haddad, R and Alcantara, LCJ and Elias, MC and Sampaio, SC and Covas, DT and Kashima, S and Slavov, SN}, title = {Exploring Viral Metagenomics in Pediatric Patients with Acute Respiratory Infections: Unveiling Pathogens beyond SARS-CoV-2.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004755}, issn = {2076-2607}, support = {2022/00910-6; 2021/09446-8; 2021/11944-6 (CeVIVAS); 2018/15826-5; 2017/23205-8//São Paulo Research Foundation/ ; }, abstract = {The emergence of SARS-CoV-2 and the subsequent pandemic have prompted extensive diagnostic and clinical efforts to mitigate viral spread. However, these strategies have largely overlooked the presence of other respiratory viruses. Acute respiratory diseases in pediatric patients can be caused by a diverse range of viral agents, and metagenomics represents a powerful tool for their characterization. This study aimed to investigate the viral abundance in pediatric patients with acute respiratory symptoms who tested negative for SARS-CoV-2 during the Omicron pandemic wave. To achieve this, viral metagenomics and next-generation sequencing were employed on 96 nasopharyngeal swab samples, which were organized into 12 pools, with each pool consisting of eight individual samples. Metagenomic analysis revealed that the most prevalent viruses associated with acute disease in pediatric patients were respiratory syncytial virus (detected in all pools) and enteroviruses, which are known to cause significant morbidity and mortality in children. Additionally, clinically significant viruses such as mumps orthorubulavirus, human metapneumovirus, influenza A, and a wide array of human herpesviruses (1, 3-7) were identified. These findings highlight the extensive potential of viral metagenomics in identifying viruses other than SARS-CoV-2 that contribute to acute infections in children. Consequently, this methodology should garner clinical attention in terms of differential diagnosis and the development of public policies to address such conditions in the global pediatric population.}, } @article {pmid38004753, year = {2023}, author = {Mathlouthi, NEH and Belguith, I and Yengui, M and Oumarou Hama, H and Lagier, JC and Ammar Keskes, L and Grine, G and Gdoura, R}, title = {The Archaeome's Role in Colorectal Cancer: Unveiling the DPANN Group and Investigating Archaeal Functional Signatures.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004753}, issn = {2076-2607}, abstract = {BACKGROUND AND AIMS: Gut microbial imbalances are linked to colorectal cancer (CRC), but archaea's role remains underexplored. Here, using previously published metagenomic data from different populations including Austria, Germany, Italy, Japan, China, and India, we performed bioinformatic and statistical analysis to identify archaeal taxonomic and functional signatures related to CRC.

METHODS: We analyzed published fecal metagenomic data from 390 subjects, comparing the archaeomes of CRC and healthy individuals. We conducted a biostatistical analysis to investigate the relationship between Candidatus Mancarchaeum acidiphilum (DPANN superphylum) and other archaeal species associated with CRC. Using the Prokka tool, we annotated the data focusing on archaeal genes, subsequently linking them to CRC and mapping them against UniprotKB and GO databases for specific archaeal gene functions.

RESULTS: Our analysis identified enrichment of methanogenic archaea in healthy subjects, with an exception for Methanobrevibacter smithii, which correlated with CRC. Notably, CRC showed a strong association with archaeal species, particularly Natrinema sp. J7-2, Ferroglobus placidus, and Candidatus Mancarchaeum acidiphilum. Furthermore, the DPANN archaeon exhibited a significant correlation with other CRC-associated archaea (p < 0.001). Functionally, we found a marked association between MvhB-type polyferredoxin and colorectal cancer. We also highlighted the association of archaeal proteins involved in the biosynthesis of leucine and the galactose metabolism process with the healthy phenotype.

CONCLUSIONS: The archaeomes of CRC patients show identifiable alterations, including a decline in methanogens and an increase in Halobacteria species. MvhB-type polyferredoxin, linked with CRC and species like Candidatus Mancarchaeum acidiphilum, Natrinema sp. J7-2, and Ferroglobus placidus emerge as potential archaeal biomarkers. Archaeal proteins may also offer gut protection, underscoring archaea's role in CRC dynamics.}, } @article {pmid38004740, year = {2023}, author = {Ossa-Trujillo, C and Taylor, EA and Sarwar, F and Vinasco, J and Jordan, ER and Buitrago, JAG and Hagevoort, GR and Lawhon, SD and Piñeiro, JM and Galloway-Peña, J and Norman, KN and Scott, HM}, title = {Two-Dose Ceftiofur Treatment Increases Cephamycinase Gene Quantities and Fecal Microbiome Diversity in Dairy Cows Diagnosed with Metritis.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004740}, issn = {2076-2607}, support = {2016-68003- 24607//United States Department of Agriculture/ ; }, abstract = {Antimicrobial resistance is a significant concern worldwide; meanwhile, the impact of 3rd generation cephalosporin (3GC) antibiotics on the microbial communities of cattle and resistance within these communities is largely unknown. The objectives of this study were to determine the effects of two-dose ceftiofur crystalline-free acid (2-CCFA) treatment on the fecal microbiota and on the quantities of second-and third-generation cephalosporin, fluoroquinolone, and macrolide resistance genes in Holstein-Friesian dairy cows in the southwestern United States. Across three dairy farms, 124 matched pairs of cows were enrolled in a longitudinal study. Following the product label regimen, CCFA was administered on days 0 and 3 to cows diagnosed with postpartum metritis. Healthy cows were pair-matched based on lactation number and calving date. Fecal samples were collected on days 0, 6, and 16 and pooled in groups of 4 (n = 192) by farm, day, and treatment group for community DNA extraction. The characterization of community DNA included real-time PCR (qPCR) to quantify the following antibiotic resistance genes: blaCMY-2, blaCTX-M, mphA, qnrB19, and the highly conserved 16S rRNA back-calculated to gene copies per gram of feces. Additionally, 16S rRNA amplicon sequencing and metagenomics analyses were used to determine differences in bacterial community composition by treatment, day, and farm. Overall, blaCMY-2 gene copies per gram of feces increased significantly (p ≤ 0.05) in the treated group compared to the untreated group on day 6 and remained elevated on day 16. However, blaCTX-M, mphA, and qnrB19 gene quantities did not differ significantly (p ≥ 0.05) between treatment groups, days, or farms, suggesting a cephamycinase-specific enhancement in cows on these farms. Perhaps unexpectedly, 16S rRNA amplicon metagenomic analyses showed that the fecal bacterial communities from treated animals on day 6 had significantly greater (p ≤ 0.05) alpha and beta diversity than the untreated group. Two-dose ceftiofur treatment in dairy cows with metritis elevates cephamycinase gene quantities among all fecal bacteria while paradoxically increasing microbial diversity.}, } @article {pmid38004707, year = {2023}, author = {Godain, A and Vogel, TM and Monnier, JM and Paitier, A and Haddour, N}, title = {Metaproteomic and Metagenomic-Coupled Approach to Investigate Microbial Response to Electrochemical Conditions in Microbial Fuel Cells.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004707}, issn = {2076-2607}, support = {ANR-11-IDEX-0007//LABEX iMUST/ ; }, abstract = {MFCs represent a promising sustainable biotechnology that enables the direct conversion of organic matter from wastewater into electricity using bacterial biofilms as biocatalysts. A crucial aspect of MFCs is how electroactive bacteria (EAB) behave and their associated mechanisms during extracellular electron transfer to the anode. A critical phase in the MFC start-up process is the initial colonization of the anode by EAB. Two MFCs were operated with an external resistance of 1000 ohms, one with an applied electrical voltage of 500 mV during the initial four days of biofilm formation and the other without any additional applied voltage. After stabilization of electricity production, total DNA and protein were extracted and sequenced from both setups. The combined metaproteomic/metagenomic analysis revealed that the application of voltage during the colonization step predominantly increased direct electron transfer via cytochrome c, mediated primarily by Geobacter sp. Conversely, the absence of applied voltage during colonization resulted in a broader diversity of bacteria, including Pseudomonas and Aeromonas, which participated in electricity production via mediated electron transfer involving flavin family members.}, } @article {pmid38004693, year = {2023}, author = {Tsouggou, N and Oikonomou, A and Papadimitriou, K and Skandamis, PN}, title = {16S and 18S rDNA Amplicon Sequencing Analysis of Aesthetically Problematic Microbial Mats on the Walls of the Petralona Cave: The Use of Essential Oils as a Cleaning Method.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004693}, issn = {2076-2607}, support = {//Palaeoanthropology Speleology Ephorate/ ; }, abstract = {The presence of microbial communities on cave walls and speleothems is an issue that requires attention. Traditional cleaning methods using water, brushes, and steam can spread the infection and cause damage to the cave structures, while chemical agents can lead to the formation of toxic compounds and damage the cave walls. Essential oils (EOs) have shown promising results in disrupting the cell membrane of bacteria and affecting their membrane permeability. In this study, we identified the microorganisms forming unwanted microbial communities on the walls and speleothems of Petralona Cave using 16S and 18S rDNA amplicon sequencing approaches and evaluated the efficacy of EOs in reducing the ATP levels of these ecosystems. The samples exhibited a variety of both prokaryotic and eukaryotic microorganisms, including Proteobacteria, Actinobacteria, Bacteroidetes, Chloroflexi, Firmicutes, the SAR supergroup, Opisthokonta, Excavata, Archaeplastida, and Amoebozoa. These phyla are often found in various habitats, including caves, and contribute to the ecological intricacy of cave ecosystems. In terms of the order and genus taxonomy, the identified biota showed abundances that varied significantly among the samples. Functional predictions were also conducted to estimate the differences in expressed genes among the samples. Oregano EO was found to reduce ATP levels by 87% and 46% for black and green spots, respectively. Consecutive spraying with cinnamon EO further reduced ATP levels, with reductions of 89% for black and 88% for green spots. The application of a mixture solution caused a significant reduction up to 96% in ATP levels of both areas. Our results indicate that EOs could be a promising solution for the treatment of microbial communities on cave walls and speleothems.}, } @article {pmid38004667, year = {2023}, author = {Kalnina, I and Gudra, D and Silamikelis, I and Viksne, K and Roga, A and Skinderskis, E and Fridmanis, D and Klovins, J}, title = {Variations in the Relative Abundance of Gut Bacteria Correlate with Lipid Profiles in Healthy Adults.}, journal = {Microorganisms}, volume = {11}, number = {11}, pages = {}, pmid = {38004667}, issn = {2076-2607}, support = {"Investigation of interaction of smoked dietary products with gut microbiota" Agreement Nr. 1.1.1.2/VIAA/1/16/128//European Regional Development Fund "On Implementation of Activity 1.1.1.2 "Post-doctoral Research Aid"/ ; }, abstract = {The gut microbiome is a versatile system regulating numerous aspects of host metabolism. Among other traits, variations in the composition of gut microbial communities are related to blood lipid patterns and hyperlipidaemia, yet inconsistent association patterns exist. This study aims to assess the relationships between the composition of the gut microbiome and variations in lipid profiles among healthy adults. This study used data and samples from 23 adult participants of a previously conducted dietary intervention study. Circulating lipid measurements and whole-metagenome sequences of the gut microbiome were derived from 180 blood and faecal samples collected from eight visits distributed across an 11-week study. Lipid-related variables explained approximately 4.5% of the variation in gut microbiome compositions, with higher effects observed for total cholesterol and high-density lipoproteins. Species from the genera Odoribacter, Anaerostipes, and Parabacteroides correlated with increased serum lipid levels, whereas probiotic species like Akkermansia muciniphila were more abundant among participants with healthier blood lipid profiles. An inverse correlation with serum cholesterol was also observed for Massilistercora timonensis, a player in regulating lipid turnover. The observed correlation patterns add to the growing evidence supporting the role of the gut microbiome as an essential regulator of host lipid metabolism.}, } @article {pmid38003681, year = {2023}, author = {Gureev, AP and Alimova, AA and Silachev, DN and Plotnikov, EY}, title = {Noncoupled Mitochondrial Respiration as Therapeutic Approach for the Treatment of Metabolic Diseases: Focus on Transgenic Animal Models.}, journal = {International journal of molecular sciences}, volume = {24}, number = {22}, pages = {}, pmid = {38003681}, issn = {1422-0067}, support = {21-75-30009//Russian Science Foundation/ ; FZGU-2023-0009//the Ministry of Science and Higher Education of the Russian Federation under the State/ ; }, mesh = {Animals ; Animals, Genetically Modified ; *Oxygen Consumption ; Mitochondria/metabolism ; Cell Respiration ; *Metabolic Diseases/metabolism ; Respiration ; Reactive Oxygen Species/metabolism ; }, abstract = {Mitochondrial dysfunction contributes to numerous chronic diseases, and mitochondria are targets for various toxins and xenobiotics. Therefore, the development of drugs or therapeutic strategies targeting mitochondria is an important task in modern medicine. It is well known that the primary, although not the sole, function of mitochondria is ATP generation, which is achieved by coupled respiration. However, a high membrane potential can lead to uncontrolled reactive oxygen species (ROS) production and associated dysfunction. For over 50 years, scientists have been studying various synthetic uncouplers, and for more than 30 years, uncoupling proteins that are responsible for uncoupled respiration in mitochondria. Additionally, the proteins of the mitochondrial alternative respiratory pathway exist in plant mitochondria, allowing noncoupled respiration, in which electron flow is not associated with membrane potential formation. Over the past two decades, advances in genetic engineering have facilitated the creation of various cellular and animal models that simulate the effects of uncoupled and noncoupled respiration in different tissues under various disease conditions. In this review, we summarize and discuss the findings obtained from these transgenic models. We focus on the advantages and limitations of transgenic organisms, the observed physiological and biochemical changes, and the therapeutic potential of uncoupled and noncoupled respiration.}, } @article {pmid38003647, year = {2023}, author = {Angelova, IY and Kovtun, AS and Averina, OV and Koshenko, TA and Danilenko, VN}, title = {Unveiling the Connection between Microbiota and Depressive Disorder through Machine Learning.}, journal = {International journal of molecular sciences}, volume = {24}, number = {22}, pages = {}, pmid = {38003647}, issn = {1422-0067}, support = {20-14-00132//Russian Science Foundation/ ; }, mesh = {Humans ; *Depressive Disorder, Major ; *Microbiota ; *Gastrointestinal Microbiome ; Metagenome ; }, abstract = {In the last few years, investigation of the gut-brain axis and the connection between the gut microbiota and the human nervous system and mental health has become one of the most popular topics. Correlations between the taxonomic and functional changes in gut microbiota and major depressive disorder have been shown in several studies. Machine learning provides a promising approach to analyze large-scale metagenomic data and identify biomarkers associated with depression. In this work, machine learning algorithms, such as random forest, elastic net, and You Only Look Once (YOLO), were utilized to detect significant features in microbiome samples and classify individuals based on their disorder status. The analysis was conducted on metagenomic data obtained during the study of gut microbiota of healthy people and patients with major depressive disorder. The YOLO method showed the greatest effectiveness in the analysis of the metagenomic samples and confirmed the experimental results on the critical importance of a reduction in the amount of Faecalibacterium prausnitzii for the manifestation of depression. These findings could contribute to a better understanding of the role of the gut microbiota in major depressive disorder and potentially lead the way for novel diagnostic and therapeutic strategies.}, } @article {pmid38003122, year = {2023}, author = {Gál, B and Varga-Kugler, R and Ihász, K and Kaszab, E and Farkas, S and Marton, S and Martella, V and Bányai, K}, title = {A Snapshot on the Genomic Epidemiology of Turkey Reovirus Infections, Hungary.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {22}, pages = {}, pmid = {38003122}, issn = {2076-2615}, support = {National Laboratory for Infectious Animal Diseases, Antimicrobial Resistance, Veterinary Public Health and Food Chain Safety RRF- 2.3.1-21-2022-00001//National Research, Development and Innovation Office/ ; TKP2021-EGA-01//National Research, Development and Innovation Office/ ; }, abstract = {Reovirus infections in turkeys are associated with arthritis and lameness. Viral genome sequence data are scarce, which makes an accurate description of the viral evolution and epidemiology difficult. In this study, we isolated and characterized turkey reoviruses from Hungary. The isolates were identified in 2016; these isolates were compared with earlier Hungarian turkey reovirus strains and turkey reoviruses isolated in the 2010s in the United States. Gene-wise sequence and phylogenetic analyses identified the cell-receptor binding protein and the main neutralization antigen, σC, to be the most conserved. The most genetically diverse gene was another surface antigen coding gene, μB. This gene was shown to undergo frequent reassortment among chicken and turkey origin reoviruses. Additional reassortment events were found primarily within members of the homologous turkey reovirus clade. Our data showed evidence for low variability among strains isolated from independent outbreaks, a finding that suggests a common source of turkey reoviruses in Hungarian turkey flocks. Given that commercial vaccines are not available, identification of the source of these founder virus strains would permit a more efficient prevention of disease outbreaks before young birds are settled to fattening facilities.}, } @article {pmid38003087, year = {2023}, author = {Kim, HR and Kim, HS and Kwon, YK}, title = {Intrahepatic Cholangiocarcinoma Identified in a Zoo-Housed Sandhill Crane (Grus canadensis): An Anatomopathological and Metagenomic Study.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {22}, pages = {}, pmid = {38003087}, issn = {2076-2615}, support = {N-1541767-2010-19-06//Animal and Plant Quarantine Agency/ ; F-1543084-2021-22-01//Animal and Plant Quarantine Agency/ ; }, abstract = {Tumors in birds can be caused by a variety of factors such as species, age, sex, virus, chemicals, and environment. In particular, tumors are a major cause of death in long-lived birds such as parrots and zoo birds. A male sandhill crane that was bred for 8 years in a zoo was diagnosed with intrahepatic cholangiocarcinoma (ICC). At necropsy, the liver revealed a multinodular mass of variable colors, and severe cirrhosis and hemorrhages were present. Histologically, ICC was characterized by the presence of both types of ICC: small-duct type and large-duct type. Large-duct-type ICC was distinguished by the presence of multifocal biliary neoplasia, characterized by the diffuse papillary proliferation of columnar cells resembling large cholangiocytes. Small-duct-type ICC was characterized by the presence of non-mucin-producing cuboidal cells such as bile duct cells. In this case, no viral cause was identified from the metagenomic analysis and PCR of ICC; however, a contributing role of Cutibacterium sp. and E. coli identified from the metagenomics could not be excluded. This study is the first to describe the anatomopathological characteristics of ICC in the studied sandhill crane and attempts to determine its potential infectious etiology using metagenomics.}, } @article {pmid38001502, year = {2023}, author = {Li, P and Hong, J and Yuan, Z and Huang, Y and Wu, M and Ding, T and Wu, Z and Sun, X and Lin, D}, title = {Gut microbiota in parasite-transmitting gastropods.}, journal = {Infectious diseases of poverty}, volume = {12}, number = {1}, pages = {105}, pmid = {38001502}, issn = {2049-9957}, support = {2020YFC1200100//the National Key R&D Program of China/ ; 2020YFC1200103//the National Key R&D Program of China/ ; 2021YFC2300800//the National Key R&D Program of China/ ; 2016YFC1200500//the National Key R&D Program of China/ ; 82202560//the National Natural Science Foundation of China/ ; 82161160343//the National Natural Science Foundation of China/ ; 82272361//the National Natural Science Foundation of China/ ; 2021B1212040017//the Science and Technology Planning Project of Guangdong Province/ ; 2022B1111030002//the R&D Program in Key Areas of Guangdong Province/ ; 22qntd4813//the Fundamental Research Funds for the Central University/ ; B12003//the 111 Project/ ; 20201192//the 6th Nuclear Energy R&D Project/ ; NPRC-2019-194-30//the National Parasitic Resource Center and Ministry of Science and Technology/ ; }, mesh = {Animals ; *Parasites ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; Snails/parasitology ; Host-Parasite Interactions ; }, abstract = {BACKGROUND: Gastropoda, the largest class within the phylum Mollusca, houses diverse gut microbiota, and some gastropods serve as intermediate hosts for parasites. Studies have revealed that gut bacteria in gastropods are associated with various biological aspects, such as growth, immunity and host-parasite interactions. Here, we summarize our current knowledge of gastropod gut microbiomes and highlight future research priorities and perspectives.

METHODS: A literature search was undertaken using PubMed, Web of Science and CNKI for the articles on the gut microbiota of gastropods until December 31, 2022. We retrieved a total of 166 articles and identified 73 eligible articles for inclusion in this review based on the inclusion and exclusion criteria.

RESULTS: Our analysis encompassed freshwater, seawater and land snails, with a specific focus on parasite-transmitting gastropods. We found that most studies on gastropod gut microbiota have primarily utilized 16S rRNA gene sequencing to analyze microbial composition, rather than employing metagenomic, metatranscriptomic, or metabolomic approaches. This comprehensive review provided an overview of the parasites carried by snail species in the context of gut microbiota studies. We presented the gut microbial trends, a comprehensive summary of the diversity and composition, influencing factors, and potential functions of gastropod gut microbiota. Additionally, we discussed the potential applications, research gaps and future perspectives of gut microbiomes in parasite-transmitting gastropods. Furthermore, several strategies for enhancing our comprehension of gut microbiomes in snails were also discussed.

CONCLUSIONS: This review comprehensively summarizes the current knowledge on the composition, potential function, influencing factors, potential applications, limitations, and challenges of gut microbiomes in gastropods, with a specific emphasis on parasite-transmitting gastropods. These findings provide important insights for future studies aiming to understand the potential role of gastropod gut microbiota in controlling snail populations and snail-borne diseases.}, } @article {pmid38001408, year = {2023}, author = {Chen, C and Zhang, Y and Yao, X and Yan, Q and Li, S and Zhong, Q and Liu, Z and Tang, F and Liu, C and Li, H and Zhu, D and Lan, W and Ling, Y and Lu, D and Xu, H and Ning, Q and Wang, Y and Jiang, Z and Zhang, Q and Gu, G and Sun, L and Wang, N and Wang, G and Zhang, A and Ullah, H and Sun, W and Ma, W}, title = {Characterizations of the multi-kingdom gut microbiota in Chinese patients with gouty arthritis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {363}, pmid = {38001408}, issn = {1471-2180}, support = {Support [2020]4Y155//Science and Technology Program of Guizhou Province/ ; Platform and talent [2020]2202//Science and Technology Program of Guizhou Province/ ; 82260894//National Natural Science Foundation of China/ ; 81902037//National Natural Science Foundation of China/ ; GZEYK-B[2021]2//Scientific Research Project of the Second Affiliated Hospital of Guizhou University of Traditional Chinese Medicine/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Arthritis, Gouty ; East Asian People ; *Microbiota ; *Mycobiome ; Bacteria/genetics ; }, abstract = {OBJECTIVE: The gut microbial composition has been linked to metabolic and autoimmune diseases, including arthritis. However, there is a dearth of knowledge on the gut bacteriome, mycobiome, and virome in patients with gouty arthritis (GA).

METHODS: We conducted a comprehensive analysis of the multi-kingdom gut microbiome of 26 GA patients and 28 healthy controls, using whole-metagenome shotgun sequencing of their stool samples.

RESULTS: Profound alterations were observed in the gut bacteriome, mycobiome, and virome of GA patients. We identified 1,117 differentially abundant bacterial species, 23 fungal species, and 4,115 viral operational taxonomic units (vOTUs). GA-enriched bacteria included Escherichia coli_D GENOME144544, Bifidobacterium infantis GENOME095938, Blautia_A wexlerae GENOME096067, and Klebsiella pneumoniae GENOME147598, while control-enriched bacteria comprised Faecalibacterium prausnitzii_G GENOME147678, Agathobacter rectalis GENOME143712, and Bacteroides_A plebeius_A GENOME239725. GA-enriched fungi included opportunistic pathogens like Cryptococcus neoformans GCA_011057565, Candida parapsilosis GCA_000182765, and Malassezia spp., while control-enriched fungi featured several Hortaea werneckii subclades and Aspergillus fumigatus GCA_000002655. GA-enriched vOTUs mainly attributed to Siphoviridae, Myoviridae, Podoviridae, and Microviridae, whereas control-enriched vOTUs spanned 13 families, including Siphoviridae, Myoviridae, Podoviridae, Quimbyviridae, Phycodnaviridae, and crAss-like. A co-abundance network revealed intricate interactions among these multi-kingdom signatures, signifying their collective influence on the disease. Furthermore, these microbial signatures demonstrated the potential to effectively discriminate between patients and controls, highlighting their diagnostic utility.

CONCLUSIONS: This study yields crucial insights into the characteristics of the GA microbiota that may inform future mechanistic and therapeutic investigations.}, } @article {pmid38001079, year = {2023}, author = {Lang, H and Liu, Y and Duan, H and Zhang, W and Hu, X and Zheng, H}, title = {Identification of peptides from honeybee gut symbionts as potential antimicrobial agents against Melissococcus plutonius.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7650}, pmid = {38001079}, issn = {2041-1723}, support = {32170495//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Bees/genetics ; Animals ; Metagenome ; Bacteria/genetics/metabolism ; Peptides/genetics/pharmacology/metabolism ; *Anti-Infective Agents/pharmacology/metabolism ; *Biological Products/metabolism ; }, abstract = {Eusocial pollinators are crucial elements in global agriculture. The honeybees and bumblebees are associated with a simple yet host-restricted gut community, which protect the hosts against pathogen infections. Recent genome mining has led to the discovery of biosynthesis pathways of bioactive natural products mediating microbe-microbe interactions from the gut microbiota. Here, we investigate the diversity of biosynthetic gene clusters in the bee gut microbiota by analyzing 477 genomes from cultivated bacteria and metagenome-assembled genomes. We identify 744 biosynthetic gene clusters (BGCs) covering multiple chemical classes. While gene clusters for the post-translationally modified peptides are widely distributed in the bee guts, the distribution of the BGC classes varies significantly in different bee species among geographic locations, which is attributed to the strain-level variation of bee gut members in the chemical repertoire. Interestingly, we find that Gilliamella strains possessing a thiopeptide-like BGC show potent activity against the pathogenic Melissococcus plutonius. The spectrometry-guided genome mining reveals a RiPP-encoding BGC from Gilliamella with a 10 amino acid-long core peptide exhibiting antibacterial potentials. This study illustrates the widespread small-molecule-encoding BGCs in the bee gut symbionts and provides insights into the bacteria-derived natural products as potential antimicrobial agents against pathogenic infections.}, } @article {pmid38000749, year = {2024}, author = {Lewin, S and Wende, S and Wehrhan, M and Verch, G and Ganugi, P and Sommer, M and Kolb, S}, title = {Cereals rhizosphere microbiome undergoes host selection of nitrogen cycle guilds correlated to crop productivity.}, journal = {The Science of the total environment}, volume = {911}, number = {}, pages = {168794}, doi = {10.1016/j.scitotenv.2023.168794}, pmid = {38000749}, issn = {1879-1026}, mesh = {*Rhizosphere ; Edible Grain/chemistry ; Nitrates ; Fertilizers/analysis ; Nitrogen Cycle ; *Microbiota/physiology ; Soil/chemistry ; Crops, Agricultural ; Nitrogen/analysis ; Soil Microbiology ; }, abstract = {Sustainable transformation of agricultural plant production requires the reduction of nitrogen (N) fertilizer application. Such a reduced N fertilizer application may impede crop production due to an altered symbiosis of crops and their rhizosphere microbiome, since reduced N input may affect the competition and synergisms with the plant. The assessment of such changes in the crop microbiome functionalities at spatial scales relevant for agricultural management remains challenging. We investigated in a field plot experiment how and if the N cycling guilds of the rhizosphere of globally relevant cereal crops - winter barley, wheat and rye - are influenced by reduced N fertilization. Crop productivity was assessed by remote sensing of the shoot biomass. Microbial N cycling guilds were investigated by metagenomics targeting diazotrophs, nitrifiers, denitrifiers and the dissimilatory nitrate to ammonium reducing guild (DNRA). The functional composition of microbial N cycling guilds was explained by crop productivity parameters and soil pH, and diverged substantially between the crop species. The responses of individual microbial N cycling guild abundances to shoot dry weight and rhizosphere nitrate content was modulated by the N fertilization treatments and the crop species, which was identified based on regression analyses. Thus, characteristic shifts in the microbial N cycling guild acquisition associated with the crop host species were resolved. Particularly, the rhizosphere of rye was enriched with potentially N-preserving microbial guilds - diazotrophs and the DNRA guild - when no fertilizer was applied. We speculate that the acquisition of microbial N cycling guilds was the result of plant species-specific acquisition strategies. Thus, the investigated cereal crop holobionts have likely different symbiotic strategies that make them differently resilient against reduced N fertilizer inputs. Furthermore, we demonstrated that these belowground patterns of N cycling guilds from the rhizosphere microbiome are linked to remotely sensed aboveground plant productivity.}, } @article {pmid38000643, year = {2023}, author = {Jiang, M and Khunjar, W and Li, A and Chandran, K}, title = {Divergent microbial structure still results in convergent microbial function during arrested anaerobic digestion of food waste at different hydraulic retention times.}, journal = {Bioresource technology}, volume = {393}, number = {}, pages = {130069}, doi = {10.1016/j.biortech.2023.130069}, pmid = {38000643}, issn = {1873-2976}, abstract = {In this study, two arrested anaerobic digestion bioreactors, fed with food waste, operated under different hydraulic retention times (HRTs) exhibited similar total volatile fatty acid (VFA) yields (p = 0.09). 16S rRNA gene sequencing revealed distinct microbial structure (p = 0.02) at the two HRTs. However, between the two HRTs, there were no differences in potential (DNA) and extant (mRNA) functionality for the production of acetic (AA)-, propionic (PA)-, butyric (BA)- and valeric-acid (VA), as indicated by the metagenome and metatranscriptome data, respectively. The highest potential and extant functionality for PA production in the reactor microbiomes mirrored the highest abundance of PA in the reactor effluents. Meta-omics analysis of BA production indicated possible metabolite exchange across different community members. Notably, the basis for similar VFA production performance observed under the HRTs tested lies in the community-level redundancy in convergent acidification functions and pathways, rather than trends in community-level structure alone.}, } @article {pmid38000633, year = {2023}, author = {Hou, J and Lam, KL and Chiu, YT and Kwong, KY and Lau, HL and Marafa, LM and Tsui, SKW and Mo, IWY and Chan, PL}, title = {Urban green waste bulking agent is the major source of antimicrobial resistance genes persisted in home compost, not animal manure.}, journal = {Environmental research}, volume = {242}, number = {}, pages = {117713}, doi = {10.1016/j.envres.2023.117713}, pmid = {38000633}, issn = {1096-0953}, abstract = {Urban green waste and food waste are often used as bulking agents to prepare home compost in combination with animal manure in urban horticulture and community gardening. Although it is known that antimicrobial resistance genes (ARGs) persist in home compost, their origins have not been determined. In addition, the factors contributing to ARGs persistence remain unclear. In this study, we aim to (i) characterize the changes in the microbiome and antimicrobial resistome during the composting process of home compost using metagenomics shotgun sequencing, (ii) identify the source of the ARGs persisted in home compost using SourceTracker, and (iii) elucidate the collective effect of compost microbiome and environmental factors, including the physicochemical properties and antibiotics concentration of home compost, in contributing to ARG persistence using Procrustes analysis, co-occurrence network analysis, variation partitioning analysis, and structural equation modeling. SourceTracker analysis indicated that urban green waste bulking agent was the major source of the persisting ARGs in home compost instead of animal manure. Procrustes analysis and co-occurrence network analysis revealed a strong association between microbiome and antimicrobial resistome. Variation partitioning analysis and structural equation modeling suggested that physicochemical properties shaped the antimicrobial resistome directly and indirectly by influencing the microbiome. Our results indicated that the persistence of ARGs in home compost might be due to the succession of microbial species from the urban green waste bulking agent, and the physicochemical properties might have defined the compost environment to shape the microbiome in the compost, thus, in turn, the persisting antimicrobial resistome.}, } @article {pmid38000281, year = {2023}, author = {Bombaywala, S and Bajaj, A and Dafale, NA}, title = {Deterministic effect of oxygen level variation on shaping antibiotic resistome.}, journal = {Journal of hazardous materials}, volume = {465}, number = {}, pages = {133047}, doi = {10.1016/j.jhazmat.2023.133047}, pmid = {38000281}, issn = {1873-3336}, abstract = {An increase in acquisition of antibiotic resistance genes (ARGs) by pathogens under antibiotic selective pressure poses public health threats. Sub-inhibitory antibiotics induce bacteria to generate reactive oxygen species (ROS) dependent on dissolved oxygen (DO) levels, while molecular connection between ROS-mediated ARG emergence through DNA damage and metabolic changes remains elusive. Thus, the study investigates antibiotic resistome dynamics, microbiome shift, and pathogen distribution in hyperoxic (5-7 mg L[-1]), normoxic (2-4 mg L[-1]), and hypoxic (0.5-1 mg L[-1]) conditions using lab-scale bioreactor. Composite inoculums in the reactor were designed to represent comprehensive microbial community and AR profile from selected activated sludge. RT-qPCR and metagenomic analysis showed an increase in ARG count (100.98 ppm) with enrichment of multidrug efflux pumps (acrAB, mexAB) in hyperoxic condition. Conversely, total ARGs decreased (0.11 ppm) under hypoxic condition marked by a major decline in int1 abundance. Prevalence of global priority pathogens increased in hyperoxic (22.5%), compared to hypoxic (0.9%) wherein major decrease were observed in Pseudomonas, Shigella, and Borrelia. The study observed an increase in superoxide dismutase (sodA, sodB), DNA repair genes (nfo, polA, recA, recB), and ROS (10.4 µmol L[-1]) in adapted biomass with spiked antibiotics. This suggests oxidative damage that facilitates stress-induced mutagenesis providing evidence for observed hyperoxic enrichment of ARGs. Moreover, predominance of catalase (katE, katG) likely limit oxidative damage that deplete ARG breeding in hypoxic condition. The study proposes a link between oxygen levels and AR development that offers insights into mitigation and intervention of AR by controlling oxygen-related stress and strategic selection of bacterial communities.}, } @article {pmid37999453, year = {2023}, author = {Yan, Z and He, X and Ayala, J and Xu, Q and Yu, X and Hou, R and Yao, Y and Huang, H and Wang, H}, title = {The Impact of Bamboo Consumption on the Spread of Antibiotic Resistance Genes in Giant Pandas.}, journal = {Veterinary sciences}, volume = {10}, number = {11}, pages = {}, pmid = {37999453}, issn = {2306-7381}, support = {2022NSFSC0131//Sichuan Science and Technology Provincial Department/ ; 2020CPB-C10//the independent project of Chengdu Research Base of Giant Panda Breeding/ ; 2021CPB-C14//the independent project of Chengdu Research Base of Giant Panda Breeding/ ; }, abstract = {The spread of antibiotic resistance genes (ARGs) in the environment exacerbates the contamination of these genes; therefore, the role plants play in the transmission of resistance genes in the food chain requires further research. Giant pandas consume different bamboo parts at different times, which provides the possibility of investigating how a single food source can affect the variation in the spread of ARGs. In this study, metagenomic analysis and the Comprehensive Antibiotic Resistance Database (CARD) database were used to annotate ARGs and the differences in gut microbiota ARGs during the consumption of bamboo shoots, leaves, and culms by captive giant pandas. These ARGs were then compared to investigate the impact of bamboo part consumption on the spread of ARGs. The results showed that the number of ARGs in the gut microbiota of the subjects was highest during the consumption of bamboo leaves, while the variety of ARGs was highest during the consumption of shoots. Escherichia coli, which poses a higher risk of ARG dissemination, was significantly higher in the leaf group, while Klebsiella, Enterobacter, and Raoultella were significantly higher in the shoot group. The ARG risk brought by bamboo shoots and leaves may originate from soil and environmental pollution. It is recommended to handle the feces of giant pandas properly and regularly monitor the antimicrobial and virulence genes in their gut microbiota to mitigate the threat of antibiotic resistance.}, } @article {pmid37999398, year = {2023}, author = {Jahajeeah, D and Ranghoo-Sanmukhiya, M and Schäfer, G}, title = {Metabolic Profiling, Antiviral Activity and the Microbiome of Some Mauritian Soft Corals.}, journal = {Marine drugs}, volume = {21}, number = {11}, pages = {}, pmid = {37999398}, issn = {1660-3397}, support = {WS/MUS22-01//International Centre for Genetic Engineering and Biotechnology/ ; }, mesh = {Animals ; *Papillomavirus Infections ; Aquatic Organisms ; *Anthozoa/chemistry ; *Microbiota ; Antiviral Agents/pharmacology/metabolism ; }, abstract = {Soft corals, recognized as sessile marine invertebrates, rely mainly on chemical, rather than physical defense, by secreting intricate secondary metabolites with plausible pharmaceutical implication. Their ecological niche encompasses a diverse community of symbiotic microorganisms which potentially contribute to the biosynthesis of these bioactive metabolites. The emergence of new viruses and heightened viral resistance underscores the urgency to explore novel pharmacological reservoirs. Thus, marine organisms, notably soft corals and their symbionts, have drawn substantial attention. In this study, the chemical composition of four Mauritian soft corals: Sinularia polydactya, Cespitularia simplex, Lobophytum patulum, and Lobophytum crassum was investigated using LC-MS techniques. Concurrently, Illumina 16S metagenomic sequencing was used to identify the associated bacterial communities in the named soft corals. The presence of unique biologically important compounds and vast microbial communities found therein was further followed up to assess their antiviral effects against SARS-CoV-2 and HPV pseudovirus infection. Strikingly, among the studied soft corals, L. patulum displayed an expansive repertoire of unique metabolites alongside a heightened bacterial consort. Moreover, L. patulum extracts exerted some promising antiviral activity against SARS-CoV-2 and HPV pseudovirus infection, and our findings suggest that L. patulum may have the potential to serve as a therapeutic agent in the prevention of infectious diseases, thereby warranting further investigation.}, } @article {pmid37999031, year = {2023}, author = {Do, TH and Dao, TK and Nguyen, HD and Truong, NH}, title = {Understanding the Role of Free-Living Bacteria in the Gut of the Lower Termite Coptotermes gestroi Based on Metagenomic DNA Analysis.}, journal = {Insects}, volume = {14}, number = {11}, pages = {}, pmid = {37999031}, issn = {2075-4450}, support = {NVCC08.08/22-23//Vietnam Academy of Sicence and Technology, Vietnam/ ; }, abstract = {Termites' digestive systems, particularly in lower termites with the presence of protozoa, are unique ecological niches that shelter a diverse microbiota with a variety of functions for the host and the environment. In 2012, the metagenomic DNA (5.4 Gb) of the prokaryotes that freely live in the gut of the lower termite Coptotermes gestroi were sequenced. A total of 125,431 genes were predicted and analyzed in order to mine lignocellulolytic genes. however, the overall picture of the structure, diversity, and function of the prokaryotic gut microbiota was not investigated. In the present study, these 125,431 genes were taxonomically classified by MEGAN and functionally annotated by the Kyoto Encyclopedia of Genes and Genomes (KEGG) and by the Carbohydrate-Active enZYmes (CAZy) and HMMER databases. As a result, 95,751 bacterial genes were classified into 35 phyla. The structure of the bacteria, typified by a high ratio of Firmicutes to Bacterioidetes, was distinct from the structure of the entirety of the bacteria in the lower or higher termites' guts. The archaea (533 genes) were distributed into 4 phyla, 10 classes, 15 orders, 21 families, 47 genera, and 61 species. Although freely living in the guts, the prokaryotic community was formed, developed, and adapted to exhibit unique interactions in order to perform mutual roles of benefit to their hosts. Methanobacteriales, accounting for 61% of the archaea symbionts, seem to play an important role in methanogenesis. Concomitantly, bacterial methanotrophs in the gut utilize methane and combine with other bacterial groups, including potential lignocellulolytic degraders, acetogens, sulfur bacteria, and nitrogen-recycling bacteria, to efficiently convert wood with little nitrogen into acetates via certain pathway modules specified by prokaryotes that freely live in the gut. This forms an important energy source for the termites. Furthermore, bacteria carry 2223 genes involved in the biosynthesis of 17 antibiotic groups. The gut bacteria also possess genes for the degradation of 18 toxic aromatic compounds, of which four are commercial pesticides against termites commonly used for the preservation of wooden constructions. Eight of the eighteen pathways were the first to be reported from the termite gut. Overall, this study sheds light on the roles of the freely living bacteria and archaea in the C. gestroi gut, providing evidence that the gut microbiome acts as the second host genome, contributing both nutrients and immunity to support the host's existence, growth, and development.}, } @article {pmid37998790, year = {2023}, author = {Rimoldi, SG and Brioschi, D and Curreli, D and Salari, F and Pagani, C and Tamoni, A and Longobardi, C and Bosari, R and Rizzo, A and Landonio, S and Coen, M and Passerini, M and Gismondo, MR and Gori, A and Manzotti, A}, title = {Traditional Cultures versus Next Generation Sequencing for Suspected Orthopedic Infection: Experience Gained from a Reference Centre.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, pmid = {37998790}, issn = {2079-6382}, support = {Project no. PE00000007, INF-ACT//EU funding within the NextGenerationEU-MUR PNRR Extended Partnership initiative on Emerging Infectious Diseases/ ; }, abstract = {(Background) The diagnosis and the antimicrobial treatment of orthopedic infection are challenging, especially in cases with culture-negative results. New molecular methods, such as next-generation sequencing (NGS), promise to overcome some limitations of the standard culture, such as the detection of difficult-to-grow bacteria. However, data are scarce regarding the impact of molecular techniques in real-life scenarios. (Methods) We included cases of suspected orthopedic infection treated with surgery from May 2021 to September 2023. We combined traditional cultures with NGS. For NGS, we performed a metagenomic analysis of ribosomal 16s, and we queried dedicated taxonomic libraries to identify the species. To avoid false positive results, we set a cut-off of 1000 counts of the percentage of frequency of reads. (Results) We included 49 patients in our study. Our results show the presence of bacteria in 36/49 (73%) and 29/49 (59%) cases studied with NGS and traditional cultures, respectively. The concordance rate was 61%. Among the 19/49 discordant cases, in 11/19 cases, cultures were negative and NGS positive; in 4/19, cultures were positive and NGS negative; and in the remaining 4/19, different species were detected by traditional cultures and NGS. (Conclusions) Difficult-to-grow microorganisms, such as slow-growing anaerobic bacteria, were better detected by NGS compared to traditional culture in our study. However, more data to distinguish between true pathogens and contaminants are needed. NGS can be an additional tool to be used for the diagnosis of orthopedic infections and the choice of appropriate antimicrobial therapy.}, } @article {pmid37998782, year = {2023}, author = {Bianconi, I and Aschbacher, R and Pagani, E}, title = {Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, pmid = {37998782}, issn = {2079-6382}, abstract = {Recent advancements in sequencing technology and data analytics have led to a transformative era in pathogen detection and typing. These developments not only expedite the process, but also render it more cost-effective. Genomic analyses of infectious diseases are swiftly becoming the standard for pathogen analysis and control. Additionally, national surveillance systems can derive substantial benefits from genomic data, as they offer profound insights into pathogen epidemiology and the emergence of antimicrobial-resistant strains. Antimicrobial resistance (AMR) is a pressing global public health issue. While clinical laboratories have traditionally relied on culture-based antimicrobial susceptibility testing, the integration of genomic data into AMR analysis holds immense promise. Genomic-based AMR data can furnish swift, consistent, and highly accurate predictions of resistance phenotypes for specific strains or populations, all while contributing invaluable insights for surveillance. Moreover, genome sequencing assumes a pivotal role in the investigation of hospital outbreaks. It aids in the identification of infection sources, unveils genetic connections among isolates, and informs strategies for infection control. The One Health initiative, with its focus on the intricate interconnectedness of humans, animals, and the environment, seeks to develop comprehensive approaches for disease surveillance, control, and prevention. When integrated with epidemiological data from surveillance systems, genomic data can forecast the expansion of bacterial populations and species transmissions. Consequently, this provides profound insights into the evolution and genetic relationships of AMR in pathogens, hosts, and the environment.}, } @article {pmid37998614, year = {2023}, author = {Klein, EJ and Almaghlouth, NK and Weigel, G and Farmakiotis, D and Hardy, E}, title = {Refractory Bilateral Tubo-Ovarian Abscesses in a Patient with Iatrogenic Hypogammaglobulinemia.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {13}, number = {22}, pages = {}, pmid = {37998614}, issn = {2075-4418}, abstract = {Genital mycoplasmas are sexually transmitted Mollicutes with a high prevalence of urogenital tract colonization among females of reproductive age. Current guidelines recommend against routine screening for these organisms, since their role in the pathogenesis of pelvic inflammatory disease and tubo-ovarian abscesses (TOAs) remains unclear. However, genital mycoplasmas harbor pathogenic potential in immunocompromised hosts, especially patients with hypogammaglobulinemia. It is important to identify such infections early, given their potential for invasive spread and the availability of easily accessible treatments. We present a young adult female with multiple sclerosis and iatrogenic hypogammaglobulinemia, with refractory, bilateral pelvic inflammatory disease and TOAs due to Ureaplasma urealyticum, identified as a single pathogen via three distinct molecular tests. To our knowledge, this is the second case of TOAs caused by U. urealyticum in the literature, and the first diagnosed by pathogen cell-free DNA metagenomic next-generation sequencing in plasma.}, } @article {pmid37998010, year = {2023}, author = {Bulaev, A and Kadnikov, V and Elkina, Y and Beletsky, A and Melamud, V and Ravin, N and Mardanov, A}, title = {Shifts in the Microbial Populations of Bioleach Reactors Are Determined by Carbon Sources and Temperature.}, journal = {Biology}, volume = {12}, number = {11}, pages = {}, pmid = {37998010}, issn = {2079-7737}, support = {21-64-00019//Russian Science Foundation/ ; }, abstract = {In the present study, the effect of additional carbon sources (carbon dioxide and molasses) on the bio-oxidation of a pyrite-arsenopyrite concentrate at temperatures of 40-50 °C was studied, and novel data regarding the patterns of the bio-oxidation of gold-bearing sulfide concentrates and the composition of the microbial populations performing these processes were obtained. At 40 °C, additional carbon sources did not affect the bio-oxidation efficiency. At the same time, the application of additional carbon dioxide improved the bio-oxidation performance at temperatures of 45 and 50 °C and made it possible to avoid the inhibition of bio-oxidation due to an increase in the temperature. Therefore, the use of additional carbon dioxide may be proposed to prevent the negative effect of an increase in temperature on the bio-oxidation of sulfide concentrates. 16S rRNA gene profiling revealed archaea of the family Thermoplasmataceae (Acidiplasma, Ferroplasma, Cuniculiplasma, and A-plasma group) and bacteria of the genera Leptospirillum, with Sulfobacillus and Acidithiobacillus among the dominant groups in the community. Temperature influenced the composition of the communities to a greater extent than the additional sources of carbon and the mode of operation of the bioreactor. Elevating the temperature from 40 °C to 50 °C resulted in increases in the shares of Acidiplasma and Sulfobacillus and decreases in the relative abundances of Ferroplasma, Leptospirillum, and Acidithiobacillus, while Cuniculiplasma and A-plasma were more abundant at 45 °C. A metagenomic analysis of the studied population made it possible to characterize novel archaea belonging to an uncultivated, poorly-studied group of Thermoplasmatales which potentially plays an important role in the bio-oxidation process. Based on an analysis of the complete genome, we propose describing the novel species and novel genus as "Candidatus Carboxiplasma ferriphilum" gen. nov., spec. nov.}, } @article {pmid37996679, year = {2024}, author = {Tilahun, L and Asrat, A and Wessel, GM and Simachew, A}, title = {Ancestors in the Extreme: A Genomics View of Microbial Diversity in Hypersaline Aquatic Environments.}, journal = {Results and problems in cell differentiation}, volume = {71}, number = {}, pages = {185-212}, pmid = {37996679}, issn = {0080-1844}, mesh = {Humans ; Phylogeny ; *Bacteria/genetics/metabolism ; Archaea/genetics/metabolism ; Sodium Chloride/metabolism ; *Microbiota/genetics ; Metagenomics ; }, abstract = {The origin of eukaryotic cells, and especially naturally occurring syncytial cells, remains debatable. While a majority of our biomedical research focuses on the eukaryotic result of evolution, our data remain limiting on the prokaryotic precursors of these cells. This is particularly evident when considering extremophile biology, especially in how the genomes of organisms in extreme environments must have evolved and adapted to unique habitats. Might these rapidly diversifying organisms have created new genetic tools eventually used to enhance the evolution of the eukaryotic single nuclear or syncytial cells? Many organisms are capable of surviving, or even thriving, in conditions of extreme temperature, acidity, organic composition, and then rapidly adapt to yet new conditions. This study identified organisms found in extremes of salinity. A lake and a nearby pond in the Ethiopian Rift Valley were interrogated for life by sequencing the DNA of populations of organism collected from the water in these sites. Remarkably, a vast diversity of microbes were identified, and even though the two sites were nearby each other, the populations of organisms were distinctly different. Since these microbes are capable of living in what for humans would be inhospitable conditions, the DNA sequences identified should inform the next step in these investigations; what new gene families, or modifications to common genes, do these organisms employ to survive in these extreme conditions. The relationship between organisms and their environment can be revealed by decoding genomes of organisms living in extreme environments. These genomes disclose new biological mechanisms that enable life outside moderate environmental conditions, new gene functions for application in biotechnology, and may even result in identification of new species. In this study, we have collected samples from two hypersaline sites in the Danakil depression, the shorelines of Lake As'ale and an actively mixing salt pond called Muda'ara (MUP), to identify the microbial community by metagenomics. Shotgun sequencing was applied to high density sampling, and the relative abundance of Operational Taxonomic Units (OTUs) was calculated. Despite the broad taxonomic similarities among the salt-saturated metagenomes analyzed, MUP stood out from Lake As'ale samples. In each sample site, Archaea accounted for 95% of the total OTUs, largely to the class Halobacteria. The remaining 5% of organisms were eubacteria, with an unclassified strain of Salinibacter ruber as the dominant OTU in both the Lake and the Pond. More than 40 different genes coding for stress proteins were identified in the three sample sites of Lake As'ale, and more than 50% of the predicted stress-related genes were associated with oxidative stress response proteins. Chaperone proteins (DnaK, DnaJ, GrpE, and ClpB) were predicted, with percentage of query coverage and similarities ranging between 9.5% and 99.2%. Long reads for ClpB homologous protein from Lake As'ale metagenome datasets were modeled, and compact 3D structures were generated. Considering the extreme environmental conditions of the Danakil depression, this metagenomics dataset can add and complement other studies on unique gene functions on stress response mechanisms of thriving bio-communities that could have contributed to cellular changes leading to single and/or multinucleated eukaryotic cells.}, } @article {pmid37996661, year = {2023}, author = {Romanowicz, KJ and Crump, BC and Kling, GW}, title = {Genomic evidence that microbial carbon degradation is dominated by iron redox metabolism in thawing permafrost.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {124}, pmid = {37996661}, issn = {2730-6151}, support = {DEB-1637459//National Science Foundation (NSF)/ ; DEB-1754835//National Science Foundation (NSF)/ ; DEB-22-24743//National Science Foundation (NSF)/ ; OPP-1936769//National Science Foundation (NSF)/ ; }, abstract = {Microorganisms drive many aspects of organic carbon cycling in thawing permafrost soils, but the compositional trajectory of the post-thaw microbiome and its metabolic activity remain uncertain, which limits our ability to predict permafrost-climate feedbacks in a warming world. Using quantitative metabarcoding and metagenomic sequencing, we determined relative and absolute changes in microbiome composition and functional gene abundance during thaw incubations of wet sedge tundra collected from northern Alaska, USA. Organic soils from the tundra active-layer (0-50 cm), transition-zone (50-70 cm), and permafrost (70+ cm) depths were incubated under reducing conditions at 4 °C for 30 days to mimic an extended thaw duration. Following extended thaw, we found that iron (Fe)-cycling Gammaproteobacteria, specifically the heterotrophic Fe(III)-reducing Rhodoferax sp. and chemoautotrophic Fe(II)-oxidizing Gallionella sp., increased by 3-5 orders of magnitude in absolute abundance within the transition-zone and permafrost microbiomes, accounting for 65% of community abundance. We also found that the abundance of genes for Fe(III) reduction (e.g., MtrE) and Fe(II) oxidation (e.g., Cyc1) increased concurrently with genes for benzoate degradation and pyruvate metabolism, in which pyruvate is used to generate acetate that can be oxidized, along with benzoate, to CO2 when coupled with Fe(III) reduction. Gene abundance for CH4 metabolism decreased following extended thaw, suggesting dissimilatory Fe(III) reduction suppresses acetoclastic methanogenesis under reducing conditions. Our genomic evidence indicates that microbial carbon degradation is dominated by iron redox metabolism via an increase in gene abundance associated with Fe(III) reduction and Fe(II) oxidation during initial permafrost thaw, likely increasing microbial respiration while suppressing methanogenesis in wet sedge tundra.}, } @article {pmid37996631, year = {2023}, author = {Messenger, SR and McGuinniety, EMR and Stevenson, LJ and Owen, JG and Challis, GL and Ackerley, DF and Calcott, MJ}, title = {Metagenomic domain substitution for the high-throughput modification of nonribosomal peptides.}, journal = {Nature chemical biology}, volume = {}, number = {}, pages = {}, pmid = {37996631}, issn = {1552-4469}, support = {16/172//Manatu Hauora | Health Research Council of New Zealand (HRC)/ ; 2020-129624//Lottery Health Research/ ; }, abstract = {The modular nature of nonribosomal peptide biosynthesis has driven efforts to generate peptide analogs by substituting amino acid-specifying domains within nonribosomal peptide synthetase (NRPS) enzymes. Rational NRPS engineering has increasingly focused on finding evolutionarily favored recombination sites for domain substitution. Here we present an alternative evolution-inspired approach that involves large-scale diversification and screening. By amplifying amino acid-specifying domains en masse from soil metagenomic DNA, we substitute more than 1,000 unique domains into a pyoverdine NRPS. Initial fluorescence and mass spectrometry screens followed by sequencing reveal more than 100 functional domain substitutions, collectively yielding 16 distinct pyoverdines as major products. This metagenomic approach does not require the high success rates demanded by rational NRPS engineering but instead enables the exploration of large numbers of substitutions in parallel. This opens possibilities for the discovery and production of nonribosomal peptides with diverse biological activities.}, } @article {pmid37996432, year = {2023}, author = {Wu, R and Davison, MR and Nelson, WC and Smith, ML and Lipton, MS and Jansson, JK and McClure, RS and McDermott, JE and Hofmockel, KS}, title = {Hi-C metagenome sequencing reveals soil phage-host interactions.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7666}, pmid = {37996432}, issn = {2041-1723}, support = {FWP 70880//U.S. Department of Energy (DOE)/ ; }, mesh = {*Bacteriophages/genetics ; Metagenome ; Soil ; Bacteria/genetics ; Lysogeny/genetics ; }, abstract = {Bacteriophages are abundant in soils. However, the majority are uncharacterized, and their hosts are unknown. Here, we apply high-throughput chromosome conformation capture (Hi-C) to directly capture phage-host relationships. Some hosts have high centralities in bacterial community co-occurrence networks, suggesting phage infections have an important impact on the soil bacterial community interactions. We observe increased average viral copies per host (VPH) and decreased viral transcriptional activity following a two-week soil-drying incubation, indicating an increase in lysogenic infections. Soil drying also alters the observed phage host range. A significant negative correlation between VPH and host abundance prior to drying indicates more lytic infections result in more host death and inversely influence host abundance. This study provides empirical evidence of phage-mediated bacterial population dynamics in soil by directly capturing specific phage-host interactions.}, } @article {pmid37996002, year = {2023}, author = {Yao, Q and Xu, J and Tang, N and Chen, W and Gu, Q and Li, H}, title = {Screening, cloning, immobilization and application prospects of a novel β-glucosidase from the soil metagenome.}, journal = {Environmental research}, volume = {244}, number = {}, pages = {117676}, doi = {10.1016/j.envres.2023.117676}, pmid = {37996002}, issn = {1096-0953}, abstract = {The soil environment for straw return is a rich and valuable library containing many microorganisms and proteins. In this study, we aimed to screen a high-quality β-glucosidase (BGL) from the soil metagenomic library and to overcome the limitation of the low extraction rate of resveratrol in Polygonum cuspidatum. This includes the construction of a soil metagenomic library, screening of BGL, bioinformatics analysis, cloning, expression, immobilization, enzymatic property analysis, and application for the transformation of polydatin. The results showed that the soil metagenomic library of straw return was successfully constructed, and a novel BGL was screened. The identified 1356 bp long BGL belonged to the glycoside hydrolase 1 (GH1) family and was named Bgl1356. After successful cloning and expression of Bgl1356, it was immobilized using chitosan. The optimum temperature of immobilized Bgl1356 was 50 °C, and the pH was 5. It exhibited good tolerance for various metal ions (CO[2+], Ni[2+], Cu[2+], Mn[2+], Na[2+], Ca[2+], and Ag[+]) and organic solvents (DMSO, Triton-X-10, and ethanol). Enzymatic kinetics assays showed that Bgl1356 had good affinity for the substrate, and the specific enzyme activity was 234.03 U/mg. The conversion rate of polydatin by immobilized Bgl1356 was 95.70 ± 1.08%, facilitating the production of high amounts of resveratrol. Thus, this paper reports a novel temperature-, organic solvent-, and metal ion-tolerant BGL that has good application prospects in the pharmaceutical industry.}, } @article {pmid37995844, year = {2023}, author = {Bonnici, V and Mengoni, C and Mangoni, M and Franco, G and Giugno, R}, title = {PanDelos-frags: A methodology for discovering pangenomic content of incomplete microbial assemblies.}, journal = {Journal of biomedical informatics}, volume = {148}, number = {}, pages = {104552}, doi = {10.1016/j.jbi.2023.104552}, pmid = {37995844}, issn = {1532-0480}, mesh = {Humans ; *Ecosystem ; *Genomics/methods ; Genome ; Metagenomics/methods ; Software ; }, abstract = {Pangenomics was originally defined as the problem of comparing the composition of genes into gene families within a set of bacterial isolates belonging to the same species. The problem requires the calculation of sequence homology among such genes. When combined with metagenomics, namely for human microbiome composition analysis, gene-oriented pangenome detection becomes a promising method to decipher ecosystem functions and population-level evolution. Established computational tools are able to investigate the genetic content of isolates for which a complete genomic sequence is available. However, there is a plethora of incomplete genomes that are available on public resources, which only a few tools may analyze. Incomplete means that the process for reconstructing their genomic sequence is not complete, and only fragments of their sequence are currently available. However, the information contained in these fragments may play an essential role in the analyses. Here, we present PanDelos-frags, a computational tool which exploits and extends previous results in analyzing complete genomes. It provides a new methodology for inferring missing genetic information and thus for managing incomplete genomes. PanDelos-frags outperforms state-of-the-art approaches in reconstructing gene families in synthetic benchmarks and in a real use case of metagenomics. PanDelos-frags is publicly available at https://github.com/InfOmics/PanDelos-frags.}, } @article {pmid37995518, year = {2024}, author = {Liu, Z and Liu, J and Geng, J and Wu, E and Zhu, J and Cong, B and Wu, R and Sun, H}, title = {Metatranscriptomic characterization of six types of forensic samples and its potential application to body fluid/tissue identification: A pilot study.}, journal = {Forensic science international. Genetics}, volume = {68}, number = {}, pages = {102978}, doi = {10.1016/j.fsigen.2023.102978}, pmid = {37995518}, issn = {1878-0326}, mesh = {Female ; Humans ; Pilot Projects ; *Body Fluids/chemistry ; Saliva/chemistry ; Bodily Secretions ; Semen/chemistry ; RNA ; Forensic Genetics/methods ; }, abstract = {Microorganisms are potential markers for identifying body fluids (venous and menstrual blood, semen, saliva, and vaginal secretion) and skin tissue in forensic genetics. Existing published studies have mainly focused on investigating microbial DNA by 16 S rRNA gene sequencing or metagenome shotgun sequencing. We rarely find microbial RNA level investigations on common forensic body fluid/tissue. Therefore, the use of metatranscriptomics to characterize common forensic body fluids/tissue has not been explored in detail, and the potential application of metatranscriptomics in forensic science remains unknown. Here, we performed 30 metatranscriptome analyses on six types of common forensic sample from healthy volunteers by massively parallel sequencing. After quality control and host RNA filtering, a total of 345,300 unigenes were assembled from clean reads. Four kingdoms, 137 phyla, 267 classes, 488 orders, 985 families, 2052 genera, and 4690 species were annotated across all samples. Alpha- and beta-diversity and differential analysis were also performed. As a result, the saliva and skin groups demonstrated high alpha diversity (Simpson index), while the venous blood group exhibited the lowest diversity despite a high Chao1 index. Specifically, we discussed potential microorganism contamination and the "core microbiome," which may be of special interest to forensic researchers. In addition, we implemented and evaluated artificial neural network (ANN), random forest (RF), and support vector machine (SVM) models for forensic body fluid/tissue identification (BFID) using genus- and species-level metatranscriptome profiles. The ANN and RF prediction models discriminated six forensic body fluids/tissue, demonstrating that the microbial RNA-based method could be applied to BFID. Unlike metagenomic research, metatranscriptomic analysis can provide information about active microbial communities; thus, it may have greater potential to become a powerful tool in forensic science for microbial-based individual identification. This study represents the first attempt to explore the application potential of metatranscriptome profiles in forensic science. Our findings help deepen our understanding of the microorganism community structure at the RNA level and are beneficial for other forensic applications of metatranscriptomics.}, } @article {pmid37995430, year = {2023}, author = {Rubin-Blum, M and Yudkovsky, Y and Marmen, S and Raveh, O and Amrani, A and Kutuzov, I and Guy-Haim, T and Rahav, E}, title = {Tar patties are hotspots of hydrocarbon turnover and nitrogen fixation during a nearshore pollution event in the oligotrophic southeastern Mediterranean Sea.}, journal = {Marine pollution bulletin}, volume = {197}, number = {}, pages = {115747}, doi = {10.1016/j.marpolbul.2023.115747}, pmid = {37995430}, issn = {1879-3363}, mesh = {Mediterranean Sea ; *Nitrogen Fixation ; Hydrocarbons/metabolism ; Alkanes/metabolism ; Bacteria/genetics ; Archaea/metabolism ; Biodegradation, Environmental ; *Petroleum Pollution ; }, abstract = {Weathered oil, that is, tar, forms hotspots of hydrocarbon degradation by complex biota in marine environment. Here, we used marker gene sequencing and metagenomics to characterize the communities of bacteria, archaea and eukaryotes that colonized tar patties and control samples (wood, plastic), collected in the littoral following an offshore spill in the warm, oligotrophic southeastern Mediterranean Sea (SEMS). We show potential aerobic and anaerobic hydrocarbon catabolism niches on tar interior and exterior, linking carbon, sulfur and nitrogen cycles. Alongside aromatics and larger alkanes, short-chain alkanes appear to fuel dominant populations, both the aerobic clade UBA5335 (Macondimonas), anaerobic Syntropharchaeales, and facultative Mycobacteriales. Most key organisms, including the hydrocarbon degraders and cyanobacteria, have the potential to fix dinitrogen, potentially alleviating the nitrogen limitation of hydrocarbon degradation in the SEMS. We highlight the complexity of these tar-associated communities, where bacteria, archaea and eukaryotes co-exist, likely exchanging metabolites and competing for resources and space.}, } @article {pmid37995287, year = {2023}, author = {Wu, J and Ouyang, J and Qin, H and Zhou, J and Roberts, R and Siam, R and Wang, L and Tong, W and Liu, Z and Shi, T}, title = {PLM-ARG: antibiotic resistance gene identification using a pretrained protein language model.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {11}, pages = {}, pmid = {37995287}, issn = {1367-4811}, support = {2017SHZDZX01//Shanghai Municipal Science and Technology/ ; //Open Research Fund of Key Laboratory of Advanced Theory and Application in Statistics and Data Science-MOE/ ; //Key Laboratory of MEA/ ; //Ministry of Education/ ; //East China Normal University/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; *Artificial Intelligence ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Metagenome ; }, abstract = {MOTIVATION: Antibiotic resistance presents a formidable global challenge to public health and the environment. While considerable endeavors have been dedicated to identify antibiotic resistance genes (ARGs) for assessing the threat of antibiotic resistance, recent extensive investigations using metagenomic and metatranscriptomic approaches have unveiled a noteworthy concern. A significant fraction of proteins defies annotation through conventional sequence similarity-based methods, an issue that extends to ARGs, potentially leading to their under-recognition due to dissimilarities at the sequence level.

RESULTS: Herein, we proposed an Artificial Intelligence-powered ARG identification framework using a pretrained large protein language model, enabling ARG identification and resistance category classification simultaneously. The proposed PLM-ARG was developed based on the most comprehensive ARG and related resistance category information (>28K ARGs and associated 29 resistance categories), yielding Matthew's correlation coefficients (MCCs) of 0.983 ± 0.001 by using a 5-fold cross-validation strategy. Furthermore, the PLM-ARG model was verified using an independent validation set and achieved an MCC of 0.838, outperforming other publicly available ARG prediction tools with an improvement range of 51.8%-107.9%. Moreover, the utility of the proposed PLM-ARG model was demonstrated by annotating resistance in the UniProt database and evaluating the impact of ARGs on the Earth's environmental microbiota.

PLM-ARG is available for academic purposes at https://github.com/Junwu302/PLM-ARG, and a user-friendly webserver (http://www.unimd.org/PLM-ARG) is also provided.}, } @article {pmid37995075, year = {2023}, author = {Yu, L and Chen, X and Bai, X and Fang, J and Sui, M}, title = {Microbiota Alters and Its Correlation with Molecular Regulation Underlying Depression in PCOS Patients.}, journal = {Molecular neurobiology}, volume = {}, number = {}, pages = {}, pmid = {37995075}, issn = {1559-1182}, support = {2022J01279//Natural Science Foundation of Fujian Province/ ; BS202203//doctoral research project of the Second Affiliated Hospital of Fujian Medical University/ ; 2019-1-48//Fujian Provincial Health Research Talents Training Project/ ; }, abstract = {Depression is one of the complications in patients with polycystic ovary syndrome (PCOS) that leads to considerable mental health. Accumulating evidence suggests that human gut microbiomes are associated with the progression of PCOS and depression. However, whether microbiota influences depression development in PCOS patients is still uncharacterized. In this study, we employed metagenomic sequencing and transcriptome sequencing (RNA-seq) to profile the composition of the fecal microbiota and gene expression of peripheral blood mononuclear cells in depressed women with PCOS (PCOS-DP, n = 27) in comparison to mentally healthy women with PCOS (PCOS, n = 18) and compared with healthy control (HC, n = 27) and patients with major depressive disorder (MDD, n = 29). Gut microbiota assessment revealed distinct patterns in the relative abundance in the PCOS-DP compared to HC, MDD, and PCOS groups. Several gut microbes exhibited uniquely and significantly higher abundance in the PCOS-DP compared to PCOS patients, inducing EC Ruminococcus torques, Coprococcus comes, Megasphaera elsdenii, Acidaminococcus intestini, and Barnesiella viscericola. Bacteroides eggerthii was a potential gut microbial biomarker for the PCOS-DP. RNA-seq profiling identified that 35 and 37 genes were significantly elevated and downregulated in the PCOS-DP, respectively. The enhanced differential expressed genes (DEGs) in the PCOS-DP were enriched in pathways involved in signal transduction and endocrine and metabolic diseases, whereas several lipid metabolism pathways were downregulated. Intriguingly, genes correlated with the gut microbiota were found to be significantly enriched in pathways of neurodegenerative diseases and the immune system, suggesting that changes in the microbiota may have a systemic impact on the expression of neurodegenerative diseases and immune genes. Gut microbe-related DEGs of CREB3L3 and CCDC173 were possible molecular biomarkers and therapeutic targets of women with PCOS-DP. Our multi-omics data indicate shifts in the gut microbiome and host gene regulation in PCOS patients with depression, which is of possible etiological and diagnostic importance.}, } @article {pmid37994699, year = {2024}, author = {Hirsch, P and Tagirdzhanov, A and Kushnareva, A and Olkhovskii, I and Graf, S and Schmartz, GP and Hegemann, JD and Bozhüyük, KAJ and Müller, R and Keller, A and Gurevich, A}, title = {ABC-HuMi: the Atlas of Biosynthetic Gene Clusters in the Human Microbiome.}, journal = {Nucleic acids research}, volume = {52}, number = {D1}, pages = {D579-D585}, pmid = {37994699}, issn = {1362-4962}, support = {//Saarland University/ ; 466168626//DFG/ ; }, mesh = {Humans ; *Biosynthetic Pathways/genetics ; Computational Biology/instrumentation ; *Databases, Genetic ; Internet ; *Microbiota/genetics ; *Multigene Family/genetics ; Metagenome/genetics ; }, abstract = {The human microbiome has emerged as a rich source of diverse and bioactive natural products, harboring immense potential for therapeutic applications. To facilitate systematic exploration and analysis of its biosynthetic landscape, we present ABC-HuMi: the Atlas of Biosynthetic Gene Clusters (BGCs) in the Human Microbiome. ABC-HuMi integrates data from major human microbiome sequence databases and provides an expansive repository of BGCs compared to the limited coverage offered by existing resources. Employing state-of-the-art BGC prediction and analysis tools, our database ensures accurate annotation and enhanced prediction capabilities. ABC-HuMi empowers researchers with advanced browsing, filtering, and search functionality, enabling efficient exploration of the resource. At present, ABC-HuMi boasts a catalog of 19 218 representative BGCs derived from the human gut, oral, skin, respiratory and urogenital systems. By capturing the intricate biosynthetic potential across diverse human body sites, our database fosters profound insights into the molecular repertoire encoded within the human microbiome and offers a comprehensive resource for the discovery and characterization of novel bioactive compounds. The database is freely accessible at https://www.ccb.uni-saarland.de/abc_humi/.}, } @article {pmid37994269, year = {2024}, author = {Rocha, U and Coelho Kasmanas, J and Kallies, R and Saraiva, JP and Toscan, RB and Štefanič, P and Bicalho, MF and Borim Correa, F and Baştürk, MN and Fousekis, E and Viana Barbosa, LM and Plewka, J and Probst, AJ and Baldrian, P and Stadler, PF and , }, title = {MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy.}, journal = {Molecular ecology resources}, volume = {24}, number = {2}, pages = {e13904}, doi = {10.1111/1755-0998.13904}, pmid = {37994269}, issn = {1755-0998}, support = {460129525//Deutsche Forschungsgemeinschaft/ ; 2019/03396-9//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2022/03534-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; //German Network for Bioinformatics Infrastructure/ ; VH-NG-1248//Helmholtz-Gemeinschaft/ ; //Lundin Energy Norway/ ; }, mesh = {*Metagenome ; Metagenomics ; Software ; Bacteria/genetics ; Phylogeny ; *Viruses/genetics ; }, abstract = {Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes and viruses from metagenomes exist. Yet, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user-friendly tool tailored for those familiar with Unix command-line environment that makes it easy to recover genomes of prokaryotes, eukaryotes and viruses from metagenomes, either alone or in combination. We tested MuDoGeR using 24 individual-isolated genomes and 574 metagenomes, demonstrating the applicability for a few samples and high throughput. While MuDoGeR can recover eukaryotic viral sequences, its characterization is predominantly skewed towards bacterial and archaeal viruses, reflecting the field's current state. However, acting as a dynamic wrapper, the MuDoGeR is designed to constantly incorporate updates and integrate new tools, ensuring its ongoing relevance in the rapidly evolving field. MuDoGeR is open-source software available at https://github.com/mdsufz/MuDoGeR. Additionally, MuDoGeR is also available as a Singularity container.}, } @article {pmid37994021, year = {2023}, author = {Duan, Y and Feng, W and Shen, Y and Li, Y and Li, N and Chen, X and Wang, Y}, title = {Severe pneumonia with empyema caused by Parvimonas micra and Streptococcus constellatus co-infection: a case report.}, journal = {The Journal of international medical research}, volume = {51}, number = {11}, pages = {3000605231210657}, pmid = {37994021}, issn = {1473-2300}, mesh = {Humans ; Male ; *Streptococcus constellatus/genetics ; *Empyema, Pleural/complications/diagnosis/microbiology ; *Coinfection ; *Pneumonia/complications/diagnosis ; *Pleural Effusion ; }, abstract = {Empyema is a common complication of pneumonia, caused by the accumulation of purulent exudate due to pathogenic bacteria invading the pleural cavity. Parvimonas micra and Streptococcus constellatus are pathogens that rarely cause pneumonia with empyema. Herein, a case of severe empyema caused by these two pathogens, confirmed by metagenomic next-generation sequencing (mNGS) of pleural effusion cultures, is reported. A male Chinese patient in his late sixties presented with wheezing, cough, sputum expectoration, and fever. Blood and sputum cultures were negative for pathogens, but the pleural effusion culture was positive for S. constellatus, and was also found to contain P. micra, confirmed by mNGS. The patient's symptoms improved after treatment with cefoperazone/sulbactam and moxifloxacin. Pneumonia caused by P. micra and S. constellatus is rare; however, coinfection with these pathogens may cause severe pneumonia, with or without empyema.}, } @article {pmid37993724, year = {2023}, author = {Gutiérrez-García, K and Whitaker, MRL and Bustos-Díaz, ED and Salzman, S and Ramos-Aboites, HE and Reitz, ZL and Pierce, NE and Cibrián-Jaramillo, A and Barona-Gómez, F}, title = {Gut microbiomes of cycad-feeding insects tolerant to β-methylamino-L-alanine (BMAA) are rich in siderophore biosynthesis.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {122}, pmid = {37993724}, issn = {2730-6151}, support = {1541560, 1309425, 1906333//National Science Foundation (NSF)/ ; NAF/R2/180631//Newton Fund/ ; 169701, 179290, 177568, FON.INST./265/2016 285746,//Consejo Nacional de Ciencia y Tecnología (National Council of Science and Technology, Mexico)/ ; }, abstract = {Ingestion of the cycad toxins β-methylamino-L-alanine (BMAA) and azoxyglycosides is harmful to diverse organisms. However, some insects are specialized to feed on toxin-rich cycads with apparent immunity. Some cycad-feeding insects possess a common set of gut bacteria, which might play a role in detoxifying cycad toxins. Here, we investigated the composition of gut microbiota from a worldwide sample of cycadivorous insects and characterized the biosynthetic potential of selected bacteria. Cycadivorous insects shared a core gut microbiome consisting of six bacterial taxa, mainly belonging to the Proteobacteria, which we were able to isolate. To further investigate selected taxa from diverging lineages, we performed shotgun metagenomic sequencing of co-cultured bacterial sub-communities. We characterized the biosynthetic potential of four bacteria from Serratia, Pantoea, and two different Stenotrophomonas lineages, and discovered a suite of biosynthetic gene clusters notably rich in siderophores. Siderophore semi-untargeted metabolomics revealed a broad range of chemically related yet diverse iron-chelating metabolites, including desferrioxamine B, suggesting the occurrence of an unprecedented desferrioxamine-like biosynthetic pathway that remains to be identified. These results provide a foundation for future investigations into how cycadivorous insects tolerate diets rich in azoxyglycosides, BMAA, and other cycad toxins, including a possible role for bacterial siderophores.}, } @article {pmid37993433, year = {2023}, author = {Lin, J and Moradi, E and Salenius, K and Lehtipuro, S and Häkkinen, T and Laiho, JE and Oikarinen, S and Randelin, S and Parikh, HM and Krischer, JP and Toppari, J and Lernmark, Å and Petrosino, JF and Ajami, NJ and She, JX and Hagopian, WA and Rewers, MJ and Lloyd, RE and Rautajoki, KJ and Hyöty, H and Nykter, M and , }, title = {Distinct transcriptomic profiles in children prior to the appearance of type 1 diabetes-linked islet autoantibodies and following enterovirus infection.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7630}, pmid = {37993433}, issn = {2041-1723}, support = {U01 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK063863/DK/NIDDK NIH HHS/United States ; U01 DK063836/DK/NIDDK NIH HHS/United States ; UL1 TR002535/TR/NCATS NIH HHS/United States ; U01 DK128847/DK/NIDDK NIH HHS/United States ; U01 DK063790/DK/NIDDK NIH HHS/United States ; U01 DK063829/DK/NIDDK NIH HHS/United States ; U01 DK063865/DK/NIDDK NIH HHS/United States ; UC4 DK095300/DK/NIDDK NIH HHS/United States ; UC4 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK063829/DK/NIDDK NIH HHS/United States ; UC4 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK117483/DK/NIDDK NIH HHS/United States ; UC4 DK063836/DK/NIDDK NIH HHS/United States ; UC4 DK112243/DK/NIDDK NIH HHS/United States ; U01 DK124166/DK/NIDDK NIH HHS/United States ; U01 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK063865/DK/NIDDK NIH HHS/United States ; U01 DK063863/DK/NIDDK NIH HHS/United States ; UC4 DK106955/DK/NIDDK NIH HHS/United States ; UC4 DK100238/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Child ; Autoantibodies ; *Diabetes Mellitus, Type 1 ; Transcriptome ; Autoimmunity/genetics ; Insulin/metabolism ; *Enterovirus Infections/genetics ; *Islets of Langerhans/metabolism ; }, abstract = {Although the genetic basis and pathogenesis of type 1 diabetes have been studied extensively, how host responses to environmental factors might contribute to autoantibody development remains largely unknown. Here, we use longitudinal blood transcriptome sequencing data to characterize host responses in children within 12 months prior to the appearance of type 1 diabetes-linked islet autoantibodies, as well as matched control children. We report that children who present with insulin-specific autoantibodies first have distinct transcriptional profiles from those who develop GADA autoantibodies first. In particular, gene dosage-driven expression of GSTM1 is associated with GADA autoantibody positivity. Moreover, compared with controls, we observe increased monocyte and decreased B cell proportions 9-12 months prior to autoantibody positivity, especially in children who developed antibodies against insulin first. Lastly, we show that control children present transcriptional signatures consistent with robust immune responses to enterovirus infection, whereas children who later developed islet autoimmunity do not. These findings highlight distinct immune-related transcriptomic differences between case and control children prior to case progression to islet autoimmunity and uncover deficient antiviral response in children who later develop islet autoimmunity.}, } @article {pmid37993375, year = {2023}, author = {Mouzan, ME and Hussaini, AA and Sarkhy, AA and Assiri, A}, title = {Intestinal fungal profile in healthy Saudi children.}, journal = {Arab journal of gastroenterology : the official publication of the Pan-Arab Association of Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajg.2023.11.001}, pmid = {37993375}, issn = {2090-2387}, abstract = {BACKGROUND AND STUDY AIM: Fungi have a well-established role in medicine. Herein, we describe the fungal profile and abundance in the gut of healthy Saudi children.

PATIENTS AND METHODS: Fecal samples from a random sample of 20 school-age Saudi children were collected, stored at -80 °C, and dispatched to the laboratory in the USA where fungal DNAs were isolated and shotgun metagenomic sequencing was performed. Abundance was presented as average percentage of fungal taxa.

RESULTS: The median age of the participants was 12.5 years (range: 7-16 years), and 35 % were male. Ascomycota were the most abundant phyla and Eurotiomycetes, Saccharomycetes, were the most abundant class. The average abundance of fungal genera were Histoplasma (36 %) and Saccharomyces (31 %). The most abundant species were Histoplasma capsulatum (36 %) and Saccharomyces pastorianus (23 %). Other less abundant but may be functionally important genera and species included Candida (2.6 %) and Saccharomycescerevisiae (8 %).

CONCLUSION: The profile and abundance of the gut fungi in healthy Saudi children reveals important differences compared to Western literature. Accordingly, this report represents a more appropriate reference than Western data to use as controls for regional studies aiming to identify fungi associated with disease.}, } @article {pmid37992864, year = {2023}, author = {Jiang, ZJ and Hong, JC and Tang, QX and Lin, BW and Zhang, WQ and Xia, H and Yao, XP}, title = {Streptococcus suis meningoencephalitis diagnosed with metagenomic next-generation sequencing: A case report with literature review.}, journal = {Journal of infection and chemotherapy : official journal of the Japan Society of Chemotherapy}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jiac.2023.11.017}, pmid = {37992864}, issn = {1437-7780}, abstract = {Streptococcus suis is a pathogen of emerging zoonotic diseases and meningoencephalitis is the most frequent clinical symptom of S. suis infection in humans. Rapid diagnosis of S. suis meningoencephalitis is critical for the treatment of the disease. While the current routine microbiological tests including bacterial culture and gram staining are poorly sensitive, diagnosis of S. suis meningoencephalitis by metagenomic next-generation sequencing (mNGS) has been rarely reported. Here, we report a 52-year-old female pork food producer with a broken finger developed S. suis meningoencephalitis. After her admission, no pathogenic bacteria were detected through bacterial culture and Gram staining microscopy in the cerebrospinal fluid obtained via lumbar puncture. However, mNGS identified the presence of S. suis in the sample. mNGS is a promising diagnostic tool for rapid diagnosis of rare infectious diseases in the central nervous system.}, } @article {pmid37992830, year = {2023}, author = {Pan, Z and Wang, W and Chen, J and Chen, Z and Avellán-Llaguno, RD and Xu, W and Duan, Y and Liu, B and Huang, Q}, title = {Temporal dynamics of microbial composition and antibiotic resistome in fermentation bed culture pig farms across various ages.}, journal = {The Science of the total environment}, volume = {912}, number = {}, pages = {168728}, doi = {10.1016/j.scitotenv.2023.168728}, pmid = {37992830}, issn = {1879-1026}, abstract = {The discharge from pig farms presents significant challenges to the environment and human health, specifically regarding the dissemination of antimicrobial resistance (AMR). Fermentation bed culture has emerged as an increasingly popular and environmentally friendly pig farming model in China, as it minimizes the release of harmful substances into the environment. However, there remains a limited understanding of the occurrence and dynamics of microbiome and antibiotic resistome in fermentation bed culture. Herein, we collected fermentation bed materials (FBM) from four fermentation bed culture pig farms with varying service ages and investigated their bacterial communities, antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), metal resistance genes (MRGs) and potential antibiotic-resistant bacterial hosts through metagenomics. Pseudomonadota, Actinomycetota, Bacteroidota and Bacillota were identified as the dominant phyla present in the FBM. In total, we detected 258 unique ARGs in the FBM samples, with 79 core ARGs shared by all FBM samples, accounting for 95 % of the total ARG abundance. Our results revealed significant variations in microbial communities and ARG profiles across varying service ages of FBM. Compared to long-term FBW, short-term FBM exhibited higher numbers and abundances of ARGs, MRGs and MGEs, along with higher levels of potential bacterial pathogens and high-risk ARGs. Further analysis of metagenome-assembled genome (MAG) indicated that the putative hosts of ARGs primarily belonged to Pseudomonadota, Actinomycetota and Bacillota. Alarmingly, among the 80 recovered ARG-carrying MAGs, 23 MAGs encoded multi-resistance, including clinically significant species that require urgent attention. Overall, this study provided valuable insights into the temporal patterns of antibiotic resistome and bacterial communities within FBM, enhancing our understanding of FBM in pig farming. The findings could potentially contribute to the development of effective strategies for evaluating and regulating fermentation bed culture practices in pig farming.}, } @article {pmid37992406, year = {2023}, author = {Jesser, KJ and Trueba, G and Konstantinidis, KT and Levy, K}, title = {Why are so many enteric pathogen infections asymptomatic? Pathogen and gut microbiome characteristics associated with diarrhea symptoms and carriage of diarrheagenic E. coli in northern Ecuador.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2281010}, pmid = {37992406}, issn = {1949-0984}, support = {K01 AI103544/AI/NIAID NIH HHS/United States ; T32 ES007032/ES/NIEHS NIH HHS/United States ; T32 ES012870/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; Escherichia coli ; *Escherichia coli Infections/microbiology ; *Gastrointestinal Microbiome/genetics ; Ecuador ; Case-Control Studies ; Diarrhea/microbiology ; }, abstract = {A high proportion of enteric infections, including those caused by diarrheagenic Escherichia coli (DEC), are asymptomatic for diarrhea. The factors responsible for the development of diarrhea symptoms, or lack thereof, remain unclear. Here, we used DEC isolate genome and whole stool microbiome data from a case-control study of diarrhea in Ecuador to examine factors associated with diarrhea symptoms accompanying DEC carriage. We investigated i) pathogen abundance, ii) gut microbiome characteristics, and iii) strain-level pathogen characteristics from DEC infections with diarrhea symptoms (symptomatic infections) and without diarrhea symptoms (asymptomatic infections). We also included data from individuals with and without diarrhea who were not infected with DEC (uninfected cases and controls). i) E. coli relative abundance in the gut microbiome was highly variable, but higher on-average in individuals with symptomatic compared to asymptomatic DEC infections. Similarly, the number and relative abundances of virulence genes in the gut were higher in symptomatic than asymptomatic DEC infections. ii) Measures of microbiome diversity were similar regardless of diarrhea symptoms or DEC carriage. Proteobacterial families that have been described as pathobionts were enriched in symptomatic infections and uninfected cases, whereas potentially beneficial taxa, including the Bacteroidaceae and Bifidobacteriaceae, were more abundant in individuals without diarrhea. An analysis of high-level gene functions recovered in metagenomes revealed that genes that were differentially abundant by diarrhea and DEC infection status were more abundant in symptomatic than asymptomatic DEC infections. iii) DEC isolates from symptomatic versus asymptomatic individuals showed no significant differences in virulence or accessory gene content, and there was no phylogenetic signal associated with diarrhea symptoms. Together, these data suggest signals that distinguish symptomatic from asymptomatic DEC infections. In particular, the abundance of E. coli, the virulence gene content of the gut microbiome, and the taxa present in the gut microbiome have an apparent role.}, } @article {pmid37992299, year = {2023}, author = {Petriglieri, F and Kondrotaite, Z and Singleton, C and Nierychlo, M and Dueholm, MKD and Nielsen, PH}, title = {A comprehensive overview of the Chloroflexota community in wastewater treatment plants worldwide.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0066723}, pmid = {37992299}, issn = {2379-5077}, support = {Dark Matter grant 13351//Villum Fonden (Villum Foundation)/ ; Microflora Danica//Poul Due Jensens Fond (Grundfos Foundation) (PDJF)/ ; }, mesh = {Sewage ; *Chloroflexi ; *Water Purification ; Biomass ; Phylogeny ; }, abstract = {Chloroflexota are often abundant members of the biomass in wastewater treatment plants (WWTPs) worldwide, typically with a filamentous morphology, forming the backbones of the activated sludge floc. However, their overgrowth can often cause operational issues connected to poor settling or foaming, impairing effluent quality and increasing operational costs. Despite their importance, few Chloroflexota genera have been characterized so far. Here, we present a comprehensive overview of Chloroflexota abundant in WWTPs worldwide and an in-depth characterization of their morphology, phylogeny, and ecophysiology, obtaining a broad understanding of their ecological role in activated sludge.}, } @article {pmid37991826, year = {2023}, author = {Song, H and Xue, H and Zhang, Z and Wang, J and Li, A and Zhang, J and Luo, P and Zhan, M and Zhou, X and Chen, L and Fang, Y}, title = {Amelioration of Type 2 Diabetes Using Four Strains of Lactobacillus Probiotics: Effects on Gut Microbiota Reconstitution-Mediated Regulation of Glucose Homeostasis, Inflammation, and Oxidative Stress in Mice.}, journal = {Journal of agricultural and food chemistry}, volume = {71}, number = {51}, pages = {20801-20814}, doi = {10.1021/acs.jafc.3c04665}, pmid = {37991826}, issn = {1520-5118}, mesh = {Mice ; Animals ; Lactobacillus ; *Diabetes Mellitus, Type 2 ; *Gastrointestinal Microbiome/physiology ; Inflammation ; *Probiotics ; Glucose ; Diet, High-Fat ; Oxidative Stress ; Homeostasis ; }, abstract = {This study aims to explore the preventive effects and underlying mechanisms of Lactobacillus fermentum CKCC1858 (CKCC1), L. fermentum CKCC1369 (CKCC2), Lactobacillus plantarum CKCC1312 (CKCC3), and Lactobacillus gasseri CKCC1913 (CKCC4) on high-fat diet combined with streptozotocin (HFD/STZ)-stimulated type 2 diabetes (T2D) in mice. Generally, the results indicated that most of the four probiotics reduced weight loss and liver and pancreas damage, significantly (p < 0.05) improved glucose metabolism by regulating glucagon-like peptide-1 (GLP-1), fasting glucose and insulin levels, and increasing expression of glucose transporters. Probiotics improved hyperlipemia, inflammation, and oxidative stress by reducing the secretion of blood lipids and proinflammatory cytokines, increasing antioxidant enzymes. Metagenomic results revealed that probiotics restored gut microbiota via enhancing (reducing) the relative abundance of beneficial bacteria (harmful bacteria) and altered specific metabolic pathways in T2D mice. CKCC1, CKCC3, and CKCC4 showed excellent effects compared to CKCC2. These results indicated that probiotics potentially prevented T2D, which is strain-specific.}, } @article {pmid37991356, year = {2023}, author = {Hollensteiner, J and Schneider, D and Poehlein, A and Himmelbach, A and Daniel, R}, title = {Metagenome-assembled genomes from particle-associated microbial communities in the mesopelagic zone of the Pacific Ocean.}, journal = {Microbiology resource announcements}, volume = {12}, number = {12}, pages = {e0061423}, pmid = {37991356}, issn = {2576-098X}, support = {TRR51-3//Deutsche Forschungsgemeinschaft (DFG)/ ; TRR51-1-3//Deutsche Forschungsgemeinschaft (DFG)/ ; }, abstract = {We report 10 particle-associated metagenome-assembled genomes (MAGs) from the mesopelagic zone of Pacific Ocean seawaters. MAGs comprise members of Flavobacteria Halomonas, Blastomonas, Brevundimonas, Alteromonas, Shingomonas, Sphingopyxis, Tabrizicola, Proteobacteria, and Gammaproteobacteria. Functional annotation suggests that these bacteria are involved in central particulate organic carbon conversion, nitrogen cycling, and phosphorus cycling.}, } @article {pmid37990114, year = {2023}, author = {Apenteng, OO and Aarestrup, FM and Vigre, H}, title = {Modelling the effectiveness of surveillance based on metagenomics in detecting, monitoring, and forecasting antimicrobial resistance in livestock production under economic constraints.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {20410}, pmid = {37990114}, issn = {2045-2322}, support = {NNF16OC0021856//Novo Nordisk Fonden/ ; 773830//European Union's Horizon 2020/ ; }, mesh = {Animals ; Swine ; *Anti-Bacterial Agents/pharmacology ; *Livestock ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Microbial Sensitivity Tests ; Metagenomics/methods ; }, abstract = {Current surveillance of antimicrobial resistance (AMR) is mostly based on testing indicator bacteria using minimum inhibitory concentration (MIC) panels. Metagenomics has the potential to identify all known antimicrobial resistant genes (ARGs) in complex samples and thereby detect changes in the occurrence earlier. Here, we simulate the results of an AMR surveillance program based on metagenomics in the Danish pig population. We modelled both an increase in the occurrence of ARGs and an introduction of a new ARG in a few farms and the subsequent spread to the entire population. To make the simulation realistic, the total cost of the surveillance was constrained, and the sampling schedule was set at one pool per month with 5, 20, 50, or 100 samples. Our simulations demonstrate that a pool of 20-50 samples and a sequencing depth of 250 million fragments resulted in the shortest time to detection in both scenarios, with a time delay to detection of change of [Formula: see text]15 months in all scenarios. Compared with culture-based surveillance, our simulation indicates that there are neither significant reductions nor increases in time to detect a change using metagenomics. The benefit of metagenomics is that it is possible to monitor all known resistance in one sampling and laboratory procedure in contrast to the current monitoring that is based on the phenotypic characterisation of selected indicator bacterial species. Therefore, overall changes in AMR in a population will be detected earlier using metagenomics due to the fact that the resistance gene does not have to be transferred to and expressed by an indicator bacteria before it is possible to detect.}, } @article {pmid37989857, year = {2023}, author = {Licandro, H and Truntzer, C and Fromentin, S and Morabito, C and Quinquis, B and Pons, N and Martin, C and Blottière, HM and Neyraud, E}, title = {The bacterial species profiles of the lingual and salivary microbiota differ with basic tastes sensitivity in human.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {20339}, pmid = {37989857}, issn = {2045-2322}, support = {ANR-15-IDEX-0003//"Investissements d'Avenir" program, project ISITE-BFC/ ; ANR-15-IDEX-0003//"Investissements d'Avenir" program, project ISITE-BFC/ ; ANR-15-IDEX-0003//"Investissements d'Avenir" program, project ISITE-BFC/ ; ANR-15-IDEX-0003//"Investissements d'Avenir" program, project ISITE-BFC/ ; }, mesh = {Humans ; *Taste Perception ; Taste ; Saliva ; Tongue ; *Microbiota ; }, abstract = {Taste perception is crucial and impairments, which can be linked to pathologies, can lead to eating disorders. It is triggered by taste compounds stimulating receptors located on the tongue. However, the tongue is covered by a film containing saliva and microorganisms suspected to modulate the taste receptor environment. The present study aimed to elucidate the links between taste sensitivity (sweetness, sourness, bitterness, saltiness, umami) and the salivary as well as the tongue microbiota using shotgun metagenomics. 109 bacterial species were correlated with at least one taste. Interestingly, when a species was correlated with at least two tastes, the correlations were unidirectional, indicating a putative global implication. Some Streptococcus, SR1 and Rickenellaceae species correlated with five tastes. When comparing both ecosystems, saliva appears to be a better taste predictor than tongue. This work shows the implication of the oral microbiota in taste and exhibits specificities depending on the ecosystem considered.}, } @article {pmid37989418, year = {2023}, author = {Xu, J and Xu, L and Zong, Y and Lin, R and He, Y and Xie, L}, title = {Electrically-assisted anaerobic digestion under ammonia stress: Facilitating propionate oxidation and activating methanogenesis via direct interspecies electron transfer.}, journal = {Bioresource technology}, volume = {393}, number = {}, pages = {130067}, doi = {10.1016/j.biortech.2023.130067}, pmid = {37989418}, issn = {1873-2976}, abstract = {Electrical assistance is an effective strategy for promoting anaerobic digestion (AD) under ammonia stress. However, the underlying mechanism of electrical assistance affecting AD is insufficiently understood. Here, electrical assistance to AD under 5 g N/L ammonia stress was provided, by employing a 0.6 V voltage to the carbon electrodes. The results demonstrated remarkable enhancements in methane production (104.6 %) and the maximal methane production rate (207.7 %). The critical segment facilitated by electro-stimulation was the microbial metabolism of propionate-to-methane, rather than ammonia removal. Proteins in extracellular polymer substances were enriched, boosting microbial resilience to ammonia intrusion. Concurrently, the promoted humic/fulvic-substances amplified the microbial electron transfer capacity. Metagenomics analysis identified the upsurge of propionate oxidation at the anode (by e.g. unclassified_c__Bacteroidia), and the stimulations of acetoclastic and direct interspecies electron transfer-dependent CO2-reducing methanogenesis at the cathode (by e.g. Methanothrix). This study provides novel insights into the effect of electrical assistance on ammonia-stressed AD.}, } @article {pmid37988265, year = {2023}, author = {Bars-Cortina, D and Moratalla-Navarro, F and García-Serrano, A and Mach, N and Riobó-Mayo, L and Vea-Barbany, J and Rius-Sansalvador, B and Murcia, S and Obón-Santacana, M and Moreno, V}, title = {Improving Species Level-taxonomic Assignment from 16S rRNA Sequencing Technologies.}, journal = {Current protocols}, volume = {3}, number = {11}, pages = {e930}, doi = {10.1002/cpz1.930}, pmid = {37988265}, issn = {2691-1299}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Bacteria/genetics ; Metagenome ; Databases, Factual ; }, abstract = {Analysis of the bacterial community from a 16S rRNA gene sequencing technologies requires comparing the reads to a reference database. The challenging task involved in annotation relies on the currently available tools and 16S rRNA databases: SILVA, Greengenes and RDP. A successful annotation depends on the quality of the database. For instance, Greengenes and RDP have not been updated since 2013 and 2016, respectively. In addition, the nature of 16S sequencing technologies (short reads) focuses mainly on the V3-V4 hypervariable region sequencing and hinders the species assignment, in contrast to whole shotgun metagenome sequencing. Here, we combine the results of three standard protocols for 16S rRNA amplicon annotation that utilize homology-based methods, and we propose a new re-annotation strategy to enlarge the percentage of amplicon sequence variants (ASV) classified up to the species level. Following the pattern (reference) method: DADA2 pipeline and SILVA v.138.1 reference database classification (Basic Protocol 1), our method maps the ASV sequences to custom nucleotide BLAST with the SILVA v.138.1 (Basic Protocol 2), and to the 16S database of Bacteria and Archaea of NCBI RefSeq Targeted Loci Project databases (Basic Protocol 3). This new re-annotation workflow was tested in 16S rRNA amplicon data from 156 human fecal samples. The proposed new strategy achieved an increase of nearly eight times the proportion of ASV classified at the species level in contrast to the reference method for the database used in the present research. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Sample inference and taxonomic profiling through DADA2 algorithm. Basic Protocol 2: Custom BLASTN database creation and ASV taxonomical assignment. Basic Protocol 3: ASV taxonomical assignment using NCBI RefSeq Targeted Loci Project database. Basic Protocol 4: Definitive selection of lineages among the three methods.}, } @article {pmid37987855, year = {2023}, author = {Carvalho, CR and Souza, BCE and Bieluczyk, W and Feitosa, YB and Delbaje, E and Camargo, PB and Tsai, SM and Fiore, MF}, title = {Phosphonate consumers potentially contributing to methane production in Brazilian soda lakes.}, journal = {Extremophiles : life under extreme conditions}, volume = {28}, number = {1}, pages = {4}, pmid = {37987855}, issn = {1433-4909}, support = {2016/14227-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, mesh = {*Lakes ; Brazil ; Extreme Environments ; Methane ; *Organophosphonates ; }, abstract = {Oxic methane production (OMP) has been reported to significantly contribute to methane emissions from oxic surface waters. Demethylation of organic compounds, photosynthesis-associated methane production, and (bacterio)chlorophyll reduction activity are some of the investigated mechanisms as potential OMP sources related to photosynthetic organisms. Recently, cyanobacteria have often been correlated with methane accumulation and emission in freshwater, marine, and saline systems. The Brazilian Pantanal is the world's largest wetland system, with approximately 10,000 shallow lakes, most of which are highly alkaline and saline extreme environments. We initiated this study with an overall investigation using genetic markers, from which we explored metagenomic and limnological data from the Pantanal soda for five potential OMP pathways. Our results showed a strong positive correlation between dissolved methane concentrations and bloom events. Metagenomic data and nutrients, mainly orthophosphate, nitrogen, iron, and methane concentrations, suggest that the organic phosphorous demethylation pathway has the most potential to drive OMP in lakes with blooms. A specialized bacterial community was identified, including the Cyanobacteria Raphidiopsis, although the bloom does not contain the genes to carry out this process. These data showed enough evidence to infer the occurrence of an OMP pathway at Pantanal soda lakes, including the microbial sources and their relation to the cyanobacterial blooms.}, } @article {pmid37987582, year = {2023}, author = {Hurley, S and Eden, JS and Bingham, J and Rodriguez, M and Neave, MJ and Johnson, A and Howard-Jones, AR and Kok, J and Anazodo, A and McMullan, B and Williams, DT and Watson, J and Solinas, A and Kim, KW and Rawlinson, W}, title = {Fatal Human Neurologic Infection Caused by Pigeon Avian Paramyxovirus-1, Australia.}, journal = {Emerging infectious diseases}, volume = {29}, number = {12}, pages = {2482-2487}, pmid = {37987582}, issn = {1080-6059}, mesh = {Animals ; Child, Preschool ; Humans ; Australia/epidemiology ; Columbidae ; *Communicable Diseases ; *Newcastle Disease/epidemiology/pathology ; Newcastle disease virus ; Phylogeny ; }, abstract = {Avian paramyxovirus type 1 (APMV-1) is a virus of birds that results in a range of outcomes, from asymptomatic infections to outbreaks of systemic respiratory and neurologic disease, depending on the virus strain and the avian species affected. Humans are rarely affected; those who are predominantly experience mild conjunctivitis. We report a fatal case of neurologic disease in a 2-year-old immunocompromised child in Australia. Metagenomic sequencing and histopathology identified the causative agent as the pigeon variant of APMV-1. This diagnosis should be considered in neurologic conditions of undefined etiologies. Agnostic metagenomic sequencing methods are useful in such settings to direct diagnostic and therapeutic efforts.}, } @article {pmid37987083, year = {2023}, author = {Yavorov-Dayliev, D and Milagro, FI and López-Yoldi, M and Clemente, I and Riezu-Boj, JI and Ayo, J and Oneca, M and Aranaz, P}, title = {Pediococcus acidilactici (pA1c®) alleviates obesity-related dyslipidemia and inflammation in Wistar rats by activating beta-oxidation and modulating the gut microbiota.}, journal = {Food & function}, volume = {14}, number = {24}, pages = {10855-10867}, doi = {10.1039/d3fo01651j}, pmid = {37987083}, issn = {2042-650X}, mesh = {Rats ; Male ; Animals ; Mice ; Rats, Wistar ; *Pediococcus acidilactici ; *Gastrointestinal Microbiome ; Obesity/metabolism ; Inflammation/drug therapy/prevention & control ; Diet, High-Fat/adverse effects ; *Hypercholesterolemia ; Cholesterol ; Mice, Inbred C57BL ; }, abstract = {Due to the importance of the gut microbiota in the regulation of energy homeostasis, probiotics have emerged as an alternative therapy to ameliorate obesity-related disturbances, including cholesterol metabolism dysregulation, dyslipidemia and inflammation. Therefore, the objectives of this study were to evaluate the effect of the probiotic strain Pediococcus acidilactici (pA1c®) on the regulation of adiposity, cholesterol and lipid metabolism, inflammatory markers and gut microbiota composition in diet-induced obese rats. Twenty-nine four-week-old male Wistar rats were divided into three groups: rats fed a control diet (CNT group, n = 8), rats fed a high fat/high sucrose diet (HFS group, n = 11), and rats fed a HFS diet supplemented with pA1c® (pA1c®group, n = 10). Organs and fat depots were weighed, and different biochemical parameters were analysed in serum. Gene expression analyses in the adipose tissue were conducted using real-time quantitative-PCR. Faecal microbiota composition was evaluated using 16S metagenomics. Animals supplemented with pA1c® exhibited a lower proportion of visceral adiposity, a higher proportion of muscle, an improvement in the total-cholesterol/HDL-cholesterol ratio and a decrease in the total cholesterol, triglyceride and aspartate aminotransaminase (AST) serum levels, together with a decrease in several inflammation-related molecules. The expression of key genes related to adipose (Adipoq, Cebpa and Pparg) and glucose (Slc2a1 and Slc2a4) metabolism in the adipose tissue was normalized by pA1c®. Moreover, it was demonstrated that pA1c® supplementation activated fatty acid β-oxidation in the adipose tissue and the liver. Metagenomics demonstrated the presence of pA1c® in the faecal samples, an increase in alpha diversity, an increase in the abundance of beneficial bacteria, and a decrease in the abundance of harmful micro-organisms, including the Streptococcus genus. Thus, our data suggest the potential of pA1c® in the prevention of obesity-related disturbances including hypercholesterolemia, hypertriglyceridemia, inflammation and gut microbiota dysbiosis.}, } @article {pmid37987001, year = {2023}, author = {Sarkar, S and Kazarina, A and Hansen, PM and Ward, K and Hargreaves, C and Reese, N and Ran, Q and Kessler, W and de Souza, LFT and Loecke, TD and Sarto, MVM and Rice, CW and Zeglin, LH and Sikes, BA and Lee, STM}, title = {Ammonia-oxidizing archaea and bacteria differentially contribute to ammonia oxidation in soil under precipitation gradients and land legacy.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37987001}, support = {P30 GM122731/GM/NIGMS NIH HHS/United States ; S10 OD021743/OD/NIH HHS/United States ; U54 HD090216/HD/NICHD NIH HHS/United States ; UL1 TR002366/TR/NCATS NIH HHS/United States ; }, abstract = {BACKGROUND: Global change has accelerated the nitrogen cycle. Soil nitrogen stock degradation by microbes leads to the release of various gases, including nitrous oxide (N2O), a potent greenhouse gas. Ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB) participate in the soil nitrogen cycle, producing N2O. There are outstanding questions regarding the impact of environmental processes such as precipitation and land use legacy on AOA and AOB structurally, compositionally, and functionally. To answer these questions, we analyzed field soil cores and soil monoliths under varying precipitation profiles and land legacies.

RESULTS: We resolved 28 AOA and AOB metagenome assembled genomes (MAGs) and found that they were significantly higher in drier environments and differentially abundant in different land use legacies. We further dissected AOA and AOB functional potentials to understand their contribution to nitrogen transformation capabilities. We identified the involvement of stress response genes, differential metabolic functional potentials, and subtle population dynamics under different environmental parameters for AOA and AOB. We observed that AOA MAGs lacked a canonical membrane-bound electron transport chain and F-type ATPase but possessed A/A-type ATPase, while AOB MAGs had a complete complex III module and F-type ATPase, suggesting differential survival strategies of AOA and AOB.

CONCLUSIONS: The outcomes from this study will enable us to comprehend how drought-like environments and land use legacies could impact AOA- and AOB-driven nitrogen transformations in soil.}, } @article {pmid37986521, year = {2023}, author = {Dartora, B and Hickert, LR and Fabricio, MF and Ayub, MAZ and Furlan, JM and Wagner, R and Perez, KJ and Sant'Anna, V}, title = {Understanding the effect of fermentation time on physicochemical characteristics, sensory attributes, and volatile compounds in green tea kombucha.}, journal = {Food research international (Ottawa, Ont.)}, volume = {174}, number = {Pt 1}, pages = {113569}, doi = {10.1016/j.foodres.2023.113569}, pmid = {37986521}, issn = {1873-7145}, mesh = {*Tea ; *Acetic Acid/analysis ; Fermentation ; Beverages/analysis ; Ethanol/analysis ; Polyphenols/analysis ; }, abstract = {Kombuchas are a trend in the fermented beverage field and the effect of fermentation time on their characteristics is necessary to better understand the process, mainly concerning volatile compounds, which are scarce information in the current literature. Thus, the present work aimed to evaluate the features of green tea kombucha during fermentation, monitoring the changes in pH, acidity, turbidity, polyphenols, ethanol, acetic acid, volatile compounds, and sensory profile and acceptance up to 14 days of fermentation. Kombuchas' pH and acidity decreased through time as expected, but after 4 days of fermentation, the beverage exceeded the Brazilian legal limits of acidity (130 mEq/L) and produced more than 0.5% AVB, which labels the beverage as alcoholic. Total polyphenols and condensed tannins content enhanced until the seventh day of fermentation and remained constant. Fermentation highly impacted the aroma of the infusion with a high formation of volatile acids, such as alcohols, esters, and ketones. Aldehydes were degraded during the bioprocess. Sensory characterization of kombucha showed that fermentation of 4 days increased perceived turbidity; vinegar, citric fruit, acid, and alcoholic aroma; and produced the beverage with sour, bitter, and vinegar flavor. Thus, the fermentation time of kombuchas must be controlled as they rapidly change and impact on the physicochemical parameters and sensory profile of the beverage can be negative.}, } @article {pmid37986012, year = {2023}, author = {Basbas, C and Garzon, A and Schlesener, C and van Heule, M and Profeta, R and Weimer, BC and Silva-Del-Rio, N and Byrne, BA and Karle, B and Aly, SS and Lima, FS and Pereira, RV}, title = {Unveiling the microbiome during post-partum uterine infection: a deep shotgun sequencing approach to characterize the dairy cow uterine microbiome.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {59}, pmid = {37986012}, issn = {2524-4671}, abstract = {BACKGROUND: The goal of this study was to assess the microbial ecology and diversity present in the uterus of post-partum dairy cows with and without metritis from 24 commercial California dairy farms using shotgun metagenomics. A set subset of 95 intrauterine swab samples, taken from a larger selection of 307 individual cow samples previously collected, were examined for α and β diversity and differential abundance associated with metritis. Cows within 21 days post-partum were categorized into one of three clinical groups during sample collection: control (CT, n = 32), defined as cows with either no vaginal discharge or a clear, non-purulent mucus vaginal discharge; metritis (MET, n = 33), defined as a cow with watery, red or brown colored, and fetid vaginal discharge; and purulent discharge cows (PUS, n = 31), defined as a non-fetid purulent or mucopurulent vaginal discharge.

RESULTS: All three clinical groups (CT, MET, and PUS) were highly diverse, with the top 12 most abundant genera accounting for 10.3%, 8.8%, and 10.1% of mean relative abundance, respectively. The α diversity indices revealed a lower diversity from samples collected from MET and PUS when compared to CT cows. PERMANOVA statistical testing revealed a significant difference (P adjusted < 0.01) in the diversity of genera between CT and MET samples (R2 = 0.112, P = 0.003) and a non-significant difference between MET and PUS samples (R2 = 0.036, P = 0.046). ANCOM-BC analysis revealed that from the top 12 most abundant genera, seven genera were increased in the natural log fold change (LFC) of abundance in MET when compared to CT samples: Bacteroides, Clostridium, Fusobacterium, Phocaeicola, Porphyromonas, Prevotella, and Streptococcus. Two genera, Dietzia and Microbacterium, were decreased in natural LFC of abundance when comparing MET (regardless of treatment) and CT, while no changes in natural LFC of abundance were observed for Escherichia, Histophilus, and Trueperella.

CONCLUSIONS: The results presented here, are the current deepest shotgun metagenomic analyses conducted on the bovine uterine microbiome to date (mean of 256,425 genus-level reads per sample). Our findings support that uterine samples from cows without metritis (CT) had increased α-diversity but decreased β-diversity when compared to metritis or PUS cows, characteristic of dysbiosis. In summary, our findings highlight that MET cows have an increased abundance of Bacteroides, Porphyromonas, and Fusobacterium when compared to CT and PUS, and support the need for further studies to better understand their potential causal role in metritis pathogenesis.}, } @article {pmid37985857, year = {2023}, author = {Qi, Y and Lin, WQ and Liao, B and Chen, JW and Chen, ZS}, title = {Blood plasma metagenomic next-generation sequencing for identifying pathogens of febrile neutropenia in acute leukemia patients.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {20297}, pmid = {37985857}, issn = {2045-2322}, mesh = {Humans ; Retrospective Studies ; *Leukemia, Myeloid, Acute/complications/genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Plasma ; *Febrile Neutropenia/diagnosis ; Sensitivity and Specificity ; }, abstract = {To investigate the value of metagenomic next-generation sequencing (mNGS) in acute leukemia (AL) patients with febrile neutropenia (FN). We retrospectively reviewed 37 AL patients with FN and compared the results of mNGS with blood culture (BC) and the clinical features of the mNGS-positive group and the mNGS-negative group. A total of 14 detected pathogens were the final clinical diagnosis, of which 9 strains were detected only by mNGS and 5 strains were detected by both mNGS and BC. The top pathogens were Klebsiella pneumoniae, Pseudomonas aeruginosa and Stenotrophomonas maltophilia. A total of 67.57% (25/37) were bacterial infections, and 2.7% (1/37) were fungal or viral infections. The diagnostic positivity rate of mNGS (25/37, 67.6%) was significantly higher than that of BC (7/37, 18.9%), and the difference was statistically significant (p < 0.05). Then, we explored the clinical distinction between the mNGS-positive group and the mNGS-negative group, and 3 features were filtered, including lymphocyte count (LY), creatinine levels (Cr), and white blood cell count (WBC). Our study demonstrated that early implementation of mNGS can effectively improve the efficacy of pathogen detection in AL patients with FN. The higher diagnostic positivity rate and the ability to detect additional pathogens compared to BC made mNGS a valuable tool in the management of infectious complications in this patient population. Furthermore, the identified clinical features associated with mNGS results provided additional insights for the clinical indication of infection in AL patients with FN.}, } @article {pmid37985845, year = {2023}, author = {Ye, Q and Sun, S and Deng, J and Chen, X and Zhang, J and Lin, S and Du, H and Gao, J and Zou, X and Lin, X and Cai, Y and Lu, Z}, title = {Using 16S rDNA and metagenomic sequencing technology to analyze the fecal microbiome of children with avoidant/restrictive food intake disorder.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {20253}, pmid = {37985845}, issn = {2045-2322}, mesh = {Humans ; Child ; Anti-Bacterial Agents ; *Avoidant Restrictive Food Intake Disorder ; Drug Resistance, Bacterial ; Macrolides ; *Microbiota ; Bacteria/genetics ; *Actinobacteria/genetics ; Eating ; RNA, Ribosomal, 16S/genetics ; }, abstract = {To investigate the gut microbiota distribution and its functions in children with avoidant/restrictive food intake disorder (ARFID). A total of 135 children were enrolled in the study, including 102 children with ARFID and 33 healthy children. Fecal samples were analyzed to explore differences in gut microbiota composition and diversity and functional differences between the ARFID and healthy control (HC) groups via 16S rDNA and metagenomic sequencing. The gut microbiota composition and diversity in children with ARFID were different from those in heathy children, but there is no difference in the composition and diversity of gut microbiota between children at the age of 3-6 and 7-12 with ARFID. At the phylum level, the most abundant microbes in the two groups identified by 16S rDNA and metagenomic sequencing were the same. At the genus level, the abundance of Bacteroides was higher in the ARFID group (P > 0.05); however, different from the result of 16SrDNA sequencing, metagenomic sequencing showed that the abundance of Bacteroides in the ARFID group was significantly higher than that in the HC group (P = 0.041). At the species level, Escherichia coli, Streptococcus thermophilus and Lachnospira eligens were the most abundant taxa in the ARFID group, and Prevotella copri, Bifidobacterium pseudocatenulatum, and Ruminococcus gnavus were the top three microbial taxa in the HC group; there were no statistically significant differences between the abundance of these microbial taxa in the two groups. LefSe analysis indicated a greater abundance of the order Enterobacterales and its corresponding family Enterobacteriaceae, the family Bacteroidaceae and corresponding genus Bacteroides, the species Bacteroides vulgatus in ARFID group, while the abundance of the phylum Actinobacteriota and its corresponding class Actinobacteria , the order Bifidobacteriales and corresponding family Bifidobacteriaceae, the genus Bifidobacterium were enriched in the HC group. There were no statistically significant differences in the Chao1, Shannon and Simpson indices between the Y1 and Y2 groups (P = 0.1, P = 0.06, P = 0.06). At the phylum level, Bacillota, Bacteroidota, Proteobacteria and Actinobacteriota were the most abundant taxa in both groups, but there were no statistically significant differences among the abundance of these bacteria (P = 0.958, P = 0.456, P = 0.473, P = 0.065). At the genus level, Faecalibacterium was more abundant in the Y2 group than in the Y1 group, and the difference was statistically significant (P = 0.037). The KEGG annotation results showed no significant difference in gut microbiota function between children with ARFID and healthy children; however, GT26 was significantly enriched in children with ARFID based on the CAZy database. The most abundant antibiotic resistance genes in the ARFID group were the vanT, tetQ, adeF, ermF genes, and the abundance of macrolide resistance genes in the ARFID group was significantly higher than that in the HC group (P = 0.041). Compared with healthy children, children with ARFID have a different distribution of the gut microbiota and functional genes. This indicates that the gut microbiome might play an important role in the pathogenesis of ARFID.Clinical trial registration: ChiCTR2300074759.}, } @article {pmid37985659, year = {2023}, author = {Mejia, ME and Mercado-Evans, V and Zulk, JJ and Ottinger, S and Ruiz, K and Ballard, MB and Fowler, SW and Britton, RA and Patras, KA}, title = {Vaginal microbial dynamics and pathogen colonization in a humanized microbiota mouse model.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {87}, pmid = {37985659}, issn = {2055-5008}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; T32 GM136554/GM/NIGMS NIH HHS/United States ; R01 DK128053/DK/NIDDK NIH HHS/United States ; F31 AI167547/AI/NIAID NIH HHS/United States ; F31 HD111236/HD/NICHD NIH HHS/United States ; F31 AI167538/AI/NIAID NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Female ; Animals ; Mice ; RNA, Ribosomal, 16S/genetics ; *Escherichia coli/genetics ; Mice, Inbred C57BL ; Vagina ; *Microbiota ; Disease Models, Animal ; Streptococcus agalactiae/genetics ; }, abstract = {Vaginal microbial composition is associated with differential risk of urogenital infection. Although Lactobacillus spp. are thought to confer protection against infection, the lack of in vivo models resembling the human vaginal microbiota remains a prominent barrier to mechanistic discovery. Using 16S rRNA amplicon sequencing of C57BL/6J female mice, we found that vaginal microbial composition varies within and between colonies across three vivaria. Noting vaginal microbial plasticity in conventional mice, we assessed the vaginal microbiome of humanized microbiota mice ([HMb]mice). Like the community structure in conventional mice, [HMb]mice vaginal microbiota clustered into community state types but, uniquely, [HMb]mice communities were frequently dominated by Lactobacillus or Enterobacteriaceae. Compared to conventional mice, [HMb]mice were less susceptible to uterine ascension by urogenital pathobionts group B Streptococcus (GBS) and Prevotella bivia. Although Escherichia and Lactobacillus both correlated with the absence of uterine GBS, vaginal pre-inoculation with exogenous [HMb]mouse-derived E. coli, but not Ligilactobacillus murinus, reduced vaginal GBS burden. Overall, [HMb]mice serve as a useful model to elucidate the role of endogenous microbes in conferring protection against urogenital pathogens.}, } @article {pmid37985465, year = {2023}, author = {Mou, Y and Liu, J and Ji, C and Cheng, W and Ren, H and Mou, X and Hu, W}, title = {Diagnosis of cutaneous primary nocardiosis in patients with normal immune function by metagenomic next-generation sequencing.}, journal = {The Australasian journal of dermatology}, volume = {}, number = {}, pages = {}, doi = {10.1111/ajd.14187}, pmid = {37985465}, issn = {1440-0960}, abstract = {Nocardia primarily affects immunocompromised individuals, and Infection with Nocardia is uncommon and primary cutaneous nocardiosis caused by percutaneous inoculation is even rarer. Primary cutaneous nocardiosis remains a diagnostic challenge and should be considered in the differential diagnosis for any superficial cutaneous infection that arises in patients with normal immune function. We report a case that was diagnosed with primary cutaneous Nocardia by metagenomic next-generation sequencing technology.}, } @article {pmid37984782, year = {2024}, author = {Venkatachalam, S and Vipindas, PV and Jabir, T and Jain, A and Krishnan, KP}, title = {Metagenomic insights into novel microbial lineages with distinct ecological functions in the Arctic glacier foreland ecosystems.}, journal = {Environmental research}, volume = {241}, number = {}, pages = {117726}, doi = {10.1016/j.envres.2023.117726}, pmid = {37984782}, issn = {1096-0953}, mesh = {*Metagenome ; Ice Cover/microbiology ; Phylogeny ; *Microbiota/genetics ; Carbon/metabolism ; Sulfur ; Nitrogen ; }, abstract = {Land-terminating glaciers are retreating globally, resulting in the expansion of the ice-free glacier forelands (GFs). These GFs act as a natural laboratory to study microbial community succession, soil formation, and ecosystem development. Here, we have employed gene-centric and genome-resolved metagenomic approaches to disseminate microbial diversity, community structure, and their associated biogeochemical processes involved in the carbon, nitrogen, and sulfur cycling across three GF ecosystems. Here, we present a compendium of draft Metagenome Assembled Genomes (MAGs) belonging to bacterial (n = 899) and archaeal (n = 4) domains. These MAGs were reconstructed using a total of 27 shotgun metagenomic datasets obtained from three different GFs, including Midtre Lovénbreen glacier (Svalbard), Russell glacier (Greenland), and Storglaciaren (Sweden). The taxonomic classification revealed that 98% of MAGs remained unclassified at species levels, suggesting the presence of novel microbial lineages. The abundance of metabolic genes associated with carbon, nitrogen, and sulfur cycling pathways varied between and within the samples collected across the three GF ecosystems. Our findings indicate that MAGs from different GFs share close phylogenetic relationships but exhibit significant differences in abundance, distribution patterns, and metabolic functions. This compendium of novel MAGs, encompassing autotrophic, phototrophic, and chemolithoautotrophic microbial groups reconstructed from GF ecosystems, represents a valuable resource for further studies.}, } @article {pmid37984648, year = {2024}, author = {Bhattarai, B and Bhattacharjee, AS and Coutinho, FH and Goel, R}, title = {Investigating the viral ecology and contribution to the microbial ecology in full-scale mesophilic anaerobic digesters.}, journal = {Chemosphere}, volume = {349}, number = {}, pages = {140743}, doi = {10.1016/j.chemosphere.2023.140743}, pmid = {37984648}, issn = {1879-1298}, mesh = {Anaerobiosis ; *Bioreactors/microbiology ; *Methane/metabolism ; Bacteria/metabolism ; Sewage ; }, abstract = {In an attempt to assess the diversity of viruses and their potential to modulate the metabolism of functional microorganisms in anaerobic digesters, we collected digestate from three mesophilic anaerobic digesters in full-scale wastewater treatment plants treating real municipal wastewater. The reads were analyzed using bioinformatics algorithms to elucidate viral diversity, identify their potential role in modulating the metabolism of functional microorganisms, and provide essential genomic information for the potential use of virus-mediated treatment in controlling the anaerobic digester microbiome. We found that Siphoviridae was the dominant family in mesophilic anaerobic digesters, followed by Myoviridae and Podoviridae. Lysogeny was prevalent in mesophilic anaerobic digesters as the majority of metagenome-assembled genomes contained at least one viral genome within them. One virus within the genome of an acetoclastic methanogen (Methanothrix soehngenii) was observed with a gene (fwdE) acquired via lateral transfer from hydrogenotrophic methanogens. The virus-mediated acquisition of fwdE gene enables possibility of mixotrophic methanogenesis in Methanothrix soehngenii. This evidence highlighted that lysogeny provides fitness advantage to methanogens in anaerobic digesters by adding flexibility to changing substrates. Similarly, we found auxiliary metabolic genes, such as cellulase and alpha glucosidase, of bacterial origin responsible for sludge hydrolysis in viruses. Additionally, we discovered novel viral genomes and provided genomic information on viruses infecting acidogenic, acetogenic, and pathogenic bacteria that can potentially be used for virus-mediated treatment to deal with the souring problem in anaerobic digesters and remove pathogens from biosolids before land application. Collectively, our study provides a genome-level understanding of virome in conjunction with the microbiome in anaerobic digesters that can be used to optimize the anaerobic digestion process for efficient biogas generation.}, } @article {pmid37984292, year = {2023}, author = {Zhang, H and Shen, T and Tang, J and Ling, H and Wu, X}, title = {Key taxa and mobilome-mediated responses co-reshape the soil antibiotic resistome under dazomet fumigation stress.}, journal = {Environment international}, volume = {182}, number = {}, pages = {108318}, doi = {10.1016/j.envint.2023.108318}, pmid = {37984292}, issn = {1873-6750}, mesh = {*Anti-Bacterial Agents/toxicity/analysis ; *Soil/chemistry ; Genes, Bacterial ; RNA, Ribosomal, 16S/genetics ; Fumigation ; Soil Microbiology ; Bacteria/genetics ; Real-Time Polymerase Chain Reaction ; }, abstract = {Agrochemicals are emergingly being implicated in the widespread dissemination of antibiotic resistance genes (ARGs) in agroecosystems. However, minimal research exists on the disturbance of fumigant on soil ARGs. Focusing on a typical fumigant dazomet in a simulated soil microcosm, we characterized the dazomet-triggered timely response and longstanding dynamic of ARGs at one-fold and two-fold field recommended doses using metagenome and quantitative PCR. Dazomet treatments reduced 13.17%-69.98% of absolute abundance of 16S rRNA gene and targeted ARGs, but, awfully, boosted diversity and relative abundance of ARGs up to 1.33-1.60 and 1.62-1.90 folds, respectively. Approximately 77.28% of changes in relative abundance of ARGs could be explained by bacterial community and mobile genetic elements (MGEs). Mechanistically, primary hosts of ARGs shifted from Proteobacteria (control) to Firmicutes and Actinobacteria (treatments) accompanied with corresponding changes in their abundance by combining community analysis, host tracking analysis and antibiotic resistant bacteria assay. Meanwhile, dazomet exposure significantly increased the incidence of MGEs and stimulated the conjugation of antibiotic-resistant plasmid. In addition, absolute abundance of targeted ARGs gradually recovered in the post-fumigation stage. Collectively, our results elucidate the dazomet-triggered emergence and spread of soil ARGs and highlight the importance of navigating toward rational use of fumigant in agricultural fields.}, } @article {pmid37984136, year = {2024}, author = {Zhang, M and Xiong, Y and Sun, H and Xiao, T and Xiao, E and Sun, X and Li, B and Sun, W}, title = {Selective pressure of arsenic and antimony co-contamination on microbial community in alkaline sediments.}, journal = {Journal of hazardous materials}, volume = {464}, number = {}, pages = {132948}, doi = {10.1016/j.jhazmat.2023.132948}, pmid = {37984136}, issn = {1873-3336}, mesh = {Antimony ; *Arsenic/analysis ; Environmental Monitoring ; *Microbiota ; Biodegradation, Environmental ; }, abstract = {Although response of microbial community to arsenic (As) and antimony (Sb) co-contamination has been investigated in neutral and acidic environments, little is known in alkaline environment. Herein, the microbial response and survival strategies under the stress of As and Sb co-contamination were determined in the alkaline sediments. Elevated concentrations of As (13700 ± 5012 mg/kg) and Sb (10222 ± 1619 mg/kg) were introduced into the alkaline sediments by the mine drainage, which was partially adopted in the aquatic environment and resulted in a relatively lower contamination (As, 6633 ± 1707 mg/kg; Sb, 6108 ± 1095 mg/kg) in the downstream sediments. The microbial richness was significantly damaged and the microbial compositions were dramatically shifted by the As and Sb co-contamination. Metagenomic analysis shed light on the survival strategies of the microbes under the pressure of As and Sb co-contamination including metal oxidation coupled with denitrification, metal reduction, and metal resistance. The representative microbes were revealed in the sediments with higher (Halomonas) and lower (Thiobacillus, Hydrogenophaga and Flavihumibacter) As and Sb concentration, respectively. In addition, antibiotic resistance genes were found to co-occur with metal resistance genes in the assembled bins. These findings might provide theoretical guidance for bioremediation of As and Sb co-contamination in alkaline environment.}, } @article {pmid37983802, year = {2023}, author = {Battistuzzi, L and Oliani, C and Sciallero, S and Tibiletti, MG and Turchetti, D and Varesco, L}, title = {Population Genomic Screening for Three Common Hereditary Conditions.}, journal = {Annals of internal medicine}, volume = {176}, number = {11}, pages = {eL230321}, doi = {10.7326/L23-0321}, pmid = {37983802}, issn = {1539-3704}, mesh = {Humans ; *Metagenomics ; *Genetic Testing ; }, } @article {pmid37983801, year = {2023}, author = {Peterson, JF and Veenstra, DL and Williams, MS and Hao, J and Guzauskas, GF}, title = {Population Genomic Screening for Three Common Hereditary Conditions.}, journal = {Annals of internal medicine}, volume = {176}, number = {11}, pages = {eL230322}, doi = {10.7326/L23-0322}, pmid = {37983801}, issn = {1539-3704}, mesh = {Humans ; *Metagenomics ; *Genetic Testing ; }, } @article {pmid37982653, year = {2023}, author = {Jang, Y and Kang, J-S and Bae, EH and Lee, J}, title = {Metagenome-assembled genomes of the GU0601 sample (the Han River, South Korea).}, journal = {Microbiology resource announcements}, volume = {12}, number = {12}, pages = {e0068823}, pmid = {37982653}, issn = {2576-098X}, support = {NIBR202314101//Ministry of Environment (MOE)/ ; RS-2023-00209930//National Research Foundation of Korea (NRF)/ ; }, abstract = {We generated metagenome sequences of the GU0601 sample collected from the Han River and constructed metagenome-assembled genomes (MAGs) to identify their bacterial composition. We identified six MAGs belonging to Alphaproteobacteria, Cyanobacteria, and Flavobacteria.}, } @article {pmid37982636, year = {2023}, author = {Gaudino, M and Salem, E and Ducatez, MF and Meyer, G}, title = {Identification of Astrovirus in the virome of the upper and lower respiratory tracts of calves with acute signs of bronchopneumonia.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0302623}, pmid = {37982636}, issn = {2165-0497}, support = {FluD//Agence Nationale de la Recherche (ANR)/ ; RespiCare//Institut Carnot Santé Animale (ICSA)/ ; }, mesh = {Animals ; Cattle ; Humans ; Swine ; *Astroviridae Infections/veterinary ; *Bronchopneumonia/veterinary ; Virome ; Phylogeny ; *Astroviridae/genetics ; *Cattle Diseases/diagnosis ; *Encephalitis ; Respiratory System ; Feces ; }, abstract = {Astroviruses (AstV) are known suspects of enteric disease in humans and livestock. Recently, AstV have been linked to encephalitis in immunocompromised patients and other animals, such as cattle, minks, and swine. In our study, we also identified AstV in the respiratory samples of calves with signs of bronchopneumonia, suggesting that their tropism could be even broader. We obtained one bovine AstV (BAstV) complete genome sequence by next-generation sequencing and showed that respiratory and enteric AstV from different species formed a divergent genetic cluster with AstV isolated from encephalitis cases, indicating that tropism might be strain-specific. These data provide further insight into understanding the biology of these understudied pathogens and suggest BAstV as a potential new candidate for bovine respiratory disease.}, } @article {pmid37982612, year = {2023}, author = {Fu, Z and Ai, J and Zhang, H and Cui, P and Xu, T and Zhang, Y and Zhang, Y and Wu, H and Shen, A and Lin, K and Zhang, M and Qiu, C and Jiang, N and Zhou, Y and Zhang, W}, title = {Pathogen quantitative efficacy of different spike-in internal controls and clinical application in central nervous system infection with metagenomic sequencing.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0113923}, pmid = {37982612}, issn = {2165-0497}, support = {82002141//MOST | National Natural Science Foundation of China (NSFC)/ ; 82161138018//MOST | National Natural Science Foundation of China (NSFC)/ ; 20dz2260100//Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Responese/ ; HS2021SHZX001//Shanghai Municipal Science and Technology Major Project/ ; 21NL2600100//Shanghai Municipal Science and Technology Major Project/ ; 2022YFC0869900//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Central Nervous System Infections ; High-Throughput Nucleotide Sequencing ; *Bacteriophages ; Metagenome ; Metagenomics ; }, abstract = {Metagenomic next-generation sequencing (mNGS) has been used broadly for pathogens detection of infectious diseases. However, there is a lack of method for the absolute quantitation of pathogens by mNGS. We compared the quantitative efficiency of three mNGS internal controls (ICs) Thermus thermophilus, T1 phages, and artificial DNA sequence and developed the most applicable strategies for pathogen quantitation via mNGS in central nervous system infection. The IC application strategy we developed will enable mNGS analysis to assess the pathogen load simultaneously with the detection of pathogens, which should provide critical information for quick decision-making of treatment as well as clinical prognosis.}, } @article {pmid37981129, year = {2024}, author = {Sun, X and Wang, X and Han, Q and Yu, Q and Wanyan, R and Li, H}, title = {Bibliometric analysis of papers on antibiotic resistance genes in aquatic environments on a global scale from 2012 to 2022: Evidence from universality, development and harmfulness.}, journal = {The Science of the total environment}, volume = {909}, number = {}, pages = {168597}, doi = {10.1016/j.scitotenv.2023.168597}, pmid = {37981129}, issn = {1879-1026}, mesh = {Humans ; *Anti-Bacterial Agents/analysis ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Water ; Bibliometrics ; }, abstract = {Antibiotic resistance genes (ARGs), emerging pollutants, are widely distributed in aquatic environments, and are tightly linked to human health. However, the research progress and trends in recent years on ARGs of aquatic environments are still unclear. This paper made a comprehensive understanding of the research advance, study trends and key topics of 1592 ARGs articles from 2012 to 2022 by bibliometrics. Publications on ARGs increased rapidly from 2012 to 2022, and scholars paid closer attention to the field of Environmental Sciences & Ecology. The most influential country and institution was mainly China and Chinese Academy of Sciences, respectively. The most articles (14.64 %) were published in the journal Science of the total environment. China and USA had the most cooperation, and USA was more inclined to international cooperation. PCR-based methods for water ARG research were the most widely used, followed by metagenomics. The most studied ARG types were sulfonamides, tetracyclines. Moreover, ARGs from wastewater and rivers were popularly concerned. Current topics mainly included pollution investigation, characteristics, transmission, reduction and risk identification of ARGs. Additionally, future research directions were proposed. Generally, by bibliometrics, this paper reviews the research hotspots and future directions of ARGs on a global scale, and summarizes the more important categories of ARGs, the pollution degree of ARGs in the relevant water environment and the research methods, which can provide a more comprehensive information for the future breakthrough of resistance mechanism, prevention and control standard formulation of ARGs.}, } @article {pmid37980948, year = {2023}, author = {Cai, Y and Liu, F and He, G and Kong, X and Jiang, Y and Liu, J and Yan, B and Zhang, S and Zhang, J and Yan, Z}, title = {Mechanisms of total phosphorus removal and reduction of β-lactam antibiotic resistance genes by exogenous fungal combination activated sludge.}, journal = {Bioresource technology}, volume = {393}, number = {}, pages = {130046}, doi = {10.1016/j.biortech.2023.130046}, pmid = {37980948}, issn = {1873-2976}, abstract = {This study utilized Trichoderma and activated sludge to construct combined activated sludge (TAS). The metagenomic approach was employed to examine the shifts in microbial community structure and function of TAS under amoxicillin stress and investigate the mechanism underlying the reduction of β-lactam antibiotic resistance genes (β-ARGs). The findings demonstrated that the elevated aundance of glpa, glpd, ugpq, glpq, and glpb were primarily responsible for the reduction in total phosphorus (TP) removal by TAS. The increased abundance of Proteobacteria and Verrucomicrobia led to enhanced expression of ugpb, phnd, and phne, thereby improving the TP removal of TAS. Furthermore, antibiotic inactivation has gradually become the primary antibiotic resistance mechanism in TAS. Specifically, an increase in the abundance of OXA-309 in TAS will decrease the probability of amoxicillin accumulation in TAS. A decrease in β-ARGs diversity confirmed this. This study presents a novel approach to reducing antibiotic and ARG accumulation in sludge.}, } @article {pmid37980461, year = {2023}, author = {Cunningham-Oakes, E and Bronowski, C and Chinyama, E and Jere, KC and Sindhu, KNC and Kang, G and Iturriza-Gómara, M and Darby, AC and Parker, EPK}, title = {Increased bacterial taxonomic and functional diversity is associated with impaired rotavirus vaccine immunogenicity in infants from India and Malawi.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {354}, pmid = {37980461}, issn = {1471-2180}, support = {MR/N006259/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; Infant ; *Rotavirus/genetics ; *Rotavirus Vaccines ; Malawi ; Prospective Studies ; Immunogenicity, Vaccine ; *Rotavirus Infections/prevention & control ; India ; Vaccines, Attenuated ; Antibodies, Viral ; }, abstract = {The immunogenicity and effectiveness of oral rotavirus vaccines (ORVs) against severe rotavirus-associated gastroenteritis are impaired in low- and middle-income countries (LMICs) where the burden of disease is highest. Determining risk factors for impaired ORV response may help identify strategies to enhance vaccine effectiveness. In this study, we use metagenomic sequencing to provide a high-resolution taxonomic analysis of stool samples collected at 6 weeks of age (coinciding with the first ORV dose) during a prospective study of ORV immunogenicity in India and Malawi. We then analyse the functional capacity of the developing microbiome in these cohorts. Microbiome composition differed significantly between countries, although functional capacity was more similar than taxonomic composition. Our results confirm previously reported findings that the developing microbiome is more diverse in taxonomic composition in ORV non-seroconverters compared with seroconverters, and we additionally demonstrate a similar pattern in functional capacity. Although taxonomic or functional feature abundances are poor predictors of ORV response, we show that skews in the direction of associations within these microbiome data can be used to identify consistent markers of ORV response across LMIC infant cohorts. We also highlight the systemic under-representation of reference genes from LMICs that limit functional annotation in our study (7% and 13% annotation at pathway and enzyme commission level, respectively). Overall, higher microbiome diversity in early life may act as marker for impaired ORV response in India and Malawi, whilst a holistic perspective of functional capacity may be hidden in the "dark matter" of the microbiome.}, } @article {pmid37980332, year = {2023}, author = {Zeamer, AL and Salive, MC and An, X and Beaudoin, FL and House, SL and Stevens, JS and Zeng, D and Neylan, TC and Clifford, GD and Linnstaedt, SD and Rauch, SL and Storrow, AB and Lewandowski, C and Musey, PI and Hendry, PL and Sheikh, S and Jones, CW and Punches, BE and Swor, RA and Hudak, LA and Pascual, JL and Seamon, MJ and Harris, E and Pearson, C and Peak, DA and Merchant, RC and Domeier, RM and Rathlev, NK and O'Neil, BJ and Sergot, P and Sanchez, LD and Bruce, SE and Kessler, RC and Koenen, KC and McLean, SA and Bucci, V and Haran, JP}, title = {Association between microbiome and the development of adverse posttraumatic neuropsychiatric sequelae after traumatic stress exposure.}, journal = {Translational psychiatry}, volume = {13}, number = {1}, pages = {354}, pmid = {37980332}, issn = {2158-3188}, support = {RF1 AG067483/AG/NIA NIH HHS/United States ; U01 MH110925/MH/NIMH NIH HHS/United States ; }, mesh = {Adult ; Humans ; *Microbiota ; *Stress Disorders, Post-Traumatic/metabolism ; *Gastrointestinal Microbiome ; Feces/microbiology ; Biological Availability ; }, abstract = {Patients exposed to trauma often experience high rates of adverse post-traumatic neuropsychiatric sequelae (APNS). The biological mechanisms promoting APNS are currently unknown, but the microbiota-gut-brain axis offers an avenue to understanding mechanisms as well as possibilities for intervention. Microbiome composition after trauma exposure has been poorly examined regarding neuropsychiatric outcomes. We aimed to determine whether the gut microbiomes of trauma-exposed emergency department patients who develop APNS have dysfunctional gut microbiome profiles and discover potential associated mechanisms. We performed metagenomic analysis on stool samples (n = 51) from a subset of adults enrolled in the Advancing Understanding of RecOvery afteR traumA (AURORA) study. Two-, eight- and twelve-week post-trauma outcomes for post-traumatic stress disorder (PTSD) (PTSD checklist for DSM-5), normalized depression scores (PROMIS Depression Short Form 8b) and somatic symptom counts were collected. Generalized linear models were created for each outcome using microbial abundances and relevant demographics. Mixed-effect random forest machine learning models were used to identify associations between APNS outcomes and microbial features and encoded metabolic pathways from stool metagenomics. Microbial species, including Flavonifractor plautii, Ruminococcus gnavus and, Bifidobacterium species, which are prevalent commensal gut microbes, were found to be important in predicting worse APNS outcomes from microbial abundance data. Notably, through APNS outcome modeling using microbial metabolic pathways, worse APNS outcomes were highly predicted by decreased L-arginine related pathway genes and increased citrulline and ornithine pathways. Common commensal microbial species are enriched in individuals who develop APNS. More notably, we identified a biological mechanism through which the gut microbiome reduces global arginine bioavailability, a metabolic change that has also been demonstrated in the plasma of patients with PTSD.}, } @article {pmid37979958, year = {2023}, author = {Prinz, E and Schlupp, L and Dyson, G and Barrett, M and Szymczak, A and Velasco, C and Izda, V and Dunn, CM and Jeffries, MA}, title = {OA susceptibility in mice is partially mediated by the gut microbiome, is transferrable via microbiome transplantation and is associated with immunophenotype changes.}, journal = {Annals of the rheumatic diseases}, volume = {}, number = {}, pages = {}, doi = {10.1136/ard-2023-224907}, pmid = {37979958}, issn = {1468-2060}, abstract = {OBJECTIVES: The Murphy Roths Large (MRL)/MpJ 'superhealer' mouse strain is protected from post-traumatic osteoarthritis (OA), although no studies have evaluated the microbiome in the context of this protection. This study characterised microbiome differences between MRL and wild-type mice, evaluated microbiome transplantation and OA and investigated microbiome-associated immunophenotypes.

METHODS: Cecal material from mixed sex C57BL6/J (B6) or female MRL/MpJ (MRL) was transplanted into B6 and MRL mice, then OA was induced by disruption of the medial meniscus surgery (DMM). In other experiments, transplantation was performed after DMM and transplantation was performed into germ-free mice. Transplanted mice were bred through F2. OARSI, synovitis and osteophyte scores were determined blindly 8 weeks after DMM. 16S microbiome sequencing was performed and metagenomic function was imputed. Immunophenotypes were determined using mass cytometry.

RESULTS: MRL-into-B6 transplant prior to DMM showed reduced OA histopathology (OARSI score 70% lower transplant vs B6 control), synovitis (60% reduction) and osteophyte scores (30% reduction) 8 weeks after DMM. When performed 48 hours after DMM, MRL-into-B6 transplant improved OA outcomes but not when performed 1-2 weeks after DMM. Protection was seen in F1 (60% reduction) and F2 progeny (30% reduction). Several cecal microbiome clades were correlated with either better (eg, Lactobacillus, R=-0.32, p=0.02) or worse (eg, Rikenellaceae, R=0.43, p=0.001) OA outcomes. Baseline immunophenotypes associated with MRL-into-B6 transplants and MRL included reduced double-negative T cells and increased CD25+CD4+ T cells.

CONCLUSION: The gut microbiome is responsible in part for OA protection in MRL mice and is transferrable by microbiome transplantation. Transplantation induces resting systemic immunophenotyping changes that correlate with OA protection.}, } @article {pmid37979928, year = {2024}, author = {Zeng, Y and Liu, H and Chen, W and Li, H and Dong, H and Wu, H and Xu, H and Sun, D and Liu, X and Li, P and Qiu, B and Dang, Y}, title = {Riboflavin-loaded carbon cloth aids the anaerobic digestion of cow dung by promoting direct interspecies electron transfer.}, journal = {Environmental research}, volume = {241}, number = {}, pages = {117660}, doi = {10.1016/j.envres.2023.117660}, pmid = {37979928}, issn = {1096-0953}, mesh = {Cattle ; Animals ; *Carbon ; Anaerobiosis ; *Electrons ; Methane ; Bioreactors ; Sewage ; }, abstract = {Cow dung generates globally due to increased beef and milk consumption, but its treatment efficiency remains low. Previous studies have shown that riboflavin-loaded conductive materials can improve anaerobic digestion through enhance direct interspecies electron transfer (DIET). However, its effect on the practical anaerobic digestion of cow dung remained unclear. In this study, carbon cloth loaded with riboflavin (carbon cloth-riboflavin) was added into an anaerobic digester treating cow dung. The carbon cloth-riboflavin reactor showed a better performance than other two reactors. The metagenomic analysis revealed that Methanothrix on the surface of the carbon cloth predominantly utilized the CO2 reduction for methane production, further enhanced after riboflavin addition, while Methanothrix in bulk sludge were using the acetate decarboxylation pathway. Furthermore, the carbon cloth-riboflavin enriched various major methanogenic pathways and activated a large number of enzymes associated with DIET. Riboflavin's presence altered the microbial communities and the abundance of functional genes relate to DIET, ultimately leading to a better performance of anaerobic digestion for cow dung.}, } @article {pmid37979711, year = {2023}, author = {Chen, Q and Luo, Y and Shen, Y and Li, X and Yang, H and Li, J and Wang, J and Xiao, Y}, title = {Fructose corn syrup induces inflammatory injury and obesity by altering gut microbiota and gut microbiota-related arachidonic acid metabolism.}, journal = {The Journal of nutritional biochemistry}, volume = {124}, number = {}, pages = {109527}, doi = {10.1016/j.jnutbio.2023.109527}, pmid = {37979711}, issn = {1873-4847}, abstract = {Excessive fructose corn syrup (FCS) intake brings a series of health problems. The aim of the present study was to explore the mechanism of FCS-induced metabolic disorders from the perspective of gut microbiota. Mice were fed for 16 weeks with normal or 30% FCS drinking water. Compared to the control group, FCS caused significantly higher fat deposition, hepatic steatosis, liver and intestinal inflammatory damages (P<.05). FCS increased the abundance of Muribaculaceae in vivo and in vitro, which was positively correlated with the indices of metabolic disorders (P<.05). In vivo and in vitro data indicated that FCS enhanced the microbial function involved in pentose phosphate pathway and arachidonic acid metabolism, metabolomics further demonstrated that FCS led to an increase in prostaglandins (the catabolites of arachidonic acid) (P<.05). Our study confirmed that FCS can directly promote gut microbiota to synthesize inflammatory factor prostaglandins, which provides new insights and directions for the treatment of FCS-induced metabolic disorders and inflammation.}, } @article {pmid37979651, year = {2024}, author = {Zhang, H and Xu, Y and Shen, T and Jia, X and Xu, Y and Shi, T and Pan, D and Hua, R and Wu, X}, title = {Chicken feedlot revisited: Co-dispersal of antibiotic and metal resistome under banning in-feed veterinary antibiotics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {341}, number = {}, pages = {122932}, doi = {10.1016/j.envpol.2023.122932}, pmid = {37979651}, issn = {1873-6424}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology/analysis ; *Chickens ; Genes, Bacterial ; Bacteria/genetics ; Metals ; Water ; }, abstract = {Intensive livestock farming has been implicated as a notorious hotspot for antibiotic resistance genes (ARGs) due to the excessive or inappropriate use of in-feed antibiotics over the past few decades. Since China implemented a ban on the use of antibiotics in animal feed since 2020, the dissemination of ARGs in the vicinity of feedlots has remained unclear. This study presents a case study that aims to investigate the dispersal of antibiotics and ARGs from a chicken feedlot (established in 2020) to the adjacent aquatic and soil environments. Comparing the sample collected from upstream area, the water and sediment samples from midstream and downstream areas showed an increase in total antibiotic residues and metal content (Cu and Zn) by 4.2-5.3 fold and 1.3-22.6 fold, respectively. The downstream water samples exhibited a 2.49-2.93-fold increase in the abundance of ARGs and a 1.48-1.75-fold increase in the abundance of metal resistance genes (MRGs). The results of Pearson correlation and metagenome-assembled genome revealed a tendency for the co-occurrence of ARGs and MRGs. The dissemination of ARGs and MRGs is primarily driven by tetracycline, tylosin, Cu, and, Mn, with mobile genetic elements playing a more significant role than bacterial communities. These findings shed light on the overlooked co-dispersal pattern of ARGs and MRGs in the environment surrounding feedlots, particularly in the context of banning in-feed veterinary antibiotics.}, } @article {pmid37979578, year = {2023}, author = {Liu, AK and Kaeser, B and Chen, L and West-Roberts, J and Taylor-Kearney, LJ and Lavy, A and Günzing, D and Li, WJ and Hammel, M and Nogales, E and Banfield, JF and Shih, PM}, title = {Deep-branching evolutionary intermediates reveal structural origins of form I rubisco.}, journal = {Current biology : CB}, volume = {33}, number = {24}, pages = {5316-5325.e3}, doi = {10.1016/j.cub.2023.10.053}, pmid = {37979578}, issn = {1879-0445}, mesh = {*Ribulose-Bisphosphate Carboxylase/genetics/chemistry/metabolism ; }, abstract = {The enzyme rubisco (ribulose-1,5-bisphosphate carboxylase/oxygenase) catalyzes the majority of biological carbon fixation on Earth. Although the vast majority of rubiscos across the tree of life assemble as homo-oligomers, the globally predominant form I enzyme-found in plants, algae, and cyanobacteria-forms a unique hetero-oligomeric complex. The recent discovery of a homo-oligomeric sister group to form I rubisco (named form I') has filled a key gap in our understanding of the enigmatic origins of the form I clade. However, to elucidate the series of molecular events leading to the evolution of form I rubisco, we must examine more distantly related sibling clades to contextualize the molecular features distinguishing form I and form I' rubiscos. Here, we present a comparative structural study retracing the evolutionary history of rubisco that reveals a complex structural trajectory leading to the ultimate hetero-oligomerization of the form I clade. We structurally characterize the oligomeric states of deep-branching form Iα and I'' rubiscos recently discovered from metagenomes, which represent key evolutionary intermediates preceding the form I clade. We further solve the structure of form I'' rubisco, revealing the molecular determinants that likely primed the enzyme core for the transition from a homo-oligomer to a hetero-oligomer. Our findings yield new insight into the evolutionary trajectory underpinning the adoption and entrenchment of the prevalent assembly of form I rubisco, providing additional context when viewing the enzyme family through the broader lens of protein evolution.}, } @article {pmid37979568, year = {2024}, author = {Peng, Y and Gu, X and Zhang, M and Yan, P and Sun, S and He, S}, title = {Simultaneously enhanced autotrophic-heterotrophic denitrification in iron-based ecological floating bed by plant biomass: Metagenomics insights into microbial communities, functional genes and nitrogen metabolic pathways.}, journal = {Water research}, volume = {248}, number = {}, pages = {120868}, doi = {10.1016/j.watres.2023.120868}, pmid = {37979568}, issn = {1879-2448}, mesh = {*Denitrification ; Nitrogen ; Iron ; Biomass ; Bioreactors ; Autotrophic Processes ; *Microbiota ; Bacteria/genetics ; Metabolic Networks and Pathways ; Water ; Nitrates ; }, abstract = {In this study, the ecological floating bed supporting with zero-valent iron (ZVI) and plant biomass (EFB-IB) was constructed to improve nitrogen removal from low-polluted water. The effects of ZVI coupling with plant biomass on microbial community structure, metabolic pathways and functional genes were analyzed by metagenomic sequencing, and the mechanism for nitrogen removal was revealed. Results showed that compared with mono-ZVI system (EFB-C), the denitrification efficiencies of EFB-IB were effectively enhanced, with the higher average NO3[-]-N removal efficiencies of 22.60-59.19%. Simultaneously, the average NH4[+]-N removal efficiencies were 73.08-91.10%. Metagenomic analyses showed that EFB-IB enriched microbes that involved in iron cycle, lignocellulosic degradation and nitrogen metabolism. Plant biomass addition simultaneously increased the relative abundances of autotrophic and heterotrophic denitrifying bacteria. Network analysis showed the cooperation between autotrophic and heterotrophic denitrifying bacteria in EFB-IB. Moreover, compared with EFB-C, plant biomass addition increased the relative abundances of genes related to iron cycle, lignocellulose degradation and glycolysis processes, ensuring the production of autotrophic and heterotrophic electron donors. Therefore, the relative abundances of key enzymes and functional genes related to denitrification were higher in EFB-IB, being beneficial to the NO3[-]-N removal. Additionally, the correlation analysis of nitrogen removal and functional genes verified the synergistic mechanism of iron-based autotrophic denitrification and plant biomass-mediated heterotrophic denitrification in EFB-IB. In summary, plant biomass has excellent potential to improve the nitrogen removal of iron-based EFB from low-polluted water.}, } @article {pmid37979403, year = {2024}, author = {Rojas-Araos, F and Rojas-Hernández, N and Cornejo-Guzmán, S and Ernst, B and Dewitte, B and Parada, C and Veliz, D}, title = {Population genomic and biophysical modeling show different patterns of population connectivity in the spiny lobster Jasus frontalis inhabiting oceanic islands.}, journal = {Marine environmental research}, volume = {193}, number = {}, pages = {106253}, doi = {10.1016/j.marenvres.2023.106253}, pmid = {37979403}, issn = {1879-0291}, mesh = {Animals ; *Palinuridae/genetics ; Islands ; Metagenomics ; Genetics, Population ; Oceans and Seas ; }, abstract = {Knowledge about connectivity between populations is essential for the fisheries management of commercial species. The lobster Jasus frontalis inhabits two oceanic island groups, the Juan Fernández Archipelago and the Desventuradas Islands, separated by 800 km. Since this species is primarily exploited in the Juan Fernández Archipelago, knowledge of the connectivity patterns among islands is foundational for species management. Here, we used variability at single-nucleotide polymorphisms (SNPs) and individual-based modeling (IBM) to estimate the genetic structure and connectivity between J. frontalis populations in these island groups. The variability at 9090 SNPs suggests two genetic populations, one in the Juan Fernández Archipelago and one in the Desventuradas Islands. Furthermore, IBM suggests an asymmetric connectivity pattern, with particles moving from the Juan Fernández Archipelago to the Desventuradas Islands but not vice versa. Since the IBM analysis suggests asymmetric larval movement between the islands, and the genetic analysis indicates isolation between the Juan Fernández Archipelago and the Desventuradas Islands, larval retention mechanisms such as small-scale oceanographic processes or behavior could hinder larval movement between islands. This study highlights the importance of using more than one methodology to estimate population connectivity.}, } @article {pmid37978289, year = {2023}, author = {Wang, C and Yu, QY and Ji, NN and Zheng, Y and Taylor, JW and Guo, LD and Gao, C}, title = {Bacterial genome size and gene functional diversity negatively correlate with taxonomic diversity along a pH gradient.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7437}, pmid = {37978289}, issn = {2041-1723}, mesh = {*Ecosystem ; *Biodiversity ; RNA, Ribosomal, 16S/genetics ; Genome Size ; Proton-Motive Force ; Bacteria/genetics ; Soil/chemistry ; Genome, Bacterial/genetics ; Soil Microbiology ; }, abstract = {Bacterial gene repertoires reflect adaptive strategies, contribute to ecosystem functioning and are limited by genome size. However, gene functional diversity does not necessarily correlate with taxonomic diversity because average genome size may vary by community. Here, we analyse gene functional diversity (by shotgun metagenomics) and taxonomic diversity (by 16S rRNA gene amplicon sequencing) to investigate soil bacterial communities along a natural pH gradient in 12 tropical, subtropical, and temperate forests. We find that bacterial average genome size and gene functional diversity decrease, whereas taxonomic diversity increases, as soil pH rises from acid to neutral; as a result, bacterial taxonomic and functional diversity are negatively correlated. The gene repertoire of acid-adapted oligotrophs is enriched in functions of signal transduction, cell motility, secretion system, and degradation of complex compounds, while that of neutral pH-adapted copiotrophs is enriched in functions of energy metabolism and membrane transport. Our results indicate that a mismatch between taxonomic and functional diversity can arise when environmental factors (such as pH) select for adaptive strategies that affect genome size distributions.}, } @article {pmid37978236, year = {2023}, author = {Khater, DZ and Amin, RS and Fetohi, AE and Mahmoud, M and El-Khatib, KM}, title = {Insights on hexavalent chromium(VI) remediation strategies in abiotic and biotic dual chamber microbial fuel cells: electrochemical, physical, and metagenomics characterizations.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {20184}, pmid = {37978236}, issn = {2045-2322}, support = {33445//The Science, Technology & Innovation Funding Authority, Egypt/ ; }, mesh = {*Bioelectric Energy Sources/microbiology ; Chromium/chemistry ; Bacteria/genetics ; Wastewater ; }, abstract = {Hexavalent chromium [Cr(VI)] is one of the most carcinogenic and mutagenic toxins, and is commonly released into the environemt from different industries, including leather tanning, pulp and paper manufacturing, and metal finishing. This study aimed to investigate the performance of dual chamber microbial fuel cells (DMFCs) equipped with a biocathode as alternative promising remediation approaches for the biological reduction of hexavalent chromium [Cr(VI)] with instantaneous power generation. A succession batch under preliminary diverse concentrations of Cr(VI) (from 5 to 60 mg L[-1]) was conducted to investigate the reduction mechanism of DMFCs. Compared to abiotic-cathode DMFC, biotic-cathode DMFC exhibited a much higher power density, Cr(VI) reduction, and coulombic efficiency over a wide range of Cr(VI) concentrations (i.e., 5-60 mg L[-1]). Furthermore, the X-ray photoelectron spectroscopy (XPS) revealed that the chemical functional groups on the surface of biotic cathode DMFC were mainly trivalent chromium (Cr(III)). Additionally, high throughput sequencing showed that the predominant anodic bacterial phyla were Firmicutes, Proteobacteria, and Deinococcota with the dominance of Clostridiumsensu strict 1, Enterobacter, Pseudomonas, Clostridiumsensu strict 11 and Lysinibacillus in the cathodic microbial community. Collectively, our results showed that the Cr(VI) removal occurred through two different mechanisms: biosorption and bioelectrochemical reduction. These findings confirmed that the DMFC could be used as a bioremediation approach for the removal of Cr(VI) commonly found in different industrial wastewater, such as tannery effluents. with simultaneous bioenergy production.}, } @article {pmid37978200, year = {2023}, author = {Rodríguez-Gijón, A and Hampel, JJ and Dharamshi, J and Bertilsson, S and Garcia, SL}, title = {Shotgun metagenomes from productive lakes in an urban region of Sweden.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {810}, pmid = {37978200}, issn = {2052-4463}, support = {UPD2021-0051//Wenner-Gren Foundation (Wenner-Gren Foundation for Anthropological Research, Inc.)/ ; UPD2020-0040//Wenner-Gren Foundation (Wenner-Gren Foundation for Anthropological Research, Inc.)/ ; }, mesh = {Bacteria/genetics ; Drinking Water ; *Lakes ; *Metagenome ; Metagenomics ; Sweden ; }, abstract = {Urban lakes provide multiple benefits to society while influencing life quality. Moreover, lakes and their microbiomes are sentinels of anthropogenic impact and can be used for natural resource management and planning. Here, we release original metagenomic data from several well-characterized and anthropogenically impacted eutrophic lakes in the vicinity of Stockholm (Sweden). Our goal was to collect representative microbial community samples and use shotgun sequencing to provide a broad view on microbial diversity of productive urban lakes. Our dataset has an emphasis on Lake Mälaren as a major drinking water reservoir under anthropogenic impact. This dataset includes short-read sequence data and metagenome assemblies from each of 17 samples collected from eutrophic lakes near the greater Stockholm area. We used genome-resolved metagenomics and obtained 2378 metagenome assembled genomes that de-replicated into 514 species representative genomes. This dataset adds new datapoints to previously sequenced lakes and it includes the first sequenced set of metagenomes from Lake Mälaren. Our dataset serves as a baseline for future monitoring of drinking water reservoirs and urban lakes.}, } @article {pmid37977851, year = {2023}, author = {Sardar, P and Elhottová, D and Pérez-Valera, E}, title = {Soil-specific responses in the antibiotic resistome of culturable Acinetobacter spp. and other non-fermentative Gram-negative bacteria following experimental manure application.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {12}, pages = {}, doi = {10.1093/femsec/fiad148}, pmid = {37977851}, issn = {1574-6941}, support = {17-25660S//Czech Science Foundation/ ; //Czech Academy of Sciences/ ; }, mesh = {Animals ; Cattle ; Female ; *Anti-Bacterial Agents/pharmacology ; Soil ; Manure/microbiology ; Genes, Bacterial ; Bacteria/genetics ; *Acinetobacter/genetics ; Gram-Negative Bacteria/genetics ; Soil Microbiology ; }, abstract = {Acinetobacter spp. and other non-fermenting Gram-negative bacteria (NFGNB) represent an important group of opportunistic pathogens due to their propensity for multiple, intrinsic, or acquired antimicrobial resistance (AMR). Antimicrobial resistant bacteria and their genes can spread to the environment through livestock manure. This study investigated the effects of fresh manure from dairy cows under antibiotic prophylaxis on the antibiotic resistome and AMR hosts in microcosms using pasture soil. We specifically focused on culturable Acinetobacter spp. and other NFGNB using CHROMagar Acinetobacter. We conducted two 28-days incubation experiments to simulate natural deposition of fresh manure on pasture soil and evaluated the effects on antibiotic resistance genes (ARGs) and bacterial hosts through shotgun metagenomics. We found that manure application altered the abundance and composition of ARGs and their bacterial hosts, and that the effects depended on the soil source. Manure enriched the antibiotic resistome of bacteria only in the soil where native bacteria had a low abundance of ARGs. Our study highlights the role of native soil bacteria in modulating the consequences of manure deposition on soil and confirms the potential of culturable Acinetobacter spp. and other NFGNB to accumulate AMR in pasture soil receiving fresh manure.}, } @article {pmid37977508, year = {2023}, author = {Liu, Y and Wang, C and Xie, L and Du, S and Ding, L and Cui, Y and Chen, R and Zhang, J and Wang, W and Liu, X and Wang, Y and Chen, S and Tan, T and Zhao, Q and Yin, L and Li, C and Chen, Y and Ding, T}, title = {Metagenomics analysis identifies oral Streptococcus as potential biomarkers for nasopharyngeal carcinoma.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2023.11.003}, pmid = {37977508}, issn = {1673-8527}, } @article {pmid37977163, year = {2023}, author = {Wheeler, NE and Price, V and Cunningham-Oakes, E and Tsang, KK and Nunn, JG and Midega, JT and Anjum, MF and Wade, MJ and Feasey, NA and Peacock, SJ and Jauneikaite, E and Baker, KS and , }, title = {Innovations in genomic antimicrobial resistance surveillance.}, journal = {The Lancet. Microbe}, volume = {4}, number = {12}, pages = {e1063-e1070}, doi = {10.1016/S2666-5247(23)00285-9}, pmid = {37977163}, issn = {2666-5247}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Drug Resistance, Bacterial/genetics ; Genomics/methods ; Genome ; Whole Genome Sequencing/methods ; }, abstract = {Whole-genome sequencing of antimicrobial-resistant pathogens is increasingly being used for antimicrobial resistance (AMR) surveillance, particularly in high-income countries. Innovations in genome sequencing and analysis technologies promise to revolutionise AMR surveillance and epidemiology; however, routine adoption of these technologies is challenging, particularly in low-income and middle-income countries. As part of a wider series of workshops and online consultations, a group of experts in AMR pathogen genomics and computational tool development conducted a situational analysis, identifying the following under-used innovations in genomic AMR surveillance: clinical metagenomics, environmental metagenomics, gene or plasmid tracking, and machine learning. The group recommended developing cost-effective use cases for each approach and mapping data outputs to clinical outcomes of interest to justify additional investment in capacity, training, and staff required to implement these technologies. Harmonisation and standardisation of methods, and the creation of equitable data sharing and governance frameworks, will facilitate successful implementation of these innovations.}, } @article {pmid37976954, year = {2024}, author = {Wang, D and Shang, J and Lin, H and Liang, J and Wang, C and Sun, Y and Bai, Y and Qu, J}, title = {Identifying ARG-carrying bacteriophages in a lake replenished by reclaimed water using deep learning techniques.}, journal = {Water research}, volume = {248}, number = {}, pages = {120859}, doi = {10.1016/j.watres.2023.120859}, pmid = {37976954}, issn = {1879-2448}, mesh = {*Bacteriophages/genetics ; Water ; Lakes ; *Deep Learning ; Genes, Bacterial ; Anti-Bacterial Agents ; }, abstract = {As important mobile genetic elements, phages support the spread of antibiotic resistance genes (ARGs). Previous analyses of metaviromes or metagenome-assembled genomes (MAGs) failed to assess the extent of ARGs transferred by phages, particularly in the generation of antibiotic pathogens. Therefore, we have developed a bioinformatic pipeline that utilizes deep learning techniques to identify ARG-carrying phages and predict their hosts, with a special focus on pathogens. Using this method, we discovered that the predominant types of ARGs carried by temperate phages in a typical landscape lake, which is fully replenished by reclaimed water, were related to multidrug resistance and β-lactam antibiotics. MAGs containing virulent factors (VFs) were predicted to serve as hosts for these ARG-carrying phages, which suggests that the phages may have the potential to transfer ARGs. In silico analysis showed a significant positive correlation between temperate phages and host pathogens (R = 0.503, p < 0.001), which was later confirmed by qPCR. Interestingly, these MAGs were found to be more abundant than those containing both ARGs and VFs, especially in December and March. Seasonal variations were observed in the abundance of phages harboring ARGs (from 5.62 % to 21.02 %) and chromosomes harboring ARGs (from 18.01 % to 30.94 %). In contrast, the abundance of plasmids harboring ARGs remained unchanged. In summary, this study leverages deep learning to analyze phage-transferred ARGs and demonstrates an alternative method to track the production of potential antibiotic-resistant pathogens by metagenomics that can be extended to microbiological risk assessment.}, } @article {pmid37976796, year = {2024}, author = {Gobikrushanth, M and Dos Santos, SJ and Champika, F and Hill, JE and Dadarwal, D}, title = {Uterine microbial profiles in healthy postpartum dairy cows do not vary with sampling techniques or phases of estrous cycle.}, journal = {Theriogenology}, volume = {214}, number = {}, pages = {298-306}, doi = {10.1016/j.theriogenology.2023.11.004}, pmid = {37976796}, issn = {1879-3231}, mesh = {Female ; Cattle ; Animals ; RNA, Ribosomal, 16S/genetics ; *Postpartum Period ; *Uterus/microbiology ; Estrous Cycle ; Estrus ; Bacteria ; }, abstract = {In this study, we aimed to compare uterine microbial profiles in postpartum dairy cows, determined by bacteriological culture and next-generation sequencing, using three uterine sampling techniques (swab, cytobrush, and lavage) and induced phases of the estrous cycle (estrus and diestrus). Fifteen healthy postpartum dairy cows at 53 ± 5 days postpartum were enrolled in the study. Uterine samples were collected during a fixed-time artificial insemination protocol. Viable bacteria were aerobically cultured from part of each sample, and bacterial isolates were identified through Sanger sequencing of the 16S rRNA gene. Total genomic DNA was extracted from the remainder of undiluted samples to quantify bacterial load using 16S rRNA qPCR and characterize the microbiome by metagenomic sequencing of the V1-V3 region of the 16S rRNA gene. Microbial profiles and composition were analyzed using the Shannon-Weaver diversity index and principal component analysis, respectively. Out of 87 samples, 88 % (77/87) were culture positive. The proportion of culture-positive uterine samples did not differ between sampling techniques (P = 0.39) or estrous cycle phases (P = 0.99). However, swab, cytobrush, and lavage techniques yielded 1.5, 9 and 9 times greater bacterial loads (P < 0.01), respectively, during diestrus than estrus phase. Moreover, during diestrus phase, the cytobrush method yielded 3 and 6 times more bacteria (P < 0.01) than both the lavage and swab methods. The most abundant bacterial genera identified from both bacteriological culture and metagenomic sequencing were Bacillus and Enterococcus, regardless of sampling technique or phases of the estrous cycle. Bacterial genera in moderate to low abundance through metagenomic sequencing included Streptococcus, Oscillospiraceae, and Lachnospiraceae. Notably, the uterine microbial profiles and composition, determined by metagenomic sequencing, did not differ by sampling techniques (P = 0.55 and P = 0.60, respectively) or estrous cycle phases (P = 0.34 and P = 0.17, respectively). In conclusion, our results suggest that any of the sampling techniques can be reliably used to study the uterine microbiome of healthy cows at random phases of the estrous cycle. However, it is important to consider potential differences in bacterial yield as a confounding factor.}, } @article {pmid37976735, year = {2024}, author = {Gao, Y and Liu, J and Fang, Y and Xu, X and Wang, F and Tang, Y and Yin, D and Cookson, AL and Zhu, W and Mao, S and Zhong, R}, title = {Straw-based compost cultivation disproportionally contributes to the environmental persistence of antibiotic resistance from raw cattle manure to organic vegetables.}, journal = {Microbiological research}, volume = {278}, number = {}, pages = {127540}, doi = {10.1016/j.micres.2023.127540}, pmid = {37976735}, issn = {1618-0623}, mesh = {Cattle ; Animals ; *Manure ; Vegetables ; *Composting ; Drug Resistance, Microbial/genetics ; Metagenome ; Anti-Bacterial Agents/pharmacology ; Soil/chemistry ; }, abstract = {Cattle manure, is a reservoir of antimicrobial resistance genes, but the mechanisms by which they migrate from farm to table remain obscure. Here, we chose Agaricus bisporus as a model vegetable to examine such migration and characterized the resistome in 112 metagenomes covering samples from raw manure, composting substrates, rhizosphere, and surfaces of mushrooms. A total of 1864 resistance genes, representing 113 unique mechanisms of resistance, were identified. Monensin treatment on beef specifically enriched fecal resistance genes within Moraxellaceae, but this effect did not persist in downstream mushrooms. Interestingly, we found that resistance genes were significantly more enriched on mushroom surfaces when cultivated with corn-based compost compared to rice and wheat, likely a result of the disproportional propagation of Pseudomonadaceae and varied ability of lateral gene transfer. Importantly, our sequence alignment together with genome-centric analysis observed that 89 resistance genes, mainly conferring resistance to drug and biocide (20.22%) and mercury (19.10%), were shared across all types of samples, indicating an efficient transmission of resistance in food production. Moreover, co-occurrence of genes conferring resistance to different compounds frequently occurred in parallel with microbial migration. Together, we present the influences of antibiotic treatment and straw-based composting on resistome along the mushroom production chain (from manure to straw-based compost, rhizosphere of compost cultivated mushroom and surface of mushroom) and highlighted the risks of resistance genes migration.}, } @article {pmid37975314, year = {2023}, author = {Liu, H and Ji, S and Fang, Y and Yi, X and Wu, F and Xing, F and Wang, C and Zhou, H and Xu, J and Sun, W}, title = {Microbiome Alteration in Lung Tissues of Tuberculosis Patients Revealed by Metagenomic Next-Generation Sequencing and Immune-Related Transcriptional Profile Identified by Transcriptome Sequencing.}, journal = {ACS infectious diseases}, volume = {9}, number = {12}, pages = {2572-2582}, pmid = {37975314}, issn = {2373-8227}, mesh = {Humans ; Transcriptome ; *Tuberculosis/microbiology ; Lung/microbiology ; *Microbiota ; High-Throughput Nucleotide Sequencing ; }, abstract = {This study explored alterations in the respiratory microbiome and transcriptome after Mycobacterium tuberculosis infection in tuberculosis (TB) patients. Metagenomic next-generation sequencing (mNGS) was adopted to reveal the microbiome in lung tissues from 110 TB and 25 nontuberculous (NonTB) patients. Transcriptome sequencing was performed in TB tissues (n = 3), tissues adjacent to TB (ParaTB, n = 3), and NonTB tissues (n = 3) to analyze differentially expressed genes (DEGs) and functional pathways. The microbial β diversity (p = 0.01325) in TB patients differed from that in the NonTB group, with 17 microbial species distinctively distributed. Eighty-three co-up-regulated DEGs were identified in the TB versus NonTB and the TB versus ParaTB comparison groups, and six were associated with immune response to Mtb. These DEGs were significantly enriched in the signaling pathways such as immune response, NF-κB, and B cell receptor. Data in the lung tissue microbiome and transcriptome in TB patients offer a sufficient understanding of the pathogenesis of TB.}, } @article {pmid37974926, year = {2023}, author = {Rathinam, AJ and Santhaseelan, H and Dahms, HU and Dinakaran, VT and Murugaiah, SG}, title = {Bioprospecting of unexplored halophilic actinobacteria against human infectious pathogens.}, journal = {3 Biotech}, volume = {13}, number = {12}, pages = {398}, pmid = {37974926}, issn = {2190-572X}, abstract = {Human pathogenic diseases received much attention recently due to their uncontrolled spread of antimicrobial resistance (AMR) which causes several threads every year. Effective alternate antimicrobials are urgently required to combat those disease causing infectious microbes. Halophilic actinobacteria revealed huge potentials and unexplored cultivable/non-cultivable actinobacterial species producing enormous antimicrobials have been proved in several genomics approaches. Potential gene clusters, PKS and NRPKS from Nocardia, Salinospora, Rhodococcus, and Streptomyces have wide range coding genes of secondary metabolites. Biosynthetic pathways identification via various approaches like genome mining, In silico, OSMAC (one strain many compound) analysis provides better identification of knowing the active metabolites using several databases like AMP, APD and CRAMPR, etc. Genome constellations of actinobacteria particularly the prediction of BGCs (Biosynthetic Gene Clusters) to mine the bioactive molecules such as pigments, biosurfactants and few enzymes have been reported for antimicrobial activity. Saltpan, saltlake, lagoon and haloalkali environment exploring potential actinobacterial strains Micromonospora, Kocuria, Pseudonocardia, and Nocardiopsis revealed several acids and ester derivatives with antimicrobial potential. Marine sediments and marine macro organisms have been found as significant population holders of potential actinobacterial strains. Deadly infectious diseases (IDs) including tuberculosis, ventilator-associated pneumonia and Candidiasis, have been targeted by halo-actinobacterial metabolites with promising results. Methicillin resistant Staphylococus aureus and virus like Encephalitic alphaviruses were potentially targeted by halophilic actinobacterial metabolites by the compound Homoseongomycin from sponge associated antinobacterium. In this review, we discuss the potential antimicrobial properties of various biomolecules extracted from the unexplored halophilic actinobacterial strains specifically against human infectious pathogens along with prospective genomic constellations.}, } @article {pmid37974518, year = {2023}, author = {Leontidou, K and Abad-Recio, IL and Rubel, V and Filker, S and Däumer, M and Thielen, A and Lanzén, A and Stoeck, T}, title = {Simultaneous analysis of seven 16S rRNA hypervariable gene regions increases efficiency in marine bacterial diversity detection.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {3484-3501}, doi = {10.1111/1462-2920.16530}, pmid = {37974518}, issn = {1462-2920}, support = {STO 414/19-1//Deutsche Forschungsgemeinschaft/ ; Fi 2089/3-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *High-Throughput Nucleotide Sequencing ; Bacteria/genetics ; Sequence Analysis, DNA ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Environmental DNA sequencing is the gold standard to reveal microbial community structures. In most applications, a one-fragment PCR approach is applied to amplify a taxonomic marker gene, usually a hypervariable region of the 16S rRNA gene. We used a new reverse complement (RC)-PCR-based assay that amplifies seven out of the nine hypervariable regions of the 16S rRNA gene, to interrogate bacterial communities in sediment samples collected from different coastal marine sites with an impact gradient. In parallel, we employed a traditional one-fragment analysis of the hypervariable V3-V4 region to investigate whether the RC-PCR reveals more of the 'unseen' diversity obtained by the one-fragment approach. As a benchmark for the full deck of diversity, we subjected the samples to PCR-free metagenomic sequencing. None of the two PCR-based approaches recorded the full taxonomic repertoire obtained from the metagenomics datasets. However, the RC-PCR approach detected 2.8 times more bacterial genera compared to the near-saturation sequenced V3-V4 samples. RC-PCR is an ideal compromise between the standard one-fragment approach and metagenomics sequencing and may guide future environmental sequencing studies, in which bacterial diversity is a central subject.}, } @article {pmid37974504, year = {2023}, author = {Mehić, S and Saltikov, C}, title = {Genome sequence and characterisation of a freshwater photoarsenotroph, Cereibacter azotoformans strain ORIO, isolated from sediments capable of cyclic light-dark arsenic oxidation and reduction.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {3738-3752}, doi = {10.1111/1462-2920.16542}, pmid = {37974504}, issn = {1462-2920}, support = {EAR-349366//National Science Foundation/ ; }, mesh = {*Arsenic ; *Arsenites ; Phylogeny ; Oxidation-Reduction ; Fresh Water ; Rhodobacter ; }, abstract = {A freshwater photosynthetic arsenite-oxidizing bacterium, Cereibacter azotoformans strain ORIO, was isolated from Owens River, CA, USA. The waters from Owens River are elevated in arsenic and serve as the headwaters to the Los Angeles Aqueduct. The complete genome sequence of strain ORIO is 4.8 Mb genome (68% G + C content) and comprises two chromosomes and six plasmids. Taxonomic analysis placed ORIO within the Cereibacter genus (formerly Rhodobacter). The ORIO genome contains arxB2 AB1 CD (encoding an arsenite oxidase), arxXSR (regulators) and several ars arsenic resistance genes all co-localised on a 136 kb plasmid, named pORIO3. Phylogenetic analysis of ArxA, the molybdenum-containing arsenite oxidase catalytic subunit, demonstrated photoarsenotrophy is likely to occur within members of the Alphaproteobacteria. ORIO is a mixotroph, oxidises arsenite to arsenate (As(V)) photoheterotrophically, and expresses arxA in cultures grown with arsenite. Further ecophysiology studies with Owens River sediment demonstrated the interconversion of arsenite and As(V) was dependent on light-dark cycling. arxA and arrA (As(V) respiratory reductase) genes were detected in the light-dark cycled sediment metagenomes suggesting syntrophic interactions among arsenotrophs. This work establishes C. azotoformans str. ORIO as a new model organism for studying photoarsenotrophy and light-dark arsenic biogeochemical cycling.}, } @article {pmid37974296, year = {2023}, author = {Sun, Y and Wang, M and Cao, L and Seim, I and Zhou, L and Chen, J and Wang, H and Zhong, Z and Chen, H and Fu, L and Li, M and Li, C and Sun, S}, title = {Mosaic environment-driven evolution of the deep-sea mussel Gigantidas platifrons bacterial endosymbiont.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {253}, pmid = {37974296}, issn = {2049-2618}, mesh = {Animals ; Phylogeny ; *Mytilidae/genetics/microbiology ; Bacteria ; Ecosystem ; Methane/metabolism ; Symbiosis ; *Hydrothermal Vents ; }, abstract = {BACKGROUND: The within-species diversity of symbiotic bacteria represents an important genetic resource for their environmental adaptation, especially for horizontally transmitted endosymbionts. Although strain-level intraspecies variation has recently been detected in many deep-sea endosymbionts, their ecological role in environmental adaptation, their genome evolution pattern under heterogeneous geochemical environments, and the underlying molecular forces remain unclear.

RESULTS: Here, we conducted a fine-scale metagenomic analysis of the deep-sea mussel Gigantidas platifrons bacterial endosymbiont collected from distinct habitats: hydrothermal vent and methane seep. Endosymbiont genomes were assembled using a pipeline that distinguishes within-species variation and revealed highly heterogeneous compositions in mussels from different habitats. Phylogenetic analysis separated the assemblies into three distinct environment-linked clades. Their functional differentiation follows a mosaic evolutionary pattern. Core genes, essential for central metabolic function and symbiosis, were conserved across all clades. Clade-specific genes associated with heavy metal resistance, pH homeostasis, and nitrate utilization exhibited signals of accelerated evolution. Notably, transposable elements and plasmids contributed to the genetic reshuffling of the symbiont genomes and likely accelerated adaptive evolution through pseudogenization and the introduction of new genes.

CONCLUSIONS: The current study uncovers the environment-driven evolution of deep-sea symbionts mediated by mobile genetic elements. Its findings highlight a potentially common and critical role of within-species diversity in animal-microbiome symbioses. Video Abstract.}, } @article {pmid37974294, year = {2023}, author = {Heston, SM and Lim, CSE and Ong, C and Chua, MC and Kelly, MS and Yeo, KT}, title = {Strain-resolved metagenomic analysis of the gut as a reservoir for bloodstream infection pathogens among premature infants in Singapore.}, journal = {Gut pathogens}, volume = {15}, number = {1}, pages = {55}, pmid = {37974294}, issn = {1757-4749}, support = {K12 HD105253/HD/NICHD NIH HHS/United States ; K23 AI135090/AI/NIAID NIH HHS/United States ; K23-AI135090/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Gut dysbiosis contributes to the high risk of bloodstream infection (BSI) among premature infants. Most prior studies of the premature infant gut microbiota were conducted in Western countries and prior to development of current tools for strain-resolved analysis.

METHODS: We performed metagenomic sequencing of weekly fecal samples from 75 premature infants at a single hospital in Singapore. We evaluated associations between clinical factors and gut microbiota composition using PERMANOVA and mixed effects linear regression. We used inStrain to perform strain-level analyses evaluating for gut colonization by BSI-causing strains.

RESULTS: Median (interquartile range) gestation was 27 (25, 29) weeks, and 63% of infants were born via Cesarean section. Antibiotic exposures (PERMANOVA; R[2] = 0.017, p = 0.001) and postnatal age (R[2] = 0.015, p = 0.001) accounted for the largest amount of variability in gut microbiota composition. Increasing postnatal age was associated with higher relative abundances of several common pathogens (Enterococcus faecalis: p < 0.0001; Escherichia coli: p < 0.0001; Klebsiella aerogenes: p < 0.0001; Klebsiella pneumoniae: p < 0.0001). Antibiotic exposures were generally associated with lower relative abundances of both frequently beneficial bacteria (e.g., Bifidobacterium species) and common enteric pathogens (e.g., Enterobacter, Klebsiella species). We identified strains identical to the blood culture isolate in fecal samples from 12 of 16 (75%) infants who developed BSI, including all infections caused by typical enteric bacteria.

CONCLUSIONS: Antibiotic exposures were the dominant modifiable factor affecting gut microbiota composition in a large cohort of premature infants from South-East Asia. Strain-resolved analyses indicate that the gut is an important reservoir for organisms causing BSI among premature infants.}, } @article {pmid37974273, year = {2023}, author = {Zhao, X and Qin, X and Jing, X and Wang, T and Qiao, Q and Li, X and Yan, P and Li, Y}, title = {Key genes of electron transfer, the nitrogen cycle and tetracycline removal in bioelectrochemical systems.}, journal = {Biotechnology for biofuels and bioproducts}, volume = {16}, number = {1}, pages = {174}, pmid = {37974273}, issn = {2731-3654}, support = {42007121//National Natural Science Foundation of China/ ; 41977133//National Natural Science Foundation of China/ ; 2020L0536//Shanxi Provincial Education Department/ ; }, abstract = {BACKGROUND: Soil microbial fuel cells (MFCs) can remove antibiotics and antibiotic resistance genes (ARGs) simultaneously, but their removal mechanism is unclear. In this study, metagenomic analysis was employed to reveal the functional genes involved in degradation, electron transfer and the nitrogen cycle in the soil MFC.

RESULTS: The results showed that the soil MFC effectively removed tetracycline in the overlapping area of the cathode and anode, which was 64% higher than that of the control. The ARGs abundance increased by 14% after tetracycline was added (54% of the amplified ARGs belonged to efflux pump genes), while the abundance decreased by 17% in the soil MFC. Five potential degraders of tetracycline were identified, especially the species Phenylobacterium zucineum, which could secrete the 4-hydroxyacetophenone monooxygenase encoded by EC 1.14.13.84 to catalyse deacylation or decarboxylation. Bacillus, Geobacter, Anaerolinea, Gemmatirosa kalamazoonesis and Steroidobacter denitrificans since ubiquinone reductase (encoded by EC 1.6.5.3), succinate dehydrogenase (EC 1.3.5.1), Coenzyme Q-cytochrome c reductase (EC 1.10.2.2), cytochrome-c oxidase (EC 1.9.3.1) and electron transfer flavoprotein-ubiquinone oxidoreductase (EC 1.5.5.1) served as complexes I, II, III, IV and ubiquinone, respectively, to accelerate electron transfer. Additionally, nitrogen metabolism-related gene abundance increased by 16% to support the microbial efficacy in the soil MFC, and especially EC 1.7.5.1, and coding the mutual conversion between nitrite and nitrate was obviously improved.

CONCLUSIONS: The soil MFC promoted functional bacterial growth, increased functional gene abundance (including nitrogen cycling, electron transfer, and biodegradation), and facilitated antibiotic and ARG removal. Therefore, soil MFCs have expansive prospects in the remediation of antibiotic-contaminated soil. This study provides insight into the biodegradation mechanism at the gene level in soil bioelectrochemical remediation.}, } @article {pmid37974247, year = {2023}, author = {Gonçalves, OS and Creevey, CJ and Santana, MF}, title = {Designing a synthetic microbial community through genome metabolic modeling to enhance plant-microbe interaction.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {81}, pmid = {37974247}, issn = {2524-6372}, support = {88887.696147/2022-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; APQ-02381-21//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 402644/2021-2//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; }, abstract = {BACKGROUND: Manipulating the rhizosphere microbial community through beneficial microorganism inoculation has gained interest in improving crop productivity and stress resistance. Synthetic microbial communities, known as SynComs, mimic natural microbial compositions while reducing the number of components. However, achieving this goal requires a comprehensive understanding of natural microbial communities and carefully selecting compatible microorganisms with colonization traits, which still pose challenges. In this study, we employed multi-genome metabolic modeling of 270 previously described metagenome-assembled genomes from Campos rupestres to design a synthetic microbial community to improve the yield of important crop plants.

RESULTS: We used a targeted approach to select a minimal community (MinCom) encompassing essential compounds for microbial metabolism and compounds relevant to plant interactions. This resulted in a reduction of the initial community size by approximately 4.5-fold. Notably, the MinCom retained crucial genes associated with essential plant growth-promoting traits, such as iron acquisition, exopolysaccharide production, potassium solubilization, nitrogen fixation, GABA production, and IAA-related tryptophan metabolism. Furthermore, our in-silico selection for the SymComs, based on a comprehensive understanding of microbe-microbe-plant interactions, yielded a set of six hub species that displayed notable taxonomic novelty, including members of the Eremiobacterota and Verrucomicrobiota phyla.

CONCLUSION: Overall, the study contributes to the growing body of research on synthetic microbial communities and their potential to enhance agricultural practices. The insights gained from our in-silico approach and the selection of hub species pave the way for further investigations into the development of tailored microbial communities that can optimize crop productivity and improve stress resilience in agricultural systems.}, } @article {pmid37974103, year = {2023}, author = {Khan, FA and Pandupuspitasari, NS and Huang, C and Negara, W and Ahmed, B and Putri, EM and Lestari, P and Priyatno, TP and Prima, A and Restitrisnani, V and Surachman, M and Akhadiarto, S and Darmawan, IWA and Wahyuni, DS and Herdis, H}, title = {Unlocking gut microbiota potential of dairy cows in varied environmental conditions using shotgun metagenomic approach.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {344}, pmid = {37974103}, issn = {1471-2180}, mesh = {Female ; Cattle ; Animals ; *Lactation ; Diet/veterinary ; *Gastrointestinal Microbiome ; Milk Proteins ; Gases ; Methane/metabolism ; }, abstract = {Food security and environmental pollution are major concerns for the expanding world population, where farm animals are the largest source of dietary proteins and are responsible for producing anthropogenic gases, including methane, especially by cows. We sampled the fecal microbiomes of cows from varying environmental regions of Pakistan to determine the better-performing microbiomes for higher yields and lower methane emissions by applying the shotgun metagenomic approach. We selected managed dairy farms in the Chakwal, Salt Range, and Patoki regions of Pakistan, and also incorporated animals from local farmers. Milk yield and milk fat, and protein contents were measured and correlated with microbiome diversity and function. The average milk protein content from the Salt Range farms was 2.68%, with an average peak milk yield of 45 litters/head/day, compared to 3.68% in Patoki farms with an average peak milk yield of 18 litters/head/day. Salt-range dairy cows prefer S-adenosyl-L-methionine (SAMe) to S-adenosyl-L-homocysteine (SAH) conversion reactions and are responsible for low milk protein content. It is linked to Bacteroides fragilles which account for 10% of the total Bacteroides, compared to 3% in the Patoki region. The solid Non-Fat in the salt range was 8.29%, whereas that in patoki was 6.34%. Moreover, Lactobacillus plantarum high abundance in Salt Range provided propionate as alternate sink to [H], and overcoming a Methanobrevibacter ruminantium high methane emissions in the Salt Range. Furthermore, our results identified ruminant fecal microbiomes that can be used as fecal microbiota transplants (FMT) to high-methane emitters and low-performing herds to increase farm output and reduce the environmental damage caused by anthropogenic gases emitted by dairy cows.}, } @article {pmid37973978, year = {2023}, author = {Grégoire, DS and George, NA and Hug, LA}, title = {Microbial methane cycling in a landfill on a decadal time scale.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7402}, pmid = {37973978}, issn = {2041-1723}, mesh = {*Solid Waste ; *Methane/metabolism ; Waste Disposal Facilities ; Ecosystem ; Oxidation-Reduction ; }, abstract = {Landfills generate outsized environmental footprints due to microbial degradation of organic matter in municipal solid waste, which produces the potent greenhouse gas methane. With global solid waste production predicted to increase substantially in the next few decades, there is a pressing need to better understand the temporal dynamics of biogeochemical processes that control methane cycling in landfills. Here, we use metagenomic approaches to characterize microbial methane cycling in waste that was landfilled over 39 years. Our analyses indicate that newer waste supports more diverse communities with similar composition compared to older waste, which contains lower diversity and more varied communities. Older waste contains primarily autotrophic organisms with versatile redox metabolisms, whereas newer waste is dominated by anaerobic fermenters. Methane-producing microbes are more abundant, diverse, and metabolically versatile in new waste compared to old waste. Our findings indicate that predictive models for methane emission in landfills overlook methane oxidation in the absence of oxygen, as well as certain microbial lineages that can potentially contribute to methane sinks in diverse habitats.}, } @article {pmid37973916, year = {2023}, author = {Liu, R and Zou, Y and Wang, WQ and Chen, JH and Zhang, L and Feng, J and Yin, JY and Mao, XY and Li, Q and Luo, ZY and Zhang, W and Wang, DM}, title = {Gut microbial structural variation associates with immune checkpoint inhibitor response.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7421}, pmid = {37973916}, issn = {2041-1723}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Immune Checkpoint Inhibitors/pharmacology/therapeutic use ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics ; *Neoplasms/genetics ; }, abstract = {The gut microbiota may have an effect on the therapeutic resistance and toxicity of immune checkpoint inhibitors (ICIs). However, the associations between the highly variable genomes of gut bacteria and the effectiveness of ICIs remain unclear, despite the fact that merely a few gene mutations between similar bacterial strains may cause significant phenotypic variations. Here, using datasets from the gut microbiome of 996 patients from seven clinical trials, we systematically identify microbial genomic structural variants (SVs) using SGV-Finder. The associations between SVs and response, progression-free survival, overall survival, and immune-related adverse events are systematically explored by metagenome-wide association analysis and replicated in different cohorts. Associated SVs are located in multiple species, including Akkermansia muciniphila, Dorea formicigenerans, and Bacteroides caccae. We find genes that encode enzymes that participate in glucose metabolism be harbored in these associated regions. This work uncovers a nascent layer of gut microbiome heterogeneity that is correlated with hosts' prognosis following ICI treatment and represents an advance in our knowledge of the intricate relationships between microbiota and tumor immunotherapy.}, } @article {pmid37973867, year = {2023}, author = {Goossens, P and Spooren, J and Baremans, KCM and Andel, A and Lapin, D and Echobardo, N and Pieterse, CMJ and Van den Ackerveken, G and Berendsen, RL}, title = {Obligate biotroph downy mildew consistently induces near-identical protective microbiomes in Arabidopsis thaliana.}, journal = {Nature microbiology}, volume = {8}, number = {12}, pages = {2349-2364}, pmid = {37973867}, issn = {2058-5276}, support = {grant no. 024.004.014//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; grant no. OCENW.GROOT.2019.063//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; t no. OCENW.GROOT.2019.063//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, mesh = {*Arabidopsis/genetics/microbiology ; Plant Diseases/microbiology ; *Oomycetes/genetics ; *Arabidopsis Proteins ; *Microbiota ; }, abstract = {Hyaloperonospora arabidopsidis (Hpa) is an obligately biotrophic downy mildew that is routinely cultured on Arabidopsis thaliana hosts that harbour complex microbiomes. We hypothesized that the culturing procedure proliferates Hpa-associated microbiota (HAM) in addition to the pathogen and exploited this model system to investigate which microorganisms consistently associate with Hpa. Using amplicon sequencing, we found nine bacterial sequence variants that are shared between at least three out of four Hpa cultures in the Netherlands and Germany and comprise 34% of the phyllosphere community of the infected plants. Whole-genome sequencing showed that representative HAM bacterial isolates from these distinct Hpa cultures are isogenic and that an additional seven published Hpa metagenomes contain numerous sequences of the HAM. Although we showed that HAM benefit from Hpa infection, HAM negatively affect Hpa spore formation. Moreover, we show that pathogen-infected plants can selectively recruit HAM to both their roots and shoots and form a soil-borne infection-associated microbiome that helps resist the pathogen. Understanding the mechanisms by which infection-associated microbiomes are formed might enable breeding of crop varieties that select for protective microbiomes.}, } @article {pmid37973864, year = {2023}, author = {Littlejohn, PT and Metcalfe-Roach, A and Cardenas Poire, E and Holani, R and Bar-Yoseph, H and Fan, YM and Woodward, SE and Finlay, BB}, title = {Multiple micronutrient deficiencies in early life cause multi-kingdom alterations in the gut microbiome and intrinsic antibiotic resistance genes in mice.}, journal = {Nature microbiology}, volume = {8}, number = {12}, pages = {2392-2405}, pmid = {37973864}, issn = {2058-5276}, mesh = {Humans ; Child ; Animals ; Mice ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/genetics ; *Malnutrition ; Drug Resistance, Microbial ; Bacteria/genetics ; Micronutrients ; }, abstract = {Globally, ~340 million children suffer from multiple micronutrient deficiencies, accompanied by high pathogenic burden and death due to multidrug-resistant bacteria. The microbiome is a reservoir of antimicrobial resistance (AMR), but the implications of undernutrition on the resistome is unclear. Here we used a postnatal mouse model that is deficient in multiple micronutrients (that is, zinc, folate, iron, vitamin A and vitamin B12 deficient) and shotgun metagenomic sequencing of faecal samples to characterize gut microbiome structure and functional potential, and the resistome. Enterobacteriaceae were enriched in micronutrient-deficient mice compared with mice fed an isocaloric experimental control diet. The mycobiome and virome were also altered with multiple micronutrient deficiencies including increased fungal pathogens such as Candida dubliniensis and bacteriophages. Despite being antibiotic naïve, micronutrient deficiency was associated with increased enrichment of genes and gene networks encoded by pathogenic bacteria that are directly or indirectly associated with intrinsic antibiotic resistance. Bacterial oxidative stress was associated with intrinsic antibiotic resistance in these mice. This analysis reveals multi-kingdom alterations in the gut microbiome as a result of co-occurring multiple micronutrient deficiencies and the implications for antibiotic resistance.}, } @article {pmid37973815, year = {2023}, author = {Lou, YC and Rubin, BE and Schoelmerich, MC and DiMarco, KS and Borges, AL and Rovinsky, R and Song, L and Doudna, JA and Banfield, JF}, title = {Infant microbiome cultivation and metagenomic analysis reveal Bifidobacterium 2'-fucosyllactose utilization can be facilitated by coexisting species.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7417}, pmid = {37973815}, issn = {2041-1723}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; }, mesh = {Female ; Child ; Humans ; Infant ; *Bifidobacterium/genetics/metabolism ; Trisaccharides/metabolism ; Milk, Human/chemistry ; Oligosaccharides/metabolism ; *Microbiota ; }, abstract = {The early-life gut microbiome development has long-term health impacts and can be influenced by factors such as infant diet. Human milk oligosaccharides (HMOs), an essential component of breast milk that can only be metabolized by some beneficial gut microorganisms, ensure proper gut microbiome establishment and infant development. However, how HMOs are metabolized by gut microbiomes is not fully elucidated. Isolate studies have revealed the genetic basis for HMO metabolism, but they exclude the possibility of HMO assimilation via synergistic interactions involving multiple organisms. Here, we investigate microbiome responses to 2'-fucosyllactose (2'FL), a prevalent HMO and a common infant formula additive, by establishing individualized microbiomes using fecal samples from three infants as the inocula. Bifidobacterium breve, a prominent member of infant microbiomes, typically cannot metabolize 2'FL. Using metagenomic data, we predict that extracellular fucosidases encoded by co-existing members such as Ruminococcus gnavus initiate 2'FL breakdown, thus critical for B. breve's growth. Using both targeted co-cultures and by supplementation of R. gnavus into one microbiome, we show that R. gnavus can promote extensive growth of B. breve through the release of lactose from 2'FL. Overall, microbiome cultivation combined with genome-resolved metagenomics demonstrates that HMO utilization can vary with an individual's microbiome.}, } @article {pmid37973062, year = {2023}, author = {Diop, S and Pons, S and Kapandji, N and Kallel, H and Woerther, PL and Mekontso-Dessap, A and Rodriguez, C and Mongardon, N and Roujansky, A and Mounier, R}, title = {Biofilm Assessment and Metagenomic Analysis of Venoarterial Extracorporeal Membrane Oxygenation Cannulas and Membrane Oxygenators.}, journal = {ASAIO journal (American Society for Artificial Internal Organs : 1992)}, volume = {}, number = {}, pages = {}, doi = {10.1097/MAT.0000000000002095}, pmid = {37973062}, issn = {1538-943X}, abstract = {Venoarterial extracorporeal membrane oxygenation (VA-ECMO) exposes the patient to infectious complications related to the cannulas or the site of insertion. The aim of the current study was to investigate and compare the prevalence of cannula and membrane oxygenators colonization using three different methods: microbiological culture, scanning electron microscopy, and metagenomic (rRNA 16S analysis). A monocentric prospective study was conducted between December 2017 and June 2018. Consecutive patients undergoing VA-ECMO support for refractory cardiac arrest or cardiogenic shock were included. Ten patients were included with a median age of 64 (52-62) years. Venoarterial extracorporeal membrane oxygenation was inserted for refractory cardiac arrest in five (50%), cardiogenic shock in four (40%), and self-poisoning in one (10%) cases. Microbiological culture of all (8/8, 100%) membrane oxygenators was negative, whereas all (10/10, 100%) were colonized by biofilm, and eight (8/9, 89%) presented bacterial DNA. Three (3/9, 33%) arterial and venous cannulas were positive in culture and seven (7/9, 78%) were colonized by biofilm, respectively. Seven (7/9, 78%) arterial and four (4/9, 44%) venous cannulas presented bacterial DNA. Colonization of cannulas and membranes is more frequent when assessed by electron microscopy or metagenomic analysis than with culture. Membrane oxygenators are more often colonized than cannulas.}, } @article {pmid37972872, year = {2024}, author = {Tekin, B and Enninga, EAL and Norgan, AP and Erickson, LA and Vanderbilt, C and Gupta, S and Guo, R}, title = {Panviral metagenomic sequencing provides further evidence for human papillomavirus 42 association with digital papillary adenocarcinoma.}, journal = {Human pathology}, volume = {143}, number = {}, pages = {77-80}, doi = {10.1016/j.humpath.2023.10.004}, pmid = {37972872}, issn = {1532-8392}, mesh = {Humans ; *Adenocarcinoma, Clear Cell ; *Adenocarcinoma, Papillary/genetics ; DNA, Viral/genetics ; *Human Papillomavirus Viruses ; Papillomaviridae/genetics ; *Papillomavirus Infections ; Metagenomics ; }, } @article {pmid37972721, year = {2023}, author = {Russo, MA and Garaci, E and Frustaci, A and Fini, M and Costantini, C and Oikonomou, V and Nunzi, E and Puccetti, P and Romani, L}, title = {Host-microbe tryptophan partitioning in cardiovascular diseases.}, journal = {Pharmacological research}, volume = {198}, number = {}, pages = {106994}, doi = {10.1016/j.phrs.2023.106994}, pmid = {37972721}, issn = {1096-1186}, mesh = {Humans ; *Tryptophan ; *Cardiovascular Diseases ; Genomics/methods ; Proteomics/methods ; Gene Expression Profiling/methods ; Metabolomics/methods ; }, abstract = {The functional interdependencies between the molecular components of a biological process demand for a network medicine platform that integrates systems biology and network science, to explore the interactions among biological components in health and disease. Access to large-scale omics datasets (genomics, transcriptomics, proteomics, metabolomics, metagenomics, phenomics, etc.) has significantly advanced our opportunity along this direction. Studies utilizing these techniques have begun to provide us with a deeper understanding of how the interaction between the intestinal microbes and their host affects the cardiovascular system in health and disease. Within the framework of a multiomics network approach, we highlight here how tryptophan metabolism may orchestrate the host-microbes interaction in cardiovascular diseases and the implications for precision medicine and therapeutics, including nutritional interventions.}, } @article {pmid37972468, year = {2024}, author = {Lu, Y and Wu, Y and Huang, M and Chen, J and Zhang, Z and Li, J and Yang, R and Liu, Y and Cai, S}, title = {Fuzhengjiedu formula exerts protective effect against LPS-induced acute lung injury via gut-lung axis.}, journal = {Phytomedicine : international journal of phytotherapy and phytopharmacology}, volume = {123}, number = {}, pages = {155190}, doi = {10.1016/j.phymed.2023.155190}, pmid = {37972468}, issn = {1618-095X}, abstract = {BACKGROUND: Acute lung injury (ALI) is distinguished by rapid and severe respiratory distress and prolonged hypoxemia. A traditional Chinese medicine (TCM), known as the Fuzhengjiedu formula (FZJDF), has been shown to have anti-inflammatory benefits in both clinical and experimental studies. The precise underlying processes, nevertheless, are yet unclear.

PURPOSE: This study sought to enlighten the protective mechanism of FZJDF in ALI through the standpoint of the gut-lung crosstalk.

METHODS: The impact of FZJDF on lipopolysaccharide (LPS)-induced ALI murine model were investigated, and the lung injury score, serum interleukin-1β (IL-1β), and tumor necrosis factor-α (TNF-α) expression were measured to confirm its anti-inflammatory effects. Additionally, gut microbiota analysis and serum and fecal samples metabolomics were performed using metagenomic sequencing and high-performance liquid chromatography-quadrupole-time-of-flight mass spectrometry, respectively.

RESULTS: FZJDF significantly induced histopathological changes caused by LPS-induced ALI as well as downregulated the serum concentration of IL-1β and TNF-α. Furthermore, FZJDF had an effect in gut microbiota disturbances, and linear discriminant effect size analysis identified signal transduction, cell motility, and amino acid metabolism as the potential mechanisms of action in the FZJDF-treated group. Several metabolites in the LPS and FZJDF groups were distinguished by untargeted metabolomic analysis. Correlations were observed between the relative abundance of microbiota and metabolic products. Comprehensive network analysis revealed connections among lung damage, gut microbes, and metabolites. The expression of glycine, serine, glutamate, cysteine, and methionine in the lung and colon tissues was dysregulated in LPS-induced ALI, and FZJDF reversed these trends.

CONCLUSION: This study revealed that FZJDF considerably protected against LPS-induced ALI in mice by regulating amino acid metabolism via the gut-microbiota-lung axis and offered thorough and in-depth knowledge of the multi-system linkages of systemic illnesses.}, } @article {pmid37972321, year = {2023}, author = {Liu, J and Tan, Y and Song, S and Liu, J and Zou, S and Luo, M and Guo, W and Liang, K}, title = {Case Report: Giant Oral Ulcers Attributed to Cytomegalovirus Infection in a Patient with AIDS.}, journal = {The American journal of tropical medicine and hygiene}, volume = {109}, number = {6}, pages = {1274-1276}, doi = {10.4269/ajtmh.22-0775}, pmid = {37972321}, issn = {1476-1645}, mesh = {Humans ; *Oral Ulcer/etiology ; *Acquired Immunodeficiency Syndrome/complications ; *Cytomegalovirus Infections/complications/diagnosis ; Staining and Labeling ; }, abstract = {Oral ulcers are often neglected in patients with AIDS. However, giant oral ulcers are uncommon and are usually suspected to be malignant lesions. Our study presents a case of giant ulcers in an AIDS patient that were initially suspected to be oral cancer. To assist with diagnosis, conventional microbiological tests, metagenomic next-generation sequencing, and a pathological examination were conducted on oral lesion biopsy specimens. The case was finally confirmed via hematoxylin-eosin staining and immunohistochemical staining to be a cytomegalovirus infection.}, } @article {pmid37972312, year = {2023}, author = {McMinn, RJ and Chacon, A and Rückert, C and Scorza, V and Young, MC and Worthington, D and Lamb, MM and Medrano, RE and Harris, EK and Arias, K and Lopez, MR and Asturias, EJ and Foy, BD and Stenglein, MD and Olson, D and Ebel, GD}, title = {Evaluation of Vector-Enabled Xenosurveillance in Rural Guatemala.}, journal = {The American journal of tropical medicine and hygiene}, volume = {109}, number = {6}, pages = {1303-1310}, doi = {10.4269/ajtmh.22-0774}, pmid = {37972312}, issn = {1476-1645}, mesh = {Animals ; Humans ; Guatemala/epidemiology ; Prospective Studies ; Mosquito Vectors ; *Culex ; *Aedes ; *Viruses ; Mammals ; Chickens ; }, abstract = {Surveillance methods that permit rapid detection of circulating pathogens in low-resource settings are desperately needed. In this study, we evaluated a mosquito bloodmeal-based surveillance method ("xenosurveillance") in rural Guatemala. Twenty households from two villages (Los Encuentros and Chiquirines) in rural southwest Guatemala were enrolled and underwent weekly prospective surveillance from August 2019 to December 2019 (16 weeks). When febrile illness was reported in a household, recently blood-fed mosquitoes were collected from within dwellings and blood samples taken from each member of the household. Mosquitoes were identified to species and blood sources identified by sequencing. Shotgun metagenomic sequencing was used to identify circulating viruses. Culex pipiens (60.9%) and Aedes aegypti (18.6%) were the most abundant mosquitoes collected. Bloodmeal sources were most commonly human (32.6%) and chicken (31.6%), with various other mammal and avian hosts detected. Several mosquito-specific viruses were detected, including Culex orthophasma virus. Human pathogens were not detected. Therefore, xenosurveillance may require more intensive sampling to detect human pathogens in Guatemala and ecologically similar localities in Central America.}, } @article {pmid37972223, year = {2023}, author = {Zhang, L and Wang, B and Su, Y and Wu, D and Wang, Z and Li, K and Xie, B}, title = {Pathogenic Bacteria Are the Primary Determinants Shaping PM2.5-Borne Resistomes in the Municipal Food Waste Treatment System.}, journal = {Environmental science & technology}, volume = {57}, number = {48}, pages = {19965-19978}, doi = {10.1021/acs.est.3c04681}, pmid = {37972223}, issn = {1520-5851}, mesh = {Humans ; *Genes, Bacterial ; Food ; RNA, Ribosomal, 16S ; *Refuse Disposal ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Particulate Matter ; }, abstract = {Bioaerosol pollution poses a substantial threat to human health during municipal food waste (FW) recycling. However, bioaerosol-borne antibiotic-resistant genes (ARGs) have received little attention. Herein, 48 metagenomic data were applied to study the prevalence of PM2.5-borne ARGs in and around full-scale food waste treatment plants (FWTPs). Overall, FWTP PM2.5 (2.82 ± 1.47 copies/16S rRNA gene) harbored comparable total abundance of ARGs to that of municipal wastewater treatment plant PM2.5 (WWTP), but was significantly enriched with the multidrug type (e.g., AdeC/I/J; p < 0.05), especially the abundant multidrug ARGs could serve as effective indicators to define resistome profiles of FWTPs (Random Forest accuracy >92%). FWTP PM2.5 exhibited a decreasing enrichment of total ARGs along the FWTP-downwind-boundary gradient, eventually reaching levels comparable to urban PM2.5 (1.46 ± 0.21 copies/16S rRNA gene, N = 12). The combined analysis of source-tracking, metagenome-assembled genomes (MAGs), and culture-based testing provides strong evidence that Acinetobacter johnsonii-dominated pathogens contributed significantly to shaping and disseminating multidrug ARGs, while abiotic factors (i.e., SO4[2-]) indirectly participated in these processes, which deserves more attention in developing strategies to mitigate airborne ARGs. In addition, the exposure level of FWTP PM2.5-borne resistant pathogens was about 5-11 times higher than those in urban PM2.5, and could be more severe than hospital PM2.5 in certain scenarios (<41.53%). This work highlights the importance of FWTP in disseminating airborne multidrug ARGs and the need for re-evaluating the air pollution induced by municipal FWTP in public health terms.}, } @article {pmid37972203, year = {2023}, author = {Zheng, L and Wang, H and Lin, J and Zhou, Y and Xiao, J and Li, K}, title = {Population genomics provides insights into the genetic diversity and adaptation of the Pieris rapae in China.}, journal = {PloS one}, volume = {18}, number = {11}, pages = {e0294521}, pmid = {37972203}, issn = {1932-6203}, mesh = {Humans ; Animals ; *Butterflies/genetics ; Metagenomics ; Biodiversity ; Temperature ; *Brassica ; Genetic Variation ; }, abstract = {The cabbage white butterfly (Pieris rapae), a major agricultural pest, has become one of the most abundant and destructive butterflies in the world. It is widely distributed in a large variety of climates and terrains of China due to its strong adaptability. To gain insight into the population genetic characteristics of P. rapae in China, we resequenced the genome of 51 individuals from 19 areas throughout China. Using population genomics approaches, a dense variant map of P. rapae was observed, indicating a high level of polymorphism that could result in adaptation to a changing environment. The feature of the genetic structure suggested considerable genetic admixture in different geographical groups. Additionally, our analyses suggest that physical barriers may have played a more important role than geographic distance in driving genetic differentiation. Population history showed the effective population size of P. rapae was greatly affected by global temperature changes, with mild periods (i.e., temperatures warmer than those during glaciation but not excessively hot) leading to an increase in population size. Furthermore, by comparing populations from south and north China, we have identified selected genes related to sensing temperature, growth, neuromodulation and immune response, which may reveal the genetic basis of adaptation to different environments. Our study is the first to illustrate the genetic signatures of P. rapae in China at the population genomic level, providing fundamental knowledge of the genetic diversity and adaptation of P. rapae.}, } @article {pmid37972047, year = {2023}, author = {Fakhraldeen, SA and Al-Haddad, S and Habibi, N and Alagarsamy, S and F K Habeebullah, S and Ali, AK and Al-Zakri, WM}, title = {Diversity and spatiotemporal variations in bacterial and archaeal communities within Kuwaiti territorial waters of the Northwest Arabian Gulf.}, journal = {PloS one}, volume = {18}, number = {11}, pages = {e0291167}, pmid = {37972047}, issn = {1932-6203}, mesh = {*Archaea/genetics ; Kuwait ; Ecosystem ; *Cyanobacteria/genetics ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Kuwaiti territorial waters of the northwest Arabian Gulf represent a unique aquatic ecosystem prone to various environmental and anthropogenic stressors that pose significant constraints on the resident biota which must withstand extreme temperatures, salinity levels, and reducing conditions, among other factors to survive. Such conditions create the ideal environment for investigations into novel functional genetic adaptations of resident organisms. Firstly, however, it is essential to identify said organisms and understand the dynamic nature of their existence. Thus, this study provides the first comprehensive analysis of bacterial and archaeal community structures in the unique waters of Kuwait located in the Northwest Arabian Gulf and analyzes their variations with respect to depth, season, and location, as well as their susceptibility to changes in abundance with respect to various physicochemical parameters. Importantly, this study is the first of its kind to utilize a shotgun metagenomics approach with sequencing performed at an average depth of 15 million paired end reads per sample, which allows for species-level community profiling and sets the framework for future functional genomic investigations. Results showed an approximately even abundance of both archaeal (42.9%) and bacterial (57.1%) communities, but significantly greater diversity among the bacterial population, which predominantly consisted of members of the Proteobacteria, Cyanobacteria, and Bacteroidetes phyla in decreasing order of abundance. Little to no significant variations as assessed by various metrics including alpha and beta diversity analyses were observed in the abundance of archaeal and bacterial populations with respect to depth down the water column. Furthermore, although variations in differential abundance of key genera were detected at each of the three sampling locations, measurements of species richness and evenness revealed negligible variation (ANOVA p<0.05) and only a moderately defined community structure (ANOSIM r2 = 0.243; p>0.001) between the various locations. Interestingly, abundance of archaeal community members showed a significant increase (log2 median ratio of RA = 2.6) while the bacterial population showed a significant decrease (log2 median ratio = -1.29) in the winter season. These findings were supported by alpha and beta diversity analyses as well (ANOSIM r2 = 0.253; p>0.01). Overall, this study provides the first in-depth analysis of both bacterial and archaeal community structures developed using a shotgun metagenomic approach in the waters of the Northwest Arabian Gulf thus providing a framework for future investigations of functional genetic adaptations developed by resident biota attempting to survive in the uniquely extreme conditions to which they are exposed.}, } @article {pmid37971255, year = {2023}, author = {Martínez-Alvarez, L and Ramond, J-B and Vikram, S and León-Sobrino, C and Maggs-Kölling, G and Cowan, DA}, title = {With a pinch of salt: metagenomic insights into Namib Desert salt pan microbial mats and halites reveal functionally adapted and competitive communities.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {12}, pages = {e0062923}, pmid = {37971255}, issn = {1098-5336}, support = {113308//National Research Foundation (NRF)/ ; }, mesh = {*Bacteria/genetics ; Desert Climate ; Soil Microbiology ; Sodium Chloride ; *Microbiota ; }, abstract = {The hyperarid Namib Desert is one of the oldest deserts on Earth. It contains multiple clusters of playas which are saline-rich springs surrounded by halite evaporites. Playas are of great ecological importance, and their indigenous (poly)extremophilic microorganisms are potentially involved in the precipitation of minerals such as carbonates and sulfates and have been of great biotechnological importance. While there has been a considerable amount of microbial ecology research performed on various Namib Desert edaphic microbiomes, little is known about the microbial communities inhabiting its multiple playas. In this work, we provide a comprehensive taxonomic and functional potential characterization of the microbial, including viral, communities of sediment mats and halites from two distant salt pans of the Namib Desert, contributing toward a better understanding of the ecology of this biome.}, } @article {pmid37971224, year = {2023}, author = {Williams, AD and Rousham, E and Neal, AL and Amin, MB and Hobman, JL and Stekel, D and Islam, MA}, title = {Impact of contrasting poultry exposures on human, poultry, and wastewater antibiotic resistomes in Bangladesh.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0176323}, pmid = {37971224}, issn = {2165-0497}, support = {NE/N019555/1//UK Research and Innovation (UKRI)/ ; NE/N01961X/1//UKRI | Natural Environment Research Council (NERC)/ ; }, mesh = {Animals ; Humans ; *Poultry ; *Drug Resistance, Bacterial/genetics ; Wastewater ; Anti-Bacterial Agents/pharmacology ; Bangladesh ; }, abstract = {Through the use of DNA sequencing, our study shows that there is no significant difference in the antibiotic resistance genes found in stool samples taken from individuals with high exposure to poultry routinely fed antibiotics and those without such exposure. This finding is significant as it suggests limited transmission of antibiotic resistance genes between poultry and humans in these circumstances. However, our research also demonstrates that commercially reared poultry are more likely to possess resistance genes to antibiotics commonly administered on medium-sized farms. Additionally, our study highlights the under-explored potential of wastewater as a source of various antibiotic resistance genes, some of which are clinically relevant.}, } @article {pmid37971141, year = {2024}, author = {Pečnerová, P and Lord, E and Garcia-Erill, G and Hanghøj, K and Rasmussen, MS and Meisner, J and Liu, X and van der Valk, T and Santander, CG and Quinn, L and Lin, L and Liu, S and Carøe, C and Dalerum, F and Götherström, A and Måsviken, J and Vartanyan, S and Raundrup, K and Al-Chaer, A and Rasmussen, L and Hvilsom, C and Heide-Jørgensen, MP and Sinding, MS and Aastrup, P and Van Coeverden de Groot, PJ and Schmidt, NM and Albrechtsen, A and Dalén, L and Heller, R and Moltke, I and Siegismund, HR}, title = {Population genomics of the muskox' resilience in the near absence of genetic variation.}, journal = {Molecular ecology}, volume = {33}, number = {2}, pages = {e17205}, doi = {10.1111/mec.17205}, pmid = {37971141}, issn = {1365-294X}, support = {CF20-0539//Carlsbergfondet/ ; 8021-00344B//Danmarks Frie Forskningsfond/ ; }, mesh = {Humans ; Animals ; Infant, Newborn ; *Metagenomics ; *Resilience, Psychological ; Biological Evolution ; Genomics ; Ruminants/genetics ; Genetic Variation/genetics ; }, abstract = {Genomic studies of species threatened by extinction are providing crucial information about evolutionary mechanisms and genetic consequences of population declines and bottlenecks. However, to understand how species avoid the extinction vortex, insights can be drawn by studying species that thrive despite past declines. Here, we studied the population genomics of the muskox (Ovibos moschatus), an Ice Age relict that was at the brink of extinction for thousands of years at the end of the Pleistocene yet appears to be thriving today. We analysed 108 whole genomes, including present-day individuals representing the current native range of both muskox subspecies, the white-faced and the barren-ground muskox (O. moschatus wardi and O. moschatus moschatus) and a ~21,000-year-old ancient individual from Siberia. We found that the muskox' demographic history was profoundly shaped by past climate changes and post-glacial re-colonizations. In particular, the white-faced muskox has the lowest genome-wide heterozygosity recorded in an ungulate. Yet, there is no evidence of inbreeding depression in native muskox populations. We hypothesize that this can be explained by the effect of long-term gradual population declines that allowed for purging of strongly deleterious mutations. This study provides insights into how species with a history of population bottlenecks, small population sizes and low genetic diversity survive against all odds.}, } @article {pmid37971084, year = {2023}, author = {Conteville, LC and Oliveira-Ferreira, J and Vicente, ACP}, title = {Heavy metal resistance in the Yanomami and Tunapuco microbiome.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {118}, number = {}, pages = {e230086}, pmid = {37971084}, issn = {1678-8060}, mesh = {Humans ; Copper ; Nickel ; Silver ; *Metals, Heavy ; *Mercury ; Gold ; *Microbiota/genetics ; }, abstract = {BACKGROUND: The Amazon Region hosts invaluable and unique biodiversity as well as mineral resources. Consequently, large illegal and artisanal gold mining areas exist in indigenous territories. Mercury has been used in gold mining, and some has been released into the environment and atmosphere, primarily affecting indigenous people such as the Yanomami. In addition, other heavy metals have been associated with gold mining and other metal-dispersing activities in the region.

OBJECTIVE: Investigate the gut microbiome of two semi-isolated groups from the Amazon, focusing on metal resistance.

METHODS: Metagenomic data from the Yanomami and Tunapuco gut microbiome were assembled into contigs, and their putative proteins were searched against a database of metal resistance proteins.

FINDINGS: Proteins associated with mercury resistance were exclusive in the Yanomami, while proteins associated with silver resistance were exclusive in the Tunapuco. Both groups share 77 non-redundant metal resistance (MR) proteins, mostly associated with multi-MR and operons with potential resistance to arsenic, nickel, zinc, copper, copper/silver, and cobalt/nickel. Although both groups harbour operons related to copper resistance, only the Tunapuco group had the pco operon.

CONCLUSION: The Yanomami and Tunapuco gut microbiome shows that these people have been exposed directly or indirectly to distinct scenarios concerning heavy metals.}, } @article {pmid37970720, year = {2023}, author = {Koponen, K and Kambur, O and Joseph, B and Ruuskanen, MO and Jousilahti, P and Salido, R and Brennan, C and Jain, M and Meric, G and Inouye, M and Lahti, L and Niiranen, T and Havulinna, AS and Knight, R and Salomaa, V}, title = {Role of Gut Microbiota in Statin-Associated New-Onset Diabetes-a Cross-Sectional and Prospective Analysis of the FINRISK 2002 Cohort.}, journal = {Arteriosclerosis, thrombosis, and vascular biology}, volume = {}, number = {}, pages = {}, doi = {10.1161/ATVBAHA.123.319458}, pmid = {37970720}, issn = {1524-4636}, abstract = {BACKGROUND: Dyslipidemia is treated effectively with statins, but treatment has the potential to induce new-onset type-2 diabetes. Gut microbiota may contribute to this outcome variability. We assessed the associations of gut microbiota diversity and composition with statins. Bacterial associations with statin-associated new-onset type-2 diabetes (T2D) risk were also prospectively evaluated.

METHODS: We examined shallow-shotgun-sequenced fecal samples from 5755 individuals in the FINRISK-2002 population cohort with a 17+-year-long register-based follow-up. Alpha-diversity was quantified using Shannon index and beta-diversity with Aitchison distance. Species-specific differential abundances were analyzed using general multivariate regression. Prospective associations were assessed with Cox regression. Applicable results were validated using gradient boosting.

RESULTS: Statin use associated with differing taxonomic composition (R[2], 0.02%; q=0.02) and 13 differentially abundant species in fully adjusted models (MaAsLin; q<0.05). The strongest positive association was with Clostridium sartagoforme (β=0.37; SE=0.13; q=0.02) and the strongest negative association with Bacteroides cellulosilyticus (β=-0.31; SE=0.11; q=0.02). Twenty-five microbial features had significant associations with incident T2D in statin users, of which only Bacteroides vulgatus (HR, 1.286 [1.136-1.457]; q=0.03) was consistent regardless of model adjustment. Finally, higher statin-associated T2D risk was seen with [Ruminococcus] torques (ΔHRstatins, +0.11; q=0.03), Blautia obeum (ΔHRstatins, +0.06; q=0.01), Blautia sp. KLE 1732 (ΔHRstatins, +0.05; q=0.01), and beta-diversity principal component 1 (ΔHRstatin, +0.07; q=0.03) but only when adjusting for demographic covariates.

CONCLUSIONS: Statin users have compositionally differing microbiotas from nonusers. The human gut microbiota is associated with incident T2D risk in statin users and possibly has additive effects on statin-associated new-onset T2D risk.}, } @article {pmid37970497, year = {2023}, author = {Lee, JH and Kim, S and Kim, ES and Keum, GB and Doo, H and Kwak, J and Pandey, S and Cho, JH and Ryu, S and Song, M and Cho, JH and Kim, S and Kim, HB}, title = {Comparative analysis of the pig gut microbiome associated with the pig growth performance.}, journal = {Journal of animal science and technology}, volume = {65}, number = {4}, pages = {856-864}, pmid = {37970497}, issn = {2055-0391}, abstract = {There are a variety of microorganisms in the animal intestine, and it has been known that they play important roles in the host such as suppression of potentially pathogenic microorganisms, modulation of the gut immunity. In addition, the gut microbiota and the livestock growth performance have long been known to be related. Therefore, we evaluated the interrelation between the growth performance and the gut microbiome of the pigs from 3 different farms, with pigs of varied ages ready to be supplied to the market. When pigs reached average market weight of 118 kg, the average age of pigs in three different farms were < 180 days, about 190 days, and > 200 days, respectively. Fecal samples were collected from pigs of age of 70 days, 100 days, 130 days, and 160 days. The output data of the 16S rRNA gene sequencing by the Illumina Miseq platform was filtered and analyzed using Quantitative Insights into Microbial Ecology (QIIME)2, and the statistical analysis was performed using Statistical Analysis of Metagenomic Profiles (STAMP). The results of this study showed that the gut microbial communities shifted as pigs aged along with significant difference in the relative abundance of different phyla and genera in different age groups of pigs from each farm. Even though, there was no statistical differences among groups in terms of Chao1, the number of observed operational taxonomic units (OTUs), and the Shannon index, our results showed higher abundances of Bifidobacterium, Clostridium and Lactobacillus in the feces of pigs with rapid growth rate. These results will help us to elucidate important gut microbiota that can affect the growth performance of pigs.}, } @article {pmid37970089, year = {2023}, author = {Lin, L and Shen, K and Xiao, L and Lin, Y and Feng, E and Zhang, Y}, title = {Identification of prosthetic joint infection by Candida using metagenomic shotgun sequencing.}, journal = {Access microbiology}, volume = {5}, number = {10}, pages = {000425}, pmid = {37970089}, issn = {2516-8290}, abstract = {BACKGROUND: Periprosthetic joint infection (PJI) is a serious complication after total knee arthroplasty. Fungal infections are prone to biofilm formation, which makes it hard to diagnose and clarify the pathogenic species.

CASE PRESENTATION: This case study provides evidence of a novel PJI pathogen that is otherwise difficult to detect using conventional methods. A patient was reviewed with persistent postoperative pain, swelling and eventually drainage around the left knee after undergoing a bilateral total knee arthroplasty 2 years previously for progressive osteoarthritis. By using metagenomic shotgun sequencing to analyse both bacterial and fungal agent sequences, we were able to identify fungal strains of Candida tropicalis, a rarely reported and difficult-to-culture PJI pathogen.

CONCLUSION: Metagenomic shotgun sequencing enables the detection of difficult-to-detect pathogens and the formulation of treatment recommendations for fungal infections with low positive rates based on gene content analysis.}, } @article {pmid37969059, year = {2023}, author = {Staudacher, HM and Mahoney, S and Canale, K and Opie, RS and Loughman, A and So, D and Beswick, L and Hair, C and Jacka, FN}, title = {Clinical trial: A Mediterranean diet is feasible and improves gastrointestinal and psychological symptoms in irritable bowel syndrome.}, journal = {Alimentary pharmacology & therapeutics}, volume = {}, number = {}, pages = {}, doi = {10.1111/apt.17791}, pmid = {37969059}, issn = {1365-2036}, support = {n/a//Alfred Deakin Postdoctoral Research Fellowship/ ; }, abstract = {BACKGROUND: Diet is fundamental to the care of irritable bowel syndrome (IBS). However, some approaches are not appropriate for individuals experiencing psychological symptoms.

AIMS: To assess feasibility of a Mediterranean diet in IBS and its impact on gastrointestinal and psychological symptoms.

METHODS: We recruited adults with Rome IV IBS and mild or moderate anxiety and/or depressive symptoms to an unblinded 6-week randomised controlled trial. Patients were randomised to Mediterranean diet counselling or habitual diet. We collected gastrointestinal and psychological symptom data, dietary data and stool samples for metagenomic sequencing.

RESULTS: We randomised 59 individuals (29 Mediterranean diet, 30 control); 48 completed the study. The Mediterranean Diet Adherence Screener score was higher in the Mediterranean diet group than controls at week 6 (7.5 [95% CI: 6.9-8.0] vs. 5.7 [5.2-6.3], p < 0.001), and there was a greater score increase than controls (2.1 [95% CI: 1.3-2.9] vs. 0.5 [95% CI: 0.1-1.0], p = 0.004), demonstrating Mediterranean diet feasibility. There was a greater proportion of gastrointestinal symptom responders in the Mediterranean diet group than controls (24/29, 83% vs. 11/30, 37%, p < 0.001) and depression responders (15/29, 52% vs. 6/30 20%, p = 0.015). There was no difference in FODMAP intake at week 6 (p = 0.51). Gastrointestinal adverse events were similar (p = 0.588). There were no differences in change in microbiome parameters between groups.

CONCLUSIONS: A Mediterranean diet is feasible in IBS and leads to improvement in gastrointestinal and psychological symptoms. Although this study was unblinded, these findings together with the broader benefits of the Mediterranean diet, provide strong impetus for future research in IBS. Australia New Zealand Clinical Trials Registry: ACTRN12620001362987.}, } @article {pmid37968659, year = {2023}, author = {Abouelkhair, MA and Roozitalab, A and Elsakhawy, OK}, title = {Molecular characterization of a reptarenavirus detected in a Colombian Red-Tailed Boa (Boa constrictor imperator).}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {265}, pmid = {37968659}, issn = {1743-422X}, mesh = {Humans ; Animals ; *Arenaviridae/genetics ; *Boidae ; Colombia ; Biological Evolution ; Genotype ; }, abstract = {The global decline in biodiversity is a matter of great concern for members of the class Reptilia. Reptarenaviruses infect snakes, and have been linked to various clinical conditions, such as Boid Inclusion Body Disease (BIBD) in snakes belonging to the families Boidae and Pythonidae. However, there is a scarcity of information regarding reptarenaviruses found in snakes in both the United States and globally. This study aimed to contribute to the understanding of reptarenavirus diversity by molecularly characterizing a reptarenavirus detected in a Colombian Red-Tailed Boa (Boa constrictor imperator). Using a metagenomics approach, we successfully identified, and de novo assembled the whole genomic sequences of a reptarenavirus in a Colombian Red-Tailed Boa manifesting clinically relevant symptoms consistent with BIBD. The analysis showed that the Colombian Red-Tailed Boa in this study carried the University of Giessen virus (UGV-1) S or S6 (UGV/S6) segment and L genotype 7. The prevalence of the UGV/S6 genotype, in line with prior research findings, implies that this genotype may possess specific advantageous characteristics or adaptations that give it a competitive edge over other genotypes in the host population. This research underscores the importance of monitoring and characterizing viral pathogens in captive and wild snake populations. Knowledge of such viruses is crucial for the development of effective diagnostic methods, potential intervention strategies, and the conservation of vulnerable reptilian species. Additionally, our study provides valuable insights for future studies focusing on the evolutionary history, molecular epidemiology, and biological properties of reptarenaviruses in boas and other snake species.}, } @article {pmid37968636, year = {2023}, author = {Heitz, M and Levrat, A and Lazarevic, V and Barraud, O and Bland, S and Santiago-Allexant, E and Louis, K and Schrenzel, J and Hauser, S}, title = {Metagenomics for the microbiological diagnosis of hospital-acquired pneumonia and ventilator-associated pneumonia (HAP/VAP) in intensive care unit (ICU): a proof-of-concept study.}, journal = {Respiratory research}, volume = {24}, number = {1}, pages = {285}, pmid = {37968636}, issn = {1465-993X}, mesh = {Humans ; *Pneumonia, Ventilator-Associated/microbiology ; Prospective Studies ; Bronchoalveolar Lavage Fluid/microbiology ; *Pneumonia/diagnosis/microbiology ; Intensive Care Units ; Hospitals ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Hospital-acquired and ventilator-associated-pneumonia (HAP/VAP) are one of the most prevalent health-care associated infections in the intensive care unit (ICU). Culture-independent methods were therefore developed to provide faster route to diagnosis and treatment. Among these, metagenomic next-generation sequencing (mNGS) has shown considerable promise.

METHODS: This proof-of-concept study describes the technical feasibility and evaluates the clinical validity of the mNGS for the detection and characterization of the etiologic agents causing hospital-acquired and ventilator-associated pneumonia. We performed a prospective study of all patients with HAP/VAP hospitalized in our intensive care unit for whom a bronchoalveolar lavage (BAL) was performed between July 2017 and November 2018. We compared BAL fluid culture and mNGS results of these patients.

RESULTS: A total of 32 BAL fluids were fully analyzed. Of these, 22 (69%) were positive by culture and all pathogens identified were also reported by mNGS. Among the culture-positive BAL samples, additional bacterial species were revealed by mNGS for 12 patients, raising the issue of their pathogenic role (colonization versus coinfection). Among BALF with culture-negative test, 5 were positive in mNGS test.

CONCLUSIONS: This study revealed concordant results for pneumonia panel pathogens between mNGS and culture-positive tests and identified additional pathogens potentially implicated in pneumonia without etiologic diagnosis by culture. mNGS has emerged as a promising methodology for infectious disease diagnoses to support conventional methods. Prospective studies with real-time mNGS are warranted to examine the impact on antimicrobial decision-making and clinical outcome.}, } @article {pmid37968548, year = {2023}, author = {Naidoo, Y and Pierneef, RE and Cowan, DA and Valverde, A}, title = {Characterization of the soil resistome and mobilome in Namib Desert soils.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {37968548}, issn = {1618-1905}, abstract = {The study of the soil resistome is important in understanding the evolution of antibiotic resistance and its dissemination between the clinic and the environment. However, very little is known about the soil resistome, especially of those from deserts. Here, we characterize the bacterial communities, using targeted sequencing of the 16S rRNA genes, and both the resistome and the mobilome in Namib Desert soils, using shotgun metagenomics. We detected a variety of antibiotic resistance genes (ARGs) that conferred resistance to antibiotics such as elfamycin, rifampicin, and fluoroquinolones, metal/biocide resistance genes (MRGs/BRGs) conferring resistance to metals such as arsenic and copper, and mobile genetic elements (MGEs) such as the ColE1-like plasmid. The presence of metal/biocide resistance genes in close proximity to ARGs indicated a potential for co-selection of resistance to antibiotics and metals/biocides. The co-existence of MGEs and horizontally acquired ARGs most likely contributed to a decoupling between bacterial community composition and ARG profiles. Overall, this study indicates that soil bacterial communities in Namib Desert soils host a diversity of resistance elements and that horizontal gene transfer, rather than host phylogeny, plays an essential role in their dynamics.}, } @article {pmid37968499, year = {2023}, author = {Pfister, CA and Cardini, U and Mirasole, A and Montilla, LM and Veseli, I and Gattuso, JP and Teixido, N}, title = {Microbial associates of an endemic Mediterranean seagrass enhance the access of the host and the surrounding seawater to inorganic nitrogen under ocean acidification.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {19996}, pmid = {37968499}, issn = {2045-2322}, mesh = {*Seawater/chemistry ; Carbon Dioxide/metabolism ; Nitrogen/metabolism ; Hydrogen-Ion Concentration ; Ocean Acidification ; *Alismatales/metabolism ; Mediterranean Sea ; Water/metabolism ; Ecosystem ; }, abstract = {Seagrasses are important primary producers in oceans worldwide. They live in shallow coastal waters that are experiencing carbon dioxide enrichment and ocean acidification. Posidonia oceanica, an endemic seagrass species that dominates the Mediterranean Sea, achieves high abundances in seawater with relatively low concentrations of dissolved inorganic nitrogen. Here we tested whether microbial metabolisms associated with P. oceanica and surrounding seawater enhance seagrass access to nitrogen. Using stable isotope enrichments of intact seagrass with amino acids, we showed that ammonification by free-living and seagrass-associated microbes produce ammonium that is likely used by seagrass and surrounding particulate organic matter. Metagenomic analysis of the epiphytic biofilm on the blades and rhizomes support the ubiquity of microbial ammonification genes in this system. Further, we leveraged the presence of natural carbon dioxide vents and show that the presence of P. oceanica enhanced the uptake of nitrogen by water column particulate organic matter, increasing carbon fixation by a factor of 8.6-17.4 with the greatest effect at CO2 vent sites. However, microbial ammonification was reduced at lower pH, suggesting that future ocean climate change will compromise this microbial process. Thus, the seagrass holobiont enhances water column productivity, even in the context of ocean acidification.}, } @article {pmid37967575, year = {2024}, author = {Adnan, D and Trinh, JQ and Sharma, D and Alsayid, M and Bishehsari, F}, title = {Early-onset Colon Cancer Shows a Distinct Intestinal Microbiome and a Host-Microbe Interaction.}, journal = {Cancer prevention research (Philadelphia, Pa.)}, volume = {17}, number = {1}, pages = {29-38}, doi = {10.1158/1940-6207.CAPR-23-0091}, pmid = {37967575}, issn = {1940-6215}, support = {AA025387//National Institute on Alcohol Abuse and Alcoholism (NIAAA)/ ; CA279487//National Cancer Institute (NCI)/ ; CA277110//National Cancer Institute (NCI)/ ; TL1TR002388//National Center for Advancing Translational Sciences (NCATS)/ ; }, mesh = {Humans ; Middle Aged ; *Gastrointestinal Microbiome ; Host Microbial Interactions ; *Colonic Neoplasms ; *Microbiota ; Feces ; *Colorectal Neoplasms/genetics ; }, abstract = {UNLABELLED: The incidence rate of colorectal cancer in younger adults has been rising in developed countries. This trend may be attributed to environmental exposures as a result of lifestyle changes. Many of the lifestyle factors that promote colorectal cancer can also affect the gut microbiome, which may be associated with colorectal cancer risks. The role of the microbiome in the ongoing rise of early-onset colorectal cancer is unknown. Here, we aimed to investigate age-related differences in the gut microbiome of patients with colorectal cancer and healthy individuals by examining both the fecal and tumor microbiomes. We utilized the publicly accessible data on fecal shotgun metagenomics from CuratedMetagenomeData and TCGA via the GDC Data Portal. Comparison of 701 colorectal cancer and 693 controls revealed that microbial features were age dependent, with a significant difference in species enrichment between early-onset (<50 years) and late-onset (>65 years) patients with colorectal cancer. Analysis of the tumor-associated microbiome in a separate dataset of 85 patients with colorectal cancer verified age-specific differences in taxon abundance between early- and late-onset patients with colorectal cancer. Finally, using host gene expression data, we found a stronger microbe-host interaction in early- vs. late-onset colorectal cancers. Altogether, these findings indicate that microbial features were age-dependent with stronger microbial-host interactions at the tumor site in early-onset colorectal cancers, suggesting a direct role of microbes in tumorigenesis via interaction with cancer-related pathways in this age group.

PREVENTION RELEVANCE: Early-onset colorectal cancer is on the rise, presumably because of changes in environmental exposures. Lifestyle changes may contribute to colorectal cancer via alterations in gut microbes. Here, we show that microbial association with colorectal cancer is age-dependent, and microbe interactions with tumor pathways are stronger in young versus older colorectal cancers.}, } @article {pmid37967226, year = {2023}, author = {Pan, M and Fang, G and Zheng, F and Lin, F and Zeng, W and Qiu, Y and Deng, J and Chen, X and Zhang, J}, title = {Clinical characteristics of tracheobronchial Talaromyces marneffei infection in non-HIV-infected patients in South China.}, journal = {Annals of medicine}, volume = {55}, number = {2}, pages = {2276310}, pmid = {37967226}, issn = {1365-2060}, mesh = {Humans ; Middle Aged ; *Amphotericin B/therapeutic use ; *Antifungal Agents/therapeutic use ; Voriconazole ; China/epidemiology ; }, abstract = {OBJECTIVES: Tracheobronchial Talaromyces marneffei (T. marneffei) infections among non-HIV-infected patients are rare. To improve understanding, we analysed the clinical features, immune mechanisms, treatment, and prognosis.

METHODS: Data on hospitalized patients with tracheobronchial T. marneffei infections from September 2013 to May 2022 were collected. The clinical and imaging features were analysed.

RESULTS: Nineteen patients were enrolled, with a median age of 52 years (45-62 years). The most common symptoms were cough, expectoration, fever, weight loss, and anaemia. The total white blood cell and neutrophil counts, erythrocyte sedimentation rate, C-reactive protein, procalcitonin and globulin were increased, and the serum albumin levels were decreased. Chest CT manifestations included patchy shadows, masses, obstructive atelectasis, cavities, pleural effusion, and hilar and mediastinal lymphadenopathy. The fibreoptic bronchoscopy findings included masses, polyps or nodules with mucosal oedema, hypertrophic bulges, lumen stenosis or obstruction, and purulent secretions. T. marneffei infection was confirmed in 10 patients by positive culture, in five by both culture and metagenomic next-generation sequencing (mNGS), in two by mNGS, in one by culture and pathology and in 1 by histopathology. BALF (15/19, 78.9%) had the highest culture positive rate, followed by sputum (3/19), bronchial mucosa (1/1), lung biopsy (1/2); 36.8% of the patients were coinfected with other pathogens. For induction therapy, 7, 6, 2, and 4 patients received voriconazole, amphotericin B, voriconazole combined with amphotericin B, and fluconazole therapy, respectively, and 26.3% received treatment combined with nebulization and/or administration of amphotericin B under fibreoptic bronchoscopy. Four patients were treated for underlying diseases or coinfection, 31.6% were cured, 42.1% improved, and 26.3% died.

CONCLUSIONS: T. marneffei infection is common in the tracheobronchial airway tissue or secretions, and bronchoscopy has important diagnostic and treatment value. Antifungal therapy, including systemic therapy, involves triazoles and amphotericin administration, and aerosol inhalation and administration of amphotericin B under bronchoscopy are important.}, } @article {pmid37967008, year = {2023}, author = {Yew, WC and Young, GR and Nelson, A and Cheung, W and Stewart, CJ and Bridge, SH and Granger, C and Berrington, JE and Embleton, ND and Smith, DL}, title = {The core phageome and its interrelationship with preterm human milk lipids.}, journal = {Cell reports}, volume = {42}, number = {11}, pages = {113373}, doi = {10.1016/j.celrep.2023.113373}, pmid = {37967008}, issn = {2211-1247}, mesh = {Infant ; Female ; Humans ; Infant, Newborn ; *Milk, Human ; Infant, Premature ; Virome ; Lactation ; *Bacteriophages ; Fatty Acids ; }, abstract = {Phages and lipids in human milk (HM) may benefit preterm infant health by preventing gastrointestinal pathobiont overgrowth and microbiome modulation. Lipid association may promote vertical transmission of phages to the infant. Despite this, interrelationships between lipids and phages are poorly characterized in preterm HM. Shotgun metagenomics and untargeted lipidomics of phage and lipid profiles from 99 preterm HM samples reveals that phages are abundant and prevalent from the first week and throughout the first 100 days of lactation. Phage-host richness of preterm HM increases longitudinally. Core phage communities characterized by Staphylococcus- and Propionibacterium-infecting phages are significantly correlated with long-chain fatty acid abundances over lactational age. We report here a phage-lipid interaction in preterm HM, highlighting the potential importance of phage carriage in preterm HM. These results reveal possible strategies for phage carriage in HM and their importance in early-life microbiota development.}, } @article {pmid37966603, year = {2024}, author = {Álvarez-Espejo, DM and Rivera, D and Moreno-Switt, AI}, title = {Bacteriophage-Host Interactions and Coevolution.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2738}, number = {}, pages = {231-243}, pmid = {37966603}, issn = {1940-6029}, mesh = {*Bacteriophages/genetics ; Biological Evolution ; Metagenomics ; }, abstract = {Bacteriophages are the most abundant entity on the planet and play very relevant roles in the diversity and abundance of their bacterial hosts. These interactions are subject to several factors, such as the first encounter of the phage with its host bacterium, in which molecular interactions are fundamental. Along with this, these interactions depend on the environment and other communities present. This chapter focuses on these phage-bacteria interactions, reviewing the knowledge of the early stage (receptor-binding proteins), host responses (resistance and counter-resistance), and ecological and evolutionary models described to date. In general, knowledge has focused on a few phage-bacteria models and has been deepened by sequencing and metagenomics. The study of phage-bacteria interactions is an essential step for the development of therapies and other applications of phages in the clinical and productive environment.}, } @article {pmid37966600, year = {2024}, author = {White, K and Eraclio, G and Lugli, GA and Ventura, M and Mahony, J and Bello, FD and van Sinderen, D}, title = {A Metagenomics Approach to Enumerate Bacteriophages in a Food Niche.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2738}, number = {}, pages = {185-199}, pmid = {37966600}, issn = {1940-6029}, mesh = {Food ; *Bacteriophages/genetics ; Fermentation ; Industry ; *Lactobacillales ; }, abstract = {Dairy fermentation relies on the activity of starter cultures composed primarily of lactic acid bacteria such as Lactococcus and Streptococcus thermophilus strains to produce consistent, high-quality products. Bacteriophages are a constant threat to the industry, often causing slowed or failed fermentation resulting in significant economic losses. To ensure the continuation of reliable fermentation practices, it is important to detect and monitor the phage populations impacting different starter cultures. This has traditionally been done primarily through culture-dependent methods but has since expanded into viral metagenomics. Here we outline a protocol for a targeted virome extraction from a dairy whey sample, followed by subsequent sequencing and phageome analysis of the sample.}, } @article {pmid37966591, year = {2024}, author = {Heinrichs, ME and Piedade, GJ and Popa, O and Sommers, P and Trubl, G and Weissenbach, J and Rahlff, J}, title = {Breaking the Ice: A Review of Phages in Polar Ecosystems.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2738}, number = {}, pages = {31-71}, pmid = {37966591}, issn = {1940-6029}, mesh = {*Bacteriophages ; Ecosystem ; Biomass ; Biological Evolution ; Cell Death ; *Viroids ; }, abstract = {Bacteriophages, or phages, are viruses that infect and replicate within bacterial hosts, playing a significant role in regulating microbial populations and ecosystem dynamics. However, phages from extreme environments such as polar regions remain relatively understudied due to challenges such as restricted ecosystem access and low biomass. Understanding the diversity, structure, and functions of polar phages is crucial for advancing our knowledge of the microbial ecology and biogeochemistry of these environments. In this review, we will explore the current state of knowledge on phages from the Arctic and Antarctic, focusing on insights gained from -omic studies, phage isolation, and virus-like particle abundance data. Metagenomic studies of polar environments have revealed a high diversity of phages with unique genetic characteristics, providing insights into their evolutionary and ecological roles. Phage isolation studies have identified novel phage-host interactions and contributed to the discovery of new phage species. Virus-like particle abundance and lysis rate data, on the other hand, have highlighted the importance of phages in regulating bacterial populations and nutrient cycling in polar environments. Overall, this review aims to provide a comprehensive overview of the current state of knowledge about polar phages, and by synthesizing these different sources of information, we can better understand the diversity, dynamics, and functions of polar phages in the context of ongoing climate change, which will help to predict how polar ecosystems and residing phages may respond to future environmental perturbations.}, } @article {pmid37966589, year = {2024}, author = {Ely, B and Lenski, J and Mohammadi, T}, title = {Structural and Genomic Diversity of Bacteriophages.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2738}, number = {}, pages = {3-16}, pmid = {37966589}, issn = {1940-6029}, mesh = {*Bacteriophages/genetics ; Genomics ; Metagenomics ; Metagenome ; Genome, Viral ; }, abstract = {Bacteriophage diversity is a relatively unknown frontier that is rapidly being explored, leading to a wealth of new information. New bacteriophages are being discovered at an astounding rate via both phage isolation studies and metagenomic analyses. In addition, a nucleotide sequence-based viral taxonomic system has been developed to better handle this wealth of new information. As a result of these developments, phage scientists are transitioning from knowing that there must be huge numbers of diverse kinds of phage particles in natural environments to identifying the actual abundance and phage diversity that is present in specific environments. This review documents the beginning of this transition, offering a glimpse into the magnitude of change unfolding in the field. It stands as a testament to the expanding frontiers of phage research, illuminating the remarkable progress made in unraveling the intricate world of bacteriophage diversity and advancing our understanding of these enigmatic viral entities.}, } @article {pmid37966405, year = {2023}, author = {Liu, J and Jiang, J and Lan, Y and Li, C and Han, R and Wang, J and Wang, T and Zhao, Z and Fan, Z and He, L and Fang, J}, title = {Metagenomic analysis of oral and intestinal microbiome of patients during the initial stage of orthodontic treatment.}, journal = {American journal of orthodontics and dentofacial orthopedics : official publication of the American Association of Orthodontists, its constituent societies, and the American Board of Orthodontics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.ajodo.2023.07.019}, pmid = {37966405}, issn = {1097-6752}, abstract = {INTRODUCTION: This prospective study analyzed changes in the oral and intestinal microbiomes in patients before and after fixed orthodontic treatment, elucidating the impacts of fixed orthodontic treatment on patient health and metabolism.

METHODS: Metagenomic analysis was conducted on stool, dental plaque, and saliva samples from 10 fixed orthodontic patients. All the samples were sequenced with Illumina NovaSeq 6000 with a paired-end sequencing length of 150 bp. Identification of taxa in metagenomes and functional annotation of genes of the microbiota were performed using the data after quality control. Clinical periodontal parameters, including the gingiva index, plaque index, and pocket probing depth, were examined at each time point in triplicates. Patients also received a table to record their oral hygiene habits of brushing, flossing, and dessert consumption frequency over 1 month.

RESULTS: The brushing and flossing times per day of patients were significantly increased after treatment compared with baseline. The number of times a patient ate dessert daily was also fewer after treatment than at baseline. In addition, the plaque index decreased significantly, whereas the pH value of saliva, gingiva index, and pocket probing depth did not change. No significant differences were observed between the participants before and after orthodontic treatment regarding alpha-diversity analysis of the gut, dental plaque, or saliva microbiota. However, on closer analysis, periodontal disease-associated bacteria levels in the oral cavity remain elevated. Alterations in gut microbiota were also observed after orthodontic treatment.

CONCLUSIONS: The richness and diversity of the microbiome did not change significantly during the initial stage of fixed orthodontic treatment. However, the levels of periodontal disease-associated bacteria increased.}, } @article {pmid37965694, year = {2023}, author = {Stilwell, JM and Camus, AC and Woodyard, ET and Ware, C and Rosser, TG and Gunn, MA and López-Porras, A and Khoo, LH and Wise, DJ and Griffin, MJ}, title = {Species-specific in situ hybridization confirms arrested development of Henneguya ictaluri in hybrid catfish (Channel Catfish × Blue Catfish) under experimental conditions, with notes on mixed-species infections in clinical cases of proliferative gill disease from Mississippi catfish aquaculture.}, journal = {Journal of aquatic animal health}, volume = {35}, number = {4}, pages = {223-237}, doi = {10.1002/aah.10196}, pmid = {37965694}, issn = {1548-8667}, support = {6066-31320-006-00D//United States Department of Agriculture Agricultural Research Service/ ; 6066-31320-007-00D//United States Department of Agriculture Agricultural Research Service/ ; }, mesh = {Animals ; *Ictaluridae ; *Catfishes/genetics ; Gills/parasitology ; Mississippi ; *Coinfection/veterinary ; *Fish Diseases/epidemiology ; *Parasitic Diseases, Animal/parasitology ; *Myxozoa/genetics ; Aquaculture ; }, abstract = {OBJECTIVE: Proliferative gill disease (PGD) in Channel Catfish Ictalurus punctatus and hybrid catfish (Channel Catfish × Blue Catfish I. furcatus) is attributed to the myxozoan Henneguya ictaluri. Despite evidence of decreased H. ictaluri transmission and impaired parasite development in hybrid catfish, PGD still occurs in hybrid production systems. Previous metagenomic assessments of clinical PGD cases revealed numerous myxozoans within affected gill tissues in addition to H. ictaluri. The objective of this study was to investigate the development and pathologic contributions of H. ictaluri and other myxozoans in naturally and experimentally induced PGD.

METHODS: Henneguya species-specific in situ hybridization (ISH) assays were developed using RNAscope technology. Natural infections were sourced from diagnostic case submissions in 2019. Experimental challenges involved Channel Catfish and hybrid catfish exposed to pond water from an active PGD outbreak, and the fish were sampled at 1, 7, 10, 12, 14, 16, 18, and 20 weeks postchallenge.

RESULT: Nine unique ISH probes were designed, targeting a diagnostic variable region of the 18S ribosomal RNA gene of select myxozoan taxa identified in clinical PGD cases. Partial validation from pure H. ictaluri, H. adiposa, H. postexilis, and H. exilis infections illustrated species-specific labeling and no cross-reactivity between different myxozoan species or the catfish hosts. After experimental challenge, mature plasmodia of H. ictaluri and H. postexilis formed in Channel Catfish but were not observed in hybrids, suggesting impaired or delayed sporogenesis in the hybridized host. These investigations also confirmed the presence of mixed infections in clinical PGD cases.

CONCLUSION: Although H. ictaluri appears to be the primary cause of PGD, presporogonic stages of other myxozoans were also present, which may contribute to disease pathology and exacerbate respiratory compromise by further altering normal gill morphology. This work provides molecular confirmation and more resolute developmental timelines of H. ictaluri and H. postexilis in Channel Catfish and supports previous research indicating impaired or precluded H. ictaluri sporogony in hybrid catfish.}, } @article {pmid37965640, year = {2023}, author = {Steinberg, HE and Ramachandran, PS and Diestra, A and Pinchi, L and Ferradas, C and Kirwan, DE and Diaz, MM and Sciaudone, M and Wapniarski, A and Zorn, KC and Calderón, M and Cabrera, L and Pinedo-Cancino, V and Wilson, MR and Asayag, CR and Gilman, RH and Bowman, NM and , }, title = {Clinical and Metagenomic Characterization of Neurological Infections of People With Human Immunodeficiency Virus in the Peruvian Amazon.}, journal = {Open forum infectious diseases}, volume = {10}, number = {11}, pages = {ofad515}, pmid = {37965640}, issn = {2328-8957}, abstract = {BACKGROUND: Neurological opportunistic infections cause significant morbidity and mortality in people with human immunodeficiency virus (HIV) but are difficult to diagnose.

METHODS: One hundred forty people with HIV with acute neurological symptoms from Iquitos, Peru, were evaluated for cerebral toxoplasmosis with quantitative polymerase chain reaction (qPCR) of cerebrospinal fluid (CSF) and for cryptococcal meningitis with cryptococcal antigen test (CrAg) in serum or CSF. Differences between groups were assessed with standard statistical methods. A subset of samples was evaluated by metagenomic next-generation sequencing (mNGS) of CSF to compare standard diagnostics and identify additional diagnoses.

RESULTS: Twenty-seven participants were diagnosed with cerebral toxoplasmosis by qPCR and 13 with cryptococcal meningitis by CrAg. Compared to participants without cerebral toxoplasmosis, abnormal Glasgow Coma Scale score (P = .05), unilateral focal motor signs (P = .01), positive Babinski reflex (P = .01), and multiple lesions on head computed tomography (CT) (P = .002) were associated with cerebral toxoplasmosis. Photophobia (P = .03) and absence of lesions on head CT (P = .02) were associated with cryptococcal meningitis. mNGS of 42 samples identified 8 cases of cerebral toxoplasmosis, 7 cases of cryptococcal meningitis, 5 possible cases of tuberculous meningitis, and incidental detections of hepatitis B virus (n = 1) and pegivirus (n = 1). mNGS had a positive percentage agreement of 71% and a negative percentage agreement of 91% with qPCR for T gondii. mNGS had a sensitivity of 78% and specificity of 100% for Cryptococcus diagnosis.

CONCLUSIONS: An infection was diagnosed by any method in only 34% of participants, demonstrating the challenges of diagnosing neurological opportunistic infections in this population and highlighting the need for broader, more sensitive diagnostic tests for central nervous system infections.}, } @article {pmid37965618, year = {2023}, author = {Ogola, HJO and Ijoma, GN and Edokpayi, JN}, title = {Sediment microbiome diversity and functional profiles of unprotected arid-tropical natural wetlands in South Africa revealed by shotgun metagenomics data.}, journal = {Data in brief}, volume = {51}, number = {}, pages = {109726}, pmid = {37965618}, issn = {2352-3409}, abstract = {The Limpopo province, located in the arid-tropical region in northeastern South Africa, is renowned for its diverse natural wetlands, some of which are currently unprotected. These wetlands play a crucial role in preserving biodiversity, purifying water, controlling floods, and supporting agricultural production for rural communities. Unfortunately, human activities such as agricultural effluents, run-offs, domestic wastewater, and plastics pollution, along with the impacts of climate change, are mounting pressures on these ecosystems. However, there is limited information on the microbial ecology of natural wetlands in this region, considering the changing anthropogenic activities. The data presented represents the first report on the microbial and functional diversity of sediment microbiomes associated with unprotected arid-tropical natural wetlands in South Africa. Metagenomic shotgun sequencing was performed on sediment samples from ten different wetlands using the Illumina NextSeq 2000 platform. Taxonomic profiling of 328,625,930 high-quality sequencing reads using the MetaPhlAn v3.0 pipeline revealed that Bacteria were the most abundant kingdom (54.5 %), followed by Viruses (0.40 %), Archaea (0.01 %), and Eukaryota (0.36 %). Among bacteria, the most prevalent taxa belonged to the phylum Proteobacteria, particularly the classes Gammaproteobacteria and Betaproteobacteria, which accounted for 83 % of bacterial sequences. The Terrabacteria group, consisting of the phyla Firmicutes and Actinobacteria, made up 3 % of the bacterial population. The abundance of these top bacterial taxa varied across different wetland samples, both at the genus and species levels. In addition, hierarchical clustering based on Bray-Curtis dissimilarity distances of fungal, protist, archaea, and virus species showed distinct clustering of sediment samples from different wetlands. Functional annotation of the metagenomes identified 1224-1702 enzyme classes, 84,833-198,397 gene families, and 280-400 pathways across the various wetland sediments. The data provide crucial baseline information on the microbial and functional diversity of sediment communities in arid tropical wetlands. This knowledge will contribute to a better understanding of these unique environments and can aid in their management and conservation efforts in rural South Africa.}, } @article {pmid37965552, year = {2023}, author = {Zhang, J and Jiang, P and Zhang, Y and Liu, W and Kong, S and Hou, X and Qi, Z and Sun, Y and Jiang, G}, title = {Effects of wearing masks during COVID-19 pandemic on the composition and diversity of skin bacteria and fungi in medical workers.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1274050}, pmid = {37965552}, issn = {1664-302X}, abstract = {BACKGROUND: Although studies have shown that wearing masks can affect the skin microbiome, more detailed and comprehensive research on wearing masks needs to be further explored.

OBJECTIVE: This study aimed to characterize the influence of mask wearing on the diversity and structural characteristics of the facial skin microbial community of medical staff during the COVID-19 pandemic by means of metagenomic sequencing (mNGS).

METHODS: A total of 40 samples were taken by swabbing the cheek in the 2 × 2 cm[2] area before and after wearing the masks. DNA was extracted for metagenomic sequencing.

RESULTS: A statistically significant decrease was found in the α diversity between BN and AN groups and between B2 h and A2 h groups. BN and AN mean groups before and after 8 h of wearing the medical protective mask (N95), including 10 volunteers, respectively. B2 h and A2 h mean groups before and after 8 h of wearing masks, including 10 volunteers changing mask every 2 h, respectively. The β diversity was found to be statistically reduced between BS and AS groups (p = 0.025), BN and AN groups (p = 0.009), and B2 h and A2 h group (p = 0.042). The fungal beta diversity was significantly decreased in every group before and after wearing masks. The main bacteria on the face before and after wearing masks were Cutibacterium (68.02 and 71.73%). Among the fungi, Malassezia predominated the facial skin surface before and after wearing masks (35.81 and 39.63%, respectively).

CONCLUSION: Wearing different types of masks and changing masks according to different frequency will have different effects on the facial skin's microbiota.}, } @article {pmid37965487, year = {2023}, author = {Alnezary, FS and Almutairi, MS and Alhifany, AA and Almangour, TA}, title = {Assessing Galleria mellonella as a preliminary model for systemic Staphylococcus aureus infection: Evaluating the efficacy and impact of vancomycin and Nigella sativa oil on gut microbiota.}, journal = {Saudi pharmaceutical journal : SPJ : the official publication of the Saudi Pharmaceutical Society}, volume = {31}, number = {12}, pages = {101824}, pmid = {37965487}, issn = {1319-0164}, abstract = {BACKGROUND: Staphylococcus aureus is a Gram-positive bacterium that can cause various infections. The Galleria mellonella has been used as a preliminary test for infection model. The study aimed to evaluate the effectiveness of G. mellonella as a microbiome model and compare the efficacy of vancomycin and antimicrobial activity of Nigella sativa (NS) on the gut flora.

METHODS: G. mellonella larvae were subjected to metagenomic analysis. The larvae's guts were collected, homogenized in phosphate-buffered saline (PBS), and the gut contents isolated for bacterial DNA extraction. Larvae were assigned into the following groups: negative control (PBS only); positive control (MRSA only); vancomycin treated group; NS oil treated group and combination (vancomycin and NS oil) treated group. Larvae were cultured, inoculated with S. aureus, and treated with vancomycin and NS oil. Larval activity, cocoon formation, growth, melanization, and survival were monitored. The toxicity of vancomycin and NS oil was tested, and S. aureus burden and natural microbiota were determined. Hemocyte density was measured. Statistical analysis was conducted using R.

RESULTS: Enterococcus related species dominated approximately 90 % of the gastrointestinal tract of the larvae. The survival rate following treatment was 85 % with vancomycin, 64 % with NS oil, and 73 % with a combination of both. The count of Enterococcus Colony Forming Units (CFUs) was significantly lower in the vancomycin treatment group (8.14E+04) compared to those treated with NS oil (1.97E+06) and the combination treatment (8.95E+05). Furthermore, the S. aureus burden was found to be lower in the NS oil (1.04E+06) and combination treatment groups (9.02E+05) compared to the vancomycin treatment group (3.38E+06). Hemocyte densities were significantly higher in the NS oil (8.29E+06) and combination treatment groups (8.18E+06) compared to the vancomycin treatment group (4.89E+06).

CONCLUSIONS: The study supported the use of G. mellonella model as a preliminary test to assess the effect of different antimicrobials against S. aureus and gut microbiota. NS oil showed more selectivity against S. aureus and protectiveness for the natural Enterococcus gut flora.}, } @article {pmid37965266, year = {2023}, author = {Piazzesi, A and Pane, S and Russo, A and Del Chierico, F and Francalanci, P and Cotugno, N and Rossi, P and Locatelli, F and Palma, P and Putignani, L}, title = {Case Report: The impact of severe cryptosporidiosis on the gut microbiota of a pediatric patient with CD40L immunodeficiency.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1281440}, pmid = {37965266}, issn = {2235-2988}, abstract = {Cryptosporidium parvum is a protozoan parasite and one of the leading causes of gastroenteritis in the world, primarily affecting very young children and immunocompromised patients. While infection is usually self-limiting, it can become chronic and even lethal in these vulnerable populations, in whom Cryptosporidium treatments are generally ineffective, due to their acting in concert with a functioning immune system. Here, we describe a case of chronic cryptosporidiosis in a European child with severe CD40L immunodeficiency infected with Cryptosporidium parvum of the IIa20G1 subgenotype, a lineage which has thus far only ever been described in the Middle East. After years of on-off treatment with conventional and non-conventional anti-parasitic drugs failed to clear parasitosis, we performed targeted metagenomics to observe the bacterial composition of the patient's gut microbiota (GM), and to evaluate fecal microbiota transplantation (FMT) as a potential treatment option. We found that C. parvum infection led to significant shifts in GM bacterial composition in our patient, with consequent shifts in predicted intestinal functional signatures consistent with a state of persistent inflammation. This, combined with the patient's poor prognosis and increasing parasitic burden despite many rounds of anti-parasitic drug treatments, made the patient a potential candidate for an experimental FMT procedure. Unfortunately, given the many comorbidities that were precipitated by the patient's immunodeficiency and chronic C. parvum infection, FMT was postponed in favor of more urgently necessary liver and bone marrow transplants. Tragically, after the first liver transplant failed, the patient lost his life before undergoing FMT and a second liver transplant. With this case report, we present the first description of how cryptosporidiosis can shape the gut microbiota of a pediatric patient with severe immunodeficiency. Finally, we discuss how both our results and the current scientific literature suggest that GM modulations, either by probiotics or FMT, can become novel treatment options for chronic Cryptosporidium infection and its consequent complications, especially in those patients who do not respond to the currently available anti-parasitic therapies.}, } @article {pmid37965251, year = {2023}, author = {Liu, X and Wang, J and Liu, J and Li, X and Guan, Y and Qian, S and Jia, X}, title = {Cryptosporidiosis diagnosed using metagenomic next-generation sequencing in a healthy child admitted to pediatric intensive care unit: a case report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1269963}, pmid = {37965251}, issn = {2235-2988}, abstract = {BACKGROUND: Cryptosporidium infections in humans typically result in symptoms such as abdominal pain and diarrhea. When the diarrhea is severe, it can cause serious complications and even be life-threatening, especially in patients with compromised immune systems.

CASE PRESENTATION: Here, we reported the use of metagenomic next-generation sequencing (mNGS) to assist in the diagnosis and treatment of a 10-year-old boy with severe Cryptosporidium infection. Despite the absence of any history of immunocompromise, the infection still resulted in severe symptoms, including shock, as well as damage to his pancreas and kidneys. The mNGS tests detected the presence of Cryptosporidium parvum when conventional methods failed. The patient received anti-parasite treatment along with supportive care to manage the condition. With disease surveillance based on regular clinical tests and sequential mNGS tests, the child recovered from the severe conditions.

CONCLUSION: Our study emphasized the importance of recognizing the potential severity of Cryptosporidium infection, even among individuals with normal immune systems. Timely diagnosis and ongoing monitoring are essential for patient prognosis.}, } @article {pmid37965142, year = {2023}, author = {Lisius, G and Duttagupta, R and Ahmed, AA and Hensley, M and Al-Yousif, N and Lu, M and Bain, W and Shah, F and Blauwkamp, TA and Bercovici, S and Schaefer, C and Qin, S and Wang, X and Zhang, Y and Mitchell, KJ and Hughes, EK and Jacobs, JL and Naqvi, A and Haidar, G and Mellors, JW and Methé, B and McVerry, BJ and Morris, A and Kitsios, GD}, title = {Noninvasive diagnosis of secondary infections in COVID-19 by sequencing of plasma microbial cell-free DNA.}, journal = {iScience}, volume = {26}, number = {11}, pages = {108093}, pmid = {37965142}, issn = {2589-0042}, abstract = {Secondary infection (SI) diagnosis in severe COVID-19 remains challenging. We correlated metagenomic sequencing of plasma microbial cell-free DNA (mcfDNA-Seq) with clinical SI assessment, immune response, and outcomes. We classified 42 COVID-19 inpatients as microbiologically confirmed-SI (Micro-SI, n = 8), clinically diagnosed-SI (Clinical-SI, n = 13, i.e., empiric antimicrobials), or no-clinical-suspicion-for-SI (No-Suspected-SI, n = 21). McfDNA-Seq was successful in 73% of samples. McfDNA detection was higher in Micro-SI (94%) compared to Clinical-SI (57%, p = 0.03), and unexpectedly high in No-Suspected-SI (83%), similar to Micro-SI. We detected culture-concordant mcfDNA species in 81% of Micro-SI samples. McfDNA correlated with LRT 16S rRNA bacterial burden (r = 0.74, p = 0.02), and biomarkers (white blood cell count, IL-6, IL-8, SPD, all p < 0.05). McfDNA levels were predictive of worse 90-day survival (hazard ratio 1.30 [1.02-1.64] for each log10 mcfDNA, p = 0.03). High mcfDNA levels in COVID-19 patients without clinical SI suspicion may suggest SI under-diagnosis. McfDNA-Seq offers a non-invasive diagnostic tool for pathogen identification, with prognostic value on clinical outcomes.}, } @article {pmid37964716, year = {2023}, author = {Momper, L and Casar, CP and Osburn, MR}, title = {A metagenomic view of novel microbial and metabolic diversity found within the deep terrestrial biosphere at DeMMO: A microbial observatory in South Dakota, USA.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {3719-3737}, doi = {10.1111/1462-2920.16543}, pmid = {37964716}, issn = {1462-2920}, support = {//CIFAR: Canadian Institute for the Advancement of Research - Earth 4D/ ; //David and Lucile Packard Foundation/ ; NNX15AM086//National Aeronautics and Space Administration Exobiology/ ; NNH14ZDA001N//National Aeronautics and Space Administration Exobiology/ ; }, mesh = {*Bacteria/metabolism ; *Metagenome ; South Dakota ; Phylogeny ; Metagenomics ; }, abstract = {The deep terrestrial subsurface is a large and diverse microbial habitat and vast repository of biomass. However, in relation to its size and physical heterogeneity we have limited understanding of taxonomic and metabolic diversity in this realm. Here we present a detailed metagenomic analysis of samples from the Deep Mine Microbial Observatory (DeMMO) spanning depths from the surface to 1.5 km into the crust. From eight geochemically and spatially distinct fluid samples we reconstructed ~600 partial to near-complete metagenome-assembled genomes (MAGs), representing 50 distinct phyla and including 18 candidate phyla. These novel clades include members of the candidate phyla radiation, two new MAGs from OLB16, a phylum originally identified in DeMMO fluids and for which only one other MAG is currently available, and new MAGs from the Eisenbacteria, Omnitrophota, and Edwardsbacteria. We find that microbes spanning this expansive phylogenetic diversity and physical subsurface space gain a competitive edge by maintaining a wide variety of functional pathways, are often capable of numerous dissimilatory energy metabolisms and poised to take advantage of nutrients as they become available in isolated fracture fluids. Our results support and expand on emerging themes of tight nutrient cycling and genomic plasticity in deep subsurface biosphere taxa.}, } @article {pmid37964633, year = {2023}, author = {Bassani, I and Bellini, R and Vizzarro, A and Coti, C and Pozzovivo, V and Barbieri, D and Pirri, CF and Verga, F and Menin, B}, title = {Biogeochemical characterization of four depleted gas reservoirs for conversion into underground hydrogen storage.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {3683-3702}, doi = {10.1111/1462-2920.16538}, pmid = {37964633}, issn = {1462-2920}, mesh = {*Oil and Gas Fields ; RNA, Ribosomal, 16S/genetics/metabolism ; Bacteria/genetics ; Archaea/genetics ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Depleted gas reservoirs are a valuable option for underground hydrogen storage (UHS). However, different classes of microorganisms, which are capable of using free H2 as a reducing agent for their metabolism, inhabit deep underground formations and can potentially affect the storage. This study integrates metagenomics based on Illumina-NGS sequencing of bacterial and archaeal 16S rRNA and dsrB and mcrA functional genes to unveil the composition and the variability of indigenous microbial populations of four Italian depleted reservoirs. The obtained mcrA sequences allow us to implement the existing taxonomic database for mcrA gene sequences with newly classified sequences obtained from the Italian gas reservoirs. Moreover, the KEGG and COG predictive functional annotation was used to highlight the metabolic pathways potentially associated with hydrogenotrophic metabolisms. The analyses revealed the specificity of each reservoir microbial community, and taxonomic and functional data highlighted the presence of an enriched number of taxa, whose activity depends on both reservoir hydrochemical composition and nutrient availability, of potential relevance in the context of UHS. This study is the very first to address the profiling of the microbial population and allowed us to perform a preliminary assessment of UHS feasibility in Italy.}, } @article {pmid37964391, year = {2023}, author = {Yokota, C and Fujimoto, K and Yamakawa, N and Kono, M and Miyaoka, D and Shimohigoshi, M and Uematsu, M and Watanabe, M and Kamei, Y and Sugimoto, A and Kawasaki, N and Yabuno, T and Okamura, T and Kuroda, E and Hamaguchi, S and Sato, S and Hotomi, M and Akeda, Y and Ishii, KJ and Yasutomi, Y and Sunami, K and Uematsu, S}, title = {Prime-boost-type PspA3 + 2 mucosal vaccine protects cynomolgus macaques from intratracheal challenge with pneumococci.}, journal = {Inflammation and regeneration}, volume = {43}, number = {1}, pages = {55}, pmid = {37964391}, issn = {1880-9693}, support = {19K17932//Grant-in-Aid for Early-Career Scientists/ ; 17K19543//Grant-in-Aid for Challenging Research (Exploratory)/ ; JPMJCR18H1//Japan Science and Technology Agency/ ; 21ak0101069h005//the Japan Agency for Medical Research and Development/ ; 22ak0101161h002//the Japan Agency for Medical Research and Development/ ; 223fa727001h0001//the Japan Agency for Medical Research and Development/ ; 20fk0108113h0001//the Japan Agency for Medical Research and Development/ ; 223fa627001//the Japan Agency for Medical Research and Development/ ; 20nk0101625h0201//the Japan Agency for Medical Research and Development/ ; }, abstract = {BACKGROUND: Although vaccination is recommended for protection against invasive pneumococcal disease, the frequency of pneumococcal pneumonia is still high worldwide. In fact, no vaccines are effective for all pneumococcal serotypes. Fusion pneumococcal surface protein A (PspA) has been shown to induce a broad range of cross-reactivity with clinical isolates and afford cross-protection against pneumococcal challenge in mice. Furthermore, we developed prime-boost-type mucosal vaccines that induce both antigen-specific IgG in serum and antigen-specific IgA in targeted mucosal organs in previous studies. We investigated whether our prime-boost-type immunization with a fusion PspA was effective against pneumococcal infection in mice and cynomolgus macaques.

METHODS: C57BL/6 mice were intramuscularly injected with fusion PspA combined with CpG oligodeoxynucleotides and/or curdlan. Six weeks later, PspA was administered intranasally. Blood and bronchoalveolar lavage fluid were collected and antigen-specific IgG and IgA titers were measured. Some mice were given intranasal Streptococcus pneumoniae and the severity of infection was analyzed. Macaques were intramuscularly injected with fusion PspA combined with CpG oligodeoxynucleotides and/or curdlan at week 0 and week 4. Then, 13 or 41 weeks later, PspA was administered intratracheally. Blood and bronchoalveolar lavage fluid were collected and antigen-specific IgG and IgA titers were measured. Some macaques were intranasally administered S. pneumoniae and analyzed for the severity of pneumonia.

RESULTS: Serum samples from mice and macaques injected with antigens in combination with CpG oligodeoxynucleotides and/or curdlan contained antigen-specific IgG. Bronchial samples contained antigen-specific IgA after the fusion PspA boosting. This immunization regimen effectively prevented S. pneumoniae infection.

CONCLUSIONS: Prime-boost-type immunization with a fusion PspA prevented S. pneumoniae infection in mice and macaques.}, } @article {pmid37964026, year = {2023}, author = {Chen, X and Liu, J and Zhu, XY and Xue, CX and Yao, P and Fu, L and Yang, Z and Sun, K and Yu, M and Wang, X and Zhang, XH}, title = {Phylogenetically and metabolically diverse autotrophs in the world's deepest blue hole.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {117}, pmid = {37964026}, issn = {2730-6151}, abstract = {The world's deepest yongle blue hole (YBH) is characterized by sharp dissolved oxygen (DO) gradients, and considerably low-organic-carbon and high-inorganic-carbon concentrations that may support active autotrophic communities. To understand metabolic strategies of autotrophic communities for obtaining carbon and energy spanning redox gradients, we presented finer characterizations of microbial community, metagenome and metagenome-assembled genomes (MAGs) in the YBH possessing oxic, hypoxic, essentially anoxic and completely anoxic zones vertically. Firstly, the YBH microbial composition and function shifted across the four zones, linking to different biogeochemical processes. The recovery of high-quality MAGs belonging to various uncultivated lineages reflected high novelty of the YBH microbiome. Secondly, carbon fixation processes and associated energy metabolisms varied with the vertical zones. The Calvin-Benson-Bassham (CBB) cycle was ubiquitous but differed in affiliated taxa at different zones. Various carbon fixation pathways were found in the hypoxic and essentially anoxic zones, including the 3-hyroxypropionate/4-hydroxybutyrate (3HP/4HB) cycle affiliated to Nitrososphaeria, and Wood-Ljungdahl (WL) pathway affiliated to Planctomycetes, with sulfur oxidation and dissimilatory nitrate reduction as primary energy-conserving pathways. The completely anoxic zone harbored diverse taxa (Dehalococcoidales, Desulfobacterales and Desulfatiglandales) utilizing the WL pathway coupled with versatile energy-conserving pathways via sulfate reduction, fermentation, CO oxidation and hydrogen metabolism. Finally, most of the WL-pathway containing taxa displayed a mixotrophic lifestyle corresponding to flexible carbon acquisition strategies. Our result showed a vertical transition of microbial lifestyle from photo-autotrophy, chemoautotrophy to mixotrophy in the YBH, enabling a better understanding of carbon fixation processes and associated biogeochemical impacts with different oxygen availability.}, } @article {pmid37963929, year = {2023}, author = {Ergunay, K and Bourke, BP and Reinbold-Wasson, DD and Nikolich, MP and Nelson, SP and Caicedo-Quiroga, L and Vaydayko, N and Kirkitadze, G and Chunashvili, T and Long, LS and Blackburn, JK and Cleary, NG and Tucker, CL and Linton, YM}, title = {The expanding range of emerging tick-borne viruses in Eastern Europe and the Black Sea Region.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {19824}, pmid = {37963929}, issn = {2045-2322}, mesh = {Animals ; Black Sea ; Europe, Eastern ; *Ixodes ; Phylogeny ; *Ticks ; *Viruses/genetics ; }, abstract = {We analysed both pooled and individual tick samples collected from four countries in Eastern Europe and the Black Sea region, using metagenome-based nanopore sequencing (NS) and targeted amplification. Initially, 1337 ticks, belonging to 11 species, were screened in 217 pools. Viruses (21 taxa) and human pathogens were detected in 46.5% and 7.3%, respectively. Tick-borne viral pathogens comprised Tacheng Tick Virus 2 (TTV2, 5.9%), Jingmen Tick Virus (JMTV, 0.9%) and Tacheng Tick Virus 1 (TTV1, 0.4%). An association of tick species with individual virus taxa was observed, with the exception of TTV2, which was observed in both Dermacentor and Haemaphysalis species. Individual ticks from pools with pathogen detection were then further screened by targeted amplification and then NS, which provided extensive genome data and revealed probable pathogen Haseki Tick Virus (HTV, 10.2%). Two distinct TTV2 clades were observed in phylogenetic analysis, one of which included closely related Dermacentor reticulatus Uukuviruses. JMTV detection indicated integrated virus sequences. Overall, we observed an expansion of newly documented pathogenic tick-borne viruses into Europe, with TTV1 being identified on the continent for the first time. These viruses should be included in the diagnostic assessment of symptomatic cases associated with tick bites and vector surveillance efforts. NS is shown as a useful tool for monitoring tick-associated pathogens in pooled or individual samples.}, } @article {pmid37963868, year = {2023}, author = {Diebold, PJ and Rhee, MW and Shi, Q and Trung, NV and Umrani, F and Ahmed, S and Kulkarni, V and Deshpande, P and Alexander, M and Thi Hoa, N and Christakis, NA and Iqbal, NT and Ali, SA and Mathad, JS and Brito, IL}, title = {Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7366}, pmid = {37963868}, issn = {2041-1723}, support = {DP2 HL141007/HL/NHLBI NIH HHS/United States ; R01 AI151059/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/genetics ; Drug Resistance, Microbial/genetics ; *Microbiota/genetics ; Genes, Bacterial/genetics ; }, abstract = {The acquisition of antimicrobial resistance (AR) genes has rendered important pathogens nearly or fully unresponsive to antibiotics. It has been suggested that pathogens acquire AR traits from the gut microbiota, which collectively serve as a global reservoir for AR genes conferring resistance to all classes of antibiotics. However, only a subset of AR genes confers resistance to clinically relevant antibiotics, and, although these AR gene profiles are well-characterized for common pathogens, less is known about their taxonomic associations and transfer potential within diverse members of the gut microbiota. We examined a collection of 14,850 human metagenomes and 1666 environmental metagenomes from 33 countries, in addition to nearly 600,000 isolate genomes, to gain insight into the global prevalence and taxonomic range of clinically relevant AR genes. We find that several of the most concerning AR genes, such as those encoding the cephalosporinase CTX-M and carbapenemases KPC, IMP, NDM, and VIM, remain taxonomically restricted to Proteobacteria. Even cfiA, the most common carbapenemase gene within the human gut microbiome, remains tightly restricted to Bacteroides, despite being found on a mobilizable plasmid. We confirmed these findings in gut microbiome samples from India, Honduras, Pakistan, and Vietnam, using a high-sensitivity single-cell fusion PCR approach. Focusing on a set of genes encoding carbapenemases and cephalosporinases, thus far restricted to Bacteroides species, we find that few mutations are required for efficacy in a different phylum, raising the question of why these genes have not spread more widely. Overall, these data suggest that globally prevalent, clinically relevant AR genes have not yet established themselves across diverse commensal gut microbiota.}, } @article {pmid37963293, year = {2023}, author = {Ma, YJ and Zhao, L and Li, JQ and Yang, L and Yan, YM and Li, JB and Gao, LH}, title = {Epstein-Barr virus infection with non-tumor-associated Anti-N-Methyl-D-Aspartate receptor encephalitis: a case report and review of literature.}, journal = {Neurocase}, volume = {29}, number = {1}, pages = {1-5}, doi = {10.1080/13554794.2023.2280276}, pmid = {37963293}, issn = {1465-3656}, mesh = {Middle Aged ; Humans ; Male ; *Anti-N-Methyl-D-Aspartate Receptor Encephalitis/complications/diagnosis ; *Epstein-Barr Virus Infections/complications/diagnosis ; Herpesvirus 4, Human ; *Hashimoto Disease/complications ; }, abstract = {To study a case of a middle-aged male with a non-tumor-associated Epstein-Barr virus (EBV) infection associated with Anti-N-methyl-D-aspartate receptor encephalitis (NMDARE), to explore the role of EBV in the pathogenesis of anti-NMDARE. The patient was diagnosed with "Anti-NMDARE, EBV infection" by using Cerebrospinal fluid (CSF) autoimmune encephalitis profile, and Metagenomics Next-Generation Sequencing (mNGS) pathogenic microbial assays, we discuss the relationship between EBV and NMDARE by reviewed literature. EBV infection may trigger and enhance anti-NMDARE, and the higher the titer of NMDAR antibody, the more severe the clinical presentation.}, } @article {pmid37962956, year = {2023}, author = {Wu, Q and Badu, S and So, SY and Treangen, TJ and Savidge, TC}, title = {The pan-microbiome profiling system Taxa4Meta identifies clinical dysbiotic features and classifies diarrheal disease.}, journal = {The Journal of clinical investigation}, volume = {134}, number = {2}, pages = {}, pmid = {37962956}, issn = {1558-8238}, abstract = {Targeted metagenomic sequencing is an emerging strategy to survey disease- specific microbiome biomarkers for clinical diagnosis and prognosis. However, this approach often yields inconsistent or conflicting results due to inadequate study power and sequencing bias. We introduce Taxa4Meta, a bioinformatics pipeline explicitly designed to compensate for technical and demographic bias. We designed and validated Taxa4Meta for accurate taxonomic profiling of 16S rRNA amplicon data acquired from different sequencing strategies. Taxa4Meta offers significant potential in identifying clinical dysbiotic features that can reliably predict human disease, validated comprehensively via re-analysis of individual patient 16S datasets. We leveraged the power of Taxa4Meta's pan-microbiome profiling to generate 16S-based classifiers that exhibited excellent utility for stratification of diarrheal patients with Clostridioides difficile infection, irritable bowel syndrome or inflammatory bowel diseases, which represent common misdiagnoses and pose significant challenges for clinical management. We believe that Taxa4Meta represents a new "best practices" approach to individual microbiome surveys that can be used to define gut dysbiosis at a population-scale level.}, } @article {pmid37962425, year = {2024}, author = {Haft, DH and Badretdin, A and Coulouris, G and DiCuccio, M and Durkin, AS and Jovenitti, E and Li, W and Mersha, M and O'Neill, KR and Virothaisakun, J and Thibaud-Nissen, F}, title = {RefSeq and the prokaryotic genome annotation pipeline in the age of metagenomes.}, journal = {Nucleic acids research}, volume = {52}, number = {D1}, pages = {D762-D769}, pmid = {37962425}, issn = {1362-4962}, support = {/LM/NLM NIH HHS/United States ; /NH/NIH HHS/United States ; /LM/NLM NIH HHS/United States ; /NH/NIH HHS/United States ; }, mesh = {*Archaea/genetics ; *Bacteria/genetics ; *Databases, Nucleic Acid/standards/trends ; Genome, Archaeal/genetics ; Genome, Bacterial/genetics ; Internet ; *Metagenome ; Molecular Sequence Annotation ; Proteins/genetics ; }, abstract = {The Reference Sequence (RefSeq) project at the National Center for Biotechnology Information (NCBI) contains over 315 000 bacterial and archaeal genomes and 236 million proteins with up-to-date and consistent annotation. In the past 3 years, we have expanded the diversity of the RefSeq collection by including the best quality metagenome-assembled genomes (MAGs) submitted to INSDC (DDBJ, ENA and GenBank), while maintaining its quality by adding validation checks. Assemblies are now more stringently evaluated for contamination and for completeness of annotation prior to acceptance into RefSeq. MAGs now account for over 17000 assemblies in RefSeq, split over 165 orders and 362 families. Changes in the Prokaryotic Genome Annotation Pipeline (PGAP), which is used to annotate nearly all RefSeq assemblies include better detection of protein-coding genes. Nearly 83% of RefSeq proteins are now named by a curated Protein Family Model, a 4.7% increase in the past three years ago. In addition to literature citations, Enzyme Commission numbers, and gene symbols, Gene Ontology terms are now assigned to 48% of RefSeq proteins, allowing for easier multi-genome comparison. RefSeq is found at https://www.ncbi.nlm.nih.gov/refseq/. PGAP is available as a stand-alone tool able to produce GenBank-ready files at https://github.com/ncbi/pgap.}, } @article {pmid37962419, year = {2023}, author = {Tang, J and Li, W and Zhou, Q and Fang, Z and Lin, Y and Xu, S and Feng, B and Zhuo, Y and Jiang, X and Zhao, H and Wu, D and Trabalza-Marinucci, M and Che, L}, title = {Effect of heating, microbial fermentation, and enzymatic hydrolysis of soybean meal on growth performance, nutrient digestibility, and intestinal microbiota of weaned piglets.}, journal = {Journal of animal science}, volume = {101}, number = {}, pages = {}, pmid = {37962419}, issn = {1525-3163}, support = {2021ZDZX0011//Sichuan Science and Technology Program/ ; ARS-35//China Agriculture Research System/ ; 2022ZYDF036//Central Government Funds of Guiding Local Scientific and Technological Development/ ; }, mesh = {Animals ; Swine ; Fermentation ; *Gastrointestinal Microbiome ; Heating ; Flour ; Hydrolysis ; Digestion ; Animal Feed/analysis ; Glycine max ; Diet/veterinary ; Nutrients ; Diarrhea/veterinary ; }, abstract = {The macromolecular proteins, anti-nutritional factors, and allergens contained in soybean meal (SBM) have a negative impact on the growth of weaned piglets. The objective of this study was to investigate the effects of heating, microbial fermentation, and enzymatically hydrolyzed SBM on the growth performance, nutrient digestibility, serum biochemistry, intestinal morphology, volatile fatty acids, and microbiota of weaned piglets. After the preparation of soaked SBM (SSBM), enzymatically hydrolyzed SBM (ESBM), and microbial fermented and enzymatically hydrolyzed SBM (MESBM), 72 weaned piglets were randomly allocated to three groups for a 21-d trial. In the three groups, 17% of conventional SBM in basal corn-soybean meal diet was replaced by an equivalent amount of SSBM (control group), ESBM, or MESBM. The results showed that the contents of glycinin, β-conglycinin, trypsin inhibitor, and proteins above 20 kDa were significantly decreased in ESBM and MESBM, compared with SSBM, and the surface of ESBM and MESBM had more pores and fragmented structure. In the second week and throughout the entire experimental period, the diarrhea index was reduced (P < 0.01) in ESBM and MESBM in contrast with SSBM. Furthermore, the inclusion of ESBM and MESBM in the diet improved the apparent total tract digestibility of dry matter and crude protein (P < 0.05), and increased the abundances of the genera Lactobacillus and Clostridium_sensu_stricto_1, respectively. Metagenomic sequencing further identified that members of six species of Proteobacteria, four species of Clostridiales, and three species of Negativiautes were enriched in the colon of piglets fed MESBM, while two bacterial species, Lachnoclostridium and Lactobacillus_points, were enriched in the colon of piglets fed ESBM. In conclusion, replacing SSBM with ESBM or MESBM in the diet decreased the diarrhea index, which could be associated with improved nutrient digestibility and microbial composition.}, } @article {pmid37961710, year = {2023}, author = {Zhang, IH and Borer, B and Zhao, R and Wilbert, S and Newman, DK and Babbin, AR}, title = {Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen deficient zones with diverse metabolic potential.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37961710}, support = {R01 HL152190/HL/NHLBI NIH HHS/United States ; }, abstract = {Archaea belonging to the DPANN superphylum have been found within an expanding number of environments and perform a variety of biogeochemical roles, including contributing to carbon, sulfur, and nitrogen cycling. Generally characterized by ultrasmall cell sizes and reduced genomes, DPANN archaea may form mutualistic, commensal, or parasitic interactions with various archaeal and bacterial hosts, influencing the ecology and functioning of microbial communities. While DPANN archaea reportedly comprise 15-26% of the archaeal community within marine oxygen deficient zone (ODZ) water columns, little is known about their metabolic capabilities in these ecosystems. We report 33 novel metagenome-assembled genomes belonging to DPANN phyla Nanoarchaeota, Pacearchaeota, Woesarchaeota, Undinarchaeota, Iainarchaeota, and SpSt-1190 from pelagic ODZs in the Eastern Tropical North Pacific and Arabian Sea. We find these archaea to be permanent, stable residents of all 3 major ODZs only within anoxic depths, comprising up to 1% of the total microbial community and up to 25-50% of archaea. ODZ DPANN appear capable of diverse metabolic functions, including fermentation, organic carbon scavenging, and the cycling of sulfur, hydrogen, and methane. Within a majority of ODZ DPANN, we identify a gene homologous to nitrous oxide reductase. Modeling analyses indicate the feasibility of a nitrous oxide reduction metabolism for host-attached symbionts, and the small genome sizes and reduced metabolic capabilities of most DPANN MAGs suggest host-associated lifestyles within ODZs.}, } @article {pmid37961379, year = {2023}, author = {Thurimella, K and Mohamed, AMT and Graham, DB and Owens, RM and La Rosa, SL and Plichta, DR and Bacallado, S and Xavier, RJ}, title = {Protein Language Models Uncover Carbohydrate-Active Enzyme Function in Metagenomics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37961379}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 DK127171/DK/NIDDK NIH HHS/United States ; R01 HL157717/HL/NHLBI NIH HHS/United States ; }, abstract = {In metagenomics, the pool of uncharacterized microbial enzymes presents a challenge for functional annotation. Among these, carbohydrate-active enzymes (CAZymes) stand out due to their pivotal roles in various biological processes related to host health and nutrition. Here, we present CAZyLingua, the first tool that harnesses protein language model embeddings to build a deep learning framework that facilitates the annotation of CAZymes in metagenomic datasets. Our benchmarking results showed on average a higher F1 score (reflecting an average of precision and recall) on the annotated genomes of Bacteroides thetaiotaomicron, Eggerthella lenta and Ruminococcus gnavus compared to the traditional sequence homology-based method in dbCAN2. We applied our tool to a paired mother/infant longitudinal dataset and revealed unannotated CAZymes linked to microbial development during infancy. When applied to metagenomic datasets derived from patients affected by fibrosis-prone diseases such as Crohn's disease and IgG4-related disease, CAZyLingua uncovered CAZymes associated with disease and healthy states. In each of these metagenomic catalogs, CAZyLingua discovered new annotations that were previously overlooked by traditional sequence homology tools. Overall, the deep learning model CAZyLingua can be applied in combination with existing tools to unravel intricate CAZyme evolutionary profiles and patterns, contributing to a more comprehensive understanding of microbial metabolic dynamics.}, } @article {pmid37961349, year = {2023}, author = {Horigan, S and Kistler, A and Ranaivoson, HC and Andrianianina, A and Andry, S and Kettenburg, G and Raharinosy, V and Randriambolamanantsoa, TH and Tato, CM and Lacoste, V and Heraud, JM and Dussart, P and Brook, CE}, title = {Detection, characterization, and phylogenetic analysis of a near-whole genome sequence of a novel astrovirus in an endemic Malagasy fruit bat, Rousettus madagascariensis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.10.27.564436}, pmid = {37961349}, abstract = {Bats (order: Chiroptera) are known to host a diverse range of viruses, some of which present a public health risk. Thorough viral surveillance is therefore essential to predict and potentially mitigate zoonotic spillover. Astroviruses (family: Astroviridae) are an understudied group of viruses with a growing amount of indirect evidence for zoonotic transfer. Astroviruses have been detected in bats with significant prevalence and diversity, suggesting that bats may act as important astrovirus hosts. Most astrovirus surveillance in wild bat hosts has, to date, been restricted to single-gene PCR detection and concomitant Sanger sequencing; additionally, many bat species and many geographic regions have not yet been surveyed for astroviruses at all. Here, we use metagenomic Next Generation Sequencing (mNGS) to detect astroviruses in three species of Madagascar fruit bats, Eidolon dupreanum, Pteropus rufus, and Rousettus madagascariensis . We detect numerous partial sequences from all three species and one near-full length astrovirus sequence from Rousettus madagascariensis , which we use to characterize the evolutionary history of astroviruses both within bats and the broader mammalian clade, Mamastrovirus . Taken together, applications of mNGS implicate bats as important astrovirus hosts and demonstrate novel patterns of bat astrovirus evolutionary history, particularly in the Southwest Indian Ocean region.}, } @article {pmid37960810, year = {2023}, author = {Li, Z and Wang, J and Gou, X and Guo, Z and Xu, F}, title = {Trichomonas vaginalis in bronchoalveolar lavage fluid of a patient with severe pneumonia detected by metagenomic next-generation sequencing: A case report.}, journal = {Medicine}, volume = {102}, number = {45}, pages = {e35777}, pmid = {37960810}, issn = {1536-5964}, mesh = {Humans ; Female ; Aged, 80 and over ; Bronchoalveolar Lavage Fluid ; *Trichomonas vaginalis/genetics ; Coma ; *Diabetes Mellitus, Type 2 ; *Pneumonia ; High-Throughput Nucleotide Sequencing ; Fever ; }, abstract = {RATIONALE: Trichomonas vaginalis (T. vaginalis) is a common anaerobic parasitic protozoan. However, to the best of our knowledge, there are few reports documenting T. vaginalis infection outside the genitourinary tract. Severe pneumonia caused by T. vaginalis infection has been rarely reported.

PATIENT CONCERNS: The 80-year-old female patient had a 20-year history of type II diabetes; however, she was not on regular medication. She was hospitalized due to a coma which continued 2 hours caused by trauma after a car accident. After her admission, she was provided with continuous mechanical ventilation; during the ventilation, she was still in a coma, accompanied by repeated fever and presence of much yellow sticky phlegm. The head CT scan indicated temporal lobe hematoma and subarachnoid hemorrhage. The lung CT scan showed bilateral pulmonary inflammatory consolidation and mass lesions.

DIAGNOSES: She was initially diagnosed with severe pneumonia and acute respiratory distress syndrome. Subsequently, fiberoptic bronchoscopy was conducted, and bronchoalveolar lavage fluid (BALF) was collected and sent for metagenomic next-generation sequencing (mNGS). The result indicated the presence of abundant sequences from the T. vaginalis genome. Thus, she was diagnosed with pulmonary T. vaginalis infection.

INTERVENTION: Anti-infective ornidazole treatment has significantly improved her symptoms.

OUTCOMES: After treatment, the patient regained consciousness and was able to communicate, and there was no obvious expectoration, fever, or positive bronchus sign in the lungs. Thereby, she was discharged from the hospital.

LESSONS: Special attention should be paid to infections other than common bacterial infections, such as T. vaginalis. Moreover, infection of rare pathogenic microorganisms might show symptoms similar to common bacterial infection, leading to misdiagnosis, further highlighting the usefulness of mNGS in detecting pathogens in a timely, sensitive, and accurate manner.}, } @article {pmid37960282, year = {2023}, author = {Rohwer, N and El Hage, R and Smyl, C and Ocvirk, S and Goris, T and Grune, T and Swidsinski, A and Weylandt, KH}, title = {Ketogenic Diet Has Moderate Effects on the Fecal Microbiota of Wild-Type Mice.}, journal = {Nutrients}, volume = {15}, number = {21}, pages = {}, pmid = {37960282}, issn = {2072-6643}, support = {WE2908/13-1//Deutsche Forschungsgemeinschaft/ ; GR1240/20-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Female ; Mice ; Animals ; *Diet, Ketogenic ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; *Neuroprotective Agents ; *Microbiota ; Diet, High-Fat ; Bacteria/genetics ; *Actinobacteria/genetics ; Mice, Inbred C57BL ; }, abstract = {The ketogenic diet (KD) is a high-fat, low-carbohydrate diet that has been reported to have neuroprotective effects. The health effects of KD might be linked to an altered gut microbiome, which plays a major role in host health, leading to neuroprotective effects via the gut-brain axis. However, results from different studies, most often based on the 16S rRNA gene and metagenome sequencing, have been inconsistent. In this study, we assessed the effect of a 4-week KD compared to a western diet (WD) on the colonic microbiome of female C57Bl/6J mice by analyzing fecal samples using fluorescence in situ hybridization. Our results showed distinct changes in the total number of gut bacteria following the 4-week KD, in addition to changes in the composition of the microbiome. KD-fed mice showed higher absolute numbers of Actinobacteria (especially Bifidobacteria spp.) and lower absolute levels of Proteobacteria, often linked to gut inflammation, in comparison with WD-fed mice. Furthermore, an increased abundance of the typically rare genus Atopobium was observed. These changes may indicate the possible anti-inflammatory effects of the KD. However, since the overall changes in the microbiota seem low, the KD effects might be linked to the differential abundance of only a few key genera in mice.}, } @article {pmid37960207, year = {2023}, author = {Li, T and Rui, Z and Mao, L and Chang, Y and Shao, J and Chen, Y and Han, Q and Sui, X and An, N and Li, H and Feng, H and Jiang, T and Wang, Q}, title = {Eight Weeks of Bifidobacterium lactis BL-99 Supplementation Improves Lipid Metabolism and Sports Performance through Short-Chain Fatty Acids in Cross-Country Skiers: A Preliminary Study.}, journal = {Nutrients}, volume = {15}, number = {21}, pages = {}, pmid = {37960207}, issn = {2072-6643}, support = {2019YFF0301700//National Key R&D Program of China/ ; }, mesh = {Humans ; Male ; *Athletic Performance ; *Bifidobacterium animalis ; Bile Acids and Salts ; Dietary Supplements ; Fatty Acids, Volatile/analysis ; Lipid Metabolism ; *Probiotics ; Single-Blind Method ; }, abstract = {(1) Background: Probiotics in the form of nutritional supplements are safe and potentially useful for strategic application among endurance athletes. Bifidobacterium animalis lactis BL-99 (BL-99) was isolated from the intestines of healthy Chinese infants. We combined plasma-targeted metabolomics and fecal metagenomics to explore the effect of 8 weeks of BL-99 supplementation on cross-country skiers' metabolism and sports performance. (2) Methods: Sixteen national top-level male cross-country skiers were recruited and randomly divided into a placebo group (C) and a BL-99 group (E). The participants took the supplements four times/day (with each of three meals and at 21:00) consistently for 8 weeks. The experiment was conducted in a single-blind randomized fashion. The subject's dietary intake and total daily energy consumption were recorded. Blood and stool samples were collected before and after the 8-week intervention, and body composition, muscle strength, blood biochemical parameters, plasma-targeted metabolomic data, and fecal metagenomic data were then analyzed. (3) Results: The following changes occurred after 8 weeks of BL-99 supplementation: (a) There was no significant difference in the average total daily energy consumption and body composition between the C and E groups. (b) The VO2max and 60°/s and 180°/s knee joint extensor strength significantly increased in both the C and E groups. By the eighth week, the VO2max and 60 s knee-joint extensor strength were significantly higher in the E group than in the C group. (c) The triglyceride levels significantly decreased in both the C and E groups. In addition, the LDL-C levels significantly decreased in the E group. (d) The abundance of Bifidobacterium animalis increased two-fold in the C group and forty-fold in the E group. (e) Plasma-targeted metabolomic analysis showed that, after eight weeks of BL-99 supplementation, the increases in DHA, adrenic acid, linoleic acid, and acetic acid and decreases in glycocholic acid and glycodeoxycholic acid in the E group were significantly higher than those in the C group. (f) Spearman correlation analysis showed that there was a significant positive correlation between Bifidobacterium animalis' abundance and SCFAs, PUFAs, and bile acids. (g) There was a significant correlation between the most significantly regulated metabolites and indicators related to sports performance and lipid metabolism. (4) Conclusions: Eight weeks of BL-99 supplementation combined with training may help to improve lipid metabolism and sports performance by increasing the abundance of Bifidobacterium, which can promote the generation of short-chain fatty acids and unsaturated fatty acids, and inhibit the synthesis of bile acids.}, } @article {pmid37958120, year = {2023}, author = {Li, S and Wang, S and Pan, C and Luo, Y and Liang, S and Long, S and Yang, X and Wang, B}, title = {Differences in Physiological Performance and Gut Microbiota between Deep-Sea and Coastal Aquaculture of Thachinotus Ovatus: A Metagenomic Approach.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {21}, pages = {}, pmid = {37958120}, issn = {2076-2615}, support = {(2021-928)//Shenzhen Special Fund for Agricultural Development (fishery) Agricultural high-tech projects/ ; (2020YFD0901002)//National Key Research and Development Program of China/ ; (KCXST20221021111206015)//Shenzhen Science and Technology Program/ ; Shenzhen University//Shenzhen University Testing Center; Public service platform for large-scale instruments and equipment of College of Life Sciences and Oceanography/ ; }, abstract = {Aquaculture has become the fastest growing sector in global agriculture. The environmental degradation, diseases, and high density of mariculture has made for an inevitable shift in mariculture production from coastal to deep-sea areas. The influence that traditional coastal and emerging deep-sea farming environments exert on aquatic growth, immunity and gut microbial flora is unclear. To address this question, we compared the growth performance, physiological indicators and intestinal microbiological differences of deep-sea and coastal aquaculture in the Guangxi Beibu Gulf of China. The results showed that the growth performance and the complement of C3 and C4 (C3, C4), superoxide dismutase (SOD), and lysozyme (LYS), these physiological and biochemical indicators in the liver, kidney, and muscle of Trachinotus ovatus (T. ovatus), showed significant differences under different rearing conditions. Metagenome sequencing analysis showed Ascomycota, Pseudomonadota, and Bacillota were the three dominant phyla, accounting for 52.98/53.32 (coastal/deep sea), 24.30/22.13, and 10.39/11.82%, respectively. Aligned against the CARD database, a total of 23/2 (coastal/deep-sea) antibiotic resistance genes were screened and grouped into 4/2 genotypes. It indicated that compared with deep-sea fish, higher biological oxygen levels (3.10 times), inorganic nitrogen (110.00 times) and labile phosphate levels (29.00 times) in coastal waters might contributed to the existence of eutrophication with antibiotic resistance. The results of the study can provide complementary data on the study of the difference between deep-sea farming and traditional coastal farming, serving as a reference to future in-depth work on the transformation of fisheries development and scientific standardization of deep-sea farming.}, } @article {pmid37957747, year = {2023}, author = {Quan, J and Xu, C and Ruan, D and Ye, Y and Qiu, Y and Wu, J and Zhou, S and Luan, M and Zhao, X and Chen, Y and Lin, D and Sun, Y and Yang, J and Zheng, E and Cai, G and Wu, Z and Yang, J}, title = {Composition, function, and timing: exploring the early-life gut microbiota in piglets for probiotic interventions.}, journal = {Journal of animal science and biotechnology}, volume = {14}, number = {1}, pages = {143}, pmid = {37957747}, issn = {1674-9782}, support = {2022B0202090002//Key Technologies R&D Program of Guangdong Province project/ ; 2021M701263//China Postdoctoral Science Foundation/ ; 2019BT02N630//Local Innovative and Research Teams Project of Guangdong Province/ ; 2023KJ126//Project of Swine Innovation Team in the Guangdong Modern Agricultural Research System/ ; }, abstract = {BACKGROUND: The establishment of a robust gut microbiota in piglets during their early developmental stage holds the potential for long-term advantageous effects. However, the optimal timeframe for introducing probiotics to achieve this outcome remains uncertain.

RESULTS: In the context of this investigation, we conducted a longitudinal assessment of the fecal microbiota of 63 piglets at three distinct pre-weaning time points. Simultaneously, we gathered vaginal and fecal samples from 23 sows. Employing 16S rRNA gene and metagenomic sequencing methodologies, we conducted a comprehensive analysis of the fluctuation patterns in microbial composition, functional capacity, interaction networks, and colonization resistance within the gut microbiota of piglets. As the piglets progressed in age, discernible modifications in intestinal microbial diversity, composition, and function were observed. A source-tracking analysis unveiled the pivotal role of fecal and vaginal microbiota derived from sows in populating the gut microbiota of neonatal piglets. By D21, the microbial interaction network displayed a more concise and efficient configuration, accompanied by enhanced colonization resistance relative to the other two time points. Moreover, we identified three strains of Ruminococcus sp. at D10 as potential candidates for improving piglets' weight gain during the weaning phase.

CONCLUSIONS: The findings of this study propose that D10 represents the most opportune juncture for the introduction of external probiotic interventions during the early stages of piglet development. This investigation augments our comprehension of the microbiota dynamics in early-life of piglets and offers valuable insights for guiding forthcoming probiotic interventions.}, } @article {pmid37957556, year = {2023}, author = {Ji, J and Wang, W and Xiang, S and Wei, X and Pang, G and Shi, H and Dong, J and Pang, J}, title = {Diagnosis of leptospira by metagenomics next-generation sequencing with extracorporeal membrane oxygenation support: a case report.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {788}, pmid = {37957556}, issn = {1471-2334}, support = {2019036//Guangxi Zhuang Autonomous Region Nanning Qingxiu District Key Research and Development Program Project/ ; Gui Ke AD22035101//Guangxi Clinical Medical Research Center for Critical Care of Major Infectious Diseases/ ; ZZH2020013//Guangxi Key Laboratory of Acute Respiratory Distress Syndrome Diagnosis and Treatment Research/ ; }, mesh = {Male ; Humans ; Animals ; Swine ; Adult ; *Leptospira/genetics ; *Extracorporeal Membrane Oxygenation ; High-Throughput Nucleotide Sequencing ; *Leptospirosis/diagnosis/therapy ; Cognition ; }, abstract = {BACKGROUND: Leptospirosis is an infectious disease caused by pathogenic Leptospira spp., which could result in severe illnesses. Indirect contact with these pathogens is more common. Individuals could contract this disease through contact with contaminated water or during floods. In this case, we present the details of a 40-year-old male pig farmer who suffered from severe pulmonary hemorrhagic leptospirosis and multiple organ failure. The diagnosis of leptospirosis was confirmed through metagenomics next-generation sequencing (mNGS) while the patient received extracorporeal membrane oxygenation (ECMO) support, and antibiotic treatment was adjusted accordingly. The patient underwent comprehensive treatment and rehabilitation in the intensive care unit.

CONCLUSION: This case illustrates the importance of early diagnosis and treatment of leptospirosis. While obtaining the epidemiological history, second-generation metagenomics sequencing was utilized to confirm the etiology. The prompt initiation of ECMO therapy provided a crucial window of opportunity for addressing the underlying cause. This case report offers valuable insights for diagnosing patients with similar symptoms.}, } @article {pmid37956948, year = {2024}, author = {Saidulu, D and Agrawal, S and Bhatnagar, A and Gupta, AK}, title = {Sulfamethoxazole removal from wastewater via anoxic/oxic moving bed biofilm reactor: Degradation pathways and toxicity assessment.}, journal = {Bioresource technology}, volume = {392}, number = {}, pages = {129998}, doi = {10.1016/j.biortech.2023.129998}, pmid = {37956948}, issn = {1873-2976}, mesh = {*Wastewater ; *Sulfamethoxazole ; Biofilms ; Bioreactors/microbiology ; Anti-Bacterial Agents ; Waste Disposal, Fluid ; Nitrogen/analysis ; }, abstract = {The effects of sulfamethoxazole (SMZ), an antibiotic commonly detected in the water environment, on the performance of a single staged anoxic/oxic moving bed biofilm reactor (A/O MBBR), was investigated. The anoxic zone played a key role in the removal of SMZ with a percentage of contribution accounting for around 85% in the overall removal. Denitrifying heterotrophic microbes present in the anoxic zone showed relatively more resistance to higher SMZ loads. It was found that in extracellular polymeric substances, protein content was increased consistently with the increase in SMZ concentration. Based on the detected biotransformation products, four degradation pathways were proposed and the toxicity was evaluated. Metagenomic analysis revealed that at higher SMZ load the activity of genera, such as Proteobacteria and Actinobacteria was significantly affected. In summary, proper design and operation of staged A/O MBBR can offer a resilient and robust treatment towards SMZ removal from wastewater.}, } @article {pmid37956947, year = {2023}, author = {Huang, R and Geng, M and Gao, S and Yin, X and Tian, J}, title = {In-depth insight into improvement of simultaneous nitrification and denitrification/biofouling control by increasing sludge concentration in membrane reactor: performance, microbial assembly and metagenomic analysis.}, journal = {Bioresource technology}, volume = {393}, number = {}, pages = {130013}, doi = {10.1016/j.biortech.2023.130013}, pmid = {37956947}, issn = {1873-2976}, abstract = {Currently, severe membrane fouling and inefficient nitrogen removal were two main issues that hindered the sustainable operation and further application of membrane bioreactor (MBR). This study aimed to simultaneously alleviate membrane fouling and improve nitrogen removal by applying high sludge concentration in MBR. Results showed that high sludge concentration (12000 mg/L) enhanced total nitrogen removal efficiency (78 %) and reduced transmembrane pressure development rate. Microbial community analysis revealed that high sludge concentration enriched functional bacteria associated with nitrogen removal, increased filamentous bacteria fraction in bio-cake and inhibited Thiothrix overgrowth in bulk sludge. From molecular level, the key genes involved in nitrogen metabolism, electron donor/adenosine triphosphate production and amino acid degradation were up-regulated under high sludge concentration. Overall, high sludge concentration improved microbial assembly and functional gene abundance, which not only enhanced nitrogen removal but also alleviated membrane fouling. This study provided an effective strategy for sustainable operation of MBR.}, } @article {pmid37956857, year = {2023}, author = {Scro, AK and Bojko, J and Behringer, DC}, title = {Symbiotic survey of the bay scallop (Argopecten irradians) from the Gulf coast of Florida, USA.}, journal = {Journal of invertebrate pathology}, volume = {201}, number = {}, pages = {108019}, doi = {10.1016/j.jip.2023.108019}, pmid = {37956857}, issn = {1096-0805}, mesh = {Animals ; Florida ; *Conservation of Natural Resources ; Fisheries ; Gene Library ; *Pectinidae ; }, abstract = {The bay scallop Argopecten irradians supported a commercial fishery in Florida but their population declined and the fishery closed in 1994. A recreational fishery remains open along the west coast of Florida despite continued threats from overfishing and a changing environment. Disease is among those threats, as it is for bivalve fisheries globally. We examined the relationship between bay scallop population density, its symbiotic microbiome, and geographic location. We focused on three sites within the range of Florida's recreational scallop fishery: St. Joseph Bay (northern extent), offshore of the Steinhatchee River (central), and offshore of Hernando County (southern extent). The study was conducted prior to the seasonal opening of the fishery to minimize the impact of fishing on our results. We also sampled caged scallops that are used for restocking in St. Joseph Bay to assess the effect of artificially high density and confinement on the scallop pathobiome. Using a combination of traditional histological methods, molecular diagnostics, and metagenomics, a suite of 15 symbionts were identified. Among them, RNA-seq data revealed four novel + ssRNA viral genomes: three picorna-like viruses and one hepe-like virus. The DNA-seq library revealed a novel Mycoplasma species. Histological evaluation revealed that protozoan, helminth and crustacean infections were common in A. irradians. These potential pathogens add to those already known for A. irradians and underscores the risk they pose to the fishery.}, } @article {pmid37956562, year = {2024}, author = {Ou, D and Ni, Y and Li, W and He, W and Wang, L and Huang, H and Pan, Z}, title = {Psychrobacter species enrichment as potential microplastic degrader and the putative biodegradation mechanism in Shenzhen Bay sediment, China.}, journal = {Journal of hazardous materials}, volume = {464}, number = {}, pages = {132971}, doi = {10.1016/j.jhazmat.2023.132971}, pmid = {37956562}, issn = {1873-3336}, mesh = {Microplastics/analysis ; Plastics/analysis ; *Psychrobacter/genetics ; Bays ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring ; Biodegradation, Environmental ; China ; Bacteria/genetics ; Geologic Sediments/microbiology ; }, abstract = {Microplastic (MP) pollution has emerged as a pressing environmental concern due to its ubiquity and longevity. Biodegradation of MPs has garnered significant attention in combatting global MP contamination. This study focused on MPs within sediments near the sewage outlet of Shenzhen Bay. The objective was to elucidate the microbial communities in sediments with varying MPs, particularly those with high MP loads, and to identify microorganisms associated with MP degradation. The results revealed varying MP abundance, ranging from 211 to 4140 items kg[-1] dry weight (d. w.), with the highest concentration observed near the outfall. Metagenomic analysis confirmed the enrichment of Psychrobacter species in sediments with high MP content. Psychrobacter accounted for ∼16.71% of the total bacterial community and 41.71% of hydrocarbon degrading bacteria at the S3 site, exhibiting a higher abundance than at other sampling sites. Psychrobacter contributed significantly to bacterial function at S3, as evidenced by the Kyoto Encyclopedia of Genes and Genomes pathway and enzyme analysis. Notably, 28 enzymes involved in MP biodegradation were identified, predominantly comprising oxidoreductases, hydrolases, transferases, ligases, lyases, and isomerases. We propose a putative mechanism for MP biodegradation, involving the breakdown of long-chain plastic polymers and subsequent oxidation of short-chain oligomers, ultimately leading to thorough mineralization.}, } @article {pmid37956203, year = {2023}, author = {Brunner, JD and Gallegos-Graves, LA and Kroeger, ME}, title = {Inferring microbial interactions with their environment from genomic and metagenomic data.}, journal = {PLoS computational biology}, volume = {19}, number = {11}, pages = {e1011661}, pmid = {37956203}, issn = {1553-7358}, mesh = {Humans ; *Genomics ; Metagenomics/methods ; Metagenome/genetics ; *Microbiota/genetics ; Microbial Interactions/genetics ; }, abstract = {Microbial communities assemble through a complex set of interactions between microbes and their environment, and the resulting metabolic impact on the host ecosystem can be profound. Microbial activity is known to impact human health, plant growth, water quality, and soil carbon storage which has lead to the development of many approaches and products meant to manipulate the microbiome. In order to understand, predict, and improve microbial community engineering, genome-scale modeling techniques have been developed to translate genomic data into inferred microbial dynamics. However, these techniques rely heavily on simulation to draw conclusions which may vary with unknown parameters or initial conditions, rather than more robust qualitative analysis. To better understand microbial community dynamics using genome-scale modeling, we provide a tool to investigate the network of interactions between microbes and environmental metabolites over time. Using our previously developed algorithm for simulating microbial communities from genome-scale metabolic models (GSMs), we infer the set of microbe-metabolite interactions within a microbial community in a particular environment. Because these interactions depend on the available environmental metabolites, we refer to the networks that we infer as metabolically contextualized, and so name our tool MetConSIN: Metabolically Contextualized Species Interaction Networks.}, } @article {pmid37956179, year = {2023}, author = {Sauters, TJC and Roth, C and Murray, D and Sun, S and Floyd Averette, A and Onyishi, CU and May, RC and Heitman, J and Magwene, PM}, title = {Amoeba predation of Cryptococcus: A quantitative and population genomic evaluation of the accidental pathogen hypothesis.}, journal = {PLoS pathogens}, volume = {19}, number = {11}, pages = {e1011763}, pmid = {37956179}, issn = {1553-7374}, support = {R01 AI039115/AI/NIAID NIH HHS/United States ; R01 AI133654/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Humans ; Mice ; *Amoeba/microbiology ; Metagenomics ; Predatory Behavior ; *Cryptococcus neoformans/genetics ; *Cryptococcosis/genetics/microbiology ; }, abstract = {The "Amoeboid Predator-Fungal Animal Virulence Hypothesis" posits that interactions with environmental phagocytes shape the evolution of virulence traits in fungal pathogens. In this hypothesis, selection to avoid predation by amoeba inadvertently selects for traits that contribute to fungal escape from phagocytic immune cells. Here, we investigate this hypothesis in the human fungal pathogens Cryptococcus neoformans and Cryptococcus deneoformans. Applying quantitative trait locus (QTL) mapping and comparative genomics, we discovered a cross-species QTL region that is responsible for variation in resistance to amoeba predation. In C. neoformans, this same QTL was found to have pleiotropic effects on melanization, an established virulence factor. Through fine mapping and population genomic comparisons, we identified the gene encoding the transcription factor Bzp4 that underlies this pleiotropic QTL and we show that decreased expression of this gene reduces melanization and increases susceptibility to amoeba predation. Despite the joint effects of BZP4 on amoeba resistance and melanin production, we find no relationship between BZP4 genotype and escape from macrophages or virulence in murine models of disease. Our findings provide new perspectives on how microbial ecology shapes the genetic architecture of fungal virulence, and suggests the need for more nuanced models for the evolution of pathogenesis that account for the complexities of both microbe-microbe and microbe-host interactions.}, } @article {pmid37956168, year = {2023}, author = {Stegmüller, S and Qi, W and Torgerson, PR and Fraefel, C and Kubacki, J}, title = {Hazard potential of Swiss Ixodes ricinus ticks: Virome composition and presence of selected bacterial and protozoan pathogens.}, journal = {PloS one}, volume = {18}, number = {11}, pages = {e0290942}, pmid = {37956168}, issn = {1932-6203}, mesh = {Humans ; Animals ; *Ixodes/microbiology ; Switzerland/epidemiology ; Virome/genetics ; Nymph ; *Encephalitis, Tick-Borne/epidemiology ; *Tick-Borne Diseases ; *Encephalitis Viruses, Tick-Borne/genetics ; }, abstract = {Ticks play an important role in transmitting many different emerging zoonotic pathogens that pose a significant threat to human and animal health. In Switzerland and abroad, the number of tick-borne diseases, in particular tick-borne encephalitis (TBE), has been increasing over the last few years. Thus, it remains essential to investigate the pathogen spectrum of ticks to rapidly detect emerging pathogens and initiate the necessary measures. To assess the risk of tick-borne diseases in different regions of Switzerland, we collected a total of 10'286 ticks from rural and urban areas in ten cantons in 2021 and 2022. Ticks were pooled according to species, developmental stage, gender, and collection site, and analyzed using next generation sequencing (NGS) and quantitative polymerase chain reaction (qPCR). The metagenomic analysis revealed for the first time the presence of Alongshan virus (ALSV) in Swiss ticks. Interestingly, the pool-prevalence of ALSV was higher than that of tick-borne encephalitis virus (TBEV). Furthermore, several TBEV foci have been identified and pool prevalence of selected non-viral pathogens determined.}, } @article {pmid37955733, year = {2023}, author = {Bombaywala, S and Dafale, NA}, title = {Mapping the spread and mobility of antibiotic resistance in wastewater due to COVID-19 surge.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {58}, pages = {121734-121747}, pmid = {37955733}, issn = {1614-7499}, mesh = {Humans ; *Wastewater ; Genes, Bacterial ; Pandemics ; *COVID-19/genetics ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Large amounts of antibiotics have been discharged into wastewater during the COVID-19 pandemic due to overuse and misuse of antibiotics to treat patients. Wastewater-based surveillance can be used as an early warning for antibiotic resistance (AR) emergence. The present study analyzed municipal wastewater corresponding to the major pandemic waves (WW1, WW2, and WW3) in India along with hospital wastewater (Ho) taken as a benchmark for AR. Commonly prescribed antibiotics during a pandemic, azithromycin and cefixime residues, were found in the range of 2.1-2.6 μg/L in Ho and WW2. Total residual antibiotic concentration was less in WW2; however, the total antibiotic resistance gene (ARG) count was 1065.6 ppm compared to 85.2 ppm in Ho. Metagenome and RT-qPCR analysis indicated a positive correlation between antibiotics and non-corresponding ARGs (blaOXA, aadA, cat, aph3, and ere), where 7.2-7.5% was carried by plasmid in the bacterial community of WW1 and WW2. Moreover, as the abundance of the dfrA and int1 genes varied most among municipal wastewater, they can be suggested as AR markers for the pandemic. The common pathogens Streptococcus, Escherichia, Shigella, and Aeromonas were putative ARG hosts in metagenome-assembled genomes. The ARG profile and antibiotic levels varied between municipal wastewaters but were fairly similar for WW2 and Ho, suggesting the impact of the pandemic in shaping the resistome pattern. The study provides insights into the resistome dynamic, AR markers, and host-ARG association in wastewater during the COVID-19 surge. Continued surveillance and identification of intervention points for AR beyond the pandemic are essential to curbing the environmental spread of ARGs in the near future.}, } @article {pmid37954503, year = {2023}, author = {Fang, C and Xu, L}, title = {Chlamydia psittaci Pneumonia-Induced Pulmonary Thrombosis: A Case Report.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {7063-7069}, pmid = {37954503}, issn = {1178-6973}, abstract = {Chlamydia psittaci pneumonia frequently leads to various extrapulmonary complications; however, reports of C. psittaci-pneumonia complicated by pulmonary thrombosis are uncommon. We report a case of severe C. psittaci pneumonia in a patient with a history of poultry contact and clinical manifestations including hyperpyrexia, dyspnea, and respiratory failure, which necessitated tracheal intubation for assisted ventilation. C. psittaci in bronchoalveolar lavage fluid was detected with metagenomic next-generation sequencing. Following targeted antibiotic therapy, the fever subsided, although dyspnea persisted without significant improvement, and chest pain developed. Compared to previous measurements, the D-dimer level increased, and CT pulmonary angiography revealed thromboses in the pulmonary artery trunk and left pulmonary artery. The symptoms improved after anticoagulant treatment, and the patient was discharged subsequently. This study suggests that C. psittaci infection may be associated with the formation of pulmonary thrombosis. Additional clinical data are required to support this inference. Following targeted antibiotic therapy, if persistent dyspnea, chest pain, and increased D-dimer level are present, pulmonary thrombosis should be considered, and pulmonary artery angiography can confirm the diagnosis.}, } @article {pmid37954240, year = {2023}, author = {Yan, P and Ma, H and Tian, W and Liu, J and Yan, X and Ma, L and Wei, S and Zhu, J and Zhu, Y and Lai, J}, title = {Methadone maintenance treatment is more effective than compulsory detoxification in addressing gut microbiota dysbiosis caused by heroin abuse.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1283276}, pmid = {37954240}, issn = {1664-302X}, abstract = {INTRODUCTION: Heroin use disorder (HUD) is commonly accompanied by gut dysbiosis, but the roles of gut microbiota in HUD treatment, such as compulsory detoxification and methadone maintenance treatment (MMT), remain poorly understood.

METHODS: In this study, we performed 16 s rDNA and whole metagenome sequencing to analyze the gut microbial profiles of HUD patients undergoing heroin addiction, heroin withdrawal (compulsory detoxification), and MMT.

RESULTS: Our findings revealed that, compared to healthy controls, microbial diversity was significantly decreased in HUD patients who were in a state of heroin addiction and withdrawal, but not in those receiving MMT. We observed significant alterations in 10 bacterial phyla and 20 bacterial families in HUD patients, while MMT partially restored these changes. Whole metagenome sequencing indicated gut microbiota functions were significantly disrupted in HUD patients experiencing heroin addiction and withdrawal, but MMT was found to almost reverse these dysfunctions. In addition, we identified 24 featured bacteria at the genus level that could be used to effectively distinguish between healthy individuals and those with heroin addiction, heroin withdrawal, or receiving MMT. Furthermore, we found the relative abundance of Actinomyces, Turicibacter and Weissella were positively associated with the Hamilton Depression Scale score in different states of HUD patients.

DISCUSSION: This study provides evidence from the gut microbiota perspective that MMT is a more effective approach than compulsory detoxification for HUD treatment.}, } @article {pmid37954099, year = {2023}, author = {Jiang, J and Lv, M and Yang, K and Zhao, G and Fu, Y}, title = {A case report of diagnosis and dynamic monitoring of Listeria monocytogenes meningitis with NGS.}, journal = {Open life sciences}, volume = {18}, number = {1}, pages = {20220738}, pmid = {37954099}, issn = {2391-5412}, abstract = {Listeria monocytogenes (LM) infections of the central nervous system are deadly and have vague symptoms. Traditional cerebro spinal fluid culture has a low positive rate, and because antibiotic use is common following therapy, it is more challenging to assess the response from pathogen content. In this case, a 66-year-old man who had a fever, a headache, and vomit was admitted to the hospital. He had diabetes, decline in thyroid function, and a history of pituitary tumor removal surgery. His initial treatment with ribavirin, ceftriaxone antibiotic, and moxifloxacin did not go well. Using two etiological tests (culture and metagenomic next-generation sequencing [mNGS]), his cerebrospinal fluid tested positively for LM. Ampicillin-sulbactam and meropenem were used as treatments once LM meningitis was identified. After treatment, his cerebrospinal fluid was assessed once more. Culture: negative; targeted next-generation sequencing (tNGS): positive and shows changes in the copy number of the LM. After 44 days of treatment, the patient finally stopped taking antibiotics, and the prognosis was good. Our study showed that mNGS and tNGS, as novel approaches for pathogen detection, are capable of identifying pathogens quickly, sensitively, and accurately, especially when there are few infections present (such as after antibiotic treatment). The two methods can be a powerful assistance for helping clinicians to choose the best course of action.}, } @article {pmid37953802, year = {2023}, author = {Jia, H and Liu, H and Tu, M and Wang, Y and He, X and Zhang, G}, title = {Pleural cryptococcosis diagnosed by pleural biopsy in an immunocompromised patient: a case report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1258021}, pmid = {37953802}, issn = {2235-2988}, mesh = {Humans ; Pleura ; *Cryptococcosis/microbiology ; *Pleural Effusion ; Biopsy/adverse effects ; Immunocompromised Host ; }, abstract = {OBJECTIVE: The aim of this study is to report an isolated pleural cryptococcosis with pleural effusion as the only manifestation, confirmed by pleural biopsy in a patient with thymoma combined with myasthenia gravis, who developed pleural effusion of unknown origin after long-term glucocorticoids and tacrolimus therapy.

METHODS: Pathological examination of the right pleural biopsy tissue from a patient with unexplained recurrent pleural effusion was implemented. Morphological analysis of the fungal component and metagenomic next-generation sequencing (mNGS) on the pleural tissue were performed.

RESULTS: A biopsy specimen of the right pleura revealed numerous yeast-like organisms surrounded by mucous capsules and Cryptococcus neoformans was detected by mNGS with a species-specific read number (SSRN) of 4, confirming the diagnosis of pleural cryptococcosis. Pleural effusion was eliminated with amphotericin B and fluconazole, and healthy status was maintained at the time of review 1 year later.

CONCLUSION: Cryptococcosis, manifested by simple pleural effusion, is extremely rare, but when repeated pleural effusion occurs in immunocompromised patients or in patients with malignant tumors, the possibility of cryptococcosis should be treated with high vigilance and pleural biopsy is recommended if necessary in order to confirm the diagnosis.}, } @article {pmid37953793, year = {2023}, author = {Boueroy, P and Chopjitt, P and Hatrongjit, R and Morita, M and Sugawara, Y and Akeda, Y and Iida, T and Hamada, S and Kerdsin, A}, title = {Fluoroquinolone resistance determinants in carbapenem-resistant Escherichia coli isolated from urine clinical samples in Thailand.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16401}, pmid = {37953793}, issn = {2167-8359}, mesh = {Humans ; Escherichia coli/genetics ; Fluoroquinolones/pharmacology ; *Escherichia coli Infections/drug therapy ; Thailand/epidemiology ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; *Carbapenem-Resistant Enterobacteriaceae ; beta-Lactamases/genetics ; }, abstract = {BACKGROUND: Escherichia coli is the most common cause of urinary tract infections and has fluoroquinolone (FQ)-resistant strains, which are a worldwide concern.

OBJECTIVES: To characterize FQ-resistant determinants among 103 carbapenem-resistant E. coli (CREc) urinary isolates using WGS.

METHODS: Antimicrobial susceptibility, biofilm formation, and short-read sequencing were applied to these isolates. Complete genome sequencing of five CREcs was conducted using short- and long-read platforms.

RESULTS: ST410 (50.49%) was the predominant ST, followed by ST405 (12.62%) and ST361 (11.65%). Clermont phylogroup C (54.37%) was the most frequent. The genes NDM-5 (74.76%) and CTX-M-15 (71.84%) were the most identified. Most CREcs were resistant to ciprofloxacin (97.09%) and levofloxacin (94.17%), whereas their resistance rate to nitrofurantoin was 33.98%. Frequently, the gene aac(6')-Ib (57.28%) was found and the coexistence of aac(6')-Ib and blaCTX-M-15 was the most widely predominant. All isolates carried the gyrA mutants of S83L and D87N. In 12.62% of the isolates, the coexistence was detected of gyrA, gyrB, parC, and parE mutations. Furthermore, the five urinary CREc-complete genomes revealed that blaNDM-5 or blaNDM-3 were located on two plasmid Inc types, comprising IncFI (60%, 3/5) and IncFI/IncQ (40%, 2/5). In addition, both plasmid types carried other resistance genes, such as blaOXA-1, blaCTX-M-15, blaTEM-1B, and aac(6')-Ib. Notably, the IncFI plasmid in one isolate carried three copies of the blaNDM-5 gene.

CONCLUSIONS: This study showed FQ-resistant determinants in urinary CREc isolates that could be a warning sign to adopt efficient strategies or new control policies to prevent further spread and to help in monitoring this microorganism.}, } @article {pmid37953104, year = {2023}, author = {Sim, S and Park, HJ and Kim, YK and Choi, Y and Park, HS}, title = {Lactobacillus paracasei-derived extracellular vesicles alleviate neutrophilic asthma by inhibiting the JNK pathway in airway epithelium.}, journal = {Allergology international : official journal of the Japanese Society of Allergology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.alit.2023.10.008}, pmid = {37953104}, issn = {1440-1592}, abstract = {BACKGROUND: Lactobacillus paracasei has been known to reduce airway resistance and inflammation in asthma. However, the therapeutic effect of its extracellular vesicles (EVs) in patients with asthma remains unclear.

METHODS: To validate the clinical relevance of L. paracasei-derived EVs (LpEV) in asthma, the composition of gut microbial EVs was verified by metagenomics in LPS-induced C57BL/6 mice. The components of proteins and metabolites in LpEV were identified by peptide mass fingerprinting and metabolomic analysis. The serum levels of specific IgG1 or IgG4 antibodies to LpEV were compared by ELISA between patients with eosinophilic asthma (EA, n = 10) and those with neutrophilic asthma (NA, n = 10) as well as with healthy controls (HCs, n = 10). Finally, therapeutic effects of LpEV and their metabolites in asthma were validated in vivo/in vitro.

RESULTS: Significantly lower proportions of EVs derived from Lactobacillus at the genus level were noted in mice with NA than in control mice. Moreover, the serum levels of LpEV-specific IgG4, but not IgG1, were lower in patients with NA than in those with EA or in HCs and positively correlated with FEV1 (%) values. In addition, oral administration of LpEV reduced airway resistance and inflammation in mice with NA. Finally, LpEV and their 3 metabolites (dodecanoic acid, palmitoleic acid, and D-(-)-tagatose) significantly inhibited JNK phosphorylation/IL-8 production in airway epithelium in vitro.

CONCLUSIONS: These findings suggest that LpEV may have a therapeutic potential targeting NA by suppressing the JNK pathway and proinflammatory cytokine production in airway epithelium.}, } @article {pmid37952948, year = {2023}, author = {Yamada, K and Koyauchi, T and Yokomura, K and Fujita, T and Sugiyama, H and Shimota, R and Shimura, N and Matsumoto, Y and Nakamura, S and Chikamatsu, K and Mitarai, S and Suda, T}, title = {Non-tuberculosis Mycobacterial Pulmonary Disease Caused by Mycobacterium kiyosense, a New Species.}, journal = {Internal medicine (Tokyo, Japan)}, volume = {}, number = {}, pages = {}, doi = {10.2169/internalmedicine.2785-23}, pmid = {37952948}, issn = {1349-7235}, abstract = {Non-tuberculosis mycobacterial (NTM) pulmonary disease (NTM-PD) is quite common, and newly identified species are being reported increasingly frequently thanks to advances in identification technologies. A 56-year-old woman had mild sputum production showed bronchiectasis with multiple small nodules, consistent with NTM-PD, on chest computed tomography. Mycobacterial species were isolated from the specimens; however, conventional methods could not identify the species. We conducted whole-genome sequencing and identified the NTM isolates as Mycobacterium kiyosense, a species newly registered in 2023 from Japan. She was diagnosed with NTM-PD caused by M. kiyosense and received watchful waiting.}, } @article {pmid37952327, year = {2024}, author = {Shuai, X and Zhou, Z and Ba, X and Lin, Y and Lin, Z and Liu, Z and Yu, X and Zhou, J and Zeng, G and Ge, Z and Chen, H}, title = {Bacteriophages: Vectors of or weapons against the transmission of antibiotic resistance genes in hospital wastewater systems?.}, journal = {Water research}, volume = {248}, number = {}, pages = {120833}, doi = {10.1016/j.watres.2023.120833}, pmid = {37952327}, issn = {1879-2448}, mesh = {Humans ; *Wastewater ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Bacteriophages/genetics ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Microbial/genetics ; beta-Lactams ; Hospitals ; }, abstract = {Antimicrobial resistance poses a serious threat to human health and is responsible for the death of millions of people annually. Hospital wastewater is an important hotspot for antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB). However, little is known about the relationship between phages and ARGs in hospital wastewater systems (HWS). In the present study, the viral diversity of 12 HWSs using data from public metagenomic databases was investigated. Viruses were widely found in both the influent and effluent of each HWS. A total of 45 unique ARGs were carried by 85 viral contigs, which accounted for only 0.14% of the total viral populations, implying that ARGs were not commonly present in phages. Three efflux pump genes were identified as shared between phages and bacterial genomes. However, the predominant types of ARGs in HWS such as aminoglycoside- and beta-lactam-resistance genes were rarely found in phages. Based on CRISPR spacer and tRNA matches, interactions between 171 viral contigs and 60 antibiotic-resistant genomes were predicted, including interactions involving phages and vancomycin-resistant Enterococcus_B faecium or beta-lactam-resistant Klebsiella pneumoniae. More than half (56.1%) of these viral contigs indicated lytic and none of them carried ARGs. As the vOTUs in this study had few ARGs and were primarily lytic, HWS may be a valuable source for phage discovery. Future studies will be able to experimentally validate these sequence-based results to confirm the suitability of HWS phages for pathogen control measures in wastewater.}, } @article {pmid37952062, year = {2023}, author = {Bloemen, B and Gand, M and Vanneste, K and Marchal, K and Roosens, NHC and De Keersmaecker, SCJ}, title = {Development of a portable on-site applicable metagenomic data generation workflow for enhanced pathogen and antimicrobial resistance surveillance.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {19656}, pmid = {37952062}, issn = {2045-2322}, mesh = {*Anti-Bacterial Agents ; Workflow ; Drug Resistance, Bacterial/genetics ; Metagenome ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; DNA ; Sequence Analysis, DNA/methods ; *Nanopores ; }, abstract = {Rapid, accurate and comprehensive diagnostics are essential for outbreak prevention and pathogen surveillance. Real-time, on-site metagenomics on miniaturized devices, such as Oxford Nanopore Technologies MinION sequencing, could provide a promising approach. However, current sample preparation protocols often require substantial equipment and dedicated laboratories, limiting their use. In this study, we developed a rapid on-site applicable DNA extraction and library preparation approach for nanopore sequencing, using portable devices. The optimized method consists of a portable mechanical lysis approach followed by magnetic bead-based DNA purification and automated sequencing library preparation, and resulted in a throughput comparable to a current optimal, laboratory-based protocol using enzymatic digestion to lyse cells. By using spike-in reference communities, we compared the on-site method with other workflows, and demonstrated reliable taxonomic profiling, despite method-specific biases. We also demonstrated the added value of long-read sequencing by recovering reads containing full-length antimicrobial resistance genes, and attributing them to a host species based on the additional genomic information they contain. Our method may provide a rapid, widely-applicable approach for microbial detection and surveillance in a variety of on-site settings.}, } @article {pmid37952001, year = {2023}, author = {Boulanger, N and Insonere, JL and Van Blerk, S and Barthel, C and Serres, C and Rais, O and Roulet, A and Servant, F and Duron, O and Lelouvier, B}, title = {Cross-alteration of murine skin and tick microbiome concomitant with pathogen transmission after Ixodes ricinus bite.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {250}, pmid = {37952001}, issn = {2049-2618}, mesh = {Humans ; Animals ; Female ; Mice ; *Ixodes/genetics/microbiology ; *Tick Bites ; RNA, Ribosomal, 16S/genetics ; *Borrelia/genetics ; *Microbiota ; Nymph/microbiology ; }, abstract = {BACKGROUND: Ticks are major vectors of diseases affecting humans such as Lyme disease or domestic animals such as anaplasmosis. Cross-alteration of the vertebrate host skin microbiome and the tick microbiome may be essential during the process of tick feeding and for the mechanism of pathogen transmission. However, it has been poorly investigated.

METHODS: We used mice bitten by field-collected ticks (nymphs and adult ticks) in different experimental conditions to investigate, by 16S rRNA gene metabarcoding, the impact of blood feeding on both the mouse skin microbiome and the tick microbiome. We also investigated by PCR and 16S rRNA gene metabarcoding, the diversity of microorganisms transmitted to the host during the process of tick bite at the skin interface and the dissemination of the pathogen in host tissues (blood, heart, and spleen).

RESULTS: Most of the commensal bacteria present in the skin of control mice were replaced during the blood-feeding process by bacteria originating from the ticks. The microbiome of the ticks was also impacted by the blood feeding. Several pathogens including tick-borne pathogens (Borrelia/Borreliella, Anaplasma, Neoehrlichia, Rickettsia) and opportunistic bacteria (Williamsia) were transmitted to the skin microbiome and some of them disseminated to the blood or spleen of the mice. In the different experiments of this study, skin microbiome alteration and Borrelia/Borreliella transmission were different depending on the tick stages (nymphs or adult female ticks).

CONCLUSIONS: Host skin microbiome at the bite site was deeply impacted by the tick bite, to an extent which suggests a role in the tick feeding, in the pathogen transmission, and a potentially important impact on the skin physiopathology. The diversified taxonomic profiles of the tick microbiome were also modified by the blood feeding. Video Abstract.}, } @article {pmid37951952, year = {2023}, author = {Ma, B and Lu, C and Wang, Y and Yu, J and Zhao, K and Xue, R and Ren, H and Lv, X and Pan, R and Zhang, J and Zhu, Y and Xu, J}, title = {A genomic catalogue of soil microbiomes boosts mining of biodiversity and genetic resources.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7318}, pmid = {37951952}, issn = {2041-1723}, mesh = {*Soil ; *Microbiota/genetics ; Metagenome/genetics ; Biodiversity ; Genomics ; Soil Microbiology ; }, abstract = {Soil harbors a vast expanse of unidentified microbes, termed as microbial dark matter, presenting an untapped reservo)ir of microbial biodiversity and genetic resources, but has yet to be fully explored. In this study, we conduct a large-scale excavation of soil microbial dark matter by reconstructing 40,039 metagenome-assembled genome bins (the SMAG catalogue) from 3304 soil metagenomes. We identify 16,530 of 21,077 species-level genome bins (SGBs) as unknown SGBs (uSGBs), which expand archaeal and bacterial diversity across the tree of life. We also illustrate the pivotal role of uSGBs in augmenting soil microbiome's functional landscape and intra-species genome diversity, providing large proportions of the 43,169 biosynthetic gene clusters and 8545 CRISPR-Cas genes. Additionally, we determine that uSGBs contributed 84.6% of previously unexplored viral-host associations from the SMAG catalogue. The SMAG catalogue provides an useful genomic resource for further studies investigating soil microbial biodiversity and genetic resources.}, } @article {pmid37951913, year = {2023}, author = {Mousavinasab, F and Karimi, R and Taheri, S and Ahmadvand, F and Sanaaee, S and Najafi, S and Halvaii, MS and Haghgoo, A and Zamany, M and Majidpoor, J and Khosravifar, M and Baniasadi, M and Talebi, M and Movafagh, A and Aghaei-Zarch, SM and Khorram, N and Farnia, P and Kalhor, K}, title = {Microbiome modulation in inflammatory diseases: Progress to microbiome genetic engineering.}, journal = {Cancer cell international}, volume = {23}, number = {1}, pages = {271}, pmid = {37951913}, issn = {1475-2867}, abstract = {Recent developments in sequencing technology and analytical approaches have allowed researchers to show that the healthy gut microbiome is very varied and capable of performing a wide range of tasks. The importance of gut microbiota in controlling immunological, neurological, and endocrine function is becoming well-recognized. Thereby, numerous inflammatory diseases, including those that impact the gastrointestinal system, as well as less obvious ones, including Rheumatoid arthritis (RA), cancer, gestational diabetes (GD), type 1 diabetes (T1D), and type 2 diabetes (T2D), have been linked to dysbiotic gut microbiota. Microbiome engineering is a rapidly evolving frontier for solutions to improve human health. Microbiome engineering seeks to improve the function of an ecosystem by manipulating the composition of microbes. Thereby, generating potential therapies against metabolic, inflammatory, and immunological diseases will be possible through microbiome engineering. This essay first provides an overview of the traditional technological instruments that might be used for microbiome engineering, such as Fecal Microbiota Transplantation (FMT), prebiotics, and probiotics. Moreover, we will also discuss experimental genetic methods such as Metagenomic Alteration of Gut microbiome by In situ Conjugation (MAGIC), Bacteriophage, and Conjugative plasmids in manipulating intestinal microbiota.}, } @article {pmid37951857, year = {2023}, author = {Kang, DY and Park, JL and Yeo, MK and Kang, SB and Kim, JM and Kim, JS and Kim, SY}, title = {Diagnosis of Crohn's disease and ulcerative colitis using the microbiome.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {336}, pmid = {37951857}, issn = {1471-2180}, mesh = {Humans ; *Colitis, Ulcerative/therapy ; *Crohn Disease/diagnosis/microbiology ; *Inflammatory Bowel Diseases/microbiology ; *Gastrointestinal Microbiome ; Bacteria/genetics ; Biomarkers ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a multifactorial chronic inflammatory disease resulting from dysregulation of the mucosal immune response and gut microbiota. Crohn's disease (CD) and ulcerative colitis (UC) are difficult to distinguish, and differential diagnosis is essential for establishing a long-term treatment plan for patients. Furthermore, the abundance of mucosal bacteria is associated with the severity of the disease. This study aimed to differentiate and diagnose these two diseases using the microbiome and identify specific biomarkers associated with disease activity.

RESULTS: Differences in the abundance and composition of the microbiome between IBD patients and healthy controls (HC) were observed. Compared to HC, the diversity of the gut microbiome in patients with IBD decreased; the diversity of the gut microbiome in patients with CD was significantly lower. Sixty-eight microbiota members (28 for CD and 40 for UC) associated with these diseases were identified. Additionally, as the disease progressed through different stages, the diversity of the bacteria decreased. The abundances of Alistipes shahii and Pseudodesulfovibrio aespoeensis were negatively correlated with the severity of CD, whereas the abundance of Polynucleobacter wianus was positively correlated. The severity of UC was negatively correlated with the abundance of A. shahii, Porphyromonas asaccharolytica and Akkermansia muciniphilla, while it was positively correlated with the abundance of Pantoea candidatus pantoea carbekii. A regularized logistic regression model was used for the differential diagnosis of the two diseases. The area under the curve (AUC) was used to examine the performance of the model. The model discriminated UC and CD at an AUC of 0.873 (train set), 0.778 (test set), and 0.633 (validation set) and an area under the precision-recall curve (PRAUC) of 0.888 (train set), 0.806 (test set), and 0.474 (validation set).

CONCLUSIONS: Based on fecal whole-metagenome shotgun (WMS) sequencing, CD and UC were diagnosed using a machine-learning predictive model. Microbiome biomarkers associated with disease activity (UC and CD) are also proposed.}, } @article {pmid37951618, year = {2023}, author = {Laux, M and Piroupo, CM and Setubal, JC and Giani, A}, title = {The Raphidiopsis (= Cylindrospermopsis) raciborskii pangenome updated: Two new metagenome-assembled genomes from the South American clade.}, journal = {Harmful algae}, volume = {129}, number = {}, pages = {102518}, doi = {10.1016/j.hal.2023.102518}, pmid = {37951618}, issn = {1878-1470}, mesh = {*Cylindrospermopsis/genetics ; Saxitoxin/genetics/metabolism ; Phylogeny ; Metagenome ; *Cyanobacteria/genetics ; Lakes ; Brazil ; }, abstract = {Two Raphidiopsis (=Cylindrospermopsis) raciborskii metagenome-assembled genomes (MAGs) were recovered from two freshwater metagenomic datasets sampled in 2011 and 2012 in Pampulha Lake, a hypereutrophic, artificial, shallow reservoir, located in the city of Belo Horizonte (MG), Brazil. Since the late 1970s, the lake has undergone increasing eutrophication pressure, due to wastewater input, leading to the occurrence of frequent cyanobacterial blooms. The major difference observed between PAMP2011 and PAMP2012 MAGs was the lack of the saxitoxin gene cluster in PAMP2012, which also presented a smaller genome, while PAMP2011 presented the complete sxt cluster and all essential proteins and clusters. The pangenome analysis was performed with all Raphidiopsis/Cylindrospermopsis genomes available at NCBI to date, with the addition of PAMP2011 and PAMP2012 MAGs (All33 subset), but also without the South American strains (noSA subset), and only among the South American strains (SA10 and SA8 subsets). We observed a substantial increase in the core genome size for the 'noSA' subset, in comparison to 'All33' subset, and since the core genome reflects the closeness among the pangenome members, the results strongly suggest that the conservation level of the essential gene repertoire seems to be affected by the geographic origin of the strains being analyzed, supporting the existence of a distinct SA clade. The Raphidiopsis pangenome comprised a total of 7943 orthologous protein clusters, and the two new MAGs increased the pangenome size by 11%. The pangenome based phylogenetic relationships among the 33 analyzed genomes showed that the SA genomes clustered together with 99% bootstrap support, reinforcing the metabolic particularity of the Raphidiopsis South American clade, related to its saxitoxin producing unique ability, while also indicating a different evolutionary history due to its geographic isolation.}, } @article {pmid37950955, year = {2023}, author = {Li, Y and Wang, H and Wang, M and Wang, Y and Shi, B}, title = {The perfluoroalkyl substances influenced the distribution of bacterial communities and their functions from source water to tap water.}, journal = {Water research}, volume = {247}, number = {}, pages = {120831}, doi = {10.1016/j.watres.2023.120831}, pmid = {37950955}, issn = {1879-2448}, mesh = {Humans ; *Drinking Water ; *Alkanesulfonic Acids/analysis ; *Fluorocarbons/analysis ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring ; }, abstract = {Perfluoroalkyl substances (PFASs) and antibiotic resistance genes (ARGs) in drinking water are environmental issues that require special attention. The objective of this study was to know the effects of PFASs on microbial communities and their functional genes from source water to tap water. PFASs were detected by mass-labeled internal standards method, and the microbial communities and functional genes were analyzed by metagenomics. Our results indicated that the concentration of total PFASs in the water ranged from 47.7 to 171.4 ng/L, with perfluorobutanoic acid (PFBA) and perfluorooctanoic acid (PFOA) being the dominant types. The PFASs concentration decreased slowly from source to tap water in some months. PFBA, PFOA, perfluorooctane sulfonic acid (PFOS) and perfluorohexanoic acid (PFHxA) influenced the functional genes related to two-component system, bacterial secretion system and flagellar assembly of Aquabacterium, Methylobacterium, and Curvibacter, which contributed significantly to macB and evgS. Therefore, the bacterial communities enhanced adaptation to fluctuating environments by upregulating some functional genes under the PFASs stress, with concomitant changes in the expression of ARGs. Moreover, PFASs also promoted the expression of functional genes associated with human diseases, such as shigellosis and tuberculosis, which increased the risk of human pathogenicity. The bench scale experiment results also suggested that PFOA and PFOS in drinking water can promote the ARGs proliferation and induce microbial risk. Therefore, it is necessary to take measures to prevent the risks caused by PFASs and ARGs in drinking water.}, } @article {pmid37950185, year = {2023}, author = {Khajah, MA and Hawai, S}, title = {Effect of minocycline, methyl prednisolone, or combination treatment on the colonic bacterial population in a state of colonic inflammation using the murine dextran sulfate sodium model.}, journal = {Microbial cell factories}, volume = {22}, number = {1}, pages = {232}, pmid = {37950185}, issn = {1475-2859}, mesh = {Mice ; Animals ; *Minocycline/pharmacology/therapeutic use/metabolism ; Dextran Sulfate/metabolism/pharmacology/therapeutic use ; Methylprednisolone/metabolism/pharmacology/therapeutic use ; Colon ; *Colitis/drug therapy ; Inflammation/drug therapy ; Bacteria ; Anti-Inflammatory Agents/pharmacology/therapeutic use/metabolism ; Disease Models, Animal ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND: Several reports demonstrated anti-inflammatory properties of minocycline in various inflammatory disorders including colitis. We have experimental evidence suggesting synergistic anti-inflammatory effect of minocycline with methyl prednisolone in reducing colitis severity in mice, but if this effect is in part related to modulating the composition of colonic microbiota is still unknown.

METHODS: the effect of vehicle (V), minocycline (M), methyl prednisolone (MP), or combination (C) regimen on the composition of the microbiota of mice in a state of colon inflammation compared to untreated (UT) healthy mice was determined using 16s metagenomic sequencing, and the taxonomic and functional profiles were summarized.

RESULTS: Overall, the bacterial flora from the phylum Firmicutes followed by Bacteroidota were found to be predominant in all the samples. However, the composition of Firmicutes was decreased relatively in all the treatment groups compared to UT group. A relatively higher percentage of Actinobacteriota was observed in the samples from the C group. At the genus level, Muribaculaceae, Bacteroides, Bifidobacterium, and Lactobacillus were found to be predominant in the samples treated with both drugs (C). Whereas "Lachnospiraceae NK4A136 group" and Helicobacter in the M group, and Helicobacter in the MP group were found to be predominant. But, in the UT group, Weissella and Staphylococcus were found to be predominant. Eubacterium siraeum group, Clostridia vadinBB60 group, Erysipelatoclostridium and Anaeroplasma genera were identified to have a significant (FDR p < 0.05) differential abundance in V compared to C and UT groups. While at the species level, the abundance of Helicobacter mastomyrinus, Massiliomicrobiota timonensis and uncultured Anaeroplasma were identified as significantly low in UT, C, and M compared to V group. Functional categories related to amino acid, carbohydrate, and energy metabolism, cell motility and cell cycle control were dominated overall across all the samples. Methane metabolism was identified as an enriched pathway. For the C group, "Colitis (decrease)" was among the significant (p = 1.81E-6) associations based on the host-intrinsic taxon set.

CONCLUSION: Combination regimen of minocycline plus methyl prednisolone produces a synergistic anti-inflammatory effect which is part related to alternation in the colonic microbiota composition.}, } @article {pmid37949415, year = {2023}, author = {Kahleova, H and Holtz, DN and Strom, N and La Reau, A and Kolipaka, S and Schmidt, N and Hata, E and Znayenko-Miller, T and Holubkov, R and Barnard, ND}, title = {A dietary intervention for postmenopausal hot flashes: A potential role of gut microbiome. An exploratory analysis.}, journal = {Complementary therapies in medicine}, volume = {79}, number = {}, pages = {103002}, doi = {10.1016/j.ctim.2023.103002}, pmid = {37949415}, issn = {1873-6963}, mesh = {Female ; Humans ; *Hot Flashes/drug therapy ; Postmenopause/physiology ; *Gastrointestinal Microbiome ; Menopause ; }, abstract = {OBJECTIVE: This study examined the role of gut microbiome changes in mediating the effects of a dietary intervention on the frequency and severity of postmenopausal vasomotor symptoms METHODS: Postmenopausal women (n = 84) reporting ≥2 moderate-to-severe hot flashes daily were randomly assigned, in 2 successive cohorts, to an intervention including a low-fat, vegan diet and cooked soybeans (½ cup [86 g] daily) or to stay on their usual diet. Over a 12-week period, frequency and severity of hot flashes were recorded with a mobile application. In a subset of 11 women, gut microbiome was analyzed at baseline and after 12 weeks of the dietary intervention (low-fat vegan diet with soybeans), using deep shotgun metagenomic sequencing. Differences in the microbiome between baseline and 12 weeks were assessed by comparing alpha diversity with Wilcoxon signed rank tests, beta diversity with permanovaFL, and taxon abundance with Wilcoxon signed rank tests. Pearson correlations were used to assess the association between changes in hot flashes and gut bacteria.

RESULTS: In the subset for which microbiome testing was done, total hot flashes decreased by 95 % during the dietary intervention (p = 0.007); severe hot flashes disappeared (from 0.6 to 0.0/day; p = 0.06); and moderate-to-severe hot flashes decreased by 96 % (p = 0.01). Daytime and nighttime hot flashes were reduced by 96 % (p = 0.01) and 94 % (p = 0.004), respectively. Alpha and beta diversity did not significantly differ in the intervention group between baseline and 12 weeks. Two families (Enterobacteriaceae and Veillonellaceae), 5 genera (Erysipelatoclostridium, Fusicatenibacter, Holdemanella, Intestinimonas, and Porphyromonas), and 6 species (Clostridium asparagiforme, Clostridium innocuum, Bacteroides thetaiotaomicron, Fusicatenibacter saccharivorans, Intestinimonas butyriciproducens, Prevotella corporis, and Streptococcus sp.) were differentially abundant, but after correction for multiple comparisons, these differences were no longer significant. Changes in the relative abundance of Porphyromonas and Prevotella corporis were associated with the reduction in severe day hot flashes both unadjusted (r = 0.61; p = 0.047; and r = 0.69; p = 0.02), respectively), and after adjustment for changes in body mass index (r = 0.63; p = 0.049; and r = 0.73; p = 0.02), respectively). Changes in relative abundance of Clostridium asparagiforme were associated with the reduction in total severe hot flashes (r = 0.69; p = 0.019) and severe night hot flashes (r = 0.82; p = 0.002) and the latter association remained significant after adjustment for changes in body mass index (r = 0.75; p = 0.01).

CONCLUSIONS: This exploratory analysis revealed potential associations between changes in vasomotor symptoms in response to a diet change and changes in the gut microbiome. Larger randomized clinical trials are needed to investigate these findings.}, } @article {pmid37949212, year = {2023}, author = {Xu, HS and Chen, Y and Patel, A and Wang, Z and McDonough, C and Guo, TL}, title = {Chronic exposure to nanocellulose altered depression-related behaviors in mice on a western diet: The role of immune modulation and the gut microbiome.}, journal = {Life sciences}, volume = {335}, number = {}, pages = {122259}, doi = {10.1016/j.lfs.2023.122259}, pmid = {37949212}, issn = {1879-0631}, mesh = {Male ; Animals ; Mice ; Mice, Inbred NOD ; *Gastrointestinal Microbiome ; Diet, Western/adverse effects ; RNA, Ribosomal, 16S/genetics ; Depression ; Mice, Inbred C57BL ; }, abstract = {AIMS: To determine if cellulose nanofibrils (CNF) have potential applications as food additives.

MATERIALS AND METHODS: Male C57BL/6 mice on a Western diet were exposed to CNF for one month at a dose of 30 mg/kg by gavage. Male NOD mice, a model for type 1 diabetes (T1D), were used in a six-month study.

KEY FINDINGS: Sequencing analysis of 16S rRNA genes suggested significant changes in gut microbiome of male C57BL/6 mice exposed to CNF. Analysis of functional metagenomics indicated that many of the functional contents that might be altered following CNF ingestion were associated with lipid and carbohydrate processing. Further studies in NOD mice suggested that there were some decreases in the blood glucose levels during the insulin tolerance test and glucose tolerance test following CNF treatment. However, these small decreases were not considered biologically meaningful as there were no significant changes in either the area under the curve or the first-order rate constant for glucose disappearance. Moreover, serum concentrations of cytokines/chemokines including IL-3, IL-12(p70) and the keratinocyte chemoattractant were increased following chronic exposure to CNF. In addition, behavioral studies suggested that the percentage of immobility time during the tail-suspension test was significantly increased following six months of exposure to CNF in NOD mice, signifying an increase in depression-related behavior.

SIGNIFICANCE: Collectively, long-term CNF consumption was associated with changes in the ecology of the gut microbiome, immune homeostasis, and possibly energy metabolism and mental health in male NOD mice on a Western diet.}, } @article {pmid37949148, year = {2023}, author = {Hosseini, H and Saadaoui, I and Cherif, M and Amir Siddiqui, S and Sayadi, S}, title = {Exploring the dynamics of algae-associated microbiome during the scale-up process of Tetraselmis sp. microalgae: A metagenomics approach.}, journal = {Bioresource technology}, volume = {393}, number = {}, pages = {129991}, doi = {10.1016/j.biortech.2023.129991}, pmid = {37949148}, issn = {1873-2976}, abstract = {Microalgae have become a key source of valuable compounds, promoting commercial scale applications. However, biological contamination is one of the most critical problems associated with large scale algal production, especially in open systems such as raceway ponds. The current research is the first to assess the effectiveness of open raceway ponds in maintaining a pure culture of Tetraselmis sp., starting from 20 L culture up to 10,000 L culture. Microbial profiling of each successive stage revealed lower abundance of eukaryotic organisms, whereas bacterial abundance increased notably resulting in a significant decrease in Tetraselmis sp. abundance. Furthermore, several bacteria with algae growth-promoting properties were found throughout the various culture stages including Balneola, Roseovarius, and Marinobacter. However, some algae-suppressive bacteria were evidenced at later stages such as Ulvibacter, Aestuariicoccus, and Defluviimonas. Overall, due to the increasing bacterial concentration, considerations limiting bacterial contamination need to be taken.}, } @article {pmid37949114, year = {2024}, author = {Shinn, LM and Mansharamani, A and Baer, DJ and Novotny, JA and Charron, CS and Khan, NA and Zhu, R and Holscher, HD}, title = {Fecal Metagenomics to Identify Biomarkers of Food Intake in Healthy Adults: Findings from Randomized, Controlled, Nutrition Trials.}, journal = {The Journal of nutrition}, volume = {154}, number = {1}, pages = {271-283}, doi = {10.1016/j.tjnut.2023.11.001}, pmid = {37949114}, issn = {1541-6100}, mesh = {Adult ; Humans ; *Gastrointestinal Microbiome ; Metagenome ; Diet ; *Juglans ; Feces ; Biomarkers ; Eating ; Metagenomics/methods ; }, abstract = {BACKGROUND: Undigested components of the human diet affect the composition and function of the microorganisms present in the gastrointestinal tract. Techniques like metagenomic analyses allow researchers to study functional capacity, thus revealing the potential of using metagenomic data for developing objective biomarkers of food intake.

OBJECTIVES: As a continuation of our previous work using 16S and metabolomic datasets, we aimed to utilize a computationally intensive, multivariate, machine-learning approach to identify fecal KEGG (Kyoto encyclopedia of genes and genomes) Orthology (KO) categories as biomarkers that accurately classify food intake.

METHODS: Data were aggregated from 5 controlled feeding studies that studied the individual impact of almonds, avocados, broccoli, walnuts, barley, and oats on the adult gastrointestinal microbiota. Deoxyribonucleic acid from preintervention and postintervention fecal samples underwent shotgun genomic sequencing. After preprocessing, sequences were aligned and functionally annotated with Double Index AlignMent Of Next-generation sequencing Data v2.0.11.149 and MEtaGenome ANalyzer v6.12.2, respectively. After the count normalization, the log of the fold change ratio for resulting KOs between pre- and postintervention of the treatment group against its corresponding control was utilized to conduct differential abundance analysis. Differentially abundant KOs were used to train machine-learning models examining potential biomarkers in both single-food and multi-food models.

RESULTS: We identified differentially abundant KOs in the almond (n = 54), broccoli (n = 2474), and walnut (n = 732) groups (q < 0.20), which demonstrated classification accuracies of 80%, 87%, and 86% for the almond, broccoli, and walnut groups using a random forest model to classify food intake into each food group's respective treatment and control arms, respectively. The mixed-food random forest achieved 81% accuracy.

CONCLUSIONS: Our findings reveal promise in utilizing fecal metagenomics to objectively complement self-reported measures of food intake. Future research on various foods and dietary patterns will expand these exploratory analyses for eventual use in feeding study compliance and clinical settings.}, } @article {pmid37947418, year = {2023}, author = {Nemet, I and Funabashi, M and Li, XS and Dwidar, M and Sangwan, N and Skye, SM and Romano, KA and Cajka, T and Needham, BD and Mazmanian, SK and Hajjar, AM and Rey, FE and Fiehn, O and Tang, WHW and Fischbach, MA and Hazen, SL}, title = {Microbe-derived uremic solutes enhance thrombosis potential in the host.}, journal = {mBio}, volume = {14}, number = {6}, pages = {e0133123}, pmid = {37947418}, issn = {2150-7511}, support = {R01 DK101674/DK/NIDDK NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; R01 HL103866/HL/NHLBI NIH HHS/United States ; T32 HL134622/HL/NHLBI NIH HHS/United States ; R01 HL160747/HL/NHLBI NIH HHS/United States ; }, abstract = {p-Cresol sulfate (pCS) and indoxyl sulfate (IS), gut microbiome-derived metabolites, are traditionally associated with cardiovascular disease (CVD) risks in the setting of impaired kidney function. While pharmacologic provision of pCS or IS can promote pro-thrombotic phenotypes, neither the microbial enzymes involved nor direct gut microbial production have been linked to CVD. Untargeted metabolomics was performed on a discovery cohort (n = 1,149) with relatively preserved kidney function, followed by stable isotope-dilution mass spectrometry quantification of pCS and IS in an independent validation cohort (n = 3,954). Genetic engineering of human commensals to produce p-cresol and indole gain-of-function and loss-of-function mutants, followed by colonization of germ-free mice, and studies on host thrombosis were performed. Systemic pCS and IS levels were independently associated with all-cause mortality. Both in vitro and within colonized germ-free mice p-cresol productions were recapitulated by collaboration of two organisms: a Bacteroides strain that converts tyrosine to 4-hydroxyphenylacetate, and a Clostridium strain that decarboxylates 4-hydroxyphenylacetate to p-cresol. We then engineered a single organism, Bacteroides thetaiotaomicron, to produce p-cresol, indole, or both metabolites. Colonizing germ-free mice with engineered strains, we show the gut microbial genes for p-cresol (hpdBCA) and indole (tryptophanase) are sufficient to confer a pro-thrombotic phenotype in vivo. Moreover, human fecal metagenomics analyses show that abundances of hpdBCA and tryptophanase are associated with CVD. These studies show that pCS and IS, two abundant microbiome-derived metabolites, play a broader potential role in CVD than was previously known. They also suggest that therapeutic targeting of gut microbial p-cresol- and indole-producing pathways represent rational targets for CVD.IMPORTANCEAlterations in gut microbial composition and function have been linked to numerous diseases. Identifying microbial pathways responsible for producing molecules that adversely impact the host is an important first step in the development of therapeutic interventions. Here, we first use large-scale clinical observations to link blood levels of defined microbial products to cardiovascular disease risks. Notably, the previously identified uremic toxins p-cresol sulfate and indoxyl sulfate were shown to predict 5-year mortality risks. After identifying the microbes and microbial enzymes involved in the generation of these uremic toxins, we used bioengineering technologies coupled with colonization of germ-free mice to show that the gut microbial genes that generate p-cresol and indole are sufficient to confer p-cresol sulfate and indoxyl sulfate formation, and a pro-thrombotic phenotype in vivo. The findings and tools developed serve as a critical step in both the study and targeting of these gut microbial pathways in vivo.}, } @article {pmid37947402, year = {2023}, author = {Alexander, H and Hu, SK and Krinos, AI and Pachiadaki, M and Tully, BJ and Neely, CJ and Reiter, T}, title = {Eukaryotic genomes from a global metagenomic data set illuminate trophic modes and biogeography of ocean plankton.}, journal = {mBio}, volume = {14}, number = {6}, pages = {e0167623}, pmid = {37947402}, issn = {2150-7511}, abstract = {Metagenomics is a powerful method for interpreting the ecological roles and physiological capabilities of mixed microbial communities. Yet, many tools for processing metagenomic data are neither designed to consider eukaryotes nor are they built for an increasing amount of sequence data. EukHeist is an automated pipeline to retrieve eukaryotic and prokaryotic metagenome-assembled genomes (MAGs) from large-scale metagenomic sequence data sets. We developed the EukHeist workflow to specifically process large amounts of both metagenomic and/or metatranscriptomic sequence data in an automated and reproducible fashion. Here, we applied EukHeist to the large-size fraction data (0.8-2,000 µm) from Tara Oceans to recover both eukaryotic and prokaryotic MAGs, which we refer to as TOPAZ (Tara Oceans Particle-Associated MAGs). The TOPAZ MAGs consisted of >900 environmentally relevant eukaryotic MAGs and >4,000 bacterial and archaeal MAGs. The bacterial and archaeal TOPAZ MAGs expand upon the phylogenetic diversity of likely particle- and host-associated taxa. We use these MAGs to demonstrate an approach to infer the putative trophic mode of the recovered eukaryotic MAGs. We also identify ecological cohorts of co-occurring MAGs, which are driven by specific environmental factors and putative host-microbe associations. These data together add to a number of growing resources of environmentally relevant eukaryotic genomic information. Complementary and expanded databases of MAGs, such as those provided through scalable pipelines like EukHeist, stand to advance our understanding of eukaryotic diversity through increased coverage of genomic representatives across the tree of life.IMPORTANCESingle-celled eukaryotes play ecologically significant roles in the marine environment, yet fundamental questions about their biodiversity, ecological function, and interactions remain. Environmental sequencing enables researchers to document naturally occurring protistan communities, without culturing bias, yet metagenomic and metatranscriptomic sequencing approaches cannot separate individual species from communities. To more completely capture the genomic content of mixed protistan populations, we can create bins of sequences that represent the same organism (metagenome-assembled genomes [MAGs]). We developed the EukHeist pipeline, which automates the binning of population-level eukaryotic and prokaryotic genomes from metagenomic reads. We show exciting insight into what protistan communities are present and their trophic roles in the ocean. Scalable computational tools, like EukHeist, may accelerate the identification of meaningful genetic signatures from large data sets and complement researchers' efforts to leverage MAG databases for addressing ecological questions, resolving evolutionary relationships, and discovering potentially novel biodiversity.}, } @article {pmid37946771, year = {2023}, author = {Cao, LJ and Zheng, YM and Li, F and Hao, HJ and Gao, F}, title = {Varicella-zoster virus meningitis with hypoglycorrhachia: A case report.}, journal = {World journal of clinical cases}, volume = {11}, number = {29}, pages = {7101-7106}, pmid = {37946771}, issn = {2307-8960}, abstract = {BACKGROUND: Varicella-zoster virus (VZV) is a common viral infection, but meningitis is a rare complication of VZV infection. The cerebrospinal fluid glucose of viral meningitis is usually within the normal range, which is different from bacteria, fungi, and cancerous meningitis. This paper reports a case of VZV meningitis with hypoglycorrhachia and the relevant literature was reviewed.

CASE SUMMARY: We report a case of an immunocompetent 39-year-old male, presenting with severe headache and fevers, without meningeal signs or exanthem, found to have VZV meningitis by the metagenomic next-generation sequencing of cerebrospinal fluid. The cerebrospinal fluid analysis revealed hypoglycorrhachia (cerebrospinal fluid glucose of 2.16) and he was treated successfully with intravenous acyclovir. Our literature review identified only ten cases diagnosed with VZV meningitis with hypoglycorrhachia previously reported to date in the English literature whose cerebrospinal fluid glucose was from 1.6 to 2.7mmol/L, with a ratio of cerebrospinal fluid to serum glucose from 0.30 to 0.49.

CONCLUSION: Although rare, the cerebrospinal fluid of patients with VZV meningitis may have hypoglycorrhachia, which broadens the understanding of the disease.}, } @article {pmid37946302, year = {2023}, author = {Shen, Z and Robert, L and Stolpman, M and Che, Y and Allen, KJ and Saffery, R and Walsh, A and Young, A and Eckert, J and Deming, C and Chen, Q and Conlan, S and Laky, K and Li, JM and Chatman, L and Kashaf, SS and , and , and Kong, HH and Frischmeyer-Guerrerio, PA and Perrett, KP and Segre, JA}, title = {A genome catalog of the early-life human skin microbiome.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {252}, pmid = {37946302}, issn = {1474-760X}, support = {UM1AI109565/NH/NIH HHS/United States ; }, mesh = {Humans ; Infant ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics ; Australia ; North America ; Metagenomics ; }, abstract = {BACKGROUND: Metagenome-assembled genomes have greatly expanded the reference genomes for skin microbiome. However, the current reference genomes are largely based on samples from adults in North America and lack representation from infants and individuals from other continents.

RESULTS: Here we use deep shotgun metagenomic sequencing to profile the skin microbiota of 215 infants at age 2-3 months and 12 months who are part of the VITALITY trial in Australia as well as 67 maternally matched samples. Based on the infant samples, we present the Early-Life Skin Genomes (ELSG) catalog, comprising 9483 prokaryotic genomes from 1056 species, 206 fungal genomes from 13 species, and 39 eukaryotic viral sequences. This genome catalog substantially expands the diversity of species previously known to comprise human skin microbiome and improves the classification rate of sequenced data by 21%. The protein catalog derived from these genomes provides insights into the functional elements such as defense mechanisms that distinguish early-life skin microbiome. We also find evidence for microbial sharing at the community, bacterial species, and strain levels between mothers and infants.

CONCLUSIONS: Overall, the ELSG catalog uncovers the skin microbiome of a previously underrepresented age group and population and provides a comprehensive view of human skin microbiome diversity, function, and development in early life.}, } @article {pmid37946273, year = {2023}, author = {Lao, X and Hu, D and Ji, L and Zhan, T and Li, T and Luo, S and Xu, X and Zhang, C and Chen, M}, title = {Magnetic resonance imaging and next-generation sequencing for the diagnosis of cystic echinococcosis in the intradural spine: a case report.}, journal = {Journal of medical case reports}, volume = {17}, number = {1}, pages = {466}, pmid = {37946273}, issn = {1752-1947}, mesh = {Female ; Humans ; Middle Aged ; *Echinococcosis/diagnostic imaging ; Magnetic Resonance Imaging ; Lumbar Vertebrae/pathology ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Cystic echinococcosis (CE) is a parasitic zoonotic disease caused by the larval stage of Echinococcus granulosus. The liver and lungs are the most common sites for infection. Infection of the intradural spine is rare.

CASE PRESENTATION: A 45-year-old woman of Han ethnicity presented with a chronic history of recurrent lumbar pain. Magnetic resonance imaging of the lumbar spine revealed the classical characteristic of multiple cystic lesions of variable sizes, manifesting a "bunch of grapes" appearance, localized within the spinal canal at the L4-L5 vertebral level. In the meanwhile, metagenomic next-generation sequencing identified Echinococcosis granulosa. The patient underwent surgery to remove the cyst entirely and subsequently took albendazole 400 mg orally twice daily for 6 months.

CONCLUSION: Spinal CE should be suspected in patients with multiple spinal cystic lesions and zoonotic exposure. metagenomic next-generation sequencing serves as a robust diagnostic tool for atypical pathogens, particularly when conventional tests are inconclusive. Prompt and aggressive treatment for spinal cystic echinococcosis is imperative, and further research is warranted for improved diagnostic and therapeutic strategies.}, } @article {pmid37946266, year = {2023}, author = {Vasco, KA and Carbonell, S and Sloup, RE and Bowcutt, B and Colwell, RR and Graubics, K and Erskine, R and Norby, B and Ruegg, PL and Zhang, L and Manning, SD}, title = {Persistent effects of intramammary ceftiofur treatment on the gut microbiome and antibiotic resistance in dairy cattle.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {56}, pmid = {37946266}, issn = {2524-4671}, support = {2019-67017-29112//U.S. Department of Agriculture/ ; 6NU50CK000510-02-07//Michigan Sequencing and Academic Partnerships for Public Health Innovation and Response (MI-SAPPHIRE) initiative at the Michigan Department of Health and Human Services via the Centers for Disease Control and Prevention through the Epidemiology and Laboratory Capacity for Prevention and Control of Emerging Infectious Diseases Enhancing Detection Expansion program/ ; }, abstract = {BACKGROUND: Intramammary (IMM) ceftiofur treatment is commonly used in dairy farms to prevent mastitis, though its impact on the cattle gut microbiome and selection of antibiotic-resistant bacteria has not been elucidated. Herein, we enrolled 40 dairy (Holstein) cows at the end of the lactation phase for dry-cow therapy: 20 were treated with IMM ceftiofur (Spectramast®DC) and a non-antibiotic internal teat sealant (bismuth subnitrate) and 20 (controls) received only bismuth subnitrate. Fecal grab samples were collected before and after treatment (weeks 1, 2, 3, 5, 7, and 9) for bacterial quantification and metagenomic next-generation sequencing.

RESULTS: Overall, 90% and 24% of the 278 samples had Gram-negative bacteria with resistance to ampicillin and ceftiofur, respectively. Most of the cows treated with ceftiofur did not have an increase in the number of resistant bacteria; however, a subset (25%) shed higher levels of ceftiofur-resistant bacteria for up to 2 weeks post-treatment. At week 5, the antibiotic-treated cows had lower microbiota abundance and richness, whereas a greater abundance of genes encoding extended-spectrum β-lactamases (ESBLs), CfxA, ACI-1, and CMY, was observed at weeks 1, 5 and 9. Moreover, the contig and network analyses detected associations between β-lactam resistance genes and phages, mobile genetic elements, and specific genera. Commensal bacterial populations belonging to Bacteroidetes most commonly possessed ESBL genes followed by members of Enterobacteriaceae.

CONCLUSION: This study highlights variable, persistent effects of IMM ceftiofur treatment on the gut microbiome and resistome in dairy cattle. Antibiotic-treated cattle had an increased abundance of specific taxa and genes encoding ESBL production that persisted for 9 weeks. Fecal shedding of ESBL-producing Enterobacteriaceae, which was classified as a serious public health threat, varied across animals. Together, these findings highlight the need for additional studies aimed at identifying factors associated with shedding levels and the dissemination and persistence of antibiotic resistance determinants on dairy farms across geographic locations.}, } @article {pmid37946167, year = {2023}, author = {Cecchini, L and Barmaz, C and Cea, MJC and Baeschlin, H and Etter, J and Netzer, S and Bregy, L and Marchukov, D and Trigo, NF and Meier, R and Hirschi, J and Wyss, J and Wick, A and Zingg, J and Christensen, S and Radan, AP and Etter, A and Müller, M and Kaess, M and Surbek, D and Yilmaz, B and Macpherson, AJ and Sokollik, C and Misselwitz, B and Ganal-Vonarburg, SC}, title = {The Bern Birth Cohort (BeBiCo) to study the development of the infant intestinal microbiota in a high-resource setting in Switzerland: rationale, design, and methods.}, journal = {BMC pediatrics}, volume = {23}, number = {1}, pages = {560}, pmid = {37946167}, issn = {1471-2431}, mesh = {Child ; Infant ; Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; Cohort Studies ; Birth Cohort ; Prospective Studies ; Switzerland/epidemiology ; }, abstract = {BACKGROUND: Microbiota composition is fundamental to human health with the intestinal microbiota undergoing critical changes within the first two years of life. The developing intestinal microbiota is shaped by maternal seeding, breast milk and its complex constituents, other nutrients, and the environment. Understanding microbiota-dependent pathologies requires a profound understanding of the early development of the healthy infant microbiota.

METHODS: Two hundred and fifty healthy pregnant women (≥20 weeks of gestation) from the greater Bern area will be enrolled at Bern University hospital's maternity department. Participants will be followed as mother-baby pairs at delivery, week(s) 1, 2, 6, 10, 14, 24, 36, 48, 96, and at years 5 and 10 after birth. Clinical parameters describing infant growth and development, morbidity, and allergic conditions as well as socio-economic, nutritional, and epidemiological data will be documented. Neuro-developmental outcomes and behavior will be assessed by child behavior checklists at and beyond 2 years of age. Maternal stool, milk, skin and vaginal swabs, infant stool, and skin swabs will be collected at enrolment and at follow-up visits. For the primary outcome, the trajectory of the infant intestinal microbiota will be characterized by 16S and metagenomic sequencing regarding composition, metabolic potential, and stability during the first 2 years of life. Secondary outcomes will assess the cellular and chemical composition of maternal milk, the impact of nutrition and environment on microbiota development, the maternal microbiome transfer at vaginal or caesarean birth and thereafter on the infant, and correlate parameters of microbiota and maternal milk on infant growth, development, health, and mental well-being.

DISCUSSION: The Bern birth cohort study will provide a detailed description and normal ranges of the trajectory of microbiota maturation in a high-resource setting. These data will be compared to data from low-resource settings such as from the Zimbabwe-College of Health-Sciences-Birth-Cohort study. Prospective bio-sampling and data collection will allow studying the association of the microbiota with common childhood conditions concerning allergies, obesity, neuro-developmental outcomes , and behaviour. Trial registration The trial has been registered at www.

CLINICALTRIALS: gov , Identifier: NCT04447742.}, } @article {pmid37946009, year = {2023}, author = {Izda, V and Schlupp, L and Prinz, E and Dyson, G and Barrett, M and Dunn, CM and Nguyen, E and Sturdy, C and Jeffries, MA}, title = {Murine cartilage microbial DNA deposition occurs rapidly following the introduction of a gut microbiome and changes with obesity, aging, and knee osteoarthritis.}, journal = {GeroScience}, volume = {}, number = {}, pages = {}, pmid = {37946009}, issn = {2509-2723}, support = {K08AR070891/AR/NIAMS NIH HHS/United States ; R61AR078075/AR/NIAMS NIH HHS/United States ; R01AR076440/AR/NIAMS NIH HHS/United States ; P20GM125528/GM/NIGMS NIH HHS/United States ; }, abstract = {Cartilage microbial DNA patterns have been recently characterized in osteoarthritis (OA). The objectives of this study were to evaluate the gut origins of cartilage microbial DNA, to characterize cartilage microbial changes with age, obesity, and OA in mice, and correlate these to gut microbiome changes. We used 16S rRNA sequencing performed longitudinally on articular knee cartilage from germ-free (GF) mice following oral microbiome inoculation and cartilage and cecal samples from young and old wild-type mice with/without high-fat diet-induced obesity (HFD) and with/without OA induced by destabilization of the medial meniscus (DMM) to evaluate gut and cartilage microbiota. Microbial diversity was assessed, groups compared, and functional metagenomic profiles reconstructed. Findings were confirmed in an independent cohort by clade-specific qPCR. We found that cartilage microbial patterns developed at 48 h and later timepoints following oral microbiome inoculation of GF mice. Alpha diversity was increased in SPF mouse cartilage samples with age (P = 0.013), HFD (P = 5.6E-4), and OA (P = 0.029) but decreased in cecal samples with age (P = 0.014) and HFD (P = 1.5E-9). Numerous clades were altered with aging, HFD, and OA, including increases in Verrucomicrobia in both cartilage and cecal samples. Functional analysis suggested changes in dihydroorotase, glutamate-5-semialdehyde dehydrogenase, glutamate-5-kinase, and phosphoribosylamine-glycine ligase, in both cecum and cartilage, with aging, HFD, and OA. In conclusion, cartilage microbial DNA patterns develop rapidly after the introduction of a gut microbiome and change in concert with the gut microbiome during aging, HFD, and OA in mice. DMM-induced OA causes shifts in both cartilage and cecal microbiome patterns independent of other factors.}, } @article {pmid37945978, year = {2023}, author = {Spreckels, JE and Fernández-Pato, A and Kruk, M and Kurilshikov, A and Garmaeva, S and Sinha, T and Ghosh, H and Harmsen, H and Fu, J and Gacesa, R and Zhernakova, A}, title = {Analysis of microbial composition and sharing in low-biomass human milk samples: a comparison of DNA isolation and sequencing techniques.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {116}, pmid = {37945978}, issn = {2730-6151}, abstract = {Human milk microbiome studies are currently hindered by low milk bacterial/human cell ratios and often rely on 16S rRNA gene sequencing, which limits downstream analyses. Here, we aimed to find a method to study milk bacteria and assess bacterial sharing between maternal and infant microbiota. We tested four DNA isolation methods, two bacterial enrichment methods and three sequencing methods on mock communities, milk samples and negative controls. Of the four DNA isolation kits, the DNeasy PowerSoil Pro (PS) and MagMAX Total Nucleic Acid Isolation (MX) kits provided consistent 16S rRNA gene sequencing results with low contamination. Neither enrichment method substantially decreased the human metagenomic sequencing read-depth. Long-read 16S-ITS-23S rRNA gene sequencing biased the mock community composition but provided consistent results for milk samples, with little contamination. In contrast to 16S rRNA gene sequencing, 16S-ITS-23S rRNA gene sequencing of milk, infant oral, infant faecal and maternal faecal DNA from 14 mother-infant pairs provided sufficient resolution to detect significantly more frequent sharing of bacteria between related pairs compared to unrelated pairs. In conclusion, PS or MX kit-DNA isolation followed by 16S rRNA gene sequencing reliably characterises human milk microbiota, and 16S-ITS-23S rRNA gene sequencing enables studies of bacterial transmission in low-biomass samples.}, } @article {pmid37945964, year = {2023}, author = {Liu, C and Yue, Y and Zheng, S and Liu, X and Pang, L and Yang, Z}, title = {Impacts of substrate properties and aquatic nutrient concentrations on the relative abundance of nitrifying/denitrifying genes and the associated microbes in epilithic biofilms.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {57}, pages = {120930-120944}, pmid = {37945964}, issn = {1614-7499}, support = {52079094//National Natural Science Foundation of China/ ; 52079095//National Natural Science Foundation of China/ ; }, mesh = {*Denitrification ; *Nitrification ; Bacteria/genetics ; Biofilms ; Carbon ; Nitrogen ; Soil Microbiology ; }, abstract = {Substrates like sand or gravels and aquatic nutrient concentrations of rivers are highly heterogeneous, influencing the abundance of functional genes in epilithic biofilms where nitrification-denitrification processes take place. To analyze how the relative abundance of nitrifying/denitrifying genes and the associated microbes changes with the physical properties of substrates and aquatic concentrations of nutrients, this paper utilized metagenomics to comprehensively characterize these functional genes (i.e., amoA, hao, and nxrB involved in nitrification, and napA, narG, nirS, norB, and nosZ associated with denitrification) from epilithic biofilms collected along the Shitingjiang River in Southwest China and further obtained the relative abundance of major nitrifiers and denitrifiers. The results show that substrate size most significantly affects the relative abundance of hao and norB by altering the hydrodynamic conditions. In sampling sites with high heterogeneity in substrate size distribution, the relative abundance of most denitrifying genes is also higher. The carbon-nitrogen ratio negatively correlates with the relative abundance of all the nitrifying genes, while ammonium, total inorganic carbon, and total organic carbon concentrations positively affect the relative abundance of amoA and nxrB. As to the relative abundance of nitrifiers and denitrifiers, mainly belonging to phyla Proteobacteria and Actinobacteria, substrate heterogeneity and the aquatic concentrations of nutrients have greater influences than substrate size. Also, the substrate heterogeneity exerted positive influence on functional species of Pseudogemmobacter bohemicus and Paracoccus zhejiangensis. Considering the genes' functions and the dominant species linked to denitrification, nitrous oxide is more likely to occur in rivers with higher heterogeneity and larger substrates.}, } @article {pmid37945565, year = {2023}, author = {Chen, HC and Liu, YW and Chang, KC and Wu, YW and Chen, YM and Chao, YK and You, MY and Lundy, DJ and Lin, CJ and Hsieh, ML and Cheng, YC and Prajnamitra, RP and Lin, PJ and Ruan, SC and Chen, DH and Shih, ESC and Chen, KW and Chang, SS and Chang, CMC and Puntney, R and Moy, AW and Cheng, YY and Chien, HY and Lee, JJ and Wu, DC and Hwang, MJ and Coonen, J and Hacker, TA and Yen, CE and Rey, FE and Kamp, TJ and Hsieh, PCH}, title = {Gut butyrate-producers confer post-infarction cardiac protection.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7249}, pmid = {37945565}, issn = {2041-1723}, mesh = {Humans ; Animals ; Mice ; Butyrates/metabolism ; Heart ; *Myocardial Infarction ; *ST Elevation Myocardial Infarction ; Ketone Bodies ; }, abstract = {The gut microbiome and its metabolites are increasingly implicated in several cardiovascular diseases, but their role in human myocardial infarction (MI) injury responses have yet to be established. To address this, we examined stool samples from 77 ST-elevation MI (STEMI) patients using 16 S V3-V4 next-generation sequencing, metagenomics and machine learning. Our analysis identified an enriched population of butyrate-producing bacteria. These findings were then validated using a controlled ischemia/reperfusion model using eight nonhuman primates. To elucidate mechanisms, we inoculated gnotobiotic mice with these bacteria and found that they can produce beta-hydroxybutyrate, supporting cardiac function post-MI. This was further confirmed using HMGCS2-deficient mice which lack endogenous ketogenesis and have poor outcomes after MI. Inoculation increased plasma ketone levels and provided significant improvements in cardiac function post-MI. Together, this demonstrates a previously unknown role of gut butyrate-producers in the post-MI response.}, } @article {pmid37945272, year = {2023}, author = {Nasir, AZ and Egwuatu, N and Jameson, A}, title = {Metagenomic next-generation sequencing identifying a rare case of Mycobacterium xenopi discitis.}, journal = {BMJ case reports}, volume = {16}, number = {11}, pages = {}, pmid = {37945272}, issn = {1757-790X}, mesh = {Female ; Humans ; *Discitis/diagnosis/drug therapy/microbiology ; Ethambutol ; High-Throughput Nucleotide Sequencing ; *Mycobacterium ; *Mycobacterium Infections, Nontuberculous/diagnosis/drug therapy/microbiology ; *Mycobacterium xenopi/genetics ; Middle Aged ; }, abstract = {Mycobacterium xenopi is a non-tuberculous mycobacterium (NTM) that sporadically causes infections in humans and can cause rare bone and joint infections in immunocompromised hosts with history of spinal surgery. This slow-growing mycobacterium takes 8-12 weeks to grow on culture. Metagenomic next-generation sequencing (MNGS) is a highly sensitive and specific plasma-based microbial cell-free DNA test that can detect M. xenopi weeks prior to culture growth. We present a case of M. xenopi lumbosacral discitis with presacral abscess in an immunocompromised woman without history of spinal surgery which was detected by MNGS 8 weeks prior to culture growth. The patient's discitis resolved with an M. xenopi-directed regimen of ethambutol, rifampin and azithromycin. This case illustrates the utility of next-generation sequencing tests in rapid diagnosis of rare and opportunistic infections, as compared with traditional diagnostic tests, with supporting contextual clinical and diagnostic findings.}, } @article {pmid37944820, year = {2023}, author = {Zeng, K and Brewster, R and Kang, JB and Tkachenko, E and Brooks, E and Bhatt, AS and Fodor, AA and Andermann, TM}, title = {Acute Steroid-Refractory Gastrointestinal Graft-Versus-Host Disease Is Not Associated With Significant Differences in Gut Taxonomic Composition Compared to Steroid-Sensitive Gastrointestinal Graft-Versus-Host Disease Immediately Before Onset of Disease.}, journal = {Transplantation and cellular therapy}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jtct.2023.11.006}, pmid = {37944820}, issn = {2666-6367}, support = {K23 AI163365/AI/NIAID NIH HHS/United States ; }, abstract = {Taxonomic composition of the gut microbiota at the time of neutrophil engraftment is associated with the development of acute gastrointestinal graft-versus-host disease (GI GVHD) in patients undergoing allogeneic hematopoietic stem cell transplantation. However, less is known about the relationship between the gut microbiota and development of steroid-refractory GI GVHD immediately before the onset of disease. Markers of steroid-refractory GI GVHD are needed to identify patients who may benefit from the early initiation of non-corticosteroid-based GVHD treatment. Our aim was to identify differences in taxonomic composition in stool samples from patients without GVHD, with steroid-responsive GVHD and with steroid-refractory GI GVHD to identify predictive microbiome biomarkers of steroid-refractory GI GVHD. We conducted a retrospective case-control, single institution study, performing shotgun metagenomic sequencing on stool samples from patients with (n = 36) and without GVHD (n = 34) matched for time since transplantation. We compared the taxonomic composition of the gut microbiome in those with steroid-sensitive GI GVHD (n = 17) and steroid-refractory GI GVHD (n = 19) to each other and to those without GVHD. We also performed associations between steroid-refractory GI GVHD, gut taxonomic composition, and fecal calprotectin, a marker of GI GVHD to develop composite fecal markers of steroid-refractory GVHD before the onset of GI disease. We found that fecal samples within 30 days of GVHD onset from patients with and without GVHD or with and without steroid-refractory GI GVHD did not differ significantly in Shannon diversity (alpha-diversity) or in overall taxonomic composition (beta-diversity). Although those patients without GVHD had higher relative abundance of Clostridium spp., those with and without steroid-refractory GI GVHD did not significantly differ in taxonomic composition between one another. In our study, fecal calprotectin before disease onset was significantly higher in patients with GVHD compared to those without GVHD and higher in patients with steroid-refractory GI GVHD compared to steroid-sensitive GI GVHD. No taxa were significantly associated with higher levels of calprotectin.}, } @article {pmid37944617, year = {2023}, author = {Fossa, SL and Anton, BP and Kneller, DW and Petralia, LMC and Ganatra, MB and Boisvert, ML and Vainauskas, S and Chan, SH and Hokke, CH and Foster, JM and Taron, CH}, title = {A novel family of sugar-specific phosphodiesterases that remove zwitterionic modifications of GlcNAc.}, journal = {The Journal of biological chemistry}, volume = {299}, number = {12}, pages = {105437}, pmid = {37944617}, issn = {1083-351X}, mesh = {Humans ; *Sugars ; *Phosphoric Diester Hydrolases/genetics ; Carbohydrates ; Glycoconjugates/chemistry ; Polysaccharides/metabolism ; Acetylglucosamine/metabolism ; }, abstract = {The zwitterions phosphorylcholine (PC) and phosphoethanolamine (PE) are often found esterified to certain sugars in polysaccharides and glycoconjugates in a wide range of biological species. One such modification involves PC attachment to the 6-carbon of N-acetylglucosamine (GlcNAc-6-PC) in N-glycans and glycosphingolipids (GSLs) of parasitic nematodes, a modification that helps the parasite evade host immunity. Knowledge of enzymes involved in the synthesis and degradation of PC and PE modifications is limited. More detailed studies on such enzymes would contribute to a better understanding of the function of PC modifications and have potential application in the structural analysis of zwitterion-modified glycans. In this study, we used functional metagenomic screening to identify phosphodiesterases encoded in a human fecal DNA fosmid library that remove PC from GlcNAc-6-PC. A novel bacterial phosphodiesterase was identified and biochemically characterized. This enzyme (termed GlcNAc-PDase) shows remarkable substrate preference for GlcNAc-6-PC and GlcNAc-6-PE, with little or no activity on other zwitterion-modified hexoses. The identified GlcNAc-PDase protein sequence is a member of the large endonuclease/exonuclease/phosphatase superfamily where it defines a distinct subfamily of related sequences of previously unknown function, mostly from Clostridium bacteria species. Finally, we demonstrate use of GlcNAc-PDase to confirm the presence of GlcNAc-6-PC in N-glycans and GSLs of the parasitic nematode Brugia malayi in a glycoanalytical workflow.}, } @article {pmid37944612, year = {2024}, author = {Wang, Y and Xu, N and Chen, B and Zhang, Z and Lei, C and Zhang, Q and Gu, Y and Wang, T and Wang, M and Penuelas, J and Qian, H}, title = {Metagenomic analysis of antibiotic-resistance genes and viruses released from glaciers into downstream habitats.}, journal = {The Science of the total environment}, volume = {908}, number = {}, pages = {168310}, doi = {10.1016/j.scitotenv.2023.168310}, pmid = {37944612}, issn = {1879-1026}, mesh = {*Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Ice Cover ; Drug Resistance, Microbial/genetics ; Ecosystem ; *Viruses/genetics ; }, abstract = {Glaciers serve as effective reservoirs of antibiotic resistance genes (ARGs) and viruses for millions of years. Climate change and anthropogenic activity have accelerated the melting of glaciers, but the patterns of release of ARGs and viruses from melting glaciers into downstream habitats remain unknown. We analyzed 171 metagenomic samples from glaciers and their downstream habitats and found that the abundance and diversity of ARGs were higher in glaciers (polar and plateau glaciers) than downstream habitats (Arctic Ocean, Qinghai Lake, and Yangtze River Basin), with the diversity of viruses having the opposite pattern. Proteobacteria and Actinobacteria were the main potential hosts of ARGs and viruses, and the richness of ARGs carried by the hosts was positively correlated with viral abundance, suggesting that the transmission of viruses in the hosts could disseminate ARGs. Source tracking indicated that >18 % of the ARGs and >25 % of the viruses detected in downstream habitats originated from glaciers, demonstrating that glaciers could be one of the potential sources of ARGs and viruses in downstream habitats. Increased solar radiation and emission of carbon dioxide mainly influenced the release of the ARGs and viruses from glaciers into downstream habitats. This study provides a systematic insight demonstrating the release of ARGs and viruses from the melting glaciers, potentially increasing ecological pressure.}, } @article {pmid37944495, year = {2023}, author = {Huang, X and Hu, M and Sun, T and Li, J and Zhou, Y and Yan, Y and Xuan, B and Wang, J and Xiong, H and Ji, L and Zhu, X and Tong, T and Ning, L and Ma, Y and Zhao, Y and Ding, J and Guo, Z and Zhang, Y and Fang, JY and Hong, J and Chen, H}, title = {Multi-kingdom gut microbiota analyses define bacterial-fungal interplay and microbial markers of pan-cancer immunotherapy across cohorts.}, journal = {Cell host & microbe}, volume = {31}, number = {11}, pages = {1930-1943.e4}, doi = {10.1016/j.chom.2023.10.005}, pmid = {37944495}, issn = {1934-6069}, mesh = {Humans ; *Gastrointestinal Microbiome ; Metagenome ; Immunotherapy ; Bacteria/genetics ; *Neoplasms/therapy ; }, abstract = {The effect of gut bacteria on the response to immune checkpoint inhibitors (ICIs) has been studied, but the relationship between fungi and ICI responses is not fully understood. Herein, 862 fecal metagenomes from 9 different cohorts were integrated for the identification of differentially abundant fungi and subsequent construction of random forest (RF) models to predict ICI responses. Fungal markers demonstrate excellent performance, with an average area under the curve (AUC) of 0.87. Their performance improves even further, reaching an average AUC of 0.89 when combined with bacterial markers. Higher enrichment of exhausted T cells is detected in responders, as predicted by fungal markers. Multi-kingdom network and functional analysis reveal that the fungus Schizosaccharomyces octosporus may ferment starch into short-chain fatty acids in responders. This study provides a fungal profile of the ICI response and the identification of multi-kingdom microbial markers with good performance that may improve the overall applicability of ICI therapy.}, } @article {pmid37944355, year = {2024}, author = {Godain, A and Vogel, TM and Fongarland, P and Haddour, N}, title = {Influence of shear stress on electroactive biofilm characteristics and performance in microbial fuel cells.}, journal = {Biosensors & bioelectronics}, volume = {244}, number = {}, pages = {115806}, doi = {10.1016/j.bios.2023.115806}, pmid = {37944355}, issn = {1873-4235}, mesh = {*Bioelectric Energy Sources ; RNA, Ribosomal, 16S ; *Biosensing Techniques ; Electricity ; Biofilms ; Electrodes ; }, abstract = {This study has provided comprehensive insights into the intricate relationship between shear stress and the development, structure, and functionality of electroactive biofilms in Microbial Fuel Cells (MFCs). A multichannel microfluidic MFC reactors that created specific shear stress on the anode, were designed for the simultaneous study of multiple flow conditions using the same medium. Then, the evolution of the biofilm growth under different shear stress conditions (1, 5 and 10 mPa) were compared. The taxonomic and functional structure was studied by 16S rRNA gene and metagenomic sequencing and the physical biofilm characteristics were measured via fluorescence microscopy. The results demonstrate the pivotal role of shear stress in influencing the growth kinetics, electrical performance, and physical structure of anodic biofilms. Notably, the selection of specific EAB was observed to be shear stress-dependent, with a marked increase in specific EAB abundance as shear stress increased. The power density, while not directly correlated with the relative abundance of specific or nonspecific EAB, exhibited a strong linear relationship with biofilm coverage. This suggests that factors beyond the microbial composition, potentially including mass transport or electrochemical conditions, might be instrumental in determining electricity production. The functional metagenomic analysis further highlighted the complexities of extracellular electron transfer (EET) mechanisms in electroactive biofilm. While certain genes associated with EET in known species such as Geobacter and Shewanella were identified, the study also examined the limitations of solely relying on genetic markers to infer EET capabilities, emphasizing the need for complementary metaproteomic analyses. This study demonstrates the multifaceted impact of shear stress on electroactive biofilm and paves the way for future investigations aimed at harnessing the potential of electroactive biofilms in microbial fuel cell applications.}, } @article {pmid37944273, year = {2023}, author = {Farias-Jofre, M and Romero, R and Galaz, J and Xu, Y and Miller, D and Garcia-Flores, V and Arenas-Hernandez, M and Winters, AD and Berkowitz, BA and Podolsky, RH and Shen, Y and Kanninen, T and Panaitescu, B and Glazier, CR and Pique-Regi, R and Theis, KR and Gomez-Lopez, N}, title = {Blockade of IL-6R prevents preterm birth and adverse neonatal outcomes.}, journal = {EBioMedicine}, volume = {98}, number = {}, pages = {104865}, pmid = {37944273}, issn = {2352-3964}, mesh = {Animals ; Child ; Female ; Humans ; Infant, Newborn ; Mice ; Pregnancy ; Amniotic Fluid ; Inflammation/metabolism ; Interleukin-6/metabolism ; *Premature Birth/prevention & control ; Proteomics ; *Receptors, Interleukin-6/antagonists & inhibitors ; Antibodies, Monoclonal/therapeutic use ; }, abstract = {BACKGROUND: Preterm birth preceded by spontaneous preterm labour often occurs in the clinical setting of sterile intra-amniotic inflammation (SIAI), a condition that currently lacks treatment.

METHODS: Proteomic and scRNA-seq human data were analysed to evaluate the role of IL-6 and IL-1α in SIAI. A C57BL/6 murine model of SIAI-induced preterm birth was developed by the ultrasound-guided intra-amniotic injection of IL-1α. The blockade of IL-6R by using an aIL-6R was tested as prenatal treatment for preterm birth and adverse neonatal outcomes. QUEST-MRI evaluated brain oxidative stress in utero. Targeted transcriptomic profiling assessed maternal, foetal, and neonatal inflammation. Neonatal biometrics and neurodevelopment were tested. The neonatal gut immune-microbiome was evaluated using metagenomic sequencing and immunophenotyping.

FINDINGS: IL-6 plays a critical role in the human intra-amniotic inflammatory response, which is associated with elevated concentrations of the alarmin IL-1α. Intra-amniotic injection of IL-1α resembles SIAI, inducing preterm birth (7% vs. 50%, p = 0.03, Fisher's exact test) and neonatal mortality (18% vs. 56%, p = 0.02, Mann-Whitney U-test). QUEST-MRI revealed no foetal brain oxidative stress upon in utero IL-1α exposure (p > 0.05, mixed linear model). Prenatal treatment with aIL-6R abrogated IL-1α-induced preterm birth (50% vs. 7%, p = 0.03, Fisher's exact test) by dampening inflammatory processes associated with the common pathway of labour. Importantly, aIL-6R reduces neonatal mortality (56% vs. 22%, p = 0.03, Mann-Whitney U-test) by crossing from the mother to the amniotic cavity, dampening foetal organ inflammation and improving growth. Beneficial effects of prenatal IL-6R blockade carried over to neonatal life, improving survival, growth, neurodevelopment, and gut immune homeostasis.

INTERPRETATION: IL-6R blockade can serve as a strategy to treat SIAI, preventing preterm birth and adverse neonatal outcomes.

FUNDING: NICHD/NIH/DHHS, Contract HHSN275201300006C. WSU Perinatal Initiative in Maternal, Perinatal and Child Health.}, } @article {pmid37943504, year = {2023}, author = {Gámbaro, F and Pérez, AB and Prot, M and Agüera, E and Baidaliuk, A and Sánchez-Seco, MP and Martínez-Martínez, L and Vázquez, A and Fernandez-Garcia, MD and Simon-Loriere, E}, title = {Untargeted metagenomic sequencing identifies Toscana virus in patients with idiopathic meningitis, southern Spain, 2015 to 2019.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {28}, number = {45}, pages = {}, pmid = {37943504}, issn = {1560-7917}, mesh = {Humans ; Male ; Adult ; *Sandfly fever Naples virus/genetics ; *Insect Bites and Stings ; Phylogeny ; Retrospective Studies ; Spain/epidemiology ; *Meningitis ; }, abstract = {BackgroundVarious pathogens, including bacteria, fungi, parasites, and viruses can lead to meningitis. Among viruses causing meningitis, Toscana virus (TOSV), a phlebovirus, is transmitted through sandfly bites. TOSV infection may be suspected if patients with enterovirus- and herpesvirus-negative aseptic (non-bacterial) meningitis recall recent insect bites. Other epidemiological factors (season, rural area) may be considered. The broad range of possible meningitis aetiologies poses considerable diagnosis challenges. Untargeted metagenomic next-generation sequencing (mNGS) can potentially identify pathogens, which are not considered or detected in routine diagnostic panels.AimIn this retrospective, single-centre observational study, we investigated mNGS usefulness to understand the cause of meningitis when conventional approaches fail.MethodsCerebrospinal fluid (CSF) samples from patients hospitalised in southern Spain in 2015-2019 with aseptic meningitis and no aetiology found by conventional testing, were subjected to mNGS. Patients' demographic characteristics had been recorded and physicians had asked them about recent insect bites. Obtained viral genome sequences were phylogenetically analysed.ResultsAmong 23 idiopathic cases, TOSV was identified in eight (all male; median age: 39 years, range: 15-78 years). Five cases lived in an urban setting, three occurred in autumn and only one recalled insect bites. Phylogenetic analysis of TOSV segment sequences supported one intra-genotype reassortment event.ConclusionsOur study highlights the usefulness of mNGS for identifying viral pathogens directly in CSF. In southern Spain, TOSV should be considered regardless of recalling of insect bites or other epidemiological criteria. Detection of a disease-associated reassortant TOSV emphasises the importance of monitoring the spread and evolution of phleboviruses in Mediterranean countries.}, } @article {pmid37943043, year = {2023}, author = {Berthold, M and Albrecht, M and Campbell, DA and Omar, NM}, title = {Draft genomes of 3 cyanobacteria strains and 17 co-habiting proteobacteria assembled from metagenomes.}, journal = {Microbiology resource announcements}, volume = {12}, number = {12}, pages = {e0046023}, pmid = {37943043}, issn = {2576-098X}, support = {426659886//Deutsche Forschungsgemeinschaft (DFG)/ ; //Canada Research Chairs (Chaires de recherche du Canada)/ ; }, abstract = {Cyanobium and Synechococcus are prominent, globally distributed cyanobacteria genera with ecological significance. Here, we report the genomes of the marine Synechococcus sp. CCMP836 and two strains of Cyanobium (CZS25K and CZS48M) along with the genomes of 17 co-occurring proteobacteria. These genomes will improve the strain-specific ecological positions.}, } @article {pmid37942080, year = {2023}, author = {Shi, Y and Zhang, C and Pan, S and Chen, Y and Miao, X and He, G and Wu, Y and Ye, H and Weng, C and Zhang, H and Zhou, W and Yang, X and Liang, C and Chen, D and Hong, L and Su, F}, title = {The diagnosis of tuberculous meningitis: advancements in new technologies and machine learning algorithms.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1290746}, pmid = {37942080}, issn = {1664-302X}, abstract = {Tuberculous meningitis (TBM) poses a diagnostic challenge, particularly impacting vulnerable populations such as infants and those with untreated HIV. Given the diagnostic intricacies of TBM, there's a pressing need for rapid and reliable diagnostic tools. This review scrutinizes the efficacy of up-and-coming technologies like machine learning in transforming TBM diagnostics and management. Advanced diagnostic technologies like targeted gene sequencing, real-time polymerase chain reaction (RT-PCR), miRNA assays, and metagenomic next-generation sequencing (mNGS) offer promising avenues for early TBM detection. The capabilities of these technologies are further augmented when paired with mass spectrometry, metabolomics, and proteomics, enriching the pool of disease-specific biomarkers. Machine learning algorithms, adept at sifting through voluminous datasets like medical imaging, genomic profiles, and patient histories, are increasingly revealing nuanced disease pathways, thereby elevating diagnostic accuracy and guiding treatment strategies. While these burgeoning technologies offer hope for more precise TBM diagnosis, hurdles remain in terms of their clinical implementation. Future endeavors should zero in on the validation of these tools through prospective studies, critically evaluating their limitations, and outlining protocols for seamless incorporation into established healthcare frameworks. Through this review, we aim to present an exhaustive snapshot of emerging diagnostic modalities in TBM, the current standing of machine learning in meningitis diagnostics, and the challenges and future prospects of converging these domains.}, } @article {pmid37941937, year = {2023}, author = {Zhang, H and Wei, T and Li, Q and Fu, L and He, L and Wang, Y}, title = {Metagenomic 16S rDNA reads of in situ preserved samples revealed microbial communities in the Yongle blue hole.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16257}, pmid = {37941937}, issn = {2167-8359}, mesh = {DNA, Ribosomal/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Water ; *Microbiota/genetics ; Sulfates ; }, abstract = {Our knowledge on biogeochemistry and microbial ecology of marine blue holes is limited due to challenges in collecting multilayered water column and oxycline zones. In this study, we collected samples from 16 water layers in Yongle blue hole (YBH) located in the South China Sea using the in situ microbial filtration and fixation (ISMIFF) apparatus. The microbial communities based on 16S rRNA metagenomic reads for the ISMIFF samples showed high microbial diversity and consistency among samples with similar dissolved oxygen levels. At the same depth of the anoxic layer, the ISMIFF samples were dominated by sulfate-reducing bacteria from Desulfatiglandales (17.96%). The sulfide concentration is the most significant factor that drives the division of microbial communities in YBH, which might support the prevalence of sulfate-reducing microorganisms in the anoxic layers. Our results are different from the microbial community structures of a Niskin sample of this study and the reported samples collected in 2017, in which a high relative abundance of Alteromonadales (26.59%) and Thiomicrospirales (38.13%), and Arcobacteraceae (11.74%) was identified. We therefore demonstrate a new profile of microbial communities in YBH probably due to the effect of sampling and molecular biological methods, which provides new possibilities for further understanding of the material circulation mechanism of blue holes and expanding anoxic marine water zones under global warming.}, } @article {pmid37941936, year = {2023}, author = {Liao, F and Xia, Y and Gu, W and Fu, X and Yuan, B}, title = {Comparative analysis of shotgun metagenomics and 16S rDNA sequencing of gut microbiota in migratory seagulls.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16394}, pmid = {37941936}, issn = {2167-8359}, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/genetics ; DNA, Ribosomal/genetics ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; *Salmonella enterica/genetics ; }, abstract = {BACKGROUND: Shotgun metagenomic and 16S rDNA sequencing are commonly used methods to identify the taxonomic composition of microbial communities. Previously, we analysed the gut microbiota and intestinal pathogenic bacteria configuration of migratory seagulls by using 16S rDNA sequencing and culture methods.

METHODS: To continue in-depth research on the gut microbiome and reveal the applicability of the two methods, we compared the metagenome and 16S rDNA amplicon results to further demonstrate the features of this animal.

RESULTS: The number of bacterial species detected by metagenomics gradually increased from the phylum to species level, consistent with 16S rDNA sequencing. Several taxa were commonly shared by both sequencing methods. However, Escherichia, Shigella, Erwinia, Klebsiella, Salmonella, Escherichia albertii, Shigella sonnei, Salmonella enterica, and Shigella flexneri were unique taxa for the metagenome compared with Escherichia-Shigella, Hafnia-Obesumbacterium, Catellicoccus marimammalium, Lactococcus garvieae, and Streptococcus gallolyticus for 16S rDNA sequencing. The largest differences in relative abundance between the two methods were identified at the species level, which identified many pathogenic bacteria to humans using metagenomic sequencing. Pearson correlation analysis indicated that the correlation coefficient for the two methods gradually decreased with the refinement of the taxonomic levels. The high consistency of the correlation coefficient was identified at the genus level for the beta diversity of the two methods.

CONCLUSIONS: In general, relatively consistent patterns and reliability could be identified by both sequencing methods, but the results varied following the refinement of taxonomic levels. Metagenomic sequencing was more suitable for the discovery and detection of pathogenic bacteria of gut microbiota in seagulls. Although there were large differences in the numbers and abundance of bacterial species of the two methods in terms of taxonomic levels, the patterns and reliability results of the samples were consistent.}, } @article {pmid37941738, year = {2023}, author = {Wizenberg, SB and Newburn, LR and Richardson, RT and Pepinelli, M and Conflitti, IM and Moubony, M and Borges, D and Guarna, MM and Guzman-Novoa, E and Foster, LJ and Zayed, A}, title = {Environmental metagenetics unveil novel plant-pollinator interactions.}, journal = {Ecology and evolution}, volume = {13}, number = {11}, pages = {e10645}, pmid = {37941738}, issn = {2045-7758}, abstract = {Honey bees are efficient pollinators of flowering plants, aiding in the plant reproductive cycle and acting as vehicles for evolutionary processes. Their role as agents of selection and drivers of gene flow is instrumental to the structure of plant populations, but historically, our understanding of their influence has been limited to predominantly insect-dispersed flowering species. Recent metagenetic work has provided evidence that honey bees also forage on pollen from anemophilous species, suggesting that their role as vectors for transmission of plant genetic material is not confined to groups designated as entomophilous, and leading us to ask: could honey bees act as dispersal agents for non-flowering plant taxa? Using an extensive pollen metabarcoding dataset from Canada, we discovered that honey bees may serve as dispersal agents for an array of sporophytes (Anchistea, Claytosmunda, Dryopteris, Osmunda, Osmundastrum, Equisetum) and bryophytes (Funaria, Orthotrichum, Sphagnum, Ulota). Our findings also suggest that honey bees may occasionally act as vectors for the dispersal of aquatic phototrophs, specifically Coccomyxa and Protosiphon, species of green algae. Our work has shed light on the broad resource-access patterns that guide plant-pollinator interactions and suggests that bees could act as vectors of gene flow, and potentially even agents of selection, across Plantae.}, } @article {pmid37941395, year = {2022}, author = {Blumberg, K and Miller, M and Ponsero, A and Hurwitz, B}, title = {Ontology-driven analysis of marine metagenomics: what more can we learn from our data?.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {37941395}, issn = {2047-217X}, mesh = {*Ecology ; *Microbiota/genetics ; Metagenome ; Metagenomics ; }, abstract = {BACKGROUND: The proliferation of metagenomic sequencing technologies has enabled novel insights into the functional genomic potentials and taxonomic structure of microbial communities. However, cyberinfrastructure efforts to manage and enable the reproducible analysis of sequence data have not kept pace. Thus, there is increasing recognition of the need to make metagenomic data discoverable within machine-searchable frameworks compliant with the FAIR (Findability, Accessibility, Interoperability, and Reusability) principles for data stewardship. Although a variety of metagenomic web services exist, none currently leverage the hierarchically structured terminology encoded within common life science ontologies to programmatically discover data.

RESULTS: Here, we integrate large-scale marine metagenomic datasets with community-driven life science ontologies into a novel FAIR web service. This approach enables the retrieval of data discovered by intersecting the knowledge represented within ontologies against the functional genomic potential and taxonomic structure computed from marine sequencing data. Our findings highlight various microbial functional and taxonomic patterns relevant to the ecology of prokaryotes in various aquatic environments.

CONCLUSIONS: In this work, we present and evaluate a novel Semantic Web architecture that can be used to ask novel biological questions of existing marine metagenomic datasets. Finally, the FAIR ontology searchable data products provided by our API can be leveraged by future research efforts.}, } @article {pmid37941137, year = {2023}, author = {Asin-Garcia, E and Garcia-Morales, L and Bartholet, T and Liang, Z and Isaacs, FJ and Martins Dos Santos, VAP}, title = {Metagenomics harvested genus-specific single-stranded DNA-annealing proteins improve and expand recombineering in Pseudomonas species.}, journal = {Nucleic acids research}, volume = {51}, number = {22}, pages = {12522-12536}, pmid = {37941137}, issn = {1362-4962}, support = {15814/NWO_/Dutch Research Council/Netherlands ; }, mesh = {DNA, Single-Stranded/genetics/metabolism ; *Gene Editing/methods ; Metabolic Engineering ; *Pseudomonas/genetics ; Pseudomonas putida/genetics ; }, abstract = {The widespread Pseudomonas genus comprises a collection of related species with remarkable abilities to degrade plastics and polluted wastes and to produce a broad set of valuable compounds, ranging from bulk chemicals to pharmaceuticals. Pseudomonas possess characteristics of tolerance and stress resistance making them valuable hosts for industrial and environmental biotechnology. However, efficient and high-throughput genetic engineering tools have limited metabolic engineering efforts and applications. To improve their genome editing capabilities, we first employed a computational biology workflow to generate a genus-specific library of potential single-stranded DNA-annealing proteins (SSAPs). Assessment of the library was performed in different Pseudomonas using a high-throughput pooled recombinase screen followed by Oxford Nanopore NGS analysis. Among different active variants with variable levels of allelic replacement frequency (ARF), efficient SSAPs were found and characterized for mediating recombineering in the four tested species. New variants yielded higher ARFs than existing ones in Pseudomonas putida and Pseudomonas aeruginosa, and expanded the field of recombineering in Pseudomonas taiwanensisand Pseudomonas fluorescens. These findings will enhance the mutagenesis capabilities of these members of the Pseudomonas genus, increasing the possibilities for biotransformation and enhancing their potential for synthetic biology applications. .}, } @article {pmid37941060, year = {2023}, author = {Ma, L and Song, Y and Lyu, W and Chen, Q and Xiao, X and Jin, Y and Yang, H and Wang, W and Xiao, Y}, title = {Longitudinal metagenomic study reveals the dynamics of fecal antibiotic resistome in pigs throughout the lifetime.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {55}, pmid = {37941060}, issn = {2524-4671}, support = {2021M702905//Postdoctoral Science Foundation of China/ ; 2022C02049//Key Research and Development Program of Zhejiang Province/ ; UA2020-152, UA2021-247//Walmart Foundation/ ; 31972999//National Natural Science Foundation of China/ ; 2010DS700124-ZZ1905//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products/ ; }, abstract = {BACKGROUND: The dissemination of antibiotic resistance genes (ARGs) poses a substantial threat to environmental safety and human health. Herein, we present a longitudinal paired study across the swine lifetime from birth to market, coupled with metagenomic sequencing to explore the dynamics of ARGs and their health risk in the swine fecal microbiome.

RESULTS: We systematically characterized the composition and distribution of ARGs among the different growth stages. In total, 829 ARG subtypes belonging to 21 different ARG types were detected, in which tetracycline, aminoglycoside, and MLS were the most abundant types. Indeed, 134 core ARG subtypes were shared in all stages and displayed a growth stage-associated pattern. Furthermore, the correlation between ARGs, gut microbiota and mobile genetic elements (MGEs) revealed Escherichia coli represented the main carrier of ARGs. We also found that in most cases, the dominant ARGs could be transmitted to progeny piglets, suggesting the potential ARGs generation transmission. Finally, the evaluation of the antibiotic resistance threats provides us some early warning of those high health risk ARGs.

CONCLUSIONS: Collectively, this relatively more comprehensive study provides a primary overview of ARG profile in swine microbiome across the lifetime and highlights the health risk and the intergenerational spread of ARGs in pig farm.}, } @article {pmid37940842, year = {2023}, author = {Liang, Y and Lin, M and Qiu, L and Chen, M and Tan, C and Tu, C and Zheng, X and Liu, J}, title = {Clinical characteristics of hospitalized patients with Nocardia genus detection by metagenomic next generation sequencing in a tertiary hospital from southern China.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {772}, pmid = {37940842}, issn = {1471-2334}, support = {A2020176//Medical Scientific Research Foundation of Guangdong Province of China/ ; ZH2202200012HJL//Science and Technology Planning Project for meidicine of Zhuhai City/ ; }, mesh = {Humans ; Aged ; Tertiary Care Centers ; High-Throughput Nucleotide Sequencing ; *Nocardia/genetics ; *Nocardia Infections/diagnosis/drug therapy ; Sulfamethoxazole/therapeutic use ; Sulfanilamide ; China ; }, abstract = {OBJECTIVE: As an opportunistic pathogen, Nocardia often occurring in the immunocompromised hosts. As the unspecifc clinical presentation and low identification rate of the culture dependent methods, Nocardia infection may be under-diagnosis. Recent study have reported physicians could benefit from metagenomic next-generation sequencing (mNGS) in Nocardia diagnosis. Herein, we present patients with a positive detection of nocardiosis in mNGS, aiming to provide useful information for an differential diagnosis and patients management.

METHODS: A total of 3756 samples detected for mNGS from March 2019 to April 2022 at the Fifth Affifiliated Hospital of Sun Yat-sen University, were screened. Clinical records, laboratory finding, CT images and mNGS results were reviewed for 19 patients who were positive for Nocardia genus.

RESULTS: Samples from low respiratory tract obtained by bronchoscope took the major part of the positive (15/19). 12 of 19 cases were diagnosis as Nocardiosis Disease (ND) and over half of the ND individuals (7/12) were geriatric. Nearly all of them (10/12) were immunocompetent and 2 patients in ND group were impressively asymptomatic. Cough was the most common symptom. Nocardia cyriacigeorgica (4/12) was more frequently occurring in ND, followed by Nocardia abscessus (3/12). There are 3 individuals detected more than one kind of Nocardia species (Supplementary table 1). Except one with renal failure and one allergic to sulfamethoxazole, all of them received co-sulfonamide treatment and relieved eventually.

CONCLUSION: Our study deciphered the clinical features of patients with positive nocardiosis detected by mNGS. Greater attention should be paid to the ND that occurred in the immunocompetent host and the geriatric. Due to the difficulties in establishing diagnosis of Nocardiosis disease, mNGS should play a much more essential role for a better assessment in those intractable cases. Co-sulfonamide treatment should still be the first choice of Nocardiosis disease.}, } @article {pmid37940706, year = {2023}, author = {Gondard, M and Lane, M and Barratt, J and Talundzic, E and Qvarnstrom, Y}, title = {Simultaneous targeted amplicon deep sequencing and library preparation for a time and cost-effective universal parasite diagnostic sequencing approach.}, journal = {Parasitology research}, volume = {122}, number = {12}, pages = {3243-3256}, pmid = {37940706}, issn = {1432-1955}, support = {CC999999/ImCDC/Intramural CDC HHS/United States ; }, mesh = {Animals ; Humans ; *Parasites/genetics ; Cost-Benefit Analysis ; *Plasmodium/genetics ; Plasmodium falciparum/genetics ; DNA, Ribosomal/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Babesia/genetics ; }, abstract = {We recently described a targeted amplicon deep sequencing (TADS) strategy that utilizes a nested PCR targeting the 18S rDNA gene of blood-borne parasites. The assay facilitates selective digestion of host DNA by targeting enzyme restriction sites present in vertebrates but absent in parasites. This enriching of parasite-derived amplicon drastically reduces the proportion of host-derived reads during sequencing and results in the sensitive detection of several clinically important blood parasites including Plasmodium spp., Babesia spp., kinetoplastids, and filarial nematodes. Despite these promising results, high costs and the laborious nature of metagenomics sequencing are prohibitive to the routine use of this assay in most laboratories. We describe and evaluate a new metagenomic approach that utilizes a set of primers modified from our original assay that incorporates Illumina barcodes and adapters during the PCR steps. This modification makes amplicons immediately compatible with sequencing on the Illumina MiSeq platform, removing the need for a separate library preparation, which is expensive and time-consuming. We compared this modified assay to our previous nested TADS assay in terms of preparation speed, limit of detection (LOD), and cost. Our modifications reduced assay turnaround times from 7 to 5 days. The cost decreased from approximately $40 per sample to $11 per sample. The modified assay displayed comparable performance in the detection and differentiation of human-infecting Plasmodium spp., Babesia spp., kinetoplastids, and filarial nematodes in clinical samples. The LOD of this modified approach was determined for malaria parasites and remained similar to that previously reported for our earlier assay (0.58 Plasmodium falciparum parasites/µL of blood). These modifications markedly reduced costs and turnaround times, making the assay more amenable to routine diagnostic applications.}, } @article {pmid37940667, year = {2023}, author = {Hu, M and Caldarelli, G and Gili, T}, title = {Inflammatory bowel disease biomarkers revealed by the human gut microbiome network.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {19428}, pmid = {37940667}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/microbiology ; *Crohn Disease/genetics/microbiology ; *Microbiota ; *Colitis, Ulcerative/genetics ; Biomarkers ; Escherichia coli ; }, abstract = {Inflammatory bowel diseases (IBDs) are complex medical conditions in which the gut microbiota is attacked by the immune system of genetically predisposed subjects when exposed to yet unclear environmental factors. The complexity of this class of diseases makes them suitable to be represented and studied with network science. In this paper, the metagenomic data of control, Crohn's disease, and ulcerative colitis subjects' gut microbiota were investigated by representing this data as correlation networks and co-expression networks. We obtained correlation networks by calculating Pearson's correlation between gene expression across subjects. A percolation-based procedure was used to threshold and binarize the adjacency matrices. In contrast, co-expression networks involved the construction of the bipartite subjects-genes networks and the monopartite genes-genes projection after binarization of the biadjacency matrix. Centrality measures and community detection were used on the so-built networks to mine data complexity and highlight possible biomarkers of the diseases. The main results were about the modules of Bacteroides, which were connected in the control subjects' correlation network, Faecalibacterium prausnitzii, where co-enzyme A became central in IBD correlation networks and Escherichia coli, whose module has different patterns of integration within the whole network in the different diagnoses.}, } @article {pmid37940330, year = {2023}, author = {Ismaeel, A and Valentino, TR and Burke, B and Goh, J and Saliu, TP and Albathi, F and Owen, A and McCarthy, JJ and Wen, Y}, title = {Acetate and succinate benefit host muscle energetics as exercise-associated post-biotics.}, journal = {Physiological reports}, volume = {11}, number = {21}, pages = {e15848}, pmid = {37940330}, issn = {2051-817X}, support = {5K99AR081367//HHS | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)/ ; 5R21AG071888//HHS | NIH | National Institute on Aging (NIA)/ ; 2022-67012-38533//USDA | National Institute of Food and Agriculture (NIFA)/ ; }, mesh = {Mice ; Animals ; *Succinic Acid ; Muscle, Skeletal/metabolism ; *Microbiota ; Bacteria ; Bacteroidetes ; Acetates/pharmacology ; Hypertrophy/metabolism ; }, abstract = {Recently, the gut microbiome has emerged as a potent modulator of exercise-induced systemic adaptation and appears to be crucial for mediating some of the benefits of exercise. This study builds upon previous evidence establishing a gut microbiome-skeletal muscle axis, identifying exercise-induced changes in microbiome composition. Metagenomics sequencing of fecal samples from non-exercise-trained controls or exercise-trained mice was conducted. Biodiversity indices indicated exercise training did not change alpha diversity. However, there were notable differences in beta-diversity between trained and untrained microbiomes. Exercise significantly increased the level of the bacterial species Muribaculaceae bacterium DSM 103720. Computation simulation of bacterial growth was used to predict metabolites that accumulate under in silico culture of exercise-responsive bacteria. We identified acetate and succinate as potential gut microbial metabolites that are produced by Muribaculaceae bacterium, which were then administered to mice during a period of mechanical overload-induced muscle hypertrophy. Although no differences were observed for the overall muscle growth response to succinate or acetate administration during the first 5 days of mechanical overload-induced hypertrophy, acetate and succinate increased skeletal muscle mitochondrial respiration. When given as post-biotics, succinate or acetate treatment may improve oxidative metabolism during muscle hypertrophy.}, } @article {pmid37940329, year = {2023}, author = {Kurokawa, M and Higashi, K and Yoshida, K and Sato, T and Maruyama, S and Mori, H and Kurokawa, K}, title = {Metagenomic Thermometer.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {30}, number = {6}, pages = {}, pmid = {37940329}, issn = {1756-1663}, mesh = {Humans ; *Thermometers ; *Metagenome ; Metagenomics ; Genomics ; }, abstract = {Various microorganisms exist in environments, and each of them has its optimal growth temperature (OGT). The relationship between genomic information and OGT of each species has long been studied, and one such study revealed that OGT of prokaryotes can be accurately predicted based on the fraction of seven amino acids (IVYWREL) among all encoded amino-acid sequences in its genome. Extending this discovery, we developed a 'Metagenomic Thermometer' as a means of predicting environmental temperature based on metagenomic sequences. Temperature prediction of diverse environments using publicly available metagenomic data revealed that the Metagenomic Thermometer can predict environmental temperatures with small temperature changes and little influx of microorganisms from other environments. The accuracy of the Metagenomic Thermometer was also confirmed by a demonstration experiment using an artificial hot water canal. The Metagenomic Thermometer was also applied to human gut metagenomic samples, yielding a reasonably accurate value for human body temperature. The result further suggests that deep body temperature determines the dominant lineage of the gut community. Metagenomic Thermometer provides a new insight into temperature-driven community assembly based on amino-acid composition rather than microbial taxa.}, } @article {pmid37940209, year = {2023}, author = {Njage, PMK and van Bunnik, B and Munk, P and Marques, ARP and Aarestrup, FM}, title = {Association of health, nutrition, and socioeconomic variables with global antimicrobial resistance: a modelling study.}, journal = {The Lancet. Planetary health}, volume = {7}, number = {11}, pages = {e888-e899}, doi = {10.1016/S2542-5196(23)00213-9}, pmid = {37940209}, issn = {2542-5196}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; Sewage/microbiology ; *Anti-Infective Agents/pharmacology ; Bacteria/genetics ; Socioeconomic Factors ; }, abstract = {BACKGROUND: Although antimicrobial use is a key selector for antimicrobial resistance, recent studies have suggested that the ecological context in which antimicrobials are used might provide important factors for the prediction of the emergence and spread of antimicrobial resistance.

METHODS: We used 1547 variables from the World Bank dataset consisting of socioeconomic, developmental, health, and nutritional indicators; data from a global sewage-based study on antimicrobial resistance (abundance of antimicrobial resistance genes [ARGs]); and data on antimicrobial usage computed from the ECDC database and the IQVIA database. We characterised and built models predicting the global resistome at an antimicrobial class level. We used a generalised linear mixed-effects model to estimate the association between antimicrobial usage and ARG abundance in the sewage samples; a multivariate random forest model to build predictive models for each antimicrobial resistance class and to select the most important variables for ARG abundance; logistic regression models to test the association between the predicted country-level antimicrobial resistance abundance and the country-level proportion of clinical resistant bacterial isolates; finite mixture models to investigate geographical heterogeneities in the abundance of ARGs; and multivariate finite mixture models with covariates to investigate the effect of heterogeneity in the association between the most important variables and the observed ARG abundance across the different country subgroups. We compared our predictions with available clinical phenotypic data from the SENTRY Antimicrobial Surveillance Program from eight antimicrobial classes and 12 genera from 56 countries.

FINDINGS: Using antimicrobial use data from between Jan 1, 2016, and Dec 31, 2019, we found that antimicrobial usage was not significantly associated with the global ARG abundance in sewage (p=0·72; incidence rate ratio 1·02 [95% CI 0·92-1·13]), whereas country-specific World Bank's variables explained a large amount of variation. The importance of the World Bank variables differed between antimicrobial classes and countries. Generally, the estimated global ARG abundance was positively associated with the prevalence of clinical phenotypic resistance, with a strong association for bacterial groups in the human gut. The associations between bacterial groups and ARG abundance were positive and significantly different from zero for the aminoglycosides (three of the four of the taxa tested), β-lactam (all the six microbial groups), fluoroquinolones (seven of nine of the microbial groups), glycopeptide (one microbial group tested), folate pathway antagonists (four of five microbial groups), and tetracycline (two of nine microbial groups).

INTERPRETATION: Metagenomic analysis of sewage is a robust approach for the surveillance of antimicrobial resistance in pathogens, especially for bacterial groups associated with the human gut. Additional studies on the associations between important socioeconomic, nutritional, and health factors and antimicrobial resistance should consider the variation in these associations between countries and antimicrobial classes.

FUNDING: EU Horizon 2020 and Novo Nordisk Foundation.}, } @article {pmid37938762, year = {2022}, author = {Lesser, MP and Sabrina Pankey, M and Slattery, M and Macartney, KJ and Gochfeld, DJ}, title = {Microbiome diversity and metabolic capacity determines the trophic ecology of the holobiont in Caribbean sponges.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {112}, pmid = {37938762}, issn = {2730-6151}, support = {OCE 1638296//National Science Foundation (NSF)/ ; OCE 1638296//National Science Foundation (NSF)/ ; OCE 1638289//National Science Foundation (NSF)/ ; OCE 1638296//National Science Foundation (NSF)/ ; OCE 1638289//National Science Foundation (NSF)/ ; }, abstract = {Sponges are increasingly recognized as an ecologically important taxon on coral reefs, representing significant biomass and biodiversity where sponges have replaced scleractinian corals. Most sponge species can be divided into two symbiotic states based on symbiont community structure and abundance (i.e., the microbiome), and are characterized as high microbial abundance (HMA) or low microbial abundance (LMA) sponges. Across the Caribbean, sponge species of the HMA or LMA symbiotic states differ in metabolic capacity, as well as their trophic ecology. A metagenetic analysis of symbiont 16 S rRNA and metagenomes showed that HMA sponge microbiomes are more functionally diverse than LMA microbiomes, offer greater metabolic functional capacity and redundancy, and encode for the biosynthesis of secondary metabolites. Stable isotope analyses showed that HMA and LMA sponges primarily consume dissolved organic matter (DOM) derived from external autotrophic sources, or live particulate organic matter (POM) in the form of bacterioplankton, respectively, resulting in a low degree of resource competition between these symbiont states. As many coral reefs have undergone phase shifts from coral- to macroalgal-dominated reefs, the role of DOM, and the potential for future declines in POM due to decreased picoplankton productivity, may result in an increased abundance of chemically defended HMA sponges on tropical coral reefs.}, } @article {pmid37938735, year = {2022}, author = {Breusing, C and Osborn, KJ and Girguis, PR and Reese, AT}, title = {Composition and metabolic potential of microbiomes associated with mesopelagic animals from Monterey Canyon.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {117}, pmid = {37938735}, issn = {2730-6151}, abstract = {There is growing recognition that microbiomes play substantial roles in animal eco-physiology and evolution. To date, microbiome research has largely focused on terrestrial animals, with far fewer studies on aquatic organisms, especially pelagic marine species. Pelagic animals are critical for nutrient cycling, yet are also subject to nutrient limitation and might thus rely strongly on microbiome digestive functions to meet their nutritional requirements. To better understand the composition and metabolic potential of midwater host-associated microbiomes, we applied amplicon and shotgun metagenomic sequencing to eleven mesopelagic animal species. Our analyses reveal that mesopelagic animal microbiomes are typically composed of bacterial taxa from the phyla Proteobacteria, Firmicutes, Bacteroidota and, in some cases, Campylobacterota. Overall, compositional and functional microbiome variation appeared to be primarily governed by host taxon and depth and, to a lesser extent, trophic level and diel vertical migratory behavior, though the impact of host specificity seemed to differ between migrating and non-migrating species. Vertical migrators generally showed lower intra-specific microbiome diversity (i.e., higher host specificity) than their non-migrating counterparts. These patterns were not linked to host phylogeny but may reflect differences in feeding behaviors, microbial transmission mode, environmental adaptations and other ecological traits among groups. The results presented here further our understanding of the factors shaping mesopelagic animal microbiomes and also provide some novel, genetically informed insights into their diets.}, } @article {pmid38046907, year = {2022}, author = {Ventura, M and van Sinderen, D and Turroni, F}, title = {New research frontiers pertaining to the infant gut microbiota.}, journal = {Microbiome research reports}, volume = {1}, number = {4}, pages = {24}, pmid = {38046907}, issn = {2771-5965}, abstract = {The human gut microbiota is believed to be responsible for multiple health-impacting host effects. The influence of gut microorganisms on the human host begins immediately after birth, having long-lasting health effects, while the gut microbiota itself continues to develop throughout the host's entire life. The purported health-associated effects of the gut microbiota have fueled extensive and ongoing research efforts. Nonetheless, the precise mode of action of functionalities exerted by microbial colonizers of the infant intestine is still largely unknown. The current perspective intends to illustrate major future investigative directions concerning the human gut microbiota with a specific focus on infant-associated gut microbes.}, } @article {pmid37938754, year = {2022}, author = {Díaz Rodríguez, CA and Díaz-García, L and Bunk, B and Spröer, C and Herrera, K and Tarazona, NA and Rodriguez-R, LM and Overmann, J and Jiménez, DJ}, title = {Novel bacterial taxa in a minimal lignocellulolytic consortium and their potential for lignin and plastics transformation.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {89}, pmid = {37938754}, issn = {2730-6151}, abstract = {The understanding and manipulation of microbial communities toward the conversion of lignocellulose and plastics are topics of interest in microbial ecology and biotechnology. In this study, the polymer-degrading capability of a minimal lignocellulolytic microbial consortium (MELMC) was explored by genome-resolved metagenomics. The MELMC was mostly composed (>90%) of three bacterial members (Pseudomonas protegens; Pristimantibacillus lignocellulolyticus gen. nov., sp. nov; and Ochrobactrum gambitense sp. nov) recognized by their high-quality metagenome-assembled genomes (MAGs). Functional annotation of these MAGs revealed that Pr. lignocellulolyticus could be involved in cellulose and xylan deconstruction, whereas Ps. protegens could catabolize lignin-derived chemical compounds. The capacity of the MELMC to transform synthetic plastics was assessed by two strategies: (i) annotation of MAGs against databases containing plastic-transforming enzymes; and (ii) predicting enzymatic activity based on chemical structural similarities between lignin- and plastics-derived chemical compounds, using Simplified Molecular-Input Line-Entry System and Tanimoto coefficients. Enzymes involved in the depolymerization of polyurethane and polybutylene adipate terephthalate were found to be encoded by Ps. protegens, which could catabolize phthalates and terephthalic acid. The axenic culture of Ps. protegens grew on polyhydroxyalkanoate (PHA) nanoparticles and might be a suitable species for the industrial production of PHAs in the context of lignin and plastic upcycling.}, } @article {pmid37938749, year = {2022}, author = {Debroas, D and Hochart, C and Galand, PE}, title = {Seasonal microbial dynamics in the ocean inferred from assembled and unassembled data: a view on the unknown biosphere.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {87}, pmid = {37938749}, issn = {2730-6151}, support = {ANR-14-CE02-0004-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-14-CE02-0004-01//Agence Nationale de la Recherche (French National Research Agency)/ ; ANR-14-CE02-0004-01//Agence Nationale de la Recherche (French National Research Agency)/ ; }, abstract = {In environmental metagenomic experiments, a very high proportion of the microbial sequencing data (> 70%) remains largely unexploited because rare and closely related genomes are missed in short-read assemblies. The identity and the potential metabolisms of a large fraction of natural microbial communities thus remain inaccessible to researchers. The purpose of this study was to explore the genomic content of unassembled metagenomic data and test their level of novelty. We used data from a three-year microbial metagenomic time series of the NW Mediterranean Sea, and conducted reference-free and database-guided analysis. The results revealed a significant genomic difference between the assembled and unassembled reads. The unassembled reads had a lower mean identity against public databases, and fewer metabolic pathways could be reconstructed. In addition, the unassembled fraction presented a clear temporal pattern, unlike the assembled ones, and a specific community composition that was similar to the rare communities defined by metabarcoding using the 16S rRNA gene. The rare gene pool was characterised by keystone bacterial taxa, and the presence of viruses, suggesting that viral lysis could maintain some taxa in a state of rarity. Our study demonstrates that unassembled metagenomic data can provide important information on the structure and functioning of microbial communities.}, } @article {pmid37938755, year = {2022}, author = {Khanongnuch, R and Mangayil, R and Svenning, MM and Rissanen, AJ}, title = {Characterization and genome analysis of a psychrophilic methanotroph representing a ubiquitous Methylobacter spp. cluster in boreal lake ecosystems.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {85}, pmid = {37938755}, issn = {2730-6151}, support = {201803224//Koneen Säätiö (Kone Foundation)/ ; 201803224//Koneen Säätiö (Kone Foundation)/ ; 323214//Academy of Finland (Suomen Akatemia)/ ; }, abstract = {Lakes and ponds are considered as a major natural source of CH4 emissions, particularly during the ice-free period in boreal ecosystems. Aerobic methane-oxidizing bacteria (MOB), which utilize CH4 using oxygen as an electron acceptor, are one of the dominant microorganisms in the CH4-rich water columns. Metagenome-assembled genomes (MAGs) have revealed the genetic potential of MOB from boreal aquatic ecosystems for various microaerobic/anaerobic metabolic functions. However, experimental proof of these functions, i.e., organic acid production via fermentation, by lake MOB is lacking. In addition, psychrophilic (i.e., cold-loving) MOB and their CH4-oxidizing process have rarely been investigated. In this study, we isolated, provided a taxonomic description, and analyzed the genome of Methylobacter sp. S3L5C, a psychrophilic MOB, from a boreal lake in Finland. Based on phylogenomic comparisons to MAGs, Methylobacter sp. S3L5C represented a ubiquitous cluster of Methylobacter spp. in boreal aquatic ecosystems. At optimal temperatures (3-12 °C) and pH (6.8-8.3), the specific growth rates (µ) and CH4 utilization rate were in the range of 0.018-0.022 h[-1] and 0.66-1.52 mmol l[-1] d[-1], respectively. In batch cultivation, the isolate could produce organic acids, and the concentrations were elevated after replenishing CH4 and air into the headspace. Up to 4.1 mM acetate, 0.02 mM malate, and 0.07 mM propionate were observed at the end of the test under optimal operational conditions. The results herein highlight the key role of Methylobacter spp. in regulating CH4 emissions and their potential to provide CH4-derived organic carbon compounds to surrounding heterotrophic microorganisms in cold ecosystems.}, } @article {pmid37938746, year = {2022}, author = {Palladino, G and Caroselli, E and Tavella, T and D'Amico, F and Prada, F and Mancuso, A and Franzellitti, S and Rampelli, S and Candela, M and Goffredo, S and Biagi, E}, title = {Correction to: Metagenomic shifts in mucus, tissue and skeleton of the coral Balanophyllia europaea living along a natural CO2 gradient.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {79}, doi = {10.1038/s43705-022-00165-w}, pmid = {37938746}, issn = {2730-6151}, } @article {pmid38077626, year = {2022}, author = {Madhogaria, B and Bhowmik, P and Kundu, A}, title = {Correlation between human gut microbiome and diseases.}, journal = {Infectious medicine}, volume = {1}, number = {3}, pages = {180-191}, pmid = {38077626}, issn = {2772-431X}, abstract = {Human gut microbiome is a major source of human bacterial population and a significant contribution to both positive and harmful effects. Due to its involvement in a variety of interactions, gut microorganisms have a great impact on our health throughout our lives. The impact of gut microbial population is been studied intensively in last two decades. Extensive literature survey focusing developments in the field were searched in English language Electronic Databases like PubMed, Google Scholar, Pubag, Google books, and Research Gate were mostly used to understand the role of human gut mirobiome and its role in different human diseases. Gut microbiome in healthy subjects differs from those who suffer from diseases. Type 2 diabetes, obesity, non-alcoholic liver disease, and cardiometabolic diseases have all been linked to dysbiosis of the gut microbiota. Pathogenesis of many disorders is also linked to changes in gut microbiota. Other diseases like cancer, arithritis, autism, depression, anxiety, sleep disorder, HIV, hypertension, and gout are also related to gut microbiota dysbiosis. We focus in this review on recent studies looking into the link between gut microbiome dysbiosis and disease etiology. Research on how gut microbiota affects host metabolism has been changed in past decades from descriptive analyses to high throughput integrative omics data analysis such as metagenomics and metabolomics. Identification of molecular mechanisms behind reported associations is been carried out in human, animals, and cells for measure of host physiology and mechanics. Still many the mechanisms are not completely understood.}, } @article {pmid37938724, year = {2022}, author = {Blakeley-Ruiz, JA and McClintock, CS and Shrestha, HK and Poudel, S and Yang, ZK and Giannone, RJ and Choo, JJ and Podar, M and Baghdoyan, HA and Lydic, R and Hettich, RL}, title = {Morphine and high-fat diet differentially alter the gut microbiota composition and metabolic function in lean versus obese mice.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {66}, pmid = {37938724}, issn = {2730-6151}, abstract = {There are known associations between opioids, obesity, and the gut microbiome, but the molecular connection/mediation of these relationships is not understood. To better clarify the interplay of physiological, genetic, and microbial factors, this study investigated the microbiome and host inflammatory responses to chronic opioid administration in genetically obese, diet-induced obese, and lean mice. Samples of feces, urine, colon tissue, and plasma were analyzed using targeted LC-MS/MS quantification of metabolites, immunoassays of inflammatory cytokine levels, genome-resolved metagenomics, and metaproteomics. Genetic obesity, diet-induced obesity, and morphine treatment in lean mice each showed increases in distinct inflammatory cytokines. Metagenomic assembly and binning uncovered over 400 novel gut bacterial genomes and species. Morphine administration impacted the microbiome's composition and function, with the strongest effect observed in lean mice. This microbiome effect was less pronounced than either diet or genetically driven obesity. Based on inferred microbial physiology from the metaproteome datasets, a high-fat diet transitioned constituent microbes away from harvesting diet-derived nutrients and towards nutrients present in the host mucosal layer. Considered together, these results identified novel host-dependent phenotypes, differentiated the effects of genetic obesity versus diet induced obesity on gut microbiome composition and function, and showed that chronic morphine administration altered the gut microbiome.}, } @article {pmid37938729, year = {2022}, author = {Wang, L and Wang, Y and Huang, X and Ma, R and Li, J and Wang, F and Jiao, N and Zhang, R}, title = {Potential metabolic and genetic interaction among viruses, methanogen and methanotrophic archaea, and their syntrophic partners.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {50}, pmid = {37938729}, issn = {2730-6151}, support = {91951209//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42006097//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2020M671942//China Postdoctoral Science Foundation/ ; }, abstract = {The metabolism of methane in anoxic ecosystems is mainly mediated by methanogens and methane-oxidizing archaea (MMA), key players in global carbon cycling. Viruses are vital in regulating their host fate and ecological function. However, our knowledge about the distribution and diversity of MMA viruses and their interactions with hosts is rather limited. Here, by searching metagenomes containing mcrA (the gene coding for the α-subunit of methyl-coenzyme M reductase) from a wide variety of environments, 140 viral operational taxonomic units (vOTUs) that potentially infect methanogens or methane-oxidizing archaea were retrieved. Four MMA vOTUs (three infecting the order Methanobacteriales and one infecting the order Methanococcales) were predicted to cross-domain infect sulfate-reducing bacteria. By facilitating assimilatory sulfur reduction, MMA viruses may increase the fitness of their hosts in sulfate-depleted anoxic ecosystems and benefit from synthesis of the sulfur-containing amino acid cysteine. Moreover, cell-cell aggregation promoted by MMA viruses may be beneficial for both the viruses and their hosts by improving infectivity and environmental stress resistance, respectively. Our results suggest a potential role of viruses in the ecological and environmental adaptation of methanogens and methane-oxidizing archaea.}, } @article {pmid38073879, year = {2022}, author = {Wang, Y and Zhang, A and Wei, X and Zhang, Z and Bi, X and Yuan, X and Geng, Y and He, N and Chen, M and Xu, X and Xia, H and Wen, H and Xu, Y}, title = {Metagenomic next-generation sequencing identified psittacosis among poultry processing workers in Shandong Province, China.}, journal = {Infectious medicine}, volume = {1}, number = {2}, pages = {135-139}, pmid = {38073879}, issn = {2772-431X}, abstract = {Human infection with Chlamydia psittaci is rare but difficult to recognize. We report an outbreak of psittacosis among poultry processing workers in China. We applied metagenomic next-generation sequencing and identified Chlamydia psittaci reads from samples of all seven patients, four of which were subsequently confirmed by PCR. Epidemiological results suggested that the poultry processed in the factory was the possible source of human infection.}, } @article {pmid38046362, year = {2022}, author = {Nakajima, A and Yoshida, K and Gotoh, A and Katoh, T and Ojima, MN and Sakanaka, M and Xiao, JZ and Odamaki, T and Katayama, T}, title = {A simple method that enhances minority species detection in the microbiota: 16S metagenome-DRIP (Deeper Resolution using an Inhibitory Primer).}, journal = {Microbiome research reports}, volume = {1}, number = {3}, pages = {20}, pmid = {38046362}, issn = {2771-5965}, abstract = {Aim: 16S rRNA gene-based microbiota analyses (16S metagenomes) using next-generation sequencing (NGS) technologies are widely used to examine the microbial community composition in environmental samples. However, the sequencing capacity of NGS is sometimes insufficient to cover the whole microbial community, especially when analyzing soil and fecal microbiotas. This limitation may have hampered the detection of minority species that potentially affect microbiota formation and structure. Methods: We developed a simple method, termed 16S metagenome-DRIP (Deeper Resolution using an Inhibitory Primer), that not only enhances minority species detection but also increases the accuracy of their abundance estimation. The method relies on the inhibition of normal amplicon formation of the 16S rRNA gene of a target major (abundant) species during the first PCR step. The addition of a biotinylated primer that is complementary to the variable sequence of the V3-V4 region of the target species inhibits a normal amplification process to form an aberrant short amplicon. The fragment is then captured by streptavidin beads for removal from the reaction mixture, and the resulting mixture is utilized for the second PCR with barcode-tag primers. Thus, this method only requires two additional experimental procedures to the conventional 16S metagenome analysis. A proof-of-concept experiment was first conducted using a mock sample consisting of the genomes of 14 bacterial species. Then, the method was applied to infant fecal samples using a Bifidobacterium-specific inhibitory primer (n = 11). Results: As a result, the reads assigned to the family Bifidobacteriaceae decreased on average from 16,657 to 1718 per sample without affecting the total read counts (36,073 and 34,778 per sample for the conventional and DRIP methods, respectively). Furthermore, the minority species detection rate increased with neither affecting Bray-Curtis dissimilarity calculated by omitting the target Bifidobacterium species (median: 0.049) nor changing the relative abundances of the non-target species. While 115 amplicon sequence variants (ASVs) were unique to the conventional method, 208 ASVs were uniquely detected for the DRIP method. Moreover, the abundance estimation for minority species became more accurate, as revealed thorough comparison with the results of quantitative PCR analysis. Conclusion: The 16S metagenome-DRIP method serves as a useful technique to grasp a deeper and more accurate microbiota composition when combined with conventional 16S metagenome analysis methods.}, } @article {pmid37938728, year = {2022}, author = {Halter, T and Köstlbacher, S and Collingro, A and Sixt, BS and Tönshoff, ER and Hendrickx, F and Kostanjšek, R and Horn, M}, title = {Ecology and evolution of chlamydial symbionts of arthropods.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {45}, pmid = {37938728}, issn = {2730-6151}, support = {DOC 69-B//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; P32112//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; uni:docs//Universität Wien (University of Vienna)/ ; }, abstract = {The phylum Chlamydiae consists of obligate intracellular bacteria including major human pathogens and diverse environmental representatives. Here we investigated the Rhabdochlamydiaceae, which is predicted to be the largest and most diverse chlamydial family, with the few described members known to infect arthropod hosts. Using published 16 S rRNA gene sequence data we identified at least 388 genus-level lineages containing about 14 051 putative species within this family. We show that rhabdochlamydiae are mainly found in freshwater and soil environments, suggesting the existence of diverse, yet unknown hosts. Next, we used a comprehensive genome dataset including metagenome assembled genomes classified as members of the family Rhabdochlamydiaceae, and we added novel complete genome sequences of Rhabdochlamydia porcellionis infecting the woodlouse Porcellio scaber, and of 'Candidatus R. oedothoracis' associated with the linyphiid dwarf spider Oedothorax gibbosus. Comparative analysis of basic genome features and gene content with reference genomes of well-studied chlamydial families with known host ranges, namely Parachlamydiaceae (protist hosts) and Chlamydiaceae (human and other vertebrate hosts) suggested distinct niches for members of the Rhabdochlamydiaceae. We propose that members of the family represent intermediate stages of adaptation of chlamydiae from protists to vertebrate hosts. Within the genus Rhabdochlamydia, pronounced genome size reduction could be observed (1.49-1.93 Mb). The abundance and genomic distribution of transposases suggests transposable element expansion and subsequent gene inactivation as a mechanism of genome streamlining during adaptation to new hosts. This type of genome reduction has never been described before for any member of the phylum Chlamydiae. This study provides new insights into the molecular ecology, genomic diversity, and evolution of representatives of one of the most divergent chlamydial families.}, } @article {pmid37938726, year = {2022}, author = {Skoog, EJ and Moore, KR and Gong, J and Ciccarese, D and Momper, L and Cutts, EM and Bosak, T}, title = {Metagenomic, (bio)chemical, and microscopic analyses reveal the potential for the cycling of sulfated EPS in Shark Bay pustular mats.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {43}, pmid = {37938726}, issn = {2730-6151}, support = {327126//Simons Foundation/ ; 344707//Simons Foundation/ ; 327126//Simons Foundation/ ; 344707//Simons Foundation/ ; 327126//Simons Foundation/ ; 344707//Simons Foundation/ ; }, abstract = {Cyanobacteria and extracellular polymeric substances (EPS) in peritidal pustular microbial mats have a two-billion-year-old fossil record. To understand the composition, production, degradation, and potential role of EPS in modern analogous communities, we sampled pustular mats from Shark Bay, Australia and analyzed their EPS matrix. Biochemical and microscopic analyses identified sulfated organic compounds as major components of mat EPS. Sulfur was more abundant in the unmineralized regions with cyanobacteria and less prevalent in areas that contained fewer cyanobacteria and more carbonate precipitates. Sequencing and assembly of the pustular mat sample resulted in 83 high-quality metagenome-assembled genomes (MAGs). Metagenomic analyses confirmed cyanobacteria as the primary sources of these sulfated polysaccharides. Genes encoding for sulfatases, glycosyl hydrolases, and other enzymes with predicted roles in the degradation of sulfated polysaccharides were detected in the MAGs of numerous clades including Bacteroidetes, Chloroflexi, Hydrogenedentes, Myxococcota, Verrucomicrobia, and Planctomycetes. Measurable sulfatase activity in pustular mats and fresh cyanobacterial EPS confirmed the role of sulfatases in the degradation of sulfated EPS. These findings suggest that the synthesis, modification, and degradation of sulfated polysaccharides influence microbial interactions, carbon cycling, and biomineralization processes within peritidal pustular microbial mats.}, } @article {pmid38046358, year = {2022}, author = {Altermann, E and Tegetmeyer, HE and Chanyi, RM}, title = {The evolution of bacterial genome assemblies - where do we need to go next?.}, journal = {Microbiome research reports}, volume = {1}, number = {3}, pages = {15}, pmid = {38046358}, issn = {2771-5965}, abstract = {Genome sequencing has fundamentally changed our ability to decipher and understand the genetic blueprint of life and how it changes over time in response to environmental and evolutionary pressures. The pace of sequencing is still increasing in response to advances in technologies, paving the way from sequenced genes to genomes to metagenomes to metagenome-assembled genomes (MAGs). Our ability to interrogate increasingly complex microbial communities through metagenomes and MAGs is opening up a tantalizing future where we may be able to delve deeper into the mechanisms and genetic responses emerging over time. In the near future, we will be able to detect MAG assembly variations within strains originating from diverging sub-populations, and one of the emerging challenges will be to capture these variations in a biologically relevant way. Here, we present a brief overview of sequencing technologies and the current state of metagenome assemblies to suggest the need to develop new data formats that can capture the genetic variations within strains and communities, which previously remained invisible due to sequencing technology limitations.}, } @article {pmid38045646, year = {2022}, author = {Lugli, GA and Ventura, M}, title = {A breath of fresh air in microbiome science: shallow shotgun metagenomics for a reliable disentangling of microbial ecosystems.}, journal = {Microbiome research reports}, volume = {1}, number = {2}, pages = {8}, pmid = {38045646}, issn = {2771-5965}, abstract = {Next-generation sequencing technologies allow accomplishing massive DNA sequencing, uncovering the microbial composition of many different ecological niches. However, the various strategies developed to profile microbiomes make it challenging to retrieve a reliable classification that is able to compare metagenomic data of different studies. Many limitations have been overcome thanks to shotgun sequencing, allowing a reliable taxonomic classification of microbial communities at the species level. Since numerous bioinformatic tools and databases have been implemented, the sequencing methodology is only the first of many choices to make for classifying metagenomic data. Here, we discuss the importance of choosing a reliable methodology to achieve consistent information in uncovering microbiomes.}, } @article {pmid38089066, year = {2022}, author = {White, K and Yu, JH and Eraclio, G and Dal Bello, F and Nauta, A and Mahony, J and van Sinderen, D}, title = {Bacteriophage-host interactions as a platform to establish the role of phages in modulating the microbial composition of fermented foods.}, journal = {Microbiome research reports}, volume = {1}, number = {1}, pages = {3}, pmid = {38089066}, issn = {2771-5965}, abstract = {Food fermentation relies on the activity of robust starter cultures, which are commonly comprised of lactic acid bacteria such as Lactococcus and Streptococcus thermophilus. While bacteriophage infection represents a persistent threat that may cause slowed or failed fermentations, their beneficial role in fermentations is also being appreciated. In order to develop robust starter cultures, it is important to understand how phages interact with and modulate the compositional landscape of these complex microbial communities. Both culture-dependent and -independent methods have been instrumental in defining individual phage-host interactions of many lactic acid bacteria (LAB). This knowledge needs to be integrated and expanded to obtain a full understanding of the overall complexity of such interactions pertinent to fermented foods through a combination of culturomics, metagenomics, and phageomics. With such knowledge, it is believed that factory-specific detection and monitoring systems may be developed to ensure robust and reliable fermentation practices. In this review, we explore/discuss phage-host interactions of LAB, the role of both virulent and temperate phages on the microbial composition, and the current knowledge of phageomes of fermented foods.}, } @article {pmid37938717, year = {2022}, author = {Lazarevic, V and Gaïa, N and Girard, M and Mauffrey, F and Ruppé, E and Schrenzel, J}, title = {Effect of bacterial DNA enrichment on detection and quantification of bacteria in an infected tissue model by metagenomic next-generation sequencing.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {122}, pmid = {37938717}, issn = {2730-6151}, abstract = {Before implementing metagenomic next-generation sequencing (mNGS) in the routine diagnostic laboratory, several challenges need to be resolved. To address strengths and limitations of mNGS in bacterial detection and quantification in samples with overwhelming host DNA abundance, we used the pig muscle tissue spiked with a home-made bacterial mock community, consisting of four species from different phyla. From the spiked tissue, we extracted DNA using: (i) a procedure based on mechanical/chemical lysis (no bacterial DNA enrichment); (ii) the Ultra-Deep Microbiome Prep (Molzym) kit for bacterial DNA enrichment; and (iii) the same enrichment kit but replacing the original proteinase K treatment for tissue solubilization by a collagenases/thermolysin digestion and cell filtration. Following mNGS, we determined bacterial: 'host' read ratios and taxonomic abundance profiles. We calculated the load of each mock-community member by combining its read counts with read counts and microscopically-determined cell counts of other co-spiked bacteria. In unenriched samples, bacterial quantification and taxonomic profiling were fairly accurate but at the expense of the sensitivity of detection. The removal of 'host' DNA by the modified enrichment protocol substantially improved bacterial detection in comparison to the other two extraction procedures and generated less distorted taxonomic profiles as compared to the original enrichment protocol.}, } @article {pmid37938339, year = {2022}, author = {Mise, K and Iwasaki, W}, title = {Unexpected absence of ribosomal protein genes from metagenome-assembled genomes.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {118}, pmid = {37938339}, issn = {2730-6151}, support = {19H05688//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22H04925//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22H04894//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 19J14142//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 22K18029//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; JPMJCR19S2//MEXT | JST | Core Research for Evolutional Science and Technology (CREST)/ ; }, abstract = {Metagenome-assembled genomes (MAGs) have revealed the hidden diversity and functions of uncultivated microbes, but their reconstruction from metagenomes remains a computationally difficult task. Repetitive or exogenous sequences, such as ribosomal RNA and horizontally transferred genes, are frequently absent from MAGs because of misassembly and binning errors. Here, we report that ribosomal protein genes are also often absent from MAGs, although they are neither repetitive nor exogenous. Comprehensive analyses of more than 190,000 MAGs revealed that these genes could be missing in more than 20-40% of near-complete (i.e., with completeness of 90% or higher) MAGs. While some uncultivated environmental microbes intrinsically lack some ribosomal protein genes, we found that this unexpected absence is largely due to special evolutionary patterns of codon usage bias in ribosomal protein genes and algorithmic characteristics of metagenomic binning, which is dependent on tetranucleotide frequencies of contigs. This problem reflects the microbial life-history strategy. Fast-growing microbes tend to have this difficulty, likely because of strong evolutionary pressures on ribosomal protein genes toward the efficient assembly of ribosomes. Our observations caution those who study genomics and phylogeny of uncultivated microbes, the diversity and evolution of microbial genes in the central dogma, and bioinformatics in metagenomics.}, } @article {pmid37938241, year = {2023}, author = {Rojas, CA and Marks, SL and Borras, E and Lesea, H and McCartney, MM and Coil, DA and Davis, CE and Eisen, JA}, title = {Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {19382}, pmid = {37938241}, issn = {2045-2322}, support = {U01 TR004083/TR/NCATS NIH HHS/United States ; P30 ES023513/ES/NIEHS NIH HHS/United States ; UL1 TR001860/TR/NCATS NIH HHS/United States ; U18 TR003795/TR/NCATS NIH HHS/United States ; UG3 OD023365/OD/NIH HHS/United States ; }, mesh = {Cats ; Animals ; *Anal Canal ; Metabolomics ; *Microbiota/genetics ; Metagenome ; Metabolome ; Mammals ; }, abstract = {Many mammals rely on volatile organic chemical compounds (VOCs) produced by bacteria for their communication and behavior, though little is known about the exact molecular mechanisms or bacterial species that are responsible. We used metagenomic sequencing, mass-spectrometry based metabolomics, and culturing to profile the microbial and volatile chemical constituents of anal gland secretions in twenty-three domestic cats (Felis catus), in attempts to identify organisms potentially involved in host odor production. We found that the anal gland microbiome was dominated by bacteria in the genera Corynebacterium, Bacteroides, Proteus, Lactobacillus, and Streptococcus, and showed striking variation among individual cats. Microbiome profiles also varied with host age and obesity. Metabolites such as fatty-acids, ketones, aldehydes and alcohols were detected in glandular secretions. Overall, microbiome and metabolome profiles were modestly correlated (r = 0.17), indicating that a relationship exists between the bacteria in the gland and the metabolites produced in the gland. Functional analyses revealed the presence of genes predicted to code for enzymes involved in VOC metabolism such as dehydrogenases, reductases, and decarboxylases. From metagenomic data, we generated 85 high-quality metagenome assembled genomes (MAGs). Of importance were four MAGs classified as Corynebacterium frankenforstense, Proteus mirabilis, Lactobacillus johnsonii, and Bacteroides fragilis. They represent strong candidates for further investigation of the mechanisms of volatile synthesis and scent production in the mammalian anal gland.}, } @article {pmid37938235, year = {2023}, author = {Chen, Z and Lou, M and Fang, P and Xiao, D and Zhu, W and Chen, H and Qian, W}, title = {Impact of different sulfur sources on the structure and function of sulfur autotrophic denitrification bacteria.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {19404}, pmid = {37938235}, issn = {2045-2322}, mesh = {*Denitrification ; Nitrates ; Sulfur ; Bacteria/genetics ; *Thiobacillus/genetics ; }, abstract = {Nitrate pollution in surface water has become a significant environmental concern. Sulfur autotrophic denitrification (SAD) technology is gaining attention for its cost-effectiveness and efficiency in nitrate removal. This study aimed to investigate the structure and function of sulfur autotrophic denitrification microbial communities in systems using sodium thiosulfate (Group A) and elemental sulfur (Group B) as the sole electron donors. Metagenomic amplicon sequencing and physicochemical analysis were performed to examine the microbial communities. The results revealed that on day 13, the nitrate nitrogen removal rate in Group A was significantly higher (89.2%) compared to Group B (74.4%). The dominant genus in both Groups was Thiobacillus, with average abundances of 34.15% and 16.34% in Groups A and B, respectively. β-diversity analysis based on species level showed significant differences in bacterial community structure between the two Groups (P < 0.001). Group A exhibited a greater potential for nitrate reduction and utilized both thiosulfate and elemental sulfur (P < 0.01) compared to Group B. This study provides a sufficient experimental basis for improving the start-up time and operating cost of SAD system through sulfur source switching and offers new prospects for in-depth mechanistic analysis.}, } @article {pmid37938162, year = {2024}, author = {Charalampous, T and Alcolea-Medina, A and Snell, LB and Alder, C and Tan, M and Williams, TGS and Al-Yaakoubi, N and Humayun, G and Meadows, CIS and Wyncoll, DLA and Paul, R and Hemsley, CJ and Jeyaratnam, D and Newsholme, W and Goldenberg, S and Patel, A and Tucker, F and Nebbia, G and Wilks, M and Chand, M and Cliff, PR and Batra, R and O'Grady, J and Barrett, NA and Edgeworth, JD}, title = {Routine Metagenomics Service for ICU Patients with Respiratory Infection.}, journal = {American journal of respiratory and critical care medicine}, volume = {209}, number = {2}, pages = {164-174}, doi = {10.1164/rccm.202305-0901OC}, pmid = {37938162}, issn = {1535-4970}, support = {MC_PC_19041/MRC_/Medical Research Council/United Kingdom ; MR/T005416/1/MRC_/Medical Research Council/United Kingdom ; MR/W025140/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; Pilot Projects ; London ; *Anti-Infective Agents ; Intensive Care Units ; *Respiratory Tract Infections/diagnosis/drug therapy ; }, abstract = {Rationale: Respiratory metagenomics (RMg) needs evaluation in a pilot service setting to determine utility and inform implementation into routine clinical practice. Objectives: Feasibility, performance, and clinical impacts on antimicrobial prescribing and infection control were recorded during a pilot RMg service. Methods: RMg was performed on 128 samples from 87 patients with suspected lower respiratory tract infection (LRTI) on two general and one specialist respiratory ICUs at Guy's and St Thomas' NHS Foundation Trust, London. Measurements and Main Results: During the first 15 weeks, RMg provided same-day results for 110 samples (86%), with a median turnaround time of 6.7 hours (interquartile range = 6.1-7.5 h). RMg was 93% sensitive and 81% specific for clinically relevant pathogens compared with routine testing. Forty-eight percent of RMg results informed antimicrobial prescribing changes (22% escalation; 26% deescalation) with escalation based on speciation in 20 out of 24 cases and detection of acquired-resistance genes in 4 out of 24 cases. Fastidious or unexpected organisms were reported in 21 samples, including anaerobes (n = 12), Mycobacterium tuberculosis, Tropheryma whipplei, cytomegalovirus, and Legionella pneumophila ST1326, which was subsequently isolated from the bedside water outlet. Application to consecutive severe community-acquired LRTI cases identified Staphylococcus aureus (two with SCCmec and three with luk F/S virulence determinants), Streptococcus pyogenes (emm1-M1uk clone), S. dysgalactiae subspecies equisimilis (STG62647A), and Aspergillus fumigatus with multiple treatments and public health impacts. Conclusions: This pilot study illustrates the potential of RMg testing to provide benefits for antimicrobial treatment, infection control, and public health when provided in a real-world critical care setting. Multicenter studies are now required to inform future translation into routine service.}, } @article {pmid37937972, year = {2023}, author = {Tian, Y and Gao, R and Wang, Y and Zhou, Y and Xu, S and Duan, Y and Lv, W and Wang, S and Hou, M and Chen, Y and Li, F and Gao, W and Zhang, L and Zhou, J-X}, title = {Economic impact of metagenomic next-generation sequencing versus traditional bacterial culture for postoperative central nervous system infections using a decision analysis mode: study protocol for a randomized controlled trial.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0058123}, pmid = {37937972}, issn = {2379-5077}, mesh = {Humans ; High-Throughput Nucleotide Sequencing ; *Central Nervous System Infections ; *Central Nervous System Bacterial Infections ; Economics, Medical ; Decision Support Techniques ; Randomized Controlled Trials as Topic ; }, abstract = {Diagnosing and treating postoperative central nervous system infections (PCNSIs) remains challenging due to the low detection rate and time-consuming nature of traditional methods for identifying microorganisms in cerebrospinal fluid. Metagenomic next-generation sequencing (mNGS) technology provides a rapid and comprehensive understanding of microbial composition in PCNSIs by swiftly sequencing and analyzing the microbial genome. The current study aimed to assess the economic impact of using mNGS versus traditional bacterial culture-directed PCNSIs diagnosis and therapy in post-neurosurgical patients from Beijing Tiantan Hospital. mNGS is a relatively expensive test item, and whether it has the corresponding health-economic significance in the clinical application of diagnosing intracranial infection has not been studied clearly. Therefore, the investigators hope to explore the clinical application value of mNGS detection in PCNSIs after neurosurgery.}, } @article {pmid37937832, year = {2023}, author = {Hay, MC and Mitchell, AC and Soares, AR and Debbonaire, AR and Mogrovejo, DC and Els, N and Edwards, A}, title = {Metagenome-assembled genomes from High Arctic glaciers highlight the vulnerability of glacier-associated microbiota and their activities to habitat loss.}, journal = {Microbial genomics}, volume = {9}, number = {11}, pages = {}, pmid = {37937832}, issn = {2057-5858}, mesh = {Humans ; *Ice Cover/chemistry/microbiology ; Metagenome ; *Microbiota/genetics ; Biodiversity ; Sulfur ; }, abstract = {The rapid warming of the Arctic is threatening the demise of its glaciers and their associated ecosystems. Therefore, there is an urgent need to explore and understand the diversity of genomes resident within glacial ecosystems endangered by human-induced climate change. In this study we use genome-resolved metagenomics to explore the taxonomic and functional diversity of different habitats within glacier-occupied catchments. Comparing different habitats within such catchments offers a natural experiment for understanding the effects of changing habitat extent or even loss upon Arctic microbiota. Through binning and annotation of metagenome-assembled genomes (MAGs) we describe the spatial differences in taxon distribution and their implications for glacier-associated biogeochemical cycling. Multiple taxa associated with carbon cycling included organisms with the potential for carbon monoxide oxidation. Meanwhile, nitrogen fixation was mediated by a single taxon, although diverse taxa contribute to other nitrogen conversions. Genes for sulphur oxidation were prevalent within MAGs implying the potential capacity for sulphur cycling. Finally, we focused on cyanobacterial MAGs, and those within cryoconite, a biodiverse microbe-mineral granular aggregate responsible for darkening glacier surfaces. Although the metagenome-assembled genome of Phormidesmis priestleyi, the cyanobacterium responsible for forming Arctic cryoconite was represented with high coverage, evidence for the biosynthesis of multiple vitamins and co-factors was absent from its MAG. Our results indicate the potential for cross-feeding to sustain P. priestleyi within granular cryoconite. Taken together, genome-resolved metagenomics reveals the vulnerability of glacier-associated microbiota to the deletion of glacial habitats through the rapid warming of the Arctic.}, } @article {pmid37937647, year = {2023}, author = {Ermakov, VS and Granados, JC and Nigam, SK}, title = {Remote effects of kidney drug transporter OAT1 on gut microbiome composition and urate homeostasis.}, journal = {JCI insight}, volume = {8}, number = {21}, pages = {}, pmid = {37937647}, issn = {2379-3708}, support = {R01 DK109392/DK/NIDDK NIH HHS/United States ; R01 GM132938/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Homeostasis ; Kidney/metabolism ; Membrane Transport Proteins ; *Renal Insufficiency, Chronic/metabolism ; Tryptophan/metabolism ; Uric Acid/metabolism ; }, abstract = {The organic anion transporter OAT1 (SLC22A6, originally identified as NKT) is a multispecific transporter responsible for the elimination by the kidney of small organic anions that derive from the gut microbiome. Many are uremic toxins associated with chronic kidney disease (CKD). OAT1 is among a group of "drug" transporters that act as hubs in a large homeostatic network regulating interorgan and interorganismal communication via small molecules. The Remote Sensing and Signaling Theory predicts that genetic deletion of such a key hub in the network results in compensatory interorganismal communication (e.g., host-gut microbe dynamics). Recent metabolomics data from Oat1-KO mice indicate that some of the most highly affected metabolites derive from bacterial tyrosine, tryptophan, purine, and fatty acid metabolism. Functional metagenomic analysis of fecal 16S amplicon and whole-genome sequencing revealed that loss of OAT1 was impressively associated with microbial pathways regulating production of urate, gut-derived p-cresol, tryptophan derivatives, and fatty acids. Certain changes, such as alterations in gut microbiome urate metabolism, appear compensatory. Thus, Oat1 in the kidney appears to mediate remote interorganismal communication by regulating the gut microbiome composition and metabolic capability. Since OAT1 function in the proximal tubule is substantially affected in CKD, our results may shed light on the associated alterations in gut-microbiome dynamics.}, } @article {pmid37937256, year = {2023}, author = {Geli-Cruz, OJ and Santos-Flores, CJ and Cafaro, MJ and Ropelewski, A and Van Dam, AR}, title = {Benchmarking assembly free nanopore read mappers to classify complex millipede gut microbiota via Oxford Nanopore Sequencing Technology.}, journal = {Journal of biological methods}, volume = {10}, number = {}, pages = {e99010003}, pmid = {37937256}, issn = {2326-9901}, abstract = {Millipedes are key players in recycling leaf litter into soil in tropical ecosystems. To elucidate their gut microbiota, we collected millipedes from different municipalities of Puerto Rico. Here we aim to benchmark which method is best for metagenomic skimming of this highly complex millipede microbiome. We sequenced the gut DNA with Oxford Nanopore Technologies' (ONT) MinION sequencer, then analyzed the data using MEGAN-LR, Kraken2 protein mode, Kraken2 nucleotide mode, GraphMap, and Minimap2 to classify these long ONT reads. From our two samples, we obtained a total of 87,110 and 99,749 ONT reads, respectively. Kraken2 nucleotide mode classified the most reads compared to all other methods at the phylum and class taxonomic level, classifying 75% of the reads in the two samples, the other methods failed to assign enough reads to either phylum or class to yield asymptotes in the taxa rarefaction curves indicating that they required more sequencing depth to fully classify this community. The community is hyper diverse with all methods classifying 20-50 phyla in the two samples. There was significant overlap in the reads used and phyla classified between the five methods benchmarked. Our results suggest that Kraken2 nucleotide mode is the most appropriate tool for the application of metagenomic skimming of this highly complex community.}, } @article {pmid37937217, year = {2023}, author = {Suzuki, S and Pruden, A and Virta, M and Zhang, T}, title = {Editorial: Antibiotic resistance in aquatic systems, volume II.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1298681}, pmid = {37937217}, issn = {1664-302X}, } @article {pmid37936065, year = {2023}, author = {Li, Z and Cui, R and Wang, YB and Luo, YB and Xue, PX and Tang, QG and Fang, MY}, title = {Specific gastrointestinal microbiota profiles in Chinese Tan sheep are associated with lauric acid content in muscle.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {331}, pmid = {37936065}, issn = {1471-2180}, mesh = {Sheep ; Animals ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Bacteria ; Muscles ; Fatty Acids/metabolism ; Bacteroidetes ; Lauric Acids/metabolism ; }, abstract = {The biological mechanisms underlying meat quality remain unclear. Currently, many studies report that the gastrointestinal microbiota is essential for animal growth and performance. However, it is uncertain which bacterial species are specifically associated with the meat quality traits. In this study, 16S rDNA and metagenomic sequencing were performed to explore the composition and function of microbes in various gastrointestinal segments of Tan sheep and Dorper sheep, as well as the relationship between microbiota and meat quality (specifically, the fatty acid content of the muscle). In the ruminal, duodenal, and colonic microbiome, several bacteria were uniquely identified in respective breeds, including Agrobacterium tumefaciens, Bacteroidales bacterium CF, and several members of the family Oscillospiraceae. The annotation of GO, KEGG, and CAZYme revealed that these different bacterial species were linked to the metabolism of glucose, lipids, and amino acids. Additionally, our findings suggested that 16 microbial species may be essential to the content of fatty acids in the muscle, especially C12:0 (lauric acid). 4 bacterial species, including Achromobacter xylosoxidans, Mageeibacillus indolicus, and Mycobacterium dioxanotrophicus, were positively correlated with C12:0, while 13 bacteria, including Methanobrevibacter millerae, Bacteroidales bacterium CF, and Bacteroides coprosuis were negatively correlated with C12:0. In a word, this study provides a basic data for better understanding the interaction between ruminant gastrointestinal microorganisms and the meat quality traits of hosts.}, } @article {pmid37935462, year = {2023}, author = {Gaike, AH and Kalamkar, SD and Gajjar, V and Divate, U and Karandikar-Iyer, S and Goel, P and Shouche, YS and Ghaskadbi, SS}, title = {Effect of long-term oral glutathione supplementation on gut microbiome of type 2 diabetic individuals.}, journal = {FEMS microbiology letters}, volume = {370}, number = {}, pages = {}, doi = {10.1093/femsle/fnad116}, pmid = {37935462}, issn = {1574-6968}, support = {//UGC/ ; //CAS/ ; //DST/ ; //Savitribai Phule Pune University/ ; //National Centre for Cell Science/ ; //IISER Pune/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Glutathione ; *Diabetes Mellitus, Type 2/drug therapy ; Dietary Supplements ; }, abstract = {The aim of this study was to check the effect of long-term oral glutathione (GSH) supplementation on alteration in gut microbiome of Indian diabetic individuals. Early morning fresh stool sample of diabetic individuals recruited in a randomized clinical trial wherein they were given 500 mg GSH supplementation orally once a day for a period of 6 months was collected and gut microbiome was analysed using high throughput 16S rRNA metagenomic sequencing. Long-term GSH supplementation as reported in our earlier work showed significant increase in body stores of GSH and stabilized decreased glycated haemoglobin (HbA1c). Analysis of gut microbiome revealed that abundance of phylum Proteobacteria significantly decreased (P < 0.05) in individuals with GSH supplementation after 6 months compared to those without it. Beneficial dominant genera such as Megasphaera, Bacteroides, and Megamonas were found to be significantly enriched (P < 0.05), while pathogenic Escherichia/Shigella was found to be depleted (P < 0.05) after supplementation. Data clearly demonstrate that GSH supplementation along with antidiabetic treatment helps restore the gut microbiome by enriching beneficial bacteria of healthy gut and reducing significantly the load of pathogenic bacteria of diabetic gut.}, } @article {pmid37935197, year = {2023}, author = {Tomofuji, Y and Kishikawa, T and Sonehara, K and Maeda, Y and Ogawa, K and Kawabata, S and Oguro-Igashira, E and Okuno, T and Nii, T and Kinoshita, M and Takagaki, M and Yamamoto, K and Arase, N and Yagita-Sakamaki, M and Hosokawa, A and Motooka, D and Matsumoto, Y and Matsuoka, H and Yoshimura, M and Ohshima, S and Nakamura, S and Fujimoto, M and Inohara, H and Kishima, H and Mochizuki, H and Takeda, K and Kumanogoh, A and Okada, Y}, title = {Analysis of gut microbiome, host genetics, and plasma metabolites reveals gut microbiome-host interactions in the Japanese population.}, journal = {Cell reports}, volume = {42}, number = {11}, pages = {113324}, doi = {10.1016/j.celrep.2023.113324}, pmid = {37935197}, issn = {2211-1247}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Genome-Wide Association Study ; East Asian People ; Metabolome ; *Blood Group Antigens ; Repressor Proteins/genetics ; Homeodomain Proteins/genetics ; }, abstract = {Interaction between the gut microbiome and host plays a key role in human health. Here, we perform a metagenome shotgun-sequencing-based analysis of Japanese participants to reveal associations between the gut microbiome, host genetics, and plasma metabolome. A genome-wide association study (GWAS) for microbial species (n = 524) identifies associations between the PDE1C gene locus and Bacteroides intestinalis and between TGIF2 and TGIF2-RAB5IF gene loci and Bacteroides acidifiaciens. In a microbial gene ortholog GWAS, agaE and agaS, which are related to the metabolism of carbohydrates forming the blood group A antigen, are associated with blood group A in a manner depending on the secretor status determined by the East Asian-specific FUT2 variant. A microbiome-metabolome association analysis (n = 261) identifies associations between bile acids and microbial features such as bile acid metabolism gene orthologs including bai and 7β-hydroxysteroid dehydrogenase. Our publicly available data will be a useful resource for understanding gut microbiome-host interactions in an underrepresented population.}, } @article {pmid37934028, year = {2024}, author = {Lin, Q and Yao, Y and Li, X and Zhang, S and Guo, H and Ma, X and Chen, W and Ru, C and Wang, L and Wang, B and Ma, Q and Zhu, J and Lin, X and Chen, Q and Lou, H and Chen, Q and Chen, J and Zeng, Z and Zhou, J and Chen, Y and Yu, Y and Zhou, H}, title = {The application of nanopore targeted sequencing for pathogen diagnosis in bronchoalveolar lavage fluid of patients with pneumonia: a prospective multicenter study.}, journal = {Infectious diseases (London, England)}, volume = {56}, number = {2}, pages = {128-137}, doi = {10.1080/23744235.2023.2276785}, pmid = {37934028}, issn = {2374-4243}, mesh = {Humans ; Bronchoalveolar Lavage Fluid ; Prospective Studies ; *Nanopores ; *Pneumonia/diagnosis ; Streptococcus pneumoniae ; High-Throughput Nucleotide Sequencing ; Sensitivity and Specificity ; }, abstract = {OBJECTIVE: To evaluate the value of nanopore targeted sequencing in diagnosing pneumonia pathogens.

METHODS: This large-scale multicentre prospective study performed in 8 hospitals across China from April to October 2022. Hospitalised patients with a diagnosis of pneumonia at admission were included. Complete clinical data were collected, and bronchoalveolar lavage fluid were obtained from each patient. These samples underwent simultaneous testing using conventional microbial testing, metagenomic next-generation sequencing, and nanopore targeted sequencing.

RESULTS: A total of 218 patients were included. Among the 168 cases of pulmonary infection, 246 strains of pathogens were confirmed. Nanopore targeted sequencing outperformed conventional microbial testing, identifying more pathogens with a sensitivity increase of 47.9% (77.2% vs. 29.3%). Metagenomic next-generation sequencing had a sensitivity of 82.9%. Total of 70.1% patients had consistent results in both metagenomic next-generation sequencing and nanopore targeted sequencing. Nanopore targeted sequencing exhibited significantly higher sensitivity in detecting Pneumocystis jiroveci, cytomegalovirus, Mycobacterium tuberculosis, Nontuberculous mycobacteria, Streptococcus pneumoniae, and Mycoplasma pneumoniae compared to conventional microbial testing. However, metagenomic next-generation sequencing demonstrated higher sensitivity than nanopore targeted sequencing for Aspergillus (88.5% vs. 53.8%). Regarding the detection of co-infections, nanopore targeted sequencing displayed significantly higher sensitivity than conventional microbial testing (76.7% vs. 28.7%) and was on par with metagenomic next-generation sequencing (76.7% vs. 82.9%).

CONCLUSION: Nanopore targeted sequencing performs equally well as metagenomic next-generation sequencing in bronchoalveolar lavage fluid for pathogen diagnosis in pneumonia, both methods showing higher sensitivity than conventional microbial testing. Nanopore targeted sequencing can be considered a reliable method for diagnosing pathogens in pneumonia.}, } @article {pmid37934008, year = {2023}, author = {de Menezes Souza, J and de Menezes Fonseca, D and Pinheiro de Souza, J and Cordeiro do Nascimento, L and Mendes Hughes, F and Pereira Bezerra, JD and Góes-Neto, A and Ferreira-Silva, A}, title = {Cactus Endophytic Fungi and Bioprospecting for their Enzymes and Bioactive Molecules: A Systematic Review.}, journal = {Chemistry & biodiversity}, volume = {20}, number = {12}, pages = {e202301413}, doi = {10.1002/cbdv.202301413}, pmid = {37934008}, issn = {1612-1880}, support = {#88887.717880/2022-0//Research Support Foundation of the state of Paraíba (FAPESQ)/ ; //Coordination for the Training of Higher Education Personnel (Brazilian CAPES Foundation)/ ; 318103/2021-4//Brazilian Council for Scientific and Technological Development/ ; //Graduate Program in Biotechnology (UEFS)/ ; }, mesh = {Humans ; *Bioprospecting ; Fungi ; *Cactaceae ; Ecosystem ; Antifungal Agents ; Endophytes ; Plants ; }, abstract = {Endophytic fungi are associated with plant health and represent a remarkable source of potential of enzymes and bioactive compounds, but the diversity of endophytes remains uncertain and poorly explored, especially in Cactaceae, one of the most species-rich families adapted to growing in arid and semi-arid regions. The aim of this study was to conduct a systematic review on the diversity and bioprospecting of endophytic fungi from Cactaceae. We analysed peer-reviewed articles from seven databases using PRISMA guidelines. The results showed that the Cactaceae family is a source of new taxa, but the diversity of endophytic fungi of Cactaceae is little explored, mainly the diversity among tissues and by metagenomics. Bioprospecting studies have shown that these microorganisms can be used in the production of enzymes and larvicidal and antifungal compounds. Our results are relevant as a starting point for researchers to develop studies that expand the knowledge of plant mycobiota in arid and semi-arid ecosystems, as well as comprising a remarkable source of fungal compounds with several biotechnological applications.}, } @article {pmid37932283, year = {2023}, author = {Simpson, AC and Sengupta, P and Zhang, F and Hameed, A and Parker, CW and Singh, NK and Miliotis, G and Rekha, PD and Raman, K and Mason, CE and Venkateswaran, K}, title = {Phylogenomics, phenotypic, and functional traits of five novel (Earth-derived) bacterial species isolated from the International Space Station and their prevalence in metagenomes.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {19207}, pmid = {37932283}, issn = {2045-2322}, support = {R01 MH117406/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Prevalence ; Phenotype ; *Paenibacillus/genetics ; Fatty Acids/analysis ; DNA ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; }, abstract = {With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habitats, and how microbes survive, proliferate and spread in space conditions, is becoming more important. The microbial tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-stain-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the ISS. The analysis of their 16S rRNA gene sequences revealed > 99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing was undertaken. For all strains, the gyrB gene exhibited < 93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average nucleotide identity and digital DNA-DNA hybridization values, when compared to any known bacterial species, were < 94% and <50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters. Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10[T] (= NRRL B-65660[T] = DSM 115933[T]), Leifsonia virtsii F6_8S_P_1A[T] (= NRRL B-65661[T] = DSM 115931[T]), Leifsonia williamsii F6_8S_P_1B[T] (= NRRL B-65662[T] = DSM 115932[T]), Paenibacillus vandeheii F6_3S_P_1C[T] (= NRRL B-65663[T] = DSM 115940[T]), and Sporosarcina highlanderae F6_3S_P_2[T] (= NRRL B-65664[T] = DSM 115943[T]). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.}, } @article {pmid37932275, year = {2023}, author = {Good, BH and Rosenfeld, LB}, title = {Eco-evolutionary feedbacks in the human gut microbiome.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7146}, pmid = {37932275}, issn = {2041-1723}, support = {R35 GM146949/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Feedback ; *Microbiota ; Metagenome ; }, abstract = {Gut microbiota can evolve within their hosts on human-relevant timescales, but little is known about how these changes influence (or are influenced by) the composition of their local community. Here, by combining ecological and evolutionary analyses of a large cohort of human gut metagenomes, we show that the short-term evolution of the microbiota is linked with shifts in its ecological structure. These correlations are not simply explained by expansions of the evolving species, and often involve additional fluctuations in distantly related taxa. We show that similar feedbacks naturally emerge in simple resource competition models, even in the absence of cross-feeding or predation. These results suggest that the structure and function of host microbiota may be shaped by their local evolutionary history, which could have important implications for personalized medicine and microbiome engineering.}, } @article {pmid37932270, year = {2023}, author = {Ning, L and Zhou, YL and Sun, H and Zhang, Y and Shen, C and Wang, Z and Xuan, B and Zhao, Y and Ma, Y and Yan, Y and Tong, T and Huang, X and Hu, M and Zhu, X and Ding, J and Zhang, Y and Cui, Z and Fang, JY and Chen, H and Hong, J}, title = {Microbiome and metabolome features in inflammatory bowel disease via multi-omics integration analyses across cohorts.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {7135}, pmid = {37932270}, issn = {2041-1723}, mesh = {Humans ; Multiomics ; *Inflammatory Bowel Diseases/metabolism ; Metabolome ; *Microbiota ; Biomarkers/metabolism ; }, abstract = {The perturbations of the gut microbiota and metabolites are closely associated with the progression of inflammatory bowel disease (IBD). However, inconsistent findings across studies impede a comprehensive understanding of their roles in IBD and their potential as reliable diagnostic biomarkers. To address this challenge, here we comprehensively analyze 9 metagenomic and 4 metabolomics cohorts of IBD from different populations. Through cross-cohort integrative analysis (CCIA), we identify a consistent characteristic of commensal gut microbiota. Especially, three bacteria, namely Asaccharobacter celatus, Gemmiger formicilis, and Erysipelatoclostridium ramosum, which are rarely reported in IBD. Metagenomic functional analysis reveals that essential gene of Two-component system pathway, linked to fecal calprotectin, are implicated in IBD. Metabolomics analysis shows 36 identified metabolites with significant differences, while the roles of these metabolites in IBD are still unknown. To further elucidate the relationship between gut microbiota and metabolites, we construct multi-omics biological correlation (MOBC) maps, which highlights gut microbial biotransformation deficiencies and significant alterations in aminoacyl-tRNA synthetases. Finally, we identify multi-omics biomarkers for IBD diagnosis, validated across multiple global cohorts (AUROC values ranging from 0.92 to 0.98). Our results offer valuable insights and a significant resource for developing mechanistic hypotheses on host-microbiome interactions in IBD.}, } @article {pmid37932168, year = {2023}, author = {Dike, CR and Ollberding, NJ and Thompson, T and Kotha, N and Minar, P and Vitale, DS and Lin, TK and Nasr, A and Denson, LA and Haslam, DB and Abu-El-Haija, M}, title = {Acute pancreatitis is associated with gut dysbiosis in children.}, journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.dld.2023.10.011}, pmid = {37932168}, issn = {1878-3562}, abstract = {BACKGROUND: Pediatric acute pancreatitis (AP) is associated with significant morbidity. Therefore, improved understanding of children who will develop severe AP is critical. Adult studies have reported AP associated gut dysbiosis, but pediatric studies are lacking.

AIMS: Assess stool microbial taxonomic and functional profiles of children with first attack of AP compared to those of healthy controls (HC), and between mild and severe AP METHODS: Children under 21 years hospitalized at a tertiary center (n = 30) with first AP attack were recruited including HC (n = 34) from same region. Shotgun metagenomic sequencing was performed on extracted DNA.

RESULTS: Demographics were similar between AP and HC. Alpha diversity (-0.68 ± 0.13, p-value < 0.001), and beta-diversity (R[2]=0.13, p-value < 0.001) differed, in children with AP compared to HC. Species including R.gnavus, V.parvula, E.faecalis, C.innocuum were enriched in AP. MetaCyc pathways involved in amino acid metabolism and fatty acid beta-oxidation were enriched in AP. Beta-diversity (R[2]=0.06, p-value = 0.02) differed for severe AP compared to mild AP with enrichment in E.faecalis and C.citroniae.

CONCLUSIONS: Gut dysbiosis occurs in pediatric AP and is associated with AP severity. A multicenter study confirming these findings could pave way for interventional trials manipulating the gut microbiome to mitigate AP severity.}, } @article {pmid37931760, year = {2024}, author = {Xiang, Y and Jia, M and Xu, R and Xu, J and He, L and Peng, H and Sun, W and Wang, D and Xiong, W and Yang, Z}, title = {Carbamazepine facilitated horizontal transfer of antibiotic resistance genes by enhancing microbial communication and aggregation.}, journal = {Bioresource technology}, volume = {391}, number = {Pt A}, pages = {129983}, doi = {10.1016/j.biortech.2023.129983}, pmid = {37931760}, issn = {1873-2976}, mesh = {*Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Anaerobiosis ; Drug Resistance, Microbial/genetics ; Sewage ; Carbamazepine/pharmacology ; }, abstract = {Antimicrobial resistance is a global health security issue of widespread concern. Recent studies have unveiled the potential contribution of non-antibiotics to the emergence of antimicrobial resistance. This study investigated the effect of carbamazepine, a non-antibiotic pharmaceutical, on the fate of antibiotic resistance genes (ARGs) during anaerobic digestion. The results, as revealed by both metagenomic sequencing and absolute quantification, demonstrated that carbamazepine induced the enrichment of ARGs and increased the abundance of ARGs hosts by 1.2-2.1 times. Carbamazepine facilitated microbial aggregation and intercellular communication by upregulating functional genes associated with two-component systems, quorum sensing and type IV secretion systems, thereby increasing the frequency of ARGs conjugation. Furthermore, carbamazepine induced the acquisition of ARGs by pathogens and elevated the overall pathogenic abundance. This study revealed the mechanisms of microbial self-regulation and ARGs transmission under carbamazepine stress, highlighting the potential health risks posed by non-antibiotic pharmaceuticals during the safe disposal of sludge.}, } @article {pmid37931127, year = {2023}, author = {Brumfield, KD and Usmani, M and Santiago, S and Singh, K and Gangwar, M and Hasan, NA and Netherland, M and Deliz, K and Angelini, C and Beatty, NL and Huq, A and Jutla, AS and Colwell, RR}, title = {Genomic diversity of Vibrio spp. and metagenomic analysis of pathogens in Florida Gulf coastal waters following Hurricane Ian.}, journal = {mBio}, volume = {14}, number = {6}, pages = {e0147623}, pmid = {37931127}, issn = {2150-7511}, support = {R01 ES030317/ES/NIEHS NIH HHS/United States ; }, abstract = {Changing climatic conditions influence parameters associated with the growth of pathogenic Vibrio spp. in the environment and, hence, are linked to increased incidence of vibriosis. Between 1992 and 2022, a long-term increase in Vibrio spp. infections was reported in Florida, USA. Furthermore, a spike in Vibrio spp. infections was reported post Hurricane Ian, a category five storm that made landfall in Florida on 28 September 2022. During October 2022, water and oyster samples were collected from three stations in Lee County in an area significantly impacted by Ian. Vibrio spp. were isolated, and whole-genome sequencing and phylogenetic analysis were done, with a focus on Vibrio parahaemolyticus and Vibrio vulnificus to provide genetic insight into pathogenic strains circulating in the environment. Metagenomic analysis of water samples provided insight with respect to human health-related factors, notably the detection of approximately 12 pathogenic Vibrio spp., virulence and antibiotic resistance genes, and mobile genetic elements, including the SXT/R391 family of integrative conjugative elements. Environmental parameters were monitored as part of a long-term time series analysis done using satellite remote sensing. In addition to anomalous rainfall and storm surge, changes in sea surface temperature and chlorophyll concentration during and after Ian favored the growth of Vibrio spp. In conclusion, genetic analysis coupled with environmental data and remote sensing provides useful public health information and, hence, constitute a valuable tool to proactively detect and characterize environmental pathogens, notably vibrios. These data can aid the development of early warning systems by yielding a larger source of information for public health during climate change. Evidence suggests warming temperatures are associated with the spread of potentially pathogenic Vibrio spp. and the emergence of human disease globally. Following Hurricane Ian, the State of Florida reported a sharp increase in the number of reported Vibrio spp. infections and deaths. Hence, monitoring of pathogens, including vibrios, and environmental parameters influencing their occurrence is critical to public health. Here, DNA sequencing was used to investigate the genomic diversity of Vibrio parahaemolyticus and Vibrio vulnificus, both potential human pathogens, in Florida coastal waters post Hurricane Ian, in October 2022. Additionally, the microbial community of water samples was profiled to detect the presence of Vibrio spp. and other microorganisms (bacteria, fungi, protists, and viruses) present in the samples. Long-term environmental data analysis showed changes in environmental parameters during and after Ian were optimal for the growth of Vibrio spp. and related pathogens. Collectively, results will be used to develop predictive risk models during climate change.}, } @article {pmid37931016, year = {2024}, author = {Zhang, M and Chen, L and Zhao, H and Qiao, T and Jiang, L and Wang, C and Zhong, X and Li, X and Xu, Y}, title = {Metagenomic next-generation sequencing for diagnosis of infectious encephalitis and meningitis: a retrospective study of 90 patients.}, journal = {Neurological research}, volume = {46}, number = {2}, pages = {187-194}, doi = {10.1080/01616412.2023.2265243}, pmid = {37931016}, issn = {1743-1328}, mesh = {Humans ; Retrospective Studies ; *Meningitis/diagnosis ; *Infectious Encephalitis/diagnosis ; *Encephalitis/diagnosis ; Sensitivity and Specificity ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {BACKGROUND: Infections of the central nervous system (CNS) are potentially life-threatening and can cause serious morbidity. We evaluated the clinical value of metagenomic next-generation sequencing (mNGS) in the diagnosis of infectious encephalitis and meningitis and explored the factors affecting the results of mNGS.

METHODS: Patients with suspected cases of encephalitis or meningitis who presented in Northern Jiangsu People's Hospital from 1 March 2018 to 30 September 2022 were collected. Demographic, historical, and clinical information were obtained, and cerebrospinal fluid (CSF) samples were treated with mNGS. The pathogen was identified using National Center for Biotechnology Information (NCBI) GenBank sequence data.

RESULTS: Ninety-six patients were screened and finally 90 subjects enrolled. Of the 90 enrolled cases, 67 (74.4%) were diagnosed with central nervous system infections, which included 48 cases (71.6%) of viral infection, 11 (12.2%) of bacterial infection, 5 (7.5%) of mycobacterium tuberculosis, 2 (3.0%) of fungal infection, and 1 (1.5%) of rickettsia infection. From these cases, mNGS identified 40 (44.4%) true-positive cases, 3 (3.3%) false-positive case, 22 (24.4%) true-negative cases, and 25 (27.8%) false-negative cases. The sensitivity and specificity of mNGS were 61.5% and 88%, respectively. mNGS of CSF could show a higher positive rate in patients with marked CSF abnormalities, including elevated protein concentrations and monocyte counts.

CONCLUSION: mNGS of CSF is an effective method for detecting infectious encephalitis and meningitis, and the results should be analyzed combined with conventional microbiological testing results.}, } @article {pmid37930866, year = {2024}, author = {Camargo, AP and Call, L and Roux, S and Nayfach, S and Huntemann, M and Palaniappan, K and Ratner, A and Chu, K and Mukherjeep, S and Reddy, TBK and Chen, IA and Ivanova, NN and Eloe-Fadrosh, EA and Woyke, T and Baltrus, DA and Castañeda-Barba, S and de la Cruz, F and Funnell, BE and Hall, JPJ and Mukhopadhyay, A and Rocha, EPC and Stalder, T and Top, E and Kyrpides, NC}, title = {IMG/PR: a database of plasmids from genomes and metagenomes with rich annotations and metadata.}, journal = {Nucleic acids research}, volume = {52}, number = {D1}, pages = {D164-D173}, pmid = {37930866}, issn = {1362-4962}, support = {//U.S. Department of Energy/ ; //Joint Genome Institute/ ; DE-AC02-05CH11231//DOE Office of Science User Facilities/ ; 17-SC-20-SC//Exascale Computing Project/ ; //U.S. Department of Energy Office of Science/ ; //National Nuclear Security Administration/ ; MR/W02666X/1//MRC Career Development Award/ ; //Office of Science of the US Department of Science/ ; }, mesh = {Humans ; *Metagenome ; Metadata ; Software ; Databases, Genetic ; Plasmids/genetics ; *Microbiota ; }, abstract = {Plasmids are mobile genetic elements found in many clades of Archaea and Bacteria. They drive horizontal gene transfer, impacting ecological and evolutionary processes within microbial communities, and hold substantial importance in human health and biotechnology. To support plasmid research and provide scientists with data of an unprecedented diversity of plasmid sequences, we introduce the IMG/PR database, a new resource encompassing 699 973 plasmid sequences derived from genomes, metagenomes and metatranscriptomes. IMG/PR is the first database to provide data of plasmid that were systematically identified from diverse microbiome samples. IMG/PR plasmids are associated with rich metadata that includes geographical and ecosystem information, host taxonomy, similarity to other plasmids, functional annotation, presence of genes involved in conjugation and antibiotic resistance. The database offers diverse methods for exploring its extensive plasmid collection, enabling users to navigate plasmids through metadata-centric queries, plasmid comparisons and BLAST searches. The web interface for IMG/PR is accessible at https://img.jgi.doe.gov/pr. Plasmid metadata and sequences can be downloaded from https://genome.jgi.doe.gov/portal/IMG_PR.}, } @article {pmid37930845, year = {2024}, author = {Tadaka, S and Kawashima, J and Hishinuma, E and Saito, S and Okamura, Y and Otsuki, A and Kojima, K and Komaki, S and Aoki, Y and Kanno, T and Saigusa, D and Inoue, J and Shirota, M and Takayama, J and Katsuoka, F and Shimizu, A and Tamiya, G and Shimizu, R and Hiratsuka, M and Motoike, IN and Koshiba, S and Sasaki, M and Yamamoto, M and Kinoshita, K}, title = {jMorp: Japanese Multi-Omics Reference Panel update report 2023.}, journal = {Nucleic acids research}, volume = {52}, number = {D1}, pages = {D622-D632}, pmid = {37930845}, issn = {1362-4962}, support = {JP21tm0124005//Japan Agency for Medical Research and Development/ ; JP21tm0424601//ToMMo supercomputer system, which is supported by AMED/ ; }, mesh = {Humans ; Prospective Studies ; Japan ; *Multiomics ; *Population Health ; Genomics/methods ; }, abstract = {Modern medicine is increasingly focused on personalized medicine, and multi-omics data is crucial in understanding biological phenomena and disease mechanisms. Each ethnic group has its unique genetic background with specific genomic variations influencing disease risk and drug response. Therefore, multi-omics data from specific ethnic populations are essential for the effective implementation of personalized medicine. Various prospective cohort studies, such as the UK Biobank, All of Us and Lifelines, have been conducted worldwide. The Tohoku Medical Megabank project was initiated after the Great East Japan Earthquake in 2011. It collects biological specimens and conducts genome and omics analyses to build a basis for personalized medicine. Summary statistical data from these analyses are available in the jMorp web database (https://jmorp.megabank.tohoku.ac.jp), which provides a multidimensional approach to the diversity of the Japanese population. jMorp was launched in 2015 as a public database for plasma metabolome and proteome analyses and has been continuously updated. The current update will significantly expand the scale of the data (metabolome, genome, transcriptome, and metagenome). In addition, the user interface and backend server implementations were rewritten to improve the connectivity between the items stored in jMorp. This paper provides an overview of the new version of the jMorp.}, } @article {pmid37930569, year = {2023}, author = {Wang, F and Zhao, Q and Zhang, L and Chen, J and Wang, T and Qiao, L and Zhang, L and Ding, C and Yuan, Y and Qi, Z and Chen, T}, title = {Co-digestion of chicken manure and sewage sludge in black soldier fly larvae bioconversion system: bacterial biodiversity and nutrients quality of residues for biofertilizer application.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {57}, pages = {119804-119813}, pmid = {37930569}, issn = {1614-7499}, support = {Grant Nos. 42272211//National Natural Science Foundation of China/ ; BK20210946//Natural Science Foundation of Jiangsu Province/ ; No. xjr2021051//School-level research projects of Yancheng Institute of Technology/ ; }, mesh = {Animals ; Larva ; *Sewage ; Manure ; Chickens ; *Diptera ; Nutrients ; Bacteria ; Digestion ; }, abstract = {Black soldier fly larvae (BSFL) bioconversion system is emerging as an effective approach for organic waste pollution treatment. Co-digestion of different organic matters with BSFL can be an effective way to realize the innovative biowaste circular economy. In this study, organic waste mixture of chicken manure and sewage sludge was chosen as substrate for BSFL growth. The bacterial biodiversity and nutrients quality of BSFL residue were evaluated through gene sequencing and other characterizations to confirm their application potential as biofertilizers. The dominant bacteria in BSFL residue were Firmicutes (75.39%) at phylum level, Bacilli (71.61%) at class level and Pseudogracilibacillus (11.08%) at genus level. Antibiotic resistance genes (ARGs) were used to assess the harmlessness of BSFL residue. After BSFL treatment, 36.2% decrease in ARGs was observed. Taking nutrients quality into consideration, dissolved organic carbon, dissolved nitrogen, available phosphorous, and available potassium significantly increased in the co-digestion system. These results demonstrated that co-digestion of chicken manure and excess sludge in BSFL bioconversion system could improve the nutrients quality of residues. However, removal of ARGs in the bioconversion process should be further explored to eliminate environmental concerns associated with application of BSFL residue as biofertilizers.}, } @article {pmid37930060, year = {2023}, author = {Tan, Y and Yu, P and Huang, D and Yuan, MM and Yu, Z and Lu, H and Alvarez, PJJ and Zhu, L}, title = {Enhanced Bacterium-Phage Symbiosis in Attached Microbial Aggregates on a Membrane Surface Facing Elevated Hydraulic Stress.}, journal = {Environmental science & technology}, volume = {57}, number = {45}, pages = {17324-17337}, doi = {10.1021/acs.est.3c05452}, pmid = {37930060}, issn = {1520-5851}, mesh = {*Bacteriophages/genetics ; Symbiosis ; Bacteria/genetics ; *Microbiota ; Metagenome ; }, abstract = {Phages are increasingly recognized for their importance in microbial aggregates, including their influence on microbial ecosystem services and biotechnology applications. However, the adaptive strategies and ecological functions of phages in different aggregates remain largely unexplored. Herein, we used membrane bioreactors to investigate bacterium-phage interactions and related microbial functions within suspended and attached microbial aggregates (SMA vs AMA). SMA and AMA represent distinct microbial habitats where bacterial communities display distinct patterns in terms of dominant species, keystone species, and bacterial networks. However, bacteria and phages in both aggregates exhibited high lysogenicity, with 60% lysogenic phages in the virome and 70% lysogenic metagenome-assembled genomes of bacteria. Moreover, substantial phages exhibited broad host ranges (34% in SMA and 42% in AMA) and closely interacted with habitat generalist species (43% in SMA and 49% in AMA) as adaptive strategies in stressful operation environments. Following a mutualistic pattern, phage-carried auxiliary metabolic genes (pAMGs; 238 types in total) presumably contributed to the bacterial survival and aggregate stability. The SMA-pAMGs were mainly associated with energy metabolism, while the AMA-pAMGs were mainly associated with antioxidant biosynthesis and the synthesis of extracellular polymeric substances, representing habitat-dependent patterns. Overall, this study advanced our understanding of phage adaptive strategies in microbial aggregate habitats and emphasized the importance of bacterium-phage symbiosis in the stability of microbial aggregates.}, } @article {pmid37930030, year = {2023}, author = {Jiang, Y and Hu, X and Fan, S and Liu, W and Chen, J and Wang, L and Deng, Q and Yang, J and Yang, A and Lou, Z and Guan, Y and Xia, H and Gu, B}, title = {RVFScan predicts virulence factor genes and hypervirulence of the clinical metagenome.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {6}, pages = {}, pmid = {37930030}, issn = {1477-4054}, mesh = {Humans ; *Virulence Factors/genetics ; Metagenome ; Virulence/genetics ; Klebsiella pneumoniae/genetics ; *Bacterial Infections/genetics ; }, abstract = {Bacterial infections often involve virulence factors that play a crucial role in the pathogenicity of bacteria. Accurate detection of virulence factor genes (VFGs) is essential for precise treatment and prognostic management of hypervirulent bacterial infections. However, there is a lack of rapid and accurate methods for VFG identification from the metagenomic data of clinical samples. Here, we developed a Reads-based Virulence Factors Scanner (RVFScan), an innovative user-friendly online tool that integrates a comprehensive VFG database with similarity matrix-based criteria for VFG prediction and annotation using metagenomic data without the need for assembly. RVFScan demonstrated superior performance compared to previous assembly-based and read-based VFG predictors, achieving a sensitivity of 97%, specificity of 98% and accuracy of 98%. We also conducted a large-scale analysis of 2425 clinical metagenomic datasets to investigate the utility of RVFScan, the species-specific VFG profiles and associations between VFGs and virulence phenotypes for 24 important pathogens were analyzed. By combining genomic comparisons and network analysis, we identified 53 VFGs with significantly higher abundances in hypervirulent Klebsiella pneumoniae (hvKp) than in classical K. pneumoniae. Furthermore, a cohort of 1256 samples suspected of K. pneumoniae infection demonstrated that RVFScan could identify hvKp with a sensitivity of 90%, specificity of 100% and accuracy of 98.73%, with 90% of hvKp samples consistent with clinical diagnosis (Cohen's kappa, 0.94). RVFScan has the potential to detect VFGs in low-biomass and high-complexity clinical samples using metagenomic reads without assembly. This capability facilitates the rapid identification and targeted treatment of hvKp infections and holds promise for application to other hypervirulent pathogens.}, } @article {pmid37929976, year = {2023}, author = {Rasmussen, AN and Francis, CA}, title = {Pelagic metagenome-assembled genomes from an estuarine salinity gradient in San Francisco Bay.}, journal = {Microbiology resource announcements}, volume = {12}, number = {12}, pages = {e0080023}, pmid = {37929976}, issn = {2576-098X}, support = {OCE-0847266//National Science Foundation (NSF)/ ; }, abstract = {San Francisco Bay (SFB) is a large and highly human-impacted estuarine system. We produced 449 metagenome-assembled genomes from SFB waters, collected along the salinity gradient, providing a rich data set to compare the metabolic potential of microorganisms from different salinity zones within SFB and to other estuarine systems.}, } @article {pmid37929823, year = {2023}, author = {Yi, X and Lu, H and Liu, X and He, J and Li, B and Wang, Z and Zhao, Y and Zhang, X and Yu, X}, title = {Unravelling the enigma of the human microbiome: Evolution and selection of sequencing technologies.}, journal = {Microbial biotechnology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1751-7915.14364}, pmid = {37929823}, issn = {1751-7915}, support = {82202569//National Natural Science Foundation of China/ ; 20210302124635//Shanxi Province Basic Research Program Project/ ; }, abstract = {The human microbiome plays a crucial role in maintaining health, with advances in high-throughput sequencing technology and reduced sequencing costs triggering a surge in microbiome research. Microbiome studies generally incorporate five key phases: design, sampling, sequencing, analysis, and reporting, with sequencing strategy being a crucial step offering numerous options. Present mainstream sequencing strategies include Amplicon sequencing, Metagenomic Next-Generation Sequencing (mNGS), and Targeted Next-Generation Sequencing (tNGS). Two innovative technologies recently emerged, namely MobiMicrobe high-throughput microbial single-cell genome sequencing technology and 2bRAD-M simplified metagenomic sequencing technology, compensate for the limitations of mainstream technologies, each boasting unique core strengths. This paper reviews the basic principles and processes of these three mainstream and two novel microbiological technologies, aiding readers in understanding the benefits and drawbacks of different technologies, thereby guiding the selection of the most suitable method for their research endeavours.}, } @article {pmid37929182, year = {2023}, author = {Hashemi, M and Amiel, A and Zouaoui, M and Adam, K and Clemente, HS and Aguilar, M and Pendaries, R and Couzigou, JM and Marti, G and Gaulin, E and Roy, S and Rey, T and Dumas, B}, title = {The mycoparasite Pythium oligandrum induces legume pathogen resistance and shapes rhizosphere microbiota without impacting mutualistic interactions.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1156733}, pmid = {37929182}, issn = {1664-462X}, abstract = {Pythium oligandrum is a soil-borne oomycete associated with rhizosphere and root tissues. Its ability to enhance plant growth, stimulate plant immunity and parasitize fungal and oomycete preys has led to the development of agricultural biocontrol products. Meanwhile, the effect of P. oligandrum on mutualistic interactions and more generally on root microbial communities has not been investigated. Here, we developed a biological system comprising P. oligandrum interacting with two legume plants, Medicago truncatula and Pisum sativum. P. oligandrum activity was investigated at the transcriptomics level through an RNAseq approach, metabolomics and finally metagenomics to investigate the impact of P. oligandrum on root microbiota. We found that P. oligandrum promotes plant growth in these two species and protects them against infection by the oomycete Aphanomyces euteiches, a devastating legume root pathogen. In addition, P. oligandrum up-regulated more than 1000 genes in M. truncatula roots including genes involved in plant defense and notably in the biosynthesis of antimicrobial compounds and validated the enhanced production of M. truncatula phytoalexins, medicarpin and formononetin. Despite this activation of plant immunity, we found that root colonization by P. oligandrum did not impaired symbiotic interactions, promoting the formation of large and multilobed symbiotic nodules with Ensifer meliloti and did not negatively affect the formation of arbuscular mycorrhizal symbiosis. Finally, metagenomic analyses showed the oomycete modifies the composition of fungal and bacterial communities. Together, our results provide novel insights regarding the involvement of P. oligandrum in the functioning of plant root microbiota.}, } @article {pmid37928975, year = {2023}, author = {Hodzhev, Y and Tsafarova, B and Tolchkov, V and Youroukova, V and Ivanova, S and Kostadinov, D and Yanev, N and Zhelyazkova, M and Tsonev, S and Kalfin, R and Panaiotov, S}, title = {Visualization of the individual blood microbiome to study the etiology of sarcoidosis.}, journal = {Computational and structural biotechnology journal}, volume = {22}, number = {}, pages = {50-57}, pmid = {37928975}, issn = {2001-0370}, abstract = {INTRODUCTION: Single microbial pathogens or host-microbiome dysbiosis are the causes of lung diseases with suspected infectious etiology. Metagenome sequencing provides an overview of the microbiome content. Due to the rarity of most granulomatous lung diseases collecting large systematic datasets is challenging. Thus, single-patient data often can only be summarized visually.

OBJECTIVE: To increase the information gain from a single-case metagenome analysis we suggest a quantitative and qualitative approach.

RESULTS: The 16S metagenomic results of 7 patients with pulmonary sarcoidosis were compared with those of 22 healthy individuals. From lysed blood, total microbial DNA was extracted and sequenced. Cleaned data reads were identified taxonomically using Kraken 2 software. Individual metagenomic data were visualized with a Sankey diagram, Krona chart, and a heat-map. We identified five genera that were exclusively present or significantly enhanced in patients with sarcoidosis - Veillonella, Prevotella, Cutibacterium, Corynebacterium, and Streptococcus.

CONCLUSIONS: Our approach can characterize the blood microbiome composition and diversity in rare diseases at an individual level. Investigation of the blood microbiome in patients with granulomatous lung diseases of unknown etiology, such as sarcoidosis could enhance our comprehension of their origin and pathogenesis and potentially uncover novel personalized therapeutics.}, } @article {pmid37928876, year = {2023}, author = {He, T and Luo, N and Kang, J and Ling, N and Zhang, D}, title = {Use of metagenomic next-generation sequencing for diagnosis of peritonitis in end-stage liver disease.}, journal = {International journal of medical sciences}, volume = {20}, number = {13}, pages = {1698-1704}, pmid = {37928876}, issn = {1449-1907}, mesh = {Humans ; Ascites ; *End Stage Liver Disease ; High-Throughput Nucleotide Sequencing ; *Peritonitis/diagnosis/etiology ; Dietary Supplements ; Sensitivity and Specificity ; }, abstract = {Background: Conventional methods are low in positive rates and time-consuming for ascites pathogen detection in patients with end-stage liver disease (ESLD). With many advantages, metagenomic next-generation sequencing (mNGS) may be a good alternative method. However, the related studies are still lacking. Methods: Ascites from 50 ESLD patients were sampled for pathogen detection using mNGS and conventional methods (culture and polymorphonuclear neutrophils detection) in this prospective observational study. Results: Forty-two samples were detected positive using mNGS. 29 strains of bacteria, 11 strains of fungi, and 9 strains of viruses were detected. 46% of patients were detected to be co-infected with 2 or more pathogens by mNGS. Moreover, mNGS showed similar and high positive rates in ESLD patients with different clinical characteristics. Compared to conventional methods, mNGS had higher positivity rates (84% vs. 20%, P<0.001), sensitivity (45.2% vs. 23.8%, P=0.039), broader pathogen spectrum, shorter detection time (24 hours vs. 3-7 days), but lower specificity (25% vs 100%, P = 0.010). Furthermore, compared to conventional methods, mNGS showed similar consistence with final diagnosis (42% vs. 36%, P=0.539). Conclusions: mNGS may be a good supplement for conventional methods and helpful to early etiological diagnosis of peritonitis, and thus improve ESLD patients' survival.}, } @article {pmid37928816, year = {2023}, author = {Jin, S and Guo, X and Xing, H and Li, D and Wang, Y and Ma, W}, title = {Multiple brain abscesses caused by Nocardia asiatica: Case report and literature review.}, journal = {IDCases}, volume = {34}, number = {}, pages = {e01903}, pmid = {37928816}, issn = {2214-2509}, abstract = {Nocardia are opportunistic pathogens mainly affecting immunocompromised individuals. Nocardia asiatica, a novel species, can cause severe infections. We present a case of multiple brain abscesses due to Nocardia asiatica, discussing its diagnosis and treatment. In January 2022, a 27-year-old Chinese woman with a history of atypical membranous nephropathy presented with low-grade fever, cough, limb weakness, and headaches. Imaging revealed lung and brain lesions. Neurological symptoms worsened over time, culminating in recurrent seizures and severe headaches. A brain MRI confirmed multiple abscesses. Craniotomy and lesion removal were performed, leading to a diagnosis of brain abscesses caused by Nocardia asiatica. Empirical antibiotics were followed by targeted regimen. After successful treatment, the patient remained symptom-free during follow-ups. Nocardia asiatica multiple brain abscesses are exceedingly rare. This case underscores the importance of considering nocardiosis in immunosuppressed patients presenting with neurological symptoms. Timely neurosurgical intervention and effective antibiotic therapy are crucial. Metagenomic next-generation sequencing proved invaluable for rapid diagnosis. Treatment with trimethoprim-sulfamethoxazole (TMP-SMX) and a carbapenem followed by TMP-SMX alone achieved disease control. This case contributes to the understanding of Nocardia asiatica infections and highlights the role of neurosurgical procedures in managing disseminated nocardiosis.}, } @article {pmid37928691, year = {2023}, author = {André, MR and Ikeda, P and Lee, DAB and do Amaral, RB and Carvalho, LAL and Pinheiro, DG and Torres, JM and de Mello, VVC and Rice, GK and Cer, RZ and Lourenço, EC and Oliveira, CE and Herrera, HM and Barros-Battesti, DM and Machado, RZ and Bishop-Lilly, KA and Dalgard, CL and Dumler, JS}, title = {Characterization of the bacterial microbiome of non-hematophagous bats and associated ectoparasites from Brazil.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1261156}, pmid = {37928691}, issn = {1664-302X}, abstract = {INTRODUCTION: Bats, along with their ectoparasites, harbor a wide diversity of symbiotic and potential pathogenic bacteria. Despite the enormous diversity of bats (181 species), few studies aimed to investigate the bacterial microbiome of Brazilian chiropterans and associated ectoparasites. This study aimed to characterize the bacterial microbiome of non-hematophagous bats and associated Streblidae flies and Macronyssidae and Spinturnicidae mites in the state of Mato Grosso do Sul, midwestern Brazil.

METHODS: Oral and rectal swabs were collected from 30 bats (Artibeus lituratus [n = 13], Artibeus planirostris [n  =  9], Eptesicus furinalis [n = 5], Carollia perspicillata [n = 2], and Platyrrhinus lineatus [n = 1]). In addition, a total of 58 mites (15 Macronyssidae and 43 Spinturnicidae) and 48 Streblidae bat flies were collected from the captured bats. After DNA extraction and purification, each sample's bacterial composition was analyzed with metagenomic sequencing.

RESULTS: The microbiome composition of both oral and rectal bat swab samples showed that Gammaproteobacteria was the most abundant bacterial class. Spiroplasma, Wolbachia and Bartonella represented the most abundant genera in Streblidae flies. While Wolbachia (Alphaproteobacteria) was the most abundant genus found in Spinturnicidae, Arsenophonus (Gammaproteobacteria) was found in high abundance in Macronyssidae mites. In addition to characterizing the microbiome of each sample at the class and genus taxonomic levels, we identified medically significant bacteria able to infect both animals and humans in oral (Streptococcus and Anaplasma) and rectal swabs (Enterobacter, Klebsiella, Escherichia, Enterococcus, Streptococcus), Macronyssidae (Anaplasma, Bartonella, Ehrlichia) and Spinturnicidae (Anaplasma, Bartonella) mites as well as Streblidae flies (Spiroplasma, Bartonella).

DISCUSSION AND CONCLUSION: Besides expanding the knowledge on the bacterial microbiome of non-hematophagous bats and Streblidae flies from Brazil, the present work showed, for the first time, the bacterial community of bat-associated Macronyssidae and Spinturnicidae mites.}, } @article {pmid37928679, year = {2023}, author = {Gangola, S and Joshi, S and Bhandari, G and Pant, G and Sharma, A and Perveen, K and Bukhari, NA and Rani, R}, title = {Exploring microbial diversity responses in agricultural fields: a comparative analysis under pesticide stress and non-stress conditions.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1271129}, pmid = {37928679}, issn = {1664-302X}, abstract = {Exposure to pesticides changes the microbial community structure in contaminated agricultural fields. To analyze the changes in the native microbial composition qRT-PCR, a metagenomic study was conducted. The qRT-PCR results exhibited that the uncontaminated soil has a higher copy number of 16S rDNA relative to the soil contaminated with pesticide. Metagenome analysis interprets that uncontaminated soil is enriched with proteobacteria in comparison with pesticide-contaminated soil. However, the presence of Actinobacteria, Firmicutes, and Bacteroides was found to be dominant in the pesticide-spiked soil. Additionally, the presence of new phyla such as Chloroflexi, Planctomycetes, and Verrucomicrobia was noted in the pesticide-spiked soil, while Acidobacteria and Crenarchaeota were observed to be extinct. These findings highlight that exposure to pesticides on soil significantly impacts the biological composition of the soil. The abundance of microbial composition under pesticide stress could be of better use for the treatment of biodegradation and bioremediation of pesticides in contaminated environments.}, } @article {pmid37928672, year = {2023}, author = {Farkas, C and Retamal-Fredes, E and Ávila, A and Fehlings, MG and Vidal, PM}, title = {Degenerative Cervical Myelopathy induces sex-specific dysbiosis in mice.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1229783}, pmid = {37928672}, issn = {1664-302X}, abstract = {Degenerative Cervical Myelopathy (DCM) is the most common cause of spinal cord impairment in elderly populations. It describes a spectrum of disorders that cause progressive spinal cord compression, neurological impairment, loss of bladder and bowel functions, and gastrointestinal dysfunction. The gut microbiota has been recognized as an environmental factor that can modulate both the function of the central nervous system and the immune response through the microbiota-gut-brain axis. Changes in gut microbiota composition or microbiota-producing factors have been linked to the progression and development of several pathologies. However, little is known about the potential role of the gut microbiota in the pathobiology of DCM. Here, DCM was induced in C57BL/6 mice by implanting an aromatic polyether material underneath the C5-6 laminae. The extent of DCM-induced changes in microbiota composition was assessed by 16S rRNA sequencing of the fecal samples. The immune cell composition was assessed using flow cytometry. To date, several bacterial members have been identified using BLAST against the largest collection of metagenome-derived genomes from the mouse gut. In both, female and males DCM caused gut dysbiosis compared to the sham group. However, dysbiosis was more pronounced in males than in females, and several bacterial members of the families Lachnospiraceae and Muribaculaceae were significantly altered in the DCM group. These changes were also associated with altered microbe-derived metabolic changes in propionate-, butyrate-, and lactate-producing bacterial members. Our results demonstrate that DCM causes dynamic changes over time in the gut microbiota, reducing the abundance of butyrate-producing bacteria, and lactate-producing bacteria to a lesser extent. Genome-scale metabolic modeling using gapseq successfully identified pyruvate-to-butanoate and pyruvate-to-propionate reactions involving genes such as Buk and ACH1, respectively. These results provide a better understanding of the sex-specific molecular effects of changes in the gut microbiota on DCM pathobiology.}, } @article {pmid37928606, year = {2023}, author = {Lv, H and Zhuang, Y and Wu, W}, title = {Lung Abscess Caused by Tannerella forsythia Infection: A Case Report.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {6975-6981}, pmid = {37928606}, issn = {1178-6973}, abstract = {BACKGROUND: Tannerella forsythia is a gram-negative anaerobic bacterium commonly found in the oral cavity. It is among the common pathogenic bacteria associated with gingivitis, chronic periodontitis, and aggressive periodontitis. However, there is currently no literature discussing lung abscesses primarily caused by T. forsythia infection.

PRESENTATION: This article presents the case of a 55-year-old male with a massive lung abscess. The patient underwent ultrasound-guided percutaneous drainage, and the sample was sent for pathogen metagenomic next-generation sequencing (mNGS) testing. The test indicated that the lung abscess was primarily caused by T. forsythia infection. A literature review was conducted to understand the characteristics of this pathogen as well as its clinical features and suitable treatment approaches.

CONCLUSION: Currently, there is no literature specifically mentioning T. forsythia as a primary pathogen causing lung abscesses. This anaerobic bacterium is commonly found in the oral cavity and is difficult to cultivate using routine culture methods. mNGS emerges as a value diagnostic method for identifying this pathogen. Treatment recommendations include drainage and antibiotic selection encompassing common periodontal pathogens such as red complex bacteria and Actinomyces.}, } @article {pmid37928602, year = {2023}, author = {Liu, J and Ye, SY and Xu, XD and Liu, Q and Ma, F and Yu, X and Luo, YH and Chen, LL and Zeng, X}, title = {Multiomics analysis reveals the genetic and metabolic characteristics associated with the low prevalence of dental caries.}, journal = {Journal of oral microbiology}, volume = {15}, number = {1}, pages = {2277271}, pmid = {37928602}, issn = {2000-2297}, abstract = {BACKGROUND: Despite poor oral hygiene, the Baiku Yao (BKY) ethnic group in China presents a low prevalence of dental caries, which may be related to genetic susceptibility. Due to strict intra-ethnic marriage rule, this ethnic has an advantage in studying the interaction between genetic factors and other regulatory factors related to dental caries.

METHODS: Peripheral blood from a caries-free adult male was used for whole genome sequencing, and the BKY assembled genome was compared to the Han Chinese genome. Oral saliva samples were collected from 51 subjects for metabolomic and metagenomic analysis. Multiomics data were integrated for combined analysis using bioinformatics approaches.

RESULTS: Comparative genomic analysis revealed the presence of structural variations in several genes associated with dental caries. Metabolomic and metagenomic sequencing demonstrated the caries-free group had significantly higher concentration of antimicrobials and higher abundance of core oral health-related microbiota. The functional analysis indicated that cationic antimicrobial peptide resistance and the lipopolysaccharide biosynthesis pathway were enriched in the caries-free group.

CONCLUSIONS: Our study provided new insights into the specific regulatory mechanisms that contribute to the low prevalence of dental caries in the specific population and may provide new evidence for the genetic diagnosis and control of dental caries.}, } @article {pmid37928212, year = {2023}, author = {Angchagun, K and Boonklang, P and Chomkatekaew, C and Pakdeerat, S and Wongsuwan, G and Amornchai, P and Wuthiekanun, V and Panapipat, S and Ngernseng, T and Waithira, N and Walton, S and Limmathurotsakul, D and Surawong, A and Siriboon, S and Chamnan, P and Chantratita, N and Dunachie, S and Corander, J and Davenport, EE and Knight, J and Parkhill, J and Peacock, SJ and Thomson, NR and Day, NPJ and Chewapreecha, C}, title = {BurkHostGEN: a study protocol for evaluating variations in the Burkholderia pseudomallei and host genomes associated with melioidosis infection.}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {347}, pmid = {37928212}, issn = {2398-502X}, abstract = {BACKGROUND: Melioidosis is a frequently fatal disease caused by an environmental bacterium Burkholderia pseudomallei. The disease is prevalent in northeast Thailand, particularly among rice field farmers who are at risk of bacterial exposure through contact with contaminated soil and water. However, not all exposure results in disease, and infection can manifest diverse outcomes. We postulate that genetic factors, whether from the bacterium, the host or the combination of both, may influence disease outcomes. To address this hypothesis, we aim to collect, sequence, and analyse genetic data from melioidosis patients and controls, along with isolates of B. pseudomallei obtained from patients. Additionally, we will study the metagenomics of the household water supply for both patients and controls, including the presence of B. pseudomallei.

METHODS: BurkHostGEN is an ongoing observational study being conducted at Sunpasitthiprasong Hospital, Ubon Ratchathani, Thailand. We are obtaining consent from 600 melioidosis patients and 700 controls, spanning both sexes, to collect 1 mL of blood for host DNA analysis, 3 mL of blood for RNA analysis, as well as 5 L of household water supply for metagenomic analysis. Additionally, we are isolating B. pseudomallei from the melioidosis patients to obtain bacterial DNA. This comprehensive approach will allow us to identify B. pseudomallei and their paired host genetic factors associated with disease acquisition and severity. Ethical approvals have been obtained for BurkHostGEN. Host and bacterial genetic data will be uploaded to European Genome-Phenome Archive (EGA) and European Nucleotide Archive (ENA), respectively.

CONCLUSIONS: BurkHostGEN holds the potential to discover bacterial and host genetic factors associated with melioidosis infection and severity of illness. It can also support various study designs, including biomarker validation, disease pathogenesis, and epidemiological analysis not only for melioidosis but also for other infectious diseases.}, } @article {pmid37927778, year = {2023}, author = {Guo, Y and Zhang, D and Qi, W}, title = {Bacterial diversity of herbal rhizospheric soils in Ordos desert steppes under different degradation gradients.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16289}, pmid = {37927778}, issn = {2167-8359}, mesh = {Humans ; *Soil/chemistry ; *Rhizosphere ; Bacteria/genetics ; Proteobacteria/genetics ; Acidobacteria/genetics ; Plants ; }, abstract = {OBJECTIVES: This study explored the effects of different degradation gradients on bacterial diversity in the rhizospheric soils of herb plants.

METHODS: The alpha diversity, species composition and correlations of bacterial communities in the rhizospheric soils of herb plants were studied using metagenomics 16SrDNA gene high-throughput sequencing.

RESULTS: The diversity of bacterial communities in the rhizospheric soils of herb plants differed during the degradation of desert steppes. An analysis of bacterial community alpha diversity indices showed the bacterial diversity and species evenness of rhizospheric soils were best in moderately degraded desert steppes. Among all samples, a total of 43 phyla, 133 classes, 261 orders, 421 families, 802 genera and 1,129 species were detected. At the phylum level, the predominant bacterial phyla were: Actinobacteria, Proteobacteria, Acidobacteria, Gemmatimonadetes, Chloroflexi, Planctomycetes and Bacteroidetes. At the genus level, the predominant bacterial genera were: RB41, Sphingomonas, WD2101_soil_group_unclassified, Pseudomonas and Actinomyces. The relative abundance of unknown genera was very large, which deserves further research. At the phylum and genus levels, the species abundance levels under slight and moderate degradation were significantly higher than those under extreme degradation. Correlation network diagrams showed there were many nodes in both slightly deteriorated and moderately deteriorated soils, and the node proportions were large and mostly positively correlated. These results indicate the bacterial communities in rhizospheric soils under slight or moderate deterioration are relatively stable. The rhizospheric soil microbes of desert steppes can form a stable network structure, allowing them to adequately respond to environmental conditions.

CONCLUSIONS: The bacterial communities in the rhizospheric soils of herb plants differ between different degradation gradients. The species number, abundance and diversity of bacterial communities in rhizospheric soils are not directly correlated with degree of degradation. The abundance, species diversity and species abundance of bacterial communities in the rhizospheric soils of moderately degraded desert steppes are the highest and most stable. The soil bacterial diversity is lowest in severely degraded desert steppes.}, } @article {pmid37926838, year = {2023}, author = {Su, Y and Xu, MY and Cui, Y and Chen, RZ and Xie, LX and Zhang, JX and Chen, YQ and Ding, T}, title = {Bacterial quorum sensing orchestrates longitudinal interactions to shape microbiota assembly.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {241}, pmid = {37926838}, issn = {2049-2618}, mesh = {Humans ; *Quorum Sensing ; Bacterial Proteins/metabolism ; Bacteria/genetics/metabolism ; Biofilms ; Streptococcus/genetics/metabolism ; *Microbiota ; }, abstract = {BACKGROUND: The mechanism of microbiota assembly is one of the main problems in microbiome research, which is also the primary theoretical basis for precise manipulation of microbial communities. Bacterial quorum sensing (QS), as the most common means for bacteria to exchange information and interactions, is characterized by universality, specificity, and regulatory power, which therefore may influence the assembly processes of human microbiota. However, the regulating role of QS in microbiota assembly is rarely reported. In this study, we developed an optimized in vitro oral biofilm microbiota assembling (OBMA) model to simulate the time-series assembly of oral biofilm microbiota (OBM), by which to excavate the QS network and its regulating power in the process.

RESULTS: By using the optimized OBMA model, we were able to restore the assembly process of OBM and generate time-series OBM metagenomes of each day. We discovered a total of 2291 QS protein homologues related to 21 QS pathways. Most of these pathways were newly reported and sequentially enriched during OBM assembling. These QS pathways formed a comprehensive longitudinal QS network that included successively enriched QS hubs, such as Streptococcus, Veillonella-Megasphaera group, and Prevotella-Fusobacteria group, for information delivery. Bidirectional cross-talk among the QS hubs was found to play critical role in the directional turnover of microbiota structure, which in turn, influenced the assembly process. Subsequent QS-interfering experiments accurately predicted and experimentally verified the directional shaping power of the longitudinal QS network in the assembly process. As a result, the QS-interfered OBM exhibited delayed and fragile maturity with prolonged membership of Streptococcus and impeded membership of Prevotella and Fusobacterium.

CONCLUSION: Our results revealed an unprecedented longitudinal QS network during OBM assembly and experimentally verified its power in predicting and manipulating the assembling process. Our work provides a new perspective to uncover underlying mechanism in natural complex microbiota assembling and a theoretical basis for ultimately precisely manipulating human microbiota through intervention in the QS network. Video Abstract.}, } @article {pmid37926832, year = {2023}, author = {Duitama González, C and Vicedomini, R and Lemane, T and Rascovan, N and Richard, H and Chikhi, R}, title = {decOM: similarity-based microbial source tracking of ancient oral samples using k-mer-based methods.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {243}, pmid = {37926832}, issn = {2049-2618}, mesh = {Animals ; Humans ; *Metagenome ; *Metagenomics/methods ; }, abstract = {BACKGROUND: The analysis of ancient oral metagenomes from archaeological human and animal samples is largely confounded by contaminant DNA sequences from modern and environmental sources. Existing methods for Microbial Source Tracking (MST) estimate the proportions of environmental sources, but do not perform well on ancient metagenomes. We developed a novel method called decOM for Microbial Source Tracking and classification of ancient and modern metagenomic samples using k-mer matrices.

RESULTS: We analysed a collection of 360 ancient oral, modern oral, sediment/soil and skin metagenomes, using stratified five-fold cross-validation. decOM estimates the contributions of these source environments in ancient oral metagenomic samples with high accuracy, outperforming two state-of-the-art methods for source tracking, FEAST and mSourceTracker.

CONCLUSIONS: decOM is a high-accuracy microbial source tracking method, suitable for ancient oral metagenomic data sets. The decOM method is generic and could also be adapted for MST of other ancient and modern types of metagenomes. We anticipate that decOM will be a valuable tool for MST of ancient metagenomic studies. Video Abstract.}, } @article {pmid37926481, year = {2023}, author = {Huang, Y and Gao, S and Li, Y}, title = {[The first imported case of visceral leishmaniasis in Shenzhen City].}, journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control}, volume = {35}, number = {4}, pages = {424-426}, doi = {10.16250/j.32.1374.2023105}, pmid = {37926481}, issn = {1005-6661}, support = {SZXK064//Infectious Disease Prevention and Control Project of Key Medical Disciplines in Shenzhen City/ ; }, mesh = {Humans ; Fever ; High-Throughput Nucleotide Sequencing ; *Leishmania donovani/genetics ; *Leishmaniasis, Visceral/diagnosis/drug therapy ; }, abstract = {A patient with fever, chills, and pancytopenia as major clinical manifestations was presented. To investigate the cause, the patient's peripheral blood was collected for pathogen screening using metagenomic next - generation sequencing (mNGS). The DNA sequence of Leishmania donovani was detected, and Leishmania amastigotes were found in bone marrow smears using microscopy. The case was therefore definitively diagnosed as visceral leishmaniasis, and was cured and discharged from hospital following treatment with liposomal amphotericin B for 14 days. This is the first imported case of visceral leishmaniasis since the founding of Shenzhen City in 1979.}, } @article {pmid37926226, year = {2024}, author = {Lin, M and Pan, C and Qian, C and Tang, F and Zhao, S and Guo, J and Zhang, Y and Song, J and Rittmann, BE}, title = {Core taxa, co-occurrence pattern, diversity, and metabolic pathways contributing to robust anaerobic biodegradation of chlorophenol.}, journal = {Environmental research}, volume = {241}, number = {}, pages = {117591}, doi = {10.1016/j.envres.2023.117591}, pmid = {37926226}, issn = {1096-0953}, mesh = {*Chlorophenols ; Anaerobiosis ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Bacteria/metabolism ; Biodegradation, Environmental ; }, abstract = {It is hard to achieve robustness in anaerobic biodegradation of trichlorophenol (TCP). We hypothesized that specific combinations of environmental factors determine phylogenetic diversity and play important roles in the decomposition and stability of TCP-biodegrading bacteria. The anaerobic bioreactor was operated at 35 °C (H condition) or 30 °C (L condition) and mainly fed with TCP (from 28 μM to 180 μM) and organic material. Metagenome sequencing was combined with 16S rRNA gene amplicon sequencing for the microbial community analysis. The results exhibited that the property of robustness occurred in specific conditions. The corresponding co-occurrence and diversity patterns suggest high collectivization, degree and evenness for robust communities. Two types of core functional taxa were recognized: dechlorinators (unclassified Anaerolineae, Thermanaerothrix and Desulfovibrio) and ring-opening members (unclassified Proteobacteria, Methanosarcina, Methanoperedens, and Rubrobacter). The deterministic process of the expansion of niche of syntrophic bacteria at higher temperatures was confirmed. The reductive and hydrolytic dechlorination mechanisms jointly lead to C-Cl bond cleavage. H ultimately adapted to the stress of high TCP loading, with more abundant ring-opening enzyme (EC 3.1.1.45, ∼55%) and hydrolytic dechlorinase (EC 3.8.1.5, 26.5%) genes than L (∼47%, 10.5%). The functional structure (based on KEGG) in H was highly stable despite the high loading of TCP (up to 60 μM), but not in L. Furthermore, an unknown taxon with multiple functions (dechlorinating and ring-opening) was found based on genetic sequencing; its functional contribution of EC 3.8.1.5 in H (26.5%) was higher than that in L (10.5%), and it possessed a new metabolic pathway for biodegradation of halogenated aromatic compounds. This new finding is supplementary to the robust mechanisms underlying organic chlorine biodegradation, which can be used to support the engineering, regulation, and design of synthetic microbiomes.}, } @article {pmid37925989, year = {2023}, author = {Sun, X and Tong, W and Wu, G and Yang, G and Zhou, J and Feng, L}, title = {A collaborative effect of solid-phase denitrification and algae on secondary effluent purification.}, journal = {Journal of environmental management}, volume = {348}, number = {}, pages = {119393}, doi = {10.1016/j.jenvman.2023.119393}, pmid = {37925989}, issn = {1095-8630}, mesh = {*Chlorella vulgaris ; Denitrification ; Nitrates ; Organic Chemicals ; Bacteria ; Nitrogen ; Phosphorus ; Bioreactors/microbiology ; }, abstract = {This study explored the collaborative effect on nutrients removal performance and microbial community in solid-phase denitrification based bacteria-algae symbiosis system. Three biodegradable carriers (apple wood, poplar wood and corncob) and two algae species (Chlorella vulgaris and Chlorella pyrenoidosa) were selected in these bacteria-algae symbiosis systems. Results demonstrated that corncob as the carrier exhibited the highest average removal efficiencies of total nitrogen (83.7%-85.1%) and phosphorus removal (38.1%-49.1%) in comparison with apple wood (65.8%-71.5%, 25.5%-32.7%) and poplar wood (42.5%-49.1%, 14.2%-20.7%), which was mainly attributed to the highest organics availability of corncob. The addition of Chlorella acquired approximately 3%-5% of promotion rates for nitrated removal among three biodegradable carriers, but only corncob reactor acquired significant promotions by 3%-11% for phosphorous removal. Metagenomics sequencing analysis further indicated that Proteobacteria was the largest phylum in all wood reactors (77.1%-93.3%) and corncob reactor without Chlorella (85.8%), while Chlorobi became the most dominant phylum instead of Proteobacteria (20.5%-41.3%) in the corncob with addition of Chlorella vulgaris (54.5%) and Chlorella pyrenoidosa (76.3%). Thus, the higher organics availability stimulated the growth of algae, and promoted the performance of bacteria-algae symbiosis system based biodegradable carriers.}, } @article {pmid37925777, year = {2023}, author = {Guo, Y and Li, Z and Li, L and Li, S and Sun, L and Yang, X and Dai, Y and Gu, J and Yang, L and Liu, X and Lu, B and Han, J and Chang, K and Gu, L and Yin, Y and Sun, S and Jing, C and Chen, H and Liu, M and Xu, H and Liu, R and Ren, Y and Guo, H and Wang, H}, title = {A dual-process of targeted and unbiased Nanopore sequencing enables accurate and rapid diagnosis of lower respiratory infections.}, journal = {EBioMedicine}, volume = {98}, number = {}, pages = {104858}, pmid = {37925777}, issn = {2352-3964}, mesh = {Humans ; *Nanopore Sequencing ; *Respiratory Tract Infections/diagnosis/genetics ; Bacteria/genetics ; Metagenome ; China ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {BACKGROUND: Nanopore metagenomics has been used for infectious disease diagnosis for bacterial pathogens. However, this technology currently lacks comprehensive performance studies in clinical settings for simultaneous detection of bacteria, fungi, and viruses.

METHODS: We developed a dual-process of Nanopore sequencing for one sample, with unbiased metagenomics in Meta process and target enrichment in Panel process (Nanopore Meta-Panel process, NanoMP) and prospectively enrolled 450 respiratory specimens from multiple centers. The filter system of pathogen detection was established with machine learning and receiver operator characteristic (ROC) curve to optimize the detection accuracy based on orthogonal test of 21 species. Antimicrobial resistance (AMR) genes were identified based on the Comprehensive Antibiotic Resistance Database (CARD) and single-nucleotide polymorphism matrix.

FINDINGS: Our approach showed high sensitivity in Meta process, with 82.9%, 88.7%, and 75.0% for bacteria, fungi (except Aspergillus), and Mycobacterium tuberculosis groups, respectively. Moreover, target amplification improved the sensitivity of virus (>80.0% vs. 39.4%) and Aspergillus (81.8% vs. 42.3%) groups in Panel process compared with Meta process. Overall, NanoMP achieved 80.2% sensitivity and 98.8% specificity compared with the composite reference standard, and we were able to accurately detect AMR genes including blaKPC-2, blaOXA-23 and mecA and distinguish their parent organisms in patients with mixed infections.

INTERPRETATION: We combined metagenomic and enriched Nanopore sequencing for one sample in parallel. Our NanoMP approach simultaneously covered bacteria, viruses and fungi in respiratory specimens and demonstrated good diagnostic performance in real clinical settings.

FUNDING: National Key Research and Development Program of China and National Natural Science Foundation of China.}, } @article {pmid37923454, year = {2024}, author = {Han, Z and Luan, X and Feng, H and Deng, Y and Yang, M and Zhang, Y}, title = {Metagenomic insights into microorganisms and antibiotic resistance genes of waste antibiotic fermentation residues along production, storage and treatment processes.}, journal = {Journal of environmental sciences (China)}, volume = {136}, number = {}, pages = {45-55}, doi = {10.1016/j.jes.2022.10.035}, pmid = {37923454}, issn = {1001-0742}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Fermentation ; Drug Resistance, Microbial/genetics ; Bacteria ; }, abstract = {Antibiotic fermentation residue (AFR) is nutrient-rich solid waste generated from fermentative antibiotic production process. It is demonstrated that AFR contains high-concentration of remaining antibiotics, and thus may promote antibiotic resistance development in receiving environment or feeding farmed animals. However, the dominate microorganisms and antibiotic resistance genes (ARGs) in AFRs have not been adequately explored, hampering understanding on the potential antibiotic resistance risk development caused by AFRs. Herein, seven kinds of representative AFRs along their production, storage, and treatment processes were collected, and multiple methods including amplicon sequencing, metagenomic sequencing, and bioinformatic approaches were adopted to explore the biological characteristics of AFRs. As expected, antibiotic fermentation producer was found as the predominant species in raw AFRs, which were collected at the outlet of fermentation tanks. However, except for producer species, more environment-derived species persisted in stored AFRs, which were temporarily stored at a semi-open space. Lactobacillus genus, classified as Firmicutes phylum and Bacilli class, became predominant bacterial taxa in stored AFRs, which might attribute to its tolerance to high concentration of antibiotics. Results from metagenomic sequencing together with assembly and binning approaches showed that these newly-colonizing species (e.g., Lactobacillus genus) tended to carry ARGs conferring resistance to the remaining antibiotic. However, after thermal treatment, remaining antibiotic could be efficiently removed from AFRs, and microorganisms together with DNA could be strongly destroyed. In sum, the main risk from the AFRs was the remaining antibiotic, while environment-derived bacteria which tolerate extreme environment, survived in ARFs with high content antibiotics, and may carry ARGs. Thus, hydrothermal or other harmless treatment technologies are recommended to remove antibiotic content and inactivate bacteria before recycling of AFRs in pharmaceutical industry.}, } @article {pmid37923262, year = {2024}, author = {Fracasso, I and Zaccone, C and Oskolkov, N and Da Ros, L and Dinella, A and Belelli Marchesini, L and Buzzini, P and Sannino, C and Turchetti, B and Cesco, S and Le Roux, G and Tonon, G and Vernesi, C and Mimmo, T and Ventura, M and Borruso, L}, title = {Exploring different methodological approaches to unlock paleobiodiversity in peat profiles using ancient DNA.}, journal = {The Science of the total environment}, volume = {908}, number = {}, pages = {168159}, doi = {10.1016/j.scitotenv.2023.168159}, pmid = {37923262}, issn = {1879-1026}, mesh = {Humans ; *Soil ; *DNA, Ancient ; Ecosystem ; Bacteria/genetics ; Metagenome ; Fungi/genetics ; }, abstract = {Natural and human-induced environmental changes deeply affected terrestrial ecosystems throughout the Holocene. Paleoenvironmental reconstructions provide information about the past and allow us to predict/model future scenarios. Among potential records, peat bogs are widely used because they present a precise stratigraphy and act as natural archives of highly diverse organic remains. Over the decades, several techniques have been developed to identify debris occurring in peat, including their morphological description. However, this is strongly constrained by the researcher's ability to distinguish residues at the species level, which typically requires many years of experience. In addition, potential contamination hampers using these techniques to obtain information from organisms such as fungi or bacteria. Environmental DNA metabarcoding and shotgun metagenome sequencing could represent a solution to detect specific groups of organisms without any a priori knowledge of their characteristics and/or to identify organisms that have rarely been considered in previous investigations. Moreover, shotgun metagenomics may allow the identification of bacteria and fungi (including both yeast and filamentous life forms), ensuring discrimination between ancient and modern organisms through the study of deamination/damage patterns. In the present review, we aim to i) present the state-of-the-art methodologies in paleoecological and paleoclimatic studies focusing on peat core analyses, proposing alternative approaches to the classical morphological identification of plant residues, and ii) suggest biomolecular approaches that will allow the use of proxies such as invertebrates, fungi, and bacteria, which are rarely employed in paleoenvironmental reconstructions.}, } @article {pmid37923227, year = {2024}, author = {Lu, J and Dong, L and Guo, Z and Hu, Z and Dai, P and Zhang, J and Wu, H}, title = {Highly efficient nitrate removal in sulfur-based constructed wetlands: Microbial mechanisms and environmental risks.}, journal = {Bioresource technology}, volume = {391}, number = {Pt A}, pages = {129970}, doi = {10.1016/j.biortech.2023.129970}, pmid = {37923227}, issn = {1873-2976}, mesh = {Humans ; *Nitrates ; Wetlands ; Nitrogen ; Sulfur ; *Groundwater ; Denitrification ; Waste Disposal, Fluid ; }, abstract = {Nitrate is widely distributed in groundwater, posing an increasing threat to both water resources and human health. In this study, the treatment performance, removal mechanisms and environmental risks of sulfur-based constructed wetlands (CWs) for purifying nitrate-contaminated groundwater were investigated. Results showed that sulfur-based CWs could achieve the highest nitrate removal (95%). However, sulfate was largely produced as a by-product in sulfur-based CWs, which declined the nitrogen and phosphorus assimilation by plants. Metagenomic analysis indicated that autotrophs denitrifiers (e.g., Thiobacillus) were enriched, and the abundance of nitrate removal genes was enhanced in sulfur-based CWs. Additionally, sulfur cycle was formed in sulfur-based CWs, which explained the highest nitrate removal reasonably. This study provides comprehensive insights into the nitrate removal mechanisms in sulfur-based CWs and the associated environmental risks in purifying the polluted groundwater.}, } @article {pmid37923065, year = {2024}, author = {Carrascosa-Carrillo, JM and Aterido, A and Li, T and Guillén, Y and Martinez, S and Marsal, S and Julià, A}, title = {Toward Precision Medicine in Atopic Dermatitis Using Molecular-Based Approaches.}, journal = {Actas dermo-sifiliograficas}, volume = {115}, number = {1}, pages = {T66-T75}, doi = {10.1016/j.ad.2023.10.032}, pmid = {37923065}, issn = {1578-2190}, mesh = {Child ; Humans ; *Dermatitis, Atopic/genetics/therapy ; Precision Medicine ; Skin/pathology ; T-Lymphocytes ; Biomarkers/metabolism ; }, abstract = {Atopic dermatitis is the most common chronic inflammatory skin disorder, affecting up to 20% of children and 10% of adults in developed countries. The pathophysiology of atopic dermatitis is complex and involves a strong genetic predisposition and T-cell driven inflammation. Although our understanding of the pathology and drivers of this disease has improved in recent years, there are still knowledge gaps in the immune pathways involved. Therefore, advances in new omics technologies in atopic dermatitis will play a key role in understanding the pathogenesis of this burden disease and could develop preventive strategies and personalized treatment strategies. In this review, we discuss the latest developments in genetics, transcriptomics, epigenomics, proteomics, and metagenomics and understand how integrating multiple omics datasets will identify potential biomarkers and uncover nets of associations between several molecular levels.}, } @article {pmid37922638, year = {2023}, author = {Zhang, Y and Bao, J and Du, J and Mao, Q and Cheng, B}, title = {Comprehensive metagenomic and enzyme activity analysis reveals the inhibitory effects and potential toxic mechanism of tetracycline on denitrification in groundwater.}, journal = {Water research}, volume = {247}, number = {}, pages = {120803}, doi = {10.1016/j.watres.2023.120803}, pmid = {37922638}, issn = {1879-2448}, mesh = {*Nitrites ; Denitrification ; Tetracycline/pharmacology ; Anti-Bacterial Agents/pharmacology ; Nitrates/metabolism ; *Groundwater/chemistry ; }, abstract = {The widespread use of tetracycline (TC) inevitably leads to its increasing emission into groundwater. However, the potential risks of TC to denitrification in groundwater remain unclear. In this study, the effects of TC on denitrification in groundwater were systematically investigated at both the protein and gene levels from the electron behavior aspect for the first time. The results showed that increasing TC from 0 to 10 µg·L[-1] decreased the nitrate removal rate from 0.41 to 0.26 mg·L[-1]·h[-1] while enhancing the residual nitrite concentration from 0.52 mg·L[-1] to 50.60 mg·L[-1] at the end of the experiment. From a macroscopic view, 10 µg·L[-1] TC significantly inhibited microbial growth and altered microbial community structure and function in groundwater, which induced the degeneration of denitrification. From the electron behavior aspect (the electron production, electron transport and electron consumption processes), 10 µg·L[-1] TC decreased the concentration of electron donors (nicotinamide adenine dinucleotide, NADH), electron transport system activity, and denitrifying enzyme activities at the protein level. At the gene level, 10 µg·L[-1] TC restricted the replication of genes related to carbon metabolism, the electron transport system and denitrification. Moreover, discrepant inhibitory effects of TC on individual denitrification steps, which led to the accumulation of nitrite, were observed in this study. These results provide the information that is necessary for evaluating the potential environmental risk of antibiotics on groundwater denitrification and bring more attention to their effects on geochemical nitrogen cycles.}, } @article {pmid37925010, year = {2024}, author = {Liu, C and Shan, X and Chen, J and Zhang, Y and Wang, J and Chen, H}, title = {Fate, risk and sources of antibiotic resistome and its attenuation dynamics in the river water-sediment system: Field and microcosm study.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {340}, number = {Pt 2}, pages = {122853}, doi = {10.1016/j.envpol.2023.122853}, pmid = {37925010}, issn = {1873-6424}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Fresh Water ; Rivers ; Water ; Machine Learning ; }, abstract = {Antibiotic resistance genes (ARGs) in rivers have received widespread attentions. Deciphering the fate and spread mechanisms of ARGs in river system can contribute to the design of effective strategies for reducing resistome risk in the environment. Although some studies have reported the prevalence and distribution of ARGs in rivers worldwide, few have systematically explored their fates, sources and risks in river water-sediment system. Also, the role of natural sunlight on the attenuation and fate of ARGs in river remains to be demonstrated. To fill the gaps, field investigation and microcosm experiment have been conducted in this study to reveal the fate, risk, source-sink relationship and attenuation dynamics of ARGs in an urban river water-sediment system, by utilizing high-throughput sequencing-based metagenomic assembly analysis and machine-learning-based source tracking tool. In all, 527 unique ARGs belonging to 29 antimicrobial classes were identified in the river. Relatively, the level of ARGs in the sediments were significantly higher (p < 0.05) than that in the waters. Variance partitioning analysis indicated the biotic and abiotic factors co-governed the riverine resistome, totally explaining 76% and 83% variations of ARGs in the waters and sediments, respectively. Microcosm experiment under natural light and dark condition showed that light induced the decay of ARGs in the waters and might promote their transfers from waters to sediments, which were also confirmed by the attenuation dynamics of bacteria in the experimental water-sediment system. Notably, the co-occurrences of ARGs with MGEs and VFs on the same contigs suggested resistome risk in the river, and relatively, the risk scores in the sediments were significantly higher (p < 0.05) than those in the waters. Source apportionment with metagenomic resistome signatures showed the Wenyu River was the most dominant contributor of ARGs in the downstream, with average contributions of 44.5% and 40.8% in the waters and sediments, respectively.}, } @article {pmid37924576, year = {2024}, author = {Qu, Z and Wu, S and Zheng, Y and Bing, Y and Liu, X and Li, S and Li, W and Zou, X}, title = {Fecal metabolomics combined with metagenomics sequencing to analyze the antidepressant mechanism of Yueju Wan.}, journal = {Journal of pharmaceutical and biomedical analysis}, volume = {238}, number = {}, pages = {115807}, doi = {10.1016/j.jpba.2023.115807}, pmid = {37924576}, issn = {1873-264X}, mesh = {Rats ; Animals ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Metabolomics/methods ; Antidepressive Agents/pharmacology/therapeutic use/analysis ; Feces/chemistry ; Medicine, Chinese Traditional ; Metabolome ; Depression/drug therapy/metabolism ; }, abstract = {BACKGROUND: Yueju Wan (YJW), defined in Danxi's Mastery of Medicine, has Qi-regulating and Qi-promoting effects. YJW has frequently been applied in the clinic for the treatment of depression. Substantial evidence has shown that depression is related to metabolic abnormalities of the gut microbiota, and traditional Chinese medicine (TCM) can treat depression by adjusting gut microbiota metabolism. The antidepressant effect of YJW is well established, but thus far, whether its mechanism of action is achieved by regulating the intestinal flora has not been elucidated.

METHODS: In this study, chronic unpredictable mild stress (CUMS) along with isolated feeding created a rat depression model, and YJW was administered for intervention. Rats were put through behavioral tests to determine their level of depression, and ELISA was utilized for measuring the level of monoamine neurotransmitters (MNTs) in the hippocampus. Metagenomic gene sequencing analysis was used to study the effect of depression on the intestinal flora in rats and the regulatory mechanism of YJW on the intestinal flora. Furthermore, ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q/TOF-MS) was utilized for fecal metabolomics studies to further reveal the antidepressant mechanism of YJW. The antidepressant mechanism of YJW was explored and further verified by Western blot analysis.

RESULTS: Different doses of YJW improved the depressive state of rats and raised the levels of MNTs in the hippocampus. The results of metagenomic sequencing indicated that the YJW recovered the structure and diversity of the intestinal flora in depressed rats. Metabolomics revealed sustained changes in 21 metabolites after the treatment of YJW, suggesting that YJW can play an antidepressant role by improving abnormal metabolic pathways. The results of correlation analysis suggested that YJW might mediate Eubacterium, Oscillibacter, Roseburia, Romboutsia and Bacterium to regulate purine metabolism, tryptophan metabolism, primary bile acid biosynthesis, and glutamate metabolism and exert antidepressant effects. Western blot analysis showed that YJW reduced the content of IL-1β in the hippocampus, inhibited the activation of the NLRP3 inflammasome in the hippocampus of rats, and increased the content of ZO-1 in the colon of rats.

CONCLUSION: YJW can alleviate depressive symptoms in depressed rats, and its mechanism is connected to improving intestinal flora and regulating body metabolism.}, } @article {pmid37924150, year = {2023}, author = {Li, Y and Mao, K and Zang, Y and Lu, G and Qiu, Q and Ouyang, K and Zhao, X and Song, X and Xu, L and Liang, H and Qu, M}, title = {Revealing the developmental characterization of rumen microbiome and its host in newly received cattle during receiving period contributes to formulating precise nutritional strategies.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {238}, pmid = {37924150}, issn = {2049-2618}, mesh = {Cattle ; Animals ; *Diet/veterinary ; Rumen/microbiology ; *Microbiota ; Bacteria/genetics/metabolism ; Archaea/metabolism ; Inflammation/metabolism ; Methane/metabolism ; Ornithine/metabolism ; Polyamines/metabolism ; Animal Feed/analysis ; Fermentation ; }, abstract = {BACKGROUND: Minimizing mortality losses due to multiple stress and obtaining maximum performance are the production goals for newly received cattle. In recent years, vaccination and metaphylaxis treatment significantly decreased the mortality rate of newly received cattle, while the growth block induced by treatment is still obvious. Assessment of blood metabolites and behavior monitoring offer potential for early identification of morbid animals. Moreover, the ruminal microorganisms' homeostasis is a guarantee of beef steers' growth and health. The most critical period for newly received cattle is the first-month post-transport. Therefore, analyzing rumen metagenomics, rumen metabolomics, host metabolomics, and their interaction during receiving period (1 day before transport and at days 1/4, 16, and 30 after transport) is key to revealing the mechanism of growth retardation, and then to formulating management and nutritional practices for newly received cattle.

RESULTS: The levels of serum hormones (COR and ACTH), and pro-inflammatory factors (IL-1β, TNF-α, and IL-6) were highest at day 16, and lowest at day 30 after arrival. Meanwhile, the antioxidant capacity (SOD, GSH-Px, and T-AOC) was significantly decreased at day 16 and increased at day 30 after arrival. Metagenomics analysis revealed that rumen microbes, bacteria, archaea, and eukaryota had different trends among the four different time points. At day 16 post-transport, cattle had a higher abundance of ruminal bacteria and archaea than those before transport, but the eukaryote abundance was highest at day 30 post-transport. Before transport, most bacteria were mainly involved in polysaccharides digestion. At day 4 post-transport, the most significantly enriched KEGG pathways were nucleotide metabolism (pyrimidine metabolism and purine metabolism). At day 16 post-transport, the energy metabolism (glycolysis/gluconeogenesis, pyruvate metabolism) and ruminal contents of MCP and VFAs were significantly increased, but at the same time, energy loss induced by methane yields (Methanobrevibacter) together with pathogenic bacteria (Saccharopolyspora rectivirgula) were also significantly increased. At this time, the most upregulated ruminal L-ornithine produces more catabolite polyamines, which cause oxidative stress to rumen microbes and their host; the most downregulated ruminal 2',3'-cAMP provided favorable growth conditions for pathogenic bacteria, and the downregulated ruminal vitamin B6 metabolism and serum PC/LysoPC disrupt immune function and inflammation reaction. At day 30 post-transport, the ruminal L-ornithine and its catabolites (mainly spermidine and 1,3-propanediamine) were decreased, and the serum PC/LysoPC and 2',3'-cNMPs pools were increased. This is also consistent with the changes in redox, inflammation, and immune status of the host.

CONCLUSIONS: This study provides new ideas for regulating the health and performance of newly received cattle during the receiving period. The key point is to manage the newly received cattle about day 16 post-transport, specifically to inhibit the production of methane and polyamines, and the reproduction of harmful bacteria in the rumen, therefore improving the immunity and performance of newly received cattle. Video Abstract.}, } @article {pmid37924056, year = {2023}, author = {Sun, J and Chen, J and Xie, Q and Sun, M and Zhang, W and Wang, H and Liu, N and Wang, Q and Wang, M}, title = {Sodium butyrate alleviates R97-116 peptide-induced myasthenia gravis in mice by improving the gut microbiota and modulating immune response.}, journal = {Journal of inflammation (London, England)}, volume = {20}, number = {1}, pages = {37}, pmid = {37924056}, issn = {1476-9255}, abstract = {Fermented butyrate exhibits an anti-inflammatory response to maintain immune homeostasis within the gut. However, the effect and underlying mechanism of butyrate on myasthenia gravis (MG) remain unclear. The changes in the gut microbiota and fecal contents of SCFAs in MG patients were examined. R97-116 peptide was used to induce the experimental autoimmune myasthenia gravis (EAMG) mice and sodium butyrate (NaB) was gavaged to the EAMG mice. Gut microbiota, the frequency of Th1, Th17, Treg, Tfh, and B cells, the levels of IFN-γ, IL-17 A, IL-10, IL-21, and anti-R97-116 IgG, RNA-seq of total B cells in the spleen were explored by metagenomics, flow cytometry, ELISA, and transcriptomics. A significant reduction in SCFA-producing bacteria including Butyricimonas synergistica and functional modules including butyrate synthesis/production II was observed in MG patients and fecal SCFAs detection confirmed the increase. The EAMG mice were successfully constructed and NaB supplementation has changed the composition and function of the gut microbiota. The numbers of Th1, Th17, Tfh, and B cells were significantly increased while that of Treg cells was obviously decreased in EAMG mice compared with controls. Interestingly, NaB treatment has reduced the amounts of Th17, Tfh, and B cells but increased that of Treg cells. Accordingly, the levels of IL-17 A, IL-21, and IgG were increased while IL-10 was decreased in EAMG mice. However, NaB treatment reduced IL-17 A and IL-21 but increased that of IL-10. RNA-seq of B cells has revealed 4577 deferentially expressed genes (DEGs), in which 1218 DEGs were up-regulated while 3359 DEGs were down-regulated in NaB-treated EAMG mice. GO enrichment and KEGG pathway analysis unveiled that the function of these DEGs was mainly focused on immunoglobulin production, mitochondrial respiratory chain complex, ribosome, oxidative phosphorylation, and CNS diseases including amyotrophic lateral sclerosis. We have found that butyrate was significantly reduced in MG patients and NaB gavage could evidently improve MG symptoms in EAMG mice by changing the gut microbiota, regulating the immune response, and altering the gene expression and function of B cells, suggesting NaB might be a potential immunomodulatory supplement for MG drugs.}, } @article {pmid37923779, year = {2023}, author = {Flores, GAM and Lopez, RP and Cerrudo, CS and Perotti, MA and Consolo, VF and Berón, CM}, title = {Wolbachia dominance influences the Culex quinquefasciatus microbiota.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {18980}, pmid = {37923779}, issn = {2045-2322}, mesh = {Animals ; *Aedes/genetics ; Bacteria/genetics ; *Culex/genetics ; *Microbiota ; Mosquito Vectors/microbiology ; RNA, Ribosomal, 16S/genetics ; *Wolbachia/genetics ; }, abstract = {Microorganisms present in mosquitoes and their interactions are key factors affecting insect development. Among them, Wolbachia is closely associated with the host and affects several fitness parameters. In this study, the bacterial and fungal microbiota from two laboratory Culex quinquefasciatus isolines (wild type and tetracycline-cured) were characterized by metagenome amplicon sequencing of the ITS2 and 16S rRNA genes at different developmental stages and feeding conditions. We identified 572 bacterial and 61 fungal OTUs. Both isolines presented variable bacterial communities and different trends in the distribution of diversity among the groups. The lowest bacterial richness was detected in sugar-fed adults of the cured isoline, whereas fungal richness was highly reduced in blood-fed mosquitoes. Beta diversity analysis indicated that isolines are an important factor in the differentiation of mosquito bacterial communities. Considering composition, Penicillium was the dominant fungal genus, whereas Wolbachia dominance was inversely related to that of Enterobacteria (mainly Thorsellia and Serratia). This study provides a more complete overview of the mosquito microbiome, emphasizing specific highly abundant components that should be considered in microorganism manipulation approaches to control vector-borne diseases.}, } @article {pmid37921501, year = {2023}, author = {Wang, H and Bi, H and Yang, M and Wang, X and Song, C and Yang, W and Wang, Y and Xie, D and Li, H and Zhou, Z}, title = {Intestinal flora altered and correlated with interleukin-2/4 in patients with primary immune thrombocytopenia.}, journal = {Hematology (Amsterdam, Netherlands)}, volume = {28}, number = {1}, pages = {2277501}, doi = {10.1080/16078454.2023.2277501}, pmid = {37921501}, issn = {1607-8454}, mesh = {Humans ; *Gastrointestinal Microbiome ; Interleukin-2 ; Interleukin-4 ; *Purpura, Thrombocytopenic, Idiopathic ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Little is known about the changes and mechanisms of intestinal flora in primary immune thrombocytopenia (ITP) patients.

AIM: To explore the structural and functional differences of intestinal flora between ITP patients and healthy controls, and clarify the correlation between intestinal flora and Th1/Th2 imbalance.

METHODS: Feces from ITP patients and healthy controls were studied by 16S rRNA and metagenomic techniques at phylum, genus, species or functional levels. Blood samples were collected for the detection of interleukin -2 (IL-2) and IL-4 concentrations.

RESULTS: The following changes in ITP patients were found: a decrease of Bacteroidetes phylum, an increase of Proteobacteria phylum and alterations of ten genera and 1045 species. IL-2 and IL-4 were significantly correlated with six and five genera, respectively. Species of C. freundii, C. rodentium, and C. youngae were negatively correlated with bleeding scores, and S. infantis was positively related to platelet counts. Functionally, the intestinal flora of ITP patients changed mainly in terms of motility, chemotaxis, membrane transport, and metabolism.

CONCLUSION: The mechanism underlying functional and structural changes of intestinal flora in ITP patients may be related to inflammation and immunity, providing possibilities of probiotics or fecal transplants for ITP.}, } @article {pmid37921472, year = {2023}, author = {Hribovšek, P and Olesin Denny, E and Dahle, H and Mall, A and Øfstegaard Viflot, T and Boonnawa, C and Reeves, EP and Steen, IH and Stokke, R}, title = {Putative novel hydrogen- and iron-oxidizing sheath-producing Zetaproteobacteria thrive at the Fåvne deep-sea hydrothermal vent field.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0054323}, pmid = {37921472}, issn = {2379-5077}, mesh = {*Iron ; Seawater/microbiology ; Hydrogen ; *Hydrothermal Vents/microbiology ; Proteobacteria/genetics ; Oxidation-Reduction ; Ferric Compounds ; }, abstract = {Knowledge on microbial iron oxidation is important for understanding the cycling of iron, carbon, nitrogen, nutrients, and metals. The current study yields important insights into the niche sharing, diversification, and Fe(III) oxyhydroxide morphology of Ghiorsea, an iron- and hydrogen-oxidizing Zetaproteobacteria representative belonging to Zetaproteobacteria operational taxonomic unit 9. The study proposes that Ghiorsea exhibits a more extensive morphology of Fe(III) oxyhydroxide than previously observed. Overall, the results increase our knowledge on potential drivers of Zetaproteobacteria diversity in iron microbial mats and can eventually be used to develop strategies for the cultivation of sheath-forming Zetaproteobacteria.}, } @article {pmid37920597, year = {2023}, author = {Li, H and Wei, L and Li, F}, title = {Diagnosis of mycobacterium avium complex infection utilizing metagenomics next-generation sequencing: a case report.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1247034}, pmid = {37920597}, issn = {2296-858X}, abstract = {Mycobacterium avium-intracellulare complex (MAC) is a type of nontuberculous mycobacteria (NTM) and is associated with underlying pulmonary diseases, such as chronic obstructive pulmonary disease, bronchiectasis, chronic aspiration or recurrent pneumonia, inactive or active tuberculosis, pneumoconiosis, and bronchogenic carcinoma. The risk factors for NTM-PD include host, drug, and environmental factors. In this report, we present the case of a 61-year-old man who developed bilateral lung nodules and was experiencing severe hemoptysis. The repeat acid-fast bacilli test performed on both sputum and bronchoalveolar lavage fluid (BALF) samples showed a negative result, as did the GeneXpert test. We employed metagenomic next-generation sequencing (mNGS) to analyze the lung nodule and BALF samples collected from the patient. Both samples tested positive for MAC within 3 days. In addition, traditional MAC culture, conducted for 2 months, confirmed the growth of MAC in the patient's BALF. Then, the patient was treated accordingly. Following treatment, a high-resolution chest computed tomography scan revealed a significant reduction in lung nodules of the patient after 2 months. These results indicate that MAC-associated lung nodules were responsible for the patient's symptoms, emphasizing the need for vigilance in diagnosing MAC infection in the patient without predisposing conditions. Furthermore, these results highlight the potential utility of mNGS as a promising rapid diagnostic tool for MAC infection and its potential role in the diagnosis of NTM disease.}, } @article {pmid37920490, year = {2023}, author = {Nevalainen, T and Autio, A and Hurme, M}, title = {Human endogenous retroviruses of the HERV-K (HML-2) family are expressed in the brain of healthy individuals and modify the composition of the brain-infiltrating immune cells.}, journal = {Heliyon}, volume = {9}, number = {11}, pages = {e21283}, pmid = {37920490}, issn = {2405-8440}, abstract = {Human endogenous retroviruses (HERVs) are remnants of ancient retroviral infections in the human genome. RNA expression of individual HERVs has frequently been observed in various pathologic conditions, but some activity can also be seen in healthy individuals, e.g. in the blood. To quantitate the basal expression levels of HERVs in the brain, we now used high-throughput sequencing-based metagenomic analysis to characterize the expression profiles of the HERV-K (HML-2) family proviruses in different brain regions of healthy brain tissue. To this end, RNA-seq data from the Genotype-Tissue Expression (GTEx) project was used. The GTEx project is a public resource to study tissue-specific gene expression and regulation, consisting of a large selection of sequenced samples from different tissues. The GTEx data used in this study consisted of 378 samples taken from 13 brain regions from 55 individuals. The data demonstrated that out of 99 intact proviruses in the family 58 were expressed, but the expression profiles were highly divergent and there were no significant differences in the expression profiles between the various anatomic regions of the brain. It is known that the brain contains a variety of infiltrating immune cells, which are probably of great importance both in the normal defense mechanisms as well as in the various pathogenic processes. Digital cytometry (CIBERSORTx) was used to quantify the proportions of the infiltrating immune cells in the same brain samples. Six most abundant (>5 % of the total population) cell types were observed to be CD4 memory resting T cells, M0 macrophages, plasma cells, CD8 T cells, CD4 memory activated T cells, and monocytes. Analysis of the correlations between the individual HERVs and infiltrating cell types indicated that a cluster of 6 HERVs had a notable correlation signature between T cell type infiltrating cell proportions and HERV RNA expression intensity. The correlations between inflammatory type infiltrating cells were negative or weak. Taken together, these data indicate that the expression of HERVs is associated with a T cell type immunity.}, } @article {pmid37919871, year = {2023}, author = {Santana, CEM and Barros, GP and Canuto, NS and Dos Santos, TE and Bharagava, RN and Liu, J and Ferreira, LFR and Souza, RL}, title = {Thermosensitive polymer-assisted extraction and purification of fungal laccase from citrus pulp wash effluent.}, journal = {Journal of the science of food and agriculture}, volume = {}, number = {}, pages = {}, doi = {10.1002/jsfa.13094}, pmid = {37919871}, issn = {1097-0010}, support = {//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {BACKGROUND: This study explores the use of liquid-liquid extraction with thermosensitive polymers for producing laccase (Lac) from Pleurotus sajor-caju. This process leverages liquid waste from the citrus industry, specifically pulp wash. The research delves into extractive fermentation and thermoseparation, both processes being facilitated by a polymer exhibiting a lower critical solution temperature transition.

RESULTS: Key factors considered include the choice of polymer, its concentration, pH, separation temperature, and the behavior of the polymer-rich phase post-extractive fermentation concerning the lower critical solution temperature. Notably, under conditions of 45% by weight of Pluronic L-61 and pH 5.0 at 25 °C, the Lac resulted in an enhancement in the purification factor of 28.4-fold, compared with the Lac obtained directly from the fermentation process on the eighth day. There was an 83.6% recovery of the Lac enzyme in the bottom phase of the system. Additionally, the unique properties of Pluronic L-61, which can induce phase separation and also allow for thermoseparation, led to a secondary fraction (aqueous solution) of Lac with purification factor of 2.1 ± 0.1-fold (at 32 ± 0.9 °C and 30 ± 0.3 min without stirring) from the polymeric phase (top phase). Fourier-transform infrared analysis validated the separation data, particularly highlighting the α-helix content in the amide I region (1600-1700 cm[-1]).

CONCLUSION: In summary, the insights from this study pave the way for broader industrial applications of these techniques, underscoring benefits like streamlined process integration, heightened selectivity, and superior separation efficacy. © 2023 Society of Chemical Industry.}, } @article {pmid37919749, year = {2023}, author = {Yi, XZ and Yang, JH and Huang, Y and Han, XR and Li, HM and Cen, LJ and Lin, ZH and Pan, CX and Wang, Z and Guan, WJ}, title = {Differential airway resistome and its correlations with clinical characteristics in Haemophilus- or Pseudomonas-predominant microbial subtypes of bronchiectasis.}, journal = {Respiratory research}, volume = {24}, number = {1}, pages = {264}, pmid = {37919749}, issn = {1465-993X}, support = {(2019A1515011395) (to Prof. Wang)//the Science and Technology Foundation of Guangdong Province/ ; No. 82222001//National Science Foundation - Outstanding Youth Fund/ ; No. ZNSA-2020013//Zhongnanshan Medical Foundation of Guangdong Province/ ; No. 2023B03J0407 and No. 202102010372//Guangzhou Science and Technology Plans/ ; (grant number not available) (to Prof. Guan)//Plan on enhancing scientific research in Guangzhou Medical University/ ; 31970112, 32170109, 41907211//National Natural Science Foundation of China/ ; }, mesh = {Adult ; Humans ; *Haemophilus ; Pseudomonas ; Longitudinal Studies ; *Bronchiectasis/diagnosis/genetics ; Respiratory System ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {The prevalence and clinical correlates of antibiotic resistance genes (ARGs) in bronchiectasis are not entirely clear. We aimed to profile the ARGs in sputum from adults with bronchiectasis, and explore the association with airway microbiome and disease severity and subtypes. In this longitudinal study, we prospectively collected 118 sputum samples from stable and exacerbation visits of 82 bronchiectasis patients and 19 healthy subjects. We profiled ARGs with shotgun metagenomic sequencing, and linked these to sputum microbiome and clinical characteristics, followed by validation in an international cohort. We compared ARG profiles in bronchiectasis according to disease severity, blood and sputum inflammatory subtypes. Unsupervised clustering revealed a Pseudomonas predominant subgroup (n = 16), Haemophilus predominant subgroup (n = 48), and balanced microbiome subgroup (N = 54). ARGs of multi-drug resistance were over-dominant in the Pseudomonas-predominant subgroup, while ARGs of beta-lactam resistance were most abundant in the Haemophilus-predominant subgroup. Pseudomonas-predominant subgroup yielded the highest ARG diversity and total abundance, while Haemophilus-predominant subgroup and balanced microbiota subgroup were lowest in ARG diversity and total abundance. PBP-1A, ksgA and emrB (multidrug) were most significantly enriched in Haemophilus-predominant subtype. ARGs generally correlated positively with Bronchiectasis Severity Index, fluoroquinolone use, and modified Reiff score. 68.6% of the ARG-clinical correlations could be validated in an independent international cohort. In conclusion, ARGs are differentially associated with the dominant microbiome and clinical characteristics in bronchiectasis.}, } @article {pmid37919496, year = {2023}, author = {Sahasa, RGK and Dhevagi, P and Poornima, R and Ramya, A and Karthikeyan, S and Priyatharshini, S}, title = {Dose-dependent toxicity of polyethylene microplastics (PE-MPs) on physiological and biochemical response of blackgram and its associated rhizospheric soil properties.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {56}, pages = {119168-119186}, pmid = {37919496}, issn = {1614-7499}, mesh = {*Polyethylene ; Microplastics ; Plastics ; *Vigna ; Chlorophyll A ; Ecosystem ; Carbon ; Soil ; }, abstract = {Microplastic contamination in terrestrial ecosystem is emerging as a global threat due to rapid production of plastic waste and its mismanagement. It affects all living organisms including plants. Hence, the current study aims at understanding the effect of polyethylene microplastics (PE-MPs) at different concentrations (0, 0.25, 0.50, 0.75, and 1.00% w/w) on the plant growth and yield attributes. With blackgram as a test crop, results revealed that a maximum reduction in physiological traits like photosynthetic rate; chlorophyll a, b; and total chlorophyll by 5, 14, 10, and 13% at flowering stage; and an increase in biochemical traits like ascorbic acid, malondialdehyde, proline, superoxide dismutase, and catalase by 11, 29.7, 16, 22, and 30% during vegetative stage was observed with 1% PE-MP application. Moreover, a reduction in growth and yield attributes was also observed with increasing concentration of microplastics. Additionally, application of 1% PE-MPs decreased the soil bulk density, available phosphorus, and potassium, whereas the EC, organic carbon, microbial biomass carbon, NO3-N, and NH4-N significantly increased. Moreover, the presence of PE-MPs in soil also had a significant influence on the soil enzyme activities. Metagenomic analysis (16 s) reveals that at genus level, Bacillus (19%) was predominant in control, while in 1% PE-MPs, Rubrobacter (28%) genus was dominant. Microvirga was found exclusively in T5, while the relative abundance of Gemmatimonas declined from T1 to T5. This study thus confirms that microplastics exert a dose-dependent effect on soil and plant characteristics.}, } @article {pmid37919437, year = {2023}, author = {Zahavi, L and Lavon, A and Reicher, L and Shoer, S and Godneva, A and Leviatan, S and Rein, M and Weissbrod, O and Weinberger, A and Segal, E}, title = {Bacterial SNPs in the human gut microbiome associate with host BMI.}, journal = {Nature medicine}, volume = {29}, number = {11}, pages = {2785-2792}, pmid = {37919437}, issn = {1546-170X}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Body Mass Index ; Polymorphism, Single Nucleotide/genetics ; Genome-Wide Association Study ; *Microbiota ; Bacteria/genetics ; }, abstract = {Genome-wide association studies (GWASs) have provided numerous associations between human single-nucleotide polymorphisms (SNPs) and health traits. Likewise, metagenome-wide association studies (MWASs) between bacterial SNPs and human traits can suggest mechanistic links, but very few such studies have been done thus far. In this study, we devised an MWAS framework to detect SNPs and associate them with host phenotypes systematically. We recruited and obtained gut metagenomic samples from a cohort of 7,190 healthy individuals and discovered 1,358 statistically significant associations between a bacterial SNP and host body mass index (BMI), from which we distilled 40 independent associations. Most of these associations were unexplained by diet, medications or physical exercise, and 17 replicated in a geographically independent cohort. We uncovered BMI-associated SNPs in 27 bacterial species, and 12 of them showed no association by standard relative abundance analysis. We revealed a BMI association of an SNP in a potentially inflammatory pathway of Bilophila wadsworthia as well as of a group of SNPs in a region coding for energy metabolism functions in a Faecalibacterium prausnitzii genome. Our results demonstrate the importance of considering nucleotide-level diversity in microbiome studies and pave the way toward improved understanding of interpersonal microbiome differences and their potential health implications.}, } @article {pmid37919157, year = {2023}, author = {Meng, Q and Zhou, Q and Shi, S and Xiao, J and Ma, Q and Yu, J and Chen, J and Kang, Y}, title = {VTwins: inferring causative microbial features from metagenomic data of limited samples.}, journal = {Science bulletin}, volume = {68}, number = {22}, pages = {2806-2816}, doi = {10.1016/j.scib.2023.10.024}, pmid = {37919157}, issn = {2095-9281}, support = {31970568 AND 32371537//National Natural Science Foundation of China/ ; 2018ZX10712001-018-002 AND 2021YFC2301003)//National Science and Technology Major Project of China/ ; }, mesh = {Humans ; *Algorithms ; *Metagenome/genetics ; Software ; Metagenomics/methods ; }, abstract = {It is difficult to infer causality from high-dimension metagenomic data due to interference from numerous confounders. By imitating the twin studies in genetic research, we develop a straightforward method-virtual twins (VTwins)-to eliminate the confounder effects by transforming the original cohort into a paired cohort of "Twin" samples with distinct phenotypes but matched taxonomic profiles. The results show that VTwins outperforms the conventional approach in the sensitivity of identifying causative features and only requires a 10-fold reduced sample size for recalling disease-associated microbes or pathways, as tested by simulated and empirical data. Benchmark test with other 16 kinds of software further validates the power and applicability of VTwins for handling high-dimension compositional datasets and mining causalities in metagenomic research. In conclusion, VTwins is straightforward and effective in handling high-diversity, high-dimension compositional data, promising applications in mining causalities for metagenomic and potentially other omics data. VTwins is open access and available at https://github.com/mengqingren/VTwins.}, } @article {pmid37919016, year = {2024}, author = {Kothe, CI and Rasmussen, JA and Mak, SST and Gilbert, MTP and Evans, J}, title = {Exploring the microbial diversity of novel misos with metagenomics.}, journal = {Food microbiology}, volume = {117}, number = {}, pages = {104372}, doi = {10.1016/j.fm.2023.104372}, pmid = {37919016}, issn = {1095-9998}, mesh = {*Fabaceae ; Glycine max ; *Soy Foods ; *Fermented Foods ; Metagenomics ; Flavoring Agents/analysis ; Fermentation ; }, abstract = {Interest in fermented foods, especially plant-based ones, has increased considerably in the last decade. Miso-a Japanese paste traditionally fermented with soybeans, salt, and kōji (Aspergillus oryzae grown on grains or beans)-has gained attention among chefs for its rich flavour and versatility. Some chefs have even been experimenting with making novel misos with untraditional substrates to create new flavours. Such novel fermented foods also offer new scientific opportunities. To explore the microbial diversity of these new traditional foods, we sampled six misos made by the team at a leading restaurant called Noma in Copenhagen (Denmark), using yellow peas (including a nixtamalised treatment), lupin seeds, Swedish Vreta peas, grey peas, and Gotland lentils as substrates. All misos were made with the same recipe and fermented for 3 months at 28 °C. Samples were collected at the end of fermentation for subsequent shotgun metagenomic sequencing and a genome-resolved metagenomic analysis. The taxonomic profile of the samples revealed the presence of kōji mould (A. oryzae) and Bacillus amyloliquefaciens in all misos. Various species of the genera Latilactobacillus, Lactiplantibacillus, Pediococcus and Staphylococcus were also detected. The Metagenome-Assembled Genomes (MAGs) revealed genomic sequences belonging to 12 different species and functional analyses of these MAGs were performed. Notably, we detected the presence of Exiguobacterium-the first reported instance of the genus in miso-and Average Nucleotide Identity (ANI) analyses suggest a potentially new species. We hope these results will improve the scientific literature on misos and contribute to developing novel fermented plant-based foods.}, } @article {pmid37919000, year = {2024}, author = {Mun, SY and Lee, W and Lee, SY and Chang, JY and Chang, HC}, title = {Pediococcus inopinatus with a well-developed CRISPR-Cas system dominates in long-term fermented kimchi, Mukeunji.}, journal = {Food microbiology}, volume = {117}, number = {}, pages = {104385}, doi = {10.1016/j.fm.2023.104385}, pmid = {37919000}, issn = {1095-9998}, mesh = {CRISPR-Cas Systems ; *Lactobacillales ; Pediococcus/genetics ; *Fermented Foods ; }, abstract = {Kimchi is produced through a low-temperature fermentation without pre-sterilization, resulting in a heterogeneous microbial community. As fermentation progresses, dominant lactic acid bacteria (LAB) species emerge and undergo a transition process. In this study, LAB were isolated from Mukeunji, a long-term fermented kimchi that is in the final stage of kimchi fermentation process. It was confirmed, through culture-dependent and independent analysis, as well as metagenome analysis, that Pediococcus inopinatus are generally dominant in long-term fermented kimchi. Comparative analysis of the de novo assembled whole genome of P. inopinatus with other kimchi LAB revealed that this species has a well-developed clustered regularly interspaced short palindromic repeats (CRISPR) system. The CRISPR system of P. inopinatus has an additional copy of the csa3 gene, a transcription factor for cas genes. Indeed, this species not only highly expresses cas1 and cas2, which induce spacer acquisition, but also has many diverse spacers that are actively expressed. These findings indicate that the well-developed CRISPR-Cas system is enabling P. inopinatus to dominate in long-fermented kimchi. Overall, this study revealed that LAB with a robust defense system dominate in the final stage of kimchi fermentation and presented a model for the succession mechanism of kimchi LAB.}, } @article {pmid37918732, year = {2024}, author = {Li, Y and Miyani, B and Childs, KL and Shiu, SH and Xagoraraki, I}, title = {Effect of wastewater collection and concentration methods on assessment of viral diversity.}, journal = {The Science of the total environment}, volume = {908}, number = {}, pages = {168128}, doi = {10.1016/j.scitotenv.2023.168128}, pmid = {37918732}, issn = {1879-1026}, mesh = {Humans ; Wastewater ; Wastewater-Based Epidemiological Monitoring ; *Viruses ; SARS-CoV-2 ; *Bacteriophages ; }, abstract = {Monitoring of potentially pathogenic human viruses in wastewater is of crucial importance to understand disease trends in communities, predict potential outbreaks, and boost preparedness and response by public health departments. High throughput metagenomic sequencing opens an opportunity to expand the capabilities of wastewater surveillance. However, there are major bottlenecks in the metagenomic enabled wastewater surveillance, including the complexities in selecting appropriate sampling and concentration/virus enrichment methods as well as in bioinformatic analysis of complex samples with low human virus concentrations. To evaluate the abilities of two commonly used sampling and concentration methods in virus identification, virus communities concentrated with Virus Adsorption-Elution (VIRADEL) and PolyEthylene Glycol (PEG) precipitation were compared for three interceptor sites. Results indicated that more viral reads were obtained by the VIRADEL concentration method, with 2.84 ± 0.57 % viral reads in the sample. For samples concentrated with PEG, the average proportion of viral reads in the sample was 0.63 ± 0.19 %. In all wastewater samples, bacteriophage affiliated with the families Siphoviridae, Myoviridae and Podoviridae were found to be the abundant populations. Comparison against a custom Swiss-Prot human virus database indicated that the relatively abundant human viruses (average proportions in human virus community greater than 1.00 %) in samples concentrated with the VIRADEL method were Orthopoxvirus, Rhadinovirus, Parapoxvirus, Varicellovirus, Hepatovirus, Simplexvirus, Molluscipoxvirus, Parechovirus, Lymphocryptovirus, and Spumavirus. In samples concentrated with the PEG method, fewer human viruses were found to be relatively abundant. These were Orthopoxvirus, Rhadinovirus, Varicellovirus, Simplexvirus, Molluscipoxvirus, Lymphocryptovirus, and Betacoronavirus. Contigs of Betacoronavirus, which contains severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), were identified in VIRADEL and PEG samples. Our study demonstrates the feasibility of using metagenomics in wastewater surveillance as a first screening tool and the need for selecting the appropriate virus concentration methods and optimizing bioinformatic approaches in analyzing metagenomic data of wastewater samples.}, } @article {pmid37918466, year = {2023}, author = {Wang, C and Wang, Y and Wang, F and Zhang, J and Sun, Z and Zhang, H and Fu, L}, title = {High intestinal isoleucine is a potential risk factor for food allergy by regulating the mTOR/AKT pathway in dendritic cells.}, journal = {Clinical immunology (Orlando, Fla.)}, volume = {257}, number = {}, pages = {109818}, doi = {10.1016/j.clim.2023.109818}, pmid = {37918466}, issn = {1521-7035}, mesh = {Animals ; Humans ; Mice ; Allergens ; Dendritic Cells ; *Food Hypersensitivity ; *Isoleucine/metabolism ; Molecular Docking Simulation ; Proto-Oncogene Proteins c-akt ; Risk Factors ; *Intestines/metabolism ; }, abstract = {Food allergy is a global food safety problem with a growing prevalence. People in industrial regions are more susceptible to allergy, but the mechanisms behind this are not fully understood. In this study, the probiotic Lactobacillus casei Zhang (LcZ) was administered to allergic individuals and the impact on allergy-related factors were determined. LcZ alleviated allergenic responses, and there was a significant correlation between the intestinal isoleucine content and IgE concentration. Metagenomics results suggest that the metabolism of the gut microbiota is a source of isoleucine. In a mouse model of food allergy, a high isoleucine diet exacerbated allergic responses and increased the activity of allergenic dendritic cell. In a dendritic cell model, a protein array revealed that the mTOR/AKT pathway mediated the function of isoleucine, and molecular docking suggested that Sestrin2 could be the potential receptor. Overall, this study revealed the role of isoleucine in promoting food allergy, elucidated the underlying mechanisms, and suggested that a high intake of isoleucine could be a potential risk factor for food allergy.}, } @article {pmid37918202, year = {2023}, author = {Huo, W and Ye, R and Hu, T and Lu, W}, title = {CO2 uptake in ethanol-driven chain elongation system: Microbial metabolic mechanisms.}, journal = {Water research}, volume = {247}, number = {}, pages = {120810}, doi = {10.1016/j.watres.2023.120810}, pmid = {37918202}, issn = {1879-2448}, mesh = {*Caproates/metabolism ; *Carbon Dioxide ; Ethanol/metabolism ; Fermentation ; Bioreactors ; }, abstract = {CO2 as a byproduct of organic waste/wastewater fermentation has an important impact on the carboxylate chain elongation. In this study, a semi-continuous flow reactor was used to investigate the effects of CO2 loading rates (Low = 0.5 LCO2·L[-1]·d[-1], Medium = 1.0 LCO2·L[-1]·d[-1], High = 2.0 LCO2·L[-1]·d[-1]) on chain elongation system Ethanol and acetate were utilized as the electron donor and electron acceptor, respectively. The results demonstrate that low loading rate of CO2 has a positive effect on chain elongation. The maximum production of caproate and CH4 were observed at a low CO2 loading rate. Caproate production reached 1.88 g COD·L[-1]·d[-1] with a selectivity of 62.55 %, while CH4 production reached 129.7 ml/d, representing 47.4 % of the total. Metagenomic analysis showed that low loading rate of CO2 favored the enrichment of Clostridium kluyveri, with its abundance being 3.8 times higher than at of high CO2 loading rate. Metatranscriptomic analysis revealed that high CO2 loading rate induced oxidative stress in microorganisms, as evidenced by increased expression of heat shock proteins and superoxide dismutase genes. Further investigation suggested that genes associated with the reverse β-oxidation pathway, CO2 uptake pathway and hydrogenotrophic methanogenesis pathway were reduced at high CO2 loading rate. These findings provide insight into the underlying mechanisms of how CO2 affects chain elongation, and it could be a crucial reason for the poor performance of chain elongation systems with high endogenous CO2 production.}, } @article {pmid37917929, year = {2023}, author = {Delikanlı-Kıyak, B and Yılmaz, İ}, title = {Metataxonomic Sequencing to Assess Microbial Safety of Buffalo Yogurts in Amasra Region.}, journal = {Foodborne pathogens and disease}, volume = {}, number = {}, pages = {}, doi = {10.1089/fpd.2023.0082}, pmid = {37917929}, issn = {1556-7125}, abstract = {Interest in the "microbiota" of dairy products and studies on this subject is increasing day by day. In this study, homemade buffalo yogurt was collected from five different local producers in Amasra province, and their microbiota was evaluated by next-generation sequencing. Salmonella enterica was found in all yogurts (1.2-3.17%). Klebsiella pneumoniae was found to be 1.12% and 5.15% in two of the samples. Staphylococcus aureus was found to be 3.17% in only a single sample. The presence of these potentially pathogenic bacteria suggests that more attention should be paid to hygiene rules during homemade production, processing, and distribution of these products being offered for sale in public markets. These yogurt products can potentially carry risks of contamination and should be periodically checked by the relevant authorities.}, } @article {pmid37916972, year = {2023}, author = {Mostacci, N and Wüthrich, TM and Siegwald, L and Kieser, S and Steinberg, R and Sakwinska, O and Latzin, P and Korten, I and Hilty, M}, title = {Informed interpretation of metagenomic data by StrainPhlAn enables strain retention analyses of the upper airway microbiome.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0072423}, pmid = {37916972}, issn = {2379-5077}, support = {159791//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Haemophilus influenzae/genetics ; Nose ; Trachea ; *Microbiota/genetics ; }, abstract = {The usage of 16S rRNA gene sequencing has become the state-of-the-art method for the characterization of the microbiota in health and respiratory disease. The method is reliable for low biomass samples due to prior amplification of the 16S rRNA gene but has limitations as species and certainly strain identification is not possible. However, the usage of metagenomic tools for the analyses of microbiome data from low biomass samples is not straight forward, and careful optimization is needed. In this work, we show that by validating StrainPhlAn 3 results with the data from bacterial cultures, the strain-level tracking of the respiratory microbiome is feasible despite the high content of host DNA being present when parameters are carefully optimized to fit low biomass microbiomes. This work further proposes that strain retention analyses are feasible, at least for more abundant species. This will help to better understand the longitudinal dynamics of the upper respiratory microbiome during health and disease.}, } @article {pmid37916828, year = {2023}, author = {Cocconcelli, PS and Gatti, M and Giraffa, G and Gobbetti, M and Lanciotti, R and Morelli, L and Neviani, E and Parente, E}, title = {Should the microbiota of raw milk cheeses play a role in the definition of geographical indications and quality schemes within the European Union?.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0052023}, pmid = {37916828}, issn = {2379-5077}, mesh = {Animals ; *Cheese/analysis ; Milk ; European Union ; *Microbiota ; }, } @article {pmid37916816, year = {2023}, author = {Koedooder, C and Zhang, F and Wang, S and Basu, S and Haley, ST and Tolic, N and Nicora, CD and Glavina Del Rio, T and Dyhrman, ST and Gledhill, M and Boiteau, RM and Rubin-Blum, M and Shaked, Y}, title = {Taxonomic distribution of metabolic functions in bacteria associated with Trichodesmium consortia.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0074223}, pmid = {37916816}, issn = {2379-5077}, support = {EMSL 50403//Joint Genome Institute (JGI)/ ; EMSL 50403//Joint Genome Institute (JGI)/ ; 2020041//United States-Israel Binational Science Foundation (BSF)/ ; 2020041//United States-Israel Binational Science Foundation (BSF)/ ; 001126//Ministry of Science, Technology and Space (MOST)/ ; 721225//Simons Foundation (SF)/ ; }, mesh = {*Trichodesmium/genetics ; *Cyanobacteria/genetics ; Nitrogen Fixation ; }, abstract = {Colonies of the cyanobacteria Trichodesmium act as a biological hotspot for the usage and recycling of key resources such as C, N, P, and Fe within an otherwise oligotrophic environment. While Trichodesmium colonies are known to interact and support a unique community of algae and particle-associated microbes, our understanding of the taxa that populate these colonies and the gene functions they encode is still limited. Characterizing the taxa and adaptive strategies that influence consortium physiology and its concomitant biogeochemistry is critical in a future ocean predicted to have increasingly resource-depleted regions.}, } @article {pmid37916453, year = {2023}, author = {Lu, Z and Qin, G and Gan, S and Liu, H and Macreadie, PI and Cheah, W and Wang, F}, title = {Blue carbon sink capacity of mangroves determined by leaves and their associated microbiome.}, journal = {Global change biology}, volume = {}, number = {}, pages = {e17007}, doi = {10.1111/gcb.17007}, pmid = {37916453}, issn = {1365-2486}, support = {YSBR-037//2022 CAS Project for Young Scientists in Basic Research/ ; ANSO-CR-KP-2022-11//ANSO collaborative research/ ; DP200100575//Australian Research Council Discovery Grant/ ; 2021B1212110004//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2021B1515020011//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2023A1515010946//Basic and Applied Basic Research Foundation of Guangdong Province/ ; 2022-8//Natural Resources Affairs Management-Ecological Forestry Construction Special Project of Forestry Administration of Guangdong Province/ ; 2021347//CAS Youth Innovation Promotion Association/ ; VRMDE2204//Key Laboratory of Vegetation Restoration and Management of Degraded Ecosystems, South China Botanical Garden, Chinese Academy of Sciences/ ; 2022B1111230001//Key-Area Research and Development Program of Guangdong Province/ ; 2020BJ003//National Forestry and Grassland Administration Youth Talent Support Program/ ; 2021YFC3100402//National Key Research and Development Program of China/ ; 32301398//National Natural Science Foundation of China/ ; 32011530164//National Natural Science Foundation of China/ ; 32171594//National Natural Science Foundation of China/ ; 42007230//National Natural Science Foundation of China/ ; U2106209//National Natural Science Foundation of China/ ; 2018B030324003//R & D program of Guangdong Provincial Department of Science and Technology/ ; QNXM-08//South China Botanical Garden, Chinese Academy of Sciences/ ; }, abstract = {Mangroves play a globally significant role in carbon capture and storage, known as blue carbon ecosystems. Yet, there are fundamental biogeochemical processes of mangrove blue carbon formation that are inadequately understood, such as the mechanisms by which mangrove afforestation regulates the microbial-driven transfer of carbon from leaf to below-ground blue carbon pool. In this study, we addressed this knowledge gap by investigating: (1) the mangrove leaf characteristics using state-of-the-art FT-ICR-MS; (2) the microbial biomass and their transformation patterns of assimilated plant-carbon; and (3) the degradation potentials of plant-derived carbon in soils of an introduced (Sonneratia apetala) and a native mangrove (Kandelia obovata). We found that biogeochemical cycling took entirely different pathways for S. apetala and K. obovata. Blue carbon accumulation and the proportion of plant-carbon for native mangroves were high, with microbes (dominated by K-strategists) allocating the assimilated-carbon to starch and sucrose metabolism. Conversely, microbes with S. apetala adopted an r-strategy and increased protein- and nucleotide-biosynthetic potentials. These divergent biogeochemical pathways were related to leaf characteristics, with S. apetala leaves characterized by lower molecular-weight, C:N ratio, and lignin content than K. obovata. Moreover, anaerobic-degradation potentials for lignin were high in old-aged soils, but the overall degradation potentials of plant carbon were age-independent, explaining that S. apetala age had no significant influences on the contribution of plant-carbon to blue carbon. We propose that for introduced mangroves, newly fallen leaves release nutrient-rich organic matter that favors growth of r-strategists, which rapidly consume carbon to fuel growth, increasing the proportion of microbial-carbon to blue carbon. In contrast, lignin-rich native mangrove leaves shape K-strategist-dominated microbial communities, which grow slowly and store assimilated-carbon in cells, ultimately promoting the contribution of plant-carbon to the remarkable accumulation of blue carbon. Our study provides new insights into the molecular mechanisms of microbial community responses during reforestation in mangrove ecosystems.}, } @article {pmid37915946, year = {2023}, author = {Chen, X and Guo, Q and Li, YY and Song, TY and Ge, JQ}, title = {Metagenomic analysis fecal microbiota of dysentery-like diarrhoea in a pig farm using next-generation sequencing.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1257573}, pmid = {37915946}, issn = {2297-1769}, abstract = {Porcine enteric diseases including swine dysentery involves a wide range of possible aetiologies and seriously damages the intestine of pigs of all ages. Metagenomic next-generation sequencing is commonly used in research for detecting and analyzing pathogens. In this study, the feces of pigs from a commercial swine farm with dysentery-like diarrhea was collected and used for microbiota analysis by next-generation sequencing. While Brachyspira spp. was not detected in diarrheal pig fecal samples, indicating that the disease was not swine dysentery. The quantity of microbial population was extremely lowered, and the bacterial composition was altered with a reduction in the relative abundance of the probiotics organisms, Firmicutes and Bacteroidetes, with an increase in pathogens like Fusobacterium and Proteobacteria, in which the specific bacteria were identified at species-level. Viral pathogens, porcine circovirus type 2, porcine lymphotropic herpesviruses 1, and porcine mastadenovirus A were also detected at pretty low levels. Carbohydrate-active enzymes (CAZy) analysis indicated that the constitute of Firmicutes and Bacteroidete were also changed. Further, the Kyoto Encyclopedia of Genes and Genomes (KEGG) alignment analysis indicated that the microbiota of diarrheal pigs had a lower ability in utilizing energy sources but were enriched in multi-drug resistance pathways. Comprehensive Antibiotic Resistance Database (CARD) and Virulence Factors of Pathogenic Bacteria (VFDB) analysis indicated that genes for elfamycin and sulfonamide resistance and the iron uptake system were enriched in diarrheal pigs. This revealed potential bacterial infection and can guide antibiotic selection for treating dysentery. Overall, our data suggested that alterations in both the population and functional attributes of microbiota in diarrheal pigs with decreased probiotic and increased pathogenic microorganisms. These results will help elucidate the mechanism of dysentery-like diarrhea and the development of approaches to control the disease.}, } @article {pmid37915853, year = {2023}, author = {Gomez-Alvarez, V and Ryu, H and Tang, M and McNeely, M and Muhlen, C and Urbanic, M and Williams, D and Lytle, D and Boczek, L}, title = {Assessing residential activity in a home plumbing system simulator: monitoring the occurrence and relationship of major opportunistic pathogens and phagocytic amoebas.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1260460}, pmid = {37915853}, issn = {1664-302X}, abstract = {Opportunistic premise plumbing pathogens (OPPPs) have been detected in buildings' plumbing systems causing waterborne disease outbreaks in the United States. In this study, we monitored the occurrence of OPPPs along with free-living amoeba (FLA) and investigated the effects of residential activities in a simulated home plumbing system (HPS). Water samples were collected from various locations in the HPS and analyzed for three major OPPPs: Legionella pneumophila, nontuberculous mycobacterial species (e.g., Mycobacterium avium, M. intracellulare, and M. abscessus), and Pseudomonas aeruginosa along with two groups of amoebas (Acanthamoeba and Vermamoeba vermiformis). A metagenomic approach was also used to further characterize the microbial communities. Results show that the microbial community is highly diverse with evidence of spatial and temporal structuring influenced by environmental conditions. L. pneumophila was the most prevalent pathogen (86% of samples), followed by M. intracellulare (66%) and P. aeruginosa (21%). Interestingly, M. avium and M. abscessus were not detected in any samples. The data revealed a relatively low prevalence of Acanthamoeba spp. (4%), while V. vermiformis was widely detected (81%) across all the sampling locations within the HPS. Locations with a high concentration of L. pneumophila and M. intracellulare coincided with the highest detection of V. vermiformis, suggesting the potential growth of both populations within FLA and additional protection in drinking water. After a period of stagnation lasting at least 2-weeks, the concentrations of OPPPs and amoeba immediately increased and then decreased gradually back to the baseline. Furthermore, monitoring the microbial population after drainage of the hot water tank and partial drainage of the entire HPS demonstrated no significant mitigation of the selected OPPPs. This study demonstrates that these organisms can adjust to their environment during such events and may survive in biofilms and/or grow within FLA, protecting them from stressors in the supplied water.}, } @article {pmid37915846, year = {2023}, author = {Zhang, Y and Chen, X and Wang, Y and Li, L and Ju, Q and Zhang, Y and Xi, H and Wang, F and Qiu, D and Liu, X and Chang, N and Zhang, W and Zhang, C and Wang, K and Li, L and Zhang, J}, title = {Alterations of lower respiratory tract microbiome and short-chain fatty acids in different segments in lung cancer: a multiomics analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1261284}, pmid = {37915846}, issn = {2235-2988}, mesh = {Humans ; *Lung Neoplasms ; Multiomics ; *Microbiota/genetics ; Fatty Acids, Volatile/metabolism ; Carcinogenesis ; }, abstract = {INTRODUCTION: The lower respiratory tract microbiome is widely studied to pinpoint microbial dysbiosis of diversity or abundance that is linked to a number of chronic respiratory illnesses. However, it is vital to clarify how the microbiome, through the release of microbial metabolites, impacts lung health and oncogenesis.

METHODS: In order to discover the powerful correlations between microbial metabolites and disease, we collected, under electronic bronchoscopy examinations, samples of paired bronchoalveolar lavage fluids (BALFs) from tumor-burden lung segments and ipsilateral non-tumor sites from 28 lung cancer participants, further performing metagenomic sequencing, short-chain fatty acid (SCFA) metabolomics, and multiomics analysis to uncover the potential correlations of the microbiome and SCFAs in lung cancer.

RESULTS: In comparison to BALFs from normal lung segments of the same participant, those from lung cancer burden lung segments had slightly decreased microbial diversity in the lower respiratory tract. With 18 differentially prevalent microbial species, including the well-known carcinogens Campylobacter jejuni and Nesseria polysaccharea, the relative species abundance in the lower respiratory tract microbiome did not significantly differ between the two groups. Additionally, a collection of commonly recognized probiotic metabolites called short-chain fatty acids showed little significance in either group independently but revealed a strong predictive value when using an integrated model by machine learning. Multiomics also discovered particular species related to SCFAs, showing a positive correlation with Brachyspira hydrosenteriae and a negative one with Pseudomonas at the genus level, despite limited detection in lower airways. Of note, these distinct microbiota and metabolites corresponded with clinical traits that still required confirmation.

CONCLUSIONS: Further analysis of metagenome functional capacity revealed that genes encoding environmental information processing and metabolism pathways were enriched in the lower respiratory tract metagenomes of lung cancer patients, further supporting the oncogenesis function of various microbial species by different metabolites. These findings point to a potent relationship between particular components of the integrated microbiota-metabolites network and lung cancer, with implications for screening and diagnosis in clinical settings.}, } @article {pmid37915503, year = {2023}, author = {Shen, H and Zhou, H and Zhang, F and Wang, J and Wang, R and Wang, J}, title = {Case Report: Successful Treatment of Recurrent Candida Albicans Meningitis with Kimura's Disease Using Amphotericin B Colloidal Dispersion Combined with Fluconazole.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {6905-6909}, pmid = {37915503}, issn = {1178-6973}, abstract = {BACKGROUND: Candida albicans meningitis is a fungal infectious disease of the central nervous system that most often occurs in immunodeficient populations. Kimura's disease is an IgE-mediated inflammatory reactive disease that is a chronic immune disorder with predominantly lymph node, soft tissue, and salivary gland damage, the treatment of which is hormone-based. The combination of Kimura's disease with C. albicans meningitis is relatively uncommon. Herein, we report a case of C. albicans meningitis in combination with Kimura's disease.

CASE PRESENTATION: The case is a 26-year-old male with a medical history of Kimura, who presented with symptoms of dizziness, headache, and double vision. Lumbar puncture and cerebrospinal fluid examination revealed an increased white blood cell count. Further analysis through cerebrospinal fluid culture and metagenomic second-generation sequencing (mNGS) led to the final diagnosis of C. albicans meningitis. The patient was treated with fluconazole after the onset of C. albicans meningitis and had a good response. During the treatment, changes in the pathogen genome sequences were monitored dynamically using metagenomic next-generation sequencing. After 1 year, the patient had a recurrence of Candida meningitis. Treatment with fluconazole alone was ineffective, while antifungal treatment with amphotericin B colloidal dispersion was effective with no detectable renal injury.

CONCLUSION: Candida meningitis can occur in the context of Kimura disease. In patients with mild disease, the possibility of recurrence exists with fluconazole treatment alone, and the efficacy of amphotericin B colloidal dispersion combined with fluconazole is better than fluconazole alone in patients with a recurrence. No nephrotoxicity was observed during amphotericin B colloidal dispersion treatment. The mNGS allows dynamic monitoring of pathogen sequencing reads, and for Candida meningitis, there may be a mismatch between peak sequencing reads and disease during treatment, the basis for which is unclear.}, } @article {pmid37914776, year = {2023}, author = {Zorz, J and Paquette, AJ and Gillis, T and Kouris, A and Khot, V and Demirkaya, C and De La Hoz Siegler, H and Strous, M and Vadlamani, A}, title = {Coordinated proteome change precedes cell lysis and death in a mat-forming cyanobacterium.}, journal = {The ISME journal}, volume = {17}, number = {12}, pages = {2403-2414}, pmid = {37914776}, issn = {1751-7370}, mesh = {*Proteome/genetics/metabolism ; *Cyanobacteria/metabolism ; Harmful Algal Bloom ; Biomass ; Cell Death ; }, abstract = {Cyanobacteria form dense multicellular communities that experience transient conditions in terms of access to light and oxygen. These systems are productive but also undergo substantial biomass turnover through cell death, supplementing heightened heterotrophic respiration. Here we use metagenomics and metaproteomics to survey the molecular response of a mat-forming cyanobacterium undergoing mass cell lysis after exposure to dark and anoxic conditions. A lack of evidence for viral, bacterial, or eukaryotic antagonism contradicts commonly held beliefs on the causative agent for cyanobacterial death during dense growth. Instead, proteogenomics data indicated that lysis likely resulted from a genetically programmed response triggered by a failure to maintain osmotic pressure in the wake of severe energy limitation. Cyanobacterial DNA was rapidly degraded, yet cyanobacterial proteins remained abundant. A subset of proteins, including enzymes involved in amino acid metabolism, peptidases, toxin-antitoxin systems, and a potentially self-targeting CRISPR-Cas system, were upregulated upon lysis, indicating possible involvement in the programmed cell death response. We propose this natural form of cell death could provide new pathways for controlling harmful algal blooms and for sustainable bioproduct production.}, } @article {pmid37914423, year = {2023}, author = {Han, L and Sun, LX and Chen, YL and Shao, HJ and Zhou, LF}, title = {[Clinical characteristics of a case of severe pneumonia caused by coinfection of COVID-19 and Chlamydia Psittaci].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {46}, number = {11}, pages = {1118-1120}, doi = {10.3760/cma.j.cn112147-20230906-00143}, pmid = {37914423}, issn = {1001-0939}, support = {2022YFF0710800//National Key Research and Development Program of China/ ; 81820108001//Major International (Regional) Joint Research Project of China/ ; ZDRCA2016018//Jiangsu Key Principal Investigator of Medicine/ ; BRA2019078//Jiangsu Provincial Project 333 for Cultivation of High-Level Talents/ ; }, mesh = {Female ; Humans ; Aged ; *Chlamydophila psittaci ; *Coinfection ; *COVID-19 ; *Pneumonia ; Lung ; }, abstract = {A 69-year-old female patient was admitted to the Department of Respiratory and Critical Care Medicine, Affiliated Hospital of Xuzhou Medical University due to a "cough and fever for eight days". On admission, a coronavirus disease (COVID-19) nucleic acid test was positive, and a chest CT scan showed progressive patchy shadows and consolidation shadows in both lungs. Arterial blood gas analysis showed type Ⅰ respiratory failure. The primary diagnosis was severe community-acquired pneumonia in an older adult without underlying disease. However, oxygen inhalation, steroid, anti-inflammatory, and antibacterial empirical treatment with piperacillin/tazobactam was ineffective. Metagenomic next-generation sequencing of bronchoscopy alveolar lavage fluid showed Chlamydia psittaci(C. psittaci). Severe pneumonia was confirmed, caused by coinfection with severe acute respiratory syndrome coronavirus 2 and C. psittaci. A combination of doxycycline and moxifloxacin significantly improved the targeted and symptomatic treatment of the underlying cause. After discharge, the patient recovered within four weeks of follow-up. Therefore, clinicians should be alert to the possibility of coinfection of C. psittaci in patients already diagnosed with COVID-19.}, } @article {pmid37914040, year = {2024}, author = {Wani, AK and Chopra, C and Dhanjal, DS and Akhtar, N and Singh, H and Bhau, P and Singh, A and Sharma, V and Pinheiro, RSB and Américo-Pinheiro, JHP and Singh, R}, title = {Metagenomics in the fight against zoonotic viral infections: A focus on SARS-CoV-2 analogues.}, journal = {Journal of virological methods}, volume = {323}, number = {}, pages = {114837}, doi = {10.1016/j.jviromet.2023.114837}, pmid = {37914040}, issn = {1879-0984}, mesh = {Animals ; Humans ; SARS-CoV-2/genetics ; *COVID-19 ; Viral Zoonoses ; Ecosystem ; Pandemics/prevention & control ; *Viruses/genetics ; Metagenomics ; }, abstract = {Zoonotic viral infections continue to pose significant threats to global public health, as highlighted by the COVID-19 pandemic caused by the SARS-CoV-2 virus. The emergence of SARS-CoV-2 served as a stark reminder of the potential for zoonotic transmission of viruses from animals to humans. Understanding the origins and dynamics of zoonotic viruses is critical for early detection, prevention, and effective management of future outbreaks. Metagenomics has emerged as a powerful tool for investigating the virome of diverse ecosystems, shedding light on the diversity of viral populations, their hosts, and potential zoonotic spillover events. We provide an in-depth examination of metagenomic approaches, including, NGS metagenomics, shotgun metagenomics, viral metagenomics, and single-virus metagenomics, highlighting their strengths and limitations in identifying and characterizing zoonotic viral pathogens. This review underscores the pivotal role of metagenomics in enhancing our ability to detect, monitor, and mitigate zoonotic viral infections, using SARS-CoV-2 analogues as a case study. We emphasize the need for continued interdisciplinary collaboration among virologists, ecologists, and bioinformaticians to harness the full potential of metagenomic approaches in safeguarding public health against emerging zoonotic threats.}, } @article {pmid37913976, year = {2024}, author = {Gao, L and Wang, S and Xu, X and Zheng, J and Cai, T and Jia, S}, title = {Metagenomic analysis reveals the distribution, function, and bacterial hosts of degradation genes in activated sludge from industrial wastewater treatment plants.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {340}, number = {Pt 2}, pages = {122802}, doi = {10.1016/j.envpol.2023.122802}, pmid = {37913976}, issn = {1873-6424}, mesh = {Sewage/microbiology ; Wastewater ; Bacteria/genetics/metabolism ; *Water Purification ; *Environmental Pollutants/metabolism ; Genes, Bacterial ; }, abstract = {For comprehensive insights into the bacterial community and its functions during industrial wastewater treatment, with a particular emphasis on its pivotal role in the bioremediation of organic pollutants, this study utilized municipal samples as a control group for metagenomic analysis. This approach allowed us to investigate the distribution, function, and bacterial hosts of biodegradation genes (BDGs) and organic degradation genes (ODGs), as well as the dynamics of bacterial communities during the industrial wastewater bioprocess. The results revealed that BDGs and ODGs associated with the degradation of benzoates, biphenyls, triazines, nitrotoluenes, and chlorinated aromatics were notably more abundant in the industrial samples. Specially, genes like clcD, linC, catE, pcaD, hbaB, hcrC, and badK, involved in the peripheral pathways for the catabolism of aromatic compounds, benzoate transport, and central aromatic intermediates, showed a significantly higher abundance of industrial activated sludge (AS) than municipal AS. Additionally, the BDG/ODG co-occurrence contigs in industrial samples exhibited a higher diversity in terms of degradation gene carrying capacity. Functional analysis of Clusters of Orthologous Groups (COGs) indicated that the primary function of bacterial communities in industrial AS was associated with the category of "metabolism". Furthermore, the presence of organic pollutants in industrial wastewater induced alterations in the bacterial community, particularly impacting the abundance of key hosts harboring BDGs and ODGs (e.g. Bradyrhizobium, Hydrogenophaga, and Mesorhizobium). The specific hosts of BDG/ODG could explain the distribution characteristics of degradation genes. For example, the prevalence of the Adh1 gene, primarily associated with Mesorhizobium, was notably more prevalent in the industrial AS. Overall, this study provides valuable insights into the development of more effective strategies for the industrial wastewater treatment and the mitigation of organic pollutant contamination.}, } @article {pmid37913769, year = {2023}, author = {Collier, JL and Rest, JS and Gallot-Lavallée, L and Lavington, E and Kuo, A and Jenkins, J and Plott, C and Pangilinan, J and Daum, C and Grigoriev, IV and Filloramo, GV and Novák Vanclová, AMG and Archibald, JM}, title = {The protist Aurantiochytrium has universal subtelomeric rDNAs and is a host for mirusviruses.}, journal = {Current biology : CB}, volume = {33}, number = {23}, pages = {5199-5207.e4}, doi = {10.1016/j.cub.2023.10.009}, pmid = {37913769}, issn = {1879-0445}, mesh = {DNA, Ribosomal ; *Viruses ; Genome ; Heterochromatin ; Eukaryota ; Telomere ; Phylogeny ; }, abstract = {Viruses are the most abundant biological entities in the world's oceans, where they play important ecological and biogeochemical roles. Metagenomics is revealing new groups of eukaryotic viruses, although disconnected from known hosts. Among these are the recently described mirusviruses, which share some similarities with herpesviruses.[1] 50 years ago, "herpes-type" viral particles[2] were found in a thraustochytrid member of the labyrinthulomycetes, a diverse group of abundant and ecologically important marine eukaryotes,[3][,][4] but could not be further characterized by methods then available. Long-read sequencing has allowed us to connect the biology of mirusviruses and thraustochytrids. We sequenced the genome of the genetically tractable model thraustochytrid Aurantiochytrium limacinum ATCC MYA-1381 and found that its 26 linear chromosomes have an extraordinary configuration. Subtelomeric ribosomal DNAs (rDNAs) found at all chromosome ends are interspersed with long repeated sequence elements denoted as long repeated-telomere and rDNA spacers (LORE-TEARS). We identified two genomic elements that are related to mirusvirus genomes. The first is a ∼300-kbp episome (circular element 1 [CE1]) present at a high copy number. Strikingly, the second, distinct, mirusvirus-like element is integrated between two sets of rDNAs and LORE-TEARS at the left end of chromosome 15 (LE-Chr15). Similar to metagenomically derived mirusviruses, these putative A. limacinum mirusviruses have a virion module related to that of herpesviruses along with an informational module related to nucleocytoplasmic large DNA viruses (NCLDVs). CE1 and LE-Chr15 bear striking similarities to episomal and endogenous latent forms of herpesviruses, respectively, and open new avenues of research into marine virus-host interactions.}, } @article {pmid37913618, year = {2024}, author = {Lu, Z and Cheng, X and Xie, J and Li, Z and Li, X and Jiang, X and Zhu, D}, title = {Iron-based multi-carbon composite and Pseudomonas furukawaii ZS1 co-affect nitrogen removal, microbial community dynamics and metabolism pathways in low-temperature aquaculture wastewater.}, journal = {Journal of environmental management}, volume = {349}, number = {}, pages = {119471}, doi = {10.1016/j.jenvman.2023.119471}, pmid = {37913618}, issn = {1095-8630}, mesh = {*Wastewater ; Denitrification ; Temperature ; Nitrogen/metabolism ; Carbon ; Pseudomonas/metabolism ; *Microbiota ; Bioreactors/microbiology ; Nitrification ; }, abstract = {Aerobic denitrification is the key process in the elimination of nitrogen from aquaculture wastewater, especially for wastewater with high dissolved oxygen and low carbon/nitrogen (C/N) ratio. However, a low C/N ratio, especially in low-temperature environments, restricts the activity of aerobic denitrifiers and decreases the nitrogen elimination efficiency. In this study, an iron-based multi-solid carbon source composite that immobilized aerobic denitrifying bacteria ZS1 (IMCSCP) was synthesized to treat aerobic (DO > 5 mg/L), low temperature (<15 °C) and low C/N ratio (C/N = 4) aquaculture wastewater. The results showed that the sequencing batch biofilm reactor (SBBR) packed with IMCSCP exhibited the highest nitrogen removal performance, with removal rates of 95.63% and 85.44% for nitrate nitrogen and total nitrogen, respectively, which were 33.03% and 30.75% higher than those in the reactor filled with multi-solid carbon source composite (MCSC). Microbial community and network analysis showed that Pseudomonas furukawaii ZS1 successfully colonized the SBBR filled with IMCSCP, and Exiguobacterium, Cellulomonas and Pseudomonas were essential for the nitrogen elimination. Metagenomic analysis showed that an increase in gene abundance related to carbon metabolism, nitrogen metabolism, extracellular polymer substance synthesis and electron transfer in the IMCSCP, enabling denitrification in the SBBR to be achieved via multiple pathways. The results of this study provided new insights into the microbial removal mechanism of nitrogen in SBBR packed with IMCSCP at low temperatures.}, } @article {pmid37910603, year = {2023}, author = {Woodworth, MH and Conrad, RE and Haldopoulos, M and Pouch, SM and Babiker, A and Mehta, AK and Sitchenko, KL and Wang, CH and Strudwick, A and Ingersoll, JM and Philippe, C and Lohsen, S and Kocaman, K and Lindner, BG and Hatt, JK and Jones, RM and Miller, C and Neish, AS and Friedman-Moraco, R and Karadkhele, G and Liu, KH and Jones, DP and Mehta, CC and Ziegler, TR and Weiss, DS and Larsen, CP and Konstantinidis, KT and Kraft, CS}, title = {Fecal microbiota transplantation promotes reduction of antimicrobial resistance by strain replacement.}, journal = {Science translational medicine}, volume = {15}, number = {720}, pages = {eabo2750}, doi = {10.1126/scitranslmed.abo2750}, pmid = {37910603}, issn = {1946-6242}, support = {K23 AI144036/AI/NIAID NIH HHS/United States ; P30 AI050409/AI/NIAID NIH HHS/United States ; UL1 TR002378/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *Fecal Microbiota Transplantation/adverse effects ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome ; Drug Resistance, Bacterial ; Feces/microbiology ; Treatment Outcome ; }, abstract = {Multidrug-resistant organism (MDRO) colonization is a fundamental challenge in antimicrobial resistance. Limited studies have shown that fecal microbiota transplantation (FMT) can reduce MDRO colonization, but its mechanisms are poorly understood. We conducted a randomized, controlled trial of FMT for MDRO decolonization in renal transplant recipients called PREMIX (NCT02922816). Eleven participants were enrolled and randomized 1:1 to FMT or an observation period followed by delayed FMT if stool cultures were MDRO positive at day 36. Participants who were MDRO positive after one FMT were treated with a second FMT. At last visit, eight of nine patients who completed all treatments were MDRO culture negative. FMT-treated participants had longer time to recurrent MDRO infection versus PREMIX-eligible controls who were not treated with FMT. Key taxa (Akkermansia muciniphila, Alistipes putredinis, Phocaeicola dorei, Phascolarctobacterium faecium, Alistipes species, Mesosutterella massiliensis, Barnesiella intestinihominis, and Faecalibacterium prausnitzii) from the single feces donor used in the study that engrafted in recipients and metabolites such as short-chain fatty acids and bile acids in FMT-responding participants uncovered leads for rational microbiome therapeutic and diagnostic development. Metagenomic analyses revealed a previously unobserved mechanism of MDRO eradication by conspecific strain competition in an FMT-treated subset. Susceptible Enterobacterales strains that replaced baseline extended-spectrum β-lactamase-producing strains were not detectable in donor microbiota manufactured as FMT doses but in one case were detectable in the recipient before FMT. These data suggest that FMT may provide a path to exploit strain competition to reduce MDRO colonization.}, } @article {pmid37910478, year = {2023}, author = {Lee, J and Peesh, P and Quaicoe, V and Tan, C and Banerjee, A and Mooz, P and Ganesh, BP and Petrosino, J and Bryan, RM and McCullough, LD and Venna, VR}, title = {Estradiol mediates colonic epithelial protection in aged mice after stroke and is associated with shifts in the gut microbiome.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2271629}, pmid = {37910478}, issn = {1949-0984}, support = {R01 NS094543/NS/NINDS NIH HHS/United States ; R21 AG072380/AG/NIA NIH HHS/United States ; R01 NS103592/NS/NINDS NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R35 NS132265/NS/NINDS NIH HHS/United States ; }, mesh = {Mice ; Female ; Male ; Animals ; *Gastrointestinal Microbiome ; Intestinal Mucosa/microbiology ; Estradiol ; RNA, Ribosomal, 16S/genetics ; Mucins/metabolism ; *Brain Injuries/metabolism ; }, abstract = {The gut is a major source of bacteria and antigens that contribute to neuroinflammation after brain injury. Colonic epithelial cells (ECs) are responsible for secreting major cellular components of the innate defense system, including antimicrobial proteins (AMP) and mucins. These cells serve as a critical regulator of gut barrier function and maintain host-microbe homeostasis. In this study, we determined post-stroke host defense responses at the colonic epithelial surface in mice. We then tested if the enhancement of these epithelial protective mechanisms is beneficial in young and aged mice after stroke. AMPs were significantly increased in the colonic ECs of young males, but not in young females after experimental stroke. In contrast, mucin-related genes were enhanced in young females and contributed to mucus formation that maintains the distance between the host and gut bacteria. Bacterial community profiling was done using universal amplification of 16S rRNA gene sequences. The sex-specific colonic epithelial defense responses after stroke in young females were reversed with ovariectomy and led to a shift from a predominately mucin response to the enhanced AMP expression seen in males after stroke. Estradiol (E2) replacement prior to stroke in aged females increased mucin gene expression in the colonic ECs. Interestingly, we found that E2 treatment reduced stroke-associated neuronal hyperactivity in the insular cortex, a brain region that interacts with visceral organs such as the gut, in parallel to an increase in the composition of Lactobacillus and Bifidobacterium in the gut microbiota. This is the first study demonstrating sex differences in host defense mechanisms in the gut after brain injury.}, } @article {pmid37909786, year = {2023}, author = {Richie, TG and Heeren, L and Kamke, A and Monk, K and Pogranichniy, S and Summers, T and Wiechman, H and Ran, Q and Sarkar, S and Plattner, BL and Lee, STM}, title = {Limitation of amino acid availability by bacterial populations during enhanced colitis in IBD mouse model.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0070323}, pmid = {37909786}, issn = {2379-5077}, support = {P30 GM122731/GM/NIGMS NIH HHS/United States ; P20 GM103418/GM/NIGMS NIH HHS/United States ; U54 HD090216/HD/NICHD NIH HHS/United States ; S10 OD021743/OD/NIH HHS/United States ; UL1 TR002366/TR/NCATS NIH HHS/United States ; }, mesh = {Mice ; Animals ; Amino Acids ; *Gastrointestinal Microbiome ; *Colitis/microbiology ; Inflammation ; *Inflammatory Bowel Diseases/drug therapy ; Bacteria ; }, abstract = {Inflammatory bowel disease is associated with an increase in Enterobacteriaceae and Enterococcus species; however, the specific mechanisms are unclear. Previous research has reported the associations between microbiota and inflammation, here we investigate potential pathways that specific bacteria populations use to drive gut inflammation. Richie et al. show that these bacterial populations utilize an alternate sulfur metabolism and are tolerant of host-derived immune-response products. These metabolic pathways drive host gut inflammation and fuel over colonization of these pathobionts in the dysbiotic colon. Cultured isolates from dysbiotic mice indicated faster growth supplemented with L-cysteine, showing these microbes can utilize essential host nutrients.}, } @article {pmid37909332, year = {2023}, author = {Poplaski, V and Bomidi, C and Kambal, A and Nguyen-Phuc, H and Di Rienzi, SC and Danhof, HA and Zeng, XL and Feagins, LA and Deng, N and Vilar, E and McAllister, F and Coarfa, C and Min, S and Kim, HJ and Shukla, R and Britton, R and Estes, MK and Blutt, SE}, title = {Human intestinal organoids from Cronkhite-Canada syndrome patients reveal link between serotonin and proliferation.}, journal = {The Journal of clinical investigation}, volume = {133}, number = {21}, pages = {}, pmid = {37909332}, issn = {1558-8238}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; P42 ES027725/ES/NIEHS NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; R21 CA236690/CA/NCI NIH HHS/United States ; U01 DK103168/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Serotonin ; Intestines ; Organoids/pathology ; *Colorectal Neoplasms/pathology ; *Intestinal Polyposis/genetics/pathology ; }, abstract = {Cronkhite-Canada Syndrome (CCS) is a rare, noninherited polyposis syndrome affecting 1 in every million individuals. Despite over 50 years of CCS cases, the etiopathogenesis and optimal treatment for CCS remains unknown due to the rarity of the disease and lack of model systems. To better understand the etiology of CCS, we generated human intestinal organoids (HIOs) from intestinal stem cells isolated from 2 patients. We discovered that CCS HIOs are highly proliferative and have increased numbers of enteroendocrine cells producing serotonin (also known as 5-hydroxytryptamine or 5HT). These features were also confirmed in patient tissue biopsies. Recombinant 5HT increased proliferation of non-CCS donor HIOs and inhibition of 5HT production in the CCS HIOs resulted in decreased proliferation, suggesting a link between local epithelial 5HT production and control of epithelial stem cell proliferation. This link was confirmed in genetically engineered HIOs with an increased number of enteroendocrine cells. This work provides a new mechanism to explain the pathogenesis of CCS and illustrates the important contribution of HIO cultures to understanding disease etiology and in the identification of novel therapies. Our work demonstrates the principle of using organoids for personalized medicine and sheds light on how intestinal hormones can play a role in intestinal epithelial proliferation.}, } @article {pmid37909046, year = {2023}, author = {Nijkamp, E and Ruffolo, JA and Weinstein, EN and Naik, N and Madani, A}, title = {ProGen2: Exploring the boundaries of protein language models.}, journal = {Cell systems}, volume = {14}, number = {11}, pages = {968-978.e3}, doi = {10.1016/j.cels.2023.10.002}, pmid = {37909046}, issn = {2405-4720}, mesh = {*Proteins/genetics ; *Artificial Intelligence ; Amino Acid Sequence ; Language ; Databases, Factual ; }, abstract = {Attention-based models trained on protein sequences have demonstrated incredible success at classification and generation tasks relevant for artificial-intelligence-driven protein design. However, we lack a sufficient understanding of how very large-scale models and data play a role in effective protein model development. We introduce a suite of protein language models, named ProGen2, that are scaled up to 6.4B parameters and trained on different sequence datasets drawn from over a billion proteins from genomic, metagenomic, and immune repertoire databases. ProGen2 models show state-of-the-art performance in capturing the distribution of observed evolutionary sequences, generating novel viable sequences, and predicting protein fitness without additional fine-tuning. As large model sizes and raw numbers of protein sequences continue to become more widely accessible, our results suggest that a growing emphasis needs to be placed on the data distribution provided to a protein sequence model. Our models and code are open sourced for widespread adoption in protein engineering. A record of this paper's Transparent Peer Review process is included in the supplemental information.}, } @article {pmid37908544, year = {2023}, author = {Hai, Q and Wang, J and Kang, W and Cheng, S and Li, J and Lyu, N and Li, Y and Luo, Z and Liu, Z}, title = {Metagenomic and metabolomic analysis of changes in intestinal contents of rainbow trout (Oncorhynchus mykiss) infected with infectious hematopoietic necrosis virus at different culture water temperatures.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1275649}, pmid = {37908544}, issn = {1664-302X}, abstract = {Infectious hematopoietic necrosis (IHN) is a major disease that limits the culture of rainbow trout. In practical production, it has been found that the temperature of the culture water is a crucial factor affecting its mortality. Currently, little is known about how temperature affects the immune response of rainbow trout gut microbiota and metabolites to IHNV. In this study, our main objective is to analyze the changes in gut microorganisms of rainbow trout (juvenile fish with a consistent genetic background) after 14 days of infection with IHNV (5 × 10[5] pfu/fish) at 12-13°C (C: injected with saline, A: injected with IHNV) and 16-17°C (D: injected with saline, B: injected with IHNV) using metagenomic and metabolomic analyses, and to screen for probiotics that are effective against IHNV. The results showed that infection with IHNV at 12-13°C caused Eukaryote loss. Compared to Group C, Group A showed a significant increase in harmful pathogens, such as Yersiniaceae, and a significant alteration of 4,087 gut metabolites. Compared to group D, group B showed a significant increase in the abundance of Streptococcaceae and Lactococcus lactis, along with significant changes in 4,259 intestinal metabolites. Compared with their respective groups, the levels of two immune-related metabolites, 1-Octadecanoyl-glycero-3-phosphoethanolamine and L-Glutamate, were significantly upregulated in groups A and B. Compared to group B, Group A showed significantly higher pathogenic bacteria including Aeromonas, Pseudomonas, and Yersiniaceae, while group B showed a significant increase in Streptococcaceae and Lactococcus lactis. Additionally, there were 4,018 significantly different metabolites between the two groups. Interestingly, 1-Octadecanoyl-sn-glycero-3-phosphoethanolamine and L-Glutamate were significantly higher in group A than in group B. Some of the different metabolites in C vs. A are correlated with Fomitopsis pinicola, while in D vs. B they were correlated with Lactococcus raffinolactis, and in A vs. B they were correlated with Hypsizygus marmoreus. This study exposed how rainbow trout gut microbiota and metabolites respond to IHNV at different temperatures, and screens beneficial bacteria with potential resistance to IHN, providing new insights and scientific basis for the prevention and treatment of IHN.}, } @article {pmid37908118, year = {2023}, author = {Igo, M and Xu, L and Krishna, A and Stewart, S and Xu, L and Li, Z and Weaver, JL and Stone, H and Sacks, L and Bensman, T and Florian, J and Rouse, R and Han, X}, title = {A metagenomic analysis for combination therapy of multiple classes of antibiotics on the prevention of the spread of antibiotic-resistant genes.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2271150}, pmid = {37908118}, issn = {1949-0984}, mesh = {Animals ; Mice ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome ; Ampicillin/pharmacology ; *Microbiota ; Ciprofloxacin/pharmacology ; Bacteria/genetics ; Genes, Bacterial ; }, abstract = {Antibiotics used systemically to treat infections may have off-target effects on the gut microbiome, potentially resulting in the emergence of drug-resistant bacteria or selection of pathogenic species. These organisms may present a risk to the host and spread to the environment with a risk of transmission in the community. To investigate the risk of emergent antibiotic resistance in the gut microbiome following systemic treatment with antibiotics, this metagenomic analysis project used next-generation sequencing, a custom-built metagenomics pipeline, and differential abundance analysis to study the effect of antibiotics (ampicillin, ciprofloxacin, and fosfomycin) in monotherapy and different combinations at high and low doses, to determine the effect on resistome and taxonomic composition in the gut of Balb/c mice. The results showed that low-dose monotherapy treatments showed little change in microbiome composition but did show an increase in expression of many antibiotic-resistant genes (ARGs) posttreatment. Dual combination treatments allowed the emergence of some conditionally pathogenic bacteria and some increase in the abundance of ARGs despite a general decrease in microbiota diversity. Triple combination treatment was the most successful in inhibiting emergence of relevant opportunistic pathogens and completely suppressed all ARGs after 72 h of treatment. The relative abundances of mobile genetic elements that can enhance transmission of antibiotic resistance either decreased or remained the same for combination therapy while increasing for low-dose monotherapy. Combination therapy prevented the emergence of ARGs and decreased bacterial diversity, while low-dose monotherapy treatment increased ARGs and did not greatly change bacterial diversity.}, } @article {pmid37908022, year = {2023}, author = {Zadjelovic, V and Wright, RJ and Borsetto, C and Quartey, J and Cairns, TN and Langille, MGI and Wellington, EMH and Christie-Oleza, JA}, title = {Microbial hitchhikers harbouring antimicrobial-resistance genes in the riverine plastisphere.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {225}, pmid = {37908022}, issn = {2049-2618}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Lincosamides ; Genes, Bacterial/genetics ; *Microbiota/genetics ; Water ; }, abstract = {BACKGROUND: The widespread nature of plastic pollution has given rise to wide scientific and social concern regarding the capacity of these materials to serve as vectors for pathogenic bacteria and reservoirs for Antimicrobial Resistance Genes (ARG). In- and ex-situ incubations were used to characterise the riverine plastisphere taxonomically and functionally in order to determine whether antibiotics within the water influenced the ARG profiles in these microbiomes and how these compared to those on natural surfaces such as wood and their planktonic counterparts.

RESULTS: We show that plastics support a taxonomically distinct microbiome containing potential pathogens and ARGs. While the plastisphere was similar to those biofilms that grew on wood, they were distinct from the surrounding water microbiome. Hence, whilst potential opportunistic pathogens (i.e. Pseudomonas aeruginosa, Acinetobacter and Aeromonas) and ARG subtypes (i.e. those that confer resistance to macrolides/lincosamides, rifamycin, sulfonamides, disinfecting agents and glycopeptides) were predominant in all surface-related microbiomes, especially on weathered plastics, a completely different set of potential pathogens (i.e. Escherichia, Salmonella, Klebsiella and Streptococcus) and ARGs (i.e. aminoglycosides, tetracycline, aminocoumarin, fluoroquinolones, nitroimidazole, oxazolidinone and fosfomycin) dominated in the planktonic compartment. Our genome-centric analysis allowed the assembly of 215 Metagenome Assembled Genomes (MAGs), linking ARGs and other virulence-related genes to their host. Interestingly, a MAG belonging to Escherichia -that clearly predominated in water- harboured more ARGs and virulence factors than any other MAG, emphasising the potential virulent nature of these pathogenic-related groups. Finally, ex-situ incubations using environmentally-relevant concentrations of antibiotics increased the prevalence of their corresponding ARGs, but different riverine compartments -including plastispheres- were affected differently by each antibiotic.

CONCLUSIONS: Our results provide insights into the capacity of the riverine plastisphere to harbour a distinct set of potentially pathogenic bacteria and function as a reservoir of ARGs. The environmental impact that plastics pose if they act as a reservoir for either pathogenic bacteria or ARGs is aggravated by the persistence of plastics in the environment due to their recalcitrance and buoyancy. Nevertheless, the high similarities with microbiomes growing on natural co-occurring materials and even more worrisome microbiome observed in the surrounding water highlights the urgent need to integrate the analysis of all environmental compartments when assessing risks and exposure to pathogens and ARGs in anthropogenically-impacted ecosystems. Video Abstract.}, } @article {pmid37907736, year = {2023}, author = {Kim, DY and Park, JY and Gee, HY}, title = {Lactobacillus plantarum ameliorates NASH-related inflammation by upregulating L-arginine production.}, journal = {Experimental & molecular medicine}, volume = {55}, number = {11}, pages = {2332-2345}, pmid = {37907736}, issn = {2092-6413}, support = {2018R1A5A2025079//National Research Foundation of Korea (NRF)/ ; 2020M3A9E4038694//National Research Foundation of Korea (NRF)/ ; }, mesh = {Mice ; Humans ; Animals ; *Non-alcoholic Fatty Liver Disease/drug therapy/etiology ; *Lactobacillus plantarum/metabolism ; Disease Models, Animal ; Liver/metabolism ; Inflammation/metabolism ; *Hepatitis/pathology ; Methionine ; Choline/metabolism ; Diet, High-Fat/adverse effects ; Mice, Inbred C57BL ; }, abstract = {Lactobacillus is a probiotic with therapeutic potential for several diseases, including liver disease. However, the therapeutic effect of L. plantarum against nonalcoholic steatohepatitis (NASH) and its underlying mechanisms remain unelucidated. Therefore, we delineated the L. plantarum-mediated NASH regulation in a mouse model to understand its therapeutic effect. We used a choline-deficient high-fat diet (CD-HFD)-induced murine model that recapitulated the critical features of human metabolic syndrome and investigated the effect of L. plantarum on NASH pathogenesis using transcriptomic, metagenomic, and immunohistochemistry analyses. Validation experiments were performed using liver organoids and a murine model fed a methionine-choline-deficient (MCD) diet. L. plantarum treatment in mice significantly decreased liver inflammation and improved metabolic phenotypes, such as insulin tolerance and the hepatic lipid content, compared with those in the vehicle group. RNA-sequencing analysis revealed that L. plantarum treatment significantly downregulated inflammation-related pathways. Shotgun metagenomic analysis revealed that L-arginine biosynthesis-related microbial genes were significantly upregulated in the L. plantarum group. We also confirmed the elevated arginine levels in the serum of the L. plantarum group. We further used liver organoids and mice fed an MCD diet to demonstrate that L-arginine alone was sufficient to alleviate liver inflammation. Our data revealed a novel and counterintuitive therapeutic effect of L. plantarum on alleviating NASH-related liver inflammation by increasing circulating L-arginine.}, } @article {pmid37907561, year = {2023}, author = {Li, H and Ma, X and Li, Y and Liu, Q and Tian, Q and Yang, X and Zhou, Z and Ren, J and Sun, B and Feng, X and Zhang, H and Yin, X and Li, H and Ding, X}, title = {The metagenomic and metabolomic profile of the gut microbes in Chinese full-term and late preterm infants treated with Clostridium butyricum.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {18775}, pmid = {37907561}, issn = {2045-2322}, mesh = {Humans ; Infant, Newborn ; Infant ; Infant, Premature ; *Clostridium butyricum/genetics ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Biotin/pharmacology ; East Asian People ; *Probiotics ; }, abstract = {The present study investigated the composition, abundance, and diversity of gut microbes in full-term and late-preterm infants from a medical center in eastern China. A total of 144 genomes of stool samples were captured for 16S rRNA metagenomic analyses. A high abundance of commensal intestinal bacteria was detected in these samples such as Phocaeicola vulgatus, Escherichia coli, and Faecalibacterium prausnitzii, indicating a relatively consistent diversity of gut microbes in the present full-term infants aged 38-40 weeks. However, late preterm infants (n = 50) with mandatory antimicrobials feeding exhibited lower diversity but a higher composition of opportunistic pathogens such as Enterococcus species. Centralized on the situation, we explored the regulatory effect of Clostridium butyricum as probiotics on these late preterm infants. The consumption of C. butyricum did not restore the composition of gut microbes altered by antimicrobials to normal levels, although several opportunistic pathogens decreased significantly after probiotic therapy including Staphylococcus aureus, Sphingomonas echinoides, and Pseudomonas putida. We also compared the effects of day-fed versus night-fed probiotics. Intriguingly, the nighttime feeding showed a higher proportion of C. butyricum compared with probiotic day-feeding. Finally, fecal metabolome and metabolites were analyzed in late preterm infants with (n = 20) or without probiotic therapy (n = 20). The KEGG enrichment analysis demonstrated that vitamin digestion and absorption, synaptic vesicle cycle, and biotin metabolism were significantly increased in the probiotic-treated group, while MSEA indicated that a series of metabolism were significantly enriched in probiotic-treated infants including glycerolipid, biotin, and lysine, indicating the complex effects of probiotic therapy on glutathione metabolism and nutrients digestion and absorption in late preterm infants. Overall, this study provided metagenomic and metabolomic profile of the gut microbes in full-term newborns and late preterm infants in eastern China. Further studies are needed to support and elucidate the role of probiotic feeding in late preterm infants with mandatory antimicrobial treatment.}, } @article {pmid37907101, year = {2024}, author = {Mugnai, G and Borruso, L and Wu, YL and Gallinaro, M and Cappitelli, F and Zerboni, A and Villa, F}, title = {Ecological strategies of bacterial communities in prehistoric stone wall paintings across weathering gradients: A case study from the Borana zone in southern Ethiopia.}, journal = {The Science of the total environment}, volume = {907}, number = {}, pages = {168026}, doi = {10.1016/j.scitotenv.2023.168026}, pmid = {37907101}, issn = {1879-1026}, mesh = {RNA, Ribosomal, 16S/genetics ; Ethiopia ; *Bacteria/metabolism ; *Microbiota/genetics ; Biodiversity ; Phylogeny ; Soil Microbiology ; }, abstract = {Rock art paintings represent fragile ecosystems supporting complex microbial communities tuned to the lithic substrate and climatic conditions. The composition and activity of these microbial communities associated with different weathering patterns affecting rock art sites remain unexplored. This study aimed to explore how bacterial communities adapt their ecological strategies based on substrate weathering, while also examining the role of their metabolic pathways in either biodeterioration or bioprotection of the underlying stone. SEM-EDS investigations coupled with 16S rRNA gene sequencing and PICRUSt2 analysis were applied on different weathered surfaces that affect southern Ethiopian rock paintings to investigate the relationships between the current stone microbiome and weathering patterns. The findings revealed that samples experiencing low and high weathering reached a climax stage characterized by stable microenvironments and limited resources. This condition favored K-strategist microorganisms, leading to reduced α-biodiversity and a community with a positive or neutral impact on the substrate. In contrast, moderately-weathered samples displayed diverse microhabitats, resulting in the prevalence of r-strategist bacteria, increased α-biodiversity, and the presence of specialist microorganisms. Moreover, the bacterial communities in moderately-weathered samples demonstrated the highest potential for carbon fixation, stress responses, and complete nitrogen and sulfur cycles. This bacterial community also showed the potential to negatively impact the underlying substrate. This research provided valuable insights into the little-understood ecology of bacterial communities inhabiting deteriorated surfaces, shedding light on the potential role of these microorganisms in the sustainable conservation of rock art.}, } @article {pmid37906569, year = {2023}, author = {Deng, Y and Yang, X and Chen, J and Yang, S and Chi, H and Chen, C and Yang, X and Hou, C}, title = {Jute (Corchorus olitorius L.) Nanocrystalline Cellulose Inhibits Insect Virus via Gut Microbiota and Metabolism.}, journal = {ACS nano}, volume = {17}, number = {21}, pages = {21662-21677}, doi = {10.1021/acsnano.3c06824}, pmid = {37906569}, issn = {1936-086X}, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome ; Cellulose/pharmacology ; *Corchorus/genetics ; *Dicistroviridae ; Antiviral Agents/pharmacology ; }, abstract = {Natural plant nanocrystalline cellulose (NCC), exhibiting a number of exceptional performance characteristics, is widely used in food fields. However, little is known about the relationship between NCC and the antiviral effect in animals. Here, we tested the function of NCC in antiviral methods utilizing honey bees as the model organism employing Israeli acute paralysis virus (IAPV), a typical RNA virus of honey bees. In both the lab and the field, we fed the IAPV-infected bees various doses of jute NCC (JNCC) under carefully controlled conditions. We found that JNCC can reduce IAPV proliferation and improve gut health. The metagenome profiling suggested that IAPV infection significantly decreased the abundance of gut core bacteria, while JNCC therapy considerably increased the abundance of the gut core bacteria Snodgrassella alvi and Lactobacillus Firm-4. Subsequent metabolome analysis further revealed that JNCC promoted the biosynthesis of fatty acids and unsaturated fatty acids, accelerated the purine metabolism, and then increased the expression of antimicrobial peptides (AMPs) and the genes involved in the Wnt and apoptosis signaling pathways against IAPV infection. Our results highlighted that JNCC could be considered as a prospective candidate agent against a viral infection.}, } @article {pmid37905808, year = {2023}, author = {Ma, C and Zhang, Y and Jiang, S and Teng, F and Huang, S and Zhang, J}, title = {Cross-cohort single-nucleotide-variant profiling of gut microbiota suggests a novel gut-health assessment approach.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0082823}, pmid = {37905808}, issn = {2379-5077}, support = {32160545//National Natural Science Foundation of China/ ; 22-3-7-lczx-7-nsh//Qingdao University (QDU)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Metagenome/genetics ; Metagenomics ; Nucleotides ; }, abstract = {Most studies focused much on the change in abundance and often failed to explain the microbiome variation related to disease conditions, Herein, we argue that microbial genetic changes can precede the ecological changes associated with the host physiological changes and, thus, would offer a new information layer from metagenomic data for predictive modeling of diseases. Interestingly, we preliminarily found a few genetic biomarkers on SCFA production can cover most chronic diseases involved in the meta-analysis. In the future, it is of both scientific and clinical significance to further explore the dynamic interactions between adaptive evolution and ecology of gut microbiota associated with host health status.}, } @article {pmid37905155, year = {2023}, author = {Antillon, SF and Bernhardt, TG and Chamakura, K and Young, R}, title = {Physiological characterization of single gene lysis proteins.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37905155}, support = {R35 GM136396/GM/NIGMS NIH HHS/United States ; T32 GM135748/GM/NIGMS NIH HHS/United States ; }, abstract = {Until recently only 11 distinct Sgls (single gene lysis proteins) have been experimentally identified. Of these, three have been shown to be specific inhibitors of different steps in the pathway that supplies Lipid II to the peptidoglycan (PG) biosynthesis machinery: Qβ A2 inhibits MurA, ϕX174 E inhibits MraY, and Lys from coliphage M inhibits MurJ. These Sgls have been called "protein antibiotics" because the lytic event is a septal catastrophe indistinguishable from that caused by cell wall antibiotics. Here we propose to designate these as members of type I Sgls, to distinguish them from another Sgl, the L protein of the paradigm ssRNA phage MS2. Although none of the other distinct Sgls have significant sequence similarity to L, alignments suggested the presence of four domains distinguished by hydrophobic and polar character. The simplest notion is that these other Sgls have the same autolytic mechanism and, based on this, constitute type II. Although the number of experimentally confirmed Sgls has not changed, recent environmental metagenomes and metatranscriptomes have revealed thousands of new ssRNA phage genomes, each of which presumably has at least one Sgl gene. Here we report on methods to distinguish type I and type II Sgls. Using phase-contrast microscopy, we show that both classes of Sgls cause the formation of blebs prior to lysis, but the location of the blebs differs significantly. In addition, we show that L and other type II Sgls do not inhibit net synthesis of PG, as measured by incorporation of [3][H]-diaminopimelic acid. Finally, we provide support for the unexpected finding by Adler and colleagues that the Sgl from Pseudomonas phage PP7 is a type I Sgl, as determined by the two methods. This shows that the sharing the putative 4-domain structure suggested for L is not a reliable discriminator for operational characterization of Sgls. Overall, this study establishes new ways to rapidly classify novel Sgls and thus may facilitate the identification of new cell envelope targets that will help generate new antibiotics.}, } @article {pmid37904928, year = {2023}, author = {Kosmopoulos, JC and Klier, KM and Langwig, MV and Tran, PQ and Anantharaman, K}, title = {Viromes vs. mixed community metagenomes: choice of method dictates interpretation of viral community ecology.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37904928}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: Viruses, the majority of which are uncultivated, are among the most abundant biological entities on Earth. From altering microbial physiology to driving community dynamics, viruses are fundamental members of microbiomes. While the number of studies leveraging viral metagenomics (viromics) for studying uncultivated viruses is growing, standards for viromics research are lacking. Viromics can utilize computational discovery of viruses from total metagenomes of all community members (hereafter metagenomes) or use physical separation of virus-specific fractions (hereafter viromes). However, differences in the recovery and interpretation of viruses from metagenomes and viromes obtained from the same samples remain understudied.

RESULTS: Here, we compare viral communities from paired viromes and metagenomes obtained from 60 diverse samples across human gut, soil, freshwater, and marine ecosystems. Overall, viral communities obtained from viromes were more abundant and species rich than those obtained from metagenomes, although there were some exceptions. Despite this, metagenomes still contained many viral genomes not detected in viromes. We also found notable differences in the predicted lytic state of viruses detected in viromes vs metagenomes at the time of sequencing. Other forms of variation observed include genome presence/absence, genome quality, and encoded protein content between viromes and metagenomes, but the magnitude of these differences varied by environment.

CONCLUSIONS: Overall, our results show that the choice of method can lead to differing interpretations of viral community ecology. We suggest that the choice of whether to target a metagenome or virome to study viral communities should be dependent on the environmental context and ecological questions being asked. However, our overall recommendation to researchers investigating viral ecology and evolution is to pair both approaches to maximize their respective benefits.}, } @article {pmid37904422, year = {2023}, author = {Li, K and Li, S and Hong, J and Cheng, W and Zhang, Y and Liang, Z and Tang, Q and Shen, B}, title = {Meningitis and sepsis caused by Streptococcus suis in an elderly woman: A CARE-compliant case report.}, journal = {Medicine}, volume = {102}, number = {43}, pages = {e35780}, pmid = {37904422}, issn = {1536-5964}, mesh = {Humans ; Female ; Aged ; *Streptococcus suis/genetics ; *Streptococcal Infections/diagnosis/drug therapy/microbiology ; *Sepsis/diagnosis/drug therapy/complications ; *Meningitis, Bacterial/diagnosis/drug therapy ; *Intracranial Hypertension/complications ; }, abstract = {RATIONALE: Streptococcus suis (S suis)-associated infections are uncommon but life-threatening diseases. The clinical manifestations vary from general symptoms of bacterial infection to fatal meningitis. The clinical manifestation and routine diagnostic testing is not specific enough to obtain well-time diagnosis.

We report a case of meningitis and sepsis caused by S suis infection. A 70-year-old woman presented to our emergency department with generalized pain. After hospital admission, her condition rapidly deteriorated to fever, intracranial hypertension, and disturbance of consciousness. Examination of the blood and cerebrospinal fluid with metagenomic next-generation sequencing and bacterial cultures revealed S suis infection.

INTERVENTIONS AND OUTCOMES: After anti-infection therapy with meropenem and vancomycin, the patient recovered and was discharged from the hospital with no residual effects.

LESSONS: Human infections with S suis are extremely rare. If clinicians encounter a patient with fever, disturbance of consciousness, and intracranial hypertension, especially those who have been exposed to raw pork, S suis infection should be considered. Metagenomic next-generation sequencing can be a useful adjunct for the rapid diagnosis of S suis infection and aid in the planning of clinical treatment. Meanwhile, public health awareness is necessary to limit the risk of S suis infection.}, } @article {pmid37904420, year = {2023}, author = {Cheng, J and Qu, JY and Hamblin, MR and Hao, D and Wen, X}, title = {Disseminated disease caused by Mycobacterium marseillense: A case report and literature review.}, journal = {Medicine}, volume = {102}, number = {43}, pages = {e35781}, pmid = {37904420}, issn = {1536-5964}, mesh = {Male ; Humans ; Aged ; Mycobacterium avium Complex ; *Mycobacterium ; *Mycobacterium Infections, Nontuberculous/diagnosis ; Clarithromycin/therapeutic use ; }, abstract = {RATIONALE: Among numerous types of nontuberculous mycobacterial infections, Mycobacterium avium complex is a related group of species, which can cause various diseases in humans. Mycobacterium marseillense is a member of the Mycobacterium avium complex, which accounts for only a small proportion of species, but causes rare diseases affecting the lungs, lymph nodes, skin, and tendon sheath. So far, very few cases have been reported.

PATIENT CONCERNS: A 76-year-old male of peculiar skin infection. Metagenomic Next Generation Sequencing and bacterial culture of skin secretions revealed M marseillense. To the best of our knowledge, we report the first patient diagnosed with disseminated M marseillense infection. Here, we identified only 8 other reports of patients with M marseillense infection.

DIAGNOSES: Disseminated M marseillense infection.

INTERVENTIONS: The patient was treated with clarithromycin, rifampicin, moxifloxacin, and ethambutol.

OUTCOMES: The skin lesions of the patient showed significant improvement, and his pruritus and limb pain were notably reduced after 7 months of follow-up.

LESSONS: Metagenomic Next Generation Sequencing may be a useful tool to diagnose M marseillense infection, but the results should be confirmed by culture and mycobacterial identification.}, } @article {pmid37903314, year = {2023}, author = {Zhang, T and Huang, X and Xu, T and Li, S and Cui, M}, title = {Pyogenic liver abscess caused by extended-spectrum β-lactamase-producing hypervirulent Klebsiella pneumoniae diagnosed by third-generation sequencing: a case report and literature review.}, journal = {The Journal of international medical research}, volume = {51}, number = {10}, pages = {3000605231206296}, pmid = {37903314}, issn = {1473-2300}, mesh = {Female ; Humans ; *Liver Abscess, Pyogenic/diagnosis/drug therapy ; Klebsiella pneumoniae/genetics ; *Klebsiella Infections/diagnosis/drug therapy ; *Choledocholithiasis ; *Diabetes Mellitus ; beta-Lactamases/genetics ; }, abstract = {We report a case of a woman with diabetes mellitus and choledocholithiasis who had a low fever with chills and severe weakness for 7 days. The patient's abdominal tenderness was positive. Computed tomography and magnetic resonance imaging showed a giant abscess in the liver. The production of extended-spectrum β-lactamases by hypervirulent Klebsiella pneumoniae was found in the purulent fluid of the liver by nanopore-based metagenomic third-generation sequencing combined with an antibiotic susceptibility test. The patient recovered after intravenous antibiotic therapy and percutaneous drainage. Patients with a history of diabetes mellitus and choledocholithiasis should be aware of the possibility of pyogenic liver abscesses caused by hypervirulent Klebsiella pneumoniae. To rapidly control the development of this disease, nanopore-based metagenomic third-generation sequencing plays an important role not only in rapidly identifying pathogens, but also in guiding the use of antibiotics.}, } @article {pmid37902877, year = {2023}, author = {Jiao, Y and Li, Y and Dou, W and Zhang, W and Liu, H}, title = {Biochar alleviates the crop failure of rice production induced by low-nitrogen cultivation mode by regulating the soil microbes taxa composition.}, journal = {Archives of microbiology}, volume = {205}, number = {12}, pages = {361}, pmid = {37902877}, issn = {1432-072X}, support = {51479033//National Natural Science Foundation Project/ ; 51479033//National Natural Science Foundation Project/ ; 51479033//National Natural Science Foundation Project/ ; 51479033//National Natural Science Foundation Project/ ; 51479033//National Natural Science Foundation Project/ ; }, mesh = {*Soil/chemistry ; *Oryza ; Nitrogen/analysis ; Fertilizers/analysis ; Bacteria/genetics ; Soil Microbiology ; }, abstract = {To improve the nitrogen utilization efficiency and a series of environmental problems caused by excessive application of nitrogen fertilizer, actual agricultural production often reduced the usage ratio of nitrogen fertilizer. However, the reduction in nitrogen fertilizer not only affects the soil microenvironment but also leads to adverse effects on rice yield. Due to its unique properties, biochar can regulate soil nutrient distribution and significantly affect soil microbial community structure/functions. To further understand the effects of different levels of biochar on soil nutrient indicators, soil microorganisms and crop growth under the nitrogen-reduction condition, our experiment with four groups was set up as followed: 0%, 2.5% and 5% biochar application rates with 99 kg/hm[2] nitrogen fertilizer and one control group (the actual fertilizer standard used in the field:110 kg/hm[2]) without no exogenous biochar supplement. The rice yield and soil nutrient indexes were observed, and the differences between groups were analyzed based on multiple comparisons. 16S ribosomal RNA and ITS sequencing were used to analyze the community structure of soil bacteria and fungi. Redundancy analysis was performed to obtain the correlation relationships between microbial community marker species, soil nutrient indexes, and rice yield. Path analysis was used to determine the mechanism by which soil nutrient indexes affect rice yield. The results showed that a higher application rate of biochar led to a significant increased trend in the soil pH, organic matter and total nitrogen content. In addition, a high concentration of biochar under nitrogen-reduction condition decreased the soil bacterial diversity but elevated the fungal diversity. Different concentrations of biochar resulted in these changes in the relative abundance of soil bacteria/fungi but did not alter the dominant species taxa. Taken together, appropriate usage for biochar under the nitrogen-reduction background could induce alteration in soil nutrient indicators, microbial communities and crop yields. These results provide a theoretical basis for exploring scientific, green and efficient fertilization strategies in the rice cultivation industry. Notably, the interaction relationship between rhizosphere microorganisms in rice and soil microbial taxa are not yet clear, so further research on its detailed effects on rice production is needed. In addition, the Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis for the physiological functions of the soil microbes could only predict the potential metabolic pathways. Therefore, the next-generation metagenome techonology might be performed to explore detailed metabolic differences and accurate taxa alteration at the "species" level.}, } @article {pmid37902391, year = {2023}, author = {Liu, L and Chen, Y and Shen, J and Pan, Y and Lin, W}, title = {Metabolic versatility of soil microbial communities below the rocks of the hyperarid Dalangtan Playa.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {11}, pages = {e0107223}, pmid = {37902391}, issn = {1098-5336}, support = {T2225011//National Natural Science Foundation of China (NSFC)/ ; ZDBS-SSW-TLC001//Key Research Program of the Chinese Academy of Sciences/ ; IGGCAS-201904, IGGCAS-202102//Key Research Programs of the Institute of Geology and Geophysics, Chinese Academy of Sciences/ ; }, mesh = {*Soil ; China ; Soil Microbiology ; *Microbiota ; Desert Climate ; }, abstract = {The hyperarid Dalangtan Playa in the western Qaidam Basin, northwestern China, is a unique terrestrial analog of Mars. Despite the polyextreme environments of this area, habitats below translucent rocks capable of environmental buffering could serve as refuges for microbial life. In this study, the hybrid assembly of Illumina short reads and Nanopore long reads recovered high-quality and high-continuity genomes, allowing for high-accuracy analysis and a deeper understanding of extremophiles in the sheltered soils of the Dalangtan Playa. Our findings reveal self-supporting and metabolically versatile sheltered soil communities adapted to a hyperarid and hypersaline playa, which provides implications for the search for life signals on Mars.}, } @article {pmid37901819, year = {2023}, author = {Cheng, W and Fan, H and Yun, Y and Zhao, X and Su, Z and Tian, X and Liu, D and Ma, T and Li, G}, title = {Effects of nutrient injection on the Xinjiang oil field microbial community studied in a long core flooding simulation device.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1230274}, pmid = {37901819}, issn = {1664-302X}, abstract = {Microbial Enhanced Oil Recovery (MEOR) is an option for recovering oil from depleted reservoirs. Numerous field trials of MEOR have confirmed distinct microbial community structure in diverse production wells within the same block. The variance in the reservoir microbial communities, however, remains ambiguously documented. In this study, an 8 m long core microbial flooding simulation device was built on a laboratory scale to study the dynamic changes of the indigenous microbial community structure in the Qizhong Block, Xinjiang oil field. During the MEOR, there was an approximate 34% upswing in oil extraction. Based on the 16S rRNA gene high-throughput sequencing, our results indicated that nutrition was one of the factors affecting the microbial communities in oil reservoirs. After the introduction of nutrients, hydrocarbon oxidizing bacteria became active, followed by the sequential activation of facultative anaerobes and anaerobic fermenting bacteria. This was consistent with the hypothesized succession of a microbial ecological "food chain" in the reservoir, which preliminarily supported the two-step activation theory for reservoir microbes transitioning from aerobic to anaerobic states. Furthermore, metagenomic results indicated that reservoir microorganisms had potential functions of hydrocarbon degradation, gas production and surfactant production. Understanding reservoir microbial communities and improving oil recovery are both aided by this work.}, } @article {pmid37901815, year = {2023}, author = {Ding, J and Yang, W and Liu, X and Zhao, Q and Dong, W and Zhang, C and Liu, H and Zhao, Y}, title = {Unraveling the rate-limiting step in microorganisms' mediation of denitrification and phosphorus absorption/transport processes in a highly regulated river-lake system.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1258659}, pmid = {37901815}, issn = {1664-302X}, abstract = {River-lake ecosystems are indispensable hubs for water transfers and flow regulation engineering, which have frequent and complex artificial hydrological regulation processes, and the water quality is often unstable. Microorganisms usually affect these systems by driving the nutrient cycling process. Thus, understanding the key biochemical rate-limiting steps under highly regulated conditions was critical for the water quality stability of river-lake ecosystems. This study investigated how the key microorganisms and genes involving nitrogen and phosphorus cycling contributed to the stability of water by combining 16S rRNA and metagenomic sequencing using the Dongping river-lake system as the case study. The results showed that nitrogen and phosphorus concentrations were significantly lower in lake zones than in river inflow and outflow zones (p < 0.05). Pseudomonas, Acinetobacter, and Microbacterium were the key microorganisms associated with nitrate and phosphate removal. These microorganisms contributed to key genes that promote denitrification (nirB/narG/narH/nasA) and phosphorus absorption and transport (pstA/pstB/pstC/pstS). Partial least squares path modeling (PLS-PM) revealed that environmental factors (especially flow velocity and COD concentration) have a significant negative effect on the key microbial abundance (p < 0.001). Our study provides theoretical support for the effective management and protection of water transfer and the regulation function of the river-lake system.}, } @article {pmid37901812, year = {2023}, author = {Potter-Birriel, JM and Pollio, AR and Knott, BD and Chunashvili, T and Fung, CK and Conte, MA and Reinbold-Wasson, DD and Hang, J}, title = {Metagenomics analysis reveals presence of the Merida-like virus in Georgia.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1258810}, pmid = {37901812}, issn = {1664-302X}, abstract = {Arbovirus surveillance is fundamental for the discovery of novel viruses and prevention of febrile vector-borne illnesses. Vector-borne pathogens can rapidly expand and adapt in new geographic and environmental conditions. In this study, metagenomic surveillance was conducted to identify novel viruses in the Country of Georgia. A total of 521 mosquitoes were captured near a military training facility and pooled from species Culex pipiens (Linnaeus) (87%) and Aedes albopictus (Skuse) (13%). We decided to further analyze the Culex pipiens mosquitoes, due to the more extensive number of samples collected. Our approach was to utilize an unbiased total RNA-seq for pathogen discovery in order to explore the mosquito virome. The viral reads from this analysis were mostly aligned to Insect-specific viruses from two main families, the Iflaviridae; a positive-stranded RNA virus and the Rhabdoviridae; a negative- and single-stranded RNA virus. Our pathogen discovery analysis revealed viral reads aligning to the Merida-like virus Turkey (MERDLVT) strain among the Rhabdoviridae. To further validate this result, we conducted a BLAST sequence comparison analysis of our samples with the MERDLVT strain. Our positive samples aligned to the MERDLVT strain with 96-100% sequence identity and 99.7-100% sequence coverage. A bootstrapped maximum-likelihood phylogenetic tree was used to evaluate the evolutionary relationships among these positive pooled specimens with the (MERDLVT) strain. The Georgia samples clustered most closely with two strains from Turkey, the Merida-like virus KE-2017a isolate 139-1-21 and the Merida-like virus Turkey isolate P431. Collectively, these results show the presence of the MERDLVT strain in Georgia.}, } @article {pmid37900734, year = {2023}, author = {Sytar, O and Kumar, A}, title = {Editorial: The adaptation strategies of plants to alleviate important environmental stresses.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1307399}, pmid = {37900734}, issn = {1664-462X}, } @article {pmid37900322, year = {2023}, author = {Zhan, D and Li, D and Yuan, K and Sun, Y and He, L and Zhong, J and Wang, L}, title = {Characteristics of the pulmonary microbiota in patients with mild and severe pulmonary infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1227581}, pmid = {37900322}, issn = {2235-2988}, mesh = {Humans ; *Pneumonia ; *Microbiota/genetics ; Bronchoalveolar Lavage Fluid ; Metagenome ; *Micrococcaceae ; *Acinetobacter ; *Bacillus ; *Coinfection ; *Fabaceae ; High-Throughput Nucleotide Sequencing ; Klebsiella ; Lung ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Lung infection is a global health problem associated with high morbidity and mortality and increasing rates of hospitalization. The correlation between pulmonary microecology and infection severity remains unclear. Therefore, the purpose of this study was to investigate the differences in lung microecology and potential biomarkers in patients with mild and severe pulmonary infection.

METHOD: Patients with pulmonary infection or suspected infection were divided into the mild group (140 cases) and the severe group (80 cases) according to pneomonia severity index (PSI) scores. Here, we used metagenomic next-generation sequencing (mNGS) to detect DNA mainly from bronchoalveolar lavage fluid (BALF) collected from patients to analyze changes in the lung microbiome of patients with different disease severity.

RESULT: We used the mNGS to analyze the pulmonary microecological composition in patients with pulmonary infection. The results of alpha diversity and beta diversity analysis showed that the microbial composition between mild and severe groups was similar on the whole. The dominant bacteria were Acinetobacter, Bacillus, Mycobacterium, Staphylococcus, and Prevotella, among others. Linear discriminant analysis effect size (LEfSe) results showed that there were significant differences in virus composition between the mild and severe patients, especially Simplexvirus and Cytomegalovirus, which were prominent in the severe group. The random forest model screened 14 kinds of pulmonary infection-related pathogens including Corynebacterium, Mycobacterium, Streptococcus, Klebsiella, and Acinetobacter. In addition, it was found that Rothia was negatively correlated with Acinetobacter, Mycobacterium, Bacillus, Enterococcus, and Klebsiella in the mild group through co-occurrence network, while no significant correlation was found in the severe group.

CONCLUSION: Here, we describe the composition and diversity of the pulmonary microbiome in patients with pulmonary infection. A significant increase in viral replication was found in the severe group, as well as a significant difference in microbial interactions between patients with mild and severe lung infections, particularly the association between the common pathogenic bacteria and Rothia. This suggests that both pathogen co-viral infection and microbial interactions may influence the course of disease. Of course, more research is needed to further explore the specific mechanisms by which microbial interactions influence disease severity.}, } @article {pmid37900317, year = {2023}, author = {Li, XX and Niu, CZ and Zhao, YC and Fu, GW and Zhao, H and Huang, MJ and Li, J}, title = {Clinical application of metagenomic next-generation sequencing in non-immunocompromised patients with severe pneumonia supported by veno-venous extracorporeal membrane oxygenation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1269853}, pmid = {37900317}, issn = {2235-2988}, mesh = {Humans ; Male ; Female ; *Extracorporeal Membrane Oxygenation ; Retrospective Studies ; High-Throughput Nucleotide Sequencing ; *Acinetobacter baumannii ; Metagenomics ; *Pneumonia/diagnosis/therapy ; Sensitivity and Specificity ; }, abstract = {OBJECTIVES: This study aims to explore the pathogen-detected effect of mNGS technology and its clinical application in non-immunocompromised patients with severe pneumonia supported by vv-ECMO.

METHODS: A retrospective analysis was conducted on a cohort of 50 non-immunocompromised patients who received vv-ECMO support for severe pneumonia between January 2016 and December 2022. These patients were divided into two groups based on their discharge outcomes: the deterioration group (Group D), which included 31 cases, and the improvement group (Group I), consisting of 19 cases. Baseline characteristics and clinical data were collected and analyzed.

RESULTS: Among the 50 patients enrolled, Group D exhibited a higher prevalence of male patients (80.6% vs. 52.6%, p < 0.05), more smokers (54.8% vs. 21.1%, p < 0.05), and were older than those in Group I (55.16 ± 16.34 years vs. 42.32 ± 19.65 years, p < 0.05). Out of the 64 samples subjected to mNGS detection, 55 (85.9%) yielded positive results, with a positivity rate of 83.7% (36/43) in Group D and 90.5% (19/21) in Group I. By contrast, the positive rate through traditional culture stood at 64.9% (74/114). Among the 54 samples that underwent both culture and mNGS testing, 23 (42.6%) displayed consistent pathogen identification, 13 (24.1%) exhibited partial consistency, and 18 (33.3%) showed complete inconsistency. Among the last cases with complete inconsistency, 14 (77.8%) were culture-negative, while two (11.1%) were mNGS-negative, and the remaining two (11.1%) presented mismatches. Remarkably, mNGS surpassed traditional culture in pathogen identification (65 strains vs. 23 strains). Within these 65 strains, 56 were found in Group D, 26 in Group I, and 17 were overlapping strains. Interestingly, a diverse array of G+ bacteria, fungi, viruses, and special pathogens were exclusive to Group D. Furthermore, Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae were more prevalent in Group D compared to Group I. Importantly, mNGS prompted antibiotic treatment adjustments in 26 patients (52.0%).

CONCLUSIONS: Compared with the conventional culture, mNGS demonstrated a higher positive rate, and emerges as a promising method for identifying mixed pathogens in non-immunodeficient patients with severe pneumonia supported by vv-ECMO. However, it is crucial to combine the interpretation of mNGS data with clinical information and traditional culture results for a comprehensive assessment.}, } @article {pmid37900308, year = {2023}, author = {Ye, X and Yu, F and Zhou, J and Zhao, C and Wu, J and Ni, X}, title = {Analysis of the gut microbiota in children with gastroesophageal reflux disease using metagenomics and metabolomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1267192}, pmid = {37900308}, issn = {2235-2988}, mesh = {Humans ; Child ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Metabolomics/methods ; Bacteria/genetics ; Metagenomics ; *Gastroesophageal Reflux ; }, abstract = {BACKGROUND: There is no direct evidence of gut microbiota disturbance in children with gastroesophageal reflux disease (GERD). This study aimed to provide direct evidence and a comprehensive understanding of gut microbiota disturbance in children with GERD through combined metagenomic and metabolomic analysis.

METHODS: 30 children with GERD and 30 healthy controls (HCs) were continuously enrolled, and the demographic and clinical characteristics of the subjects were collected. First, 16S rRNA sequencing was used to evaluate differences in the gut microbiota between children with GERD and HC group, and 10 children with GERD and 10 children in the HC group were selected for metagenomic analysis. Nontargeted metabolomic analysis was performed using liquid chromatography/mass spectrometry (LC/MS), and metagenomic and metabolomic data were analyzed together.

RESULTS: There were significant differences in the gut microbiota diversity and composition between children with GERD and HCs. The dominant bacteria in children with GERD were Proteobacteria and Bacteroidota. At the species level, the top three core bacterial groups were Bacteroides stercoris, Bacteroides vulgatus and Alistipes putredinis. The main differential pathways were identified to be related to energy, amino acid, vitamin, carbohydrate and lipid metabolism. LC/MS detected 288 different metabolites in the positive and negative ion modes between children with GERD and HCs, which were mainly involved in arachidonic acid (AA), tyrosine, glutathione and caffeine metabolism.

CONCLUSION: This study provides new evidence of the pathogenesis of GERD. There are significant differences in the gut microbiota, metabolites and metabolic pathways between HCs and children with GERD, and the differences in metabolites are related to specific changes in bacterial abundance. In the future, GERD may be treated by targeting specific bacteria related to AA metabolism.}, } @article {pmid37898635, year = {2023}, author = {de Oliveira Vieira, KC and da Silva, ABB and Felício, SA and Lira, FS and de Figueiredo, C and Bezirtzoglou, E and Pereira, VC and Nakagaki, WR and Nai, GA and Winkelströter, LK}, title = {Orange juice containing Pediococcus acidilactici CE51 modulates the intestinal microbiota and reduces induced inflammation in a murine model of colitis.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {18513}, pmid = {37898635}, issn = {2045-2322}, mesh = {Male ; Mice ; Animals ; *Gastrointestinal Microbiome ; *Pediococcus acidilactici/metabolism ; *Citrus sinensis/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; C-Reactive Protein/metabolism ; Disease Models, Animal ; *Colitis/chemically induced/drug therapy ; Inflammation/pathology ; Dextran Sulfate/toxicity ; *Probiotics/pharmacology/therapeutic use ; Mice, Inbred C57BL ; Colon/pathology ; }, abstract = {The management of inflammatory bowel diseases has been widely investigated, especially ulcerative colitis. Thus, studies with the application of new probiotic products are needed in the prevention/treatment of these clinical conditions. The objective of this work was to evaluate the effects of probiotic orange juice containing Pediococcus acidilactici CE51 in a murine model of colitis. 45 male Swiss lineage mice were used, divided into five groups (n = 9): control, colitis, colitis + probiotic (probiotic orange juice containing CE51), colitis + placebo (orange juice) and colitis + sulfasalazine (10 mg/kg/Weight). The induction of colitis was performed with dextran sodium sulfate (3%). The treatment time was 5 and 15 days after induction. Histopathological analysis, serum measurements of TNF-α and C-reactive protein and metagenomic analysis of feces were performed after euthanasia. Probiotic treatment reduced inflammation in the small intestine, large intestine and spleen. The probiotic did not alter the serum dosages of TNF-α and C-reactive protein. Their use maintained the quantitative ratio of the phylum Firmicutes/Bacteroidetes and increased Lactobacillus helveticus with 15 days of treatment (p < 0.05). The probiotic orange juice containing P. acidilactici CE51 positively modulated the gut microbiota composition and attenuated the inflammation induced in colitis.}, } @article {pmid37898601, year = {2023}, author = {Tisza, M and Javornik Cregeen, S and Avadhanula, V and Zhang, P and Ayvaz, T and Feliz, K and Hoffman, KL and Clark, JR and Terwilliger, A and Ross, MC and Cormier, J and Moreno, H and Wang, L and Payne, K and Henke, D and Troisi, C and Wu, F and Rios, J and Deegan, J and Hansen, B and Balliew, J and Gitter, A and Zhang, K and Li, R and Bauer, CX and Mena, KD and Piedra, PA and Petrosino, JF and Boerwinkle, E and Maresso, AW}, title = {Wastewater sequencing reveals community and variant dynamics of the collective human virome.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6878}, pmid = {37898601}, issn = {2041-1723}, mesh = {Humans ; *Virome/genetics ; Wastewater ; Cities ; Disease Outbreaks ; *Poliovirus ; SARS-CoV-2/genetics ; }, abstract = {Wastewater is a discarded human by-product, but its analysis may help us understand the health of populations. Epidemiologists first analyzed wastewater to track outbreaks of poliovirus decades ago, but so-called wastewater-based epidemiology was reinvigorated to monitor SARS-CoV-2 levels while bypassing the difficulties and pit falls of individual testing. Current approaches overlook the activity of most human viruses and preclude a deeper understanding of human virome community dynamics. Here, we conduct a comprehensive sequencing-based analysis of 363 longitudinal wastewater samples from ten distinct sites in two major cities. Critical to detection is the use of a viral probe capture set targeting thousands of viral species or variants. Over 450 distinct pathogenic viruses from 28 viral families are observed, most of which have never been detected in such samples. Sequencing reads of established pathogens and emerging viruses correlate to clinical data sets of SARS-CoV-2, influenza virus, and monkeypox viruses, outlining the public health utility of this approach. Viral communities are tightly organized by space and time. Finally, the most abundant human viruses yield sequence variant information consistent with regional spread and evolution. We reveal the viral landscape of human wastewater and its potential to improve our understanding of outbreaks, transmission, and its effects on overall population health.}, } @article {pmid37898385, year = {2023}, author = {Mannen, K and Nagata, T and Rozenberg, A and Konno, M and Del Carmen Marín, M and Bagherzadeh, R and Béjà, O and Uchihashi, T and Inoue, K}, title = {Multiple Roles of a Conserved Glutamate Residue for Unique Biophysical Properties in a New Group of Microbial Rhodopsins Homologous to TAT Rhodopsin.}, journal = {Journal of molecular biology}, volume = {}, number = {}, pages = {168331}, doi = {10.1016/j.jmb.2023.168331}, pmid = {37898385}, issn = {1089-8638}, abstract = {TAT rhodopsin, a microbial rhodopsin found in the marine SAR11 bacterium HIMB114, uniquely possesses a Thr-Ala-Thr (TAT) motif in the third transmembrane helix. Because of a low pKa value of the retinal Schiff base (RSB), TAT rhodopsin exhibits both a visible light-absorbing state with the protonated RSB and a UV-absorbing state with the deprotonated RSB at a neutral pH. The UV-absorbing state, in contrast to the visible light-absorbing one, converts to a long-lived photointermediate upon light absorption, implying that TAT rhodopsin functions as a pH-dependent light sensor. Despite detailed biophysical characterization and mechanistic studies on the TAT rhodopsin, it has been unknown whether other proteins with similarly unusual features exist. Here, we identified several new rhodopsin genes homologous to the TAT rhodopsin of HIMB114 (TATHIMB) from metagenomic data. Based on the absorption spectra of expressed proteins from these genes with visible and UV peaks similar to that of TATHIMB, they were classified as Twin-peaked Rhodopsin (TwR) family. TwR genes form a gene cluster with a set of 13 ORFs conserved in subclade IIIa of SAR11 bacteria. A glutamic acid in the second transmembrane helix, Glu54, is conserved in all of the TwRs. We investigated E54Q mutants of two TwRs and revealed that Glu54 plays critical roles in regulating the RSB pKa, oligomer formation, and the efficient photoreaction of the UV-absorbing state. The discovery of novel TwRs enables us to study the universality and individuality of the characteristics revealed so far in the original TATHIMB and contributes to further studies on mechanisms of unique properties of TwRs.}, } @article {pmid37898120, year = {2023}, author = {Rich, MH and Sharrock, AV and Mulligan, TS and Matthews, F and Brown, AS and Lee-Harwood, HR and Williams, EM and Copp, JN and Little, RF and Francis, JJB and Horvat, CN and Stevenson, LJ and Owen, JG and Saxena, MT and Mumm, JS and Ackerley, DF}, title = {A metagenomic library cloning strategy that promotes high-level expression of captured genes to enable efficient functional screening.}, journal = {Cell chemical biology}, volume = {30}, number = {12}, pages = {1680-1691.e6}, doi = {10.1016/j.chembiol.2023.10.001}, pmid = {37898120}, issn = {2451-9448}, mesh = {Animals ; *Metronidazole/pharmacology/metabolism ; *Zebrafish/genetics/metabolism ; Metagenome ; Cloning, Molecular ; Nitroreductases/genetics ; }, abstract = {Functional screening of environmental DNA (eDNA) libraries is a potentially powerful approach to discover enzymatic "unknown unknowns", but is usually heavily biased toward the tiny subset of genes preferentially transcribed and translated by the screening strain. We have overcome this by preparing an eDNA library via partial digest with restriction enzyme FatI (cuts CATG), causing a substantial proportion of ATG start codons to be precisely aligned with strong plasmid-encoded promoter and ribosome-binding sequences. Whereas we were unable to select nitroreductases from standard metagenome libraries, our FatI strategy yielded 21 nitroreductases spanning eight different enzyme families, each conferring resistance to the nitro-antibiotic niclosamide and sensitivity to the nitro-prodrug metronidazole. We showed expression could be improved by co-expressing rare tRNAs and encoded proteins purified directly using an embedded His6-tag. In a transgenic zebrafish model of metronidazole-mediated targeted cell ablation, our lead MhqN-family nitroreductase proved ∼5-fold more effective than the canonical nitroreductase NfsB.}, } @article {pmid37898002, year = {2023}, author = {Elahinik, A and Li, L and Pabst, M and Abbas, B and Xevgenos, D and van Loosdrecht, MCM and Pronk, M}, title = {Aerobic granular sludge phosphate removal using glucose.}, journal = {Water research}, volume = {247}, number = {}, pages = {120776}, doi = {10.1016/j.watres.2023.120776}, pmid = {37898002}, issn = {1879-2448}, mesh = {*Sewage ; *Glucose ; Bioreactors ; Polyphosphates/metabolism ; Phosphorus/metabolism ; Lactates ; }, abstract = {Enhanced biological phosphate removal and aerobic sludge granulation are commonly studied with fatty acids as substrate. Fermentative substrates such as glucose have received limited attention. In this work, glucose conversion by aerobic granular sludge and its impact on phosphate removal was studied. Long-term stable phosphate removal and successful granulation were achieved. Glucose was rapidly taken up (273 mg/gVSS/h) at the start of the anaerobic phase, while phosphate was released during the full anaerobic phase. Some lactate was produced during glucose consumption, which was anaerobically consumed once glucose was depleted. The phosphate release appeared to be directly proportional to the uptake of lactate. The ratio of phosphorus released to glucose carbon taken up over the full anaerobic phase was 0.25 Pmol/Cmol. Along with glucose and lactate uptake in the anaerobic phase, poly‑hydroxy-alkanoates and glycogen storage were observed. There was a linear correlation between glucose consumption and lactate formation. While lactate accounted for approximately 89 % of the observed products in the bulk liquid, minor quantities of formate (5 %), propionate (4 %), and acetate (3 %) were also detected (mass fraction). Formate was not consumed anaerobically. Quantitative fluorescence in-situ hybridization (qFISH) revealed that polyphosphate accumulating organisms (PAO) accounted for 61 ± 15 % of the total biovolume. Metagenome evaluation of the biomass indicated a high abundance of Micropruina and Ca. Accumulibacter in the system, which was in accordance with the microscopic observations and the protein mass fraction from metaproteome analysis. Anaerobic conversions were evaluated based on theoretical ATP balances to provide the substrate distribution amongst the dominant genera. This research shows that aerobic granular sludge technology can be applied to glucose-containing effluents and that glucose is a suitable substrate for achieving phosphate removal. The results also show that for fermentable substrates a microbial community consisting of fermentative organisms and PAO develop.}, } @article {pmid37897999, year = {2023}, author = {Ke, Y and Sun, W and Liu, S and Zhu, Y and Yan, S and Chen, X and Xie, S}, title = {Seasonal variations of biofilm C, N and S cycling genes in a pilot-scale chlorinated drinking water distribution system.}, journal = {Water research}, volume = {247}, number = {}, pages = {120759}, doi = {10.1016/j.watres.2023.120759}, pmid = {37897999}, issn = {1879-2448}, mesh = {*Drinking Water ; Seasons ; Nitrates ; Extracellular Polymeric Substance Matrix/metabolism ; Biofilms ; Sulfur ; Nitrogen/metabolism ; *Ammonium Compounds ; }, abstract = {Biofilms in drinking water distribution systems (DWDS) host diverse microorganisms. However, the functional attributes of DWDS biofilms and their associations with seasonality remain unclear. This study aims to characterize variations in the microbial metabolic traits of DWDS biofilms collected during different seasons, using a pilot-scale DWDS in dark under plug-flow conditions during one-year operation period. Network analysis was used to predict the functional gene hosts. The overall functional attributes determined by shotgun metagenomics exhibited significant differences among seasons. Genes associated with aromatic metabolism, fatty acid biosynthesis and degradation, and capsular extracellular polymeric substance (EPS) were significantly upregulated in summer owing to the higher temperatures and chlorine in the influent of the DWDS. Moreover, the pathways associated with nitrogen, sulfur, glycolysis, and tricarboxylic acid (TCA) cycling, as well as carbon fixation were reconstructed and displayed according to the sampling season. Nitrogen reduction pathways [dissimilatory nitrate reduction to ammonium (DNRA) 73 %, assimilatory nitrate reduction to ammonium (ANRA) 21 %] were identified in DWDS biofilms, but nitrogen oxidation pathways were not. Sulfur cycling were involved in diverse pathways and genes. Glycolysis and TCA cycling offered electron donors and energy sources for nitrogen and sulfur reduction in biofilms. Carbon fixation was observed in DWDS biofilms, with the predominant pathway for fixing carbon dioxide being the reductive citrate cycle (38 %). Constructed functional gene networks composed of carbon, nitrogen, and sulfur cycling-related genes demonstrated synergistic effects (Positive proportion: 63.52-71.09 %). In addition, from spring to autumn, the network complexity decreased and network modularity increased. The assembly mechanism of carbon, nitrogen and sulfur cycling-related genes was driven by stochastic processes for all samples. These results highlight the diverse functional genes in DWDS biofilms, their synergetic interrelationships, and the seasonality effect on functional attributes.}, } @article {pmid37897998, year = {2023}, author = {Zhang, H and Gong, W and Xue, Y and Zeng, W and Bai, L and Li, G and Liang, H and Ng, HY}, title = {Simulated-sunlight enhances membrane aerated biofilm reactor performance in sulfamethoxazole removal and antibiotic resistance genes reduction.}, journal = {Water research}, volume = {247}, number = {}, pages = {120747}, doi = {10.1016/j.watres.2023.120747}, pmid = {37897998}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents/metabolism ; *Wastewater ; Sulfamethoxazole/metabolism ; Sunlight ; Bioreactors/microbiology ; Bacteria/metabolism ; Biofilms ; Drug Resistance, Microbial/genetics ; }, abstract = {Membrane aerated biofilm reactors (MABRs) can be used to treat domestic wastewater containing sulfamethoxazole (SMX) because of their favorable performance in the treatment of refractory pollutants. However, biologics are generally subjected to antibiotics stress, which induces the production of antibiotic resistance genes (ARGs). In this study, a simulated-sunlight assisted MABR (L-MABR) was used to promote SMX removal and reduce ARGs production. The SMX removal efficiency of the l-MABR system was 9.62 % superior to that of the MABR system (83.13 %). In contrast from MABR, in the l-MABR, only 28.75 % of SMX was removed through microbial activity because functional bacteria were inactivated through radiation by simulated sunlight. In addition, photolysis (64.61 %) dominated SMX removal, and the best performing indirect photolysis process was the excited state of effluent organic matters ([3]EfOMs*). Through photolysis, ultraviolet (UV) and reactive oxygen species (ROS) enriched the SMX removal route, resulting in the SMX removal pathway in the l-MABR no longer being limited by enzyme catalysis. More importantly, because of the inactivation of functional bacteria, whether in the effluent or biofilm, the copy number of ARGs in the l-MABR was 1-3 orders of magnitude lower than that in the MABR. Our study demonstrates the feasibility of utilizing simulated-sunlight to enhance the antibiotic removal efficiency while reducing ARG production, thus providing a novel idea for the removal of antibiotics from wastewater.}, } @article {pmid37897905, year = {2024}, author = {Qin, R and Dai, X and Xian, Y and Zhou, Y and Su, C and Chen, Z and Lu, X and Ai, C and Lu, Y}, title = {Assessing the effect of sulfate on the anaerobic oxidation of methane coupled with Cr(VI) bioreduction by sludge characteristic and metagenomics analysis.}, journal = {Journal of environmental management}, volume = {349}, number = {}, pages = {119398}, doi = {10.1016/j.jenvman.2023.119398}, pmid = {37897905}, issn = {1095-8630}, mesh = {*Sewage/chemistry ; Anaerobiosis ; *Methane ; Extracellular Polymeric Substance Matrix/chemistry/metabolism ; Sulfates ; Chromium/analysis ; Oxidation-Reduction ; }, abstract = {Methane-driven hexavalent chromium (Cr(VI)) reduction in a microbial fuel cell (MFC) has attracted much attention. However, whether the presence of sulfate (SO4[2-]) affects the reduction of Cr(VI) is still lacking in systematic studies. This study involved constructing a MFC-granular sludge (MFC-GS) coupling system with dissolved methane (CH4) was used as the electron donor to investigate the effect of SO4[2-] on Cr(VI) bioreduction, sludge characteristic, and functional metabolic mechanisms. When the SO4[2-] concentration was 10 mg/L, the average removal rate of Cr(VI) in the anaerobic stage decreased to the lowest value (22.25 ± 2.06%). Adding 10 mg/L SO4[2-] obviously inhibited the electrochemical performance of the system. Increasing SO4[2-] concentration weakened the fluorescence peaks of tryptophan and aromatic proteins in the extracellular polymeric substance of sludge. Under the influence of SO4[2-], Methanothrix_soehngenii decreased from 14.44% to 5.89%. The relative abundance of methane metabolic was down-regulated from 1.47% to 0.98%, while the sulfur metabolic was up-regulated from 0.09% to 0.21% when SO4[2-] was added. These findings provided some reference for the treatment of wastewater containing Cr(VI) and SO4[2-] complex pollutants in the MFC-GS coupling system.}, } @article {pmid37897901, year = {2024}, author = {González-Martín, J and Cantera, S and Muñoz, R and Lebrero, R}, title = {Indoor air VOCs biofiltration by bioactive coating packed bed bioreactors.}, journal = {Journal of environmental management}, volume = {349}, number = {}, pages = {119362}, doi = {10.1016/j.jenvman.2023.119362}, pmid = {37897901}, issn = {1095-8630}, mesh = {*Air Pollution, Indoor/prevention & control/analysis ; Hexanes/analysis ; *Volatile Organic Compounds/analysis ; *Air Pollutants/analysis ; Bioreactors/microbiology ; Toluene ; Filtration ; }, abstract = {Bioactive coatings are envisaged as a promising biotechnology to tackle the emerging problem of indoor air pollution. This solution could cope with the low concentrations, the wide range of compounds and the hydrophobicity of some indoor air VOCs, which are the most important bottlenecks regarding the implementation of conventional biotechnologies for indoor air treatment. A bioactive coating-based bioreactor was tested in this study for the abatement of different VOCs (n-hexane, toluene and α-pinene) at different empty bed residence times (EBRT) and inlet VOC concentrations. The performance of this reactor was compared with a conventional biofilm-based bioreactor operated with the same microbial inoculum. After an acclimation period, the bioactive coating-based bioreactor achieved abatements of over 50% for hexane, 80% for toluene and 70% for pinene at EBRTs of 112-56 s and inlet concentrations of 9-15 mg m[-3]. These results were about 25, 10 and 20% lower than the highest removals recorded in the biofilm-based bioreactor. Both bioreactors experienced a decrease in VOC abatement by ∼25% for hexane, 45% for toluene and 40% for pinene, after reducing the EBRT to 28 s. When inlet VOC concentrations were progressively reduced, VOC abatement efficiencies did not improve. This fact suggested that low EBRTs and low inlet VOCs concentration hindered indoor air pollutant abatement as a result of a limited mass transfer and bioavailability. Metagenomic analyses showed that process operation with toluene, hexane and pinene as the only carbon and energy sources favored an enriched bacterial community represented by the genera Devosia, Mesorhizobium, Sphingobacterium and Mycobacterium, regardless of the bioreactor configuration. Bioactive coatings were used in this work as packing material of a conventional bioreactor, achieving satisfactory VOC abatement similar to a conventional bioreactor.}, } @article {pmid37897871, year = {2023}, author = {Kim, MJ and Kang, D and Lee, G and Kim, K and Kim, J and Shin, JH and Lee, S}, title = {Interplays between cyanobacterial blooms and antibiotic resistance genes.}, journal = {Environment international}, volume = {181}, number = {}, pages = {108268}, doi = {10.1016/j.envint.2023.108268}, pmid = {37897871}, issn = {1873-6750}, mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; Dysbiosis/genetics ; *Cyanobacteria/genetics ; Drug Resistance, Microbial/genetics ; *Microcystis ; Genes, Bacterial ; }, abstract = {Cyanobacterial harmful algal blooms (cyanoHABs), which are a form of microbial dysbiosis in freshwater environments, are an emerging environmental and public health concern. Additionally, the freshwater environment serves as a reservoir of antibiotic resistance genes (ARGs), which pose a risk of transmission during microbial dysbiosis, such as cyanoHABs. However, the interactions between potential synergistic pollutants, cyanoHABs, and ARGs remain poorly understood. During cyanoHABs, Microcystis and high microcystin levels were dominant in all the nine regions of the river sampled. The resistome, mobilome, and microbiome were interrelated and linked to the physicochemical properties of freshwater. Planktothrix and Pseudanabaena competed with Actinobacteriota and Proteobacteria during cyanoHABs. Forty two ARG carriers were identified, most of which belonged to Actinobacteriota and Proteobacteria. ARG carriers showed a strong correlation with ARGs density, which decreased with the severity of cyanoHAB. Although ARGs decreased due to a reduction of ARG carriers during cyanoHABs, mobile gene elements (MGEs) and virulence factors (VFs) genes increased. We explored the relationship between cyanoHABs and ARGs for potential synergistic interaction. Our findings demonstrated that cyanobacteria compete with freshwater commensal bacteria such as Actinobacteriota and Proteobacteria, which carry ARGs in freshwater, resulting in a reduction of ARGs levels. Moreover, cyanoHABs generate biotic and abiotic stress in the freshwater microbiome, which may lead to an increase in MGEs and VFs. Exploration of the intricate interplays between microbiome, resistome, mobilome, and pathobiome during cyanoHABs not only revealed that the mechanisms underlying the dynamics of microbial dysbiosis but also emphasizes the need to prioritize the prevention of microbial dysbiosis in the risk management of ARGs.}, } @article {pmid37897361, year = {2024}, author = {Hu, R and Li, F and Chen, Y and Liu, C and Li, J and Ma, Z and Wang, Y and Cui, C and Luo, C and Zhou, P and Ni, W and Yang, QY and Hu, S}, title = {AnimalMetaOmics: a multi-omics data resources for exploring animal microbial genomes and microbiomes.}, journal = {Nucleic acids research}, volume = {52}, number = {D1}, pages = {D690-D700}, pmid = {37897361}, issn = {1362-4962}, support = {2021ZD01//Foundation of state key laboratory of sheep genetic improvement and healthy production/ ; //Tianshan Talent Project/ ; 2022xjkk1202//The Tird Xinjiang Scientifc Expedition Program/ ; }, mesh = {Animals ; *Multiomics ; *Microbiota/genetics ; Genome, Microbial ; Bacteria/genetics ; Metagenome/genetics ; }, abstract = {The Animal Meta-omics landscape database (AnimalMetaOmics, https://yanglab.hzau.edu.cn/animalmetaomics#/) is a comprehensive and freely available resource that includes metagenomic, metatranscriptomic, and metaproteomic data from various non-human animal species and provides abundant information on animal microbiomes, including cluster analysis of microbial cognate genes, functional gene annotations, active microbiota composition, gene expression abundance, and microbial protein identification. In this work, 55 898 microbial genomes were annotated from 581 animal species, including 42 924 bacterial genomes, 12 336 virus genomes, 496 archaea genomes and 142 fungi genomes. Moreover, 321 metatranscriptomic datasets were analyzed from 31 animal species and 326 metaproteomic datasets from four animal species, as well as the pan-genomic dynamics and compositional characteristics of 679 bacterial species and 13 archaea species from animal hosts. Researchers can efficiently access and acquire the information of cross-host microbiota through a user-friendly interface, such as species, genomes, activity levels, expressed protein sequences and functions, and pan-genome composition. These valuable resources provide an important reference for better exploring the classification, functional diversity, biological process diversity and functional genes of animal microbiota.}, } @article {pmid37897342, year = {2024}, author = {Schmidt, TSB and Fullam, A and Ferretti, P and Orakov, A and Maistrenko, OM and Ruscheweyh, HJ and Letunic, I and Duan, Y and Van Rossum, T and Sunagawa, S and Mende, DR and Finn, RD and Kuhn, M and Pedro Coelho, L and Bork, P}, title = {SPIRE: a Searchable, Planetary-scale mIcrobiome REsource.}, journal = {Nucleic acids research}, volume = {52}, number = {D1}, pages = {D777-D783}, pmid = {37897342}, issn = {1362-4962}, support = {NFDI4Microbiota//European Molecular Biology Laboratory/ ; NFDI4Microbiota//German Research Foundation/ ; LAMarCK//German Federal Ministry of Education and Research/ ; 22JC1410900//The Science and Technology Commission of Shanghai Municipality/ ; 51NF40_180575//NCCR Microbiomes/ ; }, mesh = {*Microbiota/genetics ; Metagenome/genetics ; Metagenomics ; Databases, Factual ; }, abstract = {Meta'omic data on microbial diversity and function accrue exponentially in public repositories, but derived information is often siloed according to data type, study or sampled microbial environment. Here we present SPIRE, a Searchable Planetary-scale mIcrobiome REsource that integrates various consistently processed metagenome-derived microbial data modalities across habitats, geography and phylogeny. SPIRE encompasses 99 146 metagenomic samples from 739 studies covering a wide array of microbial environments and augmented with manually-curated contextual data. Across a total metagenomic assembly of 16 Tbp, SPIRE comprises 35 billion predicted protein sequences and 1.16 million newly constructed metagenome-assembled genomes (MAGs) of medium or high quality. Beyond mapping to the high-quality genome reference provided by proGenomes3 (http://progenomes.embl.de), these novel MAGs form 92 134 novel species-level clusters, the majority of which are unclassified at species level using current tools. SPIRE enables taxonomic profiling of these species clusters via an updated, custom mOTUs database (https://motu-tool.org/) and includes several layers of functional annotation, as well as crosslinks to several (micro-)biological databases. The resource is accessible, searchable and browsable via http://spire.embl.de.}, } @article {pmid37897301, year = {2023}, author = {Dawson, KLD and Wildi, N and Cavalli, M and Rubbenstroth, D and Oevermann, A and Seuberlich, T}, title = {Feline morbillivirus infection associated with fatal encephalitis in a Bengal cat.}, journal = {Journal of veterinary internal medicine}, volume = {37}, number = {6}, pages = {2510-2513}, pmid = {37897301}, issn = {1939-1676}, mesh = {Cats ; Animals ; Phylogeny ; *Morbillivirus/genetics ; *Morbillivirus Infections/veterinary ; *Encephalitis/veterinary ; *Cat Diseases ; }, abstract = {Feline morbillivirus (FeMV) is a recently discovered morbillivirus of the family Paramyxoviridae, which include several highly contagious viruses with zoonotic potential. In this case report we describe the detection of FeMV in archived brain tissue of a 2-month-old Bengal cat with nonsuppurative encephalitis from the year 2011 in Switzerland by high-throughput sequencing (HTS). Our metagenomics approach was able to obtain a full-length sequence covering the entire FeMV genome. Phylogenetic analysis showed that our FeMV strain clustered within FeMV genotype 1. We were able to detect FeMV RNA by in situ hybridization (ISH) in brain sections with inflammatory lesions and demonstrated its potential neurotropism and association with encephalitis. Our results provide further insight into this recently discovered morbillivirus and encourage further investigations into the pathogenesis and epidemiology of associated diseases in cats and potentially other species.}, } @article {pmid37896894, year = {2023}, author = {Louge Uriarte, EL and Badaracco, A and Spetter, MJ and Miño, S and Armendano, JI and Zeller, M and Heylen, E and Späth, E and Leunda, MR and Moreira, AR and Matthijnssens, J and Parreño, V and Odeón, AC}, title = {Molecular Epidemiology of Rotavirus A in Calves: Evolutionary Analysis of a Bovine G8P[11] Strain and Spatio-Temporal Dynamics of G6 Lineages in the Americas.}, journal = {Viruses}, volume = {15}, number = {10}, pages = {}, pmid = {37896894}, issn = {1999-4915}, mesh = {Animals ; Cattle ; *Rotavirus/genetics ; Molecular Epidemiology ; Phylogeny ; *Rotavirus Infections/epidemiology/veterinary ; Diarrhea/epidemiology/veterinary ; Genotype ; Feces ; *Cattle Diseases/epidemiology ; }, abstract = {Rotavirus A (RVA) causes diarrhea in calves and frequently possesses the G6 and P[5]/P[11] genotypes, whereas G8 is less common. We aimed to compare RVA infections and G/P genotypes in beef and dairy calves from major livestock regions of Argentina, elucidate the evolutionary origin of a G8 strain and analyze the G8 lineages, infer the phylogenetic relationship of RVA field strains, and investigate the evolution and spatio-temporal dynamics of the main G6 lineages in American countries. Fecal samples (n = 422) from diarrheic (beef, 104; dairy, 137) and non-diarrheic (beef, 78; dairy, 103) calves were analyzed by ELISA and semi-nested multiplex RT-PCR. Sequencing, phylogenetic, phylodynamic, and phylogeographic analyses were performed. RVA infections were more frequent in beef (22.0%) than in dairy (14.2%) calves. Prevalent genotypes and G6 lineages were G6(IV)P[5] in beef (90.9%) and G6(III)P[11] (41.2%) or mixed genotypes (23.5%) in dairy calves. The only G8 strain was phylogenetically related to bovine and artiodactyl bovine-like strains. Re-analyses inside the G8 genotype identified G8(I) to G8(VIII) lineages. Of all G6 strains characterized, the G6(IV)P[5](I) strains from "Cuenca del Salado" (Argentina) and Uruguay clustered together. According to farm location, a clustering pattern for G6(IV)P[5] strains of beef farms was observed. Both G6 lineage strains together revealed an evolutionary rate of 1.24 × 10[-3] substitutions/site/year, and the time to the most recent common ancestor was dated in 1853. The most probable ancestral locations were Argentina in 1981 for G6(III) strains and the USA in 1940 for G6(IV) strains. The highest migration rates for both G6 lineages together were from Argentina to Brazil and Uruguay. Altogether, the epidemiology, genetic diversity, and phylogeny of RVA in calves can differ according to the production system and farm location. We provide novel knowledge about the evolutionary origin of a bovine G8P[11] strain. Finally, bovine G6 strains from American countries would have originated in the USA nearly a century before its first description.}, } @article {pmid37896845, year = {2023}, author = {Zhao, Q and Zhao, R and Sun, Y and Ji, L and Xi, Y and Wang, X and Shen, Q and Ji, L and Wang, Y and You, Z and Yang, S and Zhang, W}, title = {Identification of Multiple Novel Viruses in Fecal Samples of Black-Necked Cranes Using Viral Metagenomic Methods.}, journal = {Viruses}, volume = {15}, number = {10}, pages = {}, pmid = {37896845}, issn = {1999-4915}, mesh = {Humans ; Phylogeny ; *Viruses/genetics ; Metagenome ; Feces ; *Virus Diseases/genetics ; *Picornaviridae/genetics ; }, abstract = {The black-necked crane is the only species of crane that lives in the high-altitude region of the Tibet Plateau. At present, there is little research on viral diseases of the black-necked crane (Grus nigricollis). In this study, a viral metagenomic approach was employed to investigate the fecal virome of black-necked cranes in Saga County, Shigatse City, Tibet, China. The identified virus families carried by black-necked cranes mainly include Genomoviridae, Parvoviridae, and Picornaviridae. The percentages of sequence reads belonging to these three virus families were 1.6%, 3.1%, and 93.7%, respectively. Among them, one genome was characterized as a novel species in the genus Grusopivirus of the family Picornaviridae, four new parvovirus genomes were obtained and classified into four different novel species within the genus Chaphamaparvovirus of the subfamily Hamaparvovirinae, and four novel genomovirus genomes were also acquired and identified as members of three different species, including Gemykroznavirus haeme1, Gemycircularvirus ptero6, and Gemycircularvirus ptero10. All of these viruses were firstly detected in fecal samples of black-necked cranes. This study provides valuable information for understanding the viral community composition in the digestive tract of black-necked cranes in Tibet, which can be used for monitoring, preventing, and treating potential viral diseases in black-necked cranes.}, } @article {pmid37896825, year = {2023}, author = {Diederich, S and Babiuk, S and Boshra, H}, title = {A Survey of Henipavirus Tropism-Our Current Understanding from a Species/Organ and Cellular Level.}, journal = {Viruses}, volume = {15}, number = {10}, pages = {}, pmid = {37896825}, issn = {1999-4915}, mesh = {Humans ; Animals ; Horses ; Swine ; *Henipavirus Infections ; Phylogeny ; *Hendra Virus ; Viral Tropism ; Tropism ; *Nipah Virus ; }, abstract = {Henipaviruses are single-stranded RNA viruses that have been shown to be virulent in several species, including humans, pigs, horses, and rodents. Isolated nearly 30 years ago, these viruses have been shown to be of particular concern to public health, as at least two members (Nipah and Hendra viruses) are highly virulent, as well as zoonotic, and are thus classified as BSL4 pathogens. Although only 5 members of this genus have been isolated and characterized, metagenomics analysis using animal fluids and tissues has demonstrated the existence of other novel henipaviruses, suggesting a far greater degree of phylogenetic diversity than is currently known. Using a variety of molecular biology techniques, it has been shown that these viruses exhibit varying degrees of tropism on a species, organ/tissue, and cellular level. This review will attempt to provide a general overview of our current understanding of henipaviruses, with a particular emphasis on viral tropism.}, } @article {pmid37896815, year = {2023}, author = {Cai, H and Zhou, Y and Li, X and Xu, T and Ni, Y and Wu, S and Yu, Y and Wang, Y}, title = {Genomic Analysis and Taxonomic Characterization of Seven Bacteriophage Genomes Metagenomic-Assembled from the Dishui Lake.}, journal = {Viruses}, volume = {15}, number = {10}, pages = {}, pmid = {37896815}, issn = {1999-4915}, mesh = {*Bacteriophages/genetics ; Lakes/microbiology ; Ecosystem ; China ; Genomics ; *Viruses/genetics ; Phylogeny ; Genome, Viral ; }, abstract = {Viruses in aquatic ecosystems exhibit remarkable abundance and diversity. However, scattered studies have been conducted to mine uncultured viruses and identify them taxonomically in lake water. Here, whole genomes (29-173 kbp) of seven uncultured dsDNA bacteriophages were discovered in Dishui Lake, the largest artificial lake in Shanghai. We analyzed their genomic signatures and found a series of viral auxiliary metabolic genes closely associated with protein synthesis and host metabolism. Dishui Lake phages shared more genes with uncultivated environmental viruses than with reference viruses based on the gene-sharing network classification. Phylogeny of proteomes and comparative genomics delineated three new genera within two known viral families of Kyanoviridae and Autographiviridae, and four new families in Caudoviricetes for these seven novel phages. Their potential hosts appeared to be from the dominant bacterial phyla in Dishui Lake. Altogether, our study provides initial insights into the composition and diversity of bacteriophage communities in Dishui Lake, contributing valuable knowledge to the ongoing research on the roles played by viruses in freshwater ecosystems.}, } @article {pmid37896809, year = {2023}, author = {Hufsky, F and Abecasis, AB and Babaian, A and Beck, S and Brierley, L and Dellicour, S and Eggeling, C and Elena, SF and Gieraths, U and Ha, AD and Harvey, W and Jones, TC and Lamkiewicz, K and Lovate, GL and Lücking, D and Machyna, M and Nishimura, L and Nocke, MK and Renard, BY and Sakaguchi, S and Sakellaridi, L and Spangenberg, J and Tarradas-Alemany, M and Triebel, S and Vakulenko, Y and Wijesekara, RY and González-Candelas, F and Krautwurst, S and Pérez-Cataluña, A and Randazzo, W and Sánchez, G and Marz, M}, title = {The International Virus Bioinformatics Meeting 2023.}, journal = {Viruses}, volume = {15}, number = {10}, pages = {}, pmid = {37896809}, issn = {1999-4915}, mesh = {Humans ; Computational Biology ; *Viruses/genetics ; *RNA Viruses ; *Virus Diseases ; *Bacteriophages ; }, abstract = {The 2023 International Virus Bioinformatics Meeting was held in Valencia, Spain, from 24-26 May 2023, attracting approximately 180 participants worldwide. The primary objective of the conference was to establish a dynamic scientific environment conducive to discussion, collaboration, and the generation of novel research ideas. As the first in-person event following the SARS-CoV-2 pandemic, the meeting facilitated highly interactive exchanges among attendees. It served as a pivotal gathering for gaining insights into the current status of virus bioinformatics research and engaging with leading researchers and emerging scientists. The event comprised eight invited talks, 19 contributed talks, and 74 poster presentations across eleven sessions spanning three days. Topics covered included machine learning, bacteriophages, virus discovery, virus classification, virus visualization, viral infection, viromics, molecular epidemiology, phylodynamic analysis, RNA viruses, viral sequence analysis, viral surveillance, and metagenomics. This report provides rewritten abstracts of the presentations, a summary of the key research findings, and highlights shared during the meeting.}, } @article {pmid37896763, year = {2023}, author = {Thongchol, J and Lill, Z and Hoover, Z and Zhang, J}, title = {Recent Advances in Structural Studies of Single-Stranded RNA Bacteriophages.}, journal = {Viruses}, volume = {15}, number = {10}, pages = {}, pmid = {37896763}, issn = {1999-4915}, support = {R21 AI156846/AI/NIAID NIH HHS/United States ; R01 GM141659/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteriophages/genetics/metabolism ; Escherichia coli/genetics ; RNA, Viral/genetics ; Virus Assembly ; *RNA Phages/genetics ; Genome, Viral ; }, abstract = {Positive-sense single-stranded RNA (ssRNA) bacteriophages (phages) were first isolated six decades ago. Since then, extensive research has been conducted on these ssRNA phages, particularly those infecting E. coli. With small genomes of typically 3-4 kb that usually encode four essential proteins, ssRNA phages employ a straightforward infectious cycle involving host adsorption, genome entry, genome replication, phage assembly, and host lysis. Recent advancements in metagenomics and transcriptomics have led to the identification of ~65,000 sequences from ssRNA phages, expanding our understanding of their prevalence and potential hosts. This review article illuminates significant investigations into ssRNA phages, with a focal point on their structural aspects, providing insights into the various stages of their infectious cycle.}, } @article {pmid37896354, year = {2023}, author = {Kadoya, R and Soga, H and Matsuda, M and Sato, M and Taguchi, S}, title = {Bacterial Population Changes during the Degradation Process of a Lactate (LA)-Enriched Biodegradable Polymer in River Water: LA-Cluster Preferable Bacterial Consortium.}, journal = {Polymers}, volume = {15}, number = {20}, pages = {}, pmid = {37896354}, issn = {2073-4360}, support = {JPNP18016//New Energy and Industrial Technology Development Organization/ ; }, abstract = {The lactate-based polyester poly[lactate (LA)-co-3-hydroxybutyrate (3HB)], termed LAHB, is a highly transparent and flexible bio-based polymeric material. There are many unknowns regarding its degradation process in riverine environments, especially the changes in bacterial flora that might result from its degradation and the identities of any LAHB-degrading bacteria. LAHB were immersed in the river water samples (A and B), and LAHB degradation was observed in terms of the weight change of the polymer and the microscopic changes on the polymer surfaces. A metagenomic analysis of microorganisms was conducted to determine the effect of LAHB degradation on the aquatic environment. The bacterial flora obtained from beta diversity analysis differed between the two river samples. The river A water sample showed the simultaneous degradation of LA and 3HB even though the copolymer was LA-enriched, suggesting preferable hydrolysis of the LA-enriched segments. In contrast, only 3HB degraded for the LAHB in the river B water sample. The linear discriminant analysis effect size (LEfSe) analysis revealed 14 bacteria that were significantly increased in the river A water sample during LAHB degradation, suggesting that these bacteria preferentially degraded and assimilated LA-clustering polymers. Our metagenomic analysis provides useful insights into the dynamic changes in microbial communities and LA-clustering polymer-degrading bacteria.}, } @article {pmid37895005, year = {2023}, author = {Seton, KA and Defernez, M and Telatin, A and Tiwari, SK and Savva, GM and Hayhoe, A and Noble, A and de Carvalho-KoK, ALS and James, SA and Bansal, A and Wileman, T and Carding, SR}, title = {Investigating Antibody Reactivity to the Intestinal Microbiome in Severe Myalgic Encephalomyelitis/Chronic Fatigue Syndrome (ME/CFS): A Feasibility Study.}, journal = {International journal of molecular sciences}, volume = {24}, number = {20}, pages = {}, pmid = {37895005}, issn = {1422-0067}, support = {BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *Fatigue Syndrome, Chronic ; *Gastrointestinal Microbiome ; Feasibility Studies ; Bacteria ; Immunoglobulin G ; }, abstract = {Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a multisystemic disease of unknown aetiology that is characterised by disabling chronic fatigue and involves both the immune and gastrointestinal (GI) systems. Patients display alterations in GI microbiome with a significant proportion experiencing GI discomfort and pain and elevated blood biomarkers for altered intestinal permeability compared with healthy individuals. To investigate a possible GI origin of ME/CFS we designed a feasibility study to test the hypothesis that ME/CFS pathogenesis is a consequence of increased intestinal permeability that results in microbial translocation and a breakdown in immune tolerance leading to generation of antibodies reactive to indigenous intestinal microbes. Secretory immunoglobulin (Ig) A and serum IgG levels and reactivity to intestinal microbes were assessed in five pairs of severe ME/CFS patients and matched same-household healthy controls. For profiling serum IgG, we developed IgG-Seq which combines flow-cytometry based bacterial cell sorting and metagenomics to detect mucosal IgG reactivity to the microbiome. We uncovered evidence for immune dysfunction in severe ME/CFS patients that was characterised by reduced capacity and reactivity of serum IgG to stool microbes, irrespective of their source. This study provides the rationale for additional studies in larger cohorts of ME/CFS patients to further explore immune-microbiome interactions.}, } @article {pmid37894982, year = {2023}, author = {Babkin, I and Tikunov, A and Morozova, V and Matveev, A and Morozov, VV and Tikunova, N}, title = {Genomes of a Novel Group of Phages That Use Alternative Genetic Code Found in Human Gut Viromes.}, journal = {International journal of molecular sciences}, volume = {24}, number = {20}, pages = {}, pmid = {37894982}, issn = {1422-0067}, support = {21-14-00360//Russian Science Foundation/ ; 121031300043-8//Ministry of Education and Science/ ; }, mesh = {Humans ; *Bacteriophages/genetics ; Virome ; Codon, Terminator/genetics ; Genome, Viral ; Genetic Code ; RNA, Transfer/genetics ; Phylogeny ; }, abstract = {Metagenomics provides detection of phage genome sequences in various microbial communities. However, the use of alternative genetic codes by some phages precludes the correct analysis of their genomes. In this study, the unusual phage genome (phAss-1, 135,976 bp) was found after the de novo assembly of the human gut virome. Genome analysis revealed the presence of the TAG stop codons in 41 ORFs, including characteristic phage ORFs, and three genes of suppressor tRNA. Comparative analysis indicated that no phages with similar genomes were described. However, two phage genomes (BK046881_ctckW2 and BK025033_ct6IQ4) with substantial similarity to phAss-1 were extracted from the human gut metagenome data. These two complete genomes demonstrated 82.7% and 86.4% of nucleotide identity, respectively, similar genome synteny to phAss-1, the presence of suppressor tRNA genes and suppressor TAG stop codons in many characteristic phage ORFs. These data indicated that phAss-1, BK046881_ctckW2, and BK025033_ct6IQ4 are distinct species within the proposed Phassvirus genus. Moreover, a monophyletic group of divergent phage genomes containing the proposed Phassvirus genus was found among metagenome data. Several phage genomes from the group also contain ORFs with suppressor TAG stop codons, indicating the need to use various translation tables when depositing phage genomes in GenBank.}, } @article {pmid37894951, year = {2023}, author = {Korobeinikova, AV and Zlobovskaya, OA and Sheptulina, AF and Ashniev, GA and Bobrova, MM and Yafarova, AA and Akasheva, DU and Kabieva, SS and Bakoev, SY and Zagaynova, AV and Lukashina, MV and Abramov, IA and Pokrovskaya, MS and Doludin, YV and Tolkacheva, LR and Kurnosov, AS and Zyatenkova, EV and Lavrenova, EA and Efimova, IA and Glazunova, EV and Kiselev, AR and Shipulin, GA and Kontsevaya, AV and Keskinov, AA and Yudin, VS and Makarov, VV and Drapkina, OM and Yudin, SM}, title = {Gut Microbiota Patterns in Patients with Non-Alcoholic Fatty Liver Disease: A Comprehensive Assessment Using Three Analysis Methods.}, journal = {International journal of molecular sciences}, volume = {24}, number = {20}, pages = {}, pmid = {37894951}, issn = {1422-0067}, support = {Contract n. 388-00154-22-00//Federal Medical Biological Agency/ ; }, mesh = {Adult ; Humans ; *Non-alcoholic Fatty Liver Disease/pathology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Fibrosis ; *Microbiota ; Bacteroidetes ; Liver/pathology ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD) is considered the most common chronic liver disease worldwide, affecting nearly 25% of the global adult population. Increasing evidence suggests that functional and compositional changes in the gut microbiota may contribute to the development and promote the progression of NAFLD. 16S rRNA gene next-generation sequencing is widely used to determine specific features of the NAFLD microbiome, but a complex system such as the gut microbiota requires a comprehensive approach. We used three different approaches: MALDI-TOF-MS of bacterial cultures, qPCR, and 16S NGS sequencing, as well as a wide variety of statistical methods to assess the differences in gut microbiota composition between NAFLD patients without significant fibrosis and the control group. The listed methods showed enrichment in Collinsella sp. and Oscillospiraceae for the control samples and enrichment in Lachnospiraceae (and in particular Dorea sp.) and Veillonellaceae in NAFLD. The families, Bifidobacteriaceae, Lactobacillaceae, and Enterococcaceae (particularly Enterococcus faecium and Enterococcus faecalis), were also found to be important taxa for NAFLD microbiome evaluation. Considering individual method observations, an increase in Candida krusei and a decrease in Bacteroides uniformis for NAFLD patients were detected using MALDI-TOF-MS. An increase in Gracilibacteraceae, Chitinophagaceae, Pirellulaceae, Erysipelatoclostridiaceae, Muribaculaceae, and Comamonadaceae, and a decrease in Acidaminococcaceae in NAFLD were observed with 16S NGS, and enrichment in Fusobacterium nucleatum was shown using qPCR analysis. These findings confirm that NAFLD is associated with changes in gut microbiota composition. Further investigations are required to determine the cause-and-effect relationships and the impact of microbiota-derived compounds on the development and progression of NAFLD.}, } @article {pmid37894923, year = {2023}, author = {Vásquez, C and Leyton-Carcaman, B and Cid-Alda, FP and Segovia, I and Pinto, F and Abanto, M}, title = {Physical Pretreatments Applied in Three Commercial Kits for the Extraction of High-Quality DNA from Activated Sewage Sludge.}, journal = {International journal of molecular sciences}, volume = {24}, number = {20}, pages = {}, pmid = {37894923}, issn = {1422-0067}, mesh = {*Sewage ; DNA, Bacterial/genetics ; *DNA ; Genomics ; Soil ; }, abstract = {Obtaining sufficient and high-quality genomic DNA from sludge samples is a fundamental issue of feasibility and comparability in genomic studies of microbial diversity. Commercial kits for soil are often used for the extraction of gDNA from sludge samples due to the lack of specific kits. However, the evaluation of the performance of commercial kits for sludge DNA extraction is scarce and optimization of these methods to obtain a high quantity and quality of DNA is necessary, especially for downstream genomic sequencing. Sequential batch reactors (SBRs) loaded with lignocellulosic biomass are used for the synthesis of renewable resources such as levulinic acid (LA), adipic acid (AA), and polyhydroxyalkanoates (PHAs), and the biochemical synthesis of these compounds is conducted through the inoculation of microbes present in the residual activated sludge (AS) obtained from a municipal wastewater treatment plant. To characterize these microbes, the extraction of DNA from residual sewage sludge was conducted with three different commercial kits: Nucleospin[®] Soil from Macherey-Nagel, DNEasy[®] PowerSoil[®] from Qiagen, and E.Z.N.A.[®] Plant DNA Kit from Omega BIO-TEK. Nevertheless, to obtain the highest load and quality of DNA for next-generation sequencing (NGS) analysis, different pretreatments and different combinations of these pretreatments were used. The pretreatments considered were an ultrasonic bath and a temperature of 80 °C, together and separately with different incubation time periods of 30, 60, and 90 min. The results obtained suggest a significant improvement in the efficiency and quality of DNA extraction with the three commercial extraction kits when used together with the ultrasonic bath and 80 °C for 60 min. Here, we were able to prove that physical pretreatments are a viable alternative to chemical lysis for DNA extraction from complex samples such as sludge.}, } @article {pmid37894726, year = {2023}, author = {Zhu, N and Yu, Q and Song, L and Sheng, H}, title = {The Inhibiting Effects of High-Dose Biochar Application on Soil Microbial Metagenomics and Rice (Oryza sativa L.) Production.}, journal = {International journal of molecular sciences}, volume = {24}, number = {20}, pages = {}, pmid = {37894726}, issn = {1422-0067}, support = {BE2022312//the Special Technology Innovation Fund of Carbon Neutrality in Jiangsu Province/ ; }, mesh = {*Soil/chemistry ; *Oryza/metabolism ; Soil Microbiology ; Charcoal/pharmacology/chemistry ; Arachis ; }, abstract = {Biochar is usually considered as an organic improver which can improve soil and increase crop yields. However, the unrestricted application of biochar to normal-fertility farmland will cause chemical stress on crops and affect agricultural production. At present, the effects and mechanisms of high-dose applications of biochar on rice (Oryza sativa L.) production and soil biological characteristics have not been fully studied. In this greenhouse pot experiment, combined with soil microbial metagenomics, three treatments in triplicates were conducted to explore the responses of rice production, soil chemical properties, and soil biological properties to high-dose applications of biochar (5%, w/w) prepared using peanut waste (peanut hulls and straw). The results show that peanut hulls, with a loose texture and pore structure, are a raw material with stronger effects for preparing biochar than peanut straw in terms of its physical structure. In a rice monoculture system, high-dose applications of biochar (5%, w/w) can slightly increase the grains per spike, while significantly inhibiting the spike number per pot and the percentage of setting. High-dose applications of biochar also have significant negative effects on the diversity and stability of soil bacterial and archaeal communities. Moreover, the microbial metabolism and nutrient cycling processes are also significantly affected by changing the soil carbon/nitrogen ratio. This study discusses the response mechanisms of rice production and soil biology to high-dose biochar applications, and complements the understanding of irrational biochar application on agricultural production and land sustainability.}, } @article {pmid37894458, year = {2023}, author = {Dora, D and Weiss, GJ and Megyesfalvi, Z and Gállfy, G and Dulka, E and Kerpel-Fronius, A and Berta, J and Moldvay, J and Dome, B and Lohinai, Z}, title = {Computed Tomography-Based Quantitative Texture Analysis and Gut Microbial Community Signatures Predict Survival in Non-Small Cell Lung Cancer.}, journal = {Cancers}, volume = {15}, number = {20}, pages = {}, pmid = {37894458}, issn = {2072-6694}, support = {2018//LCFA-BMS/IASLC Young Investigator Scholarship Award/ ; 142287; KH130356; KKP126790; 2020-1.1.6-JÖVŐ//Hungarian National Research, Development and Innovation Office/ ; FWF I3522; FWF I3977; I4677//FWF Austrian Science Fund/ ; UNKP-20-3; UNKP-21-3//New National Excellence Program of the Ministry for Innovation and Technology of Hungary/ ; 2022//Bolyai Fellowship of the Hungarian Academy of Sciences/ ; 2020//Hungarian Respiratory Society/ ; }, abstract = {This study aims to combine computed tomography (CT)-based texture analysis (QTA) and a microbiome-based biomarker signature to predict the overall survival (OS) of immune checkpoint inhibitor (ICI)-treated non-small cell lung cancer (NSCLC) patients by analyzing their CT scans (n = 129) and fecal microbiome (n = 58). One hundred and five continuous CT parameters were obtained, where principal component analysis (PCA) identified seven major components that explained 80% of the data variation. Shotgun metagenomics (MG) and ITS analysis were performed to reveal the abundance of bacterial and fungal species. The relative abundance of Bacteroides dorei and Parabacteroides distasonis was associated with long OS (>6 mo), whereas the bacteria Clostridium perfringens and Enterococcus faecium and the fungal taxa Cortinarius davemallochii, Helotiales, Chaetosphaeriales, and Tremellomycetes were associated with short OS (≤6 mo). Hymenoscyphus immutabilis and Clavulinopsis fusiformis were more abundant in patients with high (≥50%) PD-L1-expressing tumors, whereas Thelephoraceae and Lachnospiraceae bacterium were enriched in patients with ICI-related toxicities. An artificial intelligence (AI) approach based on extreme gradient boosting evaluated the associations between the outcomes and various clinicopathological parameters. AI identified MG signatures for patients with a favorable ICI response and high PD-L1 expression, with 84% and 79% accuracy, respectively. The combination of QTA parameters and MG had a positive predictive value of 90% for both therapeutic response and OS. According to our hypothesis, the QTA parameters and gut microbiome signatures can predict OS, the response to therapy, the PD-L1 expression, and toxicity in NSCLC patients treated with ICI, and a machine learning approach can combine these variables to create a reliable predictive model, as we suggest in this research.}, } @article {pmid37894270, year = {2023}, author = {Wiegand, S and Sobol, M and Schnepp-Pesch, LK and Yan, G and Iqbal, S and Vollmers, J and Müller, JA and Kaster, AK}, title = {Taxonomic Re-Classification and Expansion of the Phylum Chloroflexota Based on over 5000 Genomes and Metagenome-Assembled Genomes.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894270}, issn = {2076-2607}, support = {320579085//Deutsche Forschungsgemeinschaft/ ; }, abstract = {The phylum Chloroflexota (formerly Chloroflexi) encompasses metabolically diverse bacteria that often have high prevalence in terrestrial and aquatic habitats, some even with biotechnological application. However, there is substantial disagreement in public databases which lineage should be considered a member of the phylum and at what taxonomic level. Here, we addressed these issues through extensive phylogenomic analyses. The analyses were based on a collection of >5000 Chloroflexota genomes and metagenome-assembled genomes (MAGs) from public databases, novel environmental sites, as well as newly generated MAGs from publicly available sequence reads via an improved binning approach incorporating covariance information. Based on calculated relative evolutionary divergence, we propose that Candidatus Dormibacterota should be listed as a class (i.e., Ca. Dormibacteria) within Chloroflexota together with the classes Anaerolineae, Chloroflexia, Dehalococcoidia, Ktedonobacteria, Ca. Limnocylindria, Thermomicrobia, and two other classes containing only uncultured members. All other Chloroflexota lineages previously listed at the class rank appear to be rather orders or families in the Anaerolineae and Dehalococcoidia, which contain the vast majority of genomes and exhibited the strongest phylogenetic radiation within the phylum. Furthermore, the study suggests that a common ecophysiological capability of members of the phylum is to successfully cope with low energy fluxes.}, } @article {pmid37894218, year = {2023}, author = {Wang, L and Ding, R and He, S and Wang, Q and Zhou, Y}, title = {A Pipeline for Constructing Reference Genomes for Large Cohort-Specific Metagenome Compression.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894218}, issn = {2076-2607}, abstract = {Metagenomic data compression is very important as metagenomic projects are facing the challenges of larger data volumes per sample and more samples nowadays. Reference-based compression is a promising method to obtain a high compression ratio. However, existing microbial reference genome databases are not suitable to be directly used as references for compression due to their large size and redundancy, and different metagenomic cohorts often have various microbial compositions. We present a novel pipeline that generated simplified and tailored reference genomes for large metagenomic cohorts, enabling the reference-based compression of metagenomic data. We constructed customized reference genomes, ranging from 2.4 to 3.9 GB, for 29 real metagenomic datasets and evaluated their compression performance. Reference-based compression achieved an impressive compression ratio of over 20 for human whole-genome data and up to 33.8 for all samples, demonstrating a remarkable 4.5 times improvement than the standard Gzip compression. Our method provides new insights into reference-based metagenomic data compression and has a broad application potential for faster and cheaper data transfer, storage, and analysis.}, } @article {pmid37894190, year = {2023}, author = {Roev, GV and Borisova, NI and Chistyakova, NV and Agletdinov, MR and Akimkin, VG and Khafizov, K}, title = {Unlocking the Viral Universe: Metagenomic Analysis of Bat Samples Using Next-Generation Sequencing.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894190}, issn = {2076-2607}, support = {22-24-00078//Russian Science Foundation/ ; }, abstract = {Next-generation sequencing technologies have revolutionized the field of virology by enabling the reading of complete viral genomes, extensive metagenomic studies, and the identification of novel viral pathogens. Although metagenomic sequencing has the advantage of not requiring specific probes or primers, it faces significant challenges in analyzing data and identifying novel viruses. Traditional bioinformatics tools for sequence identification mainly depend on homology-based strategies, which may not allow the detection of a virus significantly different from known variants due to the extensive genetic diversity and rapid evolution of viruses. In this work, we performed metagenomic analysis of bat feces from different Russian cities and identified a wide range of viral pathogens. We then selected sequences with minimal homology to a known picornavirus and used "Switching Mechanism at the 5' end of RNA Template" technology to obtain a longer genome fragment, allowing for more reliable identification. This study emphasizes the importance of integrating advanced computational methods with experimental strategies for identifying unknown viruses to better understand the viral universe.}, } @article {pmid37894156, year = {2023}, author = {Gu, S and Zhang, P and Luo, S and Chen, K and Jiang, C and Xiong, J and Miao, W}, title = {Microbial Community Colonization Process Unveiled through eDNA-PFU Technology in Mesocosm Ecosystems.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894156}, issn = {2076-2607}, support = {2022FY100400//the Science & Technology Fundamental Resources Investigation Program/ ; 2021xjkk0604//the Third Xinjiang Scientific Expedition Program/ ; U22A20454//the National Natural Science Foundation of China/ ; }, abstract = {Microbial communities are essential components of aquatic ecosystems and are widely employed for the detection, protection, and restoration of water ecosystems. The polyurethane foam unit (PFU) method, an effective and widely used environmental monitoring technique, has been improved with the eDNA-PFU method, offering efficiency, rapidity, and standardization advantages. This research aimed to explore the colonization process of microbial communities within PFUs using eDNA-PFU technology. To achieve this, we conducted ten-day monitoring and sequencing of microbial communities within PFUs in a stable and controlled artificial aquatic ecosystem, comparing them with water environmental samples (eDNA samples). Results showed 1065 genera in eDNA-PFU and 1059 in eDNA, with eDNA-PFU detecting 99.95% of eDNA-identified species. Additionally, the diversity indices of bacteria and eukaryotes in both methods showed similar trends over time in the colonization process; however, relative abundance differed. We further analyzed the colonization dynamics of microbes in eDNA-PFU and identified four clusters with varying colonization speeds. Notably, we found differences in colonization rates between bacteria and eukaryotes. Furthermore, the Molecular Ecological Networks (MEN) showed that the network in eDNA-PFU was more modular, forming a unique microbial community differentiated from the aquatic environment. In conclusion, this study, using eDNA-PFU, comprehensively explored microbial colonization and interrelationships in a controlled mesocosm system, providing foundational data and reference standards for its application in aquatic ecosystem monitoring and beyond.}, } @article {pmid37894148, year = {2023}, author = {Baraka, V and Andersson, T and Makenga, G and Francis, F and Minja, DTR and Overballe-Petersen, S and Tang, ME and Fuursted, K and Lood, R}, title = {Unveiling Rare Pathogens and Antibiotic Resistance in Tanzanian Cholera Outbreak Waters.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894148}, issn = {2076-2607}, support = {2017-00100//Swedish Research Council Formas/ ; 7044-00005B//Innovation Fund Denmark/ ; }, abstract = {The emergence of antibiotic resistance is a global health concern. Therefore, understanding the mechanisms of its spread is crucial for implementing evidence-based strategies to tackle resistance in the context of the One Health approach. In developing countries where sanitation systems and access to clean and safe water are still major challenges, contamination may introduce bacteria and bacteriophages harboring antibiotic resistance genes (ARGs) into the environment. This contamination can increase the risk of exposure and community transmission of ARGs and infectious pathogens. However, there is a paucity of information on the mechanisms of bacteriophage-mediated spread of ARGs and patterns through the environment. Here, we deploy Droplet Digital PCR (ddPCR) and metagenomics approaches to analyze the abundance of ARGs and bacterial pathogens disseminated through clean and wastewater systems. We detected a relatively less-studied and rare human zoonotic pathogen, Vibrio metschnikovii, known to spread through fecal--oral contamination, similarly to V. cholerae. Several antibiotic resistance genes were identified in both bacterial and bacteriophage fractions from water sources. Using metagenomics, we detected several resistance genes related to tetracyclines and beta-lactams in all the samples. Environmental samples from outlet wastewater had a high diversity of ARGs and contained high levels of blaOXA-48. Other identified resistance profiles included tetA, tetM, and blaCTX-M9. Specifically, we demonstrated that blaCTX-M1 is enriched in the bacteriophage fraction from wastewater. In general, however, the bacterial community has a significantly higher abundance of resistance genes compared to the bacteriophage population. In conclusion, the study highlights the need to implement environmental monitoring of clean and wastewater to inform the risk of infectious disease outbreaks and the spread of antibiotic resistance in the context of One Health.}, } @article {pmid37894136, year = {2023}, author = {Pusadkar, V and Azad, RK}, title = {Benchmarking Metagenomic Classifiers on Simulated Ancient and Modern Metagenomic Data.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894136}, issn = {2076-2607}, abstract = {Taxonomic profiling of ancient metagenomic samples is challenging due to the accumulation of specific damage patterns on DNA over time. Although a number of methods for metagenome profiling have been developed, most of them have been assessed on modern metagenomes or simulated metagenomes mimicking modern metagenomes. Further, a comparative assessment of metagenome profilers on simulated metagenomes representing a spectrum of degradation depth, from the extremity of ancient (most degraded) to current or modern (not degraded) metagenomes, has not yet been performed. To understand the strengths and weaknesses of different metagenome profilers, we performed their comprehensive evaluation on simulated metagenomes representing human dental calculus microbiome, with the level of DNA damage successively raised to mimic modern to ancient metagenomes. All classes of profilers, namely, DNA-to-DNA, DNA-to-protein, and DNA-to-marker comparison-based profilers were evaluated on metagenomes with varying levels of damage simulating deamination, fragmentation, and contamination. Our results revealed that, compared to deamination and fragmentation, human and environmental contamination of ancient DNA (with modern DNA) has the most pronounced effect on the performance of each profiler. Further, the DNA-to-DNA (e.g., Kraken2, Bracken) and DNA-to-marker (e.g., MetaPhlAn4) based profiling approaches showed complementary strengths, which can be leveraged to elevate the state-of-the-art of ancient metagenome profiling.}, } @article {pmid37894125, year = {2023}, author = {Kamalanathan, V and Sevugapperumal, N and Nallusamy, S and Ashraf, S and Kailasam, K and Afzal, M}, title = {Metagenomic Approach Deciphers the Role of Community Composition of Mycobiome Structured by Bacillus velezensis VB7 and Trichoderma koningiopsis TK in Tomato Rhizosphere to Suppress Root-Knot Nematode Infecting Tomato.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894125}, issn = {2076-2607}, support = {RSPD2023R979//Researchers Supporting Projects at King Saud University, Riyadh, Saudi Arabia./ ; }, abstract = {The soil microbiome is crucial for maintaining the sustainability of the agricultural environment. Concerning the role of diverse mycobiomes and their abundance toward the suppression of root-knot nematode (RKN) infection in vegetable crops, our understanding is unclear. To unveil this issue, we examined the fungal microbiome in tomato rhizosphere augmented with bioagents challenged against RKN at taxonomic and functional levels. Composition of the mycobiome in tomato rhizosphere treated with Bacillus velezensis VB7 and Trichoderma koningiopsis TK differed significantly from the infected tomato rhizosphere. The abundance and diversity of fungal species, however, were significantly higher in the combined treatments of bioagents than for individual treatments. Fungal microbiome diversity was negatively correlated in the RKN-associated soil. Network analysis of the fungal biome indicated a larger and complex network of fungal biome diversity in bioagent-treated soil than in nematode-associated tomato rhizosphere. The diversity index represented by that challenging the RKN by drenching with consortia of B. velezensis VB7 and T. koningiopsis TK, or applying them individually, constituted the maximum abundance and richness of the mycobiome compared to the untreated control. Thus, the increased diverse nature and relative abundance of the mycobiome in tomato rhizosphere was mediated through the application of either T. koningiopsis TK or B. velezensis VB7, individually or as a consortium comprising both fungal and bacterial antagonists, which facilitated engineering the community composition of fungal bioagents. This in turn inhibited the infestation of RKN in tomato. It would be interesting to explore further the possibility of combined applications of B. velezensis VB7 and T. koningiopsis TK to manage root-knot nematodes as an integrated approach for managing plant parasitic nematodes at the field level.}, } @article {pmid37894119, year = {2023}, author = {Shi, W and Tian, J and Xu, H and Qin, M}, title = {Microbial Relationship of Carious Deciduous Molars and Adjacent First Permanent Molars.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894119}, issn = {2076-2607}, support = {PKUSSNMP-201904 and PKUSSNMP-202008//the National Clinical Key Discipline Construction Project/ ; Z181100001618008//Beijing Municipal Science & Technology Commision/ ; }, abstract = {(1) Epidemiological studies have shown that deciduous molar caries are related to and more severe than permanent molar caries. This study aimed to investigate whether caries subtypes in deciduous molars were associated with caries in first permanent molars and to explore taxonomic and functional profiles of the microbiota involved in different subtypes. (2) 42 mixed-dentition children were recruited and were divided into DMC (carious deciduous molars but caries-free first permanent molars; n = 14), C (carious deciduous and first permanent molars; n = 13), and control (n = 15) groups. Metagenomic sequencing was performed for supragingival plaque samples obtained separately from deciduous and first permanent molars. (3) The microbiota of deciduous molars in the DMC and C groups differed not only in species-based beta diversity but also in compositional and functional profiles. In the C group-like subtype, 14 caries-related species and potential pathways were identified that could be responsible for the caries relationship between the deciduous and permanent molars. In the DMC group-like subtype, the overall functional structure, the levels of Leptotrichia wadei, Streptococcus anginosus, and Stomatobaculum longum and KOs in sugar transporters and fermentation, quorum sensing, and TCA cycle in their first permanent molars surprisingly resembled those of the C group rather than the control group. This suggested that these clinically sound first permanent molars were at a greater risk for caries. (4) Classification of deciduous molar caries according to the microbiota could serve as a caries risk predictor for adjacent first permanent molars.}, } @article {pmid37894093, year = {2023}, author = {Magdy Wasfy, R and Mbaye, B and Borentain, P and Tidjani Alou, M and Murillo Ruiz, ML and Caputo, A and Andrieu, C and Armstrong, N and Million, M and Gerolami, R}, title = {Ethanol-Producing Enterocloster bolteae Is Enriched in Chronic Hepatitis B-Associated Gut Dysbiosis: A Case-Control Culturomics Study.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894093}, issn = {2076-2607}, support = {ANR-15-CE36-0004-01//Agence Nationale de la Recherche/ ; 10-IAHU-03//Méditerranée Infection Foundation/ ; }, abstract = {BACKGROUND: Hepatitis B virus (HBV) infection is a global health epidemic that causes fatal complications, leading to liver cirrhosis and hepatocellular carcinoma. The link between HBV-related dysbiosis and specific bacterial taxa is still under investigation. Enterocloster is emerging as a new genus (formerly Clostridium), including Enterocloster bolteae, a gut pathogen previously associated with dysbiosis and human diseases such as autism, multiple sclerosis, and inflammatory bowel diseases. Its role in liver diseases, especially HBV infection, is not reported.

METHODS: The fecal samples of eight patients with chronic HBV infection and ten healthy individuals were analyzed using the high-throughput culturomics approach and compared to 16S rRNA sequencing. Quantification of ethanol, known for its damaging effect on the liver, produced from bacterial strains enriched in chronic HBV was carried out by gas chromatography-mass spectrometry.

RESULTS: Using culturomics, 29,120 isolated colonies were analyzed by Matrix-Assisted Laser Desorption/Ionization Mass Spectrometry (MALDI-TOF); 340 species were identified (240 species in chronic HBV samples, 254 species in control samples) belonging to 169 genera and 6 phyla. In the chronic HBV group, 65 species were already known in the literature; 48 were associated with humans but had not been previously found in the gut, and 17 had never been associated with humans previously. Six species were newly isolated in our study. By comparing bacterial species frequency, three bacterial genera were serendipitously found with significantly enriched bacterial diversity in patients with chronic HBV: Enterocloster, Clostridium, and Streptococcus (p = 0.0016, p = 0.041, p = 0.053, respectively). However, metagenomics could not identify this enrichment, possibly concerning its insufficient taxonomical resolution (equivocal assignment of operational taxonomic units). At the species level, the significantly enriched species in the chronic HBV group almost all belonged to class Clostridia, such as Clostridium perfringens, Clostridium sporogenes, Enterocloster aldenensis, Enterocloster bolteae, Enterocloster clostridioformis, and Clostridium innocuum. Two E. bolteae strains, isolated from two patients with chronic HBV infection, showed high ethanol production (27 and 200 mM).

CONCLUSIONS: Culturomics allowed us to identify Enterocloster species, specifically, E. bolteae, enriched in the gut microbiota of patients with chronic HBV. These species had never been isolated in chronic HBV infection before. Moreover, ethanol production by E. bolteae strains isolated from the chronic HBV group could contribute to liver disease progression. Additionally, culturomics might be critical for better elucidating the relationship between dysbiosis and chronic HBV infection in the future.}, } @article {pmid37894081, year = {2023}, author = {Wang, J and Zhao, K and Li, M and Fan, H and Wang, M and Xia, S and Chen, Y and Bai, X and Liu, Z and Ni, J and Sun, W and Jia, X and Lai, S}, title = {A Preliminary Study of the Potential Molecular Mechanisms of Individual Growth and Rumen Development in Calves with Different Feeding Patterns.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894081}, issn = {2076-2607}, support = {2021YFYZ0001//high quality cattle breeding materials and methods innovation and new variety breeding, key R & D project of Sichuan Province/ ; SCCXTD-2022-13//National modern agricultural industry technology system Sichuan innovation team technical R&D and integrated application post of beef cattle industry in agricultural area/ ; }, abstract = {At present, it is common to feed calves with "Concentrate", "Concentrate + hay" and TMR "Total Mixed Rations" feeding patterns in China, which achieved well feeding efficiency, but the three feeding patterns molecular regulation mechanism in actual production is still unclear. The study aimed to explore the most suitable feeding pattern for Chinese Holstein calves to improve the rumen fermentation function and growth performance of calves. In this regard, the interactions between rumen microorganisms and host metabolism were investigated. The rumen volume and weight of calves in the GF group were significantly higher than those in the GFF and TMR groups (p < 0.05), and the rumen pH of calves in the GF group was 6.47~6.79. Metagenomics analysis revealed that the rumen microbiome of GF and GFF calves had higher relative abundances of Methanobrevibacter, Methanosphaera, and Methanolacinia (p < 0.05). Prevotella multisaccharivorax was significantly more abundant in the rumen of GF calves (p < 0.05), indicating that GF group calves had a stronger ability to ferment sugars. Notably, in the pyruvate metabolic pathway, phosphoenolpyruvate carboxylase was significantly up-regulated in GF calves compared with the TMR group, and pyruvate-phosphate dikinase was significantly down-regulated. Metabolomic results showed that Ursodeoxycholic acid was significantly up-regulated in GF calves, and most of the differential metabolites were enriched in Bile secretion pathways. The association analysis study found that the microorganisms of Prevotella and Ruminococcaceae might cooperate with the host, which was helpful for the digestion and absorption of lipids and made the calves have better growth. The three feeding modes had similar effects, but the 'GF' feeding pattern was more beneficial to the individual growth and ruminal development regarding ruminal morphology, contents physiology and microorganisms. Furthermore, the synergistic effect of rumen microorganisms and the host could more effectively hydrolyze lipid substances and promote the absorption of lipids, which was of great significance to the growth of calves.}, } @article {pmid37894077, year = {2023}, author = {Li, P and Hong, J and Wu, M and Yuan, Z and Li, D and Wu, Z and Sun, X and Lin, D}, title = {Metagenomic Analysis Reveals Variations in Gut Microbiomes of the Schistosoma mansoni-Transmitting Snails Biomphalaria straminea and Biomphalaria glabrata.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894077}, issn = {2076-2607}, support = {Nos. 82202560, 82161160343 and 82272361//the National Natural Science Foundation of China/ ; Nos. 2020YFC1200100 and 2016YFC1200500//the National Key R&D Program of China/ ; No. 2022B1111030002//the R&D Program in Key Areas of Guangdong Province/ ; No. 22qntd4813//the Fundamental Research Funds for the Central University/ ; No. NPRC-2019-194-30//the National Parasitic Resource Center of China and the Ministry of Science and Technology/ ; No. 2021B1212040017//the Science and Technology Planning Project of Guangdong Province/ ; No. 20201192//the 6th Nuclear Energy R&D Project/ ; No. B12003//the 111 Project/ ; }, abstract = {Biomphalaria snails play a crucial role in the transmission of the human blood fluke Schistosoma mansoni. The gut microbiota of intermediate hosts is known to influence their physiological functions, but little is known about its composition and role in Biomphalaria snails. To gain insights into the biological characteristics of these freshwater intermediate hosts, we conducted metagenomic sequencing on Biomphalaria straminea and B. glabrata to investigate variations in their gut microbiota. This study revealed that the dominant members of the gut microbiota in B. glabrata belong to the phyla Bacteroidetes and Proteobacteria, which were also found to be the top two most abundant gut bacteria in B. straminea. We identified Firmicutes, Acidovorax and Bosea as distinctive gut microbes in B. straminea, while Aeromonas, Cloacibacterium and Chryseobacterium were found to be dependent features of the B. glabrata gut microbiota. We observed significant differences in the community structures and bacterial functions of the gut microbiota between the two host species. Notably, we found a distinctive richness of antibiotic resistance genes (ARGs) associated with various classes of antibiotics, including bacitracin, chloramphenicol, tetracycline, sulfonamide, penicillin, cephalosporin_ii and cephalosporin_i, fluoroquinolone, aminoglycoside, beta-lactam, multidrug and trimethoprim, in the digestive tracts of the snails. Furthermore, this study revealed the potential correlations between snail gut microbiota and the infection rate of S. mansoni using Spearman correlation analysis. Through metagenomic analysis, our study provided new insights into the gut microbiota of Biomphalaria snails and how it is influenced by host species, thereby enhancing our understanding of variant patterns of gut microbial communities in intermediate hosts. Our findings may contribute to future studies on gastropod-microbe interactions and may provide valuable knowledge for developing snail control strategies to combat schistosomiasis in the future.}, } @article {pmid37894074, year = {2023}, author = {Mugge, RL and Moseley, RD and Hamdan, LJ}, title = {Substrate Specificity of Biofilms Proximate to Historic Shipwrecks.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894074}, issn = {2076-2607}, support = {D18AC00018//Defense Advanced Research Projects Agency/ ; NA18OAR0110286//National Oceanic and Atmospheric Administration Ocean Exploration and Research Program/ ; }, abstract = {The number of built structures on the seabed, such as shipwrecks, energy platforms, and pipelines, is increasing in coastal and offshore regions. These structures, typically composed of steel or wood, are substrates for microbial attachment and biofilm formation. The success of biofilm growth depends on substrate characteristics and local environmental conditions, though it is unclear which feature is dominant in shaping biofilm microbiomes. The goal of this study was to understand the substrate- and site-specific impacts of built structures on short-term biofilm composition and functional potential. Seafloor experiments were conducted wherein steel and wood surfaces were deployed for four months at distances extending up to 115 m away from three historic (>50 years old) shipwrecks in the Gulf of Mexico. DNA from biofilms on the steel and wood was extracted, and metagenomes were sequenced on an Illumina NextSeq. A bioinformatics analysis revealed that the taxonomic composition was significantly different between substrates and sites, with substrate being the primary determining factor. Regardless of site, the steel biofilms had a higher abundance of genes related to biofilm formation, and sulfur, iron, and nitrogen cycling, while the wood biofilms showed a higher abundance of manganese cycling and methanol oxidation genes. This study demonstrates how substrate composition shapes biofilm microbiomes and suggests that marine biofilms may contribute to nutrient cycling at depth. Analyzing the marine biofilm microbiome provides insight into the ecological impact of anthropogenic structures on the seabed.}, } @article {pmid37894070, year = {2023}, author = {Hassa, J and Tubbesing, TJ and Maus, I and Heyer, R and Benndorf, D and Effenberger, M and Henke, C and Osterholz, B and Beckstette, M and Pühler, A and Sczyrba, A and Schlüter, A}, title = {Uncovering Microbiome Adaptations in a Full-Scale Biogas Plant: Insights from MAG-Centric Metagenomics and Metaproteomics.}, journal = {Microorganisms}, volume = {11}, number = {10}, pages = {}, pmid = {37894070}, issn = {2076-2607}, abstract = {The current focus on renewable energy in global policy highlights the importance of methane production from biomass through anaerobic digestion (AD). To improve biomass digestion while ensuring overall process stability, microbiome-based management strategies become more important. In this study, metagenomes and metaproteomes were used for metagenomically assembled genome (MAG)-centric analyses to investigate a full-scale biogas plant consisting of three differentially operated digesters. Microbial communities were analyzed regarding their taxonomic composition, functional potential, as well as functions expressed on the proteome level. Different abundances of genes and enzymes related to the biogas process could be mostly attributed to different process parameters. Individual MAGs exhibiting different abundances in the digesters were studied in detail, and their roles in the hydrolysis, acidogenesis and acetogenesis steps of anaerobic digestion could be assigned. Methanoculleus thermohydrogenotrophicum was an active hydrogenotrophic methanogen in all three digesters, whereas Methanothermobacter wolfeii was more prevalent at higher process temperatures. Further analysis focused on MAGs, which were abundant in all digesters, indicating their potential to ensure biogas process stability. The most prevalent MAG belonged to the class Limnochordia; this MAG was ubiquitous in all three digesters and exhibited activity in numerous pathways related to different steps of AD.}, } @article {pmid37893946, year = {2023}, author = {Jakab, S and Bali, K and Freytag, C and Pataki, A and Fehér, E and Halas, M and Jerzsele, Á and Szabó, I and Szarka, K and Bálint, Á and Bányai, K}, title = {Deep Sequencing of Porcine Reproductive and Respiratory Syndrome Virus ORF7: A Promising Tool for Diagnostics and Epidemiologic Surveillance.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {20}, pages = {}, pmid = {37893946}, issn = {2076-2615}, support = {RRF- 2.3.1-21-2022-00001//National Research, Development and Innovation Fund/ ; Doctoral Student Scholarship Program of the Co-operative Doctoral Program//National Research, Development and Innovation Fund/ ; }, abstract = {Porcine reproductive and respiratory syndrome virus (PRRSV) is a major concern worldwide. Control of PRRSV is a challenging task due to various factors, including the viral diversity and variability. In this study, we evaluated an amplicon library preparation protocol targeting the ORF7 region of both PRRSV species, Betaarterivirus suid 1 and Betaarterivirus suid 2. We designed tailed primers for a two-step PCR procedure that generates ORF7-specific amplicon libraries suitable for use on Illumina sequencers. We tested the method with serum samples containing common laboratory strains and with pooled serum samples (n = 15) collected from different pig farms during 2019-2021 in Hungary. Testing spiked serum samples showed that the newly designed method is highly sensitive and detects the viral RNA even at low copy numbers (corresponding to approx. Ct 35). The ORF7 sequences were easily assembled even from clinical samples. Two different sequence variants were identified in five samples, and the Porcilis MLV vaccine strain was identified as the minor variant in four samples. An in-depth analysis of the deep sequencing results revealed numerous polymorphic sites along the ORF7 gene in a total of eight samples, and some sites (positions 12, 165, 219, 225, 315, 345, and 351) were found to be common in several clinical specimens. We conclude that amplicon deep sequencing of a highly conserved region of the PRRSV genome could support both laboratory diagnosis and epidemiologic surveillance of the disease.}, } @article {pmid37893918, year = {2023}, author = {Li, X and Chen, J and Zhang, C and Zhang, S and Shen, Q and Wang, B and Bao, M and Xu, B and Wu, Q and Han, N and Huang, Z}, title = {Fecal Metagenomics Study Reveals That a Low-Fiber Diet Drives the Migration of Wild Asian Elephants in Xishuangbanna, China.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {20}, pages = {}, pmid = {37893918}, issn = {2076-2615}, support = {2023J0202//Scientific Research Foundation of Education Department of Yunnan Province/ ; 32260015//National Natural Science Foundation of China/ ; }, abstract = {The rare northward migration of wild Asian elephants in Xishuangbanna, China, has attracted global attention. Elephant migration is a complex ecological process, and the factors driving this long-distance migration remain elusive. In this study, fresh fecal samples were collected from both captive and wild Asian elephants, along with breastfed calves residing within the Wild Elephant Valley of Xishuangbanna. Our aim was to investigate the relationship between diet, gut microbiota, and migration patterns in Asian elephants through comprehensive metagenomic sequencing analyses. Among the breastfed Asian elephant group, Bacteroidales and Escherichia emerged as the dominant bacterial taxa, while the primary carbohydrate-active enzymes (CAZymes) enriched in this group were GH2, GH20, GH92, GH97, GH38, GH23, and GH43, aligning with their dietary source, namely breast milk. The bacterial taxa enriched in captive Asian elephants (CAEs) were mainly Butyrivibrio, Treponema, and Fibrobacter, and the enriched lignocellulose-degrading enzymes mainly included GH25, GH10, GH9, and cellulase (EC 3.2.1.4). These findings are consistent with the high-fiber diet of captive elephants. In contrast, the main bacterial taxa enriched in wild Asian elephants (WAEs) were Ruminococcus and Eubacterium, and the enriched CAZymes included GH109, GH20, GH33, GH28, GH106, and GH39. The abundance of lignocellulose-degrading bacteria and CAZyme content was low in WAEs, indicating challenges in processing high-fiber foods and explaining the low-fiber diet in this group. These findings suggest that wild elephant herds migrate in search of nutritionally suitable, low-fiber food sources.}, } @article {pmid37893676, year = {2023}, author = {Tsoungos, A and Pemaj, V and Slavko, A and Kapolos, J and Papadelli, M and Papadimitriou, K}, title = {The Rising Role of Omics and Meta-Omics in Table Olive Research.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {20}, pages = {}, pmid = {37893676}, issn = {2304-8158}, support = {MIS 5047289//Operational Program Competitiveness, Entrepreneurship, and Innovation, under the call Support for Regional Excellence/ ; }, abstract = {Table olives are often the result of fermentation, a process where microorganisms transform raw materials into the final product. The microbial community can significantly impact the organoleptic characteristics and safety of table olives, and it is influenced by various factors, including the processing methods. Traditional culture-dependent techniques capture only a fraction of table olives' intricate microbiota, prompting a shift toward culture-independent methods to address this knowledge gap. This review explores recent advances in table olive research through omics and meta-omics approaches. Genomic analysis of microorganisms isolated from table olives has revealed multiple genes linked to technological and probiotic attributes. An increasing number of studies concern metagenomics and metabolomics analyses of table olives. The former offers comprehensive insights into microbial diversity and function, while the latter identifies aroma and flavor determinants. Although proteomics and transcriptomics studies remain limited in the field, they have the potential to reveal deeper layers of table olives' microbiome composition and functionality. Despite the challenges associated with implementing multi-omics approaches, such as the reliance on advanced bioinformatics tools and computational resources, they hold the promise of groundbreaking advances in table olive processing technology.}, } @article {pmid37893675, year = {2023}, author = {Fusco, V and Fanelli, F and Chieffi, D}, title = {Recent and Advanced DNA-Based Technologies for the Authentication of Probiotic, Protected Designation of Origin (PDO) and Protected Geographical Indication (PGI) Fermented Foods and Beverages.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {20}, pages = {}, pmid = {37893675}, issn = {2304-8158}, abstract = {The authenticity of probiotic products and fermented foods and beverages that have the status of protected designation of origin (PDO) or geographical indication (PGI) can be assessed via numerous methods. DNA-based technologies have emerged in recent decades as valuable tools to achieve food authentication, and advanced DNA-based methods and platforms are being developed. The present review focuses on the recent and advanced DNA-based techniques for the authentication of probiotic, PDO and PGI fermented foods and beverages. Moreover, the most promising DNA-based detection tools are presented. Strain- and species-specific DNA-based markers of microorganisms used as starter cultures or (probiotic) adjuncts for the production of probiotic and fermented food and beverages have been exploited for valuable authentication in several detection methods. Among the available technologies, propidium monoazide (PMA) real-time polymerase chain reaction (PCR)-based technologies allow for the on-time quantitative detection of viable microbes. DNA-based lab-on-a-chips are promising devices that can be used for the on-site and on-time quantitative detection of microorganisms. PCR-DGGE and metagenomics, even combined with the use of PMA, are valuable tools allowing for the fingerprinting of the microbial communities, which characterize PDO and PGI fermented foods and beverages, and they are necessary for authentication besides permitting the detection of extra or mislabeled species in probiotic products. These methods, in relation to the authentication of probiotic foods and beverages, need to be used in combination with PMA, culturomics or flow cytometry to allow for the enumeration of viable microorganisms.}, } @article {pmid37892391, year = {2023}, author = {Xiang, X and Chen, J and Zhu, M and Gao, H and Liu, X and Wang, Q}, title = {Multiomics Revealed the Multi-Dimensional Effects of Late Sleep on Gut Microbiota and Metabolites in Children in Northwest China.}, journal = {Nutrients}, volume = {15}, number = {20}, pages = {}, pmid = {37892391}, issn = {2072-6643}, mesh = {Adult ; Animals ; Humans ; Child ; *Gastrointestinal Microbiome ; Multiomics ; Amino Acids ; Sleep ; China ; Amines ; Bile Acids and Salts ; }, abstract = {Background Sleep plays a pivotal role in children's mental and physical development and has been linked to the gut microbiota in animals and adults. However, the characteristics of the gut microbiota and metabolites and the relationship to late bedtimes in children remain unclear. Methods In total, 88 eligible children, aged from 3 to 8 years, were recruited and divided into two groups according to the bedtime collected by designed questionnaires (early, before 22:00: n = 48; late, after 22:00, n = 40). Stools and plasma samples were collected to examine the characteristics of the gut microbiota and metabolites by shotgun metagenomics and metabolomics. Results The richness and diversity of the gut microbiota in children with early bedtime were significantly increased compared with the late ones. Coprococcus, Collinsella, Akkermansia muciniphila, and Bifidobacterium adolescentis were significantly more abundant in children with early bedtime, while Bacteroides and Clostridium sp. CAG-253 were obviously enriched in the late ones. A total of 106 metabolic pathways, including biosynthesis of ribonucleotide, peptidoglycan, and amino acids, and starch degradation were enriched in children with early bedtime, while 42 pathways were abundant in those with late bedtime. Notably, more gut microbial metabolites were observed in children with late bedtime, which included aldehyde, ketones, esters, amino acids and their metabolites, benzene and substituted derivatives, bile acids, heterocyclic compounds, nucleotide and metabolites, organic acid and derivatives, sugars and acyl carnitine. In plasma, fatty amides, lipids, amino acids, metabolites, hormones, and related compounds were enriched in children with early bedtime, while bile acids were higher in children with late bedtime. Association studies revealed that the different microbial species were correlated with metabolites from gut microbiota and plasma. Conclusions The results of our study revealed that the gut microbiota diversity and richness, and metabolic pathways were significantly extensive in children with early bedtime, whereas the gut microbial metabolites were significantly decreased, which might be related to gut microbial differences.}, } @article {pmid37892187, year = {2023}, author = {Meslier, V and Menozzi, E and David, A and Morabito, C and Lucas Del Pozo, S and Famechon, A and North, J and Quinquis, B and Koletsi, S and Macnaughtan, J and Mezabrovschi, R and Ehrlich, SD and Schapira, AHV and Almeida, M}, title = {Evaluation of an Adapted Semi-Automated DNA Extraction for Human Salivary Shotgun Metagenomics.}, journal = {Biomolecules}, volume = {13}, number = {10}, pages = {}, pmid = {37892187}, issn = {2218-273X}, mesh = {Humans ; Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; *DNA/genetics/chemistry ; *Microbiota/genetics ; Metagenome ; }, abstract = {Recent attention has highlighted the importance of oral microbiota in human health and disease, e.g., in Parkinson's disease, notably using shotgun metagenomics. One key aspect for efficient shotgun metagenomic analysis relies on optimal microbial sampling and DNA extraction, generally implementing commercial solutions developed to improve sample collection and preservation, and provide high DNA quality and quantity for downstream analysis. As metagenomic studies are today performed on a large number of samples, the next evolution to increase study throughput is with DNA extraction automation. In this study, we proposed a semi-automated DNA extraction protocol for human salivary samples collected with a commercial kit, and compared the outcomes with the DNA extraction recommended by the manufacturer. While similar DNA yields were observed between the protocols, our semi-automated DNA protocol generated significantly higher DNA fragment sizes. Moreover, we showed that the oral microbiome composition was equivalent between DNA extraction methods, even at the species level. This study demonstrates that our semi-automated protocol is suitable for shotgun metagenomic analysis, while allowing for improved sample treatment logistics with reduced technical variability and without compromising the structure of the oral microbiome.}, } @article {pmid37892148, year = {2023}, author = {Janusz, G and Mazur, A and Pawlik, A and Kołodyńska, D and Jaroszewicz, B and Marzec-Grządziel, A and Koper, P}, title = {Metagenomic Analysis of the Composition of Microbial Consortia Involved in Spruce Degradation over Time in Białowieża Natural Forest.}, journal = {Biomolecules}, volume = {13}, number = {10}, pages = {}, pmid = {37892148}, issn = {2218-273X}, mesh = {*Microbial Consortia/genetics ; Forests ; Wood/microbiology ; *Microbiota/genetics ; Soil ; Fungi/genetics ; }, abstract = {Deadwood plays an important role in forest ecology; its degradation and, therefore, carbon assimilation is carried out by fungi and bacteria. To quantify the abundance and distribution of microbial taxa inhabiting dead spruce logs fallen over a span of 50 years and the soil beneath, we used taxonomic profiling with NGS sequencing of hypervariable DNA fragments of ITS1 and 16S V3-V4, respectively. The analysis of sequencing data revealed a high level of diversity in microbial communities participating in the degradation of spruce logs. Differences in the relative abundance of microbial taxa between the samples of the wood that died in 1974 and 2014, and of the soil in its immediate vicinity, were visible, especially at the genus level. Based on the Lefse analysis significantly higher numbers of classified bacterial taxa were observed in the wood and soil samples from 2014 (wood: 1974-18 and 2014-28 taxa; soil: 1974-8 and 2014-41 taxa) while the number of classified fungal taxa was significantly higher in the wood and soil samples from 1974 (wood: 1974-17 and 2014-9 taxa; soil: 1974-57 and 2014-28 taxa). Most of the bacterial and fungal amplicon sequence variants (ASVs) unique to wood were found in the samples from 1974, while those unique to soil were detected in the samples from 2014. The ATR-FTIR method supported by CHN analysis revealed physicochemical changes in deadwood induced by the activity of fungal and bacterial organisms.}, } @article {pmid37892039, year = {2023}, author = {Zheng, X and He, P and Zhong, R and Chen, G and Xia, J and Li, C}, title = {Weil's Disease in an HIV-Infected Patient: A Case Report and Literature Review.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {13}, number = {20}, pages = {}, pmid = {37892039}, issn = {2075-4418}, abstract = {Weil's disease, an icterohemorrhagic infection, is the most severe and fatal form of leptospirosis and is characterized by jaundice, renal dysfunction, and hemorrhagic predisposition. Weil's disease with HIV infection has rarely been reported. A 68-year-old male with HIV infection presented to our hospital with fever and dyspnea that progressed to severe hemoptysis and systemic multiple organ failure, necessitating a tracheal intubation ventilator. A diagnosis of Weil's disease was made after Leptospira interrogans was identified via metagenomic next-generation sequencing (mNGS) in bronchoalveolar lavage fluid (BALF). After immediately receiving supportive therapy and targeted antimicrobial agents, the patient achieved complete recovery upon discharge. The co-infection of HIV infection and leptospirosis resulting in systemic multi-organ failure is rare, but awareness should be raised of the differential diagnosis. mNGS can help identify pathogens and facilitate the use of targeted and efficacious antimicrobial therapy in unusual clinical environments.}, } @article {pmid37891627, year = {2023}, author = {Coclet, C and Sorensen, PO and Karaoz, U and Wang, S and Brodie, EL and Eloe-Fadrosh, EA and Roux, S}, title = {Virus diversity and activity is driven by snowmelt and host dynamics in a high-altitude watershed soil ecosystem.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {237}, pmid = {37891627}, issn = {2049-2618}, mesh = {Humans ; Ecosystem ; Soil ; Altitude ; *Viruses/genetics ; *Bacteriophages/genetics ; Soil Microbiology ; *Microbiota/genetics ; DNA ; }, abstract = {BACKGROUND: Viruses impact nearly all organisms on Earth, including microbial communities and their associated biogeochemical processes. In soils, highly diverse viral communities have been identified, with a global distribution seemingly driven by multiple biotic and abiotic factors, especially soil temperature and moisture. However, our current understanding of the stability of soil viral communities across time and their response to strong seasonal changes in environmental parameters remains limited. Here, we investigated the diversity and activity of environmental soil DNA and RNA viruses, focusing especially on bacteriophages, across dynamics' seasonal changes in a snow-dominated mountainous watershed by examining paired metagenomes and metatranscriptomes.

RESULTS: We identified a large number of DNA and RNA viruses taxonomically divergent from existing environmental viruses, including a significant proportion of fungal RNA viruses, and a large and unsuspected diversity of positive single-stranded RNA phages (Leviviricetes), highlighting the under-characterization of the global soil virosphere. Among these, we were able to distinguish subsets of active DNA and RNA phages that changed across seasons, consistent with a "seed-bank" viral community structure in which new phage activity, for example, replication and host lysis, is sequentially triggered by changes in environmental conditions. At the population level, we further identified virus-host dynamics matching two existing ecological models: "Kill-The-Winner" which proposes that lytic phages are actively infecting abundant bacteria, and "Piggyback-The-Persistent" which argues that when the host is growing slowly, it is more beneficial to remain in a dormant state. The former was associated with summer months of high and rapid microbial activity, and the latter with winter months of limited and slow host growth.

CONCLUSION: Taken together, these results suggest that the high diversity of viruses in soils is likely associated with a broad range of host interaction types each adapted to specific host ecological strategies and environmental conditions. As our understanding of how environmental and host factors drive viral activity in soil ecosystems progresses, integrating these viral impacts in complex natural microbiome models will be key to accurately predict ecosystem biogeochemistry. Video Abstract.}, } @article {pmid37891621, year = {2023}, author = {Erculiani, M and Poluzzi, F and Mottadelli, G and Felici, E and Ml, N and Caraccia, M and Grandi, A and Casella, S and Giacometti, L and Montobbio, G and Ceccherini, I and Di Marco, E and Bonaretti, C and Biassoni, R and Squillario, M and Pietrantoni, A and Villanacci, V and Pini Prato, A}, title = {A unicentric cross-sectional observational study on chronic intestinal inflammation in total colonic aganglionosis: beware of an underestimated condition.}, journal = {Orphanet journal of rare diseases}, volume = {18}, number = {1}, pages = {339}, pmid = {37891621}, issn = {1750-1172}, support = {Ricerca Corrente//Ministero della Salute/ ; 2019.0880 - ID ROL 32612//Compagnia di San Paolo/ ; }, mesh = {Humans ; *Hirschsprung Disease/genetics/pathology ; Cross-Sectional Studies ; *Inflammatory Bowel Diseases/complications/pathology ; Inflammation ; }, abstract = {BACKGROUND: Inflammatory Bowel Diseases (IBD) are known to occur in association with Hirschsprung disease (HSCR). Most of cases are represented by Crohn Disease (CD) occurring in patients with Total Colonic Aganglionosis (TCSA) with an estimated prevalence of around 2%. Based on these considerations and on a number of provisional data belonging to our Center for Digestive Diseases, we developed a unicentric cross-sectional observational study aimed at describing phenotype, genotype, pathology and metagenomics of all patients with TCSA and Crohn-like lesions.

RESULTS: Out of a series of 62 eligible TCSA patients, 48 fulfilled inclusion criteria and were enrolled in the study. Ten patients did not complete the study due to non-compliance or withdrawal of consent and were subsequently dropped out. A total of 38 patients completed the study. All patients were tested for chronic intestinal inflammation by a combination of fecal calprotectine (FC) or occult fecal blood (OFB) and underwent fecal metagenomics. Nineteen (50%) tested positive for FC, OFB, or both and subsequently underwent retrograde ileoscopy. Fourteen patients (36.8%) presented Crohn-like lesions, occurring after a median of 11.5 years after surgery (range 8 months - 21.5 years). No statistically significant differences regarding demographic, phenotype and genotype were observed comparing patients with and without lesions, except for need for blood transfusion that was more frequent in those with lesions. Faecal microbiome of patients with lesions (not that of caregivers) was less biodiverse and characterized by a reduction of Bacteroidetes, and an overabundance of Proteobacteria. FC tested negative in 3/14 patients with lesions (21%).

CONCLUSIONS: Our study demonstrated an impressive 10-folds higher incidence of chronic inflammation in TCSA. Up to 50% of patients may develop IBD-like lesions postoperatively. Nonetheless, we failed in identifying specific risk factors to be used to implement prevention strategies. Based on the results of our study, we suggest screening all TCSA patients with retrograde ileoscopy regardless of FC/OFB values. The frequency of endoscopic assessments and the role of FC/OFB screening in prompting endoscopy is yet to be determined.}, } @article {pmid37891594, year = {2023}, author = {Chen, X and Wang, H and Li, Q and Qi, Y and Li, F and He, W and Wang, Q and Jin, F and Guo, Y and Hei, M and Xie, Z}, title = {A fatal case of neonatal viral sepsis caused by human parainfluenza virus type 3.}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {248}, pmid = {37891594}, issn = {1743-422X}, mesh = {Child ; Male ; Humans ; Infant, Newborn ; Parainfluenza Virus 3, Human/genetics ; *Shock, Septic/diagnosis ; *Respiratory Tract Infections ; Viremia ; Mutation ; Parainfluenza Virus 2, Human ; }, abstract = {BACKGROUND: Sepsis is a systemic inflammatory response syndrome caused by severe infection in children, but cases of sepsis associated with human parainfluenza virus (HPIV) have been rarely reported in newborns.

CASE PRESENTATION: We report a case of HPIV-3 positive full-term newborn admitted to the Neonatal Intensive Care Unit of Beijing Children's Hospital due to hematuria, gloomy spirit, inactivity and loss of appetite for 6 h. He had septic shock when he arrived the Accident & Emergency Department requiring immediate intubation and mechanical ventilation. Intravenous antibiotics were started. He had completely negative response to all anti-shock treatments including fluid resuscitation and vasopressor supports, and died 14 h later. Viral nucleic acid detection and metagenomic next-generation sequencing (mNGS) analyses of nasopharyngeal aspirate and blood specimens verified an HPIV-3 infection, with negative bacterial culture results. The HPIV-3 strain detected in this patient was subtyped as HPIV C3a, and two unreported amino acid mutations were found in the HN protein region.

CONCLUSION: The patient had a severe infection associated with HPIV-3, which was the cause of sepsis and septic shock. This study showed the diagnostic value of mNGS in etiological diagnosis, especially in severe neonatal case.}, } @article {pmid37891586, year = {2023}, author = {Wang, Y and Chen, T and Zhang, S and Zhang, L and Li, Q and Lv, Q and Kong, D and Jiang, H and Ren, Y and Jiang, Y and Li, Y and Huang, W and Liu, P}, title = {Clinical evaluation of metagenomic next-generation sequencing in unbiased pathogen diagnosis of urinary tract infection.}, journal = {Journal of translational medicine}, volume = {21}, number = {1}, pages = {762}, pmid = {37891586}, issn = {1479-5876}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Urinary Tract Infections/diagnosis ; Cluster Analysis ; Computational Biology ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Early availability of pathogen identification in urinary tract infections (UTIs) has critical importance in disease management. Metagenomic next-generation sequencing (mNGS) has the potential to transform how acute and serious infections are diagnosed by offering unbiased and culture-free pathogen detection. However, clinical experience with application of the mNGS test is relatively limited.

METHODS: We therefore established a MinION-based mNGS pathogens diagnostic platform and evaluated its potential for clinical implementation in UTIs with clinical samples. 213 urine samples from patients with suspected UTIs were included and subjected to mNGS testing using the MinION platform. mNGS results were compared to the gold standard of clinical culture and composite standard of combining clinical testing, confirmatory qPCR testing, and clinical adjudication by doctors.

RESULTS: The mNGS exhibited a sensitivity of 81.4% and a specificity of 92.3%, along with a positive predictive value of 96.6%, a negative predictive value of 64.9%, and an overall accuracy of 84.4%, all of which were determined based on the gold standard of routine culture results. When assessed against the composite standard, the sensitivity and specificity both increased to 89.9% and 100%, respectively, while the accuracy rose to 92.4%. Notably, the positive predictive value and negative predictive value also saw improvements, reaching 100% and 76.8%, respectively. Moreover, this diagnostic platform successfully identified dsDNA viruses. Among the 65 culture-negative samples, the viral detection rate reached 33.8% (22/65) and was subsequently validated through qPCR. Furthermore, the automatic bioinformatics pipeline we developed enabled one-click analysis from data to results, leading to a significant reduction in diagnosis time.

CONCLUSION: These results demonstrate that the pathogen detection performance of mNGS is sufficient for diagnostic testing in clinical settings. As the method is generally unbiased, it can improve diagnostic testing of UTIs and other microbial infections.}, } @article {pmid37891467, year = {2023}, author = {Zhang, K and Bai, YZ and Liu, C and Liu, SS and Lu, XX and Yang, RG}, title = {Composition of pathogenic microorganism in chronic osteomyelitis based on metagenomic sequencing and its application value in etiological diagnosis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {313}, pmid = {37891467}, issn = {1471-2180}, mesh = {Humans ; Saccharomyces cerevisiae ; High-Throughput Nucleotide Sequencing ; *Osteomyelitis/diagnosis ; Anti-Bacterial Agents ; *Coinfection ; Metagenomics ; *Mycobacterium tuberculosis ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Traditionally, conventional microbiological culture methods have been used to detect pathogenic microorganisms in chronic osteomyelitis. However, these methods have been found to have a low detection rate, complicating the precise guidance of infection treatment. This study employed metagenomic next-generation sequencing (mNGS) to detect these microorganisms in chronic osteomyelitis with three main objectives: 1). Gain a deeper understanding of the composition of pathogenic microorganisms in chronic osteomyelitis. 2). Compare the microbial detection rates between mNGS and the standard culture methods used in laboratories to enhance the effectiveness of the traditional culture methods. 3). Explore the potential of mNGS in etiological diagnosis.

METHODS: Fifty clinically confirmed intraoperative bone tissue samples of chronic osteomyelitis from January 2021 to December 2021 were collected and subjected to mNGS and microbiological testing, respectively. The orthopaedic surgeon combined clinical manifestations and related examinations to determine the causative pathogens.

RESULTS: The culture method obtained 29 aerobic and parthenogenic anaerobic bacteria, 3 specific anaerobic bacteria, and 1 yeast-like fungus. Thirty-six aerobic and parthenogenic anaerobic bacteria, 11 specific anaerobic bacteria, and 1 yeast-like fungus were obtained by mNGS, and 2 Mycobacterium tuberculosis(MTB) strains were detected. However, there was no significant difference in the overall positive detection rate between mNGS and the culture method (P = 0.07), and the two were not statistically significant in detecting aerobic and partly anaerobic bacteria (P = 0.625). But, mNGS was significantly superior to culture in detecting anaerobic bacteria and Mycobacterium tuberculosis (P<0.05).

CONCLUSIONS: The mNGS method has enhanced our understanding of the distribution of pathogenic microorganisms in chronic osteomyelitis. Traditional culture methods help isolate and cultivate aerobic and facultative anaerobic bacteria, and fungi, and are also utilized for antibacterial drug sensitivity tests. However, mNGS has shown superior capabilities in detecting anaerobic bacteria, MTB, and mixed infection bacteria. This finding offers invaluable guidance for improving laboratory microbial culture and detection conditions. Hence, mNGS should be judiciously used for chronic osteomyelitis, and PCR can be implemented for certain difficult-to-culture microorganisms, such as MTB.}, } @article {pmid37891427, year = {2023}, author = {Starke, S and Harris, DMM and Zimmermann, J and Schuchardt, S and Oumari, M and Frank, D and Bang, C and Rosenstiel, P and Schreiber, S and Frey, N and Franke, A and Aden, K and Waschina, S}, title = {Amino acid auxotrophies in human gut bacteria are linked to higher microbiome diversity and long-term stability.}, journal = {The ISME journal}, volume = {17}, number = {12}, pages = {2370-2380}, pmid = {37891427}, issn = {1751-7370}, support = {EXC2167//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; RU5042//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 1289/17-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, mesh = {Humans ; *Amino Acids/metabolism ; Bacteria/genetics/metabolism ; Metabolomics ; Metabolome ; *Gastrointestinal Microbiome/genetics ; }, abstract = {Amino acid auxotrophies are prevalent among bacteria. They can govern ecological dynamics in microbial communities and indicate metabolic cross-feeding interactions among coexisting genotypes. Despite the ecological importance of auxotrophies, their distribution and impact on the diversity and function of the human gut microbiome remain poorly understood. This study performed the first systematic analysis of the distribution of amino acid auxotrophies in the human gut microbiome using a combined metabolomic, metagenomic, and metabolic modeling approach. Results showed that amino acid auxotrophies are ubiquitous in the colon microbiome, with tryptophan auxotrophy being the most common. Auxotrophy frequencies were higher for those amino acids that are also essential to the human host. Moreover, a higher overall abundance of auxotrophies was associated with greater microbiome diversity and stability, and the distribution of auxotrophs was found to be related to the human host's metabolome, including trimethylamine oxide, small aromatic acids, and secondary bile acids. Thus, our results suggest that amino acid auxotrophies are important factors contributing to microbiome ecology and host-microbiome metabolic interactions.}, } @article {pmid37891335, year = {2023}, author = {Arana, A and Esteves, J and Ramírez, R and Galetti, PM and Pérez Z, J and Ramirez, JL}, title = {Population genomics reveals how 5 ka of human occupancy led the Lima leaf-toed gecko (Phyllodactylus sentosus) to the brink of extinction.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {18465}, pmid = {37891335}, issn = {2045-2322}, mesh = {Male ; Humans ; Animals ; *Metagenomics ; Ecosystem ; Heterozygote ; *Lizards/genetics ; Peru ; Genetic Variation ; Endangered Species ; }, abstract = {Small species with high home fidelity, high ecological specialization or low vagility are particularly prone to suffer from habitat modification and fragmentation. The Lima leaf-toed gecko (Phyllodactylus sentosus) is a critically endangered Peruvian species that shelters mostly in pre-Incan archeological areas called huacas, where the original environmental conditions are maintained. We used genotyping by sequencing to understand the population genomic history of P. sentosus. We found low genetic diversity (He 0.0406-0.134 and nucleotide diversity 0.0812-0.145) and deviations of the observed heterozygosity relative to the expected heterozygosity in some populations (Fis - 0.0202 to 0.0187). In all analyses, a clear population structuring was observed that cannot be explained by isolation by distance alone. Also, low levels of historical gene flow were observed between most populations, which decreased as shown in contemporary migration rate analysis. Demographic inference suggests these populations experienced bottleneck events during the last 5 ka. These results indicate that habitat modification since pre-Incan civilizations severely affected these populations, which currently face even more drastic urbanization threats. Finally, our predictions show that this species could become extinct in a decade without further intervention, which calls for urgent conservation actions being undertaken.}, } @article {pmid37891329, year = {2023}, author = {Lin, X and Xiao, HM and Liu, HM and Lv, WQ and Greenbaum, J and Gong, R and Zhang, Q and Chen, YC and Peng, C and Xu, XJ and Pan, DY and Chen, Z and Li, ZF and Zhou, R and Wang, XF and Lu, JM and Ao, ZX and Song, YQ and Zhang, YH and Su, KJ and Meng, XH and Ge, CL and Lv, FY and Luo, Z and Shi, XM and Zhao, Q and Guo, BY and Yi, NJ and Shen, H and Papasian, CJ and Shen, J and Deng, HW}, title = {Gut microbiota impacts bone via Bacteroides vulgatus-valeric acid-related pathways.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6853}, pmid = {37891329}, issn = {2041-1723}, support = {R01 AG061917/AG/NIA NIH HHS/United States ; R01 MH104680/MH/NIMH NIH HHS/United States ; P20 GM109036/GM/NIGMS NIH HHS/United States ; R01 AR069055/AR/NIAMS NIH HHS/United States ; U19 AG055373/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Female ; Mice ; Animals ; *Gastrointestinal Microbiome ; *Bone Resorption ; *Osteoporosis ; }, abstract = {Although the gut microbiota has been reported to influence osteoporosis risk, the individual species involved, and underlying mechanisms, remain largely unknown. We performed integrative analyses in a Chinese cohort of peri-/post-menopausal women with metagenomics/targeted metabolomics/whole-genome sequencing to identify novel microbiome-related biomarkers for bone health. Bacteroides vulgatus was found to be negatively associated with bone mineral density (BMD), which was validated in US white people. Serum valeric acid (VA), a microbiota derived metabolite, was positively associated with BMD and causally downregulated by B. vulgatus. Ovariectomized mice fed B. vulgatus demonstrated increased bone resorption and poorer bone micro-structure, while those fed VA demonstrated reduced bone resorption and better bone micro-structure. VA suppressed RELA protein production (pro-inflammatory), and enhanced IL10 mRNA expression (anti-inflammatory), leading to suppressed maturation of osteoclast-like cells and enhanced maturation of osteoblasts in vitro. The findings suggest that B. vulgatus and VA may represent promising targets for osteoporosis prevention/treatment.}, } @article {pmid37889849, year = {2023}, author = {Rafieyan, S and Amoozegar, MA and Makzum, S and Salimi-Ashtiani, M and Nikou, MM and Ventosa, A and Sanchez-Porro, C}, title = {Marinobacter iranensis sp. nov., a slightly halophilic bacterium from a hypersaline lake.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {10}, pages = {}, doi = {10.1099/ijsem.0.006083}, pmid = {37889849}, issn = {1466-5034}, mesh = {*Fatty Acids/chemistry ; Lakes/microbiology ; *Marinobacter ; Sodium Chloride ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Base Composition ; Bacterial Typing Techniques ; Phospholipids/chemistry ; }, abstract = {A novel halophilic bacterium, strain 71-i[T], was isolated from Inche-Broun hypersaline lake in Golestan province, in the north of Iran. It was a Gram-stain-negative, non-endospore forming, rod-shaped bacterium. It grew at 4-40 °C (optimum 30 °C), pH 6.0-11.0 (optimum pH 7.5) and with 0.5-15 % (w/v) NaCl [optimum 3 % (w/v) NaCl]. The results of phylogenetic analyses based on the 16S rRNA gene sequence comparison indicated its affiliation to the genus Marinobacter and the low percentage of identity with the most closely related species (97.5 %), indicated its placement as a novel species within this genus. Digital DNA-DNA hybridization (dDDH) values and average nucleotide identity (ANI) analyses of this strain against closely related species confirmed its condition of novel taxon. On the other hand, the percentage of the average amino acid identity (AAI) affiliated strain 71-i[T] within the genus Marinobacter. The DNA G+C content of this isolate was 57.7 mol%. The major fatty acids were C16 : 0 and C16 : 1ω7c and/or C16 : 1 ω6c. Ubiquinone-9 was the major isoprenoid quinone and diphosphatidylglycerol (DPG), phosphatidylglycerol (PG) and phosphatidylethanolamine (PE) were the main polar lipids of this strain. On the basis of the phylogenomic and phenotypic (including chemotaxonomic) features, we propose strain 71-i[T] (= IBRC M 11023[T] = CECT 30160[T] = LMG 29252[T]) as the type strain of a novel species within the genus Marinobacter, with the name Marinobacter iranensis sp. nov. Genomic detections of this strain in various metagenomic databases indicate that it is a relatively abundant species in environments with low salinities (approximately 5 % salinity), but not in hypersaline habitats with high salt concentrations.}, } @article {pmid37889679, year = {2023}, author = {Sutera, AM and Arfuso, F and Tardiolo, G and Riggio, V and Fazio, F and Aiese Cigliano, R and Paytuví, A and Piccione, G and Zumbo, A}, title = {Effect of a Co-Feed Liquid Whey-Integrated Diet on Crossbred Pigs' Fecal Microbiota.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {11}, pages = {}, pmid = {37889679}, issn = {2076-2615}, abstract = {This study assessed the potential effect of a co-feed liquid whey-integrated diet on the fecal microbiota of 14 crossbred pigs. The experimental design was as follows: seven pigs were in the control group, fed with a control feed, and seven were in the experimental group, fed with the same control feed supplemented daily with liquid whey. The collection of fecal samples was conducted on each animal before the dietary treatment (T0) and one (T1), and two (T2) months after the beginning of the co-feed integration. In addition, blood samples were collected from each pig at the same time points in order to evaluate the physiological parameters. Taxonomic analysis showed a bacterial community dominated by Firmicutes, Bacteroidetes, Spirochaetes, and Proteobacteria phyla that populated the crossbred pig feces. The diversity metrics suggested that the co-feed supplementation affected some alpha diversity indexes of the fecal microbiota. In addition, the differential abundance analysis at the genus level revealed significant differences for various genera, suggesting that the liquid whey supplementation potentially influenced a part of the bacterial community over time. Spearman's correlations revealed that the differential abundant genera identified are positively or negatively correlated with the physiological parameters.}, } @article {pmid37889636, year = {2023}, author = {Yamazaki, Y and Yamabe, S and Komori, S and Yoshitake, K and Fukuoka, M and Sato, S and Takada, K}, title = {Structure Determination of Kahalalide Analogues Based on Metagenomic Analysis of a Bryopsis sp. Marine Green Alga.}, journal = {Journal of natural products}, volume = {86}, number = {11}, pages = {2539-2545}, doi = {10.1021/acs.jnatprod.3c00760}, pmid = {37889636}, issn = {1520-6025}, mesh = {Animals ; *Mollusca/chemistry ; *Chlorophyta/chemistry ; Amino Acid Sequence ; Magnetic Resonance Spectroscopy ; Amino Acids ; Molecular Structure ; }, abstract = {Two kahalalide analogues were isolated from a Bryopsis sp. marine green alga. Even though our initial structure determination of the peptides by NMR and MS identified them as kahalalide Z1 (KZ1; 3) and Z2 (KZ2; 4), the absolute configuration of the Thr residues by Marfey's analysis was different from those found in kahalalide F (KF), 3, and 4. To ascertain the absolute configuration of the amino acid residues genetically, we conducted a metagenomic analysis for symbiotic bacteria in the alga, leading to the biosynthetic gene cluster (BGC) responsible for producing the kahalalides named kahalalides Z3 (KZ3; 1) and Z4 (KZ4; 2). The identification of amino acid residues based on the A-domain suggested these peptides possess the amino acid sequence d-allo-Thr-l-Val-l-Val-d-Val residues at the N-terminus, instead of the d-Val-l-Thr-l-Val-d-Val residues found in KF, 3, and 4. The N-terminal amino acid sequence including absolute configuration was unambiguously determined by a comparison of LCMS data of synthetic tetrapeptides and the hydrolysates derived from 1 and 2. This structural difference is caused by swapping the substrate specificities of the first two A-domains.}, } @article {pmid37889119, year = {2023}, author = {Seong, HJ and Kim, JJ and Sul, WJ}, title = {ACR: metagenome-assembled prokaryotic and eukaryotic genome refinement tool.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {6}, pages = {}, doi = {10.1093/bib/bbad381}, pmid = {37889119}, issn = {1477-4054}, mesh = {*Metagenome ; Eukaryota/genetics ; *Microbiota/genetics ; Algorithms ; Metagenomics/methods ; Cluster Analysis ; }, abstract = {Microbial genome recovery from metagenomes can further explain microbial ecosystem structures, functions and dynamics. Thus, this study developed the Additional Clustering Refiner (ACR) to enhance high-purity prokaryotic and eukaryotic metagenome-assembled genome (MAGs) recovery. ACR refines low-quality MAGs by subjecting them to iterative k-means clustering predicated on contig abundance and increasing bin purity through validated universal marker genes. Synthetic and real-world metagenomic datasets, including short- and long-read sequences, evaluated ACR's effectiveness. The results demonstrated improved MAG purity and a significant increase in high- and medium-quality MAG recovery rates. In addition, ACR seamlessly integrates with various binning algorithms, augmenting their strengths without modifying core features. Furthermore, its multiple sequencing technology compatibilities expand its applicability. By efficiently recovering high-quality prokaryotic and eukaryotic genomes, ACR is a promising tool for deepening our understanding of microbial communities through genome-centric metagenomics.}, } @article {pmid37889000, year = {2023}, author = {Hauser, S and Lazarevic, V and Tournoud, M and Ruppé, E and Santiago Allexant, E and Guigon, G and Schicklin, S and Lanet, V and Girard, M and Mirande, C and Gervasi, G and Schrenzel, J}, title = {A metagenomics method for the quantitative detection of bacterial pathogens causing hospital-associated and ventilator-associated pneumonia.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0129423}, pmid = {37889000}, issn = {2165-0497}, mesh = {Humans ; *Pneumonia, Ventilator-Associated/diagnosis/drug therapy/microbiology ; Bacteria/genetics ; Metagenomics ; Risk Factors ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {The management of ventilator-associated pneumonia and hospital-acquired pneumonia requires rapid and accurate quantitative detection of the infecting pathogen. To this end, we propose a metagenomic sequencing assay that includes the use of an internal sample processing control for the quantitative detection of 20 relevant bacterial species from bronchoalveolar lavage samples.}, } @article {pmid37888981, year = {2023}, author = {Schönegger, D and Moubset, O and Margaria, P and Menzel, W and Winter, S and Roumagnac, P and Marais, A and Candresse, T}, title = {Benchmarking of virome metagenomic analysis approaches using a large, 60+ members, viral synthetic community.}, journal = {Journal of virology}, volume = {97}, number = {11}, pages = {e0130023}, pmid = {37888981}, issn = {1098-5514}, support = {GA 813542//EC | Horizon 2020 Framework Programme (H2020)/ ; 871029//EC | Horizon 2020 Framework Programme (H2020)/ ; ANR-19-CE35-0008-02//Agence Nationale de la Recherche (ANR)/ ; }, mesh = {DNA Viruses/classification/genetics ; *Metagenomics/methods/standards ; Virion/genetics ; *Virome/genetics ; *Synthetic Biology/methods ; RNA, Double-Stranded/genetics ; *Viruses/classification/genetics ; Plant Viruses/classification/genetics ; }, abstract = {We report here efforts to benchmark performance of two widespread approaches for virome analysis, which target either virion-associated nucleic acids (VANA) or highly purified double-stranded RNAs (dsRNAs). This was achieved using synthetic communities of varying complexity levels, up to a highly complex community of 72 viral agents (115 viral molecules) comprising isolates from 21 families and 61 genera of plant viruses. The results obtained confirm that the dsRNA-based approach provides a more complete representation of the RNA virome, in particular, for high complexity ones. However, for viromes of low to medium complexity, VANA appears a reasonable alternative and would be the preferred choice if analysis of DNA viruses is of importance. Several parameters impacting performance were identified as well as a direct relationship between the completeness of virome description and sample sequencing depth. The strategy, results, and tools used here should prove useful in a range of virome analysis efforts.}, } @article {pmid37887819, year = {2023}, author = {Xoconostle-Cázares, B and Ramírez-Pool, JA and Núñez-Muñoz, LA and Calderón-Pérez, B and Vargas-Hernández, BY and Bujanos-Muñiz, R and Ruiz-Medrano, R}, title = {The Characterization of Melanaphis sacchari Microbiota and Antibiotic Treatment Effect on Insects.}, journal = {Insects}, volume = {14}, number = {10}, pages = {}, pmid = {37887819}, issn = {2075-4450}, support = {grant CF-2023-G-731//Consejo Nacional de Humanidades Ciencias y Tecnologias/ ; }, abstract = {Insects are under constant selective pressure, which has resulted in adaptations to novel niches such as crops. This is the case of the pest Melanaphis sacchari, the sugarcane aphid, native to Africa and currently spreading worldwide. The aphid undergoes successful parthenogenesis, causing important damage to a variety of crops and leading to important economic losses for farmers. A natural M. sacchari population grown in sorghum was studied to identify its microbiome through the sequencing of its 16S rDNA metagenome. A high proportion of Proteobacteria, followed by Firmicutes, Bacteroidetes, and Actinobacteria, was observed. We also detected Wolbachia, which correlates with the asexual reproduction of its host. M. sacchari was challenged in a bioassay with the antibiotics oxytetracycline and streptomycin, resulting in a dose-dependent decay of its survival rate. The possibility of controlling this pest by altering its microbiota is proposed.}, } @article {pmid37887409, year = {2023}, author = {Neophytou, C and Soteriou, E and Pitsouli, C}, title = {The Sterol Transporter Npc2c Controls Intestinal Stem Cell Mitosis and Host-Microbiome Interactions in Drosophila.}, journal = {Metabolites}, volume = {13}, number = {10}, pages = {}, pmid = {37887409}, issn = {2218-1989}, support = {EXCELLENCE/0918/0082//Cyprus Research and Innovation Foundation/ ; }, abstract = {Cholesterol is necessary for all cells to function. The intracellular cholesterol transporters Npc1 and Npc2 control sterol trafficking and their malfunction leads to Neimann-Pick Type C disease, a rare disorder affecting the nervous system and the intestine. Unlike humans that encode single Npc1 and Npc2 transporters, flies encompass two Npc1 (Npc1a-1b) and eight Npc2 (Npc2a-2h) members, and most of the Npc2 family genes remain unexplored. Here, we focus on the intestinal function of Npc2c in the adult. We find that Npc2c is necessary for intestinal stem cell (ISC) mitosis, maintenance of the ISC lineage, survival upon pathogenic infection, as well as tumor growth. Impaired mitosis of Npc2c-silenced midguts is accompanied by reduced expression of Cyclin genes, and genes encoding ISC regulators, such as Delta, unpaired1 and Socs36E. ISC-specific Npc2c silencing induces Attacin-A expression, a phenotype reminiscent of Gram-negative bacteria overabundance. Metagenomic analysis of Npc2c-depleted midguts indicates intestinal dysbiosis, whereby decreased commensal complexity is accompanied by increased gamma-proteobacteria. ISC-specific Npc2c silencing also results in increased cholesterol aggregation. Interestingly, administration of the non-steroidal ecdysone receptor agonist, RH5849, rescues mitosis of Npc2c-silenced midguts and increases expression of the ecdysone response gene Broad, underscoring the role of Npc2c and sterols in ecdysone signaling. Assessment of additional Npc2 family members indicates potential redundant roles with Npc2c in ISC control and response to ecdysone signaling. Our results highlight a previously unidentified essential role of Npc2c in ISC mitosis, as well as an important role in ecdysone signaling and microbiome composition in the Drosophila midgut.}, } @article {pmid37887365, year = {2023}, author = {Zhang, M and Tang, H and Yuan, Y and Ou, Z and Chen, Z and Xu, Y and Fu, X and Zhao, Z and Sun, Y}, title = {The Role of Indoor Microbiome and Metabolites in Shaping Children's Nasal and Oral Microbiota: A Pilot Multi-Omic Analysis.}, journal = {Metabolites}, volume = {13}, number = {10}, pages = {}, pmid = {37887365}, issn = {2218-1989}, support = {81861138005//Zhuohui Zhao/ ; 2021A1515010492//Yu Sun/ ; GWV-10.1-XK11//Zhuohui Zhao/ ; }, abstract = {Maintaining a diverse and well-balanced nasal and oral microbiota is vital for human health. However, the impact of indoor microbiome and metabolites on nasal and oral microbiota remains largely unknown. Fifty-six children in Shanghai were surveyed to complete a questionnaire about their personal and environmental characteristics. The indoor microbiome and metabolites from vacuumed indoor dust were profiled via shotgun metagenomics and untargeted liquid chromatography-mass spectrometry (LC-MS). The nasal and oral microbiota in children was characterized using full-length 16S rRNA sequencing from PacBio. Associations between personal/environmental characteristics and the nasal/oral microbiota were calculated using PERMANOVA and regression analyses. We identified 6247, 431, and 342 microbial species in the indoor dust, nasal, and oral cavities, respectively. The overall nasal and oral microbial composition showed significant associations with environmental tobacco smoke (ETS) exposure during pregnancy and early childhood (p = 0.005 and 0.03, respectively), and the abundance of total indoor flavonoids and two mycotoxins (deoxynivalenol and nivalenol) (p = 0.01, 0.02, and 0.03, respectively). Notably, the abundance of several flavonoids, such as baicalein, eupatilin, isoliquiritigenin, tangeritin, and hesperidin, showed positive correlations with alpha diversity and the abundance of protective microbial taxa in nasal and oral cavities (p < 0.02), suggesting their potential beneficial roles in promoting nasal/oral health. Conversely, high carbohydrate/fat food intake and ETS exposure diminished protective microorganisms while augmenting risky microorganisms in the nasal/oral cavities. Further, potential microbial transfer was observed from the indoor environment to the childhood oral cavity (Moraxella catarrhalis, Streptococcus mitis, and Streptococcus salivarius), which could potentially increase virulence factors related to adherence and immune modulation and vancomycin resistance genes in children. This is the first study to reveal the association between the indoor microbiome/metabolites and nasal/oral microbiota using multi-omic approaches. These findings reveal potential protective and risk factors related to the indoor microbial environment.}, } @article {pmid37887255, year = {2023}, author = {Šakarnytė, L and Šiugždinienė, R and Žymantienė, J and Ruzauskas, M}, title = {Comparison of Oral Microbial Composition and Determinants Encoding Antimicrobial Resistance in Dogs and Their Owners.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {10}, pages = {}, pmid = {37887255}, issn = {2079-6382}, abstract = {Consolidated studies on animal, human, and environmental health have become very important for understanding emerging zoonotic diseases and the spread of antimicrobial resistance (AMR). The aim of this study was to analyse the oral microbiomes of healthy dogs and their owners, including determinants of AMR. Shotgun metagenomic sequencing detected 299 bacterial species in pets and their owners, from which 70 species were carried by dogs and 229 species by humans. Results demonstrated a unique microbial composition of dogs and their owners. At an order level, Bacteroidales were the most prevalent oral microbiota of dogs with significantly lower prevalence in their owners where Actinomycetales and Lactobacillales predominated. Porphyromonas and Corynebacterium were the most prevalent genera in dogs, whereas Streptococcus and Actinomyces were in animal owners. The resistances to macrolides, tetracyclines, lincosamides and Cfx family A class broad-spectrum β-lactamase were detected in both animal and human microbiomes. Resistance determinants to amphenicols, aminoglycosides, sulphonamides, and quaternary ammonium compounds were detected exceptionally in dogs. In conclusion, the study demonstrated different bacterial composition in oral microbiomes of healthy dogs without clinical signs of periodontal disease and their owners. Due to the low numbers of the samples tested, further investigations with an increased number of samples should be performed.}, } @article {pmid37887010, year = {2023}, author = {Kadnikov, VV and Ravin, NV and Sokolova, DS and Semenova, EM and Bidzhieva, SK and Beletsky, AV and Ershov, AP and Babich, TL and Khisametdinov, MR and Mardanov, AV and Nazina, TN}, title = {Metagenomic and Culture-Based Analyses of Microbial Communities from Petroleum Reservoirs with High-Salinity Formation Water, and Their Biotechnological Potential.}, journal = {Biology}, volume = {12}, number = {10}, pages = {}, pmid = {37887010}, issn = {2079-7737}, support = {21-64-00019//Russian Science Foundation/ ; No grant number//Ministry of Science and Higher Education of Russian Federation/ ; }, abstract = {The reserves of light conditional oil in reservoirs with low-salinity formation water are decreasing worldwide, necessitating the extraction of heavy oil from petroleum reservoirs with high-salinity formation water. As the first stage of defining the microbial-enhanced oil recovery (MEOR) strategies for depleted petroleum reservoirs, microbial community composition was studied for petroleum reservoirs with high-salinity formation water located in Tatarstan (Russia) using metagenomic and culture-based approaches. Bacteria of the phyla Desulfobacterota, Halanaerobiaeota, Sinergistota, Pseudomonadota, and Bacillota were revealed using 16S rRNA-based high-throughput sequencing in halophilic microbial communities. Sulfidogenic bacteria predominated in the studied oil fields. The 75 metagenome-assembled genomes (MAGs) of prokaryotes reconstructed from water samples were assigned to 16 bacterial phyla, including Desulfobacterota, Bacillota, Pseudomonadota, Thermotogota, Actinobacteriota, Spirochaetota, and Patescibacteria, and to archaea of the phylum Halobacteriota (genus Methanohalophilus). Results of metagenomic analyses were supported by the isolation of 20 pure cultures of the genera Desulfoplanes, Halanaerobium, Geotoga, Sphaerochaeta, Tangfeifania, and Bacillus. The isolated halophilic fermentative bacteria produced oil-displacing metabolites (lower fatty acids, alcohols, and gases) from sugar-containing and proteinaceous substrates, which testify their potential for MEOR. However, organic substrates stimulated the growth of sulfidogenic bacteria, in addition to fermenters. Methods for enhanced oil recovery should therefore be developed, combining the production of oil-displacing compounds with fermentative bacteria and the suppression of sulfidogenesis.}, } @article {pmid37887008, year = {2023}, author = {Cembrowska-Lech, D and Krzemińska, A and Miller, T and Nowakowska, A and Adamski, C and Radaczyńska, M and Mikiciuk, G and Mikiciuk, M}, title = {An Integrated Multi-Omics and Artificial Intelligence Framework for Advance Plant Phenotyping in Horticulture.}, journal = {Biology}, volume = {12}, number = {10}, pages = {}, pmid = {37887008}, issn = {2079-7737}, abstract = {This review discusses the transformative potential of integrating multi-omics data and artificial intelligence (AI) in advancing horticultural research, specifically plant phenotyping. The traditional methods of plant phenotyping, while valuable, are limited in their ability to capture the complexity of plant biology. The advent of (meta-)genomics, (meta-)transcriptomics, proteomics, and metabolomics has provided an opportunity for a more comprehensive analysis. AI and machine learning (ML) techniques can effectively handle the complexity and volume of multi-omics data, providing meaningful interpretations and predictions. Reflecting the multidisciplinary nature of this area of research, in this review, readers will find a collection of state-of-the-art solutions that are key to the integration of multi-omics data and AI for phenotyping experiments in horticulture, including experimental design considerations with several technical and non-technical challenges, which are discussed along with potential solutions. The future prospects of this integration include precision horticulture, predictive breeding, improved disease and stress response management, sustainable crop management, and exploration of plant biodiversity. The integration of multi-omics and AI holds immense promise for revolutionizing horticultural research and applications, heralding a new era in plant phenotyping.}, } @article {pmid37886989, year = {2023}, author = {Vu, M and McFadden-Smith, W and Poojari, S}, title = {Monitoring the Spread of Grapevine Viruses in Vineyards of Contrasting Agronomic Practices: A Metagenomic Investigation.}, journal = {Biology}, volume = {12}, number = {10}, pages = {}, pmid = {37886989}, issn = {2079-7737}, support = {189GRP//Genome Canada/ ; }, abstract = {This study investigated the transmission of grapevine viruses, specifically grapevine red blotch virus (GRBV) and grapevine Pinot gris virus (GPGV), in vineyards in Niagara Region, Ontario, Canada. Forty sentinel vines that were confirmed free of GRBV and GPGV by both high-throughput sequencing (HTS) and endpoint polymerase chain reaction (PCR) were introduced to two vineyards (one organic and one conventional) that were heavily infected with both GRBV and GPGV. Four months post-introduction, the sentinel vines were relocated to a phytotron. The HTS results from 15 months post-introduction revealed a widespread infection of GPGV among the sentinel vines but did not detect any GRBV. The GPGV infection rate of sentinel vines in the organic vineyard (13/18) was higher than in the conventional vineyard (1/19). The possibility of an alternative viral reservoir was assessed by testing the most abundant plants in between rows (Medicago sativa, Trifolium repens, Cirsium arvense and Taraxacum officinale), perennial plants in border areas (Fraxinus americana, Ulmus americana, Rhamnus cathartica) and wild grape (unknown Vitis sp.). The HTS result showed that cover crops and perennial plants did not harbor any grapevine viruses, while 4/5 wild grapes tested positive for GPGV but not GRBV. A pairwise sequence identity analysis revealed high similarities between the GPGV isolates found in the established vines on the vineyard and the newly contracted GPGV isolates in the sentinel vines, implicating a recent transmission event. This work provides novel insights into the spread of grapevine viruses in Niagara Region and is also the first direct proof of the spread of GPGV in natural vineyard conditions in North America.}, } @article {pmid37886817, year = {2023}, author = {Kiki, C and Qin, D and Liu, L and Qiao, M and Adyari, B and Ifon, BE and Adeoye, ABE and Zhu, L and Cui, L and Sun, Q}, title = {Unraveling the Role of Microalgae in Mitigating Antibiotics and Antibiotic Resistance Genes in Photogranules Treating Antibiotic Wastewater.}, journal = {Environmental science & technology}, volume = {57}, number = {44}, pages = {16940-16952}, doi = {10.1021/acs.est.3c04798}, pmid = {37886817}, issn = {1520-5851}, mesh = {*Anti-Bacterial Agents/pharmacology ; Wastewater ; *Microalgae ; Sewage/microbiology ; Genes, Bacterial ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; }, abstract = {Harnessing the potential of specific antibiotic-degrading microalgal strains to optimize microalgal-bacterial granular sludge (MBGS) technology for sustainable antibiotic wastewater treatment and antibiotic resistance genes (ARGs) mitigation is currently limited. This article examined the performance of bacterial granular sludge (BGS) and MBGS (of Haematococcus pluvialis, an antibiotic-degrading microalga) systems in terms of stability, nutrient and antibiotic removal, and fate of ARGs and mobile genetic elements (MGEs) under multiclass antibiotic loads. The systems exhibited excellent performance under none and 50 μg/L mixed antibiotics and a decrease in performance at a higher concentration. The MBGS showed superior potential, higher nutrient removal, 53.9 mg/L/day higher chemical oxygen demand (COD) removal, and 5.2-8.2% improved antibiotic removal, notably for refractory antibiotics, and the system removal capacity was predicted. Metagenomic analysis revealed lower levels of ARGs and MGEs in effluent and biomass of MBGS compared to the BGS bioreactor. Particle association niche and projection pursuit regression models indicated that microalgae in MBGS may limit gene transfers among biomass and effluent, impeding ARG dissemination. Moreover, a discrepancy was found in the bacterial antibiotic-degrading biomarkers of BGS and MBGS systems due to the microalgal effect on the microcommunity. Altogether, these findings deepened our understanding of the microalgae's value in the MBGS system for antibiotic remediation and ARG propagation control.}, } @article {pmid37886529, year = {2023}, author = {Yue, Y and Read, TD and Fedirko, V and Satten, GA and Hu, YJ}, title = {Integrative analysis of microbial 16S gene and shotgun metagenomic sequencing data improves statistical efficiency.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {37886529}, support = {R01 GM141074/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND: The most widely used technologies for profiling microbial communities are 16S marker-gene sequencing and shotgun metagenomic sequencing. Interestingly, many microbiome studies have performed both sequencing experiments on the same cohort of samples. The two sequencing datasets often reveal consistent patterns of microbial signatures, highlighting the potential for an integrative analysis to improve power of testing these signatures. However, differential experimental biases, partially overlapping samples, and differential library sizes pose tremendous challenges when combining the two datasets. Currently, researchers either discard one dataset entirely or use different datasets for different objectives.

METHODS: In this article, we introduce the first method of this kind, named Com-2seq, that combines the two sequencing datasets for testing differential abundance at the genus and community levels while overcoming these difficulties. The new method is based on our LOCOM model (Hu et al., 2022), which employs logistic regression for testing taxon differential abundance while remaining robust to experimental bias. To benchmark the performance of Com-2seq, we introduce two ad hoc approaches: applying LOCOM to pooled taxa count data and combining LOCOM p-values from analyzing each dataset separately.

RESULTS: Our simulation studies indicate that Com-2seq substantially improves statistical efficiency over analysis of either dataset alone and works better than the two ad hoc approaches. An application of Com-2seq to two real microbiome studies uncovered scientifically plausible findings that would have been missed by analyzing individual datasets.

CONCLUSIONS: Com-2seq performs integrative analysis of 16S and metagenomic sequencing data, which improves statistical efficiency and has the potential to accelerate the search of microbial communities and taxa that are involved in human health and diseases.}, } @article {pmid37886447, year = {2023}, author = {Tierney, BT and Kim, J and Overbey, EG and Ryon, KA and Foox, J and Sierra, M and Bhattacharya, C and Damle, N and Najjar, D and Park, J and Garcia Medina, S and Houerbi, N and Meydan, C and Wain Hershberg, J and Qiu, J and Kleinman, A and Al Ghalith, G and MacKay, M and Afshin, EE and Dhir, R and Borg, J and Gatt, C and Brereton, N and Readhead, B and Beyaz, S and Venkateswaran, KJ and Blease, K and Moreno, J and Boddicker, A and Zhao, J and Lajoie, B and Scott, RT and Altomare, A and Kruglyak, S and Levy, S and Church, G and Mason, CE}, title = {Viral activation and ecological restructuring characterize a microbiome axis of spaceflight-associated immune activation.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {37886447}, support = {R01 CA249054/CA/NCI NIH HHS/United States ; R01 MH117406/MH/NIMH NIH HHS/United States ; }, abstract = {Maintenance of astronaut health during spaceflight will require monitoring and potentially modulating their microbiomes, which play a role in some space-derived health disorders. However, documenting the response of microbiota to spaceflight has been difficult thus far due to mission constraints that lead to limited sampling. Here, we executed a six-month longitudinal study centered on a three-day flight to quantify the high-resolution microbiome response to spaceflight. Via paired metagenomics and metatranscriptomics alongside single immune profiling, we resolved a microbiome "architecture" of spaceflight characterized by time-dependent and taxonomically divergent microbiome alterations across 750 samples and ten body sites. We observed pan-phyletic viral activation and signs of persistent changes that, in the oral microbiome, yielded plaque-associated pathobionts with strong associations to immune cell gene expression. Further, we found enrichments of microbial genes associated with antibiotic production, toxin-antitoxin systems, and stress response enriched universally across the body sites. We also used strain-level tracking to measure the potential propagation of microbial species from the crew members to each other and the environment, identifying microbes that were prone to seed the capsule surface and move between the crew. Finally, we identified associations between microbiome and host immune cell shifts, proposing both a microbiome axis of immune changes during flight as well as the sources of some of those changes. In summary, these datasets and methods reveal connections between crew immunology, the microbiome, and their likely drivers and lay the groundwork for future microbiome studies of spaceflight.}, } @article {pmid37886359, year = {2023}, author = {Fang, C and Xie, Y and Mai, H and Xu, L}, title = {Acute abdominal pain as the first symptom of Chlamydia psittaci pneumonia complicated by acute pancreatitis: a case report.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1253859}, pmid = {37886359}, issn = {2296-858X}, abstract = {BACKGROUND: Chlamydia psittaci infections primarily cause damage to the lungs but may also affect the cardiovascular system, gastrointestinal tract, liver, kidney, and brain, resulting in a variety of extrapulmonary complications. However, reports regarding C. psittaci infection-associated pancreatitis are rare. In this report, a patient with C. psittaci pneumonia complicated by acute pancreatitis is presented.

CASE DESCRIPTION: The patient presented with acute upper abdominal pain and developed severe pyrexia and dyspnoea one day later. A chest computed tomography image revealed patchy consolidation in the left lung. The disease progressed rapidly, and the patient exhibited liver and kidney damage and type 1 respiratory failure within a short period of time. Metagenomic next-generation sequencing of alveolar lavage fluid revealed the presence of C. psittaci. The patient was administered doxycycline and moxifloxacin, after which the patient's abdominal pain and lung infection significantly resolved.

CONCLUSION: This case report demonstrates that extrapulmonary C. psittaci infections due to secondary acute pancreatitis can manifest as abdominal pain, although the exact mechanisms of C. psittaci caused by acute pancreatitis remain unclear. Timely diagnoses and treatments of such infections are necessary to achieve favorable clinical outcomes.}, } @article {pmid37884755, year = {2023}, author = {Saleem, M and Yahya, S and Razzak, SA and Khawaja, S and Ali, A}, title = {Shotgun metagenomics and computational profiling of the plastisphere microbiome: unveiling the potential of enzymatic production and plastic degradation.}, journal = {Archives of microbiology}, volume = {205}, number = {11}, pages = {359}, pmid = {37884755}, issn = {1432-072X}, mesh = {*Bacteria/genetics ; *Microbiota/genetics ; Proteobacteria/genetics ; Archaea/genetics ; Metagenome ; Metagenomics ; }, abstract = {Plastic pollution is one of the most resilient types of pollution and is considered a global environmental threat, particularly in the marine environment. This study aimed to identify plastic-degrading bacteria from the plastisphere and their pharmaceutical and therapeutic potential. We collected samples from soil and aquatic plastisphere to identify the bacterial communities using shotgun metagenomic sequencing and bioinformatic tools. Results showed that the microbiome comprised 93% bacteria, 0.29% archaea, and 3.87% unidentified microbes. Of these 93% of bacteria, 54% were Proteobacteria, 23.9% were Firmicutes, 13% were Actinobacteria, and 2.1% were other phyla. We found that the plastisphere microbiome was involved in degrading synthetic and polyhydroxy alkanoate (PHA) plastic, biosurfactant production, and can thrive under high temperatures. However, no association existed between thermophiles, synthetic plastic or PHA degraders, and biosurfactant-producing bacterial species except for Pseudomonas. Other plastisphere inhabiting plastic degrading microbes include Streptomyces, Bacillus, Achromobacter, Azospirillum, Bacillus, Brevundimonas, Clostridium, Paenibacillus, Rhodococcus, Serratia, Staphylococcus, Thermobifida, and Thermomonospora. However, the plastisphere microbiome showed potential for producing secondary metabolites that were found to act as anticancer, antitumor, anti-inflammatory, antimicrobial, and enzyme stabilizers. These results revealed that the plastisphere microbiome upholds clinical and environmental significance as it can open future portals in a multi-directional way.}, } @article {pmid37884410, year = {2023}, author = {Karadayı, B and Karaismailoğlu, B and Karadayı, S and Arslan, A and Gözen, ED and Özbek, T}, title = {The uselessness of using salivary microbiota in forensic identification purposes of a person with recent antibiotic use.}, journal = {Legal medicine (Tokyo, Japan)}, volume = {}, number = {}, pages = {102338}, doi = {10.1016/j.legalmed.2023.102338}, pmid = {37884410}, issn = {1873-4162}, abstract = {The detection of microbial flora changes in saliva samples because of antibiotic use through advanced molecular genetic analysis is important for forensic and clinical applications. This study aims to reveal the variability in the microbial structure of human saliva after antibiotic use with metagenomic analysis techniques from a forensic point of view. Within the scope of the study, saliva samples were collected from patients who were under the effect of regional anesthesia to be administered a standardized course of antibiotic therapy that lasted for a week. The analysis was conducted on 56 saliva samples from 14 individuals over four different time intervals. Isolation of the 16S rRNA region and PCR analysis were performed prior to sequence analysis to determine the microbiome structure of the samples at phylum, genus, and species levels. As expected, changes were observed in bacterial species found in saliva samples after administration of antibiotics and this was linked to the specific type of antibiotics that were administered. This change was statistically significant for Firmicutes, Spirochetes, and Verrucomicrobiota. Furthermore, although the oral microbiome tends to return to its former state at the phylum and genus level within a 4-week period after the start of antibiotic use, it is observed that the change, especially in some bacterial species, still continues. The findings of this study show that because of the inability of stabilization at species-level in a period of 4 weeks from the start of antibiotic use, it is not suitable to assess saliva samples at species-level for forensic identification.}, } @article {pmid37884341, year = {2023}, author = {Deng, J and Liu, YJ and Wei, WT and Huang, QX and Zhao, LP and Luo, LY and Zhu, Q and Zhang, L and Chen, Y and Ren, YL and Jia, SG and Lin, YL and Yang, J and Lv, FH and Zhang, HP and Li, FE and Li, L and Li, MH}, title = {Single-cell transcriptome and metagenome profiling reveals the genetic basis of rumen functions and convergent developmental patterns in ruminants.}, journal = {Genome research}, volume = {33}, number = {10}, pages = {1690-1707}, pmid = {37884341}, issn = {1549-5469}, mesh = {Sheep/genetics ; Animals ; *Metagenome ; Transcriptome ; Rumen ; Ruminants/genetics ; *Microbiota ; }, abstract = {The rumen undergoes developmental changes during maturation. To characterize this understudied dynamic process, we profiled single-cell transcriptomes of about 308,000 cells from the rumen tissues of sheep and goats at 17 time points. We built comprehensive transcriptome and metagenome atlases from early embryonic to rumination stages, and recapitulated histomorphometric and transcriptional features of the rumen, revealing key transitional signatures associated with the development of ruminal cells, microbiota, and core transcriptional regulatory networks. In addition, we identified and validated potential cross-talk between host cells and microbiomes and revealed their roles in modulating the spatiotemporal expression of key genes in ruminal cells. Cross-species analyses revealed convergent developmental patterns of cellular heterogeneity, gene expression, and cell-cell and microbiome-cell interactions. Finally, we uncovered how the interactions can act upon the symbiotic rumen system to modify the processes of fermentation, fiber digestion, and immune defense. These results significantly enhance understanding of the genetic basis of the unique roles of rumen.}, } @article {pmid37883976, year = {2023}, author = {Blanco-Míguez, A and Gálvez, EJC and Pasolli, E and De Filippis, F and Amend, L and Huang, KD and Manghi, P and Lesker, TR and Riedel, T and Cova, L and Punčochář, M and Thomas, AM and Valles-Colomer, M and Schober, I and Hitch, TCA and Clavel, T and Berry, SE and Davies, R and Wolf, J and Spector, TD and Overmann, J and Tett, A and Ercolini, D and Segata, N and Strowig, T}, title = {Extension of the Segatella copri complex to 13 species with distinct large extrachromosomal elements and associations with host conditions.}, journal = {Cell host & microbe}, volume = {31}, number = {11}, pages = {1804-1819.e9}, pmid = {37883976}, issn = {1934-6069}, support = {U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Male ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Microbiota ; Phylogeny ; Prevotella ; Female ; }, abstract = {The Segatella copri (formerly Prevotella copri) complex (ScC) comprises taxa that are key members of the human gut microbiome. It was previously described to contain four distinct phylogenetic clades. Combining targeted isolation with large-scale metagenomic analysis, we defined 13 distinct Segatella copri-related species, expanding the ScC complex beyond four clades. Complete genome reconstruction of thirteen strains from seven species unveiled the presence of genetically diverse large circular extrachromosomal elements. These elements are consistently present in most ScC species, contributing to intra- and inter-species diversities. The nine species-level clades present in humans display striking differences in prevalence and intra-species genetic makeup across human populations. Based on a meta-analysis, we found reproducible associations between members of ScC and the male sex and positive correlations with lower visceral fat and favorable markers of cardiometabolic health. Our work uncovers genomic diversity within ScC, facilitating a better characterization of the human microbiome.}, } @article {pmid37883717, year = {2023}, author = {Sandler, G and Agrawal, AF and Wright, SI}, title = {Population Genomics of the Facultatively Sexual Liverwort Marchantia polymorpha.}, journal = {Genome biology and evolution}, volume = {15}, number = {11}, pages = {}, pmid = {37883717}, issn = {1759-6653}, mesh = {*Marchantia/genetics ; Metagenomics ; }, abstract = {The population genomics of facultatively sexual organisms are understudied compared with their abundance across the tree of life. We explore patterns of genetic diversity in two subspecies of the facultatively sexual liverwort Marchantia polymorpha using samples from across Southern Ontario, Canada. Despite the ease with which M. polymorpha should be able to propagate asexually, we find no evidence of strictly clonal descent among our samples and little to no signal of isolation by distance. Patterns of identity-by-descent tract sharing further showed evidence of recent recombination and close relatedness between geographically distant isolates, suggesting long distance gene flow and at least a modest frequency of sexual reproduction. However, the M. polymorpha genome contains overall very low levels of nucleotide diversity and signs of inefficient selection evidenced by a relatively high fraction of segregating deleterious variants. We interpret these patterns as possible evidence of the action of linked selection and a small effective population size due to past generations of asexual propagation. Overall, the M. polymorpha genome harbors signals of a complex history of both sexual and asexual reproduction.}, } @article {pmid37882797, year = {2023}, author = {Cheng, K and Li, X and Tong, M and Jong, M-C and Cai, Z and Zheng, H and Xiao, B and Zhou, J}, title = {Integrated metagenomic and metaproteomic analyses reveal bacterial micro-ecological mechanisms in coral bleaching.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0050523}, pmid = {37882797}, issn = {2379-5077}, support = {42106096//MOST | National Natural Science Foundation of China (NSFC)/ ; KCXFZ20211020165547011, RCJC20200714114433069, JCYJ20200109142818589//Project of Shenzhen Science and Technology Innovation Committee/ ; ZDYF2021SHFZ059//Hainan Key Research and Development Program/ ; 2021M691804//China Postdoctoral Science Foundation (China Postdoctoral Foundation Project)/ ; JC2022004//Cross Research and Innovation Funding of Tsinghua SIGS/ ; 2023N007//Sustainable Development Special Project of Shenzhen Science and Technology Innovation Committee/ ; }, mesh = {Animals ; *Coral Bleaching ; Coral Reefs ; *Anthozoa/metabolism ; Bacteria/genetics ; Energy Metabolism ; }, abstract = {Coral reefs worldwide are facing rapid decline due to coral bleaching. However, knowledge of the physiological characteristics and molecular mechanisms of coral symbionts respond to stress is scarce. Here, metagenomic and metaproteomic approaches were utilized to shed light on the changes in the composition and functions of coral symbiotic bacteria during coral bleaching. The results demonstrated that coral bleaching significantly affected the composition of symbionts, with bacterial communities dominating in bleached corals. Through differential analyses of gene and protein expression, it becomes evident that symbionts experience functional disturbances in response to heat stress. These disturbances result in abnormal energy metabolism, which could potentially compromise the health and resilience of the symbionts. Furthermore, our findings highlighted the highly diverse microbial communities of coral symbionts, with beneficial bacteria providing critical services to corals in stress responses and pathogenic bacteria driving coral bleaching. This study provides comprehensive insights into the complex response mechanisms of coral symbionts under heat stress from the micro-ecological perspective and offers fundamental data for future monitoring of coral health.}, } @article {pmid37882788, year = {2024}, author = {Qian, Z and Xia, H and Zhou, J and Wang, R and Zhu, D and Chen, L and Kang, H and Feng, J and Hu, X and Wang, L and Xu, S and Lou, Z and Tao, Y}, title = {Performance of Metagenomic Next-Generation Sequencing of Cell-Free DNA From Vitreous and Aqueous Humor for Diagnoses of Intraocular Infections.}, journal = {The Journal of infectious diseases}, volume = {229}, number = {1}, pages = {252-261}, doi = {10.1093/infdis/jiad363}, pmid = {37882788}, issn = {1537-6613}, support = {82101142//National Natural Science Foundation of China/ ; //Scientific and Technological Innovation Foundation of Beijing Chaoyang Hospital/ ; //Beijing Hospitals Authority Youth Programme/ ; //Shunyi District Beijing Science and technology/ ; 21RGSF0013//Science and Technology Project of Xi'an/ ; }, mesh = {Humans ; Aqueous Humor ; *Cell-Free Nucleic Acids/genetics ; Prospective Studies ; *Eye Infections ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Delayed diagnosis and improper therapy for intraocular infections usually result in poor prognosis. Due to limitations of conventional culture and polymerase chain reaction methods, most causative pathogens cannot be identified from vitreous humor (VH) or aqueous humor (AH) samples with limited volume.

METHODS: Patients with suspected intraocular infections were enrolled from January 2019 to August 2021. Metagenomic next-generation sequencing (mNGS) was used to detected causative pathogens.

RESULTS: This multicenter prospective study enrolled 488 patients, from whom VH (152) and AH (336) samples were respectively collected and analyzed using mNGS of cell-free DNA (cfDNA). Taking final comprehensive clinical diagnosis as the gold standard, there were 39 patients with indefinite final diagnoses, whereas 288 and 161 patients were diagnosed as definite infectious and noninfectious diseases, respectively. Based on clinical adjudication, the sensitivity (92.2%) and total coincidence rate (81.3%) of mNGS using VH samples were slightly higher than those of mNGS using AH samples (85.4% and 75.4%, respectively).

CONCLUSIONS: Using mNGS of cfDNA, an era with clinical experience for more rapid, independent, and impartial diagnosis of bacterial and other intraocular infections can be expected.}, } @article {pmid37882765, year = {2023}, author = {Hong, X and Ji, Y and Chen, M and Su, F and Zhu, Y and Ge, Y}, title = {Varicella Zoster viral encephalitis without herpes: diagnosis by metagenomic next-generation sequencing of cerebrospinal fluid.}, journal = {Future microbiology}, volume = {18}, number = {}, pages = {1217-1223}, doi = {10.2217/fmb-2023-0107}, pmid = {37882765}, issn = {1746-0921}, support = {20211214//New Project of Zhejiang Provincial People's Hospital entitled 'Construction of Rapid Nucleic Acid Detection Platform for Invasive Fungi'/ ; }, mesh = {Female ; Humans ; Young Adult ; *Chickenpox/drug therapy ; *Encephalitis, Varicella Zoster/diagnosis/drug therapy ; *Herpes Zoster/diagnosis/drug therapy ; High-Throughput Nucleotide Sequencing ; Antiviral Agents/therapeutic use ; }, abstract = {Acute Varicella Zoster viral encephalitis in immunocompetent adult patients without cutaneous herpes has rarely been reported. A 24-year-old female was hospitalized for a headache with a fever but without other obvious symptoms. Multiple routine examinations showed no abnormalities. Lumbar puncture indicated intracranial hypertension. The examination of cerebrospinal fluid by metagenomic next-generation sequencing demonstrated acute Varicella Zoster viral encephalitis. The patient's condition improved by treatment with acyclovir for antiviral therapy and mannitol dehydration to lower cranial pressure. Central Varicella Zoster viral infection should be emphasized as it is easily misdiagnosed and rare in clinical settings. Metagenomic next-generation sequencing of cerebrospinal fluid has significant advantages in the diagnosis of Varicella Zoster viral encephalitis.}, } @article {pmid37882525, year = {2023}, author = {Zhu, Y and Gan, M and Ge, M and Dong, X and Yan, G and Zhou, Q and Yu, H and Wang, X and Cao, Y and Lu, G and Wu, B and Zhou, W}, title = {Correction for Zhu et al., "Diagnostic Performance and Clinical Impact of Metagenomic Next-Generation Sequencing for Pediatric Infectious Diseases".}, journal = {Journal of clinical microbiology}, volume = {61}, number = {11}, pages = {e0115023}, doi = {10.1128/jcm.01150-23}, pmid = {37882525}, issn = {1098-660X}, } @article {pmid37881577, year = {2023}, author = {Yadav, SK and Ahmad, R and Moshfegh, CM and Sankarasubramanian, J and Joshi, V and Elkhatib, SK and Chhonker, YS and Murry, DJ and Talmon, GA and Guda, C and Case, AJ and Singh, AB}, title = {Repeated Social Defeat Stress Induces an Inflammatory Gut Milieu by Altering the Mucosal Barrier Integrity and Gut Microbiota Homeostasis.}, journal = {Biological psychiatry global open science}, volume = {3}, number = {4}, pages = {824-836}, pmid = {37881577}, issn = {2667-1743}, support = {R01 HL158521/HL/NHLBI NIH HHS/United States ; }, abstract = {BACKGROUND: Posttraumatic stress disorder (PTSD) is a mental health condition triggered by exposure to traumatic events in an individual's life. Patients with PTSD are also at a higher risk for comorbidities. However, it is not well understood how PTSD affects human health and/or promotes the risk for comorbidities. Nevertheless, patients with PTSD harbor a proinflammatory milieu and dysbiotic gut microbiota. Gut barrier integrity helps to maintain normal gut homeostasis and its dysregulation promotes gut dysbiosis and inflammation.

METHODS: We used a mouse model of repeated social defeat stress (RSDS), a preclinical model of PTSD. Behavioral studies, metagenomics analysis of the microbiome, gut permeability assay (on mouse colon, using an Ussing chamber), immunoblotting, and immunohistochemical analyses were performed. Polarized intestinal epithelial cells and 3-dimensional crypt cultures were used for mechanistic analysis.

RESULTS: The RSDS mice harbor a heightened proinflammatory gut environment and microbiota dysbiosis. The RSDS mice further showed significant dysregulation of gut barrier functions, including transepithelial electrical resistance, mucin homeostasis, and antimicrobial responses. RSDS mice also showed a specific increase in intestinal expression of claudin-2, a tight junction protein, and epinephrine, a stress-induced neurotransmitter. Treating intestinal epithelial cells or 3-dimensional cultured crypts with norepinephrine or intestinal luminal contents (fecal contents) upregulated claudin-2 expression and inhibited transepithelial electrical resistance.

CONCLUSIONS: Traumatic stress induces dysregulation of gut barrier functions, which may underlie the observed gut microbiota changes and proinflammatory gut milieu, all of which may have an interdependent effect on the health and increased risk of comorbidities in patients with PTSD.}, } @article {pmid37881335, year = {2023}, author = {García-López, JD and Barbieri, F and Baños, A and Madero, JMG and Gardini, F and Montanari, C and Tabanelli, G}, title = {Use of two autochthonous bacteriocinogenic strains as starter cultures in the production of salchichónes, a type of Spanish fermented sausages.}, journal = {Current research in food science}, volume = {7}, number = {}, pages = {100615}, pmid = {37881335}, issn = {2665-9271}, abstract = {In this work, two autochthonous LAB strains (Lactiplantibacillus paraplantarum BPF2 and Pediococcus acidilactici ST6), isolated from spontaneously fermented sausages produced in Spain, were tested to produce Spanish fermented sausages (salchichón) in pilot plants, due to their promising technological and anti-listerial activity. These products were compared with a sample obtained with a commercial starter (RAP) and a spontaneously fermented control sample. Physico-chemical parameters, microbial counts, metagenomic analysis, biogenic amines content and organoleptic profile of the obtained samples were studied to assess the performances of the native starters. In fact, traditional and artisanal products obtained through spontaneous fermentations can represent an important biodiversity reservoir of strains to be exploited as new potential starter cultures, to improve the safety, quality and local differentiation of traditional products. The data underlined that ST6 strain resulted in a final lower percentage if compared with the other LAB used as starter cultures. The use of starters reduced the BA concentration observed in the sausages obtained with spontaneous fermentation and the BPF2 and ST6 strains were able to decrease the level of products rancidity. Moreover, a challenge test against L. monocytogenes were performed. The data confirmed the effectiveness in the inhibition of L. monocytogenes by the two bacteriocinogenic strains tested, with respect to RAP and control samples, highlighting their ability to produce bacteriocins in real food systems. This work demonstrated the promising application in meat industry of these autochthonous strains as starter cultures to improve sensory differentiation and recognizability of typical fermented sausages.}, } @article {pmid37881119, year = {2023}, author = {Da Costa, AC and Bortoletto, P and Spandorfer, SD and Tozetto-Mendoza, TR and Linhares, IM and Mendes-Correa, MC and Witkin, SS}, title = {Association between torquetenovirus in vaginal secretions and infertility: An exploratory metagenomic analysis.}, journal = {American journal of reproductive immunology (New York, N.Y. : 1989)}, volume = {90}, number = {5}, pages = {e13788}, doi = {10.1111/aji.13788}, pmid = {37881119}, issn = {1600-0897}, mesh = {Male ; Humans ; Female ; *Infertility, Female ; *Torque teno virus/genetics ; Semen ; Vagina ; *Lactobacillus crispatus ; *Infertility, Male ; }, abstract = {PROBLEM: The association of viruses with infertility remains incompletely evaluated.

METHOD OF STUDY: Vaginal secretions from 46 women seeking treatment in the Center for Reproductive Medicine and Infertility at Weill Cornell Medicine were tested for viruses by metagenomic analysis by lab personnel blinded to all clinical data.

RESULTS: Torquetenovirus (TTV) was identified in 16 women, alphapapillomavirus in seven women and most were positive for bacteriophages. Twelve of the subjects were fertile and sought to freeze their oocytes for future implantation. These women were all negative for TTV. In contrast, 16 of the 34 women (47.1%) being treated for infertility were TTV-positive (p = .0035). Evaluating the women by cause of infertility, five of nine women (55.6%) whose male partner had inadequate sperm parameters and six of 14 women (42.9%) with defective ovulation were TTV positive (p = .0062 and p = .0171, respectively, vs. the fertile women). Alphapapillomavirus was identified in one (8.3%) fertile woman, five (35.7%) women with ovulation deficiency, and one (11.1%) woman with male factor infertility. These differences were not statistically significant. There were no differences in bacteriophage families or the presence of Lactobacillus phages between fertile or infertile women or between different causes of infertility. There was a negative association between TTV detection and Lactobacillus crispatus dominance in the vaginal microbiota (p = .0184), but no association between TTV detection and the presence of alphapapillomavirus or Candida species.

CONCLUSION: Detection of TTV in the vagina might be a biomarker for specific causes of infertility.}, } @article {pmid37881064, year = {2023}, author = {Torres, C and Correa, RM and Picconi, MA and Buck, CB and Mbayed, VA}, title = {Identification of a new polyomavirus in distinct human populations and tissues.}, journal = {Journal of medical virology}, volume = {95}, number = {10}, pages = {e29197}, doi = {10.1002/jmv.29197}, pmid = {37881064}, issn = {1096-9071}, mesh = {Humans ; Argentina ; *Polyomavirus/genetics ; *Polyomavirus Infections ; Skin ; }, abstract = {Several human polyomaviruses (HPyVs) have been described in the last 15 years. This work aimed to characterize a novel HPyV with cutaneous tropism. Swabs of healthy skin (forehead) of 75 immunocompetent individuals from Argentina were screened for HPyV through sequence amplification techniques. Publicly available metagenomic data sets were also analyzed. A previously unknown polyomavirus sequence was detected in two skin swab samples. A nearly identical sequence was detected in public data sets representing metagenomic surveys of human skin and feces. Further analyses showed that the new polyomavirus diverges from its nearest relative, human polyomavirus 6 (HPyV6), by 17.3%-17.7% (in nucleotides for the large T antigen), which meets criteria for a new species designation in the genus Deltapolyomavirus. The screening also revealed more distant HPyV6 relatives in macaque genital and chimpanzee fecal data sets. Since polyomaviruses are generally thought to cospeciate with mammalian hosts, the high degree of similarity to HPyV6 suggests the new polyomavirus species is human-tropic. Therefore, a novel polyomavirus was identified and characterized from samples of distinct populations and tissues. We suggest the common name human polyomavirus 16 (HPyV16).}, } @article {pmid37880979, year = {2023}, author = {Alessandri, G and Sangalli, E and Facchi, M and Fontana, F and Mancabelli, L and Donofrio, G and Ventura, M}, title = {Metataxonomic analysis of milk microbiota in the bovine subclinical mastitis.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {12}, pages = {}, doi = {10.1093/femsec/fiad136}, pmid = {37880979}, issn = {1574-6941}, mesh = {Cattle ; Animals ; Female ; Humans ; Milk/microbiology ; RNA, Ribosomal, 16S/genetics ; Pilot Projects ; *Mastitis, Bovine/microbiology/pathology ; *Microbiota/genetics ; }, abstract = {Subclinical mastitis is one of the most widespread diseases affecting dairy herds with detrimental effects on animal health, milk productivity, and quality. Despite its multifactorial nature, the presence of pathogenic bacteria is regarded one of the main drivers of subclinical mastitis, causing a disruption of the homeostasis of the bovine milk microbial community. However, bovine milk microbiota alterations associated with subclinical mastitis still represents a largely unexplored research area. Therefore, the species-level milk microbiota of a total of 75 milk samples, collected from both healthy and subclinical mastitis-affected cows from two different stables, was deeply profiled through an ITS, rather than a traditional, and less informative, 16S rRNA gene microbial profiling. Surprisingly, the present pilot study not only revealed that subclinical mastitis is characterized by a reduced biodiversity of the bovine milk microbiota, but also that this disease does not induce standard alterations of the milk microbial community across stables. In addition, a flow cytometry-based total bacterial cell enumeration highlighted that subclinical mastitis is accompanied by a significant increment in the number of milk microbial cells. Furthermore, the combination of the metagenomic and flow cytometry approaches allowed to identify different potential microbial marker strictly correlated with subclinical mastitis across stables.}, } @article {pmid37880617, year = {2023}, author = {Li, Z and Yuan, Z and Cao, H and Huan, D and Qiu, Y and Xia, T and Shen, J}, title = {A case report on Mycobacterium houstonense infection after total hip arthroplasty.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {722}, pmid = {37880617}, issn = {1471-2334}, mesh = {Aged ; Female ; Humans ; Anti-Bacterial Agents/therapeutic use ; *Arthroplasty, Replacement, Hip/adverse effects ; *Mycobacteriaceae ; *Mycobacterium Infections/diagnosis/drug therapy/complications ; *Prosthesis-Related Infections/diagnosis/drug therapy/etiology ; Reoperation ; }, abstract = {BACKGROUND: Mycobacterium houstonense is a category of rapidly growing mycobacteria that is gram-positive, acid-fast, polycrystalline, and non-spore-forming. There have been few reports of human infection caused by Mycobacterium houstonense worldwide.

CASE PRESENTATION: We present a case of chronic periprosthetic joint infection caused by Mycobacterium houstonense in an elderly female patient. The patient developed signs of infection after undergoing total hip arthroplasty. Despite receiving antibiotic treatment and revision surgery, the signs of infection recurred repeatedly. Multiple bacterial cultures during the treatment period were negative. Later, we identified the pathogenic bacteria Mycobacterium houstonense through mNGS testing, isolated the bacteria from the ultrasonically centrifuged fluid of the prosthesis and obtained drug sensitivity results. Finally, we performed a revision surgery and treated the patient with moxifloxacin and clindamycin. After treatment, the patient did not show signs of infection recurrence during 24 months of follow-up.

CONCLUSION: Through a relevant literature search, we believe that Mycobacterium houstonense may show higher sensitivity to amikacin and quinolone antibiotics. Additionally, clarifying occult infection sources through methods such as gene testing will improve the diagnosis and treatment of periprosthetic joint infection.}, } @article {pmid37880542, year = {2023}, author = {Tebbe, DA and Gruender, C and Dlugosch, L and Lõhmus, K and Rolfes, S and Könneke, M and Chen, Y and Engelen, B and Schäfer, H}, title = {Microbial drivers of DMSO reduction and DMS-dependent methanogenesis in saltmarsh sediments.}, journal = {The ISME journal}, volume = {17}, number = {12}, pages = {2340-2351}, pmid = {37880542}, issn = {1751-7370}, support = {TRR51//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; FOR 2716//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; EP/L016494/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; EP/L016494/1//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {Dimethyl Sulfoxide/metabolism ; Oxidoreductases/genetics/metabolism ; Bacteria/genetics/metabolism ; *Alphaproteobacteria/metabolism ; Sulfides/metabolism ; *Sulfonium Compounds/metabolism ; }, abstract = {Saltmarshes are highly productive environments, exhibiting high abundances of organosulfur compounds. Dimethylsulfoniopropionate (DMSP) is produced in large quantities by algae, plants, and bacteria and is a potential precursor for dimethylsulfoxide (DMSO) and dimethylsulfide (DMS). DMSO serves as electron acceptor for anaerobic respiration leading to DMS formation, which is either emitted or can be degraded by methylotrophic prokaryotes. Major products of these reactions are trace gases with positive (CO2, CH4) or negative (DMS) radiative forcing with contrasting effects on the global climate. Here, we investigated organic sulfur cycling in saltmarsh sediments and followed DMSO reduction in anoxic batch experiments. Compared to previous measurements from marine waters, DMSO concentrations in the saltmarsh sediments were up to ~300 fold higher. In batch experiments, DMSO was reduced to DMS and subsequently consumed with concomitant CH4 production. Changes in prokaryotic communities and DMSO reductase gene counts indicated a dominance of organisms containing the Dms-type DMSO reductases (e.g., Desulfobulbales, Enterobacterales). In contrast, when sulfate reduction was inhibited by molybdate, Tor-type DMSO reductases (e.g., Rhodobacterales) increased. Vibrionales increased in relative abundance in both treatments, and metagenome assembled genomes (MAGs) affiliated to Vibrio had all genes encoding the subunits of DMSO reductases. Molar conversion ratios of <1.3 CH4 per added DMSO were accompanied by a predominance of the methylotrophic methanogens Methanosarcinales. Enrichment of mtsDH genes, encoding for DMS methyl transferases in metagenomes of batch incubations indicate their role in DMS-dependent methanogenesis. MAGs affiliated to Methanolobus carried the complete set of genes encoding for the enzymes in methylotrophic methanogenesis.}, } @article {pmid37880541, year = {2023}, author = {McDaniel, EA and Scarborough, M and Mulat, DG and Lin, X and Sampara, PS and Olson, HM and Young, RP and Eder, EK and Attah, IK and Markillie, LM and Hoyt, DW and Lipton, MS and Hallam, SJ and Ziels, RM}, title = {Diverse electron carriers drive syntrophic interactions in an enriched anaerobic acetate-oxidizing consortium.}, journal = {The ISME journal}, volume = {17}, number = {12}, pages = {2326-2339}, pmid = {37880541}, issn = {1751-7370}, support = {RGPIN-2018-04585//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; SIP06//Genome British Columbia/ ; DE-AC05-76RL01830//DOE | SC | Biological and Environmental Research (BER)/ ; }, mesh = {Anaerobiosis ; *Ecosystem ; Electrons ; Acetates/metabolism ; Bacteria ; Archaea ; *Euryarchaeota/metabolism ; Oxidation-Reduction ; Hydrogen/metabolism ; Formates/metabolism ; Methane/metabolism ; }, abstract = {In many anoxic environments, syntrophic acetate oxidation (SAO) is a key pathway mediating the conversion of acetate into methane through obligate cross-feeding interactions between SAO bacteria (SAOB) and methanogenic archaea. The SAO pathway is particularly important in engineered environments such as anaerobic digestion (AD) systems operating at thermophilic temperatures and/or with high ammonia. Despite the widespread importance of SAOB to the stability of the AD process, little is known about their in situ physiologies due to typically low biomass yields and resistance to isolation. Here, we performed a long-term (300-day) continuous enrichment of a thermophilic (55 °C) SAO community from a municipal AD system using acetate as the sole carbon source. Over 80% of the enriched bioreactor metagenome belonged to a three-member consortium, including an acetate-oxidizing bacterium affiliated with DTU068 encoding for carbon dioxide, hydrogen, and formate production, along with two methanogenic archaea affiliated with Methanothermobacter_A. Stable isotope probing was coupled with metaproteogenomics to quantify carbon flux into each community member during acetate conversion and inform metabolic reconstruction and genome-scale modeling. This effort revealed that the two Methanothermobacter_A species differed in their preferred electron donors, with one possessing the ability to grow on formate and the other only consuming hydrogen. A thermodynamic analysis suggested that the presence of the formate-consuming methanogen broadened the environmental conditions where ATP production from SAO was favorable. Collectively, these results highlight how flexibility in electron partitioning during SAO likely governs community structure and fitness through thermodynamic-driven mutualism, shedding valuable insights into the metabolic underpinnings of this key functional group within methanogenic ecosystems.}, } @article {pmid37880540, year = {2023}, author = {Liu, S and Hu, R and Peng, N and Zhou, Z and Chen, R and He, Z and Wang, C}, title = {Phylogenetic and ecophysiological novelty of subsurface mercury methylators in mangrove sediments.}, journal = {The ISME journal}, volume = {17}, number = {12}, pages = {2313-2325}, pmid = {37880540}, issn = {1751-7370}, mesh = {*Mercury/metabolism ; Phylogeny ; Geologic Sediments/microbiology ; *Methylmercury Compounds/metabolism ; Bacteria/genetics/metabolism ; *Water Pollutants, Chemical/metabolism ; }, abstract = {Mangrove sediment is a crucial component in the global mercury (Hg) cycling and acts as a hotspot for methylmercury (MeHg) production. Early evidence has documented the ubiquity of well-studied Hg methylators in mangrove superficial sediments; however, their diversity and metabolic adaptation in the more anoxic and highly reduced subsurface sediments are lacking. Through MeHg biogeochemical assay and metagenomic sequencing, we found that mangrove subsurface sediments (20-100 cm) showed a less hgcA gene abundance but higher diversity of Hg methylators than superficial sediments (0-20 cm). Regional-scale investigation of mangrove subsurface sediments spanning over 1500 km demonstrated a prevalence and family-level novelty of Hg-methylating microbial lineages (i.e., those affiliated to Anaerolineae, Phycisphaerae, and Desulfobacterales). We proposed the candidate phylum Zixibacteria lineage with sulfate-reducing capacity as a currently understudied Hg methylator across anoxic environments. Unlike other Hg methylators, the Zixibacteria lineage does not use the Wood-Ljungdahl pathway but has unique capabilities of performing methionine synthesis to donate methyl groups. The absence of cobalamin biosynthesis pathway suggests that this Hg-methylating lineage may depend on its syntrophic partners (i.e., Syntrophobacterales members) for energy in subsurface sediments. Our results expand the diversity of subsurface Hg methylators and uncover their unique ecophysiological adaptations in mangrove sediments.}, } @article {pmid37879367, year = {2024}, author = {D'Addiego, J and Wand, N and Afrough, B and Fletcher, T and Kurosaki, Y and Leblebicioglu, H and Hewson, R}, title = {Recovery of complete genome sequences of Crimean-Congo haemorrhagic fever virus (CCHFV) directly from clinical samples: A comparative study between targeted enrichment and metagenomic approaches.}, journal = {Journal of virological methods}, volume = {323}, number = {}, pages = {114833}, doi = {10.1016/j.jviromet.2023.114833}, pmid = {37879367}, issn = {1879-0984}, mesh = {Humans ; *Hemorrhagic Fever Virus, Crimean-Congo/genetics ; *Hemorrhagic Fever, Crimean/epidemiology ; RNA, Viral/genetics ; Sequence Analysis, DNA ; *Vaccines ; }, abstract = {Crimean-Congo haemorrhagic fever (CCHF) is the most prevalent human tick-borne viral disease, endemic to the Balkans, Africa, Middle East and Asia. There are currently no licensed vaccines or effective antivirals against CCHF. CCHF virus (CCHFV) has a negative sense segmented tripartite RNA genome consisting of the small (S), medium (M) and large (L) segments. Depending on the segment utilised for genetic affiliation, there are up to 7 circulating lineages of CCHFV. The current lack of geographical representation of CCHFV sequences in various repositories highlights a requirement for increased CCHFV sequencing capabilities in endemic regions. We have optimised and established a multiplex PCR tiling methodology for the targeted enrichment of complete genomes of Europe 1 CCHFV lineage directly from clinical samples and compared its performance to a non-targeted enrichment approach on both short-read and long-read sequencing platforms. We have found a statistically significant increase in mapped viral sequencing reads produced with our targeted enrichment approach. This has allowed us to recover near complete S segment sequences and above 90% of the M and L segment sequences for samples with Ct values as high as 31.3. This study demonstrates the superiority of a targeted enrichment approach for recovery of CCHFV genomic sequences from samples with low virus titre. CCHFV is an important vector-borne human pathogen with wide geographical distribution. The validated methodology reported here adds value to front-line public health laboratories employing genomic sequencing for CCHFV Europe 1 lineage surveillance, particularly in the Balkan and Middle Eastern territories currently monitoring the spread of the pathogen. Tracking the genomic evolution of the virus across regions improves risk assessment and directly informs the development of diagnostics, therapeutics, and vaccines.}, } @article {pmid37879180, year = {2023}, author = {Hu, M and Liu, X and Liu, S and Ya, T and Zhang, M and Zhang, T and Gao, X and Wang, X}, title = {Responses of microbial interactions and functional genes to sulfamethoxazole in anammox consortia.}, journal = {Journal of environmental management}, volume = {348}, number = {}, pages = {119408}, doi = {10.1016/j.jenvman.2023.119408}, pmid = {37879180}, issn = {1095-8630}, mesh = {*Sulfamethoxazole/pharmacology ; *Anaerobic Ammonia Oxidation ; Nitrogen ; Microbial Interactions ; }, abstract = {Sulfamethoxazole (SMX) has been widely detected in various environments and its potential environmental risks have caused great concerns. However, the impact mechanism of SMX on microbial interactions among anammox consortia remain unknown. A long-term exposure experiments (140 d) was carried out to systematically examine the influence of SMX (0-1000 μg/L) on the anammox system, especially microbial network dynamics and variations of key metabolic genes. Results showed that anammox system could adapt to SMX below 500 μg/L and maintain a high nitrogen removal efficiency (NRE) of 85.35 ± 2.42%, while 1000 μg/L SMX significantly decreased the abundance of functional microbes and deteriorated denitrification performance with NRE dropped to 36.92 ± 15.01%. Co-occurrence network analysis indicated that 1000 μg/L SMX decreased the interactions between Proteobacteria and Chloroflexi and limited AnAOB from playing an important role as central nodes in the subnetwork of Planctomycetes. Metagenomics analysis found that genes associated with nitrogen removal (i.e., hdh, hzs, nirS, and hao) showed lower expression level after addition of SMX, while SMX-related ARGs (sul1 and sul2) increased by 1.22 and 2.68 times. This study provided us a relatively comprehensive perspective in response of microbial interactions and metabolic activity to various SMX concentrations.}, } @article {pmid37878710, year = {2023}, author = {Xi, H and Nie, X and Gao, F and Liang, X and Li, H and Zhou, H and Cai, Y and Yang, C}, title = {A bacterial spermidine biosynthetic pathway via carboxyaminopropylagmatine.}, journal = {Science advances}, volume = {9}, number = {43}, pages = {eadj9075}, pmid = {37878710}, issn = {2375-2548}, mesh = {*Spermidine ; Putrescine ; Biosynthetic Pathways ; Aspartic Acid ; Ecosystem ; *Cyanobacteria/metabolism ; }, abstract = {Spermidine, a ubiquitous polyamine, is known to be required for critical physiological functions in bacteria. Two principal pathways are known for spermidine biosynthesis, both of which involve aminopropylation of putrescine. Here, we identified a spermidine biosynthetic pathway via a previously unknown metabolite, carboxyaminopropylagmatine (CAPA), in a model cyanobacterium Synechocystis sp. PCC 6803 through an approach combining [13]C and [15]N tracers, metabolomics, and genetic and biochemical characterization. The CAPA pathway starts with reductive condensation of agmatine and l-aspartate-β-semialdehyde into CAPA by a previously unknown CAPA dehydrogenase, followed by decarboxylation of CAPA to form aminopropylagmatine, and ends with conversion of aminopropylagmatine to spermidine by an aminopropylagmatine ureohydrolase. Thus, the pathway does not involve putrescine and depends on l-aspartate-β-semialdehyde as the aminopropyl group donor. Genomic, biochemical, and metagenomic analyses showed that the CAPA-pathway genes are widespread in 15 different phyla of bacteria distributed in marine, freshwater, and other ecosystems.}, } @article {pmid37878664, year = {2023}, author = {Midya, V and Lane, JM and Gennings, C and Torres-Olascoaga, LA and Gregory, JK and Wright, RO and Arora, M and Téllez-Rojo, MM and Eggers, S}, title = {Prenatal Lead Exposure Is Associated with Reduced Abundance of Beneficial Gut Microbial Cliques in Late Childhood: An Investigation Using Microbial Co-Occurrence Analysis (MiCA).}, journal = {Environmental science & technology}, volume = {57}, number = {44}, pages = {16800-16810}, pmid = {37878664}, issn = {1520-5851}, mesh = {Pregnancy ; Female ; Humans ; Child ; Lead ; *Gastrointestinal Microbiome ; *Microbiota ; Bacteria ; }, abstract = {Many analytical methods used in gut microbiome research focus on either single bacterial taxa or the whole microbiome, ignoring multibacteria relationships (microbial cliques). We present a novel analytical approach to identify microbial cliques within the gut microbiome of children at 9-11 years associated with prenatal lead (Pb) exposure. Data came from a subset of participants (n = 123) in the Programming Research in Obesity, Growth, Environment and Social Stressors cohort. Pb concentrations were measured in maternal whole blood from the second and third trimesters of pregnancy. Stool samples collected at 9-11 years old underwent metagenomic sequencing to assess the gut microbiome. Using a novel analytical approach, Microbial Co-occurrence Analysis (MiCA), we paired a machine learning algorithm with randomization-based inference to first identify microbial cliques that were predictive of prenatal Pb exposure and then estimate the association between prenatal Pb exposure and microbial clique abundance. With second-trimester Pb exposure, we identified a two-taxa microbial clique that included Bifidobacterium adolescentis and Ruminococcus callidus and a three-taxa clique that also included Prevotella clara. Increasing second-trimester Pb exposure was associated with significantly increased odds of having the two-taxa microbial clique below the median relative abundance (odds ratio (OR) = 1.03, 95% confidence interval (CI) [1.01-1.05]). Using a novel combination of machine learning and causal inference, MiCA identified a significant association between second-trimester Pb exposure and the reduced abundance of a probiotic microbial clique within the gut microbiome in late childhood.}, } @article {pmid37877794, year = {2023}, author = {Morissette, A and André, DM and Agrinier, AL and Varin, TV and Pilon, G and Flamand, N and Houde, VP and Marette, A}, title = {The metabolic benefits of substituting sucrose for maple syrup are associated with a shift in carbohydrate digestion and gut microbiota composition in high-fat high-sucrose diet-fed mice.}, journal = {American journal of physiology. Endocrinology and metabolism}, volume = {325}, number = {6}, pages = {E661-E671}, doi = {10.1152/ajpendo.00065.2023}, pmid = {37877794}, issn = {1522-1555}, support = {//Producteurs et productrices acericoles du Quebec/ ; }, mesh = {Male ; Animals ; Mice ; Sucrose ; *Gastrointestinal Microbiome ; *Acer ; Mice, Obese ; Liver/metabolism ; Diet, High-Fat ; Sweetening Agents ; Digestion ; Mice, Inbred C57BL ; }, abstract = {Overconsumption of added sugars is now largely recognized as a major culprit in the global situation of obesity and metabolic disorders. Previous animal studies reported that maple syrup (MS) is less deleterious than refined sugars on glucose metabolism and hepatic health, but the mechanisms remain poorly studied. Beyond its content in sucrose, MS is a natural sweetener containing several bioactive compounds, such as polyphenols and inulin, which are potential gut microbiota modifiers. We aimed to investigate the impact of MS on metabolic health and gut microbiota in male C57Bl/6J mice fed a high-fat high-sucrose (HFHS + S) diet or an isocaloric HFHS diet in which a fraction (10% of the total caloric intake) of the sucrose was substituted by MS (HFHS + MS). Insulin and glucose tolerance tests were performed at 5 and 7 wk into the diet, respectively. The fecal microbiota was analyzed by whole-genome shotgun sequencing. Liver lipids and inflammation were determined, and hepatic gene expression was assessed by transcriptomic analysis. Maple syrup was less deleterious on insulin resistance and decreased liver steatosis compared with mice consuming sucrose. This could be explained by the decreased intestinal α-glucosidase activity, which is involved in carbohydrate digestion and absorption. Metagenomic shotgun sequencing analysis revealed that MS intake increased the abundance of Faecalibaculum rodentium, Romboutsia ilealis, and Lactobacillus johnsonii, which all possess gene clusters involved in carbohydrate metabolism, such as sucrose utilization and butyric acid production. Liver transcriptomic analyses revealed that the cytochrome P450 (Cyp450) epoxygenase pathway was differently modulated between HFHS + S- and HFHS + MS-fed mice. These results show that substituting sucrose for MS alleviated dysmetabolism in diet-induced obese mice, which were associated with decreased carbohydrate digestion and shifting gut microbiota.NEW & NOTEWORTHY The natural sweetener maple syrup has sparked much interest as an alternative to refined sugars. This study aimed to investigate whether the metabolic benefits of substituting sucrose with an equivalent dose of maple syrup could be linked to changes in gut microbiota composition and digestion of carbohydrates in obese mice. We demonstrated that maple syrup is less detrimental than sucrose on metabolic health and possesses a prebiotic-like activity through novel gut microbiota and liver mechanisms.}, } @article {pmid37877702, year = {2023}, author = {Child, HT and Airey, G and Maloney, DM and Parker, A and Wild, J and McGinley, S and Evens, N and Porter, J and Templeton, K and Paterson, S and van Aerle, R and Wade, MJ and Jeffries, AR and Bassano, I}, title = {Comparison of metagenomic and targeted methods for sequencing human pathogenic viruses from wastewater.}, journal = {mBio}, volume = {14}, number = {6}, pages = {e0146823}, pmid = {37877702}, issn = {2150-7511}, abstract = {Wastewater-based epidemiology is a powerful tool for monitoring the emergence and spread of viral pathogens at the population scale. Typical polymerase chain reaction (PCR)-based methods of quantitative and genomic monitoring of viruses in wastewater provide high sensitivity and specificity. However, these methods are limited to the surveillance of target viruses in a single assay and require prior knowledge of the target genome(s). Metagenomic sequencing methods may represent a target-agnostic approach to viral wastewater monitoring, allowing for the detection of a broad range of target viruses, including potentially novel and emerging pathogens. In this study, targeted and untargeted metagenomic sequencing methods were compared with tiled-PCR sequencing for the detection and genotyping of viral pathogens in wastewater samples. Deep shotgun metagenomic sequencing was unable to generate sufficient genome coverage of human pathogenic viruses for robust genomic epidemiology, with samples dominated by bacteria. Hybrid-capture enrichment of shotgun libraries for respiratory viruses led to significant increases in genome coverage for a range of targets. Tiled-PCR sequencing led to further improvements in genome coverage compared to hybrid capture for severe acute respiratory syndrome coronavirus 2, enterovirus D68, norovirus GII, and human adenovirus F41 in wastewater samples. In conclusion, untargeted shotgun sequencing was unsuitable for genomic monitoring of the low virus concentrations in wastewater samples analyzed in this study. Hybrid-capture enrichment represented a viable method for simultaneous genomic epidemiology of a range of viral pathogens, while tiled-PCR sequencing provided the optimal genome coverage for individual viruses with the minimum sequencing depth. IMPORTANCE Most public health initiatives that monitor viruses in wastewater have utilized quantitative polymerase chain reaction (PCR) and whole genome PCR sequencing, mirroring techniques used for viral epidemiology in individuals. These techniques require prior knowledge of the target viral genome and are limited to monitoring individual or small groups of viruses. Metagenomic sequencing may offer an alternative strategy for monitoring a broad spectrum of viruses in wastewater, including novel and emerging pathogens. In this study, while amplicon sequencing gave high viral genome coverage, untargeted shotgun sequencing of total nucleic acid samples was unable to detect human pathogenic viruses with enough sensitivity for use in genomic epidemiology. Enrichment of shotgun libraries for respiratory viruses using hybrid-capture technology provided genotypic information on a range of viruses simultaneously, indicating strong potential for wastewater surveillance. This type of targeted metagenomics could be used for monitoring diverse targets, such as pathogens or antimicrobial resistance genes, in environmental samples.}, } @article {pmid37877698, year = {2023}, author = {Avelar-Barragan, J and Mendez Luque, LF and Nguyen, J and Nguyen, H and Odegaard, AO and Fleischman, AG and Whiteson, KL}, title = {Characterizing the microbiome of patients with myeloproliferative neoplasms during a Mediterranean diet intervention.}, journal = {mBio}, volume = {14}, number = {6}, pages = {e0230823}, pmid = {37877698}, issn = {2150-7511}, support = {P30 CA062203/CA/NCI NIH HHS/United States ; R25 GM055246/GM/NIGMS NIH HHS/United States ; }, abstract = {Myeloproliferative neoplasms (MPNs) are a class of rare hematological malignancies that result in the overproduction of myeloid lineage cells. These malignancies result in increased cytokine production and inflammation, which correlate with worsened symptom burden and prognosis. Other than bone marrow transplantation, there is no cure for myeloproliferative neoplasms. As such, treatments focus on reducing thrombotic risk, inflammation, and symptom burden. Because current pharmacological treatments carry significant side effects, there is a need to explore low-risk therapies that may modulate inflammation and alleviate symptom burden. One potential way to achieve this is adherence to a Mediterranean (MED) diet, which is rich in anti-inflammatory foods, reduces inflammatory biomarkers, and beneficially alters the gut microbiome. We performed a 15-week clinical trial of 28 individuals with MPN who were randomized to dietary counseling based on either a Mediterranean diet or standard U.S. Guidelines for Americans. Our primary objective was to determine whether MPN patients could adopt a Mediterranean eating pattern when supported with dietician counseling. As exploratory endpoints, we investigated the impact of diet and inflammation on the gut microbiome. Using shotgun metagenomic sequencing, we found that microbiome diversity and composition were stable throughout the study duration in both cohorts. Furthermore, we discovered significant differences in the microbiomes between MPN subtypes, such as increased beta-dispersion in subjects with myelofibrosis. Lastly, we found several significant correlations between the abundance of multiple bacterial taxa and cytokine levels. Together, this study provides insight into the interaction between diet, inflammation, and the gut microbiome. IMPORTANCE The gut microbiome serves as an interface between the host and the diet. Diet and the gut microbiome both play important roles in managing inflammation, which is a key aspect of myeloproliferative neoplasm (MPN). Studies have shown that a Mediterranean (MED) diet can reduce inflammation. Therefore, we longitudinally characterized the gut microbiomes of MPN patients in response to Mediterranean or standard 2020 US Guidelines for Americans dietary counseling to determine whether there were microbiome-associated changes in inflammation. We did not find significant changes in the gut microbiome associated with diet, but we did find several associations with inflammation. This research paves the way for future studies by identifying potential mechanistic targets implicated in inflammation within the MPN gut microbiome.}, } @article {pmid37877655, year = {2023}, author = {Ahmad, N and Ritz, M and Calchera, A and Otte, J and Schmitt, I and Brueck, T and Mehlmer, N}, title = {Biosynthetic gene cluster synteny: Orthologous polyketide synthases in Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata.}, journal = {MicrobiologyOpen}, volume = {12}, number = {5}, pages = {e1386}, pmid = {37877655}, issn = {2045-8827}, mesh = {*Polyketide Synthases/genetics/metabolism ; Depsides/metabolism ; Synteny ; *Lichens/genetics/microbiology ; Fungi/genetics ; Multigene Family ; Phylogeny ; }, abstract = {Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus), which together generate a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here, we provide a comparative view of the biosynthetic gene clusters of three lichen mycobionts derived from Hypogymnia physodes, Hypogymnia tubulosa, and Parmelia sulcata. In addition, we present a high-quality PacBio metagenome of Parmelia sulcata, from which we extracted the mycobiont bin containing 214 biosynthetic gene clusters. Most biosynthetic gene clusters in these genomes were associated with T1PKSs, followed by NRPSs and terpenes. This study focused on biosynthetic gene clusters related to polyketide synthesis. Based on ketosynthase homology, we identified nine highly syntenic clusters present in all three species. Among the four clusters belonging to nonreducing PKSs, two are putatively linked to lichen substances derived from orsellinic acid (orcinol depsides and depsidones, e.g., lecanoric acid, physodic acid, lobaric acid), one to compounds derived from methylated forms of orsellinic acid (beta orcinol depsides, e.g., atranorin), and one to melanins. Five clusters with orthologs in all three species are linked to reducing PKSs. Our study contributes to sorting and dereplicating the vast PKS diversity found in lichenized fungi. High-quality sequences of biosynthetic gene clusters of these three common species provide a foundation for further exploration into biotechnological applications and the molecular evolution of lichen substances.}, } @article {pmid37876815, year = {2023}, author = {Duitama González, C and Rangavittal, S and Vicedomini, R and Chikhi, R and Richard, H}, title = {aKmerBroom: Ancient oral DNA decontamination using Bloom filters on k-mer sets.}, journal = {iScience}, volume = {26}, number = {11}, pages = {108057}, pmid = {37876815}, issn = {2589-0042}, abstract = {Dental calculus samples are modeled as a mixture of DNA coming from dental plaque and contaminants. Current computational decontamination methods such as Recentrifuge and DeconSeq require either a reference database or sequenced negative controls, and therefore have limited use cases. We present a reference-free decontamination tool tailored for the removal of contaminant DNA of ancient oral sample called aKmerBroom. Our tool builds a Bloom filter of known ancient and modern oral k-mers, then scans an input set of ancient metagenomic reads using multiple passes to iteratively retain reads likely to be of oral origin. On synthetic data, aKmerBroom achieves over 89.53% sensitivity and 94.00% specificity. On real datasets, aKmerBroom shows higher read retainment (+60% on average) than other methods. We anticipate aKmerBroom will be a valuable tool for the processing of ancient oral samples as it will prevent contaminated datasets from being completely discarded in downstream analyses.}, } @article {pmid37876810, year = {2023}, author = {Mao, Y and Liu, X and Zhang, N and Wang, Z and Han, M}, title = {NCRD: A non-redundant comprehensive database for detecting antibiotic resistance genes.}, journal = {iScience}, volume = {26}, number = {11}, pages = {108141}, pmid = {37876810}, issn = {2589-0042}, abstract = {Antibiotic resistance genes (ARGs) are emerging pollutants present in various environments. Identifying ARGs has become a growing concern in recent years. Several databases, including the Antibiotic Resistance Genes Database (ARDB), Comprehensive Antibiotic Resistance Database (CARD), and Structured Antibiotic Resistance Genes (SARG), have been applied to detect ARGs. However, these databases have limitations, which hinder the comprehensive profiling of ARGs in environmental samples. To address these issues, we constructed a non-redundant antibiotic resistance genes database (NRD) by consolidating sequences from ARDB, CARD, and SARG. We identified the homologous proteins of NRD from Non-redundant Protein Database (NR) and the Protein DataBank Database (PDB) and clustered them to establish a non-redundant comprehensive antibiotic resistance genes database (NCRD) with similarities of 100% (NCRD100) and 95% (NCRD95). To demonstrate the advantages of NCRD, we compared it with other databases by using metagenome datasets. Results revealed its strong ability in detecting potential ARGs.}, } @article {pmid37876012, year = {2023}, author = {Yu, J and Jiang, C and Yamano, R and Koike, S and Sakai, Y and Mino, S and Sawabe, T}, title = {Unveiling the early life core microbiome of the sea cucumber Apostichopus japonicus and the unexpected abundance of the growth-promoting Sulfitobacter.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {54}, pmid = {37876012}, issn = {2524-4671}, abstract = {BACKGROUND: Microbiome in early life has long-term effects on the host's immunological and physiological development and its disturbance is known to trigger various diseases in host Deuterostome animals. The sea cucumber Apostichopus japonicus is one of the most valuable marine Deuterostome invertebrates in Asia and a model animal in regeneration studies. To understand factors that impact on host development and holobiont maintenance, host-microbiome association has been actively studied in the last decade. However, we currently lack knowledge of early life core microbiome during its ontogenesis and how it benefits the host's growth.

RESULTS: We analyzed the microbial community in 28 sea cucumber samples from a laboratory breeding system, designed to replicate aquaculture environments, across six developmental stages (fertilized eggs to the juvenile stage) over a three years-period to examine the microbiomes' dynamics and stability. Microbiome shifts occurred during sea cucumber larval ontogenesis in every case. Application of the most sophisticated core microbiome extraction methodology, a hybrid approach with abundance-occupancy core microbiome analyses (top 75% of total reads and > 70% occupation) and core index calculation, first revealed early life core microbiome consisted of Alteromonadaceae and Rhodobacteraceae, as well as a stage core microbiome consisting of pioneer core microbe Pseudoalteromonadaceae in A. japonicus, suggesting a stepwise establishment of microbiome related to ontogenesis and feeding behavior in A. japonicus. More interestingly, four ASVs affiliated to Alteromonadaceae and Rhodobacteraceae were extracted as early life core microbiome. One of the ASV (ASV0007) was affiliated to the Sulfitobactor strain BL28 (Rhodobacteraceae), isolated from blastula larvae in the 2019 raring batch. Unexpectedly, a bioassay revealed the BL28 strain retains a host growth-promoting ability. Further meta-pangenomics approach revealed the BL28 genome reads were abundant in the metagenomic sequence pool, in particular, in that of post-gut development in early life stages of A. japonicus.

CONCLUSION: Repeated rearing efforts of A. japonicus using laboratory aquaculture replicating aquaculture environments and hybrid core microbiome extraction approach first revealed particular ASVs affiliated to Alteromonadaceae and Rhodobacteraceae as the A. japonicus early life core microbiome. Further bioassay revealed the growth promoting ability to the host sea cucumber in one of the core microbes, the Sulfitobactor strain BL28 identified as ASV0007. Genome reads of the BL28 were abundant in post-gut development of A. japonicus, which makes us consider effective probiotic uses of those core microbiome for sea cucumber resource production and conservation. The study also emphasizes the importance of the core microbiome in influencing early life stages in marine invertebrates. Understanding these dynamics could offer pathways to improve growth, immunity, and disease resistance in marine invertebrates.}, } @article {pmid37875803, year = {2023}, author = {Salman, MM and Nawaz, M and Yaqub, T and Mushtaq, MH}, title = {Investigation of milk microbiota of healthy and mastitic Sahiwal cattle.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {304}, pmid = {37875803}, issn = {1471-2180}, mesh = {Animals ; Cattle ; Female ; Humans ; Milk/microbiology ; RNA, Ribosomal, 16S/genetics ; *Mastitis, Bovine/microbiology ; *Microbiota ; }, abstract = {BACKGROUND: Sahiwal cattle is an indigenous cattle breed of Pakistan and mastitis is one of the major problems faced by Sahiwal cattle which hinders its production potential. The study was designed to investigate the milk microbiota of healthy and mastitic Sahiwal cattle as part of a multistep project to develop probiotics for the mitigation and control of mastitis. Milk samples of Sahiwal cattle (healthy clinical mastitis and subclinical mastitis) reared under similar husbandry and management practices were processed for 16S rRNA gene base metagenomics analysis.

RESULTS: Results revealed that Proteobacteria were dominant in the healthy group and subclinical mastitis group (56.48% and 48.77%, respectively) as compared to the clinical mastitis group (2.68%). In contrast, Firmicutes were abundant in the clinical mastitis group (64%) as compared to the healthy and subclinical mastitis groups (15.87% and 38.98%, respectively). Dominant species assigned in the healthy group were Ignavibacterium album, Novosphingobium capsulatum, Akkermansia muciniphila and Lactobacillus fermentum.The clinical mastitis group was dominated by Streptococcus dysgalactiae and Corynebacterium bovis, while subclinical mastitis group included Lactobacillus fermentum and uncultured acidobacteriales and Akkermansia muciniphila as dominant species. Alpha diversity indices showed higher microbial diversity in the healthy group compared to the clinical and sub-clinical mastitis groups.

CONCLUSION: It is concluded that the milk microbiota of healthy sahiwal cattle has higher diversity and dominant taxa in the different groups may be used as signature microbes for mastitis susceptibility. Akkermansia muciniphila is one of candidate specie that was identified and may be used for development of probiotics.}, } @article {pmid37875797, year = {2023}, author = {Fu, Y and Zhang, K and Shan, F and Li, J and Wang, Y and Li, X and Xu, H and Qin, Z and Zhang, L}, title = {Metagenomic analysis of gut microbiome and resistome of Whooper and Black Swans: a one health perspective.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {635}, pmid = {37875797}, issn = {1471-2164}, support = {U1904203//Key program of National Natural Science Foundation of China - Henan Province Joint Fund/ ; 2019YFC1605700//National Key Research and Development Program of China/ ; 19CZ0122//Leading Talents of Thousand Talents Program of Central China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *One Health ; *Anseriformes ; China ; *Microbiota ; Ducks ; Anti-Bacterial Agents/pharmacology ; }, abstract = {BACKGROUND: With the promotion of "One Health," the health of animals and their impact on the environment have become major concerns recently. Widely distributed in China, the whooper swans (Cygnus cygnus) and black swans (Cygnus atratus) are not only important to the ecological environment, but they may also potentially influence public health security. The metagenomic approach was adopted to uncover the impacts of the gut microbiota of swans on host and public health.

RESULTS: In this study, the intestinal microbiome and resistome of migratory whooper swans and captive-bred black swans were identified. The results revealed similar gut microbes and functional compositions in whooper and black swans. Interestingly, different bacteria and probiotics were enriched by overwintering whooper swans. We also found that Acinetobacter and Escherichia were significantly enriched in early wintering period swans and that clinically important pathogens were more abundant in black swans. Whooper swans and black swans are potential reservoirs of antibiotic resistance genes (ARGs) and novel ARGs, and the abundance of novel ARGs in whooper swans was significantly higher than that in black swans. Metagenomic assembly-based host tracking revealed that most ARG-carrying contigs originated from Proteobacteria (mainly Gammaproteobacteria).

CONCLUSIONS: The results revealed spatiotemporal changes in microbiome and resistome in swans, providing a reference for safeguarding public health security and preventing animal epidemics.}, } @article {pmid37875603, year = {2023}, author = {Zhou, K and Wong, TY and Long, L and Anantharaman, K and Zhang, W and Wong, WC and Zhang, R and Qian, PY}, title = {Genomic and transcriptomic insights into complex virus-prokaryote interactions in marine biofilms.}, journal = {The ISME journal}, volume = {17}, number = {12}, pages = {2303-2312}, pmid = {37875603}, issn = {1751-7370}, mesh = {Transcriptome ; *Viruses/genetics ; Seawater/microbiology ; Genomics ; *Cyanobacteria/genetics ; Biofilms ; }, abstract = {Marine biofilms are complex communities of microorganisms that play a crucial ecological role in oceans. Although prokaryotes are the dominant members of these biofilms, little is known about their interactions with viruses. By analysing publicly available and newly sequenced metagenomic data, we identified 2446 virus-prokaryote connections in 84 marine biofilms. Most of these connections were between the bacteriophages in the Uroviricota phylum and the bacteria of Proteobacteria, Cyanobacteria and Bacteroidota. The network of virus-host pairs is complex; a single virus can infect multiple prokaryotic populations or a single prokaryote is susceptible to several viral populations. Analysis of genomes of paired prokaryotes and viruses revealed the presence of 425 putative auxiliary metabolic genes (AMGs), 239 viral genes related to restriction-modification (RM) systems and 38,538 prokaryotic anti-viral defence-related genes involved in 15 defence systems. Transcriptomic evidence from newly established biofilms revealed the expression of viral genes, including AMGs and RM, and prokaryotic defence systems, indicating the active interplay between viruses and prokaryotes. A comparison between biofilms and seawater showed that biofilm prokaryotes have more abundant defence genes than seawater prokaryotes, and the defence gene composition differs between biofilms and the surrounding seawater. Overall, our study unveiled active viruses in natural biofilms and their complex interplay with prokaryotes, which may result in the blooming of defence strategists in biofilms. The detachment of bloomed defence strategists may reduce the infectivity of viruses in seawater and result in the emergence of a novel role of marine biofilms.}, } @article {pmid37875417, year = {2023}, author = {Li, J and Yang, Z and Yuan, W and Bao, Z and Li, MD}, title = {Heme metabolism mediates the effects of smoking on gut microbiome.}, journal = {Nicotine & tobacco research : official journal of the Society for Research on Nicotine and Tobacco}, volume = {}, number = {}, pages = {}, doi = {10.1093/ntr/ntad209}, pmid = {37875417}, issn = {1469-994X}, abstract = {INTRODUCTION: The number of smokers worldwide increased greatly during the past decades and reached 1.14 billion in 2019, becoming a leading risk factor for human health. Tobacco smoking has wide effects on human genetics, epigenetics, transcriptome, and gut microbiome. Although many studies have revealed effects of smoking on host transcriptome, research on the relationship among smoking, host gene expression, and the gut microbiome is limited.

METHODS: We first explored transcriptome and metagenome profile differences between smokers and non-smokers. To evaluate the relationship between host gene expression and gut microbiome, we then applied bi-directional mediation analysis to infer causal relationships between smoking, gene expression, and gut microbes.

RESULTS: Metagenome and transcriptome analyses revealed 71 differential species and 324 differential expressed genes between smokers and non-smokers. With smoking as an exposure variable, we identified 272 significant causal relationships between gene expression and gut microbes, among which there were 247 genes that mediate the effect of smoking on gut microbes. Pathway-based enrichment analysis showed that these genes were significantly enriched in heme metabolic pathway, which mainly mediated the changes of Bacteroides finegoldii and Lachnospiraceae bacterium 9_1_43BFAA. Additionally, by performing metabolome data analysis in the Integrated Human Microbiome project (iHMP) database, we verified the correlation between the intermediate products of the heme metabolism pathway (porphobilinogen, bilirubin, and biliverdin) and gut microbiome.

CONCLUSIONS: By investigating the bi-directional interaction between smoking-related host gene expression and gut microbes, this study provided evidence for the mediation of smoking on gut microbes through co-involvement or interaction of heme metabolism.

IMPLICATIONS: By comparing the metagenome and transcriptome sequencing profiles between 34 smokers and 33 age- and gender-matched non-smokers, we are the first to reveal causal relationships among tobacco smoking, host gene expression and gut microbes. These findings offer insight into how smoking affects gut microbes through host gene expression and metabolism, which highlights the importance of heme metabolism in modulating the effects of smoking on gut microbiome.}, } @article {pmid37875356, year = {2023}, author = {Cheng, X and Zhang, Z and Dong, W and Lun, Y and Liu, B}, title = {Characteristics of intestinal flora in patients with cerebral infarction complicated with Type 2 diabetes mellitus.}, journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences}, volume = {48}, number = {8}, pages = {1163-1175}, doi = {10.11817/j.issn.1672-7347.2023.220558}, pmid = {37875356}, issn = {1672-7347}, support = {2020J01903//the grants from the Natural Science Foundations of Fujian Province/ ; 2019013//the Talents Research Project of Putian University/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/complications ; Retrospective Studies ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {OBJECTIVES: The intestinal microbial characteristics of patients with simple cerebral infarction (CI) and CI complicated with Type 2 diabetes mellitus (CI-T2DM) are still not clear. This study aims to analyze the differences in the variable characteristics of intestinal flora between patients simply with CI and CI-T2DM.

METHODS: This study retrospectively collected the patients who were admitted to the Affiliated Hospital of Putian University from September 2021 to September 2022. The patients were divided into a CI group (n=12) and a CI-T2DM group (n=12). Simultaneously, 12 healthy people were selected as a control group. Total DNA was extracted from feces specimens. Illumina Novaseq sequencing platform was used for metagenomic sequencing. The Knead Data software, Kraken2 software, and Bracken software were applied for sequencing analysis.

RESULTS: At phylum level, the average ratio of Firmicutes, Bacteroidetes, and Proteobacteria in the CI-T2DM group were 33.07%, 54.80%, and 7.00%, respectively. In the CI group, the ratios of each were 14.03%, 69.62%, and 11.13%, respectively, while in the control group, the ratios were 50.99%, 37.67%, and 5.24%, respectively. There was significant differences in the distribution of Firmicutes (F=6.130, P=0.011) among the 3 groups. At the family level, compared with the CI group, the relative abundance of Eubacteriaceae (t=8.062, P<0.001) in the CI-T2DM group was significantly increased, while Corynebacteriaceae (t=4.471, P<0.001), Methanobacteriaceae (t=3.406, P=0.003), and Pseudomonadaceae (t=2.352, P=0.028) were decreased significantly. At the genus level, compared with the CI group, there was a relative abundance of Cutibacterium (t=6.242, P<0.001), Eubacterium (t=8.448, P<0.001), and Blautia (t=3.442, P=0.002) in the CI-T2DM group which was significantly increased. In terms of Methanobrevibacter (t=3.466, P=0.002), Pyramidobacter (t=2.846, P=0.009) and Pseudomonas (t=2.352, P=0.028), their distributions were decreased significantly in the CI-T2DM group. At the species level, compared with the CI group, the relative abundance of Cutibacterium acnes (t=6.242, P<0.001) in the CI-T2DM group was significantly increased, while Pseudomonas aeruginosa (t=2.352, P=0.028) was decreased significantly. Still at the genus level, linear discriminant analysis effect size (LEfSe) analysis showed that the distributions of Pseudomonas and Blautia were determined to be the most significantly different between the CI-T2DM and the CI group. At the species level, the total number of operational taxonomic units (OTUs) in the 3 groups was 1 491. There were 169, 221, and 192 kinds of OTUs unique to the CI-T2DM, CI, and control group, respectively.

CONCLUSIONS: From phylum level to species level, the composition of intestinal flora in the patients with CI-T2DM is different from those in the patients simply with CI. The change in the proportion of Firmicutes, Bacteroidetes and Proteus compared with the healthy population is an important feature of intestinal flora imbalance in the patients with CI and with CI-T2DM. Attention should be paid to the differential distribution of Bacteroides monocytogenes and butyrate producing bacteria.}, } @article {pmid37875211, year = {2024}, author = {Go, K and Horiba, K and Yamamoto, H and Morimoto, Y and Fukasawa, Y and Ohashi, N and Yasuda, K and Ishikawa, Y and Kuraishi, K and Suzuki, K and Ito, Y and Takahashi, Y and Kato, T}, title = {Dysbiosis of gut microbiota in patients with protein-losing enteropathy after the Fontan procedure.}, journal = {International journal of cardiology}, volume = {396}, number = {}, pages = {131554}, doi = {10.1016/j.ijcard.2023.131554}, pmid = {37875211}, issn = {1874-1754}, mesh = {Humans ; *Fontan Procedure/adverse effects ; *Protein-Losing Enteropathies/diagnosis/etiology ; *Gastrointestinal Microbiome ; Case-Control Studies ; Dysbiosis/diagnosis/complications ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: There is a lack of predictive biomarkers for the onset or activity of protein-losing enteropathy (PLE), a Fontan procedure-associated complication. Here, we aimed to identify the gut microbiota composition of patients with active PLE and investigate its relationship with PLE activity.

METHODS: This multicenter case-control study involved patients who developed PLE (n = 16) after the Fontan procedure and those who did not (non-PLE; n = 20). Patients with PLE who maintained a serum albumin level of ≥3 g/dL for >1 year were included in the remissive-stage-PLE group (n = 9) and those who did not maintain this level were included in the active-PLE group (n = 7). 16S rRNA gene sequencing analysis of fecal samples was performed using QIIME2 pipeline. Alpha (Shannon and Faith's phylogenetic diversity indices) and beta diversity was assessed using principal coordinate analysis based on unweighted UniFrac distances.

RESULTS: Shannon and Faith's phylogenetic diversity indices were lower in the active-PLE group than in the remissive-stage- (q = 0.028 and 0.025, respectively) and non-PLE (q = 0.028 and 0.017, respectively) groups. Analysis of beta diversity revealed a difference in the microbiota composition between the active-PLE and the other two groups. Linear discriminant effect size analysis demonstrated differences in the relative abundance of Bifidobacterium and Granulicatella spp., and Ruminococcus torques between patients with active- and those with remissive-stage-PLE.

CONCLUSIONS: Gut microbiota dysbiosis was observed in patients with active PLE. Changes in the bacterial composition of the gut microbiota and decreased diversity may be associated with the severity of PLE.}, } @article {pmid37874143, year = {2023}, author = {Kok, CR and Mulakken, N and Thissen, JB and Grey, SF and Avila-Herrera, A and Upadhyay, MM and Lisboa, FA and Mabery, S and Elster, EA and Schobel, SA and Be, NA}, title = {Targeted metagenomic assessment reflects critical colonization in battlefield injuries.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0252023}, pmid = {37874143}, issn = {2165-0497}, mesh = {Humans ; *Wound Infection/diagnosis/microbiology ; *Metagenome ; *War-Related Injuries/diagnosis/microbiology ; }, abstract = {Microbial contamination in combat wounds can lead to opportunistic infections and adverse outcomes. However, current microbiological detection has a limited ability to capture microbial functional genes. This work describes the application of targeted metagenomic sequencing to profile wound bioburden and capture relevant wound-associated signatures for clinical utility. Ultimately, the ability to detect such signatures will help guide clinical decisions regarding wound care and management and aid in the prediction of wound outcomes.}, } @article {pmid37874137, year = {2023}, author = {Taraboletti, A and King, A and Dixon, Y and Orr, O and Parnell, C and Watson, Y and Nash, B and Esimai, C and Ude, G}, title = {Assessing microbial diversity in soil samples along the Potomac River: implications for environmental health.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0254023}, pmid = {37874137}, issn = {2165-0497}, support = {1438902//National Science Foundation (NSF)/ ; 1622811, 183365//National Science Foundation (NSF)/ ; }, mesh = {Humans ; *Rivers ; Environmental Pollution ; *Microbiota ; Environmental Health ; Soil ; Soil Microbiology ; }, abstract = {This study integrates microbial analysis into an undergraduate chemistry class, offering students a hands-on approach to environmental research. We examined the soil along the urbanized Potomac River, discovering a mix of common marine microbes and others that are indicators of urban waste and pollution. Our findings provide valuable insights into the environmental impacts of urbanization on soil health and reveal the effectiveness of using modern genetic tools to teach students about real-world issues. This innovative educational approach not only deepens students' understanding of chemistry and ecology but also prepares them to be thoughtful, informed participants in addressing contemporary environmental challenges while shedding light on the state of the soil microbiome near and around the DC metro area.}, } @article {pmid37873767, year = {2023}, author = {Xu, J and Chen, L and Cen, T and Zeng, Y and Liu, Q}, title = {HHV-6B- and HHV-7-associated choroiditis secondary to acute myelogenous leukemia: a case report.}, journal = {The Journal of international medical research}, volume = {51}, number = {10}, pages = {3000605231204479}, pmid = {37873767}, issn = {1473-2300}, mesh = {Humans ; Female ; Adult ; *Herpesvirus 6, Human/genetics ; *Herpesvirus 7, Human/genetics ; *Choroiditis/diagnosis/pathology ; Choroid/pathology ; *Leukemia, Myeloid, Acute/complications/pathology ; Tomography, Optical Coherence ; }, abstract = {We report a case of human herpes virus 6 (HHV-6)- and human herpes virus 7 (HHV-7)-associated choroiditis in an immunocompromised woman. A 42-year-old Chinese woman with a history of acute myelogenous leukemia presented with blurred vision and black floaters in her right eye. Anterior segment examination findings were normal. Ophthalmoscopic examination revealed a subretinal lesion in the superonasal peripapillary region with several punctate hemorrhages. Optical coherence tomography showed a crater-like choroidal protuberance, associated with retinal pigment epithelium rupture and full-thickness retinal edema in the involved area. Indocyanine green angiography demonstrated a broad hypofluorescent lesion in the choroid. The patient was diagnosed with choroiditis. Subsequently, metagenomic next-generation sequencing revealed HHV-6B and HHV-7 DNA in the aqueous humor. Therefore, antiviral therapy was initiated. The patient experienced resolution of all symptoms and signs after treatment with intravenous foscarnet and oral acyclovir. The findings in this case indicate that HHV-6 and HHV-7 can cause ocular infection, particularly in immunocompromised patients.}, } @article {pmid37873403, year = {2023}, author = {Erawijantari, PP and Kartal, E and Liñares-Blanco, J and Laajala, TD and Feldman, LE and , and Carmona-Saez, P and Shigdel, R and Claesson, MJ and Bertelsen, RJ and Gomez-Cabrero, D and Minot, S and Albrecht, J and Chung, V and Inouye, M and Jousilahti, P and Schultz, JH and Friederich, HC and Knight, R and Salomaa, V and Niiranen, T and Havulinna, AS and Saez-Rodriguez, J and Levinson, RT and Lahti, L}, title = {Microbiome-based risk prediction in incident heart failure: a community challenge.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {37873403}, support = {T32 GM007635/GM/NIGMS NIH HHS/United States ; }, abstract = {Heart failure (HF) is a major public health problem. Early identification of at-risk individuals could allow for interventions that reduce morbidity or mortality. The community-based FINRISK Microbiome DREAM challenge (synapse.org/finrisk) evaluated the use of machine learning approaches on shotgun metagenomics data obtained from fecal samples to predict incident HF risk over 15 years in a population cohort of 7231 Finnish adults (FINRISK 2002, n=559 incident HF cases). Challenge participants used synthetic data for model training and testing. Final models submitted by seven teams were evaluated in the real data. The two highest-scoring models were both based on Cox regression but used different feature selection approaches. We aggregated their predictions to create an ensemble model. Additionally, we refined the models after the DREAM challenge by eliminating phylum information. Models were also evaluated at intermediate timepoints and they predicted 10-year incident HF more accurately than models for 5- or 15-year incidence. We found that bacterial species, especially those linked to inflammation, are predictive of incident HF. This highlights the role of the gut microbiome as a potential driver of inflammation in HF pathophysiology. Our results provide insights into potential modeling strategies of microbiome data in prospective cohort studies. Overall, this study provides evidence that incorporating microbiome information into incident risk models can provide important biological insights into the pathogenesis of HF.}, } @article {pmid37873265, year = {2023}, author = {Chang, D and Gupta, VK and Hur, B and Cobo-López, S and Cunningham, KY and Han, NS and Lee, I and Kronzer, VL and Teigen, LM and Karnatovskaia, LV and Longbrake, EE and Davis, JM and Nelson, H and Sung, J}, title = {Gut Microbiome Wellness Index 2 for Enhanced Health Status Prediction from Gut Microbiome Taxonomic Profiles.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37873265}, support = {UL1 TR002494/TR/NCATS NIH HHS/United States ; }, abstract = {Recent advancements in human gut microbiome research have revealed its crucial role in shaping innovative predictive healthcare applications. We introduce Gut Microbiome Wellness Index 2 (GMWI2), an advanced iteration of our original GMWI prototype, designed as a robust, disease-agnostic health status indicator based on gut microbiome taxonomic profiles. Our analysis involved pooling existing 8069 stool shotgun metagenome data across a global demographic landscape to effectively capture biological signals linking gut taxonomies to health. GMWI2 achieves a cross-validation balanced accuracy of 80% in distinguishing healthy (no disease) from non-healthy (diseased) individuals and surpasses 90% accuracy for samples with higher confidence (i.e., outside the "reject option"). The enhanced classification accuracy of GMWI2 outperforms both the original GMWI model and traditional species-level α-diversity indices, suggesting a more reliable tool for differentiating between healthy and non-healthy phenotypes using gut microbiome data. Furthermore, by reevaluating and reinterpreting previously published data, GMWI2 provides fresh insights into the established understanding of how diet, antibiotic exposure, and fecal microbiota transplantation influence gut health. Looking ahead, GMWI2 represents a timely pivotal tool for evaluating health based on an individual's unique gut microbial composition, paving the way for the early screening of adverse gut health shifts. GMWI2 is offered as an open-source command-line tool, ensuring it is both accessible to and adaptable for researchers interested in the translational applications of human gut microbiome science.}, } @article {pmid37873088, year = {2023}, author = {Kirsch, JM and Hryckowian, AJ and Duerkop, BA}, title = {Insertion sequence driven evolution of the microbiota revealed by a novel metagenomics pipeline.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37873088}, support = {F31 AI169976/AI/NIAID NIH HHS/United States ; R01 AI141479/AI/NIAID NIH HHS/United States ; R35 GM150996/GM/NIGMS NIH HHS/United States ; T32 AI052066/AI/NIAID NIH HHS/United States ; }, abstract = {Insertion sequence (IS) elements are mobile genetic elements in bacterial genomes that support adaptation. We developed a database of IS elements coupled to a computational pipeline that identifies IS element insertions in the microbiota. We discovered that diverse IS elements insert into the genomes of intestinal bacteria regardless of human host lifestyle. These insertions targeted bacterial accessory genes that aid in their adaptation to unique environmental conditions. Using IS element expansion in Bacteroides, we show that IS element activity leads to insertion "hot spots" in accessory genes. We show that IS element insertions are stable and can be transferred between humans. Extreme environmental perturbations force IS element insertions to fall out of the microbiota and many fail to rebound following homeostasis. Our work shows that IS elements drive bacterial genome diversification within the microbiota and establishes a framework for understanding how strain level variation within the microbiota impacts human health.}, } @article {pmid37872759, year = {2023}, author = {Hurle, GR and Brainard, J and Tyler, KM}, title = {Microbiome diversity is a modifiable virulence factor for cryptosporidiosis.}, journal = {Virulence}, volume = {14}, number = {1}, pages = {2273004}, pmid = {37872759}, issn = {2150-5608}, mesh = {Animals ; Child ; Humans ; Child, Preschool ; *Cryptosporidiosis/parasitology ; *Cryptosporidium ; *Cryptosporidium parvum ; Bacteria/genetics ; *Gastrointestinal Microbiome ; Feces/parasitology ; }, abstract = {Cryptosporidium spp. infection causes significant disease in immunosuppressed individuals and children under the age of 5 years. The severity of the pathological presentation of cryptosporidiosis is a function of the host and parasite genotypes, host immune status, and the enteric environment or microbiome of the host. Cryptosporidiosis often presents with abdominal pain and severe diarrhoea and is associated with intestinal dysbiosis and inflammation. Our systematic analysis of the available literature revealed that bacterial diversity is reduced during infection in larger animal models, lending support to recent studies which indicate that the use of probiotics or the presence of a naturally diverse gut microbiome can prevent or minimise pathology caused by gastrointestinal pathogens. In summary, we present evidence that the presence of a diverse gut microbiome, natural or induced, reduces both symptomatic pathology and oocyst output.}, } @article {pmid37872584, year = {2023}, author = {Yang, Y and Hu, X and Cai, S and Hu, N and Yuan, Y and Wu, Y and Wang, Y and Mi, J and Liao, X}, title = {Pet cats may shape the antibiotic resistome of their owner's gut and living environment.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {235}, pmid = {37872584}, issn = {2049-2618}, mesh = {Animals ; Humans ; Cats ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial/genetics ; Aminoglycosides ; Tetracycline ; Enterobacteriaceae ; }, abstract = {BACKGROUND: Companion animals can contribute to the physical and mental health of people and often live in very close association with their owners. However, the antibiotic resistome carried by companion animals and the impact they have on their owners and living environment remain unclear. In this study, we compared the ARG profiles of cats, humans, and their living environments using metagenomic analysis to identify the core ARGs in the cat and human gut and explore the potential impact of cats on ARGs in the human gut through the environment.

RESULTS: Results showed that the abundance of ARGs in the cat gut was significantly higher than that in the human gut (P < 0.0001), with aminoglycoside and tetracycline resistance genes being the dominant ARGs in the cat gut. There was no significant difference in the abundance of total ARGs in the guts of cat owners and non-owners (P > 0.05). However, the abundance of aminoglycoside resistance genes including APH(2'')-IIa and AAC(6')-Im was significantly higher in cat owners than that in non-cat owners (P < 0.001). Also, ARG abundance was positively correlated with the frequency of cat activity in the living environment. Enterobacteriaceae was the dominant ARG host co-occurring in the cat gut, human gut, and living environment.

CONCLUSIONS: Our results show that cats may shape the living environment resistome and thus the composition of some ARGs in the human gut, highlighting the importance of companion animal environment health. Video Abstract.}, } @article {pmid37872569, year = {2023}, author = {Pochon, Z and Bergfeldt, N and Kırdök, E and Vicente, M and Naidoo, T and van der Valk, T and Altınışık, NE and Krzewińska, M and Dalén, L and Götherström, A and Mirabello, C and Unneberg, P and Oskolkov, N}, title = {aMeta: an accurate and memory-efficient ancient metagenomic profiling workflow.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {242}, pmid = {37872569}, issn = {1474-760X}, mesh = {Workflow ; *Metagenome ; *Metagenomics ; Archaeology ; DNA, Ancient ; }, abstract = {Analysis of microbial data from archaeological samples is a growing field with great potential for understanding ancient environments, lifestyles, and diseases. However, high error rates have been a challenge in ancient metagenomics, and the availability of computational frameworks that meet the demands of the field is limited. Here, we propose aMeta, an accurate metagenomic profiling workflow for ancient DNA designed to minimize the amount of false discoveries and computer memory requirements. Using simulated data, we benchmark aMeta against a current state-of-the-art workflow and demonstrate its superiority in microbial detection and authentication, as well as substantially lower usage of computer memory.}, } @article {pmid37872501, year = {2023}, author = {Ye, Z and He, J and Ji, H and Xu, H and Zhang, Y and Zhou, K and Liu, H}, title = {Case report: isolated prevotella intermedia causing intracranial infection detected using metagenomic next generation sequencing.}, journal = {BMC neurology}, volume = {23}, number = {1}, pages = {383}, pmid = {37872501}, issn = {1471-2377}, support = {2022ZA184//Traditional Chinese Medicine Health Science and Technology Plan Project of Zhejiang Province/ ; 22ywb54//Science and Technology Plan Project of Taizhou/ ; }, mesh = {Humans ; Female ; Middle Aged ; *High-Throughput Nucleotide Sequencing ; Base Composition ; Phylogeny ; Prevotella intermedia/genetics ; RNA, Ribosomal, 16S ; Sequence Analysis, DNA ; *Anti-Bacterial Agents/therapeutic use ; }, abstract = {BACKGROUND: Isolated Prevotella intermedia, a rare gram-negative, rod-shaped, anaerobic bacterium, is rarely detected in clinical practice. It has been associated with infections of the oral cavity and female genital tract, but has never been detected in cerebrospinal fluid (CSF) of patients in China. Accurate detection of causative pathogens is still an arduous task owing to the difficult conditions of anaerobic bacterial culture. Isolated Prevotella intermedia can be detected by metagenomic next generation sequencing (mNGS) of the CSF. Correct diagnosis and antibiotic treatment can help patients avoid life-threatening events.

CASE PRESENTATION: Herein, we describe the case of a 64-year-old Chinese woman who presented with typical features of meningoencephalitis. Routine CSF culture failed to identify the causative pathogen. Isolated Prevotella intermedia was detected by mNGS, and the patient was treated with antibacterial agents including ceftriaxone, vancomycin, moxifloxacin, meropenem, metronidazole, and linezolid. The patient underwent surgical treatment for abscess of left frontal parietal lobe, which was observed on magnetic resonance imaging (MRI) and was suspected to be caused by Prevotella intermedia. It was further confirmed that it was a secondary infection from the oral cavity, and the possible etiology might have been dental surgery. Treatment was rendered to the patient based on metagenomic test result, and her condition improved after two months.

CONCLUSIONS: This case highlights the role of mNGS in accurate diagnosis of patients with central nervous system infection. In particular, mNGS can be used to identify rare pathogens and confirm the diagnosis in patients with unknown etiology.}, } @article {pmid37872393, year = {2023}, author = {Li, Y and Xiong, L and Yu, H and Zeng, K and Wei, Y and Li, H and Zeng, W and Ji, X}, title = {Function and distribution of nitrogen-cycling microbial communities in the Napahai plateau wetland.}, journal = {Archives of microbiology}, volume = {205}, number = {11}, pages = {357}, pmid = {37872393}, issn = {1432-072X}, support = {(32160294, 31960033)//the National Natural Science Foundation of China/ ; }, mesh = {*Wetlands ; Phylogeny ; Nitrogen/metabolism ; Nitrates ; *Microbiota/genetics ; }, abstract = {Nitrogen is an essential component of living organisms and a major nutrient that limits life on Earth. Until now, freely available nitrogen mainly comes from atmospheric nitrogen, but most organisms rely on bioavailable forms of nitrogen, which depends on the complex network of microorganisms with a wide variety of metabolic functions. Microbial-mediated nitrogen cycling contributes to the biogeochemical cycling of wetlands, but its specific microbial abundance, composition, and distribution need to be studied. Based on the metagenomic data, we described the composition and functional characteristics of microbial nitrogen cycle-related genes in the Napahai plateau wetland. Six nitrogen cycling pathways existed, such as dissimilatory nitrate reduction, denitrification, nitrogen fixation, nitrification, anammox, and nitrate assimilation. Most genes related to the nitrogen cycling in this region come from bacteria, mainly from Proteobacteria and Acidobacteria. Habitat types and nitrogen cycle-related genes largely explained the relative abundance of total nitrogen pathways. Phylogenetic trees were constructed based on nitrogen cycle-related genes from different habitats and sources, combined with PCoA analysis, most of them clustered separately, indicating richness and uniqueness. Some microbial groups seemed to be special or general in the nitrogen cycling. In conclusion, it suggested that microorganisms regulated the N cycling process, and may lead to N loss throughout the wetland, thus providing a basis for further elucidation of the microbial regulation of N cycling processes and the Earth's elemental cycles.}, } @article {pmid37872094, year = {2023}, author = {Luan, YT and Liu, CH and Jiang, SL and Gu, HT and Lyu, J and Xing, F and Zhao, CQ and Yuan, JL and Liu, P and Mu, YP}, title = {[Comparative analysis of intestinal microbiota distribution characteristics based on metagenomics in patients with hepatitis B cirrhosis with or without ascites].}, journal = {Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology}, volume = {31}, number = {9}, pages = {974-985}, doi = {10.3760/cma.j.cn501113-20220830-00440}, pmid = {37872094}, issn = {1007-3418}, support = {81874390//National Natural Science Foundation of China/ ; shslczdzk01201//Shanghai Key Specialty of Traditional Chinese Clinical Medicine/ ; 21ZR1464100//Shanghai Natural Science Foundation/ ; 22S11901700//Special Project for Biomedical Science and Technology Support of the "Science and Technology Innovation Action Plan" of Shanghai Science and Technology Commission in 2022/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Ascites/complications ; RNA, Ribosomal, 16S/genetics ; Liver Cirrhosis/complications ; *Hepatitis B/complications ; Amino Acids ; }, abstract = {Objective: To use metagenomic sequencing to compare the differences in intestinal microbiota species and metabolic pathways in patients with hepatitis B cirrhosis with or without ascites and further explore the correlation between the differential microbiota and clinical indicators and metabolic pathways. Methods: 20 hepatitis B cirrhosis cases [10 without ascites (HBLC-WOA), 10 with ascites (HBLC-WA), and 5 healthy controls (HC)] were selected from the previously studied 16S rRNA samples. Metagenome sequencing was performed on the intestinal microbiota samples. The Kruskal-Wallis rank sum test and Spearman test were used to identify and analyse differential intestinal microbiota populations, metabolic pathways, and their correlations. Results: (1) The overall structure of the intestinal microbiota differed significantly among the three groups (R = 0.19, P = 0.018). The HC group had the largest abundance of Firmicutes and the lowest abundance of Proteobacteria at the genus level. Firmicutes abundance was significantly decreased (P(fdr) < 0.01), while Proteobacteria abundance was significantly increased (P(fdr) < 0.01) in patients with cirrhosis accompanied by ascites; (2) LEfSe analysis revealed that 29 intestinal microbiota (18 in the HBLC-WA group and 11 in the HBLC-WOA group) played a significant role in the disease group. The unclassified Enterobacteriaceae and Klebsiella species in the HBLC-WA group and Enterobacteriaceae in the HBLC-WOA group were positively correlated with the Child-Turcotte-Pugh (CTP) score, prothrombin time, and international normalized ratio score and negatively correlated with albumin and hemoglobin levels (P < 0.05). Escherichia and Shigella in the HBLC-WA group were positively correlated with CTP scores (P < 0.05); (3) The correlation analysis results between the KEGG pathway and 29 specific intestinal microbiota revealed that Enterobacteriaceae and arachidonic acid, α-linolenic acid, glycerolipid metabolism, and fatty acid degradation were positively correlated in the lipid metabolism pathway, while most Enterobacteriaceae were positively correlated with branched-chain amino acid degradation and negatively correlated with aromatic amino acid biosynthesis in the amino acid metabolic pathway. Conclusion: A significant increment of Enterobacteriaceae in the intestines of HBLC-WA patients influenced hepatic reserve function and was associated with amino acid and lipid metabolic pathways. Therefore, attention should be paid to controlling the intestinal microbiota to prevent complications and improve the prognosis in patients with hepatitis B cirrhosis, especially in those with ascites.}, } @article {pmid37871736, year = {2024}, author = {Chai, L and Song, Y and Chen, A and Jiang, L and Deng, H}, title = {Gut microbiota perturbations during larval stages in Bufo gargarizans tadpoles after Cu exposure with or without the presence of Pb.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {340}, number = {Pt 2}, pages = {122774}, doi = {10.1016/j.envpol.2023.122774}, pmid = {37871736}, issn = {1873-6424}, mesh = {Animals ; Larva ; *Gastrointestinal Microbiome ; Lead/toxicity ; Bufonidae ; Bacteria ; }, abstract = {Cu and Pb are ubiquitous environmental contaminants, but there is limited information on their potential impacts on gut microbiota profile in anuran amphibians at different developmental stages during metamorphosis. In this study, Bufo gargarizans tadpoles were chronically exposed to Cu alone or Cu combined with Pb from Gs26 throughout metamorphosis. Morphology of tadpoles, histological characteristic and bacterial community of intestines were evaluated at three developmental stages: Gs33, Gs36, and Gs42. Results showed that Cu and Cu + Pb exposure caused various degrees of morphological and histological changes in guts at tested three stages. In addition, bacterial richness and diversity in tadpoles especially at Gs33 and Gs42 were disturbed by Cu and Cu + Pb. Beta diversity demonstrated that the bacterial community structures were influenced by both heavy metals exposure and developmental stages. Alterations in taxonomic composition were characterized by increased abundance of Proteobacteria and Firmicutes, reduction of Fusobacteriota, as well as decreased Cetobacterium and increased C39 at all three stages. Overall, response of gut bacterial diversity and composition to Cu stress depends on the developmental stage, while the altered patterns of bacterial community at Cu stress could be modified further by the presence of Pb. Moreover, predicted metabolic disorders were associated with shifts in bacterial community, but needs integrated information from metagenomic and metatranscriptomic analyses. These results contribute to the growing body of research about potential ecotoxicological effects of heavy metals on amphibian gut microbiota during metamorphosis.}, } @article {pmid37871727, year = {2023}, author = {Zhao, H and Zhao, Y and Yan, N and Wang, Y and Li, W and Zhao, J and Xu, Y and Tang, H and Liu, X}, title = {Metagenomic next-generation sequencing of bronchoalveolar lavage fluid in non-severe and severe pneumonia patients.}, journal = {Journal of microbiological methods}, volume = {215}, number = {}, pages = {106848}, doi = {10.1016/j.mimet.2023.106848}, pmid = {37871727}, issn = {1872-8359}, mesh = {Humans ; Bronchoalveolar Lavage Fluid ; *High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents ; Metagenome ; Metagenomics ; *Pneumonia/diagnosis ; Sensitivity and Specificity ; }, abstract = {Metagenomic next-generation sequencing (mNGS) is widely used as a more promising technology than conventional tests. However, its clinical utility in the context of bronchoalveolar lavage fluid (BALF) samples for discriminating between non-severe and severe pneumonia is not well established. Thus, this study aimed to investigate the diagnostic performance of mNGS on BALF samples from 100 individuals suspected of pneumonia, and compared it with conventional microbiological tests (CMT) of BALF samples and the final clinical diagnosis. Twenty-seven cases of non-severe pneumonia and 73 cases of severe pneumonia patients were finally clinically diagnosed. Among 100 cases, diagnostic performance of mNGS and culture showed a significant difference; 65 cases had the same sample types, of which 25 cases were diagnosed as positive by mNGS only (38.46%) and 1 was diagnosed as positive by culture only (1.54%). Moreover, 24 cases were diagnosed positive in both mNGS and culture (36.92%) and 15 cases tested negative in both mNGS and culture (23.08%). Among 35 cases, 28 out of 35 cases were diagnosed as positive by mNGS, while only 4 out of 35 cases were diagnosed as positive by the indirect immunofluorescence method (IIFT). In addition, the positive rate of mNGS was higher than that of culture in cases regardless of prior antibiotic exposure. Mixed pathogens were found to be significantly more prevalent in severe pneumonia patients than in non-severe pneumonia patients. Importantly, among 38 cases who were diagnosed solely by mNGS, 25 patients experienced an improved outcome after physicians changed the therapy according to the mNGS results. In conclusion, the results showed that mNGS of BALF represents a potentially effective tool for detection of mixed pathogens in severe pneumonia.}, } @article {pmid37871447, year = {2023}, author = {Wu, C and Yu, X and Gai, W and Liu, Y and Qi, Y and Zheng, Y and Zhang, N and Cai, X and Li, G and Chen, B}, title = {Diagnostic value of plasma and blood cells metagenomic next-generation sequencing in patients with sepsis.}, journal = {Biochemical and biophysical research communications}, volume = {683}, number = {}, pages = {149079}, doi = {10.1016/j.bbrc.2023.10.011}, pmid = {37871447}, issn = {1090-2104}, mesh = {Humans ; Prospective Studies ; Reproducibility of Results ; *Sepsis/diagnosis ; Blood Cells ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Several studies have investigated the detection of plasma cell-free DNA (cfDNA) using metagenomic next-generation sequencing (mNGS). However, to our knowledge, no study has evaluated the diagnostic value of mNGS detection using blood cells. In this study, we aimed to evaluate the performance of a whole blood mNGS assay which includes the results of plasma and blood cells mNGS detection.

METHODS: We selected a panel of seven microorganisms to validate both the plasma and blood cells assay for their limits of detection (LoD), linearity, precision, and robustness to interference. In a multicentered prospective study conducted from January 2021 to April 2022, we tested 253 septic patients with plasma and blood cells mNGS and compared it with blood cultures (BCs). The performance of pathogen detection was compared between mNGS and BCs.

RESULTS: The LoD for plasma and blood cells mNGS was 8.3-140 genome equivalents (GE)/mL and 26 to 534 colony-forming units (CFU) or copies/mL, respectively. The inter- and intra-assay reproducibility of both plasma and blood cells mNGS was 100%. Compared to plasma mNGS alone, the sensitivity of whole blood mNGS was increased by 18.04% when using BCs as the standard (67.21% vs 85.25%). Furthermore, the sensitivity of whole blood mNGS in diagnosing bloodstream infections (BSIs) was 85.21%, which was significantly higher than that of BCs (36.09%, P＜0.0001) and plasma mNGS (69.82%; P = 0.0007). Additional analysis showed that blood cells mNGS was able to detect bacteria missed by plasma mNGS, while plasma mNGS was effective at detecting viruses.

CONCLUSIONS: Our findings indicate that whole blood mNGS shows great potential as a promising diagnostic technique for BSIs owing to its ability to identify pathogens with higher sensitivity.}, } @article {pmid37871442, year = {2024}, author = {Tiwari, N and Santhiya, D and Sharma, JG}, title = {Significance of landfill microbial communities in biodegradation of polyethylene and nylon 6,6 microplastics.}, journal = {Journal of hazardous materials}, volume = {462}, number = {}, pages = {132786}, doi = {10.1016/j.jhazmat.2023.132786}, pmid = {37871442}, issn = {1873-3336}, mesh = {*Microplastics/metabolism ; Polyethylene/chemistry ; Plastics/chemistry ; *Microbiota ; Waste Disposal Facilities ; Biodegradation, Environmental ; }, abstract = {Plastic pollution, particularly microplastics, poses a significant environmental challenge. This study aimed to address the urgent need for sustainable solutions to manage plastic waste. The degradation of polyethylene microplastics (PEMPs) and nylon 6,6 microplastics (NMPs) were investigated using bacterial culture isolates, isolated from a municipal landfill site and identified through 16 S rDNA as well as metagenomics techniques.The study demonstrated for the first time along with degradation mechanism. The isolates identified as Achromobacter xylosoxidans and mixed culture species in dominance of Pulmonis sp. were used to degrade PEMPs and NMPs. Achromobacter xylosoxidans reduced microplastic's dry weight by 26.7% (PEMPs) and 21.3% (NMPs) in 40 days, while the mixed culture achieved weight reductions of 19.3% (PEMPs) and 20% (NMPs). The release of enzymes, laccase and peroxidases revealed C-C bond cleavage and reduced polymer chain length. The thermal studies (TGA and DSC) revealed changes in the thermal stability and transition characteristics of microplastics. The structural alterations on PEMPs and NMPs were recorded by FTIR analysis. Byproducts such as alkanes, esters, aromatic compounds and carboxylic acids released were identified by GC-MS. These results suggest the effectiveness of bacterial isolates in degrading PEMPs and NMPs, with potential for sustainable plastic waste management solutions.}, } @article {pmid37871298, year = {2023}, author = {Kolodnitsky, AS and Ionov, NS and Rudik, AV and Filimonov, DA and Poroikov, VV}, title = {HGMMX: Host Gut Microbiota Metabolism Xenobiotics Database.}, journal = {Journal of chemical information and modeling}, volume = {63}, number = {21}, pages = {6463-6468}, doi = {10.1021/acs.jcim.3c00837}, pmid = {37871298}, issn = {1549-960X}, mesh = {Humans ; *Gastrointestinal Microbiome ; Xenobiotics/chemistry/metabolism/pharmacology ; *Microbiota ; Biotransformation ; Databases, Factual ; }, abstract = {The metagenome of bacteria colonizing the human intestine is a set of genes that is almost 150 times greater than the set of host genes. Some of these genes encode enzymes whose functioning significantly expands the number of potential pathways for xenobiotic metabolism. The resulting metabolites can exhibit activity different from that of the parent compound. This can decrease the efficacy of pharmacotherapy as well as induce undesirable and potentially life-threatening side effects. Thus, analysis of the biotransformation of small drug-like compounds mediated by the gut microbiota is an important step in the development of new pharmaceutical agents and repurposing of the approved drugs. In vitro research, the interaction of drug-like compounds with the gut microbiota is a multistep and time-consuming process. Systematic testing of large sets of chemical structures is associated with a number of challenges, including the lack of standardized techniques and significant financial costs to identify the structure of the final metabolites. Estimation of the compounds' ability to be biotransformed by the gut microbiota and prediction of the structures of their metabolites are possible in silico. However, the development of computational approaches is limited by the lack of information about chemical structures metabolized by microbiota enzymes. The aim of this study is to create a database containing information on the metabolism of drug-like compounds by the gut microbiota. We created the data set containing information about 368 structures metabolized and 310 structures not metabolized by the human gut microbiota. The HGMMX database is freely available at https://www.way2drug.com/hgmmx. The information presented will be useful in the development of computational approaches for analyzing the impact of the human microbiota on metabolism of drug-like molecules.}, } @article {pmid37870692, year = {2023}, author = {Camacho, J and Negredo, A and Carrilero, B and Segovia, M and Moreno, A and Pozo, F and Echevarría, JE and Echevarría, JM and Sánchez-Seco, MP and Tarragó, D}, title = {Mutations in Coding and Non-Coding Regions in Varicella-Zoster Virus Causing Fatal Hemorrhagic Fever Without Rash in an Immunocompetent Patient: Case Report.}, journal = {Infectious diseases and therapy}, volume = {12}, number = {11}, pages = {2621-2630}, pmid = {37870692}, issn = {2193-8229}, support = {MPY1372/12//Instituto de Salud Carlos III/ ; }, abstract = {INTRODUCTION: We report the case of a fatal hemorrhagic varicella primary infection in an immunocompetent man and whole-genome characterization of the virus for the investigation of biomarkers of virulence.

CASE: A 38-year-old patient born in Nigeria presented to the emergency department with abdominal pain and subsequently developed fatal hemorrhagic disease without skin rash. Extensive laboratory tests including serology and PCR for arenaviruses, bunyaviruses and ebolaviruses were negative. Varicella-zoster virus (VZV) PCR of sera, liver and spleen tissue samples from autopsy revealed the presence of VZV DNA. Primary infection by varicella-zoster virus with hemorrhagic manifestations was diagnosed after virological testing. The VZV genome was sequenced using a mWGS approach. Bioinformatic analysis showed 53 mutations across the genome, 33 of them producing non-synonymous variants affecting up to 14 genes. Some of them, such as ORF11 and ORF 62, encoded for essential functions related to skin or neurotropism. To our knowledge, the mutations reported here have never been described in a VZV causing such a devastating outcome.

DISCUSSION: In immunocompetent patients, viral factors should be considered in patients with uncommon symptoms or severe diseases. Some relevant mutations revealed by using whole genome sequencing (WGS) directly from clinical samples may be involved in this case and deserves further investigation.

CONCLUSION: Differential diagnosis of varicella-zoster virus in immunocompetent adults should be considered among patients with suspected VHF, even if the expected vesicular rash is not present at admission and does not arise thereafter. Whole genome sequencing of strains causing uncommon symptoms and/or mortality is needed for epidemiological surveillance and further characterization of putative markers of virulence. Additionally, this report highlights the recommendation for a VZV vaccination policy in non-immunized migrants from developing countries.}, } @article {pmid37870180, year = {2023}, author = {Zhang, Q and Xu, N and Lei, C and Chen, B and Wang, T and Ma, Y and Lu, T and Penuelas, J and Gillings, M and Zhu, YG and Fu, Z and Qian, H}, title = {Metagenomic Insight into The Global Dissemination of The Antibiotic Resistome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {10}, number = {33}, pages = {e2303925}, pmid = {37870180}, issn = {2198-3844}, support = {2022YFD1700400//National Key Research and Development Program of China/ ; 21976161//National Natural Science Foundation of China/ ; 22376187//National Natural Science Foundation of China/ ; 42307158//National Natural Science Foundation of China/ ; LZ23B070001//Natural Science Foundation of Zhejiang Province/ ; TED2021-132627B-I00//Department of Local Government, Sport and cultural industries/ ; }, mesh = {Animals ; Humans ; *Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Metagenome/genetics ; Feces ; }, abstract = {The global crisis in antimicrobial resistance continues to grow. Estimating the risks of antibiotic resistance transmission across habitats is hindered by the lack of data on mobility and habitat-specificity. Metagenomic samples of 6092 are analyzed to delineate the unique core resistomes from human feces and seven other habitats. This is found that most resistance genes (≈85%) are transmitted between external habitats and human feces. This suggests that human feces are broadly representative of the global resistome and are potentially a hub for accumulating and disseminating resistance genes. The analysis found that resistance genes with ancient horizontal gene transfer (HGT) events have a higher efficiency of transfer across habitats, suggesting that HGT may be the main driver for forming unique but partly shared resistomes in all habitats. Importantly, the human fecal resistome is historically different and influenced by HGT and age. The most important routes of cross-transmission of resistance are from the atmosphere, buildings, and animals to humans. These habitats should receive more attention for future prevention of antimicrobial resistance. The study will disentangle transmission routes of resistance genes between humans and other habitats in a One Health framework and can identify strategies for controlling the ongoing dissemination and antibiotic resistance.}, } @article {pmid37869650, year = {2023}, author = {Ibrahimi, E and Lopes, MB and Dhamo, X and Simeon, A and Shigdel, R and Hron, K and Stres, B and D'Elia, D and Berland, M and Marcos-Zambrano, LJ}, title = {Overview of data preprocessing for machine learning applications in human microbiome research.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1250909}, pmid = {37869650}, issn = {1664-302X}, abstract = {Although metagenomic sequencing is now the preferred technique to study microbiome-host interactions, analyzing and interpreting microbiome sequencing data presents challenges primarily attributed to the statistical specificities of the data (e.g., sparse, over-dispersed, compositional, inter-variable dependency). This mini review explores preprocessing and transformation methods applied in recent human microbiome studies to address microbiome data analysis challenges. Our results indicate a limited adoption of transformation methods targeting the statistical characteristics of microbiome sequencing data. Instead, there is a prevalent usage of relative and normalization-based transformations that do not specifically account for the specific attributes of microbiome data. The information on preprocessing and transformations applied to the data before analysis was incomplete or missing in many publications, leading to reproducibility concerns, comparability issues, and questionable results. We hope this mini review will provide researchers and newcomers to the field of human microbiome research with an up-to-date point of reference for various data transformation tools and assist them in choosing the most suitable transformation method based on their research questions, objectives, and data characteristics.}, } @article {pmid37868933, year = {2023}, author = {Xin, G and Kuang, Q and Le, S and Wu, W and Gao, Q and Gao, H and Xu, Z and Zheng, Z and Lu, G and Gong, L and Wang, H and Zhang, G and Shi, M and Sun, Y}, title = {Origin, genomic diversity and evolution of African swine fever virus in East Asia.}, journal = {Virus evolution}, volume = {9}, number = {2}, pages = {vead060}, pmid = {37868933}, issn = {2057-1577}, abstract = {Since 2018, the outbreaks of genotype II African swine fever virus (ASFV) in China and several eastern Asian countries have caused a huge impact on the local swine industry, resulting in huge economic losses. However, little is known about the origin, genomic diversity, evolutionary features, and epidemiological history of the genotype II ASFV. Here, 14 high-quality complete genomes of ASFVs were generated via sequencing of samples collected from China over the course of 3 years, followed by phylogenetic and phylodynamic analyses. The strains identified were relatively homogeneous, with a total of 52 SNPs and 11 indels compared with the prototype strain HLJ/2018, among which there were four exceptionally large deletions (620-18,023 nt). Evolutionary analyses revealed that ASFV strains distributed in eastern Asia formed a monophyly and a 'star-like' structure centered around the prototype strain, suggesting a single origin. Additionally, phylogenetic network analysis and ancestral reconstruction of geographic state indicated that genotype II ASFV strains in eastern Asia likely originated from Western Europe. Overall, these results contribute to the understanding of the history and current status of genotype II ASFV strains in eastern Asian, which could be of considerable importance in disease control and prevention.}, } @article {pmid37867968, year = {2023}, author = {Gao, J and Yi, X and Wang, Z}, title = {The application of multi-omics in the respiratory microbiome: Progresses, challenges and promises.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {4933-4943}, pmid = {37867968}, issn = {2001-0370}, abstract = {The study of the respiratory microbiome has entered a multi-omic era. Through integrating different omic data types such as metagenome, metatranscriptome, metaproteome, metabolome, culturome and radiome surveyed from respiratory specimens, holistic insights can be gained on the lung microbiome and its interaction with host immunity and inflammation in respiratory diseases. The power of multi-omics have moved the field forward from associative assessment of microbiome alterations to causative understanding of the lung microbiome in the pathogenesis of chronic, acute and other types of respiratory diseases. However, the application of multi-omics in respiratory microbiome remains with unique challenges from sample processing, data integration, and downstream validation. In this review, we first introduce the respiratory sample types and omic data types applicable to studying the respiratory microbiome. We next describe approaches for multi-omic integration, focusing on dimensionality reduction, multi-omic association and prediction. We then summarize progresses in the application of multi-omics to studying the microbiome in respiratory diseases. We finally discuss current challenges and share our thoughts on future promises in the field.}, } @article {pmid37867962, year = {2023}, author = {Bárdy, P and MacDonald, CIW and Pantůček, R and Antson, AA and Fogg, PCM}, title = {Jorvik: A membrane-containing phage that will likely found a new family within Vinavirales.}, journal = {iScience}, volume = {26}, number = {11}, pages = {108104}, pmid = {37867962}, issn = {2589-0042}, abstract = {Although membrane-containing dsDNA bacterial viruses are some of the most prevalent predators in aquatic environments, we know little about how they function due to their intractability in the laboratory. Here, we have identified and thoroughly characterized a new type of membrane-containing bacteriophage, Jorvik, that infects the freshwater mixotrophic model bacterium Rhodobacter capsulatus. Jorvik is extremely virulent, can persist in the host integrated into the RuBisCo operon and encodes two experimentally verified cell wall hydrolases. Jorvik-like prophages are abundant in the genomes of Alphaproteobacteria, are distantly related to known viruses of the class Tectiliviricetes, and we propose they should be classified as a new family. Crucially, we demonstrate how widely used phage manipulation methods should be adjusted to prevent loss of virus infectivity. Our thorough characterization of environmental phage Jorvik provides important experimental insights about phage diversity and interactions in microbial communities that are often unexplored in common metagenomic analyses.}, } @article {pmid37867065, year = {2023}, author = {Brookes, Z and Teoh, L and Cieplik, F and Kumar, P}, title = {Mouthwash Effects on the Oral Microbiome: Are They Good, Bad, or Balanced?.}, journal = {International dental journal}, volume = {73 Suppl 2}, number = {Suppl 2}, pages = {S74-S81}, pmid = {37867065}, issn = {1875-595X}, mesh = {Humans ; Mouthwashes/pharmacology ; Chlorhexidine/pharmacology ; Mouth ; *Anti-Infective Agents ; Bacteria ; *Microbiota ; }, abstract = {This narrative review describes the oral microbiome, and its role in oral health and disease, before considering the impact of commonly used over-the-counter (OTC) mouthwashes on oral bacteria, viruses, bacteriophages, and fungi that make up these microbial communities in different niches of the mouth. Whilst certain mouthwashes have proven antimicrobial actions and clinical effectiveness supported by robust evidence, this review reports more recent metagenomics evidence, suggesting that mouthwashes such as chlorhexidine may cause "dysbiosis," whereby certain species of bacteria are killed, leaving others, sometimes unwanted, to predominate. There is little known about the effects of mouthwashes on fungi and viruses in the context of the oral microbiome (virome) in vivo, despite evidence that they "kill" certain viral pathogens ex vivo. Evidence for mouthwashes, much like antibiotics, is also emerging with regards to antimicrobial resistance, and this should further be considered in the context of their widespread use by clinicians and patients. Therefore, considering the potential of currently available OTC mouthwashes to alter the oral microbiome, this article finally proposes that the ideal mouthwash, whilst combatting oral disease, should "balance" antimicrobial communities, especially those associated with health. Which antimicrobial mouthwash best fits this ideal remains uncertain.}, } @article {pmid37866373, year = {2023}, author = {Schwartz, DJ and Langdon, A and Sun, X and Langendorf, C and Berthé, F and Grais, RF and Trehan, I and Isanaka, S and Dantas, G}, title = {Effect of amoxicillin on the gut microbiome of children with severe acute malnutrition in Madarounfa, Niger: a retrospective metagenomic analysis of a placebo-controlled trial.}, journal = {The Lancet. Microbe}, volume = {4}, number = {11}, pages = {e931-e942}, pmid = {37866373}, issn = {2666-5247}, support = {R01 GM099538/GM/NIGMS NIH HHS/United States ; 2021081/DDCF/Doris Duke Charitable Foundation/United States ; R01 AI123394/AI/NIAID NIH HHS/United States ; TL1 TR000449/TR/NCATS NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; K08 AI159384/AI/NIAID NIH HHS/United States ; }, mesh = {Child, Preschool ; Humans ; Infant ; Amoxicillin/pharmacology ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/genetics ; Niger ; Randomized Controlled Trials as Topic ; Retrospective Studies ; *Severe Acute Malnutrition/drug therapy ; }, abstract = {BACKGROUND: Children with severe acute malnutrition are treated with antibiotics as outpatients. We aimed to determine the effect of 7 days of amoxicillin on acute and long-term changes to the gut microbiome and antibiotic resistome in children treated for severe acute malnutrition.

METHODS: We conducted a secondary analysis of a randomised, double-blinded, placebo-controlled trial (NCT01613547) of amoxicillin in children (aged 6-59 months) with severe acute malnutrition treated as outpatients in Madarounfa, Niger. We randomly selected 161 children from the overall cohort (n=2399) for initial 12-week follow-up from Sept 23, 2013 to Feb 3, 2014. We selected a convenience sample of those 161 children, on the basis of anthropometric measures, for follow-up 2 years later (Sept 28 to Oct 27, 2015). Children provided faecal samples at baseline, week 1, week 4, week 8, week 12, and, for those in the 2-year follow-up cohort, week 104. We conducted metagenomic sequencing followed by microbiome and resistome profiling of faecal samples. 38 children without severe acute malnutrition and six children with severe acute malnutrition matching the baseline ages of the original cohort were used as reference controls.

FINDINGS: In the 12-week follow-up group, amoxicillin led to an immediate decrease in gut microbiome richness from 37·6 species (95% CI 32·6-42·7) and Shannon diversity index (SDI) 2·18 (95% CI 1·97-2·39) at baseline to 27·7 species (95% CI 22·9-32·6) species and SDI 1·55 (95% CI 1·35-1·75) at week 1. Amoxicillin increased gut antibiotic resistance gene abundance to 6044 reads per kilobase million (95% CI 4704-7384) at week 1, up from 4800 (3391-6208) at baseline, which returned to baseline 3 weeks later. 35 children were included in the 2-year follow-up; the amoxicillin-treated children (n=22) had increased number of species in the gut microbiome compared with placebo-treated children (n=13; 60·7 [95% CI 54·7-66·6] vs 36·9 [29·4-44·3]). Amoxicillin-treated children had increased Prevotella spp and decreased Bifidobacterium spp relative to age-matched placebo-treated children, indicating a more mature, adult-like microbiome.

INTERPRETATION: Amoxicillin treatment led to acute but not sustained increases in antimicrobial resistance genes and improved gut microbiome maturation 2 years after severe acute malnutrition treatment.

FUNDING: Bill & Melinda Gates Foundation; Médecins sans Frontières Operational Center Paris; National Institute of Allergy and Infectious Diseases; National Institute of General Medical Sciences; Eunice Kennedy Shriver National Institute of Child Health and Human Development; Edward Mallinckrodt Jr Foundation; Doris Duke Foundation.}, } @article {pmid37866247, year = {2023}, author = {Kleikamp, HBC and Grouzdev, D and Schaasberg, P and van Valderen, R and van der Zwaan, R and Wijgaart, RV and Lin, Y and Abbas, B and Pronk, M and van Loosdrecht, MCM and Pabst, M}, title = {Metaproteomics, metagenomics and 16S rRNA sequencing provide different perspectives on the aerobic granular sludge microbiome.}, journal = {Water research}, volume = {246}, number = {}, pages = {120700}, doi = {10.1016/j.watres.2023.120700}, pmid = {37866247}, issn = {1879-2448}, mesh = {*Sewage/chemistry ; RNA, Ribosomal, 16S/genetics ; Bioreactors ; *Microbiota ; Metagenome ; Metagenomics/methods ; }, abstract = {The tremendous progress in sequencing technologies has made DNA sequencing routine for microbiome studies. Additionally, advances in mass spectrometric techniques have extended conventional proteomics into the field of microbial ecology. However, systematic studies that provide a better understanding of the complementary nature of these 'omics' approaches, particularly for complex environments such as wastewater treatment sludge, are urgently needed. Here, we describe a comparative metaomics study on aerobic granular sludge from three different wastewater treatment plants. For this, we employed metaproteomics, whole metagenome, and 16S rRNA amplicon sequencing to study the same granule material with uniform size. We furthermore compare the taxonomic profiles using the Genome Taxonomy Database (GTDB) to enhance the comparability between the different approaches. Though the major taxonomies were consistently identified in the different aerobic granular sludge samples, the taxonomic composition obtained by the different omics techniques varied significantly at the lower taxonomic levels, which impacts the interpretation of the nutrient removal processes. Nevertheless, as demonstrated by metaproteomics, the genera that were consistently identified in all techniques cover the majority of the protein biomass. The established metaomics data and the contig classification pipeline are publicly available, which provides a valuable resource for further studies on metabolic processes in aerobic granular sludge.}, } @article {pmid37866246, year = {2023}, author = {Zheng, CW and Luo, YH and Lai, YS and Ilhan, ZE and Ontiveros-Valencia, A and Krajmalnik-Brown, R and Jin, Y and Gu, H and Long, X and Zhou, D and Rittmann, BE}, title = {Identifying biodegradation pathways of cetrimonium bromide (CTAB) using metagenome, metatranscriptome, and metabolome tri-omics integration.}, journal = {Water research}, volume = {246}, number = {}, pages = {120738}, doi = {10.1016/j.watres.2023.120738}, pmid = {37866246}, issn = {1879-2448}, mesh = {Cetrimonium ; *Metagenome ; Cetrimonium Compounds ; Metabolome ; *Environmental Pollutants ; }, abstract = {Traditional research on biodegradation of emerging organic pollutants involves slow and labor-intensive experimentation. Currently, fast-developing metagenome, metatranscriptome, and metabolome technologies promise to expedite mechanistic research on biodegradation of emerging organic pollutants. Integrating the metagenome, metatranscriptome, and metabolome (i.e., tri-omics) makes it possible to link gene abundance and expression with the biotransformation of the contaminant and the formation of metabolites from this biotransformation. In this study, we used this tri-omics approach to study the biotransformation pathways for cetyltrimethylammonium bromide (CTAB) under aerobic conditions. The tri-omics analysis showed that CTAB undergoes three parallel first-step mono-/di-oxygenations (to the α, β, and ω-carbons); intermediate metabolites and expressed enzymes were identified for all three pathways, and the β-carbon mono-/di-oxygenation is a novel pathway; and the genes related to CTAB biodegradation were associated with Pseudomonas spp. Four metabolites - palmitic acid, trimethylamine N-oxide (TMAO), myristic acid, and betaine - were the key identified biodegradation intermediates of CTAB, and they were associated with first-step mono-/di-oxygenations at the α/β-C. This tri-omics approach with CTAB demonstrates its power for identifying promising paths for future research on the biodegradation of complex organics by microbial communities.}, } @article {pmid37866244, year = {2023}, author = {Hu, X and Yue, J and Yao, D and Zhang, X and Li, Y and Hu, Z and Liang, S and Wu, H and Xie, H and Zhang, J}, title = {Plant development alters the nitrogen cycle in subsurface flow constructed wetlands: Implications to the strategies for intensified treatment performance.}, journal = {Water research}, volume = {246}, number = {}, pages = {120750}, doi = {10.1016/j.watres.2023.120750}, pmid = {37866244}, issn = {1879-2448}, mesh = {*Wetlands ; Denitrification ; Nitrogen Cycle ; *Microbiota ; Nitrogen ; Plant Development ; Waste Disposal, Fluid/methods ; }, abstract = {Plant development greatly influences the composition structure and functions of microbial community in constructed wetlands (CWs) via plant root activities. However, our knowledge of the effect of plant development on microbial nitrogen (N) cycle is poorly understood. Here, we investigated the N removal performance and microbial structure in subsurface flow CWs at three time points corresponding to distinct stages of plant development: seedling, mature and wilting. Overall, the water parameters were profoundly affected by plant development with the increased root activities including radial oxygen loss (ROL) and root exudates (REs). The removal efficiency of NH4[+]-N was significantly highest at the mature stage (p < 0.01), while the removal performance of NO3[-]-N at the seedling stage. The highest relative abundances of nitrification- and anammox-related microbes (Nitrospira, Nitrosomonas, and Candidatus Brocadia, etc.) and functional genes (Amo, Hdh, and Hzs) were observed in CWs at the mature stage, which can be attributed to the enhanced intensity of ROL, creating micro-habitat with high DO concentration. On the other hand, the highest relative abundances of denitrification- and DNRA-related microbes (Petrimonas, Geobacter, and Pseudomonas, etc.) and functional genes (Nxr, Nir, and Nar, etc.) were observed in CWs at the seedling and wilting stages, which can be explained by the absence of ROL and biological denitrification inhibitor derived from REs. Results give insights into microbial N cycle in CWs with different stages of plant development. More importantly, a potential solution for intensified N removal via the combination of practical operation and natural regulation is proposed.}, } @article {pmid37866200, year = {2023}, author = {Wang, X and Sun, T and Yan, S and Chen, S and Zhang, Y}, title = {Sediment microbial community characteristics in sea cucumber restocking area.}, journal = {Marine environmental research}, volume = {192}, number = {}, pages = {106233}, doi = {10.1016/j.marenvres.2023.106233}, pmid = {37866200}, issn = {1879-0291}, mesh = {Animals ; Humans ; Geologic Sediments/chemistry ; *Sea Cucumbers/microbiology ; *Microbiota ; Bacteria ; Water ; Nitrogen ; }, abstract = {Variations of microbial species and functional composition in coastal sediment are usually taken as the results of the provision of supplementary nutrients affected by human activities. However, responses of microbiome stability to restocking biological resources remain less understood in coastal benthic systems without nutrient supplements. Here, combined with metagenomics and microbiome co-occurrence networks, the composition, function, and community stability of microbes were evaluated in a coastal area where sea cucumbers (Apostichopus japonicus) restocked after six months. Also, the physicochemical characteristics of sediments and bottom water were analyzed. We found the total organic carbon, total nitrogen, and total phosphorus of sediment did not change significantly in the restocking area after six months, whereas the concentration of dissolved inorganic nitrogen in bottom water increased significantly. Moreover, the relative abundance of Nitrospina at the class level was increased significantly in the restocking area. Also, enzymes related to nitrate reduction and nitrous oxide reductase were increased in the restocking area. Of note, stock enhancement of sea cucumbers altered associations between bacteria rather than their composition. The elimination of negative associations and reduction of the potential keystone taxa in the restocking area indicated destabilized bacterial communities. Our work may contribute to elucidating the response of microbial stability to stock enhancement. This finding also suggests that microbial community stability can be considered as an indicator of ecological risk under the influence of stock enhancement.}, } @article {pmid37865678, year = {2023}, author = {Líndez, PP and Johansen, J and Kutuzova, S and Sigurdsson, AI and Nissen, JN and Rasmussen, S}, title = {Adversarial and variational autoencoders improve metagenomic binning.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {1073}, pmid = {37865678}, issn = {2399-3642}, mesh = {*Metagenome ; *Genome, Microbial ; Metagenomics/methods ; Cluster Analysis ; Benchmarking ; }, abstract = {Assembly of reads from metagenomic samples is a hard problem, often resulting in highly fragmented genome assemblies. Metagenomic binning allows us to reconstruct genomes by re-grouping the sequences by their organism of origin, thus representing a crucial processing step when exploring the biological diversity of metagenomic samples. Here we present Adversarial Autoencoders for Metagenomics Binning (AAMB), an ensemble deep learning approach that integrates sequence co-abundances and tetranucleotide frequencies into a common denoised space that enables precise clustering of sequences into microbial genomes. When benchmarked, AAMB presented similar or better results compared with the state-of-the-art reference-free binner VAMB, reconstructing ~7% more near-complete (NC) genomes across simulated and real data. In addition, genomes reconstructed using AAMB had higher completeness and greater taxonomic diversity compared with VAMB. Finally, we implemented a pipeline Integrating VAMB and AAMB that enabled improved binning, recovering 20% and 29% more simulated and real NC genomes, respectively, compared to VAMB, with moderate additional runtime.}, } @article {pmid37865320, year = {2024}, author = {Wang, G and Sun, C and Fu, P and Zhang, B and Zhu, J and Li, Q and Zhang, J and Chen, R}, title = {Mechanistic insights into synergistic facilitation of copper/zinc ions and dewatered swine manure-derived biochar on anaerobic digestion of swine wastewater.}, journal = {Environmental research}, volume = {240}, number = {Pt 2}, pages = {117429}, doi = {10.1016/j.envres.2023.117429}, pmid = {37865320}, issn = {1096-0953}, mesh = {Animals ; Swine ; Anaerobiosis ; *Copper ; *Manure ; Wastewater ; Ions ; Methane ; Zinc ; }, abstract = {Biochar-assisted anaerobic digestion (AD) has been proposed an advanced system for swine wastewater (SW) management. However, the effects of metallic nutrients in SW, such as copper/zinc ions (Cu[2+]/Zn[2+]), on the biochar-assisted AD of SW are not well understood. This study investigated the influences of individual Cu[2+]/Zn[2+] or dewatered swine manure-derived biochar, as well as their combined additions, on the AD of SW. The results showed that exposure to 50 mg/L Cu[2+]/Zn[2+] temporary inhibited methane production, but the addition of 20 g/L biochar alleviated this inhibition by shortening the methanogenic lag time and increasing methane yield. Following a period of acclimation, both Cu[2+]/Zn[2+] and biochar promoted methane production, although metagenomic analysis revealed distinct mechanisms underlying their promotion. Cu[2+]/Zn[2+] enhanced ATP processing, including electron exchange between NADH/NAD[+] and succinate/fumarate transformation, by 26.0-35.8%. Additionally, the gene encoding Coenzyme M methylation was upregulated by 36.2% along with enrichments of Methanocullus and Methanosarcina, contributing to accelerated hydrolysis and methanogenesis rates by 54.7% and 44.8%, respectively. On the other hand, biochar mainly stimulated bacterial F-type ATPase activities by 28.4%, likely facilitating direct interspecies electron transfer between Geobacter and Methanosarcina for syntrophic methanogenesis. The combined addition of Cu[2+]/Zn[2+] and biochar resulted in "win-win" benefits, significantly increasing the maximum methane production rate from 40.3 mL CH4/d to 53.7 mL CH4/d. Moreover, the introduction of biochar into AD of SW facilitated the transformation of more Cu[2+]/Zn[2+] from a reducible Fe-Mn oxides form to a residual form, which potentially reduced the metallic toxicity of the digestate for soil amendment. The findings of this study provide novel insights into understanding the synergistic impacts of heavy metals and biochar in regulating SW during AD, as well as the management of associated digestate.}, } @article {pmid37865178, year = {2023}, author = {Fu, Y and Zhang, C and Xie, H and Wu, Z and Tao, Y and Wang, Z and Gu, M and Wei, P and Lin, S and Li, R and He, Y and Sheng, J and Xu, J and Wang, J and Pan, Y}, title = {Human umbilical cord mesenchymal stem cells alleviated TNBS-induced colitis in mice by restoring the balance of intestinal microbes and immunoregulation.}, journal = {Life sciences}, volume = {334}, number = {}, pages = {122189}, doi = {10.1016/j.lfs.2023.122189}, pmid = {37865178}, issn = {1879-0631}, mesh = {Humans ; Mice ; Animals ; Trinitrobenzenesulfonic Acid/toxicity ; *Colitis/chemically induced/therapy ; Cytokines/metabolism ; *Inflammatory Bowel Diseases/chemically induced/therapy ; T-Lymphocytes, Regulatory ; Immunity ; *Mesenchymal Stem Cells/metabolism ; Umbilical Cord/metabolism ; Disease Models, Animal ; }, abstract = {AIMS: Human umbilical cord mesenchymal stem cells (HUMSCs) have been documented to be effective for several immune disorders including inflammatory bowel diseases (IBD). However, it remains unclear how HUMSCs function in regulating immune responses and intestinal flora in the trinitrobenzene sulfonic acid (TNBS)-induced IBD model.

MATERIALS AND METHODS: We assessed the regulatory effects of HUMSCs on the gut microbiota, T lymphocyte subpopulations and related immune cytokines in the TNBS-induced IBD model. The mice were divided into the normal, TNBS, and HUMSC-treated groups. The effect of HUMSCs was evaluated by Hematoxylin and Eosin (H&E) staining, fluorescence-activated cell sorting (FACS), and enzyme-linked immunosorbent assay (ELISA) analyses. Metagenomics Illumina sequencing was conducted for fecal samples.

KEY FINDINGS: We demonstrated that the disease symptoms and pathological changes in the colon tissues of TNBS-induced colitis mice were dramatically ameliorated by HUMSCs, which improved the gut microbiota and rebalanced the immune system, increasing the abundance of healthy bacteria (such as Lactobacillus murinus and Lactobacillus johnsonii), the Firmicutes/Bacteroidetes ratio, and the proportion of Tregs; the Th1/Th17 ratio was decreased. Consistently, the expression levels of IFN-γ and IL-17 were significantly decreased, and transforming growth factor-β1 (TGF-β1) levels were significantly increased in the plasma of colitis mice HUMSC injection.

SIGNIFICANCE: Our experiment revealed that HUMSCs mitigate acute colitis by regulating the rebalance of Th1/Th17/Treg cells and related cytokines and remodeling the gut microbiota, providing potential future therapeutic targets in IBD.}, } @article {pmid37864263, year = {2023}, author = {Blanco-Fuertes, M and Sibila, M and Franzo, G and Obregon-Gutierrez, P and Illas, F and Correa-Fiz, F and Aragón, V}, title = {Ceftiofur treatment of sows results in long-term alterations in the nasal microbiota of the offspring that can be ameliorated by inoculation of nasal colonizers.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {53}, pmid = {37864263}, issn = {2524-4671}, support = {AGL2016-77361-R and PID2019-106233RB-I00 /AEI/10.13039/501100011033//Ministerio de Ciencia e Innovación/ ; }, abstract = {BACKGROUND: The nasal microbiota of the piglet is a reservoir for opportunistic pathogens that can cause polyserositis, such as Glaesserella parasuis, Mycoplasma hyorhinis or Streptococcus suis. Antibiotic treatment is a strategy to control these diseases, but it has a detrimental effect on the microbiota. We followed the piglets of 60 sows from birth to 8 weeks of age, to study the effect of ceftiofur on the nasal microbiota and the colonization by pathogens when the treatment was administered to sows or their litters. We also aimed to revert the effect of the antibiotic on the nasal microbiota by the inoculation at birth of nasal colonizers selected from healthy piglets. Nasal swabs were collected at birth, and at 7, 15, 21 and 49 days of age, and were used for pathogen detection by PCR and bacterial culture, 16S rRNA amplicon sequencing and whole shotgun metagenomics. Weights, clinical signs and production parameters were also recorded during the study.

RESULTS: The composition of the nasal microbiota of piglets changed over time, with a clear increment of Clostridiales at the end of nursery. The administration of ceftiofur induced an unexpected temporary increase in alpha diversity at day 7 mainly due to colonization by environmental taxa. Ceftiofur had a longer impact on the nasal microbiota of piglets when administered to their sows before farrowing than directly to them. This effect was partially reverted by the inoculation of nasal colonizers to newborn piglets and was accompanied by a reduction in the number of animals showing clinical signs (mainly lameness). Both interventions altered the colonization pattern of different strains of the above pathogens. In addition, the prevalence of resistance genes increased over time in all the groups but was significantly higher at weaning when the antibiotic was administered to the sows. Also, ceftiofur treatment induced the selection of more beta-lactams resistance genes when it was administered directly to the piglets.

CONCLUSIONS: This study shed light on the effect of the ceftiofur treatment on the piglet nasal microbiota over time and demonstrated for the first time the possibility of modifying the piglets' nasal microbiota by inoculating natural colonizers of the upper respiratory tract.}, } @article {pmid37863966, year = {2023}, author = {Marcelino, VR and Welsh, C and Diener, C and Gulliver, EL and Rutten, EL and Young, RB and Giles, EM and Gibbons, SM and Greening, C and Forster, SC}, title = {Disease-specific loss of microbial cross-feeding interactions in the human gut.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6546}, pmid = {37863966}, issn = {2041-1723}, support = {R01 DK133468/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Case-Control Studies ; *Microbiota ; Metagenome ; *Crohn Disease ; }, abstract = {Many gut microorganisms critical to human health rely on nutrients produced by each other for survival; however, these cross-feeding interactions are still challenging to quantify and remain poorly characterized. Here, we introduce a Metabolite Exchange Score (MES) to quantify those interactions. Using metabolic models of prokaryotic metagenome-assembled genomes from over 1600 individuals, MES allows us to identify and rank metabolic interactions that are significantly affected by a loss of cross-feeding partners in 10 out of 11 diseases. When applied to a Crohn's disease case-control study, our approach identifies a lack of species with the ability to consume hydrogen sulfide as the main distinguishing microbiome feature of disease. We propose that our conceptual framework will help prioritize in-depth analyses, experiments and clinical targets, and that targeting the restoration of microbial cross-feeding interactions is a promising mechanism-informed strategy to reconstruct a healthy gut ecosystem.}, } @article {pmid37863223, year = {2024}, author = {Jiménez-Volkerink, SN and Jordán, M and Smidt, H and Minguillón, C and Vila, J and Grifoll, M}, title = {Metagenomic insights into the microbial cooperative networks of a benz(a)anthracene-7,12-dione degrading community from a creosote-contaminated soil.}, journal = {The Science of the total environment}, volume = {907}, number = {}, pages = {167832}, doi = {10.1016/j.scitotenv.2023.167832}, pmid = {37863223}, issn = {1879-1026}, mesh = {Microbial Consortia ; Creosote ; Sand ; *Polycyclic Aromatic Hydrocarbons/metabolism ; Biodegradation, Environmental ; Carbon ; *Soil Pollutants/metabolism ; Soil Microbiology ; Soil ; }, abstract = {Genotoxicity of PAH-contaminated soils can eventually increase after bioremediation due to the formation and accumulation of polar transformation products, mainly oxygenated PAHs (oxy-PAHs). Biodegradation of oxy-PAHs has been described in soils, but information on the microorganisms and mechanisms involved is still scarce. Benz(a)anthracene-7,12-dione (BaAQ), a transformation product from benz(a)anthracene frequently detected in soils, presents higher genotoxic potential than its parent PAH. Here, using sand-in-liquid microcosms we identified a specialized BaAQ-degrading subpopulation in a PAH-contaminated soil. A BaAQ-degrading microbial consortium was obtained by enrichment in sand-in-liquid cultures with BaAQ as sole carbon source, and its metagenomic analysis identified members of Sphingobium, Stenotrophomonas, Pusillimonas, Olivibacter, Pseudomonas, Achromobacter, and Hyphomicrobiales as major components. The integration of data from metabolomic and metagenomic functional gene analyses of the consortium revealed that the BaAQ metabolic pathway was initiated by Baeyer-Villiger monooxygenases (BVMOs). The presence of plasmid pANTQ-1 in the metagenomic sequences, identified in a previous multi-omic characterization of a 9,10-anthraquinone-degrading isolate recovered from the same soil, suggested the occurrence of a horizontal gene transfer event. Further metagenomic analysis of the BaAQ-degrading consortium also provided insights into the potential roles and interactions within the consortium members. Several potential auxotrophies were detected, indicating that relevant nutritional interdependencies and syntrophic associations were taking place within the community members, not only to provide suitable carbon and energy sources, but also to supply essential nutrients and cofactors. Our work confirms the essential role that BVMO may play as a detoxification mechanism to mitigate the risk posed by oxy-PAH formation during bioremediation of contaminated soils.}, } @article {pmid37863091, year = {2023}, author = {Hu, Y and Hu, Y and Zhou, W and Wei, F}, title = {Conservation Genomics and Metagenomics of Giant and Red Pandas in the Wild.}, journal = {Annual review of animal biosciences}, volume = {}, number = {}, pages = {}, doi = {10.1146/annurev-animal-021022-054730}, pmid = {37863091}, issn = {2165-8110}, abstract = {Giant pandas and red pandas are endangered species with similar specialized bamboo diet and partial sympatric distribution in China. Over the last two decades, the rapid development of genomics and metagenomics research on these species has enriched our knowledge of their biology, ecology, physiology, genetics, and evolution, which is crucial and useful for their conservation. We describe the evolutionary history, endangerment processes, genetic diversity, and population structure of wild giant pandas and two species of red pandas (Chinese and Himalayan red pandas). In addition, we explore how genomics and metagenomics studies have provided insight into the convergent adaptation of pandas to the specialized bamboo diet. Finally, we discuss how these findings are applied to effective conservation management of giant and red pandas in the wild and in captivity to promote the long-term persistence of these species. Expected final online publication date for the Annual Review of Animal Biosciences, Volume 12 is February 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.}, } @article {pmid37863066, year = {2023}, author = {Colbert, LE and El Alam, MB and Wang, R and Karpinets, T and Lo, D and Lynn, EJ and Harris, TA and Elnaggar, JH and Yoshida-Court, K and Tomasic, K and Bronk, JK and Sammouri, J and Yanamandra, AV and Olvera, AV and Carlin, LG and Sims, T and Delgado Medrano, AY and Napravnik, TC and O'Hara, M and Lin, D and Abana, CO and Li, HX and Eifel, PJ and Jhingran, A and Joyner, M and Lin, L and Ramondetta, LM and Futreal, AM and Schmeler, KM and Mathew, G and Dorta-Estremera, S and Zhang, J and Wu, X and Ajami, NJ and Wong, M and Taniguchi, C and Petrosino, JF and Sastry, KJ and Okhuysen, PC and Martinez, SA and Tan, L and Mahmud, I and Lorenzi, PL and Wargo, JA and Klopp, AH}, title = {Tumor-resident Lactobacillus iners confer chemoradiation resistance through lactate-induced metabolic rewiring.}, journal = {Cancer cell}, volume = {41}, number = {11}, pages = {1945-1962.e11}, doi = {10.1016/j.ccell.2023.09.012}, pmid = {37863066}, issn = {1878-3686}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; U54 CA096300/CA/NCI NIH HHS/United States ; }, mesh = {Female ; Humans ; Lactic Acid/metabolism ; *Uterine Cervical Neoplasms/radiotherapy ; Lactobacillus/genetics/metabolism ; *Microbiota ; Tumor Microenvironment ; }, abstract = {Tumor microbiota can produce active metabolites that affect cancer and immune cell signaling, metabolism, and proliferation. Here, we explore tumor and gut microbiome features that affect chemoradiation response in patients with cervical cancer using a combined approach of deep microbiome sequencing, targeted bacterial culture, and in vitro assays. We identify that an obligate L-lactate-producing lactic acid bacterium found in tumors, Lactobacillus iners, is associated with decreased survival in patients, induces chemotherapy and radiation resistance in cervical cancer cells, and leads to metabolic rewiring, or alterations in multiple metabolic pathways, in tumors. Genomically similar L-lactate-producing lactic acid bacteria commensal to other body sites are also significantly associated with survival in colorectal, lung, head and neck, and skin cancers. Our findings demonstrate that lactic acid bacteria in the tumor microenvironment can alter tumor metabolism and lactate signaling pathways, causing therapeutic resistance. Lactic acid bacteria could be promising therapeutic targets across cancer types.}, } @article {pmid37862709, year = {2023}, author = {Giangeri, G and Tsapekos, P and Gaspari, M and Ghofrani-Isfahani, P and Hong Lin, MKT and Treu, L and Kougias, P and Campanaro, S and Angelidaki, I}, title = {Magnetite Alters the Metabolic Interaction between Methanogens and Sulfate-Reducing Bacteria.}, journal = {Environmental science & technology}, volume = {57}, number = {43}, pages = {16399-16413}, pmid = {37862709}, issn = {1520-5851}, mesh = {Ferrosoferric Oxide/metabolism ; Biofuels ; *Hydrogen Sulfide/metabolism ; *Euryarchaeota/metabolism ; Anaerobiosis ; Bacteria/metabolism ; Acetates/metabolism ; Butyrates/metabolism ; Methane ; Sulfates ; Bioreactors ; }, abstract = {It is known that the presence of sulfate decreases the methane yield in the anaerobic digestion systems. Sulfate-reducing bacteria can convert sulfate to hydrogen sulfide competing with methanogens for substrates such as H2 and acetate. The present work aims to elucidate the microbial interactions in biogas production and assess the effectiveness of electron-conductive materials in restoring methane production after exposure to high sulfate concentrations. The addition of magnetite led to a higher methane content in the biogas and a sharp decrease in the level of hydrogen sulfide, indicating its beneficial effects. Furthermore, the rate of volatile fatty acid consumption increased, especially for butyrate, propionate, and acetate. Genome-centric metagenomics was performed to explore the main microbial interactions. The interaction between methanogens and sulfate-reducing bacteria was found to be both competitive and cooperative, depending on the methanogenic class. Microbial species assigned to the Methanosarcina genus increased in relative abundance after magnetite addition together with the butyrate oxidizing syntrophic partners, in particular belonging to the Syntrophomonas genus. Additionally, Ruminococcus sp. DTU98 and other species assigned to the Chloroflexi phylum were positively correlated to the presence of sulfate-reducing bacteria, suggesting DIET-based interactions. In conclusion, this study provides new insights into the application of magnetite to enhance the anaerobic digestion performance by removing hydrogen sulfide, fostering DIET-based syntrophic microbial interactions, and unraveling the intricate interplay of competitive and cooperative interactions between methanogens and sulfate-reducing bacteria, influenced by the specific methanogenic group.}, } @article {pmid37862695, year = {2023}, author = {Xiong, W and Ye, Y and He, D and He, S and Xiang, Y and Xiao, J and Feng, W and Wu, M and Yang, Z and Wang, D}, title = {Deregulation of Ribosome Biogenesis in Nitrite-Oxidizing Bacteria Leads to Nitrite Accumulation.}, journal = {Environmental science & technology}, volume = {57}, number = {43}, pages = {16673-16684}, doi = {10.1021/acs.est.3c06002}, pmid = {37862695}, issn = {1520-5851}, mesh = {*Nitrites/metabolism ; *Nitrogen Dioxide ; Bioreactors/microbiology ; Nitrification ; Bacteria/genetics/metabolism ; Ammonia/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Ribosomal Proteins/metabolism ; Ribosomes/metabolism ; Sewage/microbiology ; }, abstract = {Nitrite (NO2[-]) accumulation caused by nitrite-oxidizing bacteria (NOB) inhibition in nitrification is a double-edged sword, i.e., a disaster in aquatic environments but a hope for innovating nitrogen removal technology in wastewater treatment. However, little information is available regarding the molecular mechanism of NOB inhibition at the cellular level. Herein, we investigate the response of NOB inhibition on NO2[-] accumulation established by a side-stream free ammonia treatment unit in a nitrifying reactor using integrated metagenomics and metaproteomics. Results showed that compared with the baseline, the relative abundance and activity of NOB in the experimental stage decreased by 91.64 and 68.66%, respectively, directly resulting in a NO2[-] accumulation rate of 88%. Moreover, RNA polymerase, translation factors, and aa-tRNA ligase were significantly downregulated, indicating that protein synthesis in NOB was interfered during NO2[-] accumulation. Further investigations showed that ribosomal proteins and GTPases, responsible for bindings between either ribosomal proteins and rRNA or ribosome subunits, were remarkably downregulated. This suggests that ribosome biogenesis was severely disrupted, which might be the key reason for the inhibited protein synthesis. Our findings fill a knowledge gap regarding the underlying mechanisms of NO2[-] accumulation, which would be beneficial for regulating the accumulation of NO2[-] in aquatic environments and engineered systems.}, } @article {pmid37861738, year = {2023}, author = {Zheng, M and Kang, Y and Shen, Y and Xu, Y and Xu, F and Chen, Y}, title = {Genomic Features and Comparative Genomic Analysis of Streptococcus sp. v1. nov., Isolated from an Endophthalmitis Patient.}, journal = {Current microbiology}, volume = {80}, number = {12}, pages = {378}, pmid = {37861738}, issn = {1432-0991}, support = {2018ZX10201001//National Science and Technology Major Project/ ; Y20190171//the Science and Technology Bureau of Wenzhou/ ; }, mesh = {Humans ; *Streptococcus/genetics ; *Endophthalmitis ; Streptococcus mitis ; Genomics ; Virulence Factors/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; }, abstract = {Endophthalmitis is an acute inflammatory intraocular condition that can cause permanent vision loss. The treatment strategy and visual outcome partly depend on the identification of the agents of pathogens. In this study, metagenomic sequencing was conducted to investigate the microbial and antibiotic resistance genes (ARGs) composition in the vitreous (intraocular body fluid) of an endophthalmitis patient, who progressed rapidly and accompanied by severe pain. Metagenomic sequencing data revealed that the vitreous sample was predominated by Streptococcus, with a low-diversity microbiome in the vitreous. This strain harbor's the ARGs mainly against beta-lactam, macrolide-lincosamide-streptogramin, and multidrug. Additionally, metagenome-assembled genome sequence of Streptococcus sp. v1. nov. was identified. The Tetra Correlation Search (TCS) analysis uncovered that the closest relative of the Streptococcus sp. v1. nov. was Streptococcus mitis SK321. Pan/core genome analysis for Streptococcus sp. v1. nov. and TCS top 25 hits strains revealed that most unique genes of Streptococcus sp. v1. nov. were linked to ATP-binding cassette transport system, which could indicate unique virulence and pathogenic potentials of Streptococcus sp. v1. nov. In addition, a total of 7 virulence factors were identified, and the overwhelming of them were classified into "offensive virulence factors". The high pathogenicity of Streptococcus sp. v1. nov. could be a reason for the patient's rapid disease progression. Our study was first isolated an ocular pathogen with highly virulent based on metagenomic sequencing and bioinformatics analysis, which has important reference value for revealing the composition and genome characteristics of pathogens in endophthalmitis patient in the future.}, } @article {pmid37861560, year = {2023}, author = {Zhang, C and Zhang, J and Liao, Z}, title = {A case of successful hormone therapy for refractory hypotension following viral encephalitis: Case report.}, journal = {Medicine}, volume = {102}, number = {42}, pages = {e34988}, pmid = {37861560}, issn = {1536-5964}, mesh = {Male ; Humans ; Aged ; Acyclovir/therapeutic use ; *Encephalitis, Herpes Simplex/drug therapy ; *Encephalitis, Viral/diagnosis/drug therapy ; Methylprednisolone/therapeutic use ; *Hypotension/etiology/complications ; Anti-Inflammatory Agents/therapeutic use ; Hormones/therapeutic use ; Antiviral Agents/therapeutic use ; }, abstract = {RATIONALE: Refractory hypotension is a life-threatening condition that can result from various causes. We report a rare case of refractory hypotension following herpes simplex virus type 1 encephalitis that was successfully treated with hormone therapy.

PATIENT CONCERNS: The patient was a 66-year-old male who was admitted to the hospital because of fever, chills, convulsions, and impaired consciousness. He developed respiratory failure and was intubated. Cerebrospinal fluid metagenomic sequencing confirmed herpes simplex virus type 1 infection. He received piperacillin-tazobactam for anti-infection, acyclovir for antiviral therapy, and dexamethasone for anti-inflammatory therapy. He had repeated episodes of hypotension despite fluid resuscitation and vasopressor therapy.

DIAGNOSIS: The diagnosis of herpes simplex virus type 1 encephalitis complicated by refractory hypotension was based on the patient's epidemiological history, clinical manifestations, laboratory tests, and imaging studies. Cerebrospinal fluid examination was the most important diagnostic method, which could detect viral nucleic acids. Head magnetic resonance imaging showed a large recent lesion in the right temporal-parietal and insular lobes.

INTERVENTIONS: The treatment of refractory hypotension mainly included anti-infection, antiviral, anti-inflammatory, and hormone therapy. Hormone therapy used methylprednisolone shock treatment until tapering withdrawal. Other treatments included fluid resuscitation, vasopressors, anticonvulsants, etc.

OUTCOMES: The patient's blood pressure stabilized after receiving methylprednisolone shock treatment, and his mean arterial pressure increased from 73 mm Hg to 92 mm Hg within 24 hours. Three months later, the patient's blood pressure was normal without medication, and he had a good social and physical recovery.

LESSONS: This case illustrates the possible role of hormone therapy in restoring blood pressure in patients with refractory hypotension following viral encephalitis. It suggests that adrenal insufficiency or autonomic dysfunction may be involved in the pathophysiology of this condition. Further studies are needed to confirm the efficacy and safety of hormone therapy in this setting.}, } @article {pmid37861333, year = {2023}, author = {Khanongnuch, R and Mangayil, R and Rissanen, AJ}, title = {Conversion of methane to organic acids is a widely found trait among gammaproteobacterial methanotrophs of freshwater lake and pond ecosystems.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0174223}, pmid = {37861333}, issn = {2165-0497}, support = {346751//Academy of Finland (AKA)/ ; 353750//Academy of Finland (AKA)/ ; 346983//Academy of Finland (AKA)/ ; 201803224//Koneen Säätiö (Kone Foundation)/ ; }, mesh = {*Lakes/microbiology ; *Ecosystem ; Ponds ; Methane/metabolism ; Bacteria ; Acids ; }, abstract = {Aerobic gammaproteobacterial methanotrophic bacteria (gMOB) play an important role in reducing methane emissions from freshwater ecosystems. In hypoxic conditions prevalent near oxic-anoxic interfaces, gMOB potentially shift their metabolism to fermentation, resulting in the conversion of methane to extracellular organic acids, which would serve as substrates for non-methanotrophic microbes. We intended to assess the prevalence of fermentation traits among freshwater gMOB. Therefore, we isolated two strains representing relevant freshwater gMOB genera, i.e., Methylovulum and Methylomonas, from boreal lakes, experimentally showed that they convert methane to organic acids and demonstrated via metagenomics that the fermentation potential is widely dispersed among lake and pond representatives of these genera. Combined with our recent study showing coherent results from another relevant freshwater gMOB genus, i.e., Methylobacter, we conclude that the conversion of methane to organic acids is a widely found trait among freshwater gMOB, highlighting their role as pivotal mediators of methane carbon into microbial food webs.}, } @article {pmid37861083, year = {2023}, author = {Fuchsman, CA and Hays, MD}, title = {Increased cyanophage infection at the bottom of the euphotic zone, especially in the fall.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {3349-3363}, doi = {10.1111/1462-2920.16525}, pmid = {37861083}, issn = {1462-2920}, support = {IDP2021//GEOTRACES 2021 Intermediate Data Product/ ; //Scientific Committee on Oceanic Research (SCOR)/ ; #1756517//Hawaii Ocean Time-series observations supported by the U.S. National Science Foundation/ ; //Horn Point Laboratory start up/ ; }, mesh = {Seasons ; Seawater/microbiology ; Photosynthesis ; *Cyanobacteria/genetics ; Pacific Ocean ; *Prochlorococcus/genetics ; }, abstract = {Picocyanobacteria contribute greatly to offshore primary production with cells extending through the deep euphotic zone. Literature indicates high viral infection of cyanobacteria in ocean transition zones. We postulate that the bottom of the euphotic zone is a transition zone, where communities transition from phototrophic to aphotic processes. We use single-copy core genes to examine cyanophage to cyanobacteria ratios in cellular metagenomes in the subtropical North Atlantic and Pacific. Cyanophage to cyanobacteria terL/rpoB ratios generally increase to >10 in the deep euphotic zone. As light levels decrease in the fall, Prochlorococcus in the deep euphotic zone experience reduced light levels. We find clear differences between spring (Geotraces GA02) and fall (GA03) in the North Atlantic, with terL/rpoB ratios increasing to >40 in the fall. When examining 23 months of the North Pacific Hawaii Ocean Timeseries, the depth of elevated cyanophage to cyanobacteria ratios in cellular metagenomes negatively correlated with surface photosynthetic radiation (PAR), particularly with the change in PAR, which reflected the season. In fall, all picocyanobacteria ecotypes were found at depths enriched with viruses, while in summer, only low light ecotypes were affected. Thus, we find high cyanophage infection both in the deep euphotic zone and during seasonal transitions.}, } @article {pmid37860140, year = {2023}, author = {Tibihenda, C and Zhong, H and Liu, K and Dai, J and Lin, X and Motelica-Heino, M and Hou, S and Zhang, M and Lu, Y and Xiao, L and Zhang, C}, title = {Ecologically different earthworm species are the driving force of microbial hotspots influencing Pb uptake by the leafy vegetable Brassica campestris.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1240707}, pmid = {37860140}, issn = {1664-302X}, abstract = {Food chain contamination by soil lead (Pb), beginning with Pb uptake by leafy vegetables, is a threat to food safety and poses a potential risk to human health. This study highlights the importance of two ecologically different earthworm species (the anecic species Amynthas aspergillum and the epigeic species Eisenia fetida) as the driving force of microbial hotspots to enhance Pb accumulation in the leafy vegetable Brassica campestris at different Pb contamination levels (0, 100, 500, and 1,000 mg·kg[-1]). The fingerprints of phospholipid fatty acids (PLFAs) were employed to reveal the microbial mechanism of Pb accumulation involving earthworm-plant interaction, as PLFAs provide a general profile of soil microbial biomass and community structure. The results showed that Gram-positive (G[+]) bacteria dominated the microbial community. At 0 mg·kg[-1] Pb, the presence of earthworms significantly reduced the total PLFAs. The maximum total of PLFAs was found at 100 mg·kg[-1] Pb with E. fetida inoculation. A significant shift in the bacterial community was observed in the treatments with E. fetida inoculation at 500 and 1,000 mg·kg[-1] Pb, where the G[+]/G[-] bacteria ratio was significantly decreased compared to no earthworm inoculation. Principal component analysis (PCA) showed that E. fetida had a greater effect on soil microbial hotspots than A. aspergillum, thus having a greater effect on the Pb uptake by B. campestris. Redundancy analysis (RDA) showed that soil microbial biomass and structure explained 43.0% (R[2] = 0.53) of the total variation in Pb uptake by B. campestris, compared to 9.51% of microbial activity. G[-] bacteria explained 23.2% of the total variation in the Pb uptake by B. campestris, significantly higher than the other microbes. The Mantel test showed that microbial properties significantly influenced Pb uptake by B. campestris under the driving force of earthworms. E. fetida inoculation was favorable for the G[-] bacterial community, whereas A. aspergillum inoculation was favorable for the fungal community. Both microbial communities facilitated the entry of Pb into the vegetable food chain system. This study delivers novel evidence and meaningful insights into how earthworms prime the microbial mechanism of Pb uptake by leafy vegetables by influencing soil microbial biomass and community composition. Comprehensive metagenomics analysis can be employed in future studies to identify the microbial strains promoting Pb migration and develop effective strategies to mitigate Pb contamination in food chains.}, } @article {pmid37860094, year = {2023}, author = {Wong, CKF and Chong, TY and Tan, J and Wong, WL}, title = {Isolation and Characterisation of Culturable Thermophilic Cyanobacteria from Perak Hot Springs and their Plant Growth Promoting Properties Effects on Rice Seedlings (Oryza sativa L.).}, journal = {Tropical life sciences research}, volume = {34}, number = {3}, pages = {1-22}, pmid = {37860094}, issn = {1985-3718}, abstract = {Malaysia is home to a number of hot springs that are rich in microbial diversity including the photosynthetic cyanobacteria. Although this microbial community has been characterised based on metagenomics approach, the culturable thermophilic isolates have not been isolated and characterised extensively. Compared to the mesophiles, information on plant growth promoting (PGP) properties of these thermophiles remain largely untapped. As the amount of arable land for microbial bioprospecting is decreasing due to extensive human activities, the search for alternative source for microbial strains with PGP properties is important for the development of potential biofertilisers. This study sought to isolate and characterise culturable cyanobacteria strains from two local hot springs - Sungai Klah (SK) and Lubuk Timah (LT) located in Perak using morphological and molecular methods. The IAA production from the axenic cultures were measured. The PGP properties were also measured by priming the rice seeds with cyanobacterial water extracts. A total of six strains were isolated from both hot springs. Strains LTM and LTW from LT were identified as Leptolyngbya sp. whereas strains SEM, SEH, STH and STM were identified as Thermosynechococcus elongatus. All six strains produced IAA ranged from 670.10 pg/μL to 2010 pg/μL. The water extracts were found to increase the seed amylase activity of the rice seeds from 5th day of germination (DAG) to 10th DAG. In general, the IAA production and increased seed amylase activity might have contributed in enhancing the longest root length, shoot length and root-to-shoot (RS) ratio. To conclude, the thermophilic cyanobacteria from hot springs can be further exploited as a novel source of PGP microbes for the development of biofertilsers.}, } @article {pmid37860065, year = {2023}, author = {Chen, G and Ma, N and Zhu, D and Zhou, H and Liang, Q and Meng, J and Shen, Y and Liu, H and Liu, L and He, Z and Qin, Z}, title = {Accurate diagnosis of bronchopulmonary Talaromyces marneffei infection in an anti-IFN-γ autoantibodies positive patient assisted by endobronchial ultrasound-guided TBNA and mNGS: a case report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1186335}, pmid = {37860065}, issn = {2235-2988}, mesh = {Humans ; Male ; Middle Aged ; Autoantibodies/blood/immunology ; *Cough/pathology ; Interferon-gamma ; Lymph Nodes/pathology ; *Mycoses/diagnosis ; Ultrasonography, Interventional ; }, abstract = {RATIONALE: T. marneffei is opportunistic and dimorphic fungus, which can cause systemic mycosis in human beings. It's being difficult to obtain histopathological or microbiological evidence in T. marneffei infection. We reported a rare non-HIV case of T. marneffei infection of bronchopulmonary and mediastinal lymph nodes which was diagnosed by EBUS-TBNA combined with mNGS. The high titer of anti-IFN-γ autoantibodies in serum was probably the cause of T. marneffei infection,which has yet to be fully known.

PATIENT CONCERNS: A 56-year-old Chinese man presented with a 5-month history of intermittent low or high fever and dry cough, followed by fatigue, night sweating, and chest pain when coughing. A large hilar lesion in the left lung and multiple mediastinal lymph node enlargements were found on his chest CT scan.

DIAGNOSES: The patient received EBUS-TBNA of hilar tissue and lymph node biopsy for mNGS at the second Ultrasonic bronchoscopy. No fungal hyphae or spores were found in the histopathology. There were high sequencing reads of T. marneffei in samples of lymph node fluid and bronchogenesis tissue detected by mNGS. His plasma anti-IFN-γ autoantibodies level was positive with a high titer at 1:2500↑.

INTERVENTION: The patient went through atrial fibrillation at the first dose of amphotericin B liposomes and treated with voriconazole later.

OUTCOMES: His fever, cough and dyspnea quickly disappeared since the fourth day of treatment. After six months, there was not any focus in his chest CT scans. But his plasma anti-IFN-γ autoantibodies remained unchanged.

LESSONS: Complementing the traditional laboratory and bronchoscopy, mNGS combined with EBUS-TBNA facilitate rapid and precise diagnosis of bronchopulmonary mediastinal lymph nodes T. marneffei infection. Clinicians should be aware of anti-INF-γ autoantibodies in opportunistic infections of non-HIV patients.}, } @article {pmid37859795, year = {2023}, author = {Abadikhah, M and Liu, M and Persson, F and Wilén, BM and Farewell, A and Sun, J and Modin, O}, title = {Effect of anode material and dispersal limitation on the performance and biofilm community in microbial electrolysis cells.}, journal = {Biofilm}, volume = {6}, number = {}, pages = {100161}, pmid = {37859795}, issn = {2590-2075}, abstract = {In a microbial electrolysis cell (MEC), the oxidization of organic compounds is facilitated by an electrogenic biofilm on the anode surface. The biofilm community composition determines the function of the system. Both deterministic and stochastic factors affect the community, but the relative importance of different factors is poorly understood. Anode material is a deterministic factor as materials with different properties may select for different microorganisms. Ecological drift is a stochastic factor, which is amplified by dispersal limitation between communities. Here, we compared the effects of three anode materials (graphene, carbon cloth, and nickel) with the effect of dispersal limitation on the function and biofilm community assembly. Twelve MECs were operated for 56 days in four hydraulically connected loops and shotgun metagenomic sequencing was used to analyse the microbial community composition on the anode surfaces at the end of the experiment. The anode material was the most important factor affecting the performance of the MECs, explaining 54-80 % of the variance observed in peak current density, total electric charge generation, and start-up lag time, while dispersal limitation explained 10-16 % of the variance. Carbon cloth anodes had the highest current generation and shortest lag time. However, dispersal limitation was the most important factor affecting microbial community structure, explaining 61-98 % of the variance in community diversity, evenness, and the relative abundance of the most abundant taxa, while anode material explained 0-20 % of the variance. The biofilms contained nine Desulfobacterota metagenome-assembled genomes (MAGs), which made up 64-89 % of the communities and were likely responsible for electricity generation in the MECs. Different MAGs dominated in different MECs. Particularly two different genotypes related to Geobacter benzoatilyticus competed for dominance on the anodes and reached relative abundances up to 83 %. The winning genotype was the same in all MECs that were hydraulically connected irrespective of anode material used.}, } @article {pmid37858800, year = {2023}, author = {Liu, Z and Awasthi, MK and Zhao, J and Liu, G and Syed, A and Al-Shwaiman, HA and Fang, J}, title = {Unraveling impacts of inoculating novel microbial agents on nitrogen conversion during cattle manure composting: Core microorganisms and functional genes.}, journal = {Bioresource technology}, volume = {390}, number = {}, pages = {129887}, doi = {10.1016/j.biortech.2023.129887}, pmid = {37858800}, issn = {1873-2976}, mesh = {Cattle ; Animals ; *Composting ; Manure ; Nitrogen ; Soil ; Bacteria/genetics ; }, abstract = {The impacts of microbial agents on nitrogen conversion during composting is still not entirely clear. In this research, a novel microbial agent containing two thermotolerant nitrifying bacteria was identified and its impacts on nitrogen conversion, bacterial structure and functional genes during cattle manure composting were investigated. The results revealed that the inoculation enhancing the maturation of compost, increased the total nitrogen by 13.6-26.8%, reduced NH3 emission and the N2O emission by 24.8-36.1% and 22.7-32.1%, respectively. Particularly, the microbial agents mixed Acinetobacter radioresistens and Bacillus nitratireducens (1:1, treatment group 1) had the best nitrogen preservation effect. Furthermore, the inoculation not only produced diverse diazotroph community but could strength the co-occurrence between core microorganisms to promote nitrogen metabolism. The metagenomic analysis demonstrated that the inoculation decreased the abundance of nitrate reduction gene (nirS, norC, nap and nif), and increased the abundance of hao, thus facilitating nitrification and suppressing NH3 and N2O emission.}, } @article {pmid37858797, year = {2023}, author = {Yang, J and Wei, H and Lin, Y and Chu, ESH and Zhou, Y and Gou, H and Guo, S and Lau, HCH and Cheung, AHK and Chen, H and To, KF and Sung, JJY and Wang, Y and Yu, J}, title = {High Soluble Fiber Promotes Colorectal Tumorigenesis Through Modulating Gut Microbiota and Metabolites in Mice.}, journal = {Gastroenterology}, volume = {}, number = {}, pages = {}, doi = {10.1053/j.gastro.2023.10.012}, pmid = {37858797}, issn = {1528-0012}, abstract = {BACKGROUND & AIMS: Dietary fibers are mainly fermented by the gut microbiota, but their roles in colorectal cancer (CRC) are largely unclear. Here, we investigated the associations of different fibers with colorectal tumorigenesis in mice.

METHODS: Apc[min/+] mice and C57BL/6 mice with azoxymethane (AOM) injection were used as CRC mouse models. Mice were fed with mixed high-fiber diet (20% soluble fiber and 20% insoluble fiber), high-inulin diet, high-guar gum diet, high-cellulose diet, or diets with different inulin dose. Germ-free mice were used for validation. Fecal microbiota and metabolites were profiled by shotgun metagenomic sequencing and liquid chromatography-mass spectrometry, respectively.

RESULTS: Mixed high-fiber diet promoted colorectal tumorigenesis with increased tumor number and tumor load in AOM-treated and Apc[min/+] mice. Antibiotics use abolished the pro-tumorigenic effect of mixed high-fiber diet, while transplanting stools from mice fed with mixed high-fiber diet accelerated tumor growth in AOM-treated germ-free mice. We therefore characterized the contribution of soluble and insoluble fiber in CRC separately. Our results revealed that soluble fiber inulin or guar gum, but not insoluble fiber cellulose, promoted colorectal tumorigenesis in AOM-treated and Apc[min/+] mice. Soluble fiber induced gut dysbiosis with Bacteroides uniformis enrichment and Bifidobacterium pseudolongum depletion, accompanied by increased fecal butyrate and serum bile acids and decreased inosine. We also identified a positive correlation between inulin dosage and colorectal tumorigenesis. Moreover, transplanting stools from mice fed with high-inulin diet increased colonic cell proliferation and oncogene expressions in germ-free mice.

CONCLUSION: High-dose soluble but not insoluble fiber potentiates colorectal tumorigenesis in a dose-dependent manner by dysregulating gut microbiota and metabolites in mice.}, } @article {pmid37858269, year = {2023}, author = {Labarthe, S and Plancade, S and Raguideau, S and Plaza Oñate, F and Le Chatelier, E and Leclerc, M and Laroche, B}, title = {Four functional profiles for fibre and mucin metabolism in the human gut microbiome.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {231}, pmid = {37858269}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Mucins ; Dysbiosis ; *Microbiota/genetics ; Metagenome ; Dietary Fiber ; Inflammation ; Metagenomics/methods ; }, abstract = {BACKGROUND: With the emergence of metagenomic data, multiple links between the gut microbiome and the host health have been shown. Deciphering these complex interactions require evolved analysis methods focusing on the microbial ecosystem functions. Despite the fact that host or diet-derived fibres are the most abundant nutrients available in the gut, the presence of distinct functional traits regarding fibre and mucin hydrolysis, fermentation and hydrogenotrophic processes has never been investigated.

RESULTS: After manually selecting 91 KEGG orthologies and 33 glycoside hydrolases further aggregated in 101 functional descriptors representative of fibre and mucin degradation pathways in the gut microbiome, we used nonnegative matrix factorization to mine metagenomic datasets. Four distinct metabolic profiles were further identified on a training set of 1153 samples, thoroughly validated on a large database of 2571 unseen samples from 5 external metagenomic cohorts and confirmed with metatranscriptomic data. Profiles 1 and 2 are the main contributors to the fibre-degradation-related metagenome: they present contrasted involvement in fibre degradation and sugar metabolism and are differentially linked to dysbiosis, metabolic disease and inflammation. Profile 1 takes over Profile 2 in healthy samples, and unbalance of these profiles characterize dysbiotic samples. Furthermore, high fibre diet favours a healthy balance between profiles 1 and profile 2. Profile 3 takes over profile 2 during Crohn's disease, inducing functional reorientations towards unusual metabolism such as fucose and H2S degradation or propionate, acetone and butanediol production. Profile 4 gathers under-represented functions, like methanogenesis. Two taxonomic makes up of the profiles were investigated, using either the covariation of 203 prevalent genomes or metagenomic species, both providing consistent results in line with their functional characteristics. This taxonomic characterization showed that profiles 1 and 2 were respectively mainly composed of bacteria from the phyla Bacteroidetes and Firmicutes while profile 3 is representative of Proteobacteria and profile 4 of methanogens.

CONCLUSIONS: Integrating anaerobic microbiology knowledge with statistical learning can narrow down the metagenomic analysis to investigate functional profiles. Applying this approach to fibre degradation in the gut ended with 4 distinct functional profiles that can be easily monitored as markers of diet, dysbiosis, inflammation and disease. Video Abstract.}, } @article {pmid37858227, year = {2023}, author = {Jia, P and Dong, LF and Tu, Y and Diao, QY}, title = {Bacillus subtilis and Macleaya cordata extract regulate the rumen microbiota associated with enteric methane emission in dairy cows.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {229}, pmid = {37858227}, issn = {2049-2618}, mesh = {Female ; Cattle ; Animals ; *Lactation ; Bacillus subtilis ; Rumen/microbiology ; Propionates/metabolism ; Methane/metabolism ; Diet/veterinary ; *Microbiota ; Acetates/metabolism ; Butyrates/metabolism ; Plant Extracts ; Fermentation ; }, abstract = {BACKGROUND: Ruminant livestock production is a considerable source of enteric methane (CH4) emissions. In a previous study, we found that dietary inclusions of Bacillus subtilis (BS) and Macleaya cordata extract (MCE) increased dry matter intake and milk production, while reduced enteric CH4 emission in dairy cows. The objective of this study was to further elucidate the impact of feeding BS and MCE on rumen methanogenesis in dairy cows using rumen metagenomics techniques.

RESULTS: Sixty dairy cows were blocked in 20 groups of 3 cows accordingly to their live weight, milk yield, and days in milk, and within each group, the 3 cows were randomly allocated to 1 of 3 treatments: control diet (CON), control diet plus BS (BS), and control diet plus MCE (MCE). After 75 days of feeding experimental diets, 12 cows were selected from each treatment for collection of rumen samples for the metagenomic sequencing. Results showed that BS decreased ruminal acetate and butyrate, while increased propionate concentrations, resulting in decreased acetate:propionate ratio. The metagenomics analysis revealed that MCE reduced relative abundances of Methanobrevibacter wolinii, Methanobrevibacter sp. AbM4, Candidatus Methanomassiliicoccus intestinalis, Methanobrevibacter cuticularis, Methanomicrobium mobile, Methanobacterium formicicum, and Methanobacterium congolense. Both BS and MCE reduced relative abundances of Methanosphaera sp. WGK6 and Methanosphaera stadtmanae. The co-occurrence network analysis of rumen bacteria and archaea revealed that dietary treatments influenced microbial interaction patterns, with BS and MCE cows having more and stronger associations than CON cows. The random forest and heatmaps analysis demonstrated that the Halopenitus persicus was positively correlated with fat- and protein-corrected milk yield; Clostridium sp. CAG 269, Clostridium sp. 27 14, Haloarcula rubripromontorii, and Methanobrevibacter curvatus were negatively correlated with rumen acetate and butyrate concentrations, and acetate:propionate ratio, whereas Selenomonas rumiantium was positively correlated with those variables.

CONCLUSIONS: The present results provided new information for mitigation of enteric methane emissions of dairy cows by feeding BS and MCE to influence rumen microbial activities. This fundamental knowledge is essential for developing enteric CH4 reduction strategies to mitigate climate change and reduce dietary energy waste. Video Abstract.}, } @article {pmid37857845, year = {2023}, author = {Wu, J and Song, W and Yan, H and Luo, C and Hu, W and Xie, L and Shen, N and Cao, Q and Mo, X and An, K and Tao, Y}, title = {Metagenomic next-generation sequencing in detecting pathogens in pediatric oncology patients with suspected bloodstream infections.}, journal = {Pediatric research}, volume = {}, number = {}, pages = {}, pmid = {37857845}, issn = {1530-0447}, abstract = {BACKGROUND: Studies on mNGS application in pediatric oncology patients, who are at high risk of infection, are quite limited.

METHODS: From March 2020 to June 2022, a total of 224 blood samples from 195 pediatric oncology patients who were suspected as bloodstream infections were enrolled in this study. Their clinical and laboratory data were retrospectively reviewed, and the diagnostic performance of mNGS was assessed.

RESULTS: Compared to the reference tests, mNGS showed significantly higher sensitivity (89.8% vs 32.5%, P < 0.001) and clinical agreement (76.3% vs 51.3%, P < 0.001) in detecting potential pathogens and distinguishing BSI from non-BSI. Especially, mNGS had an outstanding performance for virus detection, contributing to 100% clinical diagnosed virus. Samples from patients with neutropenia showed higher incidence of bacterial infections (P = 0.035). The most identified bacteria were Escherichia coli, and the overall infections by gram-negative bacteria were significantly more prevalent than those by gram-positive ones (90% vs 10%, P < 0.001). Overall, mNGS had an impact on the antimicrobial regimens' usage in 54.3% of the samples in this study.

CONCLUSIONS: mNGS has the advantage of rapid and effective pathogen diagnosis in pediatric oncology patients with suspected BSI, especially for virus.

IMPACT: Compared with reference tests, mNGS showed significantly higher sensitivity and clinical agreement in detecting potential pathogens and distinguishing bloodstream infections (BSI) from non-BSI. mNGS is particularly prominent in clinical diagnosed virus detection. The incidence of bacterial infection was higher in patients with neutropenia, and the overall infection rate of Gram-negative bacteria was significantly higher than that of Gram-positive bacteria. mNGS affects the antimicrobial regimens' usage in more than half of patients.}, } @article {pmid37856954, year = {2024}, author = {Chu, G and Qi, W and Chen, W and Zhang, Y and Gao, S and Wang, Q and Gao, C and Gao, M}, title = {Metagenomic insights into the nitrogen metabolism, antioxidant pathway, and antibiotic resistance genes of activated sludge from a sequencing batch reactor under tetracycline stress.}, journal = {Journal of hazardous materials}, volume = {462}, number = {}, pages = {132788}, doi = {10.1016/j.jhazmat.2023.132788}, pmid = {37856954}, issn = {1873-3336}, mesh = {*Sewage/microbiology ; *Anti-Bacterial Agents ; Antioxidants/pharmacology ; Wastewater ; Denitrification ; Nitrification ; Tetracycline/pharmacology ; Bioreactors/microbiology ; Nitrogen/analysis ; Drug Resistance, Microbial/genetics ; }, abstract = {Tetracycline is prevalent in wastewater treatment plants and poses a potential threat to biological nitrogen removal under long-term exposure. In the present study, the influence of different tetracycline concentrations on the nitrogen removal, bioactivity response, and the spread of antibiotic resistance genes (ARGs) was assessed in sequencing batch reactor (SBR). The nitrogen removal efficiency, nitrification rate, and denitrification rate and their corresponding enzymatic activities gradually decreased with an increase in tetracycline concentration from 0.5 to 15 mg/L. The remarkable toxicity induced by tetracycline led to a significant increase in the peroxidation and the response of antioxidant system, as evidenced by strengthened antioxidant enzymatic activity and abundant genes (SOD12, katG, PXDN, gpx, and apx). Tetracycline addition significantly inhibited the ammonia-oxidizing bacterium Nitrosomonas and functional genes (amoA, amoB, and amoC). The presence of tetracycline decreased the abundance of citrate synthase and genes (CS, IDH3, and acnA) and interfered with carbon source metabolism, leading to impaired bioactivity and treatment performance. In addition, the presence of tetracycline induces diversity and differences in ARGs. The results provide reliable basic data for a deeper understanding of the effects of tetracycline on the nitrogen removal performance of bioreactors and provide a theoretical basis to build a promising strategy for relieving antibiotic-caused process fluctuations.}, } @article {pmid37856784, year = {2023}, author = {Dang, H and Ewald, JM and Mattes, TE}, title = {Genome-Resolved Metagenomics and Metatranscriptomics Reveal Insights into the Ecology and Metabolism of Anaerobic Microbial Communities in PCB-Contaminated Sediments.}, journal = {Environmental science & technology}, volume = {57}, number = {43}, pages = {16386-16398}, pmid = {37856784}, issn = {1520-5851}, support = {P30 ES005605/ES/NIEHS NIH HHS/United States ; R01 ES032671/ES/NIEHS NIH HHS/United States ; P42 ES013661/ES/NIEHS NIH HHS/United States ; }, mesh = {*Polychlorinated Biphenyls/analysis/chemistry/metabolism ; *Chloroflexi/genetics/chemistry/metabolism ; Anaerobiosis ; Biodegradation, Environmental ; *Microbiota ; Acetates/metabolism ; Geologic Sediments/analysis ; }, abstract = {Growth of organohalide-respiring bacteria such as Dehalococcoides mccartyi on halogenated organics (e.g., polychlorinated biphenyls (PCBs)) at contaminated sites or in enrichment culture requires interaction and support from other microbial community members. To evaluate naturally occurring interactions between Dehalococcoides and key supporting microorganisms (e.g., production of H2, acetate, and corrinoids) in PCB-contaminated sediments, metagenomic and metatranscriptomic sequencing was conducted on DNA and RNA extracted from sediment microcosms, showing evidence of both Dehalococcoides growth and PCB dechlorination. Using a genome-resolved approach, 160 metagenome-assembled genomes (MAGs), including three Dehalococcoides MAGs, were recovered. A novel reductive dehalogenase gene, distantly related to the chlorophenol dehalogenase gene cprA (pairwise amino acid identity: 23.75%), was significantly expressed. Using MAG gene expression data, 112 MAGs were assigned functional roles (e.g., corrinoid producers, acetate/H2 producers, etc.). A network coexpression analysis of all 160 MAGs revealed correlations between 39 MAGs and the Dehalococcoides MAGs. The network analysis also showed that MAGs assigned with functional roles that support Dehalococcoides growth (e.g., corrinoid assembly, and production of intermediates required for corrinoid synthesis) displayed significant coexpression correlations with Dehalococcoides MAGs. This work demonstrates the power of genome-resolved metagenomic and metatranscriptomic analyses, which unify taxonomy and function, in investigating the ecology of dehalogenating microbial communities.}, } @article {pmid37856515, year = {2023}, author = {Johansson, MHK and Aarestrup, FM and Petersen, TN}, title = {Importance of mobile genetic elements for dissemination of antimicrobial resistance in metagenomic sewage samples across the world.}, journal = {PloS one}, volume = {18}, number = {10}, pages = {e0293169}, pmid = {37856515}, issn = {1932-6203}, mesh = {*Sewage/microbiology ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Interspersed Repetitive Sequences/genetics ; }, abstract = {We are facing an ever-growing threat from increasing antimicrobial resistance (AMR) in bacteria. To mitigate this, we need a better understanding of the global spread of antimicrobial resistance genes (ARGs). ARGs are often spread among bacteria by horizontal gene transfer facilitated by mobile genetic elements (MGE). Here we use a dataset consisting of 677 metagenomic sequenced sewage samples from 97 countries or regions to study how MGEs are geographically distributed and how they disseminate ARGs worldwide. The ARGs, MGEs, and bacterial abundance were calculated by reference-based read mapping. We found systematic differences in the abundance of MGEs and ARGs, where some elements were prevalent on all continents while others had higher abundance in separate geographic areas. Different MGEs tended to be localized to temperate or tropical climate zones, while different ARGs tended to separate according to continents. This suggests that the climate is an important factor influencing the local flora of MGEs. MGEs were also found to be more geographically confined than ARGs. We identified several integrated MGEs whose abundance correlated with the abundance of ARGs and bacterial genera, indicating the ability to mobilize and disseminate these genes. Some MGEs seemed to be more able to mobilize ARGs and spread to more bacterial species. The host ranges of MGEs seemed to differ between elements, where most were associated with bacteria of the same family. We believe that our method could be used to investigate the population dynamics of MGEs in complex bacterial populations.}, } @article {pmid37855961, year = {2023}, author = {Machineni, L and Anupoju, GR}, title = {Optimization of biomethane production from sweet sorghum bagasse using artificial neural networks combined with particle swarm algorithm.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {53}, pages = {114095-114110}, pmid = {37855961}, issn = {1614-7499}, mesh = {Anaerobiosis ; *Sorghum ; RNA, Ribosomal, 16S ; Algorithms ; Neural Networks, Computer ; Methane ; Biofuels ; Bioreactors ; }, abstract = {In the face of international movement away from fossil fuels caused pollution menace, many research labs are rushing towards next big breakthrough via effective biorefinery development employing non-edible agro-residues as feedstock. This work aims to evaluate and optimize the methane potential of underutilized full strength sweet sorghum bagasse (SSB) via anaerobic digestion (AD). Biochemical methane potential assays are set up for SSB AD under mesophilic and thermophilic conditions at four substrate-o-inoculum ratios (SIR) 3, 5, 7, and 9 with pH 6.5, 7.5, and 8.5 and with 80, 90, and 100 rpm mixing speed over 50 days. SIR 5 produced the highest cumulative biomethane yield of 4.25 L methane g[-1] VS with a shorter lag time of 7.5 days and technical digestion time of 24 days. The influence of physio-chemical parameters on AD process dynamics is supported with 16s rRNA metagenomic sequencing. Based on complete experimental data sets, two artificial neural network (ANN) models are developed to identify the relevant significance of process parameters and to predict bagasse methane potential. Further, the developed ANN model is integrated with particle swarm optimization algorithm to create ideal AD process operating conditions which maximize the target variable, biomethane. The trained and cross-validated ANN-PSO model showed good-fit-accuracy with R[2] > 0.995 and demonstrated satisfactory performance in the biomethane yield prediction from AD of non-edible agri-residues.}, } @article {pmid37855624, year = {2023}, author = {Salmaso, N and Boscaini, A and Cerasino, L and Pindo, M and Pinto, F and Segata, N and Donati, C}, title = {Draft genome sequence of the anatoxin-a producing cyanobacterium Tychonema bourrellyi B0820 isolated from the epilimnion of the deep Alpine Lake Garda.}, journal = {Microbiology resource announcements}, volume = {12}, number = {11}, pages = {e0084423}, pmid = {37855624}, issn = {2576-098X}, support = {PNRR Missione 4 Componente 2 Dalla ricerca all'impresa Investimento 1.4 Project CN00000033//Italian Ministry of University and Research - NBFC/ ; HORIZON MSCA 2021 SE 01 AlgaeNet4AV Project ID 101086437//EC | Horizon Europe | Excellent Science | HORIZON EUROPE Marie Sklodowska-Curie Actions (MSCA)/ ; }, abstract = {We report the draft genome sequence of strain B0820 of the cyanobacterium Tychonema bourrellyi isolated from the epilimnion of Lake Garda and assembled from a metagenome of a non-axenic culture. The strain analyzed was shown to produce anatoxin-a, a potent neurotoxin that can cause fatal intoxication in exposed organisms.}, } @article {pmid37855616, year = {2023}, author = {Zhang, Y and Zheng, T and Ma, D and Shi, P and Zhang, H and Li, J and Sun, Z}, title = {Probiotics Bifidobacterium lactis M8 and Lactobacillus rhamnosus M9 prevent high blood pressure via modulating the gut microbiota composition and host metabolic products.}, journal = {mSystems}, volume = {8}, number = {6}, pages = {e0033123}, pmid = {37855616}, issn = {2379-5077}, mesh = {Adult ; Mice ; Animals ; Female ; Humans ; *Gastrointestinal Microbiome ; *Bifidobacterium animalis ; *Lacticaseibacillus rhamnosus ; *Probiotics/therapeutic use ; *Hypertension/prevention & control ; }, abstract = {Elevated blood pressure affects 40% of the adult population, which accounts for high cardiovascular disease risk and further high mortality yearly. The global understanding of the gut microbiome for hypertension may provide important insights into the prevention. Bifidobacterium lactis M8 and Lactobacillus rhamnosus M9 originated from human breast milk, were able to decrease blood pressure, and modified metabolites in a high fructose-induced elevated blood pressure mouse model. Moreover, we found there was a close relationship between unexplored gut microbes and elevated blood pressure. Also, subsequently, the cross-link was explored among gut microbes, metabolites, and some metabolic pathways in gut microbial environment through introducing novel prediction methodology and bioinformatic analysis. It allowed us to hypothesize that probiotics can prevent elevated blood pressure via gut microbiota and related metabolism.Thus, utilization of dietary strategies (such as probiotics) to maintain the blood pressure level is of crucial importance.}, } @article {pmid37855604, year = {2023}, author = {Amundson, KK and Wolfe, BA and Wilkins, MJ}, title = {Twenty-five metagenome-assembled genomes recovered from the gut microbiome of the domestic ferret, Mustela putorius.}, journal = {Microbiology resource announcements}, volume = {12}, number = {11}, pages = {e0036423}, pmid = {37855604}, issn = {2576-098X}, abstract = {With the advent of metagenomics has come an increased appreciation for the gut microbiome's role in overall health of mammalian organisms. Even so, studies characterizing taxonomic and functional diversity of the ferret gut microbiome remain limited. Here, we present 25 metagenome-assembled genomes recovered from the gut microbiome of domestic ferrets.}, } @article {pmid37854337, year = {2023}, author = {Sang, X and Li, S and Guo, R and Yan, Q and Liu, C and Zhang, Y and Lv, Q and Wu, L and Ma, J and You, W and Feng, L and Sun, W}, title = {Dynamics and ecological reassembly of the human gut microbiome and the host metabolome in response to prolonged fasting.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1265425}, pmid = {37854337}, issn = {1664-302X}, abstract = {INTRODUCTION: Prolonged fasting is an intervention approach with potential benefits for individuals with obesity or metabolic disorders. Changes in gut microbiota during and after fasting may also have significant effects on the human body.

METHODS: Here we conducted a 7-days medically supervised water-only fasting for 46 obese volunteers and characterized their gut microbiota based on whole-metagenome sequencing of feces at five timepoints.

RESULTS: Substantial changes in the gut microbial diversity and composition were observed during fasting, with rapid restoration after fasting. The ecological pattern of the microbiota was also reassembled during fasting, reflecting the reduced metabolic capacity of diet-derived carbohydrates, while other metabolic abilities such as degradation of glycoproteins, amino acids, lipids, and organic acid metabolism, were enhanced. We identified a group of species that responded significantly to fasting, including 130 fasting-resistant (consisting of a variety of members of Bacteroidetes, Proteobacteria, and Fusobacteria) and 140 fasting-sensitive bacteria (mainly consisting of Firmicutes members). Functional comparison of the fasting-responded bacteria untangled the associations of taxon-specific functions (e.g., pentose phosphate pathway modules, glycosaminoglycan degradation, and folate biosynthesis) with fasting. Furthermore, we found that the serum and urine metabolomes of individuals were also substantially changed across the fasting procedure, and particularly, these changes were largely affected by the fasting-responded bacteria in the gut microbiota.

DISCUSSION: Overall, our findings delineated the patterns of gut microbiota alterations under prolonged fasting, which will boost future mechanistic and clinical intervention studies.}, } @article {pmid37853813, year = {2023}, author = {Yu, S and Wang, H and Cui, L and Wang, J and Zhang, Z and Wu, Z and Lin, X and He, N and Zou, Y and Li, S}, title = {Pectic oligosaccharides ameliorate high-fat diet-induced obesity and hepatic steatosis in association with modulating gut microbiota in mice.}, journal = {Food & function}, volume = {14}, number = {21}, pages = {9892-9906}, doi = {10.1039/d3fo02168h}, pmid = {37853813}, issn = {2042-650X}, mesh = {Animals ; Mice ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Pectins/pharmacology ; Obesity/prevention & control ; *Fatty Liver/drug therapy/etiology/prevention & control ; Oligosaccharides/pharmacology ; Mice, Inbred C57BL ; }, abstract = {Accumulating evidence has shown that gut microbiota and its metabolites have important significance in the etiology of obesity and related disorders. Prebiotics prevent and alleviate obesity by modulating the gut microbiota. However, how pectin oligosaccharides (POS) derived from pectin degradation affect gut microbiota and obesity remains unclear. To investigate the potential anti-obesity effects of POS, mice were fed a high-fat diet (HFD) for 12 weeks and a POS supplement with drinking water during the last 8 weeks. The outcomes demonstrated that POS supplementation in HFD-fed mice decreased body weight (P < 0.01), improved glucose tolerance (P < 0.001), reduced fat accumulation (P < 0.0001) and hepatic steatosis, protected intestinal barrier, and reduced pro-inflammatory cytokine levels. After fecal metagenomic sequencing, the POS corrected the gut microbiota dysbiosis caused by the HFD, as shown by the increased populations of Bifidobacterium, Lactobacillus taiwanensis, and Bifidobacterium animalis, and decreased populations of Alistipes and Erysipelatoclostridium, which were previously considered harmful bacteria. Notably, the changed gut microbiota was associated with the obesity prevention of POS. These findings demonstrate that POS regulates particular gut microbiota, which is essential owing to its ability to prevent disorders associated with obesity.}, } @article {pmid37853312, year = {2023}, author = {Li, Z and Wang, J and Xiu, X and Shi, Z and Zhang, Q and Chen, D}, title = {Evaluation of different diagnostic methods for spinal tuberculosis infection.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {695}, pmid = {37853312}, issn = {1471-2334}, mesh = {Humans ; *Mycobacterium tuberculosis/genetics ; *Tuberculosis, Spinal/diagnosis/drug therapy ; Sensitivity and Specificity ; Rifampin/pharmacology/therapeutic use ; Predictive Value of Tests ; Sputum/microbiology ; }, abstract = {BACKGROUND AND PURPOSE: Tuberculosis (TB) is the most fatal infectious disease worldwide. Approximately 24.6% of tuberculosis cases are extrapulmonary and predominantly affect the spine. It is difficult to diagnose spinal TB (STB). We aimed to evaluate the diagnostic performance of the Mycobacteria Growth Indicator Tube (MGIT)-960 culture, T-SPOT.TB, Xpert Mycobacterium tuberculosis complex (MTB)/resistance to rifampin (RIF), and Metagenomic Next-Generation Sequencing (mNGS) to detect STB.

METHODS: We assessed 126 patients presumed to have STB using these four methods. The sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) were calculated using clinical diagnosis as a reference.

RESULTS: Of the patients, 41 were diagnosed with STB and 85 with non-STB. In the STB group, the sensitivity, specificity, PPV, and NPV of the MGIT-960 culture were 29.3% (12/41), 100% (85/85), 100% (12/12), and 74.6% (85/114), respectively. The sensitivity, specificity, PPV, and NPV of T-SPOT.TB were 92.7% (38/41), 82.4% (70/85), 58.5% (31/53), and 95.9% (70/73), respectively. The sensitivity, specificity, PPV, and NPV of the Xpert MTB/RIF assay were 53.7% (22/41), 100% (85/85), 100% (22/22), and 81.7% (85/104), respectively. The sensitivity, specificity, PPV, and NPV of mNGS were 39.0% (16/41), 98.8% (84/85), 94.1% (16/17), and 77.1% (84/109), respectively. The sensitivity, specificity, PPV, and NPV of mNGS + Xpert MTB/RIF were 73.2% (30/41), 100% (85/85), 96.8% (30/31), and 72.0% (85/118), respectively. The sensitivity, specificity, PPV, and NPV of the mNGS + T-spot assay were 97.6% (40/41), 100% (85/85), 67.9% (38/56), and 75.9% (85/113), respectively. Moreover, the sensitivity, specificity, PPV, and NPV of T-spot + Xpert MTB/RIF were 95.1% (39/41), 100% (85/85), 72.2% (39/54), and 81.0% (85/105), respectively.

CONCLUSIONS: T-SPOT.TB is the most effective method for diagnosing STB; however, Xpert MTB/RIF is more reliable and can detect RIF resistance. Clinicians can use mNGS to identify pathogens in patients with spinal infections; these pathogens appeared to be more meaningful in guiding the clinical management of patients in the non-STB group. The combination of Xpert MTB/RIF and mNGS can improve the early diagnosis rate and drug resistance detection, reduce the diagnostic cycle, and provide early targeted anti-TB treatment for patients with STB.}, } @article {pmid37853183, year = {2023}, author = {Schober, I and Bunk, B and Carril, G and Freese, HM and Ojeda, N and Riedel, T and Meier-Kolthoff, JP and Göker, M and Spröer, C and Flores-Herrera, PA and Nourdin-Galindo, G and Gómez, F and Cárdenas, C and Vásquez-Ponce, F and Labra, A and Figueroa, J and Olivares-Pacheco, J and Nübel, U and Sikorski, J and Marshall, SH and Overmann, J}, title = {Ongoing diversification of the global fish pathogen Piscirickettsia salmonis through genetic isolation and transposition bursts.}, journal = {The ISME journal}, volume = {17}, number = {12}, pages = {2247-2258}, pmid = {37853183}, issn = {1751-7370}, mesh = {Animals ; Humans ; *Piscirickettsia/genetics ; *Piscirickettsiaceae Infections/veterinary/microbiology ; RNA, Ribosomal, 16S/genetics ; Fishes ; *Fish Diseases/microbiology ; }, abstract = {The management of bacterial pathogens remains a key challenge of aquaculture. The marine gammaproteobacterium Piscirickettsia salmonis is the etiological agent of piscirickettsiosis and causes multi-systemic infections in different salmon species, resulting in considerable mortality and substantial commercial losses. Here, we elucidate its global diversity, evolution, and selection during human interventions. Our comprehensive analysis of 73 closed, high quality genome sequences covered strains from major outbreaks and was supplemented by an analysis of all P. salmonis 16S rRNA gene sequences and metagenomic reads available in public databases. Genome comparison showed that Piscirickettsia comprises at least three distinct, genetically isolated species of which two showed evidence for continuing speciation. However, at least twice the number of species exist in marine fish or seawater. A hallmark of Piscirickettsia diversification is the unprecedented amount and diversity of transposases which are particularly active in subgroups undergoing rapid speciation and are key to the acquisition of novel genes and to pseudogenization. Several group-specific genes are involved in surface antigen synthesis and may explain the differences in virulence between strains. However, the frequent failure of antibiotic treatment of piscirickettsiosis outbreaks cannot be explained by horizontal acquisition of resistance genes which so far occurred only very rarely. Besides revealing a dynamic diversification of an important pathogen, our study also provides the data for improving its surveillance, predicting the emergence of novel lineages, and adapting aquaculture management, and thereby contributes towards the sustainability of salmon farming.}, } @article {pmid37853062, year = {2023}, author = {Marimón, JM and Sorrarain, A and Ercibengoa, M and Azcue, N and Alonso, M and Vidaur, L}, title = {Lung microbiome on admission in critically ill patients with acute bacterial and viral pneumonia.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {17724}, pmid = {37853062}, issn = {2045-2322}, mesh = {Humans ; *Pneumonia, Pneumococcal ; *Influenza, Human ; Critical Illness ; *COVID-19 ; SARS-CoV-2 ; Lung/microbiology ; Bacteria/genetics ; *Microbiota ; *Pneumonia, Viral ; Firmicutes ; Proteobacteria ; *Community-Acquired Infections/microbiology ; }, abstract = {Composition of pulmonary microbiome of patients with severe pneumonia is poorly known. The aim of this work was to analyse the lung microbiome of patients admitted to the intensive care unit (ICU) with severe community acquired pneumonia (CAP) between 2019 and 2021 in comparison with a control group of 6 patients undergoing digestive surgery. As a second objective, the diagnostic capabilities of metagenomics was also studied in a small group of selected patients. The lung microbiome of patients with viral (5 with Influenza A and 8 with SARS-CoV-2) pneumonia at admission showed a similar diversity as the control group (p = 0.140 and p = 0.213 respectively). Contrarily, the group of 12 patients with pneumococcal pneumonia showed a significant lower Simpson´s index (p = 0.002). In the control group (n = 6) Proteobacteria (36.6%), Firmicutes (24.2%) and Actinobacteria (23.0%) were the predominant phyla. In SARS-CoV-2 patients (n = 8), there was a predominance of Proteobacteria (mean 41.6%) (Moraxella and Pelomonas at the genus level), Actinobacteria (24.6%) (Microbacterium) and Firmicutes (22.8%) mainly Streptococcus, Staphylococcus and Veillonella. In patients with Influenza A pneumonia (n = 5) there was a predominance of Firmicutes (35.1%) mainly Streptococcus followed by Proteobacteria (29.2%) (Moraxella, Acinetobacter and Pelomonas). In the group of pneumococcal pneumonia (n = 12) two phyla predominated: Firmicutes (53.1%) (Streptococcus) and Proteobacteria (36.5%) (Haemophilus). In the 7 patients with non-pneumococcal bacterial pneumonia Haemophilus influenzae (n = 2), Legionella pneumophila (n = 2), Klebsiella pneumoniae, Streptococcus pyogenes and Leptospira were detected by metagenomics, confirming the diagnosis done using conventional microbiological techniques. The diversity of the respiratory microbiome in patients with severe viral pneumonia at ICU admission was similar to that of the control group. Contrarily, patients with pneumococcal pneumonia showed a lower grade of diversity. At initial stages of SARS-CoV-2 infection, no important alterations in the pulmonary microbiome were observed. The analysis of bacterial microbiome showed promising results as a diagnostic tool.}, } @article {pmid37852478, year = {2023}, author = {Marais, G and Valley-Omar, Z and Marais, S and McMullen, K and Bateman, K and der Westhuizen, DV and Maseko, M and Hardie, D and Brink, A}, title = {Clinical metagenomics in a resource-limited setting.}, journal = {The Journal of infection}, volume = {87}, number = {6}, pages = {604-606}, doi = {10.1016/j.jinf.2023.10.007}, pmid = {37852478}, issn = {1532-2742}, mesh = {Humans ; *Resource-Limited Settings ; *Metagenomics ; }, } @article {pmid37852461, year = {2024}, author = {Ghiotto, G and Zampieri, G and Campanaro, S and Treu, L}, title = {Strain-resolved metagenomics approaches applied to biogas upgrading.}, journal = {Environmental research}, volume = {240}, number = {Pt 2}, pages = {117414}, doi = {10.1016/j.envres.2023.117414}, pmid = {37852461}, issn = {1096-0953}, mesh = {*Biofuels ; *Computational Biology ; Hydrogen ; Metagenomics ; Nucleotides ; }, abstract = {Genetic heterogeneity is a common trait in microbial populations, caused by de novo mutations and changes in variant frequencies over time. Microbes can thus differ genetically within the same species and acquire different phenotypes. For instance, performance and stability of anaerobic reactors are linked to the composition of the microbiome involved in the digestion process and to the environmental parameters imposing selective pressure on the metagenome, shaping its evolution. Changes at the strain level have the potential to determine variations in microbial functions, and their characterization could provide new insight into ecological and evolutionary processes driving anaerobic digestion. In this work, single nucleotide variant dynamics were studied in two time-course biogas upgrading experiments, testing alternative carbon sources and the response to exogenous hydrogen addition. A cumulative total of 76,229 and 64,289 high-confidence single nucleotide variants were discerned in the experiments related to carbon substrate availability and hydrogen addition, respectively. By combining complementary bioinformatic approaches, the study reconstructed the precise strain count-two for both hydrogenotrophic archaea-and tracked their abundance over time, while also characterizing tens of genes under strong selection. Results in the dominant archaea revealed the presence of nearly 100 variants within genes encoding enzymes involved in hydrogenotrophic methanogenesis. In the bacterial counterparts, 119 mutations were identified across 23 genes associated with the Wood-Ljungdahl pathway, suggesting a possible impact on the syntrophic acetate-oxidation process. Strain replacement events took place in both experiments, confirming the trends suggested by the variants trajectories and providing a comprehensive understanding of the biogas upgrading microbiome at the strain level. Overall, this resolution level allowed us to reveal fine-scale evolutionary mechanisms, functional dynamics, and strain-level metabolic variation that could contribute to the selection of key species actively involved in the carbon dioxide fixation process.}, } @article {pmid37852332, year = {2023}, author = {Cui, T and Bai, Q and Yu, W and Guo, D and Ban, Y and Chen, K and Raza, A and Zhou, G and Wu, Q}, title = {Chromosome-level genome assembly and population genomic analysis provide novel insights into the immunity and evolution of Sogatella furcifera.}, journal = {Genomics}, volume = {115}, number = {6}, pages = {110729}, doi = {10.1016/j.ygeno.2023.110729}, pmid = {37852332}, issn = {1089-8646}, mesh = {Humans ; Animals ; *Metagenomics ; Genomics ; China ; Asia ; *Hemiptera/genetics ; Chromosomes ; }, abstract = {Sogatella furcifera is a destructive agricultural pest causing large threats to rice production in China and Southeast Asian countries. Despite recent breakthroughs in long-read sequencing, high quality genomic data are very limited in S. furcifera. In present study, a chromosome-level assembly of the S. furcifera genome was completed (0.64 GB), comprising 15 chromosomes covered 95.04% of the estimated genome size, along with other 624 small scaffolds making up the remaining 4.96% of the genome of S. furcifera. A total of 24,669 protein-coding genes, 1211 long noncoding RNA and 7595 circular RNA transcripts were predicted in this study. Comparative genomic analysis revealed rapidly evolved genes were associated with multiple immune-related pathways in S. furcifera. Genome resequencing of 44 individuals from 12 geographic populations revealed frequent gene flow among populations. The systemic genomic analysis will provide more insights into the understanding of the immunity and evolutionary adaptation of S. furcifera.}, } @article {pmid37851310, year = {2023}, author = {Park, Y and Kim, W and Kim, M and Park, W}, title = {The β-Lactamase Activity at the Community Level Confers β-Lactam Resistance to Bloom-Forming Microcystis aeruginosa Cells.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {61}, number = {9}, pages = {807-820}, pmid = {37851310}, issn = {1976-3794}, support = {NIBR202324201//National Institute of Biological Resources/ ; }, mesh = {*Microcystis/genetics ; Anti-Bacterial Agents/pharmacology ; Ampicillin/pharmacology ; beta-Lactam Resistance/genetics ; beta-Lactamases/genetics ; Microbial Sensitivity Tests ; }, abstract = {Many freshwater cyanobacteria, including Microcystis aeruginosa, lack several known antibiotic resistance genes; however, both axenic and xenic M. aeruginosa strains exhibited high antibiotic resistance against many antibiotics under our tested concentrations, including colistin, trimethoprim, and kanamycin. Interestingly, axenic PCC7806, although not the xenic NIBR18 and NIBR452 strains, displayed susceptibility to ampicillin and amoxicillin, indicating that the associated bacteria in the phycosphere could confer such antibiotic resistance to xenic strains. Fluorescence and scanning electron microscopic observations revealed their tight association, leading to possible community-level β-lactamase activity. Combinatory treatment of ampicillin with a β-lactamase inhibitor, sulbactam, abolished the ampicillin resistance in the xenic stains. The nitrocefin-based assay confirmed the presence of significant community-level β-lactamase activity. Our tested low ampicillin concentration and high β-lactamase activity could potentially balance the competitive advantage of these dominant species and provide opportunities for the less competitive species, thereby resulting in higher bacterial diversity under ampicillin treatment conditions. Non-PCR-based metagenome data from xenic NIBR18 cultures revealed the dominance of blaOXA-related antibiotic resistance genes followed by other class A β-lactamase genes (AST-1 and FAR-1). Alleviation of ampicillin toxicity could be observed only in axenic PCC7806, which had been cocultured with β-lactamase from other freshwater bacteria. Our study suggested M. aeruginosa develops resistance to old-class β-lactam antibiotics through altruism, where associated bacteria protect axenic M. aeruginosa cells.}, } @article {pmid37850871, year = {2022}, author = {Zafeiropoulos, H and Beracochea, M and Ninidakis, S and Exter, K and Potirakis, A and De Moro, G and Richardson, L and Corre, E and Machado, J and Pafilis, E and Kotoulas, G and Santi, I and Finn, RD and Cox, CJ and Pavloudi, C}, title = {metaGOflow: a workflow for the analysis of marine Genomic Observatories shotgun metagenomics data.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {37850871}, issn = {2047-217X}, mesh = {Workflow ; *Software ; *Genomics ; Metagenomics ; Computational Biology ; Metagenome ; }, abstract = {BACKGROUND: Genomic Observatories (GOs) are sites of long-term scientific study that undertake regular assessments of the genomic biodiversity. The European Marine Omics Biodiversity Observation Network (EMO BON) is a network of GOs that conduct regular biological community samplings to generate environmental and metagenomic data of microbial communities from designated marine stations around Europe. The development of an effective workflow is essential for the analysis of the EMO BON metagenomic data in a timely and reproducible manner.

FINDINGS: Based on the established MGnify resource, we developed metaGOflow. metaGOflow supports the fast inference of taxonomic profiles from GO-derived data based on ribosomal RNA genes and their functional annotation using the raw reads. Thanks to the Research Object Crate packaging, relevant metadata about the sample under study, and the details of the bioinformatics analysis it has been subjected to, are inherited to the data product while its modular implementation allows running the workflow partially. The analysis of 2 EMO BON samples and 1 Tara Oceans sample was performed as a use case.

CONCLUSIONS: metaGOflow is an efficient and robust workflow that scales to the needs of projects producing big metagenomic data such as EMO BON. It highlights how containerization technologies along with modern workflow languages and metadata package approaches can support the needs of researchers when dealing with ever-increasing volumes of biological data. Despite being initially oriented to address the needs of EMO BON, metaGOflow is a flexible and easy-to-use workflow that can be broadly used for one-sample-at-a-time analysis of shotgun metagenomics data.}, } @article {pmid37850517, year = {2023}, author = {Varadi, M and Tsenkov, M and Velankar, S}, title = {Challenges in bridging the gap between protein structure prediction and functional interpretation.}, journal = {Proteins}, volume = {}, number = {}, pages = {}, doi = {10.1002/prot.26614}, pmid = {37850517}, issn = {1097-0134}, support = {//Google DeepMind/ ; }, abstract = {The rapid evolution of protein structure prediction tools has significantly broadened access to protein structural data. Although predicted structure models have the potential to accelerate and impact fundamental and translational research significantly, it is essential to note that they are not validated and cannot be considered the ground truth. Thus, challenges persist, particularly in capturing protein dynamics, predicting multi-chain structures, interpreting protein function, and assessing model quality. Interdisciplinary collaborations are crucial to overcoming these obstacles. Databases like the AlphaFold Protein Structure Database, the ESM Metagenomic Atlas, and initiatives like the 3D-Beacons Network provide FAIR access to these data, enabling their interpretation and application across a broader scientific community. Whilst substantial advancements have been made in protein structure prediction, further progress is required to address the remaining challenges. Developing training materials, nurturing collaborations, and ensuring open data sharing will be paramount in this pursuit. The continued evolution of these tools and methodologies will deepen our understanding of protein function and accelerate disease pathogenesis and drug development discoveries.}, } @article {pmid37849822, year = {2023}, author = {Arrieta-Echeverri, MC and Fernandez, GJ and Duarte-Riveros, A and Correa-Álvarez, J and Bardales, JA and Villanueva-Mejía, DF and Sierra-Zapata, L}, title = {Multi-omics characterization of the microbial populations and chemical space composition of a water kefir fermentation.}, journal = {Frontiers in molecular biosciences}, volume = {10}, number = {}, pages = {1223863}, pmid = {37849822}, issn = {2296-889X}, abstract = {In recent years, the popularity of fermented foods has strongly increased based on their proven health benefits and the adoption of new trends among consumers. One of these health-promoting products is water kefir, which is a fermented sugary beverage based on kefir grains (symbiotic colonies of yeast, lactic acid and acetic acid bacteria). According to previous knowledge and the uniqueness of each water kefir fermentation, the following project aimed to explore the microbial and chemical composition of a water kefir fermentation and its microbial consortium, through the integration of culture-dependent methods, compositional metagenomics, and untargeted metabolomics. These methods were applied in two types of samples: fermentation grains (inoculum) and fermentation samples collected at different time points. A strains culture collection of ∼90 strains was established by means of culture-dependent methods, mainly consisting of individuals of Pichia membranifaciens, Acetobacter orientalis, Lentilactobacillus hilgardii, Lacticaseibacillus paracasei, Acetobacter pomorum, Lentilactobacillus buchneri, Pichia kudriavzevii, Acetobacter pasteurianus, Schleiferilactobacillus harbinensis, and Kazachstania exigua, which can be further studied for their use in synthetic consortia formulation. In addition, metabarcoding of each fermentation time was done by 16S and ITS sequencing for bacteria and yeast, respectively. The results show strong population shifts of the microbial community during the fermentation time course, with an enrichment of microbial groups after 72 h of fermentation. Metataxonomics results revealed Lactobacillus and Acetobacter as the dominant genera for lactic acid and acetic acid bacteria, whereas, for yeast, P. membranifaciens was the dominant species. In addition, correlation and systematic analyses of microbial growth patterns and metabolite richness allowed the recognition of metabolic enrichment points between 72 and 96 h and correlation between microbial groups and metabolite abundance (e.g., Bile acid conjugates and Acetobacter tropicalis). Metabolomic analysis also evidenced the production of bioactive compounds in this fermented matrix, which have been associated with biological activities, including antimicrobial and antioxidant. Interestingly, the chemical family of Isoschaftosides (C-glycosyl flavonoids) was also found, representing an important finding since this compound, with hepatoprotective and anti-inflammatory activity, had not been previously reported in this matrix. We conclude that the integration of microbial biodiversity, cultured species, and chemical data enables the identification of relevant microbial population patterns and the detection of specific points of enrichment during the fermentation process of a food matrix, which enables the future design of synthetic microbial consortia, which can be used as targeted probiotics for digestive and metabolic health.}, } @article {pmid37849433, year = {2023}, author = {Valadez-Cano, C and Reyes-Prieto, A and Lawrence, J}, title = {Novel virulent and temperate cyanophages predicted to infect Microcoleus associated with anatoxin-producing benthic mats.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {3319-3332}, doi = {10.1111/1462-2920.16527}, pmid = {37849433}, issn = {1462-2920}, support = {GCXE22S001//Environment and Climate Change Canada/ ; //Government of New Brunswick's Environmental Trust Fund/ ; }, mesh = {*Cyanobacteria/genetics ; Cyanobacteria Toxins ; Tropanes ; Rivers/microbiology ; }, abstract = {Cyanophages are crucial for regulating cyanobacterial populations, but their influence on anatoxin-producing Microcoleus mat dynamics remains unexplored. Here, we use metagenomics to explore phage presence in benthic mats from the Wolastoq|Saint John River (New Brunswick, Canada) and the Eel River (California, USA). We recovered multiple viral-like sequences associated with different putative bacterial hosts, including two cyanophage genomes with apparently different replication strategies. A temperate cyanophage was found integrated in the genomes of Microcoleus sp. 3 recovered from the Eel River and is phylogenetically related to Phormidium phages. We also recovered novel virulent cyanophage genomes from Wolastoq and Eel River mats that were dominated by anatoxin-producing Microcoleus species predicted to be the host. Despite the geographical distance, these genomes have similar sizes (circa 239 kbp) and share numerous orthologous genes with high sequence identity. A considerable reduction of the anatoxin-producing Microcoleus species in Wolastoq mats following the emergence of the virulent phage suggests that phage infections have an important role in limiting the abundance of this toxigenic cyanobacterium and releasing anatoxins into the surrounding water. Our results constitute the first report of cyanophages predicted to infect mat-forming Microcoleus species associated with anatoxin production.}, } @article {pmid37848997, year = {2023}, author = {Zhang, Z and Liu, Y and Zhao, W and Ji, M}, title = {Radiation impacts gene redundancy and biofilm regulation of cryoconite microbiomes in Northern Hemisphere glaciers.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {228}, pmid = {37848997}, issn = {2049-2618}, mesh = {*Ecosystem ; Ice Cover ; *Microbiota/genetics ; Multigene Family ; Climate Change ; }, abstract = {BACKGROUND: Glaciers harbor diverse microorganisms adapted to extreme conditions with high radiation, fluctuating temperature, and low nutrient availability. In glacial ecosystems, cryoconite granules are hotspots of microbial metabolic activity and could influences the biogeochemical cycle on glacier surface. Climate change could influence glacier dynamics by changing regional meteorological factors (e.g., radiation, precipitation, temperature, wind, and evaporation). Moreover, meteorological factors not only influence glacier dynamics but also directly or indirectly influence cryoconite microbiomes. However, the relationship of the meteorological factors and cryoconite microbiome are poorly understood.

RESULTS: Here, we collected 88 metagenomes from 26 glaciers distributed in the Northern Hemisphere with corresponding public meteorological data to reveal the relationship between meteorological factors and variation of cryoconite microbiome. Our results showed significant differences in taxonomic and genomic characteristics between cryoconite generalists and specialists. Additionally, we found that the biogeography of both generalists and specialists was influenced by solar radiation. Specialists with smaller genome size and lower gene redundancy were more abundant under high radiation stress, implying that streamlined genomes are more adapted to high radiation conditions. Network analysis revealed that biofilm regulation is a ubiquitous function in response to radiation stress, and hub genes were associated with the formation and dispersion of biofilms.

CONCLUSION: These findings enhance our understanding of glacier cryoconite microbiome variation on a hemispheric scale and indicate the response mechanisms to radiation stress, which will support forecasts of the ecological consequences of future climate change. Video Abstract.}, } @article {pmid37848554, year = {2023}, author = {Lücking, D and Mercier, C and Alarcón-Schumacher, T and Erdmann, S}, title = {Extracellular vesicles are the main contributor to the non-viral protected extracellular sequence space.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {112}, pmid = {37848554}, issn = {2730-6151}, support = {Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; Max Planck Research Group Archaeal Virology//Max-Planck-Gesellschaft (Max Planck Society)/ ; }, abstract = {Environmental virus metagenomes, commonly referred to as "viromes", are typically generated by physically separating virus-like particles (VLPs) from the microbial fraction based on their size and mass. However, most methods used to purify VLPs, enrich extracellular vesicles (EVs) and gene transfer agents (GTAs) simultaneously. Consequently, the sequence space traditionally referred to as a "virome" contains host-associated sequences, transported via EVs or GTAs. We therefore propose to call the genetic material isolated from size-fractionated (0.22 µm) and DNase-treated samples protected environmental DNA (peDNA). This sequence space contains viral genomes, DNA transduced by viruses and DNA transported in EVs and GTAs. Since there is no genetic signature for peDNA transported in EVs, GTAs and virus particles, we rely on the successful removal of contaminating remaining cellular and free DNA when analyzing peDNA. Using marine samples collected from the North Sea, we generated a thoroughly purified peDNA dataset and developed a bioinformatic pipeline to determine the potential origin of the purified DNA. This pipeline was applied to our dataset as well as existing global marine "viromes". Through this pipeline, we identified known GTA and EV producers, as well as organisms with actively transducing proviruses as the source of the peDNA, thus confirming the reliability of our approach. Additionally, we identified novel and widespread EV producers, and found quantitative evidence suggesting that EV-mediated gene transfer plays a significant role in driving horizontal gene transfer (HGT) in the world's oceans.}, } @article {pmid37848489, year = {2023}, author = {Bertagnolli, AD and Maritan, AJ and Tumolo, BB and Fritz, SF and Oakland, HC and Mohr, EJ and Poole, GC and Albertson, LK and Stewart, FJ}, title = {Net-spinning caddisflies create denitrifier-enriched niches in the stream microbiome.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {111}, pmid = {37848489}, issn = {2730-6151}, support = {1945941//National Science Foundation (NSF)/ ; }, abstract = {Larval net-spinning caddisflies (Hydropsychidae) function as ecosystem engineers in streams where they construct protective retreats composed of organic and inorganic material affixed with silk filtration nets that alter streambed hydrology. We hypothesized that hydropsychid bio-structures (retreats, nets) are microhabitats for microbes with oxygen-sensitive metabolisms, and therefore increase the metabolic heterogeneity of streambed microbial assemblages. Metagenomic and 16 S rRNA gene amplicon analysis of samples from a montane stream (Cherry Creek, Montana, USA) revealed that microbiomes of caddisfly bio-structures are taxonomically and functionally distinct from those of the immediately adjacent rock biofilm (~2 cm distant) and enriched in microbial taxa with established roles in denitrification, nitrification, and methane production. Genes for denitrification, high oxygen affinity terminal oxidases, hydrogenases, oxidative dissimilatory sulfite reductases, and complete ammonia oxidation are significantly enriched in caddisfly bio-structures. The results suggest a novel ecosystem engineering effect of caddisflies through the creation of low-oxygen, denitrifier-enriched niches in the stream microbiome. Facilitation of metabolic diversity in streambeds may be a largely unrecognized mechanism by which caddisflies alter whole-stream biogeochemistry.}, } @article {pmid37848477, year = {2023}, author = {Rajeev, M and Jung, I and Lim, Y and Kim, S and Kang, I and Cho, JC}, title = {Metagenome sequencing and recovery of 444 metagenome-assembled genomes from the biofloc aquaculture system.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {707}, pmid = {37848477}, issn = {2052-4463}, support = {KIMST-20210646//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; NRF-2022R1A2C3008502//National Research Foundation of Korea (NRF)/ ; }, mesh = {Animals ; Aquaculture ; Bacteria ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Biofloc technology is increasingly recognised as a sustainable aquaculture method. In this technique, bioflocs are generated as microbial aggregates that play pivotal roles in assimilating toxic nitrogenous substances, thereby ensuring high water quality. Despite the crucial roles of the floc-associated bacterial (FAB) community in pathogen control and animal health, earlier microbiota studies have primarily relied on the metataxonomic approaches. Here, we employed shotgun sequencing on eight biofloc metagenomes from a commercial aquaculture system. This resulted in the generation of 106.6 Gbp, and the reconstruction of 444 metagenome-assembled genomes (MAGs). Among the recovered MAGs, 230 were high-quality (≥90% completeness, ≤5% contamination), and 214 were medium-quality (≥50% completeness, ≤10% contamination). Phylogenetic analysis unveiled Rhodobacteraceae as dominant members of the FAB community. The reported metagenomes and MAGs are crucial for elucidating the roles of diverse microorganisms and their functional genes in key processes such as nitrification, denitrification, and remineralization. This study will contribute to scientific understanding of phylogenetic diversity and metabolic capabilities of microbial taxa in aquaculture environments.}, } @article {pmid37848186, year = {2023}, author = {Cai, Y and Gu, H and Kenney, T}, title = {Rank selection for non-negative matrix factorization.}, journal = {Statistics in medicine}, volume = {42}, number = {30}, pages = {5676-5693}, doi = {10.1002/sim.9934}, pmid = {37848186}, issn = {1097-0258}, support = {RGPIN-2017-05108//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN/4945-2014//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Humans ; *Algorithms ; *Microbiota ; Research Design ; }, abstract = {Non-Negative Matrix Factorization (NMF) is a widely used dimension reduction method that factorizes a non-negative data matrix into two lower dimensional non-negative matrices: one is the basis or feature matrix which consists of the variables and the other is the coefficients matrix which is the projections of data points to the new basis. The features can be interpreted as sub-structures of the data. The number of sub-structures in the feature matrix is also called the rank. This parameter controls the model complexity and is the only tuning parameter for the NMF model. An appropriate rank will extract the key latent features while minimizing the noise from the original data. However due to the large amount of optimization error always present in the NMF computation, the rank selection has been a difficult problem. We develop a novel rank selection method based on hypothesis testing, using a deconvolved bootstrap distribution to assess the significance level accurately. Through simulations, we compare our method with a rank selection method based on hypothesis testing using bootstrap distribution without deconvolution and a method based on cross-validation; we demonstrate that our method is not only accurate at estimating the true ranks for NMF, especially when the features are hard to distinguish, but also efficient at computation. When applied to real microbiome data (eg, OTU data and functional metagenomic data), our method also shows the ability to extract interpretable subcommunities in the data.}, } @article {pmid37848139, year = {2024}, author = {Liu, C and Shan, X and Song, L and Wang, J and Chen, H}, title = {Metagenomics-assembled analysis revealed the characteristics of antibiotic resistome and community coalescence in the soils irrigated with different irrigation materials.}, journal = {The Science of the total environment}, volume = {907}, number = {}, pages = {167868}, doi = {10.1016/j.scitotenv.2023.167868}, pmid = {37848139}, issn = {1879-1026}, mesh = {*Soil/chemistry ; *Anti-Bacterial Agents/analysis ; Wastewater ; Genes, Bacterial ; Ecosystem ; Manure ; Water/analysis ; Soil Microbiology ; }, abstract = {Antibiotic resistance has received widespread attention in recent years. Soil irrigation and fertilization are routine agricultural practices, but also lead to the spread of antibiotic resistance genes (ARGs) in soil-crop system such as via resistome coalescence. Despite community coalescence being ubiquitous and important in natural ecosystems, little research has been done to investigate resistome coalescence during soil irrigation activities. In this study, the characteristics of antibiotic resistome and community coalescence in the soils irrigated with different irrigation materials (wastewater, wastewater-river water, and wastewater-manure) have been revealed by utilizing microcosm experiments and high-throughput sequencing-based metagenomic assembly approaches. Results showed irrigation and coalescence changed soil quality and resistome. Totally, 789 unique ARGs were identified in the irrigation system, including some emerging ARGs. The abundance and diversity of ARGs increased in the coalesced soils, mainly due to the newly imported ARGs from irrigation materials. Relatively, the soils irrigated with wastewater and manure showed higher level of ARGs. Irrigation with the mixtures containing river water caused greater loss of indigenous taxa, while the community structure of mixing treatment with manure changed more dramatically. Interestingly, the succession of community in coalesced soils was influenced by transient competition for resources and ecological niche width, and the highest abundance and diversity of microorganisms and ARGs were found in the initial phase of coalescence, followed by a gradual succession towards the original community. With increasement of wastewater in the irrigation materials, the soil community showed a stepwise change rather than linear change. Notably, natural deposit of irrigation materials reduced their impacts on the ARGs in the coalesced soils. Findings provide new insights into the resistome coalescence during agricultural practices for reducing the spread risks of ARGs.}, } @article {pmid37847957, year = {2023}, author = {Davison, HR and Hurst, GDD}, title = {Hidden from plain sight: Novel Simkaniaceae and Rhabdochlamydiaceae diversity emerging from screening genomic and metagenomic data.}, journal = {Systematic and applied microbiology}, volume = {46}, number = {6}, pages = {126468}, doi = {10.1016/j.syapm.2023.126468}, pmid = {37847957}, issn = {1618-0984}, mesh = {Animals ; *Metagenome ; *Chlamydiales/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Bacteria ; Metagenomics/methods ; Mammals/genetics ; }, abstract = {Chlamydiota are an ancient and hyperdiverse phylum of obligate intracellular bacteria. The best characterized representatives are pathogens or parasites of mammals, but it is thought that their most common hosts are microeukaryotes like Amoebozoa. The diversity in taxonomy, evolution, and function of non-pathogenic Chlamydiota are slowly being described. Here we use data mining techniques and genomic analysis to extend our current knowledge of Chlamydiota diversity and its hosts, in particular the Order Parachlamydiales. We extract one Rhabdochlamydiaceae and three Simkaniaceae Metagenome-Assembled Genomes (MAGs) from NCBI Short Read Archive deposits of ciliate and algal genome sequencing projects. We then use these to identify a further 14 and 8 MAGs respectively amongst existing, unidentified environmental assemblies. From these data we identify two novel clades with host associated data, for which we propose the names "Sacchlamyda saccharinae" (Family Rhabdochlamydiaceae) and "Amphrikana amoebophyrae" (Family Simkaniaceae), as well as a third new clade of environmental MAGs "Acheromyda pituitae" (Family Rhabdochlamydiaceae). The extent of uncharacterized diversity within the Rhabdochlamydiaceae and Simkaniaceae is indicated by 16 of the 22 MAGs being evolutionarily distant from currently characterised genera. Within our limited data, there was great predicted diversity in Parachlamydiales metabolism and evolution, including the potential for metabolic and defensive symbioses as well as pathogenicity. These data provide an imperative to link genomic diversity in metagenomics data to their associated eukaryotic host, and to develop onward understanding of the functional significance of symbiosis with this hyperdiverse clade.}, } @article {pmid37846988, year = {2023}, author = {Langat, SK and Kerich, G and Cinkovich, S and Johnson, J and Ambale, J and Yalwala, S and Opot, B and Garges, E and Ojwang, E and Eyase, F}, title = {Genome sequences of Phasi Charoen-like phasivirus and Fako virus from Aedes aegypti mosquitoes collected in coastal Kenya.}, journal = {Microbiology resource announcements}, volume = {12}, number = {11}, pages = {e0067823}, pmid = {37846988}, issn = {2576-098X}, support = {P0116_22_KY//Global Emerging Infections Surveillance (GEIS)/ ; }, abstract = {We report the sequencing of two viruses, Phasi Charoen-like phasivirus (PCLV) and Fako virus (FAKV), which were detected in a pool of Aedes aegypti from Kenya. Analysis showed a high similarity of PCLV to publicly available PCLV genomes from Kenya. FAKV showed a high genetic divergence from publicly available FAKV genomes.}, } @article {pmid37846986, year = {2023}, author = {Jiang, H and Luo, J and Liu, Q and Ogunyemi, SO and Ahmed, T and Li, B and Yu, S and Wang, X and Yan, C and Chen, J and Li, B}, title = {Rice bacterial leaf blight drives rhizosphere microbial assembly and function adaptation.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0105923}, pmid = {37846986}, issn = {2165-0497}, support = {27306C2006/ES/NIEHS NIH HHS/United States ; }, mesh = {*Oryza ; Rhizosphere ; Soil Microbiology ; Bacteria ; *Microbiota ; }, abstract = {Our results suggest that rhizosphere bacteria are more sensitive to bacterial leaf blight (BLB) than fungi. BLB infection decreased the diversity of the rhizosphere bacterial community but increased the complexity and size of the rhizosphere microbial community co-occurrence networks. In addition, the relative abundance of the genera Streptomyces, Chitinophaga, Sphingomonas, and Bacillus increased significantly. Finally, these findings contribute to the understanding of plant-microbiome interactions by providing critical insight into the ecological mechanisms by which rhizosphere microbes respond to phyllosphere diseases. In addition, it also lays the foundation and provides data to support the use of plant microbes to promote plant health in sustainable agriculture, providing critical insight into ecological mechanisms.}, } @article {pmid37846981, year = {2023}, author = {Uchimiya, M and Elliott, LE and Derito, CM and Hay, AG}, title = {Metagenome-assembled genomes from sugarcane mill mud.}, journal = {Microbiology resource announcements}, volume = {12}, number = {11}, pages = {e0056823}, pmid = {37846981}, issn = {2576-098X}, support = {//U.S. Department of Agriculture (USDA)/ ; }, abstract = {The genomes of 11 bacteria and 3 archaea were assembled from metagenomic DNA extracted from sugarcane mill mud. These metagenome-assembled genomes ranged from 1.79 to 6.45 Mb, with 2,263 to 5,551 predicted proteins, 80.65% to 100% genome completeness, and 43.19% to 68.02% G+C content.}, } @article {pmid37846600, year = {2023}, author = {Li, Y and Liu, Q and Zhang, L and Zou, J and He, R and Zhou, Y and Qian, C and Zhu, Y and Chen, R and Zhang, Y and Cai, P and Wang, M and Shao, W and Ji, M and Wu, H and Zhang, F and Liu, Z and Liu, Y}, title = {Washed microbiota transplantation reduces glycemic variability in unstable diabetes.}, journal = {Journal of diabetes}, volume = {}, number = {}, pages = {}, doi = {10.1111/1753-0407.13485}, pmid = {37846600}, issn = {1753-0407}, support = {2022YFA0806103//National Key R&D Program of China/ ; 81770778//National Natural Science Foundation of China/ ; 81800724//National Natural Science Foundation of China/ ; 81800735//National Natural Science Foundation of China/ ; 82070849//National Natural Science Foundation of China/ ; 82270871//National Natural Science Foundation of China/ ; BK20180672//Natural Science Foundation of Jiangsu Province/ ; 18KJB310005//Natural Science Foundation of the Jiangsu Higher Education Institutions/ ; BE2022794//the Jiangsu Provincial Key Research Development Program/ ; }, abstract = {BACKGROUND: Dysbiosis of gut microbiota is causally linked to impaired host glucose metabolism. We aimed to study effects of the new method of fecal microbiota transplantation, washed microbiota transplantation (WMT), on reducing glycemic variability (GV) in unstable diabetes.

METHODS: Fourteen eligible patients received three allogenic WMTs and were followed up at 1 week, 1 month, and 3 months. Primary outcomes were daily insulin dose, glucose excursions during meal tests, and GV indices calculated from continuous monitoring or self-monitoring glucose values. Secondary outcomes were multiomics data, including 16S rRNA gene sequencing, metagenomics, and metabolomics to explore underlying mechanisms.

RESULTS: Daily insulin dose and glucose excursions markedly dropped, whereas GV indices significantly improved up to 1 month. WMT increased gut microbial alpha diversity, beta diversity, and network complexity. Taxonomic changes featured lower abundance of genera Bacteroides and Escherichia-Shigella, and higher abundance of genus Prevotella. Metagenomics functional annotations revealed enrichment of distinct microbial metabolic pathways, including methane biosynthesis, citrate cycle, amino acid degradation, and butyrate production. Derived metabolites correlated significantly with improved GV indices. WMT did not change circulating inflammatory cytokines, enteroendocrine hormones, or C-peptide.

CONCLUSIONS: WMT showed strong ameliorating effect on GV, raising the possibility of targeting gut microbiota as an effective regimen to reduce GV in diabetes.}, } @article {pmid37846356, year = {2023}, author = {Mathur, H and Mechoud, MA and Matthews, C and Lordan, C and FitzGerald, JA and Beresford, T and Cotter, PD}, title = {Methods to mitigate Escherichia coli blooms in human ex vivo colon model experiments using the high throughput micro-Matrix bioreactor fermentation system.}, journal = {MethodsX}, volume = {11}, number = {}, pages = {102393}, pmid = {37846356}, issn = {2215-0161}, abstract = {Ex vivo colon model experiments are frequently employed as a means to assess the gut microbiome modulating potential of different foods, food ingredients and dietary supplements. A number of useful models already exist; however, they tend to be relatively low in terms of throughput (3-4 samples per experiment) with a long experiment duration of one to a number of weeks. Therefore, a need for a high-throughput system with a short duration time is required to enable screening of large numbers of samples. Therefore, we report here on the development of a system based on the Applikon micro-Matrix bioreactor which has the capacity to run 24 samples with an experiment duration of 48 h. However, Escherichia coli blooms are a common problem encountered in this model. Here, we describe the factors that contribute to such blooms and provide approaches to address them, providing:•Step by step optimisation of processes involved in conducting ex vivo distal colon experiments using the micro-Matrix bioreactor fermentation platform•Recommended steps for users on how to attenuate E. coli blooms in such ex vivo colon model experiments.}, } @article {pmid37846203, year = {2023}, author = {Bhat, AH and Tak, H and Ganai, BA and Malik, IM and Bhat, TA}, title = {Bacteria associated with ovine gut parasites Trichuris ovis and Haemonchus contortus.}, journal = {Journal of helminthology}, volume = {97}, number = {}, pages = {e75}, doi = {10.1017/S0022149X23000573}, pmid = {37846203}, issn = {1475-2697}, mesh = {Animals ; Sheep ; *Haemonchus/genetics ; *Parasites/genetics ; Trichuris ; RNA, Ribosomal, 16S/genetics ; *Nematoda/genetics ; Bacteria/genetics ; *Sheep Diseases/parasitology ; *Haemonchiasis/parasitology ; }, abstract = {An associated microbiome of any host helps it in different metabolic processes ranging from the decomposition of food to the maturation of gametes. Organisms with a parasitic mode of life, though present at nutritious sites inside their host, maintain their own microbiome. Nevertheless, the comprehensive characterization and functionality of microbiome in parasitic organisms remain understudied. We selected two nematode parasites of Kashmir Merino sheep viz;Haemonchus contortus and Trichuris ovis based on their higher prevalence, difference in mode of nutrition, habitation site and effect on host. The objective of the study was to explore the bacteria associated with these parasitic nematodes of sheep. We adopted a 16S rRNA metagenomic sequencing approach to estimate and compare the bacterial communities present in these two nematode species. Nematode parasites from Kashmir Merino sheep were identified morphologically and confirmed with DNA characterization. H. contortus was dominated by phylum Proteobacteria (57%), Firmicutes (25%), Bacteroidota (15%) and Actinobacteriota (3%). Conversely, T. ovis showed Proteobacteria (78%) followed by Firmicutes (8%), Bacteroidota (8%), Actinobacteriota (1%), Fusobacteriota (1%) and other phyla (4%). This study provides a comprehensive account of the microbiome composition of H. contortus and T. ovis, both of which are highly prevalent among Kashmir Merino sheep. Additionally, T. ovis exhibited a greater bacterial diversity compared to H. contortus. Notably, these nematodes were found to harbor certain pathogenic bacteria. This study can further be carried forward in gaining insights into the complex relationship between the microbiota of a parasite and its pathogenicity, reproductive potential and host microbiome modification.}, } @article {pmid37846038, year = {2023}, author = {Sato, N and Uematsu, M and Fujimoto, K and Uematsu, S and Imoto, S}, title = {ggkegg: analysis and visualization of KEGG data utilizing the grammar of graphics.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {10}, pages = {}, pmid = {37846038}, issn = {1367-4811}, mesh = {*Genome ; *Software ; Documentation ; }, abstract = {SUMMARY: The Kyoto Encyclopedia of Genes and Genomes (KEGG) database serves as a valuable systems biology resource and is widely utilized in diverse research fields. However, existing software does not allow flexible visualization and network analyses of the vast and complex KEGG data. We developed ggkegg, an R package that integrates KEGG information with ggplot2 and ggraph. ggkegg enables enhanced visualization and network analyses of KEGG data. We demonstrate the utility of the package by providing examples of its application in single-cell, bulk transcriptome, and microbiome analyses. ggkegg may empower researchers to analyze complex biological networks and present their results effectively.

The package and user documentation are available at: https://github.com/noriakis/ggkegg.}, } @article {pmid37845315, year = {2023}, author = {Odenwald, MA and Lin, H and Lehmann, C and Dylla, NP and Cole, CG and Mostad, JD and Pappas, TE and Ramaswamy, R and Moran, A and Hutchison, AL and Stutz, MR and Dela Cruz, M and Adler, E and Boissiere, J and Khalid, M and Cantoral, J and Haro, F and Oliveira, RA and Waligurski, E and Cotter, TG and Light, SH and Beavis, KG and Sundararajan, A and Sidebottom, AM and Reddy, KG and Paul, S and Pillai, A and Te, HS and Rinella, ME and Charlton, MR and Pamer, EG and Aronsohn, AI}, title = {Bifidobacteria metabolize lactulose to optimize gut metabolites and prevent systemic infection in patients with liver disease.}, journal = {Nature microbiology}, volume = {8}, number = {11}, pages = {2033-2049}, pmid = {37845315}, issn = {2058-5276}, support = {T32DK007074//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; U01AA026975//U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)/ ; }, mesh = {Humans ; Mice ; Animals ; *Lactulose ; *Hepatic Encephalopathy/drug therapy/prevention & control ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {Progression of chronic liver disease is precipitated by hepatocyte loss, inflammation and fibrosis. This process results in the loss of critical hepatic functions, increasing morbidity and the risk of infection. Medical interventions that treat complications of hepatic failure, including antibiotic administration for systemic infections and lactulose treatment for hepatic encephalopathy, can impact gut microbiome composition and metabolite production. Here, using shotgun metagenomic sequencing and targeted metabolomic analyses on 847 faecal samples from 262 patients with acute or chronic liver disease, we demonstrate that patients hospitalized for liver disease have reduced microbiome diversity and a paucity of bioactive metabolites, including short-chain fatty acids and bile acid derivatives, that impact immune defences and epithelial barrier integrity. We find that patients treated with the orally administered but non-absorbable disaccharide lactulose have increased densities of intestinal bifidobacteria and reduced incidence of systemic infections and mortality. Bifidobacteria metabolize lactulose, produce high concentrations of acetate and acidify the gut lumen in humans and mice, which, in combination, can reduce the growth of antibiotic-resistant bacteria such as vancomycin-resistant Enterococcus faecium in vitro. Our studies suggest that lactulose and bifidobacteria serve as a synbiotic to reduce rates of infection in patients with severe liver disease.}, } @article {pmid37844141, year = {2023}, author = {Wu, D and Xie, J and Liu, Y and Jin, L and Li, G and An, T}, title = {Metagenomic and Machine Learning Meta-Analyses Characterize Airborne Resistome Features and Their Hosts in China Megacities.}, journal = {Environmental science & technology}, volume = {57}, number = {43}, pages = {16414-16423}, doi = {10.1021/acs.est.3c02593}, pmid = {37844141}, issn = {1520-5851}, mesh = {*Genes, Bacterial ; *Metagenome ; Cities ; Anti-Bacterial Agents/pharmacology ; China ; }, abstract = {Urban ambient air contains a cocktail of antibiotic resistance genes (ARGs) emitted from various anthropogenic sites. However, what is largely unknown is whether the airborne ARGs exhibit site-specificity or their pathogenic hosts persistently exist in the air. Here, by retrieving 1.2 Tb metagenomic sequences (n = 136), we examined the airborne ARGs from hospitals, municipal wastewater treatment plants (WWTPs) and landfills, public transit centers, and urban sites located in seven of China's megacities. As validated by the multiple machine learning-based classification and optimization, ARGs' site-specificity was found to be the most apparent in hospital air, with featured resistances to clinical-used rifamycin and (glyco)peptides, whereas the more environmentally prevalent ARGs (e.g., resistance to sulfonamide and tetracycline) were identified being more specific to the nonclinical ambient air settings. Nearly all metagenome-assembled genomes (MAGs) that possessed the site-featured resistances were identified as pathogenic taxa, which occupied the upper-representative niches in all the neutrally distributed airborne microbial community (P < 0.01, m = 0.22-0.50, R[2] = 0.41-0.86). These niche-favored putative resistant pathogens highlighted the enduring antibiotic resistance hazards in the studied urban air. These findings are critical, albeit the least appreciated until our study, to gauge the airborne dimension of resistomes' features and fates in urban atmospheric environments.}, } @article {pmid37844077, year = {2023}, author = {Gao, Y and Sun, F}, title = {Batch normalization followed by merging is powerful for phenotype prediction integrating multiple heterogeneous studies.}, journal = {PLoS computational biology}, volume = {19}, number = {10}, pages = {e1010608}, pmid = {37844077}, issn = {1553-7358}, support = {R01 GM131407/GM/NIGMS NIH HHS/United States ; }, mesh = {Reproducibility of Results ; *Algorithms ; *Machine Learning ; Genomics ; Phenotype ; }, abstract = {Heterogeneity in different genomic studies compromises the performance of machine learning models in cross-study phenotype predictions. Overcoming heterogeneity when incorporating different studies in terms of phenotype prediction is a challenging and critical step for developing machine learning algorithms with reproducible prediction performance on independent datasets. We investigated the best approaches to integrate different studies of the same type of omics data under a variety of different heterogeneities. We developed a comprehensive workflow to simulate a variety of different types of heterogeneity and evaluate the performances of different integration methods together with batch normalization by using ComBat. We also demonstrated the results through realistic applications on six colorectal cancer (CRC) metagenomic studies and six tuberculosis (TB) gene expression studies, respectively. We showed that heterogeneity in different genomic studies can markedly negatively impact the machine learning classifier's reproducibility. ComBat normalization improved the prediction performance of machine learning classifier when heterogeneous populations are present, and could successfully remove batch effects within the same population. We also showed that the machine learning classifier's prediction accuracy can be markedly decreased as the underlying disease model became more different in training and test populations. Comparing different merging and integration methods, we found that merging and integration methods can outperform each other in different scenarios. In the realistic applications, we observed that the prediction accuracy improved when applying ComBat normalization with merging or integration methods in both CRC and TB studies. We illustrated that batch normalization is essential for mitigating both population differences of different studies and batch effects. We also showed that both merging strategy and integration methods can achieve good performances when combined with batch normalization. In addition, we explored the potential of boosting phenotype prediction performance by rank aggregation methods and showed that rank aggregation methods had similar performance as other ensemble learning approaches.}, } @article {pmid37843556, year = {2023}, author = {Zheng, X and Hu, N and Liu, J and Zhao, K and Li, H and Wang, J and Zhang, M and Zhang, L and Song, L and Lyu, Y and Cui, M and Ding, L and Wang, J}, title = {Cervicovaginal microbiota disorder combined with the change of cytosine phosphate guanine motif- toll like receptor 9 axis was associated with cervical cancerization.}, journal = {Journal of cancer research and clinical oncology}, volume = {149}, number = {19}, pages = {17371-17381}, pmid = {37843556}, issn = {1432-1335}, mesh = {Female ; Humans ; Bacteria ; *Carcinogenesis ; *Microbiota ; Phosphates ; *Toll-Like Receptor 9/genetics/metabolism ; *Uterine Cervical Dysplasia/genetics/microbiology/pathology ; *Uterine Cervical Neoplasms/genetics/microbiology/pathology ; *Vagina/microbiology ; *Cervix Uteri/microbiology ; }, abstract = {BACKGROUND: Convincing studies demonstrated that cervicovaginal microbiota disorder and toll-like receptor 9 (TLR9) high expression were related to cervical carcinogenesis. However, the effects of cervicovaginal microbiota integration TLR9 in cervical cancerization are unclear. Based on the biological basis that unmethylated cytosine-phosphate-guanine (CpG) motifs of bacteria could activate TLR9, we explored the effects of cervicovaginal microbiota disorder and CpG motif-TLR9 axis change in cervical carcinogenesis.

METHODS: A total of 341 participants, including 124 normal cervical (NC), 90 low-grade cervical intraepithelial neoplasia (CIN1), 78 high-grade cervical intraepithelial neoplasia (CIN2/3) and 49 squamous cervical cancer (SCC), diagnosed by pathology were enrolled in the study. Here, metagenomic shotgun sequencing was used to reveal cervicovaginal microbiota characteristics, and TLR9 protein was detected by western blotting.

RESULTS: Our results showed that the diversity of cervicovaginal microbiota gradually increased along with the poor development of cervical lesions, showing the abundance of Lactobacillus crispatus and Lactobacillus iners decreased, while the abundance of pathogenic bacteria gradually increased. The level of TLR9 expression was gradually increased with cervicovaginal microbiota diversity increasing, the abundance of Lactobacillus decreasing, and we found a positive correlation dependency relationship (r = 0.384, P = 0.002) between TLR9 and GTCGTT motif content. Stratified analysis based on HPV16 infection, we found that the characteristics of cervicovaginal microbiota and increased TLR9 expression were also closely related to HPV16 infection.

CONCLUSIONS: Cervicovaginal microbiota dysbiosis might lead to the CpG motif increased, which was closely associated with TLR9 high expression, and ultimately might promote the progression of cervical lesions.}, } @article {pmid37843377, year = {2023}, author = {Ang, WSL and Burleigh, O and Frail, S and Santos, YVS and Tyagi, B and Li, F-W}, title = {Genome sequence of a symbiotic cyanobacterium from the flowering plant Gunnera tinctoria.}, journal = {Microbiology resource announcements}, volume = {12}, number = {11}, pages = {e0056323}, pmid = {37843377}, issn = {2576-098X}, support = {1831428//National Science Foundation (NSF)/ ; }, abstract = {Metagenomic analysis of the symbiotic cyanobacteria colonies within Gunnera tinctoria stems revealed a new strain of Nostoc. Here, we report its genome sequence.}, } @article {pmid37843286, year = {2023}, author = {Claesen, J and Brown, JM}, title = {Predicting cardiovascular disease risk from gut microbial genes.}, journal = {mBio}, volume = {14}, number = {6}, pages = {e0197023}, pmid = {37843286}, issn = {2150-7511}, support = {R01 DK120679/DK/NIDDK NIH HHS/United States ; R01 AI153173/AI/NIAID NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; R01 DK130227/DK/NIDDK NIH HHS/United States ; P50 AA024333/AA/NIAAA NIH HHS/United States ; }, abstract = {Gut bacteria-driven production of trimethylamine (TMA) is strongly associated with cardiovascular disease. Borton et al. (mBio 14:e01511-23, 2023, https://doi.org/10.1128/mbio.01511-23) introduce the Methylated Amine Gene Inventory of Catabolism database (MAGICdb), comprehensively cataloging pathways involved in TMA metabolism. By integrating transcriptomics, proteomics, and metagenomic data, this work identifies key bacterial players in the process and can link gut microbial gene content to fecal TMA concentrations. This work shows that methylated amine metabolism is a keystone microbiome process carried out by a small proportion of the community. Proatherogenic pathways are more widely distributed among the gut microbiota, and new TMA-reducing genera were identified that might offer new potential for probiotic strategies or targeted microbiome interventions. Remarkably, MAGICdb's power to predict cardiovascular disease risk matches an approach using more traditional lipid risk factors. This open source will be a valuable tool for the community to link methylated amine metabolism to gut microbiome-related human health conditions.}, } @article {pmid37843219, year = {2024}, author = {Liu, X and Liu, Y and Liu, J and Zhang, H and Shan, C and Guo, Y and Gong, X and Cui, M and Li, X and Tang, M}, title = {Correlation between the gut microbiome and neurodegenerative diseases: a review of metagenomics evidence.}, journal = {Neural regeneration research}, volume = {19}, number = {4}, pages = {833-845}, pmid = {37843219}, issn = {1673-5374}, abstract = {A growing body of evidence suggests that the gut microbiota contributes to the development of neurodegenerative diseases via the microbiota-gut-brain axis. As a contributing factor, microbiota dysbiosis always occurs in pathological changes of neurodegenerative diseases, such as Alzheimer's disease, Parkinson's disease, and amyotrophic lateral sclerosis. High-throughput sequencing technology has helped to reveal that the bidirectional communication between the central nervous system and the enteric nervous system is facilitated by the microbiota's diverse microorganisms, and for both neuroimmune and neuroendocrine systems. Here, we summarize the bioinformatics analysis and wet-biology validation for the gut metagenomics in neurodegenerative diseases, with an emphasis on multi-omics studies and the gut virome. The pathogen-associated signaling biomarkers for identifying brain disorders and potential therapeutic targets are also elucidated. Finally, we discuss the role of diet, prebiotics, probiotics, postbiotics and exercise interventions in remodeling the microbiome and reducing the symptoms of neurodegenerative diseases.}, } @article {pmid37842616, year = {2023}, author = {Yang, SL and Gao, Y and Han, ZY and Du, X and Liu, W and Jin, SG and Bi, Y and Chen, PF and Yue, CS and Wu, JH and Lai, QQ and Tang, YJ and Wang, XT and Ji, YY and Zhao, MY and Kang, K and Yu, KJ}, title = {Successful treatment of near-fatal pulmonary embolism and cardiac arrest in an adult patient with fulminant psittacosis-induced severe acute respiratory distress syndrome after veno-venous extracorporeal membrane oxygenation rescue: A case report and follow-up.}, journal = {Heliyon}, volume = {9}, number = {10}, pages = {e20562}, pmid = {37842616}, issn = {2405-8440}, abstract = {BACKGROUND: Veno-venous extracorporeal membrane oxygenation (ECMO) was successfully performed for the rescue of an adult patient with severe acute respiratory distress syndrome (ARDS) induced by fulminant psittacosis, and then a near-fatal pulmonary embolism (PE) and cardiac arrest (CA) of the same patient was cured through catheter-directed thrombolysis.

CASE PRESENTATION: A 51-year-old female patient was admitted to the hospital on September 10, 2021 due to slurred speech, weakness in lower limbs, dizziness, and nausea. Subsequently, she developed confusion and was transferred to the intensive care unit (ICU), where she received anti-shock, antibiotics, invasive mechanical ventilation (IMV), and veno-venous ECMO due to the diagnosis of severe pneumonia, severe ARDS, and septic shock based on comprehensive physical examination, laboratory tests, and imaging findings. The metagenomic next-gengeration sequencing (m-NGS) in the bronchoalveolar lavage fluid (BALF) suggested that the pathogen was chlamydia psittaci, so the antibiotics were adjusted to doxycycline combined with azithromycin. After withdrawal from ECMO, ultrasound (US) re-examination of the left lower limb revealed inter-muscular vein thrombosis, following which heparin was replaced by subcutaneous injection of 0.4ml enoxaparin sodium twice daily for anti-coagulation therapy. After withdrawal from IMV, the patient suffered sudden CA and successful cardiopulmonary resuscitation (CPR), and emergency pulmonary angiography (PA) was performed to show bilateral main pulmonary artery embolism. After immediate catheter-directed thrombolysis and placement of an inferior vena cava filter, the patient's condition gradually stabilized.

CONCLUSIONS: Veno-venous ECMO can be successfully performed as an emergency life-saving treatment for patients with severe ARDS induced by fulminant psittacosis, and during ECMO regular examinations should be conducted to detect and manage thrombosis in time, thereby avoiding the occurrence of near-fatal PE and CA.}, } @article {pmid37842004, year = {2023}, author = {Xu, L and Fang, C}, title = {Case Report: Omadacycline in the treatment of macrolide-unresponsive Mycoplasma pneumoniae pneumonia in an adolescent patient.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1244398}, pmid = {37842004}, issn = {2235-2988}, mesh = {Adult ; Humans ; Adolescent ; Child ; Macrolides ; Mycoplasma pneumoniae ; Drug Resistance, Bacterial ; Anti-Bacterial Agents/adverse effects ; *Pneumonia, Mycoplasma/drug therapy ; Tetracyclines/therapeutic use/pharmacology ; *Community-Acquired Infections/drug therapy/microbiology ; }, abstract = {Omadacycline is a novel tetracycline antibiotic that exhibits good in vitro antibacterial activity against atypical pathogens such as Mycoplasma pneumoniae. It is approved for the treatment of adults with community-acquired bacterial pneumonia. However, the safety and efficacy of omadacycline in pediatric patients under 18 years of age have not yet been established. In the present paper, we report a case of pediatric community-acquired pneumonia in which initial empirical anti-infective therapy had failed. The patient received empirical anti-infective therapy with azithromycin and other antimicrobial agents upon admission but showed a poor clinical response and developed secondary tinnitus and liver dysfunction. After the confirmation of M. pneumoniae infection through metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid, an antibiotic switch to omadacycline was made. Thereafter, the patient's condition improved, and no adverse reactions were observed. These findings demonstrate that mNGS enables the identification of infection-causing pathogens in patients with unresponsive pneumonia. Omadacycline can be considered as an alternative option for anti-infective therapy in pediatric M. pneumoniae pneumonia, especially when the presence of bacterial resistance, adverse drug reactions, or organ failure are taken into consideration.}, } @article {pmid37841999, year = {2023}, author = {Rodenes-Gavidia, A and Lamelas, A and Bloor, S and Hobson, A and Treadway, S and Haworth, J and Vijayakumar, V and Naghibi, M and Day, R and Chenoll, E}, title = {An insight into the functional alterations in the gut microbiome of healthy adults in response to a multi-strain probiotic intake: a single arm open label trial.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1240267}, pmid = {37841999}, issn = {2235-2988}, mesh = {Humans ; Young Adult ; Dietary Supplements ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; *Lacticaseibacillus rhamnosus ; *Probiotics ; }, abstract = {BACKGROUND: Probiotic supplements, by definition, provide a benefit to the host, but few studies have investigated the effect of probiotic supplements in healthy adult populations.

PURPOSE: The present, single arm, open label clinical trial, evaluated compositional and functional changes in the fecal microbiome of healthy adults after supplementation with a 14-strain probiotic.

METHODS: We analysed the effect of a 14-strain probiotic blend (Bacillus subtilis NCIMB 30223, Bifidobacterium bifidum NCIMB 30179, B. breve NCIMB 30180, B. infantis NCIMB 30181, B. longum NCIMB 30182, Lactobacillus helveticus NCIMB 30184, L. delbrueckii subsp. bulgaricus NCIMB 30186, Lacticaseibacillus paracasei NCIMB 30185, Lactiplantibacillus plantarum NCIMB 30187, Lacticaseibacillus rhamnosus NCIMB 30188, L. helveticus NCIMB 30224, Lactobacillus salivarius NCIMB 30225, Lactococcus lactis subsp. lactis NCIMB 30222, and Streptococcus thermophilus NCIMB 30189), on the faecal microbiota of healthy young adults (n=41) in a single arm study. The adults consumed 4 capsules daily of the 14 strain blend(8 billion colony forming units/day) for 8 weeks. Compositional and functional changes in faecal microbiota before and after supplementation were assessed using shotgun metagenomic sequencing. Fasting breath analysis, faecal biochemistry and bowel habits were also assessed.

RESULTS: In healthy adult participants, no significant changes to the overall alpha- or beta-diversity was observed after 8 weeks of multi-strain probiotic supplementation. However, in a simplified model that considered only time and individual differences, significant decreases (p < 0.05) in family Odoribacteraceae and Bacteroidaceae abundance and a significant increase (p < 0.05) in genus Megamonas abundance were observed. At a functional level, there were significant changes in functional gene abundance related to several functional pathways, including phenylalanine metabolism, O-antigen nucleotide sugar biosynthesis, bacterial chemotaxis, and flagellar assembly. No significant changes in stool form or frequency, fecal biochemistry, or methane and hydrogen breath tests were observed.

CONCLUSION: In healthy young adults, overall alpha- and beta-diversity did not change in response to probiotic intake even though modest compositional changes at the family and genus level were observed. However, at functional level, results identified changes in gene abundance for several functional pathways.}, } @article {pmid37841844, year = {2023}, author = {Benton, L and Lopez-Galvez, N and Herman, C and Caporaso, G and Cope, E and Rosales, C and Gameros, M and Lothrop, N and Martínez, F and Wright, A and Carr, T and Beamer, P}, title = {Environmental and Structural Factors Associated with Bacterial Diversity in Household Dust Across the Arizona-Sonora Border.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {37841844}, support = {UH3 HL147016/HL/NHLBI NIH HHS/United States ; R21 AI176305/AI/NIAID NIH HHS/United States ; P30 ES006694/ES/NIEHS NIH HHS/United States ; R01 AI146131/AI/NIAID NIH HHS/United States ; R01 AI149754/AI/NIAID NIH HHS/United States ; R01 HD104618/HD/NICHD NIH HHS/United States ; P01 AI148104/AI/NIAID NIH HHS/United States ; UG1 HL139054/HL/NHLBI NIH HHS/United States ; U01 HL130045/HL/NHLBI NIH HHS/United States ; UH3 OD023282/OD/NIH HHS/United States ; UG3 HL147016/HL/NHLBI NIH HHS/United States ; R01 HL132523/HL/NHLBI NIH HHS/United States ; R01 AI135108/AI/NIAID NIH HHS/United States ; }, abstract = {We previously reported that asthma prevalence was higher in the United States (US) compared to Mexico (MX) (25.8% vs 8.4%). This investigation assessed differences in microbial dust composition in relation to demographic and housing characteristics on both sides of the US-MX Border. Forty homes were recruited in the US and MX. Home visits collected floor dust and documented occupants' demographics, asthma prevalence, and housing structure and use characteristics. US households were more likely to have inhabitants who reported asthma when compared with MX households (30% vs 5%) and had significantly different flooring types. The percentage of households on paved roads, with flushing toilets, with piped water and with air conditioning was higher in the US, while dust load was higher in MX. Significant differences exist between countries in the microbial composition of the floor dust. Dust from US homes was enriched with Geodermatophilus, whereas dust from Mexican homes was enriched with Alishewanella and Chryseomicrobium. A predictive metagenomics analysis identified 68 significantly differentially abundant functional pathways between US and MX. This study documented multiple structural, environmental, and demographic differences between homes in the US and MX that may contribute to significantly different microbial composition of dust observed in these two countries.}, } @article {pmid37841727, year = {2023}, author = {Yu, CW and Zhu, XF and Huang, C and Meng, HD and Cao, XG}, title = {Case report: A toxoplasmic encephalitis in an immunocompromised child detected through metagenomic next-generation sequencing.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1247233}, pmid = {37841727}, issn = {2296-2565}, mesh = {Humans ; Child, Preschool ; Brain/diagnostic imaging ; *Central Nervous System Infections ; High-Throughput Nucleotide Sequencing/methods ; *Encephalitis/diagnosis/cerebrospinal fluid ; }, abstract = {UNLABELLED: There exist numerous pathogens that are capable of causing infections within the central nervous system (CNS); however, conventional detection and analysis methods prove to be challenging. Clinical diagnosis of CNS infections often depends on clinical characteristics, cerebrospinal fluid (CSF) analysis, imaging, and molecular detection assays. Unfortunately, these methods can be both insensitive and time consuming, which can lead to missed diagnoses and catastrophic outcomes, especially in the case of infrequent diseases. Despite the application of appropriate prophylactic regimens and evidence-based antimicrobial agents, CNS infections continue to result in significant morbidity and mortality in hospital settings. Metagenomic next-generation sequencing (mNGS) is a novel tool that enables the identification of thousands of pathogens in a target-independent manner in a single run. The role of this innovative detection method in clinical pathogen diagnostics has matured over time. In this particular research, clinicians employed mNGS to investigate a suspected CNS infection in a child with leukemia, and unexpectedly detected Toxoplasma gondii.

CASE: A 3-year-old child diagnosed with T-cell lymphoblastic lymphoma was admitted to our hospital due to a 2-day history of fever and headache, along with 1 day of altered consciousness. Upon admission, the patient's Glasgow Coma Scale score was 14. Brain magnetic resonance imaging revealed multiple abnormal signals. Due to the patient's atypical clinical symptoms and laboratory test results, determining the etiology and treatment plan was difficulty.Subsequently, the patient underwent next-generation sequencing examination of cerebrospinal fluid. The following day, the results indicated the presence of Toxoplasma gondii. The patient received treatment with a combination of sulfamethoxazole (SMZ) and azithromycin. After approximately 7 days, the patient's symptoms significantly improved, and they were discharged from the hospital with oral medication to continue at home. A follow-up polymerase chain reaction (PCR) testing after about 6 weeks revealed the absence of Toxoplasma.

CONCLUSION: This case highlights the potential of mNGS as an effective method for detecting toxoplasmic encephalitis (TE). Since mNGS can identify thousands of pathogens in a single run, it may be a promising detection method for investigating the causative pathogens of central nervous system infections with atypical features.}, } @article {pmid37841598, year = {2023}, author = {Walsh, LH and Coakley, M and Walsh, AM and Crispie, F and O'Toole, PW and Cotter, PD}, title = {Analysis of the milk kefir pan-metagenome reveals four community types, core species, and associated metabolic pathways.}, journal = {iScience}, volume = {26}, number = {10}, pages = {108004}, pmid = {37841598}, issn = {2589-0042}, abstract = {A comprehensive metagenomics-based investigation of the microorganisms present within milk kefir communities from across the globe was carried out with a view to defining the milk kefir pan-metagenome, including details relating to core and non-core components. Milk kefir samples, generated by inoculating full fat, pasteurized cow's milk with 64 kefir grains sourced from 25 different countries, were analyzed. We identified core features, including a consistent pattern of domination by representatives from the species Lactobacillus helveticus or the sub-species Lactobacillus kefiranofaciens subsp. kefiranofaciens, Lactococcus lactis subsp. lactis or Lla. cremoris subsp. cremoris in each kefir. Notably, even in kefirs where the lactococci did not dominate, they and 51 associated metabolic pathways were identified across all metagenomes. These insights can contribute to future efforts to create tailored kefir-based microbial communities for different applications and assist regulators and producers to ensure that kefir products have a microbial composition that reflects the artisanal beverage.}, } @article {pmid37841475, year = {2023}, author = {Liang, X and Zhai, Z and Ren, F and Jie, Y and Kim, SK and Niu, KM and Wu, X}, title = {Metagenomic characterization of the cecal microbiota community and functions in finishing pigs fed fermented Boehmeria nivea.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1253778}, pmid = {37841475}, issn = {2297-1769}, abstract = {Ramie (Boehmeria nivea, BN) is used as livestock forage through suitable silage fermentation owing to its nutritional value. To date, relatively few studies have investigated the effects of dietary fermented BN (FBN) on gut health in finishing pigs. The aim of the present study was to investigate the effects of dietary supplementation with 20% FBN on intestinal morphology, gene expression, and the functional response of the gut microbiota in finishing pigs. We found that FBN did not significantly affect serum antioxidant enzyme activities, ileal morphology, or the expression of genes encoding antioxidant enzymes, inflammatory cytokines, or tight junction proteins in the liver of the pigs. However, the gene expression levels of aryl hydrocarbon receptor (AHR) and interleukin 6 (IL6) were significantly downregulated in the ileum. A metagenomic analysis demonstrated that, compared with that seen in the control group, the cecal microbiota of pigs in the FBN treatment group was more closely clustered and contained a greater number of unique microbes. Bacteria were the predominant kingdom in the cecal microbiota, while Firmicutes, Bacteroidetes, and Proteobacteria were the dominant phyla, and Streptococcus, Lactobacillus, and Prevotella were the dominant genera. Dietary FBN significantly increased the abundance of the probiotic bacterium Roseburia inulinivorans (p < 0.05). Functional analysis of the cecal microbiota showed that ABC transporter levels and glycolysis/gluconeogenesis-associated functions were diminished in FBN-fed pigs. Meanwhile, CAZyme analysis revealed that dietary FBN significantly downregulated the contents of carbohydrate-active enzymes, such as GT2, GH1, GH25, and GH13_31. In addition, cytochrome P450 analysis revealed that the abundance of CYP51 and CYP512 decreased with FBN treatment. An assessment of antibiotic resistance based on the Comprehensive Antibiotic Resistance Database (CARD) annotation indicated that the cecal microbes from pigs in the FBN treatment group had increased resistance to lincosamide, streptogramin, and chloramphenicol and reduced resistance to amikacin, isepamicin, neomycin, lividomycin, gentamicin, paromomycin, ribostamycin, and butirosin. Finally, virulence factor-related analysis showed that putative hemolysin-associated functions were decreased, whereas fibronectin-binding protein, flagella, and alginate-associated functions were increased. Taken together, our data showed that FBN supplementation exerted only minor effects on intestinal morphology and microbial community composition, suggesting that it is potentially safe for use as a supplement in the diets of finishing pigs. However, more studies are needed to validate its functionality.}, } @article {pmid37840989, year = {2023}, author = {Dixit, S and Sahoo, K and Gaur, M and Subudhi, E}, title = {Investigating microbiome and transcriptome data to uncover the key microbial community involved in lignocellulose degradation within the Deulajhari hot spring consortium.}, journal = {Data in brief}, volume = {51}, number = {}, pages = {109648}, pmid = {37840989}, issn = {2352-3409}, abstract = {Geothermally heated spring water contaminated with decomposed leaf biomass creates unique hot spring ecosystems that support the recycling of diverse nutrients and harbor microbial consortia capable of degrading lignocellulose. We present microbiome and transcriptome data from the bacterial consortium of Deulajhari hot springs, characterized by a temperature of approximately 58 °C and surrounded by a dense population of pandanus plants in Angul, Odisha, India. Metagenomics and metatranscriptomics datasets were generated by extracting total DNA and RNA from the consortium sample of hotspring sediment, followed by shotgun sequencing using the Illumina HiSeq 2500 platform. The metagenomics dataset produced approximately 38,694 contigs, while the metatranscriptomics dataset yielded 9226 contigs, resulting in a total nucleotide size of 89,857,616 and 15,541,403 bps, respectively. Analysis using MEGAN6 against the NCBI "taxonomy" database revealed the presence of 18 and 12 phyla, including candidate phyla, in respective datasets. Proteobacteria exhibited the highest relative abundance in the metagenomics dataset, while Firmicutes was highly abundant in the metatranscriptomics dataset. At the genus level, a total of 92 and 25 genera were predicted in both datasets, with lignocellulose degrading Meiothermus being highly abundant in both metagenomics and metatranscriptomics datasets. We also observed that the unknown bacteria and unidentified sequences were found in significant proportion in the metatranscriptomics dataset. We assembled and functionally annotated approximately 23,960 contigs using the Prokka pipeline. Among the SEED category, the most expressed and annotated microbial genes fall under the unknown category as well as Biotin synthesis and their utilization. Furthermore, some of these genes were implicated in the degradation of aromatic amino acids, D-mannitol, and D-mannose. These findings contribute to our understanding of how the composition and abundance of bacterial communities facilitate lignocellulose degradation in extreme environments and biofuel generation.}, } @article {pmid37840986, year = {2023}, author = {Akanmu, AM and van Marle-Kӧster, E and Hassen, A and Adejoro, FA}, title = {Datasets of shotgun metagenomics evaluation of rumen microbiota of South African mutton merino sheep.}, journal = {Data in brief}, volume = {51}, number = {}, pages = {109629}, pmid = {37840986}, issn = {2352-3409}, abstract = {The rumen microbial consortium plays a crucial role in the production performance and health of the ruminant animal. They are responsible for breaking down complex plant materials such as cellulose and hemicellulose to release usable energy by the host animal. Rumen microbial diversity manipulation through dietary strategies can be used to achieve several goals such as improved feed efficiency, reduced environmental impact or better utilization of low-quality forages. The dataset, deposited in the National Centre for Biotechnology Information SRA with project number PRJNA775821, comprises sequenced DNA extracted from the rumen content of 16 South African Merino sheep supplemented with different plant extracts. Illumina HiSeq™ 6000 technology was utilised to generate a total of approximately 46.7 Gb in raw nucleotide data. The data consists of 700,318,582 sequences, each with an average length of 184 base pairs. Taxonomic annotation conducted through the MG-RAST server showed the dominant phylum averages are Bacteroidetes (51 %) and Firmicutes (28 %), while Euryarchaeota, Actinobacteria, and Proteobacteria each account for approximately 3 % of the population. This dataset also enables us to identify and profile all expressed genes related to metabolic and chemical processes. The dataset is a valuable tool, offering insights that can lead to enhanced sustainability, profitability and reduced environmental impact within the context of ruminant production process.}, } @article {pmid37840855, year = {2023}, author = {Brzychczy-Sroka, B and Talaga-Ćwiertnia, K and Sroka-Oleksiak, A and Gurgul, A and Zarzecka-Francica, E and Ostrowski, W and Kąkol, J and Zarzecka, J and Brzychczy-Włoch, M}, title = {Oral microbiota study of the patients after hospitalisation for COVID-19, considering selected dental indices and antibiotic therapy using the next generation sequencing method (NGS).}, journal = {Journal of oral microbiology}, volume = {15}, number = {1}, pages = {2264591}, pmid = {37840855}, issn = {2000-2297}, abstract = {BACKGROUND: Poor oral hygiene and the increased incidence and severity of periodontitis may exacerbate SARS-CoV-2 infection. The aim was to evaluate the oral microbiota of 60 participants divided into groups: COVID-19 convalescents who received antibiotics during hospitalization (I), COVID-19 convalescents without antibiotic therapy (II) and healthy individuals (III).

MATERIALS AND METHODS: Dental examination was conducted, and oral health status was evaluated using selected dental indexes. Clinical samples (saliva, dorsal swabs, supragingival and subgingival plaque) were collected and used for metagenomic library to the next-generation sequencing (NGS) preparation.

RESULTS: Each of the clinical materials in particular groups of patients showed a statistically significant and quantitatively different bacterial composition. Patients from group I showed significantly worse oral health, reflected by higher average values of dental indexes and also a higher percentage of Veillonella, Tannerella, Capnocytophaga and Selenomonas genera in comparison to other groups. Additionally, a statistically significant decrease in the amount of Akkermansia type in both groups with COVID-19 was observed for all materials.

CONCLUSIONS: The primary factor affecting the composition of oral microbiota was not the SARS-CoV-2 infection itself, but the use of antibiotic therapy. The increased percentage of pro-inflammatory pathogens observed in COVID-19 patients underscores the importance of preventing periodontal disease and improving oral hygiene in the future.}, } @article {pmid37840832, year = {2023}, author = {}, title = {Erratum: The Performance of Metagenomic Next-Generation Sequence in the Diagnosis of Suspected Opportunistic Infections in Patients with Acquired Immunodeficiency Syndrome [Corrigendum].}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {6617-6618}, doi = {10.2147/IDR.S442294}, pmid = {37840832}, issn = {1178-6973}, abstract = {[This corrects the article DOI: 10.2147/IDR.S378249.].}, } @article {pmid37840830, year = {2023}, author = {Chai, S and Wang, C and Liu, Y and Xia, J and Wang, X and Shi, J}, title = {Distribution Patterns of Pathogens Causing Lower Respiratory Tract Infection Based on Metagenomic Next-Generation Sequencing.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {6635-6645}, pmid = {37840830}, issn = {1178-6973}, abstract = {PURPOSE: Lower Respiratory Tract Infection (LRTI) is a leading cause of morbidity and mortality worldwide. In this study, the distribution patterns of causative pathogens in LRTI were evaluated within a city-level hospital by combining conventional microbiological tests (CMT) with metagenomic next-generation sequencing (mNGS).

PATIENTS AND METHODS: This retrospective cohort study involved 160 patients suspected of having LRTI in a single center. Specimens, including bronchoalveolar lavage fluid (BALF), blood, tissue, sputum, and pus were utilized to identify pathogens. The seasonal prevalence of pathogens and co-pathogens involved in multiple infections was analyzed.

RESULTS: A total of 137 patients with 156 samples were included in this study. Pseudomonas aeruginosa, Corynebacterium striatum, Klebsiella pneumoniae, Candida, and human herpesvirus were the top prevalent pathogens. We observed seasonal dynamic variation in the top prevalent bacteria (Pseudomonas aeruginosa and Klebsiella pneumoniae) and herpesvirus (Epstein-Barr virus and Human herpesvirus-7). The majority of patients had single bacterial infections, followed by instances of bacterial-viral co-infections, as well as mixed infections involving bacteria, fungi, and viruses. Notably, the spectrum of co-infecting pathogens was broader among the elderly population, and positive Spearman correlations were observed among these co-infecting pathogens.

CONCLUSION: Co-infections were prevalent among patients with LRTI, and the pathogens displayed distinct seasonal distribution patterns. The findings underscored the significance of comprehending pathogen distribution and epidemic patterns, which can serve as a basis for early etiological identification.}, } @article {pmid37840773, year = {2023}, author = {Laue, HE and Moroishi, Y and Jackson, BP and Palys, TJ and Baker, ER and Korrick, SA and Madan, JC and Karagas, MR}, title = {Bacterial Modification of the Association Between Arsenic and Autism-Related Social Behavior Scores.}, journal = {Exposure and health}, volume = {15}, number = {2}, pages = {347-354}, pmid = {37840773}, issn = {2451-9766}, support = {UH3 OD023275/OD/NIH HHS/United States ; P42 ES007373/ES/NIEHS NIH HHS/United States ; P20 ES018175/ES/NIEHS NIH HHS/United States ; P01 ES022832/ES/NIEHS NIH HHS/United States ; UG3 OD023275/OD/NIH HHS/United States ; P20 GM104416/GM/NIGMS NIH HHS/United States ; }, abstract = {Arsenic is related to neurodevelopmental outcomes and is associated with the composition of the gut microbiome. Data on the modifying role of the microbiome are limited. We probed suggestive relationships between arsenic and social behaviors to quantify the modifying role of the infant gut microbiome. We followed children for whom arsenic concentrations were quantified in 6-week-old toenail clippings. Scores on the Social Responsiveness Scale (SRS-2), which measures autism-related social behaviors, were provided by caregivers when the child was approximately 3 years of age. Metagenomic sequencing was performed on infant stools collected at 6 weeks and 1 year of age. To evaluate modification by the top ten most abundant species and functional pathways, we modeled SRS-2 total T-scores as a function of arsenic concentrations, microbiome features dichotomized at their median, and an interaction between exposure and the microbiome, adjusting for other trace elements and sociodemographic characteristics. As compared to the standardized population (SRS-2 T-scores = 50), participants in our study had lower SRS-2 scores (n = 78, mean = 44, SD = 5).The relative abundances of several functional pathways identified in 6-week stool samples modified the arsenic-SRS-2 association, including the pathways of valine and isoleucine biosynthesis; we observed no association among those with high relative abundance of each pathway [β = - 0.67 (95% CI - 1.46, 0.12)], and an adverse association [β = 1.67 (95% CI 0.3, 3.04), pinteraction= 0.05] among infants with low relative abundance. Our findings indicate the infant gut microbiome may alter neurodevelopmental susceptibility to environmental exposures.}, } @article {pmid37840743, year = {2023}, author = {Pérez Gallego, R and Bale, NJ and Sinninghe Damste, JS and Villanueva, L}, title = {Developing a genetic approach to target cyanobacterial producers of heterocyte glycolipids in the environment.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1257040}, pmid = {37840743}, issn = {1664-302X}, abstract = {Heterocytous cyanobacteria are important players in the carbon and nitrogen cycle. They can fix dinitrogen by using heterocytes, specialized cells containing the oxygen-sensitive nitrogenase enzyme surrounded by a thick polysaccharide and glycolipid layer which prevents oxygen diffusion and nitrogenase inactivation. Heterocyte glycolipids can be used to detect the presence of heterocytous cyanobacteria in present-day and past environments, providing insight into the functioning of the studied ecosystems. However, due to their good preservation throughout time, heterocyte glycolipids are not ideal to detect and study living communities, instead methods based on DNA are preferred. Currently cyanobacteria can be detected using untargeted genomic approaches such as metagenomics, or they can be specifically targeted by, for example, the use of primers that preferentially amplify their 16S rRNA gene or their nifH gene in the case of nitrogen fixing cyanobacteria. However, since not all cyanobacterial nitrogen fixers are heterocytous, there is currently no fast gene-based method to specifically detect and distinguish heterocytous cyanobacteria. Here, we developed a PCR-based method to specifically detect heterocytous cyanobacteria by designing primers targeting the gene (hglT) encoding the enzyme responsible for the last step in the biosynthesis of heterocyte glycolipid (i.e., a glycosyltransferase). We designed several primer sets using the publicly available sequences of 23 heterocytous cyanobacteria, after testing them on DNA extracts of 21 heterocyte-forming and 7 non-heterocyte forming freshwater cyanobacteria. The best primer set was chosen and successfully used to confirm the presence of heterocytous cyanobacteria in a marine environmental sample.}, } @article {pmid37840734, year = {2023}, author = {Li, Y and Fan, Y and Ma, X and Wang, Y and Liu, J}, title = {Metagenomic survey reveals global distribution and evolution of microbial sialic acid catabolism.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1267152}, pmid = {37840734}, issn = {1664-302X}, abstract = {Sialic acids comprise a varied group of nine-carbon amino sugars found mostly in humans and other higher metazoans, playing major roles in cell interactions with external environments as well as other cells. Microbial sialic acid catabolism (SAC) has long been considered a virulence determinant, and appears to be mainly the purview of pathogenic and commensal bacterial species associated with eukaryotic hosts. Here, we used 2,521 (pre-)assembled metagenomes to evaluate the distribution of SAC in microbial communities from diverse ecosystems and human body parts. Our results demonstrated that microorganisms possessing SAC globally existed in non-host associated environments, although much less frequently than in mammal hosts. We also showed that the ecological significance and taxonomic diversity of microbial SAC have so far been largely underestimated. Phylogenetic analysis revealed a strong signal of horizontal gene transfer among distinct taxa and habitats, and also suggested a specific ecological pressure and a relatively independent evolution history in environmental communities. Our study expanded the known diversity of microbial SAC, and has provided the backbone for further studies on its ecological roles and potential pathogenesis.}, } @article {pmid37840730, year = {2023}, author = {Cai, Y and Luo, Y and Dai, N and Yang, Y and He, Y and Chen, H and Zhao, M and Fu, X and Chen, T and Xing, Z}, title = {Functional metagenomic and metabolomics analysis of gut dysbiosis induced by hyperoxia.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1197970}, pmid = {37840730}, issn = {1664-302X}, abstract = {BACKGROUND: Inhaled oxygen is the first-line therapeutic approach for maintaining tissue oxygenation in critically ill patients, but usually exposes patients to damaging hyperoxia. Hyperoxia adversely increases the oxygen tension in the gut lumen which harbors the trillions of microorganisms playing an important role in host metabolism and immunity. Nevertheless, the effects of hyperoxia on gut microbiome and metabolome remain unclear, and metagenomic and metabolomics analysis were performed in this mouse study.

METHODS: C57BL/6 mice were randomly divided into a control (CON) group exposed to room air with fractional inspired oxygen (FiO2) of 21% and a hyperoxia (OXY) group exposed to FiO2 of 80% for 7 days, respectively. Fecal pellets were collected on day 7 and subjected to metagenomic sequencing. Another experiment with the same design was performed to explore the impact of hyperoxia on gut and serum metabolome. Fecal pellets and blood were collected and high-performance liquid chromatography with mass spectrometric analysis was carried out.

RESULTS: At the phylum level, hyperoxia increased the ratio of Firmicutes/Bacteroidetes (p = 0.049). At the species level, hyperoxia reduced the abundance of Muribaculaceae bacterium Isolate-037 (p = 0.007), Isolate-114 (p = 0.010), and Isolate-043 (p = 0.011) etc. Linear discriminant analysis effect size (LEfSe) revealed that Muribaculaceae and Muribaculaceae bacterium Isolate-037, both belonging to Bacteroidetes, were the marker microbes of the CON group, while Firmicutes was the marker microbes of the OXY group. Metagenomic analysis using Kyoto Encyclopedia of Genes and Genomes (KEGG) and Carbohydrate-Active enZYmes (CAZy) revealed that hyperoxia provoked disturbances in carbohydrate and lipid metabolism. Fecal metabolomics analysis showed hyperoxia reduced 11-dehydro Thromboxane B2-d4 biosynthesis (p = 1.10 × 10[-11]). Hyperoxia blunted fecal linoleic acid metabolism (p = 0.008) and alpha-linolenic acid metabolism (p = 0.014). We showed that 1-docosanoyl-glycer-3-phosphate (p = 1.58 × 10[-10]) was the most significant differential serum metabolite inhibited by hyperoxia. In addition, hyperoxia suppressed serum hypoxia-inducible factor-1 (HIF-1, p = 0.007) and glucagon signaling pathways (p = 0.007).

CONCLUSION: Hyperoxia leads to gut dysbiosis by eliminating beneficial and oxygen strictly intolerant Muribaculaceae with genomic dysfunction of carbohydrate and lipid metabolism. In addition, hyperoxia suppresses unsaturated fatty acid metabolism in the gut and inhibits the HIF-1 and glucagon signaling pathways in the serum.}, } @article {pmid37840729, year = {2023}, author = {Mengucci, C and Rampelli, S and Picone, G and Lucchi, A and Litta, G and Biagi, E and Candela, M and Manfreda, G and Brigidi, P and Capozzi, F and De Cesare, A}, title = {Application of multi-omic features clustering and pathway enrichment to clarify the impact of vitamin B2 supplementation on broiler caeca microbiome.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1264361}, pmid = {37840729}, issn = {1664-302X}, abstract = {BACKGROUND: The results of omic methodologies are often reported as separate datasets. In this study we applied for the first time multi-omic features clustering and pathway enrichment to clarify the biological impact of vitamin B2 supplementation on broiler caeca microbiome.

METHODS: The caeca contents of broilers fed +50 and +100 mg/kg vitamin B2 were analyzed by shotgun metagenomic and metabolomic. Latent variables extracted from NMR spectra, as well as taxonomic and functional features profiled from metagenomes, were integrated to characterize the effect of vitamin B2 in modulating caeca microbiome. A pathway-based network was obtained by mapping the observed input genes and compounds, highlighting connected strands of metabolic ways through pathway-enrichment analysis.

RESULTS: At day 14, the taxonomic, functional and metabolomic features in the caeca of tested broilers showed some degree of separation between control and treated groups, becoming fully clear at 28 days and persisting up to 42 days. In the caeca of birds belonging to the control group Alistipes spp. was the signature species, while the signature species in the caeca of broilers fed +50 and +100 mg/kg vitamin B2 were Bacteroides fragilis and Lactobacillus crispatus, Lactobacillus reuteri, Ruminococcus torques, Subdoligranum spp., respectively. The pathway enrichment analysis highlighted that the specific biochemical pathways enhanced by the supplementations of vitamin B2 were N-Formyl-L-aspartate amidohydrolase, producing Aspartate and Formate; L-Alanine:2-oxoglutarate amino transferase, supporting the conversion of L-Alanine and 2-Oxoglutarate in Pyruvate and L-Glutamate; 1D-myo-inositol 1/4 phosphate phosphohydrolase, converting Inositol 1/4-phosphate and water in myo-Inositol and Orthophosphate. The results of this study demonstrated that the caeca of birds fed +50 and + 100 mg/kg were those characterized by taxonomic groups more beneficial to the host and with a higher concentration of myo-inositol, formic acid, amino acids and pyruvate involved in glycolysis and amino acid biosynthesis.

CONCLUSION: In this study we demonstrated how to perform multi-omic features integration to describe the biochemical mechanisms enhanced by the supplementation of different concentrations of vitamin B2 in the poultry diet. The relationship between vitamin B2 supplementation and myo-inositol production was highlighted in our study for the first time.}, } @article {pmid37840722, year = {2023}, author = {Shukla, S and Srivastava, A and Verma, D and Gangopadhyay, S and Chauhan, A and Srivastava, V and Budhwar, S and Tyagi, D and Sharma, DC}, title = {Analysis of gut bacteriome of in utero arsenic-exposed mice using 16S rRNA-based metagenomic approach.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1147505}, pmid = {37840722}, issn = {1664-302X}, abstract = {INTRODUCTION: Approximately 200 million people worldwide are affected by arsenic toxicity emanating from the consumption of drinking water containing inorganic arsenic above the prescribed maximum contaminant level. The current investigation deals with the role of prenatal arsenic exposure in modulating the gut microbial community and functional pathways of the host.

METHOD: 16S rRNA-based next-generation sequencing was carried out to understand the effects of in utero 0.04 mg/kg (LD) and 0.4 mg/kg (HD) of arsenic exposure. This was carried out from gestational day 15 (GD-15) until the birth of pups to understand the alterations in bacterial diversity.

RESULTS: The study focused on gestational exposure to arsenic and the altered gut microbial community at phyla and genus levels, along with diversity indices. A significant decrease in firmicutes was observed in the gut microbiome of mice treated with arsenic. Functional analysis revealed that a shift in genes involved in crucial pathways such as insulin signaling and non-alcoholic fatty liver disease pathways may lead to metabolic diseases in the host.

DISCUSSION: The present investigation may hypothesize that in utero arsenic exposure can perturb the gut bacterial composition significantly as well as the functional pathways of the gestationally treated pups. This research paves the way to further investigate the probable mechanistic insights in the field of maternal exposure environments, which may play a key role in epigenetic modulations in developing various disease endpoints in the progeny.}, } @article {pmid37840720, year = {2023}, author = {Hartmann, M and Herzog, C and Brunner, I and Stierli, B and Meyer, F and Buchmann, N and Frey, B}, title = {Long-term mitigation of drought changes the functional potential and life-strategies of the forest soil microbiome involved in organic matter decomposition.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1267270}, pmid = {37840720}, issn = {1664-302X}, abstract = {Climate change can alter the flow of nutrients and energy through terrestrial ecosystems. Using an inverse climate change field experiment in the central European Alps, we explored how long-term irrigation of a naturally drought-stressed pine forest altered the metabolic potential of the soil microbiome and its ability to decompose lignocellulolytic compounds as a critical ecosystem function. Drought mitigation by a decade of irrigation stimulated profound changes in the functional capacity encoded in the soil microbiome, revealing alterations in carbon and nitrogen metabolism as well as regulatory processes protecting microorganisms from starvation and desiccation. Despite the structural and functional shifts from oligotrophic to copiotrophic microbial lifestyles under irrigation and the observation that different microbial taxa were involved in the degradation of cellulose and lignin as determined by a time-series stable-isotope probing incubation experiment with [13]C-labeled substrates, degradation rates of these compounds were not affected by different water availabilities. These findings provide new insights into the impact of precipitation changes on the soil microbiome and associated ecosystem functioning in a drought-prone pine forest and will help to improve our understanding of alterations in biogeochemical cycling under a changing climate.}, } @article {pmid37840718, year = {2023}, author = {Zehnle, H and Otersen, C and Benito Merino, D and Wegener, G}, title = {Potential for the anaerobic oxidation of benzene and naphthalene in thermophilic microorganisms from the Guaymas Basin.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1279865}, pmid = {37840718}, issn = {1664-302X}, abstract = {Unsubstituted aromatic hydrocarbons (UAHs) are recalcitrant molecules abundant in crude oil, which is accumulated in subsurface reservoirs and occasionally enters the marine environment through natural seepage or human-caused spillage. The challenging anaerobic degradation of UAHs by microorganisms, in particular under thermophilic conditions, is poorly understood. Here, we established benzene- and naphthalene-degrading cultures under sulfate-reducing conditions at 50°C and 70°C from Guaymas Basin sediments. We investigated the microorganisms in the enrichment cultures and their potential for UAH oxidation through short-read metagenome sequencing and analysis. Dependent on the combination of UAH and temperature, different microorganisms became enriched. A Thermoplasmatota archaeon was abundant in the benzene-degrading culture at 50°C, but catabolic pathways remained elusive, because the archaeon lacked most known genes for benzene degradation. Two novel species of Desulfatiglandales bacteria were strongly enriched in the benzene-degrading culture at 70°C and in the naphthalene-degrading culture at 50°C. Both bacteria encode almost complete pathways for UAH degradation and for downstream degradation. They likely activate benzene via methylation, and naphthalene via direct carboxylation, respectively. The two species constitute the first thermophilic UAH degraders of the Desulfatiglandales. In the naphthalene-degrading culture incubated at 70°C, a Dehalococcoidia bacterium became enriched, which encoded a partial pathway for UAH degradation. Comparison of enriched bacteria with related genomes from environmental samples indicated that pathways for benzene degradation are widely distributed, while thermophily and capacity for naphthalene activation are rare. Our study highlights the capacities of uncultured thermophilic microbes for UAH degradation in petroleum reservoirs and in contaminated environments.}, } @article {pmid37840709, year = {2023}, author = {Huanca-Juarez, J and Nascimento-Silva, EA and Silva, NH and Silva-Rocha, R and Guazzaroni, ME}, title = {Identification and functional analysis of novel protein-encoding sequences related to stress-resistance.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1268315}, pmid = {37840709}, issn = {1664-302X}, abstract = {Currently, industrial bioproducts are less competitive than chemically produced goods due to the shortcomings of conventional microbial hosts. Thus, is essential developing robust bacteria for improved cell tolerance to process-specific parameters. In this context, metagenomic approaches from extreme environments can provide useful biological parts to improve bacterial robustness. Here, in order to build genetic constructs that increase bacterial resistance to diverse stress conditions, we recovered novel protein-encoding sequences related to stress-resistance from metagenomic databases using an in silico approach based on Hidden-Markov-Model profiles. For this purpose, we used metagenomic shotgun sequencing data from microbial communities of extreme environments to identify genes encoding chaperones and other proteins that confer resistance to stress conditions. We identified and characterized 10 novel protein-encoding sequences related to the DNA-binding protein HU, the ATP-dependent protease ClpP, and the chaperone protein DnaJ. By expressing these genes in Escherichia coli under several stress conditions (including high temperature, acidity, oxidative and osmotic stress, and UV radiation), we identified five genes conferring resistance to at least two stress conditions when expressed in E. coli. Moreover, one of the identified HU coding-genes which was retrieved from an acidic soil metagenome increased E. coli tolerance to four different stress conditions, implying its suitability for the construction of a synthetic circuit directed to expand broad bacterial resistance.}, } @article {pmid37840698, year = {2023}, author = {Zhao, Y and Chen, L and Yao, S and Chen, L and Huang, J and Chen, S and Yu, Z}, title = {Genome-centric investigation of the potential succession pattern in gut microbiota and altered functions under high-protein diet.}, journal = {Current research in food science}, volume = {7}, number = {}, pages = {100600}, pmid = {37840698}, issn = {2665-9271}, abstract = {Excessive intake of protein has been considered as a factor leading to intestinal microecological disorder, but why and how intestinal microbes change under the high-protein diet (HPD) have yet to be fully elucidated. Here, we performed 16S rRNA gene amplicon sequencing and metagenomic sequencing on contents of cecum, colon and feces from two groups of mice with standard diet (SD) and HPD. And then the microbial alteration of composition and function were deeply analyzed by using several statistical models and bioinformatic methods. Among the three niches, the microbes in the colon are observed to show the most significant change with lower alpha-diversity and higher beta-diversity after HPD. In addition, this alteration of microbial structure may be related to the replacement process and co-occurring community. Most species are also enriched or impoverished in the colon during this process. After analyzing the functional genes related to protein and carbohydrate hydrolysis in different niches, we found that the carbon source provided by poor carbohydrates compared with the rich protein may be the potential factor driving the enrichment of mucin degraders and desulphaters in the colon under HPD. Therefore, our study provided a new insight to understand the underlying mechanism of HPD affecting intestinal health from the perspective of microbial functional ecology.}, } @article {pmid37839685, year = {2024}, author = {Xiang, F and Zhang, Q and Xu, X and Zhang, Z}, title = {Black soldier fly larvae recruit functional microbiota into the intestines and residues to promote lignocellulosic degradation in domestic biodegradable waste.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {340}, number = {Pt 1}, pages = {122676}, doi = {10.1016/j.envpol.2023.122676}, pmid = {37839685}, issn = {1873-6424}, mesh = {Animals ; Larva ; *Microbiota ; Intestines ; *Diptera ; }, abstract = {Lignocellulose is an important component of domestic biodegradable waste (DBW), and its complex structure makes it an obstacle in the biological treatment of DBW. Here, we identify black soldier fly larvae (Hermetia illucens L., BSFL) as a bioreactor for lignocellulose degradation in DBW based on their ability to effectively recruit lignocellulose-degrading bacteria. This study mainly examined the lignocellulose degradation, dynamic succession of the microbial community, gene expression of carbohydrate-active enzymes (CAZymes), and co-occurrence network analysis. Investigation of lignocellulose degradation by BSFL within 14 days indicated that the lignocellulose biodegradation rate in the larvae treatment (LT, 26.5%) group was higher than in natural composting (NC, 4.06%). In order to gain a more comprehensive understanding of microbiota, we conducted metagenomic sequencing of larvae intestines (LI), along with the LT and NC. The relative abundance of lignocellulose-degrading bacteria and CAZymes genes in LT and LI were higher than those in NC based on metagenomics sequencing. Importantly, genes coding cellulase and hemicellulase in LI were 3.36- and 2.79-fold higher, respectively, than that in LT, while the ligninase genes in LT were 1.82-fold higher than in LI. A co-occurrence network analysis identified Enterocluster and Luteimonas as keystone taxa in larvae intestines and residues, respectively, with a synergistic relationship to lignocellulose-degrading bacteria. The mechanism of recruiting functional bacteria through the larvae intestines promoted lignocellulose degradation in DBW, improving the efficiency of BSFL biotechnology and resource regeneration.}, } @article {pmid37839679, year = {2023}, author = {Rockwell, NC and Lagarias, JC}, title = {Cyanobacteriochromes from Gloeobacterales Provide New Insight into the Diversification of Cyanobacterial Photoreceptors.}, journal = {Journal of molecular biology}, volume = {}, number = {}, pages = {168313}, doi = {10.1016/j.jmb.2023.168313}, pmid = {37839679}, issn = {1089-8638}, abstract = {The phytochrome superfamily comprises three groups of photoreceptors sharing a conserved GAF (cGMP-specific phosphodiesterases, cyanobacterial adenylate cyclases, and formate hydrogen lyase transcription activator FhlA) domain that uses a covalently attached linear tetrapyrrole (bilin) chromophore to sense light. Knotted red/far-red phytochromes are widespread in both bacteria and eukaryotes, but cyanobacteria also contain knotless red/far-red phytochromes and cyanobacteriochromes (CBCRs). Unlike typical phytochromes, CBCRs require only the GAF domain for bilin binding, chromophore ligation, and full, reversible photoconversion. CBCRs can sense a wide range of wavelengths (ca. 330-750 nm) and can regulate phototaxis, second messenger metabolism, and optimization of the cyanobacterial light-harvesting apparatus. However, the origins of CBCRs are not well understood: we do not know when or why CBCRs evolved, or what selective advantages led to retention of early CBCRs in cyanobacterial genomes. In the current work, we use the increasing availability of genomes and metagenome-assembled-genomes from early-branching cyanobacteria to explore the origins of CBCRs. We reaffirm the earliest branches in CBCR evolution. We also show that early-branching cyanobacteria contain late-branching CBCRs, implicating early appearance of CBCRs during cyanobacterial evolution. Moreover, we show that early-branching CBCRs behave as integrators of light and pH, providing a potential unique function for early CBCRs that led to their retention and subsequent diversification. Our results thus provide new insight into the origins of these diverse cyanobacterial photoreceptors.}, } @article {pmid37839225, year = {2023}, author = {Chen, L and Wei, G and Zhang, Y and Wang, K and Wang, C and Deng, X and Li, Y and Xie, X and Chen, J and Huang, F and Chen, H and Zhang, B and Wei, C and Qiu, G}, title = {Candidatus Accumulibacter use fermentation products for enhanced biological phosphorus removal.}, journal = {Water research}, volume = {246}, number = {}, pages = {120713}, doi = {10.1016/j.watres.2023.120713}, pmid = {37839225}, issn = {1879-2448}, mesh = {*Phosphorus/metabolism ; Fermentation ; Protons ; Bioreactors ; *Betaproteobacteria/metabolism ; Polyphosphates/metabolism ; Lactates/metabolism ; Alanine ; Succinates/metabolism ; Carbon/metabolism ; Acetates/metabolism ; }, abstract = {Previous research suggested that two major groups of polyphosphate-accumulating organisms (PAOs), i.e., Ca. Accumulibacter and Tetrasphaera, play cooperative roles in enhanced biological phosphorus removal (EBPR). The fermentation of complex organic compounds by Tetrasphaera provides carbon sources for Ca. Accumulibacter. However, the viability of the fermentation products (e.g., lactate, succinate, alanine) as carbon sources for Ca. Accumulibacter and their potential effects on the metabolism of Ca. Accumulibacter were largely unknown. This work for the first time investigated the capability and metabolic details of Ca. Accumulibacter cognatus clade IIC strain SCUT-2 (enriched in a lab-scale reactor with a relative abundance of 42.8%) in using these fermentation products for EBPR. The enrichment culture was able to assimilate lactate and succinate with the anaerobic P release to carbon uptake ratios of 0.28 and 0.36 P mol/C mol, respectively. In the co-presence of acetate, the uptake of lactate was strongly inhibited, since two substrates shared the same transporter as suggested by the carbon uptake bioenergetic analysis. When acetate and succinate were fed at the same time, Ca. Accumulibacter assimilated two carbon sources simultaneously. Proton motive force (PMF) was the key driving force (up to 90%) for the uptake of lactate and succinate by Ca. Accumulibacter. Apart from the efflux of proton in symport with phosphate via the inorganic phosphate transport system, translocation of proton via the activity of fumarate reductase contributed to the generation of PMF, which agreed with the fact that PHV was a major component of PHA when lactate and succinate were used as carbon sources, involving the succinate-propionate pathway. Metabolic models for the usage of lactate and succinate by Ca. Accumulibacter for EBPR were built based on the combined physiological, biochemical, metagenomic, and metatranscriptomic analyses. Alanine was shown as an invalid carbon source for Ca. Accumulibacter. Instead, it significantly and adversely affected Ca. Accumulibacter-mediated EBPR. Phosphate release was observed without alanine uptake. Significant inhibitions on the aerobic phosphate uptake was also evident. Overall, this study suggested that there might not be a simply synergic relationship between Ca. Accumulibacter and Tetrasphaera. Their interactions would largely be determined by the kind of fermentation products released by the latter.}, } @article {pmid37838745, year = {2023}, author = {Huang, J and Gao, K and Yang, L and Lu, Y}, title = {Successional action of Bacteroidota and Firmicutes in decomposing straw polymers in a paddy soil.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {76}, pmid = {37838745}, issn = {2524-6372}, support = {91951206//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Decomposition of plant biomass is vital for carbon cycling in terrestrial ecosystems. In waterlogged soils including paddy fields and natural wetlands, plant biomass degradation generates the largest natural source of global methane emission. However, the intricate process of plant biomass degradation by diverse soil microorganisms remains poorly characterized. Here we report a chemical and metagenomic investigation into the mechanism of straw decomposition in a paddy soil.

RESULTS: The chemical analysis of 16-day soil microcosm incubation revealed that straw decomposition could be divided into two stages based on the dynamics of methane, short chain fatty acids, dissolved organic carbon and monosaccharides. Metagenomic analysis revealed that the relative abundance of glucoside hydrolase (GH) encoding genes for cellulose decomposition increased rapidly during the initial stage (3-7 days), while genes involved in hemicellulose decomposition increased in the later stage (7-16 days). The increase of cellulose GH genes in initial stage was derived mainly from Firmicutes while Bacteroidota contributed mostly to the later stage increase of hemicellulose GH genes. Flagella assembly genes were prevalent in Firmicutes but scarce in Bacteroidota. Wood-Ljungdahl pathway (WLP) was present in Firmicutes but not detected in Bacteroidota. Overall, Bacteroidota contained the largest proportion of total GHs and the highest number of carbohydrate active enzymes gene clusters in our paddy soil metagenomes. The strong capacity of the Bacteroidota phylum to degrade straw polymers was specifically attributed to Bacteroidales and Chitinophagales orders, the latter has not been previously recognized.

CONCLUSIONS: This study revealed a collaborating sequential contribution of microbial taxa and functional genes in the decomposition of straw residues in a paddy soil. Firmicutes with the property of mobility, WLP and cellulose decomposition could be mostly involved in the initial breakdown of straw polymers, while Bacteroidota became abundant and possibly responsible for the decomposition of hemicellulosic polymers during the later stage.}, } @article {pmid37838714, year = {2023}, author = {Schaerer, L and Putman, L and Bigcraft, I and Byrne, E and Kulas, D and Zolghadr, A and Aloba, S and Ong, R and Shonnard, D and Techtmann, S}, title = {Coexistence of specialist and generalist species within mixed plastic derivative-utilizing microbial communities.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {224}, pmid = {37838714}, issn = {2049-2618}, mesh = {Polyethylene/chemistry/metabolism ; *Microbiota ; Metagenome ; *Phthalic Acids ; }, abstract = {BACKGROUND: Plastic-degrading microbial isolates offer great potential to degrade, transform, and upcycle plastic waste. Tandem chemical and biological processing of plastic wastes has been shown to substantially increase the rates of plastic degradation; however, the focus of this work has been almost entirely on microbial isolates (either bioengineered or naturally occurring). We propose that a microbial community has even greater potential for plastic upcycling. A microbial community has greater metabolic diversity to process mixed plastic waste streams and has built-in functional redundancy for optimal resilience.

RESULTS: Here, we used two plastic-derivative degrading communities as a model system to investigate the roles of specialist and generalist species within the microbial communities. These communities were grown on five plastic-derived substrates: pyrolysis treated high-density polyethylene, chemically deconstructed polyethylene terephthalate, disodium terephthalate, terephthalamide, and ethylene glycol. Short-read metagenomic and metatranscriptomic sequencing were performed to evaluate activity of microorganisms in each treatment. Long-read metagenomic sequencing was performed to obtain high-quality metagenome assembled genomes and evaluate division of labor.

CONCLUSIONS: Data presented here show that the communities are primarily dominated by Rhodococcus generalists and lower abundance specialists for each of the plastic-derived substrates investigated here, supporting previous research that generalist species dominate batch culture. Additionally, division of labor may be present between Hydrogenophaga terephthalate degrading specialists and lower abundance protocatechuate degrading specialists. Video Abstract.}, } @article {pmid37837778, year = {2024}, author = {Wu, Z and Yu, X and Ji, Y and Liu, G and Gao, P and Xia, L and Li, P and Liang, B and Freilich, S and Gu, L and Qiao, W and Jiang, J}, title = {Flexible catabolism of monoaromatic hydrocarbons by anaerobic microbiota adapting to oxygen exposure.}, journal = {Journal of hazardous materials}, volume = {462}, number = {}, pages = {132762}, doi = {10.1016/j.jhazmat.2023.132762}, pmid = {37837778}, issn = {1873-3336}, mesh = {Benzene/metabolism ; Anaerobiosis ; Nitrates ; Hydrocarbons/metabolism ; Benzene Derivatives/metabolism ; Toluene/metabolism ; Xylenes/metabolism ; Biodegradation, Environmental ; *Microbiota ; Oxygen ; *Ammonium Compounds ; Carbon ; }, abstract = {Microbe-mediated anaerobic degradation is a practical method for remediation of the hazardous monoaromatic hydrocarbons (BTEX, including benzene, toluene, ethylbenzene and xylenes) under electron-deficient contaminated sites. However, how do the anaerobic functional microbes adapt to oxygen exposure and flexibly catabolize BTEX remain poorly understood. We investigated the switches of substrate spectrum and bacterial community upon oxygen perturbation in a nitrate-amended anaerobic toluene-degrading microbiota which was dominated by Aromatoleum species. DNA-stable isotope probing demonstrated that Aromatoleum species was involved in anaerobic mineralization of toluene. Metagenome-assembled genome of Aromatoleum species harbored both the nirBD-type genes for nitrate reduction to ammonium coupled with toluene oxidation and the additional meta-cleavage pathway for aerobic benzene catabolism. Once the anaerobic microbiota was fully exposed to oxygen and benzene, 1.05 ± 0.06% of Diaphorobacter species rapidly replaced Aromatoleum species and flourished to 96.72 ± 0.01%. Diaphorobacter sp. ZM was isolated, which was not only able to utilize benzene as the sole carbon source for aerobic growth and but also innovatively reduce nitrate to ammonium with citrate/lactate/glucose as the carbon source under anaerobic conditions. This study expands our understanding of the adaptive mechanism of microbiota for environmental redox disturbance and provides theoretical guidance for the bioremediation of BTEX-contaminated sites.}, } @article {pmid37837767, year = {2023}, author = {Lyu, Y and Zhang, J and Chen, Y and Li, Q and Ke, Z and Zhang, S and Li, J}, title = {Distinct diversity patterns and assembly mechanisms of prokaryotic microbial sub-community in the water column of deep-sea cold seeps.}, journal = {Journal of environmental management}, volume = {348}, number = {}, pages = {119240}, doi = {10.1016/j.jenvman.2023.119240}, pmid = {37837767}, issn = {1095-8630}, mesh = {*Ecosystem ; Water ; Geologic Sediments ; Archaea/genetics ; Bacteria/genetics ; *Microbiota ; Methane ; Sulfur ; Phylogeny ; }, abstract = {Methane leakage from deep-sea cold seeps has a major impact on marine ecosystems. Microbes sequester methane in the water column of cold seeps and can be divided into abundant and rare groups. Both abundant and rare groups play an important role in cold seep ecosystems, and the environmental heterogeneity in cold seeps may enhance conversion between taxa with different abundances. Yet, the environmental stratification and assembly mechanisms of these microbial sub-communities remain unclear. We investigated the diversities and assembly mechanisms in microbial sub-communities with distinct abundance in the deep-sea cold seep water column, from 400 m to 1400 m. We found that bacterial β-diversity, as measured by Sørensen dissimilarities, exhibited a significant species turnover pattern that was influenced by several environmental factors including depth, temperature, SiO3[2-], and salinity. In contrast, archaeal β-diversity showed a relatively high percentage of nestedness pattern, which was driven by the levels of soluble reactive phosphate and SiO3[2-]. During the abundance dependency test, abundant taxa of both bacteria and archaea showed a significant species turnover, while the rare taxa possessed a higher percentage of nestedness. Stochastic processes were prominent in shaping the prokaryotic community, but deterministic processes were more pronounced for the abundant taxa than rare ones. Furthermore, the metagenomics results revealed that the abundances of methane oxidation, sulfur oxidation, and nitrogen fixation-related genes and related microbial groups were significantly higher in the bottom water. Our results implied that the carbon, sulfur, and nitrogen cycles were potentially strongly coupled in the bottom water. Overall, the results obtained in this study highlight taxonomic and abundance-dependent microbial community diversity patterns and assembly mechanisms in the water column of cold seeps, which will help understand the impacts of fluid seepage from the sea floor on the microbial community in the water column and further provide guidance for the management of cold seep ecosystem under future environmental pressures.}, } @article {pmid37837552, year = {2023}, author = {Werneburg, GT and Adler, A and Khooblall, P and Wood, HM and Gill, BC and Vij, SC and Angermeier, KW and Lundy, SD and Miller, AW and Bajic, P}, title = {Penile prostheses harbor biofilms driven by individual variability and manufacturer even in the absence of clinical infection.}, journal = {The journal of sexual medicine}, volume = {20}, number = {12}, pages = {1431-1439}, doi = {10.1093/jsxmed/qdad124}, pmid = {37837552}, issn = {1743-6109}, support = {//2020 Sexual Medicine Society of North America Young Clinicians Research Grant/ ; }, mesh = {Humans ; Middle Aged ; Aged ; *Penile Prosthesis ; Biofilms ; Anti-Bacterial Agents/therapeutic use ; Prosthesis Implantation ; *Diabetes Mellitus ; }, abstract = {BACKGROUND: Culture-based studies have shown that penile prostheses harbor biofilms in the presence and absence of infection, but these findings have not been adequately validated using contemporary microbiome analytic techniques.

AIM: The study sought to characterize microbial biofilms of indwelling penile prosthesis devices according to patient factors, device components, manufacturer, and infection status.

METHODS: Upon penile prostheses surgical explantation, device biofilms were extracted, sonicated, and characterized using shotgun metagenomics and culture-based approaches. Device components were also analyzed using scanning electron microscopy.

OUTCOMES: Outcomes included the presence or absence of biofilms, alpha and beta diversity, specific microbes identified and the presence of biofilm, and antibiotic resistance genes on each prosthesis component.

RESULTS: The average age of participants from whom devices were explanted was 61 ± 11 years, and 9 (45%) of 20 had a diagnosis of diabetes mellitus. Seventeen devices were noninfected, and 3 were associated with clinical infection. Mean device indwelling time prior to explant was 5.1 ± 5.1 years. All analyzed components from 20 devices had detectable microbial biofilms, both in the presence and absence of infection. Scanning electron microscopy corroborated the presence of biofilms across device components. Significant differences between viruses, prokaryotes, and metabolic pathways were identified between individual patients, device manufacturers, and infection status. Mobiluncus curtisii was enriched in manufacturer A device biofilms relative to manufacturer B device biofilms. Bordetella bronchialis, Methylomicrobium alcaliphilum, Pseudoxanthomonas suwonensis, and Porphyrobacter sp. were enriched in manufacturer B devices relative to manufacturer A devices. The most abundant bacterial phyla were the Proteobacteria, Actinobacteria, and Firmicutes. Glycogenesis, the process of glycogen synthesis, was among the predominant metabolic pathways detected across device components. Beta diversity of bacteria, viruses, protozoa, and pathways did not differ among device components.

CLINICAL IMPLICATIONS: All components of all penile prostheses removed from infected and noninfected patients have biofilms. The significance of biofilms on noninfected devices remains unknown and merits further investigation.

STRENGTHS AND LIMITATIONS: Strengths include the multipronged approach to characterize biofilms and being the first study to include all components of penile prostheses in tandem. Limitations include the relatively few number of infected devices in the series, a relatively small subset of devices included in shotgun metagenomics analysis, and the lack of anaerobic and other expanded conditions for culture.

CONCLUSION: Penile prosthesis biofilms are apparent in the presence and absence of infection, and the composition of biofilms was driven primarily by device manufacturer, individual variability, and infection, while being less impacted by device component.}, } @article {pmid37836508, year = {2023}, author = {Greff, D and Váncsa, S and Váradi, A and Szinte, J and Park, S and Hegyi, P and Nyirády, P and Ács, N and Horváth, EM and Várbíró, S}, title = {Myoinositols Prevent Gestational Diabetes Mellitus and Related Complications: A Systematic Review and Meta-Analysis of Randomized Controlled Trials.}, journal = {Nutrients}, volume = {15}, number = {19}, pages = {}, pmid = {37836508}, issn = {2072-6643}, support = {NFKIH-FK 129206//Hungarian National Research, Development and Innovation Office/ ; }, mesh = {Pregnancy ; Infant, Newborn ; Female ; Humans ; *Diabetes, Gestational/prevention & control ; *Premature Birth ; *Pre-Eclampsia ; *Hypertension, Pregnancy-Induced ; Randomized Controlled Trials as Topic ; *Hypoglycemia ; Insulin ; Inositol/therapeutic use ; }, abstract = {Although gestational diabetes mellitus (GDM) has several short- and long-term adverse effects on the mother and the offspring, no medicine is generally prescribed to prevent GDM. The present systematic review and meta-analysis aimed to investigate the effect of inositol supplementation in preventing GDM and related outcomes. Systematic search was performed in CENTRAL, MEDLINE, and Embase until 13 September 2023. Eligible randomized controlled trials (RCTs) compared the efficacy of inositols to placebo in pregnant women at high risk for GDM. Our primary outcome was the incidence of GDM, whereas secondary outcomes were oral glucose tolerance test (OGTT) and maternal and fetal complications. (PROSPERO registration number: CRD42021284939). Eight eligible RCTs were identified, including the data of 1795 patients. The incidence of GDM was halved by inositols compared to placebo (RR = 0.42, CI: 0.26-0.67). Fasting, 1-h, and 2-h OGTT glucose levels were significantly decreased by inositols. The stereoisomer myoinositol also reduced the risk of insulin need (RR = 0.29, CI: 0.13-0.68), preeclampsia or gestational hypertension (RR = 0.38, CI: 0.2-0.71), preterm birth (RR = 0.44, CI: 0.22-0.88), and neonatal hypoglycemia (RR = 0.12, CI: 0.03-0.55). Myoinositol decrease the incidence of GDM in pregnancies high-risk for GDM. Moreover, myoinositol supplementation reduces the risk of insulin need, preeclampsia or gestational hypertension, preterm birth, and neonatal hypoglycemia. Based on the present study 2-4 g myoinositol canbe suggested from the first trimester to prevent GDM and related outcomes.}, } @article {pmid37836447, year = {2023}, author = {Wang, H and Lv, X and Zhao, S and Yuan, W and Zhou, Q and Sadiq, FA and Zhao, J and Lu, W and Wu, W}, title = {Weight Loss Promotion in Individuals with Obesity through Gut Microbiota Alterations with a Multiphase Modified Ketogenic Diet.}, journal = {Nutrients}, volume = {15}, number = {19}, pages = {}, pmid = {37836447}, issn = {2072-6643}, support = {2022YFF1100403//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diet, Ketogenic ; Obesity ; Diet, Reducing ; Ketone Bodies ; Weight Loss ; }, abstract = {The occurrence of obesity and related metabolic disorders is rising, necessitating effective long-term weight management strategies. With growing interest in the potential role of gut microbes due to their association with responses to different weight loss diets, understanding the mechanisms underlying the interactions between diet, gut microbiota, and weight loss remains a challenge. This study aimed to investigate the potential impact of a multiphase dietary protocol, incorporating an improved ketogenic diet (MDP-i-KD), on weight loss and the gut microbiota. Using metagenomic sequencing, we comprehensively analyzed the taxonomic and functional composition of the gut microbiota in 13 participants before and after a 12-week MDP-i-KD intervention. The results revealed a significant reduction in BMI (9.2% weight loss) among obese participants following the MDP-i-KD intervention. Machine learning analysis identified seven key microbial species highly correlated with MDP-i-KD, with Parabacteroides distasonis exhibiting the highest response. Additionally, the co-occurrence network of the gut microbiota in post-weight-loss participants demonstrated a healthier state. Notably, metabolic pathways related to nucleotide biosynthesis, aromatic amino acid synthesis, and starch degradation were enriched in pre-intervention participants and positively correlated with BMI. Furthermore, species associated with obesity, such as Blautia obeum and Ruminococcus torques, played pivotal roles in regulating these metabolic activities. In conclusion, the MDP-i-KD intervention may assist in weight management by modulating the composition and metabolic functions of the gut microbiota. Parabacteroides distasonis, Blautia obeum, and Ruminococcus torques could be key targets for gut microbiota-based obesity interventions.}, } @article {pmid37835689, year = {2023}, author = {Zou, S and Yuan, T and Lu, T and Yan, J and Kang, D and Li, D}, title = {Human Disturbance Increases Health Risks to Golden Snub-Nosed Monkeys and the Transfer Risk of Pathogenic Antibiotic-Resistant Bacteria from Golden Snub-Nosed Monkeys to Humans.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {19}, pages = {}, pmid = {37835689}, issn = {2076-2615}, support = {32200403//Shuzhen Zou/ ; 32270548//Dayong Li/ ; S202210638075//Tingting Yuan/ ; 2023NSFSC5206//Shuzhen Zou/ ; 2023NSFSC0143//Di Kang/ ; XNYB22KP-05//Shuzhen Zou/ ; }, abstract = {From the perspective of interactions in the human-animal-ecosystem, the study and control of pathogenic bacteria that can cause disease in animals and humans is the core content of "One Health". In order to test the effect of human disturbance (HD) on the health risk of pathogenic antibiotic-resistant bacteria (PARBs) to wild animals and transfer risk of the PARBs from wild animals to humans, golden snub-nosed monkeys (Rhinopithecus roxellana) were used as sentinel animals. Metagenomic analysis was used to analyze the characteristics of PARBs in the gut microbiota of golden snub-nosed monkeys. Then, the total contribution of antibiotic resistance genes (ARGs) and virulence factors (VFs) of the PARBs were used to assess the health risk of PARBs to golden snub-nosed monkeys, and the antimicrobial drug resistance and bacterial infectious disease of PARBs were determined to assess the transfer risk of PARBs from golden snub-nosed monkeys to humans. There were 18 and 5 kinds of PARBs in the gut microbiota of golden snub-nosed monkeys under HD (HD group) and wild habitat environments (W group), respectively. The total health risks of PARBs to the W group and the HD group were -28.5 × 10[-3] and 125.8 × 10[-3], respectively. There were 12 and 16 kinds of KEGG pathways of human diseases in the PARBs of the W group and the HD group, respectively, and the gene numbers of KEGG pathways in the HD group were higher than those in the W group. HD increased the pathogenicity of PARBs to golden snub-nosed monkeys, and the PARBs in golden snub-nosed monkeys exhibited resistance to lincosamide, aminoglycoside, and streptogramin antibiotics. If these PARBs transfer from golden snub-nosed monkeys to humans, then humans may acquire symptoms of pathogens including Tubercle bacillus, Staphylococcus, Streptococcus, Yersinia, Pertussis, and Vibrio cholera.}, } @article {pmid37835198, year = {2023}, author = {Andreson, M and Kazantseva, J and Malv, E and Kuldjärv, R and Priidik, R and Kütt, ML}, title = {Evaluation of Microbial Dynamics of Kombucha Consortia upon Continuous Backslopping in Coffee and Orange Juice.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {19}, pages = {}, pmid = {37835198}, issn = {2304-8158}, support = {2014-2020.4.02.19-0228//European Regional Development Fund/ ; }, abstract = {The kombucha market is diverse, and competitors constantly test new components and flavours to satisfy customers' expectations. Replacing the original brewing base, adding flavours, or using "backslopping" influence the composition of the symbiotic starter culture of bacteria and yeast (SCOBY). Yet, deep characterisation of microbial and chemical changes in kombucha consortia in coffee and orange juice during backslopping has not been implemented. This study aimed to develop new kombucha beverages in less-conventional matrices and characterise their microbiota. We studied the chemical properties and microbial growth dynamics of lactic-acid-bacteria-tailored (LAB-tailored) kombucha culture by 16S rRNA next-generation sequencing in coffee and orange juice during a backslopping process that spanned five cycles, each lasting two to four days. The backslopping changed the culture composition and accelerated the fermentation. This study gives an overview of the pros and cons of backslopping technology for the production of kombucha-based beverages. Based on research conducted using two different media, this work provides valuable information regarding the aspects to consider when using the backslopping method to produce novel kombucha drinks, as well as identifying the main drawbacks that need to be addressed.}, } @article {pmid37835192, year = {2023}, author = {Çelik Doğan, C and Yüksel Dolgun, HT and İkiz, S and Kırkan, Ş and Parın, U}, title = {Detection of the Microbial Composition of Some Commercial Fermented Liquid Products via Metagenomic Analysis.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {19}, pages = {}, pmid = {37835192}, issn = {2304-8158}, support = {35313//Istanbul University Cerrahpaşa/ ; }, abstract = {The fermented liquid sector is developing all over the world due to its contribution to health. Our study has contributed to the debate about whether industrially manufactured fermented liquids live up to their claims by analyzing pathogens and beneficial bacteria using a 16S rRNA sequencing technique called metagenomic analysis. Paenibacillus, Lentibacillus, Bacillus, Enterococcus, Levilactobacillus, and Oenococcus were the most abundant bacterial genera observed as potential probiotics. Pseudomonas stutzeri, Acinetobacter, and Collimonas, which have plant-growth-promoting traits, were also detected. The fact that we encounter biocontroller bacteria that promote plant growth demonstrates that these organisms are widely used in foods and emphasizes the necessity of evaluating them in terms of public health. Their potential applications in agriculture may pose a danger to food hygiene and human health in the long term, so our data suggest that this should be evaluated.}, } @article {pmid37835190, year = {2023}, author = {Feng, L and Gao, S and Liu, P and Wang, S and Zheng, L and Wang, X and Teng, J and Ye, F and Gui, A and Xue, J and Zheng, P}, title = {Microbial Diversity and Characteristic Quality Formation of Qingzhuan Tea as Revealed by Metagenomic and Metabolomic Analysis during Pile Fermentation.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {19}, pages = {}, pmid = {37835190}, issn = {2304-8158}, support = {2022CFB472//Hubei Provincial Natural Science Foundation/ ; 2023AFB850//Hubei Provincial Natural Science Foundation/ ; 31902081//National Natural Science Foundation of China/ ; 2023//the cultivation Plan for Young Backbone Talents of the Fruit and Tea Research Institute of the Hubei Academy of Agricultural Sciences/ ; 2022//Wuhan Knowledge Innovation Special Project-Dawn Program/ ; CARS-19//the China Agriculture Research System of MOF and MARA/ ; 2023BBB154//Hubei Agricultural Science and Technology Achievement Transformation Fund Project/ ; }, abstract = {In order to analyze the changes in the microbial community structure during the pile fermentation of Qingzhuan tea and their correlation with the formation of quality compounds in Qingzhuan tea, this study carried out metagenomic and metabolomic analyses of tea samples during the fermentation process of Qingzhuan tea. The changes in the expression and abundance of microorganisms during the pile fermentation were investigated through metagenomic assays. During the processing of Qingzhuan tea, there is a transition from a bacterial dominated ecosystem to an ecosystem enriched with fungi. The correlation analyses of metagenomics and metabolomics showed that amino acids and polyphenol metabolites with relatively simple structures exhibited a significant negative correlation with target microorganisms, while the structurally complicated B-ring dihydroxy puerin, B-ring trihydroxy galloyl puerlin, and other compounds showed a significant positive correlation with target microorganisms. Aspergillus niger, Aspergillus glaucus, Penicillium in the Aspergillaceae family, and Talaromyces and Rasamsonia emersonii in Trichocomaceae were the key microorganisms involved in the formation of the characteristic qualities of Qingzhuan tea.}, } @article {pmid37834997, year = {2023}, author = {Rocha-de-Lossada, C and Mazzotta, C and Gabrielli, F and Papa, FT and Gómez-Huertas, C and García-López, C and Urbinati, F and Rachwani-Anil, R and García-Lorente, M and Sánchez-González, JM and Rechichi, M and Rubegni, G and Borroni, D}, title = {Ocular Surface Microbiota in Naïve Keratoconus: A Multicenter Validation Study.}, journal = {Journal of clinical medicine}, volume = {12}, number = {19}, pages = {}, pmid = {37834997}, issn = {2077-0383}, abstract = {In the field of Ophthalmology, the mNGS 16S rRNA sequencing method of studying the microbiota and ocular microbiome is gaining more and more weight in the scientific community. This study aims to characterize the ocular microbiota of patients diagnosed with keratoconus who have not undergone any prior surgical treatment using the mNGS 16S rRNA sequencing method. Samples of naïve keratoconus patients were collected with an eNAT with 1 mL of Liquid Amies Medium (Copan Brescia, Italy), and DNA was extracted and analyzed with 16S NGS. The microbiota analysis showed a relative abundance of microorganisms at the phylum level in each sample collected from 38 patients with KC and 167 healthy controls. A comparison between healthy control and keratoconus samples identified two genera unique to keratoconus, Pelomonas and Ralstonia. Our findings suggest that alterations in the microbiota may play a role in the complex scenario of KC development.}, } @article {pmid37833917, year = {2023}, author = {Baćmaga, M and Wyszkowska, J and Borowik, A and Kucharski, J}, title = {Bacteria, Fungi, and Enzymes in Soil Treated with Sulcotrione and Terbuthylazine.}, journal = {International journal of molecular sciences}, volume = {24}, number = {19}, pages = {}, pmid = {37833917}, issn = {1422-0067}, support = {30.610.006-110//This research was funded by the University of Warmia and Mazury in Olsztyn, Faculty of Agri-culture and Forestry, Department of Soil Science and Microbiology/ ; }, mesh = {Soil/chemistry ; Fungi ; Bacteria ; *Ascomycota ; *Herbicides/pharmacology ; Soil Microbiology ; *Soil Pollutants ; Zea mays ; }, abstract = {Soil's biological equilibrium, disturbed by the uncontrolled penetration of pesticides, can be restored by the activity of native microorganisms, which show abilities in neutralizing these xenobiotics. Therefore, this research is necessary in the search for new microorganisms used in the process of the bioremediation of contaminated soils. The aim of this study was to evaluate the effects of the herbicides, Sulcogan 300 SC, Tezosar 500 SC, and Sulcotrek 500 SC, applied to soil at the manufacturers' recommended dosage as well as 10-fold higher, on the abundance of microorganisms, the diversity and structure of bacterial and fungal communities, the activity of soil enzymes, and the growth and development of Zea mays L. It was found that herbicides in contaminating amounts stimulated the proliferation of organotrophic bacteria and inhibited the growth of fungi. Organotrophic bacteria and actinobacteria were represented by K-strategies and fungi by r-strategies. Bacteria belonging to the phylum, Actinobacteriota, represented by the genus, Cellulosimicrobium, were most abundant in the soil, while among the fungi, it was the phylum, Ascomycota, represented by the genus, Humicola and Chaetomium. The herbicides decreased urease activity while increasing arylsulfatase and acid phosphatase activity. They had a positive effect on the growth and development of Zea mays L., as evidenced by an increase in the values of the plant tolerance index (TI) and the maize leaf greenness index (SPAD). The results indicate that soil microorganisms and enzymes are suitable indicators reflecting the quality of herbicide-treated soil.}, } @article {pmid37833777, year = {2023}, author = {Van Camp, PJ and Prasath, VBS and Haslam, DB and Porollo, A}, title = {MGS2AMR: a gene-centric mining of metagenomic sequencing data for pathogens and their antimicrobial resistance profile.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {223}, pmid = {37833777}, issn = {2049-2618}, support = {R21 AI143467/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Metagenome ; Drug Resistance, Bacterial/genetics ; Bacteria ; Metagenomics/methods ; }, abstract = {BACKGROUND: Identification of pathogenic bacteria from clinical specimens and evaluating their antimicrobial resistance (AMR) are laborious tasks that involve in vitro cultivation, isolation, and susceptibility testing. Recently, a number of methods have been developed that use machine learning algorithms applied to the whole-genome sequencing data of isolates to approach this problem. However, making AMR assessments from more easily available metagenomic sequencing data remains a big challenge.

RESULTS: We present the Metagenomic Sequencing to Antimicrobial Resistance (MGS2AMR) pipeline, which detects antibiotic resistance genes (ARG) and their possible organism of origin within a sequenced metagenomics sample. This in silico method allows for the evaluation of bacterial AMR directly from clinical specimens, such as stool samples. We have developed two new algorithms to optimize and annotate the genomic assembly paths within the raw Graphical Fragment Assembly (GFA): the GFA Linear Optimal Path through seed segments (GLOPS) algorithm and the Adapted Dijkstra Algorithm for GFA (ADAG). These novel algorithms improve the sensitivity of ARG detection and aid in species annotation. Tests based on 1200 microbiome samples show a high ARG recall rate and correct assignment of the ARG origin. The MGS2AMR output can further be used in many downstream applications, such as evaluating AMR to specific antibiotics in samples from emerging intestinal infections. We demonstrate that the MGS2AMR-derived data is as informative for the entailing prediction models as the whole-genome sequencing (WGS) data. The performance of these models is on par with our previously published method (WGS2AMR), which is based on the sequencing data of bacterial isolates.

CONCLUSIONS: MGS2AMR can provide researchers with valuable insights into the AMR content of microbiome environments and may potentially improve patient care by providing faster quantification of resistance against specific antibiotics, thereby reducing the use of broad-spectrum antibiotics. The presented pipeline also has potential applications in other metagenome analyses focused on the defined sets of genes. Video Abstract.}, } @article {pmid37833740, year = {2023}, author = {Rollin, J and Rong, W and Massart, S}, title = {Cont-ID: detection of sample cross-contamination in viral metagenomic data.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {217}, pmid = {37833740}, issn = {1741-7007}, mesh = {Humans ; *RNA, Viral/analysis/genetics ; Reproducibility of Results ; *Viruses/genetics ; Metagenomics/methods ; Computational Biology ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {BACKGROUND: High-throughput sequencing (HTS) technologies completed by the bioinformatic analysis of the generated data are becoming an important detection technique for virus diagnostics. They have the potential to replace or complement the current PCR-based methods thanks to their improved inclusivity and analytical sensitivity, as well as their overall good repeatability and reproducibility. Cross-contamination is a well-known phenomenon in molecular diagnostics and corresponds to the exchange of genetic material between samples. Cross-contamination management was a key drawback during the development of PCR-based detection and is now adequately monitored in routine diagnostics. HTS technologies are facing similar difficulties due to their very high analytical sensitivity. As a single viral read could be detected in millions of sequencing reads, it is mandatory to fix a detection threshold that will be informed by estimated cross-contamination. Cross-contamination monitoring should therefore be a priority when detecting viruses by HTS technologies.

RESULTS: We present Cont-ID, a bioinformatic tool designed to check for cross-contamination by analysing the relative abundance of virus sequencing reads identified in sequence metagenomic datasets and their duplication between samples. It can be applied when the samples in a sequencing batch have been processed in parallel in the laboratory and with at least one specific external control called Alien control. Using 273 real datasets, including 68 virus species from different hosts (fruit tree, plant, human) and several library preparation protocols (Ribodepleted total RNA, small RNA and double-stranded RNA), we demonstrated that Cont-ID classifies with high accuracy (91%) viral species detection into (true) infection or (cross) contamination. This classification raises confidence in the detection and facilitates the downstream interpretation and confirmation of the results by prioritising the virus detections that should be confirmed.

CONCLUSIONS: Cross-contamination between samples when detecting viruses using HTS (Illumina technology) can be monitored and highlighted by Cont-ID (provided an alien control is present). Cont-ID is based on a flexible methodology relying on the output of bioinformatics analyses of the sequencing reads and considering the contamination pattern specific to each batch of samples. The Cont-ID method is adaptable so that each laboratory can optimise it before its validation and routine use.}, } @article {pmid37833670, year = {2023}, author = {Pu, S and Wang, M and Wang, J and Zhang, Q and Ma, X and Wang, R and Yu, S and Wang, L and Pan, Y}, title = {Metagenomic analysis reveals a dynamic microbiome with diversified adaptive functions that respond to ovulation regulation in the mouse endometrium.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {615}, pmid = {37833670}, issn = {1471-2164}, support = {Grant No. 20JR10RA561//National Science Foundation for Distinguished Young Scholars of Gansu province/ ; No. 20200624RCC0022//Innovative Talent Project of Gansu Province/ ; Grant No. 32160859//National Natural Science Foundation of China/ ; No. Gaufx-02Y10//Fuxi Foundation for Youth Talent at Gansu Agricultural University/ ; Grant No. GSAU-RCZX201701//Scientific Research Foundation for the New Scholars, Gansu Agricultural University/ ; }, mesh = {Female ; Animals ; Mice ; *Endometrium/metabolism ; Reproduction ; Ovulation/genetics ; *Microbiota/genetics ; Steroids ; }, abstract = {Understanding the microflora inhabiting the reproductive tract is important for a better understanding of female physiology and reproductive health. The endometrial fluid from mice in three reproductive stages (A: Unproductive mice; B: Postovulatory mice; C: Postpartum mice) was extracted for microbial DNA extraction and sequencing. Phenotypic and functional analyses of endometrial microbial enrichment was undertaken using LefSe. The results showed 95 genera and 134 species of microorganisms in the uteri of mice. There were differentially distributed genera, among which Lactobacillus, Enterococcus, and Streptococcus were more abundant in the endometrial fluid of mice in the unproductive group. That of mice in the postovulatory group was colonized with Salmonella enterica and Campylobacter and was mainly enriched in metabolic pathways and steroid biosynthesis. The presence of Chlamydia, Enterococcus, Pseudomonadales, Acinetobacter, and Clostridium in the endometrial fluid of postpartum mice, in addition to the enrichment of the endocrine system and the Apelin and FoxO signaling pathways, resulted in a higher number of pathogenic pathways than in the other two groups. The results showed that the microbial diversity characteristics in the endometrium of mice in different reproductive states differed and that they could be involved in the regulation of animal reproduction through metabolic pathways and steroid biosynthesis, suggesting that reproductive diseases induced by microbial diversity alterations in the regulation of animal reproduction cannot be ignored.}, } @article {pmid37833524, year = {2023}, author = {Michalik, A and Bauer, E and Szklarzewicz, T and Kaltenpoth, M}, title = {Nutrient supplementation by genome-eroded Burkholderia symbionts of scale insects.}, journal = {The ISME journal}, volume = {17}, number = {12}, pages = {2221-2231}, pmid = {37833524}, issn = {1751-7370}, support = {2021/41/B/NZ8/04526//Narodowe Centrum Nauki (National Science Centre)/ ; }, mesh = {Animals ; *Hemiptera/microbiology ; Tryptophan/genetics ; *Burkholderia/genetics ; Phylogeny ; Dietary Supplements ; Vitamin B 12 ; Nutrients ; Symbiosis/genetics ; Genome, Bacterial ; }, abstract = {Hemipterans are known as hosts to bacterial or fungal symbionts that supplement their unbalanced diet with essential nutrients. Among them, scale insects (Coccomorpha) are characterized by a particularly large diversity of symbiotic systems. Here, using microscopic and genomic approaches, we functionally characterized the symbionts of two scale insects belonging to the Eriococcidae family, Acanthococcus aceris and Gossyparia spuria. These species host Burkholderia bacteria that are localized in the cytoplasm of the fat body cells. Metagenome sequencing revealed very similar and highly reduced genomes (<900KBp) with a low GC content (~38%), making them the smallest and most AT-biased Burkholderia genomes yet sequenced. In their eroded genomes, both symbionts retain biosynthetic pathways for the essential amino acids leucine, isoleucine, valine, threonine, lysine, arginine, histidine, phenylalanine, and precursors for the semi-essential amino acid tyrosine, as well as the cobalamin-dependent methionine synthase MetH. A tryptophan biosynthesis pathway is conserved in the symbiont of G. spuria, but appeared pseudogenized in A. aceris, suggesting differential availability of tryptophan in the two host species' diets. In addition to the pathways for essential amino acid biosynthesis, both symbionts maintain biosynthetic pathways for multiple cofactors, including riboflavin, cobalamin, thiamine, and folate. The localization of Burkholderia symbionts and their genome traits indicate that the symbiosis between Burkholderia and eriococcids is younger than other hemipteran symbioses, but is functionally convergent. Our results add to the emerging picture of dynamic symbiont replacements in sap-sucking Hemiptera and highlight Burkholderia as widespread and versatile intra- and extracellular symbionts of animals, plants, and fungi.}, } @article {pmid37833297, year = {2023}, author = {Li, L and Huang, D and Hu, Y and Rudling, NM and Canniffe, DP and Wang, F and Wang, Y}, title = {Globally distributed Myxococcota with photosynthesis gene clusters illuminate the origin and evolution of a potentially chimeric lifestyle.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6450}, pmid = {37833297}, issn = {2041-1723}, support = {BB/W008076/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; Phylogeny ; *Bacteria/genetics ; *Photosynthesis/genetics ; Multigene Family ; }, abstract = {Photosynthesis is a fundamental biogeochemical process, thought to be restricted to a few bacterial and eukaryotic phyla. However, understanding the origin and evolution of phototrophic organisms can be impeded and biased by the difficulties of cultivation. Here, we analyzed metagenomic datasets and found potential photosynthetic abilities encoded in the genomes of uncultivated bacteria within the phylum Myxococcota. A putative photosynthesis gene cluster encoding a type-II reaction center appears in at least six Myxococcota families from three classes, suggesting vertical inheritance of these genes from an early common ancestor, with multiple independent losses in other lineages. Analysis of metatranscriptomic datasets indicate that the putative myxococcotal photosynthesis genes are actively expressed in various natural environments. Furthermore, heterologous expression of myxococcotal pigment biosynthesis genes in a purple bacterium supports that the genes can drive photosynthetic processes. Given that predatory abilities are thought to be widespread across Myxococcota, our results suggest the intriguing possibility of a chimeric lifestyle (combining predatory and photosynthetic abilities) in members of this phylum.}, } @article {pmid37832871, year = {2023}, author = {Nagy, JB and Koleszár, B and Khayer, B and Róka, E and Laczkó, L and Ungvári, E and Kaszab, E and Bali, K and Bányai, K and Vargha, M and Lovas-Kiss, Á and Tóth, Á and Kardos, G}, title = {Carbapenem-resistant Escherichia coli in Black-headed gulls, the Danube, and human clinical samples: A One Health comparison of contemporary isolates.}, journal = {Journal of global antimicrobial resistance}, volume = {35}, number = {}, pages = {257-261}, doi = {10.1016/j.jgar.2023.10.002}, pmid = {37832871}, issn = {2213-7173}, mesh = {Animals ; Humans ; *Charadriiformes ; *One Health ; Escherichia coli/genetics ; *Carbapenem-Resistant Enterobacteriaceae/genetics ; Carbapenems/pharmacology ; Cefotaxime/pharmacology ; Water ; }, abstract = {OBJECTIVES: Our aim was to characterize and compare contemporary carbapenem-resistant Enterobacterales (CRE) isolates from gulls, the River Danube, and humans in Hungary, Budapest.

METHODS: Multiresistant Enterobacterales were sought for in 227 gull faecal and 24 Danube water samples from 2019 to 2020. Eosin-methylene blue agar containing 2 mg/L cefotaxime and Colilert-test containing 10 mg/L cefotaxime were used for gull and water samples, respectively. Isolates were characterized by polymerase chain reactions (PCRs); acquired carbapenemase producers were further analysed by whole-genome sequencing, together with 21 Hungarian human CR Escherichia coli (CREc) isolates.

RESULTS: Gull and water samples exhibited a CRE prevalence of 7.4% (9/122) and 6.7% (7/105), none and 5/12 water samples yielded CRE from 2019 and 2020, respectively; CRE were found only in samples taken downstream of Budapest. The dominant species was Escherichia coli and the most prevalent carbapenemase was blaNDM-1. High-risk CREc clones were found both in gulls (ST224, ST372, ST744) and the Danube (ST10, ST354, ST410); the closest associations were between ST410 from humans and the Danube, among ST1437 among gulls, and between ST1437 in gulls and the Danube (46, 0, and 22-24 allelic distances, respectively). Direct links between human and gull isolates were not demonstrated.

CONCLUSION: The study demonstrates potential epidemiological links among humans, a river crossing a city, and urbanised birds, suggesting a local transmission network. Water bodies receiving influent wastewater, together with animals using such habitats, may serve as a local reservoir system for CRE, highlighting the importance of One Health in CRE transmission, even in a country with a low CRE prevalence in humans.}, } @article {pmid37832571, year = {2023}, author = {Musisi, E and Wyness, A and Eldirdiri, S and Dombay, E and Mtafya, B and Ntinginya, NE and Heinrich, N and Kibiki, GS and Hoelscher, M and Boeree, M and Aarnoutse, R and Gillespie, SH and Sabiiti, W and , }, title = {Effect of seven anti-tuberculosis treatment regimens on sputum microbiome: a retrospective analysis of the HIGHRIF study 2 and PanACEA MAMS-TB clinical trials.}, journal = {The Lancet. Microbe}, volume = {4}, number = {11}, pages = {e913-e922}, doi = {10.1016/S2666-5247(23)00191-X}, pmid = {37832571}, issn = {2666-5247}, mesh = {Humans ; Antitubercular Agents/pharmacology ; Drug Therapy, Combination ; *Microbiota ; Moxifloxacin/pharmacology ; Retrospective Studies ; RNA, Ribosomal, 16S ; Sputum/microbiology ; Tanzania ; *Tuberculosis/drug therapy ; *Tuberculosis, Pulmonary/drug therapy ; Clinical Trials as Topic ; }, abstract = {BACKGROUND: Respiratory tract microbiota has been described as the gatekeeper for respiratory health. We aimed to assess the impact of standard-of-care and experimental anti-tuberculosis treatment regimens on the respiratory microbiome and implications for treatment outcomes.

METHODS: In this retrospective study, we analysed the sputum microbiome of participants with tuberculosis treated with six experimental regimens versus standard-of-care who were part of the HIGHRIF study 2 (NCT00760149) and PanACEA MAMS-TB (NCT01785186) clinical trials across a 3-month treatment follow-up period. Samples were from participants in Mbeya, Kilimanjaro, Bagamoyo, and Dar es Salaam, Tanzania. Experimental regimens were composed of different combinations of rifampicin (R), isoniazid (H), pyrazinamide (Z), ethambutol (E), moxifloxacin (M), and a new drug, SQ109 (Q). Reverse transcription was used to create complementary DNA for each participant's total sputum RNA and the V3-V4 region of the 16S rRNA gene was sequenced using the Illumina metagenomic technique. Qiime was used to analyse the amplicon sequence variants and estimate alpha diversity. Descriptive statistics were applied to assess differences in alpha diversity pre-treatment and post-treatment initiation and the effect of each treatment regimen.

FINDINGS: Sequence data were obtained from 397 pre-treatment and post-treatment samples taken between Sept 26, 2008, and June 30, 2015, across seven treatment regimens. Pre-treatment microbiome (206 genera) was dominated by Firmicutes (2860 [44%] of 6500 amplicon sequence variants [ASVs]) at the phylum level and Streptococcus (2340 [36%] ASVs) at the genus level. Two regimens had a significant depressing effect on the microbiome after 2 weeks of treatment, HR20mg/kgZM (Shannon diversity index p=0·0041) and HR35mg/kgZE (p=0·027). Gram-negative bacteria were the most sensitive to bactericidal activity of treatment with the highest number of species suppressed being under the moxifloxacin regimen. By week 12 after treatment initiation, microbiomes had recovered to pre-treatment level except for the HR35mg/kgZE regimen and for genus Mycobacterium, which did not show recovery across all regimens. Tuberculosis culture conversion to negative by week 8 of treatment was associated with clearance of genus Neisseria, with a 98% reduction of the pre-treatment level.

INTERPRETATION: HR20mg/kgZM was effective against tuberculosis without limiting microbiome recovery, which implies a shorter efficacious anti-tuberculosis regimen with improved treatment outcomes might be achieved without harming the commensal microbiota.

FUNDING: European and Developing Countries Clinical Trials Partnership and German Ministry of Education and Research.}, } @article {pmid37832484, year = {2023}, author = {Zhao, Z and Yang, C and Gao, B and Wu, Y and Ao, Y and Ma, S and Jiménez, N and Zheng, L and Huang, F and Tomberlin, JK and Ren, Z and Yu, Z and Yu, C and Zhang, J and Cai, M}, title = {Insights into the reduction of antibiotic-resistant bacteria and mobile antibiotic resistance genes by black soldier fly larvae in chicken manure.}, journal = {Ecotoxicology and environmental safety}, volume = {266}, number = {}, pages = {115551}, doi = {10.1016/j.ecoenv.2023.115551}, pmid = {37832484}, issn = {1090-2414}, mesh = {Animals ; Larva/genetics ; *Manure/analysis ; Chickens/genetics ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; *Diptera/genetics ; Bacteria ; Drug Resistance, Microbial ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The increasing prevalence of antibiotic-resistant bacteria (ARB) from animal manure has raised concerns about the potential threats to public health. The bioconversion of animal manure with insect larvae, such as the black soldier fly larvae (BSFL, Hermetia illucens [L.]), is a promising technology for quickly attenuating ARB while also recycling waste. In this study, we investigated BSFL conversion systems for chicken manure. Using metagenomic analysis, we tracked ARB and evaluated the resistome dissemination risk by investigating the co-occurrence of antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), and bacterial taxa in a genetic context. Our results indicated that BSFL treatment effectively mitigated the relative abundance of ARB, ARGs, and MGEs by 34.9%, 53.3%, and 37.9%, respectively, within 28 days. Notably, the transferable ARGs decreased by 30.9%, indicating that BSFL treatment could mitigate the likelihood of ARG horizontal transfer and thus reduce the risk of ARB occurrence. In addition, the significantly positive correlation links between antimicrobial concentration and relative abundance of ARB reduced by 44.4%. Moreover, using variance partition analysis (VPA), we identified other bacteria as the most important factor influencing ARB, explaining 20.6% of the ARB patterns. Further analysis suggested that antagonism of other bacteria on ARB increased by 1.4 times, while nutrient competition on both total nitrogen and crude fat increased by 2.8 times. Overall, these findings provide insight into the mechanistic understanding of ARB reduction during BSFL treatment of chicken manure and provide a strategy for rapidly mitigating ARB in animal manure.}, } @article {pmid37832249, year = {2023}, author = {Wang, C and Yang, H and Liu, H and Zhang, XX and Ma, L}, title = {Anthropogenic contributions to antibiotic resistance gene pollution in household drinking water revealed by machine-learning-based source-tracking.}, journal = {Water research}, volume = {246}, number = {}, pages = {120682}, doi = {10.1016/j.watres.2023.120682}, pmid = {37832249}, issn = {1879-2448}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Drinking Water ; Drug Resistance, Microbial/genetics ; Machine Learning ; }, abstract = {Although the presence of antibiotic resistance genes (ARGs) in drinking water and their potential horizontal gene transfer to pathogenic microbes are known to pose a threat to human health, their pollution levels and potential anthropogenic sources are poorly understood. In this study, broad-spectrum ARG profiling combined with machine-learning-based source classification SourceTracker was performed to investigate the pollution sources of ARGs in household drinking water collected from 95 households in 47 cities of eight countries/regions. In total, 451 ARG subtypes belonging to 19 ARG types were detected with total abundance in individual samples ranging from 1.4 × 10[-4] to 1.5 × 10° copies per cell. Source tracking analysis revealed that many ARGs were highly contributed by anthropogenic sources (37.1%), mainly wastewater treatment plants. The regions with the highest detected ARG contribution from wastewater (∼84.3%) used recycled water as drinking water, indicating the need for better ARG control strategies to ensure safe water quality in these regions. Among ARG types, sulfonamide, rifamycin and tetracycline resistance genes were mostly anthropogenic in origin. The contributions of anthropogenic sources to the 20 core ARGs detected in all of the studied countries/regions varied from 36.6% to 84.1%. Moreover, the anthropogenic contribution of 17 potential mobile ARGs identified in drinking water was significantly higher than other ARGs, and metagenomic assembly revealed that these mobile ARGs were carried by diverse potential pathogens. These results indicate that human activities have exacerbated the constant input and transmission of ARGs in drinking water. Our further risk classification framework revealed three ARGs (sul1, sul2 and aadA) that pose the highest risk to public health given their high prevalence, anthropogenic sources and mobility, facilitating accurate monitoring and control of anthropogenic pollution in drinking water.}, } @article {pmid37832205, year = {2024}, author = {Zhang, J and Du, R and Niu, J and Ban, S and Zhang, Y and Xu, L and Nie, H and Wu, Q and Xu, Y}, title = {Daqu and environmental microbiota regulate fatty acid biosynthesis via driving the core microbiota in soy sauce aroma type liquor fermentation.}, journal = {International journal of food microbiology}, volume = {408}, number = {}, pages = {110423}, doi = {10.1016/j.ijfoodmicro.2023.110423}, pmid = {37832205}, issn = {1879-3460}, mesh = {Fermentation ; Odorants/analysis ; *Soy Foods/analysis ; Pichia/genetics ; *Microbiota/genetics ; Alcoholic Beverages/analysis ; Fatty Acids/analysis ; }, abstract = {Fatty acids are considered as important compounds for the aroma and taste of Chinese liquor. Revealing the core microbiota related with fatty acid biosynthesis and how they are influenced are essential to control fatty acids in spontaneous Chinese liquor fermentation. Herein, we identified the core microbiota related with fatty acid biosynthesis based on their microbial abundance, abundance and expression level of genes related with fatty acid biosynthesis, using high-throughput amplicon sequencing, metagenomic and metatranscriptomic analysis, respectively. Acetilactobacillus, Kroppenstedtia, Saccharomyces, Paecilomyces and Pichia were identified as the core microbiota (the criteria for identifying core microbiota: average relative abundance ≥1 %, average abundance of related genes >400 fragments per kilobase of transcript per million fragments mapped [FPKM], and expression level of related genes >1000 FPKM) related with fatty acid biosynthesis. SourceTracker analysis showed that Daqu mainly provided Kroppenstedtia (34.01 %) and Acetilactobacillus (3.31 %). Ground mainly provided Pichia (47.47 %), Saccharomyces (16.17 %) and Paecilomyces (8.55 %). Structural equation model revealed that Daqu and environmental microbiota drove the core microbiota (P < 0.05), and the core microbiota drove the biosynthesis of fatty acids (P < 0.05). This work revealed the important role of Daqu and environmental microbiota in fatty acid biosynthesis in liquor fermentation. It would benefit controlling fatty acids in liquor fermentation, and improving the liquor quality.}, } @article {pmid37831725, year = {2023}, author = {Ventolero, M and Wang, S and Hu, H and Li, X}, title = {Are the predicted known bacterial strains in a sample really present? A case study.}, journal = {PloS one}, volume = {18}, number = {10}, pages = {e0291964}, pmid = {37831725}, issn = {1932-6203}, mesh = {*Staphylococcus aureus/genetics ; *Metagenome ; Genome, Bacterial ; Bacteria/genetics ; Metagenomics ; }, abstract = {With mutations constantly accumulating in bacterial genomes, it is unclear whether the previously identified bacterial strains are really present in an extant sample. To address this question, we did a case study on the known strains of the bacterial species S. aureus and S. epidermis in 68 atopic dermatitis shotgun metagenomic samples. We evaluated the likelihood of the presence of all sixteen known strains predicted in the original study and by two popular tools in this study. We found that even with the same tool, only two known strains were predicted by the original study and this study. Moreover, none of the sixteen known strains was likely present in these 68 samples. Our study thus indicates the limitation of the known-strain-based studies, especially those on rapidly evolving bacterial species. It implies the unlikely presence of the previously identified known strains in a current environmental sample. It also called for de novo bacterial strain identification directly from shotgun metagenomic reads.}, } @article {pmid37831715, year = {2023}, author = {Alarcón-Schumacher, T and Lücking, D and Erdmann, S}, title = {Revisiting evolutionary trajectories and the organization of the Pleolipoviridae family.}, journal = {PLoS genetics}, volume = {19}, number = {10}, pages = {e1010998}, pmid = {37831715}, issn = {1553-7404}, mesh = {Australia ; *Viruses/genetics ; *Archaeal Viruses/genetics ; Biological Evolution ; Integrases/genetics ; Archaea/genetics ; Genome, Viral/genetics ; }, abstract = {Archaeal pleomorphic viruses belonging to the Pleolipoviridae family represent an enigmatic group as they exhibit unique genomic features and are thought to have evolved through recombination with different archaeal plasmids. However, most of our understanding of the diversity and evolutionary trajectories of this clade comes from a handful of isolated representatives. Here we present 164 new genomes of pleolipoviruses obtained from metagenomic data of Australian hypersaline lakes and publicly available metagenomic data. We perform a comprehensive analysis on the diversity and evolutionary relationships of the newly discovered viruses and previously described pleolipoviruses. We propose to classify the viruses into five genera within the Pleolipoviridae family, with one new genus represented only by virus genomes retrieved in this study. Our data support the current hypothesis that pleolipoviruses reshaped their genomes through recombining with multiple different groups of plasmids, which is reflected in the diversity of their predicted replication strategies. We show that the proposed genus Epsilonpleolipovirus has evolutionary ties to pRN1-like plasmids from Sulfolobus, suggesting that this group could be infecting other archaeal phyla. Interestingly, we observed that the genome size of pleolipoviruses is correlated to the presence or absence of an integrase. Analyses of the host range revealed that all but one virus exhibit an extremely narrow range, and we show that the predicted tertiary structure of the spike protein is strongly associated with the host family, suggesting a specific adaptation to the host S-layer glycoprotein organization.}, } @article {pmid37831420, year = {2023}, author = {Mozhaitseva, K and Tourrain, Z and Branca, A}, title = {Population Genomics of the Mostly Thelytokous Diplolepis rosae (Linnaeus, 1758) (Hymenoptera: Cynipidae) Reveals Population-specific Selection for Sex.}, journal = {Genome biology and evolution}, volume = {15}, number = {10}, pages = {}, pmid = {37831420}, issn = {1759-6653}, mesh = {Animals ; Female ; Male ; Base Sequence ; *Hymenoptera/genetics ; Metagenomics ; Parthenogenesis ; Semen ; *Wasps/genetics ; }, abstract = {In Hymenoptera, arrhenotokous parthenogenesis (arrhenotoky) is a common reproductive mode. Thelytokous parthenogenesis (thelytoky), when virgin females produce only females, is less common and is found in several taxa. In our study, we assessed the efficacy of recombination and the effect of thelytoky on the genome structure of Diplolepis rosae, a gall wasp-producing bedeguars in dog roses. We assembled a high-quality reference genome using Oxford Nanopore long-read technology and sequenced 17 samples collected in France with high-coverage Illumina reads. We found two D. rosae peripatric lineages that differed in the level of recombination and homozygosity. One of the D. rosae lineages showed a recombination rate that was 13.2 times higher and per-individual heterozygosity that was 1.6 times higher. In the more recombining lineage, the genes enriched in functions related to male traits ('sperm competition", "insemination", and "copulation" gene ontology terms) showed signals of purifying selection, whereas in the less recombining lineage, the same genes showed traces pointing towards balancing or relaxed selection. Thus, although D. rosae reproduces mainly by thelytoky, selection may act to maintain sexual reproduction.}, } @article {pmid37831075, year = {2023}, author = {Xu, H and Xiao, Q and Dai, Y and Chen, D and Zhang, C and Jiang, Y and Xie, J}, title = {Selected Bacteria Are Critical for Karst River Carbon Sequestration via Integrating Multi-omics and Hydrochemistry Data.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {3043-3056}, pmid = {37831075}, issn = {1432-184X}, mesh = {*Rivers/chemistry ; *Carbon Sequestration ; Dissolved Organic Matter ; Leucine/metabolism ; Multiomics ; Carbon/metabolism ; Bacteria/genetics/metabolism ; Water/metabolism ; }, abstract = {Recalcitrant dissolved organic carbon (RDOC) produced by microbial carbon pumps (MCPs) in the ocean is crucial for carbon sequestration and regulating climate change in the history of Earth. However, the importance of microbes on RDOC formation in terrestrial aquatic systems, such as rivers and lakes, remains to be determined. By integrating metagenomic (MG) and metatranscriptomic (MT) sequencing, we defined the microbial communities and their transcriptional activities in both water and silt of a typical karst river, the Lijiang River, in Southwest China. Betaproteobacteria predominated in water, serving as the most prevalent population remodeling components of dissolved organic carbon (DOC). Binning method recovered 45 metagenome-assembled genomes (MAGs) from water and silt. Functional annotation of MAGs showed Proteobacteria was less versatile in degrading complex carbon, though cellulose and chitin utilization genes were widespread in this phylum, whereas Bacteroidetes had high potential for the utilization of macro-molecular organic carbon. Metabolic remodeling revealed that increased shared metabolites within the bacterial community are associated with increased concentration of DOC, highlighting the significance of microbial cooperation during producing and remodeling of carbon components. Beta-oxidation, leucine degradation, and mevalonate (MVA) modules were significantly positively correlated with the concentration of RDOC. Blockage of the leucine degradation pathway in Limnohabitans and UBA4660-related MAGs were associated with decreased RDOC in the karst river, while the Fluviicola-related MAG containing a complete leucine degradation pathway was positively correlated with RDOC concentration. Collectively, our study revealed the linkage between bacteria metabolic processes and carbon sequestration. This provided novel insights into the microbial roles in karst-rivers carbon sink.}, } @article {pmid37830937, year = {2023}, author = {Rasool, N}, title = {Ophthalmic manifestations of Whipple's disease.}, journal = {Current opinion in ophthalmology}, volume = {}, number = {}, pages = {}, doi = {10.1097/ICU.0000000000000989}, pmid = {37830937}, issn = {1531-7021}, abstract = {PURPOSE OF REVIEW: Whipple's disease is an infectious cause of uveitis that may present with nonspecific findings of intraocular inflammation, which can precede the development of neurologic symptoms and signs. Whipple's disease, then, may evade consideration in the differential diagnosis for uveitis.

RECENT FINDINGS: Molecular tests can be helpful in identifying the presence of Tropheryma whipplei from ocular specimens. The application of metagenomic sequencing for ocular specimens is promising, as it offers the opportunity to identify the pathogen when suspicion for an intraocular infection is high. Whipple's disease demonstrates the ability to abrogate the host immune response, which gives some insight into its pathogenesis.

SUMMARY: Whipple's disease should be suspected in patients who have uveitis refractory to anti-inflammatory therapy. Knowledge of this important pathogen can help direct the timely implementation of diagnostic testing.}, } @article {pmid37830816, year = {2023}, author = {Dudas, G and Batson, J}, title = {Accumulated metagenomic studies reveal recent migration, whole genome evolution, and undiscovered diversity of orthomyxoviruses.}, journal = {Journal of virology}, volume = {97}, number = {10}, pages = {e0105623}, pmid = {37830816}, issn = {1098-5514}, support = {IG-5305-2023//European Molecular Biology Organization (EMBO)/ ; }, mesh = {Evolution, Molecular ; *Genome, Viral ; *Orthomyxoviridae/genetics ; Phylogeny ; Metagenomics ; }, abstract = {The number of known virus species has increased dramatically through metagenomic studies, which search genetic material sampled from a host for non-host genes. Here, we focus on an important viral family that includes influenza viruses, the Orthomyxoviridae, with over 100 recently discovered viruses infecting hosts from humans to fish. We find that one virus called Wǔhàn mosquito virus 6, discovered in mosquitoes in China, has spread across the globe very recently. Surface proteins used to enter cells show signs of rapid evolution in Wǔhàn mosquito virus 6 and its relatives which suggests an ability to infect vertebrate animals. We compute the rate at which new orthomyxovirus species discovered add evolutionary history to the tree of life, predict that many viruses remain to be discovered, and discuss what appropriately designed future studies can teach us about how diseases cross between continents and species.}, } @article {pmid37830742, year = {2024}, author = {Wigren, MA and Johnson, TA and Griffitt, RJ and Hay, AG and Knott, JA and Sepúlveda, MS}, title = {Limited impact of weathered residues from the Deepwater Horizon oil spill on the gut-microbiome and foraging behavior of sheepshead minnows (Cyprinodon variegatus).}, journal = {Journal of toxicology and environmental health. Part A}, volume = {87}, number = {1}, pages = {1-21}, doi = {10.1080/15287394.2023.2265413}, pmid = {37830742}, issn = {1528-7394}, mesh = {Animals ; *Killifishes/genetics ; *Petroleum/toxicity ; *Gastrointestinal Microbiome ; *Petroleum Pollution/adverse effects ; RNA, Ribosomal, 16S ; *Microbiota ; *Cyprinidae ; Hydrocarbons ; Gulf of Mexico ; *Water Pollutants, Chemical/toxicity ; *Polycyclic Aromatic Hydrocarbons ; }, abstract = {The Deepwater Horizon disaster of April 2010 was the largest oil spill in U.S. history and exerted catastrophic effects on several ecologically important fish species in the Gulf of Mexico (GoM). Within fish, the microbiome plays a key symbiotic role in maintaining host health and aids in acquiring nutrients, supporting immune function, and modulating behavior. The aim of this study was to examine if exposure to weathered oil might produce significant shifts in fish gut-associated microbial communities as determined from taxa and genes known for hydrocarbon degradation, and whether foraging behavior was affected. The gut microbiome (16S rRNA and shotgun metagenomics) of sheepshead minnow (Cyprinodon variegatus) was characterized after fish were exposed to oil in High Energy Water Accommodated Fractions (HEWAF; tPAH = 81.1 ± 12.4 µg/L) for 7 days. A foraging behavioral assay was used to determine feeding efficiency before and after oil exposure. The fish gut microbiome was not significantly altered in alpha or beta diversity. None of the most abundant taxa produced any significant shifts as a result of oil exposure, with only rare taxa showing significant shifts in abundance between treatments. However, several bioindicator taxa known for hydrocarbon degradation were detected in the oil treatment, primarily Sphingomonas and Acinetobacter. Notably, the genus Stenotrophomonas was detected in high abundance in 16S data, which previously was not described as a core member of fish gut microbiomes. Data also demonstrated that behavior was not significantly affected by oil exposure. Potential low bioavailability of the oil may have been a factor in our observation of minor shifts in taxa and no behavioral effects. This study lays a foundation for understanding the microbiome of captive sheepshead minnows and indicates the need for further research to elucidate the responses of the fish gut-microbiome under oil spill conditions.}, } @article {pmid37830211, year = {2023}, author = {Hoang, J and Gilbertson-White, S and Cady, N and Yadav, M and Shahi, S and Aguilar, L and Mangalam, AK and Cherwin, C}, title = {Preliminary Analysis of Gut Microbiome and Gastrointestinal Symptom Burden in Breast Cancer Patients Receiving Chemotherapy Compared to Healthy Controls.}, journal = {Biological research for nursing}, volume = {}, number = {}, pages = {10998004231205277}, doi = {10.1177/10998004231205277}, pmid = {37830211}, issn = {1552-4175}, support = {P30 ES005605/ES/NIEHS NIH HHS/United States ; }, abstract = {BACKGROUND: Alterations in the naturally occurring bacteria of the gut, known as the gastrointestinal (GI) microbiome, may influence GI symptoms in women with breast cancer.

OBJECTIVE: This work aims to describe GI symptom occurrence, duration, severity, and distress and measures of the GI microbiome among women with breast cancer receiving chemotherapy compared to age- and sex-matched healthy controls.

INTERVENTIONS/METHODS: 22 women with breast cancer receiving chemotherapy and 17 healthy control women provided stool specimens and GI symptom data using the modified Memorial Symptom Assessment Scale (MSAS). The fecal microbiome was profiled by metagenomic sequencing of 16S Ribosomal RNA (rRNA). GI microbiome was compared between groups using alpha-diversity (Observed OTU number and Shannon index), beta-diversity (UniFrac distances), and relative abundance of select genera.

RESULTS: GI symptoms with high symptom reports among breast cancer patients included nausea, diarrhea, flatulence, dry mouth, taste change, and poor appetite. Indices of differential abundance (beta diversity) significantly distinguished between breast cancer patients and healthy controls. Unique bacterial features differentiating the 2 groups were Prevotella_9, Akkermansia, Lachnospira, Lachnospiraceae_NK4A136, Lachnoclostridium, and Oscillibacter.

CONCLUSIONS: Gut bacteria are associated with GI inflammation and mucus degradation, suggesting the potential role of the GI microbiome in GI symptom burden. Understanding the influence of GI bacteria on gut health and symptoms will help harness the enormous potential of the GI microbiome as a future diagnostic and therapeutic agent to reduce the symptom burden associated with chemotherapy.}, } @article {pmid37830115, year = {2023}, author = {Choi, SI and Kim, N and Nam, RH and Jang, JY and Kim, EH and Ha, S and Kang, K and Lee, W and Choi, H and Kim, YR and Seok, YJ and Shin, CM and Lee, DH}, title = {The Protective Effect of Roseburia faecis Against Repeated Water Avoidance Stress-induced Irritable Bowel Syndrome in a Wister Rat Model.}, journal = {Journal of cancer prevention}, volume = {28}, number = {3}, pages = {93-105}, pmid = {37830115}, issn = {2288-3649}, abstract = {Roseburia faecis, a butyrate-producing, gram-positive anaerobic bacterium, was evaluated for its usefulness against repeated water avoidance stress (WAS)-induced irritable bowel syndrome (IBS) in a rat model, and the underlying mechanism was explored. We divided the subjects into three groups: one without stress exposure, another subjected to daily 1-hour WAS for 10 days, and a third exposed to the same WAS regimen while also receiving two different R. faecis strains (BBH024 or R22-12-24) via oral gavage for the same 10-day duration. Fecal pellet output (FPO), a toluidine blue assay for mast cell infiltration, and fecal microbiota analyses were conducted using 16S rRNA metagenomic sequencing. Predictive functional profiling of microbial communities in metabolism was also conducted. FPO and colonic mucosal mast cell counts were significantly higher in the WAS group than in the control group (male, P = 0.004; female, P = 0.027). The administration of both BBH024 (male, P = 0.015; female, P = 0.022) and R22-12-24 (male, P = 0.003; female, P = 0.040) significantly reduced FPO. Submucosal mast cell infiltration in the colon showed a similar pattern in males. In case of fecal microbiota, the WAS with R. faecis group showed increased abundance of the Roseburia genus compared to WAS alone. Moreover, the expression of a gene encoding a D-methionine transport system substrate-binding protein was significantly elevated in the WAS with R. faecis group compared to that in the WAS (male, P = 0.028; female, P = 0.025) group. These results indicate that R. faecis is a useful probiotic for treating IBS and colonic microinflammation.}, } @article {pmid37829673, year = {2023}, author = {Lynch, M and Nedjat-Haiem, M and Abeson, K and Chang, C}, title = {Limbic Encephalitis Associated with Human Herpesvirus-7 Infection in an Immunocompetent Adolescent.}, journal = {Child neurology open}, volume = {10}, number = {}, pages = {2329048X231206935}, pmid = {37829673}, issn = {2329-048X}, abstract = {Despite the ubiquitous nature of human herpesvirus-7 (HHV-7) infection, its clinical significance in the central nervous system (CNS) is poorly understood. However, the related human herpesvirus-6 (HHV-6), which has remarkable genomic similarity to HHV-7, is linked to encephalitis. We present the case of a 17-year-old immunocompetent male with remote history of seizure who arrived in status epilepticus. Upon resolution, he required hospitalization for worsening encephalopathy. Electroencephalogram (EEG) revealed bilateral temporal lobe dysfunction and magnetic resonance imaging (MRI) showed increased signaling in bilateral medial temporal lobes with hippocampal microhemorrhages. Empiric intravenous (IV) acyclovir was initiated despite initially negative cerebrospinal fluid (CSF) studies due to concern for herpes simplex virus (HSV) encephalitis. The patient improved and was discharged on hospital day 13 (HD13). After discharge, a human metagenomics CSF panel resulted positive only for HHV-7, making a case for possible etiology and empiric treatment of HHV-7 despite delayed CSF and serum studies.}, } @article {pmid37829447, year = {2023}, author = {Guo, DJ and Li, DP and Yang, B and Verma, KK and Singh, RK and Singh, P and Khan, Q and Sharma, A and Qin, Y and Zhang, BQ and Song, XP and Li, YR}, title = {Corrigendum: Effect of endophytic diazotroph Enterobacter roggenkampii ED5 on nitrogen-metabolism-related microecology in the sugarcane rhizosphere at different nitrogen levels.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1290575}, doi = {10.3389/fmicb.2023.1290575}, pmid = {37829447}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2023.1132016.].}, } @article {pmid37828802, year = {2023}, author = {Zhao, J and Feng, T and An, X and Chen, X and Han, N and Wang, J and Chang, G and Hou, X}, title = {Livestock grazing is associated with the gut microbiota and antibiotic resistance genes in sympatric plateau pika (Ochotona curzoniae).}, journal = {Integrative zoology}, volume = {}, number = {}, pages = {}, doi = {10.1111/1749-4877.12778}, pmid = {37828802}, issn = {1749-4877}, support = {2019QZKK0501//Second Tibetan Plateau Scientific Expedition and Research Program (STEP)/ ; 32172436//National Natural Science Foundation of China/ ; 2022K-16//Science and Technology Program of Shaanxi Academy of Science/ ; 2019QZKK0501//Scond Tibetan Plateau Scientific Expedition and Research/ ; 32172436//National Natural Science Foundation of China/ ; 2022K-16//Science and Technology Program of Shaanxi Academy of Science/ ; }, abstract = {With the overuse of antibiotics in health care and animal husbandry, antibiotic resistance becomes a serious threat to public health. Antibiotic residues from veterinary medicine have increased the dissemination of antibiotic resistance genes (ARGs) by horizontal gene transfer globally, leading to the enrichment of ARGs in wildlife. Plateau pika (Ochotona curzoniae) is a small herbivore endemic to the Qinghai-Tibetan Plateau. Previous studies reveal that pika evolves a coprophagy behavior toward cohabitated yak, which makes the pika population a potential reservoir of ARGs. Yet, little is known about the resistome of pika under different grazing intensities. Here, we sampled the cecum content of pika from three different grazing intensity areas in the Qinghai-Tibetan Plateau to evaluate the effect of grazing on its gut microbiota and resistome. By using the 16S full-length amplicon and metagenomic sequencing, our study revealed that livestock grazing significantly altered the gut microbial community of plateau pika as compared to prohibited grazing areas. We found bacterial lineage Prevotellaceae, Lachnospirales, and RF39 increased in grazing areas. Analysis of the resistome revealed that pika from continuous grazing areas enriched a higher abundance of colistin (MCR) and streptogramin (vat) resistance genes. Moreover, we observed significant correlations between the gut microbial community, ARGs, and mobile genetic element profiles, hinting that pika gut microbiota was an important shaping force of the resistome. In future studies, the continuous monitoring of wildlife gut resistome and environmental antibiotic residues is imperative for a better understanding and for tackling the horizontal gene transfer of ARGs across the wildlife-livestock interface.}, } @article {pmid37828586, year = {2023}, author = {Zhang, P and Wang, X and Li, S and Cao, X and Zou, J and Fang, Y and Shi, Y and Xiang, F and Shen, B and Li, Y and Fang, B and Zhang, Y and Guo, R and Lv, Q and Zhang, L and Lu, Y and Wang, Y and Yu, J and Xie, Y and Wang, R and Chen, X and Yu, J and Zhang, Z and He, J and Zhan, J and Lv, W and Nie, Y and Cai, J and Xu, X and Hu, J and Zhang, Q and Gao, T and Jiang, X and Tan, X and Xue, N and Wang, Y and Ren, Y and Wang, L and Zhang, H and Ning, Y and Chen, J and Zhang, L and Jin, S and Ren, F and Ehrlich, SD and Zhao, L and Ding, X}, title = {Metagenome-wide analysis uncovers gut microbial signatures and implicates taxon-specific functions in end-stage renal disease.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {226}, pmid = {37828586}, issn = {1474-760X}, mesh = {Humans ; Metagenome ; *Gastrointestinal Microbiome ; *Kidney Failure, Chronic ; *Microbiota ; *Renal Insufficiency, Chronic/genetics/metabolism ; Feces ; Clostridiales ; }, abstract = {BACKGROUND: The gut microbiota plays a crucial role in regulating host metabolism and producing uremic toxins in patients with end-stage renal disease (ESRD). Our objective is to advance toward a holistic understanding of the gut ecosystem and its functional capacity in such patients, which is still lacking.

RESULTS: Herein, we explore the gut microbiome of 378 hemodialytic ESRD patients and 290 healthy volunteers from two independent cohorts via deep metagenomic sequencing and metagenome-assembled-genome-based characterization of their feces. Our findings reveal fundamental alterations in the ESRD microbiome, characterized by a panel of 348 differentially abundant species, including ESRD-elevated representatives of Blautia spp., Dorea spp., and Eggerthellaceae, and ESRD-depleted Prevotella and Roseburia species. Through functional annotation of the ESRD-associated species, we uncover various taxon-specific functions linked to the disease, such as antimicrobial resistance, aromatic compound degradation, and biosynthesis of small bioactive molecules. Additionally, we show that the gut microbial composition can be utilized to predict serum uremic toxin concentrations, and based on this, we identify the key toxin-contributing species. Furthermore, our investigation extended to 47 additional non-dialyzed chronic kidney disease (CKD) patients, revealing a significant correlation between the abundance of ESRD-associated microbial signatures and CKD progression.

CONCLUSION: This study delineates the taxonomic and functional landscapes and biomarkers of the ESRD microbiome. Understanding the role of gut microbiota in ESRD could open new avenues for therapeutic interventions and personalized treatment approaches in patients with this condition.}, } @article {pmid37828452, year = {2023}, author = {Shangguan, L and Xue, L and Shang, J and Wang, H}, title = {The application value of metagenomic next-generation sequencing in community-acquired purulent meningitis after antibiotic intervention.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {683}, pmid = {37828452}, issn = {1471-2334}, mesh = {Humans ; Retrospective Studies ; *Meningitis, Bacterial/diagnosis/drug therapy ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/therapeutic use ; Blood Culture ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Bacteria account for nearly one third of the causes of community-acquired central nervous system infections, and traditional diagnostic methods are based on culture results, which are time-consuming and have a low detection rate leading to delayed diagnosis and treatment. Since metagenomic next-generation sequencing (mNGS) has the advantages of high timeliness and only detecting microbial trace gene fragments, it has been used more widely in recent years. Based on this, we explored whether the application of cerebrospinal fluid (CSF) mNGS is advantageous in patients with community-acquired purulent meningitis, especially in people who have already used antibiotics.

METHODS: This was a retrospective study of 63 patients with community-acquired purulent meningitis admitted to the Department of Neurology of Shanxi Bethune Hospital from March 2018 to November 2022. Data were systematically collected and classified into CSF culture group, blood culture group and CSF mNGS group according to different detection methods, and the total detection rate of each method was calculated. Each group of patients was divided into two subgroups according to whether antibiotics were used before sampling. The detection rates of the three groups were compared within and between groups to explore whether mNGS has advantages over traditional methods and the influence of antibiotic use on detection rates of the three methods.

RESULTS: Among the 63 patients, the cases of CSF culture, blood culture and CSF mNGS were 56, 46, 44, respectively. The total detection rates of the three methods were 17.86%, 36.96%, 81.82%, with statistical differences (p < 0.05),suggesting that the detection rate of mNGS was higher than CSF culture (p < 0.05) and blood culture (p < 0.05),and the detection rate of blood culture higher than CSF culture (p < 0.05). Further grouping found that without antibiotics, the detection rates of CSF culture, blood culture and CSF mNGS were 28.57%, 56.25% and 88.89%, with statistical differences (p < 0.05), and the detection rate of CSF mNGS was higher than that of CSF culture (p < 0.05), but there was no statistical difference between CSF and blood culture (p > 0.05), nor between blood culture and CSF mNGS (p > 0.05). The detection rates of the three groups with antibiotics were 14.29%, 26.67% and 80.00%, with statistical differences (p < 0.05), and the detection rate of CSF mNGS was still higher than CSF culture (p < 0.05) and blood culture (p < 0.05). However, the detection rate of CSF mNGS also decreased after antibiotics were used for more than 3 days.

CONCLUSIONS: The detection rate of CSF mNGS in patients with purulent meningitis is higher than traditional methods, especially in patients who have been given antibiotics, but the detection rate will decrease with the extension of antibiotic use.}, } @article {pmid37828152, year = {2023}, author = {Wu-Woods, NJ and Barlow, JT and Trigodet, F and Shaw, DG and Romano, AE and Jabri, B and Eren, AM and Ismagilov, RF}, title = {Microbial-enrichment method enables high-throughput metagenomic characterization from host-rich samples.}, journal = {Nature methods}, volume = {20}, number = {11}, pages = {1672-1682}, pmid = {37828152}, issn = {1548-7105}, support = {RC2 DK133947/DK/NIDDK NIH HHS/United States ; T32 GM150375/GM/NIGMS NIH HHS/United States ; RC2 DK122394/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Metagenome ; *Microbiota/genetics ; Bacteria/genetics ; DNA ; Gastrointestinal Tract ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Mammals/genetics ; }, abstract = {Host-microbe interactions have been linked to health and disease states through the use of microbial taxonomic profiling, mostly via 16S ribosomal RNA gene sequencing. However, many mechanistic insights remain elusive, in part because studying the genomes of microbes associated with mammalian tissue is difficult due to the high ratio of host to microbial DNA in such samples. Here we describe a microbial-enrichment method (MEM), which we demonstrate on a wide range of sample types, including saliva, stool, intestinal scrapings, and intestinal mucosal biopsies. MEM enabled high-throughput characterization of microbial metagenomes from human intestinal biopsies by reducing host DNA more than 1,000-fold with minimal microbial community changes (roughly 90% of taxa had no significant differences between MEM-treated and untreated control groups). Shotgun sequencing of MEM-treated human intestinal biopsies enabled characterization of both high- and low-abundance microbial taxa, pathways and genes longitudinally along the gastrointestinal tract. We report the construction of metagenome-assembled genomes directly from human intestinal biopsies for bacteria and archaea at relative abundances as low as 1%. Analysis of metagenome-assembled genomes reveals distinct subpopulation structures between the small and large intestine for some taxa. MEM opens a path for the microbiome field to acquire deeper insights into host-microbe interactions by enabling in-depth characterization of host-tissue-associated microbial communities.}, } @article {pmid37827037, year = {2023}, author = {Yu, J and You, J and Lens, PNL and Lu, L and He, Y and Ji, Z and Chen, J and Cheng, Z and Chen, D}, title = {Biofilm metagenomic characteristics behind high coulombic efficiency for propanethiol deodorization in two-phase partitioning microbial fuel cell.}, journal = {Water research}, volume = {246}, number = {}, pages = {120677}, doi = {10.1016/j.watres.2023.120677}, pmid = {37827037}, issn = {1879-2448}, mesh = {*Bioelectric Energy Sources/microbiology ; Silicone Oils ; Sulfhydryl Compounds ; Sulfur ; Biofilms ; Electrodes ; Electricity ; }, abstract = {Hydrophobic volatile organic sulfur compounds (VOSCs) are frequently found during sewage treatment, and their effective management is crucial for reducing malodorous complaints. Microbial fuel cells (MFC) are effective for both VOSCs abatement and energy recovery. However, the performance of MFC on VOSCs remains limited by the mass transfer efficiency of MFC in aqueous media. Inspired by two-phase partitioning biotechnology, silicone oil was introduced for the first time into MFC as a non-aqueous phase (NAP) medium to construct two-phase partitioning microbial fuel cell (TPPMFC) and augment the mass transfer of target VOSCs of propanethiol (PT) in the liquid phase. The PT removal efficiency within 32 h increased by 11-20% compared with that of single-phase MFC, and the coulombic efficiency of TPPMFC (11.01%) was 4.32-2.68 times that of single-phase MFC owing to the fact that highly active desulfurization and thiol-degrading bacteria (e.g., Pseudomonas, Achromobacter) were attached to the silicone oil surface, whereas sulfur-oxidizing bacteria (e.g., Thiobacillus, Commonas, Ottowia) were dominant on the anodic biofilm. The outer membrane cytochrome-c content and NADH dehydrogenase activity improved by 4.15 and 3.36 times in the TPPMFC, respectively. The results of metagenomics by KEGG and COG confirmed that the metabolism of PT in TPPMFC was comprehensive, and that the addition of a NAP upregulates the expression of genes related to sulfur metabolism, energy generation, and amino acid synthesis. This finding indicates that the NAP assisted bioelectrochemical systems would be promising to solve mass-transfer restrictions in low solubility contaminates removal.}, } @article {pmid37824825, year = {2023}, author = {Park, SY and Lindner, MS and Brick, K and Noll, N and Ounit, R and Noa, LJ and Sabzwari, R and Trible, R and Sniffen, JC and Roth, P and Khan, A and Rodriguez, A and Sahra, S and Davis, MJ and Brar, IS and Balasundaram, G and Nolte, FS and Blauwkamp, TA and Perkins, BA and Bercovici, S}, title = {Detection of Mpox Virus Using Microbial Cell-free DNA: the Potential of Pathogen-Agnostic Sequencing for Rapid Identification of Emerging Pathogens.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiad452}, pmid = {37824825}, issn = {1537-6613}, abstract = {BACKGROUND: The 2022 global outbreak of mpox virus (MPXV) highlighted challenges with PCR detection as divergent strains emerged and atypical presentations limited the applicability of swab sampling. Recommended testing in the United States requires a swab of lesions, which arise late in infection and may be unrecognized. We present MPXV detections using plasma microbial cell-free DNA (mcfDNA) sequencing.

METHODS: Fifteen plasma samples from 12 case-patients were characterized through mcfDNA sequencing. Assay performance was confirmed through in-silico inclusivity and exclusivity assessments. MPXV isolates were genotyped using mcfDNA, and phylodynamic information imputed using publicly available sequences.

RESULTS: MPXV mcfDNA was detected in 12 case-patients. Mpox was not suspected in 5, with one having documented resolution of mpox >6 months previously. Six had moderate to severe mpox, supported by high MPXV mcfDNA concentration; 4 died. In 7 case-patients, mcfDNA sequencing detected co-infections. Genotyping by mcfDNA sequencing identified 22 MPXV mutations at 10 genomic loci in 9 case-patients. Consistent with variation observed in the 2022 outbreak, 21/22 variants were G > A/C > T. Phylogenetic analyses imputed isolates to sublineages arising at different time points and from different geographic locations.

CONCLUSIONS: We demonstrate the potential of plasma mcfDNA sequencing to detect, quantify, and, for acute infections with high sequencing coverage, subtype MPXV using a single non-invasive test. Sequencing plasma mcfDNA may augment existing mpox testing in vulnerable patient populations or in patients with atypical symptoms or unrecognized mpox. Strain type information may supplement disease surveillance and facilitate tracking emerging pathogens.}, } @article {pmid37824740, year = {2023}, author = {Adams, AK and Kristy, BD and Gorman, M and Balint-Kurti, P and Yencho, GC and Olukolu, BA}, title = {Qmatey: an automated pipeline for fast exact matching-based alignment and strain-level taxonomic binning and profiling of metagenomes.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {6}, pages = {}, pmid = {37824740}, issn = {1477-4054}, mesh = {*Metagenome ; Sequence Analysis, DNA ; *Metagenomics ; Databases, Factual ; }, abstract = {Metagenomics is a powerful tool for understanding organismal interactions; however, classification, profiling and detection of interactions at the strain level remain challenging. We present an automated pipeline, quantitative metagenomic alignment and taxonomic exact matching (Qmatey), that performs a fast exact matching-based alignment and integration of taxonomic binning and profiling. It interrogates large databases without using metagenome-assembled genomes, curated pan-genes or k-mer spectra that limit resolution. Qmatey minimizes misclassification and maintains strain level resolution by using only diagnostic reads as shown in the analysis of amplicon, quantitative reduced representation and shotgun sequencing datasets. Using Qmatey to analyze shotgun data from a synthetic community with 35% of the 26 strains at low abundance (0.01-0.06%), we revealed a remarkable 85-96% strain recall and 92-100% species recall while maintaining 100% precision. Benchmarking revealed that the highly ranked Kraken2 and KrakenUniq tools identified 2-4 more taxa (92-100% recall) than Qmatey but produced 315-1752 false positive taxa and high penalty on precision (1-8%). The speed, accuracy and precision of the Qmatey pipeline positions it as a valuable tool for broad-spectrum profiling and for uncovering biologically relevant interactions.}, } @article {pmid37824622, year = {2023}, author = {Pinko, D and Abramovich, S and Rahav, E and Belkin, N and Rubin-Blum, M and Kucera, M and Morard, R and Holzmann, M and Abdu, U}, title = {Shared ancestry of algal symbiosis and chloroplast sequestration in foraminifera.}, journal = {Science advances}, volume = {9}, number = {41}, pages = {eadi3401}, pmid = {37824622}, issn = {2375-2548}, mesh = {Phylogeny ; *Symbiosis/genetics ; *Foraminifera/genetics ; Chloroplasts/genetics ; }, abstract = {Foraminifera are unicellular organisms that established the most diverse algal symbioses in the marine realm. Endosymbiosis repeatedly evolved in several lineages, while some engaged in the sequestration of chloroplasts, known as kleptoplasty. So far, kleptoplasty has been documented exclusively in the rotaliid clade. Here, we report the discovery of kleptoplasty in the species Hauerina diversa that belongs to the miliolid clade. The existence of kleptoplasty in the two main clades suggests that it is more widespread than previously documented. We observed chloroplasts in clustered structures within the foraminiferal cytoplasm and confirmed their functionality. Phylogenetic analysis of 18S ribosomal RNA gene sequences showed that H. diversa branches next to symbiont-bearing Alveolinidae. This finding represents evidence of of a relationship between kleptoplastic and symbiotic foraminifera.. Analysis of ribosomal genes and metagenomics revealed that alveolinid symbionts and kleptoplasts belong to the same clade, which suggests a common ancestry.}, } @article {pmid37823957, year = {2023}, author = {Hernandez, SAV and Salamat, SEA and Galay, RL}, title = {Analysis of the bacterial community in female Rhipicephalus microplus ticks from selected provinces in Luzon, Philippines, using next-generation sequencing.}, journal = {Experimental & applied acarology}, volume = {91}, number = {3}, pages = {463-475}, pmid = {37823957}, issn = {1572-9702}, mesh = {Female ; Animals ; Cattle ; *Rhipicephalus/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Philippines ; Bacteria/genetics ; *Tick-Borne Diseases/veterinary ; High-Throughput Nucleotide Sequencing ; DNA ; *Cattle Diseases/parasitology ; *Tick Infestations/veterinary/parasitology ; }, abstract = {Analysis of the tick microbiome can help understand tick-symbiont interactions and identify undiscovered pathogens, which may aid in implementing control of ticks and tick-borne diseases. The tropical cattle tick Rhipicephalus microplus is a widespread ectoparasite of cattle in the Philippines, negatively affecting animal productivity and health. This study characterized the bacterial community of R. microplus from Luzon, Philippines, through next-generation sequencing of 16s rRNA. DNA was extracted from 45 partially engorged female ticks from nine provinces. The DNA samples were pooled per province and then sequenced and analyzed using an open-source bioinformatics platform. In total, 667 operational taxonomic units (OTUs) were identified. The ticks in all nine provinces were found to have Coxiella, Corynebacterium, Staphylococcus, and Acinetobacter. Basic local alignment search tool (BLAST) analysis revealed the presence of known pathogens of cattle, such as Bartonella, Ehrlichia minasensis, and Dermatophilus congolensis. The tick samples from Laguna, Quezon, and Batangas had the most diverse bacterial species, whereas the tick samples from Ilocos Norte had the lowest diversity. Similarities in the composition of the bacterial community in ticks from provinces near each other were also observed. This is the first study on metagenomic analysis of cattle ticks in the Philippines, providing new insights that may be useful for controlling ticks and tick-borne diseases.}, } @article {pmid37823665, year = {2023}, author = {Liu, B and Gao, J and Liu, XF and Rao, G and Luo, J and Han, P and Hu, W and Zhang, Z and Zhao, Q and Han, L and Jiang, Z and Zhou, M}, title = {Direct prediction of carbapenem resistance in Pseudomonas aeruginosa by whole genome sequencing and metagenomic sequencing.}, journal = {Journal of clinical microbiology}, volume = {61}, number = {11}, pages = {e0061723}, pmid = {37823665}, issn = {1098-660X}, support = {2017YFC1309700, 2017YFC1309701//MOST | National Key Research and Development Program of China (NKPs)/ ; shslczdzk02202//Shanghai Municipal Key Clinical Specialty/ ; 2017ZZ02014//Shanghai Top-Priority Clinical Key Disciplines Construction Project/ ; 20dz2261100//Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases/ ; 20dz2210500//Cultivation Projection of Shanghai Major Infectious Disease Research Base/ ; }, mesh = {Humans ; *Pseudomonas aeruginosa/genetics ; *Pseudomonas Infections/drug therapy ; Bacterial Proteins/genetics ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Meropenem ; Carbapenems/pharmacology/therapeutic use ; Whole Genome Sequencing ; beta-Lactamases/genetics ; Porins/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Carbapenem resistance is a major concern in the management of antibiotic-resistant Pseudomonas aeruginosa infections. The direct prediction of carbapenem-resistant phenotype from genotype in P. aeruginosa isolates and clinical samples would promote timely antibiotic therapy. The complex carbapenem resistance mechanism and the high prevalence of variant-driven carbapenem resistance in P. aeruginosa make it challenging to predict the carbapenem-resistant phenotype through the genotype. In this study, using whole genome sequencing (WGS) data of 1,622 P. aeruginosa isolates followed by machine learning, we screened 16 and 31 key gene features associated with imipenem (IPM) and meropenem (MEM) resistance in P. aeruginosa, including oprD(HIGH), and constructed the resistance prediction models. The areas under the curves of the IPM and MEM resistance prediction models were 0.906 and 0.925, respectively. For the direct prediction of carbapenem resistance in P. aeruginosa from clinical samples by the key gene features selected and prediction models constructed, 72 P. aeruginosa-positive sputum samples were collected and sequenced by metagenomic sequencing (MGS) based on next-generation sequencing (NGS) or Oxford Nanopore Technology (ONT). The prediction applicability of MGS based on NGS outperformed that of MGS based on ONT. In 72 P. aeruginosa-positive sputum samples, 65.0% (26/40) of IPM-insensitive and 63.2% (24/38) of MEM-insensitive P. aeruginosa were directly predicted by NGS-based MGS with positive predictive values of 0.897 and 0.889, respectively. By the direct detection of the key gene features associated with carbapenem resistance of P. aeruginosa, the carbapenem resistance of P. aeruginosa could be directly predicted from cultured isolates by WGS or from clinical samples by NGS-based MGS, which could assist the timely treatment and surveillance of carbapenem-resistant P. aeruginosa.}, } @article {pmid37823484, year = {2023}, author = {Straub, TJ and Lombardo, MJ and Bryant, JA and Diao, L and Lodise, T and Freedberg, DE and Wortman, J and Litcofsky, KD and Hasson, BR and McGovern, BH and Ford, CB and Henn, MR}, title = {Impact of a purified microbiome therapeutic on abundance of antimicrobial resistance genes in patients with recurrent Clostridioides difficile infection.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciad636}, pmid = {37823484}, issn = {1537-6591}, abstract = {BACKGROUND: The gastrointestinal microbiota is an important line of defense against colonization with antimicrobial resistant (AR) bacteria. In this post hoc analysis of the Phase 3 ECOSPOR III trial, we assessed impact of a microbiota-based oral therapeutic (fecal microbiota spores, live [VOWSTTM Oral Spores; VOS, formerly SER-109]) compared with placebo, on AR gene (ARG) abundance in patients with recurrent Clostridioides difficile infection (rCDI).

METHODS: Adults with rCDI were randomized to receive VOS or placebo orally for 3 days following standard-of-care antibiotics. ARG and taxonomic profiles were generated using whole metagenomic sequencing of stool at baseline and Weeks 1, 2, 8, and 24 post-treatment.

RESULTS: Baseline (n=151) and serial post-treatment stool samples collected through 24 weeks (total n=472) from 182 patients (59.9% female; mean age 65.5 years) in ECOSPOR III as well as 68 stool samples obtained at a single timepoint from a healthy cohort were analyzed. Baseline ARG abundance was similar between arms and significantly elevated vs. the healthy cohort. By Week 1, there was a greater decline in ARG abundance in VOS vs. placebo (p=0.003) in association with marked decline of Proteobacteria and repletion of spore-forming Firmicutes, as compared with baseline. We observed abundance of Proteobacteria and non-spore forming Firmicutes were associated with ARG abundance, while spore-forming Firmicutes abundance was negatively associated.

CONCLUSIONS: This proof-of-concept analysis suggests that microbiome remodeling with Firmicutes spores may be a potential novel approach to reduce ARG colonization in the gastrointestinal tract.}, } @article {pmid37823388, year = {2023}, author = {Motahar, SFS and Tiyoula, FN and Motamedi, E and Zeinalabedini, M and Kavousi, K and Ariaeenejad, S}, title = {Computational Insights into the Selecting Mechanism of α-Amylase Immobilized on Cellulose Nanocrystals: Unveiling the Potential of α-Amylases Immobilized for Efficient Poultry Feed Hydrolysis.}, journal = {Bioconjugate chemistry}, volume = {34}, number = {11}, pages = {2034-2048}, doi = {10.1021/acs.bioconjchem.3c00304}, pmid = {37823388}, issn = {1520-4812}, mesh = {Animals ; *alpha-Amylases/chemistry/metabolism ; Hydrolysis ; Cellulose/chemistry ; Molecular Docking Simulation ; Poultry/metabolism ; Sodium Chloride ; *Nanoparticles ; }, abstract = {The selection of an appropriate amylase for hydrolysis poultry feed is crucial for achieving improved digestibility and high-quality feed. Cellulose nanocrystals (CNCs), which are known for their high surface area, provide an excellent platform for enzyme immobilization. Immobilization greatly enhances the operational stability of α-amylases and the efficiency of starch bioconversion in poultry feeds. In this study, we immobilized two metagenome-derived α-amylases, PersiAmy2 and PersiAmy3, on CNCs and employed computational methods to characterize and compare the degradation efficiencies of these enzymes for poultry feed hydrolysis. Experimental in vitro bioconversion assessments were performed to validate the computational outcomes. Molecular docking studies revealed the superior hydrolysis performance of PersiAmy3, which displayed stronger electrostatic interactions with CNCs. Experimental characterization demonstrated the improved performance of both α-amylases after immobilization at high temperatures (80 °C). A similar trend was observed under alkaline conditions, with α-amylase activity reaching 88% within a pH range of 8.0 to 9.0. Both immobilized α-amylases exhibited halotolerance at NaCl concentrations up to 3 M and retained over 50% of their initial activity after 13 use cycles. Notably, PersiAmy3 displayed more remarkable improvements than PersiAmy2 following immobilization, including a significant increase in activity from 65 to 80.73% at 80 °C, an increase in activity to 156.48% at a high salinity of 3 M NaCl, and a longer half-life, indicating greater thermal stability within the range of 60 to 80 °C. These findings were substantiated by the in vitro hydrolysis of poultry feed, where PersiAmy3 generated 53.53 g/L reducing sugars. This comprehensive comparison underscores the utility of computational methods as a faster and more efficient approach for selecting optimal enzymes for poultry feed hydrolysis, thereby providing valuable insights into enhancing feed digestibility and quality.}, } @article {pmid37823365, year = {2023}, author = {Li, J and Zhang, D and Luo, C and Li, B and Zhang, G}, title = {In Situ Discrimination and Cultivation of Active Degraders in Soils by Genome-Directed Cultivation Assisted by SIP-Raman-Activated Cell Sorting.}, journal = {Environmental science & technology}, volume = {57}, number = {44}, pages = {17087-17098}, doi = {10.1021/acs.est.3c04247}, pmid = {37823365}, issn = {1520-5851}, mesh = {*Soil ; Isotopes/chemistry ; Toluene/metabolism ; DNA ; *Petroleum ; Biodegradation, Environmental ; Soil Microbiology ; }, abstract = {The identification and in situ cultivation of functional yet uncultivable microorganisms are important to confirm inferences regarding their ecological functions. Here, we developed a new method that couples Raman-activated cell sorting (RACS), stable-isotope probing (SIP), and genome-directed cultivation (GDC)─namely, RACS-SIP-GDC─to identify, sort, and cultivate the active toluene degraders from a complex microbial community in petroleum-contaminated soil. Using SIP, we successfully identified the active toluene degrader Pigmentiphaga, the single cells of which were subsequently sorted and isolated by RACS. We further successfully assembled the genome of Pigmentiphaga based on the metagenomic sequencing of [13]C-DNA and genomic sequencing of sorted cells, which was confirmed by gyrB gene comparison and average nucleotide identity determination. Additionally, the genotypes and phenotypes of this degrader were directly linked at the single-cell level, and its complete toluene metabolic pathways in petroleum-contaminated soil were reconstructed. Based on its unique metabolic properties uncovered by genome sequencing, we modified the traditional cultivation medium with antibiotics, amino acids, carbon sources, and growth factors (e.g., vitamins and metals), achieving the successful cultivation of RACS-sorted active degrader Pigmentiphaga sp. Our results implied that RACS-SIP-GDC is a state-of-the-art approach for the precise identification, targeted isolation, and cultivation of functional microbes from complex communities in natural habitats. RACS-SIP-GDC can be used to explore specific and targeted organic-pollution-degrading microorganisms at the single-cell level and provide new insights into their biodegradation mechanisms.}, } @article {pmid37822937, year = {2023}, author = {Xiang, ZB and Leng, EL and Cao, WF and Liu, SM and Zhou, YL and Luo, CQ and Hu, F and Wen, A}, title = {A systematic review and meta-analysis of the diagnostic accuracy of metagenomic next-generation sequencing for diagnosing tuberculous meningitis.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1223675}, pmid = {37822937}, issn = {1664-3224}, mesh = {Humans ; *Tuberculosis, Meningeal/diagnosis ; Sensitivity and Specificity ; ROC Curve ; High-Throughput Nucleotide Sequencing ; Databases, Factual ; }, abstract = {OBJECTIVE: The utility of metagenomic next-generation sequencing (mNGS) in the diagnosis of tuberculous meningitis (TBM) remains uncertain. We performed a meta-analysis to comprehensively evaluate its diagnostic accuracy for the early diagnosis of TBM.

METHODS: English (PubMed, Medline, Web of Science, Cochrane Library, and Embase) and Chinese (CNKI, Wanfang, and CBM) databases were searched for relevant studies assessing the diagnostic accuracy of mNGS for TBM. Review Manager was used to evaluate the quality of the included studies, and Stata was used to perform the statistical analysis.

RESULTS: Of 495 relevant articles retrieved, eight studies involving 693 participants (348 with and 345 without TBM) met the inclusion criteria and were included in the meta-analysis. The pooled sensitivity, specificity, positive likelihood ratio, negative likelihood ratio, diagnostic odds ratio, and area under the summary receiver-operating characteristic curve of mNGS for diagnosing TBM were 62% (95% confidence interval [CI]: 0.46-0.76), 99% (95% CI: 0.94-1.00), 139.08 (95% CI: 8.54-2266), 0.38 (95% CI: 0.25-0.58), 364.89 (95% CI: 18.39-7239), and 0.97 (95% CI: 0.95-0.98), respectively.

CONCLUSIONS: mNGS showed good specificity but moderate sensitivity; therefore, a more sensitive test should be developed to assist in the diagnosis of TBM.}, } @article {pmid37822757, year = {2023}, author = {Yousefi-Behzadi, M and Mehrabi, A and Ahmadinezhad, M and Rohani, M and Naddaf, SR and Bagheri, A and Shams-Ghahfarokhi, M and Maghsoudlou, E and Mojahed, N and Mounesan, L and Tahmasebi, Z and Sohrabi, A and Salehi-Vaziri, M and Salehi, Z and Razzaghi-Abyaneh, M}, title = {Metagenomics Characterization of Ixodes ricinus Intestinal Microbiota as Major Vector of Tick-Borne Diseases in Domestic Animals.}, journal = {Journal of arthropod-borne diseases}, volume = {17}, number = {2}, pages = {152-164}, pmid = {37822757}, issn = {2322-1984}, abstract = {BACKGROUND: Understanding the microbiota of disease vectors can help for developing new strategies to prevent the transmission of vector pathogens. Ixodes ricinus is one of the most notorious tick vectors with increasing importance in Iran and other parts of the world while there is limited data on its microbiota. This study aimed to use metagenomics for identifying the I. ricinus tick's microbiota of Iran.

METHODS: A total of 39 adult ticks were collected from Mazandaran (21 females), Gilan (17 females), and Golestan (1 male). Five tick pools prepared from 39 adults of I. ricinus were subjected to metagenomics analysis. The data were analyzed by targeting the V6 region of the 16S rRNA gene by Illumina 4000 Hiseq sequencing.

RESULTS: Among hundreds of intestinal microbiota identified by metagenomics, various pathogenic microorganisms distributed in 30 genera and species including those responsible for tick-borne diseases resided in the genera Coxiella, Rickettsia, and Burkholderia were found.

CONCLUSION: Our results indicated that metagenomics identifies bacteria genera and species which cannot be easily recognized by routine methods. The presence of such pathogenic bacteria indicates the importance of possible zoonotic diseases in this region which could affect public health. These results further substantiate the importance of advanced metagenomics analyses to identify neglected tick-borne pathogens which enable researchers to provide efficient mapping roads for the management of emerging and re-emerging infectious diseases.}, } @article {pmid37822749, year = {2023}, author = {Wang, T and Liu, J and Luo, Y and Yu, B and Kong, X and Zheng, P and Huang, Z and Mao, X and Yu, J and Luo, J and Yan, H and He, J}, title = {Combined effects of host genetics and diet on porcine intestinal fungi and their pathogenic genes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1192288}, pmid = {37822749}, issn = {1664-302X}, abstract = {As research on gut microbes progresses, it becomes increasingly clear that a small family of microbiota--fungi, plays a crucial role in animal health. However, little is known about the fungal composition in the pig intestine, especially after a dietary fiber diet and hybrid genetics, and the changes in host pathogenicity-associated genes they carry. The purpose of this study is to investigate the effects of diet and genetics on the diversity and structure of porcine intestinal fungi and to describe, for the first time, the host pathogenicity-related genes carried by porcine intestinal fungi. Samples of colonic contents were collected for metagenomic analysis using a 3 × 2 parsing design, where three pig breeds (Taoyuan, Duroc, and crossbred Xiangcun) were fed high or low fiber diets (n = 10). In all samples, we identified a total of 281 identifiable fungal genera, with Ascomycota and Microsporidia being the most abundant fungi. Compared to Duroc pigs, Taoyuan and Xiangcun pigs had higher fungal richness. Interestingly, the fiber diet significantly reduced the abundance of the pathogenic fungus Mucor and significantly increased the abundance of the fiber digestion-associated fungus Neocallimastix. Pathogenic fungi exert their pathogenicity through the genes they carry that are associated with host pathogenicity. Therefore, we obtained 839 pathogenicity genes carried by the spectrum of fungi in the pig intestine by comparing the PHI-base database. Our results showed that fungi in the colon of Taoyuan pigs carried the highest abundance of different classes of host pathogenicity-related genes, and the lowest in Duroc pigs. Specifically, Taoyuan pigs carried high abundance of animal pathogenicity-related genes (CaTUP1, CPAR2_106400, CaCDC35, Tfp1, CaMNT2), and CaTUP1 was the key gene for Candida pathogenicity. The intestinal fungal composition of crossbred Xiangcun pigs and the abundance of host pathogenicity-associated genes they carried exhibited a mixture of characteristics of Taoyuan and Duroc pigs. In conclusion, our results provide the first comprehensive report on the effects of dietary fiber and genetics on the composition of intestinal fungi and the host-associated pathogenicity genes they carry in pigs. These findings provide a reference for subsequent pig breeding and development of anti-pathogenic fungal drugs.}, } @article {pmid37822741, year = {2023}, author = {Džunková, M and Moraru, C and Anantharaman, K}, title = {Editorial: Advances in viromics: new tools, challenges, and data towards characterizing human and environmental viromes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1290062}, pmid = {37822741}, issn = {1664-302X}, } @article {pmid37822701, year = {2023}, author = {Wang, C and Yang, Y and Cai, Q and Gao, Y and Cai, H and Wu, J and Zheng, W and Long, J and Shu, XO}, title = {Oral microbiome and ischemic stroke risk among elderly Chinese women.}, journal = {Journal of oral microbiology}, volume = {15}, number = {1}, pages = {2266655}, pmid = {37822701}, issn = {2000-2297}, abstract = {BACKGROUND: Stroke, a leading cause of disability worldwide, has been associated with periodontitis. However, whether stroke risk is related to oral microbiota remains unknown. This study aims to evaluate the associations between the oral microbiome and ischemic stroke risk.

METHODS: In a case-control study of 134 case-control pairs nested within a prospective cohort study, we examined pre-diagnostic oral microbiome in association with stroke risk via shotgun metagenomic sequencing. The microbial sub-community and functional profiling were performed using Latent Dirichlet Allocation and HUMAnN2. Associations of microbial diversity, sub-community structure, and individual microbial features with ischemic stroke risk were evaluated via conditional logistic regression.

RESULTS: Alpha and beta diversities differ significantly between cases and controls. One genus- and two species-level sub-communities were significantly associated with decreased ischemic stroke risk, with odds ratios (95% confidence intervals) of 0.52 (0.31-0.90), 0.51 (0.31-0.84), and 0.60 (0.36-0.99), respectively. These associations were potentially driven by the representative taxa in these sub-communities, i.e., genus Corynebacterium and Lautropia, and species Lautropia mirabilis and Neisseria elongate (p < 0.05). Additionally, 55 taxa, 1,237 gene families, and 90 metabolic pathways were associated with ischemic stroke risk at p < 0.05.

CONCLUSION: Our study highlights the role of oral microbiota in the etiology of ischemic stroke and calls for further research.}, } @article {pmid37822360, year = {2023}, author = {Xu, Y and Jiang, Y and Wang, Y and Meng, F and Qin, W and Lin, Y}, title = {Metagenomic next-generation sequencing of bronchoalveolar lavage fluid assists in the diagnosis of pathogens associated with lower respiratory tract infections in children.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1220943}, pmid = {37822360}, issn = {2235-2988}, mesh = {Humans ; Child ; Bronchoalveolar Lavage Fluid ; *Respiratory Tract Infections/diagnosis ; High-Throughput Nucleotide Sequencing ; Streptococcus pneumoniae ; *Bacteriophages ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {Worldwide, lower respiratory tract infections (LRTI) are an important cause of hospitalization in children. Due to the relative limitations of traditional pathogen detection methods, new detection methods are needed. The purpose of this study was to evaluate the value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) samples for diagnosing children with LRTI based on the interpretation of sequencing results. A total of 211 children with LRTI admitted to the First Affiliated Hospital of Guangzhou Medical University from May 2019 to December 2020 were enrolled. The diagnostic performance of mNGS versus traditional methods for detecting pathogens was compared. The positive rate for the BALF mNGS analysis reached 95.48% (95% confidence interval [CI] 92.39% to 98.57%), which was superior to the culture method (44.07%, 95% CI 36.68% to 51.45%). For the detection of specific pathogens, mNGS showed similar diagnostic performance to PCR and antigen detection, except for Streptococcus pneumoniae, for which mNGS performed better than antigen detection. S. pneumoniae, cytomegalovirus and Candida albicans were the most common bacterial, viral and fungal pathogens. Common infections in children with LRTI were bacterial, viral and mixed bacterial-viral infections. Immunocompromised children with LRTI were highly susceptible to mixed and fungal infections. The initial diagnosis was modified based on mNGS in 29.6% (37/125) of patients. Receiver operating characteristic (ROC) curve analysis was performed to predict the relationship between inflammation indicators and the type of pathogen infection. BALF mNGS improves the sensitivity of pathogen detection and provides guidance in clinical practice for diagnosing LRTI in children.}, } @article {pmid37821827, year = {2023}, author = {Zhu, X and Zhao, L and Huang, L and Yang, W and Wang, L and Yu, R}, title = {cgMSI: pathogen detection within species from nanopore metagenomic sequencing data.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {387}, pmid = {37821827}, issn = {1471-2105}, mesh = {Metagenome ; *Nanopore Sequencing ; *Nanopores ; Alleles ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {BACKGROUND: Metagenomic sequencing is an unbiased approach that can potentially detect all the known and unidentified strains in pathogen detection. Recently, nanopore sequencing has been emerging as a highly potential tool for rapid pathogen detection due to its fast turnaround time. However, identifying pathogen within species is nontrivial for nanopore sequencing data due to the high sequencing error rate.

RESULTS: We developed the core gene alleles metagenome strain identification (cgMSI) tool, which uses a two-stage maximum a posteriori probability estimation method to detect pathogens at strain level from nanopore metagenomic sequencing data at low computational cost. The cgMSI tool can accurately identify strains and estimate relative abundance at 1× coverage.

CONCLUSIONS: We developed cgMSI for nanopore metagenomic pathogen detection within species. cgMSI is available at https://github.com/ZHU-XU-xmu/cgMSI .}, } @article {pmid37821698, year = {2023}, author = {Pavlopoulos, GA and Baltoumas, FA and Liu, S and Selvitopi, O and Camargo, AP and Nayfach, S and Azad, A and Roux, S and Call, L and Ivanova, NN and Chen, IM and Paez-Espino, D and Karatzas, E and , and Iliopoulos, I and Konstantinidis, K and Tiedje, JM and Pett-Ridge, J and Baker, D and Visel, A and Ouzounis, CA and Ovchinnikov, S and Buluç, A and Kyrpides, NC}, title = {Unraveling the functional dark matter through global metagenomics.}, journal = {Nature}, volume = {622}, number = {7983}, pages = {594-602}, pmid = {37821698}, issn = {1476-4687}, support = {DP5 OD026389/OD/NIH HHS/United States ; P20 GM103475/GM/NIGMS NIH HHS/United States ; }, mesh = {Cluster Analysis ; *Metagenome/genetics ; *Metagenomics/methods ; *Proteins/chemistry/classification/genetics ; Databases, Protein ; Protein Conformation ; *Microbiology ; }, abstract = {Metagenomes encode an enormous diversity of proteins, reflecting a multiplicity of functions and activities[1,2]. Exploration of this vast sequence space has been limited to a comparative analysis against reference microbial genomes and protein families derived from those genomes. Here, to examine the scale of yet untapped functional diversity beyond what is currently possible through the lens of reference genomes, we develop a computational approach to generate reference-free protein families from the sequence space in metagenomes. We analyse 26,931 metagenomes and identify 1.17 billion protein sequences longer than 35 amino acids with no similarity to any sequences from 102,491 reference genomes or the Pfam database[3]. Using massively parallel graph-based clustering, we group these proteins into 106,198 novel sequence clusters with more than 100 members, doubling the number of protein families obtained from the reference genomes clustered using the same approach. We annotate these families on the basis of their taxonomic, habitat, geographical and gene neighbourhood distributions and, where sufficient sequence diversity is available, predict protein three-dimensional models, revealing novel structures. Overall, our results uncover an enormously diverse functional space, highlighting the importance of further exploring the microbial functional dark matter.}, } @article {pmid37821414, year = {2023}, author = {Panyako, PM and Ommeh, SC and Kuria, SN and Lichoti, JK and Musina, J and Nair, V and Nene, V and Oyola, SO and Munir, M}, title = {Metagenomic characterization reveals virus coinfections associated with Newcastle disease virus among poultry in Kenya.}, journal = {Journal of basic microbiology}, volume = {63}, number = {12}, pages = {1383-1396}, doi = {10.1002/jobm.202300390}, pmid = {37821414}, issn = {1521-4028}, support = {NRF/Newton Utafiti Fund/1/04//Biotechnology and Biological Sciences Research Council (BBSRC) and the National Commission of Science, Technology and Innovation (NACOSTI)'s National Research Fund/ ; }, mesh = {Animals ; Newcastle disease virus/genetics ; *Newcastle Disease/diagnosis/epidemiology/prevention & control ; Poultry ; Chickens ; *Coinfection/epidemiology/veterinary ; Kenya/epidemiology ; Cross-Sectional Studies ; *Poultry Diseases/epidemiology/prevention & control ; }, abstract = {Newcastle disease (ND) is an endemic viral disease affecting poultry and causing massive economic losses. This cross-sectional purposive study detected coinfections that are associated with the Newcastle disease virus among poultry from selected regions in Kenya. Cloacal (n = 599) and oral-pharyngeal (n = 435) swab samples were collected and pooled into 17 and 15 samples, respectively. A total of 17,034,948 and 7,751,974 paired-end reads with an average of 200 nucleotides were generated from the cloacal and oral-pharyngeal swab samples, respectively. Analysis of the de novo assembled contigs identified 177 and 18 cloacal and oral-pharyngeal contigs, respectively with hits to viral sequences, as determined by BLASTx and BLASTn analyses. Several known and unknown representatives of Coronaviridae, Picobirnaviridae, Reoviridae, Retroviridae, and unclassified Deltavirus were identified in the cloacal swab samples. However, no Newcastle disease virus (family Paramyxoviridae) was detected in the cloacal swabs, although they were detected in the oropharyngeal swabs of chickens sampled in Nairobi, Busia, and Trans Nzoia. Additionally, sequences representative of Paramyxoviridae, Coronaviridae, and Retroviridae were identified in the oral-pharyngeal swab samples. Infectious bronchitis virus and rotavirus were chickens' most prevalent coinfections associated with the Newcastle disease virus. The detection of these coinfections suggests that these viruses are significant threats to the control of Newcastle disease as the Newcastle disease virus vaccines are known to fail because of these coinfections. Therefore, this study provides important information that will help improve disease diagnosis and vaccine development for coinfections associated with the Newcastle disease virus.}, } @article {pmid37820967, year = {2023}, author = {Zhang, G and An, Y and Zabed, HM and Yun, J and Parvez, A and Zhao, M and Zhang, C and Ravikumar, Y and Li, J and Qi, X}, title = {Rewiring Bacillus subtilis and bioprocess optimization for oxidoreductive reaction-mediated biosynthesis of D-tagatose.}, journal = {Bioresource technology}, volume = {389}, number = {}, pages = {129843}, doi = {10.1016/j.biortech.2023.129843}, pmid = {37820967}, issn = {1873-2976}, mesh = {*Bacillus subtilis/genetics/metabolism ; *Hexoses ; Galactose/metabolism ; Oxidation-Reduction ; }, abstract = {D-tagatose holds significant importance as a functional monosaccharide with diverse applications in food, medicine, and other fields. This study aimed to explore the oxidoreductive pathway for D-tagatose production, surpassing the contemporary isomerization-mediated biosynthesis approach in order to enhance the thermodynamic equilibrium of the reactions. Initially, a novel galactitol dehydrogenase was discovered through biochemical and bioinformatics analyses. By co-expressing the galactitol dehydrogenase and xylose reductase, the oxidoreductive pathway for D-tagatose synthesis was successfully established in Bacillus subtilis. Subsequently, pathway fine-tuning was achieved via promoter regulation and dehydrogenase-mediated cofactor regeneration, resulting in 6.75-fold higher D-tagatose compared to that produced by the strain containing the unmodified promoter. Finally, optimization of fermentation conditions and medium composition produced 39.57 g/L D-tagatose in a fed-batch experiment, with a productivity of 0.33 g/L/h and a yield of 0.55 mol/mol D-galactose. These findings highlight the potential of the constructed redox pathway as an effective approach for D-tagatose production.}, } @article {pmid37820966, year = {2023}, author = {Ma, Z and Lin, L and Xi, J and Gong, X and Wang, J and Peng, P and An, Y and Hu, W and Cao, J and Wu, Z and Zhou, Z}, title = {Nitrogen removal from dewatering liquid of landfill sludge by partial nitrification and denitrification.}, journal = {Bioresource technology}, volume = {390}, number = {}, pages = {129856}, doi = {10.1016/j.biortech.2023.129856}, pmid = {37820966}, issn = {1873-2976}, mesh = {*Nitrification ; Sewage ; Denitrification ; Ammonia ; Nitrites ; Nitrogen ; Bioreactors/microbiology ; Oxygen ; Waste Disposal Facilities ; *Betaproteobacteria ; Oxidation-Reduction ; }, abstract = {Two pilot-scale two-stage anoxic/oxic membrane bioreactors were operated at different dissolved oxygen (DO) levels to evaluate nitrogen removal performances for treating landfill sludge dewatering liquid. Under either high (5.0-6.0 mg/L) or conventional DO (2.0-3.0 mg/L) conditions, partial nitrification (PN)-denitrification was both achieved, and high-concentration free ammonia (FA) ensured stable PN. The high DO system exhibited higher nitrite accumulation (98.5 %) and nitrogen removal (98.0 %), and its nitrogen removal was mainly ascribed to PN-denitrification (53.8 %). Kinetic inhibition tests and microbial sequencing results demonstrated that high DO condition improved the abundance and ability of ammonia-oxidizing bacteria (AOB) rather than nitrite-oxidizing bacteria under the FA inhibition. Pseudomonas, Thauera, and Soehngenia were characteristic genus in the high DO system, and Nitrosomonas was only AOB. Metagenomic analysis confirmed the important role of PN on nitrogen removal in high DO system. This provides valuable references for the efficient and economic treatment of ammonia-rich wastewater.}, } @article {pmid37819893, year = {2023}, author = {Reynoso-García, J and Santiago-Rodriguez, TM and Narganes-Storde, Y and Cano, RJ and Toranzos, GA}, title = {Edible flora in pre-Columbian Caribbean coprolites: Expected and unexpected data.}, journal = {PloS one}, volume = {18}, number = {10}, pages = {e0292077}, pmid = {37819893}, issn = {1932-6203}, support = {R25 GM061151/GM/NIGMS NIH HHS/United States ; P20 GM103475/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *DNA, Ancient ; Puerto Rico ; *Diet ; Ethnicity ; Fungi ; }, abstract = {Coprolites, or mummified feces, are valuable sources of information on ancient cultures as they contain ancient DNA (aDNA). In this study, we analyzed ancient plant DNA isolated from coprolites belonging to two pre-Columbian cultures (Huecoid and Saladoid) from Vieques, Puerto Rico, using shotgun metagenomic sequencing to reconstruct diet and lifestyles. We also analyzed DNA sequences of putative phytopathogenic fungi, likely ingested during food consumption, to further support dietary habits. Our findings show that pre-Columbian Caribbean cultures had a diverse diet consisting of maize (Zea mays), sweet potato (Ipomoea batatas), chili peppers (Capsicum annuum), peanuts (Arachis spp.), papaya (Carica papaya), tomato (Solanum lycopersicum) and, very surprisingly cotton (Gossypium barbadense) and tobacco (Nicotiana sylvestris). Modelling of putative phytopathogenic fungi and plant interactions confirmed the potential consumption of these plants as well as edible fungi, particularly Ustilago spp., which suggest the consumption of maize and huitlacoche. These findings suggest that a variety of dietary, medicinal, and hallucinogenic plants likely played an important role in ancient human subsistence and societal customs. We compared our results with coprolites found in Mexico and the United States, as well as present-day faeces from Mexico, Peru, and the United States. The results suggest that the diet of pre-Columbian cultures resembled that of present-day hunter-gatherers, while agriculturalists exhibited a transitional state in dietary lifestyles between the pre-Columbian cultures and larger scale farmers and United States individuals. Our study highlights differences in dietary patterns related to human lifestyles and provides insight into the flora present in the pre-Columbian Caribbean area. Importantly, data from ancient fecal specimens demonstrate the importance of ancient DNA studies to better understand pre-Columbian populations.}, } @article {pmid37819800, year = {2023}, author = {Li, H and Bhattarai, B and Barber, M and Goel, R}, title = {Stringent Response of Cyanobacteria and Other Bacterioplankton during Different Stages of a Harmful Cyanobacterial Bloom.}, journal = {Environmental science & technology}, volume = {57}, number = {42}, pages = {16016-16032}, doi = {10.1021/acs.est.3c03114}, pmid = {37819800}, issn = {1520-5851}, mesh = {Guanosine Pentaphosphate ; Nitrates ; *Cyanobacteria/genetics ; *Microcystis ; Lakes ; Aquatic Organisms ; }, abstract = {We conducted a field study to investigate the role of stringent response in cyanobacteria and coexisting bacterioplankton during nutrient-deprived periods at various stages of bloom in a freshwater lake (Utah Lake) for the first time. Using metagenomics and metatranscriptomics analyses, we examined the cyanobacterial ecology and expression of important functional genes related to stringent response, N and P metabolism, and regulation. Our findings mark a significant advancement in understanding the mechanisms by which toxic cyanobacteria survive and proliferate during nitrogen (N) and phosphorus (P) limitations. We successfully identified and analyzed the metagenome-assembled genomes (MAGs) of the dominant bloom-forming cyanobacteria, namely, Dolichospermum circinale, Aphanizomenon flos-aquae UKL13-PB, Planktothrix agardhii, and Microcystis aeruginosa. By mapping RNA-seq data to the coding sequences of the MAGs, we observed that these four prevalent cyanobacteria species activated multiple functions to adapt to the depletion of inorganic nutrients. During and after the blooms, the four dominant cyanobacteria species expressed high levels of transcripts related to toxin production, such as microcystins (mcy), anatoxins (ana), and cylindrospermopsins (cyr). Additionally, genes associated with polyphosphate (poly-P) storage and the stringent response alarmone (p)ppGpp synthesis/hydrolysis, including ppk, relA, and spoT, were highly activated in both cyanobacteria and bacterioplankton. Under N deficiency, the main N pathways shifted from denitrification and dissimilatory nitrate reduction in bacterioplankton toward N2-fixing and assimilatory nitrate reduction in certain cyanobacteria with a corresponding shift in the community composition. P deprivation triggered a stringent response mediated by spoT-dependent (p)ppGpp accumulation and activation of the Pho regulon in both cyanobacteria and bacterioplankton, facilitating inorganic and organic P uptake. The dominant cyanobacterial MAGs exhibited the presence of multiple alkaline phosphatase (APase) transcripts (e.g., phoA in Dolichospermum, phoX in Planktothrix, and Microcystis), suggesting their ability to synthesize and release APase enzymes to convert ambient organic P into bioavailable forms. Conversely, transcripts associated with bacterioplankton-dominated pathways like denitrification were low and did not align with the occurrence of intense cyanoHABs. The strong correlations observed among N, P, stringent response metabolisms and the succession of blooms caused by dominant cyanobacterial species provide evidence that the stringent response, induced by nutrient limitation, may activate unique N and P functions in toxin-producing cyanobacteria, thereby sustaining cyanoHABs.}, } @article {pmid37819146, year = {2023}, author = {Park, YR and Lee, HL and Hyun, JY and Choi, J and Moon, JH and Kim, BY and Yang, S-J and Lee, JH and Kim, BK and Park, T-S and Suk, KT and Lee, DY}, title = {Systemic multiomics evaluation of the therapeutic effect of Bacteroides species on liver cirrhosis in male mice.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0534922}, doi = {10.1128/spectrum.05349-22}, pmid = {37819146}, issn = {2165-0497}, support = {NRF-2021M3A9I4021433, NRF-2020R1A6A1A03043026//Basic Science Research Program through the National Research Foundation of Korea funded by the Ministry of Education, Science and Technology/ ; //Hallym University Research Fund/ ; Project No. PJ015865012021//Cooperative Research Program for Agriculture Science and Technology Development (Rural Development Administration, Republic of Korea)/ ; 20163MFDS120//Ministry of Food and Drug Safety (MFDS)/ ; }, mesh = {Male ; Humans ; Animals ; Mice ; *Multiomics ; Liver Cirrhosis/therapy ; Liver/metabolism ; *Liver Diseases ; Bacteroides/genetics ; }, abstract = {The human gut microbiome mediates bidirectional interaction within the gut-liver axis, while liver diseases, including liver cirrhosis, are very closely related to the state of the gut environment. Thus, improving the health of the gut-liver axis by targeting the intestinal microbiota is a potential therapeutic approach in hepatic diseases. This study examines changes in metabolomics and microbiome composition by treating bacteria derived from the human gut in mice with liver cirrhosis. Interorgan-based multiomics profiling coupled with functional examination demonstrated that the treatment of Bacteroides dorei pertained to protective effects on liver cirrhosis by normalizing the functional, metabolic, and metagenomic environment through the gut-liver axis. The study provides the potential value of a multiomics-based and interorgan-targeted evaluation platform for the comprehensive examination and mechanistic understanding of a wide range of biologics, including gut microbes. Furthermore, the current finding also suggests in-depth future research focusing on the discovery and validation of next-generation probiotics and products (postbiotics).}, } @article {pmid37819096, year = {2023}, author = {Khot, V and Strous, M and Dong, X and Kiesser, AK}, title = {Viral diversity and dynamics and CRISPR-Cas-mediated immunity in a robust alkaliphilic cyanobacterial consortium.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0221723}, pmid = {37819096}, issn = {2165-0497}, support = {//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; //Canada First Research Excellence Fund (CFREF)/ ; //Alberta Innovates (AI)/ ; Alberta Graduate Excellence//Government of Alberta (Alberta Government)/ ; Faculty of Graduate Studies Doctoral Scholarship//University of Calgary (U of C)/ ; }, mesh = {CRISPR-Cas Systems ; *Cyanobacteria/genetics ; *Viruses ; }, abstract = {Biotechnology applications utilizing the function of microbial communities have become increasingly important solutions as we strive for sustainable applications. Although viral infections are known to have a significant impact on microbial turnover and nutrient cycling, viral dynamics have remained largely overlooked in these engineered communities. Predatory perturbations to the functional stability of these microbial biotechnology applications must be investigated in order to design more robust applications. In this study, we closely examine virus-microbe dynamics in a model microbial community used in a biotechnology application. Our findings suggest that viral dynamics change significantly with environmental conditions and that microbial immunity may play an important role in maintaining functional stability. We present this study as a comprehensive template for other researchers interested in exploring predatory dynamics in engineered microbial communities.}, } @article {pmid37818528, year = {2023}, author = {Rocha, LF and Kinsel, ME and Bond, JP and Fakhoury, AM}, title = {Chemical Profiles of Heterodera glycines Suppressive Soils in Double Cropping Soybean Production.}, journal = {Journal of nematology}, volume = {55}, number = {1}, pages = {20230030}, pmid = {37818528}, issn = {0022-300X}, abstract = {We previously reported soybean fields double-cropped with winter wheat having reduced soybean cyst nematode (SCN) (Heterodera glycines) counts compared to fallow. A follow-up metagenomics study identified several fungal and bacterial taxa enriched in wheat fields, and some were reported to parasitize SCN. Knowing that phytocompounds with potential nematicidal activity are released via wheat roots and stubble, we implemented a dichloromethane-based extraction method and a gas chromatography-mass spectrometry (GCMS) system to investigate soil chemical profiles of samples collected from these fields and review the potential nematicidal activity of compounds with higher concentration in double cropping fields. 51 compounds were detected during the GCMS analysis, eight with unknown identification. Several compounds, including multiple fatty acids, had larger relative peak areas when double-cropped, compared to fallow samples. This study, along with our previously published one, provided a better understanding of the mechanisms that govern the effect of wheat on SCN populations. Rather than driven by a single mechanism, the suppression of SCN in soybean fields double-cropped with winter wheat was potentially linked to enriched microbial communities, increased populations of beneficial organisms, and higher concentrations of chemicals with potential nematicidal activity. To our knowledge, this is the first study using GCMS to characterize soil chemical profiles in soybean fields double-cropped with winter wheat regarding the suppression of SCN populations.}, } @article {pmid37817022, year = {2023}, author = {Salazar-Ardiles, C and Asserella-Rebollo, L and Cornejo, C and Arias, D and Vasquez-Muñoz, M and Toledo, C and Andrade, DC}, title = {Molecular diagnostic approaches for SARS-CoV-2 detection and pathophysiological consequences.}, journal = {Molecular biology reports}, volume = {50}, number = {12}, pages = {10367-10382}, pmid = {37817022}, issn = {1573-4978}, support = {11220870//Agencia Nacional de Investigación y Desarrollo/ ; 11220962//Agencia Nacional de Investigación y Desarrollo/ ; ACT210083//Agencia Nacional de Investigación y Desarrollo/ ; 2203//MEL/ ; }, mesh = {Humans ; SARS-CoV-2/genetics ; *COVID-19/diagnosis ; Pathology, Molecular ; *Pneumonia, Viral/diagnosis ; RNA, Viral/genetics ; Sensitivity and Specificity ; COVID-19 Testing ; }, abstract = {SARS-CoV-2, a novel coronavirus within the Coronaviridae family, is the causative agent behind the respiratory ailment referred to as COVID-19. Operating on a global scale, COVID-19 has led to a substantial number of fatalities, exerting profound effects on both public health and the global economy. The most frequently reported symptoms encompass fever, cough, muscle or body aches, loss of taste or smell, headaches, and fatigue. Furthermore, a subset of individuals may manifest more severe symptoms, including those consistent with viral pneumonitis, which can be so profound as to result in fatalities. Consequently, this situation has spurred the rapid advancement of disease diagnostic technologies worldwide. Predominantly employed in diagnosing COVID-19, the real-time quantitative reverse transcription PCR has been the foremost diagnostic method, effectively detecting SARS-CoV-2 viral RNA. As the pandemic has evolved, antigen and serological tests have emerged as valuable diagnostic tools. Antigen tests pinpoint specific viral proteins of SARS-CoV-2, offering swift results, while serological tests identify the presence of antibodies in blood samples. Additionally, there have been notable strides in sample collection methods, notably with the introduction of saliva-based tests, presenting a non-invasive substitute to nasopharyngeal swabs. Given the ongoing mutations in SARS-CoV-2, there has been a continuous need for genomic surveillance, encompassing full genome sequencing and the identification of new variants through Illumina technology and, more recently, nanopore metagenomic sequencing (SMTN). Consequently, while diagnostic testing methods for COVID-19 have experienced remarkable progress, no test is flawless, and there exist limitations with each technique, including sensitivity, specificity, sample collection, and the minimum viral load necessary for accurate detection. These aspects are comprehensively addressed within this current review.}, } @article {pmid37816749, year = {2023}, author = {Dyksma, S and Pester, M}, title = {Oxygen respiration and polysaccharide degradation by a sulfate-reducing acidobacterium.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6337}, pmid = {37816749}, issn = {2041-1723}, mesh = {*Sulfates/metabolism ; *Oxygen/metabolism ; Anaerobiosis ; Acidobacteria/metabolism ; Respiration ; Polysaccharides ; Oxidation-Reduction ; }, abstract = {Sulfate-reducing microorganisms represent a globally important link between the sulfur and carbon cycles. Recent metagenomic surveys expanded the diversity of microorganisms putatively involved in sulfate reduction underscoring our incomplete understanding of this functional guild. Here, we use genome-centric metatranscriptomics to study the energy metabolism of Acidobacteriota that carry genes for dissimilation of sulfur compounds in a long-term continuous culture running under alternating anoxic and oxic conditions. Differential gene expression analysis reveals the unique metabolic flexibility of a pectin-degrading acidobacterium to switch from sulfate to oxygen reduction when shifting from anoxic to oxic conditions. The combination of facultative anaerobiosis and polysaccharide degradation expands the metabolic versatility among sulfate-reducing microorganisms. Our results highlight that sulfate reduction and aerobic respiration are not mutually exclusive in the same organism, sulfate reducers can mineralize organic polymers, and anaerobic mineralization of complex organic matter is not necessarily a multi-step process involving different microbial guilds but can be bypassed by a single microbial species.}, } @article {pmid37816747, year = {2023}, author = {Rahlff, J and Esser, SP and Plewka, J and Heinrichs, ME and Soares, A and Scarchilli, C and Grigioni, P and Wex, H and Giebel, HA and Probst, AJ}, title = {Marine viruses disperse bidirectionally along the natural water cycle.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6354}, pmid = {37816747}, issn = {2041-1723}, mesh = {*Ecosystem ; Water Cycle ; Seawater/analysis ; *Viruses/genetics ; Aerosols/analysis ; }, abstract = {Marine viruses in seawater have frequently been studied, yet their dispersal from neuston ecosystems at the air-sea interface towards the atmosphere remains a knowledge gap. Here, we show that 6.2% of the studied virus population were shared between air-sea interface ecosystems and rainwater. Virus enrichment in the 1-mm thin surface microlayer and sea foams happened selectively, and variant analysis proved virus transfer to aerosols collected at ~2 m height above sea level and rain. Viruses detected in rain and these aerosols showed a significantly higher percent G/C base content compared to marine viruses. CRISPR spacer matches of marine prokaryotes to foreign viruses from rainwater prove regular virus-host encounters at the air-sea interface. Our findings on aerosolization, adaptations, and dispersal support transmission of viruses along the natural water cycle.}, } @article {pmid37816408, year = {2024}, author = {Huang, W and Dong, X and Tu, C and Yang, H and Chang, Y and Yang, X and Chen, H and Che, F}, title = {Response mechanism of sediment endogenous phosphorus release to functional microorganisms and its cyanobacterial growth and disappearance effects.}, journal = {The Science of the total environment}, volume = {906}, number = {}, pages = {167676}, doi = {10.1016/j.scitotenv.2023.167676}, pmid = {37816408}, issn = {1879-1026}, mesh = {*Phosphorus/analysis ; *Cyanobacteria ; Lakes/chemistry ; Eutrophication ; Proteobacteria ; Geologic Sediments/chemistry ; China ; }, abstract = {Endogenous phosphorus (P) release from lake sediments is an important factor in the eutrophication of overlying waters, as P is the limiting nutrient salt affecting cyanobacterial growth. Microorganisms are also key to the evolution of cyanobacterial growth and disappearance, as they can influence the release of endogenous P. Meanwhile, endogenous phosphorus can also have an impact on microbial structure. However, there is a lack of studies on the response mechanisms between endogenous P release and microorganisms, as well as the exploration of endogenous P release on the whole cyanobacterial growth and disappearance evolution process. In this study, metagenome sequencing was used to characterize the microbial community structure at different times and to explain the P cycle from the perspective of functional genes. The results showed that the number of sediment microorganisms (genes) gradually increased with the P release capacity, and the outbreak with the strongest P release capacity possessed the most abundant microorganisms (genes). Proteobacteria with P solubilizing functions were consistently the most abundant phylum in all four periods and were positively correlated with P release potential assessment factors EPC0, EPC0F, and NAP. Functional genes affect the P cycle by acting primarily on inorganic P solubilization, organic P mineralization, and P transport. These P-functional genes are mainly found in Proteobacteria, Acidobacteria, Chloroflexi, and Actinobacteria microorganisms. In addition, the P form in the sediments was dominated by IP, with the highest concentration (704.86 mg/kg) occurring during the dormant period. Sediments from this period acted as a strong P "sink", creating a precondition for cyanobacterial recovery and outbreaks to provide a source of P. The results of this study can provide a theoretical basis for controlling endogenous P release at the microscopic level of cyanobacterial growth and disappearance.}, } @article {pmid37816267, year = {2023}, author = {Berglund, F and Rodríguez-Molina, D and Gradisteanu Pircalabioru, G and Blaak, H and Chifiriuc, MC and Czobor Barbu, I and Flach, CF and Gheorghe-Barbu, I and Măruțescu, L and Popa, M and de Roda Husman, AM and Wengenroth, L and Schmitt, H and Larsson, DGJ}, title = {The resistome and microbiome of wastewater treatment plant workers - The AWARE study.}, journal = {Environment international}, volume = {180}, number = {}, pages = {108242}, doi = {10.1016/j.envint.2023.108242}, pmid = {37816267}, issn = {1873-6750}, mesh = {Humans ; Female ; Wastewater ; Genes, Bacterial ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology/analysis ; *Microbiota/genetics ; *Water Purification ; *Disinfectants ; }, abstract = {Urban wastewater treatment plants harbor a large collection of antibiotic resistant enteric bacteria. It is therefore reasonable to hypothesize that workers at such plants would possess a more diverse set of resistant enteric bacteria, compared to the general population. To address this hypothesis, we have compared the fecal microbiome and resistome of 87 workers at wastewater treatment plants (WWTPs) from Romania and the Netherlands to those of 87 control individuals, using shotgun metagenomics. Controlling for potential confounders, neither the total antibiotic resistance gene (ARG) abundance, nor the overall bacterial composition were significantly different between the two groups. If anything, the ARG richness was slightly lower in WWTP workers, and in a stratified analysis the total ARG abundance was significantly lower in Dutch workers compared to Dutch control participants. We identified country of residence, together with recent antibiotic intake in the Dutch population, as the largest contributing factors to the total abundance of ARGs. A striking side-finding was that sex was associated with carriage of disinfectant resistance genes, with women in both Romania and the Netherlands having significantly higher abundance compared to men. A follow up investigation including an additional 313 publicly available samples from healthy individuals from three additional countries showed that the difference was significant for three genes conferring resistance to chemicals commonly used in cosmetics and cleaning products. We therefore hypothesize that the use of cosmetics and, possibly, cleaning products leads to higher abundance of disinfectant resistance genes in the microbiome of the users. Altogether, this study shows that working at a WWTP does not lead to a higher abundance or diversity of ARGs and no large shifts in the overall gut microbial composition in comparison to participants not working at a WWTP. Instead, other factors such as country of residence, recent antibiotic intake and sex seem to play a larger role.}, } @article {pmid37816004, year = {2023}, author = {Gu, CH and Khatib, LA and Fitzgerald, AS and Graham-Wooten, J and Ittner, CA and Sherrill-Mix, S and Chuang, Y and Glaser, LJ and Meyer, NJ and Bushman, FD and Collman, RG}, title = {Tracking gut microbiome and bloodstream infection in critically ill adults.}, journal = {PloS one}, volume = {18}, number = {10}, pages = {e0289923}, pmid = {37816004}, issn = {1932-6203}, support = {R33 HL137063/HL/NHLBI NIH HHS/United States ; R01 HL137006/HL/NHLBI NIH HHS/United States ; R01 HL137915/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; Adult ; *Gastrointestinal Microbiome/genetics ; *Bacteremia/microbiology ; Critical Illness ; *Sepsis ; Bacteria/genetics ; }, abstract = {BACKGROUND: The gut microbiome is believed to contribute to bloodstream infection (BSI) via translocation of dominant gut bacteria in vulnerable patient populations. However, conclusively linking gut and blood organisms requires stringent approaches to establish strain-level identity.

METHODS: We enrolled a convenience cohort of critically ill patients and investigated 86 bloodstream infection episodes that occurred in 57 patients. Shotgun metagenomic sequencing was used to define constituents of their gut microbiomes, and whole genome sequencing and assembly was done on 23 unique bloodstream isolates that were available from 21 patients. Whole genome sequences were downloaded from public databases and used to establish sequence-identity distribution and define thresholds for unrelated genomes of BSI species. Gut microbiome reads were then aligned to whole genome sequences of the cognate bloodstream isolate and unrelated database isolates to assess identity.

RESULTS: Gut microbiome constituents matching the bloodstream infection species were present in half of BSI episodes, and represented >30% relative abundance of gut sequences in 10% of episodes. Among the 23 unique bloodstream organisms that were available for whole genome sequencing, 14 were present in gut at the species level. Sequence alignment applying defined thresholds for identity revealed that 6 met criteria for identical strains in blood and gut, but 8 did not. Sequence identity between BSI isolates and gut microbiome reads was more likely when the species was present at higher relative abundance in gut.

CONCLUSION: In assessing potential gut source for BSI, stringent sequence-based approaches are essential to determine if organisms responsible for BSI are identical to those in gut: of 14 evaluable patients in which the same species was present in both sites, they were identical in 6/14, but were non-identical in 8/14 and thus inconsistent with gut source. This report demonstrates application of sequencing as a key tool to investigate infection tracking within patients.}, } @article {pmid37815749, year = {2023}, author = {Adıgüzel, AO and Şen, F and Könen-Adıgüzel, S and Kıdeyş, AE and Karahan, A and Doruk, T and Tunçer, M}, title = {Identification of Cutinolytic Esterase from Microplastic-Associated Microbiota Using Functional Metagenomics and Its Plastic Degrading Potential.}, journal = {Molecular biotechnology}, volume = {}, number = {}, pages = {}, pmid = {37815749}, issn = {1559-0305}, support = {120Z329//Türkiye Bilimsel ve Teknolojik Araştırma Kurumu/ ; }, abstract = {Plastic pollution has threatened biodiversity and human health by shrinking habitats, reducing food quality, and limiting the activities of organisms. Therefore, global interest in discovering novel enzymes capable of degrading plastics has increased considerably. Within this context, the functional metagenomic approach, which allows for unlocking the functional potential of uncultivable microbial biodiversity, was used to discover a plastic-degrading enzyme. First, metagenomic libraries derived from microplastic-associated microbiota were screened for esterases capable of degrading both tributyrin and polycaprolactone. Clone KAD01 produced esterase highly active against p-nitrophenyl esters (C2-C16). The gene corresponding to the enzyme activity showed moderate identity (≤ 55.94%) to any known esterases/cutinases. The gene was extracellularly expressed with a 6× histidine tag in E. coli BL21(DE3), extracellularly. Titer of the enzyme (CEstKAD01) was raised from 21.32 to 35.17 U/mL by the statistical optimization of expression conditions and media components. CEstKAD01 was most active at pH 7.0 and 30 °C. It was noteworthy stable over a wide pH (6.0-10.0) and temperature (20-50 °C). The enzyme was active and stable in elevated NaCl concentrations up to 12% (w/v). Pre-incubation of CEstKAD01 with Mg[2+], Mn[2+], and Ca[2+] increased the enzyme activity. CEstKAD01 displayed an excellent tolerance against various chemicals and solvents. It was determined that 1 mg of the enzyme caused the release of 5.39 ± 0.18 mM fatty acids from 1 g apple cutin in 120 min. Km and Vmax values of CEstKAD01 against p-nitrophenyl butyrate were calculated to be 1.48 mM and 20.37 µmol/min, respectively. The enzyme caused 6.94 ± 0.55, 8.71 ± 0.56, 7.47 ± 0.47, and 9.22 ± 0.18% of weight loss in polystyrene, high-density polyethylene, low-density polyethylene, and polyvinyl chloride after 30-day incubation. The scanning electron microscopy (SEM) analysis indicated the formation of holes and pits on the plastic surfaces supporting the degradation. In addition, the change in chemical structure in plastics treated with the enzyme was determined by Fourier Transform Infrared Spectroscopy (FTIR) analysis. Finally, the degradation products were found to have no genotoxic potential. To our knowledge, no cutinolytic esterase with the potential to degrade polystyrene (PS), high-density polyethylene (HDPE), low-density polyethylene (LDPE), and polyvinyl chloride (PVC) has been identified from metagenomes derived from microplastic-associated microbiota.}, } @article {pmid37814055, year = {2023}, author = {Wang, Y and Gai, J and Hou, Q and Zhao, H and Shan, C and Guo, Z}, title = {Ultra-high-depth macrogenomic sequencing revealed differences in microbial composition and function between high temperature and medium-high temperature Daqu.}, journal = {World journal of microbiology & biotechnology}, volume = {39}, number = {12}, pages = {337}, pmid = {37814055}, issn = {1573-0972}, support = {2023//Science and technology plan project of Xinjiang Production and Construction Corps/ ; 2023//Science and technology plan project of Xinjiang Production and Construction Corps/ ; 2020kypytd009//Hubei university of arts and science cultivation fund for teachers' scientific research ability: technological innovation team/ ; }, mesh = {*Alcoholic Beverages/microbiology ; Temperature ; Bacteria/genetics ; *Microbiota ; Fermentation ; }, abstract = {Complex microorganisms in Daqu of different temperatures play a vital role in the taste, flavor and quality of Baijiu during fermentation. However, understanding the functional diversity of the whole microbial community between the Daqus of two different temperatures (high temperature Daqu, HD and medium-high temperature Daqu, MD) remains a major challenge. Here, a systematic study of the microbial diversity, functions as well as physiological and biochemical indexes of Daqu are described. The results revealed that the Daqu exhibited unique characteristics. In particular, the diversity of microorganisms in HD and MD was high, with 44 species including 14 novel species (Sphingomonas sp. is the main novel species) detected in all samples. Their profiles of carbohydrate-active enzymes and specific functional components supported the fact that these species were involved in flavor formation. The Daqu microbiome consisted of a high proportion of phage, providing evidence of phage infection/genome integration and horizontal gene transfer from phage to bacteria. Such processes would also regulate Daqu microbiomes and thus flavor quality. These results enrich current knowledge of Daqu and can be used to promote the development of Baijiu fermentation technology.}, } @article {pmid37813636, year = {2023}, author = {Kim, H and Kim, J and Choi, JW and Ahn, KS and Park, DI and Kim, S}, title = {A streamlined pipeline based on HmmUFOtu for microbial community profiling using 16S rRNA amplicon sequencing.}, journal = {Genomics & informatics}, volume = {21}, number = {3}, pages = {e40}, pmid = {37813636}, issn = {1598-866X}, abstract = {Microbial community profiling using 16S rRNA amplicon sequencing allows for taxonomic characterization of diverse microorganisms. While amplicon sequence variant (ASV) methods are increasingly favored for their fine-grained resolution of sequence variants, they often discard substantial portions of sequencing reads during quality control, particularly in datasets with large number samples. We present a streamlined pipeline that integrates FastP for read trimming, HmmUFOtu for operational taxonomic units (OTU) clustering, Vsearch for chimera checking, and Kraken2 for taxonomic assignment. To assess the pipeline's performance, we reprocessed two published stool datasets of normal Korean populations: one with 890 and the other with 1,462 independent samples. In the first dataset, HmmUFOtu retained 93.2% of over 104 million read pairs after quality trimming, discarding chimeric or unclassifiable reads, while DADA2, a commonly used ASV method, retained only 44.6% of the reads. Nonetheless, both methods yielded qualitatively similar β-diversity plots. For the second dataset, HmmUFOtu retained 89.2% of read pairs, while DADA2 retained a mere 18.4% of the reads. HmmUFOtu, being a closed-reference clustering method, facilitates merging separately processed datasets, with shared OTUs between the two datasets exhibiting a correlation coefficient of 0.92 in total abundance (log scale). While the first two dimensions of the β-diversity plot exhibited a cohesive mixture of the two datasets, the third dimension revealed the presence of a batch effect. Our comparative evaluation of ASV and OTU methods within this streamlined pipeline provides valuable insights into their performance when processing large-scale microbial 16S rRNA amplicon sequencing data. The strengths of HmmUFOtu and its potential for dataset merging are highlighted.}, } @article {pmid37813622, year = {2023}, author = {Ling, CW and Zhong, H and Zeng, FF and Chen, G and Fu, Y and Wang, C and Zhang, ZQ and Cao, WT and Sun, TY and Ding, D and Liu, YH and Dong, HL and Jing, LP and Ling, W and Zheng, JS and Chen, YM}, title = {Cohort Profile: Guangzhou Nutrition and Health Study (GNHS): A Population-Based Multi-Omics Study.}, journal = {Journal of epidemiology}, volume = {}, number = {}, pages = {}, doi = {10.2188/jea.JE20230108}, pmid = {37813622}, issn = {1349-9092}, abstract = {BACKGROUND: The Guangzhou Nutrition and Health Study (GNHS) aims to assess the determinants of metabolic disease in nutritional aspects, as well as other environmental and genetic factors, and explore possible biomarkers and mechanisms with multi-omics integration.

METHODS: The population-based sample of adults in Guangzhou, China (baseline: 40-83 years old; n = 5118) was followed up about every 3 years. All will be tracked via on-site follow-up and health information systems. We assessed detailed information on lifestyle factors, physical activities, dietary assessments, psychological health, cognitive function, body measurements, and muscle function. Instrument tests included dual-energy X-ray absorptiometry scanning, carotid artery and liver ultrasonography evaluations, vascular endothelial function evaluation, upper-abdomen and brain magnetic resonance imaging, and 14-d real-time continuous glucose monitoring tests. We also measured multi-omics, including host genome-wide genotyping, serum metabolome and proteome, gut microbiome (16S rRNA sequencing, metagenome, and internal transcribed spacer 2 sequencing), and fecal metabolome and proteome.

RESULTS: The baseline surveys were conducted from 2008 to 2015. Now, we have completed 3 waves. The 3rd and 4th follow-ups have started but have yet to end. A total of 5118 participants aged 40-83 took part in the study. The median age at baseline was approximately 59.0 years and the proportion of female participants was about 69.4%. Among all the participants, 3628 (71%) completed at least one on-site follow-up with a median duration of 9.48 years.

CONCLUSION: The cohort will provide data that have been influential in establishing the role of nutrition in metabolic diseases with multi-omics.}, } @article {pmid37813263, year = {2024}, author = {Peng, H and Xu, T and Wang, L and Yu, J and Chen, X and Cheng, X and Li, H and Huang, L and Wei, L and Wei, S}, title = {Effect of Streptomyces JD211 application on soil physicochemical properties and N2O emission characteristics of rice rhizosphere.}, journal = {The Science of the total environment}, volume = {906}, number = {}, pages = {167673}, doi = {10.1016/j.scitotenv.2023.167673}, pmid = {37813263}, issn = {1879-1026}, mesh = {Soil/chemistry ; *Oryza ; *Streptomyces ; RNA, Ribosomal, 16S ; Rhizosphere ; Nitrous Oxide/analysis ; Soil Microbiology ; }, abstract = {Biocontrol agent, as a pollution-free and sustainable plant disease control method, can inhibit the spread of soil-borne diseases and promote the growth of crops. However, there are few studies on the effect of biocontrol agent on N2O emission in rice soil. In this study, after the application of the biocontrol agent Streptomyces JD211, N2O emission from rice soil were measured, and the relationship between the agent and soil N2O emissions were studied in soil chemistry and molecular biology. The results showed that the application of Streptomyces JD211 can significantly reduce the rate of N2O emission from rice soil. The NH4[+]-N and NO3[-]-N contents in rice soil decreased in a short period of time after the application of Streptomyces JD211, while the mineral N content in the soil remained stable with rice growth. 16S rRNA gene sequencing and metagenomic sequencing revealed Streptomyces JD211 application mainly increased the relative abundance of Burkholderia and Streptomyces in the soil microbial community, reduced the relative abundance of hao, norB, norC genes, and increased the relative abundance of nosZ and hcp genes. Streptomyces JD211 application promoted N2O transformation and weakened N2O production pathways, which ultimately reduced N2O emissions from rice soils. This study provided new insight of biocontrol agents to regulate soil N2O emissions, which is of great significance for the development and application of biocontrol bacteria and farmland environmental protection.}, } @article {pmid37812548, year = {2023}, author = {Ma, L and Deng, W and Bai, Y and Du, Z and Xiao, M and Wang, L and Li, J and Nandi, AK}, title = {Identifying Phage Sequences From Metagenomic Data Using Deep Neural Network With Word Embedding and Attention Mechanism.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {20}, number = {6}, pages = {3772-3785}, doi = {10.1109/TCBB.2023.3322870}, pmid = {37812548}, issn = {1557-9964}, mesh = {*Bacteriophages/genetics ; Neural Networks, Computer ; Algorithms ; Metagenome/genetics ; *Microbiota ; }, abstract = {Phages are the functional viruses that infect bacteria and they play important roles in microbial communities and ecosystems. Phage research has attracted great attention due to the wide applications of phage therapy in treating bacterial infection in recent years. Metagenomics sequencing technique can sequence microbial communities directly from an environmental sample. Identifying phage sequences from metagenomic data is a vital step in the downstream of phage analysis. However, the existing methods for phage identification suffer from some limitations in the utilization of the phage feature for prediction, and therefore their prediction performance still need to be improved further. In this article, we propose a novel deep neural network (called MetaPhaPred) for identifying phages from metagenomic data. In MetaPhaPred, we first use a word embedding technique to encode the metagenomic sequences into word vectors, extracting the latent feature vectors of DNA words. Then, we design a deep neural network with a convolutional neural network (CNN) to capture the feature maps in sequences, and with a bi-directional long short-term memory network (Bi-LSTM) to capture the long-term dependencies between features from both forward and backward directions. The feature map consists of a set of feature patterns, each of which is the weighted feature extracted by a convolution filter with convolution kernels in the CNN slide along the input feature vectors. Next, an attention mechanism is used to enhance contributions of important features. Experimental results on both simulated and real metagenomic data with different lengths demonstrate the superiority of the proposed MetaPhaPred over the state-of-the-art methods in identifying phage sequences.}, } @article {pmid37812012, year = {2023}, author = {Kocurek, B and Ramachandran, P and Grim, CJ and Morin, P and Howard, L and Ottesen, A and Timme, R and Leonard, SR and Rand, H and Strain, E and Tadesse, D and Pettengill, JB and Lacher, DW and Mammel, M and Jarvis, KG}, title = {Application of quasimetagenomics methods to define microbial diversity and subtype Listeria monocytogenes in dairy and seafood production facilities.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0148223}, pmid = {37812012}, issn = {2165-0497}, mesh = {Humans ; *Listeria monocytogenes/genetics ; Food Microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Seafood ; }, abstract = {In developed countries, the human diet is predominated by food commodities, which have been manufactured, processed, and stored in a food production facility. Little is known about the application of metagenomic sequencing approaches for detecting foodborne pathogens, such as L. monocytogenes, and characterizing microbial diversity in food production ecosystems. In this work, we investigated the utility of 16S rRNA amplicon and quasimetagenomic sequencing for the taxonomic and phylogenetic classification of Listeria culture enrichments of environmental swabs collected from dairy and seafood production facilities. We demonstrated that single-nucleotide polymorphism (SNP) analyses of L. monocytogenes metagenome-assembled genomes (MAGs) from quasimetagenomic data sets can achieve similar resolution as culture isolate whole-genome sequencing. To further understand the impact of genome coverage on MAG SNP cluster resolution, an in silico downsampling approach was employed to reduce the percentage of target pathogen sequence reads, providing an initial estimate of required MAG coverage for subtyping resolution of L. monocytogenes.}, } @article {pmid37811944, year = {2023}, author = {Gihawi, A and Ge, Y and Lu, J and Puiu, D and Xu, A and Cooper, CS and Brewer, DS and Pertea, M and Salzberg, SL}, title = {Major data analysis errors invalidate cancer microbiome findings.}, journal = {mBio}, volume = {14}, number = {5}, pages = {e0160723}, pmid = {37811944}, issn = {2150-7511}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Computational Biology ; Metagenomics ; *Microbiota ; *Neoplasms ; Data Analysis ; }, abstract = {Recent reports showing that human cancers have a distinctive microbiome have led to a flurry of papers describing microbial signatures of different cancer types. Many of these reports are based on flawed data that, upon re-analysis, completely overturns the original findings. The re-analysis conducted here shows that most of the microbes originally reported as associated with cancer were not present at all in the samples. The original report of a cancer microbiome and more than a dozen follow-up studies are, therefore, likely to be invalid.}, } @article {pmid37811892, year = {2024}, author = {Baltoumas, FA and Karatzas, E and Liu, S and Ovchinnikov, S and Sofianatos, Y and Chen, IM and Kyrpides, NC and Pavlopoulos, GA}, title = {NMPFamsDB: a database of novel protein families from microbial metagenomes and metatranscriptomes.}, journal = {Nucleic acids research}, volume = {52}, number = {D1}, pages = {D502-D512}, pmid = {37811892}, issn = {1362-4962}, support = {1855-BOLOGNA//HFRI/ ; 838018//Marie Sklodowska-Curie/ ; //Fondation Sante/ ; //U.S. Department of Energy Joint Genome Institute/ ; DE-AC02-05CH11231//U.S. Department of Energy/ ; }, mesh = {*Metagenome ; *Ecosystem ; Proteins/chemistry ; Amino Acid Sequence ; Databases, Factual ; Databases, Protein ; }, abstract = {The Novel Metagenome Protein Families Database (NMPFamsDB) is a database of metagenome- and metatranscriptome-derived protein families, whose members have no hits to proteins of reference genomes or Pfam domains. Each protein family is accompanied by multiple sequence alignments, Hidden Markov Models, taxonomic information, ecosystem and geolocation metadata, sequence and structure predictions, as well as 3D structure models predicted with AlphaFold2. In its current version, NMPFamsDB hosts over 100 000 protein families, each with at least 100 members. The reported protein families significantly expand (more than double) the number of known protein sequence clusters from reference genomes and reveal new insights into their habitat distribution, origins, functions and taxonomy. We expect NMPFamsDB to be a valuable resource for microbial proteome-wide analyses and for further discovery and characterization of novel functions. NMPFamsDB is publicly available in http://www.nmpfamsdb.org/ or https://bib.fleming.gr/NMPFamsDB.}, } @article {pmid37811141, year = {2023}, author = {Liang, X and Zhang, J and Kim, Y and Ho, J and Liu, K and Keenum, I and Gupta, S and Davis, B and Hepp, SL and Zhang, L and Xia, K and Knowlton, KF and Liao, J and Vikesland, PJ and Pruden, A and Heath, LS}, title = {ARGem: a new metagenomics pipeline for antibiotic resistance genes: metadata, analysis, and visualization.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1219297}, pmid = {37811141}, issn = {1664-8021}, abstract = {Antibiotic resistance is of crucial interest to both human and animal medicine. It has been recognized that increased environmental monitoring of antibiotic resistance is needed. Metagenomic DNA sequencing is becoming an attractive method to profile antibiotic resistance genes (ARGs), including a special focus on pathogens. A number of computational pipelines are available and under development to support environmental ARG monitoring; the pipeline we present here is promising for general adoption for the purpose of harmonized global monitoring. Specifically, ARGem is a user-friendly pipeline that provides full-service analysis, from the initial DNA short reads to the final visualization of results. The capture of extensive metadata is also facilitated to support comparability across projects and broader monitoring goals. The ARGem pipeline offers efficient analysis of a modest number of samples along with affordable computational components, though the throughput could be increased through cloud resources, based on the user's configuration. The pipeline components were carefully assessed and selected to satisfy tradeoffs, balancing efficiency and flexibility. It was essential to provide a step to perform short read assembly in a reasonable time frame to ensure accurate annotation of identified ARGs. Comprehensive ARG and mobile genetic element databases are included in ARGem for annotation support. ARGem further includes an expandable set of analysis tools that include statistical and network analysis and supports various useful visualization techniques, including Cytoscape visualization of co-occurrence and correlation networks. The performance and flexibility of the ARGem pipeline is demonstrated with analysis of aquatic metagenomes. The pipeline is freely available at https://github.com/xlxlxlx/ARGem.}, } @article {pmid37810788, year = {2023}, author = {Ochoa-Sánchez, M and Acuña Gomez, EP and Ramírez-Fenández, L and Eguiarte, LE and Souza, V}, title = {Current knowledge of the Southern Hemisphere marine microbiome in eukaryotic hosts and the Strait of Magellan surface microbiome project.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15978}, pmid = {37810788}, issn = {2167-8359}, mesh = {Animals ; *Eukaryota/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenome ; Fishes/genetics ; Aquatic Organisms/genetics ; Mammals/genetics ; }, abstract = {Host-microbe interactions are ubiquitous and play important roles in host biology, ecology, and evolution. Yet, host-microbe research has focused on inland species, whereas marine hosts and their associated microbes remain largely unexplored, especially in developing countries in the Southern Hemisphere. Here, we review the current knowledge of marine host microbiomes in the Southern Hemisphere. Our results revealed important biases in marine host species sampling for studies conducted in the Southern Hemisphere, where sponges and marine mammals have received the greatest attention. Sponge-associated microbes vary greatly across geographic regions and species. Nevertheless, besides taxonomic heterogeneity, sponge microbiomes have functional consistency, whereas geography and aging are important drivers of marine mammal microbiomes. Seabird and macroalgal microbiomes in the Southern Hemisphere were also common. Most seabird microbiome has focused on feces, whereas macroalgal microbiome has focused on the epibiotic community. Important drivers of seabird fecal microbiome are aging, sex, and species-specific factors. In contrast, host-derived deterministic factors drive the macroalgal epibiotic microbiome, in a process known as "microbial gardening". In turn, marine invertebrates (especially crustaceans) and fish microbiomes have received less attention in the Southern Hemisphere. In general, the predominant approach to study host marine microbiomes has been the sequencing of the 16S rRNA gene. Interestingly, there are some marine holobiont studies (i.e., studies that simultaneously analyze host (e.g., genomics, transcriptomics) and microbiome (e.g., 16S rRNA gene, metagenome) traits), but only in some marine invertebrates and macroalgae from Africa and Australia. Finally, we introduce an ongoing project on the surface microbiome of key species in the Strait of Magellan. This is an international project that will provide novel microbiome information of several species in the Strait of Magellan. In the short-term, the project will improve our knowledge about microbial diversity in the region, while long-term potential benefits include the use of these data to assess host-microbial responses to the Anthropocene derived climate change.}, } @article {pmid37810463, year = {2023}, author = {Ye, G and Yang, L and Dong, Z}, title = {Severe intracranial infection caused by community-acquired hypervirulent Klebsiella pneumoniae: A case report.}, journal = {IDCases}, volume = {34}, number = {}, pages = {e01902}, pmid = {37810463}, issn = {2214-2509}, abstract = {Hypervirulent Klebsiella pneumoniae (HvKp) is a dynamic pathotype characterized by heightened mucoviscosity and virulence, typically afflicting individuals within the community, who commonly exhibit good health. We presented a case study of a 65-year-old male with diabetes who developed community acquired pneumonia, septic shock, and intracranial infection. The diagnosis was established through cranial magnetic resonance imaging (MRI), typical clinical presentation, and biological culture. The presence of HvKp infection was confirmed by cerebrospinal fluid (CSF) metagenomic next-generation sequencing (mNGS) and blood culture. Treatment consisted of Amikacin 0.8 g qd in combination with meropenem 2.0 g q8h, based on drug sensitivity testing. The patient experienced symptom relief, with the CSF becoming clear and the elimination of the pathogen, ultimately resulting in a successful recovery. The clinical data, diagnosis, and treatment of the patient were documented, and a review of the literature was conducted to offer clinical guidance regarding the intracranial infection resulting from community-acquired HvKp.}, } @article {pmid37810459, year = {2023}, author = {Frolov, AV and Akhmetova, LA and Vishnevskaya, MS and Kiriukhin, BA and Montreuil, O and Lopes, F and Tarasov, SI}, title = {Amplicon metagenomics of dung beetles (Coleoptera, Scarabaeidae, Scarabaeinae) as a proxy for lemur (Primates, Lemuroidea) studies in Madagascar.}, journal = {ZooKeys}, volume = {1181}, number = {}, pages = {29-39}, pmid = {37810459}, issn = {1313-2989}, abstract = {Dung beetles (Scarabaeidae, Scarabaeinae) are among the most cost-effective and informative biodiversity indicator groups, conveying rich information about the status of habitats and faunas of an area. Yet their use for monitoring the mammal species, that are the main providers of the food for the dung beetles, has only recently been recognized. In the present work, we studied the diet of four endemic Madagascan dung beetles (Helictopleurusfissicollis (Fairmaire), H.giganteus (Harold), Nanosagaboides (Boucomont), and Epilissussplendidus Fairmaire) using high-throughput sequencing and amplicon metagenomics. For all beetle species, the ⅔-¾ of reads belonged to humans, suggesting that human feces are the main source of food for the beetles in the examined areas. The second most abundant were the reads of the cattle (Bostaurus Linnaeus). We also found lower but significant number of reads of six lemur species belonging to three genera. Our sampling localities agree well with the known ranges of these lemur species. The amplicon metagenomics method proved a promising tool for the lemur inventories in Madagascar.}, } @article {pmid37810127, year = {2023}, author = {Uemura, T and Kawashima, A and Jingushi, K and Motooka, D and Saito, T and Nesrine, S and Oka, T and Okuda, Y and Yamamoto, A and Yamamichi, G and Tomiyama, E and Ishizuya, Y and Yamamoto, Y and Kato, T and Hatano, K and Tsujikawa, K and Wada, H and Nonomura, N}, title = {Bacteria-derived DNA in serum extracellular vesicles are biomarkers for renal cell carcinoma.}, journal = {Heliyon}, volume = {9}, number = {9}, pages = {e19800}, pmid = {37810127}, issn = {2405-8440}, abstract = {This is the first study to determine the clinical importance of circulating bacterial DNA in patients with renal cell carcinoma (RCC). We performed 16S rRNA metagenomic analysis of serum extracellular vesicles (EVs) from 88 patients with RCC and 10 healthy donors and identified three abundant bacterial DNA: Bacteroidia, TM7-1, and Sphingomonadales. Combining characteristic bacterial DNA information (three bacteria-derived DNA), a BTS index was created to diagnose patients with RCC. The BTS index showed high sensitivity not only in the discovery cohort, but also in the validation cohort, suggesting that it was useful as a screening test. Furthermore, in nivolumab treatment of RCC, patients with higher levels of Bacteroidia DNA in serum EVs had significantly poorer progression-free and overall survival than did those with lower levels. This study showed that circulating Bacteria-derived DNA could be used as a biomarker for RCC.}, } @article {pmid37809773, year = {2023}, author = {Chen, M and Song, X and Shi, M and Zhang, M and Hu, X}, title = {Case presentation of Campylobacter rectus leading to pneumonia and literature review.}, journal = {Heliyon}, volume = {9}, number = {9}, pages = {e20014}, pmid = {37809773}, issn = {2405-8440}, abstract = {Pneumonia caused by Campylobacter rectus is very rare. Herein, we describe the treatment course and experiences of a patient with pneumonia caused by Campylobacter rectus. A 64-year-old woman with intermittent hemoptysis and part lung necrosis indicated by radiography was admitted to our hospital on March 15, 2021. After admission, a CT (Computer tomography)-guided percutaneous lung biopsy was identified as Campylobacter rectus positive by bacterial culture and metagenomic sequencing. The hemoptysis resolved, and the lesions in the right lower lung were gradually absorbed after treatment with anti-Campylobacter rectus drugs. In cases of pneumonia which unresolved by initial therapy and associated with more severe oral hygiene problems, the possibility of infection with oral pathogens (eg, Campylobacter rectus) should be considered. This case suggests that bacterial culture and metagenomic sequencing of the diseased tissue, particularly anaerobic culture, helps to clarify the etiological diagnosis.}, } @article {pmid37809666, year = {2023}, author = {Atkinson, L and Lee, JC and Lennon, A and Shah, D and Storey, N and Morfopoulou, S and Harris, KA and Breuer, J and Brown, JR}, title = {Untargeted metagenomics protocol for the diagnosis of infection from CSF and tissue from sterile sites.}, journal = {Heliyon}, volume = {9}, number = {9}, pages = {e19854}, pmid = {37809666}, issn = {2405-8440}, abstract = {Metagenomic next-generation sequencing (mNGS) is an untargeted technique capable of detecting all microbial nucleic acid within a sample. This protocol outlines our wet laboratory method for mNGS of cerebrospinal fluid (CSF) specimens and tissues from sterile sites. We use this method routinely in our clinical service, processing 178 specimens over the past 2.5 years in a laboratory that adheres to ISO:15189 standards. We have successfully used this protocol to diagnose multiple cases of encephalitis and hepatitis.}, } @article {pmid37809439, year = {2023}, author = {Liu, H and Xu, H and Liu, H and Zhao, Z and Zhang, X}, title = {Metagenomic next-generation sequencing in the diagnose of pulmonary infection with airway complications in a lung transplant recipient.}, journal = {Heliyon}, volume = {9}, number = {9}, pages = {e19611}, pmid = {37809439}, issn = {2405-8440}, abstract = {We reported a case of a 60-year-old male with fever, cough, expectoration, and chest distress after right lung transplanted. Blood examination showed elevated C-reaction protein (CRP), white blood cell (WBC), and ammonia. Computed tomography (CT) revealed patchy high-density shadows and few pleural effusions in the transplanted lung. Bronchoscopy illustrated anastomotic fistula, and pseudomembrane and mucus plugs around the right main bronchial anastomosis. Carbapenem-resistant Klebsiella pneumoniae, Ureaplasma urealyticum, and Aspergillus flavus was successively detected by metagenomic next-generation sequencing (mNGS). Targeted anti-microbial agents were administered and patient was successfully discharged. Unfortunately, a year later, patient died of respiratory failure due to recurrent pulmonary infections.}, } @article {pmid37809036, year = {2023}, author = {Li, H and Niu, E and Fu, J and Huang, Y and Gao, Y and Chai, W and Chen, J}, title = {The Clinical Impact of Metagenomic Next-Generation Sequencing for the Diagnosis of Periprosthetic Joint Infection.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {6521-6533}, pmid = {37809036}, issn = {1178-6973}, abstract = {BACKGROUND: Synovial fluid metagenomic next-generation sequencing was introduced into the diagnosis of periprosthetic joint infection (PJI) in recent years. However, the clinical impact of mNGS remains unknown. Therefore, we performed a prospective cohort study to evaluate the clinical impact of mNGS for PJI diagnosis.

MATERIALS AND METHODS: Between April 2019 and April 2021, a total of 201 patients with suspected PJI were recruited in a high-volume PJI revision center. All patients underwent joint aspiration before surgeries and the obtained synovial fluids were sent to tests for the diagnosis of PJI. Based on the clinical evaluation of these patients, the patients were categorized into three groups: Group A: the mNGS reports were not acted upon. Group B: mNGS confirmed the standard diagnostic tests of PJI and generated identical clinical impact compared to standard diagnostic tests. Group C: mNGS results guided clinical therapy. Then, the concordance between synovial mNGS and cultures was analyzed. After that, multivariate regressions were performed to explore the "targeted populations" of mNGS tests.

RESULTS: A total of 107 patients were diagnosed with PJI based on the 2014 MSIS criteria and there were 33, 123, 45 patients in the group A, B, C respectively. The predictive factors of mNGS inducing clinical impact compared to standard diagnostic tests were negative culture results (adjusted OR: 5.88), previous history of joint infection (adjusted OR: 5.97), polymicrobial PJI revealed by culture (adjusted OR: 4.39) and PJI identified by MSIS criteria (adjusted OR: 17.06).

CONCLUSION: When standard diagnostic tests for PJI were performed, about 22% of synovial fluid mNGS tests can change the treatment protocols built on standard diagnostic tests and affect the clinical practice. Thus, the use of synovial fluid mNGS in some "target" populations is more valuable compared to others such as patients with previous joint infection, polymicrobial PJI, and culture-negative PJI.

EVIDENCE LEVEL: Level I.}, } @article {pmid37808911, year = {2023}, author = {Lei, Y and Guo, Q and Liu, J and Huang, H and Han, P}, title = {Staphylococcus cohnii infection diagnosed by metagenomic next generation sequencing in a patient on hemodialysis with cirrhotic ascites: a case report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1240283}, pmid = {37808911}, issn = {2235-2988}, mesh = {Male ; Humans ; Middle Aged ; Ascites/diagnosis/microbiology ; High-Throughput Nucleotide Sequencing/methods ; *Staphylococcal Infections/diagnosis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; Liver Cirrhosis/complications/diagnosis ; *Peritonitis/diagnosis/microbiology ; Abdominal Pain/drug therapy ; Metagenomics/methods ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Patients with spontaneous bacterial peritonitis (SBP) often just receive empirical antibiotic therapy, as pathogens can be identified in only few patients using the techniques of conventional culture. Metagenomic next generation sequencing (mNGS) is a useful tool for diagnosis of infectious diseases. However, clinical application of mNGS in diagnosis of infected ascites of cirrhotic patients is rarely reported.

CASE PRESENTATION: A 53-year-old male with cirrhosis on regular hemodialysis presented with continuous abdominal pain. After treatment with empiric antibiotics, his inflammatory parameters decreased without significant relief of abdominal pain. Finally, based on ascites mNGS detection, he was diagnosed as infection of Staphylococcus cohnii (S.cohnii), a gram-positive opportunistic pathogen. With targeted antibiotic treatment, the bacterial peritonitis was greatly improved and the patient's abdominal pain was significantly alleviated.

CONCLUSIONS: When conventional laboratory diagnostic methods and empirical antibiotic therapy fail, proper application of mNGS can help identify pathogens and significantly improve prognosis and patients' symptoms.}, } @article {pmid37808738, year = {2023}, author = {Tisza, M and Lloyd, R and Hoffman, K and Smith, D and Rewers, M and , and Cregeen, SJ and Petrosino, JF}, title = {Phage-bacteria dynamics during the first years of life revealed by trans-kingdom marker gene analysis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37808738}, support = {U01 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK063863/DK/NIDDK NIH HHS/United States ; UL1 TR002535/TR/NCATS NIH HHS/United States ; U01 DK128847/DK/NIDDK NIH HHS/United States ; U01 DK063790/DK/NIDDK NIH HHS/United States ; UL1 TR000064/TR/NCATS NIH HHS/United States ; HHSN267200700014C/LM/NLM NIH HHS/United States ; U01 DK063836/DK/NIDDK NIH HHS/United States ; U01 DK063829/DK/NIDDK NIH HHS/United States ; U01 DK063865/DK/NIDDK NIH HHS/United States ; UC4 DK095300/DK/NIDDK NIH HHS/United States ; UC4 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK063829/DK/NIDDK NIH HHS/United States ; UC4 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK117483/DK/NIDDK NIH HHS/United States ; UC4 DK063836/DK/NIDDK NIH HHS/United States ; UC4 DK112243/DK/NIDDK NIH HHS/United States ; U01 DK124166/DK/NIDDK NIH HHS/United States ; U01 DK063861/DK/NIDDK NIH HHS/United States ; UC4 DK063865/DK/NIDDK NIH HHS/United States ; U01 DK063863/DK/NIDDK NIH HHS/United States ; UC4 DK106955/DK/NIDDK NIH HHS/United States ; UC4 DK100238/DK/NIDDK NIH HHS/United States ; }, abstract = {Humans are colonized with commensal bacteria soon after birth, and, while this colonization is affected by lifestyle and other factors, bacterial colonization proceeds through well-studied phases. However, less is known about phage communities in early human development due to small study sizes, inability to leverage large databases, and lack of appropriate bioinformatics tools. In this study, whole genome shotgun sequencing data from the TEDDY study, composed of 12,262 longitudinal samples from 887 children in 4 countries, is reanalyzed to assess phage and bacterial dynamics simultaneously. Reads from these samples were mapped to marker genes from both bacteria and a new database of tens of thousands of phage taxa from human microbiomes. We uncover that each child is colonized by hundreds of different phages during the early years, and phages are more transitory than bacteria. Participants' samples continually harbor new phage species over time whereas the diversification of bacterial species begins to saturate. Phage data improves the ability for machine learning models to discriminate samples by country. Finally, while phage populations were individual-specific, striking patterns arose from the larger dataset, showing clear trends of ecological succession amongst phages, which correlated well with putative host bacteria. Improved understanding of phage-bacterial relationships may reveal new means by which to shape and modulate the microbiome and its constituents to improve health and reduce disease, particularly in vulnerable populations where antibiotic use and/or other more drastic measures may not be advised.}, } @article {pmid37808673, year = {2023}, author = {Lee, J and Wellenstein, K and Rahnavard, A and Nelson, AT and Holter, MM and Cummings, B and Yeliseyev, V and Castoldi, A and Clish, CB and Bry, L and Siegel, D and Kahn, BB}, title = {Beneficial metabolic effects of PAHSAs depend on the gut microbiota in diet-induced obese mice.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.09.28.558803}, pmid = {37808673}, abstract = {Dietary lipids play an essential role in regulating the function of the gut microbiota and gastrointestinal tract, and these luminal interactions contribute to mediating host metabolism. PAHSAs are a class of lipids with anti-diabetic and anti-inflammatory properties, but whether the gut microbiota contributes to their beneficial effects on host metabolism is unknown. Here, we report that treating high fat diet (HFD)-fed germ-free mice with PAHSAs does not improve insulin sensitivity. However, transfer of feces from PAHSA-treated, but not Vehicle-treated, chow-fed mice increases insulin-sensitivity in HFD-fed germ free mice. Thus, the gut microbiota is necessary for and can transmit the insulin-sensitizing effects of PAHSAs in HFD-fed germ-free mice. Functional analyses of the cecal metagenome and lipidome of PAHSA-treated mice identified multiple lipid species that associate with the gut commensal Bacteroides thetaiotaomicron (Bt) and with insulin sensitivity resulting from PAHSA treatment. Bt supplementation in HFD-fed female mice prevented weight gain, reduced adiposity, improved glucose tolerance, fortified the colonic mucus barrier and reduced systemic inflammation versus chow-fed controls, effects that were not observed in HFD-fed male mice. Furthermore, ovariectomy partially reversed the beneficial Bt effects on host metabolism, indicating a role for sex hormones in mediating probiotic effects. Altogether, these studies highlight the fact that lipids can modulate the gut microbiota resulting in improvement in host metabolism and that PAHSA-induced changes in the microbiota result in at least some of their insulin-sensitizing effects in female mice.}, } @article {pmid37808316, year = {2023}, author = {Vigil, K and Aw, TG}, title = {Comparison of de novo assembly using long-read shotgun metagenomic sequencing of viruses in fecal and serum samples from marine mammals.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1248323}, pmid = {37808316}, issn = {1664-302X}, abstract = {INTRODUCTION: Viral diseases of marine mammals are difficult to study, and this has led to a limited knowledge on emerging known and unknown viruses which are ongoing threats to animal health. Viruses are the leading cause of infectious disease-induced mass mortality events among marine mammals.

METHODS: In this study, we performed viral metagenomics in stool and serum samples from California sea lions (Zalophus californianus) and bottlenose dolphins (Tursiops truncates) using long-read nanopore sequencing. Two widely used long-read de novo assemblers, Canu and Metaflye, were evaluated to assemble viral metagenomic sequencing reads from marine mammals.

RESULTS: Both Metaflye and Canu assembled similar viral contigs of vertebrates, such as Parvoviridae, and Poxviridae. Metaflye assembled viral contigs that aligned with one viral family that was not reproduced by Canu, while Canu assembled viral contigs that aligned with seven viral families that was not reproduced by Metaflye. Only Canu assembled viral contigs from dolphin and sea lion fecal samples that matched both protein and nucleotide RefSeq viral databases using BLASTx and BLASTn for Anelloviridae, Parvoviridae and Circoviridae families. Viral contigs assembled with Canu aligned with torque teno viruses and anelloviruses from vertebrate hosts. Viruses associated with invertebrate hosts including densoviruses, Ambidensovirus, and various Circoviridae isolates were also aligned. Some of the invertebrate and vertebrate viruses reported here are known to potentially cause mortality events and/or disease in different seals, sea stars, fish, and bivalve species.

DISCUSSION: Canu performed better by producing the most viral contigs as compared to Metaflye with assemblies aligning to both protein and nucleotide databases. This study suggests that marine mammals can be used as important sentinels to surveil marine viruses that can potentially cause diseases in vertebrate and invertebrate hosts.}, } @article {pmid37808297, year = {2023}, author = {Zhang, Y and Ruff, SE and Oskolkov, N and Tierney, BT and Ryon, K and Danko, D and Mason, CE and Elhaik, E}, title = {The microbial biodiversity at the archeological site of Tel Megiddo (Israel).}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1253371}, pmid = {37808297}, issn = {1664-302X}, abstract = {INTRODUCTION: The ancient city of Tel Megiddo in the Jezreel Valley (Israel), which lasted from the Neolithic to the Iron Age, has been continuously excavated since 1903 and is now recognized as a World Heritage Site. The site features multiple ruins in various areas, including temples and stables, alongside modern constructions, and public access is allowed in designated areas. The site has been studied extensively since the last century; however, its microbiome has never been studied. We carried out the first survey of the microbiomes in Tel Megiddo. Our objectives were to study (i) the unique microbial community structure of the site, (ii) the variation in the microbial communities across areas, (iii) the similarity of the microbiomes to urban and archeological microbes, (iv) the presence and abundance of potential bio-corroding microbes, and (v) the presence and abundance of potentially pathogenic microbes.

METHODS: We collected 40 swab samples from ten major areas and identified microbial taxa using next-generation sequencing of microbial genomes. These genomes were annotated and classified taxonomically and pathogenetically.

RESULTS: We found that eight phyla, six of which exist in all ten areas, dominated the site (>99%). The relative sequence abundance of taxa varied between the ruins and the sampled materials and was assessed using all metagenomic reads mapping to a respective taxon. The site hosted unique taxa characteristic of the built environment and exhibited high similarity to the microbiome of other monuments. We identified acid-producing bacteria that may pose a risk to the site through biocorrosion and staining and thus pose a danger to the site's preservation. Differences in the microbiomes of the publicly accessible or inaccessible areas were insignificant; however, pathogens were more abundant in the former.

DISCUSSION: We found that Tel Megiddo combines microbiomes of arid regions and monuments with human pathogens. The findings shed light on the microbial community structures and have relevance for bio-conservation efforts and visitor health.}, } @article {pmid37808290, year = {2023}, author = {Bailey, NP and Shao, Y and Du, S and Foster, PG and Fettweis, J and Hall, N and Wang, Z and Hirt, RP}, title = {Evolutionary conservation of Trichomonas-mycoplasma symbiosis across the host species barrier.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1242275}, pmid = {37808290}, issn = {1664-302X}, abstract = {INTRODUCTION: The protozoan parasite Trichomonas vaginalis is the most common cellular sexually transmitted disease in humans, and the closely related species Trichomonas gallinae is an avian parasite of ecological and economic importance. Phylogenetic evidence suggests T. vaginalis arose during bird to human transmission of a T. gallinae-like ancestor. Trichomonas vaginalis shares a strong clinical association with the independent sexually transmitted pathogen Metamycoplasma (formerly Mycoplasma) hominis, and the uncultured bacterium "Candidatus Malacoplasma (formerly Mycoplasma) girerdii," with the latter association being an order of magnitude stronger. Both bacterial species have been shown to profoundly influence T. vaginalis growth, energy production and virulence-associated mechanisms.

METHODS: Evidence for a novel Malacoplasma sp. was discovered by in vivo Illumina metatranscriptomics sequencing of the T. gallinae-infected pigeon mouth. We leveraged published 16S rDNA profiling data from digestive tract of 12 healthy and 24 T. gallinae-infected pigeons to investigate association between the novel Malacoplasma sp. and T. gallinae. We utilised Illumina metagenomics sequencing targeted to pigeon oral and crop samples infected with the novel Malacoplasma sp. to generate its full-length genome sequence. Sequence similarity network analysis was used to compare annotated proteins from the novel Malacoplasma sp. with a range of other related species.

RESULTS: Here we present evidence for a novel Malacoplasma species, related to "Ca. M. girerdii," that is strongly associated with T. gallinae in the upper digestive tract of domestic pigeons. Analysis of the genome sequence revealed gene features apparently specific to a Trichomonas-symbiotic Malacoplasma lineage.

DISCUSSION: These data support a model of long-term association between Trichomonas and Malacoplasma spp. that has been conserved across diversification of the Trichomonas lineage and the host species barrier from birds to human.}, } @article {pmid37808286, year = {2023}, author = {Papoutsoglou, G and Tarazona, S and Lopes, MB and Klammsteiner, T and Ibrahimi, E and Eckenberger, J and Novielli, P and Tonda, A and Simeon, A and Shigdel, R and Béreux, S and Vitali, G and Tangaro, S and Lahti, L and Temko, A and Claesson, MJ and Berland, M}, title = {Machine learning approaches in microbiome research: challenges and best practices.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1261889}, pmid = {37808286}, issn = {1664-302X}, abstract = {Microbiome data predictive analysis within a machine learning (ML) workflow presents numerous domain-specific challenges involving preprocessing, feature selection, predictive modeling, performance estimation, model interpretation, and the extraction of biological information from the results. To assist decision-making, we offer a set of recommendations on algorithm selection, pipeline creation and evaluation, stemming from the COST Action ML4Microbiome. We compared the suggested approaches on a multi-cohort shotgun metagenomics dataset of colorectal cancer patients, focusing on their performance in disease diagnosis and biomarker discovery. It is demonstrated that the use of compositional transformations and filtering methods as part of data preprocessing does not always improve the predictive performance of a model. In contrast, the multivariate feature selection, such as the Statistically Equivalent Signatures algorithm, was effective in reducing the classification error. When validated on a separate test dataset, this algorithm in combination with random forest modeling, provided the most accurate performance estimates. Lastly, we showed how linear modeling by logistic regression coupled with visualization techniques such as Individual Conditional Expectation (ICE) plots can yield interpretable results and offer biological insights. These findings are significant for clinicians and non-experts alike in translational applications.}, } @article {pmid37807043, year = {2023}, author = {Hayes, MG and Langille, MGI and Gu, H}, title = {Cross-study analyses of microbial abundance using generalized common factor methods.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {380}, pmid = {37807043}, issn = {1471-2105}, support = {CGS-M Alexander Graham Bell Scholarship//Natural Sciences and Engineering Research Council of Canada/ ; RGPIN/05108-2017//Natural Sciences and Engineering Research Council of Canada/ ; Scotia Scholars Award//Nova Scotia Health Research Foundation/ ; }, mesh = {*Metagenome ; *Microbiota/genetics ; Metagenomics/methods ; Genomics ; Computational Biology/methods ; }, abstract = {BACKGROUND: By creating networks of biochemical pathways, communities of micro-organisms are able to modulate the properties of their environment and even the metabolic processes within their hosts. Next-generation high-throughput sequencing has led to a new frontier in microbial ecology, promising the ability to leverage the microbiome to make crucial advancements in the environmental and biomedical sciences. However, this is challenging, as genomic data are high-dimensional, sparse, and noisy. Much of this noise reflects the exact conditions under which sequencing took place, and is so significant that it limits consensus-based validation of study results.

RESULTS: We propose an ensemble approach for cross-study exploratory analyses of microbial abundance data in which we first estimate the variance-covariance matrix of the underlying abundances from each dataset on the log scale assuming Poisson sampling, and subsequently model these covariances jointly so as to find a shared low-dimensional subspace of the feature space.

CONCLUSIONS: By viewing the projection of the latent true abundances onto this common structure, the variation is pared down to that which is shared among all datasets, and is likely to reflect more generalizable biological signal than can be inferred from individual datasets. We investigate several ways of achieving this, demonstrate that they work well on simulated and real metagenomic data in terms of signal retention and interpretability, and recommend a particular implementation.}, } @article {pmid37806995, year = {2023}, author = {Rick, K and Byrne, M and Cameron, S and Cooper, SJB and Dunlop, J and Hill, B and Lohr, C and Mitchell, NJ and Moritz, C and Travouillon, KJ and von Takach, B and Ottewell, K}, title = {Population genomic diversity and structure in the golden bandicoot: a history of isolation, extirpation, and conservation.}, journal = {Heredity}, volume = {131}, number = {5-6}, pages = {374-386}, pmid = {37806995}, issn = {1365-2540}, mesh = {*Genetics, Population ; *Genetic Variation ; Ecosystem ; Metagenomics ; Genetic Drift ; Conservation of Natural Resources ; }, abstract = {Using genetic information to develop and implement conservation programs is vital for maintaining biodiversity and ecosystem resilience. Evaluation of the genetic variability within and among remnant populations can inform management of both natural and translocated populations to maximise species' adaptive potential, mitigate negative impacts of inbreeding, and subsequently minimise risk of extinction. Here we use reduced representation sequencing to undertake a genetic assessment of the golden bandicoot (Isoodon auratus), a threatened marsupial endemic to Australia. The currently recognised taxon consists of three subspecies distributed among multiple natural and translocated populations. After confirming the genetic distinctiveness of I. auratus from two closely related taxa, I. fusciventer and I. macrourus, we identified four genetic clusters within I. auratus. These clusters exhibited substantial genetic differentiation (pairwise FST values ranging from 0.18 to 0.65, pairwise DXY ranging from 0.1 to 0.168), reflecting long-term isolation of some populations on offshore islands and the influence of genetic drift. Mainland natural populations in the Kimberley region had the highest genetic diversity and the largest contribution to overall allelic and gene diversity compared to both natural and translocated island populations. A population translocated to Guluwuru Island in the Northern Territory had the lowest genetic diversity. Our data suggest that island populations can appear genetically unique due to genetic drift and this needs to be taken into account when considering genetic diversity in conservation efforts to maintain overall genetic diversity of the species. We effectively demonstrate how genomic information can guide practical conservation planning, especially when declining species are represented by multiple isolated populations.}, } @article {pmid37806587, year = {2024}, author = {Lin, X and Liu, Z and Wang, W and Duan, G and Zhu, Y}, title = {Effects of artificial sweetener acesulfame on soil-dwelling earthworms (Eisenia fetida) and its gut microbiota.}, journal = {The Science of the total environment}, volume = {907}, number = {}, pages = {167641}, doi = {10.1016/j.scitotenv.2023.167641}, pmid = {37806587}, issn = {1879-1026}, mesh = {Animals ; Soil ; *Oligochaeta/physiology ; *Gastrointestinal Microbiome ; Sweetening Agents/analysis ; *Soil Pollutants/analysis ; }, abstract = {Artificial sweeteners (AS) are the emerging contaminants with potential toxicity to living organisms. The effects of AS to soil typical invertebrates have not been revealed. In this study, the responses of earthworms (Eisenia fetida) and gut microbial communities to acesulfame-contaminated soils (0.1, 1 and 10 mg kg[-1]) were studied using transcriptomics, metabolomics and metagenomics analyses. The fresh weight of earthworms was significantly stimulated by acesulfame at concentrations of 1 mg kg[-1]. Sphingolipid metabolism, purine metabolism, cutin, suberine and wax biosynthesis pathways were significantly affected. At 10 mg kg[-1] treatment, the amount and weight of cocoons were significantly increased and decreased, respectively, accompanied by the significant disorder of ECM-receptor interaction, and carbon fixation in photosynthetic organisms pathways. Lysosome pathway was significantly affected in all the treatments. Moreover, the acesulfame significantly increased the relative abundance of Bacteroidetes and Mucoromycota, and decreased Proteobacteria in the gut of earthworms. Our multi-level investigation indicated that AS at a relatively low concentration induced toxicity to earthworms and AS pollution has significant environmental risks for soil fauna.}, } @article {pmid37806429, year = {2023}, author = {Yang, S and Wu, J and Wang, H and Yang, Q and Zhang, H and Yang, L and Li, D and Deng, Y and Zhong, Y and Peng, P}, title = {New dechlorination products and mechanisms of tris(2-chloroethyl) phosphate by an anaerobic enrichment culture from a vehicle dismantling site.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {338}, number = {}, pages = {122704}, doi = {10.1016/j.envpol.2023.122704}, pmid = {37806429}, issn = {1873-6424}, mesh = {Anaerobiosis ; RNA, Ribosomal, 16S/genetics ; *Flame Retardants/analysis ; Organophosphates ; Phosphates/analysis ; Esters ; China ; }, abstract = {End-of-life vehicles (ELVs) dismantling sites are the notorious hotspots of chlorinated organophosphate esters (Cl-OPEs). However, the microbial-mediated dechlorination of Cl-OPEs at such sites has not yet been explored. Herein, the dechlorination products, pathways and mechanisms of tris(2-chloroethyl) phosphate (TCEP, a representative Cl-OPE) by an anaerobic enrichment culture (ZNE) from an ELVs dismantling plant were investigated. Our results showed that dechlorination of TCEP can be triggered by reductive transformation to form bis(2-chloroethyl) phosphate (BCEP), mono-chloroethyl phosphate (MCEP) and by hydrolytic dechlorination to form bis(2-chloroethyl) 2-hydroxyethyl phosphate (TCEP-OH), 2-chloroethyl bis(2-hydroxyethyl) phosphate (TCEP-2OH), 2-chloroethyl (2-hydroxyethyl) hydrogen phosphate (BCEP-OH). The combination of 16S rRNA gene amplicon sequencing, quantitative real-time PCR (qPCR) and metagenomics revealed that the Dehalococcoides played an important role in the reductive transformation of TCEP to BCEP and MCEP. A high-quality metagenome-assembled genome (completeness >99% and contamination <1%) of Dehalococcoides was obtained. The sulfate-reducing bacteria harboring haloacid dehalogenase genes (had) may be responsible for the hydrolytic dechlorination of TCEP. These findings provide insights into microbial-mediated anaerobic transformation products and mechanisms of TCEP at ELVs dismantling sites, having implications for the environmental fate and risk assessment of Cl-OPEs at those sites.}, } @article {pmid37806360, year = {2023}, author = {Yang, L and Li, W and Zhu, H and Dong, S and Mu, H and Hu, K and Wang, T and Li, J}, title = {Functions and mechanisms of sponge iron-mediated multiple metabolic processes in anaerobic ammonium oxidation.}, journal = {Bioresource technology}, volume = {390}, number = {}, pages = {129821}, doi = {10.1016/j.biortech.2023.129821}, pmid = {37806360}, issn = {1873-2976}, mesh = {Anaerobiosis ; Oxidation-Reduction ; *Wastewater ; *Ammonium Compounds/metabolism ; Iron ; Bioreactors ; Nitrogen/metabolism ; Denitrification ; Sewage ; }, abstract = {Sponge iron (SI) is a promising material for nitrogen removal from wastewater. This study reveals the potential functions and mechanisms of SI-mediated multiple metabolic processes in the nitrogen removal of Anammox. The results showed that although the SI application prolonged the start-up time of the reactor, achieved efficient and stable nitrogen removal after a successful start-up. The total nitrogen removal efficiency of the SI-Anammox system (92.62%) was 13.30% higher than that of R0 without SI (79.32%). The increase in nitrogen removal performance was accompanied by an increase in SAA and EPS content. Further microbial analysis showed significant enrichment of functional microorganisms, such as Candidatus_Brocadia, Nitrosomonas, Ellin6067, and Nitrospira. Multi-omics evidence suggests that efficient nitrogen removal is ultimately attributable to the enhancement of the specific key Fe- and N-functional genes in Anammox.}, } @article {pmid37806267, year = {2023}, author = {Zhang, X and Usman, S and Bature, I and Xu, D and Guo, X}, title = {Occurrence and fate of antibiotic-resistance genes and their potential hosts in high-moisture alfalfa silage treated with or without formic acid bactericide.}, journal = {Journal of environmental management}, volume = {347}, number = {}, pages = {119235}, doi = {10.1016/j.jenvman.2023.119235}, pmid = {37806267}, issn = {1095-8630}, mesh = {Animals ; *Silage/analysis/microbiology ; *Anti-Bacterial Agents/pharmacology ; Medicago sativa ; Formates/pharmacology ; Fermentation ; }, abstract = {Silage as the main forage for ruminants could be a reservoir for antibiotic resistance genes (ARGs) through which these genes got access into the animals' system causing a latent health risk. This study employed metagenomics and investigated the ARGs' fate and transmission mechanism in high-moisture alfalfa silage treated with formic acid bactericide. The results showed that there were 22 ARGs types, in which multidrug, macrolide-lincosamide-streptogramine, bacitracin, beta-lactam, fosmidomycin, kasugamycin, and polymycin resistance genes were the most prevalent ARGs types in the ensiled alfalfa. The natural ensiling process increased ARGs enrichment. Intriguingly, after 5 days of ensiling, formic acid-treated silage reduced ARGs abundances by inhibiting host bacterial and plasmids. Although formic acid bactericide enhanced the fermentation characteristics of the high-moisture alfalfa by lowering silage pH, butyric acid concentration, dry matter losses and proteolysis, it increased ARGs abundances in alfalfa silage owing to increases in abundances of ARGs carriers and transposase after 90 days of ensiling. Notably, several pathogens like Staphylococcus, Clostridium, and Pseudomonas were inferred as potential ARGs hosts in high-moisture alfalfa silage, and high-moisture alfalfa silage may harbor a portion of the clinical ARGs. Fundamentally, microbes were distinguished as the foremost driving factor of ARGs propagation in ensiling microecosystem. In conclusion, although formic acid bactericide improved the fermentation characteristics of high-moisture alfalfa during ensiling and reduced ARGs enrichment at the initial ensiling stage, it increased ARGs enrichment at the end of ensiling.}, } @article {pmid37805868, year = {2023}, author = {Sahu, S and Shah, S and Supriti, - and Joshi, A and Patel J, D and Yadav, A}, title = {THE GUT-BRAIN AXIS: IMPLICATIONS FOR NEUROLOGICAL DISORDERS, MENTAL HEALTH, AND IMMUNE FUNCTION.}, journal = {Georgian medical news}, volume = {}, number = {340-341}, pages = {17-24}, pmid = {37805868}, issn = {1512-0112}, mesh = {Infant ; Adult ; Infant, Newborn ; Humans ; Brain-Gut Axis ; *Enterocolitis, Necrotizing/microbiology ; Dysbiosis ; Mental Health ; *Neonatal Sepsis ; *Infant, Newborn, Diseases ; *Nervous System Diseases ; Immunity ; }, abstract = {A gut-brain axis (GBA) has a long history of conceptual development. Intestinal dysbiosis has now been recognized as a key player in the development of adult neurodevelopmental disorders, obesity, and inflammatory bowel disease. Recent developments in metagenomics suggest those nutrition and gut microbiotas (GM) are important regulators of the gut-brain communication pathways that cause neurodevelopmental and psychiatric problems in adulthood. Intestinal dysbiosis and neurodevelopmental disease outcomes in preterm newborns are being linked by recent research. Recent clinical investigations demonstrate that in critical care units, intestinal dysbiosis occurs before late-onset newborn sepsis and necrotizing enterocolitis. Strong epidemiologic data also shows a connection between necrotizing enterocolitis and extremely low birth weight babies' long-term psychomotor impairments and late-onset neonatal sepsis. The GBA theory suggests that intestinal bacteria may indirectly affect preterm newborns' developing brains. In this review, we emphasize the structure and function of the GBA and discuss how immune-microbial dysfunction in the gut affects the transmission of stress signals to the brain. Preterm babies who are exposed to these signals develop neurologic disorders. Understanding neuronal and humoral communication through the GBA may provide insight into therapeutic and nutritional strategies that may enhance the results of very low-birth-weight babies.}, } @article {pmid37805557, year = {2023}, author = {Huang, G and Shi, W and Wang, L and Qu, Q and Zuo, Z and Wang, J and Zhao, F and Wei, F}, title = {PandaGUT provides new insights into bacterial diversity, function, and resistome landscapes with implications for conservation.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {221}, pmid = {37805557}, issn = {2049-2618}, mesh = {Animals ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Animals, Wild/microbiology ; Metagenome/genetics ; Bacteria/genetics ; Mammals/genetics ; }, abstract = {BACKGROUND: The gut microbiota play important roles in host adaptation and evolution, but are understudied in natural population of wild mammals. To address host adaptive evolution and improve conservation efforts of threatened mammals from a metagenomic perspective, we established a high-quality gut microbiome catalog of the giant panda (pandaGUT) to resolve the microbiome diversity, functional, and resistome landscapes using approximately 7 Tbp of long- and short-read sequencing data from 439 stool samples.

RESULTS: The pandaGUT catalog comprises 820 metagenome-assembled genomes, including 40 complete closed genomes, and 64.5% of which belong to species that have not been previously reported, greatly expanding the coverage of most prokaryotic lineages. The catalog contains 2.37 million unique genes, with 74.8% possessing complete open read frames, facilitating future mining of microbial functional potential. We identified three microbial enterotypes across wild and captive panda populations characterized by Clostridium, Pseudomonas, and Escherichia, respectively. We found that wild pandas exhibited host genetic-specific microbial structures and functions, suggesting host-gut microbiota phylosymbiosis, while the captive cohorts encoded more multi-drug resistance genes.

CONCLUSIONS: Our study provides largely untapped resources for biochemical and biotechnological applications as well as potential intervention avenues via the rational manipulation of microbial diversity and reducing antibiotic usage for future conservation management of wildlife. Video Abstract.}, } @article {pmid37805087, year = {2023}, author = {Zhang, Y and Yun, J and Zhang, G and Parvez, A and Zhou, L and Zabed, HM and Li, J and Qi, X}, title = {Efficient biosynthesis of 3-hydroxypropionic acid from glucose through multidimensional engineering of Escherichia coli.}, journal = {Bioresource technology}, volume = {389}, number = {}, pages = {129822}, doi = {10.1016/j.biortech.2023.129822}, pmid = {37805087}, issn = {1873-2976}, mesh = {Escherichia coli/genetics/metabolism ; Glycerol/metabolism ; Glucose/metabolism ; Metabolic Engineering/methods ; *Aquaporins/metabolism ; *Escherichia coli Proteins ; }, abstract = {3-Hydroxypropionic acid (3-HP) is a top value-added chemical with multifaceted application in chemical, material, and food field. However, limited availability of robust strains and elevated fermentation costs currently impose constraints on sustainable biosynthesis of 3-HP. Herein, transporter engineering, metabolic dynamic modulation, and enzyme engineering were combined to address above limitations. First, a glucose-utilizing 3-HP biosynthetic pathway was constructed in Escherichia coli, followed by recruiting alternative glucose transport system to overcome center metabolism overflow. Next, the Cra (a transcription factor)-dependent switch was applied to autonomously fine-tune carbon flux, which alleviated growth retardation and improved the 3-HP production. Subsequently, inactivation of glycerol facilitator (GlpF) increased intracellular glycerol levels and boosted 3-HP biosynthesis, but caused toxic intermediate 3-hydroxypropionaldehyde (3-HPA) accumulation. Furthermore, semi-rational design of aldehyde dehydrogenase (YdcW) increased its activity and eliminated 3-HPA accumulation. Finally, fed-batch fermentation of the final strain resulted in 52.73 g/L 3-HP, with a yield of 0.59 mol/mol glucose.}, } @article {pmid37804990, year = {2024}, author = {Wang, J and Xu, X and Liu, Y and Wang, W and Ren, C and Guo, Y and Wang, J and Wang, N and He, L and Zhao, F}, title = {Unknown bacterial species lead to soil CO2 emission reduction by promoting lactic fermentation in alpine meadow on the Qinghai-Tibetan Plateau.}, journal = {The Science of the total environment}, volume = {906}, number = {}, pages = {167610}, doi = {10.1016/j.scitotenv.2023.167610}, pmid = {37804990}, issn = {1879-1026}, mesh = {Tibet ; *Grassland ; *Carbon Dioxide ; Fermentation ; Soil ; }, abstract = {Highly variable soil microbial respiration among grasslands has been identified as a major cause of uncertainty in regional carbon (C) budget estimation in the Qinghai-Tibetan Plateau; microbial metabolism mechanisms might explain this variation, but remain elusive. Therefore, we investigated soil CO2 production in incubated soils and detected the associated functional genes at four sampling sites from two major alpine grasslands on the Qinghai-Tibetan Plateau. The results showed that the cumulative CO2 emissions from alpine meadow soils were 71 %-83 % lower than those from alpine steppe soils. Both the enriched genes abundance encoding fermentation and glycolysis (Embden-Meyerhof pathway (EMP)) and the diminished genes encoding tricarboxylic acid cycle (TCA) and phosphate pentose pathway (PPP) explained the CO2 emission reduction in the alpine meadow soils. The EMP: PPP and fermentation: TCA cycle ratios in alpine meadow soils were 1.45- and 1.50-fold higher than those in alpine steppe soils, respectively. Such shifts in metabolic pathways were primarily caused by the increasing dominance of an unknown species of Desulfobacteraceae with high glycolytic potential, carrying a higher abundance of ldh genes during fermentation. These unknown species were promoted by warmer temperatures and higher precipitation in the alpine meadows. Further studies on the unknown species would enhance our understanding and predictability of C cycling in alpine grasslands.}, } @article {pmid37804763, year = {2024}, author = {Xu, C and Hu, C and Lu, J and Yang, T and Shen, C and Li, F and Wang, J}, title = {Lake plastisphere as a new biotope in the Anthropocene: Potential pathogen colonization and distinct microbial functionality.}, journal = {Journal of hazardous materials}, volume = {461}, number = {}, pages = {132693}, doi = {10.1016/j.jhazmat.2023.132693}, pmid = {37804763}, issn = {1873-3336}, mesh = {*Lakes/microbiology ; Plastics ; Nitrification ; *Microbiota ; Sulfur/metabolism ; }, abstract = {The not-homogenous microplastics (MPs) distribution in freshwaters results in distinct microbial communities. Yet knowledge regarding plastisphere in metabolic pathways and element cycling behaviors remains limited. In this study, we collected MPs from 15 sampling sites in the Taihu Lake in China, and found that MPs were widely distributed in this freshwater lake, and dominantly composed of fibrous polyethylene terephthalate. Based on the metagenomic analysis, we found that MPs were colonized by Bacteroidia, Alpha-Proteobacteria, and Bacilli as a filter, but depleted in Verrucomicrobiae. Potential pathogens of plant eudicots and monocots were significantly enriched in plastisphere. Predicted functional profiles involved in the metabolism of other amino acids, biosynthesis of other secondary metabolites, and glycan biosynthesis and metabolism were overrepresented in plastisphere. Regarding elemental cycling, functional genes related to nitrogen fixation and nitrification showed 39.6% and 67.5% decline in plastisphere, whereas the genes involved in denitrification and nitrate reduction were significantly enriched. For sulfur cycles, the plastisphere exhibited higher sulfate reduction and sulfur oxidation system activities. Additionally, the taxonomic compositions and predicted functions in the plastispheres were mainly driven by the stochastic processes, while the deterministic processes were more important for the planktonic communities. The distinctions in the microbial composition, the predicted functionality, and the underly mechanisms between plastisphere and planktonic communities illustrated the unique ecology of the new anthropogenic-related plastisphere ecosystems.}, } @article {pmid37804571, year = {2023}, author = {Matthijnssens, J and Adriaenssens, E}, title = {Editorial overview: The virome in health and disease (2022).}, journal = {Current opinion in virology}, volume = {63}, number = {}, pages = {101376}, doi = {10.1016/j.coviro.2023.101376}, pmid = {37804571}, issn = {1879-6265}, } @article {pmid37804481, year = {2023}, author = {Regueira-Iglesias, A and Balsa-Castro, C and Blanco-Pintos, T and Tomás, I}, title = {Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis.}, journal = {Molecular oral microbiology}, volume = {38}, number = {5}, pages = {347-399}, doi = {10.1111/omi.12434}, pmid = {37804481}, issn = {2041-1014}, support = {PI21/00588//Instituto de Salud Carlos III (ISCIII) and co-funded by the European Union/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; Phylogeny ; Workflow ; *High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; }, abstract = {The multi-batch reanalysis approach of jointly reevaluating gene/genome sequences from different works has gained particular relevance in the literature in recent years. The large amount of 16S ribosomal ribonucleic acid (rRNA) gene sequence data stored in public repositories and information in taxonomic databases of the same gene far exceeds that related to complete genomes. This review is intended to guide researchers new to studying microbiota, particularly the oral microbiota, using 16S rRNA gene sequencing and those who want to expand and update their knowledge to optimise their decision-making and improve their research results. First, we describe the advantages and disadvantages of using the 16S rRNA gene as a phylogenetic marker and the latest findings on the impact of primer pair selection on diversity and taxonomic assignment outcomes in oral microbiome studies. Strategies for primer selection based on these results are introduced. Second, we identified the key factors to consider in selecting the sequencing technology and platform. The process and particularities of the main steps for processing 16S rRNA gene-derived data are described in detail to enable researchers to choose the most appropriate bioinformatics pipeline and analysis methods based on the available evidence. We then produce an overview of the different types of advanced analyses, both the most widely used in the literature and the most recent approaches. Several indices, metrics and software for studying microbial communities are included, highlighting their advantages and disadvantages. Considering the principles of clinical metagenomics, we conclude that future research should focus on rigorous analytical approaches, such as developing predictive models to identify microbiome-based biomarkers to classify health and disease states. Finally, we address the batch effect concept and the microbiome-specific methods for accounting for or correcting them.}, } @article {pmid37803833, year = {2023}, author = {, }, title = {[Chinese expert consensus on the application of metagenomic next-generation sequencing technology in the diagnosis of pathogens in hematological patients (2023)].}, journal = {Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi}, volume = {44}, number = {8}, pages = {617-623}, pmid = {37803833}, issn = {0253-2727}, mesh = {Humans ; Consensus ; *High-Throughput Nucleotide Sequencing ; Sensitivity and Specificity ; *Hematologic Diseases ; *Infections/diagnosis ; China ; }, } @article {pmid37803772, year = {2023}, author = {You, L and Lv, R and Jin, H and Ma, T and Zhao, Z and Kwok, LY and Sun, Z}, title = {A large-scale comparative genomics study reveals niche-driven and within-sample intra-species functional diversification in Lacticaseibacillus rhamnosus.}, journal = {Food research international (Ottawa, Ont.)}, volume = {173}, number = {Pt 2}, pages = {113446}, doi = {10.1016/j.foodres.2023.113446}, pmid = {37803772}, issn = {1873-7145}, mesh = {*Lacticaseibacillus rhamnosus/genetics ; Genome, Bacterial/genetics ; Lacticaseibacillus ; Phylogeny ; Genomics/methods ; Phosphorylases/genetics ; }, abstract = {Lacticaseibacillus rhamnosus (L. rhamnosus) is widely recognized as a probiotic species, and it exists in a variety of environments including host gut and dairy products. This work aimed at conducting a large-scale comparative genomics analysis of 384 L. rhamnosus genomes (257 whole-sequence or metagenomic-assembled genomes from gut-associated isolates [122 and 135 retrieved from the UHGG and NCBI databases, respectively] and 127 genomes from dairy isolates [34 from the NCBI database; 93 isolated from a cheese sample and sequenced here]). Our results showed that L. rhamnosus had a large and open pan-genome (15,253 pan-genes identified from all 384 genomes; 15,028 pan-genes if the 93 cheese-originated isolates were excluded). The core-gene phylogenetic tree constructed from the 384 L. rhamnosus genomes comprised five phylogenetic branches, with a random distribution of dairy and gut-associated isolates/genomes across the tree. No significant difference was identified in the overall profile of metabolism-related genes between dairy and gut-associated genomes; however, notably, the gut-associated strains/isolates contained more genes coding for specific metabolic pathways and carbohydrate-active enzymes, e.g., lacto-N-biosidase (EC 3.2.1.140; GT20) and lacto-N-biose phosphorylase/galacto-N-biose phosphorylase (EC 2.4.1.211; GH112). Further, we found that there was obvious intra-species diversification of the 93 cheese-originated L. rhamnosus isolates, forming three clades (Clades A, B, and C) in the reconstructed core-gene phylogenetic tree. There were numerous single nucleotide variations (over 10,000) across the three clades. Moreover, significant differences were observed in the content of metabolism-related genes across clades (p < 0.05, Adonis test), characterized by the enrichment in glycoside hydrolases in Clade C and the possession of unique metabolic pathways in each clade. These results implicated genomics/functional diversification of L. rhamnosus in a single food matrix and niche-driven adaptive evolution of isolates from dairy and host gut-associated origins. Our study shed insights into the selection of candidate strains for food industry applications.}, } @article {pmid37803768, year = {2023}, author = {Alvarez-Molina, A and Cobo-Díaz, JF and Alexa, EA and Crispie, F and Prieto, M and López, M and Cotter, PD and Alvarez-Ordóñez, A}, title = {Sequencing-based analysis of the microbiomes of Spanish food processing facilities reveals environment-specific variation in the dominant taxa and antibiotic resistance genes.}, journal = {Food research international (Ottawa, Ont.)}, volume = {173}, number = {Pt 2}, pages = {113442}, doi = {10.1016/j.foodres.2023.113442}, pmid = {37803768}, issn = {1873-7145}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Microbiota/genetics ; Drug Resistance, Microbial/genetics ; Bacteria ; Aminoglycosides ; Food Handling ; Tetracyclines ; }, abstract = {In the last years, advances in high throughput sequencing technologies have opened the possibility to broaden environmental monitoring activities in facilities processing food, offering expanded opportunities for characterizing in an untargeted manner the microbiome and resistome of foods and food processing environments (FPE) with huge potential benefits in food safety management systems. Here the microbiome and resistome of FPE from slaughterhouses (n = 3), dairy (n = 12) and meat (n = 10) processing plants were assessed through whole metagenome sequencing of 2 composite samples for each facility, comprising 10 FPE swabs taken from food contact surfaces and 10 FPE samples from non-food contact surfaces, respectively. FPE from slaughterhouses had more diverse microbiomes and resistomes, while FPE from dairy processing plants showed the highest β-dispersion, consistent with a more heterogeneous microbiome and resistome composition. The predominant bacterial genera depended on the industry type, with Pseudomonas and Psychrobacter being highly dominant in surfaces from slaughterhouses and meat industries, while different lactic acid bacteria predominated in dairy industries. The most abundant antimicrobial resistance genes (ARG) found were associated with resistance to aminoglycosides, tetracyclines and quaternary ammonium compounds (QAC). ARGs relating to resistance to aminoglycosides and tetracyclines were significantly more prevalent in slaughterhouses than in food processing plants, while QAC resistance genes were particularly abundant in some food contact surfaces from dairy and meat processing plants, suggesting that daily sanitation under suboptimal conditions may be selecting for persistent microbiota tolerant to these biocides in some facilities. The taxonomic mapping of ARG pointed to specific bacterial genera, such as Escherichia, Bacillus, or Staphylococcus, as carriers of the most relevant resistance determinants. About 63% of all ARG reads were assigned to contigs classified as plasmid-associated, indicating that the resistome of FPE may be strongly shaped through the spread of mobile genetic elements. Overall, the relevance of FPE as reservoirs of ARG was confirmed and it was demonstrated that next generation sequencing technologies allowing a deep characterisation of sources and routes of spread of microorganisms and antimicrobial resistance determinants in food industry settings hold promise to be integrated in monitoring and food safety management programmes.}, } @article {pmid37803714, year = {2023}, author = {Li, Q and Wang, H and Xu, R and Su, Y and Zhu, W}, title = {Dynamic analysis of metabolomics reveals the potential associations between colonic peptides and serum appetite-related hormones.}, journal = {Food research international (Ottawa, Ont.)}, volume = {173}, number = {Pt 2}, pages = {113376}, doi = {10.1016/j.foodres.2023.113376}, pmid = {37803714}, issn = {1873-7145}, mesh = {Animals ; Swine ; *Appetite ; *Amino Acids ; Glucagon-Like Peptide 1 ; Peptides ; Lipids ; }, abstract = {Gut signals, including hormones and metabolites are crucial zeitgebers that regulate the circadian rhythm of host metabolism, but the potential links have been explored more in rodents. Herein, we performed an hour-scale metabolomics analysis of serum and colonic digesta to characterize the circadian rhythmic metabolic patterns using a pig model under ad libitum feeding conditions. Importantly, our findings identified potential associations between colonic and body metabolism, revealing the potential relationships between colonic peptides and host appetite regulation. Concretely, amino acids accounted for the highest proportion in rhythmic serum metabolites, whereas lipids accounted for the highest proportion in rhythmic colonic metabolites. The diurnal difference analysis revealed that the levels of most amino acids and peptides were higher in the light phase, while the levels of most lipids were higher in the dark phase. And more correlations were be checked between serum amino acids, lipids, peptides and colonic metabolites in the light and more correlations were be checked between serum carbohydrates, cofactors and vitamins, energy, nucleotides, xenobiotics and colonic metabolites in the dark. Interestingly, peptides oscillated to a similar extent in serum and colonic digesta. Of note, colonic peptides composed of valine, proline and leucine were checked in positive associations to glucagon-like peptide-1 (GLP-1) in serum. And these peptides were positive with the genera Butyricicoccus, Streptococcus, Clostridioides, Bariatricus and Coriobacteriia_norank, and negative with Prevotella, and showed the potential relationships with colonic microbial biosynthesis of amino acids. Collectively, we mapped the rhythmic profiling on pig serum and colonic metabolites and revealed the relationships between host and gut metabolism. However, the underlying regulatory mechanisms remains to be further investigated.}, } @article {pmid37803564, year = {2023}, author = {Liu, Y and Yu, L and Tian, F and Chen, W and Zhai, Q}, title = {Meta-analysis of microbiomes reveals metagenomic features of fermented vegetables.}, journal = {Food research international (Ottawa, Ont.)}, volume = {173}, number = {Pt 1}, pages = {113248}, doi = {10.1016/j.foodres.2023.113248}, pmid = {37803564}, issn = {1873-7145}, mesh = {Metagenome ; Vegetables/genetics ; *Microbiota/genetics ; *Lactobacillales/genetics ; Drug Resistance, Microbial ; }, abstract = {An insightful exploration of the fermented vegetable microbiome is the key to improving food quality and sustainability. Based on 57 fermented vegetable samples from China, Ireland, the UK, and Germany retrieved from public genome databases, we conducted a high-resolution meta-analysis of the fermented vegetable microbiomes. There were significant differences in the microbiota composition and functional pathway diversity of the tested samples, as reflected by the differences in their geographical origins. Metagenomic analysis also revealed the metagenomic features of carbohydrate-active enzymes and antibiotic resistance genes in the fermented vegetable metagenomes. Five putative new species were detected by recovering 221 metagenome-assembled genomes belonging to the genera Rubrobacteraceae, Bifidobacteriaceae, and Ruminococcaceae. Our results provide new ecological insights into the implications of fermented vegetable microbiota composition and functional potential and highlight the importance of high-resolution metagenomic analysis to further investigate the fermented food microbiome.}, } @article {pmid37803284, year = {2023}, author = {Chen, Z and Xiao, Y and Jia, Y and Lin, Q and Qian, Y and Cui, L and Xiang, Z and Li, M and Yang, C and Zou, H}, title = {Metagenomic analysis of microbiological changes on the ocular surface of diabetic children and adolescents with a dry eye.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {286}, pmid = {37803284}, issn = {1471-2180}, mesh = {Humans ; Adolescent ; Child ; Metagenome ; China ; *Dry Eye Syndromes ; *Diabetes Mellitus/genetics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Microbiome changes on the ocular surface may cause dry eyes. A metagenome assay was used to compare the microbiome composition and function of the ocular surface between diabetic children and adolescents with dry eye, diabetic children and adolescents without dry eye, and normal children.

MATERIALS AND METHODS: Twenty children and adolescents aged 8 to 16 with diabetes were selected from the Shanghai Children and Adolescent Diabetes Eye Study. Ten healthy children and adolescents belonging to the same age group were selected from the outpatient clinic during the same period. The participants were classified into the dry eye group (DM-DE group, n = 10), the non-dry eye group (DM-NDE group, n = 10) and the normal group (NDM group, n = 10). A conjunctival sac swab was collected for metagenomic sequencing, and the relationship between the microbiome composition and functional gene differences on the ocular surface with dry eye was studied.

RESULTS: The classification composition and metabolic function of the microorganisms on the ocular surface of children in the 3 groups were analyzed. It was found that children's ocular microbiota was composed of bacteria, viruses and fungi. There were significant differences in α diversity and β diversity of microbial composition of ocular surface between DM-DE group and NDM group(P<0.05). There were significant differences in α and β diversity of metabolic pathways between the two groups(P<0.05). The functional pathways of ocular surface microorganisms in diabetic children with dry eyes were mainly derived from human disease, antibiotic resistance genes, carbohydrate, coenzyme and lipid transport and metabolism-related functional genes; In normal children, the functional pathways were mainly derived from replication, recombination, repair, signal transduction and defense-related functional genes.

CONCLUSION: The DM-DE group have unique microbial composition and functional metabolic pathways. The dominant species and unique metabolic pathways of the ocular surface in the DM-DE group may be involved in the pathogenesis of dry eye in diabetic children.}, } @article {pmid37802989, year = {2023}, author = {Du, Y and Sun, F}, title = {MetaCC allows scalable and integrative analyses of both long-read and short-read metagenomic Hi-C data.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {6231}, pmid = {37802989}, issn = {2041-1723}, mesh = {Animals ; Sheep ; *Algorithms ; Sequence Analysis, DNA/methods ; *Metagenome/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; }, abstract = {Metagenomic Hi-C (metaHi-C) can identify contig-to-contig relationships with respect to their proximity within the same physical cell. Shotgun libraries in metaHi-C experiments can be constructed by next-generation sequencing (short-read metaHi-C) or more recent third-generation sequencing (long-read metaHi-C). However, all existing metaHi-C analysis methods are developed and benchmarked on short-read metaHi-C datasets and there exists much room for improvement in terms of more scalable and stable analyses, especially for long-read metaHi-C data. Here we report MetaCC, an efficient and integrative framework for analyzing both short-read and long-read metaHi-C datasets. MetaCC outperforms existing methods on normalization and binning. In particular, the MetaCC normalization module, named NormCC, is more than 3000 times faster than the current state-of-the-art method HiCzin on a complex wastewater dataset. When applied to one sheep gut long-read metaHi-C dataset, MetaCC binning module can retrieve 709 high-quality genomes with the largest species diversity using one single sample, including an expansion of five uncultured members from the order Erysipelotrichales, and is the only binner that can recover the genome of one important species Bacteroides vulgatus. Further plasmid analyses reveal that MetaCC binning is able to capture multi-copy plasmids.}, } @article {pmid37802717, year = {2023}, author = {Ellison, JS and Atkinson, SN and Hayward, M and Hokanson, E and Sheridan, KR and Salzman, N}, title = {The intestinal microbiome of children with initial and recurrent nephrolithiasis: A pilot study and exploratory analysis.}, journal = {Journal of pediatric urology}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jpurol.2023.09.015}, pmid = {37802717}, issn = {1873-4898}, abstract = {INTRODUCTION: Kidney stone disease in children is rising disproportionate to the general population, representing a disease population with a distinct biological mechanism as compared to adults. Factors influencing recurrent kidney stone disease in children are poorly characterized and the associations of the intestinal microbiome within sub-populations of kidney stone formers, however, are not well described. We evaluated a pilot cohort of children with nephrolithiasis comparing patients based on recurrent kidney stone episodes and abnormal 24-h urinary parameters, with dual aims to compare the microbiome signal in children with initial and recurrent nephrolithiasis and to explore additional associations in microbiome composition and diversity within this population.

METHODS: Children aged 6-18 with a history of nephrolithiasis, without an active ureteral calculus or antibiotic exposure within 30 days of study entry were eligible to participate. All participants had a 24-h urine study within 6 months of study entry and provided a fecal sample. Microbiome samples were analyzed using 16S ribosomal DNA sequencing techniques for alpha and beta diversity comparing initial and recurrent stone formers as well as microbiome multivariate association (MaAsLin2) to determine differentially abundant taxa. Shotgun sequencing reads were aligned to custom oxidase degradation and butyrate production gene databases (5 databases total). Comparisons for MaAsLin2 and shotgun metagenomics, normalized to sequencing depth, were based on stone recurrence, sex, hypercalcuria (≤4 mg/kg/day), hyperoxaluria (≥45 mg/1.73 m[2]), and hypocitraturia (<310 mg/1.73 m[2] [females] or < 365 mg/1.73 m[2] [males]).

RESULTS: A total of 16 enrolled children provided samples sufficient for analyses, including 9 girls and 7 boys, of whom 5 had experienced recurrent kidney stone events. Three participants had hypercalcuria, 2 had hyperoxaluria, and 4 had hypocitraturia. Comparisons of Formyl-CoA transferase between index and recurrent urinary stone disease revealed a trend towards higher mean abundance of the gene in initial stone formers (0.166% vs 0.0343%, p = 0.2847) (Summary Figure), while trends toward lower biodiversity were also noted in the recurrent stone cohort on both Faith (p = 0.06) and Shannon (p = 0.05) indices. Exploratory analyses found Eubacterium siraeum to be significantly greater in relative abundance in children with documented hypercalciuria (p = 0.001).

DISCUSSION: Our pilot study demonstrates possible signals in both microbial diversity and oxalate gene expression, both of which are lower in recurrent pediatric kidney stone patients. These findings warrant further investigation as a potential diagnostic marker for future kidney stone events.}, } @article {pmid37802272, year = {2023}, author = {Jangi, S and Hsia, K and Zhao, N and Kumamoto, CA and Friedman, S and Singh, S and Michaud, DS}, title = {Dynamics of the Gut Mycobiome in Patients With Ulcerative Colitis.}, journal = {Clinical gastroenterology and hepatology : the official clinical practice journal of the American Gastroenterological Association}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.cgh.2023.09.023}, pmid = {37802272}, issn = {1542-7714}, abstract = {BACKGROUND & AIMS: Intestinal fungi have been implicated in the pathogenesis of ulcerative colitis (UC). However, it remains unclear if fungal composition is altered during active versus quiescent disease.

METHODS: We analyzed clinical and metagenomic data from the Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease (SPARC IBD), available via the IBD Plexus Program of the Crohn's & Colitis Foundation. We evaluated the fungal composition of fecal samples from 421 patients with UC during clinical activity and remission. Within a longitudinal subcohort (n = 52), we assessed for dynamic taxonomic changes across alterations in clinical activity over time. We examined if fungal amplicon sequence variants and fungal-bacterial relationships were altered during activity versus remission. Finally, we classified activity in UC using a supervised machine learning random forest model trained on fungal abundance data.

RESULTS: During clinical activity, the relative abundance of genus Candida was increased 3.5-fold (P-adj < 1 × 10[-4]) compared with during remission. Patients with longitudinal reductions in clinical activity demonstrated parallel reductions in Candida relative abundance (P < .05). Candida relative abundance correlated with Parabacteroides diastonis, Faecalibacterium prausnitzii, and Bacteroides dorei relative abundance (P < .05) during remission; however, these correlations were disrupted during activity. Fungal abundance data successfully classified patients with active or quiescent UC (area under the curve ∼0.80), with Candida relative abundance critical to the success of the model.

CONCLUSIONS: Clinical activity in UC is associated with an increased relative abundance of Candida, cross-sectionally and dynamically over time. The role of fecal Candida as a target for therapeutics in UC should be evaluated.}, } @article {pmid37801779, year = {2023}, author = {Floridia, V and Russo, N and D'Alessandro, E and Lopreiato, V and Pino, A and Amato, A and Liotta, L and Caggia, C and Randazzo, CL}, title = {Effect of olive cake supplementation on faecal microbiota profile of Holstein and Modicana dairy cattle.}, journal = {Microbiological research}, volume = {277}, number = {}, pages = {127510}, doi = {10.1016/j.micres.2023.127510}, pmid = {37801779}, issn = {1618-0623}, mesh = {Female ; Cattle ; Animals ; *Olea ; Milk ; Diet/veterinary ; Dietary Supplements ; *Microbiota ; Animal Feed ; }, abstract = {The present study aimed to investigate the effect of olive cake supplementation on faecal microbiota of Holstein (n = 16) and Modicana (n = 16) dairy cows. Although no difference in richness was detected, within breeds and between the two dietary treatment, the PERMANOVA analysis applied to the beta diversity allowed to discriminate samples according to breeds (p < 0.001) and treatment (p < 0.001). In Holstein cows, the olive cake supplementation led to the increase of Pseudobutyrivibrio and Christensenellaceae_R7-group genera (p < 0.05) recognized as health-promoting or associated with feed efficiency. Differently, no difference was detected between control and treated groups for Modicana suggesting a high adaptive capacity to diet changes. In addition, the higher prevalence of Firmicutes phyla in the Modicana microbiota reflected its better capacity to digest the fibrous sources. Our study supports the suitability of olive cake as a feed supplement for cows and could help validating a sustainable livestock system in the Mediterranean area, characterized by a relevant oil production and by a native breeds reared with extensive systems.}, } @article {pmid37801397, year = {2023}, author = {Jenks, JD and White, PL and Kidd, SE and Goshia, T and Fraley, SI and Hoenigl, M and Thompson, GR}, title = {An update on current and novel molecular diagnostics for the diagnosis of invasive fungal infections.}, journal = {Expert review of molecular diagnostics}, volume = {23}, number = {12}, pages = {1135-1152}, doi = {10.1080/14737159.2023.2267977}, pmid = {37801397}, issn = {1744-8352}, mesh = {Humans ; Antifungal Agents/therapeutic use ; *Mycoses/diagnosis/microbiology ; Pathology, Molecular ; Fungi/genetics ; *Invasive Fungal Infections/diagnosis ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Invasive fungal infections cause millions of infections annually, but diagnosis remains challenging. There is an increased need for low-cost, easy to use, highly sensitive and specific molecular assays that can differentiate between colonized and pathogenic organisms from different clinical specimens.

AREAS COVERED: We reviewed the literature evaluating the current state of molecular diagnostics for invasive fungal infections, focusing on current and novel molecular tests such as polymerase chain reaction (PCR), digital PCR, high-resolution melt (HRM), and metagenomics/next generation sequencing (mNGS).

EXPERT OPINION: PCR is highly sensitive and specific, although performance can be impacted by prior/concurrent antifungal use. PCR assays can identify mutations associated with antifungal resistance, non-Aspergillus mold infections, and infections from endemic fungi. HRM is a rapid and highly sensitive diagnostic modality that can identify a wide range of fungal pathogens, including down to the species level, but multiplex assays are limited and HRM is currently unavailable in most healthcare settings, although universal HRM is working to overcome this limitation. mNGS offers a promising approach for rapid and hypothesis-free diagnosis of a wide range of fungal pathogens, although some drawbacks include limited access, variable performance across platforms, the expertise and costs associated with this method, and long turnaround times in real-world settings.}, } @article {pmid37801152, year = {2023}, author = {Onohuean, H and Nwodo, UU}, title = {Polymorphism and mutational diversity of virulence (vcgCPI/vcgCPE) and resistance determinants (aac(3)-IIa, (aacC2, strA, Sul 1, and 11) among human pathogenic Vibrio species recovered from surface waters in South-Western districts of Uganda.}, journal = {Journal, genetic engineering & biotechnology}, volume = {21}, number = {1}, pages = {94}, pmid = {37801152}, issn = {2090-5920}, abstract = {BACKGROUND: Vibrio species are among the autochthonous bacterial populations found in surface waters and associated with various life-threatening extraintestinal diseases, especially in human populations with underlying illnesses and wound infections. Presently, very diminutive information exists regarding these species' mutational diversity of virulence and resistance genes. This study evaluated variations in endonucleases and mutational diversity of the virulence and resistance genes of Vibrio isolates, harboring virulence-correlated gene (vcgCPI), dihydropteroate synthase type 1 and type II genes (Sul 1 and 11), (aadA) aminoglycoside (3'') (9) adenylyltransferase gene, (aac(3)-IIa, (aacC2)a, aminoglycoside N(3)-acetyltransferase III, and (strA) aminoglycoside 3'-phosphotransferase resistance genes.

METHODS: Using combinations of molecular biology techniques, bioinformatics tools, and sequence analysis.

RESULTS: Our result revealed various nucleotide variations in virulence determinants of V. vulnificus (vcgCPI) at nucleotide positions (codon) 73-75 (A → G) and 300-302 (N → S). The aminoglycosides resistance gene (aadA) of Vibrio species depicts a nucleotide difference at position 482 (A → G), while the aminoglycosides resistance gene (sul 1 and 11) showed two variable regions of nucleotide polymorphism (102 and 140). The amino acid differences exist with the nucleotide polymorphism at position 140 (A → E). The banding patterns produced by the restriction enzymes HinP1I, MwoI, and StyD4I showed significant variations. Also, the restriction enzyme digestion of protein dihydropteroate synthase type 1 and type II genes (Sul 1 and 11) differed significantly, while enzymes DpnI and Hinf1 indicate no significant differences. The restriction enzyme NlaIV showed no band compared to reference isolates from the GenBank. However, the resistant determinants show significant point nucleotide mutation, which does not produce any amino acid change with diverse polymorphic regions, as revealed in the restriction digest profile.

CONCLUSION: The described virulence and resistance determinants possess specific polymorphic locus relevant to pathogenomics studies, pharmacogenomic, and control of such water-associated strains.}, } @article {pmid37800932, year = {2023}, author = {Viljoen, N and Ismail, A and Weyer, J and Markotter, W}, title = {A rabies-related lyssavirus from a Nycticeinops schlieffeni bat with neurological signs, South Africa.}, journal = {Microbiology resource announcements}, volume = {12}, number = {11}, pages = {e0062123}, pmid = {37800932}, issn = {2576-098X}, support = {98339//National Research Foundation (NRF)/ ; //National Institute for Communicable Diseases, South Africa/ ; //University of Pretoria, South Africa/ ; }, abstract = {We report the coding-complete sequence of a lyssavirus, provisionally designated Phala bat lyssavirus (PBLV), characterized using a metagenomics approach. PBLV was identified in a Nycticeinops schlieffeni bat that exhibited neurological signs and died within 24 hours of admission to a wildlife rehabilitation center in Phalaborwa, South Africa.}, } @article {pmid37799600, year = {2023}, author = {Balbay, MG and Shlafstein, MD and Cockell, C and Cady, SL and Prescott, RD and Lim, DSS and Chain, PSG and Donachie, SP and Decho, AW and Saw, JH}, title = {Metabolic versatility of Caldarchaeales from geothermal features of Hawai'i and Chile as revealed by five metagenome-assembled genomes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1216591}, pmid = {37799600}, issn = {1664-302X}, abstract = {Members of the archaeal order Caldarchaeales (previously the phylum Aigarchaeota) are poorly sampled and are represented in public databases by relatively few genomes. Additional representative genomes will help resolve their placement among all known members of Archaea and provide insights into their roles in the environment. In this study, we analyzed 16S rRNA gene amplicons belonging to the Caldarchaeales that are available in public databases, which demonstrated that archaea of the order Caldarchaeales are diverse, widespread, and most abundant in geothermal habitats. We also constructed five metagenome-assembled genomes (MAGs) of Caldarchaeales from two geothermal features to investigate their metabolic potential and phylogenomic position in the domain Archaea. Two of the MAGs were assembled from microbial community DNA extracted from fumarolic lava rocks from Mauna Ulu, Hawai'i, and three were assembled from DNA obtained from hot spring sinters from the El Tatio geothermal field in Chile. MAGs from Hawai'i are high quality bins with completeness >95% and contamination <1%, and one likely belongs to a novel species in a new genus recently discovered at a submarine volcano off New Zealand. MAGs from Chile have lower completeness levels ranging from 27 to 70%. Gene content of the MAGs revealed that these members of Caldarchaeales are likely metabolically versatile and exhibit the potential for both chemoorganotrophic and chemolithotrophic lifestyles. The wide array of metabolic capabilities exhibited by these members of Caldarchaeales might help them thrive under diverse harsh environmental conditions. All the MAGs except one from Chile harbor putative prophage regions encoding several auxiliary metabolic genes (AMGs) that may confer a fitness advantage on their Caldarchaeales hosts by increasing their metabolic potential and make them better adapted to new environmental conditions. Phylogenomic analysis of the five MAGs and over 3,000 representative archaeal genomes showed the order Caldarchaeales forms a monophyletic group that is sister to the clade comprising the orders Geothermarchaeales (previously Candidatus Geothermarchaeota), Conexivisphaerales and Nitrososphaerales (formerly known as Thaumarchaeota), supporting the status of Caldarchaeales members as a clade distinct from the Thaumarchaeota.}, } @article {pmid37799597, year = {2023}, author = {Ren, H and Zhang, F and Zhu, X and Lamlom, SF and Zhao, K and Zhang, B and Wang, J}, title = {Manipulating rhizosphere microorganisms to improve crop yield in saline-alkali soil: a study on soybean growth and development.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1233351}, pmid = {37799597}, issn = {1664-302X}, abstract = {INTRODUCTION: Rhizosphere microorganisms can effectively promote the stress resistance of plants, and some beneficial rhizosphere microorganisms can significantly promote the growth of crops under salt stress, which has the potential to develop special microbial fertilizers for increasing the yield of saline-alkali land and provides a low-cost and environmentally friendly new strategy for improving the crop yield of saline-alkali cultivated land by using agricultural microbial technology.

METHODS: In May 2022, a field study in a completely randomized block design was conducted at the Heilongjiang Academy of Agricultural Sciences to explore the correlation between plant rhizosphere microorganisms and soybean growth in saline-alkali soil. Two soybean cultivars (Hening 531, a salt-tolerant variety, and 20_1846, a salt-sensitive variety) were planted at two experimental sites [Daqing (normal condition) and Harbin (saline-alkali conditions)], aiming to investigate the performance of soybean in saline-alkali environments.

RESULTS: Soybeans grown in saline-alkali soil showed substantial reductions in key traits: plant height (25%), pod number (26.6%), seed yield (33%), and 100 seed weight (13%). This underscores the unsuitability of this soil type for soybean cultivation. Additionally, microbial analysis revealed 43 depleted and 56 enriched operational taxonomic units (OTUs) in the saline-alkali soil compared to normal soil. Furthermore, an analysis of ion-associated microbes identified 85 mOTUs with significant correlations with various ions. A co-occurrence network analysis revealed strong relationships between specific mOTUs and ions, such as Proteobacteria with multiple ions. In addition, the study investigated the differences in rhizosphere species between salt-tolerant and salt-sensitive soybean varieties under saline-alkali soil conditions. Redundancy analysis (RDA) indicated that mOTUs in saline-alkali soil were associated with pH and ions, while mOTUs in normal soil were correlated with Ca[2+] and K[+]. Comparative analyses identified significant differences in mOTUs between salt-tolerant and salt-sensitive varieties under both saline-alkali and normal soil conditions. Planctomycetes, Proteobacteria, and Actinobacteria were dominant in the bacterial community of saline-alkali soil, with significant enrichment compared to normal soil. The study explored the functioning of the soybean rhizosphere key microbiome by comparing metagenomic data to four databases related to the carbon, nitrogen, phosphorus, and sulfur cycles. A total of 141 KOs (KEGG orthologues) were identified, with 66 KOs related to the carbon cycle, 16 KOs related to the nitrogen cycle, 48 KOs associated with the phosphorus cycle, and 11 KOs linked to the sulfur cycle. Significant correlations were found between specific mOTUs, functional genes, and phenotypic traits, including per mu yield (PMY), grain weight, and effective pod number per plant.

CONCLUSION: Overall, this study provides comprehensive insights into the structure, function, and salt-related species of soil microorganisms in saline-alkali soil and their associations with salt tolerance and soybean phenotype. The identification of key microbial species and functional categories offers valuable information for understanding the mechanisms underlying plant-microbe interactions in challenging soil conditions.}, } @article {pmid37799596, year = {2023}, author = {Yan, Y and Shi, T and Bao, X and Gai, Y and Liang, X and Jiang, Y and Li, Q}, title = {Combined network analysis and interpretable machine learning reveals the environmental adaptations of more than 10,000 ruminant microbial genomes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1147007}, pmid = {37799596}, issn = {1664-302X}, abstract = {BACKGROUND: The ruminant gastrointestinal contains numerous microbiomes that serve a crucial role in sustaining the host's productivity and health. In recent times, numerous studies have revealed that variations in influencing factors, including the environment, diet, and host, contribute to the shaping of gastrointestinal microbial adaptation to specific states. Therefore, understanding how host and environmental factors affect gastrointestinal microbes will help to improve the sustainability of ruminant production systems.

RESULTS: Based on a graphical analysis perspective, this study elucidates the microbial topology and robustness of the gastrointestinal of different ruminant species, showing that the microbial network is more resistant to random attacks. The risk of transmission of high-risk metagenome-assembled genome (MAG) was also demonstrated based on a large-scale survey of the distribution of antibiotic resistance genes (ARG) in the microbiota of most types of ecosystems. In addition, an interpretable machine learning framework was developed to study the complex, high-dimensional data of the gastrointestinal microbial genome. The evolution of gastrointestinal microbial adaptations to the environment in ruminants were analyzed and the adaptability changes of microorganisms to different altitudes were identified, including microbial transcriptional repair.

CONCLUSION: Our findings indicate that the environment has an impact on the functional features of microbiomes in ruminant. The findings provide a new insight for the future development of microbial resources for the sustainable development in agriculture.}, } @article {pmid37799338, year = {2023}, author = {Xu, W and Wang, Q and Li, L and Zhu, B and Cai, Q and Yi, X and Fang, R and Wang, Q}, title = {Case Report: Metagenomic next-generation sequencing applied in diagnosing psittacosis caused by Chlamydia psittaci infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1249225}, pmid = {37799338}, issn = {2235-2988}, mesh = {Humans ; *Psittacosis/diagnosis ; *Chlamydophila psittaci/genetics ; Multilocus Sequence Typing ; Anti-Bacterial Agents ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Chlamydia psittaci is the causative agent of psittacosis in humans, while its rapid identification is hampered due to the lack of specificity of laboratory testing methods.

CASE PRESENTATION: This study reports four cases of C. psittaci infection after contact with a domestic parrot, all belonging to the same family. Common manifestations like fever, cough, headache, nausea, and hypodynamia appeared in the patients. Metagenomic next-generation sequencing (mNGS) aided the etiological diagnosis of psittacosis, revealing 58318 and 7 sequence reads corresponding to C. psittaci in two cases. The detected C. psittaci was typed as ST100001 in the Multilocus-sequence typing (MLST) system, a novel strain initially reported. Based on the results of pathogenic identification by mNGS, the four patients were individually, treated with different antibiotics, and discharged with favorable outcomes.

CONCLUSION: In diagnosing psittacosis caused by a rare C. psittaci agent, mNGS provides rapid etiological identification, contributing to targeted antibiotic therapy and favorable outcomes. This study also reminds clinicians to raise awareness of psittacosis when encountering family members with a fever of unknown origin.}, } @article {pmid37798850, year = {2023}, author = {Lee, JG and Seo, H and Son, SS and Jeong, HS and Lee, KM and Cho, NJ and Park, S and Gil, HW and Park, HA and Kim, S and Lee, EY}, title = {Loss of Cutibacterium is responsible for chronic kidney disease-associated pruritus in patients on dialysis.}, journal = {Kidney research and clinical practice}, volume = {}, number = {}, pages = {}, doi = {10.23876/j.krcp.23.057}, pmid = {37798850}, issn = {2211-9132}, abstract = {BACKGROUND: Chronic kidney disease (CKD)-associated pruritus is a severe distressing condition that frequently occurs in patients undergoing dialysis. In this study, the profile of the skin microbiome was analyzed to understand the underlying etiology and potential treatments.

METHODS: Seventy-six end-stage kidney disease (ESKD) patients (hemodialysis, 40; peritoneal dialysis, 36) and 15 healthy controls were enrolled and swabbed at three sites: back, antecubital fossa, and shin. The pruritus severity of the enrolled subjects was validated by the Worst Itch Numeric Rating Scale (WI-NRS), 5-D itch scale, and Uremic Pruritus in Dialysis Patients (UP-Dial). The 16S gene-based metagenomics method was applied to skin microbiome analysis.

RESULTS: In the comparison of bacterial communities of ESKD patients and the control group, there was a significant difference on back. Specifically, the average composition ratio of the Cutibacterium in the back samples was significantly lower in ESKD patients than in healthy controls (p < 0.01). In further analysis of ESKD patients, Cutibacterium was significantly lower in the high pruritus group than in the low pruritus group (p < 0.05), even though other clinical parameters such as age, calcium-phosphorus product, and intact parathyroid hormone showed no significance difference between the groups.

CONCLUSION: In ESKD patients, the skin microbiome of the back was significantly altered, and the severity of itching was related to the reduction of Cutibacterium. This research reveals the relationship between skin microbiota and CKD-associated pruritus in multiple skin sites for the first time. The results of this study suggest a potential data basis for the diagnosis and treatment of CKD-associated pruritus.}, } @article {pmid37798783, year = {2023}, author = {Kim, HS and Kim, SH and Song, HS and Kwon, YK and Park, CK and Kim, HR}, title = {Application of metagenomics for diagnosis of broilers displaying neurological symptoms.}, journal = {BMC veterinary research}, volume = {19}, number = {1}, pages = {190}, pmid = {37798783}, issn = {1746-6148}, support = {M-1543084-2023-25-01//Animal and Plant Quarantine Agency (APQA), Ministry of Agriculture, Food and Rural Affairs, the Republic of Korea./ ; M-1543084-2023-25-01//Animal and Plant Quarantine Agency (APQA), Ministry of Agriculture, Food and Rural Affairs, the Republic of Korea./ ; M-1543084-2023-25-01//Animal and Plant Quarantine Agency (APQA), Ministry of Agriculture, Food and Rural Affairs, the Republic of Korea./ ; M-1543084-2023-25-01//Animal and Plant Quarantine Agency (APQA), Ministry of Agriculture, Food and Rural Affairs, the Republic of Korea./ ; M-1543084-2023-25-01//Animal and Plant Quarantine Agency (APQA), Ministry of Agriculture, Food and Rural Affairs, the Republic of Korea./ ; }, mesh = {Animals ; Chickens/microbiology ; Newcastle disease virus ; *Newcastle Disease ; Brain/pathology ; *Meningoencephalitis/diagnosis/veterinary ; *Poultry Diseases/microbiology ; }, abstract = {BACKGROUND: Thirty-two-day-old broiler chickens at a farm located in northwestern South Korea displayed adverse neurological symptoms including limping, lying down, and head shaking. Approximately 2.1% of chickens died or were culled due to severe symptoms. Five carcasses were submitted to the Avian Disease Division of the Animal and Plant Quarantine Agency (APQA) for disease diagnosis.

RESULTS: Broilers displayed severe pericarditis and perihepatitis associated with gross lesions. Broilers also displayed microscopic lesions in the cerebrum and in the granular layer of the cerebellum, which were associated with multifocal perivascular cuffing and purulent necrosis in the cerebrum, and severe meningitis with heterophil and lymphocyte infiltration. Staphylococcus spp. were identified in the liver and heart using bacteriological culture. PCR/RT-PCR assays revealed that broilers were negative for avian Clostridium botulinum, Newcastle disease virus, and avian encephalomyelitis virus. Bacterial and viral metagenomic analysis of brain sample further revealed the presence of Pseudomonas spp. and Marek's disease virus, which are known etiological agents of chicken meningoencephalitis.

CONCLUSIONS: This study reports a diagnostic analysis of gross and histopathological lesions from 32-day-old broilers displaying unique neurological symptoms that revealed the presence of the several neurological diseases including meningoencephalitis. The causative agents associated with meningoencephalitis of broilers that had not been identified by routine diagnostic methods could be diagnosed by metagenomics, which proves the usefulness of metagenomics as a diagnostic tool for unknown neurological diseases in broilers.}, } @article {pmid37798675, year = {2023}, author = {Avila Santos, AP and Kabiru Nata'ala, M and Kasmanas, JC and Bartholomäus, A and Keller-Costa, T and Jurburg, SD and Tal, T and Camarinha-Silva, A and Saraiva, JP and Ponce de Leon Ferreira de Carvalho, AC and Stadler, PF and Sipoli Sanches, D and Rocha, U}, title = {The AnimalAssociatedMetagenomeDB reveals a bias towards livestock and developed countries and blind spots in functional-potential studies of animal-associated microbiomes.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {48}, pmid = {37798675}, issn = {2524-4671}, abstract = {BACKGROUND: Metagenomic data can shed light on animal-microbiome relationships and the functional potential of these communities. Over the past years, the generation of metagenomics data has increased exponentially, and so has the availability and reusability of data present in public repositories. However, identifying which datasets and associated metadata are available is not straightforward. We created the Animal-Associated Metagenome Metadata Database (AnimalAssociatedMetagenomeDB - AAMDB) to facilitate the identification and reuse of publicly available non-human, animal-associated metagenomic data, and metadata. Further, we used the AAMDB to (i) annotate common and scientific names of the species; (ii) determine the fraction of vertebrates and invertebrates; (iii) study their biogeography; and (iv) specify whether the animals were wild, pets, livestock or used for medical research.

RESULTS: We manually selected metagenomes associated with non-human animals from SRA and MG-RAST.  Next, we standardized and curated 51 metadata attributes (e.g., host, compartment, geographic coordinates, and country). The AAMDB version 1.0 contains 10,885 metagenomes associated with 165 different species from 65 different countries. From the collected metagenomes, 51.1% were recovered from animals associated with medical research or grown for human consumption (i.e., mice, rats, cattle, pigs, and poultry). Further, we observed an over-representation of animals collected in temperate regions (89.2%) and a lower representation of samples from the polar zones, with only 11 samples in total. The most common genus among invertebrate animals was Trichocerca (rotifers).

CONCLUSION: Our work may guide host species selection in novel animal-associated metagenome research, especially in biodiversity and conservation studies. The data available in our database will allow scientists to perform meta-analyses and test new hypotheses (e.g., host-specificity, strain heterogeneity, and biogeography of animal-associated metagenomes), leveraging existing data. The AAMDB WebApp is a user-friendly interface that is publicly available at https://webapp.ufz.de/aamdb/ .}, } @article {pmid37798477, year = {2023}, author = {Piton, G and Allison, SD and Bahram, M and Hildebrand, F and Martiny, JBH and Treseder, KK and Martiny, AC}, title = {Life history strategies of soil bacterial communities across global terrestrial biomes.}, journal = {Nature microbiology}, volume = {8}, number = {11}, pages = {2093-2102}, pmid = {37798477}, issn = {2058-5276}, support = {DE-SC0020382//DOE | SC | Biological and Environmental Research (BER)/ ; DE-SC0016410//DOE | SC | Biological and Environmental Research (BER)/ ; erc-stg-948219, EPYC//EC | EU Framework Programme for Research and Innovation H2020 | H2020 Excellent Science (H2020 Priority Excellent Science)/ ; BBS/e/F/000Pr10355//RCUK | Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {*Life History Traits ; Soil/chemistry ; Soil Microbiology ; Ecosystem ; Bacteria ; }, abstract = {The life history strategies of soil microbes determine their metabolic potential and their response to environmental changes. Yet these strategies remain poorly understood. Here we use shotgun metagenomes from terrestrial biomes to characterize overarching covariations of the genomic traits that capture dominant life history strategies in bacterial communities. The emerging patterns show a triangle of life history strategies shaped by two trait dimensions, supporting previous theoretical and isolate-based studies. The first dimension ranges from streamlined genomes with simple metabolisms to larger genomes and expanded metabolic capacities. As metabolic capacities expand, bacterial communities increasingly differentiate along a second dimension that reflects a trade-off between increasing capacities for environmental responsiveness or for nutrient recycling. Random forest analyses show that soil pH, C:N ratio and precipitation patterns together drive the dominant life history strategy of soil bacterial communities and their biogeographic distribution. Our findings provide a trait-based framework to compare life history strategies of soil bacteria.}, } @article {pmid37797927, year = {2023}, author = {Lu, J and Li, M and Tan, J and He, M and Wu, H and Kang, Y and Hu, Z and Zhang, J and Guo, Z}, title = {Distribution, sources, ecological risk and microbial response of polycyclic aromatic hydrocarbons in Qingdao bays, China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {338}, number = {}, pages = {122687}, doi = {10.1016/j.envpol.2023.122687}, pmid = {37797927}, issn = {1873-6424}, mesh = {Geologic Sediments/chemistry ; Ecosystem ; *Water Pollutants, Chemical/analysis ; Bays/chemistry ; *Polycyclic Aromatic Hydrocarbons/analysis ; Environmental Monitoring/methods ; Risk Assessment ; China ; }, abstract = {Bay ecosystem has garnered significant attention due to the severe threat posed by organic pollutants, particularly polycyclic aromatic hydrocarbons (PAHs). However, there is a dearth of information regarding the extent of PAHs pollutant risk and its impact on microbial communities and metabolism within this environment. In this study, the distribution, sources, ecological risk, and microbial community and metabolic response of PAHs in Jiaozhou Bay, Aoshan Bay, and Lingshan Bay in Qingdao, China were investigated. The results showed that the average concentration of ∑PAHs ranged from 120 to 614 ng/L across three bays, with Jiaozhou and Aoshan Bay exhibiting a higher risk than Lingshan Bay due to an increased concentration of high-molecular-weight PAHs. Further analysis revealed a negative correlation between dissolved organic carbon concentration and ∑PAHs concentration in water. Metagenomic analysis demonstrated that higher levels of PAHs can lead to decreased microbial diversity, while the abundance of PAHs-degrading bacteria is enhanced. Additionally, the Erythrobacter, Jannaschia and Ruegeria genera were found to have a significant correlation with low-molecular-weight PAH concentrations. In terms of microbial metabolism, higher PAH concentrations were beneficial for carbohydrate metabolic pathway but unfavorable for amino acid metabolic pathways and membrane transport pathways in natural bay environments. These findings provide a foundation for controlling PAHs pollution and offer insights into the impact of PAHs on bacterial communities and metabolism in natural bay environments.}, } @article {pmid37797495, year = {2023}, author = {Zhao, W and Zhang, Z and Wang, Z and Ma, P and Pan, Y and Wang, Q and Zhang, Z}, title = {Factors affecting the accuracy of genomic prediction in joint pig populations.}, journal = {Animal : an international journal of animal bioscience}, volume = {17}, number = {10}, pages = {100980}, doi = {10.1016/j.animal.2023.100980}, pmid = {37797495}, issn = {1751-732X}, mesh = {Animals ; Swine/genetics ; *Quantitative Trait Loci ; *Models, Genetic ; Genomics/methods ; Phenotype ; Metagenomics ; Polymorphism, Single Nucleotide ; Genotype ; }, abstract = {Genomic prediction (GP) has greatly advanced animal and plant breeding over the past two decades. GP in joint populations is a feasible method to improve the accuracy of genomic estimated breeding values in small populations. However, there is still a need to understand the factors that influence GP in joint populations. This study used simulated data and real data from Duroc pig populations to examine the impact of linkage disequilibrium (LD), causal variants effect sizes (CVESs), and minor allele frequencies (MAF) of SNPs on the accuracy of genomic prediction in joint populations. Three prediction methods were used: genomic best linear unbiased prediction (GBLUP), single-step GBLUP and multi-trait GBLUP. Results from the simulated datasets showed that the accuracies of GP in joint populations were always higher than those in a single population when only LD inconsistencies existed. However, single-step GBLUP accuracy in joint populations decreased as the correlation of MAF between populations decreased, while the accuracy of GBLUP is consistently higher in joint populations than in a single population. As the correlation of CVES between populations decreased, the accuracy of both GBLUP and single-step GBLUP in joint populations declined. Analysis of real Duroc populations showed low genetic correlation, similar to the simulated relationship between the most distant populations. In most cases in Duroc populations, GP have higher accuracies in joint populations than in individual population. In conclusion, the consistency of CVES plays a more important role in multi-population GP. The genetic relatedness of the Duroc populations is so weak that the prediction accuracy of GP in joint populations is reduced in some traits. Multi-trait GBLUP is a competitive method for the joint breeding evaluation.}, } @article {pmid37797086, year = {2024}, author = {Feng, Y and Comes, HP and Chen, J and Zhu, S and Lu, R and Zhang, X and Li, P and Qiu, J and Olsen, KM and Qiu, Y}, title = {Genome sequences and population genomics provide insights into the demographic history, inbreeding, and mutation load of two 'living fossil' tree species of Dipteronia.}, journal = {The Plant journal : for cell and molecular biology}, volume = {117}, number = {1}, pages = {177-192}, doi = {10.1111/tpj.16486}, pmid = {37797086}, issn = {1365-313X}, support = {2017YFA0605100//National Key R&D Program of China/ ; 2022YFF1301703//National Key R&D Program of China/ ; 31872652//National Natural Science Foundation of China/ ; 32161143003//National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Fossils ; Genetic Variation ; *Inbreeding ; Metagenomics ; Mutation ; *Trees/genetics ; }, abstract = {'Living fossils', that is, ancient lineages of low taxonomic diversity, represent an exceptional evolutionary heritage, yet we know little about how demographic history and deleterious mutation load have affected their long-term survival and extinction risk. We performed whole-genome sequencing and population genomic analyses on Dipteronia sinensis and D. dyeriana, two East Asian Tertiary relict trees. We found large-scale genome reorganizations and identified species-specific genes under positive selection that are likely involved in adaptation. Our demographic analyses suggest that the wider-ranged D. sinensis repeatedly recovered from population bottlenecks over late Tertiary/Quaternary periods of adverse climate conditions, while the population size of the narrow-ranged D. dyeriana steadily decreased since the late Miocene, especially after the Last Glacial Maximum (LGM). We conclude that the efficient purging of deleterious mutations in D. sinensis facilitated its survival and repeated demographic recovery. By contrast, in D. dyeriana, increased genetic drift and reduced selection efficacy, due to recent severe population bottlenecks and a likely preponderance of vegetative propagation, resulted in fixation of strongly deleterious mutations, reduced fitness, and continuous population decline, with likely detrimental consequences for the species' future viability and adaptive potential. Overall, our findings highlight the significant impact of demographic history on levels of accumulation and purging of putatively deleterious mutations that likely determine the long-term survival and extinction risk of Tertiary relict trees.}, } @article {pmid37796924, year = {2023}, author = {Tesolato, S and Ortega-Hernández, A and Gómez-Garre, D and Claver, P and De Juan, C and De la Serna, S and Paz, M and Domínguez-Serrano, I and Dziakova, J and Rivera, D and Torres, A and Iniesta, P}, title = {Gut microbiota profiles in feces and paired tumor and non-tumor tissues from Colorectal Cancer patients. Relationship to the Body Mass Index.}, journal = {PloS one}, volume = {18}, number = {10}, pages = {e0292551}, pmid = {37796924}, issn = {1932-6203}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Body Mass Index ; Bacteria/genetics ; *Colonic Neoplasms ; Feces/microbiology ; Obesity ; RNA, Ribosomal, 16S/genetics ; *Colorectal Neoplasms/pathology ; }, abstract = {Colorectal Cancer (CRC) and Obesity constitute two of the most common malignancies in the western world, and previously have been associated with intestinal microbial composition alterations. Our main aim in this study is to provide molecular data on intestinal microbiota patterns in subjects with CRC, as well as to establish possible associations with their Body Mass Index (BMI). A total of 113 samples from 45 subjects were collected and submitted to metagenomics analysis for gut microbiota. This study was performed by 16S ribosomal RNA bacterial gene amplification and sequencing using the Ion Torrent™ technology. The same dominant phyla were observed in feces and colorectal tissues, although a greater proportion of Fusobacteriota was found in tumor samples. Moreover, at the genus level, LEfSe analysis allowed us to detect a significant increase in Fusobacterium and Streptococcus in colorectal tissues with respect to fecal samples, with a significant preponderance of Fusobacterium in tumor tissues. Also, our data revealed relevant associations between gut microbiota composition and tumor location. When comparing bacterial profiles between right and left colon cancers, those from the left-sided colon showed a significant preponderance, among others, of the order Staphylococcales. Moreover, phyla Firmicutes and Spirochaetota were more abundant in the group of right-sided CRCs and phylum Proteobacteria was increased in rectal cancers. In relation to BMI of patients, we detected significant differences in beta diversity between the normal weight and the obese groups of cases. Microbiota from obese patients was significantly enriched, among others, in Bacteroidales. Therefore, our results are useful in the molecular characterization of CRC in obese and non-obese patients, with a clear impact on the establishment of diagnostic and prognosis of CRC.}, } @article {pmid37796897, year = {2023}, author = {Diao, M and Dyksma, S and Koeksoy, E and Ngugi, DK and Anantharaman, K and Loy, A and Pester, M}, title = {Global diversity and inferred ecophysiology of microorganisms with the potential for dissimilatory sulfate/sulfite reduction.}, journal = {FEMS microbiology reviews}, volume = {47}, number = {5}, pages = {}, pmid = {37796897}, issn = {1574-6976}, support = {P 31996-B/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Oxidation-Reduction ; *Bacteria/metabolism ; *Archaea/metabolism ; Sulfates/metabolism ; Sulfites/metabolism ; Sulfur/metabolism ; Phylogeny ; }, abstract = {Sulfate/sulfite-reducing microorganisms (SRM) are ubiquitous in nature, driving the global sulfur cycle. A hallmark of SRM is the dissimilatory sulfite reductase encoded by the genes dsrAB. Based on analysis of 950 mainly metagenome-derived dsrAB-carrying genomes, we redefine the global diversity of microorganisms with the potential for dissimilatory sulfate/sulfite reduction and uncover genetic repertoires that challenge earlier generalizations regarding their mode of energy metabolism. We show: (i) 19 out of 23 bacterial and 2 out of 4 archaeal phyla harbor uncharacterized SRM, (ii) four phyla including the Desulfobacterota harbor microorganisms with the genetic potential to switch between sulfate/sulfite reduction and sulfur oxidation, and (iii) the combination as well as presence/absence of different dsrAB-types, dsrL-types and dsrD provides guidance on the inferred direction of dissimilatory sulfur metabolism. We further provide an updated dsrAB database including > 60% taxonomically resolved, uncultured family-level lineages and recommendations on existing dsrAB-targeted primers for environmental surveys. Our work summarizes insights into the inferred ecophysiology of newly discovered SRM, puts SRM diversity into context of the major recent changes in bacterial and archaeal taxonomy, and provides an up-to-date framework to study SRM in a global context.}, } @article {pmid37796016, year = {2023}, author = {Kamer, O and Rinott, E and Tsaban, G and Kaplan, A and Yaskolka Meir, A and Zelicha, H and Knights, D and Tuohy, K and Fava, F and Uwe Scholz, M and Ziv, O and Rubin, E and Blüher, M and Stumvoll, M and Ceglarek, U and Clément, K and Koren, O and Hu, FB and Stampfer, MJ and Wang, DD and Youngster, I and Shai, I}, title = {Successful weight regain attenuation by autologous fecal microbiota transplantation is associated with non-core gut microbiota changes during weight loss; randomized controlled trial.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2264457}, pmid = {37796016}, issn = {1949-0984}, support = {R00 DK119412/DK/NIDDK NIH HHS/United States ; R01 AG077489/AG/NIA NIH HHS/United States ; R01 NR019992/NR/NINR NIH HHS/United States ; }, mesh = {Humans ; Middle Aged ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome ; Feces ; Weight Loss ; Weight Gain ; }, abstract = {We previously reported that autologous-fecal-microbiota-transplantation (aFMT), following 6 m of lifestyle intervention, attenuated subsequent weight regain and insulin rebound for participants consuming a high-polyphenol green-Mediterranean diet. Here, we explored whether specific changes in the core (abundant) vs. non-core (low-abundance) gut microbiome taxa fractions during the weight-loss phase (0-6 m) were differentially associated with weight maintenance following aFMT. Eighty-two abdominally obese/dyslipidemic participants (age = 52 years; 6 m weightloss = -8.3 kg) who provided fecal samples (0 m, 6 m) were included. Frozen 6 m's fecal samples were processed into 1 g, opaque and odorless aFMT capsules. Participants were randomly assigned to receive 100 capsules containing their own fecal microbiota or placebo over 8 m-14 m in ten administrations (adherence rate > 90%). Gut microbiome composition was evaluated using shotgun metagenomic sequencing. Non-core taxa were defined as ≤ 66% prevalence across participants. Overall, 450 species were analyzed. At baseline, 13.3% were classified as core, and Firmicutes presented the highest core proportion by phylum. During 6 m weight-loss phase, abundance of non-core species changed more than core species (P < .0001). Subject-specific changes in core and non-core taxa fractions were strongly correlated (Jaccard Index; r = 0.54; P < .001). Following aFMT treatment, only participants with a low 6 m change in core taxa, and a high change in non-core taxa, avoided 8-14 m weight regain (aFMT = -0.58 ± 2.4 kg, corresponding placebo group = 3.18 ± 3.5 kg; P = .02). In a linear regression model, low core/high non-core 6 m change was the only combination that was significantly associated with attenuated 8-14 m weight regain (P = .038; P = .002 for taxa patterns/treatment intervention interaction). High change in non-core, low-abundance taxa during weight-loss might mediate aFMT treatment success for weight loss maintenance.ClinicalTrials.gov: NCT03020186.}, } @article {pmid37796012, year = {2023}, author = {Strochkov, V and Beloussov, V and Solomadin, M and Granica, J and Yegorov, S and Orkara, S and Sandybayev, N}, title = {Full genome sequence of a human rhinovirus A1B, obtained in Kazakhstan.}, journal = {Microbiology resource announcements}, volume = {12}, number = {11}, pages = {e0074923}, pmid = {37796012}, issn = {2576-098X}, abstract = {Here, we report the full nucleotide sequence of the RvA1B/KZ/2021/87 rhinovirus, identified through metagenomic sequencing of nasopharyngeal swabs collected from patients exhibiting respiratory symptoms in Kazakhstan during 2021.}, } @article {pmid37795995, year = {2023}, author = {Cao, Y and Wang, J and Hou, W and Ding, Y and Zhu, Y and Zheng, J and Huang, Q and Cao, Z and Xie, R and Wei, Q and Qin, H}, title = {Colorectal cancer-associated T cell receptor repertoire abnormalities are linked to gut microbiome shifts and somatic cell mutations.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2263934}, pmid = {37795995}, issn = {1949-0984}, mesh = {Humans ; *Colorectal Neoplasms ; *Gastrointestinal Microbiome ; Fusobacterium nucleatum ; Biomarkers ; Mutation ; Receptors, Antigen, T-Cell/genetics ; }, abstract = {As with many diseases, tumor formation in colorectal cancer (CRC) is multifactorial and involves immune, environmental factors and various genetics that contribute to disease development. Accumulating evidence suggests that the gut microbiome is linked to the occurrence and development of CRC, and these microorganisms are important for immune maturation. However, a systematic perspective integrating microbial profiling, T cell receptor (TCR) and somatic mutations in humans with CRC is lacking. Here, we report distinct features of the expressed TCRβ repertoires in the peripheral blood of and CRC patients (n = 107) and healthy donors (n = 30). CRC patients have elevated numbers of large TCRβ clones and they have very low TCR diversity. The metagenomic sequencing data showed that the relative abundance of Fusobacterium nucleatum (F. nucleatum), Escherichia coli and Dasheen mosaic virus were elevated consistently in CRC patients (n = 97) compared to HC individuals (n = 30). The abundance of Faecalibacterium prausnitzii and Roseburia intestinalis was reduced in CRC (n = 97) compared to HC (n = 30). The correlation between somatic mutations of target genes (16 genes, n = 79) and TCR clonality and microbial biomarkers in CRC had been investigated. Importantly, we constructed a random forest classifier (contains 15 features) based on microbiome and TCR repertoires, which can be used as a clinical detection method to screen patients for CRC. We also analysis of F. nucleatum-specific TCR repertoire characteristics. Collectively, our large-cohort multi-omics data aimed to identify novel biomarkers to inform clinical decision-making in the detection and diagnosis of CRC, which is of possible etiological and diagnostic significance.}, } @article {pmid37795951, year = {2023}, author = {Samake, JN and Lavretsky, P and Gunarathna, I and Follis, M and Brown, JI and Ali, S and Yared, S and Carter, TE}, title = {Population genomic analyses reveal population structure and major hubs of invasive Anopheles stephensi in the Horn of Africa.}, journal = {Molecular ecology}, volume = {32}, number = {21}, pages = {5695-5708}, doi = {10.1111/mec.17136}, pmid = {37795951}, issn = {1365-294X}, support = {Research Enhancement Award (R15AI151766)/NH/NIH HHS/United States ; Research Enhancement Award (R15AI151766)/NH/NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Anopheles/genetics ; Mosquito Vectors/genetics ; Gene Regulatory Networks ; Metagenomics ; *Malaria/epidemiology/genetics ; Genomics ; Ethiopia ; }, abstract = {Anopheles stephensi invasion in the Horn of Africa (HoA) poses a substantial risk of increased malaria disease burden in the region. An understanding of the history of introduction(s), establishment(s) and potential A. stephensi sources in the HoA is needed to predict future expansions and establish where they may be effectively controlled. To this end, we take a landscape genomic approach to assess A. stephensi origins and spread throughout the HoA, information essential for vector control. Specifically, we assayed 2070 genome-wide single nucleotide polymorphisms across 214 samples spanning 13 populations of A. stephensi from Ethiopia and Somaliland collected in 2018 and 2020, respectively. Principal component and genetic ancestry analyses revealed clustering that followed an isolation-by-distance pattern, with genetic divergence among the Ethiopian samples significantly correlating with geographical distance. Additionally, genetic relatedness was observed between the northeastern and east central Ethiopian A. stephensi populations and the Somaliland A. stephensi populations. These results reveal population differentiation and genetic connectivity within HoA A. stephensi populations. Furthermore, based on genetic network analysis, we uncovered that Dire Dawa, the site of a spring 2022 malaria outbreak, was one of the major hubs from which sequential founder events occurred in the rest of the eastern Ethiopian region. These findings can be useful for the selection of sites for heightened control to prevent future malaria outbreaks. Finally, we did not detect significant genotype-environmental associations, potentially due to the recency of their colonization and/or other anthropogenic factors leading to the initial spread and establishment of A. stephensi. Our study highlights how coupling genomic data at landscape levels can shed light into even ongoing invasions.}, } @article {pmid37795928, year = {2024}, author = {Terlouw, D and Boot, A and Ducarmon, QR and Nooij, S and Jessurun, MA and van Leerdam, ME and Tops, CM and Langers, AMJ and Morreau, H and van Wezel, T and Nielsen, M}, title = {Colibactin mutational signatures in NTHL1 tumor syndrome and MUTYH associated polyposis patients.}, journal = {Genes, chromosomes & cancer}, volume = {63}, number = {1}, pages = {e23208}, doi = {10.1002/gcc.23208}, pmid = {37795928}, issn = {1098-2264}, support = {11292//KWF Kankerbestrijding/ ; }, mesh = {Humans ; *Adenomatous Polyposis Coli/genetics/pathology ; Mutation ; *Colorectal Neoplasms/genetics/pathology ; Deoxyribonuclease (Pyrimidine Dimer)/genetics ; }, abstract = {Polyketide synthase (pks) island harboring Escherichia coli are, under the right circumstances, able to produce the genotoxin colibactin. Colibactin is a risk factor for the development of colorectal cancer and associated with mutational signatures SBS88 and ID18. This study explores colibactin-associated mutational signatures in biallelic NTHL1 and MUTYH patients. Targeted Next Generation Sequencing (NGS) was performed on colorectal adenomas and carcinomas of one biallelic NTHL and 12 biallelic MUTYH patients. Additional fecal metagenomics and genome sequencing followed by mutational signature analysis was conducted for the NTHL1 patient. Targeted NGS of the NTHL1 patient showed somatic APC variants fitting SBS88 which was confirmed using WGS. Furthermore, fecal metagenomics revealed pks genes. Also, in 1 out of 11 MUTYH patient a somatic variant was detected fitting SBS88. This report shows that colibactin may influence development of colorectal neoplasms in predisposed patients.}, } @article {pmid37795586, year = {2023}, author = {Hanson, KE and Caliendo, AM}, title = {Plasma cell free DNA metagenomic sequencing: new insights from the PICKUP study.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {}, number = {}, pages = {}, doi = {10.1093/cid/ciad600}, pmid = {37795586}, issn = {1537-6591}, } @article {pmid37795307, year = {2023}, author = {Huang, X and Zheng, Y and Li, P and Cui, J and Sui, P and Chen, Y and Gao, W}, title = {Organic management increases beneficial microorganisms and promotes the stability of microecological networks in tea plantation soil.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1237842}, pmid = {37795307}, issn = {1664-302X}, abstract = {INTRODUCTION: Organic agriculture is highly regarded by people for its commitment to health, ecology, care, and fairness. The soil microbial community responds quickly to environmental changes and is a good indicator for evaluating soil microecology. Therefore, from the perspective of soil microbial communities, elucidating the impact of organic management on soil microecology in tea plantations has great significance for improving local tea plantation systems.

METHODS: The study collected bulk soil from organic management (OM) and conventional management (CM) tea plantations in Pu'er City, a major tea-producing area in China, and analyzed their species diversity, structural composition, and co-occurrence networks using metagenomics technology.

RESULTS: Compared with CM, the diversity index (Shannon) and evenness index (Heip) of soil fungi increased by 7.38% and 84.2% in OM tea plantations, respectively. The relative abundance of microorganisms related to the nitrogen cycle increased. Specifically, there was a significant increase in Rhodobiales, a 2-fold increase in Nitrospirae, and approximately 1.95 and 2.03 times increases in unclassified genera within Betaproteobacteria and Deltaproteobacteria, respectively. The relative abundance of plant residue degradation species, Gemmatimonadetes, Ascomycota, and Basidiomycota, increased by 2.8, 1, and 1.4 times, respectively. The OM was conducive to the establishment of collaborative relationships among bacterial species and increased the diversity and complexity of species relationships in fungal communities. The network stability of soil ecosystems was promoted. The organic tea plantations' keystone taxa contained mycorrhizal fungi (Pezoloma_ericae, Rhizophagus_irregularis, Rhizophagus_clarus), as well as species involved in soil nitrogen metabolism (Acidobacteria_bacterium, Acidobacteriia_bacterium_AA117, Sphingomonas_sp._URHD0007, Enhydrobacter_aerosaccus), pathogen (Erysiphe_pulchra), and parasites (Paramycosporidium saccamoeba). The partial least squares method (PLS-SEM) indicated that OM affected N-NH4+ negatively, increasing the abundance of fungi, and thereby positively affecting the Shannon index.

CONCLUSION: In brief, reasonable organic management can improve the diversity of soil microorganisms, increase the relative abundance of beneficial bacteria in tea plantation soil, and promote the stability of the soil microbial ecological network.}, } @article {pmid37795292, year = {2023}, author = {Liu, X and Ma, Z and Wang, Y and Jia, H and Wang, Z and Zhang, L}, title = {Heat stress exposure cause alterations in intestinal microbiota, transcriptome, and metabolome of broilers.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1244004}, pmid = {37795292}, issn = {1664-302X}, abstract = {INTRODUCTION: Heat stress can affect the production of poultry through complex interactions between genes, metabolites and microorganisms. At present, it is unclear how heat stress affects genetic, metabolic and microbial changes in poultry, as well as the complex interactions between them.

METHODS: Thus, at 28  days of age a total of 200 Arbor Acres broilers with similar body weights were randomly divided into the control (CON) and heat stress treatment (HS). There were 5 replicates in CON and HS, respectively, 20 per replication. From the 28-42  days, the HS was kept at 31 ± 1°C (9:00-17:00, 8 h) and other time was maintained at 21 ± 1°C as in the CON. At the 42nd day experiment, we calculated the growth performance (n = 8) of broilers and collected 3 and 6 cecal tissues for transcriptomic and metabolomic investigation and 4 cecal contents for metagenomic investigation of each treatment.

RESULTS AND DISCUSSION: The results indicate that heat stress significantly reduced the average daily gain and body weight of broilers (value of p < 0.05). Transcriptome KEGG enrichment showed that the differential genes were mainly enriched in the NF-kB signaling pathway. Metabolomics results showed that KEGG enrichment showed that the differential metabolites were mainly enriched in the mTOR signaling pathway. 16S rDNA amplicon sequencing results indicated that heat stress increased the relative abundance of Proteobacteria decreased the relative abundance of Firmicutes. Multi-omics analysis showed that the co-participating pathway of differential genes, metabolites and microorganisms KEGG enrichment was purine metabolism. Pearson correlation analysis found that ornithine was positively correlated with SULT1C3, GSTT1L and g_Lactobacillus, and negatively correlated with CALB1. PE was negatively correlated with CALB1 and CHAC1, and positively with g_Alistipes. In conclusion, heat stress can generate large amounts of reactive oxygen and increase the types of harmful bacteria, reduce intestinal nutrient absorption and antioxidant capacity, and thereby damage intestinal health and immune function, and reduce growth performance indicators. This biological process is manifested in the complex regulation, providing a foundational theoretical basis for solving the problem of heat stress.}, } @article {pmid37795207, year = {2023}, author = {Rao, Z and Wang, Z and Tang, M and Zhang, K}, title = {Optimal Perioperative Antimicrobial Management Strategies of Kidney Transplant Recipients Guided by Metagenomic Next-Generation Sequencing of Deceased Donors' Microbiology Samples.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {6473-6486}, pmid = {37795207}, issn = {1178-6973}, abstract = {BACKGROUND: There is no consensus on the optimal use of perioperative antibiotics prophylaxis after kidney transplantation, but there is a common trend to limit the duration of antibiotic use worldwide. Metagenomic next-generation sequencing (mNGS) has emerged as a novel technology for pathogen detection in clinical practice due to its noninvasive, rapid, precise and high susceptibility to detect infectious pathogens. However, data are lacking on whether mNGS analyses could be used to detect pathogens and guide anti-infection regimens in kidney transplant donors and recipients.

METHODS: We conducted a retrospective study to review all clinic data of mNGS and traditional laboratory methods (TMs) for pathogen detection in kidney transplant recipients and their corresponding deceased donors from August 1, 2021 to October 30, 2022 in our center.

RESULTS: A total of 57 donors and 112 of their corresponding recipients were included. The antimicrobial strategy mainly depended on mNGS results combined with traditional pathogen culture and clinical conditions. The percentages of positive pathogen detected by mNGS in blood, urine, bronchoalveolar lavage fluid (BALF) and preservation fluids (PFs) were 50.9% (29/57), 35.1% (20/57), 84.2% (48/57) and 54.4% (31/57) respectively, and were 24.6% (14/57), 15.8% (9/57), 57.9% (33/57) and 14.1% (8/57) respectively when using TMs. mNGS could detected all of pathogens which were detected by TMs. However, samples with negative TMs testing can be additionally detected as positive by mNGS (15/43 in blood, 11/48 in urine, 15/24 in BALF and 23/49 in PFs). Drug resistance genes were detected in 9 donors by mNGS,which were consistent with 6 donors by TMs. There was only one case of donor-derived infection in this study.

CONCLUSION: This study showed that it is effective to combine mNGS with traditional pathogen detection methods and clinical features to develop optimal perioperative antimicrobial management strategies for deceased donor kidney transplantation.}, } @article {pmid37795203, year = {2023}, author = {Chen, R and Xie, M and Wang, S and Yu, F and Zhang, D and Yuan, L and Zheng, J and Wang, J and Zhou, J and Li, B and Zheng, S and Fan, Y and Han, D}, title = {Secondary Infection Surveillance with Metagenomic Next-Generation Sequencing in COVID-19 Patients: A Cross-Sectional Study.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {6463-6472}, pmid = {37795203}, issn = {1178-6973}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a promising tool for improving antimicrobial therapy and infection control decision-making in complex infections. Secondary infection surveillance using mNGS in COVID-19 patients has rarely been reported.

METHODS: Respiratory pathogen and antibiotic resistance prediction were evaluated by BALF mNGS for 192 hospitalized COVID-19 patients between December 2022 and February 2023.

RESULTS: Secondary infection was confirmed in 83.3% (160/192) of the COVID-19 patients, with bacterial infections (45%, 72/160) predominating, followed by mixed bacterial and fungal infections (20%, 32/160), and fungal infections (17.5%, 28/160). The incidence of bacterial or viral secondary infection was significantly higher in patients who were admitted to the ICU, received mechanical ventilation, or developed severe pneumonia (all p<0.05). Klebsiella pneumoniae (n=30, 8.4%) was the most prevalent pathogen associated with secondary infection followed by Acinetobacter baumannii (n=29, 8.1%), Candida albicans (n=29, 8.1%), Aspergillus fumigatus (n=27, 7.6%), human herpes simplex virus type 1 (n=23, 6.4%), Staphylococcus aureus (n=20, 5.6%) and Pneumocystis jiroveci (n=14, 3.9%). The overall concordance between the resistance genes detected by mNGS and the reported phenotypic resistance in 69 samples containing five clinically important pathogens (ie, K. pneumoniae, A. baumannii, S. aureus, P. aeruginosa and E. coli) that caused secondary infection was 85.5% (59/69).

CONCLUSION: mNGS can detect pathogens causing secondary infection and predict antimicrobial resistance for COVID19 patients. This is crucial for initiating targeted treatment and rapidly detect unsuspected spread of multidrug-resistant pathogens.}, } @article {pmid37794500, year = {2023}, author = {Costa, FF and Souza, RSC and Voidaleski, MF and Gomes, RR and Reis, GF and Lima, BJFS and Candido, GZ and Geraldo, MR and Soares, JMB and Schneider, GX and Trindade, EDS and Bini, IH and Moreno, LF and Bombassaro, A and Queiroz-Telles, F and Raittz, RT and Quan, Y and Arruda, P and Attili-Angelis, D and de Hoog, S and Vicente, VA}, title = {Sugarcane: an unexpected habitat for black yeasts in Chaetothyriales.}, journal = {IMA fungus}, volume = {14}, number = {1}, pages = {20}, pmid = {37794500}, issn = {2210-6340}, support = {312811/2018-7//CNPq/ ; 0592012//CAPES PVE/ ; }, abstract = {Sugarcane (Saccharum officinarum, Poaceae) is cultivated on a large scale in (sub)tropical regions such as Brazil and has considerable economic value for sugar and biofuel production. The plant is a rich substrate for endo- and epiphytic fungi. Black yeasts in the family Herpotrichiellaceae (Chaetothyriales) are colonizers of human-dominated habitats, particularly those rich in toxins and hydrocarbon pollutants, and may cause severe infections in susceptible human hosts. The present study assessed the diversity of Herpotrichiellaceae associated with sugarcane, using in silico identification and selective isolation. Using metagenomics, we identified 5833 fungal sequences, while 639 black yeast-like isolates were recovered in vitro. In both strategies, the latter fungi were identified as members of the genera Cladophialophora, Exophiala, and Rhinocladiella (Herpotrichiellaceae), Cyphellophora (Cyphellophoraceae), and Knufia (Trichomeriaceae). In addition, we discovered new species of Cladophialophora and Exophiala from sugarcane and its rhizosphere. The first environmental isolation of Cladophialophora bantiana is particularly noteworthy, because this species up to now is exclusively known from the human host where it mostly causes fatal brain disease in otherwise healthy patients.}, } @article {pmid37793587, year = {2023}, author = {Ni, M and Pan, Y and Li, D and Huang, Y and Chen, Z and Li, L and Bi, Z and Wu, R and Song, Z}, title = {Metagenomics, metatranscriptomics, and proteomics reveal the metabolic mechanism of biofilm sequencing batch reactor with higher phosphate enrichment capacity under low phosphorus load.}, journal = {Environmental research}, volume = {238}, number = {Pt 2}, pages = {117237}, doi = {10.1016/j.envres.2023.117237}, pmid = {37793587}, issn = {1096-0953}, mesh = {*NAD ; *Proteomics ; Phosphorus ; Biofilms ; Adenosine Triphosphate ; Bioreactors ; Sewage ; }, abstract = {The biofilm sequencing batch reactor (BSBR) process has higher phosphate recovery efficiency and enrichment multiple when the phosphorus load is lower, but the mechanism of phosphate enrichment at low phosphorus load remains unclear. In this study, we operated two BSBR operating under low and high phosphorus load (0.012 and 0.032 kg/(m[3]·d)) respectively, and used metagenomic, metatranscriptomic, and proteomics methods to analyze the community structure of the phosphorus accumulating organisms (PAOs) in the biofilm, the transcription and protein expression of key functional genes and enzymes, and the metabolism of intracellular polymers. Compared with at high phosphorus load, the BSBR at low phosphorus load have different PAOs and fewer types of PAOs, but in both cases the PAOs must have the PHA, PPX, Pst, and acs genes to become dominant. Some key differences in the metabolism of PAOs from the BSBR with different phosphorus load can be identified as follows. When the phosphorus load is low, the adenosine triphosphoric acid (ATP) and NAD(P)H in the anaerobic stage come from the TCA cycle and the second half of the EMP pathway. The key genes that are upregulated include GAPDH, PGK, ENO, ppdk in the EMP pathway, actP in acetate metabolism, phnB in polyhydroxybutyrate (PHB) synthesis, and aceA, mdh, sdhA, and IDH1 in the TCA cycle. In the meantime, the ccr gene in the PHV pathway is inhibited. As a result, the metabolism of the PAOs features low glycogen with high PHB, Pupt, Prel, and low PHV. That is, more ATP and NAD(P)H flow to phosphorus enrichment metabolism, thus allowing the highly efficient enrichment of phosphorus from low concentration phosphate thanks to the higher abundance of PAOs. The current results provide theoretical support and a new technical option for the enrichment and recovery of low concentrations of phosphate from wastewater by the BSBR process.}, } @article {pmid37792894, year = {2023}, author = {Pompei, S and Bella, E and Weitz, JS and Grilli, J and Lagomarsino, MC}, title = {Metacommunity structure preserves genome diversity in the presence of gene-specific selective sweeps under moderate rates of horizontal gene transfer.}, journal = {PLoS computational biology}, volume = {19}, number = {10}, pages = {e1011532}, pmid = {37792894}, issn = {1553-7358}, mesh = {Humans ; *Gene Transfer, Horizontal/genetics ; *Bacteria/genetics ; Biological Evolution ; Genome ; }, abstract = {The horizontal transfer of genes is fundamental for the eco-evolutionary dynamics of microbial communities, such as oceanic plankton, soil, and the human microbiome. In the case of an acquired beneficial gene, classic population genetics would predict a genome-wide selective sweep, whereby the genome spreads clonally within the community and together with the beneficial gene, removing genome diversity. Instead, several sources of metagenomic data show the existence of "gene-specific sweeps", whereby a beneficial gene spreads across a bacterial community, maintaining genome diversity. Several hypotheses have been proposed to explain this process, including the decreasing gene flow between ecologically distant populations, frequency-dependent selection from linked deleterious allelles, and very high rates of horizontal gene transfer. Here, we propose an additional possible scenario grounded in eco-evolutionary principles. Specifically, we show by a mathematical model and simulations that a metacommunity where species can occupy multiple patches, acting together with a realistic (moderate) HGT rate, helps maintain genome diversity. Assuming a scenario of patches dominated by single species, our model predicts that diversity only decreases moderately upon the arrival of a new beneficial gene, and that losses in diversity can be quickly restored. We explore the generic behaviour of diversity as a function of three key parameters, frequency of insertion of new beneficial genes, migration rates and horizontal transfer rates.Our results provides a testable explanation for how diversity can be maintained by gene-specific sweeps even in the absence of high horizontal gene transfer rates.}, } @article {pmid37792198, year = {2023}, author = {Qaria, MA and Xu, C and Hussain, A and Nawaz, MZ and Zhu, D}, title = {Metagenomic investigations on antibiotic resistance and microbial virulence in oil-polluted soils from China.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {51}, pages = {110590-110599}, pmid = {37792198}, issn = {1614-7499}, mesh = {Humans ; Virulence ; *Bacteria/genetics ; *Genes, Bacterial ; Soil ; Drug Resistance, Microbial/genetics ; China ; Virulence Factors ; Soil Microbiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Engine oil spills have been associated with a wide range of human health problems. However, little is known about the effects of petroleum hydrocarbon pollution on soil microbial communities. In this study, three samples were collected from oil-polluted soils (OPS), and one control soil (CS) from Taolin town, China, near the old engine's scrapes was used. The aims of this study were to conduct metagenomic sequencing and subsequently perform resistome and virulome analysis. We also aimed to validate anti-microbial resistance and virulence genes and anti-bacterial sensitivity profiles among the isolates from oil-polluted soils. The OPS microbial community was dominated by bacterial species compared to the control samples which were dominated by metazoans and other organisms. Secondly, the resistosome and virulome analysis showed that ARGs and virulence factors were higher among OPS microbial communities. Antibiotic susceptibility assay and qPCR analysis for ARGs and virulence factors showed that the oil-polluted soil samples had remarkably enhanced expression of these ARGs and some virulence genes. Our study suggests that oil pollution contributes to shifting microbial communities to more resilient types that could survive the toxicity of oil pollution and subsequently become more resilient in terms of higher resistance and virulence potential.}, } @article {pmid37791884, year = {2024}, author = {Gumerov, VM and Ulrich, LE and Zhulin, IB}, title = {MiST 4.0: a new release of the microbial signal transduction database, now with a metagenomic component.}, journal = {Nucleic acids research}, volume = {52}, number = {D1}, pages = {D647-D653}, pmid = {37791884}, issn = {1362-4962}, support = {R35 GM131760/GM/NIGMS NIH HHS/United States ; R35GM131760/NH/NIH HHS/United States ; }, mesh = {*Metagenome ; *Genome, Bacterial ; Bacteria/genetics ; Archaea/genetics ; Metagenomics ; Signal Transduction/genetics ; }, abstract = {Signal transduction systems in bacteria and archaea link environmental stimuli to specific adaptive cellular responses. They control gene expression, motility, biofilm formation, development and other processes that are vital to survival. The microbial signal transduction (MiST) database is an online resource that stores tens of thousands of genomes and allows users to explore their signal transduction profiles, analyze genomes in bulk using the database application programming interface (API) and make testable hypotheses about the functions of newly identified signaling systems. However, signal transduction in metagenomes remained completely unexplored. To lay the foundation for research in metagenomic signal transduction, we have prepared a new release of the MiST database, MiST 4.0, which features over 10 000 metagenome-assembled genomes (MAGs), a scaled representation of proteins and detailed BioSample information. In addition, several thousands of new genomes have been processed and stored in the database. A new interface has been developed that allows users to seamlessly switch between genomes and MAGs. MiST 4.0 is freely available at https://mistdb.com; metagenomes and MAGs can also be explored using the API available on the same page.}, } @article {pmid37791757, year = {2023}, author = {Rønne, ME and Tandrup, T and Madsen, M and Hunt, CJ and Myers, PN and Moll, JM and Holck, J and Brix, S and Strube, ML and Aachmann, FL and Wilkens, C and Svensson, B}, title = {Three alginate lyases provide a new gut Bacteroides ovatus isolate with the ability to grow on alginate.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {10}, pages = {e0118523}, pmid = {37791757}, issn = {1098-5336}, mesh = {Humans ; *Alginates/metabolism ; *Bacteria/metabolism ; Oligosaccharides/metabolism ; Polysaccharide-Lyases/metabolism ; Substrate Specificity ; }, abstract = {Humans consume alginate in the form of seaweed, food hydrocolloids, and encapsulations, making the digestion of this mannuronic acid (M) and guluronic acid (G) polymer of key interest for human health. To increase knowledge on alginate degradation in the gut, a gene catalog from human feces was mined for potential alginate lyases (ALs). The predicted ALs were present in nine species of the Bacteroidetes phylum, of which two required supplementation of an endo-acting AL, expected to mimic cross-feeding in the gut. However, only a new isolate grew on alginate. Whole-genome sequencing of this alginate-utilizing isolate suggested that it is a new Bacteroides ovatus strain harboring a polysaccharide utilization locus (PUL) containing three ALs of families: PL6, PL17, and PL38. The BoPL6 degraded polyG to oligosaccharides of DP 1-3, and BoPL17 released 4,5-unsaturated monouronate from polyM. BoPL38 degraded both alginates, polyM, polyG, and polyMG, in endo-mode; hence, it was assumed to deliver oligosaccharide substrates for BoPL6 and BoPL17, corresponding well with synergistic action on alginate. BoPL17 and BoPL38 crystal structures, determined at 1.61 and 2.11 Å, respectively, showed (α/α)6-barrel + anti-parallel β-sheet and (α/α)7-barrel folds, distinctive for these PL families. BoPL17 had a more open active site than the two homologous structures. BoPL38 was very similar to the structure of an uncharacterized PL38, albeit with a different triad of residues possibly interacting with substrate in the presumed active site tunnel. Altogether, the study provides unique functional and structural insights into alginate-degrading lyases of a PUL in a human gut bacterium.IMPORTANCEHuman ingestion of sustainable biopolymers calls for insight into their utilization in our gut. Seaweed is one such resource with alginate, a major cell wall component, used as a food hydrocolloid and for encapsulation of pharmaceuticals and probiotics. Knowledge is sparse on the molecular basis for alginate utilization in the gut. We identified a new Bacteroides ovatus strain from human feces that grew on alginate and encoded three alginate lyases in a gene cluster. BoPL6 and BoPL17 show complementary specificity toward guluronate (G) and mannuronate (M) residues, releasing unsaturated oligosaccharides and monouronic acids. BoPL38 produces oligosaccharides degraded by BoPL6 and BoPL17 from both alginates, G-, M-, and MG-substrates. Enzymatic and structural characterization discloses the mode of action and synergistic degradation of alginate by these alginate lyases. Other bacteria were cross-feeding on alginate oligosaccharides produced by an endo-acting alginate lyase. Hence, there is an interdependent community in our guts that can utilize alginate.}, } @article {pmid37791411, year = {2023}, author = {Jaarsma, AH and Sipes, K and Zervas, A and Jiménez, FC and Ellegaard-Jensen, L and Thøgersen, MS and Stougaard, P and Benning, LG and Tranter, M and Anesio, AM}, title = {Exploring microbial diversity in Greenland Ice Sheet supraglacial habitats through culturing-dependent and -independent approaches.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {11}, pages = {}, pmid = {37791411}, issn = {1574-6941}, mesh = {*Ice Cover/microbiology ; Greenland ; Biodiversity ; *Microbiota/genetics ; Metagenome ; }, abstract = {The microbiome of Greenland Ice Sheet supraglacial habitats is still underinvestigated, and as a result there is a lack of representative genomes from these environments. In this study, we investigated the supraglacial microbiome through a combination of culturing-dependent and -independent approaches. We explored ice, cryoconite, biofilm, and snow biodiversity to answer: (1) how microbial diversity differs between supraglacial habitats, (2) if obtained bacterial genomes reflect dominant community members, and (3) how culturing versus high throughput sequencing changes our observations of microbial diversity in supraglacial habitats. Genomes acquired through metagenomic sequencing (133 high-quality MAGs) and whole genome sequencing (73 bacterial isolates) were compared to the metagenome assemblies to investigate abundance within the total environmental DNA. Isolates obtained in this study were not dominant taxa in the habitat they were sampled from, in contrast to the obtained MAGs. We demonstrate here the advantages of using metagenome SSU rRNA genes to reflect whole-community diversity. Additionally, we demonstrate a proof-of-concept of the application of in situ culturing in a supraglacial setting.}, } @article {pmid37791400, year = {2023}, author = {Billaud, M and Petit, MA and Lossouarn, J}, title = {The Clostridium-infecting filamentous phage CAK1 genome analysis allows to define a new potential clade of Tubulavirales.}, journal = {FEMS microbiology letters}, volume = {370}, number = {}, pages = {}, doi = {10.1093/femsle/fnad099}, pmid = {37791400}, issn = {1574-6968}, mesh = {Animals ; Swine ; *Viruses/genetics ; Genome ; Clostridium/genetics ; Computational Biology ; *Bacteriophages/genetics ; Genome, Viral ; Phylogeny ; }, abstract = {What we know about Tubulavirales, i.e. filamentous phages, essentially comes from Gram-negative-infecting Inoviridae. However, metagenomics recently suggests filamentous phages are much more widespread and diverse. Here, we report the complete sequence and functional annotation of CAK1, a 6.6 kb filamentous phage that was shown to chronically infect Clostridium beijerinckii 30 years ago and only represents the second filamentous phage cultivated on a Gram-positive bacterium. CAK1 has a typical filamentous phage modular genome with no homologs in databases and we were interested to compare it with a pig gut filamentous phage metagenomics dataset that we previously assembled and for which many filamentous phages were predicted to infect Clostridium species by bioinformatics means. CAK1 is distantly related to nine of these sequences, two of which have been predicted as Clostridium-associated. In itself, this small cluster of CAK1-connected sequences sheds light on the diversity of filamentous phages that putatively infect Clostridium species, and probably many other Gram-positive genera.}, } @article {pmid37791391, year = {2023}, author = {Mason, CN and Shahar, S and Beals, KK and Kelley, ST and Lipson, DA and Swingley, WD and Barber, NA}, title = {Taxonomic and functional restoration of tallgrass prairie soil microbial communities in comparison to remnant and agricultural soils.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {11}, pages = {}, doi = {10.1093/femsec/fiad120}, pmid = {37791391}, issn = {1574-6941}, mesh = {*Soil ; Ecosystem ; Grassland ; Soil Microbiology ; Agriculture ; *Microbiota/genetics ; }, abstract = {Restoring ecosystems requires the re-establishment of diverse soil microbial communities that drive critical ecosystem functions. In grasslands, restoration and management require the application of disturbances like fire and grazing. Disturbances can shape microbial taxonomic composition and potentially functional composition as well. We characterized taxonomic and functional gene composition of soil communities using whole genome shotgun metagenomic sequencing to determine how restored soil communities differed from pre-restoration agricultural soils and original remnant soils, how management affects soil microbes, and whether restoration and management affect the number of microbial genes associated with carbohydrate degradation. We found distinct differences in both taxonomic and functional diversity and composition among restored, remnant, and agricultural soils. Remnant soils had low taxonomic and functional richness and diversity, as well as distinct composition, indicating that restoration of agricultural soils does not re-create soil microbial communities that match remnants. Prescribed fire management increased functional diversity, which also was higher in more recently planted restorations. Finally, restored and post-fire soils included high abundances of genes encoding cellulose-degrading enzymes, so restorations and their ongoing management can potentially support functions important in carbon cycling.}, } @article {pmid37790619, year = {2023}, author = {Waiho, K and Abd Razak, MS and Abdul Rahman, MZ and Zaid, Z and Ikhwanuddin, M and Fazhan, H and Shu-Chien, AC and Lau, NS and Azmie, G and Ishak, AN and Syahnon, M and Kasan, NA}, title = {A metagenomic comparison of clearwater, probiotic, and Rapid BFT[TM] on Pacific whiteleg shrimp, Litopenaeus vannamei cultures.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15758}, pmid = {37790619}, issn = {2167-8359}, mesh = {Animals ; Metagenome ; *Penaeidae ; Seafood ; Aquaculture ; *Probiotics ; }, abstract = {Biofloc technology improves water quality and promote the growth of beneficial bacteria community in shrimp culture. However, little is known about the bacteria community structure in both water and gut of cultured organisms. To address this, the current study characterised the metagenomes derived from water and shrimp intestine samples of novel Rapid BFT[TM] with probiotic and clearwater treatments using 16S V4 region and full length 16S sequencing. Bacteria diversity of water and intestine samples of Rapid BFT[TM] and probiotic treatments were similar. Based on the 16S V4 region, water samples of >20 μm biofloc had the highest abundance of amplicon sequence variant (ASV). However, based on full length 16S, no clear distinction in microbial diversity was observed between water samples and intestine samples. Proteobacteria was the most abundant taxon in all samples based on both 16S V4 and full length 16S sequences. Vibrio was among the highest genus based on 16S V4 region but only full length 16S was able to discern up to species level, with three Vibrios identified-V. harveyi, V. parahaemolyticus and V. vulnificus. Vibrio harveyi being the most abundant species in all treatments. Among water samples, biofloc water samples had the lowest abundance of all three Vibrios, with V. vulnificus was present only in bioflocs of <20 μm. Predicted functional profiles of treatments support the beneficial impacts of probiotic and biofloc inclusion into shrimp culture system. This study highlights the potential displacement of opportunistic pathogens by the usage of biofloc technology (Rapid BFT[TM]) in shrimp culture.}, } @article {pmid37790580, year = {2023}, author = {Abate, A and Li, X and Xu, L and Demaree, B and Noecker, C and Bisanz, J and Weisgerber, D and Modavi, C and Turnbaugh, P}, title = {Microbiome single cell atlases generated with a commercial instrument.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {37790580}, abstract = {Single cell sequencing is useful for resolving complex systems into their composite cell types and computationally mining them for unique features that are masked in pooled sequencing. However, while commercial instruments have made single cell analysis widespread for mammalian cells, analogous tools for microbes are limited. Here, we present EASi-seq (Easily Accessible Single microbe sequencing). By adapting the single cell workflow of the commercial Mission Bio Tapestri instrument, this method allows for efficient sequencing of individual microbes' genomes. EASi-seq allows thousands of microbes to be sequenced per run and, as we show, can generate detailed atlases of human and environmental microbiomes. The ability to capture large shotgun genome datasets from thousands of single microbes provides new opportunities in discovering and analyzing species subpopulations. To facilitate this, we develop a companion bioinformatic pipeline that clusters microbes by similarity, improving whole genome assembly, strain identification, taxonomic classification, and gene annotation. In addition, we demonstrate integration of metagenomic contigs with the EASi-seq datasets to reduce capture bias and increase coverage. Overall, EASi-seq enables high quality single cell genomic data for microbiome samples using an accessible workflow that can be run on a commercially available platform.}, } @article {pmid37790403, year = {2023}, author = {Ma, B and Gavzy, SJ and France, M and Song, Y and Lwin, HW and Kensiski, A and Saxena, V and Piao, W and Lakhan, R and Iyyathurai, J and Li, L and Paluskievicz, C and Wu, L and WillsonShirkey, M and Mongodin, EF and Mas, VR and Bromberg, J}, title = {Rapid intestinal and systemic metabolic reprogramming in an immunosuppressed environment.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {37790403}, support = {R01 HL148672/HL/NHLBI NIH HHS/United States ; T32 AI095190/AI/NIAID NIH HHS/United States ; U01 AI170050/AI/NIAID NIH HHS/United States ; }, abstract = {Intrinsic metabolism shapes the immune environment associated with immune suppression and tolerance in settings such as organ transplantation and cancer. However, little is known about the metabolic activities in an immunosuppressive environment. In this study, we employed metagenomic, metabolomic, and immunological approaches to profile the early effects of the immunosuppressant drug tacrolimus, antibiotics, or both in gut lumen and circulation using a murine model. Tacrolimus induced rapid and profound alterations in metabolic activities within two days of treatment, prior to alterations in gut microbiota composition and structure. The metabolic profile and gut microbiome after seven days of treatment was distinct from that after two days of treatment, indicating continuous drug effects on both gut microbial ecosystem and host metabolism. The most affected taxonomic groups are Clostriales and Verrucomicrobiae (i.e., Akkermansia muciniphila), and the most affected metabolic pathways included a group of interconnected amino acids, bile acid conjugation, glucose homeostasis, and energy production. Highly correlated metabolic changes were observed between lumen and serum metabolism, supporting their significant interactions. Despite a small sample size, this study explored the largely uncharacterized microbial and metabolic events in an immunosuppressed environment and demonstrated that early changes in metabolic activities can have significant implications that may serve as antecedent biomarkers of immune activation or quiescence. To understand the intricate relationships among gut microbiome, metabolic activities, and immune cells in an immune suppressed environment is a prerequisite for developing strategies to monitor and optimize alloimmune responses that determine transplant outcomes.}, } @article {pmid37789859, year = {2023}, author = {Qiao, C and He, M and Wang, S and Jiang, X and Wang, F and Li, X and Tan, S and Chao, Z and Xin, W and Gao, S and Yuan, J and Li, Q and Xu, Z and Zheng, X and Zhao, J and Liu, G}, title = {Multi-omics analysis reveals substantial linkages between the oral-gut microbiomes and inflamm-aging molecules in elderly pigs.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1250891}, pmid = {37789859}, issn = {1664-302X}, abstract = {INTRODUCTION: The accelerated aging of the global population has emerged as a critical public health concern, with increasing recognition of the influential role played by the microbiome in shaping host well-being. Nonetheless, there remains a dearth of understanding regarding the functional alterations occurring within the microbiota and their intricate interactions with metabolic pathways across various stages of aging.

METHODS: This study employed a comprehensive metagenomic analysis encompassing saliva and stool samples obtained from 45 pigs representing three distinct age groups, alongside serum metabolomics and lipidomics profiling.

RESULTS: Our findings unveiled discernible modifications in the gut and oral microbiomes, serum metabolome, and lipidome at each age stage. Specifically, we identified 87 microbial species in stool samples and 68 in saliva samples that demonstrated significant age-related changes. Notably, 13 species in stool, including Clostridiales bacterium, Lactobacillus johnsonii, and Oscillibacter spp., exhibited age-dependent alterations, while 15 salivary species, such as Corynebacterium xerosis, Staphylococcus sciuri, and Prevotella intermedia, displayed an increase with senescence, accompanied by a notable enrichment of pathogenic organisms. Concomitant with these gut-oral microbiota changes were functional modifications observed in pathways such as cell growth and death (necroptosis), bacterial infection disease, and aging (longevity regulating pathway) throughout the aging process. Moreover, our metabolomics and lipidomics analyses unveiled the accumulation of inflammatory metabolites or the depletion of beneficial metabolites and lipids as aging progressed. Furthermore, we unraveled a complex interplay linking the oral-gut microbiota with serum metabolites and lipids.

DISCUSSION: Collectively, our findings illuminate novel insights into the potential contributions of the oral-gut microbiome and systemic circulating metabolites and lipids to host lifespan and healthy aging.}, } @article {pmid37789855, year = {2023}, author = {Zhao, M and Li, Y and Wei, W and Zhang, Z and Zhou, H}, title = {The distribution variation of pathogens and virulence factors in different geographical populations of giant pandas.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1264786}, pmid = {37789855}, issn = {1664-302X}, abstract = {Intestinal diseases caused by opportunistic pathogens seriously threaten the health and survival of giant pandas. However, our understanding of gut pathogens in different populations of giant pandas, especially in the wild populations, is still limited. Here, we conducted a study based on 52 giant panda metagenomes to investigate the composition and distribution of gut pathogens and virulence factors (VFs) in five geographic populations (captive: GPCD and GPYA; wild: GPQIN, GPQIO, and GPXXL). The results of the beta-diversity analyzes revealed a close relationship and high similarity in pathogen and VF compositions within the two captive groups. Among all groups, Proteobacteria, Firmicutes, and Bacteroidetes emerged as the top three abundant phyla. By using the linear discriminant analysis effect size method, we identified pathogenic bacteria unique to different populations, such as Klebsiella in GPCD, Salmonella in GPYA, Hafnia in GPQIO, Pedobacter in GPXXL, and Lactococcus in GPQIN. In addition, we identified 12 VFs that play a role in the intestinal diseases of giant pandas, including flagella, CsrA, enterobactin, type IV pili, alginate, AcrAB, capsule, T6SS, urease, type 1 fimbriae, polar flagella, allantoin utilization, and ClpP. These VFs influence pathogen motility, adhesion, iron uptake, acid resistance, and protein regulation, thereby contributing to pathogen infection and pathogenicity. Notably, we also found a difference in virulence of Pseudomonas aeruginosa between GPQIN and non-GPQIN wild populations, in which the relative abundance of VFs (0.42%) of P. aeruginosa was the lowest in GPQIN and the highest in non-GPQIN wild populations (GPXXL: 23.55% and GPQIO: 10.47%). In addition to enhancing our understanding of gut pathogens and VFs in different geographic populations of giant pandas, the results of this study provide a specific theoretical basis and data support for the development of effective conservation measures for giant pandas.}, } @article {pmid37789830, year = {2023}, author = {Ling, Y and Hu, X and Zheng, G and Ye, W and Yuan, K and Ye, L and Huang, W and Tian, B and Gu, B}, title = {Metagenomics as New Tool for Diagnosis of Scrub Typhus: Two Case Reports.}, journal = {International medical case reports journal}, volume = {16}, number = {}, pages = {617-622}, pmid = {37789830}, issn = {1179-142X}, abstract = {Scrub typhus is a vector-borne infectious disease caused by Orientia tsutsugamushi. Accurate and timely diagnosis at the early infection stage could save the patients' lives. Traditional technologies were limited to rapidly and successfully detecting Orientia tsutsugamushi due to poor specificity, especially in the condition of atypical symptoms. The technology of Metagenomic next-generation sequencing (mNGS) is amenable to finding the real pathogen because it holds potential as a diagnostic platform for unbiased pathogen identification and precision medicine. Herein, we reported two clinical case reports relative to the Orientia tsutsugamushi infection diagnosed by mNGS. We hope these two cases will improve clinical diagnosis.}, } @article {pmid37789449, year = {2023}, author = {Yang, J and Woo, JJ and Oh, SY and Kim, W and Hur, JS}, title = {Fungal community inside lichen: a curious case of sparse diversity and high modularity.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {73}, pmid = {37789449}, issn = {2524-6372}, support = {NRF-2020R1I1A2073283//National Research Foundation of Korea/ ; NRF-2020R1I1A2073283//National Research Foundation of Korea/ ; NRF-2020R1I1A2073283//National Research Foundation of Korea/ ; NRF-2020R1I1A2073283//National Research Foundation of Korea/ ; NRF-2020R1I1A2073283//National Research Foundation of Korea/ ; }, abstract = {BACKGROUND: Lichens represent not only the mutualism of fungal and photosynthetic partners but also are composed of microbial consortium harboring diverse fungi known as endolichenic fungi. While endolichenic fungi are known to exert a remarkable influence on lichen ecology through their crucial roles in nutrient cycling, bioprospecting and biodiversity, the enigmatic community structures of these fungal inhabitants remain shrouded in mystery, awaiting further exploration and discovery. To address knowledge gap, we conducted metabarcoding on two lichens using 18S gene amplification, Dirinara applanta and Parmotrema tinctorum, and compared their microbial communities to those found in the pine bark to which the lichens were attached. Our hypothesis was that the endolichenic communities would exhibit distinct diversity patterns, community structures, network structures, and specialist composition compared to the surrounding epiphytic community.

RESULTS: Our investigation has shed light on the clear demarcation between the endolichenic and epiphytic fungal communities, as they exhibit markedly different characteristics that set them apart from each other. This research demonstrated that the endolichenic communities are less diverse as compared to the epiphytic communities. Through community similarity analysis, we observed that two endolichenic communities are more similar to each other in terms of community composition than with the adjacent epiphytic communities. Moreover, we unveiled a striking contrast in the network structures between the endolichenic and epiphytic communities, as the former displayed a more modular and less nested features that is evocative of a potent host-filtration mechanism.

CONCLUSIONS: Through our investigation, we have discovered that lichens harbor less intricate and interconnected fungal communities compared to the neighboring epiphytic environment. These observations provide valuable insights into the metagenomic architecture of lichens and offer a tantalizing glimpse into the unique mycobiome.}, } @article {pmid37789379, year = {2023}, author = {Zhao, S and Chi, L and Chen, H}, title = {CEGA: a method for inferring natural selection by comparative population genomic analysis across species.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {219}, pmid = {37789379}, issn = {1474-760X}, mesh = {Animals ; Humans ; *Metagenomics ; Selection, Genetic ; Polymorphism, Genetic ; *Hominidae ; Genome ; }, abstract = {We developed maximum likelihood method for detecting positive selection or balancing selection using multilocus or genomic polymorphism and divergence data from two species. The method is especially useful for investigating natural selection in noncoding regions. Simulations demonstrate that the method outperforms existing methods in detecting both positive and balancing selection. We apply the method to population genomic data from human and chimpanzee. The list of genes identified under selection in the noncoding regions is prominently enriched in pathways related to the brain and nervous system. Therefore, our method will serve as a useful tool for comparative population genomic analysis.}, } @article {pmid37789055, year = {2023}, author = {Flahaut, M and Leprohon, P and Pham, NP and Gingras, H and Bourbeau, J and Papadopoulou, B and Maltais, F and Ouellette, M}, title = {Distinctive features of the oropharyngeal microbiome in Inuit of Nunavik and correlations of mild to moderate bronchial obstruction with dysbiosis.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {16622}, pmid = {37789055}, issn = {2045-2322}, mesh = {Humans ; *Bronchial Diseases/epidemiology ; *Dysbiosis/epidemiology ; Inuit ; Lung ; *Microbiota ; *Oropharynx/microbiology ; }, abstract = {Inuit of Nunavik are coping with living conditions that can influence respiratory health. Our objective was to investigate associations between respiratory health in Inuit communities and their airway microbiome. Oropharyngeal samples were collected during the Qanuilirpitaa? 2017 Inuit Health Survey and subjected to metagenomic analyses. Participants were assigned to a bronchial obstruction group or a control group based on their clinical history and their pulmonary function, as monitored by spirometry. The Inuit microbiota composition was found to be distinct from other studied populations. Within the Inuit microbiota, differences in diversity measures tend to distinguish the two groups. Bacterial taxa found to be more abundant in the control group included candidate probiotic strains, while those enriched in the bronchial obstruction group included opportunistic pathogens. Crossing taxa affiliation method and machine learning consolidated our finding of distinct core microbiomes between the two groups. More microbial metabolic pathways were enriched in the control participants and these were often involved in vitamin and anti-inflammatory metabolism, while a link could be established between the enriched pathways in the disease group and inflammation. Overall, our results suggest a link between microbial abundance, interactions and metabolic activities and respiratory health in the Inuit population.}, } @article {pmid37788797, year = {2023}, author = {Xu, D and Zhang, X and Yuan, X and Han, H and Xue, Y and Guo, X}, title = {Hazardous risk of antibiotic resistance genes: Host occurrence, distribution, mobility and vertical transmission from different environments to corn silage.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {338}, number = {}, pages = {122671}, doi = {10.1016/j.envpol.2023.122671}, pmid = {37788797}, issn = {1873-6424}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Zea mays ; Silage/analysis ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; }, abstract = {Antibiotic resistance genes (ARGs) are one of the emerging contaminants posing a great deal of hazardous risk to public health. This study employed metagenomics and deciphered the potential risk of the antibiotic resistome and their vertical transfer to ensiled whole-crop corn silage harvested from six climate zones: 1. Warm temperate-fully humid-hot summer (Cfa), 2. Arid-desert-cold arid (BWk), 3. Snow-desert-cold summer (Dwc), 4. Snow-desert-hot summer (Dwa), 5. Arid-steppe-cold arid (BSk), and 6. Equatorial-desert (Aw) based on the Köppen-Geiger climate classification in China. The findings demonstrate a high diversity of ARGs, which is related to the drug classes of tetracycline, ciprofloxacin, lincosamide, fosfomycin, and beta lactam. Resistome variations are mostly related to variations in microbial composition and fermentation characteristics of the silages from different climate zones, which are indirectly influenced by environmental conditions. The most dominating ARGs in corn silage were tetM, acrA, H-NS, lnuA, emrR, and KpnG, which is primarily hosted by Klebsiella and Lactobacilli. There were 5 high-risk ARGs (tetM, bacA, SHV-1, dfrA17, and QnrS1) in silage from different climate zones, and the tetM was the most prevalent high-risk ARG. However, throughout the ensiling process, the abundance of ARGs, and mobile ARGs were reduced. The resistome contamination in silage from Tibet (Dwc) with high altitude and harsh environment was relatively low due to the low variety and abundance of ARGs, the low abundance of mobile ARGs and high-risk ARGs. In addition, most of the bacteria responsible for the silage fermentation were also found to be the hosts to the ARGs, although their abundance decreased after 90 d of silage fermentation. Hence, we alert the existence of ARGs-related biosafety risk in silages and call for more attention to the silage ARGs, their hosts, and mobile genetic elements in order to curtail their possible risk to public health.}, } @article {pmid37788637, year = {2023}, author = {Kazemzadeh, K and Pelosi, L and Chenal, C and Chobert, SC and Hajj Chehade, M and Jullien, M and Flandrin, L and Schmitt, W and He, Q and Bouvet, E and Jarzynka, M and Varoquaux, N and Junier, I and Pierrel, F and Abby, SS}, title = {Diversification of Ubiquinone Biosynthesis via Gene Duplications, Transfers, Losses, and Parallel Evolution.}, journal = {Molecular biology and evolution}, volume = {40}, number = {10}, pages = {}, pmid = {37788637}, issn = {1537-1719}, mesh = {*Gene Duplication ; *Ubiquinone/genetics/metabolism ; Mixed Function Oxygenases/genetics ; Iron/metabolism ; }, abstract = {The availability of an ever-increasing diversity of prokaryotic genomes and metagenomes represents a major opportunity to understand and decipher the mechanisms behind the functional diversification of microbial biosynthetic pathways. However, it remains unclear to what extent a pathway producing a specific molecule from a specific precursor can diversify. In this study, we focus on the biosynthesis of ubiquinone (UQ), a crucial coenzyme that is central to the bioenergetics and to the functioning of a wide variety of enzymes in Eukarya and Pseudomonadota (a subgroup of the formerly named Proteobacteria). UQ biosynthesis involves three hydroxylation reactions on contiguous carbon atoms. We and others have previously shown that these reactions are catalyzed by different sets of UQ-hydroxylases that belong either to the iron-dependent Coq7 family or to the more widespread flavin monooxygenase (FMO) family. Here, we combine an experimental approach with comparative genomics and phylogenetics to reveal how UQ-hydroxylases evolved different selectivities within the constrained framework of the UQ pathway. It is shown that the UQ-FMOs diversified via at least three duplication events associated with two cases of neofunctionalization and one case of subfunctionalization, leading to six subfamilies with distinct hydroxylation selectivity. We also demonstrate multiple transfers of the UbiM enzyme and the convergent evolution of UQ-FMOs toward the same function, which resulted in two independent losses of the Coq7 ancestral enzyme. Diversification of this crucial biosynthetic pathway has therefore occurred via a combination of parallel evolution, gene duplications, transfers, and losses.}, } @article {pmid37788456, year = {2023}, author = {Toyoshima, K and Ohsugi, Y and Lin, P and Komatsu, K and Shiba, T and Takeuchi, Y and Hirota, T and Shimohira, T and Tsuchiya, Y and Katagiri, S and Iwata, T and Aoki, A}, title = {Blue Light-Emitting Diode Irradiation Without a Photosensitizer Alters Oral Microbiome Composition of Ligature-Induced Periodontitis in Mice.}, journal = {Photobiomodulation, photomedicine, and laser surgery}, volume = {41}, number = {10}, pages = {549-559}, doi = {10.1089/photob.2023.0061}, pmid = {37788456}, issn = {2578-5478}, mesh = {Mice ; Male ; Animals ; Photosensitizing Agents/pharmacology ; X-Ray Microtomography/adverse effects ; RNA, Ribosomal, 16S ; *Alveolar Bone Loss/etiology/metabolism ; *Periodontitis/therapy/complications/metabolism ; *Microbiota ; }, abstract = {Objective: This study investigated the suppressive effects of blue light-emitting diode (LED) irradiation on bone resorption and changes in the oral microbiome of mice with ligature-induced periodontitis. Background: Wavelength of blue light has antimicrobial effects; however, whether blue LED irradiation alone inhibits the progression of periodontitis remains unclear. Methods: Nine-week-old male mice ligated ligature around the right maxillary second molar was divided into ligation alone (Li) and ligation with blue LED irradiation (LiBL) groups. The LiBL group underwent blue LED (wavelength, 455 nm) irradiation four times in a week at 150 mW/cm[2] without a photosensitizer on the gingival tissue around the ligated tooth at a distance of 5 mm for 5 min. The total energy density per day was 45 J/cm[2]. Bone resorption was evaluated using micro-computed tomography at 8 days. Differences in the oral microbiome composition of the collected ligatures between the Li and LiBL groups were analyzed using next-generation sequencing based on the 16S rRNA gene from the ligatures. Results: Blue LED irradiation did not suppress bone resorption caused by ligature-induced periodontitis. However, in the LiBL group, the α-diversity, number of observed features, and Chao1 were significantly decreased. The relative abundances in phylum Myxococcota and Bacteroidota were underrepresented, and the genera Staphylococcus, Lactococcus, and Lactobacillus were significantly overrepresented by blue LED exposure. Metagenomic function prediction indicated an increase in the downregulated pathways related to microbial energy metabolism after irradiation. The co-occurrence network was altered to a simpler structure in the LiBL group, and the number of core genera decreased. Conclusions: Blue LED irradiation altered the composition and network of the oral microbiome of ligature-induced periodontitis in mice.}, } @article {pmid37788279, year = {2023}, author = {Wang, J and Liu, X and Sun, R and Mao, H and Liu, M and Jin, X}, title = {Akkermansia muciniphila participates in the host protection against helminth-induced cardiac fibrosis via TLR2.}, journal = {PLoS pathogens}, volume = {19}, number = {10}, pages = {e1011683}, pmid = {37788279}, issn = {1553-7374}, mesh = {Animals ; Humans ; Mice ; Fibrosis ; RNA, Ribosomal, 16S/genetics ; *Toll-Like Receptor 2/genetics ; *Verrucomicrobia/genetics ; Trichinella spiralis ; *Trichinellosis/immunology ; }, abstract = {Helminth Trichinella spiralis (Ts) is one of the major pathogens of human infective myocarditis that can lead to cardiac fibrosis (CF). The gut microbiota involved in this pathology are of interest. Here, we use mice infected with Ts as a model to examine the interactions between gut microbes and host protection to CF. Infected mice show enhanced CF severity. We find that antibiotics treatment to deplete the microbiota aggravates the disease phenotype. Attempts to restore microbiota using fecal microbiota transplantation ameliorates helminth-induced CF. 16S rRNA gene sequencing and metagenomics sequencing reveal a higher abundance of Akkermansia muciniphila in gut microbiomes of Ts-infected mice. Oral supplementation with alive or pasteurized A. muciniphila improves CF via TLR2. This work represents a substantial advance toward our understanding of causative rather than correlative relationships between the gut microbiota and CF.}, } @article {pmid37788167, year = {2023}, author = {Wu, Y and Huang, L and Li, M and Cui, X and Zhan, Q and Wang, C}, title = {The role of lung microbiota in primary graft dysfunction in lung transplant recipients.}, journal = {Clinical transplantation}, volume = {37}, number = {12}, pages = {e15152}, doi = {10.1111/ctr.15152}, pmid = {37788167}, issn = {1399-0012}, support = {2022-HX-53//the Internal cross-cutting projects at China-Japan Friendship Hospital/ ; MTP2022A004//the Medical Talent Program for High-hroughput Sequencing Technology in Infectious Diseases, China/ ; }, mesh = {Humans ; Retrospective Studies ; *Primary Graft Dysfunction/diagnosis/etiology ; Dysbiosis/complications ; Transplant Recipients ; Lung ; *Lung Transplantation/adverse effects ; }, abstract = {BACKGROUND: Recent studies have shown that the lung microbiota is altered in critically ill patients and predicts clinical outcomes. Primary graft dysfunction (PGD) is a common complication and a leading cause of death within 1 month of lung transplantation, but the clinical significance of changes in the lung bacterial community during PGD is unclear. The aim of this study was to determine the contribution of the lung microbiota to the development and course of severe PGD.

METHODS: We conducted a retrospective study to characterize the lung microbiota of 32 lung transplant patients with combined PGD using next-generation sequencing of bronchoalveolar lavage samples. The relationship between lung flora dysbiosis and lung immunity in PGD was assessed by quantification of alveolar cytokines. The contribution of microbiota characteristics to patient outcomes was assessed by estimating overall survival.

RESULTS: Patients diagnosed with PGD grade 3 showed a reduction in alpha diversity, driven by a significant increase in the abundance of the genera Modestobacter, Scardovia and Selenomonas, and a reduction in the proportion of the genera Klebsiella and Oribacterium. Alpha diversity of the lung microbiota in PGD3 patients was negatively correlated with BALF interleukin (IL)-2 (r = -.752, p < .05). In addition, bacterial diversity in the lung microbiota of non-survivors was lower than that of survivors (p = .041).

CONCLUSIONS: There is variation in the lung microbiota of PGD grade 3 patients and dysbiosis of the lung microbiota is associated with lung immunity. The lung microbiota has potential in the diagnosis and treatment of PGD grade 3.}, } @article {pmid37787745, year = {2024}, author = {Yu, KD and Betts, MN and Urban, GM and Schwartz, MLB and Robinson, TO and Moyer, RJ and Taddonio, SW and Vasudevan, A and Johns, A and Sturm, AC and Kelly, MA and Williams, MS and Poler, SM and Buchanan, AH}, title = {Evaluation of Malignant Hyperthermia Features in Patients with Pathogenic or Likely Pathogenic RYR1 Variants Disclosed through a Population Genomic Screening Program.}, journal = {Anesthesiology}, volume = {140}, number = {1}, pages = {52-61}, doi = {10.1097/ALN.0000000000004786}, pmid = {37787745}, issn = {1528-1175}, mesh = {Humans ; Genetic Testing ; *Malignant Hyperthermia/diagnosis/genetics/pathology ; Metagenomics ; Mutation ; Phenotype ; *Ryanodine Receptor Calcium Release Channel/genetics ; }, abstract = {BACKGROUND: Malignant hyperthermia (MH) susceptibility is a heritable musculoskeletal disorder that can present as a potentially fatal hypermetabolic response to triggering anesthesia agents. Genomic screening for variants in MH-associated genes RYR1 and CACNA1S provides an opportunity to prevent morbidity and mortality. There are limited outcomes data from disclosing variants in RYR1, the most common MH susceptibility gene, in unselected populations. The authors sought to identify the rate of MH features or fulminant episodes after triggering agent exposure in an unselected population undergoing genomic screening including actionable RYR1 variants.

METHODS: The MyCode Community Health Initiative by Geisinger (USA) is an electronic health record-linked biobank that discloses pathogenic and likely pathogenic variants in clinically actionable genes to patient-participants. Available electronic anesthesia and ambulatory records for participants with actionable RYR1 results returned through December 2020 were evaluated for pertinent findings via double-coded chart reviews and reconciliation. Descriptive statistics for observed phenotypes were calculated.

RESULTS: One hundred fifty-two participants had an actionable RYR1 variant disclosed during the study period. None had previous documented genetic testing for MH susceptibility; one had previous contracture testing diagnosing MH susceptibility. Sixty-eight participants (44.7%) had anesthesia records documenting triggering agent exposure during at least one procedure. None received dantrolene treatment or had documented muscle rigidity, myoglobinuria, hyperkalemia, elevated creatine kinase, severe myalgia, or tea-colored urine. Of 120 possibly MH-related findings (postoperative intensive care unit admissions, hyperthermia, arterial blood gas evaluation, hypercapnia, or tachycardia), 112 (93.3%) were deemed unlikely to be MH events; 8 (6.7%) had insufficient records to determine etiology.

CONCLUSIONS: Results demonstrate a low frequency of classic intraanesthetic hypermetabolic phenotypes in an unselected population with actionable RYR1 variants. Further research on the actionability of screening for MH susceptibility in unselected populations, including economic impact, predictors of MH episodes, and expanded clinical phenotypes, is necessary.}, } @article {pmid37787536, year = {2023}, author = {Sapula, SA and Amsalu, A and Whittall, JJ and Hart, BJ and Siderius, NL and Nguyen, L and Gerber, C and Turnidge, J and Venter, H}, title = {The scope of antimicrobial resistance in residential aged care facilities determined through analysis of Escherichia coli and the total wastewater resistome.}, journal = {Microbiology spectrum}, volume = {11}, number = {6}, pages = {e0073123}, pmid = {37787536}, issn = {2165-0497}, support = {GN1152556//Medical Research Future Fund/ ; }, mesh = {Humans ; Aged ; *Escherichia coli ; Anti-Bacterial Agents/pharmacology ; *Escherichia coli Infections/epidemiology/microbiology ; Wastewater ; Drug Resistance, Bacterial ; Drug Resistance, Multiple, Bacterial/genetics ; beta-Lactamases/genetics ; Microbial Sensitivity Tests ; }, abstract = {Antimicrobial resistance (AMR) is a global threat that imposes a heavy burden on our health and economy. Residential aged care facilities (RACFs), where frequent inappropriate antibiotic use creates a selective environment that promotes the development of bacterial resistance, significantly contribute to this problem. We used wastewater-based epidemiology to provide a holistic whole-facility assessment and comparison of antimicrobial resistance in two RACFs and a retirement village. Resistant Escherichia coli, a common and oftentimes problematic pathogen within RACFs, was isolated from the wastewater, and the phenotypic and genotypic AMR was determined for all isolates. We observed a high prevalence of an international high-risk clone, carrying an extended-spectrum beta-lactamase in one facility. Analysis of the entire resistome also revealed a greater number of mobile resistance genes in this facility. Finally, both facilities displayed high fluoroquinolone resistance rates-a worrying trend seen globally despite measures in place aimed at limiting their use.}, } @article {pmid37787419, year = {2023}, author = {Zhang, Y and Zhou, Y and Humbert, P and Yuan, D and Yuan, C}, title = {Effect on the Skin Microbiota of Oral Minocycline for Rosacea.}, journal = {Acta dermato-venereologica}, volume = {103}, number = {}, pages = {adv10331}, pmid = {37787419}, issn = {1651-2057}, mesh = {Humans ; Anti-Bacterial Agents/therapeutic use ; *Microbiota ; Minocycline ; RNA, Ribosomal, 16S/genetics ; *Rosacea/diagnosis/drug therapy ; Skin/microbiology ; }, abstract = {In the rosacea an unstable skin microbiota is significant for disease progression. However, data on the influence on the skin microbiota of treatment with systemic antibiotics are limited. This single-arm trial recruited patients with rosacea. Oral minocycline 50 mg was administered twice daily for 6 weeks. The lesions on the cheek and nose were sampled for 16S rRNA amplicon sequencing and metagenomic sequencing at baseline, 3 weeks and 6 weeks of treatment. Physiological parameters were detected using non-invasive instruments. After treatment, distribution of the Investigator Global Assessment scores changed significantly. For the skin microbiota, a notable increase in α-diversity and a shift of structure were observed after treatment. Treatment was accompanied by a reduction in the relative abundance of Cutibacterium and Staphylococcus, indicating negative correlations with increased bacterial metabolic pathways, such as butyrate synthesis and L-tryptophan degradation. The increased butyrate and tryptophan metabolites would be conducive to inhibiting skin inflammation and promoting skin barrier repair. In addition, the abundance of skin bacterial genes related to tetracycline resistance and multidrug resistance increased notably after antibiotic treatment.}, } @article {pmid37786716, year = {2023}, author = {Benoit, G and Raguideau, S and James, R and Phillippy, AM and Chikhi, R and Quince, C}, title = {Efficient High-Quality Metagenome Assembly from Long Accurate Reads using Minimizer-space de Bruijn Graphs.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37786716}, abstract = {We introduce a novel metagenomics assembler for high-accuracy long reads. Our approach, implemented as metaMDBG, combines highly efficient de Bruijn graph assembly in minimizer space, with both a multi-k' approach for dealing with variations in genome coverage depth and an abundance-based filtering strategy for simplifying strain complexity. The resulting algorithm is more efficient than the state-of-the-art but with better assembly results. metaMDBG was 1.5 to 12 times faster than competing assemblers and requires between one-tenth and one-thirtieth of the memory across a range of data sets. We obtained up to twice as many high-quality circularised prokaryotic metagenome assembled genomes (MAGs) on the most complex communities, and a better recovery of viruses and plasmids. metaMDBG performs particularly well for abundant organisms whilst being robust to the presence of strain diversity. The result is that for the first time it is possible to efficiently reconstruct the majority of complex communities by abundance as near-complete MAGs.}, } @article {pmid37786251, year = {2023}, author = {Wang, Y and Ma, W and Mehta, R and Nguyen, LH and Song, M and Drew, DA and Asnicar, F and Huttenhower, C and Segata, N and Wolf, J and Spector, T and Berry, S and Staller, K and Chan, AT}, title = {Diet and gut microbial associations in irritable bowel syndrome according to disease subtype.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2262130}, pmid = {37786251}, issn = {1949-0984}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; K23 DK120945/DK/NIDDK NIH HHS/United States ; K23 DK125838/DK/NIDDK NIH HHS/United States ; /MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; R35 CA253185/CA/NCI NIH HHS/United States ; U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Irritable Bowel Syndrome/microbiology ; *Gastrointestinal Microbiome ; Diarrhea/microbiology ; Constipation/complications ; Diet ; }, abstract = {The role of diet and the gut microbiome in the etiopathogenesis of irritable bowel syndrome (IBS) is not fully understood. Therefore, we investigated the interplay between dietary risk factors and gut microbiota in IBS subtypes using a food frequency questionnaire and stool metagenome data from 969 participants aged 18-65 years in the ZOE PREDICT 1 study, an intervention study designed to predict postprandial metabolic responses. We identified individuals with IBS subtype according to the Rome III criteria based on predominant bowel habits during symptom onset: diarrhea (i.e. looser), constipation (i.e. harder), and mixed. Participants with IBS-D (n = 59) consumed more healthy plant-based foods (e.g. whole grains, leafy vegetables) and fiber, while those with IBS-C (n = 49) tended to consume more unhealthy plant-based foods (e.g. refined grains, fruit juice) than participants without IBS (n = 797). Microbial diversity was nominally lower in patients with IBS-D than in participants without IBS or with IBS-C. Using multivariable-adjusted linear regression, we identified specific microbiota variations in IBS subtypes, including slight increases in pro-inflammatory taxa in IBS-C (e.g. Escherichia coli) and loss of strict anaerobes in IBS-D (e.g. Faecalibacterium prausnitzii). Our analysis also revealed intriguing evidence of interactions between diet and Faecalibacterium prausnitzii. The positive associations between fiber and iron intake and IBS-diarrhea were stronger among individuals with a higher relative abundance of Faecalibacterium prausnitzii, potentially driven by carbohydrate metabolic pathways, including the superpathway of β-D-glucuronide and D-glucuronate degradation. In conclusion, our findings suggest subtype-specific variations in dietary habits, gut microbial composition and function, and diet-microbiota interactions in IBS, providing insights into potential microbiome-informed dietary interventions.}, } @article {pmid37784018, year = {2023}, author = {Tang, X and Yang, L and Miao, Y and Ha, W and Li, Z and Mi, D}, title = {Angelica polysaccharides relieve blood glucose levels in diabetic KKAy mice possibly by modulating gut microbiota: an integrated gut microbiota and metabolism analysis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {281}, pmid = {37784018}, issn = {1471-2180}, mesh = {Mice ; Male ; Animals ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/drug therapy/microbiology ; Blood Glucose/metabolism ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred C57BL ; Polysaccharides/pharmacology ; }, abstract = {BACKGROUND: Angelica polysaccharides (AP) have numerous benefits in relieving type 2 diabetes (T2D). However, the underlying mechanisms have yet to be fully understood. Recent many reports have suggested that altering gut microbiota can have adverse effects on the host metabolism and contribute to the development of T2D. Here, we successfully established the T2D model using the male KKAy mice with high-fat and high-sugar feed. Meanwhile, the male C57BL/6 mice were fed with a normal feed. T2D KKAy mice were fed either with or without AP supplementation. In each group, we measured the mice's fasting blood glucose, weight, and fasting serum insulin levels. We collected the cecum content of mice, the gut microbiota was analyzed by targeted full-length 16S rRNA metagenomic sequencing and metabolites were analyzed by untargeted-metabolomics.

RESULTS: We found AP effectively alleviated glycemic disorders of T2D KKAy mice, with the changes in gut microbiota composition and function. Many bacteria species and metabolites were markedly changed in T2D KKAy mice and reversed by AP. Additionally, 16 altered metabolic pathways affected by AP were figured out by combining metagenomic pathway enrichment analysis and metabolic pathway enrichment analysis. The key metabolites in 16 metabolic pathways were significantly associated with the gut microbial alteration. Together, our findings showed that AP supplementation could attenuate the diabetic phenotype. Significant gut microbiota and gut metabolite changes were observed in the T2D KKAy mice and AP intervention.

CONCLUSIONS: Administration of AP has been shown to improve the composition of intestinal microbiota in T2D KKAy mice, thus providing further evidence for the potential therapeutic application of AP in the treatment of T2D.}, } @article {pmid37784008, year = {2023}, author = {Rumbavicius, I and Rounge, TB and Rognes, T}, title = {HoCoRT: host contamination removal tool.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {371}, pmid = {37784008}, issn = {1471-2105}, support = {190179 and 198048//Kreftforeningen/ ; }, mesh = {Humans ; *Software ; Metagenome ; Sequence Analysis, DNA/methods ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {BACKGROUND: Shotgun metagenome sequencing data obtained from a host environment will usually be contaminated with sequences from the host organism. Host sequences should be removed before further analysis to avoid biases, reduce downstream computational load, or ensure privacy in the case of a human host. The tools that we identified, as designed specifically to perform host contamination sequence removal, were either outdated, not maintained, or complicated to use. Consequently, we have developed HoCoRT, a fast and user-friendly tool that implements several methods for optimised host sequence removal. We have evaluated the speed and accuracy of these methods.

RESULTS: HoCoRT is an open-source command-line tool for host contamination removal. It is designed to be easy to install and use, offering a one-step option for genome indexing. HoCoRT employs a variety of well-known mapping, classification, and alignment methods to classify reads. The user can select the underlying classification method and its parameters, allowing adaptation to different scenarios. Based on our investigation of various methods and parameters using synthetic human gut and oral microbiomes, and on assessment of publicly available data, we provide recommendations for typical datasets with short and long reads.

CONCLUSIONS: To decontaminate a human gut microbiome with short reads using HoCoRT, we found the optimal combination of speed and accuracy with BioBloom, Bowtie2 in end-to-end mode, and HISAT2. Kraken2 consistently demonstrated the highest speed, albeit with a trade-off in accuracy. The same applies to an oral microbiome, but here Bowtie2 was notably slower than the other tools. For long reads, the detection of human host reads is more difficult. In this case, a combination of Kraken2 and Minimap2 achieved the highest accuracy and detected 59% of human reads. In comparison to the dedicated DeconSeq tool, HoCoRT using Bowtie2 in end-to-end mode proved considerably faster and slightly more accurate. HoCoRT is available as a Bioconda package, and the source code can be accessed at https://github.com/ignasrum/hocort along with the documentation. It is released under the MIT licence and is compatible with Linux and macOS (except for the BioBloom module).}, } @article {pmid37783796, year = {2023}, author = {Sharpe, G and Zhao, L and Meyer, MG and Gong, W and Burns, SM and Tagliabue, A and Buck, KN and Santoro, AE and Graff, JR and Marchetti, A and Gifford, S}, title = {Synechococcus nitrogen gene loss in iron-limited ocean regions.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {107}, pmid = {37783796}, issn = {2730-6151}, support = {80NSSC17K0552//National Aeronautics and Space Administration (NASA)/ ; 80NSSC17K0552//National Aeronautics and Space Administration (NASA)/ ; 80NSSC17K0568//National Aeronautics and Space Administration (NASA)/ ; 80NSSC17K0552//National Aeronautics and Space Administration (NASA)/ ; OCE-1756433//National Science Foundation (NSF)/ ; }, abstract = {Synechococcus are the most abundant cyanobacteria in high latitude regions and are responsible for an estimated 17% of annual marine net primary productivity. Despite their biogeochemical importance, Synechococcus populations have been unevenly sampled across the ocean, with most studies focused on low-latitude strains. In particular, the near absence of Synechococcus genomes from high-latitude, High Nutrient Low Chlorophyll (HNLC) regions leaves a gap in our knowledge of picocyanobacterial adaptations to iron limitation and their influence on carbon, nitrogen, and iron cycles. We examined Synechococcus populations from the subarctic North Pacific, a well-characterized HNLC region, with quantitative metagenomics. Assembly with short and long reads produced two near complete Synechococcus metagenome-assembled genomes (MAGs). Quantitative metagenome-derived abundances of these populations matched well with flow cytometry counts, and the Synechococcus MAGs were estimated to comprise >99% of the Synechococcus at Station P. Whereas the Station P Synechococcus MAGs contained multiple genes for adaptation to iron limitation, both genomes lacked genes for uptake and assimilation of nitrate and nitrite, suggesting a dependence on ammonium, urea, and other forms of recycled nitrogen leading to reduced iron requirements. A global analysis of Synechococcus nitrate reductase abundance in the TARA Oceans dataset found nitrate assimilation genes are also lower in other HNLC regions. We propose that nitrate and nitrite assimilation gene loss in Synechococcus may represent an adaptation to severe iron limitation in high-latitude regions where ammonium availability is higher. Our findings have implications for models that quantify the contribution of cyanobacteria to primary production and subsequent carbon export.}, } @article {pmid37783332, year = {2023}, author = {Wang, J and Cheng, Z and Wang, J and Chen, D and Chen, J and Yu, J and Qiu, S and Dionysiou, DD}, title = {Enhancement of bio-S[0] recovery and revealing the inhibitory effect on microorganisms under high sulfide loading.}, journal = {Environmental research}, volume = {238}, number = {Pt 2}, pages = {117214}, doi = {10.1016/j.envres.2023.117214}, pmid = {37783332}, issn = {1096-0953}, mesh = {Oxidation-Reduction ; *Sulfides ; Bacteria/metabolism ; Bioreactors ; *Hydrogen Sulfide ; }, abstract = {Biodesulfurization is a mature technology, but obtaining biosulfur (S[0]) that can be easily settled naturally is still a challenge. Increasing the sulfide load is one of the known methods to obtain better settling of S[0]. However, the inhibitory effect of high levels of sulfide on microbes has also not been well studied. We constructed a high loading sulfide (1.55-10.86 kg S/m[3]/d) biological removal system. 100% sulfide removal and 0.56-2.53 kg S/m[3]/d S[0] (7.0 ± 0.09-16.4 ± 0.25 μm) recovery were achieved at loads of 1.55-7.75 kg S/m[3]/d. Under the same load, S[0] in the reflux sedimentation tank, which produced larger S[0] particles (24.2 ± 0.73-53.8 ± 0.70 μm), increased the natural settling capacity and 45% recovery. For high level sulfide inhibitory effect, we used metagenomics and metatranscriptomics analyses. The increased sulfide load significantly inhibited the expression of flavin cytochrome c sulfide dehydrogenase subunit B (fccB) (Decreased from 615 ± 75 to 30 ± 5 TPM). At this time sulfide quinone reductase (SQR) (324 ± 185-1197 ± 51 TPM) was mainly responsible for sulfide oxidation and S[0] production. When the sulfide load reached 2800 mg S/L, the SQR (730 ± 100 TPM) was also suppressed. This resulted in the accumulation of sulfide, causing suppression of carbon sequestration genes (Decreased from 3437 ± 842 to 665 ± 175 TPM). Other inhibitory effects included inhibition of microbial respiration, production of reactive oxygen species, and DNA damage. More sulfide-oxidizing bacteria (SOB) and newly identified potential SOB (99.1%) showed some activity (77.6%) upon sulfide accumulation. The main microorganisms in the sulfide accumulation environment were Thiomicrospiracea and Burkholderiaceae, whose sulfide oxidation capacity and respiration were not significantly inhibited. This study provides a new approach to enhance the natural sedimentation of S[0] and describes new microbial mechanisms for the inhibitory effects of sulfide.}, } @article {pmid37781761, year = {2023}, author = {Chandel, N and Somvanshi, PR and Thakur, V}, title = {Characterization of Indian gut microbiome for B-vitamins production and its comparison with Chinese cohort.}, journal = {The British journal of nutrition}, volume = {}, number = {}, pages = {1-28}, doi = {10.1017/S0007114523002179}, pmid = {37781761}, issn = {1475-2662}, abstract = {The human gut microbiota can biosynthesize essential micronutrients such as B-vitamins, and is also known for its metabolic cooperative behaviour. The current study characterizes such B-vitamin biosynthesizers, their biosynthetic pathways, explores their prevalence and abundance, and examines how lifestyle or diet affects them in multiple Indian cohorts, and compares it with the Chinese cohort. To achieve this, publicly available fecal metagenome data of healthy individuals from multiple Indian (two urban and three tribal populations) and a Chinese cohort were analyzed. The distribution of prevalence and abundance of B vitamin biosynthesizers showed similar profiles to that of the entire gut community of the Indian cohort, and there were 28 B-vitamin biosynthesizers that had modest or higher prevalence and abundance. The omnivorous diet affected only the prevalence of a few B-vitamin biosynthesizers, however, lifestyle and/or location affected both prevalence and abundance. A comparison with the Chinese cohort showed that fourteen B-vitamin biosynthesizers were significantly more prevalent and abundant in Chinese as compared to Indian samples (FDR <= 0.05). The metabolic potential of the entire gut community for B-vitamin production showed that within India, the tribal cohort has a higher abundance of B-vitamin biosynthesis pathways as compared to two urban cohorts namely, Bhopal and Kasargod, and comparison with the Chinese cohort revealed a higher abundance in the latter group. Potential metabolic cooperative behaviour of the Indian gut microbiome for biosynthesis of the B vitamins showed multiple pairs of species showed theoretical complementarity for complete biosynthetic pathways genes of thiamin, riboflavin, niacin and pantothenate.}, } @article {pmid37781628, year = {2023}, author = {Duan, C and Liu, Y and Liu, Y and Liu, L and Cai, M and Zhang, R and Zeng, Q and Koonin, EV and Krupovic, M and Li, M}, title = {Diversity of Bathyarchaeia viruses in metagenomes and virus-encoded CRISPR system components.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37781628}, abstract = {Bathyarchaeia represent a class of archaea common and abundant in sedimentary ecosystems. The virome of Bathyarchaeia so far has not been characterized. Here we report 56 metagenome-assembled genomes of Bathyarchaeia viruses identified in metagenomes from different environments. Gene sharing network and phylogenomic analyses led to the proposal of four virus families, including viruses of the realms Duplodnaviria and Adnaviria, and archaea-specific spindle-shaped viruses. Genomic analyses uncovered diverse CRISPR elements in these viruses. Viruses of the proposed family 'Fuxiviridae' harbor an atypical type IV-B CRISPR-Cas system and a Cas4 protein that might interfere with host immunity. Viruses of the family 'Chiyouviridae' encode a Cas2-like endonuclease and two mini-CRISPR arrays, one with a repeat identical to that in the host CRISPR array, potentially allowing the virus to recruit the host CRISPR adaptation machinery to acquire spacers that could contribute to competition with other mobile genetic elements or to inhibition of host defenses. These findings present an outline of the Bathyarchaeia virome and offer a glimpse into their counter-defense mechanisms.}, } @article {pmid37781531, year = {2023}, author = {Jimoh, AA and Booysen, E and van Zyl, L and Trindade, M}, title = {Do biosurfactants as anti-biofilm agents have a future in industrial water systems?.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {11}, number = {}, pages = {1244595}, pmid = {37781531}, issn = {2296-4185}, abstract = {Biofilms are bacterial communities embedded in exopolymeric substances that form on the surfaces of both man-made and natural structures. Biofilm formation in industrial water systems such as cooling towers results in biofouling and biocorrosion and poses a major health concern as well as an economic burden. Traditionally, biofilms in industrial water systems are treated with alternating doses of oxidizing and non-oxidizing biocides, but as resistance increases, higher biocide concentrations are needed. Using chemically synthesized surfactants in combination with biocides is also not a new idea; however, these surfactants are often not biodegradable and lead to accumulation in natural water reservoirs. Biosurfactants have become an essential bioeconomy product for diverse applications; however, reports of their use in combating biofilm-related problems in water management systems is limited to only a few studies. Biosurfactants are powerful anti-biofilm agents and can act as biocides as well as biodispersants. In laboratory settings, the efficacy of biosurfactants as anti-biofilm agents can range between 26% and 99.8%. For example, long-chain rhamnolipids isolated from Burkholderia thailandensis inhibit biofilm formation between 50% and 90%, while a lipopeptide biosurfactant from Bacillus amyloliquefaciens was able to inhibit biofilms up to 96% and 99%. Additionally, biosurfactants can disperse preformed biofilms up to 95.9%. The efficacy of antibiotics can also be increased by between 25% and 50% when combined with biosurfactants, as seen for the V9T14 biosurfactant co-formulated with ampicillin, cefazolin, and tobramycin. In this review, we discuss how biofilms are formed and if biosurfactants, as anti-biofilm agents, have a future in industrial water systems. We then summarize the reported mode of action for biosurfactant molecules and their functionality as biofilm dispersal agents. Finally, we highlight the application of biosurfactants in industrial water systems as anti-fouling and anti-corrosion agents.}, } @article {pmid37781016, year = {2023}, author = {Rao, A and Lokesh, J and D'Souza, C and Prithvisagar, KS and Subramanyam, K and Karunasagar, I and Kumar, BK}, title = {Metagenomic Analysis to Uncover the Subgingival and Atherosclerotic Plaque Microbiota in Patients with Coronary Artery Disease.}, journal = {Indian journal of microbiology}, volume = {63}, number = {3}, pages = {281-290}, pmid = {37781016}, issn = {0046-8991}, abstract = {The role of periodontal pathogens in the initiation and progression of atherosclerosis has been extensively researched, yet a precise causal mechanism has not been established. The subgingival microbiota may be a source of dissemination and may contribute to the development of atherosclerosis; hence this study attempted to characterize and compare the subgingival and atherosclerotic plaques. Plaque samples were subjected to 16S rRNA-based metagenomics to study microbiota associated with subgingival and atherosclerotic plaques collected from patients with coronary artery disease. The PCoA analysis showed that the microbiomes of subgingival plaques were highly scattered and showed a diverse microbial composition, unlike the atherosclerotic plaques that did not show evident variability in the microbial composition and formed a close distinct group. The abundance of various genera in the subgingival plaques revealed Fusobacterium (11%), Acinetobacter (13%), Veillonella (9%), and Prevotella (11%) among the top ten genera. The atherosclerotic plaques contained Acinetobacter (39%), Chryseobacterium (9%), Rhizobium (5%), and Staphylococcus (4%). All the patients examined in this study had either generalized or localized periodontitis with varying degrees of severity. The community microbiota analysis revealed that 22 bacterial genera were shared between two different plaques, with Acinetobacter being dominant. Based on the Human Oral Microbiome Database, 55% of the shared microbiota in this study have been listed as periodontal microbiota, with some of them found in increased proportions in patients with periodontitis suggesting the translocation of bacteria from the periodontal pockets into the circulation. This study provides valuable insights into the possible relationship between periodontal pathogens and atherosclerotic cardiovascular disease.}, } @article {pmid37781005, year = {2023}, author = {Andraskar, J and Yadav, S and Khan, D and Kapley, A}, title = {Treatment Options for Municipal Solid Waste by Composting and Its Challenges.}, journal = {Indian journal of microbiology}, volume = {63}, number = {3}, pages = {235-243}, pmid = {37781005}, issn = {0046-8991}, abstract = {UNLABELLED: Recovery and recycling of municipal solid waste biodegradable fraction (50-55%) are essential for attaining sustainability and a circular economy. Among organic waste treatment methods, composting is used to recycle organic fractions of waste. However, only 10-12% of municipal solid waste is utilized for composting treatment due to a lack of segregation practices and process challenges, including long process periods, odorous and greenhouse gas emissions, nitrogen loss, and low compost quality, which hinders large-scale practice. The current review paper discusses the challenges of composting treatment and its possible solutions. Various strategies were explored to address these challenges, such as utilizing microbial inoculum, additives, and optimization of physicochemical parameters. It also emphasizes the application of metagenomics for exploring key species. The knowledge about the microbial community and biochemical pathways (genome mining) can be exploited for the improvement of treatment efficiency.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-023-01087-4.}, } @article {pmid37780855, year = {2023}, author = {Oh, S and Lee, HJ and Park, KU}, title = {Metagenomic characterization of the microbiomes in five different body habitats of otherwise healthy individuals with periodontal disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1257816}, pmid = {37780855}, issn = {2235-2988}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Dental Plaque ; *Microbiota/genetics ; *Periodontal Diseases ; Metagenome ; }, abstract = {INTRODUCTION: Recent studies have proposed several plausible mechanisms supporting the association between periodontal disease and systemic disease. However, characterizing the microbial communities in individuals with periodontal disease before onset of other diseases is an important first step in determining how the altered microbial state contributes to disease progression. This study established microbiome profiles for five body habitats of carefully selected, otherwise healthy individuals with periodontal disease.

METHODS: Blood, oral (buccal mucosa, dental plaque, and saliva), and stool samples were collected from ten healthy subjects with periodontal disease. Using 16S rRNA metagenomics, the taxonomic and functional compositions of microbiomes were investigated.

RESULTS: The most predominant phylum in blood and stool was Bacillota. Pseudomonadota accounted for the largest proportion of microbes in the buccal mucosa and saliva, whereas Bacteroidota were the most prevalent in dental plaque. Differential abundance analysis revealed that 12 phyla and 139 genera were differentially abundant between body habitats. Comparison of alpha diversity showed that the blood microbiome has the most diverse community close to neither oral nor stool microbiomes. We also predicted the functional configurations of the microbiome in otherwise healthy subjects with periodontal disease. Principal coordinate analysis based on functional abundance revealed distinct clustering of the microbial communities between different body habitats, as also observed for taxonomic abundance. In addition, 13 functional pathways, including lipopolysaccharide biosynthesis, glutathione metabolism, and proteasome, showed differential expression between habitats.

DISCUSSION: Our results offer insight into the effects of the microbiome on systemic health and disease in people with periodontal disease.}, } @article {pmid37780852, year = {2023}, author = {Huang, J and Zhao, Y and Jiang, C and Han, D and Pan, Z and Zhang, Z and Wang, L and Chen, W and Li, S and Zhao, Y and Hu, X}, title = {Diagnostic efficiency of metagenomic next-generation sequencing for suspected infection in allogeneic hematopoietic stem cell transplantation recipients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1251509}, pmid = {37780852}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Immunosuppression Therapy ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {INTRODUCTION: Immunosuppression predisposes allogeneic hematopoietic stem cell transplantation (allo-HSCT) recipients to infection. Prompt and accurate identification of pathogens is crucial to optimize treatment strategies. This multi-center retrospective study aimed to assess the ability of metagenomic next-generation sequencing (mNGS) to detect causative pathogens in febrile allo-HSCT recipients and examined its concordance with conventional microbiological tests (CMT).

METHODS: We performed mNGS and CMT on samples obtained from 153 patients with suspected infection during allo-HSCT. Patients were grouped based on their neutropenic status at the time of sampling.

RESULTS: The mNGS test was more sensitive than CMT (81.1% vs. 53.6%, P<0.001) for diagnosing clinically suspected infection, especially in the non-neutropenia cohort. mNGS could detect fungi and viruses better than bacteria, with a higher sensitivity than CMT. Immune events were diagnosed in 57.4% (35/61) of the febrile events with negative mNGS results, and 33.5% (48/143) with negative CMT results (P=0.002). The treatment success rate of the targeted anti-infection strategy was significantly higher when based on mNGS than on empirical antibiotics (85% vs. 56.5%, P=0.004).

CONCLUSION: The mNGS test is superior to CMT for identifying clinically relevant pathogens, and provides valuable information for anti-infection strategies in allo-HSCT recipients. Additionally, attention should be paid to immune events in patients with negative mNGS results.}, } @article {pmid37780531, year = {2023}, author = {He, Y and Geng, S and Mei, Q and Zhang, L and Yang, T and Zhu, C and Fan, X and Wang, Y and Tong, F and Gao, Y and Fang, X and Bao, R and Sheng, X and Pan, A}, title = {Diagnostic Value and Clinical Application of Metagenomic Next-Generation Sequencing for Infections in Critically Ill Patients.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {6309-6322}, pmid = {37780531}, issn = {1178-6973}, abstract = {OBJECTIVE: To evaluate the diagnostic value and clinical application of metagenomic next-generation sequencing (mNGS) for infections in critically ill patients.

METHODS: Comparison of diagnostic performance of mNGS and conventional microbiological testing for pathogens was analyzed in 234 patients. The differences between immunocompetent and immunocompromised individuals in mNGS-guided anti-infective treatment adjustment were also analyzed.

RESULTS: The sensitivity and specificity of mNGS for bacterial and fungal detection were 96.6% (95% confidence interval [CI], 93.5%-99.6%) and 83.1% (95% CI, 75.2%-91.1%), and 85.7% (95% CI, 71.9%-99.5%) and 93.2% (95% CI, 89.7%-96.7%), respectively. Overall, 152 viruses were detected by mNGS, but in which 28 viruses were considered causative agents. The proportion of mNGS-guided beneficial anti-infective therapy adjustments in the immunocompromised group was greater than in the immunocompetent group (48.5% vs 30.1%; P=0.008). In addition, mNGS-guided anti-infective regimens with peripheral blood and BALF specimens had the highest proportion (39.0%; 40.0%), but the proportion of patients not helpful due to peripheral blood mNGS was also as high as 22.0%.

CONCLUSION: mNGS might be a promising technology to provide precision medicine for critically ill patients with infection.}, } @article {pmid37779688, year = {2023}, author = {González, D and Morales-Olavarria, M and Vidal-Veuthey, B and Cárdenas, JP}, title = {Insights into early evolutionary adaptations of the Akkermansia genus to the vertebrate gut.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1238580}, pmid = {37779688}, issn = {1664-302X}, abstract = {Akkermansia, a relevant mucin degrader from the vertebrate gut microbiota, is a member of the deeply branched Verrucomicrobiota, as well as the only known member of this phylum to be described as inhabitants of the gut. Only a few Akkermansia species have been officially described so far, although there is genomic evidence addressing the existence of more species-level variants for this genus. This niche specialization makes Akkermansia an interesting model for studying the evolution of microorganisms to their adaptation to the gastrointestinal tract environment, including which kind of functions were gained when the Akkermansia genus originated or how the evolutionary pressure functions over those genes. In order to gain more insight into Akkermansia adaptations to the gastrointestinal tract niche, we performed a phylogenomic analysis of 367 high-quality Akkermansia isolates and metagenome-assembled genomes, in addition to other members of Verrucomicrobiota. This work was focused on three aspects: the definition of Akkermansia genomic species clusters and the calculation and functional characterization of the pangenome for the most represented species; the evolutionary relationship between Akkermansia and their closest relatives from Verrucomicrobiota, defining the gene families which were gained or lost during the emergence of the last Akkermansia common ancestor (LAkkCA) and; the evaluation of the evolutionary pressure metrics for each relevant gene family of main Akkermansia species. This analysis found 25 Akkermansia genomic species clusters distributed in two main clades, divergent from their non-Akkermansia relatives. Pangenome analyses suggest that Akkermansia species have open pangenomes, and the gene gain/loss model indicates that genes associated with mucin degradation (both glycoside hydrolases and peptidases), (micro)aerobic metabolism, surface interaction, and adhesion were part of LAkkCA. Specifically, mucin degradation is a very ancestral innovation involved in the origin of Akkermansia. Horizontal gene transfer detection suggests that Akkermansia could receive genes mostly from unknown sources or from other Gram-negative gut bacteria. Evolutionary metrics suggest that Akkemansia species evolved differently, and even some conserved genes suffered different evolutionary pressures among clades. These results suggest a complex evolutionary landscape of the genus and indicate that mucin degradation could be an essential feature in Akkermansia evolution as a symbiotic species.}, } @article {pmid37779687, year = {2023}, author = {Karnachuk, OV and Rusanov, II and Panova, IA and Kadnikov, VV and Avakyan, MR and Ikkert, OP and Lukina, AP and Beletsky, AV and Mardanov, AV and Knyazev, YV and Volochaev, MN and Pimenov, NV and Ravin, NV}, title = {The low-temperature germinating spores of the thermophilic Desulfofundulus contribute to an extremely high sulfate reduction in burning coal seams.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1204102}, pmid = {37779687}, issn = {1664-302X}, abstract = {Burning coal seams, characterized by massive carbon monoxide (CO) emissions, the presence of secondary sulfates, and high temperatures, represent suitable environments for thermophilic sulfate reduction. The diversity and activity of dissimilatory sulfate reducers in these environments remain unexplored. In this study, using metagenomic approaches, in situ activity measurements with a radioactive tracer, and cultivation we have shown that members of the genus Desulfofundulus are responsible for the extremely high sulfate reduction rate (SRR) in burning lignite seams in the Altai Mountains. The maximum SRR reached 564 ± 21.9 nmol S cm[-3] day[-1] at 60°C and was of the same order of magnitude for both thermophilic (60°C) and mesophilic (23°C) incubations. The 16S rRNA profiles and the search for dsr gene sequences in the metagenome revealed members of the genus Desulfofundulus as the main sulfate reducers. The thermophilic Desulfofundulus sp. strain Al36 isolated in pure culture, did not grow at temperatures below 50°C, but produced spores that germinated into metabolically active cells at 20 and 15°C. Vegetative cells germinating from spores produced up to 0.738 ± 0.026 mM H2S at 20°C and up to 0.629 ± 0.007 mM H2S at 15°C when CO was used as the sole electron donor. The Al36 strain maintains significant production of H2S from sulfate over a wide temperature range from 15°C to 65°C, which is important in variable temperature biotopes such as lignite burning seams. Burning coal seams producing CO are ubiquitous throughout the world, and biogenic H2S may represent an overlooked significant flux to the atmosphere. The thermophilic spore outgrowth and their metabolic activity at temperatures below the growth minimum may be important for other spore-forming bacteria of environmental, industrial and clinical importance.}, } @article {pmid37779211, year = {2023}, author = {Cao, Y and Feng, T and Wu, Y and Xu, Y and Du, L and Wang, T and Luo, Y and Wang, Y and Li, Z and Xuan, Z and Chen, S and Yao, N and Gao, NL and Xiao, Q and Huang, K and Wang, X and Cui, K and Rehman, SU and Tang, X and Liu, D and Han, H and Li, Y and Chen, WH and Liu, Q}, title = {The multi-kingdom microbiome of the goat gastrointestinal tract.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {219}, pmid = {37779211}, issn = {2049-2618}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; Gastrointestinal Tract/microbiology ; *Goats ; Methane ; *Microbiota ; }, abstract = {BACKGROUND: Goat is an important livestock worldwide, which plays an indispensable role in human life by providing meat, milk, fiber, and pelts. Despite recent significant advances in microbiome studies, a comprehensive survey on the goat microbiomes covering gastrointestinal tract (GIT) sites, developmental stages, feeding styles, and geographical factors is still unavailable. Here, we surveyed its multi-kingdom microbial communities using 497 samples from ten sites along the goat GIT.

RESULTS: We reconstructed a goat multi-kingdom microbiome catalog (GMMC) including 4004 bacterial, 71 archaeal, and 7204 viral genomes and annotated over 4,817,256 non-redundant protein-coding genes. We revealed patterns of feeding-driven microbial community dynamics along the goat GIT sites which were likely associated with gastrointestinal food digestion and absorption capabilities and disease risks, and identified an abundance of large intestine-enriched genera involved in plant fiber digestion. We quantified the effects of various factors affecting the distribution and abundance of methane-producing microbes including the GIT site, age, feeding style, and geography, and identified 68 virulent viruses targeting the methane producers via a comprehensive virus-bacterium/archaea interaction network.

CONCLUSIONS: Together, our GMMC catalog provides functional insights of the goat GIT microbiota through microbiome-host interactions and paves the way to microbial interventions for better goat and eco-environmental qualities. Video Abstract.}, } @article {pmid37778843, year = {2024}, author = {Liu, S and Han, Z and Zhu, D and Luan, X and Deng, L and Dong, L and Yang, M and Zhang, Y}, title = {Field-based evidence for the enrichment of intrinsic antibiotic resistome stimulated by plant-derived fertilizer in agricultural soil.}, journal = {Journal of environmental sciences (China)}, volume = {135}, number = {}, pages = {728-740}, doi = {10.1016/j.jes.2022.08.009}, pmid = {37778843}, issn = {1001-0742}, mesh = {Animals ; *Soil ; *Anti-Bacterial Agents/pharmacology ; Fertilizers/analysis ; Genes, Bacterial ; Manure/analysis ; Soil Microbiology ; Bacteria/genetics ; }, abstract = {Animal manures have been demonstrated to enhance antibiotic resistance in agricultural soils. However, little is known about the effects of plant-derived fertilizer on soil antibiotic resistome. Herein, metagenomic sequencing was used to investigate the effects of a plant-derived fertilizer processed from sugarcane and beet on soil antibiotic resistance genes (ARGs) in a soybean field along crop growth stages. ARG profiles in the soils amended by plant-derived fertilizer were compared with those in the soils amended by chicken manure. The abundance and diversity of total ARGs in the soils amended by plant-derived fertilizer were significantly (P < 0.05) elevated at the sprout stage, to a level comparable to that in the manured soils. Whereas, unlike chicken manure mainly introducing manure-borne ARGs to soil, the plant-derived fertilizer was indicated to mainly enrich multidrug resistance genes in soil by nourishing indigenous bacteria. ARGs with abundances in amended soils significantly (P < 0.05) higher than in unamended soils at the sprout stage of soybean were considered as enriched ARGs. Decrease in the abundance of the enriched ARGs was observed in both the amended soils from the sprout to the harvest. Network analysis further identified Proteobacteria and Bacteroidetes as the primary bacterial taxa involved in the temporal variation of the enriched ARGs in the soils amended by plant-derived fertilizer, while in manured soils were Firmicutes and Actinobacteria. As revealed by multivariate statistical analyses, variation of the enriched ARGs in the soils amended by plant-derived fertilizer was majorly attributed to the response of co-occurred bacteria to depleting nutrients, which was different from the failed establishment of manure-borne bacteria in the manured soils. Our study provided field-based evidence that plant-derived fertilizer stimulated the intrinsic antibiotic resistome, and proposed attention to the un-perceived risk since some clinically relevant ARGs originate and evolve from natural resistome.}, } @article {pmid37778796, year = {2024}, author = {Wang, H and Gong, H and Dai, X and Yang, M}, title = {Metagenomics reveals the microbial community and functional metabolism variation in the partial nitritation-anammox process: From collapse to recovery.}, journal = {Journal of environmental sciences (China)}, volume = {135}, number = {}, pages = {210-221}, doi = {10.1016/j.jes.2023.01.002}, pmid = {37778796}, issn = {1001-0742}, mesh = {Anaerobic Ammonia Oxidation ; Oxidation-Reduction ; Bioreactors ; Nitrification ; *Microbiota ; Nitrogen ; *Ammonium Compounds ; Denitrification ; Sewage ; }, abstract = {Mainstream partial nitritation-anammox (PNA) process easily suffers from performance instability and even reactor collapse in application. Thus, it is of great significance to unveil the characteristic of performance recovery, understand the intrinsic mechanism and then propose operational strategy. In this study, we combined long-term reactor operation, batch tests, and metagenomics to reveal the succession of microbial community and functional metabolism variation from system collapse to recovery. Proper aeration control (0.10-0.25 mg O2/L) was critical for performance recovery. It was also found that Candidatus Brocadia became the dominant flora and its abundance increased from 3.5% to 11.0%. Significant enhancements in carbon metabolism and phospholipid biosynthesis were observed during system recovery, and the genes abundance related to signal transduction was dramatically increased. The up-regulation of sdh and suc genes showed the processes of succinate dehydrogenation and succinyl-CoA synthesis might stimulate the production of amino acids and the synthesis of proteins, thereby possibly improving the activity and abundance of AnAOB, which was conducive to the performance recovery. Moreover, the increase in abundance of hzs and hdh genes suggested the enhancement of the anammox process. Changes in the abundance of key genes involved in nitrogen metabolism indicated that nitrogen removal pathway was more diverse after system recovery. The achievement of performance recovery was driven by anammox, nitrification and denitrification coupled with dissimilatory nitrate reduction to ammonium. These results provide deeper insights into the recovery mechanism of PNA system and also provide a potential regulation strategy for the stable operation of the mainstream PNA process.}, } @article {pmid37778792, year = {2024}, author = {Wu, L and Wang, M and Rong, L and Wang, W and Chen, L and Wu, Q and Sun, H and Huang, X and Zou, X}, title = {Structural effects of sulfonamides on the proliferation dynamics of sulfonamide resistance genes in the sequencing batch reactors and the mechanism.}, journal = {Journal of environmental sciences (China)}, volume = {135}, number = {}, pages = {161-173}, doi = {10.1016/j.jes.2022.11.014}, pmid = {37778792}, issn = {1001-0742}, mesh = {*Sulfonamides ; *Sewage ; Anti-Bacterial Agents/pharmacology ; Sulfanilamide ; Genes, Bacterial ; Cell Proliferation ; }, abstract = {Antibiotic resistance genes (ARGs) can be easily promoted by antibiotics, however, the structural effects of antibiotics on the proliferation of ARGs dynamic and the associated mechanisms remain obscure in, especially, activated sludge sequencing batch reactors. In the present study, the effects of 9 sulfonamides (SAs) with different structures on the proliferation dynamic of sulfonamide resistance genes (Suls) in the activated sludge sequencing batch reactors and the corresponding mechanisms were determined (30 days), and the results showed that the largest proliferation value (∆A[R]) of Suls dynamic for SAs (sulfachloropyridazine) was approximately 2.9 times than that of the smallest one (sulfadiazine). The proliferation of Suls was significantly related to the structural features (minHBint6, SssNH, SHBd and SpMax2_Bhm) that represent the biological activity of SAs. To interpret the phenomenon, a mechanistic model was developed and the results indicated that the biodegradation of SAs (T1/2) rather than conjugative transfer frequency or mutation frequency tends to be the key process for affecting Suls proliferation. T1/2 was proved to be dependent on the interactions between SAs and receptors (Ebinding), the cleavage mode (bond dissociation energy), and the site of nucleophilic assault. Besides, the metagenomic analysis showed that SAs posed significant effect on antibiotic resistome and Tnp31 played a vital role in the proliferation of Suls. Overall, our findings provide important insight into a theoretical basis for understanding the structural effects of SAs on the proliferation of ARGs in SBR systems.}, } @article {pmid37778610, year = {2023}, author = {Wang, H and Fan, Y and Zhou, M and Liu, J and Li, X and Wang, Y}, title = {Metagenomics insight into the long-term effect of ferrous ions on the mainstream anammox system.}, journal = {Environmental research}, volume = {238}, number = {Pt 2}, pages = {117243}, doi = {10.1016/j.envres.2023.117243}, pmid = {37778610}, issn = {1096-0953}, mesh = {Anaerobiosis ; *Anaerobic Ammonia Oxidation ; Bacteria/metabolism ; Iron ; Oxidation-Reduction ; Ions ; Bioreactors/microbiology ; Nitrogen/metabolism ; *Ammonium Compounds/metabolism ; Sewage ; }, abstract = {Anaerobic ammonium oxidation (anammox) bacteria have a high requirement for iron for their growth and metabolism. However, it remains unclear whether iron supplementation can sustain the stability of mainstream anammox systems at varying temperatures. Here, we investigated the long-term effects of Fe[2+] on the mainstream anammox systems. Our findings revealed that the nitrogen removal efficiency (NRE) of the anammox system supplemented with 5 mg/L Fe[2+] decreased from 76.5 ± 0.76% at 35 °C to 39.0 ± 9.9% at 25 °C. Notably, higher dosages of Fe[2+] (15 mg/L and 30 mg/L) inhibited the anammox system, resulting in NREs of 15.9 ± 8.1% and 2.5 ± 1.1% at 25 °C, respectively. The results of microbial communities and function profiles suggested that the high Fe[2+] dosage seriously affected the iron assimilation and utilization in the mainstream anammox system. This was evident from the decreased abundance of genes associated with Fe(II) transport and uptake, which in turn hindered the biosynthesis of intracellular iron-cofactors, resulting in decrease in the absolute abundance of Candidatus Brocadia, a key anammox bacterium, as well as a decline in NRE. Furthermore, our results showed that the anammox process was more susceptible to iron supplementation at 25 °C compared to 35 °C, which may be due to the oxidative stress reactions induced by combined lowered temperature and a high Fe[2+] dosage. Overall, these findings offer a deeper understanding of the effect of iron in mainstream anammox systems, which can contribute to improved stability maintenance and effectiveness of anammox processes.}, } @article {pmid37778601, year = {2023}, author = {Yu, Q and Han, Q and Li, T and Kou, Y and Zhang, X and Wang, Y and Li, G and Zhou, H and Qu, J and Li, H}, title = {Metagenomics reveals the self-recovery and risk of antibiotic resistomes during carcass decomposition of wild mammals.}, journal = {Environmental research}, volume = {238}, number = {Pt 2}, pages = {117222}, doi = {10.1016/j.envres.2023.117222}, pmid = {37778601}, issn = {1096-0953}, mesh = {Animals ; *Genes, Bacterial ; *Anti-Bacterial Agents ; RNA, Ribosomal, 16S ; Mammals/genetics ; Cadaver ; }, abstract = {Animal carcass decomposition may bring serious harm to the environment, including pathogenic viruses, toxic gases and metabolites, and antibiotic resistance genes (ARGs). However, how wild mammal corpses decomposition influence and change ARGs in the environment has less explored. Through metagenomics, 16S rRNA gene sequencing, and physicochemical analysis, this study explored the succession patterns, influencing factors, and assembly process of ARGs and mobile genetic elements (MGEs) in gravesoil during long-term corpse decomposition of wild mammals. Our results indicate that the ARG and MGE communities related to wildlife corpses exhibited a pattern of differentiation first and then convergence. Different from the farmed animals, the decomposition of wild animals first reduced the diversity of ARGs and MGEs, and then recovered to a level similar to that of the control group (untreated soil). ARGs and MGEs of the gravesoil are mainly affected by deterministic processes in different stages. MGEs and bacterial community are the two most important factors affecting ARGs in gravesoil. It is worth noting that the decomposition of wild animal carcasses enriched different high-risk ARGs at different stages (bacA, mecA and floR), which have co-occurrence patterns with opportunistic pathogens (Comamonas and Acinetobacter), thereby posing a great threat to public health. These results are of great significance for wildlife corpse management and environmental and ecological safety.}, } @article {pmid37778491, year = {2023}, author = {Liu, C and Shan, X and Zhang, Y and Song, L and Chen, H}, title = {Microcosm experiments revealed resistome coalescence of sewage treatment plant effluents in river environment.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {338}, number = {}, pages = {122661}, doi = {10.1016/j.envpol.2023.122661}, pmid = {37778491}, issn = {1873-6424}, mesh = {*Sewage ; *Anti-Bacterial Agents/pharmacology ; Rivers ; Drug Resistance, Microbial/genetics ; Water ; Genes, Bacterial ; }, abstract = {Sewage treatment plant (STP) effluents are important contributors of antibiotic resistance (AR) pollution in rivers. Effluent discharging into rivers causes resistome coalescence. However, their mechanisms and dynamic processes are poorly understood, especially for the effects of dilution, diffusion, and sunlight-induced attenuation on coalescence. In this study, we have constructed microcosmic experiments based on in-situ investigation to explore these issues. The first batch experiment revealed the effects of dilution and diffusion. The coverage of water coalesced resistomes ranged 66.26∼152.18 × /Gb and was positively correlated with effluent volume (Mann-Kendall test, p < 0.01). Principal coordinate analysis (PCoA) and source tracking analysis demonstrated that dilution and diffusion stepwise reduced AR pollution. The second batch experiment explored the temporal dynamics and sunlight attenuation on coalesced resistomes. Under natural light, the coverage and diversity of water resistomes posed decreasing trends, primarily attributed to drastic erasure of effluent traces. The proportion of effluent-specific ARGs in coalesced resistomes significantly declined over time (Spearman's r = -0.83 and -0.94 in coverage and richness). While under dark condition, the coverage and diversity increased. Sunlight radiation intensified the interactions between water and sediment resistomes, as evidenced by more shared ARGs and less dissimilarities across niches. Network analysis, metagenome-assembled genome (MAG) analysis and variation partitioning analysis (VPA) showed that microbiome controlled resistome coalescence, explaining 56.5% and 58.4% of resistomes in water and sediment, respectively. Biotic and abiotic factors synergistically explained 40% of water resistomes. This study offers a comprehensive understanding of AR transmission and provides theoretical bases for grasping AR pollution and developing effective suppression strategies.}, } @article {pmid37778473, year = {2023}, author = {Mageiros, L and Megremis, S and Papadopoulos, NG}, title = {The virome in allergy and asthma: A nascent, ineffable player.}, journal = {The Journal of allergy and clinical immunology}, volume = {152}, number = {6}, pages = {1347-1351}, doi = {10.1016/j.jaci.2023.09.022}, pmid = {37778473}, issn = {1097-6825}, mesh = {Humans ; Virome ; Prospective Studies ; *Viruses ; *Bacteriophages/genetics ; *Asthma ; }, abstract = {Allergic diseases can be affected by virus-host interactions and are increasingly linked with the tissue-specific microbiome. High-throughput metagenomic sequencing has offered the opportunity to study the presence of viruses as an ecologic system, namely, the virome. Even though virome studies are technically challenging conceptually and analytically, they are already producing novel data expanding our understanding of the pathophysiologic mechanisms related to chronic inflammation and allergy. The importance of interspecies and intraspecies interactions is becoming apparent, as they can significantly, directly or indirectly, affect the host's response and antigenic state. Here, we emphasize the challenges and potential insights related to study of the virome in the context of allergy and asthma. We review the limited number of studies that have investigated the virome in these conditions, underlining the need for prospective, repeated sampling designs to unravel the virome's impact on disease development and its interplay with microbiota and immunity. The potential therapeutic use of bacteriophages, which are highly complex components of the virome, is discussed. There is clearly a need for further in-depth investigation of the virome as a system in allergic diseases.}, } @article {pmid37778348, year = {2023}, author = {Sturm, G and Mojarrad, M and Kaster, AK}, title = {Targeted Cell Labeling and Sorting of Prokaryotes for Cultivation and Omics Approaches.}, journal = {Microbial physiology}, volume = {33}, number = {1}, pages = {63-84}, doi = {10.1159/000532088}, pmid = {37778348}, issn = {2673-1673}, mesh = {*Metagenomics/methods ; *Prokaryotic Cells ; Genome ; Cell Separation ; }, abstract = {To date, the vast majority of prokaryotic organisms escapes detailed characterization because they cannot be isolated in axenic cultures. These organisms are referred to as microbial dark matter. Targeted labelling and sorting of these microorganisms pave the way for single-cell, enrichment, or cultivation approaches. In this review, we describe an array of different methods ranging from labeling-free to specific labelling techniques. In addition, different cell sorting methods and their combinations with targeting strategies are summarized and downstream applications like sequencing and cultivation are reviewed. Recent advances, challenges, and limitations of the particular methods are discussed with respect to cell viability, genome integrity as well as throughput, in order to help researchers select the most suitable methods for their specific research questions.}, } @article {pmid37777783, year = {2023}, author = {Xu, F and Wang, Q and Zhang, N and Xing, X and Liu, Z and Li, K and Ma, Y and Ou, Q and Jia, Y and Chen, X and Zhang, C and Pan, J and Che, N}, title = {Simultaneous diagnosis of tuberculous pleurisy and malignant pleural effusion using metagenomic next-generation sequencing (mNGS).}, journal = {Journal of translational medicine}, volume = {21}, number = {1}, pages = {680}, pmid = {37777783}, issn = {1479-5876}, mesh = {Humans ; *Tuberculosis, Pleural/diagnosis ; *Pleural Effusion, Malignant/diagnosis/genetics ; *Pleural Effusion ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has become a powerful tool for pathogen detection, but the value of human sequencing reads generated from it is underestimated.

METHODS: A total of 138 patients with pleural effusion (PE) were diagnosed with tuberculous pleurisy (TBP, N = 82), malignant pleural effusion (MPE, N = 35), or non-TB infection (N = 21), whose PE samples all underwent mNGS analysis. Clinical TB tests including culture, Acid-Fast Bacillus (AFB) test, Xpert, and T-SPOT, were performed. To utilize mNGS for MPE identification, 25 non-MPE samples (20 TBP and 5 non-TB infection) were randomly selected to set human chromosome copy number baseline and generalized linear modeling was performed using copy number variant (CNV) features of the rest 113 samples (35 MPE and 78 non-MPE).

RESULTS: The performance of TB detection was compared among five methods. T-SPOT demonstrated the highest sensitivity (61% vs. culture 32%, AFB 12%, Xpert 35%, and mNGS 49%) but with the highest false-positive rate (10%) as well. In contrast, mNGS was able to detect TB-genome in nearly half (40/82) of the PE samples from TBP subgroup, with 100% specificity. To evaluate the performance of using CNV features of the human genome for MPE prediction, we performed the leave-one-out cross-validation (LOOCV) in the subcohort excluding the 25 non-MPE samples for setting copy number standards, which demonstrated 54.1% sensitivity, 80.8% specificity, 71.7% accuracy, and an AUC of 0.851.

CONCLUSION: In summary, we exploited the value of human and non-human sequencing reads generated from mNGS, which showed promising ability in simultaneously detecting TBP and MPE.}, } @article {pmid37777765, year = {2023}, author = {Wen, Y and Yang, L and Wang, Z and Liu, X and Gao, M and Zhang, Y and Wang, J and He, P}, title = {Blocked conversion of Lactobacillus johnsonii derived acetate to butyrate mediates copper-induced epithelial barrier damage in a pig model.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {218}, pmid = {37777765}, issn = {2049-2618}, mesh = {Mice ; Animals ; Swine ; Butyrates/metabolism ; *Lactobacillus johnsonii/metabolism ; Copper ; Acetates ; *Microbiota ; }, abstract = {BACKGROUND: High-copper diets have been widely used to promote growth performance of pigs, but excess copper supplementation can also produce negative effects on ecosystem stability and organism health. High-copper supplementation can damage the intestinal barrier and disturb the gut microbiome community. However, the specific relationship between high-copper-induced intestinal damage and gut microbiota or its metabolites is unclear.

OBJECTIVE: Using fecal microbiota transplantation and metagenomic sequencing, responses of colonic microbiota to a high-copper diet was profiled. In addition, via comparison of specific bacteria and its metabolites rescue, we investigated a network of bacteria-metabolite interactions involving conversion of specific metabolites as a key mechanism linked to copper-induced damage of the colon.

RESULTS: High copper induced colonic damage, Lactobacillus extinction, and reduction of SCFA (acetate and butyrate) concentrations in pigs. LefSe analysis and q-PCR results confirmed the extinction of L. johnsonii. In addition, transplanting copper-rich fecal microbiota to ABX mice reproduced the gut characteristics of the pig donors. Then, L. johnsonii rescue could restore decreased SCFAs (mainly acetate and butyrate) and colonic barrier damage including thinner mucus layer, reduced colon length, and tight junction protein dysfunction. Given that acetate and butyrate concentrations exhibited a positive correlation with L. johnsonii abundance, we investigated how L. johnsonii exerted its effects by supplementing acetate and butyrate. L. johnsonii and butyrate administration but not acetate could correct the damaged colonic barrier. Acetate administration had no effects on butyrate concentration, indicating blocked conversion from acetate to butyrate. Furthermore, L. johnsonii rescue enriched a series of genera with butyrate-producing ability, mainly Lachnospiraceae NK4A136 group.

CONCLUSIONS: For the first time, we reveal the microbiota-mediated mechanism of high-copper-induced colonic damage in piglets. A high-copper diet can induce extinction of L. johnsonii which leads to colonic barrier damage and loss of SCFA production. Re-establishment of L. johnsonii normalizes the SCFA-producing pathway and restores colonic barrier function. Mechanistically, Lachnospiraceae NK4A136 group mediated conversion of acetate produced by L. johnsonii to butyrate is indispensable in the protection of colonic barrier function. Collectively, these findings provide a feasible mitigation strategy for gut damage caused by high-copper diets. Video Abstract.}, } @article {pmid37777252, year = {2023}, author = {Asao, K and Hashida, N and Motooka, D and Tsukamoto, T and Nakamura, S and Maruyama, K and Nishida, K}, title = {Fungal dysbiosis and decreased tear mucin at the conjunctiva in patients with conjunctival mucosa-associated lymphoid tissue lymphoma.}, journal = {BMJ open ophthalmology}, volume = {8}, number = {1}, pages = {}, pmid = {37777252}, issn = {2397-3269}, mesh = {Humans ; *Lymphoma, B-Cell, Marginal Zone/microbiology ; Case-Control Studies ; Mucins ; Dysbiosis/pathology ; Conjunctiva/pathology ; *Conjunctival Neoplasms/microbiology ; *Lacerations/pathology ; *Neoplasms, Connective Tissue/pathology ; *Skin Neoplasms/pathology ; }, abstract = {OBJECTIVE: This study aimed to examine the differences in the fungal microbiome between patients with conjunctival mucosa-associated lymphoid tissue (MALT) and healthy controls using metagenomic analysis.

METHODS AND ANALYSIS: This case-control study was conducted at Osaka University Hospital in Osaka, Japan, from April 2015 to March 2022. Twenty-five consecutive patients with conjunctival MALT lymphoma and 25 healthy volunteers were included. Metagenomic analysis using Internal Transcribed Spacer (ITS)1 deep sequencing and hierarchical clustering was performed to investigate differences in the fungal microbiome. To assess tear environmental change, we measured tear mucin concentrations using ELISA.

RESULTS: Detailed analyses showed fungal dysbiosis and changes in β-diversity within the conjunctiva of patients with conjunctival MALT lymphoma. Hierarchical clustering revealed that the participants could be divided into three clusters according to the Malassezia abundance: cluster I (Malassezia abundance above 70%), cluster II (Malassezia abundance 25%-70%) and cluster II (Malassezia abundance below 25%). Most patients were included in cluster I, whereas most of healthy controls were included in cluster III. The differences were significant. Tear mucin concentrations were significantly lower in patients with MALT compared with healthy controls.

CONCLUSION: The metagenomic analysis using ITS1 deep sequencing was useful for identifying the differences in commensal fungi between patients with MALT lymphoma and healthy individuals. The increased prevalence of the Malassezia genus and the decreased levels of tear mucin can lead to an allergic response of the conjunctiva, resulting in the pathogenesis associated with conjunctival MALT lymphoma. Therefore, it may be beneficial to initiate treatment when a high abundance Malassezia is detected.}, } @article {pmid37777125, year = {2023}, author = {Sieber, G and Drees, F and Shah, M and Stach, TL and Hohrenk-Danzouma, L and Bock, C and Vosough, M and Schumann, M and Sures, B and Probst, AJ and Schmidt, TC and Beisser, D and Boenigk, J}, title = {Exploring the efficacy of metabarcoding and non-target screening for detecting treated wastewater.}, journal = {The Science of the total environment}, volume = {903}, number = {}, pages = {167457}, doi = {10.1016/j.scitotenv.2023.167457}, pmid = {37777125}, issn = {1879-1026}, abstract = {Wastewater treatment processes can eliminate many pollutants, yet remainder pollutants contain organic compounds and microorganisms released into ecosystems. These remainder pollutants have the potential to adversely impact downstream ecosystem processes, but their presence is currently not being monitored. This study was set out with the aim of investigating the effectiveness and sensitivity of non-target screening of chemical compounds, 18S V9 rRNA gene, and full-length 16S rRNA gene metabarcoding techniques for detecting treated wastewater in receiving waters. We aimed at assessing the impact of introducing 33 % treated wastewater into a triplicated large-scale mesocosm setup during a 10-day exposure period. Discharge of treated wastewater significantly altered the chemical signature as well as the microeukaryotic and prokaryotic diversity of the mesocosms. Non-target screening, 18S V9 rRNA gene, and full-length 16S rRNA gene metabarcoding detected these changes with significant covariation of the detected pattern between methods. The 18S V9 rRNA gene metabarcoding exhibited superior sensitivity immediately following the introduction of treated wastewater and remained one of the top-performing methods throughout the study. Full-length 16S rRNA gene metabarcoding demonstrated sensitivity only in the initial hour, but became insignificant thereafter. The non-target screening approach was effective throughout the experiment and in contrast to the metabarcoding methods the signal to noise ratio remained similar during the experiment resulting in an increasing relative strength of this method. Based on our findings, we conclude that all methods employed for monitoring environmental disturbances from various sources are suitable. The distinguishing factor of these methods is their ability to detect unknown pollutants and organisms, which sets them apart from previously utilized approaches and allows for a more comprehensive perspective. Given their diverse strengths, particularly in terms of temporal resolution, these methods are best suited as complementary approaches.}, } @article {pmid37776859, year = {2023}, author = {Hino, T and Omura, SN and Nakagawa, R and Togashi, T and Takeda, SN and Hiramoto, T and Tasaka, S and Hirano, H and Tokuyama, T and Uosaki, H and Ishiguro, S and Kagieva, M and Yamano, H and Ozaki, Y and Motooka, D and Mori, H and Kirita, Y and Kise, Y and Itoh, Y and Matoba, S and Aburatani, H and Yachie, N and Karvelis, T and Siksnys, V and Ohmori, T and Hoshino, A and Nureki, O}, title = {An AsCas12f-based compact genome-editing tool derived by deep mutational scanning and structural analysis.}, journal = {Cell}, volume = {186}, number = {22}, pages = {4920-4935.e23}, doi = {10.1016/j.cell.2023.08.031}, pmid = {37776859}, issn = {1097-4172}, mesh = {Animals ; Humans ; Mice ; *CRISPR-Cas Systems ; Cryoelectron Microscopy ; *Gene Editing ; Mutation ; Genetic Therapy ; }, abstract = {SpCas9 and AsCas12a are widely utilized as genome-editing tools in human cells. However, their relatively large size poses a limitation for delivery by cargo-size-limited adeno-associated virus (AAV) vectors. The type V-F Cas12f from Acidibacillus sulfuroxidans is exceptionally compact (422 amino acids) and has been harnessed as a compact genome-editing tool. Here, we developed an approach, combining deep mutational scanning and structure-informed design, to successfully generate two AsCas12f activity-enhanced (enAsCas12f) variants. Remarkably, the enAsCas12f variants exhibited genome-editing activities in human cells comparable with those of SpCas9 and AsCas12a. The cryoelectron microscopy (cryo-EM) structures revealed that the mutations stabilize the dimer formation and reinforce interactions with nucleic acids to enhance their DNA cleavage activities. Moreover, enAsCas12f packaged with partner genes in an all-in-one AAV vector exhibited efficient knock-in/knock-out activities and transcriptional activation in mice. Taken together, enAsCas12f variants could offer a minimal genome-editing platform for in vivo gene therapy.}, } @article {pmid37776796, year = {2023}, author = {Wang, Y and Yang, L and Ma, J and Tang, J and Chen, M}, title = {Unraveling the antibiotic resistome in backwater zones of large cascade reservoirs: Co-occurrence patterns, horizontal transfer directions and health risks.}, journal = {Journal of environmental management}, volume = {347}, number = {}, pages = {119144}, doi = {10.1016/j.jenvman.2023.119144}, pmid = {37776796}, issn = {1095-8630}, mesh = {*Genes, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Metagenome ; Water ; }, abstract = {The widespread occurrence of antibiotic resistant genes (ARGs) throughout aquatic environments has raised global concerns for public health. However, the profiles and patterns of antibiotic resistome in backwater zone of cascade reservoirs, where water flow is slowed down, are still poorly understood. Here, we proposed a metagenomic analysis framework to comprehensively reveal the diversity, abundance, co-occurrence patterns and transfer direction of ARGs in cascade reservoirs system and evaluated their health risks through a procedure based on contigs. A total of 364 ARGs subtypes conferring resistance to different antibiotics classes were detected in our water samples, and the dominant ARGs (macB, bacA, vanRA, bcrA) were similar in different reservoirs. Meanwhile, the distribution of ARGs was influenced by the presence of biotic factors such as metal resistant genes (MRGs) and mobile genetic elements (MGEs), as well as abiotic factors such as dissolved oxygen (DO) and pH. Remarkably, ARGs (vanR, rosB, MexT) co-occurred with plasmids and virulence factor genes (VFGs), which can lead to the emergence and spread of highly virulent and antibiotic resistant bacteria in microbial communities. Overall, this study helps administrators to better understand the complex patterns of ARGs in backwater zones of large cascade reservoirs and provides a proper procedure for detecting the presence of high-risk of ARGs.}, } @article {pmid37776739, year = {2023}, author = {Ji, M and Smith, AF and Rattray, JE and England, WE and Hubert, CRJ}, title = {Potential for natural attenuation of crude oil hydrocarbons in benthic microbiomes near coastal communities in Kivalliq, Nunavut, Canada.}, journal = {Marine pollution bulletin}, volume = {196}, number = {}, pages = {115557}, doi = {10.1016/j.marpolbul.2023.115557}, pmid = {37776739}, issn = {1879-3363}, mesh = {*Petroleum/metabolism ; Nunavut ; RNA, Ribosomal, 16S/genetics ; Hydrocarbons/metabolism ; Canada ; *Microbiota ; Biodegradation, Environmental ; *Petroleum Pollution ; }, abstract = {Oil spilled in marine environments can settle to the seafloor through aggregation and sedimentation processes. This has been predicted to be especially relevant in the Arctic due to plankton blooms initiated by melting sea ice. These conditions exist in the Kivalliq region in Nunavut, Canada, where elevated shipping traffic has increased the risk of accidental spills. Experimental microcosms combining surface sediment and crude oil were incubated at 4 °C over 21 weeks to evaluate the biodegradation potential of seabed microbiomes. Sediments sampled near the communities of Arviat and Chesterfield Inlet were assessed for biodegradation capabilities by combining hydrocarbon geochemistry with 16S rRNA gene and metagenomic sequencing, revealing decreased microbial diversity but enrichment of oil-degrading taxa. Alkane and aromatic hydrocarbon losses corresponded to detection of genes and genomes that encode enzymes for aerobic biodegradation of these compounds, pointing to the utility of marine microbiome surveys for predicting the fate of oil released into Arctic marine environments.}, } @article {pmid37775739, year = {2023}, author = {Zhong, X and Wang, M and Meng, Q and Jiang, X and Guo, Z and Zhang, Y and Gao, D}, title = {Meningitis caused by oral anaerobes detected using mNGS tool: a case report and review of literature.}, journal = {BMC neurology}, volume = {23}, number = {1}, pages = {344}, pmid = {37775739}, issn = {1471-2377}, support = {2020YFC2005403//National Key Research and Development Program of China Stem Cell and Translational Research/ ; 2020YFC2005403//National Key Research and Development Program of China Stem Cell and Translational Research/ ; 2020YFC2005403//National Key Research and Development Program of China Stem Cell and Translational Research/ ; 2020YFC2005403//National Key Research and Development Program of China Stem Cell and Translational Research/ ; 2020YFC2005403//National Key Research and Development Program of China Stem Cell and Translational Research/ ; 2020YFC2005403//National Key Research and Development Program of China Stem Cell and Translational Research/ ; 2020YFC2005403//National Key Research and Development Program of China Stem Cell and Translational Research/ ; }, mesh = {Humans ; Middle Aged ; Female ; Animals ; *Ceftriaxone ; *Meningitis, Bacterial/diagnosis/drug therapy ; Brain/diagnostic imaging ; Meninges ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {BACKGROUND: Bacterial meningitis is a central nervous system (CNS) infection disease of the meninges and brain parenchyma caused by the bacteria. Few cases of meningitis related to oral anaerobes have been reported in the literature. Here, we report a case of meningitis in a middle-aged woman, caused by oral anaerobes.

CASE PRESENTATION: A 58-year-old woman was admitted to hospital with fever, headache for 21 days and left limb weakness for 2 days. The blood cell counts (11.73 × 10[9]/L), neutrophil counts (9.22 × 10[9]/L) and high-sensitivity C-reactive protein levels (> 5.00 mg/L) were elevated. The brain computerized tomography (CT) scanning indicated the new right thalamus infarct. The brain cranial-enhanced magnetic resonance imaging (MRI) showed the right lateral paraventricular and right thalamic infarct, and abnormal signal in occipital horns of bilateral lateral ventricles were increased. In addition, the brain enhanced nuclear magnetic resonance (NMR) scanning suggested that meninges were thickened and enhanced at the base of the brain, with meningitis changes. The neck CT angiography (CTA) revealed arteriosclerotic changes. The metagenomic next-generation sequencing (mNGS) revealed Eubacterium brachy, Porphyromonas gingivalis, Fusobacterium nucleatum and Torque teno virus in her cerebrospinal fluid (CSF). The patient was diagnosed with purulent meningitis caused by infection of oral anaerobes, and treated with mannitol, ceftriaxone and vancomycin. Her symptoms alleviated. Subsequently, she was transferred to the infectious department and treated with ceftriaxone plus metronidazole (anti-anaerobes) and mannitol (reduce intracranial pressure). Her symptoms improved and currently received rehabilitation treatment.

CONCLUSION: We herein report a rare case involving meningitis caused by infection of oral anaerobes. The mNGS can accurately detect the pathogens of infectious diseases.}, } @article {pmid37775503, year = {2023}, author = {Qi, X and Ji, M and Yin, CF and Zhou, NY and Liu, Y}, title = {Glacier as a source of novel polyethylene terephthalate hydrolases.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {2822-2833}, doi = {10.1111/1462-2920.16516}, pmid = {37775503}, issn = {1462-2920}, support = {91851207//Major Research plan of the National Natural Science Foundation of China/ ; 42171138//National Natural Science Foundation of China/ ; 918512//National Natural Science Foundation of China/ ; 23050202//The Seed Industry Revitalization Project of Guangdong Province/ ; 2019QZKK0503//Second Tibetan Plateau Scientific Expedition and Research Program (STEP)/ ; 2021YFC2300904//the National Key Research and Development Plans/ ; }, mesh = {*Polyethylene Terephthalates/metabolism ; *Hydrolases/genetics/metabolism ; Ice Cover ; Plastics ; Carbon ; }, abstract = {Polyethylene terephthalate (PET) is a major component of microplastic contamination globally, which is now detected in pristine environments including Polar and mountain glaciers. As a carbon-rich molecule, PET could be a carbon source for microorganisms dwelling in glacier habitats. Thus, glacial microorganisms may be potential PET degraders with novel PET hydrolases. Here, we obtained 414 putative PET hydrolase sequences by searching a global glacier metagenome dataset. Metagenomes from the Alps and Tibetan glaciers exhibited a higher relative abundance of putative PET hydrolases than those from the Arctic and Antarctic. Twelve putative PET hydrolase sequences were cloned and expressed, with one sequence (designated as GlacPETase) proven to degrade amorphous PET film with a similar performance as IsPETase, but with a higher thermostability. GlacPETase exhibited only 30% sequence identity to known active PET hydrolases with a novel disulphide bridge location and, therefore may represent a novel PET hydrolases class. The present work suggests that extreme carbon-poor environments may harbour a diverse range of known and novel PET hydrolases for carbon acquisition as an environmental adaptation mechanism.}, } @article {pmid37775319, year = {2023}, author = {Ma, C and Li, Y and Mei, Z and Yuan, C and Kang, JH and Grodstein, F and Ascherio, A and Willett, WC and Chan, AT and Huttenhower, C and Stampfer, MJ and Wang, DD}, title = {Association Between Bowel Movement Pattern and Cognitive Function: Prospective Cohort Study and a Metagenomic Analysis of the Gut Microbiome.}, journal = {Neurology}, volume = {101}, number = {20}, pages = {e2014-e2025}, pmid = {37775319}, issn = {1526-632X}, support = {R00 DK119412/DK/NIDDK NIH HHS/United States ; R01 AG077489/AG/NIA NIH HHS/United States ; R01 NR019992/NR/NINR NIH HHS/United States ; K99 DK119412/DK/NIDDK NIH HHS/United States ; UM1 CA186107/CA/NCI NIH HHS/United States ; U01 CA176726/CA/NCI NIH HHS/United States ; U01 CA167552/CA/NCI NIH HHS/United States ; }, mesh = {Male ; Humans ; Female ; Aged ; Prospective Studies ; Follow-Up Studies ; *Gastrointestinal Microbiome ; Defecation ; Cohort Studies ; Cognition/physiology ; }, abstract = {BACKGROUND AND OBJECTIVES: Little is known regarding the association between intestinal motility patterns and cognitive function in individuals who are baseline cognitively healthy. The gut microbiome may contribute to the association. We examined the association between bowel movement (BM) pattern and cognitive function and explored the role of the gut microbiome in explaining this association.

METHODS: In this prospective study, we leveraged 3 cohort studies, Nurses' Health Study (NHS), NHSII, and Health Professionals Follow-Up Study (HPFS). Participants reported BM frequency and subjective cognitive function. In a subset of NHSII participants, we assessed cognitive function using an objective neuropsychological battery. We profiled the gut microbiome in a subset of participants using whole-genome shotgun metagenomics. General linear models, Poisson regression, and logistic regression were used to quantify the association of BM frequency with different cognitive measurements.

RESULTS: We followed 112,753 men and women (women: 87.6%) with a mean age of 67.2 years at baseline (NHS: 76 years, NHSII: 59 years, HPFS: 75 years) for a median follow-up of 4 years (NHSII and HPFS: 4 years, NHS: 2 years). Compared with those with BM once daily, participants with BM frequency every 3+ days had significantly worse objective cognitive function, equivalent to 3.0 (95% confidence interval [CI],1.2-4.7) years of chronological cognitive aging. We observed similar J-shape dose-response relationships of BM frequency with the odds of subjective cognitive decline and the likelihood of having more subsequent subjective cognitive complaints (both p nonlinearity < 0.001). BM frequencies of every 3+ days and ≥twice/day, compared with once daily, were associated with the odds ratios of subjective cognitive decline of 1.73 (95% CI 1.60-1.86) and 1.37 (95% CI 1.33-1.44), respectively. BM frequency and subjective cognitive decline were significantly associated with the overall gut microbiome configuration (both p < 0.005) and specific microbial species in the 515 participants with microbiome data. Butyrate-producing microbial species were depleted in those with less frequent BM and worse cognition, whereas a higher abundance of proinflammatory species was associated with BM frequency of ≥twice/day and worse cognition.

DISCUSSION: Lower BM frequency was associated with worse cognitive function. The gut microbial dysbiosis may be a mechanistic link underlying the association.}, } @article {pmid37775014, year = {2023}, author = {Xu, M and Lyu, Y and Cheng, K and Zhang, B and Cai, Z and Chen, G and Zhou, J}, title = {Interactions between quorum sensing/quorum quenching and virulence genes may affect coral health by regulating symbiotic bacterial community.}, journal = {Environmental research}, volume = {238}, number = {Pt 2}, pages = {117221}, doi = {10.1016/j.envres.2023.117221}, pmid = {37775014}, issn = {1096-0953}, mesh = {Animals ; *Quorum Sensing/genetics ; Virulence ; *Anthozoa ; Bacteria/metabolism ; Virulence Factors ; }, abstract = {Quorum sensing (QS) and quorum quenching (QQ) are two antagonistic processes that may regulate the composition, function and structure of bacterial community. In coral holobiont, autoinducers signaling mediate the communication pathways between interspecies and intraspecies bacteria, which regulate the expression of the virulence factors that can damage host health. However, under environmental stressors, the interaction between the QS/QQ gene and virulence factors and their role in the bacterial communities and coral bleaching is still not fully clear. To address this question, here, metagenomics method was used to examine the profile of QS/QQ and virulence genes from a deeply sequenced microbial database, obtained from three bleached and non-bleached corals species. The prediction of bacterial genes of bleached samples involved in functional metabolic pathways were remarkably decreased, and the bacterial community structure on bleached samples was significantly different compared to non-bleached samples. The distribution and significant difference in QS/QQ and virulence genes were also carried out. We found that Proteobacteria was dominant bacteria among all samples, and AI-1 system is widespread within this group of bacteria. The identified specific genes consistently exhibited a trend of increased pathogenicity in bleached corals relative to non-bleached corals. The abundance of pathogenicity-associated QS genes, including bapA, pfoA and dgcB genes, were significantly increased in bleached corals and can encode the protein of biofilm formation and the membrane damaging toxins promoting pathogenic adhesion and infection. Similarly, the virulence genes, such as superoxide dismutase (Mn-SOD gene), metalloproteinase (yme1, yydH and zmpB), glycosidases (malE, malF, malG, and malK) and LodAB (lodB) genes significantly increased. Conversely, QQ genes that inhibit QS activity and virulence factors to defense the pathogens, including blpA, lsrK, amiE, aprE and gmuG showed a significant decrease in bleached groups. Furthermore, the significant correlations were found among virulence, QS/QQ genes, and coral associated bacterial community, and the virulence genes interact with key QS/QQ genes, directly or indirectly influence symbiotic bacterial communities homeostasis, thereby impacting coral health. It suggested that the functional and structural divergence in the symbiont bacteria may be partially attribute to the interplay, involving interactions among the host, bacterial communication signal systems, and bacterial virulence factors. In conclusion, these data helped to reveal the characteristic behavior of coral symbiotic bacteria, and facilitated a better understanding of bleaching mechanism from a chemical ecological perspective.}, } @article {pmid37774801, year = {2023}, author = {Chen, J and Cai, Y and Wang, Z and Xu, Z and Li, J and Ma, X and Zhuang, W and Liu, D and Wang, S and Song, A and Xu, J and Ying, H}, title = {Construction of a synthetic microbial community based on multiomics linkage technology and analysis of the mechanism of lignocellulose degradation.}, journal = {Bioresource technology}, volume = {389}, number = {}, pages = {129799}, doi = {10.1016/j.biortech.2023.129799}, pmid = {37774801}, issn = {1873-2976}, abstract = {The efficient degradation of lignocellulose is a bottleneck for its integrated utilization. This research performed species analysis and made functional predictions in various ecosystems using multiomics coupling to construct a core synthetic microbial community with efficient lignocellulose degradation function. The synthetic microbial community was employed to degrade corn straw via solid-state fermentation. The degradation mechanisms were resolved using proteomics. The optimum culture conditions included 10% inoculum level (w/v), 4% nitrogen source ratio and a fermentation time of 23 d. Under these conditions, the degradation rates of cellulose, hemicellulose, and lignin were 34.91%, 45.94%, and 23.34%, respectively. Proteomic analysis revealed that lignin 1,4-β-xylanase, β-xylosidase and endo-1,4-β-xylanase were closely related to lignocellulose degradation. The metabolic pathways involved in lignocellulose degradation and the functional roles of eight strains were obtained. The synthesis of a microbial community via multiomics linkage technology can effectively decompose lignocellulose, which is useful for their further utilization.}, } @article {pmid37774634, year = {2023}, author = {Kharnaior, P and Tamang, JP}, title = {Microbiome and metabolome in home-made fermented soybean foods of India revealed by metagenome-assembled genomes and metabolomics.}, journal = {International journal of food microbiology}, volume = {407}, number = {}, pages = {110417}, doi = {10.1016/j.ijfoodmicro.2023.110417}, pmid = {37774634}, issn = {1879-3460}, mesh = {Humans ; Metagenome ; Glycine max/microbiology ; *Microbiota/genetics ; *Fermented Foods/microbiology ; Metabolome ; Metagenomics ; }, abstract = {Grep-chhurpi, peha, peron namsing and peruñyaan are lesser-known home-made fermented soybean foods prepared by the native people of Arunachal Pradesh in India. Present work aims to study the microbiome, their functional annotations, metabolites and recovery of metagenome-assembled genomes (MAGs) in these four fermented soybean foods. Metagenomes revealed the dominance of bacteria (97.80 %) with minor traces of viruses, eukaryotes and archaea. Bacillota is the most abundant phylum with Bacillus subtilis as the abundant species. Metagenome also revealed the abundance of lactic acid bacteria such as Enterococcus casseliflavus, Enterococcus faecium, Mammaliicoccus sciuri and Staphylococcus saprophyticus in all samples. B. subtilis was the major species found in all products. Predictive metabolic pathways showed the abundance of genes associated with metabolisms. Metabolomics analysis revealed both targeted and untargeted metabolites, which suggested their role in flavour development and therapeutic properties. High-quality MAGs, identified as B. subtilis, Enterococcus faecalis, Pediococcus acidilactici and B. velezensis, showed the presence of several biomarkers corresponding to various bio-functional properties. Gene clusters of secondary metabolites (antimicrobial peptides) and CRISPR-Cas systems were detected in all MAGs. This present work also provides key elements related to the cultivability of identified species of MAGs for future use as starter cultures in fermented soybean food product development. Additionally, comparison of microbiome and metabolites of grep-chhurpi, peron namsing and peruñyaan with that of other fermented soybean foods of Asia revealed a distinct difference.}, } @article {pmid37774604, year = {2024}, author = {Yuan, W and She, J and Liu, J and Zhang, Q and Wei, X and Huang, L and Zeng, X and Wang, J}, title = {Insight into microbial functional genes' role in geochemical distribution and cycling of uranium: The evidence from covering soils of uranium tailings dam.}, journal = {Journal of hazardous materials}, volume = {461}, number = {}, pages = {132630}, doi = {10.1016/j.jhazmat.2023.132630}, pmid = {37774604}, issn = {1873-3336}, mesh = {*Uranium/chemistry ; Nitrates/analysis ; Soil/chemistry ; RNA, Ribosomal, 16S/genetics ; Environmental Pollution ; }, abstract = {There exists a research gap on microbial functional genes' role in U geochemical behavior and cycling in U contaminated soils, which has been poorly understood. Herein, 16S rRNA sequencing gene amplifiers and metagenome analysis were applied to probe microbial community structure and functional metabolism of different depth layers of covering soils in U tailings dam. Results showed that the soils were highly enriched with U (47.5-123.3 mg/kg) and a remarkable portion of 35-70% was associated with the labile fractions. It was found that U geochemical distribution was notably interacted with functional genes from N, S, Fe and P related microbes. Importantly, diminution in gene NirK and amplification in nrfH involving in nitrate reduction could induce microbial tolerance to U. Moreover, gene Sat in microbial sulfate reduction, NosZ and NorB in nitrate reduction, phnD, upgA and upgC in P transportation and phnI, phnK, phoA and opd in microbial organic P mineralization, were all closely linked to U geochemical distribution, species and cycling. All these findings disclose the functional genes that may control the transfer and transformation behavior of U in soil environment, which provides important and novel indications for the bio-remediation strategies towards U polluted sites.}, } @article {pmid37774127, year = {2023}, author = {Kirchberger, PC and Ochman, H}, title = {Microviruses: A World Beyond phiX174.}, journal = {Annual review of virology}, volume = {10}, number = {1}, pages = {99-118}, doi = {10.1146/annurev-virology-100120-011239}, pmid = {37774127}, issn = {2327-0578}, mesh = {Microvirus/genetics ; *Microviridae/genetics ; *Bacteriophages/genetics ; Phylogeny ; Metagenomics ; }, abstract = {Two decades of metagenomic analyses have revealed that in many environments, small (∼5 kb), single-stranded DNA phages of the family Microviridae dominate the virome. Although the emblematic microvirus phiX174 is ubiquitous in the laboratory, most other microviruses, particularly those of the gokushovirus and amoyvirus lineages, have proven to be much more elusive. This puzzling lack of representative isolates has hindered insights into microviral biology. Furthermore, the idiosyncratic size and nature of their genomes have resulted in considerable misjudgments of their actual abundance in nature. Fortunately, recent successes in microvirus isolation and improved metagenomic methodologies can now provide us with more accurate appraisals of their abundance, their hosts, and their interactions. The emerging picture is that phiX174 and its relatives are rather rare and atypical microviruses, and that a tremendous diversity of other microviruses is ready for exploration.}, } @article {pmid37774039, year = {2023}, author = {Ma, L and Hou, C and Yang, H and Chen, Q and Lyu, W and Wang, Z and Wang, J and Xiao, Y}, title = {Multi-omics analysis reveals the interaction of gut microbiome and host microRNAs in ulcerative colitis.}, journal = {Annals of medicine}, volume = {55}, number = {2}, pages = {2261477}, pmid = {37774039}, issn = {1365-2060}, mesh = {Humans ; Animals ; Mice ; *Colitis, Ulcerative/genetics ; *MicroRNAs/genetics/metabolism ; *Gastrointestinal Microbiome ; Multiomics ; *Colitis/chemically induced/genetics ; Inflammation ; *Inflammatory Bowel Diseases ; Mice, Inbred C57BL ; Disease Models, Animal ; }, abstract = {BACKGROUND: Inflammatory bowel disease (IBD) is a chronic inflammation of the gastrointestinal tract that co-occurs with gut microbiota dysbiosis; however, its etiology remains unclear. MicroRNA (miRNA)-microbiome interactions play an essential role in host health and disease.

METHODS: To investigate the gut microbiome and host miRNA profiles in colitis, we used a Dextran Sulfate Sodium (DSS)-induced ulcerative colitis (UC) model. Metagenomic sequencing and metabolome profiling were performed to explore typical microbiota and metabolite signatures in colitis, whereas mRNA and miRNA sequencing were used to determine differentially expressed miRNAs and their target genes in the inflamed colon.

RESULTS: A total of 986 miRNAs were identified between the two groups, with 41 upregulated and 21 downregulated miRNAs in colitis mice compared to the control group. Notably, the target genes of these significantly altered miRNAs were primarily enriched in the immune and inflammation-related pathways. Second, LEfSe analysis revealed bacterial biomarkers distinguishing the two groups, with significantly higher levels of commonly encountered pathogens such as Escherichia coli and Shigella flexneri in the UC group, whereas beneficial species such as Bifidobacterium pseudolongum were more abundant in the control group. Microbiota metabolites histamine, N-acetylhistamine, and glycocholic acid were found to be downregulated in colitis mice. Spearman correlation further revealed the potential crosstalk between the microbiota profile and colonic miRNA, revealing the possibility of microbiome-miRNA interactions involved in IBD development.

CONCLUSIONS: Our data reveal the relationships between multi-omic features during UC and suggest that targeting specific miRNAs may provide new avenues for the development of effective miRNA-based therapeutics.}, } @article {pmid37774017, year = {2023}, author = {Wielscher, M and Pfisterer, K and Samardzic, D and Balsini, P and Bangert, C and Jäger, K and Buchberger, M and Selitsch, B and Pjevac, P and Willinger, B and Weninger, W}, title = {The phageome in normal and inflamed human skin.}, journal = {Science advances}, volume = {9}, number = {39}, pages = {eadg4015}, pmid = {37774017}, issn = {2375-2548}, mesh = {Humans ; *Virome ; Skin/microbiology ; *Microbiota ; Metagenome ; Bacteria/genetics ; DNA, Viral/genetics ; }, abstract = {Dysbiosis of skin microbiota drives the progression of atopic dermatitis (AD). The contribution of bacteriophages to bacterial community compositions in normal and inflamed skin is unknown. Using shotgun metagenomics from skin swabs of healthy individuals and patients with AD, we found 13,586 potential viral contiguous DNA sequences, which could be combined into 164 putative viral genomes including 133 putative phages. The Shannon diversity index for the viral metagenome-assembled genomes (vMAGs) did not correlate with AD. In total, we identified 28 vMAGs that differed significantly between normal and AD skin. Quantitative polymerase chain reaction validation of three complete vMAGs revealed their independence from host bacterium abundance. Our data indicate that normal and inflamed skin harbor distinct phageomes and suggest a causative relationship between changing viral and bacterial communities as a driver of skin pathology.}, } @article {pmid37773207, year = {2023}, author = {Wang, D and Chen, L and Tang, G and Yu, J and Chen, J and Li, Z and Cao, Y and Lei, X and Deng, L and Wu, S and Guan, LL and Yao, J}, title = {Multi-omics revealed the long-term effect of ruminal keystone bacteria and the microbial metabolome on lactation performance in adult dairy goats.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {215}, pmid = {37773207}, issn = {2049-2618}, mesh = {Humans ; Animals ; Female ; Adolescent ; *Lactation ; *Diet/veterinary ; Propionates/metabolism ; Multiomics ; Bacteria/genetics ; Metabolome ; Goats ; Carbohydrates ; Rumen/microbiology ; Fermentation ; Animal Feed/analysis ; }, abstract = {BACKGROUND: The increased growth rate of young animals can lead to higher lactation performance in adult goats; however, the effects of the ruminal microbiome on the growth of young goats, and the contribution of the early-life rumen microbiome to lifelong growth and lactation performance in goats has not yet been well defined. Hence, this study assessed the rumen microbiome in young goats with different average daily gains (ADG) and evaluated its contribution to growth and lactation performance during the first lactation period.

RESULTS: Based on monitoring of a cohort of 99 goats from youth to first lactation, the 15 highest ADG (HADG) goats and 15 lowest ADG (LADG) goats were subjected to rumen fluid microbiome and metabolome profiling. The comparison of the rumen metagenome of HADG and LADG goats revealed that ruminal carbohydrate metabolism and amino acid metabolism function were enhanced in HADG goats, suggesting that the rumen fluid microbiome of HADG goats has higher feed fermentation ability. Co-occurrence network and correlation analysis revealed that Streptococcus, Candidatus Saccharimonans, and Succinivibrionaceae UCG-001 were significantly positively correlated with young goats' growth rates and some HADG-enriched carbohydrate and protein metabolites, such as propionate, butyrate, maltoriose, and amino acids, while several genera and species of Prevotella and Methanogens exhibited a negative relationship with young goats' growth rates and correlated with LADG-enriched metabolites, such as rumen acetate as well as methane. Additionally, some functional keystone bacterial taxa, such as Prevotella, in the rumen of young goats were significantly correlated with the same taxa in the rumen of adult lactation goats. Prevotella also enriched the rumen of LADG lactating goats and had a negative effect on rumen fermentation efficiency in lactating goats. Additional analysis using random forest machine learning showed that rumen fluid microbiota and their metabolites of young goats, such as Prevotellaceae UCG-003, acetate to propionate ratio could be potential microbial markers that can potentially classify high or low ADG goats with an accuracy of prediction of > 81.3%. Similarly, the abundance of Streptococcus in the rumen of young goats could be predictive of milk yield in adult goats with high accuracy (area under the curve 91.7%).

CONCLUSIONS: This study identified the keystone bacterial taxa that influence carbohydrate and amino acid metabolic functions and shape the rumen fluid microbiota in the rumen of adult animals. Keystone bacteria and their effects on rumen fluid microbiota and metabolome composition during early life can lead to higher lactation performance in adult ruminants. These findings suggest that the rumen microbiome together with their metabolites in young ruminants have long-term effect on feed efficiency and animal performance. The fundamental knowledge may allow us to develop advanced methods to manipulate the rumen microbiome and improve production efficiency of ruminants. Video Abstract.}, } @article {pmid37773143, year = {2023}, author = {Malik, M and Chiers, K and Theuns, S and Vereecke, N and Chantziaras, I and Croubels, S and Maes, D}, title = {Porcine ear necrosis: characterization of lesions and associated pathogens.}, journal = {Veterinary research}, volume = {54}, number = {1}, pages = {85}, pmid = {37773143}, issn = {1297-9716}, mesh = {Animals ; Swine ; *Bites and Stings/veterinary ; *Swine Diseases/pathology ; Necrosis/veterinary ; Skin ; *Mycotoxins ; }, abstract = {Porcine ear necrosis (PEN) is characterized by ulcerative lesions of the ear auricle. To investigate that problem, three farms with PEN in nursery pigs were included, and the study aim was to characterize PEN and the potential role of pathogens and mycotoxins. Within each farm, one batch of weaned piglets was included and the prevalence and severity of PEN were monitored for 6-7 weeks. Within each batch, 30 PEN-affected/non-affected animals were randomly selected. Blood samples were taken from these animals, to assess the systemic presence of pathogens and mycotoxins, as well as punch biopsies from the ear auricle for histopathological examination. From 10 animals, scrapings and swabs from the lesions were subjected to nanopore metagenomic sequencing and bacteriological cultivation, respectively. In all three farms, lesions appeared within 3-4 weeks post-weaning. The prevalence at the end of the nursery was 33%, 24%, and 46% for farms A, B, and C, respectively. Most affected pigs had mild to moderate lesions. Blood samples revealed low to very low levels of pathogens and mycotoxins. Different bacteria such as Staphylococcus, Streptococcus, Fusobacterium, Mycoplasma, and Clostridium species were identified by sequencing in the scrapings. The first two pathogens were also most often identified in bacterial cultures. Mycoplasma hyopharyngis was only found in PEN-affected pigs. Histopathological changes were primarily observed in the outer layer of the epidermis. The results suggest that PEN lesions develop by damage to the outer part of the skin e.g. by ear suckling or biting, followed by multiplication of opportunistic pathogens.}, } @article {pmid37773075, year = {2023}, author = {Trinh, P and Clausen, DS and Willis, AD}, title = {happi: a hierarchical approach to pangenomics inference.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {214}, pmid = {37773075}, issn = {1474-760X}, mesh = {*Metagenomics ; *Microbiota/genetics ; Metagenome ; Computer Simulation ; Sequence Analysis, DNA ; }, abstract = {Recovering metagenome-assembled genomes (MAGs) from shotgun sequencing data is an increasingly common task in microbiome studies, as MAGs provide deeper insight into the functional potential of both culturable and non-culturable microorganisms. However, metagenome-assembled genomes vary in quality and may contain omissions and contamination. These errors present challenges for detecting genes and comparing gene enrichment across sample types. To address this, we propose happi, an approach to testing hypotheses about gene enrichment that accounts for genome quality. We illustrate the advantages of happi over existing approaches using published Saccharibacteria MAGs, Streptococcus thermophilus MAGs, and via simulation.}, } @article {pmid37772760, year = {2024}, author = {Ko, JT and Li, YY and Chen, PY and Liu, PY and Ho, MY}, title = {Use of 16S rRNA gene sequences to identify cyanobacteria that can grow in far-red light.}, journal = {Molecular ecology resources}, volume = {24}, number = {1}, pages = {e13871}, doi = {10.1111/1755-0998.13871}, pmid = {37772760}, issn = {1755-0998}, support = {109V1102//Ministry of Education, Taiwan/ ; 110V1102//Ministry of Education, Taiwan/ ; 111V1102-4//Ministry of Education, Taiwan/ ; 112V1102-5//Ministry of Education, Taiwan/ ; 109-2636-B-002-013-//Ministry of Science and Technology, Taiwan/ ; 110-2628-B-002-065-//Ministry of Science and Technology, Taiwan/ ; 111-2628-B-002-041-//National Science and Technology Council/ ; 112-2628-B-002-031-//National Science and Technology Council/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Red Light ; Genes, rRNA ; Photosynthesis/genetics ; *Cyanobacteria/genetics ; }, abstract = {Although most cyanobacteria use visible light (VL; λ = 400-700 nm) for photosynthesis, some have evolved strategies to use far-red light (FRL; λ = 700-800 nm). These cyanobacteria are defined as far-red light-utilizing cyanobacteria (FRLCyano), including two groups: (1) chlorophyll d-producing Acaryochloris spp. and (2) polyphyletic cyanobacteria that produce chlorophylls d and f in response to FRL. Numerous ecological studies examine pigments, such as chlorophylls d and f, to investigate the presence of FRLCyano in the environment. This method is not ideal because it can only detect FRLCyano that have made chlorophylls d or f. Here we develop a new method, far-red cyanobacteria identification (FRCI), to identify FRLCyano based on 16S rRNA gene sequences. From public databases and published articles, 62 16S rRNA gene sequences of FRLCyano were extracted. Comparing with related lineages, we determined that 97% sequence identity is the optimal cut-off for distinguishing FRLCyano from other cyanobacteria. To test the method experimentally, we collected samples from 17 sites in Taipei, Taiwan, and conducted VL and FRL enrichments. Our results demonstrate that FRCI can detect FRLCyano during FRL enrichments more sensitively than pigment analysis. FRCI can also resolve the composition of FRLCyano at the genus level, which pigment analysis cannot do. In addition, we applied FRCI to published datasets and discovered putative FRLCyano in diverse environments, including soils, hot springs and deserts. Overall, our results indicate that FRCI is a sensitive and high-resolution method using 16S rRNA gene sequences to identify FRLCyano.}, } @article {pmid37772420, year = {2023}, author = {Xia, Q and Liu, F and Sun, S and Huang, W and Zhao, Z and Yang, F and Lei, Z and Huang, W and Yi, X}, title = {Coupling Iron Sludge Addition and Intermittent Aeration for Achieving Simultaneous Methanogenesis, Feammox, and Denitrification in a Single Reactor Treating Fish Sludge.}, journal = {Environmental science & technology}, volume = {57}, number = {40}, pages = {15065-15075}, doi = {10.1021/acs.est.3c03009}, pmid = {37772420}, issn = {1520-5851}, mesh = {*Sewage ; *Denitrification ; Iron ; Bioreactors ; Carbon ; Nitrogen ; Ferric Compounds ; Waste Disposal, Fluid/methods ; }, abstract = {An integrated anaerobic digestion system for the simultaneous removal of carbon and nitrogen from fish sludge was developed by coupling iron sludge supplementation with intermittent aeration. In terms of nitrogen removal, Fe(III) in iron sludge could trigger Feammox reactions and intermittent aeration could drive the Fe(II)/Fe(III) cycle to sustain continuous ammonia removal. Mass balance analysis suggested that nitrate was the main product of Feammox, which was subsequently removed through heterotrophic denitrification. In terms of carbon removal, the Fe(III)-induced dissimilatory iron reduction (DIR) process significantly promoted fish sludge hydrolysis and provided more simple organics for methanogens and denitrifiers, but aeration showed a negative impact on methanogenesis. To promote nitrogen removal and avoid serious methanogenesis inhibition, different aeration intensities were studied. Results showed that compared with the control without aeration or iron sludge addition, aeration for 5 min every 3 days (150 mL/min) contributed to a 29.0% lower NH4[+]-N concentration and a 12.1% lower total chemical oxygen demand level on day 28, and the decline in methane yield was acceptable (only 13.5% lower). Simultaneous methanogenesis, Feammox, and denitrification in a single reactor treating fish sludge were achieved, which provides a simple and low-cost strategy for the treatment of organic wastewater.}, } @article {pmid37772263, year = {2023}, author = {Zheng, X and Wu, C and Jiang, B and Qin, G and Zeng, M}, title = {Clinical analysis of severe Chlamydia psittaci pneumonia: Case series study.}, journal = {Open life sciences}, volume = {18}, number = {1}, pages = {20220698}, pmid = {37772263}, issn = {2391-5412}, abstract = {The clinical characteristics and diagnosis of ten cases with severe Chlamydia psittaci pneumonia were analyzed. Ten patients had high fever, cough, or diarrhea, and all had a history of contact with birds or poultry. The white blood cell count of the patients was normal or slightly increased. The percentage of neutrophils (N%) and C reactive protein of the patients were significantly increased. Chest computer tomography showed patchy consolidation of both lungs, with one-sided lung lobes prominent, and bronchial inflation signs. All the patients were admitted to the intensive care unit due to respiratory failure. Nine patients needed ventilator-assisted ventilation therapy, and one patient needed high-flow oxygen therapy. All patients had sepsis, and five patients developed septic shock. The patients were diagnosed with severe C. psittaci pneumonia by clinical manifestations and contact history. After timely adjustment of tetracycline-based treatment, eight patients recovered and were discharged, and two patients died of septic shock and respiratory failure. Patients with poultry contact should be cautious toward C. psittaci pneumonia. A better method for the detection of C. psittaci is metagenomic next-generation sequencing. Its examination can shorten the diagnosis time. In a later stage, large-sample research is needed to guide clinical diagnosis and treatment.}, } @article {pmid37771751, year = {2023}, author = {Arikawa, K and Hosokawa, M}, title = {Uncultured prokaryotic genomes in the spotlight: An examination of publicly available data from metagenomics and single-cell genomics.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {4508-4518}, pmid = {37771751}, issn = {2001-0370}, abstract = {Owing to the ineffectiveness of traditional culture techniques for the vast majority of microbial species, culture-independent analyses utilizing next-generation sequencing and bioinformatics have become essential for gaining insight into microbial ecology and function. This mini-review focuses on two essential methods for obtaining genetic information from uncultured prokaryotes, metagenomics and single-cell genomics. We analyzed the registration status of uncultured prokaryotic genome data from major public databases and assessed the advantages and limitations of both the methods. Metagenomics generates a significant quantity of sequence data and multiple prokaryotic genomes using straightforward experimental procedures. However, in ecosystems with high microbial diversity, such as soil, most genes are presented as brief, disconnected contigs, and lack association of highly conserved genes and mobile genetic elements with individual species genomes. Although technically more challenging, single-cell genomics offers valuable insights into complex ecosystems by providing strain-resolved genomes, addressing issues in metagenomics. Recent technological advancements, such as long-read sequencing, machine learning algorithms, and in silico protein structure prediction, in combination with vast genomic data, have the potential to overcome the current technical challenges and facilitate a deeper understanding of uncultured microbial ecosystems and microbial dark matter genes and proteins. In light of this, it is imperative that continued innovation in both methods and technologies take place to create high-quality reference genome databases that will support future microbial research and industrial applications.}, } @article {pmid37771005, year = {2023}, author = {Park, S and Kang, S}, title = {Association of Pooled Fecal Microbiota on Height Growth in Children According to Enterotypes.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {77}, number = {6}, pages = {801-810}, doi = {10.1097/MPG.0000000000003949}, pmid = {37771005}, issn = {1536-4801}, mesh = {Child ; Humans ; *Phosphatidylinositol 3-Kinases ; Bacteria ; *Gastrointestinal Microbiome/physiology ; Feces/microbiology ; }, abstract = {OBJECTIVES: The association between fecal microbiota and height in children has yielded conflicting findings, warranting further investigation into potential differences in fecal bacterial composition between children with short stature and those of standard height based on enterotypes (ETs).

METHODS: According to the height z score for age and gender, the children were categorized into normal-stature (NS; n = 335) and short-stature (SS; n = 152) groups using a z score of -1.15 as a separator value. The human fecal bacterial FASTA/Q files (n = 487) were pooled and analyzed with the QIIME 2 platform with the National Center for Biotechnology Information alignment search tool. According to ETs, the prediction models by the machine learning algorithms were used for explaining SS, and their quality was validated.

RESULTS: The proportion of SS was 16.4% in ET Enterobacteriaceae (ET-E) and 68.1% in Prevotellaceae (ET-P). The Chao1 and Shannon indexes were significantly lower in the SS than in the NS groups only in ET-P. The fecal bacteria related to SS from the prediction models were similar regardless of ETs. However, in network analysis, the negative correlations between fecal bacteria in the NS and SS groups were much higher in the ET-P than in the ET-E. In the metagenome function, fecal bacteria showed an inverse association of biotin and secondary bile acid synthesis and downregulation of insulin/insulin-like growth factor-1-driven phosphoinositide 3-kinase Akt signaling and AMP-kinase signaling in the SS group compared with the NS group in both ETs.

CONCLUSION: The gut microbial compositions in children were associated with height. Strategies to modify and optimize the gut microbiota composition should be investigated for any potential in promoting height in children.}, } @article {pmid37771003, year = {2023}, author = {Gautam, A and Bhowmik, D and Basu, S and Zeng, W and Lahiri, A and Huson, DH and Paul, S}, title = {Microbiome Metabolome Integration Platform (MMIP): a web-based platform for microbiome and metabolome data integration and feature identification.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {6}, pages = {}, doi = {10.1093/bib/bbad325}, pmid = {37771003}, issn = {1477-4054}, mesh = {*Metabolome ; *Microbiota ; Metabolomics/methods ; Internet ; }, abstract = {A microbial community maintains its ecological dynamics via metabolite crosstalk. Hence, knowledge of the metabolome, alongside its populace, would help us understand the functionality of a community and also predict how it will change in atypical conditions. Methods that employ low-cost metagenomic sequencing data can predict the metabolic potential of a community, that is, its ability to produce or utilize specific metabolites. These, in turn, can potentially serve as markers of biochemical pathways that are associated with different communities. We developed MMIP (Microbiome Metabolome Integration Platform), a web-based analytical and predictive tool that can be used to compare the taxonomic content, diversity variation and the metabolic potential between two sets of microbial communities from targeted amplicon sequencing data. MMIP is capable of highlighting statistically significant taxonomic, enzymatic and metabolic attributes as well as learning-based features associated with one group in comparison with another. Furthermore, MMIP can predict linkages among species or groups of microbes in the community, specific enzyme profiles, compounds or metabolites associated with such a group of organisms. With MMIP, we aim to provide a user-friendly, online web server for performing key microbiome-associated analyses of targeted amplicon sequencing data, predicting metabolite signature, and using learning-based linkage analysis, without the need for initial metabolomic analysis, and thereby helping in hypothesis generation.}, } @article {pmid37770615, year = {2023}, author = {Coe, K and Bostan, H and Rolling, W and Turner-Hissong, S and Macko-Podgórni, A and Senalik, D and Liu, S and Seth, R and Curaba, J and Mengist, MF and Grzebelus, D and Van Deynze, A and Dawson, J and Ellison, S and Simon, P and Iorizzo, M}, title = {Population genomics identifies genetic signatures of carrot domestication and improvement and uncovers the origin of high-carotenoid orange carrots.}, journal = {Nature plants}, volume = {9}, number = {10}, pages = {1643-1658}, pmid = {37770615}, issn = {2055-0278}, support = {2016-51181-25400//United States Department of Agriculture | Agricultural Research Service (USDA Agricultural Research Service)/ ; 2022-51181-38321//United States Department of Agriculture/ ; 1008691//United States Department of Agriculture/ ; NSF//National Science Foundation/ ; }, mesh = {*beta Carotene/metabolism ; *Daucus carota/genetics/metabolism ; Domestication ; Metagenomics ; Plant Breeding ; Carotenoids/metabolism ; }, abstract = {Here an improved carrot reference genome and resequencing of 630 carrot accessions were used to investigate carrot domestication and improvement. The study demonstrated that carrot was domesticated during the Early Middle Ages in the region spanning western Asia to central Asia, and orange carrot was selected during the Renaissance period, probably in western Europe. A progressive reduction of genetic diversity accompanied this process. Genes controlling circadian clock/flowering and carotenoid accumulation were under selection during domestication and improvement. Three recessive genes, at the REC, Or and Y2 quantitative trait loci, were essential to select for the high α- and β-carotene orange phenotype. All three genes control high α- and β-carotene accumulation through molecular mechanisms that regulate the interactions between the carotenoid biosynthetic pathway, the photosynthetic system and chloroplast biogenesis. Overall, this study elucidated carrot domestication and breeding history and carotenoid genetics at a molecular level.}, } @article {pmid37770548, year = {2023}, author = {Santos-Medellín, C and Blazewicz, SJ and Pett-Ridge, J and Firestone, MK and Emerson, JB}, title = {Viral but not bacterial community successional patterns reflect extreme turnover shortly after rewetting dry soils.}, journal = {Nature ecology & evolution}, volume = {7}, number = {11}, pages = {1809-1822}, pmid = {37770548}, issn = {2397-334X}, support = {DE-SC0020163//DOE | SC | Biological and Environmental Research (BER)/ ; }, mesh = {*Ecosystem ; *Soil/chemistry ; Seasons ; Bacteria/genetics ; DNA ; }, abstract = {As central members of soil trophic networks, viruses have the potential to drive substantial microbial mortality and nutrient turnover. Pinpointing viral contributions to terrestrial ecosystem processes remains a challenge, as temporal dynamics are difficult to unravel in the spatially and physicochemically heterogeneous soil environment. In Mediterranean grasslands, the first rainfall after seasonal drought provides an ecosystem reset, triggering microbial activity during a tractable window for capturing short-term dynamics. Here, we simulated precipitation in microcosms from four distinct dry grassland soils and generated 144 viromes, 84 metagenomes and 84 16S ribosomal RNA gene amplicon datasets to characterize viral, prokaryotic and relic DNA dynamics over 10 days. Vastly different viral communities in each soil followed remarkably similar successional trajectories. Wet-up triggered a significant increase in viral richness, followed by extensive compositional turnover. Temporal succession in prokaryotic communities was much less pronounced, perhaps suggesting differences in the scales of activity captured by viromes (representing recently produced, ephemeral viral particles) and total DNA. Still, differences in the relative abundances of Actinobacteria (enriched in dry soils) and Proteobacteria (enriched in wetted soils) matched those of their predicted phages, indicating viral predation of dominant bacterial taxa. Rewetting also rapidly depleted relic DNA, which subsequently reaccumulated, indicating substantial new microbial mortality in the days after wet-up, particularly of the taxa putatively under phage predation. Production of abundant, diverse viral particles via microbial host cell lysis appears to be a conserved feature of the early response to soil rewetting, and results suggest the potential for 'Cull-the-Winner' dynamics, whereby viruses infect and cull but do not decimate dominant host populations.}, } @article {pmid37769470, year = {2023}, author = {Li, X and Zhu, L and Ma, R and Zhang, X and Lin, C and Tang, Y and Huang, Z and Wang, C}, title = {Effects of iron additives on the removal of antibiotics and antibiotic resistance genes in anaerobic fermentation of food waste.}, journal = {Journal of environmental management}, volume = {347}, number = {}, pages = {119038}, doi = {10.1016/j.jenvman.2023.119038}, pmid = {37769470}, issn = {1095-8630}, mesh = {*Iron ; Fermentation ; Anti-Bacterial Agents/pharmacology ; Anaerobiosis ; Food ; Ferrosoferric Oxide ; *Refuse Disposal ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; }, abstract = {The presence of antibiotics and antibiotic resistance genes (ARGs) in food waste (FW) during anaerobic fermentation poses significant environmental and health risks. This study elucidated the potential of iron additives, specifically 500-nm and 50-nm zero-valent iron (ZVI) and magnetite, in mitigating these contaminants. These findings revealed that 500-nm magnetite significantly reduced tetracyclines by 81.04%, while 500-nm ZVI effectively reduced cefotaxime by 89.90%. Furthermore, both 500-nm and 50-nm ZVI were observed to decrease different types and abundance of heavy metal resistance and virulence genes. Interestingly, while 500-nm ZVI reduced the overall abundance of ARGs by 50%, 500-nm magnetite primarily reduced the diversity of ARGs without significantly impacting their abundance. These results elucidate the efficacy of iron additives in addressing antibiotic contamination and resistance during the anaerobic fermentation process of FW. The findings acquired from this study mitigate the development of innovative and environmentally sustainable technologies for FW treatment, emphasizing the reduction of environmental risks and enhancement of treatment efficiency.}, } @article {pmid37769091, year = {2023}, author = {Enbody, ED and Sendell-Price, AT and Sprehn, CG and Rubin, CJ and Visscher, PM and Grant, BR and Grant, PR and Andersson, L}, title = {Community-wide genome sequencing reveals 30 years of Darwin's finch evolution.}, journal = {Science (New York, N.Y.)}, volume = {381}, number = {6665}, pages = {eadf6218}, doi = {10.1126/science.adf6218}, pmid = {37769091}, issn = {1095-9203}, mesh = {Animals ; *Beak/anatomy & histology ; Ecuador ; *Finches/anatomy & histology/genetics ; Gene Frequency ; Metagenomics ; *Selection, Genetic ; *Adaptation, Biological ; *Genetic Speciation ; *Genetic Introgression ; Genetic Loci ; }, abstract = {A fundamental goal in evolutionary biology is to understand the genetic architecture of adaptive traits. Using whole-genome data of 3955 of Darwin's finches on the Galápagos Island of Daphne Major, we identified six loci of large effect that explain 45% of the variation in the highly heritable beak size of Geospiza fortis, a key ecological trait. The major locus is a supergene comprising four genes. Abrupt changes in allele frequencies at the loci accompanied a strong change in beak size caused by natural selection during a drought. A gradual change in Geospiza scandens occurred across 30 years as a result of introgressive hybridization with G. fortis. This study shows how a few loci with large effect on a fitness-related trait contribute to the genetic potential for rapid adaptive radiation.}, } @article {pmid37768448, year = {2023}, author = {Manara, S and Beghini, F and Masetti, G and Armanini, F and Geat, D and Galligioni, G and Segata, N and Farina, S and Cristofolini, M}, title = {Thermal Therapy Modulation of the Psoriasis-Associated Skin and Gut Microbiome.}, journal = {Dermatology and therapy}, volume = {13}, number = {11}, pages = {2769-2783}, pmid = {37768448}, issn = {2193-8210}, abstract = {INTRODUCTION: Psoriasis is a systemic immune-mediated disease primarily manifesting as skin redness and inflammation. Balneotherapy proved to be a successful non-pharmacological option to reduce the skin areas affected by the disease, but the specific mechanisms underlying this effect have not been elucidated yet. Here we test the hypothesis that the effect of thermal treatments on psoriatic lesions could be partially mediated by changes in the resident microbial population, i.e., the microbiome.

METHODS: In this study, we enrolled patients with psoriasis and monitored changes in their skin and gut microbiome after a 12-bath balneotherapy course with a combination of 16S rRNA amplicon sequencing and metagenomics. Changes in the resident microbiome were then correlated with thermal therapy outcomes evaluated as changes in Psoriasis Area and Severity Index (PASI) and Body Surface Area index (BSA).

RESULTS: The amplicon sequencing analysis of the skin microbiome showed that after thermal treatment the microbiome composition of affected areas improved to approach that typical of unaffected skin. We moreover identified some low-abundance bacterial biomarkers indicative of disease status and treatment efficacy, and we showed via metagenomic sequencing that thermal treatments and thermal water drinking affect the fecal microbiome to host more species associated with favorable metabolic health.

CONCLUSIONS: Changes in lower-abundance microbial taxa presence and abundance could be the basis for the positive effect of thermal water treatment and drinking on the cutaneous and systemic symptomatology of psoriasis.}, } @article {pmid37768349, year = {2023}, author = {Hong, H and Yang, SM and Kim, E and Kim, HJ and Park, SH}, title = {Correction: Comprehensive metagenomic analysis of stress‑resistant and‑sensitive Listeria monocytogenes.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {21}, pages = {6733-6734}, doi = {10.1007/s00253-023-12793-w}, pmid = {37768349}, issn = {1432-0614}, } @article {pmid37768087, year = {2023}, author = {Wang, M and Lu, J and Qin, P and Wang, S and Ding, W and Fu, H-H and Zhang, Y-Z and Zhang, W}, title = {Biofilm formation stabilizes metabolism in a Roseobacteraceae bacterium under temperature increase.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {10}, pages = {e0060123}, pmid = {37768087}, issn = {1098-5336}, mesh = {Temperature ; *Bacteria/genetics ; *Carbohydrate Metabolism ; Glycolysis ; Biofilms ; }, abstract = {Ocean warming profoundly impacts microbes in marine environments; yet, how lifestyle (e.g., free living versus biofilm associated) affects the bacterial response to rising temperature is not clear. Here, we compared transcriptional, enzymatic, and physiological responses of free-living and biofilm-associated Leisingera aquaemixtae M597, a member of the Roseobacteraceae family isolated from marine biofilms, to the increase in temperature from 25℃ to 31℃. Complete genome sequencing and metagenomics revealed the prevalence of M597 in global ocean biofilms. Transcriptomics suggested a significant effect on the expression of genes related to carbohydrate metabolism, nitrogen and sulfur metabolism, and phosphorus utilization of free-living M597 cells due to temperature increase, but such drastic alterations were not observed in its biofilms. In the free-living state, the transcription of the key enzyme participating in the Embden-Meyerhof-Parnas pathway was significantly increased due to the increase in temperature, accompanied by a substantial decrease in the Entner-Doudoroff pathway, but transcripts of these glycolytic enzymes in biofilm-forming strains were independent of the temperature variation. The correlation between the growth condition and the shift in glycolytic pathways under temperature change was confirmed by enzymatic activity assays. Furthermore, the rising temperature affected the growth rate and the production of intracellular reactive oxygen species when M597 cells were free living rather than in biofilms. Thus, biofilm formation stabilizes metabolism in M597 when grown under high temperature and this homeostasis is probably related to the glycolytic pathways.IMPORTANCEBiofilm formation is one of the most successful strategies employed by microbes against environmental fluctuations. In this study, using a marine Roseobacteraceae bacterium, we studied how biofilm formation affects the response of marine bacteria to the increase in temperature. This study enhances our understanding of the function of bacterial biofilms and the microbe-environment interactions in the framework of global climate change.}, } @article {pmid37768075, year = {2023}, author = {Kumari, S and Leon Magdaleno, JS and Grewal, RK and Narsing Rao, MP and Rajjak Shaikh, A and Cavallo, L and Chawla, M and Kumar, M}, title = {High potential for biomass-degrading CAZymes revealed by pine forest soil metagenomics.}, journal = {Journal of biomolecular structure & dynamics}, volume = {}, number = {}, pages = {1-12}, doi = {10.1080/07391102.2023.2262600}, pmid = {37768075}, issn = {1538-0254}, abstract = {The undisturbed environment in Netarhat, with its high levels of accumulated lignocellulosic biomass, presents an opportunity to identify microbes for biomass digestion. This study focuses on the bioprospecting of native soil microbes from the Netarhat forest in Jharkhand, India, with the potential for lignocellulosic substrate digestion. These biocatalysts could help overcome the bottleneck of biomass saccharification and reduce the overall cost of biofuel production, replacing harmful fossil fuels. The study used metagenomic analysis of pine forest soil via whole genome shotgun sequencing, revealing that most of the reads matched with the bacterial species, very low percentage of reads (0.1%) belongs to fungal species, with 13% of unclassified reads. Actinobacteria were found to be predominant among the bacterial species. MetaErg annotation identified 11,830 protein family genes and 2 metabolic marker genes in the soil samples. Based on the Carbohydrate Active EnZyme (CAZy) database, 3,996 carbohydrate enzyme families were identified, with family Glycosyl hydrolase (GH) dominating with 1,704 genes. Most observed GH families in the study were GH0, 3, 5, 6. 9, 12. 13, 15, 16, 39, 43, 57, and 97. Modelling analysis of a representative GH 43 gene suggested a strong affinity for cellulose than xylan. This study highlights the lignocellulosic digestion potential of the native microfauna of the lesser-known pine forest of Netarhat.Communicated by Ramaswamy H. Sarma.}, } @article {pmid37768069, year = {2023}, author = {Dittmer, J and Corretto, E and Štarhová Serbina, L and Michalik, A and Nováková, E and Schuler, H}, title = {Division of labor within psyllids: metagenomics reveals an ancient dual endosymbiosis with metabolic complementarity in the genus Cacopsylla.}, journal = {mSystems}, volume = {8}, number = {5}, pages = {e0057823}, pmid = {37768069}, issn = {2379-5077}, support = {I 4639-B//Province Bolzano, Austrian Science Fund FWF/ ; 2017/26/D/NZ8/00799//Polish National Science Center/ ; }, mesh = {Animals ; *Hemiptera/genetics ; Symbiosis/genetics ; Phylogeny ; Bacteria ; Enterobacteriaceae/genetics ; }, abstract = {Heritable beneficial bacterial endosymbionts have been crucial for the evolutionary success of numerous insects by enabling the exploitation of nutritionally limited food sources. Herein, we describe a previously unknown dual endosymbiosis in the psyllid genus Cacopsylla, consisting of the primary endosymbiont "Candidatus Carsonella ruddii" and a co-occurring Enterobacteriaceae bacterium for which we propose the name "Candidatus Psyllophila symbiotica." Its localization within the bacteriome and its small genome size confirm that Psyllophila is a co-primary endosymbiont widespread within the genus Cacopsylla. Despite its highly eroded genome, Psyllophila perfectly complements the tryptophan biosynthesis pathway that is incomplete in the co-occurring Carsonella. Moreover, the genome of Psyllophila is almost as small as Carsonella's, suggesting an ancient dual endosymbiosis that has now reached a precarious stage where any additional gene loss would make the system collapse. Hence, our results shed light on the dynamic interactions of psyllids and their endosymbionts over evolutionary time.}, } @article {pmid37767011, year = {2023}, author = {Dayer, R and De Marco, G and Vazquez, O and Tabard-Fougère, A and Cochard, B and Gavira, N and Di Laura Frattura, G and Guanziroli Pralong, N and Steiger, C and Ceroni, D}, title = {Laboratory diagnostics for primary spinal infections in pediatric and adult populations: a narrative review.}, journal = {North American Spine Society journal}, volume = {16}, number = {}, pages = {100270}, pmid = {37767011}, issn = {2666-5484}, abstract = {Primary spinal infection (PSI) is a generic term covering a heterogeneous group of infections that can affect the vertebral body, intervertebral disks, the content of the medullary cavity, and adjacent paraspinal tissues. Patients' characteristics can vary significantly, notably according to their age, and some of these characteristics undoubtedly play a primordial role in the occurrence of a PSI and in the type of offending pathogen. Before approaching the subject of laboratory diagnostics, it is essential to define the characteristics of the patient and their infection, which can then guide the physician toward specific diagnostic approaches. This review critically examined the roles and usefulness of traditional and modern laboratory diagnostics in supporting clinicians' decision-making in cases of pediatric and adult primary spinal infection (PSI). It appears impossible to compare PSIs in children and adults, whether from an epidemiological, clinical, bacteriological, or biological perspective. The recipients are really too different, and the responsible germs are closely correlated to their age. Secondly, the interpretation of traditional laboratory blood tests appears to contribute little guidance for clinicians attempting to diagnose a PSI. Biopsy or needle aspiration for bacterial identification remains a controversial subject, as the success rates of these procedures for identifying causative organisms are relatively uncertain in pediatric populations.Using nucleic acid amplification assays (NAAAs) on biopsy samples has been demonstrated to be more sensitive than conventional cultures for diagnosing PSI. Recent advances in next-generation sequencing (NGS) are particularly interesting for establishing a microbiological diagnosis of a PSI when standard cultures and NAAAs have failed to detect the culprit. We can even imagine that plasma metagenomic NGS using plasma (known as "liquid biopsy") is a diagnostic approach that can detect not only pathogens circulating in the bloodstream but also those causing focal infections, and thus eliminate the need for source sample collection using costly invasive surgical procedures.}, } @article {pmid37766921, year = {2023}, author = {Cao, L and Sun, Y and Chen, F}, title = {Pulmonary nocardiosis following COVID-19 in a patient with idiopathic pulmonary fibrosis and lung transplantation: a case report.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1266857}, pmid = {37766921}, issn = {2296-858X}, abstract = {BACKGROUND: Nocardiosis is an opportunistic infection that primarily affects immunocompromised patients. Pulmonary nocardiosis is the most prevalent form, but can also spread to other organs. Potential causes contributing to opportunistic infection may include immunosuppression and disruption of tight junctions, both of which can result from COVID-19.

CASE PRESENTATION: We reported a case of a 68-year-old male patient who presented with a 10-day history of fever, cough, and productive sputum. Upon physical examination, velcro rales were detected in the right lung, while breath sounds in the left lung were clear. The patient had previously undergone left lung transplantation due to idiopathic pulmonary fibrosis four years ago. He was initially hospitalized and treated for COVID-19 but was readmitted due to worsening symptoms. Subsequently, pulmonary nocardiosis was diagnosed utilizing metagenomic next-generation sequencing of bronchoalveolar lavage fluid. The above-mentioned condition was improved following treatment with cancidas and linezolid. Now, he is under regular follow-up.

CONCLUSION: This case highlights the complexity of COVID-19 and the occurrence of secondary opportunistic infections, which require further investigation.}, } @article {pmid37766363, year = {2023}, author = {Lee, CK and Ng, SY and Chai, CN and Lim, YF and Hu, TJ and Lee, OF and Yan, G}, title = {Successful Confirmation of Dual Genital Herpes Co-Infection with Herpes Simplex Virus 1 and Herpes Simplex Virus 2 Using Unbiased Metagenomic Next-Generation Sequencing.}, journal = {Viruses}, volume = {15}, number = {9}, pages = {}, pmid = {37766363}, issn = {1999-4915}, abstract = {Dual co-infection with both HSV-1 and HSV-2 is rare, with few cases reported in the literature. In this case report, we describe the successful use of unbiased metagenomic next-generation sequencing (mNGS) as a rapid and alternative method for confirming dual genital herpes co-infection. Our case involves a 74-year-old woman who presented with genital lesions and initially tested positive for both HSV-1 and HSV-2 via the Luminex ARIES HSV 1&2 assay. The entire mNGS process, from nucleic acid extraction to result analysis, was completed in less than 48 h. Using mNGS, we identified mapped reads specific to either HSV-1 or HSV-2 and screened the sequences to rule out mis-genotyping by the Luminex ARIES assay. Notably, the generated sequences can reveal sequence variations within multiple gene regions, demonstrating the potential of mNGS for identifying novel HSV-1 and HSV-2 variants. Our findings suggest that mNGS can serve as a rapid and reliable alternative confirmatory method for dual genital herpes infections, providing valuable information to guide appropriate treatment options for patients. By eliminating the need for prior knowledge of causative agents, mNGS offers an unbiased approach for detecting and characterizing viral co-infections.}, } @article {pmid37766355, year = {2023}, author = {Xiao, H and Meng, B}, title = {Molecular and Metagenomic Analyses Reveal High Prevalence and Complexity of Viral Infections in French-American Hybrids and North American Grapes.}, journal = {Viruses}, volume = {15}, number = {9}, pages = {}, pmid = {37766355}, issn = {1999-4915}, mesh = {*Vitis ; Prevalence ; *Virus Diseases ; *Wine ; North America/epidemiology ; }, abstract = {French-American hybrids and North American grape species play a significant role in Canada's grape and wine industry. Unfortunately, the occurrence of viruses and viral diseases among these locally important non-vinifera grapes remains understudied. We report here the results from a large-scale survey to assess the prevalence of 14 viruses among 533 composite samples representing 2665 vines from seven French-American hybrid wine grape cultivars, two North American juice grape cultivars (Concord and Niagara), and the table grape cultivar Sovereign coronation. Based on reverse transcription polymerase chain reaction (RT-PCR) assays, ten viruses were detected. Grapevine rupestris stem pitting-associated virus, grapevine leafroll-associated virus 3, grapevine Pinot gris virus and grapevine red blotch virus were detected with the highest frequency. As expected, mixed infections were common; 62% of the samples contained two or more viruses. Overall, hybrid wine grapes were infected with more viruses and a higher prevalence of individual viruses than juice and table grapes. To validate these findings and to refine the virome of these non-European grapes, high-throughput sequencing (HTS) analyses of five composite samples representing each category of grapevine cultivars was performed. Results from HTS agreed with those from RT-PCR. Importantly, Vidal, a widely grown white-wine grape with international recognition due to its use in the award-winning icewine, is host to 14 viruses, four of which comprise multiple and distinct genetic variants. This comprehensive survey represents the most extensive examination of viruses among French-American hybrids and North American grapes to date.}, } @article {pmid37766302, year = {2023}, author = {Ternovoi, VA and Shvalov, AN and Kartashov, MY and Ponomareva, EP and Tupota, NL and Khoroshavin, YA and Bayandin, RB and Gladysheva, AV and Mikryukova, TP and Tregubchak, TV and Loktev, VB}, title = {The Viromes of Mosquitoes from the Natural Landscapes of Western Siberia.}, journal = {Viruses}, volume = {15}, number = {9}, pages = {}, pmid = {37766302}, issn = {1999-4915}, mesh = {Humans ; Animals ; Virome ; Siberia ; *Nodaviridae ; Capsid Proteins/genetics ; *Culicidae ; }, abstract = {The metagenomic analysis of mosquitoes allows for the genetic characterization of mosquito-associated viruses in different regions of the world. This study applied a metagenomic approach to identify novel viral sequences in seven species of mosquitoes collected from the Novosibirsk region of western Siberia. Using NGS sequencing, we identified 15 coding-complete viral polyproteins (genomes) and 15 viral-like partial sequences in mosquitoes. The complete sequences for novel viruses or the partial sequences of capsid proteins, hypothetical viral proteins, and RdRps were used to identify their taxonomy. The novel viral sequences were classified within the orders Tymovirales and Picornavirales and the families Partitiviridae, Totiviridae, Tombusviridae, Iflaviridae, Nodaviridae, Permutotetraviridae, and Solemoviridae, with several attributed to four unclassified RNA viruses. Interestingly, the novel putative viruses and viral sequences were mainly associated with the mosquito Coquillettidia richardii. This study aimed to increase our understanding of the viral diversity in mosquitoes found in the natural habitats of Siberia, which is characterized by very long, snowy, and cold winters.}, } @article {pmid37766257, year = {2023}, author = {de Santana, SF and Santos, VC and Lopes, ÍS and Porto, JAM and Mora-Ocampo, IY and Sodré, GA and Pirovani, CP and Góes-Neto, A and Pacheco, LGC and Fonseca, PLC and Costa, MA and Aguiar, ERGR}, title = {Mining Public Data to Investigate the Virome of Neglected Pollinators and Other Floral Visitors.}, journal = {Viruses}, volume = {15}, number = {9}, pages = {}, pmid = {37766257}, issn = {1999-4915}, mesh = {Humans ; Bees ; Animals ; *Virome ; Phylogeny ; Insecta ; *Viruses/genetics ; Crops, Agricultural ; }, abstract = {This study reports the virome investigation of pollinator species and other floral visitors associated with plants from the south of Bahia: Aphis aurantii, Atrichopogon sp., Dasyhelea sp., Forcipomyia taiwana, and Trigona ventralis hoozana. Studying viruses in insects associated with economically important crops is vital to understand transmission dynamics and manage viral diseases that pose as threats for global food security. Using literature mining and public RNA next-generation sequencing data deposited in the NCBI SRA database, we identified potential vectors associated with Malvaceae plant species and characterized the microbial communities resident in these insects. Bacteria and Eukarya dominated the metagenomic analyses of all taxon groups. We also found sequences showing similarity to elements from several viral families, including Bunyavirales, Chuviridae, Iflaviridae, Narnaviridae, Orthomyxoviridae, Rhabdoviridae, Totiviridae, and Xinmoviridae. Phylogenetic analyses indicated the existence of at least 16 new viruses distributed among A. aurantii (3), Atrichopogon sp. (4), Dasyhelea sp. (3), and F. taiwana (6). No novel viruses were found for T. ventralis hoozana. For F. taiwana, the available libraries also allowed us to suggest possible vertical transmission, while for A. aurantii we followed the infection profile along the insect development. Our results highlight the importance of studying the virome of insect species associated with crop pollination, as they may play a crucial role in the transmission of viruses to economically important plants, such as those of the genus Theobroma, or they will reduce the pollination process. This information may be valuable in developing strategies to mitigate the spread of viruses and protect the global industry.}, } @article {pmid37766237, year = {2023}, author = {Mohamed Ali, S and Rakotonirina, A and Heng, K and Jacquemet, E and Volant, S and Temmam, S and Boyer, S and Eloit, M}, title = {Longitudinal Study of Viral Diversity Associated with Mosquito Species Circulating in Cambodia.}, journal = {Viruses}, volume = {15}, number = {9}, pages = {}, pmid = {37766237}, issn = {1999-4915}, support = {U01 AI151758/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Animals ; Cambodia/epidemiology ; Longitudinal Studies ; Mosquito Vectors ; *Birnaviridae ; *Culicidae ; }, abstract = {Arthropod-borne viruses (arboviruses) pose a significant global health threat and are primarily transmitted by mosquitoes. In Cambodia, there are currently 290 recorded mosquito species, with at least 17 of them considered potential vectors of arboviruses to humans. Effective surveillance of virome profiles in mosquitoes from Cambodia is vital, as it could help prevent and control arbovirus diseases in a country where epidemics occur frequently. The objective of this study was to identify and characterize the viral diversity in mosquitoes collected during a one-year longitudinal study conducted in various habitats across Cambodia. For this purpose, we used a metatranscriptomics approach and detected the presence of chikungunya virus in the collected mosquitoes. Additionally, we identified viruses categorized into 26 taxa, including those known to harbor arboviruses such as Flaviviridae and Orthomyxoviridae, along with a group of viruses not yet taxonomically identified and provisionally named "unclassified viruses". Interestingly, the taxa detected varied in abundance and composition depending on the mosquito genus, with no significant influence of the collection season. Furthermore, most of the identified viruses were either closely related to viruses found exclusively in insects or represented new viruses belonging to the Rhabdoviridae and Birnaviridae families. The transmission capabilities of these novel viruses to vertebrates remain unknown.}, } @article {pmid37766228, year = {2023}, author = {Paietta, EN and Kraberger, S and Custer, JM and Vargas, KL and Espy, C and Ehmke, E and Yoder, AD and Varsani, A}, title = {Characterization of Diverse Anelloviruses, Cressdnaviruses, and Bacteriophages in the Human Oral DNA Virome from North Carolina (USA).}, journal = {Viruses}, volume = {15}, number = {9}, pages = {}, pmid = {37766228}, issn = {1999-4915}, mesh = {Humans ; Animals ; *Bacteriophages ; *Anelloviridae ; North Carolina ; Pilot Projects ; Virome ; DNA ; *Lemur ; }, abstract = {The diversity of viruses identified from the various niches of the human oral cavity-from saliva to dental plaques to the surface of the tongue-has accelerated in the age of metagenomics. This rapid expansion demonstrates that our understanding of oral viral diversity is incomplete, with only a few studies utilizing passive drool collection in conjunction with metagenomic sequencing methods. For this pilot study, we obtained 14 samples from healthy staff members working at the Duke Lemur Center (Durham, NC, USA) to determine the viral diversity that can be identified in passive drool samples from humans. The complete genomes of 3 anelloviruses, 9 cressdnaviruses, 4 Caudoviricetes large bacteriophages, 29 microviruses, and 19 inoviruses were identified in this study using high-throughput sequencing and viral metagenomic workflows. The results presented here expand our understanding of the vertebrate-infecting and microbe-infecting viral diversity of the human oral virome in North Carolina (USA).}, } @article {pmid37766190, year = {2023}, author = {Hille, F and Gieschler, S and Brinks, E and Franz, CMAP}, title = {Characterisation of the Novel Filamentous Phage PMBT54 Infecting the Milk Spoilage Bacteria Pseudomonas carnis and Pseudomonas lactis.}, journal = {Viruses}, volume = {15}, number = {9}, pages = {}, pmid = {37766190}, issn = {1999-4915}, mesh = {Humans ; Animals ; Milk ; *Inovirus/genetics ; Pseudomonas ; Bacteria ; *Bacteriophages/genetics ; }, abstract = {Filamentous bacteriophages are lysogenic and pseudo-lysogenic viruses that do not lyse their host but are often continuously secreted from the infected cell. They belong to the order Tubulavirales, which encompasses three families, with the Inoviridae being the largest. While the number of identified inoviral sequences has greatly increased in recent years due to metagenomic studies, morphological and physiological characterisation is still restricted to only a few members of the filamentous phages. Here, we describe the novel filamentous phage PMBT54, which infects the spoilage-relevant Pseudomonas species P. carnis and P. lactis. Its genome is 7320 bp in size, has a mol% GC content of 48.37, and codes for 13 open-reading frames, two of which are located on the (-) strand. The virion exhibits a typical filamentous morphology and is secreted from the host cell at various lengths. The phage was shown to promote biofilm formation in both host strains and, therefore, has potential implications for milk spoilage, as biofilms are a major concern in the dairy industry.}, } @article {pmid37765456, year = {2023}, author = {Vinogradova, S and Porotikova, E and Navrotskaya, E and Galbacs, ZN and Massart, S and Varallyay, E}, title = {The First Virome of a Russian Vineyard.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {18}, pages = {}, pmid = {37765456}, issn = {2223-7747}, support = {19-76-10029//Russian Science Foundation/ ; 122112300055-6//Ministry of Education and Science of Russian Federation/ ; K131679//National Research, Development and Innovation Office (NKFIH)/ ; K119783//National Research, Development and Innovation Office (NKFIH)/ ; }, abstract = {Among other pathogens, more than 80 viruses infect grapevine. The aim of this work was to study the virome diversity of grapevine viruses and mycoviruses of a vineyard using high-throughput sequencing technologies. The grapevine virome was studied in symptomatic vines of the Rkatsiteli cultivar (V. vinifera) collected at the vineyards of the Krasnodar Krai in Russia. Ribosomal-depleted total RNA and isolated small RNAs were used for library preparation and high-throughput sequencing. Six grapevine-infecting viruses and two viroids were validated by RT-PCR and analyzed phylogenetically. We identified the presence of grapevine leafroll-associated virus 3, grapevine Pinot gris virus, grapevine virus T, grapevine rupestris stem-pitting-associated virus, grapevine fleck virus, and grapevine rupestris vein feathering virus, as well as two viroids, grapevine yellow speckle viroid 1 and hop stunt viroid. We also studied the mycovirome of the vineyard and identified nine viruses with single-stranded positive-sense RNA genomes: alternaria arborescens mitovirus 1, botrytis cinerea mitovirus 1, botrytis cinerea mitovirus 2, botrytis cinerea mitovirus 3, botrytis cinerea mitovirus 4, sclerotinia sclerotiorum mitovirus 3, botrytis cinerea hypovirus 1, grapevine-associated narnavirus 1, and botrytis virus F. In addition, we identified botrytis cinerea hypovirus 1 satellite-like RNA and two single-stranded negative-sense RNA viruses. This is the first study of grapevine mycoviruses in Russia. The obtained result will contribute to the development of biocontrol strategies in the future.}, } @article {pmid37764930, year = {2023}, author = {da Silva, AS and de Campos, GM and Villanova, MG and Bezerra, RDS and Santiago, LMM and Haddad, R and Covas, DT and Giovanetti, M and Alcantara, LCJ and Elias, MC and Sampaio, SC and Kashima, S and Slavov, SN}, title = {Human Pegivirus-1 Detection and Genotyping in Brazilian Patients with Fulminant Hepatitis.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {9}, pages = {}, pmid = {37764930}, issn = {2076-0817}, support = {2018/15826-5//São Paulo Research Foundation/ ; 2017/23205-8//São Paulo Research Foundation/ ; 2019/08528-0//São Paulo Research Foundation/ ; 2021/11944-6//São Paulo Research Foundation/ ; 2022/00910-6//São Paulo Research Foundation/ ; 2022/10278-5//São Paulo Research Foundation/ ; }, abstract = {Fulminant hepatitis is a severe clinical disease characterized by a marked decline in liver function and encephalopathy. In a previous survey, using metagenomics in a group of 27 patients with this clinical condition, we observed an expressive quantity of reads of the Human pegivirus-1 (HPgV-1). Therefore, the objective of this study was to evaluate the frequency, molecular features, and HPgV-1 circulating genotypes in patients with fulminant hepatitis. After testing the collected plasma samples, we discovered twelve samples (44.4%) that were positive for HPgV-1 RNA (using both real-time and nested PCR). The positive samples presented a mean cycle threshold (Ct) of 28.5 (±7.3). Genotyping assignments revealed that all HPgV-1 positive samples belonged to the HPgV-1 genotype 2 (both subgenotypes 2A and 2B were identified). Although HPgV-1 is considered a commensal virus, little is known regarding its prevalence and genotypes in cases of fulminant hepatitis. More research is needed to understand whether HPgV-1 can be implicated in clinical disorders and infectious diseases.}, } @article {pmid37764838, year = {2023}, author = {Bastos-Moreira, Y and Ouédraogo, L and De Boevre, M and Argaw, A and de Kok, B and Hanley-Cook, GT and Deng, L and Ouédraogo, M and Compaoré, A and Tesfamariam, K and Ganaba, R and Huybregts, L and Toe, LC and Lachat, C and Kolsteren, P and De Saeger, S and Dailey-Chwalibóg, T}, title = {A Multi-Omics and Human Biomonitoring Approach to Assessing the Effectiveness of Fortified Balanced Energy-Protein Supplementation on Maternal and Newborn Health in Burkina Faso: A Study Protocol.}, journal = {Nutrients}, volume = {15}, number = {18}, pages = {}, pmid = {37764838}, issn = {2072-6643}, support = {OPP1175213/GATES/Bill & Melinda Gates Foundation/United States ; 946192/ERC_/European Research Council/International ; }, mesh = {Pregnancy ; Infant ; Infant, Newborn ; Humans ; Female ; Burkina Faso ; *Infant Health ; *Biological Monitoring ; Lactation ; Multiomics ; Folic Acid ; Iron ; Dietary Supplements ; Randomized Controlled Trials as Topic ; }, abstract = {Fortified balanced energy-protein (BEP) supplementation is a promising intervention for improving maternal health, birth outcomes and infant growth in low- and middle-income countries. This nested biospecimen sub-study aimed to evaluate the physiological effect of multi-micronutrient-fortified BEP supplementation on pregnant and lactating women and their infants. Pregnant women (15-40 years) received either fortified BEP and iron-folic acid (IFA) (intervention) or IFA only (control) throughout pregnancy. The same women were concurrently randomized to receive either a fortified BEP supplement during the first 6 months postpartum in combination with IFA for the first 6 weeks (i.e., intervention) or the postnatal standard of care, which comprised IFA alone for 6 weeks postpartum (i.e., control). Biological specimens were collected at different timepoints. Multi-omics profiles will be characterized to assess the mediating effect of BEP supplementation on the different trial arms and its effect on maternal health, as well as birth and infant growth outcomes. The mediating effect of the exposome in the relationship between BEP supplementation and maternal health, birth outcomes and infant growth were characterized via biomonitoring markers of air pollution, mycotoxins and environmental contaminants. The results will provide holistic insight into the granular physiological effects of prenatal and postnatal BEP supplementation.}, } @article {pmid37764199, year = {2023}, author = {Williams, RAJ and Sánchez-Llatas, CJ and Doménech, A and Madrid, R and Fandiño, S and Cea-Callejo, P and Gomez-Lucia, E and Benítez, L}, title = {Emerging and Novel Viruses in Passerine Birds.}, journal = {Microorganisms}, volume = {11}, number = {9}, pages = {}, pmid = {37764199}, issn = {2076-2607}, abstract = {There is growing interest in emerging viruses that can cause serious or lethal disease in humans and animals. The proliferation of cloacal virome studies, mainly focused on poultry and other domestic birds, reveals a wide variety of viruses, although their pathogenic significance is currently uncertain. Analysis of viruses detected in wild birds is complex and often biased towards waterfowl because of the obvious interest in avian influenza or other zoonotic viruses. Less is known about the viruses present in the order Passeriformes, which comprises approximately 60% of extant bird species. This review aims to compile the most significant contributions on the DNA/RNA viruses affecting passerines, from traditional and metagenomic studies. It highlights that most passerine species have never been sampled. Especially the RNA viruses from Flaviviridae, Orthomyxoviridae and Togaviridae are considered emerging because of increased incidence or avian mortality/morbidity, spread to new geographical areas or hosts and their zoonotic risk. Arguably poxvirus, and perhaps other virus groups, could also be considered "emerging viruses". However, many of these viruses have only recently been described in passerines using metagenomics and their role in the ecosystem is unknown. Finally, it is noteworthy that only one third of the viruses affecting passerines have been officially recognized.}, } @article {pmid37764193, year = {2023}, author = {Loughrin, JH and Parekh, RR and Agga, GE and Silva, PJ and Sistani, KR}, title = {Microbiome Diversity of Anaerobic Digesters Is Enhanced by Microaeration and Low Frequency Sound.}, journal = {Microorganisms}, volume = {11}, number = {9}, pages = {}, pmid = {37764193}, issn = {2076-2607}, abstract = {Biogas is produced by a consortium of bacteria and archaea. We studied how the microbiome of poultry litter digestate was affected by time and treatments that enhanced biogas production. The microbiome was analyzed at six, 23, and 42 weeks of incubation. Starting at week seven, the digesters underwent four treatments: control, microaeration with 6 mL air L[-1] digestate per day, treatment with a 1000 Hz sine wave, or treatment with the sound wave and microaeration. Both microaeration and sound enhanced biogas production relative to the control, while their combination was not as effective as microaeration alone. At week six, over 80% of the microbiome of the four digesters was composed of the three phyla Actinobacteria, Proteobacteria, and Firmicutes, with less than 10% Euryarchaeota and Bacteroidetes. At week 23, the digester microbiomes were more diverse with the phyla Spirochaetes, Synergistetes, and Verrucomicrobia increasing in proportion and the abundance of Actinobacteria decreasing. At week 42, Firmicutes, Bacteroidetes, Euryarchaeota, and Actinobacteria were the most dominant phyla, comprising 27.8%, 21.4%, 17.6%, and 12.3% of the microbiome. Other than the relative proportions of Firmicutes being increased and proportions of Bacteroidetes being decreased by the treatments, no systematic shifts in the microbiomes were observed due to treatment. Rather, microbial diversity was enhanced relative to the control. Given that both air and sound treatment increased biogas production, it is likely that they improved poultry litter breakdown to promote microbial growth.}, } @article {pmid37764172, year = {2023}, author = {Gomeiz, AT and Sun, Y and Newborn, A and Wang, ZW and Angelotti, B and Van Aken, B}, title = {Metagenomic Analysis of a Continuous-Flow Aerobic Granulation System for Wastewater Treatment.}, journal = {Microorganisms}, volume = {11}, number = {9}, pages = {}, pmid = {37764172}, issn = {2076-2607}, abstract = {Aerobic granulation is an emerging process in wastewater treatment that has the potential to accelerate sedimentation of the microbial biomass during secondary treatment. Aerobic granulation has been difficult to achieve in the continuous flow reactors (CFRs) used in modern wastewater treatment plants. Recent research has demonstrated that the alternation of nutrient-abundant (feast) and nutrient-limiting (famine) conditions is able to promote aerobic granulation in a CFR. In this study, we conducted a metagenomic analysis with the objective of characterizing the bacterial composition of the granular biomass developed in three simulated plug flow reactors (PFRs) with different feast-to-famine ratios. Phylogenetic analyses revealed a clear distinction between the bacterial composition of aerobic granules in the pilot simulated PFRs as compared with conventional activated sludge. Larger and denser granules, showing improved sedimentation properties, were observed in the PFR with the longest famine time and were characterized by a greater proportion of bacteria producing abundant extracellular polymeric substances (EPS). Functional metagenomic analysis based on KEGG pathways indicated that the large and dense aerobic granules in the PFR with the longest famine time showed increased functionalities related to secretion systems and quorum sensing, which are characteristics of bacteria in biofilms and aerobic granules. This study contributes to a further understanding of the relationship between aerobic granule morphology and the bacterial composition of the granular biomass.}, } @article {pmid37764151, year = {2023}, author = {Nagakubo, D and Kaibori, Y}, title = {Oral Microbiota: The Influences and Interactions of Saliva, IgA, and Dietary Factors in Health and Disease.}, journal = {Microorganisms}, volume = {11}, number = {9}, pages = {}, pmid = {37764151}, issn = {2076-2607}, abstract = {Recent advances in metagenomic analyses have made it easier to analyze microbiota. The microbiota, a symbiotic community of microorganisms including bacteria, archaea, fungi, and viruses within a specific environment in tissues such as the digestive tract and skin, has a complex relationship with the host. Recent studies have revealed that microbiota composition and balance particularly affect the health of the host and the onset of disease. Influences such as diet, food preferences, and sanitation play crucial roles in microbiota composition. The oral cavity is where the digestive tract directly communicates with the outside. Stable temperature and humidity provide optimal growth environments for many bacteria. However, the oral cavity is a unique environment that is susceptible to pH changes, salinity, food nutrients, and external pathogens. Recent studies have emphasized the importance of the oral microbiota, as changes in bacterial composition and balance could contribute to the development of systemic diseases. This review focuses on saliva, IgA, and fermented foods because they play critical roles in maintaining the oral bacterial environment by regulating its composition and balance. More attention should be paid to the oral microbiota and its regulatory factors in oral and systemic health.}, } @article {pmid37764032, year = {2023}, author = {Qu, H and Long, Y and Wang, X and Wang, K and Chen, L and Yang, Y and Chen, L}, title = {Diversity and Abundance of Bacterial and Fungal Communities Inhabiting Camellia sinensis Leaf, Rhizospheric Soil, and Gut of Agriophara rhombata.}, journal = {Microorganisms}, volume = {11}, number = {9}, pages = {}, pmid = {37764032}, issn = {2076-2607}, support = {202101BD07001-029//Agricultural Joint Special Project of Yunnan/ ; 32160724//National Natural Science Foundation of China/ ; }, abstract = {Agriophara rhombata is a tea leaf moth that is considered one of the most destructive pests of Camellia sinensis (tea plant). Several recent studies have shown that many insects acquire part of the microbiome from their host and soil, but the pattern and diversity of their microbiome have not been clearly demonstrated. The present study aimed to investigate the bacterial and fungal communities present in the rhizospheric soil and leaf of tea plant compared to the gut of tea moth at different developmental stages (larvae, pupae, adult female and male) using Illumina MiSeq technology. Alpha diversity (Shannon index) showed higher (p < 0.05) bacterial and fungal diversity in soil samples than in leaf and tea moth larvae, pupae, and adult gut samples. However, during different developmental stages of tea moth, bacterial and fungal diversity did not differ (p > 0.05) between larvae, pupae, female, and male guts. Beta diversity also revealed more distinct bacterial and fungal communities in soil and leaf samples compared with tea moth gut samples, which had a more similar microbiome. Furthermore, Proteobacteria, Firmicutes, and Tenericutes were detected as the dominant bacterial phyla, while Ascomycota, Basidiomycota, and Mortierellomycota were the most abundant fungal phyla among all groups, but their relative abundance was comparatively higher (p < 0.05) in soil and leaf samples compared to tea moth gut samples. Similarly, Klebsiella, Streptophyta, and Enterococcus were the top three bacterial genera, while Candida, Aureobasidium, and Strelitziana were the top three fungal genera, and their relative abundance varied significantly (p < 0.05) among all groups. The KEGG analysis also revealed significantly higher (p < 0.5) enrichment of the functional pathways of bacterial communities in soil and leaf samples than in tea moth gut samples. Our study concluded that the bacterial and fungal communities of soil and tea leaves were more diverse and were significantly different from the tea moth gut microbiome at different developmental stages. Our findings contribute to our understanding of the gut microbiota of the tea moth and its potential application in the development of pest management techniques.}, } @article {pmid37763986, year = {2023}, author = {Kimura, H and Hayashi, Y and Kitagawa, M and Yoshizaki, M and Saito, K and Harada, K and Okayama, K and Miura, Y and Kimura, R and Shirai, T and Fujita, K and Machida, S and Ito, K and Kurosawa, I}, title = {Pathogen Profiles in Outpatients with Non-COVID-19 during the 7th Prevalent Period of COVID-19 in Gunma, Japan.}, journal = {Microorganisms}, volume = {11}, number = {9}, pages = {}, pmid = {37763986}, issn = {2076-2607}, support = {Takara Bio Inc//This research was supported by Takara Bio Inc/ ; }, abstract = {The identification of pathogens associated with respiratory symptoms other than the novel coronavirus disease 2019 (COVID-19) can be challenging. However, the diagnosis of pathogens is crucial for assessing the clinical outcome of patients. We comprehensively profiled pathogens causing non-COVID-19 respiratory symptoms during the 7th prevalent period in Gunma, Japan, using deep sequencing combined with a next-generation sequencer (NGS) and advanced bioinformatics technologies. The study included nasopharyngeal swabs from 40 patients who tested negative for severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2) using immuno-chromatography and/or quantitative reverse transcription polymerase chain reaction (qRT-PCR) methods. Comprehensive pathogen sequencing was conducted through deep sequencing using NGS. Additionally, short reads obtained from NGS were analyzed for comprehensive pathogen estimation using MePIC (Metagenomic Pathogen Identification Pipeline for Clinical Specimens) and/or VirusTap. The results revealed the presence of various pathogens, including respiratory viruses and bacteria, in the present subjects. Notably, human adenovirus (HAdV) was the most frequently detected virus in 16 of the 40 cases (40.0%), followed by coryneforms, which were the most frequently detected bacteria in 21 of the 40 cases (52.5%). Seasonal human coronaviruses (NL63 type, 229E type, HKU1 type, and OC43 type), human bocaviruses, and human herpesviruses (human herpesvirus types 1-7) were not detected. Moreover, multiple pathogens were detected in 50% of the subjects. These results suggest that various respiratory pathogens may be associated with non-COVID-19 patients during the 7th prevalent period in Gunma Prefecture, Japan. Consequently, for an accurate diagnosis of pathogens causing respiratory infections, detailed pathogen analyses may be necessary. Furthermore, it is possible that various pathogens, excluding SARS-CoV-2, may be linked to fever and/or respiratory infections even during the COVID-19 pandemic.}, } @article {pmid37763247, year = {2023}, author = {Gong, X and Li, S and Wu, Z and Alhaj Hamoud, Y and Shaghaleh, H and Kalkhajeh, YK and Si, C and Zhu, L and Ma, C}, title = {Biochar Enhances Soil Resource Availability and Suppresses Microbial Metabolism Genes in the Rhizosphere of Wheat.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {9}, pages = {}, pmid = {37763247}, issn = {2075-1729}, abstract = {Despite the well-documented role of biochar in promoting soil quality and crop productivity, the underlying biological mechanisms remain poorly understood. Here, we explored the effects of straw biochar on soil microbiome in the rhizosphere from wheat using metagenomic sequencing. Our results showed that straw return decreased the yields of wheat, while the straw biochar return increased the wheat yields. Further, both the richness and community composition confirmed different effects of the straw return and straw biochar return. The straw biochar return also resulted in greater rhizosphere effects from wheat, represented by resource availability, including soil organic carbon, soil total nitrogen, available phosphorus, and available potassium. The rhizosphere effects from wheat, represented by microbial metabolism genes involved in carbon, nitrogen, phosphorus, and potassium cycling, however, were decreased by straw biochar returning. In addition, the rhizosphere effects from nitrogen content and the nitrogen cycling genes showed negative relationships with wheat yields. Together, these results revealed that straw biochar enhanced soil resource availability but suppressed microbial metabolism genes in the rhizosphere from wheat, supporting the idea that straw biochar serves as a nutrient pool for crops.}, } @article {pmid37762905, year = {2023}, author = {Baek, YJ and Lee, YJ and Lee, JA and Kim, JH and Kwon, HM and Yeom, JS and Park, KK and Jeong, SJ}, title = {Role of α-Defensin and the Microbiome in Prosthetic Joint Infection: A Prospective Cohort Study in Korea.}, journal = {Journal of clinical medicine}, volume = {12}, number = {18}, pages = {}, pmid = {37762905}, issn = {2077-0383}, support = {C-2020-0018//Severance Hospital Research Fund for Clinical Excellence/ ; }, abstract = {The utility of α-defensin (AD), leukocyte esterase (LE) levels, and metagenomics sequencing as diagnostic tools for prosthetic joint infection (PJI) has been suggested, but there are few studies among the Asian population. This study aimed to evaluate the diagnostic performance of various biomarkers for PJI and the role of the microbiome in the synovial fluid of patients with prostheses. Patients with suspected knee PJI were enrolled, and their blood and synovial fluid were collected. The cases were classified into the PJI and non-PJI groups. Significant differences between the two groups were observed in the levels of AD (4698 µg/L vs. 296 µg/L, p < 0.001) and positivity for LE (62.5% vs. 21.1%, p = 0.01). AD had 94.4% sensitivity and 89.5% specificity for diagnosing PJI, whereas LE had 37.5% sensitivity and 100% specificity. Microbiome taxonomic profiling showed high sensitivity. The number of operational taxonomic units and the richness of the microbiome in the synovial fluid were higher in the non-PJI than in the PJI group. AD has shown encouraging results in the Asian population as a diagnostic biomarker for PJI, and LE can be used as a diagnostic adjunct. The bacterial richness of the synovial fluid is likely associated with infections.}, } @article {pmid37762727, year = {2023}, author = {Kamal, S and Parkash, N and Beattie, W and Christensen, B and Segal, JP}, title = {Are We Ready to Reclassify Crohn's Disease Using Molecular Classification?.}, journal = {Journal of clinical medicine}, volume = {12}, number = {18}, pages = {}, pmid = {37762727}, issn = {2077-0383}, abstract = {Crohn's disease (CD) is a type of inflammatory bowel disease. The number of IBD cases worldwide was estimated to be 4.9 million in 2019. CD exhibits heterogeneity in clinical presentation, anatomical involvement, disease behaviour, clinical course and response to treatment. The classical description of CD involves transmural inflammation with skip lesions anywhere along the entire gastrointestinal tract. The complexity and heterogeneity of Crohn's disease is not currently reflected in the conventional classification system. Though the knowledge of Crohn's pathophysiology remains far from understood, the established complex interplay of the omics-genomics, transcriptomics, proteomics, epigenomics, metagenomics, metabolomics, lipidomics and immunophenomics-provides numerous targets for potential molecular markers of disease. Advancing technology has enabled identification of small molecules within these omics, which can be extrapolated to differentiate types of Crohn's disease. The multi-omic future of Crohn's disease is promising, with potential for advancements in understanding of its pathogenesis and implementation of personalised medicine.}, } @article {pmid37762509, year = {2023}, author = {Zabolotneva, AA and Gaponov, AM and Roumiantsev, SA and Vasiliev, IY and Grigoryeva, TV and Kit, OI and Zlatnik, EY and Maksimov, AY and Goncharova, AS and Novikova, IA and Appolonova, SA and Markin, PA and Shestopalov, AV}, title = {Alkylresorcinols as New Modulators of the Metabolic Activity of the Gut Microbiota.}, journal = {International journal of molecular sciences}, volume = {24}, number = {18}, pages = {}, pmid = {37762509}, issn = {1422-0067}, abstract = {Alkylresorcinols (ARs) are polyphenolic compounds with a wide spectrum of biological activities and are potentially involved in the regulation of host metabolism. The present study aims to establish whether ARs can be produced by the human gut microbiota and to evaluate alterations in content in stool samples as well as metabolic activity of the gut microbiota of C57BL, db/db, and LDLR (-/-) mice according to diet specifications and olivetol (5-n-pentylresorcinol) supplementation to estimate the regulatory potential of ARs. Gas chromatography with mass spectrometric detection was used to quantitatively analyse AR levels in mouse stool samples; faecal microbiota transplantation (FMT) from human donors to germ-free mice was performed to determine whether the intestinal microbiota could produce AR molecules; metagenome sequencing analysis of the mouse gut microbiota followed by reconstruction of its metabolic activity was performed to investigate olivetol's regulatory potential. A significant increase in the amounts of individual members of AR homologues in stool samples was revealed 14 days after FMT. Supplementation of 5-n-Pentylresorcinol to a regular diet influences the amounts of several ARs in the stool of C57BL/6 and LDLR (-/-) but not db/db mice, and caused a significant change in the predicted metabolic activity of the intestinal microbiota of C57BL/6 and LDLR (-/-) but not db/db mice. For the first time, we have shown that several ARs can be produced by the intestinal microbiota. Taking into account the dependence of AR levels in the gut on olivetol supplementation and microbiota metabolic activity, AR can be assumed to be potential quorum-sensing molecules, which also influence gut microbiota composition and host metabolism.}, } @article {pmid37762502, year = {2023}, author = {Ravin, NV and Muntyan, MS and Smolyakov, DD and Rudenko, TS and Beletsky, AV and Mardanov, AV and Grabovich, MY}, title = {Metagenomics Revealed a New Genus 'Candidatus Thiocaldithrix dubininis' gen. nov., sp. nov. and a New Species 'Candidatus Thiothrix putei' sp. nov. in the Family Thiotrichaceae, Some Members of Which Have Traits of Both Na[+]- and H[+]-Motive Energetics.}, journal = {International journal of molecular sciences}, volume = {24}, number = {18}, pages = {}, pmid = {37762502}, issn = {1422-0067}, support = {20-14-00137//Russian Science Foundation/ ; }, mesh = {*Thiothrix/genetics ; Phylogeny ; *Thiotrichaceae/genetics ; Bacteria/genetics ; DNA, Ribosomal/genetics ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; RNA, Ribosomal, 16S/genetics ; Fatty Acids ; Bacterial Typing Techniques ; }, abstract = {Two metagenome-assembled genomes (MAGs), GKL-01 and GKL-02, related to the family Thiotrichaceae have been assembled from the metagenome of bacterial mat obtained from a sulfide-rich thermal spring in the North Caucasus. Based on average amino acid identity (AAI) values and genome-based phylogeny, MAG GKL-01 represented a new genus within the Thiotrichaceae family. The GC content of the GKL-01 DNA (44%) differed significantly from that of other known members of the genus Thiothrix (50.1-55.6%). We proposed to assign GKL-01 to a new species and genus 'Candidatus Thiocaldithrix dubininis' gen. nov., sp. nov. GKL-01. The phylogenetic analysis and estimated distances between MAG GKL-02 and the genomes of the previously described species of the genus Thiothrix allowed assigning GKL-02 to a new species with the proposed name 'Candidatus Thiothrix putei' sp. nov. GKL-02 within the genus Thiothrix. Genome data first revealed the presence of both Na[+]-ATPases and H[+]-ATPases in several Thiothrix species. According to genomic analysis, bacteria GKL-01 and GKL-02 are metabolically versatile facultative aerobes capable of growing either chemolithoautotrophically or chemolithoheterotrophically in the presence of hydrogen sulfide and/or thiosulfate or chemoorganoheterotrophically.}, } @article {pmid37762390, year = {2023}, author = {Schlegel, I and De Goüyon Matignon de Pontourade, CMF and Lincke, JB and Keller, I and Zinkernagel, MS and Zysset-Burri, DC}, title = {The Human Ocular Surface Microbiome and Its Associations with the Tear Proteome in Dry Eye Disease.}, journal = {International journal of molecular sciences}, volume = {24}, number = {18}, pages = {}, pmid = {37762390}, issn = {1422-0067}, support = {CF10000044-EPFL SCR0237812//Fondation Bertarelli/ ; n.a.//OPOS foundation/ ; }, mesh = {Humans ; Proteome ; Eye ; *Dry Eye Syndromes ; Face ; *Microbiota ; }, abstract = {Although dry eye disease (DED) is one of the most common ocular surface diseases worldwide, its pathogenesis is incompletely understood, and treatment options are limited. There is growing evidence that complex interactions between the ocular surface microbiome (OSM) and tear fluid constituents, potentially leading to inflammatory processes, are associated with ocular surface diseases such as DED. In this study, we aimed to find unique compositional and functional features of the OSM associated with human and microbial tear proteins in patients with DED. Applying whole-metagenome shotgun sequencing of forty lid and conjunctival swabs, we identified 229 taxa, with Actinobacteria and Proteobacteria being the most abundant phyla and Propionibacterium acnes the dominating species in the cohort. When DED patients were compared to controls, the species Corynebacterium tuberculostearicum was more abundant in conjunctival samples, whereas the family Propionibacteriaceae was more abundant in lid samples. Functional analysis showed that genes of L-lysine biosynthesis, tetrapyrrole biosynthesis, 5-aminoimidazole ribonucleotide biosynthesis, and the super pathway of L-threonine biosynthesis were enriched in conjunctival samples of controls. The relative abundances of Acinetobacter johnsonii correlated with seven human tear proteins, including mucin-16. The three most abundant microbial tear proteins were the chaperone protein DnaK, the arsenical resistance protein ArsH, and helicase. Compositional and functional features of the OSM and the tear proteome are altered in patients with DED. Ultimately, this may help to design novel interventional therapeutics to target DED.}, } @article {pmid37762139, year = {2023}, author = {Gryaznova, M and Kozarenko, O and Smirnova, Y and Burakova, I and Syromyatnikov, M and Maslov, A and Lebedeva, O}, title = {Cervical and Vaginal Microbiomes in Early Miscarriages and Ongoing Pregnancy with and without Dydrogesterone Usage.}, journal = {International journal of molecular sciences}, volume = {24}, number = {18}, pages = {}, pmid = {37762139}, issn = {1422-0067}, support = {22-24-00802//Russian Science Foundation/ ; }, mesh = {Pregnancy ; Female ; Humans ; *Abortion, Spontaneous ; Dydrogesterone/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Vagina ; *Microbiota/genetics ; }, abstract = {Emerging evidence suggests that the reproductive tract microbiota is a key modulator of local inflammatory and immune pathways throughout pregnancy and may subsequently impact pregnancy outcomes. In this study, our objective was to analyze the cervical and vaginal microbiomes during early pregnancy among three groups: women with healthy ongoing pregnancies, women undergoing dydrogesterone treatment, and those who experienced miscarriages. The experiment involved 51 women at 8-11 weeks of gestation. The microbiome was examined using 16S rRNA sequencing on the Ion Torrent PGM platform. Across all groups, Lactobacillus iners was predominant, suggesting that the vaginal community type CST III is common among the majority of participants. Notably, our data highlighted the significant roles of Gardnerella vaginalis and Mycoplasma girerdii in the pathogenesis of early miscarriage. Conversely, L. iners and Bifidobacterium longum have a protective effect in early pregnancy. Moreover, dydrogesterone intake appeared to influence notable differences between the cervical and vaginal microbiomes. Overall, our study enhanced our understanding of the cervical and vaginal microbiome composition in the eastern European population during early pregnancy.}, } @article {pmid37762102, year = {2023}, author = {Aida, N and Saito, A and Azuma, T}, title = {Current Status of Next-Generation Sequencing in Bone Genetic Diseases.}, journal = {International journal of molecular sciences}, volume = {24}, number = {18}, pages = {}, pmid = {37762102}, issn = {1422-0067}, support = {21H03146//Japan Society for the Promotion of Science/ ; 20K10170//Japan Society for the Promotion of Science/ ; 23K09342//Japan Society for the Promotion of Science/ ; MRCJD//the private university research baranding project from MEXT of Japan/ ; }, mesh = {Humans ; *Bone and Bones ; *Bone Diseases/genetics ; High-Throughput Nucleotide Sequencing ; Osteoblasts ; Osteoclasts ; }, abstract = {The development of next-generation sequencing (NGS) has dramatically increased the speed and volume of genetic analysis. Furthermore, the range of applications of NGS is rapidly expanding to include genome, epigenome (such as DNA methylation), metagenome, and transcriptome analyses (such as RNA sequencing and single-cell RNA sequencing). NGS enables genetic research by offering various sequencing methods as well as combinations of methods. Bone tissue is the most important unit supporting the body and is a reservoir of calcium and phosphate ions, which are important for physical activity. Many genetic diseases affect bone tissues, possibly because metabolic mechanisms in bone tissue are complex. For instance, the presence of specialized immune cells called osteoclasts in the bone tissue, which absorb bone tissue and interact with osteoblasts in complex ways to support normal vital functions. Moreover, the many cell types in bones exhibit cell-specific proteins for their respective activities. Mutations in the genes encoding these proteins cause a variety of genetic disorders. The relationship between age-related bone tissue fragility (also called frailty) and genetic factors has recently attracted attention. Herein, we discuss the use of genomic, epigenomic, transcriptomic, and metagenomic analyses in bone genetic disorders.}, } @article {pmid37762088, year = {2023}, author = {Aitmanaitė, L and Širmonaitis, K and Russo, G}, title = {Microbiomes, Their Function, and Cancer: How Metatranscriptomics Can Close the Knowledge Gap.}, journal = {International journal of molecular sciences}, volume = {24}, number = {18}, pages = {}, pmid = {37762088}, issn = {1422-0067}, mesh = {Humans ; *Neoplasms/genetics ; Metagenomics ; *Microbiota/genetics ; Transcriptome ; }, abstract = {The interaction between the microbial communities in the human body and the onset and progression of cancer has not been investigated until recently. The vast majority of the metagenomics research in this area has concentrated on the composition of microbiomes, attempting to link the overabundance or depletion of certain microorganisms to cancer proliferation, metastatic behaviour, and its resistance to therapies. However, studies elucidating the functional implications of the microbiome activity in cancer patients are still scarce; in particular, there is an overwhelming lack of studies assessing such implications directly, through analysis of the transcriptome of the bacterial community. This review summarises the contributions of metagenomics and metatranscriptomics to the knowledge of the microbial environment associated with several cancers; most importantly, it highlights all the advantages that metatranscriptomics has over metagenomics and suggests how such an approach can be leveraged to advance the knowledge of the cancer bacterial environment.}, } @article {pmid37762071, year = {2023}, author = {Fernandez-Lopez, L and Roda, S and Robles-Martín, A and Muñoz-Tafalla, R and Almendral, D and Ferrer, M and Guallar, V}, title = {Enhancing the Hydrolytic Activity of a Lipase towards Larger Triglycerides through Lid Domain Engineering.}, journal = {International journal of molecular sciences}, volume = {24}, number = {18}, pages = {}, pmid = {37762071}, issn = {1422-0067}, support = {101000327//European Commission (SOCIETAL CHALLENGES - Food security, sustainable agriculture and forestry, marine, maritime and inland water research, and the bioeconomy))/ ; PID2020-112758RB-I00 (M.F.), PDC2021-121534-I00 (M.F.), TED2021-130544B-I00 (M.F.), PID2019-106370RB-I00 (V.G.)//Agencia Estatal de Investigación (AEI) (Digital Object Identifier 10.13039/501100011033)/ ; PDC2021-121534-I00 (M.F.), TED2021-130544B-I00 (M.F.)//European Union ("NextGenerationEU/PRTR")/ ; PRE2020-091825//Ministerio de Ciencia e Innovación/ ; FPU19/00608//Ministerio de Ciencia e Innovación/ ; }, mesh = {*Lipase/genetics ; Hydrolysis ; Esterases ; *Actinomycetales ; Amino Acids ; }, abstract = {Lipases have valuable potential for industrial use, particularly those mostly active against water-insoluble substrates, such as triglycerides composed of long-carbon chain fatty acids. However, in most cases, engineered variants often need to be constructed to achieve optimal performance for such substrates. Protein engineering techniques have been reported as strategies for improving lipase characteristics by introducing specific mutations in the cap domain of esterases or in the lid domain of lipases or through lid domain swapping. Here, we improved the lipase activity of a lipase (WP_075743487.1, or LipMRD) retrieved from the Marine Metagenomics MarRef Database and assigned to the Actinoalloteichus genus. The improvement was achieved through site-directed mutagenesis and by substituting its lid domain (FRGTEITQIKDWLTDA) with that of Rhizopus delemar lipase (previously R. oryzae; UniProt accession number, I1BGQ3) (FRGTNSFRSAITDIVF). The results demonstrated that the redesigned mutants gain activity against bulkier triglycerides, such as glyceryl tridecanoate and tridodecanoate, olive oil, coconut oil, and palm oil. Residue W89 (LipMRD numbering) appears to be key to the increase in lipase activity, an increase that was also achieved with lid swapping. This study reinforces the importance of the lid domains and their amino acid compositions in determining the substrate specificity of lipases, but the generalization of the lid domain swapping between lipases or the introduction of specific mutations in the lid domain to improve lipase activity may require further investigation.}, } @article {pmid37761051, year = {2023}, author = {Yasir, M and Alkhaldy, AA and Soliman, SA and Turkistani, SA and Azhar, EI}, title = {Metagenomic Insights into the Microbiome and Resistance Genes of Traditional Fermented Foods in Arabia.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {18}, pages = {}, pmid = {37761051}, issn = {2304-8158}, support = {IFPRC-014-290-2020//Deputyship for Research & Innovation, Ministry of Education Saudi Arabia/ ; }, abstract = {This study uncovered microbial communities and evaluated the microbiological safety of traditional fermented foods consumed in the Arab region. Samples of dairy and non-dairy fermented foods-mish, jibneh, zabadi, and pickles-were collected from local markets in Saudi Arabia. Using the MiSeq system, samples were sequenced using 16S amplicons and shotgun metagenomics. Alpha and beta diversity indicated inter- and intra-variation in the studied fermented foods' bacterial communities. In the case of mish, the replicates were clustered. Twenty-one genera were found to be significantly different (FDR < 0.05) in abundance in pairwise comparison of fermented foods. Five high-quality, metagenome-assembled genomes (MAGs) of Lactococcus lactis, Lactobacillus helveticus, Pseudoalteromonas nigrifaciens, Streptococcus thermophiles, and Lactobacillus acetotolerans were retrieved from the shotgun sequencing representing the dominant taxa in the studied fermented foods. Additionally, 33 genes that cause antimicrobial resistance (ARGs) against ten different antibiotic classes were detected. Metabolic pathways were abundant in the studied metagenomes, such as amino acid metabolism, carbohydrate metabolism, cofactors, and vitamin biosynthesis. Metagenomic evaluation of Arabian fermented foods, including the identification of probiotics, pathogenic bacteria, and ARGs, illustrates the importance of microbiological analysis in evaluating their health effects.}, } @article {pmid37760793, year = {2023}, author = {Park, SY and Lee, SP and Kim, D and Kim, WJ}, title = {Gut Dysbiosis: A New Avenue for Stroke Prevention and Therapeutics.}, journal = {Biomedicines}, volume = {11}, number = {9}, pages = {}, pmid = {37760793}, issn = {2227-9059}, support = {NRF-2018R1D1A1B07041747//National Research Foundation of Korea/ ; }, abstract = {A stroke is a serious life-threatening condition and a leading cause of death and disability that happens when the blood vessels to part of the brain are blocked or burst. While major advances in the understanding of the ischemic cascade in stroke was made over several decades, limited therapeutic options and high mortality and disability have caused researchers to extend the focus toward peripheral changes beyond brain. The largest proportion of microbes in human body reside in the gut and the interaction between host and microbiota in health and disease is well known. Our study aimed to explore the gut microbiota in patients with stroke with comparison to control group. Fecal samples were obtained from 51 subjects: 25 stroke patients (18 hemorrhagic, 7 ischemic) and 26 healthy control subjects. The variable region V3-V4 of the 16S rRNA gene was sequenced using the Illumina MiSeq platform. PICRUSt2 was used for prediction of metagenomics functions. Our results show taxonomic dysbiosis in stroke patients in parallel with functional dysbiosis. Here, we show that stroke patients have (1) increased Parabacteroides and Escherichia_Shigella, but decreased Prevotella and Fecalibacterium; (2) higher transposase and peptide/nickel transport system substrate-binding protein, but lower RNA polymerase sigma-70 factor and methyl-accepting chemotaxis protein, which are suggestive of malnutrition. Nutrients are essential regulators of both host and microbial physiology and function as key coordinators of host-microbe interactions. Manipulation of nutrition is expected to alleviate gut dysbiosis and prognosis and improve disability and mortality in the management of stroke.}, } @article {pmid37759740, year = {2023}, author = {Witkowska, AM and Salem, JE}, title = {Pharmacological and Nutritional Modulation of Metabolome and Metagenome in Cardiometabolic Disorders.}, journal = {Biomolecules}, volume = {13}, number = {9}, pages = {}, pmid = {37759740}, issn = {2218-273X}, abstract = {Cardiometabolic disorders are major causes of morbidity and mortality worldwide. A growing body of research indicates that the gut microbiota, whether it interacts favorably or not, plays an important role in host metabolism. Elucidating metabolic pathways may be crucial in preventing and treating cardiometabolic diseases, and omics methods are key to studying the interaction between the fecal microbiota and host metabolism. This review summarizes available studies that combine metabolomic and metagenomic approaches to describe the effects of drugs, diet, nutrients, and specific foods on cardiometabolic health and to identify potential targets for future research.}, } @article {pmid37759653, year = {2023}, author = {Ford, T and McAdams, ZL and Townsend, KS and Martin, LM and Johnson, PJ and Ericsson, AC}, title = {Effect of Sugar Beet Pulp on the Composition and Predicted Function of Equine Fecal Microbiota.}, journal = {Biology}, volume = {12}, number = {9}, pages = {}, pmid = {37759653}, issn = {2079-7737}, support = {T32 GM008396/GM/NIGMS NIH HHS/United States ; }, abstract = {The purpose of this study is to determine the effect of the partial replacement of dietary hay with sugar beet pulp (SBP) on the composition and predicted function of the fecal microbiota of healthy adult horses. Fecal samples were collected daily for 12 days from six adult horses after removal from pasture, including a five-day acclimation period, and a seven-day period following the introduction of SBP into their diet, and compared to six untreated horses over a comparable period. Fecal DNA was subjected to 16S rRNA amplicon sequencing and a longitudinal analysis was performed comparing the composition and predicted function. While no significant treatment-associated changes in the richness, alpha diversity, or beta diversity were detected, random forest regression identified several high-importance taxonomic features associated with change over time in horses receiving SBP. A similar analysis of the predicted functional pathways identified several high-importance pathways, including those involved in the production of L-methionine and butyrate. These data suggest that feeding SBP to healthy adult horses acutely increases the relative abundance of several Gram-positive taxa, including Cellulosilyticum sp., Moryella sp., and Weissella sp., and mitigates the predicted functional changes associated with removal from pasture. Large-scale studies are needed to assess the protective effect of SBP on the incidence of the gastrointestinal conditions of horses.}, } @article {pmid37759605, year = {2023}, author = {Lin, WH and Tsai, TS}, title = {Comparisons of the Oral Microbiota from Seven Species of Wild Venomous Snakes in Taiwan Using the High-Throughput Amplicon Sequencing of the Full-Length 16S rRNA Gene.}, journal = {Biology}, volume = {12}, number = {9}, pages = {}, pmid = {37759605}, issn = {2079-7737}, support = {110-2621-B-020-001//Ministry of Science and Technology, Taiwan/ ; }, abstract = {A venomous snake's oral cavity may harbor pathogenic microorganisms that cause secondary infection at the wound site after being bitten. We collected oral samples from 37 individuals belonging to seven species of wild venomous snakes in Taiwan, including Naja atra (Na), Bungarus multicinctus (Bm), Protobothrops mucrosquamatus (Pm), Trimeresurus stejnegeri (Ts), Daboia siamensis (Ds), Deinagkistrodon acutus (Da), and alpine Trimeresurus gracilis (Tg). Bacterial species were identified using full-length 16S rRNA amplicon sequencing analysis, and this is the first study using this technique to investigate the oral microbiota of multiple Taiwanese snake species. Up to 1064 bacterial species were identified from the snake's oral cavities, with 24 pathogenic and 24 non-pathogenic species among the most abundant ones. The most abundant oral bacterial species detected in our study were different from those found in previous studies, which varied by snake species, collection sites, sampling tissues, culture dependence, and analysis methods. Multivariate analysis revealed that the oral bacterial species compositions in Na, Bm, and Pm each were significantly different from the other species, whereas those among Ts, Ds, Da, and Tg showed fewer differences. Herein, we reveal the microbial diversity in multiple species of wild snakes and provide potential therapeutic implications regarding empiric antibiotic selection for wildlife medicine and snakebite management.}, } @article {pmid37759232, year = {2023}, author = {Li, C and Lv, C and Yu, M and Zhang, Y and Ling, L and Yue, W}, title = {A case report of a brain abscess due to prevotella oris and a review of the literature.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {633}, pmid = {37759232}, issn = {1471-2334}, mesh = {Male ; Humans ; Middle Aged ; *Brain Abscess/diagnosis/drug therapy ; Prevotella/genetics ; Brain/diagnostic imaging ; Combined Modality Therapy ; }, abstract = {BACKGROUND: Brain abscesses caused by Prevotella oris are rarely reported. Here, we described a case of a brain infection caused by Prevotella oris that was detected by metagenomic next-generation sequencing (mNGS).

CASE PRESENTATION: A 63-year-old man with no medical history reported headache in the right frontotemporal region, fever, and intermittent diplopia. Magnetic resonance imaging (MRI) revealed abnormal signals and enhancement changes in the superior sellar region. mNGS testing showed that cerebrospinal fluid collected from the spine was positive for Prevotella oris. After receiving a combined treatment of antibiotic therapy, the patient recovered well.

CONCLUSION: We reviewed the relevant literature and summarized the characteristics and prognosis of this type of bacterial infection to provide ideas for clinicians to diagnose and treat this disease.}, } @article {pmid37757827, year = {2023}, author = {Blaustein, RA and Shen, Z and Kashaf, SS and Lee-Lin, S and Conlan, S and , and Bosticardo, M and Delmonte, OM and Holmes, CJ and Taylor, ME and Banania, G and Nagao, K and Dimitrova, D and Kanakry, JA and Su, H and Holland, SM and Bergerson, JRE and Freeman, AF and Notarangelo, LD and Kong, HH and Segre, JA}, title = {Expanded microbiome niches of RAG-deficient patients.}, journal = {Cell reports. Medicine}, volume = {4}, number = {10}, pages = {101205}, pmid = {37757827}, issn = {2666-3791}, mesh = {Humans ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Skin ; Metagenome ; }, abstract = {The complex interplay between microbiota and immunity is important to human health. To explore how altered adaptive immunity influences the microbiome, we characterize skin, nares, and gut microbiota of patients with recombination-activating gene (RAG) deficiency-a rare genetically defined inborn error of immunity (IEI) that results in a broad spectrum of clinical phenotypes. Integrating de novo assembly of metagenomes from RAG-deficient patients with reference genome catalogs provides an expansive multi-kingdom view of microbial diversity. RAG-deficient patient microbiomes exhibit inter-individual variation, including expansion of opportunistic pathogens (e.g., Corynebacterium bovis, Haemophilus influenzae), and a relative loss of body site specificity. We identify 35 and 27 bacterial species derived from skin/nares and gut microbiomes, respectively, which are distinct to RAG-deficient patients compared to healthy individuals. Underscoring IEI patients as potential reservoirs for viral persistence and evolution, we further characterize the colonization of eukaryotic RNA viruses (e.g., Coronavirus 229E, Norovirus GII) in this patient population.}, } @article {pmid37757683, year = {2023}, author = {Wang, Z and Tang, K and Struik, PC and Ashraf, MN and Zhang, T and Zhao, Y and Wu, R and Jin, K and Li, Y}, title = {Alteration of microbial carbon and nitrogen metabolism within the soil metagenome with grazing intensity at semiarid steppe.}, journal = {Journal of environmental management}, volume = {347}, number = {}, pages = {119078}, doi = {10.1016/j.jenvman.2023.119078}, pmid = {37757683}, issn = {1095-8630}, mesh = {Animals ; Sheep ; *Soil/chemistry ; *Grassland ; Metagenome ; Carbon/analysis ; Nitrogen/analysis ; Soil Microbiology ; }, abstract = {Grazing causes changes in microbiome metabolic pathways affecting plant growth and soil physicochemical properties. However, how grazing intensity affects microbial processes is poorly understood. In semiarid steppe grassland in northern China, shotgun metagenome sequencing was used to investigate variations in soil carbon (C) and nitrogen (N) cycling-related genes after six years of the following grazing intensities: G0, control, no grazing; G1, 170 sheep days ha[-1] year[-1]; G2, 340 sheep days ha[-1] year[-1]; and G3, 510 sheep days ha[-1] year[-1]. Taxa and functions of the soil microbiome associated with the C cycle decreased with increasing grazing intensity. Abundances of genes involved in C fixation and organic matter decomposition were altered in grazed sites, which could effects on vegetation decomposition and soil dissolved organic carbon (DOC) content. Compared with the control, the abundances of nitrification genes were higher in G1, but the abundances of N reduction and denitrification genes were lower, suggesting that light grazing promoted nitrification, inhibited denitrification, and increased soil NO3[-] content. Q-PCR further revealed that the copies of genes responsible for carbon fixation (cbbL) and denitrification (norB) decreased with increasing grazing intensity. The highest copy numbers of the nitrification genes AOA and AOB were in G1, whereas copy numbers of the denitrification gene nirK were the lowest. A multivariate regression tree indicated that changes in C fixation genes were linked to changes in soil DOC content, whereas soil NO3[-] content was linked with nitrification and denitrification under grazing. Thus, genes associated with C fixation and the N cycle affected how C fixation and N storage influenced soil physicochemical properties under grazing. The findings indicate that grazing intensity affected C and N metabolism. Proper grassland management regimes (e.g., G1) are beneficial to the balances between ecological protection of grasslands and plant production in the semiarid steppe.}, } @article {pmid37756379, year = {2023}, author = {Tse, LV and Hou, YJ and McFadden, E and Lee, RE and Scobey, TD and Leist, SR and Martinez, DR and Meganck, RM and Schäfer, A and Yount, BL and Mascenik, T and Powers, JM and Randell, SH and Zhang, Y and Wang, L and Mascola, J and McLellan, JS and Baric, RS}, title = {A MERS-CoV antibody neutralizes a pre-emerging group 2c bat coronavirus.}, journal = {Science translational medicine}, volume = {15}, number = {715}, pages = {eadg5567}, doi = {10.1126/scitranslmed.adg5567}, pmid = {37756379}, issn = {1946-6242}, mesh = {Humans ; Animals ; Mice ; *Middle East Respiratory Syndrome Coronavirus ; Dipeptidyl Peptidase 4/genetics/metabolism ; *Chiroptera ; Cryoelectron Microscopy ; *Coronavirus Infections ; Antibodies, Monoclonal/metabolism ; }, abstract = {The repeated emergence of zoonotic human betacoronaviruses (β-CoVs) dictates the need for broad therapeutics and conserved epitope targets for countermeasure design. Middle East respiratory syndrome (MERS)-related coronaviruses (CoVs) remain a pressing concern for global health preparedness. Using metagenomic sequence data and CoV reverse genetics, we recovered a full-length wild-type MERS-like BtCoV/li/GD/2014-422 (BtCoV-422) recombinant virus, as well as two reporter viruses, and evaluated their human emergence potential and susceptibility to currently available countermeasures. Similar to MERS-CoV, BtCoV-422 efficiently used human and other mammalian dipeptidyl peptidase protein 4 (DPP4) proteins as entry receptors and an alternative DPP4-independent infection route in the presence of exogenous proteases. BtCoV-422 also replicated efficiently in primary human airway, lung endothelial, and fibroblast cells, although less efficiently than MERS-CoV. However, BtCoV-422 shows minor signs of infection in 288/330 human DPP4 transgenic mice. Several broad CoV antivirals, including nucleoside analogs and 3C-like/M[pro] protease inhibitors, demonstrated potent inhibition against BtCoV-422 in vitro. Serum from mice that received a MERS-CoV mRNA vaccine showed reduced neutralizing activity against BtCoV-422. Although most MERS-CoV-neutralizing monoclonal antibodies (mAbs) had limited activity, one anti-MERS receptor binding domain mAb, JC57-11, neutralized BtCoV-422 potently. A cryo-electron microscopy structure of JC57-11 in complex with BtCoV-422 spike protein revealed the mechanism of cross-neutralization involving occlusion of the DPP4 binding site, highlighting its potential as a broadly neutralizing mAb for group 2c CoVs that use DPP4 as a receptor. These studies provide critical insights into MERS-like CoVs and provide candidates for countermeasure development.}, } @article {pmid37756074, year = {2023}, author = {Kilburn-Kappeler, LR and Doerksen, T and Lu, A and Palinski, RM and Lu, N and Aldrich, CG}, title = {Comparison of the Effect of Corn-fermented Protein and Traditional Ingredients on the Fecal Microbiota of Dogs.}, journal = {Veterinary sciences}, volume = {10}, number = {9}, pages = {}, pmid = {37756074}, issn = {2306-7381}, abstract = {Corn-fermented protein (CFP), a co-product from the ethanol industry, is produced using post-fermentation technology to split the protein and yeast from fiber prior to drying. The objective of this study was to determine the effect of CFP compared to traditional ingredients on the fecal microbiota of dogs. The four experimental diets included a control with no yeast and diets containing either 3.5% brewer's dried yeast, 2.5% brewer's dried yeast plus 17.5% distiller's dried grains with solubles, or 17.5% CFP. The experimental diets were fed to adult dogs (n = 12) in a 4 × 4 replicated Latin square design. Fresh fecal samples (n = 48) were analyzed by 16S metagenomic sequencing. Raw sequences were processed through mothur. Community diversity was evaluated in R. Relative abundance data were analyzed within the 50 most abundant operational taxonomic units using a mixed model of SAS. Alpha and beta diversity were similar for all treatments. Predominant phyla among all samples were Firmicutes (73%), Bacteroidetes (15%), Fusobacteria (8%), and Actinobacteria (4%). There were no quantifiable (p > 0.05) shifts in the predominant phyla among the treatments. However, nine genera resulted in differences in relative abundance among the treatments. These data indicate that compared to traditional ingredients, CFP did not alter the overall diversity of the fecal microbiota of healthy adult dogs over 14 days.}, } @article {pmid37755512, year = {2023}, author = {Peters, MK and Astafyeva, Y and Han, Y and Macdonald, JFH and Indenbirken, D and Nakel, J and Virdi, S and Westhoff, G and Streit, WR and Krohn, I}, title = {Novel marine metalloprotease-new approaches for inhibition of biofilm formation of Stenotrophomonas maltophilia.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {23}, pages = {7119-7134}, pmid = {37755512}, issn = {1432-0614}, support = {SuReMetS (FKZ 031B0944A)//Bundesministerium für Bildung und Forschung/ ; AquaHealth (FKZ 031B0945C)//Bundesministerium für Bildung und Forschung/ ; MarBioTech (FKZ 031A565)//Bundesministerium für Bildung und Forschung/ ; }, mesh = {Humans ; *Stenotrophomonas maltophilia/genetics ; Proteome ; Anti-Bacterial Agents/pharmacology ; Biofilms ; Metalloproteases/genetics/pharmacology ; *Gram-Negative Bacterial Infections ; }, abstract = {Many marine organisms produce bioactive molecules with unique characteristics to survive in their ecological niches. These enzymes can be applied in biotechnological processes and in the medical sector to replace aggressive chemicals that are harmful to the environment. Especially in the human health sector, there is a need for new approaches to fight against pathogens like Stenotrophomonas maltophilia which forms thick biofilms on artificial joints or catheters and causes serious diseases. Our approach was to use enrichment cultures of five marine resources that underwent sequence-based screenings in combination with deep omics analyses in order to identify enzymes with antibiofilm characteristics. Especially the supernatant of the enrichment culture of a stony coral caused a 40% reduction of S. maltophilia biofilm formation. In the presence of the supernatant, our transcriptome dataset showed a clear stress response (upregulation of transcripts for metal resistance, antitoxins, transporter, and iron acquisition) to the treatment. Further investigation of the enrichment culture metagenome and proteome indicated a series of potential antimicrobial enzymes. We found an impressive group of metalloproteases in the proteome of the supernatant that is responsible for the detected anti-biofilm effect against S. maltophilia. KEY POINTS: • Omics-based discovery of novel marine-derived antimicrobials for human health management by inhibition of S. maltophilia • Up to 40% reduction of S. maltophilia biofilm formation by the use of marine-derived samples • Metalloprotease candidates prevent biofilm formation of S. maltophilia K279a by up to 20.}, } @article {pmid37755279, year = {2023}, author = {Wu, CY and Huang, CK and Hong, WS and Liu, YH and Shih, MC and Lin, JC}, title = {Influence of Symbiotic Fermentation Broth on Regulating Metabolism with Gut Microbiota and Metabolite Profiles Is Estimated Using a Third-Generation Sequencing Platform.}, journal = {Metabolites}, volume = {13}, number = {9}, pages = {}, pmid = {37755279}, issn = {2218-1989}, support = {110-6603-005-400//Ministry of Education, Taiwan/ ; A-111-008//Sagittarius Life Science Corporations, Taiwan/ ; }, abstract = {Overnutrition with a high-fat or high-sugar diet is widely considered to be the risk factor for various metabolic, chronic, or malignant diseases that are accompanied by alterations in gut microbiota, metabolites, and downstream pathways. In this study, we investigated supplementation with soybean fermentation broth containing saponin (SFBS, also called SAPOZYME) in male C57BL/6 mice fed a high-fat-fructose diet or normal chaw. In addition to the lessening of weight gain, the influence of SFBS on reducing hyperlipidemia and hyperglycemia associated with a high-fat-fructose diet was estimated using the results of related biological tests. The results of gut microbial profiling indicated that the high-fat-fructose diet mediated increases in opportunistic pathogens. In contrast, SFBS supplementation reprogrammed the high-fat-fructose diet-related microbial community with a relatively high abundance of potential probiotics, including Akkermansia and Lactobacillus genera. The metagenomic functions of differential microbial composition in a mouse model and enrolled participants were assessed using the PICRUSt2 algorithm coupled with the MetaCyc and the KEGG Orthology databases. SFBS supplementation exerted a similar influence on an increase in the level of 4-aminobutanoate (also called GABA) through the L-glutamate degradation pathway in the mouse model and the enrolled healthy population. These results suggest the beneficial influence of SFBS supplementation on metabolic disorders associated with a high-fat-fructose diet, and SFBS may function as a nutritional supplement for people with diverse requirements.}, } @article {pmid37755060, year = {2023}, author = {Mihai, RA and Melo Heras, EJ and Landazuri Abarca, PA and Catana, RD}, title = {The Fungal, Nutritional, and Metabolomic Diagnostics of the Oil Palm Elaeis guineensis Affected by Bud Rot Disease in Esmeraldas, Ecuador.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {9}, pages = {}, pmid = {37755060}, issn = {2309-608X}, abstract = {The oil palm Elaeis guineensis represents one of the most important crops in Ecuador. Considering that bud rot disease is deadly in Ecuador, more attention has been given to identifying possible causes for palm debility from this disease. We studied the involvement of fungi and nutrients in triggering bud rot disease in E. guineensis. Special emphasis was given to the molecules synthesized by the plant to protect against this devastating disease. Techniques like Diagnosis and Recommendation Integrated System (DRIS) and metagenomic analysis were used to understand the possible implications of biotic and abiotic factors in the development of bud rot disease in oil palm in Ecuador. Liquid chromatography-mass spectrometry (LC-MS) analysis was used to identify the phenolic protection barrier of the palm facing the disease. Our results indicate that fungi from Ascomyceta phylum were found in the tested samples. The species directly involved are different in soil compared with plants. The results indicate a deficiency of chemical elements, such as Ca, Mn, Mg, and Fe, which are responsible for palm debility from bud rot disease. More than 30 compounds with protective roles were identified in the leaves of symptomatic plants from the first stage of the infection.}, } @article {pmid37754998, year = {2023}, author = {Pagani, DM and Ventura, SPR and Vu, D and Mendes-Pereira, T and Ribeiro Tomé, LM and Carvalho, DS and Costa-Rezende, DH and Kato, RB and García, GJY and Geml, J and Robert, V and They, NH and Brenig, B and Azevedo, V and Scroferneker, ML and Valente, P and Góes-Neto, A}, title = {Unveiling Fungal Community Structure along Different Levels of Anthropic Disturbance in a South American Subtropical Lagoon.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {9}, pages = {}, pmid = {37754998}, issn = {2309-608X}, support = {NA//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; NA//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; APQ-01411-22//Fundação de Amparo à Pesquisa do Estado de Minas Gerais (FAPEMIG)/ ; 308880/2022-6//CNPq/ ; }, abstract = {Studies of fungal communities through amplicon metagenomics in aquatic environments, particularly in freshwater ecosystems, are still relatively recent. Unfortunately, many of these water bodies are facing growing threats from human expansion, such as effluent discharge from various human activities. As a result, these effluents have the potential to significantly alter the characteristics of water bodies and, subsequently, impact the diversity of their resident microorganisms. In this context, our objective was to investigate whether the fungal community structure varies according to the presence of different anthropic disturbances. We expect (i) the diversity of fungi will be greater and (ii) more specific unique operational taxonomic units (OTUs) related to each ecotonal system will be found compared to other sites of a lagoon. The study was conducted in the Tramandaí Lagoon (subtropical southern Brazil) at four distinct sampling points (estuary, middle of the lagoon, crop field area, and near a residential area where the Tramandaí River flows into the lagoon). As expected, the estuary and residential zones, which are ecotones, exhibited greater fungal diversity and more specific OTUs compared to the middle of the lagoon and crop field area. Moreover, a substantial proportion of fungal taxa could not be identified at the genus level, with many only classified at the phylum level, indicating potential new lineages. These findings underscore our limited understanding of the subtropical freshwater mycobiota.}, } @article {pmid37754709, year = {2023}, author = {Chen, S and Zhou, A and Xu, Y}, title = {Symbiotic Bacteria Regulating Insect-Insect/Fungus/Virus Mutualism.}, journal = {Insects}, volume = {14}, number = {9}, pages = {}, pmid = {37754709}, issn = {2075-4450}, support = {32261160374//National Natural Science Foundation of China/ ; 2021N007//Special Project for Sustainable Development Science and Technology of Shenzhen/ ; }, abstract = {Bacteria associated with insects potentially provide many beneficial services and have been well documented. Mutualism that relates to insects is widespread in ecosystems. However, the interrelation between "symbiotic bacteria" and "mutualism" has rarely been studied. We introduce three systems of mutualism that relate to insects (ants and honeydew-producing Hemiptera, fungus-growing insects and fungi, and plant persistent viruses and vector insects) and review the species of symbiotic bacteria in host insects, as well as their functions in host insects and the mechanisms underlying mutualism regulation. A deeper understanding of the molecular mechanisms and role of symbiotic bacteria, based on metagenomics, transcriptomics, proteomics, metabolomics, and microbiology, will be required for describing the entire interaction network.}, } @article {pmid37754684, year = {2023}, author = {Zhang, Y and Kitazumi, A and Liao, YT and de Los Reyes, BG and Wu, VCH}, title = {Metagenomic investigation reveals bacteriophage-mediated horizontal transfer of antibiotic resistance genes in microbial communities of an organic agricultural ecosystem.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0022623}, pmid = {37754684}, issn = {2165-0497}, abstract = {Agricultural microbiomes are major reservoirs of antibiotic resistance genes (ARGs), posing continuous risks to human health. To understand the role of bacteriophages as vehicles for the horizontal transfer of ARGs in the agricultural microbiome, we investigated the diversity of bacterial and viral microbiota from fecal and environmental samples on an organic farm. The profiles of the microbiome indicated the highest abundance of Bacteroidetes, Firmicutes, and Proteobacteria phyla in animal feces, with varying Actinobacteria and Spirochaetes abundance across farm animals. The most predominant composition in environmental samples was the phylum Proteobacteria. Compared to the microbiome profiles, the trends in virome indicated much broader diversity with more specific signatures between the fecal and environmental samples. Overall, viruses belonging to the order Caudovirales were the most prevalent across the agricultural samples. Additionally, the similarities within and between fecal and environmental components of the agricultural environment based on ARG-associated bacteria alone were much lower than those of total microbiome composition. However, there were significant similarities in the profiles of ARG-associated viruses across the fecal and environmental components. Moreover, the predictive models of phage-bacterial interactions on bipartite ARG transfer networks indicated that phages belonging to the order Caudovirales, particularly in the Siphoviridae family, contained diverse ARG types in different samples. Their interaction with various bacterial hosts further implied the important role of bacteriophages in ARG transmission across bacterial populations. Our findings provided a novel insight into the potential mechanisms of phage-mediated ARG transmission and their correlation with resistome evolution in natural agricultural environments. IMPORTANCE Antibiotic resistance has become a serious health concern worldwide. The potential impact of viruses, bacteriophages in particular, on spreading antibiotic resistance genes is still controversial due to the complexity of bacteriophage-bacterial interactions within diverse environments. In this study, we determined the microbiome profiles and the potential antibiotic resistance gene (ARG) transfer between bacterial and viral populations in different agricultural samples using a high-resolution analysis of the metagenomes. The results of this study provide compelling genetic evidence for ARG transfer through bacteriophage-bacteria interactions, revealing the inherent risks associated with bacteriophage-mediated ARG transfer across the agricultural microbiome.}, } @article {pmid37754563, year = {2023}, author = {Zhang, A and de Ángel Solá, D and Acevedo Flores, M and Cao, L and Wang, L and Kim, JG and Tarr, PI and Warner, BB and Rosario Matos, N and Wang, L}, title = {Infants exposed in utero to Hurricane Maria have gut microbiomes with reduced diversity and altered metabolic capacity.}, journal = {mSphere}, volume = {8}, number = {5}, pages = {e0013423}, pmid = {37754563}, issn = {2379-5042}, support = {1R21AI139649-01A1/AI/NIAID NIH HHS/United States ; UL1TR002345/TR/NCATS NIH HHS/United States ; }, mesh = {Pregnancy ; Female ; Humans ; Infant ; *Gastrointestinal Microbiome ; *Cyclonic Storms ; Cohort Studies ; Feces/microbiology ; Breast Feeding ; }, abstract = {The gut microbiome is a potentially important mechanism that links prenatal disaster exposures with increased disease risks. However, whether prenatal disaster exposures are associated with alterations in the infant's gut microbiome remains unknown. We established a birth cohort study named Hurricane as the Origin of Later Alterations in Microbiome (HOLA) after Hurricane Maria struck Puerto Rico in 2017. We enrolled vaginally born Latino term infants aged 2 to 6 months, including n = 29 infants who were exposed in utero to Hurricane Maria in Puerto Rico and n = 34 infants who were conceived at least 5 months after the hurricane as controls. Shotgun metagenomic sequencing was performed on infant stool swabs. Infants exposed in utero to Hurricane Maria had a reduced diversity in their gut microbiome compared to the control infants, which was mainly seen in the exclusively formula-fed group (P = 0.02). Four bacterial species, including Bacteroides vulgatus, Clostridium innocuum, Bifidobacterium pseudocatenulatum, and Clostridium neonatale, were depleted in the exposure group compared to the control group. Compositional differences in the microbial community and metabolic genes between the exposure and control groups were significant, which were driven by the formula feeding group (P = 0.02 for the microbial community and P = 0.008 for the metabolic genes). Metabolic modules involved in carbohydrate metabolism were reduced in the exposure group. Prenatal maternal exposure to Hurricane Maria was associated with a reduced gut commensal and an altered microbial composition and metabolic potential in the offspring's gut. Breastfeeding can adjust the composition of the gut microbiomes of exposed infants. IMPORTANCE Climate change is a serious issue that is affecting human health. With more frequent and intense weather disasters due to climate change, there is an urgent need to evaluate and understand the impacts of prenatal disaster exposures on the offspring. The prenatal stage is a particularly vulnerable stage for disease origination. However, the impact of prenatal weather disaster exposures on the offspring's gut microbiome has not been evaluated. Our HOLA study starts to fill this knowledge gap and provides novel insights into the microbiome as a mechanism that links prenatal disaster exposures with elevated disease risks. Our major finding that reduced microbial diversity and altered metabolic capacity are associated with prenatal hurricane exposures warrants further studies to evaluate the impact of weather disasters on the unborn.}, } @article {pmid37754561, year = {2023}, author = {Liu, WW and Pan, P and Zhou, NY}, title = {The presence of benzene ring activating CoA ligases for aromatics degradation in the ANaerobic MEthanotrophic (ANME) archaea.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0176623}, pmid = {37754561}, issn = {2165-0497}, abstract = {Petroleum-source and black carbon-source aromatic compounds are present in the cold seep environments, where ANaerobic MEthanotrophic (ANME) archaea as the dominant microbial community mediates the anaerobic oxidation of methane to produce inorganic and organic carbon. Here, by predicting the aromatics catabolic pathways in ANME metagenome-assembled genomes, we provide genomic and biochemical evidences that ANME have the potential of metabolizing aromatics via the strategy of CoA activation of the benzene ring using phenylacetic acid and benzoate as the substrates. Two ring-activating enzymes phenylacetate-CoA ligase (PaaKANME) and benzoate-CoA ligase (BadAANME) are able to convert phenylacetate to phenylacetyl-CoA and benzoate to benzoyl-CoA in vitro, respectively. They are mesophilic, alkali resistance, and with broad substrate spectra showing different affinity with various substrates. An exploration of the relative gene abundance in ANME genomes and cold seep environments indicates that about 50% of ANME genomes contain PCL genes, and various bacteria and archaea contain PCL and BCL genes. The results provide evidences for the capability of heterotrophic metabolism of aromatic compounds by ANME. This has not only enhanced our understanding of the nutrient range of ANME but also helped to explore the additional ecological and biogeochemical significance of this ubiquitous sedimentary archaea in the carbon flow in the cold seep environments. IMPORTANCE ANaerobic MEthanotrophic (ANME) archaea is the dominant microbial community mediating the anaerobic oxidation of methane in the cold seep environments, where aromatic compounds are present. Then it is hypothesized that ANME may be involved in the metabolism of aromatics. Here, we provide genomic and biochemical evidences for the heterotrophic metabolism of aromatic compounds by ANME, enhancing our understanding of their nutrient range and also shedding light on the ecological and biogeochemical significance of these ubiquitous sedimentary archaea in carbon flow within cold seep environments. Overall, this study offers valuable insights into the metabolic capabilities of ANME and their potential contributions to the global carbon cycle.}, } @article {pmid37754261, year = {2023}, author = {Mathlouthi, NEH and Oumarou Hama, H and Belguith, I and Charfi, S and Boudawara, T and Lagier, JC and Ammar Keskes, L and Grine, G and Gdoura, R}, title = {Colorectal Cancer Archaeome: A Metagenomic Exploration, Tunisia.}, journal = {Current issues in molecular biology}, volume = {45}, number = {9}, pages = {7572-7581}, pmid = {37754261}, issn = {1467-3045}, support = {_952583//Twinning European project MICAfrica/ ; }, abstract = {Colorectal cancer (CRC) is a serious public health problem known to have a multifactorial etiology. The association between gut microbiota and CRC has been widely studied; however, the link between archaea and CRC has not been sufficiently studied. To investigate the involvement of archaea in colorectal carcinogenesis, we performed a metagenomic analysis of 68 formalin-embedded paraffin fixed tissues from tumoral (n = 33) and healthy mucosa (n = 35) collected from 35 CRC Tunisian patients. We used two DNA extraction methods: Generead DNA FFPE kit (Qiagen, Germantown, MD, USA) and Chelex. We then sequenced the samples using Illumina Miseq. Interestingly, DNA extraction exclusively using Chelex generated enough DNA for sequencing of all samples. After data filtering and processing, we reported the presence of archaeal sequences, which represented 0.33% of all the reads generated. In terms of abundance, we highlighted a depletion in methanogens and an enrichment in Halobacteria in the tumor tissues, while the correlation analysis revealed a significant association between the Halobacteria and the tumor mucosa (p < 0.05). We reported a strong correlation between Natrialba magadii, Sulfolobus acidocaldarius, and tumor tissues, and a weak correlation between Methanococcus voltae and healthy adjacent mucosa. Here, we demonstrated the feasibility of archaeome analysis from formol fixed paraffin-embedded (FFPE) tissues using simple protocols ranging from sampling to data analysis, and reported a significant association between Halobacteria and tumor tissues in Tunisian patients with CRC. The importance of our study is that it represents the first metagenomic analysis of Tunisian CRC patients' gut microbiome, which consists of sequencing DNA extracted from paired tumor-adjacent FFPE tissues collected from CRC patients. The detection of archaeal sequences in our samples confirms the feasibility of carrying out an archaeome analysis from FFPE tissues using a simple DNA extraction protocol. Our analysis revealed the enrichment of Halobacteria, especially Natrialba magadii, in tumor mucosa compared to the normal mucosa in CRC Tunisian patients. Other species were also associated with CRC, including Sulfolobus acidocaldarius and Methanococcus voltae, which is a methanogenic archaea; both species were found to be correlated with adjacent healthy tissues.}, } @article {pmid37754236, year = {2023}, author = {Shibata, M and Ozato, N and Tsuda, H and Mori, K and Kinoshita, K and Katashima, M and Katsuragi, Y and Nakaji, S and Maeda, H}, title = {Mouse Model of Anti-Obesity Effects of Blautia hansenii on Diet-Induced Obesity.}, journal = {Current issues in molecular biology}, volume = {45}, number = {9}, pages = {7147-7160}, pmid = {37754236}, issn = {1467-3045}, support = {he Center of　Innovation Program (JPMJCE1302)//Japan Science and Technology Agency/ ; 07010-3216001-3310199004//Kao Corp. (Tokyo, Japan)/ ; }, abstract = {Reportedly, a relationship exists between intestinal microflora and obesity-related lifestyle diseases. Blautia spp. a major intestinal microbiota, accounts for 3-11% of human intestinal microflora. Epidemiological reports have described that people with more visceral fat have less Blautia hansenii in their intestinal tract irrespective of age or gender. However, the effect of oral administration of heat-sterilized Blautia hansenii on obesity has not been clarified. Therefore, the aim of this study was to evaluate the effects of dietary Blautia hansenii administration on obesity in high-fat-diet-induced obesity in a mouse model. Heat-sterilized cells of Blautia hansenii were used. C57BL/6J mice (normal mice, n = 7) were fed with each experimental diet for nine weeks. Diets for experimentation were: normal-fat (NF) diets, high-fat (HF) diets, and high-fat + Blautia hansenii (HF + Blautia) diets. The HF + Blautia group was administered about 1 × 10[9] (CFU/mouse/day) of Blautia hansenii. During the periods of experimentation, body weight, food intake, water consumption, and fecal weight were recorded, and glucose tolerance tests were performed. Subsequently, the white adipose tissue (WAT) weight and serum components were measured. Short-chain fatty acid contents in the feces and cecum were analyzed. Furthermore, changes in the intestinal microflora were analyzed using meta-genomics analysis. Results showed that the total weight of WAT in the HF + Blautia group was significantly lower (13.2%) than that of the HF group. Moreover, the HF + Blautia group exhibited better glucose tolerance than the HF group. Productivity of short-chain fatty acids in the intestinal tract was at a significantly (p < 0.05) low level in the HF group; on the other hand, it recovered in the HF + Blautia group. Furthermore, there was a higher ratio of Blautia (p < 0.05) in the intestinal tracts of the HF + Blautia group than in the HF group. These results suggest that Blautia hansenii administration suppresses obesity induced by a high-fat diet.}, } @article {pmid37754223, year = {2023}, author = {Ferreira, NE and da Costa, AC and Kallas, EG and Silveira, CGT and de Oliveira, ACS and Honorato, L and Paião, HGO and Lima, SH and de M Vasconcelos, D and Côrtes, MF and Costa, SF and Mendoza, TRT and Gomes, HR and Witkin, SS and Mendes-Correa, MC}, title = {Encephalopathy Caused by Human Parvovirus B19 Genotype 1 Associated with Haemophilus influenzae Meningitis in a Newborn.}, journal = {Current issues in molecular biology}, volume = {45}, number = {9}, pages = {6958-6966}, pmid = {37754223}, issn = {1467-3045}, support = {201710264-6//FAPESP: Research Support Foundation of the State of São Paulo-SP/ ; }, abstract = {Parvovirus B19 infection is associated with a wide range of clinical manifestations, from asymptomatic to severe neurological disorders. Its major clinical symptoms, fever and rash, are common to multiple viruses, and laboratory tests to detect B19 are frequently not available. Thus, the impact of B19 on public health remains unclear. We report the case of a 38-day old girl admitted to São Paulo Clinical Hospital, Brazil, with an initial diagnosis of bacterial meningitis, seizures, and acute hydrocephalus. Antibiotic therapy was maintained for one week after admission and discontinued after negative laboratory results were obtained. Nine days after symptoms onset, a cerebral spinal fluid (CSF) sample revealed persistent pleocytosis. The complete B19 complete genome was subsequently identified in her CSF by a metagenomic next-generation sequencing approach. This report highlights the possible involvement of B19 in the occurrence of acute neurological manifestations and emphasizes that its possible involvement might be better revealed by the use of metagenomic technology to detect viral agents in clinical situations of unknown or uncertain etiology.}, } @article {pmid37753177, year = {2023}, author = {Ho, H and Chovatia, M and Egan, R and He, G and Yoshinaga, Y and Liachko, I and O'Malley, R and Wang, Z}, title = {Integrating chromatin conformation information in a self-supervised learning model improves metagenome binning.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e16129}, pmid = {37753177}, issn = {2167-8359}, support = {R44 AI162570/AI/NIAID NIH HHS/United States ; }, mesh = {*Chromatin/genetics ; *Metagenome/genetics ; Algorithms ; Benchmarking ; Supervised Machine Learning ; }, abstract = {Metagenome binning is a key step, downstream of metagenome assembly, to group scaffolds by their genome of origin. Although accurate binning has been achieved on datasets containing multiple samples from the same community, the completeness of binning is often low in datasets with a small number of samples due to a lack of robust species co-abundance information. In this study, we exploited the chromatin conformation information obtained from Hi-C sequencing and developed a new reference-independent algorithm, Metagenome Binning with Abundance and Tetra-nucleotide frequencies-Long Range (metaBAT-LR), to improve the binning completeness of these datasets. This self-supervised algorithm builds a model from a set of high-quality genome bins to predict scaffold pairs that are likely to be derived from the same genome. Then, it applies these predictions to merge incomplete genome bins, as well as recruit unbinned scaffolds. We validated metaBAT-LR's ability to bin-merge and recruit scaffolds on both synthetic and real-world metagenome datasets of varying complexity. Benchmarking against similar software tools suggests that metaBAT-LR uncovers unique bins that were missed by all other methods. MetaBAT-LR is open-source and is available at https://bitbucket.org/project-metabat/metabat-lr.}, } @article {pmid37752797, year = {2023}, author = {Quinn, G and Ali, RO and Zhang, GY and Hill, K and Townsend, E and Umarova, R and Chakraborty, M and Ahmad, MF and Gewirtz, M and Haddad, J and Rosenzweig, S and Rampertaap, S and Schoenfeld, M and Yang, S and Koh, C and Levy, E and Kleiner, DE and Etzion, O and Heller, T}, title = {Non-selective dampening of the host immune response after hepatitis C clearance and its association with circulating chemokine and endotoxin levels.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {43}, number = {12}, pages = {2701-2712}, doi = {10.1111/liv.15737}, pmid = {37752797}, issn = {1478-3231}, support = {/CA/NCI NIH HHS/United States ; /DK/NIDDK NIH HHS/United States ; /CA/NCI NIH HHS/United States ; /DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Antiviral Agents/therapeutic use ; Hepacivirus ; *Hepatitis C, Chronic/complications ; Endotoxins/therapeutic use ; RNA, Ribosomal, 16S/genetics ; *Hepatitis C/complications ; Sustained Virologic Response ; Chemokines/therapeutic use ; Immunity ; }, abstract = {BACKGROUND & AIMS: Direct-acting antiviral (DAA) therapy has revolutionized treatment for the hepatitis C virus (HCV). While DAA therapy is common, little is known about the intrahepatic immunological changes after sustained virologic response (SVR). We aim to describe transcriptional alterations of the gut microbiome and the liver after SVR.

METHODS: Twenty-two HCV patients were evaluated before and 9 months after 12 weeks of sofosbuvir/velpatasvir treatment. All achieved SVR. A liver biopsy, portal blood (direct portal vein cannulation), peripheral blood and stool samples were obtained. RNA-seq and immunofluorescent staining were performed on liver biopsies. RNA-seq and 16S rRNA metagenomics were performed on stool.

RESULTS: Differential expression within liver transcription showed 514 downregulated genes (FDR q < .05; foldchange > 2) enriched in inflammatory pathways; of note, GO:0060337, type 1 IFN signalling (p = 8e-23) and GO:0042742, defence response to bacterium (p = 8e-3). Interestingly, microbial products increased in the portal blood and liver after SVR. Due to the increase in microbial products, the gut microbiome was investigated. There was no dysbiosis by Shannon diversity index or Bacteroides/Firmicutes ratio. There was a differential increase in genes responsible for bacterial lipopolysaccharide production after SVR.

CONCLUSIONS: The decrease in the antiviral interferon pathway expression was expected after SVR; however, there was an unanticipated decrease in the transcription of genes involved in recognition and response to bacteria, which was associated with increased levels of microbial products. Finally, the alterations in the function of the gut microbiome are a promising avenue for further investigation of the gut-liver axis, especially in the context of the significant immunological changes noted after SVR.}, } @article {pmid37752615, year = {2023}, author = {Jin, Z and Yang, Y and Cao, Y and Wen, Q and Xi, Y and Cheng, J and Zhao, Q and Weng, J and Hong, K and Jiang, H and Hang, J and Zhang, Z}, title = {The gut metabolite 3-hydroxyphenylacetic acid rejuvenates spermatogenic dysfunction in aged mice through GPX4-mediated ferroptosis.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {212}, pmid = {37752615}, issn = {2049-2618}, mesh = {Mice ; Male ; Animals ; *Ferroptosis ; Semen ; *Gastrointestinal Microbiome/physiology ; Fecal Microbiota Transplantation ; Spermatogenesis ; }, abstract = {BACKGROUND: Aging-related fertility decline is a prevalent concern globally. Male reproductive system aging is mainly characterized by a decrease in sperm quality and fertility. While it is known that intestinal physiology changes with age and that microbiota is shaped by physiology, the underlying mechanism of how the microbiota affects male reproductive aging is still largely unexplored.

RESULTS: Here, we utilized fecal microbiota transplantation (FMT) to exchange the fecal microbiota between young and old mice. Cecal shotgun metagenomics and metabolomics were used to identify differences in gut microbiota composition and metabolic regulation during aging. Our results demonstrated that FMT from young to old mice alleviated aging-associated spermatogenic dysfunction through an unexpected mechanism mediated by a gut bacteria-derived metabolite, 3-hydroxyphenylacetic acid (3-HPAA). 3-HPAA treatment resulted in an improvement of spermatogenesis in old mice. RNA sequencing analysis, qRT-PCR and Western blot revealed that 3-HPAA induced an upregulation of GPX4, thereby restraining ferroptosis and restoring spermatogenesis. These findings were further confirmed by in vitro induction of ferroptosis and inhibition of GPX4 expression.

CONCLUSIONS: Our results demonstrate that the microbiome-derived metabolite, 3-HPAA, facilitates spermatogenesis of old mice through a ferroptosis-mediated mechanism. Overall, these findings provide a novel mechanism of dysregulated spermatogenesis of old mice, and suggest that 3-HPAA could be a potential therapy for fertility decline of aging males in clinical practice. Video Abstract.}, } @article {pmid37752498, year = {2023}, author = {Fan, Z and Zhang, L and Wei, L and Huang, X and Yang, M and Xing, X}, title = {Tracheal microbiome and metabolome profiling in iatrogenic subglottic tracheal stenosis.}, journal = {BMC pulmonary medicine}, volume = {23}, number = {1}, pages = {361}, pmid = {37752498}, issn = {1471-2466}, support = {202201AY070001-277//the Special and Joint Program of the Yunnan Provincial Science and Technology Department and Kunming Medical University/ ; 202201AY070001-265//the Special and Joint Program of the Yunnan Provincial Science and Technology Department and Kunming Medical University/ ; 2022J0019//Science Research Foundation of Yunnan Provincial Education Department/ ; No. 82160016//the National Natural Science Foundation of China/ ; No. YNWR-MY-2020-013//Famous Doctors of High-level Talent Training Support Program of Yunnan Province/ ; }, mesh = {Humans ; *Tracheal Stenosis ; *Laryngostenosis ; Cicatrix ; Iatrogenic Disease ; *Microbiota ; Metabolome ; Carnitine ; }, abstract = {BACKGROUND: To study the role of microecology and metabolism in iatrogenic tracheal injury and cicatricial stenosis, we investigated the tracheal microbiome and metabolome in patients with tracheal stenosis after endotracheal intubation.

METHODS: We collected 16 protected specimen brush (PSB) and 8 broncho-alveolar lavage (BAL) samples from 8 iatrogenic subglottic tracheal stenosis patients, including 8 PSB samples from tracheal scar sites, 8 PSB samples from scar-free sites and 8 BAL samples, by lavaging the subsegmental bronchi of the right-middle lobe. Metagenomic sequencing was performed to characterize the microbiome profiling of 16 PSB and 8 BAL samples. Untargeted metabolomics was performed in 6 PSB samples (3 from tracheal scar PSB and 3 from tracheal scar-free PSB) using high-performance liquid chromatography‒mass spectrometry (LC‒MS).

RESULTS: At the species level, the top four bacterial species were Neisseria subflava, Streptococcus oralis, Capnocytophaga gingivals, and Haemophilus aegyptius. The alpha and beta diversity among tracheal scar PSB, scar-free PSB and BAL samples were compared, and no significant differences were found. Untargeted metabolomics was performed in 6 PSB samples using LC‒MS, and only one statistically significant metabolite, carnitine, was identified. Pathway enrichment analysis of carnitine revealed significant enrichment in fatty acid oxidation.

CONCLUSION: Our study found that carnitine levels in tracheal scar tissue were significantly lower than those in scar-free tissue, which might be a new target for the prevention and treatment of iatrogenic tracheal stenosis in the future.}, } @article {pmid37752225, year = {2023}, author = {Luo, Y and Liu, C and Luo, Y and Zhang, X and Li, J and Hu, C and Yang, S}, title = {Thiostrepton alleviates experimental colitis by promoting RORγt ubiquitination and modulating dysbiosis.}, journal = {Cellular & molecular immunology}, volume = {20}, number = {11}, pages = {1352-1366}, pmid = {37752225}, issn = {2042-0226}, mesh = {Animals ; Mice ; *Interleukin-17/metabolism ; Thiostrepton/metabolism/pharmacology/therapeutic use ; Immunity, Innate ; Nuclear Receptor Subfamily 1, Group F, Member 3/metabolism ; Dysbiosis ; Lymphocytes/metabolism ; *Colitis/chemically induced/therapy ; Colon/metabolism ; Inflammation/metabolism ; Ubiquitination ; Dextran Sulfate ; Mice, Inbred C57BL ; Disease Models, Animal ; }, abstract = {Thiostrepton (TST) is a natural antibiotic with pleiotropic properties. This study aimed to elucidate the therapeutic effect of TST on experimental colitis and identify its targets. The effect of TST on colon inflammation was evaluated in a dextran sulfate sodium (DSS)-induced colitis model and a T-cell transfer colitis model. The therapeutic targets of TST were investigated by cytokine profiling, immunophenotyping and biochemical approaches. The effect of TST on the gut microbiota and its contribution to colitis were evaluated in mice with DSS-induced colitis that were subjected to gut microbiota depletion and fecal microbiota transplantation (FMT). Alterations in the gut microbiota caused by TST were determined by 16S rDNA and metagenomic sequencing. Here, we showed that TST treatment significantly ameliorated colitis in the DSS-induced and T-cell transfer models. Specifically, TST targeted the retinoic acid-related orphan nuclear receptor RORγt to reduce the production of IL-17A by γδ T cells, type 3 innate lymphoid cells (ILC3s) and Th17 cells in mice with DSS-induced colitis. Similarly, TST selectively prevented the development of Th17 cells in the T-cell transfer colitis model and the differentiation of naïve CD4[+] T cells into Th17 cells in vitro. Mechanistically, TST induced the ubiquitination and degradation of RORγt by promoting the binding of Itch to RORγt. Moreover, TST also reversed dysbiosis to control colonic inflammation. Taken together, these results from our study describe the previously unexplored role of TST in alleviating colonic inflammation by reducing IL-17A production and modulating dysbiosis, suggesting that TST is a promising candidate drug for the treatment of IBD.}, } @article {pmid37750599, year = {2023}, author = {Moeller, AH and Sanders, JG and Sprockett, DD and Landers, A}, title = {Assessing co-diversification in host-associated microbiomes.}, journal = {Journal of evolutionary biology}, volume = {36}, number = {12}, pages = {1659-1668}, doi = {10.1111/jeb.14221}, pmid = {37750599}, issn = {1420-9101}, support = {R35GM138284/GM/NIGMS NIH HHS/United States ; R35GM138284/GM/NIGMS NIH HHS/United States ; }, mesh = {Phylogeny ; *Biological Evolution ; *Microbiota ; Evolution, Molecular ; Genome ; Symbiosis ; }, abstract = {When lineages of hosts and microbial symbionts engage in intimate interactions over evolutionary timescales, they can diversify in parallel (i.e., co-diversify), producing associations between the lineages' phylogenetic histories. Tests for co-diversification of individual microbial lineages and their hosts have been developed previously, and these have been applied to discover ancient symbioses in diverse branches of the tree of life. However, most host-microbe relationships are not binary but multipartite, in that a single host-associated microbiota can contain many microbial lineages, generating challenges for assessing co-diversification. Here, we review recent evidence for co-diversification in complex microbiota, highlight the limitations of prior studies, and outline a hypothesis testing approach designed to overcome some of these limitations. We advocate for the use of microbiota-wide scans for co-diversifying symbiont lineages and discuss tools developed for this purpose. Tests for co-diversification for simple host symbiont systems can be extended to entire phylogenies of microbial lineages (e.g., metagenome-assembled or isolate genomes, amplicon sequence variants) sampled from host clades, thereby providing a means for identifying co-diversifying symbionts present within complex microbiota. The relative ages of symbiont clades can corroborate co-diversification, and multi-level permutation tests can account for multiple comparisons and phylogenetic non-independence introduced by repeated sampling of host species. Discovering co-diversifying lineages will generate powerful opportunities for interrogating the molecular evolution and lineage turnover of ancestral, host-species specific symbionts within host-associated microbiota.}, } @article {pmid37749663, year = {2023}, author = {Shen, S and Wang, J and Ma, C and Chen, Y and Ding, H and Zhang, J}, title = {Understanding the "individual drug reaction" from the perspective of the interaction between probiotics and lovastatin in vitro and in vivo.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {209}, pmid = {37749663}, issn = {2049-2618}, mesh = {Animals ; Cricetinae ; Humans ; Lovastatin/pharmacology ; Liver ; Chromatography, High Pressure Liquid ; *Drug-Related Side Effects and Adverse Reactions ; *Gastrointestinal Microbiome ; *Probiotics ; }, abstract = {BACKGROUND: The existence of the gut microbiota produces an "individual drug reaction." As members of the intestinal microbiota, probiotics, although they have prebiotic functions, may accelerate the degradation of drugs, thereby affecting drug efficacy. Lovastatin is one of the well-recognized lipid-lowering drugs. Its main action site is the liver. Therefore, if it is degraded in advance by gastrointestinal probiotics, its efficacy may be reduced.

RESULTS: Here, we designed a two-stage experiment in vitro and in vivo to explore the degradation of lovastatin by probiotics. In vitro, the degradation of lovastatin by 83 strains of Lactiplantibacillus plantarum and the "star strain" Lacticaseibacillus paracasei strain Shirota was investigated by high-performance liquid chromatography (HPLC). The results showed that probiotics could degrade lovastatin to varying degrees. Subsequently, we selected Lactiplantibacillus plantarum A5 (16.87%) with the strongest ability to degrade lovastatin, Lactiplantibacillus plantarum C3 (4.61%) with the weakest ability to degrade lovastatin and Lacticaseibacillus paracasei strain Shirota (17.6%) as representative probiotics for in vivo experiments. In vivo, the therapeutic effect of lovastatin combined with probiotics on golden hamsters with mixed hyperlipidemia was evaluated by measuring blood indicators, intestinal microbiota metagenomic sequencing, and the liver transcriptome. The results showed that the intake of probiotics did not affect the efficacy of lovastatin and could slow the inflammatory reaction of the liver.

CONCLUSIONS: The supplementation of probiotics produced beneficial metabolites in the intestine by promoting beneficial microbes. Intestinal metabolites affected the expression of the liver genes through the gut-liver axis, increased the relative content of the essential amino acids, and finally improved the liver inflammatory response of the host. This study aims to reveal the impact of probiotics on the human body from a unique perspective, suggesting the impact of taking probiotics while taking drugs. Video Abstract.}, } @article {pmid37749660, year = {2023}, author = {Wegner, CE and Stahl, R and Velsko, I and Hübner, A and Fagernäs, Z and Warinner, C and Lehmann, R and Ritschel, T and Totsche, KU and Küsel, K}, title = {A glimpse of the paleome in endolithic microbial communities.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {210}, pmid = {37749660}, issn = {2049-2618}, mesh = {*Genomics ; Paleontology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenome ; }, abstract = {BACKGROUND: The terrestrial subsurface is home to a significant proportion of the Earth's microbial biomass. Our understanding about terrestrial subsurface microbiomes is almost exclusively derived from groundwater and porous sediments mainly by using 16S rRNA gene surveys. To obtain more insights about biomass of consolidated rocks and the metabolic status of endolithic microbiomes, we investigated interbedded limestone and mudstone from the vadose zone, fractured aquifers, and deep aquitards.

RESULTS: By adapting methods from microbial archaeology and paleogenomics, we could recover sufficient DNA for downstream metagenomic analysis from seven rock specimens independent of porosity, lithology, and depth. Based on the extracted DNA, we estimated between 2.81 and 4.25 × 10[5] cells × g[-1] rock. Analyzing DNA damage patterns revealed paleome signatures (genetic records of past microbial communities) for three rock specimens, all obtained from the vadose zone. DNA obtained from deep aquitards isolated from surface input was not affected by DNA decay indicating that water saturation and not flow is controlling subsurface microbial survival. Decoding the taxonomy and functional potential of paleome communities revealed increased abundances for sequences affiliated with chemolithoautotrophs and taxa such as Cand. Rokubacteria. We also found a broader metabolic potential in terms of aromatic hydrocarbon breakdown, suggesting a preferred utilization of sedimentary organic matter in the past.

CONCLUSIONS: Our study suggests that limestones function as archives for genetic records of past microbial communities including those sensitive to environmental stress at modern times, due to their specific conditions facilitating long-term DNA preservation. Video Abstract.}, } @article {pmid37749507, year = {2023}, author = {Pan, J and Ji, L and Wu, H and Wang, X and Wang, Y and Wu, Y and Yang, S and Shen, Q and Liu, Y and Zhang, W and Zhang, K and Shan, T}, title = {Metagenomic analysis of herbivorous mammalian viral communities in the Northwest Plateau.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {568}, pmid = {37749507}, issn = {1471-2164}, support = {No.2022YFC2603801//National Key Research and Development Programs of China/ ; No.2022YFC2603801//National Key Research and Development Programs of China/ ; No.2022YFC2603801//National Key Research and Development Programs of China/ ; No.2022YFC2603801//National Key Research and Development Programs of China/ ; No.2022YFC2603801//National Key Research and Development Programs of China/ ; No.2022YFC2603801//National Key Research and Development Programs of China/ ; No.2022YFC2603801//National Key Research and Development Programs of China/ ; No.2022YFC2603801//National Key Research and Development Programs of China/ ; No.2022YFC2603801//National Key Research and Development Programs of China/ ; No.2022YFC2603801//National Key Research and Development Programs of China/ ; No.2022YFC2603801//National Key Research and Development Programs of China/ ; No.2022YFC2603801//National Key Research and Development Programs of China/ ; No. 20220817004//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents/ ; No. 20220817004//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents/ ; No. 20220817004//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents/ ; No. 20220817004//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents/ ; No. 20220817004//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents/ ; No. 20220817004//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents/ ; No. 20220817004//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents/ ; No. 20220817004//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents/ ; No. 20220817004//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents/ ; No. 20220817004//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents/ ; No. 20220817004//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents/ ; No. 20220817004//Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship talents - Leading Talents/ ; }, mesh = {Animals ; Humans ; *Deer ; Phylogeny ; *Brassicaceae ; Vegetables ; Cloning, Molecular ; }, abstract = {BACKGROUND: Mammals are potential hosts for many infectious diseases. However, studies on the viral communities of herbivorous mammals in the Northwest Plateau are limited. Here, we studied the viral communities of herbivorous mammals in the Northwest Plateau using virus metagenomic analysis to analyze and compare the viral community composition of seven animal species.

RESULTS: By library construction and next-generation sequencing, contigs and singlets reads with similar viral sequences were classified into 24 viral families. Analyzed from the perspective of sampling areas, the virus community composition was relatively similar in two areas of Wuwei and Jinchang, Gansu Province. Analyzed from the perspective of seven animal species, the viral reads of seven animal species were mostly ssDNA and dominated by CRESS-DNA viruses. Phylogenetic analysis based on viral marker genes indicated that CRESS-DNA viruses and microviruses have high genetic diversity. In addition to DNA viruses, nodaviruses, pepper mild mottle viruses and picornaviruses were RNA viruses that we performed by phylogenetic analysis. The CRESS-DNA viruses and nodaviruses are believed to infect plants and insects, and microviruses can infect bacteria, identifying that they were likely from the diet of herbivorous mammals. Notably, two picornaviruses were identified from red deer and wild horse, showing that the picornavirus found in red deer had the relatively high similarity with human hepatitis A virus, and the picornavirus carried by wild horse could potentially form a new species within the Picornaviridae family.

CONCLUSIONS: This study explored the herbivorous mammalian virus community in the Northwest Plateau and the genetic characteristics of viruses that potentially threaten human health. It reveals the diversity and stability of herbivorous mammalian virus communities in the Northwest Plateau and helps to expand our knowledge of various herbivorous mammalian potentially pathogenic viruses.}, } @article {pmid37749471, year = {2023}, author = {Lu, Y and Pang, L and Chatzisymeon, E and Liu, X and Xu, K and Yang, P and Gou, M}, title = {Copper in different forms and tetracycline affect behavior and risk of antibiotic resistome in thermophilic anaerobic digestion of cattle manure.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {49}, pages = {108162-108175}, pmid = {37749471}, issn = {1614-7499}, mesh = {Humans ; Cattle ; Animals ; *Anti-Bacterial Agents/pharmacology ; *Manure ; Copper ; Copper Sulfate ; Anaerobiosis ; Genes, Bacterial ; Tetracycline/pharmacology ; Oxides ; }, abstract = {The metagenomics-based behavior and risk of antibiotic resistance genes (ARGs) were investigated during cattle manure thermophilic anaerobic digestion with tetracycline and copper, namely, bulk-copper oxide, nano-copper oxide, and copper sulfate, which are common feed additives. Although bulk-copper oxide reduced ARGs' diversity, it enriched high-risk ARGs the most than the other two copper species, while copper sulfate could strongly mitigate the ARG risk by decreasing their abundances. Compared to corresponding individual effects, copper and tetracycline combinations may decrease ARGs' co-occurrence potential by 22.0%, and particularly, tetracycline combined separately with copper sulfate and nano-copper oxide reduces the ARGs' risk in abundance (by 7.2%) and human health (by 4.0%). These were mainly driven by bioavailable copper, volatile fatty acids, and pH, as well as the main potential hosts in phyla Firmicutes, Coprothermobacterota, and Euryarchaeota. Notably, the twin risks of pathogenicity and ARGs should be emphasized due to the ARGs' positive correlation with human pathogens of Clostridioides difficile and Arcobacter peruensis. These findings are important for understanding the potential ARGs' risk in treatments of livestock wastes containing feed additives of different sizes and speciation.}, } @article {pmid37749431, year = {2023}, author = {Arumugam, U and Sudarsanan, GB and Karuppannan, AK and Palaniappan, S}, title = {Metagenomic Studies Reveal the Evidence of Akkermansia muciniphila and Other Probiotic Bacteria in the Gut of Healthy and Enterocytozoon hepatopenaei (EHP)-Infected Farmed Penaeus vannamei.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {37749431}, issn = {1867-1314}, abstract = {Penaeus vannamei (whiteleg shrimp) is the most widely cultured shrimp globally. Enterocytozoon hepatopenaei (EHP), a microsporidian parasite, infects P. vannamei and causes severe growth retardation, subsequent production, and economic losses in the shrimp culture. The influence of EHP infection in the shrimp gut microbiota is poorly studied, and this would be an interesting area to investigate since the gut microbiome of shrimp influences a number of key host processes such as digestion and immunity. In this study, a metagenomic approach was followed to compare the overall species richness of the gut microbiota of EHP-infected and healthy P. vannamei. Bacterial genomic DNA from the healthy and EHP-infected gut sample were profiled for the bacterial 16S rRNA gene, targeting the V3-V4 conserved region. Operational taxonomic units (OTUs), an approximation of definitive taxonomic identity, were identified based on the sequence similarity within the sample reads and clustered together using a cut-off of 97% identity using UCLUST. The OTUs were then used for the computation of alpha diversity and beta diversity for each sample. EHP-infected gut sample showed lower bacterial abundance throughout the family, class, order, genus, and species levels when compared to healthy gut sample. This study shows that the shrimp gut microbiota is sensitive and exhibits a high level of plasticity during a microsporidian infection like EHP. Furthermore, Akkermansia muciniphila, a novel probiotic bacterium, has been reported in the shrimp gut for the first time.}, } @article {pmid37749380, year = {2023}, author = {Jahanshahi, DA and Ariaeenejad, S and Kavousi, K}, title = {A metagenomic catalog for exploring the plastizymes landscape covering taxa, genes, and proteins.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {16029}, pmid = {37749380}, issn = {2045-2322}, mesh = {*Metagenome ; *Bacterial Proteins/metabolism ; Metagenomics/methods ; }, abstract = {There are significant environmental and health concerns associated with the current inefficient plastic recycling process. This study presents the first integrated reference catalog of plastic-contaminated environments obtained using an insilico workflow that could play a significant role in discovering new plastizymes. Here, we combined 66 whole metagenomic data from plastic-contaminated environment samples from four previously collected metagenome data with our new sample. In this study, an integrated plastic-contaminated environment gene, protein, taxa, and plastic degrading enzyme catalog (PDEC) was constructed. These catalogs contain 53,300,583 non-redundant genes and proteins, 691 metagenome-assembled genomes, and 136,654 plastizymes. Based on KEGG and eggNOG annotations, 42% of recognized genes lack annotations, indicating their functions remain elusive and warrant further investigation. Additionally, the PDEC catalog highlights hydrolases, peroxidases, and cutinases as the prevailing plastizymes. Ultimately, following multiple validation procedures, our effort focused on pinpointing enzymes that exhibited the highest similarity to the introduced plastizymes in terms of both sequence and three-dimensional structural aspects. This encompassed evaluating the linear composition of constituent units as well as the complex spatial conformation of the molecule. The resulting catalog is expected to improve the resolution of future multi-omics studies, providing new insights into plastic-pollution related research.}, } @article {pmid37749192, year = {2023}, author = {Akter, S and Rahman, MS and Ali, H and Minch, B and Mehzabin, K and Siddique, MM and Galib, SM and Yesmin, F and Azmuda, N and Adnan, N and Hasan, NA and Rahman, SR and Moniruzzaman, M and Ahmed, MF}, title = {Phylogenetic diversity and functional potential of the microbial communities along the Bay of Bengal coast.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15976}, pmid = {37749192}, issn = {2045-2322}, mesh = {Bays ; Phylogeny ; *Microbiota ; *Alteromonas ; *Dinoflagellida ; }, abstract = {The Bay of Bengal, the world's largest bay, is bordered by populous countries and rich in resources like fisheries, oil, gas, and minerals, while also hosting diverse marine ecosystems such as coral reefs, mangroves, and seagrass beds; regrettably, its microbial diversity and ecological significance have received limited research attention. Here, we present amplicon (16S and 18S) profiling and shotgun metagenomics data regarding microbial communities from BoB's eastern coast, viz., Saint Martin and Cox's Bazar, Bangladesh. From the 16S barcoding data, Proteobacteria appeared to be the dominant phylum in both locations, with Alteromonas, Methylophaga, Anaerospora, Marivita, and Vibrio dominating in Cox's Bazar and Pseudoalteromonas, Nautella, Marinomonas, Vibrio, and Alteromonas dominating the Saint Martin site. From the 18S barcoding data, Ochrophyta, Chlorophyta, and Protalveolata appeared among the most abundant eukaryotic divisions in both locations, with significantly higher abundance of Choanoflagellida, Florideophycidae, and Dinoflagellata in Cox's Bazar. The shotgun sequencing data reveals that in both locations, Alteromonas is the most prevalent bacterial genus, closely paralleling the dominance observed in the metabarcoding data, with Methylophaga in Cox's Bazar and Vibrio in Saint Martin. Functional annotations revealed that the microbial communities in these samples harbor genes for biofilm formation, quorum sensing, xenobiotics degradation, antimicrobial resistance, and a variety of other processes. Together, these results provide the first molecular insight into the functional and phylogenetic diversity of microbes along the BoB coast of Bangladesh. This baseline understanding of microbial community structure and functional potential will be critical for assessing impacts of climate change, pollution, and other anthropogenic disturbances on this ecologically and economically vital bay.}, } @article {pmid37749183, year = {2023}, author = {Yin, YR and Li, XW and Long, CH and Li, L and Hang, YY and Rao, MD and Yan, X and Liu, QL and Sang, P and Li, WJ and Yang, LQ}, title = {Characterization of a GH10 extremely thermophilic xylanase from the metagenome of hot spring for prebiotic production.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {16053}, pmid = {37749183}, issn = {2045-2322}, mesh = {China ; *Hot Springs ; Metagenome ; Amino Acid Sequence ; Biofuels ; Escherichia coli/genetics ; }, abstract = {A xylanase gene (named xyngmqa) was identified from the metagenomic data of the Gumingquan hot spring (92.5 °C, pH 9.2) in Tengchong City, Yunnan Province, southwest China. It showed the highest amino acid sequence identity (82.70%) to endo-1,4-beta-xylanase from Thermotoga caldifontis. A constitutive expression plasmid (denominated pSHY211) and double-layer plate (DLP) method were constructed for cloning, expression, and identification of the XynGMQA gene. The XynGMQA gene was synthesized and successfully expressed in Escherichia coli DH5α. XynGMQA exhibited optimal activity at 90 °C and pH 4.6, being thermostable by maintaining 100% of its activity after 2 h incubated at 80 °C. Interestingly, its enzyme activity was enhanced by high temperatures (70 and 80 °C) and low pH (3.0-6.0). About 150% enzyme activity was detected after incubation at 70 °C for 20 to 60 min or 80 °C for 10 to 40 min, and more than 140% enzyme activity after incubation at pH 3.0 to 6.0 for 12 h. Hydrolytic products of beechwood xylan with XynGMQA were xylooligosaccharides, including xylobiose (X2), xylotriose (X3), and xylotetraose (X4). These properties suggest that XynGMQA as an extremely thermophilic xylanase, may be exploited for biofuel and prebiotic production from lignocellulosic biomass.}, } @article {pmid37748599, year = {2024}, author = {Teng, M and Zhao, X and Zhou, L and Yan, H and Zhao, L and Sun, J and Li, Y and Zhu, W and Wu, F}, title = {An integrated analysis of the fecal metabolome and metagenome reveals the distinct effects of differentially charged nanoplastics on the gut microbiota-associated metabolites in mice.}, journal = {The Science of the total environment}, volume = {906}, number = {}, pages = {167287}, doi = {10.1016/j.scitotenv.2023.167287}, pmid = {37748599}, issn = {1879-1026}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Metagenome ; Microplastics ; Metabolome ; Polystyrenes ; Biomarkers ; RNA, Ribosomal, 16S ; }, abstract = {Whether nanoplastics with differential charges cause intestinal impairment via distinct mechanisms remains unclear. We investigated the relationship between fecal metabolites and the gut microbiome, and potential biomarkers thereof, in mice following exposure to differentially charged polystyrene nanoplastics (PS-NPs). Metagenomic analysis revealed that exposure to differentially charged PS-NPs resulted in alterations in the abundances of Bilophila_wadsworthia, Helicobacter apodemus, and Helicobacter typhlonius. A total of 237 fecal metabolites were significantly altered in mice that exhibited intestinal impairment, and these included 10 gut microbiota-related fecal metabolites that accurately discriminated impaired intestinal samples from the control. Additionally, the specific gut microbiome-related fecal metabolite-based model approach for the prediction of intestinal impairment in mice had an area under the curve (AUC) of 1.0 in the PS (without charge) group, an AUC of 0.94 in the PS-NH2 (positive charge) group, and an AUC of 0.86 in the PS-COOH (negative charge) group. Thus, the model showed promising evaluable accuracy for the prediction of intestinal impairment induced by nanoplastics in a charge-specific manner. Our study demonstrates that the fecal metabolome of mice with intestinal impairment following exposure to differentially charged nanoplastics is associated with changes in the gut microbiome. The identified biomarkers have potential application for the detection of intestinal impairment after exposure to negative, positive, or noncharged nanomaterials.}, } @article {pmid37748347, year = {2023}, author = {Palomo, A and Dechesne, A and Smets, BF and Zheng, Y}, title = {Narrow host range phages infect essential bacteria for water purification reactions in groundwater-fed rapid sand filters.}, journal = {Water research}, volume = {245}, number = {}, pages = {120655}, doi = {10.1016/j.watres.2023.120655}, pmid = {37748347}, issn = {1879-2448}, abstract = {Biofiltration is used worldwide to provide safe potable water due to its low energy demand and excellent treatment performance. For instance, in Denmark, over 95% of drinking water is supplied through groundwater-fed rapid sand filters (RSF). Bacteriophages, viruses that infect bacteria, have been shown to shape the taxonomic and functional composition of microbial communities across a range of natural and engineering systems. However, phages in the biofiltration systems are rarely studied, despite the central role microbes play in water purification. To probe this, metagenomic data from surface water, groundwater and mixed source water biofiltration units (n = 26 from China, Europe and USA) for drinking water production were analysed to characterize prokaryotic viruses and to identify their potential microbial hosts. The source water type and geographical location are found to exert influence on the composition of the phageome in biofilters. Although the viral abundance (71,676 ± 17,841 RPKM) in biofilters is only 14.4% and 17.0% lower than those of the nutrient-rich wastewater treatment plants and fresh surface waters, the richness (1,441 ± 1,046) and diversity (Inverse Simpson: 91 ± 61) in biofiltration units are significantly less by a factor of 2-5 and 3-4, respectively. In depth analysis of data from 24 groundwater-fed RSFs in Denmark revealed a core phageome shared by most RSFs, which was consistently linked to dominant microbial hosts involved in key biological reactions for water purification. Finally, the high number of specific links detected between phages and bacterial species and the large proportion of lytic phages (77%) led to the conjecture that phages regulate bacterial populations through predation, preventing the proliferation of dominant species and contributing to the established functional redundancy among the dominant microbial groups. In conclusion, bacteriophages are likely to play a significant role in water treatment within biofilters, particularly through interactions with key bacterial species.}, } @article {pmid37748344, year = {2023}, author = {Yang, Y and Deng, Y and Liu, L and Yin, X and Xu, X and Wang, D and Zhang, T}, title = {Establishing reference material for the quest towards standardization in environmental microbial metagenomic studies.}, journal = {Water research}, volume = {245}, number = {}, pages = {120641}, doi = {10.1016/j.watres.2023.120641}, pmid = {37748344}, issn = {1879-2448}, abstract = {Breakthroughs in DNA-based technologies, especially in metagenomic sequencing, have drastically enhanced researchers' ability to explore environmental microbiome and the associated interplays within. However, as new methodologies are being actively developed for improvements in different aspects, metagenomic workflows become diversified and heterogeneous. Through a single-variable control approach, we quantified the microbial profiling variations arising from 6 common technical variables associated with metagenomic workflows for both simple and complex samples. The incurred variations were constantly the lowest in replicates of DNA isolation and DNA sequencing library construction. Different DNA extraction kits often caused the highest variation among all the tested variables. Additionally, sequencing run batch was an important source of variability for targeted platforms. As such, the development of an environmental reference material for complex environmental samples could be beneficial in benchmarking accrued non-biological variability within and between protocols and insuring reliable and reproducible sequencing outputs immediately upstream of bioinformatic analysis. To develop an environment reference material, sequencing of a well-homogenized environmental sample composed of activated sludge was performed using different pre-analytical assays in replications. In parallel, a certified mock community was processed and sequenced. Assays were ranked based on the reconstruction of the theoretical mock community profile. The reproducibility of the best-performing assay and the microbial profile of the reference material were further ascertained. We propose the adoption of our complex environmental reference material, which could reflect the degree of diversity in environmental microbiome studies, to facilitate accurate, reproducible, and comparable environmental metagenomics-based studies.}, } @article {pmid37748307, year = {2024}, author = {Gao, J and Xing, X and Cai, W and Li, Z and Shi, G and Chen, Y and Liang, H and Chen, C and Ma, K and Chen, J and Hu, C}, title = {Effect of micropollutants on disinfection byproducts and antibiotic resistance genes in drinking water in the process of biological activated carbon treatment.}, journal = {Journal of hazardous materials}, volume = {461}, number = {}, pages = {132304}, doi = {10.1016/j.jhazmat.2023.132304}, pmid = {37748307}, issn = {1873-3336}, mesh = {Disinfection ; *Drinking Water ; Charcoal ; Extracellular Polymeric Substance Matrix/chemistry ; Anti-Bacterial Agents ; *Water Purification ; *Water Pollutants, Chemical/toxicity/analysis ; *Disinfectants/pharmacology ; }, abstract = {The biofilm stress response of biological activated carbon (BAC) was investigated under prolonged exposure to sulfadiazine and 2,4-Dichlorophenoxyacetic acid, simulating complex emerging organic contaminants (EOCs) that are mainly involved in the formation of nitrogenous disinfection byproducts (N-DBPs) and antibiotic resistance genes (ARGs). Under trace complex EOCs condition (2 µg/L), N-DBP precursors and abundance of ARGs increased significantly in BAC effluent. The total formation potential of haloacetonitriles (HANs) and halonitromethanes (HNMs) was 751.47 ± 2.98 ng/L, which was much higher than the control group (440.67 ± 13.38 ng/L without EOCs). Similarly, the relative abundance of ARGs was more than twice that in the control group. The complex EOCs induce excessive extracellular polymeric substance secretion (EPS), thereby causing more N-DBP precursors and stronger horizontal gene transfer. Metagenome analysis revealed that functional amino acid and protein biosynthesis genes were overexpressed compared to the control group, causing more EPS to be secreted into the external environment. Complex EOCs promote Cobetia, Clostridium, and Streptomyces dominance, contributing to the production of N-DBP precursors and ARGs. For the first time, in addition to the direct hazards of the EOCs, this study successfully revealed the indirect water quality risks of complex EOCs from the microbial stress response during BAC treatment. Synergistic regulation of EOCs and microorganisms is important for tap water security.}, } @article {pmid37748299, year = {2023}, author = {Lu, J and Dong, L and Guo, Z and Hu, Z and Dai, P and Zhang, J and Wu, H}, title = {Highly efficient phosphorous removal in constructed wetland with iron scrap: Insights into the microbial removal mechanism.}, journal = {Journal of environmental management}, volume = {347}, number = {}, pages = {119076}, doi = {10.1016/j.jenvman.2023.119076}, pmid = {37748299}, issn = {1095-8630}, mesh = {*Wastewater ; Wetlands ; Iron ; *Bioelectric Energy Sources ; Phosphorus ; }, abstract = {Excessive phosphorus (P) in surface water can lead to serious eutrophication and economic losses. Iron-based constructed wetland (CW) is considered as a promising solution to eliminate P effectively due to the advantage of low-cost. However, there is limited available information on the microbial removal mechanism of P in iron-based CW up to now. Therefore, CW with iron scrap was constructed to investigate the treatment performance and microbial removal mechanism in this study. Results showed that efficient and stable P removal (97.09 ± 1.90%) was achieved in iron scrap-based CW during the experiment period, which was attributed to the precipitation of iron and P and improved microbially mediated P removal. Metagenomic analysis showed that microbial diversity was enhanced and phosphate accumulating organisms (e.g., Dechloromonas and Tetrasphaera) were enriched in CW with iron scrap, which explained higher P removal reasonably. In addition, the abundance of genes involved in the P starvation (e.g., phoB), uptake and transport (e.g., pstB) were enhanced in iron scrap-based CW. Enrichment analysis demonstrated that phosphotransferase pathway was also significantly up-regulated in CW with iron scraps, indicating that the energy supply of microbial P removal was enhanced. These findings provide a better understanding of the microbial removal mechanism of P in iron-based CW.}, } @article {pmid37747940, year = {2023}, author = {Murali, R and Yu, H and Speth, DR and Wu, F and Metcalfe, KS and Crémière, A and Laso-Pèrez, R and Malmstrom, RR and Goudeau, D and Woyke, T and Hatzenpichler, R and Chadwick, GL and Connon, SA and Orphan, VJ}, title = {Physiological potential and evolutionary trajectories of syntrophic sulfate-reducing bacterial partners of anaerobic methanotrophic archaea.}, journal = {PLoS biology}, volume = {21}, number = {9}, pages = {e3002292}, pmid = {37747940}, issn = {1545-7885}, mesh = {*Archaea ; Anaerobiosis ; *Sulfates/metabolism ; Geologic Sediments/microbiology ; Bacteria/genetics ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Sulfate-coupled anaerobic oxidation of methane (AOM) is performed by multicellular consortia of anaerobic methanotrophic archaea (ANME) in obligate syntrophic partnership with sulfate-reducing bacteria (SRB). Diverse ANME and SRB clades co-associate but the physiological basis for their adaptation and diversification is not well understood. In this work, we used comparative metagenomics and phylogenetics to investigate the metabolic adaptation among the 4 main syntrophic SRB clades (HotSeep-1, Seep-SRB2, Seep-SRB1a, and Seep-SRB1g) and identified features associated with their syntrophic lifestyle that distinguish them from their non-syntrophic evolutionary neighbors in the phylum Desulfobacterota. We show that the protein complexes involved in direct interspecies electron transfer (DIET) from ANME to the SRB outer membrane are conserved between the syntrophic lineages. In contrast, the proteins involved in electron transfer within the SRB inner membrane differ between clades, indicative of convergent evolution in the adaptation to a syntrophic lifestyle. Our analysis suggests that in most cases, this adaptation likely occurred after the acquisition of the DIET complexes in an ancestral clade and involve horizontal gene transfers within pathways for electron transfer (CbcBA) and biofilm formation (Pel). We also provide evidence for unique adaptations within syntrophic SRB clades, which vary depending on the archaeal partner. Among the most widespread syntrophic SRB, Seep-SRB1a, subclades that specifically partner ANME-2a are missing the cobalamin synthesis pathway, suggestive of nutritional dependency on its partner, while closely related Seep-SRB1a partners of ANME-2c lack nutritional auxotrophies. Our work provides insight into the features associated with DIET-based syntrophy and the adaptation of SRB towards it.}, } @article {pmid37747624, year = {2023}, author = {das Neves Costa, LCP and Siqueira, JAM and Teixeira, DM and da Piedade, GJL and Júnior, ECS and Ferreira, JL and da Silva, LD and Gabbay, YB}, title = {Circulation of adenovirus and other viruses in urban drainage channels: an environmental surveillance in Belém, Amazon region, Brazil.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {54}, number = {4}, pages = {2939-2949}, pmid = {37747624}, issn = {1678-4405}, mesh = {Humans ; *Adenoviridae ; Brazil ; *Adenoviruses, Human/genetics ; Environmental Monitoring ; Real-Time Polymerase Chain Reaction ; }, abstract = {Urban channels in amazon cities are very polluted, with garbage and sewage disposal in these aquatic environments, favoring the high dissemination of waterborne viruses such as human adenovirus (HAdV). The aim of this study was to perform the detection and molecular characterization of adenovirus in urban channels and in a wastewater treatment plant located in a metropolitan city in the Amazon. Additionally, metagenomic analyses were performed to assess viral diversity. Samples were concentrated by organic flocculation, analyzed by quantitative real time PCR (qPCR) and sequenced (Sanger e next generation sequencing). Cell culture was performed to verify the viability of HAdV particles. A total of 104 samples were collected, being the HAdV positivity of 76% (79/104). Among the positive samples, 29.1% (23/79) were characterized as HAdV-F40 (87%, 20/23), HAdV-F41 (8.7%, 2/23), and HAdV-B (4.3%, 1/23). Average precipitation rates ranged from 163 to 614 mm, while the pH ranged from 6.9 to 7.6. Eight positive samples were inoculated into A549 cells and in 4 of these, was observed changes in the structure of the cell monolayer, alteration in the structure of the cell monolayer was observed, but without amplification when analyzed by PCR. The metagenomic data demonstrated the presence of 14 viral families, being the most abundant: Myoviridae (41% of available reads), Siphoviridae (24.5%), Podoviridae (14.1%), and Autographiviridae (6.9%) with more than 85% of the total number of identified reads. This study reinforcing that continuous surveillance may contribute to monitoring viral diversity in aquatic environments and provide early warning of potential outbreaks.}, } @article {pmid37747192, year = {2023}, author = {Islam, T and Hoque, MN}, title = {Gut and flesh microbiome sequencing of the Bangladesh national fish hilsa (Tenualosa ilisha).}, journal = {Microbiology resource announcements}, volume = {12}, number = {10}, pages = {e0044823}, pmid = {37747192}, issn = {2576-098X}, abstract = {The gut and flesh microbiome of the national fish of Bangladesh, Tenualosa ilisha, were analyzed using 16S rRNA gene sequencing. Our findings revealed a significant microbial disparity between sample categories and the habitat of hilsa fish, which will serve as a valuable foundation for further comprehensive studies on the hilsa microbiome.}, } @article {pmid37747149, year = {2023}, author = {Luo, S and Ru, J and Mirzaei, MK and Xue, J and Peng, X and Ralser, A and Mejías-Luque, R and Gerhard, M and Deng, L}, title = {Gut virome profiling identifies an association between temperate phages and colorectal cancer promoted by Helicobacter pylori infection.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2257291}, pmid = {37747149}, issn = {1949-0984}, mesh = {Animals ; Mice ; *Bacteriophages/genetics ; *Helicobacter pylori ; Virome ; *Helicobacter Infections/microbiology ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; *Colorectal Neoplasms/microbiology ; Carcinogenesis ; }, abstract = {Colorectal cancer (CRC) is one of the most commonly diagnosed cancers worldwide. While a close correlation between chronic Helicobacter pylori infection and CRC has been reported, the role of the virome has been overlooked. Here, we infected Apc-mutant mouse models and C57BL/6 mice with H. pylori and conducted a comprehensive metagenomics analysis of H. pylori-induced changes in lower gastrointestinal tract bacterial and viral communities. We observed an expansion of temperate phages in H. pylori infected Apc[+/1638N] mice at the early stage of carcinogenesis. Some of the temperate phages were predicted to infect bacteria associated with CRC, including Enterococcus faecalis. We also observed a high prevalence of virulent genes, such as flgJ, cwlJ, and sleB, encoded by temperate phages. In addition, we identified phages associated with pre-onset and onset of H. pylori-promoted carcinogenesis. Through co-occurrence network analysis, we found strong associations between the viral and bacterial communities in infected mice before the onset of carcinogenesis. These findings suggest that the expansion of temperate phages, possibly caused by prophage induction triggered by H. pylori infection, may have contributed to the development of CRC in mice by interacting with the bacterial community.}, } @article {pmid37746927, year = {2023}, author = {Simpkin, AJ and Mesdaghi, S and Sánchez Rodríguez, F and Elliott, L and Murphy, DL and Kryshtafovych, A and Keegan, RM and Rigden, DJ}, title = {Tertiary structure assessment at CASP15.}, journal = {Proteins}, volume = {91}, number = {12}, pages = {1616-1635}, doi = {10.1002/prot.26593}, pmid = {37746927}, issn = {1097-0134}, support = {/GM/NIGMS NIH HHS/United States ; /BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /GM/NIGMS NIH HHS/United States ; }, mesh = {*Furylfuramide ; *Computational Biology/methods ; Models, Molecular ; Proteins/chemistry ; Sequence Alignment ; }, abstract = {The results of tertiary structure assessment at CASP15 are reported. For the first time, recognizing the outstanding performance of AlphaFold 2 (AF2) at CASP14, all single-chain predictions were assessed together, irrespective of whether a template was available. At CASP15, there was no single stand-out group, with most of the best-scoring groups-led by PEZYFoldings, UM-TBM, and Yang Server-employing AF2 in one way or another. Many top groups paid special attention to generating deep Multiple Sequence Alignments (MSAs) and testing variant MSAs, thereby allowing them to successfully address some of the hardest targets. Such difficult targets, as well as lacking templates, were typically proteins with few homologues. Local divergence between prediction and target correlated with localization at crystal lattice or chain interfaces, and with regions exhibiting high B-factor factors in crystal structure targets, and should not necessarily be considered as representing error in the prediction. However, analysis of exposed and buried side chain accuracy showed room for improvement even in the latter. Nevertheless, a majority of groups produced high-quality predictions for most targets, which are valuable for experimental structure determination, functional analysis, and many other tasks across biology. These include those applying methods similar to those used to generate major resources such as the AlphaFold Protein Structure Database and the ESM Metagenomic atlas: the confidence estimates of the former were also notably accurate.}, } @article {pmid37746273, year = {2023}, author = {Peng, X and Wei, Z and Wang, L and Cheng, J}, title = {Invasive splenic mucormycosis due to Rhizopus microsporus during chemotherapy for acute monocytic leukemia: a case report and literature review.}, journal = {Frontiers in oncology}, volume = {13}, number = {}, pages = {1237807}, pmid = {37746273}, issn = {2234-943X}, abstract = {Mucormycosis is a rare opportunistic fungal infection associated with high mortality that typically occurs in immunocompromised patients. It is difficult to diagnose owing to non-specific clinical manifestations, the serologic index, imaging features, and the limitations of diagnostic methods. The incidence of invasive splenic mucormycosis is extremely rare, with only a few cases documented in the literature. We report a survival case of invasive splenic mucormycosis involving the liver caused by Rhizopus microsporus in a patient during consolidation therapy for acute monocytic leukemia (AML-M5). The patient initially presented with recurrent fever and splenomegaly accompanied by multiple focal hypodensities unresponsive to empiric anti-infective treatment. Splenic mucormycosis was diagnosed by Contrast-Enhanced Ultrasonography (CEUS) and metagenomic next-generation sequencing (mNGS). However, surgical intervention carries a high risk due to the progressive involvement of the liver in invasive splenic mucormycosis. Fortunately, monotherapy with amphotericin B was effective, and the patient underwent allo-HSCT. This case aims to emphasize the importance of utilizing mNGS and CEUS for the timely diagnosis of mucormycosis to help clinicians identify splenic mucormycosis and initiate appropriate therapy as soon as possible to improve therapeutic efficacy and prognosis.}, } @article {pmid37746004, year = {2023}, author = {Khan, AL}, title = {The phytomicrobiome: solving plant stress tolerance under climate change.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1219366}, pmid = {37746004}, issn = {1664-462X}, abstract = {With extraordinary global climate changes, increased episodes of extreme conditions result in continuous but complex interaction of environmental variables with plant life. Exploring natural phytomicrobiome species can provide a crucial resource of beneficial microbes that can improve plant growth and productivity through nutrient uptake, secondary metabolite production, and resistance against pathogenicity and abiotic stresses. The phytomicrobiome composition, diversity, and function strongly depend on the plant's genotype and climatic conditions. Currently, most studies have focused on elucidating microbial community abundance and diversity in the phytomicrobiome, covering bacterial communities. However, least is known about understanding the holistic phytomicrobiome composition and how they interact and function in stress conditions. This review identifies several gaps and essential questions that could enhance understanding of the complex interaction of microbiome, plant, and climate change. Utilizing eco-friendly approaches of naturally occurring synthetic microbial communities that enhance plant stress tolerance and leave fewer carbon-foot prints has been emphasized. However, understanding the mechanisms involved in stress signaling and responses by phytomicrobiome species under spatial and temporal climate changes is extremely important. Furthermore, the bacterial and fungal biome have been studied extensively, but the holistic interactome with archaea, viruses, oomycetes, protozoa, algae, and nematodes has seldom been studied. The inter-kingdom diversity, function, and potential role in improving environmental stress responses of plants are considerably important. In addition, much remains to be understood across organismal and ecosystem-level responses under dynamic and complex climate change conditions.}, } @article {pmid37745602, year = {2023}, author = {Crits-Christoph, A and Levy, JI and Pekar, JE and Goldstein, SA and Singh, R and Hensel, Z and Gangavarapu, K and Rogers, MB and Moshiri, N and Garry, RF and Holmes, EC and Koopmans, MPG and Lemey, P and Popescu, S and Rambaut, A and Robertson, DL and Suchard, MA and Wertheim, JO and Rasmussen, AL and Andersen, KG and Worobey, M and Débarre, F}, title = {Genetic tracing of market wildlife and viruses at the epicenter of the COVID-19 pandemic.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37745602}, support = {U19 AI135995/AI/NIAID NIH HHS/United States ; R01 AI153044/AI/NIAID NIH HHS/United States ; T15 LM011271/LM/NLM NIH HHS/United States ; T32 AI007244/AI/NIAID NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; U01 AI151812/AI/NIAID NIH HHS/United States ; R01 AI135992/AI/NIAID NIH HHS/United States ; }, abstract = {Zoonotic spillovers of viruses have occurred through the animal trade worldwide. The start of the COVID-19 pandemic was traced epidemiologically to the Huanan Wholesale Seafood Market, the site with the most reported wildlife vendors in the city of Wuhan, China. Here, we analyze publicly available qPCR and sequencing data from environmental samples collected in the Huanan market in early 2020. We demonstrate that the SARS-CoV-2 genetic diversity linked to this market is consistent with market emergence, and find increased SARS-CoV-2 positivity near and within a particular wildlife stall. We identify wildlife DNA in all SARS-CoV-2 positive samples from this stall. This includes species such as civets, bamboo rats, porcupines, hedgehogs, and one species, raccoon dogs, known to be capable of SARS-CoV-2 transmission. We also detect other animal viruses that infect raccoon dogs, civets, and bamboo rats. Combining metagenomic and phylogenetic approaches, we recover genotypes of market animals and compare them to those from other markets. This analysis provides the genetic basis for a short list of potential intermediate hosts of SARS-CoV-2 to prioritize for retrospective serological testing and viral sampling.}, } @article {pmid37745216, year = {2023}, author = {Wang, J and Chen, Y and Li, M and Xia, S and Zhao, K and Fan, H and Ni, J and Sun, W and Jia, X and Lai, S}, title = {The effects of differential feeding on ileum development, digestive ability and health status of newborn calves.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1255122}, pmid = {37745216}, issn = {2297-1769}, abstract = {Pre-weaning is the most important period for the growth and development of calves. Intestinal morphology, microbial community and immunity are initially constructed at this stage, and even have a lifelong impact on calves. Early feeding patterns have a significant impact on gastrointestinal development and microbial communities. This study mainly analyzed the effects of three feeding methods on the gastrointestinal development of calves, and provided a theoretical basis for further improving the feeding mode of calves. it is very important to develop a suitable feeding mode. In this study, we selected nine newborn healthy Holstein bull calves were randomly selected and divided into three groups (n = 3), which were fed with starter + hay + milk (SH group), starter + milk (SF group), total mixed ration + milk (TMR group). After 80 days of feeding Feeding to 80 days of age after, the ileum contents and blood samples were collected, and the differences were compared and analyzed by metagenomic analysis and serum metabolomics analysis. Results show that compared with the other two groups, the intestinal epithelium of the SH group was more complete and the goblet cells developed better. The feeding method of SH group was more conducive to the development of calves, with higher daily gain and no pathological inflammatory reaction. The intestinal microbial community was more conducive to digestion and absorption, and the immunity was stronger. These findings are helpful for us to explore better calf feeding patterns. In the next step, we will set up more biological replicates to study the deep-seated reasons for the differences in the development of pre-weaning calves. At the same time, the new discoveries of neuro microbiology broaden our horizons and are the focus of our future attention.}, } @article {pmid37745000, year = {2023}, author = {Qian, X and Wu, Y and Zuo, X and Peng, X and Guo, Y and Yang, R and Zhang, X and Cui, Y}, title = {mStrain: strain-level identification of Yersinia pestis using metagenomic data.}, journal = {Bioinformatics advances}, volume = {3}, number = {1}, pages = {vbad115}, pmid = {37745000}, issn = {2635-0041}, abstract = {MOTIVATION: High-resolution target pathogen detection using metagenomic sequencing data represents a major challenge due to the low concentration of target pathogens in samples. We introduced mStrain, a novel Yesinia pestis strain/lineage-level identification tool that utilizes metagenomic data. mStrain successfully identified Y. pestis at the strain/lineage level by extracting sufficient information regarding single-nucleotide polymorphisms (SNPs), which can therefore be an effective tool for identification and source tracking of Y. pestis based on metagenomic data during a plague outbreak.

DEFINITION:  .

STRAIN-LEVEL IDENTIFICATION: Assigning the reads in the metagenomic sequencing data to an exactly known or most closely representative Y. pestis strain.

LINEAGE-LEVEL IDENTIFICATION: Assigning the reads in the metagenomic sequencing data to a specific lineage on the phylogenetic tree.

CANOSNPS: The unique and typical SNPs present in all representative strains.

ANCESTOR/DERIVED STATE: An SNP is defined as the ancestor state when consistent with the allele of Yersinia pseudotuberculosis strain IP32953; otherwise, the SNP is defined as the derived state.

The code for running mStrain, the test dataset, and instructions for running the code can be found at the following GitHub repository: https://github.com/xwqian1123/mStrain.}, } @article {pmid37744933, year = {2023}, author = {Chhimwal, J and Anand, P and Mehta, P and Swarnkar, MK and Patial, V and Pandey, R and Padwad, Y}, title = {Metagenomic signatures reveal the key role of phloretin in amelioration of gut dysbiosis attributed to metabolic dysfunction-associated fatty liver disease by time-dependent modulation of gut microbiome.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1210517}, pmid = {37744933}, issn = {1664-302X}, abstract = {The importance of gut-liver axis in the pathophysiology of metabolic dysfunction-associated fatty liver disease (MAFLD) is being investigated more closely in recent times. However, the inevitable changes in gut microbiota during progression of the disease merits closer look. The present work intends to assess the time-dependent gut dysbiosis in MAFLD, its implications in disease progression and role of plant-derived prebiotics in its attenuation. Male C57BL/6J mice were given western diet (WD) for up to 16 weeks and phloretin was administered orally. The fecal samples of mice were collected every fourth week for 16 weeks. The animals were sacrificed at the end of the study and biochemical and histological analyses were performed. Further, 16S rRNA amplicon sequencing analysis was performed to investigate longitudinal modification of gut microbiome at different time points. Findings of our study corroborate that phloretin alleviated the metabolic changes and mitigated circulating inflammatory cytokines levels. Phloretin treatment resists WD induced changes in microbial diversity of mice and decreased endotoxin content. Prolonged exposure of WD changed dynamics of gut microbiota abundance and distribution. Increased abundance of pathogenic taxa like Desulfovibrionaceae, Peptostreptococcus, Clostridium, and Terrisporobacter was noted. Phloretin treatment not only reversed this dysbiosis but also modulated taxonomic signatures of beneficial microbes like Ruminococcus, Lactobacillus, and Alloprevotella. Therefore, the potential of phloretin to restore gut eubiosis could be utilized as an intervention strategy for the prevention of MAFLD and related metabolic disorders.}, } @article {pmid37744910, year = {2023}, author = {Peng, K and Deng, J and Zou, N and Sun, X and Huang, W and Li, R and Yang, X}, title = {Emergence of the fourth mobile sulfonamide resistance gene sul4 in clinical Salmonella enterica.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1242369}, pmid = {37744910}, issn = {1664-302X}, abstract = {The fourth mobile sulfonamide resistance gene sul4 has been discovered in many metagenomic datasets. However, there is no reports of it in cultured bacteria. In this study, a sul4 positive clinical Salmonella enterica SC2020597 was obtained by conventional Salmonella isolation methods and characterized by species identification and antimicrobial susceptibility testing. Meanwhile, the genomic DNA was sequenced using both long-read and short-read methods. Following that, the complete genome was analyzed by bioinformatic methods. The sul4 gene in S. enterica SC2020597 differed from the sul4 identified in metagenomic data by one amino acid and could confer full resistance to sulfamethoxazole. Genetic location analysis showed that the sul4 in SC2020597 was carried by a complex chromosomally integrated hybrid plasmid. ISCR20-like was strongly associated with the mobilization of sul4 by core genetic context analysis. To the best of our knowledge, this is the first report of the emergence of sul4 in clinically cultured S. enterica. More important, the sul4 has the potential to spread to other bacteria with the help of mobile elements.}, } @article {pmid37744909, year = {2023}, author = {Angamarca, E and Castillejo, P and Tenea, GN}, title = {Microbiota and its antibiotic resistance profile in avocado Guatemalan fruits (Persea nubigena var. guatemalensis) sold at retail markets of Ibarra city, northern Ecuador.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1228079}, pmid = {37744909}, issn = {1664-302X}, abstract = {INTRODUCTION: Avocados are typically sold in unsanitary conditions at the retail markets in Ecuador, which can raise the risk of microbial contamination. These microorganisms could exhibit multi-antibiotic resistance (MAR), being a serious threat concern to human health. In this study, we aimed to evaluate the microbiota and its antibiotic resistance profile in avocado Guatemalan fruits (Persea nubigena var. guatemalensis), at ripe stage: immature, firm light green (ready to eat in 4 days), peel (AFPE) and pulp (AFPU), and mature intense green (ready to eat) peel (AMPE) and pulp (AMPU), to gain baseline information on the prevalence of MAR bacteria.

METHODS: Culture-independent (16S rRNA metagenomics) and culture-dependent approach (to detect specific indicator microorganisms) were used. Moreover, antibiotic susceptibility of selected target indicator bacteria was assessed providing information about the antibiotic resistance (AR) among the groups.

RESULTS: Based on 16S rRNA gene metagenomic analysis, over 99.78% of reads were classified as bacteria in all samples. Shannon diversity index varies from 1.22 to 2.22, with the highest bacterial population assigned to AFPE samples (1327 species). The highest microbial counts of indicator Staphylococcus spp. (STAPHY), Enterobacter spp. (ENT), and Listeria spp. (LIST), were detected in AMPE samples. Thirty percent of the selected STAPHYs, and 20.91% of Enterobacter (ENT) clones were resistant to various classes of antibiotics. The MAR index varies between 0.25 to 0.88 and was clone-, and fruit ripe stage-dependent.

CONCLUSIONS: The results indicated that ready to eat avocados contained detectable levels of MAR bacteria, including methicillin resistant (MR)-STAPHY, which may act as a potential vector for the spread of antibiotic resistance. To achieve the increase of the production and marketing of Fuerte cultivar in Ecuador, it is vitally important to consider valuable strategies to protect the fruits at the early ripe stage in future. Thus, it is crucial to set up efficient control measures and develop coordinated strategies to guarantee the microbiological quality of the food.}, } @article {pmid37744031, year = {2023}, author = {Zhao, ZS and Yang, LY and Li, FX and Cun, W and Wang, XY and Cao, CQ and Zhang, QL}, title = {Gut flora alterations among aquatic firefly Aquatica leii inhabiting various dissolved oxygen in fresh water.}, journal = {iScience}, volume = {26}, number = {10}, pages = {107809}, pmid = {37744031}, issn = {2589-0042}, abstract = {Knowledge about the impact of different dissolved oxygen (DO) on the composition and function of gut bacteria of aquatic insects is largely unknown. Herein, we constructed freshwater environments with different DOs (hypoxia: 2.50 ± 0.50, normoxia: 7.00 ± 0.50, and hyperoxia: 13.00 ± 0.50 mg/L) where aquatic firefly Aquatica leii larvae lived for three months. Their gut flora was analyzed using the combination of 16S rRNA amplicon sequencing and metagenomics. The results showed no difference in alpha diversity of the gut flora between A. leii inhabiting various DOs. However, the relative abundance of several bacterial lineages presented significant changes, such as Pseudomonas. In addition, bacterial genes with an altered relative abundance in response to various DOs were primarily related to metabolism. The alteration of these functions correlated with the DO change. This is the first to uncover structure of gut flora under various DOs in aquatic insect larvae.}, } @article {pmid37743884, year = {2023}, author = {Tran, DM and Nguyen, TH}, title = {Rice (Oryza sativa L.) cultivated in the Central Highlands of Vietnam: Dataset on the endophytic microbiome.}, journal = {Data in brief}, volume = {50}, number = {}, pages = {109551}, pmid = {37743884}, issn = {2352-3409}, abstract = {Rice (Oryza sativa L.) is the main annual crop cultivated in the Central Highlands region of Vietnam. Understanding the endophytic bacterial community of this plant, a new technique for sustainable production can be developed. In this work, a representative sample was obtained by combining rice (RVT variety) root samples collected from five different fields in Dray Sap Commune, Krong Ana District, Dak Lak Province, the Central Highlands of Vietnam. Using the Illumina MiSeq technology, the 16S rRNA metagenomics was applied to the sequencing amplicons library. The QIIME2 matched with the SILVA SSURef reference database was employed to analyze the taxonomic profile, and the PICRUSt2 and MetaCyc databases were used to predict the functional profile of rice endophytic prokaryotes. Results revealed that Enterobacterales was the most predominant class (57.7%) in the bacterial community, and biosynthesis was the primary function of the rice endophytic microbiome (75.95%). Raw sequences obtained in this work are available from the National Center for Biotechnology Information (NCBI) (Bioproject ID: PRJNA994482) and Mendeley Data [1]. Data in this work provide insight into the endophytic microbiome of rice (RVT variety) cultivated in the Central Highlands of Vietnam. These data are valuable for developing a new method for producing locally sustainable rice employing endophytic bacteria. This is the first report on the endophytic microbiome of rice cultivated in this region.}, } @article {pmid37743871, year = {2023}, author = {Liu, Y and Chan, MTV and Chan, FKL and Wu, WKK and Ng, SC and Zhang, L}, title = {Lower gut abundance of Eubacterium rectale is linked to COVID-19 mortality.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1249069}, pmid = {37743871}, issn = {2235-2988}, mesh = {Adult ; Humans ; Eubacterium ; *COVID-19 ; Butyrates ; *Gastrointestinal Microbiome ; Metagenome ; }, abstract = {INTRODUCTION: Emerging preclinical and clinical studies suggest that altered gut microbiome composition and functions are associated with coronavirus 2019 (COVID- 19) severity and its long-term complications. We hypothesize that COVID-19 outcome is associated with gut microbiome status in population-based settings.

METHODS: Gut metagenomic data of the adult population consisting of 2871 subjects from 16 countries were obtained from ExperimentHub through R, while the dynamic death data of COVID-19 patients between January 22, 2020 and December 8, 2020 in each country was acquired from Johns Hopkins Coronavirus Resource Center. An adjusted stable mortality rate (SMR) was used to represent these countries' mortality and correlated with the mean relative abundance (mRA) of healthy adult gut microbiome species.

RESULTS: After excluding bacterial species with low prevalence (prevalence <0.2 in the included countries), the β-diversity was significantly higher in the countries with high SMR when compared with those with median or low SMR (p <0.001). We then identified the mRA of two butyrate producers, Eubacterium rectale and Roseburia intestinalis, that were negatively correlated with SMR during the study period. And the reduction of these species was associated with severer COVID-19 manifestation.

CONCLUSION: Population-based microbiome signatures with the stable mortality rate of COVID-19 in different countries suggest that altered gut microbiome composition and functions are associated with mortality of COVID-19.}, } @article {pmid37743870, year = {2023}, author = {Palanisamy, V and Bosilevac, JM and Barkhouse, DA and Velez, SE and Chitlapilly Dass, S}, title = {Shotgun-metagenomics reveals a highly diverse and communal microbial network present in the drains of three beef-processing plants.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1240138}, pmid = {37743870}, issn = {2235-2988}, abstract = {BACKGROUND: Multi-species biofilms pose a problem in various environments, especially food-processing environments. The diversity of microorganisms in these biofilms plays a critical role in their integrity and protection against external biotic and abiotic factors. Compared to single-species biofilms, mixed-species biofilms are more resistant to various stresses, including antimicrobials like sanitizers. Therefore, understanding the microbiome composition and diversity in biofilms and their metabolic potential is a priority when developing intervention techniques to combat foodborne pathogens in food processing environments.

METHODS: This study aimed to describe and compare the microbiome profile of 75 drain biofilm samples obtained from five different locations (Hotscale, Hotbox, Cooler, Processing, & Grind room) of three beef-processing plants (Plant A, B & C) taken over two timepoints 2017-18 (T1) and 2021 (T2) by shotgun sequencing.

RESULTS: Core microbiome analysis found Pseudomonas, Psychrobacter, and Acinetobacter to be the top three prevalent genera among the plants and locations. Alpha diversity analysis demonstrated a high diversity of microbiome present in all the plants and locations across the time points. Functional analysis showed the high metabolic potential of the microbial community with abundance of genes in metabolism, cell-adhesion, motility, and quorum sensing. Moreover, Quaternary Ammonium Compound (QAC) resistance genes were also observed, this is significant as QAC sanitizers are commonly used in many food processing facilities. Multi-functional genes such as transposases, polymerases, permeases, flagellar proteins, and Mobile Genetic Elements (MGEs) were found suggesting these are dynamic microbial communities that work together to protect themselves against environmental stresses through multiple defense mechanisms.

CONCLUSION: This study provides a framework for understanding the collective microbial network spanning a beef processing system. The results can be used to develop intervention strategies to best control these highly communicative microbial networks.}, } @article {pmid37743869, year = {2023}, author = {Li, Y and Lei, J and Ren, Z and Ma, X}, title = {Case Report: Metagenomic next-generation sequencing assists in dynamic pathogen monitoring: powerful tool for progressing severe pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1230813}, pmid = {37743869}, issn = {2235-2988}, mesh = {Male ; Humans ; Adolescent ; *Influenza, Human/diagnosis ; *Methicillin-Resistant Staphylococcus aureus ; High-Throughput Nucleotide Sequencing ; *Pneumonia, Staphylococcal/diagnosis ; *Cross Infection ; }, abstract = {BACKGROUND: Severe community-acquired pneumonia (sCAP) is life-threatening and characterized by intensive care unit (ICU) admission and high mortality. And they are vulnerable to hospital-acquired infection. In such a severe condition, metagenomic next-generation sequencing (mNGS) outperforms for short turnaround time and broad detection spectrum.

CASE PRESENTATION: A 15-year-old male with severe influenza and methicillin-resistant Staphylococcus aureus (MRSA) pneumonia progressed rapidly, initially misdiagnosed as influenza co-infected with Aspergillus for misleading bronchoscopy manifestations. The turnaround time of mNGS is 13 h, which has the potential to expedite the clinical medication process. With the powerful support of mNGS and extracorporeal membrane oxygenation (ECMO), anti-infective therapy was adjusted accordingly, and vital signs gradually stabilized. After tortuous treatment and unremitting efforts, the patient recovered well.

CONCLUSIONS: Rapid mNGS applications, timely medication adjustments, strong ECMO support and active family compliance contribute to this miracle of life. False-negative or false-positive results are alarming, anti-infective medications should be adjusted after a comprehensive review of physical status and other indicators.}, } @article {pmid37743240, year = {2023}, author = {Ramachandran, PS and Williamson, DA}, title = {The transformative potential of metagenomics in microbiology: advancements and implications.}, journal = {Internal medicine journal}, volume = {53}, number = {9}, pages = {1520-1523}, doi = {10.1111/imj.16228}, pmid = {37743240}, issn = {1445-5994}, mesh = {*Metagenomics ; *Microbiology ; }, } @article {pmid37742984, year = {2023}, author = {Xu, K and Liu, X and Pang, L and Yue, Y and Chatzisymeon, E and Yang, P}, title = {Response behavior of antibiotic resistance genes and human pathogens to slope gradient and position: An environmental risk analysis in sloping cultivated land.}, journal = {The Science of the total environment}, volume = {905}, number = {}, pages = {166994}, doi = {10.1016/j.scitotenv.2023.166994}, pmid = {37742984}, issn = {1879-1026}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Soil/chemistry ; Risk Assessment ; Nitrogen ; Soil Microbiology ; }, abstract = {Soils, especially in farmlands, are key media for the transmission of antibiotic resistance genes (ARGs) and their hosts from the environment to humans. Sloping farmland is an important agricultural resource, but there lack of studies on the fate and risk of ARGs in sloping land. Also, the behavior and drivers of ARGs in response to slope gradient and position are unclear. Here, metagenomics was used to investigate the profiles of ARGs, mobile genetic elements, and microbial communities in soils from lands of five slope gradients (5°, 10°, 15°, 20°, and 25°) with two slope positions (uphill and downhill). Results showed that while the abundance (except 15°) and diversity (except 20°) of ARGs increased as the slope gradient increased, the diversity of ARGs with health risk, especially the high-risk ones, decreased. For slope positions, abundant and diverse ARGs were more likely to accumulate at downhill. Furthermore, 52 bacterial genera and 12 human pathogenic bacteria (HPB) species were identified as the potential hosts for ARGs with high risk, and abundant HPB species were also detected in the soils with low gradients at downhill. Moreover, the structural equation model analysis revealed that the slope gradient and the slope position have both direct and indirect effects on the abundance of ARGs. Further correlation analysis revealed that the slope gradient has a positive effect (p < 0.05) on nitrite nitrogen in the soils. Also, the slope position has a negative effect (p < 0.05) on total phosphorus and microbial nitrogen, while positively affected (p < 0.05) on particulate nitrogen and microbial carbon, which were the key factors driving the behavior of ARGs. Overall, this study provided comprehensive information on ARGs with health risks and their potential pathogenic hosts in sloping farmland. It can be important for controlling antibiotic resistance transmission and be consistent with the One Health framework.}, } @article {pmid37742860, year = {2023}, author = {Shan, X and Liu, C and Song, L and Huan, H and Chen, H}, title = {Risk characteristics of resistome coalescence in irrigated soils and effect of natural storage of irrigation materials on risk mitigation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {338}, number = {}, pages = {122575}, doi = {10.1016/j.envpol.2023.122575}, pmid = {37742860}, issn = {1873-6424}, mesh = {*Soil ; *Genes, Bacterial ; Manure/microbiology ; Fertilizers ; Soil Microbiology ; Anti-Bacterial Agents ; }, abstract = {Irrigation and fertilization are the routinely agricultural practices but also cause resistome coalescence, by which the entire microbiomes from irrigation materials invade soil microbial community, to transfer antibiotic resistance genes (ARGs) in the coalesced soils. Although studies have reported the effect of irrigation or fertilization on the prevalence and spread of ARGs in soils, risk characteristics of resistome coalescence in irrigation system remain to be demonstrated and few has shown whether natural storage of irrigation materials will reduce resistance risks. To fill the gaps, two microscopic experiments were conducted for deeply exploring resistance risks in the soils irrigated with wastewater and manure fertilizer from a perspective of community coalescence by metagenomic analysis, and to reveal the effect of natural storage of irrigation materials on the reduction of resistance risks in the coalesced soils. Results showed irrigation and coalescence significantly increased the abundance and diversity of ARGs in the soils, and introduced some emerging resistance genes into the coalesced community, including mcr-type, tetX, qacB, and an array of genes conferring resistance to carbapenem. Procrustes analysis demonstrated microbial community was significantly correlated with the ARGs in coalesced soils, and variance partitioning analysis quantified its dominant role on shaping resistome profile in the environment. Besides ARGs, abundant and diverse mobile genetic elements (MGEs) were also identified in the coalesced soils and co-existed on the ARG-carrying contigs, implying potential transfer risk of ARGs in the irrigation system. Further, the analysis of metagenome-assembled genomes (MAGs) confirmed the risk by recovering 358 ARGs-carrying MAGs and identifying the resistant bacteria that co-carried multiple ARGs and MGEs. As expected, the natural storage of irrigation water and manure fertilizer reduced about 27%-54% of ARGs, MGEs and virulence factors in the coalesced soils, thus caused the soils to move towards lower resistance risks to a certain extent.}, } @article {pmid37742563, year = {2023}, author = {Li, H and Tan, L and Xu, Y and Zheng, X}, title = {Metagenomics insights into the performance and mechanism of soil infiltration systems on removing antibiotic resistance genes in rural sewage.}, journal = {Journal of environmental management}, volume = {346}, number = {}, pages = {118981}, doi = {10.1016/j.jenvman.2023.118981}, pmid = {37742563}, issn = {1095-8630}, abstract = {The removal of antibiotic resistance genes (ARGs) in sewage is of great concern, but advanced sewage treatment technologies are not suitable for rural areas, so the multi-layer soil infiltration system (MSL) has been developed for rural sewage treatment. However, little is known about the performance and function of MSL in the treatment of ARGs in rural sewage. Here, we optimized the matrix composition and structure of MSL and explored the efficacy and mechanism of MSL systems for ARG removal under different hydraulic conditions. The ARGs removal rate of MSL ranged from 41.51% to 99.67%, in which MSL with the middle hydraulic load, high pollution load, and continuous inflowing conditions showed the best removal performance. In addition, this system can operate stably and resist the temperature fluctuation, which showed an equivalent removal rate of ARGs in warm and cold seasons, amounting to 69.0%. The structural equation model revealed that microorganisms in sewage could significantly affect ARG removal (path coefficient = 0.91), probably owing to their interspecies competition. As for the internal system, the reduction of ARGs was mainly driven by microorganisms in the system matrix (path coefficient = 0.685), especially soil-mixture-block (SMB) microorganisms. The physicochemical factors of the matrix indirectly reduce ARGs by affecting the microorganisms that adhere to the matrices. Note that the pairwise alignment of nucleotide analysis demonstrated that the system matrix, especially biochar in the SMB, adsorbed ARGs and their hosts from the sewage, and in turn eliminated them by inhibiting the spread and colonization of hosts, thereby reducing the abundance of ARGs. Collectively, this study provides a deeper insight into the removal of ARGs from rural sewage by MSL, which can help improve sewage treatment technologies.}, } @article {pmid37741805, year = {2023}, author = {Wicaksono, WA and Cernava, T and Wassermann, B and Abdelfattah, A and Soto-Giron, MJ and Toledo, GV and Virtanen, SM and Knip, M and Hyöty, H and Berg, G}, title = {The edible plant microbiome: evidence for the occurrence of fruit and vegetable bacteria in the human gut.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2258565}, pmid = {37741805}, issn = {1949-0984}, mesh = {Humans ; Vegetables ; Plants, Edible ; Fruit ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Bacteria/genetics ; }, abstract = {Diversity of the gut microbiota is crucial for human health. However, whether fruit and vegetable associated bacteria contribute to overall gut bacterial diversity is still unknown. We reconstructed metagenome-assembled genomes from 156 fruit and vegetable metagenomes to investigate the prevalence of associated bacteria in 2,426 publicly available gut metagenomes. The microbiomes of fresh fruits and vegetables and the human gut are represented by members in common such as Enterobacterales, Burkholderiales, and Lactobacillales. Exposure to bacteria via fruit and vegetable consumption potentially has a beneficial impact on the functional diversity of gut microbiota particularly due to the presence of putative health-promoting genes for the production of vitamin and short-chain fatty acids. In the human gut, they were consistently present, although at a low abundance, approx. 2.2%. Host age, vegetable consumption frequency, and the diversity of plants consumed were drivers favoring a higher proportion. Overall, these results provide one of the primary links between the human microbiome and the environmental microbiome. This study revealed evidence that fruit and vegetable-derived microbes could be found in the human gut and contribute to gut microbiome diversity.}, } @article {pmid37741505, year = {2023}, author = {Shahila Ismail, KI and Kumar, CVS and Aneesha, U and Syama, PS and Sajini, KP}, title = {Comparative analysis of gut bacteria of silkworm Bombyx mori L. on exposure to temperature through 16S rRNA high throughput metagenomic sequencing.}, journal = {Journal of invertebrate pathology}, volume = {201}, number = {}, pages = {107992}, doi = {10.1016/j.jip.2023.107992}, pmid = {37741505}, issn = {1096-0805}, mesh = {Animals ; *Bombyx ; RNA, Ribosomal, 16S/genetics ; Temperature ; Bacteria ; Hot Temperature ; Larva ; }, abstract = {Global warming is one of the serious threats that adversely affects the development and reproduction of silkworms. The ideal temperature for silkworms to carryout normal life activities is 20-30 °C. Certain bivoltine silkworms that are raised in tropical regions are thermotolerant. But, prolonged exposure to high temperatures may be fatal. In the present study, fifth instar larvae of bivoltine silkworm were exposed to heat shock at 40 ± 2 °C for a short period of one hour per day to examine the changes in the gut microflora. The study used high throughput sequencing to evaluate the impact of intestinal microbes of silkworms in response to high temperature. The findings demonstrated that elevated temperature has a negative impact on the intestinal microbes of silkworm compared to the control which were reared under the optimum temperature (25 ± 3° C). Four hundred and fifty eight (458) species of microbes were reported in the control group whereas only 434 species were reported in the temperature exposed group. The digestive process of silkworms may also be impaired by heat shock due to their effect on digestive enzymes. So, the results indicated that heat shock has an impact on the intestinal microflora of silkworms that control the activity of associated digestive enzymes which affects the digestion and nutritional intake, eventually impacting the growth and development of silkworm larvae and cocoons produced. The morphometric parameters of silkworm larvae and cocoons also showed a considerable drop when exposed to heat shock.}, } @article {pmid37741393, year = {2024}, author = {Welman-Purchase, MD and Castillo, J and Gomez-Arias, A and Matu, A and Hansen, RN}, title = {First insight into the natural biodegradation of cyanide in a gold tailings environment enriched in cyanide compounds.}, journal = {The Science of the total environment}, volume = {906}, number = {}, pages = {167174}, doi = {10.1016/j.scitotenv.2023.167174}, pmid = {37741393}, issn = {1879-1026}, mesh = {*Cyanides/chemistry ; *Gold/chemistry ; Biodegradation, Environmental ; South Africa ; }, abstract = {The disposal of mining wastes that contain cyanide are dumped in tailings from gold extraction is a public concern in mining countries such as South Africa. Many studies have shown the potential of microorganisms to degrade cyanide. However, no in-situ exploration, in tailings contaminated with cyanide, of the capability of indigenous microorganisms to act as a natural barrier for cyanide attenuation has been performed. Here we aim to combine geochemical and metagenomics techniques to reveal the genomic machinery of indigenous bacteria to degrade cyanide in gold tailings. Indigenous bacteria (i.e., Alicyclobacillus, Sulfobacillus, Acinetobacter, Achromobacter, and among others) pose the genomic machinery to trigger hydrolytic cyanide degradation using enzymes such as nitrilase, nitrile hydratase (Nhase) and thiocyanate. It seems that the lack of nitrogen sources induces the use of cyanide, which would contribute to its natural attenuation in the gold tailings. Therefore, the bacteria identified could represent the first barrier for the detoxification and degradation of cyanide in the outermost layer of the tailings.}, } @article {pmid37741388, year = {2023}, author = {Zhou, T and Xiang, Y and Liu, S and Ma, H and Shao, Z and He, Q and Chai, H}, title = {Microbial community dynamics and metagenomics reveal the potential role of unconventional functional microorganisms in nitrogen and phosphorus removal biofilm system.}, journal = {The Science of the total environment}, volume = {905}, number = {}, pages = {167194}, doi = {10.1016/j.scitotenv.2023.167194}, pmid = {37741388}, issn = {1879-1026}, mesh = {*Ammonia/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; Bacteria/genetics/metabolism ; Archaea/metabolism ; Nitrification ; *Microbiota ; }, abstract = {The conventional functional microorganisms for nitrogen and phosphorus removal, such as Nitrosomonas, Nitrobacter, Nitrospira and Candidatus Accumulibacter, were hotspots in past research. However, the role of diverse unconventional functional microorganisms was neglected. In this study, a biofilm system was developed to explore the potential role of unconventional functional microorganisms in nutrients removal. According to the results of microbial community dynamics and metagenomics, complete ammonia oxidizing (comammox) bacteria was 20 times more abundant than ammonia-oxidizing bacteria (AOB) at day 121 and its abundance of amoA gene was almost the same as AOB. Although Nitrospira dominated the nitrite-oxidizing bacteria (NOB), diverse unconventional nxrB-containing microorganisms, particularly Chloroflexi, also significantly contributed to the nitrite oxidation. Binning analysis showed that Myxococcota-affiliated Haliangium had the necessary genes owns by phosphorus-accumulating organisms (PAO) and was likely to be the primary PAO since its abundance (6.38 %) was much higher than other conventional PAO (0.70 %). Comparing metagenome-assembled genomes of comammox bacteria with AOB and ammonia-oxidizing archaea (AOA), it possessed potential metabolic versatility in hydrogen and phosphorus, which may be the primary reason for the positive effect of the alternating anaerobic and aerobic conditions on the enrichment of comammox bacteria. Collectively, our findings broaden the understanding on the microbial mechanism of nitrogen and phosphorus removal in biofilm system.}, } @article {pmid37741262, year = {2023}, author = {Robinson, SL}, title = {Structure-guided metagenome mining to tap microbial functional diversity.}, journal = {Current opinion in microbiology}, volume = {76}, number = {}, pages = {102382}, doi = {10.1016/j.mib.2023.102382}, pmid = {37741262}, issn = {1879-0364}, mesh = {Humans ; *Metagenome ; *Microbiota/genetics ; Soil Microbiology ; Phenotype ; Drug Resistance, Microbial/genetics ; }, abstract = {Scientists now have access to millions of accurate three-dimensional (3D) models of protein structures. How do we leverage 3D structural models to learn about microbial functions encoded in metagenomes? Here, we review recent developments using protein structural features to mine metagenomes from diverse environments ranging from the human gut to soil and ocean viromes. We compare 3D protein structural methods to characterize antibiotic resistance phenotypes, nutrient cycling, and host-drug-microbe interactions. Broadly, we encourage the scientific community to look beyond global sequence and structure alignments by considering fine-grained descriptors such as distance to ligand, active site, and tertiary interactions between amino acid residues scaling to microbiomes. Finally, we highlight structure-inspired approaches to chart new areas of microbial protein-coding sequence space.}, } @article {pmid37741170, year = {2023}, author = {Son, H and Moon, J and Ha, EJ and Kim, N and Kim, EY and Lee, HS and Koh, EJ and Phi, JH and Park, CK and Kim, JE and Kim, SK and Lee, ST and Jung, KH and Lee, SK and Cho, WS and Chu, K}, title = {Identification of bacterial pathogens in brain abscesses by metagenomic approach using nanopore 16S amplicon sequencing.}, journal = {Diagnostic microbiology and infectious disease}, volume = {107}, number = {4}, pages = {116041}, doi = {10.1016/j.diagmicrobio.2023.116041}, pmid = {37741170}, issn = {1879-0070}, mesh = {Humans ; *Nanopore Sequencing ; RNA, Ribosomal, 16S/genetics ; *Nanopores ; *Coinfection ; DNA, Bacterial/genetics/analysis ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; *Brain Abscess/diagnosis/microbiology ; }, abstract = {Brain abscess is medically challenging. In this study, we applied nanopore sequencing for 16S rRNA analysis and investigated its efficacy and diagnostic value for patients with brain abscesses. Genomic DNA was extracted from the pus samples (n = 27) of brain abscess, and 16S rRNA genes were amplified by PCR. Sequencing libraries were generated using a rapid barcoding kit, and the generated reads were analyzed using the EPI2ME16S workflow. A conventional culture study was performed. More sensitive identification of pathogens was made by 16S sequencing, faster than the culture study. The proportion of anaerobic bacteria identified by 16S sequencing was higher (75%) than that obtained by culturing (32%). Polymicrobial infections were identified in 10 cases (40%) by 16S sequencing, while the culture study identified multiple bacteria in only 2 cases (8%). 16S sequencing was useful for identifying the composition of polymicrobial infections, including rare pathogens, and for the initial diagnosis of space-occupying lesions.}, } @article {pmid37740386, year = {2023}, author = {Adams, JN and Escalona, M and Marimuthu, MPA and Fairbairn, CW and Beraut, E and Seligmann, W and Nguyen, O and Chumchim, N and Stajich, JE}, title = {The reference genome assembly of the bright cobblestone lichen, Acarospora socialis.}, journal = {The Journal of heredity}, volume = {114}, number = {6}, pages = {707-714}, pmid = {37740386}, issn = {1465-7333}, support = {S10 OD016290/OD/NIH HHS/United States ; S10 OD018174/OD/NIH HHS/United States ; S10 OD010786/OD/NIH HHS/United States ; }, mesh = {*Lichens/genetics ; Molecular Sequence Annotation ; Genomics ; *Ascomycota/genetics ; }, abstract = {Acarospora socialis, the bright cobblestone lichen, is commonly found in southwestern North America. This charismatic yellow lichen is a species of key ecological significance as it is often a pioneer species in new environments. Despite their ecological importance virtually no research has been conducted on the genomics of A. socialis. To address this, we used long-read sequencing to generate the first high-quality draft genome of A. socialis. Lichen thallus tissue was collected from Pinkham Canyon in Joshua Tree National Park, California and deposited in the UC Riverside herbarium under accession #295874. The de novo assembly of the mycobiont partner of the lichen was generated from Pacific Biosciences HiFi long reads and Dovetail Omni-C chromatin capture data. After removing algal and bacterial contigs, the fungal genome was approximately 31.2 Mb consisting of 38 scaffolds with contig and scaffold N50 of 2.4 Mb. The BUSCO completeness score of the assembled genome was 97.5% using the Ascomycota gene set. Information on the genome of A. socialis is important for California conservation purposes given that this lichen is threatened in some places locally by wildfires due to climate change. This reference genome will be used for understanding the genetic diversity, population genomics, and comparative genomics of A. socialis species. Genomic resources for this species will support population and landscape genomics investigations, exploring the use of A. socialis as a bioindicator species for climate change, and in studies of adaptation by comparing populations that occur across aridity gradients in California.}, } @article {pmid37740058, year = {2023}, author = {Komori, E and Kato-Kogoe, N and Imai, Y and Sakaguchi, S and Taniguchi, K and Omori, M and Ohmichi, M and Nakamura, S and Nakano, T and Lee, SW and Ueno, T}, title = {Changes in salivary microbiota due to gastric cancer resection and its relation to gastric fluid microbiota.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15863}, pmid = {37740058}, issn = {2045-2322}, mesh = {Humans ; *Stomach Neoplasms/surgery ; RNA, Ribosomal, 16S/genetics ; Gastrectomy ; *Microbiota/genetics ; }, abstract = {Gastric cancer is one of the leading causes of death worldwide, and resections are performed to cure the disease. We have previously reported the changes in the gastric microbiota after gastric cancer resection, which may be associated with the oral microbiota; however, the changes in the oral microbiota remain uncharacterized. This study aimed to characterize the changes in the salivary microbiota caused by gastric cancer resection and to evaluate their association with the gastric fluid microbiota. Saliva and gastric fluid samples were collected from 63 patients who underwent gastrectomy before and after surgery, and a 16S rRNA metagenomic analysis was performed to compare the microbiota composition. The number of bacterial species in the salivary microbiota decreased, and the bacterial composition changed after the resection of gastric cancer. In addition, we identified several bacterial genera that varied significantly in the salivary microbiota, some of which also showed similar changes in the gastric fluid microbiota. These findings indicate that changes in the gastric environment affect the oral microbiota, emphasizing the close association between the oral and gastric fluid microbiota. Our study signifies the importance of focusing on the oral microbiota in the perioperative period of gastrectomy in patients with gastric cancer.}, } @article {pmid37739268, year = {2023}, author = {Ge, F and Guo, R and Liang, Y and Chen, Y and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M}, title = {Characterization and genomic analysis of Stutzerimonas stutzeri phage vB_PstS_ZQG1, representing a novel viral genus.}, journal = {Virus research}, volume = {336}, number = {}, pages = {199226}, pmid = {37739268}, issn = {1872-7492}, mesh = {*Bacteriophages ; Phylogeny ; Sequence Analysis, DNA ; Genome, Viral ; Myoviridae ; Genomics ; Nucleotides ; }, abstract = {Stutzerimonas stutzeri is an opportunistic pathogenic bacterium belonging to the Gammaproteobacteria, exhibiting wide distribution in the environment and playing significant ecological roles such as nitrogen fixation or pollutant degradation. Despite its ecological importance, only two S. stutzeri phages have been isolated to date. Here, a novel S. stutzeri phage, vB_PstS_ZQG1, was isolated from the surface seawater of Qingdao, China. Transmission electron microscopy analysis indicates that vB_PstS_ZQG1 has a morphology characterized by a long non-contractile tail. The genomic sequence of vB_PstS_ZQG1 contains a linear, double-strand 61,790-bp with the G+C content of 53.24% and encodes 90 putative open reading frames. Two auxiliary metabolic genes encoding TolA protein and nucleotide pyrophosphohydrolase were identified, which are likely involved in host adaptation and phage reproduction. Phylogenetic and comparative genomic analyses demonstrated that vB_PstS_ZQG1 exhibits low similarity with previously isolated phages or uncultured viruses (average nucleotide identity values range from 21.7 to 29.4), suggesting that it represents a novel viral genus by itself, here named as Fuevirus. Biogeographic analysis showed that vB_PstS_ZQG1 was only detected in epipelagic and mesopelagic zone with low abundance. In summary, our findings of the phage vB_PstS_ZQG1 will provide helpful insights for further research on the interactions between S. stutzeri phages and their hosts, and contribute to discovering unknown viral sequences in the metagenomic database.}, } @article {pmid37738973, year = {2023}, author = {Liu, NN and Yi, CX and Wei, LQ and Zhou, JA and Jiang, T and Hu, CC and Wang, L and Wang, YY and Zou, Y and Zhao, YK and Zhang, LL and Nie, YT and Zhu, YJ and Yi, XY and Zeng, LB and Li, JQ and Huang, XT and Ji, HB and Kozlakidis, Z and Zhong, L and Heeschen, C and Zheng, XQ and Chen, C and Zhang, P and Wang, H}, title = {The intratumor mycobiome promotes lung cancer progression via myeloid-derived suppressor cells.}, journal = {Cancer cell}, volume = {41}, number = {11}, pages = {1927-1944.e9}, doi = {10.1016/j.ccell.2023.08.012}, pmid = {37738973}, issn = {1878-3686}, mesh = {Humans ; Animals ; Mice ; *Lung Neoplasms/genetics ; *Myeloid-Derived Suppressor Cells ; *Mycobiome ; CD8-Positive T-Lymphocytes ; Lung ; }, abstract = {Although polymorphic microbiomes have emerged as hallmarks of cancer, far less is known about the role of the intratumor mycobiome as living microorganisms in cancer progression. Here, using fungi-enriched DNA extraction and deep shotgun metagenomic sequencing, we have identified enriched tumor-resident Aspergillus sydowii in patients with lung adenocarcinoma (LUAD). By three different syngeneic lung cancer mice models, we find that A. sydowii promotes lung tumor progression via IL-1β-mediated expansion and activation of MDSCs, resulting in suppressed activity of cytotoxic T lymphocyte cells and accumulation of PD-1[+] CD8[+] T cells. This is mediated by IL-1β secretion via β-glucan/Dectin-1/CARD9 pathway. Analysis of human samples confirms that enriched A. sydowii is associated with immunosuppression and poor patient outcome. Our findings suggest that intratumor mycobiome, albeit at low biomass, promotes lung cancer progression and could be targeted at the strain level to improve patients with LUAD outcome.}, } @article {pmid37738943, year = {2023}, author = {Zhang, J and Xu, Z and Chu, W and Ju, F and Jin, W and Li, P and Xiao, R}, title = {Residual chlorine persistently changes antibiotic resistance gene composition and increases the risk of antibiotic resistance in sewer systems.}, journal = {Water research}, volume = {245}, number = {}, pages = {120635}, doi = {10.1016/j.watres.2023.120635}, pmid = {37738943}, issn = {1879-2448}, abstract = {During the COVID-19 pandemic, excessive amounts of disinfectants and their transformation products entered sewer systems worldwide, which was an extremely rare occurrence before. The stress of residual chlorine and disinfection by-products is not only likely to promote the spread of antibiotic resistance genes (ARGs), but also leads to the enrichment of chlorine-resistant bacteria that may also be resistant to antibiotics. Therefore, the potential impact of such discharge on ARG composition should be studied and the health risks should be assessed. Thus, this study combined high-throughput 16S rRNA gene amplicon sequencing and metagenomic analysis with long-term batch tests that involved two stages of stress and recovery to comprehensively evaluate the impact of residual chlorine on the microbial community and ARG compositions in sewer systems. The tests demonstrated that the disturbance of the microbial community structure by residual chlorine was reversible, but the change in ARG composition was persistent. This study found that vertical propagation and horizontal gene transfer jointly drove ARG composition succession in the biofilm, while the driving force was mainly horizontal gene transfer in the sediment. In this process, the biocide resistance gene (BRG) subtype chtR played an important role in promoting co-selection with ARGs through plasmids and integrative and conjugative elements. Moreover, it was further shown that the addition of sodium hypochlorite increased the risk of ARGs to human health, even after discontinuation of dosing, signifying that the impact was persistent. In general, this study strengthens the co-selection theory of ARGs and BRGs, and calls for improved disinfection strategies and more environmentally friendly disinfectants.}, } @article {pmid37738938, year = {2023}, author = {Zhuo, T and He, L and Chai, B and Zhou, S and Wan, Q and Lei, X and Zhou, Z and Chen, B}, title = {Micro-pressure promotes endogenous phosphorus release in a deep reservoir by favouring microbial phosphate mineralisation and solubilisation coupled with sulphate reduction.}, journal = {Water research}, volume = {245}, number = {}, pages = {120647}, doi = {10.1016/j.watres.2023.120647}, pmid = {37738938}, issn = {1879-2448}, mesh = {*Phosphorus/analysis ; Phosphates/analysis ; *Water Pollutants, Chemical/analysis ; Geologic Sediments/analysis ; Environmental Monitoring ; Water/analysis ; Sulfates ; }, abstract = {Deep reservoirs vary in their hydrostatic pressure owing to artificial water level control. The potential migration of phosphorus (P) in reservoir sediments raises the risk of harmful algal blooms. To ascertain the mechanisms of endogenous P release in reservoirs, we characterised aquatic microbial communities associated with coupled iron (Fe), P and sulphur (S) cycling at the sediment-water interface. The responses of microbial communities to hydrostatic pressures of 0.2-0.7 mega pascals (MPa; that is, micro-pressures) were investigated through a 30-day simulation experiment. Our findings unravelled a potential mechanism that micro-pressure enhanced the solubilisation of Fe/aluminium (Al)-bound P caused by microbially-driven sulphate reduction, leading to endogenous P release in the deep reservoir. Although the vertical distribution of labile Fe was not affected by pressure changes, we did observe Fe resupply at sediment depths of 2-5 cm. Metagenomic analysis revealed increased abundances of functional genes for P mineralisation (phoD, phoA), P solubilisation (pqqC, ppx-gppA) and sulphate reduction (cysD, cysC) in sediments subjected to micro-pressure, which contrasted with the pattern of S oxidation gene (soxB). There was a tight connection between P and S cycling-related microbial communities, based on significant positive correlations between labile element (P and S) concentrations and functional gene (phoD, cysD) abundances. This provided strong support that Fe-P-S coupling processes were governed by micro-pressure through modulation of P and S cycling-related microbial functions. Key taxa involved in P and S cycling (for example, Bradyrhizobium, Methyloceanibacter) positively responded to micro-pressure and as such, indirectly drove P release from sediments by facilitating P mineralisation and solubilisation coupled with sulphate reduction.}, } @article {pmid37738905, year = {2023}, author = {Garg, R and Prasad, D}, title = {Carbon dots and their interactions with recognition molecules for enhanced nucleic acid detection.}, journal = {Biochemical and biophysical research communications}, volume = {680}, number = {}, pages = {93-107}, doi = {10.1016/j.bbrc.2023.09.033}, pmid = {37738905}, issn = {1090-2104}, mesh = {*Quantum Dots/chemistry ; Carbon/chemistry ; Optical Imaging/methods ; DNA ; Fluorescent Dyes/chemistry ; *Biosensing Techniques/methods ; }, abstract = {Carbon Dots (C-dots) have exceptional fluorescence and incident wavelength alteration capabilities because of their π-π* electron transitions between the surface-trapped charges. They have clear, considerate and cost-effective applications in the domain of bio-sensing, optical imaging, medical diagnostics, fluorescence chemotherapy, forensics, and environmentology. Advances in the production process of C-dots can change their optical and chemical characteristics, allowing them to interact with a variety of chemicals and ions that can be exploited for the DNA detection in point-of-care devices. In the current scenario of pathogenic disease prevention, metagenomics and industrial processes, alternative genetic material identification is critical. This review focuses on the existing carbon dots-based DNA detection technologies and their interactions with other components such as metallic salts, dyes, and biological chemicals based on their surface charge distribution (positive or negative) employed in the DNA diagnostic devices and biosensors with their operating mechanism regarding their target component. These intriguing scientific discoveries and technologies will be extensively examined to translate them into real-world solutions which will have a significant societal and economic impact on overall well-being and innovation.}, } @article {pmid37738757, year = {2023}, author = {Hui, C and Yu, Q and Liu, B and Zhu, M and Long, Y and Shen, D}, title = {Microbial contamination risk of landfilled waste with different ages.}, journal = {Waste management (New York, N.Y.)}, volume = {170}, number = {}, pages = {297-307}, doi = {10.1016/j.wasman.2023.09.021}, pmid = {37738757}, issn = {1879-2456}, abstract = {Landfills are reservoirs of antibiotic resistance genes (ARGs) and pathogens, and humans are exposed to these pollutants during extensive excavation of old landfills. However, the microbial contamination risk of landfilled waste with different ages has not been assessed. In this study, human bacterial pathogens (HBPs), ARGs, and virulence factors (VFs) were systematically determined using metagenomic analysis. Results showed that the abundance of HBPs, ARGs, and VFs increased with landfill age, the percentage of HBPs in refuse with deposit age of 10-12 years (Y10) was 23.75 ± 0.49%, which was higher than that in fresh refuse (Y0, 17.99 ± 0.14%) and refuse with deposit age of 5-6 years (Y5, 19.14 ± 0.15%), indicating that old refuse had higher microbial contamination risk than fresh refuse. Multidrug, macrolide, lincosamide, streptogramine, and tetracycline resistance genes were the primary ARGs, whereas lipooligosaccharides, type IV pili, and polar flagella were the dominant VFs in refuse. The HBPs showed a significant positive correlation with ARGs and VFs. Listeria monocytogenes, Salmonella enterica, Streptococcus pneumoniae, Acinetobacter baumannii, and Escherichia coli possibly possess both multiple ARGs and VFs and could be listed as high-risk HBPs in refuse. Mobile genetic elements, especially transposons, showed positive correlations with most ARGs and VFs, and they were identified as the primary factors accounting for the variations in ARGs and VFs. These findings will help understand the spread of ARGs and VFs in landfills and evaluate the potential risk of microbiological contamination in refuse of different landfill ages, thus providing guidance for preventing disease infection during landfill excavations.}, } @article {pmid37738590, year = {2023}, author = {Mallawaarachchi, V and Roach, MJ and Decewicz, P and Papudeshi, B and Giles, SK and Grigson, SR and Bouras, G and Hesse, RD and Inglis, LK and Hutton, ALK and Dinsdale, EA and Edwards, RA}, title = {Phables: from fragmented assemblies to high-quality bacteriophage genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {10}, pages = {}, pmid = {37738590}, issn = {1367-4811}, support = {RC2DK116713/DK/NIDDK NIH HHS/United States ; }, abstract = {MOTIVATION: Microbial communities have a profound impact on both human health and various environments. Viruses infecting bacteria, known as bacteriophages or phages, play a key role in modulating bacterial communities within environments. High-quality phage genome sequences are essential for advancing our understanding of phage biology, enabling comparative genomics studies and developing phage-based diagnostic tools. Most available viral identification tools consider individual sequences to determine whether they are of viral origin. As a result of challenges in viral assembly, fragmentation of genomes can occur, and existing tools may recover incomplete genome fragments. Therefore, the identification and characterization of novel phage genomes remain a challenge, leading to the need of improved approaches for phage genome recovery.

RESULTS: We introduce Phables, a new computational method to resolve phage genomes from fragmented viral metagenome assemblies. Phables identifies phage-like components in the assembly graph, models each component as a flow network, and uses graph algorithms and flow decomposition techniques to identify genomic paths. Experimental results of viral metagenomic samples obtained from different environments show that Phables recovers on average over 49% more high-quality phage genomes compared to existing viral identification tools. Furthermore, Phables can resolve variant phage genomes with over 99% average nucleotide identity, a distinction that existing tools are unable to make.

Phables is available on GitHub at https://github.com/Vini2/phables.}, } @article {pmid37738438, year = {2023}, author = {Khatun, MA and Hoque, MA and Koffas, M and Feng, Y}, title = {Reducing the virulence of Pseudomonas aeruginosa by using multiple quorum-quenching enzymes.}, journal = {Journal of industrial microbiology & biotechnology}, volume = {50}, number = {1}, pages = {}, pmid = {37738438}, issn = {1476-5535}, support = {15JC1400402//Science and Technology Commission of Shanghai Municipality/ ; }, mesh = {*Quorum Sensing ; Virulence ; *Pseudomonas aeruginosa/genetics ; Biofilms ; Virulence Factors ; Bacterial Proteins/genetics ; }, abstract = {UNLABELLED: The emergence of multidrug-resistant Pseudomonas aeruginosa in healthcare settings poses a tremendous challenge to traditional antibiotic therapy. Pseudomonas aeruginosa utilizes quorum sensing (QS) to coordinate the production of virulence factors and the formation of drug-resistant biofilms. QS is mediated by signal compounds produced by P. aeruginosa as well as signal molecules produced by other non-pseudomonad bacteria. A potential strategy to prevent bacterial pathogenicity is utilizing enzymes to interfere with QS. Here, we used AidC, a quorum-quenching (QQ) enzyme from Chryseobacterium sp. strain StRB126 that can effectively hydrolyze N-(3-oxododecanoyl) homoserine lactone (3OC12-HSL) and N-butanoyl-homoserine lactone (C4-HSL), the major signal molecules synthesized by P. aeruginosa. The exogenous addition of AidC to P. aeruginosa wild-type strain PAO1 cultures significantly reduced the total protease and elastase activities and the production of pyocyanin. In addition, the application of AidC resulted in thin and sparse biofilm formation. Later, we used a metagenomic-derived QQ enzyme, QQ-2, in combination with AidC to attenuate PAO1 virulence when the presence of a non-pseudomonad signal compound, autoinducer-2, aggravated it. These findings suggest that using a combined antimicrobial approach may lead to a more efficacious therapeutic intervention against P. aeruginosa PAO1 infection, as its behavior is modulated in the presence of intraspecies and interspecies signal compounds.

ONE-SENTENCE SUMMARY: In this work, the potential of dual enzymes was investigated to interfere with quorum sensing as a novel concept for reducing the virulence of P. aeruginosa, which is influenced by both intra species and interspecies communication.}, } @article {pmid37738420, year = {2023}, author = {Welgemoed, T and Duong, TA and Barnes, I and Stukenbrock, EH and Berger, DK}, title = {Population genomic analyses suggest recent dispersal events of the pathogen Cercospora zeina into East and Southern African maize cropping systems.}, journal = {G3 (Bethesda, Md.)}, volume = {13}, number = {11}, pages = {}, pmid = {37738420}, issn = {2160-1836}, mesh = {*Zea mays/genetics ; Phylogeny ; *Metagenomics ; South Africa ; }, abstract = {A serious factor hampering global maize production is gray leaf spot disease. Cercospora zeina is one of the causative pathogens, but population genomics analysis of C. zeina is lacking. We conducted whole-genome Illumina sequencing of a representative set of 30 C. zeina isolates from Kenya and Uganda (East Africa) and Zambia, Zimbabwe, and South Africa (Southern Africa). Selection of the diverse set was based on microsatellite data from a larger collection of the pathogen. Pangenome analysis of the C. zeina isolates was done by (1) de novo assembly of the reads with SPAdes, (2) annotation with BRAKER, and (3) protein clustering with OrthoFinder. A published long-read assembly of C. zeina (CMW25467) from Zambia was included and annotated using the same pipeline. This analysis revealed 790 non-shared accessory and 10,677 shared core orthogroups (genes) between the 31 isolates. Accessory gene content was largely shared between isolates from all countries, with a few genes unique to populations from Southern Africa (32) or East Africa (6). There was a significantly higher proportion of effector genes in the accessory secretome (44%) compared to the core secretome (24%). PCA, ADMIXTURE, and phylogenetic analysis using a neighbor-net network indicated a population structure with a geographical subdivision between the East African isolates and the Southern African isolates, although gene flow was also evident. The small pangenome and partial population differentiation indicated recent dispersal of C. zeina into Africa, possibly from 2 regional founder populations, followed by recurrent gene flow owing to widespread maize production across sub-Saharan Africa.}, } @article {pmid37738402, year = {2023}, author = {Cho, H and Qu, Y and Liu, C and Tang, B and Lyu, R and Lin, BM and Roach, J and Azcarate-Peril, MA and Aguiar Ribeiro, A and Love, MI and Divaris, K and Wu, D}, title = {Comprehensive evaluation of methods for differential expression analysis of metatranscriptomics data.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {5}, pages = {}, pmid = {37738402}, issn = {1477-4054}, support = {R03 DE028983/DE/NIDCR NIH HHS/United States ; U01 DE025046/DE/NIDCR NIH HHS/United States ; }, mesh = {Child ; Humans ; Child, Preschool ; *Benchmarking ; Biofilms ; Computer Simulation ; Lactic Acid ; *Stomatognathic Diseases ; }, abstract = {Understanding the function of the human microbiome is important but the development of statistical methods specifically for the microbial gene expression (i.e. metatranscriptomics) is in its infancy. Many currently employed differential expression analysis methods have been designed for different data types and have not been evaluated in metatranscriptomics settings. To address this gap, we undertook a comprehensive evaluation and benchmarking of 10 differential analysis methods for metatranscriptomics data. We used a combination of real and simulated data to evaluate performance (i.e. type I error, false discovery rate and sensitivity) of the following methods: log-normal (LN), logistic-beta (LB), MAST, DESeq2, metagenomeSeq, ANCOM-BC, LEfSe, ALDEx2, Kruskal-Wallis and two-part Kruskal-Wallis. The simulation was informed by supragingival biofilm microbiome data from 300 preschool-age children enrolled in a study of childhood dental disease (early childhood caries, ECC), whereas validations were sought in two additional datasets from the ECC study and an inflammatory bowel disease study. The LB test showed the highest sensitivity in both small and large samples and reasonably controlled type I error. Contrarily, MAST was hampered by inflated type I error. Upon application of the LN and LB tests in the ECC study, we found that genes C8PHV7 and C8PEV7, harbored by the lactate-producing Campylobacter gracilis, had the strongest association with childhood dental disease. This comprehensive model evaluation offers practical guidance for selection of appropriate methods for rigorous analyses of differential expression in metatranscriptomics. Selection of an optimal method increases the possibility of detecting true signals while minimizing the chance of claiming false ones.}, } @article {pmid37737585, year = {2023}, author = {Jensen, EEB and Sedor, V and Eshun, E and Njage, P and Otani, S and Aarestrup, FM}, title = {The resistomes of rural and urban pigs and poultry in Ghana.}, journal = {mSystems}, volume = {8}, number = {5}, pages = {e0062923}, pmid = {37737585}, issn = {2379-5077}, support = {NNF16OC0021856: Global Surveillance of Antimicrobial Resistance//Novo Nordisk Foundation/ ; Fellowships//The Fleming Fund/ ; }, mesh = {Animals ; Swine ; Poultry ; Anti-Bacterial Agents ; Ghana ; Bacteria ; *Microbiota/genetics ; *Anti-Infective Agents ; }, abstract = {To the best of our knowledge, this is the first report on the resistomes that are measured using metagenomics in livestock from Sub-Saharan Africa. We find notable differences in the microbiomes between both pigs and poultry, and those also varied markedly compared to similar samples from Europe. However, for both animal species, the same bacterial taxa drove such differences. In pigs and urban free-range poultry, we find a very low abundance of antimicrobial resistance genes (ARGs), whereas rural free-range poultry displayed similarity to the European average, and industrialized poultry exhibited higher levels. These findings show how different African livestock bacterial communities and resistomes are from their European counterparts. They also underscore the importance of continued surveillance and investigation into antimicrobial resistance across diverse ecosystems, contributing significantly to global efforts toward combating the threat of antibiotic resistance.}, } @article {pmid37737276, year = {2023}, author = {Lim, Y and Yang, SJ and Kang, I and Cho, JC}, title = {Metagenomic data from surface seawater of the east coast of South Korea.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {647}, pmid = {37737276}, issn = {2052-4463}, support = {KIMST-20210646//Korea Institute of Marine Science and Technology promotion (Korea Institute of Marine Science & Technology promotion)/ ; 2022R1A2C3008502//National Research Foundation of Korea (NRF)/ ; 2022R1A6A3A01087360//National Research Foundation of Korea (NRF)/ ; }, mesh = {*Ecosystem ; *Metagenome ; Republic of Korea ; Seawater ; }, abstract = {The East Sea, also known as the Sea of Japan, is a marginal sea located in the western Pacific Ocean, displaying comparable characteristics to Earth's oceans, thereby meriting its recognition as a "miniature ocean". The East Sea exhibits a range of annually-recurring biogeochemical features in accordance with seasonal fluctuations, such as phytoplankton blooms during the spring and autumn seasons. Despite ongoing monitoring efforts focused on water quality and physicochemical parameters, the investigation of prokaryotic assemblages in the East Sea, encompassing seasonal variations, has been infrequently pursued. Here, we present a monthly time-series metagenomic dataset spanning a one-year period in 2009, obtained from surface (10 m) seawater samples collected off the coast of the East Sea. The dataset encompasses 12 metagenomes, amounting 195 Gbp, with 14.73-22.52 Gbp per sample. This dataset is accompanied by concurrently measured physicochemical parameters. Our anticipation is that these metagenomes will facilitate extensive investigations aimed at elucidating various aspects of the marine microbial ecosystems in the East Sea.}, } @article {pmid37737154, year = {2023}, author = {Luan, M and Niu, M and Yang, P and Han, D and Zhang, Y and Li, W and He, Q and Zhao, Y and Mao, B and Chen, J and Mou, K and Li, P}, title = {Metagenomic sequencing reveals altered gut microbial compositions and gene functions in patients with non-segmental vitiligo.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {265}, pmid = {37737154}, issn = {1471-2180}, mesh = {Humans ; *Vitiligo/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Bacteroides fragilis ; Clostridiales ; }, abstract = {BACKGROUND: Vitiligo has been correlated with an abnormal gut microbiota. We aimed to systematically identify characteristics of the gut microbial compositions, genetic functions, and potential metabolic features in patients with non-segmental vitiligo.

METHODS: Twenty-five patients with non-segmental vitiligo and 25 matched healthy controls (HCs) were enrolled. Metagenomic sequencing and bioinformatic analysis were performed to determine the gut microbiota profiles. Differences in gut microbiota diversity and composition between patients with vitiligo and HCs were analyzed. Gene functions and gut metabolic modules were predicted with the Kyoto Encyclopedia of Gene and Genomes (KEGG) and MetaCyc databases.

RESULTS: Compared with HCs, alpha diversity of intestinal microbiome in vitiligo patients was significantly reduced. At the species level, the relative abundance of Staphylococcus thermophiles was decreased, and that of Bacteroides fragilis was increased in patients with vitiligo compared with those of the HCs. Linear discriminant analysis (LDA) effect size (LEfSe) analysis revealed representative microbial markers of Lachnospiraceae_bacterium_BX3, Massilioclostridium_coli, TM7_phylum_sp_oral_taxon_348 and Bacteroides_fragilis for patients with vitiligo. KEGG gene function analysis showed that the NOD-like receptor signaling pathway was significantly enriched in patients with vitiligo. Gut metabolic modules (GMMs) analysis showed that cysteine degradation was significantly down-regulated, and galactose degradation was up-regulated in patients with vitiligo. A panel of 28 microbial features was constructed to distinguish patients with vitiligo from HCs.

CONCLUSIONS: The gut microbial profiles and genetic functions of patients with vitiligo were distinct from those of the HCs. The identified gut microbial markers may potentially be used for earlier diagnosis and treatment targets.}, } @article {pmid37737118, year = {2023}, author = {Tang, ST and Song, XW and Chen, J and Shen, J and Ma, B and Rosen, BP and Zhang, J and Zhao, FJ}, title = {Widespread Distribution of the arsO Gene Confers Bacterial Resistance to Environmental Antimony.}, journal = {Environmental science & technology}, volume = {57}, number = {39}, pages = {14579-14588}, pmid = {37737118}, issn = {1520-5851}, support = {R35 GM136211/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Antimony/chemistry/metabolism ; *Arsenic ; Flavin-Adenine Dinucleotide/metabolism ; Interleukin-1 Receptor-Like 1 Protein/metabolism ; Oxidoreductases/metabolism ; Oxidation-Reduction ; Escherichia coli/metabolism ; }, abstract = {Microbial oxidation of environmental antimonite (Sb(III)) to antimonate (Sb(V)) is an antimony (Sb) detoxification mechanism. Ensifer adhaerens ST2, a bacterial isolate from a Sb-contaminated paddy soil, oxidizes Sb(III) to Sb(V) under oxic conditions by an unknown mechanism. Genomic analysis of ST2 reveals a gene of unknown function in an arsenic resistance (ars) operon that we term arsO. The transcription level of arsO was significantly upregulated by the addition of Sb(III). ArsO is predicted to be a flavoprotein monooxygenase but shows low sequence similarity to other flavoprotein monooxygenases. Expression of arsO in the arsenic-hypersensitive Escherichia coli strain AW3110Δars conferred increased resistance to Sb(III) but not arsenite (As(III)) or methylarsenite (MAs(III)). Purified ArsO catalyzes Sb(III) oxidation to Sb(V) with NADPH or NADH as the electron donor but does not oxidize As(III) or MAs(III). The purified enzyme contains flavin adenine dinucleotide (FAD) at a ratio of 0.62 mol of FAD/mol protein, and enzymatic activity was increased by addition of FAD. Bioinformatic analyses show that arsO genes are widely distributed in metagenomes from different environments and are particularly abundant in environments affected by human activities. This study demonstrates that ArsO is an environmental Sb(III) oxidase that plays a significant role in the detoxification of Sb(III).}, } @article {pmid37737001, year = {2023}, author = {Bernadus, JBB and Pelealu, J and Kandou, GD and Pinaria, AG and Mamahit, JME and Tallei, TE}, title = {Metagenomic Insight into the Microbiome and Virome Associated with Aedes aegypti Mosquitoes in Manado (North Sulawesi, Indonesia).}, journal = {Infectious disease reports}, volume = {15}, number = {5}, pages = {549-563}, pmid = {37737001}, issn = {2036-7430}, abstract = {The aim of this study was to investigate the microbial diversity encompassing bacteria, fungi, and viruses within the composite microbial community associated with Aedes aegypti mosquitoes in Manado, Indonesia, using a whole-genome shotgun metagenomics approach. Female mosquitoes were collected and grouped into pools of 50 individuals, from which genomic DNA (gDNA) and RNA were extracted separately. Whole-genome shotgun metagenomics were performed on gDNA samples. The bioinformatics analysis encompassed quality assessment, taxonomic classification, and visualization. The evaluation of the microbial community entailed an assessment of taxa abundance and diversity using Kraken version 2.1.2. The study delineated the prevalence of dominant bacterial phyla, including Proteobacteria, with varying abundance of Firmicutes, Bacteroidota, and Actinobacteria, and notable occurrence of Tenericutes. Furthermore, the presence of the fungal phylum Ascomycota was also detected. Among the identified barcodes, Barcode04 emerged as the most abundant and diverse, while Barcode06 exhibited greater evenness. Barcode03, 05, and 07 displayed moderate richness and diversity. Through an analysis of the relative abundance, a spectrum of viruses within Ae. aegypti populations was unveiled, with Negarnaviricota constituting the most prevalent phylum, followed by Nucleocytoviricota, Uroviricota, Artverviricota, Kitrinoviricota, Peploviricota, Phixviricota, and Cossaviricota. The presence of Negarnaviricota viruses raises pertinent public health concerns. The presence of other viral phyla underscores the intricate nature of virus-mosquito interactions. The analysis of viral diversity provides valuable insights into the range of viruses carried by Ae. aegypti. The community exhibits low biodiversity, with a few dominant species significantly influencing its composition. This has implications for healthcare and ecological management, potentially simplifying control measures but also posing risks if the dominant species are harmful. This study enriches our comprehension of the microbiome and virome associated with Ae. aegypti mosquitoes, emphasizing the importance of further research to fully comprehend their ecological significance and impact on public health. The findings shed light on the microbial ecology of Ae. aegypti, offering potential insights into mosquito biology, disease transmission, and strategies for vector control. Future studies should endeavor to establish specific associations with Ae. aegypti, elucidate the functional roles of the identified microbial and viral species, and investigate their ecological implications.}, } @article {pmid37736853, year = {2023}, author = {Das, S and Bhattacharjee, MJ and Mukherjee, AK and Khan, MR}, title = {Comprehensive bacterial-metabolite profiles of Hawaijar, Bekang, and Akhone: a comparative study on traditional fermented soybeans of north-east India.}, journal = {World journal of microbiology & biotechnology}, volume = {39}, number = {11}, pages = {315}, pmid = {37736853}, issn = {1573-0972}, mesh = {Humans ; Animals ; Glycine max ; India ; Ethnicity ; *Brevibacillus ; *Coleoptera ; *Fermented Foods ; }, abstract = {Preparation of traditionally fermented soybeans varies across ethnicities with distinct tastes, flavour, and nutritional values. The fermented soybean varieties Hawaijar, Bekang, and Akhone of north-east India are associated with diverse ethnic groups from Manipur, Mizoram, and Nagaland, respectively. These varieties differ in substrate and traditional practice that exerts differential bacterial-metabolite profile, which needs an in-depth analysis i. Culture-dependent and independent techniques investigated the bacterial diversity of the fermented soybean varieties. Gas chromatography and mass spectroscopy (GC-MS) studied these varieties' metabolite profiles. The common dominant bacterial genera detected in Hawaijar, Bekang, and Akhone were Bacillus, Ignatzschinaria, and Corynebacterium, with the presence of Brevibacillus and Staphylococcus exclusively in Hawaijar and Oceanobacillus in Bekang and Akhone. The metabolite analysis identified a higher abundance of essential amino acids, amino and nucleotide sugars, and vitamins in Hawaijar, short-chain fatty acids in Bekang, polyunsaturated fatty acids in Akhone and Hawaijar, and prebiotics in Akhone. The bacteria-metabolite correlation analysis predicted four distinct bacterial clusters associated with the differential synthesis of the functional metabolites. While B. subtilis is ubiquitous, cluster-1 comprised B. thermoamylovorans/B. amyloliquefaciens, cluster-2 comprised B. tropicus, cluster-3 comprised B. megaterium/B. borstelensis, and cluster-4 comprised B. rugosus. To the best of our knowledge, this is the first comparative study on traditional fermented soybean varieties of north-east India linking bacterial-metabolite profiles which may help in designing starters for desired functionalities in the future.}, } @article {pmid37736746, year = {2023}, author = {Li, S and Lian, WH and Han, JR and Ali, M and Lin, ZL and Liu, YH and Li, L and Zhang, DY and Jiang, XZ and Li, WJ and Dong, L}, title = {Capturing the microbial dark matter in desert soils using culturomics-based metagenomics and high-resolution analysis.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {67}, pmid = {37736746}, issn = {2055-5008}, mesh = {*Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Biodiversity ; Metagenome ; Soil ; }, abstract = {Deserts occupy one-third of the Earth's terrestrial surface and represent a potentially significant reservoir of microbial biodiversity, yet the majority of desert microorganisms remain uncharacterized and are seen as "microbial dark matter". Here, we introduce a multi-omics strategy, culturomics-based metagenomics (CBM) that integrates large-scale cultivation, full-length 16S rRNA gene amplicon, and shotgun metagenomic sequencing. The results showed that CBM captured a significant amount of taxonomic and functional diversity missed in direct sequencing by increasing the recovery of amplicon sequence variants (ASVs) and high/medium-quality metagenome-assembled genomes (MAGs). Importantly, CBM allowed the post hoc recovery of microbes of interest (e.g., novel or specific taxa), even those with extremely low abundance in the culture. Furthermore, strain-level analyses based on CBM and direct sequencing revealed that the desert soils harbored a considerable number of novel bacterial candidates (1941, 51.4%), of which 1095 (from CBM) were culturable. However, CBM would not exactly reflect the relative abundance of true microbial composition and functional pathways in the in situ environment, and its use coupled with direct metagenomic sequencing could provide greater insight into desert microbiomes. Overall, this study exemplifies the CBM strategy with high-resolution is an ideal way to deeply explore the untapped novel bacterial resources in desert soils, and substantially expands our knowledge on the microbial dark matter hidden in the vast expanse of deserts.}, } @article {pmid37736702, year = {2023}, author = {Kragsnaes, MS and Miguens Blanco, J and Mullish, BH and Serrano-Contreras, JI and Kjeldsen, J and Horn, HC and Pedersen, JK and Munk, HL and Nilsson, AC and Salam, A and Lewis, MR and Chekmeneva, E and Kristiansen, K and Marchesi, JR and Ellingsen, T}, title = {Small Intestinal Permeability and Metabolomic Profiles in Feces and Plasma Associate With Clinical Response in Patients With Active Psoriatic Arthritis Participating in a Fecal Microbiota Transplantation Trial: Exploratory Findings From the FLORA Trial.}, journal = {ACR open rheumatology}, volume = {5}, number = {11}, pages = {583-593}, pmid = {37736702}, issn = {2578-5745}, support = {21228/VAC_/Versus Arthritis/United Kingdom ; }, abstract = {OBJECTIVE: We investigated intestinal permeability and fecal, plasma, and urine metabolomic profiles in methotrexate-treated active psoriatic arthritis (PsA) and how this related to clinical response following one sham or fecal microbiota transplantation (FMT).

METHODS: This exploratory study is based on the FLORA trial cohort, in which 31 patients with moderate-to-high peripheral PsA disease activity, despite at least 3 months of methotrexate-treatment, were included in a 26-week, double-blind, 1:1 randomized, sham-controlled trial. Participants were randomly allocated to receive either one healthy donor FMT (n = 15) or sham (n = 16) via gastroscopy. The primary trial end point was the proportion of treatment failures through 26 weeks. We performed a lactulose-to-mannitol ratio (LMR) test at baseline (n = 31) and at week 26 (n = 26) to assess small intestinal permeability. Metabolomic profiles in fecal, plasma, and urine samples collected at baseline, weeks 4, 12, and 26 were measured using [1] H Nuclear Magnetic Resonance.

RESULTS: Trial failures (n = 7) had significantly higher LMR compared with responders (n = 19) at week 26 (0.027 [0.017-0.33]) vs. 0.012 [0-0.064], P = 0.013), indicating increased intestinal permeability. Multivariate analysis revealed a significant model for responders (n = 19) versus failures (n = 12) at all time points based on their fecal (P < 0.0001) and plasma (P = 0.005) metabolomic profiles, whereas urine metabolomic profiles did not differ between groups (P = 1). Fecal N-acetyl glycoprotein GlycA correlated with Health Assessment Questionnaire Disability Index (coefficient = 0.50; P = 0.03) and fecal propionate correlated with American College of Rheumatology 20 response at week 26 (coefficient = 27, P = 0.02).

CONCLUSION: Intestinal permeability and fecal and plasma metabolomic profiles of patients with PsA were associated with the primary clinical trial end point, failure versus responder.}, } @article {pmid37736390, year = {2023}, author = {Dweh, TJ and Pattnaik, S and Sahoo, JP}, title = {Assessing the impact of meta-genomic tools on current cutting-edge genome engineering and technology.}, journal = {International journal of biochemistry and molecular biology}, volume = {14}, number = {4}, pages = {62-75}, pmid = {37736390}, issn = {2152-4114}, abstract = {Metagenomics is defined as the study of the genome of the total microbiota found in nature and is often referred to as microbial environmental genomics because it entails the examination of a group of genetic components (genomes) from a diverse community of organisms in a particular setting. It is a sub-branch of omics technology that encompasses Deoxyribonucleic Acid (DNA), Ribonucleic acid (DNA), proteins, and various components associated with comprehensive analysis of all aspects of biological molecules in a system-wide manner. Clustered regularly interspaced palindromic repeats and its endonuclease, CRISPR-associated protein which forms a complex called CRISPR-cas9 technology, though it is a different technique used to make precise changes to the genome of an organism, it can be used in conjunction with metagenomic approaches to give a better, rapid, and more accurate description of genomes and sequence reads. There have been ongoing improvements in sequencing that have deepened our understanding of microbial genomes forever. From the time when only a small amount of gene could be sequenced using traditional methods (e.g., "the plus and minus" method developed by Allan and Sanger and the "chemical cleavage" method that is known for its use in the sequencing the phiX174 bacteriophage genome via radio-labeled DNA polymerase-primer in a polymerization reaction aided by polyacrylamide gel) to the era of total genomes sequencing which includes "sequencing-by-ligation" and the "sequencing-by-synthesis" that detects hydrogen ions when new DNA is synthesized (Second Generation) and then Next Generation Sequencing technologies (NGS). With these technologies, the Human Genome Project (HGP) was made possible. The study looks at recent advancements in metagenomics in plants and animals by examining findings from randomly selected research papers. All selected case studies examined the functional and taxonomical analysis of different microbial communities using high-throughput sequencing to generate different sequence reads. In animals, five studies indicated how Zebrafish, Livestock, Poultry, cattle, niches, and the human microbiome were exploited using environmental samples, such as soil and water, to identify microbial communities and their functions. It has also been used to study the microbiome of humans and other organisms, including gut microbiomes. Recent studies demonstrated how these technologies have allowed for faster and more accurate identification of pathogens, leading to improved disease diagnostics. They have also enabled the development of personalized medicine by allowing for the identification of genetic variations that can impact drug efficacy and toxicity. Continued advancements in sequencing techniques and the refinement of CRISPR-Cas9 tools offer even greater potential for transformative breakthroughs in scientific research and applications. On the other hand, metagenomic data are always large and uneasy to handle. The complexity of taxonomical profiling, functional annotation, and mechanisms of complex interaction still needs better bioinformatics tools. Current review focuses on better (e.g., AI-driven algorithms) tools that can predict metabolic pathways and interactions, and manipulate complex data to address potential bias for accurate interpretation.}, } @article {pmid37736325, year = {2023}, author = {Hammond, TC and Green, SJ and Jacobs, Y and Chlipala, GE and Xing, X and Heil, S and Chen, A and Aware, C and Flemister, A and Stromberg, A and Balchandani, P and Lin, AL}, title = {Gut microbiome association with brain imaging markers, APOE genotype, calcium and vegetable intakes, and obesity in healthy aging adults.}, journal = {Frontiers in aging neuroscience}, volume = {15}, number = {}, pages = {1227203}, pmid = {37736325}, issn = {1663-4365}, abstract = {INTRODUCTION: Advanced age is a significant factor in changes to brain physiology and cognitive functions. Recent research has highlighted the critical role of the gut microbiome in modulating brain functions during aging, which can be influenced by various factors such as apolipoprotein E (APOE) genetic variance, body mass index (BMI), diabetes, and dietary intake. However, the associations between the gut microbiome and these factors, as well as brain structural, vascular, and metabolic imaging markers, have not been well explored.

METHODS: We recruited 30 community dwelling older adults between age 55-85 in Kentucky. We collected the medical history from the electronic health record as well as the Dietary Screener Questionnaire. We performed APOE genotyping with an oral swab, gut microbiome analysis using metagenomics sequencing, and brain structural, vascular, and metabolic imaging using MRI.

RESULTS: Individuals with APOE e2 and APOE e4 genotypes had distinct microbiota composition, and higher level of pro-inflammatory microbiota were associated higher BMI and diabetes. In contrast, calcium- and vegetable-rich diets were associated with microbiota that produced short chain fatty acids leading to an anti-inflammatory state. We also found that important gut microbial butyrate producers were correlated with the volume of the thalamus and corpus callosum, which are regions of the brain responsible for relaying and processing information. Additionally, putative proinflammatory species were negatively correlated with GABA production, an inhibitory neurotransmitter. Furthermore, we observed that the relative abundance of bacteria from the family Eggerthellaceae, equol producers, was correlated with white matter integrity in tracts connecting the brain regions related to language, memory, and learning.

DISCUSSION: These findings highlight the importance of gut microbiome association with brain health in aging population and could have important implications aimed at optimizing healthy brain aging through precision prebiotic, probiotic or dietary interventions.}, } @article {pmid37736247, year = {2023}, author = {Nanfack-Minkeu, F and Delong, A and Morgan, W}, title = {Complete genome of Aedes japonicus narnavirus from wild caught mosquitoes collected in Ohio, USA.}, journal = {microPublication biology}, volume = {2023}, number = {}, pages = {}, pmid = {37736247}, issn = {2578-9430}, abstract = {Narnaviruses infect several genera of mosquitoes including Culex and Aedes . The narnavirus genome is a positive, single stranded RNA encoding an RNA-dependent RNA polymerase gene. The partial genome of a narnavirus identified in wild Aedes japonicus mosquitoes collected in Wooster, Ohio, USA was obtained using metagenomic analyses. Rapid amplification of 5'-cDNA ends (RACE) and Sanger sequencing were used to obtain the remaining genomic sequence of this strain. The complete genome is composed of 3153 nucleotides and has 98.4% and 99.1% nucleotide sequence identity with Aedes japonicus narnavirus genomes identified in Netherlands and Japan.}, } @article {pmid37735616, year = {2023}, author = {Ter Horst, AM and Fudyma, JD and Sones, JL and Emerson, JB}, title = {Dispersal, habitat filtering, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {2079-2089}, pmid = {37735616}, issn = {1751-7370}, mesh = {*Ecosystem ; *Wetlands ; Soil ; Metagenome ; Carbon/metabolism ; }, abstract = {Wetlands store 20-30% of the world's soil carbon, and identifying the microbial controls on these carbon reserves is essential to predicting feedbacks to climate change. Although viral infections likely play important roles in wetland ecosystem dynamics, we lack a basic understanding of wetland viral ecology. Here 63 viral size-fraction metagenomes (viromes) and paired total metagenomes were generated from three time points in 2021 at seven fresh- and saltwater wetlands in the California Bodega Marine Reserve. We recovered 12,826 viral population genomic sequences (vOTUs), only 4.4% of which were detected at the same field site two years prior, indicating a small degree of population stability or recurrence. Viral communities differed most significantly among the seven wetland sites and were also structured by habitat (plant community composition and salinity). Read mapping to a new version of our reference database, PIGEONv2.0 (515,763 vOTUs), revealed 196 vOTUs present over large geographic distances, often reflecting shared habitat characteristics. Wetland vOTU microdiversity was significantly lower locally than globally and lower within than between time points, indicating greater divergence with increasing spatiotemporal distance. Viruses tended to have broad predicted host ranges via CRISPR spacer linkages to metagenome-assembled genomes, and increased SNP frequencies in CRISPR-targeted major tail protein genes suggest potential viral eco-evolutionary dynamics in response to both immune targeting and changes in host cell receptors involved in viral attachment. Together, these results highlight the importance of dispersal, environmental selection, and eco-evolutionary dynamics as drivers of local and global wetland viral biogeography.}, } @article {pmid37735571, year = {2023}, author = {}, title = {Skani enables accurate and efficient genome comparison for modern metagenomic datasets.}, journal = {Nature methods}, volume = {20}, number = {11}, pages = {1633-1634}, pmid = {37735571}, issn = {1548-7105}, support = {RGPIN-2022-03074//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; CGS-D//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; }, mesh = {*Metagenomics ; *Metagenome ; Algorithms ; Software ; }, } @article {pmid37735570, year = {2023}, author = {Shaw, J and Yu, YW}, title = {Fast and robust metagenomic sequence comparison through sparse chaining with skani.}, journal = {Nature methods}, volume = {20}, number = {11}, pages = {1661-1665}, pmid = {37735570}, issn = {1548-7105}, support = {RGPIN-2022-03074//Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology)/ ; CGS-D//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; }, mesh = {*Metagenome ; *Prokaryotic Cells ; Metagenomics/methods ; }, abstract = {Sequence comparison tools for metagenome-assembled genomes (MAGs) struggle with high-volume or low-quality data. We present skani (https://github.com/bluenote-1577/skani), a method for determining average nucleotide identity (ANI) via sparse approximate alignments. skani outperforms FastANI in accuracy and speed (>20× faster) for fragmented, incomplete MAGs. skani can query genomes against >65,000 prokaryotic genomes in seconds and 6 GB memory. skani unlocks higher-resolution insights for extensive, noisy metagenomic datasets.}, } @article {pmid37735392, year = {2023}, author = {Liu, H and Huang, J and Lu, ZS and Li, LX and Liang, XT and Tang, T and Sun, WC and Lu, HJ and Jin, NY and Bai, X and Si, XK}, title = {Isolation and characterization of a novel parvovirus from a red-crowned crane, China, 2021.}, journal = {BMC veterinary research}, volume = {19}, number = {1}, pages = {169}, pmid = {37735392}, issn = {1746-6148}, support = {32273097//National Natural Sciences Foundation of China/ ; 32273097//National Natural Sciences Foundation of China/ ; SKLVBF202211//State Key Laboratory of Veterinary Biotechnology Foundation/ ; SKLVBF202211//State Key Laboratory of Veterinary Biotechnology Foundation/ ; SKLVBF202211//State Key Laboratory of Veterinary Biotechnology Foundation/ ; SKLVBF202211//State Key Laboratory of Veterinary Biotechnology Foundation/ ; YDWS202205//Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, P.R. China; Key Laboratory of Livestock Disease Prevention of Guangdong Province/ ; YDWS202205//Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, P.R. China; Key Laboratory of Livestock Disease Prevention of Guangdong Province/ ; YDWS202205//Key Laboratory for prevention and control of Avian Influenza and Other Major Poultry Diseases, Ministry of Agriculture and Rural Affairs, P.R. China; Key Laboratory of Livestock Disease Prevention of Guangdong Province/ ; }, mesh = {Animals ; Phylogeny ; *Parvoviridae Infections/veterinary ; Chickens ; Ducks ; Geese ; China ; Diarrhea/veterinary ; *Parvovirus/genetics ; }, abstract = {BACKGROUND: Parvoviruses are icosahedral, nonenveloped viruses with single-stranded DNA genomes of approximately 5 kb in length. In recent years, parvoviruses have frequently mutated and expanded their host range to cause disease in many wild animals by altering their tissue tropism. Animal infection mainly results in acute enteritis and inflammation of other organs. In this study, we used a viral metagenomic method to detect a novel parvovirus species in a red-crowned crane that died due to severe diarrhea in China.

RESULTS: The presence of the viral genome in the kidney, lung, heart, liver, and intestine were confirmed by PCR. Histopathological examination of the intestine showed a large number of infiltrated inflammatory cells. The JL21/10 strain of the red-crowned crane parvovirus was first isolated from the intestine. Whole-genome sequence analysis showed that JL21/10 shared high identity with the red-crowned crane Parvovirinae strains yc-8 at the nucleotide level (96.61%). Phylogenetic analysis of the complete genome and NS1 gene revealed that the JL21/10 strain clustered with strains in chicken and revealed a close genetic relationship with the red-crowned crane parvovirus strains.The complete of VP2 gene analysis showed that JL21/10 shared identity with the red-crowned crane yc-8 strains (97.7%), chicken (55.4%),ducks(31.0%) and geese(30.1%) at the amino acid level. The result showed that red-crowned crane parvovirus may be cross-species transmission to chicken. However, There is little possibility of transmission to ducks and geese.

CONCLUSION: This is the first isolation and identification of a parvovirus in red-crowned crane that was associated with severe diarrhea.}, } @article {pmid37735195, year = {2023}, author = {Malukiewicz, J and D'arc, M and Dias, CA and Cartwright, RA and Grativol, AD and Moreira, SB and Souza, AR and Tavares, MCH and Pissinatti, A and Ruiz-Miranda, CR and Santos, AFA}, title = {Bifidobacteria define gut microbiome profiles of golden lion tamarin (Leontopithecus rosalia) and marmoset (Callithrix sp.) metagenomic shotgun pools.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15679}, pmid = {37735195}, issn = {2045-2322}, mesh = {Humans ; Animals ; *Callithrix ; *Gastrointestinal Microbiome ; Bifidobacterium ; Callitrichinae ; }, abstract = {Gut microbiome disruptions may lead to adverse effects on wildlife fitness and viability, thus maintaining host microbiota biodiversity needs to become an integral part of wildlife conservation. The highly-endangered callitrichid golden lion tamarin (GLT-Leontopithecus rosalia) is a rare conservation success, but allochthonous callitrichid marmosets (Callithrix) serve as principle ecological GLT threats. However, incorporation of microbiome approaches to GLT conservation is impeded by limited gut microbiome studies of Brazilian primates. Here, we carried out analysis of gut metagenomic pools from 114 individuals of wild and captive GLTs and marmosets. More specifically, we analyzed the bacterial component of ultra filtered samples originally collected as part of a virome profiling study. The major findings of this study are consistent with previous studies in showing that Bifidobacterium, a bacterial species important for the metabolism of tree gums consumed by callitrichids, is an important component of the callitrichid gut microbiome - although GTLs and marmosets were enriched for different species of Bifidobacterium. Additionally, the composition of GLT and marmoset gut microbiota is sensitive to host environmental factors. Overall, our data expand baseline gut microbiome data for callitrichids to allow for the development of new tools to improve their management and conservation.}, } @article {pmid37734616, year = {2023}, author = {Sang, Y and Mo, S and Zeng, S and Wu, X and Kashif, M and Song, J and Yu, D and Bai, L and Jiang, C}, title = {Model of shrimp pond-mediated spatiotemporal dynamic distribution of antibiotic resistance genes in the mangrove habitat of a subtropical gulf.}, journal = {The Science of the total environment}, volume = {905}, number = {}, pages = {167199}, doi = {10.1016/j.scitotenv.2023.167199}, pmid = {37734616}, issn = {1879-1026}, mesh = {Animals ; Humans ; *Genes, Bacterial ; Ponds/analysis ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Microbiota ; Crustacea ; China ; }, abstract = {Aquacultures are the main reason for the environmental selection of antibiotic resistance genes (ARGs), resulting in the enrichment of ARGs. As a filter, a marine mangrove ecosystem can reduce antimicrobial resistance (AMR) or eliminate ARGs; however, its elimination mechanism remains unclear. This study investigated the spatiotemporal dynamic distribution of ARGs in two different types of mangrove habitats (shrimp ponds and virgin forests), within a subtropical gulf located in the Beibu Gulf, China, during dry and wet seasons by using metagenomics and real time quantitative polymerase chain reaction (RT-qPCR) analysis. As the key environmental factors, sulfide, salinity, and mobile genetic elements significantly were found to contribute to ARGs distribution, respectively. Wet and dry seasons influenced the dispersal of ARGs but did not affect the microbial community structure. Three potential biomarkers, TEM-116, smeD, and smeE, played key roles in seasonal differences. The key different genes in the biological relevance of absolute abundance were demonstrated by RT-qPCR. Co-occurrence network analysis indicated that high-abundance ARGs were distributed in a modular manner. For the first time, a risk index weighted by risk rank (RIR) was proposed and used to quantify the human risk of ARGs in the mangrove metagenome. The shrimp ponds during the wet season showed the highest RIR detected. In addition to offering a perspective on reducing AMR in mangrove wetlands, this study constructed the first spatiotemporal dynamic model of ARGs in the Beibu Gulf, China and contributed to revealing the global spread of ARGs. Meanwhile, this study proposes a new pipeline for assessing the risk of ARGs, while also exploring the concept of "One Health."}, } @article {pmid37734503, year = {2023}, author = {Yuan, X and Cui, K and Chen, Y and Zhang, Y and Wu, S and Xie, X and Liu, T and Yao, H}, title = {Microbial community and gene dynamics response to high concentrations of gadolinium and sulfamethoxazole in biological nitrogen removal system.}, journal = {Chemosphere}, volume = {342}, number = {}, pages = {140218}, doi = {10.1016/j.chemosphere.2023.140218}, pmid = {37734503}, issn = {1879-1298}, mesh = {Sulfamethoxazole/pharmacology ; Gadolinium ; Denitrification ; Nitrogen ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; *Metals, Heavy ; *Microbiota ; }, abstract = {The impact of high antibiotic and heavy metal pollution levels on biological nitrogen removal in wastewater treatment plants (WWTPs) remains poorly understood, posing a global concern regarding the issue spread of antibiotic resistance induced by these contaminants. Herein, we investigated the effects of gadolinium (Gd) and sulfamethoxazole (SMX), commonly found in medical wastewater, on biological nitrogen removal systems and microbial characteristics, and the fate of antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs). Our findings indicated that high SMX and Gd(III) concentrations adversely affected nitrification and denitrification, with Gd(III) exerting a strong inhibitory effect on microbial activity. Metagenomic analysis revealed that high SMX and Gd(III) concentrations could reduce microbial diversity, with Thauera and Pseudomonas emerging as dominant genera across all samples. While the relative abundance of most ARGs decreased under single Gd(III) stress, MRGs increased, and nitrification functional genes were inhibited. Conversely, combined SMX and Gd(III) pollution increased the relative abundance of intl1. Correlation analysis revealed that most genera could host ARGs and MRGs, indicating co-selection and competition between these resistance genes. However, most denitrifying functional genes exhibited a positive correlation with MRGs. Overall, our study provides novel insights into the impact of high concentrations of antibiotics and heavy metal pollution in WWTPs, and laying the groundwork for the spread and proliferation of resistance genes under combined SMX and Gd pollution.}, } @article {pmid37733635, year = {2023}, author = {Luo, T and Dai, X and Wei, W and Xu, Q and Ni, BJ}, title = {Microplastics Enhance the Prevalence of Antibiotic Resistance Genes in Anaerobic Sludge Digestion by Enriching Antibiotic-Resistant Bacteria in Surface Biofilm and Facilitating the Vertical and Horizontal Gene Transfer.}, journal = {Environmental science & technology}, volume = {57}, number = {39}, pages = {14611-14621}, doi = {10.1021/acs.est.3c02815}, pmid = {37733635}, issn = {1520-5851}, mesh = {Humans ; *Sewage/microbiology ; *Microplastics ; Plastics ; Genes, Bacterial ; Anaerobiosis ; Gene Transfer, Horizontal ; Prevalence ; Angiotensin Receptor Antagonists ; Polyethylene ; Anti-Bacterial Agents/pharmacology ; Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Digestion ; }, abstract = {Antibiotic resistance genes (ARGs) and microplastics (MPs) are recognized as emerging contaminants and threats to global human health. Despite both of them being significantly detected in their "hotspots", i.e., waste activated sludge (WAS), rare studies on how MPs affect ARGs and antibiotic-resistant bacteria (ARB) in anaerobic sludge digestion are available. Herein, the fate of ARGs and ARB after exposure to MPs of three dosages (10, 30, and 80 particles/g-TS), three polymer types (LDPE, PET, and PS), and three branching extents (LDPE, LLDPE, and HDPE) in anaerobic sludge digestion was investigated. Metagenomic results indicated that all variants of MPs resulted in an increase of the relative abundance of ARGs in the digester compared to the control. The abundance of ARGs demonstrated a dosage-dependent relationship within the range from 10 to 80 particles/g-TS, resulting in an increase from 4.5 to 27.9% compared to the control. Branching structure and polymer type influence ARG level in the sludge digester as well. Mechanism studies revealed that LDPE selectively enriched potential ARB and ARGs in the surface biofilm, possibly creating a favorable environment for ARB proliferation and ARG exchange. Furthermore, vertical transfer of ARGs was facilitated by LDPE through increasing bacterial cell proliferation accompanied by the enhancement of relevant functional genes. The elevated abundance of mobile genetic elements (MGEs) and ARGs-carrying plasmids also demonstrated that MGE-mediated horizontal transfer was promoted by LDPE at 80 particles/g-TS. This effect was compounded by increased oxidative stress, cell membrane permeability, and cell cohesion, collectively facilitating horizontal ARG transfer. Consequently, both vertical and horizontal transfer of ARGs could be concurrently promoted by LDPE an in anaerobic sludge digester.}, } @article {pmid37733134, year = {2023}, author = {Lema, NK and Gemeda, MT and Woldesemayat, AA}, title = {Recent Advances in Metagenomic Approaches, Applications, and Challenge.}, journal = {Current microbiology}, volume = {80}, number = {11}, pages = {347}, pmid = {37733134}, issn = {1432-0991}, mesh = {Humans ; *Metagenome ; Metagenomics ; *COVID-19 ; SARS-CoV-2/genetics ; Genomics ; }, abstract = {Advances in metagenomics analysis with the advent of next-generation sequencing have extended our knowledge of microbial communities as compared to conventional techniques providing advanced approach to identify novel and uncultivable microorganisms based on their genetic information derived from a particular environment. Shotgun metagenomics involves investigating the DNA of the entire community without the requirement of PCR amplification. It provides access to study all genes present in the sample. On the other hand, amplicon sequencing targets taxonomically important marker genes, the analysis of which is restricted to previously known DNA sequences. While sequence-based metagenomics is used to analyze DNA sequences directly from the environment without the requirement of library construction and with limited identification of novel genes and products that can be complemented by functional genomics, function-based metagenomics requires fragmentation and cloning of extracted metagenome DNA in a suitable host with subsequent functional screening and sequencing clone for detection of a novel gene. Although advances were made in metagenomics, different challenges arise. This review provides insight into advances in the metagenomic approaches combined with next-generation sequencing, their recent applications highlighting the emerging ones, such as in astrobiology, forensic sciences, and SARS-CoV-2 infection diagnosis, and the challenges associated. This review further discusses the different types of metagenomics and outlines advancements in bioinformatics tools and their significance in the analysis of metagenomic datasets.}, } @article {pmid37732845, year = {2024}, author = {Osborne, CM and Langelier, C and Kamm, J and Williamson, K and Ambroggio, L and Reeder, RW and Locandro, C and Kirk Harris, J and Wagner, BD and Maddux, AB and Caldera, S and Lyden, A and Soesanto, V and Simões, EAF and Leroue, MK and Carpenter, TC and Hall, MW and Zuppa, AF and Carcillo, JA and Meert, KL and Pollack, MM and McQuillen, PS and Notterman, DA and DeRisi, J and Mourani, PM and , }, title = {Viral Detection by Reverse Transcriptase Polymerase Chain Reaction in Upper Respiratory Tract and Metagenomic RNA Sequencing in Lower Respiratory Tract in Critically Ill Children With Suspected Lower Respiratory Tract Infection.}, journal = {Pediatric critical care medicine : a journal of the Society of Critical Care Medicine and the World Federation of Pediatric Intensive and Critical Care Societies}, volume = {25}, number = {1}, pages = {e1-e11}, pmid = {37732845}, issn = {1529-7535}, support = {UG1 HD049983/HD/NICHD NIH HHS/United States ; UG1 HD063108/HD/NICHD NIH HHS/United States ; R01 HL155418/HL/NHLBI NIH HHS/United States ; K23 HL138461/HL/NHLBI NIH HHS/United States ; U01 HD049934/HD/NICHD NIH HHS/United States ; UG1 HD049981/HD/NICHD NIH HHS/United States ; K23 HD096018/HD/NICHD NIH HHS/United States ; UG1 HD050096/HD/NICHD NIH HHS/United States ; UG1 HD083170/HD/NICHD NIH HHS/United States ; UG1 HD083166/HD/NICHD NIH HHS/United States ; R01 HL124103/HL/NHLBI NIH HHS/United States ; UG1 HD083171/HD/NICHD NIH HHS/United States ; }, mesh = {Child ; Humans ; Infant ; Reverse Transcriptase Polymerase Chain Reaction ; Prospective Studies ; *Critical Illness ; *Respiratory Tract Infections/diagnosis ; Nasopharynx ; Sequence Analysis, RNA ; }, abstract = {OBJECTIVES: Viral lower respiratory tract infection (vLRTI) contributes to substantial morbidity and mortality in children. Diagnosis is typically confirmed by reverse transcriptase polymerase chain reaction (RT-PCR) of nasopharyngeal specimens in hospitalized patients; however, it is unknown whether nasopharyngeal detection accurately reflects presence of virus in the lower respiratory tract (LRT). This study evaluates agreement between viral detection from nasopharyngeal specimens by RT-PCR compared with metagenomic next-generation RNA sequencing (RNA-Seq) from tracheal aspirates (TAs).

DESIGN: This is an analysis of of a seven-center prospective cohort study.

SETTING: Seven PICUs within academic children's hospitals in the United States.

PATIENTS: Critically ill children (from 1 mo to 18 yr) who required mechanical ventilation via endotracheal tube for greater than or equal to 72 hours.

INTERVENTIONS: We evaluated agreement in viral detection between paired upper and LRT samples. Results of clinical nasopharyngeal RT-PCR were compared with TA RNA-Seq. Positive and negative predictive agreement and Cohen's Kappa were used to assess agreement.

MEASUREMENTS AND MAIN RESULTS: Of 295 subjects with paired testing available, 200 (68%) and 210 (71%) had positive viral testing by RT-PCR from nasopharyngeal and RNA-Seq from TA samples, respectively; 184 (62%) were positive by both nasopharyngeal RT-PCR and TA RNA-Seq for a virus, and 69 (23%) were negative by both methods. Nasopharyngeal RT-PCR detected the most abundant virus identified by RNA-Seq in 92.4% of subjects. Among the most frequent viruses detected, respiratory syncytial virus demonstrated the highest degree of concordance (κ = 0.89; 95% CI, 0.83-0.94), whereas rhinovirus/enterovirus demonstrated lower concordance (κ = 0.55; 95% CI, 0.44-0.66). Nasopharyngeal PCR was more likely to detect multiple viruses than TA RNA-Seq (54 [18.3%] vs 24 [8.1%], p ≤ 0.001).

CONCLUSIONS: Viral nucleic acid detection in the upper versus LRT reveals good overall agreement, but concordance depends on the virus. Further studies are indicated to determine the utility of LRT sampling or the use of RNA-Seq to determine LRTI etiology.}, } @article {pmid37732776, year = {2023}, author = {Mujakić, I and Cabello-Yeves, PJ and Villena-Alemany, C and Piwosz, K and Rodriguez-Valera, F and Picazo, A and Camacho, A and Koblížek, M}, title = {Multi-environment ecogenomics analysis of the cosmopolitan phylum Gemmatimonadota.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0111223}, pmid = {37732776}, issn = {2165-0497}, abstract = {Gemmatimonadota is a diverse bacterial phylum commonly found in environments such as soils, rhizospheres, fresh waters, and sediments. So far, the phylum contains just six cultured species (five of them sequenced), which limits our understanding of their diversity and metabolism. Therefore, we analyzed over 400 metagenome-assembled genomes (MAGs) and 5 culture-derived genomes representing Gemmatimonadota from various aquatic environments, hydrothermal vents, sediments, soils, and host-associated (with marine sponges and coral) species. The principal coordinate analysis based on the presence/absence of genes in Gemmatimonadota genomes and phylogenomic analysis documented that marine and host-associated Gemmatimonadota were the most distant from freshwater and wastewater species. A smaller genome size and coding sequences (CDS) number reduction were observed in marine MAGs, pointing to an oligotrophic environmental adaptation. Several metabolic pathways are restricted to specific environments. For example, genes for anoxygenic phototrophy were found only in freshwater, wastewater, and soda lake sediment genomes. There were several genomes from soda lake sediments and wastewater containing type IC/ID ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO). Various genomes from wastewater harbored bacterial type II RuBisCO, whereas RuBisCO-like protein was found in genomes from fresh waters, soil, host-associated, and marine sediments. Gemmatimonadota does not contain nitrogen fixation genes; however, the nosZ gene, involved in the reduction of N2O, was present in genomes from most environments, missing only in marine water and host-associated Gemmatimonadota. The presented data suggest that Gemmatimonadota evolved as an organotrophic species relying on aerobic respiration and then remodeled its genome inventory when adapting to particular environments. IMPORTANCE Gemmatimonadota is a rarely studied bacterial phylum consisting of a handful of cultured species. Recent culture-independent studies documented that these organisms are distributed in many environments, including soil, marine, fresh, and waste waters. However, due to the lack of cultured species, information about their metabolic potential and environmental role is scarce. Therefore, we collected Gemmatimonadota metagenome-assembled genomes (MAGs) from different habitats and performed a systematic analysis of their genomic characteristics and metabolic potential. Our results show how Gemmatimonadota have adapted their genomes to different environments.}, } @article {pmid37732569, year = {2023}, author = {O'Brien, PA and Tan, S and Frade, PR and Robbins, SJ and Engelberts, JP and Bell, SC and Vanwonterghem, I and Miller, DJ and Webster, NS and Zhang, G and Bourne, DG}, title = {Validation of key sponge symbiont pathways using genome-centric metatranscriptomics.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {3207-3224}, doi = {10.1111/1462-2920.16509}, pmid = {37732569}, issn = {1462-2920}, support = {//Beijing Genomics Institute/ ; //Earthwatch Institute/ ; //Mitsubishi International Corporation/ ; //AIMS@JCU/ ; }, mesh = {Animals ; Phylogeny ; *Cyanobacteria/genetics ; *Microbiota/genetics ; Vitamins/metabolism ; Carbohydrates ; *Porifera ; Symbiosis ; }, abstract = {The sponge microbiome underpins host function through provision and recycling of essential nutrients in a nutrient poor environment. Genomic data suggest that carbohydrate degradation, carbon fixation, nitrogen metabolism, sulphur metabolism and supplementation of B-vitamins are central microbial functions. However, validation beyond the genomic potential of sponge symbiont pathways is rarely explored. To evaluate metagenomic predictions, we sequenced the metagenomes and metatranscriptomes of three common coral reef sponges: Ircinia ramosa, Ircinia microconulosa and Phyllospongia foliascens. Multiple carbohydrate active enzymes were expressed by Poribacteria, Bacteroidota and Cyanobacteria symbionts, suggesting these lineages have a central role in assimilating dissolved organic matter. Expression of entire pathways for carbon fixation and multiple sulphur compound transformations were observed in all sponges. Gene expression for anaerobic nitrogen metabolism (denitrification and nitrate reduction) were more common than aerobic metabolism (nitrification), where only the I. ramosa microbiome expressed the nitrification pathway. Finally, while expression of the biosynthetic pathways for B-vitamins was common, the expression of additional transporter genes was far more limited. Overall, we highlight consistencies and disparities between metagenomic and metatranscriptomic results when inferring microbial activity, while uncovering new microbial taxa that contribute to the health of their sponge host via nutrient exchange.}, } @article {pmid37732381, year = {2023}, author = {Wang, HJ and Chen, W and Wang, HZ and Zhao, HL and Wang, DH and Long, Y and Xing, XZ and , }, title = {Expert Consensus on Acute Respiratory Failure in Critically Ill Cancer Patients (2023).}, journal = {Chinese medical sciences journal = Chung-kuo i hsueh k'o hsueh tsa chih}, volume = {38}, number = {3}, pages = {163-177}, doi = {10.24920/004203}, pmid = {37732381}, issn = {1001-9294}, mesh = {Humans ; Consensus ; Critical Illness/therapy ; *Neoplasms/complications/therapy ; Oxygen ; *Pneumonia ; *Respiratory Distress Syndrome/therapy/drug therapy ; *Respiratory Insufficiency/etiology/therapy ; }, abstract = {Objective This consensus aims to provide evidence-based recommendations on common questions in the diagnosis and treatment of acute respiratory failure (ARF) for critically ill cancer patients.Methods We developed six clinical questions using the PICO (Population, Intervention, Comparison, and Outcome) principle in diagnosis and treatment for critical ill cancer patients with ARF. Based on literature searching and meta-analyses, recommendations were devised. The GRADE (Grading of Recommendation Assessment, Development and Evaluation) method was applied to each question to reach consensus in the expert panel. Results The panel makes strong recommendations in favor of (1) metagenomic next-generation sequencing (mNGS) tests may aid clinicians in rapid diagnosis in critically ill cancer patients suspected of pulmonary infections; (2) extracorporeal membrane oxygenation (ECMO) therapy should not be used as a routine rescue therapy for acute respiratory distress syndrome in critically ill cancer patients but may benefit highly selected patients after multi-disciplinary consultations; (3) cancer patients who have received immune checkpoint inhibitor therapy have an increased incidence of pneumonitis compared with standard chemotherapy; (4) critically ill cancer patients who are on invasive mechanical ventilation and estimated to be extubated after 14 days may benefit from early tracheotomy; and (5) high-flow nasal oxygen and noninvasive ventilation therapy can be used as a first-line oxygen strategy for critically ill cancer patients with ARFs. A weak recommendation is: (6) for critically ill cancer patients with ARF caused by tumor compression, urgent chemotherapy may be considered as a rescue therapy only in patients determined to be potentially sensitive to the anticancer therapy after multidisciplinary consultations. Conclusions The recommendations based on the available evidence can guide diagnosis and treatment in critically ill cancer patients with acute respiratory failure and improve outcomes.}, } @article {pmid37732272, year = {2023}, author = {Pan, YF and Zhao, H and Gou, QY and Shi, PB and Tian, JH and Feng, Y and Li, K and Yang, WH and Wu, D and Tang, G and Zhang, B and Ren, Z and Peng, S and Luo, GY and Le, SJ and Xin, GY and Wang, J and Hou, X and Peng, MW and Kong, JB and Chen, XX and Yang, CH and Mei, SQ and Liao, YQ and Cheng, JX and Wang, J and Chaolemen, and Wu, YH and Wang, JB and An, T and Huang, X and Eden, JS and Li, J and Guo, D and Liang, G and Jin, X and Holmes, EC and Li, B and Wang, D and Li, J and Wu, WC and Shi, M}, title = {Metagenomic analysis of individual mosquitos reveals the ecology of insect viruses.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37732272}, support = {U01 AI151810/AI/NIAID NIH HHS/United States ; }, abstract = {Mosquito transmitted viruses are responsible for an increasing burden of human disease. Despite this, little is known about the diversity and ecology of viruses within individual mosquito hosts. Using a meta-transcriptomic approach, we analysed the virome of 2,438 individual mosquitos (79 species), spanning ~4000 km along latitudes and longitudes in China. From these data we identified 393 core viral species associated with mosquitos, including seven (putative) arbovirus species. We identified potential species and geographic hotspots of viral richness and arbovirus occurrence, and demonstrated that host phylogeny had a strong impact on the composition of individual mosquito viromes. Our data revealed a large number of viruses shared among mosquito species or genera, expanding our knowledge of host specificity of insect-associated viruses. We also detected multiple virus species that were widespread throughout the country, possibly facilitated by long-distance mosquito migrations. Together, our results greatly expand the known mosquito virome, linked the viral diversity at the scale of individual insects to that at a country-wide scale, and offered unique insights into the ecology of viruses of insect vectors.}, } @article {pmid37731932, year = {2023}, author = {Jácome-Hernández, A and Lamelas, A and Desgarennes, D and Huerta, C and Cruz-Rosales, M and Favila, ME}, title = {Influence of phylogenetic, environmental, and behavioral factors on the gut bacterial community structure of dung beetles (Scarabaeidae: Scarabaeinae) in a Neotropical Biosphere Reserve.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1224601}, pmid = {37731932}, issn = {1664-302X}, abstract = {Gut bacteria help dung beetles metabolize nutrients contained and synthesize those unavailable in their food, depending on the ecological scenario in which they develop. However, less is known about the influence of environmental and behavioral factors on the taxonomic composition of bacterial gut communities in Scarabaeinae beetles. To address this research topic, we analyzed 13 tropical dung beetle species in the Los Tuxtlas Biosphere Reserve, Mexico, to understand how the beetle tribe, habitat, food preference, food relocation, and parental care influence the composition of gut bacterial communities. We found that the beetle tribe is the primary factor impacting the taxonomic composition of gut bacterial communities. Among them, Deltochilini displayed the highest variability in diversity due to the different combinations of habitat and food preferences among its species. On the other hand, the other tribes studied did not exhibit such variable combinations. Habitat emerged as the second most influential factor, with forest-dwelling beetles displaying higher diversity. This can be attributed to the heterogeneous environments within tropical forests, which offer a greater diversity of food resources. In contrast, grassland beetles, living in more homogeneous environments and relying on cow feces as their main food source, exhibited lower diversity. Our findings suggest a correlation between bacterial diversity and food resource availability in complex habitats, such as tropical forests, which offer a wider array of food sources compared to simpler environments like grasslands.}, } @article {pmid37731926, year = {2023}, author = {Dikareva, E and Matharu, D and Lahtinen, E and Kolho, KL and De Vos, WM and Salonen, A and Ponsero, AJ}, title = {An extended catalog of integrated prophages in the infant and adult fecal microbiome shows high prevalence of lysogeny.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1254535}, pmid = {37731926}, issn = {1664-302X}, abstract = {BACKGROUND AND AIMS: The acquisition and gradual maturation of gut microbial communities during early childhood is central to an individual's healthy development. Bacteriophages have the potential to shape the gut bacterial communities. However, the complex ecological interactions between phages and their bacterial host are still poorly characterized. In this study, we investigated the abundance and diversity of integrated prophages in infant and adult gut bacteria by detecting integrated prophages in metagenome assembled genomes (MAGs) of commensal bacteria.

METHODS: Our study included 88 infants sampled at 3 weeks, 3 months, 6 months, and 12 months (n = 323 total samples), and their parents around delivery time (n = 138 total samples). Fecal DNA was extracted and characterized by using shotgun metagenomic sequencing, and a collection of prokaryotic MAGs was generated. The MAG collection was screened for the presence of integrated bacteriophage sequences, allowing their taxonomic and functional characterization.

RESULTS: A large collection of 6,186 MAGs from infant and adult gut microbiota was obtained and screened for integrated prophages, allowing the identification of 7,165 prophage sequences longer than 10 kb. Strikingly, more than 70% of the near-complete MAGs were identified as lysogens. The prevalence of prophages in MAGs varied across bacterial families, with a lower prevalence observed among Coriobacteriaceae, Eggerthellaceae, Veillonellaceae and Burkholderiaceae, while a very high prevalence of lysogen MAGs were observed in Oscillospiraceae, Enterococcaceae, and Enterobacteriaceae. Interestingly for several bacterial families such as Bifidobacteriaceae and Bacteroidaceae, the prevalence of prophages in MAGs was higher in early infant time point (3 weeks and 3 months) than in later sampling points (6 and 12 months) and in adults. The prophage sequences were clustered into 5,616 species-like vOTUs, 77% of which were novel. Finally, we explored the functional repertoire of the potential auxiliary metabolic genes carried by these prophages, encoding functions involved in carbohydrate metabolism and degradation, amino acid metabolism and carbon metabolism.

CONCLUSION: Our study provides an enhanced understanding of the diversity and prevalence of lysogens in infant and adult gut microbiota and suggests a complex interplay between prophages and their bacterial hosts.}, } @article {pmid37731925, year = {2023}, author = {Xiong, M and Jiang, W and Zou, S and Kang, D and Yan, X}, title = {Microbial carbohydrate-active enzymes influence soil carbon by regulating the of plant- and fungal-derived biomass decomposition in plateau peat wetlands under differing water conditions.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1266016}, pmid = {37731925}, issn = {1664-302X}, abstract = {Peatlands are important carbon sinks and water sources in terrestrial ecosystems. It is important to explore their microbial-driven water-carbon synergistic mechanisms to understand the driving mechanisms of carbon processes in peatlands. Based on macrogenomic sequencing techniques, located on the peatland of the eastern margin of the Tibetan Plateau with similar stand and different water conditions, we taken soil properties, microbiome abundance, CAZyme abundance and enzyme gene pathways as the object of study, investigated the characterization of soil microbial carbohydrate-active enzymes (CAZymes) under different water gradients in peatland. According to the results, these three phyla (Chloroflexi, Gemmatimonadetes, and Verrucomicrobia) differed significantly between water gradients. Under dried wetlands, the abundance of CAZymes involved in hemicellulose and glucan degradation increased by 3.0 × 10[-5] and 3.0 × 10[-6], respectively. In contrast, the abundance of CAZymes involved in chitin degradation decreased by 1.1 × 10[-5] (p < 0.05). It highlights that regulating plant- and fungus-derived carbon metabolism processes by soil microorganisms in highland peatlands is a crucial mechanism for their response to water changes. Most plant-derived carbon fractions are regulated by soil enzymes (endo-beta 1,4-xylanase, alpha-L-arabinofuranosidase, and alpha-L-fucosidase) containing CAZymes functional genes. Additional findings in this enzyme gene pathway indicate that water changes that affect soil carbon fractions indirectly influence the three enzyme gene metabolic pathways related to plant carbon sources (the glycolysis/gluconeogenesis, other glycan degradation and amino sugar, and nucleotide sugar metabolism). Overall, this study highlights the significance of microbial CAZymes in highland peatland soil carbon processes and indicates that microbial conversion of plant and fungal biomass carbon is more sensitive to water changes.}, } @article {pmid37731580, year = {2023}, author = {Pan, FY and Fan, HZ and Zhuang, SH and Pan, LF and Ye, XH and Tong, HJ}, title = {Severe inflammatory disorder in trisomy 8 without myelodysplastic syndrome and response to methylprednisolone: A case report.}, journal = {World journal of clinical cases}, volume = {11}, number = {26}, pages = {6206-6212}, pmid = {37731580}, issn = {2307-8960}, abstract = {BACKGROUND: Patients with trisomy 8 consistently present with myeloid neoplasms and/or auto-inflammatory syndrome. A possible link between myelodysplastic syndromes (MDS) with trisomy 8 (+8-MDS) and inflammatory disorders is well recognized, several cases having been reported. However, inflammatory disorders in patients without MDS have been largely overlooked. Generally, Behçet's disease is the most common type in +8-MDS. However, inflammatory disorders with pulmonary involvement are less frequent, and no effective treatment has been established.

CASE SUMMARY: A 27-year-old man with recurrent fever, fatigue for > 2 mo, and unconsciousness for 1 day was admitted to our emergency department with a provisional diagnosis of severe pneumonia. Vancomycin and imipenem were administered and sputum collected for metagenomic next-generation sequencing. Epstein-Barr virus and Mycobacterium kansasii were detected. Additionally, chromosomal analysis showed duplications on chromosome 8. Two days later, repeat metagenomic next-generation sequencing was performed with blood culture. Cordyceps portugal, M. kansasii, and Candida portugal were detected, and duplications on chromosome 8 confirmed. Suspecting hematological disease, we aspirated a bone marrow sample from the iliac spine, examination of which showed evidence of infection. We added fluconazole as further antibiotic therapy. Seven days later, the patient's condition had not improved, prompting addition of methylprednisolone as an anti-inflammatory agent. Fortunately, this treatment was effective and the patient eventually recovered.

CONCLUSION: Severe inflammatory disorders with pulmonary involvement can occur in patients with trisomy 8. Methylprednisolone may be an effective treatment.}, } @article {pmid37731336, year = {2023}, author = {Aizpurua, O and Dunn, RR and Hansen, LH and Gilbert, MTP and Alberdi, A}, title = {Field and laboratory guidelines for reliable bioinformatic and statistical analysis of bacterial shotgun metagenomic data.}, journal = {Critical reviews in biotechnology}, volume = {}, number = {}, pages = {1-19}, doi = {10.1080/07388551.2023.2254933}, pmid = {37731336}, issn = {1549-7801}, abstract = {Shotgun metagenomics is an increasingly cost-effective approach for profiling environmental and host-associated microbial communities. However, due to the complexity of both microbiomes and the molecular techniques required to analyze them, the reliability and representativeness of the results are contingent upon the field, laboratory, and bioinformatic procedures employed. Here, we consider 15 field and laboratory issues that critically impact downstream bioinformatic and statistical data processing, as well as result interpretation, in bacterial shotgun metagenomic studies. The issues we consider encompass intrinsic properties of samples, study design, and laboratory-processing strategies. We identify the links of field and laboratory steps with downstream analytical procedures, explain the means for detecting potential pitfalls, and propose mitigation measures to overcome or minimize their impact in metagenomic studies. We anticipate that our guidelines will assist data scientists in appropriately processing and interpreting their data, while aiding field and laboratory researchers to implement strategies for improving the quality of the generated results.}, } @article {pmid37731212, year = {2023}, author = {Ji, C and Liu, J and Mou, Y and Cheng, W and Hu, W}, title = {Rapid Diagnosis of Mycobacterium marinum Infection on Both Hands using a Combination of Skin Trephination and Metagenomic Next-generation Sequencing.}, journal = {Acta dermato-venereologica}, volume = {103}, number = {}, pages = {adv13360}, pmid = {37731212}, issn = {1651-2057}, mesh = {Humans ; *Trephining ; *Hand ; Upper Extremity ; High-Throughput Nucleotide Sequencing ; }, } @article {pmid37731192, year = {2024}, author = {Faber, A and Fritz, G}, title = {Seek and you shall find-news on the quest for novel PET-degrading enzymes.}, journal = {The FEBS journal}, volume = {291}, number = {1}, pages = {57-60}, doi = {10.1111/febs.16958}, pmid = {37731192}, issn = {1742-4658}, support = {FT230100283//Australian Research Council/ ; //Forrest Research Foundation/ ; //Jock Clough Marine Foundation/ ; //Centre for Entrepreneurial Research and Innovation/ ; //Woodside Energy Ltd./ ; }, mesh = {*Polyethylene Terephthalates/chemistry ; *Hydrolases/chemistry ; Esterases ; Hydrolysis ; }, abstract = {Plastic-degrading enzymes hold immense potential for eco-friendly recycling methods. However, the catalytic rates of current enzymes do not stack up against the mammoth task of degrading millions of tons of plastic waste per year. In the quest for more efficient polyethylene terephthalate (PET)-degrading enzymes, Zhang et al. report the discovery and characterization of PET40, a versatile PET-hydrolyzing esterase that is divergent from most characterized PETases. While PET40 has comparably low hydrolytic activity on PET, Zhang et al. demonstrate its broad activity on an expanded substrate pool. This sheds light on the potential ecological role of these esterases and suggests that PET might be only a recent addition to their substrate spectrum.}, } @article {pmid37730729, year = {2023}, author = {Nicolas, AM and Sieradzki, ET and Pett-Ridge, J and Banfield, JF and Taga, ME and Firestone, MK and Blazewicz, SJ}, title = {A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5835}, pmid = {37730729}, issn = {2041-1723}, mesh = {*Ecosystem ; Grassland ; California ; Soil ; *Viruses ; }, abstract = {Viruses are abundant, ubiquitous members of soil communities that kill microbial cells, but how they respond to perturbation of soil ecosystems is essentially unknown. Here, we investigate lineage-specific virus-host dynamics in grassland soil following "wet-up", when resident microbes are both resuscitated and lysed after a prolonged dry period. Quantitative isotope tracing, time-resolved metagenomics and viromic analyses indicate that dry soil holds a diverse but low biomass reservoir of virions, of which only a subset thrives following wet-up. Viral richness decreases by 50% within 24 h post wet-up, while viral biomass increases four-fold within one week. Though recent hypotheses suggest lysogeny predominates in soil, our evidence indicates that viruses in lytic cycles dominate the response to wet-up. We estimate that viruses drive a measurable and continuous rate of cell lysis, with up to 46% of microbial death driven by viral lysis one week following wet-up. Thus, viruses contribute to turnover of soil microbial biomass and the widely reported CO2 efflux following wet-up of seasonally dry soils.}, } @article {pmid37730174, year = {2023}, author = {Benjamim da Silva, É and Polukis, SA and Smith, ML and Voshell, RS and Leggett, MJ and Jones, PB and Kung, L}, title = {The use of Lentilactobacillus buchneri PJB1 and Lactiplantibacillus plantarum MTD1 on the ensiling of whole-plant corn silage, snaplage, and high-moisture corn.}, journal = {Journal of dairy science}, volume = {}, number = {}, pages = {}, doi = {10.3168/jds.2023-23672}, pmid = {37730174}, issn = {1525-3198}, abstract = {Experiments were conducted over a 3-year period to evaluate the effects of bacterial inoculants on the fermentation profile and aerobic stability of whole-plant corn silage (WPC), snaplage (SNP), and high-moisture corn (HMC). Whole-plant corn was inoculated with Lentilactobacillus buchneri PJB1 in combination with Lactiplantibacillus plantarum MTD1or with L. plantarum alone (Experiments 1 and 2). Snaplage (Experiment 3) and HMC (Experiments 4 and 5) were inoculated with L. buchneri in combination with L. plantarum or with L. buchneri alone. After inoculation, the feedstuffs were ensiled in 7.57-L silos and stored at 21 ± 2°C for 30 or 90 d. In Experiment 5, silage was subjected to air stress for 2 h every 2 weeks through 42 d and then for 2 h/week until 90 d and had samples analyzed for their bacterial community composition by metagenomics. Overall, in all experiments, silages inoculated with L. buchneri alone or in combination with L. plantarum had more acetic acid and 1,2-propanediol and fewer yeasts than uninoculated silages. After 30 d of ensiling, inoculation with L. buchneri alone or in combination with L. plantarum did not affect the aerobic stability of SNP, but it slightly increased the stability of WPC and markedly improved the stability of HMC. After 90 d of ensiling, inoculation with L. buchneri alone or in combination with L. plantarum markedly improved the aerobic stability of WPC, SNP, and HMC. In Experiment 5, inoculation increased the relative abundance (RA) of Lactobacillaceae and reduced the RA of Enterobacteriaceae and Leuconostocaceae in HMC at 30 and 90 d and the RA of Clostridiaceae in non-air-stressed HMC at 90 d. Air-stressed HMC inoculated with L. buchneri had less lactic acid, more acetic acid and 1,2-propanediol, and markedly greater aerobic stability than uninoculated air-stressed HMC at 90 d. In conclusion, inoculation with L. buchneri PJB1 alone or in combination with L. plantarum MTD1 increased the production of acetic acid and 1,2-propanediol, inhibited yeasts development, and improved the aerobic stability of WPC, SNP, and HMC. In HMC, inoculation markedly improved aerobic stability as soon as after 30 d of ensiling, and after 90 d, it improved stability even under air stress conditions.}, } @article {pmid37730069, year = {2023}, author = {Chen, L and Zhou, LT and Ding, YC and Wu, D and Feng, HJ}, title = {Enhancing microbial salt tolerance through low-voltage stimulation for improved p-chloronitrobenzene (p-CNB) removal in high-salinity wastewater.}, journal = {The Science of the total environment}, volume = {905}, number = {}, pages = {167164}, doi = {10.1016/j.scitotenv.2023.167164}, pmid = {37730069}, issn = {1879-1026}, mesh = {*Wastewater ; *Salinity ; Salt Tolerance ; Sodium Chloride ; Bioreactors ; Sewage/chemistry ; }, abstract = {As an important raw material for the synthesis of chemical and pharmaceutical, hazardous carcinogen p-chloronitrobenzene (p-CNB) has been widely found in high-salinity wastewater which need to be treated carefully. Due to the high-salinity shock on microorganisms, conventional microbial treatment technologies usually show poor effluent quality. This study initially investigated the p-CNB removal performance of microorganisms stimulated by 1.2 V low-voltage in high-salinity wastewater under facultative anaerobic conditions and further revealed the enhanced mechanisms. The results showed that the p-CNB removal kinetic parameter kp-CNB in the electrostimulating microorganism reactor (EMR) increased by 104.37 % to 155.30 % compared to the microorganism reactor (MR) as the control group under the varying salinities (0-45 g/L NaCl). The secretion of extracellular polymeric substances (EPS) in halotolerant microorganisms mainly enhanced by 1.2 V voltage stimulation ranging from 0 g/L NaCl to 30 g/L NaCl. Protein concentration ratio of EMR to MR in loosely bound EPS achieved maximum value of 1.77 at the salinity of 15 g/L NaCl, and the same ratio in tightly bound EPS also peaked at 1.39 under the salinity of 30 g/L NaCl. At the salinity of 45 g/L NaCl, 1.2 V voltage stimulation mainly enhanced salt-in strategy of halotolerant microorganisms, and the intracellular Na[+] and K[+] concentration ratio of EMR to MR reached maximum and minimum values of 0.65 and 1.92, respectively. Furthermore, the results of microbial metagenomic and metatranscriptomic analysis showed the halotolerant microorganisms Pseudomonas_A and Nitratireductor with p-CNB removal ability were enriched significantly under 1.2 V voltage stimulation. And the gene expression of p-CNB removal, salt-in strategy and betaine transporter were enhanced under voltage stimulation at varying salinities. Our investigation provided a new solution which combined with 1.2 V voltage stimulation and halotolerant microorganisms for the treatment of high-salinity wastewater.}, } @article {pmid37729847, year = {2023}, author = {Perlejewski, K and Radkowski, M and Pawełczyk, A and Rydzanicz, M and Dzieciątkowski, T and Makowiecki, M and Paciorek, M and Welc-Falęciak, R and Horban, A and Laskus, T}, title = {Enteroviral central nervous system infections in patients with Lyme neuroborreliosis.}, journal = {Ticks and tick-borne diseases}, volume = {14}, number = {6}, pages = {102253}, doi = {10.1016/j.ttbdis.2023.102253}, pmid = {37729847}, issn = {1877-9603}, mesh = {Humans ; *Lyme Neuroborreliosis/diagnosis/cerebrospinal fluid ; *Epstein-Barr Virus Infections ; Herpesvirus 4, Human ; *Central Nervous System Infections ; Polymerase Chain Reaction ; }, abstract = {Patients with Lyme neuroborreliosis (LNB) are rarely tested for the presence of neurovirulent viruses other than tick-borne encephalitis virus (TBEV); however, such coinfections could be of clinical importance. The aim of the study was to search for the presence of neurotropic viruses in a LNB patients. Fourteen patients admitted with signs and symptoms of neuroinfection who were eventually diagnosed to have LNB (according to the guidelines of the European Federation of Neurological Societies) were subjects of the study. Sera and cerebrospinal fluid (CSF) collected at the time of initial presentation were tested for viral pathogens most common in our geographical area: human enteroviruses (EV), herpes simplex virus type 1 and 2, varicella-zoster virus, Epstein-Barr virus, cytomegalovirus, human herpesvirus type 6, human adenoviruses, and TBEV using PCR/RT-PCR and serological assays. RNA and DNA-based metagenomic next-generation sequencing (mNGS) was used to detect other viral pathogens. EV was detected in CSF from two (14 %) LNB patients and viral loads were similar (220 and 270 copies/ml). The mMGS analysis were performed on CSFs from 10 patients and generated a total 213,750,885 NGS reads, 0.05 % of which were viral. However, none of potential pathogens fulfilled the criteria for positive viral detection by mNGS. Using a number of PCR/RT-PCR assays and mNGS we identified EV infection in two out of 14 LNB patients. The possible co-occurrence of enterovirus and Lyme neuroborreliosis infections may warrant further research.}, } @article {pmid37729842, year = {2023}, author = {Ao, Z and Li, Y and Li, Y and Zhao, Z and Zhang, Y}, title = {Facilitating direct interspecies electron transfer in anaerobic digestion via speeding up transmembrane transport of electrons and CO2 reduction in methanogens by Na[+] adjustment.}, journal = {Waste management (New York, N.Y.)}, volume = {170}, number = {}, pages = {252-260}, doi = {10.1016/j.wasman.2023.09.017}, pmid = {37729842}, issn = {1879-2456}, abstract = {The possibility of facilitating direct interspecies electron transfer (DIET) in anaerobic digestion with different concentrations of NaCl was explored. Additional NaCl at 2 or 4 g/L strengthened anaerobic digestion to resist the high-organic loading rate impacts, whereas the higher concentrations of NaCl (6 or 8 g/L) suppressed methanogenesis. Additional MgCl2 with the same ion strength as NaCl at 2 g/L had no effect on performances. Additional NaCl at 2 or 4 g/L dramatically increased the abundance of Methanosarcina species (20.7%/23.4% vs 8.6%) and stimulated the growth of Sphaerochaeta and Petrimonas species that could transfer electrons to the soluble Fe(III) or elemental sulfur. Electrochemical evidences showed that, additional NaCl at 2 or 4 g/L increased capacitances and decreased charge transfer resistances of Methanosarcina-dominant communities. Metagenomic evidences showed that, additional NaCl at 2 or 4 g/L increased the abundance of genes that encoded the type IV pilus assembly proteins (1.98E-04/1.87E-04 vs 1.85E-04) and cytochrome c-like proteins (5.51E-04/5.60E-04 vs 5.31E-04). In addition, additional NaCl at 2 or 4 g/L increased the abundance of genes for methanophenazine (MP)/MPH2 transformation (1.04E-05/1.24E-05 vs 8.06E-06) and CO2 reduction (1.64E-03/1.86E-03 vs 1.06E-03), suggesting a rapid transmembrane transport of electrons and CO2 reduction in methanogens. Both processes were closely associated with F420/F420H2 transformation that required ATP. Additional NaCl at 2 or 4 g/L increased the yield of ATP (256.0/249.3 vs 231.8 nmol/L) that might promote F420/F420H2 transformation in methanogens, which overcame the thermodynamic limitations of combining electrons with protons for the reduction of CO2 to methane and facilitated DIET.}, } @article {pmid37729712, year = {2024}, author = {Lu, J and Liu, Y and Zhang, R and Hu, Z and Xue, K and Dong, B}, title = {Biochar inoculated with Pseudomonas putida alleviates its inhibitory effect on biodegradation pathways in phenanthrene-contaminated soil.}, journal = {Journal of hazardous materials}, volume = {461}, number = {}, pages = {132550}, doi = {10.1016/j.jhazmat.2023.132550}, pmid = {37729712}, issn = {1873-3336}, mesh = {*Pseudomonas putida/metabolism ; *Soil Pollutants/metabolism ; Soil Microbiology ; *Phenanthrenes/pharmacology/metabolism ; Biodegradation, Environmental ; *Polycyclic Aromatic Hydrocarbons/analysis ; Soil ; }, abstract = {Controversial results are reported whereby biodegradation of polycyclic aromatic hydrocarbons (PAHs) can be promoted or inhibited by biochar amendment of soil. Metabolomics was applied to analyze the metabolic profiles of amendment with biochar (BB) and biochar inoculated with functional bacteria (Pseudomonas putida) (BP) involved in phenanthrene (PHE) degradation. Additionally, metagenomic analysis was utilized to assess the impact of different treatments on PHE degradation by soil microorganisms. Results indicated that BB treatment decreased the PHE biodegradation of the soil indigenous bacterial consortium, but BP treatment alleviated this inhibitory effect. Metabolomics revealed the differential metabolite 9-phenanthrol was absent in the BB treatment, but was found in the control group (CK), and in the treatment inoculated with the Pseudomonas putida (Ps) and the BP treatment. Metagenomic analysis showed that biochar decreased the abundance of the cytochrome P450 monooxygenase (CYP116), which was detected in the Pseudomonas putida, thus alleviating the inhibitory effect of biochar on PHE degradation. Moreover, a noticeable delayed increase of functional gene abundance and enzymes abundance in the BB treatment was observed in the PHE degradation pathway. Our findings elucidate the mechanism of inhibition with biochar amendment and the alleviating effect of biochar inoculated with degrading bacteria.}, } @article {pmid37729205, year = {2023}, author = {Yan, Z and Du, K and Yan, Y and Huang, R and Zhu, F and Yuan, X and Wang, S and Ferry, JG}, title = {Respiration-driven methanotrophic growth of diverse marine methanogens.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {39}, pages = {e2303179120}, pmid = {37729205}, issn = {1091-6490}, mesh = {*Respiration ; *Euryarchaeota ; Archaea/genetics ; Atmosphere ; Consensus ; }, abstract = {Anaerobic marine environments are the third largest producer of the greenhouse gas methane. The release to the atmosphere is prevented by anaerobic 'methanotrophic archaea (ANME) dependent on a symbiotic association with sulfate-reducing bacteria or direct reduction of metal oxides. Metagenomic analyses of ANME are consistent with a reverse methanogenesis pathway, although no wild-type isolates have been available for validation and biochemical investigation. Herein is reported the characterization of methanotrophic growth for the diverse marine methanogens Methanosarcina acetivorans C2A and Methanococcoides orientis sp. nov. Growth was dependent on reduction of either ferrihydrite or humic acids revealing a respiratory mode of energy conservation. Acetate and/or formate were end products. Reversal of the well-characterized methanogenic pathways is remarkably like the consensus pathways for uncultured ANME based on extensive metagenomic analyses.}, } @article {pmid37728942, year = {2023}, author = {Subirats, J and Sharpe, H and Tai, V and Fruci, M and Topp, E}, title = {Metagenome meta-analysis reveals an increase in the abundance of some multidrug efflux pumps and mobile genetic elements in chemically polluted environments.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {10}, pages = {e0104723}, pmid = {37728942}, issn = {1098-5336}, mesh = {Humans ; *Metagenome ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Interspersed Repetitive Sequences ; *Petroleum ; }, abstract = {Many human activities contaminate terrestrial and aquatic environments with numerous chemical pollutants that not only directly alter the environment but also affect microbial communities in ways that are potentially concerning to human health, such as selecting for the spread of antibiotic-resistance genes (ARGs) through horizontal gene transfer. In the present study, metagenomes available in the public domain from polluted (with antibiotics, with petroleum, with metal mining, or with coal-mining effluents) and unpolluted terrestrial and aquatic environments were compared to examine whether pollution has influenced the abundance and composition of ARGs and mobile elements, with specific focus on IS26 and class 1 integrons (intI1). When aggregated together, polluted environments had a greater relative abundance of ARGs than unpolluted environments and a greater relative abundance of IS26 and intI1. In general, chemical pollution, notably with petroleum, was associated with an increase in the prevalence of ARGs linked to multidrug efflux pumps. Included in the suite of efflux pumps were mexK, mexB, mexF, and mexW that are polyspecific and whose substrate ranges include multiple classes of critically important antibiotics. Also, in some instances, β-lactam resistance (TEM181 and OXA-541) genes increased, and genes associated with rifampicin resistance (RNA polymerases subunits rpoB and rpoB2) decreased in relative abundance. This meta-analysis suggests that different types of chemical pollution can enrich populations that carry efflux pump systems associated with resistance to multiple classes of medically critical antibiotics.IMPORTANCEThe United Nations has identified chemical pollution as being one of the three greatest threats to environmental health, through which the evolution of antimicrobial resistance, a seminally important public health challenge, may be favored. While this is a very plausible outcome of continued chemical pollution, there is little evidence or research evaluating this risk. The objective of the present study was to examine existing metagenomes from chemically polluted environments and evaluate whether there is evidence that pollution increases the relative abundance of genes and mobile genetic elements that are associated with antibiotic resistance. The key finding is that for some types of pollution, particularly in environments exposed to petroleum, efflux pumps are enriched, and these efflux pumps can confer resistance to multiple classes of medically important antibiotics that are typically associated with Pseudomonas spp. or other Gram-negative bacteria. This finding makes clear the need for more investigation on the impact of chemical pollution on the environmental reservoir of ARGs and their association with mobile genetic elements that can contribute to horizontal gene transfer events.}, } @article {pmid37728722, year = {2023}, author = {Zhong, ML and Cai, YQ and Tang, YF and Dai, YL and Jiang, YH and Ni, Y and Zou, CC}, title = {Gut microbiota, a potential cause of higher insulin sensitivity in children with Prader-Willi syndrome.}, journal = {Journal of endocrinological investigation}, volume = {}, number = {}, pages = {}, pmid = {37728722}, issn = {1720-8386}, support = {81371215//National Natural Science Foundation of China/ ; 81670786//National Natural Science Foundation of China/ ; }, abstract = {PURPOSE: Obesity is the main driving factor for comorbidities in Prader-Willi syndrome (PWS) patients due to overeating behaviors. The gut microbiota has been implicated in the etiology of obesity and associated comorbidities. The purpose of the present study was to characterize the fecal microbiota in Chinese patients with PWS and compare it to that of patients with obesity as well as healthy controls.

METHODS: We conducted a cross-sectional study with 35 PWS patients (PWS), 35 patients with obesity (OB), and 35 healthy controls (HC). Metagenomic sequencing was performed in stool samples.

RESULTS: The composition of the fecal microbiota in PWS patients differed from that of participants in the OB and HC groups. It was characterized by increased Akkermansia Eubacterium, Eubacterium rectale, and Roseburia intestinalis and decreased Parabacteroides and Phascolarctobacterium. Additionally, the homeostatic model assessment of insulin resistance (HOMA-IR) was lower in PWS patients than in patients with obesity. Spearman rank correlation analysis showed that Achromobacter, Acidiphilium, Xylophilus, and Frisingicoccus were significantly negatively correlated with HOMA-IR.

CONCLUSION: The composition of the gut microbiota in Chinese PWS patients differed from that in patients with obesity, which might contribute to higher insulin sensitivity in PWS patients.}, } @article {pmid37728335, year = {2023}, author = {Mancabelli, L and Taurino, G and Ticinesi, A and Ciociola, T and Vacondio, F and Milani, C and Fontana, F and Lugli, GA and Tarracchini, C and Alessandri, G and Viappiani, A and Bianchi, M and Nouvenne, A and Chetta, AA and Turroni, F and Meschi, T and Mor, M and Bussolati, O and Ventura, M}, title = {Disentangling the interactions between nasopharyngeal and gut microbiome and their involvement in the modulation of COVID-19 infection.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0219423}, pmid = {37728335}, issn = {2165-0497}, abstract = {The human organism is inhabited by trillions of microorganisms, known as microbiota, which are considered to exploit a pivotal role in the regulation of host health and immunity. Recent investigations have suggested a relationship between the composition of the human microbiota and COVID-19 infection, highlighting a possible role of bacterial communities in the modulation of the disease severity. In this study, we performed a shotgun metagenomics analysis to explore and compare the nasopharyngeal microbiota of 38 hospitalized Italian patients with and without COVID-19 infection during the third and fourth pandemic waves. In detail, the metagenomic analysis combined with specific correlation analyses suggested a positive association of several microbial species, such as S. parasanguinis and P. melaninogenica, with the severity of COVID-19 infection. Furthermore, the comparison of the microbiota composition between the nasopharyngeal and their respective fecal samples highlighted an association between these different compartments represented by a sharing of several bacterial species. Additionally, lipidomic and deep-shotgun functional analyses of the fecal samples suggested a metabolic impact of the microbiome on the host's immune response, indicating the presence of key metabolic compounds in COVID-19 patients, such as lipid oxidation end products, potentially related to the inflammatory state. Conversely, the patients without COVID-19 displayed enzymatic patterns associated with the biosynthesis and degradation of specific compounds like lysine (synthesis) and phenylalanine (degradation) that could positively impact disease severity and contribute to modulating COVID-19 infection. IMPORTANCE The human microbiota is reported to play a major role in the regulation of host health and immunity, suggesting a possible impact on the severity of COVID-19 disease. This preliminary study investigated the possible correlation between nasopharyngeal microbiota and COVID-19 infection. In detail, the analysis of the nasopharyngeal microbiota of hospitalized Italian patients with and without COVID-19 infection suggested a positive association of several microbial species with the severity of the disease and highlighted a sharing of several bacteria species with the respective fecal samples. Moreover, the metabolic analyses suggested a possible impact of the microbiome on the host's immune response and the disease severity.}, } @article {pmid37727808, year = {2023}, author = {Herzog, EL and Kreuzer, M and Zinkernagel, MS and Zysset-Burri, DC}, title = {Challenges and insights in the exploration of the low abundance human ocular surface microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1232147}, pmid = {37727808}, issn = {2235-2988}, mesh = {Humans ; *Nylons ; Reproducibility of Results ; Face ; Conjunctiva ; *Microbiota ; }, abstract = {PURPOSE: The low microbial abundance on the ocular surface results in challenges in the characterization of its microbiome. The purpose of this study was to reveal factors introducing bias in the pipeline from sample collection to data analysis of low-abundant microbiomes.

METHODS: Lower conjunctiva and lower lid swabs were collected from six participants using either standard cotton or flocked nylon swabs. Microbial DNA was isolated with two different kits (with or without prior host DNA depletion and mechanical lysis), followed by whole-metagenome shotgun sequencing with a high sequencing depth set at 60 million reads per sample. The relative microbial compositions were generated using the two different tools MetaPhlan3 and Kraken2.

RESULTS: The total amount of extracted DNA was increased by using nylon flocked swabs on the lower conjunctiva. In total, 269 microbial species were detected. The most abundant bacterial phyla were Actinobacteria, Firmicutes and Proteobacteria. Depending on the DNA extraction kit and tool used for profiling, the microbial composition and the relative abundance of viruses varied.

CONCLUSION: The microbial composition on the ocular surface is not dependent on the swab type, but on the DNA extraction method and profiling tool. These factors have to be considered in further studies about the ocular surface microbiome and other sparsely colonized microbiomes in order to improve data reproducibility. Understanding challenges and biases in the characterization of the ocular surface microbiome may set the basis for microbiome-altering interventions for treatment of ocular surface associated diseases.}, } @article {pmid37727483, year = {2023}, author = {Chen, Q and Niu, YL and Zhang, T}, title = {Diagnosis and treatment of Whipple disease after kidney transplantation: A case report.}, journal = {World journal of clinical cases}, volume = {11}, number = {25}, pages = {6019-6024}, pmid = {37727483}, issn = {2307-8960}, abstract = {BACKGROUND: Kidney transplantation is the standard treatment for end-stage renal disease. Particularly, rare and specific pathogenic infections which are asymptomatic are often difficult to diagnose, causing delayed and ineffective treatment and thus seriously affecting prognosis. Tropheryma whipplei (T. whipplei) is a Gram-positive actinomycete widely found in soil, sewage, and other external environments and is present in the population as an asymptomatic pathogen. There is relatively little documented research on T. whipplei in renal transplant patients, and there are no uniform criteria for treating this group of post-transplant patients. This article describes the treatment of a 42-year-old individual with post-transplant T. whipplei infection following kidney transplantation.

CASE SUMMARY: To analyze clinical features of Whipple's disease and summarize its diagnosis and treatment effects after renal transplantation. Clinical data of a Whipple's disease patient treated in the affiliated hospital of Guizhou Medical University were collected and assessed retrospectively. The treatment outcomes and clinical experience were then summarized via literature review. The patient was admitted to the hospital due to recurrent diarrhea for 1 mo, shortness of breath, and 1 wk of fever, after 3 years of renal transplantation. The symptoms of the digestive and respiratory systems were not significantly improved after adjusting immunosuppressive regimen and anti-diarrheal, empirical antibiotic treatments. Bronchoscopic alveolar fluid was collected for meta-genomic next-generation sequencing (mNGS). The deoxyribonucleic acid sequence of Tropheryma whipplei was detected, and Whipple's disease was diagnosed. Meropenem, ceftriaxone, and other symptomatic treatments were given, and water-electrolyte balance was maintained. Symptoms resolved quickly, and the patient was discharged after 20 d of hospitalization. The compound sulfamethoxazole tablet was continued for 3 mo after discharge. No diarrhea, fever, and other symptoms occurred during the 6-month follow-up.

CONCLUSION: Whipple's disease is rare, with no specific symptoms, which makes diagnosis difficult. Polymerase chain reaction or mNGS should be immediately performed when the disease is suspected to confirm the diagnosis.}, } @article {pmid37727275, year = {2023}, author = {Li, J and Yan, C and Wei, D and Gong, X}, title = {Streptococcus gallolyticus Subspecies pasteurianus Meningitis in an Infant with Hypothyroidism and Diarrhea.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {6217-6223}, pmid = {37727275}, issn = {1178-6973}, abstract = {Streptococcus gallolyticus subspecies pasteurianus, formerly classified as S. bovis biotype II/2 until 2003, is a rare cause of infant meningitis. Over the past 2 decades, only a few individual case reports and limited case series exist in the English-language literature. Moreover, the pathogenesis of S. gallolyticus subsp. pasteurianus meningitis in infants is unclear. Here we report a case of meningitis in a 6-week-old infant with hypothyroidism and preceding diarrhea. In this case, S. gallolyticus was cultured from cerebrospinal fluid, and then S. gallolyticus subspecies pasteurianus was identified by metagenomic next-generation Sequencing. The infant recovered uneventfully after a 4-week antibiotic course with ceftriaxone and vancomycin. Then combined with the literature of S. gallolyticus subsp. pasteurianus meningitis in infants, we discuss the possible etiology.}, } @article {pmid37726374, year = {2023}, author = {Hansen, ZA and Vasco, K and Rudrik, JT and Scribner, KT and Zhang, L and Manning, SD}, title = {Recovery of the gut microbiome following enteric infection and persistence of antimicrobial resistance genes in specific microbial hosts.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15524}, pmid = {37726374}, issn = {2045-2322}, support = {U01 CK000510/CK/NCEZID CDC HHS/United States ; U01CK000510/ACL/ACL HHS/United States ; U19 AI090872/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome/genetics ; Drug Resistance, Bacterial/genetics ; *Anti-Infective Agents ; Aminoglycosides ; }, abstract = {Enteric pathogens cause widespread foodborne illness and are increasingly resistant to important antibiotics yet their ecological impact on the gut microbiome and resistome is not fully understood. Herein, shotgun metagenome sequencing was applied to stool DNA from 60 patients (cases) during an enteric bacterial infection and after recovery (follow-ups). Overall, the case samples harbored more antimicrobial resistance genes (ARGs) with greater resistome diversity than the follow-up samples (p < 0.001), while follow-ups had more diverse gut microbiota (p < 0.001). Although cases were primarily defined by genera Escherichia, Salmonella, and Shigella along with ARGs for multi-compound and multidrug resistance, follow-ups had a greater abundance of Bacteroidetes and Firmicutes phyla and resistance genes for tetracyclines, macrolides, lincosamides, and streptogramins, and aminoglycosides. A host-tracking analysis revealed that Escherichia was the primary bacterial host of ARGs in both cases and follow-ups, with a greater abundance occurring during infection. Eleven distinct extended spectrum beta-lactamase (ESBL) genes were identified during infection, with some detectable upon recovery, highlighting the potential for gene transfer within the community. Because of the increasing incidence of disease caused by foodborne pathogens and their role in harboring and transferring resistance determinants, this study enhances our understanding of how enteric infections impact human gut ecology.}, } @article {pmid37726348, year = {2023}, author = {Warner, BB and Rosa, BA and Ndao, IM and Tarr, PI and Miller, JP and England, SK and Luby, JL and Rogers, CE and Hall-Moore, C and Bryant, RE and Wang, JD and Linneman, LA and Smyser, TA and Smyser, CD and Barch, DM and Miller, GE and Chen, E and Martin, J and Mitreva, M}, title = {Social and psychological adversity are associated with distinct mother and infant gut microbiome variations.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5824}, pmid = {37726348}, issn = {2041-1723}, support = {UL1 TR002345/TR/NCATS NIH HHS/United States ; }, mesh = {Female ; Pregnancy ; Humans ; Infant ; *Gastrointestinal Microbiome/genetics ; Mothers ; Case-Control Studies ; Bifidobacterium/genetics ; Cytokines ; Vitamins ; }, abstract = {Health disparities are driven by underlying social disadvantage and psychosocial stressors. However, how social disadvantage and psychosocial stressors lead to adverse health outcomes is unclear, particularly when exposure begins prenatally. Variations in the gut microbiome and circulating proinflammatory cytokines offer potential mechanistic pathways. Here, we interrogate the gut microbiome of mother-child dyads to compare high-versus-low prenatal social disadvantage, psychosocial stressors and maternal circulating cytokine cohorts (prospective case-control study design using gut microbiomes from 121 dyads profiled with 16 S rRNA sequencing and 89 dyads with shotgun metagenomic sequencing). Gut microbiome characteristics significantly predictive of social disadvantage and psychosocial stressors in the mothers and children indicate that different discriminatory taxa and related pathways are involved, including many species of Bifidobacterium and related pathways across several comparisons. The lowest inter-individual gut microbiome similarity was observed among high-social disadvantage/high-psychosocial stressors mothers, suggesting distinct environmental exposures driving a diverging gut microbiome assembly compared to low-social disadvantage/low-psychosocial stressors controls (P = 3.5 × 10[-5] for social disadvantage, P = 2.7 × 10[-15] for psychosocial stressors). Children's gut metagenome profiles at 4 months also significantly predicted high/low maternal prenatal IL-6 (P = 0.029), with many bacterial species overlapping those identified by social disadvantage and psychosocial stressors. These differences, based on maternal social and psychological status during a critical developmental window early in life, offer potentially modifiable targets to mitigate health inequities.}, } @article {pmid37726290, year = {2023}, author = {Liu, S and Zhang, ZF and Mao, J and Zhou, Z and Zhang, J and Shen, C and Wang, S and Marco, ML and Mao, J}, title = {Integrated meta-omics approaches reveal Saccharopolyspora as the core functional genus in huangjiu fermentations.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {65}, pmid = {37726290}, issn = {2055-5008}, mesh = {Fermentation ; *Saccharopolyspora/genetics ; Saccharomyces cerevisiae ; Amino Acids ; Cellulose ; }, abstract = {Identification of the core functional microorganisms in food fermentations is necessary to understand the ecological and functional processes for making those foods. Wheat qu, which provides liquefaction and saccharifying power, and affects the flavor quality, is a key ingredient in ancient alcoholic huangjiu fermentation, while core microbiota of them still remains indistinct. In this study, metagenomics, metabolomics, microbial isolation and co-fermentation were used to investigate huangjiu. Although Aspergillus is usually regarded as core microorganism in wheat qu to initiate huangjiu fermentations, our metagenomic analysis showed that bacteria Saccharopolyspora are predominant in wheat qu and responsible for breakdown of starch and cellulose. Metabolic network and correlation analysis showed that Saccharopolyspora rectivirgula, Saccharopolyspora erythraea, and Saccharopolyspora hirsuta made the greatest contributions to huangjiu's metabolites, consisting of alcohols (phenylethanol, isoamylol and isobutanol), esters, amino acids (Pro, Arg, Glu and Ala) and organic acids (lactate, tartrate, acetate and citrate). S. hirsuta J2 isolated from wheat qu had the highest amylase, glucoamylase and protease activities. Co-fermentations of S. hirsuta J2 with S. cerevisiae HJ resulted in a higher fermentation rate and alcohol content, and huangjiu flavors were more similar to that of traditional huangjiu compared to co-fermentations of Aspergillus or Lactiplantibacillus with S. cerevisiae HJ. Genome of S. hirsuta J2 contained genes encoding biogenic amine degradation enzymes. By S. hirsuta J2 inoculation, biogenic amine content was reduced by 45%, 43% and 62% in huangjiu, sausage and soy sauce, respectively. These findings show the utility of Saccharopolyspora as a key functional organism in fermented food products.}, } @article {pmid37726263, year = {2023}, author = {Xu, F and Liao, H and Yang, J and Zhang, Y and Yu, P and Cao, Y and Fang, J and Chen, S and Li, L and Sun, L and Du, C and Wang, K and Dang, X and Feng, Z and Cao, Y and Li, Y and Zhang, J and Xu, W}, title = {Auxin-producing bacteria promote barley rhizosheath formation.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5800}, pmid = {37726263}, issn = {2041-1723}, mesh = {*Hordeum ; Bacteria/genetics ; Desiccation ; Indoleacetic Acids ; Soil ; }, abstract = {The rhizosheath, or the layer of soil closely adhering to roots, can help plants to tolerate drought under moderate soil drying conditions. Rhizosheath formation is the result of poorly understood interactions between root exudates, microbes, and soil conditions. Here, we study the roles played by the soil microbiota in rhizosheath formation in barley (a dry crop). We show that barley rhizosheath formation is greater in acid soil than in alkaline soil, and inoculation with microbiota from acid soil enhances rhizosheath formation in alkaline soil. The rhizosheath-promoting activity is associated with the presence of Flavobacteriaceae and Paenibacillaceae bacteria that express genes for biosynthesis of indole-3-acetic acid (IAA, a common auxin), as determined by metagenomics and metatranscriptomics. Two bacterial strains isolated from rhizosheath (Chryseobacterium culicis and Paenibacillus polymyxa) produce IAA and enhance barley rhizosheath formation, while their IAA-defective mutants are unable to promote rhizosheath formation. Co-inoculation with the IAA-producing strains enhances barley grain yield in field experiments through an increase in spike number. Our findings contribute to our understanding of barley rhizosheath formation, and suggest potential strategies for crop improvement.}, } @article {pmid37725594, year = {2023}, author = {Madison, JD and LaBumbard, BC and Woodhams, DC}, title = {Shotgun metagenomics captures more microbial diversity than targeted 16S rRNA gene sequencing for field specimens and preserved museum specimens.}, journal = {PloS one}, volume = {18}, number = {9}, pages = {e0291540}, pmid = {37725594}, issn = {1932-6203}, mesh = {Genes, rRNA ; *Metagenomics ; *Museums ; RNA, Ribosomal, 16S/genetics ; Benchmarking ; }, abstract = {The use of museum specimens for research in microbial evolutionary ecology remains an under-utilized investigative dimension with important potential. Despite this potential, there remain barriers in methodology and analysis to the wide-spread adoption of museum specimens for such studies. Here, we hypothesized that there would be significant differences in taxonomic prediction and related diversity among sample type (museum or fresh) and sequencing strategy (medium-depth shotgun metagenomic or 16S rRNA gene). We found dramatically higher predicted diversity from shotgun metagenomics when compared to 16S rRNA gene sequencing in museum and fresh samples, with this differential being larger in museum specimens. Broadly confirming these hypotheses, the highest diversity found in fresh samples was with shotgun sequencing using the Rep200 reference inclusive of viruses and microeukaryotes, followed by the WoL reference database. In museum-specimens, community diversity metrics also differed significantly between sequencing strategies, with the alpha-diversity ACE differential being significantly greater than the same comparisons made for fresh specimens. Beta diversity results were more variable, with significance dependent on reference databases used. Taken together, these findings demonstrate important differences in diversity results and prompt important considerations for future experiments and downstream analyses aiming to incorporate microbiome datasets from museum specimens.}, } @article {pmid37725182, year = {2023}, author = {Yaragal, RR and Mutnuri, S}, title = {Diversity and functional annotation of microorganisms in anaerobic chamber treating nitrate-rich wastewater.}, journal = {World journal of microbiology & biotechnology}, volume = {39}, number = {11}, pages = {311}, pmid = {37725182}, issn = {1573-0972}, mesh = {*Nitrates ; Wastewater ; Anaerobiosis ; Archaea ; Carbon ; *Environmental Pollutants ; Nitrogen ; }, abstract = {The vertical flow constructed wetlands (VFCW) for the treatment of domestic wastewater has become a conventional and cost effective treatment system with one of the major disadvantage of elevated nitrate concentrations. The present study makes an effort in providing a new design of anaerobic denitrification unit termed as anaerobic chamber (AC) which was introduced after two-stage VFCW to remove nitrates from the treated wastewater (WW). The AC provided all the essential conditions of effective denitrification such as anaerobic environment with enough carbon and nitrogen source. To understand the pollutant removal mechanism in AC, microbial diversity and functional annotation was studied by metagenomic analysis of sequences obtained from biofilm formed in AC. The efficiency of AC was measured with respect to physicochemical wastewater quality parameters. The removal efficiencies were 88, 65, 43 and 27% for total nitrogen, nitrate (NO3), ammoniacal-nitrogen (NH4) and ortho-phosphate respectively. The microbial flora was much more diverse and unique pertaining to anaerobic microbes in AC compared to WW with total of 954 and 1191 genuses respectively with minimum abundance of 10 hits. The metagenomes exhibited 188% more Archaea in the AC than WW where Crenarchaeota, Euryarchaeota, Korarchaeota, Nanoarchaeota and Thaumarchaeota were major phyla with 60 genuses. The nitrogen metabolism was reported in terms of assimilatory nitrate reductase. As the class, Proteobacteria, Actinobacteria were prominent in WW, whereas Proteobacteria, Chloroflexi in AC were abundant. From functional annotation of sequences, the microbial flora in AC has the potential of removal of pollutants present in the form of carbon, nitrogen, and phosphorus.}, } @article {pmid37724888, year = {2023}, author = {Jiang, X and Liu, J and Xi, Y and Zhang, Q and Wang, Y and Zhao, M and Lu, X and Wu, H and Shan, T and Ni, B and Zhang, W and Ma, X}, title = {Virome of high-altitude canine digestive tract and genetic characterization of novel viruses potentially threatening human health.}, journal = {mSphere}, volume = {8}, number = {5}, pages = {e0034523}, pmid = {37724888}, issn = {2379-5042}, mesh = {Animals ; Humans ; Dogs ; *Virome ; Phylogeny ; Altitude ; *Viruses/genetics ; Zoonoses ; Gastrointestinal Tract ; }, abstract = {The majority of currently emerging infectious illnesses are zoonotic infections, which have caused serious public health and economic implications. The development of viral metagenomics has helped us to explore unknown viruses. We collected 1,970 canine feces from Yushu and Guoluo in the plateau region of China for this study to do a metagenomics analysis of the viral community of the canine digestive tract. Our analysis identified 203 novel viruses, classified into 11 known families and 2 unclassified groups. These viruses include the hepatitis E virus, first identified in dogs, and the astrovirus, coronavirus, polyomavirus, and others. The relationship between the newly identified canine viruses and known viruses was investigated through the use of phylogenetic analysis. Furthermore, we demonstrated the cross-species transmission of viruses and predicted new viruses that may cause diseases in both humans and animals, providing technical support for the prevention and control of diseases caused by environmental pollution viruses. IMPORTANCE Most emerging infectious diseases are due to zoonotic disease agents. Because of their effects on the security of human or animal life, agriculture production, and food safety, zoonotic illnesses and livestock diseases are of worldwide significance. Because dogs are closely related to humans and domestic animals, they serve as one of the important links in the transmission of zoonotic and livestock diseases. Canines can contaminate the environment in which humans live such as water and soil through secretions, potentially altering the human gut microbiota or causing diseases. Our study enriched the viral community in the digestive tract microbiome of dogs and found types of viruses that threaten human health, providing technical support for the prevention and control of early warning of diseases caused by environmental contaminant viruses.}, } @article {pmid37724866, year = {2023}, author = {van der Loos, LM and De Coninck, L and Zell, R and Lequime, S and Willems, A and De Clerck, O and Matthijnssens, J}, title = {Highly divergent CRESS DNA and picorna-like viruses associated with bleached thalli of the green seaweed Ulva.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0025523}, pmid = {37724866}, issn = {2165-0497}, abstract = {Marine macroalgae (seaweeds) are important primary producers and foundation species in coastal ecosystems around the world. Seaweeds currently contribute to an estimated 51% of the global mariculture production, with a long-term growth rate of 6% per year, and an estimated market value of more than US$11.3 billion. Viral infections could have a substantial impact on the ecology and aquaculture of seaweeds, but surprisingly little is known about virus diversity in macroalgal hosts. Using metagenomic sequencing, we characterized viral communities associated with healthy and bleached specimens of the commercially important green seaweed Ulva. We identified 20 putative new and divergent viruses, of which the majority belonged to the Circular Rep-Encoding Single-Stranded (CRESS) DNA viruses [single-stranded (ss)DNA genomes], Durnavirales [double-stranded (ds)RNA], and Picornavirales (ssRNA). Other newly identified RNA viruses were related to the Ghabrivirales, the Mitoviridae, and the Tombusviridae. Bleached Ulva samples contained particularly high viral read numbers. While reads matching assembled CRESS DNA viruses and picorna-like viruses were nearly absent from the healthy Ulva samples (confirmed by qPCR), they were very abundant in the bleached specimens. Therefore, bleaching in Ulva could be caused by one or a combination of the identified viruses but may also be the result of another causative agent or abiotic stress, with the viruses simply proliferating in already unhealthy seaweed tissue. This study highlights how little we know about the diversity and ecology of seaweed viruses, especially in relation to the health and diseases of the algal host, and emphasizes the need to better characterize the algal virosphere. IMPORTANCE Green seaweeds of the genus Ulva are considered a model system to study microbial interactions with the algal host. Remarkably little is known, however, about viral communities associated with green seaweeds, especially in relation to the health of the host. In this study, we characterized the viral communities associated with healthy and bleached Ulva. Our findings revealed the presence of 20 putative novel viruses associated with Ulva, encompassing both DNA and RNA viruses. The majority of these viruses were found to be especially abundant in bleached Ulva specimens. This is the first step toward understanding the role of viruses in the ecology and aquaculture of this green seaweed.}, } @article {pmid37724865, year = {2023}, author = {Sabatino, R and Sbaffi, T and Sivalingam, P and Corno, G and Fontaneto, D and Di Cesare, A}, title = {Bacteriophages limitedly contribute to the antimicrobial resistome of microbial communities in wastewater treatment plants.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0110123}, pmid = {37724865}, issn = {2165-0497}, abstract = {Bacteriophages are known as players in the transmission of antimicrobial resistance genes (ARGs) by horizontal gene transfer. In this study, we characterized the bacteriophage community and the associated ARGs to estimate the potential for phages to spread ARGs in aquatic ecosystems analyzing the intra- and extracellular DNA isolated from two wastewater treatment plants (WWTPs) by shotgun metagenomics. We compared the phage antimicrobial resistome with the bacterial resistome and investigated the effect of the final disinfection treatment on the phage community and its resistome. Phage community was mainly composed by Siphoviridae and other members of the order Caudovirales. The final disinfection only marginally affected the composition of the phage community, and it was not possible to measure its effect on the antimicrobial resistome. Indeed, only three phage metagenome-assembled genomes (pMAGs) annotated as Siphoviridae, Padoviridae, and Myoviridae were positive for putative ARGs. Among the detected ARGs, i.e., dfrB6, rpoB mutants, and EF-Tu mutants, the first one was not annotated in the bacterial MAGs. Overall, these results demonstrate that bacteriophages limitedly contribute to the whole antimicrobial resistome. However, in order to obtain a comprehensive understanding of the antimicrobial resistome within a microbial community, the role of bacteriophages needs to be investigated. IMPORTANCE WWTPs are considered hotspots for the spread of ARGs by horizontal gene transfer. In this study, we evaluated the phage composition and the associated antimicrobial resistome by shotgun metagenomics of samples collected before and after the final disinfection treatment. Only a few bacteriophages carried ARGs. However, since one of the detected genes was not found in the bacterial metagenome-assembled genomes, it is necessary to investigate the phage community in order to gain a comprehensive overview of the antimicrobial resistome. This investigation could help assess the potential threats to human health.}, } @article {pmid37724520, year = {2023}, author = {Yan, Z and Wang, Y and Zeng, W and Xia, R and Liu, Y and Wu, Z and Deng, W and Zhu, M and Xu, J and Deng, H and Miao, Y}, title = {Microbiota of long-term indwelling hemodialysis catheters during renal transplantation perioperative period: a cross-sectional metagenomic microbial community analysis.}, journal = {Renal failure}, volume = {45}, number = {2}, pages = {2256421}, pmid = {37724520}, issn = {1525-6049}, mesh = {Humans ; *Kidney Transplantation/adverse effects ; Cross-Sectional Studies ; Catheters, Indwelling/adverse effects ; *Microbiota ; *Catheter-Related Infections/diagnosis ; Renal Dialysis/adverse effects ; }, abstract = {Background: Catheter-related infection (CRI) is a major complication in patients undergoing hemodialysis. The lack of high-throughput research on catheter-related microbiota makes it difficult to predict the occurrence of CRI. Thus, this study aimed to delineate the microbial structure and diversity landscape of hemodialysis catheter tips among patients during the perioperative period of kidney transplantation (KTx) and provide insights into predicting the occurrence of CRI.Methods: Forty patients at the Department of Transplantation undergoing hemodialysis catheter removal were prospectively included. Samples, including catheter tip, catheter outlet skin swab, catheter blood, peripheral blood, oropharynx swab, and midstream urine, from the separate pre- and post-KTx groups were collected and analyzed using metagenomic next-generation sequencing (mNGS). All the catheter tips and blood samples were cultured conventionally.Results: The positive detection rates for bacteria using mNGS and traditional culture were 97.09% (200/206) and 2.65% (3/113), respectively. Low antibiotic-sensitivity biofilms with colonized bacteria were detected at the catheter tip. In asymptomatic patients, no statistically significant difference was observed in the catheter tip microbial composition and diversity between the pre- and post-KTx group. The catheter tip microbial composition and diversity were associated with fasting blood glucose levels. Microorganisms at the catheter tip most likely originated from catheter outlet skin and peripheral blood.Conclusions: The long-term colonization microbiota at the catheter tip is in a relatively stable state and is not readily influenced by KTx. It does not act as the source of infection in all CRIs, but could reflect hematogenous infection to some extent.}, } @article {pmid37724414, year = {2023}, author = {Zhang, Y and Yang, M}, title = {Leukemia followed by mixed infection with mucormycosis and aspergillosis: A case report and literature review.}, journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences}, volume = {48}, number = {7}, pages = {1105-1112}, doi = {10.11817/j.issn.1672-7347.2023.230039}, pmid = {37724414}, issn = {1672-7347}, support = {81974000 and 82270185//the National Natural Science Foundation/ ; 2021JJ10077//the Natural Science Foundation of Hunan Province/ ; 2022RC3077//the Science and Technology Innovation Plan Program of Hunan Province/ ; }, mesh = {Male ; Child ; Humans ; *Mucormycosis/diagnosis/therapy ; *Coinfection/diagnosis ; Antifungal Agents/therapeutic use ; *Aspergillosis/diagnosis/drug therapy ; *Leukemia ; }, abstract = {Leukemia complicated with Mucor and Aspergillus coinfection is very rare, which is difficult to diagnose, and life-threatening. The clinical characteristics, diagnosis and treatment in a child with acute myeloid leukemia (AML), who developed mucormycosis and aspergillus coinfection after chemotherapy, was reported. This case was a 12-year-old boy who presented with fever and cough during chemotherapy. Rhizomucor pusillus and Aspergillus flavus were detected in his blood, cerebrospinal fluid and alveolar lavage fluid by metagenomic next-generation sequencing (mNGS). Amphotericin B, posaconazole, and voriconazole were successively used for antifungal therapy. Skin debridement, bronchoalveolar lavage and local perfusion under bronchoscopy were performed. The infection of children was well controlled. The clinical manifestations of leukemia with mixed fungal infection are non-specific. The disease progresses rapidly and is prone to spread. Early diagnosis and treatment should be carried out. Combined antifungal therapy is recommended, and surgery is helpful to improve the patient's condition.}, } @article {pmid37724290, year = {2023}, author = {Liang, X and Wang, Q and Liu, J and Ma, J and Zhang, Y and Wang, M and Yu, Y and Wang, L}, title = {Coinfection of SARS-CoV-2 and influenza A (H3N2) detected in bronchoalveolar lavage fluid of a patient with long COVID using metagenomic next-generation sequencing: a case report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1224794}, pmid = {37724290}, issn = {2235-2988}, mesh = {Humans ; SARS-CoV-2/genetics ; *Coinfection/diagnosis ; *Influenza, Human/diagnosis ; Influenza A Virus, H3N2 Subtype ; Post-Acute COVID-19 Syndrome ; Bronchoalveolar Lavage Fluid ; *COVID-19/diagnosis ; High-Throughput Nucleotide Sequencing ; Dyspnea ; Fatigue ; }, abstract = {The growing number of long COVID cases has drawn clinical attention to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which has been spreading worldwide since winter 2019. Its symptoms are not limited to fatigue and shortness of breath but also affect daily life. We report the use of metagenomic next-generation sequencing (mNGS) to detect coinfection with SARS-CoV-2 and influenza A virus in a patient with long COVID. The patient was admitted with fever, expectoration, fatigue, and shortness of breath. The PCR test was negative due to possible clearance of SARS-Cov-2 in the upper respiratory tract of patients with long COVID. Other routine microbiological tests were also negative, making the clinical diagnosis difficult. Bronchoalveolar lavage fluid (BALF) samples were tested using mNGS. The patient was diagnosed and treated promptly, recovered quickly, and continued taking azvudine after discharge; his condition was stable. This study illustrates that mNGS may be valuable for the timely diagnosis of patients with long COVID and their mixed infections.}, } @article {pmid37724093, year = {2023}, author = {Zhang, X and Lin, Y and Chen, H and Hu, J and Zhao, H and Yang, M and Han, D}, title = {Diagnostic Performance of Metagenomic Next-Generation Sequencing in Central Nervous System Cryptococcosis Using Cerebrospinal Fluid.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {6175-6183}, pmid = {37724093}, issn = {1178-6973}, abstract = {PURPOSE: Metagenomic next-generation sequencing (mNGS) has been widely used to diagnose infectious diseases. However, there are few studies on its diagnostic performance in the central nervous system (CNS) cryptococcosis. This study examined the diagnostic efficacy of mNGS in identifying Cryptococcus spp. in cerebrospinal fluid (CSF) samples.

PATIENTS AND METHODS: From March 2021 to March 2023, 290 patients with suspected CNS infection were recruited from the First Affiliated Hospital, School of Medicine, Zhejiang University, and 74 patients were ultimately included in the study. Lastly, 22 patients with CNS cryptococcosis were included. Of these patients, 25 CSF samples were enrolled. The diagnostic performance of conventional assays [including India ink, cryptococcal antigen (CrAg) testing, and culture] and mNGS was evaluated for CNS cryptococcosis.

RESULTS: In the 25 samples collected, the coincidence rates of mNGS with India ink, CrAg, and culture were 64.0% (16/25), 80.0% (20/25), and 80.0% (20/25), respectively. Without antifungal drug exposure, the coincidence rates were increased to 66.7% (10/15), 100.0% (15/15), and 93.3% (14/15), respectively. The coincidence rates after antifungal therapy were all decreased to 60.0% (6/10), 50.0% (5/10), and 60.0% (6/10), respectively. Moreover, in the 25 samples, the sensitivity of mNGS reached 80.0%, and of India ink, CrAg testing, and culture were 68.0, 100.0, and 60.0%, respectively. The mNGS showed an excellent positive rate (100.0%) in the 15 samples collected without antifungal drug exposure, which was significantly higher than the antifungal drug-exposed group (n = 10) (50.0%) (P = 0.005). The reads of Cryptococcus spp. before antifungal therapy were significantly higher than after it (median, 25,915 vs 2, P = 0.008).

CONCLUSION: mNGS is an effective tool for diagnosing CNS cryptococcosis using CSF; however, its sensitivity decreases considerably in patients who have been effectively treated with antifungal drugs.}, } @article {pmid37724091, year = {2023}, author = {Zhu, L and Xu, H and Pu, Y and Fu, C and Pan, Q and Zhao, H}, title = {Case Report: Comprehensive Management of Pneumocystis Jiroveci Pneumonia (PJP) and Secondary Infections of Multiple-Drug Resistant Enterobacter cloacae complex and Pseudomonas aeruginosa in a Kidney Transplant Recipient with Sulfonamide Allergies.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {6185-6193}, pmid = {37724091}, issn = {1178-6973}, abstract = {We report a case of pneumocystis jiroveci pneumonia (PJP) in a 46-year-old woman, who previously underwent kidney transplant for chronic renal failure. She did not receive PJP prophylaxis treatment for the history of sulfonamide allergies. Four months after renal transplantation, the patient had cough, chest tightness, and shortness of breath. Procalcitonin (PCT) (0.06 ng/mL) and C-reactive protein (CRP) (5.33 mg/L) were normal, but the level of 1, 3-β-D-glucan test (G test, 193.89 pg/mL) were elevated. Metagenomics next-generation sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) rapidly and accurately identified P. jiroveci. Through sulfonamide desensitization and sulfamethoxazole-trimethoprim (TMP-SMX) combined with caspofungin (CAS) treatment, PJP was controlled. However, the patients' conditions were worsen for the hospital-acquired secondary pulmonary infection. A second BALF mNGS identified Enterobacter cloacae complex and Pseudomonas aeruginosa carrying carbapenem drug resistance genes, which were confirmed by subsequent culture and antimicrobial susceptibility test within 3 days. Finally, symptoms, such as chest tightness, cough, and shortness of breath, were improved and she was discharged after combined treatment with meropenem (MEM), polymyxin B (PMB), CAS, and TMP-SMX. In this case, mNGS, culture, and drug susceptibility testing were combined to monitor pathogenic microbial and adjust medication. At present, there are no case reports of mNGS use and sulfonamide desensitization in a kidney transplant recipient with sulfonamide allergies.}, } @article {pmid37723435, year = {2023}, author = {LaPolice, TM and Huang, YF}, title = {An unsupervised deep learning framework for predicting human essential genes from population and functional genomic data.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {347}, pmid = {37723435}, issn = {1471-2105}, support = {R35 GM142560/GM/NIGMS NIH HHS/United States ; T32 GM102057/GM/NIGMS NIH HHS/United States ; T32 GM102057 Computation, Bioinformatics, and Statistics (CBIOS) Training Program Grant/NH/NIH HHS/United States ; R35GM142560/NH/NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; *Genes, Essential ; *Deep Learning ; Genomics ; Metagenomics ; Cell Line ; }, abstract = {BACKGROUND: The ability to accurately predict essential genes intolerant to loss-of-function (LOF) mutations can dramatically improve the identification of disease-associated genes. Recently, there have been numerous computational methods developed to predict human essential genes from population genomic data. While the existing methods are highly predictive of essential genes of long length, they have limited power in pinpointing short essential genes due to the sparsity of polymorphisms in the human genome.

RESULTS: Motivated by the premise that population and functional genomic data may provide complementary evidence for gene essentiality, here we present an evolution-based deep learning model, DeepLOF, to predict essential genes in an unsupervised manner. Unlike previous population genetic methods, DeepLOF utilizes a novel deep learning framework to integrate both population and functional genomic data, allowing us to pinpoint short essential genes that can hardly be predicted from population genomic data alone. Compared with previous methods, DeepLOF shows unmatched performance in predicting ClinGen haploinsufficient genes, mouse essential genes, and essential genes in human cell lines. Notably, at a false positive rate of 5%, DeepLOF detects 50% more ClinGen haploinsufficient genes than previous methods. Furthermore, DeepLOF discovers 109 novel essential genes that are too short to be identified by previous methods.

CONCLUSION: The predictive power of DeepLOF shows that it is a compelling computational method to aid in the discovery of essential genes.}, } @article {pmid37723422, year = {2023}, author = {Hess, MK and Hodgkinson, HE and Hess, AS and Zetouni, L and Budel, JCC and Henry, H and Donaldson, A and Bilton, TP and van Stijn, TC and Kirk, MR and Dodds, KG and Brauning, R and McCulloch, AF and Hickey, SM and Johnson, PL and Jonker, A and Morton, N and Hendy, S and Oddy, VH and Janssen, PH and McEwan, JC and Rowe, SJ}, title = {Large-scale analysis of sheep rumen metagenome profiles captured by reduced representation sequencing reveals individual profiles are influenced by the environment and genetics of the host.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {551}, pmid = {37723422}, issn = {1471-2164}, support = {SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; SOW14-AGR-GPLER-SP5-SR//Livestock Research Group of the Global Research Alliance on Agricultural Greenhouse Gasses/ ; Curiosity Fund//AgResearch/ ; Curiosity Fund//AgResearch/ ; 119400343//Meat and Livestock Australia and the Australian Commonwealth Government/ ; 119400343//Meat and Livestock Australia and the Australian Commonwealth Government/ ; Breeding low emitting ruminants MET5.1//New Zealand Agricultural Greenhouse Gas Research Centre/ ; Breeding low emitting ruminants MET5.1//New Zealand Agricultural Greenhouse Gas Research Centre/ ; Breeding low emitting ruminants MET5.1//New Zealand Agricultural Greenhouse Gas Research Centre/ ; Breeding low emitting ruminants MET5.1//New Zealand Agricultural Greenhouse Gas Research Centre/ ; C10X1306//Ministry of Business, Innovation and Employment/ ; }, mesh = {Animals ; Sheep/genetics ; *Metagenome ; Rumen ; *Microbiota ; Livestock ; Methane ; }, abstract = {BACKGROUND: Producing animal protein while reducing the animal's impact on the environment, e.g., through improved feed efficiency and lowered methane emissions, has gained interest in recent years. Genetic selection is one possible path to reduce the environmental impact of livestock production, but these traits are difficult and expensive to measure on many animals. The rumen microbiome may serve as a proxy for these traits due to its role in feed digestion. Restriction enzyme-reduced representation sequencing (RE-RRS) is a high-throughput and cost-effective approach to rumen metagenome profiling, but the systematic (e.g., sequencing) and biological factors influencing the resulting reference based (RB) and reference free (RF) profiles need to be explored before widespread industry adoption is possible.

RESULTS: Metagenome profiles were generated by RE-RRS of 4,479 rumen samples collected from 1,708 sheep, and assigned to eight groups based on diet, age, time off feed, and country (New Zealand or Australia) at the time of sample collection. Systematic effects were found to have minimal influence on metagenome profiles. Diet was a major driver of differences between samples, followed by time off feed, then age of the sheep. The RF approach resulted in more reads being assigned per sample and afforded greater resolution when distinguishing between groups than the RB approach. Normalizing relative abundances within the sampling Cohort abolished structures related to age, diet, and time off feed, allowing a clear signal based on methane emissions to be elucidated. Genus-level abundances of rumen microbes showed low-to-moderate heritability and repeatability and were consistent between diets.

CONCLUSIONS: Variation in rumen metagenomic profiles was influenced by diet, age, time off feed and genetics. Not accounting for environmental factors may limit the ability to associate the profile with traits of interest. However, these differences can be accounted for by adjusting for Cohort effects, revealing robust biological signals. The abundances of some genera were consistently heritable and repeatable across different environments, suggesting that metagenomic profiles could be used to predict an individual's future performance, or performance of its offspring, in a range of environments. These results highlight the potential of using rumen metagenomic profiles for selection purposes in a practical, agricultural setting.}, } @article {pmid37723360, year = {2023}, author = {Xu, S and Zhang, X and Yang, Q and Li, J and Yu, Z}, title = {Identification of Microbial Community in Otomycosis by Metagenomic Next Generation Sequencing (mNGS): Potential Implication of Treatment with Terbinafine.}, journal = {Mycopathologia}, volume = {188}, number = {6}, pages = {995-1005}, pmid = {37723360}, issn = {1573-0832}, support = {82071039//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 82101215//Innovative Research Group Project of the National Natural Science Foundation of China/ ; }, mesh = {Humans ; Terbinafine/therapeutic use ; *Otomycosis/drug therapy/microbiology ; Antifungal Agents/pharmacology/therapeutic use ; High-Throughput Nucleotide Sequencing ; Aspergillus/genetics ; Fungi/genetics ; *Microbiota ; }, abstract = {The present study was designed to identify the microbial community as well as to analyze its diversity by means of metagenomic Next Generation Sequencing (mNGS) in 17 patients with otomycosis treated with terbinafine in the Department of Otolaryngology of Shandong Provincial Hospital from June 2021 to June 2022, so as to evaluate the relationship between microbial community and terbinafine resistance. Those 17 patients were divided into two groups, i.e., Terbinafine Effective Group (TEG, n = 14 cases) and Terbinafine Resistance Group (TRG, n = 3 cases) according to the therapy effect, whose microbial community of secretion of external auditory canal was identified using mNGS. We found that the sequence of bacteria was significantly more than that of fungi and, whereas, the difference between the two groups of bacteria was not significant. There were significant differences in fungal community between the two groups. Aspergillus was the main pathogenic fungus of TEG patients while Malassezia was a dominant fungus in TRG patients. In conclusion, the results from this work indicate that Aspergillus terreusis is the main pathogenic fungus in this cohort of otomycosis patients and MNGS sequencing can offer comprehensive information about the microbial community of otomycosis. The fungus community dominated by Malassezia is more likely to be resistant to terbinafine, which provides certain guidance for clinical treatment of otomycosis with terbinafine.}, } @article {pmid37723339, year = {2023}, author = {Li, S and Mosier, D and Dong, X and Kouris, A and Ji, G and Strous, M and Diao, M}, title = {Frequency of change determines effectiveness of microbial response strategies.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {2047-2057}, pmid = {37723339}, issn = {1751-7370}, mesh = {RNA, Ribosomal, 16S/genetics/metabolism ; *Microbiota ; Bacteria ; Metagenome ; Bacteroidetes/genetics ; Metagenomics/methods ; }, abstract = {Nature challenges microbes with change at different frequencies and demands an effective response for survival. Here, we used controlled laboratory experiments to investigate the effectiveness of different response strategies, such as post-translational modification, transcriptional regulation, and specialized versus adaptable metabolisms. For this, we inoculated replicated chemostats with an enrichment culture obtained from sulfidic stream microbiomes 16 weeks prior. The chemostats were submitted to alternatingly oxic and anoxic conditions at three frequencies, with periods of 1, 4 and 16 days. The microbial response was recorded with 16S rRNA gene amplicon sequencing, shotgun metagenomics, transcriptomics and proteomics. Metagenomics resolved provisional genomes of all abundant bacterial populations, mainly affiliated with Proteobacteria and Bacteroidetes. Almost all these populations maintained a steady growth rate under both redox conditions at all three frequencies of change. Our results supported three conclusions: (1) Oscillating oxic/anoxic conditions selected for generalistic species, rather than species specializing in only a single condition. (2) A high frequency of change selected for strong codon usage bias. (3) Alignment of transcriptomes and proteomes required multiple generations and was dependent on a low frequency of change.}, } @article {pmid37723220, year = {2023}, author = {Rahlff, J and Wietz, M and Giebel, HA and Bayfield, O and Nilsson, E and Bergström, K and Kieft, K and Anantharaman, K and Ribas-Ribas, M and Schweitzer, HD and Wurl, O and Hoetzinger, M and Antson, A and Holmfeldt, K}, title = {Ecogenomics and cultivation reveal distinctive viral-bacterial communities in the surface microlayer of a Baltic Sea slick.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {97}, pmid = {37723220}, issn = {2730-6151}, support = {RA3432/1-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 34509606//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 451574234//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 451574234//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; CR2019-0034//Crafoordska Stiftelsen (Crafoord Foundation)/ ; CR2019-0034//Crafoordska Stiftelsen (Crafoord Foundation)/ ; 2018-05973//Vetenskapsrådet (Swedish Research Council)/ ; }, abstract = {Visible surface films, termed slicks, can extensively cover freshwater and marine ecosystems, with coastal regions being particularly susceptible to their presence. The sea-surface microlayer (SML), the upper 1-mm at the air-water interface in slicks (herein slick SML) harbors a distinctive bacterial community, but generally little is known about SML viruses. Using flow cytometry, metagenomics, and cultivation, we characterized viruses and bacteria in a brackish slick SML in comparison to non-slick SML as well as seawater below slick and non-slick areas (subsurface water = SSW). Size-fractionated filtration of all samples distinguished viral attachment to hosts and particles. The slick SML contained higher abundances of virus-like particles, prokaryotic cells, and dissolved organic carbon compared to non-slick SML and SSW. The community of 428 viral operational taxonomic units (vOTUs), 426 predicted as lytic, distinctly differed across all size fractions in the slick SML compared to non-slick SML and SSW. Specific metabolic profiles of bacterial metagenome-assembled genomes and isolates in the slick SML included a prevalence of genes encoding motility and carbohydrate-active enzymes (CAZymes). Several vOTUs were enriched in slick SML, and many virus variants were associated with particles. Nine vOTUs were only found in slick SML, six of them being targeted by slick SML-specific clustered-regularly interspaced short palindromic repeats (CRISPR) spacers likely originating from Gammaproteobacteria. Moreover, isolation of three previously unknown lytic phages for Alishewanella sp. and Pseudoalteromonas tunicata, abundant and actively replicating slick SML bacteria, suggests that viral activity in slicks contributes to biogeochemical cycling in coastal ecosystems.}, } @article {pmid37723166, year = {2023}, author = {Ye, H and Borusak, S and Eberl, C and Krasenbrink, J and Weiss, AS and Chen, SC and Hanson, BT and Hausmann, B and Herbold, CW and Pristner, M and Zwirzitz, B and Warth, B and Pjevac, P and Schleheck, D and Stecher, B and Loy, A}, title = {Ecophysiology and interactions of a taurine-respiring bacterium in the mouse gut.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5533}, pmid = {37723166}, issn = {2041-1723}, mesh = {Humans ; Animals ; Mice ; *Affect ; Bile Acids and Salts ; *Salmonella enterica ; Taurine ; Sulfur ; }, abstract = {Taurine-respiring gut bacteria produce H2S with ambivalent impact on host health. We report the isolation and ecophysiological characterization of a taurine-respiring mouse gut bacterium. Taurinivorans muris strain LT0009 represents a new widespread species that differs from the human gut sulfidogen Bilophila wadsworthia in its sulfur metabolism pathways and host distribution. T. muris specializes in taurine respiration in vivo, seemingly unaffected by mouse diet and genotype, but is dependent on other bacteria for release of taurine from bile acids. Colonization of T. muris in gnotobiotic mice increased deconjugation of taurine-conjugated bile acids and transcriptional activity of a sulfur metabolism gene-encoding prophage in other commensals, and slightly decreased the abundance of Salmonella enterica, which showed reduced expression of galactonate catabolism genes. Re-analysis of metagenome data from a previous study further suggested that T. muris can contribute to protection against pathogens by the commensal mouse gut microbiota. Together, we show the realized physiological niche of a key murine gut sulfidogen and its interactions with selected gut microbiota members.}, } @article {pmid37722584, year = {2023}, author = {Wang, S and Han, Y and Wu, X and Sun, H}, title = {Metagenomics reveals the effects of glyphosate on soil microbial communities and functional profiles of C and P cycling in the competitive vegetation control process of Chinese fir plantation.}, journal = {Environmental research}, volume = {238}, number = {Pt 1}, pages = {117162}, doi = {10.1016/j.envres.2023.117162}, pmid = {37722584}, issn = {1096-0953}, mesh = {Soil ; *Cunninghamia ; RNA, Ribosomal, 16S ; Soil Microbiology ; *Microbiota ; Bacteria ; Glyphosate ; }, abstract = {Although considerable efforts have been devoted to investigate the behavior of glyphosate on microbiome in various environment, knowledge about the soil microbial community and functional profile in weeds control process of the Chinese fir plantation are limited. In this study, shotgun metagenomic sequencing was used to determine the abundance and diversity of microbial communities and functional genes after foliar application of glyphosate for 1, 2, 3 and 4 months in a Chinese fir plantation. The results showed that glyphosate increased the copy numbers (qPCR) of 16S rRNA gene for 16.9%, improved the bacterial diversity (Shannon index) and complexity of bacterial co-occurrence network, and changed the abundances of some bacterial and fungal taxa, but had no effects on ITS gene copy numbers, fungal Shannon index, and bacterial and fungal communities (PCoA). Glyphosate application significantly decreased the amount of microbial function potentials involved in organic P mineralization for 10.7%, chitin degradation for 13.1%, and CAZy gene families with an exception of PL for 11.5% at the first month, while did not affect the profile of microbial genes response to P and C cycling in longer term. In addition, glyphosate reduced the contents of soil TOC, DOC and NH4[+]-H for 17.6%, 52.3% and 44.6% respectively, and decreased the starch, soluble sugar, Zn and Fe of Chinese fir leaves for 20.6%, 19.8%, 32.8% and 48.4% respectively. Mantle test, Spearman's correlation, and PLS-PM model revealed the connections among soil properties, tree nutrients, bacterial and fungal communities, and microbial function potentials were influenced by glyphosate. While our findings need to be validated in other filed and mechanistic studies, they may indicate that the foliar application of glyphosate has a potential effect on Chinese fir seedlings, and this effect may contribute to the changes of the bacterial community and soil properties including AN, DON and NH4[+]-H.}, } @article {pmid37722545, year = {2023}, author = {Zhang, Y and Qi, W and Chu, G and Wang, Q and Gao, C and Chen, W and Liu, J and Gao, M}, title = {Performance evaluation, enzymatic activity change and metagenomic analysis of sequencing batch reactor under divalent zinc stress.}, journal = {Bioresource technology}, volume = {388}, number = {}, pages = {129774}, doi = {10.1016/j.biortech.2023.129774}, pmid = {37722545}, issn = {1873-2976}, abstract = {Divalent zinc (Zn[2+]) are widely detected in domestic and industrial wastewater, and it is essential to evaluate the effect of Zn[2+] on wastewater biological treatment process due to its bio-toxicity. In this study, the nitrogen removal rates and their corresponding enzymatic activities of sequencing batch reactor decreased with the increase of Zn[2+] concentration. The Zn[2+] accumulation in activated sludge caused significant antioxidant response, and the reactive oxygen species (ROS) production and antioxidant enzymatic activities were positively correlated with Zn[2+] concentration. The presence of Zn[2+] inhibited the metabolic pathways related to energy production and electron transport. The abundance decreases of nitrification and denitrification functional genes led to the deterioration of nitrogen removal performance under Zn[2+] stress. The correlation analysis between functional gene modules and microbial genera revealed that Zoogloea had obvious Zn[2+] resistance. This study can provide the insights into the influencing mechanism of Zn[2+] on the biological nitrogen removal process.}, } @article {pmid37722541, year = {2023}, author = {Wang, Y and Li, J and Liu, M and Gu, L and Xu, L and Li, J and Ao, L}, title = {Enhancement of anaerobic digestion of high salinity food waste by magnetite and potassium ions: Digestor performance, microbial and metabolomic analyses.}, journal = {Bioresource technology}, volume = {388}, number = {}, pages = {129769}, doi = {10.1016/j.biortech.2023.129769}, pmid = {37722541}, issn = {1873-2976}, abstract = {The study investigated the effectiveness of magnetite and potassium ions (K[+]) in enhancing anaerobic digestion of high salinity food waste. Results indicated that both magnetite and K[+] improved anaerobic digestion in high-salt environments, and their combination yielded even better results. The combination of magnetite and K[+] promoted microorganism activity, and resulted in increased abundance of DMER64, Halobacteria and Methanosaeta. Metabolomic analysis revealed that magnetite mainly influenced quorum sensing, while K[+] mainly stimulated the synthesis of compatible solutes, aiding in maintaining osmotic balance. The combined additives regulated pathways such as ATP binding cassette transport, methane metabolism, and inhibitory substance metabolism, enabling cells to resist environmental stress and maintain normal metabolic activity. Overall, this study demonstrated the potential of magnetite and K[+] to enhance food waste anaerobic digestion in high salt conditions and provided valuable insights into the molecular mechanism.}, } @article {pmid37722141, year = {2023}, author = {Chen, T and Deng, C and Wu, Z and Liu, T and Zhang, Y and Xu, X and Zhao, X and Li, J and Li, S and Xu, N and Yu, K}, title = {Metagenomic analysis unveils the underexplored roles of prokaryotic viruses in a full-scale landfill leachate treatment plant.}, journal = {Water research}, volume = {245}, number = {}, pages = {120611}, doi = {10.1016/j.watres.2023.120611}, pmid = {37722141}, issn = {1879-2448}, abstract = {Enormous viral populations have been identified in activated sludge systems, but their ecological and biochemical roles in landfill leachate treatment plants remain poorly understood. To address this knowledge gap, we conducted an in-depth analysis using 36 metagenomic datasets that we collected and sequenced during a half-year time-series sampling campaign at six sites in a full-scale landfill leachate treatment plant (LLTP), elucidating viral distribution, virus‒host dynamics, virus-encoded auxiliary metabolic genes (AMGs), and viral contributions to the spread of virulence and antibiotic resistance genes. Our findings demonstrated that viral and prokaryotic communities differed widely among different treatment units, with stability over time. LLTP viruses were linked to various prokaryotic hosts, spanning 35 bacterial phyla and one archaeal phylum, which included the core microbes involved in biological treatments, as well as some of the less well-characterized microbial dark matter phyla. By encoding 2364 auxiliary metabolic genes (AMGs), viruses harbored the potential to regulate microbial nucleotide metabolism, facilitate the biodegradation of complex organic matter, and enhance flocculation and settling in biological treatment plants. The abundance distribution of AMGs varied considerably across treatment units and showed a lifestyle-dependent pattern with temperate virus-associated AMGs exhibiting a higher average abundance in downstream biological treatment units and effluent water. Meanwhile, temperate viruses tended to carry a higher load of virulence factor genes (VFGs), antibiotic resistance genes (ARGs), and biotic and metal resistance genes (BMRGs), and engaged in more frequent gene exchanges with prokaryotes than lytic viruses, thus acting as a pivotal contributor to the dissemination of pathogenicity and resistance genes in downstream LLTP units. This study provided a comprehensive profile of viral and prokaryotic communities in the LLTP and unveiled the varying roles of different-lifestyle viruses in biochemical processes and water quality safety.}, } @article {pmid37721240, year = {2023}, author = {Zhou, D and Zhu, N and Li, S and Dong, L and Xia, J and Zhang, X and Li, S}, title = {Characteristics and comparison of rapidly growing and slowly growing nontuberculous mycobacterial pulmonary disease.}, journal = {International journal of mycobacteriology}, volume = {12}, number = {3}, pages = {324-331}, doi = {10.4103/ijmy.ijmy_145_23}, pmid = {37721240}, issn = {2212-554X}, mesh = {Humans ; Male ; Female ; Nontuberculous Mycobacteria/genetics ; *Mycobacterium Infections, Nontuberculous/microbiology ; *Bronchiectasis ; Hemoptysis ; *Mycobacterium tuberculosis ; }, abstract = {BACKGROUND: Nontuberculous mycobacterial (NTM) pulmonary disease (PD) has rapidly increased globally. The characteristics and comparison of rapidly growing mycobacteria PD (RGM-PD) and slowly growing mycobacteria PD (SGM-PD) are still unclear.

METHODS: Our study enrolled 31 NTM-PD patients. Clinical data, including baseline, symptoms, underlying disease, laboratory tests, metagenomic next-generation sequencing (mNGS) results, radiological images, treatment, and outcome were recorded and analyzed.

RESULTS: Of the 31 patients with NTM-PD, 22 patients were female and 9 were male. It included 11 RGM-PD and 20 SGM-PD. There was no difference in age (P = 0.425) and body mass index (P = 0.152) between the two groups. The common respiratory diseases in prevalence included bronchiectasis and chronic obstructive pulmonary disease. Three patients had positive results of T-SPOT tuberculosis (TB), and none had positive Xpert-Mycobacterium tuberculosis/rifampin results. On admission, patients were symptomatic and included cough/sputum production, fever, weight loss, fatigue, and hemoptysis. In comparison to RGM-PD, patients with SGM-PD had a greater chance of experiencing fatigue (P = 0.012). No significance was found in serum biomarkers between RGM and SGM-PD, including CD4/CD8 ratio, white blood cells, neutrophils, lymphocytes, procalcitonin, ferritin, C-reactive protein, and erythrocyte sedimentation rate. No liver or kidney impairment was found. Patients with RGM-PD were more likely to have right lower lobe (RLL) impairment (P = 0.021) and a cavity characteristic (P = 0.012). All 31 cases had positive mNGS results. The duration of mNGS was shorter than conventional methods (3.4 ± 0.7 vs. 26.4 ± 20.9, P < 0.001).

CONCLUSIONS: Patients with SGM-PD were more likely to experience fatigue. The cavity and RLL involvement were more frequent in the RGM-PD. mNGS increases the identification of NTM specimens and complements the capabilities of conventional methods.}, } @article {pmid37720160, year = {2023}, author = {Maguire, M and Ramachandran, P and Tallent, S and Mammel, MK and Brown, EW and Allard, MW and Musser, SM and González-Escalona, N}, title = {Precision metagenomics sequencing for food safety: hybrid assembly of Shiga toxin-producing Escherichia coli in enriched agricultural water.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1221668}, pmid = {37720160}, issn = {1664-302X}, abstract = {Culture-independent metagenomic sequencing of enriched agricultural water could expedite the detection and virulotyping of Shiga toxin-producing Escherichia coli (STEC). We previously determined the limits of a complete, closed metagenome-assembled genome (MAG) assembly and of a complete, fragmented MAG assembly for O157:H7 in enriched agricultural water using long reads (Oxford Nanopore Technologies, Oxford), which were 10[7] and 10[5] CFU/ml, respectively. However, the nanopore assemblies did not have enough accuracy to be used in Single Nucleotide Polymorphism (SNP) phylogenies and cannot be used for the precise identification of an outbreak STEC strain. The present study aimed to determine the limits of detection and assembly for STECs in enriched agricultural water by Illumina MiSeq sequencing technology alone, followed by establishing the limit of hybrid assembly with nanopore long-read sequencing using three different hybrid assemblers (SPAdes, Unicycler, and OPERA-MS). We also aimed to generate a genome with enough accuracy to be used in a SNP phylogeny. The classification of MiSeq and nanopore sequencing identified the same highly abundant species. Using the totality of the MiSeq output and a precision metagenomics approach in which the E. coli reads are binned before assembly, the limit of detection and assembly of STECs by MiSeq were determined to be 10[5] and 10[7] CFU/ml, respectively. While a complete, closed MAG could not be generated at any concentration, a complete, fragmented MAG was produced using the SPAdes assembler with an STEC concentration of at least 10[7] CFU/ml. At this concentration, hybrid assembled contigs aligned to the nanopore-assembled genome could be accurately placed in a neighbor-joining tree. The MiSeq limit of detection and assembly was less sensitive than nanopore sequencing, which was likely due to factors including the small starting material (50 vs. 1 μg) and the dilution of the library loaded on the cartridge. This pilot study demonstrates that MiSeq sequencing requires higher coverage in precision metagenomic samples; however, with sufficient concentration, STECs can be characterized and phylogeny can be accurately determined.}, } @article {pmid37720151, year = {2023}, author = {Campos-Madueno, EI and Aldeia, C and Perreten, V and Sendi, P and Moser, AI and Endimiani, A}, title = {Detection of blaCTX-M and blaDHA genes in stool samples of healthy people: comparison of culture- and shotgun metagenomic-based approaches.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1236208}, pmid = {37720151}, issn = {1664-302X}, abstract = {We implemented culture- and shotgun metagenomic sequencing (SMS)-based methods to assess the gut colonization with extended-spectrum cephalosporin-resistant Enterobacterales (ESC-R-Ent) in 42 volunteers. Both methods were performed using native and pre-enriched (broth supplemented with cefuroxime) stools. Native culture screening on CHROMID[®] ESBL plates resulted in 17 positive samples, whereas the pre-enriched culture (gold-standard) identified 23 carriers. Overall, 26 ESC-R-Ent strains (24 Escherichia coli) were identified: 25 CTX-M and 3 DHA-1 producers (2 co-producing CTX-Ms). Using the SMS on native stool ("native SMS") with thresholds ≥60% for both identity and coverage, only 7 of the 23 pre-enriched culture-positive samples resulted positive for blaCTX-M/blaDHA genes (native SMS reads mapping to blaCTX-M/blaDHAs identified in gold-standard: sensitivity, 59.0%; specificity 100%). Moreover, an average of 31.5 and 24.6 antimicrobial resistance genes (ARGs) were detected in the 23 pre-enriched culture-positive and the 19 negative samples, respectively. When the pre-enriched SMS was implemented, more blaCTX-M/blaDHA genes were detected than in the native assay, including in stools that were pre-enriched culture-negative (pre-enriched SMS reads mapping to blaCTX-M/blaDHAs identified in gold-standard: sensitivity, 78.3%; specificity 75.0%). In addition, the pre-enriched SMS identified on average 38.6 ARGs/sample, whereas for the corresponding native SMS it was 29.4 ARGs/sample. Notably, stools resulting false-negative by using the native SMS had lower concentrations of ESC-R-Ent (average: ~10[5] vs. ~10[7] CFU/g) and E. coli classified reads (average: 193,959 vs. 1.45 million) than those of native SMS positive samples. Finally, the detection of blaCTX-M/blaDHA genes was compared with two well-established bioinformatic tools. In conclusion, only the pre-enriched SMS assured detection of most carriers of ESC-R-Ent. However, its performance was not comparable to the pre-enriched culture-based approach.}, } @article {pmid37719779, year = {2023}, author = {Gil, P and Exbrayat, A and Loire, E and Rakotoarivony, I and Charriat, F and Morel, C and Baldet, T and Boisseau, M and Marie, A and Frances, B and L'Ambert, G and Bessat, M and Otify, Y and Goffredo, M and Mancini, G and Busquets, N and Birnberg, L and Talavera, S and Aranda, C and Ayari, E and Mejri, S and Sghaier, S and Bennouna, A and El Rhaffouli, H and Balenghien, T and Chlyeh, G and Fassi Fihri, O and Reveillaud, J and Simonin, Y and Eloit, M and Gutierrez, S}, title = {Spatial scale influences the distribution of viral diversity in the eukaryotic virome of the mosquito Culex pipiens.}, journal = {Virus evolution}, volume = {9}, number = {2}, pages = {vead054}, pmid = {37719779}, issn = {2057-1577}, abstract = {Our knowledge of the diversity of eukaryotic viruses has recently undergone a massive expansion. This diversity could influence host physiology through yet unknown phenomena of potential interest to the fields of health and food production. However, the assembly processes of this diversity remain elusive in the eukaryotic viromes of terrestrial animals. This situation hinders hypothesis-driven tests of virome influence on host physiology. Here, we compare taxonomic diversity between different spatial scales in the eukaryotic virome of the mosquito Culex pipiens. This mosquito is a vector of human pathogens worldwide. The experimental design involved sampling in five countries in Africa and Europe around the Mediterranean Sea and large mosquito numbers to ensure a thorough exploration of virus diversity. A group of viruses was found in all countries. This core group represented a relatively large and diverse fraction of the virome. However, certain core viruses were not shared by all host individuals in a given country, and their infection rates fluctuated between countries and years. Moreover, the distribution of coinfections in individual mosquitoes suggested random co-occurrence of those core viruses. Our results also suggested differences in viromes depending on geography, with viromes tending to cluster depending on the continent. Thus, our results unveil that the overlap in taxonomic diversity can decrease with spatial scale in the eukaryotic virome of C. pipiens. Furthermore, our results show that integrating contrasted spatial scales allows us to identify assembly patterns in the mosquito virome. Such patterns can guide future studies of virome influence on mosquito physiology.}, } @article {pmid37719750, year = {2023}, author = {Becker, CC and Weber, L and Zgliczynski, B and Sullivan, C and Sandin, S and Muller, E and Clark, AS and Kido Soule, MC and Longnecker, K and Kujawinski, EB and Apprill, A}, title = {Microorganisms and dissolved metabolites distinguish Florida's Coral Reef habitats.}, journal = {PNAS nexus}, volume = {2}, number = {9}, pages = {pgad287}, pmid = {37719750}, issn = {2752-6542}, abstract = {As coral reef ecosystems experience unprecedented change, effective monitoring of reef features supports management, conservation, and intervention efforts. Omic techniques show promise in quantifying key components of reef ecosystems including dissolved metabolites and microorganisms that may serve as invisible sensors for reef ecosystem dynamics. Dissolved metabolites are released by reef organisms and transferred among microorganisms, acting as chemical currencies and contributing to nutrient cycling and signaling on reefs. Here, we applied four omic techniques (taxonomic microbiome via amplicon sequencing, functional microbiome via shotgun metagenomics, targeted metabolomics, and untargeted metabolomics) to waters overlying Florida's Coral Reef, as well as microbiome profiling on individual coral colonies from these reefs to understand how microbes and dissolved metabolites reflect biogeographical, benthic, and nutrient properties of this 500-km barrier reef. We show that the microbial and metabolite omic approaches each differentiated reef habitats based on geographic zone. Further, seawater microbiome profiling and targeted metabolomics were significantly related to more reef habitat characteristics, such as amount of hard and soft coral, compared to metagenomic sequencing and untargeted metabolomics. Across five coral species, microbiomes were also significantly related to reef zone, followed by species and disease status, suggesting that the geographic water circulation patterns in Florida also impact the microbiomes of reef builders. A combination of differential abundance and indicator species analyses revealed metabolite and microbial signatures of specific reef zones, which demonstrates the utility of these techniques to provide new insights into reef microbial and metabolite features that reflect broader ecosystem processes.}, } @article {pmid37719673, year = {2023}, author = {Wang, S and Xing, L}, title = {Metagenomic next-generation sequencing assistance in identifying non-tuberculous mycobacterial infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1253020}, pmid = {37719673}, issn = {2235-2988}, mesh = {Humans ; *Nontuberculous Mycobacteria/genetics ; Metagenomics ; Retrospective Studies ; Metagenome ; High-Throughput Nucleotide Sequencing ; *Mycobacterium abscessus ; }, abstract = {INTRODUCTION: The advent of metagenomics next-generation sequencing (mNGS) has garnered attention as a novel method for detecting pathogenic infections, including Non-Tuberculous Mycobacterial (NTM) and tuberculosis (TB).However, the robustness and specificity of mNGS in NTM diagnostics have not been fully explored.

METHODS: In this retrospective study, we enrolled 27 patients with NTM genomic sequences via mNGS and conducted a comprehensive clinical evaluation.

RESULTS: Pulmonary NTM disease was the most commonly observed presentation, with a subset of patients also presenting with extrapulmonary NTM infections.mNGS analysis identified six distinct NTM species, primarily Mycobacteriumavium complex (MAC), followed by Mycobacterium intracellulare andMycobacterium abscessus. Conventional routine culture methods encountered challenges, resulting in negative results for all available 22 samples. Among the 10 patients who underwent quantitative polymerase chain reaction (qPCR) testing, five tested positive for NTM.

DISCUSSION: It is important to note that further species typing is necessary to determine the specific NTM type, as traditional pathogen detection methods serve as an initial step. In contrast, when supplemented with pathogen data, enables the identification of specific species, facilitating precise treatment decisions. In conclusion, mNGS demonstrates significant potential in aidingthe diagnosis of NTMdisease by rapidly detecting NTM pathogens and guiding treatment strategies. Its enhanced performance, faster turnaround time (TAT), and species identification capabilities make mNGS a promising tool for managing NTM infections.}, } @article {pmid37719652, year = {2023}, author = {Mu, X and Liang, J and Qian, L and Zhou, B and Zou, X and Fu, Y and Zhu, Y and Li, X and Shi, J}, title = {Genome Analysis of ST1 Bartonella henselae, a Zoonotic Pathogen Causing Endocarditis in an Elderly Patient in China.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {6079-6084}, pmid = {37719652}, issn = {1178-6973}, abstract = {Infective endocarditis (IE) is a rare disease but with high associated mortality. Currently, the mainstays of diagnosis are still echocardiography and blood cultures. Here, we reported a case of infective endocarditis with negative blood cultures, and blood and aortic valve tissue metagenomic next-generation sequencing (mNGS) results suggested Bartonella henselae. In addition, we obtained the whole genomic sequence of B. henselae ZJBH strain. To our knowledge, this is the first report of B. henselae genomic analysis isolated from clinic in China. Furthermore, we described the whole genome sequencing (WGS) data incorporating all B. henselae from diverse sources worldwide and shed light on underlying risk of B. henselae transmitted between cats and humans.}, } @article {pmid37719281, year = {2023}, author = {Prajna, NV and Prajna, L and Teja, V and Gunasekaran, R and Chen, C and Ruder, K and Zhong, L and Yu, D and Liu, D and Abraham, T and Ao, W and Deiner, M and Hinterwirth, A and Seitzman, G and Doan, T and Lietman, T}, title = {Apollo Rising: Acute Conjunctivitis Outbreak in India, 2022.}, journal = {Cornea open}, volume = {2}, number = {2}, pages = {}, pmid = {37719281}, issn = {2833-6992}, support = {R01 EY032041/EY/NEI NIH HHS/United States ; }, abstract = {PURPOSE: To identify pathogens associated with the 2022 conjunctivitis outbreak in Tamil Nadu, India.

METHODS: This prospective study was conducted in November of 2022. Patients with presumed acute infectious conjunctivitis presenting to the Aravind Eye Clinic in Madurai, India were eligible. Anterior nares and conjunctival samples from participants were obtained and processed for metagenomic RNA deep sequencing (RNA-seq).

RESULTS: Samples from 29 patients were sequenced. A pathogen was identified in 28/29 (97%) patients. Coxsackievirus A24v, a highly infectious RNA virus, was the predominant pathogen and detected in 23/29 patients. Human adenovirus D (HAdV-D), a DNA virus commonly associated with conjunctivitis outbreaks, was detected in the remaining patients (5/29). Hemorrhagic conjunctiva was documented in both HAdV-D and coxsackievirus A24v affected patients but was not the predominant clinical presentation. Phylogenetic analysis of coxsackievirus A24v revealed a recent divergence from the 2015 outbreak.

CONCLUSIONS: Coxsackievirus A24v and HAdV-D were co-circulating during the 2022 conjunctivitis outbreak in Tamil Nadu, India. Clinical findings were similar between patients with HAD-V and coxsackievirus A24v associated conjunctivitis. As high-throughput technologies become more readily accessible and cost-effective, unbiased pathogen surveillance may prove useful for outbreak surveillance and control.}, } @article {pmid37718237, year = {2023}, author = {You, L and Jin, H and Kwok, LY and Lv, R and Zhao, Z and Bilige, M and Sun, Z and Liu, W and Zhang, H}, title = {Intraspecific microdiversity and ecological drivers of lactic acid bacteria in naturally fermented milk ecosystem.}, journal = {Science bulletin}, volume = {68}, number = {20}, pages = {2405-2417}, doi = {10.1016/j.scib.2023.09.001}, pmid = {37718237}, issn = {2095-9281}, mesh = {Animals ; Milk/microbiology ; *Lactobacillales/genetics ; Lactobacillus/genetics ; Ecosystem ; Phylogeny ; *Lactobacillus delbrueckii/genetics ; *Lactococcus lactis ; }, abstract = {Traditional fermented milks are produced by inoculating technique, which selects well-adapted microorganisms that have been passed on through generations. Few reports have used naturally fermented milks as model ecosystems to investigate the mechanism of formation of intra-species microbial diversity. Here, we isolated and whole-genome-sequenced a total of 717 lactic acid bacterial isolates obtained from 12 independent naturally fermented milks collect from 12 regions across five countries. We further analyzed the within-sample intra-species phylogenies of 214 Lactobacillus helveticus isolates, 97 Lactococcus lactis subsp. lactis isolates, and 325 Lactobacillus delbrueckii subsp. bulgaricus isolates. We observed a high degree of intra-species genomic and functional gene diversity within-/between-sample(s). Single nucleotide polymorphism-based phylogenetic reconstruction revealed great within-sample intra-species heterogeneity, evolving from multiple lineages. Further phylogenetic reconstruction (presence-absence gene profile) revealed within-sample inter-clade functional diversity (based on carbohydrate-active enzyme- and peptidase-encoding genes) in all three investigated species/subspecies. By identifying and mapping clade-specific genes of intra-sample clades of the three species/subspecies to the respective fermented milk metagenome, we found extensive potential inter-/intra-species horizontal gene transfer events. Finally, the microbial composition of the samples is closely linked to the nucleotide diversity of the respective species/subspecies. Overall, our results contribute to the conservation of lactic acid bacteria resources, providing ecological insights into the microbial ecosystem of naturally fermented dairy products.}, } @article {pmid37717754, year = {2023}, author = {Jain, R and Gaur, A and Suravajhala, R and Chauhan, U and Pant, M and Tripathi, V and Pant, G}, title = {Microplastic pollution: Understanding microbial degradation and strategies for pollutant reduction.}, journal = {The Science of the total environment}, volume = {905}, number = {}, pages = {167098}, doi = {10.1016/j.scitotenv.2023.167098}, pmid = {37717754}, issn = {1879-1026}, mesh = {Humans ; Microplastics ; Plastics/chemistry ; *Environmental Pollutants ; Ecosystem ; *Water Pollutants, Chemical/analysis ; Environmental Pollution ; *Microbiota ; Environmental Monitoring ; }, abstract = {Microplastics are ubiquitous environmental pollutants with the potential for adverse impacts on ecosystems and human health. These particles originate from the fragmentation of larger plastic items, shedding from synthetic fibers, tire abrasions, and direct release from personal care products and industrial processes. Once released into the environment, microplastics can disrupt ecosystems, accumulate in organisms, cause physical harm, and carry chemical pollutants that pose risks to both wildlife and human health. There is an urgent need to comprehensively explore the multifaceted issue of microplastic pollution and understand microbial degradation to reduce environmental pollution caused by microplastics. This paper presents a comprehensive exploration of microplastics, including their types, composition, advantages, and disadvantages, as well as the journey and evolution of microplastic pollution. The impact of microplastics on the microbiome and microbial communities is elucidated, highlighting the intricate interactions between microplastics and microbial ecosystems. Furthermore, the microbial degradation of microplastics is discussed, including the identification, characterization, and culturing methods of microplastic-degrading microorganisms. Mechanisms of microplastic degradation and the involvement of microbial enzymes are elucidated to shed light on potential biotechnological applications. Strategies for reducing microplastic pollution are presented, encompassing policy recommendations and the importance of enhanced waste management practices. Finally, the paper addresses future challenges and prospects in the field, emphasizing the need for international collaboration, research advancements, and public engagement. Overall, this study underscores the urgent need for concerted efforts to mitigate microplastic pollution and offers valuable insights for researchers, policymakers, and stakeholders involved in environmental preservation.}, } @article {pmid37717394, year = {2023}, author = {Chen, Y and Zhang, X and Gong, X and Tao, T and Wang, Z and Zhang, J and Zhu, Y}, title = {Recovery and utilization of waste filtrate from industrial biological fermentation: Development and metabolite profile of the Bacillus cereus liquid bio-fertilizer.}, journal = {Journal of environmental management}, volume = {346}, number = {}, pages = {118945}, doi = {10.1016/j.jenvman.2023.118945}, pmid = {37717394}, issn = {1095-8630}, abstract = {Most fermentation waste filtrates can be used as raw materials for producing bio-fertilizers to reduce wastewater emissions and environmental pollution, but their bio-fertilizer utilization depends on the nutrients contained and their metabolized by functional microorganism. To achieve bio-fertilizer utilization of Acremonium terricola fermented waste filtrate, this study systematically explored the functional microbial species for making good use of waste liquid, optimized material process parameters for bio-fertilizer production based on D-optimal mixture design method, and analyzed the composition of the waste filtrate and its metabolism by functional microorganisms using a non-targeted LC-MS metagenomics technique. The results showed that Bacillus cereus was the functional microbial candidate for producing bio-fertilizer because of its more efficiently utilize the waste filtrate than other Bacillus sp. The optimal material process parameters of the liquid bio-fertilizer were the inoculum dose of 5% (v:v, %), 80% of waste filtrate, 0.25% of N, 3.5% of P2O5, 3.25% of K2O of mass percentage. Under these conditions, the colony forming unit (CFU) of Bacillus cereus could reach (1.59 ± 0.01) × 10[8] CFU/mL, which met the bio-fertilizer standard requirements of the People's Republic of China (NY/T798). Furthermore, the potential functions of bio-fertilizer were studied based on comparison of raw materials and production components: on the one hand, waste filtrate contained abundant of nitrogen and carbon sources, and bioactive substances secreted by Acremonium terricola, such as β-alanyl-L-lysine, anserine, UMP, L-lactic acid and etc., which could meet the nutrient requirements of the growth of Bacillus cereus; On the other hand, some compounds of waste filtrate with the potential to benefit the plant growth and defense, such as betaine aldehyde, (2E,6E)-farnesol, homogentisic acid and etc., were significantly up regulated by Bacillus cereus utilization of the filtrate. To sum up, this work highlighted that the waste filtrate could be efficiently developed into liquid bio-fertilizer by Bacillus cereus.}, } @article {pmid37716381, year = {2023}, author = {Zhang, Z and Liu, T and Li, X and Ye, Q and Bangash, HI and Zheng, J and Peng, N}, title = {Metagenome-assembled genomes reveal carbohydrate degradation and element metabolism of microorganisms inhabiting Tengchong hot springs, China.}, journal = {Environmental research}, volume = {238}, number = {Pt 1}, pages = {117144}, doi = {10.1016/j.envres.2023.117144}, pmid = {37716381}, issn = {1096-0953}, mesh = {*Hot Springs/chemistry/microbiology ; Metagenome ; Archaea/genetics/metabolism ; Bacteria/metabolism ; China ; Carbohydrates ; Sulfur/metabolism ; Nitrogen/metabolism ; Phylogeny ; }, abstract = {A hot spring is a distinctive aquatic environment that provides an excellent system to investigate microorganisms and their function in elemental cycling processes. Previous studies of terrestrial hot springs have been mostly focused on the microbial community, one special phylum or category, or genes involved in a particular metabolic step, while little is known about the overall functional metabolic profiles of microorganisms inhabiting the terrestrial hot springs. Here, we analyzed the microbial community structure and their functional genes based on metagenomic sequencing of six selected hot springs with different temperature and pH conditions. We sequenced a total of 11 samples from six hot springs and constructed 162 metagenome-assembled genomes (MAGs) with completeness above 70% and contamination lower than 10%. Crenarchaeota, Euryarchaeota and Aquificae were found to be the dominant phyla. Functional annotation revealed that bacteria encode versatile carbohydrate-active enzymes (CAZYmes) for the degradation of complex polysaccharides, while archaea tend to assimilate C1 compounds through carbon fixation. Under nitrogen-deficient conditions, there were correspondingly fewer genes involved in nitrogen metabolism, while abundant and diverse set of genes participating in sulfur metabolism, particularly those associated with sulfide oxidation and thiosulfate disproportionation. In summary, archaea and bacteria residing in the hot springs display distinct carbon metabolism fate, while sharing the common energy preference through sulfur metabolism. Overall, this research contributes to a better comprehension of biogeochemistry of terrestrial hot springs.}, } @article {pmid37716364, year = {2023}, author = {Worby, CJ and Sridhar, S and Turbett, SE and Becker, MV and Kogut, L and Sanchez, V and Bronson, RA and Rao, SR and Oliver, E and Walker, AT and Walters, MS and Kelly, P and Leung, DT and Knouse, MC and Hagmann, SHF and Harris, JB and Ryan, ET and Earl, AM and LaRocque, RC}, title = {Gut microbiome perturbation, antibiotic resistance, and Escherichia coli strain dynamics associated with international travel: a metagenomic analysis.}, journal = {The Lancet. Microbe}, volume = {4}, number = {10}, pages = {e790-e799}, pmid = {37716364}, issn = {2666-5247}, support = {U01 CK000490/CK/NCEZID CDC HHS/United States ; U01 CK000633/CK/NCEZID CDC HHS/United States ; U01CK000490/ACL/ACL HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; }, mesh = {United States ; Humans ; *Escherichia coli/genetics ; *Gastrointestinal Microbiome/genetics ; Travel ; Metagenome ; Travel-Related Illness ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Microbial ; beta-Lactamases/genetics ; DNA ; }, abstract = {BACKGROUND: Culture-based studies have shown that acquisition of extended-spectrum β-lactamase-producing Enterobacterales is common during international travel; however, little is known about the role of the gut microbiome before and during travel, nor about acquisition of other antimicrobial-resistant organisms. We aimed to identify (1) whether the gut microbiome provided colonisation resistance against antimicrobial-resistant organism acquisition, (2) the effect of travel and travel behaviours on the gut microbiome, and (3) the scale and global heterogeneity of antimicrobial-resistant organism acquisition.

METHODS: In this metagenomic analysis, participants were recruited at three US travel clinics (Boston, MA; New York, NY; and Salt Lake City, UT) before international travel. Participants had to travel internationally between Dec 8, 2017, and April 30, 2019, and have DNA extractions for stool samples both before and after travel for inclusion. Participants were excluded if they had at least one low coverage sample (<1 million read pairs). Stool samples were collected at home before and after travel, sent to a clinical microbiology laboratory to be screened for three target antimicrobial-resistant organisms (extended-spectrum β-lactamase-producing Enterobacterales, carbapenem-resistant Enterobacterales, and mcr-mediated colistin-resistant Enterobacterales), and underwent DNA extraction and shotgun metagenomic sequencing. We profiled metagenomes for taxonomic composition, antibiotic-resistant gene content, and characterised the Escherichia coli population at the strain level. We analysed pre-travel samples to identify the gut microbiome risk factors associated with acquisition of the three targeted antimicrobial resistant organisms. Pre-travel and post-travel samples were compared to identify microbiome and resistome perturbation and E coli strain acquisition associated with travel.

FINDINGS: A total of 368 individuals travelled between the required dates, and 296 had DNA extractions available for both before and after travel. 29 travellers were excluded as they had at least one low coverage sample, leaving a final group of 267 participants. We observed a perturbation of the gut microbiota, characterised by a significant depletion of microbial diversity and enrichment of the Enterobacteriaceae family. Metagenomic strain tracking confirmed that 67% of travellers acquired new strains of E coli during travel that were phylogenetically distinct from their pre-travel strains. We observed widespread enrichment of antibiotic-resistant genes in the gut, with a median 15% (95% CI 10-20, p<1 × 10[-10]) increase in burden (reads per kilobase per million reads). This increase included antibiotic-resistant genes previously classified as threats to public health, which were 56% (95% CI 36-91, p=2 × 10[-11]) higher in abundance after travel than before. Fluoroquinolone antibiotic-resistant genes were aquired by 97 (54%) of 181 travellers with no detected pre-travel carriage. Although we found that visiting friends or relatives, travel to south Asia, and eating uncooked vegetables were risk factors for acquisition of the three targeted antimicrobial resistant organisms, we did not observe an association between the pre-travel microbiome structure and travel-related antimicrobial-resistant organism acquisition.

INTERPRETATION: This work highlights a scale of E coli and antimicrobial-resistant organism acquisition by US travellers not apparent from previous culture-based studies, and suggests that strategies to control antimicrobial-resistant organisms addressing international traveller behaviour, rather than modulating the gut microbiome, could be worthwhile.

FUNDING: US Centers for Disease Control and Prevention and National Institute of Allergy and Infectious Diseases.}, } @article {pmid37716295, year = {2023}, author = {Ahmad, HA and Ahmad, S and Gao, L and Ismail, S and Wang, Z and El-Baz, A and Ni, SQ}, title = {Multi-omics analysis revealed the selective enrichment of partial denitrifying bacteria for the stable coupling of partial-denitrification and anammox process under the influence of low strength magnetic field.}, journal = {Water research}, volume = {245}, number = {}, pages = {120619}, doi = {10.1016/j.watres.2023.120619}, pmid = {37716295}, issn = {1879-2448}, abstract = {The microbial consortium involving anaerobic ammonium oxidation (anammox) and partial denitrification (PD), known as PD-anammox, is an emerging energy-efficient and lower carbon nitrogen removal process from wastewater. However, maintaining a stable PD process by locking nitrate reduction until nitrite was challenging. This study established the first stable connection of anammox with constant nitrite generation by PD bacteria under a low-strength (1.3 mT) magnetic field (MF). When the nitrogen loading rate was 1.81 kg-N/m[3]/d, the nitrogen removal efficiency of the control reactor (R1) was 75%, lower than that of the experimental reactor (R2), which was 85%. The expression of Thauera and Zoogloea, potential PD bacteria was substantially lower in R1 (5.75% and 1.21%, respectively) than in R2 (10.25 and 6.61%, respectively), according to a meta-transcriptomic analysis. At the same time, the mRNA expression of anammox genera Candidatus Brocadia and Candidatus Kuenenia was 33.53% and 3.83% in R1 and 22.86% and 1.87% in R2. Moreover, carbon and nitrogen metabolism pathways were more abundant under the influence of low-strength MF. The selective enrichment of PD bacteria can be attributed to the increased expression of carbon metabolic pathways like the citrate cycle, glycolysis/gluconeogenesis, and pyruvate metabolism. Interestingly, the control reactor was dominated by a hydroxylamine-dependent anammox process while a low-strength MF-enhanced nitric-oxide-dependent anammox process. For successful anammox-centered nitrogen removal from wastewater, this study demonstrated that low-strength MF is a convenient and applicable technique to lock the nitrate reduction until nitrite.}, } @article {pmid37716235, year = {2023}, author = {Wang, H and Zhao, X and Wen, J and Wang, C and Zhang, X and Ren, X and Zhang, J and Li, H and Muhatai, G and Qu, L}, title = {Comparative population genomics analysis uncovers genomic footprints and genes influencing body weight trait in Chinese indigenous chicken.}, journal = {Poultry science}, volume = {102}, number = {11}, pages = {103031}, pmid = {37716235}, issn = {1525-3171}, mesh = {Animals ; Body Weight/genetics ; *Chickens/genetics ; Genomics ; Metagenomics ; Polymorphism, Single Nucleotide ; China ; Selective Breeding/genetics ; }, abstract = {Body weight of chicken is a typical quantitative trait, which shows phenotypic variations due to selective breeding. Despite some QTL loci have been obtained, the body weight of native chicken breeds in different geographic regions varies greatly, its genetic basis remains unresolved questions. To address this issue, we analyzed 117 Chinese indigenous chickens from 10 breeds (Huiyang Bearded, Xinhua, Hotan Black, Baicheng You, Liyang, Yunyang Da, Jining Bairi, Lindian, Beijing You, Tibetan). We applied fixation index (FST) analysis to find selected genomic regions and genes associated with body weight traits. Our study suggests that NELL1, XYLT1, and NCAPG/LCORL genes are strongly selected in the body weight trait of Chinese indigenous chicken breeds. In addition, the IL1RAPL1 gene was strongly selected in large body weight chickens, while the PCDH17 and CADM2 genes were strongly selected in small body weight chickens. This result suggests that the patterns of genetic variation of native chicken and commercial chicken, and/or distinct local chicken breeds may follow different evolutionary mechanisms.}, } @article {pmid37715108, year = {2023}, author = {Vargas, KL and Kraberger, S and Custer, JM and Paietta, EN and Culver, M and Munguia-Vega, A and Dolby, GA and Varsani, A}, title = {Identification of a novel polyomavirus in wild Sonoran Desert rodents of the family Heteromyidae.}, journal = {Archives of virology}, volume = {168}, number = {10}, pages = {253}, pmid = {37715108}, issn = {1432-8798}, support = {2109458//National Science Foundation/ ; 1925535//National Science Foundation/ ; 2305608//National Science Foundation/ ; 1925771//National Science Foundation/ ; 1925771//National Science Foundation/ ; }, mesh = {Animals ; Humans ; Mice ; *Rodentia ; *Polyomavirus/genetics ; Mexico ; Polyomaviridae ; Animals, Domestic ; }, abstract = {Rodents are the largest and most diverse group of mammals. Covering a wide range of structural and functional adaptations, rodents successfully occupy virtually every terrestrial habitat, and they are often found in close association with humans, domestic animals, and wildlife. Although a significant amount of research has focused on rodents' prominence as known reservoirs of zoonotic viruses, there has been less emphasis on the viral ecology of rodents in general. Here, we utilized a viral metagenomics approach to investigate polyomaviruses in wild rodents from the Baja California peninsula, Mexico, using fecal samples. We identified a novel polyomavirus in fecal samples from two rodent species, a spiny pocket mouse (Chaetodipus spinatus) and a Dulzura kangaroo rat (Dipodomys simulans). These two polyomaviruses represent a new species in the genus Betapolyomavirus. Sequences of this polyomavirus cluster phylogenetically with those of other rodent polyomaviruses and two other non-rodent polyomaviruses (WU and KI) that have been identified in the human respiratory tract. Through our continued work on seven species of rodents, we endeavor to explore the viral diversity associated with wild rodents on the Baja California peninsula and expand on current knowledge of rodent viral ecology and evolution.}, } @article {pmid37715043, year = {2023}, author = {Liu, X and Li, P and Wang, H and Han, LL and Yang, K and Wang, Y and Jiang, Z and Cui, L and Kao, SJ}, title = {Nitrogen fixation and diazotroph diversity in groundwater systems.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {2023-2034}, pmid = {37715043}, issn = {1751-7370}, mesh = {*Nitrogen Fixation ; China ; Pseudomonas ; *Groundwater/chemistry ; Nitrogen/analysis ; Ferrous Compounds ; }, abstract = {Biological nitrogen fixation (BNF), the conversion of N2 into bioavailable nitrogen (N), is the main process for replenishing N loss in the biosphere. However, BNF in groundwater systems remains poorly understood. In this study, we examined the activity, abundance, and community composition of diazotrophs in groundwater in the Hetao Plain of Inner Mongolia using [15]N tracing methods, reverse transcription qPCR (RT-qPCR), and metagenomic/metatranscriptomic analyses. [15]N2 tracing incubation of near in situ groundwater (9.5-585.4 nmol N L[-1] h[-1]) and N2-fixer enrichment and isolates (13.2-1728.4 nmol N g[-1] h[-1], as directly verified by single-cell resonance Raman spectroscopy), suggested that BNF is a non-negligible source of N in groundwater in this region. The expression of nifH genes ranged from 3.4 × 10[3] to 1.2 × 10[6] copies L[-1] and was tightly correlated with dissolved oxygen (DO), Fe(II), and NH4[+]. Diazotrophs in groundwater were chiefly aerobes or facultative anaerobes, dominated by Stutzerimonas, Pseudomonas, Paraburkholderia, Klebsiella, Rhodopseudomonas, Azoarcus, and additional uncultured populations. Active diazotrophs, which prefer reducing conditions, were more metabolically diverse and potentially associated with nitrification, sulfur/arsenic mobilization, Fe(II) transport, and CH4 oxidation. Our results highlight the importance of diazotrophs in subsurface geochemical cycles.}, } @article {pmid37714908, year = {2023}, author = {Miyata, R and Miyabe, C and Oki, H and Motooka, D and Nakamura, S and Miyabe, Y and Takenaka, Y and Fukuya, Y and Yudo, K and Ishiguro, N}, title = {Alteration of microbial composition in the skin and blood in vasculitis.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15317}, pmid = {37714908}, issn = {2045-2322}, mesh = {Humans ; *Vasculitis ; Skin ; Leukocytes ; *Actinomycetales ; Discriminant Analysis ; }, abstract = {Vasculitis is a systemic autoimmune disease characterized by leukocyte infiltration into blood vessels. Various microorganisms have been associated with the pathogenesis of vasculitis; however, the causal microbial agents and underlying mechanisms are not fully understood, possibly because of the technical limitations of pathogen detection. In the present study, we characterized the microbiome profile of patients with cutaneous vasculitis using comprehensive metagenome shotgun sequencing. We found that the abundance of the SEN virus was increased in the affected skin and serum of patients with vasculitis compared to healthy donors. In particular, the abundance of SEN virus reads was increased in the sera of patients with cutaneous arteritis. Among the bacteria identified, Corynebacteriales was the most differentially associated with vasculitis. Linear discriminant analysis effect size also indicated differences in the microbial taxa between patients with vasculitis and healthy donors. These findings demonstrate that vasculitis is associated with considerable alteration of the microbiome in the blood and skin and suggest a role for the infectious trigger in vasculitis.}, } @article {pmid37714737, year = {2023}, author = {Guo, Z and Yiu, N and Hu, Z and Zhou, W and Long, X and Yang, M and Liao, J and Zhang, G and Lu, Q and Zhao, M}, title = {Alterations of fecal microbiome and metabolome in pemphigus patients.}, journal = {Journal of autoimmunity}, volume = {141}, number = {}, pages = {103108}, doi = {10.1016/j.jaut.2023.103108}, pmid = {37714737}, issn = {1095-9157}, mesh = {Humans ; *Pemphigus/diagnosis ; *Microbiota ; Metabolome ; Feces/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; }, abstract = {The role of gut microbiome and metabolic substances in the development of autoimmune diseases has gradually been revealed. However, the relevant gut features in pemphigus have not been well clarified. We collected stool samples from pemphigus patients and healthy controls (HCs). Metagenomic sequencing and liquid chromatography-mass spectrometry (LC/MS) metabolome sequencing were performed to analyze the compositional and metabolic alternations of the gut microbiome in pemphigus patients and HCs. We observed the reduced richness and diversity and greater heterogeneity in pemphigus patients, which was characterized by a significant decrease in Firmicutes and an increase in Proteobacteria. At the species level, Intestinal pathogenic bacteria such as Escherichia coli and Bacteroides fragilis were significantly enriched, while anti-inflammatory bacteria and butyric acid-producing bacteria were significantly reduced, which were related to clinical indicators (Dsg1/3 and PDAI). 4 species were selected by the machine learning algorithm to better distinguish pemphigus patients from healthy people. Metabolomic analysis showed that the composition of pemphigus patients was different from that of HCs. PE (18:3 (6Z,9Z, 12Z)/14:1 (9Z)) was the main metabolic substance in pemphigus and involved in a variety of metabolic pathways. While Retinol, flavonoid compounds and various amino acids decreased significantly compared with HCs. Furthermore, we found that differences in the levels of these metabolites correlated with changes in the abundance of specific species. Our study provides a comprehensive picture of gut microbiota and metabolites in pemphigus patients and suggests a potential mechanism of the aberrant gut microbiota and metabolites in the pathogenesis of pemphigus.}, } @article {pmid37714509, year = {2023}, author = {Wang, G and Tian, X and Peng, R and Huang, Y and Li, Y and Li, Z and Hu, X and Luo, Z and Zhang, Y and Cui, X and Niu, L and Lu, G and Yang, F and Gao, L and Chan, JF and Jin, Q and Yin, F and Tang, C and Ren, Y and Du, J}, title = {Genomic and phylogenetic profiling of RNA of tick-borne arboviruses in Hainan Island, China.}, journal = {Microbes and infection}, volume = {}, number = {}, pages = {105218}, doi = {10.1016/j.micinf.2023.105218}, pmid = {37714509}, issn = {1769-714X}, abstract = {Ticks act as vectors and hosts of numerous arboviruses. Examples of medically important arboviruses include the tick-borne encephalitis virus, Crimean Congo hemorrhagic fever, and severe fever with thrombocytopenia syndrome. Recently, some novel arboviruses have been identified in blood specimens of patients with unexplained fever and a history of tick bites in Inner Mongolia. Consequently, tick-borne viruses are a major focus of infectious disease research. However, the spectrum of tick-borne viruses in subtropical areas of China has yet to be sufficiently characterized. In this study, we collected 855 ticks from canine and bovine hosts in four locations in Hainan Province. The ticks were combined into 18 pools according to genus and location. Viral RNA-sequence libraries were subjected to transcriptome sequencing analysis. Molecular clues from metagenomic analyses were used to classify sequence reads into virus species, genera, or families. The diverse viral reads closely associated with mammals were assigned to 12 viral families and important tick-borne viruses, such as Jingmen, Beiji nairovirus, and Colorado tick fever. Our virome and phylogenetic analyses of the arbovirus strains provide basic data for preventing and controlling human infectious diseases caused by tick-borne viruses in the subtropical areas of China.}, } @article {pmid37714349, year = {2023}, author = {Sun, Y and Hao, Y and Zhang, Q and Liu, X and Wang, L and Li, J and Li, M and Li, D}, title = {Coping with extremes: Alternations in diet, gut microbiota, and hepatic metabolic functions in a highland passerine.}, journal = {The Science of the total environment}, volume = {905}, number = {}, pages = {167079}, doi = {10.1016/j.scitotenv.2023.167079}, pmid = {37714349}, issn = {1879-1026}, mesh = {Animals ; Male ; Female ; Humans ; *Gastrointestinal Microbiome/physiology ; RNA, Ribosomal, 16S/genetics ; Diet/veterinary ; *Microbiota ; Adaptation, Psychological ; *Passeriformes ; }, abstract = {In wild animals, diet and gut microbiota interactions are critical moderators of metabolic functions and are highly contingent on habitat conditions. Challenged by the extreme conditions of high-altitude environments, the strategies implemented by highland animals to adjust their diet and gut microbial composition and modulate their metabolic substrates remain largely unexplored. By employing a typical human commensal species, the Eurasian tree sparrow (Passer montanus, ETS), as a model species, we studied the differences in diet, digestive tract morphology and enzyme activity, gut microbiota, and metabolic energy profiling between highland (the Qinghai-Tibet Plateau, QTP; 3230 m) and lowland (Shijiazhuang, Hebei; 80 m) populations. Our results showed that highland ETSs had enlarged digestive organs and longer small intestinal villi, while no differences in key digestive enzyme activities were observed between the two populations. The 18S rRNA sequencing results revealed that the dietary composition of highland ETSs were more animal-based and less plant-based than those of the lowland ones. Furthermore, 16S rRNA sequencing results suggested that the intestinal microbial communities were structurally segregated between populations. PICRUSt metagenome predictions further indicated that the expression patterns of microbial genes involved in material and energy metabolism, immune system and infection, and xenobiotic biodegradation were strikingly different between the two populations. Analysis of liver metabolomics revealed significant metabolic differences between highland and lowland ETSs in terms of substrate utilization, as well as distinct sex-specific alterations in glycerophospholipids. Furthermore, the interplay between diet, liver metabolism, and gut microbiota suggests a dietary shift resulting in corresponding changes in gut microbiota and metabolic functions. Our findings indicate that highland ETSs have evolved to optimize digestion and absorption, rely on more protein-rich foods, and possess gut microbiota tailored to their dietary composition, likely adaptive physiological and ecological strategies adopted to cope with extreme highland environments.}, } @article {pmid37714338, year = {2023}, author = {Liu, D and Gao, X and Huang, X and Fan, Y and Wang, YE and Zhang, Y and Chen, X and Wen, J and He, H and Hong, Y and Liang, Y and Zhang, Y and Liu, Z and Chen, S and Li, X}, title = {Moderate altitude exposure impacts host fasting blood glucose and serum metabolome by regulation of the intestinal flora.}, journal = {The Science of the total environment}, volume = {905}, number = {}, pages = {167016}, doi = {10.1016/j.scitotenv.2023.167016}, pmid = {37714338}, issn = {1879-1026}, mesh = {Humans ; Mice ; Animals ; *Gastrointestinal Microbiome ; Blood Glucose ; Propionates ; Glutamic Acid ; Altitude ; Escherichia coli ; Metabolome ; Glucose ; Fasting ; }, abstract = {Moderate altitude exposure has shown beneficial effects on diabetes incidence but the underlying mechanisms are not understood. Our study aimed to investigate how the human gut microbiome impacted the serum metabolome and associated with glucose homeostasis in healthy Chinese individuals upon moderate-altitude exposure. Faecal microbiome composition was assessed using shotgun metagenomic sequencing. Serum metabolome was acquired by untargeted metabolomics technology, and amino acids (AAs) and propionic acid in serum were quantified by targeted metabolomics technology. The results indicated that the moderate-altitude exposed individuals presented lowered fasting blood glucose (FBG) and propionic acid, increased circulating L-Glutamine but decreased L-Glutamate and L-Valine, which correlated with enriched Bacteroidetes and decreased Proteobacteria. Additionally, the silico causality associations among gut microbiota, serum metabolome and host FBG were analyzed by mediation analysis. It showed that increased Bacteroides ovatus (B. ovatus) and decreased Escherichia coli (E. coli) were identified as the main antagonistic species driving the association between L-Glutamate and FBG in silico causality. Furthermore, the high-fat diet (HFD) fed mice subjected to faecal microbiota transplantation (FMT) were applied to validate the cause-in-fact effects of gut microbiota on the beneficial glucose response. We found that microbiome in the moderate-altitude exposed donor could predict the extent of the FBG response in recipient mice, which showed lowered FBG, L-Glutamate and Firmicutes/Bacteroidetes ratio. Our findings suggest that moderate-altitude exposure targeting gut microbiota and circulating metabolome, may pave novel avenues to counter dysglycemia.}, } @article {pmid37714224, year = {2024}, author = {Lu, Y and Gao, X and Mohammed, SAD and Wang, T and Fu, J and Wang, Y and Nan, Y and Lu, F and Liu, S}, title = {Efficacy and mechanism study of Baichanting compound, a combination of Acanthopanax senticosus (Rupr. and Maxim.) Harms, Paeonia lactiflora Pall and Uncaria rhynchophylla (Miq.) Miq. ex Havil, on Parkinson's disease based on metagenomics and metabolomics.}, journal = {Journal of ethnopharmacology}, volume = {319}, number = {Pt 1}, pages = {117182}, doi = {10.1016/j.jep.2023.117182}, pmid = {37714224}, issn = {1872-7573}, mesh = {Mice ; Animals ; *Parkinson Disease/drug therapy ; Dopamine/metabolism ; *Eleutherococcus ; *Paeonia ; Glutamic Acid ; Tumor Necrosis Factor-alpha/metabolism ; Chromatography, Liquid ; Interleukin-6 ; Mice, Inbred C57BL ; Tandem Mass Spectrometry ; Antioxidants/therapeutic use ; Metabolomics ; Glutamine ; Superoxide Dismutase ; Malondialdehyde ; }, abstract = {Parkinson's disease (PD) is a rapidly progressing neurological disorder. Currently, Medication for PD has numerous limitations. Baichanting Compound (BCT) is a Chinese herbal prescription, a Combination of Acanthopanax senticosus (Rupr. and Maxim.) Harms, Paeonia lactiflora Pall and Uncaria rhynchophylla (Miq.) Miq. ex Havil, that was developed to treat PD and holds a national patent (ZL, 201110260536.3).

AIM OF THE STUDY: To clarify the therapeutic effect of BCT on PD and explore its possible mechanism based on metabolomics and metagenomics.

MATERIALS AND METHODS: C57BL/6 mice were used as a control group, and α-syn transgenic C57BL/6 mice were randomly assigned to the PD (without treatment) or BCT (with BCT treatment) group. UPLC-MS was performed to detect dopamine levels in brain tissue, while ELISA was used to determine inflammatory factors such as IL-1β, IL-6, TNF-α, IFN-γ and NO, and oxidative stress indicators such as malondialdehyde, superoxide dismutase and glutathione peroxidase enzyme activity. Fecal metabolomics was used to detect fecal metabolic profiles, screen differential metabolic markers, and predict metabolic pathways by KEGG enrichment analysis. Metagenomics was used to determine the intestinal microbial composition, and KO enrichment analysis was performed to predict the potential function of different gut microbiota. Finally, Spearman correlation analysis was used to find the possible relationships among intestinal flora, metabolic markers, inflammatory factors, oxidative stress and dopamine levels.

RESULTS: BCT increased the superoxide dismutase activity of α-Syn transgenic C57BL/6 mice (P < 0.01), decreased the levels of TNF-α, IFN-γ, IL-1β, IL-6, NO and malondialdehyde (P < 0.01, 0.05), and increased the release of dopamine (P < 0.01). Metabolomics results show that BCT could regulate Acetatifactor, Marvinbryantia, Faecalitalea, Anaeromassilibacillus, Anaerobium, Pseudobutyrivibrio and Lachnotalea and Acetatifactor_muris, Marvinbryantia_formatexigens, Lachnotalea_sp_AF33_28, Faecalitalea_sp_Marseille_P3755 and Anaerobium_acetethylicum, Gemmiger_sp_An120 abundance to restore intestinal flora function, and reverse fecal metabolism trend, restoring the content of α-D-glucose, cytidine, L-glutamate, L-glutamine, N-acetyl-L-glutamate, raffinose and uracil. In addition, it regulates arginine biosynthesis, D-glutamine and D-glutamate, pyrimidine, galactose and alanine, aspartate and glutamate metabolic pathways.

CONCLUSION: BCT may regulate the composition of the gut microbiota to reverse fecal metabolism in PD mice to protect the substantia nigra and striatum from oxidative stress and inflammatory factors and ultimately play an anti-PD role.}, } @article {pmid37713802, year = {2023}, author = {Vieira, TR and de Oliveira, EFC and Cibulski, SP and Silva, NMV and Borba, MR and Oliveira, CJB and Cardoso, M}, title = {Comparative resistome, mobilome, and microbial composition of retail chicken originated from conventional, organic, and antibiotic-free production systems.}, journal = {Poultry science}, volume = {102}, number = {11}, pages = {103002}, pmid = {37713802}, issn = {1525-3171}, abstract = {The aim of this study was to investigate the microbial composition, and the profiles of antimicrobial resistance genes (ARGs, resistome) and mobile genetic elements (mobilome) of retail chicken carcasses originated from conventional intensive production systems (CO), certified antimicrobial-free intensive production systems (AF), and certified organic production systems with restricted antimicrobial use (OR). DNA samples were collected from 72 chicken carcasses according to a cross-sectional study design. Shot-gun metagenomics was performed by means of Illumina high throughput DNA sequencing followed by downstream bioinformatic analyses. Gammaproteobacteria was the most abundant bacterial class in all groups. Although CO, AF, and OR did not differ in terms of alpha- and beta-microbial diversity, the abundance of some taxa differed significantly across the groups, including spoilage-associated organisms such as Pseudomonas and Acinetobacter. The co-resistome comprised 29 ARGs shared by CO, AF and OR, including genes conferring resistance to beta-lactams (blaACT-8, 10, 13, 29; blaOXA-212;blaOXA-275 and ompA), aminoglycosides (aph(3')-IIIa, VI, VIa and spd), tetracyclines (tet KL (W/N/W and M), lincosamides (inu A,C) and fosfomycin (fosA). ARGs were significantly less abundant (P < 0.05) in chicken carcasses from AF and OR compared with CO. Regarding mobile genetic elements (MGEs), transposases accounted for 97.2% of the mapped genes. A higher abundance (P = 0.037) of MGEs was found in CO compared to OR. There were no significant differences in ARGs or MGEs diversity among groups according to the Simpson´s index. In summary, retail frozen chicken carcasses from AF and OR systems show similar ARGs, MGEs and microbiota profiles compared with CO, even though the abundance of ARGs and MGEs was higher in chicken carcasses from CO, probably due to a higher selective pressure.}, } @article {pmid37713776, year = {2023}, author = {Wu, Y and Li, S and Yu, K and Hu, J and Chen, Q and Sun, W}, title = {Wastewater treatment plant effluents exert different impacts on antibiotic resistome in water and sediment of the receiving river: Metagenomic analysis and risk assessment.}, journal = {Journal of hazardous materials}, volume = {460}, number = {}, pages = {132528}, doi = {10.1016/j.jhazmat.2023.132528}, pmid = {37713776}, issn = {1873-3336}, mesh = {*Water ; *Escherichia coli ; Rivers ; Risk Assessment ; Anti-Bacterial Agents/pharmacology ; Pseudomonas aeruginosa ; }, abstract = {Wastewater treatment plants (WWTPs) are considered as hotspots for the spread of antibiotic resistome into the environment. However, the differential contributions of WWTPs to the antibiotic resistome in the receiving river water and sediment are poorly understood. Here, based on metagenomic analysis, we found that the WWTP effluents significantly elevated the diversities and abundances of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in the receiving river water from the Qinghai-Tibet Plateau, but showed less interference with the antibiotic resistome in sediment. Estimated by SourceTracker, WWTPs contributed 60.691.8% of ARGs in downstream river water, much higher than those for sediment (7.7568.0%). A holistic comparison of ARG risks based on analysis of ARG combination, mobility risk, ARG hosts and ARG-carrying pathogens further revealed the great impacts of WWTP effluents on downstream river water rather than sediment. Among various MGEs, tnpA exhibited the greatest potential for the dissemination of ARGs, and displayed highest co-occurrence frequency with multiple ARGs. P. aeruginosa, E. cloacae, and E. coli were identified as the critical-priority pathogens of ARG hosts. This study demonstrated the much greater impacts of WWTP effluents on the downstream water compared with sediment, which is significant for developing effective strategies to mitigate ARG risks.}, } @article {pmid37712982, year = {2023}, author = {Xiao, ST and Zhang, HQ and Wang, YX}, title = {Isolated neural arch tuberculosis with tuberculomas: case report.}, journal = {Skeletal radiology}, volume = {}, number = {}, pages = {}, pmid = {37712982}, issn = {1432-2161}, support = {2020JJ4913//Natural Science Foundation of Hunan Province/ ; 2021JGB082//Research project on postgraduate education and teaching reform of Central South University/ ; 2022YJSKS032//Graduate course ideological and political construction project of Central South University/ ; }, abstract = {We reported a case of atypical spinal tuberculosis on the posterior elements of lumbar spine in a 52-year-old female. It was easy to be misdiagnosed as spinal tumor due to its imaging characteristics. We performed puncture biopsy to initially consider tuberculosis, and then the patient was accepted surgical treatment. The intraoperative removed specimen was sent to pathological examination, microbial culture, Xpert MTB/RIF and metagenomic next-generation sequencing (mNGS) and then the diagnosis of neural arch tuberculosis was confirmed. After operation, the patient obtained stable effect by anti-tuberculosis drug treatment. In a word, the uncommon case had an important reference significance for the diagnosis of atypical spine tuberculosis and differentiation from spinal tumors. It is critical to make right preliminary diagnosis by appropriate examination as it determined the next diagnosis and treatment in special and rare clinical cases.}, } @article {pmid37712673, year = {2023}, author = {Alidjinou, EK and De Coninck, L and Swinnen, J and Lazrek, M and Hober, D and Matthijnssens, J}, title = {Four complete genomes of human parvovirus B19 from amniotic fluid specimens.}, journal = {Microbiology resource announcements}, volume = {12}, number = {10}, pages = {e0055623}, pmid = {37712673}, issn = {2576-098X}, abstract = {We report the sequences of four complete genomes of parvovirus B19, extracted from human amniotic fluid specimens collected from pregnant women with abnormal ultrasound features in France. The genome sequences are 5,596 nucleotides long and include long terminal repeats. Several amino acid substitutions were observed in nonstructural protein (NS1).}, } @article {pmid37712061, year = {2023}, author = {Yuan, C and Xu, W and Zhao, C and Gao, W and Wu, G}, title = {Case Report: Detection of Treponema phagedenis in cerebrospinal fluid of a neurosyphilis patient by metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1218049}, pmid = {37712061}, issn = {2235-2988}, mesh = {Animals ; Cattle ; Male ; Humans ; *Treponema/genetics ; *Neurosyphilis/diagnosis ; High-Throughput Nucleotide Sequencing ; Penicillin G Benzathine ; }, abstract = {Treponema phagedenis, a human commensal spirochete, has been reported world-wide as a key factor in the pathogenesis of bovine digital dermatitis. Here we report a case of T. phagedenis sequence detection in the cerebrospinal fluid (CSF) of a patient. The patient was diagnosed with neurosyphilis, and T. phagedenis was detected as the only microorganism in his CSF by metagenomic sequencing. The patient went through a round of penicillin therapy previously (2.4 million units of Benzathine Penicillin intramuscularly once a week for three weeks) that did not resolve the symptoms; after the diagnosis of neurosyphilis he was treated with Penicillin G Sodium 4.0 million units q4h intravenous for 14 days then his symptoms resolved. To the best of our knowledge, T. phagedenis has never been reported to be detected in a human's CSF before. This was also the first time it was detected by metagenomic next-generation sequencing. We propose that more etiological tests should be performed including culture and sequencing for more patients with syphilis, which will contribute to a deeper understanding of the pathogenicity of the spirochete.}, } @article {pmid37711695, year = {2023}, author = {Zhou, J and Chen, T and Cui, J and Chen, Y and Zhao, S and Qu, JH and Wang, Z and Pan, J and Fan, L}, title = {Responses of the microbial community and the production of extracellular polymeric substances to sulfamethazine shocks in a novel two-stage biological contact oxidation system.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1240435}, pmid = {37711695}, issn = {1664-302X}, abstract = {INTRODUCTION: The biological contact oxidation reactor is an effective technology for the treatment of antibiotic wastewater, but there has been little research investigating its performance on the sulfamethazine wastewater treatment.

METHODS: In this study, a novel two-stage biological contact oxidation reactor was used for the first time to explore the impact of sulfamethazine (SMZ) on the performance, microbial community, extracellular polymeric substances (EPS), and antibiotic-resistant genes (ARGs).

RESULTS: The chemical oxygen demand (COD) and ammonia nitrogen (NH4+-N) removal efficiencies kept stable at 86.93% and 83.97% with 0.1-1 mg/L SMZ addition and were inhibited at 3 mg/L SMZ. The presence of SMZ could affect the production and chemical composition of EPS in the biofilm, especially for the pronounced increase in TB-PN yield in response against the threat of SMZ. Metagenomics sequencing demonstrated that SMZ could impact on the microbial community, a high abundance of Candidatus_Promineofilum, unclassified_c__Anaerolineae, and unclassified_c__Betaproteobacteria were positively correlated to SMZ, especially for Candidatus_Promineofilum.

DISCUSSION: Candidatus_Promineofilum not only had the ability of EPS secretion, but also was significantly associated with the primary SMZ resistance genes of sul1 and sul2, which developed resistance against SMZ pressure through the mechanism of targeted gene changes, further provided a useful and easy-implement technology for sulfamethazine wastewater treatment.}, } @article {pmid37709944, year = {2023}, author = {Bermingham, KM and May, A and Asnicar, F and Capdevila, J and Leeming, ER and Franks, PW and Valdes, AM and Wolf, J and Hadjigeorgiou, G and Delahanty, LM and Segata, N and Spector, TD and Berry, SE}, title = {Snack quality and snack timing are associated with cardiometabolic blood markers: the ZOE PREDICT study.}, journal = {European journal of nutrition}, volume = {}, number = {}, pages = {}, pmid = {37709944}, issn = {1436-6215}, abstract = {BACKGROUND: Snacking is a common diet behaviour which accounts for a large proportion of daily energy intake, making it a key determinant of diet quality. However, the relationship between snacking frequency, quality and timing with cardiometabolic health remains unclear.

DESIGN: Demography, diet, health (fasting and postprandial cardiometabolic blood and anthropometrics markers) and stool metagenomics data were assessed in the UK PREDICT 1 cohort (N = 1002) (NCT03479866). Snacks (foods or drinks consumed between main meals) were self-reported (weighed records) across 2-4 days. Average snacking frequency and quality [snack diet index (SDI)] were determined (N = 854 after exclusions). Associations between snacking frequency, quality and timing with cardiometabolic blood and anthropometric markers were assessed using regression models (adjusted for age, sex, BMI, education, physical activity level and main meal quality).

RESULTS: Participants were aged (mean, SD) 46.1 ± 11.9 years, had a mean BMI of 25.6 ± 4.88 kg/m[2] and were predominantly female (73%). 95% of participants were snackers (≥ 1 snack/day; n = 813); mean daily snack intake was 2.28 snacks/day (24 ± 16% of daily calories; 203 ± 170 kcal); and 44% of participants were discordant for meal and snack quality. In snackers, overall snacking frequency and quantity of snack energy were not associated with cardiometabolic risk markers. However, lower snack quality (SDI range 1-11) was associated with higher blood markers, including elevated fasting triglycerides (TG (mmol/L) β; - 0.02, P = 0.02), postprandial TGs (6hiAUC (mmol/L.s); β; - 400, P = 0.01), fasting insulin (mIU/L) (β; - 0.15, P = 0.04), insulin resistance (HOMA-IR; β; - 0.04, P = 0.04) and hunger (scale 0-100) (β; - 0.52, P = 0.02) (P values non-significant after multiple testing adjustments). Late-evening snacking (≥ 9 pm; 31%) was associated with lower blood markers (HbA1c; 5.54 ± 0.42% vs 5.46 ± 0.28%, glucose 2hiAUC; 8212 ± 5559 vs 7321 ± 4928 mmol/L.s, P = 0.01 and TG 6hiAUC; 11,638 ± 8166 vs 9781 ± 6997 mmol/L.s, P = 0.01) compared to all other snacking times (HbA1c remained significant after multiple testing).

CONCLUSION: Snack quality and timing of consumption are simple diet features which may be targeted to improve diet quality, with potential health benefits.

NCT03479866, https://clinicaltrials.gov/ct2/show/NCT03479866?term=NCT03479866&draw=2&rank=1.}, } @article {pmid37709803, year = {2023}, author = {Mukohda, M and Yano, T and Matsui, T and Nakamura, S and Miyamae, J and Toyama, K and Mitsui, R and Mizuno, R and Ozaki, H}, title = {Treatment with Ligilactobacillus murinus lowers blood pressure and intestinal permeability in spontaneously hypertensive rats.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15197}, pmid = {37709803}, issn = {2045-2322}, mesh = {Animals ; Rats ; Blood Pressure ; Rats, Inbred SHR ; Claudin-4 ; *Intestines ; *Hypertension ; }, abstract = {One feature of hypertension is a microbial imbalance with increased intestinal permeability. In this study, we examined whether an alteration in the microbiota affects blood pressure and intestinal permeability in spontaneously hypertensive rats (SHRs). We performed a 16S metagenome analysis of feces from 10- to 15-week-old SHRs using a synthetic long-read sequencing approach, and found a candidate for the microbiome treatment, Ligilactobacillus murinus (L. murinus), that was robustly decreased. Oral administration of L. murinus to SHRs for 2 weeks significantly inhibited blood pressure elevation and improved endothelium-dependent vasodilation but did not attenuate enhanced vascular contraction in SHR mesenteric arteries. The proximal colon of SHRs exhibited increased intestinal permeability with decreased levels of the tight junction protein claudin 4, morphological changes such as decreased intestinal crypts and elevated TNF-α levels, which was reversed by treatment with L. murinus. Consistent with these intestinal phenotypes, plasma lipopolysaccharides levels were elevated in SHR but decreased following L. murinus administration. We concluded that oral administration of L. murinus to SHRs exerts protective effects on intestinal permeability via restoration of claudin 4 expression and reversal of morphologic disorder, which may improve low-grade endotoxemia and thus reduce development of hypertension via recovery of endothelial vasodilating functions.}, } @article {pmid37709733, year = {2023}, author = {Lim, JJ and Diener, C and Wilson, J and Valenzuela, JJ and Baliga, NS and Gibbons, SM}, title = {Growth phase estimation for abundant bacterial populations sampled longitudinally from human stool metagenomes.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5682}, pmid = {37709733}, issn = {2041-1723}, mesh = {Animals ; Humans ; *Metagenome ; Ecosystem ; Feces ; *Body Fluids ; Population Density ; Escherichia coli/genetics ; }, abstract = {Longitudinal sampling of the stool has yielded important insights into the ecological dynamics of the human gut microbiome. However, human stool samples are available approximately once per day, while commensal population doubling times are likely on the order of minutes-to-hours. Despite this mismatch in timescales, much of the prior work on human gut microbiome time series modeling has assumed that day-to-day fluctuations in taxon abundances are related to population growth or death rates, which is likely not the case. Here, we propose an alternative model of the human gut as a stationary system, where population dynamics occur internally and the bacterial population sizes measured in a bolus of stool represent a steady-state endpoint of these dynamics. We formalize this idea as stochastic logistic growth. We show how this model provides a path toward estimating the growth phases of gut bacterial populations in situ. We validate our model predictions using an in vitro Escherichia coli growth experiment. Finally, we show how this method can be applied to densely-sampled human stool metagenomic time series data. We discuss how these growth phase estimates may be used to better inform metabolic modeling in flow-through ecosystems, like animal guts or industrial bioreactors.}, } @article {pmid37709670, year = {2023}, author = {Asao, K and Hashida, N and Maruyama, K and Motooka, D and Tsukamoto, T and Usui, Y and Nakamura, S and Nishida, K}, title = {Comparative evaluation of 16S rRNA metagenomic sequencing in the diagnosis and understanding of bacterial endophthalmitis.}, journal = {BMJ open ophthalmology}, volume = {8}, number = {1}, pages = {}, pmid = {37709670}, issn = {2397-3269}, mesh = {Male ; Humans ; Female ; Adult ; Middle Aged ; Aged ; Aged, 80 and over ; RNA, Ribosomal, 16S/genetics ; *Endophthalmitis/diagnosis ; *Eye Infections, Bacterial ; Vitreous Body ; *Libraries ; }, abstract = {OBJECTIVE: To evaluate the usefulness of metagenomic analysis in the search for causative organisms of bacterial endophthalmitis.

METHODS AND ANALYSIS: Twenty-one consecutive treatment-naïve patients (13 men and 8 women; mean age, 60.8±19.8 years) with suspected endophthalmitis were recruited. Vitrectomy was performed to diagnose and treat endophthalmitis. Bacterial culture and metagenomic analysis of the vitreous body were performed. Extracted DNA was analysed using 16S rRNA sequences, and libraries were sequenced on an Illumina MiSeq sequencer. To compare the bacterial composition in each case, α and β diversities were determined.

RESULTS: Patients were categorised into three groups: endophthalmitis cases with matching predominant organisms according to metagenomic analysis and bacterial culture, those with negative results for bacterial culture and those with negative results in both cases. In 7 of 15 culture-negative cases, results from metagenomic analysis could detect pathogens. The diversity of bacterial populations was significantly lower in the group with positive results for predominant bacteria according to culture and metagenomic analysis. All patients with uveitis were included in the group for which the causative pathogen could not be determined by culture or metagenomic analysis. The structures of bacterial populations significantly differed between the positive and negative groups by culture and metagenomic analysis.

CONCLUSIONS: Metagenomic analysis could be useful for prompt detection of causative pathogens, for precise diagnosis of infection, and as a marker of inflammation processes such as uveitis.}, } @article {pmid37708700, year = {2023}, author = {Zhao, J and He, X and Min, J and Yao, RSY and Chen, Y and Chen, Z and Huang, Y and Zhu, Z and Gong, Y and Xie, Y and Li, Y and Luo, W and Shi, D and Xu, J and Shen, A and Wang, Q and Sun, R and He, B and Lin, Y and Shen, N and Cao, B and Yang, L and She, D and Shi, Y and Zhou, J and Su, X and Zhou, H and Ma, Z and Fan, H and Lin, Y and Ye, F and Nie, X and Zhang, Q and Tian, X and Lai, G and Zhou, M and Ma, J and Zhang, J and Qu, J}, title = {A multicenter prospective study of comprehensive metagenomic and transcriptomic signatures for predicting outcomes of patients with severe community-acquired pneumonia.}, journal = {EBioMedicine}, volume = {96}, number = {}, pages = {104790}, pmid = {37708700}, issn = {2352-3964}, abstract = {BACKGROUND: Severe community-acquired pneumonia (SCAP) results in high mortality as well as massive economic burden worldwide, yet limited knowledge of the bio-signatures related to prognosis has hindered the improvement of clinical outcomes. Pathogen, microbes and host are three vital elements in inflammations and infections. This study aims to discover the specific and sensitive biomarkers to predict outcomes of SCAP patients.

METHODS: In this study, we applied a combined metagenomic and transcriptomic screening approach to clinical specimens gathered from 275 SCAP patients of a multicentre, prospective study.

FINDINGS: We found that 30-day mortality might be independent of pathogen category or microbial diversity, while significant difference in host gene expression pattern presented between 30-day mortality group and the survival group. Twelve outcome-related clinical characteristics were identified in our study. The underlying host response was evaluated and enrichment of genes related to cell activation, immune modulation, inflammatory and metabolism were identified. Notably, omics data, clinical features and parameters were integrated to develop a model with six signatures for predicting 30-day mortality, showing an AUC of 0.953 (95% CI: 0.92-0.98).

INTERPRETATION: In summary, our study linked clinical characteristics and underlying multi-omics bio-signatures to the differential outcomes of patients with SCAP. The establishment of a comprehensive predictive model will be helpful for future improvement of treatment strategies and prognosis with SCAP.

FUNDING: National Natural Science Foundation of China (No. 82161138018), Shanghai Municipal Key Clinical Specialty (shslczdzk02202), Shanghai Top-Priority Clinical Key Disciplines Construction Project (2017ZZ02014), Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases (20dz2261100).}, } @article {pmid37708410, year = {2023}, author = {Khachaturyan, M and Reusch, TBH and Dagan, T}, title = {Worldwide Population Genomics Reveal Long-Term Stability of the Mitochondrial Genome Architecture in a Keystone Marine Plant.}, journal = {Genome biology and evolution}, volume = {15}, number = {9}, pages = {}, pmid = {37708410}, issn = {1759-6653}, mesh = {Humans ; Metagenomics ; *Genome, Mitochondrial ; DNA, Mitochondrial/genetics ; Mitochondria/genetics ; *Magnoliopsida/genetics ; }, abstract = {Mitochondrial genomes (mitogenomes) of flowering plants are composed of multiple chromosomes. Recombination within and between the mitochondrial chromosomes may generate diverse DNA molecules termed isoforms. The isoform copy number and composition can be dynamic within and among individual plants due to uneven replication and homologous recombination. Nonetheless, despite their functional importance, the level of mitogenome conservation within species remains understudied. Whether the ontogenetic variation translates to evolution of mitogenome composition over generations is currently unknown. Here we show that the mitogenome composition of the seagrass Zostera marina is conserved among worldwide populations that diverged ca. 350,000 years ago. Using long-read sequencing, we characterized the Z. marina mitochondrial genome and inferred the repertoire of recombination-induced configurations. To characterize the mitochondrial genome architecture worldwide and study its evolution, we examined the mitogenome in Z. marina meristematic region sampled in 16 populations from the Pacific and Atlantic oceans. Our results reveal a striking similarity in the isoform relative copy number, indicating a high conservation of the mitogenome composition among distantly related populations and within the plant germline, despite a notable variability during individual ontogenesis. Our study supplies a link between observations of dynamic mitogenomes at the level of plant individuals and long-term mitochondrial evolution.}, } @article {pmid37707732, year = {2023}, author = {Liu, JL and Yao, J and Zhou, DL and Liu, B and Liu, H and Li, M and Zhao, C and Sunahara, G and Duran, R}, title = {Mining-related multi-resistance genes in sulfate-reducing bacteria treatment of typical karst nonferrous metal(loid) mine tailings in China.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {47}, pages = {104753-104766}, pmid = {37707732}, issn = {1614-7499}, mesh = {RNA, Ribosomal, 16S ; *Metals/analysis ; *Bacteria/metabolism ; Anti-Bacterial Agents/pharmacology ; China ; Sulfates/analysis ; Genes, Bacterial ; }, abstract = {Management of tailings at metal mine smelter sites can reduce the potential hazards associated with exposure to toxic metal(loid)s and residual organic flotation reagents. In addition, microbes in the tailings harboring multi-resistance genes (e.g., tolerance to multiple antimicrobial agents) can cause high rates of morbidity and global economic problems. The potential co-selection mechanisms of antibiotic resistance genes (ARGs) and metal(loid) resistance genes (MRGs) during tailings sulfate-reducing bacteria (SRB) treatment have been poorly investigated. Samples were collected from a nonferrous metal mine tailing site treated with an established SRB protocol and were analyzed for selected geochemical properties and high throughput sequencing of 16S rRNA gene barcoding. Based on the shotgun metagenomic analysis, the bacterial domain was dominant in nonferrous metal(loid)-rich tailings treated with SRB for 12 months. KEGGs related to ARGs and MRGs were detected. Thiobacillus and Sphingomonas were the main genera carrying the bacA and mexEF resistance operons, along with Sulfuricella which were also found as the main genera carrying MRGs. The SRB treatment may mediate the distribution of numerous resistance genes. KOs based on the metagenomic database indicated that ARGs (mexNW, merD, sul, and bla) and MRGs (czcABCR and copRS genes) were found on the same contig. The SRB strains (Desulfosporosinus and Desulfotomaculum), and the acidophilic strain Acidiphilium significantly contributed to the distribution of sul genes. The functional metabolic pathways related to siderophores metabolism were largely from anaerobic genera of Streptomyces and Microbacterium. The presence of arsenate reductase, metal efflux pump, and Fe transport genes indicated that SRB treatment plays a key role in the metal(loid)s transformation. Overall, our findings show that bio-treatment is an effective tool for managing ARGs/MRGs and metals in tailings that contain numerous metal(loid) contaminants.}, } @article {pmid37707718, year = {2023}, author = {Rambia, A and Veluchamy, C and Rawat, JM and Jamdhade, MD and Purohit, S and Pawar, KD and Rajasekaran, C and Rawat, B and Sharma, A}, title = {Revealing bacterial and fungal communities of the untapped forest and alpine grassland zones of the Western-Himalayan region.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {37707718}, issn = {1618-1905}, abstract = {The Western Himalayas offer diverse environments for investigating the diversity and distribution of microbial communities and their response to both the abiotic and biotic factors across the entire altitudinal gradient. Such investigations contribute significantly to our understanding of the complex ecological processes that shape microbial diversity. The proposed study focuses on the investigation of the bacterial and fungal communities in the forest and alpine grasslands of the Western Himalayan region, as well as their relationship with the physicochemical parameters of soil. A total of 185 isolates were obtained using the culture-based technique belonging to Bacillus (37%), Micrococcus (16%), and Staphylococcus (7%). Targeted metagenomics revealed the abundance of bacterial phyla Pseudomonadota (23%) followed by Acidobacteriota (20.2%), Chloroflexota (15%), and Bacillota (11.3%). At the genera level, CandidatusUdaeobacter (6%), Subgroup_2 (5.5%) of phylum Acidobacteriota, and uncultured Ktedonobacterales HSB_OF53-F07 (5.2%) of Choloroflexota phylum were found to be preponderant. Mycobiome predominantly comprised of phyla Ascomycota (54.1%), Basidiomycota (24%), and Mortierellomycota (19.1%) with Archaeorhizomyces (19.1%), Mortierella (19.1%), and Russula (5.4%) being the most abundant genera. Spearman's correlation revealed that the bacterial community was most influenced by total nitrogen in the soil followed by soil organic carbon as compared to other soil physicochemical factors. The study establishes a fundamental relationship between microbial communities and the physicochemical properties of soil. Furthermore, the study provides valuable insights into the complex interplay between biotic and abiotic factors that influence the microbial community composition of this unique region across various elevations.}, } @article {pmid37705831, year = {2023}, author = {Wichmann, A and Buschong, E and Müller, A and Jünger, D and Hildebrandt, A and Hankeln, T and Schmidt, B}, title = {MetaTransformer: deep metagenomic sequencing read classification using self-attention models.}, journal = {NAR genomics and bioinformatics}, volume = {5}, number = {3}, pages = {lqad082}, pmid = {37705831}, issn = {2631-9268}, abstract = {Deep learning has emerged as a paradigm that revolutionizes numerous domains of scientific research. Transformers have been utilized in language modeling outperforming previous approaches. Therefore, the utilization of deep learning as a tool for analyzing the genomic sequences is promising, yielding convincing results in fields such as motif identification and variant calling. DeepMicrobes, a machine learning-based classifier, has recently been introduced for taxonomic prediction at species and genus level. However, it relies on complex models based on bidirectional long short-term memory cells resulting in slow runtimes and excessive memory requirements, hampering its effective usability. We present MetaTransformer, a self-attention-based deep learning metagenomic analysis tool. Our transformer-encoder-based models enable efficient parallelization while outperforming DeepMicrobes in terms of species and genus classification abilities. Furthermore, we investigate approaches to reduce memory consumption and boost performance using different embedding schemes. As a result, we are able to achieve 2× to 5× speedup for inference compared to DeepMicrobes while keeping a significantly smaller memory footprint. MetaTransformer can be trained in 9 hours for genus and 16 hours for species prediction. Our results demonstrate performance improvements due to self-attention models and the impact of embedding schemes in deep learning on metagenomic sequencing data.}, } @article {pmid37705113, year = {2023}, author = {De Filippis, F and Bonelli, M and Bruno, D and Sequino, G and Montali, A and Reguzzoni, M and Pasolli, E and Savy, D and Cangemi, S and Cozzolino, V and Tettamanti, G and Ercolini, D and Casartelli, M and Caccia, S}, title = {Plastics shape the black soldier fly larvae gut microbiome and select for biodegrading functions.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {205}, pmid = {37705113}, issn = {2049-2618}, mesh = {Animals ; Larva ; *Gastrointestinal Microbiome/genetics ; Plastics ; RNA, Ribosomal, 16S/genetics ; *Diptera ; }, abstract = {BACKGROUND: In the last few years, considerable attention has been focused on the plastic-degrading capability of insects and their gut microbiota in order to develop novel, effective, and green strategies for plastic waste management. Although many analyses based on 16S rRNA gene sequencing are available, an in-depth analysis of the insect gut microbiome to identify genes with plastic-degrading potential is still lacking.

RESULTS: In the present work, we aim to fill this gap using Black Soldier Fly (BSF) as insect model. BSF larvae have proven capability to efficiently bioconvert a wide variety of organic wastes but, surprisingly, have never been considered for plastic degradation. BSF larvae were reared on two widely used plastic polymers and shotgun metagenomics was exploited to evaluate if and how plastic-containing diets affect composition and functions of the gut microbial community. The high-definition picture of the BSF gut microbiome gave access for the first time to the genomes of culturable and unculturable microorganisms in the gut of insects reared on plastics and revealed that (i) plastics significantly shaped bacterial composition at species and strain level, and (ii) functions that trigger the degradation of the polymer chains, i.e., DyP-type peroxidases, multicopper oxidases, and alkane monooxygenases, were highly enriched in the metagenomes upon exposure to plastics, consistently with the evidences obtained by scanning electron microscopy and [1]H nuclear magnetic resonance analyses on plastics.

CONCLUSIONS: In addition to highlighting that the astonishing plasticity of the microbiota composition of BSF larvae is associated with functional shifts in the insect microbiome, the present work sets the stage for exploiting BSF larvae as "bioincubators" to isolate microbial strains and enzymes for the development of innovative plastic biodegradation strategies. However, most importantly, the larvae constitute a source of enzymes to be evolved and valorized by pioneering synthetic biology approaches. Video Abstract.}, } @article {pmid37705082, year = {2023}, author = {Kaur, K and Rinaldo, A and Lovelock, D and Rodoni, B and Constable, F}, title = {The genetic variability of grapevine Pinot gris virus (GPGV) in Australia.}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {211}, pmid = {37705082}, issn = {1743-422X}, mesh = {Australia ; Phylogeny ; *Flexiviridae/genetics ; Europe ; Fruit ; }, abstract = {Grapevine Pinot gris virus (GPGV; genus Trichovirus in the family Betaflexiviridae) was detected in Australia in 2016, but its impact on the production of nursery material and fruit in Australia is still currently unknown. This study investigated the prevalence and genetic diversity of GPGV in Australia. GPGV was detected by reverse transcription-polymerase chain reaction (RT-PCR) in a range of rootstock, table and wine grape varieties from New South Wales, South Australia, and Victoria, with 473/2171 (21.8%) samples found to be infected. Genomes of 32 Australian GPGV isolates were sequenced and many of the isolates shared high nucleotide homology. Phylogenetic and haplotype analyses demonstrated that there were four distinct clades amongst the 32 Australian GPGV isolates and that there were likely to have been at least five separate introductions of the virus into Australia. Recombination and haplotype analysis indicate the emergence of new GPGV strains after introduction into Australia. When compared with 168 overseas GPGV isolates, the analyses suggest that the most likely origin of Australian GPGV isolates is from Europe. There was no correlation between specific GPGV genotypes and symptoms such as leaf mottling, leaf deformation, and shoot stunting, which were observed in some vineyards, and the virus was frequently found in symptomless grapevines.}, } @article {pmid37704808, year = {2023}, author = {Pan, Z and Chen, Z and Zhu, L and Avellán-Llaguno, RD and Liu, B and Huang, Q}, title = {Antibiotic resistome and associated bacterial communities in agricultural soil following the amendments of swine manure-derived fermentation bed waste.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {47}, pages = {104520-104531}, pmid = {37704808}, issn = {1614-7499}, support = {(2020R1034002//Fujian Special Fund for Scientific Research Institutes in the Public Interest/ ; 3502Z20227240//Natural Science Foundation of Xiamen City/ ; DWHZ2021-15//External cooperation project of Fujian Academy of Agricultural Sciences/ ; }, mesh = {Swine ; Animals ; *Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; Manure/analysis ; Fermentation ; Genes, Bacterial ; Soil Microbiology ; Agriculture ; Bacteria/genetics ; *Microbiota ; }, abstract = {The practice of utilizing animal manures on land is widespread in agriculture, but it has raised concerns about the possible spread of antibiotic resistance genes (ARGs) and the potential risk it poses to public health through food production. Fermentation bed culture is an effective circular agricultural practice commonly utilized in pig farming that minimizes the environmental impact of livestock farming. However, this method generates a significant amount of fermentation bed waste (FBW), which can be turned into organic fertilizer for land application. The objective of this research was to examine the impacts of amending agricultural soil samples with swine manure-derived FBW on microbial communities, mobile genetic elements (MGEs), and ARG profiles over different periods. The study findings indicated that the amendment of swine manure-derived FBW significantly increased the diversity and abundance of ARGs and MGEs during the early stages of amendment, but this effect diminished over time, and after 12 months of FBW amendments, the levels returned to those comparable to control samples. The shift in the bacterial communities played a significant role in shaping the patterns of ARGs. Actinobacteriota, Proteobacteria, and Bacteroidetes were identified as the primary potential hosts of ARGs through metagenomic binning analysis. Furthermore, the pH of soil samples was identified as the most important property in driving the composition of the bacterial community and soil resistome. These findings provided valuable insights into the temporal patterns and dissemination risks of ARGs in FBW-amended agriculture soil, which could contribute to the development of effective strategies to manage the dissemination risks of FBW-derived ARGs.}, } @article {pmid37704738, year = {2023}, author = {Chang, YH and Yanckello, LM and Chlipala, GE and Green, SJ and Aware, C and Runge, A and Xing, X and Chen, A and Wenger, K and Flemister, A and Wan, C and Lin, AL}, title = {Prebiotic inulin enhances gut microbial metabolism and anti-inflammation in apolipoprotein E4 mice with sex-specific implications.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {15116}, pmid = {37704738}, issn = {2045-2322}, support = {RF1 AG062480/AG/NIA NIH HHS/United States ; UL1 TR002003/TR/NCATS NIH HHS/United States ; }, mesh = {Female ; Male ; Animals ; Mice ; Apolipoprotein E4/genetics ; Apolipoprotein E3 ; Dysbiosis ; *Gastrointestinal Microbiome ; Inulin/pharmacology ; *Alzheimer Disease ; Anti-Inflammatory Agents ; Escherichia coli ; }, abstract = {Gut dysbiosis has been identified as a crucial factor of Alzheimer's disease (AD) development for apolipoprotein E4 (APOE4) carriers. Inulin has shown the potential to mitigate dysbiosis. However, it remains unclear whether the dietary response varies depending on sex. In the study, we fed 4-month-old APOE4 mice with inulin for 16 weeks and performed shotgun metagenomic sequencing to determine changes in microbiome diversity, taxonomy, and functional gene pathways. We also formed the same experiments with APOE3 mice to identify whether there are APOE-genotype dependent responses to inulin. We found that APOE4 female mice fed with inulin had restored alpha diversity, significantly reduced Escherichia coli and inflammation-associated pathway responses. However, compared with APOE4 male mice, they had less metabolic responses, including the levels of short-chain fatty acids-producing bacteria and the associated kinases, especially those related to acetate and Erysipelotrichaceae. These diet- and sex- effects were less pronounced in the APOE3 mice, indicating that different APOE variants also play a significant role. The findings provide insights into the higher susceptibility of APOE4 females to AD, potentially due to inefficient energy production, and imply the importance of considering precision nutrition for mitigating dysbiosis and AD risk in the future.}, } @article {pmid37704113, year = {2023}, author = {Gou, H and Su, H and Liu, D and Wong, CC and Shang, H and Fang, Y and Zeng, X and Chen, H and Li, Y and Huang, Z and Fan, M and Wei, C and Wang, X and Zhang, X and Li, X and Yu, J}, title = {Traditional Medicine Pien Tze Huang Suppresses Colorectal Tumorigenesis Through Restoring Gut Microbiota and Metabolites.}, journal = {Gastroenterology}, volume = {165}, number = {6}, pages = {1404-1419}, doi = {10.1053/j.gastro.2023.08.052}, pmid = {37704113}, issn = {1528-0012}, mesh = {Mice ; Animals ; Signal Transduction ; *Gastrointestinal Microbiome ; Dextran Sulfate/toxicity ; Phosphatidylinositol 3-Kinases/metabolism ; Apoptosis ; Medicine, Traditional ; *Colorectal Neoplasms/chemically induced/prevention & control/metabolism ; Carcinogenesis ; Azoxymethane/toxicity ; }, abstract = {BACKGROUND & AIMS: Pien Tze Huang (PZH) is a well-established traditional medicine with beneficial effects against inflammation and cancer. We aimed to explore the chemopreventive effect of PZH in colorectal cancer (CRC) through modulating gut microbiota.

METHODS: CRC mouse models were established by azoxymethane plus dextran sulfate sodium treatment or in Apc[min/+] mice treated with or without PZH (270 mg/kg and 540 mg/kg). Gut barrier function was determined by means of intestinal permeability assays and transmission electron microscopy. Fecal microbiota and metabolites were analyzed by means of metagenomic sequencing and liquid chromatography mass spectrometry, respectively. Germ-free mice or antibiotic-treated mice were used as models of microbiota depletion.

RESULTS: PZH inhibited colorectal tumorigenesis in azoxymethane plus dextran sulfate sodium-treated mice and in Apc[min/+] mice in a dose-dependent manner. PZH treatment altered the gut microbiota profile, with an increased abundance of probiotics Pseudobutyrivibrio xylanivorans and Eubacterium limosum, while pathogenic bacteria Aeromonas veronii, Campylobacter jejuni, Collinsella aerofaciens, and Peptoniphilus harei were depleted. In addition, PZH increased beneficial metabolites taurine and hypotaurine, bile acids, and unsaturated fatty acids, and significantly restored gut barrier function. Transcriptomic profiling revealed that PZH inhibited PI3K-Akt, interleukin-17, tumor necrosis factor, and cytokine-chemokine signaling. Notably, the chemopreventive effect of PZH involved both microbiota-dependent and -independent mechanisms. Fecal microbiota transplantation from PZH-treated mice to germ-free mice partly recapitulated the chemopreventive effects of PZH. PZH components ginsenoside-F2 and ginsenoside-Re demonstrated inhibitory effects on CRC cells and primary organoids, and PZH also inhibited tumorigenesis in azoxymethane plus dextran sulfate sodium-treated germ-free mice.

CONCLUSIONS: PZH manipulated gut microbiota and metabolites toward a more favorable profile, improved gut barrier function, and suppressed oncogenic and pro-inflammatory pathways, thereby suppressing colorectal carcinogenesis.}, } @article {pmid37703713, year = {2023}, author = {Liu, Z and Wang, Q and Ma, A and Feng, S and Chung, D and Zhao, J and Ma, Q and Liu, B}, title = {Inference of disease-associated microbial gene modules based on metagenomic and metatranscriptomic data.}, journal = {Computers in biology and medicine}, volume = {165}, number = {}, pages = {107458}, doi = {10.1016/j.compbiomed.2023.107458}, pmid = {37703713}, issn = {1879-0534}, mesh = {Humans ; Gene Regulatory Networks ; Reproducibility of Results ; *Diabetes Mellitus, Type 1/genetics ; *Inflammatory Bowel Diseases/genetics ; Genes, Microbial ; }, abstract = {The identification of microbial characteristics associated with diseases is crucial for disease diagnosis and therapy. However, the presence of heterogeneity, high dimensionality, and large amounts of microbial data presents tremendous challenges in discovering key microbial features. In this paper, we present IDAM, a novel computational method for inferring disease-associated gene modules from metagenomic and metatranscriptomic data. This method integrates gene context conservation (uber-operons) and regulatory mechanisms (gene co-expression patterns) within a mathematical graph model to explore gene modules associated with specific diseases. It alleviates reliance on prior meta-data. We applied IDAM to publicly available datasets from inflammatory bowel disease, melanoma, type 1 diabetes mellitus, and irritable bowel syndrome. The results demonstrated the superior performance of IDAM in inferring disease-associated characteristics compared to existing popular tools. Furthermore, we showcased the high reproducibility of the gene modules inferred by IDAM using independent cohorts with inflammatory bowel disease. We believe that IDAM can be a highly advantageous method for exploring disease-associated microbial characteristics. The source code of IDAM is freely available at https://github.com/OSU-BMBL/IDAM, and the web server can be accessed at https://bmblx.bmi.osumc.edu/idam/.}, } @article {pmid37702952, year = {2024}, author = {Townsend-Nicholson, A}, title = {Teaching Medical Students to Use Supercomputers: A Personal Reflection.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2716}, number = {}, pages = {413-420}, pmid = {37702952}, issn = {1940-6029}, mesh = {Humans ; *Students, Medical ; Computers ; Industry ; *Physicians ; Research Personnel ; }, abstract = {At the "Kick Off" meeting for CompBioMed (compbiomed.eu), which was first funded in October 2016, I had no idea that one single sentence ("I wish I could teach this to medical students") would lead to a dedicated program of work to engage the clinicians and biomedical researchers of the future with supercomputing. This program of work which, within the CompBiomed Centre of Excellence, we have been calling "the CompBioMed Education and Training Programme," is a holistic endeavor that has been developed by and continues to be delivered with the expertise and support from experimental researchers, computer scientists, clinicians, HPC centers, and industrial partners within or associated with CompBioMed. The original description of the initial educational approach to training has previously been published (Townsend-Nicholson Interface Focus 10:20200003, 2020). In this chapter, I describe the refinements to the program and its delivery, emphasizing the highs and lows of delivering this program over the past 6 years. I conclude with suggestions for feasible measures that I believe will help overcome the barriers and challenges we have encountered in bringing a community of users with little familiarity of computing beyond the desktop to the petascale and beyond.}, } @article {pmid37702790, year = {2023}, author = {Zou, D and Chen, J and Zhang, C and Kao, SJ and Liu, H and Li, M}, title = {Diversity and salinity adaptations of ammonia oxidizing archaea in three estuaries of China.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {22}, pages = {6897-6909}, pmid = {37702790}, issn = {1432-0614}, support = {32225003//National Natural Science Foundation of China/ ; 31970105//National Natural Science Foundation of China/ ; 2022M722175//Postdoctoral Research Foundation of China/ ; JCYJ20200109105010363//Shenzhen Science and Technology Innovation Program/ ; }, abstract = {Ammonia-oxidizing archaea (AOA) are ubiquitously found in diverse habitats and play pivotal roles in the nitrogen and carbon cycle, especially in estuarine and coastal environments. Despite the fact that the diversity and distribution of AOA are thought to be tightly linked to habitats, little is known about the relationship that underpins their genomic traits, adaptive potentials, and ecological niches. Here, we have characterized and compared the AOA community in three estuaries of China using metagenomics. AOA were the dominant ammonia oxidizers in the three estuaries. Through phylogenetic analyses, five major AOA groups were identified, including the Nitrosomarinus-like, Nitrosopumilus-like, Aestuariumsis-like, Nitrosarchaeum-like, and Nitrosopelagicus-like groups. Statistical analyses showed that the aquatic and sedimentary AOA communities were mainly influenced by spatial factors (latitude and water depth) and environmental factors (salinity, pH, and dissolved oxygen) in estuaries, respectively. Compared to AOA dwelling in terrestrial and marine habitats, estuarine AOA encoded more genes involved in glucose and amino acid metabolism, transport systems, osmotic control, and cell motility. The low proteome isoelectric points (pI), high content of acidic amino acids, and the presence of potassium ion and mechanosensitive channels suggest a "salt-in" strategy for estuarine AOA to counteract high osmolarity in their surroundings. Our findings have indicated potential adaptation strategies and highlighted their importance in the estuarine nitrogen and carbon cycles. KEY POINTS: • Spatial and environmental factors influence water and sediment AOA respectively. • Estuarine AOA share low proteome isoelectric value and high acid amino acids content. • AOA adaptation to estuaries is likely resulted from their unique genomic features.}, } @article {pmid37702690, year = {2023}, author = {Wang, D and Cheng, J and Peng, L and Li, Y}, title = {Comparison of Metagenomic Second- and Third-Generation Sequencing by Diagnostic Sensitivity and Specificity in Tuberculosis Patients.}, journal = {Clinical laboratory}, volume = {69}, number = {9}, pages = {}, doi = {10.7754/Clin.Lab.2023.230124}, pmid = {37702690}, issn = {1433-6510}, mesh = {Humans ; *Tuberculosis/diagnosis ; High-Throughput Nucleotide Sequencing ; *Tuberculosis, Pulmonary/diagnosis ; *Mycobacterium tuberculosis/genetics ; Hospitals ; }, abstract = {BACKGROUND: The third-generation sequencing (TGS) of Mycobacterium tuberculosis (MTB) is rarely reported in clinical practice. This study aims to compare the efficacy difference between next-generation sequencing (NGS) and TGS in the diagnosis of MTB and share the experience of NGS/TGS in the diagnosis of PTB.

METHODS: The past cases of suspected pulmonary tuberculosis (PTB) in our hospital were reviewed. Patients suspected of PTB who had undergone NGS/TGS detection, MTB culture, and molecular biology detection were included in the study. The clinical data of patients were reviewed, and the clinical comprehensive diagnosis of patients was used as the gold standard to analyze the efficacy of four methods for diagnosis of MTB infection, namely, metagenomic sequencing, MTB culture, molecular biology, and MTB culture + molecular biology. Then, we analyzed the results of NGS and TGS and compared the efficacy of the two metagenomic sequencing methods in the diagnosis of MTB infection.

RESULTS: Ninety patients suspected of PTB were included in the study. 37 patients (41.11%) completed NGS and 53 patients (58.89%) completed TGS. Sixty-five patients (72.11%) had MTB infection in the lung or other parts of the body, and the remaining 25 patients (27.89%) had no MTB infection. Traditional laboratory tests such as MTB culture have low sensitivity and accuracy in diagnosing MTB. The sensitivity, specificity, and detection accuracy of metagenomic sequencing are significantly higher than those of other detection methods. The diagnostic accuracy of TGS reached 88.68%, which is significantly higher than that of NGS (64.86%).

CONCLUSIONS: Compared with NGS, TGS has higher sensitivity and specificity in the diagnosis of MTB. In clinical practice, TGS is a better choice for patients who are suspected of MTB infection but cannot be diagnosed by traditional laboratory indicators.}, } @article {pmid37702502, year = {2023}, author = {Vázquez Rosas Landa, M and De Anda, V and Rohwer, RR and Angelova, A and Waldram, G and Gutierrez, T and Baker, BJ}, title = {Exploring novel alkane-degradation pathways in uncultured bacteria from the North Atlantic Ocean.}, journal = {mSystems}, volume = {8}, number = {5}, pages = {e0061923}, pmid = {37702502}, issn = {2379-5077}, support = {687165//Simons Foundation (SF)/ ; NE/S007342/1//NERC Scottish Universities Partnership for Environmental Research (SUPER)/ ; NE/S007342/1//Doctoral Training Partnership/ ; 503341//DOE-JGI/ ; //Heriot-Watt University (HWU)/ ; NEAMO//Royal Society Research Grant/ ; //Society for Applied Microbiology (SFAM)/ ; NEADMICRO//MASTS PECRE/ ; }, mesh = {Biodegradation, Environmental ; *Hydrocarbons/analysis ; *Bacteria/genetics ; Atlantic Ocean ; Alkanes/metabolism ; }, abstract = {Petroleum pollution in the ocean has increased because of rapid population growth and modernization, requiring urgent remediation. Our understanding of the metabolic response of native microbial communities to oil spills is not well understood. Here, we explored the baseline hydrocarbon-degrading communities of a subarctic Atlantic region to uncover the metabolic potential of the bacteria that inhabit the surface and subsurface water. We conducted enrichments with a [13]C-labeled hydrocarbon to capture the fraction of the community actively using the hydrocarbon. We then combined this approach with metagenomics to identify the metabolic potential of this hydrocarbon-degrading community. This revealed previously undescribed uncultured bacteria with unique metabolic mechanisms involved in aerobic hydrocarbon degradation, indicating that temperature may be pivotal in structuring hydrocarbon-degrading baseline communities. Our findings highlight gaps in our understanding of the metabolic complexity of hydrocarbon degradation by native marine microbial communities.}, } @article {pmid37702461, year = {2023}, author = {Hussan, H and Clinton, SK and Grainger, EM and Webb, M and Wang, C and Webb, A and Needleman, B and Noria, S and Zhu, J and Choueiry, F and Pietrzak, M and Bailey, MT}, title = {Distinctive patterns of sulfide- and butyrate-metabolizing bacteria after bariatric surgery: potential implications for colorectal cancer risk.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2255345}, pmid = {37702461}, issn = {1949-0984}, support = {R35 GM133510/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Female ; Middle Aged ; Aged ; Male ; Butyrates ; Cross-Sectional Studies ; Escherichia coli ; *Gastrointestinal Microbiome ; *Bariatric Surgery ; Bacteria/genetics ; *Colorectal Neoplasms/surgery ; }, abstract = {Despite improved cardiometabolic outcomes following bariatric surgery, its long-term impact on colorectal cancer (CRC) risk remains uncertain. In parallel, the influence of bariatric surgery on the host microbiome and relationships with disease outcomes is beginning to be appreciated. Therefore, we investigated the impact of Roux-en-Y gastric bypass (RYGB) and vertical sleeve gastrectomy (VSG) on the patterns of sulfide-reducing and butyrate-producing bacteria, which are hypothesized to modulate CRC risk after bariatric surgery. In this single-center, cross-sectional study, we included 15 pre-surgery subjects with severe obesity and patients who are at a median (range) of 25.6 (9.9-46.5) months after RYGB (n = 16) or VSG (n = 10). The DNA abundance of fecal bacteria and enzymes involved in butyrate and sulfide metabolism were identified using metagenomic sequencing. Differences between pre-surgery and post-RYGB or post-VSG cohorts were quantified using the linear discriminant analysis (LDA) effect size (LEfSe) method. Our sample was predominantly female (87%) with a median (range) age of 46 (23-71) years. Post-RYGB and post-VSG patients had a higher DNA abundance of fecal sulfide-reducing bacteria than pre-surgery controls (LDA = 1.3-4.4, p < .05). The most significant enrichments were for fecal E. coli, Acidaminococcus and A. finegoldii after RYGB, and for A. finegoldii, S. vestibularis, V. parvula after VSG. As for butyrate-producing bacteria, R. faecis was more abundant, whereas B. dentium and A. hardus were lower post-RYGB vs. pre-surgery. B. dentium was also lower in post-VSG vs. pre-surgery. Consistent with these findings, our analysis showed a greater enrichment of sulfide-reducing enzymes after bariatric surgery, especially RYGB, vs. pre-surgery. The DNA abundance of butyrate-producing enzymes was lower post-RYGB. In conclusion, the two most used bariatric surgeries, RYGB and VSG, are associated with microbiome patterns that are potentially implicated in CRC risk. Future studies are needed to validate and understand the impact of these microbiome changes on CRC risk after bariatric surgery.}, } @article {pmid37701837, year = {2023}, author = {Bulygin, I and Shatov, V and Rykachevskiy, A and Raiko, A and Bernstein, A and Burnaev, E and Gelfand, MS}, title = {Absence of enterotypes in the human gut microbiomes reanalyzed with non-linear dimensionality reduction methods.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15838}, pmid = {37701837}, issn = {2167-8359}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Metagenome ; Algorithms ; }, abstract = {Enterotypes of the human gut microbiome have been proposed to be a powerful prognostic tool to evaluate the correlation between lifestyle, nutrition, and disease. However, the number of enterotypes suggested in the literature ranged from two to four. The growth of available metagenome data and the use of exact, non-linear methods of data analysis challenges the very concept of clusters in the multidimensional space of bacterial microbiomes. Using several published human gut microbiome datasets of variable 16S rRNA regions, we demonstrate the presence of a lower-dimensional structure in the microbiome space, with high-dimensional data concentrated near a low-dimensional non-linear submanifold, but the absence of distinct and stable clusters that could represent enterotypes. This observation is robust with regard to diverse combinations of dimensionality reduction techniques and clustering algorithms.}, } @article {pmid37701569, year = {2023}, author = {Turchi, R and Sciarretta, F and Ceci, V and Tiberi, M and Audano, M and Pedretti, S and Panebianco, C and Nesci, V and Pazienza, V and Ferri, A and Carotti, S and Chiurchiù, V and Mitro, N and Lettieri-Barbato, D and Aquilano, K}, title = {Butyrate prevents visceral adipose tissue inflammation and metabolic alterations in a Friedreich's ataxia mouse model.}, journal = {iScience}, volume = {26}, number = {10}, pages = {107713}, pmid = {37701569}, issn = {2589-0042}, abstract = {Friedreich's ataxia (FA) is a neurodegenerative disease resulting from a mutation in the FXN gene, leading to mitochondrial frataxin deficiency. FA patients exhibit increased visceral adiposity, inflammation, and heightened diabetes risk, negatively affecting prognosis. We investigated visceral white adipose tissue (vWAT) in a murine model (KIKO) to understand its role in FA-related metabolic complications. RNA-seq analysis revealed altered expression of inflammation, angiogenesis, and fibrosis genes. Diabetes-like traits, including larger adipocytes, immune cell infiltration, and increased lactate production, were observed in vWAT. FXN downregulation in cultured adipocytes mirrored vWAT diabetes-like features, showing metabolic shifts toward glycolysis and lactate production. Metagenomic analysis indicated a reduction in fecal butyrate-producing bacteria, known to exert antidiabetic effects. A butyrate-enriched diet restrained vWAT abnormalities and mitigated diabetes features in KIKO mice. Our work emphasizes the role of vWAT in FA-related metabolic issues and suggests butyrate as a safe and promising adjunct for FA management.}, } @article {pmid37701436, year = {2023}, author = {Guan, Y and Yu, C and Fei, Y and Wang, Q and Wang, P and Zuo, W and Wu, H and Qi, X and Shi, Q}, title = {Case Report: Four cases of SARS-CoV-2-associated Guillain-Barré Syndrome with SARS-CoV-2-positive cerebrospinal fluid detected by metagenomic next-generation sequencing: a retrospective case series from China.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1258579}, pmid = {37701436}, issn = {1664-3224}, mesh = {Humans ; SARS-CoV-2 ; *Guillain-Barre Syndrome/diagnosis ; RNA, Viral/genetics ; Retrospective Studies ; *COVID-19/complications/diagnosis ; China ; High-Throughput Nucleotide Sequencing ; }, abstract = {Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is often absent or at low levels in the cerebrospinal fluid (CSF) of patients with previous SARS-CoV-2-associated Guillain-Barré syndrome (GBS). This has led to speculation that SARS-CoV-2-associated GBS is more likely mediated by post-infectious immunity or a parainfection. This understanding has influenced the development of treatment regimens for SARS-CoV-2-associated GBS. This paper reports our experience with four Chinese patients with SARS-CoV-2-associated GBS who tested positive for SARS-CoV-2 RNA in the CSF. They developed symptoms of peripheral nerve damage 4-15 days after fever and confirmed SARS-CoV-2 infection, all of whom presented with progressive weakness of both lower limbs; three with autonomic nerve function impairment such as constipation and urination disorder; and one with polycranial neuritis and Miller-Fisher syndrome. Three patients were tested for anti-ganglioside antibodies, and one tested positive for GD1a-IgG. Four patients recovered well after treatment with anti-viral drugs combined with intravenous immunoglobulin. The present results showed that SARS-CoV-2 RNA can be detected via mNGS in the CSF of some patients with SARS-CoV-2-associated GBS, suggesting that SARS-CoV-2-associated GBS may have multiple pathogeneses.}, } @article {pmid37700874, year = {2023}, author = {Wan, J and Song, J and Lv, Q and Zhang, H and Xiang, Q and Dai, H and Zheng, H and Lin, X and Zhang, W}, title = {Alterations in the Gut Microbiome of Young Children with Airway Allergic Disease Revealed by Next-Generation Sequencing.}, journal = {Journal of asthma and allergy}, volume = {16}, number = {}, pages = {961-972}, pmid = {37700874}, issn = {1178-6965}, abstract = {PURPOSE: Recent studies had shown that gut microbiota played a significant role in the development of the immune system and may affect the course of airway allergic disease. We conducted this study to determine unique gut microbial associated with allergic disease in children by shotgun gene sequencing.

METHODS: We collected fecal samples from children with allergic asthma (n = 23) and allergic rhinitis (n = 18), and healthy control (n = 19). The gut microbiota of specimens was analyzed by high-throughput metagenomic shotgun gene sequencing.

RESULTS: The intestinal microbiota of children with allergic asthma and allergic rhinitis was characterized by increased microbial richness and diversity. Simpson and Shannon were significantly elevated in children with allergic asthma. Principal coordinates analysis (PCoA) showed that the gut microbial communities cluster patterns of children with asthma or rhinitis were significantly different from those of healthy controls. However, no significant difference was found between asthma group and rhinitis group At the phylum level, higher relative abundance of Firmicutes was found in the allergic rhinitis group and allergic asthma group, while the level of Bacteroidetes was significantly lower. At the genus level, Corynebacterium, Streptococcus, Dorea, Actinomyces, Bifidobacterium, Blautia, and Rothia were significantly enriched in the allergic asthma group. Finally, a random forest classifier model selected 16 general signatures to discriminate the allergic asthma group from the healthy control group.

CONCLUSION: In conclusion, children in the allergic rhinitis group and allergic asthma group had altered gut microbiomes in comparison with the healthy control group. Compared to healthy children, the gut microbiome in children with allergic diseases has higher pro-inflammatory potential and increased production of pro-inflammatory molecules.}, } @article {pmid37700802, year = {2023}, author = {Chang, C and Wang, H and Zhang, L and Hao, J and Wang, X and Wang, Y and Qi, F and Lou, J and Zhao, J and Dong, J}, title = {Clinical Efficiency of Metagenomic Next-Generation Sequencing in Sputum for Pathogen Detection of Patients with Pneumonia According to Disease Severity and Host Immune Status.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {5869-5885}, pmid = {37700802}, issn = {1178-6973}, abstract = {PURPOSE: Severe pneumonia causes the highest mortality rate in immunocompromised patients. This study aimed to investigate the pathogen diagnostic efficacy of metagenomic next-generation sequencing (mNGS) using sputum sample in patients with pneumonia according to patients' disease severity and immune conditions.

PATIENTS AND METHODS: A total of 180 patients suffering from pneumonia were recruited, and sputum samples were collected in duplicate for pathogen detection by both conventional microbiological tests (CMT) and mNGS. Then, the performance of pathogen identification was examined between two methods, according to disease severity and patients' immune status.

RESULTS: In comparison to CMT, mNGS had higher positivity rates in all patients with pneumonia (85.0% vs 62.2%, P=9.445e-07). The most commonly detected microorganism in sputum of pneumonia patients was Acinetobacter baumannii (42/180, 23.3%) in bacterum level, Candida albicans in fungus level (44/180, 24.4%), and Human herpesvirus 1 (39/180, 27.5%) in virus level. However, for mNGS results, Candida albicans in 34.9% of positive patients, and Human herpesvirus 1 in 7.7% of positive cases were confirmed as pathogens causing pneumonia. Acinetobacter baumannii detected by mNGS in 75% of positive patients was diagnosed as pathogen of pneumonia. The microorganism profile of sputum mNGS differed according to disease severity and immune status of patients. Pneumocystis jirovecii was more likely to infect immunocompromised patients (P=0.002). Pseudomonas aeruginosa (14.8% vs 0.0%, P=0.008) and Human herpesvirus 1 (26.1% vs 5.3%, P=0.004) had higher infection rate in patients with severe pneumonia compared with non-severe cases. mNGS had overwhelming advantages over CMT in detecting a lot of microorganisms including Streptococcus pneumoniae, Enterococcus faecium, Pneumocystis jirovecii, and majority of viruses.

CONCLUSION: mNGS is a complementary tool of CMT for detecting suspected pathogens for patients with lower respiratory infections. The interpretation of opportunistic pathogens identified by mNGS is challenging, and needs comprehensive consideration of sequencing data and clinical factors.}, } @article {pmid37700798, year = {2023}, author = {Xu, X and Shan, Y and Cen, Y and Zhao, J and Yang, X and Liu, R and Tan, Q and Ma, Y and He, M and Zhang, J and Yang, F and Yu, S}, title = {Clinical Characteristics and Treatment of Listeria monocytogenes Infections in the Central Nervous System.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {5899-5909}, pmid = {37700798}, issn = {1178-6973}, abstract = {PURPOSE: Listeria monocytogenes infections are rare in the central nervous system (CNS) and frequently difficult-to-diagnose. Our goal is to assess CNS listeriosis patients' clinical characteristics, diagnosis, treatment, and prognosis.

PATIENTS AND METHODS: Patients with CNS listeriosis admitted to the Department of neurology, the first medical center of the Chinese PLA general hospital, were enrolled in this study from March 2018 to August 2022.

RESULTS: This study analyzed eight adults, including five males and three females. The average age of onset was (50.25 ± 11.52) years. The clinical manifestations included fever, headache, altered mental status, vomiting, seizures, neck rigidity, hemiplegia and cranial nerve palsies. Cerebrospinal fluid (CSF) tests revealed intracranial hypertension, elevated cell count and protein concentration, and decreased glucose levels. The positive rates of blood and CSF culture were 40% and 28.57%, respectively. All patients underwent CSF metagenomic next-generation sequencing (mNGS), with a 100% positive rate and the specific read number 12-20394. Magnetic resonance imaging (MRI) exhibited leptomeningitis, meningoencephalitis, and brain abscess, and no specific changes were discovered in two patients. All patients received antibiotic treatment, seven were cured, and one died.

CONCLUSION: Monitoring the proportion of monocytes in blood and mNGS results of CSF can play a crucial role in diagnosing pathogens. Early and sufficient application of two to three sensitive antibiotics with a BBB permeability of 20-30% for at least 2-3 months can significantly improve CNS listeriosis prognosis.}, } @article {pmid37700504, year = {2023}, author = {Bender, SF and Schulz, S and Martínez-Cuesta, R and Laughlin, RJ and Kublik, S and Pfeiffer-Zakharova, K and Vestergaard, G and Hartman, K and Parladé, E and Römbke, J and Watson, CJ and Schloter, M and van der Heijden, MGA}, title = {Simplification of soil biota communities impairs nutrient recycling and enhances above- and belowground nitrogen losses.}, journal = {The New phytologist}, volume = {240}, number = {5}, pages = {2020-2034}, doi = {10.1111/nph.19252}, pmid = {37700504}, issn = {1469-8137}, support = {31003A-166079//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, mesh = {*Soil ; *Nitrogen/analysis ; Agriculture ; Gases ; Biota ; Nutrients ; Nitrous Oxide ; Fertilizers ; }, abstract = {Agriculture is a major source of nutrient pollution, posing a threat to the earth system functioning. Factors determining the nutrient use efficiency of plant-soil systems need to be identified to develop strategies to reduce nutrient losses while ensuring crop productivity. The potential of soil biota to tighten nutrient cycles by improving plant nutrition and reducing soil nutrient losses is still poorly understood. We manipulated soil biota communities in outdoor lysimeters, planted maize, continuously collected leachates, and measured N2 O- and N2 -gas emissions after a fertilization pulse to test whether differences in soil biota communities affected nutrient recycling and N losses. Lysimeters with strongly simplified soil biota communities showed reduced crop N (-20%) and P (-58%) uptake, strongly increased N leaching losses (+65%), and gaseous emissions (+97%) of N2 O and N2 . Soil metagenomic analyses revealed differences in the abundance of genes responsible for nutrient uptake, nitrate reduction, and denitrification that helped explain the observed nutrient losses. Soil biota are major drivers of nutrient cycling and reductions in the diversity or abundance of certain groups (e.g. through land-use intensification) can disrupt nutrient cycling, reduce agricultural productivity and nutrient use efficiency, and exacerbate environmental pollution and global warming.}, } @article {pmid37700361, year = {2023}, author = {Huda, N and Ullah, S and Wahab, RA and Lani, MN and Daud, NHA and Shariff, AHM and Ismail, NI and Hamid, AAA and Mohamad, MAN and Huyop, F}, title = {The first ITS2 sequence data set of eDNA from honey of Malaysian giant honeybees (Apis dorsata) and stingless bees (Heterotrigona itama) reveals plant species diversity.}, journal = {BMC research notes}, volume = {16}, number = {1}, pages = {211}, pmid = {37700361}, issn = {1756-0500}, mesh = {Bees/genetics ; Animals ; *Honey ; Ecosystem ; *DNA, Environmental ; Pollen/genetics ; Metagenomics ; }, abstract = {OBJECTIVES: Pollen is a useful tool for identifying the provenance and complex ecosystems surrounding honey production in Malaysian forests. As native key pollinators in Malaysia, Apis dorsata and Heterotrigona itama forage on various plant/pollen species to collect honey. This study aims to generate a dataset that uncovers the presence of these plant/pollen species and their relative abundance in the honey of A. dorsata and H. itama. The information gathered from this study can be used to determine the geographical and botanical origin and authenticity of the honey produced by these two species.

RESULTS: Sequence data were obtained for both A. dorsata and H. itama. The raw sequence data for A. dorsata was 5 Mb, which was assembled into 5 contigs with a size of 6,098,728 bp, an N50 of 15,534, and a GC average of 57.42. Similarly, the raw sequence data for H. itama was 6.3 Mb, which was assembled into 11 contigs with a size of 7,642,048 bp, an N50 of 17,180, and a GC average of 55.38. In the honey sample of A. dorsata, we identified five different plant/pollen species, with only one of the five species exhibiting a relative abundance of less than 1%. For H. itama, we identified seven different plant/pollen species, with only three of the species exhibiting a relative abundance of less than 1%. All of the identified plant species were native to Peninsular Malaysia, especially the East Coast area of Terengganu.

DATA DESCRIPTION: Our data offers valuable insights into honey's geographical and botanical origin and authenticity. Metagenomic studies could help identify the plant species that honeybees forage and provide preliminary data for researchers studying the biological development of A. dorsata and H. itama. The identification of various flowers from the eDNA of honey that are known for their medicinal properties could aid in regional honey with accurate product origin labeling, which is crucial for guaranteeing product authenticity to consumers.}, } @article {pmid37700351, year = {2023}, author = {Hares, MF and Griffiths, BE and Johnson, F and Nelson, C and Haldenby, S and Stewart, CJ and Duncan, JS and Oikonomou, G and Coombes, JL}, title = {Specific pathway abundances in the neonatal calf faecal microbiome are associated with susceptibility to Cryptosporidium parvum infection: a metagenomic analysis.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {43}, pmid = {37700351}, issn = {2524-4671}, support = {/WT_/Wellcome Trust/United Kingdom ; BB/M011186/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {BACKGROUND: Cryptosporidium parvum is the main cause of calf scour worldwide. With limited therapeutic options and research compared to other Apicomplexa, it is important to understand the parasites' biology and interactions with the host and microbiome in order to develop novel strategies against this infection. The age-dependent nature of symptomatic cryptosporidiosis suggests a link to the undeveloped immune response, the immature intestinal epithelium, and its associated microbiota. This led us to hypothesise that specific features of the early life microbiome could predict calf susceptibility to C. parvum infection.

RESULTS: In this study, a single faecal swab sample was collected from each calf within the first week of life in a cohort of 346 animals. All 346 calves were subsequently monitored for clinical signs of cryptosporidiosis, and calves that developed diarrhoea were tested for Rotavirus, Coronavirus, E. coli F5 (K99) and C. parvum by lateral flow test (LFT). A retrospective case-control approach was taken whereby a subset of healthy calves (Control group; n = 33) and calves that went on to develop clinical signs of infectious diarrhoea and test positive for C. parvum infection via LFT (Cryptosporidium-positive group; n = 32) were selected from this cohort, five of which were excluded due to low DNA quality. A metagenomic analysis was conducted on the faecal microbiomes of the control group (n = 30) and the Cryptosporidium-positive group (n = 30) prior to infection, to determine features predictive of cryptosporidiosis. Taxonomic analysis showed no significant differences in alpha diversity, beta diversity, and taxa relative abundance between controls and Cryptosporidium-positive groups. Analysis of functional potential showed pathways related to isoprenoid precursor, haem and purine biosynthesis were significantly higher in abundance in calves that later tested positive for C. parvum (q ≤ 0.25). These pathways are either absent or streamlined in the C. parvum parasites. Though the de novo production of isoprenoid precursors, haem and purines are absent, C. parvum has been shown to encode enzymes that catalyse the downstream reactions of these pathway metabolites, indicating that C. parvum may scavenge those products from an external source.

CONCLUSIONS: The host has previously been put forward as the source of essential metabolites, but our study suggests that C. parvum may also be able to harness specific metabolic pathways of the microbiota in order to survive and replicate. This finding is important as components of these microbial pathways could be exploited as potential therapeutic targets for the prevention or mitigation of cryptosporidiosis in bovine neonates.}, } @article {pmid37700137, year = {2023}, author = {Rajput, V and Yadav, R and Dharne, MS}, title = {Correction to: Metagenomic exploration reveals a differential patterning of antibiotic resistance genes in urban and peri‑urban stretches of a riverine system.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {46}, pages = {103361}, doi = {10.1007/s11356-023-29845-3}, pmid = {37700137}, issn = {1614-7499}, } @article {pmid37699793, year = {2023}, author = {Chakraborty, M and Acharya, D and Dutta, TK}, title = {Diversity analysis of hilsa (Tenualosa ilisha) gut microbiota using culture-dependent and culture-independent approaches.}, journal = {Journal of applied microbiology}, volume = {134}, number = {9}, pages = {}, doi = {10.1093/jambio/lxad208}, pmid = {37699793}, issn = {1365-2672}, support = {760/CSIR-UGC NET/June 2017//University Grants Commission/ ; //Department of Science and Technology, Government of West Bengal/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Fishes ; Firmicutes/genetics ; Bacteroidetes/genetics ; Bangladesh ; Proteobacteria/genetics ; }, abstract = {AIMS: The bacterial communities associated with the gastrointestinal (GI) tract are primarily involved in digestion, physiology, and the immune response against pathogenic bacteria for the overall development and health of the host. Hilsa shad (Tenualosa ilisha), a tropical anadromous fish, found predominantly in Bangladesh and India, has so far been poorly investigated for its gut bacterial communities. In this study, both culture-based and metagenomic approaches were used to detect intestinal isolates of hilsa, captured from both freshwater and seawater to investigate the community structure of intestinal microbiota.

METHODS AND RESULTS: Culture-dependent approach allowed to isolate a total of 23 distinct bacterial species comprising 16 Gram-negative, and 7 Gram-positive isolates, where Proteobacteria and Firmicutes were identified as the two most dominant phyla. While metagenomic approach explored a wide range of important GI bacteria, primarily dominated by Proteobacteria, Firmicutes, and Bacteroidetes, with Proteobacteria and Firmicutes, being the most abundant in freshwater and seawater samples, respectively.

CONCLUSIONS: A combination of these approaches provided the differential GI-associated bacterial diversity in freshwater and seawater hilsa with the prediction of overall functional potential.

IMPACT STATEMENT: The study explored the diversity of gut microbiota in hilsa, one of the most preferred nutritious dietary fish, captured from freshwater and seawater habitats, which may encourage to comprehend the composition of the gut microbiome in relation to the migratory behavior and polyunsaturated fatty acid profile of anadromous fish in general.}, } @article {pmid37699790, year = {2023}, author = {Lee, JY and Kim, S and Kim, D and Cho, Y and Kim, KP}, title = {The influence of dietary patterns on skin bacterial diversity, composition, and co-occurrence relationships at forearm and neck sites of healthy Korean adults.}, journal = {Journal of applied microbiology}, volume = {134}, number = {9}, pages = {}, doi = {10.1093/jambio/lxad211}, pmid = {37699790}, issn = {1365-2672}, support = {//National Research Foundation/ ; 2019R1I1A1A01041799//Ministry of Education/ ; }, mesh = {Animals ; *Forearm ; *Skin ; Bacteria/genetics ; Vegetables ; Republic of Korea ; }, abstract = {AIMS: Diet and nutrition are important aspects of skin physiology and health. However, the influence of diet on the bacterial flora of different skin sites is not well understood. Therefore, we investigated the relationship between dietary patterns (DPs) and skin bacterial flora on the forearm (a dry site) and the neck (a sebaceous site) of healthy Korean adults.

METHODS AND RESULTS: In metagenomics analysis, Shannon and Simpson indices were higher on the forearm than on the neck and were negatively correlated with the two dominant species, Cutibacterium acnes and Staphylococcus epidermidis, on two skin sites. In addition, the Simpson index of the forearm was positively associated with DP1 (characterized by a high intake of vegetables, mushrooms, meat, fish and shellfish, seaweed, and fat and oil), while that on the neck was negatively associated with DP2 (characterized by a high intake of fast food). A high intake of DP1 was associated with a lower abundance of dominant species, including C. acnes, and higher degrees of the co-occurrence network, whereas a high intake of DP2 was associated with the opposite pattern.

CONCLUSIONS: Specific diets may impact both skin bacterial diversity and composition, as well as the co-occurrence of bacteria, which may vary across different skin sites.}, } @article {pmid37699502, year = {2023}, author = {Lee, C and Polo, RO and Zaheer, R and Van Domselaar, G and Zovoilis, A and McAllister, TA}, title = {Evaluation of metagenomic assembly methods for the detection and characterization of antimicrobial resistance determinants and associated mobilizable elements.}, journal = {Journal of microbiological methods}, volume = {213}, number = {}, pages = {106815}, doi = {10.1016/j.mimet.2023.106815}, pmid = {37699502}, issn = {1872-8359}, abstract = {Antimicrobial resistance genes (ARGs) can be transferred between members of a bacterial population by mobile genetic elements (MGE). Understanding the risk of these transfer events is important in monitoring and predicting antimicrobial resistance (AMR), especially in the context of a One Health Continuum. However, there is no universally accepted method for detection of ARGs and MGEs, and especially for determining their linkages. This study used publicly available shotgun metagenomic DNA short-read (Illumina, 100 bp paired-end) sequence data from samples across the One Health Continuum (including beef cattle composite feces from feedlots, catch basin water at feedlots, agricultural soil from feedlot manured surrounding fields, and urban/municipal sewage influent from two municipal wastewater treatment plants) to develop a workflow to identify and associate ARGs and MGEs. ARG- and MGE-based targeted-assemblies with available short-read data were unable to meet this analysis goal. In contrast, de novo assembly of contigs provided enough sequence context to associate ARGs and MGEs, without compromising discovery rate. However, to estimate the relative abundance of these elements, unassembled sequence data must still be used.}, } @article {pmid37698879, year = {2023}, author = {Danhof, HA and Lee, J and Thapa, A and Britton, RA and Di Rienzi, SC}, title = {Microbial stimulation of oxytocin release from the intestinal epithelium via secretin signaling.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2256043}, pmid = {37698879}, issn = {1949-0984}, support = {R01 DK056388/DK/NIDDK NIH HHS/United States ; F32 AI136404/AI/NIAID NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; Secretin ; Oxytocin ; *Gastrointestinal Microbiome ; *Gastrointestinal Hormones ; Intestinal Mucosa ; *Limosilactobacillus reuteri ; }, abstract = {Intestinal microbes impact the health of the intestine and organs distal to the gut. Limosilactobacillus reuteri is a human intestinal microbe that promotes normal gut transit, the anti-inflammatory immune system, wound healing, normal social behavior in mice, and prevents bone reabsorption. Oxytocin impacts these functions and oxytocin signaling is required for L. reuteri-mediated wound healing and social behavior; however, the events in the gut leading to oxytocin stimulation and beneficial effects are unknown. Here we report evolutionarily conserved oxytocin production in the intestinal epithelium through analysis of single-cell RNA-Seq datasets and imaging of human and mouse intestinal tissues. Moreover, human intestinal organoids produce oxytocin, demonstrating that the intestinal epithelium is sufficient to produce oxytocin. We find that L. reuteri facilitates oxytocin secretion from human intestinal tissue and human intestinal organoids. Finally, we demonstrate that stimulation of oxytocin secretion by L. reuteri is dependent on the gut hormone secretin, which is produced in enteroendocrine cells, while oxytocin itself is produced in enterocytes. Altogether, this work demonstrates that oxytocin is produced and secreted from enterocytes in the intestinal epithelium in response to secretin stimulated by L. reuteri. This work thereby identifies oxytocin as an intestinal hormone and provides mechanistic insight into avenues by which gut microbes promote host health.}, } @article {pmid37698609, year = {2023}, author = {Zhang, A and Cao, Z and Zhao, L and Zhang, Q and Fu, L and Li, J and Liu, T}, title = {Characterization of bifunctional alginate lyase Aly644 and antimicrobial activity of enzymatic hydrolysates.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {22}, pages = {6845-6857}, pmid = {37698609}, issn = {1432-0614}, support = {IRFSOCC2023-2025//Impact and Response of Antarctic Seas to Climate Change/ ; }, abstract = {An alginate lyase gene aly644 encoding a member of polysaccharide lyase family 6 was obtained from a metagenome of Antarctic macroalgae-associated microbes. The gene was expressed heterologously in Escherichia coli, and the recombinant protein was purified using a Ni-NTA His Tag Kit. With sodium alginate as the substrate, recombinant Aly644 exhibited an optimum reaction temperature of 50°C and an optimum reaction pH of 7.0. The Vmax and Km values of Aly644 toward sodium alginate were 112.36 mg/mL·min and 16.75 mg/mL, respectively. Substrate specificity analysis showed that Aly644 was a bifunctional alginate lyase that hydrolyzed both polyguluronic acid and polymannuronic acid. The hydrolysis products of Aly644 with sodium alginate as the substrate were detected by thin-layer chromatography, and were mainly di- and trisaccharides. The oligosaccharides produced by degradation of sodium alginate by Aly644 inhibited the mycelial growth of the plant pathogens Phytophthora capsici and Fulvia fulva; the 50% maximal effective concentration (EC50) values were 297.45 and 452.89 mg/L, and the 90% maximal effective concentration (EC90) values were 1341.45 and 2693.83 mg/L, respectively. This highlights that Aly644 is a potential candidate enzyme for the industrial production of alginate oligosaccharides with low degree of polymerization. Enzyme-hydrolyzed alginate oligosaccharides could support the development of green agriculture as natural antimicrobial agents. KEY POINTS: • An alginate lyase was obtained from a metagenome of Antarctic macroalgae-associated microbes. • Aly644 is a bifunctional alginate lyase with excellent thermostability and pH stability. • The enzymatic hydrolysates of Aly644 directly inhibited Phytophthora capsici and Fulvia fulva.}, } @article {pmid37698429, year = {2023}, author = {Wang, Z and Guo, M and Li, J and Jiang, C and Yang, S and Zheng, S and Li, M and Ai, X and Xu, X and Zhang, W and He, X and Wang, Y and Chen, Y}, title = {Composition and functional profiles of gut microbiota reflect the treatment stage, severity, and etiology of acute pancreatitis.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0082923}, pmid = {37698429}, issn = {2165-0497}, abstract = {Acute pancreatitis (AP) is a type of digestive system disease with high mortality. Previous studies have shown that gut microbiota can participate in developing and treating acute pancreatitis by affecting the host's metabolism. In this study, we followed 20 AP patients to generate longitudinal gut microbiota profiles and activity during disease (before treatment, on the third day of treatment, and 1 month after discharge). We analyzed species composition and metabolic pathways' changes across the treatment phase, severity, and etiology. The diversity of the gut microbiome of patients with AP did not show much variation with treatment. In contrast, the metabolic functions of the gut microbiota, such as the essential chemical reactions that produce energy and maintain life, were partially reinstated after treatment. The severe AP (SAP) patients contained less beneficial bacteria (i.e., Bacteroides xylanisolvens, Clostridium lavalense, and Roseburia inulinivorans) and weaker sugar degradation function than mild AP patients before treatment. Moreover, etiology was one of the drivers of gut microbiome composition and explained the 3.54% variation in species' relative abundance. The relative abundance of pathways related to lipid synthesis was higher in the gut of hyperlipidemia AP patients than in biliary AP patients. The composition and functional profiles of the gut microbiota reflect the severity and etiology of AP. Otherwise, we also identified bacterial species associated with SAP, i.e., Oscillibacter sp. 57_20, Parabacteroides johnsonii, Bacteroides stercoris, Methanobrevibacter smithii, Ruminococcus lactaris, Coprococcus comes, and Dorea formicigenerans, which have the potential to identify the SAP at an early stage. IMPORTANCE Acute pancreatitis (AP) is a type of digestive system disease with high mortality. Previous studies have shown that gut microbiota can participate in the development and treatment of acute pancreatitis by affecting the host's metabolism. However, fewer studies acquired metagenomic sequencing data to associate species to functions intuitively and performed longitudinal analysis to explore how gut microbiota influences the development of AP. We followed 20 AP patients to generate longitudinal gut microbiota profiles and activity during disease and studied the differences in intestinal flora under different severities and etiologies. We have two findings. First, the gut microbiota profile has the potential to identify the severity and etiology of AP at an early stage. Second, gut microbiota likely acts synergistically in the development of AP. This study provides a reference for characterizing the driver flora of severe AP to identify the severity of acute pancreatitis at an early stage.}, } @article {pmid37697496, year = {2023}, author = {Zhang, P and Fang, Z and Zhao, M and Yi, B and Huang, Y and Yang, H and Guo, N and Zhao, C}, title = {Ethanol extract of Pueraria lobata improve acute myocardial infarction in rats via regulating gut microbiota and bile acid metabolism.}, journal = {Phytotherapy research : PTR}, volume = {37}, number = {12}, pages = {5932-5946}, doi = {10.1002/ptr.8005}, pmid = {37697496}, issn = {1099-1573}, support = {2017YFC1702901//the National Key Research and Development Program of China/ ; 2019YFC1708900//the National Key Research and Development Program of China/ ; CI2021A05031//CACMS Innovation Fund/ ; CI2021B017//Scientific and Technological Innovation Project of China Academy of Chinese Medical Sciences/ ; 2019-0894//Shandong Province Traditional Chinese Medicine Science and Technology Development Plan Project/ ; JBGS2021002//the Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; 81370095//Innovative Research Group Project of the National Natural Science Foundation of China/ ; }, mesh = {Rats ; Animals ; Ethanol ; *Gastrointestinal Microbiome ; *Pueraria ; Chromatography, Liquid ; Tandem Mass Spectrometry ; *Myocardial Infarction/drug therapy ; Plant Extracts/pharmacology ; Bile Acids and Salts ; }, abstract = {BACKGROUND AND AIM: Acute myocardial infarction (AMI) is a multifactorial disease with high mortality rate worldwide. Ethanol extract of Pueraria lobata (EEPL) has been widely used in treating cardiovascular diseases in China. This study aimed to explore the underlying therapeutic mechanism of EEPL in AMI rats.

EXPERIMENTAL PROCEDURE: We first evaluated the anti-AMI efficacy of EEPL through immunohistochemistry staining and biochemical indexes. Then, UPLC-MS/MS, 16S rDNA, and shotgun metagenomic sequencing were used to analyze the alterations in bile acid metabolism and intestinal flora. Finally, the influence of EEPL on ilem bile acid metabolism, related enzymes expression, and transporter proteins expression in rats were verified by mass spectrometry image and ELISA.

KEY RESULTS: The results showed that EEPL can reduce cardiac impairment in AMI rats. Besides, EEPL effectively increased bile acid levels and regulated gut microbiota disturbance in AMI rats via increasing CYP7A1 expression and restoring intestinal microbiota diversity, separately. Moreover, it can increase bile acids reabsorption and fecal excretion through inhibiting FXR-FGF15 signaling pathway and increasing OST-α expression, which associated with Lachnoclostridium.

CONCLUSIONS AND IMPLICATIONS: Our findings demonstrated that EEPL alleviated AMI partially by remediating intestinal dysbiosis and promoting bile acid biosynthesis, which provided new targets for AMI treatment.}, } @article {pmid37697305, year = {2023}, author = {Magnuson, E and Altshuler, I and Freyria, NJ and Leveille, RJ and Whyte, LG}, title = {Sulfur-cycling chemolithoautotrophic microbial community dominates a cold, anoxic, hypersaline Arctic spring.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {203}, pmid = {37697305}, issn = {2049-2618}, mesh = {Calcium Sulfate ; Canada ; *Microbiota/genetics ; Oxygen ; Sulfates ; *Gammaproteobacteria ; }, abstract = {BACKGROUND: Gypsum Hill Spring, located in Nunavut in the Canadian High Arctic, is a rare example of a cold saline spring arising through thick permafrost. It perennially discharges cold (~ 7 °C), hypersaline (7-8% salinity), anoxic (~ 0.04 ppm O2), and highly reducing (~ - 430 mV) brines rich in sulfate (2.2 g.L[-1]) and sulfide (9.5 ppm), making Gypsum Hill an analog to putative sulfate-rich briny habitats on extraterrestrial bodies such as Mars.

RESULTS: Genome-resolved metagenomics and metatranscriptomics were utilized to describe an active microbial community containing novel metagenome-assembled genomes and dominated by sulfur-cycling Desulfobacterota and Gammaproteobacteria. Sulfate reduction was dominated by hydrogen-oxidizing chemolithoautotrophic Desulfovibrionaceae sp. and was identified in phyla not typically associated with sulfate reduction in novel lineages of Spirochaetota and Bacteroidota. Highly abundant and active sulfur-reducing Desulfuromusa sp. highly transcribed non-coding RNAs associated with transcriptional regulation, showing potential evidence of putative metabolic flexibility in response to substrate availability. Despite low oxygen availability, sulfide oxidation was primarily attributed to aerobic chemolithoautotrophic Halothiobacillaceae. Low abundance and transcription of photoautotrophs indicated sulfur-based chemolithoautotrophy drives primary productivity even during periods of constant illumination.

CONCLUSIONS: We identified a rare surficial chemolithoautotrophic, sulfur-cycling microbial community active in a unique anoxic, cold, hypersaline Arctic spring. We detected Mars-relevant metabolisms including hydrogenotrophic sulfate reduction, sulfur reduction, and sulfide oxidation, which indicate the potential for microbial life in analogous S-rich brines on past and present Mars. Video Abstract.}, } @article {pmid37697264, year = {2023}, author = {Wang, Y and Fang, Y and Yan, Z and Xia, R and Zeng, W and Deng, W and Xu, J and Feng, X and Peng, J and Miao, Y}, title = {Fatal BK polyomavirus-associated pneumonia: report of two cases with literature review.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {592}, pmid = {37697264}, issn = {1471-2334}, support = {82270784//National Natural Science Foundation of China/ ; 82070770//National Natural Science Foundation of China/ ; 2023A1515012276//Natural Science Foundation of Guangdong Province/ ; }, mesh = {Humans ; *BK Virus/genetics ; *Pneumonia ; Antiviral Agents ; *Cystitis ; Heart Rate ; }, abstract = {BACKGROUND: In immunocompromised populations, such as patients with AIDS and recipients of solid organ and hematopoietic stem cell transplants, BK polyomavirus (BKPyV) can reactivate and cause several diseases, which can lead to death in their severe forms. Unlike hemorrhagic cystitis and BKPyV-associated nephropathy, BKPyV-associated pneumonia is rare, with only seven known cases worldwide. However, the disease can rapidly progress with extremely high mortality.

CASE PRESENTATION: Herein, we report two cases of BKPyV-associated pneumonia following hematopoietic stem cell transplantation. Both patients had consistent infectious pneumonia and graft-versus-host disease after stem cell transplantation. The diagnosis of BKPyV-associated pneumonia was confirmed by metagenomic next-generation sequencing and polymerase chain reaction after the sudden worsening of the pulmonary infection signs and symptoms concomitant with renal dysfunction and systemic immune weakening. Both patients eventually died of systemic multi-organ failure caused by severe pneumonia.

CONCLUSIONS: Currently, BKPyV reactivation cannot be effectively prevented. Immunocompromised patients must actively manage their primary lung infections, pay close attention to pulmonary signs and imaging changes. Especially during and after steroid pulse therapy or immunosuppressive therapy for graft versus host diseases, BKPyV load in blood/urine needs to be regularly measured, and the immunosuppressive intensity should be adjusted properly after the BKPyV reactivation diagnosis. Clinical trials of new antiviral drugs and therapies for BKPyV are urgently needed.}, } @article {pmid37697032, year = {2023}, author = {Perez-Garcia, P and Chow, J and Costanzi, E and Gurschke, M and Dittrich, J and Dierkes, RF and Molitor, R and Applegate, V and Feuerriegel, G and Tete, P and Danso, D and Thies, S and Schumacher, J and Pfleger, C and Jaeger, KE and Gohlke, H and Smits, SHJ and Schmitz, RA and Streit, WR}, title = {An archaeal lid-containing feruloyl esterase degrades polyethylene terephthalate.}, journal = {Communications chemistry}, volume = {6}, number = {1}, pages = {193}, pmid = {37697032}, issn = {2399-3669}, support = {101000327//European Commission (EC)/ ; 031B867B//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B867F//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0837B//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 031B0837A//Bundesministerium für Bildung und Forschung (Federal Ministry of Education and Research)/ ; 417919780//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; INST 208/740-1 FUGG//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Polyethylene terephthalate (PET) is a commodity polymer known to globally contaminate marine and terrestrial environments. Today, around 80 bacterial and fungal PET-active enzymes (PETases) are known, originating from four bacterial and two fungal phyla. In contrast, no archaeal enzyme had been identified to degrade PET. Here we report on the structural and biochemical characterization of PET46 (RLI42440.1), an archaeal promiscuous feruloyl esterase exhibiting degradation activity on semi-crystalline PET powder comparable to IsPETase and LCC (wildtypes), and higher activity on bis-, and mono-(2-hydroxyethyl) terephthalate (BHET and MHET). The enzyme, found by a sequence-based metagenome search, is derived from a non-cultivated, deep-sea Candidatus Bathyarchaeota archaeon. Biochemical characterization demonstrated that PET46 is a promiscuous, heat-adapted hydrolase. Its crystal structure was solved at a resolution of 1.71 Å. It shares the core alpha/beta-hydrolase fold with bacterial PETases, but contains a unique lid common in feruloyl esterases, which is involved in substrate binding. Thus, our study widens the currently known diversity of PET-hydrolyzing enzymes, by demonstrating PET depolymerization by a plant cell wall-degrading esterase.}, } @article {pmid37696680, year = {2023}, author = {Del Chierico, F and Cardile, S and Baldelli, V and Alterio, T and Reddel, S and Bramuzzo, M and Knafelz, D and Lega, S and Bracci, F and Torre, G and Maggiore, G and Putignani, L}, title = {Characterization of the Gut Microbiota and Mycobiota in Italian Pediatric Patients With Primary Sclerosing Cholangitis and Ulcerative Colitis.}, journal = {Inflammatory bowel diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/ibd/izad203}, pmid = {37696680}, issn = {1536-4844}, support = {//Italian Ministry of Health/ ; }, abstract = {BACKGROUND: Primary sclerosing cholangitis (PSC) is a chronic, fibroinflammatory, cholestatic liver disease of unknown etiopathogenesis, often associated with inflammatory bowel diseases. Recent evidence ascribes, together with immunologic and environmental components, a significant role to the intestinal microbiota or its molecules in the PSC pathogenesis.

METHODS: By metagenomic sequencing of 16S rRNA and ITS2 loci, we describe the fecal microbiota and mycobiota of 26 pediatric patients affected by PSC and concomitant ulcerative colitis (PSC-UC), 27 patients without PSC but with UC (UC), and 26 healthy subjects (CTRLs).

RESULTS: Compared with CTRL, the bacterial and fungal gut dysbiosis was evident for both PSC-UC and UC groups; in particular, Streptococcus, Saccharomyces, Sporobolomyces, Tilletiopsis, and Debaryomyces appeared increased in PSC-UC, whereas Klebsiella, Haemophilus, Enterococcus Collinsella, Piptoporus, Candida, and Hyphodontia in UC. In both patient groups, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma and Malassezia were decreased. Co-occurrence analysis evidenced the lowest number of nodes and edges for fungi networks compared with bacteria. Finally, we identified a specific patient profile, based on liver function tests, bacterial and fungal signatures, that is able to distinguish PSC-UC from UC patients.

CONCLUSIONS: We describe the gut microbiota and mycobiota dysbiosis associated to PSC-UC disease. Our results evidenced a gut imbalance, with the reduction of gut commensal microorganisms with stated anti-inflammatory properties (ie, Akkermansia, Bacteroides, Parabacteroides, Oscillospira, Meyerozyma, and Malassezia) and the increase of pathobionts (ie, Streptococcus, Saccharomyces, and Debaryomyces) that could be involved in PSC progression. Altogether, these events may concur in the pathophysiology of PSC in the framework of UC.}, } @article {pmid37696473, year = {2023}, author = {Kelly, SA and O'Connell, NH and Thompson, TP and Dillon, L and Wu, J and Creevey, C and Kiely, P and Slevin, B and Powell, J and Gilmore, BF and Dunne, CP}, title = {Large-scale characterization of hospital wastewater system microbiomes and clinical isolates from infected patients: profiling of multi-drug-resistant microbial species.}, journal = {The Journal of hospital infection}, volume = {141}, number = {}, pages = {152-166}, doi = {10.1016/j.jhin.2023.09.001}, pmid = {37696473}, issn = {1532-2939}, mesh = {Humans ; Wastewater ; *Microbiota/genetics ; Hospitals, Teaching ; Anti-Bacterial Agents ; *Biological Products ; *Cross Infection/epidemiology ; Genes, Bacterial ; }, abstract = {BACKGROUND: Hospital-acquired infections (HAIs) and infectious agents exhibiting antimicrobial resistance (AMR) are challenges globally. Environmental patient-facing wastewater apparatus including handwashing sinks, showers and toilets are increasingly identified as sources of infectious agents and AMR genes.

AIM: To provide large-scale metagenomics analysis of wastewater systems in a large teaching hospital in the Republic of Ireland experiencing multi-drug-resistant HAI outbreaks.

METHODS: Wastewater pipe sections (N=20) were removed immediately prior to refurbishment of a medical ward where HAIs had been endemic. These comprised toilet U-bends, and sink and shower drains. Following DNA extraction, each pipe section underwent metagenomic analysis.

FINDINGS: Diverse taxonomic and resistome profiles were observed, with members of phyla Proteobacteria and Actinobacteria dominating (38.23 ± 5.68% and 15.78 ± 3.53%, respectively). Genomes of five clinical isolates were analysed. These AMR bacterial isolates were from patients >48 h post-admission to the ward. Genomic analysis determined that the isolates bore a high number of antimicrobial resistance genes (ARGs).

CONCLUSION: Comparison of resistome profiles of isolates and wastewater metagenomes revealed high degrees of similarity, with many identical ARGs shared, suggesting probable acquisition post-admission. The highest numbers of ARGs observed were those encoding resistance to clinically significant and commonly used antibiotic classes. Average nucleotide identity analysis confirmed the presence of highly similar or identical genomes in clinical isolates and wastewater pipes. These unique large-scale analyses reinforce the need for regular cleaning and decontamination of patient-facing hospital wastewater pipes and effective infection control policies to prevent transmission of nosocomial infection and emergence of AMR within potential wastewater reservoirs.}, } @article {pmid37695138, year = {2023}, author = {Borton, MA and Shaffer, M and Hoyt, DW and Jiang, R and Ellenbogen, JB and Purvine, S and Nicora, CD and Eder, EK and Wong, AR and Smulian, AG and Lipton, MS and Krzycki, JA and Wrighton, KC}, title = {Targeted curation of the gut microbial gene content modulating human cardiovascular disease.}, journal = {mBio}, volume = {14}, number = {5}, pages = {e0151123}, pmid = {37695138}, issn = {2150-7511}, support = {P30 CA016058/CA/NCI NIH HHS/United States ; P30 CA046934/CA/NCI NIH HHS/United States ; R01 DK109345/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Cardiovascular Diseases/genetics ; *Microbiota ; *Gastrointestinal Microbiome ; Amines ; Genes, Microbial ; Methylamines/metabolism ; }, abstract = {One of the most-cited examples of the gut microbiome modulating human disease is the microbial metabolism of quaternary amines from protein-rich foods. By-products of this microbial processing promote atherosclerotic heart disease, a leading cause of human mortality globally. Our research addresses current knowledge gaps in our understanding of this microbial metabolism by holistically inventorying the microorganisms and expressed genes catalyzing critical atherosclerosis-promoting and -ameliorating reactions in the human gut. This led to the creation of an open-access resource, the Methylated Amine Gene Inventory of Catabolism database, the first systematic inventory of gut methylated amine metabolism. More importantly, using this resource we deliver here, we show for the first time that these gut microbial genes can predict human disease, paving the way for microbiota-inspired diagnostics and interventions.}, } @article {pmid37695121, year = {2023}, author = {Rojas, CA and Gardy, J and Eisen, JA and Ganz, HH}, title = {Recovery of 52 bacterial genomes from the fecal microbiome of the domestic cat (Felis catus) using Hi-C proximity ligation and shotgun metagenomics.}, journal = {Microbiology resource announcements}, volume = {12}, number = {10}, pages = {e0060123}, pmid = {37695121}, issn = {2576-098X}, support = {//AnimalBiome/ ; //Phase Genomics/ ; }, abstract = {We used Hi-C proximity ligation with shotgun sequencing to retrieve metagenome-assembled genomes (MAGs) from the fecal microbiomes of two domestic cats (Felis catus). The genomes were assessed for completeness and contamination, classified taxonomically, and annotated for putative antimicrobial resistance (AMR) genes.}, } @article {pmid37695076, year = {2023}, author = {Sarode, GV and Mazi, TA and Neier, K and Shibata, NM and Jospin, G and Harder, NHO and Caceres, A and Heffern, MC and Sharma, AK and More, SK and Dave, M and Schroeder, SM and Wang, L and LaSalle, JM and Lutsenko, S and Medici, V}, title = {The role of intestine in metabolic dysregulation in murine Wilson disease.}, journal = {Hepatology communications}, volume = {7}, number = {10}, pages = {}, pmid = {37695076}, issn = {2471-254X}, support = {R01 AA027075/AA/NIAAA NIH HHS/United States ; R01 DK104770/DK/NIDDK NIH HHS/United States ; P30 ES023513/ES/NIEHS NIH HHS/United States ; R01 DK071865/DK/NIDDK NIH HHS/United States ; UL1 TR001860/TR/NCATS NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Hepatolenticular Degeneration/genetics ; Lipid Metabolism/genetics ; Disease Models, Animal ; Sphingolipids ; Intestines ; }, abstract = {BACKGROUND: The clinical manifestations of Wilson disease (WD) are related to copper accumulation in the liver and the brain, but little is known about other tissue involvement regarding metabolic changes in WD. In vitro studies suggested that the loss of intestinal ATP7B affects metabolic dysregulation in WD. We tested this hypothesis by evaluating the gut microbiota and lipidome in 2 mouse models of WD and by characterizing a new mouse model with a targeted deletion of Atp7b in the intestine.

METHODS: Cecal content 16S sequencing and untargeted hepatic and plasma lipidome analyses in the Jackson Laboratory toxic-milk and the Atp7b null global knockout mouse models of WD were profiled and integrated. Intestine-specific Atp7b knockout mice (Atp7bΔIEC) were generated and characterized using targeted lipidome analysis following a high-fat diet challenge.

RESULTS: Gut microbiota diversity was reduced in animal models of WD. Comparative prediction analysis revealed amino acid, carbohydrate, and lipid metabolism functions to be dysregulated in the WD gut microbial metagenome. Liver and plasma lipidomic profiles showed dysregulated triglyceride and diglyceride, phospholipid, and sphingolipid metabolism in WD models. However, Atp7bΔIEC mice did not show gut microbiome differences compared to wild type. When challenged with a high-fat diet, Atp7bΔIEC mice exhibited profound alterations to fatty acid desaturation and sphingolipid metabolism pathways as well as altered APOB48 distribution in intestinal epithelial cells.

CONCLUSIONS: Gut microbiome and lipidome underlie systemic metabolic manifestations in murine WD. Intestine-specific ATP7B deficiency affected both intestinal and systemic response to a high-fat challenge but not the microbiome profile, at least at early stages. WD is a systemic disease in which intestinal-specific ATP7B loss and diet influence the phenotype and the lipidome profile.}, } @article {pmid37695074, year = {2023}, author = {Park, H and Lim, SJ and Cosme, J and O'Connell, K and Sandeep, J and Gayanilo, F and Cutter, GR and Montes, E and Nitikitpaiboon, C and Fisher, S and Moustahfid, H and Thompson, LR}, title = {Investigation of machine learning algorithms for taxonomic classification of marine metagenomes.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0523722}, pmid = {37695074}, issn = {2165-0497}, abstract = {Microbial communities play key roles in ocean ecosystems through regulation of biogeochemical processes such as carbon and nutrient cycling, food web dynamics, and gut microbiomes of invertebrates, fish, reptiles, and mammals. Assessments of marine microbial diversity are therefore critical to understanding spatiotemporal variations in microbial community structure and function in ocean ecosystems. With recent advances in DNA shotgun sequencing for metagenome samples and computational analysis, it is now possible to access the taxonomic and genomic content of ocean microbial communities to study their structural patterns, diversity, and functional potential. However, existing taxonomic classification tools depend upon manually curated phylogenetic trees, which can create inaccuracies in metagenomes from less well-characterized communities, such as from ocean water. Herein, we explore the utility of deep learning tools-DeepMicrobes and a novel Residual Network architecture-that leverage natural language processing and convolutional neural network architectures to map input sequence data (k-mers) to output labels (taxonomic groups) without reliance on a curated taxonomic tree. We trained both models using metagenomic reads simulated from marine microbial genomes in the MarRef database. The performance of both models (accuracy, precision, and percent microbe predicted) was compared with the standard taxonomic classification tool Kraken2 using 10 complex metagenomic data sets simulated from MarRef. Our results demonstrate that time, compute power, and microbial genomic diversity still pose challenges for machine learning (ML). Moreover, our results suggest that high genome coverage and rectification of class imbalance are prerequisites for a well-trained model, and therefore should be a major consideration in future ML work. IMPORTANCE Taxonomic profiling of microbial communities is essential to model microbial interactions and inform habitat conservation. This work develops approaches in constructing training/testing data sets from publicly available marine metagenomes and evaluates the performance of machine learning (ML) approaches in read-based taxonomic classification of marine metagenomes. Predictions from two models are used to test accuracy in metagenomic classification and to guide improvements in ML approaches. Our study provides insights on the methods, results, and challenges of deep learning on marine microbial metagenomic data sets. Future machine learning approaches can be improved by rectifying genome coverage and class imbalance in the training data sets, developing alternative models, and increasing the accessibility of computational resources for model training and refinement.}, } @article {pmid37695063, year = {2023}, author = {Cerri, A and Bolatti, EM and Zorec, TM and Montani, ME and Rimondi, A and Hosnjak, L and Casal, PE and Di Domenica, V and Barquez, RM and Poljak, M and Giri, AA}, title = {Identification and characterization of novel alphacoronaviruses in Tadarida brasiliensis (Chiroptera, Molossidae) from Argentina: insights into recombination as a mechanism favoring bat coronavirus cross-species transmission.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0204723}, pmid = {37695063}, issn = {2165-0497}, abstract = {Bats are reservoirs of various coronaviruses that can jump between bat species or other mammalian hosts, including humans. This article explores coronavirus infection in three bat species (Tadarida brasiliensis, Eumops bonariensis, and Molossus molossus) of the family Molossidae from Argentina using whole viral metagenome analysis. Fecal samples of 47 bats from three semiurban or highly urbanized areas of the province of Santa Fe were investigated. After viral particle enrichment, total RNA was sequenced using the Illumina NextSeq 550 instrument; the reads were assembled into contigs and taxonomically and phylogenetically analyzed. Three novel complete Alphacoronavirus (AlphaCoV) genomes (Tb1-3) and two partial sequences were identified in T. brasiliensis (Tb4-5), and an additional four partial sequences were identified in M. molossus (Mm1-4). Phylogenomic analysis showed that the novel AlphaCoV clustered in two different lineages distinct from the 15 officially recognized AlphaCoV subgenera. Tb2 and Tb3 isolates appeared to be variants of the same virus, probably involved in a persistent infectious cycle within the T. brasiliensis colony. Using recombination analysis, we detected a statistically significant event in Spike gene, which was reinforced by phylogenetic tree incongruence analysis, involving novel Tb1 and AlphaCoVs identified in Eptesicus fuscus (family Vespertilionidae) from the U.S. The putative recombinant region is in the S1 subdomain of the Spike gene, encompassing the potential receptor-binding domain of AlphaCoVs. This study reports the first AlphaCoV genomes in molossids from the Americas and provides new insights into recombination as an important mode of evolution of coronaviruses involved in cross-species transmission. IMPORTANCE This study generated three novel complete AlphaCoV genomes (Tb1, Tb2, and Tb3 isolates) identified in individuals of Tadarida brasiliensis from Argentina, which showed two different evolutionary patterns and are the first to be reported in the family Molossidae in the Americas. The novel Tb1 isolate was found to be involved in a putative recombination event with alphacoronaviruses identified in bats of the genus Eptesicus from the U.S., whereas isolates Tb2 and Tb3 were found in different collection seasons and might be involved in persistent viral infections in the bat colony. These findings contribute to our knowledge of the global diversity of bat coronaviruses in poorly studied species and highlight the different evolutionary aspects of AlphaCoVs circulating in bat populations in Argentina.}, } @article {pmid37694653, year = {2023}, author = {Yao, ZX and Wang, LP and Li, D and Li, YP and He, SL and Zhao, YQ}, title = {[Remediation of Petroleum-contaminated Soil by Highly Efficient Oil-degrading Bacteria and Analysis of Its Enhancement Mechanism].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {44}, number = {8}, pages = {4599-4610}, doi = {10.13227/j.hjkx.202210004}, pmid = {37694653}, issn = {0250-3301}, mesh = {Bacteria/genetics ; Proteobacteria ; *Actinobacteria ; Agriculture ; *Petroleum ; }, abstract = {A 120-day in situ remediation of oil-contaminated soil was carried out by using highly efficient oil-degrading bacteria. The effects of bio-enhanced remediation and changes in soil physicochemical properties and enzyme activities were investigated. Combined with metagenomic sequencing and bioinformatics analysis, the strengthening mechanism was revealed. The results showed that compared with the blank control group (Ctrl), the degradation rate of total petroleum hydrocarbons in the bioremediation group (Exp-BT) was significantly increased, reaching 81.23%. During enhanced bioremediation by highly efficient oil-degrading bacteria, the pH of the soil was stable, the oxidation capacity of the system was improved, and the electrical conductivity was in the range suitable for agricultural activities. Lipase and dehydrogenase maintained high activity during repair. In addition, the analysis of the initial contaminated soil (B0), the highly efficient oil-degrading bacteria obtained from domestication (GZ), and the soil samples after bioremediation (BT) in the obtained samples showed that, at the phylum level, the total proportion of Proteobacteria and Actinobacteria increased by 17.1%. At the genus level, the abundance of Nocardioides, Achromobacter, Gordonia, and Rhodococcus increased significantly. The species and function contribution analysis of COG and KEGG proved that the above bacterial genera had important contributions to the degradation of petroleum hydrocarbons. A high abundance of petroleum hydrocarbon-related metabolic enzymes and five petroleum hydrocarbon-related degradation genes was found in the soil after remediation:alkM, tamA, rubB, ladA, and alkB. The analysis showed that the introduction of the exogenous petroleum hydrocarbon-degrading bacteria group enhanced the metabolic activity of microorganism-related enzymes and the expression of corresponding functional genes.}, } @article {pmid37693522, year = {2023}, author = {Santos-Júnior, CD and Der Torossian Torres, M and Duan, Y and Del Río, ÁR and Schmidt, TSB and Chong, H and Fullam, A and Kuhn, M and Zhu, C and Houseman, A and Somborski, J and Vines, A and Zhao, XM and Bork, P and Huerta-Cepas, J and de la Fuente-Nunez, C and Coelho, LP}, title = {Computational exploration of the global microbiome for antibiotic discovery.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37693522}, abstract = {Novel antibiotics are urgently needed to combat the antibiotic-resistance crisis. We present a machine learning-based approach to predict prokaryotic antimicrobial peptides (AMPs) by leveraging a vast dataset of 63,410 metagenomes and 87,920 microbial genomes. This led to the creation of AMPSphere, a comprehensive catalog comprising 863,498 non-redundant peptides, the majority of which were previously unknown. We observed that AMP production varies by habitat, with animal-associated samples displaying the highest proportion of AMPs compared to other habitats. Furthermore, within different human-associated microbiota, strain-level differences were evident. To validate our predictions, we synthesized and experimentally tested 50 AMPs, demonstrating their efficacy against clinically relevant drug-resistant pathogens both in vitro and in vivo. These AMPs exhibited antibacterial activity by targeting the bacterial membrane. Additionally, AMPSphere provides valuable insights into the evolutionary origins of peptides. In conclusion, our approach identified AMP sequences within prokaryotic microbiomes, opening up new avenues for the discovery of antibiotics.}, } @article {pmid37693489, year = {2023}, author = {Rice, MC and Elde, NC and Gagnon, JA and Balla, KM}, title = {Microbe transmission from pet shop to lab-reared zebrafish reveals a pathogenic birnavirus.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37693489}, support = {R35 GM134936/GM/NIGMS NIH HHS/United States ; R35 GM142950/GM/NIGMS NIH HHS/United States ; T32 AI055434/AI/NIAID NIH HHS/United States ; }, abstract = {Zebrafish are popular research organisms selected for laboratory use due in part to widespread availability from the pet trade. Many contemporary colonies of laboratory zebrafish are maintained in aquaculture facilities that monitor and aim to curb infections that can negatively affect colony health and confound experiments. The impact of laboratory control on the microbial constituents associated with zebrafish in research environments compared to the pet trade are unclear. Diseases of unknown causes are common in both environments. We conducted a metagenomic survey to broadly compare the zebrafish-associated microbes in pet trade and laboratory environments. We detected many microbes in animals from the pet trade that were not found in laboratory animals. Co-housing experiments revealed several transmissible microbes including a newly described non-enveloped, double-stranded RNA virus in the Birnaviridae family we name Rocky Mountain birnavirus (RMBV). Infections were detected in asymptomatic animals from the pet trade, but when transmitted to laboratory animals RMBV was associated with pronounced antiviral responses and hemorrhagic disease. These experiments highlight the pet trade as a distinct source of diverse microbes that associate with zebrafish and establish a paradigm for the discovery of newly described pathogenic viruses and other infectious microbes that can be developed for study in the laboratory.}, } @article {pmid37693399, year = {2023}, author = {Torres, MDT and Brooks, E and Cesaro, A and Sberro, H and Nicolaou, C and Bhatt, AS and de la Fuente-Nunez, C}, title = {Human gut metagenomic mining reveals an untapped source of peptide antibiotics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37693399}, abstract = {Drug-resistant bacteria are outpacing traditional antibiotic discovery efforts. Here, we computationally mined 444,054 families of putative small proteins from 1,773 human gut metagenomes, identifying 323 peptide antibiotics encoded in small open reading frames (smORFs). To test our computational predictions, 78 peptides were synthesized and screened for antimicrobial activity in vitro, with 59% displaying activity against either pathogens or commensals. Since these peptides were unique compared to previously reported antimicrobial peptides, we termed them smORF-encoded peptides (SEPs). SEPs killed bacteria by targeting their membrane, synergized with each other, and modulated gut commensals, indicating that they may play a role in reconfiguring microbiome communities in addition to counteracting pathogens. The lead candidates were anti-infective in both murine skin abscess and deep thigh infection models. Notably, prevotellin-2 from Prevotella copri presented activity comparable to the commonly used antibiotic polymyxin B. We report the discovery of hundreds of peptide sequences in the human gut.}, } @article {pmid37692394, year = {2023}, author = {Nemchinov, LG and Irish, BM and Uschapovsky, IV and Grinstead, S and Shao, J and Postnikova, OA}, title = {Composition of the alfalfa pathobiome in commercial fields.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1225781}, pmid = {37692394}, issn = {1664-302X}, abstract = {Through the recent advances of modern high-throughput sequencing technologies, the "one microbe, one disease" dogma is being gradually replaced with the principle of the "pathobiome". Pathobiome is a comprehensive biotic environment that not only includes a diverse community of all disease-causing organisms within the plant but also defines their mutual interactions and resultant effect on plant health. To date, the concept of pathobiome as a major component in plant health and sustainable production of alfalfa (Medicago sativa L.), the most extensively cultivated forage legume in the world, is non-existent. Here, we approached this subject by characterizing the biodiversity of the alfalfa pathobiome using high-throughput sequencing technology. Our metagenomic study revealed a remarkable abundance of different pathogenic communities associated with alfalfa in the natural ecosystem. Profiling the alfalfa pathobiome is a starting point to assess known and identify new and emerging stress challenges in the context of plant disease management. In addition, it allows us to address the complexity of microbial interactions within the plant host and their impact on the development and evolution of pathogenesis.}, } @article {pmid37692168, year = {2023}, author = {Jia, H and Liu, H and Tu, M and Wang, Y and Wang, X and Li, J and Zhang, G}, title = {Diagnostic efficacy of metagenomic next generation sequencing in bronchoalveolar lavage fluid for proven invasive pulmonary aspergillosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1223576}, pmid = {37692168}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Invasive Pulmonary Aspergillosis/diagnosis ; Bronchoalveolar Lavage Fluid ; Retrospective Studies ; Biopsy ; }, abstract = {OBJECTIVE: To assess the diagnostic efficacy of metagenomic next generation sequencing (mNGS) for proven invasive pulmonary aspergillosis (IPA).

METHODS: A total of 190 patients including 53 patients who had been diagnosed with proven IPA were retrospectively analyzed. Using the pathological results of tissue biopsy specimens as gold standard, we ploted the receiver operating characteristic (ROC) curve to determine the optimal cut-off value of mNGS species-specific read number (SSRN) of Aspergillus in bronchoalveolar lavage fluid (BALF)for IPA. Furthermore, we evaluated optimal cut-off value of mNGS SSRN in different populations.

RESULTS: The optimal cut-off value of Aspergillus mNGS SSRN in BALF for IPA diagnosis was 2.5 for the whole suspected IPA population, and 1 and 4.5 for immunocompromised and diabetic patients, respectively. The accuracy of mNGS was 80.5%, 73.7% and 85.3% for the whole population, immunocompromised and diabetic patients, respectively.

CONCLUSIONS: The mNGS in BALF has a high diagnostic efficacy for proven IPA, superioring to Aspergillus culture in sputum and BALF and GM test in blood and BALF. However, the cut-off value of SSRN should be adjusted when in different population.}, } @article {pmid37692161, year = {2023}, author = {Zhang, JX and Yuan, Y and Hu, QH and Jin, DZ and Bai, Y and Xin, WW and Kang, L and Wang, JL}, title = {Identification of potential pathogenic targets and survival strategies of Vibrio vulnificus through population genomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1254379}, pmid = {37692161}, issn = {2235-2988}, mesh = {*Metagenomics ; *Vibrio vulnificus/genetics ; Genome-Wide Association Study ; Amino Acids ; Biological Transport ; }, abstract = {Vibrio vulnificus, a foodborne pathogen, has a high mortality rate. Despite its relevance to public health, the identification of virulence genes associated with the pathogenicity of currently known clinical isolates of V. vulnificus is incomplete and its synergistic pathogenesis remains unclear. Here, we integrate whole genome sequencing (WGS), genome-wide association studies (GWAS), and genome-wide epistasis studies (GWES), along with phenotype characterization to investigate the pathogenesis and survival strategies of V. vulnificus. GWAS and GWES identified a total of six genes (purH, gmr, yiaV, dsbD, ramA, and wbpA) associated with the pathogenicity of clinical isolates related to nucleotide/amino acid transport and metabolism, cell membrane biogenesis, signal transduction mechanisms, and protein turnover. Of these, five were newly discovered potential specific virulence genes of V. vulnificus in this study. Furthermore, GWES combined with phenotype experiments indicated that V. vulnificus isolates were clustered into two ecological groups (EGs) that shared distinct biotic and abiotic factors, and ecological strategies. Our study reveals pathogenic mechanisms and their evolution in V. vulnificus to provide a solid foundation for designing new vaccines and therapeutic targets.}, } @article {pmid37691847, year = {2023}, author = {Mutinda, J and Mwamburi, SM and Oduor, KO and Vincent Omolo, M and Ntabo, RM and Gathiru, JM and Mwangangi, J and Nonoh, JOM}, title = {Profiles of bacterial communities and environmental factors associated with proliferation of malaria vector mosquitoes within the Kenyan Coast.}, journal = {Access microbiology}, volume = {5}, number = {8}, pages = {}, pmid = {37691847}, issn = {2516-8290}, abstract = {BACKGROUND: Since Anopheles mosquitoes which transmit and maintain the malaria parasite breed in the outdoor environment, there is an urgent need to manage these mosquito breeding sites. In order to elaborate more on the ecological landscape of mosquito breeding sites, the bacterial community structure and their interactions with physicochemical factors in mosquito larval habitats was characterised in Kwale County (Kenya), where malaria is endemic.

METHODS: The physical characteristics and water physicochemical parameters of the habitats were determined and recorded. Water samples were also collected from the identified sites for total metagenomic DNA extraction in order to characterise the bacterial communities within the breeding sites.

RESULTS AND DISCUSSION: Sites where mosquito larvae were found were described as positive and those without mosquito larvae as negative. Electrical conductivity, total dissolved solids, salinity and ammonia were lower in the rainy season than in the dry season, which also coincided with a high proportion of positive sites. Pseudomonadota was the most common phyla recovered in all samples followed by Bacteroidota and then Actinomycetota. The presence or absence of mosquito larvae in a potential proliferation site was not related to the bacterial community structure in the sampled sites, but was positively correlated with bacterial richness and evenness.

CONCLUSION: Generally, the presence of Anopheles mosquito larvae was found to be positively correlated with rainy season, bacterial richness and evenness, and negatively correlated with electrical conductivity, total dissolved solids, salinity and ammonia. The findings of this study have implications for predicting the potential of environmental water samples to become mosquito proliferation sites.}, } @article {pmid37691669, year = {2023}, author = {Pindling, S and Klugman, M and Lan, Q and Hosgood, HD}, title = {Narrative review: respiratory tract microbiome and never smoking lung cancer.}, journal = {Journal of thoracic disease}, volume = {15}, number = {8}, pages = {4522-4529}, pmid = {37691669}, issn = {2072-1439}, abstract = {BACKGROUND AND OBJECTIVE: The lung microbiome was previously thought to be a sterile environment where only gaseous exchange takes place, but recent studies have shown the presence of microbiota in the lung. This review investigates the current literature on the effects of an environmental driven dysbiosis on the healthy oral and respiratory microbiome and its relationship to lung cancer risk in never-smokers.

METHODS: An online electronic search was performed on PubMed of all English-language literature using combinations of the following keywords: "lung cancer", "dysbiosis", "non-smokers", "oral microbiome", and "respiratory microbiome". All population-based studies reporting results on oral and/or respiratory microbiome in adults were considered for our narrative review.

KEY CONTENT AND FINDINGS: Metagenomic analyses have been performed on isolated samples from healthy participants and compared to samples from those with lung cancer. Research shows that a decrease in alpha diversity of microbes in the oral microbiome is associated with increased risk of lung cancer, along with differences in beta diversity in the sputum of lung cancer cases and healthy controls. Further, several studies have observed that significant changes in the abundance of genera such as increased abundance of Lactobacillales, Bacilli, and Firmicutes associated with an increased lung cancer risk among participants with exposure to certain household solid fuels.

CONCLUSIONS: These findings suggest potential carcinogenic processes such as increased inflammation associated with changes in flora. Additionally, studies showed that increase in certain taxa such as Bacteroides and Spirochetes might have a protective effect on lung cancer risk. The review also provides insight into how understanding the microbial changes can be beneficial for lung cancer treatment and disease-free survival. Larger studies in different populations need to be performed to strengthen the current associations between microbial diversity and lung cancer risk.}, } @article {pmid37691054, year = {2023}, author = {Dwivedi, S and Yadav, K and Gupta, S and Tanveer, A and Yadav, S and Yadav, D}, title = {Fungal pectinases: an insight into production, innovations and applications.}, journal = {World journal of microbiology & biotechnology}, volume = {39}, number = {11}, pages = {305}, pmid = {37691054}, issn = {1573-0972}, support = {DST/INSPIRE Fellowship/2019/IF190080//DST-INSPIRE Fellowship/ ; Grant. No. DST/WOS-B/2018/1707//DST, Women Scientist-B , New Delhi INDIA/ ; }, mesh = {Animals ; *Polygalacturonase/genetics ; *Actinobacteria ; Bioreactors ; Catalysis ; Eukaryota ; }, abstract = {The fungal system holds morphological plasticity and metabolic versatility which makes it unique. Fungal habitat ranges from the Arctic region to the fertile mainland, including tropical rainforests, and temperate deserts. They possess a wide range of lifestyles behaving as saprophytic, parasitic, opportunistic, and obligate symbionts. These eukaryotic microbes can survive any living condition and adapt to behave as extremophiles, mesophiles, thermophiles, or even psychrophile organisms. This behaviour has been exploited to yield microbial enzymes which can survive in extreme environments. The cost-effective production, stable catalytic behaviour and ease of genetic manipulation make them prominent sources of several industrially important enzymes. Pectinases are a class of pectin-degrading enzymes that show different mechanisms and substrate specificities to release end products. The pectinase family of enzymes is produced by microbial sources such as bacteria, fungi, actinomycetes, plants, and animals. Fungal pectinases having high specificity for natural sources and higher stabilities and catalytic activities make them promising green catalysts for industrial applications. Pectinases from different microbial sources have been investigated for their industrial applications. However, their relevance in the food and textile industries is remarkable and has been extensively studied. The focus of this review is to provide comprehensive information on the current findings on fungal pectinases targeting diverse sources of fungal strains, their production by fermentation techniques, and a summary of purification strategies. Studies on pectinases regarding innovations comprising bioreactor-based production, immobilization of pectinases, in silico and expression studies, directed evolution, and omics-driven approaches specifically by fungal microbiota have been summarized.}, } @article {pmid37690547, year = {2023}, author = {Li, D and Ping, Q and Guo, W and Chen, Y and Wang, L and Li, Y}, title = {Evaluating effects of biochar on anaerobic digestion of dewatered waste activated sludge: Digester performance, microbial co-metabolism and underlying mechanism.}, journal = {Chemosphere}, volume = {341}, number = {}, pages = {140139}, doi = {10.1016/j.chemosphere.2023.140139}, pmid = {37690547}, issn = {1879-1298}, mesh = {Anaerobiosis ; *Sewage ; *Biofuels ; Electron Transport ; }, abstract = {Biochar has been proven to be capable of improving the performance of anaerobic digestion (AD). However, the effect of biochar on microbial communities remains ambiguous. In this study, the influence of pH was excluded in a semi-continuous anaerobic digestor for the treatment of dewatered waste activated sludge (WAS) to determine the effect of biochar on microbes. Compared with the control group, the average methane production increased by 24.5% and 23.2% at the organic loading rates (OLRs) of 1.56 and 3.00 gTS/L/d, respectively, in the presence of biochar. This study innovatively found biochar accelerated the enrichment of Methanofastidiosaceae, which competed with Methanobacteriaceae for H2, and its abundance increased from 0.99% at the OLR of 1.56 g TS/L/d to 16.57% and 38.11% at the OLR of 3.00 and 5.60 gTS/L/d, respectively. The efficient metabolic network of f__norank_o__Aminicenantales, syntrophic bacteria, Methanofastidiosaceae and Methanosaetaceae promoted the conversion of WAS to CH4 in the biochar group. In addition, metagenome analysis revealed that biochar optimized the metabolites related to energy conservation and electron transfer, particularly for hydrogenase (frhABG, mbhLHK and hndA-D), confirming that biochar changed the way H2 was involved in methanogenesis. These findings provide novel insights into the direct effect of biochar on microbial evolution and facilitate the reduction of WAS to achieve higher economic benefits in biogas production.}, } @article {pmid37690533, year = {2023}, author = {Zhao, X and Zhao, J and Li, D and Yang, H and Chen, C and Qin, M and Wen, Z and He, Z and Xu, L}, title = {Akkermansia muciniphila: A potential target and pending issues for oncotherapy.}, journal = {Pharmacological research}, volume = {196}, number = {}, pages = {106916}, doi = {10.1016/j.phrs.2023.106916}, pmid = {37690533}, issn = {1096-1186}, abstract = {In the wake of the development of metagenomic, metabolomic, and metatranscriptomic approaches, the intricate interactions between the host and various microbes are now being progressively understood. Numerous studies have demonstrated evident changes in gut microbiota during the process of a variety of diseases, such as diabetes, obesity, aging, and cancers. Notably, gut microbiota is viewed as a potential source of novel therapeutics. Currently, Next-generation probiotics (NGPs) are gaining popularity as therapeutic agents that alter the gut microbiota and affect cancer development. Akkermansia muciniphila (A. muciniphila), a representative commensal bacterium, has received substantial attention over the past decade as a promising NGP. The components and metabolites of A. muciniphila can directly or indirectly affect tumorigenesis, in particular through its effects on antitumor immunosurveillance, including the stimulation of pattern recognition receptors (PRRs), which also leads to better outcomes in a variety of situations, including the prevention and curation of cancers. In this article, we systematically summarize the role of A. muciniphila in tumorigenesis (involving gastrointestinal and non-gastrointestinal cancers) and in tumor therapy. In particular, we carefully discuss some critical scientific issues that need to be solved for the future using A. muciniphila as a representative beneficial bacterium in tumor treatment, which might provide bright clues and assistance for the application of drugs targeting A. muciniphila in clinical oncotherapy.}, } @article {pmid37690468, year = {2023}, author = {Liu, L and Hu, J and Teng, Y and Wang, J and Chen, H and Guo, X and Zhai, Y}, title = {Response of microbial community to different media in start-up period of Annan constructed wetland in Beijing of China.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {337}, number = {}, pages = {122529}, doi = {10.1016/j.envpol.2023.122529}, pmid = {37690468}, issn = {1873-6424}, mesh = {Humans ; *Wetlands ; Beijing ; Bacteria/genetics ; *Microbiota ; China ; }, abstract = {Microbial community, as the decomposers of constructed wetland (CW), plays crucial role in biodegradation and biotransformation of pollutants, nutrient cycling and the maintenance of ecosystem balance. In this study, 9 water samples, 6 sediment samples, and 8 plant samples were collected in Annan CW, which has the functions of water treatment and wetland culture park. The characteristics of microbial community structure in different media were illustrated by using of high-throughput sequencing-based metagenomics approach and statistical analysis. Meanwhile, this study identified and classified human pathogens in CW to avoid potential risks to human health. The results showed that dominant bacteria phyla in CW include Proteobacteria, Bacteroides, Actinobacteria, Firmicutes and Verrucomicrobia. The distribution of microorganisms in three media is different, but not significant. And the pH and DO profoundly affected microbe abundance, followed by water temperature. The microbial diversity in sediments is the highest, which is similar with the detection of human pathogens in sediments. Moreover, compared with Calamus, Lythrum salicaria and Reed, Scirpus tabernaemontani has fewer pathogenic microorganisms. The distribution of microorganisms in the CW is complex, and a variety of human pathogens are detected, which is more prone to create potential risks to human health and should receive additional attention.}, } @article {pmid37689952, year = {2023}, author = {Das, S and Tamang, JP}, title = {Metagenomics and metabolomics of Toddy, an Indian fermented date palm beverage.}, journal = {Food research international (Ottawa, Ont.)}, volume = {172}, number = {}, pages = {113205}, doi = {10.1016/j.foodres.2023.113205}, pmid = {37689952}, issn = {1873-7145}, mesh = {Humans ; *Metagenomics ; *Phoeniceae ; Metabolomics ; Acetic Acid ; Beverages ; }, abstract = {Toddy is a popular fermented palm beverage of India. No scientific information on shotgun metagenomics and metabolomics are available on toddy of India till date. Hence, we choose the fermented date palm beverage, locally called khejur toddy, of West Bengal and Jharkhand states of India, to profile microbial community, their targeted and untargeted metabolites to study the putative bio-functional genes corresponding to regulatory metabolic pathways. Shotgun-based metataxonomic analyses revealed the existence of all domains where bacteria were the most abundant domain (94.48%) followed by eukaryotes (3.38%), viruses (1.53%) and archaea (0.61%). Overall, 54 phyla, 363 families, 1087 genera and 1885 species were observed and identified. Bacillota (49.3%) was the most abundant bacterial phylum. At species level, several species of bacteria and yeasts were detected in toddy samples which included Leuconostoc mesenteroides,Leuconostoc citreum,Lactobacillus helveticus,Lactiplantibacillus plantarum,Lactococcus lactis, Acetobacter malorum, Gluconobacter japonicus, Gluconacetobacter liquefaciens, Fructobacillus durionis, Zymomonas mobilis and yeastsSaccharomyces cerevisiae, Hanseniaspora uvarumandHanseniaspora guilliermondii. Toddy metagenome was also compared with metagenome of pulque, the Mexican fermented fresh sap ofAgave, which was retrieved from NCBI database, and also with metagenomic data of some amplicon-based previous studies on toddy and African fermented palm drink for similarity, dissimilarity and uniqueness among them. Predictive biosynthesis of ethanol, acetic acid, butanoate, linalool, staurosporine, prodigiosin, folic acid, riboflavin, etc. were annotated by KEGG/COG database. Clustered regularly interspaced short palindromic repeats (CRISPR) analysis detected 23 arrays (average length 23.69 bp ± 4.28). Comprehensive Antibiotic Resistance Database (CARD) analysis did not show the presence of any momentous antibiotic resistance gene among the major microbial members. Metabolomics analysis detected many primary and secondary metabolites. We believe this is the first report on complete shotgun metagenomics, and metabolomics of fermented palm drink of India as well as Eastern India.}, } @article {pmid37689895, year = {2023}, author = {Shangpliang, HNJ and Tamang, JP}, title = {Metagenomics and metagenome-assembled genomes mining of health benefits in jalebi batter, a naturally fermented cereal-based food of India.}, journal = {Food research international (Ottawa, Ont.)}, volume = {172}, number = {}, pages = {113130}, doi = {10.1016/j.foodres.2023.113130}, pmid = {37689895}, issn = {1873-7145}, mesh = {*Metagenome ; *Edible Grain ; Metagenomics ; India ; }, abstract = {Jalebi is one of the oldest Indian traditional fermented wheat-based confectioneries. Since jalebi is prepared by natural fermentation, diverse microbial community is expected to play bio-functional activities. Due to limited studies, information on microbial community structure in jalebi is unknown. Hence, the present study is aimed to profile the microbial community in jalebi by shotgun metagenomics and also to predict putative probiotic and functional genes by metagenome-assembled genome (MAG). Bacteria were the most abundant domain (91.91%) under which Bacillota was the most abundant phylum (82%). The most abundant species was Lapidilactobacillus dextrinicus followed by several species of lactic acid bacteria, acetic acid bacteria including few yeasts. Lap. dextrinicus was also significantly abundant in jalebi when compared to similar fermented wheat-based sourdough. Additionally, Lap. bayanensis, Pediococcus stilesii, and yeast- Candida glabrata, Gluconobacter japonicus, Pichia kudriavzevii, Wickerhamomyces anomalus were only detected in jalebi, which are not detected in sourdough. Few viruses and archaea were detected with < 1 % abundance. In silico screening of genes from the abundant species was mined using both KEGG and EggNOG database for putative health beneficial attributes. Circular genomes of five high-quality MAGs, identified as Lapidilactobacillus dextrinicus, Enterococcus hirae, Pediococcus stilesii, Acetobacter indonesiensis and Acetobacter cibinongensis, were constructed separately and putative genes were mapped and annotated. The CRISPR/Cas gene clusters in the genomes of four MAGs except Acetobacter cibinongensis were detected. MAGs also showed several secondary metabolites. Since, the identified MAGs have different putative genes for bio-functional properties, this may pave the way to selectively culture the uncultivated putative microbes for jalebi production. We believe this is the first report on metagenomic and MAGs of jalebi.}, } @article {pmid37689857, year = {2023}, author = {Zhu, C and Cheng, Y and Shi, Q and Ge, X and Yang, Y and Huang, Y}, title = {Metagenomic analyses reveal microbial communities and functional differences between Daqu from seven provinces.}, journal = {Food research international (Ottawa, Ont.)}, volume = {172}, number = {}, pages = {113076}, doi = {10.1016/j.foodres.2023.113076}, pmid = {37689857}, issn = {1873-7145}, mesh = {Metagenome ; *Microbiota ; *Bacillus ; Amino Acids ; Lactic Acid ; *Lactobacillales/genetics ; }, abstract = {Microbial communities perform the brewing function in Daqu. Macrogenomics and PICRUST II analyses revealed the differences in microbes and metabolic functions among Daqu from the seven Baijiu-producing provinces. Jiang-flavored Daqu (Guizhou, Shandong, and Hubei provinces) generally forms an aroma-producing functional microbiota with Kroppenstedtia, Bacillus, Thermoascus, Virgibacillus, and Thermomyces as the core, which promotes the metabolism of various amino acids and aroma compounds. Light-flavored Daqu (Shanxi Province) enriched the Saccharomycopsis, Saccharomyces, and lactic acid bacteria (LAB) microbiota through low-temperature fermentation. These microbes can synthesize alcohol and lactic acid but inhibit amino acid metabolism within the Light-flavored Daqu. Bifidobacterium and Saccharomycopsis were dominant in the Tao-flavored Daqu (Henan province). This unique microbial structure is beneficial for pyruvate fermentation to lactate. Research also found that Strong-flavored Daqu from Jiangsu and Sichuan provinces differed significantly. The microbial communities and metabolic pathways within Jiangsu Daqu were similar to those within Jiang-flavored Daqu, but Sichuan Daqu was dominated by Thermoascus, LAB, and Thermoactinomyces. In addition, Spearman correlation analysis indicated that Kroppenstedtia, Bacillus, and Thermomyces were not only positively related to flavor metabolism but also negatively correlated with Saccharomycopsis. This research will help establish a systematic understanding of the microbial community and functional characteristics in Daqu.}, } @article {pmid37689612, year = {2023}, author = {Lin, W and Xie, F and Li, X and Yang, R and Lu, J and Ruan, Z and Ou, D and Wang, Z}, title = {Diagnostic performance of metagenomic next-generation sequencing and conventional microbial culture for spinal infection: a retrospective comparative study.}, journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society}, volume = {32}, number = {12}, pages = {4238-4245}, pmid = {37689612}, issn = {1432-0932}, support = {2021A1515011508//Guangdong Basic and Applied Basic Research Foundation/ ; CRSP2019010//Scientific Research Start Plan of Shunde Hospital, Southern Medical University/ ; SRSP2021007//Scientific Research Start Plan of Shunde Hospital, Southern Medical University/ ; }, mesh = {Male ; Humans ; Female ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; *Affect ; DNA ; Sensitivity and Specificity ; }, abstract = {PURPOSE: The study evaluated the diagnostic performance of metagenomic next-generation sequencing (mNGS) as a diagnostic test for biopsy samples from patients with suspected spinal infection (SI) and compared the diagnostic performance of mNGS with that of microbial culture.

METHODS: All patients diagnosed with clinical suspicion of SI were enrolled, and data were collected through a retrospective chart review of patient records. Biopsy specimens obtained from each patient were tested via mNGS and microbial culture. Samples were enriched for microbial DNA using the universal DNA extraction kit, whole-genome amplified, and sequenced using MGISEQ-200 instrument. After Low-quality reads removed, the remaining sequences for microbial content were analyzed and aligned using SNAP and kraken2 tools.

RESULTS: A total of 39 patients (19 men and 20 women) were deemed suitable for enrollment. The detection rate for pathogens of mNGS was 71.8% (28/39), which was significantly higher than that of microbial culture (23.1%, p = 0.016). Mycobacterium tuberculosis complex was the most frequently isolated. Using pathologic test as the standard reference for SI, thirty-one cases were classified as infected, and eight cases were considered aseptic. The sensitivity and specificity values for detecting pathogens with mNGS were 87.1% and 87.5%, while these rates were 25.8% and 87.5% with conventional culture. mNGS was able to detect 88.9% (8/9) of pathogens identified by conventional culture, with a genus-level sensitivity of 100% (8/8) and a species-level sensitivity of 87.5% (7/8).

CONCLUSION: The present work suggests that mNGS might be superior to microbial culture for detecting SI pathogens.}, } @article {pmid37689208, year = {2023}, author = {Thompson, C and Bacha, L and Paz, PHC and de Assis Passos Oliveira, M and Oliveira, BCV and Omachi, C and Chueke, C and de Lima Hilário, M and Lima, M and Leomil, L and Felix-Cordeiro, T and da Cruz, TLC and Otsuki, K and Vidal, L and Thompson, M and Ribeiro E Silva, R and Cabezas, CMV and Veríssimo, BM and Zaganelli, JL and Botelho, ACN and Teixeira, L and Cosenza, C and Costa, PM and Landuci, F and Tschoeke, DA and Silva, TA and Attias, M and de Souza, W and de Rezende, CE and Thompson, F}, title = {Collapse of scallop Nodipecten nodosus production in the tropical Southeast Brazil as a possible consequence of global warming and water pollution.}, journal = {The Science of the total environment}, volume = {904}, number = {}, pages = {166873}, doi = {10.1016/j.scitotenv.2023.166873}, pmid = {37689208}, issn = {1879-1026}, mesh = {Animals ; Chlorophyll A ; Brazil ; *Global Warming ; *Pectinidae ; Water Pollution ; }, abstract = {Mollusc rearing is a relevant global socioeconomic activity. However, this activity has faced severe problems in the last years in southeast Brazil. The mariculture scallop production dropped from 51,2 tons in 2016 to 10,2 tons in 2022 in the Baia da Ilha Grande (BIG; Rio de Janeiro). However, the possible causes of this collapse are unknown. This study aimed to analyze decadal trends of water quality in Nodipecten nodosus spat and adult production in BIG. We also performed physical-chemical and biological water quality analyses of three scallop farms and two nearby locations at BIG in 2022 to evaluate possible environmental stressors and risks. Scallop spat production dropped drastically in the last five years (2018-2022: mean ± stdev: 0.47 ± 0.45 million). Spat production was higher in colder waters and during peaks of Chlorophyll a in the last 13 years. Reduction of Chlorophyll a coincided with decreasing spat production in the last five years. Warmer periods (>27 °C) of the year may hamper scallop development. Counts of potentially pathogenic bacteria (Vibrios) and Escherichia coli were significantly higher in warmer periods which may further reduce scallop productivity. Shotgun metagenomics of seawater samples from the five studied corroborated these culture-based counts. Vibrios and fecal indicator bacteria metagenomic sequences were abundant across the entire study area throughout 2022. The results of this study suggest the collapse of scallop mariculture is the result of a synergistic negative effect of global warming and poor seawater quality.}, } @article {pmid37688754, year = {2023}, author = {Fehér, E and Kaszab, E and Mótyán, JA and Máté, D and Bali, K and Hoitsy, M and Sós, E and Jakab, F and Bányai, K}, title = {Structural similarity of human papillomavirus E4 and polyomaviral VP4 exhibited by genomic analysis of the common kestrel (Falco tinnunculus) polyomavirus.}, journal = {Veterinary research communications}, volume = {}, number = {}, pages = {}, pmid = {37688754}, issn = {1573-7446}, abstract = {Polyomaviruses are widely distributed viruses of birds that may induce developmental deformities and internal organ disorders primarily in nestlings. In this study, polyomavirus sequence was detected in kidney and liver samples of a common kestrel (Falco tinnunculus) that succumbed at a rescue station in Hungary. The amplified 5025 nucleotide (nt) long genome contained the early (large and small T antigen, LTA and STA) and late (viral proteins, VP1, VP2, VP3) open reading frames (ORFs) typical for polyomaviruses. One of the additional putative ORFs (named VP4) showed identical localization with the VP4 and ORF-X of gammapolyomaviruses, but putative splicing sites could not be found in its sequence. Interestingly, the predicted 123 amino acid (aa) long protein sequence showed the highest similarity with human papillomavirus E4 early proteins in respect of the aa distribution and motif arrangement implying similar functions. The LTA of the kestrel polyomavirus shared <59.2% nt and aa pairwise identity with the LTA sequence of other polyomaviruses and formed a separated branch in the phylogenetic tree among gammapolyomaviruses. Accordingly, the kestrel polyomavirus may be the first member of a novel species within the Gammapolyomavirus genus, tentatively named Gammapolyomavirus faltin.}, } @article {pmid37688597, year = {2023}, author = {Wang, L and Lian, C and Wan, W and Qiu, Z and Luo, X and Huang, Q and Deng, Y and Zhang, T and Yu, K}, title = {Salinity-triggered homogeneous selection constrains the microbial function and stability in lakes.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {21}, pages = {6591-6605}, pmid = {37688597}, issn = {1432-0614}, abstract = {Climate change and anthropogenic exploitation have led to the gradual salinization of inland waters worldwide. However, the impacts of this process on the prokaryotic plankton communities and their role in biogeochemical cycles in the inland lake are poorly known. Here, we take a space-for-time substitution approach, using 16S rRNA gene amplicon sequencing and metagenomic sequencing. We analyzed the prokaryotic plankton communities of 11 lakes in northwest China, with average water salinities ranging from 0.002 to 14.370%. The results demonstrated that, among the various environmental parameters, salinity was the most important driver of prokaryotic plankton β-diversity (Mantel test, r = 0.53, P < 0.001). (1) Under low salinity, prokaryotic planktons were assembled by stochastic processes and employed diverse halotolerant strategies, including the synthesis and uptake of compatible solutes and extrusion of Na[+] or Li[+] in exchange for H[+]. Under elevated salinity pressure, strong homogeneous selection meant that only planktonic prokaryotes showing an energetically favorable halotolerant strategy employing an Mnh-type Na[+]/H[+] antiporter remained. (2) The decreasing taxonomic diversity caused by intense environmental filtering in high-salinity lakes impaired functional diversity related to substance metabolism. The prokaryotes enhanced the TCA cycle, carbon fixation, and low-energy-consumption amino acid biosynthesis in high-salinity lakes. (3) Elevated salinity pressure decreased the negative:positive cohesion and the modularity of the molecular ecology networks for the planktonic prokaryotes, indicating a precarious microbial network. Our findings provide new insights into plankton ecology and are helpful for the protecting of the biodiversity and function of inland lakes against the background of salinization. KEY POINTS: • Increased salinity enhances homogeneous selection in the microbial assembly. • Elevated salinity decreases the microbial co-occurrence networks stability. • High salinity damages the microbial function diversity.}, } @article {pmid37688461, year = {2023}, author = {Feng, M and Varliero, G and Qi, W and Stierli, B and Edwards, A and Robinson, S and van der Heijden, MGA and Frey, B}, title = {Microbial dynamics in soils of the Damma glacier forefield show succession in the functional genetic potential.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {3116-3138}, doi = {10.1111/1462-2920.16497}, pmid = {37688461}, issn = {1462-2920}, support = {201904910436//Chinese Government Scholarship/ ; 675546//Horizon 2020 Framework Programme (Marie Sklodowska Curie Actions program)/ ; 5233.00388.001.01//Swiss Federal Institute for Forest, Snow and Landscape Research (WSL)/ ; }, mesh = {*Ice Cover ; *Soil ; Soil Microbiology ; Plants ; Nitrification ; }, abstract = {Glacier retreat is a visible consequence of climate change worldwide. Although taxonomic change of the soil microbiomes in glacier forefields have been widely documented, how microbial genetic potential changes along succession is little known. Here, we used shotgun metagenomics to analyse whether the soil microbial genetic potential differed between four stages of soil development (SSD) sampled along three transects in the Damma glacier forefield (Switzerland). The SSDs were characterized by an increasing vegetation cover, from barren soil, to biological soil crust, to sparsely vegetated soil and finally to vegetated soil. Results suggested that SSD significantly influenced microbial genetic potential, with the lowest functional diversity surprisingly occurring in the vegetated soils. Overall, carbohydrate metabolism and secondary metabolite biosynthesis genes overrepresented in vegetated soils, which could be partly attributed to plant-soil feedbacks. For C degradation, glycoside hydrolase genes enriched in vegetated soils, while auxiliary activity and carbohydrate esterases genes overrepresented in barren soils, suggested high labile C degradation potential in vegetated, and high recalcitrant C degradation potential in barren soils. For N-cycling, organic N degradation and synthesis genes dominated along succession, and gene families involved in nitrification were overrepresented in barren soils. Our study provides new insights into how the microbial genetic potential changes during soil formation along the Damma glacier forefield.}, } @article {pmid37688275, year = {2023}, author = {Dudun, AA and Chesnokova, DV and Voinova, VV and Bonartsev, AP and Bonartseva, GA}, title = {Changes in the Gut Microbiota Composition during Implantation of Composite Scaffolds Based on Poly(3-hydroxybutyrate) and Alginate on the Large-Intestine Wall.}, journal = {Polymers}, volume = {15}, number = {17}, pages = {}, pmid = {37688275}, issn = {2073-4360}, support = {20-64-47008//Russian Science Foundation/ ; }, abstract = {The development of biopolymer scaffolds for intestine regeneration is one of the most actively developing areas in tissue engineering. However, intestinal regenerative processes after scaffold implantation depend on the activity of the intestinal microbial community that is in close symbiosis with intestinal epithelial cells. In this work, we study the impact of different scaffolds based on biocompatible poly(3-hydroxybutyrate) (PHB) and alginate (ALG) as well as PHB/ALG scaffolds seeded with probiotic bacteria on the composition of gut microbiota of Wistar rats. Implantation of PHB/ALG scaffolds on the large-intestine wall to close its injury showed that alpha diversity of the gut microbiota was not reduced in rats implanted with different PHB/ALG scaffolds except for the PHB/ALG scaffolds with the inclusion of Lactobacillus spheres (PHB/ALG-L). The composition of the gut microbiota of rats implanted with PHB/ALG scaffolds with probiotic bacteria or in simultaneous use of an antimicrobial agent (PHB/ALG-AB) differed significantly from other experimental groups. All rats with implanted scaffolds demonstrated shifts in the composition of the gut microbiota by individual operational taxonomic units. The PHB/ALG-AB construct led to increased abundance of butyrate-producing bacteria: Ileibacterium sp. dominated in rats with implanted PHB/ALG-L and Lactobacillus sp. and Bifidobacterium sp. dominated in the control group. In addition, the PHB/ALG scaffolds had a favourable effect on the growth of commensal bacteria. Thus, the effect of implantation of the PHB/ALG scaffold compared to other scaffolds on the composition of the gut microbiota was closest to the control variant, which may demonstrate the biocompatibility of this device with the microbiota.}, } @article {pmid37686487, year = {2023}, author = {Mauceri, R and Coppini, M and Vacca, D and Bertolazzi, G and Cancila, V and Tripodo, C and Campisi, G}, title = {No Clear Clustering Dysbiosis from Salivary Microbiota Analysis by Long Sequencing Reads in Patients Affected by Oral Squamous Cell Carcinoma: A Single Center Study.}, journal = {Cancers}, volume = {15}, number = {17}, pages = {}, pmid = {37686487}, issn = {2072-6694}, abstract = {BACKGROUND: Advancements in DNA sequencing technology have facilitated the assessment of the connection between the oral microbiome and various diseases. The aim of the present study was to investigate the salivary microbiota composition employing for the first time in the literature the Oxford Nanopore Technology in patients affected by oral squamous cell carcinoma (OSCC).

METHODS: Unstimulated saliva samples of 31 patients were collected (24 OSCC patients and 7 controls). DNA was extracted using the QIAamp DNA Blood Kit and metagenomic long sequencing reads were performed using the MinION device.

RESULTS: In the OSCC group, 13 were males and 11 were females, with a mean age of 65.5 ± 13.9 years; in the control group, 5 were males and 2 were females, with a mean age of 51.4 ± 19.2 years. The border of the tongue was the most affected OSCC site. The microorganisms predominantly detected in OSCC patients were Prevotella, Chlamydia, Tissierellia, Calothrix, Leotiomycetes, Firmicutes and Zetaproteobacteria.

CONCLUSIONS: This study confirmed the predominance of periodontopathic bacteria in the salivary microbiome in the OSCC group. If a direct correlation between oral dysbiosis and OSCC onset was proven, it could lead to new prevention strategies and early diagnostic tools.}, } @article {pmid37685932, year = {2023}, author = {Milicevic, O and Loncar, A and Abazovic, D and Vukcevic, M and Despot, D and Djukic, T and Djukic, V and Milovanovic, A and Panic, N and Plecic, N and Banko, A}, title = {Transcriptome from Paired Samples Improves the Power of Comprehensive COVID-19 Host-Viral Characterization.}, journal = {International journal of molecular sciences}, volume = {24}, number = {17}, pages = {}, pmid = {37685932}, issn = {1422-0067}, mesh = {Humans ; *SARS-CoV-2/genetics ; Transcriptome ; *COVID-19/genetics ; Gene Expression Profiling ; Computational Biology ; }, abstract = {Previous transcriptome profiling studies showed significantly upregulated genes and altered biological pathways in acute COVID-19. However, changes in the transcriptional signatures during a defined time frame are not yet examined and described. The aims of this study included viral metagenomics and evaluation of the total expression in time-matched and tissue-matched paired COVID-19 samples with the analysis of the host splicing profile to reveal potential therapeutic targets. Prospective analysis of paired nasopharyngeal swabs (NPS) and blood (BL) samples from 18 COVID-19 patients with acute and resolved infection performed using Kallisto, Suppa2, Centrifuge, EdgeR, PantherDB, and L1000CDS2 tools. In NPS, we discovered 6 genes with changed splicing and 40 differentially expressed genes (DEG) that yielded 88 altered pathways. Blood samples yielded 15 alternatively spliced genes. Although the unpaired DEG analysis failed, pairing identified 78 genes and 242 altered pathways with meaningful clinical interpretation and new candidate drug combinations with up to 65% overlap. Metagenomics analyses showed SARS-CoV-2 dominance during and after the acute infection, with a significant reduction in NPS (0.008 vs. 0.002, p = 0.019). Even though both NPS and BL give meaningful insights into expression changes, this is the first demonstration of how the power of blood analysis is vastly maximized by pairing. The obtained results essentially showed that pairing is a determinant between a failed and a comprehensive study. Finally, the bioinformatics results prove to be a comprehensive tool for full-action insights, drug development, and infectious disease research when designed properly.}, } @article {pmid37684694, year = {2023}, author = {Liu, S and Men, X and Guo, Y and Cai, W and Wu, R and Gao, R and Zhong, W and Guo, H and Ruan, H and Chou, S and Mai, J and Ping, S and Jiang, C and Zhou, H and Mou, X and Zhao, W and Lu, Z}, title = {Gut microbes exacerbate systemic inflammation and behavior disorders in neurologic disease CADASIL.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {202}, pmid = {37684694}, issn = {2049-2618}, mesh = {Animals ; Mice ; *CADASIL ; *Gastrointestinal Microbiome ; *Mental Disorders ; Cytokines ; gamma-Aminobutyric Acid ; }, abstract = {BACKGROUND: Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL) is a cerebral small vessel disease that carries mutations in NOTCH3. The clinical manifestations are influenced by genetic and environmental factors that may include gut microbiome.

RESULTS: We investigated the fecal metagenome, fecal metabolome, serum metabolome, neurotransmitters, and cytokines in a cohort of 24 CADASIL patients with 28 healthy household controls. The integrated-omics study showed CADASIL patients harbored an altered microbiota composition and functions. The abundance of bacterial coenzyme A, thiamin, and flavin-synthesizing pathways was depleted in patients. Neurotransmitter balance, represented by the glutamate/GABA (4-aminobutanoate) ratio, was disrupted in patients, which was consistent with the increased abundance of two major GABA-consuming bacteria, Megasphaera elsdenii and Eubacterium siraeum. Essential inflammatory cytokines were significantly elevated in patients, accompanied by an increased abundance of bacterial virulence gene homologs. The abundance of patient-enriched Fusobacterium varium positively correlated with the levels of IL-1β and IL-6. Random forest classification based on gut microbial species, serum cytokines, and neurotransmitters showed high predictivity for CADASIL with AUC = 0.89. Targeted culturomics and mechanisms study further showed that patient-derived F. varium infection caused systemic inflammation and behavior disorder in Notch3[R170C/+] mice potentially via induction of caspase-8-dependent noncanonical inflammasome activation in macrophages.

CONCLUSION: These findings suggested the potential linkage among the brain-gut-microbe axis in CADASIL. Video Abstract.}, } @article {pmid37684563, year = {2023}, author = {Liang, W and Feng, Y and Yang, D and Qin, J and Zhi, X and Wu, W and Jie, Q}, title = {Oral probiotics increased the proportion of Treg, Tfr, and Breg cells to inhibit the inflammatory response and impede gestational diabetes mellitus.}, journal = {Molecular medicine (Cambridge, Mass.)}, volume = {29}, number = {1}, pages = {122}, pmid = {37684563}, issn = {1528-3658}, mesh = {Female ; Pregnancy ; Humans ; Animals ; Mice ; *B-Lymphocytes, Regulatory ; Asparagine ; Aspartic Acid ; *Diabetes Mellitus, Type 2 ; *Diabetes, Gestational ; Dysbiosis ; Leptin ; T-Lymphocytes, Regulatory ; Inflammation ; }, abstract = {BACKGROUND: Children of mothers with gestational diabetes mellitus (GDM) are more prone to acquire type 2 diabetes and obesity as adults. Due to this link, early intervention strategies that alter the gut microbiome may benefit the mother and kid long-term. This work uses metagenomic and transcriptome sequencing to investigate how probiotics affect gut microbiota dysbiosis and inflammation in GDM.

METHODS: GDM and control metagenomic sequencing data were obtained from the SRA database. This metagenomic data helped us understand gut microbiota abundance and function. KEGG detected and extracted functional pathway genes. Transcriptome sequencing data evaluated GDM-related gene expression. Finally, GDM animal models were given probiotics orally to evaluate inflammatory response, regulatory immune cell fractions, and leptin protein levels.

RESULTS: GDM patients had more Fusobacteria and Firmicutes, while healthy people had more Bacteroidetes. Gut microbiota composition may affect GDM by altering the L-aspartate and L-asparagine super pathways. Mannan degradation and the super pathway of L-aspartate and L-asparagine synthesis enhanced in GDM mice with leptin protein overexpression. Oral probiotics prevent GDM by lowering leptin. Oral probiotics increased Treg, Tfr, and Breg cells, which decreased TNF-α and IL-6 and increased TGF-β and IL-10, preventing inflammation and preserving mouse pregnancy.

CONCLUSION: Dysbiosis of the gut microbiota may increase leptin expression and cause GDM. Oral probiotics enhance Treg, Tfr, and Breg cells, which limit the inflammatory response and assist mice in sustaining normal pregnancy. Thus, oral probiotics may prevent GDM, enabling targeted gut microbiota modulation and maternal and fetal health.}, } @article {pmid37684524, year = {2023}, author = {Lee, J and Ju, F and Beck, K and Bürgmann, H}, title = {Differential effects of wastewater treatment plant effluents on the antibiotic resistomes of diverse river habitats.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {1993-2002}, pmid = {37684524}, issn = {1751-7370}, mesh = {*Anti-Bacterial Agents/pharmacology ; Wastewater ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; *Microbiota ; Water ; beta-Lactamases/genetics ; }, abstract = {Wastewater treatment plants (WWTPs) are key sources of antimicrobial resistance genes (ARGs) that could influence the resistomes of microbial communities in various habitats of the receiving river ecosystem. However, it is currently unknown which habitats are most impacted and whether ARGs, like certain chemical contaminants, could be accumulated or enriched in the river ecosystem. We conducted a systematic metagenomic survey on the antibiotic resistomes of WWTP effluent, four riverine habitats (water, suspended particles, sediment, epilithic biofilm), and freshwater amphipod gut microbiomes. The impact of WWTP effluent on the downstream habitats was assessed in nine Swiss rivers. While there were significant differences in resistomes across habitats, the wastewater resistome was more similar to the resistome of receiving river water than to the resistomes of other habitats, and river water was the habitat most strongly impacted by the WWTPs effluent. The sulfonamide, beta-lactam, and aminoglycoside resistance genes were among the most abundant ARGs in the WWTP effluents, and especially aadA, sul1, and class A beta-lactamase genes showed significantly increased abundance in the river water of downstream compared to upstream locations (p < 0.05). However, this was not the case for the sediment, biofilm, and amphipod gut habitats. Accordingly, evidence for accumulation or enrichment of ARGs through the riverine food web was not identified. Our study suggests that monitoring riverine antimicrobial resistance determinants could be conducted using "co-occurrence" of aadA, sul1, and class A beta-lactamase genes as an indicator of wastewater-related pollution and should focus on the water as the most affected habitat.}, } @article {pmid37684331, year = {2023}, author = {Sun, J and Germain, A and Kaglan, G and Servant, F and Lelouvier, B and Federici, M and Fernandez-Real, JM and Sala, DT and Neagoe, RM and Bouloumié, A and Burcelin, R}, title = {Correction: The visceral adipose tissue bacterial microbiota provides a signature of obesity based on inferred metagenomic functions.}, journal = {International journal of obesity (2005)}, volume = {47}, number = {10}, pages = {1028}, doi = {10.1038/s41366-023-01377-3}, pmid = {37684331}, issn = {1476-5497}, } @article {pmid37684300, year = {2023}, author = {Kozhar, O and Sitz, RA and Woyda, R and Legg, L and Ibarra Caballero, JR and Pearse, IS and Abdo, Z and Stewart, JE}, title = {Population genomic analysis of an emerging pathogen Lonsdalea quercina affecting various species of oaks in western North America.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {14852}, pmid = {37684300}, issn = {2045-2322}, mesh = {*Quercus/genetics ; Ecosystem ; Metagenomics ; Phylogeny ; Enterobacteriaceae ; *Geraniaceae ; North America ; }, abstract = {Understanding processes leading to disease emergence is important for effective disease management and prevention of future epidemics. Utilizing whole genome sequencing, we studied the phylogenetic relationship and diversity of two populations of the bacterial oak pathogen Lonsdalea quercina from western North America (Colorado and California) and compared these populations to other Lonsdalea species found worldwide. Phylogenetic analysis separated Colorado and California populations into two Lonsdalea clades, with genetic divergence near species boundaries, suggesting long isolation and populations that differ in genetic structure and distribution and possibly their polyphyletic origin. Genotypes collected from different host species and habitats were randomly distributed within the California cluster. Most Colorado isolates from introduced planted trees, however, were distinct from three isolates collected from a natural stand of Colorado native Quercus gambelii, indicating cryptic population structure. The California identical core genotypes distribution varied, while Colorado identical core genotypes were always collected from neighboring trees. Despite its recent emergence, the Colorado population had higher nucleotide diversity, possibly due to its long presence in Colorado or due to migrants moving with nursery stock. Overall, results suggest independent pathogen emergence in two states likely driven by changes in host-microbe interactions due to ecosystems changes. Further studies are warranted to understand evolutionary relationships among L. quercina from different areas, including the red oak native habitat in northeastern USA.}, } @article {pmid37684262, year = {2023}, author = {Han, Y and Zhang, C and Zhao, Z and Peng, Y and Liao, J and Jiang, Q and Liu, Q and Shao, Z and Dong, X}, title = {A comprehensive genomic catalog from global cold seeps.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {596}, pmid = {37684262}, issn = {2052-4463}, support = {2023M734096//China Postdoctoral Science Foundation/ ; 2022M723709//China Postdoctoral Science Foundation/ ; }, mesh = {Databases, Factual ; *Genomics ; Knowledge ; *Metagenome ; Metagenomics ; Bacteria ; Archaea ; }, abstract = {Cold seeps harbor abundant and diverse microbes with tremendous potential for biological applications and that have a significant influence on biogeochemical cycles. Although recent metagenomic studies have expanded our understanding of the community and function of seep microorganisms, knowledge of the diversity and genetic repertoire of global seep microbes is lacking. Here, we collected a compilation of 165 metagenomic datasets from 16 cold seep sites across the globe to construct a comprehensive gene and genome catalog. The non-redundant gene catalog comprised 147 million genes, and 36% of them could not be assigned to a function with the currently available databases. A total of 3,164 species-level representative metagenome-assembled genomes (MAGs) were obtained, most of which (94%) belonged to novel species. Of them, 81 ANME species were identified that cover all subclades except ANME-2d, and 23 syntrophic SRB species spanned the Seep-SRB1a, Seep-SRB1g, and Seep-SRB2 clades. The non-redundant gene and MAG catalog is a valuable resource that will aid in deepening our understanding of the functions of cold seep microbiomes.}, } @article {pmid37683845, year = {2023}, author = {Kang, J and Qiu, W and Zhang, W and Liu, J and Yang, Z and Wu, Z and Ge, J}, title = {Understanding how various forms of phosphorus stress affect microbiome functions and boost plant disease resistance: Insights from metagenomic analysis.}, journal = {The Science of the total environment}, volume = {904}, number = {}, pages = {166899}, doi = {10.1016/j.scitotenv.2023.166899}, pmid = {37683845}, issn = {1879-1026}, mesh = {*Disease Resistance ; Soil Microbiology ; *Microbiota ; Metagenome ; Plant Diseases/microbiology ; Rhizosphere ; Soil ; Plant Roots/microbiology ; }, abstract = {The plant's response to phosphorus (P) starvation suppresses its immunity and regulates rhizosphere microbial colonization. However, the impact of various P forms on plant disease resistance and microbial composition remains underreported. This paper examines the soybean rhizosphere microbiome facing co-stress from Fusarium oxysporum and diverse P forms. Macrogenomic analysis evaluates whether P addition enhances plant disease resistance and rhizosphere microbial function, and if such effects relate to P forms. Results show that different P forms mitigate F. oxysporum-induced plant inhibition by promoting P turnover. P forms predominantly affect microbial composition, followed by soil and plant properties. In soybean, the phosphate transport strategy (ugpA/Q) was selected to maintain high P to enhance immunity in the KH2PO4 treatment, while organo-P mineralization (phnH/F/W/G) was selected for superphosphate treatment. The Frankiales, a P-turnover microorganism, copiotrophic microorganisms, and indicator bacteria of plant properties, initially increase after F. oxysporum inoculation and then decrease post P addition, regardless of P forms. Additionally, the rhizosphere microbial community's metabolic activities and compounds significantly aid soybean defense against F. oxysporum, with functional types depending on P forms. Therefore, these findings establish a novel approach to enhance host defense against soil-borne diseases through P nutrition regulation to mediate host-driven metabolic activities of microbial communities.}, } @article {pmid37683634, year = {2023}, author = {Wang, Y and Gallagher, LA and Andrade, PA and Liu, A and Humphreys, IR and Turkarslan, S and Cutler, KJ and Arrieta-Ortiz, ML and Li, Y and Radey, MC and McLean, JS and Cong, Q and Baker, D and Baliga, NS and Peterson, SB and Mougous, JD}, title = {Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle.}, journal = {Cell}, volume = {186}, number = {22}, pages = {4803-4817.e13}, pmid = {37683634}, issn = {1097-4172}, support = {R01 AI128215/AI/NIAID NIH HHS/United States ; R01 AI141953/AI/NIAID NIH HHS/United States ; R01 DE023810/DE/NIDCR NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {*Bacteria/classification/genetics/growth & development ; Metagenome ; Metagenomics ; Phylogeny ; Actinobacteria/physiology ; }, abstract = {Patescibacteria, also known as the candidate phyla radiation (CPR), are a diverse group of bacteria that constitute a disproportionately large fraction of microbial dark matter. Its few cultivated members, belonging mostly to Saccharibacteria, grow as epibionts on host Actinobacteria. Due to a lack of suitable tools, the genetic basis of this lifestyle and other unique features of Patescibacteira remain unexplored. Here, we show that Saccharibacteria exhibit natural competence, and we exploit this property for their genetic manipulation. Imaging of fluorescent protein-labeled Saccharibacteria provides high spatiotemporal resolution of phenomena accompanying epibiotic growth, and a transposon-insertion sequencing (Tn-seq) genome-wide screen reveals the contribution of enigmatic Saccharibacterial genes to growth on their hosts. Finally, we leverage metagenomic data to provide cutting-edge protein structure-based bioinformatic resources that support the strain Southlakia epibionticum and its corresponding host, Actinomyces israelii, as a model system for unlocking the molecular underpinnings of the epibiotic lifestyle.}, } @article {pmid37683504, year = {2023}, author = {Chao, H and Balcazar, JL and Wu, Y and Cai, A and Ye, M and Sun, M and Hu, F}, title = {Phages in vermicomposts enrich functional gene content and facilitate pesticide degradation in soil.}, journal = {Environment international}, volume = {179}, number = {}, pages = {108175}, doi = {10.1016/j.envint.2023.108175}, pmid = {37683504}, issn = {1873-6750}, mesh = {Animals ; Cattle ; Swine ; *Pesticides/toxicity ; Fertilizers ; *Bacteriophages/genetics ; Biodegradation, Environmental ; Manure ; Soil ; }, abstract = {Organic fertilizer microbiomes play substantial roles in soil ecological functions, including improving soil structure, crop yield, and pollutant dissipation. However, limited information is available about the ecological functions of phages and phage-encoded auxiliary metabolic genes (AMGs) in orga9nic fertilizers. Here we used a combination of metagenomics and phage transplantation trials to investigate the phage profiles and their potential roles in pesticide degradation in four organic fertilizers from different sources. Phage annotation results indicate that the two vermicomposts made from swine (PV) and cattle (CV) dung had more similar phage community structures than the swine (P) and cattle (C) manures. After vermicomposting, the organic fertilizers (PV and CV) exhibited enriched phage-host pairings and phage AMG diversity in relative to the two organic fertilizers (P and C) without composting. In addition, the number of broad-host-range phages in the vermicomposts (182) was higher than that in swine (153) and cattle (103) manures. Notably, phage AMGs associated with metabolism and pesticide biodegradation were detected across the four organic fertilizers. The phage transplantation demonstrated that vermicompost phages were most effective at facilitating the degradation of pesticide precursor p-nitrochlorobenzene (p-NCB) in soil, as compared to swine and cattle manures (P < 0.05). Taken together, our findings highlight the significance of phages in vermicompost for biogeochemical cycling and biodegradation of pesticide-associated chemicals in contaminated soils.}, } @article {pmid37683382, year = {2023}, author = {Li, X and Ma, R and Zhu, L and Zhang, X and Lin, C and Tang, Y and Huang, Z and Wang, C}, title = {Effects of zero-valent iron and magnetite on ethanol and lactic acid production in the anaerobic fermentation of food waste.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118928}, doi = {10.1016/j.jenvman.2023.118928}, pmid = {37683382}, issn = {1095-8630}, mesh = {Fermentation ; Anaerobiosis ; *Ferrosoferric Oxide ; Food ; *Refuse Disposal ; Ethanol ; Iron ; Lactic Acid ; }, abstract = {With the increasing global concern about food waste management, finding efficient ways to convert it into valuable products is crucial. The addition of zero-valent iron and magnetite to enhance ethanol and lactic acid fermentation yields from food waste emerges as a potential solution. This study compared the effects of 50-nm and 500-nm particle sizes of zero-valent iron and magnetite on ethanol and lactic acid fermentation and analyzed the mechanism of action from the perspective of organic matter material transformation and microbiology. The experimental results showed that 500-nm particle size magnetite and zero-valent iron could promote the hydrolysis of polysaccharides and proteins. 500-nm particle size magnetite could increase ethanol production (1.4-fold of the control), while 500-nm particle size zero-valent iron could increase lactic acid production (2.8-fold of the control). Metagenomic analysis showed that 500-nm magnetite increased the abundance of genes for amino acid metabolic functions, while 500-nm zero-valent iron increased the abundance of glycoside hydrolase genes (1.3-fold of the control). It's worth noting that while these findings are promising, they are based on controlled experimental conditions, and real-world applications may vary. his research not only offers a novel approach to augmenting anaerobic fermentation yields but also contributes to sustainable food waste management practices, potentially reducing environmental impacts and creating valuable products.}, } @article {pmid37683380, year = {2023}, author = {Gong, X and Hou, F and Pang, H and Guo, Y and Zhang, Q and Li, X and Zhang, L and Peng, Y}, title = {Robust and high-efficient nitrogen removal from real sewage and waste activated sludge (WAS) reduction in zero-external carbon PN/A combined with in-situ fermentation-denitrification process under decreased temperatures.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118761}, doi = {10.1016/j.jenvman.2023.118761}, pmid = {37683380}, issn = {1095-8630}, mesh = {Fermentation ; *Sewage ; *Denitrification ; Nitrogen Dioxide ; Temperature ; Carbon ; Nitrogen ; }, abstract = {Despite the advantages of the combined anammox and fermentation-driven denitrification process in nitrogen removal and energy consumption, stable performance at decreased temperatures remains a challenge. In this study, a robust and high-efficient nitrogen removal efficiency (95.0-93.1 ∼ 86.8-93.4%) with desirable effluent quality (3.0-4.1 ∼ 7.9-4.9 mg/L) under long-term decreased temperatures (30 °C→25 °C→20 °C) was achieved in a zero-external carbon Partial Nitritation/Anammox combined with in-situ sludge Fermentation-Denitrification process treating sewage. Excellent sludge reduction averaged at 14.9% assuming no microbial growth. Increased hzsB mRNA (2.2-fold) and reduced Ea (80.9 kJ/mol) proved resilient anammox to lower temperature. RT-qPCR tests revealed increased NarG/NirK (5.1) and NarG/NirS (4.9) mRNA at 20 °C, suggesting higher NO3[-]→NO2[-] over NO2[-]→N2 pathway. Metagenomics unraveled dominant anammox bacteria (Candidatus_Brocadia, 2.27%), increased denitritation bacteria containing more NarG (Hyphomicrobium, 0.8%), fatty acid biosynthesis and CAZymes genes. Enhanced denitritation with recovered organics from sludge reserved nitrite for anammox and facilitated higher anammox contribution to N removal at 20 °C (42.4%) than 30 °C (39.5%). This study proposed an innovative low-temperature strategy for in-situ sludge fermentation, and demonstrated stability of advanced municipal wastewater treatment and sludge disposal through energy savings and carbon recovery under decreased temperatures.}, } @article {pmid37682363, year = {2023}, author = {Sepúlveda-Correa, A and Monsalve, L and Polania, J and Mestanza, O and Vanegas, J}, title = {Effect of salinity on genes involved in the stress response in mangrove soils.}, journal = {Antonie van Leeuwenhoek}, volume = {116}, number = {11}, pages = {1171-1184}, pmid = {37682363}, issn = {1572-9699}, support = {123365944129//Ministerio de Ciencia, Tecnología e Innovación de Colombia/ ; }, mesh = {*Ecosystem ; *Salinity ; Soil ; Metagenome ; Caribbean Region ; }, abstract = {Mangroves are a challenging ecosystem for the microorganisms that inhabit them, considering they are subjected to stressful conditions such as high and fluctuating salinity. Metagenomic analysis of mangrove soils under contrasting salinity conditions was performed at the mouth of the Ranchera River to the Caribbean Sea in La Guajira, Colombia, using shotgun sequencing and the Illumina Hiseq 2500 platform. Functional gene analysis demonstrated that salinity could influence the abundance of microbial genes involved in osmoprotectant transport, DNA repair, heat shock proteins (HSP), and Quorum Sensing, among others. In total, 135 genes were discovered to be linked to 12 pathways. Thirty-four genes out of 10 pathways had statistical differences for a p-value and FDR < 0.05. UvrA and uvrB (nucleotide excision repair), groEL (HSP), and secA (bacterial secretion system) genes were the most abundant and were enriched by high salinity. The results of this study showed the prevalence of diverse genetic mechanisms that bacteria use as a response to survive in the challenging mangrove, as well as the presence of various genes that are recruited in order to maintain bacterial homeostasis under conditions of high salinity.}, } @article {pmid37680745, year = {2023}, author = {Yang, L and Peng, L and Yuan, K and Cai, K and Feng, C and Yang, G and Wang, S and Zhu, X and Zhang, J and Wang, F and Lu, H}, title = {Case Report: Mycobacterium kansasii causing infective endocarditis explored by metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1227537}, pmid = {37680745}, issn = {2235-2988}, mesh = {Male ; Humans ; Middle Aged ; *Mycobacterium kansasii/genetics ; DNA Copy Number Variations ; *Endocarditis/diagnosis ; *Endocarditis, Bacterial/diagnosis ; High-Throughput Nucleotide Sequencing ; }, abstract = {In this report, we describe the first case of infective endocarditis caused by Mycobacterium kansasii in a 45-year-old male patient who presented with a 10-day fever and decompensated cirrhosis. Despite negative results in blood culture and pathology, we employed metagenomic next-generation sequencing (mNGS) to analyze the genome sequences of both the host and microbe. The copy number variation (CNV) indicated a high risk of liver disease in the patient, which correlated with biochemical examination findings. Notably, M. kansasii sequences were detected in peripheral blood samples and confirmed through Sanger sequencing. Unfortunately, the patient's condition deteriorated, leading to his demise prior to heart surgery. Nevertheless, we propose that mNGS could be a novel approach for diagnosing M. kansasii infection, particularly in cases where blood culture and pathology results are unavailable. It is important to consider M. kansasii infection as a potential cause of endocarditis and initiate appropriate anti-infection treatment.}, } @article {pmid37680532, year = {2023}, author = {Katagiri, S and Ohsugi, Y and Shiba, T and Yoshimi, K and Nakagawa, K and Nagasawa, Y and Uchida, A and Liu, A and Lin, P and Tsukahara, Y and Iwata, T and Tohara, H}, title = {Homemade blenderized tube feeding improves gut microbiome communities in children with enteral nutrition.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1215236}, pmid = {37680532}, issn = {1664-302X}, abstract = {Enteral nutrition for children is supplied through nasogastric or gastrostomy tubes. Diet not only influences nutritional intake but also interacts with the composition and function of the gut microbiota. Homemade blenderized tube feeding has been administered to children receiving enteral nutrition, in addition to ready-made tube feeding. The purpose of this study was to evaluate the oral/gut microbial communities in children receiving enteral nutrition with or without homemade blenderized tube feeding. Among a total of 30 children, 6 receiving mainly ready-made tube feeding (RTF) and 5 receiving mainly homemade blenderized tube feeding (HBTF) were analyzed in this study. Oral and gut microbiota community profiles were evaluated through 16S rRNA sequencing of saliva and fecal samples. The α-diversity representing the number of observed features, Shannon index, and Chao1 in the gut were significantly increased in HBTF only in the gut microbiome but not in the oral microbiome. In addition, the relative abundances of the phylum Proteobacteria, class Gammaproteobacteria, and genus Escherichia-Shigella were significantly low, whereas that of the genus Ruminococcus was significantly high in the gut of children with HBTF, indicating HBTF altered the gut microbial composition and reducing health risks. Metagenome prediction showed enrichment of carbon fixation pathways in prokaryotes at oral and gut microbiomes in children receiving HBTF. In addition, more complex network structures were observed in the oral cavity and gut in the HBTF group than in the RTF group. In conclusion, HBTF not only provides satisfaction and enjoyment during meals with the family but also alters the gut microbial composition to a healthy state.}, } @article {pmid37680465, year = {2023}, author = {Liu, H and Liu, WW and Haro-Moreno, JM and Xu, B and Zheng, Y and Liu, J and Tian, J and Zhang, XH and Zhou, NY and Qin, L and Zhu, Y and Rodriguez-Valera, F and Zhang, C}, title = {A moderately thermophilic origin of a novel family of marine group II euryarchaeota from deep ocean.}, journal = {iScience}, volume = {26}, number = {9}, pages = {107664}, pmid = {37680465}, issn = {2589-0042}, abstract = {Marine group II (MGII) is the most abundant planktonic heterotrophic archaea in the ocean. The evolutionary history of MGII archaea is elusive. In this study, 13 new MGII metagenome-assembled genomes were recovered from surface to the hadal zone in Challenger Deep of the Mariana Trench; four of them from the deep ocean represent a novel group. The optimal growth temperature (OGT) of the common ancestor of MGII has been estimated to be at about 60°C and OGTs of MGIIc, MGIIb, and MGIIa at 47°C-50ºC, 37°C-44ºC, and 30°C-37ºC, respectively, suggesting the adaptation of these species to different temperatures during evolution. The estimated OGT range of MGIIc was supported by experimental measurements of cloned β-galactosidase that showed optimal enzyme activity around 50°C. These results indicate that MGIIc may have originated from a common ancestor that lived in warm or even hot marine environment, such as hydrothermal vents.}, } @article {pmid37680359, year = {2023}, author = {Yuan, T and Qazi, IH and Li, J and Yang, P and Yang, H and Zhang, X and Liu, W and Liu, J}, title = {Analysis of changes in bacterial diversity in healthy and bacterial wilt mulberry samples using metagenomic sequencing and culture-dependent approaches.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1206691}, pmid = {37680359}, issn = {1664-462X}, abstract = {INTRODUCTION: Mulberry bacterial wilt is a serious destructive soil-borne disease caused by a complex and diverse group of pathogenic bacteria. Given that the bacterial wilt has been reported to cause a serious damage to the yield and quality of mulberry, therefore, elucidation of its main pathogenic groups is essential in improving our understanding of this disease and for the development of its potential control measures.

METHODS: In this study, combined metagenomic sequencing and culture-dependent approaches were used to investigate the microbiome of healthy and bacterial wilt mulberry samples.

RESULTS: The results showed that the healthy samples had higher bacterial diversity compared to the diseased samples. Meanwhile, the proportion of opportunistic pathogenic and drug-resistant bacterial flora represented by Acinetobacter in the diseased samples was increased, while the proportion of beneficial bacterial flora represented by Proteobacteria was decreased. Ralstonia solanacearum species complex (RSSC), Enterobacter cloacae complex (ECC), Klebsiella pneumoniae, K. quasipneumoniae, K. michiganensis, K. oxytoca, and P. ananatis emerged as the main pathogens of the mulberry bacterial wilt.

DISCUSSION: In conclusion, this study provides a valuable reference for further focused research on the bacterial wilt of mulberry and other plants.}, } @article {pmid37680093, year = {2023}, author = {de la Cuesta-Zuluaga, J and Huus, KE and Youngblut, ND and Escobar, JS and Ley, RE}, title = {Obesity is the main driver of altered gut microbiome functions in the metabolically unhealthy.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2246634}, pmid = {37680093}, issn = {1949-0984}, mesh = {Adult ; Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Obesity ; Adipose Tissue ; Anthropometry ; }, abstract = {Obesity (OB) and cardiometabolic disease are major public health issues linked to changes in the gut microbiome. OB and poor cardiometabolic health status (CHS) are often comorbid, which hinders efforts to identify components of the microbiome uniquely linked to either one. Here, we used a deeply phenotyped cohort of 408 adults from Colombia, including subjects with OB, unhealthy CHS, or both, to validate previously reported features of gut microbiome function and diversity independently correlated with OB or CHS using fecal metagenomes. OB was defined by body mass index, waist circumference, and body fat; CHS as healthy or unhealthy according to blood biochemistry and anthropometric data. We found that OB, more so than metabolic status, drove associations with gut microbiome structure and functions. The microbiome of obese individuals with and without co-existing unhealthy CHS was characterized by reduced metagenomic diversity, reduced fermentative potential and elevated capacity to respond to oxidative stress and produce bacterial antigens. Disease-linked features were correlated with increased host blood pressure and inflammatory markers, and were mainly contributed by members of the family Enterobacteriaceae. Our results link OB with a microbiome able to tolerate an inflammatory and oxygenated gut state, and suggest that OB is the main driver of microbiome functional differences when poor CHS is a comorbidity.}, } @article {pmid37679777, year = {2023}, author = {Huang, W and Wang, F and Cai, Q and Xu, H and Hong, D and Wu, H and Zhou, L and Hu, L and Lu, Y}, title = {Epidemiological and clinical characteristics of psittacosis among cases with complicated or atypical pulmonary infection using metagenomic next-generation sequencing: a multi-center observational study in China.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {22}, number = {1}, pages = {80}, pmid = {37679777}, issn = {1476-0711}, support = {ZD2021CY001//Science and Technology Commission of Shanghai Municipality/ ; }, mesh = {Humans ; Middle Aged ; *Psittacosis/diagnosis/epidemiology ; *Coinfection ; High-Throughput Nucleotide Sequencing ; Candida albicans ; China/epidemiology ; *Pneumonia/epidemiology ; }, abstract = {BACKGROUND: Chlamydia psittaci (C. psittaci) causes parrot fever in humans. Development of metagenomic next-generation sequencing (mNGS) enables the identification of C. psittaci.

METHODS: This study aimed to determine the epidemiological and clinical characteristics of parrot fever cases in China. A multi-center observational study was conducted in 44 tertiary and secondary hospitals across 14 provinces and municipalities between April 2019 and October 2021.

RESULTS: A total of 4545 patients with complicated or atypical pulmonary infection were included in the study, among which the prevalence of C. psittaci was determined to be 2.1% using mNGS. The prevalence of C. psittaci was further determined across demographic groups and types of specimens. It was significantly higher in patients with senior age (2.6% in those > 50 years), winter-spring (3.6%; particularly in December, January, and February), and southwestern (3.4%) and central and southern China (2.7%) (each P < 0.001). Moreover, the prevalence was the highest in bronchoalveolar lavage fluid (BALF) (2.9%), compared with sputum (1.1%) and peripheral blood specimens (0.9%). Additionally, co-infection of principal microorganisms was compared. Certain microorganisms were more likely to co-infect in parrot fever cases, such as Candida albicans in BALF (26.7%) and peripheral blood (6.3%), compared with non-parrot fever cases (19.7% and 1.3%); however, they did not significantly differ (each P > 0.05).

CONCLUSION: Parrot fever remains low in patients with complicated or atypical pulmonary infection. It is likely to occur in winter-spring and southwestern region in China. BALF may be the optimal specimen in the application of mNGS. Co-infection of multiple microorganisms should be further considered.}, } @article {pmid37679638, year = {2023}, author = {Heine, PA and Ballmann, R and Thevarajah, P and Russo, G and Moreira, GMSG and Hust, M}, title = {Biomarker Discovery by ORFeome Phage Display.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2702}, number = {}, pages = {543-561}, pmid = {37679638}, issn = {1940-6029}, mesh = {*Biomedical Research ; Antibodies ; Bacteriophage M13/genetics ; Biological Assay ; Cell Surface Display Techniques ; }, abstract = {Phage display is an efficient and robust method for protein-protein interaction studies. Although it is mostly used for antibody generation, it can be also utilized for the discovery of immunogenic proteins that could be used as biomarkers. Through this technique, a genome or metagenome is fragmented and cloned into a phagemid vector. The resulting protein fragments from this genetic material are displayed on M13 phage surface, while the corresponding gene fragments are packaged. This packaging process uses the pIII deficient helperphage, called Hyperphage (M13KO7 ΔpIII), so open reading frames (ORFs) are enriched in these libraries, giving the name to this method: ORFeome phage display. After conducting a selection procedure, called "bio-panning," relevant immunogenic peptides or protein fragments are selected using purified antibodies or serum samples, and can be used as potential biomarkers. As ORFeome phage display is an in vitro method, only the DNA or cDNA of the species of interest is needed. Therefore, this approach is also suitable for organisms that are hard to cultivate, or metagenomic samples, for example. An additional advantage is that the biomarker discovery is not limited to surface proteins due to the presentation of virtually every kind of peptide or protein fragment encoded by the ORFeome on the phage surface. At last, the selected biomarkers can be the start for the development of diagnostic assays, vaccines, or protein interaction studies.}, } @article {pmid37679429, year = {2023}, author = {Singh, A and Schnürer, A and Dolfing, J and Westerholm, M}, title = {Syntrophic entanglements for propionate and acetate oxidation under thermophilic and high-ammonia conditions.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {1966-1978}, pmid = {37679429}, issn = {1751-7370}, mesh = {*Propionates/metabolism ; Ammonia/metabolism ; Anaerobiosis ; Bacteria/genetics/metabolism ; Acetates/metabolism ; Methanobacteriaceae ; *Euryarchaeota/metabolism ; Formates/metabolism ; Hydrogen/metabolism ; Methane/metabolism ; }, abstract = {Propionate is a key intermediate in anaerobic digestion processes and often accumulates in association with perturbations, such as elevated levels of ammonia. Under such conditions, syntrophic ammonia-tolerant microorganisms play a key role in propionate degradation. Despite their importance, little is known about these syntrophic microorganisms and their cross-species interactions. Here, we present metagenomes and metatranscriptomic data for novel thermophilic and ammonia-tolerant syntrophic bacteria and the partner methanogens enriched in propionate-fed reactors. A metagenome for a novel bacterium for which we propose the provisional name 'Candidatus Thermosyntrophopropionicum ammoniitolerans' was recovered, together with mapping of its highly expressed methylmalonyl-CoA pathway for syntrophic propionate degradation. Acetate was degraded by a novel thermophilic syntrophic acetate-oxidising candidate bacterium. Electron removal associated with syntrophic propionate and acetate oxidation was mediated by the hydrogen/formate-utilising methanogens Methanoculleus sp. and Methanothermobacter sp., with the latter observed to be critical for efficient propionate degradation. Similar dependence on Methanothermobacter was not seen for acetate degradation. Expression-based analyses indicated use of both H2 and formate for electron transfer, including cross-species reciprocation with sulphuric compounds and microbial nanotube-mediated interspecies interactions. Batch cultivation demonstrated degradation rates of up to 0.16 g propionate L[-1] day[-1] at hydrogen partial pressure 4-30 Pa and available energy was around -20 mol[-1] propionate. These observations outline the multiple syntrophic interactions required for propionate oxidation and represent a first step in increasing knowledge of acid accumulation in high-ammonia biogas production systems.}, } @article {pmid37679419, year = {2023}, author = {Lagou, V and Jiang, L and Ulrich, A and Zudina, L and González, KSG and Balkhiyarova, Z and Faggian, A and Maina, JG and Chen, S and Todorov, PV and Sharapov, S and David, A and Marullo, L and Mägi, R and Rujan, RM and Ahlqvist, E and Thorleifsson, G and Gao, Η and Εvangelou, Ε and Benyamin, B and Scott, RA and Isaacs, A and Zhao, JH and Willems, SM and Johnson, T and Gieger, C and Grallert, H and Meisinger, C and Müller-Nurasyid, M and Strawbridge, RJ and Goel, A and Rybin, D and Albrecht, E and Jackson, AU and Stringham, HM and Corrêa, IR and Farber-Eger, E and Steinthorsdottir, V and Uitterlinden, AG and Munroe, PB and Brown, MJ and Schmidberger, J and Holmen, O and Thorand, B and Hveem, K and Wilsgaard, T and Mohlke, KL and Wang, Z and , and Shmeliov, A and den Hoed, M and Loos, RJF and Kratzer, W and Haenle, M and Koenig, W and Boehm, BO and Tan, TM and Tomas, A and Salem, V and Barroso, I and Tuomilehto, J and Boehnke, M and Florez, JC and Hamsten, A and Watkins, H and Njølstad, I and Wichmann, HE and Caulfield, MJ and Khaw, KT and van Duijn, CM and Hofman, A and Wareham, NJ and Langenberg, C and Whitfield, JB and Martin, NG and Montgomery, G and Scapoli, C and Tzoulaki, I and Elliott, P and Thorsteinsdottir, U and Stefansson, K and Brittain, EL and McCarthy, MI and Froguel, P and Sexton, PM and Wootten, D and Groop, L and Dupuis, J and Meigs, JB and Deganutti, G and Demirkan, A and Pers, TH and Reynolds, CA and Aulchenko, YS and Kaakinen, MA and Jones, B and Prokopenko, I and , }, title = {GWAS of random glucose in 476,326 individuals provide insights into diabetes pathophysiology, complications and treatment stratification.}, journal = {Nature genetics}, volume = {55}, number = {9}, pages = {1448-1461}, pmid = {37679419}, issn = {1546-1718}, support = {/WT_/Wellcome Trust/United Kingdom ; R01 DK072193/DK/NIDDK NIH HHS/United States ; U01 DK105535/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Glucose ; Genome-Wide Association Study ; Blood Glucose/genetics ; *Diabetes Mellitus, Type 2/genetics ; Colon ; }, abstract = {Conventional measurements of fasting and postprandial blood glucose levels investigated in genome-wide association studies (GWAS) cannot capture the effects of DNA variability on 'around the clock' glucoregulatory processes. Here we show that GWAS meta-analysis of glucose measurements under nonstandardized conditions (random glucose (RG)) in 476,326 individuals of diverse ancestries and without diabetes enables locus discovery and innovative pathophysiological observations. We discovered 120 RG loci represented by 150 distinct signals, including 13 with sex-dimorphic effects, two cross-ancestry and seven rare frequency signals. Of these, 44 loci are new for glycemic traits. Regulatory, glycosylation and metagenomic annotations highlight ileum and colon tissues, indicating an underappreciated role of the gastrointestinal tract in controlling blood glucose. Functional follow-up and molecular dynamics simulations of lower frequency coding variants in glucagon-like peptide-1 receptor (GLP1R), a type 2 diabetes treatment target, reveal that optimal selection of GLP-1R agonist therapy will benefit from tailored genetic stratification. We also provide evidence from Mendelian randomization that lung function is modulated by blood glucose and that pulmonary dysfunction is a diabetes complication. Our investigation yields new insights into the biology of glucose regulation, diabetes complications and pathways for treatment stratification.}, } @article {pmid37679294, year = {2023}, author = {Umar, M and Bowman, JP and Asis, C and McConchie, C and Eyles, A and Stanley, R and Gracie, A}, title = {Microbial communities associated with resin canal discoloration in mango fruit.}, journal = {Letters in applied microbiology}, volume = {76}, number = {9}, pages = {}, doi = {10.1093/lambio/ovad104}, pmid = {37679294}, issn = {1472-765X}, support = {IC140100024//Australian Research Council/ ; }, mesh = {*Mangifera ; Fruit ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Enterobacteriaceae ; }, abstract = {Resin canal discoloration (RCD) severely impacts the fruit quality of mango, diminishes consumer confidence, and reduces sales, but the biological cause is still unclear. Using next-generation sequencing, the overall microbial community composition of RCD+ and visually healthy mango fruits was determined for the first time to examine the possible role of bacterial and fungal pathogens in RCD. The diversity profile of bacterial and fungal communities was determined using primers targeting the 16S rRNA gene and Internal Transcribed Spacer (ITS) regions. Results showed that bacterial communities in healthy fruits are clustered together and significantly different from those in RCD+ fruits. Tatumella and Pantoea species were the most abundant bacterial taxa on RCD+ fruit, and both have been linked to disease outbreaks in a variety of fruit crops. Fungal communities were generally similar between RCD+ and normal samples, though non-pathogenic yeasts Meyerozyma and Naganishia tended to dominate the fungal communities on RCD+ fruit. The study indicates that bacteria rather than fungal organisms are more likely to be associated with RCD in mango. This finding will facilitate the isolation and confirmation of RCD-causing organisms and the development of control strategies to manage RCD problem in mango.}, } @article {pmid37678712, year = {2023}, author = {Bohn, T and Balbuena, E and Ulus, H and Iddir, M and Wang, G and Crook, N and Eroglu, A}, title = {Carotenoids in Health as Studied by Omics-Related Endpoints.}, journal = {Advances in nutrition (Bethesda, Md.)}, volume = {14}, number = {6}, pages = {1538-1578}, pmid = {37678712}, issn = {2156-5376}, mesh = {Animals ; Humans ; *Carotenoids/metabolism ; *Diabetes Mellitus, Type 2 ; Inflammation ; Antioxidants/pharmacology ; Lutein ; Mammals/metabolism ; }, abstract = {Carotenoids have been associated with risk reduction for several chronic diseases, including the association of their dietary intake/circulating levels with reduced incidence of obesity, type 2 diabetes, certain types of cancer, and even lower total mortality. In addition to some carotenoids constituting vitamin A precursors, they are implicated in potential antioxidant effects and pathways related to inflammation and oxidative stress, including transcription factors such as nuclear factor κB and nuclear factor erythroid 2-related factor 2. Carotenoids and metabolites may also interact with nuclear receptors, mainly retinoic acid receptor/retinoid X receptor and peroxisome proliferator-activated receptors, which play a role in the immune system and cellular differentiation. Therefore, a large number of downstream targets are likely influenced by carotenoids, including but not limited to genes and proteins implicated in oxidative stress and inflammation, antioxidation, and cellular differentiation processes. Furthermore, recent studies also propose an association between carotenoid intake and gut microbiota. While all these endpoints could be individually assessed, a more complete/integrative way to determine a multitude of health-related aspects of carotenoids includes (multi)omics-related techniques, especially transcriptomics, proteomics, lipidomics, and metabolomics, as well as metagenomics, measured in a variety of biospecimens including plasma, urine, stool, white blood cells, or other tissue cellular extracts. In this review, we highlight the use of omics technologies to assess health-related effects of carotenoids in mammalian organisms and models.}, } @article {pmid37676707, year = {2023}, author = {Kapel, N and Kalimeris, E and Lumley, S and Decano, A and Rodger, G and Lopes Alves, M and Dingle, K and Oakley, S and Barrett, L and Barnett, S and Crook, D and Eyre, DW and Matthews, PC and Street, T and Stoesser, N}, title = {Evaluation of sequence hybridization for respiratory viruses using the Twist Bioscience Respiratory Virus Research panel and the OneCodex Respiratory Virus sequence analysis workflow.}, journal = {Microbial genomics}, volume = {9}, number = {9}, pages = {}, pmid = {37676707}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; /DH_/Department of Health/United Kingdom ; 110110/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Workflow ; *Hybridization, Genetic ; Nucleic Acid Hybridization ; *Computational Biology ; Multiplex Polymerase Chain Reaction ; }, abstract = {Respiratory viral infections are a major global clinical problem, and rapid, cheap, scalable and agnostic diagnostic tests that capture genome-level information on viral variation are urgently needed. Metagenomic approaches would be ideal, but remain currently limited in that much of the genetic content in respiratory samples is human, and amplifying and sequencing the viral/pathogen component in an unbiased manner is challenging. PCR-based tests, including those which detect multiple pathogens, are already widely used, but do not capture information on strain-level variation; tests with larger viral repertoires are also expensive on a per-test basis. One intermediate approach is the use of large panels of viral probes or 'baits', which target or 'capture' sequences representing complete genomes amongst several different common viral pathogens; these are then amplified, sequenced and analysed with a sequence analysis workflow. Here we evaluate one such commercial bait capture method (the Twist Bioscience Respiratory Virus Research Panel) and sequence analysis workflow (OneCodex), using control (simulated) and patient samples head-to-head with a validated multiplex PCR clinical diagnostic test (BioFire FilmArray). We highlight the limited sensitivity and specificity of the joint Twist Bioscience/OneCodex approach, which are further reduced by shortening workflow times and increasing sample throughput to reduce per-sample costs. These issues with performance may be driven by aspects of both the laboratory (e.g. capacity to enrich for viruses present in low numbers), bioinformatics methods used (e.g. a limited viral reference database) and thresholds adopted for calling a virus as present or absent. As a result, this workflow would require further optimization prior to any implementation for respiratory virus characterization in a routine diagnostic healthcare setting.}, } @article {pmid37675977, year = {2023}, author = {King, WL and Yates, CF and Cao, L and O'Rourke-Ibach, S and Fleishman, SM and Richards, SC and Centinari, M and Hafner, BD and Goebel, M and Bauerle, T and Kim, YM and Nicora, CD and Anderton, CR and Eissenstat, DM and Bell, TH}, title = {Functionally discrete fine roots differ in microbial assembly, microbial functional potential, and produced metabolites.}, journal = {Plant, cell & environment}, volume = {46}, number = {12}, pages = {3919-3932}, doi = {10.1111/pce.14705}, pmid = {37675977}, issn = {1365-3040}, support = {//USDA National Institute of Food and Agriculture/ ; //DOE Biological and Environmental Research program/ ; //DOE Environmental Molecular Sciences Laboratory/ ; //NSF Centre for Research on Programmable Plant Systems/ ; }, mesh = {*Plant Roots/microbiology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics ; Rhizosphere ; Fungi ; Soil Microbiology ; }, abstract = {Traditionally, fine roots were grouped using arbitrary size categories, rarely capturing the heterogeneity in physiology, morphology and functionality among different fine root orders. Fine roots with different functional roles are rarely separated in microbiome-focused studies and may result in confounding microbial signals and host-filtering across different root microbiome compartments. Using a 26-year-old common garden, we sampled fine roots from four temperate tree species that varied in root morphology and sorted them into absorptive and transportive fine roots. The rhizoplane and rhizosphere were characterized using 16S rRNA gene and internal transcribed spacer region amplicon sequencing and shotgun metagenomics for the rhizoplane to identify potential microbial functions. Fine roots were subject to metabolomics to spatially characterize resource availability. Both fungi and bacteria differed according to root functional type. We observed additional differences between the bacterial rhizoplane and rhizosphere compartments for absorptive but not transportive fine roots. Rhizoplane bacteria, as well as the root metabolome and potential microbial functions, differed between absorptive and transportive fine roots, but not the rhizosphere bacteria. Functional differences were driven by sugar transport, peptidases and urea transport. Our data highlights the importance of root function when examining root-microbial relationships, emphasizing different host selective pressures imparted on different root microbiome compartments.}, } @article {pmid37675433, year = {2023}, author = {Wei, J and Chen, J and Fang, X and Liu, T and Yuan, Y and Zhang, J}, title = {Protocol for the safety and efficacy of fecal microbiota transplantation liquid in children with autism spectrum disorder: a randomized controlled study.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1236904}, pmid = {37675433}, issn = {1664-302X}, abstract = {BACKGROUND: Autism Spectrum Disorder (ASD) is a neurodevelopmental disorder characterized by deficits in social interaction, repetitive behavior and language impairment, and its worldwide prevalence has been found to be increasing annually in recent years. Till now, ASD is uncurable as its pathogenesis remains unknown. However, studies on both animals and humans have demonstrated that fecal microbiota transplantation (FMT) may ameliorate the symptoms of ASD, as well as gastrointestinal symptoms. Nonetheless, there is still no agreement regarding the optimal dosage or duration of FMT treatment for individuals with ASD.

METHODS: This clinical study is a double-blind, randomized, interventional trial conducted at a single center. The aim is to investigate the safety and efficacy of a pediatric formulation of FMT for ASD. A total of 42 children between the ages of 3-9 with ASD will be randomly assigned in a 2:1 ratio to either an FMT treatment group (n = 28) or a placebo group (n = 14), forming cohort 1. Additionally, 30 healthy children of similar age and gender will be recruited as the control group (cohort 2). Cohort 1 will be assessed using a variety of scales, including the Autism Behavior Checklist, Childhood Autism Rating Scale, Social Responsiveness Scale, Gastrointestinal Symptom Rating Scale, Children's Sleep Habits Questionnaire, and Psychoeducational Profile (Third Edition). These assessments will evaluate the effectiveness of FMT in reducing core symptoms and comorbidities (such as gastrointestinal symptoms and sleep disturbances) in children with ASD. The study will use metagenomic and metabolomic sequencing to assess changes in the composition and structure of the intestinal flora and its metabolites in blood, urine, and feces following treatment. Furthermore, the study will evaluate the acceptability of the FMT formulation by participants' legal guardians and investigate differences in the intestinal flora and metabolism in the FMT group before and after treatment compared to 30 healthy children.

CLINICAL TRIAL REGISTRATION: https://www.chictr.org.cn/, identifier ChiCTR2200058459.}, } @article {pmid37675126, year = {2023}, author = {Shan, H and Wei, C and Zhang, J and He, M and Zhang, Z}, title = {Case Report: Severe Diarrhea Caused by Cryptosporidium Diagnosed by Metagenome Next-Generation Sequencing in Blood.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {5777-5782}, pmid = {37675126}, issn = {1178-6973}, abstract = {BACKGROUND: Cryptosporidium is one of the major pathogens causing diarrhea worldwide. At present, cryptosporidiosis is difficult to prevent and control, especially in immunocompromised hosts. It may cause life-threatening diarrhea and malabsorption among children and immunocompromised patients. Therefore, it is very important to explore rapid diagnostic tools and treatment methods for Cryptosporidium infection.

CASE PRESENTATION: We reported a case of severe diarrhea caused by cryptosporidiosis in a liver transplant recipient, whose condition was finally confirmed by metagenomic next-generation sequencing (mNGS) and fecal microscopy. His illness was resolved with immunosuppression regulation, nitazoxanide administration, and infection control.

CONCLUSION: So far, nitazoxanide is still the first choice for the treatment of cryptosporidiosis. Our institutional experience suggested that nitazoxanide alone may be effective on the basis of adjusting immunosuppressant. In addition, even though diagnosis of Cryptosporidium infection is a challenge, mNGS can serve as a rapid screening tool in low-prevalence setting.}, } @article {pmid37674900, year = {2023}, author = {Moon, JH and Roh, DH and Kwack, KH and Lee, JH}, title = {Bacterial single-cell transcriptomics: Recent technical advances and future applications in dentistry.}, journal = {The Japanese dental science review}, volume = {59}, number = {}, pages = {253-262}, pmid = {37674900}, issn = {1882-7616}, abstract = {Metagenomics and metatranscriptomics have enhanced our understanding of the oral microbiome and its impact on oral health. However, these approaches have inherent limitations in exploring individual cells and the heterogeneity within mixed microbial communities, which restricts our current understanding to bulk cells and species-level information. Fortunately, recent technical advances have enabled the application of single-cell RNA sequencing (scRNA-seq) for studying bacteria, shedding light on cell-to-cell diversity and interactions between host-bacterial cells at the single-cell level. Here, we address the technical barriers in capturing RNA from single bacterial cells and highlight pioneering studies from the past decade. We also discuss recent achievements in host-bacterial dual transcriptional profiling at the single-cell level. Bacterial scRNA-seq provides advantages in various research fields, including the investigation of phenotypic heterogeneity within genetically identical bacteria, identification of rare cell types, detection of antibiotic-resistant or persistent cells, analysis of individual gene expression patterns and metabolic activities, and characterization of specific microbe-host interactions. Integrating single-cell techniques with bulk approaches is essential to gain a comprehensive understanding of oral diseases and develop targeted and personalized treatment in dentistry. The reviewed pioneering studies are expected to inspire future research on the oral microbiome at the single-cell level.}, } @article {pmid37674817, year = {2023}, author = {Cao, L and Ma, Y and Wan, Z and Li, B and Tian, W and Zhang, C and Li, Y}, title = {Longitudinal anellome dynamics in the upper respiratory tract of children with acute respiratory tract infections.}, journal = {Virus evolution}, volume = {9}, number = {2}, pages = {vead045}, pmid = {37674817}, issn = {2057-1577}, abstract = {Anelloviruses (AVs) are ubiquitous in humans and are the most abundant components of the commensal virome. Previous studies on the diversity, transmission, and persistence of AVs mainly focused on the blood or transplanted tissues from adults; however, the profile of the anellome in the respiratory tract in children are barely known. We investigated the anellome profile and their dynamics in the upper respiratory tract from a cohort of children with acute respiratory tract infections (ARTIs). Different to that in adult, betatorquevirus is the most abundant genus, followed by alphatorquevirus. We found that the relative abundance of betatorquevirus was higher in earlier time points, and in contrast, the abundance of alphatorquevirus was higher in later time points; these results might suggest that betatorquevirus decreased with age and alphatorquevirus increased with age in childhood. No difference regarding the diversity and abundance of anellome was found between single and multiple ARTIs, consistent with the idea that AV is not associated with certain disease. Most AVs are transient, and a small proportion (8 per cent) of them were found to be possibly persistent, with persistence time ranging from 1 month to as long as 56 months. Furthermore, the individual respiratory anellome appeared to be unique and dynamic, and the replacement of existing AVs with new ones are common over different time points. These findings demonstrate that betatorquevirus may be the early colonizer in children, and the individual respiratory anellome is unique, which are featured by both chronic infections and AV community replacement.}, } @article {pmid37674718, year = {2023}, author = {Wang, Q and Wang, BY and Pratap, S and Xie, H}, title = {Oral microbiome associated with differential ratios of Porphyromonas gingivalis and Streptococcus cristatus.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {37674718}, support = {R16 GM149359/GM/NIGMS NIH HHS/United States ; U54 MD007586/MD/NIMHD NIH HHS/United States ; }, abstract = {BACKGROUND: Periodontitis has been recently defined as a dysbiotic disease resulting from imbalanced oral microbiota. The transition of microbial communities from commensal to periodontitis-associated ones likely requires colonization by specific pathogens, including Porphyromonas gingivalis. We previously reported an antagonistic relationship between Streptococcus cristatus and P. gingivalis and the role of S. cristatus in inhibition of the biofilm formation, invasion, and gingipain enzymatic activity of P. gingivalis. Given the importance of P. gingivalis as a keystone pathogen of polymicrobial communities, the determinants of P. gingivalis levels, its interaction with the core microbiota, and association with the pathogenic potential of the microbial communities need to be addressed.

RESULTS: This present study intends to determine the role of S. cristatus in altering interactions of P. gingivalis with other oral bacteria in a complex context. We collected dental plaque samples from periodontitis patients and assigned them into two groups based on their ratios of S. cristatus and P. gingivalis. We then characterized microbial profiles of the dental plaque samples using shotgun metagenomic sequencing and subsequently compared oral microbial composition and functional capabilities between groups with high or low S. cristatus-P. gingivalis ratios. Taxonomic annotation showed significant differences in microbial compositions at both genus and species levels between the two groups. Notably, a higher microbial composition diversity was observed in the samples with low S. cristatus-P. gingivalis ratios. The antibiotic resistance gene profiles of the two groups are also distinct, with significantly increased diversity and abundance of antibiotic resistance genes in the dental plaque samples with low S. cristatus-P. gingivalis ratios, which likely lead to elevated virulence potential.

CONCLUSIONS: Overall, our work highlights the importance of S. cristatus-P. gingivalis ratios in influencing the virulence of the oral microbiome. Approaches to enhance S. cristatus-P. gingivalis ratios in oral microbial communities will be attractive for revising the dysbiotic oral microbiome.}, } @article {pmid37674635, year = {2023}, author = {Tekin, A and Truong, HH and Rovati, L and Lal, A and Gerberi, DJ and Gajic, O and O'Horo, JC}, title = {The Diagnostic Accuracy of Metagenomic Next-Generation Sequencing in Diagnosing Pneumocystis Pneumonia: A Systemic Review and Meta-analysis.}, journal = {Open forum infectious diseases}, volume = {10}, number = {9}, pages = {ofad442}, pmid = {37674635}, issn = {2328-8957}, abstract = {BACKGROUND: Pneumocystis pneumonia (PCP) is a growing concern as the immunocompromised population expands. Current laboratory approaches are limited. This systematic review aimed to evaluate metagenomic next-generation sequencing (MNGS) tests' performance in detecting PCP.

METHODS: Five databases were searched through December 19, 2022, to identify original studies comparing MNGS with clinically diagnosed PCP. To assess the accuracy, symmetric hierarchical summary receiver operating characteristic models were used.

RESULTS: Eleven observational studies reporting 1442 patients (424 with PCP) were included. Six studies focused exclusively on recipients of biologic immunosuppression (none with HIV-associated immunosuppression). Six were exclusively on bronchoalveolar lavage, while 1 was on blood samples. The sensitivity of MGNS was 0.96 (95% CI, 0.90-0.99), and specificity was 0.96 (95% CI, 0.92-0.98), with negative and positive likelihood ratios of 0.02 (95% CI, 0.01-0.05) and 19.31 (95% CI, 10.26-36.36), respectively. A subgroup analysis of studies exclusively including bronchoalveolar lavage (BAL) and blood samples demonstrated a sensitivity of 0.94 (95% CI, 0.78-0.99) and 0.93 (95% CI, 0.80-0.98) and a specificity of 0.96 (95% CI, 0.88-0.99) and 0.98 (95% CI, 0.76-1.00), respectively. The sensitivity analysis on recipients of biologic immunosuppression showed a sensitivity and specificity of 0.96 (95% CI, 0.90-0.98) and 0.94 (95% CI, 0.84-0.98), respectively. The overall confidence in the estimates was low.

CONCLUSIONS: Despite the low certainty of evidence, MNGS detects PCP with high sensitivity and specificity. This also applies to recipients of biologic immunosuppression and tests performed exclusively on blood samples without the need for BAL. Further studies are required in individuals with HIV-associated immunosuppression.}, } @article {pmid37674580, year = {2023}, author = {Song, J and Zhu, K and Wang, X and Yang, Q and Yu, S and Zhang, Y and Fu, Z and Wang, H and Zhao, Y and Lin, K and Yuan, G and Guo, J and Shi, Y and Liu, C and Ai, J and Zhang, H and Zhang, W}, title = {Utility of clinical metagenomics in diagnosing malignancies in a cohort of patients with Epstein-Barr virus positivity.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1211732}, pmid = {37674580}, issn = {2235-2988}, mesh = {Humans ; Herpesvirus 4, Human/genetics ; *Epstein-Barr Virus Infections/complications/diagnosis ; Metagenomics ; Retrospective Studies ; *Neoplasms/complications/diagnosis ; *Fever of Unknown Origin ; }, abstract = {BACKGROUNDS: Differentiation between benign and malignant diseases in EBV-positive patients poses a significant challenge due to the lack of efficient diagnostic tools. Metagenomic Next-Generation Sequencing (mNGS) is commonly used to identify pathogens of patients with fevers of unknown-origin (FUO). Recent studies have extended the application of Next-Generation Sequencing (NGS) in identifying tumors in body fluids and cerebrospinal fluids. In light of these, we conducted this study to develop and apply metagenomic methods to validate their role in identifying EBV-associated malignant disease.

METHODS: We enrolled 29 patients with positive EBV results in the cohort of FUO in the Department of Infectious Diseases of Huashan Hospital affiliated with Fudan University from 2018 to 2019. Upon enrollment, these patients were grouped for benign diseases, CAEBV, and malignant diseases according to their final diagnosis, and CNV analysis was retrospectively performed in 2022 using samples from 2018 to 2019.

RESULTS: Among the 29 patients. 16 of them were diagnosed with benign diseases, 3 patients were diagnosed with CAEBV and 10 patients were with malignant diseases. 29 blood samples from 29 patients were tested for mNGS. Among all 10 patients with malignant diagnosis, CNV analysis suggested neoplasms in 9 patients. Of all 19 patients with benign or CAEBV diagnosis, 2 patients showed abnormal CNV results. The sensitivity and specificity of CNV analysis for the identification for tumors were 90% and 89.5%, separately.

CONCLUSIONS: The application of mNGS could assist in the identification of microbial infection and malignancies in EBV-related diseases. Our results demonstrate that CNV detection through mNGS is faster compared to conventional oncology tests. Moreover, the convenient collection of peripheral blood samples adds to the advantages of this approach.}, } @article {pmid37674579, year = {2023}, author = {Zhang, X and Wang, Y and Pen, D and Liu, J and Zhou, Q and Wang, Y and Zhong, H and Liu, T and Chen, W and Wu, B and Zhou, Y and Wang, C and Li, X and Yu, F and Wang, X and Lu, G and Yan, G}, title = {Diagnosis of mixed infection and a primary immunodeficiency disease using next-generation sequencing: a case report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1179090}, pmid = {37674579}, issn = {2235-2988}, mesh = {Male ; Child ; Humans ; *Coinfection ; Aftercare ; Patient Discharge ; High-Throughput Nucleotide Sequencing ; *Primary Immunodeficiency Diseases/diagnosis/genetics ; }, abstract = {Major Histocompatibility Complex Class II (MHC II) deficiency is a rare primary immunodeficiency disorder (PID) with autosomal recessive inheritance pattern. The outcome is almost fatal owing to delayed diagnosis and lacking of effective therapy. Therefore, prompt diagnosis, timely and effective treatment are critical. Here, we report a 117-day-old boy with diarrhea, cough, cyanosis and tachypnea who was failed to be cured by empiric antimicrobial therapy initially and progressed to severe pneumonia and respiratory failure. The patient was admitted to the pediatric intensive care unit (PICU) immediately and underwent a series of tests. Blood examination revealed elevated levels of inflammatory markers and cytomegalovirus DNA. Imaging findings showed signs of severe infection of lungs. Finally, the diagnosis was obtained mainly through next-generation sequencing (NGS). We found out what pathogenic microorganism he was infected via repeated conventional detection methods and metagenomic next-generation sequencing (mNGS) of sputum and bronchoalveolar lavage fluid (BALF). And his whole exome sequencing (WES) examination suggested that CIITA gene was heterozygous mutation, a kind of MHC II deficiency diseases. After aggressive respiratory support and repeated adjustment of antimicrobial regimens, the patient was weaned from ventilator on the 56th day of admission and transferred to the immunology ward on the 60th day. The patient was successful discharged after hospitalizing for 91 days, taking antimicrobials orally to prevent infections post-discharge and waiting for stem cell transplantation. This case highlights the potential importance of NGS in providing better diagnostic testing for unexplained infection and illness. Furthermore, pathogens would be identified more accurately if conventional detection techniques were combined with mNGS.}, } @article {pmid37674578, year = {2023}, author = {Hou, Y and Zhang, M and Jiang, Q and Yang, Y and Liu, J and Yuan, K and Sun, Z and Liu, X}, title = {Microbial signatures of neonatal bacterial meningitis from multiple body sites.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1169101}, pmid = {37674578}, issn = {2235-2988}, mesh = {Infant, Newborn ; Humans ; *Meningitis, Bacterial/diagnosis ; Biomass ; Hospitalization ; Metagenome ; Metagenomics ; }, abstract = {As a common central nervous system infection in newborns, neonatal bacterial meningitis (NBM) can seriously affect their health and growth. However, although metagenomic approaches are being applied in clinical diagnostic practice, there are some limitations for whole metagenome sequencing and amplicon sequencing in handling low microbial biomass samples. Through a newly developed ultra-sensitive metagenomic sequencing method named 2bRAD-M, we investigated the microbial signatures of central nervous system infections in neonates admitted to the neonatal intensive care unit. Particularly, we recruited a total of 23 neonates suspected of having NBM and collected their blood, cerebrospinal fluid, and skin samples for 2bRAD-M sequencing. Then we developed a novel decontamination method (Reads Level Decontamination, RLD) for 2bRAD-M by which we efficiently denoised the sequencing data and found some potential biomarkers that have significantly different relative abundance between 12 patients that were diagnosed as NBM and 11 Non-NBM based on their cerebrospinal fluid (CSF) examination results. Specifically, we discovered 11 and 8 potential biomarkers for NBM in blood and CSF separately and further identified 16 and 35 microbial species that highly correlated with the physiological indicators in blood and CSF. Our study not only provide microbiological evidence to aid in the diagnosis of NBM but also demonstrated the application of an ultra-sensitive metagenomic sequencing method in pathogenesis study.}, } @article {pmid37673908, year = {2023}, author = {Hodgins, HP and Chen, P and Lobb, B and Wei, X and Tremblay, BJM and Mansfield, MJ and Lee, VCY and Lee, PG and Coffin, J and Duggan, AT and Dolphin, AE and Renaud, G and Dong, M and Doxey, AC}, title = {Ancient Clostridium DNA and variants of tetanus neurotoxins associated with human archaeological remains.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5475}, pmid = {37673908}, issn = {2041-1723}, mesh = {Humans ; Animals ; Mice ; *DNA, Ancient ; Neurotoxins ; *Tetanus ; Phylogeny ; Clostridium ; Chile ; Mammals ; }, abstract = {The analysis of microbial genomes from human archaeological samples offers a historic snapshot of ancient pathogens and provides insights into the origins of modern infectious diseases. Here, we analyze metagenomic datasets from 38 human archaeological samples and identify bacterial genomic sequences related to modern-day Clostridium tetani, which produces the tetanus neurotoxin (TeNT) and causes the disease tetanus. These genomic assemblies had varying levels of completeness, and a subset of them displayed hallmarks of ancient DNA damage. Phylogenetic analyses revealed known C. tetani clades as well as potentially new Clostridium lineages closely related to C. tetani. The genomic assemblies encode 13 TeNT variants with unique substitution profiles, including a subgroup of TeNT variants found exclusively in ancient samples from South America. We experimentally tested a TeNT variant selected from an ancient Chilean mummy sample and found that it induced tetanus muscle paralysis in mice, with potency comparable to modern TeNT. Thus, our ancient DNA analysis identifies DNA from neurotoxigenic C. tetani in archaeological human samples, and a novel variant of TeNT that can cause disease in mammals.}, } @article {pmid37673353, year = {2023}, author = {Mao, X and Li, Y and Shi, P and Zhu, Z and Sun, J and Xue, Y and Wan, Z and Yang, D and Ma, T and Wang, J and Zhu, R}, title = {Analysis of sputum microbial flora in chronic obstructive pulmonary disease patients with different phenotypes during acute exacerbations.}, journal = {Microbial pathogenesis}, volume = {184}, number = {}, pages = {106335}, doi = {10.1016/j.micpath.2023.106335}, pmid = {37673353}, issn = {1096-1208}, mesh = {Humans ; *Bronchitis, Chronic ; Sputum ; *Pulmonary Disease, Chronic Obstructive ; Phenotype ; *Asthma ; *Emphysema ; Inflammation ; }, abstract = {BACKGROUND: Increasing studies have shown that the imbalance of the respiratory microbial flora is related to the occurrence of COPD, the severity and frequency of exacerbations and mortality.However, it remains unclear how the sputum microbial flora differs during exacerbations in COPD patients manifesting emphysema phenotype, chronic bronchitis with emphysema phenotype and asthma-COPD overlap phenotype.

METHODS: Sputum samples were obtained from 29 COPD patients experiencing acute exacerbations who had not received antibiotics or systemic corticosteroids within the past four weeks.Patients were divided into three groups;emphysema phenotype(E);chronic bronchitis with emphysema phenotype(B+E) and asthma-COPD overlap phenotype(ACO).We utilized metagenomic Next Generation Sequencing (mNGS) technology to analyze the sputum microbial flora in COPD patients with different phenotypes during exacerbations.

RESULTS: There was no significant difference in alpha diversity and beta diversity among three groups.The microbial flora composition was similar in all three groups during exacerbations except for a significant increase in Streptococcus mitis in ACO.Through network analysis,we found Candidatus Saccharibacteria oral taxon TM7x and Fusobacterium necrophorum were the core nodes of the co-occurrence network in ACO and E respectively.They were positively correlated with some species and play a synergistic role.In B+E,Haemophilus pittmaniae and Klebsiella pneumoniae had a synergistic effect.Besides,some species among the three groups play a synergistic or antagonistic role.Through Spearman analysis,we found the relative abundance of Streptococcus mitis was negatively correlated with the number of hospitalizations in the past year(r = -0.410,P = 0.027).We also observed that the relative abundance of Prevotella and Prevotella melaninogenica was negatively correlated with age(r = -0.534,P = 0.003;r = -0.567,P = 0.001),while the relative abundance of Streptococcus oralis and Actinomyces odontolyticus was positively correlated with age(r = 0.570,P = 0.001;r = 0.480,P = 0.008).In addition,the relative abundance of Prevotella melaninogenica was negatively correlated with peripheral blood neutrophil ratio and neutrophil to lymphocyte ratio(r = -0.479,P = 0.009;r = -0.555,P = 0.002),while the relative abundance of Streptococcus sanguinis was positively correlated with peripheral blood neutrophil ratio and neutrophil to lymphocyte ratio (r = 0.450,P = 0.014;r = 0.501,P = 0.006).There was also a significant positive correlation between Oribacterium and blood eosinophil counts(r = 0.491,P = 0.007).

CONCLUSION: Overall,we analyzed the sputum microbiota of COPD patients with different phenotypes and its relationship with clinical indicators, and explored the relationships between microbiota and inflammation in COPD.We hope to alter the prognosis of patients by inhibiting specific bacterial taxa related to inflammation and using guide individualized treatment in the future research.}, } @article {pmid37673239, year = {2023}, author = {Irit, N and Hana, B and Laura, R and Arielle, K and Mariela, P and Esti, KW and Guadalupe, P and Katja, S and Ariel, K}, title = {Trichocoleus desertorum isolated from Negev desert petroglyphs: Characterization, adaptation and bioerosion potential.}, journal = {The Science of the total environment}, volume = {904}, number = {}, pages = {166739}, doi = {10.1016/j.scitotenv.2023.166739}, pmid = {37673239}, issn = {1879-1026}, mesh = {*Cyanobacteria/metabolism ; Minerals/metabolism ; Weather ; Africa, Northern ; RNA, Ribosomal, 16S ; }, abstract = {The Negev petroglyphs are considered valuable cultural heritage sites, but unfortunately, they are exposed to deterioration processes caused by anthropogenic and natural forces. Despite the many studies that have already pointed to the role of cyanobacteria in biogenic rock weathering, the knowledge involved in the process is still lacking. In this study, a cyanobacterial strain was isolated from the Negev Desert petroglyphs aiming to reveal its involvement in geochemical cycles and in the weathering processes of the rock substrate. The strain was characterized using morphological, molecular, and microscopic studies. The morphological research revealed a green-bluish, bundle-forming filamentous strain characterized by trichomes embedded in a common sheath. A combination of Nanopore and Illumina sequencing technologies facilitated the assembly of a near-complete genome containing 5,458,034 base pairs. A total of 5027 coding sequences were revealed by implementing PROKKA software. Annotation of five replicas of the 16S ribosomal RNA genes revealed that the Negev cyanobacteria isolate is closely (99.73 %) related to Trichocoleus desertorum LSB90_MW403957 isolated from the Sahara Desert, Algeria. The local strain was thus named Trichocoleus desertorum NBK24 CP116619. Several gene sequences that code for possible environmental adaptation mechanisms were found. Our study also identified genes for membrane transporters involved in the exchange of chemical elements, suggesting a possible interaction with rock minerals. Microscopic observations of T. desertorum NBK24 CP116619 infected onto calcareous stone slabs under laboratory conditions demonstrated the effect of the isolated cyanobacteria on stone surface degradation. In conclusion, the findings of this study further our understanding of terrestrial cyanobacterial genomes and functions and highlight the role of T. desertorum NBK24 CP116619 in stone weathering processes. This information may contribute to the creation of efficient restoration strategies for stone monuments affected by cyanobacteria.}, } @article {pmid37673036, year = {2023}, author = {Ni, Y and Qian, L and Siliceo, SL and Long, X and Nychas, E and Liu, Y and Ismaiah, MJ and Leung, H and Zhang, L and Gao, Q and Wu, Q and Zhang, Y and Jia, X and Liu, S and Yuan, R and Zhou, L and Wang, X and Li, Q and Zhao, Y and El-Nezami, H and Xu, A and Xu, G and Li, H and Panagiotou, G and Jia, W}, title = {Resistant starch decreases intrahepatic triglycerides in patients with NAFLD via gut microbiome alterations.}, journal = {Cell metabolism}, volume = {35}, number = {9}, pages = {1530-1547.e8}, doi = {10.1016/j.cmet.2023.08.002}, pmid = {37673036}, issn = {1932-7420}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Microbiota ; *Non-alcoholic Fatty Liver Disease ; Resistant Starch ; Triglycerides ; Humans ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD) is a hepatic manifestation of metabolic dysfunction for which effective interventions are lacking. To investigate the effects of resistant starch (RS) as a microbiota-directed dietary supplement for NAFLD treatment, we coupled a 4-month randomized placebo-controlled clinical trial in individuals with NAFLD (ChiCTR-IOR-15007519) with metagenomics and metabolomics analysis. Relative to the control (n = 97), the RS intervention (n = 99) resulted in a 9.08% absolute reduction of intrahepatic triglyceride content (IHTC), which was 5.89% after adjusting for weight loss. Serum branched-chain amino acids (BCAAs) and gut microbial species, in particular Bacteroides stercoris, significantly correlated with IHTC and liver enzymes and were reduced by RS. Multi-omics integrative analyses revealed the interplay among gut microbiota changes, BCAA availability, and hepatic steatosis, with causality supported by fecal microbiota transplantation and monocolonization in mice. Thus, RS dietary supplementation might be a strategy for managing NAFLD by altering gut microbiota composition and functionality.}, } @article {pmid37672426, year = {2023}, author = {Prado, T and Magalhães, MGP and Moreira, DA and Brandão, ML and Fumian, TM and Ferreira, FC and Chame, M and Leomil, L and Degrave, WMS and Leite, JPG and Miagostovich, MP}, title = {Microbiome and virome on indoor surfaces of an Antarctic research ship.}, journal = {Memorias do Instituto Oswaldo Cruz}, volume = {118}, number = {}, pages = {e230084}, pmid = {37672426}, issn = {1678-8060}, mesh = {Humans ; *Virome ; Ships ; Antarctic Regions ; *Microbiota ; Archaea/genetics ; }, abstract = {BACKGROUND: Few studies have focused on microbial diversity in indoor environments of ships, as well as the role of the microbiome and its ecological interconnections. In this study, we investigated the microbiome and virome present on the internal surfaces of a polar ship in different stages (beginning, during, and at the end) of the Brazilian Antarctic expedition in order to evaluate abundance of microorganisms in different periods.

OBJECTIVES AND METHODS: We used shotgun metagenomic analysis on pooled samples from sampling surfaces in the ship's interior to track the microbial diversity.

FINDINGS: Considering the total fraction of the microbiome, the relative abundance of bacteria, eukaryotes, viruses, and archaea was 83.7%, 16.2%, 0.04%, and 0.002%, respectively. Proteobacteria was the most abundant bacterial phyla, followed by Firmicutes, Actinobacteria, and Bacteroidetes. Concerning the virome, the greatest richness of viral species was identified during the middle of the trip, including ten viral families after de novo assembly: Autographiviridae, Chrysoviridae, Genomoviridae, Herelleviridae, Myoviridae, Partitiviridae, Podoviridae, Potyviridae, Siphoviridae, and Virgaviridae.

MAIN CONCLUSIONS: This study contributed to the knowledge of microbial diversity in naval transportation facilities, and variations in the abundance of microorganisms probably occurred due to factors such as the number of passengers and activities on the ship.}, } @article {pmid37672120, year = {2023}, author = {Díaz-Palafox, G and Tamayo-Ordoñez, YJ and Bello-López, JM and Ayil-Gutiérrez, BA and RodrÍguez-Garza, MM and Antonio Rodríguez-de la Garza, J and Sosa-Santillán, GJ and Acosta-Cruz, E and Ruiz-Marín, A and Córdova-Quiroz, AV and Pérez-Reda, LJ and Tamayo-Ordoñez, FA and Tamayo-Ordoñez, MC}, title = {Regulation Transcriptional of Antibiotic Resistance Genes (ARGs) in Bacteria Isolated from WWTP.}, journal = {Current microbiology}, volume = {80}, number = {10}, pages = {338}, pmid = {37672120}, issn = {1432-0991}, mesh = {*Anti-Bacterial Agents ; *Wastewater ; Bacteria ; Sulfanilamide ; Drug Resistance, Microbial ; }, abstract = {The incidence of antibiotics and transcriptional regulation of ARGs in isolated bacteria from wastewater needs to be explored. By HPLC, in samples of untreated wastewater, ampicillin (49.74 ± 5.70 µg/mL), chloramphenicol (0.60 ± 0.03 µg/mL), tylosin (72.95 ± 2.03 µg/mL), and oxytetracycline (0.22 ± 0.01 µg/mL) was determined. Through metagenomic analysis identified 58 bacterial species belonging to 9 phyla and at least 14 species have shown resistance to a variety of antibiotics. Twenty-two bacterial isolates were proved to be resistant to fifteen antibiotics of new generation and used in medical research to combat infectious diseases. Fourteen strains were shown to harbor plasmids in size ranges of 2-5 Kb, 6-10 Kb and plasmids with size greater than 10 Kb. By quantitative PCR it was possible to identify genes sul, qnr, cat1, aadA1, and sat-1 gene were shown to be present in gDNA samples from treated and untreated samples of wastewater and by relative expression analysis, differential expression of cat1, ermB, act, and tetA genes was demonstrated in strains that showed identity with Escherichia coli, Bacteroides fragilis, and Salmonella thyphi, and that were stressed with different concentrations of antibiotics. The presence of ARGs in untreated water samples, as well as in bacterial isolates, was indicative that in these habitats there are microorganisms that can resist β-lactams, aminoglycosides, tetracyclines, sulfonamides, and quinolones.}, } @article {pmid37671399, year = {2023}, author = {Gao, Y and Wu, Y and Xu, D and Bao, L and Ding, X and Lv, L and Ma, C and Bian, T and Han, S}, title = {Chlamydia psittaci pneumonia in Wuxi, China: retrospective analysis of 55 cases and predictors of severe disease.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1150746}, pmid = {37671399}, issn = {2296-858X}, abstract = {PURPOSE: More and more patients with community-acquired pneumonia have been detected with Chlamydia psittaci (C. psittaci) infected using metagenomic next-generation sequencing (mNGS). Previously, this was unheard of, and several patients presented with severe pneumonia and even required ECMO. We aimed to clarify the clinical characteristics of C. psittaci pneumonia and find out if there are any possible predictors of severe C. psittaci pneumonia.

METHODS: In this retrospective study, we included all confirmed cases of C. psittaci pneumonia in Wuxi. Epidemiological, clinical, and radiological features, as well as laboratory data, were collected and analyzed.

RESULTS: We enrolled 55 patients with C. psittaci pneumonia, with 30 (54.5%) having a history of exposure to birds or their internal organs. 50 (90.9%) patients were diagnosed by mNGS. Patients with C. psittaci pneumonia had many complications, among which, that deserve sufficient attention from clinicians were vascular embolic events (3, 5.5%). High fever was the most common clinical manifestation (41, 74.5%). The majority of patients had a significant increase in neutrophils ratio, neutrophils to lymphocytes ratio (NLR), rapid c-reactive protein, creatine kinase (CK), and lactate dehydrogenase (LDH), as well as a decrease in lymphocytes ratio, albumin, serum sodium, serum potassium, and serum phosphorus. Chest computed tomography scans revealed unilateral pneumonia (70.9%), consolidation (87.3%), air bronchogram (76.4%), and ground-glass opacity (69.1%). The neutrophil ratio, NLR, LDH, and CK were all factors that could identify severe pneumonia. Both AUCs exceeded 0.8; the respective 95% CIs were 0.715-0.944, 0.710-0.963, 0.677-0.937, and 0.718-0.950; all p < 0.05 (0.01, 0.001, 0.007, 0.007 respectively). The ORs were 10.057, 9.750, 10.057, and 9.667, respectively; the 95% CIs were 2.643-38.276, 2.339-40.649, and 2.643-38.276, respectively; all p-values were less than 0.05 (0.001, 0.002, 0.001, 0.001 respectively).

CONCLUSION: C. psittaci pneumonia is a very complex disease that changes all the time. Some patients showed severe pneumonia. Patients will have a poor prognosis if they are not treated promptly and effectively. We discovered that many clinical indicators were typical. Meanwhile, significant increases in neutrophil ratio, NLR, LDH, and CK predicted severe pneumonia. Timely detection of mNGS provided substantial help for clinical diagnosis and early treatment.}, } @article {pmid37670353, year = {2023}, author = {Gofton, AW and Popa-Baez, A and Takano, A and Soennichsen, K and Michie, M and Short, M and Supriyono, S and Pascoe, J and Cusbert, S and Mulley, R}, title = {Characterisation and comparative genomics of three new Varanus-associated Borrelia spp. from Indonesia and Australia.}, journal = {Parasites & vectors}, volume = {16}, number = {1}, pages = {317}, pmid = {37670353}, issn = {1756-3305}, mesh = {Animals ; Humans ; *Borrelia ; Indonesia ; Phylogeny ; Genomics ; *Lizards ; Australia ; *Relapsing Fever ; }, abstract = {BACKGROUND: Borrelia are important disease-causing tick- and louse-borne spirochaetes than can infect a wide variety of vertebrates, including humans and reptiles. Reptile-associated (REP) Borrelia, once considered a peculiarity, are now recognised as a distinct and important evolutionary lineage, and are increasingly being discovered worldwide in association with novel hosts. Numerous novel Borrelia spp. associated with monitor lizards (Varanus spp.) have been recently identified throughout the Indo-Pacific region; however, there is a lack of genomic data on these Borrelia.

METHODS: We used metagenomic techniques to sequence almost complete genomes of novel Borrelia spp. from Varanus varius and Varanus giganteus from Australia, and used long- and short-read technologies to sequence the complete genomes of two strains of a novel Borrelia sp. previously isolated from ticks infesting Varanus salvator from Indonesia. We investigated intra- and interspecies genomic diversity, including plasmid diversity and relatedness, among Varanus-associated Borrelia and other available REP Borrelia and, based on 712 whole genome orthologues, produced the most complete phylogenetic analysis, to the best of our knowledge, of REP Borrelia to date.

RESULTS: The genomic architecture of Varanus-associated Borrelia spp. is similar to that of Borrelia spp. that cause relapsing fever (RF), and includes a highly conserved megaplasmid and numerous smaller linear and circular plasmids that lack structural consistency between species. Analysis of PF32 and PF57/62 plasmid partitioning genes indicated that REP Borrelia plasmids fall into at least six distinct plasmid families, some of which are related to previously defined Borrelia plasmid families, whereas the others appear to be unique. REP Borrelia contain immunogenic variable major proteins that are homologous to those found in Borrelia spp. that cause RF, although they are limited in copy number and variability and have low sequence identities to RF variable major proteins. Phylogenetic analyses based on single marker genes and 712 single copy orthologs also definitively demonstrated the monophyly of REP Borrelia as a unique lineage.

CONCLUSIONS: In this work we present four new genomes from three novel Borrelia, and thus double the number of REP Borrelia genomes publicly available. The genomic characterisation of these Borrelia clearly demonstrates their distinctiveness as species, and we propose the names Borrelia salvatorii, 'Candidatus Borrelia undatumii', and 'Candidatus Borrelia rubricentralis' for them.}, } @article {pmid37670231, year = {2023}, author = {Guo, R and Zhang, W and Shen, W and Zhang, G and Xie, T and Li, L and Jinmei, J and Liu, Y and Kong, F and Guo, B and Li, B and Sun, Y and Liu, S}, title = {Analysis of gut microbiota in chinese donkey in different regions using metagenomic sequencing.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {524}, pmid = {37670231}, issn = {1471-2164}, support = {SDAIT-27//Donkey Innovation Team of Shandong Modern Agricultural Industry Technology System/ ; SD2019 XM 008//Major Agricultural Application Technology Innovation Projects of Shandong Province/ ; 225A6601D//Hebei Provincial science and Technology Planning Project/ ; 2022DZ01//Systematic Evaluation and Screening of donkey germplasm Resources in the Yellow River Basin/ ; 2021E02035//Autonomous region science and technology branch Xinjiang project/ ; ZR2022QC091//Shandong Province Natural Science Foundation/ ; 20210021//Experimental Technology Research Pro-gramme of Qingdao Agriculture University/ ; }, mesh = {Bacteroidetes ; China ; Clostridiales ; Firmicutes ; *Gastrointestinal Microbiome ; *Equidae/microbiology ; }, abstract = {BACKGROUND: Gut microbiota plays a significant role in host survival, health, and diseases; however, compared to other livestock, research on the gut microbiome of donkeys is limited.

RESULTS: In this study, a total of 30 donkey samples of rectal contents from six regions, including Shigatse, Changdu, Yunnan, Xinjiang, Qinghai, and Dezhou, were collected for metagenomic sequencing. The results of the species annotation revealed that the dominant phyla were Firmicutes and Bacteroidetes, and the dominant genera were Bacteroides, unclassified_o_Clostridiales (short for Clostridiales) and unclassified_f_Lachnospiraceae (short for Lachnospiraceae). The dominant phyla, genera and key discriminators were Bacteroidetes, Clostridiales and Bacteroidetes in Tibet donkeys (Shigatse); Firmicutes, Clostridiales and Clostridiales in Tibet donkeys (Changdu); Firmicutes, Fibrobacter and Tenericutes in Qinghai donkeys; Firmicutes, Clostridiales and Negativicutes in Yunnan donkeys; Firmicutes, Fibrobacter and Fibrobacteres in Xinjiang donkeys; Firmicutes, Clostridiales and Firmicutes in Dezhou donkeys. In the functional annotation, it was mainly enriched in the glycolysis and gluconeogenesis of carbohydrate metabolism, and the abundance was the highest in Dezhou donkeys. These results combined with altitude correlation analysis demonstrated that donkeys in the Dezhou region exhibited strong glucose-conversion ability, those in the Shigatse region exhibited strong glucose metabolism and utilization ability, those in the Changdu region exhibited a strong microbial metabolic function, and those in the Xinjiang region exhibited the strongest ability to decompose cellulose and hemicellulose.

CONCLUSION: According to published literature, this is the first study to construct a dataset with multi-regional donkey breeds. Our study revealed the differences in the composition and function of gut microbes in donkeys from different geographic regions and environmental settings and is valuable for donkey gut microbiome research.}, } @article {pmid37669363, year = {2023}, author = {Sireci, M and Muñoz, MA and Grilli, J}, title = {Environmental fluctuations explain the universal decay of species-abundance correlations with phylogenetic distance.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {37}, pages = {e2217144120}, pmid = {37669363}, issn = {1091-6490}, mesh = {Phylogeny ; Cross-Sectional Studies ; *Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Multiple ecological forces act together to shape the composition of microbial communities. Phyloecology approaches-which combine phylogenetic relationships between species with community ecology-have the potential to disentangle such forces but are often hard to connect with quantitative predictions from theoretical models. On the other hand, macroecology, which focuses on statistical patterns of abundance and diversity, provides natural connections with theoretical models but often neglects interspecific correlations and interactions. Here, we propose a unified framework combining both such approaches to analyze microbial communities. In particular, by using both cross-sectional and longitudinal metagenomic data for species abundances, we reveal the existence of an empirical macroecological law establishing that correlations in species-abundance fluctuations across communities decay from positive to null values as a function of phylogenetic dissimilarity in a consistent manner across ecologically distinct microbiomes. We formulate three variants of a mechanistic model-each relying on alternative ecological forces-that lead to radically different predictions. From these analyses, we conclude that the empirically observed macroecological pattern can be quantitatively explained as a result of shared population-independent fluctuating resources, i.e., environmental filtering and not as a consequence of, e.g., species competition. Finally, we show that the macroecological law is also valid for temporal data of a single community and that the properties of delayed temporal correlations can be reproduced as well by the model with environmental filtering.}, } @article {pmid37667515, year = {2023}, author = {Baker, JL}, title = {Illuminating the oral microbiome and its host interactions: recent advancements in omics and bioinformatics technologies in the context of oral microbiome research.}, journal = {FEMS microbiology reviews}, volume = {47}, number = {5}, pages = {}, pmid = {37667515}, issn = {1574-6976}, support = {K99 DE029228/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Quality of Life ; Computational Biology ; Genomics ; Metabolomics ; *Microbiota/genetics ; }, abstract = {The oral microbiota has an enormous impact on human health, with oral dysbiosis now linked to many oral and systemic diseases. Recent advancements in sequencing, mass spectrometry, bioinformatics, computational biology, and machine learning are revolutionizing oral microbiome research, enabling analysis at an unprecedented scale and level of resolution using omics approaches. This review contains a comprehensive perspective of the current state-of-the-art tools available to perform genomics, metagenomics, phylogenomics, pangenomics, transcriptomics, proteomics, metabolomics, lipidomics, and multi-omics analysis on (all) microbiomes, and then provides examples of how the techniques have been applied to research of the oral microbiome, specifically. Key findings of these studies and remaining challenges for the field are highlighted. Although the methods discussed here are placed in the context of their contributions to oral microbiome research specifically, they are pertinent to the study of any microbiome, and the intended audience of this includes researchers would simply like to get an introduction to microbial omics and/or an update on the latest omics methods. Continued research of the oral microbiota using omics approaches is crucial and will lead to dramatic improvements in human health, longevity, and quality of life.}, } @article {pmid37667485, year = {2023}, author = {Xu, R and Cui, H and Fan, F and Zhang, M and Yuan, S and Wang, D and Gan, Z and Yu, Z and Wang, C and Meng, F}, title = {Combination of Sequencing Batch Operation and A/O Process to Achieve Partial Mainstream Anammox: Pilot-Scale Demonstration and Microbial Ecological Mechanism.}, journal = {Environmental science & technology}, volume = {57}, number = {37}, pages = {13887-13900}, doi = {10.1021/acs.est.3c03022}, pmid = {37667485}, issn = {1520-5851}, mesh = {*Anaerobic Ammonia Oxidation ; *Biofilms ; Biological Transport ; Bioreactors ; Fermentation ; }, abstract = {In this study, sequencing batch operation was successfully combined with a pilot-scale anaerobic biofilm-modified anaerobic/aerobic membrane bioreactor to achieve anaerobic ammonium oxidation (anammox) without inoculation of anammox aggregates for municipal wastewater treatment. Both total nitrogen and phosphorus removal efficiencies of the reactor reached up to 80% in the 250-day operation, with effluent concentrations of 4.95 mg-N/L and 0.48 mg-P/L. In situ enrichment of anammox bacteria with a maximum relative abundance of 7.86% was observed in the anaerobic biofilm, contributing to 18.81% of nitrogen removal, with denitrification being the primary removal pathway (38.41%). Denitrifying phosphorus removal (DPR) (40.54%) and aerobic phosphorus uptake (48.40%) played comparable roles in phosphorus removal. Metagenomic sequencing results showed that the biofilm contained significantly lower abundances of NO-reducing functional genes than the bulk sludge (p < 0.01), favoring anammox catabolism in the former. Interactions between the anammox bacteria and flanking community were dominated by cooperation behaviors (e.g., nitrite supply, amino acids/vitamins exchange) in the anaerobic biofilm community network. Moreover, the hydrolytic/fermentative bacteria and endogenous heterotrophic bacteria (Dechloromonas, Candidatus competibacter) were substantially enriched under sequencing batch operation, which could alleviate the inhibition of anammox bacteria by complex organics. Overall, this study provides a feasible and promising strategy for substantially enriching anammox bacteria and achieving partial mainstream anammox as well as DPR.}, } @article {pmid37666833, year = {2023}, author = {Baillie, VL and Madhi, SA and Ahyong, V and Olwagen, CP}, title = {Metagenomic sequencing of post-mortem tissue samples for the identification of pathogens associated with neonatal deaths.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5373}, pmid = {37666833}, issn = {2041-1723}, mesh = {Infant, Newborn ; Female ; Humans ; *Perinatal Death ; South Africa ; High-Throughput Nucleotide Sequencing ; *Acinetobacter baumannii ; Autopsy ; Escherichia coli ; }, abstract = {Postmortem minimally invasive tissue sampling together with the detailed review of clinical records has been shown to be highly successful in determining the cause of neonatal deaths. However, conventional tests including traditional culture methods and nucleic acid amplification tests have periodically proven to be insufficient to detect the causative agent in the infectious deaths. In this study, metagenomic next generation sequencing was used to explore for putative pathogens associated with neonatal deaths in post-mortem blood and lung tissue samples, in Soweto, South Africa. Here we show that the metagenomic sequencing results corroborate the findings using conventional methods of culture and nucleic acid amplifications tests on post-mortem samples in detecting the pathogens attributed in the causal pathway of death in 90% (18/20) of the decedents. Furthermore, metagenomic sequencing detected a putative pathogen, including Acinetobacter baumannii, Klebsiella pneumoniae, Escherichia coli, and Serratia marcescens, in a further nine of 11 (81%) cases where no causative pathogen was identified. The antimicrobial susceptibility profile was also determined by the metagenomic sequencing for all pathogens with numerous multi drug resistant organism identified. In conclusion, metagenomic sequencing is able to successfully identify pathogens contributing to infection associated deaths on postmortem blood and tissue samples.}, } @article {pmid37666802, year = {2023}, author = {Kieft, B and Finke, N and McLaughlin, RJ and Nallan, AN and Krzywinski, M and Crowe, SA and Hallam, SJ}, title = {Genome-resolved correlation mapping links microbial community structure to metabolic interactions driving methane production from wastewater.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5380}, pmid = {37666802}, issn = {2041-1723}, mesh = {*Wastewater ; *Metagenome ; Microbial Consortia/genetics ; Sewage ; Methane ; }, abstract = {Anaerobic digestion of municipal mixed sludge produces methane that can be converted into renewable natural gas. To improve economics of this microbial mediated process, metabolic interactions catalyzing biomass conversion to energy need to be identified. Here, we present a two-year time series associating microbial metabolism and physicochemistry in a full-scale wastewater treatment plant. By creating a co-occurrence network with thousands of time-resolved microbial populations from over 100 samples spanning four operating configurations, known and novel microbial consortia with potential to drive methane production were identified. Interactions between these populations were further resolved in relation to specific process configurations by mapping metagenome assembled genomes and cognate gene expression data onto the network. Prominent interactions included transcriptionally active Methanolinea methanogens and syntrophic benzoate oxidizing Syntrophorhabdus, as well as a Methanoregulaceae population and putative syntrophic acetate oxidizing bacteria affiliated with Bateroidetes (Tenuifilaceae) expressing the glycine cleavage bypass of the Wood-Ljungdahl pathway.}, } @article {pmid37666200, year = {2023}, author = {Xu, M and Wang, W and Su, S and Li, W and Hu, X and Zhang, J}, title = {Arecoline alleviated loperamide induced constipation by regulating gut microbes and the expression of colonic genome.}, journal = {Ecotoxicology and environmental safety}, volume = {264}, number = {}, pages = {115423}, doi = {10.1016/j.ecoenv.2023.115423}, pmid = {37666200}, issn = {1090-2414}, abstract = {This study aimed to investigate the effects of arecoline on constipation by intervening at different times to explore its preventive and therapeutic effects. Symptoms related to constipation, gut microbes, short-chain fatty acid (SCFA) content in the cecum, and gene expression in the colon were measured to examine the effect of arecoline on relieving constipation. The results showed that arecoline intervention alleviated loperamide-induced constipation, as evidenced by significantly shortened intestinal transit time, increased fecal water content, improved small bowel propulsion, and increased defecation frequency. In addition, arecoline significantly reduced the levels of gastrointestinal regulatory peptides such as somatostatin and vasoactive intestinal peptide in the serum, thereby regulating intestinal peristalsis. Histopathological analysis showed that arecoline ameliorated intestinal injury caused by constipation. Gut microbial analysis indicated that arecoline altered the taxonomic composition and levels of its metabolite SCFAs in the gut microbiota. Furthermore, the colonic transcriptome results indicated that genes expression related to intestinal diseases were significantly down-regulated by arecoline intervention. In conclusion, the results of the correlation analysis propose a possible mechanism of arecoline in alleviating constipation by modulating the gut microbes and their metabolites and regulating the gut genome.}, } @article {pmid37666133, year = {2023}, author = {Ahmed, B and Gahlot, P and Balasundaram, G and Tyagi, VK and Banu J, R and Vivekanand, V and Kazmi, AA}, title = {Semi-continuous anaerobic co-digestion of thermal and thermal-alkali processed organic fraction of municipal solid waste: Methane yield, energy analysis, anaerobic microbiome.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118907}, doi = {10.1016/j.jenvman.2023.118907}, pmid = {37666133}, issn = {1095-8630}, mesh = {Anaerobiosis ; *Solid Waste ; *Microbiota ; Alkalies ; Methane ; Digestion ; }, abstract = {The semi-continuous anaerobic co-digestion (AcoD) of thermal and thermal-alkali pretreated organic fraction of municipal solid waste (OFMSW) and sewage sludge (SS) was studied under varying hydraulic retention times (HRT) and organic loading rates (OLR Three semi-continuous digesters were operated under control (non-pre-treated), thermally pretreated (125 °C), and thermal-alkali pretreated (125°C-3g/L NaOH) conditions at variable OLRs at 2.5, 4.0, 5.1, and 7.6 kgVS/m[3].d and corresponding HRTs of 30, 20, 15, and 10 days. The 10 and 43% higher methane yield (0.445 m[3]/kgVS) and 11 and 57% higher VS removal (52%) was achieved for thermal-alkali pretreated digester at 5.1 kgVS/m[3].d OLR over thermally pretreated (0.408 m[3]/kgVS, 45% VS removal) and control digesters (0.310 m[3]/kgVS, 33% VS removal), respectively. Thermal and thermal-alkali digesters failed on increasing the OLR to 7.6 kgVS/m[3].d, whereas the control digester becomes upset at 5.1 kgVS/m[3].d OLR. The metagenomic study revealed that Firmicutes, Bacteroidetes, Chloroflexi, Euryarchaeota, Proteobacteria, and Actinobacteria were the predominant bacterial population, whereas Methanosarcina and Methanothrix dominated the archaeal community. Energy balance analysis revealed that thermal alkali pretreatment showed the highest positive energy balance of 114.6 MJ/ton with an energy ratio of 1.25 compared with thermally pretreated (81.5 MJ/ton) and control samples (-46.9 MJ/ton). This work pave the way for scaleup of both thermal and thermal-alkali pre-treatment at 125 °C to realize the techno-economic and energy potential of the process.}, } @article {pmid37666128, year = {2023}, author = {Wang, S and Chen, D and Liu, Q and Zang, L and Zhang, G and Sui, M and Dai, Y and Zhou, C and Li, Y and Yang, Y and Ding, F}, title = {Dominant influence of plants on soil microbial carbon cycling functions during natural restoration of degraded karst vegetation.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118889}, doi = {10.1016/j.jenvman.2023.118889}, pmid = {37666128}, issn = {1095-8630}, mesh = {*Ecosystem ; Soil ; Soil Microbiology ; Plants ; China ; *Microbiota ; Carbon ; }, abstract = {The impacts of natural restoration projects on soil microbial carbon (C) cycling functions have not been well recognized despite their wide implementation in the degraded karst areas of southwest China. In this study, metagenomic sequencing assays were conducted on functional genes and microorganisms related to soil C-cycling at three natural restoration stages (shrubbery, TG; secondary forest, SG; old-growth forest, OG) in the southeast of Guizhou Province, China. The aims were to investigate the changes in microbial potentials responsible for soil C cycling and the underlying driving forces. The natural restoration resulted in vegetation establishment at all three restoration stages, rendering alterations of soil microbial C cycle functions as indicated by metagenomic gene assays. When TG was restored into OG, the number and diversity of genes and microorganisms involved in soil C cycling remained unchanged, but their composition underwent significant shifts. Specifically, microbial potentials for soil C decomposition exhibited an increase driven by the collaborative efforts of plants and soils, while microbial potentials for soil C biosynthesis displayed an initial upswing followed by a subsequent decline which was primarily influenced by plants alone. In comparison to soil nutrients, it was determined that plant diversities served as the primary driving factor for the alterations in microbial carbon cycle potentials. Soil microbial communities involved in C cycling were predominantly attributed to Proteobacteria (31.87%-40.25%) and Actinobacteria (11.29%-26.07%), although their contributions varied across the three restoration stages. The natural restoration of degraded karst vegetation thus influences soil microbial C cycle functions by enhancing C decomposition potentials and displaying a nuanced pattern of biosynthesis potentials, primarily influenced by above-ground plants. These results provide valuable new insights into the regulation of soil C cycling during the restoration of degraded karst vegetation from genetic and microbial perspectives.}, } @article {pmid37665521, year = {2023}, author = {Khatua, S and Simal-Gandara, J and Acharya, K}, title = {Myco-remediation of plastic pollution: current knowledge and future prospects.}, journal = {Biodegradation}, volume = {}, number = {}, pages = {}, pmid = {37665521}, issn = {1572-9729}, support = {CRUE/CSIC//Universidade de Vigo/ ; }, abstract = {To date, enumerable fungi have been reported to participate in the biodegradation of several notorious plastic materials following their isolation from soil of plastic-dumping sites, marine water, waste of mulch films, landfills, plant parts and gut of wax moth. The general mechanism begins with formation of hydrophobin and biofilm proceding to secretion of specific plastic degarding enzymes (peroxidase, hydrolase, protease and urease), penetration of three dimensional substrates and mineralization of plastic polymers into harmless products. As a result, several synthetic polymers including polyethylene, polystyrene, polypropylene, polyvinyl chloride, polyurethane and/or bio-degradable plastics have been validated to deteriorate within months through the action of a wide variety of fungal strains predominantly Ascomycota (Alternaria, Aspergillus, Cladosporium, Fusarium, Penicillium spp.). Understanding the potential and mode of operation of these organisms is thus of prime importance inspiring us to furnish an up to date view on all the presently known fungal strains claimed to mitigate the plastic waste problem. Future research henceforth needs to be directed towards metagenomic approach to distinguish polymer degrading microbial diversity followed by bio-augmentation to build fascinating future of waste disposal.}, } @article {pmid37665120, year = {2023}, author = {Kado, T and Akbary, Z and Motooka, D and Sparks, IL and Melzer, ES and Nakamura, S and Rojas, ER and Morita, YS and Siegrist, MS}, title = {A cell wall synthase accelerates plasma membrane partitioning in mycobacteria.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {37665120}, issn = {2050-084X}, support = {T32 GM008515/GM/NIGMS NIH HHS/United States ; T32 GM139789/GM/NIGMS NIH HHS/United States ; DP2 AI138238/AI/NIAID NIH HHS/United States ; R35 GM143057/GM/NIGMS NIH HHS/United States ; R21 AI144748/AI/NIAID NIH HHS/United States ; R03 AI140259/AI/NIAID NIH HHS/United States ; R35GM143057/GM/NIGMS NIH HHS/United States ; }, mesh = {Cell Membrane ; *Benzyl Alcohol ; *Cell Wall ; Mycobacterium smegmatis ; }, abstract = {Lateral partitioning of proteins and lipids shapes membrane function. In model membranes, partitioning can be influenced both by bilayer-intrinsic factors like molecular composition and by bilayer-extrinsic factors such as interactions with other membranes and solid supports. While cellular membranes can departition in response to bilayer-intrinsic or -extrinsic disruptions, the mechanisms by which they partition de novo are largely unknown. The plasma membrane of Mycobacterium smegmatis spatially and biochemically departitions in response to the fluidizing agent benzyl alcohol, then repartitions upon fluidizer washout. By screening for mutants that are sensitive to benzyl alcohol, we show that the bifunctional cell wall synthase PonA2 promotes membrane partitioning and cell growth during recovery from benzyl alcohol exposure. PonA2's role in membrane repartitioning and regrowth depends solely on its conserved transglycosylase domain. Active cell wall polymerization promotes de novo membrane partitioning and the completed cell wall polymer helps to maintain membrane partitioning. Our work highlights the complexity of membrane-cell wall interactions and establishes a facile model system for departitioning and repartitioning cellular membranes.}, } @article {pmid37665015, year = {2023}, author = {Sinjab, K and Sawant, S and Ou, A and Fenno, JC and Wang, HL and Kumar, P}, title = {Impact of surface characteristics on the peri-implant microbiome in health and disease.}, journal = {Journal of periodontology}, volume = {}, number = {}, pages = {}, doi = {10.1002/JPER.23-0205}, pmid = {37665015}, issn = {1943-3670}, abstract = {BACKGROUND: Because little is known about the impact of implant surface modifications on the peri-implant microbiome, we aimed to examine peri-implant communities in various surface types in order to better understand the impact of these surfaces on the development of peri-implantitis (PI).

METHODS: One hundred and six systemically healthy individuals with anodized (AN), hydroxyapatite-coated (HA), or sandblasted acid-etched (SLA) implants that were >6 months in function were recruited and categorized into health (H) or PI. Peri-implant biofilm was analyzed using 16S rRNA gene sequencing and compared between health/disease and HA/SLA/AN using community-level and taxa-level metrics.

RESULTS: Healthy implants did not demonstrate significant differences in clustering, alpha- or beta-diversity based on surface modification. AN and HA surfaces displayed significant differences between health and PI (p < 0.05); however, such a clustering was not evident with SLA (p > 0.05). AN and HA surfaces also differed in the magnitude and diversity of differences between health and PI. Six species belonging to the genera Shuttleworthia, Scardovia, and Prevotella demonstrated lower abundances in AN implants with PI, and 18 species belonging to the genera Fretibacterium, Tannerella, Treponema, and Fusobacterium were elevated, while in HA implants with PI, 20 species belonging to the genera Streptococcus, Lactobacillus, Veillonella, Rothia, and family Ruminococcaceae were depleted and Peptostreptococcaceae, Atopobiaceae, Veillonellaceae, Porphyromonadaceae, Desulfobulbaceae, and order Synergistales were enriched.

CONCLUSIONS: Within the limitations of this study, we demonstrate that implant surface can differentially modify the disease-associated microbiome, suggesting that surface topography must be considered in the multi-factorial etiology of peri-implant diseases.}, } @article {pmid37664974, year = {2023}, author = {Schuetz, R and Claypool, J and Sfriso, R and Vollhardt, JH}, title = {Sunscreens can preserve human skin microbiome upon erythemal UV exposure.}, journal = {International journal of cosmetic science}, volume = {}, number = {}, pages = {}, doi = {10.1111/ics.12910}, pmid = {37664974}, issn = {1468-2494}, abstract = {OBJECTIVE: Ultraviolet radiation (UVR) is a known environmental key factor for premature skin ageing. Only few scientific evidence is available to support the effects of UVR on the skin microbiome. This in vivo pilot study aimed to evaluate the impact on the skin microbiome upon erythemal UV exposure and the protection of UV-exposed skin microbiome by UV filters.

METHODS: Ten female volunteers were treated with an sun protection factor (SPF) 20 sunscreen and placebo formulation (without UV filters) on their upper middle backs and irradiated with an erythemal dose (2 MED) by a solar simulator. Skin swabbing samples from four zones (i.e., unexposed, exposed, sunscreen- and placebo-treated on exposed skin) were collected for the microbiome analysis before and 2 h after UV exposure, respectively, and processed via shallow 16S rRNA Amplicon and Shotgun metagenomic sequencing. An in vitro UV method was developed to confirm the protection of isolated bacterial strains by single UV filters and combinations.

RESULTS: Alpha diversity was impacted by significant inter-individual differences and by treatment rather than by irradiation. Cutibacterium acnes was found to be the most abundant and a confounding factor for diversity. On a species level, Lactobacillus crispatus was negatively associated with UVR and placebo treatment, whereas there was a positive association with sunscreen treatment. The sunscreen treatment also favoured an interaction network with central Micrococcus genus. The in vitro results showed that both single UV filters and combinations had specific effects on the survival rates of L. crispatus, C. acnes, and Staphylococcus epidermidis.

CONCLUSION: We identified potential microorganisms and bacterial interactions that were associated with an SPF 20 sunscreen treatment. The specific protection of L. crispatus as a key player in the UV-exposed skin microbiome and reduction of C. acnes population by UV filters might lead to new cosmetic concepts for photoprotection.}, } @article {pmid37664620, year = {2023}, author = {Mao, C and Li, Q and Komijani, M and Huang, J and Li, T}, title = {Metagenomic analysis reveals the dissemination mechanisms and risks of resistance genes in plateau lakes.}, journal = {iScience}, volume = {26}, number = {9}, pages = {107508}, pmid = {37664620}, issn = {2589-0042}, abstract = {Antibiotic resistance genes (ARGs) are emerging as environmental pollutants that can persist and disseminate in aquatic environments. Lakes, as important sources of freshwater, also serve as potential natural reservoirs of ARGs. In this study, we analyzed the distribution and potential risks of resistance genes in five typical freshwater lakes on the Yunnan-Guizhou Plateau. Our findings revealed that multidrug and MLS ARGs dominated in the studied lakes. Notably, while Lugu Lake exhibited higher abundance of ARGs, mobile genetic elements (MGEs), and metal resistance genes (MRGs), a greater resistome risk was observed in the eutrophic Xingyun Lake. The dissemination processes of ARGs and MRGs are primarily driven by microbial communities and the horizontal gene transfer via MGEs. Limnohabitans, Flavobacterium, and Acinetobacter were identified as key players in the dissemination of ARGs. Our study highlights the persistence of ARGs and provides valuable baseline data and risk assessment of ARGs in plateau freshwater lakes.}, } @article {pmid37663996, year = {2023}, author = {Huang, L and Suhler, EB and Rosenberg, C and Ta Kim, D and Winthrop, KL and Doan, T and Lin, P}, title = {Acanthamoeba-associated retinitis successfully treated with intravitreal and systemic antimicrobials.}, journal = {American journal of ophthalmology case reports}, volume = {32}, number = {}, pages = {101902}, pmid = {37663996}, issn = {2451-9936}, abstract = {PURPOSE: To describe a case of unilateral Acanthamoeba-associated retinitis in the absence of concomitant corneal infection in an immunocompetent host without risk factors.

OBSERVATIONS: A 37-year-old woman presented with unilateral multifocal retinitis with minimal vitritis. Anterior segment was normal. Conventional diagnostics of bacterial, fungal, viral, Toxoplasma and Toxocara etiologies all returned negative. Empiric treatments were unsuccessful, including oral valacyclovir, oral fluconazole, as well as intravitreal injection of vancomycin and ceftazidime. Metagenomic deep sequencing (MDS) identified Acanthamoeba genomic fragments in the vitreous sample. Multiple intravitreal voriconazole injections were performed and achieved partial suppression of lesion growth. Subsequent dual therapy of oral voriconazole and trimethoprim-sulfamethoxazole led to resolution of the lesions and vision improvement without further injections.

CONCLUSIONS AND IMPORTANCE: This is an unusual case of unilateral Acanthamoeba-associated retinitis without concomitant corneal infection, diagnosed via unbiased DNA and RNA deep sequencing, with other etiologies ruled out by conventional approaches. Treatment with systemic and intravitreal therapy led to a successful resolution of retinitis and vision improvement. Our case demonstrates the potential of MDS as an unbiased diagnostic tool for rare ocular pathogens and the therapeutic effect of oral voriconazole with trimethoprim-sulfamethoxazole for Acanthamoeba intraocular infection.}, } @article {pmid37663603, year = {2023}, author = {Hu, C and He, T and Zou, B and Li, H and Zhao, J and Hu, C and Cui, J and Huang, Z and Shu, S and Hao, Y}, title = {Fecal microbiota transplantation in a child with severe ASD comorbidities of gastrointestinal dysfunctions-a case report.}, journal = {Frontiers in psychiatry}, volume = {14}, number = {}, pages = {1219104}, pmid = {37663603}, issn = {1664-0640}, abstract = {Autism spectrum disorder (ASD) is a neurodevelopmental disorder defined by social communication impairments and restricted, repetitive behaviors. In addition to behavioral interventions and psychotherapies, and pharmacological interventions, in-depth studies of intestinal microbiota in ASD has obvious abnormalities which may effectively influenced in ASD. Several attempts have been made to indicate that microbiota can reduce the occurrence of ASD effectively. Fecal microbiota transplantation (FMT) is a type of biological therapy that involves the transplant of intestinal microbiota from healthy donors into the patient's gastrointestinal tract to improve the gut microenvironment. In this case report, we describe a case of child ASD treated by FMT. The patient have poor response to long-term behavioral interventions. After five rounds of FMT, clinical core symptoms of ASD and gastrointestinal(GI) symptoms were significantly altered. Moreover, the multiple levels of functional development of child were also significantly ameliorated. We found that FMT changed the composition of the intestinal microbiota as well as the metabolites, intestinal inflammatory manifestations, and these changes were consistent with the patient's symptoms. This report suggests further FMT studies in ASD could be worth pursuing, and more studies are needed to validate the effectiveness of FMT in ASD and its mechanisms.}, } @article {pmid37663136, year = {2023}, author = {Meng, X and Liu, Y and Li, J and Wang, L and Shi, R and Chen, Y and Zhu, Y and Zhuang, S}, title = {Metagenomic next-generation sequencing for diagnosis and efficacy evaluation of a critical case of SFTS complicated by invasive pulmonary aspergillosis.}, journal = {IDCases}, volume = {33}, number = {}, pages = {e01884}, pmid = {37663136}, issn = {2214-2509}, abstract = {Severe fever with thrombocytopenia syndrome (SFTS) is an emerging infectious disease caused by SFTS virus (SFTSV). SFTS patients were prone to invasive pulmonary aspergillosis (IPA), which was directly related to increased mortality. Here, we present a critical case of SFTS complicated by IPA in a previously healthy 58-year-old woman. On day 1, SFTSV and three different Aspergillus species were both detected in the patient's bronchoalveolar lavage fluid and blood through metagenomic next-generation sequencing (mNGS). After 17 days of treatment, the patient was still in poor condition and A. fumigatus was once again detected in her blood through mNGS. Then her family decided to give up treatment because of financial problems and grave prognosis. She was discharged home and died the next day. Medical personnel should be alter to the possibility of IPA in SFTS patients due to its high mortality. mNGS may be used as an auxiliary diagnostic tool and efficacy-monitoring method for suspected SFTS complicated by IPA.}, } @article {pmid37663088, year = {2023}, author = {Zhang, H and Shen, D and Zhou, J and Yang, Q and Ying, Y and Li, N and Cao, L and Wang, W and Ma, X}, title = {The Utility of Metagenomic Next-Generation Sequencing (mNGS) in the Management of Patients With Bronchiectasis: A Single-Center Retrospective Study of 93 Cases.}, journal = {Open forum infectious diseases}, volume = {10}, number = {8}, pages = {ofad425}, pmid = {37663088}, issn = {2328-8957}, abstract = {BACKGROUND: Bronchiectasis is a chronic inflammatory respiratory disease mainly caused by pathogenic infections. However, standard methods of pathogen detection show prolonged cycle durations and unsatisfactory sensitivity and detection rates. Macrogenomic next-generation sequencing (mNGS) emerges as a promising technique for swift, effective, and unbiased pathogen detection and subsequent data interpretation.

METHODS: Here, a retrospective analysis of 93 patients with suspected bronchiectasis was performed to assess the clinical applicability of mNGS. Bronchoalveolar alveolar lavage fluid (BALF) samples were collected from these subjects, followed by standard assays and mNGS separately. The turnaround time, detection rate, and pathogen identification using mNGS were compared with those of standard methods.

RESULTS: mNGS identified a greater number of bacteria (72 vs 16), fungi (26 vs 19), and viruses (14 vs 0) than standard methods. Specifically, the commonly identified bacteria were Haemophilus, Mycobacterium intracellulare, Pseudomonas, and Streptococcus pneumoniae, while the most detected fungi were Aspergillus and the most prevalent viruses were human herpesviruses. Of note, 29 out of 30 patients (96.67%) who received optimized treatment strategies based on mNGS results experienced recovery.

CONCLUSIONS: Collectively, these findings suggest that mNGS has the potential to improve the diagnosis and treatment of bronchiectasis patients by enabling rapid and precise pathogen detection, which can lead to timely and effective treatment strategies.}, } @article {pmid37663038, year = {2023}, author = {Gimenez-Miranda, L and Samhouri, BF and Wolf, MJ and Anderson, DK and Midthun, DE and Lim, KG and Kern, RM and Patel, R and Carmona, EM}, title = {Diagnostic Yield of 16S Ribosomal Ribonucleic Acid Gene-Based Targeted Metagenomic Sequencing for Evaluation of Pleural Space Infection: A Prospective Study.}, journal = {Mayo Clinic proceedings. Innovations, quality & outcomes}, volume = {7}, number = {5}, pages = {373-381}, pmid = {37663038}, issn = {2542-4548}, abstract = {OBJECTIVE: To better understand the microbial profile of complicated parapneumonic effusions and empyema, and to evaluate whether antimicrobial selection would differ if guided by targeted metagenomic sequencing (tMGS) vs conventional cultures (CCs) alone.

PATIENTS AND METHODS: We analyzed the pleural fluid of a cohort of 47 patients undergoing thoracentesis from January 1, 2017 to August 31, 2019, to characterize their microbial profile. All samples underwent 16S ribosomal ribonucleic acid gene polymerase chain reaction, followed by tMGS.

RESULTS: Pleural space infection was deemed clinically present in 20 of the 47 (43%) participants. Of those, n=7 (35%) had positive pleural fluid cultures and n=14 (70%) had positive tMGS results. The organisms identified by tMGS were concordant with CCs; however, tMGS detected additional bacterial species over CCs alone. Streptococcus and Staphylococcus species were the most common organisms identified, with Streptococcus intermedius/constellatus identified in 5 patients. Polymicrobial infections were found in 6 of the 20 patients, with anaerobes being the most common organisms identified in these cases.

CONCLUSION: Streptococci and staphylococci were the most common organisms identified in infected pleural fluid. Anaerobes were common in polymicrobial infections. When compared with CCs, tMGS had higher sensitivity than CCs. Targeted metagenomic sequencing identified additional organisms, not identified by CCs, with associated potential management implications.}, } @article {pmid37662426, year = {2023}, author = {Kuroda, K and Tomita, S and Kurashita, H and Hatamoto, M and Yamaguchi, T and Hori, T and Aoyagi, T and Sato, Y and Inaba, T and Habe, H and Tamaki, H and Hagihara, Y and Tamura, T and Narihiro, T}, title = {Metabolic implications for predatory and parasitic bacterial lineages in activated sludge wastewater treatment systems.}, journal = {Water research X}, volume = {20}, number = {}, pages = {100196}, pmid = {37662426}, issn = {2589-9147}, abstract = {Deciphering unclear microbial interactions is key to improving biological wastewater treatment processes. Microbial predation and parasitism in wastewater treatment ecosystems are unexplored survival strategies that have long been known and have recently attracted attention because these interspecies interactions may contribute to the reduction of excess sludge. Here, microbial community profiling of 600 activated sludge samples taken from six industrial and one municipal wastewater treatment processes (WWTPs) was conducted. To identify the shared lineages in the WWTPs, the shared microbial constituents were defined as the family level taxa that had ≥ 0.1% average relative abundance and detected in all processes. The microbial community analysis assigned 106 families as the shared microbial constituents in the WWTPs. Correlation analysis showed that 98 of the 106 shared families were significantly correlated with total carbon (TC) and/or total nitrogen (TN) concentrations, suggesting that they may contribute to wastewater remediation. Most possible predatory or parasitic bacteria belonging to the phyla Bdellovibrionota, Myxococcota, and Candidatus Patescibacteria were found to be the shared families and negatively correlated with TC/TN; thus, they were frequently present in the WWTPs and could be involved in the removal of carbon/nitrogen derived from cell components. Shotgun metagenome-resolved metabolic reconstructions indicated that gene homologs associated with predation or parasitism are conserved in the Bdellovibrionota, Myxococcota, and Ca. Patescibacteria genomes (e.g., host interaction (hit) locus, Tad-like secretion complexes, and type IV pilus assembly proteins). This study provides insights into the complex microbial interactions potentially linked to the reduction of excess sludge biomass in these processes.}, } @article {pmid37662302, year = {2023}, author = {Jeong, DE and Sundrani, S and Hall, RN and Krupovic, M and Koonin, EV and Fire, AZ}, title = {DNA polymerase diversity reveals multiple incursions of Polintons during nematode evolution.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.08.22.554363}, pmid = {37662302}, abstract = {Polintons are dsDNA, virus-like self-synthesizing transposons widely found in eukaryotic genomes. Recent metagenomic discoveries of Polinton-like viruses are consistent with the hypothesis that Polintons invade eukaryotic host genomes through infectious viral particles. Nematode genomes contain multiple copies of Polintons and provide an opportunity to explore the natural distribution and evolution of Polintons during this process. We performed an extensive search of Polintons across nematode genomes, identifying multiple full-length Polinton copies in several species. We provide evidence of both ancient Polinton integrations and recent mobility in strains of the same nematode species. In addition to the major nematode Polinton family, we identified a group of Polintons that are overall closely related to the major family, but encode a distinct protein-primed B family DNA polymerase (pPolB) that is related to homologs from a different group of Polintons present outside of the Nematoda . Phylogenetic analyses on the pPolBs support the evolutionary scenarios in which these extrinsic pPolBs that seem to derive from Polinton families present in oomycetes and molluscs replaced the canonical pPolB in subsets of Polintons found in terrestrial and marine nematodes, respectively, suggesting inter-phylum horizontal gene transfers. The pPolBs of the terrestrial nematode and oomycete Polintons share a unique feature, an insertion of a HNH nuclease domain, whereas the pPolBs in the marine nematode Polintons share an insertion of a VSR nuclease domain with marine mollusc pPolBs. We hypothesize that horizontal gene transfer occurs among Polintons from widely different but cohabiting hosts.}, } @article {pmid37662279, year = {2023}, author = {Mullinax, SR and Darby, AM and Gupta, A and Chan, P and Smith, BR and Unckless, RL}, title = {A suite of selective pressures supports the maintenance of alleles of a Drosophila immune peptide.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37662279}, support = {P20 GM103638/GM/NIGMS NIH HHS/United States ; R01 AI139154/AI/NIAID NIH HHS/United States ; }, abstract = {The innate immune system provides hosts with a crucial first line of defense against pathogens. While immune genes are often among the fastest evolving genes in the genome, in Drosophila, antimicrobial peptides (AMPs) are notable exceptions. Instead, AMPs may be under balancing selection, such that over evolutionary timescales multiple alleles are maintained in populations. In this study, we focus on the Drosophila antimicrobial peptide Diptericin A, which has a segregating amino acid polymorphism associated with differential survival after infection with the Gram-negative bacteria Providencia rettgeri. Diptericin A also helps control opportunistic gut infections by common Drosophila gut microbes, especially those of Lactobacillus plantarum. In addition to genotypic effects on gut immunity, we also see strong sex-specific effects that are most prominent in flies without functional diptericin A. To further characterize differences in microbiomes between different diptericin genotypes, we used 16S metagenomics to look at the microbiome composition. We used both lab reared and wild caught flies for our sequencing and looked at overall composition as well as the differential abundance of individual bacterial families. Overall, we find flies that are homozygous serine for diptericin A are better equipped to survive a systemic infection from P. rettgeri, but in general homozygous arginine flies have a longer lifespan after being fed common gut commensals. Our results suggest a possible mechanism for the maintenance of genetic variation of diptericin A through the complex interactions of sex, systemic immunity, and the maintenance of the gut microbiome.}, } @article {pmid37662255, year = {2023}, author = {Jean Wilson, E and Sirpu Natesh, N and Ghadermazi, P and Pothuraju, R and Shanmugam, M and Prajapati, DR and Pandey, S and Kaifi, JT and Dodam, JR and Bryan, J and Lorson, CL and Watrelot, AA and Foster, JM and Mansel, TJ and Joshua Chan, SH and Batra, SK and Subbiah, J and Rachagani, S}, title = {Red cabbage juice-mediated gut microbiota modulation improves intestinal epithelial homeostasis and ameliorates colitis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.08.23.554560}, pmid = {37662255}, abstract = {Gut microbiota plays a crucial role in inflammatory bowel disease (IBD) and has therapeutic benefits. Thus, targeting the gut microbiota is a promising therapeutic approach for IBD treatment. We recently found that red cabbage juice (RCJ) ameliorates dextran sulfate sodium (DSS)-induced colitis in mice. However, the underlying mechanisms remain unknown. The current study investigated the modulation of gut microbiota in response to treatment with RCJ to ameliorate the DSS colitis. The initial results demonstrated that mice treated with DSS + RCJ showed increased body weight and decreased diarrhea and blood in feces compared to the DSS alone group. RCJ ameliorated colitis by regulating the intestinal barrier function by reducing the number of apoptotic cells, improving colonic protective mucin, and increasing tight junction protein in RCJ + DSS groups compared to the DSS group. Short-gun metagenomic analysis revealed significant enrichment of short-chain fatty acid (SCFAs)-producing bacteria (Butyrivibrio, Ruminococcaceae, Acetatifactor muris, Rosburia Sp. CAG:303 , Dorea Sp. 5-2) increased PPAR-© activation, leading to repression of the nuclear factor κB (NFκB) signaling pathway, thus decreasing the production of crucial inflammatory cytokines and chemokines in the RCJ + DSS groups compared to the DSS group. Pathway abundance analysis showed an increased abundance of the SCFA pathway, reduced histidine degradation (Bacteroides sartorii, and Bacteroides caecimuris), and LCFA production in the RCJ+DSS treated group, suggesting the promotion of good colonic health. Furthermore, increased T-reg (FOXP3+) cells in the colon were due to SCFAs produced by the gut microbiota, which was corroborated by an increase in IL-10, a vital anti-inflammatory cytokine. Thus, our study provides the first evidence that RCJ ameliorates colonic inflammation by modulating the gut microbiota.}, } @article {pmid37662006, year = {2023}, author = {Liu, H and Zhang, Y and Liu, Y and Xiao, J and Huang, Z and Li, Y and Li, H and Li, P}, title = {Virome analysis of an ectomycorrhizal fungus Suillus luteus revealing potential evolutionary implications.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1229859}, pmid = {37662006}, issn = {2235-2988}, mesh = {*Basidiomycota/virology ; *Fungal Viruses/classification/genetics/isolation & purification ; Metagenomics ; Biological Evolution ; RNA Viruses/classification/genetics/isolation & purification ; }, abstract = {Suillus luteus is a widespread edible ectomycorrhizal fungus that holds significant importance in both ecological and economic value. Mycoviruses are ubiquitous infectious agents hosted in different fungi, with some known to exert beneficial or detrimental effects on their hosts. However, mycoviruses hosted in ectomycorrhizal fungi remain poorly studied. To address this gap in knowledge, we employed next-generation sequencing (NGS) to investigate the virome of S. luteus. Using BLASTp analysis and phylogenetic tree construction, we identified 33 mycovirus species, with over half of them belonging to the phylum Lenarviricota, and 29 of these viruses were novel. These mycoviruses were further grouped into 11 lineages, with the discovery of a new negative-sense single-stranded RNA viral family in the order Bunyavirales. In addition, our findings suggest the occurrence of cross-species transmission (CST) between the fungus and ticks, shedding light on potential evolutionary events that have shaped the viral community in different hosts. This study is not only the first study to characterize mycoviruses in S. luteus but highlights the enormous diversity of mycoviruses and their implications for virus evolution.}, } @article {pmid37662001, year = {2023}, author = {Shi, R and Wang, Y and Zhou, S and Zhang, Y and Zheng, S and Zhang, D and Du, X and Gu, W and Xu, Y and Zhu, C}, title = {Metagenomic next-generation sequencing for detecting lower respiratory tract infections in sputum and bronchoalveolar lavage fluid samples from children.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1228631}, pmid = {37662001}, issn = {2235-2988}, mesh = {Humans ; Child ; *Sputum ; Bronchoalveolar Lavage Fluid ; *Respiratory Tract Infections/diagnosis ; High-Throughput Nucleotide Sequencing ; Metagenome ; }, abstract = {Lower respiratory tract infections are common in children. Bronchoalveolar lavage fluid has long been established as the best biological sample for detecting respiratory tract infections; however, it is not easily collected in children. Sputum may be used as an alternative yet its diagnostic accuracy remains controversial. Therefore, this study sought to evaluate the diagnostic accuracy of sputum for detecting lower respiratory tract infections using metagenomic next-generation sequencing. Paired sputum and bronchoalveolar lavage fluid samples were obtained from 68 patients; pathogens were detected in 67 sputum samples and 64 bronchoalveolar lavage fluid samples by metagenomic next-generation sequencing, respectively. The combined pathogen-detection rates in the sputum and bronchoalveolar lavage fluid samples were 80.90% and 66.2%, respectively. For sputum, the positive predictive values (PPVs) and negative predictive values (NPVs) for detecting bacteria were 0.72 and 0.73, respectively, with poor Kappa agreement (0.30; 95% confidence interval: 0.218-0.578, P < 0.001). However, viral detection in sputum had good sensitivity (0.87), fair specificity (0.57), and moderate Kappa agreement (0.46; 95% confidence interval: 0.231-0.693, P < 0.001). The PPVs and NPVs for viral detection in sputum were 0.82 and 0.67, respectively. The consistency between the sputum and bronchoalveolar lavage fluid was poor for bacterial detection yet moderate for viral detection. Thus, clinicians should be cautious when interpreting the results of sputum in suspected cases of lower respiratory tract infections, particularly with regards to bacterial detection in sputum. Viral detection in sputum appears to be more reliable; however, clinicians must still use comprehensive clinical judgment.}, } @article {pmid37661684, year = {2023}, author = {Ding, M and Yang, C and Li, Y}, title = {Clinical application of metagenomic next-generation sequencing in purulent meningitis: a case seri.}, journal = {The Turkish journal of pediatrics}, volume = {65}, number = {4}, pages = {679-686}, doi = {10.24953/turkjped.2022.691}, pmid = {37661684}, issn = {2791-6421}, mesh = {Child ; Humans ; High-Throughput Nucleotide Sequencing ; Polymerase Chain Reaction ; *Staphylococcal Infections ; Staphylococcus aureus ; *Meningitis ; }, abstract = {BACKGROUND: Purulent meningitis remains an important cause of mortality and morbidity among children worldwide. An immediate diagnosis of the causative microorganism is critical to significantly improving the outcome of this condition.

CASE: In this study, we collected cerebrospinal fluid (CSF) samples from four patients clinically diagnosed with purulent meningitis. Patients with purulent meningitis may present with a variety of clinical symptoms or laboratory results. Infectious microorganisms including Pseudomonas aeruginosa, Staphylococcus aureus, Streptococcus pneumonia, and Haemophilus influenzae were identified in the CSF samples via metagenomic nextgeneration sequencing (mNGS).

CONCLUSIONS: mNGS is effective for the immediate detection of pathogens, which can in turn facilitate prompt diagnosis and treatment among individuals with purulent meningitis, especially if conventional CSF results (such as CSF culture and polymerase chain reaction) are negative.}, } @article {pmid37661068, year = {2023}, author = {Zhang, D and Wang, H and Liu, A and Wang, S and Xu, C and Lan, K and Xiang, W and Zhu, K and Xiao, Y and Fu, J and Jiang, R and Chen, W and Ni, Y}, title = {The chronic consumption of dietary fructose promotes the gut Clostridium species imbalance and bile acid alterations in developing nonalcoholic fatty liver disease.}, journal = {The Journal of nutritional biochemistry}, volume = {121}, number = {}, pages = {109434}, doi = {10.1016/j.jnutbio.2023.109434}, pmid = {37661068}, issn = {1873-4847}, mesh = {Mice ; Animals ; Male ; *Non-alcoholic Fatty Liver Disease/metabolism ; Bile Acids and Salts/metabolism ; Fructose/adverse effects/metabolism ; Dysbiosis/metabolism ; Mice, Inbred C57BL ; Liver/metabolism ; Diet, High-Fat/adverse effects ; Clostridium ; Water/metabolism ; }, abstract = {Excessive fructose intake is associated with the rising prevalence of nonalcoholic fatty liver disease (NAFLD). The gut microbiome (GM) and bile acids (BAs) are involved in the pathogenesis of NAFLD, but the impact of fructose on their cross-talk is unclear. In this study, adult male C57BL/6J mice were fed a normal diet with tap water (ND) or with 4% fructose in the drinking water (Fru), 60% high-fat diet with tap water (HF) or with 4% fructose solution (HFF) for 12 weeks. Targeted BA analysis was performed in five anatomical sites including the liver, ileum contents, portal serum, cecum contents, and feces. Metagenomic sequencing was performed to explore gut dysbiosis. Within 12 weeks, the 4% fructose diet could initially stimulate gut dysbiosis and BA upregulation in the ileum, portal serum, and cecum when the intestinal and hepatic transport system remained stable without hepatic lipid accumulation. However, the chronic consumption of fructose promoted HF-induced NAFLD, with significantly increased body weight, impaired glucose tolerance, and advanced liver steatosis. BA transporters were inhibited in HFF, causing the block of internal BA circulation and increased BA secretion via cecum contents and feces. Notably, lithocholic acid (LCA) and its taurine conjugates were elevated within the enterohepatic circulation. Meanwhile, the Clostridium species were significantly altered in both Fru and HFF groups and were closely associated with fructose and BA metabolism. In summary, excessive fructose caused gut dysbiosis and BA alterations, promoting HF-induced NAFLD. The crosstalk between Clostridium sp. and LCA species were potential targets in fructose-mediated NAFLD.}, } @article {pmid37660873, year = {2023}, author = {Bhardwaj, L and Reddy, B and Dubey, SK}, title = {Deciphering insights into rhizospheric microbial community and soil parameters under the influence of herbicides in zero-tillage tropical rice-agroecosystem.}, journal = {Environmental research}, volume = {237}, number = {Pt 2}, pages = {117033}, doi = {10.1016/j.envres.2023.117033}, pmid = {37660873}, issn = {1096-0953}, abstract = {Extensive use of chemicals like herbicides in rice and other fields to manage weeds is expected to have a lasting influence on the soil environment. Considering this rationale, we aimed to decipher the effects of herbicides, Pendimethalin and Pretilachlor, applied at 0.5 and 0.6 kg ha[-1], respectively on the rhizosphere microbial community and soil characteristics in the tropical rice field, managed under zero tillage cultivation. The quantity of herbicide residues declined gradually since application up to 60 days thereafter it reached the non-detectable level. Most of the soil variables viz., microbial biomass, soil enzymes etc., exhibited slight reduction in the treated soils compared to the control. A gradual decline was observed in Mineral-N, MBC, MBN and enzyme activities. Quantitative polymerase chain reaction results showed maximal microbial abundance of bacteria, fungi and archaea at mid-flowering stage of rice crop. The 16 rRNA and ITS region targeted amplicons high throughput sequencing microbial metagenomic approach revealed total of 94, 1353, and 510 species for archaea, bacteria and fungi, respectively. The metabarcoding of core microbiota revealed that the archaea comprised of Nitrososphaera, Nitrosocosmicus, and Methanosarcina. In the bacterial core microbiome, Neobacillus, Nitrospira, Thaurea, and Microvigra were found as the predominant taxa. Fusarium, Clonostachys, Nigrospora, Mortierella, Chaetomium, etc., were found in core fungal microbiome. Overall, the study exhibited that the recommended dose of herbicides found to be detrimental to the microbial dynamics, though a negative relation between residues and soil variables was observed that might alter the microbial diversity. The outcomes offer a comprehensive understanding of how herbicides affect the microbial community in zero tillage rice soil, thus has a critical imputation for eco-friendly and sustainable rice agriculture. Further, the long-term studies will be helpful in elucidating the role of identified microbial groups in sustaining the soil fertility and crop productivity.}, } @article {pmid37660237, year = {2023}, author = {Li, R and Hu, M and Jiang, X and Xu, C}, title = {Metagenomic insights into the microbiota involved in lactate and butyrate production and manipulating their synthesis in alfalfa silage.}, journal = {Journal of applied microbiology}, volume = {134}, number = {9}, pages = {}, doi = {10.1093/jambio/lxad197}, pmid = {37660237}, issn = {1365-2672}, support = {31872420//National Natural Science Foundation of China/ ; }, mesh = {*Lactic Acid ; Medicago sativa/genetics ; Butyrates ; L-Lactate Dehydrogenase/genetics ; Silage ; *Microbiota/genetics ; Escherichia coli ; }, abstract = {AIMS: Lactate and butyrate are important indicators of silage quality. However, the microorganisms and mechanisms responsible for lactate and butyrate production in silage are not well documented.

METHODS AND RESULTS: whole-metagenomic sequencing was used to analyse metabolic pathways, microbiota composition, functional genes, and their contributions to lactate and butyrate production in alfalfa silage with (SA) and without (CK) sucrose addition. Carbon metabolism was the most abundant metabolic pathway. We identified 11 and 2 functional genes associated with lactate and butyrate metabolism, respectively. Among them, D-lactate dehydrogenase (ldhA) and L-lactate dehydrogenase (ldhB) were most important for the transition between D/L-lactate and pyruvate and were primarily related to Lactobacillus in the SA group. The genes encoding L-lactate dehydrogenase (lldD), which decomposes lactate, were the most abundant and primarily associated with Enterobacter cloacae. Butyrate-related genes, mainly encoding butyryl-CoA: acetate CoA-transferase (but), were predominantly associated with Klebsiella oxytoca and Escherichia coli in the CK group.

CONCLUSIONS: Enterobacteriaceae and Lactobacillaceae were mainly responsible for butyrate and lactate formation, respectively.}, } @article {pmid37659809, year = {2023}, author = {Li, Z and Wen, Q and Pi, J and Zhang, D and Nie, J and Wei, W and Li, W and Guo, DA}, title = {An inulin-type fructan isolated from Serratula chinensis alleviated the dextran sulfate sodium-induced colitis in mice through regulation of intestinal barrier and gut microbiota.}, journal = {Carbohydrate polymers}, volume = {320}, number = {}, pages = {121206}, doi = {10.1016/j.carbpol.2023.121206}, pmid = {37659809}, issn = {1879-1344}, mesh = {Animals ; Mice ; Inulin/pharmacology/therapeutic use ; Fructans/pharmacology/therapeutic use ; *Gastrointestinal Microbiome ; Dextran Sulfate/toxicity ; Spectroscopy, Fourier Transform Infrared ; *Colitis/chemically induced/drug therapy ; }, abstract = {Herein, we aimed to explore the polysaccharide material basis of Serratula chinensis and establish its beneficial effects against colitis. A neutral polysaccharide (SCP) was extracted from S. chinensis in high yield using hot water. The molecular weights were calculated by HPSEC as Mw = 2928 Da, Mn = 2634 Da, and Mw/Mn = 1.11. FT-IR and 1D/2D-NMR spectroscopic analyses confirmed that SCP was an inulin-type fructan with α-D-Glcp-(1 → [1)-β-D-Fruf-(2]17) linkages. Treatment with SCP (200 or 400 mg/kg) alleviated dextran sulfate sodium (DSS)-induced mouse colitis symptoms, including the loss of body weight, increase of disease activity index score, and shortening of colon length. Histopathological and immunofluorescence assessments revealed that SCP could reduce pathological damage to the colon, restore the number of goblet cells, increase the content of glycoproteins in goblet cells and mucins in crypts, and enhance the expression of tight junction proteins ZO-1 and occludin. In addition, metagenomic sequencing revealed that SCP could improve the dysbiosis of gut microbiomes and act on multiple microbial functions. Moreover, SCP treatment increased the content of colonic acetic acid and butanoic acid. Collectively, these results indicated that SCP could alleviate the DSS-induced colitis in mice through regulation of intestinal barrier and gut microbiota.}, } @article {pmid37659640, year = {2023}, author = {Zheng, N and Hu, W and Zhou, X and Liu, Y and Bartlam, M and Wang, Y}, title = {Influence of phycospheric bacterioplankton disruption or removal on algae growth and survival.}, journal = {Environmental research}, volume = {237}, number = {Pt 2}, pages = {117060}, doi = {10.1016/j.envres.2023.117060}, pmid = {37659640}, issn = {1096-0953}, abstract = {Phycospheric bacteria play a crucial role in the survival of microalgae. However, the potential of using the growth regulation and community structure modulation of phycospheric bacteria to prevent the occurrence of blooms is yet to be verified. The phycospheric bacterioplankton of Cyclotella sp. can be categorized into HNA (high nucleic acid) bacteria and LNA (low nucleic acid) bacteria. 16S rRNA sequencing showed that the HNA bacteria exhibited higher α-diversity compared to the LNA bacteria, and the microbial community composition also exhibited variations. Metagenomic sequencing further indicated the distinct ecological functions between HNA and LNA bacteria. Furthermore, the study showcased the restorative capacity of the phycospheric bacterioplankton. Biomass analysis revealed that the recovery of phycospheric bacterioplankton positively influenced the microalgae growth, thus affirming the significance of phycospheric bacterioplankton to microalgae. The community structure of phycospheric bacterioplankton demonstrated a notable decrease in the abundance of restored LNA core bacteria. Additionally, the restored phycospheric bacterioplankton exhibited a more complex co-occurrence network structure, resulting in decreased resistance and sensitivity of microalgae to adverse environments. The presence of phycospheric bacterioplankton provides a protective shield for microalgae, and thus destabilizing or removing phycospheric bacterioplankton may effectively inhibit growth of microalgae.}, } @article {pmid37659531, year = {2023}, author = {Wang, Q and Hou, J and Huang, Y and Liu, W and Christie, P}, title = {Metagenomics reveals mechanism of pyrene degradation by an enriched bacterial consortium from a coking site contaminated with PAHs.}, journal = {The Science of the total environment}, volume = {904}, number = {}, pages = {166759}, doi = {10.1016/j.scitotenv.2023.166759}, pmid = {37659531}, issn = {1879-1026}, mesh = {*Polycyclic Aromatic Hydrocarbons/metabolism ; *Coke ; Pyrenes/metabolism ; Bacteria/metabolism ; Biodegradation, Environmental ; *Soil Pollutants/metabolism ; }, abstract = {A bacterial consortium, termed WPB, was obtained from polycyclic aromatic hydrocarbons (PAHs) contaminated soil from a coking site. The consortium effectively degraded 100 mg L[-1] pyrene by 94.8 % within 12 days. WPB was also able to degrade phenanthrene (98.3 %) and benzo[a]pyrene (24.6 %) in 12 days, while the individual isolates showed no PAHs degrading ability. Paracoccus sp. dominated the bacterial consortium (65.0-86.2 %) throughout the degradation process. Metagenomic sequencing reveals the proportion of sequences with xenobiotics biodegradation and metabolism increased throughout the degradation process indicating the great potential of WPB to degrade pollutants. The annotation of genes by metagenomic analysis help reconstruct the degradation pathways ("phthalate pathway" and "naphthalene degradation") and reveal how different bacteria contribute to the degradation process. Mycobacterium gilvum was found to carry nidAB genes that catalyze the first step of high-molecular-weight (HMW) PAHs in the degradation process despite Mycobacterium gilvum accounting for only 0.005-0.06 %. In addition, genomes of Paracoccus denitrificans and some other genera affiliated with Devosia, Pusillimonas caeni and Eoetvoesia caeni were successfully recovered and were found to carry genes responsible for the degradation of the intermediates of pyrene. These results enable further understanding of the metabolic patterns of pyrene-degrading consortia and provide direction for further cultivation and discovery of key players in complex microbial consortia.}, } @article {pmid37658654, year = {2023}, author = {Couso, LL and Soler-Bistué, A and Aptekmann, AA and Sánchez, IE}, title = {Ecology theory disentangles microbial dichotomies.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {3052-3063}, doi = {10.1111/1462-2920.16495}, pmid = {37658654}, issn = {1462-2920}, mesh = {*Bacteria/genetics ; *Microbiota ; Heterotrophic Processes ; Metagenomics ; Carbon ; }, abstract = {Microbes are often discussed in terms of dichotomies such as copiotrophic/oligotrophic and fast/slow-growing microbes, defined using the characterisation of microbial growth in isolated cultures. The dichotomies are usually qualitative and/or study-specific, sometimes precluding clear-cut results interpretation. We can unravel microbial dichotomies as life history strategies by combining ecology theory with Monod curves, a laboratory mathematical tool of bacterial physiology that relates the specific growth rate of a microbe with the concentration of a limiting nutrient. Fitting of Monod curves provides quantities that directly correspond to key parameters in ecological theories addressing species coexistence and diversity, such as r/K selection theory, resource competition and community structure theory and the CSR triangle of life strategies. The resulting model allows us to reconcile the copiotrophic/oligotrophic and fast/slow-growing dichotomies as different subsamples of a life history strategy triangle that also includes r/K strategists. We also used the number of known carbon sources together with community structure theory to partially explain the diversity of heterotrophic microbes observed in metagenomics experiments. In sum, we propose a theoretical framework for the study of natural microbial communities that unifies several existing proposals. Its application would require the integration of metagenomics, metametabolomics, Monod curves and carbon source data.}, } @article {pmid37658443, year = {2023}, author = {Paulo, AC and Lança, J and Almeida, ST and Hilty, M and Sá-Leão, R}, title = {The upper respiratory tract microbiota of healthy adults is affected by Streptococcus pneumoniae carriage, smoking habits, and contact with children.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {199}, pmid = {37658443}, issn = {2049-2618}, mesh = {Adult ; Child ; Humans ; Streptococcus pneumoniae/genetics ; Smoking ; Nose ; *Microbiota ; Metagenome ; *Bacillus ; Firmicutes ; }, abstract = {BACKGROUND: The microbiota of the upper respiratory tract is increasingly recognized as a gatekeeper of respiratory health. Despite this, the microbiota of healthy adults remains understudied. To address this gap, we investigated the composition of the nasopharyngeal and oropharyngeal microbiota of healthy adults, focusing on the effect of Streptococcus pneumoniae carriage, smoking habits, and contact with children.

RESULTS: Differential abundance analysis indicated that the microbiota of the oropharynx was significantly different from that of the nasopharynx (P < 0.001) and highly discriminated by a balance between the classes Negativicutes and Bacilli (AUC of 0.979). Moreover, the oropharynx was associated with a more homogeneous microbiota across individuals, with just two vs. five clusters identified in the nasopharynx. We observed a shift in the nasopharyngeal microbiota of carriers vs. noncarriers with an increased relative abundance of Streptococcus, which summed up to 30% vs. 10% in noncarriers and was not mirrored in the oropharynx. The oropharyngeal microbiota of smokers had a lower diversity than the microbiota of nonsmokers, while no differences were observed in the nasopharyngeal microbiota. In particular, the microbiota of smokers, compared with nonsmokers, was enriched (on average 16-fold) in potential pathogenic taxa involved in periodontal diseases of the genera Bacillus and Burkholderia previously identified in metagenomic studies of cigarettes. The microbiota of adults with contact with children resembled the microbiota of children. Specifically, the nasopharyngeal microbiota of these adults had, on average, an eightfold increase in relative abundance in Streptococcus sp., Moraxella catarrhalis, and Haemophilus influenzae, pathobionts known to colonize the children's upper respiratory tract, and a fourfold decrease in Staphylococcus aureus and Staphylococcus lugdunensis.

CONCLUSIONS: Our study showed that, in adults, the presence of S. pneumoniae in the nasopharynx is associated with a shift in the microbiota and dominance of the Streptococcus genus. Furthermore, we observed that smoking habits are associated with an increase in bacterial genera commonly linked to periodontal diseases. Interestingly, our research also revealed that adults who have regular contact with children have a microbiota enriched in pathobionts frequently carried by children. These findings collectively contribute to a deeper understanding of how various factors influence the upper respiratory tract microbiota in adults. Video Abstract.}, } @article {pmid37658428, year = {2023}, author = {Mao, Q and Liu, Y and Zhang, J and Li, W and Zhang, W and Zhou, C}, title = {Blood virome of patients with traumatic sepsis.}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {198}, pmid = {37658428}, issn = {1743-422X}, mesh = {Humans ; Virome ; *Sepsis/diagnosis ; *Anelloviridae/genetics ; Immunocompromised Host ; Metagenome ; }, abstract = {Sepsis is one of the possible outcomes of severe trauma, and it poses a dire threat to human life, particularly in immunocompromised people. The most prevalent pathogens are bacteria and fungi, but viruses should not be overlooked. For viral metagenomic analysis, we collected blood samples from eight patients with post-traumatic sepsis before and seven days after treatment. The results demonstrated that Anellovirus predominated the viral community, followed by Siphoviridae and Myoviridae, and that the variations in viral community and viral load before and after treatment were not statistically significant. This study allows us to investigate methods for establishing NGS-based viral diagnostic instruments for detecting viral infections in the blood of sepsis patients so that antiviral therapy can be administered quickly.}, } @article {pmid37658324, year = {2023}, author = {Laso-Jadart, R and O'Malley, M and Sykulski, AM and Ambroise, C and Madoui, MA}, title = {Holistic view of the seascape dynamics and environment impact on macro-scale genetic connectivity of marine plankton populations.}, journal = {BMC ecology and evolution}, volume = {23}, number = {1}, pages = {46}, pmid = {37658324}, issn = {2730-7182}, mesh = {Animals ; *Plankton/genetics ; *Acclimatization ; Zooplankton/genetics ; Genomics ; Atlantic Ocean ; Eukaryota ; }, abstract = {BACKGROUND: Plankton seascape genomics studies have revealed different trends from large-scale weak differentiation to microscale structures. Previous studies have underlined the influence of the environment and seascape on species differentiation and adaptation. However, these studies have generally focused on a few single species, sparse molecular markers, or local scales. Here, we investigated the genomic differentiation of plankton at the macro-scale in a holistic approach using Tara Oceans metagenomic data together with a reference-free computational method.

RESULTS: We reconstructed the FST-based genomic differentiation of 113 marine planktonic taxa occurring in the North and South Atlantic Oceans, Southern Ocean, and Mediterranean Sea. These taxa belong to various taxonomic clades spanning Metazoa, Chromista, Chlorophyta, Bacteria, and viruses. Globally, population genetic connectivity was significantly higher within oceanic basins and lower in bacteria and unicellular eukaryotes than in zooplankton. Using mixed linear models, we tested six abiotic factors influencing connectivity, including Lagrangian travel time, as proxies of oceanic current effects. We found that oceanic currents were the main population genetic connectivity drivers, together with temperature and salinity. Finally, we classified the 113 taxa into parameter-driven groups and showed that plankton taxa belonging to the same taxonomic rank such as phylum, class or order presented genomic differentiation driven by different environmental factors.

CONCLUSION: Our results validate the isolation-by-current hypothesis for a non-negligible proportion of taxa and highlight the role of other physicochemical parameters in large-scale plankton genetic connectivity. The reference-free approach used in this study offers a new systematic framework to analyse the population genomics of non-model and undocumented marine organisms from a large-scale and holistic point of view.}, } @article {pmid37658057, year = {2023}, author = {Sun, Z and Liu, J and Zhang, M and Wang, T and Huang, S and Weiss, ST and Liu, YY}, title = {Removal of false positives in metagenomics-based taxonomy profiling via targeting Type IIB restriction sites.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5321}, pmid = {37658057}, issn = {2041-1723}, support = {K99 HL163519/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Metagenomics ; Base Sequence ; Benchmarking ; Computer Simulation ; *Inflammatory Bowel Diseases ; }, abstract = {Accurate species identification and abundance estimation are critical for the interpretation of whole metagenome sequencing (WMS) data. Yet, existing metagenomic profilers suffer from false-positive identifications, which can account for more than 90% of total identified species. Here, by leveraging species-specific Type IIB restriction endonuclease digestion sites as reference instead of universal markers or whole microbial genomes, we present a metagenomic profiler, MAP2B (MetAgenomic Profiler based on type IIB restriction sites), to resolve those issues. We first illustrate the pitfalls of using relative abundance as the only feature in determining false positives. We then propose a feature set to distinguish false positives from true positives, and using simulated metagenomes from CAMI2, we establish a false-positive recognition model. By benchmarking the performance in metagenomic profiling using a simulation dataset with varying sequencing depth and species richness, we illustrate the superior performance of MAP2B over existing metagenomic profilers in species identification. We further test the performance of MAP2B using real WMS data from an ATCC mock community, confirming its superior precision against sequencing depth. Finally, by leveraging WMS data from an IBD cohort, we demonstrate the taxonomic features generated by MAP2B can better discriminate IBD and predict metabolomic profiles.}, } @article {pmid37657702, year = {2023}, author = {Lu, Q and Wang, S and Ping, Q and Li, Y}, title = {A novel approach to enhance methane production during anaerobic digestion of waste activated sludge by combined addition of trypsin, nano-zero-valent iron and activated carbon.}, journal = {Chemosphere}, volume = {341}, number = {}, pages = {140007}, doi = {10.1016/j.chemosphere.2023.140007}, pmid = {37657702}, issn = {1879-1298}, mesh = {*Iron/metabolism ; *Sewage/microbiology ; Charcoal ; Trypsin/metabolism ; Anaerobiosis ; Methane/metabolism ; Bioreactors/microbiology ; }, abstract = {A novel approach with a combination of trypsin, nano-zero-valent iron (NZVI) and activated carbon (AC) was conducted to promote the methane production of waste activated sludge (WAS) during the anaerobic digestion (AD) processes. Results showed that the combined addition of trypsin-NZVI-AC exhibited the synergistic effect during different AD stages. Trypsin mainly facilitated the hydrolysis process and the acetic acid conversion, while NZVI-AC enhanced the substrate metabolism and the electronic transfer to subsequently produce methane. A dose of 1000 mg/L trypsin was optimal to maximize this synergistic effect. Metagenomic analysis showed that trypsin-NZVI-AC addition effectively improved the relative abundance of acetyl-CoA carboxylase, and then strengthened both acetoclastic methanogenesis (M00357) and hydrogenotrophic methanogenesis (M00567). Hydrogenotrophic methanogens such as Methanobacterium, Methanoculleus, and Methanosarcina were greatly enriched with trypsin-NZVI-AC compared with trypsin or NZVI-AC addition. Moreover, electroactive bacteria G. sulfurreducens and G. metallireducens were also enriched by this method to conduct direct interspecies electron transfer among methanogens, leading to the better improvement of methane production. These findings supply a promising way to optimize the enzyme pretreatment technology and elevate the methanogenic efficiency of WAS.}, } @article {pmid37657648, year = {2023}, author = {Yao, W and Feng, S and Yang, L and Lin, Y and Zhang, M and Cai, K and Xing, L and Yuan, K and Lu, H and Wang, F}, title = {Differences caused by blood and secretion samples for the detection of Klebsiella pneumoniae using metagenomic next-generation sequencing: A comparative analysis.}, journal = {The Journal of infection}, volume = {87}, number = {5}, pages = {438-444}, doi = {10.1016/j.jinf.2023.08.011}, pmid = {37657648}, issn = {1532-2742}, } @article {pmid37657643, year = {2023}, author = {Osman, A and Mervosh, NL and Strat, AN and Euston, TJ and Zipursky, G and Pollak, RM and Meckel, KR and Tyler, SR and Chan, KL and Buxbaum Grice, A and Drapeau, E and Litichevskiy, L and Gill, J and Zeldin, SM and Thaiss, CA and Buxbaum, JD and Breen, MS and Kiraly, DD}, title = {Acetate supplementation rescues social deficits and alters transcriptional regulation in prefrontal cortex of Shank3 deficient mice.}, journal = {Brain, behavior, and immunity}, volume = {114}, number = {}, pages = {311-324}, doi = {10.1016/j.bbi.2023.08.020}, pmid = {37657643}, issn = {1090-2139}, abstract = {BACKGROUND: The pathophysiology of autism spectrum disorder (ASD) involves genetic and environmental factors. Mounting evidence demonstrates a role for the gut microbiome in ASD, with signaling via short-chain fatty acids (SCFA) as one mechanism. Here, we utilize mice carrying deletion to exons 4-22 of Shank3 (Shank3[KO]) to model gene by microbiome interactions in ASD. We identify SCFA acetate as a mediator of gut-brain interactions and show acetate supplementation reverses social deficits concomitant with alterations to medial prefrontal cortex (mPFC) transcriptional regulation independent of microbiome status.

METHODS: Shank3[KO] and wild-type (Wt) littermates were divided into control, Antibiotic (Abx), Acetate and Abx + Acetate groups upon weaning. After six weeks, animals underwent behavioral testing. Molecular analysis including 16S and metagenomic sequencing, metabolomic and transcriptional profiling were conducted. Additionally, targeted serum metabolomic data from Phelan McDermid Syndrome (PMS) patients (who are heterozygous for the Shank3 gene) were leveraged to assess levels of SCFA's relative to ASD clinical measures.

RESULTS: Shank3[KO] mice were found to display social deficits, dysregulated gut microbiome and decreased cecal levels of acetate - effects exacerbated by Abx treatment. RNA-sequencing of mPFC showed unique gene expression signature induced by microbiome depletion in the Shank3[KO] mice. Oral treatment with acetate reverses social deficits and results in marked changes in gene expression enriched for synaptic signaling, pathways among others, even in Abx treated mice. Clinical data showed sex specific correlations between levels of acetate and hyperactivity scores.

CONCLUSION: These results suggest a key role for the gut microbiome and the neuroactive metabolite acetate in regulating ASD-like behaviors.}, } @article {pmid37657622, year = {2023}, author = {Dong, Z and Xie, Q and Yuan, Y and Shen, X and Hao, Y and Li, J and Xu, H and Kuang, W}, title = {Strain-level structure of gut microbiome showed potential association with cognitive function in major depressive disorder: A pilot study.}, journal = {Journal of affective disorders}, volume = {341}, number = {}, pages = {236-247}, doi = {10.1016/j.jad.2023.08.129}, pmid = {37657622}, issn = {1573-2517}, mesh = {Animals ; Humans ; *Depressive Disorder, Major ; *Gastrointestinal Microbiome/genetics ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Cognition ; }, abstract = {BACKGROUND: Although the association between gut microbiota and the pathogenesis of major depressive disorder (MDD) has been well studied, it is unclear whether gut microbiota affects cognitive function in patients with MDD. In this study, we explored the association between gut microbiota and cognitive function in MDD and its possible mechanisms.

METHODS: We enrolled 57 patients with MDD and 30 healthy controls (HCs) and used 16S rRNA gene sequencing analysis and shotgun metagenomic sequencing analysis to determine gut microbial composition.

RESULTS: The richness and diversity of gut microbiota in patients with MDD were the same as those in HCs, but there were differences in the abundance of Bifidobacterium and Blautia. Compared with HCs, two strains (bin_32 and bin_55) were significantly increased, and one strain (bin_31) was significantly decreased in patients with MDD based on the strain-level meta-analysis. Time to complete the Stroop-C had significant negative correlations with bin_31 and bin_32. Bin_55 had significant negative correlations with time to complete the Stroop-C, time to complete the Stroop-CW, and repeated animal words in 60 s but significant positive correlations with correct answers in 120 s on the Stroop-CW.

LIMITATIONS: This study only tested the cognitive function of MDD in a small sample, which may have caused some bias.

CONCLUSIONS: Based on our strain-level analysis, we found that gut microbiota may be associated with the pathogenesis of MDD and may have potential effects on cognitive function.}, } @article {pmid37657296, year = {2023}, author = {Fu, S and Zhang, Y and Wang, R and Qiu, Z and Song, W and Yang, Q and Shen, L}, title = {A novel culture-enriched metagenomic sequencing strategy effectively guarantee the microbial safety of drinking water by uncovering the low abundance pathogens.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118737}, doi = {10.1016/j.jenvman.2023.118737}, pmid = {37657296}, issn = {1095-8630}, mesh = {*Metagenome ; *Drinking Water ; Phylogeny ; Anti-Bacterial Agents ; Risk Management ; }, abstract = {Assessing the presence of waterborne pathogens and antibiotic resistance genes (ARGs) is crucial for managing the environmental quality of drinking water sources. However, detecting low abundance pathogens in such settings is challenging. In this study, a workflow was developed to enrich for broad spectrum pathogens from drinking water samples. A mock community was used to evaluate the effectiveness of various enrichment broths in detecting low-abundance pathogens. Monthly metagenomic surveillance was conducted in a drinking water source from May to September 2021, and water samples were subjected to five enrichment procedures for 6 h to recover the majority of waterborne bacterial pathogens. Oxford Nanopore Technology (ONT) was used for metagenomic sequencing of enriched samples to obtain high-quality pathogen genomes. The results showed that selective enrichment significantly increased the proportions of targeted bacterial pathogens. Compared to direct metagenomic sequencing of untreated water samples, targeted enrichment followed by ONT sequencing significantly improved the detection of waterborne pathogens and the quality of metagenome-assembled genomes (MAGs). Eighty-six high-quality MAGs, including 70 pathogen MAGs, were obtained from ONT sequencing, while only 12 MAGs representing 10 species were obtained from direct metagenomic sequencing of untreated water samples. In addition, ONT sequencing improved the recovery of mobile genetic elements and the accuracy of phylogenetic analysis. This study highlights the urgent need for efficient methodologies to detect and manage microbial risks in drinking water sources. The developed workflow provides a cost-effective approach for environmental management of drinking water sources with microbial risks. The study also uncovered pathogens that were not detected by traditional methods, thereby advancing microbial risk management of drinking water sources.}, } @article {pmid37655346, year = {2023}, author = {Gutierrez, T and Liu, H}, title = {Editorial: Rising stars in aquatic microbiology: 2022.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1265720}, doi = {10.3389/fmicb.2023.1265720}, pmid = {37655346}, issn = {1664-302X}, } @article {pmid37655299, year = {2023}, author = {Shen, H and Liu, T and Shen, M and Zhang, Y and Chen, W and Chen, H and Wang, Y and Liu, J and Tao, J and He, L and Lu, G and Yan, G}, title = {Utilizing metagenomic next-generation sequencing for diagnosis and lung microbiome probing of pediatric pneumonia through bronchoalveolar lavage fluid in pediatric intensive care unit: results from a large real-world cohort.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1200806}, pmid = {37655299}, issn = {2235-2988}, mesh = {Humans ; Child ; Bronchoalveolar Lavage Fluid ; Retrospective Studies ; *Pneumonia/diagnosis ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; Intensive Care Units, Pediatric ; Lung ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a powerful method for pathogen detection in various infections. In this study, we assessed the value of mNGS in the pathogen diagnosis and microbiome analysis of pneumonia in pediatric intensive care units (PICU) using bronchoalveolar lavage fluid (BALF) samples.

METHODS: A total of 104 pediatric patients with pneumonia who were admitted into PICU between June 2018 and February 2020 were retrospectively enrolled. Among them, 101 subjects who had intact clinical information were subject to parallel comparison of mNGS and conventional microbiological tests (CMTs) for pathogen detection. The performance was also evaluated and compared between BALF-mNGS and BALF-culture methods. Moreover, the diversity and structure of all 104 patients' lung BALF microbiomes were explored using the mNGS data.

RESULTS: Combining the findings of mNGS and CMTs, 94.06% (95/101) pneumonia cases showed evidence of causative pathogenic infections, including 79.21% (80/101) mixed and 14.85% (15/101) single infections. Regarding the pathogenesis of pneumonia in the PICU, the fungal detection rates were significantly higher in patients with immunodeficiency (55.56% vs. 25.30%, P =0.025) and comorbidities (40.30% vs. 11.76%, P=0.007). There were no significant differences in the α-diversity either between patients with CAP and HAP or between patients with and without immunodeficiency. Regarding the diagnostic performance, the detection rate of DNA-based BALF-mNGS was slightly higher than that of the BALF-culture although statistically insignificant (81.82% vs.77.92%, P=0.677) and was comparable to CMTs (81.82% vs. 89.61%, P=0.211). The overall sensitivity of DNA-based mNGS was 85.14% (95% confidence interval [CI]: 74.96%-92.34%). The detection rate of RNA-based BALF-mNGS was the same with CMTs (80.00% vs 80.00%, P>0.999) and higher than BALF-culture (80.00% vs 52.00%, P=0.045), with a sensitivity of 90.91% (95%CI: 70.84%-98.88%).

CONCLUSIONS: mNGS is valuable in the etiological diagnosis of pneumonia, especially in fungal infections, and can reveal pulmonary microecological characteristics. For pneumonia patients in PICU, the mNGS should be implemented early and complementary to CMTs.}, } @article {pmid37655298, year = {2023}, author = {Qin, L and Wang, S and Zheng, Z and Zhang, W and Qu, Q and Li, J and Tan, Y and Cao, L}, title = {A complicated infection by cutaneous Nocardia wallacei and pulmonary Mycobacterium abscessus in a Chinese immunocompetent patient: a case report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1229298}, pmid = {37655298}, issn = {2235-2988}, mesh = {Female ; Humans ; Middle Aged ; *Mycobacterium abscessus/genetics ; Abscess ; East Asian People ; *Nocardia/genetics ; *Nocardia Infections/diagnosis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; Lung ; }, abstract = {Nocardiosis is an infectious disease caused by Nocardia that primarily affects immunocompromised hosts. Mycobacterium abscessus is a common opportunistic pathogen that causes disease in humans, including pulmonary and extrapulmonary infection. Nocardia spp. infection is uncommon, and infection with Nocardia wallacei and Mycobacterium abscessus is even rarer. A 59-year-old immunocompetent woman with risk factors for environmental exposure developed nocardiosis and presented to the hospital with a cough, shortness of breath, hemoptysis, and a back abscess. An enhanced computed tomography (CT) of the chest revealed partial destruction of the right lung, as well as consolidation of the right upper lobe. Rare pathogens N. wallacei and Mycobacterium abscessus were detected by metagenomic next-generation sequencing (mNGS) from abscess on the back and lung puncture tissue, respectively. She was treated with a combination of antibiotics and was finally discharged with a good prognosis. In this case, we present a patient who was successfully diagnosed with N. wallacei and Mycobacterium abscessus infection using mNGS. This importance of using mNGS in pathogen detection and the effective use of antibiotics in treating patients with long-term rare infections is highlighted in this report.}, } @article {pmid37653687, year = {2023}, author = {Dixon, TA and Walker, RSK and Pretorius, IS}, title = {Visioning synthetic futures for yeast research within the context of current global techno-political trends.}, journal = {Yeast (Chichester, England)}, volume = {40}, number = {10}, pages = {443-456}, doi = {10.1002/yea.3897}, pmid = {37653687}, issn = {1097-0061}, support = {//Australian Research Council/ ; }, abstract = {Yeast research is entering into a new period of scholarship, with new scientific tools, new questions to ask and new issues to consider. The politics of emerging and critical technology can no longer be separated from the pursuit of basic science in fields, such as synthetic biology and engineering biology. Given the intensifying race for technological leadership, yeast research is likely to attract significant investment from government, and that it offers huge opportunities to the curious minded from a basic research standpoint. This article provides an overview of new directions in yeast research with a focus on Saccharomyces cerevisiae, and places these trends in their geopolitical context. At the highest level, yeast research is situated within the ongoing convergence of the life sciences with the information sciences. This convergent effect is most strongly pronounced in areas of AI-enabled tools for the life sciences, and the creation of synthetic genomes, minimal genomes, pan-genomes, neochromosomes and metagenomes using computer-assisted design tools and methodologies. Synthetic yeast futures encompass basic and applied science questions that will be of intense interest to government and nongovernment funding sources. It is essential for the yeast research community to map and understand the context of their research to ensure their collaborations turn global challenges into research opportunities.}, } @article {pmid37653056, year = {2023}, author = {Takahashi, K and Kuwahara, H and Horikawa, Y and Izawa, K and Kato, D and Inagaki, T and Yuki, M and Ohkuma, M and Hongoh, Y}, title = {Emergence of putative energy parasites within Clostridia revealed by genome analysis of a novel endosymbiotic clade.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {1895-1906}, pmid = {37653056}, issn = {1751-7370}, mesh = {Animals ; Humans ; *Parasites ; Phylogeny ; Eukaryota/genetics ; Bacteria/genetics ; Bacteria, Anaerobic ; Firmicutes ; Mitochondrial ADP, ATP Translocases/genetics ; Adenosine Triphosphate ; Symbiosis/genetics ; *Isoptera/microbiology ; }, abstract = {The Clostridia is a dominant bacterial class in the guts of various animals and are considered to nutritionally contribute to the animal host. Here, we discovered clostridial endosymbionts of cellulolytic protists in termite guts, which have never been reported with evidence. We obtained (near-)complete genome sequences of three endosymbiotic Clostridia, each associated with a different parabasalid protist species with various infection rates: Trichonympha agilis, Pseudotrichonympha grassii, and Devescovina sp. All these protists are previously known to harbor permanently-associated, mutualistic Endomicrobia or Bacteroidales that supplement nitrogenous compounds. The genomes of the endosymbiotic Clostridia were small in size (1.0-1.3 Mbp) and exhibited signatures of an obligately-intracellular parasite, such as an extremely limited capability to synthesize amino acids, cofactors, and nucleotides and a disrupted glycolytic pathway with no known net ATP-generating system. Instead, the genomes encoded ATP/ADP translocase and, interestingly, regulatory proteins that are unique to eukaryotes in general and are possibly used to interfere with host cellular processes. These three genomes formed a clade with metagenome-assembled genomes (MAGs) derived from the guts of other animals, including human and ruminants, and the MAGs shared the characteristics of parasites. Gene flux analysis suggested that the acquisition of the ATP/ADP translocase gene in a common ancestor was probably key to the emergence of this parasitic clade. Taken together, we provide novel insights into the multilayered symbiotic system in the termite gut by adding the presence of parasitism and present an example of the emergence of putative energy parasites from a dominant gut bacterial clade.}, } @article {pmid37653019, year = {2023}, author = {Yue, X and Xi, X and Zhang, M and Bian, J and Chen, Y}, title = {[Pulmonary Mucinous Adenocarcinoma Combined with Bronchial Squamous Cell Papilloma and Infection with Tropheryma Whipplei: A Case Report].}, journal = {Zhongguo fei ai za zhi = Chinese journal of lung cancer}, volume = {26}, number = {7}, pages = {553-558}, pmid = {37653019}, issn = {1999-6187}, mesh = {Humans ; *Lung Neoplasms/complications/diagnosis ; Tropheryma ; *Adenocarcinoma of Lung ; Lung ; Epithelial Cells ; }, abstract = {Simultaneous multiple primary tumors on the same side of the lung with Tropheryma whipplei (TW) infection are rare. We reviewed the clinical data, imaging manifestations, pathological results, diagnosis and treatment of a primary pulmonary mucinous adenocarcinoma (PPMA) patient with bronchial squamous cell papilloma (BSCP) and TW infection, and discussed our treatment experience. The patient mainly presented with chronic cough and sputum, and computed tomography (CT) showed inflammatory changes with multiple nodular shadows. Biopsy of the lower lobe of the right lung showed PPMA, and right lung sub-branchial nodules discovered during bronchoscope revealed BSCP. Metagenomics next generation sequencing (mNGS) of bronchoalveolar lavage fluid showed mixed infection of Streptococcus pneumoniae and TW with a poor anti-infective effect. No clear genetic mutation was detected, and the patient was treated with chemotherapy and regularly followed up. We should improve the awareness of multiple pulmonary pathologies during clinical practice, avoid missed diagnosis and misdiagnosis, and carry out comprehensive treatment after clarifying the diagnosis as soon as possible. .}, } @article {pmid37652953, year = {2023}, author = {Wu, J and Li, C and Gao, P and Zhang, C and Zhang, P and Zhang, L and Dai, C and Zhang, K and Shi, B and Liu, M and Zheng, J and Pan, B and Chen, Z and Zhang, C and Liao, W and Pan, W and Fang, W and Chen, C}, title = {Intestinal microbiota links to allograft stability after lung transplantation: a prospective cohort study.}, journal = {Signal transduction and targeted therapy}, volume = {8}, number = {1}, pages = {326}, pmid = {37652953}, issn = {2059-3635}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Prospective Studies ; *Lung Transplantation ; Cytokines ; Allografts ; }, abstract = {Whether the alternated microbiota in the gut contribute to the risk of allograft rejection (AR) and pulmonary infection (PI) in the setting of lung transplant recipients (LTRs) remains unexplored. A prospective multicenter cohort of LTRs was identified in the four lung transplant centers. Paired fecal and serum specimens were collected and divided into AR, PI, and event-free (EF) groups according to the diagnosis at sampling. Fecal samples were determined by metagenomic sequencing. And metabolites and cytokines were detected in the paired serum to analyze the potential effect of the altered microbiota community. In total, we analyzed 146 paired samples (AR = 25, PI = 43, and EF = 78). Notably, we found that the gut microbiome of AR followed a major depletion pattern with decreased 487 species and compositional diversity. Further multi-omics analysis showed depleted serum metabolites and increased inflammatory cytokines in AR and PI. Bacteroides uniformis, which declined in AR (2.4% vs 0.6%) and was negatively associated with serum IL-1β and IL-12, was identified as a driven specie in the network of gut microbiome of EF. Functionally, the EF specimens were abundant in probiotics related to mannose and cationic antimicrobial peptide metabolism. Furthermore, a support-vector machine classifier based on microbiome, metabolome, and clinical parameters highly predicted AR (AUPRC = 0.801) and PI (AUPRC = 0.855), whereby the microbiome dataset showed a particularly high diagnostic power. In conclusion, a disruptive gut microbiota showed a significant association with allograft rejection and infection and with systemic cytokines and metabolites in LTRs.}, } @article {pmid37652940, year = {2023}, author = {Jacobs, JP and Lee, ML and Rechtman, DJ and Sun, AK and Autran, C and Niklas, V}, title = {Human milk oligosaccharides modulate the intestinal microbiome of healthy adults.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {14308}, pmid = {37652940}, issn = {2045-2322}, mesh = {Adult ; Female ; Humans ; Infant, Newborn ; *Gastrointestinal Microbiome ; *Milk, Human/chemistry ; *Oligosaccharides/pharmacology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Human milk contains over 200 distinct oligosaccharides, which are critical to shaping the developing neonatal gut microbiome. To investigate whether a complex mixture of human milk oligosaccharides (HMOs) would similarly modulate the adult gut microbiome, HMO-Concentrate derived from pooled donor breast milk was administered orally to 32 healthy adults for 7 days followed by 21 days of monitoring. Fecal samples were collected for 16S rRNA gene sequencing, shotgun metagenomics, and metabolomics analyses. HMO-Concentrate induced dose-dependent Bifidobacterium expansion, reduced microbial diversity, and altered microbial gene content. Following HMO cessation, a microbial succession occurred with diverse taxonomic changes-including Bacteroides expansion-that persisted through day 28. This was associated with altered microbial gene content, shifts in serum metabolite levels, and increased circulating TGFβ and IL-10. Incubation of cultured adult microbiota with HMO-Concentrate induced dose-dependent compositional shifts that were not recapitulated by individual HMOs or defined mixtures of the 10 most abundant HMOs in HMO-Concentrate at their measured concentrations. These findings support that pooled donor HMOs can exert direct effects on adult gut microbiota and that complex mixtures including low abundance HMOs present in donor milk may be required for maximum effect.Registration: ClinicalTrials.gov NCT05516225.}, } @article {pmid37652786, year = {2023}, author = {Delavy, M and Sertour, N and d'Enfert, C and Bougnoux, ME}, title = {Metagenomics and metabolomics approaches in the study of Candida albicans colonization of host niches: a framework for finding microbiome-based antifungal strategies.}, journal = {Trends in microbiology}, volume = {31}, number = {12}, pages = {1276-1286}, doi = {10.1016/j.tim.2023.08.002}, pmid = {37652786}, issn = {1878-4380}, mesh = {Female ; Humans ; Candida albicans/genetics ; Antifungal Agents/pharmacology ; *Gastrointestinal Microbiome ; *Microbiota ; Metabolomics ; Bacteria ; }, abstract = {In silico and experimental approaches have allowed an ever-growing understanding of the interactions within the microbiota. For instance, recently acquired data have increased knowledge of the mechanisms that support, in the gut and vaginal microbiota, the resistance to colonization by Candida albicans, an opportunistic fungal pathogen whose overgrowth can initiate severe infections in immunocompromised patients. Here, we review how bacteria from the microbiota interact with C. albicans. We show how recent OMICs-based pipelines, using metagenomics and/or metabolomics, have identified bacterial species and metabolites modulating C. albicans growth. We finally discuss how the combined use of cutting-edge OMICs-based and experimental approaches could provide new means to control C. albicans overgrowth within the microbiota and prevent its consequences.}, } @article {pmid37652370, year = {2023}, author = {Xin, M and Sun, Y and Li, W and Li, X and Long, Y and Bian, R and Wang, YN and Wang, H and Huang, Q}, title = {Metagenomics insights into the effect of co-landfill of incineration fly ash and refuse for bacterial community succession and metabolism pathway of VFAs production.}, journal = {The Science of the total environment}, volume = {904}, number = {}, pages = {166705}, doi = {10.1016/j.scitotenv.2023.166705}, pmid = {37652370}, issn = {1879-1026}, mesh = {*Incineration ; Coal Ash/chemistry ; Solid Waste/analysis ; *Refuse Disposal/methods ; Waste Disposal Facilities ; }, abstract = {With the development of incineration technologies, incineration has become the most common treatment method of municipal solid waste in China. However, stabilized fly ash may enter landfills during the transition from landfill to incineration, which caused uncertain impact on landfill waste stabilization. Two simulated co-landfill columns were constructed based on different co-landfill methods (layer co-landfill and mixed co-landfill) to investigate the effect of stabilized fly ash co-landfilled municipal solid waste for bacterial community succession and change in metabolic pathways during hydrolysis-acidogenesis stage. The mixed co-landfill method resulted in higher degree of organic matter degradation, and the concentrations of volatile fatty acids (VFA) and chemical oxygen demand (COD) in leachate were higher. The dominant phyla were Firmicutes in the layered co-landfill column and Bacteroidetes in mixed co-landfill column. The dominant genera for the total bacterial composition and VFA production were different, Pseudomonas and Propionibacterium, Proteiniphilum and unclassified Bacteroides were the dominant genera responsible for VFA generation in the layered and mixed co-landfill columns. The genes for butyrate production were enriched in the layered co-landfill column, whereas those related to acetate production were enriched in mixed co-landfill column. However, the layered co-landfill inhibited the microbial metabolic activity at the end of the co-landfill process.}, } @article {pmid37652264, year = {2023}, author = {Zhang, B and Zhang, X and Luo, Z and Ren, J and Yu, X and Zhao, H and Wang, Y and Zhang, W and Tian, W and Wei, X and Ding, Q and Yang, H and Jin, Z and Tong, X and Wang, J and Zhao, L}, title = {Microbiome and metabolome dysbiosis analysis in impaired glucose tolerance for the prediction of progression to diabetes mellitus.}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jgg.2023.08.005}, pmid = {37652264}, issn = {1673-8527}, abstract = {Gut microbiota and circulating metabolite dysbiosis predate important pathological changes in glucose metabolic disorders; however, comprehensive studies on impaired glucose tolerance (IGT), a diabetes mellitus (DM) precursor, are lacking. Here, we perform metagenomic sequencing and metabolomics on 47 pairs of individuals with IGT and newly diagnosed DM and 46 controls with normal glucose tolerance (NGT); patients with IGT are followed-up after 4 years for progression to DM. Analysis of baseline data reveals significant differences in gut microbiota and serum metabolites among the IGT, DM, and NGT groups. In addition, 13 types of gut microbiota and 17 types of circulating metabolites showed significant differences at baseline before IGT progressed to DM, including higher levels of Eggerthella unclassified, Coprobacillus unclassified, Clostridium ramosum, L-valine, L-norleucine, and L-isoleucine, and lower levels of Eubacterium eligens, Bacteroides faecis, Lachnospiraceae bacterium 3_1_46FAA, Alistipes senegalensis, Megaspaera elsdenii, Clostridium perfringens, α-linolenic acid, 10E, 12Z octadecadienoic acid, and dodecanoic acid. A random forest model based on differential intestinal microbiota and circulating metabolites can predict the progression from IGT to DM (AUC = 0.87). These results suggest that microbiome and metabolome dysbiosis occur in individuals with IGT and have important predictive values and potential for intervention in preventing IGT from progressing to DM.}, } @article {pmid37652096, year = {2024}, author = {Carrascosa-Carrillo, JM and Aterido, A and Li, T and Guillén, Y and Martinez, S and Marsal, S and Julià, A}, title = {Toward Precision Medicine in Atopic Dermatitis Using Molecular-Based Approaches.}, journal = {Actas dermo-sifiliograficas}, volume = {115}, number = {1}, pages = {66-75}, doi = {10.1016/j.ad.2023.08.003}, pmid = {37652096}, issn = {1578-2190}, mesh = {Child ; Humans ; *Dermatitis, Atopic/genetics/therapy ; Precision Medicine ; Skin/pathology ; T-Lymphocytes ; Biomarkers/metabolism ; }, abstract = {Atopic dermatitis is the most common chronic inflammatory skin disorder, affecting up to 20% of children and 10% of adults in developed countries. The pathophysiology of atopic dermatitis is complex and involves a strong genetic predisposition and T-cell driven inflammation. Although our understanding of the pathology and drivers of this disease has improved in recent years, there are still knowledge gaps in the immune pathways involved. Therefore, advances in new omics technologies in atopic dermatitis will play a key role in understanding the pathogenesis of this burden disease and could develop preventive strategies and personalized treatment strategies. In this review, we discuss the latest developments in genetics, transcriptomics, epigenomics, proteomics, and metagenomics and understand how integrating multiple omics datasets will identify potential biomarkers and uncover nets of associations between several molecular levels.}, } @article {pmid37651462, year = {2023}, author = {Charlys da Costa, A and Mendes-Correa, MC and Tozetto-Mendoza, TR and Villas-Boas, LS and de Paula, AV and Paiao, HGO and Leal, FE and Ferreira, NE and Honorato, L and Leal, E and Grandi, G and Dos Santos Morais, V and Manuli, ER and Sabino, EC and Witkin, SS}, title = {Detailed characterization of Redondovirus in saliva of SARS-CoV-2-infected individuals in Sao Paulo, Brazil.}, journal = {PloS one}, volume = {18}, number = {8}, pages = {e0291027}, pmid = {37651462}, issn = {1932-6203}, mesh = {Female ; Male ; Humans ; *SARS-CoV-2 ; *COVID-19 ; Brazil/epidemiology ; Phylogeny ; Saliva ; }, abstract = {BACKGROUND: Redondovirus (ReDoV) is a DNA virus present in the respiratory tract of many healthy individuals. Since SARS-CoV-2, the virus responsible for COVID-19, also primarily infects the same site, we evaluated whether ReDoV was present at increased frequency in patients with COVID-19 and influenced infection parameters.

METHODS: Saliva samples were collected weekly from 59 individuals with COVID-19 and from 132 controls. ReDoV was detected by polymerase chain reaction and the genotypes were identified by metagenomics. Torque Teno Virus (TTV) in these samples were previously reported.

RESULTS: ReDoV was detected in saliva more frequently from COVID-19 patients (72.9%) than from controls (50.0%) (p = 0.0015). There were no associations between ReDoV detection and either continuous or intermittent SARS-CoV-2 shedding, the duration of SARS-CoV-2 detection in saliva, patients' sex or if infection was by the B1 or Gamma strain. The two ReDoV strains, Brisavirus and Vientovirus, were present in equivalent frequencies in ReDoV-positive COVID-19 patients and controls. Phylogenetic analysis suggested that the two ReDoV strains in Brazil were similar to strains previously detected on other continents.

CONCLUSION: ReDoV expression in saliva is increased in males and females in Brazil with mild COVID-19 but its presence does not appear to influence properties of the SARS-CoV-2 infection.}, } @article {pmid37651004, year = {2023}, author = {Saini, N and Aamir, M and Singh, VK and Deepak, B and Mona, S}, title = {Unveiling the microbial diversity and functional dynamics of Shiv Kund, Sohna hot spring, India through a shotgun metagenomics approach.}, journal = {Archives of microbiology}, volume = {205}, number = {9}, pages = {323}, pmid = {37651004}, issn = {1432-072X}, mesh = {*Hot Springs ; Metagenomics ; India ; *Acinetobacter baumannii/genetics ; Biological Evolution ; }, abstract = {In this research, we examined the microbial diversity in Sohna hot spring, Haryana, India using shotgun metagenome sequencing based on the Illumina Hiseq 4000 sequencing technology. The raw sequence data from metagenomic paired-end libraries were analysed for taxonomic classification, diversity, and functional annotation using MG-RAST online server. The results showed the presence of total of 57 phyla, 931 genera, and 2068 species, predominantly occupied by Moraxellaceae (Gammaproteobacteria). However, at the species level, we reported the presence of some representative pathogenic taxa, such as Acinetobacter baumannii and Moraxella osloensis. The functional annotation predicted at various levels based on SEED-based subsystem, KEGG ortholog identity (KO), Cluster of Orthologous Groups (COGs) database identified the predominance of genes associated with primary and secondary metabolism along with a crucial role in environmental and genetic signals, cellular communication, and cell signalling. Comparative Genome Analysis (CGA) using The Pathosystem Resource Integration Centre (PATRIC) tool based on genome annotation and assembly of the metagenomic libraries for representative taxon Acinetobacter baumannii (NCBI tax id:470) characterized the reads with a unique genome identifier of 470.20380 (A. baumannii DDLJ4) which is evolutionary closer to A. baumannii ATCC 470.17978 400667.7. In addition, the CARD database results about the presence of potential AMR pathotypes and the prevalence of adeABC, adeIJK, abeM gene-specific clusters that function as multidrug efflux pumps. Overall, the results provided a comprehensive insight into virulence and anti-microbial resistance mechanism and could be useful for developing potential drug targets against the possible AMR pathotypes.}, } @article {pmid37650684, year = {2023}, author = {Chaudhary, M and Sitaula, S and Ruder, K and Chen, C and Zhong, L and Heng Lu, Y and Abraham, T and Yu, D and Hinterwirth, A and Lietman, TM and Doan, T and Seitzman, GD and , }, title = {Heterogenous pathogen profile associated with acute conjunctivitis in Nepal.}, journal = {International health}, volume = {}, number = {}, pages = {}, doi = {10.1093/inthealth/ihad079}, pmid = {37650684}, issn = {1876-3405}, support = {R01 EY032041/EY/NEI NIH HHS/United States ; /NH/NIH HHS/United States ; R01EY032041/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Infectious conjunctivitis is common in Nepal.

MATERIALS AND METHODS: This prospective study recruited 60 patients with presumed acute infectious conjunctivitis from the B.P. Koirala Lions Center for Ophthalmic Studies in Kathmandu, Nepal. Swabs from the conjunctiva and anterior nares were processed for metagenomic RNA deep sequencing (RNA-seq).

RESULTS: Pathogens were identified in 55% of cases. RNA viruses were the most common pathogen class identified. Severe acute respiratory syndrome coronavirus 2 was the most common RNA virus identified.

CONCLUSIONS: Acute infectious conjunctivitis varies by location. Contrary to expectations, RNA viruses predominated. Repeat surveillance may be useful and RNA-seq allows for detection of the unexpected pathogen including RNA viruses.}, } @article {pmid37650630, year = {2023}, author = {Koziol, A and Odriozola, I and Leonard, A and Eisenhofer, R and San José, C and Aizpurua, O and Alberdi, A}, title = {Mammals show distinct functional gut microbiome dynamics to identical series of environmental stressors.}, journal = {mBio}, volume = {14}, number = {5}, pages = {e0160623}, pmid = {37650630}, issn = {2150-7511}, support = {R250-2017-1351//Lundbeck Foundation (Lundbeckfonden)/ ; DNRF143//Danmarks Grundforskningsfond (DNRF)/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Phylogeny ; Mammals ; *Microbiota ; Metagenomics ; RNA, Ribosomal, 16S ; }, abstract = {In our manuscript, we report the first interspecific comparative study about the plasticity of the gut microbiota. We conducted a captivity experiment that exposed wild-captured mammals to a series of environmental challenges over 45 days. We characterized their gut microbial communities using genome-resolved metagenomics and modeled how the taxonomic, phylogenetic, and functional microbial dynamics varied across a series of disturbances in both species. Our results indicate that the intrinsic properties (e.g., diversity and functional redundancy) of microbial communities coupled with physiological attributes (e.g., thermal plasticity) of hosts shape the taxonomic, phylogenetic, and functional response of gut microbiomes to environmental stressors, which might influence their contribution to the acclimation and adaptation capacity of animal hosts.}, } @article {pmid37650612, year = {2023}, author = {Teullet, S and Tilak, M-K and Magdeleine, A and Schaub, R and Weyer, NM and Panaino, W and Fuller, A and Loughry, WJ and Avenant, NL and de Thoisy, B and Borrel, G and Delsuc, F}, title = {Metagenomics uncovers dietary adaptations for chitin digestion in the gut microbiota of convergent myrmecophagous mammals.}, journal = {mSystems}, volume = {8}, number = {5}, pages = {e0038823}, pmid = {37650612}, issn = {2379-5077}, support = {683257//EC | European Research Council (ERC)/ ; ANR-10-LABX-0025//Agence Nationale de la Recherche (ANR)/ ; ANR-10-LABX-0004//Agence Nationale de la Recherche (ANR)/ ; }, mesh = {Pregnancy ; Animals ; Female ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; Chitin ; Placenta ; Mammals/microbiology ; Digestion ; }, abstract = {Myrmecophagous mammals are specialized in the consumption of ants and/or termites. They do not share a direct common ancestor and evolved convergently in five distinct placental orders raising questions about the underlying adaptive mechanisms involved and the relative contribution of natural selection and phylogenetic constraints. Understanding how these species digest their prey can help answer these questions. More specifically, the role of their gut microbial symbionts in the digestion of the insect chitinous exoskeleton has not been investigated in all myrmecophagous orders. We generated 29 new gut metagenomes from nine myrmecophagous species to reconstruct more than 300 bacterial genomes in which we identified chitin-degrading enzymes. Studying the distribution of these chitinolytic bacteria among hosts revealed both shared and specific bacteria between ant-eating species. Overall, our results highlight the potential role of gut symbionts in the convergent dietary adaptation of myrmecophagous mammals and the evolutionary mechanisms shaping their gut microbiota.}, } @article {pmid37650395, year = {2023}, author = {Huang, G and Qi, D and Yang, Z and Hou, R and Shi, W and Zhao, F and Li, Z and Yan, L and Wei, F}, title = {Gut microbiome as a key monitoring indicator for reintroductions of captive animals.}, journal = {Conservation biology : the journal of the Society for Conservation Biology}, volume = {}, number = {}, pages = {e14173}, doi = {10.1111/cobi.14173}, pmid = {37650395}, issn = {1523-1739}, support = {31821001//National Natural Science Foundation of China/ ; 31970386//National Natural Science Foundation of China/ ; 2023090//Chinese Academy of Sciences/ ; XDB31000000//Chinese Academy of Sciences/ ; }, abstract = {Reintroduction programs seek to restore degraded populations and reverse biodiversity loss. To examine the hypothesis that gut symbionts could be used as an indicator of reintroduction success, we performed intensive metagenomic monitoring over 10 years to characterize the ecological succession and adaptive evolution of the gut symbionts of captive giant pandas reintroduced to the wild. We collected 63 fecal samples from 3 reintroduced individuals and 22 from 9 wild individuals and used 96 publicly available samples from another 3 captive individuals. By microbial composition analysis, we identified 3 community clusters of the gut microbiome (here termed enterotypes) with interenterotype succession that was closely related to the reintroduction process. Each of the 3 enterotypes was identified based on significant variation in the levels of 1 of 3 genera: Clostridium, Pseudomonas, and Escherichia. The enterotype of captive pandas was Escherichia. This enterotype was gradually replaced by the Clostridium enterotype during the wild-training process, which in turn was replaced by the Pseudomonas enterotype that resembled the enterotype of wild pandas, an indicator of conversion to wildness and a successful reintroduction. We also isolated 1 strain of Pseudomonas protegens from the wild enterotype, a previously reported free-living microbe, and found that its within-host evolution contributed to host dietary adaptation in the wild. Monitoring gut microbial structure provides a novel, noninvasive tool that can be used as an indicator of successful reintroduction of a captive individual to the wild.}, } @article {pmid37649627, year = {2023}, author = {Guo, DJ and Li, DP and Yang, B and Verma, KK and Singh, RK and Singh, P and Khan, Q and Sharma, A and Qin, Y and Zhang, BQ and Song, XP and Li, YR}, title = {Effect of endophytic diazotroph Enterobacter roggenkampii ED5 on nitrogen-metabolism-related microecology in the sugarcane rhizosphere at different nitrogen levels.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1132016}, pmid = {37649627}, issn = {1664-302X}, abstract = {Sugarcane is an important sugar and energy crop worldwide, requiring a large amount of nitrogen (N). However, excessive application of synthetic N fertilizer causes environmental pollution in farmland. Endophytic nitrogen-fixing bacteria (ENFB) provide N nutrition for plants through biological N fixation, thus reducing the need for chemical fertilizers. The present study investigated the effect of the N-fixing endophytic strain Enterobacter roggenkampii ED5 on phytohormone indole-3-acetic acid (IAA), N-metabolism enzyme activities, microbial community compositions, and N cycle genes in sugarcane rhizosphere soil at different N levels. Three levels of [15]N-urea, such as low N (0 kg/ha), medium N (150 kg/ha), and high N (300 kg/ha), were applied. The results showed that, after inoculating strain ED5, the IAA content in sugarcane leaves was significantly increased by 68.82% under low N condition at the seedling stage (60 days). The nitrate reductase (NR) activity showed a downward trend. However, the glutamine synthase (GS) and NADH-glutamate dehydrogenase (NADH-GDH) activities were significantly enhanced compared to the control under the high N condition, and the GS and NR genes had the highest expression at 180 and 120 days, respectively, at the low N level. The total N content in the roots, stems, and leaves of sugarcane was higher than the control. The [15]N atom % excess of sugarcane decreased significantly under medium N condition, indicating that the medium N level was conducive to N fixation in strain ED5. Metagenome analysis of sugarcane rhizosphere soil exhibited that the abundance of N-metabolizing microbial richness was increased under low and high N conditions after inoculation of strain ED5 at the genus level, while it was increased at the phylum level only under the low N condition. The LefSe (LDA > 2, p < 0.05) found that the N-metabolism-related differential microorganisms under the high N condition were higher than those under medium and low N conditions. It was also shown that the abundance of nifDHK genes was significantly increased after inoculation of ED5 at the medium N level, and other N cycle genes had high abundance at the high N level after inoculation of strain ED5. The results of this study provided a scientific reference for N fertilization in actual sugarcane production.}, } @article {pmid37649454, year = {2023}, author = {Alidjinou, EK and De Coninck, L and Swinnen, J and Lazrek, M and Hober, D and Matthijnssens, J}, title = {Viral metagenomics enables accurate detection of viral pathogens in amniotic fluid samples from pregnant women with suspicion of congenital infection.}, journal = {Journal of medical virology}, volume = {95}, number = {9}, pages = {e29045}, doi = {10.1002/jmv.29045}, pmid = {37649454}, issn = {1096-9071}, mesh = {Pregnancy ; Female ; Humans ; Infant, Newborn ; Pregnant Women ; Amniotic Fluid ; Metagenomics ; *Communicable Diseases ; *Infant, Newborn, Diseases ; }, } @article {pmid37649370, year = {2023}, author = {Wu, J and Qing, H and Ouyang, J and Zhou, J and Gao, Z and Mason, CE and Liu, Z and Shi, T}, title = {HiFun: homology independent protein function prediction by a novel protein-language self-attention model.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {5}, pages = {}, doi = {10.1093/bib/bbad311}, pmid = {37649370}, issn = {1477-4054}, mesh = {Amino Acid Sequence ; *Benchmarking ; *Language ; Metagenomics ; Molecular Sequence Annotation ; }, abstract = {Protein function prediction based on amino acid sequence alone is an extremely challenging but important task, especially in metagenomics/metatranscriptomics field, in which novel proteins have been uncovered exponentially from new microorganisms. Many of them are extremely low homology to known proteins and cannot be annotated with homology-based or information integrative methods. To overcome this problem, we proposed a Homology Independent protein Function annotation method (HiFun) based on a unified deep-learning model by reassembling the sequence as protein language. The robustness of HiFun was evaluated using the benchmark datasets and metrics in the CAFA3 challenge. To navigate the utility of HiFun, we annotated 2 212 663 unknown proteins and discovered novel motifs in the UHGP-50 catalog. We proved that HiFun can extract latent function related structure features which empowers it ability to achieve function annotation for non-homology proteins. HiFun can substantially improve newly proteins annotation and expand our understanding of microorganisms' adaptation in various ecological niches. Moreover, we provided a free and accessible webservice at http://www.unimd.org/HiFun, requiring only protein sequences as input, offering researchers an efficient and practical platform for predicting protein functions.}, } @article {pmid37649255, year = {2023}, author = {Zhang, K and He, Y and Lu, X and Shi, Y and Zhao, H and Li, X and Li, J and Liu, Y and Ouyang, Y and Tang, Y and Ren, X and Zhang, X and Yang, W and Sun, Z and Zhang, C and Quinet, M and Luthar, Z and Germ, M and Kreft, I and Janovská, D and Meglič, V and Pipan, B and Georgiev, MI and Studer, B and Chapman, MA and Zhou, M}, title = {Comparative and population genomics of buckwheat species reveal key determinants of flavor and fertility.}, journal = {Molecular plant}, volume = {16}, number = {9}, pages = {1427-1444}, pmid = {37649255}, issn = {1752-9867}, mesh = {*Fagopyrum/genetics ; Metagenomics ; DNA Copy Number Variations ; Genome-Wide Association Study ; Plant Breeding ; Fertility ; *Biological Products ; }, abstract = {Common buckwheat (Fagopyrum esculentum) is an ancient crop with a world-wide distribution. Due to its excellent nutritional quality and high economic and ecological value, common buckwheat is becoming increasingly important throughout the world. The availability of a high-quality reference genome sequence and population genomic data will accelerate the breeding of common buckwheat, but the high heterozygosity due to the outcrossing nature has greatly hindered the genome assembly. Here we report the assembly of a chromosome-scale high-quality reference genome of F. esculentum var. homotropicum, a homozygous self-pollinating variant of common buckwheat. Comparative genomics revealed that two cultivated buckwheat species, common buckwheat (F. esculentum) and Tartary buckwheat (F. tataricum), underwent metabolomic divergence and ecotype differentiation. The expansion of several gene families in common buckwheat, including FhFAR genes, is associated with its wider distribution than Tartary buckwheat. Copy number variation of genes involved in the metabolism of flavonoids is associated with the difference of rutin content between common and Tartary buckwheat. Furthermore, we present a comprehensive atlas of genomic variation based on whole-genome resequencing of 572 accessions of common buckwheat. Population and evolutionary genomics reveal genetic variation associated with environmental adaptability and floral development between Chinese and non-Chinese cultivated groups. Genome-wide association analyses of multi-year agronomic traits with the content of flavonoids revealed that Fh05G014970 is a potential major regulator of flowering period, a key agronomic trait controlling the yield of outcrossing crops, and that Fh06G015130 is a crucial gene underlying flavor-associated flavonoids. Intriguingly, we found that the gene translocation and sequence variation of FhS-ELF3 contribute to the homomorphic self-compatibility of common buckwheat. Collectively, our results elucidate the genetic basis of speciation, ecological adaptation, fertility, and unique flavor of common buckwheat, and provide new resources for future genomics-assisted breeding of this economically important crop.}, } @article {pmid37648982, year = {2023}, author = {Diba, F and Hoque, MN and Rahman, MS and Haque, F and Rahman, KMJ and Moniruzzaman, M and Khan, M and Hossain, MA and Sultana, M}, title = {Metagenomic and culture-dependent approaches unveil active microbial community and novel functional genes involved in arsenic mobilization and detoxification in groundwater.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {241}, pmid = {37648982}, issn = {1471-2180}, mesh = {*Arsenic ; *Arsenites ; Phylogeny ; *Microbiota ; }, abstract = {BACKGROUND: Arsenic (As) and its species are major pollutants in ecological bodied including groundwater in Bangladesh rendering serious public health concern. Bacteria with arsenotrophic genes have been found in the aquifer, converting toxic arsenite [As (III)] to less toxic arsenate [As (V)] that is easily removed using chemical and biological trappers. In this study, genomic and metagenomic approaches parallel to culture-based assay (Graphical abstract) have made it possible to decipher phylogenetic diversity of groundwater arsenotrophic microbiomes along with elucidation of their genetic determinants.

RESULTS: Seventy-two isolates were retrieved from six As-contaminated (average As concentration of 0.23 mg/L) groundwater samples from Munshiganj and Chandpur districts of Bangladesh. Twenty-three isolates harbored arsenite efflux pump (arsB) gene with high abundance, and ten isolates possessing arsenite oxidase (aioA) gene, with a wide range of minimum inhibitory concentration, MICAs (2 to 32 mM), confirming their role in arsenite metabolism. There was considerable heterogeneity in species richness and microbial community structure. Microbial taxa from Proteobacteria, Firmicutes and Acidobacteria dominated these diversities. Through these combinatorial approaches, we have identified potential candidates such as, Pseudomonas, Acinetobacter, Stenotrophomonas, Achromobacter, Paraburkholderia, Comamonas and Klebsiella and associated functional genes (arsB, acr3, arsD, arsH, arsR) that could significantly contribute to arsenite detoxification, accumulation, and immobilization.

CONCLUSIONS: Culture-dependent and -independent shotgun metagenomic investigation elucidated arsenotrophic microbiomes and their functions in As biogeochemical transformation. These findings laid a foundation for further large-scale researches on the arsenotrophic microbiomes and their concurrent functions in As biogeochemical transformation in As-contaminated areas of Bangladesh and beyond.}, } @article {pmid37648978, year = {2023}, author = {Yang, J and Shang, P and Zhang, B and Wang, J and Du, Z and Wang, S and Xing, J and Zhang, H}, title = {Genomic and metabonomic methods reveal the probiotic functions of swine-derived Ligilactobacillus salivarius.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {242}, pmid = {37648978}, issn = {1471-2180}, mesh = {Humans ; Animals ; Swine ; *Ligilactobacillus salivarius ; Phylogeny ; Genomics ; Metabolomics ; Anti-Bacterial Agents ; Antioxidants ; }, abstract = {BACKGROUND: As substitutes for antibiotics, probiotic bacteria protect against digestive infections caused by pathogenic bacteria. Ligilactobacillus salivarius is a species of native lactobacillus found in both humans and animals. Herein, a swine-derived Ligilactobacillus salivarius was isolated and shown to colonize the ileal mucous membrane, thereby promoting nutritional digestion, absorption, and immunity. To evaluate its probiotic role, the entire genome was sequenced, the genetic information was annotated, and the metabolic information was analyzed.

RESULTS: The phylogenetic relationship indicated that the bacteria was closer to L. salivarius MT573555.1 and MT585431.1. Functional genes included transporters, membrane proteins, enzymes, heavy metal resistance proteins, and putative proteins; metabolism-related genes were the most abundant. The six types of metabolic pathways secreted by L. salivarius were mainly composed of secretory transmembrane proteins and peptides. The secretory proteins of L. salivarius were digestive enzymes, functional proteins that regulate apoptosis, antibodies, and hormones. Non-targeted metabolomic analysis of L. salivarius metabolites suggested that ceramide, pyrrolidone- 5- carboxylic acid, N2-acetyl-L-ornithine, 2-ethyl-2-hydroxybutyric acid, N-lactoyl-phenylalanine, and 12 others were involved in antioxidation, repair of the cellular membrane, anticonvulsant, hypnosis, and appetite inhibition. Metabolites of clavaminic acid, antibiotic X14889C, and five other types of bacteriocins were identified, namely phenyllactic acid, janthitrem G, 13-demethyl tacrolimus, medinoside E, and tertonasin. The adherence and antioxidation of L. salivarius were also predicted. No virulence genes were found.

CONCLUSION: The main probiotic properties of L. salivarius were identified using genomic, metabonomic, and biochemical assays, which are beneficial for porcine feeding. Our results provided deeper insights into the probiotic effects of L. salivarius.}, } @article {pmid37648852, year = {2023}, author = {Takeuchi, T and Kubota, T and Nakanishi, Y and Tsugawa, H and Suda, W and Kwon, AT and Yazaki, J and Ikeda, K and Nemoto, S and Mochizuki, Y and Kitami, T and Yugi, K and Mizuno, Y and Yamamichi, N and Yamazaki, T and Takamoto, I and Kubota, N and Kadowaki, T and Arner, E and Carninci, P and Ohara, O and Arita, M and Hattori, M and Koyasu, S and Ohno, H}, title = {Gut microbial carbohydrate metabolism contributes to insulin resistance.}, journal = {Nature}, volume = {621}, number = {7978}, pages = {389-395}, pmid = {37648852}, issn = {1476-4687}, mesh = {Animals ; Humans ; Mice ; *Carbohydrate Metabolism ; Diabetes Mellitus, Type 2/metabolism ; *Gastrointestinal Microbiome/physiology ; *Insulin Resistance/physiology ; Monosaccharides/metabolism ; Insulin/metabolism ; Metabolic Syndrome/metabolism ; Feces/chemistry/microbiology ; Metabolomics ; }, abstract = {Insulin resistance is the primary pathophysiology underlying metabolic syndrome and type 2 diabetes[1,2]. Previous metagenomic studies have described the characteristics of gut microbiota and their roles in metabolizing major nutrients in insulin resistance[3-9]. In particular, carbohydrate metabolism of commensals has been proposed to contribute up to 10% of the host's overall energy extraction[10], thereby playing a role in the pathogenesis of obesity and prediabetes[3,4,6]. Nevertheless, the underlying mechanism remains unclear. Here we investigate this relationship using a comprehensive multi-omics strategy in humans. We combine unbiased faecal metabolomics with metagenomics, host metabolomics and transcriptomics data to profile the involvement of the microbiome in insulin resistance. These data reveal that faecal carbohydrates, particularly host-accessible monosaccharides, are increased in individuals with insulin resistance and are associated with microbial carbohydrate metabolisms and host inflammatory cytokines. We identify gut bacteria associated with insulin resistance and insulin sensitivity that show a distinct pattern of carbohydrate metabolism, and demonstrate that insulin-sensitivity-associated bacteria ameliorate host phenotypes of insulin resistance in a mouse model. Our study, which provides a comprehensive view of the host-microorganism relationships in insulin resistance, reveals the impact of carbohydrate metabolism by microbiota, suggesting a potential therapeutic target for ameliorating insulin resistance.}, } @article {pmid37648570, year = {2023}, author = {Robinson, JM and Hodgson, R and Krauss, SL and Liddicoat, C and Malik, AA and Martin, BC and Mohr, JJ and Moreno-Mateos, D and Muñoz-Rojas, M and Peddle, SD and Breed, MF}, title = {Opportunities and challenges for microbiomics in ecosystem restoration.}, journal = {Trends in ecology & evolution}, volume = {38}, number = {12}, pages = {1189-1202}, doi = {10.1016/j.tree.2023.07.009}, pmid = {37648570}, issn = {1872-8383}, mesh = {*Ecosystem ; Soil Microbiology ; Ecology ; Soil/chemistry ; *Microbiota ; Plants ; }, abstract = {Microbiomics is the science of characterizing microbial community structure, function, and dynamics. It has great potential to advance our understanding of plant-soil-microbe processes and interaction networks which can be applied to improve ecosystem restoration. However, microbiomics may be perceived as complex and the technology is not accessible to all. The opportunities of microbiomics in restoration ecology are considerable, but so are the practical challenges. Applying microbiomics in restoration must move beyond compositional assessments to incorporate tools to study the complexity of ecosystem recovery. Advances in metaomic tools provide unprecedented possibilities to aid restoration interventions. Moreover, complementary non-omic applications, such as microbial inoculants and biopriming, have the potential to improve restoration objectives by enhancing the establishment and health of vegetation communities.}, } @article {pmid37648499, year = {2023}, author = {Hagihara, M and Kato, H and Shibata, Y and Umemura, T and Ariyoshi, T and Hirai, J and Asai, N and Mori, N and Mikamo, H}, title = {Mycobiome and Mycobiome-Associated Diseases.}, journal = {Medical mycology journal}, volume = {64}, number = {3}, pages = {55-62}, doi = {10.3314/mmj.23-002}, pmid = {37648499}, issn = {1882-0476}, mesh = {Humans ; *Mycobiome ; Carcinogenesis ; Knowledge ; Metagenome ; Metagenomics ; }, abstract = {The human body is host to a large number of commensal microbial species such as bacteria, fungi, and viruses. Among these, the human mycobiome is often neglected as a potential cause of disease, as it is thought to be comparatively much less abundant and less diverse than the human bacteriome. Additionally, most fungi are not easily cultured, even in specific media. Hence, their study has been limited to date, mainly because of the unavailability of methods used for their detection. However, the utilization of a novel metagenomic methodology will enable the identification of well-characterized mycobiomes in several parts of the human body and broaden our knowledge of their contribution to human health and disease. In this article, we review the role of the human mycobiome in the gut, respiratory organs, skin, genital tract, and carcinogenesis, highlighting the correlations between the human mycobiome and mycobiome-associated diseases.}, } @article {pmid37648438, year = {2023}, author = {Lajoie, G and Kembel, SW}, title = {Data-driven identification of major axes of functional variation in bacteria.}, journal = {Environmental microbiology}, volume = {25}, number = {11}, pages = {2580-2591}, doi = {10.1111/1462-2920.16487}, pmid = {37648438}, issn = {1462-2920}, mesh = {*Ecosystem ; Phylogeny ; *Biodiversity ; Plants ; Bacteria/genetics ; }, abstract = {The discovery of major axes of correlated functional variation among species and habitats has revealed the fundamental trade-offs structuring both functional and taxonomic diversity in eukaryotes such as plants. Whether such functional axes exist in the bacterial realm and whether they could explain bacterial taxonomic turnover among ecosystems remains unknown. Here, we use a data-driven approach to leverage global genomic and metagenomic datasets to reveal the existence of major axes of functional variation explaining both evolutionary differentiation within Bacteria and their ecological sorting across diverse habitats. We show that metagenomic variation among bacterial communities from various ecosystems is structured along a few axes of correlated functional pathways. Similar clusters of traits explained phylogenetic trait variation among >16,000 bacterial genomes, suggesting that functional turnover among bacterial communities from distinct habitats does not only result from the differential filtering of similar functions among communities, but also from phylogenetic correlations among these functions. Concordantly, functional pathways associated with trait clusters that were most important for defining functional turnover among bacterial communities were also those that had the highest phylogenetic signal in the bacterial genomic phylogeny. This study overall underlines the important role of evolutionary history in shaping contemporary distributions of bacteria across ecosystems.}, } @article {pmid37648194, year = {2023}, author = {Kakakhel, MA and Narwal, N and Kataria, N and Johari, SA and Zaheer Ud Din, S and Jiang, Z and Khoo, KS and Xiaotao, S}, title = {Deciphering the dysbiosis caused in the fish microbiota by emerging contaminants and its mitigation strategies-A review.}, journal = {Environmental research}, volume = {237}, number = {Pt 2}, pages = {117002}, doi = {10.1016/j.envres.2023.117002}, pmid = {37648194}, issn = {1096-0953}, abstract = {The primary barrier to nutrient absorption in fish is the intestinal epithelium, followed by a community of microorganisms known as the gut microbiota, which can be thought of as a hidden organ. The gastrointestinal microbiota of fish plays a key role in the upholding of overall health by maintaining the homeostasis and disease resistance of the host. However, emerging contaminants as the result of anthropogenic activities have significantly led to disruptions and intestinal dysbiosis in fish. Which probably results in fish mortalities and disrupts the balance of an ecosystem. Therefore, we comprehensively seek to compile the effects and consequences of emerging contaminations on fish intestinal microbiota. Additionally, the mitigation strategies including prebiotics, probiotics, plant-based diet, and Biofloc technology are being outlined. Biofloc technology (BFT) can treat toxic materials, i.e., nitrogen components, and convert them into a useful product such as proteins and demonstrated promising elevating technique for the fish intestinal bacterial composition. However, it remains unclear whether the bacterial isolate is primarily responsible for the BFT's removal of nitrate and ammonia and the corresponding removal mechanism. To answer this, real time polymerase chain reaction (RT-PCR) with metagenomics, transcriptomics, and proteomics techniques probably provides a possible solution.}, } @article {pmid37647948, year = {2023}, author = {Jian, C and Hao, Y and Liu, R and Qi, X and Chen, M and Liu, N}, title = {Mixotrophic denitrification process driven by lime sulfur and butanediol: Denitrification performance and metagenomic analysis.}, journal = {The Science of the total environment}, volume = {903}, number = {}, pages = {166654}, doi = {10.1016/j.scitotenv.2023.166654}, pmid = {37647948}, issn = {1879-1026}, abstract = {Heterotrophic sulfur-based autotrophic denitrification is a promising biological denitrification technology for low COD/TN (C/N) wastewater due to its high efficiency and low cost. Compared to the conventional autotrophic denitrification process driven by elemental sulfur, the presence of polysulfide in the system can promote high-speed nitrogen removal. However, autotrophic denitrification mediated by polysulfide has not been reported. This study investigated the denitrification performance and microbial metabolic mechanism of heterotrophic denitrification, sulfur-based autotrophic denitrification, and mixotrophic denitrification using lime sulfur and butanediol as electron donors. When the influent C/N was 1, the total nitrogen removal efficiency of the mixotrophic denitrification process was 1.67 and 1.14 times higher than that of the heterotrophic and sulfur-based autotrophic denitrification processes, respectively. Microbial community alpha diversity and principal component analysis indicated different electron donors lead to different evolutionary directions in microbial communities. Metagenomic analysis showed the enriched denitrifying bacteria (Thauera, Pseudomonas, and Pseudoxanthomonas), dissimilatory nitrate reduction to ammonia bacteria (Hydrogenophaga), and sulfur oxidizing bacteria (Thiobacillus) can stably support nitrate reduction. Analysis of metabolic pathways revealed that complete denitrification, dissimilatory nitrate reduction to ammonia, and sulfur disproportionation are the main pathways of the N and S cycle. This study demonstrates the feasibility of a mixotrophic denitrification process driven by a combination of lime sulfur and butanediol as a cost-effective solution for treating nitrogen pollution in low C/N wastewater and elucidates the N and S metabolic pathways involved.}, } @article {pmid37647765, year = {2023}, author = {Young, GR and Nelson, A and Stewart, CJ and Smith, DL}, title = {Bacteriophage communities are a reservoir of unexplored microbial diversity in neonatal health and disease.}, journal = {Current opinion in microbiology}, volume = {75}, number = {}, pages = {102379}, doi = {10.1016/j.mib.2023.102379}, pmid = {37647765}, issn = {1879-0364}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Infant, Newborn ; Infant ; Humans ; Infant Health ; Infant, Premature ; *Microbiota ; *Bacteriophages/genetics ; *Gastrointestinal Microbiome ; }, abstract = {Acquisition and development of the gut microbiome are vital for immune education in neonates, especially those born preterm. As such, microbial communities have been extensively studied in the context of postnatal health and disease. Bacterial communities have been the focus of research in this area due to the relative ease of targeted bacterial sequencing and the availability of databases to align and validate sequencing data. Recent increases in high-throughput metagenomic sequencing accessibility have facilitated research to investigate bacteriophages within the context of neonatal gut microbial communities. Focusing on unexplored viral diversity, has identified novel bacteriophage species and previously uncharacterised viral diversity. In doing so, studies have highlighted links between bacteriophages and bacterial community structure in the context of health and disease. However, much remains unknown about the complex relationships between bacteriophages, the bacteria they infect and their human host. With a particular focus on preterm infants, this review highlights opportunities to explore the influence of bacteriophages on developing microbial communities and the tripartite relationships between bacteriophages, bacteria and the neonatal human host. We suggest a focus on expanding collections of isolated bacteriophages that will further our understanding of the growing numbers of bacteriophages identified in metagenomes.}, } @article {pmid37647089, year = {2023}, author = {Zhu, Z and Yu, C and Dong, Z and Mo, R and Zhang, C and Liu, X and Zuo, Y and Li, Y and Deng, W and Hu, X}, title = {Phylogeny and Fungal Community Structures of Helotiales Associated with Sclerotial Disease of Mulberry Fruits in China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-02-23-0223-RE}, pmid = {37647089}, issn = {0191-2917}, abstract = {Mulberry fruit sclerotiniose is a prevalent disease caused by the fungal species Ciboria shiraiana, Ciboria carunculoides, and Scleromitrula shiraiana of the order Helotiales, and severely affects the production of mulberry. However, these species have only been identified using morphological and rDNA-ITS sequence analyses, and their genetic variation is unclear. To address this, morphological and two-locus phylogenetic (ITS and RPB2) analyses were conducted using culture-dependent and independent methods for 49 samples from 31 orchards across four provinces in China. Illumina MiSeq sequencing was used to assess the fungal communities collected from fruits varying in disease severity and color from an orchard in Wuhan. Conidial suspensions of C. shiraiana and C. carunculoides isolated from diseased fruits, disease fruits affected with hypertrophy and pellet sorosis sclerotiniose, and mycelia of Sclerotinia sclerotiorum were determined to be pathogenic to the mulberry cultivar 'YSD10'. However, fruits inoculated with S. sclerotiorum mycelia exhibited non-typical disease symptoms, and mycelia and conidia obtained from C. carunculoides and S. shiraiana strains were not pathogenic. Maximum parsimony and Bayesian analyses using the sequences of the assessed loci indicated species variability with no evidence of geographic specialization. Metagenomic analysis revealed that the diversity of fungal communities was reduced with disease progression. Furthermore, within a single fruit, the presence of two Ciboria spp. was detected. These results provide novel insights into Ciboria spp., revealing the secondary infections caused by conidia in diseased fruit, genetic variations of the pathogens, and the occurrence of coinfection. This improved understanding of fungal pathogens will aid in developing effective disease control strategies.}, } @article {pmid37646836, year = {2023}, author = {Alshehri, WA and Abulfaraj, AA and Alqahtani, MD and Alomran, MM and Alotaibi, NM and Alwutayd, K and Aloufi, AS and Alshehrei, FM and Alabbosh, KF and Alshareef, SA and Ashy, RA and Refai, MY and Jalal, RS}, title = {Abundant resistome determinants in rhizosphere soil of the wild plant Abutilon fruticosum.}, journal = {AMB Express}, volume = {13}, number = {1}, pages = {92}, pmid = {37646836}, issn = {2191-0855}, support = {PNURSP2023R355//Deanship of Scientific Research, Princess Nourah Bint Abdulrahman University/ ; }, abstract = {A metagenomic whole genome shotgun sequencing approach was used for rhizospheric soil micribiome of the wild plant Abutilon fruticosum in order to detect antibiotic resistance genes (ARGs) along with their antibiotic resistance mechanisms and to detect potential risk of these ARGs to human health upon transfer to clinical isolates. The study emphasized the potential risk to human health of such human pathogenic or commensal bacteria, being transferred via food chain or horizontally transferred to human clinical isolates. The top highly abundant rhizospheric soil non-redundant ARGs that are prevalent in bacterial human pathogens or colonizers (commensal) included mtrA, soxR, vanRO, golS, rbpA, kdpE, rpoB2, arr-1, efrA and ileS genes. Human pathogenic/colonizer bacteria existing in this soil rhizosphere included members of genera Mycobacterium, Vibrio, Klebsiella, Stenotrophomonas, Pseudomonas, Nocardia, Salmonella, Escherichia, Citrobacter, Serratia, Shigella, Cronobacter and Bifidobacterium. These bacteria belong to phyla Actinobacteria and Proteobacteria. The most highly abundant resistance mechanisms included antibiotic efflux pump, antibiotic target alteration, antibiotic target protection and antibiotic inactivation. antimicrobial resistance (AMR) families of the resistance mechanism of antibiotic efflux pump included resistance-nodulation-cell division (RND) antibiotic efflux pump (for mtrA, soxR and golS genes), major facilitator superfamily (MFS) antibiotic efflux pump (for soxR gene), the two-component regulatory kdpDE system (for kdpE gene) and ATP-binding cassette (ABC) antibiotic efflux pump (for efrA gene). AMR families of the resistance mechanism of antibiotic target alteration included glycopeptide resistance gene cluster (for vanRO gene), rifamycin-resistant beta-subunit of RNA polymerase (for rpoB2 gene) and antibiotic-resistant isoleucyl-tRNA synthetase (for ileS gene). AMR families of the resistance mechanism of antibiotic target protection included bacterial RNA polymerase-binding protein (for RbpA gene), while those of the resistance mechanism of antibiotic inactivation included rifampin ADP-ribosyltransferase (for arr-1 gene). Better agricultural and food transport practices are required especially for edible plant parts or those used in folkloric medicine.}, } @article {pmid37646508, year = {2023}, author = {Strutt, JPB and Natarajan, M and Lee, E and Teo, DBL and Sin, WX and Cheung, KW and Chew, M and Thazin, K and Barone, PW and Wolfrum, JM and Williams, RBH and Rice, SA and Springs, SL}, title = {Machine learning-based detection of adventitious microbes in T-cell therapy cultures using long-read sequencing.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0135023}, pmid = {37646508}, issn = {2165-0497}, abstract = {Assuring that cell therapy products are safe before releasing them for use in patients is critical. Currently, compendial sterility testing for bacteria and fungi can take 7-14 days. The goal of this work was to develop a rapid untargeted approach for the sensitive detection of microbial contaminants at low abundance from low volume samples during the manufacturing process of cell therapies. We developed a long-read sequencing methodology using Oxford Nanopore Technologies MinION platform with 16S and 18S amplicon sequencing to detect USP <71> organisms and other microbial species. Reads are classified metagenomically to predict the microbial species. We used an extreme gradient boosting machine learning algorithm (XGBoost) to first assess if a sample is contaminated, and second, determine whether the predicted contaminant is correctly classified or misclassified. The model was used to make a final decision on the sterility status of the input sample. An optimized experimental and bioinformatics pipeline starting from spiked species through to sequenced reads allowed for the detection of microbial samples at 10 colony-forming units (CFU)/mL using metagenomic classification. Machine learning can be coupled with long-read sequencing to detect and identify sample sterility status and microbial species present in T-cell cultures, including the USP <71> organisms to 10 CFU/mL. IMPORTANCE This research presents a novel method for rapidly and accurately detecting microbial contaminants in cell therapy products, which is essential for ensuring patient safety. Traditional testing methods are time-consuming, taking 7-14 days, while our approach can significantly reduce this time. By combining advanced long-read nanopore sequencing techniques and machine learning, we can effectively identify the presence and types of microbial contaminants at low abundance levels. This breakthrough has the potential to improve the safety and efficiency of cell therapy manufacturing, leading to better patient outcomes and a more streamlined production process.}, } @article {pmid37645824, year = {2023}, author = {Hibberd, MC and Webber, DM and Rodionov, DA and Henrissat, S and Chen, RY and Zhou, C and Lynn, HM and Wang, Y and Chang, HW and Lee, EM and Lelwala-Guruge, J and Kazanov, MD and Arzamasov, AA and Leyn, SA and Lombard, V and Terrapon, N and Henrissat, B and Castillo, JJ and Couture, G and Bacalzo, NP and Chen, Y and Lebrilla, CB and Mostafa, I and Das, S and Mahfuz, M and Barratt, MJ and Osterman, AL and Ahmed, T and Gordon, JI}, title = {Bioactive glycans in a microbiome-directed food for malnourished children.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {37645824}, support = {R01 DK030292/DK/NIDDK NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; }, abstract = {Evidence is accumulating that perturbed postnatal development of the gut microbiome contributes to childhood malnutrition[1-4]. Designing effective microbiome-directed therapeutic foods to repair these perturbations requires knowledge about how food components interact with the microbiome to alter its expressed functions. Here we use biospecimens from a randomized, controlled trial of a microbiome-directed complementary food prototype (MDCF-2) that produced superior rates of weight gain compared to a conventional ready-to-use supplementary food (RUSF) in 12-18-month-old Bangladeshi children with moderate acute malnutrition (MAM)4. We reconstructed 1000 bacterial genomes (metagenome-assembled genomes, MAGs) present in their fecal microbiomes, identified 75 whose abundances were positively associated with weight gain (change in weight-for-length Z score, WLZ), characterized gene expression changes in these MAGs as a function of treatment type and WLZ response, and used mass spectrometry to quantify carbohydrate structures in MDCF-2 and feces. The results reveal treatment-induced changes in expression of carbohydrate metabolic pathways in WLZ-associated MAGs. Comparing participants consuming MDCF-2 versus RUSF, and MDCF-2-treated children in the upper versus lower quartiles of WLZ responses revealed that two Prevotella copri MAGs positively associated with WLZ were principal contributors to MDCF-2-induced expression of metabolic pathways involved in utilization of its component glycans. Moreover, the predicted specificities of carbohydrate active enzymes expressed by polysaccharide utilization loci (PULs) in these two MAGs correlate with the (i) in vitro growth of Bangladeshi P. copri strains, possessing differing degrees of PUL and overall genomic content similarity to these MAGs, cultured in defined medium containing different purified glycans representative of those in MDCF-2, and (ii) levels of carbohydrate structures identified in feces from clinical trial participants. In the accompanying paper5, we use a gnotobiotic mouse model colonized with age- and WLZ-associated bacterial taxa cultured from this study population, and fed diets resembling those consumed by study participants, to directly test the relationship between P. copri, MDCF-2 glycan metabolism, host ponderal growth responses, and intestinal gene expression and metabolism. The ability to identify bioactive glycan structures in MDCFs that are metabolized by growth-associated bacterial taxa will help guide recommendations about use of this MDCF for children with acute malnutrition representing different geographic locales and ages, as well as enable development of bioequivalent, or more efficacious, formulations composed of culturally acceptable and affordable ingredients.}, } @article {pmid37645804, year = {2023}, author = {Reasoner, SA and Bernard, R and Waalkes, A and Penewit, K and Lewis, J and Sokolow, AG and Brown, RF and Edwards, KM and Salipante, SJ and Hadjifrangiskou, M and Nicholson, MR}, title = {Longitudinal Profiling of the Intestinal Microbiome in Children with Cystic Fibrosis Treated with Elexacaftor-Tezacaftor-Ivacaftor.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {37645804}, support = {T32 DK007673/DK/NIDDK NIH HHS/United States ; K23 AI156132/AI/NIAID NIH HHS/United States ; P30 DK089507/DK/NIDDK NIH HHS/United States ; T32 GM007347/GM/NIGMS NIH HHS/United States ; F30 AI169748/AI/NIAID NIH HHS/United States ; }, abstract = {The intestinal microbiome influences growth and disease progression in children with cystic fibrosis (CF). Elexacaftor-tezacaftor-ivacaftor (ELX/TEZ/IVA), the newest pharmaceutical modulator for CF, restores function of the pathogenic mutated CFTR channel. We performed a single-center longitudinal analysis of the effect of ELX/TEZ/IVA on the intestinal microbiome, intestinal inflammation, and clinical parameters in children with CF. Following ELX/TEZ/IVA, children with CF had significant improvements in BMI, ppFEV1 and required fewer antibiotics for respiratory infections. Intestinal microbiome diversity increased following ELX/TEZ/IVA coupled with a decrease in the intestinal carriage of Staphylococcus aureus, the predominant respiratory pathogen in children with CF. There was a reduced abundance of microbiome-encoded antibiotic-resistance genes. Microbial pathways for aerobic respiration were reduced after ELX/TEZ/IVA. The abundance of microbial acid tolerance genes was reduced, indicating microbial adaptation to increased CFTR function. In all, this study represents the first comprehensive analysis of the intestinal microbiome in children with CF receiving ELX/TEZ/IVA.}, } @article {pmid37645712, year = {2023}, author = {Chang, HW and Lee, EM and Wang, Y and Zhou, C and Pruss, KM and Henrissat, S and Chen, RY and Kao, C and Hibberd, MC and Lynn, HM and Webber, DM and Crane, M and Cheng, J and Rodionov, DA and Arzamasov, AA and Castillo, JJ and Couture, G and Chen, Y and Balcazo, NP and Lebrilla, CB and Terrapon, N and Henrissat, B and Ilkayeva, O and Muehlbauer, MJ and Newgard, CB and Mostafa, I and Das, S and Mahfuz, M and Osterman, AL and Barratt, MJ and Ahmed, T and Gordon, JI}, title = {Prevotella copri-related effects of a therapeutic food for malnutrition.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37645712}, support = {F30 DK131866/DK/NIDDK NIH HHS/United States ; R01 DK030292/DK/NIDDK NIH HHS/United States ; K01 DK134840/DK/NIDDK NIH HHS/United States ; T32 HG000045/HG/NHGRI NIH HHS/United States ; R37 DK030292/DK/NIDDK NIH HHS/United States ; }, abstract = {Preclinical and clinical studies are providing evidence that the healthy growth of infants and children reflects, in part, healthy development of their gut microbiomes[1-5]. This process of microbial community assembly and functional maturation is perturbed in children with acute malnutrition. Gnotobiotic animals, colonized with microbial communities from children with severe and moderate acute malnutrition, have been used to develop microbiome-directed complementary food (MDCF) formulations for repairing the microbiomes of these children during the weaning period[5]. Bangladeshi children with moderate acute malnutrition (MAM) participating in a previously reported 3-month-long randomized controlled clinical study of one such formulation, MDCF-2, exhibited significantly improved weight gain compared to a commonly used nutritional intervention despite the lower caloric density of the MDCF[6]. Characterizing the 'metagenome assembled genomes' (MAGs) of bacterial strains present in the microbiomes of study participants revealed a significant correlation between accelerated ponderal growth and the expression by two Prevotella copri MAGs of metabolic pathways involved in processing of MDCF-2 glycans[1]. To provide a direct test of these relationships, we have now performed 'reverse translation' experiments using a gnotobiotic mouse model of mother-to-offspring microbiome transmission. Mice were colonized with defined consortia of age- and ponderal growth-associated gut bacterial strains cultured from Bangladeshi infants/children in the study population, with or without P. copri isolates resembling the MAGs. By combining analyses of microbial community assembly, gene expression and processing of glycan constituents of MDCF-2 with single nucleus RNA-Seq and mass spectrometric analyses of the intestine, we establish a principal role for P. copri in mediating metabolism of MDCF-2 glycans, characterize its interactions with other consortium members including Bifidobacterium longum subsp. infantis, and demonstrate the effects of P. copri-containing consortia in mediating weight gain and modulating the activities of metabolic pathways involved in lipid, amino acid, carbohydrate plus other facets of energy metabolism within epithelial cells positioned at different locations in intestinal crypts and villi. Together, the results provide insights into structure/function relationships between MDCF-2 and members of the gut communities of malnourished children; they also have implications for developing future prebiotic, probiotic and/or synbiotic therapeutics for microbiome restoration in children with already manifest malnutrition, or who are at risk for this pervasive health challenge.}, } @article {pmid37645461, year = {2023}, author = {Zuzolo, D and Ranauda, MA and Maisto, M and Tartaglia, M and Prigioniero, A and Falzarano, A and Marotta, G and Sciarrillo, R and Guarino, C}, title = {The rootstock shape microbial diversity and functionality in the rhizosphere of Vitis vinifera L. cultivar Falanghina.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1205451}, pmid = {37645461}, issn = {1664-462X}, abstract = {The rhizosphere effect occurring at the root-soil interface has increasingly been shown to play a key role in plant fitness and soil functionality, influencing plants resilience. Here, for the first time, we investigated whether the rootstock genotype on which Vitis vinifera L. cultivar Falanghina is grafted can influence the rhizosphere microbiome. Specifically, we evaluated to which extent the 5BB and 1103P rootstocks are able to shape microbial diversity of rhizosphere environment. Moreover, we explored the potential function of microbial community and its shift under plant genotype influence. We investigated seven vineyards subjected to the same pedo-climatic conditions, similar age, training system and management and collected twelve rhizosphere soil samples for metagenomic analyses and composite soil samples for physical-chemical properties. In this study, we used 16S rRNA gene-based metagenomic analysis to investigate the rhizosphere bacterial diversity and composition. Liner discriminant analysis effect size (LEFSe) was conducted for metagenomic biomarker discovery. The functional composition of sampled communities was determined using PICRUSt, which is based on marker gene sequencing profiles. Soil analyses involved the determination of texture, pH, Cation Exchange Capacity (CSC), Organic Carbon (OC), electrical conductivity (EC), calcium (Ca), magnesium (Mg), potassium (K) content, Phosphorous (P), nitrogen (N). The latter revealed that soil features were quite homogenous. The metagenomic data showed that the bacterial alpha-diversity (Observed OTUs) significantly increased in 1103P rhizosphere microbiota. Irrespective of cultivar, Pseudomonadota was the dominant phylum, followed by Actinomycetota > Bacteroidota > Thermoproteota. However, Actinomycetota was the major marker phyla differentiating the rhizosphere microbial communities associated with the different rootstock types. At the genus level, several taxa belonging to Actinomycetota and Alphaproteobacteria classes were enriched in 1103P genotype rhizosphere. Investigating the potential functional profile, we found that most key enzyme-encoding genes involved in N cycling were significantly more abundant in 5BB rootstock rhizosphere soil. However, we found that 1103P rhizosphere was enriched in genes involved in C cycle and Plant Growth Promotion (PGP) functionality. Our results suggest that the different rootstocks not only recruit specific bacterial communities, but also specific functional traits within the same environment.}, } @article {pmid37645381, year = {2023}, author = {Lin, T and Tu, X and Zhao, J and Huang, L and Dai, X and Chen, X and Xu, Y and Li, W and Wang, Y and Lou, J and Wu, S and Zhang, H}, title = {Corrigendum: Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1205802}, doi = {10.3389/fcimb.2023.1205802}, pmid = {37645381}, issn = {2235-2988}, abstract = {[This corrects the article DOI: 10.3389/fcimb.2023.1136588.].}, } @article {pmid37645375, year = {2023}, author = {Chen, J and Wang, Z and Starkweather, A and Chen, MH and McCauley, P and Miao, H and Ahn, H and Cong, X}, title = {Pain sensation and gut microbiota profiles in older adults with heart failure.}, journal = {Interdisciplinary nursing research}, volume = {2}, number = {2}, pages = {83-91}, pmid = {37645375}, issn = {2832-918X}, abstract = {OBJECTIVES: Patients with heart failure (HF) experience severe pain and may have altered pain sensation; however, the underlying mechanisms of these symptoms are not yet fully understood. Identifying pain sensation and genomic biomarkers of pain in older adults with HF is a critical step toward developing personalized interventions to improve pain management and outcomes. This study aimed to investigate the differences in pain sensation, gut microbiota, self-reported pain, and symptoms in older adults with and without HF.

METHODS: Twenty older adults with HF and age-matched healthy controls (HCs) were recruited in the Northeastern United States. Quantitative sensory testing and conditioned pain modulation were performed on the nondominant upper arm to detect the mechanical, thermal, and pressure pain thresholds and pain modulations. Stool samples were collected, and the 16S rRNA V4 gene region of stool samples was sequenced and processed using the Mothur 1.42.3 pipeline. Self-reported pain and symptoms were measured by the Brief Pain Inventory and the NIH Patient-reported Outcomes Measurement Information System. The associations between pain sensation, gut microbiota α-diversity indices, and pain and symptoms were explored using the Spearman correlations.

RESULTS: The HF and HC subjects' mean ages were 73.50 (SD = 8.33) and 67.10 (SD = 7.64), respectively. The HF subjects reported significantly higher pain intensity and interference, sleep disturbance, fatigue, anxiety, and depression than the HCs. The HF subjects also had a significantly lower level of physical function and participation in social roles and activities. Compared with the HCs, the HF subjects had significantly altered conditioned pain modulation heat effect and gut microbiota compositions and predicted metabolic functions. The Statistical Analysis Of Metagenomic Profiles indicated that the HF subjects had a significantly decreased cardiac muscle contraction pathway compared with the HCs. The correlation analysis showed that the quantitative sensory testing profiles and gut microbiota diversity index were significantly associated with pain and symptoms in older adults with HF.

CONCLUSIONS: Older adults with HF had more severe self-reported pain and symptoms, altered pain sensation, and different gut microbiota composition and function compared with age-matched HCs. Pain sensation and gut microbiota may contribute to pain and symptoms in older adults with HF and could serve as biomarkers of pain and symptoms of HF. Further research with a larger sample size is warranted to confirm these findings.}, } @article {pmid37644917, year = {2023}, author = {Huard, DJE and Johnson, AM and Fan, Z and Kenney, LG and Xu, M and Drori, R and Gumbart, JC and Dai, S and Lieberman, RL and Glass, JB}, title = {Molecular basis for inhibition of methane clathrate growth by a deep subsurface bacterial protein.}, journal = {PNAS nexus}, volume = {2}, number = {8}, pages = {pgad268}, pmid = {37644917}, issn = {2752-6542}, abstract = {Methane clathrates on continental margins contain the largest stores of hydrocarbons on Earth, yet the role of biomolecules in clathrate formation and stability remains almost completely unknown. Here, we report new methane clathrate-binding proteins (CbpAs) of bacterial origin discovered in metagenomes from gas clathrate-bearing ocean sediments. CbpAs show similar suppression of methane clathrate growth as the commercial gas clathrate inhibitor polyvinylpyrrolidone and inhibit clathrate growth at lower concentrations than antifreeze proteins (AFPs) previously tested. Unlike AFPs, CbpAs are selective for clathrate over ice. CbpA3 adopts a nonglobular, extended structure with an exposed hydrophobic surface, and, unexpectedly, its TxxxAxxxAxx motif common to AFPs is buried and not involved in clathrate binding. Instead, simulations and mutagenesis suggest a bipartite interaction of CbpAs with methane clathrate, with the pyrrolidine ring of a highly conserved proline residue mediating binding by filling empty clathrate cages. The discovery that CbpAs exert such potent control on methane clathrate properties implies that biomolecules from native sediment bacteria may be important for clathrate stability and habitability.}, } @article {pmid37644393, year = {2023}, author = {Khattab, RH and Abo-Hammam, RH and Salah, M and Hanora, AM and Shabayek, S and Zakeer, S}, title = {Multi-omics analysis of fecal samples in colorectal cancer Egyptians patients: a pilot study.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {238}, pmid = {37644393}, issn = {1471-2180}, mesh = {Female ; Humans ; Pilot Projects ; Chromatography, Liquid ; *Multiomics ; Tandem Mass Spectrometry ; Protein Kinases ; *Colorectal Neoplasms/genetics ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is a public health concern and the second most common disease worldwide. This is due to genetic coding and is influenced by environmental aspects, in which the gut microbiota plays a significant role. The purpose of this study was to compare the microbiota makeup of CRC patients with that of healthy control and to identify upregulated and downregulated proteins and metabolites in CRC patients. Using a next-generation sequencing approach, fecal samples of five females (4 CRC patients and one healthy control) were analyzed by BGI DNBSEQ-T7, Hong Kong, China. Furthermore, proteomics and metabolomics analysis were performed using LC-MS/MS technique.

RESULTS: Dysbiosis of gut microbiota has been observed in patients with CRC, with an increase in microbiota diversity at all taxonomic levels relative to healthy control. Where, at the functional level the bacterial species participate in many different pathways among them de novo nucleotide synthesis and amino acids pathways were aberrantly upregulated in CRC patients. Proteomics and metabolomics profiles of CRC patients showed different proteins and metabolites, a total of 360 and 158 proteins and metabolites, respectively were highly expressed compared to healthy control with fold change ≥ 1.2. Among the highly expressed proteins were transketolase, sushi domain-containing protein, sulfide quinone oxidoreductase protein, AAA family ATPase protein, carbonic anhydrase, IgG Fc-binding protein, nucleoside diphosphate kinase protein, arylsulfatase, alkaline phosphatase protein, phosphoglycerate kinase, protein kinase domain-containing protein, non-specific serine/threonine protein kinase, Acyl-CoA synthetase and EF-hand domain-containing protein. Some of the differential metabolites, Taurine, Taurocholic acid, 7-ketodeoxycholic acid, Glycochenodeoxycholic acid, Glycocholic acid, and Taurochenodeoxycholic acid that belong to bile acids metabolites.

CONCLUSIONS: Some bacterial species, proteins, and metabolites could be used as diagnostic biomarkers for CRC. Our study paves an insight into using multi-omics technology to address the relationship between gut microbiota and CRC.}, } @article {pmid37644161, year = {2023}, author = {Koo, H and Morrow, CD}, title = {Identification of donor Bacteroides vulgatus genes encoding proteins that correlate with early colonization following fecal transplant of patients with recurrent Clostridium difficile.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {14112}, pmid = {37644161}, issn = {2045-2322}, mesh = {Child ; Humans ; Animals ; Mice ; *Fecal Microbiota Transplantation ; *Clostridioides difficile/genetics ; Tissue Donors ; Bacteroides/genetics ; }, abstract = {Due to suppressive antibiotics, patients with recurrent Clostridium difficile have gut microbial communities that are devoid of most commensal microbes. Studies have shown that most of the failures using fecal microbe transplantation (FMT) for recurrent C. difficile occur during the first 4 weeks following transplantation. To identify features of donor Bacteroides vulgatus that lead to early colonization, we used two data sets that collected fecal samples from recipients at early times points post FMT. The first analysis used the shotgun metagenomic DNA sequencing data set from Aggarwala et al. consisting of 7 FMT donors and 13 patients with recurrent C. difficile with fecal samples taken as early as 24 h post FMT. We identified 2 FMT donors in which colonization of recipients by donor B. vulgatus was detected as early as 24 h post FMT. We examined a second data set from Hourigan et al. that collected fecal samples from C. difficile infected children and identified 1 of 3 FMT that also had early colonization of the donor B. vulgatus. We found 19 genes out of 4911 encoding proteins were unique to the 3 donors that had early colonization. A gene encoding a putative chitobiase was identified that was in a gene complex that had been previously identified to enhance colonization in mice. A gene encoding a unique fimbrillin (i.e., pili) family protein and 17 genes encoding hypothetical proteins were also specific for early colonizing donors. Most of the genes encoding hypothetical proteins had neighboring genes that encoded proteins involved in mobilization or transposition. Finally, analysis of 42 paired fecal samples from the human microbiome project (HMP) found no individuals had all 19 genes while 2 individuals had none of the 19 genes. Based on the results from our study, consideration should be given to the screening of FMT donors for these B. vulgatus genes found to enhance early colonization that would be of benefit to promote colonization following FMT.}, } @article {pmid37644066, year = {2023}, author = {Yan, M and Pratama, AA and Somasundaram, S and Li, Z and Jiang, Y and Sullivan, MB and Yu, Z}, title = {Interrogating the viral dark matter of the rumen ecosystem with a global virome database.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5254}, pmid = {37644066}, issn = {2041-1723}, mesh = {Humans ; Animals ; Virome ; Rumen ; *Microbiota ; *Caudovirales ; Databases, Factual ; }, abstract = {The diverse rumen virome can modulate the rumen microbiome, but it remains largely unexplored. Here, we mine 975 published rumen metagenomes for viral sequences, create a global rumen virome database (RVD), and analyze the rumen virome for diversity, virus-host linkages, and potential roles in affecting rumen functions. Containing 397,180 species-level viral operational taxonomic units (vOTUs), RVD substantially increases the detection rate of rumen viruses from metagenomes compared with IMG/VR V3. Most of the classified vOTUs belong to Caudovirales, differing from those found in the human gut. The rumen virome is predicted to infect the core rumen microbiome, including fiber degraders and methanogens, carries diverse auxiliary metabolic genes, and thus likely impacts the rumen ecosystem in both a top-down and a bottom-up manner. RVD and the findings provide useful resources and a baseline framework for future research to investigate how viruses may impact the rumen ecosystem and digestive physiology.}, } @article {pmid37644001, year = {2023}, author = {Hoskinson, C and Dai, DLY and Del Bel, KL and Becker, AB and Moraes, TJ and Mandhane, PJ and Finlay, BB and Simons, E and Kozyrskyj, AL and Azad, MB and Subbarao, P and Petersen, C and Turvey, SE}, title = {Delayed gut microbiota maturation in the first year of life is a hallmark of pediatric allergic disease.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4785}, pmid = {37644001}, issn = {2041-1723}, mesh = {Infant ; Humans ; Child ; *Gastrointestinal Microbiome/genetics ; *Hypersensitivity ; *Microbiota ; *Asthma ; *Dermatitis, Atopic ; }, abstract = {Allergic diseases affect millions of people worldwide. An increase in their prevalence has been associated with alterations in the gut microbiome, i.e., the microorganisms and their genes within the gastrointestinal tract. Maturation of the infant immune system and gut microbiota occur in parallel; thus, the conformation of the microbiome may determine if tolerant immune programming arises within the infant. Here we show, using deeply phenotyped participants in the CHILD birth cohort (n = 1115), that there are early-life influences and microbiome features which are uniformly associated with four distinct allergic diagnoses at 5 years: atopic dermatitis (AD, n = 367), asthma (As, n = 165), food allergy (FA, n = 136), and allergic rhinitis (AR, n = 187). In a subset with shotgun metagenomic and metabolomic profiling (n = 589), we discover that impaired 1-year microbiota maturation may be universal to pediatric allergies (AD p = 0.000014; As p = 0.0073; FA p = 0.00083; and AR p = 0.0021). Extending this, we find a core set of functional and metabolic imbalances characterized by compromised mucous integrity, elevated oxidative activity, decreased secondary fermentation, and elevated trace amines, to be a significant mediator between microbiota maturation at age 1 year and allergic diagnoses at age 5 years (βindirect = -2.28; p = 0.0020). Microbiota maturation thus provides a focal point to identify deviations from normative development to predict and prevent allergic disease.}, } @article {pmid37643149, year = {2023}, author = {Song, Y and Finkelstein, R and Rhoads, W and Edwards, MA and Pruden, A}, title = {Shotgun Metagenomics Reveals Impacts of Copper and Water Heater Anodes on Pathogens and Microbiomes in Hot Water Plumbing Systems.}, journal = {Environmental science & technology}, volume = {57}, number = {36}, pages = {13612-13624}, pmid = {37643149}, issn = {1520-5851}, mesh = {*Water ; Copper ; Metagenomics ; Sanitary Engineering ; *Microbiota ; Electrodes ; Phosphates ; }, abstract = {Hot water building plumbing systems are vulnerable to the proliferation of opportunistic pathogens (OPs), including Legionella pneumophila and Mycobacterium avium. Implementation of copper as a disinfectant could help reduce OPs, but a mechanistic understanding of the effects on the microbial community under real-world plumbing conditions is lacking. Here, we carried out a controlled pilot-scale study of hot water systems and applied shotgun metagenomic sequencing to examine the effects of copper dose (0-2 mg/L), orthophosphate corrosion control agent, and water heater anode materials (aluminum vs magnesium vs powered anode) on the bulk water and biofilm microbiome composition. Metagenomic analysis revealed that, even though a copper dose of 1.2 mg/L was required to reduce Legionella and Mycobacterium numbers, lower doses (e.g., ≤0.6 mg/L) measurably impacted the broader microbial community, indicating that the OP strains colonizing these systems were highly copper tolerant. Orthophosphate addition reduced bioavailability of copper, both to OPs and to the broader microbiome. Functional gene analysis indicated that both membrane damage and interruption of nucleic acid replication are likely at play in copper inactivation mechanisms. This study identifies key factors (e.g., orthophosphate, copper resistance, and anode materials) that can confound the efficacy of copper for controlling OPs in hot water plumbing.}, } @article {pmid37642853, year = {2023}, author = {Ribeiro, AL and Sánchez, M and Bosch, S and Berenguer, J and Hidalgo, A}, title = {Stabilization of Enzymes by Using Thermophiles.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2704}, number = {}, pages = {313-328}, pmid = {37642853}, issn = {1940-6029}, mesh = {*Commerce ; *Drug Industry ; Gene Library ; Half-Life ; Kanamycin ; }, abstract = {Manufactured steroid compounds have many applications in the pharmaceutical industry. Due to the chemical complexity and chirality of steroids, there is an increasing demand for enzyme-based bioconversion processes to replace those based on chemical synthesis. In this context, thermostability of the involved enzymes is a highly desirable property as both the increased half-life of the enzyme and the enhanced solubility of substrates and products will improve the yield of the reactions. Metagenomic libraries from thermal environments are potential sources of thermostable enzymes of prokaryotic origin, but the number of expected hits could be quite low for enzymes handling substrates such as steroids, rarely found in prokaryotes. An alternative to metagenome screening is the selection of thermostable variants of well-known steroid-processing enzymes. Here we review and detail a protocol for such selection, where error-prone PCR (epPCR) is used to introduce random mutations into a gene to create a variants library for further selection of thermostable variants in the thermophile Thermus thermophilus. The method involves the use of folding interference vectors where the proper folding of the enzyme of interest at high temperature is linked to the folding of a reporter encoding a selectable property such as thermostable resistance to kanamycin, leading to a life-or-death selection of variants of reinforced folding independently of the activity of the enzyme.}, } @article {pmid37641717, year = {2023}, author = {Shang, J and Peng, C and Liao, H and Tang, X and Sun, Y}, title = {PhaBOX: a web server for identifying and characterizing phage contigs in metagenomic data.}, journal = {Bioinformatics advances}, volume = {3}, number = {1}, pages = {vbad101}, pmid = {37641717}, issn = {2635-0041}, abstract = {MOTIVATION: There is accumulating evidence showing the important roles of bacteriophages (phages) in regulating the structure and functions of the microbiome. However, lacking an easy-to-use and integrated phage analysis software hampers microbiome-related research from incorporating phages in the analysis.

RESULTS: In this work, we developed a web server, PhaBOX, which can comprehensively identify and analyze phage contigs in metagenomic data. It supports integrated phage analysis, including phage contig identification from the metagenomic assembly, lifestyle prediction, taxonomic classification, and host prediction. Instead of treating the algorithms as a black box, PhaBOX also supports visualization of the essential features for making predictions. The web server is designed with a user-friendly graphical interface that enables both informatics-trained and nonspecialist users to analyze phages in microbiome data with ease.

The web server of PhaBOX is available via: https://phage.ee.cityu.edu.hk. The source code of PhaBOX is available at: https://github.com/KennthShang/PhaBOX.}, } @article {pmid37641475, year = {2023}, author = {Garcia-Serrano, A and Mukhedkar, D and Hultin, E and Rudsander, U and Wettergren, Y and Ure, AE and Dillner, J and Arroyo-Mühr, LS}, title = {Assessment of bacterial and viral gut communities in healthy and tumoral colorectal tissue using RNA and DNA deep sequencing.}, journal = {Cancer medicine}, volume = {12}, number = {18}, pages = {19291-19300}, pmid = {37641475}, issn = {2045-7634}, mesh = {Humans ; *Colorectal Neoplasms/pathology ; RNA ; Bacteria/genetics ; DNA ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is known to present a distinct microbiome profile compared to healthy mucosa. Non-targeted deep-sequencing strategies enable nowadays full microbiome characterization up to species level.

AIM: We aimed to analyze both bacterial and viral communities in CRC using these strategies.

MATERIALS & METHODS: We analyzed bacterial and viral communities using both DNA and RNA deep-sequencing (Novaseq) in colorectal tissue specimens from 10 CRC patients and 10 matched control patients. Following taxonomy classification using Kraken 2, different metrics for alpha and beta diversities as well as relative and differential abundance were calculated to compare tumoral and healthy samples.

RESULTS: No viral differences were identified between tissue types, but bacterial species Polynucleobacter necessarius had a highly increased presence for DNA in tumors (p = 0.001). RNA analyses showed that bacterial species Arabia massiliensis had a highly decreased transcription in tumors (p = 0.002) while Fusobacterium nucleatum transcription was highly increased in tumors (p = 0.002).

DISCUSSION: Sequencing of both DNA and RNA enables a wider perspective of micriobiome profiles. Lack of RNA transcription (Polynucleobacter necessarius) casts doubt on possible role of a microorganism in CRC. The association of F. nucleatum mainly with transcription, may provide further insights on its role in CRC.

CONCLUSION: Joint assessment of the metagenome (DNA) and the metatranscriptome (RNA) at the species level provided a huge coverage for both bacteria and virus and identifies differential specific bacterial species as tumor associated.}, } @article {pmid37641353, year = {2023}, author = {Moore, SG and Feehily, C and Doyle, RC and Buckley, F and Lonergan, P and Cotter, PD and Butler, ST}, title = {Associations between the postpartum uterine and vaginal microbiota and the subsequent development of purulent vaginal discharge vary with dairy cow breed and parity.}, journal = {Journal of dairy science}, volume = {106}, number = {11}, pages = {8133-8151}, doi = {10.3168/jds.2022-22720}, pmid = {37641353}, issn = {1525-3198}, abstract = {The objective of this study was to characterize the species composition and functional potential of the vaginal and uterine microbiota at 1 wk postpartum in dairy cows diagnosed with or without purulent vaginal discharge (PVD) at 3 wk postpartum. The hypothesis was that differences in the vaginal and uterine microbiota between cows diagnosed with (PVD+) or without (PVD-) PVD were dependent on parity and breed. Cytobrush samples of the vagina and uterus were collected at 1 wk postpartum from 36 Holstein-Friesian (7 primiparous and 29 multiparous) and 29 Jersey (10 primiparous and 19 multiparous) cows. Microbial DNA was isolated from each sample and processed for shotgun metagenomic sequencing. The odds of multiparous cows being diagnosed as PVD+ was less compared with primiparous cows (OR = 0.21). Neither the α-diversity nor β-diversity of the uterine and vaginal microbiota were associated with PVD but the β-diversity was different between breeds and between parities. In the vagina of primiparous cows, differences in the microbiota of PVD- and PVD+ cows were minor, but the microbiota of multiparous PVD+ cows had greater relative abundance of Fusobacterium necrophorum, Trueperella pyogenes, Porphyromonas levii, and greater functional potential for amino acid and protein synthesis, energy metabolism, and growth compared with PVD- cows. The uterus of primiparous PVD+ cows had lesser relative abundance of Bacteroides heparinolyticus compared with PVD- cows. In the uterine microbiota, differences included greater functional potential for cellulose biosynthesis and fucose catabolism in multiparous PVD+ cows compared with PVD- cows. In the uterine microbiota of primiparous PVD+ cows, the functional potential for gram-negative cell wall synthesis and for negative regulation of tumor necrosis factor signaling was lesser compared with multiparous PVD+ cows. In the vagina of Holstein-Friesian PVD+ cows, the relative abundance of Caviibacter abscessus was greater whereas in the vagina of Jersey PVD+ cows the relative abundance of Catenibacterium mitsuokai, Finegoldia magna, Klebsiella variicola, and Streptococcus anginosus was greater compared with PVD- cows. In the uterine microbiota of Holstein-Friesian cows, the functional potential for spermidine biosynthesis was reduced compared with PVD- cows. In summary, differences in the species composition and functional potential of the vaginal and uterine microbiota between PVD- and PVD+ cows were dependent on parity and breed. The findings suggest that alternative strategies may be required to treat PVD for different parities and breeds of dairy cow.}, } @article {pmid37938694, year = {2022}, author = {Nishikawa, Y and Kogawa, M and Hosokawa, M and Wagatsuma, R and Mineta, K and Takahashi, K and Ide, K and Yura, K and Behzad, H and Gojobori, T and Takeyama, H}, title = {Validation of the application of gel beads-based single-cell genome sequencing platform to soil and seawater.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {92}, pmid = {37938694}, issn = {2730-6151}, support = {17H06158//MEXT | Japan Science and Technology Agency (JST)/ ; JPMJAX20BE//MEXT | Japan Science and Technology Agency (JST)/ ; 18H01801//MEXT | Japan Science and Technology Agency (JST)/ ; JPMJPR15FA//MEXT | JST | Precursory Research for Embryonic Science and Technology (PRESTO)/ ; URF/1/1976/17/01//KAUST | Global Collaborative Research, King Abdullah University of Science and Technology (GCR, KAUST)/ ; URF/1/1976/20/01//KAUST | Global Collaborative Research, King Abdullah University of Science and Technology (GCR, KAUST)/ ; FCS/1/3326/01/01//KAUST | Global Collaborative Research, King Abdullah University of Science and Technology (GCR, KAUST)/ ; }, abstract = {Single-cell genomics is applied to environmental samples as a method to solve the problems of current metagenomics. However, in the fluorescence-activated cell sorting-based cell isolation and subsequent whole genome amplification, the sorting efficiency and the sequence quality are greatly affected by the type of target environment, limiting its adaptability. Here, we developed an improved single-cell genomics platform, named SAG-gel, which utilizes gel beads for single-cell isolation, lysis, and whole genome amplification. To validate the versatility of SAG-gel, single-cell genome sequencing was performed with model bacteria and microbial samples collected from eight environmental sites, including soil and seawater. Gel beads enabled multiple lysis treatments. The genome coverage with model bacteria was improved by 9.1-25%. A total of 734 single amplified genomes were collected from the diverse environmental samples, and almost full-length 16S rRNA genes were recovered from 57.8% of them. We also revealed two marine Rhodobacter strains harboring nearly identical 16S rRNA genes but having different genome contents. In addition, searching for viral sequences elucidated the virus-host linkage over the sampling sites, revealing the geographic distribution and diverse host range of viruses.}, } @article {pmid37938354, year = {2022}, author = {Kohtz, AJ and Jay, ZJ and Lynes, MM and Krukenberg, V and Hatzenpichler, R}, title = {Culexarchaeia, a novel archaeal class of anaerobic generalists inhabiting geothermal environments.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {86}, pmid = {37938354}, issn = {2730-6151}, support = {80NSSC19K1633//National Aeronautics and Space Administration (NASA)/ ; }, abstract = {Geothermal environments, including terrestrial hot springs and deep-sea hydrothermal sediments, often contain many poorly understood lineages of archaea. Here, we recovered ten metagenome-assembled genomes (MAGs) from geothermal sediments and propose that they constitute a new archaeal class within the TACK superphylum, "Candidatus Culexarchaeia", named after the Culex Basin in Yellowstone National Park. Culexarchaeia harbor distinct sets of proteins involved in key cellular processes that are either phylogenetically divergent or are absent from other closely related TACK lineages, with a particular divergence in cell division and cytoskeletal proteins. Metabolic reconstruction revealed that Culexarchaeia have the capacity to metabolize a wide variety of organic and inorganic substrates. Notably, Culexarchaeia encode a unique modular, membrane associated, and energy conserving [NiFe]-hydrogenase complex that potentially interacts with heterodisulfide reductase (Hdr) subunits. Comparison of this [NiFe]-hydrogenase complex with similar complexes from other archaea suggests that interactions between membrane associated [NiFe]-hydrogenases and Hdr may be more widespread than previously appreciated in both methanogenic and non-methanogenic lifestyles. The analysis of Culexarchaeia further expands our understanding of the phylogenetic and functional diversity of lineages within the TACK superphylum and the ecology, physiology, and evolution of these organisms in extreme environments.}, } @article {pmid37938674, year = {2022}, author = {Walker, JR and Woods, AC and Pierce, MK and Steichen, JL and Quigg, A and Kaiser, K and Labonté, JM}, title = {Functionally diverse microbial communities show resilience in response to a record-breaking rain event.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {81}, pmid = {37938674}, issn = {2730-6151}, support = {1801367//National Science Foundation (NSF)/ ; }, abstract = {Estuaries provide many ecosystem services and host a majority of the world's population. Here, the response of microbial communities after a record-breaking flood event in a highly urbanized estuary was followed. Hurricane Harvey (hereafter Harvey) was a category 4 hurricane that made landfall on the Texas coast in 2017 and lashed the Houston area with 1.4-1.7 × 10[10] m[3] of rainfall, disrupting the natural gradients of nutrients and salinity. Here, we utilized metagenomics to analyze how Harvey altered the microbial community of Galveston Bay over five weeks following the storm. We hypothesized that the community would shift from a marine dominated community to that of a terrestrial and freshwater origin. We found that following the storm there were changes in the distribution of species with specific metabolic capacities, such as Cyanobacteria, enriched in oxygenic photosynthesis and nitrogen fixation genes, as well as Verrucomicrobia and Betaproteobacteria, with high prevalence of the SOX complex and anoxygenic photosynthesis genes. On the other hand, dominant members of the community with more diverse metabolic capabilities showed less fluctuations in their distribution. Our results highlight how massive precipitation disturbances can alter microbial communities and how the coalescence of diverse microorganisms creates a resilient community able to maintain ecosystem services even when the system is in an altered state.}, } @article {pmid37938667, year = {2022}, author = {Kim, M and Rodriguez-R, LM and Hatt, JK and Kayali, O and Nalá, R and Dunlop, AL and Brennan, PA and Corwin, E and Smith, AK and Brown, J and Konstantinidis, KT}, title = {Higher pathogen load in children from Mozambique vs. USA revealed by comparative fecal microbiome profiling.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {74}, pmid = {37938667}, issn = {2730-6151}, support = {OPP1137224//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; OPP1137224//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; OPP1137224//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; OPP1137224//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; OPP1137224//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; OPP1137224//Bill and Melinda Gates Foundation (Bill & Melinda Gates Foundation)/ ; GHS-A-00-09-00015-00//United States Agency for International Development (U.S. Agency for International Development)/ ; GHS-A-00-09-00015-00//United States Agency for International Development (U.S. Agency for International Development)/ ; GHS-A-00-09-00015-00//United States Agency for International Development (U.S. Agency for International Development)/ ; GHS-A-00-09-00015-00//United States Agency for International Development (U.S. Agency for International Development)/ ; GHS-A-00-09-00015-00//United States Agency for International Development (U.S. Agency for International Development)/ ; R01NR014800//U.S. Department of Health & Human Services | NIH | National Institute of Nursing Research (NINR)/ ; R01NR014800//U.S. Department of Health & Human Services | NIH | National Institute of Nursing Research (NINR)/ ; R01NR014800//U.S. Department of Health & Human Services | NIH | National Institute of Nursing Research (NINR)/ ; R01NR014800//U.S. Department of Health & Human Services | NIH | National Institute of Nursing Research (NINR)/ ; R01MD009746//U.S. Department of Health & Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)/ ; R01MD009746//U.S. Department of Health & Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)/ ; R01MD009746//U.S. Department of Health & Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)/ ; R01MD009746//U.S. Department of Health & Human Services | NIH | National Institute on Minority Health and Health Disparities (NIMHD)/ ; }, abstract = {The infant gut microbiome has lifelong implications on health and immunity but there is still limited understanding of the microbiome differences and similarities between children in low- and middle-income countries (LMICs) vs. high-income countries (HICs). Here, we describe and compare the microbiome profile of children aged under 48 months in two urban areas: Maputo, Mozambique and Atlanta, USA using shotgun metagenomics. The gut microbiome of American children showed distinct development, characterized by higher alpha diversity after infancy, compared to the same age group of African children, and the microbiomes clustered separately based on geographic location or age. The abundances of antibiotic resistance genes (ARGs) and virulence factors (VFs) were significantly higher in Maputo children, driven primarily by several primary and opportunistic pathogens. Most notably, about 50% of Maputo children under the age of two were positive for enterotoxigenic (ETEC) and typical enteropathogenic (EPEC) Escherichia coli diagnostic genes while none of the Atlanta age-matched children showed such a positive signal. In contrast, commensal species such as Phocaeicola vulgatus and Bacteroides caccae were more abundant in Atlanta, potentially reflecting diets rich in animal protein and susceptibility to inflammatory diseases. Overall, our results suggest that the different environments characterizing the two cities have significant, distinctive signatures on the microbiota of children and its development over time. Lack of safe water, sanitation, and hygiene (WASH) conditions and/or unsafe food sources may explain the higher enteric pathogen load among children in Maputo.}, } @article {pmid37938723, year = {2022}, author = {Crits-Christoph, A and Diamond, S and Al-Shayeb, B and Valentin-Alvarado, L and Banfield, JF}, title = {A widely distributed genus of soil Acidobacteria genomically enriched in biosynthetic gene clusters.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {70}, pmid = {37938723}, issn = {2730-6151}, abstract = {Bacteria of the phylum Acidobacteria are one of the most abundant groups across soil ecosystems, yet they are represented by comparatively few sequenced genomes, leaving gaps in our understanding of their metabolic diversity. Recently, genomes of Acidobacteria species with unusually large repertoires of biosynthetic gene clusters (BGCs) were reconstructed from grassland soil metagenomes, but the degree to which species with this trait are widespread is still unknown. To investigate this, we assembled 46 metagenome-assembled genomes recovered from permanently saturated organic-rich soils of a vernal (spring) pool ecosystem in Northern California. We obtained high and medium-quality draft genomes for three novel species from Candidatus Angelobacter (a proposed subdivision 1 Acidobacterial genus), a genus that is genomically enriched in genes for specialized metabolite biosynthesis. Acidobacteria were particularly abundant in the vernal pool sediments, and a Ca. Angelobacter species was the most abundant bacterial species detected in some samples. We identified numerous diverse biosynthetic gene clusters in these genomes, and also in five additional genomes from other publicly available soil metagenomes for other related Ca. Angelobacter species. Metabolic analysis indicates that Ca. Angelobacter likely are aerobes that ferment organic carbon, with potential to contribute to carbon compound turnover in soils. Using metatranscriptomics, we identified in situ metabolic activity and expression of specialized metabolic traits for two species from this genus. In conclusion, we expand genomic sampling of the uncultivated Ca. Angelobacter, and show that they represent common and sometimes highly abundant members of dry and saturated soil communities, with a high degree of capacity for synthesis of diverse specialized metabolites.}, } @article {pmid37938252, year = {2022}, author = {Palladino, G and Caroselli, E and Tavella, T and D'Amico, F and Prada, F and Mancuso, A and Franzellitti, S and Rampelli, S and Candela, M and Goffredo, S and Biagi, E}, title = {Metagenomic shifts in mucus, tissue and skeleton of the coral Balanophyllia europaea living along a natural CO2 gradient.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {65}, pmid = {37938252}, issn = {2730-6151}, abstract = {Using the Mediterranean coral Balanophyllia europaea naturally growing along a pH gradient close to Panarea island (Italy) as a model, we explored the role of host-associated microbiomes in coral acclimatization to ocean acidification (OA). Coral samples were collected at three sites along the gradient, mimicking seawater conditions projected for 2100 under different IPCC (The Intergovernmental Panel on Climate Change) scenarios, and mucus, soft tissue and skeleton associated microbiomes were characterized by shotgun metagenomics. According to our findings, OA induced functional changes in the microbiomes genetic potential that could mitigate the sub-optimal environmental conditions at three levels: i. selection of bacteria genetically equipped with functions related to stress resistance; ii. shifts in microbial carbohydrate metabolism from energy production to maintenance of cell membranes and walls integrity; iii. gain of functions able to respond to variations in nitrogen needs at the holobiont level, such as genes devoted to organic nitrogen mobilization. We hence provided hypotheses about the functional role of the coral associated microbiome in favoring host acclimatation to OA, remarking on the importance of considering the crosstalk among all the components of the holobiont to unveil how and to what extent corals will maintain their functionality under forthcoming ocean conditions.}, } @article {pmid37746232, year = {2022}, author = {Flores, GAM and Lopez, RP and Cerrudo, CS and Consolo, VF and Berón, CM}, title = {Culex quinquefasciatus Holobiont: A Fungal Metagenomic Approach.}, journal = {Frontiers in fungal biology}, volume = {3}, number = {}, pages = {918052}, pmid = {37746232}, issn = {2673-6128}, abstract = {Microorganisms associated with mosquitoes have fundamental roles, not only in their nutrition, but also in physiological and immunological processes, and in their adaptation to the environment as well. Studies on mosquito hologenomes have increased significantly during the last years, achieving important advances in the characterization of the "core bacteriome" of some species of health importance. However, the fungal mycobiome has not been exhaustively researched, especially throughout the life cycle of some hematophagous mosquito species. In this work, the diversity and composition of fungal communities in different developmental stages, sexes, and adult nutrition of Culex quinquefasciatus reared on laboratory conditions were characterized, using internal transcribed spacer high throughput amplicon sequencing. Larvae presented a higher fungal richness, while sucrose-fed males and females showed a similar diversity between them. Blood-fed females presented few operational taxonomic units with an even distribution. Results are consistent with the reduction of larval microbiota after molting, observed for the bacterial microbiome in other mosquito species. The filamentous Ascomycota Penicillium polonicum and Cladosporium sp. were present in all stages of the mosquitoes; in addition, the presence of yeasts in the insects or their subsequent colonization associated with their diet is also discussed. These results suggest that some species of fungi could be essential for the nutrition and development of mosquitoes throughout their life cycle.}, } @article {pmid37938269, year = {2022}, author = {Sauk, AH and Hug, LA}, title = {Substrate-restricted methanogenesis and limited volatile organic compound degradation in highly diverse and heterogeneous municipal landfill microbial communities.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {58}, pmid = {37938269}, issn = {2730-6151}, support = {2016-03686//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; }, abstract = {Microbial communities in landfills transform waste and generate methane in an environment unique from other built and natural environments. Landfill microbial diversity has predominantly been observed at the phylum level, without examining the extent of shared organismal diversity across space or time. We used 16S rRNA gene amplicon and shotgun metagenomic sequencing to examine the taxonomic and functional diversity of the microbial communities inhabiting a Southern Ontario landfill. The microbial capacity for volatile organic compound degradation in leachate and groundwater samples was correlated with geochemical conditions. Across the landfill, 25 bacterial and archaeal phyla were present at >1% relative abundance within at least one landfill sample, with Patescibacteria, Bacteroidota, Firmicutes, and Proteobacteria dominating. Methanogens were neither numerous nor particularly abundant, and were predominantly constrained to either acetoclastic or methylotrophic methanogenesis. The landfill microbial community was highly heterogeneous, with 90.7% of organisms present at only one or two sites within this interconnected system. Based on diversity measures, the landfill is a microbial system undergoing a constant state of disturbance and change, driving the extreme heterogeneity observed. Significant differences in geochemistry occurred across the leachate and groundwater wells sampled, with calcium, iron, magnesium, boron, meta and para xylenes, ortho xylenes, and ethylbenzene concentrations contributing most strongly to observed site differences. Predicted microbial degradation capacities indicated a heterogeneous community response to contaminants, including identification of novel proteins implicated in anaerobic degradation of key volatile organic compounds.}, } @article {pmid37938683, year = {2022}, author = {Marasco, R and Fusi, M and Ramond, JB and Van Goethem, MW and Seferji, K and Maggs-Kölling, G and Cowan, DA and Daffonchio, D}, title = {The plant rhizosheath-root niche is an edaphic "mini-oasis" in hyperarid deserts with enhanced microbial competition.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {47}, pmid = {37938683}, issn = {2730-6151}, abstract = {Plants have evolved unique morphological and developmental adaptations to cope with the abiotic stresses imposed by (hyper)arid environments. Such adaptations include the formation of rhizosheath-root system in which mutualistic plant-soil microbiome associations are established: the plant provides a nutrient-rich and shielded environment to microorganisms, which in return improve plant-fitness through plant growth promoting services. We hypothesized that the rhizosheath-root systems represent refuge niches and resource islands for the desert edaphic microbial communities. As a corollary, we posited that microorganisms compete intensively to colonize such "oasis" and only those beneficial microorganisms improving host fitness are preferentially selected by plant. Our results show that the belowground rhizosheath-root micro-environment is largely more hospitable than the surrounding gravel plain soil with higher nutrient and humidity contents, and cooler temperatures. By combining metabarcoding and shotgun metagenomics, we demonstrated that edaphic microbial biomass and community stability increased from the non-vegetated soils to the rhizosheath-root system. Concomitantly, non-vegetated soil communities favored autotrophy lifestyle while those associated with the plant niches were mainly heterotrophs and enriched in microbial plant growth promoting capacities. An intense inter-taxon microbial competition is involved in the colonization and homeostasis of the rhizosheath zone, as documented by significant enrichment of antibiotic resistance genes and CRISPR-Cas motifs. Altogether, our results demonstrate that rhizosheath-root systems are "edaphic mini-oases" and microbial diversity hotspots in hyperarid deserts. However, to colonize such refuge niches, the desert soil microorganisms compete intensively and are therefore prepared to outcompete potential rivals.}, } @article {pmid37915425, year = {2022}, author = {Weinstein, SB and Stephens, WZ and Greenhalgh, R and Round, JL and Dearing, MD}, title = {Wild herbivorous mammals (genus Neotoma) host a diverse but transient assemblage of fungi.}, journal = {Symbiosis (Philadelphia, Pa.)}, volume = {87}, number = {1}, pages = {45-58}, pmid = {37915425}, issn = {0334-5114}, support = {T32 AI055434/AI/NIAID NIH HHS/United States ; }, abstract = {Fungi are often overlooked in microbiome research and, as a result, little is known about the mammalian mycobiome. Although frequently detected in vertebrate guts and known to contribute to digestion in some herbivores, whether these eukaryotes are a persistent part of the mammalian gut microbiome remains contentious. To address this question, we sampled fungi from wild woodrats (Neotoma spp.) collected from 25 populations across the southwestern United States. For each animal, we collected a fecal sample in the wild, and then re-sampled the same individual after a month in captivity on a controlled diet. We characterized and quantified fungi using three techniques: ITS metabarcoding, shotgun metagenomics and qPCR. Wild individuals contained diverse fungal assemblages dominated by plant pathogens, widespread molds, and coprophilous taxa primarily in Ascomycota and Mucoromycota. Fungal abundance, diversity and composition differed between individuals, and was primarily influenced by animal geographic origin. Fungal abundance and diversity significantly declined in captivity, indicating that most fungi in wild hosts came from diet and environmental exposure. While this suggests that these mammals lack a persistent gut mycobiome, natural fungal exposure may still impact fungal dispersal and animal health.}, } @article {pmid37938295, year = {2022}, author = {Sanchez-Cid, C and Guironnet, A and Keuschnig, C and Wiest, L and Vulliet, E and Vogel, TM}, title = {Gentamicin at sub-inhibitory concentrations selects for antibiotic resistance in the environment.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {29}, pmid = {37938295}, issn = {2730-6151}, abstract = {Antibiotics released into the environment at low (sub-inhibitory) concentrations could select for antibiotic resistance that might disseminate to the human microbiome. In this case, low-level anthropogenic sources of antibiotics would have a significant impact on human health risk. In order to provide data necessary for the evaluation of this risk, we implemented river water microcosms at both sub-inhibitory and inhibitory concentrations of gentamicin as determined previously based on bacterial growth in enriched media. Using metagenomic sequencing and qPCR/RT-qPCR, we assessed the effects of gentamicin on water bacterial communities and their resistome. A change in the composition of total and active communities, as well as a gentamicin resistance gene selection identified via mobile genetic elements, was observed during a two-day exposure. We demonstrated the effects of sub-inhibitory concentrations of gentamicin on bacterial communities and their associated resistome in microcosms (simulating in situ conditions). In addition, we established relationships between antibiotic dose and the magnitude of the community response in the environment. The scope of resistance selection under sub-inhibitory concentrations of antibiotics and the mechanisms underlying this process might provide the basis for understanding resistance dispersion and associated risks in relatively low impacted ecosystems.}, } @article {pmid37938650, year = {2022}, author = {Wu, X and Cui, Z and Peng, J and Zhang, F and Liesack, W}, title = {Genome-resolved metagenomics identifies the particular genetic traits of phosphate-solubilizing bacteria in agricultural soil.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {17}, pmid = {37938650}, issn = {2730-6151}, support = {Z191100004019013//China Agricultural University (CAU)/ ; Z191100004019013//China Agricultural University (CAU)/ ; Z191100004019013//China Agricultural University (CAU)/ ; 10020799//China Agricultural University (CAU)/ ; }, abstract = {Bacteria play a key role in phosphate solubilization, but related genome-centric research on agricultural microbiomes is scarce. Here, we reconstructed 472 metagenome-assembled genomes (MAGs) covering agricultural soils from six long-term field trials across China. A total of 79 MAGs contained gcd encoding quinoprotein glucose dehydrogenase (GCD), which is the key biomarker for phosphate solubilization. Our findings showed that all GCD-MAGs represent potentially novel species, with gcd copy numbers varying from 1 to 10 per genome. Large genome size, a high ratio of glycosyl hydrolase genes, and increased capacity for carbohydrate utilization were specific traits of GCD-MAGs. Notably, the gcd copy number showed a significant and positive correlation with genome size. Generated using a machine learning approach, our findings were validated in a dataset of 692 genotypes covering the 18 bacterial families to which the 79 GCD-MAGs belong. Our results improve the knowledge of both the diversity and the genetic composition of phosphate-solubilizing bacteria. In particular, they reveal a genomic link between phosphate solubilization capacity and increased potential for carbohydrate metabolism, which may accelerate targeted engineering and improve management practices for sustainable agriculture.}, } @article {pmid37938680, year = {2022}, author = {Jang, HB and Chittick, L and Li, YF and Zablocki, O and Sanderson, CM and Carrillo, A and van den Engh, G and Sullivan, MB}, title = {Viral tag and grow: a scalable approach to capture and characterize infectious virus-host pairs.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {12}, pmid = {37938680}, issn = {2730-6151}, support = {1829640//National Science Foundation (NSF)/ ; }, abstract = {Viral metagenomics (viromics) has reshaped our understanding of DNA viral diversity, ecology, and evolution across Earth's ecosystems. However, viromics now needs approaches to link newly discovered viruses to their host cells and characterize them at scale. This study adapts one such method, sequencing-enabled viral tagging (VT), to establish "Viral Tag and Grow" (VT + Grow) to rapidly capture and characterize viruses that infect a cultivated target bacterium, Pseudoalteromonas. First, baseline cytometric and microscopy data improved understanding of how infection conditions and host physiology impact populations in VT flow cytograms. Next, we extensively evaluated "and grow" capability to assess where VT signals reflect adsorption alone or wholly successful infections that lead to lysis. Third, we applied VT + Grow to a clonal virus stock, which, coupled to traditional plaque assays, revealed significant variability in burst size-findings that hint at a viral "individuality" parallel to the microbial phenotypic heterogeneity literature. Finally, we established a live protocol for public comment and improvement via protocols.io to maximally empower the research community. Together these efforts provide a robust foundation for VT researchers, and establish VT + Grow as a promising scalable technology to capture and characterize viruses from mixed community source samples that infect cultivable bacteria.}, } @article {pmid37938653, year = {2022}, author = {Vigneron, A and Cruaud, P and Lovejoy, C and Vincent, WF}, title = {Genomic evidence of functional diversity in DPANN archaea, from oxic species to anoxic vampiristic consortia.}, journal = {ISME communications}, volume = {2}, number = {1}, pages = {4}, pmid = {37938653}, issn = {2730-6151}, abstract = {DPANN archaea account for half of the archaeal diversity of the biosphere, but with few cultivated representatives, their metabolic potential and environmental functions are poorly understood. The extreme geochemical and environmental conditions in meromictic ice-capped Lake A, in the Canadian High Arctic, provided an isolated, stratified model ecosystem to resolve the distribution and metabolism of uncultured aquatic DPANN archaea living across extreme redox and salinity gradients, from freshwater oxygenated conditions, to saline, anoxic, sulfidic waters. We recovered 28 metagenome-assembled genomes (MAGs) of DPANN archaea that provided genetic insights into their ecological function. Thiosulfate oxidation potential was detected in aerobic Woesearchaeota, whereas diverse metabolic functions were identified in anaerobic DPANN archaea, including degradation and fermentation of cellular compounds, and sulfide and polysulfide reduction. We also found evidence for "vampiristic" metabolism in several MAGs, with genes coding for pore-forming toxins, peptidoglycan degradation, and RNA scavenging. The vampiristic MAGs co-occurred with other DPANNs having complementary metabolic capacities, leading to the possibility that DPANN form interspecific consortia that recycle microbial carbon, nutrients and complex molecules through a DPANN archaeal shunt, adding hidden novel complexity to anaerobic microbial food webs.}, } @article {pmid37938716, year = {2021}, author = {Zeugner, LE and Krüger, K and Barrero-Canosa, J and Amann, RI and Fuchs, BM}, title = {In situ visualization of glycoside hydrolase family 92 genes in marine flavobacteria.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {81}, pmid = {37938716}, issn = {2730-6151}, abstract = {Gene clusters rich in carbohydrate-active enzymes within Flavobacteriia genera provide a competitiveness for their hosts to degrade diatom-derived polysaccharides. One such widely distributed polysaccharide is glucuronomannan, a main cell wall component of diatoms. A conserved gene cluster putatively degrading glucuronomannan was found previously among various flavobacterial taxa in marine metagenomes. Here, we aimed to visualize two glycoside hydrolase family 92 genes coding for α-mannosidases with fluorescently-labeled polynucleotide probes using direct-geneFISH. Reliable in situ localization of single-copy genes was achieved with an efficiency up to 74% not only in the flavobacterial strains Polaribacter Hel1_33_49 and Formosa Hel1_33_131 but also in planktonic samples from the North Sea. In combination with high-resolution microscopy, direct-geneFISH gave visual evidence of the contrasting lifestyles of closely related Polaribacter species in those samples and allowed for the determination of gene distribution among attached and free-living cells. We also detected highly similar GH92 genes in yet unidentified taxa by broadening probe specificities, enabling a visualization of the functional trait in subpopulations across the borders of species and genera. Such a quantitative insight into the niche separation of flavobacterial taxa complements our understanding of the ecology of polysaccharide-degrading bacteria beyond omics-based techniques on a single-cell level.}, } @article {pmid37938281, year = {2021}, author = {Bramucci, AR and Focardi, A and Rinke, C and Hugenholtz, P and Tyson, GW and Seymour, JR and Raina, JB}, title = {Microvolume DNA extraction methods for microscale amplicon and metagenomic studies.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {79}, pmid = {37938281}, issn = {2730-6151}, support = {DP180100838//Department of Education and Training | Australian Research Council (ARC)/ ; DP200100919//Department of Education and Training | Australian Research Council (ARC)/ ; DP180100838//Department of Education and Training | Australian Research Council (ARC)/ ; DP200100919//Department of Education and Training | Australian Research Council (ARC)/ ; }, abstract = {Investigating the composition and metabolic capacity of aquatic microbial assemblages usually requires the filtration of multi-litre samples, which are up to 1 million-fold larger than the microenvironments within which microbes are predicted to be spatially organised. To determine if community profiles can be reliably generated from microlitre volumes, we sampled seawater at a coastal and an oceanic site, filtered and homogenised them, and extracted DNA from bulk samples (2 L) and microvolumes (100, 10 and 1 μL) using two new approaches. These microvolume DNA extraction methods involve either physical or chemical lysis (through pH/thermal shock and lytic enzymes/surfactants, respectively), directly followed by the capture of DNA on magnetic beads. Downstream analysis of extracted DNA using both amplicon sequencing and metagenomics, revealed strong correlation with standard large volume approaches, demonstrating the fidelity of taxonomic and functional profiles of microbial communities in as little as 1 μL of seawater. This volume is six orders of magnitude smaller than most standard operating procedures for marine metagenomics, which will allow precise sampling of the heterogenous landscape that microbes inhabit.}, } @article {pmid37938275, year = {2021}, author = {Ponsero, AJ and Hurwitz, BL and Magain, N and Miadlikowska, J and Lutzoni, F and U'Ren, JM}, title = {Cyanolichen microbiome contains novel viruses that encode genes to promote microbial metabolism.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {56}, pmid = {37938275}, issn = {2730-6151}, abstract = {Lichen thalli are formed through the symbiotic association of a filamentous fungus and photosynthetic green alga and/or cyanobacterium. Recent studies have revealed lichens also host highly diverse communities of secondary fungal and bacterial symbionts, yet few studies have examined the viral component within these complex symbioses. Here, we describe viral biodiversity and functions in cyanolichens collected from across North America and Europe. As current machine-learning viral-detection tools are not trained on complex eukaryotic metagenomes, we first developed efficient methods to remove eukaryotic reads prior to viral detection and a custom pipeline to validate viral contigs predicted with three machine-learning methods. Our resulting high-quality viral data illustrate that every cyanolichen thallus contains diverse viruses that are distinct from viruses in other terrestrial ecosystems. In addition to cyanobacteria, predicted viral hosts include other lichen-associated bacterial lineages and algae, although a large fraction of viral contigs had no host prediction. Functional annotation of cyanolichen viral sequences predicts numerous viral-encoded auxiliary metabolic genes (AMGs) involved in amino acid, nucleotide, and carbohydrate metabolism, including AMGs for secondary metabolism (antibiotics and antimicrobials) and fatty acid biosynthesis. Overall, the diversity of cyanolichen AMGs suggests that viruses may alter microbial interactions within these complex symbiotic assemblages.}, } @article {pmid37938319, year = {2021}, author = {Sun, X and Ward, BB}, title = {Novel metagenome-assembled genomes involved in the nitrogen cycle from a Pacific oxygen minimum zone.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {26}, pmid = {37938319}, issn = {2730-6151}, abstract = {Oxygen minimum zones (OMZs) are unique marine regions where broad redox gradients stimulate biogeochemical cycles. Despite the important and unique role of OMZ microbes in these cycles, they are less characterized than microbes from the oxic ocean. Here we recovered 39 high- and medium-quality metagenome-assembled genomes (MAGs) from the Eastern Tropical South Pacific OMZ. More than half of these MAGs were not represented at the species level among 2631 MAGs from global marine datasets. OMZ MAGs were dominated by denitrifiers catalyzing nitrogen loss and especially MAGs with partial denitrification metabolism. A novel bacterial genome with nitrate-reducing potential could only be assigned to the phylum level. A Marine-Group II archaeon was found to be a versatile denitrifier, with the potential capability to respire multiple nitrogen compounds including N2O. The newly discovered denitrifying MAGs will improve our understanding of microbial adaptation strategies and the evolution of denitrification in the tree of life.}, } @article {pmid37744149, year = {2021}, author = {Ament-Velásquez, SL and Tuovinen, V and Bergström, L and Spribille, T and Vanderpool, D and Nascimbene, J and Yamamoto, Y and Thor, G and Johannesson, H}, title = {The Plot Thickens: Haploid and Triploid-Like Thalli, Hybridization, and Biased Mating Type Ratios in Letharia.}, journal = {Frontiers in fungal biology}, volume = {2}, number = {}, pages = {656386}, pmid = {37744149}, issn = {2673-6128}, abstract = {The study of the reproductive biology of lichen fungal symbionts has been traditionally challenging due to their complex lifestyles. Against the common belief of haploidy, a recent genomic study found a triploid-like signal in Letharia. Here, we infer the genome organization and reproduction in Letharia by analyzing genomic data from a pure culture and from thalli, and performing a PCR survey of the MAT locus in natural populations. We found that the read count variation in the four Letharia specimens, including the pure culture derived from a single sexual spore of L. lupina, is consistent with haploidy. By contrast, the L. lupina read counts from a thallus' metagenome are triploid-like. Characterization of the mating-type locus revealed a conserved heterothallic configuration across the genus, along with auxiliary genes that we identified. We found that the mating-type distributions are balanced in North America for L. vulpina and L. lupina, suggesting widespread sexual reproduction, but highly skewed in Europe for L. vulpina, consistent with predominant asexuality. Taken together, we propose that Letharia fungi are heterothallic and typically haploid, and provide evidence that triploid-like individuals are hybrids between L. lupina and an unknown Letharia lineage, reconciling classic systematic and genetic studies with recent genomic observations.}, } @article {pmid37938632, year = {2021}, author = {Pribyl, AL and Parks, DH and Angel, NZ and Boyd, JA and Hasson, AG and Fang, L and MacDonald, SL and Wills, BA and Wood, DLA and Krause, L and Tyson, GW and Hugenholtz, P}, title = {Critical evaluation of faecal microbiome preservation using metagenomic analysis.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {14}, pmid = {37938632}, issn = {2730-6151}, abstract = {The ability to preserve microbial communities in faecal samples is essential as increasing numbers of studies seek to use the gut microbiome to identify biomarkers of disease. Here we use shotgun metagenomics to rigorously evaluate the technical and compositional reproducibility of five room temperature (RT) microbial stabilisation methods compared to the best practice of flash-freezing. These methods included RNALater, OMNIGene-GUT, a dry BBL swab, LifeGuard, and a novel method for preserving faecal samples, a Copan FLOQSwab in an active drying tube (FLOQSwab-ADT). Each method was assessed using six replicate faecal samples from five participants, totalling 180 samples. The FLOQSwab-ADT performed best for both technical and compositional reproducibility, followed by RNAlater and OMNIgene-GUT. LifeGuard and the BBL swab had unpredictable outgrowth of Escherichia species in at least one replicate from each participant. We further evaluated the FLOQSwab-ADT in an additional 239 samples across 10 individuals after storage at -20 °C, RT, and 50 °C for four weeks compared to fresh controls. The FLOQSwab-ADT maintained its performance across all temperatures, indicating this method is an excellent alternative to existing RT stabilisation methods.}, } @article {pmid37938245, year = {2021}, author = {Li, J and Hua, ZS and Liu, T and Wang, C and Li, J and Bai, G and Lücker, S and Jetten, MSM and Zheng, M and Guo, J}, title = {Selective enrichment and metagenomic analysis of three novel comammox Nitrospira in a urine-fed membrane bioreactor.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {7}, pmid = {37938245}, issn = {2730-6151}, support = {21876095//National Natural Science Foundation of China (National Science Foundation of China)/ ; grant 016.Vidi.189.050//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, abstract = {The discovery of complete ammonia-oxidizing (comammox) Nitrospira has added an important new process to the microbial nitrogen cycle. While comammox Nitrospira have been detected in various ecosystems, only few studies have achieved their enrichment over other canonical nitrifiers. Here, we obtained a selective enrichment of comammox Nitrospira in a urine-fed membrane bioreactor in less than 200 days. By using 16S rRNA gene amplicon sequencing and quantitative PCR of the functional marker gene amoA, we observed a dominance (up to 30% relative abundance) of comammox Nitrospira over ammonia-oxidizing bacteria and archaea. Furthermore, the complete genomes of three new clade A comammox Nitrospira were recovered by metagenomics. These three strains were divergent from previously reported comammox species according to comparative genome and amoA-based analyses. In addition to the key genes for ammonia and nitrite oxidation, the three recovered genomes contained a complete urea utilization pathway. Our findings suggest that the urea present in the urine media played a significant role in the selective enrichment of these novel comammox Nitrospira, and support the diversity and versatility of their metabolism.}, } @article {pmid37938695, year = {2021}, author = {Pust, MM and Tümmler, B}, title = {Identification of core and rare species in metagenome samples based on shotgun metagenomic sequencing, Fourier transforms and spectral comparisons.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {2}, pmid = {37938695}, issn = {2730-6151}, abstract = {In shotgun metagenomic sequencing applications, low signal-to-noise ratios may complicate species-level differentiation of genetically similar core species and impede high-confidence detection of rare species. However, core and rare species can take pivotal roles in their habitats and should hence be studied as one entity to gain insights into the total potential of microbial communities in terms of taxonomy and functionality. Here, we offer a solution towards increased species-level specificity, decreased false discovery and omission rates of core and rare species in complex metagenomic samples by introducing the rare species identifier (raspir) tool. The python software is based on discrete Fourier transforms and spectral comparisons of biological and reference frequency signals obtained from real and ideal distributions of short DNA reads mapping towards circular reference genomes. Simulation-based testing of raspir enabled the detection of rare species with genome coverages of less than 0.2%. Species-level differentiation of rare Escherichia coli and Shigella spp., as well as the clear delineation between human Streptococcus spp. was feasible with low false discovery (1.3%) and omission rates (13%). Publicly available human placenta sequencing data were reanalysed with raspir. Raspir was unable to identify placental microbial communities, reinforcing the sterile womb paradigm.}, } @article {pmid37938231, year = {2021}, author = {Damashek, J and Okotie-Oyekan, AO and Gifford, SM and Vorobev, A and Moran, MA and Hollibaugh, JT}, title = {Transcriptional activity differentiates families of Marine Group II Euryarchaeota in the coastal ocean.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {5}, pmid = {37938231}, issn = {2730-6151}, support = {1656311//National Science Foundation (NSF)/ ; }, abstract = {Marine Group II Euryarchaeota (Candidatus Poseidoniales), abundant but yet-uncultivated members of marine microbial communities, are thought to be (photo)heterotrophs that metabolize dissolved organic matter (DOM), such as lipids and peptides. However, little is known about their transcriptional activity. We mapped reads from a metatranscriptomic time series collected at Sapelo Island (GA, USA) to metagenome-assembled genomes to determine the diversity of transcriptionally active Ca. Poseidoniales. Summer metatranscriptomes had the highest abundance of Ca. Poseidoniales transcripts, mostly from the O1 and O3 genera within Ca. Thalassarchaeaceae (MGIIb). In contrast, transcripts from fall and winter samples were predominantly from Ca. Poseidoniaceae (MGIIa). Genes encoding proteorhodopsin, membrane-bound pyrophosphatase, peptidase/proteases, and part of the ß-oxidation pathway were highly transcribed across abundant genera. Highly transcribed genes specific to Ca. Thalassarchaeaceae included xanthine/uracil permease and receptors for amino acid transporters. Enrichment of Ca. Thalassarchaeaceae transcript reads related to protein/peptide, nucleic acid, and amino acid transport and metabolism, as well as transcript depletion during dark incubations, provided further evidence of heterotrophic metabolism. Quantitative PCR analysis of South Atlantic Bight samples indicated consistently abundant Ca. Poseidoniales in nearshore and inshore waters. Together, our data suggest that Ca. Thalassarchaeaceae are important photoheterotrophs potentially linking DOM and nitrogen cycling in coastal waters.}, } @article {pmid37641111, year = {2023}, author = {Mak, L and Meleshko, D and Danko, DC and Barakzai, WN and Maharjan, S and Belchikov, N and Hajirasouliha, I}, title = {Ariadne: synthetic long read deconvolution using assembly graphs.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {197}, pmid = {37641111}, issn = {1474-760X}, support = {R35 GM138152/GM/NIGMS NIH HHS/United States ; T32 GM083937/GM/NIGMS NIH HHS/United States ; }, mesh = {*Algorithms ; Genomics ; Metagenome ; *Pentaerythritol Tetranitrate ; }, abstract = {Synthetic long read sequencing techniques such as UST's TELL-Seq and Loop Genomics' LoopSeq combine 3[Formula: see text] barcoding with standard short-read sequencing to expand the range of linkage resolution from hundreds to tens of thousands of base-pairs. However, the lack of a 1:1 correspondence between a long fragment and a 3[Formula: see text] unique molecular identifier confounds the assignment of linkage between short reads. We introduce Ariadne, a novel assembly graph-based synthetic long read deconvolution algorithm, that can be used to extract single-species read-clouds from synthetic long read datasets to improve the taxonomic classification and de novo assembly of complex populations, such as metagenomes.}, } @article {pmid37641081, year = {2023}, author = {Liu, W and Chu, J and Xie, Z and Yang, L and Huang, L and Tu, S and Cai, H and Wu, Z and Wei, A and Liu, C and Cheng, Y and Zhang, K and Wang, N}, title = {Mycobacterium abscessus pulmonary disease presenting with spontaneous pneumomediastinum and subcutaneous emphysema in childhood acute lymphoblastic leukemia: a case report and literature review.}, journal = {BMC pediatrics}, volume = {23}, number = {1}, pages = {431}, pmid = {37641081}, issn = {1471-2431}, mesh = {Adult ; Child ; Female ; Humans ; Child, Preschool ; *Mycobacterium abscessus ; *Mediastinal Emphysema/diagnostic imaging/etiology ; *Subcutaneous Emphysema/diagnostic imaging/etiology ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/complications ; *Lung Diseases ; }, abstract = {INTRODUCTION: Mycobacterium abscessus is a rapidly growing mycobacterium commonly identified in adults with underlying pulmonary diseases but is rarely observed in children. A better understanding of this pathogen in children is essential.

CASE PRESENTATION: We report the case of a 49-month-old female child without previous underlying pulmonary diseases but with acute lymphoblastic leukemia (ALL). The patient was complicated with pneumonia during chemotherapy, which was primarily characterized by spontaneous pneumomediastinum and subcutaneous emphysema on chest computed tomography (CT). M. abscessus sequences were detected by metagenomic next-generation sequencing in bronchoalveolar lavage fluid. With mechanical ventilation, closed thoracic drainage, and anti-infective therapy for 6 months, the patient's infection was controlled. The patient completed 2.5 years of treatment for ALL, and the drugs were discontinued. The patient currently remains in complete hematologic remission.

DISCUSSION: We reviewed the literature on 33 children with M. abscessus pulmonary disease. These children mostly had underlying immunodeficiency. Chest CT most often showed nodular shadows, consolidation, and bronchiectasis. Spontaneous pneumomediastinum and subcutaneous emphysema were not reported as major manifestations.

CONCLUSION: Spontaneous pneumomediastinum and subcutaneous emphysema were our patient's main characteristics on chest CT, and this study enriches the knowledge regarding possible imaging changes in M. abscessus pulmonary disease in children. This case report reflects good clinical experience in maintaining the balance between chemotherapy and anti-infective therapy in childhood ALL.}, } @article {pmid37641024, year = {2023}, author = {Yu, L and Zhang, B and Shi, J and Wang, M and Wan, H}, title = {Osteoarticular infection caused by Talaromyces Marneffei and Salmonella in a person living with HIV: a case report.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {560}, pmid = {37641024}, issn = {1471-2334}, support = {2022ZB292//Zhejiang TCM Science and Technology Program of China/ ; }, mesh = {Male ; Humans ; Adult ; *Acquired Immunodeficiency Syndrome ; *Talaromyces ; Salmonella ; }, abstract = {INTRODUCTION: Talaromycosis is a common invasive fungal disease in patients with HIV. However, its association with bone destruction is unusual in AIDS patients with talaromycosis.

CASE PRESENTATION: This report covers the case of a 38-year-old male AIDS patient coinfected with Talaromyces marneffei and Salmonella. The case, which involved bone destruction, was identified via metagenomic next-generation sequencing (mNGS). Following treatment with a combination of amphotericin B and piperacillin-tazobactam, the patient's elbow motion noticeably improved. Imaging findings revealed that the progression of bony destruction had halted.

CONCLUSION: Bone damage due to Talaromyces marneffei infection is infrequent in HIV-positive patients. Therefore, healthcare professionals must be vigilant for potential bone lesions associated with this type of infection. Prompt diagnosis and antimicrobial treatment are crucial.}, } @article {pmid37641010, year = {2023}, author = {Carpenter, L and Shoubridge, AP and Flynn, E and Lang, C and Taylor, SL and Papanicolas, LE and Collins, J and Gordon, D and Lynn, DJ and Crotty, M and Whitehead, C and Leong, LEX and Wesselingh, SL and Ivey, K and Inacio, MC and Rogers, GB}, title = {Cohort profile: GRACE - a residential aged care cohort examining factors influencing antimicrobial resistance carriage.}, journal = {BMC geriatrics}, volume = {23}, number = {1}, pages = {521}, pmid = {37641010}, issn = {1471-2318}, mesh = {Humans ; Female ; Aged ; Aged, 80 and over ; Male ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Australia ; Drug Resistance, Bacterial ; Age Factors ; *Dementia/diagnosis/drug therapy/epidemiology ; }, abstract = {BACKGROUND: The emergence of antimicrobial-resistant bacteria represents a considerable threat to human health, particularly for vulnerable populations such as those living in residential aged care. However, antimicrobial resistance carriage and modes of transmission remain incompletely understood. The Generating evidence on antimicrobial Resistance in the Aged Care Environment (GRACE) study was established to determine principal risk factors of antimicrobial resistance carriage and transmission in residential aged care facilities (RACFs). This article describes the cohort characteristics, national representation, and planned analyses for this study.

METHODS: Between March 2019 and March 2020, 279 participants were recruited from five South Australian RACFs. The median age was 88.6 years, the median period in residence was 681 days, and 71.7% were female. A dementia diagnosis was recorded in 54.5% and more than two thirds had moderate to severe cognitive impairment (68.8%). 61% had received at least one course of antibiotics in the 12 months prior to enrolment.

RESULTS: To investigate the representation of the GRACE cohort to Australians in residential aged care, its characteristics were compared to a subset of the historical cohort of the Registry of Senior Australians (ROSA). This included 142,923 individuals who were permanent residents of RACFs on June 30th, 2017. GRACE and ROSA cohorts were similar in age, sex, and duration of residential care, prevalence of health conditions, and recorded dementia diagnoses. Differences were observed in care requirements and antibiotic exposure (both higher for GRACE participants). GRACE participants had fewer hospital visits compared to the ROSA cohort, and a smaller proportion were prescribed psycholeptic medications.

CONCLUSIONS: We have assembled a cohort of aged care residents that is representative of the Australian aged care population, and which provides a basis for future analyses. Metagenomic data isolated from participants and built environments will be used to determine microbiome and resistome characteristics of an individual and the facility. Individual and facility risk exposures will be aligned with metagenomic data to identify principal determinants for antimicrobial resistance carriage. Ultimately, this analysis will inform measures aimed at reducing the emergence and spread of antimicrobial resistant pathogens in this high-risk population.}, } @article {pmid37640834, year = {2023}, author = {van Dijk, B and Buffard, P and Farr, AD and Giersdorf, F and Meijer, J and Dutilh, BE and Rainey, PB}, title = {Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {90}, pmid = {37640834}, issn = {2730-6151}, abstract = {Microbial evolution is driven by rapid changes in gene content mediated by horizontal gene transfer (HGT). While mobile genetic elements (MGEs) are important drivers of gene flux, the nanobiome-the zoo of Darwinian replicators that depend on microbial hosts-remains poorly characterised. New approaches are necessary to increase our understanding beyond MGEs shaping individual populations, towards their impacts on complex microbial communities. A bioinformatic pipeline (xenoseq) was developed to cross-compare metagenomic samples from microbial consortia evolving in parallel, aimed at identifying MGE dissemination, which was applied to compost communities which underwent periodic mixing of MGEs. We show that xenoseq can distinguish movement of MGEs from demographic changes in community composition that otherwise confounds identification, and furthermore demonstrate the discovery of various unexpected entities. Of particular interest was a nanobacterium of the candidate phylum radiation (CPR) which is closely related to a species identified in groundwater ecosystems (Candidatus Saccharibacterium), and appears to have a parasitic lifestyle. We also highlight another prolific mobile element, a 313 kb plasmid hosted by a Cellvibrio lineage. The host was predicted to be capable of nitrogen fixation, and acquisition of the plasmid coincides with increased ammonia production. Taken together, our data show that new experimental strategies combined with bioinformatic analyses of metagenomic data stand to provide insight into the nanobiome as a driver of microbial community evolution.}, } @article {pmid37640519, year = {2023}, author = {Maccio, U and Gianolio, A and Rets, AV}, title = {Granulomas in bone marrow biopsies: clinicopathological significance and new perspectives.}, journal = {Journal of clinical pathology}, volume = {77}, number = {1}, pages = {8-15}, doi = {10.1136/jcp-2023-209104}, pmid = {37640519}, issn = {1472-4146}, mesh = {Humans ; Bone Marrow/pathology ; *Epstein-Barr Virus Infections/complications ; Herpesvirus 4, Human ; Granuloma/diagnosis/etiology/pathology ; *Tuberculosis/diagnosis ; Biopsy ; }, abstract = {Bone marrow granulomas in trephine biopsies are a rare and usually incidental finding. Possible causes include infectious (especially tuberculous and rarer non-tuberculous mycobacteria, but also many other bacterial, viral, fungal and parasitic agents) and non-infectious causes (especially medications, autoimmune disease, sarcoidosis, haematological and non-haematological malignancy). Necrotising granulomas are generally suggestive of an infectious aetiology (tuberculosis being the most common), whereas fibrin ring granulomas are associated with Q-fever and Epstein Barr Virus, although exceptions are possible. Every case suspicious for infectious aetiology should undergo further analysis like special staining (Ziehl-Neelsen for acid-fast rods) or molecular studies. The histomorphology should always be clinically correlated. In cases in which no infectious cause can be identified, untargeted metagenomics may represent a valid diagnostic tool that may become standard in the near future for bone marrow diagnostics. In this review, we have analysed the published data from 1956 up to today, and we report aspects of epidemiology, aetiology, diagnostic algorithms, differential diagnosis and the role of metagenomics in bone marrow biopsies with granulomas.}, } @article {pmid37640288, year = {2023}, author = {Ousmane, S and Kollo, IA and Jambou, R and Boubacar, R and Arzika, AM and Maliki, R and Amza, A and Liu, Z and Lebas, E and Colby, E and Zhong, L and Chen, C and Hinterwirth, A and Doan, T and Lietman, TM and O'Brien, KS}, title = {Wastewater-Based Surveillance of Antimicrobial Resistance in Niger: An Exploratory Study.}, journal = {The American journal of tropical medicine and hygiene}, volume = {109}, number = {4}, pages = {725-729}, pmid = {37640288}, issn = {1476-1645}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Drug Resistance, Bacterial/genetics ; Wastewater-Based Epidemiological Monitoring ; Wastewater ; Niger/epidemiology ; }, abstract = {Wastewater-based surveillance is increasingly recognized as an important approach to monitoring population-level antimicrobial resistance (AMR). In this exploratory study, we examined the use of metagenomics to evaluate AMR using untreated wastewater samples routinely collected by the Niger national polio surveillance program. Forty-eight stored samples from two seasons each year over 4 years (2016-2019) in three regions were selected for inclusion in this study and processed using unbiased DNA deep sequencing. Normalized number of reads of genetic determinants for different antibiotic classes were compared over time, by season, and by location. Correlations in resistance were examined among classes. Changes in reads per million per year were demonstrated for several classes, including decreases over time in resistance determinants for phenicols (-3.3, 95% CI: -8.7 to -0.1, P = 0.029) and increases over time for aminocoumarins (3.8, 95% CI: 0.0 to 11.4, P = 0.043), fluoroquinolones (6.8, 95% CI: 0.0 to 20.5, P = 0.048), and beta-lactams (0.85, 95% CI: 0.1 to 1.7, P = 0.006). Sulfonamide resistance was higher in the post-rainy season compared with the dry season (5.2-fold change, 95% CI: 3.4 to 7.9, P < 0.001). No differences were detected when comparing other classes by season or by site for any antibiotic class. Positive correlations were identified in genetic determinants of resistance among several antibiotic classes. These results demonstrate the potential utility of leveraging existing wastewater sample collection in this setting for AMR surveillance.}, } @article {pmid37640150, year = {2023}, author = {Astarita, G and Kelly, RS and Lasky-Su, J}, title = {Metabolomics and lipidomics strategies in modern drug discovery and development.}, journal = {Drug discovery today}, volume = {28}, number = {10}, pages = {103751}, pmid = {37640150}, issn = {1878-5832}, support = {R01 DK125273/DK/NIDDK NIH HHS/United States ; R01 HL123915/HL/NHLBI NIH HHS/United States ; R01 HL155742/HL/NHLBI NIH HHS/United States ; R01 HL141826/HL/NHLBI NIH HHS/United States ; U19 AI168643/AI/NIAID NIH HHS/United States ; K01 HL146980/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Lipidomics ; *Lipids/chemistry ; Metabolomics/methods ; Biomarkers/metabolism ; Drug Discovery ; }, abstract = {Metabolomics and lipidomics have an increasingly pivotal role in drug discovery and development. In the context of drug discovery, monitoring changes in the levels or composition of metabolites and lipids relative to genetic variations yields functional insights, bolstering human genetics and (meta)genomic methodologies. This approach also sheds light on potential novel targets for therapeutic intervention. In the context of drug development, metabolite and lipid biomarkers contribute to enhanced success rates, promising a transformative impact on precision medicine. In this review, we deviate from analytical chemist-focused perspectives, offering an overview tailored to drug discovery. We provide introductory insight into state-of-the-art mass spectrometry (MS)-based metabolomics and lipidomics techniques utilized in drug discovery and development, drawing from the collective expertise of our research teams. We comprehensively outline the application of metabolomics and lipidomics in advancing drug discovery and development, spanning fundamental research, target identification, mechanisms of action, and the exploration of biomarkers.}, } @article {pmid37639797, year = {2023}, author = {Wang, S and Yun, Y and Tian, X and Su, Z and Liao, Z and Li, G and Ma, T}, title = {HMDB: A curated database of genes involved in hydrocarbon monooxygenation reaction with homologous genes as background.}, journal = {Journal of hazardous materials}, volume = {460}, number = {}, pages = {132397}, doi = {10.1016/j.jhazmat.2023.132397}, pmid = {37639797}, issn = {1873-3336}, mesh = {*Carbon ; Carbon Cycle ; Databases, Factual ; *Environmental Restoration and Remediation ; Hydrocarbons ; Mixed Function Oxygenases/genetics ; }, abstract = {The investigation of hydrocarbon degradation potential of environmental microorganisms is an important research topic, whether for the global carbon cycle or oil pollution remediation. Under aerobic conditions, the microorganisms employ a range of monooxygenases to use hydrocarbons substrates as a source of carbon and energy. With the explosion of sequencing data, mining genes in genomes or metagenomes has become computationally expensive and time-consuming. We proposed the HMDB, which is a professional gene database of hydrocarbon monooxygenases. HMDB contains 38 genes, which encode 11 monooxygenases responsible for the hydroxylation of 8 hydrocarbons. To reduce false positives, the strategy of using homologous genes as background noise was applied for HMDB. We added 10,095 gene sequences of homologous enzymes which took non-hydrocarbons as substrates to HMDB. The classic BLAST method and best-hit strategy were recommended for HMDB usage, but not limited. The performance of HMDB was validated using 264,402 prokaryote genomes from RefSeq and 51 metagenomes from SRA. The results showed that HMDB database had high sensitivity and low false positive rate. We release the HMDB database here, hoping to speed up the process for investigation of hydrocarbon monooxygenases in massive metagenomic data. HMDB is freely available at http://www.orgene.net/HMDB/.}, } @article {pmid37639510, year = {2023}, author = {Zeng, XC and Xu, Y and Lu, H and Xiong, J and Xu, H and Wu, W}, title = {Contradictory Impacts of Nitrate on the Dissimilatory Arsenate-Respiring Prokaryotes-Induced Reductive Mobilization of Arsenic from Contaminated Sediments: Mechanism Insight from Metagenomic and Functional Analyses.}, journal = {Environmental science & technology}, volume = {57}, number = {36}, pages = {13473-13486}, doi = {10.1021/acs.est.3c02190}, pmid = {37639510}, issn = {1520-5851}, mesh = {*Nitrates ; *Arsenic ; Arsenates ; Nitrites ; }, abstract = {Dissimilatory arsenate-respiring prokaryotes (DARPs) are considered to be a key impetus of the reductive dissolution of solid-phase arsenic. However, little is known about the interaction between nitrate and DARPs so far. In this study, we showed that nitrate either inhibited or promoted the DARP population-catalyzed reductive mobilization of As in sediments. Metagenomic analysis of the microbial communities in the microcosms after seven days of As release assays suggested that microbes mainly consisted of: Type-I DARPs having potential to reduce NO3[-] into NO2[-] and Type-II DARPs having potential to reduce NO3[-] to NH4[+]. We further isolated two cultivable DARPs, Neobacillus sp. A01 and Paenibacillus sp. A02, which represent Type-I and -II DARPs, respectively. We observed that nitrate suppressed A01-mediated release of As(III) but promoted A02-mediated release of As(III). Furthermore, we demonstrated that this observation was due to the fact that nitrite, the end product of incomplete denitrification by Type-I DARPs, suppressed the arrA gene expression per cell and growth of all DARPs, whereas ammonium, the end product of dissimilatory nitrate reduction to ammonium (DNRA) by Type-II DARPs, enhanced the arrA gene expression per cell and significantly promoted the growth of all DARPs. These findings suggest that the actual effects of nitrate on DARP population-catalyzed reductive mobilization of arsenic, largely depend on the ratio of Type-I to Type-II DARPs in sediments.}, } @article {pmid37639475, year = {2023}, author = {Rangel-Pineros, G and Almeida, A and Beracochea, M and Sakharova, E and Marz, M and Reyes Muñoz, A and Hölzer, M and Finn, RD}, title = {VIRify: An integrated detection, annotation and taxonomic classification pipeline using virus-specific protein profile hidden Markov models.}, journal = {PLoS computational biology}, volume = {19}, number = {8}, pages = {e1011422}, pmid = {37639475}, issn = {1553-7358}, mesh = {Humans ; *Eukaryota ; Eukaryotic Cells ; Genome, Viral/genetics ; Metagenome/genetics ; *Microbiota ; }, abstract = {The study of viral communities has revealed the enormous diversity and impact these biological entities have on various ecosystems. These observations have sparked widespread interest in developing computational strategies that support the comprehensive characterisation of viral communities based on sequencing data. Here we introduce VIRify, a new computational pipeline designed to provide a user-friendly and accurate functional and taxonomic characterisation of viral communities. VIRify identifies viral contigs and prophages from metagenomic assemblies and annotates them using a collection of viral profile hidden Markov models (HMMs). These include our manually-curated profile HMMs, which serve as specific taxonomic markers for a wide range of prokaryotic and eukaryotic viral taxa and are thus used to reliably classify viral contigs. We tested VIRify on assemblies from two microbial mock communities, a large metagenomics study, and a collection of publicly available viral genomic sequences from the human gut. The results showed that VIRify could identify sequences from both prokaryotic and eukaryotic viruses, and provided taxonomic classifications from the genus to the family rank with an average accuracy of 86.6%. In addition, VIRify allowed the detection and taxonomic classification of a range of prokaryotic and eukaryotic viruses present in 243 marine metagenomic assemblies. Finally, the use of VIRify led to a large expansion in the number of taxonomically classified human gut viral sequences and the improvement of outdated and shallow taxonomic classifications. Overall, we demonstrate that VIRify is a novel and powerful resource that offers an enhanced capability to detect a broad range of viral contigs and taxonomically classify them.}, } @article {pmid37638757, year = {2023}, author = {Chaturvedi, A and Li, X and Dhandapani, V and Marshall, H and Kissane, S and Cuenca-Cambronero, M and Asole, G and Calvet, F and Ruiz-Romero, M and Marangio, P and Guigó, R and Rago, D and Mirbahai, L and Eastwood, N and Colbourne, JK and Zhou, J and Mallon, E and Orsini, L}, title = {The hologenome of Daphnia magna reveals possible DNA methylation and microbiome-mediated evolution of the host genome.}, journal = {Nucleic acids research}, volume = {51}, number = {18}, pages = {9785-9803}, pmid = {37638757}, issn = {1362-4962}, support = {NE/N016777/1//NERC/ ; 965406//European Union/ ; 101028700//Marie Skłodowska-Curie/ ; IC160121//Royal Society International Collaboration Award/ ; }, abstract = {Properties that make organisms ideal laboratory models in developmental and medical research are often the ones that also make them less representative of wild relatives. The waterflea Daphnia magna is an exception, by both sharing many properties with established laboratory models and being a keystone species, a sentinel species for assessing water quality, an indicator of environmental change and an established ecotoxicology model. Yet, Daphnia's full potential has not been fully exploited because of the challenges associated with assembling and annotating its gene-rich genome. Here, we present the first hologenome of Daphnia magna, consisting of a chromosomal-level assembly of the D. magna genome and the draft assembly of its metagenome. By sequencing and mapping transcriptomes from exposures to environmental conditions and from developmental morphological landmarks, we expand the previously annotates gene set for this species. We also provide evidence for the potential role of gene-body DNA-methylation as a mutagen mediating genome evolution. For the first time, our study shows that the gut microbes provide resistance to commonly used antibiotics and virulence factors, potentially mediating Daphnia's environmental-driven rapid evolution. Key findings in this study improve our understanding of the contribution of DNA methylation and gut microbiota to genome evolution in response to rapidly changing environments.}, } @article {pmid37637815, year = {2023}, author = {Li, Y and Bian, W and Wu, S and Zhang, J and Li, D}, title = {Metagenomic next-generation sequencing for Mycobacterium tuberculosis complex detection: a meta-analysis.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1224993}, pmid = {37637815}, issn = {2296-2565}, mesh = {Humans ; *Mycobacterium tuberculosis/genetics ; High-Throughput Nucleotide Sequencing ; *Coinfection ; Research Design ; Technology ; }, abstract = {OBJECTIVE: Metagenomic next-generation sequencing (mNGS) has been gradually applied to the diagnosis of tuberculosis (TB) due to its rapid and highly sensitive characteristics. Despite numerous studies on this subject, their results vary significantly. Thus, the current meta-analysis was performed to assess the performance of the mNGS on tuberculosis.

METHODS: PubMed, Embase, Web of Science, and The Cochrane Library were searched up to June 21, 2023. Studies utilizing the mNGS for tuberculosis detection were included. The risk of bias was assessed by QUADAS-2, and a meta-analysis was performed with STATA14.0 software.

RESULTS: Seventeen studies comprising 3,205 specimens were included. The combined sensitivity and specificity of mNGS for clinical specimens were 0.69[0.58-0.79] and 1.00[0.99-1.00], respectively. Subgroup analysis identified sequencing platform, diagnostic criteria, study type, sample size, and sample types as potential sources of heterogeneity. Cerebrospinal Fluid (CSF) has a lower sensitivity of 0.58 (0.39-0.75). In a population with a 10% prevalence rate, the accuracy of sensitivity reached 94%.

CONCLUSION: Metagenomic next-generation sequencing technology exhibits high sensitivity and speed in diagnosing Mycobacterium tuberculosis. Its application in mono and mixed infections peoples shows promise, and mNGS is likely to be increasingly used to address challenges posed by Mycobacterium tuberculosis complexes in the future.}, } @article {pmid37637702, year = {2023}, author = {Zhou, S and Liu, MH and Deng, XP}, title = {Critical respiratory failure due to pregnancy complicated by COVID-19 and bacterial coinfection: A case report.}, journal = {World journal of clinical cases}, volume = {11}, number = {23}, pages = {5559-5566}, pmid = {37637702}, issn = {2307-8960}, abstract = {BACKGROUND: In the past 3 years, the global pandemic of coronavirus disease 2019 (COVID-19) has posed a great threat to human life and safety. Among the causes of death in COVID-19 patients, combined or secondary bacterial infection is an important factor. As a special group, pregnant women experience varying degrees of change in their immune status, cardiopulmonary function, and anatomical structure during pregnancy, which puts them at higher risk of contracting COVID-19. COVID-19 infection during pregnancy is associated with increased adverse events such as hospitalisation, admission to the intensive care unit, and mechanical ventilation. Therefore, pregnancy combined with coinfection of COVID-19 and bacteria often leads to critical respiratory failure, posing severe challenges in the diagnosis and treatment process.

CASE SUMMARY: We report a case of COVID-19 complicated with Staphylococcus aureus (S. aureus) coinfection in a pregnant woman at 34 wk of gestation. Her rapid progression of pulmonary lesions caused severe respiratory failure, and she received non-invasive ventilator-assisted respiratory treatment. Subsequently, we delivered a foetus via emergency caesarean section after accelerating the maturity of the foetal pulmonary system, and the respiratory condition of the puerperant woman significantly improved after the delivery of the foetus. Lavage fluid was taken under tracheoscopy to quickly search for pathogens by the metagenomic next-generation sequencing (mNGS), and both COVID-19 and S. aureus were detected. After targeted anti-infective treatment, the maternal condition gradually improved, and the patient was discharged from the hospital.

CONCLUSION: The coinfection of pregnancy with COVID-19 and bacteria often leads to critical respiratory failure, which is a great challenge in the process of diagnosis and treatment. It is crucial to choose the right time to deliver the foetus and to quickly find pathogens by mNGS.}, } @article {pmid37637461, year = {2023}, author = {Zhang, C and Li, Z and Wang, M and Zhou, J and Yu, W and Liu, H and Hu, B and Wang, S}, title = {High specificity of metagenomic next-generation sequencing using protected bronchial brushing sample in diagnosing pneumonia in children.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1165432}, pmid = {37637461}, issn = {2235-2988}, mesh = {Humans ; Child ; Metagenomics ; Retrospective Studies ; *Pneumonia/diagnosis ; *Respiratory Tract Infections ; High-Throughput Nucleotide Sequencing ; Mycoplasma pneumoniae ; }, abstract = {BACKGROUND: Lower respiratory tract infections are the leading cause of morbidity and mortality in children worldwide. Timely and accurate pathogen detection is crucial for proper clinical diagnosis and therapeutic strategies. The low detection efficiency of conventional methods and low specificity using respiratory samples seriously hindered the accurate detection of pathogens.

METHODS: In this study, we retrospectively enrolled 1,032 children to evaluate the performance of metagenomics next-generation sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) sample and protected bronchial brushing (BB) sample in diagnosing pneumonia in children. In addition, conventional tests (CTs) were also performed.

RESULTS: The specificity of BB mNGS [67.3% (95% CI 58.6%-75.9%)] was significantly higher than that of BALF mNGS [38.5% (95% CI 12.0%-64.9%)]. The total coincidence rate of BB mNGS [77.6% (95% CI 74.8%-80.5%)] was slightly higher than that of BALF mNGS [76.5% (95% CI 68.8%-84.1%)] and CTs [38.5% (95% CI 35.2%-41.9%)]. During the epidemics of Mycoplasma pneumoniae, the detection rate of M. pneumoniae in the >6-year group (81.8%) was higher than that in the 3-6-year (78.9%) and <3-year groups (21.5%). The highest detection rates of bacteria, fungi, and viruses were found in the <3-year, >6-year, and 3-6-year groups, respectively. mNGS detection should be performed at the duration of 5-7 days after the start of continuous anti-microbial therapy or at the duration of 6-9 days from onset to mNGS test.

CONCLUSIONS: This is the first report to evaluate the performance of BB mNGS in diagnosing pulmonary infections in children on a large scale. Based on our findings, extensive application of BB mNGS could be expected.}, } @article {pmid37637134, year = {2023}, author = {White, C and Antell, E and Schwartz, SL and Lawrence, JE and Keren, R and Zhou, L and Yu, K and Zhuang, W and Alvarez-Cohen, L}, title = {Synergistic interactions between anammox and dissimilatory nitrate reducing bacteria sustains reactor performance across variable nitrogen loading ratios.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1243410}, pmid = {37637134}, issn = {1664-302X}, abstract = {Anaerobic ammonium oxidizing (anammox) bacteria are utilized for high efficiency nitrogen removal from nitrogen-laden sidestreams in wastewater treatment plants. The anammox bacteria form a variety of competitive and mutualistic interactions with heterotrophic bacteria that often employ denitrification or dissimilatory nitrate reduction to ammonium (DNRA) for energy generation. These interactions can be heavily influenced by the influent ratio of ammonium to nitrite, NH4[+]:NO2[-], where deviations from the widely acknowledged stoichiometric ratio (1:1.32) have been demonstrated to have deleterious effects on anammox efficiency. Thus, it is important to understand how variable NH4[+]:NO2[-] ratios impact the microbial ecology of anammox reactors. We observed the response of the microbial community in a lab scale anammox membrane bioreactor (MBR) to changes in the influent NH4[+]:NO2[-] ratio using both 16S rRNA gene and shotgun metagenomic sequencing. Ammonium removal efficiency decreased from 99.77 ± 0.04% when the ratio was 1:1.32 (prior to day 89) to 90.85 ± 0.29% when the ratio was decreased to 1:1.1 (day 89-202) and 90.14 ± 0.09% when the ratio was changed to 1:1.13 (day 169-200). Over this same timespan, the overall nitrogen removal efficiency (NRE) remained relatively unchanged (85.26 ± 0.01% from day 0-89, compared to 85.49 ± 0.01% from day 89-169, and 83.04 ± 0.01% from day 169-200). When the ratio was slightly increased to 1:1.17-1:1.2 (day 202-253), the ammonium removal efficiency increased to 97.28 ± 0.45% and the NRE increased to 88.21 ± 0.01%. Analysis of 16 S rRNA gene sequences demonstrated increased relative abundance of taxa belonging to Bacteroidetes, Chloroflexi, and Ignavibacteriae over the course of the experiment. The relative abundance of Planctomycetes, the phylum to which anammox bacteria belong, decreased from 77.19% at the beginning of the experiment to 12.24% by the end of the experiment. Analysis of metagenome assembled genomes (MAGs) indicated increased abundance of bacteria with nrfAH genes used for DNRA after the introduction of lower influent NH4[+]:NO2[-] ratios. The high relative abundance of DNRA bacteria coinciding with sustained bioreactor performance indicates a mutualistic relationship between the anammox and DNRA bacteria. Understanding these interactions could support more robust bioreactor operation at variable nitrogen loading ratios.}, } @article {pmid37636319, year = {2023}, author = {Abbo, SR and de Almeida, JPP and Olmo, RP and Balvers, C and Griep, JS and Linthout, C and Koenraadt, CJM and Silva, BM and Fros, JJ and Aguiar, ERGR and Marois, E and Pijlman, GP and Marques, JT}, title = {The virome of the invasive Asian bush mosquito Aedes japonicus in Europe.}, journal = {Virus evolution}, volume = {9}, number = {2}, pages = {vead041}, pmid = {37636319}, issn = {2057-1577}, abstract = {The Asian bush mosquito Aedes japonicus is rapidly invading North America and Europe. Due to its potential to transmit multiple pathogenic arthropod-borne (arbo)viruses including Zika virus, West Nile virus, and chikungunya virus, it is important to understand the biology of this vector mosquito in more detail. In addition to arboviruses, mosquitoes can also carry insect-specific viruses that are receiving increasing attention due to their potential effects on host physiology and arbovirus transmission. In this study, we characterized the collection of viruses, referred to as the virome, circulating in Ae. japonicus populations in the Netherlands and France. Applying a small RNA-based metagenomic approach to Ae. japonicus, we uncovered a distinct group of viruses present in samples from both the Netherlands and France. These included one known virus, Ae. japonicus narnavirus 1 (AejapNV1), and three new virus species that we named Ae. japonicus totivirus 1 (AejapTV1), Ae. japonicus anphevirus 1 (AejapAV1) and Ae. japonicus bunyavirus 1 (AejapBV1). We also discovered sequences that were presumably derived from two additional novel viruses: Ae. japonicus bunyavirus 2 (AejapBV2) and Ae. japonicus rhabdovirus 1 (AejapRV1). All six viruses induced strong RNA interference responses, including the production of twenty-one nucleotide-sized small interfering RNAs, a signature of active replication in the host. Notably, AejapBV1 and AejapBV2 belong to different viral families; however, no RNA-dependent RNA polymerase sequence has been found for AejapBV2. Intriguingly, our small RNA-based approach identified an ∼1-kb long ambigrammatic RNA that is associated with AejapNV1 as a secondary segment but showed no similarity to any sequence in public databases. We confirmed the presence of AejapNV1 primary and secondary segments, AejapTV1, AejapAV1, and AejapBV1 by reverse transcriptase polymerase chain reaction (PCR) in wild-caught Ae. japonicus mosquitoes. AejapNV1 and AejapTV1 were found at high prevalence (87-100 per cent) in adult females, adult males, and larvae. Using a small RNA-based, sequence-independent metagenomic strategy, we uncovered a conserved and prevalent virome among Ae. japonicus mosquito populations. The high prevalence of AejapNV1 and AejapTV1 across all tested mosquito life stages suggests that these viruses are intimately associated with Ae. japonicus.}, } @article {pmid37636036, year = {2023}, author = {Liu, J and Wang, X and Sheng, F and Giri, BR and Li, S and Xia, T and Li, X and Cheng, G}, title = {Metagenomic sequencing for identifying pathogen-specific circulating DNAs and development of diagnostic methods for schistosomiasis.}, journal = {iScience}, volume = {26}, number = {9}, pages = {107495}, pmid = {37636036}, issn = {2589-0042}, abstract = {Timely diagnosis of Schistosoma infection, particularly in the early stage is crucial for identifying infected hosts and then taking effective control strategies. Here, metagenomic next-generation sequencing was used to identify pathogen-specific circulating DNAs (cDNAs) in the sera/plasma of New Zealand rabbits infected with S. japonicum, and the identified cDNAs were validated by PCR and qPCR. Loop-mediated isothermal amplification (LAMP)-based CRISPR-Cas12a and recombinase polymerase amplification-based lateral flow strip (RPA-LF) methods combined with the newly identified cDNA were developed to evaluate the potentials for diagnosing murine and human schistosomiasis. The results indicated that twenty-two cDNAs were identified. The developed LAMP-based CRISPR/Cas12a and RPA-LF methods showed a good potential for diagnosing murine or human schistosomiasis as early as 5 days of post-infection with 5 cercariae infection. In a word, S. japonicum specific cDNAs in circulation of infected hosts could be effective biomarkers for detecting Schistosoma infection particularly for early stages.}, } @article {pmid37635964, year = {2023}, author = {Cariati, F and Carotenuto, C and Bagnulo, F and Pacella, D and Marrone, V and Paolillo, R and Catania, MR and Di Girolamo, R and Conforti, A and Strina, I and Alviggi, C}, title = {Endometrial microbiota profile in in-vitro fertilization (IVF) patients by culturomics-based analysis.}, journal = {Frontiers in endocrinology}, volume = {14}, number = {}, pages = {1204729}, pmid = {37635964}, issn = {1664-2392}, mesh = {Pregnancy ; Humans ; Female ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; *Fertilization in Vitro ; *Embryo Transfer ; Fertilization ; }, abstract = {INTRODUCTION: It is well recognized that the human uterus and adjoining tissues of the female reproductive tract exist in a non-sterile state where dysbiosis can impact reproductive outcomes. The endometrial microbiota is a part of this greater milieu. To date, it has largely been studied using 16S rRNA or metagenomics-based methodologies. Despite the known advantages of sequencing analysis, several difficulties have been noted including sample contamination and standardization of DNA extraction or sequencing. The aim of this study was to use a culturomics-based method to analyze the endometrial microbiota and correlate the results with ongoing pregnancy rates.

METHODS: A prospective cohort study was performed at the University of Naples from June 2022 to December 2022. Ninety-three patients undergoing an IVF cycle with single embryo transfer (ET) (fresh or frozen) were enrolled in the study. Following ET, the catheter tip was inserted into brain heart infusion (BHI) medium under sterile conditions for culture. After 24h and 48h of incubation the microorganisms in the colonies were identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS).

RESULTS: Overall, 68 (73,92%) patients resulted positive for one or more microbes and 25 patients (26,08%) had no microbial growth. Across all participants, the four most important phyla were Firmicutes (87,76%), Proteobacteria (27,94%), Actinobacteria (10,29%) and Ascomycota (8,82%). Lactobacillus species, in particular, was significantly correlated with ongoing pregnancy rate (p=0,05). On the other hand, Staphylococcus subspecies (spp.) (p<0,05) and Enterobacteriaceae (p<0,001) were found to have a negative impact on the implantation rate.

DISCUSSION: Detection of bacteria by culturomics from catheter tips used for embryo transfer has been shown to be a reliable method to detect pathogen growth. Endometrial microbiota testing in clinical practice could certainly offer a means to further improve diagnosis and treatment strategies in IVF patients.}, } @article {pmid37635357, year = {2023}, author = {Gao, W and Gao, X and Zhu, L and Gao, S and Sun, R and Feng, Z and Wu, D and Liu, Z and Zhu, R and Jiao, N}, title = {Multimodal metagenomic analysis reveals microbial single nucleotide variants as superior biomarkers for early detection of colorectal cancer.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2245562}, pmid = {37635357}, issn = {1949-0984}, mesh = {*Colorectal Neoplasms/diagnosis/microbiology ; *Polymorphism, Single Nucleotide ; *Early Detection of Cancer/methods ; Metagenomics ; *Precancerous Conditions/diagnosis/microbiology ; *Adenoma/diagnosis/microbiology ; Metagenome ; *Gastrointestinal Microbiome/genetics ; Genetic Markers ; Feces/microbiology ; Humans ; Fungi/genetics/isolation & purification ; Bacteria/genetics/isolation & purification ; Archaea/genetics/isolation & purification ; Viruses/genetics/isolation & purification ; Cohort Studies ; }, abstract = {Microbial signatures show remarkable potentials in predicting colorectal cancer (CRC). This study aimed to evaluate the diagnostic powers of multimodal microbial signatures, multi-kingdom species, genes, and single-nucleotide variants (SNVs) for detecting precancerous adenomas. We performed cross-cohort analyses on whole metagenome sequencing data of 750 samples via xMarkerFinder to identify adenoma-associated microbial multimodal signatures. Our data revealed that fungal species outperformed species from other kingdoms with an area under the ROC curve (AUC) of 0.71 in distinguishing adenomas from controls. The microbial SNVs, including dark SNVs with synonymous mutations, displayed the strongest diagnostic capability with an AUC value of 0.89, sensitivity of 0.79, specificity of 0.85, and Matthews correlation coefficient (MCC) of 0.74. SNV biomarkers also exhibited outstanding performances in three independent validation cohorts (AUCs = 0.83, 0.82, 0.76; sensitivity = 1.0, 0.72, 0.93; specificity = 0.67, 0.81, 0.67, MCCs = 0.69, 0.83, 0.72) with high disease specificity for adenoma. In further support of the above results, functional analyses revealed more frequent inter-kingdom associations between bacteria and fungi, and abnormalities in quorum sensing, purine and butanoate metabolism in adenoma, which were validated in a newly recruited cohort via qRT-PCR. Therefore, these data extend our understanding of adenoma-associated multimodal alterations in the gut microbiome and provide a rationale of microbial SNVs for the early detection of CRC.}, } @article {pmid37635262, year = {2023}, author = {Zhai, X and Castro-Mejía, JL and Gobbi, A and Aslampaloglou, A and Kot, W and Nielsen, DS and Deng, L}, title = {The impact of storage buffer and storage conditions on fecal samples for bacteriophage infectivity and metavirome analyses.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {193}, pmid = {37635262}, issn = {2049-2618}, mesh = {Humans ; *Bacteriophages/genetics ; DNA, Bacterial ; Feces ; Metagenome ; RNA ; }, abstract = {BACKGROUND: There is an increasing interest in investigating the human gut virome for its influence on the gut bacterial community and its putative influence on the trajectory towards health or disease. Most gut virome studies are based on sequencing of stored fecal samples. However, relatively little is known about how conventional storage buffers and storage conditions affect the infectivity of bacteriophages and influence the downstream metavirome sequencing.

RESULTS: We demonstrate that the infectivity and genome recovery rate of different spiked bacteriophages (T4, c2 and Phi X174) are variable and highly dependent on storage buffers. Regardless of the storage temperature and timespan, all tested phages immediately lost 100% (DNA/RNA Shield) or more than 90% (StayRNA and RNAlater) of their infectivity. Generally, in SM buffer at 4 °C phage infectivity was preserved for up to 30 days and phage DNA integrity was maintained for up to 100 days. While in CANVAX, the most effective buffer, all spiked phage genomes were preserved for at least 100 days. Prolonged storage time (500 days) at - 80 °C impacted viral diversity differently in the different buffers. Samples stored in CANVAX or DNA/RNA Shield buffer had the least shifts in metavirome composition, after prolonged storage, but they yielded more contigs classified as "uncharacterised". Moreover, in contrast to the SM buffer, these storage buffers yielded a higher fraction of bacterial DNA in metavirome-sequencing libraries. We demonstrated that the latter was due to inactivation of the DNases employed to remove extra-cellular DNA during virome extraction. The latter could be partly avoided by employing additional washing steps prior to virome extraction.

CONCLUSION: Fecal sample storage buffers and storage conditions (time and temperature) strongly influence bacteriophage infectivity and viral composition as determined by plaque assay and metavirome sequencing. The choice of buffer had a larger effect than storage temperature and storage time on the quality of the viral sequences and analyses. Based on these results, we recommend storage of fecal virome samples at in SM buffer at 4 °C for the isolation of viruses and at - 80 °C for metagenomic applications if practically feasible (i.e., access to cold storage). For fecal samples stored in other buffers, samples should be cleared of these buffers before viral extraction and sequencing. Video Abstract.}, } @article {pmid37634713, year = {2023}, author = {Wang, C and Lu, B and Chen, H and Chen, H and Li, T and Lu, W and Chai, X}, title = {Strengthen high-loading operation of wastewater treatment plants by composite micron powder carrier: Microscale control of carbon, nitrogen, and sulfur metabolic pathways.}, journal = {The Science of the total environment}, volume = {904}, number = {}, pages = {166593}, doi = {10.1016/j.scitotenv.2023.166593}, pmid = {37634713}, issn = {1879-1026}, mesh = {*Sewage/microbiology ; Carbon ; Powders ; Nitrogen ; *Water Purification/methods ; Sulfur ; Metabolic Networks and Pathways ; Bioreactors ; Waste Disposal, Fluid/methods ; }, abstract = {The concentration of activated sludge is a crucial factor influencing the capacity and efficiency of sewage wastewater treatment plants (WWTPs). However, high sludge concentrations can lead to sludge loss in the secondary sedimentation tank, resulting in reduced processing capacity, particularly during low-temperature stages and sludge bulking. This study investigated the impact of adding composite micron powder carriers (CMPC) in high-concentration powder carrier biofluidized bed (HPB) technology to the biochemical units of WWTPs on sludge concentration and settling performance. For the traditional activated sludge method (ASM), its hydraulic retention time (HRT) was 8 h, with an average effluent total nitrogen (TN) of 15.14 mg/L. Sludge bulking was prone to occur in low-temperature environments, resulting in a high average sludge volume index (SVI) of 560 mL/g. Conversely, with a CMPC dosage of 4 g/L, the HRT of HPB technology was 4.8 h, and the average effluent TN was 11.40 mg/L, with a removal efficiency of 67.43 %. During operation of HPB technology under high sludge concentration conditions (8 g/L), the average SVI remained at 85 mL/g, indicating excellent settling characteristics. Moreover, in the sequencing batch reactor (SBR), the SVI value of bulking sludge decreased from the original 695 to 111 mL/g by the 9th day of operation with the CMPC dosage of 2 g/L. At the same time, the filamentous bacteria almost disappeared, suggesting that CMPC inhibit the growth of filamentous bacteria. Metagenomic analysis demonstrated that CPMC enhance the utilization of small molecular fatty acids in activated sludge and promote electron transfer between nitrate and nitrite, thereby improving wastewater treatment capacity. Additionally, CMPC enhanced the relative abundance of Saprospiraceae in sludge, which accelerate the degradation of polysaccharides in extracellular polymeric substances, weaken sludge's hydrophilic properties, and improve sludge's settling performance. Overall, these findings suggested that CMPC effectively strengthen the high-loading operation of WWTPs by improving sludge concentration and sedimentation performance.}, } @article {pmid37634690, year = {2023}, author = {Liu, L and Xin, Y and Guang, SB and Lin, GF and Liu, CX and Zeng, LQ and He, SQ and Zheng, YM and Chen, GY and Zhao, QB}, title = {Planktonic microbial community and biological metabolism in a subtropical drinking water river-reservoir system.}, journal = {Environmental research}, volume = {237}, number = {Pt 2}, pages = {116999}, doi = {10.1016/j.envres.2023.116999}, pmid = {37634690}, issn = {1096-0953}, abstract = {To understand the dynamics of planktonic microbial community and its metabolism processes in subtropical drinking water river-reservoir system with lower man-made pollution loading, this study selected Dongzhen river-reservoir system in Mulan Creek as object to investigate spatial-temporal characteristics of community profile and functional genes involved in biological metabolism, and to analyze the influence of environmental factors. The results indicated that Proteobacteria and Actinobacteria were the most diverse phyla with proportion ranges of 9%-80% in target system, and carbohydrate metabolism (5.76-7.12 × 10[-2]), amino acid metabolism (5.78-7.21 × 10[-2]) and energy metabolism (4.07-5.17 × 10[-2]) were found to be the dominant pathways of biological metabolism. Although there were variations in biological properties both spatially and temporally, seasonal variation had a greater influence on microbial community and biological metabolism, than locational differences. Regarding the role of environmental factors, this study revealed that microbial diversity could be affected by multiple abiotic factors, with total organic carbon, total phosphorus and temperature being more influential (absolute value of standardized regression weights >2.13). Stochastic processes dominated the microbial community assembly (R[2] of neutral community model = 0.645), while niche-based processes differences represented by nutrients, temperature and pH level played secondary roles (R > 0.388, P < 0.01). Notably, the synergistic influences among the environmental factors accounted for the higher percentages of community variation (maximum proportion up to 17.6%). Additionally, pH level, temperature, and concentrations of dissolved oxygen, carbon and nitrogen were found to be the significant factors affecting carbon metabolism pathways (P < 0.05), yet only total organic carbon significantly affected on nitrogen transformation (P < 0.05). In summary, the microbial profile in reservoir is not completely dominated by that in feeding river, and planktonic microbial community and its metabolism in subtropical drinking water river-reservoir system are shaped by multiple abiotic and biotic factors with underlying interactions.}, } @article {pmid37633998, year = {2023}, author = {Odom, AR and Faits, T and Castro-Nallar, E and Crandall, KA and Johnson, WE}, title = {Metagenomic profiling pipelines improve taxonomic classification for 16S amplicon sequencing data.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13957}, pmid = {37633998}, issn = {2045-2322}, support = {R01 GM127430/GM/NIGMS NIH HHS/United States ; R21 AI154387/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Metagenome ; *Microbiota ; Bone Plates ; *Cercozoa ; *Polyarteritis Nodosa ; }, abstract = {Most experiments studying bacterial microbiomes rely on the PCR amplification of all or part of the gene for the 16S rRNA subunit, which serves as a biomarker for identifying and quantifying the various taxa present in a microbiome sample. Several computational methods exist for analyzing 16S amplicon sequencing. However, the most-used bioinformatics tools cannot produce high quality genus-level or species-level taxonomic calls and may underestimate the potential accuracy of these calls. We used 16S sequencing data from mock bacterial communities to evaluate the sensitivity and specificity of several bioinformatics pipelines and genomic reference libraries used for microbiome analyses, concentrating on measuring the accuracy of species-level taxonomic assignments of 16S amplicon reads. We evaluated the tools DADA2, QIIME 2, Mothur, PathoScope 2, and Kraken 2 in conjunction with reference libraries from Greengenes, SILVA, Kraken 2, and RefSeq. Profiling tools were compared using publicly available mock community data from several sources, comprising 136 samples with varied species richness and evenness, several different amplified regions within the 16S rRNA gene, and both DNA spike-ins and cDNA from collections of plated cells. PathoScope 2 and Kraken 2, both tools designed for whole-genome metagenomics, outperformed DADA2, QIIME 2 using the DADA2 plugin, and Mothur, which are theoretically specialized for 16S analyses. Evaluations of reference libraries identified the SILVA and RefSeq/Kraken 2 Standard libraries as superior in accuracy compared to Greengenes. These findings support PathoScope and Kraken 2 as fully capable, competitive options for genus- and species-level 16S amplicon sequencing data analysis, whole genome sequencing, and metagenomics data tools.}, } @article {pmid37633814, year = {2023}, author = {Liu, X and Xu, J and Wang, Z and Xu, X and Wen, H and Su, H and Han, Y and Luo, Y and Zhang, Y and Li, W and Yao, X}, title = {Differential changes in the gut microbiota between extrinsic and intrinsic atopic dermatitis.}, journal = {Journal of autoimmunity}, volume = {141}, number = {}, pages = {103096}, doi = {10.1016/j.jaut.2023.103096}, pmid = {37633814}, issn = {1095-9157}, mesh = {Humans ; *Dermatitis, Atopic ; *Gastrointestinal Microbiome ; Histidine ; Metagenome ; Immunoglobulin E ; }, abstract = {Elevated serum level of total and (or) allergen-specific IgE is one of the key features of atopic dermatitis (AD). Previous studies have shown that the gut microbiome mediates interactions between external exposures and the immune system in AD; however, the relationship between the gut microbiota and IgE remains unclear. In the present study, analyses of environmental exposures for 250 AD patients and 138 healthy volunteers revealed an association between hygiene levels in the residential environment and the occurrence of AD and the IgE level. Metagenomic sequencing of the gut microbiota from 68 AD patients and 77 healthy controls showed that AD patients had a distinct gut microbiota composition; moreover, while L-histidine degradation was enriched in healthy controls, L-histidine biosynthesis was enriched in AD patients. Extrinsic and intrinsic AD showed different enrichment patterns of specific microbes and differential associations of functional pathways. Our study indicated that elevated levels of IgE in AD were related to specific microbes in the gut microbiota, which showed extensive interactions with environmental factors.}, } @article {pmid37633610, year = {2023}, author = {Zhu, Y and An, M and Mamut, R and Wang, H}, title = {Comparative analysis of metabolic mechanisms in the remediation of Cd-polluted alkaline soil in cotton field by biochar and biofertilizer.}, journal = {Chemosphere}, volume = {340}, number = {}, pages = {139961}, doi = {10.1016/j.chemosphere.2023.139961}, pmid = {37633610}, issn = {1879-1298}, mesh = {*Cadmium ; *Gossypium ; Environmental Pollution ; Soil ; }, abstract = {To screen environmentally friendly and efficient Cd pollution remediation material, the effects of BC and BF on soil Cd bio-availability and cotton Cd absorption were analyzed under Cd exposure. Besides, the differences in metabolic mechanisms by which biochar (BC) and biofertilizer (BF) affect Cd-contaminated soil and cotton were also analyzed. The results showed that the application of BC and BF increased cotton dry matter accumulation, boll number, and single boll weight, and reduced the Cd content in cotton roots, stems, leaves, and bolls. At harvest, the Cd content in cotton roots in the BC and BF groups reduced by 15.23% and 16.33%, respectively, compared with that in the control. This was attributed to the conversion of carbonate-bound Cd (carbon-Cd) and exchangeable Cd (EX-Cd) by BC and BF into residual Cd (Res-Cd). It should be noted that the soil available Cd (Ava-Cd) content in the BF group was lower than that in the BC group. The metabolomic analysis results showed that for BC vs BF, the relative abundance of differential metabolites Caffeic acid, Xanthurenic acid, and Shikimic acid in soil and cotton roots were up-regulated. Mantel test found that cotton root exudate l-Histinine was correlated with the enrichment of Cd in various organs of cotton. Therefore, the application of BC and BF can alleviate Cd stress by reducing soil Ava-Cd content and cotton's Cd uptake, and BF is superior to BC in reducing Cd content in soil and cotton organs. This study will provide a reference for the development of efficient techniques for the remediation of Cd-polluted alkaline soil, and provide a basis for subsequent metagenomics analysis.}, } @article {pmid37633303, year = {2023}, author = {Sinha, P and Kerchberger, VE and Willmore, A and Chambers, J and Zhuo, H and Abbott, J and Jones, C and Wickersham, N and Wu, N and Neyton, L and Langelier, CR and Mick, E and He, J and Jauregui, A and Churpek, MM and Gomez, AD and Hendrickson, CM and Kangelaris, KN and Sarma, A and Leligdowicz, A and Delucchi, KL and Liu, KD and Russell, JA and Matthay, MA and Walley, KR and Ware, LB and Calfee, CS}, title = {Identifying molecular phenotypes in sepsis: an analysis of two prospective observational cohorts and secondary analysis of two randomised controlled trials.}, journal = {The Lancet. Respiratory medicine}, volume = {11}, number = {11}, pages = {965-974}, doi = {10.1016/S2213-2600(23)00237-0}, pmid = {37633303}, issn = {2213-2619}, support = {R35 GM142992/GM/NIGMS NIH HHS/United States ; R35 GM145330/GM/NIGMS NIH HHS/United States ; R35 HL140026/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Humans ; *Shock, Septic/diagnosis/drug therapy ; Protein C/therapeutic use ; Retrospective Studies ; Prospective Studies ; *Sepsis/diagnosis/drug therapy/complications ; Phenotype ; Biomarkers ; Vasoconstrictor Agents/therapeutic use ; *Respiratory Distress Syndrome ; Randomized Controlled Trials as Topic ; }, abstract = {BACKGROUND: In sepsis and acute respiratory distress syndrome (ARDS), heterogeneity has contributed to difficulty identifying effective pharmacotherapies. In ARDS, two molecular phenotypes (hypoinflammatory and hyperinflammatory) have consistently been identified, with divergent outcomes and treatment responses. In this study, we sought to derive molecular phenotypes in critically ill adults with sepsis, determine their overlap with previous ARDS phenotypes, and evaluate whether they respond differently to treatment in completed sepsis trials.

METHODS: We used clinical data and plasma biomarkers from two prospective sepsis cohorts, the Validating Acute Lung Injury biomarkers for Diagnosis (VALID) study (N=1140) and the Early Assessment of Renal and Lung Injury (EARLI) study (N=818), in latent class analysis (LCA) to identify the optimal number of classes in each cohort independently. We used validated models trained to classify ARDS phenotypes to evaluate concordance of sepsis and ARDS phenotypes. We applied these models retrospectively to the previously published Prospective Recombinant Human Activated Protein C Worldwide Evaluation in Severe Sepsis and Septic Shock (PROWESS-SHOCK) trial and Vasopressin and Septic Shock Trial (VASST) to assign phenotypes and evaluate heterogeneity of treatment effect.

FINDINGS: A two-class model best fit both VALID and EARLI (p<0·0001). In VALID, 804 (70·5%) of the 1140 patients were classified as hypoinflammatory and 336 (29·5%) as hyperinflammatory; in EARLI, 530 (64·8%) of 818 were hypoinflammatory and 288 (35·2%) hyperinflammatory. We observed higher plasma pro-inflammatory cytokines, more vasopressor use, more bacteraemia, lower protein C, and higher mortality in the hyperinflammatory than in the hypoinflammatory phenotype (p<0·0001 for all). Classifier models indicated strong concordance between sepsis phenotypes and previously identified ARDS phenotypes (area under the curve 0·87-0·96, depending on the model). Findings were similar excluding participants with both sepsis and ARDS. In PROWESS-SHOCK, 1142 (68·0%) of 1680 patients had the hypoinflammatory phenotype and 538 (32·0%) had the hyperinflammatory phenotype, and response to activated protein C differed by phenotype (p=0·0043). In VASST, phenotype proportions were similar to other cohorts; however, no treatment interaction with the type of vasopressor was observed (p=0·72).

INTERPRETATION: Molecular phenotypes previously identified in ARDS are also identifiable in multiple sepsis cohorts and respond differently to activated protein C. Molecular phenotypes could represent a treatable trait in critical illness beyond the patient's syndromic diagnosis.

FUNDING: US National Institutes of Health.}, } @article {pmid37633209, year = {2023}, author = {Li, RH and Huang, J and Liu, CX and Yu, K and Guo, F and Li, Y and Chen, ZH and Wang, X and Zhao, RX and Zhang, JY and Liang, JJ and Li, Y and Lin, L and Sun, L and Li, XY and Li, B}, title = {Genome-centric metagenomics provides new insights into metabolic pathways of polyhydroxyalkanoates biosynthesis and functional microorganisms subsisting on municipal organic wastes.}, journal = {Water research}, volume = {244}, number = {}, pages = {120512}, doi = {10.1016/j.watres.2023.120512}, pmid = {37633209}, issn = {1879-2448}, mesh = {Sewage ; Food ; *Polyhydroxyalkanoates ; Metagenomics ; *Refuse Disposal ; Bioreactors ; Metabolic Networks and Pathways ; }, abstract = {The microbial community of a sequencing batch reactor operated under feast and famine conditions for production of polyhydroxyalkanoates (PHAs) was characterized through high-throughput sequencing and metagenomic analysis. The fermented food waste and chemically-enhanced primary sludge was fed in this bioreactor. After acclimation, the PHA yield achieved as high as 0.60-0.69 g CODPHA/g CODS. The complete changes of microbial community structure were found during shifts of feedstock. A synthesis of SCL/MCL-PHAs pathway was established for PHA-producing bioreactor in this mixed-culture system. The structure-performance relationship of PHA-producing microbial community and feedstock composition was investigated. The results showed that microbial community tends to be decentralized and prefer team work for PHA synthesis to consume the multiple substrates and digest inevitable non-VFA contents in fermented liquor. This study also discovered unreported potential PHA producers (e.g., genera Tabrizicola, Nannocystis, Ga0077539, Ga0077559, JOSHI-001, SNC69-320 and UBA2334) subsisting on municipal organic wastes and expands the current knowledge about mixed-culture system that the PHA synthesis pathway is widely existed in activated sludge.}, } @article {pmid37632121, year = {2023}, author = {Babalola, B and Fraile, A and García-Arenal, F and McLeish, M}, title = {Ecological Strategies for Resource Use by Three Bromoviruses in Anthropic and Wild Plant Communities.}, journal = {Viruses}, volume = {15}, number = {8}, pages = {}, pmid = {37632121}, issn = {1999-4915}, mesh = {*Ecosystem ; *Bromovirus ; Genetic Drift ; High-Throughput Nucleotide Sequencing ; Host Specificity ; }, abstract = {Ecological strategies for resource utilisation are important features of pathogens, yet have been overshadowed by stronger interest in genetic mechanisms underlying disease emergence. The purpose of this study is to ask whether host range and transmission traits translate into ecological strategies for host-species utilisation in a heterogeneous ecosystem, and whether host utilisation corresponds to genetic differentiation among three bromoviruses. We combine high-throughput sequencing and population genomics with analyses of species co-occurrence to unravel the ecological strategies of the viruses across four habitat types. The results show that the bromoviruses that were more closely related genetically did not share similar ecological strategies, but that the more distantly related pair did. Shared strategies included a broad host range and more frequent co-occurrences, which both were habitat-dependent. Each habitat thus presents as a barrier to gene flow, and each virus has an ecological strategy to navigate limitations to colonising non-natal habitats. Variation in ecological strategies could therefore hold the key to unlocking events that lead to emergence.}, } @article {pmid37632061, year = {2023}, author = {Richard, JC and Blevins, E and Dunn, CD and Leis, EM and Goldberg, TL}, title = {Viruses of Freshwater Mussels during Mass Mortality Events in Oregon and Washington, USA.}, journal = {Viruses}, volume = {15}, number = {8}, pages = {}, pmid = {37632061}, issn = {1999-4915}, mesh = {Animals ; Oregon ; Washington/epidemiology ; *Fresh Water ; *Bivalvia ; Rivers ; }, abstract = {Freshwater mussels (Unionida) are globally imperiled, in part due to largely unexplained mass mortality events (MMEs). While recent studies have begun to investigate the possibility that mussel MMEs in the Eastern USA may be caused by infectious diseases, mussels in the Western USA have received relatively little attention in this regard. We conducted a two-year epidemiologic investigation of the role of viruses in ongoing MMEs of the Western pearlshell (Margaritifera falcata) and the Western ridged mussel (Gonidea angulata) in the Chehalis River and Columbia River watersheds in the Western USA. We characterized viromes of mussel hemolymph from 5 locations in 2018 and 2020 using metagenomic methods and identified 557 viruses based on assembled contiguous sequences, most of which are novel. We also characterized the distribution and diversity of a previously identified mussel Gammarhabdovirus related to pathogenic finfish viruses. Overall, we found few consistent associations between viruses and mussel health status. Variation in mussel viromes was most strongly driven by location, with little influence from date, species, or health status, though these variables together only explained ~1/3 of variation in virome composition. Our results demonstrate that Western freshwater mussels host remarkably diverse viromes, but no single virus or combination of viruses appears to be associated with morbidity or mortality during MMEs. Our findings have implications for the conservation of imperiled freshwater mussels, including efforts to enhance natural populations through captive propagation.}, } @article {pmid37631297, year = {2023}, author = {Leignadier, J and Drago, M and Lesouhaitier, O and Barreau, M and Dashi, A and Worsley, O and Attia-Vigneau, J}, title = {Lysine-Dendrimer, a New Non-Aggressive Solution to Rebalance the Microbiota of Acne-Prone Skin.}, journal = {Pharmaceutics}, volume = {15}, number = {8}, pages = {}, pmid = {37631297}, issn = {1999-4923}, abstract = {Acne is a chronic inflammatory skin disease that affects the quality of life of patients. Several treatments exist for acne, but their effectiveness tends to decrease over time due to increasing resistance to treatment and associated side effects. To circumvent these issues, a new approach has emerged that involves combating the pathogen Cutibacterium acnes while maintaining the homeostasis of the skin microbiome. Recently, it was shown that the use of a G2 lysine dendrigraft (G2 dendrimer) could specifically decrease the C. acnes phylotype (IAI) involved in acne, compared to non-acne-causing C. acnes (phylotype II) bacteria. In the present study, we demonstrate that the efficacy of this technology is related to its 3D structure, which, in contrast to the linear form, significantly decreases the inflammation factor (IL-8) linked to acne. In addition, our in-vitro data confirm the specific activity of the G2 dendrimer: after treatment of bacterial cultures and biofilms, the G2 dendrimer affected neither non-acneic C. acnes nor commensal bacteria of the skin (Staphylococcus epidermidis, S. hominis, and Corynebacterium minutissimum). In parallel, comparative in-vitro and in-vivo studies with traditional over-the-counter molecules showed G2's effects on the survival of commensal bacteria and the reduction of acne outbreaks. Finally, metagenomic analysis of the cutaneous microbiota of volunteers who applied a finished cosmetic product containing the G2 dendrimer confirmed the ability of G2 to rebalance cutaneous acne microbiota dysbiosis while maintaining commensal bacteria. These results confirm the value of using this G2 dendrimer to gently prevent the appearance of acne vulgaris while respecting the cutaneous microbiota.}, } @article {pmid37631163, year = {2023}, author = {Aleynova, OA and Nityagovsky, NN and Ananev, AA and Suprun, AR and Ogneva, ZV and Dneprovskaya, AA and Beresh, AA and Tyunin, AP and Dubrovina, AS and Kiselev, KV}, title = {The Endophytic Microbiome of Wild Grapevines Vitis amurensis Rupr. and Vitis coignetiae Pulliat Growing in the Russian Far East.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {16}, pages = {}, pmid = {37631163}, issn = {2223-7747}, support = {22-74-10001//Russian Science Foundation/ ; 121031000144-5//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Many grape endophytic microorganisms exhibit high potential for suppressing the development of grape diseases and stimulating grapevine growth and fitness, as well as beneficial properties of the crop. The microbiome of wild grapevines is a promising source of biocontrol agents, which can be beneficial for domesticated grapevines. Using next-generation sequencing (NGS) and classical microbiology techniques, we performed an analysis of bacterial and fungal endophytic communities of wild grapevines Vitis amurensis Rupr. and Vitis coignetiae Pulliat growing in the Russian Far East. According to the NGS analysis, 24 and 18 bacterial taxa from the class level were present in V. amurensis and V. coignetiae grapevines, respectively. Gammaproteobacteria (35%) was the predominant class of endophytic bacteria in V. amurensis and Alphaproteobacteria (46%) in V. coignetiae. Three taxa, namely Sphingomonas, Methylobacterium, and Hymenobacter, were the most common bacterial genera for V. amurensis and V. coignetiae. Metagenomic analysis showed the presence of 23 and 22 fungi and fungus-like taxa of class level in V. amurensis and V. coignetiae, respectively. The predominant fungal classes were Dothideomycetes (61-65%) and Tremellomycetes (10-11%), while Cladosporium and Aureobasidium were the most common fungal genera in V. amurensis and V. coignetiae, respectively. A comparative analysis of the endophytic communities of V. amurensis and V. coignetiae with the previously reported endophytic communities of V. vinifera revealed that the bacterial biodiversity of V. amurensis and V. coignetiae was similar in alpha diversity to V. vinifera's bacterial biodiversity. The fungal alpha diversity of V. amurensis and V. coignetiae was statistically different from that of V. vinifera. The beta diversity analysis of bacterial and fungal endophytes showed that samples of V. vinifera formed separate clusters, while V. amurensis samples formed a separate cluster including V. coignetiae samples. The data revealed that the endophytic community of bacteria and fungi from wild V. amurensis was richer than that from V. coignetiae grapes and cultivated V. vinifera grapes. Therefore, the data obtained in this work could be of high value in the search for potentially useful microorganisms for viticulture.}, } @article {pmid37630666, year = {2023}, author = {Jo, Y and Lee, G and Ahmad, S and Son, H and Kim, MJ and Sliti, A and Lee, S and Kim, K and Lee, SE and Shin, JH}, title = {The Alteration of the Gut Microbiome during Ramadan Offers a Novel Perspective on Ramadan Fasting: A Pilot Study.}, journal = {Microorganisms}, volume = {11}, number = {8}, pages = {}, pmid = {37630666}, issn = {2076-2607}, abstract = {An intermittent fasting regimen is widely perceived to lead to various beneficial health effects, including weight loss, the alleviation of insulin resistance, and the restructuring of a healthy gut microbiome. Because it shares certain commonalities with this dietary intervention, Ramadan fasting is sometimes misinterpreted as intermittent fasting, even though there are clear distinctions between these two regimens. The main purpose of this study is to verify whether Ramadan fasting drives the same beneficial effects as intermittent fasting by monitoring alterations in the gut microbiota. We conducted a study involving 20 Muslim individuals who were practicing Ramadan rituals and assessed the composition of their gut microbiomes during the 4-week period of Ramadan and the subsequent 8-week period post-Ramadan. Fecal microbiome analysis was conducted, and short-chain fatty acids (SCFAs) were assessed using liquid-chromatography-mass spectrometry. The observed decrease in the levels of SCFAs and beneficial bacteria during Ramadan, along with the increased microbial diversity post-Ramadan, suggests that the daily diet during Ramadan may not provide adequate nutrients to maintain robust gut microbiota. Additionally, the notable disparities in the functional genes detected through the metagenomic analysis and the strong correlation between Lactobacillus and SCFAs provide further support for our hypothesis.}, } @article {pmid37630612, year = {2023}, author = {Mohamed, HM and Barzideh, Z and Siddiqi, M and LaPointe, G}, title = {Taxonomy, Sequence Variance and Functional Profiling of the Microbial Community of Long-Ripened Cheddar Cheese Using Shotgun Metagenomics.}, journal = {Microorganisms}, volume = {11}, number = {8}, pages = {}, pmid = {37630612}, issn = {2076-2607}, support = {490979-15//Natural Sciences and Engineering Research Council/ ; OGI-134//Genome Canada/ ; }, abstract = {Shotgun metagenomic sequencing was used to investigate the diversity of the microbial community of Cheddar cheese ripened over 32 months. The changes in taxa abundance were compared from assembly-based, non-assembly-based, and mOTUs2 sequencing pipelines to delineate the community profile for each age group. Metagenomic assembled genomes (MAGs) passing the quality threshold were obtained for 11 species from 58 samples. Although Lactococcus cremoris and Lacticaseibacillus paracasei were dominant across the shotgun samples, other species were identified using MG-RAST. NMDS analysis of the beta diversity of the microbial community revealed the similarity of the cheeses in older age groups (7 months to 32 months). As expected, the abundance of Lactococcus cremoris consistently decreased over ripening, while the proportion of permeable cells increased. Over the ripening period, the relative abundance of viable Lacticaseibacillus paracasei progressively increased, but at a variable rate among trials. Reads attributed to Siphoviridae and Ascomycota remained below 1% relative abundance. The functional profiles of PMA-treated cheeses differed from those of non-PMA-treated cheeses. Starter rotation was reflected in the single nucleotide variant profiles of Lactococcus cremoris (SNVs of this species using mOTUs2), while the incoming milk was the leading factor in discriminating Lacticaseibacillus paracasei/casei SNV profiles. The relative abundance estimates from Kraken2, non-assembly-based (MG-RAST) and marker gene clusters (mOTUs2) were consistent across age groups for the two dominant taxa. Metagenomics enabled sequence variant analysis below the bacterial species level and functional profiling that may affect the metabolic interactions between subpopulations in cheese during ripening, which could help explain the overall flavour development of cheese. Future work will integrate microbial variants with volatile profiles to associate the development of compounds related to cheese flavour at each ripening stage.}, } @article {pmid37630603, year = {2023}, author = {Jaudou, S and Deneke, C and Tran, ML and Salzinger, C and Vorimore, F and Goehler, A and Schuh, E and Malorny, B and Fach, P and Grützke, J and Delannoy, S}, title = {Exploring Long-Read Metagenomics for Full Characterization of Shiga Toxin-Producing Escherichia coli in Presence of Commensal E. coli.}, journal = {Microorganisms}, volume = {11}, number = {8}, pages = {}, pmid = {37630603}, issn = {2076-2607}, abstract = {The characterization of Shiga toxin-producing Escherichia coli (STEC) is necessary to assess their pathogenic potential, but isolation of the strain from complex matrices such as milk remains challenging. In previous work, we have shown the potential of long-read metagenomics to characterize eae-positive STEC from artificially contaminated raw milk without isolating the strain. The presence of multiple E. coli strains in the sample was shown to potentially hinder the correct characterization of the STEC strain. Here, we aimed at determining the STEC:commensal ratio that would prevent the characterization of the STEC. We artificially contaminated pasteurized milk with different ratios of an eae-positive STEC and a commensal E. coli and applied the method previously developed. Results showed that the STEC strain growth was better than the commensal E. coli after enrichment in acriflavine-supplemented BPW. The STEC was successfully characterized in all samples with at least 10 times more STEC post-enrichment compared to the commensal E. coli. However, the presence of equivalent proportions of STEC and commensal E. coli prevented the full characterization of the STEC strain. This study confirms the potential of long-read metagenomics for STEC characterization in an isolation-free manner while refining its limit regarding the presence of background E. coli strains.}, } @article {pmid37630578, year = {2023}, author = {Gao, H and He, C and Xin, S and Hua, R and Du, Y and Wang, B and Gong, F and Yu, X and Pan, L and Gao, L and Xu, J}, title = {Current Insights into the Use of Probiotics and Fatty Acids in Alleviating Depression.}, journal = {Microorganisms}, volume = {11}, number = {8}, pages = {}, pmid = {37630578}, issn = {2076-2607}, support = {82174056//National Natural Science Foundation of China/ ; }, abstract = {(1) Background: Depression is the most prevalent psychiatric symptom present among individuals of all ages and backgrounds, impacting an estimated 300 million people globally. Therefore, it demands a significant amount of attention when it comes to managing depression. A growing amount of data reveal that probiotics and fatty acids could be beneficial to depression. However, the opposing position maintains that they have no influence on depression. A network meta-analyses of existing datasets aid in the estimation of comparative efficacy as well as in achieving an understanding of the relative merits of different therapies. The purpose of this study was to investigate the current evidence for probiotic or fatty acid depression therapy and to establish a practical alternative for depression patients using a meta-analysis and metagenomic data from a Wistar-Kyoto (WKY) depressed rat model. (2) Methods: Probiotic data were obtained from seven randomized controlled trial studies (n = 394), and fatty acid data were obtained from 24 randomized controlled trial studies (n = 1876). Meanwhile, a metagenomics analysis of data on animal gut flora was also applied to validate the preceding evidence. (3) Results: The fatty acid studies were separated into three sections based on the duration of probiotic delivery: ≤8 weeks, 9-12 weeks, and >12 weeks. The results were as follows: for ≤8 weeks, MD = -1.65 (95% CI: -2.96--0.15), p = 0.01; for 9-12 weeks, MD = -2.22 (95% CI: -3.03--1.22), p < 0.001; for >12 weeks, MD = -1.23 (95% CI: -2.85-0.39), p = 0.14. Regarding the probiotics, the meta-analysis revealed MD = -2.19 (95% CI: -3.38--2.43), p < 0.001. The research presented herein illustrates that probiotics and fatty acids may successfully lower depression scores. Additionally, the probiotics were drastically reduced in the WKY rats. (4) Conclusions: According to the data, a depression intervention utilizing probiotics outperformed the control, implying that the use of probiotics and fatty acids may be a successful strategy for depression treatment.}, } @article {pmid37630539, year = {2023}, author = {Peterson, CT and Iablokov, SN and Rodionov, DA and Peterson, SN}, title = {Personalized Response of Parkinson's Disease Gut Microbiota to Nootropic Medicinal Herbs In Vitro: A Proof of Concept.}, journal = {Microorganisms}, volume = {11}, number = {8}, pages = {}, pmid = {37630539}, issn = {2076-2607}, support = {Triph-2017//Samuel Lawrence Foundation/ ; 19-14-00305//Russian Science Foundation/ ; }, abstract = {Parkinson's disease (PD) is a neurodegenerative disease characterized by the loss of dopaminergic neurons. Although the etiology of PD remains elusive, it has been hypothesized that initial dysregulation may occur in the gastrointestinal tract and may be accompanied by gut barrier defects. A strong clinical interest in developing therapeutics exists, including for the treatment of gut microbiota and physiology. We previously reported the impact of healthy fecal microbiota anaerobic cultures supplemented with nootropic herbs. Here, we evaluated the effect of nootropic Ayurvedic herbs on fecal microbiota derived from subjects with PD in vitro using 16S rRNA sequencing. The microbiota underwent substantial change in response to each treatment, comparable in magnitude to that observed from healthy subjects. However, the fecal samples derived from each participant displayed unique changes, consistent with a personalized response. We used genome-wide metabolic reconstruction to predict the community's metabolic potential to produce products relevant to PD pathology, including SCFAs, vitamins and amino acid degradation products. These results suggest the potential value of conducting in vitro cultivation and analyses of PD stool samples as a means of prescreening patients to select the medicinal herbs for which that individual is most likely to respond and derive benefit.}, } @article {pmid37630519, year = {2023}, author = {Paul, SS and Rama Rao, SV and Chatterjee, RN and Raju, MVLN and Mahato, AK and Prakash, B and Yadav, SP and Kannan, A and Reddy, GN and Kumar, V and Kumar, PSP}, title = {An Immobilized Form of a Blend of Essential Oils Improves the Density of Beneficial Bacteria, in Addition to Suppressing Pathogens in the Gut and Also Improves the Performance of Chicken Breeding.}, journal = {Microorganisms}, volume = {11}, number = {8}, pages = {}, pmid = {37630519}, issn = {2076-2607}, support = {BT/IN/Indo-UK/AMR/05/NH/2018-19//Department of Biotechnology/ ; }, abstract = {Antimicrobial growth promoters (AGP) are used in chicken production to suppress pathogens in the gut and improve performance, but such products tend to suppress beneficial bacteria while favoring the development and spread of antimicrobial resistance. A green alternative to AGP with the ability to suppress pathogens, but with an additional ability to spare beneficial gut bacteria and improve breeding performance is urgently required. We investigated the effect of supplementation of a blend of select essential oils (cinnamon oil, carvacrol, and thyme oil, henceforth referred to as EO; at two doses: 200 g/t and 400 g/t feed) exhibiting an ability to spare Lactobacillus while exhibiting strong E. coli inhibition ability under in vitro tests and immobilized in a sunflower oil and calcium alginate matrix, to broiler chickens and compared the effects with those of a probiotic yeast (Y), an AGP virginiamycin (V), and a negative control (C). qPCR analysis of metagenomic DNA from the gut content of experimental chickens indicated a significantly (p < 0.05) lower density of E. coli in the EO groups as compared to other groups. Amplicon sequence data of the gut microbiome indicated that all the additives had specific significant effects (DESeq2) on the gut microbiome, such as enrichment of uncultured Clostridia in the V and Y groups and uncultured Ruminococcaceae in the EO groups, as compared to the control. LEfSe analysis of the sequence data indicated a high abundance of beneficial bacteria Ruminococcaceae in the EO groups, Faecalibacterium in the Y group, and Blautia in the V group. Supplementation of the immobilized EO at the dose rate of 400 g/ton feed improved body weight gain (by 64 g/bird), feed efficiency (by 5 points), and cellular immunity (skin thickness response to phytoheamagglutinin lectin from Phaseolus vulgaris by 58%) significantly (p < 0.05), whereas neither yeast nor virginiamycin showed a significant effect on performance parameters. Expression of genes associated with gut barrier and immunity function such as CLAUDIN1, IL6, IFNG, TLR2A, and NOD1 were significantly higher in the EO groups. This study showed that the encapsulated EO mixture can improve the density of beneficial microbes in the gut significantly, with concomitant suppression of potential pathogens such as E.coli and improved performance and immunity, and hence, has a high potential to be used as an effective alternative to AGP in poultry.}, } @article {pmid37630492, year = {2023}, author = {Pushkareva, E and Elster, J and Becker, B}, title = {Metagenomic Analysis of Antarctic Biocrusts Unveils a Rich Range of Cold-Shock Proteins.}, journal = {Microorganisms}, volume = {11}, number = {8}, pages = {}, pmid = {37630492}, issn = {2076-2607}, support = {BE1779/23-1//Deutsche Forschungsgemeinschaft/ ; 67985939//Czech Academy of Sciences/ ; }, abstract = {Microorganisms inhabiting Antarctic biocrusts develop several strategies to survive extreme environmental conditions such as severe cold and drought. However, the knowledge about adaptations of biocrusts microorganisms are limited. Here, we applied metagenomic sequencing to study biocrusts from east Antarctica. Biocrusts were dominated by cyanobacteria, actinobacteria and proteobacteria. Furthermore, the results provided insights into the presence and abundance of cold shock proteins (Csp), cold shock domain A proteins (CsdA), and antifreeze proteins (AFP) in these extreme environments. The metagenomic analysis revealed a high number of CsdA across the samples. The majority of the Csp recorded in the studied biocrusts were Csp A, C, and E. In addition, CsdA, Csp, and AFP primarily originated from proteobacteria and actinobacteria.}, } @article {pmid37630429, year = {2023}, author = {Lan, J and Ji, S and Yang, C and Cai, G and Lu, J and Li, X}, title = {Extracellular Expression of Feruloyl Esterase and Xylanase in Escherichia coli for Ferulic Acid Production from Agricultural Residues.}, journal = {Microorganisms}, volume = {11}, number = {8}, pages = {}, pmid = {37630429}, issn = {2076-2607}, support = {31701730//National Natural Science Foundation of China/ ; }, abstract = {There is still a large amount of ferulic acid (FA), an outstanding antioxidant, present in agricultural residues. Enzymatic hydrolysis has been regarded as the most effective way to release FA. This present study therefore selected feruloyl esterase (FAE) and xylanase (XYN) from the metagenomes of a cow rumen and a camel rumen, respectively, for their recombinant expression in Escherichia coli BL21 and further application in releasing FA. After screening the candidate signal peptides, the optimal one for each enzyme, which were selected as SP1 and SP4, respectively, was integrated into the vectors pET22b(+) and pETDuet-1. Among the generated E. coli strains SP1-F, SP4-X, and SP1-F-SP4-X that could express extracellular enzymes either separately or simultaneously, the latter one performed the best in relation to degrading the biomass and releasing FA. Under the optimized culture and induction conditions, the strain SP1-F-SP4-X released 90% of FA from 10% of de-starched wheat bran and produced 314.1 mg/L FA, which was deemed to be the highest obtained value to the best of our knowledge. This result could pave a way for the re-utilization of agricultural residues and enhancing their add-value.}, } @article {pmid37628701, year = {2023}, author = {Soriano, B and Hafez, AI and Naya-Català, F and Moroni, F and Moldovan, RA and Toxqui-Rodríguez, S and Piazzon, MC and Arnau, V and Llorens, C and Pérez-Sánchez, J}, title = {SAMBA: Structure-Learning of Aquaculture Microbiomes Using a Bayesian Approach.}, journal = {Genes}, volume = {14}, number = {8}, pages = {}, pmid = {37628701}, issn = {2073-4425}, mesh = {Animals ; Humans ; Bayes Theorem ; RNA, Ribosomal, 16S/genetics ; Learning ; *Microbiota/genetics ; Aquaculture ; *Sea Bream ; }, abstract = {Gut microbiomes of fish species consist of thousands of bacterial taxa that interact among each other, their environment, and the host. These complex networks of interactions are regulated by a diverse range of factors, yet little is known about the hierarchy of these interactions. Here, we introduce SAMBA (Structure-Learning of Aquaculture Microbiomes using a Bayesian Approach), a computational tool that uses a unified Bayesian network approach to model the network structure of fish gut microbiomes and their interactions with biotic and abiotic variables associated with typical aquaculture systems. SAMBA accepts input data on microbial abundance from 16S rRNA amplicons as well as continuous and categorical information from distinct farming conditions. From this, SAMBA can create and train a network model scenario that can be used to (i) infer information of how specific farming conditions influence the diversity of the gut microbiome or pan-microbiome, and (ii) predict how the diversity and functional profile of that microbiome would change under other variable conditions. SAMBA also allows the user to visualize, manage, edit, and export the acyclic graph of the modelled network. Our study presents examples and test results of Bayesian network scenarios created by SAMBA using data from a microbial synthetic community, and the pan-microbiome of gilthead sea bream (Sparus aurata) in different feeding trials. It is worth noting that the usage of SAMBA is not limited to aquaculture systems as it can be used for modelling microbiome-host network relationships of any vertebrate organism, including humans, in any system and/or ecosystem.}, } @article {pmid37628698, year = {2023}, author = {Pandey, S and Avuthu, N and Guda, C}, title = {StrainIQ: A Novel n-Gram-Based Method for Taxonomic Profiling of Human Microbiota at the Strain Level.}, journal = {Genes}, volume = {14}, number = {8}, pages = {}, pmid = {37628698}, issn = {2073-4425}, support = {P20 GM103427/GM/NIGMS NIH HHS/United States ; P30 CA036727/CA/NCI NIH HHS/United States ; U54 GM115458/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; Metagenome/genetics ; Algorithms ; Computational Biology ; High-Throughput Nucleotide Sequencing ; }, abstract = {The emergence of next-generation sequencing (NGS) technology has greatly influenced microbiome research and led to the development of novel bioinformatics tools to deeply analyze metagenomics datasets. Identifying strain-level variations in microbial communities is important to understanding the onset and progression of diseases, host-pathogen interrelationships, and drug resistance, in addition to designing new therapeutic regimens. In this study, we developed a novel tool called StrainIQ (strain identification and quantification) based on a new n-gram-based (series of n number of adjacent nucleotides in the DNA sequence) algorithm for predicting and quantifying strain-level taxa from whole-genome metagenomic sequencing data. We thoroughly evaluated our method using simulated and mock metagenomic datasets and compared its performance with existing methods. On average, it showed 85.8% sensitivity and 78.2% specificity on simulated datasets. It also showed higher specificity and sensitivity using n-gram models built from reduced reference genomes and on models with lower coverage sequencing data. It outperforms alternative approaches in genus- and strain-level prediction and strain abundance estimation. Overall, the results show that StrainIQ achieves high accuracy by implementing customized model-building and is an efficient tool for site-specific microbial community profiling.}, } @article {pmid37628619, year = {2023}, author = {Notario, E and Visci, G and Fosso, B and Gissi, C and Tanaskovic, N and Rescigno, M and Marzano, M and Pesole, G}, title = {Amplicon-Based Microbiome Profiling: From Second- to Third-Generation Sequencing for Higher Taxonomic Resolution.}, journal = {Genes}, volume = {14}, number = {8}, pages = {}, pmid = {37628619}, issn = {2073-4425}, mesh = {RNA, Ribosomal, 16S/genetics ; *Benchmarking ; Computational Biology ; *Microbiota/genetics ; Technology ; }, abstract = {The 16S rRNA amplicon-based sequencing approach represents the most common and cost-effective strategy with great potential for microbiome profiling. The use of second-generation sequencing (NGS) technologies has led to protocols based on the amplification of one or a few hypervariable regions, impacting the outcome of the analysis. Nowadays, comparative studies are necessary to assess different amplicon-based approaches, including the full-locus sequencing currently feasible thanks to third-generation sequencing (TGS) technologies. This study compared three different methods to achieve the deepest microbiome taxonomic characterization: (a) the single-region approach, (b) the multiplex approach, covering several regions of the target gene/region, both based on NGS short reads, and (c) the full-length approach, which analyzes the whole length of the target gene thanks to TGS long reads. Analyses carried out on benchmark microbiome samples, with a known taxonomic composition, highlighted a different classification performance, strongly associated with the type of hypervariable regions and the coverage of the target gene. Indeed, the full-length approach showed the greatest discriminating power, up to species level, also on complex real samples. This study supports the transition from NGS to TGS for the study of the microbiome, even if experimental and bioinformatic improvements are still necessary.}, } @article {pmid37628582, year = {2023}, author = {Gagnon, JC and Beauregard-Tousignant, S and Marcil, JS and Lazar, CS}, title = {Deep Isolated Aquifer Brines Harbor Atypical Halophilic Microbial Communities in Quebec, Canada.}, journal = {Genes}, volume = {14}, number = {8}, pages = {}, pmid = {37628582}, issn = {2073-4425}, mesh = {Humans ; Quebec ; Canada ; *Groundwater ; *Microbiota/genetics ; }, abstract = {The deep terrestrial subsurface, hundreds of meters to kilometers below the surface, is characterized by oligotrophic conditions, dark and often anoxic settings, with fluctuating pH, salinity, and water availability. Despite this, microbial populations are detected and active, contributing to biogeochemical cycles over geological time. Because it is extremely difficult to access the deep biosphere, little is known about the identity and metabolisms of these communities, although they likely possess unknown pathways and might interfere with deep waste deposits. Therefore, we analyzed rock and groundwater microbial communities from deep, isolated brine aquifers in two regions dating back to the Ordovician and Devonian, using amplicon and whole genome sequencing. We observed significant differences in diversity and community structure between both regions, suggesting an impact of site age and composition. The deep hypersaline groundwater did not contain typical halophilic bacteria, and genomes suggested pathways involved in protein and hydrocarbon degradation, and carbon fixation. We identified mainly one strategy to cope with osmotic stress: compatible solute uptake and biosynthesis. Finally, we detected many bacteriophage families, potentially indicating that bacteria are infected. However, we also found auxiliary metabolic genes in the viral genomes, probably conferring an advantage to the infected hosts.}, } @article {pmid37628073, year = {2023}, author = {Yang, Z and Li, W and Yuan, Y and Liang, Z and Yan, Y and Chen, Y and Ni, L and Lv, X}, title = {Metagenomic Insights into the Regulatory Effects of Microbial Community on the Formation of Biogenic Amines and Volatile Flavor Components during the Brewing of Hongqu Rice Wine.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {16}, pages = {}, pmid = {37628073}, issn = {2304-8158}, support = {32072204//National Natural Science Foundation of China/ ; 2022L3075//Central Leading Local Science and Technology Development Fund Project of China/ ; 2022J01101//Natural Science Foundation of Fujian Province of China/ ; GXRC21049//Outstanding Talent of "Qishan Scholar" of Fuzhou University, China/ ; }, abstract = {As one of the typical representatives of Chinese rice wine (Huangjiu), Hongqu rice wine is produced with glutinous rice as the main raw material and Hongqu as the fermentation starter. The complex microbial flora in the brewing process may have a great influence on the formation of the flavor quality and drinking safety of Hongqu rice wine. Previous studies have shown that high biogenic amine (BA) content in rice wine has potential physiological toxicity and has become a bottleneck problem restricting the development of the rice wine industry. This study aimed to evaluate the regulatory effects of the microbial community on the formation of BAs and volatile flavor components during the brewing of Hongqu rice wine. The results demonstrated that histamine, putrescine, cadaverine, tyramine, tryptamine, spermine, and spermidine were the main BAs in Hongqu rice wine. The contents of putrescine, cadaverine, histamine, tyramine, and spermidine in Hongqu rice wine of HBAs (with higher BAs content) were significantly higher than those in LBAs (with lower BAs content). GC-MS testing results showed that there were significant differences in the composition of volatile organic compounds (VOCs) between HBAs and LBAs. Among them, VOCs such as 2-methoxy-4-vinylphenol, ethyl caprate, phenethyl acetate, ethyl lactate, ethyl myristate, ethyl palmitate, ethyl n-octadecanoate, ethyl oleate, and ethyl linoleate were identified as the characteristic volatile components with significant differences between HBAs and LBAs. Microbiome analysis based on metagenomic sequencing revealed that unclassified_g_Pantoea, Klebsiella pneumoniae, Panobacter disperse, unclassified_f_Enterobacteriaceae, Leuconostoc mesenteroides, and Saccharomyces cerevisiae were the dominant microbial species in the HBA brewing process, while Weissella confuse, Pediococcus acidilactici, Saccharomyces cerevisiae, and Aspergillus niger were the dominant microbial species in the LBA brewing process. Furthermore, correlation heatmap analysis demonstrated that BAs were positively related to Lactobacillus curvatus, Lactococcus lactis, and Leuconostoc mesenteroides. Bioinformatical analysis based on the KEGG database revealed that the microbial genes encoding enzymes involved in BAs' synthesis were more abundant in HBAs, and the abundances of microbial genes encoding enzymes related to BAs' degradation and the metabolism of characteristic volatile components were higher in LBAs. Overall, this work provides important scientific data for enhancing the flavor quality of Hongqu rice wine and lays a solid foundation for the healthy development of the Hongqu rice wine industry.}, } @article {pmid37627971, year = {2023}, author = {Ding, L and Wang, S and Jiang, W and Miao, Y and Liu, W and Yang, F and Zhang, J and Chi, W and Liu, T and Liu, Y and Wang, S and Zhang, Y and Zhao, H}, title = {Identification of Intestinal Microbial Community in Gallstone Patients with Metagenomic Next-Generation Sequencing.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {13}, number = {16}, pages = {}, pmid = {37627971}, issn = {2075-4418}, support = {82272987//National Natural Science Foundation of China/ ; 82172933//National Natural Science Foundation of China/ ; 81902380//National Natural Science Foundation of China/ ; 21ZR1421700//Scientific Research Project of Shanghai Science and Technology Commission/ ; 21Y11900900//Shanghai Technological Innovation Action Projects/ ; 20204Y0296//Shanghai health and family planning commission youth project of scientific research subject/ ; ZDXK2212//Key Subject of Huadong Hospital/ ; HDLC2022007//the Clinical Research Project of Huadong Hospital/ ; 23QA1403000//Shanghai Rising-Star Program/ ; A2020567//Medical Scientific Research Foundation of Guangdong Province/ ; }, abstract = {Gallstone disease (GD) is one of the most common gastrointestinal diseases worldwide. Nowadays, intestinal microbiota are thought to play important roles in the formation of gallstones. In our study, human fecal samples were extracted for metagenomic next-generation sequencing (mNGS) on the Illumina HiSeq platform, followed by bioinformatics analyses. Our results showed that there was a particular intestinal micro-ecosystem in GD patients. In contrast to healthy people, the sequences of Bacteroidetes, Bacteroides and Thetaiotaomicron were obviously more abundant in GD patients at phylum, genus and species levels, respectively. On the other hand, the glycan metabolism and drug resistance, especially for the β-lactams, were the most profound functions of gut microbes in GD patients compared to those in normal subjects. Furthermore, a correlation analysis drew out that there existed a significant relationship between the serum levels of biochemical indicators and abundances of intestinal microbes in GD patients. Our results illuminate both the composition and functions of intestinal microbiota in GD patients. All in all, our study can broaden the insight into the potential mechanism of how gut microbes affect the progression of gallstones to some extent, which may provide potential targets for the prevention, diagnosis or treatment of GD.}, } @article {pmid37627823, year = {2023}, author = {Keng, ZX and Tan, JJM and Phoon, BL and Khoo, CC and Khoiroh, I and Chong, S and Supramaniam, C and Singh, A and Pan, GT}, title = {Aerated Static Pile Composting for Industrial Biowastes: From Engineering to Microbiology.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {10}, number = {8}, pages = {}, pmid = {37627823}, issn = {2306-5354}, support = {//KPT Recycle Sdn Bhd/ ; }, abstract = {This work demonstrated the feasibility of an industrial-scale aerated static pile composting system for treating one of the common biowastes-soybean curd residue. The mixing ratios of the feedstock were optimized to achieve a carbon-nitrogen ratio and a moisture level in the ranges of 25-35 and 60-70%, respectively. This open-air composting system required 6-7 months to obtain a mature compost. Solvita and seed germination tests further confirmed the maturity of the compost, with 25% compost extract concentration yielding the best germination index in the absence of phytotoxicity. The bacterial and fungal compositions of the compost piles were further examined with metagenomic analysis. Thermoactinomyces spp., Oceanobacillus spp., and Kroppenstedtia spp. were among the unique bacteria found, and Diutina rugosa, Thermomyces dupontii, and Candida taylorii were among the unique fungi found in the compost piles, suggesting the presence of good microorganisms for degrading the organic biowastes.}, } @article {pmid37627735, year = {2023}, author = {Patangia, DV and Grimaud, G and Linehan, K and Ross, RP and Stanton, C}, title = {Microbiota and Resistome Analysis of Colostrum and Milk from Dairy Cows Treated with and without Dry Cow Therapies.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {8}, pages = {}, pmid = {37627735}, issn = {2079-6382}, support = {12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; 101054719/ERC_/European Research Council/International ; }, abstract = {This study investigated the longitudinal impact of methods for the drying off of cows with and without dry cow therapy (DCT) on the microbiota and resistome profile in colostrum and milk samples from cows. Three groups of healthy dairy cows (n = 24) with different antibiotic treatments during DCT were studied. Colostrum and milk samples from Month 0 (M0), 2 (M2), 4 (M4) and 6 (M6) were analysed using whole-genome shotgun-sequencing. The microbial diversity from antibiotic-treated groups was different and higher than that of the non-antibiotic group. This difference was more evident in milk compared to colostrum, with increasing diversity seen only in antibiotic-treated groups. The microbiome of antibiotic-treated groups clustered separately from the non-antibiotic group at M2-, M4- and M6 milk samples, showing the effect of antibiotic treatment on between-group (beta) diversity. The non-antibiotic group did not show a high relative abundance of mastitis-causing pathogens during early lactation and was more associated with genera such as Psychrobacter, Serratia, Gordonibacter and Brevibacterium. A high relative abundance of antibiotic resistance genes (ARGs) was observed in the milk of antibiotic-treated groups with the Cephaguard group showing a significantly high abundance of genes conferring resistance to cephalosporin, aminoglycoside and penam classes. The data support the use of non-antibiotic alternatives for drying off in cows.}, } @article {pmid37627387, year = {2023}, author = {Sung, CH and Pilla, R and Chen, CC and Ishii, PE and Toresson, L and Allenspach-Jorn, K and Jergens, AE and Summers, S and Swanson, KS and Volk, H and Schmidt, T and Stuebing, H and Rieder, J and Busch, K and Werner, M and Lisjak, A and Gaschen, FP and Belchik, SE and Tolbert, MK and Lidbury, JA and Steiner, JM and Suchodolski, JS}, title = {Correlation between Targeted qPCR Assays and Untargeted DNA Shotgun Metagenomic Sequencing for Assessing the Fecal Microbiota in Dogs.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {16}, pages = {}, pmid = {37627387}, issn = {2076-2615}, abstract = {DNA shotgun sequencing is an untargeted approach for identifying changes in relative abundances, while qPCR allows reproducible quantification of specific bacteria. The canine dysbiosis index (DI) assesses the canine fecal microbiota by using a mathematical algorithm based on qPCR results. We evaluated the correlation between qPCR and shotgun sequencing using fecal samples from 296 dogs with different clinical phenotypes. While significant correlations were found between qPCR and sequencing, certain taxa were only detectable by qPCR and not by sequencing. Based on sequencing, less than 2% of bacterial species (17/1190) were consistently present in all healthy dogs (n = 76). Dogs with an abnormal DI had lower alpha-diversity compared to dogs with normal DI. Increases in the DI correctly predicted the gradual shifts in microbiota observed by sequencing: minor changes (R = 0.19, DI < 0 with any targeted taxa outside the reference interval, RI), mild-moderate changes (R = 0.24, 0 < DI < 2), and significant dysbiosis (R = 0.54, 0.73, and 0.91 for DI > 2, DI > 5, and DI > 8, respectively), compared to dogs with a normal DI (DI < 0, all targets within the RI), as higher R-values indicated larger dissimilarities. In conclusion, the qPCR-based DI is an effective indicator of overall microbiota shifts observed by shotgun sequencing in dogs.}, } @article {pmid37626951, year = {2023}, author = {Meleshko, D and Korobeynikov, A}, title = {Benchmarking State-of-the-Art Approaches for Norovirus Genome Assembly in Metagenome Sample.}, journal = {Biology}, volume = {12}, number = {8}, pages = {}, pmid = {37626951}, issn = {2079-7737}, support = {19-14-00172//Russian Science Foundation/ ; }, abstract = {A recently published article in BMCGenomics by Fuentes-Trillo et al. contains a comparison of assembly approaches of several noroviral samples via different tools and preprocessing strategies. It turned out that the study used outdated versions of tools as well as tools that were not designed for the viral assembly task. In order to improve the suboptimal assemblies, authors suggested different sophisticated preprocessing strategies that seem to make only minor contributions to the results. We have reproduced the analysis using state-of-the-art tools designed for viral assembly, and we demonstrate that tools from the SPAdes toolkit (rnaviralSPAdes and coronaSPAdes) allow one to assemble the samples from the original study into a single contig without any additional preprocessing.}, } @article {pmid37626773, year = {2023}, author = {Lelonek, E and Bouazzi, D and Jemec, GBE and Szepietowski, JC}, title = {Skin and Gut Microbiome in Hidradenitis Suppurativa: A Systematic Review.}, journal = {Biomedicines}, volume = {11}, number = {8}, pages = {}, pmid = {37626773}, issn = {2227-9059}, support = {SUBZ.C260.23.041//Wroclaw Medical University/ ; }, abstract = {Hidradenitis suppurativa (HS) is a chronic skin disease that significantly impairs the quality of life of affected individuals. The disease is characterized by persistent purulent lesions in specific anatomical areas, and its pathophysiology involves multiple factors, including inflammation, genetics, the microbiome, and environmental components. Recent research suggests a potential role for pathogenic bacteria in HS, highlighting the importance of the communication between the human host and the microbiome in maintaining homeostasis and immune system reactivity. However, the exact mechanisms underlying the gut-skin microbial interactions in HS remain unclear. This systematic review aims to examine the existing literature on the differences in skin and gut microbiome composition between HS patients and healthy controls. The review identifies methodological inconsistencies and calls for further research to elucidate the microbiome's role in HS pathogenesis and to explore new therapeutic interventions. The review highlights the need for advancements in microbiome research methodologies, such as metataxonomics and metagenomics, to improve our understanding of the microbiota's impact on health and disease.}, } @article {pmid37626632, year = {2023}, author = {López-García, E and Benítez-Cabello, A and Arenas-de Larriva, AP and Gutierrez-Mariscal, FM and Pérez-Martínez, P and Yubero-Serrano, EM and Arroyo-López, FN and Garrido-Fernández, A}, title = {Application of Compositional Data Analysis to Study the Relationship between Bacterial Diversity in Human Faeces and Sex, Age, and Weight.}, journal = {Biomedicines}, volume = {11}, number = {8}, pages = {}, pmid = {37626632}, issn = {2227-9059}, support = {RTI2018-100883-B-I00//Ministerio de Ciencia, Innovación y Universidades, España/ ; PRE2019-087812//Ministerio de Ciencia, Innovación y Universidades, España/ ; PAIDI2020- 00162//Regional Government of Andalusia/ ; }, abstract = {This work uses Compositional Data Analysis (CoDA) to examine the typical human faecal bacterial diversity in 39 healthy volunteers from the Andalusian region (Spain). Stool samples were subjected to high-throughput sequencing of the V3 and V4 regions of the 16S ribosomal RNA gene using Illumina MiSeq. The numbers of sequences per sample and their genus-level assignment were carried out using the Phyloseq R package. The alpha diversity indices of the faecal bacterial population were not influenced by the volunteer's sex (male or female), age (19-46 years), and weight (48.6-99.0 kg). To study the relationship between these variables and the faecal bacterial population, the ALDEx2 and coda4microbiome CoDA packages were used. Applying ALDEx2, a trend suggesting a connection between sex and the genera Senegalimassilia and Negatibacillus (slightly more abundant in females) and Desulfovibrio (more abundant in males) was found. Moreover, age was tentatively associated with Streptococcus, Tizzerella, and Ruminococaceae_UCG-003, while weight was linked to Senegalimassilia. The exploratory tool of the coda4microbiome package revealed numerous bacterial log-ratios strongly related to sex and, to a lesser extent, age and weight. Moreover, the cross-sectional analysis identified bacterial signature balances able to assign sex to samples regardless of controlling for volunteers' age or weight. Desulfovibrio, Faecalitalea, and Romboutsia were relevant in the numerator, while Coprococcus, Streptococcus, and Negatibacillus were prominent in the denominator; the greater presence of these could characterise the female sex. Predictions for age included Caproiciproducens, Coprobacter, and Ruminoclostridium in the numerator and Odoribacter, Ezakiella, and Tyzzerella in the denominator. The predictions depend on the relationship between both groups, but the abundance of the first group and scarcity of the second could be related to older individuals. However, the association of the faecal bacterial population with weight did not yield a satisfactory model, indicating scarce influence. These results demonstrate the usefulness of the CoDA methodology for studying metagenomics data and, specifically, human microbiota.}, } @article {pmid37626433, year = {2023}, author = {Zhou, X and Lennon, JT and Lu, X and Ruan, A}, title = {Anthropogenic activities mediate stratification and stability of microbial communities in freshwater sediments.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {191}, pmid = {37626433}, issn = {2049-2618}, mesh = {Humans ; *Anthropogenic Effects ; *Ecosystem ; Lakes ; China ; Earth, Planet ; }, abstract = {BACKGROUND: Freshwater sediment microbes are crucial decomposers that play a key role in regulating biogeochemical cycles and greenhouse gas emissions. They often exhibit a highly ordered structure along depth profiles. This stratification not only reflects redox effects but also provides valuable insights into historical transitions, as sediments serve as important archives for tracing environmental history. The Anthropocene, a candidate geological epoch, has recently garnered significant attention. However, the human impact on sediment zonation under the cover of natural redox niches remains poorly understood. Dam construction stands as one of the most far-reaching anthropogenic modifications of aquatic ecosystems. Here we attempted to identify the ecological imprint of damming on freshwater sediment microbiome.

RESULTS: We conducted a year-round survey on the sediment profiles of Lake Chaohu, a large shallow lake in China. Through depth-discrete shotgun metagenomics, metataxonomics, and geophysiochemical analyses, we unveiled a unique prokaryotic hierarchy shaped by the interplay of redox regime and historical damming (labeled by the [137]Cs peak in AD 1963). Dam-induced initial differentiation was further amplified by nitrogen and methane metabolism, forming an abrupt transition governing nitrate-methane metabolic interaction and gaseous methane sequestration depth. Using a random forest algorithm, we identified damming-sensitive taxa that possess distinctive metabolic strategies, including energy-saving mechanisms, unique motility behavior, and deep-environment preferences. Moreover, null model analysis showed that damming altered microbial community assembly, from a selection-oriented deterministic process above to a more stochastic, dispersal-limited one below. Temporal investigation unveiled the rapid transition zone as an ecotone, characterized by high species richness, low community stability, and emergent stochasticity. Path analysis revealed the observed emergent stochasticity primarily came from the high metabolic flexibility, which potentially contributed to both ecological and statistical neutralities.

CONCLUSIONS: We delineate a picture in which dam-induced modifications in nutrient availability and sedimentation rates impact microbial metabolic activities and generate great changes in the community structure, assembly, and stability of the freshwater sediment microbiome. These findings reflect profound ecological and biogeochemical ramifications of human-Earth system interactions and help re-examine the mainstream views on the formation of sediment microbial stratification. Video Abstract.}, } @article {pmid37626351, year = {2023}, author = {Ghaly, TM and Focardi, A and Elbourne, LDH and Sutcliffe, B and Humphreys, W and Paulsen, IT and Tetu, SG}, title = {Stratified microbial communities in Australia's only anchialine cave are taxonomically novel and drive chemotrophic energy production via coupled nitrogen-sulphur cycling.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {190}, pmid = {37626351}, issn = {2049-2618}, mesh = {Humans ; *Nitrogen Cycle ; *Microbiota/genetics ; Sulfur ; Nitrification ; Australia ; }, abstract = {BACKGROUND: Anchialine environments, in which oceanic water mixes with freshwater in coastal aquifers, are characterised by stratified water columns with complex physicochemical profiles. These environments, also known as subterranean estuaries, support an abundance of endemic macro and microorganisms. There is now growing interest in characterising the metabolisms of anchialine microbial communities, which is essential for understanding how complex ecosystems are supported in extreme environments, and assessing their vulnerability to environmental change. However, the diversity of metabolic strategies that are utilised in anchialine ecosystems remains poorly understood.

RESULTS: Here, we employ shotgun metagenomics to elucidate the key microorganisms and their dominant metabolisms along a physicochemical profile in Bundera Sinkhole, the only known continental subterranean estuary in the Southern Hemisphere. Genome-resolved metagenomics suggests that the communities are largely represented by novel taxonomic lineages, with 75% of metagenome-assembled genomes assigned to entirely new or uncharacterised families. These diverse and novel taxa displayed depth-dependent metabolisms, reflecting distinct phases along dissolved oxygen and salinity gradients. In particular, the communities appear to drive nutrient feedback loops involving nitrification, nitrate ammonification, and sulphate cycling. Genomic analysis of the most highly abundant members in this system suggests that an important source of chemotrophic energy is generated via the metabolic coupling of nitrogen and sulphur cycling.

CONCLUSION: These findings substantially contribute to our understanding of the novel and specialised microbial communities in anchialine ecosystems, and highlight key chemosynthetic pathways that appear to be important in these energy-limited environments. Such knowledge is essential for the conservation of anchialine ecosystems, and sheds light on adaptive processes in extreme environments. Video Abstract.}, } @article {pmid37624549, year = {2023}, author = {Pal, P and Shastry, RP}, title = {Exploring the complex role of gut microbiome in the development of precision medicine strategies for targeting microbial imbalance-induced colon cancer.}, journal = {Folia microbiologica}, volume = {68}, number = {5}, pages = {691-701}, pmid = {37624549}, issn = {1874-9356}, support = {ICMR/5/13/84/2020/NCD-III dated 16/03/2021//ICMR-DHR, Government of India, New Delhi/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Precision Medicine/methods ; Dysbiosis/therapy ; *Probiotics/therapeutic use ; *Colonic Neoplasms/therapy ; }, abstract = {The gut microbiome has been increasingly recognized as a key player in the development and progression of colon cancer. Alterations in the gut microbiota, known as dysbiosis, can lead to a variety of medical issues. Microbial adaptation through signals and small molecules can enhance pathogen colonization and modulate host immunity, significantly impacting disease progression. Quorum sensing peptides and molecules have been linked to the progression of colon cancer. Various interventions, such as fecal microbiota transplantation, probiotics, prebiotics, synbiotics, and antibiotics, have been used to reverse dysbiosis with mixed results and potential side effects. Thus, a personalized approach to treatment selection based on patient characteristics, such as individual gut microbiota manipulation, is necessary to prevent and treat diseases like colon cancer. With advances in metagenomic sequencing and other omics technologies, there has been a growing interest in developing precision medicine strategies for microbial imbalance-induced colon cancer. This review serves as a comprehensive synthesis of current knowledge on the gut microbiome involvement in colon cancer. By exploring the potential of utilizing the gut microbiome as a target for precision medicine, this review underscores the exciting opportunities that lie ahead. Although challenges exist, the integration of microbiome data into precision medicine approaches has the potential to revolutionize the management of colon cancer, providing patients with more personalized and effective treatment options.}, } @article {pmid37624284, year = {2023}, author = {Summers, S and Quimby, J and Gagné, J and Lappin, M}, title = {The Effect of Dietary Protein Concentration on the Fecal Microbiome and Serum Concentrations of Gut-Derived Uremic Toxins in Healthy Adult Cats.}, journal = {Veterinary sciences}, volume = {10}, number = {8}, pages = {}, pmid = {37624284}, issn = {2306-7381}, support = {Not applicable//Nestle Purina and Colorado State University Center for Companion Animal Studies/ ; }, abstract = {The purpose of this study was to evaluate the effect of feeding healthy adult cats with foods containing variable protein concentrations on the fecal microbiome and serum concentrations of the gut-derived uremic toxins indoxyl sulfate, p-cresol sulfate (pCS), and trimethylamine-n-oxide. Twenty healthy young adult cats were randomized into two groups and fed either a low-protein diet (LPD; 7.4 g/100 kcal ME) or a high-protein diet (HPD; 11.0 g/100 kcal ME) for a 12-week period. Serum uremic toxin concentrations were measured via liquid chromatography tandem mass spectrometry, and the fecal microbiome was characterized using shallow sequence shotgun metagenomics. Cats that consumed the HPD had higher pCS concentrations at 8 weeks (p = 0.028) when compared to baseline. After 12 weeks, cats fed the HPD had higher fecal alpha diversity indices at both the taxonomic and functional levels and lower fecal Bifidobacterium relative abundance compared to those cats fed the LPD. In conclusion, a change in diet and dietary protein concentration shifted the fecal microbial community and microbial function. Feeding cats a high amount of protein increased serum concentrations of the uremic toxin pCS; however, the effect was short-lived.}, } @article {pmid37624283, year = {2023}, author = {Kim, SH and Choi, Y and Miguel, MA and Lee, SJ and Lee, SS and Lee, SS}, title = {Analysis of Fecal Microbial Changes in Young Calves Following Bovine Rotavirus Infection.}, journal = {Veterinary sciences}, volume = {10}, number = {8}, pages = {}, pmid = {37624283}, issn = {2306-7381}, support = {NRF-2021R1C1C2014102//National Research Foundation of Korea/ ; }, abstract = {The objective of the present study was to identify changes in fecal microbiota and predict the functional features of healthy calves and those infected with rotavirus over time. Six Holstein calves (average body weight 43.63 ± 1.19 kg, age-matched within 5-7 d) were randomly selected and distributed into two groups which contained three calves each. Fecal samples were taken 3 days before inoculation and on days 1 and 7 post-inoculation. The 16S rRNA gene amplicon sequencing was performed. Bacterial diversity tended to decrease in the rota group, as indicated by the alpha (evenness, p = 0.074 and Shannon, p = 0.055) and beta (Bray-Curtis dissimilarity, p = 0.099) diversity at 1 day post-inoculation. Differences in the bacterial taxa between healthy and rota-infected calves were detected using a linear discriminant analysis effect size (LDA > 2.0, p < 0.05). Rota calves had a higher abundance of certain bacterial taxa, such as Enterococcus, Streptococcus, and Escherichia-Shigella, and a lower abundance of bacteria that contribute to the production of short-chain fatty acids, such as Alistipes, Faecalibacterium, Pseudoflavonifractor, Subdoligranulum, Alloprevotella, Butyricicoccus, and Ruminococcus, compared to the healthy calves. The observed changes in the fecal microbiota of the rota-infected group compared to the healthy group indicated potential dysbiosis. This was further supported by significant differences in the predicted functional metagenomic profiles of these microbial communities. We suggest that calves infected with bovine rotavirus had bacterial dysbiosis, which was characterized by lower diversity and fewer observed genera than the fecal microbiota of healthy calves.}, } @article {pmid37623987, year = {2023}, author = {McHugh, J and Saleh, OA}, title = {Updates in Culture-Negative Endocarditis.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {8}, pages = {}, pmid = {37623987}, issn = {2076-0817}, abstract = {Blood culture-negative infective endocarditis (BCNE) is a challenging condition associated with significant morbidity and mortality. This review discusses the epidemiology, microbiology, diagnosis, and treatment of BCNE considering advancements in molecular diagnostics and increased access to cardiac surgery. BCNE can be categorized into bacterial endocarditis with sterilized blood cultures due to previous antibiotic treatment, endocarditis caused by fastidious microorganisms, and true BCNE caused by intracellular organisms that cannot be cultured using traditional techniques. Non-infectious causes such as nonbacterial thrombotic endocarditis should also be considered. Diagnostic approaches involve thorough patient history; blood and serum testing, including appropriate handling of blood cultures; serological testing; and molecular techniques such as targeted and shotgun metagenomic sequencing. Where available, evaluation of explanted cardiac tissue through histopathology and molecular techniques is crucial. The therapy for BCNE depends on the likely causative agent and the presence of prosthetic material, with surgical intervention often required.}, } @article {pmid37623865, year = {2023}, author = {Cumeras, R and Shen, T and Valdiviez, L and Tippins, Z and Haffner, BD and Fiehn, O}, title = {Differences in the Stool Metabolome between Vegans and Omnivores: Analyzing the NIST Stool Reference Material.}, journal = {Metabolites}, volume = {13}, number = {8}, pages = {}, pmid = {37623865}, issn = {2218-1989}, support = {U2C ES030158/GF/NIH HHS/United States ; }, abstract = {To gain confidence in results of omic-data acquisitions, methods must be benchmarked using validated quality control materials. We report data combining both untargeted and targeted metabolomics assays for the analysis of four new human fecal reference materials developed by the U.S. National Institute of Standards and Technologies (NIST) for metagenomics and metabolomics measurements. These reference grade test materials (RGTM) were established by NIST based on two different diets and two different samples treatments, as follows: firstly, homogenized fecal matter from subjects eating vegan diets, stored and submitted in either lyophilized (RGTM 10162) or aqueous form (RGTM 10171); secondly, homogenized fecal matter from subjects eating omnivore diets, stored and submitted in either lyophilized (RGTM 10172) or aqueous form (RGTM 10173). We used four untargeted metabolomics assays (lipidomics, primary metabolites, biogenic amines and polyphenols) and one targeted assay on bile acids. A total of 3563 compounds were annotated by mass spectrometry, including 353 compounds that were annotated in more than one assay. Almost half of all compounds were annotated using hydrophilic interaction chromatography/accurate mass spectrometry, followed by the lipidomics and the polyphenol assays. In total, 910 metabolites were found in at least 4-fold different levels in fecal matter from vegans versus omnivores, specifically for peptides, amino acids and lipids. In comparison, only 251 compounds showed 4-fold differences between lyophilized and aqueous fecal samples, including DG O-34:0 and methionine sulfoxide. A range of diet-specific metabolites were identified to be significantly different between vegans and omnivores, exemplified by citrinin and C17:0-acylcarnitine for omnivores, and curcumin and lenticin for vegans. Bioactive molecules like acyl alpha-hydroxy-fatty acids (AAHFA) were differentially regulated in vegan versus omnivore fecal materials, highlighting the importance of diet-specific reference materials for dietary biomarker studies.}, } @article {pmid37623415, year = {2023}, author = {Nagy, A and Katona, P and Molnár, A and Rádai, Z and Tóth, M and Szanyi, K and Szanyi, S}, title = {Wide Range of Brachyceran Fly Taxa Attracted to Synthetic and Semi-Synthetic Generic Noctuid Lures and the Description of New Attractants for Sciomyzidae and Heleomyzidae Families.}, journal = {Insects}, volume = {14}, number = {8}, pages = {}, pmid = {37623415}, issn = {2075-4450}, support = {PD 138329//National Research, Development and Innovation Office/ ; }, abstract = {During field tests implemented in Transcarpathia (West Ukraine) in 2015, 6501 specimens belonging to 26 Brachyceran fly families were collected with traps baited with generic lures (originally developed for noctuid moths) based on fermenting liquid and floral compounds. Isoamyl alcohol-based baits generally attracted more flies than phenylacetaldehyde-based baits and unbaited controls; however, the phenylacetaldehyde-based traps were the most attractive to the Empididae and Milichiidae families. The isoamyl alcohol-based semisynthetic lure showed significant attractivity to the families of Muscidae, Ulidiidae, Sarcophagidae, Calliphoridae, Sciomyzidae, Heleomyzidae, Drosophilidae, Phoridae and Platystomatidae. Additionally, isoamyl alcohol-based semisynthetic lure is the first reported attractant of the Sciomyzidae family. Since our phenylacetaldehyde-based floral lure was also attractive to Heleomyzidae flies, both types of lures can be seen as the first known attractants of this family.}, } @article {pmid37623326, year = {2023}, author = {Sun, K and Yu, M and Zhu, XY and Xue, CX and Zhang, Y and Chen, X and Yao, P and Chen, L and Fu, L and Yang, Z and Zhang, XH}, title = {Microbial communities related to the sulfur cycle in the Sansha Yongle Blue Hole.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0114923}, pmid = {37623326}, issn = {2165-0497}, abstract = {The Sansha Yongle Blue Hole (SYBH), the deepest blue hole in the world, is an excellent habitat for revealing biogeochemical cycles in the anaerobic environment. However, how sulfur cycling is mediated by microorganisms in the SYBH hasn't been fully understood. In this study, the water layers of the SYBH were divided into oxic zone, hypoxic zone, anoxic zone I and II, and microbial-mediated sulfur cycling in the SYBH was comprehensively interpreted. The 16S rRNA genes/transcripts analyses showed that the microbial community structures associated with the sulfur cycling in each zone had distinctive features. Sulfur-oxidizing bacteria were mostly constituted by Gammaproteobacteria, Alphaproteobacteria, Campylobacterota, and Chlorobia above the anoxic zone I and sulfate-reducing bacteria were dominated by Desulfobacterota in anoxic zones. Metagenomic analyses showed that the sulfide-oxidation-related gene sqr and genes encoding the Sox system were mainly distributed in the anoxic zone I, while genes related to dissimilatory sulfate reduction and sulfur intermediate metabolite reduction were mainly distributed in the anoxic zone II, indicating different sulfur metabolic processes between these two zones. Moreover, sulfur-metabolism-related genes were identified in 81 metagenome-assembled genomes (MAGs), indicating a high diversity of microbial communities involved in sulfur cycling. Among them, three MAGs from the candidate phyla JdFR-76 and AABM5-125-24 with genes related to dissimilatory sulfate reduction exhibited distinctive metabolic features. Our results showed unique and novel microbial populations in the SYBH sulfur cycle correlated to the sharp redox gradients, revealing complex biogeochemical processes in this extreme environment. IMPORTANCE Oxygen-deficient regions in the global ocean are expanding rapidly and affect the growth, reproduction and ecological processes of marine organisms. The anaerobic water body of about 150 m in the Sansha Yongle Blue Hole (SYBH) provided a suitable environment to study the specific microbial metabolism in anaerobic seawater. Here, we found that the vertical distributions of the total and active communities of sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) were different in each water layer of the SYBH according to the dissolved oxygen content. Genes related to sulfur metabolism also showed distinct stratification characteristics. Furthermore, we have obtained diverse metagenome-assembled genomes, some of which exhibit special sulfur metabolic characteristics, especially candidate phyla JdFR-76 and AABM5-125-24 were identified as potential novel SRB. The results of this study will promote further understanding of the sulfur cycle in extreme environments, as well as the environmental adaptability of microorganisms in blue holes.}, } @article {pmid37622724, year = {2023}, author = {Xia, Y}, title = {Statistical normalization methods in microbiome data with application to microbiome cancer research.}, journal = {Gut microbes}, volume = {15}, number = {2}, pages = {2244139}, pmid = {37622724}, issn = {1949-0984}, mesh = {RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; *Microbiota ; Metagenome ; Research Design ; *Neoplasms ; }, abstract = {Mounting evidence has shown that gut microbiome is associated with various cancers, including gastrointestinal (GI) tract and non-GI tract cancers. But microbiome data have unique characteristics and pose major challenges when using standard statistical methods causing results to be invalid or misleading. Thus, to analyze microbiome data, it not only needs appropriate statistical methods, but also requires microbiome data to be normalized prior to statistical analysis. Here, we first describe the unique characteristics of microbiome data and the challenges in analyzing them (Section 2). Then, we provide an overall review on the available normalization methods of 16S rRNA and shotgun metagenomic data along with examples of their applications in microbiome cancer research (Section 3). In Section 4, we comprehensively investigate how the normalization methods of 16S rRNA and shotgun metagenomic data are evaluated. Finally, we summarize and conclude with remarks on statistical normalization methods (Section 5). Altogether, this review aims to provide a broad and comprehensive view and remarks on the promises and challenges of the statistical normalization methods in microbiome data with microbiome cancer research examples.}, } @article {pmid37622435, year = {2023}, author = {Juge, N}, title = {Microbe Profile: Ruminococcus gnavus: the yin and yang of human gut symbionts.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {8}, pages = {}, pmid = {37622435}, issn = {1465-2080}, support = {BB/X011054/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13630/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13631/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR13633/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *Ruminococcus/genetics ; Gastrointestinal Microbiome ; Symbiosis ; }, abstract = {Ruminococcus gnavus is a human gut symbiont, part of the infant and adult gut microbiota and associated with intestinal and extra-intestinal disorders. R. gnavus mechanisms of adaptation to the gut are strain-specific and underpinned by the capacity of R. gnavus strains to utilize mucin and dietary glycans and produce bacteriocins and adhesins. Several potential mediators underpinning the association between R. gnavus strains and diseases have been identified, including the capacity to elicit a pro- or anti-inflammatory host response and modulate host metabolism, secondary bile acids and tryptophan metabolic pathways. Based on increasing evidence from metagenomics studies in humans and functional investigations in vitro and in mouse models, R. gnavus is emerging as a main player in influencing health and disease outcomes from infants to the elderly.}, } @article {pmid37621874, year = {2023}, author = {Zhou, Q and Tao, X and Guo, F and Zhu, Y and Wu, Y and Xiang, H and Shang, D}, title = {The crosstalk between microbiota and metabolites in AP mice: an analysis based on metagenomics and untargeted metabolomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1134321}, pmid = {37621874}, issn = {2235-2988}, mesh = {Animals ; Mice ; Metagenomics ; Acute Disease ; *Pancreatitis ; *Microbiota ; Signal Transduction ; Bacteroidetes ; Lactobacillus ; }, abstract = {BACKGROUND AND PURPOSE: Microbiome dysfunction is known to aggravate acute pancreatitis (AP); however, the relationship between this dysfunction and metabolite alterations is not fully understood. This study explored the crosstalk between the microbiome and metabolites in AP mice.

METHODS: Experimental AP models were established by injecting C57/BL mice with seven doses of cerulein and one dose of lipopolysaccharide (LPS). Metagenomics and untargeted metabolomics were used to identify systemic disturbances in the microbiome and metabolites, respectively, during the progression of AP.

RESULTS: The gut microbiome of AP mice primarily included Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria, and "core microbiota" characterized by an increase in Proteobacteria and a decrease in Actinobacteria. The Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis found that significantly different microbes were involved in several signaling networks. Untargeted metabolomics identified 872 metabolites, of which lipids and lipid-like molecules were the most impacted. An integrated analysis of metagenomics and metabolomics indicated that acetate kinase (ackA) gene expression was associated with various gut microbiota, including Alistipes, Butyricimonas, and Lactobacillus, and was strongly correlated with the metabolite daphnoretin. The functional gene, O-acetyl-L-serine sulfhydrylase (cysK), was associated with Alistipes, Jeotgalicoccus, and Lactobacillus, and linked to bufalin and phlorobenzophenone metabolite production.

CONCLUSION: This study identified the relationship between the gut microbiome and metabolite levels during AP, especially the Lactobacillus-, Alistipes-, and Butyricimonas-associated functional genes, ackA and cysK. Expression of these genes was significantly correlated to the production of the anti-inflammatory and antitumor metabolites daphnoretin and bufalin.}, } @article {pmid37621652, year = {2023}, author = {Liang, J and Ali, S and Lv, C and Yang, H and Zhao, X and Ni, X and Li, C and Danzeng, B and Wang, Y and Quan, G}, title = {Dietary protein levels modulate the gut microbiome composition through fecal samples derived from lactating ewes.}, journal = {Frontiers in endocrinology}, volume = {14}, number = {}, pages = {1194425}, pmid = {37621652}, issn = {1664-2392}, mesh = {Sheep ; Animals ; Female ; *Gastrointestinal Microbiome ; Lactation ; Feces ; Dietary Proteins ; Sheep, Domestic ; Clostridiales ; }, abstract = {In ruminants, the digestion and utilization of dietary proteins are closely linked to the bacterial populations that are present in the gastrointestinal tract. In the present study, 16S rDNA sequencing, together with a metagenomic strategy was used to characterize the fecal bacteria of ewes in the early lactation stage after feeding with three levels of dietary proteins 8.58%, 10.34%, and 13.93%, in three different groups (H_1), (H_m) and (H_h), respectively. A total of 376,278,516 clean data-points were obtained by metagenomic sequencing. Firmicutes and Bacteroidetes were the dominant phyla, regardless of the dietary protein levels. In the H_h group, the phyla Proteobacteria, Caldiserica, and Candidatus_Cryosericota were less abundant than those in the H_I group. In contrast, Lentisphaerae, Chlamydiae, and Planctomycetes were significantly more abundant in the H_h group. Some genera, such as Prevotella, Roseburia, and Firmicutes_unclassified, were less abundant in the H_h group than those in the H_I group. In contrast, Ruminococcus, Ruminococcaceae_noname, Anaerotruncus, Thermotalae, Lentisphaerae_noname, and Paraprevotella were enriched in the H_h group. The acquired microbial genes were mainly clustered into biological processes; molecular functions; cytosol; cellular components; cytoplasm; structural constituents of ribosomes; plasma membranes; translation; and catalytic activities. 205987 genes were significantly enriched in the H_h group. In contrast, 108129 genes were more abundant in the H_I group. Our findings reveal that dynamic changes in fecal bacteria and their genes are strongly influenced by the levels of dietary proteins. We discovered that differentially expressed genes mainly regulate metabolic activity and KEGG demonstrated the primary involvement of these genes in the metabolism of carbohydrates, amino acids, nucleotides, and vitamins. Additionally, genes responsible for metabolism were more abundant in the H_h group. Investigating fecal bacterial characteristics may help researchers develop a dietary formula for lactating ewes to optimize the growth and health of ewes and lambs.}, } @article {pmid37621397, year = {2023}, author = {Du, X and Yan, C and Kong, S and Che, D and Peng, B and Zhu, L and Geng, S and Guo, K}, title = {Successful secukinumab therapy in plaque psoriasis is associated with altered gut microbiota and related functional changes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1227309}, pmid = {37621397}, issn = {1664-302X}, abstract = {INTRODUCTION: The role of gut microbiome dysbiosis in the pathogenesis of psoriasis has gained increasing attention in recent years. Secukinumab, targeting interleukin (IL)-17, has a promising efficacy in psoriasis treatment. However, it remains unclear the gut microbiota alteration and related functional changes caused by successful secukinumab therapy in psoriatic patients.

METHODS: In our study, we compared the fecal microbiome profile between psoriatic patients after secukinumab successful treatment (AT) and the other two groups, psoriatic patients without therapy (BT) and healthy people (H), respectively, by using next-generation sequencing targeting 16S ribosomal RNA. Then, shotgun metagenomic sequencing was first used to characterize bacterial gut microbial communities and related functional changes in the AT group.

RESULTS: We found that the diversity and structure of the microbial community in the AT group were significantly changed compared to those in the BT group and the H group. The AT group showed a microbiota profile characterized by increased proportions of the phylum Firmicute, families Ruminococcaceae, and a reduction in the phylum Bacteroidota (elevated F/B ratio). To detect functional alteration, we discovered that secukinumab treatment may construct a more stable homeostasis of the gut microbiome with functional alteration. There were different KEGG pathways, such as the downregulated cardiovascular diseases pathway and the upregulated infectious diseases in the AT group. By metagenomic analysis, the metabolic functional pathway was changed after secukinumab therapy.

DISCUSSION: It seems that gut microbiota investigation during biologic drug treatment is useful for predicting the efficacy and risks of drug treatment in disease.}, } @article {pmid37620878, year = {2023}, author = {Abrantes, J and Varsani, A and Pereira, P and Maia, C and Farias, I and Veríssimo, A and Neves, F}, title = {Identification and characterization of a polyomavirus in the thornback skate (Raja clavata).}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {190}, pmid = {37620878}, issn = {1743-422X}, mesh = {Animals ; *Polyomavirus/genetics ; *Skates, Fish ; Ecosystem ; Phylogeny ; Polyomaviridae ; Mammals ; }, abstract = {Members of the family Polyomaviridae have a circular double-stranded DNA genome that have been identified in various hosts ranging from mammals to arachnids. Here we report the identification and analysis of a complete genome sequence of a novel polyomavirus, Raja clavata polyomavirus (RcPyV1), from a cartilaginous fish, the thornback skate (Raja clavata). The genome sequence was determined using a metagenomics approach with an aim to provide baseline viral data in cartilaginous fish in different ecosystems. The RcPyV1 genome (4,195 nucleotides) had typical organization of polyomavirus, including early antigens (small T; Large T) encoded on one strand and late viral proteins (VP1; VP2) on the complementary strand. Maximum-likelihood phylogenetic analysis of the large T-antigen revealed that RcPyV1 clusters with a polyomavirus obtained from another cartilaginous fish, the guitarfish polyomavirus 1 (GfPyV1). These two share ~ 56% pairwise identity in LT and VP1 protein sequences. These analyses support the hypothesis that cartilaginous fishes have a specific lineage of polyomaviruses.}, } @article {pmid37620368, year = {2023}, author = {Mutti, G and Oteo-Garcia, G and Caldon, M and da Silva, MJF and Minhós, T and Cowlishaw, G and Gottelli, D and Huchard, E and Carter, A and Martinez, FI and Raveane, A and Capelli, C}, title = {Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13839}, pmid = {37620368}, issn = {2045-2322}, mesh = {Humans ; Male ; Animals ; *Metagenomics ; *Theropithecus ; Papio ; Macaca mulatta ; Microsatellite Repeats/genetics ; }, abstract = {Y chromosome markers can shed light on male-specific population dynamics but for many species no such markers have been discovered and are available yet, despite the potential for recovering Y-linked loci from available genome sequences. Here, we investigated how effective available bioinformatic tools are in recovering informative Y chromosome microsatellites from whole genome sequence data. In order to do so, we initially explored a large dataset of whole genome sequences comprising individuals at various coverages belonging to different species of baboons (genus: Papio) using Y chromosome references belonging to the same genus and more distantly related species (Macaca mulatta). We then further tested this approach by recovering Y-STRs from available Theropithecus gelada genomes using Papio and Macaca Y chromosome as reference sequences. Identified loci were validated in silico by a) comparing within-species relationships of Y chromosome lineages and b) genotyping male individuals in available pedigrees. Each STR was selected not to extend in its variable region beyond 100 base pairs, so that loci can be developed for PCR-based genotyping of non-invasive DNA samples. In addition to assembling a first set of Papio and Theropithecus Y-specific microsatellite markers, we released TYpeSTeR, an easy-to-use script to identify and genotype Y chromosome STRs using population genomic data which can be modulated according to available male reference genomes and genomic data, making it widely applicable across taxa.}, } @article {pmid37619978, year = {2023}, author = {Steffen, K and Proux-Wéra, E and Soler, L and Churcher, A and Sundh, J and Cárdenas, P}, title = {Whole genome sequence of the deep-sea sponge Geodia barretti (Metazoa, Porifera, Demospongiae).}, journal = {G3 (Bethesda, Md.)}, volume = {13}, number = {10}, pages = {}, pmid = {37619978}, issn = {2160-1836}, mesh = {Animals ; *Geodia/genetics ; *Genome, Mitochondrial ; Aquatic Organisms/genetics ; Sweden ; }, abstract = {Sponges are among the earliest branching extant animals. As such, genetic data from this group are valuable for understanding the evolution of various traits and processes in other animals. However, like many marine organisms, they are notoriously difficult to sequence, and hence, genomic data are scarce. Here, we present the draft genome assembly for the North Atlantic deep-sea high microbial abundance species Geodia barretti Bowerbank 1858, from a single individual collected on the West Coast of Sweden. The nuclear genome assembly has 4,535 scaffolds, an N50 of 48,447 bp and a total length of 144 Mb; the mitochondrial genome is 17,996 bp long. BUSCO completeness was 71.5%. The genome was annotated using a combination of ab initio and evidence-based methods finding 31,884 protein-coding genes.}, } @article {pmid37619305, year = {2023}, author = {Fan, SQ and Wen, WR and Xie, GJ and Lu, Y and Liu, BF and Xing, DF and Ma, J and Ren, NQ}, title = {Deep insights into the population shift of n-DAMO and Anammox in granular sludge: From sidestream to mainstream.}, journal = {Water research}, volume = {244}, number = {}, pages = {120448}, doi = {10.1016/j.watres.2023.120448}, pmid = {37619305}, issn = {1879-2448}, mesh = {*Sewage ; Anaerobiosis ; Anaerobic Ammonia Oxidation ; Bioreactors ; Denitrification ; Bacteria/genetics/metabolism ; Oxidation-Reduction ; Methane/metabolism ; *Ammonium Compounds/metabolism ; Nitrogen/metabolism ; }, abstract = {Granular sludge combined n-DAMO and Anammox (n-D/A) is an energy-efficient biotechnique for the simultaneous removal of nitrogen and dissolved methane from wastewater. However, the lack of knowledge so far about the metabolic interactions between n-DAMO and Anammox in response to operation condition in granular sludge restrains the development of this biotechnology. To address this gap, three independent membrane granular sludge reactors (MGSRs) were designed to carry out the granule-based n-D/A process under different conditions. We provided the first deep insights into the metabolic interactions between n-DAMO and Anammox in granular sludge via combined metagenomic and metatranscriptomic analyses. Our study unveiled a clear population shift of n-DAMO community from Candidatus Methanoperedens to Candidatus Methylomirabilis from sidestream to mainstream. Candidatus Methanoperedens with relative abundance of 25.2% played the major role in nitrate reduction and methane oxidation under sidestream condition, indicated by the high expression activities of mcrA and narG. Candidatus Methylomirabilis dominated the microbial community under mainstream condition with relative abundance of 32.1%, supported by the high expression activities of pmoA and hao. Furthermore, a transition of Anammox population from Candidatus Kuenenia to Candidatus Brocadia was also observed from sidestream to mainstream. Candidatus Kuenenia and Candidatus Brocadia jointly contributed to the primary anaerobic ammonium oxidation suggested by the high expression value of hdh and hzs. Candidatus Methylomirabilis was speculated to perform ammonium oxidation mediated by pMMO under mainstream condition. These findings might help to reveal the microbial interactions and ecological niches of n-DAMO and Anammox microorganisms, shedding light on the optimization and management of the granule-based n-D/A system.}, } @article {pmid37619274, year = {2023}, author = {Wu, Z and Cai, P and Liang, E and Chen, Q and Sun, W and Wang, J}, title = {Distinct adaptive strategies and microbial interactions of soil viruses under different metal(loid) contaminations.}, journal = {Journal of hazardous materials}, volume = {460}, number = {}, pages = {132347}, doi = {10.1016/j.jhazmat.2023.132347}, pmid = {37619274}, issn = {1873-3336}, mesh = {*Drug Contamination ; *Environmental Pollution ; Metagenome ; Metals ; Microbial Interactions ; Soil ; }, abstract = {Viruses, as the most abundant organisms, significantly influence ecological function and microbial survival in soils, yet little was known about how viruses and virus-microbe interactions respond to environmental stresses induced by metal(loid) contaminations. Here, we conducted the metagenomic analysis to investigate the adaptative mechanisms of soil viruses under different metal(loid) contamination levels. By capturing a catalogue of 23,066 viruses, we found that viral communities exhibited the increased richness, diversity, and the temperate to lytic ratio in facing the highest metal(loid) contaminations. Meanwhile, viruses displayed obvious lineage-specific infection modes to distinct dominant hosts under different pollution levels. Viral functions linking to the inhibition of transcription and the enhancement of DNA repairment as well as multiple resistance not only contributed to coping with elevated multiple metal(loid) stresses, but also facilitated the adaptation and functioning of viral hosts. Moreover, the harmonious coexistence of viruses and resistant/pathogenic bacteria under the heaviest contaminations potentially exacerbated disseminating resistance and pathogenicity, while viruses under the lightest contaminations might be natural predators of resistant/pathogenic bacteria through lysing host cells. Overall, this study highlights the ecological importance of viral adaptation and the interactions between viruses and resistant/pathogenic bacteria in contaminated environments, contributing to developing virus-based approaches to soil restoration.}, } @article {pmid37615434, year = {2023}, author = {Shi, Z and Wang, Y and Yan, X and Ma, X and Duan, A and Hassan, F-u and Wang, W and Deng, T}, title = {Metagenomic and metabolomic analyses reveal the role of gut microbiome-associated metabolites in diarrhea calves.}, journal = {mSystems}, volume = {8}, number = {5}, pages = {e0058223}, pmid = {37615434}, issn = {2379-5077}, support = {HARS-22-13-S//Henan Beef Cattle Industrial Technology System/ ; 2020GXNSFDA297032//Natural Science Foundation of Guangxi Zhuang Autonomous Region/ ; 2023ZC057//Independent Innovation Project of Henan Academy of Agricultural Sciences/ ; }, mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome/genetics ; Diarrhea/veterinary ; Feces ; Metagenome ; Metabolomics ; }, abstract = {Calf diarrhea is of great concern to the global dairy industry as it results in significant economic losses due to lower conception rates, reduced milk production, and early culling. Although there is evidence of an association between altered gut microbiota and diarrhea, remarkably little is known about the microbial and metabolic mechanisms underlying the link between gut microbiota dysbiosis and the occurrence of calf diarrhea. Here, we used fecal metagenomic and metabolomic analyses to demonstrate that gut microbiota-driven metabolic disorders of purine or arachidonic acid were associated with calf diarrhea. These altered gut microbiotas play vital roles in diarrhea pathogenesis and indicate that gut microbiota-targeted therapies could be useful for both prevention and treatment of diarrhea.}, } @article {pmid37615431, year = {2023}, author = {Armour, CR and Sovacool, KL and Close, WL and Topçuoğlu, BD and Wiens, J and Schloss, PD}, title = {Machine learning classification by fitting amplicon sequences to existing OTUs.}, journal = {mSphere}, volume = {8}, number = {5}, pages = {e0033623}, pmid = {37615431}, issn = {2379-5042}, support = {R01CA215574/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; Algorithms ; *Microbiota/genetics ; }, abstract = {The ability to use 16S rRNA gene sequence data to train machine learning classification models offers the opportunity to diagnose patients based on the composition of their microbiome. In some applications, the taxonomic resolution that provides the best models may require the use of de novo operational taxonomic units (OTUs) whose composition changes when new data are added. We previously developed a new reference-based approach, OptiFit, that fits new sequence data to existing de novo OTUs without changing the composition of the original OTUs. While OptiFit produces OTUs that are as high quality as de novo OTUs, it is unclear whether this method for fitting new sequence data into existing OTUs will impact the performance of classification models relative to models trained and tested only using de novo OTUs. We used OptiFit to cluster sequences into existing OTUs and evaluated model performance in classifying a dataset containing samples from patients with and without colonic screen relevant neoplasia (SRN). We compared the performance of this model to standard methods including de novo and database-reference-based clustering. We found that using OptiFit performed as well or better in classifying SRNs. OptiFit can streamline the process of classifying new samples by avoiding the need to retrain models using reclustered sequences. IMPORTANCE There is great potential for using microbiome data to aid in diagnosis. A challenge with de novo operational taxonomic unit (OTU)-based classification models is that 16S rRNA gene sequences are often assigned to OTUs based on similarity to other sequences in the dataset. If data are generated from new patients, the old and new sequences must be reclustered to OTUs and the classification model retrained. Yet there is a desire to have a single, validated model that can be widely deployed. To overcome this obstacle, we applied the OptiFit clustering algorithm to fit new sequence data to existing OTUs allowing for reuse of the model. A random forest model implemented using OptiFit performed as well as the traditional reassign and retrain approach. This result shows that it is possible to train and apply machine learning models based on OTU relative abundance data that do not require retraining or the use of a reference database.}, } @article {pmid37615407, year = {2023}, author = {Pan, X and Zhang, Y and Chen, G}, title = {The clinical utility of metagenomic next-generation sequencing for the diagnosis of central nervous system infectious diseases.}, journal = {Neurological research}, volume = {45}, number = {10}, pages = {919-925}, doi = {10.1080/01616412.2023.2247299}, pmid = {37615407}, issn = {1743-1328}, mesh = {Humans ; Chlorides ; High-Throughput Nucleotide Sequencing ; Meninges ; *Central Nervous System Infections/diagnosis ; *Encephalitis, Viral ; Glucose ; *Communicable Diseases ; }, abstract = {BACKGROUND: To evaluate the clinical utility of metagenomic next-generation sequencing (mNGS) for the diagnosis of central nervous system infections (CNSI).

METHODS: Cerebrospinal fluid (CSF) from 54 patients who were high-level clinical suspicion of CNSI was collected and sent for mNGS and conventional tests from January 2019 to March 2022.

RESULTS: Twenty out of 54 patients were diagnosed with CNSI and 34 non-CNSI. Among the 34 non-CNSI, one was false positive by mNGS. Among the 20 CNSI, 11 had presumed viral encephalitis and/or meningitis, 5 had presumed bacterial meningitis, 2 had presumed TMB, 1 had Crytococcus meningitis and 1 had neurosyphilis. The sensitivity of viral encephalitis and/or meningitis was 0.73 (8/11); 10 virus were detected; 9/10 was dsDNA; 1/10 was ssRNA. SSRN ranged from 1 to 13. The accuracy rate was 0.4, the accuracy rate was positively correlated with SSRN (r = 0.738, P = 0.015), SSRN ≥ 1, the accuracy rate was 0.4; SSRN ≥ 3, the accuracy rate was 0.66; SSRN ≥ 4, the accuracy rate was 0.75; SSRN ≥ 6, the accuracy rate was 1. The sensitivity of bacterial meningitis was 1. Seven kinds of bacteria were detected, among which 3/7 were gram positive, 3/7 were gram negative, and 1/7 was infected NTM (nontuberculous mycobacteria). The accuracy rate was 0.43 (3/7). The sensitivity of TBM was 0.66 (2/3), the accuracy rate was 1. The sensitivity of Crytococcus meningitis was 1, the accuracy rate was 0.5. PPV (positive predictive value) of mNGS was 0.94, NPV (negative predictive value) of mNGS was 0.89, specificity was 0.97 and sensitivity was 0.8. The AUG for CSF mNGS diagnosis of CNSI was 0.89 (95% CI = 0.78-0.99) Headache, meningeal irritation sign and image of meninges abnormal were correlated with the sensitivity of mNGS (r = 0.451, 0.313, 0.446; p = 0.001, 0.021, 0.001); CSF Glucose and CSF Chloride were negatively correlated with sensitivity of mNGS (r = -0.395, -0.462; p = 0.003, ＜ 0.001).

CONCLUSION: mNGS is a detection means with high sensitivity, wide coverage and strong timeliness, which can help clinicians to identify the pathogen diagnosis quickly, conduct targeted anti-infection treatment early and reduce antibiotic abuse. The pathogen which causing low CSF Glucose, low CSF Chloride or meninges infections was more likely to be detected by mNGS. It may be related to growth and structural characteristics of the pathogen and blood-brain barrier damage.}, } @article {pmid37612775, year = {2023}, author = {Fusi, M and Ngugi, DK and Marasco, R and Booth, JM and Cardinale, M and Sacchi, L and Clementi, E and Yang, X and Garuglieri, E and Fodelianakis, S and Michoud, G and Daffonchio, D}, title = {Gill-associated bacteria are homogeneously selected in amphibious mangrove crabs to sustain host intertidal adaptation.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {189}, pmid = {37612775}, issn = {2049-2618}, mesh = {Animals ; *Brachyura ; Gills ; Ecosystem ; Host Adaptation ; RNA, Ribosomal, 16S/genetics ; *Actinobacteria ; Bacteria/genetics ; }, abstract = {BACKGROUND: The transition from water to air is a key event in the evolution of many marine organisms to access new food sources, escape water hypoxia, and exploit the higher and temperature-independent oxygen concentration of air. Despite the importance of microorganisms in host adaptation, their contribution to overcoming the challenges posed by the lifestyle changes from water to land is not well understood. To address this, we examined how microbial association with a key multifunctional organ, the gill, is involved in the intertidal adaptation of fiddler crabs, a dual-breathing organism.

RESULTS: Electron microscopy revealed a rod-shaped bacterial layer tightly connected to the gill lamellae of the five crab species sampled across a latitudinal gradient from the central Red Sea to the southern Indian Ocean. The gill bacterial community diversity assessed with 16S rRNA gene amplicon sequencing was consistently low across crab species, and the same actinobacterial group, namely Ilumatobacter, was dominant regardless of the geographic location of the host. Using metagenomics and metatranscriptomics, we detected that these members of actinobacteria are potentially able to convert ammonia to amino acids and may help eliminate toxic sulphur compounds and carbon monoxide to which crabs are constantly exposed.

CONCLUSIONS: These results indicate that bacteria selected on gills can play a role in the adaptation of animals in dynamic intertidal ecosystems. Hence, this relationship is likely to be important in the ecological and evolutionary processes of the transition from water to air and deserves further attention, including the ontogenetic onset of this association. Video Abstract.}, } @article {pmid37612768, year = {2023}, author = {Zhang, ZF and Liu, LR and Pan, YP and Pan, J and Li, M}, title = {Long-read assembled metagenomic approaches improve our understanding on metabolic potentials of microbial community in mangrove sediments.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {188}, pmid = {37612768}, issn = {2049-2618}, mesh = {*Metagenome/genetics ; *Microbiota/genetics ; Metagenomics ; Fermentation ; Carbon ; }, abstract = {BACKGROUND: Mangrove wetlands are coastal ecosystems with important ecological features and provide habitats for diverse microorganisms with key roles in nutrient and biogeochemical cycling. However, the overall metabolic potentials and ecological roles of microbial community in mangrove sediment are remained unanswered. In current study, the microbial and metabolic profiles of prokaryotic and fungal communities in mangrove sediments were investigated using metagenomic analysis based on PacBio single-molecule real time (SMRT) and Illumina sequencing techniques.

RESULTS: Comparing to Illumina short reads, the incorporation of PacBio long reads significantly contributed to more contiguous assemblies, yielded more than doubled high-quality metagenome-assembled genomes (MAGs), and improved the novelty of the MAGs. Further metabolic reconstruction for recovered MAGs showed that prokaryotes potentially played an essential role in carbon cycling in mangrove sediment, displaying versatile metabolic potential for degrading organic carbons, fermentation, autotrophy, and carbon fixation. Mangrove fungi also functioned as a player in carbon cycling, potentially involved in the degradation of various carbohydrate and peptide substrates. Notably, a new candidate bacterial phylum named as Candidatus Cosmopoliota with a ubiquitous distribution is proposed. Genomic analysis revealed that this new phylum is capable of utilizing various types of organic substrates, anaerobic fermentation, and carbon fixation with the Wood-Ljungdahl (WL) pathway and the reverse tricarboxylic acid (rTCA) cycle.

CONCLUSIONS: The study not only highlights the advantages of HiSeq-PacBio Hybrid assembly for a more complete profiling of environmental microbiomes but also expands our understanding of the microbial diversity and potential roles of distinct microbial groups in biogeochemical cycling in mangrove sediment. Video Abstract.}, } @article {pmid37612723, year = {2023}, author = {Wang, X and Wang, K and Xie, F and Han, Z and Liu, Y and Pan, L and Zhu, G and Cao, Z and Yan, P and Xiao, L and Duan, Z and Hu, Y and Xiao, K and Chen, X and Fu, H and Shi, Y and Song, Y and Han, X and Xie, W and Xie, L}, title = {Protocol of a multicenter, single-blind, randomized, parallel controlled trial evaluating the effect of microbiological rapid on-site evaluation (M-ROSE) guiding anti-infection treatment in patients with severe hospital-acquired pneumonia.}, journal = {Trials}, volume = {24}, number = {1}, pages = {552}, pmid = {37612723}, issn = {1745-6215}, support = {2022-1-5091//Capital's Funds for Health Improvement and Research/ ; }, mesh = {Humans ; Adolescent ; Adult ; Prospective Studies ; Rapid On-site Evaluation ; Single-Blind Method ; *Anti-Infective Agents ; Hospitals, General ; *Pneumonia ; Randomized Controlled Trials as Topic ; Multicenter Studies as Topic ; }, abstract = {INTRODUCTION: The mortality rate of hospitalized patients with severe hospital-acquired pneumonia (SHAP) remains high. Empirical broad-spectrum antibiotic coverage and the misuse of high-grade antibiotics could lead to the emergence of multi-drug and even pandrug-resistant bacteria. In addition to metagenomic next-generation sequencing (mNGS), microbiological rapid on-site evaluation (M-ROSE) might be a useful technique to identify the pathogens in the early stage; however, the effect of M-ROSE guiding anti-infection treatment on prognostic outcomes of SHAP patients is still unclear.

METHODS/DESIGN: This is a multicenter, single-blind, prospective, randomized controlled trial to evaluate the effect of M-ROSE guiding anti-infection treatment in SHAP patients, which will provide new strategies for the prevention and control of clinical multi-drug resistance bacteria. A total of 166 patients with SHAP, aged 18 years and over, will be recruited from seven centers in Beijing and randomly assigned to the intervention group (M-ROSE combined with mNGS) or the control group (mNGS only) in a 1:1 ratio using the central randomization system. Patients in the intervention group will accept M-ROSE and mNGS analysis, and the control group will accept mNGS analysis. Individualized anti-infective treatment and routine treatment will be selected according to the analysis results. The primary outcome is the ICU outcome (mortality). The safety of the intervention measures will be evaluated during the entire trial period. This trial will be the first randomized controlled trial to evaluate the effect of M-ROSE guiding treatment on mortality in patients with SHAP and may change the prevalence of multi-drug resistant bacteria.

ETHICS AND DISSEMINATION: This trial adheres to the Declaration of Helsinki and guidelines of Good Clinical Practice. Signed informed consent will be obtained from all participants. The trial has been approved by the Chinese PLA General Hospital (Approval Number: 20220322001).

TRIAL REGISTRATION: ClinicalTrials.gov NCT05300776. Registered on 25 March 2022.}, } @article {pmid37612665, year = {2023}, author = {Hernández-Neuta, I and Magoulopoulou, A and Pineiro, F and Lisby, JG and Gulberg, M and Nilsson, M}, title = {Highly multiplexed targeted sequencing strategy for infectious disease surveillance.}, journal = {BMC biotechnology}, volume = {23}, number = {1}, pages = {31}, pmid = {37612665}, issn = {1472-6750}, mesh = {Humans ; *Communicable Diseases ; High-Throughput Nucleotide Sequencing ; Biological Assay ; Computational Biology ; Gene Library ; }, abstract = {BACKGROUND: Global efforts to characterize diseases of poverty are hampered by lack of affordable and comprehensive detection platforms, resulting in suboptimal allocation of health care resources and inefficient disease control. Next generation sequencing (NGS) can provide accurate data and high throughput. However, shotgun and metagenome-based NGS approaches are limited by low concentrations of microbial DNA in clinical samples, requirements for tailored sample and library preparations plus extensive bioinformatics analysis. Here, we adapted molecular inversion probes (MIPs) as a cost-effective target enrichment approach to characterize microbial infections from blood samples using short-read sequencing. We designed a probe panel targeting 2 bacterial genera, 21 bacterial and 6 fungi species and 7 antimicrobial resistance markers (AMRs).

RESULTS: Our approach proved to be highly specific to detect down to 1 in a 1000 pathogen DNA targets contained in host DNA. Additionally, we were able to accurately survey pathogens and AMRs in 20 out of 24 samples previously profiled with routine blood culture for sepsis.

CONCLUSIONS: Overall, our targeted assay identifies microbial pathogens and AMRs with high specificity at high throughput, without the need for extensive sample preparation or bioinformatics analysis, simplifying its application for characterization and surveillance of infectious diseases in medium- to low- resource settings.}, } @article {pmid37611017, year = {2023}, author = {Sim, EM and Wang, Q and Howard, P and Kim, R and Lim, L and Hope, K and Sintchenko, V}, title = {Persistent Salmonella enterica serovar Typhi sub-populations within host interrogated by whole genome sequencing and metagenomics.}, journal = {PloS one}, volume = {18}, number = {8}, pages = {e0289070}, pmid = {37611017}, issn = {1932-6203}, mesh = {Humans ; *Salmonella typhi/genetics ; *Typhoid Fever ; Metagenomics ; Persistent Infection ; Whole Genome Sequencing ; }, abstract = {Salmonella enterica serovar Typhi (S. Typhi) causes typhoid fever and, in some cases, chronic carriage after resolution of acute disease. This study examined sequential isolates of S. Typhi from a single host with persistent asymptomatic infection. These isolates, along with another S. Typhi isolate recovered from a household contact with typhoid fever, were subjected to whole genome sequencing and analysis. In addition, direct sequencing of the bile fluid from the host with persistent infection was also performed. Comparative analysis of isolates revealed three sub-populations of S. Typhi with distinct genetic patterns. Metagenomic sequencing recognised only two of the three sub-populations within the bile fluid. The detection and investigation of insertion sequences IS10R and associated deletions complemented analysis of single nucleotide polymorphisms. These findings improve our understanding of within-host dynamics of S. Typhi in cases of persistent infection and inform epidemiological investigations of transmission events associated with chronic carriers.}, } @article {pmid37610590, year = {2023}, author = {Antwi, J}, title = {Precision Nutrition to Improve Risk Factors of Obesity and Type 2 Diabetes.}, journal = {Current nutrition reports}, volume = {12}, number = {4}, pages = {679-694}, pmid = {37610590}, issn = {2161-3311}, mesh = {Humans ; *Diabetes Mellitus, Type 2/epidemiology/prevention & control ; Obesity/epidemiology/prevention & control ; Nutritional Status ; Risk Factors ; Diet ; }, abstract = {PURPOSE OF REVIEW: Existing dietary and lifestyle interventions and recommendations, to improve the risk factors of obesity and type 2 diabetes with the target to mitigate this double global epidemic, have produced inconsistent results due to interpersonal variabilities in response to these conventional approaches, and inaccuracies in dietary assessment methods. Precision nutrition, an emerging strategy, tailors an individual's key characteristics such as diet, phenotype, genotype, metabolic biomarkers, and gut microbiome for personalized dietary recommendations to optimize dietary response and health. Precision nutrition is suggested to be an alternative and potentially more effective strategy to improve dietary intake and prevention of obesity and chronic diseases. The purpose of this narrative review is to synthesize the current research and examine the state of the science regarding the effect of precision nutrition in improving the risk factors of obesity and type 2 diabetes.

RECENT FINDINGS: The results of the research review indicate to a large extent significant evidence supporting the effectiveness of precision nutrition in improving the risk factors of obesity and type 2 diabetes. Deeper insights and further rigorous research into the diet-phenotype-genotype and interactions of other components of precision nutrition may enable this innovative approach to be adapted in health care and public health to the special needs of individuals. Precision nutrition provides the strategy to make individualized dietary recommendations by integrating genetic, phenotypic, nutritional, lifestyle, medical, social, and other pertinent characteristics about individuals, as a means to address the challenges of generalized dietary recommendations. The evidence presented in this review shows that precision nutrition markedly improves risk factors of obesity and type 2 diabetes, particularly behavior change.}, } @article {pmid37610465, year = {2023}, author = {Szuhaj, M and Kakuk, B and Wirth, R and Rákhely, G and Kovács, KL and Bagi, Z}, title = {Regulation of the methanogenesis pathways by hydrogen at transcriptomic level in time.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {20}, pages = {6315-6324}, pmid = {37610465}, issn = {1432-0614}, support = {2020-3.1.2-ZFR-KVG-2020-00009//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; K143198//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; FK123902//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; 2019-2.1.13-TÉT_IN-2020-00016//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; PD 132145//Nemzeti Kutatási Fejlesztési és Innovációs Hivatal/ ; }, abstract = {The biomethane formation from 4 H2 + CO2 by pure cultures of two methanogens, Methanocaldococcus fervens and Methanobacterium thermophilum, has been studied. The goal of the study was to understand the regulation of the enzymatic steps associated with biomethane biosynthesis by H2, using metagenomic, pan-genomic, and transcriptomic approaches. Methanogenesis in the autotrophic methanogen M. fervens could be easily "switched off" and "switched on" by H2/CO2 within about an hour. In contrast, the heterotrophic methanogen M. thermophilum was practically insensitive to the addition of the H2/CO2 trigger although this methanogen also converted H2/CO2 to CH4. From practical points of view, the regulatory function of H2/CO2 suggests that in the power-to-gas (P2G) renewable excess electricity conversion and storage systems, the composition of the biomethane-generating methanogenic community is essential for sustainable operation. In addition to managing the specific hydrogenotrophic methanogenesis biochemistry, H2/CO2 affected several, apparently unrelated, metabolic pathways. The redox-regulated overall biochemistry and symbiotic relationships in the methanogenic communities should be explored in order to make the P2G technology more efficient. KEY POINTS : • Hydrogenotrophic methanogens may respond distinctly to H2/CO2 in bio-CH4 formation. • H2/CO2 can also activate metabolic routes, which are apparently unrelated to methanogenesis. • Sustainable conversion of the fluctuating renewable electricity to bio-CH4 is an option.}, } @article {pmid37610104, year = {2023}, author = {Lin, ZT and Du, LF and Zhang, MZ and Han, XY and Wang, BH and Meng, J and Yu, FX and Zhou, XQ and Wang, N and Li, C and Wang, XY and Liu, J and Gao, WY and Ye, RZ and Xia, LY and Sun, Y and Jia, N and Jiang, JF and Zhao, L and Cui, XM and Zhan, L and Cao, WC}, title = {Genomic Characteristics of Emerging Intraerythrocytic Anaplasma capra and High Prevalence in Goats, China.}, journal = {Emerging infectious diseases}, volume = {29}, number = {9}, pages = {1780-1788}, pmid = {37610104}, issn = {1080-6059}, mesh = {Animals ; Humans ; *Goats ; Prevalence ; Phylogeny ; *Genomics ; Anaplasma/genetics ; China/epidemiology ; }, abstract = {Anaplasma capra is an emerging tickborne human pathogen initially recognized in China in 2015; it has been reported in ticks and in a wide range of domestic and wild animals worldwide. We describe whole-genome sequences of 2 A. capra strains from metagenomic sequencing of purified erythrocytes from infected goats in China. The genome of A. capra was the smallest among members of the genus Anaplasma. The genomes of the 2 A. capra strains contained comparable G+C content and numbers of pseudogenes with intraerythrocytic Anaplasma species. The 2 A. capra strains had 54 unique genes. The prevalence of A. capra was high among goats in the 2 endemic areas. Phylogenetic analyses revealed that the A. capra strains detected in this study were basically classified into 2 subclusters with those previously detected in Asia. Our findings clarify details of the genomic characteristics of A. capra and shed light on its genetic diversity.}, } @article {pmid37609623, year = {2023}, author = {Menon, T and Kalyanaraman, S}, title = {The oral microbiota in patients undergoing coronary artery bypass graft surgery.}, journal = {Indian journal of thoracic and cardiovascular surgery}, volume = {39}, number = {5}, pages = {501-504}, pmid = {37609623}, issn = {0970-9134}, abstract = {The oral cavity houses a diverse community of microorganisms which play an important role in maintaining the health of the individual. The coexistence of periodontal infections with coronary artery disease (CAD) has been shown in many studies. We investigated the presence and abundance of periodontitis-causing bacteria in patients with CAD. The oral microbiome of five patients admitted for coronary artery bypass graft (CABG) surgery was analysed by metagenomic sequencing of 16 s ribosomal ribonucleic acid (rRNA) gene amplicons. Two samples of oral mouthwash were collected 48-72 h apart when the patients were in the intensive care unit. Abundance and diversity of oral bacterial flora were analysed. The most abundant phyla were Firmicutes and Bacteroidetes. Less than 5% of the taxa in this group of patients belonged to the phylum Proteobacteria. Though there were variations in the abundance of the bacterial species in the immediate postoperative period, there was no major change in the overall diversity. High counts of periodontal pathogens such as Tannerella forsythia, Campylobacter rectus, Fusobacterium nucleatum, Prevotella intermedia, and Treponema denticola were seen in most of the patients.}, } @article {pmid37609544, year = {2023}, author = {Aljuraiban, GS and Algabsani, SS and Sabico, S and AlShammari, S and Aljazairy, EA and Al-Musharaf, S}, title = {Types of fiber and gut microbiota composition and diversity among arab females.}, journal = {Saudi journal of biological sciences}, volume = {30}, number = {9}, pages = {103767}, pmid = {37609544}, issn = {1319-562X}, abstract = {OBJECTIVES: Dietary fiber is recognized as an important nutrient for gut health. However, research on the relations of different types of fibers (soluble and insoluble) to the human microbiota health is limited. This study aimed to identify whether higher habitual intake of soluble and/or insoluble fiber have a different influence on the composition, diversity, and abundance of microbiota.

METHODS: We examined the fecal microbial composition of 92 healthy females aged 18 and above using the novel shotgun metagenomics sequencing technique. The habitual fiber intake was determined using the Saudi food frequency questionnaire. Pearson's correlation was used for the correlations between total, soluble, and insoluble fiber and gut microbiota. α- and β-diversities were applied to acquire the distinctions in the relative abundances of bacterial taxa.

RESULTS: Our findings show that higher dietary fiber, particularly insoluble fiber, was significantly correlated with the abundances of Bacteroides_u_s, Bacteroides uniformis, and Lactobacillus acidophilus (r = 0.26, 0.29, 0.26, p-value < 0.05, respectively). Non-significant difference was noted in the microbial α-diversity and β-diversity in low and high soluble/insoluble dietary fiber.

CONCLUSIONS: Current findings suggest that insoluble dietary-fiber intake is favorably correlated with the health of the human gut microbiota. However, further investigations are necessary to identify the effect of types of fiber on the specific species identified in this study.}, } @article {pmid37609282, year = {2023}, author = {Diallo, D and Sun, S and Somboro, AM and Baya, B and Kone, A and Diarra, B and Nantoume, M and Koloma, I and Diakite, M and Holl, J and Maiga, AI and Seydi, M and Theron, G and Hou, L and Fodor, A and Maiga, M}, title = {Metabolic and Immune Consequences of Antibiotic Related Microbiome Alterations during first-line Tuberculosis Treatment in Bamako, Mali.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {37609282}, abstract = {BACKGROUND: Tuberculosis (TB) infection is known to lead to the unbalance of the gut microbiota and act synergistically on the decline of the host immune response, when untreated. Moreover, previous work has found a correlation between dysbiosis in the gut microbiota composition and the use of antibiotics. However, there is a need for an in-depth understanding of the metabolic and immune consequences of antibiotic-related microbiome alterations during first-line TB treatment.

METHODS: In a longitudinal cohort study, which included TB-infected cohorts and healthy individuals (control group), we studied the anti-TB-related changes in the gut microbiota composition and related functional consequences. Sputum, whole blood and stool samples were collected from participants at four time-points including before (Month-0), during (Month-2), at the end of drug treatment (Month-6) and 9 months after treatment (Month-15). Controls were sampled at inclusion and Month-6. We analyzed the microbiota composition and microbial functional pathways with shotgun metagenomics, analyzed the blood metabolomics using high-performance liquid chromatography (HPLC), and measured the levels of metabolites and cytokines with cytometric bead array.

RESULTS: We found that the gut microbiota of patients infected with TB was different from that of the healthy controls. The gut microbiota became similar to healthy controls after treatment but was still significantly different after 6 months treatment and at the follow up 9 months after treatment. Our data also showed disturbance in the plasma metabolites such as tryptophan and tricarboxylic acids components of patients during TB treatment. Levels of IL-4, IL-6, IL-10, and IFN-γ decreased during treatment and levels were maintained after treatment completion, while IL-17A known to have a strong link with the gut microbiota was highly expressed during treatment period and longer than the 9-month post treatment completion. We found that some fatty acids were negatively correlated with the abundance of taxa. For example, Roseburia, Megasphaera, and alpha proteobacterium HIMB5 species were negatively correlated (rho = -0.6) with the quinolinate production.

CONCLUSION: Changes in the composition and function of gut microbiota was observed in TB patients before and after treatment compared to healthy controls. The differences persisted at nine months after treatment completion. Alterations in some bacterial taxa were correlated to the changes in metabolite levels in peripheral blood, thus the altered microbial community might lead to changes in immune status that influence the disease outcome and future resistance to infections.}, } @article {pmid37609281, year = {2023}, author = {Li, X and Xu, L and Demaree, B and Noecker, C and Bisanz, JE and Weisgerber, DW and Modavi, C and Turnbaugh, PJ and Abate, AR}, title = {Microbiome single cell atlases generated with a commercial instrument.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.08.08.551713}, pmid = {37609281}, abstract = {Single cell sequencing is useful for resolving complex systems into their composite cell types and computationally mining them for unique features that are masked in pooled sequencing. However, while commercial instruments have made single cell analysis widespread for mammalian cells, analogous tools for microbes are limited. Here, we present EASi-seq (E asily A ccessible S ingle microbe seq uencing). By adapting the single cell workflow of the commercial Mission Bio Tapestri instrument, this method allows for efficient sequencing of individual microbes' genomes. EASi-seq allows thousands of microbes to be sequenced per run and, as we show, can generate detailed atlases of human and environmental microbiomes. The ability to capture large shotgun genome datasets from thousands of single microbes provides new opportunities in discovering and analyzing species subpopulations. To facilitate this, we develop a companion bioinformatic pipeline that clusters microbes by similarity, improving whole genome assembly, strain identification, taxonomic classification, and gene annotation. In addition, we demonstrate integration of metagenomic contigs with the EASi-seq datasets to reduce capture bias and increase coverage. Overall, EASi-seq enables high quality single cell genomic data for microbiome samples using an accessible workflow that can be run on a commercially available platform.}, } @article {pmid37609255, year = {2023}, author = {Jenior, ML and Leslie, JL and Kolling, GL and Archbald-Pannone, L and Powers, DA and Petri, WA and Papin, JA}, title = {Systems-ecology designed bacterial consortium protects from severe Clostridioides difficile infection.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.08.08.552483}, pmid = {37609255}, support = {R01 AI124214/AI/NIAID NIH HHS/United States ; }, abstract = {Fecal Microbiota Transplant (FMT) is an emerging therapy that has had remarkable success in treatment and prevention of recurrent Clostridioides difficile infection (rCDI). FMT has recently been associated with adverse outcomes such as inadvertent transfer of antimicrobial resistance, necessitating development of more targeted bacteriotherapies. To address this challenge, we developed a novel systems biology pipeline to identify candidate probiotic strains that would be predicted to interrupt C. difficile pathogenesis. Utilizing metagenomic characterization of human FMT donor samples, we identified those metabolic pathways most associated with successful FMTs and reconstructed the metabolism of encoding species to simulate interactions with C. difficile . This analysis resulted in predictions of high levels of cross-feeding for amino acids in species most associated with FMT success. Guided by these in silico models, we assembled consortia of bacteria with increased amino acid cross-feeding which were then validated in vitro . We subsequently tested the consortia in a murine model of CDI, demonstrating total protection from severe CDI through decreased toxin levels, recovered gut microbiota, and increased intestinal eosinophils. These results support the novel framework that amino acid cross-feeding is likely a critical mechanism in the initial resolution of CDI by FMT. Importantly, we conclude that our predictive platform based on predicted and testable metabolic interactions between the microbiota and C. difficile led to a rationally designed biotherapeutic framework that may be extended to other enteric infections.}, } @article {pmid37609252, year = {2023}, author = {Hsu, TY and Nzabarushimana, E and Wong, D and Luo, C and Beiko, RG and Langille, M and Huttenhower, C and Nguyen, LH and Franzosa, EA}, title = {Profiling novel lateral gene transfer events in the human microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37609252}, abstract = {Lateral gene transfer (LGT) is an important mechanism for genome diversification in microbial populations, including the human microbiome. While prior work has surveyed LGT events in human-associated microbial isolate genomes, the scope and dynamics of novel LGT events arising in personal microbiomes are not well understood, as there are no widely adopted computational methods to detect, quantify, and characterize LGT from complex microbial communities. We addressed this by developing, benchmarking, and experimentally validating a computational method (WAAFLE) to profile novel LGT events from assembled metagenomes. Applying WAAFLE to >2K human metagenomes from diverse body sites, we identified >100K putative high-confidence but previously uncharacterized LGT events (~2 per assembled microbial genome-equivalent). These events were enriched for mobile elements (as expected), as well as restriction-modification and transport functions typically associated with the destruction of foreign DNA. LGT frequency was quantifiably influenced by biogeography, the phylogenetic similarity of the involved taxa, and the ecological abundance of the donor taxon. These forces manifest as LGT networks in which hub species abundant in a community type donate unequally with their close phylogenetic neighbors. Our findings suggest that LGT may be a more ubiquitous process in the human microbiome than previously described. The open-source WAAFLE implementation, documentation, and data from this work are available at http://huttenhower.sph.harvard.edu/waafle.}, } @article {pmid37608803, year = {2023}, author = {Ordóñez, CD and Mayoral-Campos, C and Egas, C and Redrejo-Rodríguez, M}, title = {A primer-independent DNA polymerase-based method for competent whole-genome amplification of intermediate to high GC sequences.}, journal = {NAR genomics and bioinformatics}, volume = {5}, number = {3}, pages = {lqad073}, pmid = {37608803}, issn = {2631-9268}, abstract = {Multiple displacement amplification (MDA) has proven to be a useful technique for obtaining large amounts of DNA from tiny samples in genomics and metagenomics. However, MDA has limitations, such as amplification artifacts and biases that can interfere with subsequent quantitative analysis. To overcome these challenges, alternative methods and engineered DNA polymerase variants have been developed. Here, we present new MDA protocols based on the primer-independent DNA polymerase (piPolB), a replicative-like DNA polymerase endowed with DNA priming and proofreading capacities. These new methods were tested on a genomes mixture containing diverse sequences with high-GC content, followed by deep sequencing. Protocols relying on piPolB as a single enzyme cannot achieve competent amplification due to its limited processivity and the presence of ab initio DNA synthesis. However, an alternative method called piMDA, which combines piPolB with Φ29 DNA polymerase, allows proficient and faithful amplification of the genomes. In addition, the prior denaturation step commonly performed in MDA protocols is dispensable, resulting in a more straightforward protocol. In summary, piMDA outperforms commercial methods in the amplification of genomes and metagenomes containing high GC sequences and exhibits similar profiling, error rate and variant determination as the non-amplified samples.}, } @article {pmid37608325, year = {2023}, author = {Ghorbani, M and Ferreira, D and Maioli, S}, title = {A metagenomic study of gut viral markers in amyloid-positive Alzheimer's disease patients.}, journal = {Alzheimer's research & therapy}, volume = {15}, number = {1}, pages = {141}, pmid = {37608325}, issn = {1758-9193}, mesh = {Humans ; *Alzheimer Disease/diagnosis ; Metagenomics ; Amyloidogenic Proteins ; Biomarkers ; Computational Biology ; }, abstract = {BACKGROUND: Mounting evidence suggests the involvement of viruses in the development and treatment of Alzheimer's disease (AD). However, there remains a significant research gap in metagenomic studies investigating the gut virome of AD patients, leaving gut viral dysbiosis in AD unexplored. This study aimed to fill this gap by conducting a metagenomics analysis of the gut virome in both amyloid-positive AD patients (Aβ + ADs) and healthy controls (HCs), with the objective of identifying viral signatures linked with AD.

METHOD: Whole-genome sequence (WGS) data from 65 human participants, including 30 Aβ + ADs and 35 HCs, was obtained from the database NCBI SRA (Bio Project: PRJEB47976). The Metaphlan3 pipeline and linear discriminant analysis effect size (LEfSe) analysis were utilized for the bioinformatics process and the detection of viral signatures, respectively. In addition, the Benjamini-Hochberg method was applied with a significance cutoff of 0.05 to evaluate the false discovery rate for all biomarkers identified by LEfSe. The CombiROC model was employed to determine the discriminatory power of the viral signatures identified by LEfSe.

RESULTS: Compared to HCs, the gut virome profiles of Aβ + ADs showed lower alpha diversity, indicating a lower bacteriophage richness. The Siphoviridae family was decreased in Aβ + ADs. Significant decreases of Lactococcus phages were found in Aβ + ADs, including bIL285, Lactococcus phage bIL286, Lactococcus phage bIL309, and Lactococcus phage BK5 T, Lactococcus phage BM13, Lactococcus phage P335 sensu lato, Lactococcus phage phiLC3, Lactococcus phage r1t, Lactococcus phage Tuc2009, Lactococcus phage ul36, and Lactococcus virus bIL67. The predictive combined model of these viral signatures obtained an area under the curve of 0.958 when discriminating Aβ + ADs from HCs.

CONCLUSION: This is the first study to identify distinct viral signatures in the intestine that can be used to effectively distinguish individuals with AD from HCs.}, } @article {pmid37608207, year = {2023}, author = {Russell, AL and McAdams, ZL and Donovan, E and Seilhamer, N and Siegrist, M and Franklin, CL and Ericsson, AC}, title = {The contribution of maternal oral, vaginal, and gut microbiota to the developing offspring gut.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {13660}, pmid = {37608207}, issn = {2045-2322}, support = {U42 OD010918/NH/NIH HHS/United States ; R03 OD028259/OD/NIH HHS/United States ; }, mesh = {Female ; Animals ; Mice ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Disease Models, Animal ; Feces ; }, abstract = {There is limited understanding of how the microbiota colonizing various maternal tissues contribute to the development of the neonatal gut microbiota (GM). To determine the contribution of various maternal microbiotic sites to the offspring microbiota in the upper and lower gastrointestinal tract (GIT) during early life, litters of mice were sacrificed at 7, 9, 10, 11, 12, 14, and 21 days of age, and fecal and ileal samples were collected. Dams were euthanized alongside their pups, and oral, vaginal, ileal, and fecal samples were collected. This was done in parallel using mice with either a low-richness or high-richness microbiota to assess the consistency of findings across multiple microbial compositions. Samples were analyzed using 16S rRNA amplicon sequencing. The compositional similarity between pup and dam samples were used to determine the contribution of each maternal source to the composition of the neonate fecal and ileal samples at each timepoint. As expected, similarity between neonate and maternal feces increased significantly over time. During earlier time-points however, the offspring fecal and ileal microbiotas were closer in composition to the maternal oral microbiota than other maternal sites. Prominent taxa contributed by the maternal oral microbiota to the neonate GM were supplier-dependent and included Lactobacillus spp., Streptococcus spp., and a member of the Pasteurellaceae family. These findings align with the microbial taxa reported in infant microbiotas, highlighting the translatability of mouse models in this regard, as well as the dynamic nature of the GM during early life.}, } @article {pmid37607924, year = {2023}, author = {Li, X and Chen, D and Carrión, VJ and Revillini, D and Yin, S and Dong, Y and Zhang, T and Wang, X and Delgado-Baquerizo, M}, title = {Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {5090}, pmid = {37607924}, issn = {2041-1723}, mesh = {*Fusariosis ; *Microbiota ; *Fusarium ; Metagenome ; Hydrogen-Ion Concentration ; }, abstract = {Soil-borne pathogens pose a major threat to food production worldwide, particularly under global change and with growing populations. Yet, we still know very little about how the soil microbiome regulates the abundance of soil pathogens and their impact on plant health. Here we combined field surveys with experiments to investigate the relationships of soil properties and the structure and function of the soil microbiome with contrasting plant health outcomes. We find that soil acidification largely impacts bacterial communities and reduces the capacity of soils to combat fungal pathogens. In vitro assays with microbiomes from acidified soils further highlight a declined ability to suppress Fusarium, a globally important plant pathogen. Similarly, when we inoculate healthy plants with an acidified soil microbiome, we show a greatly reduced capacity to prevent pathogen invasion. Finally, metagenome sequencing of the soil microbiome and untargeted metabolomics reveals a down regulation of genes associated with the synthesis of sulfur compounds and reduction of key traits related to sulfur metabolism in acidic soils. Our findings suggest that changes in the soil microbiome and disruption of specific microbial processes induced by soil acidification can play a critical role for plant health.}, } @article {pmid37607639, year = {2023}, author = {Li, J and Yang, Z and Zhu, Q and Zhong, G and Liu, J}, title = {Biodegradation of soil agrochemical contamination mitigates the direct horizontal transfer risk of antibiotic resistance genes to crops.}, journal = {The Science of the total environment}, volume = {901}, number = {}, pages = {166454}, doi = {10.1016/j.scitotenv.2023.166454}, pmid = {37607639}, issn = {1879-1026}, abstract = {Microorganisms can drive a substrate-specific biodegradation process to mitigate soil contamination resulting from extensive agrochemical usage. However, microorganisms with high metabolic efficiency are capable of adapting to the co-occurrence of non-substrate contaminants in the soil (particularly antibiotics). Therefore, the utilization of active microorganisms for biodegradation raises concerns regarding the potential risk of antibiotic resistance development. Here, the horizontal transfer risk of antibiotic-resistance genes (ARGs) in the soil-plant biota was assessed during biodegradation by the newly isolated Proteus terrae ZQ02 (which shortened the half-life of fungicide chlorothalonil from 9.24 d to 2.35 d when exposed to tetracycline). Based on metagenomic analyses, the distribution of ARGs and mobile genetic elements (MGEs) was profiled. The ARGs shared with ∼118 core genes and mostly accumulated in the rhizosphere and maize roots. After ZQ02 was inoculated, the core genes of ARGs reduced significantly in roots. In addition, the Pseudomonas and Proteus genera were identified as the dominant microbial hosts of ARGs and MGEs after ZQ02 adoption. The richness of major ARG hosts increased in soil but barely changed in the roots, which contributed to the mitigation of hosts-mediated ARGs transfer from soil to maize. Finally, the risk of ARGs has been assessed. Compared with the regular planting system, the number of risky ARGs declined from 220 (occupied 4.77 % of the total ARGs) to 143 (occupied 2.67 %) after biodegradation. Among these, 23 out of 25 high-risk genes were aggregated in the soil whereas only 2 genes were identified in roots, which further verified the low antibiotic resistance risk for crop after biodegradation. In a nutshell, this work highlights the critical advantage of ZQ02-based biodegradation that alleviating the ARGs transfer risks from soil to crop, which offers deeper insights into the versatility and feasibility of bioremediation techniques in sustainable agriculture.}, } @article {pmid37607456, year = {2023}, author = {Lönnrot, M and Lynch, KF and Rewers, M and Lernmark, Å and Vehik, K and Akolkar, B and Hagopian, W and Krischer, J and McIndoe, RA and Toppari, J and Ziegler, AG and Petrosino, JF and Lloyd, R and Hyöty, H and , }, title = {Gastrointestinal Infections Modulate the Risk for Insulin Autoantibodies as the First-Appearing Autoantibody in the TEDDY Study.}, journal = {Diabetes care}, volume = {46}, number = {11}, pages = {1908-1915}, pmid = {37607456}, issn = {1935-5548}, support = {U01 DK063821/DK/NIDDK NIH HHS/United States ; UL1 TR000064/TR/NCATS NIH HHS/United States ; UC4 DK063821/DK/NIDDK NIH HHS/United States ; U01 DK128847/DK/NIDDK NIH HHS/United States ; Contract no HHSN267200700014/DK/NIDDK NIH HHS/United States ; }, mesh = {Child ; Humans ; Infant ; Child, Preschool ; Autoantibodies ; *Diabetes Mellitus, Type 1 ; Case-Control Studies ; Insulin ; Insulin Antibodies ; Glutamate Decarboxylase ; *Islets of Langerhans ; }, abstract = {OBJECTIVE: To investigate gastrointestinal infection episodes (GIEs) in relation to the appearance of islet autoantibodies in The Environmental Determinants of Diabetes in the Young (TEDDY) cohort.

RESEARCH DESIGN AND METHODS: GIEs on risk of autoantibodies against either insulin (IAA) or GAD (GADA) as the first-appearing autoantibody were assessed in a 10-year follow-up of 7,867 children. Stool virome was characterized in a nested case-control study.

RESULTS: GIE reports (odds ratio [OR] 2.17 [95% CI 1.39-3.39]) as well as Norwalk viruses found in stool (OR 5.69 [1.36-23.7]) at <1 year of age were associated with an increased IAA risk at 2-4 years of age. GIEs reported at age 1 to <2 years correlated with a lower risk of IAA up to 10 years of age (OR 0.48 [0.35-0.68]). GIE reports at any other age were associated with an increase in IAA risk (OR 2.04 for IAA when GIE was observed 12-23 months prior [1.41-2.96]). Impacts on GADA risk were limited to GIEs <6 months prior to autoantibody development in children <4 years of age (OR 2.16 [1.54-3.02]).

CONCLUSIONS: Bidirectional associations were observed. GIEs were associated with increased IAA risk when reported before 1 year of age or 12-23 months prior to IAA. Norwalk virus was identified as one possible candidate factor. GIEs reported during the 2nd year of life were associated with a decreased IAA risk.}, } @article {pmid37607408, year = {2023}, author = {Paoletti, MM and Fournier, GP and Dolan, EL and Saito, MA}, title = {Metaproteogenomic Profile of a Mesopelagic Adenylylsulfate Reductase: Course-Based Discovery Using the Ocean Protein Portal.}, journal = {Journal of proteome research}, volume = {22}, number = {9}, pages = {2871-2879}, pmid = {37607408}, issn = {1535-3907}, support = {R01 GM135709/GM/NIGMS NIH HHS/United States ; }, mesh = {Phylogeny ; *Proteomics ; Pacific Ocean ; *Sulfates ; Sulfur ; }, abstract = {Adenylylsulfate reductase (Apr) is a flavoprotein with a dissimilatory sulfate reductase function. Its ability to catalyze the reverse reaction in sulfur oxidizers has propelled a complex phylogenetic history of transfers with sulfate reducers and made this enzyme an important protein in ocean sulfur cycling. As part of a graduate course, we analyzed metaproteomic data from the Ocean Protein Portal and observed evidence of Apr alpha (AprA) and beta (AprB) subunits in the Central Pacific Ocean. The protein was originally taxonomically attributed toChlorobium tepidum TLS, a green sulfur bacterium. However, our phylogenomic and oceanographic contextual analysis contradicted this label, instead showing that this protein is consistent with the genomic material from the newly discovered Candidatus Lambdaproteobacteriaclass, implying that the ecological role of this lineage in oxygen minimum twilight zones is underappreciated. This study illustrates how metaproteogenomic analysis can contribute to more accurate metagenomic/proteomic annotations and comprehensive ocean biogeochemical processes conducive to course-based research experiences.}, } @article {pmid37607063, year = {2023}, author = {Yang, M and Du, S and Zhang, Z and Xia, Q and Liu, H and Qin, F and Wu, Z and Ying, H and Wu, Y and Shao, J and Zhao, Y}, title = {Genomic diversity and biogeographic distributions of a novel lineage of bacteriophages that infect marine OM43 bacteria.}, journal = {Microbiology spectrum}, volume = {11}, number = {5}, pages = {e0494222}, pmid = {37607063}, issn = {2165-0497}, abstract = {The marine methylotrophic OM43 clade is considered an important bacterial group in coastal microbial communities. OM43 bacteria, which are closely related to phytoplankton blooms, have small cell sizes and streamlined genomes. Bacteriophages profoundly shape the evolutionary trajectories, population dynamics, and physiology of microbes. The prevalence and diversity of several phages that infect OM43 bacteria have been reported. In this study, we isolated and sequenced two novel OM43 phages, MEP401 and MEP402. These phages share 90% of their open reading frames (ORFs) and are distinct from other known phage isolates. Furthermore, a total of 99 metagenomic viral genomes (MVGs) closely related to MEP401 and MEP402 were identified. Phylogenomic analyses suggest that MEP401, MEP402, and these identified MVGs belong to a novel subfamily in the family Zobellviridae and that they can be separated into two groups. Group I MVGs show conserved whole-genome synteny with MEP401, while group II MVGs possess the MEP401-type DNA replication module and a distinct type of morphogenesis and packaging module, suggesting that genomic recombination occurred between phages. Most members in these two groups were predicted to infect OM43 bacteria. Metagenomic read-mapping analysis revealed that the phages in these two groups are globally ubiquitous and display distinct biogeographic distributions, with some phages being predominant in cold regions, some exclusively detected in estuarine stations, and others displaying wider distributions. This study expands our knowledge of the diversity and ecology of a novel phage lineage that infects OM43 bacteria by describing their genomic diversity and global distribution patterns. IMPORTANCE OM43 phages that infect marine OM43 bacteria are important for host mortality, community structure, and physiological functions. In this study, two OM43 phages were isolated and characterized. Metagenomic viral genome (MVG) retrieval using these two OM43 phages as baits led to the identification of two phage groups of a new subfamily in the family Zobellviridae. We found that group I MVGs share similar genomic content and arrangement with MEP401 and MEP402, whereas group II MVGs only possess the MEP401-type DNA replication module. Metagenomic mapping analysis suggests that members in these two groups are globally ubiquitous with distinct distribution patterns. This study provides important insights into the genomic diversity and biogeography of the OM43 phages in the global ocean.}, } @article {pmid37606634, year = {2023}, author = {Liu, D and Wang, S and Liu, Y and Luo, Y and Wen, B and Wu, W and Zeng, H and Huang, J and Liu, Z}, title = {Fuzhuan brick tea ameliorates hepatic steatosis and steatohepatitis through gut microbiota-derived aryl hydrocarbon receptor ligands in high-fat diet-induced obese mice.}, journal = {Food & function}, volume = {14}, number = {18}, pages = {8351-8368}, doi = {10.1039/d3fo01782f}, pmid = {37606634}, issn = {2042-650X}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Diet, High-Fat/adverse effects ; Ligands ; Mice, Obese ; Receptors, Aryl Hydrocarbon/genetics ; *Fatty Liver/drug therapy ; Escherichia coli ; Tea ; }, abstract = {High-fat diet (HFD) induced obesity and its associated conditions, such as hepatic steatosis and steatohepatitis, are major health concerns worldwide. Previous studies have reported the excellent efficiency of Fuzhuan brick tea (FBT) in attenuating HFD-induced obesity and metabolic disorders. In this study, we investigated the effects of FBT on hepatic steatosis and simple steatohepatitis in HFD-induced obese mice, as well as the metabolic function of the gut microbiome using metagenomics and metabolomics. The results showed that FBT ameliorated dyslipidemia, hepatic steatosis and steatohepatitis in HFD-induced obese mice by normalizing the gut microbiota structure and tryptophan metabolism. FBT increased the cecal abundance of aryl hydrocarbon receptor (AhR)-ligand producing bacteria such as Lactobacillus_reuteri and Lactobacillus_johnsonii, at the expense of AhR-ligand consuming bacteria, such as Faecalibaculum_rodentium and Escherichia_coli, and elevated the cecal contents of AhR-ligands such as IAA, IPA, and KYNA. Furthermore, FBT regulated the expressions of AhR and its targeted lipometabolic genes such as Pemt, Fasn, and SREBP-1c, as well as other inflammatory genes including TNF-α, IL-6, and IL-1β in the liver of mice. Overall, these findings highlight the beneficial effects of FBT on obesity-related hepatic steatosis and steatohepatitis via microbiota-derived AhR signaling.}, } @article {pmid37606424, year = {2023}, author = {Yang, Z and Lou, Y and Yan, X and Pan, H and Wang, H and Yang, Q and Sun, Y and Zhuge, Y}, title = {The Microbiome and Antibiotic Resistome in Soil under Biodegradable Composite Carbon Source Amendment.}, journal = {Journal of xenobiotics}, volume = {13}, number = {3}, pages = {424-438}, pmid = {37606424}, issn = {2039-4713}, support = {52100192//National Natural Science Foundation of China/ ; 2021CXGC010804//Key Research and Development Program of Shandong Province/ ; SDBX2020013//Shandong Province Postdoctoral Innovative Talent Support Program/ ; }, abstract = {The decomposition of biodegradable composite carbon sources generates a large amount of biodegradable microplastics, which may not only furnish microbial denitrification, but might also pose potential environmental risks. In the present study, the effects of different dosages of a biodegradable composite carbon source on the microbial communities, the nitrogen metabolic pathways and the antibiotic resistome were explored through Illumina MiSeq sequencing analysis and metagenomic analysis. The results of partial least-square discriminant analysis (PLS-DA) and analysis of similarity (ANOSIM) demonstrated that the response of the bacterial community to a biodegradable composite carbon source was more obvious than the fungal community. The application of biodegradable microplastics diminished the complexity of the microbial communities to some extent and obviously stimulated denitrification. Antibiotics resistance gene (ARG) dispersal was not evidently accelerated after the addition of biodegradable composite carbon source. Lysobacter, Methylobacillus, Phyllobacterium, Sinorhizobium, Sphingomonas from Proteobacteria and Actinomadura, Agromyces, Gaiella and Micromonospora from Actinobacteria were the major ARG hosts. Overall, the addition of a biodegradable composite carbon source shaped microbial communities and their antibiotic resistance profiles in this study.}, } @article {pmid37605221, year = {2023}, author = {Tams, KW and Larsen, I and Hansen, JE and Spiegelhauer, H and Strøm-Hansen, AD and Rasmussen, S and Ingham, AC and Kalmar, L and Kean, IRL and Angen, Ø and Holmes, MA and Pedersen, K and Jelsbak, L and Folkesson, A and Larsen, AR and Strube, ML}, title = {The effects of antibiotic use on the dynamics of the microbiome and resistome in pigs.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {39}, pmid = {37605221}, issn = {2524-4671}, support = {34009-17-1246//Grønt Udviklings- og Demonstrations Program/ ; }, abstract = {Antibiotics are widely used in pig farming across the world which has led to concerns about the potential impact on human health through the selection of antibiotic resistant pathogenic bacteria. This worry has resulted in the development of a production scheme known as pigs Raised Without Antibiotics (RWA), in which pigs are produced in commercial farms, but are ear-tagged as RWA until slaughter unless they receive treatment, thus allowing the farmer to sell the pigs either as premium priced RWA or as conventional meat. Development of antibiotic resistance in pig farming has been studied in national surveys of antibiotic usage and resistance, as well as in experimental studies of groups of pigs, but not in individual pigs followed longitudinally in a commercial pig farm. In this study, a cohort of RWA designated pigs were sampled at 10 time points from birth until slaughter along with pen-mates treated with antibiotics at the same farm. From these samples, the microbiome, determined using 16S sequencing, and the resistome, as determined using qPCR for 82 resistance genes, was investigated, allowing us to examine the difference between RWA pigs and antibiotic treated pigs. We furthermore included 176 additional pigs from six different RWA farms which were sampled at the slaughterhouse as an endpoint to substantiate the cohort as well as for evaluation of intra-farm variability. The results showed a clear effect of age in both the microbiome and resistome composition from early life up until slaughter. As a function of antibiotic treatment, however, we observed a small but significant divergence between treated and untreated animals in their microbiome composition immediately following treatment, which disappeared before 8 weeks of age. The effect on the resistome was evident and an effect of treatment could still be detected at week 8. In animals sampled at the slaughterhouse, we observed no difference in the microbiome or the resistome as a result of treatment status but did see a strong effect of farm origin. Network analysis of co-occurrence of microbiome and resistome data suggested that some resistance genes may be transferred through mobile genetic elements, so we used Hi-C metagenomics on a subset of samples to investigate this. We conclude that antibiotic treatment has a differential effect on the microbiome vs. the resistome and that although resistance gene load is increased by antibiotic treatment load, this effect disappears before slaughter. More studies are needed to elucidate the optimal way to rear pigs without antibiotics.}, } @article {pmid37604918, year = {2023}, author = {Chen, C and Li, L and Wang, Y and Dong, X and Zhao, FJ}, title = {Methylotrophic methanogens and bacteria synergistically demethylate dimethylarsenate in paddy soil and alleviate rice straighthead disease.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {1851-1861}, pmid = {37604918}, issn = {1751-7370}, mesh = {Cacodylic Acid ; Soil/chemistry ; *Oryza/genetics ; RNA, Ribosomal, 16S/genetics ; *Soil Pollutants/analysis ; *Arsenic ; Bacteria/genetics ; *Euryarchaeota/genetics ; Hydrogen ; }, abstract = {Microorganisms play a key role in arsenic (As) biogeochemistry, transforming As species between inorganic and organic forms and different oxidation states. Microbial As methylation is enhanced in anoxic paddy soil, producing primarily dimethylarsenic (DMAs), which can cause rice straighthead disease and large yield losses. DMAs can also be demethylated in paddy soil, but the microorganisms driving this process remain unclear. In this study, we showed that the enrichment culture of methylotrophic methanogens from paddy soil demethylated pentavalent DMAs(V) efficiently. DMAs(V) was reduced to DMAs(III) before demethylation. 16S rRNA gene diversity and metagenomic analysis showed that Methanomassiliicoccus dominated in the enrichment culture, with Methanosarcina and Methanoculleus also being present. We isolated Methanomassiliicoccus luminyensis CZDD1 and Methanosarcina mazei CZ1 from the enrichment culture; the former could partially demethylate trivalent DMAs(III) but not DMAs(V) and the latter could demethylate neither. Addition of strain CZDD1 to the enrichment culture greatly accelerated DMAs(V) demethylation. Demethylation of DMAs(V) in the enrichment culture was suppressed by ampicillin, suggesting the involvement of bacteria. We isolated three anaerobic bacterial strains including Clostridium from the enrichment culture, which could produce hydrogen and reduce DMAs(V) to DMAs(III). Furthermore, augmentation of the Methanomassiliicoccus-Clostridium coculture to a paddy soil decreased DMAs accumulation by rice and alleviated straighthead disease. The results reveal a synergistic relationship whereby anaerobic bacteria reduce DMAs(V) to DMAs(III) for demethylation by Methanomassiliicoccus and also produce hydrogen to promote the growth of Methanomassiliicoccus; enhancing their populations in paddy soil can help alleviate rice straighthead disease.}, } @article {pmid37604238, year = {2023}, author = {Bakre, A and Kariithi, HM and Suarez, DL}, title = {Alternative probe hybridization buffers for target RNA depletion and viral sequence recovery in NGS for poultry samples.}, journal = {Journal of virological methods}, volume = {321}, number = {}, pages = {114793}, doi = {10.1016/j.jviromet.2023.114793}, pmid = {37604238}, issn = {1879-0984}, mesh = {Animals ; *RNA ; Poultry ; Nucleic Acid Hybridization ; *Nucleic Acids ; High-Throughput Nucleotide Sequencing ; }, abstract = {Non-targeted next generation sequencing (NGS) is widely applied to identify the diversity of pathogens in field samples. However, abundance of host RNA (especially rRNA) and other environmental nucleic acids can reduce the abundance of pathogen specific reads of interest, reduce depth of coverage and increase surveillance costs. We presently deplete chicken- and selected bacterial-specific rRNAs in poultry field RNA samples with complementary DNA probes in a commercially available probe hybridization buffer followed by digestion of the RNA:DNA hybrids with RNase H. Because the current buffer is an expensive special order reagent of proprietary composition, we tested in-house and other commercially available buffers and identified a viable alternative that yields equivalent host rRNA depletion and viral-specific reads in poultry samples as the current special order reagent but at a reduced cost.}, } @article {pmid37604210, year = {2023}, author = {Kimseng, H and Rossi, G and Danjean, M and Jimenez-Araya, B and Chaligne, C and Galy, A and Souhail, B and Bert, F and Leflon, V and Fihman, V and Caillault, A and Demontant, V and Seng, S and Trawinski, E and N 'Debi, M and Boizeau, L and Jacquier, H and Ronot, M and Reizine, E and Le Roy, V and Lefort, A and Rodriguez, C and Lepeule, R and Woerther, PL}, title = {Evaluation of the contribution of shotgun metagenomics in the microbiological diagnosis of liver abscesses.}, journal = {The Journal of infection}, volume = {87}, number = {5}, pages = {365-372}, doi = {10.1016/j.jinf.2023.08.004}, pmid = {37604210}, issn = {1532-2742}, abstract = {BACKGROUND: Shotgun metagenomics (SMg) sequencing has gained a considerable interest, as it enables the detection of any microorganisms through a single analysis. Due to the limitations of standard microbiological approaches, the microbial documentation of liver abscesses (LA), which is crucial for their medical management, can be difficult. Here we aimed to compare the performance of SMg with standard approaches for the microbiological documentation of LA.

METHODS: In this retrospective study conducted at two centers, we compared the results of standard microbiology with metagenomics analysis of consecutive LA samples. For samples tested positive for Klebsiella pneumoniae, we compared the analysis of virulence and resistance genes using metagenomics data to whole-genome sequencing of corresponding isolates obtained in culture.

RESULTS: Out of the 62 samples included, standard approaches and SMg yielded documentation in 80.6% and 96.8%, respectively. In 37.1% (23/62) of cases, both methods showed identical results, whereas in 43.5% (27/62) of cases, the samples were positive by both methods, but SMg found additional species in 88.9% (24/27), mostly anaerobes. When the standard approaches were negative, the SMg was able to detect microorganisms in 80.0% of cases (8/10). Overall, SMg identified significantly more microorganisms than culture (414 vs.105; p<0.05). K. pneumoniae genome analysis was able to detect resistance and virulence genes with a level of sensitivity depending on the depth of sequencing.

DISCUSSION: Overall, we showed that SMg had better performance in detecting and identifying microorganisms from LA samples and could help characterizing strain's resistome and virulome. Although still costly and requiring specific skills and expensive equipment, MGs methods are set to expand in the future.}, } @article {pmid37604017, year = {2023}, author = {Xu, N and Qiu, D and Zhang, Z and Wang, Y and Chen, B and Zhang, Q and Wang, T and Hong, W and Zhou, NY and Penuelas, J and Gillings, M and Zhu, YG and Qian, H}, title = {A global atlas of marine antibiotic resistance genes and their expression.}, journal = {Water research}, volume = {244}, number = {}, pages = {120488}, doi = {10.1016/j.watres.2023.120488}, pmid = {37604017}, issn = {1879-2448}, mesh = {Humans ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Phylogeny ; Drug Resistance, Microbial/genetics ; *Microbiota ; }, abstract = {Oceans serve as global reservoirs of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). However, little is known about the traits and expression of ARGs in response to environmental factors. We analyzed 347 metagenomes and 182 metatranscriptomes to determine the distribution, hosts, and expression of ARGs in oceans. Our study found that the diversity and abundance of ARGs varied with latitude and depth. The core marine resistome mainly conferred glycopeptide and multidrug resistance. The hosts of this resistome were mainly limited to the core marine microbiome, with phylogenetic barriers to the horizontal transfer of ARGs, transfers being more frequent within species than between species. Sixty-five percent of the marine ARGs identified were expressed. More than 90% of high-risk ARGs were more likely to be expressed. Anthropogenic activity might affect the expression of ARGs by altering nitrate and phosphate concentrations and ocean temperature. Machine-learning models predict >97% of marine ARGs will change expression by 2100. High-risk ARGs will shift to low latitudes and regions with high anthropogenic activity, such as the Pacific and Atlantic Oceans. Certain ARGs serve a dual role in antibiotic resistance and potentially participate in element cycling, along with other unknown functions. Determining whether changes in ARG expression are beneficial to ecosystems and human health is challenging without comprehensive understanding of their functions. Our study identified a core resistome in the oceans and quantified the expression of ARGs for the development of future control strategies under global change.}, } @article {pmid37603579, year = {2023}, author = {Liu, Y and Zhang, YZ and Imoto, S}, title = {Microbial Gene Ontology informed deep neural network for microbe functionality discovery in human diseases.}, journal = {PloS one}, volume = {18}, number = {8}, pages = {e0290307}, pmid = {37603579}, issn = {1932-6203}, mesh = {Humans ; *Genes, Microbial ; Benchmarking ; Gene Ontology ; *Inflammatory Bowel Diseases/genetics ; Neural Networks, Computer ; }, abstract = {The human microbiome plays a crucial role in human health and is associated with a number of human diseases. Determining microbiome functional roles in human diseases remains a biological challenge due to the high dimensionality of metagenome gene features. However, existing models were limited in providing biological interpretability, where the functional role of microbes in human diseases is unexplored. Here we propose to utilize a neural network-based model incorporating Gene Ontology (GO) relationship network to discover the microbe functionality in human diseases. We use four benchmark datasets, including diabetes, liver cirrhosis, inflammatory bowel disease, and colorectal cancer, to explore the microbe functionality in the human diseases. Our model discovered and visualized the novel candidates' important microbiome genes and their functions by calculating the important score of each gene and GO term in the network. Furthermore, we demonstrate that our model achieves a competitive performance in predicting the disease by comparison with other non-Gene Ontology informed models. The discovered candidates' important microbiome genes and their functions provide novel insights into microbe functional contribution.}, } @article {pmid37603566, year = {2023}, author = {Velasco-Álvarez, JR and Torres Y Torres, N and Chairez, I and Castrejón-Flores, JL}, title = {Microbiome distribution modeling using gradient descent strategies for mock, in vitro and clinical community distributions.}, journal = {PloS one}, volume = {18}, number = {8}, pages = {e0290082}, pmid = {37603566}, issn = {1932-6203}, mesh = {Humans ; *Microbiota ; Metagenome ; Algorithms ; Computer Simulation ; Data Analysis ; }, abstract = {The human gut is home to a complex array of microorganisms interacting with the host and each other, forming a community known as the microbiome. This community has been linked to human health and disease, but understanding the underlying interactions is still challenging for researchers. Standard studies typically use high-throughput sequencing to analyze microbiome distribution in patient samples. Recent advancements in meta-omic data analysis have enabled computational modeling strategies to integrate this information into an in silico model. However, there is a need for improved parameter fitting and data integration features in microbial community modeling. This study proposes a novel alternative strategy utilizing state-of-the-art dynamic flux balance analysis (dFBA) to provide a simple protocol enabling accurate replication of abundance data composition through dynamic parameter estimation and integration of metagenomic data. We used a recurrent optimization algorithm to replicate community distributions from three different sources: mock, in vitro, and clinical microbiome. Our results show an accuracy of 98% and 96% when using in vitro and clinical bacterial abundance distributions, respectively. The proposed modeling scheme allowed us to observe the evolution of metabolites. It could provide a deeper understanding of metabolic interactions while taking advantage of the high contextualization features of GEM schemes to fit the study case. The proposed modeling scheme could improve the approach in cases where external factors determine specific bacterial distributions, such as drug intake.}, } @article {pmid37602733, year = {2023}, author = {Budiš, J and Krampl, W and Kucharík, M and Hekel, R and Goga, A and Sitarčík, J and Lichvár, M and Smol'ak, D and Böhmer, M and Baláž, A and Ďuriš, F and Gazdarica, J and Šoltys, K and Turňa, J and Radvánszky, J and Szemes, T}, title = {SnakeLines: integrated set of computational pipelines for sequencing reads.}, journal = {Journal of integrative bioinformatics}, volume = {20}, number = {3}, pages = {}, pmid = {37602733}, issn = {1613-4516}, mesh = {Reproducibility of Results ; *Software ; *Genomics/methods ; Computational Biology/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {With the rapid growth of massively parallel sequencing technologies, still more laboratories are utilising sequenced DNA fragments for genomic analyses. Interpretation of sequencing data is, however, strongly dependent on bioinformatics processing, which is often too demanding for clinicians and researchers without a computational background. Another problem represents the reproducibility of computational analyses across separated computational centres with inconsistent versions of installed libraries and bioinformatics tools. We propose an easily extensible set of computational pipelines, called SnakeLines, for processing sequencing reads; including mapping, assembly, variant calling, viral identification, transcriptomics, and metagenomics analysis. Individual steps of an analysis, along with methods and their parameters can be readily modified in a single configuration file. Provided pipelines are embedded in virtual environments that ensure isolation of required resources from the host operating system, rapid deployment, and reproducibility of analysis across different Unix-based platforms. SnakeLines is a powerful framework for the automation of bioinformatics analyses, with emphasis on a simple set-up, modifications, extensibility, and reproducibility. The framework is already routinely used in various research projects and their applications, especially in the Slovak national surveillance of SARS-CoV-2.}, } @article {pmid37601730, year = {2023}, author = {Linder, KA and Miceli, MH}, title = {Impact of Metagenomic Next-Generation Sequencing of Plasma Cell-free DNA Testing in the Management of Patients With Suspected Infectious Diseases.}, journal = {Open forum infectious diseases}, volume = {10}, number = {8}, pages = {ofad385}, pmid = {37601730}, issn = {2328-8957}, abstract = {Metagenomic next-generation sequencing (mNGS) of cell-free DNA is an emerging modality for the diagnosis of infectious diseases, but studies on its clinical utility are limited. We conducted a retrospective single-center study including all patients who had plasma mNGS sent at the University of Michigan between 1 January 2021 and 25 July 2022. Test results were assessed for clinical impact. A total of 71 tests were sent on 69 patients; the mean ± SD age was 52 ± 19 years; and 35% of patients were immunocompromised. Forty-five (63%) mNGS test results were positive and 14 (31%) had clinical impact-from starting new antimicrobials (n = 7), discontinuing antimicrobials (n = 4), or changing antimicrobial duration (n = 2) or by affecting surgical decision making (n = 1). Twenty-six (37%) mNGS test results were negative and only 4 (15%) were impactful, leading to discontinuation of antimicrobials. Overall, just 25% of mNGS tests were clinically relevant. There was no significant difference in the proportion of tests that were clinically relevant between negative and positive results (P = .16) or if patients were immunocompromised (P = .57). Plasma mNGS was most frequently impactful (in 50% of patients) when included in the diagnostic workup of cardiovascular infection but less impactful in other clinical syndromes, including fever of unknown origin and pulmonary infection. Our findings underscore the need to further study this testing modality, particularly with prospective research including negative controls, before it is considered for widespread use.}, } @article {pmid37601681, year = {2023}, author = {Wu, X and Tang, Z and Zhao, R and Wang, Y and Wang, X and Liu, S and Zou, H}, title = {Taxonomic and functional profiling of fecal metagenomes for the early detection of colorectal cancer.}, journal = {Frontiers in oncology}, volume = {13}, number = {}, pages = {1218056}, pmid = {37601681}, issn = {2234-943X}, abstract = {OBJECTIVES: This study aimed to identify colorectal cancer (CRC)-associated phylogenetic and functional bacterial features by a large-scale metagenomic sequencing and develop a binomial classifier to accurately distinguish between CRC patients and healthy individuals.

METHODS: We conducted shotgun metagenomic analyses of fecal samples from a ZhongShanMed discovery cohort of 121 CRC and 52 controls and SouthernMed validation cohort of 67 CRC and 44 controls. Taxonomic profiling and quantification were performed by direct sequence alignment against genome taxonomy database (GTDB). High-quality reads were also aligned to IGC datasets to obtain functional profiles defined by Kyoto Encyclopedia of Genes and Genomes (KEGG). A least absolute shrinkage and selection operator (LASSO) classifier was constructed to quantify risk scores of probability of disease and to discriminate CRC from normal for discovery, validation, Fudan, GloriousMed, and HongKong cohorts.

RESULTS: A diverse spectrum of bacterial and fungi species were found to be either enriched (368) or reduced (113) in CRC patients (q<0.05). Similarly, metabolic functions associated with biosynthesis and metabolism of amino acids and fatty acids were significantly altered (q<0.05). The LASSO regression analysis of significant changes in the abundance of microbial species in CRC achieved areas under the receiver operating characteristic curve (AUROCs) of 0.94 and 0.91 in the ZhongShanMed and SouthernMed cohorts, respectively. A further analysis of Fudan, GloriousMed, and HK cohorts using the same classification model also demonstrated AUROC of 0.80, 0.78, and 0.91, respectively. Moreover, major CRC-associated bacterial biomarkers identified in this study were found to be coherently enriched or depleted across 10 metagenomic sequencing studies of gut microbiota.

CONCLUSION: A coherent signature of CRC-associated bacterial biomarkers modeled on LASSO binomial classifier maybe used accurately for early detection of CRC.}, } @article {pmid37601559, year = {2023}, author = {Li, S and Zhou, P and Yang, L and Tang, T and Qin, J and Qian, J and Bo, S and Yu, S}, title = {Clinical Value of Sampling Time of Metagenomic Next-Generation Sequencing in Patients with Severe Pneumonia.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {5263-5274}, pmid = {37601559}, issn = {1178-6973}, abstract = {OBJECTIVE: Severe pneumonia is a common infectious disease with high morbidity and mortality. Early etiological diagnosis is crucial for improving the prognosis. The aim of this study is to evaluate the clinical value of sampling time of mNGS in patients with severe pneumonia.

METHODS: This retrospective study enrolled 105 patients with severe pneumonia. mNGS was performed on bronchoalveolar lavage fluid (BALF). Patients were divided into the sampling time ≤ 72h vs sampling time >72h groups and survivors vs non-survivors groups according to their sampling time and prognosis. Clinical characteristics, the adjustment of antibiotics and clinical prognostic value were evaluated.

RESULTS: Our study showed that, early sampling of mNGS can significantly shorten the mechanical ventilation time (p = 0.007) and hospitalization time (p = 0.004). In the non-survivors group, CURB-65, SOFA, and APACHE II scores were higher. Age (OR: 1.051, 95% CI: 1.004-1.100, p = 0.034), chronic respiratory diseases (OR: 4.639, 95% CI: 1.260-17.082, p = 0.021), immunosuppression (OR: 5.008, 95% CI: 1.617-15.510, p = 0.005) and SOFA score on the day of mNGS sampling (OR: 1.492, 95% CI: 1.212-1.837, p < 0.001) were independent risk factors of in-hospital mortality. The most common pathogens were Klebsiella pneumoniae and Human gammaherpesvirus 4. The proportion of appropriate and targeted antibiotics adjusted was significantly higher than that in the sampling time > 72h group, and the proportion of antifungal and antiviral agents adjusted was lower. In the early sampling group, it was significantly decreased in the CRP, PCT level and NEU% at discharge.

CONCLUSION: This study demonstrated that early sampling of mNGS could shorten the time of mechanical ventilation and hospitalization of patients with severe pneumonia. Patients with higher SOFA score on the day of sampling had a poorer prognosis. It emphasizes that early sampling of mNGS has a positive value.}, } @article {pmid37601557, year = {2023}, author = {Su, ZQ and Rao, WY and Pan, XY and Tang, JX and Fan, MY and Chen, XB and Li, SY}, title = {Multiple Lung Cavity Lesions, Thoracic Wall Abscess and Vertebral Destruction Caused by Streptococcus constellatus Infection: A Case Report.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {5329-5333}, pmid = {37601557}, issn = {1178-6973}, abstract = {Disseminated infection caused by Streptococcus constellatus was seldom occurred. We reported a case of Streptococcus constellatus infection, presenting as multiple pulmonary cavities, thoracic wall abscess and vertebral destruction. The 37-year-old male had recurrent fever, chest wall swelling and pain, and lower limb numbness, he had weak physical condition and previously suffered from poorly controlled diabetes and severe periodontal disease for 3 years. Definite diagnosis of Streptococcus constellatus infection was made by metagenomic next‑generation sequencing (mNGS) in abscess drainage fluid. Systemic antibiotics and thoracic wall drainage were given, and the pulmonary cavity and the thoracic intermuscular abscess were significantly decreased. Few to no study reported the disseminated infection (pulmonary cavities, thoracic wall abscess and vertebral destruction) caused by Streptococcus constellatus. This case report highlighted the importance of mNGS for accurate diagnosis, as well as the timely drainage and antibiotics for effective treatment of Streptococcus constellatus infection.}, } @article {pmid37601386, year = {2023}, author = {Singh, A and Mazahar, S and Chapadgaonkar, SS and Giri, P and Shourie, A}, title = {Phyto-microbiome to mitigate abiotic stress in crop plants.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1210890}, pmid = {37601386}, issn = {1664-302X}, abstract = {Plant-associated microbes include taxonomically diverse communities of bacteria, archaebacteria, fungi, and viruses, which establish integral ecological relationships with the host plant and constitute the phyto-microbiome. The phyto-microbiome not only contributes in normal growth and development of plants but also plays a vital role in the maintenance of plant homeostasis during abiotic stress conditions. Owing to its immense metabolic potential, the phyto-microbiome provides the host plant with the capability to mitigate the abiotic stress through various mechanisms like production of antioxidants, plant growth hormones, bioactive compounds, detoxification of harmful chemicals and toxins, sequestration of reactive oxygen species and other free radicals. A deeper understanding of the structure and functions of the phyto-microbiome and the complex mechanisms of phyto-microbiome mediated abiotic stress mitigation would enable its utilization for abiotic stress alleviation of crop plants and development of stress-resistant crops. This review aims at exploring the potential of phyto-microbiome to alleviate drought, heat, salinity and heavy metal stress in crop plants and finding sustainable solutions to enhance the agricultural productivity. The mechanistic insights into the role of phytomicrobiome in imparting abiotic stress tolerance to plants have been summarized, that would be helpful in the development of novel bioinoculants. The high-throughput modern approaches involving candidate gene identification and target gene modification such as genomics, metagenomics, transcriptomics, metabolomics, and phyto-microbiome based genetic engineering have been discussed in wake of the ever-increasing demand of climate resilient crop plants.}, } @article {pmid37601366, year = {2023}, author = {Konganti, K and Reed, E and Mammel, M and Kayikcioglu, T and Binet, R and Jarvis, K and Ferreira, CM and Bell, RL and Zheng, J and Windsor, AM and Ottesen, A and Grim, CJ and Ramachandran, P}, title = {bettercallsal: better calling of Salmonella serotypes from enrichment cultures using shotgun metagenomic profiling and its application in an outbreak setting.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1200983}, pmid = {37601366}, issn = {1664-302X}, abstract = {Most current Salmonella subtyping analyses rely on whole genome sequencing (WGS), which focuses on the high-resolution analysis of single genomes or multiple single genomes from the isolated colonies on microbiological agar plates. In this study, we introduce bioinformatics innovations for a metagenomic outbreak response workflow that accurately identifies multiple Salmonella serovars at the same time. bettercallsal is one of the first analysis tools to identify multiple Salmonella enterica serotypes from metagenomic or quasi-metagenomic datasets with high accuracy, allowing these isolate-independent methods to be incorporated into surveillance and root cause investigations. It was tested on an in silico benchmark dataset comprising 29 unique Salmonella serovars, 46 non-Salmonella bacterial genomes, and 10 viral genomes at varying read depths and on previously well-characterized and sequenced non-selective primary and selective enrichments of papaya and peach samples from separate outbreak investigations that resulted in the identification of multiple Salmonella serovars using traditional isolate culturing and WGS as well as nucleic acid assays. Analyses were also conducted on these datasets using a custom-built k-mer tool, SeqSero2, and Kallisto to compare serotype calling to bettercallsal. The in silico dataset analyzed with bettercallsal achieved the maximum precision, recall, and accuracy of 100, 83, and 94%, respectively. In the papaya outbreak samples, bettercallsal identified the presence of multiple serovars in agreement with the Luminex[®] xMAP assay results and also identified more serovars per sample, as evidenced by NCBI SNP clustering. In peach outbreak samples, bettercallsal identified two serovars in concordance with k-mer analysis and the Luminex xMAP assay. The genome hit reported by bettercallsal clustered with the chicken isolate genome, as reported by the FDA peach outbreak investigation from sequenced isolates (WGS). Overall, bettercallsal outperformed k-mer, Seqsero2, and Kallisto in identifying multiple serovars from enrichment cultures using shotgun metagenomic sequencing.}, } @article {pmid37601363, year = {2023}, author = {Bing, RG and Willard, DJ and Crosby, JR and Adams, MWW and Kelly, RM}, title = {Whither the genus Caldicellulosiruptor and the order Thermoanaerobacterales: phylogeny, taxonomy, ecology, and phenotype.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1212538}, pmid = {37601363}, issn = {1664-302X}, support = {T32 GM133366/GM/NIGMS NIH HHS/United States ; }, abstract = {The order Thermoanaerobacterales currently consists of fermentative anaerobic bacteria, including the genus Caldicellulosiruptor. Caldicellulosiruptor are represented by thirteen species; all, but one, have closed genome sequences. Interest in these extreme thermophiles has been motivated not only by their high optimal growth temperatures (≥70°C), but also by their ability to hydrolyze polysaccharides including, for some species, both xylan and microcrystalline cellulose. Caldicellulosiruptor species have been isolated from geographically diverse thermal terrestrial environments located in New Zealand, China, Russia, Iceland and North America. Evidence of their presence in other terrestrial locations is apparent from metagenomic signatures, including volcanic ash in permafrost. Here, phylogeny and taxonomy of the genus Caldicellulosiruptor was re-examined in light of new genome sequences. Based on genome analysis of 15 strains, a new order, Caldicellulosiruptorales, is proposed containing the family Caldicellulosiruptoraceae, consisting of two genera, Caldicellulosiruptor and Anaerocellum. Furthermore, the order Thermoanaerobacterales also was re-assessed, using 91 genome-sequenced strains, and should now include the family Thermoanaerobacteraceae containing the genera Thermoanaerobacter, Thermoanaerobacterium, Caldanaerobacter, the family Caldanaerobiaceae containing the genus Caldanaerobius, and the family Calorimonaceae containing the genus Calorimonas. A main outcome of ANI/AAI analysis indicates the need to reclassify several previously designated species in the Thermoanaerobacterales and Caldicellulosiruptorales by condensing them into strains of single species. Comparative genomics of carbohydrate-active enzyme inventories suggested differentiating phenotypic features, even among strains of the same species, reflecting available nutrients and ecological roles in their native biotopes.}, } @article {pmid37601346, year = {2023}, author = {Zhai, J and Wang, Y and Tang, B and Zheng, S and He, S and Zhao, W and Chen, H and Lin, J and Li, F and Bao, Y and Lancuo, Z and Sharshov, K and Liu, C and Wang, W}, title = {Comparative analysis of gut DNA viromes in wild and captive Himalayan vultures.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1120838}, pmid = {37601346}, issn = {1664-302X}, abstract = {INTRODUCTION: Himalayan vultures (Gyps hinalayensis) are widely distributed on the Qinghai-Tibetan Plateau and play a crucial role in maintaining the ecological balance by feeding on decayed corpses of wild and domestic animals. Large-scale culture and metagenomics studies have broadened our understanding of viral diversity in animals' gastrointestinal tracts. However, despite the importance of gut viral communities in regulating bacterial diversity and performing symbiotic functions, no gut viral study has been conducted on Himalayan vultures. Furthermore, the impact of captivity on the gut virome of these vultures remains unknown.

METHODS: In this study, metagenomic sequencing methods targeting DNA of virus-like particles enriched from feces were used to characterize the gut DNA viromes of wild and captive Himalayan vultures.

RESULTS: In total, 22,938 unique viral operational taxonomic units (vOTUs) were identified and assigned to 140 viral genera in 41 viral families. These families included viruses associated with bacteria, animals, plants, insects, and archaea. Phage communities, including Siphoviridae, Microviridae, Myoviridae, Inoviridae, and Herelleviridae, dominated the gut virome of Himalayan vultures. Wild vultures exhibited higher viral richness and diversity compared with those in captivity. The functional capacity of the gut virome was characterized by identifying 93 KEGG pathways, which were significantly enriched in metabolism and genetic information processing. Abundant auxiliary metabolic genes, such as carbohydrate-active enzyme, and antibiotic resistance genes, were also found in the vultures' gut virome.

DISCUSSION: Our findings reveal the complex and diverse viral community present in the gut virome of Himalayan vultures, which varies between wild, and captive states. The DNA virome dataset establishes a baseline for the vultures' gut virome and will serve as a reference for future virus isolation and cultivation. Understanding the impact of captivity on the gut virome contributes to our knowledge of vultures' response to captivity and aids in optimizing their rehabilitation and implementing protective measures.}, } @article {pmid37601341, year = {2023}, author = {Gen-Jiménez, A and Flores-Félix, JD and Rincón-Molina, CI and Manzano-Gomez, LA and Rogel, MA and Ruíz-Valdiviezo, VM and Rincón-Molina, FA and Rincón-Rosales, R}, title = {Enhance of tomato production and induction of changes on the organic profile mediated by Rhizobium biofortification.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1235930}, pmid = {37601341}, issn = {1664-302X}, abstract = {INTRODUCTION: The extensive use of chemical fertilizers has served as a response to the increasing need for crop production in recent decades. While it addresses the demand for food, it has resulted in a decline in crop productivity and a heightened negative environmental impact. In contrast, plant probiotic bacteria (PPB) offer a promising alternative to mitigate the negative consequences of chemical fertilizers. PPB can enhance nutrient availability, promote plant growth, and improve nutrient uptake efficiency, thereby reducing the reliance on chemical fertilizers.

METHODS: This study aimed to evaluate the impact of native Rhizobium strains, specifically Rhizobium calliandrae LBP2-1, Rhizobium mayense NSJP1-1, and Rhizobium jaguaris SJP1- 2, on the growth, quality, and rhizobacterial community of tomato crops. Various mechanisms promoting plant growth were investigated, including phosphate solubilization, siderophore production, indole acetic acid synthesis, and cellulose and cellulase production. Additionally, the study involved the assessment of biofilm formation and root colonization by GFP-tagged strains, conducted a microcosm experiment, and analyzed the microbial community using metagenomics of rhizospheric soil.

RESULTS: The results showed that the rhizobial strains LBP2-1, NSJP1-1 and SJP1-2 had the ability to solubilize dicalcium phosphate, produce siderophores, synthesize indole acetic acid, cellulose production, biofilm production, and root colonization. Inoculation of tomato plants with native Rhizobium strains influenced growth, fruit quality, and plant microbiome composition. Metagenomic analysis showed increased Proteobacteria abundance and altered alpha diversity indices, indicating changes in rhizospheric bacterial community.

DISCUSSION: Our findings demonstrate the potential that native Rhizobium strains have to be used as a plant probiotic in agricultural crops for the generation of safe food and high nutritional value.}, } @article {pmid37600953, year = {2023}, author = {He, S and Wei, J and Feng, J and Liu, D and Wang, N and Chen, L and Xiong, Y}, title = {The application of metagenomic next-generation sequencing in pathogen diagnosis: a bibliometric analysis based on Web of Science.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1112229}, pmid = {37600953}, issn = {2235-2988}, mesh = {Humans ; *Bibliometrics ; High-Throughput Nucleotide Sequencing ; China ; Metagenome ; *Communicable Diseases/diagnosis ; }, abstract = {BACKGROUND: Infectious disease is a large burden on public health globally. Metagenomic next-generation sequencing (mNGS) has become popular as a new tool for pathogen diagnosis with numerous advantages compared to conventional methods. Recently, research on mNGS increases yearly. However, no bibliometric analysis has systematically presented the full spectrum of this research field. Therefore, we reviewed all the publications associated with this topic and performed this study to analyze the comprehensive status and future hotspots of mNGS for infectious disease diagnosis.

METHODS: The literature was searched in the Web of Science Core Collection and screened without year or language restrictions, and the characteristics of the studies were also identified. The outcomes included publication years, study types, journals, countries, authorship, institutions, frontiers, and hotspots with trends. Statistical analysis and visualization were conducted using VOSviewer (version 1.6.16) and CiteSpace (version 6.1. R3).

RESULTS: In total, 325 studies were included in the analysis after screening. Studies were published between 2009 and 2022 with a significantly increasing number from 1 to 118. Most of the studies were original articles and case reports. Frontiers in Cellular and Infection Microbiology and Clinical Infectious Disease were the most commonly cited and co-cited journals. Institutions and researchers from China contributed the most to this field, followed by those from the USA. The hotspots and frontiers of these studies are pneumonia, tuberculosis, and central nervous system infections.

CONCLUSION: This study determined that mNGS is a hot topic in the diagnosis of infectious diseases with development trends and provides insights into researchers, institutions, hotspots and frontiers in mNGS, which can offer references to related researchers and future research.}, } @article {pmid37600944, year = {2023}, author = {Xu, D and Hu, X and Zhang, H and Gao, Q and Guo, C and Liu, S and Tang, B and Zhang, G and Zhang, C and Tang, M}, title = {Analysis of risk factors for deep vein thrombosis after spinal infection surgery and construction of a nomogram preoperative prediction model.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1220456}, pmid = {37600944}, issn = {2235-2988}, mesh = {Humans ; Models, Statistical ; Nomograms ; Prognosis ; Risk Factors ; *Spinal Diseases ; *Venous Thrombosis/epidemiology/etiology ; }, abstract = {OBJECTIVE: To investigate the differences in postoperative deep venous thrombosis (DVT) between patients with spinal infection and those with non-infected spinal disease; to construct a clinical prediction model using patients' preoperative clinical information and routine laboratory indicators to predict the likelihood of DVT after surgery.

METHOD: According to the inclusion criteria, 314 cases of spinal infection (SINF) and 314 cases of non-infected spinal disease (NSINF) were collected from January 1, 2016 to December 31, 2021 at Xiangya Hospital, Central South University, and the differences between the two groups in terms of postoperative DVT were analyzed by chi-square test. The spinal infection cases were divided into a thrombotic group (DVT) and a non-thrombotic group (NDVT) according to whether they developed DVT after surgery. Pre-operative clinical information and routine laboratory indicators of patients in the DVT and NDVT groups were used to compare the differences between groups for each variable, and variables with predictive significance were screened out by least absolute shrinkage and operator selection (LASSO) regression analysis, and a predictive model and nomogram of postoperative DVT was established using multi-factor logistic regression, with a Hosmer- Lemeshow goodness-of-fit test was used to plot the calibration curve of the model, and the predictive effect of the model was evaluated by the area under the ROC curve (AUC).

RESULT: The incidence of postoperative DVT in patients with spinal infection was 28%, significantly higher than 16% in the NSINF group, and statistically different from the NSINF group (P < 0.000). Five predictor variables for postoperative DVT in patients with spinal infection were screened by LASSO regression, and plotted as a nomogram. Calibration curves showed that the model was a good fit. The AUC of the predicted model was 0.8457 in the training cohort and 0.7917 in the validation cohort.

CONCLUSION: In this study, a nomogram prediction model was developed for predicting postoperative DVT in patients with spinal infection. The nomogram included five preoperative predictor variables, which would effectively predict the likelihood of DVT after spinal infection and may have greater clinical value for the treatment and prevention of postoperative DVT.}, } @article {pmid37600604, year = {2023}, author = {Busing, JD and Fouladi, F and Bulik-Sullivan, EC and Carroll, IM and Fodor, AA and Thomsen, KF and Gulati, AS and Nicholson, MR}, title = {Gut Microbial Changes Following Fecal Microbiota Transplantation for D-Lactic Acidosis in Two Children.}, journal = {JPGN reports}, volume = {4}, number = {3}, pages = {e319}, pmid = {37600604}, issn = {2691-171X}, abstract = {D-lactic acidosis (D-LA) is an uncommon complication of short bowel syndrome characterized by elevated plasma D-lactate and encephalopathy. Treatments include rehydration, dietary carbohydrate restriction, and antibiotics to alter the gut microbiota. Fecal microbiota transplantation (FMT) has recently been used in children to successfully treat D-LA. We compared the clinical course and then utilized metagenomic shotgun sequencing to describe changes in the composition and function of the intestinal microbiome following FMT in 2 patients with recurrent D-LA. FMT altered the composition of the fecal microbiota in these 2 patients with recurrent D-LA, though not necessarily in a consistent manner. Importantly, microbial metabolic pathways were also impacted by FMT, which may be critical for achieving desired clinical outcomes. While sample size limits the generalizability of our results, these findings set the stage for further understanding of the role of microbes in the pathogenesis of recurrent D-LA.}, } @article {pmid37600181, year = {2023}, author = {Liu, C and Yu, J and Ying, J and Zhang, K and Hu, Z and Liu, Z and Chen, S}, title = {Integrated metagenomics and metabolomics analysis reveals changes in the microbiome and metabolites in the rhizosphere soil of Fritillaria unibracteata.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1223720}, pmid = {37600181}, issn = {1664-462X}, abstract = {Fritillaria unibracteata (FU) is a renowned herb in China that requires strict growth conditions in its cultivation process. During this process, the soil microorganisms and their metabolites may directly affect the growth and development of FU, for example, the pathogen infection and sipeimine production. However, few systematic studies have reported the changes in the microbiome and metabolites during FU cultivation thus far. In this work, we simultaneously used metagenomics and metabolomics technology to monitor the changes in microbial communities and metabolites in the rhizosphere of FU during its cultivation for one, two, and three years. Moreover, the interaction between microorganisms and metabolites was investigated by co-occurrence network analysis. The results showed that the microbial composition between the three cultivation-year groups was significantly different (2020-2022). The dominant genera changed from Pseudomonas and Botrytis in CC1 to Mycolicibacterium and Pseudogymnoascus in CC3. The relative abundances of beneficial microorganisms decreased, while the relative abundances of harmful microorganisms showed an increasing trend. The metabolomics results showed that significant changes of the of metabolite composition were observed in the rhizosphere soil, and the relative abundances of some beneficial metabolites showed a decreasing trend. In this study, we discussed the changes in the microbiome and metabolites during the three-year cultivation of FU and revealed the relationship between microorganisms and metabolites. This work provides a reference for the efficient and sustainable cultivation of FU.}, } @article {pmid37599833, year = {2023}, author = {Attaye, I and Lassen, PB and Adriouch, S and Steinbach, E and Patiño-Navarrete, R and Davids, M and Alili, R and Jacques, F and Benzeguir, S and Belda, E and Nemet, I and Anderson, JT and Alexandre-Heymann, L and Greyling, A and Larger, E and Hazen, SL and van Oppenraaij, SL and Tremaroli, V and Beck, K and Bergh, PO and Bäckhed, F and Ten Brincke, SPM and Herrema, H and Groen, AK and Pinto-Sietsma, SJ and Clément, K and Nieuwdorp, M}, title = {Protein supplementation changes gut microbial diversity and derived metabolites in subjects with type 2 diabetes.}, journal = {iScience}, volume = {26}, number = {8}, pages = {107471}, pmid = {37599833}, issn = {2589-0042}, abstract = {High-protein diets are promoted for individuals with type 2 diabetes (T2D). However, effects of dietary protein interventions on (gut-derived) metabolites in T2D remains understudied. We therefore performed a multi-center, randomized-controlled, isocaloric protein intervention with 151 participants following either 12-week high-protein (HP; 30Energy %, N = 78) vs. low-protein (LP; 10 Energy%, N = 73) diet. Primary objectives were dietary effects on glycemic control which were determined via glycemic excursions, continuous glucose monitors and HbA1c. Secondary objectives were impact of diet on gut microbiota composition and -derived metabolites which were determined by shotgun-metagenomics and mass spectrometry. Analyses were performed using delta changes adjusting for center, baseline, and kidney function when appropriate. This study found that a short-term 12-week isocaloric protein modulation does not affect glycemic parameters or weight in metformin-treated T2D. However, the HP diet slightly worsened kidney function, increased alpha-diversity, and production of potentially harmful microbiota-dependent metabolites, which may affect host metabolism upon prolonged exposure.}, } @article {pmid37599672, year = {2023}, author = {Castilho, TJC and Almeida, GHDR and Mello, EVSL and Campos, ACL}, title = {Metagenomics of microbiota following probiotic supplementation in rats subjected to intestinal anastomosis.}, journal = {Surgery open science}, volume = {14}, number = {}, pages = {22-30}, pmid = {37599672}, issn = {2589-8450}, abstract = {BACKGROUND: The use of probiotics positively modifies the composition and function of the intestinal flora, decreasing inflammation, and these changes improve the quality of intestinal anastomosis. Therefore, the objective of this study was to evaluate the metagenomics of the microbial community after probiotic supplementation in rats subjected to intestinal anastomosis.

METHODS: The probiotic chosen for this study was composed of the strains Lactobacillus paracasei LPC37, Bifidobacterium lactis HN0019, Lactobacillus rhamnosus HN001 and Lactobacillus acidophilus NCFM. Both groups underwent two colostomies, one in the right colon and the second in the rectosigmoid colon, followed by anastomosis with eight interrupted stitches. The rats were killed on the fifth day of PO. Changes in the intestinal microbiota were evaluated by means of a metagenomic study that evaluated bacterial alpha and beta diversity indices.

RESULTS: Although there were no significant differences for any alpha diversity index, changes were observed for beta diversity indexes in the microbiota of rats. The group that received the probiotic preserved and even increased the abundance of beneficial bacterial genera and, at the same time, decreased the abundance of potentially pathogenic bacteria, promoting a favorable environment for anastomoses' healing.

CONCLUSION: The use of probiotics had a positive impact on the quality of the intestinal microbiota.}, } @article {pmid37599091, year = {2023}, author = {Arrington, EC and Tarn, J and Kittner, HE and Kivenson, V and Liu, RM and Valentine, DL}, title = {Methylated cycloalkanes fuel a novel genus in the Porticoccaceae family (Ca. Reddybacter gen. nov).}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {2958-2971}, doi = {10.1111/1462-2920.16474}, pmid = {37599091}, issn = {1462-2920}, support = {OAC-1928147//National Science Foundation/ ; OCE-1634478//National Science Foundation/ ; OCE-1756947//National Science Foundation/ ; OCE-2126625//National Science Foundation/ ; }, mesh = {Geologic Sediments/microbiology ; *Cycloparaffins ; Hydrocarbons/metabolism ; Seawater/microbiology ; *Microbiota ; *Gammaproteobacteria/genetics ; *Petroleum/metabolism ; Gulf of Mexico ; *Petroleum Pollution ; Biodegradation, Environmental ; }, abstract = {Cycloalkanes are abundant and toxic compounds in subsurface petroleum reservoirs and their fate is important to ecosystems impacted by natural oil seeps and spills. This study focuses on the microbial metabolism of methylcyclohexane (MCH) and methylcyclopentane (MCP) in the deep Gulf of Mexico. MCH and MCP are often abundant cycloalkanes observed in petroleum and will dissolve into the water column when introduced at the seafloor via a spill or natural seep. We conducted incubations with deep Gulf of Mexico (GOM) seawater amended with MCH and MCP at four stations. Within incubations with active respiration of MCH and MCP, we found that a novel genus of bacteria belonging to the Porticoccaceae family (Candidatus Reddybacter) dominated the microbial community. Using metagenome-assembled genomes, we reconstructed the central metabolism of Candidatus Reddybacter, identifying a novel clade of the particulate hydrocarbon monooxygenase (pmo) that may play a central role in MCH and MCP metabolism. Through comparative analysis of 174 genomes, we parsed the taxonomy of the Porticoccaceae family and found evidence suggesting the acquisition of pmo and other genes related to the degradation of cyclic and branched hydrophobic compounds were likely key events in the ecology and evolution of this group of organisms.}, } @article {pmid37598984, year = {2023}, author = {Jian, J and Yuan, Y and Vilatersana, R and Li, L and Wang, Y and Zhang, W and Song, Z and Kong, H and Peter Comes, H and Yang, J}, title = {Phylogenomic and population genomic analyses reveal the spatial-temporal dynamics of diversification of the Nigella arvensis complex (Ranunculaceae) in the Aegean archipelago.}, journal = {Molecular phylogenetics and evolution}, volume = {188}, number = {}, pages = {107908}, doi = {10.1016/j.ympev.2023.107908}, pmid = {37598984}, issn = {1095-9513}, mesh = {*Ranunculaceae ; *Nigella ; Phylogeny ; Metagenomics ; Genomics ; }, abstract = {The continental-shelf islands of the Aegean Sea provide an ideal geographical setting for evolutionary-biogeographical studies but disentangling the relationships between palaeogeographical history and the times, orders of modes of taxon divergence is not straightforward. Here, we used phylogenomic and population genomic approaches, based on orthologous gene sequences and transcriptome-derived SNP data, to reconstruct the spatial-temporal evolution of the Aegean Nigella arvensis complex (Ranunculaceae; 11 out of 12 taxa). The group's early diversification in the Early/Mid-Pliocene (c. 3.77 Mya) resulted in three main lineages (Greek mainland vs. central Aegean + Turkish mainland/eastern Aegean islands), while all extant taxa are of Late Plio-/Early Pleistocene origin (c. 3.30-1.59 Mya). Demographic modelling of the outcrossing taxa uncovered disparate modes of (sub)speciation, including divergence with gene flow on the Greek mainland, para- or peripatric diversification across eastern Aegean islands, and a 'mixing-isolation-mixing (MIM)' mode of subspeciation in the Cyclades. The two selfing species (N. stricta, N. doerfleri) evolved independently from the outcrossers. Present-day island configurations are clearly insufficient to explain the spatial-temporal history of lineage diversification and modes of (sub)speciation in Aegean Nigella. Moreover, our identification of positively selected genes in almost all taxa calls into question that this plant group represents a case of 'non-adaptive' radiation. Our study revealed an episodic diversification history of the N. arvensis complex, giving new insight into the modes and drivers of island speciation and adaption across multiple spatiotemporal scales.}, } @article {pmid37598930, year = {2023}, author = {Sajjad, B and Rasool, K and Siddique, A and Jabbar, KA and El-Malaha, SS and Sohail, MU and Almomani, F and Alfarra, MR}, title = {Size-resolved ambient bioaerosols concentration, antibiotic resistance, and community composition during autumn and winter seasons in Qatar.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {336}, number = {}, pages = {122401}, doi = {10.1016/j.envpol.2023.122401}, pmid = {37598930}, issn = {1873-6424}, abstract = {This study investigates the size distribution, microbial composition, and antibiotic resistance (ABR) of airborne bioaerosols at a suburban location in Doha, Qatar between October 2021 and January 2022. Samples were collected using an Andersen six-stage viable cascade impactor and a liquid impinger. Findings showed that the mean bacteria concentration (464 CFU/m[3]) was significantly higher than that of fungi (242 CFU/m[3]) during the study period. Both bacteria and fungi were most abundant in the aerodynamic size fractions of 1.10-2.21 μm, with peak concentrations observed in the mornings and lowest concentrations in the afternoons across all size fractions. A total of 24 different culturable species were identified, with the most abundant ones being Pasteurella pneumotropica (9.71%), Pantoea spp. 1 (8.73%), and Proteus penneri (7.77%) spp. At the phylum level, the bacterial community configurations during the autumn and winter seasons were nearly identical as revealed by molecular genomics, with Proteobacteria being the most predominant, followed by Firmicutes, Bacteroidetes, Acidobacteriota, and Planctomycetota. However, there was a significant variation in dominant genera between autumn and winter. The most abundant genera included Sphingomonas, Paraburkholderia, Comamonas, Bacillus, and Lysinibacillus. Several bacterial genera identified in this study have important public health and ecological implications, including the risk of respiratory tract infections. Furthermore, the study found that ABR was highest in December, with bioaerosols exhibiting resistance to at least 5 out of 10 antibiotics, and 100% resistance to Metronidazole in all samples. Metagenomics analysis revealed the presence of various airborne bacteria that were not detected through culture-dependent methods. This study provides valuable insights into the airborne microbial composition, temporal variability and ABR in the Arabian Gulf region.}, } @article {pmid37598621, year = {2023}, author = {Zhuang, BB and Chen, J and Zhang, Q and Zhang, GL and Shi, SS}, title = {Diagnosis of pituitary abscess and treatment via transsphenoidal surgery: experience from 15 cases.}, journal = {Neuro-Chirurgie}, volume = {69}, number = {5}, pages = {101478}, doi = {10.1016/j.neuchi.2023.101478}, pmid = {37598621}, issn = {1773-0619}, abstract = {OBJECTIVE: Pituitary abscess is an often misdiagnosed, rare clinical disorder. To improve diagnostic accuracy and the efficacy of surgical and antibiotic therapy for patients with pituitary abscess, herein, we retrospectively reviewed 15 patients who presented with pituitary abscesses from 2005 to 2022.

DESIGN: Retrospective study.

PATIENTS: Fifteen patients underwent transsphenoidal surgery and received antibiotic treatment.

MEASUREMENTS: Complete details regarding medical history, clinical manifestations, laboratory examinations, imaging studies, and treatment strategies were obtained for all patients.

RESULTS: Most patients presented with hypopituitarism and headaches, while some presented with fever, visual disturbances, and diabetes insipidus (DI). Abscesses showed significant annular enhancement post gadolinium injection. In most patients, pituitary abscess can be cured via microscopic or endoscopic drainage of the abscess followed by antibiotic treatment. Complete cure of pituitary abscess was observed in nine patients, with six cases of prolonged hypopituitarism and only one case of recurrence. Long-term hormone replacement therapy was effective in the postoperative management of hypopituitarism.

CONCLUSIONS: The typical manifestations of pituitary abscess include hypopituitarism and headaches; the presence of an enhanced ring at the edge of the mass on contrast-enhanced magnetic resonance images (MRI) is highly suggestive of pituitary abscess. We recommend antibiotic treatment for 4-6 weeks postoperatively, based on the results of bacterial cultures or metagenomic next-generation sequencing (mNGS).}, } @article {pmid37598547, year = {2023}, author = {Liu, C and Mo, T and Zhong, J and Chen, H and Xu, H and Yang, X and Li, Y}, title = {Synergistic benefits of lime and 3,4-dimethylpyrazole phosphate application to mitigate the nitrous oxide emissions from acidic soils.}, journal = {Ecotoxicology and environmental safety}, volume = {263}, number = {}, pages = {115387}, doi = {10.1016/j.ecoenv.2023.115387}, pmid = {37598547}, issn = {1090-2414}, mesh = {*Soil ; *Phosphates ; Nitrous Oxide ; Dimethylphenylpiperazinium Iodide ; }, abstract = {Acidic soils cover approximately 50 % of the arable land with high N2O emission potential. 3,4-dimethylpyrazole phosphate (DMPP) inhibits N2O emission from soils; however, its efficiency is affected by acidity. Liming is used for soil conditioning to ameliorate the effects of acidity. In the present study, we investigated the effects of liming on the efficiency of DMPP in inhibiting N2O emission in acidic soils and the mechanisms involved. We evaluated the impact of liming, DMPP, and combined application and its microbial responses in two acidic soils from Zengcheng (ZC) and Shaoguan (SG) City, Guangdong Province, China. Soils were subjected to four treatments: un-limed soil (low soil pH) + urea (LU), un-limed soil + urea + DMPP (LD), limed soil (high soil pH) + urea (HU), and limed soil + urea + DMPP (HD) for analyses of the mineral N, N2O emissions, and full-length 16S and metagenome sequencing. The results revealed that, HU significantly decreased and increased the N2O emission by 17.8 % and 235.0 % in ZC and SG, respectively, compared with LU. This was caused by a trade-off between N2O production and consumption after liming, where microbial communities and N-cycling functional genes show various compositions in different acidic soils. LD reduced N2O emission by 23.5 % in ZC, whereas decreased 1.5 % was observed in SG. Interestingly, DMPP efficiency considerably improved after liming in two acidic soils. Compared with LU, HD significantly reduced N2O emissions by 61.2 % and 48.5 % in ZC and SG, respectively. Synergy of mitigation efficiency was observed by lime and DMPP application, which was attributed to the changes in the dominant nitrifiers and the increase in N2O consumption by denitrifiers. The combined application of lime and DMPP is a high-efficiency strategy for N2O mitigation can ensure agricultural sustainability in acidic arable soils with minimal environmental damage.}, } @article {pmid37597851, year = {2023}, author = {Li, J and Guo, Y and Liu, J and Guo, F and Du, L and Yang, Y and Li, X and Ma, Y}, title = {Depicting the landscape of gut microbial-metabolic interaction and microbial-host immune heterogeneity in deficient and proficient DNA mismatch repair colorectal cancers.}, journal = {Journal for immunotherapy of cancer}, volume = {11}, number = {8}, pages = {}, pmid = {37597851}, issn = {2051-1426}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; CD8-Positive T-Lymphocytes ; DNA Mismatch Repair/genetics ; Succinic Acid ; Lactic Acid ; *Colorectal Neoplasms/genetics ; }, abstract = {BACKGROUND: Accumulating evidence has indicated the role of gut microbiota in remodeling host immune signatures, but various interplays underlying colorectal cancers (CRC) with deficient DNA mismatch repair (dMMR) and proficient DNA mismatch repair (pMMR) remain poorly understood. This study aims to decipher the gut microbiome-host immune interactions between dMMR and pMMR CRC.

METHOD: We performed metagenomic sequencing and metabolomic analysis of fecal samples from a cohort encompassing 455 participants, including 21 dMMR CRC, 207 pMMR CRC, and 227 healthy controls. Among them, 50 tumor samples collected from 5 dMMR CRC and 45 pMMR CRC were conducted bulk RNA sequencing.

RESULTS: Pronounced microbiota and metabolic heterogeneity were identified with 211 dMMR-enriched species, such as Fusobacterium nucleatum and Akkermansia muciniphila, 2 dMMR-depleted species, such as Flavonifractor plautii, 13 dMMR-enriched metabolites, such as retinoic acid, and 77 dMMR-depleted metabolites, such as lactic acid, succinic acid, and 2,3-dihydroxyvaleric acid. F. plautii was enriched in pMMR CRC and it was positively associated with fatty acid degradation, which might account for the accumulation of dMMR-depleted metabolites classified as short chain organic acid (lactic acid, succinic acid, and 2,3-dihydroxyvaleric acid) in pMMR CRC. The microbial-metabolic association analysis revealed the characterization of pMMR CRC as the accumulation of lactate induced by the depletion of specific gut microbiota which was negatively associated with antitumor immune, whereas the nucleotide metabolism and peptide degradation mediated by dMMR-enriched species characterized dMMR CRC. MMR-specific metabolic landscapes were related to distinctive immune features, such as CD8[+] T cells, dendritic cells and M2-like macrophages.

CONCLUSIONS: Our mutiomics results delineate a heterogeneous landscape of microbiome-host immune interactions within dMMR and pMMR CRC from aspects of bacterial communities, metabolic features, and correlation with immunocyte compartment, which infers the underlying mechanism of heterogeneous immune responses.}, } @article {pmid37597746, year = {2023}, author = {Gu, W and Wu, S and Liu, X and Wang, L and Wang, X and Qiu, Q and Wang, G}, title = {Algal-bacterial consortium promotes carbon sink formation in saline environment.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2023.08.004}, pmid = {37597746}, issn = {2090-1224}, abstract = {INTRODUCTION: The level of atmospheric CO2 has continuously been increasing and the resulting greenhouse effects are receiving attention globally. Carbon removal from the atmosphere occurs naturally in various ecosystems. Among them, saline environments contribute significantly to the global carbon cycle. Carbonate deposits in the sediments of salt lakes are omnipresent, and the biological effects, especially driven by halophilic microalgae and bacteria, on carbonate formation remain to be elucidated.

OBJECTIVES: The present study aims to characterize the carbonates formed in saline environments and demonstrate the mechanisms underlying biological-driven CO2 removal via microalgal-bacterial consortium.

METHODS: The carbonates naturally formed in saline environments were collected and analyzed. Two saline representative organisms, the photosynthetic microalga Dunaliella salina and its mutualistic halophilic bacteria Nesterenkonia sp. were isolated from the inhabiting saline environment and co-cultivated to study their biological effects on carbonates precipitation and isotopic composition. During this process, electrochemical parameters and Ca[2+] flux, and expression of genes related to CaCO3 formation were analyzed. Genome sequencing and metagenomic analysis were conducted to provide molecular evidence.

RESULTS: The results showed that natural saline sediments are enriched with CaCO3 and enrichment of genes related to photosynthesis and ureolysis. The co-cultivation stimulated 54.54% increase in CaCO3 precipitation and significantly promoted the absorption of external CO2 by 49.63%. A pH gradient was formed between the bacteria and algae culture, creating 150.22 mV of electronic potential, which might promote Ca[2+] movement toward D. salina cells. Based on the results of lab-scale induction and [13]C analysis, a theoretical calculation indicates a non-negligible amount of 0.16 and 2.3 Tg C/year carbon sequestration in China and global saline lakes, respectively.

CONCLUSION: The combined effects of these two typical representative species have contributed to the carbon sequestration in saline environments, by promoting Ca[2+] influx and increase of pH via microalgal and bacterial metabolic processes.}, } @article {pmid37597572, year = {2023}, author = {Joslin, GR and Barber, DG and Aston, L and Liu, P and Kuloyo, O and Oentoro, K and Liu, J and Baugh, AV and Fedenko, JR and Melas, I and Hamilton, PG and Allen, DJ and Tennant, RK}, title = {Metagenomic analysis of ethylene glycol contamination in anaerobic digestion.}, journal = {Bioresource technology}, volume = {387}, number = {}, pages = {129683}, doi = {10.1016/j.biortech.2023.129683}, pmid = {37597572}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Metagenome ; *Microbiota ; Biofuels ; Ethylene Glycols ; }, abstract = {Anaerobic digestion is an established method for the biological conversion of waste feedstocks to biogas and biomethane. While anaerobic digestion is an excellent waste management technique, it can be susceptible to toxins and pollutants from contaminated feedstocks, which may have a detrimental impact on a digester's efficiency and productivity. Ethylene glycol (EG) is readily used in the heat-transfer loops of anaerobic digestion facilities to maintain reactor temperature. Failure of the structural integrity of these heat transfer loops can cause EG to leak into the digester, potentially causing a decrease in the resultant gas yields. Batch fermentations were incubated with 0, 10, 100 and 500 ppm (parts per million) of EG, and analysis showed that the EG was completely metabolised by the digester microbiome. The concentrations of EG tested showed significant increases in gas yields, however there were no significant changes to the digester microbiome.}, } @article {pmid37597444, year = {2023}, author = {Heinze, BM and Küsel, K and Jehmlich, N and von Bergen, M and Taubert, M}, title = {Metabolic versatility enables sulfur-oxidizers to dominate primary production in groundwater.}, journal = {Water research}, volume = {244}, number = {}, pages = {120426}, doi = {10.1016/j.watres.2023.120426}, pmid = {37597444}, issn = {1879-2448}, mesh = {Carbon Dioxide/metabolism ; Bacteria/metabolism ; *Microbiota ; Sulfur/metabolism ; *Groundwater/chemistry ; }, abstract = {High rates of CO2 fixation and the genetic potential of various groundwater microbes for autotrophic activity have shown that primary production is an important source of organic C in groundwater ecosystems. However, the contribution of specific chemolithoautotrophic groups such as S-oxidizing bacteria (SOB) to groundwater primary production and their adaptation strategies remain largely unknown. Here, we stimulated anoxic groundwater microcosms with reduced S and sampled the microbial community after 1, 3 and 6 weeks. Genome-resolved metaproteomics was combined with 50at-% [13]CO2 stable isotope probing to follow the C flux through the microbial food web and infer traits expressed by active SOB in the groundwater microcosms. Already after 7 days, 90% of the total microbial biomass C in the microcosms was replaced by CO2-derived C, increasing to 97% at the end of incubation. Stable Isotope Cluster Analysis revealed active autotrophs, characterized by a uniform [13]C-incorporation of 45% in their peptides, to dominate the microbial community throughout incubation. Mixo- and heterotrophs, characterized by 10 to 40% [13]C-incorporation, utilized the primarily produced organic C. Interestingly, obligate autotrophs affiliated with Sulfuricella and Sulfuritalea contained traits enabling the storage of elemental S in globules to maintain primary production under energy limitation. Others related to Sulfurimonas seemed to rapidly utilize substrates for fast proliferation, and most autotrophs further maximized their energy yield via efficient denitrification and the potential for H2 oxidation. Mixotrophic SOB, belonging to Curvibacter or Polaromonas, enhanced metabolic flexibility by using organic compounds to satisfy their C requirements. Time series data spanning eight years further revealed that key taxa of our microcosms composed up to 15% of the microbial groundwater community, demonstrating their in-situ importance. This showed that SOB, by using different metabolic strategies, are able to account for high rates of primary production in groundwater, especially at sites limited to geogenic nutrient sources. The widespread presence of SOB with traits such as S storage, H2 oxidation, and organic C utilization in many aquatic habitats further suggested that metabolic versatility governs S-fueled primary production in the environment.}, } @article {pmid37597391, year = {2023}, author = {Yao, Y and Wei, Y and Li, J and Han, R and Jing, C and Liu, R and Niu, Q}, title = {Microbial electron flow promotes naphthalene degradation in anaerobic digestion in the presence of nitrate electron acceptor: Focus on electron flow regulation and microbial interaction succession.}, journal = {Journal of hazardous materials}, volume = {459}, number = {}, pages = {132293}, doi = {10.1016/j.jhazmat.2023.132293}, pmid = {37597391}, issn = {1873-3336}, mesh = {Humans ; *Nitrates ; Anaerobiosis ; *Electrons ; Organic Chemicals ; Naphthalenes ; Microbial Interactions ; Oxidants ; }, abstract = {Microbial electron flow (MEF) is produced from microbial degradation of organic compounds. Regulating MEF to promote organic pollutants biodegradation such as naphthalene (Nap) is a potential way but remains a lack of theoretical basis. Here, we regulated MEF by adding electron acceptor NO3[-] to achieve 2.6 times increase of Nap biodegradation with cyclodextrin as co-metabolism carbon source. With the NO3[-] addition, the genes inhibited by Nap of electron generation significantly up-regulated. Especially, key genes ubiD and nahD for anaerobic Nap degradation significantly up-regulated respectively 3.7 times and 6.7 times. Moreover, the ability of electron transfer in MEF was also improved consistent with 7.2 times increase of electron transfer system (ETS) activity. Furthermore, total 60 metagenome-assembled genomes (MAGs) were reconstructed through the metagenomic sequencing data with assembly and binning strategies. Interestingly, it was also first found that the Klebsiella MAG. SDU (Shandong University) 14 had the ability of simultaneous Nap biodegradation and denitrification. Our results firstly offered an effective method of regulating MEF to promote polycyclic aromatic hydrocarbons (PAHs) degradation and simultaneous methanogenesis.}, } @article {pmid37597294, year = {2023}, author = {Liu, Y and Yuan, TQ and Zheng, JW and Li, DW and Jiao, YH and Li, HY and Li, RM and Yang, WD}, title = {Exposure to okadaic acid could disrupt the colonic microenvironment in rats.}, journal = {Ecotoxicology and environmental safety}, volume = {263}, number = {}, pages = {115376}, doi = {10.1016/j.ecoenv.2023.115376}, pmid = {37597294}, issn = {1090-2414}, mesh = {Animals ; Rats ; Okadaic Acid/toxicity ; Body Weight ; Colon ; Escherichia coli/genetics ; }, abstract = {Okadaic acid (OA) is one of the most prevalent marine phycotoxin with complex toxicity, which can lead to toxic symptoms such as diarrhea, vomiting, nausea, abdominal pain, and gastrointestinal discomfort. Studies have shown that the main affected tissue of OA is digestive tract. However, its toxic mechanism is not yet fully understood. In this study, we investigated the changes that occurred in the epithelial microenvironment following OA exposure, including the epithelial barrier and gut bacteria. We found that impaired epithelial cell junctions, mucus layer destruction, cytoskeletal remodeling, and increased bacterial invasion occurred in colon of rats after OA exposure. At the same time, the gut bacteria decreased in the abundance of beneficial bacteria and increased in the abundance of pathogenic bacteria, and there was a significant negative correlation between the abundance of pathogenic bacteria represented by Escherichia/Shigella and animal body weight. Metagenomic analysis inferred that Escherichia coli and Shigella spp. in Escherichia/Shigella may be involved in the process of cytoskeletal remodeling and mucosal layer damage caused by OA. Although more evidence is needed, our results suggest that opportunistic pathogens may be involved in the complex toxicity of OA during OA-induced epithelial barrier damage.}, } @article {pmid37596696, year = {2023}, author = {Pavia, MJ and Chede, A and Wu, Z and Cadillo-Quiroz, H and Zhu, Q}, title = {BinaRena: a dedicated interactive platform for human-guided exploration and binning of metagenomes.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {186}, pmid = {37596696}, issn = {2049-2618}, mesh = {Humans ; *Metagenome/genetics ; *Microbiota/genetics ; Algorithms ; Biological Evolution ; Diarrhea ; }, abstract = {BACKGROUND: Exploring metagenomic contigs and "binning" them into metagenome-assembled genomes (MAGs) are essential for the delineation of functional and evolutionary guilds within microbial communities. Despite the advances in automated binning algorithms, their capabilities in recovering MAGs with accuracy and biological relevance are so far limited. Researchers often find that human involvement is necessary to achieve representative binning results. This manual process however is expertise demanding and labor intensive, and it deserves to be supported by software infrastructure.

RESULTS: We present BinaRena, a comprehensive and versatile graphic interface dedicated to aiding human operators to explore metagenome assemblies via customizable visualization and to associate contigs with bins. Contigs are rendered as an interactive scatter plot based on various data types, including sequence metrics, coverage profiles, taxonomic assignments, and functional annotations. Various contig-level operations are permitted, such as selection, masking, highlighting, focusing, and searching. Binning plans can be conveniently edited, inspected, and compared visually or using metrics including silhouette coefficient and adjusted Rand index. Completeness and contamination of user-selected contigs can be calculated in real time. In demonstration of BinaRena's usability, we show that it facilitated biological pattern discovery, hypothesis generation, and bin refinement in a complex tropical peatland metagenome. It enabled isolation of pathogenic genomes within closely related populations from the gut microbiota of diarrheal human subjects. It significantly improved overall binning quality after curating results of automated binners using a simulated marine dataset.

CONCLUSIONS: BinaRena is an installation-free, dependency-free, client-end web application that operates directly in any modern web browser, facilitating ease of deployment and accessibility for researchers of all skill levels. The program is hosted at https://github.com/qiyunlab/binarena , together with documentation, tutorials, example data, and a live demo. It effectively supports human researchers in intuitive interpretation and fine tuning of metagenomic data. Video Abstract.}, } @article {pmid37596690, year = {2023}, author = {Debeljak, P and Bayer, B and Sun, Y and Herndl, GJ and Obernosterer, I}, title = {Seasonal patterns in microbial carbon and iron transporter expression in the Southern Ocean.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {187}, pmid = {37596690}, issn = {2049-2618}, mesh = {Seasons ; *Carbon ; *Iron ; Membrane Transport Proteins/genetics ; Oceans and Seas ; }, abstract = {BACKGROUND: Heterotrophic microbes in the Southern Ocean are challenged by the double constraint of low concentrations of organic carbon (C) and iron (Fe). These essential elements are tightly coupled in cellular processes; however, the prokaryotic requirements of C and Fe under varying environmental settings remain poorly studied. Here, we used a combination of metatranscriptomics and metaproteomics to identify prokaryotic membrane transporters for organic substrates and Fe in naturally iron-fertilized and high-nutrient, low-chlorophyll waters of the Southern Ocean during spring and late summer.

RESULTS: Pronounced differences in membrane transporter profiles between seasons were observed at both sites, both at the transcript and protein level. When specific compound classes were considered, the two approaches revealed different patterns. At the transcript level, seasonal patterns were only observed for subsets of genes belonging to each transporter category. At the protein level, membrane transporters of organic compounds were relatively more abundant in spring as compared to summer, while the opposite pattern was observed for Fe transporters. These observations suggest an enhanced requirement for organic C in early spring and for Fe in late summer. Mapping transcripts and proteins to 50 metagenomic-assembled genomes revealed distinct taxon-specific seasonal differences pointing to potentially opportunistic clades, such as Pseudomonadales and Nitrincolaceae, and groups with a more restricted repertoire of expressed transporters, such as Alphaproteobacteria and Flavobacteriaceae.

CONCLUSION: The combined investigations of C and Fe membrane transporters suggest seasonal changes in the microbial requirements of these elements under different productivity regimes. The taxon-specific acquisition strategies of different forms of C and Fe illustrate how diverse microbes could shape transcript and protein expression profiles at the community level at different seasons. Our results on the C- and Fe-related metabolic capabilities of microbial taxa provide new insights into their potential role in the cycling of C and Fe under varying nutrient regimes in the Southern Ocean. Video Abstract.}, } @article {pmid37596536, year = {2023}, author = {Araújo, V and Fehn, AM and Phiri, A and Wills, J and Rocha, J and Gayà-Vidal, M}, title = {Oral microbiome homogeneity across diverse human groups from southern Africa: first results from southwestern Angola and Zimbabwe.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {226}, pmid = {37596536}, issn = {1471-2180}, mesh = {Humans ; Zimbabwe ; Angola ; Africa, Southern ; *Citrobacter ; *Microbiota/genetics ; }, abstract = {BACKGROUND: While the human oral microbiome is known to play an important role in systemic health, its average composition and diversity patterns are still poorly understood. To gain better insights into the general composition of the microbiome on a global scale, the characterization of microbiomes from a broad range of populations, including non-industrialized societies, is needed. Here, we used the portion of non-human reads obtained through an expanded exome capture sequencing approach to characterize the saliva microbiomes of 52 individuals from eight ethnolinguistically diverse southern African populations from Angola (Kuvale, Kwepe, Himba, Tjimba, Kwisi, Twa, !Xun) and Zimbabwe (Tshwa), including foragers, food-producers, and peripatetic groups (low-status communities who provide services to their dominant neighbors).

RESULTS: Our results indicate that neither host genetics nor livelihood seem to influence the oral microbiome profile, with Neisseria, Streptococcus, Prevotella, Rothia, and Porphyromonas being the five most frequent genera in southern African groups, in line with what has been shown for other human populations. However, we found that some Tshwa and Twa individuals display an enrichment of pathogenic genera from the Enterobacteriaceae family (i.e. Enterobacter, Citrobacter, Salmonella) of the Proteobacteria phylum, probably reflecting deficient sanitation and poor health conditions associated with social marginalization.

CONCLUSIONS: Taken together, our results suggest that socio-economic status, rather than ethnolinguistic affiliation or subsistence mode, is a key factor in shaping the salivary microbial profiles of human populations in southern Africa.}, } @article {pmid37596518, year = {2023}, author = {Galperine, T and Choi, Y and Pagani, JL and Kritikos, A and Papadimitriou-Olivgeris, M and Méan, M and Scherz, V and Opota, O and Greub, G and Guery, B and Bertelli, C and , }, title = {Temporal changes in fecal microbiota of patients infected with COVID-19: a longitudinal cohort.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {537}, pmid = {37596518}, issn = {1471-2334}, mesh = {Humans ; *COVID-19 ; SARS-CoV-2 ; *Microbiota ; *Gastrointestinal Microbiome ; Bacteroides ; Butyrates ; }, abstract = {BACKGROUND: Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a multifaceted disease potentially responsible for various clinical manifestations including gastro-intestinal symptoms. Several evidences suggest that the intestine is a critical site of immune cell development, gut microbiota could therefore play a key role in lung immune response. We designed a monocentric longitudinal observational study to describe the gut microbiota profile in COVID-19 patients and compare it to a pre-existing cohort of ventilated non-COVID-19 patients.

METHODS: From March to December 2020, we included patients admitted for COVID-19 in medicine (43 not ventilated) or intensive care unit (ICU) (14 ventilated) with a positive SARS-CoV-2 RT-PCR assay in a respiratory tract sample. 16S metagenomics was performed on rectal swabs from these 57 COVID-19 patients, 35 with one and 22 with multiple stool collections. Nineteen non-COVID-19 ICU controls were also enrolled, among which 14 developed ventilator-associated pneumonia (pneumonia group) and five remained without infection (control group). SARS-CoV-2 viral loads in fecal samples were measured by qPCR.

RESULTS: Although similar at inclusion, Shannon alpha diversity appeared significantly lower in COVID-19 and pneumonia groups than in the control group at day 7. Furthermore, the microbiota composition became distinct between COVID-19 and non-COVID-19 groups. The fecal microbiota of COVID-19 patients was characterized by increased Bacteroides and the pneumonia group by Prevotella. In a distance-based redundancy analysis, only COVID-19 presented significant effects on the microbiota composition. Moreover, patients in ICU harbored increased Campylobacter and decreased butyrate-producing bacteria, such as Lachnospiraceae, Roseburia and Faecalibacterium as compared to patients in medicine. Both the stay in ICU and patient were significant factors affecting the microbiota composition. SARS-CoV-2 viral loads were higher in ICU than in non-ICU patients.

CONCLUSIONS: Overall, we identified distinct characteristics of the gut microbiota in COVID-19 patients compared to control groups. COVID-19 patients were primarily characterized by increased Bacteroides and decreased Prevotella. Moreover, disease severity showed a negative correlation with butyrate-producing bacteria. These features could offer valuable insights into potential targets for modulating the host response through the microbiota and contribute to a better understanding of the disease's pathophysiology.

TRIAL REGISTRATION: CER-VD 2020-00755 (05.05.2020) & 2017-01820 (08.06.2018).}, } @article {pmid37596412, year = {2023}, author = {Roux, S and Brum, JR}, title = {Counting dots or counting reads? Complementary approaches to estimate virus-to-microbe ratios.}, journal = {The ISME journal}, volume = {17}, number = {10}, pages = {1521-1522}, pmid = {37596412}, issn = {1751-7370}, mesh = {*Ecosystem ; *Metagenome ; }, } @article {pmid37596411, year = {2023}, author = {Bojanova, DP and De Anda, VY and Haghnegahdar, MA and Teske, AP and Ash, JL and Young, ED and Baker, BJ and LaRowe, DE and Amend, JP}, title = {Well-hidden methanogenesis in deep, organic-rich sediments of Guaymas Basin.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {1828-1838}, pmid = {37596411}, issn = {1751-7370}, support = {S10 OD010786/OD/NIH HHS/United States ; }, mesh = {*Geologic Sediments ; Phylogeny ; *Euryarchaeota/genetics ; Methane/metabolism ; RNA, Ribosomal, 16S ; }, abstract = {Deep marine sediments (>1mbsf) harbor ~26% of microbial biomass and are the largest reservoir of methane on Earth. Yet, the deep subsurface biosphere and controls on its contribution to methane production remain underexplored. Here, we use a multidisciplinary approach to examine methanogenesis in sediments (down to 295 mbsf) from sites with varying degrees of thermal alteration (none, past, current) at Guaymas Basin (Gulf of California) for the first time. Traditional ([13]C/[12]C and D/H) and multiply substituted ([13]CH3D and [12]CH2D2) methane isotope measurements reveal significant proportions of microbial methane at all sites, with the largest signal at the site with past alteration. With depth, relative microbial methane decreases at differing rates between sites. Gibbs energy calculations confirm methanogenesis is exergonic in Guaymas sediments, with methylotrophic pathways consistently yielding more energy than the canonical hydrogenotrophic and acetoclastic pathways. Yet, metagenomic sequencing and cultivation attempts indicate that methanogens are present in low abundance. We find only one methyl-coenzyme M (mcrA) sequence within the entire sequencing dataset. Also, we identify a wide diversity of methyltransferases (mtaB, mttB), but only a few sequences phylogenetically cluster with methylotrophic methanogens. Our results suggest that the microbial methane in the Guaymas subsurface was produced over geologic time by relatively small methanogen populations, which have been variably influenced by thermal sediment alteration. Higher resolution metagenomic sampling may clarify the modern methanogen community. This study highlights the importance of using a multidisciplinary approach to capture microbial influences in dynamic, deep subsurface settings like Guaymas Basin.}, } @article {pmid37596370, year = {2023}, author = {Vigneron, A and Vincent, WF and Lovejoy, C}, title = {Discovery of a novel bacterial class with the capacity to drive sulfur cycling and microbiome structure in a paleo-ocean analog.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {82}, pmid = {37596370}, issn = {2730-6151}, support = {Sentinel North//Canada First Research Excellence Fund (Fonds d'excellence en recherche Apogée Canada)/ ; Sentinel North//Canada First Research Excellence Fund (Fonds d'excellence en recherche Apogée Canada)/ ; Sentinel North//Canada First Research Excellence Fund (Fonds d'excellence en recherche Apogée Canada)/ ; ArcticNet//Gouvernement du Canada | Réseaux de centres d'excellence | AUTO21 Network of Centres of Excellence (Réseau de Centres d'Excellence AUTO21)/ ; Arctic Net//Gouvernement du Canada | Réseaux de centres d'excellence | AUTO21 Network of Centres of Excellence (Réseau de Centres d'Excellence AUTO21)/ ; }, abstract = {Uncultivated microbial taxa represent a large fraction of global microbial diversity and likely drive numerous biogeochemical transformations in natural ecosystems. Geographically isolated, polar ecosystems are complex microbial biomes and refuges of underexplored taxonomic and functional biodiversity. Combining amplicon sequencing with genome-centric metagenomic analysis of samples from one of the world's northernmost lakes (Lake A, Ellesmere Island, Canadian High Arctic), we identified a novel bacterial taxon that dominates in the bottom layer of anoxic, sulfidic, relict sea water that was isolated from the Arctic Ocean some 3000 years ago. Based on phylogenomic comparative analyses, we propose that these bacteria represent a new Class within the poorly described Electryoneota/AABM5-125-24 candidate phylum. This novel class, for which we propose the name Tariuqbacteria, may be either a relict of ancient ocean conditions or endemic to this High Arctic system, provisionally providing a rare example of high-taxonomy level endemism. Consistent with the geochemistry of the bottom water, the genetic composition of the Candidatus Tariuqbacter genome revealed a strictly anaerobic lifestyle with the potential for sulfate and sulfur reduction, a versatile carbon metabolism and the capability to eliminate competing bacteria through methylarsenite production, suggesting an allelochemical influence on microbiome structure by this planktonic microbe.}, } @article {pmid37596308, year = {2023}, author = {Sriaporn, C and Campbell, KA and Van Kranendonk, MJ and Handley, KM}, title = {Bacterial and archaeal community distributions and cosmopolitanism across physicochemically diverse hot springs.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {80}, pmid = {37596308}, issn = {2730-6151}, abstract = {Terrestrial hot springs harbor diverse microbial communities whose compositions are shaped by the wide-ranging physico-chemistries of individual springs. The effect of enormous physico-chemical differences on bacterial and archaeal distributions and population structures is little understood. We therefore analysed the prevalence and relative abundance of bacteria and archaea in the sediments (n = 76) of hot spring features, in the Taupō Volcanic Zone (New Zealand), spanning large differences in major anion water chemistry, pH (2.0-7.5), and temperature (17.5-92.9 °C). Community composition, based on 16S rRNA amplicon sequence variants (ASVs) was strongly influenced by both temperature and pH. However, certain lineages characterized diverse hot springs. At the domain level, bacteria and archaea shared broadly equivalent community abundances across physico-chemically diverse springs, despite slightly lower bacteria-to-archaea ratios and microbial 16S rRNA gene concentrations at higher temperatures. Communities were almost exclusively dominated by Proteobacteria, Euryarchaeota or Crenarchaeota. Eight archaeal and bacterial ASVs from Thermoplasmatales, Desulfurellaceae, Mesoaciditogaceae and Acidithiobacillaceae were unusually prevalent (present in 57.9-84.2% of samples) and abundant (1.7-12.0% sample relative abundance), and together comprised 44% of overall community abundance. Metagenomic analyses generated multiple populations associated with dominant ASVs, and showed characteristic traits of each lineage for sulfur, nitrogen and hydrogen metabolism. Differences in metabolic gene composition and genome-specific metabolism delineated populations from relatives. Genome coverage calculations showed that populations associated with each lineage were distributed across a physicochemically broad range of hot springs. Results imply that certain bacterial and archaeal lineages harbor different population structures and metabolic potentials for colonizing diverse hot spring environments.}, } @article {pmid37596226, year = {2023}, author = {Xu, L and Huang, X and Hou, J and Ji, P}, title = {Metagenomic next-generation sequencing (mNGS)-assisted diagnosis of a case with infective endocarditis caused by Bartonella species.}, journal = {Asian journal of surgery}, volume = {46}, number = {11}, pages = {4966-4967}, doi = {10.1016/j.asjsur.2023.06.018}, pmid = {37596226}, issn = {0219-3108}, mesh = {Humans ; *Bartonella ; *Endocarditis, Bacterial/diagnosis ; *Endocarditis ; High-Throughput Nucleotide Sequencing ; }, } @article {pmid37596069, year = {2023}, author = {Lyu, Y and Luo, H and Chai, S and Zhang, Y and Fan, X and Wang, S and Feng, Z}, title = {Discovery and characterization of a novel PKD-Fn3 domains containing GH44 endoglucanase from a Tibetan metagenomic library.}, journal = {Journal of applied microbiology}, volume = {134}, number = {8}, pages = {}, doi = {10.1093/jambio/lxad187}, pmid = {37596069}, issn = {1365-2672}, support = {KYRC2021009//Fundamental Research Funds for the Central Universities/ ; MMLKF21-07//State Key Laboratory of Microbial Metabolism/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; }, mesh = {*Carboxymethylcellulose Sodium ; *Cellulase/genetics ; Metagenomics ; Tibet ; Escherichia coli/genetics ; Glycoside Hydrolases ; }, abstract = {AIMS: To explore novel microbial endoglucanases with unique properties derived from extreme environments by using metagenomics approach.

METHODS AND RESULTS: A Tibetan soil metagenomic library was applied for screening cellulase-active clones by function-based metagenomics. The candidate genes in the active clones were identified through bioinformatic analyses and heterologously expressed using an Escherichia coli system. The recombinant endoglucanases were purified and characterized using enzyme assays to determine their bioactivities, stabilities, substrate specificities, and other enzymatic properties. A novel endoglucanase gene Zfeg1907 was identified, which consisted of a glycoside hydrolase family 44 (GH44) catalytic domain along with a polycystic kidney disease (PKD) domain and a fibronectin type Ⅲ (Fn3) domain at the C terminal. Recombinant enzyme ZFEG1907 and its truncated mutant ZFEG1907t (ΔPKDΔFn3) were successfully expressed and purified. The two recombinants exhibited catalytic activities toward carboxymethyl cellulose, konjac glucomannan (KGM), and lichenan. Both enzymes had an optimal temperature of 50°C and an optimal pH value of 5.0. The catalytic activities of both recombinant enzymes were promoted by adding Zn2+ and Ca2+ at the final concentration of 10 mM. The Km value of ZFEG1907 was lower, while the kcat/Km value of ZFEG1907 was higher than those of of ZFEG1907t when using carboxymethyl cellulose, KGM, and lichenan as substrates. Structure prediction of two recombinants revealed that PKD-Fn3 domains consisted of a flexible linker and formed a β-sandwich structure.

CONCLUSIONS: A novel endoglucanase ZFEG1907 contained a GH44 catalytic domain and a PKD-Fn3 domain was characterized. The PKD-Fn3 domains were not indispensable for the activity but contributed to the enzyme binding of the polysaccharide substrates as a carbohydrate-binding module (CBM).}, } @article {pmid37596061, year = {2023}, author = {Bucheli, J and Cella, H and Nader, C and Oliveira, CYB and Bastolla, CLV and Lopes, RG and Pereira, GDV and Karam, J and Derner, RB}, title = {Bacterial assemblages structure in intensive cultivations of the microalga Tetradesmus obliquus.}, journal = {Journal of basic microbiology}, volume = {63}, number = {12}, pages = {1440-1450}, doi = {10.1002/jobm.202300362}, pmid = {37596061}, issn = {1521-4028}, support = {01.10.0457.00//Funding Authority for Studies and Projects (FINEP)/ ; 407513/2013-2//National Council for Scientific and Technological Development (CNPq)/ ; }, mesh = {Humans ; *Microalgae ; *Chlorophyceae ; Bacteria/genetics ; Biomass ; }, abstract = {The present study shows the characterization of the bacterial communities associated with different systems during the cultivation of the microalga Tetradesmus obliquus. For that, sequential cultivation was performed in three different systems: (1) Photobioreactor bench-scale; (2) flat-panel photobioreactor; and (3) thin-layer cascade. Cultures were monitored daily for growth parameters and biomass samples were collected for characterization of bacterial communities using metagenomic. A total of 195,177 reads were produced, resulting in the identification of 72 OTUs. In the grouping of bacterial communities, 3 phyla, 6 classes, 28 families, and 35 taxa were found. The bacteria Brevundimonas and Porphyrobacter had a higher relative abundance compared with other taxa found. These taxa were present in all cultivation systems forming a possible core community. Bacterial communities associated with different cultivation systems of the microalga T. obliquus showed an increase in taxa richness and diversity in the super-intensive and intensive systems.}, } @article {pmid37595937, year = {2023}, author = {Li, Y and Xu, J and Hong, Y and Li, Z and Xing, X and Zhufeng, Y and Lu, D and Liu, X and He, J and Li, Y and Sun, X}, title = {Metagenome-wide association study of gut microbiome features for myositis.}, journal = {Clinical immunology (Orlando, Fla.)}, volume = {255}, number = {}, pages = {109738}, doi = {10.1016/j.clim.2023.109738}, pmid = {37595937}, issn = {1521-7035}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Escherichia coli/genetics ; *Myositis/complications ; *Lung Diseases, Interstitial ; Bacteria ; Autoantibodies ; Retrospective Studies ; }, abstract = {PURPOSE: The clinical relevance and pathogenic role of gut microbiome in both myositis and its associated interstitial lung disease (ILD) are still unclear. The purpose of this study was to investigate the role of gut microbiome in myositis through comprehensive metagenomic-wide association studies (MWAS).

METHODS: We conducted MWAS of the myositis gut microbiome in a Chinese cohort by using whole-genome shotgun sequencing of high depth, including 30 myositis patients and 31 healthy controls (HC). Among the myositis patients, 11 developed rapidly progressive interstitial lung disease (RP-ILD) and 10 had chronic ILD (C-ILD).

RESULTS: Analysis for overall distribution level of the bacteria showed Alistipes onderdonkii, Parabacteroides distasonis and Escherichia coli were upregulated, Lachnospiraceae bacterium GAM79, Roseburia intestinalis, and Akkermansia muciniphila were downregulated in patients with myositis compared to HC. Bacteroides thetaiotaomicron, Parabacteroides distasonis and Escherichia coli were upregulated, Bacteroides A1C1 and Bacteroides xylanisolvens were downregulated in RP-ILD cases compared with C-ILD cases. A variety of biological pathways related to metabolism were enriched in the myositis and HC, RP-ILD and C-ILD comparison. And in the analyses for microbial contribution in metagenomic biological pathways, we have found that E. coli played an important role in the pathway expression in both myositis group and myositis-associated RP-ILD group. Anti-PL-12 antibody, anti-Ro-52 antibody, and anti-EJ antibody were found to have positive correlation with bacterial diversity (Shannon-wiener diversity index and Chao1, richness estimator) between myositis group and control groups. The combination of E. coli and R. intestinalis could distinguish myositis group from HC effectively. R. intestinalis can also be applied in the distinguishment of RP-ILD group vs. C-ILD group in myositis patients.

CONCLUSION: Our MWAS study first revealed the link between gut microbiome and pathgenesis of myositis, which may help us understand the role of gut microbiome in the etiology of myositis and myositis-associated RP-ILD.}, } @article {pmid37595699, year = {2023}, author = {Zhi, M and Zhao, Y and Zeng, X and Maddela, NR and Xiao, Y and Chen, Y and Prasad, R and Zhou, Z}, title = {Filamentous cyanobacteria and hydrophobic protein in extracellular polymeric substances facilitate algae-bacteria aggregation during partial nitrification.}, journal = {International journal of biological macromolecules}, volume = {251}, number = {}, pages = {126379}, doi = {10.1016/j.ijbiomac.2023.126379}, pmid = {37595699}, issn = {1879-0003}, abstract = {In algae-bacteria symbiotic wastewater treatment, the excellent settling performance of algae-bacteria aggregates is critical for biomass separation and recovery. Here, the composition of extracellular polymeric substances (EPS), microbial profiles, and functional genes of algae-bacteria aggregates were investigated at different solid retention times (SRTs) (10, 20, and 40 d) during partial nitrification in photo sequencing bioreactors (PSBRs). Results showed that SRTs greatly influenced the nitrogen transformation and the formation and morphological structure of algae-bacteria aggregates. The highest nitrite accumulation, the largest particle size (~1.54 mm) and the best settling performance were observed for the algae-bacteria aggregates in the PSBR with an SRT of 10 d, where the abundant occurrence of filamentous cyanobacteria with the highest ratio of chlorophyll a/b and the lowest EPS amount with the highest protein-to-polysaccharide ratio were observed. In particular, the EPS at 10 d of SRT contained a higher amount of protein-related hydrophobic groups and a lower ratio of α-helix/(β-sheet + random coil), indicating a looser protein structure, which might facilitate the formation and stabilization of algae-bacteria aggregates. Moreover, algal-bacterial aggregation greatly depended on the composition and evolution of filamentous cyanobacteria (unclassified _o__Oscillatoriales and Phormidium accounted for 56.29 % of the identified algae at SRT 10 d). The metagenomic analysis further revealed that functional genes related to amino acid metabolism (e.g., genes of phenylalanine, tyrosine, and tryptophan biosynthesis) were expressed at high levels within 10 d of SRT. Overall, this study demonstrates the influence of EPS structures and filamentous cyanobacteria on algae-bacteria aggregation and reveals the biological mechanisms driving photogranule structure and function.}, } @article {pmid37595469, year = {2023}, author = {Rolbiecki, D and Paukszto, Ł and Krawczyk, K and Korzeniewska, E and Sawicki, J and Harnisz, M}, title = {Chlorine disinfection modifies the microbiome, resistome and mobilome of hospital wastewater - A nanopore long-read metagenomic approach.}, journal = {Journal of hazardous materials}, volume = {459}, number = {}, pages = {132298}, doi = {10.1016/j.jhazmat.2023.132298}, pmid = {37595469}, issn = {1873-3336}, mesh = {Humans ; Chlorine/pharmacology ; Wastewater ; Angiotensin Receptor Antagonists ; Disinfection ; *Nanopores ; Angiotensin-Converting Enzyme Inhibitors ; Halogens ; *Microbiota/genetics ; Chlorides ; Anti-Bacterial Agents ; Hospitals ; }, abstract = {The aim of the present study was to analyze changes in the microbiome, resistome, and mobilome of hospital wastewater (HWW) induced by disinfection with chlorine compounds. Changes in bacterial communities and specific antibiotic resistance genes (ARGs) in HWW were determined with the use of a nanopore long-read metagenomic approach. The main hosts of ARGs in HWW were identified, and the mobility of resistance mechanisms was analyzed. Special attention was paid to the prevalence of critical-priority pathogens in the HWW microbiome, which pose the greatest threat to human health. The results of this study indicate that chlorine disinfection of HWW can induce significant changes in the structure of the total bacterial population and antibiotic resistant bacteria (ARB) communities, and that it can modify the resistome and mobilome of HWW. Disinfection favored the selection of ARGs, decreased their prevalence in HWW, while increasing their diversity. The mobility of the HWW resistome increased after disinfection. Disinfection led to the emergence of new drug resistance mechanisms in previously sensitive bacterial taxa. In conclusion, this study demonstrated that HWW disinfected with low (sublethal) concentrations of free chlorine significantly contributes to the mobility and transfer of drug resistance mechanisms (including critical mechanisms) between bacteria (including pathogens).}, } @article {pmid37595295, year = {2024}, author = {Ring, HC and Thorsen, J and Lilje, B and Bay, L and Bjarnsholt, T and Fuursted, K and Saunte, DM and Jemec, GB and Thomsen, SF}, title = {Predictive metagenomic analysis identifies specific bacterial metabolic pathways in hidradenitis suppurativa tunnels.}, journal = {Journal of the European Academy of Dermatology and Venereology : JEADV}, volume = {38}, number = {1}, pages = {e63-e65}, doi = {10.1111/jdv.19433}, pmid = {37595295}, issn = {1468-3083}, mesh = {Humans ; Bacteria ; *Hidradenitis Suppurativa/genetics ; Severity of Illness Index ; Metagenomics ; }, } @article {pmid37594978, year = {2023}, author = {Paul, R and Rogers, TJ and Fullerton, KM and Selci, M and Cascone, M and Stokes, MH and Steen, AD and de Moor, JM and Chiodi, A and Stefánsson, A and Halldórsson, SA and Ramirez, CJ and Jessen, GL and Barry, PH and Cordone, A and Giovannelli, D and Lloyd, KG}, title = {Complex organic matter degradation by secondary consumers in chemolithoautotrophy-based subsurface geothermal ecosystems.}, journal = {PloS one}, volume = {18}, number = {8}, pages = {e0281277}, pmid = {37594978}, issn = {1932-6203}, abstract = {Microbial communities in terrestrial geothermal systems often contain chemolithoautotrophs with well-characterized distributions and metabolic capabilities. However, the extent to which organic matter produced by these chemolithoautotrophs supports heterotrophs remains largely unknown. Here we compared the abundance and activity of peptidases and carbohydrate active enzymes (CAZymes) that are predicted to be extracellular identified in metagenomic assemblies from 63 springs in the Central American and the Andean convergent margin (Argentinian backarc of the Central Volcanic Zone), as well as the plume-influenced spreading center in Iceland. All assemblies contain two orders of magnitude more peptidases than CAZymes, suggesting that the microorganisms more often use proteins for their carbon and/or nitrogen acquisition instead of complex sugars. The CAZy families in highest abundance are GH23 and CBM50, and the most abundant peptidase families are M23 and C26, all four of which degrade peptidoglycan found in bacterial cells. This implies that the heterotrophic community relies on autochthonous dead cell biomass, rather than allochthonous plant matter, for organic material. Enzymes involved in the degradation of cyanobacterial- and algal-derived compounds are in lower abundance at every site, with volcanic sites having more enzymes degrading cyanobacterial compounds and non-volcanic sites having more enzymes degrading algal compounds. Activity assays showed that many of these enzyme classes are active in these samples. High temperature sites (> 80°C) had similar extracellular carbon-degrading enzymes regardless of their province, suggesting a less well-developed population of secondary consumers at these sites, possibly connected with the limited extent of the subsurface biosphere in these high temperature sites. We conclude that in < 80°C springs, chemolithoautotrophic production supports heterotrophs capable of degrading a wide range of organic compounds that do not vary by geological province, even though the taxonomic and respiratory repertoire of chemolithoautotrophs and heterotrophs differ greatly across these regions.}, } @article {pmid37594964, year = {2023}, author = {Li, W and Kari, L and Yu, Y and Hug, LA}, title = {MT-MAG: Accurate and interpretable machine learning for complete or partial taxonomic assignments of metagenomeassembled genomes.}, journal = {PloS one}, volume = {18}, number = {8}, pages = {e0283536}, pmid = {37594964}, issn = {1932-6203}, mesh = {Animals ; Cattle ; Female ; Humans ; *Metagenome/genetics ; Benchmarking ; Computational Biology ; *Gastrointestinal Microbiome ; Machine Learning ; }, abstract = {We propose MT-MAG, a novel machine learning-based software tool for the complete or partial hierarchically-structured taxonomic classification of metagenome-assembled genomes (MAGs). MT-MAG is alignment-free, with k-mer frequencies being the only feature used to distinguish a DNA sequence from another (herein k = 7). MT-MAG is capable of classifying large and diverse metagenomic datasets: a total of 245.68 Gbp in the training sets, and 9.6 Gbp in the test sets analyzed in this study. In addition to complete classifications, MT-MAG offers a "partial classification" option, whereby a classification at a higher taxonomic level is provided for MAGs that cannot be classified to the Species level. MT-MAG outputs complete or partial classification paths, and interpretable numerical classification confidences of its classifications, at all taxonomic ranks. To assess the performance of MT-MAG, we define a "weighted classification accuracy," with a weighting scheme reflecting the fact that partial classifications at different ranks are not equally informative. For the two benchmarking datasets analyzed (genomes from human gut microbiome species, and bacterial and archaeal genomes assembled from cow rumen metagenomic sequences), MT-MAG achieves an average of 87.32% in weighted classification accuracy. At the Species level, MT-MAG outperforms DeepMicrobes, the only other comparable software tool, by an average of 34.79% in weighted classification accuracy. In addition, MT-MAG is able to completely classify an average of 67.70% of the sequences at the Species level, compared with DeepMicrobes which only classifies 47.45%. Moreover, MT-MAG provides additional information for sequences that it could not classify at the Species level, resulting in the partial or complete classification of 95.13%, of the genomes in the datasets analyzed. Lastly, unlike other taxonomic assignment tools (e.g., GDTB-Tk), MT-MAG is an alignment-free and genetic marker-free tool, able to provide additional bioinformatics analysis to confirm existing or tentative taxonomic assignments.}, } @article {pmid37593763, year = {2023}, author = {Cui, S and Pan, M and Tang, X and Liu, G and Mao, B and Zhao, J and Yang, K}, title = {Metagenomic insights into the effects of cosmetics containing complex polysaccharides on the composition of skin microbiota in females.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1210724}, pmid = {37593763}, issn = {2235-2988}, mesh = {Female ; Humans ; Metagenome ; *Microbiota ; *Cosmetics ; Skin ; *Actinobacteria ; Bifidobacterium ; }, abstract = {INTRODUCTION: The use of cosmetics has become a habit for women. However, their influence on the microbial diversity of the skin has rarely been studied.

METHODS: Herein, the effect of cosmetics containing complex polysaccharides on the skin bacterial microbiota of female forehead and cheek areas was analyzed. Eighty volunteers were recruited and split into two groups (40 people each); one group was treated with cosmetics containing complex polysaccharides and the other with basic cream for 28 days. Skin samples were collected using sterilized cotton swabs, and 16S rDNA high-throughput sequencing was used to analyze the changes in skin bacterial microbiota composition before and after the intervention.

RESULTS AND DISCUSSION: A total of twenty-four phyla were detected in the forehead and cheek skin samples of 80 volunteers, the top three of which were Proteobacteria, Firmicutes, and Actinobacteria. The main genera of the forehead skin bacterial microbiota were Cutibacterium (11.1%), Acinetobacter (10.4%), Enterococcus (8.9%), Ralstonia (8.8%), and Staphylococcus (8.7%), while those of the cheek skin bacterial microbiota were Staphylococcus (20.0%), Ralstonia (8.7%), Propionibacterium (7.9%), Acinetobacter (7.2%), and Bifidobacterium (6.0%). Compared with basic cream, the use of cosmetics containing complex polysaccharides significantly increased the relative abundance of Staphylococcus and Bacillus in the forehead and cheek and reduced the relative abundance of Propionibacterium and Bifidobacterium. Thus, cosmetics containing complex polysaccharides could modify the composition of skin bacterial microbiota, which may help to maintain stable conditions of the skin.}, } @article {pmid37593761, year = {2023}, author = {Fukuoka, H and Tourlousse, DM and Ohashi, A and Suzuki, S and Nakagawa, K and Ozawa, M and Ishibe, A and Endo, I and Sekiguchi, Y}, title = {Elucidating colorectal cancer-associated bacteria through profiling of minimally perturbed tissue-associated microbiota.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1216024}, pmid = {37593761}, issn = {2235-2988}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Gastrointestinal Microbiome ; Bacteria/genetics ; *Colorectal Neoplasms ; }, abstract = {Sequencing-based interrogation of gut microbiota is a valuable approach for detecting microbes associated with colorectal cancer (CRC); however, such studies are often confounded by the effect of bowel preparation. In this study, we evaluated the viability of identifying CRC-associated mucosal bacteria through centimeter-scale profiling of the microbiota in tumors and adjacent noncancerous tissue from eleven patients who underwent colonic resection without preoperative bowel preparation. High-throughput 16S rRNA gene sequencing revealed that differences between on- and off-tumor microbiota varied considerably among patients. For some patients, phylotypes affiliated with genera previously implicated in colorectal carcinogenesis, as well as genera with less well-understood roles in CRC, were enriched in tumor tissue, whereas for other patients, on- and off-tumor microbiota were very similar. Notably, the enrichment of phylotypes in tumor-associated mucosa was highly localized and no longer apparent even a few centimeters away from the tumor. Through short-term liquid culturing and metagenomics, we further generated more than one-hundred metagenome-assembled genomes, several representing bacteria that were enriched in on-tumor samples. This is one of the first studies to analyze largely unperturbed mucosal microbiota in tissue samples from the resected colons of unprepped CRC patients. Future studies with larger cohorts are expected to clarify the causes and consequences of the observed variability in the emergence of tumor-localized microbiota among patients.}, } @article {pmid37593545, year = {2023}, author = {Flores-Vargas, G and Korber, DR and Bergsveinson, J}, title = {Sub-MIC antibiotics influence the microbiome, resistome and structure of riverine biofilm communities.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1194952}, pmid = {37593545}, issn = {1664-302X}, abstract = {The effects of sub-minimum inhibitory concentrations (sub-MICs) of antibiotics on aquatic environments is not yet fully understood. Here, we explore these effects by employing a replicated microcosm system fed with river water where biofilm communities were continuously exposed over an eight-week period to sub-MIC exposure (1/10, 1/50, and 1/100 MIC) to a mix of common antibiotics (ciprofloxacin, streptomycin, and oxytetracycline). Biofilms were examined using a structure-function approach entailing microscopy and metagenomic techniques, revealing details on the microbiome, resistome, virulome, and functional prediction. A comparison of three commonly used microbiome and resistome databases was also performed. Differences in biofilm architecture were observed between sub-MIC antibiotic treatments, with an overall reduction of extracellular polymeric substances and autotroph (algal and cyanobacteria) and protozoan biomass, particularly at the 1/10 sub-MIC condition. While metagenomic analyses demonstrated that microbial diversity was lowest at the sub-MIC 1/10 antibiotic treatment, resistome diversity was highest at sub-MIC 1/50. This study also notes the importance of benchmarking analysis tools and careful selection of reference databases, given the disparity in detected antimicrobial resistance genes (ARGs) identity and abundance across methods. Ultimately, the most detected ARGs in sub-MICs exposed biofilms were those that conferred resistance to aminoglycosides, tetracyclines, β-lactams, sulfonamides, and trimethoprim. Co-occurrence of microbiome and resistome features consistently showed a relationship between Proteobacteria genera and aminoglycoside ARGs. Our results support the hypothesis that constant exposure to sub-MICs antibiotics facilitate the transmission and promote prevalence of antibiotic resistance in riverine biofilms communities, and additionally shift overall microbial community metabolic function.}, } @article {pmid37593224, year = {2023}, author = {Hu, J and Ding, J and Li, X and Li, J and Zheng, T and Xie, L and Li, C and Tang, Y and Guo, K and Huang, J and Liu, S and Yan, J and Peng, W and Hou, C and Wen, L and Xu, A and Zhou, Z and Xiao, Y}, title = {Distinct signatures of gut microbiota and metabolites in different types of diabetes: a population-based cross-sectional study.}, journal = {EClinicalMedicine}, volume = {62}, number = {}, pages = {102132}, pmid = {37593224}, issn = {2589-5370}, support = {R01 DK126809/DK/NIDDK NIH HHS/United States ; R01 DK130318/DK/NIDDK NIH HHS/United States ; }, abstract = {BACKGROUND: Patients with type 1 diabetes (T1D) and type 2 diabetes (T2D) present intestinal disturbances. Recent epidemiological data have showed that, worldwide, over half of newly diagnosed T1D patients were adults. However, the gut microbial alterations in adult-onset T1D are unclear. We aimed to identify the signatures of gut microbiota and metabolites in patients with adult-onset T1D systematically, comparing with T2D patients and healthy controls (HCs).

METHODS: This study enrolled 218 subjects from February 2019 to April 2022 (discovery cohort: 36 HCs, 51 patients with adult-onset T1D and 56 patients with T2D; validation cohort: 28 HCs, 27 patients with adult-onset T1D and 20 patients with T2D). Gut microbial profiles of the study subjects were investigated by metagenomic sequencing, and their faecal and serum metabolites were measured with targeted metabolomics. The study was registered on ClinicalTrials.gov (NCT05252728).

FINDINGS: Patients with adult-onset T1D had significant differences in the composition of bacteria and their metabolites, characterized by notable depletion of short-chain fatty acid-producing bacteria, especially Eubacterium rectale. This was associated with a severe loss of phenolic acids and their derivatives, including gallic acid (associated with glucose metabolism) and 3,4-dihydroxyhydrocinnamic acid (linked with glucose metabolism and pancreatic beta cell autoimmunity). A predictive model based on six bacteria and six metabolites simultaneously discriminated adult-onset T1D from T2D and HCs with high accuracy. Interestingly, bacterial-viral or bacterial-fungal trans-kingdom relationships, especially positive correlations between bacteriophages and beneficial bacteria, were significantly reduced in adult-onset T1D compared to HCs.

INTERPRETATION: Adult-onset T1D patients exhibit unique changes in host-microbiota-metabolite interactions. Gut microbiota and metabolite-based algorithms could be used as additional tools for differential diagnosis of different types of diabetes and beyond.

FUNDING: National Key Research and Development Program of China, the National Natural Science Foundation of China.}, } @article {pmid37592253, year = {2023}, author = {Alexander, JE and Filler, S and Bergman, PJ and Bowring, CE and Carvell-Miller, L and Fulcher, B and Haydock, R and Lightfoot, T and Logan, DW and McKee, TS and Mills, T and Morrison, J and Watson, P and Woodruff, C and , }, title = {The MARS PETCARE BIOBANK protocol: establishing a longitudinal study of health and disease in dogs and cats.}, journal = {BMC veterinary research}, volume = {19}, number = {1}, pages = {125}, pmid = {37592253}, issn = {1746-6148}, mesh = {Humans ; Cats ; Dogs ; Animals ; Longitudinal Studies ; Biological Specimen Banks ; *Cat Diseases/genetics ; Genome-Wide Association Study/veterinary ; Prospective Studies ; *Dog Diseases/genetics ; }, abstract = {BACKGROUND: The veterinary care of cats and dogs is increasingly embracing innovations first applied to human health, including an increased emphasis on preventative care and precision medicine. Large scale human population biobanks have advanced research in these areas; however, few have been established in veterinary medicine. The MARS PETCARE BIOBANK™ (MPB) is a prospective study that aims to build a longitudinal bank of biological samples, with paired medical and lifestyle data, from 20,000 initially healthy cats and dogs (10,000 / species), recruited through veterinary hospitals over a ten-year period. Here, we describe the MPB protocol and discuss its potential as a platform to increase understanding of why and how diseases develop and how to advance personalised veterinary healthcare.

METHODS: At regular intervals, extensive diet, health and lifestyle information, electronic medical records, clinicopathology and activity data are collected, genotypes, whole genome sequences and faecal metagenomes analysed, and blood, plasma, serum, and faecal samples stored for future research.

DISCUSSION: Proposed areas for research include the early detection and progression of age-related disease, risk factors for common conditions, the influence of the microbiome on health and disease and, through genome wide association studies, the identification of candidate loci for disease associated genetic variants. Genomic data will be open access and research proposals for access to data and samples will be considered. Over the coming years, the MPB will provide the longitudinal data and systematically collected biological samples required to generate important insights into companion animal health, identifying biomarkers of disease, supporting earlier identification of risk, and enabling individually tailored interventions to manage disease.}, } @article {pmid37591872, year = {2023}, author = {Liao, J and Shenhav, L and Urban, JA and Serrano, M and Zhu, B and Buck, GA and Korem, T}, title = {Microdiversity of the vaginal microbiome is associated with preterm birth.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4997}, pmid = {37591872}, issn = {2041-1723}, support = {R01 HD106017/HD/NICHD NIH HHS/United States ; }, mesh = {Infant, Newborn ; Pregnancy ; Humans ; Female ; *Premature Birth/genetics ; *Microbiota/genetics ; Metagenome/genetics ; Acclimatization ; Biological Evolution ; }, abstract = {Preterm birth (PTB) is the leading cause of neonatal morbidity and mortality. The vaginal microbiome has been associated with PTB, yet the mechanisms underlying this association are not fully understood. Understanding microbial genetic adaptations to selective pressures, especially those related to the host, may yield insights into these associations. Here, we analyze metagenomic data from 705 vaginal samples collected during pregnancy from 40 women who delivered preterm spontaneously and 135 term controls from the Multi-Omic Microbiome Study-Pregnancy Initiative. We find that the vaginal microbiome of pregnancies that ended preterm exhibited unique genetic profiles. It was more genetically diverse at the species level, a result which we validate in an additional cohort, and harbored a higher richness and diversity of antimicrobial resistance genes, likely promoted by transduction. Interestingly, we find that Gardnerella species drove this higher genetic diversity, particularly during the first half of the pregnancy. We further present evidence that Gardnerella spp. underwent more frequent recombination and stronger purifying selection in genes involved in lipid metabolism. Overall, our population genetics analyses reveal associations between the vaginal microbiome and PTB and suggest that evolutionary processes acting on vaginal microbes may play a role in adverse pregnancy outcomes such as PTB.}, } @article {pmid37591518, year = {2023}, author = {Liu, X and Wu, J and Tang, J and Xu, Z and Zhou, B and Liu, Y and Hu, F and Zhang, G and Cheng, R and Xia, X and Chen, Y and Wu, H and Wang, D and Yue, J and Dong, B and Fu, J and Yu, H and Dong, B}, title = {Prevotella copri alleviates sarcopenia via attenuating muscle mass loss and function decline.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {14}, number = {5}, pages = {2275-2288}, pmid = {37591518}, issn = {2190-6009}, support = {32100927//National Natural Science Foundation of China/ ; 82101653//National Natural Science Foundation of China/ ; 2021YFS0158//Project of the Sichuan Province Science and Technology/ ; Z2018B09//National Clinical Research Center for Geriatric, West China Hospital, Sichuan University/ ; 2020HXBH011//West China Hospital Postdoctoral Fund/ ; HXYS19005//1.3.5 Project for Disciplines of Excellence, West China Hospital, Sichuan University, Project of Max Cynader Academy of Brain Workstation, WCHSCU/ ; 2019YF0900083SN//Chengdu Science and Technology Bureau Major Science and Technology Application Demonstration Project/ ; CSC 202108510037//China Scholarship Council/ ; CVON2018-27//Dutch Heart Foundation IN-CONTROL/ ; 101001678//ERC Consolidator Grant/ ; VI.C.202.022//NWO-VICI Grant/ ; 024.003.001//The Netherlands Organ-on-Chip Initiative, an NWO Gravitation Project/ ; }, abstract = {BACKGROUND: The gut microbiome and fecal metabolites have been found to influence sarcopenia, but whether there are potential bacteria that can alleviate sarcopenia has been under-investigated, and the molecular mechanism remains unclear.

METHODS: To investigate the relationships between the gut microbiome, fecal metabolites and sarcopenia, subjects were selected from observational multi-ethnic study conducted in Western China. Sarcopenia was diagnosed according to the criteria of the Asian Working Group for Sarcopenia 2014. The gut microbiome was profiled by shotgun metagenomic sequencing. Untargeted metabolomic analysis was performed to analyse the differences in fecal metabolites. We investigated bacterium with the greatest relative abundance difference between healthy individuals and sarcopenia patients, and the differences in metabolites associated with the bacteria, to verify its effects on muscle mass and function in a mouse model.

RESULTS: The study included 283 participants (68.90% females, mean age: 66.66 years old) with and without sarcopenia (141 and 142 participants, respectively) and from the Han (98 participants), Zang (88 participants) and Qiang (97 participants) ethnic groups. This showed an overall reduction (15.03% vs. 20.77%, P = 0.01) of Prevotella copri between the sarcopenia and non-sarcopenia subjects across the three ethnic groups. Functional characterization of the differential bacteria showed enrichment (odds ratio = 15.97, P = 0.0068) in branched chain amino acid (BCAA) metabolism in non-sarcopenia group. A total of 13 BCAA and their derivatives have relatively low levels in sarcopenia. In the in vivo experiment, we found that the blood BCAA level was higher in the mice gavaged with live P. copri (LPC) (P < 0.001). The LPC mice had significantly longer wire and grid hanging time (P < 0.02), longer time on rotor (P = 0.0001) and larger grip strength (P < 0.0001), indicating better muscle function. The weight of gastrocnemius mass and rectus femoris mass (P < 0.05) was higher in LPC mice. The micro-computed tomography showed a larger leg area (P = 0.0031), and a small animal analyser showed a higher lean mass ratio in LPC mice (P = 0.0157), indicating higher muscle mass.

CONCLUSIONS: The results indicated that there were lower levels of both P. copri and BCAA in sarcopenia individuals. In vivo experiments, gavage with LPC could attenuate muscle mass and function decline, indicating alleviating sarcopenia. This suggested that P. copri may play a therapeutic potential role in the management of sarcopenia.}, } @article {pmid37591387, year = {2023}, author = {Bounaga, A and Alsanea, A and Danouche, M and Rittmann, BE and Zhou, C and Boulif, R and Zeroual, Y and Benhida, R and Lyamlouli, K}, title = {Effect of alkaline leaching of phosphogypsum on sulfate reduction activity and bacterial community composition using different sources of anaerobic microbial inoculum.}, journal = {The Science of the total environment}, volume = {904}, number = {}, pages = {166296}, doi = {10.1016/j.scitotenv.2023.166296}, pmid = {37591387}, issn = {1879-1026}, mesh = {*Sulfates/chemistry ; Anaerobiosis ; Bacteria ; *Desulfovibrio ; Water ; Sulfides ; Lactates ; Oxidation-Reduction ; }, abstract = {Phosphogypsum (PG), a by-product of the phosphate industry, is high in sulfate, (SO4[2-]), which makes it an excellent substrate for sulfate-reducing bacteria (SRB) to produce hydrogen sulfide. This work aimed to optimize SO4[2-] leaching from PG to achieve a high biological reduction of SO4[2-] and generate high sulfide concentrations for subsequent use in the biological recovery of elemental sulfur. Five SRB consortia were isolated and enriched from: IS (Industrial sludges), MS (Marine sediments), WC (Winogradsky column), SNV (petroleum industry sediments) and PG (stored Phosphogypsum). The five consortia showed reduction activity when using PG leachate (with water) as source of SO4[2-] and lactate, acetate, or glucose as the electron donor. The highest reduction rate (81.5 %) was registered using lactate and the IS consortium (81.5 %) followed by MS (79 %) and PG (71 %). To enhance the concentration of leached SO4[2-] from PG for future utilization with the isolated consortia, PG was treated with NaOH solutions (2 % and 5 %). SO4[2-] release of 97 % was achieved with a 5 % concentration and the resulting leachate was further diluted to target a SO4[2-] concentration of 12.4 g·L[-1] for utilization with the isolated consortia. Compared to water leachate, a significantly higher reduction rate was registered (2 g·L[-1] of SO4[2]) using the IS consortium, demonstrating limited inhibition effect of sulfide[-] concentration on SRB functionalities. Moreover, metagenomic analysis of the consortia revealed that using PG as a source of SO4[2-] increased the abundance of Deltaproteobacteria, including known SRB like Desulfovibrio, Desulfomicrobium, and Desulfosporosinus, as well as novel SRB genera (Cupidesulfovibrio, Desulfocurvus, Desulfococcus) that showed, for the first time, significant potential as novel sulfate-reducers using PG as a SO4[2-] source.}, } @article {pmid37591100, year = {2023}, author = {Yang, C and Chen, Y and Zhang, Q and Qie, X and Chen, J and Che, Y and Lv, D and Xu, X and Gao, Y and Wang, Z and Sun, J}, title = {Mechanism of microbial regulation on methane metabolism in saline-alkali soils based on metagenomics analysis.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118771}, doi = {10.1016/j.jenvman.2023.118771}, pmid = {37591100}, issn = {1095-8630}, mesh = {*Alkalies ; *Soil ; Carbon Dioxide/analysis ; Metagenomics ; Nitrogen Dioxide/analysis ; Methane/analysis ; Soil Microbiology ; }, abstract = {Saline-alkali soils constitute a globally important carbon pool that plays a critical role in soil carbon dioxide (CO2) and methane (CH4) fluxes. However, the relative importance of microorganisms in the regulation of CH4 emissions under elevated salinity remains unclear. Here, we report the composition of CH4 production and oxidation microbial communities under five different salinity levels in the Yellow River Delta, China. This study also obtained the gene number of microbial CH4 metabolism via testing the soil metagenomes, and further investigated the key soil factors to determine the regulation mechanism. Spearman correlation analysis showed that the soil electrical conductivity, salt content, and Na[+], and SO4[2-] concentrations showed significantly negative correlations with the CO2 and CH4 emission rates, while the NO2[-]-N concentration and NO2[-]/NO3[-] ratio showed significantly positive correlations with the CO2 and CH4 emission rates. Metabolic pathway analysis showed that the mcrA gene for CH4 production was highest in low-salinity soils. By contrast, the relative abundances of the fwdA, ftr, mch, and mer genes related to the CO2 pathway increased significantly with rising salinity. Regarding CH4 oxidation processes, the relative abundances of the pmoA, mmoB, and mdh1 genes transferred from CH4 to formaldehyde decreased significantly from the control to the extreme-salinity plot. The greater abundance and rapid increase of methanotrophic bacteria compared with the lower abundance and slow increase in methanogenic archaea communities in saline-alkali soils may have increased CH4 oxidation and reduced CH4 production in this study. Only CO2 emissions positively affected CH4 emissions from low- to medium-salinity soils, while the diversities of CH4 production and oxidation jointly influenced CH4 emissions from medium- to extreme-salinity plots. Hence, future investigations will also explore more metabolic pathways for CH4 emissions from different types of saline-alkali lands and combine the key soil enzymes and regulated biotic or abiotic factors to enrich the CH4 metabolism pathway in saline-alkali soils.}, } @article {pmid37590181, year = {2023}, author = {Huang, BC and Li, GF and Ren, ZQ and Ji, XM and Wang, Y and Gu, YN and Li, JP and Chang, RR and Fan, NS and Jin, RC}, title = {Light-Driven Electron Uptake from Nonfermentative Organic Matter to Expedite Nitrogen Dissimilation by Chemolithotrophic Anammox Consortia.}, journal = {Environmental science & technology}, volume = {57}, number = {34}, pages = {12732-12740}, doi = {10.1021/acs.est.3c04160}, pmid = {37590181}, issn = {1520-5851}, mesh = {*Anaerobic Ammonia Oxidation ; *Cytochrome-c Peroxidase ; Electrons ; Hydrogen Peroxide ; Reactive Oxygen Species ; Nitrogen ; }, abstract = {Nonphotosynthetic microorganisms are typically unable to directly utilize light energy, but light might change the metabolic pathway of these bacteria indirectly by forming intermediates such as reactive oxygen species (ROS). This work investigated the role of light on nitrogen conversion by anaerobic ammonium oxidation (anammox) consortia. The results showed that high intensity light (>20000 lx) caused ca. 50% inhibition of anammox activity, and total ROS reached 167% at 60,000 lx. Surprisingly, 200 lx light was found to induce unexpected promotion of the nitrogen conversion rate, and ultraviolet light (<420 nm) was identified as the main contributor. Metagenomic and metatranscriptomic analyses revealed that the gene encoding cytochrome c peroxidase was highly expressed only under 200 lx light. [15]N isotope tracing, gene abundance quantification, and external H2O2 addition experiments showed that photoinduced trace H2O2 triggered cytochrome c peroxidase expression to take up electrons from extracellular nonfermentative organics to synthesize NADH and ATP, thereby expediting nitrogen dissimulation of anammox consortia. External supplying reduced humic acid into a low-intensity light exposure system would result in a maximal 1.7-fold increase in the nitrogen conversion rate. These interesting findings may provide insight into the niche differentiation and widespread nature of anammox bacteria in natural ecotopes.}, } @article {pmid37589876, year = {2023}, author = {K, S and Vasanthrao, R and Chattopadhyay, I}, title = {Impact of environment on transmission of antibiotic-resistant superbugs in humans and strategies to lower dissemination of antibiotic resistance.}, journal = {Folia microbiologica}, volume = {68}, number = {5}, pages = {657-675}, pmid = {37589876}, issn = {1874-9356}, mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Microbial/genetics ; }, abstract = {Antibiotics are the most efficient type of therapy developed in the twentieth century. From the early 1960s to the present, the rate of discovery of new and therapeutically useful classes of antibiotics has significantly decreased. As a result of antibiotic use, novel strains emerge that limit the efficiency of therapies in patients, resulting in serious consequences such as morbidity or mortality, as well as clinical difficulties. Antibiotic resistance has created major concern and has a greater impact on global health. Horizontal and vertical gene transfers are two mechanisms involved in the spread of antibiotic resistance genes (ARGs) through environmental sources such as wastewater treatment plants, agriculture, soil, manure, and hospital-associated area discharges. Mobile genetic elements have an important part in microbe selection pressure and in spreading their genes into new microbial communities; additionally, it establishes a loop between the environment, animals, and humans. This review contains antibiotics and their resistance mechanisms, diffusion of ARGs, prevention of ARG transmission, tactics involved in microbiome identification, and therapies that aid to minimize infection, which are explored further below. The emergence of ARGs and antibiotic-resistant bacteria (ARB) is an unavoidable threat to global health. The discovery of novel antimicrobial agents derived from natural products shifts the focus from chemical modification of existing antibiotic chemical composition. In the future, metagenomic research could aid in the identification of antimicrobial resistance genes in the environment. Novel therapeutics may reduce infection and the transmission of ARGs.}, } @article {pmid37589603, year = {2023}, author = {Millan Arias, P and Hill, KA and Kari, L}, title = {iDeLUCS: a deep learning interactive tool for alignment-free clustering of DNA sequences.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {9}, pages = {}, pmid = {37589603}, issn = {1367-4811}, mesh = {Base Sequence ; *Deep Learning ; Algorithms ; Archaea ; Cluster Analysis ; }, abstract = {SUMMARY: We present an interactive Deep Learning-based software tool for Unsupervised Clustering of DNA Sequences (iDeLUCS), that detects genomic signatures and uses them to cluster DNA sequences, without the need for sequence alignment or taxonomic identifiers. iDeLUCS is scalable and user-friendly: its graphical user interface, with support for hardware acceleration, allows the practitioner to fine-tune the different hyper-parameters involved in the training process without requiring extensive knowledge of deep learning. The performance of iDeLUCS was evaluated on a diverse set of datasets: several real genomic datasets from organisms in kingdoms Animalia, Protista, Fungi, Bacteria, and Archaea, three datasets of viral genomes, a dataset of simulated metagenomic reads from microbial genomes, and multiple datasets of synthetic DNA sequences. The performance of iDeLUCS was compared to that of two classical clustering algorithms (k-means++ and GMM) and two clustering algorithms specialized in DNA sequences (MeShClust v3.0 and DeLUCS), using both intrinsic cluster evaluation metrics and external evaluation metrics. In terms of unsupervised clustering accuracy, iDeLUCS outperforms the two classical algorithms by an average of ∼20%, and the two specialized algorithms by an average of ∼12%, on the datasets of real DNA sequences analyzed. Overall, our results indicate that iDeLUCS is a robust clustering method suitable for the clustering of large and diverse datasets of unlabeled DNA sequences.

iDeLUCS is available at https://github.com/Kari-Genomics-Lab/iDeLUCS under the terms of the MIT licence.}, } @article {pmid37589541, year = {2023}, author = {François, S and Nazki, S and Vickers, SH and Fournié, G and Perrins, CM and Broadbent, AJ and Pybus, OG and Hill, SC}, title = {Genetic diversity, recombination and cross-species transmission of a waterbird gammacoronavirus in the wild.}, journal = {The Journal of general virology}, volume = {104}, number = {8}, pages = {}, doi = {10.1099/jgv.0.001883}, pmid = {37589541}, issn = {1465-2099}, support = {BB/T008806/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/X006204/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 102427/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; 220414/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Animals ; *Gammacoronavirus/genetics ; *Coronavirus/genetics ; Disease Outbreaks ; *Anseriformes ; *Coronavirus Infections/epidemiology/veterinary ; Animals, Wild ; Genetic Variation ; Recombination, Genetic ; }, abstract = {Viruses emerging from wildlife can cause outbreaks in humans and domesticated animals. Predicting the emergence of future pathogens and mitigating their impacts requires an understanding of what shapes virus diversity and dynamics in wildlife reservoirs. In order to better understand coronavirus ecology in wild species, we sampled birds within a coastal freshwater lagoon habitat across 5 years, focussing on a large population of mute swans (Cygnus olor) and the diverse species that they interact with. We discovered and characterised the full genome of a divergent gammacoronavirus belonging to the Goose coronavirus CB17 species. We investigated the genetic diversity and dynamics of this gammacoronavirus using untargeted metagenomic sequencing of 223 faecal samples from swans of known age and sex, and RT-PCR screening of 1632 additional bird samples. The virus circulated persistently within the bird community; virus prevalence in mute swans exhibited seasonal variations, but did not change with swan age-class or epidemiological year. One whole genome was fully characterised, and revealed that the virus originated from a recombination event involving an undescribed gammacoronavirus species. Multiple lineages of this gammacoronavirus co-circulated within our study population. Viruses from this species have recently been detected in aquatic birds from both the Anatidae and Rallidae families, implying that host species habitat sharing may be important in shaping virus host range. As the host range of the Goose coronavirus CB17 species is not limited to geese, we propose that this species name should be updated to 'Waterbird gammacoronavirus 1'. Non-invasive sampling of bird coronaviruses may provide a tractable model system for understanding the evolutionary and cross-species dynamics of coronaviruses.}, } @article {pmid37589492, year = {2023}, author = {Sawayama, E and Takahashi, M and Kitamura, SI}, title = {Metagenomic profile of caudal fin morphology of farmed red sea bream Pagrus major.}, journal = {Diseases of aquatic organisms}, volume = {155}, number = {}, pages = {79-85}, doi = {10.3354/dao03742}, pmid = {37589492}, issn = {0177-5103}, mesh = {Animals ; *Sea Bream ; RNA, Ribosomal, 16S/genetics ; *Perciformes ; Farms ; *Tenacibaculum ; }, abstract = {The morphology of farm-reared fish often differs from that of their wild counterparts, impacting their market value. Two caudal fin tip shapes, acutely angled and blunted, are recognized in farmed populations of red sea bream Pagrus major. The angled form is preferred by consumers over the blunt since it resembles that of wild fish. Discovering the cause of the blunted tip is crucial to maximizing the commercial value of farmed red sea bream. We hypothesized that the blunt fin tip is the result of opportunistic bacteria and conducted partial 16S rRNA metagenomic barcoding and generated a clone library of the 16S rRNA gene to compare bacterial communities of the 2 fin forms. Metagenomic barcoding revealed an abundance of 5 bacterial genera, Sulfitobacter, Vibrio, Tenacibaculum, Psychrobacter, and an unknown genus of Rhodobacteraceae, on the caudal fin surface. Sulfitobacter was significantly more common on the angled caudal fin than the blunted. Vibrio is the dominant genus on the blunted caudal fin. The clone library identified these genera to species level, and Sulfitobacter sp., Vibrio harveyi, Tenacibaculum maritimum, and Psychrobacter marincola were frequently observed in blunt caudal fins. Our results suggest that opportunistic pathogenic bacteria such as V. harveyi and T. maritimum are not the primary cause of caudal fin malformation, and multiple factors such as combinations of injury, stress, and pathogenic infection may be involved. The reason for the significantly greater occurrence of Sulfitobacter sp. in the angled caudal fin is unknown, and further investigation is needed.}, } @article {pmid37588054, year = {2023}, author = {Zhao, Z and Chen, X and Wang, Y and Feng, J}, title = {Comparison of quality/quantity mNGS and usual mNGS for pathogen detection in suspected pulmonary infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1184245}, pmid = {37588054}, issn = {2235-2988}, mesh = {Humans ; Prospective Studies ; *Pneumonia ; High-Throughput Nucleotide Sequencing ; Bronchoalveolar Lavage Fluid ; Metagenome ; }, abstract = {Improved metagenomic next-generation sequencing (mNGS), for example, quality/quantity mNGS (QmNGS), is being used in the diagnosis of pulmonary pathogens. There are differences between QmNGS and the usual mNGS (UmNGS), but reports that compare their detection performances are rare. In this prospective study of patients enrolled between December 2021 and March 2022, the bronchoalveolar lavage fluid of thirty-six patients with suspected pulmonary infection was assessed using UmNGS and QmNGS. The sensitivity of QmNGS was similar to that of UmNGS. The specificity of QmNGS was higher than that of UmNGS; however, the difference was not statistically significant. The positive likelihood ratios (+LR) of QmNGS and UmNGS were 3.956 and 1.394, respectively, and the negative likelihood ratios (-LR) were 0.342 and 0.527, respectively. For the co-detection of pathogens, the depth and coverage of the QmNGS sequencing were lower than those of UmNGS, while for the detection of pathogens isolated from patients with pulmonary infection, the concordance rate was 77.2%. In the eleven patients with nonpulmonary infection, only viruses were detected using QmNGS, while UmNGS detected not only viruses but also bacteria and fungi. This study provides a basis for the selection of mNGS for the diagnosis of suspected pulmonary infection.}, } @article {pmid37587900, year = {2023}, author = {Umair, M and Jamal, Z and Haider, SA and Hakim, R and Ammar, M and Ali, Q and Akhtar, N and Ikram, A and Salman, M}, title = {Genomic characterization of the first mpox and varicella-zoster co-infection in Pakistan (2023) through next-generation sequencing.}, journal = {Journal of medical virology}, volume = {95}, number = {8}, pages = {e29037}, doi = {10.1002/jmv.29037}, pmid = {37587900}, issn = {1096-9071}, mesh = {Humans ; *Chickenpox/diagnosis ; *Coinfection/diagnosis ; Genomics ; *Herpes Zoster/diagnosis ; High-Throughput Nucleotide Sequencing ; *Mpox (monkeypox) ; Pakistan ; United States ; *Varicella Zoster Virus Infection ; }, abstract = {The global mpox outbreak spanning 2022-2023 has affected numerous countries worldwide. In this study, we present the first report on the detection, whole-genome sequence, and coinfection of the mpox virus and varicella zoster virus (VZV) from Pakistan. During April-May 2023, samples from 20 suspected cases of mpox were tested at the National Institutes of Health, Islamabad among which 4 tested positive. All four cases had a travel history of Saudi Arabia. All the suspected samples were processed by using a Zymo research kit for DNA extraction, followed by qRT-PCR amplification by using a DaAn Gene detection kit for the mpox virus. Further, two of the positive samples with a low Ct value (<20) were subjected to whole-genome sequencing using a metagenomic approach on the iSeq (Illumina) platform. The sequencing results revealed Clade IIb and genotype A.2.1 of MPXV, which clustered with viruses from Slovenia and the UK in July and June 2022, respectively. Our analysis identified two novel nonsynonymous substitutions in mpox virus, namely V98I in OPG046 and P600S in OPG109. Furthermore, we successfully retrieved the complete genome of VZV from the same sample, belonging to Clade 5. This study represents the first positive case of MPXV in Pakistan and the coinfection of mpox and VZV by using a metagenome approach providing insights into their complete genomes. Our results highlight the importance of surveillance at the point of entries, strengthening lab capacities including next-generation sequencing, and using differential diagnosis for timely and accurate detection of mpox cases.}, } @article {pmid37587527, year = {2023}, author = {Liao, H and Ji, Y and Sun, Y}, title = {High-resolution strain-level microbiome composition analysis from short reads.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {183}, pmid = {37587527}, issn = {2049-2618}, mesh = {*Microbiota/genetics ; Metagenome/genetics ; Metagenomics ; Software ; }, abstract = {BACKGROUND: Bacterial strains under the same species can exhibit different biological properties, making strain-level composition analysis an important step in understanding the dynamics of microbial communities. Metagenomic sequencing has become the major means for probing the microbial composition in host-associated or environmental samples. Although there are a plethora of composition analysis tools, they are not optimized to address the challenges in strain-level analysis: highly similar strain genomes and the presence of multiple strains under one species in a sample. Thus, this work aims to provide a high-resolution and more accurate strain-level analysis tool for short reads.

RESULTS: In this work, we present a new strain-level composition analysis tool named StrainScan that employs a novel tree-based k-mers indexing structure to strike a balance between the strain identification accuracy and the computational complexity. We tested StrainScan extensively on a large number of simulated and real sequencing data and benchmarked StrainScan with popular strain-level analysis tools including Krakenuniq, StrainSeeker, Pathoscope2, Sigma, StrainGE, and StrainEst. The results show that StrainScan has higher accuracy and resolution than the state-of-the-art tools on strain-level composition analysis. It improves the F1 score by 20% in identifying multiple strains at the strain level.

CONCLUSIONS: By using a novel k-mer indexing structure, StrainScan is able to provide strain-level analysis with higher resolution than existing tools, enabling it to return more informative strain composition analysis in one sample or across multiple samples. StrainScan takes short reads and a set of reference strains as input and its source codes are freely available at https://github.com/liaoherui/StrainScan . Video Abstract.}, } @article {pmid37587369, year = {2023}, author = {Gavriilidou, A and Avcı, B and Galani, A and Schorn, MA and Ingham, CJ and Ettema, TJG and Smidt, H and Sipkema, D}, title = {Candidatus Nemesobacterales is a sponge-specific clade of the candidate phylum Desulfobacterota adapted to a symbiotic lifestyle.}, journal = {The ISME journal}, volume = {17}, number = {11}, pages = {1808-1818}, pmid = {37587369}, issn = {1751-7370}, mesh = {Animals ; *Porifera/microbiology ; Phylogeny ; In Situ Hybridization, Fluorescence ; Bacteria/genetics ; Metagenome ; }, abstract = {Members of the candidate phylum Dadabacteria, recently reassigned to the phylum Candidatus Desulfobacterota, are cosmopolitan in the marine environment found both free-living and associated with hosts that are mainly marine sponges. Yet, these microorganisms are poorly characterized, with no cultured representatives and an ambiguous phylogenetic position in the tree of life. Here, we performed genome-centric metagenomics to elucidate their phylogenomic placement and predict the metabolism of the sponge-associated members of this lineage. Rank-based phylogenomics revealed several new species and a novel family (Candidatus Spongomicrobiaceae) within a sponge-specific order, named here Candidatus Nemesobacterales. Metabolic reconstruction suggests that Ca. Nemesobacterales are aerobic heterotrophs, capable of synthesizing most amino acids, vitamins and cofactors and degrading complex carbohydrates. We also report functional divergence between sponge- and seawater-associated metagenome-assembled genomes. Niche-specific adaptations to the sponge holobiont were evident from significantly enriched genes involved in defense mechanisms against foreign DNA and environmental stressors, host-symbiont interactions and secondary metabolite production. Fluorescence in situ hybridization gave a first glimpse of the morphology and lifestyle of a member of Ca. Desulfobacterota. Candidatus Nemesobacterales spp. were found both inside sponge cells centred around sponge nuclei and in the mesohyl of the sponge Geodia barretti. This study sheds light on the enigmatic group Ca. Nemesobacterales and their functional characteristics that reflect a symbiotic lifestyle.}, } @article {pmid37587248, year = {2023}, author = {Pei, Z and Li, X and Cui, S and Yang, B and Lu, W and Zhao, J and Mao, B and Chen, W}, title = {Population genomics of Lacticaseibacillus paracasei: pan-genome, integrated prophage, antibiotic resistance, and carbohydrate utilization.}, journal = {World journal of microbiology & biotechnology}, volume = {39}, number = {10}, pages = {280}, pmid = {37587248}, issn = {1573-0972}, support = {32172173//National Natural Science Foundation of China/ ; 31972086//National Natural Science Foundation of China/ ; 2021YFD2100700//Key Technologies Research and Development Program/ ; }, mesh = {Humans ; *Lacticaseibacillus paracasei ; Metagenomics ; Lacticaseibacillus ; Prophages/genetics ; Drug Resistance, Microbial ; Carbohydrates ; }, abstract = {Lacticaseibacillus paracasei has beneficial effects on human health and holds promising potential as a probiotic for use in the development of functional foods, especially dairy products. This species can adapt to a variety of ecological niches and presents fundamental carbohydrate metabolism and tolerance to environmental stresses. However, the population structure, ecology, and antibiotic resistance of Lc. paracasei in diverse ecological niches are poorly understood. Reclassification of Lc. paracasei as a separate species of Lacticaseibacillus has stimulated renewed interest in its research, and a deeper interpretation of it will be important for screening strains beneficial to human health. Here, we collected 121 self-isolated and 268 publicly available Lc. paracasei genomes discussed how genomic approaches have advanced our understanding of its taxonomy, ecology, evolution, diversity, integrated prophage-related element distribution, antibiotic resistance, and carbohydrate utilization. Moreover, for the Lc. paracasei strains isolated in this study, we assessed the inducibility of integrated prophages in their genomes and determined the phenotypes that presented tolerance to multiple antibiotics to provide evidence for safety evaluations of Lc. paracasei during the fermentation processes.}, } @article {pmid37587110, year = {2023}, author = {Walsh, LH and Walsh, AM and Garcia-Perez, I and Crispie, F and Costabile, A and Ellis, R and Finlayson, J and Finnegan, LA and Claesson, MJ and Holmes, E and Cotter, PD}, title = {Comparison of the relative impacts of acute consumption of an inulin-enriched diet, milk kefir or a commercial probiotic product on the human gut microbiome and metabolome.}, journal = {NPJ science of food}, volume = {7}, number = {1}, pages = {41}, pmid = {37587110}, issn = {2396-8370}, abstract = {It has been established that the human gut microbiota is central to health, and, consequently, there has been a growing desire to positively modulate its composition and/or function through, for example, the use of fermented foods, prebiotics or probiotics. Here, we compare the relative impact of the daily consumption of an inulin-enriched diet (n = 10), a commercial probiotic-containing fermented milk product (FMP) (n = 10), or a traditional kefir FMP (n = 9), over a 28-day period on the gut microbiome and urine metabolome of healthy human adults. None of the treatments resulted in significant changes to clinical parameters or biomarkers tested. However, shotgun metagenomic analysis revealed that kefir consumption resulted in a significant change in taxonomy, in the form of an increased abundance of the sub-dominant FMP-associated species Lactococcus raffinolactis, which further corresponded to shifts in the urine metabolome. Overall, our results indicated that daily consumption of a single portion of kefir alone resulted in detectable changes to the gut microbiota and metabolome of consumers.}, } @article {pmid37586512, year = {2023}, author = {Wang, X and Xiang, B and Li, J and Zhang, M and Frostegard, A and Bakken, L and Zhang, X}, title = {Using adaptive and aggressive N2O-reducing bacteria to augment digestate fertilizer for mitigating N2O emissions from agricultural soils.}, journal = {The Science of the total environment}, volume = {903}, number = {}, pages = {166284}, doi = {10.1016/j.scitotenv.2023.166284}, pmid = {37586512}, issn = {1879-1026}, abstract = {Nitrous oxide (N2O) emitted from agricultural soils destroys stratospheric ozone and contributes to global warming. A promising approach to reduce emissions is fertilizing the soil using organic wastes augmented by non-denitrifying N2O-reducing bacteria (NNRB). To realize this potential, we need a suite of NNRB strains that fulfill several criteria: efficient reduction of N2O, ability to grow in organic waste, and ability to survive in farmland soil. In this study, we enriched such organisms by sequential anaerobic batch incubations with N2O and reciprocating inoculation between the sterilized substrates of anaerobic manure digestate and soils. 16S rDNA amplicon sequencing and metagenomics analysis showed that a cluster of bacteria containing nosZ genes encoding N2O-reductase, was enriched during the incubation process. Strains of several dominant members were then isolated and characterized, and three of them were found to harbor the nosZ gene but none of the other denitrifying genes, thus qualifying as NNRB. The selected isolates were tested for their capacities to reduce N2O emissions from three different typical Chinese farmland soils. The results indicated the significant mitigation effect of these isolates, even in very acidic red soil. In conclusion, this study demonstrated a strategy to engineer the soil microbiome with promising NNRB with high adaptability to livestock manure digestate as well as different agricultural soils, which would be suitable for developing novel fertilizer for farmland application to efficiently mitigate the N2O emissions from agricultural soils.}, } @article {pmid37586502, year = {2023}, author = {Menezes, CA and Almeida, PS and Camargo, FP and Delforno, TP and Oliveira, VM and Sakamoto, IK and Varesche, MBA and Silva, EL}, title = {One versus two-stage codigestion of sugarcane vinasse and glycerol: Assessing combinations at mesophilic and (hyper) thermophilic conditions.}, journal = {The Science of the total environment}, volume = {904}, number = {}, pages = {166294}, doi = {10.1016/j.scitotenv.2023.166294}, pmid = {37586502}, issn = {1879-1026}, mesh = {*Bioreactors ; *Saccharum/metabolism ; Glycerol ; Anaerobiosis ; Methane/metabolism ; Sulfates ; }, abstract = {Sugarcane vinasse exits the distillation process at high temperatures, which may differ from the optimal temperatures for dark fermentation and anaerobic digestion. A 15 °C temperature increase, for example, stops sugarcane vinasse methane generation, making distillery vinasse digestion complicated. Conversely, in other aspects, co-digesting vinasse and glycerol has been proven to stabilize methane production from vinasse because of sulfate dilution. However, glycerol has not been tested to stabilize vinasse digestion under temperature changes. Thus, this study compared the effects of different temperature settings on the co-digestion of 10 g COD L[-1] of vinasse and glycerol (50 %:50 % on a COD basis) in anaerobic fluidized bed reactors (AFBR), i.e., an acidogenic and a methanogenic one-stage AFBRs operated at 55, 60, and 65 °C, and two methanogenic AFBRs fed both with acidogenic effluent (one operated at room temperature (25 °C) and the other at 55, 60, and 65 °C). The co-digestion provided steady methane generation at all AFBRs, with methane production rates ranging from 2.27 to 2.93 L CH4 d[-1] L[-1], whether in one or two stages. A feature of this research was to unravel the black box of the role of sulfate in the digestion of sugarcane vinasse, which was rarely studied. Desulfovibrio was the primary genus degrading 1,3-propanediol into 3-hydroxypropanoate after genome sequencing. Phosphate acetyltransferase (EC: 2.3.1.8, K00625) and acetate kinase (EC: 2.7.2.1, K00925) genes were also found, suggesting propionate was metabolized. In practical aspects, regarding the two-stage systems, the thermophilic-mesophilic (acidogenic-methanogenic) configuration is best for extracting additional value-added products because 1,3-propanediol may be recovered at high yields with steady methane production at reduced energy expenditure in a reactor operated at room temperature. However, the one-stage design is best for methane generation per system volume since it remained stable with rising temperatures, and all systems presented similar methane production rates.}, } @article {pmid37586432, year = {2023}, author = {Yang, H and Chen, X and Wang, A and Liu, S and Liang, X and Lu, H and Li, Q}, title = {Regulating sludge composting with percarbonate facilitated the methylation and detoxification of arsenic mediated via reactive oxygen species.}, journal = {Bioresource technology}, volume = {387}, number = {}, pages = {129674}, doi = {10.1016/j.biortech.2023.129674}, pmid = {37586432}, issn = {1873-2976}, mesh = {*Arsenic ; Sewage ; Reactive Oxygen Species ; *Composting ; Methylation ; Hydrogen Peroxide ; }, abstract = {This study purposed to demonstrate the impact of reactive oxygen species (ROS) on arsenic detoxification mechanism in sludge composting with percarbonate. In this study, sodium percarbonate was used as an additive. Adding sodium percarbonate increased the content of H2O2 and OH, which the experimental group (SPC) was higher than the control group (CK). In addition, it decreased the bioavailability of arsenic by 19.10%. Metagenomic analysis found that Firmicutes and Pseudomonas took an active part in the overall compost as the dominant bacteria of arsenic methylation. ROS positively correlated with arsenic oxidation and methylation genes (arsC, arsM), with the gene copy number of arsC and arsM increasing to 7.74 × 10[12], 5.24 × 10[12] in SPC. In summary, the passivation of arsenic could be achieved by adding percarbonate, which promoted the methylation of arsenic, reduced the toxicity of arsenic, and provided a new idea for the harmless management of sludge.}, } @article {pmid37585451, year = {2023}, author = {Rostami, M and Karegar, A and Taghavi, SM and Ghasemi-Fasaei, R and Ghorbani, A}, title = {Effective combination of arugula vermicompost, chitin and inhibitory bacteria for suppression of the root-knot nematode Meloidogyne javanica and explanation of their beneficial properties based on microbial analysis.}, journal = {PloS one}, volume = {18}, number = {8}, pages = {e0289935}, pmid = {37585451}, issn = {1932-6203}, mesh = {Animals ; *Tylenchoidea ; Chitin ; *Chitosan/pharmacology ; Antinematodal Agents/pharmacology/chemistry ; *Bacillus ; *Ricinus communis ; }, abstract = {Root-knot nematodes (Meloidogyne spp.) are dangerous parasites of many crops worldwide. The threat of chemical nematicides has led to increasing interest in studying the inhibitory effects of organic amendments and bacteria on plant-parasitic nematodes, but their combination has been less studied. One laboratory and four glasshouse experiments were conducted to study the effect on M. javanica of animal manure, common vermicompost, shrimp shells, chitosan, compost and vermicompost from castor bean, chinaberry and arugula, and the combination of arugula vermicompost with some bacteria, isolated from vermicompost or earthworms. The extract of arugula compost and vermicompost, common vermicompost and composts from castor bean and chinaberry reduced nematode egg hatch by 12-32% and caused 13-40% mortality of second-stage juveniles in vitro. Soil amendments with the combination vermicompost of arugula + Pseudomonas. resinovorans + Sphingobacterium daejeonense + chitosan significantly increased the yield of infected tomato plants and reduced nematode reproduction factor by 63.1-76.6%. Comparison of chemical properties showed that arugula vermicompost had lower pH, EC, and C/N ratio than arugula compost. Metagenomics analysis showed that Bacillus, Geodermatophilus, Thermomonas, Lewinella, Pseudolabrys and Erythrobacter were the major bacterial genera in the vermicompost of arugula. Metagenomics analysis confirmed the presence of chitinolytic, detoxifying and PGPR bacteria in the vermicompost of arugula. The combination of arugula vermicompost + chitosan + P. resinovorans + S. daejeonense could be an environmentally friendly approach to control M. javanica.}, } @article {pmid37584775, year = {2023}, author = {Chouhan, U and Gamad, U and Choudhari, JK}, title = {Metagenomic analysis of soybean endosphere microbiome to reveal signatures of microbes for health and disease.}, journal = {Journal, genetic engineering & biotechnology}, volume = {21}, number = {1}, pages = {84}, pmid = {37584775}, issn = {2090-5920}, abstract = {BACKGROUND: Soil metagenomics is a cultivation-independent molecular strategy for investigating and exploiting the diversity of soil microbial communities. Soil microbial diversity is essential because it is critical to sustaining soil health for agricultural productivity and protection against harmful organisms. This study aimed to perform a metagenomic analysis of the soybean endosphere (all microbial communities found in plant leaves) to reveal signatures of microbes for health and disease.

RESULTS: The dataset is based on the National Center for Biotechnology Information (NCBI) Sequence Read Archive (SRA) release "microbial diversity in soybean". The quality control process rejected 21 of the evaluated sequences (0.03% of the total sequences). Dereplication determined that 68,994 sequences were artificial duplicate readings, and removed them from consideration. Ribosomal Ribonucleic acid (RNA) genes were present in 72,747 sequences that successfully passed quality control (QC). Finally, we found that hierarchical classification for taxonomic assignment was conducted using MG-RAST, and the considered dataset of the metagenome domain of bacteria (99.68%) dominated the other groups. In Eukaryotes (0.31%) and unclassified sequence 2 (0.00%) in the taxonomic classification of bacteria in the genus group, Streptomyces, Chryseobacterium, Ppaenibacillus, Bacillus, and Mitsuaria were found. We also found some biological pathways, such as CMP-KDO biosynthesis II (from D-arabinose 5-phosphate), tricarboxylic acid cycle (TCA) cycle (plant), citrate cycle (TCA cycle), fatty acid biosynthesis, and glyoxylate and dicarboxylate metabolism. Gene prediction uncovered 1,180 sequences, 15,172 of which included gene products, with the shortest sequence being 131 bases and maximum length 3829 base pairs. The gene list was additionally annotated using Integrated Microbial Genomes and Microbiomes. The annotation process yielded a total of 240 genes found in 177 bacterial strains. These gene products were found in the genome of strain 7598. Large volumes of data are generated using modern sequencing technology to sample all genes in all species present in a given complex sample.

CONCLUSIONS: These data revealed that it is a rich source of potential biomarkers for soybean plants. The results of this study will help us to understand the role of the endosphere microbiome in plant health and identify the microbial signatures of health and disease. The MG-RAST is a public resource for the automated phylogenetic and functional study of metagenomes. This is a powerful tool for investigating the diversity and function of microbial communities.}, } @article {pmid37584728, year = {2023}, author = {Yavorov-Dayliev, D and Milagro, FI and Ayo, J and Oneca, M and Goyache, I and López-Yoldi, M and Aranaz, P}, title = {Glucose-lowering effects of a synbiotic combination containing Pediococcus acidilactici in C. elegans and mice.}, journal = {Diabetologia}, volume = {66}, number = {11}, pages = {2117-2138}, pmid = {37584728}, issn = {1432-0428}, mesh = {Animals ; Mice ; Male ; *Synbiotics ; Caenorhabditis elegans/metabolism ; *Pediococcus acidilactici/metabolism ; Blood Glucose/metabolism ; *Diabetes Mellitus, Type 2 ; Mice, Obese ; RNA, Ribosomal, 16S ; Insulin-Like Growth Factor I ; Mice, Inbred C57BL ; Obesity/metabolism ; Diet, High-Fat/adverse effects ; Insulin ; Glucose ; }, abstract = {AIMS/HYPOTHESIS: Modulation of gut microbiota has emerged as a promising strategy to treat or prevent the development of different metabolic diseases, including type 2 diabetes and obesity. Previous data from our group suggest that the strain Pediococcus acidilactici CECT9879 (pA1c) could be an effective probiotic for regulating glucose metabolism. Hence, the objectives of this study were to verify the effectiveness of pA1c on glycaemic regulation in diet-induced obese mice and to evaluate whether the combination of pA1c with other normoglycaemic ingredients, such as chromium picolinate (PC) and oat β-glucans (BGC), could increase the efficacy of this probiotic on the regulation of glucose and lipid metabolism.

METHODS: Caenorhabditis elegans was used as a screening model to describe the potential synbiotic activities, together with the underlying mechanisms of action. In addition, 4-week-old male C57BL/6J mice were fed with a high-fat/high-sucrose diet (HFS) for 6 weeks to induce hyperglycaemia and obesity. Mice were then divided into eight groups (n=12 mice/group) according to dietary supplementation: control-diet group; HFS group; pA1c group (10[10] colony-forming units/day); PC; BGC; pA1c+PC+BGC; pA1c+PC; and pA1c+BGC. Supplementations were maintained for 10 weeks. Fasting blood glucose was determined and an IPGTT was performed prior to euthanasia. Fat depots, liver and other organs were weighed, and serum biochemical variables were analysed. Gene expression analyses were conducted by real-time quantitative PCR. Sequencing of the V3-V4 region of the 16S rRNA gene from faecal samples of each group was performed, and differential abundance for family, genera and species was analysed by ALDEx2R package.

RESULTS: Supplementation with the synbiotic (pA1c+PC+BGC) counteracted the effect of the high glucose by modulating the insulin-IGF-1 signalling pathway in C. elegans, through the reversal of the glucose nuclear localisation of daf-16. In diet-induced obese mice, all groups supplemented with the probiotic significantly ameliorated glucose tolerance after an IPGTT, demonstrating the glycaemia-regulating effect of pA1c. Further, mice supplemented with pA1c+PC+BGC exhibited lower fasting blood glucose, a reduced proportion of visceral adiposity and a higher proportion of muscle tissue, together with an improvement in the brown adipose tissue in comparison with the HFS group. Besides, the effect of the HFS diet on steatosis and liver damage was normalised by the synbiotic. Gene expression analyses demonstrated that the synbiotic activity was mediated not only by modulation of the insulin-IGF-1 signalling pathway, through the overexpression of GLUT-1 and GLUT-4 mediators, but also by a decreased expression of proinflammatory cytokines such as monocyte chemotactic protein-1. 16S metagenomics demonstrated that the synbiotic combinations allowed an increase in the concentration of P. acidilactici, together with improvements in the intestinal microbiota such as a reduction in Prevotella and an increase in Akkermansia muciniphila.

CONCLUSIONS/INTERPRETATION: Our data suggest that the combination of pA1c with PC and BGC could be a potential synbiotic for blood glucose regulation and may help to fight insulin resistance, diabetes and obesity.}, } @article {pmid37584000, year = {2023}, author = {Xu, WB and Fu, JJ and Yuan, XJ and Xian, QJ and Zhang, LJ and Song, PP and You, ZQ and Wang, CT and Zhao, QG and Pang, F}, title = {Metagenomic next-generation sequencing in the diagnosis of neurocysticercosis: A case report.}, journal = {World journal of clinical cases}, volume = {11}, number = {20}, pages = {4912-4919}, pmid = {37584000}, issn = {2307-8960}, abstract = {BACKGROUND: The clinical symptoms and imaging manifestations of neurocysticercosis (NCC) are very different, and the difficulty and delay of clinical diagnoses may lead to an increase in mortality and disability. Rapid and accurate pathogen identification is important for the treatment of these patients. Metagenomic next-generation sequencing (mNGS) is a powerful tool to identify pathogens, especially in infections that are difficult to identify by conventional methods.

CASE SUMMARY: A 43-year-old male patient was admitted due to a recurrent headache for a few months. Imaging examinations showed hydrocephalus and cystic lesions, which were considered to be a central nervous system infection, but no etiology was found by routine examination. mNGS of the cerebrospinal fluid revealed high Taenia solium reads, and the positive results of a cysticercosis antibody test confirmed the infection. Combined with the patient's clinical manifestations, the etiological evidence, and the imaging manifestation, the patient was finally diagnosed with NCC and he was prescribed dexamethasone, albendazole, neurotrophic drugs, and intracranial pressure reduction therapy. The headaches disappeared after anti-parasite treatment, and no associated symptoms recurred prior to the three- and six-month follow-up.

CONCLUSION: As an accurate and sensitivity detection method, mNGS can be a reliable approach for the diagnosis of NCC.}, } @article {pmid37583994, year = {2023}, author = {Jian, L and Zhao, QQ}, title = {Unexpected diffuse lung lesions in a patient with pulmonary alveolar proteinosis: A case report.}, journal = {World journal of clinical cases}, volume = {11}, number = {20}, pages = {4932-4936}, pmid = {37583994}, issn = {2307-8960}, abstract = {BACKGROUND: Pulmonary alveolar proteinosis (PAP) often presents nonspecifically and can be easily confused with: (1) Idiopathic interstitial lung fibrosis; (2) alveolar carcinoma; (3) pulmonary tuberculosis; and (4) other lung diseases such as viral pneumonia, mycoplasma pneumonia, and chlamydial pneumonia.

CASE SUMMARY: Diagnosis: In this case, a patient was diagnosed with PAP through transbronchial cryobiopsy (TBCB) and quantitative metagenomic next-generation sequencing, which confirmed the impairment of surfactant turnover as the underlying cause of PAP. Interventions: High-volume total lung lavage was performed for this patient. Outcomes: The patient's clinical condition had improved significantly by the 6-month follow-up, with a 92% finger oxygen saturation. A repeat chest computed tomography scan revealed scattered patchy ground-glass shadows in both lungs, which was consistent with alveolar protein deposition but with a lower density than in the radiograph from October 23, 2022.

CONCLUSION: TBCB has unique advantages in diagnosing atypical alveolar protein deposition, particularly for enabling the early detection of PAP. This information can help patients take preventive measures to prevent or halt PAP development by avoiding dusty environments and seeking treatment with total lung lavage and inhaled granulocyte macrophage colony-stimulating factor.}, } @article {pmid37583445, year = {2023}, author = {Zheng, H and Tan, Y and Chen, X and Chen, J and Li, L and Wang, J}, title = {Encephalitis and myositis caused by Trachipleistophora hominis diagnosed by metagenomic next-generation sequencing-a case report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1206624}, pmid = {37583445}, issn = {2235-2988}, mesh = {Male ; Humans ; Adult ; *Microsporidia ; *Myositis/diagnosis/drug therapy ; *Encephalitis/diagnosis ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Myositis is the main manifestation of Trachipleistophora hominis (T. hominis) infection and other microsporidians infection in immunocompromised patients. Clinical differential diagnosis of different microsporidians can be challenging, as the standard technique to distinguish various microsporidia species, transmission electron microscopy (TEM), is time-consuming and relies on equipment and experienced staffs who can perform the test and interpret the results.

CASE PRESENTATION: We report a 37-year-old Chinese man with acquired immune deficiency syndrome (AIDS) developed headache and muscle pain in the extremities. Tramadol was used to relieve his pain. Infectious lesions in his brain were detected by cerebral magnetic resonance imaging (MRI). Oval-shaped pathogens was observed by biopsy of right gastrocnemius. Finally, T. hominis was identified by metagenomic next-generation sequencing (mNGS) in the gastrocnemius tissue and cerebrospinal fluid. After a 12-week course of antifungal treatment and antiretroviral therapy, the patient recovered from the encephalitis and myositis caused by T. hominis.

CONCLUSION: This report described the diagnosis and treatment of the first case of encephalitis caused by T. hominis. And mNGS is recommended for the rapid diagnosis of uncommon pathogens.}, } @article {pmid37583444, year = {2023}, author = {Zhang, Y and Andreu-Sánchez, S and Vadaq, N and Wang, D and Matzaraki, V and van der Heijden, WA and Gacesa, R and Weersma, RK and Zhernakova, A and Vandekerckhove, L and de Mast, Q and Joosten, LAB and Netea, MG and van der Ven, AJAM and Fu, J}, title = {Gut dysbiosis associates with cytokine production capacity in viral-suppressed people living with HIV.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1202035}, pmid = {37583444}, issn = {2235-2988}, mesh = {Humans ; *HIV ; Interleukin-10 ; Interleukin-6 ; Dysbiosis ; *HIV Infections/drug therapy ; Cytokines ; }, abstract = {BACKGROUND: People living with human immunodeficiency virus (PLHIV) are exposed to chronic immune dysregulation, even when virus replication is suppressed by antiretroviral therapy (ART). Given the emerging role of the gut microbiome in immunity, we hypothesized that the gut microbiome may be related to the cytokine production capacity of PLHIV.

METHODS: To test this hypothesis, we collected metagenomic data from 143 ART-treated PLHIV and assessed the ex vivo production capacity of eight different cytokines [interleukin-1β (IL-1β), IL-6, IL-1Ra, IL-10, IL-17, IL-22, tumor necrosis factor, and interferon-γ] in response to different stimuli. We also characterized CD4[+] T-cell counts, HIV reservoir, and other clinical parameters.

RESULTS: Compared with 190 age- and sex-matched controls and a second independent control cohort, PLHIV showed microbial dysbiosis that was correlated with viral reservoir levels (CD4[+] T-cell-associated HIV-1 DNA), cytokine production capacity, and sexual behavior. Notably, we identified two genetically different P. copri strains that were enriched in either PLHIV or healthy controls. The control-related strain showed a stronger negative association with cytokine production capacity than the PLHIV-related strain, particularly for Pam3Cys-incuded IL-6 and IL-10 production. The control-related strain is also positively associated with CD4[+] T-cell level.

CONCLUSIONS: Our findings suggest that modulating the gut microbiome may be a strategy to modulate immune response in PLHIV.}, } @article {pmid37581914, year = {2023}, author = {Njovu, IK and Nalumaga, PP and Ampaire, L and Nuwagira, E and Mwesigye, J and Musinguzi, B and Kassaza, K and Taseera, K and Kiguli Mukasa, J and Bazira, J and Iramiot, JS and Baguma, A and Bongomin, F and Kwizera, R and Achan, B and Cox, MJ and King, JS and May, R and Ballou, ER and Itabangi, H}, title = {Investigating Metabolic and Molecular Ecological Evolution of Opportunistic Pulmonary Fungal Coinfections: Protocol for a Laboratory-Based Cross-Sectional Study.}, journal = {JMIR research protocols}, volume = {12}, number = {}, pages = {e48014}, pmid = {37581914}, issn = {1929-0748}, abstract = {BACKGROUND: Fungal-bacterial cocolonization and coinfections pose an emerging challenge among patients suspected of having pulmonary tuberculosis (PTB); however, the underlying pathogenic mechanisms and microbiome interactions are poorly understood. Understanding how environmental microbes, such as fungi and bacteria, coevolve and develop traits to evade host immune responses and resist treatment is critical to controlling opportunistic pulmonary fungal coinfections. In this project, we propose to study the coexistence of fungal and bacterial microbial communities during chronic pulmonary diseases, with a keen interest in underpinning fungal etiological evolution and the predominating interactions that may exist between fungi and bacteria.

OBJECTIVE: This is a protocol for a study aimed at investigating the metabolic and molecular ecological evolution of opportunistic pulmonary fungal coinfections through determining and characterizing the burden, etiological profiles, microbial communities, and interactions established between fungi and bacteria as implicated among patients with presumptive PTB.

METHODS: This will be a laboratory-based cross-sectional study, with a sample size of 406 participants. From each participant, 2 sputa samples (one on-spot and one early morning) will be collected. These samples will then be analyzed for both fungal and bacterial etiology using conventional metabolic and molecular (intergenic transcribed spacer and 16S ribosomal DNA-based polymerase chain reaction) approaches. We will also attempt to design a genome-scale metabolic model for pulmonary microbial communities to analyze the composition of the entire microbiome (ie, fungi and bacteria) and investigate host-microbial interactions under different patient conditions. This analysis will be based on the interplays of genes (identified by metagenomics) and inferred from amplicon data and metabolites (identified by metabolomics) by analyzing the full data set and using specific computational tools. We will also collect baseline data, including demographic and clinical history, using a patient-reported questionnaire. Altogether, this approach will contribute to a diagnostic-based observational study. The primary outcome will be the overall fungal and bacterial diagnostic profile of the study participants. Other diagnostic factors associated with the etiological profile, such as incidence and prevalence, will also be analyzed using univariate and multivariate schemes. Odds ratios with 95% CIs will be presented with a statistical significance set at P<.05.

RESULTS: The study has been approved by the Mbarara University Research Ethic Committee (MUREC1/7-07/09/20) and the Uganda National Council of Science and Technology (HS1233ES). Following careful scrutiny, the protocol was designed to enable patient enrollment, which began in March 2022 at Mbarara University Teaching Hospital. Data collection is ongoing and is expected to be completed by August 2023, and manuscripts will be submitted for publication thereafter.

CONCLUSIONS: Through this protocol, we will explore the metabolic and molecular ecological evolution of opportunistic pulmonary fungal coinfections among patients with presumptive PTB. Establishing key fungal-bacterial cross-kingdom synergistic relationships is crucial for instituting fungal bacterial coinfecting etiology.

TRIAL REGISTRATION: ISRCTN Registry ISRCTN33572982; https://tinyurl.com/caa2nw69.

DERR1-10.2196/48014.}, } @article {pmid37581868, year = {2023}, author = {Liu, Z and Mu, C and Zhu, W}, title = {Metagenomics-based inference of microbial metabolism towards neuroactive amino acids and the response to antibiotics in piglet colon.}, journal = {Amino acids}, volume = {55}, number = {10}, pages = {1333-1347}, pmid = {37581868}, issn = {1438-2199}, support = {31902166//the Natural Science Foundation of China/ ; 32030104//the Natural Science Foundation of China/ ; }, mesh = {Animals ; Swine ; *Amino Acids ; *Tryptophan/metabolism ; Kynurenine ; Anti-Bacterial Agents/pharmacology ; Putrescine ; Glutamic Acid ; gamma-Aminobutyric Acid/metabolism ; Colon/metabolism ; Transaminases/genetics ; }, abstract = {Gut-derived neuroactive metabolites from amino acids perform a broad range of physiological roles in the body. However, the interaction between microbiota and epithelium in the metabolism of amino acids with neuroactive properties remains unclear in the colon of piglets. To investigate the microbial and epithelial metabolism, metagenomics and mucosal metabolomics were performed using colonic samples from 12 ileum-canulated piglets subjected to a 25-day infusion with saline or antibiotics. We categorized 23 metabolites derived from the metabolism of tryptophan, glutamate, and tyrosine, known as precursors of neuroactive metabolites. Microbial enzymes involved in the kynurenine synthesis via arylformamidase, 4-aminobutyric acid (GABA) synthesis via putrescine aminotransferase, and tyramine synthesis via tyrosine decarboxylase were identified in Clostridiales bacterium, uncultured Blautia sp., and Methanobrevibacter wolinii, respectively. Antibiotics significantly affected the microbiota involved in tryptophan-kynurenine and glutamate-GABA metabolism. An increase in the relative abundance of putrescine aminotransferase and Blautia sp. correlated positively with an increase in luminal GABA concentration. Overall, our findings provide new insights into the microbial ability to metabolize key amino acids that are precursors of neuroactive metabolites.}, } @article {pmid37581624, year = {2023}, author = {Du, J and Li, Y and Huang, Y and Zhang, D and Li, L}, title = {Characterization of a novel monooxygenase originating from a deep-sea sediment metagenomic library.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {20}, pages = {6237-6249}, pmid = {37581624}, issn = {1432-0614}, support = {31500059//National Natural Science Foundation of China/ ; 20222100//Guangdong Provincial Bureau of Traditional Chinese Medicine Project/ ; }, mesh = {Amino Acid Sequence ; *Mixed Function Oxygenases/genetics ; Phylogeny ; *Indigo Carmine ; Gene Library ; Temperature ; Metals ; Ions ; Hydrogen-Ion Concentration ; Cloning, Molecular ; }, abstract = {Oxygenases are important biocatalysts to produce many industrially important biomolecules. Here, a novel oxygenase, named MoxA, was identified through screening of a deep-sea sediment metagenomic library. Sequence analysis showed MoxA contains 424 amino acid residues with a predicated molecular mass of 46.9 kDa. Multiple sequence alignment and phylogenetic analysis indicated the sequence might be a new member of monooxygenase subfamily. A recombinant MoxA was obtained through the functional expression of moxA gene in Escherichia coli. Characterization of the purified MoxA indicated that it is an alkaline oxygenase showing maximal activity at pH 8.0. The optimal temperature of MoxA was 37 ℃, and it retained more than 70% of its initial activity after 1 h at 20-50 ℃ exhibiting good thermostability. Furthermore, effect of metal ions and organic solvents on enzymatic activity was investigated, and the results showed that the activity of MoxA was enhanced by Cu[2+], Zn[2+], Co[2+] and Mg[2+] at 1 mM, and by Co[2+], Ca[2+] and Mg[2+] at 5 mM. Moreover, the recombinant strain harboring MoxA was used as a whole-cell biocatalyst for the efficient biosynthesis of indigo showing promising conversion efficiency. The biochemical properties of MoxA indicated that it would provide great contribution for the indigo bioproduction. KEY POINTS: • A novel monooxygenase from a metagenomic library was characterized. • The activity of MoxA was enhanced by metal ions at 1 mM and 5 mM. • MoxA has an optimal temperature of 37 ℃ and exhibited high conversion capacity.}, } @article {pmid37581165, year = {2023}, author = {Lu, D and Abudouaini, M and Kerimu, M and Leng, Q and Wu, H and Aynazar, A and Zhong, Z}, title = {Clinical Evaluation of Metagenomic Next-Generation Sequencing and Identification of Risk Factors in Patients with Severe Community-Acquired Pneumonia.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {5135-5147}, pmid = {37581165}, issn = {1178-6973}, abstract = {PURPOSE: Severe community-acquired pneumonia (SCAP) is the leading cause of death among patients with infectious diseases worldwide. This study aimed to evaluate the effectiveness of metagenomic next-generation sequencing (mNGS) through detecting pathogens in bronchoalveolar lavage fluid (BALF) and identifying risk factors for recovery in SCAP patients.

PATIENTS AND METHODS: This prospective study recruited 158 SCAP patients admitted to respiratory intensive care unit that were randomly divided into control and study groups, with receiving conventional tests and the same conventional tests plus mNGS, respectively. The diagnostic efficiency of mNGS was evaluated by comparing with conventional tests. Furthermore, univariate and multivariate logistic regression analyses were performed to determine the independent risk factors for recovery in SCAP patients, and a nomogram prediction model was established based on these factors.

RESULTS: Within the study group, the pathogen detection rate was significantly higher with mNGS than that with conventional tests (84.81% vs 45.57%, P < 0.001), with a positive coincidence rate of 94.44%. Acinetobacter baumannii (21.52%, 17/79), Candida albicans (17.72%, 14/79), and Klebsiella pneumonia (15.19%, 12/79) were the top three common pathogens detected by mNGS. Of note, the improvement rate of patients in the study group was significantly higher than that in the control group. The further analysis revealed that the increased levels of interleukin-6, blood urea nitrogen, procalcitonin, the longer length of hospital stay, and bacterial infection were independent risk factors for recovery of SCAP patients, while mNGS detection status was a protective factor. The predictive model showed a good performance for the modeling and validation sets.

CONCLUSION: Early mNGS exhibited a superior diagnostic efficiency to conventional tests in SCAP patients, which can reduce the risk of death in SCAP patients. Moreover, the clinical factors could also be used for the management and prognosis prediction of SCAP patients.}, } @article {pmid37580828, year = {2023}, author = {Deng, F and Wang, C and Li, D and Peng, Y and Deng, L and Zhao, Y and Zhang, Z and Wei, M and Wu, K and Zhao, J and Li, Y}, title = {The unique gut microbiome of giant pandas involved in protein metabolism contributes to the host's dietary adaption to bamboo.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {180}, pmid = {37580828}, issn = {2049-2618}, mesh = {Animals ; Mice ; *Ursidae ; *Gastrointestinal Microbiome/genetics ; Feces/chemistry ; Metagenome ; Diet ; }, abstract = {BACKGROUND: The gut microbiota of the giant panda (Ailuropoda melanoleuca), a global symbol of conservation, are believed to be involved in the host's dietary switch to a fibrous bamboo diet. However, their exact roles are still largely unknown.

RESULTS: In this study, we first comprehensively analyzed a large number of gut metagenomes giant pandas (n = 322), including 98 pandas sequenced in this study with deep sequencing (Illumina) and third-generation sequencing (nanopore). We reconstructed 408 metagenome-assembled genomes (MAGs), and 148 of which (36.27%) were near complete. The most abundant MAG was classified as Streptococcus alactolyticus. A pairwise comparison of the metagenomes and meta-transcriptomes in 14 feces revealed genes involved in carbohydrate metabolism were lower, but those involved in protein metabolism were greater in abundance and expression in giant pandas compared to those in herbivores and omnivores. Of note, S. alactolyticus was positively correlated to the KEGG modules of essential amino-acid biosynthesis. After being isolated from pandas and gavaged to mice, S. alactolyticus significantly increased the relative abundance of essential amino acids in mice jejunum.

CONCLUSIONS: The study highlights the unique protein metabolic profiles in the giant panda's gut microbiome. The findings suggest that S. alactolyticus is an important player in the gut microbiota that contributes to the giant panda's dietary adaptation by more involvement in protein rather than carbohydrate metabolism. Video Abstract.}, } @article {pmid37580698, year = {2023}, author = {Tang, X and Wang, N and Liu, G and Tan, H and Li, AM and Gao, YQ and Yao, MY and Wang, N and Jing, HD and Di, QG and Chen, L and Wang, R and Li, XY and Li, Y and Yuan, X and Zhao, Y and Li, Q and Tong, ZH and Sun, B}, title = {Psittacosis caused severe community-acquired pneumonia accompanied by acute hypoxic respiratory failure: a multicenter retrospective cohort study from China.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {532}, pmid = {37580698}, issn = {1471-2334}, support = {Ggyfz202332//Reform and Development Program of the Beijing Institute of Respiratory Medicine/ ; XMLX202105//the Clinical medicine development project of Beijing Hospital Authority/ ; Z201100005520030//clinical diagnosis and treatment technology and translational research project of Beijing/ ; XUEKEDAITOUREN-01-19//Excellent Talents Development Project of Public Health Technology/ ; }, mesh = {Animals ; Humans ; *Psittacosis/complications/diagnosis/drug therapy ; Retrospective Studies ; *Pneumonia ; *Community-Acquired Infections/diagnosis ; Tetracycline/therapeutic use ; Poultry ; Fluoroquinolones/therapeutic use ; China/epidemiology ; *Respiratory Insufficiency ; }, abstract = {INTRODUCTION: Psittacosis can cause severe community-acquired pneumonia (CAP). The clinical manifestations of psittacosis range from subclinical to fulminant psittacosis with multi-organ failure. It is essential to summarize the clinical characteristic of patients with severe psittacosis accompanied by acute hypoxic respiratory failure (AHRF).

METHODS: This retrospective study included patients with severe psittacosis caused CAP accompanied by AHRF from 19 tertiary hospitals of China. We recorded the clinical data, antimicrobial therapy, respiratory support, complications, and outcomes. Chlamydia psittaci was detected on the basis of metagenomic next-generation sequencing performed on bronchoalveolar lavage fluid samples. Patient outcomes were compared between the treatment methods.

RESULTS: This study included 45 patients with severe CAP and AHRF caused by psittacosis from April 2018 to May 2021. The highest incidence of these infections was between September and April. There was a history of poultry contact in 64.4% of the patients. The median PaO2/FiO2 of the patients was 119.8 (interquartile range, 73.2 to 183.6) mmHg. Four of 45 patients (8.9%) died in the ICU, and the median ICU duration was 12 days (interquartile range, 8 to 21) days. There were no significant differences between patients treated with fluoroquinolone initially and continued after the diagnosis, fluoroquinolone initially followed by tetracycline, and fluoroquinolone combined with tetracycline.

CONCLUSION: Psittacosis caused severe CAP seems not rare, especially in the patients with the history of exposure to poultry or birds. Empirical treatment that covers atypical pathogens may benefit such patients, which fluoroquinolones might be considered as an alternative.}, } @article {pmid37580683, year = {2023}, author = {Józefiak, A and Rawski, M and Kierończyk, B and Józefiak, D and Mazurkiewicz, J}, title = {Effect of two insect meals on the gut commensal microbiome of healthy sea trout (Salmo trutta vr. trutta).}, journal = {BMC veterinary research}, volume = {19}, number = {1}, pages = {124}, pmid = {37580683}, issn = {1746-6148}, support = {POIR 4.4//Narodowe Centrum Nauki/ ; TEAM TECH no. POIR.04.04.00-00-204E/16-00//Narodowe Centrum Badań i Rozwoju/ ; }, mesh = {Animals ; *Trout/microbiology ; Diet/veterinary ; Insecta ; Bacteria ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: The balance of the intestinal commensal microbiome of fish and other animals plays an important role in the physiological processes of healthy animals, contributes to the defense against pathogens, stimulates the immune system and facilitates nutrient metabolism. In the last decade, the interest in the application of the insects in fish nutrition increased, although little is known regarding the effects of insect meals on the gastrointenstinal tract microbiome of the sea trout fingerlings. The aim of this study was to evaluate the effect of two diets containing mealworm (MW) and superworm (SW) on the microbiome of the digesta of sea trout fingerlings and the relative abundances of different taxa among communities under controlled conditions.

RESULTS: The insect meals produced a similar weight gain and survival rate to sea trout fed fishmeal. The most abundant bacterial phylum in all the treatment groups was Firmicutes followed by Proteobacteria and Actinobacteria, and significant differences in the amount of Cyanobacteria were observed in the SW group.

CONCLUSIONS: The insect meals did not produce differences in the three most abundant phyla in the sea trout digesta. However, the effect of each type of meal on the lower taxonomic levels was evident, particularly in the case of the superworm meal. These microbiome differences indicated that mealworm meal was more related to fishmeal than superworm meal. Our results highlight the potential effects of insect meals, such as mealworm and superworm meals, on the microbiota of sea trout.}, } @article {pmid37579703, year = {2023}, author = {Li, Z and Wang, J and Fan, J and Yue, H and Zhang, X}, title = {Marine toxin domoic acid alters protistan community structure and assembly process in sediments.}, journal = {Marine environmental research}, volume = {191}, number = {}, pages = {106131}, doi = {10.1016/j.marenvres.2023.106131}, pmid = {37579703}, issn = {1879-0291}, mesh = {*Marine Toxins ; Kainic Acid/toxicity ; Eukaryota ; *Microbiota ; }, abstract = {Domoic acid (DA)-producing algal blooms have been the issue of worldwide concerns in recent decades, but there has never been any attempt to investigate the effects of DA on microbial ecology in marine environments. Protists are considered to be key regulators of microbial activity, community structure and evolution, we therefore explore the effect of DA on the ecology of protists via metagenome in this work. The results indicate that trace amounts of DA can act as a stressor to alter alpha and beta diversity of protistan community. Among trophic functional groups, consumers and phototrophs are negative responders of DA, implying DA is potentially capable of functional-level effects in the ocean. Moreover, microecological theory reveals that induction of DA increases the role of deterministic processes in microbial community assembly, thus altering the biotic relationships and successional processes in symbiotic patterns. Finally, we demonstrate that the mechanism by which DA shapes protistan ecological network is by acting on phototrophs, which triggers cascading effects in networks and eventually leading to shifts in ecological succession of protists. Overall, our results present the first perspective regarding the effects of DA on marine microbial ecology, which will supplement timely information on the ecological impacts of DA in the ocean.}, } @article {pmid37579601, year = {2023}, author = {Shi, X and Tan, W and Tang, S and Ling, Q and Tang, C and Qin, P and Luo, S and Zhao, Y and Yu, F and Li, Y}, title = {Metagenomics reveals taxon-specific responses of soil nitrogen cycling under different fertilization regimes in heavy metal contaminated soil.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118766}, doi = {10.1016/j.jenvman.2023.118766}, pmid = {37579601}, issn = {1095-8630}, mesh = {*Soil/chemistry ; *Metagenomics ; Soil Microbiology ; Bacteria/genetics ; Fertilization ; Nitrogen ; }, abstract = {Soil deficiency, cyclic erosion, and heavy metal pollution have led to fertility loss and ecological function decline in mining areas. Fertilization is an important way to rapidly replenish soil nutrients, which have a major influence on the soil nitrogen cycling process, but different fertilization regimes have different impacts on soil properties and microbial functional potentials. Here, metagenomic sequencing was used to investigate the different responses of key functional genes of microbial nitrogen cycling to fertilization regimes and explore the potential effects of soil physicochemical properties on the key functional genes. The results indicated that AC-HH (ammonium chloride-high frequency and concentration) treatment significantly increased the gene abundance of norC (13.40-fold), nirK (5.46-fold), and napA (5.37-fold). U-HH (urea-high frequency and concentration) treatment significantly increased the gene abundance of hao (6.24-fold), pmoA-amoA (4.32-fold) norC (7.00-fold), nosZ (3.69-fold), and nirK (6.88-fold). Functional genes were distributed differently among the 10 dominant phyla. The nifH and nifK genes were distributed only in Proteobacteria. The hao gene was distributed in Gemmatimonadetes, Nitrospirae and Proteobacteria. Fertilization regimes caused changes in functional redundancy in soil, and nirK and nirB, which are involved in denitrification, were present in different genera. Fertilization regimes with high frequency and high concentration were more likely to increase the gene abundance at the genus level. In summary, this study provides insights into the taxon-specific response of soil nitrogen cycling under different fertilization regimes, where changes in fertilization regimes affect microbial nitrogen cycling by altering soil physicochemical properties in a complex dynamic environment.}, } @article {pmid37578240, year = {2023}, author = {Cabrol, L and Capo, E and van Vliet, DM and von Meijenfeldt, FAB and Bertilsson, S and Villanueva, L and Sánchez-Andrea, I and Björn, E and G Bravo, A and Heimburger Boavida, LE}, title = {Redox gradient shapes the abundance and diversity of mercury-methylating microorganisms along the water column of the Black Sea.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0053723}, pmid = {37578240}, issn = {2379-5077}, mesh = {Humans ; *Mercury/analysis ; *Methylmercury Compounds/analysis ; Ecosystem ; Water/analysis ; Black Sea ; Bacteria/genetics ; *Chloroflexi/metabolism ; Oxidation-Reduction ; Planctomycetes ; Oxygen/analysis ; }, abstract = {In the global context of seawater deoxygenation triggered by climate change and anthropogenic activities, changes in redox gradients impacting biogeochemical transformations of pollutants, such as mercury, become more likely. Being the largest anoxic basin worldwide, with high concentrations of the potent neurotoxic methylmercury (MeHg), the Black Sea is an ideal natural laboratory to provide new insights about the link between dissolved oxygen concentration and hgcAB gene-carrying (hgc[+]) microorganisms involved in the formation of MeHg. We combined geochemical and microbial approaches to assess the effect of vertical redox gradients on abundance, diversity, and metabolic potential of hgc[+] microorganisms in the Black Sea water column. The abundance of hgcA genes [congruently estimated by quantitative PCR (qPCR) and metagenomics] correlated with MeHg concentration, both maximal in the upper part of the anoxic water. Besides the predominant Desulfobacterales, hgc[+] microorganisms belonged to a unique assemblage of diverse-previously underappreciated-anaerobic fermenters from Anaerolineales, Phycisphaerae (characteristic of the anoxic and sulfidic zone), Kiritimatiellales, and Bacteroidales (characteristic of the suboxic zone). The metabolic versatility of Desulfobacterota differed from strict sulfate reduction in the anoxic water to reduction of various electron acceptors in the suboxic water. Linking microbial activity and contaminant concentration in environmental studies is rare due to the complexity of biological pathways. In this study, we disentangle the role of oxygen in shaping the distribution of Hg-methylating microorganisms consistently with MeHg concentration, and we highlight their taxonomic and metabolic niche partitioning across redox gradients, improving the prediction of the response of marine communities to the expansion of oxygen-deficient zones. IMPORTANCE Methylmercury (MeHg) is a neurotoxin detected at high concentrations in certain marine ecosystems, posing a threat to human health. MeHg production is mainly mediated by hgcAB gene-carrying (hgc[+]) microorganisms. Oxygen is one of the main factors controlling Hg methylation; however, its effect on the diversity and ecology of hgc[+] microorganisms remains unknown. Under the current context of seawater deoxygenation, mercury cycling is expected to be disturbed. Here, we show the strong effect of oxygen gradients on the distribution of potential Hg methylators. In addition, we show for the first time the significant contribution of a unique assemblage of potential fermenters from Anaerolineales, Phycisphaerae, and Kiritimatiellales to Hg methylation, stratified in different redox niches along the Black Sea gradient. Our results considerably expand the known taxonomic diversity and ecological niches prone to the formation of MeHg and contribute to better apprehend the consequences of oxygen depletion in seawater.}, } @article {pmid37578199, year = {2023}, author = {Gwak, HJ and Lee, HA and Jeong, JY and Lee, Y and Rho, M and Cho, SH}, title = {Antibiotic Sensitivity and Nasal Microbiome in Patients with Acute Bacterial Rhinosinusitis.}, journal = {The Laryngoscope}, volume = {}, number = {}, pages = {}, doi = {10.1002/lary.30950}, pmid = {37578199}, issn = {1531-4995}, support = {RS-2023-00217123//National Research Foundation of Korea (NRF) grant and Basic Science Research Program funded by the Korean government (MSIT), South Korea/ ; 2021M3H4A4079522//National Research Foundation of Korea (NRF) grant and Basic Science Research Program funded by the Korean government (MSIT), South Korea/ ; 2021R1F1A1049413//National Research Foundation of Korea (NRF) grant and Basic Science Research Program funded by the Korean government (MSIT), South Korea/ ; }, abstract = {OBJECTIVES: Acute rhinosinusitis (ARS) is a common upper respiratory tract infection that is mostly of viral origin. However, little is known about the nasal microbiome profile at presentation and the changes caused by antibiotics in acute bacterial rhinosinusitis (ABRS).

METHODS: This was a prospective single-center study. Overall, 43 ARS patients were screened and were assessed with the symptom questionnaires, nasal endoscopy, and Water's view. Five healthy subjects were recruited as controls. Middle meatal mucus samples were obtained using a cotton swab (for bacterial culture and antimicrobial susceptibility testing) and the suction technique (for 16S rRNA sequencing). After 1 week of antibiotic use (amoxicillin with clavulanic acid), we enrolled 13 patients with ABRS with positive isolates and middle meatal samples for 16S rRNA sequencing were obtained again.

RESULTS: Overall, we demonstrated a significantly lower abundance of the Lactobacillaceae family in ABRS patients than in healthy controls. Resistant ABRS had different characteristics of middle meatal microbiomes when compared to sensitive ABRS as follows: (1) lower proportion of lactic acid bacteria, (2) increased pathogens such as Rhodococcus sp., Massila sp., Acinetobacter sp., and H. influenza, and (3) increased beta diversity. However, no remarkable changes were observed in the middle meatal microbiome after antibiotic use.

CONCLUSION: We showed the roles of Lactobacillaceae in ABRS, and Acinetobacter and Massilia in case of amoxicillin resistance.

LEVEL OF EVIDENCE: 3 Laryngoscope, 2023.}, } @article {pmid37577672, year = {2023}, author = {Real, MVF and Colvin, MS and Sheehan, MJ and Moeller, AH}, title = {Major urinary protein (Mup) gene family deletion drives sex-specific alterations on the house mouse gut microbiota.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37577672}, support = {R24 AG065172/AG/NIA NIH HHS/United States ; R35 GM138284/GM/NIGMS NIH HHS/United States ; }, abstract = {The gut microbiota is shaped by host metabolism. In house mice (Mus musculus), major urinary protein (MUP) pheromone production represents a considerable energy investment, particularly in sexually mature males. Deletion of the Mup gene family shifts mouse metabolism towards an anabolic state, marked by lipogenesis, lipid accumulation, and body mass increases. Given the metabolic implications of MUPs, they may also influence the gut microbiota. Here, we investigated the effect of deletion of the Mup gene family on the gut microbiota of sexually mature mice. Shotgun metagenomics revealed distinct taxonomic and functional profiles between wildtype and knockout males, but not females. Deletion of the Mup gene cluster significantly reduced diversity in microbial families and functions in male mice. Additionally, specific taxa of the Ruminococcaceae family, which is associated with gut health and reduced risk of developing metabolic syndrome, and several microbial functions, such as transporters involved in vitamin B5 acquisition, were significantly depleted in the microbiota of Mup-knockout males. Altogether these results show that major urinary proteins significantly affect the gut microbiota of house mouse in a sex-specific manner.}, } @article {pmid37577448, year = {2023}, author = {Bonatelli, ML and Rohwerder, T and Popp, D and Liu, Y and Akay, C and Schultz, C and Liao, KP and Ding, C and Reemtsma, T and Adrian, L and Kleinsteuber, S}, title = {Recently evolved combination of unique sulfatase and amidase genes enables bacterial degradation of the wastewater micropollutant acesulfame worldwide.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1223838}, pmid = {37577448}, issn = {1664-302X}, abstract = {Xenobiotics often challenge the principle of microbial infallibility. One example is acesulfame introduced in the 1980s as zero-calorie sweetener, which was recalcitrant in wastewater treatment plants until the early 2010s. Then, efficient removal has been reported with increasing frequency. By studying acesulfame metabolism in alphaproteobacterial degraders of the genera Bosea and Chelatococcus, we experimentally confirmed the previously postulated route of two subsequent hydrolysis steps via acetoacetamide-N-sulfonate (ANSA) to acetoacetate and sulfamate. Genome comparison of wildtype Bosea sp. 100-5 and an acesulfame degradation-defective mutant revealed the involvement of two plasmid-borne gene clusters. The acesulfame-hydrolyzing sulfatase is strictly manganese-dependent and belongs to the metallo beta-lactamase family. In all degraders analyzed, it is encoded on a highly conserved gene cluster embedded in a composite transposon. The ANSA amidase, on the other hand, is an amidase signature domain enzyme encoded in another gene cluster showing variable length among degrading strains. Transposition of the sulfatase gene cluster between chromosome and plasmid explains how the two catabolic gene clusters recently combined for the degradation of acesulfame. Searching available genomes and metagenomes for the two hydrolases and associated genes indicates that the acesulfame plasmid evolved and spread worldwide in short time. While the sulfatase is unprecedented and unique for acesulfame degraders, the amidase occurs in different genetic environments and likely evolved for the degradation of other substrates. Evolution of the acesulfame degradation pathway might have been supported by the presence of structurally related natural and anthropogenic compounds, such as aminoacyl sulfamate ribonucleotide or sulfonamide antibiotics.}, } @article {pmid37577445, year = {2023}, author = {Amorín de Hegedüs, R and Conesa, A and Foster, JS}, title = {Integration of multi-omics data to elucidate keystone unknown taxa within microbialite-forming ecosystems.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1174685}, pmid = {37577445}, issn = {1664-302X}, abstract = {Microbes continually shape Earth's biochemical and physical landscapes by inhabiting diverse metabolic niches. Despite the important role microbes play in ecosystem functioning, most microbial species remain unknown highlighting a gap in our understanding of structured complex ecosystems. To elucidate the relevance of these unknown taxa, often referred to as "microbial dark matter," the integration of multiple high throughput sequencing technologies was used to evaluate the co-occurrence and connectivity of all microbes within the community. Since there are no standard methodologies for multi-omics integration of microbiome data, we evaluated the abundance of "microbial dark matter" in microbialite-forming communities using different types meta-omic datasets: amplicon, metagenomic, and metatranscriptomic sequencing previously generated for this ecosystem. Our goal was to compare the community structure and abundances of unknown taxa within the different data types rather than to perform a functional characterization of the data. Metagenomic and metatranscriptomic data were input into SortMeRNA to extract 16S rRNA gene reads. The output, as well as amplicon sequences, were processed through QIIME2 for taxonomy analysis. The R package mdmnets was utilized to build co-occurrence networks. Most hubs presented unknown classifications, even at the phyla level. Comparisons of the highest scoring hubs of each data type using sequence similarity networks allowed the identification of the most relevant hubs within the microbialite-forming communities. This work highlights the importance of unknown taxa in community structure and proposes that ecosystem network construction can be used on several types of data to identify keystone taxa and their potential function within microbial ecosystems.}, } @article {pmid37577441, year = {2023}, author = {Santana-Pereira, ALR and Moen, FS and Severance, B and Liles, MR}, title = {Influence of soil nutrients on the presence and distribution of CPR bacteria in a long-term crop rotation experiment.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1114548}, pmid = {37577441}, issn = {1664-302X}, abstract = {Bacteria affiliated with the Candidate Phyla Radiation (CPR) are a hyper-diverse group of ultra-small bacteria with versatile yet sparse metabolisms. However, most insights into this group come from a surprisingly small number of environments, and recovery of CPR bacteria from soils has been hindered due to their extremely low abundance within complex microbial assemblages. In this study we enriched soil samples from 14 different soil fertility treatments for ultra-small (<0.45 μm) bacteria in order to study rare soil CPR. 42 samples were sequenced, enabling the reconstruction of 27 quality CPR metagenome-assembled genomes (MAGs) further classified as Parcubacteria/Paceibacteria, Saccharibacteria/Saccharimonadia and ABY1, in addition to representative genomes from Gemmatimonadetes, Dependentiae and Chlamydae phyla. These genomes were fully annotated and used to reconstruct the CPR community across all 14 plots. Additionally, for five of these plots, the entire microbiota was reconstructed using 16S amplification, showing that specific soil CPR may form symbiotic relationships with a varied and circumstantial range of hosts. Cullars CPR had a prevalence of enzymes predicted to degrade plant-derived carbohydrates, which suggests they have a role in plant biomass degradation. Parcubacteria appear to be more apt at microfauna necromass degradation. Cullars Saccharibacteria and a Parcubacteria group were shown to carry a possible aerotolerance mechanism coupled with potential for aerobic respiration, which appear to be a unique adaptation to the oxic soil environment. Reconstruction of CPR communities across treatment plots showed that they were not impacted by changes in nutrient levels or microbiota composition, being only impacted by extreme conditions, causing some CPR to dominate the community. These findings corroborate the understanding that soil-dwelling CPR bacteria have a very broad symbiont range and have metabolic capabilities associated to soil environments which allows them to scavenge resources and form resilient communities. The contributions of these microbial dark matter species to soil ecology and plant interactions will be of significant interest in future studies.}, } @article {pmid37577433, year = {2023}, author = {Laranjo, M}, title = {Editorial: Role of starters on the safety of fermented food products.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1260403}, doi = {10.3389/fmicb.2023.1260403}, pmid = {37577433}, issn = {1664-302X}, } @article {pmid37577378, year = {2023}, author = {Kulecka, M and Zeber-Lubecka, N and Bałabas, A and Czarnowski, P and Bagińska, K and Głowienka, M and Kluska, A and Piątkowska, M and Dąbrowska, M and Waker, E and Mikula, M and Ostrowski, J}, title = {Diarrheal-associated gut dysbiosis in cancer and inflammatory bowel disease patients is exacerbated by Clostridioides difficile infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1190910}, pmid = {37577378}, issn = {2235-2988}, mesh = {Humans ; *Clostridioides difficile/genetics ; Dysbiosis/complications/microbiology ; *Clostridium Infections/microbiology ; *Inflammatory Bowel Diseases/complications/microbiology ; Diarrhea/microbiology ; Bacteria/genetics ; Butyrates ; *Neoplasms/complications ; }, abstract = {INTRODUCTION: Low diversity gut dysbiosis can take different forms depending on the disease context. In this study, we used shotgun metagenomic sequencing and gas chromatography-mass spectrometry (GC-MS) to compared the metagenomic and metabolomic profiles of Clostridioides (Clostridium) difficile diarrheal cancer and inflammatory bowel disease (IBD) patients and defined the additive effect of C. difficile infection (CDI) on intestinal dysbiosis.

RESULTS: The study cohort consisted of 138 case-mix cancer patients, 43 IBD patients, and 45 healthy control individuals. Thirty-three patients were also infected with C. difficile. In the control group, three well-known enterotypes were identified, while the other groups presented with an additional Escherichia-driven enterotype. Bacterial diversity was significantly lower in all groups than in healthy controls, while the highest level of bacterial species richness was observed in cancer patients. Fifty-six bacterial species had abundance levels that differentiated diarrheal patient groups from the control group. Of these species, 52 and 4 (Bacteroides fragilis, Escherichia coli, Klebsiella pneumoniae, and Ruminococcus gnavus) were under-represented and over-represented, respectively, in all diarrheal patient groups. The relative abundances of propionate and butyrate were significantly lower in fecal samples from IBD and CDI patients than in control samples. Isobutyrate, propanate, and butyrate concentrations were lower in cancer, IBD, and CDI samples, respectively. Glycine and valine amino acids were over- represented in diarrheal patients.

CONCLUSION: Our data indicate that different external and internal factors drive comparable profiles of low diversity dysbiosis. While diarrheal-related low diversity dysbiosis may be a consequence of systemic cancer therapy, a similar phenotype is observed in cases of moderate to severe IBD, and in both cases, dysbiosis is exacerbated by incidence of CDI.}, } @article {pmid37577374, year = {2023}, author = {Avellaneda-Franco, L and Dahlman, S and Barr, JJ}, title = {The gut virome and the relevance of temperate phages in human health.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1241058}, pmid = {37577374}, issn = {2235-2988}, mesh = {Humans ; *Bacteriophages/genetics ; Virome ; Bacteria/genetics ; }, abstract = {Alterations in the gut virome impact human health. Bacteriophages, viruses that infect bacteria, dominate the gut virome and are mainly composed by virulent and temperate phages. While virulent phages exclusively replicate within and lyse their bacterial host's cell, temperate phages switch from an integrated state residing within their bacterial host's chromosome to an induced free virion state via an induction event. How often do these induction events occur and what are their implications on gut homeostasis? Here, we summarize the current knowledge of the gut virome based on metagenomics and present how the proportion of induced temperate phages varies amongst individuals, age, and disease states. Finally, we highlight the importance of building upon classical culture-dependent techniques and sequencing approaches to improve our understanding of temperate phages to enable their potential therapeutic use.}, } @article {pmid37577371, year = {2023}, author = {Naud, S and Valles, C and Abdillah, A and Abou Chacra, L and Mekhalif, FZ and Ibrahim, A and Caputo, A and Baudoin, JP and Gouriet, F and Bittar, F and Lagier, JC and Ranque, S and Fenollar, F and Tidjani Alou, M and Raoult, D}, title = {Preliminary landscape of Candidatus Saccharibacteria in the human microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1195679}, pmid = {37577371}, issn = {2235-2988}, mesh = {Female ; Humans ; Prospective Studies ; Retrospective Studies ; *Bacteria/genetics ; *Microbiota ; Real-Time Polymerase Chain Reaction ; }, abstract = {INTRODUCTION: Candidate Phyla Radiation (CPR) and more specifically Candidatus Saccharibacteria (TM7) have now been established as ubiquitous members of the human oral microbiota. Additionally, CPR have been reported in the gastrointestinal and urogenital tracts. However, the exploration of new human niches has been limited to date.

METHODS: In this study, we performed a prospective and retrospective screening of TM7 in human samples using standard PCR, real-time PCR, scanning electron microscopy (SEM) and shotgun metagenomics.

RESULTS: Using Real-time PCR and standard PCR, oral samples presented the highest TM7 prevalence followed by fecal samples, breast milk samples, vaginal samples and urine samples. Surprisingly, TM7 were also detected in infectious samples, namely cardiac valves and blood cultures at a low prevalence (under 3%). Moreover, we observed CPR-like structures using SEM in all sample types except cardiac valves. The reconstruction of TM7 genomes in oral and fecal samples from shotgun metagenomics reads further confirmed their high prevalence in some samples.

CONCLUSION: This study confirmed, through their detection in multiple human samples, that TM7 are human commensals that can also be found in clinical settings. Their detection in clinical samples warrants further studies to explore their role in a pathological setting.}, } @article {pmid37577265, year = {2023}, author = {Fuhl, W and Zabel, S and Nieselt, K}, title = {Improving taxonomic classification with feature space balancing.}, journal = {Bioinformatics advances}, volume = {3}, number = {1}, pages = {vbad092}, pmid = {37577265}, issn = {2635-0041}, abstract = {SUMMARY: Modern high-throughput sequencing technologies, such as metagenomic sequencing, generate millions of sequences that need to be assigned to their taxonomic rank. Modern approaches either apply local alignment to existing databases, such as MMseqs2, or use deep neural networks, as in DeepMicrobes and BERTax. Due to the increasing size of datasets and databases, alignment-based approaches are expensive in terms of runtime. Deep learning-based approaches can require specialized hardware and consume large amounts of energy. In this article, we propose to use k-mer profiles of DNA sequences as features for taxonomic classification. Although k-mer profiles have been used before, we were able to significantly increase their predictive power significantly by applying a feature space balancing approach to the training data. This greatly improved the generalization quality of the classifiers. We have implemented different pipelines using our proposed feature extraction and dataset balancing in combination with different simple classifiers, such as bagged decision trees or feature subspace KNNs. By comparing the performance of our pipelines with state-of-the-art algorithms, such as BERTax and MMseqs2 on two different datasets, we show that our pipelines outperform these in almost all classification tasks. In particular, sequences from organisms that were not part of the training were classified with high precision.

The open-source code and the code to reproduce the results is available in Seafile, at https://tinyurl.com/ysk47fmr.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.}, } @article {pmid37577055, year = {2023}, author = {Foo, A and Cerdeira, L and Hughes, GL and Heinz, E}, title = {Recovery of metagenomic data from the Aedes aegypti microbiome using a reproducible snakemake pipeline: MINUUR.}, journal = {Wellcome open research}, volume = {8}, number = {}, pages = {131}, pmid = {37577055}, issn = {2398-502X}, abstract = {Background: Ongoing research of the mosquito microbiome aims to uncover novel strategies to reduce pathogen transmission. Sequencing costs, especially for metagenomics, are however still significant. A resource that is increasingly used to gain insights into host-associated microbiomes is the large amount of publicly available genomic data based on whole organisms like mosquitoes, which includes sequencing reads of the host-associated microbes and provides the opportunity to gain additional value from these initially host-focused sequencing projects. Methods: To analyse non-host reads from existing genomic data, we developed a snakemake workflow called MINUUR (Microbial INsights Using Unmapped Reads). Within MINUUR, reads derived from the host-associated microbiome were extracted and characterised using taxonomic classifications and metagenome assembly followed by binning and quality assessment. We applied this pipeline to five publicly available Aedes aegypti genomic datasets, consisting of 62 samples with a broad range of sequencing depths. Results: We demonstrate that MINUUR recovers previously identified phyla and genera and is able to extract bacterial metagenome assembled genomes (MAGs) associated to the microbiome. Of these MAGS, 42 are high-quality representatives with >90% completeness and <5% contamination. These MAGs improve the genomic representation of the mosquito microbiome and can be used to facilitate genomic investigation of key genes of interest. Furthermore, we show that samples with a high number of KRAKEN2 assigned reads produce more MAGs. Conclusions: Our metagenomics workflow, MINUUR, was applied to a range of Aedes aegypti genomic samples to characterise microbiome-associated reads. We confirm the presence of key mosquito-associated symbionts that have previously been identified in other studies and recovered high-quality bacterial MAGs. In addition, MINUUR and its associated documentation are freely available on GitHub and provide researchers with a convenient workflow to investigate microbiome data included in the sequencing data for any applicable host genome of interest.}, } @article {pmid37577040, year = {2023}, author = {Han, CY and Ye, XM and Lu, JP and Jin, HY and Wang, P and Xu, WW and Zhang, M}, title = {Effect of Benaglutide on Gut Microbiota and Fecal Metabolites in Patients with Type 2 Diabetes Mellitus.}, journal = {Diabetes, metabolic syndrome and obesity : targets and therapy}, volume = {16}, number = {}, pages = {2329-2344}, pmid = {37577040}, issn = {1178-7007}, abstract = {OBJECTIVE: Benaglutide is a glucagon-like peptide-1 receptor agonist (GLP-1RA) that has been approved in the treatment of type 2 diabetes mellitus (T2DM). It is known to lead to significant weight loss, and it is hypothesized that changes in gut microbiota may play a significant role in such weight loss. However, it is unclear how gut microbiota and metabolites change as a result of benaglutide treatment.

METHODS: Healthy participants and patients with T2DM were included in this study. They received differentiated treatments, and stool specimens were collected separately. These stool specimens were subjected to 16S ribosomal RNA amplicon and metagenomic sequencing to create fecal metabolomic profiles. The diversity of gut microbiota and metabolic products in the stools of each participant was analyzed.

RESULTS: The data showed that Faecalibacterium prausnitzii was abundant in the gut microbiota of the control group, which was entirely made up of healthy individuals; however, it showed a statistically significant decrease in patients with T2DM treated with metformin alone, while no significant decrease was observed in patients treated with metformin combined with benaglutide. A metagenomic analysis revealed that benaglutide could improve the fecal microbiota diversity in patients with T2DM. Furthermore, there was a statistically significant correlation between the changes in the metabolites of patients with T2DM and the changes in their gut microbiota (including F. prausnitzii) after treatment with metformin and benaglutide.

CONCLUSION: These findings suggest that the weight-reducing effect of benaglutide is attributed to its ability to normalize the gut microbiota of patients with T2DM, particularly by increasing the abundance of F. prausnitzii.}, } @article {pmid37576519, year = {2023}, author = {Yang, J and Li, L and Zhu, X and He, C and Li, T and Qin, J and Wang, Y}, title = {Microbial Community Characterization and Molecular Resistance Monitoring in Geriatric Intensive Care Units in China Using mNGS.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {5121-5134}, pmid = {37576519}, issn = {1178-6973}, abstract = {BACKGROUND: Surface pathogens in the ICU pose a global public health threat, especially to elderly patients who are immunocompromised. To detect these pathogens, unbiased methods such as metagenomic next-generation sequencing (mNGS) are increasingly utilized for environmental microbiological surveillance.

METHODS: In a six-month study from January to July 2022, we investigated microbial communities in Chinese geriatric ICUs by regularly monitoring multiple surfaces at three-month intervals. Using mNGS sequencing, we analyzed microorganisms present at eight specific locations within the ICU. Additionally, we compared pathogen profiles and drug resistance genes between patient cultures and environmental samples collected during the same period.

RESULTS: The microbial composition remained relatively stable over time, but significant differences in alpha diversities were observed among various surfaces such as floors, hands, pumps, trolleys, and ventilator inlets/outlets. Surfaces with high contact frequency for healthcare workers, including workstations, ventilator panels, trolleys, pumps, and beds, harbored pathogenic microorganisms such as Acinetobacter baumannii, Cutibacterium acnes, Staphylococcus haemolyticus, Pseudomonas aeruginosa, and Enterococcus faecium. Acinetobacter baumannii, particularly the carbapenem-resistant strain (CRAB), was the most frequently identified pathogen in geriatric ICU patients regardless of testing method used. The mNGS approach enabled detection of viruses, fungi, and parasites that are challenging to culture. Additionally, an abundance of drug resistance genes was found in almost all environmental samples.

CONCLUSION: The microbial composition and abundance in the ICU remained relatively constant over time. The floor exhibited the highest microbial diversity and abundance in the ICU environment. Drug-resistant genes in the ICU environment may migrate between patients. Overall, mNGS is an emerging and powerful tool for microbiological monitoring of the hospital environment.}, } @article {pmid37575934, year = {2023}, author = {Kakkar, RA and Haneen, MA and Parida, AC and Sharma, G}, title = {The known, unknown, and the intriguing about members of a critically endangered traditional medicinal plant genus Aconitum.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1139215}, pmid = {37575934}, issn = {1664-462X}, abstract = {Humanity will always be indebted to plants. In the ongoing scientific era, the 'Herbal Revolution' has helped discover several valuable medicinal plants and associated novel secondary metabolites from the diverse unexplored ecosystems, treating several diseases via phytotherapy. The Aconitum genus comprises several economically-important poisonous mountainous medicinal plant species whose unique biodiversity is on the verge of extinction due to illegal human intervention triggered habitat loss, over-harvesting, and unrestricted trading. Owing to its vast diversity of diterpene alkaloids, most species are extensively used to treat several ailments in rural parts of the world. Irrespective of this, many unexplored and intriguing prospects exist to understand and utilize this critical plant for human benefit. This systematic review tries to fill this gap by compiling information from the sporadically available literature known for ~300 Aconitum spp. regarding its nomenclature and classification, endangerment, plant morphology, ploidy, secondary metabolites, drug pharmacokinetics, conservation, and omics-based computational studies. We also depicted the disparity in the studied model organisms for this diverse genus. The absence of genomic/metagenomic data is becoming a limiting factor in understanding its plant physiology, metabolic pathways, and plant-microbes interactions, and therefore must be promoted. Additionally, government support and public participation are crucial in establishing conservation protocols to save this plant from endangerment.}, } @article {pmid37575390, year = {2023}, author = {Kodackattumannil, P and Sasi, S and Krishnan, S and Lekshmi, G and Kottackal, M and Amiri, KMA}, title = {Protocol for the High-quality Plasmid Isolation from Different Recalcitrant Bacterial Species: Agrobacterium spp., Rhizobium sp., and Bacillus thuringiensis.}, journal = {Bio-protocol}, volume = {13}, number = {15}, pages = {e4788}, pmid = {37575390}, issn = {2331-8325}, abstract = {High yield of good quality plasmid DNA from gram -ve bacteria (Agrobacterium tumefaciens, A. rhizogenes, and Rhizobium sp.) and gram +ve bacterium (Bacillus thuringiensis) is difficult. The widely used plasmid extraction kits for Escherichia coli yield a low quantity of poor-quality plasmid DNA from these species. We have optimized an in-house modification of the QIAprep Spin Miniprep kit protocol of Qiagen, consisting of two extraction steps. In the first, the centrifugation after adding neutralization buffer is followed by ethanol (absolute) precipitation of plasmid DNA. In the second extraction step, the precipitated DNA is dissolved in Tris-EDTA (TE) buffer, followed by an addition of 0.5 volumes of 5 M sodium chloride and 0.1 volumes of 20% (w/v) sodium dodecyl sulfate. After incubation at 65 °C for 15 min, the plasmid DNA is extracted with an equal volume of chloroform:isoamyl alcohol (CIA). RNase (20 mg/mL) is added to the upper phase retrieved after centrifugation and is incubated at 37 °C for 15 min. The extraction of the plasmid DNA with an equal volume of CIA is followed by centrifugation and is precipitated from the retrieved upper phase by adding an equal volume of absolute ethanol. The pellet obtained after centrifugation is washed twice with 70% (v/v) ethanol, air dried, dissolved in TE buffer, and quantified. This easy-to-perform protocol is free from phenol extraction, density gradient steps, and DNA binding columns, and yields high-quality plasmid DNA. The protocol opens an easy scale up to yield a large amount of high-quality plasmid DNA, useful for high-throughput downstream applications. Key features The protocol is free from density gradient steps and use of phenol. The protocol is an extension of the QIAprep Spin Miniprep kit (Qiagen) and is applicable for plasmid DNA isolation from difficult-to-extract bacterial species. The protocol facilitates the direct transformation of the ligation product into Agrobacterium by skipping the step of E. coli transformation. The plasmids isolated are of sequencing grade and the method is useful for extracting plasmids for metagenomic studies. Graphical overview Overview of the plasmid isolation protocol (modified QIAprep Spin Miniprep kit) of the present study.}, } @article {pmid37575122, year = {2023}, author = {Zhou, Q and Zhan, Z and Huang, F and Zhao, M and Huang, D and Xu, J and Huang, L and Xie, L and Zhang, A}, title = {Case report: A rare multidrug-resistant Escherichia coli causes fatal neonatal meningoencephalitis.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1174536}, pmid = {37575122}, issn = {2296-2565}, mesh = {Infant ; Infant, Newborn ; Humans ; *Anti-Bacterial Agents/therapeutic use ; Escherichia coli ; Cefoperazone/therapeutic use ; Sulbactam/therapeutic use ; *Meningoencephalitis/diagnosis/drug therapy ; }, abstract = {Neonatal meningitis is rare but devastating disease. Multidrug-resistant (MDR, multi-drug resistant) bacteria are a major global health risk. We report an Escherichia coli meningitis isolate with multiple resistance patterns and unusual serotype (O75) that caused sudden neonatal death. The isolate was resistant to antibiotics other than cefoperazone/sulbactam and imipenem, challenging the combination of antibiotics commonly used in the empirical treatment of neonatal sepsis. Despite aggressive symptomatic and supportive treatment of the infant based on laboratory tests and clinical practice, the infant eventually died. This is the first case of meningoencephalitis due to serotype O75 reported in China. The presence of highly pathogenic multidrug-resistant microorganisms isolated in neonates underscores the need to implement rapid resistance diagnostic methods and should prompt consideration of alternatives to empiric treatment of neonatal bacterial meningitis.}, } @article {pmid37574624, year = {2023}, author = {Zhang, S and Liang, C and Xiao, M and Chui, C and Wang, N and Ji, Y and Wang, Z and Shi, J and Liu, L}, title = {Metagenomic characterization of the enhanced performance of multicomponent synergistic thermophilic anaerobic co-digestion of food waste utilizing kitchen waste or garden waste as co-substrate.}, journal = {Water research}, volume = {244}, number = {}, pages = {120457}, doi = {10.1016/j.watres.2023.120457}, pmid = {37574624}, issn = {1879-2448}, mesh = {*Refuse Disposal/methods ; Food ; Gardens ; Anaerobiosis ; Biofuels ; Bioreactors ; Methane ; Digestion ; Sewage ; }, abstract = {Food waste (FW) single-substrate anaerobic digestion usually suffers from rapid acidification and inhibition of oil and salt. To overcome these problems and improve the process efficiency, supplementing other substrates has been used in FW anaerobic digestion. This study investigated the biogas production potential through co-digestion of FW with kitchen waste (KW) or garden waste (GW) in different ratios under thermophilic conditions. The results showed that the optimal ratios were FW:KW=60:40 and FW:GW=80:20 which biogas production improved 73.33% and 68.45% compared with single FW digestion, respectively. The organic matter removal rate of co-digestion was 84.46% for FW+KW group (RFK) and 65.64% for FW+GW group (RFG). Co-digestion increased the abundance of the dominant hydrolytic bacteria Defluviitoga and Hydrogenispora and hydrogenotrophic methanogen Methanoculleus. Furthermore, glycoside hydrolases (GHs), vital carbohydrate-active enzymes (CAZymes), were improved by co-digestion. Co-digestion could also effectively promote the function of cellulase and hemicellulose. This strategy for utilizing different organic wastes together as co-substrate provides a new avenue for bioenergy production.}, } @article {pmid37574314, year = {2023}, author = {Xing, M and Fu, QY and Lin, SS and Fu, X and Wang, XX and Wang, LC and Zhu, X and Ouyang, TL}, title = {[Analysis of fast-growing culturable bacteria and pathogenic bacteria in the surface water of the northeast coast of Hainan Island in China].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {57}, number = {8}, pages = {1206-1216}, doi = {10.3760/cma.j.cn112150-20230221-00142}, pmid = {37574314}, issn = {0253-9624}, support = {20A200316//Hainan Province Medical and Health Research Project/ ; 2020SKLID303//Key Project of the National Key Laboratory of Infectious Disease Prevention and Control/ ; }, mesh = {Humans ; *Water ; *Bacteria/genetics ; Seawater/microbiology ; Escherichia coli ; Enterococcus ; Klebsiella pneumoniae ; China ; }, abstract = {Objective: To obtain the diversity and abundance of fast-growing bacteria in the surface water of the northeast coast of Hainan Island in China, different cultivation methods were employed. This study also aims to provide a reference for isolating bacterial samples from seawater sources and preventing marine-derived pathogens. Methods: Based on the principles of taxonomic design, surface seawater samples were collected from six locations along the northeast coast of Hainan Island in China in March, June, October, and December 2021. Then, bacterial enrichment was performed based on traditional cultivation methods for Salmonella, Vibrio, Burkholderia pseudomallei, Actinomycetes, and general marine bacteria. After that, bacterial species identification was conducted by 16S rDNA amplicon sequencing and metagenomic sequencing. Results: A total of 1 151 fast-growing cultivable bacteria belonging to 66 genera and 213 species were identified using five different culture protocols. In different cultivation protocols, Bacillus and Klebsiella demonstrated extensive discriminatory advantages and ranked among the top genera in terms of abundance. Protocol 1 had Escherichia, Klebsiella, and Citrobacter as dominant genera. Pathogenic bacteria detected by protocol 1 included Klebsiella pneumoniae and Escherichia coli, with 37 and 29 strains respectively, while Salmonella enterica was uniquely detected with seven isolates. Proteus, Enterococcus, and Providencia were the dominant genera in protocol 2, and Proteus mirabilis was the most abundant pathogenic bacteria detected with 66 isolates. Vibrio cholerae was uniquely detected with six isolates at a higher abundance. Klebsiella, Escherichia, and Acinetobacter were the dominant genera in protocol 3, and Klebsiella pneumoniae was the most abundant pathogenic bacteria detected with 53 isolates, while Acinetobacter nosocomialis was uniquely detected with seven isolates. Vibrio and Pseudoalteromonas were the dominant genera in protocol 4, and they showed advantages in isolating and cultivating Marine-derived Vibrio. Exiguobacterium, Staphylococcus, and Bacillus were the dominant genera in protocol 5. Bacillus cereus and Lactococcus lactis were the most abundant pathogenic bacteria detected with 20 and 15 isolates, respectively, while Lactococcus lactis was uniquely detected at higher abundance. Metagenomic sequencing showed that Klebsiella pneumoniae was significantly dominant with a gene abundance of 51.11%, followed by Alcanivorax sp. at 12.57%. Conclusion: The surface water of the northeast coast of Hainan Island in China exhibits a rich diversity of bacteria, with Klebsiella pneumoniae being highly abundant in the studied area. Different cultivation methods demonstrate distinct selective advantages in culturing bacterial genera and pathogens. Therefore, it is necessary to optimize cultivation conditions for specific marine bacteria.}, } @article {pmid37574126, year = {2023}, author = {Canouï, E and Woerther, PL and Soulier, A and Benhaddou, N and Seng, S and Belan, M and Rodriguez, C and Charlier, C}, title = {Shotgun metagenomic screening to improve the retrospective diagnosis of undocumented intrauterine infections on embedded placenta samples: Lessons from a brucellosis case.}, journal = {Infectious diseases now}, volume = {53}, number = {7}, pages = {104770}, doi = {10.1016/j.idnow.2023.104770}, pmid = {37574126}, issn = {2666-9919}, abstract = {BACKGROUND: Microbiological diagnosis of intrauterine infections (IIU) still relies on bacteriological cultures or targeted DNA amplification lacking in sensitivity. Shotgun metagenomics (SMg) is an emerging unbiased molecular approach that makes it possible to sequence all the nucleic acids from any sample. It had never previously been used for IIU.

METHODS: We here report the case of a patient with an unexplained IIU and fetal loss that could be documented by a combined SMg/microbiological approach, leading to the diagnosis of maternal brucellosis.

RESULTS: A 31-year-old woman presented with an undocumented IIU with fetal loss at 24 weeks of gestation. Culture-based work-up failed to identify the pathogen involved. Paraffin-embedded placenta sample was retrospectively analyzed by SMg. Brucella spp nucleic acids were detected, and subacute maternal brucellosis was confirmed by targeted PCR and serological testing.

CONCLUSION: This case provides grounds for further utilization of SMg for the microbiological diagnosis of unexplained obstetrical infections.}, } @article {pmid37573789, year = {2023}, author = {Sha, J and Shao, J and Lu, S and Yao, W and Deng, Y and Chen, J and Zhang, J and Feng, Y}, title = {Pyopneumothorax with bronchopleural fistula due to pulmonary infection caused by Porphyromonas gingivalis in a patient with periodontitis.}, journal = {The clinical respiratory journal}, volume = {17}, number = {9}, pages = {962-965}, pmid = {37573789}, issn = {1752-699X}, mesh = {Male ; Humans ; Middle Aged ; Porphyromonas gingivalis ; *Periodontitis/complications ; *Pleural Diseases/complications/diagnosis ; *Bronchial Fistula/complications ; *Pneumothorax/complications ; *Empyema, Pleural ; }, abstract = {Pyopneumothorax with bronchopleural fistula is a rare complication of lung infection. We herein report a case of pyopneumothorax with bronchopleural fistula caused by Porphyromonas gingivalis infection, a common pathogenic pathogen of periodontitis, in a 49-year-old man with periodontitis. The patient was admitted with respiratory failure. Pleural puncture yielded a lot of gas continually and foul-smelling light brown pus, which was found to be caused due to infection with P. gingivalis by the metagenomic next generation sequencing (mNGS) and anaerobic culture.}, } @article {pmid37573460, year = {2023}, author = {Dwiyanto, J and Huët, MAL and Hussain, MH and Su, TT and Tan, JBL and Toh, KY and Lee, JWJ and Rahman, S and Chong, CW}, title = {Social demographics determinants for resistome and microbiome variation of a multiethnic community in Southern Malaysia.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {55}, pmid = {37573460}, issn = {2055-5008}, mesh = {Humans ; Malaysia ; Escherichia coli/genetics ; Saccharomyces cerevisiae ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Demography ; }, abstract = {The prevalence of antibiotic-resistant bacteria in Southeast Asia is a significant concern, yet there is limited research on the gut resistome and its correlation with lifestyle and environmental factors in the region. This study aimed to profile the gut resistome of 200 individuals in Malaysia using shotgun metagenomic sequencing and investigate its association with questionnaire data comprising demographic and lifestyle variables. A total of 1038 antibiotic resistance genes from 26 classes were detected with a mean carriage rate of 1.74 ± 1.18 gene copies per cell per person. Correlation analysis identified 14 environmental factors, including hygiene habits, health parameters, and intestinal colonization, that were significantly associated with the resistome (adjusted multivariate PERMANOVA, p < 0.05). Notably, individuals with positive yeast cultures exhibited a reduced copy number of 15 antibiotic resistance genes. Network analysis highlighted Escherichia coli as a major resistome network hub, with a positive correlation to 36 antibiotic-resistance genes. Our findings suggest that E. coli may play a pivotal role in shaping the resistome dynamics in Segamat, Malaysia, and its abundance is strongly associated with the community's health and lifestyle habits. Furthermore, the presence of yeast appears to be associated with the suppression of antibiotic-resistance genes.}, } @article {pmid37573429, year = {2023}, author = {Zhou, Y and Li, J and Huang, F and Ai, H and Gao, J and Chen, C and Huang, L}, title = {Characterization of the pig lower respiratory tract antibiotic resistome.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4868}, pmid = {37573429}, issn = {2041-1723}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microbiota/genetics ; Respiratory System ; Swine ; }, abstract = {Respiratory diseases and its treatments are highly concerned in both the pig industry and human health. However, the composition and distribution of antibiotic resistance genes (ARGs) in swine lower respiratory tract microbiome remain unknown. The relationships of ARGs with mobile genetic elements (MGEs) and lung health are unclear. Here, we characterize antibiotic resistomes of the swine lower respiratory tract microbiome containing 1228 open reading frames belonging to 372 ARGs using 745 metagenomes from 675 experimental pigs. Twelve ARGs conferring resistance to tetracycline are related to an MGE Tn916 family, and multiple types of ARGs are related to a transposase gene tnpA. Most of the linkage complexes between ARGs and MGEs (the Tn916 family and tnpA) are also observed in pig gut microbiomes and human lung microbiomes, suggesting the high risk of these MGEs mediating ARG transfer to both human and pig health. Gammaproteobacteria are the major ARG carriers, within which Escherichia coli harbored >50 ARGs and >10 MGEs. Although the microbial compositions structure the compositions of ARGs, we identify 73 ARGs whose relative abundances are significantly associated with the severity of lung lesions. Our results provide the first overview of ARG profiles in the swine lower respiratory tract microbiome.}, } @article {pmid37572889, year = {2023}, author = {Chen, J and Zhang, X and Zhou, L and Zhu, Z and Wu, Z and Zhang, K and Wang, Y and Ju, T and Ji, X and Jin, D and Wu, P and Zhang, X}, title = {Metagenomics insights into high-rate nitrogen removal from municipal wastewater by integrated nitrification, partial denitrification and Anammox at an extremely short hydraulic retention time.}, journal = {Bioresource technology}, volume = {387}, number = {}, pages = {129606}, doi = {10.1016/j.biortech.2023.129606}, pmid = {37572889}, issn = {1873-2976}, mesh = {*Wastewater ; *Nitrification ; Denitrification ; Anaerobic Ammonia Oxidation ; Sewage ; Nitrogen ; Metagenomics ; Oxidation-Reduction ; Bioreactors ; }, abstract = {To achieve high-rate nitrogen removal in municipal wastewater treatment through anaerobic ammonia oxidation (Anammox), the nitrification, partial denitrification, and Anammox processes were integrated by a step-feed strategy. An exceptional nitrogen removal load of 0.224 kg N/(m[3]·d) was achieved by gradient-reducing the hydraulic retention time (HRT) to 5 h. Metagenomic analysis demonstrated that Nitrosospira could express all genes encoding ammonia oxidation under low nitrogen and dissolved oxygen conditions (less than 0.5 mg/L), enabling complete nitrification. With the short of HRT, the relative abundance of Thauera increased from 2.8 % to 6.4 %. Frequent substrate exchanges at such extremely short HRT facilitated enhanced synergistic interactions among Nitrosospira, Thauera, and Candidatus Brocadia. These findings provide a comprehensive understanding of the utilization of Anammox combined processes for high-speed nitrogen removal in municipal wastewater treatment and the microbial interactions involved.}, } @article {pmid37572887, year = {2023}, author = {Li, L and Guan, W and Fan, Y and He, Q and Guo, D and Yuan, A and Xing, Q and Wang, Y and Ma, Z and Ni, J and Chen, J and Zhou, Q and Zhong, Y and Li, J and Zhang, H}, title = {Zinc/carbon nanomaterials inhibit antibiotic resistance genes by affecting quorum sensing and microbial community in cattle manure production.}, journal = {Bioresource technology}, volume = {387}, number = {}, pages = {129648}, doi = {10.1016/j.biortech.2023.129648}, pmid = {37572887}, issn = {1873-2976}, mesh = {Cattle ; Animals ; Manure ; Genes, Bacterial ; Zinc ; Carbon ; Anti-Bacterial Agents/pharmacology ; *Zinc Oxide ; Quorum Sensing/genetics ; Drug Resistance, Microbial/genetics ; *Microbiota ; *Nanostructures ; }, abstract = {This study used metagenomic sequencing to examine the effects of carbon-based zinc oxide nanoparticles (CZnONPs) and graphene-based zinc oxide nanoparticles (GZnONPs) on quorum sensing (QS), antibiotic resistance genes (ARGs) and microbial community changes during cattle manure production. The manure zinc content was significantly reduced in GZnONPs group. In the QS pathway, the autoinducer gene increases significantly in Control group, while the transporter and repressor genes experience a substantial increase in CZnONPs group. These results contributed to the significantly decreased the abundance of ARGs in GZnONPs group. The co-occurrence network analysis revealed a correlation between core ARGs and QS-related KEGG Orthology or ARGs' hosts, indicating that the selective pressure of zinc influences microbial QS, forming a unique ARG pattern in in vivo anaerobic fermentation. These findings suggest that implementing nutritional regulation in farming practices can serve as a preventive measure to mitigate the potential transmission of ARGs resulting from livestock waste.}, } @article {pmid37572592, year = {2023}, author = {Wang, X and Chen, X and Song, X and Cao, L and Yang, S and Shen, Q and Ji, L and Lu, X and Zhang, W}, title = {Identification of novel anelloviruses in the blood of giant panda (Ailuropoda melanoleuca).}, journal = {Comparative immunology, microbiology and infectious diseases}, volume = {100}, number = {}, pages = {102038}, doi = {10.1016/j.cimid.2023.102038}, pmid = {37572592}, issn = {1878-1667}, abstract = {In recent years, the continuous development of metagenomics has revealed that in addition to the digestive tract, some viruses are also common in mammalian blood. To explore and monitor potential novel viruses, in April 2015, a blood sample was collected from a healthy captive giant panda at the Chengdu Research Base of Giant Panda Breeding in Sichuan Province, China. The genomes of 25 different anelloviruses containing the complete ORF1 region have been identified. The BLASTp results showed that the amino acid sequence identity of these viruses with the best match in GenBank ranged from 27.15% to 41.29%. Based on phylogenetic analysis and SDT (Species Demarcation Tool) analysis of the complete ORF1 regions of these 25 viruses, these sequences were deduced to represent one or several novel virus genera or species. This virological study has increased our understanding of the diversity of anelloviruses in the blood of giant pandas, but further laboratory analysis is needed to verify its possible pathogenicity.}, } @article {pmid37572464, year = {2023}, author = {Dang, C and Zhang, Y and Zheng, M and Meng, Q and Wang, J and Zhong, Y and Wu, Z and Liu, B and Fu, J}, title = {Effect of chlorine disinfectant influx on biological sewage treatment process under the COVID-19 pandemic: Performance, mechanisms and implications.}, journal = {Water research}, volume = {244}, number = {}, pages = {120453}, doi = {10.1016/j.watres.2023.120453}, pmid = {37572464}, issn = {1879-2448}, mesh = {Humans ; *Disinfectants/pharmacology ; Chlorine/pharmacology ; Sewage/microbiology ; Pandemics ; *COVID-19 ; SARS-CoV-2 ; Nitrogen/metabolism ; }, abstract = {Since the onset of the COVID-19 Pandemic, large amounts of chlorine-containing disinfectants have been used to interrupt the spread of SARS-CoV-2 and residual chlorine eventually entered the hospital or municipal sewage treatment facilities. However, little is known about the effect of chlorine influx on the biological sewage treatment process. Here we investigated the effect of chlorine on the microbiome and the mechanism of microbial chlorine resistance in the activated sludge of the aerobic treatment process, using metagenomic and metatranscriptomic sequencing. We found that chlorine could negatively impact the aerobic treatment performance regarding nitrogen/COD removal with a dose-dependent effect, and the dual effects of chlorine dose and interaction time differentiated the microbial community in activated sludge. The decline of nitrogen/COD removal was attributed to the compressed activity of functional microorganisms, such as the ammonia oxidation bacteria, under chlorinated conditions, and the damage cannot be recovered in a short term. In addition, some microorganisms could survive in chlorinated conditions by up-regulating the chlorine resistance genes (CRGs) expression (approximately 1.5 times) and stimulating new CRGs expression. In particular, species Acinetobacter johnsonii could resist high concentrations of chlorine through various mechanisms, especially the overexpression of efflux pump function encoded by qac genes play a key role. Based on these results, considering the persistence of the epidemic and extensive use of chlorine disinfectants, it cannot be ignored that large amounts of residual chlorine are entering the biological treatment facility, and strictly de-chlorination measures or microbial chlorine resistance regulations before entering should be implemented.}, } @article {pmid37570344, year = {2023}, author = {Yue, L and Wang, C and Meng, B and Xie, B and Cao, H and Su, H and Zhang, M}, title = {The Food Niche Overlap and Interspecific Relationship between the Sympatric Tibetan Macaque and Grey Snub-Nosed Monkey.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {15}, pages = {}, pmid = {37570344}, issn = {2076-2615}, support = {Grant No. 32260331//National Natural Science Foundation of China/ ; }, abstract = {Assessing the trophic niche and interspecific relationships between related species and determining how the species maintain differences in nutritional niches while coexisting in the same area are important topics in ecological research. Therefore, exploring the mechanism of food resource utilization, competition and coexistence among species distributed in the same region is important. In this study, we used fecal samples and metagenome sequencing technology to study the plant feeding habits and coexistence mechanisms of Tibetan macaques (Macaca thibetana) and grey snub-nosed monkeys (Rhinopithecus brelichi) within the same area. In the winter of 2020, we collected a total of 40 fecal samples from Tibetan macaques and grey snub-nosed monkeys; of those, 29 samples were considered valid and were analyzed using DNA metabarcoding. The results showed that in winter, Tibetan macaques consumed plants from 117 families and 184 genera, whereas grey snub-nosed monkeys consumed plants from 109 families and 165 genera. Diversity analysis revealed that there was a significant difference in the food composition of Tibetan macaques and grey snub-nosed monkeys. Tibetan macaques had a broader food niche width than grey snub-nosed monkeys at the family and genus levels. In winter, the food niches of Tibetan macaques and grey snub-nosed monkeys almost entirely overlapped (0.99). Our research provides detailed dietary data for Tibetan macaques and grey snub-nosed monkeys and valuable information that can aid in conservation efforts targeting these species.}, } @article {pmid37569608, year = {2023}, author = {Oñate, FP and Chamignon, C and Burz, SD and Lapaque, N and Monnoye, M and Philippe, C and Bredel, M and Chêne, L and Farin, W and Paillarse, JM and Boursier, J and Ratziu, V and Mousset, PY and Doré, J and Gérard, P and Blottière, HM}, title = {Adlercreutzia equolifaciens Is an Anti-Inflammatory Commensal Bacterium with Decreased Abundance in Gut Microbiota of Patients with Metabolic Liver Disease.}, journal = {International journal of molecular sciences}, volume = {24}, number = {15}, pages = {}, pmid = {37569608}, issn = {1422-0067}, support = {MetaGenoPolis ANR-11-DPBS-0001//Agence Nationale de la Recherche/ ; FunAMetaGen ANR-15-CE14-0021//Agence Nationale de la Recherche/ ; }, mesh = {Animals ; Mice ; *Non-alcoholic Fatty Liver Disease/metabolism ; *Gastrointestinal Microbiome ; Dysbiosis/microbiology ; Liver/metabolism ; *Metabolic Diseases/metabolism ; *Liver Neoplasms/metabolism ; Anti-Inflammatory Agents/pharmacology/therapeutic use/metabolism ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD) affects about 20-40% of the adult population in high-income countries and is now a leading indication for liver transplantation and can lead to hepatocellular carcinoma. The link between gut microbiota dysbiosis and NAFLD is now clearly established. Through analyses of the gut microbiota with shotgun metagenomics, we observe that compared to healthy controls, Adlercreutzia equolifaciens is depleted in patients with liver diseases such as NAFLD. Its abundance also decreases as the disease progresses and eventually disappears in the last stages indicating a strong association with disease severity. Moreover, we show that A. equolifaciens possesses anti-inflammatory properties, both in vitro and in vivo in a humanized mouse model of NAFLD. Therefore, our results demonstrate a link between NAFLD and the severity of liver disease and the presence of A. equolifaciens and its anti-inflammatory actions. Counterbalancing dysbiosis with this bacterium may be a promising live biotherapeutic strategy for liver diseases.}, } @article {pmid37568379, year = {2023}, author = {Stoian, IL and Botezatu, A and Fudulu, A and Ilea, CG and Socolov, DG}, title = {Exploring Microbiota Diversity in Cervical Lesion Progression and HPV Infection through 16S rRNA Gene Metagenomic Sequencing.}, journal = {Journal of clinical medicine}, volume = {12}, number = {15}, pages = {}, pmid = {37568379}, issn = {2077-0383}, support = {doctoral grant no.159/31.01.2022.//University of Medicine and Pharmacy "Grigore T. Popa"/ ; }, abstract = {(1) Background: Cervical cancer is a significant health concern, with the main cause being persistent infection with high-risk Human Papillomavirus (hrHPV). There is still no evidence for why viral persistence occurs in some women, but recent studies have revealed the interplay between cervical microbiota and hrHPV. This research aimed to characterize the cervicovaginal microbiota in cervical lesion progression and HPV infection status. (2) Methods: This study included 85 cervical specimens from women from the north-eastern region of Romania. DNA was isolated from cervical secretion for HPV genotyping and 16S ribosomal RNA gene NGS sequencing. (3) Results: Our study revealed a distinct pattern within the studied group when considering Lactobacillus species, which differs from findings reported in other populations. Specifically, the presence of Lactobacillus iners coupled with the absence of Lactobacillus crispatus alongside Atopobium spp., Prevotella spp., and Gardnerella spp. could serve as defining factors for severe cervical lesions. The results also showed a significant association between microbiota diversity, HPV infection, and cervical lesion progression. (4) Conclusions: As the microbiota profile seems to vary among different populations and individuals, a deeper comprehension of its composition has the potential to develop personalized detection and treatment approaches for cervical dysplasia and cancer.}, } @article {pmid37567350, year = {2023}, author = {Zhang, H and Zhao, J and Fu, Z and Wang, Y and Guan, D and Xie, J and Zhang, Q and Liu, Q and Wang, D and Sun, Y}, title = {Metagenomic approach reveals the mechanism of calcium oxide improving kitchen waste dry anaerobic digestion.}, journal = {Bioresource technology}, volume = {387}, number = {}, pages = {129647}, doi = {10.1016/j.biortech.2023.129647}, pmid = {37567350}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Biofuels ; *Fatty Acids, Volatile/metabolism ; Calcium Compounds ; Methane/metabolism ; Bioreactors ; }, abstract = {In light of the characteristics of excessive acidification and low biogas yield during kitchen waste (KW) dry digestion, the impact of the calcium oxide (CaO) on KW mesophilic dry digestion was investigated, and the enhanced mechanism was revealed through metagenomic approach. The results showed that CaO increased the biogas production, when the CaO dosage was 0.07 g/g (based on total solid), the biogas production reached 656.84 mL/g suspended solids (VS), approximately 8.38 times of that in the control. CaO promoted the leaching and hydrolysis of key organic matter in KW. CaO effectively promoted the conversion of volatile fatty acid (VFA) and mitigated over-acidification. Macrogenome analysis revealed that CaO increased the microbial diversity in KW dry digestion and upregulated the abundance of genes related to amino acid and carbohydrates metabolism. This study provides an effective strategy with potential economic benefits to improve the bioconversion efficiency of organic matter in KW.}, } @article {pmid37567140, year = {2023}, author = {Li, Z and Ren, L and Wang, X and Chen, M and Wang, T and Dai, R and Wang, Z}, title = {Anaerobic hydrolysis of recalcitrant tetramethylammonium from semiconductor wastewater: Performance and mechanisms.}, journal = {Journal of hazardous materials}, volume = {459}, number = {}, pages = {132239}, doi = {10.1016/j.jhazmat.2023.132239}, pmid = {37567140}, issn = {1873-3336}, mesh = {*Wastewater ; Anaerobiosis ; Hydrolysis ; Molecular Docking Simulation ; *Quaternary Ammonium Compounds/metabolism ; }, abstract = {The treatment of tetramethylammonium hydroxide (TMAH)-bearing wastewater, generated in the electronic and semiconductor industries, raises significant concerns due to the neurotoxic, recalcitrant, and bio-inhibiting effects of TMAH. In this study, we proposed the use of an anaerobic hydrolysis bioreactor (AHBR) for TMAH removal, achieving a high removal efficiency of approximately 85%, which greatly surpassed the performance of widely-used advanced oxidation processes (AOPs). Density functional theory calculations indicated that the unexpectedly poor efficiency (5.8-8.0%) of selected AOPs can be attributed to the electrostatic repulsion between oxidants and the tightly bound electrons of TMAH. Metagenomic analyses of the AHBR revealed that Proteobacteria and Euryarchaeota played a dominant role in the transformation of TMAH through processes such as methyl transfer, methanogenesis, and acetyl-coenzyme A synthesis, utilizing methyl-tetrahydromethanopterin as a substrate. Moreover, several potential functional genes (e.g., mprF, basS, bcrB, sugE) related to TMAH resistance have been identified. Molecular docking studies between five selected proteins and tetramethylammonium further provided evidence supporting the roles of these potential functional genes. This study demonstrates the superiority of AHBR as a pretreatment technology compared to several widely-researched AOPs, paving the way for the proper design of treatment processes to abate TMAH in semiconductor wastewater.}, } @article {pmid37566631, year = {2023}, author = {Cervi, GH and Flores, CD and Thompson, CE}, title = {The MetaGens algorithm for metagenomic database lossy compression and subject alignment.}, journal = {Database : the journal of biological databases and curation}, volume = {2023}, number = {}, pages = {}, pmid = {37566631}, issn = {1758-0463}, mesh = {*Data Compression/methods ; High-Throughput Nucleotide Sequencing/methods ; Algorithms ; Sequence Analysis, DNA/methods ; DNA ; Software ; }, abstract = {The advancement of genetic sequencing techniques led to the production of a large volume of data. The extraction of genetic material from a sample is one of the early steps of the metagenomic study. With the evolution of the processes, the analysis of the sequenced data allowed the discovery of etiological agents and, by corollary, the diagnosis of infections. One of the biggest challenges of the technique is the huge volume of data generated with each new technology developed. To introduce an algorithm that may reduce the data volume, allowing faster DNA matching with the reference databases. Using techniques like lossy compression and substitution matrix, it is possible to match nucleotide sequences without losing the subject. This lossy compression explores the nature of DNA mutations, insertions and deletions and the possibility that different sequences are the same subject. The algorithm can reduce the overall size of the database to 15% of the original size. Depending on parameters, it may reduce up to 5% of the original size. Although is the same as the other platforms, the match algorithm is more sensible because it ignores the transitions and transversions, resulting in a faster way to obtain the diagnostic results. The first experiment results in an increase in speed 10 times faster than Blast while maintaining high sensitivity. This performance gain can be extended by combining other techniques already used in other studies, such as hash tables. Database URL https://github.com/ghc4/metagens.}, } @article {pmid37566190, year = {2023}, author = {Tomar, S and Mitra, D and Kumar, G and Kashyap, P and Sharma, M and Kumar, S and Sridhar, K and Pant, K}, title = {Microbial Diversity and Functional Potential of Keem: A Traditional Starter Culture for Alcoholic Beverage-Application of Next-Generation Amplicon and Shotgun Metagenome Sequences.}, journal = {Molecular biotechnology}, volume = {}, number = {}, pages = {}, pmid = {37566190}, issn = {1559-0305}, support = {UCS&T/R&D-01/19/20/17530//Uttarakhand State Council for Science and Technology/ ; }, abstract = {"Pakhoi" is an ethnic drink of the Tons valley, Uttarakhand, India produced by fermenting jaggery and barley with the help of a starter culture called "keem". In the present study, we investigated the microbial diversity and associated functional potential of "keem" using shotgun metagenome sequencing and amplicon sequencing. We also compared the taxonomic data obtained using these two sequencing techniques. The results showed that shotgun sequencing revealed a higher resolution of taxonomic profiling as compared to the amplicon sequencing. Furthermore, it was found that the genera detected by shotgun sequencing were valuable for facilitating the fermentation process. Additionally, to understand the functional profiling of the genera, different databases were used for annotation, resulting in a total of 13 metabolic pathways. The five most abundant KEGG functions were genetic information processing, metabolism, translation, cofactor and vitamin metabolism and xenobiotic degradation. In contrast, the top five COG were in order of highest frequency sequences belonging to transcription, followed by general function prediction, carbohydrate transport metabolism, amino acid transport and metabolism and translation and biogenesis. Gene ontology revealed many pathways, biochemical processes and molecular functions associated with the organisms forming the starter culture. Overall, the present study can help to understand the microbial diversity and its role in fermentation of traditional alcoholic beverages using "Keem".}, } @article {pmid37566076, year = {2023}, author = {Miernikiewicz, P and Barylski, J and Wilczak, A and Dragoš, A and Rybicka, I and Bałdysz, S and Szymczak, A and Dogsa, I and Rokush, K and Harhala, MA and Ciekot, J and Ferenc, S and Gnus, J and Witkiewicz, W and Dąbrowska, K}, title = {New Phage-Derived Antibacterial Enzyme PolaR Targeting Rothia spp.}, journal = {Cells}, volume = {12}, number = {15}, pages = {}, pmid = {37566076}, issn = {2073-4409}, mesh = {Animals ; Humans ; *Bacteriophages ; *Micrococcaceae/metabolism ; Bacteria ; Anti-Bacterial Agents/pharmacology/metabolism ; Mammals ; }, abstract = {Rothia is an opportunistic pathogen, particularly life-threatening for the immunocompromised. It is associated with pneumonia, endocarditis, peritonitis and many other serious infections, including septicemia. Of note, Rothia mucilaginousa produces metabolites that support and increase overgrowth of Pseudomonas aeruginosa, one of the ESKAPE bacteria. Endolysins are considered as antibacterial enzymes derived from bacteriophages that selectively and efficiently kill susceptible bacteria without harming human cells or the normal microbiome. Here, we applied a computational analysis of metagenomic sequencing data of the gastric mucosa phageome extracted from human patients' stomach biopsies. A selected candidate anti-Rothia sequence was produced in an expression system, purified and confirmed as a Rothia mucilaginosa- and Rothia dentocariosa-specific endolysin PolaR, able to destroy bacterial cells even when aggregated, as in a biofilm. PolaR had no cytotoxic or antiproliferative effects on mammalian cells. PolaR is the first described endolysin selectively targeting Rothia species, with a high potential to combat infections caused by Rothia mucilaginosa and Rothia dentocariosa, and possibly other bacterial groups. PolaR is the first antibacterial enzyme selected from the gastric mucosa phageome, which underlines the biological complexity and probably underestimated biological role of the phageome in the human gastric mucosa.}, } @article {pmid37565218, year = {2023}, author = {And Alternative Medicine, EC}, title = {Retracted: Application Value of Metagenomics Next-Generation Sequencing (mNGS) in Detection of Mucormycosis after Chemotherapy in Childhood Acute Leukemia.}, journal = {Evidence-based complementary and alternative medicine : eCAM}, volume = {2023}, number = {}, pages = {9764181}, pmid = {37565218}, issn = {1741-427X}, abstract = {[This retracts the article DOI: 10.1155/2022/7366432.].}, } @article {pmid37564177, year = {2023}, author = {Liu, Y and Tan, Y and Huang, J and Wu, C and Fan, X and Stalin, A and Lu, S and Wang, H and Zhang, J and Zhang, F and Wu, Z and Li, B and Huang, Z and Chen, M and Cheng, G and Mou, Y and Wu, J}, title = {Corrigendum: Revealing the mechanism of Huazhi Rougan granule in the treatment of nonalcoholic fatty liver through intestinal flora based on 16S rRNA, metagenomic sequencing and network pharmacology.}, journal = {Frontiers in pharmacology}, volume = {14}, number = {}, pages = {1243304}, doi = {10.3389/fphar.2023.1243304}, pmid = {37564177}, issn = {1663-9812}, abstract = {[This corrects the article DOI: 10.3389/fphar.2022.875700.].}, } @article {pmid37564072, year = {2023}, author = {Michoud, G and Kohler, TJ and Ezzat, L and Peter, H and Nattabi, JK and Nalwanga, R and Pramateftaki, P and Styllas, M and Tolosano, M and De Staercke, V and Schön, M and Marasco, R and Daffonchio, D and Bourquin, M and Busi, SB and Battin, TJ}, title = {The dark side of the moon: first insights into the microbiome structure and function of one of the last glacier-fed streams in Africa.}, journal = {Royal Society open science}, volume = {10}, number = {8}, pages = {230329}, pmid = {37564072}, issn = {2054-5703}, abstract = {The glaciers on Africa's 'Mountains of the Moon' (Rwenzori National Park, Uganda) are predicted to disappear within the next decades owing to climate change. Consequently, the glacier-fed streams (GFSs) that drain them will vanish, along with their resident microbial communities. Despite the relevance of microbial communities for performing ecosystem processes in equatorial GFSs, their ecology remains understudied. Here, we show that the benthic microbiome from the Mt. Stanley GFS is distinct at several levels from other GFSs. Specifically, several novel taxa were present, and usually common groups such as Chrysophytes and Polaromonas exhibited lower relative abundances compared to higher-latitude GFSs, while cyanobacteria and diatoms were more abundant. The rich primary producer community in this GFS likely results from the greater environmental stability of the Afrotropics, and accordingly, heterotrophic processes dominated in the bacterial community. Metagenomics revealed that almost all prokaryotes in the Mt. Stanley GFS are capable of organic carbon oxidation, while greater than 80% have the potential for fermentation and acetate oxidation. Our findings suggest a close coupling between photoautotrophs and other microbes in this GFS, and provide a glimpse into the future for high-latitude GFSs globally where primary production is projected to increase with ongoing glacier shrinkage.}, } @article {pmid37563687, year = {2023}, author = {Lai, S and Yan, Y and Pu, Y and Lin, S and Qiu, JG and Jiang, BH and Keller, MI and Wang, M and Bork, P and Chen, WH and Zheng, Y and Zhao, XM}, title = {Enterotypes of the human gut mycobiome.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {179}, pmid = {37563687}, issn = {2049-2618}, mesh = {Humans ; Aged ; *Mycobiome/genetics ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Candida ; Aging ; }, abstract = {BACKGROUND: The fungal component of the human gut microbiome, also known as the mycobiome, plays a vital role in intestinal ecology and human health. However, the overall structure of the gut mycobiome as well as the inter-individual variations in fungal composition remains largely unknown. In this study, we collected a total of 3363 fungal sequencing samples from 16 cohorts across three continents, including 572 newly profiled samples from China.

RESULTS: We identify and characterize four mycobiome enterotypes using ITS profiling of 3363 samples from 16 cohorts. These enterotypes exhibit stability across populations and geographical locations and significant correlation with bacterial enterotypes. Particularly, we notice that fungal enterotypes have a strong age preference, where the enterotype dominated by Candida (i.e., Can_type enterotype) is enriched in the elderly population and confers an increased risk of multiple diseases associated with a compromised intestinal barrier. In addition, bidirectional mediation analysis reveals that the fungi-contributed aerobic respiration pathway associated with the Can_type enterotype might mediate the association between the compromised intestinal barrier and aging.

CONCLUSIONS: We show that the human gut mycobiome has stable compositional patterns across individuals and significantly correlates with multiple host factors, such as diseases and host age. Video Abstract.}, } @article {pmid37563539, year = {2023}, author = {Chen, J and Xu, F}, title = {Application of Nanopore Sequencing in the Diagnosis and Treatment of Pulmonary Infections.}, journal = {Molecular diagnosis & therapy}, volume = {27}, number = {6}, pages = {685-701}, pmid = {37563539}, issn = {1179-2000}, mesh = {Humans ; *Nanopore Sequencing ; Bacteria/genetics ; *Bacterial Infections/diagnosis/drug therapy ; *Pneumonia ; High-Throughput Nucleotide Sequencing ; }, abstract = {This review provides an in-depth discussion of the development, principles and utility of nanopore sequencing technology and its diverse applications in the identification of various pulmonary pathogens. We examined the emergence and advancements of nanopore sequencing as a significant player in this field. We illustrate the challenges faced in diagnosing mixed infections and further scrutinize the use of nanopore sequencing in the identification of single pathogens, including viruses (with a focus on its use in epidemiology, outbreak investigation, and viral resistance), bacteria (emphasizing 16S targeted sequencing, rare bacterial lung infections, and antimicrobial resistance studies), fungi (employing internal transcribed spacer sequencing), tuberculosis, and atypical pathogens. Furthermore, we discuss the role of nanopore sequencing in metagenomics and its potential for unbiased detection of all pathogens in a clinical setting, emphasizing its advantages in sequencing genome repeat areas and structural variant regions. We discuss the limitations in dealing with host DNA removal, the inherent high error rate of nanopore sequencing technology, along with the complexity of operation and processing, while acknowledging the possibilities provided by recent technological improvements. We compared nanopore sequencing with the BioFire system, a rapid molecular diagnostic system based on polymerase chain reaction. Although the BioFire system serves well for the rapid screening of known and common pathogens, it falls short in the identification of unknown or rare pathogens and in providing comprehensive genome analysis. As technological advancements continue, it is anticipated that the role of nanopore sequencing technology in diagnosing and treating lung infections will become increasingly significant.}, } @article {pmid37563495, year = {2023}, author = {Baker, M and Zhang, X and Maciel-Guerra, A and Dong, Y and Wang, W and Hu, Y and Renney, D and Hu, Y and Liu, L and Li, H and Tong, Z and Zhang, M and Geng, Y and Zhao, L and Hao, Z and Senin, N and Chen, J and Peng, Z and Li, F and Dottorini, T}, title = {Machine learning and metagenomics reveal shared antimicrobial resistance profiles across multiple chicken farms and abattoirs in China.}, journal = {Nature food}, volume = {4}, number = {8}, pages = {707-720}, pmid = {37563495}, issn = {2662-1355}, mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Chickens/microbiology ; Drug Resistance, Bacterial/genetics ; Farms ; Metagenomics ; Abattoirs ; Escherichia coli ; Machine Learning ; }, abstract = {China is the largest global consumer of antimicrobials and improving surveillance methods could help to reduce antimicrobial resistance (AMR) spread. Here we report the surveillance of ten large-scale chicken farms and four connected abattoirs in three Chinese provinces over 2.5 years. Using a data mining approach based on machine learning, we analysed 461 microbiomes from birds, carcasses and environments, identifying 145 potentially mobile antibiotic resistance genes (ARGs) shared between chickens and environments across all farms. A core set of 233 ARGs and 186 microbial species extracted from the chicken gut microbiome correlated with the AMR profiles of Escherichia coli colonizing the same gut, including Arcobacter, Acinetobacter and Sphingobacterium, clinically relevant for humans, and 38 clinically relevant ARGs. Temperature and humidity in the barns were also correlated with ARG presence. We reveal an intricate network of correlations between environments, microbial communities and AMR, suggesting multiple routes to improving AMR surveillance in livestock production.}, } @article {pmid37563185, year = {2023}, author = {Xue, Z and Han, Y and Tian, W and Zhang, W}, title = {Metagenome sequencing and 103 microbial genomes from ballast water and sediments.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {536}, pmid = {37563185}, issn = {2052-4463}, mesh = {Archaea/genetics ; Bacteria/genetics ; Genome, Microbial ; *Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {The great threat of microbes carried by ballast water calls for figuring out the species composition of the ballast-tank microbial community, where the dark, cold, and anoxic tank environment might select special taxa. In this study, we reconstructed 103 metagenome-assembled genomes (MAGs), including 102 bacteria and one archaea, from four vessels on international voyages. Of these MAGs, 60 were 'near complete' (completeness >90%), 34 were >80% complete, and nine were >75% complete. Phylogenomic analysis revealed that over 70% (n = 74) of these MAGs represented new taxa at different taxonomical levels, including one order, three families, 12 genera, and 58 species. The species composition of these MAGs was most consistent with the previous reports, with the most abundant phyla being Proteobacteria (n = 69), Bacteroidota (n = 17), and Actinobacteriota (n = 7). These draft genomes provided novel data on species diversity and function in the ballast-tank microbial community, which will facilitate ballast water and sediments management.}, } @article {pmid37562975, year = {2023}, author = {Thebault, S and Gandelman, S and Lane, C and Kim, EJ and Pileggi, C and Zuroff, L and Yamashita, LD and Schindler, MK and Chiu, C and Wilson, MR and Berger, JR and Markowitz, C and Bar-Or, A and Fuller, R and Brandstadter, R and Pruitt, AA and Jacobs, DA}, title = {Severe Neuroinvasive West Nile Virus in Association With Anti-CD20 Monotherapy for Multiple Sclerosis.}, journal = {Neurology(R) neuroimmunology & neuroinflammation}, volume = {10}, number = {5}, pages = {}, pmid = {37562975}, issn = {2332-7812}, mesh = {Humans ; Female ; Male ; *West Nile Fever/complications/drug therapy ; *West Nile virus ; *Multiple Sclerosis/drug therapy/complications ; Antibodies, Viral ; Immunoglobulin M ; }, abstract = {OBJECTIVES: The objective of this study was to report on the development of neuroinvasive West Nile virus (WNV) infection in the context of anti-CD20 monotherapy for multiple sclerosis (MS).

METHODS: This is a case series study.

RESULTS: In 2021-2022, we observed 4 cases of neuroinvasive WNV infection in our patient population of 2009 patients with MS on ocrelizumab, compared with a total of 46 cases of neuroinvasive WNV infection reported in Pennsylvania and 40 in New Jersey. Odds were 258 times that of the general population (95% confidence interval 97-691), χ[2] p < 0.0001). All were women aged 41-61 years with variable disease duration, level of disability, and duration of anti-CD20 therapy. All presented in summer/early fall with fever, headache, and encephalopathy consistent with meningoencephalitis. Three patients had acute cerebellitis. Two had anterior nerve root involvement progressing to quadriparesis, and 1 developed refractory nonconvulsive status epilepticus. All required intubation and experienced significant morbidity. All had CSF pleocytosis. Two patients were WNV IgM positive in both the serum and CSF, 1 patient had positive serum IgM and CSF metagenomic next-generation sequencing (mNGS), while 1 had positive CSF mNGS with negative serum and CSF antibodies.

DISCUSSION: Neuroinvasive WNV infection can develop with anti-CD20 monotherapy in the absence of additional immunosuppression. WNV serologies may be negative in the setting of anti-CD20 treatment; in the appropriate clinical context, one should consider direct detection methods such as PCR or mNGS-based testing.}, } @article {pmid37562501, year = {2023}, author = {Win, TT and Song, KG}, title = {Metagenomics and proteomics profiling of extracellular polymeric substances from municipal waste sludge and their application for soil and water bioremediation.}, journal = {Chemosphere}, volume = {339}, number = {}, pages = {139767}, doi = {10.1016/j.chemosphere.2023.139767}, pmid = {37562501}, issn = {1879-1298}, mesh = {*Sewage/chemistry ; *Extracellular Polymeric Substance Matrix/metabolism ; Biodegradation, Environmental ; Ammonia/metabolism ; Metagenomics ; Proteomics ; RNA, Ribosomal, 16S ; Tandem Mass Spectrometry ; Nitrogen/metabolism ; Bioreactors ; Waste Disposal, Fluid/methods ; }, abstract = {This study assessed the components of anaerobically digested sludge, activated sludge, and microbial and extracellular polymeric substance (EPS) enzymes to identify the mechanisms underlying nitrogen removal and soil regeneration. 16S rRNA gene amplicon-based sequencing was used to determine the microbial community composition and the related National Center for Biotechnology Information (NCBI) protein database was used to construct a conventional library from the observed community. EPS components were identified using gel-free proteomic (Liquid Chromatography with tandem mass spectrometry-LC/MS/MS) methods. Alginate-like EPS from aerobically activated sludge have strong potential for soil aggregation and water-holding capacity, whereas total EPS from anaerobic sludge have significant potential for ammonia removal under salt stress. Fourier transform infrared spectroscopy (FTIR) revealed that both EPS may contain proteins, carbohydrates, humic compounds, uronic acid, and DNA and determined the presence of O-H, N-H, C-N, CO, and C-H functional groups. These results demonstrate that the overall enzyme activity may be inactivated at 30 g L[-1] of salinity. An annotation found in Kyoto Encyclopedia of Genes and Genomes (KEGG)- KEGG Automatic Annotation Server (KAAS) revealed that the top two metabolic activities in the EPS generated from the anaerobic sludge were methane and nitrogen metabolism. Therefore, we focused on the nitrogen metabolism reference map 00910. EPS from the anaerobically digested sludge exhibited nitrate reductase, nitrite reductase, and dehydrogenase activities. Assimilatory nitrate reduction, denitrification, nitrification, and anammox removed ammonia biochemically. The influence of microbial extracellular metabolites on water-holding capacity and soil aggregation was also investigated. The KAAS-KEGG annotation server was used to identify the main enzymes in the activated sludge-derived alginate-like extracellular EPS (ALE-EPS) samples. These include hydrolases, oxidoreductases, lyases, ligases, and transporters, which contribute to soil fertility and stability. This study improves our understanding of the overall microbial community structure and the associated biochemical processes, which are related to distinct functional genes or enzymes involved in nitrogen removal and soil aggregation. In contrast to conventional methods, microbial association with proteomics can be used to investigate ecological relationships, establishments, key player species, and microbial responses to environmental changes. Linking the metagenome to off-gel proteomics and bioinformatics solves the problem of analyzing metabolic pathways in complex environmental samples in a cost-effective manner.}, } @article {pmid37562342, year = {2023}, author = {Xu, Y and Zhu, L and Chen, S and Wu, H and Li, R and Li, J and Yuan, J and Wen, T and Xue, C and Shen, Q}, title = {Risk assessment and dissemination mechanism of antibiotic resistance genes in compost.}, journal = {Environment international}, volume = {178}, number = {}, pages = {108126}, doi = {10.1016/j.envint.2023.108126}, pmid = {37562342}, issn = {1873-6750}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology/analysis ; *Composting ; Genes, Bacterial ; Manure/analysis ; Drug Resistance, Microbial/genetics ; Risk Assessment ; }, abstract = {In recent years, the excessive of antibiotics in livestock and poultry husbandry, stemming from extensive industry experience, has resulted in the accumulation of residual antibiotics and antibiotic resistance genes (ARGs) in livestock manure. Composting, as a crucial approach for the utilization of manure resources, has the potential to reduce the levels of antibiotics and ARGs in manure, although complete elimination is challenging. Previous studies have primarily focused on the diversity and abundance of ARGs in compost or have solely examined the correlation between ARGs and their carriers, potentially leading to a misjudgment of the actual risk associated with ARGs in compost. To address this gap, this study investigated the transfer potential of ARGs in compost and their co-occurrence with opportunistic pathogenic bacteria by extensively analyzing metagenomic sequencing data of compost worldwide. The results demonstrated that the potential risk of ARGs in compost was significantly lower than in manure, suggesting that composting effectively reduces the risk of ARGs. Further analysis showed that the microbes shifted their life history strategy in manure and compost due to antibiotic pressure and formed metabolic interactions dominated by antibiotic-resistant microbes, increasing ARG dissemination frequency. Therefore, husbandry practice without antibiotic addition was recommended to control ARG evolution, dissemination, and abatement both at the source and throughout processing.}, } @article {pmid37562250, year = {2023}, author = {You, A and Hua, L and Hu, J and Tian, J and Ding, T and Cheng, N and Hu, L}, title = {Patters of reactive nitrogen removal at the waters in the semi-constructed wetland.}, journal = {Journal of environmental management}, volume = {344}, number = {}, pages = {118733}, doi = {10.1016/j.jenvman.2023.118733}, pmid = {37562250}, issn = {1095-8630}, mesh = {*Wetlands ; *Denitrification ; Nitrogen ; Nitrification ; Nitrates ; }, abstract = {Protection and rectification patters of urban wetlands have been considered in strategies to balance services to society and negative consequences of excess reactive nitrogen (Nr) loading. However, the knowledge about strategies of semi-constructed wetlands on nitrogen (N) cycling pathways and removal Nr from the overlying water is limited. This study aimed to reveal considerable differences among rectification patterns of the typical semi-constructed wetland (Xixi wetland), comprising rational exploitation area (REA), rehabilitation and reconstruction area (RRA), and conservation area (CA) by analyzing the N distribution and N protentional pathways among them. Results pointed out that both NH4[+] and NO3[-] concentration were prominently higher in REA, as opposed to CA and RRA. Sediments in RRA had relatively higher NH4[+] content, indicating the efficiency of dissimilatory nitrate reduction (DNRA) in RRA. Moreover, there was a significant shift in the microbial community structure across different sites and sediments. Metagenomic analysis distinguished the N cycling pathways, with nitrification (M00804), denitrification (M00529), and DNRA (M00530) being the crucial pathways in the semi-constructed wetland. The relative abundance of N metabolic pathways (ko00910) varied among different types of sediments, being more abundant in shore and rhizosphere areas and less abundant in bottom sediments. Methylobacter and Nitrospira were the predominant nitrifiers in shore sediments, while Methylocystis was enriched in the bottom sediments and rhizosphere soils. Furthermore, Anaeromyxobacter, Anaerolinea, Dechloromonas, Nocardioides, and Methylocystis were identified as the primary denitrifiers with N reductase genes (nirK, nirS, or nosZ). Among these, Anaeromyxobacter, Dechloromonas, and Methylocystis were the primary contributors containing the nosZ gene in semi-constructed wetlands, driving the conversion of N2O to N2. This study provides important insights into rectification-dependent Nr removal from the overlying water in terms of N distribution and N metabolic functional microbial communities in the semi-constructed wetlands.}, } @article {pmid37561723, year = {2023}, author = {Gudra, D and Silamikelis, I and Pjalkovskis, J and Danenberga, I and Pupola, D and Skenders, G and Ustinova, M and Megnis, K and Leja, M and Vangravs, R and Fridmanis, D}, title = {Abundance and prevalence of ESBL coding genes in patients undergoing first line eradication therapy for Helicobacter pylori.}, journal = {PloS one}, volume = {18}, number = {8}, pages = {e0289879}, pmid = {37561723}, issn = {1932-6203}, mesh = {Humans ; *Helicobacter pylori/genetics ; Prevalence ; Klebsiella ; *Klebsiella Infections/microbiology ; Patients ; beta-Lactamases/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Microbial Sensitivity Tests ; }, abstract = {The spread of extended-spectrum beta-lactamases (ESBLs) in nosocomial and community-acquired enterobacteria is an important challenge for clinicians due to the limited therapeutic options for infections that are caused by these organisms. Here, we developed a panel of ESBL coding genes, evaluated the abundance and prevalence of ESBL encoding genes in patients undergoing H. pylori eradication therapy, and summarized the effects of eradication therapy on functional profiles of the gut microbiome. To assess the repertoire of known beta lactamase (BL) genes, they were divided into clusters according to their evolutionary relation. Primers were designed for amplification of cluster marker regions, and the efficiency of this amplification panel was assessed in 120 fecal samples acquired from 60 patients undergoing H. pylori eradication therapy. In addition, fecal samples from an additional 30 patients were used to validate the detection efficiency of the developed ESBL panel. The presence for majority of targeted clusters was confirmed by NGS of amplification products. Metagenomic sequencing revealed that the abundance of ESBL genes within the pool of microorganisms was very low. The global relative abundances of the ESBL-coding gene clusters did not differ significantly among treatment states. However, at the level of each cluster, classical ESBL producers such as Klebsiella sp. for blaOXY (p = 0.0076), Acinetobacter sp. for blaADC (p = 0.02297) and others, differed significantly with a tendency to decrease compared to the pre- and post-eradication states. Only 13 clusters were common across all three datasets, suggesting a patient-specific distribution profile of ESBL-coding genes. The number of AMR genes detected in the post-eradication state was higher than that in the pre-eradication state, which could be attributed, at least in part, to the therapy. This study demonstrated that the ESBL screening panel was effective in targeting ESBL-coding gene clusters from bacterial DNA and that minor differences exist in the abundance and prevalence of ESBL-coding gene levels before and after eradication therapy.}, } @article {pmid37561193, year = {2023}, author = {Samanta, B and Sharma, S and Budhwar, R}, title = {Metagenome Analysis of Speleothem Microbiome from Subterranean Cave Reveals Insight into Community Structure, Metabolic Potential, and BGCs Diversity.}, journal = {Current microbiology}, volume = {80}, number = {10}, pages = {317}, pmid = {37561193}, issn = {1432-0991}, support = {F. No: 2021/0003//Gandhi Institute of Technology and Management/ ; }, mesh = {Caves/microbiology ; *Metagenome ; *Microbiota/genetics ; Phylogeny ; Sulfur ; *Bacteria/chemistry/classification/isolation & purification ; }, abstract = {The Borra caves, the second largest subterranean karst cave ecosystem in the Indian sub-continent, are located at the Ananthagiri hills of Araku Valley in the Alluri district of Andhra Pradesh, India. The present investigation applied a shotgun metagenomic approach to gain insights into the microbial community structure, metabolic potential, and biosynthetic gene cluster (BGC) diversity of the microbes colonizing the surface of the speleothems from the aphotic zone of Borra caves. The taxonomic analysis of the metagenome data illustrated that the speleothem-colonizing core microbial community was dominated mainly by Alpha-, Beta-, and Gamma-Proteobacteria, Actinobacteria, Firmicutes, and Bacteroidetes. The key energy metabolic pathways analysis provides strong evidence of chemolithoautotrophic and chemoheterotrophic modes of nutrition in the speleothem-colonizing microbial community. Metagenome data suggests that sulfur reducers and sulfur-disproportionating microbes might play a vital role in energy generation in this ecosystem. Our metagenome data also suggest that the dissimilatory nitrifiers and nitrifying denitrifiers might play an essential role in conserving nitrogen pools in the ecosystem. Furthermore, metagenome-wide BGCs mining retrieved 451 putative BGCs; NRPS was the most abundant (24%). Phylogenetic analysis of the C domain of NRPS showed that sequences were distributed across all six function categories of the known C domain, including several novel subclades. For example, a novel subclade had been recovered within the LCL domain clade as a sister subclade of immunosuppressant cyclosporin encoding C domain sequences. Our result suggested that subterranean cave microbiomes might be a potential reservoir of novel microbial metabolites.}, } @article {pmid37561110, year = {2023}, author = {Le, AV and Větrovský, T and Barucic, D and Saraiva, JP and Dobbler, PT and Kohout, P and Pospíšek, M and da Rocha, UN and Kléma, J and Baldrian, P}, title = {Improved recovery and annotation of genes in metagenomes through the prediction of fungal introns.}, journal = {Molecular ecology resources}, volume = {23}, number = {8}, pages = {1800-1811}, doi = {10.1111/1755-0998.13852}, pmid = {37561110}, issn = {1755-0998}, support = {21-17749S//Grantová Agentura České Republiky/ ; e-INFRA CZ LM2018140//Ministry of Education, Youth and Sports of the Czech Republic/ ; }, abstract = {Metagenomics provides a tool to assess the functional potential of environmental and host-associated microbiomes based on the analysis of environmental DNA: assembly, gene prediction and annotation. While gene prediction is straightforward for most bacterial and archaeal taxa, it has limited applicability in the majority of eukaryotic organisms, including fungi that contain introns in gene coding sequences. As a consequence, eukaryotic genes are underrepresented in metagenomics datasets and our understanding of the contribution of fungi and other eukaryotes to microbiome functioning is limited. Here, we developed a machine intelligence-based algorithm that predicts fungal introns in environmental DNA with reasonable precision and used it to improve the annotation of environmental metagenomes. Intron removal increased the number of predicted genes by up to 9.1% and improved the annotation of several others. The proportion of newly predicted genes increased with the share of eukaryotic genes in the metagenome and-within fungal taxa-increased with the number of introns per gene. Our approach provides a tool named SVMmycointron for improved metagenome annotation, especially of microbiomes with a high proportion of eukaryotes. The scripts described in the paper are made publicly available and can be readily utilized by microbiome researchers analysing metagenomics data.}, } @article {pmid37560872, year = {2023}, author = {Pan, Y and Xiang, P and Zhang, D and Wang, W and Han, J and Tan, W and Wang, P and Li, J and Wang, Q and Liu, J}, title = {The First Human Infection Case of Macacine Alphaherpesvirus 1 Virus in China.}, journal = {Clinical laboratory}, volume = {69}, number = {8}, pages = {}, doi = {10.7754/Clin.Lab.2023.221215}, pmid = {37560872}, issn = {1433-6510}, mesh = {Male ; Humans ; Middle Aged ; *Herpesvirus 1, Cercopithecine ; China/epidemiology ; Real-Time Polymerase Chain Reaction ; Beijing ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Macacine alphaherpesvirus 1 (BV) was first reported in the 1930s and only about 60 cases have been diagnosed since then.

METHODS: A 53-year-old male who worked as a veterinary surgeon, developed a fever with nausea and vomiting in April 2021 in Beijing, China. Real-time polymerase chain reaction (PCR) and metagenomics Next Generation Sequencing (mNGS) were used for diagnosis.

RESULTS: BV DNA was confirmed by mNGS and PCR. The case died 51 days after onset, due to the damage to the brain and spinal cord caused by a viral infection and hypoxic-ischemic encephalopathy. The typical BV inclusion bodies in the brain were found for the first time.

CONCLUSIONS: Here we reported the first human infection case of BV in China. This fatal case highlights the potential threat of BV to occupational workers and the essential role of surveillance.}, } @article {pmid37560730, year = {2023}, author = {Li, HH and Zhou, XM and Liu, T and Wu, R and Huang, ZF and Sun, CW and Liu, ZA and Zheng, SY and Lai, W and Lou, H and Xiong, B}, title = {The clinical value of metagenomic next-generation sequencing for rapid microbial identification of chronic granulation wound infections.}, journal = {Archives of medical science : AMS}, volume = {19}, number = {4}, pages = {1162-1167}, pmid = {37560730}, issn = {1734-1922}, } @article {pmid37560239, year = {2023}, author = {Yang, Y and Liu, Z and Chen, X and Qin, F and Zhou, W}, title = {Association between vaginal microbiomes and neonatal septicemia in pregnant women with preterm premature rupture of membranes based on metagenome sequencing.}, journal = {American journal of translational research}, volume = {15}, number = {7}, pages = {4544-4557}, pmid = {37560239}, issn = {1943-8141}, abstract = {BACKGROUND: Preterm premature rupture of membranes (PPROM) is closely associated with pathogenic microbiomes in the female reproductive tract, and can lead to neonatal septicemia. The current study aimed to investigate potential pathogenic microbiomes associated with neonatal septicemia based on DNA metagenome sequencing.

METHODS: In this study, a total of 7 pregnant women with PPROM presenting neonatal septicemia (experimental group) and 3 pregnant women with normal newborns (control group) were enrolled. Vaginal secretions at admission and before parturition as well as placental tissues after parturition were collected for DNA metagenome sequencing using whole genome shotgun method on the Illumina NovaSeq/HiSeq platform. Raw data were processed by BioBakery workflow, and MetaPhlAn4 was implemented for qualitative and quantitative analyses of microbiome. Lactobacillus crispatus, Gardneralla vaginalis, Fannyhessea vaginae and Streptococcus suis were specifically detected from the experimental group. The two groups were compared using Student's t-tests.

RESULTS: The indexes of Chao1 (P=0.00028/P=0.00072), abundance-based coverage estimator (ACE, P=0.00059/P=0.00026), Shannon (P=0.036/P=0.0065) and Simpson (P=0.007/P=0.041) in the experimental group were increased at admission and before parturition as compared with the control group. Several microbiomes, such as Lactobacillus crispatus, Gardneralla vaginalis, Fannyhessea vaginae and Streptococcus suis, were specifically detected in the experimental group. Notably, Gardnerella vaginalis and Streptococcus gallolyticus were identified from the vaginal secretions and placenta tissues of women with neonatal septicemia. Moreover, nucleic acid synthesis and carbohydrate metabolism-related pathways were enriched in the experimental group.

CONCLUSION: This study enhanced the current understanding of the mechanisms underlying pathogenic microbiomes in PPROM-induced neonatal septicemia. The trial registry number is ChiCTR2300070666 (URL: https://www.chictr.org.cn/showproj.html?proj=195648).}, } @article {pmid37560191, year = {2023}, author = {Ladeveze, S and Zurek, PJ and Kaminski, TS and Emond, S and Hollfelder, F}, title = {Versatile Product Detection via Coupled Assays for Ultrahigh-Throughput Screening of Carbohydrate-Active Enzymes in Microfluidic Droplets.}, journal = {ACS catalysis}, volume = {13}, number = {15}, pages = {10232-10243}, pmid = {37560191}, issn = {2155-5435}, abstract = {Enzyme discovery and directed evolution are the two major contemporary approaches for the improvement of industrial processes by biocatalysis in various fields. Customization of catalysts for improvement of single enzyme reactions or de novo reaction development is often complex and tedious. The success of screening campaigns relies on the fraction of sequence space that can be sampled, whether for evolving a particular enzyme or screening metagenomes. Ultrahigh-throughput screening (uHTS) based on in vitro compartmentalization in water-in-oil emulsion of picoliter droplets generated in microfluidic systems allows screening rates >1 kHz (or >10[7] per day). Screening for carbohydrate-active enzymes (CAZymes) catalyzing biotechnologically valuable reactions in this format presents an additional challenge because the released carbohydrates are difficult to monitor in high throughput. Activated substrates with large optically active hydrophobic leaving groups provide a generic optical readout, but the molecular recognition properties of sugars will be altered by the incorporation of such fluoro- or chromophores and their typically higher reactivity, as leaving groups with lowered pKa values compared to native substrates make the observation of promiscuous reactions more likely. To overcome these issues, we designed microdroplet assays in which optically inactive carbohydrate products are made visible by specific cascades: the primary reaction of an unlabeled substrate leads to an optical signal downstream. Successfully implementing such assays at the picoliter droplet scale allowed us to detect glucose, xylose, glucuronic acid, and arabinose as final products of complex oligosaccharide degradation by glycoside hydrolases by absorbance measurements. Enabling the use of uHTS for screening CAZyme reactions that have been thus far elusive will chart a route toward faster and easier development of specific and efficient biocatalysts for biovalorization, directing enzyme discovery by challenging catalysts for reaction with natural rather than model substrates.}, } @article {pmid37559969, year = {2023}, author = {Ozga, AT and Ottoni, C}, title = {Dental calculus as a proxy for animal microbiomes.}, journal = {Quaternary international : the journal of the International Union for Quaternary Research}, volume = {653-654}, number = {}, pages = {47-52}, pmid = {37559969}, issn = {1040-6182}, abstract = {The field of dental calculus research has exploded in recent years, predominantly due to the multitude of studies related to human genomes and oral pathogens. Despite having a subset of these studies devoted to non-human primates, little progress has been made in the distribution of oral pathogens across domestic and wild animal populations. This overlooked avenue of research is particularly important at present when many animal populations with the potentiality for zoonotic transmission continue to reside in close proximity to human groups due to reasons such as deforestation and climatic impacts on resource availability. Here, we analyze all previously available published oral microbiome data recovered from the skeletal remains of animals, all of which belong to the Mammalia class. Our genus level results emphasize the tremendous diversity of oral ecologies across mammals in spite of the clustering based primarily on host species. We also discuss the caveats and flaws in analyzing ancient animal oral microbiomes at the species level of classification. Lastly, we assess the benefits, challenges, and gaps in the current knowledge of dental calculus research within animals and postulate the future of the field as a whole.}, } @article {pmid37559122, year = {2023}, author = {Van Zyl, WF and Van Staden, AD and Dicks, LMT and Trindade, M}, title = {Use of the mCherry fluorescent protein to optimize the expression of class I lanthipeptides in Escherichia coli.}, journal = {Microbial cell factories}, volume = {22}, number = {1}, pages = {149}, pmid = {37559122}, issn = {1475-2859}, support = {Self initiated//South African Medical Research Council/ ; UID87326//National Research Foundation/ ; }, mesh = {Escherichia coli/genetics/metabolism ; *Luminescent Proteins/genetics ; *Nisin ; Plasmids/genetics ; Red Fluorescent Protein ; }, abstract = {BACKGROUND: Lanthipeptides are a rapidly expanding family of ribosomally synthesized and post-translationally modified natural compounds with diverse biological functions. Lanthipeptide structural and biosynthetic genes can readily be identified in genomic datasets, which provides a substantial repository for unique peptides with a wide range of potentially novel bioactivities. To realize this potential efficiently optimized heterologous production systems are required. However, only a few class I lanthipeptides have been successfully expressed using Escherichia coli as heterologous producer. This may be attributed to difficulties experienced in the co-expression of structural genes and multiple processing genes as well as complex optimization experiments.

RESULTS: Here, an optimized modular plasmid system is presented for the complete biosynthesis for each of the class I lanthipeptides nisin and clausin, in E. coli. Genes encoding precursor lanthipeptides were fused to the gene encoding the mCherry red fluorescent protein and co-expressed along with the required synthetases from the respective operons. Antimicrobially active nisin and clausin were proteolytically liberated from the expressed mCherry fusions. The mCherry-NisA expression system combined with in vivo fluorescence monitoring was used to elucidate the effect of culture media composition, promoter arrangement, and culture conditions including choice of growth media and inducer agents on the heterologous expression of the class I lanthipeptides. To evaluate the promiscuity of the clausin biosynthetic enzymes, the optimized clausin expression system was used for the heterologous expression of epidermin.

CONCLUSION: We succeeded in developing novel mCherry-fusion based plug and play heterologous expression systems to produce two different subgroups of class I lanthipeptides. Fully modified Pre-NisA, Pre-ClausA and Pre-EpiA fused to the mCherry fluorescence gene was purified from the Gram-negative host E. coli BL21 (DE3). Our study demonstrates the potential of using in vivo fluorescence as a platform to evaluate the expression of mCherry-fused lanthipeptides in E. coli. This allowed a substantial reduction in optimization time, since expression could be monitored in real-time, without the need for extensive and laborious purification steps or the use of in vitro activity assays. The optimized heterologous expression systems developed in this study may be employed in future studies for the scalable expression of novel NisA derivatives, or novel genome mined derivatives of ClausA and other class I lanthipeptides in E. coli.}, } @article {pmid37558633, year = {2023}, author = {Ahn, KS and Kang, KJ and Kim, YH and Kim, TS and Cho, KB and Kim, HS and Baek, WK and Suh, SI and Han, JY}, title = {Diagnostic Role of Bile Pigment Components in Biliary Tract Cancer.}, journal = {Biomolecules & therapeutics}, volume = {31}, number = {6}, pages = {674-681}, pmid = {37558633}, issn = {1976-9148}, abstract = {Bile pigment, bilirubin, and biliverdin concentrations may change as a results of biliary tract cancer (BTC) altering the mechanisms of radical oxidation and heme breakdown. We explored whether changes in bile pigment components could help distinguish BTC from benign biliary illness by evaluating alterations in patients with BTC. We collected bile fluid from 15 patients with a common bile duct stone (CBD group) and 63 individuals with BTC (BTC group). We examined the bile fluid's bilirubin, biliverdin reductase (BVR), heme oxygenase (HO-1), and bacterial taxonomic abundance. Serum bilirubin levels had no impact on the amounts of bile HO-1, BVR, or bilirubin. In comparison to the control group, the BTC group had considerably higher amounts of HO-1, BVR, and bilirubin in the bile. The areas under the curve for the receiver operating characteristic curve analyses of the BVR and HO-1 were 0.832 (p<0.001) and 0.891 (p<0.001), respectively. Firmicutes was the most prevalent phylum in both CBD and BTC, according to a taxonomic abundance analysis, however the Firmicutes/Bacteroidetes ratio was substantially greater in the BTC group than in the CBD group. The findings of this study showed that, regardless of the existence of obstructive jaundice, biliary carcinogenesis impacts heme degradation and bile pigmentation, and that the bile pigment components HO-1, BVR, and bilirubin in bile fluid have a diagnostic significance in BTC. In tissue biopsies for the diagnosis of BTC, particularly for distinguishing BTC from benign biliary strictures, bile pigment components can be used as additional biomarkers.}, } @article {pmid37558566, year = {2023}, author = {Abriouel, H and Manetsberger, J and Lavilla Lerma, L and Pestaña Blanco, MD and Martínez Nogueras, R and Caballero Gómez, N and Benomar, N}, title = {Metagenomic insights into microbial contamination in critical healthcare environments and the efficacy of a novel "HLE" disinfectant.}, journal = {Infection, disease & health}, volume = {28}, number = {4}, pages = {282-289}, doi = {10.1016/j.idh.2023.07.002}, pmid = {37558566}, issn = {2468-0869}, mesh = {Humans ; *Disinfectants/pharmacology ; Disinfection ; Bacteria/genetics ; Drug Resistance, Microbial ; Delivery of Health Care ; }, abstract = {BACKGROUND: Bacterial contamination on inanimate clinical surfaces is directly linked to severe health problems, especially those caused by multidrug resistant (MDR) pathogens. Here, we evaluated the microbial burden in these environments and tested the efficacy of a novel HLE disinfectant solution.

METHODS: Microbial contamination of healthcare surfaces [Intensive Care Unit (ICU), Long Period Hospitalization Room (LPHR) and Otolaryngology Consultation (OC)] and the efficacy of HLE disinfectant solution were determined analyzing the viable counts on general and selective media, and also by molecular studies focused on metagenomic and specific qPCR.

RESULTS: Different contamination loads were detected with LPHR showing the highest contamination. Treatment with the HLE disinfectant solution curbed the spread of well-adapted pathogens on touched surfaces (ICU, LPHR and OC). Metagenomic analysis of microbial diversity of the Patient Table (most contaminated surface in LPHR) revealed the presence of mainly A. johnsonii and P. putida. Furthermore, functional annotation of toxin, virulence and antibiotic resistance sequences showed a high diversity of Acinetobacter spp. and Pseudomonas spp. In this context, specific qPCR analysis confirmed the efficacy of HLE disinfectant solution against the most prevalent and critical pathogens Pseudomonas sp. and Acinetobacter sp. achieving their complete eradication.

CONCLUSION: Given the persistence of detrimental resistant pathogens, the application of HLE disinfection solution could be a highly beneficial and effective option -used either alone or in combination-for infection prevention and control with the aim to eliminate microbial pathogens and their genes from contaminated contact-surfaces and thus limit the spread to humans and other ecological niches.}, } @article {pmid37558110, year = {2023}, author = {Tian, F and Wang, Y and Guo, G and Ding, K and Yang, F and Wang, C and Wang, H and Yan, M}, title = {Meta-genome analysis of a newly enriched azo dyes detoxification halo-thermophilic bacterial consortium.}, journal = {Environmental research}, volume = {237}, number = {Pt 1}, pages = {116828}, doi = {10.1016/j.envres.2023.116828}, pmid = {37558110}, issn = {1096-0953}, abstract = {Treating textile wastewaters were always inhibited by its higher salt concentration and temperature. In this study, a halo-thermophilic bacterial consortium YM was enriched with ability to decolorize acid brilliant scarlet GR (ABS) at 55 °C and 10% salinity. Under optimum conditions of pH (8), temperature (55 °C), and salinity (10%), YM decolorized 97% of ABS under anaerobic conditions. Alteribacillus was identified to be the dominant genus in consortium YM. Consortium YM showed significant decolorization ability under a wide range of salinity (1%-10%), pH (7-9) and temperature (45 °C-60 °C). The degradation pathway of ABS was proposed by the combination of UV-vis spectral analysis, Fourier transform infrared (FTIR), gas chromatography mass spectrometric (GC-MS), and metagenomic analysis. Azoreductase, which was an important enzyme in decolorization process, was identified with great variation in the genome of consortium YM. Meanwhile, the metabolic intermediates after decolorization was identified with low biotoxicity by phytotoxicity tests. This study first identified that Alterbacillus play an important role in azo dye decolorization and degradation process under halo-thermophlic conditions and provided significant knowledge for azo dye decolorization and degradation process.}, } @article {pmid37557958, year = {2023}, author = {Penner, J and Hassell, J and Brown, JR and Mankad, K and Storey, N and Atkinson, L and Ranganathan, N and Lennon, A and Lee, JCD and Champsas, D and Kopec, A and Shah, D and Venturini, C and Dixon, G and De, S and Hatcher, J and Harris, K and Aquilina, K and Kusters, MA and Moshal, K and Shingadia, D and Worth, AJJ and Lucchini, G and Merve, A and Jacques, TS and Bamford, A and Kaliakatsos, M and Breuer, J and Morfopoulou, S}, title = {Translating metagenomics into clinical practice for complex paediatric neurological presentations.}, journal = {The Journal of infection}, volume = {87}, number = {5}, pages = {451-458}, doi = {10.1016/j.jinf.2023.08.002}, pmid = {37557958}, issn = {1532-2742}, support = {206478/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; /DH_/Department of Health/United Kingdom ; /CRUK_/Cancer Research UK/United Kingdom ; }, mesh = {Child ; Humans ; *Metagenome ; *Nervous System Diseases/diagnosis/genetics ; }, } @article {pmid37556397, year = {2023}, author = {Hunter, S and Flaten, E and Petersen, C and Gervain, J and Werker, JF and Trainor, LJ and Finlay, BB}, title = {Babies, bugs and brains: How the early microbiome associates with infant brain and behavior development.}, journal = {PloS one}, volume = {18}, number = {8}, pages = {e0288689}, pmid = {37556397}, issn = {1932-6203}, support = {//CIHR/Canada ; }, mesh = {Humans ; Infant ; Pilot Projects ; *Gastrointestinal Microbiome ; *Microbiota ; Bacteria ; Feces/microbiology ; Brain ; }, abstract = {Growing evidence is demonstrating the connection between the microbiota gut-brain axis and neurodevelopment. Microbiota colonization occurs before the maturation of many neural systems and is linked to brain health. Because of this it has been hypothesized that the early microbiome interactions along the gut-brain axis evolved to promote advanced cognitive functions and behaviors. Here, we performed a pilot study with a multidisciplinary approach to test if the microbiota composition of infants is associated with measures of early cognitive development, in particular neural rhythm tracking; language (forward speech) versus non-language (backwards speech) discrimination; and social joint attention. Fecal samples were collected from 56 infants between four and six months of age and sequenced by shotgun metagenomic sequencing. Of these, 44 performed the behavioral Point and Gaze test to measure joint attention. Infants were tested on either language discrimination using functional near-infrared spectroscopy (fNIRS; 25 infants had usable data) or neural rhythm tracking using electroencephalogram (EEG; 15 had usable data). Infants who succeeded at the Point and Gaze test tended to have increased Actinobacteria and reduced Firmicutes at the phylum level; and an increase in Bifidobacterium and Eggerthella along with a reduction in Hungatella and Streptococcus at the genus level. Measurements of neural rhythm tracking associated negatively to the abundance of Bifidobacterium and positively to the abundance of Clostridium and Enterococcus for the bacterial abundances, and associated positively to metabolic pathways that can influence neurodevelopment, including branched chain amino acid biosynthesis and pentose phosphate pathways. No associations were found for the fNIRS language discrimination measurements. Although the tests were underpowered due to the small pilot sample sizes, potential associations were identified between the microbiome and measurements of early cognitive development that are worth exploring further.}, } @article {pmid37555072, year = {2023}, author = {Li, N and Yi, X and Chen, C and Dai, Z and Deng, Z and Pu, J and Zhou, Y and Li, B and Wang, Z and Ran, P}, title = {The gut microbiome as a potential source of non-invasive biomarkers of chronic obstructive pulmonary disease.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1173614}, pmid = {37555072}, issn = {1664-302X}, abstract = {BACKGROUND: The link between gut microbial dysbiosis and the development of chronic obstructive pulmonary disease (COPD) is of considerable interest. However, little is known regarding the potential for the use of the fecal metagenome for the diagnosis of COPD.

METHODS: A total of 80 healthy controls, 31 patients with COPD severity stages I or II, and 49 patients with COPD severity stages III or IV fecal samples were subjected to metagenomic analysis. We characterized the gut microbiome, identified microbial taxonomic and functional markers, and constructed a COPD disease classifier using samples.

RESULTS: The fecal microbial diversity of patients with COPD stages I or II was higher than that of healthy controls, but lower in patients with COPD stages III or IV. Twenty-one, twenty-four, and eleven microbial species, including potential pathogens and pro-inflammatory bacteria, were significantly enriched or depleted in healthy controls, patients with COPD stages I or II, and patients with COPD stages III & IV. The KEGG orthology (KO) gene profiles derived demonstrated notable differences in gut microbial function among the three groups. Moreover, gut microbial taxonomic and functional markers could be used to differentiate patients with COPD from healthy controls, on the basis of areas under receiver operating characteristic curves (AUCs) of 0.8814 and 0.8479, respectively. Notably, the gut microbial taxonomic features differed between healthy individuals and patients in stages I-II COPD, which suggests the utility of fecal metagenomic biomarkers for the diagnosis of COPD (AUC = 0.9207).

CONCLUSION: Gut microbiota-targeted biomarkers represent potential non-invasive tools for the diagnosis of COPD.}, } @article {pmid37554781, year = {2023}, author = {Cheng, B and Huang, M and Zhou, T and Deng, Q and Teketay Wassie, and Wu, T and Wu, X}, title = {Garlic essential oil supplementation modulates colonic microbiota compositions and regulates immune response in weaned piglets.}, journal = {Heliyon}, volume = {9}, number = {8}, pages = {e18729}, pmid = {37554781}, issn = {2405-8440}, abstract = {The objective of this study was to investigate the colonic microbiome compositions and immune response and reveal their correlations in weaned piglets fed with garlic essential oil (GEO). Twelve 21-day-old crossbred piglets with the same parity and similar weight (BW = 7.07 ± 0.37 Kg) were randomly divided into control and experimental groups based on BW and sex, which fed either a basal diet (CON group), or a basal diet supplemented with 1.5 g/kg GEO (GEO group). UHPLC-QE-MS showed the main component of GEO were belonged to carbohydrates, organic acid, flavonoids, phenylpropanoids and terpenoids. GEO decreased serum IL-1β, IL-8 content and the down-regulated mRNA expression of IFN-γ, TLR2 in jejunal mucosa but increased serum IgG, IL-4 content and up-regulated the mRNA expression of IL-4, IL-1β, TNF-α in ileal mucosa. What's more, the metagenomic analysis demonstrated that GEO increased the abundance of Bacteroidetes, Euryarchaeota and Spirochaetes, while decreased the abundance of Firmicutes and Actinobacteria at Phylum level and Selenomonas_boris, Selenomonadaceae_bacterium_DSM_108025, Clostridiales_bacterium and Phascolarctobacterium_succinatutens at species level. Notably, the main function pathway of virulence factor (VFDB) enriched in GEO group were Fibronection-binding protein, Zn[++] metallophrotease and Capsular polysaccharide, while the main function pathway of VFDB enriched in CON group were heme biosynthesis, Lap and FeoAB. Spearman correlation analysis indicated the Spirochaetes had a positive association with IL-6 and IL-4. Acinobacteria was positively correlated with IL-1β, while negative with the IL-6; In addition, Euryarchaeota had a positive correlation with IL-4, but a negative correlation with IL-1β; Tenericutes was negative with IL-8; Phascolarcolarctobacterium_succinatutens and was negative with IL-6; Ruminococcaceae_bacterium was negative with TNF-α. While Selenomonadaceae_bacterium_DSM_108025 had a positive correlation with IL-8. In conclusion, our results uncovered that immune regulation effects of GEO may be associated with the microbiome compositions in response to GEO.}, } @article {pmid37554339, year = {2023}, author = {Verstraete, B and Janssens, S and De Block, P and Asselman, P and Méndez, G and Ly, S and Hamon, P and Guyot, R}, title = {Metagenomics of African Empogona and Tricalysia (Rubiaceae) reveals the presence of leaf endophytes.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15778}, pmid = {37554339}, issn = {2167-8359}, mesh = {Endophytes/genetics ; *Rubiaceae/genetics ; Phylogeny ; Metagenomics ; *Burkholderia ; Plants ; Plant Leaves/microbiology ; *Burkholderiaceae ; }, abstract = {BACKGROUND: Leaf symbiosis is a phenomenon in which host plants of Rubiaceae interact with bacterial endophytes within their leaves. To date, it has been found in around 650 species belonging to eight genera in four tribes; however, the true extent in Rubiaceae remains unknown. Our aim is to investigate the possible occurrence of leaf endophytes in the African plant genera Empogona and Tricalysia and, if present, to establish their identity.

METHODS: Total DNA was extracted from the leaves of four species of the Coffeeae tribe (Empogona congesta, Tricalysia hensii, T. lasiodelphys, and T. semidecidua) and sequenced. Bacterial reads were filtered out and assembled. Phylogenetic analysis of the endophytes was used to reveal their identity and their relationship with known symbionts.

RESULTS: All four species have non-nodulated leaf endophytes, which are identified as Caballeronia. The endophytes are distinct from each other but related to other nodulated and non-nodulated endophytes. An apparent phylogenetic or geographic pattern appears to be absent in endophytes or host plants. Caballeronia endophytes are present in the leaves of Empogona and Tricalysia, two genera not previously implicated in leaf symbiosis. This interaction is likely to be more widespread, and future discoveries are inevitable.}, } @article {pmid37554329, year = {2023}, author = {Jeong, S and Cho, WK and Jo, Y and Choi, SR and Lee, N and Jeon, K and Park, MJ and Song, W and Lee, KY}, title = {Immune-checkpoint proteins, cytokines, and microbiome impact on patients with cervical insufficiency and preterm birth.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1228647}, pmid = {37554329}, issn = {1664-3224}, mesh = {*Immune Checkpoint Proteins/metabolism ; Humans ; Female ; Pregnancy ; *Microbiota ; *Cytokines/metabolism ; *Premature Birth/diagnosis ; Cerclage, Cervical ; *Cervix Uteri/microbiology ; Prospective Studies ; *Uterine Cervical Incompetence ; }, abstract = {BACKGROUND: Microenvironmental factors, including microbe-induced inflammation and immune-checkpoint proteins that modulate immune cells have been associated with both cervical insufficiency and preterm delivery. These factors are incompletely understood. This study aimed to explore and compare interactions among microbiome and inflammatory factors, such as cytokines and immune-checkpoint proteins, in patients with cervical insufficiency and preterm birth. In particular, factors related to predicting preterm birth were identified and the performance of the combination of these factors was evaluated.

METHODS: A total of 220 swab samples from 110 pregnant women, prospectively recruited at the High-Risk Maternal Neonatal Intensive Care Center, were collected between February 2020 and March 2021. This study included 63 patients with cervical insufficiency receiving cerclage and 47 control participants. Endo- and exocervical swabs and fluids were collected simultaneously. Shotgun metagenomic sequencing for the microbiome and the measurement of 34 immune-checkpoint proteins and inflammatory cytokines were performed.

RESULTS: First, we demonstrated that immune-checkpoint proteins, the key immune-regulatory molecules, could be measured in endocervical and exocervical samples. Secondly, we identified significantly different microenvironments in cervical insufficiency and preterm birth, with precise cervical locations, to provide information about practically useful cervical locations in clinical settings. Finally, the presence of Moraxella osloensis (odds ratio = 14.785; P = 0.037) and chemokine CC motif ligand 2 levels higher than 73 pg/mL (odds ratio = 40.049; P = 0.005) in endocervical samples were associated with preterm birth. Combining M. osloensis and chemokine CC motif ligand 2 yielded excellent performance for predicting preterm birth (area under the receiver operating characteristic curve = 0.846, 95% confidence interval = 0.733-0.925).

CONCLUSION: Multiple relationships between microbiomes, immune-checkpoint proteins, and inflammatory cytokines in the cervical microenvironment were identified. We focus on these factors to aid in the comprehensive understanding and therapeutic modulation of local microbial and immunologic compositions for the management of cervical insufficiency and preterm birth.}, } @article {pmid37553874, year = {2023}, author = {Qian, Y and Kang, Z and Zhao, L and Chen, H and Zhou, C and Gao, Q and Wang, Z and Liu, Q and Cui, Y and Li, X and Chen, Y and Zou, T and Fang, J}, title = {Berberine might block colorectal carcinogenesis by inhibiting the regulation of B-cell function by Veillonella parvula.}, journal = {Chinese medical journal}, volume = {136}, number = {22}, pages = {2722-2731}, pmid = {37553874}, issn = {2542-5641}, mesh = {Animals ; Humans ; *Berberine/pharmacology/therapeutic use ; Carcinogenesis ; Veillonella ; *Colorectal Neoplasms/genetics ; Tumor Microenvironment ; }, abstract = {BACKGROUND: Colorectal carcinogenesis and progression are related to the gut microbiota and the tumor immune microenvironment. Our previous clinical trial demonstrated that berberine (BBR) hydrochloride might reduce the recurrence and canceration of colorectal adenoma (CRA). The present study aimed to further explore the mechanism of BBR in preventing colorectal cancer (CRC).

METHODS: We performed metagenomics sequencing on fecal specimens obtained from the BBR intervention trial, and the differential bacteria before and after medication were validated using quantitative polymerase chain reaction. We further performed ApcMin/+ animal intervention tests, RNA sequencing, flow cytometry, immunohistochemistry, and enzyme-linked immunosorbent assays.

RESULTS: The abundance of fecal Veillonella parvula (V . parvula) decreased significantly after BBR administration (P = 0.0016) and increased through the development from CRA to CRC. Patients with CRC with a higher V. parvula abundance had worse tumor staging and a higher lymph node metastasis rate. The intestinal immune pathway of Immunoglobulin A production was activated, and the expression of TNFSF13B (Tumor necrosis factor superfamily 13b, encoding B lymphocyte stimulator [BLyS]), the representative gene of this pathway, and the genes encoding its receptors (interleukin-10 and transforming growth factor beta) were significantly upregulated. Animal experiments revealed that V. parvula promoted colorectal carcinogenesis and increased BLyS levels, while BBR reversed this effect.

CONCLUSION: BBR might inhibit V. parvula and further weaken the immunomodulatory effect of B cells induced by V. parvula , thereby blocking the development of colorectal tumors.

TRIAL REGISTRAION: ClinicalTrials.gov, No. NCT02226185.}, } @article {pmid37553697, year = {2023}, author = {Chen, J and Siliceo, SL and Ni, Y and Nielsen, HB and Xu, A and Panagiotou, G}, title = {Identification of robust and generalizable biomarkers for microbiome-based stratification in lifestyle interventions.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {178}, pmid = {37553697}, issn = {2049-2618}, support = {H2020-MSCA-ITN-2018/MCCC_/Marie Curie/United Kingdom ; }, mesh = {Humans ; *Microbiota ; *Gastrointestinal Microbiome ; Biomarkers ; Diet ; Life Style ; }, abstract = {BACKGROUND: A growing body of evidence suggests that the gut microbiota is strongly linked to general human health. Microbiome-directed interventions, such as diet and exercise, are acknowledged as a viable and achievable strategy for preventing disorders and improving human health. However, due to the significant inter-individual diversity of the gut microbiota between subjects, lifestyle recommendations are expected to have distinct and highly variable impacts to the microbiome structure.

RESULTS: Here, through a large-scale meta-analysis including 1448 shotgun metagenomics samples obtained longitudinally from 396 individuals during lifestyle studies, we revealed Bacteroides stercoris, Prevotella copri, and Bacteroides vulgatus as biomarkers of microbiota's resistance to structural changes, and aromatic and non-aromatic amino acid biosynthesis as important regulator of microbiome dynamics. We established criteria for distinguishing between significant compositional changes from normal microbiota fluctuation and classified individuals based on their level of response. We further developed a machine learning model for predicting "responders" and "non-responders" independently of the type of intervention with an area under the curve of up to 0.86 in external validation cohorts of different ethnicities.

CONCLUSIONS: We propose here that microbiome-based stratification is possible for identifying individuals with highly plastic or highly resistant microbial structures. Identifying subjects that will not respond to generalized lifestyle therapeutic interventions targeting the restructuring of gut microbiota is important to ensure that primary end-points of clinical studies are reached. Video Abstract.}, } @article {pmid37553373, year = {2023}, author = {Muzeniek, T and Perera, T and Siriwardana, S and Bas, D and Bayram, F and Öruc, M and Becker-Ziaja, B and Perera, I and Weerasena, J and Handunnetti, S and Schwarz, F and Premawansa, G and Premawansa, S and Yapa, W and Nitsche, A and Kohl, C}, title = {Comparative virome analysis of individual shedding routes of Miniopterus phillipsi bats inhabiting the Wavul Galge cave, Sri Lanka.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12859}, pmid = {37553373}, issn = {2045-2322}, mesh = {Animals ; Humans ; *Chiroptera ; Phylogeny ; Virome ; Sri Lanka ; *Coronavirus/genetics ; }, abstract = {Bats are described as the natural reservoir host for a wide range of viruses. Although an increasing number of bat-associated, potentially human pathogenic viruses were discovered in the past, the full picture of the bat viromes is not explored yet. In this study, the virome composition of Miniopterus phillipsi bats (formerly known as Miniopterus fuliginosus bats in Sri Lanka) inhabiting the Wavul Galge cave, Sri Lanka, was analyzed. To assess different possible excretion routes, oral swabs, feces and urine were collected and analyzed individually by using metagenomic NGS. The data obtained was further evaluated by using phylogenetic reconstructions, whereby a special focus was set on RNA viruses that are typically associated with bats. Two different alphacoronavirus strains were detected in feces and urine samples. Furthermore, a paramyxovirus was detected in urine samples. Sequences related to Picornaviridae, Iflaviridae, unclassified Riboviria and Astroviridae were identified in feces samples and further sequences related to Astroviridae in urine samples. No viruses were detected in oral swab samples. The comparative virome analysis in this study revealed a diversity in the virome composition between the collected sample types which also represent different potential shedding routes for the detected viruses. At the same time, several novel viruses represent first reports of these pathogens from bats in Sri Lanka. The detection of two different coronaviruses in the samples indicates the potential general persistence of this virus species in M. phillipsi bats. Based on phylogenetics, the identified viruses are closely related to bat-associated viruses with comparably low estimation of human pathogenic potential. In further studies, the seasonal variation of the virome will be analyzed to identify possible shedding patterns for particular viruses.}, } @article {pmid37553333, year = {2023}, author = {Hessler, T and Huddy, RJ and Sachdeva, R and Lei, S and Harrison, STL and Diamond, S and Banfield, JF}, title = {Vitamin interdependencies predicted by metagenomics-informed network analyses and validated in microbial community microcosms.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4768}, pmid = {37553333}, issn = {2041-1723}, mesh = {Metagenomics ; Vitamins ; *Microbiota/genetics ; Metagenome/genetics ; *Comamonadaceae ; Thiamine ; }, abstract = {Metagenomic or metabarcoding data are often used to predict microbial interactions in complex communities, but these predictions are rarely explored experimentally. Here, we use an organism abundance correlation network to investigate factors that control community organization in mine tailings-derived laboratory microbial consortia grown under dozens of conditions. The network is overlaid with metagenomic information about functional capacities to generate testable hypotheses. We develop a metric to predict the importance of each node within its local network environments relative to correlated vitamin auxotrophs, and predict that a Variovorax species is a hub as an important source of thiamine. Quantification of thiamine during the growth of Variovorax in minimal media show high levels of thiamine production, up to 100 mg/L. A few of the correlated thiamine auxotrophs are predicted to produce pantothenate, which we show is required for growth of Variovorax, supporting that a subset of vitamin-dependent interactions are mutualistic. A Cryptococcus yeast produces the B-vitamin pantothenate, and co-culturing with Variovorax leads to a 90-130-fold fitness increase for both organisms. Our study demonstrates the predictive power of metagenome-informed, microbial consortia-based network analyses for identifying microbial interactions that underpin the structure and functioning of microbial communities.}, } @article {pmid37551852, year = {2023}, author = {Vientós-Plotts, AI and Ericsson, AC and Reinero, CR}, title = {The respiratory microbiota and its impact on health and disease in dogs and cats: A One Health perspective.}, journal = {Journal of veterinary internal medicine}, volume = {37}, number = {5}, pages = {1641-1655}, pmid = {37551852}, issn = {1939-1676}, mesh = {Cats ; Dogs ; Humans ; Animals ; Dysbiosis/veterinary/microbiology ; *Cat Diseases ; *One Health ; *Dog Diseases ; Lung/microbiology ; *Microbiota ; *Respiratory Tract Diseases/veterinary ; }, abstract = {Healthy lungs were long thought of as sterile, with presence of bacteria identified by culture representing contamination. Recent advances in metagenomics have refuted this belief by detecting rich, diverse, and complex microbial communities in the healthy lower airways of many species, albeit at low concentrations. Although research has only begun to investigate causality and potential mechanisms, alterations in these microbial communities (known as dysbiosis) have been described in association with inflammatory, infectious, and neoplastic respiratory diseases in humans. Similar studies in dogs and cats are scarce. The microbial communities in the respiratory tract are linked to distant microbial communities such as in the gut (ie, the gut-lung axis), allowing interplay of microbes and microbial products in health and disease. This review summarizes considerations for studying local microbial communities, key features of the respiratory microbiota and its role in the gut-lung axis, current understanding of the healthy respiratory microbiota, and examples of dysbiosis in selected respiratory diseases of dogs and cats.}, } @article {pmid37550964, year = {2023}, author = {Li, J and Ghosh, TS and McCann, R and Mallon, P and Hill, C and Draper, L and Schult, D and Fanning, LJ and Shannon, R and Sadlier, C and Horgan, M and O'Mahony, L and O'Toole, PW}, title = {Robust cross-cohort gut microbiome associations with COVID-19 severity.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2242615}, pmid = {37550964}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; *COVID-19 ; RNA, Ribosomal, 16S/genetics ; SARS-CoV-2 ; Biomarkers ; }, abstract = {Although many recent studies have examined associations between the gut microbiome and COVID-19 disease severity in individual patient cohorts, questions remain on the robustness across international cohorts of the biomarkers they reported. Here, we performed a meta-analysis of eight shotgun metagenomic studies of COVID-19 patients (comprising 1,023 stool samples) and 23 > 16S rRNA gene amplicon sequencing (16S) cohorts (2,415 total stool samples). We found that disease severity (as defined by the WHO clinical progression scale) was associated with taxonomic and functional microbiome differences. This alteration in gut microbiome configuration peaks at days 7-30 post diagnosis, after which the gut microbiome returns to a configuration that becomes more similar to that of healthy controls over time. Furthermore, we identified a core set of species that were consistently associated with disease severity across shotgun metagenomic and 16S cohorts, and whose abundance can accurately predict disease severity category of SARS-CoV-2 infected subjects, with Actinomyces oris abundance predicting population-level mortality rate of COVID-19. Additionally, we used relational diet-microbiome databases constructed from cohort studies to predict microbiota-targeted diet patterns that would modulate gut microbiota composition toward that of healthy controls. Finally, we demonstrated the association of disease severity with the composition of intestinal archaeal, fungal, viral, and parasitic communities. Collectively, this study has identified robust COVID-19 microbiome biomarkers, established accurate predictive models as a basis for clinical prognostic tests for disease severity, and proposed biomarker-targeted diets for managing COVID-19 infection.}, } @article {pmid37550758, year = {2023}, author = {Hao, C and Elias, JE and Lee, PKH and Lam, H}, title = {metaSpectraST: an unsupervised and database-independent analysis workflow for metaproteomic MS/MS data using spectrum clustering.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {176}, pmid = {37550758}, issn = {2049-2618}, mesh = {Animals ; Mice ; *Tandem Mass Spectrometry ; Workflow ; Proteomics ; *Microbiota/genetics ; Peptides ; }, abstract = {BACKGROUND: The high diversity and complexity of the microbial community make it a formidable challenge to identify and quantify the large number of proteins expressed in the community. Conventional metaproteomics approaches largely rely on accurate identification of the MS/MS spectra to their corresponding short peptides in the digested samples, followed by protein inference and subsequent taxonomic and functional analysis of the detected proteins. These approaches are dependent on the availability of protein sequence databases derived either from sample-specific metagenomic data or from public repositories. Due to the incompleteness and imperfections of these protein sequence databases, and the preponderance of homologous proteins expressed by different bacterial species in the community, this computational process of peptide identification and protein inference is challenging and error-prone, which hinders the comparison of metaproteomes across multiple samples.

RESULTS: We developed metaSpectraST, an unsupervised and database-independent metaproteomics workflow, which quantitatively profiles and compares metaproteomics samples by clustering experimentally observed MS/MS spectra based on their spectral similarity. We applied metaSpectraST to fecal samples collected from littermates of two different mother mice right after weaning. Quantitative proteome profiles of the microbial communities of different mice were obtained without any peptide-spectrum identification and used to evaluate the overall similarity between samples and highlight any differentiating markers. Compared to the conventional database-dependent metaproteomics analysis, metaSpectraST is more successful in classifying the samples and detecting the subtle microbiome changes of mouse gut microbiomes post-weaning. metaSpectraST could also be used as a tool to select the suitable biological replicates from samples with wide inter-individual variation.

CONCLUSIONS: metaSpectraST enables rapid profiling of metaproteomic samples quantitatively, without the need for constructing the protein sequence database or identification of the MS/MS spectra. It maximally preserves information contained in the experimental MS/MS spectra by clustering all of them first and thus is able to better profile the complex microbial communities and highlight their functional changes, as compared with conventional approaches. tag the videobyte in this section as ESM4 Video Abstract.}, } @article {pmid37550707, year = {2023}, author = {Zhu, XY and Li, Y and Xue, CX and Lidbury, IDEA and Todd, JD and Lea-Smith, DJ and Tian, J and Zhang, XH and Liu, J}, title = {Deep-sea Bacteroidetes from the Mariana Trench specialize in hemicellulose and pectin degradation typically associated with terrestrial systems.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {175}, pmid = {37550707}, issn = {2049-2618}, support = {BB/X005968/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Bacteroidetes/genetics/metabolism ; *Ecosystem ; Polysaccharides/metabolism ; Pectins/metabolism ; }, abstract = {BACKGROUND: Hadal trenches (>6000 m) are the deepest oceanic regions on Earth and depocenters for organic materials. However, how these enigmatic microbial ecosystems are fueled is largely unknown, particularly the proportional importance of complex polysaccharides introduced through deposition from the photic surface waters above. In surface waters, Bacteroidetes are keystone taxa for the cycling of various algal-derived polysaccharides and the flux of carbon through the photic zone. However, their role in the hadal microbial loop is almost unknown.

RESULTS: Here, culture-dependent and culture-independent methods were used to study the potential of Bacteroidetes to catabolize diverse polysaccharides in Mariana Trench waters. Compared to surface waters, the bathypelagic (1000-4000 m) and hadal (6000-10,500 m) waters harbored distinct Bacteroidetes communities, with Mesoflavibacter being enriched at ≥ 4000 m and Bacteroides and Provotella being enriched at 10,400-10,500 m. Moreover, these deep-sea communities possessed distinct gene pools encoding for carbohydrate active enzymes (CAZymes), suggesting different polysaccharide sources are utilised in these two zones. Compared to surface counterparts, deep-sea Bacteroidetes showed significant enrichment of CAZyme genes frequently organized into polysaccharide utilization loci (PULs) targeting algal/plant cell wall polysaccharides (i.e., hemicellulose and pectin), that were previously considered an ecological trait associated with terrestrial Bacteroidetes only. Using a hadal Mesoflavibacter isolate (MTRN7), functional validation of this unique genetic potential was demonstrated. MTRN7 could utilize pectic arabinans, typically associated with land plants and phototrophic algae, as the carbon source under simulated deep-sea conditions. Interestingly, a PUL we demonstrate is likely horizontally acquired from coastal/land Bacteroidetes was activated during growth on arabinan and experimentally shown to encode enzymes that hydrolyze arabinan at depth.

CONCLUSIONS: Our study implies that hadal Bacteroidetes exploit polysaccharides poorly utilized by surface populations via an expanded CAZyme gene pool. We propose that sinking cell wall debris produced in the photic zone can serve as an important carbon source for hadal heterotrophs and play a role in shaping their communities and metabolism. Video Abstract.}, } @article {pmid37550406, year = {2023}, author = {Doane, MP and Reed, MB and McKerral, J and Farias Oliveira Lima, L and Morris, M and Goodman, AZ and Johri, S and Papudeshi, B and Dillon, T and Turnlund, AC and Peterson, M and Mora, M and de la Parra Venegas, R and Pillans, R and Rohner, CA and Pierce, SJ and Legaspi, CG and Araujo, G and Ramirez-Macias, D and Edwards, RA and Dinsdale, EA}, title = {Emergent community architecture despite distinct diversity in the global whale shark (Rhincodon typus) epidermal microbiome.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12747}, pmid = {37550406}, issn = {2045-2322}, mesh = {Animals ; *Sharks/physiology ; Epidermis ; Epidermal Cells ; *Microbiota/genetics ; Metagenome ; }, abstract = {Microbiomes confer beneficial physiological traits to their host, but microbial diversity is inherently variable, challenging the relationship between microbes and their contribution to host health. Here, we compare the diversity and architectural complexity of the epidermal microbiome from 74 individual whale sharks (Rhincodon typus) across five aggregations globally to determine if network properties may be more indicative of the microbiome-host relationship. On the premise that microbes are expected to exhibit biogeographic patterns globally and that distantly related microbial groups can perform similar functions, we hypothesized that microbiome co-occurrence patterns would occur independently of diversity trends and that keystone microbes would vary across locations. We found that whale shark aggregation was the most important factor in discriminating taxonomic diversity patterns. Further, microbiome network architecture was similar across all aggregations, with degree distributions matching Erdos-Renyi-type networks. The microbiome-derived networks, however, display modularity indicating a definitive microbiome structure on the epidermis of whale sharks. In addition, whale sharks hosted 35 high-quality metagenome assembled genomes (MAGs) of which 25 were present from all sample locations, termed the abundant 'core'. Two main MAG groups formed, defined here as Ecogroup 1 and 2, based on the number of genes present in metabolic pathways, suggesting there are at least two important metabolic niches within the whale shark microbiome. Therefore, while variability in microbiome diversity is high, network structure and core taxa are inherent characteristics of the epidermal microbiome in whale sharks. We suggest the host-microbiome and microbe-microbe interactions that drive the self-assembly of the microbiome help support a functionally redundant abundant core and that network characteristics should be considered when linking microbiomes with host health.}, } @article {pmid37550336, year = {2023}, author = {Peres, FV and Paula, FS and Bendia, AG and Gontijo, JB and de Mahiques, MM and Pellizari, VH}, title = {Assessment of prokaryotic communities in Southwestern Atlantic deep-sea sediments reveals prevalent methanol-oxidising Methylomirabilales.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12782}, pmid = {37550336}, issn = {2045-2322}, mesh = {*Methanol/metabolism ; *Geologic Sediments/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Prokaryotic Cells ; Bacteria ; Archaea ; }, abstract = {Continental slopes can play a significant contribution to marine productivity and carbon cycling. These regions can harbour distinct geological features, such as salt diapirs and pockmarks, in which their depressions may serve as natural sediment traps where different compounds can accumulate. We investigated the prokaryotic communities in surface (0-2 cm) and subsurface (18-20 or 22-24 cm) sediments from a salt diapir and pockmark field in Santos Basin, Southwest Atlantic Ocean. Metabarcoding of 16 samples revealed that surface sediments were dominated by the archaeal class Nitrososphaeria, while the bacterial class Dehalococcoidia was the most prevalent in subsurface samples. Sediment strata were found to be a significant factor explaining 27% of the variability in community composition. However, no significant difference was observed among geomorphological features. We also performed a metagenomic analysis of three surface samples and analysed the highest quality metagenome-assembled genome retrieved, which belonged to the family CSP1-5, phylum Methylomirabilota. This non-methanotrophic methylotroph contains genes encoding for methanol oxidation and Calvin Cycle pathways, along with diverse functions that may contribute to its adaptation to deep-sea habitats and to oscillating environmental conditions. By integrating metabarcoding and metagenomic approaches, we reported that CSP1-5 is prevalent in the sediment samples from Santos Basin slope, indicating the potential importance of methanol metabolism in this region. Finally, using a phylogenetic approach integrating 16S rRNA sequences assigned to Methylomirabilota in this study with those from a public database, we argued that CSP1-5 public sequences might be misclassified as Methylomirabilaceae (the methanotrophic clade) and, therefore, the role of these organisms and the methanol cycling could also be neglected in other environments.}, } @article {pmid37549699, year = {2023}, author = {Seshan, H and Santillan, E and Constancias, F and Chandra Segaran, US and Williams, RBH and Wuertz, S}, title = {Metagenomics and metatranscriptomics suggest pathways of 3-chloroaniline degradation in wastewater reactors.}, journal = {The Science of the total environment}, volume = {903}, number = {}, pages = {166066}, doi = {10.1016/j.scitotenv.2023.166066}, pmid = {37549699}, issn = {1879-1026}, abstract = {Biological wastewater treatment systems are often affected by shifts in influent quality, including the input of toxic chemicals. Yet the mechanisms underlying the adaptation of activated sludge process performance are rarely studied in a controlled and replicated experimental setting, particularly when challenged with a sustained toxin input. Three replicate bench-scale bioreactors were subjected to a chemical disturbance in the form of 3-chloroaniline (3-CA) over 132 days, after an acclimation period of 58 days, while three control reactors received no 3-CA input. Ammonia oxidation was initially affected by 3-CA. Within three weeks of the experiment, microbial communities in all three treatment reactors adapted to biologically degrade 3-CA resulting in partial ammonia oxidation recovery. Combining process and microbial community data from amplicon sequencing with potential functions gleaned from assembled metagenomics and metatranscriptomics data, two putative degradation pathways for 3-CA were identified. The first pathway, determined from metagenomics data, involves a benzoate dioxygenase and subsequent meta-cleavage of the aromatic ring. The second, determined from intensive short-term sampling for gene expression data in tandem with 3-CA degradation, involves a phenol monooxygenase followed by ortho-cleavage of the aromatic ring. The relative abundances of amplicon sequence variants associated with the genera Gemmatimonas, OLB8, and Taibaiella correlated significantly with 3-CA degradation. Metagenome-assembled genome data also showed the genus OLB8 to be differentially enriched in treatment reactors, making it a strong candidate as 3-CA degrader. Using replicated reactors, this study has demonstrated the impact of a sustained stress on the activated sludge process. The unique and novel features of this study include the identification of putative pathways and potential degraders of 3-CA using long-term and short-term sampling in tandem with multiple methods in a controlled and replicated experiment.}, } @article {pmid37549040, year = {2024}, author = {Zhang, H and Dierkes, RF and Perez-Garcia, P and Costanzi, E and Dittrich, J and Cea, PA and Gurschke, M and Applegate, V and Partus, K and Schmeisser, C and Pfleger, C and Gohlke, H and Smits, SHJ and Chow, J and Streit, WR}, title = {The metagenome-derived esterase PET40 is highly promiscuous and hydrolyses polyethylene terephthalate (PET).}, journal = {The FEBS journal}, volume = {291}, number = {1}, pages = {70-91}, doi = {10.1111/febs.16924}, pmid = {37549040}, issn = {1742-4658}, support = {031B0571B//Bundesministerium für Bildung und Forschung/ ; 031B0837A//Bundesministerium für Bildung und Forschung/ ; 031B0837B//Bundesministerium für Bildung und Forschung/ ; 031B867B//Bundesministerium für Bildung und Forschung/ ; 417919780//Deutsche Forschungsgemeinschaft/ ; INST 208/740-1 FUGG//Deutsche Forschungsgemeinschaft/ ; 101000327//European Commission/ ; }, mesh = {*Esterases/genetics ; Polyethylene Terephthalates/metabolism ; Metagenome ; Ecosystem ; Molecular Docking Simulation ; Hydrolases/chemistry ; *Streptomyces/genetics ; Polymers ; }, abstract = {Polyethylene terephthalate (PET) is a widely used synthetic polymer and known to contaminate marine and terrestrial ecosystems. Only few PET-active microorganisms and enzymes (PETases) are currently known, and it is debated whether degradation activity for PET originates from promiscuous enzymes with broad substrate spectra that primarily act on natural polymers or other bulky substrates, or whether microorganisms evolved their genetic makeup to accepting PET as a carbon source. Here, we present a predicted diene lactone hydrolase designated PET40, which acts on a broad spectrum of substrates, including PET. It is the first esterase with activity on PET from a GC-rich Gram-positive Amycolatopsis species belonging to the Pseudonocardiaceae (Actinobacteria). It is highly conserved within the genera Amycolatopsis and Streptomyces. PET40 was identified by sequence-based metagenome search using a PETase-specific hidden Markov model. Besides acting on PET, PET40 has a versatile substrate spectrum, hydrolyzing δ-lactones, β-lactam antibiotics, the polyester-polyurethane Impranil® DLN, and various para-nitrophenyl ester substrates. Molecular docking suggests that the PET degradative activity is likely a result of the promiscuity of PET40, as potential binding modes were found for substrates encompassing mono(2-hydroxyethyl) terephthalate, bis(2-hydroxyethyl) terephthalate, and a PET trimer. We also solved the crystal structure of the inactive PET40 variant S178A to 1.60 Å resolution. PET40 is active throughout a wide pH (pH 4-10) and temperature range (4-65 °C) and remarkably stable in the presence of 5% SDS, making it a promising enzyme as a starting point for further investigations and optimization approaches.}, } @article {pmid37548643, year = {2023}, author = {Li, Z and Ju, Y and Xia, J and Zhang, Z and Zhen, H and Tong, X and Sun, Y and Lu, H and Zong, Y and Chen, P and Cai, K and Wang, Z and Yang, H and Wang, J and Wang, J and Hou, Y and Jin, X and Zhang, T and Zhang, W and Xu, X and Xiao, L and Guo, R and Nie, C}, title = {Integrated Human Skin Bacteria Genome Catalog Reveals Extensive Unexplored Habitat-Specific Microbiome Diversity and Function.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {10}, number = {28}, pages = {e2300050}, pmid = {37548643}, issn = {2198-3844}, support = {2022ZD0211600//STI2030-Major Projects/ ; 2019-I2M-5-066//CAMS Innovation Fund for Medical Sciences/ ; }, abstract = {The skin is the largest organ in the human body. Various skin environments on its surface constitutes a complex ecosystem. One of the characteristics of the skin micro-ecosystem is low biomass, which greatly limits a comprehensive identification of the microbial species through sequencing. In this study, deep-shotgun sequencing (average 21.5 Gigabyte (Gb)) from 450 facial samples and publicly available skin metagenomic datasets of 2069 samples to assemble a Unified Human Skin Genome (UHSG) catalog is integrated. The UHSG encompasses 813 prokaryotic species derived from 5779 metagenome-assembled genomes, among which 470 are novel species covering 20 phyla with 1385 novel assembled genomes. Based on the UHSG, the core functions of the skin microbiome are described and the differences in amino acid metabolism, carbohydrate metabolism, and drug resistance functions among different phyla are identified. Furthermore, analysis of secondary metabolites of the near-complete genomes further find 1220 putative novel secondary metabolites, several of which are found in previously unknown genomes. Single nucleotide variant (SNV) reveals a possible skin protection mechanism: the negative selection process of the skin environment to conditional pathogens. UHSG offers a convenient reference database that will facilitate a more in-depth understanding of the role of skin microorganisms in the skin.}, } @article {pmid37548332, year = {2023}, author = {Wu, Y and Zhuang, J and Zhang, Q and Zhao, X and Chen, G and Han, S and Hu, B and Wu, W and Han, S}, title = {Aging characteristics of colorectal cancer based on gut microbiota.}, journal = {Cancer medicine}, volume = {12}, number = {17}, pages = {17822-17834}, pmid = {37548332}, issn = {2045-7634}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/pathology ; Bacteria/genetics ; *Microbiota ; Aging ; }, abstract = {BACKGROUND: Aging is one of the factors leading to cancer. Gut microbiota is related to aging and colorectal cancer (CRC).

METHODS: A total of 11 metagenomic data sets related to CRC were collected from the R package curated Metagenomic Data. After batch effect correction, healthy individuals and CRC samples were divided into three age groups. Ggplot2 and Microbiota Process packages were used for visual description of species composition and PCA in healthy individuals and CRC samples. LEfSe analysis was performed for species relative abundance data in healthy/CRC groups according to age. Spearman correlation coefficient of age-differentiated bacteria in healthy individuals and CRC samples was calculated separately. Finally, the age prediction model and CRC risk prediction model were constructed based on the age-differentiated bacteria.

RESULTS: The structure and composition of the gut microbiota were significantly different among the three groups. For example, the abundance of Bacteroides vulgatus in the old group was lower than that in the other two groups, the abundance of Bacteroides fragilis increased with aging. In addition, seven species of bacteria whose abundance increases with aging were screened out. Furthermore, the abundance of pathogenic bacteria (Escherichia_coli, Butyricimonas_virosa, Ruminococcus_bicirculans, Bacteroides_fragilis and Streptococcus_vestibularis) increased with aging in CRCs. The abundance of probiotics (Eubacterium_eligens) decreased with aging in CRCs. The age prediction model for healthy individuals based on the 80 age-related differential bacteria and model of CRC patients based on the 58 age-related differential bacteria performed well, with AUC of 0.79 and 0.71, respectively. The AUC of CRC risk prediction model based on 45 disease differential bacteria was 0.83. After removing the intersection between the disease-differentiated bacteria and the age-differentiated bacteria from the healthy samples, the AUC of CRC risk prediction model based on remaining 31 bacteria was 0.8. CRC risk prediction models for each of the three age groups showed no significant difference in accuracy (young: AUC=0.82, middle: AUC=0.83, old: AUC=0.85).

CONCLUSION: Age as a factor affecting microbial composition should be considered in the application of gut microbiota to predict the risk of CRC.}, } @article {pmid37547692, year = {2023}, author = {Li, L and Meng, D and Yin, H and Zhang, T and Liu, Y}, title = {Genome-resolved metagenomics provides insights into the ecological roles of the keystone taxa in heavy-metal-contaminated soils.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1203164}, pmid = {37547692}, issn = {1664-302X}, abstract = {Microorganisms that exhibit resistance to environmental stressors, particularly heavy metals, have the potential to be used in bioremediation strategies. This study aimed to explore and identify microorganisms that are resistant to heavy metals in soil environments as potential candidates for bioremediation. Metagenomic analysis was conducted using microbiome metagenomes obtained from the rhizosphere of soil contaminated with heavy metals and mineral-affected soil. The analysis resulted in the recovery of a total of 175 metagenome-assembled genomes (MAGs), 73 of which were potentially representing novel taxonomic levels beyond the genus level. The constructed ecological network revealed the presence of keystone taxa, including Rhizobiaceae, Xanthobacteraceae, Burkholderiaceae, and Actinomycetia. Among the recovered MAGs, 50 were associated with these keystone taxa. Notably, these MAGs displayed an abundance of genes conferring resistance to heavy metals and other abiotic stresses, particularly those affiliated with the keystone taxa. These genes were found to combat excessive accumulation of zinc/manganese, arsenate/arsenite, chromate, nickel/cobalt, copper, and tellurite. Furthermore, the keystone taxa were found to utilize both organic and inorganic energy sources, such as sulfur, arsenic, and carbon dioxide. Additionally, these keystone taxa exhibited the ability to promote vegetation development in re-vegetated mining areas through phosphorus solubilization and metabolite secretion. In summary, our study highlights the metabolic adaptability and ecological significance of microbial keystone taxa in mineral-affected soils. The MAGs associated with keystone taxa exhibited a markedly higher number of genes related to abiotic stress resistance and plant growth promotion compared to non-keystone taxa MAGs.}, } @article {pmid37547681, year = {2023}, author = {Wang, W and Shen, P and Lu, Z and Mo, F and Liao, Y and Wen, X}, title = {Metagenomics reveals the abundance and accumulation trend of antibiotic resistance gene profile under long-term no tillage in a rainfed agroecosystem.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1238708}, pmid = {37547681}, issn = {1664-302X}, abstract = {Widespread soil resistance can seriously endanger sustainable food production and soil health. Conservation tillage is a promising practice for improving soil structure and health. However, the impact of long-term no-tillage on the presence of antibiotic resistance genes in agricultural soils remains unexplored. Based on the long-term (>11 yr) tillage experimental fields that include both conservation tillage practices [no tillage (ZT)] and conventional tillage practices [plough tillage (PT)], we investigated the accumulation trend of antibiotic resistance genes (ARGs) in farmland soils under long-term no-tillage conditions. We aimed to provide a scientific basis for formulating agricultural production strategies to promote ecological environment safety and human health. In comparison to PT, ZT led to a considerable reduction in the relative abundance of both antibiotic resistance genes and antibiotic target gene families in the soil. Furthermore, the abundance of all ARGs were considerably lower in the ZT soil. The classification of drug resistance showed that ZT substantially decreased the relative abundance of Ethambutol (59.97%), β-lactams (44.87%), Fosfomycin (35.82%), Sulfonamides (34.64%), Polymyxins (33.67%), MLSB (32.78%), Chloramphenicol (28.57%), Multi-drug resistance (26.22%), Efflux pump (23.46%), Aminoglycosides (16.79%), Trimethoprim (13.21%), Isoniazid (11.34%), Fluoroquinolone (6.21%) resistance genes, compared to PT soil. In addition, the abundance of the bacterial phyla Proteobacteria, Actinobacteria, Acidobacteria, and Gemmatimonadetes decreased considerably. The Mantel test indicated that long-term ZT practices substantially increased the abundance of beneficial microbial flora and inhibited the enrichment of ARGs in soil by improving soil microbial diversity, metabolic activity, increasing SOC, TN, and available Zn, and decreasing pH. Overall, long-term no-tillage practices inhibit the accumulation of antibiotic resistance genes in farmland soil, which is a promising agricultural management measure to reduce the accumulation risk of soil ARGs.}, } @article {pmid37547599, year = {2023}, author = {Tozetto-Mendoza, TR and da-Costa, AC and Moron, AF and Leal, É and Lima, SH and Ferreira, NE and Honorato, L and Paião, HGO and Freire, WS and Mendes-Correa, MC and Witkin, SS}, title = {Characterization of Torquetenovirus in amniotic fluid at the time of in utero fetal surgery: correlation with early premature delivery and respiratory distress.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1161091}, pmid = {37547599}, issn = {2296-858X}, abstract = {Torquetenovirus (TTV) is a commensal virus present in many healthy individuals. Although considered to be non-pathogenic, its presence and titer have been shown to be indicative of altered immune status in individuals with chronic infections or following allogeneic transplantations. We evaluated if TTV was present in amniotic fluid (AF) at the time of in utero surgery to correct a fetal neurological defect, and whether its detection was predictive of adverse post-surgical parameters. AF was collected from 27 women by needle aspiration prior to a uterine incision. TTV titer in the AF was measured by isolation of viral DNA followed by gene amplification and analysis. The TTV genomes were further characterized and sequenced by metagenomics. Pregnancy outcome parameters were subsequently obtained by chart review. Three of the AFs (11.1%) were positive for TTV at 3.36, 4.16, and 4.19 log10 copies/mL. Analysis of their genomes revealed DNA sequences similar to previously identified TTV isolates. Mean gestational age at delivery was >2 weeks earlier (32.5 vs. 34.6 weeks) and the prevalence of respiratory distress was greater (100% vs. 20.8%) in the TTV-positive pregnancies. TTV detection in AF prior to intrauterine surgery may indicate elevated post-surgical risk for earlier delivery and newborn respiratory distress.}, } @article {pmid37545858, year = {2023}, author = {Yuan, X and Xie, L and Shi, Z and Zhou, M}, title = {Application of mNGS in the study of pulmonary microbiome in pneumoconiosis complicated with pulmonary infection patients and exploration of potential biomarkers.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1200157}, pmid = {37545858}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *Pneumonia ; *Microbiota ; High-Throughput Nucleotide Sequencing ; Biomarkers ; Lung ; Sensitivity and Specificity ; Metagenomics ; }, abstract = {BACKGROUND: Pneumoconiosis patients have a high prevalence of pulmonary infections, which can complicate diagnosis and treatment. And there is no comprehensive study of the microbiome of patients with pneumoconiosis. The application of metagenomic next-generation sequencing (mNGS) fills the gap to some extent by analyzing the lung microbiota of pneumoconiosis population while achieving accurate diagnosis.

METHODS: We retrospectively analyzed 44 patients with suspected pneumoconiosis complicated with pulmonary infection between Jan 2020 and Nov 2022. Bronchoalveolar lavage fluid (BALF) specimens from 44 patients were collected and tested using the mNGS technology.

RESULTS: Among the lung microbiome of pneumoconiosis patients with complicated pulmonary infection (P group), the most frequently detected bacteria and fungi at the genus level were Streptococcus and Aspergillus, at the species level were Streptococcus pneumoniae and Aspergillus flavus, respectively, and the most frequently detected DNA virus was Human gammaherpesvirus 4. There was no significant difference in α diversity between the P group and the non-pneumoconiosis patients complicated with pulmonary infection group (Non-P group) in pulmonary flora, while P< 0.01 for β diversity analysis, and the differential species between the two groups were Mycobacterium colombiense and Fusobacterium nucleatum. In addition, we monitored a high distribution of Malassezia and Pneumocystis in the P group, while herpes virus was detected in the majority of samples.

CONCLUSIONS: Overall, we not only revealed a comprehensive lung microbiome profile of pneumoconiosis patients, but also compared the differences between their microbiome and that of non-pneumoconiosis complicated with pulmonary infection patients. This provides a good basis for a better understanding of the relationship between pneumoconiosis and microorganisms, and for the search of potential biomarkers.}, } @article {pmid37544996, year = {2023}, author = {Hong, H and Li, T and Ying, Y and An, Q and Liu, H and Liang, K}, title = {Cat-scratch disease manifesting as uveitis and binocular fundus nodular lesions: a case report.}, journal = {BMC ophthalmology}, volume = {23}, number = {1}, pages = {345}, pmid = {37544996}, issn = {1471-2415}, mesh = {Male ; Humans ; *Cat-Scratch Disease/diagnosis/drug therapy ; *Bartonella henselae ; Fundus Oculi ; *Retinitis/diagnosis ; *Chorioretinitis ; }, abstract = {BACKGROUND: Cat-scratch disease typically presents with various ocular manifestations such as uveitis, vitritis, retinitis, retinochoroiditis, and optic neuritis. However, fundus nodular lesions was rarely reported. In our study, we reported a case of Cat-Scratch disease with binocular fundus nodular lesions.

CASE PRESENTATION: An 11-year old male presented with uveitis in the right eye and bilateral fundus nodular lesions after indirect contact with unvaccinated cats. Comprehensive ancillary examinations including wide-angle fundus photography, ultrasonography, fluorescein fundus angiography, optical coherence tomography, and orbital magnetic resonance imaging were performed to elucidate the multidimensional features of the binocular lesions. Metagenomics next-generation sequencing was utilized to confirm the diagnosis of Cat-scratch disease. The patient's condition showed improvement after a 6-month combination treatment regimen involving systemic administration of doxycycline hyclate and methylprednisolone tablets, as well as local application of mydriatic and corticosteroid eye drops.

CONCLUSIONS: We firstly reported a case of Cat-scratch disease presenting simultaneously with uveitis and fundus nodular lesions caused by Bartonella henselae infection in a child. Timely diagnosis and treatment with antibiotics and corticosteroids showed promising outcomes for the prognosis of these ocular disorders.}, } @article {pmid37544676, year = {2023}, author = {Padovan, A and Kennedy, K and Gibb, K}, title = {A microcystin synthesis mcyE/ndaF gene assay enables early detection of microcystin production in a tropical wastewater pond.}, journal = {Harmful algae}, volume = {127}, number = {}, pages = {102476}, doi = {10.1016/j.hal.2023.102476}, pmid = {37544676}, issn = {1878-1470}, mesh = {Microcystins/analysis ; Ponds ; Wastewater ; *Cyanobacteria/metabolism ; *Microcystis/genetics/metabolism ; }, abstract = {Cyanobacteria can dominate the algal community in wastewater ponds, which can lead to the production of cyanotoxins and their release into the environment. We applied traditional and molecular techniques to identify cyanotoxin hazards and high-risk periods in a tropical wastewater treatment system. Potentially toxic cyanobacteria were identified by microscopy and amplicon sequencing over the course of a year. Toxin gene levels were monitored and compared to toxin production to identify likely toxin producing species and high-risk periods. Cyanobacteria were persistent in the effluent year-round, with Planktothrix and Microcystis the most abundant genera; Microcystis could not be resolved beyond genus using amplicon sequencing, but M. flos-aquae was identified as a dominant species by microscopy. Microcystin toxin was detected for the first time in treated effluent at the beginning of the wet season (December 2018), which correlated with an increase in Microcystis amplicon sequence abundance and elevated microcystin toxin gene (mcyE/ndaF) levels. Concomitantly, microscopy data showed an increase in M. flos-aquae but not M. aeruginosa. These data informed a refined sampling campaign in 2019 and results showed a strong correlation between mcyE/ndaF gene abundance, microcystin toxin levels and Microcystis amplicon sequence abundance. Microscopy data showed that in addition to M. flos-aquae, M. aeruginosa was also abundant in February and March 2019, with highest levels coinciding with toxin detection and toxin gene levels. M. aeruginosa was the most abundant Microcystis species detected in selected treated effluent samples by metagenomics analysis, and elevated levels coincided with toxin production. All microcystin genes in the biosynthesis pathway were detected, but microcystin genes from Planktothrix agardhii were not detected. Gene toxin assays were successfully used to predict microcystin production in this wastewater system. Changes in amplicon sequence relative abundance were a useful indicator of changes in the cyanobacterial community. We found that metagenomics was useful not just for identifying the most abundant Microcystis species, but the detection of microcystin biosynthesis genes helped confirm this genus as the most likely toxin producer in this system. We recommend toxin gene testing for the early detection of potential toxin producing cyanobacteria to manage the risk of toxicity and allow the implementation of risk management strategies.}, } @article {pmid37544653, year = {2023}, author = {Zhao, H and Li, Y and Liu, M and Song, X and Liu, B and Ju, X}, title = {Metagenomic and network analyses reveal key players in nitrification in upland agricultural soils.}, journal = {Environmental microbiology}, volume = {25}, number = {11}, pages = {2636-2640}, doi = {10.1111/1462-2920.16467}, pmid = {37544653}, issn = {1462-2920}, mesh = {*Soil/chemistry ; *Nitrification ; Archaea ; Oxidation-Reduction ; Soil Microbiology ; Ammonia ; Nitrogen/chemistry ; }, abstract = {Nitrification, a key step in soil nitrogen cycling, is a biologically mediated process crucial to the ecological environment. However, how nitrifiers drive nitrification under different soil properties and climatic factors at large spatial scales is poorly understood. Here, using metagenomic sequencing and network-based approaches, we identified key nitrifying species of upland agricultural soils in northern China, which spans a wide range of climates and geographic distances. We found that potential nitrification rates (PNRs) varied in different soils and were positively correlated with soil pH (5.42-8.46) and mean annual temperature (MAT) and negatively correlated with the C/N ratio. Network analysis revealed that one module (module 3) was significantly correlated with PNR. In this module, 16 dominant nodes were associated with AOB Nitrosomonas and most nodes were significantly correlated with environmental factors, suggesting that abiotic conditions are important for determining the assembly of these key nitrifiers. Our study advanced the understanding of the key nitrifying populations and their environmental drivers in upland agricultural soil across different soil and climate types.}, } @article {pmid37544570, year = {2023}, author = {Dos Santos, MAM and Pavon, JAR and Dias, LS and Viniski, AE and Souza, CLC and de Oliveira, EC and de Azevedo, VC and da Silva, SP and Cruz, ACR and Medeiros, DBA and Nunes, MRT and Slhessarenko, RD}, title = {Dengue virus serotype 2 genotype III evolution during the 2019 outbreak in Mato Grosso, Midwestern Brazil.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {113}, number = {}, pages = {105487}, doi = {10.1016/j.meegid.2023.105487}, pmid = {37544570}, issn = {1567-7257}, mesh = {Humans ; *Dengue Virus/genetics ; *Dengue/epidemiology ; Serogroup ; Brazil/epidemiology ; Genotype ; Disease Outbreaks ; Phylogeny ; }, abstract = {DENV-2 was the main responsible for a 70% increase in dengue incidence in Brazil during 2019. That year, our metagenomic study by Illumina NextSeq on serum samples from acute febrile patients (n = 92) with suspected arbovirus infection, sampled in 22 cities of the state of Mato Grosso (MT), in the middle west of Brazil, revealed eight complete genomes and two near-complete sequences of DENV-2 genotype III, one Human parvovirus B19 genotype I (5,391 nt) and one Coxsackievirus A6 lineage D (4,514 nt). These DENV-2 sequences share the aminoacidic identities of BR4 lineage on E protein domains I, II and III, and were included in a clade with sequences of the same lineage circulating in the southeast of Brazil in the same year. Nevertheless, 11/34 non-synonymous mutations are unique to three strains inthis study, distributed in the E (n = 6), NS3 (n = 2) and NS5 (n = 3) proteins. Other 14 aa changes on C (n = 1), E (n = 3), NS1 (n = 2), NS2A (n = 1) and NS5 (n = 7) were first reported in a genotype III lineage, having been already reported only in other DENV-2 genotypes. All 10 sequences have mutations in the NS5 protein (14 different aa changes). Nine E protein aa changes found in two sequences, six of which are unique, are in the ectodomain; where the E:M272T change is on the hinge of the E protein at domain II, in a region critical for the anchoring to the host cell receptor. The NS5:G81R mutation, in the methyltransferase domain, was found in one strain of this study. Altogether, these data points to an important evolution of DENV-2 genotype III lineage BR4 during this outbreak in 2019 in MT. Genomic surveillance is essential to detect virus etiology and evolution, possibly related to immune evasion and viral fitness changes leading to future novel outbreaks.}, } @article {pmid37544548, year = {2023}, author = {Kadri, MS and Singhania, RR and Haldar, D and Patel, AK and Bhatia, SK and Saratale, G and Parameswaran, B and Chang, JS}, title = {Advances in Algomics technology: Application in wastewater treatment and biofuel production.}, journal = {Bioresource technology}, volume = {387}, number = {}, pages = {129636}, doi = {10.1016/j.biortech.2023.129636}, pmid = {37544548}, issn = {1873-2976}, mesh = {Wastewater ; Biofuels ; *Microalgae/metabolism ; *Water Purification ; Metagenomics ; Biomass ; }, abstract = {Advanced sustainable bioremediation is gaining importance with rising global pollution. This review examines microalgae's potential for sustainable bioremediation and process enhancement using multi-omics approaches. Recently, microalgae-bacterial consortia have emerged for synergistic nutrient removal, allowing complex metabolite exchanges. Advanced bioremediation requires effective consortium design or pure culture based on the treatment stage and specific roles. The strain potential must be screened using modern omics approaches aligning wastewater composition. The review highlights crucial research gaps in microalgal bioremediation. It discusses multi-omics advantages for understanding microalgal fitness concerning wastewater composition and facilitating the design of microalgal consortia based on bioremediation skills. Metagenomics enables strain identification, thereby monitoring microbial dynamics during the treatment process. Transcriptomics and metabolomics encourage the algal cell response toward nutrients and pollutants in wastewater. Multi-omics role is also summarized for product enhancement to make algal treatment sustainable and fit for sustainable development goals and growing circular bioeconomy scenario.}, } @article {pmid37544546, year = {2023}, author = {Xu, Z and Gao, X and Li, G and Nghiem, LD and Luo, W}, title = {Microbes from mature compost to promote bacterial chemotactic motility via tricarboxylic acid cycle-regulated biochemical metabolisms for enhanced composting performance.}, journal = {Bioresource technology}, volume = {387}, number = {}, pages = {129633}, doi = {10.1016/j.biortech.2023.129633}, pmid = {37544546}, issn = {1873-2976}, mesh = {*Composting ; NAD ; Citric Acid Cycle ; Biodegradation, Environmental ; Oxidation-Reduction ; Soil ; }, abstract = {This study aims to reveal the underlying mechanisms of mature compost addition for improving organic waste composting. Composting experiments and metagenomic analysis were conducted to elucidate the role of mature compost addition to regulate microbial metabolisms and physiological behaviors for composting amelioration. Mature compost with or without inactivation pretreatment was added to the composting of kitchen and garden wastes at 0%, 5%, 10%, 15%, and 20% (by wet weight) for comparison. Results show that mature compost promoted pyruvate metabolism, tricarboxylic acid (TCA) cycle, and oxidative phosphorylation to produce heat and energy to accelerate temperature increase for composting initiation and biological contaminant removal (>78%) for pasteurization. Energy requirement drives bacterial chemotactic motility towards nutrient-rich regions to sustain organic biodegradation. Nevertheless, when NADH formation exceeded NAD[+] regeneration in oxidative phosphorylation, TCA cycle was restrained to limit continuous temperature increase and recover high intracellular NAD[+]/NADH ratio to secure stable oxidation reactions.}, } @article {pmid37544539, year = {2023}, author = {Lin, B and Tan, B and Liu, X and Li, M and Peng, H and Zhang, Q and Chen, J and Shen, H and He, Q}, title = {Elucidating the roles of Cr(VI)-Cu(II) Co-pollution in the stress of aniline degradation stress: Insights into metabolic pathways and functional genes.}, journal = {Bioresource technology}, volume = {387}, number = {}, pages = {129613}, doi = {10.1016/j.biortech.2023.129613}, pmid = {37544539}, issn = {1873-2976}, mesh = {*Metals, Heavy/metabolism ; Chromium/metabolism ; Metabolic Networks and Pathways ; Nitrogen ; }, abstract = {In order to examine the impact of Cu(II)-Cr(VI) co-pollution in printing and dyeing wastewater on the aniline biodegradation system (ABS), loading experiments were conducted on ABS at varying concentrations of Cu(II)-Cr(VI). The synergistic stress imposed by Cu(II)-Cr(VI) accelerated the deterioration of the systems, with only the C2-3 (2 mg/L Cr(VI)-3 mg/L Cu(II)) sustaining stable operation for 42 days. However, its nitrogen removal performance remained significantly impaired, resulting in a total nitrogen (TN) removal rate below 40%. High-throughput sequencing analysis revealed a stronger correlation between Cr(VI) and microbial diversity compared to Cu(II). Metagenomic sequencing results demonstrated that Cu(II) emerged as the dominant factor influencing the distribution of dominant bacteria in C2-3, as well as its contribution to contaminant degradation. The complex co-pollution systems hindered aniline degradation and nitrogen metabolism through the combined bio-toxicity of heavy metals and aniline, thereby disrupting the transport chain within the systems matrix.}, } @article {pmid37544477, year = {2023}, author = {Li, T and Li, J and Wang, J and Xue, KS and Su, X and Qu, H and Duan, X and Jiang, Y}, title = {The occurrence and management of fumonisin contamination across the food production and supply chains.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2023.08.001}, pmid = {37544477}, issn = {2090-1224}, abstract = {BACKGROUND: Fumonisins (FUMs) are among the most common mycotoxins in plant-derived food products. FUMs contamination has considerably impacted human and animal health, while causing significant economic losses. Hence, management of FUMs contamination in food production and supply chains is needed. The toxicities of FUMs have been widely investigated. FUMs management has been reported and several available strategies have been developed successfully to mitigate FUMs contamination present in foods. However, currently available management of FUMs contamination from different phases of food chains and the mechanisms of some major strategies are not comprehensively summarized.

AIM OF REVIEW: This review comprehensively characterize the occurrence, impacts, and management of FUMs contamination across food production and supply chains. Pre- and post-harvest strategies to prevent FUMs contamination also are reviewed, with an emphasis on the potential applications and the mechanisms of major mitigation strategies. The presence of modified FUMs products and their potential toxic effects are also considered. Importantly, the potential application of biotechnological approaches and emerging technologies are enunciated.

Currently available pre- and post-harvest management of FUMs contamination primarily involves prevention and decontamination. Prevention strategies are mainly based on limiting fungal growth and FUMs biosynthesis. Decontamination strategies are implemented through alkalization, hydrolysis, thermal or chemical transformation, and enzymatic or chemical degradation of FUMs. Concerns have been raised about toxicities of modified FUMs derivatives, which presents challenges for reducing FUMs contamination in foods with conventional methodologies. Integrated prevention and decontamination protocols are recommended to control FUMs contamination across entire value chains in developed countries. In developing countries, several other approaches, including cultivating, introducing Bt maize, simple sorting/cleaning, and dehulling, are suggested. Future studies should focus on biotechnological approaches, emerging technologies, and metagenomic/genomic identification of new degradation enzymes that could allow better opportunities to manage FUMs contamination in the entire food system.}, } @article {pmid37544442, year = {2023}, author = {Lepper, HC and Perry, MR and Wee, BA and Wills, D and Nielsen, H and Otani, S and Simon, M and Aarestrup, FM and Woolhouse, MEJ and van Bunnik, BAD}, title = {Distinctive hospital and community resistomes in Scottish urban wastewater: Metagenomics of a paired wastewater sampling design.}, journal = {The Science of the total environment}, volume = {902}, number = {}, pages = {165978}, doi = {10.1016/j.scitotenv.2023.165978}, pmid = {37544442}, issn = {1879-1026}, mesh = {Humans ; *Wastewater ; *Sewage/microbiology ; Bacteria/genetics ; Genes, Bacterial ; Hospitals ; Anti-Bacterial Agents ; Metagenomics ; }, abstract = {The wastewater microbiome contains a multitude of resistant bacteria of human origin, presenting an opportunity for surveillance of resistance in the general population. However, wastewater microbial communities are also influenced by clinical sources, such as hospitals. Identifying signatures of the community and hospital resistome in wastewater is needed for interpretation and risk analysis. In this study, we compare the resistome and microbiome of hospital, community, and mixed municipal wastewater to investigate how and why the composition of these different sites differ. We conducted shotgun metagenomic analysis on wastewater samples from eight wastewater treatment plants (WWTPs), four hospitals, and four community sites in Scotland, using a paired sampling design. Cluster analysis and source attribution random forest models demonstrated that the hospital resistome was distinct from community and WWTP resistomes. Hospital wastewater had a higher abundance and diversity of resistance genes, in keeping with evidence that hospitals act as a reservoir and enricher of resistance. However, this distinctive 'hospital' signature appeared to be weak in the resistome of downstream WWTPs, likely due to dilution. We conclude that hospital and community wastewater resistomes differ, with the hospital wastewater representing a reservoir of patient- and hospital environment-associated bacteria. However, this 'hospital' signature is transient and does not overwhelm the community signature in the resistome of the downstream WWTP influent.}, } @article {pmid37544439, year = {2023}, author = {Shen, W and Zhang, H and Li, X and Qi, D and Liu, R and Kang, G and Liu, J and Li, N and Zhang, S and Hu, S}, title = {Pathogens and antibiotic resistance genes during the landfill leachate treatment process: Occurrence, fate, and impact on groundwater.}, journal = {The Science of the total environment}, volume = {903}, number = {}, pages = {165925}, doi = {10.1016/j.scitotenv.2023.165925}, pmid = {37544439}, issn = {1879-1026}, abstract = {Landfill leachate is an essential source of pathogens and antibiotic resistance genes (ARGs) in the environment. However, information on the removal behavior of pathogens and ARGs during the leachate treatment and the impact on surrounding groundwater is limited. In this study, we investigated the effects of leachate treatment on the removal of pathogens and ARGs with metagenomic sequencing, as well as the impact of landfill effluent on groundwater. It is shown that the leachate treatment could not completely remove pathogens and ARGs. Twenty-nine additional pathogens and twenty-nine ARGs were newly identified in the landfill effluent. The relative abundance of pathogens and multiple antibiotic resistance genes decreased after ultrafiltration but relative abundance increased after reverse osmosis. In addition, the relative abundances of Acinetobacter baumannii, Erwinia amylovora, Escherichia coli, Fusarium graminearum, Klebsiella pneumoniae, and Magnaporthe oryzae, as well as mdtH, VanZ, and blaOXA-53 increased significantly in the landfill effluent compared to the untreated leachate. The relative abundance of some mobile genetic elements (tniA, tniB, tnpA, istA, IS91) in leachate also increased after ultrafiltration and reverse osmosis. The size of pathogens, the size and properties of ARGs and mobile genetic elements, and the materials of ultrafiltration and reverse osmosis membranes may affect the removal effect of pathogens, ARGs and mobile genetic elements in leachate treatment process. Interestingly, the pathogens and ARGs in landfill effluent were transferred to groundwater according to SourceTracker. The ARGs, mobile genetic elements, and pathogens that are difficult to remove in the leachate treatment process, provide a reference for optimizing the leachate treatment process and improving the control of pathogens and ARGs. Furthermore, this study clarifies the effect of landfill leachate sources of pathogens and ARGs in groundwater.}, } @article {pmid37544313, year = {2023}, author = {Gould, CV and Free, RJ and Bhatnagar, J and Soto, RA and Royer, TL and Maley, WR and Moss, S and Berk, MA and Craig-Shapiro, R and Kodiyanplakkal, RPL and Westblade, LF and Muthukumar, T and Puius, YA and Raina, A and Hadi, A and Gyure, KA and Trief, D and Pereira, M and Kuehnert, MJ and Ballen, V and Kessler, DA and Dailey, K and Omura, C and Doan, T and Miller, S and Wilson, MR and Lehman, JA and Ritter, JM and Lee, E and Silva-Flannery, L and Reagan-Steiner, S and Velez, JO and Laven, JJ and Fitzpatrick, KA and Panella, A and Davis, EH and Hughes, HR and Brault, AC and St George, K and Dean, AB and Ackelsberg, J and Basavaraju, SV and Chiu, CY and Staples, JE and , }, title = {Transmission of yellow fever vaccine virus through blood transfusion and organ transplantation in the USA in 2021: report of an investigation.}, journal = {The Lancet. Microbe}, volume = {4}, number = {9}, pages = {e711-e721}, doi = {10.1016/S2666-5247(23)00170-2}, pmid = {37544313}, issn = {2666-5247}, mesh = {Humans ; Blood Transfusion ; *Encephalitis/chemically induced ; *Organ Transplantation/adverse effects ; United States/epidemiology ; *Yellow Fever Vaccine ; Yellow fever virus/genetics ; }, abstract = {BACKGROUND: In 2021, four patients who had received solid organ transplants in the USA developed encephalitis beginning 2-6 weeks after transplantation from a common organ donor. We describe an investigation into the cause of encephalitis in these patients.

METHODS: From Nov 7, 2021, to Feb 24, 2022, we conducted a public health investigation involving 15 agencies and medical centres in the USA. We tested various specimens (blood, cerebrospinal fluid, intraocular fluid, serum, and tissues) from the organ donor and recipients by serology, RT-PCR, immunohistochemistry, metagenomic next-generation sequencing, and host gene expression, and conducted a traceback of blood transfusions received by the organ donor.

FINDINGS: We identified one read from yellow fever virus in cerebrospinal fluid from the recipient of a kidney using metagenomic next-generation sequencing. Recent infection with yellow fever virus was confirmed in all four organ recipients by identification of yellow fever virus RNA consistent with the 17D vaccine strain in brain tissue from one recipient and seroconversion after transplantation in three recipients. Two patients recovered and two patients had no neurological recovery and died. 3 days before organ procurement, the organ donor received a blood transfusion from a donor who had received a yellow fever vaccine 6 days before blood donation.

INTERPRETATION: This investigation substantiates the use of metagenomic next-generation sequencing for the broad-based detection of rare or unexpected pathogens. Health-care workers providing vaccinations should inform patients of the need to defer blood donation for at least 2 weeks after receiving a yellow fever vaccine. Despite mitigation strategies and safety interventions, a low risk of transfusion-transmitted infections remains.

FUNDING: US Centers for Disease Control and Prevention (CDC), the Biomedical Advanced Research and Development Authority, and the CDC Epidemiology and Laboratory Capacity Cooperative Agreement for Infectious Diseases.}, } @article {pmid37544234, year = {2023}, author = {Zhu, L and Huang, C and Li, W and Wu, W and Tang, Z and Tian, Y and Xi, B}, title = {Ammonia assimilation is key for the preservation of nitrogen during industrial-scale composting of chicken manure.}, journal = {Waste management (New York, N.Y.)}, volume = {170}, number = {}, pages = {50-61}, doi = {10.1016/j.wasman.2023.07.028}, pmid = {37544234}, issn = {1879-2456}, mesh = {Animals ; *Ammonia ; Nitrogen ; Chickens/metabolism ; Manure ; *Composting ; Soil ; Bacteria/metabolism ; }, abstract = {Nitrogen loss from compost is a serious concern, causing severe environmental pollution. The NH4[+]-N content reflects the release of NH3. However, the nitrogen conversion pathway that has the greatest impact on NH4[+]-N content is still unclear. This study attempted to explore the key pathways, core functional microorganisms, and mechanisms involved in the transformation of ammonia nitrogen during composting. KEGG (Kyoto Encyclopedia of Genes and Genomes) metabolic pathways revealed that ammonia assimilation was dominated by the glutamate dehydrogenase (GDH) pathway (53.4%), which is crucial for nitrogen preservation. The combined analysis of KEGG, NR species annotation, and co-occurrence network identified 20 easy-to-regulate obligate core nitrogen-transforming functional microorganisms, including 18 ammonia-assimilating bacteria. Furthermore, the effects of environmental parameters on the obligate core functional microorganisms were investigated. The present study results provided a theoretical basis for the utilization of ten ammonia-assimilating bacteria, such as Paenibacillus, Erysipelatoclostridium, and Defluviimonas to improve the quality of compost.}, } @article {pmid37543720, year = {2023}, author = {Hikida, H and Okazaki, Y and Zhang, R and Nguyen, TT and Ogata, H}, title = {A rapid genome-wide analysis of isolated giant viruses using MinION sequencing.}, journal = {Environmental microbiology}, volume = {25}, number = {11}, pages = {2621-2635}, doi = {10.1111/1462-2920.16476}, pmid = {37543720}, issn = {1462-2920}, mesh = {*Giant Viruses/genetics ; Genomics ; Sequence Analysis, DNA ; Metagenome ; High-Throughput Nucleotide Sequencing ; }, abstract = {Following the discovery of Acanthamoeba polyphaga mimivirus, diverse giant viruses have been isolated. However, only a small fraction of these isolates have been completely sequenced, limiting our understanding of the genomic diversity of giant viruses. MinION is a portable and low-cost long-read sequencer that can be readily used in a laboratory. Although MinION provides highly error-prone reads that require correction through additional short-read sequencing, recent studies assembled high-quality microbial genomes only using MinION sequencing. Here, we evaluated the accuracy of MinION-only genome assemblies for giant viruses by re-sequencing a prototype marseillevirus. Assembled genomes presented over 99.98% identity to the reference genome with a few gaps, demonstrating a high accuracy of the MinION-only assembly. As a proof of concept, we de novo assembled five newly isolated viruses. Average nucleotide identities to their closest known relatives suggest that the isolates represent new species of marseillevirus, pithovirus and mimivirus. The assembly of subsampled reads demonstrated that their taxonomy and genomic composition could be analysed at the 50× sequencing coverage. We also identified a pithovirus gene whose homologues were detected only in metagenome-derived relatives. Collectively, we propose that MinION-only assembly is an effective approach to rapidly perform a genome-wide analysis of isolated giant viruses.}, } @article {pmid37543591, year = {2023}, author = {Inwood, SN and Skelly, J and Guhlin, JG and Harrop, TWR and Goldson, SL and Dearden, PK}, title = {Chromosome-level genome assemblies of two parasitoid biocontrol wasps reveal the parthenogenesis mechanism and an associated novel virus.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {440}, pmid = {37543591}, issn = {1471-2164}, mesh = {Animals ; *Wasps/genetics ; *Weevils/genetics ; Reproduction ; Parthenogenesis ; Chromosomes ; }, abstract = {BACKGROUND: Biocontrol is a key technology for the control of pest species. Microctonus parasitoid wasps (Hymenoptera: Braconidae) have been released in Aotearoa New Zealand as biocontrol agents, targeting three different pest weevil species. Despite their value as biocontrol agents, no genome assemblies are currently available for these Microctonus wasps, limiting investigations into key biological differences between the different species and strains.

METHODS AND FINDINGS: Here we present high-quality genomes for Microctonus hyperodae and Microctonus aethiopoides, assembled with short read sequencing and Hi-C scaffolding. These assemblies have total lengths of 106.7 Mb for M. hyperodae and 129.2 Mb for M. aethiopoides, with scaffold N50 values of 9 Mb and 23 Mb respectively. With these assemblies we investigated differences in reproductive mechanisms, and association with viruses between Microctonus wasps. Meiosis-specific genes are conserved in asexual Microctonus, with in-situ hybridisation validating expression of one of these genes in the ovaries of asexual Microctonus aethiopoides. This implies asexual reproduction in these Microctonus wasps involves meiosis, with the potential for sexual reproduction maintained. Investigation of viral gene content revealed candidate genes that may be involved in virus-like particle production in M. aethiopoides, as well as a novel virus infecting M. hyperodae, for which a complete genome was assembled.

CONCLUSION AND SIGNIFICANCE: These are the first published genomes for Microctonus wasps which have been deployed as biocontrol agents, in Aotearoa New Zealand. These assemblies will be valuable resources for continued investigation and monitoring of these biocontrol systems. Understanding the biology underpinning Microctonus biocontrol is crucial if we are to maintain its efficacy, or in the case of M. hyperodae to understand what may have influenced the significant decline of biocontrol efficacy. The potential for sexual reproduction in asexual Microctonus is significant given that empirical modelling suggests this asexual reproduction is likely to have contributed to biocontrol decline. Furthermore the identification of a novel virus in M. hyperodae highlights a previously unknown aspect of this biocontrol system, which may contribute to premature mortality of the host pest. These findings have potential to be exploited in future in attempt to increase the effectiveness of M. hyperodae biocontrol.}, } @article {pmid37543327, year = {2023}, author = {Bai, Y and Hu, H and Lee, PH and Zhussupbekova, A and Shvets, IV and Du, B and Terada, A and Zhan, X}, title = {Nitrate removal in iron sulfide-driven autotrophic denitrification biofilter: Biochemical and chemical transformation pathways and its underlying microbial mechanism.}, journal = {The Science of the total environment}, volume = {901}, number = {}, pages = {165908}, doi = {10.1016/j.scitotenv.2023.165908}, pmid = {37543327}, issn = {1879-1026}, abstract = {Iron sulfides-based autotrophic denitrification (IAD) is effective for treating nitrate-contaminated wastewater. However, the complex nitrate transformation pathways coupled with sulfur and iron cycles in IADs are still unclear. In this study, two columns (abiotic vs biotic) with iron sulfides (FeS) as the packing materials were constructed and operated continuously. In the abiotic column, FeS chemically reduced nitrate to ammonium under the ambient condition; this chemical reduction reaction pathway was spontaneous and has been overlooked in IAD reactors. In the biotic column (IAD biofilter), the complex nitrogen-transformation network was composed of chemical reduction, autotrophic denitrification, dissimilatory nitrate reduction to ammonium (DNRA) and sulfate reducing ammonium oxidation (Sulfammox). Metagenomic analysis and XPS characterization of the IAD biofilter further validated the roles of functional microbial communities (e.g., Acidovorax, Diaphorobacter, Desulfuromonas) in nitrate reduction process coupled with iron and sulfur cycles. This study gives an in-depth insight into the nitrogen transformations in IAD system and provides fundamental evidence about the underlying microbial mechanism for its further application in biological nitrogen removal.}, } @article {pmid37543322, year = {2023}, author = {Li, X and Xie, J and Ding, C and Du, H and Gao, S and Ma, W and Liang, F and Zhang, H and Wang, A}, title = {Occurrence, fate and potential health risks of antibiotic resistomes in a constructed wetlands-reservoir ecosystem for drinking water source improvement.}, journal = {The Science of the total environment}, volume = {901}, number = {}, pages = {166055}, doi = {10.1016/j.scitotenv.2023.166055}, pmid = {37543322}, issn = {1879-1026}, abstract = {The development of effective and feasible engineering technologies to control the transmission of antibiotic resistance genes (ARGs) and pathogenic antibiotic-resistant bacteria (PARB) form drinking water sources is urgently needed for ensuring drinking water safety. In this study, metagenomic analysis was applied to systematically explore the full profiles, removal, and potential health risks of antibiotic resistomes in a large constructed wetlands-reservoir ecosystem (CWs-R) for drinking water source improvement. A total of 343 ARG subtypes belonging to 18 ARG types were identified from water and sediment samples in the CWs-R ecosystem, with an average abundance of 0.339 copies/cell, and bacitracin and multidrug resistance genes were the predominant ARG types in the water and sediment, respectively. The CWs-R ecosystem showed an excellent removal efficiency of ARGs and mobile genetic elements (MGEs) in water, with the total removal rate reaching 64.82 % and 77.09 %, respectively, among which the emergent plant zone and ecological storage unit played major roles. The metagenomic assembly tracked many mobile ARGs and opportunistic pathogens in the CWs-R ecosystem and identified 19 contigs as ARG-carrying pathogens, including Staphylococcus aureus, Salmonella enterica, Escherichia coli, and Klebsiella pneumonia. Overall, the CWs-R ecosystem has an important role in reducing the potential public health risks posed by antibiotic resistomes in drinking water sources but still cannot fully eliminate them. Therefore, we further classified water and sediment samples in the CWs-R ecosystem and identified potential ARGs and PARB indicators based on the metagenomic analysis results by considering the potential for horizontal transfer of ARGs to opportunistic pathogens. Taken together, this work demonstrates the CWs-R ecosystem as an economical and feasible engineering technology to reduce the dissemination of antibiotic resistomes in the drinking water source, provides useful information for monitoring and controlling antibiotic resistance in similar water sources, and ensures biosafety of drinking water.}, } @article {pmid37543315, year = {2023}, author = {Gao, M and Zhang, Q and Lei, C and Lu, T and Qian, H}, title = {Atmospheric antibiotic resistome driven by air pollutants.}, journal = {The Science of the total environment}, volume = {902}, number = {}, pages = {165942}, doi = {10.1016/j.scitotenv.2023.165942}, pmid = {37543315}, issn = {1879-1026}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Air Pollutants ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; }, abstract = {The atmosphere is an important reservoir and habitat for antibiotic resistance genes (ARGs) and is a main pathway to cause potential health risks through inhalation and ingestion. However, the distribution characteristics of ARGs in the atmosphere and whether they were driven by atmospheric pollutants remain unclear. We annotated 392 public air metagenomic data worldwide and identified 1863 ARGs, mainly conferring to tetracycline, MLS, and multidrug resistance. We quantified these ARG's risk to human health and identified their principal pathogenic hosts, Burkholderia and Staphylococcus. Additionally, we found that bacteria in particulate contaminated air carry more ARGs than in chemically polluted air. This study revealed the influence of typical pollutants in the global atmosphere on the dissemination and risk of ARGs, providing a theoretical basis for the prevention and mitigation of the global risks associated with ARGs.}, } @article {pmid37543247, year = {2023}, author = {Mengelkoch, S and Miryam Schüssler-Fiorenza Rose, S and Lautman, Z and Alley, JC and Roos, LG and Ehlert, B and Moriarity, DP and Lancaster, S and Snyder, MP and Slavich, GM}, title = {Multi-omics approaches in psychoneuroimmunology and health research: Conceptual considerations and methodological recommendations.}, journal = {Brain, behavior, and immunity}, volume = {114}, number = {}, pages = {475-487}, doi = {10.1016/j.bbi.2023.07.022}, pmid = {37543247}, issn = {1090-2139}, support = {F32 MH130149/MH/NIMH NIH HHS/United States ; K08 ES028825/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Psychoneuroimmunology ; *Multiomics ; Metabolome ; Immune System ; Proteome ; }, abstract = {The field of psychoneuroimmunology (PNI) has grown substantially in both relevance and prominence over the past 40 years. Notwithstanding its impressive trajectory, a majority of PNI studies are still based on a relatively small number of analytes. To advance this work, we suggest that PNI, and health research in general, can benefit greatly from adopting a multi-omics approach, which involves integrating data across multiple biological levels (e.g., the genome, proteome, transcriptome, metabolome, lipidome, and microbiome/metagenome) to more comprehensively profile biological functions and relate these profiles to clinical and behavioral outcomes. To assist investigators in this endeavor, we provide an overview of multi-omics research, highlight recent landmark multi-omics studies investigating human health and disease risk, and discuss how multi-omics can be applied to better elucidate links between psychological, nervous system, and immune system activity. In doing so, we describe how to design high-quality multi-omics studies, decide which biological samples (e.g., blood, stool, urine, saliva, solid tissue) are most relevant, incorporate behavioral and wearable sensing data into multi-omics research, and understand key data quality, integration, analysis, and interpretation issues. PNI researchers are addressing some of the most interesting and important questions at the intersection of psychology, neuroscience, and immunology. Applying a multi-omics approach to this work will greatly expand the horizon of what is possible in PNI and has the potential to revolutionize our understanding of mind-body medicine.}, } @article {pmid37542576, year = {2023}, author = {Hong, H and Yang, SM and Kim, E and Kim, HJ and Park, SH}, title = {Comprehensive metagenomic analysis of stress-resistant and -sensitive Listeria monocytogenes.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {19}, pages = {6047-6056}, pmid = {37542576}, issn = {1432-0614}, support = {E0210702-01//Korea Food Research Institute/ ; }, mesh = {*Listeria monocytogenes/genetics ; Food Microbiology ; Virulence/genetics ; Virulence Factors/genetics ; Whole Genome Sequencing ; }, abstract = {Listeria monocytogenes is a pathogenic bacterium which can live in adverse environments (low pH, high salinity, and low temperature). Even though there are various whole genome sequencing (WGS) data on L. monocytogenes, investigations on genetic differences between stress-resistant and -sensitive L. monocytogenes grown under stress environments have been not fully examined. This study aims to investigate and compare genetic characteristics between stress-resistant and -sensitive L. monocytogenes using whole genome sequencing (WGS). A total of 47 L. monocytogenes strains (43 stress-resistant and 4 stress-sensitive) were selected based on the stress-resistance tests under pH 3, 5% salt concentration, and 1 °C. The sequencing library for WGS was prepared and sequenced using an Illumina MiSeq. Genetic characteristics of two different L. monocytogenes groups were examined to analyze the pangenome, functionality, virulence, antibiotic resistance, core, and unique genes. The functionality of unique genes in the stress-resistant L. monocytogenes was distinct compared to the stress-sensitive L. monocytogenes, such as carbohydrate and nucleotide transport and metabolism. The lisR virulence gene was detected more in the stress-resistant L. monocytogenes than in the stress-sensitive group. Five stress-resistant L. monocytogenes strains possessed tet(M) antibiotic resistance gene. This is the first study suggesting that deep genomic characteristics of L. monocytogenes may have different resistance level under stress conditions. This new insight will aid in understanding the genetic relationship between stress-resistant and -sensitive L. monocytogenes strains isolated from diverse resources. KEY POINTS: • Whole genomes of L. monocytogenes isolated from three different sources were analyzed. • Differences in two L. monocytogenes groups were identified in functionality, virulence, and antibiotic resistance genes. • This study first examines the association between resistances and whole genomes of stress-resistant and -sensitive L. monocytogenes.}, } @article {pmid37542330, year = {2023}, author = {Shahin, K and Soleimani-Delfan, A and He, Z and Sansonetti, P and Collard, JM}, title = {Metagenomics revealed a correlation of gut phageome with autism spectrum disorder.}, journal = {Gut pathogens}, volume = {15}, number = {1}, pages = {39}, pmid = {37542330}, issn = {1757-4749}, support = {#2019SHZDZX02//Shanghai Municipal Science and Technology Major Project/ ; }, abstract = {The human gut bacteriome is believed to have pivotal influences on human health and disease while the particular roles associated with the gut phageome have not been fully characterized yet with few exceptions. It is argued that gut microbiota can have a potential role in autism spectrum disorders (ASD). The public microbiota database of ASD and typically developing (TD) Chinese individuals were analyzed for phage protein-coding units (pPCU) to find any link between the phageome and ASD. The gut phageome of ASD individuals showed a wider diversity and higher abundance compared to TD individuals. The ASD phageome was associated with a significant expansion of Caudoviricetes bacteriophages. Phages infecting Bacteroidaceae and prophages encoded within Faecalibacterium were more frequent in ASD than in TD individuals. The expansion and diversification of ASD phageome can influence the bacterial homeostasis by imposing pressure on the bacterial communities. In conclusion, the differences of phages community in in ASD and TD can be used as potential diagnosis biomarkers of ASD. Further investigations are needed to verify the role of gut phage communities in the pathogenesis of ASD.}, } @article {pmid37542071, year = {2023}, author = {Oguzie, JU and Petros, BA and Oluniyi, PE and Mehta, SB and Eromon, PE and Nair, P and Adewale-Fasoro, O and Ifoga, PD and Odia, I and Pastusiak, A and Gbemisola, OS and Aiyepada, JO and Uyigue, EA and Edamhande, AP and Blessing, O and Airende, M and Tomkins-Tinch, C and Qu, J and Stenson, L and Schaffner, SF and Oyejide, N and Ajayi, NA and Ojide, K and Ogah, O and Abejegah, C and Adedosu, N and Ayodeji, O and Liasu, AA and Okogbenin, S and Okokhere, PO and Park, DJ and Folarin, OA and Komolafe, I and Ihekweazu, C and Frost, SDW and Jackson, EK and Siddle, KJ and Sabeti, PC and Happi, CT}, title = {Metagenomic surveillance uncovers diverse and novel viral taxa in febrile patients from Nigeria.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4693}, pmid = {37542071}, issn = {2041-1723}, support = {U01 HG007480/HG/NHGRI NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; T32 GM007753/GM/NIGMS NIH HHS/United States ; T32 GM144273/GM/NIGMS NIH HHS/United States ; U01 AI151812/AI/NIAID NIH HHS/United States ; U54 HG007480/HG/NHGRI NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Nigeria/epidemiology ; Metagenomics ; *Lassa Fever/diagnosis/epidemiology ; Lassa virus/genetics ; *Viruses/genetics ; }, abstract = {Effective infectious disease surveillance in high-risk regions is critical for clinical care and pandemic preemption; however, few clinical diagnostics are available for the wide range of potential human pathogens. Here, we conduct unbiased metagenomic sequencing of 593 samples from febrile Nigerian patients collected in three settings: i) population-level surveillance of individuals presenting with symptoms consistent with Lassa Fever (LF); ii) real-time investigations of outbreaks with suspected infectious etiologies; and iii) undiagnosed clinically challenging cases. We identify 13 distinct viruses, including the second and third documented cases of human blood-associated dicistrovirus, and a highly divergent, unclassified dicistrovirus that we name human blood-associated dicistrovirus 2. We show that pegivirus C is a common co-infection in individuals with LF and is associated with lower Lassa viral loads and favorable outcomes. We help uncover the causes of three outbreaks as yellow fever virus, monkeypox virus, and a noninfectious cause, the latter ultimately determined to be pesticide poisoning. We demonstrate that a local, Nigerian-driven metagenomics response to complex public health scenarios generates accurate, real-time differential diagnoses, yielding insights that inform policy.}, } @article {pmid37541984, year = {2023}, author = {Shen, Z and Wang, Y and Bao, A and Yang, J and Sun, X and Cai, Y and Wan, L and Huang, C and Xu, X and Niu, J and Xia, X and Shen, C and Wei, Y and Qiu, H and Zhou, K and Zhang, M and Tong, Y and Song, X}, title = {Metagenomic Next-Generation Sequencing for Pathogens in Bronchoalveolar Lavage Fluid Improves the Survival of Patients with Pulmonary Complications After Allogeneic Hematopoietic Stem Cell Transplantation.}, journal = {Infectious diseases and therapy}, volume = {12}, number = {8}, pages = {2103-2115}, pmid = {37541984}, issn = {2193-8229}, support = {SHDC2020CR1012B//Shanghai Shen Kang Hospital Development Center/ ; 19411970000//Shanghai Science and Technology Commission Western Medicine Guidance Project/ ; CTCCR-2019D02//Clinical Research Special Clinical Research Innovation Plan of Shanghai General Hospital/ ; CTCCR-2019B03//Clinical Research Special Clinical Research Innovation Plan of Shanghai General Hospital/ ; }, abstract = {INTRODUCTION: Unbiased metagenomic next-generation sequencing (mNGS) has been used for infection diagnosis. In this study, we explored the clinical diagnosis value of mNGS for pulmonary complications after allogeneic hematopoietic stem cell transplantation (allo-HSCT).

METHODS: From August 2019 to June 2021, a prospective study was performed to comparatively analyze the pathogenic results of mNGS and conventional tests for bronchoalveolar lavage fluid (BALF) from 134 cases involving 101 patients with pulmonary complications after allo-HSCT.

RESULTS: More pathogens were identified by mNGS than with conventional tests (226 vs 120). For bacteria, the diagnostic sensitivity (P = 0.144) and specificity (P = 0.687) were similar between the two methods. For fungus except Pneumocystis jirovecii (PJ), conventional tests had a significantly higher sensitivity (P = 0.013) with a similarly high specificity (P = 0.109). The sensitivities for bacteria and fungi could be increased with the combination of the two methods. As for PJ, both the sensitivity (100%) and specificity (99.12%) of mNGS were very high. For viruses, the sensitivity of mNGS was significantly higher (P = 0.021) and the negative predictive value (NPV) was 95.74% (84.27-99.26%). Pulmonary infection complications accounted for 90.30% and bacterium was the most common pathogen whether in single infection (63.43%) or mixed infection (81.08%). The 6-month overall survival (OS) of 88.89% in the early group (mNGS ≤ 7 days) was significantly higher than that of 65.52% (HR 0.287, 95% CI 0.101-0.819, P = 0.006) in the late group (mNGS > 7 days).

CONCLUSIONS: mNGS for BALF could facilitate accurate and fast diagnosis for pulmonary complications. Early mNGS could improve the prognosis of patients with pulmonary complications after allo-HSCT.

TRIAL REGISTRATION: ClinicalTrials.gov identifier, NCT04051372.}, } @article {pmid37541958, year = {2023}, author = {Patil, PK and Nagaraju, VT and Baskaran, V and Avunje, S and Rameshbabu, R and Ghate, SD and Solanki, HG}, title = {Development of microbial enrichments for simultaneous removal of sulfur and nitrogenous metabolites in saline water aquaculture.}, journal = {Journal of applied microbiology}, volume = {134}, number = {8}, pages = {}, doi = {10.1093/jambio/lxad173}, pmid = {37541958}, issn = {1365-2672}, abstract = {AIM: The aim of the study was to develop microbial enrichments from the nitrifying microbial consortia and the environment for simultaneous removal of ammonia, nitrate, and sulfide in aquaculture systems at varied salinities.

METHODS AND RESULTS: Sulfur and nitrogen metabolites are the major factors affecting the farmed aquatic animal species and deteriorate the receiving environments causing ecological damage. The present study reports the development of microbial enrichments from the nitrifying microbial consortia and the environment. The enrichments used thiosulfate or thiocyanate as an energy source and simultaneously removed sulfur, ammonia, and nitrite in spiked medium (125 mg/l ammonia; 145 mg/l nitrite). Further, the microbes in the enrichments could grow up to 30 g/l salinity. Metagenomic studies revealed limited microbial diversity suggesting the enrichment of highly specialized taxa, and co-occurrence network analysis showed the formation of three micro-niches with multiple interactions at different taxonomic levels.

CONCLUSIONS: The ability of the enrichments to grow in both organic and inorganic medium and simultaneous removal of sulfide, ammonia, and nitrite under varied salinities suggests their potential application in sulfur, nitrogen, and organic matter-rich aquaculture pond environments and other industrial effluents.}, } @article {pmid37541957, year = {2023}, author = {Vineis, JH and Bulseco, AN and Bowen, JL}, title = {Microbial chemolithoautotrophs are abundant in salt marsh sediment following long-term experimental nitrate enrichment.}, journal = {FEMS microbiology letters}, volume = {370}, number = {}, pages = {}, doi = {10.1093/femsle/fnad082}, pmid = {37541957}, issn = {1574-6968}, mesh = {*Wetlands ; *Nitrates/metabolism ; Geologic Sediments ; Phylogeny ; Sulfur/metabolism ; Carbon/metabolism ; Denitrification ; Nitrogen/metabolism ; }, abstract = {Long-term anthropogenic nitrate (NO3-) enrichment is a serious threat to many coastal systems. Nitrate reduction coupled with the oxidation of reduced forms of sulfur is conducted by chemolithoautotrophic microbial populations in a process that decreases nitrogen (N) pollution. However, little is known about the diversity and distribution of microbes capable of carbon fixation within salt marsh sediment and how they respond to long-term NO3- loading. We used genome-resolved metagenomics to characterize the distribution, phylogenetic relationships, and adaptations important to microbial communities within NO3--enriched sediment. We found NO3- reducing sulfur oxidizers became dominant members of the microbial community throughout the top 25 cm of the sediment following long-term NO3- enrichment. We also found that most of the chemolithoautotrophic genomes recovered contained striking metabolic versatility, including the potential for complete denitrification and evidence of mixotrophy. Phylogenetic reconstruction indicated that similar carbon fixation strategies and metabolic versatility can be found in several phylogenetic groups, but the genomes recovered here represent novel organisms. Our results suggest that the role of chemolithoautotrophy within NO3--enriched salt marsh sediments may be quantitatively more important for retaining carbon and filtering NO3- than previously indicated and further inquiry is needed to explicitly measure their contribution to carbon turnover and removal of N pollution.}, } @article {pmid37541802, year = {2023}, author = {Pfisterer, N and Ammer-Herrmenau, C and Antweiler, K and Küffer, S and Ellenrieder, V and Neesse, A}, title = {Dynamics of intestinal and intratumoral microbiome signatures in genetically engineered mice and human pancreatic ductal adenocarcinoma.}, journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]}, volume = {23}, number = {6}, pages = {663-673}, doi = {10.1016/j.pan.2023.07.008}, pmid = {37541802}, issn = {1424-3911}, mesh = {Humans ; Mice ; Animals ; In Situ Hybridization, Fluorescence ; RNA, Ribosomal, 16S ; *Pancreatic Neoplasms/genetics/pathology ; *Carcinoma, Pancreatic Ductal/genetics/pathology ; Disease Models, Animal ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Emerging evidence has recently revealed a prominent role of the microbiome in pancreatic ductal adenocarcinoma (PDAC). However, while most observations were made in patients, mouse models still require a precise characterization of their disease-related microbiome to employ them for mechanistic and interventional preclinical studies.

METHODS: To investigate the fecal and tumoral microbiome of LSL-Kras[G12D/+];LSL-Trp53[R172H/+];Pdx-1-Cre (KPC) and control (CTRL) mice, Oxford Nanopore sequencing was applied. Feces were collected from 10 KPC mice and 10 CTRLs at 3 timepoints (6 weeks, 12 weeks, and when tumor-bearing (KPC) or 6 months (CTRL), respectively). Metagenomic sequencing was performed on feces DNA. KPC tumor and healthy pancreas DNA samples were subjected to 16S rRNA gene sequencing. Bacterial marker components were detected in KPC tumor tissue over time by fluorescence in situ hybridization (FISH) and immunohistochemistry (IHC).

RESULTS: Murine fecal samples showed a significantly different microbiome compared to age-matched healthy CTRLs regarding beta diversity (p = 0.001, R2 = 0.2-0.25 for Bray-Curtis). Adjusted human PDAC classifiers predicted disease status from feces of KPC mice achieving area under the receiver operating characteristic (AUROC) values of 80%. Furthermore, KPC tumors harbored significantly more bacterial components than healthy pancreas. Also the microbial composition differs significantly between KPC tumors and healthy pancreas tissue (p = 0.042 for Bray-Curtis). Microbiota found highly abundant in human PDAC samples were considerably more abundant in KPC tumors as compared to healthy pancreas samples (p-value <0.001).

CONCLUSION: KPC fecal samples show similarities with the microbial composition of stool samples from human PDAC patients.}, } @article {pmid37541570, year = {2023}, author = {Liu, YC and Chen, TH and Huang, YF and Chen, CL and Nai, YS}, title = {Investigation of the fall armyworm (Spodoptera frugiperda) gut microbiome and entomopathogenic fungus-induced pathobiome.}, journal = {Journal of invertebrate pathology}, volume = {200}, number = {}, pages = {107976}, doi = {10.1016/j.jip.2023.107976}, pmid = {37541570}, issn = {1096-0805}, mesh = {Animals ; Spodoptera ; *Gastrointestinal Microbiome ; Zea mays ; *Beauveria ; Larva ; }, abstract = {The gut microflora plays an important role in insect development and physiology. The gut bacterial microbiome of the fall armyworm (FAW), Spodoptera frugiperda, in both cornfield and laboratory-reared populations was investigated using a 16S metagenomic approach. The alpha- and beta-diversity of the cornfield FAW populations varied among sampling sites and were higher than those of the laboratory-reared FAW population, indicating that different diets and environments influence the gut bacterial composition. To better understand the interaction between the microbiome and entomopathogenic fungi (EPF), FAWs from organic and conventionally managed corn fields and from the laboratory-reared colony were inoculated with Beauveria bassiana NCHU-153 (Bb-NCHU-153). A longer median lethal time (LT50) was observed in the Bb-NCHU-153-infected cornfield FAW population than in the laboratory-reared FAWs. In terms of the microbiome, three Bb-NCHU-153-infected FAW groups showed different gut bacterial compositions compared to noninfected FAW. Further investigation of the cooccurrence network and linear discriminant analysis (LDA) of effect size (LEfSe) revealed that the enriched bacterial genera, such as Enterococcus, Serratia, Achromobacter, and Tsukamurella, in the gut might play the role of opportunistic pathogens after fungal infection; in contrast, some gut bacteria of Methylobacterium, Marinomonas, Paenochrobactrum, Pseudomonas, Acinetobacter, Delftia, Dietzia, Gordonia, Leucobacter, Paracoccus, and Stenotrophomonas might be probiotics against EPF infection. These results indicated that EPF infection can change the gut bacterial composition and lead to a pathobiome in the FAW and that some bacterial species might protect the FAW from EPF infection. These findings could be applied to the design of pathobiome-inducing biocontrol strategies.}, } @article {pmid37540923, year = {2023}, author = {Li, S and Diao, M and Liao, Y and Ji, G}, title = {Performance, microbial growth and community interactions of iron-dependent denitrification in freshwaters.}, journal = {Environment international}, volume = {178}, number = {}, pages = {108124}, doi = {10.1016/j.envint.2023.108124}, pmid = {37540923}, issn = {1873-6750}, mesh = {*Iron/metabolism ; *Denitrification ; Fresh Water ; Nitrogen/metabolism ; Bioreactors ; Nitrates/metabolism ; }, abstract = {Iron-dependent denitrification is a safe and promising technology for nitrogen removal in freshwaters. However, the understanding of microbial physiology and interactions during the process was limited. Denitrifying systems inoculated with freshwater samples were operated with and without iron(II) at a low C/N ratio for 54 days. Iron addition improved nitrogen removal. Batch experiments confirmed that microbially mediated reaction rather than abiotic reaction dominated during the process. Metagenomics recovered genomes of the five most abundant microorganisms, which accounted for over 99% of the community in every triplicate of the iron-based system. Based on codon usage bias, all of them were fast-growing organisms. The total abundance of fast-growing organisms was 38% higher in the system with iron than in the system without iron. Notably, the most abundant organism Diaphorobacter did not have enzymes for asparagine and aspartate biosynthesis, whereas Rhodanobacter could not produce serine and cobalamin. Algoriphagus and Areminomonas lost synthesis enzymes for more amino acids and vitamins. However, they could always obtain these growth-required substances from another microorganism in the community. The two-partner relationship minimized the limitation on microbial reproduction and increased community stability. Our results indicated that iron addition improved nitrogen removal by supplying electron donors, promoting microbial growth, and building up syntrophic interactions among microorganisms with timely communications. The findings provided new insights into the process, with implications for freshwater remediation.}, } @article {pmid37539288, year = {2023}, author = {Kumburu, HH and Shayo, M and van Zwetslaar, M and Njau, J and Kuchaka, DJ and Ignas, IP and Wadugu, B and Kasworm, R and Masaki, LJ and Hallgren, MB and Clausen, PTLC and Mmbaga, BT and Aarestrup, FM and Sonda, TB}, title = {Nanopore sequencing technology for clinical diagnosis of infectious diseases where laboratory capacity is meager: A case report.}, journal = {Heliyon}, volume = {9}, number = {7}, pages = {e17439}, pmid = {37539288}, issn = {2405-8440}, abstract = {In resource-limited settings, patients are often first presented to clinical settings when seriously ill and access to proper clinical microbial diagnostics is often very limited or non-existing. On February 16th[,] 2022 we were on a field trip to test a completely field-deployable metagenomics sequencing set-up, that includes DNA purification, sequencing, and bioinformatics analyses using bioinformatics tools installed on a laptop for water samples, just outside Moshi, Tanzania. On our way to the test site, we were contacted by the nearby Machame hospital regarding a child seriously ill with diarrhea and not responding to treatment. Within the same day, we conducted an onsite metagenomics examination of a fecal sample from the child, and Campylobacter jejuni was identified as the causative agent. The treatment was subsequently changed, with almost immediate improvement, and the child was discharged on February 21st.}, } @article {pmid37537681, year = {2023}, author = {Mendes, LW and Raaijmakers, JM and de Hollander, M and Sepo, E and Gómez Expósito, R and Chiorato, AF and Mendes, R and Tsai, SM and Carrión, VJ}, title = {Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {68}, pmid = {37537681}, issn = {2524-6372}, support = {2014/03217-3, 2015/00251-9, 2020/00469-2//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 408191/2018-0, 307670/2021-0, 302591/2019-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 88887.185941/2018-00//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, abstract = {BACKGROUND: Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar.

RESULTS: Integration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion.

CONCLUSION: Collectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.}, } @article {pmid37537673, year = {2023}, author = {Ferrocino, I and Biasato, I and Dabbou, S and Colombino, E and Rantsiou, K and Squara, S and Gariglio, M and Capucchio, MT and Gasco, L and Cordero, CE and Liberto, E and Schiavone, A and Cocolin, L}, title = {Lactiplantibacillus plantarum, lactiplantibacillus pentosus and inulin meal inclusion boost the metagenomic function of broiler chickens.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {36}, pmid = {37537673}, issn = {2524-4671}, abstract = {BACKGROUND: The inclusion of alternative ingredients in poultry feed is foreseen to impact poultry gut microbiota. New feeding strategies (probiotics/prebiotics) must be adopted to allow sustainable productions. Therefore, the current study aimed to use metagenomics approaches to determine how dietary inclusion of prebiotic (inulin) plus a multi-strain probiotic mixture of Lactiplantibacillus plantarum and Lactiplantibacillus pentosus affected microbiota composition and functions of the gastro-intestinal tract of the broilers during production. Fecal samples were collected at the beginning of the trial and after 5, 11 and 32 days for metataxonomic analysis. At the end of the trial, broilers were submitted to anatomo-pathological investigations and caecal content was subjected to volatilome analysis and DNAseq.

RESULTS: Probiotic plus prebiotic inclusion did not significantly influence bird performance and did not produce histopathological alterations or changes in blood measurements, which indicates that the probiotic did not impair the overall health status of the birds. The multi-strain probiotic plus inulin inclusion in broilers increased the abundance of Blautia, Faecalibacterium and Lachnospiraceae and as a consequence an increased level of butyric acid was observed. In addition, the administration of probiotics plus inulin modified the gut microbiota composition also at strain level since probiotics alone or in combination with inulin select specific Faecalibacterium prausnitzi strain populations. The metagenomic analysis showed in probiotic plus prebiotic fed broilers a higher number of genes required for branched-chain amino acid biosynthesis belonging to selected F. prausnitzi strains, which are crucial in increasing immune function resistance to pathogens. In the presence of the probiotic/prebiotic a reduction in the occurrence of antibiotic resistance genes belonging to aminoglycoside, beta-lactamase and lincosamide family was observed.

CONCLUSIONS: The positive microbiome modulation observed is particularly relevant, since the use of these alternative ingredients could promote a healthier status of the broiler's gut.}, } @article {pmid37537550, year = {2023}, author = {Gand, M and Bloemen, B and Vanneste, K and Roosens, NHC and De Keersmaecker, SCJ}, title = {Comparison of 6 DNA extraction methods for isolation of high yield of high molecular weight DNA suitable for shotgun metagenomics Nanopore sequencing to detect bacteria.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {438}, pmid = {37537550}, issn = {1471-2164}, mesh = {Metagenomics/methods ; *Nanopore Sequencing ; *Nanopores ; Molecular Weight ; High-Throughput Nucleotide Sequencing/methods ; DNA ; Sequence Analysis, DNA/methods ; Bacteria/genetics ; }, abstract = {BACKGROUND: Oxford Nanopore Technologies (ONT) offers an accessible platform for long-read sequencing, which improves the reconstruction of genomes and helps to resolve complex genomic contexts, especially in the case of metagenome analysis. To take the best advantage of long-read sequencing, DNA extraction methods must be able to isolate pure high molecular weight (HMW) DNA from complex metagenomics samples, without introducing any bias. New methods released on the market, and protocols developed at the research level, were specifically designed for this application and need to be assessed.

RESULTS: In this study, with different bacterial cocktail mixes, analyzed as pure or spiked in a synthetic fecal matrix, we evaluated the performances of 6 DNA extraction methods using various cells lysis and purification techniques, from quick and easy, to more time-consuming and gentle protocols, including a portable method for on-site application. In addition to the comparison of the quality, quantity and purity of the extracted DNA, the performance obtained when doing Nanopore sequencing on a MinION flow cell was also tested. From the obtained results, the Quick-DNA HMW MagBead Kit (Zymo Research) was selected as producing the best yield of pure HMW DNA. Furthermore, this kit allowed an accurate detection, by Nanopore sequencing, of almost all the bacterial species present in a complex mock community.

CONCLUSION: Amongst the 6 tested methods, the Quick-DNA HMW MagBead Kit (Zymo Research) was considered as the most suitable for Nanopore sequencing and would be recommended for bacterial metagenomics studies using this technology.}, } @article {pmid37536450, year = {2023}, author = {Gomes, RAL and Zerbini, FM}, title = {ConCreT, a 2D convolutional neural network for taxonomic classification applied to viruses in the phylum Cressdnaviricota.}, journal = {Journal of virological methods}, volume = {320}, number = {}, pages = {114789}, doi = {10.1016/j.jviromet.2023.114789}, pmid = {37536450}, issn = {1879-0984}, mesh = {Humans ; Phylogeny ; *Viruses/genetics ; Neural Networks, Computer ; Metagenomics/methods ; Machine Learning ; }, abstract = {Taxonomic assignments allow scientists to communicate better with each other. In virology, taxonomy is continually improving towards a more precise and comprehensive framework. With the huge numbers of new viruses being described in metagenomic studies, automated taxonomy tools are urgently needed. A number of such tools have been proposed, and those applying machine learning (ML), mainly in the deep learning branch, stand out with accurate results. Still, there is a demand for tools that are less computationally intensive and that can classify viruses down to the ranks of genus and species. Cressdnaviruses are good subjects for testing such tools, due to their small, circular genomes and the existence of several families and genera with a highly imbalanced number of species. We developed a 2D convolutional neural network for virus taxonomy and tested it for classification of viruses from the phylum Cressdnaviricota. We obtained >98 % accuracy in the final pipeline tested, which we named ConCreT (Convolutional Neural Network for Cressdnavirus Taxonomy). The mixture of augmentation for more imbalanced groups with no augmentation for more balanced ones achieved the best score in the final test.}, } @article {pmid37535713, year = {2023}, author = {Jackson, FLC}, title = {Community-initiated genomics.}, journal = {Science (New York, N.Y.)}, volume = {381}, number = {6657}, pages = {482-483}, doi = {10.1126/science.adj2380}, pmid = {37535713}, issn = {1095-9203}, mesh = {Humans ; *Black or African American/genetics ; *DNA, Ancient ; Metagenomics ; *Enslavement/history ; }, abstract = {Ancient DNA is used to connect enslaved African Americans to modern descendants.}, } @article {pmid37535671, year = {2023}, author = {Mattock, J and Martínez-Álvaro, M and Cleveland, MA and Roehe, R and Watson, M}, title = {KOunt: a reproducible KEGG orthologue abundance workflow.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {8}, pages = {}, pmid = {37535671}, issn = {1367-4811}, support = {BB/S006567/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S006680/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Software ; Workflow ; *Metagenome ; Databases, Factual ; }, abstract = {SUMMARY: Accurate gene prediction is essential for successful metagenome analysis. We present KOunt, a Snakemake pipeline, that precisely quantifies KEGG orthologue abundance.

KOunt is available on GitHub: https://github.com/WatsonLab/KOunt. The KOunt reference database is available on figshare: https://doi.org/10.6084/m9.figshare.21269715. Test data are available at https://doi.org/10.6084/m9.figshare.22250152 and version 1.2.0 of KOunt at https://doi.org/10.6084/m9.figshare.23607834.}, } @article {pmid37535472, year = {2023}, author = {Motro, Y and Wajnsztajn, D and Michael-Gayego, A and Mathur, S and Marano, RB and Salah, I and Rosenbluh, C and Temper, V and Strahilevitz, J and Moran-Gilad, J}, title = {Metagenomic sequencing for investigation of a national keratoconjunctivitis outbreak, Israel, 2022.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {28}, number = {31}, pages = {}, pmid = {37535472}, issn = {1560-7917}, mesh = {Humans ; Metagenome ; Metagenomics ; Israel/epidemiology ; *Keratoconjunctivitis/diagnosis/epidemiology/genetics ; *Microsporidia/genetics ; Disease Outbreaks ; High-Throughput Nucleotide Sequencing ; }, abstract = {BackgroundEpidemics of keratoconjunctivitis may involve various aetiological agents. Microsporidia are an uncommon difficult-to-diagnose cause of such outbreaks.AimDuring the third quarter of 2022, a keratoconjunctivitis outbreak was reported across Israel, related to common water exposure to the Sea of Galilee. We report a comprehensive diagnostic approach that identified Vittaforma corneae as the aetiology, serving as proof of concept for using real-time metagenomics for outbreak investigation.MethodsCorneal scraping samples from a clinical case were subjected to standard microbiological testing. Samples were tested by calcofluor white staining and metagenomic short-read sequencing. We analysed the metagenome for taxonomical assignment and isolation of metagenome-assembled genome (MAG). Targets for a novel PCR were identified, and the assay was applied to clinical and environmental samples and confirmed by long-read metagenomic sequencing.ResultsFluorescent microscopy was suggestive of microsporidiosis. The most abundant species (96.5%) on metagenomics analysis was V. corneae. Annotation of the MAG confirmed the species assignment. A unique PCR target in the microsporidian rRNA gene was identified and validated against the clinical sample. The assay and metagenomic sequencing confirmed V. corneae in an environmental sludge sample collected at the exposure site.ConclusionsThe real-time utilisation of metagenomics allowed species detection and development of diagnostic tools, which aided in outbreak source tracking and can be applied for future cases. Metagenomics allows a fully culture-independent investigation and is an important modality for public health microbiology.}, } @article {pmid37534530, year = {2023}, author = {Graf, EH}, title = {We All Know Standardization Is Key, But How Do We Get There with Clinical Metagenomics?.}, journal = {Clinical chemistry}, volume = {69}, number = {9}, pages = {948-950}, doi = {10.1093/clinchem/hvad101}, pmid = {37534530}, issn = {1530-8561}, mesh = {Humans ; *Metagenomics/standards ; *Respiratory Tract Infections ; High-Throughput Nucleotide Sequencing ; Reference Standards ; }, } @article {pmid37534320, year = {2023}, author = {Li, M and Mao, J and Diaz, I and Kopylova, E and Melnik, AV and Aksenov, AA and Tipton, CD and Soliman, N and Morgan, AM and Boyd, T}, title = {Multi-omic approach to decipher the impact of skincare products with pre/postbiotics on skin microbiome and metabolome.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1165980}, pmid = {37534320}, issn = {2296-858X}, abstract = {INTRODUCTION: Although pre/pro/postbiotics have become more prevalent in dermatologic and cosmetic fields, the mode of action when topically applied is largely unknown. A multi-omic approach was applied to decipher the impact of the skincare products with pre/postbiotics on skin microbiome and metabolome.

METHODS: Subjects with dry skin applied a body wash and body lotion with or without pre/postbiotics for 6 weeks. Skin hydration was measured at baseline, 3 and 6 weeks. Skin swabs were collected for 16S rRNA gene sequencing, metagenomics and metabolomics analysis.

RESULTS: Skin hydration significantly increased in both groups. The prebiotic group significantly reduced opportunistic pathogens, e.g., Pseudomonas stutzeri and Sphingomonas anadarae, and increased the commensals, e.g., Staphylococcus equorum, Streptococcus mitis, Halomonas desiderata. Bacterial sugar degradation pathways were enriched in the prebiotic group, while fatty acid biosynthesis pathways were reduced in control. The changes on skin metabolome profiles by the products were more prominent. The prebiotic group performed greater modulation on many clinically-relevant metabolites compared to control. Correlation analysis showed H. desiderata and S. mitis positively correlated with skin hydration, P. stutzeri and S. anadarae negatively correlated with the metabolites that are positively associated with skin hydration improvement.

CONCLUSION: This holistic study supported a hypothesis that the pre/postbiotics increased skin hydration through the modulation of skin microbiome, metabolic pathways and metabolome.}, } @article {pmid37534074, year = {2023}, author = {Safika, S and Indrawati, A and Afif, U and Hidayat, R and Sunartatie, T}, title = {Metagenomic analysis of mycobiome in wild and captivity Sumatran orangutans (Pongo abelii).}, journal = {Journal of advanced veterinary and animal research}, volume = {10}, number = {2}, pages = {228-236}, pmid = {37534074}, issn = {2311-7710}, abstract = {OBJECTIVE: This study analyzes the mycobiome in wild and captive Sumatran orangutans.

MATERIALS AND METHODS: Nine orangutan feces samples from the wild and nine from captivity were divided into three repeats from 11- to 15-year-olds in good health. The Illumina platform for analysis of ITS bioinformatics was used according to the Qiime2 and CCMetagen approaches.

RESULTS: Wild Sumatran orangutans include 53% Ascomycota, 38% uncultured fungi, and 4% Basidiomycota. Orangutans in captivity are 57% Ascomycota, 26% uncultured fungi, and 2% Basidiomycota. Based on genus level, uncultured Neurospora (31%), Penicillium (10%), Aspergillus (3%), Fusarium (3%), Candida (2%), Cutaneotrichosporon (2%), and Limonomyces (2%) are found in wild orangutans. The most prevalent genus among captivity orangutans is Aspergillus (32%), followed by fungal sp. (11%), Lasiodiplodia (18%), Devriesia (2%), and Sordariomycetes (2%). According to the Chao1 diversity index and Shannon and Simpson, there was no significant difference between wild and captive Sumatran orangutans.

CONCLUSION: Neurospora is unique to wild Sumatran orangutans, although Aspergillus predominates in captive orangutans. We hypothesize that the gut mycobiome of wild orangutans will resemble that of orangutans in captivity. The excellent range of food sources in the forest does not result in the prevalence of fungi in the typical gut microbiome.}, } @article {pmid37533931, year = {2023}, author = {Zou, Y and Zeng, S and Chen, M and Li, S and Fu, Q and Zhou, S and Zhou, J}, title = {Gut microbiota in children with split-dose bowel preparations revealed by metagenomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1202007}, pmid = {37533931}, issn = {2235-2988}, mesh = {Humans ; Child ; *Cathartics/adverse effects ; *Gastrointestinal Microbiome ; Metagenomics ; Polyethylene Glycols ; Colonoscopy/adverse effects ; }, abstract = {OBJECTIVE: Split-dose polyethylene glycol (PEG) is routinely used for bowel preparation before colonoscopy. This study aimed to investigate the composition of gut microbiota and its functions in pediatric patients undergoing split-dose PEG bowel preparation for colonoscopy to understand the stability and resilience of gut microbiota.

MATERIAL AND METHODS: From September to December 2021, 19 pediatric patients were enrolled at Shenzhen Children's Hospital and 76 samples (4 time points) were analyzed using metagenomics. Time points included Time_1 (one day before bowel preparation), Time_2 (one day after colonoscopy), Time_3 (two weeks after bowel preparation), and Time_4 (four weeks after bowel preparation).

RESULT: Alpha diversity comparison at both the species and gene levels showed a decrease in community richness after colonoscopy, with little statistical significance. However, the Shannon diversity index significantly decreased (P<0.05) and gradually returned to pre-preparation levels at two weeks after bowel preparation. The genus level analysis showed six genera (Eubacterium, Escherichia, Intertinibacter, Veillonella, Ruminococcaceae unclassified, and Coprobacillus) significantly different across the four time periods. Additionally, at the species level, the abundance of Escherichia coli, Bacteroides fragilis, and Veillonella parvula significantly increased at one day after colonoscopy before gradually decreasing at two weeks after bowel preparation. In contrast, the abundance of Intertinibacter bartlettii decreased at one day after colonoscopy but then recovered at two weeks after bowel preparation, reaching the preoperative level at four weeks after bowel preparation. Furthermore, five functional pathways (base excision repair, biosynthesis of ansamycins, biosynthesis of siderophore group nonribosomal peptide, flavonoid biosynthesis, and biosynthesis of type II polyketide products) were significantly different across the four time periods, with recovery at two weeks after bowel preparation and reaching preoperative levels at four weeks after bowel preparation.

CONCLUSIONS: Gut microbiota at the genus level, species level, and functional pathways are impacted in pediatric patients undergoing split-dose PEG bowel preparation and colonoscopy, with recovery two weeks following bowel preparation. However, the phylum level was not impacted. Modifications in gut microbiota composition and function may be investigated in future studies of bowel preparation. This study highlights the stability and resilience of gut microbiota among pediatric patients during bowel preparation.}, } @article {pmid37533383, year = {2023}, author = {Liu, J and Li, XY and Song, WT and Zeng, XX and Li, H and Yang, L and Wang, DY}, title = {Metagenomic Analysis of Environmental Samples from Wildlife Rescue Station at Poyang Lake, China.}, journal = {Biomedical and environmental sciences : BES}, volume = {36}, number = {7}, pages = {595-603}, doi = {10.3967/bes2023.087}, pmid = {37533383}, issn = {2214-0190}, mesh = {Animals ; Animals, Wild/genetics ; Lakes ; Phylogeny ; *Picornaviridae/genetics ; *Viruses/genetics ; China ; Metagenomics ; Genome, Viral ; }, abstract = {OBJECTIVE: To improve the understanding of the virome and bacterial microbiome in the wildlife rescue station of Poyang Lake, China.

METHODS: Ten smear samples were collected in March 2019. Metagenomic sequencing was performed to delineate bacterial and viral diversity. Taxonomic analysis was performed using the Kraken2 and Bracken methods. A maximum-likelihood tree was constructed based on the RNA-dependent RNA polymerase (RdRp) region of picornavirus.

RESULTS: We identified 363 bacterial and 6 viral families. A significant difference in microbial and viral abundance was found between samples S01-S09 and S10. In S01-S09, members of Flavobacteriia and Gammaproteobacteria were the most prevalent, while in S10, the most prevalent bacteria class was Actinomycetia. Among S01-S09, members of Myoviridae and Herelleviridae were the most prevalent, while the dominant virus family of S10 was Picornaviridae. The full genome of the pigeon mesivirus-like virus (NC-BM-233) was recovered from S10 and contained an open reading frame of 8,124 nt. It showed the best hit to the pigeon mesivirus 2 polyprotein, with 84.10% amino acid identity. Phylogenetic analysis showed that RdRp clustered into Megrivirus B.

CONCLUSION: This study provides an initial assessment of the bacteria and viruses in the cage-smeared samples, broadens our knowledge of viral and bacterial diversity, and is a way to discover potential pathogens in wild birds.}, } @article {pmid37532998, year = {2023}, author = {Syama, K and Jothi, JAA and Khanna, N}, title = {Correction: Automatic disease prediction from human gut metagenomic data using boosting GraphSAGE.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {307}, pmid = {37532998}, issn = {1471-2105}, } @article {pmid37532062, year = {2023}, author = {Liu, J and Yu, J and Tan, Y and Dang, R and Zhou, M and Hernández, M and Lichtfouse, E and Xiao, L}, title = {Biomethane is produced by acetate cleavage, not direct interspecies electron transfer: genome-centric view and carbon isotope.}, journal = {Bioresource technology}, volume = {387}, number = {}, pages = {129589}, doi = {10.1016/j.biortech.2023.129589}, pmid = {37532062}, issn = {1873-2976}, mesh = {Electrons ; Carbon Isotopes ; Carbon Dioxide/metabolism ; Bacteria/metabolism ; Acetates ; Anaerobiosis ; *Microbiota ; *Euryarchaeota/metabolism ; Methane/metabolism ; }, abstract = {Understanding the source of methane (CH4) is of great significance for improving the anaerobic fermentation efficiency in bioengineering, and for mitigating the emission potential of natural ecosystems. Microbes involved in the process named direct interspecies electron transfer coupling with CO2 reduction, i.e., electrons released from electroactive bacteria to reduce CO2 into CH4, have attracted considerable attention for wastewater treatment in the past decade. However, how the synergistic effect of microbiota contributes to this anaerobic carbon metabolism accompanied by CH4 production still remains poorly understood, especial for wastewater with antibiotic exposure. Results show that enhancing lower-abundant acetoclastic methanogens and acetogenic bacteria, rather than electroactive bacteria, contributed to CH4 production, based on a metagenome-assembled genomes network analysis. Natural and artificial isotope tracing of CH4 further confirmed that CH4 mainly originated from acetoclastic methanogenesis. These findings reveal the contribution of direct acetate cleavage (acetoclastic methanogenesis) and provide insightsfor further regulation of methanogenic strategies.}, } @article {pmid37531452, year = {2023}, author = {Kaličanin, N and Balaž, AM and Prodanović, O and Prodanović, R}, title = {Heterologous Expression and Partial Characterization of a Putative Opine Dehydrogenase from a Metagenomic Sequence of Desulfohalobium retbaense.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {24}, number = {20}, pages = {e202300414}, doi = {10.1002/cbic.202300414}, pmid = {37531452}, issn = {1439-7633}, mesh = {Gene Library ; *Salts ; *Sodium Chloride ; Oxidoreductases ; Substrate Specificity ; Enzyme Stability ; Hydrogen-Ion Concentration ; }, abstract = {The aim of this research was to prove the function of the putative opine dehydrogenase from Desulfohalobium retbaense and to characterize the enzyme in terms of functional and kinetic parameters. A putative opine dehydrogenase was identified from a metagenomic library by a sequence-based technique search of the metagenomic library, and afterward was successfully heterologously produced in Escherichia coli. In order to examine its potential for applications in the synthesis of secondary amines, first the substrate specificity of the enzyme towards different amino donors and amino acceptors was determined. The highest affinity was observed towards small amino acids, preferentially L-alanine, and when it comes to α-keto acids, pyruvate proved to be a preferential amino acceptor. The highest activity was observed at pH 6.5 in the absence of salts. The enzyme showed remarkable stability in a wide range of experimental conditions, such as broad pH stability (from 6.0-11.0 after 30 min incubation in buffers at a certain pH), stability in the presence of NaCl up to 3.0 M for 24 h, it retained 80 % of the initial activity after 1 h incubation at 45 °C, and 65 % of the initial activity after 24 h incubation in 30 % dimethyl sulfoxide.}, } @article {pmid37531160, year = {2023}, author = {Fan, G and Li, S and Tian, F and Yang, L and Yi, S and Chen, S and Li, C and Zhang, R and He, X and Ma, X}, title = {RNA-sequencing-based detection of human viral pathogens in cerebrospinal fluid and serum samples from children with meningitis and encephalitis.}, journal = {Microbial genomics}, volume = {9}, number = {8}, pages = {}, pmid = {37531160}, issn = {2057-5858}, mesh = {Infant ; Humans ; Child ; *Meningitis ; *Encephalitis/cerebrospinal fluid/diagnosis ; *Viruses/genetics ; *Enterovirus/genetics ; Sequence Analysis, RNA ; RNA ; }, abstract = {Encephalitis and meningitis are notable global public health concerns, especially among infants or children. Metagenomic next-generation sequencing (mNGS) has greatly advanced our understanding of the viruses responsible for these diseases. However, the detection rate of the aetiology remains low. We conducted RNA sequencing and virome analysis on cerebrospinal fluid (CSF) and serum samples commonly used in the clinical diagnosis to detect viral pathogens. In total, 226 paired CSF and serum samples from 113 children with encephalitis and meningitis were enrolled. The results showed that the diversity of viruses was higher in CSF, with a total of 12 viral taxa detected, including one case each of herpesvirus, coronavirus and enterovirus, and six cases of adenovirus related to human diseases. In contrast, the Anelloviridae was the most abundant viral family detected in serum, and only a few samples contained human viral pathogens, including one case of enterovirus and two cases of adenovirus. The detection rate for human viral pathogens increases to 10.6 %(12/113) when both types of samples are used simultaneously, compared to CSF along 7.9 % (9/113) or serum alone 2.6 % (3/113). However, we did not detect these viruses simultaneously in paired samples from the same case. These results suggest that CSF samples still have irreplaceable advantages for using mNGS to detect viruses in patients with meningitis and encephalitis, and serum can supplement to improve the detection rate of viral encephalitis and meningitis. The findings of this study could help improve the etiological diagnosis, clinical management and prognosis of patients with meningitis and encephalitis in children.}, } @article {pmid37531005, year = {2023}, author = {da Silva, LA and de Camargo, BR and Rodrigues, BMP and Berlitz, DL and Fiuza, LM and Ardisson-Araújo, DMP and Ribeiro, BM}, title = {Exploring viral infections in honey bee colonies: insights from a metagenomic study in southern Brazil.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {54}, number = {3}, pages = {1447-1458}, pmid = {37531005}, issn = {1678-4405}, support = {304223/2021-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 193001532/2016//Fundação de Apoio à Pesquisa do Distrito Federal/ ; 193.00001749/2022-31//Fundação de Apoio à Pesquisa do Distrito Federal/ ; }, mesh = {*Bees/virology ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Brazil ; *Insect Viruses/classification/genetics/isolation & purification ; Phylogeny ; Viral Proteins/chemistry/genetics ; }, abstract = {The decline in honey bee colonies in different parts of the world in recent years is due to different reasons, such as agricultural practices, climate changes, the use of chemical insecticides, and pests and diseases. Viral infections are one of the main causes leading to honey bee population declines, which have a major economic impact due to honey production and pollination. To investigate the presence of viruses in bees in southern Brazil, we used a metagenomic approach to sequence adults' samples of concentrated extracts from Apis mellifera collected in fifteen apiaries of six municipalities in the Rio Grande do Sul state, Brazil, between 2016 and 2017. High-throughput sequencing (HTS) of these samples resulted in the identification of eight previously known viruses (Apis rhabdovirus 1 (ARV-1), Acute bee paralysis virus (ABPV), Aphid lethal paralysis virus (ALPV), Black queen cell virus (BQCV), Bee Macula-like virus (BeeMLV), Deformed wing virus (DWV), Lake Sinai Virus NE (LSV), and Varroa destructor virus 3 (VDV-3)) and a thogotovirus isolate. This thogotovirus shares high amino acid identities in five of the six segments with Varroa orthomyxovirus 1, VOV-1 (98.36 to 99.34% identity). In contrast, segment 4, which codes for the main glycoprotein (GP), has no identity with VOV-1, as observed for the other segments, but shares an amino acid identity of 34-38% with other glycoproteins of viruses from the Orthomyxoviridae family. In addition, the putative thogotovirus GP also shows amino acid identities ranging from 33 to 41% with the major glycoprotein (GP64) of insect viruses of the Baculoviridae family. To our knowledge, this is the second report of a thogotovirus found in bees and given this information, this thogotovirus isolate was tentatively named Apis thogotovirus 1 (ATHOV-1). The detection of multiple viruses in bees is important to better understand the complex interactions between viruses and their hosts. By understanding these interactions, better strategies for managing viral infections in bees and protecting their populations can be developed.}, } @article {pmid37530925, year = {2023}, author = {Wei, YR and Mi, XY and Wu, JY}, title = {Genome sequence of a Sobemovirus from the feces of Northern Pintail (Anas acuta).}, journal = {Virus genes}, volume = {59}, number = {5}, pages = {786-789}, pmid = {37530925}, issn = {1572-994X}, support = {2020D01A43//the Natural Science Foundation Project of Xinjiang Uygur Autonomous Region/ ; }, mesh = {Animals ; *Capsid Proteins/genetics ; Phylogeny ; Ducks ; *RNA Viruses/genetics ; Feces ; Genome, Viral/genetics ; Open Reading Frames ; }, abstract = {Northern pintail (Anas acuta) is a migratory waterfowl that can transmit various viruses. The genome sequence of a Sobemovirus was determined using metagenomic sequencing from the feces of northern pintail (Anas acuta) in Xinjiang, northwest China. The virus possesses a linear RNA molecule of 4177 bp and is most closely related to isolates SoMV-WA (GenBank accession no. HM163159.1) and ATCC PV-109 (GenBank accession no. GQ845002.2), with a nucleotide identity of 86.7%. The virus encodes four open reading frames (ORF) coding for four proteins, and phylogenetic analysis of capsid protein and RNA-dependent RNA polymerase (RdRp) showed that the strain was clustered into the species Sowbane Mosaic Virus (SoMV). The amino acid sequence identity of capsid protein was 89.6-90.9% to other isolates of SoMV, but 17.6-31.4% similar to other strains in the genus Sobemovirus, indicating a strain of Sowbane Mosaic Virus. This is the first report of SoMV in the feces of wild birds and in China, and it suggested that northern pintail likely plays an alternative role in the transmission of SoMV.}, } @article {pmid37530473, year = {2023}, author = {Abdelrazek, S and Bush, E and Oliver, CL and Liu, H and Sharma, P and Aguilera Flores, M and Donegan, MA and Almeida, R and Nita, M and Vinatzer, B}, title = {A survey of Xylella fastidiosa in the US state of Virginia reveals wide distribution of both subspecies fastidiosa and multiplex in grapevine.}, journal = {Phytopathology}, volume = {}, number = {}, pages = {}, doi = {10.1094/PHYTO-06-23-0212-R}, pmid = {37530473}, issn = {0031-949X}, abstract = {Global travel and trade in combination with climate change are expanding the geographic distribution of plant pathogens. The bacterium Xylella fastidiosa is a prime example. Native to the Americas, it has spread to Europe, Asia, and the Middle East. To assess the risk that pathogen introductions pose to crops in newly invaded areas, it is key to survey their diversity, host range, and disease incidence in relation to climatic conditions where they are already present. We performed a survey of X. fastidiosa in grapevine in Virginia, USA, using a combination of quantitative PCR, multilocus sequencing, and metagenomics. We also analyzed samples from deciduous trees with leaf scorch symptoms. X. fastidiosa subspecies fastidiosa was identified in grapevines in all regions of the state, even in Northern Virginia where the temperature was below -9ºC for 10 days/year on average in the years preceding sampling. Unexpectedly, we also found for the first time grapevine samples infected with X. fastidiosa subspecies multiplex (Xfm). The Xfm lineage found in grapevines had been previously isolated from blueberries in the Southeastern US and was distinct from that found in deciduous trees in Virginia. The obtained results will be important for risk assessment of X. fastidiosa introductions in other parts of the world.}, } @article {pmid37529954, year = {2023}, author = {Zhong, S and Yang, MH}, title = {[Value of metagenomic next-generation sequencing in children with hematological malignancies complicated with infections].}, journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics}, volume = {25}, number = {7}, pages = {718-725}, pmid = {37529954}, issn = {1008-8830}, mesh = {Humans ; Child ; Retrospective Studies ; *Hematologic Neoplasms/complications ; High-Throughput Nucleotide Sequencing ; Bronchoalveolar Lavage Fluid ; Hospitals ; Sensitivity and Specificity ; }, abstract = {OBJECTIVES: To explore the value of metagenomic next-generation sequencing (mNGS) in the pathogen identification in children with hematological malignancies complicated with infections.

METHODS: A retrospective analysis was conducted on clinical data and pathogenic test results of 43 children with hematological malignancies who underwent microbial culture and mNGS due to infections in the Third Xiangya Hospital of Central South University between June 2020 and July 2022. Differences in detection rates and characteristics of pathogenic microorganisms detected by mNGS and microbial culture were compared.

RESULTS: A total of 54 specimens were examined, and the overall detection rate of pathogen by mNGS (80%, 43/54) was significantly higher than that by microbial culture (30%, 16/54) (P<0.001). The most commonly detected infection type by mNGS was viral infection, followed by fungal infection combined viral infection, while that by microbial culture was bacterial infection, followed by fungal infection. The detection rate of fungi by mNGS (33%, 18/54) was higher than that by microbial culture (6%, 3/54) (P<0.001). The detection rate of two or more pathogenic microorganisms by mNGS was higher at 48% compared to microbial culture at 9% (P<0.05). The detection rate of two or more types of pathogenic microorganisms by mNGS was also significantly higher at 33% compared to microbial culture at 2% (P<0.05). The most commonly detected bacteria and fungi by mNGS were Pseudomonas aeruginosa and Candida tropicalis, respectively, in peripheral blood, while Streptococcus pneumoniae and Pneumocystis jirovecii were most commonly detected in bronchoalveolar lavage fluid. Treatment adjustments based on mNGS results were beneficial for 35% (15/43) of the cases.

CONCLUSIONS: mNGS has a higher detection rate than microbial culture and has obvious advantages in diagnosing mixed and fungal infections, making it a useful supplementary diagnostic method to microbial culture.}, } @article {pmid37529378, year = {2023}, author = {Niyogisubizo, J and Cai, Y and Zhang, L and Zhang, X and Wei, Y}, title = {Editorial: Computational solutions for microbiome and metagenomics sequencing analyses, Volume II.}, journal = {Frontiers in molecular biosciences}, volume = {10}, number = {}, pages = {1253303}, doi = {10.3389/fmolb.2023.1253303}, pmid = {37529378}, issn = {2296-889X}, } @article {pmid37528843, year = {2023}, author = {Wrønding, T and Vomstein, K and Bosma, EF and Mortensen, B and Westh, H and Heintz, JE and Mollerup, S and Petersen, AM and Ensign, LM and DeLong, K and van Hylckama Vlieg, JET and Thomsen, AB and Nielsen, HS}, title = {Antibiotic-free vaginal microbiota transplant with donor engraftment, dysbiosis resolution and live birth after recurrent pregnancy loss: a proof of concept case study.}, journal = {EClinicalMedicine}, volume = {61}, number = {}, pages = {102070}, pmid = {37528843}, issn = {2589-5370}, abstract = {BACKGROUND: Vaginal dysbiosis covers imbalances in the vaginal microbiota, defined by altered composition of bacteria, viruses, and fungi and is associated with euploid pregnancy losses, premature birth, infertility, or bacterial vaginosis. A large proportion of women who have vaginal dysbiosis do not experience any symptoms. Antibiotics are the traditional treatment, recently combined with local probiotics in some cases. Vaginal Microbiota Transplantation (VMT) with eubiotic vaginal bacterial microbiota after antibiotic eradication of pathogens has successfully been performed in a case study with five patients, but no VMT has been performed without the use of antibiotics.

METHODS: This is a proof of concept case study. The patient was found to have vaginal dysbiosis at the RPL clinic at Copenhagen University Hospital Hvidovre, Denmark on the 23rd of June 2021. She was offered and accepted to receive experimental treatment in the form of a VMT as a compassionate use case. VMT is the transfer of cervicovaginal secretions (CVS) from a healthy donor with a Lactobacillus-dominant vaginal microbiome to a recipient with a dysbiotic vaginal microbiome. CVS is a mixture of e.g., mucus, bacteria, metabolites present in the vaginal canal. Potential donors were thoroughly screened for the absence of STIs, and the most suitable donor sample for the specific patient in this study was determined via an in vitro microbiome competition assay.

FINDINGS: A 30-year-old patient with one livebirth and a complicated pregnancy history of two stillbirths and 1 s trimester pregnancy loss in gestational weeks 27 (2019), 17 (2020) and 23 (2020) respectively with complaints of vaginal irritation and discharge that had aggravated in all her pregnancies. Her vaginal microbiome composition showed a 90% dominance of Gardnerella spp. After one VMT there was a complete shift in microbiome composition to 81.2% L. crispatus and 9% L. jensenii with a concurrent resolvement of vaginal symptoms. Single nucleotide polymorphism-analysis confirmed her microbiome to be of donor origin and it remain stable now 1.5 years after the VMT. Five months after the VMT she became pregnant and has successfully delivered a healthy baby at term.

INTERPRETATION: Here we report a successful VMT with confirmed donor strain engraftment followed by a successful pregnancy and delivery after a series of late pregnancy losses/stillbirths. Findings suggest that VMT is a potential treatment for severe vaginal dysbiosis. Further, larger studies are required.

FUNDING: The study was partially funded (i.e., analysis costs) by Freya Biosciences Aps, Fruebjergvej, 2100 Copenhagen, Denmark.}, } @article {pmid37528534, year = {2023}, author = {Hu, X and Yu, L and Li, Y and Li, X and Zhao, Y and Xiong, L and Ai, J and Chen, Q and Wang, X and Chen, X and Ba, Y and Wang, Y and Wu, X}, title = {Piperine improves levodopa availability in the 6-OHDA-lesioned rat model of Parkinson's disease by suppressing gut bacterial tyrosine decarboxylase.}, journal = {CNS neuroscience & therapeutics}, volume = {}, number = {}, pages = {}, doi = {10.1111/cns.14383}, pmid = {37528534}, issn = {1755-5949}, support = {82173943//National Natural Science Foundation of China/ ; 81473333//National Natural Science Foundation of China/ ; }, abstract = {AIM: Tyrosine decarboxylase (TDC) presented in the gut-associated strain Enterococcus faecalis can convert levodopa (L-dopa) into dopamine (DA), and its increased abundance would potentially minimize the availability and efficacy of L-dopa. However, the known human decarboxylase inhibitors are ineffective in this bacteria-mediated conversion. This study aims to investigate the inhibition of piperine (PIP) on L-dopa bacterial metabolism and evaluates the synergistic effect of PIP combined with L-dopa on Parkinson's disease (PD).

METHODS: Metagenomics sequencing was adopted to determine the regulation of PIP on rat intestinal microbiota structure, especially on the relative abundance of E. faecalis. Then, the inhibitory effects of PIP on L-dopa conversion and TDC expression of E. faecalis were tested in vitro. We examined the synergetic effect of the combination of L-dopa and PIP on 6-hydroxydopamine (6-OHDA)-lesioned rats and tested the regulations of L-dopa bioavailability and brain DA level by pharmacokinetics study and MALDI-MS imaging. Finally, we evaluated the microbiota-dependent improvement effect of PIP on L-dopa availability using pseudo-germ-free and E. faecalis-transplanted rats.

RESULTS: We found that PIP combined with L-dopa could better ameliorate the move disorders of 6-OHDA-lesioned rats by remarkably improving L-dopa availability and brain DA level than L-dopa alone, which was associated with the effect of PIP on suppressing the bacterial decarboxylation of L-dopa via effectively downregulating the abnormal high abundances of E. faecalis and TDC in 6-OHDA-lesioned rats.

CONCLUSION: Oral administration of L-dopa combined with PIP can improve L-dopa availability and brain DA level in 6-OHDA-lesioned rats by suppressing intestinal bacterial TDC.}, } @article {pmid37528457, year = {2023}, author = {Hoedt, EC and Hueston, CM and Cash, N and Bongers, RS and Keane, JM and van Limpt, K and Ben Amor, K and Knol, J and MacSharry, J and van Sinderen, D}, title = {A synbiotic mixture of selected oligosaccharides and bifidobacteria assists murine gut microbiota restoration following antibiotic challenge.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {168}, pmid = {37528457}, issn = {2049-2618}, support = {SFI/12/RC/2273_P2/SFI_/Science Foundation Ireland/Ireland ; }, mesh = {Humans ; Infant ; Animals ; Pregnancy ; Mice ; Female ; *Synbiotics ; *Gastrointestinal Microbiome ; Bifidobacterium ; Anti-Bacterial Agents/pharmacology ; Cesarean Section ; Clindamycin ; Oligosaccharides ; }, abstract = {BACKGROUND: Typically, animal models studying gastrointestinal microbiotas compromised in early life have employed either germ-free animals or mice treated with a cocktail of antibiotics. Such studies intend to mimic scenarios of infants born by caesarean section and/or subjected to antibiotic treatment. However, the antibiotics used in these studies are rarely prescribed to infants. Therefore, an early life model was developed in which the murine gastrointestinal microbiota was severely disrupted by clindamycin treatment.

RESULTS: In this mouse model, we investigated the extent supplementation with a synbiotic mixture of prebiotics, being scGOS/lcFOS with the human milk oligosaccharide 2'-Fucosyllactose (2'-FL), in combination with or without single strain or mix of "infant type" bifidobacteria, can rescue an antibiotic-compromised microbiota. Shotgun metagenomic sequencing showed that the microbiota was severely disrupted by the clindamycin challenge. No recovery was observed 3 weeks post-challenge in the scGOS/lcFOS/2'FL group, while the group that received the synbiotic treatment of scGOS/lcFOS/2'-FL with Bifidobacterium breve NRBB01 showed partial recovery. Strikingly in the scGOS/lcFOS/2'-FL group receiving the mixture of bifidobacteria resulted in a recovery of the microbiota disruption. Histological analyses showed that the clindamycin-treated animals at the end of the experiment still suffered from mild oedema and villi/colonic crypt irregularities which was ameliorated by the synbiotic intervention.

CONCLUSION: Our study demonstrates that supplementation of synbiotic mixture of scGOS/lcFOS/2'-FL in combination with a specific mix of infant-type bifidobacterial strains is able to partially revive an antibiotic-perturbed gastrointestinal microbiota. Video Abstract.}, } @article {pmid37528343, year = {2023}, author = {Chopyk, J and Cobián Güemes, AG and Ramirez-Sanchez, C and Attai, H and Ly, M and Jones, MB and Liu, R and Liu, C and Yang, K and Tu, XM and Abeles, SR and Nelson, K and Pride, DT}, title = {Common antibiotics, azithromycin and amoxicillin, affect gut metagenomics within a household.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {206}, pmid = {37528343}, issn = {1471-2180}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Amoxicillin/pharmacology ; Azithromycin/pharmacology ; Metagenomics ; Macrolides/pharmacology ; Drug Resistance, Bacterial ; }, abstract = {BACKGROUND: The microbiome of the human gut serves a role in a number of physiological processes, but can be altered through effects of age, diet, and disturbances such as antibiotics. Several studies have demonstrated that commonly used antibiotics can have sustained impacts on the diversity and the composition of the gut microbiome. The impact of the two most overused antibiotics, azithromycin, and amoxicillin, in the human microbiome has not been thoroughly described. In this study, we recruited a group of individuals and unrelated controls to decipher the effects of the commonly used antibiotics amoxicillin and azithromycin on their gut microbiomes.

RESULTS: We characterized the gut microbiomes by metagenomic sequencing followed by characterization of the resulting microbial communities. We found that there were clear and sustained effects of the antibiotics on the gut microbial community with significant alterations in the representations of Bifidobacterium species in response to azithromycin (macrolide antibiotic). These results were supported by significant increases identified in putative antibiotic resistance genes associated with macrolide resistance. Importantly, we did not identify these trends in the unrelated control individuals. There were no significant changes observed in other members of the microbial community.

CONCLUSIONS: As we continue to focus on the role that the gut microbiome plays and how disturbances induced by antibiotics might affect our overall health, elucidating members of the community most affected by their use is of critical importance to understanding the impacts of common antibiotics on those who take them. Clinical Trial Registration Number NCT05169255. This trial was retrospectively registered on 23-12-2021.}, } @article {pmid37528259, year = {2023}, author = {Bermingham, KM and Stensrud, S and Asnicar, F and Valdes, AM and Franks, PW and Wolf, J and Hadjigeorgiou, G and Davies, R and Spector, TD and Segata, N and Berry, SE and Hall, WL}, title = {Exploring the relationship between social jetlag with gut microbial composition, diet and cardiometabolic health, in the ZOE PREDICT 1 cohort.}, journal = {European journal of nutrition}, volume = {62}, number = {8}, pages = {3135-3147}, pmid = {37528259}, issn = {1436-6215}, support = {/WT_/Wellcome Trust/United Kingdom ; 212904/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Male ; *Cardiovascular Diseases/complications ; Circadian Rhythm ; Diet ; *Gastrointestinal Microbiome ; Jet Lag Syndrome/complications ; Sleep ; }, abstract = {PURPOSE: In this study, we explore the relationship between social jetlag (SJL), a parameter of circadian misalignment, and gut microbial composition, diet and cardiometabolic health in the ZOE PREDICT 1 cohort (NCT03479866).

METHODS: We assessed demographic, diet, cardiometabolic, stool metagenomics and postprandial metabolic measures (n = 1002). We used self-reported habitual sleep (n = 934) to calculate SJL (difference in mid-sleep time point of ≥ 1.5 h on week versus weekend days). We tested group differences (SJL vs no-SJL) in cardiometabolic markers and diet (ANCOVA) adjusting for sex, age, BMI, ethnicity, and socio-economic status. We performed comparisons of gut microbial composition using machine learning and association analyses on the species level genome bins present in at least 20% of the samples.

RESULTS: The SJL group (16%, n = 145) had a greater proportion of males (39% vs 25%), shorter sleepers (average sleep < 7 h; 5% vs 3%), and were younger (38.4 ± 11.3y vs 46.8 ± 11.7y) compared to the no-SJL group. SJL was associated with a higher relative abundance of 9 gut bacteria and lower abundance of 8 gut bacteria (q < 0.2 and absolute Cohen's effect size > 0.2), in part mediated by diet. SJL was associated with unfavourable diet quality (less healthful Plant-based Diet Index), higher intakes of potatoes and sugar-sweetened beverages, and lower intakes of fruits, and nuts, and slightly higher markers of inflammation (GlycA and IL-6) compared with no-SJL (P < 0.05 adjusted for covariates); rendered non-significant after multiple testing adjustments.

CONCLUSIONS: Novel associations between SJL and a more disadvantageous gut microbiome in a cohort of predominantly adequate sleepers highlight the potential implications of SJL for health.}, } @article {pmid37528119, year = {2023}, author = {Liu, S and Li, Q and Jiang, R and Liu, P and Zhang, XX}, title = {Shift of human pathogen community composition and their potential human health risk after supply suspension in tap water.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12419}, pmid = {37528119}, issn = {2045-2322}, mesh = {Humans ; *Water Supply ; *Water ; Mycobacterium avium/genetics ; Pseudomonas aeruginosa/genetics ; Water Microbiology ; }, abstract = {Water supply suspension-restoration can occur frequently due to the overhauling of civil infrastructure in developing countries and the shutdown of commercial buildings during the pandemic. For comprehensive insights into the effects of water supply suspension-restoration, this study characterized the variations of the pathogen community composition of the tap water and their infection risk under different water supply scenarios. Metagenomic sequencing revealed a significant change of the human pathogen profiles, among which the most dominant pathogen changed from Pseudomonas aeruginosa (4.91%) to Acinetobacter johnsonii (0.59%). Furthermore, absolute quantification of pathogens by propidium-monoazide-qPCR revealed that the abundance of the three typical pathogens (Pseudomonas aeruginosa, Mycobacterium avium and Salmonella sp.) showed an increase of 2.44 log to 3.60 log immediately after water supply suspension-restoration and did not return to the normal level even after 2-h supply restoration, except for Pseudomonas aeruginosa. Quantitative microbial risk assessment suggested the infection risks of the three pathogens arising from direct utilization of tap water under stable water supply, including dermal exposure and oral intake, were all above the threshold of 10[-4], and evidently increased after water supply suspension-restoration. This study warns us against the risk induced by the pathogens in tap water, especially after water supply suspension-restoration.}, } @article {pmid37526383, year = {2023}, author = {Esteban-Torres, M and Ruiz, L and Rossini, V and Nally, K and van Sinderen, D}, title = {Intracellular glycogen accumulation by human gut commensals as a niche adaptation trait.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2235067}, pmid = {37526383}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Gastrointestinal Tract/microbiology ; Bacteria/genetics ; *Microbiota ; Glycogen/metabolism ; }, abstract = {The human gut microbiota is a key contributor to host metabolism and physiology, thereby impacting in various ways on host health. This complex microbial community has developed many metabolic strategies to colonize, persist and survive in the gastrointestinal environment. In this regard, intracellular glycogen accumulation has been associated with important physiological functions in several bacterial species, including gut commensals. However, the role of glycogen storage in shaping the composition and functionality of the gut microbiota offers a novel perspective in gut microbiome research. Here, we review what is known about the enzymatic machinery and regulation of glycogen metabolism in selected enteric bacteria, while we also discuss its potential impact on colonization and adaptation to the gastrointestinal tract. Furthermore, we survey the presence of such glycogen biosynthesis pathways in gut metagenomic data to highlight the relevance of this metabolic trait in enhancing survival in the highly competitive and dynamic gut ecosystem.}, } @article {pmid37525495, year = {2023}, author = {Bui, TVA and Hwangbo, H and Lai, Y and Hong, SB and Choi, YJ and Park, HJ and Ban, K}, title = {The Gut-Heart Axis: Updated Review for The Roles of Microbiome in Cardiovascular Health.}, journal = {Korean circulation journal}, volume = {53}, number = {8}, pages = {499-518}, pmid = {37525495}, issn = {1738-5520}, support = {/MSIT/Ministry of Science and ICT, South Korea/Korea ; 21A0104L1-11/MOHW/Ministry of Health and Welfare/Korea ; 21100818//Hong Kong Research Grants Council/Hong Kong ; //CityU Applied Research Grant/Hong Kong ; //TFBC project fund/Hong Kong ; }, abstract = {Cardiovascular diseases (CVDs), including coronary artery disease, stroke, heart failure, and hypertension, are the global leading causes of death, accounting for more than 30% of deaths worldwide. Although the risk factors of CVDs have been well understood and various treatment and preventive measures have been established, the mortality rate and the financial burden of CVDs are expected to grow exponentially over time due to the changes in lifestyles and increasing life expectancies of the present generation. Recent advancements in metagenomics and metabolomics analysis have identified gut microbiome and its associated metabolites as potential risk factors for CVDs, suggesting the possibility of developing more effective novel therapeutic strategies against CVD. In addition, increasing evidence has demonstrated the alterations in the ratio of Firmicutes to Bacteroidetes and the imbalance of microbial-dependent metabolites, including short-chain fatty acids and trimethylamine N-oxide, play a crucial role in the pathogenesis of CVD. However, the exact mechanism of action remains undefined to this day. In this review, we focus on the compositional changes in the gut microbiome and its related metabolites in various CVDs. Moreover, the potential treatment and preventive strategies targeting the gut microbiome and its metabolites are discussed.}, } @article {pmid37525231, year = {2023}, author = {Fu, Y and Zhang, K and Yang, M and Li, X and Chen, Y and Li, J and Xu, H and Dhakal, P and Zhang, L}, title = {Metagenomic analysis reveals the relationship between intestinal protozoan parasites and the intestinal microecological balance in calves.}, journal = {Parasites & vectors}, volume = {16}, number = {1}, pages = {257}, pmid = {37525231}, issn = {1756-3305}, support = {U1904203//Key Program of the National Natural Science Foundation of China-Henan Province Joint Fund/ ; 2022YFD1800200//National Key Research and Development Program of China/ ; 19CZ0122//Leading Talents of Thousand Talents Program of Central China/ ; }, mesh = {Animals ; Cattle ; *Parasites/genetics ; *Cryptosporidiosis/parasitology ; *Cryptosporidium/genetics ; Metagenome ; *Intestinal Diseases, Parasitic/veterinary ; *Giardiasis/veterinary/parasitology ; Giardia/genetics ; *Giardia lamblia/genetics ; *Blastocystis/genetics ; *Eimeria/genetics ; *Entamoeba/genetics ; Feces/parasitology ; Diarrhea/veterinary/parasitology ; }, abstract = {BACKGROUND: A close connection between a protozoan parasite and the balance of the other gut microbes of the host has been demonstrated. The calves may be naturally co-infected with many parasites, and the co-effects of parasites on other intestinal microbes of calves remain unclear. This study aims to preliminarily reveal the relationship between intestinal parasites and other intestinal microbes in calves.

METHODS: Fecal samples were collected from four calves with bloody diarrhea, four calves with watery diarrhea, and seven normal calves, and the microbial flora of the samples were analyzed by whole-genome sequencing. Protozoal parasites were detected in the metagenome sequences and identified using polymerase chain reaction (PCR).

RESULTS: Cryptosporidium, Eimeria, Giardia, Blastocystis, and Entamoeba were detected by metagenomic analysis, and the identified species were Giardia duodenalis assemblage E, Cryptosporidium bovis, Cryptosporidium ryanae, Eimeria bovis, Eimeria subspherica, Entamoeba bovis, and Blastocystis ST2 and ST10. Metagenomic analysis showed that the intestinal microbes of calves with diarrhea were disordered, especially in calves with bloody diarrhea. Furthermore, different parasites show distinct relationships with the intestinal microecology. Cryptosporidium, Eimeria, and Giardia were negatively correlated with various intestinal bacteria but positively correlated with some fungi. However, Blastocystis and Entamoeba were positively associated with other gut microbes. Twenty-seven biomarkers not only were significantly enriched in bloody diarrhea, watery diarrhea, and normal calves but were also associated with Eimeria, Cryptosporidium, and Giardia. Only Eimeria showed a distinct relationship with seven genera of bacteria, which were significantly enriched in the healthy calves. All 18 genera of fungi were positively correlated with Cryptosporidium, Eimeria, and Giardia, which were also significantly enriched in calves with bloody diarrhea. Functional genes related to parasites and diseases were found mainly in fungi.

CONCLUSIONS: This study revealed the relationship between intestinal protozoan parasites and the other calf gut microbiome. Different intestinal protozoan parasites have diametrically opposite effects on other gut microecology, which not only affects bacteria in the gut, but also is significantly related to fungi and archaea.}, } @article {pmid37525141, year = {2023}, author = {Oliveros, A and Terraube, J and Levengood, AL and Powell, D and Frère, CH}, title = {Influence of scat ageing on the gut microbiome: how old is too old?.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {427}, pmid = {37525141}, issn = {1471-2164}, mesh = {Animals ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Microbiota ; Animals, Wild ; *Phascolarctidae ; }, abstract = {BACKGROUND: The study of the host-microbiome by the collection of non-invasive samples has the potential to become a powerful tool for conservation monitoring and surveillance of wildlife. However, multiple factors can bias the quality of data recovered from scats, particularly when field-collected samples are used given that the time of defecation is unknown. Previous studies using scats have shown that the impact of aerobic exposure on the microbial composition is species-specific, leading to different rates of change in microbial communities. However, the impact that this aging process has on the relationship between the bacterial and fungal composition has yet to be explored. In this study, we measured the effects of time post-defecation on bacterial and fungal compositions in a controlled experiment using scat samples from the endangered koala (Phascolarctos cinereus).

RESULTS: We found that the bacterial composition remained stable through the scat aging process, while the fungal composition did not. The absence of an increase in facultative anaerobes and the stable population of obligate anaerobic bacteria were likely due to our sampling from the inner portion of the scat. We report a cluster of fungal taxa that colonises scats after defecation which can dilute the genetic material from the autochthonous mycoflora and inhibit recovery.

CONCLUSION: We emphasize the need to preserve the integrity of scat samples collected in the wild and combat the effects of time and provide strategies for doing so.}, } @article {pmid37525113, year = {2023}, author = {Dai, J and Yao, C and Ling, H and Li, B and Chen, R and Shi, F}, title = {A rare case of severe leptospirosis infection presenting as septic shock in a non-endemic area: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {503}, pmid = {37525113}, issn = {1471-2334}, support = {2022A1515220169//Enterprises and the Basic and applied Basic Research Foundation of Guangdong Province/ ; 2022A1515220169//Enterprises and the Basic and applied Basic Research Foundation of Guangdong Province/ ; 2022A1515220169//Enterprises and the Basic and applied Basic Research Foundation of Guangdong Province/ ; 2022A1515220169//Enterprises and the Basic and applied Basic Research Foundation of Guangdong Province/ ; 2022A1515220169//Enterprises and the Basic and applied Basic Research Foundation of Guangdong Province/ ; 2022A1515220169//Enterprises and the Basic and applied Basic Research Foundation of Guangdong Province/ ; }, mesh = {Male ; Animals ; Humans ; Middle Aged ; *Shock, Septic/diagnosis/etiology ; *Leptospirosis/complications/diagnosis/drug therapy ; Zoonoses ; *Leptospira/genetics ; Hemorrhage ; *Thrombocytopenia/diagnosis ; }, abstract = {BACKGROUND: Leptospirosis is a zoonosis caused by spirochete "genus" leptospira. The clinical presentations of leptospirosis range from an influenza-like presentation of fever and myalgia, to severe forms. Leptospirosis can potentially lead to a misdiagnosis or delay in diagnosis when clinical similarities exist.

CASE PRESENTATION: A 63-year-old man presented with fever, shock and thrombocytopenia followed by diffuse pulmonary hemorrhage. Peripheral blood Metagenomic Next-generation Sequencing (mNGS) reported Leptospira interrogans. The patient was treated with piperacillin-tazobactam (TZP) plus doxycycline and improved dramatically after 7 days.

CONCLUSION: We conclude that leptospirosis can potentially lead to a misdiagnosis or delay in diagnosis. Correctly evaluation of thrombocytopenia in acute febrile illnesses facilitates the differential diagnosis of leptospirosis. mNGS can accurately detect Leptospira DNA during the early stage of the infection.}, } @article {pmid37524909, year = {2023}, author = {Chen, T and Liu, T and Wu, Z and Wang, B and Chen, Q and Zhang, M and Liang, E and Ni, J}, title = {Virus-pathogen interactions improve water quality along the Middle Route of the South-to-North Water Diversion Canal.}, journal = {The ISME journal}, volume = {17}, number = {10}, pages = {1719-1732}, pmid = {37524909}, issn = {1751-7370}, mesh = {Humans ; Water Quality ; Environment ; *Virus Diseases ; *Viruses/genetics ; Bacteria/genetics ; Phosphorus/analysis ; China ; }, abstract = {Bacterial pathogens and viruses are the leading causes of global waterborne diseases. Here, we discovered an interesting natural paradigm of water "self-purification" through virus-pathogen interactions over a 1432 km continuum along the Middle Route of the South-to-North Water Diversion Canal (MR-SNWDC) in China, the largest water transfer project in the world. Due to the extremely low total phosphorus (TP) content (ND-0.02 mg/L) in the MR-SNWDC, the whole canal has experienced long-lasting phosphorus (P) limitation since its operation in 2015. Based on 4443 metagenome-assembled genomes (MAGs) and 40,261 nonredundant viral operational taxonomic units (vOTUs) derived from our recent monitoring campaign, we found that residential viruses experiencing extreme P constraints had to adopt special adaptive strategies by harboring smaller genomes to minimize nucleotide replication, DNA repair, and posttranslational modification costs. With the decreasing P supply downstream, bacterial pathogens showed repressed environmental fitness and growth potential, and a weakened capacity to maintain P acquisition, membrane formation, and ribonucleotide biosynthesis. Consequently, the unique viral predation effects under P limitation, characterized by enhanced viral lytic infections and an increased abundance of ribonucleotide reductase (RNR) genes linked to viral nuclear DNA replication cycles, led to unexpectedly lower health risks from waterborne bacterial pathogens in the downstream water-receiving areas. These findings highlighted the great potential of water self-purification associated with virus-pathogen dynamics for water-quality improvement and sustainable water resource management.}, } @article {pmid37524805, year = {2023}, author = {Leiva, C and Pérez-Sorribes, L and González-Delgado, S and Ortiz, S and Wangensteen, OS and Pérez-Portela, R}, title = {Exceptional population genomic homogeneity in the black brittle star Ophiocomina nigra (Ophiuroidea, Echinodermata) along the Atlantic-Mediterranean coast.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {12349}, pmid = {37524805}, issn = {2045-2322}, mesh = {Humans ; Animals ; *Echinodermata/genetics ; *Metagenomics ; Genetic Drift ; Genomics ; Genetic Variation ; Genetics, Population ; }, abstract = {The Atlantic-Mediterranean marine transition is characterised by strong oceanographic barriers and steep environmental gradients that generally result in connectivity breaks between populations from both basins and may lead to local adaptation. Here, we performed a population genomic study of the black brittle star, Ophiocomina nigra, covering most of its distribution range along the Atlantic-Mediterranean region. Interestingly, O. nigra is extremely variable in its coloration, with individuals ranging from black to yellow-orange, and different colour morphs inhabiting different depths and habitats. In this work, we used a fragment of the mitochondrial COI gene and 2,374 genome-wide ddRADseq-derived SNPs to explore: (a) whether the different colour morphs of O. nigra represent different evolutionary units; (b) the disruptive effects of major oceanographic fronts on its population structure; and (c) genomic signals of local adaptation to divergent environments. Our results revealed exceptional population homogeneity, barely affected by oceanographic fronts, with no signals of local adaptation nor genetic differentiation between colour morphs. This remarkable panmixia likely results from a long pelagic larval duration, a large effective population size and recent demographic expansions. Our study unveils an extraordinary phenotypic plasticity in O. nigra, opening further research questions on the ecological and molecular mechanisms underpinning coloration in Ophiuroidea.}, } @article {pmid37524802, year = {2023}, author = {Garner, RE and Kraemer, SA and Onana, VE and Fradette, M and Varin, MP and Huot, Y and Walsh, DA}, title = {A genome catalogue of lake bacterial diversity and its drivers at continental scale.}, journal = {Nature microbiology}, volume = {8}, number = {10}, pages = {1920-1934}, pmid = {37524802}, issn = {2058-5276}, mesh = {Humans ; *Lakes/microbiology ; RNA, Ribosomal, 16S/genetics ; Canada ; Bacteria/genetics ; *Microbiota/genetics ; }, abstract = {Lakes are heterogeneous ecosystems inhabited by a rich microbiome whose genomic diversity is poorly defined. We present a continental-scale study of metagenomes representing 6.5 million km[2] of the most lake-rich landscape on Earth. Analysis of 308 Canadian lakes resulted in a metagenome-assembled genome (MAG) catalogue of 1,008 mostly novel bacterial genomospecies. Lake trophic state was a leading driver of taxonomic and functional diversity among MAG assemblages, reflecting the responses of communities profiled by 16S rRNA amplicons and gene-centric metagenomics. Coupling the MAG catalogue with watershed geomatics revealed terrestrial influences of soils and land use on assemblages. Agriculture and human population density were drivers of turnover, indicating detectable anthropogenic imprints on lake bacteria at the continental scale. The sensitivity of bacterial assemblages to human impact reinforces lakes as sentinels of environmental change. Overall, the LakePulse MAG catalogue greatly expands the freshwater genomic landscape, advancing an integrative view of diversity across Earth's microbiomes.}, } @article {pmid37524773, year = {2023}, author = {Wang, Z and Zhang, X and Lei, W and Zhu, H and Wu, S and Liu, B and Ru, D}, title = {Chromosome-level genome assembly and population genomics of Robinia pseudoacacia reveal the genetic basis for its wide cultivation.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {797}, pmid = {37524773}, issn = {2399-3642}, mesh = {*Ecosystem ; *Robinia/genetics ; Metagenomics ; Trees ; Chromosomes ; }, abstract = {Urban greening provides important ecosystem services and ideal places for urban recreation and is a serious consideration for municipal decision-makers. Among the tree species cultivated in urban green spaces, Robinia pseudoacacia stands out due to its attractive flowers, fragrances, high trunks, wide adaptability, and essential ecosystem services. However, the genomic basis and consequences of its wide-planting in urban green spaces remains unknown. Here, we report the chromosome-level genome assembly of R. pseudoacacia, revealing a genome size of 682.4 Mb and 33,187 protein-coding genes. More than 99.3% of the assembly is anchored to 11 chromosomes with an N50 of 59.9 Mb. Comparative genomic analyses among 17 species reveal that gene families related to traits favoured by urbanites, such as wood formation, biosynthesis, and drought tolerance, are notably expanded in R. pseudoacacia. Our population genomic analyses further recover 11 genes that are under recent selection. Ultimately, these genes play important roles in the biological processes related to flower development, water retention, and immunization. Altogether, our results reveal the evolutionary forces that shape R. pseudoacacia cultivated for urban greening. These findings also present a valuable foundation for the future development of agronomic traits and molecular breeding strategies for R. pseudoacacia.}, } @article {pmid37524645, year = {2023}, author = {Zhang, L and Zhou, M and Lv, W and Li, T and Xu, Y and Liu, Z}, title = {Metagenomics assists in the diagnosis of a refractory, culture-negative pyoderma gangrenosum-like ulcer caused by Helicobacter cinaedi in a patient with primary agammaglobulinemia.}, journal = {Journal of microbiology, immunology, and infection = Wei mian yu gan ran za zhi}, volume = {56}, number = {6}, pages = {1284-1287}, doi = {10.1016/j.jmii.2023.07.001}, pmid = {37524645}, issn = {1995-9133}, mesh = {Humans ; *Pyoderma Gangrenosum/diagnosis/drug therapy/complications ; Ulcer/complications ; *Agammaglobulinemia/complications/diagnosis ; *Helicobacter Infections/diagnosis/drug therapy ; Metagenomics ; }, abstract = {Helicobacter cinaedi is known to cause various infections in immunocompromised hosts ranging from skin lesions to disseminated septicemia. Identification of H. cinaedi is difficult through conventional identification methods due to its fastidious nature. We reported a refractory and culture-negative pyoderma gangrenosum-like ulcer caused by H. cinaedi in a patient with primary agammaglobulinemia. Metagenomic next-generation sequencing (mNGS) was applied for the identification of H. cinaedi and prolonged minocycline and amoxicillin-clavulanate potassium was used to eradicate the infection. Given the difficulties in culturing this organism, it's highly possible that H cinaedi infections have been overlooked. We suggest that early consideration of H. cinaedi infection should be suspected in immunocompromised patients presenting with unexplained skin lesions as the appropriate antibiotic choice plus a prolonged treatment course is essential for the prognosis. Application of mNGS could contribute to the early identification of rare and cryptogenic pathogens.}, } @article {pmid37524154, year = {2023}, author = {Yan, J and Duan, W and Gao, Q and Mao, T and Wang, M and Duan, J and Li, J}, title = {ENPP2 inhibitor improves proliferation in AOM/DSS-induced colorectal cancer mice via remodeling the gut barrier function and gut microbiota composition.}, journal = {Pharmacological research}, volume = {195}, number = {}, pages = {106877}, doi = {10.1016/j.phrs.2023.106877}, pmid = {37524154}, issn = {1096-1186}, mesh = {Animals ; Mice ; Azoxymethane/adverse effects ; Cell Proliferation ; Colitis/chemically induced ; *Colorectal Neoplasms/drug therapy/metabolism ; Dextran Sulfate/pharmacology ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; *Phosphoric Diester Hydrolases/metabolism ; }, abstract = {In our previous multicenter study, we delineated the inherent metabolic features of colorectal cancer (CRC). Therein, we identified a member of the ectonucleotide pyrophosphatase/ phosphodiesterase family (ENPP2) as a significant differential metabolite of CRC. In this study, the role of ENPP2 in CRC has been demonstrated using established in vitro and in vivo models including ENPP2 gene knockdown, and use of the ENPP2 inhibitor, GLPG1690. We found that CRC proliferation was decreased after either ENPP2 gene knockdown or use of ENPP2 inhibitors. We further evaluated the role of GLPG1690 in AOM/DSS-induced CRC mice via intestinal barrier function, macrophage polarization, inflammatory response and microbial homeostasis. Results of immunofluorescence staining and Western blotting showed that GLPG1690 can restore gut-barrier function by increasing the expression of tight junction proteins, claudin-1, occludin and ZO-1. M2 tumor-associated macrophage polarization and colonic inflammation were attenuated after treatment with GLPG1690 using the Azoxymethane/Dextran Sodium Sulfate (AOM/DSS) model. Moreover, 16 S rDNA pyrosequencing and metagenomic analysis showed that GLPG1690 could alleviate gut dysbiosis in mice. Furthermore, administration of GLPG1690 with antibiotics as well as fecal microbiota transplantation assays demonstrated a close link between the efficacy of GLPG1690 and the gut microbiota composition. Finally, results of metabolomic analysis implicated mainly the gut microbiota-derived metabolites of aromatic amino acids in CRC progression. These findings may provide novel insights into the development of small-molecule ENPP2 inhibitors for the treatment of CRC.}, } @article {pmid37523923, year = {2023}, author = {Wan, R and Ge, L and Chen, B and Tang, JM and Tan, E and Zou, W and Tian, L and Li, M and Liu, Z and Hou, L and Yin, G and Kao, SJ}, title = {Permeability decides the effect of antibiotics on sedimentary nitrogen removal in Jiulong River Estuary.}, journal = {Water research}, volume = {243}, number = {}, pages = {120400}, doi = {10.1016/j.watres.2023.120400}, pmid = {37523923}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents ; *Nitrogen/analysis ; Denitrification ; Estuaries ; Permeability ; Geologic Sediments ; }, abstract = {Sedimentary denitrification takes place beneath the oxic layer at the sediment-water interface, where nitrate and antibiotics need to diffuse through the overlying water. However, the antibiotics' effect on sedimentary N removal and associated N2O production has not been adequately investigated under in situ conditions. Here, isotope pairing techniques, including slurry incubations (potential) and intact core incubations (in situ), combined with metagenomic analysis were applied to investigate the impacts of two protein-inhibiting antibiotics (oxytetracycline and thiamphenicol) on sediment nitrogen removal in a subtropical estuary. Slurry incubations showed that the two antibiotics significantly inhibited denitrification (67-98%) and anammox (49-99%), while intact core incubations presented no antibiotic effect at upstream but significant inhibition (23%-52%) at downstream. Meanwhile, N2O yields were stimulated up to 20 folds in slurry incubations yet showing insignificant response in intact cores. Such contrasting results between up- and down-stream and between slurry and intact core incubations strongly indicated that permeability, which determines diffusion of antibiotics to microbes, is the key to exert the effect of antibiotics on in situ sedimentary nitrogen removal processes regardless the existence of antibiotics resistance genes. This diffusive obstruction may mitigate the toxic effect of antibiotics on nitrogen removal related microbes in natural environments.}, } @article {pmid37523919, year = {2023}, author = {Zhu, Q and Qian, D and Yuan, M and Li, Z and Xu, Z and Liang, S and Yu, W and Yuan, S and Yang, J and Hou, H and Hu, J}, title = {Revealing the roles of chemical communication in restoring the formation and electroactivity of electrogenic biofilm under electrical signaling disruption.}, journal = {Water research}, volume = {243}, number = {}, pages = {120421}, doi = {10.1016/j.watres.2023.120421}, pmid = {37523919}, issn = {1879-2448}, mesh = {*Biofilms ; *Quorum Sensing/physiology ; Bacterial Proteins/genetics ; Gene Expression Regulation, Bacterial ; }, abstract = {Electrogenic biofilms in microbial electrochemical systems have played significant roles in simultaneous wastewater treatment and energy recovery owing to their unique extracellular electron transfer. Their formation has been shown to be regulated by electrical and chemical communication, but the interaction between these signal communication pathways has not been studied. This research investigated the coordination between intracellular c-di-GMP signaling and reinforced quorum sensing with or without exogenous HSL (a common quorum sensing molecule), on the formation of mixed-cultured electrogenic biofilm under electrical signaling disruption by tetraethylammonium (TEA, a broad-range potassium channel blocker). Intracellular c-di-GMP was spontaneously reinforced in response to TEA stress, and metagenomic analysis revealed that the dominant DGC (the genes for producing c-di-GMP) induced the eventual biofilm formation by mediating exopolysaccharide synthesis. Meanwhile, reinforced quorum sensing by exogenous HSL could also benefit the biofilm restoration, however, it alleviated the TEA-induced communication stress, resulting in the weakening of c-di-GMP dominance. Interestingly, suppressing electrical communication with or without HSL addition both induced selective enrichment of Geobacter of 85.5% or 30.1% respectively. Functional contribution analysis revealed the significant roles of Geobacter and Thauera in c-di-GMP signaling, especially Thauera in resistance to TEA stress. This study proposed a potential strategy for electrogenic biofilm regulation from the perspectives of cell-to-cell communication.}, } @article {pmid37522759, year = {2022}, author = {Salazar, VW and Shaban, B and Quiroga, MDM and Turnbull, R and Tescari, E and Rossetto Marcelino, V and Verbruggen, H and Lê Cao, KA}, title = {Metaphor-A workflow for streamlined assembly and binning of metagenomes.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {37522759}, issn = {2047-217X}, mesh = {*Metagenome ; *Metaphor ; Workflow ; Algorithms ; Cluster Analysis ; }, abstract = {Recent advances in bioinformatics and high-throughput sequencing have enabled the large-scale recovery of genomes from metagenomes. This has the potential to bring important insights as researchers can bypass cultivation and analyze genomes sourced directly from environmental samples. There are, however, technical challenges associated with this process, most notably the complexity of computational workflows required to process metagenomic data, which include dozens of bioinformatics software tools, each with their own set of customizable parameters that affect the final output of the workflow. At the core of these workflows are the processes of assembly-combining the short-input reads into longer, contiguous fragments (contigs)-and binning, clustering these contigs into individual genome bins. The limitations of assembly and binning algorithms also pose different challenges depending on the selected strategy to execute them. Both of these processes can be done for each sample separately or by pooling together multiple samples to leverage information from a combination of samples. Here we present Metaphor, a fully automated workflow for genome-resolved metagenomics (GRM). Metaphor differs from existing GRM workflows by offering flexible approaches for the assembly and binning of the input data and by combining multiple binning algorithms with a bin refinement step to achieve high-quality genome bins. Moreover, Metaphor generates reports to evaluate the performance of the workflow. We showcase the functionality of Metaphor on different synthetic datasets and the impact of available assembly and binning strategies on the final results.}, } @article {pmid37522175, year = {2023}, author = {Li, LQ and He, Y and Liu, T and Zhou, J and Chen, EQ}, title = {Fever of unknown origin and splenomegaly: a case report of visceral leishmaniasis diagnosed by metagenomic next-generation sequencing.}, journal = {Future microbiology}, volume = {18}, number = {}, pages = {699-705}, doi = {10.2217/fmb-2023-0038}, pmid = {37522175}, issn = {1746-0921}, mesh = {Humans ; *Leishmaniasis, Visceral/diagnosis/drug therapy/epidemiology ; Splenomegaly/diagnosis ; *Fever of Unknown Origin ; *Leishmania ; High-Throughput Nucleotide Sequencing ; }, abstract = {Visceral leishmaniasis (VL) is a parasitic disease caused by Leishmania spp., which is transmitted by sandflies. As China is not the main epidemic area and VL has complex and atypical clinical manifestations, it is easily misdiagnosed or even missed in clinical practice. Without prompt and efficient treatment, the mortality rate of VL is extremely high; therefore early diagnosis of VL is crucial. Herein we describe a case of fever and splenomegaly of unknown origin, which was finally diagnosed as VL by metagenomic next-generation sequencing.}, } @article {pmid37522054, year = {2023}, author = {Cheng, J and Zeng, D and Zhang, T and Zhang, L and Han, X and Zhou, P and Wang, L and He, J and Han, Q}, title = {Microascus cirrosus SZ 2021: A potentially new genotype of Microascus cirrosus, which can cause fatal pulmonary infection in patients with acute leukemia following haplo‑HSCT.}, journal = {Experimental and therapeutic medicine}, volume = {26}, number = {2}, pages = {404}, pmid = {37522054}, issn = {1792-1015}, abstract = {Uncommon Microascus cirrosus (M. cirrosus) species have been reported to cause an increasing number of subcutaneous and invasive fungal infections worldwide; since the first human infection was reported in 1992, seven cases have been reported in PubMed. The present study reports a novel genotype named M. cirrosus SZ 2021 isolated from a patient undergoing hematopoietic stem cell transplantation, who exhibited extensive drug resistance and suffered a fatal pulmonary infection. This isolated M. cirrosus was cultured and determined by morphological observation, multi-locus sequence typing, matrix-assisted laser desorption and ionization time-of-flight mass spectrometry, and whole genome sequencing by next-generation sequencing. The whole nucleotide sequence (32.61 Mb) has been uploaded in the NCBI database (PRJNA835605). In addition, M. cirrosus SZ 2021 was not sensitive to the commonly used antifungal drugs, including fluconazole, amphotericin B, 5-flucytosine and caspofungin. The current literature on human infections by M. cirrosus was reviewed to closely define the comprehensive clinical characteristics and etiological identification. In brief, the present study identified a new M. cirrosus and summarized the clinical characteristics of fungal pneumonia by M. cirrosus species. Complete laboratory identification methods from morphology to gene sequencing were also established for an improved etiological identification and further investigation into the real prevalence of invasive pneumonia by M. cirrosus.}, } @article {pmid37521665, year = {2023}, author = {Thakur, M and Rai, AK and Singh, SP}, title = {Structural Characteristics, Physicochemical Properties, and Digestibility Analysis of Resistant Starch Type-V Prepared from Debranched Corn Starch and Fatty Acid Complexation.}, journal = {ACS omega}, volume = {8}, number = {29}, pages = {25799-25807}, pmid = {37521665}, issn = {2470-1343}, abstract = {Corn starch was gelatinized and treated with a metagenomic type 1 pullulanase (PulM), increasing the proportion of linear glucan chains. The debranched corn starch (DCS), containing amylose helices, was subjected to complexation with fatty acid molecules at moderate temperatures (50-60 °C). The amylose-lipid complexes prepared using saturated fatty acids, e.g., capric acid (CA) and lauric acid (LA), displayed higher CI values as compared to that of unsaturated fatty acid compounds, e.g., undecylenic acids (UAs) and oleic acid (OA). The DCS-fatty acid complex was estimated to contain about 14% of rapidly digested starch (RDS), 26% of slowly digested starch (SDS), and 60% of resistant starch V (RS-5). RS-5 samples exhibited high resistance toward digestive enzymatic hydrolysis. The surface microdetails of RS-5 were examined by scanning electron microscopy (SEM), depicting small spherulite-like structural aggregates. X-ray diffraction pattern analysis estimated about 46% of the crystallinity of RS-5. Thermal attributes of RS-5 were examined by thermogravimetric analysis (TGA) and differential scanning calorimetry (DSC) analysis, depicting the increase in melting enthalpies after the complexation of fatty acid molecules with debranched corn starch. Comparative DSC thermograms divulged a relatively higher stability of RS-5 as compared to that of RS-3. The findings advocated the potentiality of RS-5 (nondigestible DCS-LA complex) as a functional, valuable ingredient in the food industry.}, } @article {pmid37521121, year = {2023}, author = {Khatiebi, S and Kiprotich, K and Onyando, Z and Wekesa, C and Chi, CN and Mulambalah, C and Okoth, P}, title = {Shotgun Metagenomic Analyses of Microbial Assemblages in the Aquatic Ecosystem of Winam Gulf of Lake Victoria, Kenya Reveals Multiclass Pollution.}, journal = {BioMed research international}, volume = {2023}, number = {}, pages = {3724531}, pmid = {37521121}, issn = {2314-6141}, mesh = {Animals ; Humans ; Lakes ; Ecosystem ; Kenya ; Plastics ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring ; *Microbiota/genetics ; Water ; Pharmaceutical Preparations ; }, abstract = {Lake Victoria, the second-largest freshwater lake in the world, provides an important source of food and income, particularly fish for both domestic consumption and for export market. In recent years, Lake Victoria has suffered massive pollution from both industrial and wastewater discharge. Microplastic biomes, pharmaceutical residues, drugs of abuse, heavy metals, agrochemicals, and personal care products are ubiquitous in the aquatic ecosystem of Winam Gulf. These pollutants are known to alter microbial assemblages in aquatic ecosystems with far-reaching ramification including a calamitous consequence to human health. Indeed, some of these pollutants have been associated with human cancers and antimicrobial resistance. There is a paucity of data on the microbial profiles of this important but heavily polluted aquatic ecosystem. The current study sought to investigate the metagenomic profiles of microbial assemblages in the Winam Gulf ecosystem. Water and sediment samples were collected from several locations within the study sites. Total genomic DNA pooled from all sampling sites was extracted and analyzed by whole-genome shotgun sequencing. Analyses revealed three major kingdoms: bacteria, archaea and eukaryotes belonging to 3 phyla, 13 classes, 14 families, 9 orders, 14 genera, and 10 species. Proteobacteria, Betaproteobacteria, Comamonadaceae, Burkholdariales, and Arcobacter were the dominated phyla, class, family, order, genera, and species, respectively. The Kyoto Encyclopedia of Genes and Genomes indicated the highest number of genes involved in metabolism. The presence of carbohydrate metabolism genes and enzymes was used to infer organic pollutions from sewage and agricultural runoffs. Similarly, the presence of xylene and nutrotoluene degradation genes and enzyme was used to infer industrial pollution into the lake. Drug metabolism genes lend credence to the possibility of pharmaceutical pollutants in water. Taken together, there is a clear indication of massive pollution. In addition, carbohydrate-active enzymes were the most abundant and included genes in glycoside hydrolases. Shotgun metagenomic analyses conveyed an understanding of the microbial communities of the massively polluted aquatic ecosystem of Winam Gulf, Lake Vicoria, Kenya. The current study documents the presence of multiclass pollutants in Lake Victoria and reveals information that might be useful for a potential bioremediation strategy using the native microbial communities.}, } @article {pmid37520955, year = {2023}, author = {Kane, Y and Chen, J and Li, L and Descorps-Declère, S and Wong, G and Berthet, N}, title = {Diverse single-stranded DNA viruses from viral metagenomics on a cynopterus bat in China.}, journal = {Heliyon}, volume = {9}, number = {8}, pages = {e18270}, pmid = {37520955}, issn = {2405-8440}, abstract = {Bats serve as reservoirs for many emerging viruses. Cressdnaviruses can infect a wide range of animals, including agricultural species, such as pigs, in which porcine circoviruses cause severe gastroenteritis. New cressdnaviruses have also attracted considerable attention recently, due to their involvement with infectious diseases. However, little is known about their host range and many cressdnaviruses remain poorly characterized. We identified and characterized 11 contigs consisting of previously unknown cressdnaviruses from a rectal swab sample of a Cynopterus bat collected in Yunnan Province, China, in 2011. Full genomes of two cressdnaviruses (OQ267680, 2069 nt; OQ351951, 2382 nt), and a nearly complete genome for a third (OQ267683, 2361 nt) were obtained. Phylogenetic analyses and the characteristics of these viral genomes suggest a high degree of ssDNA virus diversity. These results shed light on cressdnavirus diversity and the probable role of Cynopterus bats as their hosts.}, } @article {pmid37520848, year = {2023}, author = {Mengyi, Z and Yuhui, L and Zhan, G and Anqing, L and Yujia, L and Shilin, L and Lei, G and Yue, L and Mei, H and Jianhua, W and Weilan, H and Wei, M and Jie, C and Jingyu, Z and Yijing, Y and Yanli, G and Qiulei, Z and Yang, H and Limin, C and Zhenxin, F and Miao, H}, title = {Plasma metagenomics reveals regional variations of emerging and re-emerging pathogens in Chinese blood donors with an emphasis on human parvovirus B19.}, journal = {One health (Amsterdam, Netherlands)}, volume = {17}, number = {}, pages = {100602}, pmid = {37520848}, issn = {2352-7714}, abstract = {At present, many infectious pathogens, especially emerging/re-emerging pathogens, exist in the blood of voluntary blood donors and may be transmitted through blood transfusions. However, most of Chinese blood centers only routinely screen for HBV, HCV, HIV, and syphilis. We employed metagenomic next-generation sequencing (mNGS) to investigate the microbiome in healthy voluntary blood donors to help assess blood safety in China by identifying infectious pathogens presented in donations that could lead to transfusion-acquired infections. We collected 10,720 plasma samples from voluntary blood donors from seven blood centers in different cities during 2012-2018 in China. A total of 562 GB of clean data was obtained. By analyzing the sequencing data, it was found that the most commonly identified bacteria found in the healthy blood were Serratia spp. (5.0176%), Pseudomonas spp. (0.6637%), and Burkholderia spp. (0.5544%). The principal eukaryote were Leishmania spp (1.3723%), Toxoplasma gondii (0.6352%), and Candida dubliniensis (0.1848%). Among viruses, Human Parvovirus B19 (B19V) accounts for the highest proportion (0.1490%), followed by Torque teno midi virus (0.0032%) and Torque teno virus (0.0015%). Since that B19V is a non-negligible threat to blood safety, we evaluated the positive samples for B19V tested by mNGS using quantitative polymerase chain reaction, Sanger sequencing, and phylogenetic analysis to achieve a better understanding of B19V in Chinese blood donors. Subsequently, 9 (0.07%) donations were positive for B19V DNA. The quantitative DNA levels ranged from 5.58 × 10[2] to 7.24 × 10[4] IU/ml. The phylogenic analyses showed that prevalent genotypes belonged to the B19-1A subtype, which disclosed previously unknown regional variability in the B19V positivity rate. The investigation revealed that many microbes dwell in the blood of healthy donors, including some pathogens that may be dormant in the blood and only cause disease under specific conditions. Thus, investigating the range and nature of potential pathogens in the qualified donations provided a framework for targeted interventions to help prevent emerging and re-emerging infectious diseases.}, } @article {pmid37520380, year = {2023}, author = {Menon, R and Khanipov, K and Radnaa, E and Ganguly, E and Bento, GFC and Urrabaz-Garza, R and Kammala, AK and Yaklic, J and Pyles, R and Golovko, G and Tantengco, OAG}, title = {Amplification of microbial DNA from bacterial extracellular vesicles from human placenta.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1213234}, pmid = {37520380}, issn = {1664-302X}, abstract = {INTRODUCTION: The placenta is essential for fetal growth and survival and maintaining a successful pregnancy. The sterility of the placenta has been challenged recently; however, the presence of a placental microbiome has been controversial. We tested the hypothesis that the bacterial extracellular vesicles (BEVs) from Gram-negative bacteria as an alternate source of microbial DNA, regardless of the existence of a microbial community in the placenta.

METHODS: Placentae from the term, not in labor Cesareans deliveries, were used for this study, and placental specimens were sampled randomly from the fetal side. We developed a protocol for the isolation of BEVs from human tissues and this is the first study to isolate the BEVs from human tissue and characterize them.

RESULTS: The median size of BEVs was 130-140 nm, and the mean concentration was 1.8-5.5 × 10[10] BEVs/g of the wet placenta. BEVs are spherical and contain LPS and ompA. Western blots further confirmed ompA but not human EVs markers ALIX confirming the purity of preparations. Taxonomic abundance profiles showed BEV sequence reads above the levels of the negative controls (all reagent controls). In contrast, the sequence reads in the same placenta were substantially low, indicating nothing beyond contamination (low biomass). Alpha-diversity showed the number of detected genera was significantly higher in the BEVs than placenta, suggesting BEVs as a likely source of microbial DNA. Beta-diversity further showed significant overlap in the microbiome between BEV and the placenta, confirming that BEVs in the placenta are likely a source of microbial DNA in the placenta. Uptake studies localized BEVs in maternal (decidual) and placental cells (cytotrophoblast), confirming their ability to enter these cells. Lastly, BEVs significantly increased inflammatory cytokine production in THP-1 macrophages in a high-dose group but not in the placental or decidual cells.

CONCLUSION: We conclude that the BEVs are normal constituents during pregnancy and likely reach the placenta through hematogenous spread from maternal body sites that harbor microbiome. Their presence may result in a low-grade localized inflammation to prime an antigen response in the placenta; however, insufficient to cause a fetal inflammatory response and adverse pregnancy events. This study suggests that BEVs can confound placental microbiome studies, but their low biomass in the placenta is unlikely to have any immunologic impact.}, } @article {pmid37520368, year = {2023}, author = {Islam, T and Fatema, and Hoque, MN and Gupta, DR and Mahmud, NU and Sakif, TI and Sharpe, AG}, title = {Improvement of growth, yield and associated bacteriome of rice by the application of probiotic Paraburkholderia and Delftia.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1212505}, pmid = {37520368}, issn = {1664-302X}, abstract = {Plant probiotic bacteria enhance growth and yield of crop plants when applied at the appropriate time and dose. Two rice probiotic bacteria, Paraburkholderia fungorum strain BRRh-4 and Delftia sp. strain BTL-M2 promote growth and yield of plants. However, no information is available on application of these two bacteria on growth, yield, and diversity and population of bacteriome in roots and rhizosphere soils of the treated rice plants. This study aimed to assess the effect of BRRh-4 and BTL-M2 application on growth, yield and bacteriome in roots and rhizosphere soil of rice under varying doses of N, P and K fertilizers. Application of BRRh-4 and BTL-M2 strains significantly (p < 0.05) increased seed germination, growth and yield of rice compared to an untreated control. Interestingly, the grain yield of rice by these bacteria with 50% less of the recommended doses of N, P, and K fertilizers were statistically similar to or better than the rice plants treated with 100% doses of these fertilizers. Targeted amplicon (16S rRNA) sequence-based analysis revealed significant differences (PERMANOVA, p = 0.00035) in alpha-diversity between the root (R) and rhizosphere soil (S) samples, showing higher diversity in the microbial ecosystem of root samples. Additionally, the bacteriome diversity in the root of rice plants that received both probiotic bacteria and chemical fertilizers were significantly higher (PERMANOVA, p = 0.0312) compared to the rice plants treated with fertilizers only. Out of 185 bacterial genera detected, Prevotella, an anaerobic and Gram-negative bacterium, was found to be the predominant genus in both rhizosphere soil and root metagenomes. However, the relative abundance of Prevotella remained two-fold higher in the rhizosphere soil metagenome (52.02%) than in the root metagenome (25.04%). The other predominant bacterial genera detected in the rice root metagenome were Bacillus (11.07%), Planctomyces (4.06%), Faecalibacterium (3.91%), Deinococcus (2.97%), Bacteroides (2.61%), and Chryseobacterium (2.30%). On the other hand, rhizosphere soil metagenome had Bacteroides (12.38%), Faecalibacterium (9.50%), Vibrio (5.94%), Roseomonas (3.40%), and Delftia (3.02%). Interestingly, we found the presence and/or abundance of specific genera of bacteria in rice associated with the application of a specific probiotic bacterium. Taken together, our results indicate that improvement of growth and yield of rice by P. fungorum strain BRRh-4 and Delftia sp. strain BTL-M2 is likely linked with modulation of diversity, structures, and signature of bacteriome in roots and rhizosphere soils. This study for the first time demonstrated that application of plant growth promoting bacteria significantly improve growth, yield and increase the diversity of bacterial community in rice.}, } @article {pmid37520363, year = {2023}, author = {Flint, A and Cooper, A and Rao, M and Weedmark, K and Carrillo, C and Tamber, S}, title = {Targeted metagenomics using bait-capture to detect antibiotic resistance genes in retail meat and seafood.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1188872}, pmid = {37520363}, issn = {1664-302X}, abstract = {Metagenomics analysis of foods has the potential to provide comprehensive data on the presence and prevalence of antimicrobial resistance (AMR) genes in the microbiome of foods. However, AMR genes are generally present in low abundance compared to other bacterial genes in the food microbiome and consequently require multiple rounds of in-depth sequencing for detection. Here, a metagenomics approach, using bait-capture probes targeting antimicrobial resistance and plasmid genes, is used to characterize the resistome and plasmidome of retail beef, chicken, oyster, shrimp, and veal enrichment cultures (n = 15). Compared to total shotgun metagenomics, bait-capture required approximately 40-fold fewer sequence reads to detect twice the number of AMR gene classes, AMR gene families, and plasmid genes across all sample types. For the detection of critically important extended spectrum beta-lactamase (ESBL) genes the bait capture method had a higher overall positivity rate (44%) compared to shotgun metagenomics (26%), and a culture-based method (29%). Overall, the results support the use of bait-capture for the identification of low abundance genes such as AMR genes from food samples.}, } @article {pmid37520352, year = {2023}, author = {Kim, J and Lee, G and Han, S and Kim, MJ and Shin, JH and Lee, S}, title = {Microbial communities in aerosol generated from cyanobacterial bloom-affected freshwater bodies: an exploratory study in Nakdong River, South Korea.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1203317}, pmid = {37520352}, issn = {1664-302X}, abstract = {Toxic blooms of cyanobacteria, which can produce cyanotoxins, are prevalent in freshwater, especially in South Korea. Exposure to cyanotoxins via ingestion, inhalation, and dermal contact may cause severe diseases. Particularly, toxic cyanobacteria and their cyanotoxins can be aerosolized by a bubble-bursting process associated with a wind-driven wave mechanism. A fundamental question remains regarding the aerosolization of toxic cyanobacteria and cyanotoxins emitted from freshwater bodies during bloom seasons. To evaluate the potential health risk of the aerosolization of toxic cyanobacteria and cyanotoxins, the objectives of this study were as follows: 1) to quantify levels of microcystin in the water and air samples, and 2) to monitor microbial communities, including toxic cyanobacteria in the water and air samples. Water samples were collected from five sites in the Nakdong River, South Korea, from August to September 2022. Air samples were collected using an air pump with a mixed cellulose ester membrane filter. Concentrations of total microcystins were measured using enzyme-linked immunosorbent assay. Shotgun metagenomic sequencing was used to investigate microbial communities, including toxic cyanobacteria. Mean concentrations of microcystins were 960 μg/L ranging from 0.73 to 5,337 μg/L in the water samples and 2.48 ng/m[3] ranging from 0.1 to 6.8 ng/m[3] in the air samples. In addition, in both the water and air samples, predominant bacteria were Microcystis (PCC7914), which has a microcystin-producing gene, and Cyanobium. Particularly, abundance of Microcystis (PCC7914) comprised more than 1.5% of all bacteria in the air samples. This study demonstrates microbial communities with genes related with microcystin synthesis, antibiotic resistance gene, and virulence factors in aerosols generated from cyanobacterial bloom-affected freshwater body. In summary, aerosolization of toxic cyanobacteria and cyanotoxins is a critical concern as an emerging exposure route for potential risk to environmental and human health.}, } @article {pmid37520002, year = {2023}, author = {Leyson, CM and Alkhamis, MA and Goraichuk, IV}, title = {Editorial: Sequencing and phylogenetic analysis as a tool in molecular epidemiology of veterinary infectious diseases.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1236155}, doi = {10.3389/fvets.2023.1236155}, pmid = {37520002}, issn = {2297-1769}, } @article {pmid37517706, year = {2023}, author = {Ma, F and Wang, Y and Quan, H and Wang, Z and Zhao, C and Li, X and Liang, B and Zhang, H and Hao, L and Zhu, T}, title = {Exploring the humification process of municipal sludge in hyperthermophilic composting through metagenomic and untargeted metabolomic.}, journal = {Bioresource technology}, volume = {387}, number = {}, pages = {129575}, doi = {10.1016/j.biortech.2023.129575}, pmid = {37517706}, issn = {1873-2976}, mesh = {*Composting ; Humic Substances/analysis ; Soil ; Sewage ; Amino Acids ; Manure ; }, abstract = {Hyperthermophilic composting (HC) has been widely recognized for the advantage of high treatment efficiency for organic wastes. However, the humification process is still unclear. In this study, the humification process of HC was investigated, compared to conventional composting (CK). The results showed that the highest composting temperature, organic matter degradation rate, and humification index in HC were 92.62 °C, 23.98%, and 1.59, while those in CK were 70.23 °C, 14.49 %, and 1.04, indicating HC accelerated humification process. Moreover, the results of metagenomic and untargeted metabolomic showed that the genes and metabolisms related to carbohydrate, lipid, amino acid, fatty acid, and nucleotide were more abundant in HC. Consequently, the metabolic pathways regarding organic matter degradation and microbial reproduction were enhanced in the high temperature stage of HC, further accelerating the humification reaction in the low temperature stage. This work contributes to the comprehension of the humification mechanism in HC.}, } @article {pmid37517669, year = {2023}, author = {Ozsefil, IC and Miraloglu, IH and Ozbayram, EG and Uzun, O and Ince, B and Ince, O}, title = {Is a floodplain forest a valuable source for lignin-degrading anaerobic microbial communities: A metagenomic approach.}, journal = {Chemosphere}, volume = {339}, number = {}, pages = {139675}, doi = {10.1016/j.chemosphere.2023.139675}, pmid = {37517669}, issn = {1879-1298}, mesh = {*Lignin/metabolism ; Anaerobiosis ; *Microbiota ; Metagenome ; Microbial Consortia ; Forests ; }, abstract = {Lignin is one of the most substantial obstacles in the evaluation of lignocellulosic compounds. Although there are numerous approaches for the enhancement of lignin digestion in the literature, there has yet to be an optimized system to date. In this study, samples taken from Igneada floodplain forests were enriched anaerobically at 25 °C and 37 °C, with alkali lignin as the sole carbon source. The activity of the anaerobic lignin-degrading microbial consortium was detected more efficiently at 37 °C, where biogas production exceeded 3.5 mLgas/mLmedium. It was observed that the microbial community initially dominated by Proteobacteria (around 60%) changed completely after enrichment and was led by members of the Firmicutes phylum (up to 90%). The dominant species (Sporomusa termitida, Desulfitobacterium hafniense, Citrobacter freundii, Citrobacter portucalensis, Alkalibacter rhizosphaerae, and Gudongella oleilytica) occupying more than 50% in the final enrichment culture were only around 2% in the raw samples. Therefore, this study, one of the few in which enriched environmental samples were sequenced using MinION, demonstrated that longoses are exceptional reservoirs for lignin-digesting anaerobic microorganisms.}, } @article {pmid37517495, year = {2023}, author = {Veerasamy, V and Jagannathan, UM and Arakkala, SD and Shafee, WA and Kaliannan, T}, title = {Exploring the bacterial genetic diversity and community structure of crude oil contaminated soils using microbiomics.}, journal = {Environmental research}, volume = {236}, number = {Pt 2}, pages = {116779}, doi = {10.1016/j.envres.2023.116779}, pmid = {37517495}, issn = {1096-0953}, mesh = {*Petroleum ; Ecosystem ; Sewage ; *Soil Pollutants/analysis ; Soil Microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Biodegradation, Environmental ; Soil/chemistry ; Genetic Variation ; }, abstract = {The impact of environmental pollution in air and water is reflected mainly in the soil ecosystem as it impairs soil functions. Also, since the soil is the habitat for billions of organisms, the biodiversity is in turn altered. Microbes are precise sensors of ecological contamination, and bacteria have a key and important function in terms of bioremediation of the contaminated soil. Hence in the current work, we aimed at assessing the unidentified bacterial population through Illumina MiSeq sequencing technology and their community structural changes in different levels of petroleum-contaminated soil and sludge samples (aged, sludge, and leakage soil) to identify unique bacteria for their potential application in remediation. The studies showed that major bacterial consortiums namely, Proteobacteria (57%), Alphaproteobacteria (31%), and Moraxellaceae (23%) were present in aged soil, whereas Proteobacteria (52%), Alphaproteobacteria (33%), and Rhodobacteraceae (28%) were dominantly found in sludge soil. In leakage soil, Proteobacteria (59%), Alphaproteobacteria (33%), and Rhodobacteraceae (29%) were abundantly present. The Venn diagrams are used to analyze the distribution of abundances in individual operational taxonomic units (OTUs) within three soil samples. After data filtering, they were grouped into OTU clusters and 329 OTUs were identified from the three soil samples. Among the 329, 160 OTUs were common in the three soil samples. The bacterial diversity is estimated using alpha diversity indices and Shanon index and was found to be 4.490, 4.073 and 4.631 in aged soil, sludge soil and leakage soil, respectively and similarly richness was found to be 618, 417 and 418. The heat map was generated by QIIME software and from the top 50 enriched genera few microbes such as Pseudomonas, Bacillus, Mycobacterium, Sphingomonas and Paracoccus, were shown across all the samples. In addition, we also analyzed various physicochemical properties of soil including pH, temperature, salinity, electrical conductivity, alkalinity, total carbon, total organic matter, nitrogen, phosphorus and potassium to calculate the soil quality index (SQI). The SQI of aged, sludge and leakage soil samples were 0.73, 0.64, and 0.89, respectively. These findings show the presence of unexplored bacterial species which could be applied for hydrocarbon remediation and further they can be exploited for the same.}, } @article {pmid37516858, year = {2023}, author = {Wu, M and Xiao, H and Xiao, Y and Chen, T and Wang, X and Xiao, X and Wang, Y and Wang, J and Ren, L and Liu, G}, title = {Pathogenesis diagnosis of a pediatric patient suffering from multi-organ abscesses.}, journal = {Diagnostic pathology}, volume = {18}, number = {1}, pages = {85}, pmid = {37516858}, issn = {1746-1596}, support = {2019PT310029//Nonprofit Central Research Institute Fund of Chinese Academy of Medical Sciences/ ; 2021-I2M-1-038//Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences/ ; Z190017//Beijing Municipal Natural Science Foundation of China/ ; 3332021092//Fundamental Research Funds for the Central Universities/ ; L202004//Beijing Natural Science Foundation/ ; XTZD20180501//The Special Fund of the Pediatric Medical Coordinated Development Center of Beijing Hospitals Authority/ ; HXZX-202106//Respiratory Research Project of National Clinical Research Center for Respiratory Diseases/ ; }, mesh = {Humans ; Child ; *Abscess ; Anti-Bacterial Agents ; Antibodies, Neutralizing ; *Bacteremia ; High-Throughput Nucleotide Sequencing ; }, abstract = {A pediatric patient suffered from renal and hepatic abscesses (through hepatorenal space) and recovered by antibiotics and other therapies. By clinical analysis, the multi-organ abscesses might be caused by bloodstream-disseminated infection. In order to identify the pathogen, we collected kidney biopsy tissue, swabs, and plasma samples, and used metagenomics next-generation sequencing (mNGS) and some traditional methods. The results revealed that polymicrobial especially anaerobic bacteremia (Bacteroides fragilis, et al.) contributed to the abscess formation. What is more, systematic human adenovirus C (HAdV-C) infection was shown, and the virus was isolated. The titer of HAdV-2 neutralizing antibodies was 1/4 in the plasma after symptoms onset. Although the exact mechanism of HAdV-2 infection in multiple abscess formation has not been clarified, the case of multi-organ abscesses in the context of polymicrobial especially anaerobic bacteremia and HAdV infection in healthy children is infrequent.}, } @article {pmid37516367, year = {2023}, author = {Pichler, I and Schmutz, S and Ziltener, G and Zaheri, M and Kufner, V and Trkola, A and Huber, M}, title = {Rapid and sensitive single-sample viral metagenomics using Nanopore Flongle sequencing.}, journal = {Journal of virological methods}, volume = {320}, number = {}, pages = {114784}, doi = {10.1016/j.jviromet.2023.114784}, pmid = {37516367}, issn = {1879-0984}, mesh = {Humans ; Metagenomics/methods ; *Nanopores ; *Virus Diseases/diagnosis ; *Viruses/genetics ; *RNA Viruses/genetics ; DNA Viruses/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; }, abstract = {The ability of viral metagenomic Next-Generation Sequencing (mNGS) to unbiasedly detect nucleic acids in a clinical sample is a powerful tool for advanced diagnosis of viral infections. When clinical symptoms do not provide a clear differential diagnosis, extensive laboratory testing with virus-specific PCR and serology can be replaced by a single viral mNGS analysis. However, widespread diagnostic use of viral mNGS is thus far limited by long sample-to-result times, as most protocols rely on Illumina sequencing, which provides high and accurate sequencing output but is time-consuming and expensive. Here, we describe the development of an mNGS protocol based on the more cost-effective Nanopore Flongle sequencing with decreased turnaround time and lower, yet sufficient sequencing output to provide sensitive virus detection. Sample preparation (6 h) and sequencing (2 h) times are substantially reduced compared to Illumina mNGS and allow detection of DNA/RNA viruses at low input (up to 33-38 cycle threshold of specific qPCR). Although Flongles yield lower sequencing output, direct comparison with Illumina mNGS on diverse clinical samples showed similar results. Collectively, the novel Nanopore mNGS approach is specifically tailored for use in clinical diagnostics and provides a rapid and cost-effective mNGS strategy for individual testing of severe cases.}, } @article {pmid37516265, year = {2023}, author = {Liu, C and Liu, H and Liu, X and Li, G and Zhang, Y and Zhang, M and Li, Z}, title = {Metagenomic analysis insights into the influence of 3,4-dimethylpyrazole phosphate application on nitrous oxide mitigation efficiency across different climate zones in Eastern China.}, journal = {Environmental research}, volume = {236}, number = {Pt 1}, pages = {116761}, doi = {10.1016/j.envres.2023.116761}, pmid = {37516265}, issn = {1096-0953}, mesh = {*Nitrous Oxide ; *Phosphates/analysis ; Dimethylphenylpiperazinium Iodide/metabolism ; Bacteria/genetics/metabolism ; Soil ; China ; Ammonia ; Nitrites/analysis/metabolism ; Soil Microbiology ; Fertilizers/analysis ; }, abstract = {Excessive nitrogen (N) fertilization in agroecological systems increases nitrous oxide (N2O) emissions. 3,4-dimethylpyrazole phosphate (DMPP) is used to mitigate N2O losses. The influence of DMPP efficiency on N2O mitigation was clearly affected by spatiotemporal heterogeneity. Using field and incubation experiments combined with metagenomic sequencing, we aimed to investigate DMPP efficiency and the underlying microbial mechanisms in dark-brown (Siping, SP), fluvo-aquic (Cangzhou, CZ; Xinxiang, XX), and red soil (Wenzhou, WZ) from diverse climatic zones. In the field experiments, the DMPP efficiency in N2O mitigation ranged from 51.6% to 89.9%, in the order of XX, CZ, SP, and WZ. The DMPP efficiency in the incubation experiments ranged from 58.3% to 93.9%, and the order of efficiency from the highest to lowest was the same as that of the field experiments. Soil organic matter, total N, pH, texture, and taxonomic and functional α-diversity were important soil environment and microbial factors for DMPP efficiency. DMPP significantly enriched ammonia-oxidizing archaea (AOA) and nitrite-oxidizing bacteria (NOB), which promoted N-cycling with low N2O emissions. Random forest (RF) and regression analyses found that an AOA (Nitrosocosmicus) and NOB (Nitrospina) demonstrated important and positive correlation with DMPP efficiency. Moreover, genes associated with carbohydrate metabolism were important for DMPP efficiency and could influenced N-cycling and DMPP metabolism. The similar DMPP efficiency indicated that the variation in DMPP efficiency was significantly due to soil physicochemical and microbial variations. In conclusion, filling the knowledge gap regarding the response of DMPP efficiency to abiotic and biotic factors could be beneficial in DMPP applications, and in adapting more efficient strategies to improve DMPP efficiency and mitigate N2O emissions in multiple regions.}, } @article {pmid37516175, year = {2023}, author = {Shivaram, KB and Bhatt, P and Verma, MS and Clase, K and Simsek, H}, title = {Bacteriophage-based biosensors for detection of pathogenic microbes in wastewater.}, journal = {The Science of the total environment}, volume = {901}, number = {}, pages = {165859}, doi = {10.1016/j.scitotenv.2023.165859}, pmid = {37516175}, issn = {1879-1026}, abstract = {Wastewater is discarded from several sources, including industry, livestock, fertilizer application, and municipal waste. If the disposed of wastewater has not been treated and processed before discharge to the environment, pathogenic microorganisms and toxic chemicals are accumulated in the disposal area and transported into the surface waters. The presence of harmful microbes is responsible for thousands of human deaths related to water-born contamination every year. To be able to take the necessary step and quick action against the possible presence of harmful microorganisms and substances, there is a need to improve the effective speed of identification and treatment of these problems. Biosensors are such devices that can give quantitative information within a short period of time. There have been several biosensors developed to measure certain parameters and microorganisms. The discovered biosensors can be utilized for the detection of axenic and mixed microbial strains from the wastewaters. Biosensors can further be developed for specific conditions and environments with an in-depth understanding of microbial organization and interaction within that community. In this regard, bacteriophage-based biosensors have become a possibility to identify specific live bacteria in an infected environment. This paper has investigated the current scenario of microbial community analysis and biosensor development in identifying the presence of pathogenic microorganisms.}, } @article {pmid37516054, year = {2023}, author = {He, S and Deng, X and Han, Y and Gong, Z and Wang, J and Tao, X and Tong, H and Chen, Y}, title = {Metabolites and metagenomic analysis reveals the quality of Pu-erh "tea head".}, journal = {Food chemistry}, volume = {429}, number = {}, pages = {136992}, doi = {10.1016/j.foodchem.2023.136992}, pmid = {37516054}, issn = {1873-7072}, mesh = {Tea/chemistry ; *Microbiota ; Bacteria/genetics ; *Catechin ; Fermentation ; }, abstract = {Tea head, a derivative product of Pu-erh tea, are tight tea lumps formed during pile-fermentation. The aim of this study was to reveal the differences of quality-related metabolites and microbial communities between ripened Pu-erh tea (PE-21) and tea heads (CT-21). Compared with PE-21, CT-21 showed a more mellow and smooth taste with slight bitterness and astringency, and can withstand multiple infusions. Metabolites analysis indicated CT-21 had more abundant water-soluble substances (47.39%) and showed significant differences with PE-21 in the main compositions of amino acids, catechins and saccharides which contributed to the viscosity of tea liquor, mellow taste and the tight tea lumps formation. Microbial communities and COG annotation analysis revealed CT-21 had lower abundance of Bacteria (84.05%), and higher abundance of Eukaryota (15.10%), carbohydrate transport and metabolism (8.28%) and glycoside hydrolases (37.36%) compared with PE-21. The different microbial communities may cause metabolites changes, forming distinct flavor of Pu-erh.}, } @article {pmid37515475, year = {2023}, author = {Tanabe, TS and Dahl, C}, title = {HMSS2: An advanced tool for the analysis of sulphur metabolism, including organosulphur compound transformation, in genome and metagenome assemblies.}, journal = {Molecular ecology resources}, volume = {23}, number = {8}, pages = {1930-1945}, doi = {10.1111/1755-0998.13848}, pmid = {37515475}, issn = {1755-0998}, support = {Da 351/13-1//Deutsche Forschungsgemeinschaft/ ; //Studienstiftung des Deutschen Volkes/ ; }, mesh = {Humans ; *Metagenome ; *Sulfur Compounds/metabolism ; Sulfur/metabolism ; }, abstract = {The global sulphur cycle has implications for human health, climate change, biogeochemistry and bioremediation. The organosulphur compounds that participate in this cycle not only represent a vast reservoir of sulphur but are also used by prokaryotes as sources of energy and/or carbon. Closely linked to the inorganic sulphur cycle, it involves the interaction of prokaryotes, eukaryotes and chemical processes. However, ecological and evolutionary studies of the conversion of organic sulphur compounds are hampered by the poor conservation of the relevant pathways and their variation even within strains of the same species. In addition, several proteins involved in the conversion of sulphonated compounds are related to proteins involved in sulphur dissimilation or turnover of other compounds. Therefore, the enzymes involved in the metabolism of organic sulphur compounds are usually not correctly annotated in public databases. To address this challenge, we have developed HMSS2, a profiled Hidden Markov Model-based tool for rapid annotation and synteny analysis of organic and inorganic sulphur cycle proteins in prokaryotic genomes. Compared to its previous version (HMS-S-S), HMSS2 includes several new features. HMM-based annotation is now supported by nonhomology criteria and covers the metabolic pathways of important organosulphur compounds, including dimethylsulphoniopropionate, taurine, isethionate, and sulphoquinovose. In addition, the calculation speed has been increased by a factor of four and the available output formats have been extended to include iTol compatible data sets, and customized sequence FASTA files.}, } @article {pmid37515283, year = {2023}, author = {Ryabov, EV and Nearman, AJ and Nessa, A and Grubbs, K and Sallmann, B and Fahey, R and Wilson, ME and Rennich, KD and Steinhauer, N and Fauvel, AM and Chen, Y and Evans, JD and vanEngelsdorp, D}, title = {Apis mellifera Solinvivirus-1, a Novel Honey Bee Virus That Remained Undetected for over a Decade, Is Widespread in the USA.}, journal = {Viruses}, volume = {15}, number = {7}, pages = {}, pmid = {37515283}, issn = {1999-4915}, mesh = {Bees/genetics ; Animals ; United States ; *RNA Viruses/genetics ; Metagenome ; RNA ; }, abstract = {A metagenomic analysis of the virome of honey bees (Apis mellifera) from an apiary with high rates of unexplained colony losses identified a novel RNA virus. The virus, which was named Apis mellifera solinvivirus 1 (AmSV1), contains a 10.6 kb positive-strand genomic RNA with a single ORF coding for a polyprotein with the protease, helicase, and RNA-dependent RNA polymerase domains, as well as a single jelly-roll structural protein domain, showing highest similarity with viruses in the family Solinviviridae. The injection of honey bee pupae with AmSV1 preparation showed an increase in virus titer and the accumulation of the negative-strand of AmSV1 RNA 3 days after injection, indicating the replication of AmSV1. In the infected worker bees, AmSV1 was present in heads, thoraxes, and abdomens, indicating that this virus causes systemic infection. An analysis of the geographic and historic distribution of AmSV1, using over 900 apiary samples collected across the United States, showed AmSV1 presence since at least 2010. In the year 2021, AmSV1 was detected in 10.45% of apiaries (95%CI: 8.41-12.79%), mostly sampled in June and July in Northwestern and Northeastern United States. The diagnostic methods and information on the AmSV1 distribution will be used to investigate the connection of AmSV1 to honey bee colony losses.}, } @article {pmid37515261, year = {2023}, author = {Laubscher, F and Kaiser, L and Cordey, S}, title = {SCANellome: Analysis of the Genomic Diversity of Human and Non-Human Primate Anelloviruses from Metagenomics Data.}, journal = {Viruses}, volume = {15}, number = {7}, pages = {}, pmid = {37515261}, issn = {1999-4915}, mesh = {Humans ; Animals ; *Anelloviridae/genetics ; Metagenomics ; *Torque teno virus ; *Viruses/genetics ; Primates ; }, abstract = {Anelloviruses are extremely prevalent in the human population and are considered to be commensal parts of the human virome. The best-known member in humans is the Torque teno virus. Recent metagenomic next-generation sequencing investigations have helped reveal the considerable number of species and genotypes from the same genus that can be co-detected within a single individual and that this diversity increases as a function of age during the first months/years of life. As a result, to date, the bioinformatics analysis of this genetic diversity remains complex and constraining for researchers. Here, we present SCANellome, a user-friendly tool to investigate the anellome composition at the genus, species, and genotype levels of samples from metagenomics data generated by the Illumina and Nanopore platforms. SCANellome is based on an in-house up-to-date database that includes all human and non-human primate anellovirus reference sequences available on GenBank and meets the latest classification criteria established by the International Committee on Taxonomy of Viruses.}, } @article {pmid37515247, year = {2023}, author = {Diaz-Lara, A and Stevens, K and Aguilar-Molina, VH and Fernández-Cortés, JM and Chabacano León, VM and De Donato, M and Sharma, A and Erickson, TM and Al Rwahnih, M}, title = {High-Throughput Sequencing of Grapevine in Mexico Reveals a High Incidence of Viruses including a New Member of the Genus Enamovirus.}, journal = {Viruses}, volume = {15}, number = {7}, pages = {}, pmid = {37515247}, issn = {1999-4915}, mesh = {*Luteoviridae ; *Vitis ; Mexico ; Incidence ; Plant Diseases ; High-Throughput Nucleotide Sequencing ; }, abstract = {This is the first viral metagenomic analysis of grapevine conducted in Mexico. During the summer of 2021, 48 plants displaying virus-like symptoms were sampled in Queretaro, an important grapevine-producing area of Mexico, and analyzed for the presence of viruses via high-throughput sequencing (HTS). The results of HTS were verified by real-time RT-PCR following a standardized testing scheme (Protocol 2010). Fourteen different viruses were identified, including grapevine asteroid mosaic-associated virus (GAMaV), grapevine Cabernet Sauvignon reovirus (GCSV), grapevine fanleaf virus (GFLV), grapevine fleck virus (GFkV), grapevine Pinot gris virus (GPGV), grapevine red globe virus (GRGV), grapevine rupestris stem pitting-associated virus (GRSPaV), grapevine rupestris vein feathering virus (GRVFV), grapevine Syrah virus 1 (GSyV-1), grapevine virus B (GVB), and grapevine leafroll-associated viruses 1, 2, 3, 4 (GLRaV1, 2, 3, 4). Additionally, divergent variants of GLRaV4 and GFkV, and a novel Enamovirus-like virus were discovered. This is the first report of GAMaV, GCSV, GLRaV4, GPGV, GRGV, GRVFV, and GSyV-1 infecting grapevines in Mexico; the impact of these pathogens on production is unknown.}, } @article {pmid37515163, year = {2023}, author = {Hardies, SC and Cho, BC and Jang, GI and Wang, Z and Hwang, CY}, title = {Identification of Structural and Morphogenesis Genes of Sulfitobacter Phage ΦGT1 and Placement within the Evolutionary History of the Podoviruses.}, journal = {Viruses}, volume = {15}, number = {7}, pages = {}, pmid = {37515163}, issn = {1999-4915}, mesh = {Prospective Studies ; Genome, Viral ; *Bacteriophages/genetics/chemistry ; *Podoviridae/genetics ; Prophages/genetics ; }, abstract = {ΦGT1 is a lytic podovirus of an alphaproteobacterial Sulfitobacter species, with few closely matching sequences among characterized phages, thus defying a useful description by simple sequence clustering methods. The history of the ΦGT1 core structure module was reconstructed using timetrees, including numerous related prospective prophages, to flesh out the evolutionary lineages spanning from the origin of the ejectosomal podovirus >3.2 Gya to the present genes of ΦGT1 and its closest relatives. A peculiarity of the ΦGT1 structural proteome is that it contains two paralogous tubular tail A (tubeA) proteins. The origin of the dual tubeA arrangement was traced to a recombination between two more ancient podoviral lineages occurring ~0.7 Gya in the alphaproteobacterial order Rhizobiales. Descendants of the ancestral dual A recombinant were tracked forward forming both temperate and lytic phage clusters and exhibiting both vertical transmission with patchy persistence and horizontal transfer with respect to host taxonomy. The two ancestral lineages were traced backward, making junctions with a major metagenomic podoviral family, the LUZ24-like gammaproteobacterial phages, and Myxococcal phage Mx8, and finally joining near the origin of podoviruses with P22. With these most conservative among phage genes, deviations from uncomplicated vertical and nonrecombinant descent are numerous but countable. The use of timetrees allowed conceptualization of the phage's evolution in the context of a sequence of ancestors spanning the time of life on Earth.}, } @article {pmid37515113, year = {2023}, author = {Thijssen, M and Khamisipour, G and Maleki, M and Devos, T and Li, G and Van Ranst, M and Matthijnssens, J and Pourkarim, MR}, title = {Characterization of the Human Blood Virome in Iranian Multiple Transfused Patients.}, journal = {Viruses}, volume = {15}, number = {7}, pages = {}, pmid = {37515113}, issn = {1999-4915}, mesh = {Humans ; Iran/epidemiology ; Virome ; *Viruses/genetics ; *Anelloviridae/genetics ; Metagenome ; Metagenomics/methods ; }, abstract = {Blood transfusion safety is an essential element of public health. Current blood screening strategies rely on targeted techniques that could miss unknown or unexpected pathogens. Recent studies have demonstrated the presence of a viral community (virobiota/virome) in the blood of healthy individuals. Here, we characterized the blood virome in patients frequently exposed to blood transfusion by using Illumina metagenomic sequencing. The virome of these patients was compared to viruses present in healthy blood donors. A total number of 155 beta-thalassemia, 149 hemodialysis, and 100 healthy blood donors were pooled with five samples per pool. Members of the Anelloviridae and Flaviviridae family were most frequently observed. Interestingly, samples of healthy blood donors harbored traces of potentially pathogenic viruses, including adeno-, rota-, and Merkel cell polyomavirus. Viruses of the Anelloviridae family were most abundant in the blood of hemodialysis patients and displayed a higher anellovirus richness. Pegiviruses (Flaviviridae) were only observed in patient populations. An overall trend of higher eukaryotic read abundance in both patient groups was observed. This might be associated with increased exposure through blood transfusion. Overall, the findings in this study demonstrated the presence of various viruses in the blood of Iranian multiple-transfused patients and healthy blood donors.}, } @article {pmid37513037, year = {2023}, author = {Lomakina, A and Bukin, S and Shubenkova, O and Pogodaeva, T and Ivanov, V and Bukin, Y and Zemskaya, T}, title = {Microbial Communities in Ferromanganese Sediments from the Northern Basin of Lake Baikal (Russia).}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, pmid = {37513037}, issn = {2076-2607}, support = {22-14-00084//Russian Science Foundation/ ; }, abstract = {We analyzed the amplicons of the 16S rRNA genes and assembled metagenome-assembled genomes (MAGs) of the enrichment culture from the Fe-Mn layer to have an insight into the diversity and metabolic potential of microbial communities from sediments of two sites in the northern basin of Lake Baikal. Organotrophic Chloroflexota, Actionobacteriota, and Acidobacteriota, as well as aerobic and anaerobic participants of the methane cycle (Methylococcales and Methylomirabilota, respectively), dominated the communities of the surface layers. With depth, one of the cores showed a decrease in the proportion of the Chloroflexota and Acidobacteriota members and a substantial increase in the sequences of the phylum Firmicutes. The proportion of the Desulfobacteriota and Thermodesulfovibronia (Nitrospirota) increased in another core. The composition of archaeal communities was similar between the investigated sites and differed in depth. Members of ammonia-oxidizing archaea (Nitrososphaeria) predominated in the surface sediments, with an increase in anaerobic methanotrophs (Methanoperedenaceae) and organoheterotrophs (Bathyarchaeia) in deep sediments. Among the 37 MAGs, Gammaproteobacteria, Desulfobacteriota, and Methylomirabilota were the most common in the microbial community. Metagenome sequencing revealed the assembled genomes genes for N, S, and CH4 metabolism for carbon fixation, and genes encoding Fe and Mn pathways, indicating the likely coexistence of the biogeochemical cycle of various elements and creating certain conditions for the development of taxonomically and functionally diverse microbial communities.}, } @article {pmid37513003, year = {2023}, author = {Riber, L and Carstens, AB and Dougherty, PE and Roy, C and Willenbücher, K and Hille, F and Franz, CMAP and Hansen, LH}, title = {Pheno- and Genotyping of Three Novel Bacteriophage Genera That Target a Wheat Phyllosphere Sphingomonas Genus.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, pmid = {37513003}, issn = {2076-2607}, support = {NNF19SA0059348//Novo Nordisk Foundation/ ; 00036150//The Velux Foundations/ ; }, abstract = {Bacteriophages are viral agents that infect and replicate within bacterial cells. Despite the increasing importance of phage ecology, environmental phages-particularly those targeting phyllosphere-associated bacteria-remain underexplored, and current genomic databases lack high-quality phage genome sequences linked to specific environmentally important bacteria, such as the ubiquitous sphingomonads. Here, we isolated three novel phages from a Danish wastewater treatment facility. Notably, these phages are among the first discovered to target and regulate a Sphingomonas genus within the wheat phyllosphere microbiome. Two of the phages displayed a non-prolate Siphovirus morphotype and demonstrated a narrow host range when tested against additional Sphingomonas strains. Intergenomic studies revealed limited nucleotide sequence similarity within the isolated phage genomes and to publicly available metagenome data of their closest relatives. Particularly intriguing was the limited homology observed between the DNA polymerase encoding genes of the isolated phages and their closest relatives. Based on these findings, we propose three newly identified genera of viruses: Longusvirus carli, Vexovirus birtae, and Molestusvirus kimi, following the latest ICTV binomial nomenclature for virus species. These results contribute to our current understanding of phage genetic diversity in natural environments and hold promising implications for phage applications in phyllosphere microbiome manipulation strategies.}, } @article {pmid37512975, year = {2023}, author = {Konrad, R and Vergara-Barros, P and Alcorta, J and Alcamán-Arias, ME and Levicán, G and Ridley, C and Díez, B}, title = {Distribution and Activity of Sulfur-Metabolizing Bacteria along the Temperature Gradient in Phototrophic Mats of the Chilean Hot Spring Porcelana.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, pmid = {37512975}, issn = {2076-2607}, support = {Doctoral fellowship N° 21191763//Agencia Nacional de Investigación y Desarrollo/ ; Postdoctoral fellowship FONDECYT N° 3170807//Agencia Nacional de Investigación y Desarrollo/ ; FONDAP CR2 Nº 15110009//Agencia Nacional de Investigación y Desarrollo/ ; regular N° 1150171//Agencia Nacional de Investigación y Desarrollo/ ; regular N° 1190998//Agencia Nacional de Investigación y Desarrollo/ ; Millennium Institute Center for Genome Regulation ICN2021_044//Agencia Nacional de Investigación y Desarrollo/ ; }, abstract = {In terrestrial hot springs, some members of the microbial mat community utilize sulfur chemical species for reduction and oxidization metabolism. In this study, the diversity and activity of sulfur-metabolizing bacteria were evaluated along a temperature gradient (48-69 °C) in non-acidic phototrophic mats of the Porcelana hot spring (Northern Patagonia, Chile) using complementary meta-omic methodologies and specific amplification of the aprA (APS reductase) and soxB (thiosulfohydrolase) genes. Overall, the key players in sulfur metabolism varied mostly in abundance along the temperature gradient, which is relevant for evaluating the possible implications of microorganisms associated with sulfur cycling under the current global climate change scenario. Our results strongly suggest that sulfate reduction occurs throughout the whole temperature gradient, being supported by different taxa depending on temperature. Assimilative sulfate reduction is the most relevant pathway in terms of taxonomic abundance and activity, whereas the sulfur-oxidizing system (Sox) is likely to be more diverse at low rather than at high temperatures. Members of the phylum Chloroflexota showed higher sulfur cycle-related transcriptional activity at 66 °C, with a potential contribution to sulfate reduction and oxidation to thiosulfate. In contrast, at the lowest temperature (48 °C), Burkholderiales and Acetobacterales (both Pseudomonadota, also known as Proteobacteria) showed a higher contribution to dissimilative sulfate reduction/oxidation as well as to thiosulfate metabolism. Cyanobacteriota and Planctomycetota were especially active in assimilatory sulfate reduction. Analysis of the aprA and soxB genes pointed to members of the order Burkholderiales (Gammaproteobacteria) as the most dominant and active along the temperature gradient for these genes. Changes in the diversity and activity of different sulfur-metabolizing bacteria in photoautotrophic microbial mats along a temperature gradient revealed their important role in hot spring environments, especially the main primary producers (Chloroflexota/Cyanobacteriota) and diazotrophs (Cyanobacteriota), showing that carbon, nitrogen, and sulfur cycles are highly linked in these extreme systems.}, } @article {pmid37512875, year = {2023}, author = {Łomża, P and Krucoń, T and Tabernacka, A}, title = {Potential of Microbial Communities to Perform Dehalogenation Processes in Natural and Anthropogenically Modified Environments-A Metagenomic Study.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, pmid = {37512875}, issn = {2076-2607}, support = {2019/33/N/NZ9/01404//National Science Centre (Poland)/ ; }, abstract = {Halogenated organic compounds (HOCs) pose a serious problem for the environment. Many are highly toxic and accumulate both in soil and in organisms. Their biological transformation takes place by dehalogenation, in which the halogen substituents are detached from the carbon in the organic compound by enzymes produced by microorganisms. This increases the compounds' water solubility and bioavailability, reduces toxicity, and allows the resulting compound to become more susceptible to biodegradation. The microbial halogen cycle in soil is an important part of global dehalogenation processes. The aim of the study was to examine the potential of microbial communities inhabiting natural and anthropogenically modified environments to carry out the dehalogenation process. The potential of microorganisms was assessed by analyzing the metagenomes from a natural environment (forest soils) and from environments subjected to anthropopression (agricultural soil and sludge from wastewater treatment plants). Thirteen genes encoding enzymes with dehalogenase activity were identified in the metagenomes of both environments, among which, 2-haloacid dehalogenase and catechol 2,3-dioxygenase were the most abundant genes. Comparative analysis, based on comparing taxonomy, identified genes, total halogens content and content of DDT derivatives, demonstrated the ability of microorganisms to transform HOCs in both environments, indicating the presence of these compounds in the environment for a long period of time and the adaptive need to develop mechanisms for their detoxification. Metagenome analyses and comparative analyses indicate the genetic potential of microorganisms of both environments to carry out dehalogenation processes, including dehalogenation of anthropogenic HOCs.}, } @article {pmid37512841, year = {2023}, author = {Santiago, BCF and de Souza, ID and Cavalcante, JVF and Morais, DAA and da Silva, MB and Pasquali, MAB and Dalmolin, RJS}, title = {Metagenomic Analyses Reveal the Influence of Depth Layers on Marine Biodiversity on Tropical and Subtropical Regions.}, journal = {Microorganisms}, volume = {11}, number = {7}, pages = {}, pmid = {37512841}, issn = {2076-2607}, support = {312305/2021-4//National Council for Scientific and Technological Development/ ; 302949/2020-8//National Council for Scientific and Technological Development/ ; xxx//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; xxxx//Propesq UFRN/ ; xxx//APC - UFCG/ ; }, abstract = {The emergence of open ocean global-scale studies provided important information about the genomics of oceanic microbial communities. Metagenomic analyses shed light on the structure of marine habitats, unraveling the biodiversity of different water masses. Many biological and environmental factors can contribute to marine organism composition, such as depth. However, much remains unknown about microbial communities' taxonomic and functional features in different water layer depths. Here, we performed a metagenomic analysis of 76 publicly available samples from the Tara Ocean Project, distributed in 8 collection stations located in tropical or subtropical regions, and sampled from three layers of depth (surface water layer-SRF, deep chlorophyll maximum layer-DCM, and mesopelagic zone-MES). The SRF and DCM depth layers are similar in abundance and diversity, while the MES layer presents greater diversity than the other layers. Diversity clustering analysis shows differences regarding the taxonomic content of samples. At the domain level, bacteria prevail in most samples, and the MES layer presents the highest proportion of archaea among all samples. Taken together, our results indicate that the depth layer influences microbial sample composition and diversity.}, } @article {pmid37512553, year = {2023}, author = {Ouyang, R and Zheng, S and Wang, X and Li, Q and Ding, J and Ma, X and Zhuo, Z and Li, Z and Xin, Q and Lu, X and Zhou, L and Ren, Z and Mei, S and Liu, X and Xu, G}, title = {Crosstalk between Breast Milk N-Acetylneuraminic Acid and Infant Growth in a Gut Microbiota-Dependent Manner.}, journal = {Metabolites}, volume = {13}, number = {7}, pages = {}, pmid = {37512553}, issn = {2218-1989}, support = {No. 2020RQ067//the Youth Science and Technology Star Project Support Program from the Scientific and Technological Office of Dalian/ ; No. 2021186//the Youth Innovation Promotion Association of Chinese Academy of Sciences/ ; DICP I202019//the Innovation Program of Science and Research from Dalian Institute of Chemical Physics, Chinese Academy of Sciences/ ; }, abstract = {The healthy growth of infants during early life is associated with lifelong consequences. Breastfeeding has positive impacts on reducing obesity risk, which is likely due to the varied components of breast milk, such as N-acetylneuraminic acid (Neu5Ac). However, the effect of breast milk Neu5Ac on infant growth has not been well studied. In this study, targeted metabolomic and metagenomic analyses were performed to illustrate the association between breast milk Neu5Ac and infant growth. Results demonstrated that Neu5Ac was significantly abundant in breast milk from infants with low obesity risk in two independent Chinese cohorts. Neu5Ac from breast milk altered infant gut microbiota and bile acid metabolism, resulting in a distinct fecal bile acid profile in the high-Neu5Ac group, which was characterized by reduced levels of primary bile acids and elevated levels of secondary bile acids. Taurodeoxycholic acid 3-sulfate and taurochenodeoxycholic acid 3-sulfate were correlated with high breast milk Neu5Ac and low obesity risk in infants, and their associations with healthy growth were reproduced in mice colonized with infant-derived microbiota. Parabacteroides might be linked to bile acid metabolism and act as a mediator between Neu5Ac and infant growth. These results showed the gut microbiota-dependent crosstalk between breast milk Neu5Ac and infant growth.}, } @article {pmid37511545, year = {2023}, author = {Lach, J and Krupińska, M and Mikołajczyk, A and Strapagiel, D and Stączek, P and Matera-Witkiewicz, A}, title = {Novel Antimicrobial Peptides from Saline Environments Active against E. faecalis and S. aureus: Identification, Characterisation and Potential Usage.}, journal = {International journal of molecular sciences}, volume = {24}, number = {14}, pages = {}, pmid = {37511545}, issn = {1422-0067}, support = {POWR.03.02.00-00-I033/16-00//National Centre for Research and Development/ ; WBIOŚ B2111000000038.01//University of Łódź/ ; SUBZ.D250.23.035//Wroclaw Medical University/ ; }, mesh = {Humans ; *Staphylococcus aureus ; *Methicillin-Resistant Staphylococcus aureus ; Antimicrobial Peptides ; Anti-Bacterial Agents/pharmacology/chemistry ; Peptides ; Microbial Sensitivity Tests ; }, abstract = {Microorganisms inhabiting saline environments have been known for decades as producers of many valuable bioproducts. These substances include antimicrobial peptides (AMPs), the most recognizable of which are halocins produced by halophilic Archaea. As agents with a different modes of action from that of most conventionally used antibiotics, usually associated with an increase in the permeability of the cell membrane as a result of a formation of channels and pores, AMPs are a currently promising object of research focused on the investigation of antibiotics with non-standard modes of action. The aim of this study was to investigate antimicrobial activity against multidrug-resistant human pathogens of three peptides, which were synthetised based on sequences identified in metagenomes from saline environments. The investigations were performed against Enterococcus faecalis, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli and Candida albicans. Subsequently, the cytotoxicity and haemolytic properties of the tested peptides were verified. An in silico analysis of the interaction of the tested peptides with molecular targets for reference antibiotics was also carried out in order to verify whether or not they can act in a similar way. The P1 peptide manifested the growth inhibition of E. faecalis at a MIC50 of 32 µg/mL and the P3 peptide at a MIC50 of 32 µg/mL was shown to inhibit the growth of both E. faecalis and S. aureus. Furthermore, the P1 and P3 peptides were shown to have no cytotoxic or haemolytic activity against human cells.}, } @article {pmid37511492, year = {2023}, author = {Qin, Y and Zhao, H and Han, H and Zhu, G and Wang, Z and Li, F}, title = {Chromosome-Level Genome Assembly and Population Genomic Analyses Reveal Geographic Variation and Population Genetic Structure of Prunus tenella.}, journal = {International journal of molecular sciences}, volume = {24}, number = {14}, pages = {}, pmid = {37511492}, issn = {1422-0067}, support = {2022YFD2200400//Ministry of Science and Technology/ ; }, mesh = {*Prunus/genetics ; Metagenomics ; Genomics/methods ; Chromosomes ; *Prunus dulcis ; Genetics, Population ; Phylogeny ; }, abstract = {Prunus tenella is a rare and precious relict plant in China. It is an important genetic resource for almond improvement and an indispensable material in ecological protection and landscaping. However, the research into molecular breeding and genetic evolution has been severely restricted due to the lack of genome information. In this investigation, we created a chromosome-level genomic pattern of P. tenella, 231 Mb in length with a contig N50 of 18.1 Mb by Hi-C techniques and high-accuracy PacBio HiFi sequencing. The present assembly predicted 32,088 protein-coding genes, and an examination of the genome assembly indicated that 94.7% among all assembled transcripts were alignable to the genome assembly; most (97.24%) were functionally annotated. By phylogenomic genome comparison, we found that P. tenella is an ancient group that diverged approximately 13.4 million years ago (mya) from 13 additional closely related species and about 6.5 Mya from the cultivated almond. Collinearity analysis revealed that P. tenella is highly syntenic and has high sequence conservation with almond and peach. However, this species also exhibits many presence/absence variants. Moreover, a large inversion at the 7588 kb position of chromosome 5 was observed, which may have a significant association with phenotypic traits. Lastly, population genetic structure analysis in eight different populations indicated a high genetic differentiation among the natural distribution of P. tenella. This high-quality genome assembly provides critical clues and comprehensive information for the systematic evolution, genetic characteristics, and functional gene research of P. tenella. Moreover, it provides a valuable genomic resource for in-depth study in protection, developing, and utilizing P. tenella germplasm resources.}, } @article {pmid37511184, year = {2023}, author = {Boulangé, CL and Pedersen, HK and Martin, FP and Siegwald, L and Pallejà Caro, A and Eklund, AC and Jia, W and Zhang, H and Berger, B and Sprenger, N and Heine, RG and Cinnamon Study Investigator Group, }, title = {An Extensively Hydrolyzed Formula Supplemented with Two Human Milk Oligosaccharides Modifies the Fecal Microbiome and Metabolome in Infants with Cow's Milk Protein Allergy.}, journal = {International journal of molecular sciences}, volume = {24}, number = {14}, pages = {}, pmid = {37511184}, issn = {1422-0067}, mesh = {Child ; Female ; Animals ; Cattle ; Humans ; Infant ; Child, Preschool ; *Milk Hypersensitivity ; Milk, Human ; Oligosaccharides ; Dietary Supplements ; *Gastrointestinal Microbiome ; Metabolome ; Infant Formula/chemistry ; }, abstract = {Cow's milk protein allergy (CMPA) is a prevalent food allergy among infants and young children. We conducted a randomized, multicenter intervention study involving 194 non-breastfed infants with CMPA until 12 months of age (clinical trial registration: NCT03085134). One exploratory objective was to assess the effects of a whey-based extensively hydrolyzed formula (EHF) supplemented with 2'-fucosyllactose (2'-FL) and lacto-N-neotetraose (LNnT) on the fecal microbiome and metabolome in this population. Thus, fecal samples were collected at baseline, 1 and 3 months from enrollment, as well as at 12 months of age. Human milk oligosaccharides (HMO) supplementation led to the enrichment of bifidobacteria in the gut microbiome and delayed the shift of the microbiome composition toward an adult-like pattern. We identified specific HMO-mediated changes in fecal amino acid degradation and bile acid conjugation, particularly in infants commencing the HMO-supplemented formula before the age of three months. Thus, HMO supplementation partially corrected the dysbiosis commonly observed in infants with CMPA. Further investigation is necessary to determine the clinical significance of these findings in terms of a reduced incidence of respiratory infections and other potential health benefits.}, } @article {pmid37511032, year = {2023}, author = {Hong, M and Tong, L and Mehta, JS and Ong, HS}, title = {Impact of Exposomes on Ocular Surface Diseases.}, journal = {International journal of molecular sciences}, volume = {24}, number = {14}, pages = {}, pmid = {37511032}, issn = {1422-0067}, mesh = {Humans ; *Exposome ; *Eye Diseases/etiology ; Inflammation ; *Corneal Neovascularization ; }, abstract = {Ocular surface diseases (OSDs) are significant causes of ocular morbidity, and are often associated with chronic inflammation, redness, irritation, discomfort, and pain. In severe OSDs, loss of vision can result from ocular surface failure, characterised by limbal stem cell deficiencies, corneal vascularisation, corneal opacification, and surface keratinisation. External and internal exposomes are measures of environmental factors that individuals are exposed to, and have been increasingly studied for their impact on ocular surface diseases. External exposomes consist of external environmental factors such as dust, pollution, and stress; internal exposomes consist of the surface microbiome, gut microflora, and oxidative stress. Concerning internal exposomes, alterations in the commensal ocular surface microbiome of patients with OSDs are increasingly reported due to advancements in metagenomics using next-generation sequencing. Changes in the microbiome may be a consequence of the underlying disease processes or may have a role in the pathogenesis of OSDs. Understanding the changes in the ocular surface microbiome and the impact of various other exposomes may also help to establish the causative factors underlying ocular surface inflammation and scarring, the hallmarks of OSDs. This review provides a summary of the current evidence on exposomes in various OSDs.}, } @article {pmid37511022, year = {2023}, author = {Neidhöfer, C and Bagniceva, M and Wetzig, N and Sieber, MA and Thiele, R and Parčina, M}, title = {Pragmatic Considerations When Extracting DNA for Metagenomics Analyses of Clinical Samples.}, journal = {International journal of molecular sciences}, volume = {24}, number = {14}, pages = {}, pmid = {37511022}, issn = {1422-0067}, mesh = {DNA, Bacterial/genetics ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; *DNA ; }, abstract = {Microbiome analyses are essential for understanding microorganism composition and diversity, but interpretation is often challenging due to biological and technical variables. DNA extraction is a critical step that can significantly bias results, particularly in samples containing a high abundance of challenging-to-lyse microorganisms. Taking into consideration the distinctive microenvironments observed in different bodily locations, our study sought to assess the extent of bias introduced by suboptimal bead-beating during DNA extraction across diverse clinical sample types. The question was whether complex targeted extraction methods are always necessary for reliable taxonomic abundance estimation through amplicon sequencing or if simpler alternatives are effective for some sample types. Hence, for four different clinical sample types (stool, cervical swab, skin swab, and hospital surface swab samples), we compared the results achieved from extracting targeted manual protocols routinely used in our research lab for each sample type with automated protocols specifically not designed for that purpose. Unsurprisingly, we found that for the stool samples, manual extraction protocols with vigorous bead-beating were necessary in order to avoid erroneous taxa proportions on all investigated taxonomic levels and, in particular, false under- or overrepresentation of important genera such as Blautia, Faecalibacterium, and Parabacteroides. However, interestingly, we found that the skin and cervical swab samples had similar results with all tested protocols. Our results suggest that the level of practical automation largely depends on the expected microenvironment, with skin and cervical swabs being much easier to process than stool samples. Prudent consideration is necessary when extending the conclusions of this study to applications beyond rough estimations of taxonomic abundance.}, } @article {pmid37510347, year = {2023}, author = {Aragão, CF and da Silva, SP and do Nascimento, BLS and da Silva, FS and Nunes Neto, JP and Pinheiro, VCS and Cruz, ACR}, title = {Shotgun Metagenomic Sequencing Reveals Virome Composition of Mosquitoes from a Transition Ecosystem of North-Northeast Brazil.}, journal = {Genes}, volume = {14}, number = {7}, pages = {}, pmid = {37510347}, issn = {2073-4425}, mesh = {Animals ; Humans ; Brazil ; Ecosystem ; Virome ; *Culex ; *Aedes ; *Viruses ; *RNA Viruses ; }, abstract = {A wide diversity of pathogenic mosquito-borne viruses circulate in the Brazilian Amazon, and the intense deforestation can contribute to the spread of these viruses. In this context, this study aimed to investigate the viral diversity in mosquitoes of the genera Aedes, Culex, Haemagogus, and Sabethes from a transition area between the Amazon, Cerrado, and Caatinga biomes in Brazil. Metagenomic high-throughput sequencing was used to characterize the virome of 20 mosquito pools. A total of 15 virus-like genomes were identified, comprising species genomically close to insect-specific viruses of the families Iflaviridae, Metaviridae, Lispiviridae, Rhabdoviridae, Xinmoviridae, and Parvoviridae and species of plant viruses of the families Solemoviridae, Virgaviridae, and Partitiviridae. However, sequences of viruses associated with human and animal diseases were not detected. Most of the recovered genomes were divergent from those previously described. These findings reveal that there are a large number of unknown viruses to be explored in the middle-north of Brazil.}, } @article {pmid37509812, year = {2023}, author = {Wang, H and Zhang, M and Qu, C and Fei, Y and Liang, J and Bai, W and Zhao, W and Xiao, G and Liu, G}, title = {Characterization and Correlation of Microbiota and Higher Alcohols Based on Metagenomic and Metabolite Profiling during Rice-Flavor Baijiu Fermentation.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {14}, pages = {}, pmid = {37509812}, issn = {2304-8158}, support = {2021ZDJS005//Research Capacity Enhancement Project of Key Discipline in Guangdong Province/ ; 202201010268//Guangzhou Science and Technology Projects/ ; 2023KJ101//Guangdong Provincial Agricultural Science and Technology Innovation and Extension Project in 2023/ ; 2021B1212040013//Guangdong Provincial Key Laboratory of Lingnan Specialty Food Science and Technology/ ; }, abstract = {Higher alcohol, as an inevitable product of fermentation, plays an important role in the flavor and quality of Baijiu. However, the relationship between the complex microbial metabolism and the formation of higher alcohols in rice-flavor Baijiu was not clear. To investigate the relationship between microorganisms and higher alcohol production, two fermentation mashes inoculated with starters from Heyuan Jinhuangtian Liquor Co., Ltd. (Heyuan, China) as JM and Guangdong Changleshao Co., Ltd. (Meizhou, China) as CM, respectively, with significant differences in higher alcohol profiles during rice-flavor Baijiu fermentation were selected. In general, higher alcohols presented a rapid accumulation during the early fermentation stages, especially in JM, with higher and faster increases than those in CM. As for their precursors including amino acids, pyruvic acid and ketoacids, complex variations were observed during the fermentation. Metagenomic results indicated that Saccharomyces cerevisiae and Rhizopus microsporus were the microorganisms present throughout the brewing process in JM and CM, and the relative abundance of R. microsporus in JM was significantly higher than that in CM. The results of higher alcohol metabolism in JM may contribute to the regulation of higher alcohols in rice-flavor Baijiu.}, } @article {pmid37509218, year = {2023}, author = {Li, G and Jin, Y and Chen, B and Lin, A and Wang, E and Xu, F and Hu, G and Xiao, C and Liu, H and Hou, X and Zhang, B and Song, J}, title = {Exploring the Relationship between the Gut Mucosal Virome and Colorectal Cancer: Characteristics and Correlations.}, journal = {Cancers}, volume = {15}, number = {14}, pages = {}, pmid = {37509218}, issn = {2072-6694}, support = {Nos. 81873553//National Natural Science Foundation of China/ ; Nos. 81800465//National Natural Science Foundation of China/ ; }, abstract = {The fecal virome has been reported to be associated with CRC. However, little is known about the mucosal virome signature in CRC. This study aimed to determine the viral community within CRC tissues and their contributions to colorectal carcinogenesis. Colonic mucosal biopsies were harvested from patients with CRC (biopsies of both neoplasia and adjacent normal tissue (CRC-A)) and healthy controls (HC). The shot-gun metagenomic sequencing of virus-like particles (VLPs) was performed on the biopsies. Viral community, functional pathways, and their correlations to clinical data were analyzed. Fluorescence in situ hybridizations (FISH) for the localization of viruses in the intestine was performed, as well as quantitative PCR for the detection of Torque teno virus load in human mucosal VLP DNA. A greater number and proportion of core species were found in CRC tissues than in CRC-A and HC tissues. The diversity of the mucosal virome in CRC tissues was significantly increased compared to that in HC and CRC-A tissues. The mucosal virome signature of CRC tissues were significantly different from those of HC and CRC-A tissues at the species level. The abundances of eukaryotic viruses from the Anelloviridae family and its sub-species Torque teno virus (TTV) were significantly higher in CRC patients than in HC. Furthermore, increased levels of TTV in the intestinal lamina propria were found in the CRC group. Multiple viral functions of TTV associated with carcinogenesis were enriched in CRC tissues. We revealed for the first time that the mucosal virobiota signature of CRC is characterized by a higher diversity and more eukaryotic viruses. The enrichment of TTV species in CRC tissues suggests that they may play an oncogenic role in CRC. Targeting eukaryotic viruses in the gut may provide novel strategies for the prevention and treatment of CRC.}, } @article {pmid37508354, year = {2023}, author = {Machuca-Sepúlveda, J and Miranda, J and Lefin, N and Pedroso, A and Beltrán, JF and Farias, JG}, title = {Current Status of Omics in Biological Quality Elements for Freshwater Biomonitoring.}, journal = {Biology}, volume = {12}, number = {7}, pages = {}, pmid = {37508354}, issn = {2079-7737}, support = {2020/06982-3//Universidad de La Frontera/ ; }, abstract = {Freshwater ecosystems have been experiencing various forms of threats, mainly since the last century. The severity of this adverse scenario presents unprecedented challenges to human health, water supply, agriculture, forestry, ecological systems, and biodiversity, among other areas. Despite the progress made in various biomonitoring techniques tailored to specific countries and biotic communities, significant constraints exist, particularly in assessing and quantifying biodiversity and its interplay with detrimental factors. Incorporating modern techniques into biomonitoring methodologies presents a challenging topic with multiple perspectives and assertions. This review aims to present a comprehensive overview of the contemporary advancements in freshwater biomonitoring, specifically by utilizing omics methodologies such as genomics, metagenomics, transcriptomics, proteomics, metabolomics, and multi-omics. The present study aims to elucidate the rationale behind the imperative need for modernization in this field. This will be achieved by presenting case studies, examining the diverse range of organisms that have been studied, and evaluating the potential benefits and drawbacks associated with the utilization of these methodologies. The utilization of advanced high-throughput bioinformatics techniques represents a sophisticated approach that necessitates a significant departure from the conventional practices of contemporary freshwater biomonitoring. The significant contributions of omics techniques in the context of biological quality elements (BQEs) and their interpretations in ecological problems are crucial for biomonitoring programs. Such contributions are primarily attributed to the previously overlooked identification of interactions between different levels of biological organization and their responses, isolated and combined, to specific critical conditions.}, } @article {pmid37508100, year = {2023}, author = {Floridia, V and Giuffrè, L and Giosa, D and Arfuso, F and Aragona, F and Fazio, F and Chen, C and Song, C and Romeo, O and D'Alessandro, E}, title = {Comparison of the Faecal Microbiota Composition Following a Dairy By-Product Supplemented Diet in Nero Siciliano and Large White × Landrace Pig Breeds.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {14}, pages = {}, pmid = {37508100}, issn = {2076-2615}, abstract = {The current study compared the faecal microbiota composition of two pig breeds (autochthonous vs. commercial) to understand what happens after the integration of liquid whey in the diet and what the role of the host genetic is. The trial was conducted for 60 days, and the faecal microbiota composition was investigated at three time points, T0, T1 (after 30 days) and T2 (after 60 days) in 30 female pigs (20 commercial crossbred and 10 Nero Siciliano pigs). The animals were divided into four groups (two control and two treatment groups). Generally, in both breeds, Firmicutes (51%) and Bacteroidota (36%) were the most abundant phylum whereas Prevotella, Treponema and Lactobacillus were the most abundant genera. The two breeds have a different reaction to a liquid whey diet. In fact, as shown by PERMANOVA analysis, the liquid whey significantly (p < 0.001) affects the microbiota composition of crossbreeds while not having an effect on the microbiota of the Nero Siciliano. Despite this, in both breeds Bifidobacterium and Ruminococcus have been positively influenced by liquid whey and they promote intestinal health, improve immunity, increase performance, and feed efficiency. In conclusion, the integration of liquid whey had a different effect on the Nero Siciliano and crossbred pig breeds, emphasizing the importance of the host genetic profile in determining the faecal bacterial composition.}, } @article {pmid37508080, year = {2023}, author = {Gryaznova, M and Smirnova, Y and Burakova, I and Morozova, P and Nesterova, E and Gladkikh, M and Mikhaylov, E and Syromyatnikov, M}, title = {Characteristics of the Fecal Microbiome of Piglets with Diarrhea Identified Using Shotgun Metagenomics Sequencing.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {14}, pages = {}, pmid = {37508080}, issn = {2076-2615}, support = {project FZGW-2020-0001, unique number of the register of State tasks 075001X39782002//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Diarrhea in piglets is one of the most common diseases leading to high mortality and, as a result, to economic losses. Shotgun metagenomic sequencing was performed on the DNBSEQ-G50, MGI system to study the role of the fecal microbiome in the development of diarrhea in newborn piglets. Analysis of the study data showed that the composition of the fecal microbiome at the level of bacteria and fungi did not differ in piglets with diarrhea from the healthy group. Bacteria belonging to the phyla Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria, and Fusobacteria were the most abundant. However, a higher level of bacterial alpha diversity was observed in the group of piglets with diarrhea, which may be due to dysbacteriosis and inflammation. The study of the virome showed the difference between the two types of phages: Bacteroides B40-8 prevailed in diseased piglets, while Escherichia virus BP4 was found in greater numbers in healthy piglets. The results of our study suggest that the association between the fecal microbiome and susceptibility to diarrhea in suckling piglets may have been previously overestimated.}, } @article {pmid37508075, year = {2023}, author = {Salman, MM and Nawaz, M and Yaqub, T and Mushtaq, MH}, title = {Exploring the Milk Microbiota of Healthy and Mastitic Nili Ravi Buffalo Using 16S rRNA Gene Base Metagenomic Analysis.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {14}, pages = {}, pmid = {37508075}, issn = {2076-2615}, support = {PHEC/ARA/PIRCA/20211/9//Punjab Higher Education Commission/ ; }, abstract = {The Nili Ravi, a buffalo breed from Pakistan, significantly contributes to the dairy industry. Mastitis is one of the major challenges affecting milk production in this breed. The objective of the current study was to identify the bacterial communities and diversity in healthy and mastitic milk of this breed. Milk samples (n = 14) were collected from Nili Ravi buffaloes with different udder health statuses, i.e., healthy (5), subclinical mastitis (4), and clinical mastitis (5). The DNAs were extracted, subjected to partial amplification of 16S rDNA (V3 and V4 regions), and sequenced using the Illumina platform. The results revealed variations in the bacterial communities in the milk of animals with different udder health statuses. Proteobacteria was the predominant phylum in the healthy group, while clinical and subclinical mastitis milk had a higher abundance of Firmicutes. Dominant bacterial genera in the healthy group were Streptococcus (11.60%), Herbaspirillum (7.65%), and Staphylococcus (4.70%), whereas the clinical mastitis group was dominated by Streptococcus (33.96%), Staphylococcus (7.87%), and Corynebacterium (2.68%), and the subclinical mastitis group was dominated by Bacillus (15.70%), Corynebacterium (6.70%), and Staphylococcus (6.58%). Assignment of operational taxonomic units at the species level resulted in most species being assigned to uncultured or unknown bacteria or remaining unassigned. Alpha diversity indices indicated lower microbial diversity in the clinical mastitis group, while beta diversity indices showed a scattered pattern of sample clustering in PCA plots among different groups. It is concluded that bacterial diversity in the milk of Nili Ravi buffaloes suffering from clinical mastitis is lower compared to healthy and subclinical mastitis cases. It is concluded that the variations in the microbiota of healthy and mastitic milk may be further investigated and exploited as signature microbes associated with the udder health status of Nili Ravi buffalo.}, } @article {pmid37507809, year = {2023}, author = {Fredriksen, S and de Warle, S and van Baarlen, P and Boekhorst, J and Wells, JM}, title = {Resistome expansion in disease-associated human gut microbiomes.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {166}, pmid = {37507809}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; }, abstract = {BACKGROUND: The resistome, the collection of antibiotic resistance genes (ARGs) in a microbiome, is increasingly recognised as relevant to the development of clinically relevant antibiotic resistance. Many metagenomic studies have reported resistome differences between groups, often in connection with disease and/or antibiotic treatment. However, the consistency of resistome associations with antibiotic- and non-antibiotic-treated diseases has not been established. In this study, we re-analysed human gut microbiome data from 26 case-control studies to assess the link between disease and the resistome.

RESULTS: The human gut resistome is highly variable between individuals both within and between studies, but may also vary significantly between case and control groups even in the absence of large taxonomic differences. We found that for diseases commonly treated with antibiotics, namely cystic fibrosis and diarrhoea, patient microbiomes had significantly elevated ARG abundances compared to controls. Disease-associated resistome expansion was found even when ARG abundance was high in controls, suggesting ongoing and additive ARG acquisition in disease-associated strains. We also found a trend for increased ARG abundance in cases from some studies on diseases that are not treated with antibiotics, such as colorectal cancer.

CONCLUSIONS: Diseases commonly treated with antibiotics are associated with expanded gut resistomes, suggesting that historical exposure to antibiotics has exerted considerable selective pressure for ARG acquisition in disease-associated strains. Video Abstract.}, } @article {pmid37507643, year = {2023}, author = {Achudhan, AB and Kannan, P and Gupta, A and Saleena, LM}, title = {A Review of Web-Based Metagenomics Platforms for Analysing Next-Generation Sequence Data.}, journal = {Biochemical genetics}, volume = {}, number = {}, pages = {}, pmid = {37507643}, issn = {1573-4927}, abstract = {Metagenomics has now evolved as a promising technology for understanding the microbial population in the environment. By metagenomics, a number of extreme and complex environment has been explored for their microbial population. Using this technology, researchers have brought out novel genes and their potential characteristics, which have robust applications in food, pharmaceutical, scientific research, and other biotechnological fields. A sequencing platform can provide a sequence of microbial populations in any given environment. The sequence needs to be analysed computationally to derive meaningful information. It is presumed that only bioinformaticians with extensive computational skills can process the sequencing data till the downstream end. However, numerous open-source software and online servers are available to analyse the metagenomic data developed for a biologist with less computational skills. This review is focused on bioinformatics tools such as Galaxy, CSI-NGS portal, ANASTASIA and SHAMAN, EBI- metagenomics, IDseq, and MG-RAST for analysing metagenomic data.}, } @article {pmid37507157, year = {2023}, author = {Wilkens, D and Simon, J}, title = {Biosynthesis and function of microbial methylmenaquinones.}, journal = {Advances in microbial physiology}, volume = {83}, number = {}, pages = {1-58}, doi = {10.1016/bs.ampbs.2023.05.002}, pmid = {37507157}, issn = {2162-5468}, mesh = {Humans ; Vitamin K 2/metabolism ; *Hydroquinones ; Phylogeny ; *Quinones/metabolism ; Methyltransferases/genetics/metabolism ; Electron Transport ; }, abstract = {The membranous quinone/quinol pool is essential for the majority of life forms and its composition has been widely used as a biomarker in microbial taxonomy. The most abundant quinone is menaquinone (MK), which serves as an essential redox mediator in various electron transport chains of aerobic and anaerobic respiration. Several methylated derivatives of MK, designated methylmenaquinones (MMKs), have been reported to be present in members of various microbial phyla possessing either the classical MK biosynthesis pathway (Men) or the futalosine pathway (Mqn). Due to their low redox midpoint potentials, MMKs have been proposed to be specifically involved in appropriate electron transport chains of anaerobic respiration. The class C radical SAM methyltransferases MqnK, MenK and MenK2 have recently been shown to catalyse specific MK methylation reactions at position C-8 (MqnK/MenK) or C-7 (MenK2) to synthesise 8-MMK, 7-MMK and 7,8-dimethylmenaquinone (DMMK). MqnK, MenK and MenK2 from organisms such as Wolinella succinogenes, Adlercreutzia equolifaciens, Collinsella tanakaei, Ferrimonas marina and Syntrophus aciditrophicus have been functionally produced in Escherichia coli, enabling extensive quinone/quinol pool engineering of the native MK and 2-demethylmenaquinone (DMK). Cluster and phylogenetic analyses of available MK and MMK methyltransferase sequences revealed signature motifs that allowed the discrimination of MenK/MqnK/MenK2 family enzymes from other radical SAM enzymes and the identification of C-7-specific menaquinone methyltransferases of the MenK2 subfamily. It is envisaged that this knowledge will help to predict the methylation status of the menaquinone/menaquinol pool of any microbial species (or even a microbial community) from its (meta)genome.}, } @article {pmid37506938, year = {2023}, author = {Rani, J and Dhoble, AS}, title = {Effect of fungal pretreatment by Pycnoporus sanguineus and Trichoderma longibrachiatum on the anaerobic digestion of rice straw.}, journal = {Bioresource technology}, volume = {387}, number = {}, pages = {129503}, doi = {10.1016/j.biortech.2023.129503}, pmid = {37506938}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Oryza ; *Polyporaceae ; Biofuels/analysis ; Methane/analysis ; }, abstract = {Rice straw is composed of complex lignocellulosic biomass, representing a major obstacle in its conversion to bioenergy. The objective of this study was to evaluate the usefulness of less explored fungal strains Trichoderma longibrachiatum (TL) and Pycnoporus sanguineus (PS) in improving hydrolysis and bioavailability of rice straw in anaerobic digestion (AD). The fungal treatment of rice straw for 10 days by PS and TL increased biogas production by 20.79% and 17.85% and reduced soluble chemical oxygen demand (sCOD) by 71.43% and 64.70%, respectively. The AD samples containing fungal-treated rice straw showed higher lignocellulolytic enzyme activities contributing to better process performance. The taxonomic profile of microbial communities in treated samples showed increased diversity that could sustain consistent system performance and exhibit enhanced resilience against pH fluctuations. Metagenomic analysis revealed 60.82% increase in Proteobacteria in PS and 11.58% increase in Bacteroidetes in TL-treated rice straw samples resulting in improved hydrolysis.}, } @article {pmid37506757, year = {2023}, author = {Muzyukina, P and Soutourina, O}, title = {CRISPR genotyping methods: Tracing the evolution from spoligotyping to machine learning.}, journal = {Biochimie}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.biochi.2023.07.017}, pmid = {37506757}, issn = {1638-6183}, abstract = {CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems provide prokaryotes with adaptive immunity defenses against foreign genetic invaders. The identification of CRISPR-Cas function is among the most impactful discoveries of recent decades that have shaped the development of genome editing in various organisms paving the way for a plethora of promising applications in biotechnology and health. Even before the discovery of CRISPR-Cas biological role, the particular structure of CRISPR loci has been explored for epidemiological genotyping of bacterial pathogens. CRISPR-Cas loci are arranged in CRISPR arrays of mostly identical direct repeats intercalated with invader-derived spacers and an operon of cas genes encoding the Cas protein components. Each small CRISPR RNA (crRNA) encoded within the CRISPR array constitutes a key functional unit of this RNA-based CRISPR-Cas defense system guiding the Cas effector proteins toward the foreign nucleic acids for their destruction. The information acquired from prior invader encounters and stored within CRISPR arrays turns out to be extremely valuable in tracing the microevolution and epidemiology of major bacterial pathogens. We review here the history of CRISPR-based typing strategies highlighting the first PCR-based methods that have set the stage for recent developments of high-throughput sequencing and machine learning-based approaches. A great amount of whole genome sequencing and metagenomic data accumulated in recent years opens up new avenues for combining experimental and computational approaches of high-resolution CRISPR-based typing.}, } @article {pmid37506647, year = {2023}, author = {Zhou, Y and Zhou, S}, title = {Role of microplastics in microbial community structure and functions in urban soils.}, journal = {Journal of hazardous materials}, volume = {459}, number = {}, pages = {132141}, doi = {10.1016/j.jhazmat.2023.132141}, pmid = {37506647}, issn = {1873-3336}, mesh = {Humans ; *Microplastics/pharmacology ; Plastics ; Soil Microbiology ; Soil/chemistry ; *Microbiota ; }, abstract = {Evidence from the laboratory suggests that microplastics (MPs) can harm soil microorganisms, affecting the structures and functions of microbial communities. The impact of soil MPs on microbes in actual urban environments with high human activity levels, however, has not been well reported. To investigate the MP effect on urban soil microorganisms under complex scenarios, we analyzed 42 soil samples from standardized plots of 7 urban functional zones. We report that urban green spaces are important for studying microbial diversity in the study area, and they also contribute to the global homogenization of soil microbes and genes. Bacterial communities in soils enriched with various MPs showed greater differences in OTUs than fungi. Compared to low-MP soils, most ARGs and nutrient cycling genes had similar or slightly lower abundances in soils with high levels of MPs. The coupling of pollutant factors with MPs as independent variables had significant explanatory power for both positive and negative correlations in PLS-PM analysis. Specifically, PET and PP MPs explained 3.54% and 6.03%, respectively, of the microbial community and functional genes. This study fills knowledge gaps on the effects of MPs on urban soil microbial communities in real environments, facilitating better management of urban green spaces.}, } @article {pmid37506645, year = {2023}, author = {Zhu, M and Li, Y and Wang, L and Zhang, W and Niu, L and Hu, T}, title = {Unraveling antibiotic resistomes associated with bacterial and viral communities in intertidal mudflat aquaculture area.}, journal = {Journal of hazardous materials}, volume = {459}, number = {}, pages = {132087}, doi = {10.1016/j.jhazmat.2023.132087}, pmid = {37506645}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents ; Phylogeny ; *Genes, Bacterial ; Bacteria/genetics ; Aquaculture ; }, abstract = {The extensive use of antibiotics in intertidal mudflat aquaculture area has substantially increased the dissemination risk of antibiotic resistance genes (ARGs). As hosts of ARGs, bacteria and virus exert vital effects on ARG dissemination. However, the insights for the interrelationships among ARGs, bacteria, and virus have not been thoroughly explored in intertidal mudflat. Therefore, this study attempts to unravel the occurrence, dissemination, evolution, and driving mechanisms of ARGs associated with bacterial and viral communities using metagenomic sequencing in a typical intertidal mudflat. Abundant and diverse ARGs (22 types and 437 subtypes) were identified and those of ARGs were higher in spring than in autumn. It is worthy noted that virus occupied a more essential position than bacteria for ARGs dissemination through network analysis. Meanwhile, nitrogen exerted indirect effect on ARG profiles by shaping viral and bacterial diversity. According to the results of neutral and null models, deterministic processes dominated the ARG community assembly by controlling sediment nitrogen and antibiotics. Homogeneous and variable selection dominated phylogenetic turnover of ARG community, contributing 46.15% and 45.90% of the total processes, respectively. This study can hence theoretically support for the ARG pollution control and management in intertidal mudflat aquaculture area.}, } @article {pmid37506636, year = {2023}, author = {Yang, T and Wang, X and Hui, X and Jiang, L and Bi, X and Ng, HY and Zheng, X and Huang, S and Jiang, B and Zhou, X}, title = {Antibiotic resistome associated with inhalable bioaerosols from wastewater to atmosphere: Mobility, bacterial hosts, source contributions and resistome risk.}, journal = {Water research}, volume = {243}, number = {}, pages = {120403}, doi = {10.1016/j.watres.2023.120403}, pmid = {37506636}, issn = {1879-2448}, mesh = {*Wastewater ; *Genes, Bacterial ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria/genetics ; Atmosphere ; Particulate Matter ; Anti-Bacterial Agents ; }, abstract = {Antibiotic resistome can be carried by the bioaerosols and propagate from wastewater treatment plants (WWTPs) to the atmosphere, but questions remain regarding their mobility, bacterial hosts, source, and resistome risk. Here, fine particulate matter (PM2.5) was collected within and around a large WWTP and analyzed by the metagenomic assembly and binning. PM2.5 was discovered with increasing enrichment of total antibiotic resistance genes (ARGs), potentially mobile ARGs, and antibiotic-resistant bacteria (ARB) along the WWTP-downwind-upwind gradient. Some ARGs were found to be flanked by certain mobile genetic elements and generally mediated by plasmids in WWTP-PM2.5. Totally, 198 metagenome assembled genomes assigning to seven phyla were identified as the ARB, and a contig-based analysis indicated that 32 pathogens were revealed harboring at least two ARGs. Despite disparate aerosolization potentials of ARGs or ARB at different WWTP units, high resistome risks were found, along with the dominant contribution of wastewater for airborne ARGs (44.79-62.82%) and ARB (35.03-40.10%). Among the detected WWTP matrices, the sludge dewatering room was characterized by the highest resistome risk associated with PM2.5. This study underscores the dispersion of ARGs and ARB from WWTPs to the atmosphere and provides a reference for managing risks of antibiotic resistance.}, } @article {pmid37506632, year = {2023}, author = {Luo, Z and Li, Y and Chen, B and Lei, M and Zhang, N and Zhang, X and Li, J}, title = {Effect of free ammonia on partial denitrification: Long-term performance, mechanism, and feasibility of PD/Anammox-FBBR for mature landfill leachate treatment.}, journal = {Water research}, volume = {243}, number = {}, pages = {120238}, doi = {10.1016/j.watres.2023.120238}, pmid = {37506632}, issn = {1879-2448}, mesh = {*Ammonia ; Denitrification ; *Water Pollutants, Chemical ; Anaerobic Ammonia Oxidation ; Feasibility Studies ; Glutamine ; Nitrogen Dioxide ; Oxidation-Reduction ; Bioreactors/microbiology ; Nitrogen ; Bacteria ; Sewage ; }, abstract = {As a stable and effective approach for NO2[-]-N accumulation, partial denitrification (PD) could significantly cut down operation cost, and PD/Anammox (PD/A) is a promising nitrogen removal process in wastewater treatment. The biotoxicity of free ammonia (FA) to nitrifying bacteria and anammox bacteria has been demonstrated, while whether FA affects PD bacteria is an open question. Here, long-term operation of PD-fixed bed biofilm reactor (PD-FBBR) treating synthetic wastewater and mature landfill leachate was conducted to reveal the mechanism concerning the effect of FA on PD bacteria. Stable NO2[-]-N accumulation was achieved with NO3[-]-N to NO2[-]-N transformation ratio (NTR) of 60-70% during 280-day operation with FA ranged from 0 to 20.71 ± 0.23 mg/L, while NTR decreased and maintained at ∼30% when FA reached 40.59 ± 0.19 mg/L. Specific NOx[-]-N reduction rate improved at low FA concentration (< 12 mg/L), while high FA level (> 25 mg/L) had inhibitory effect on PD bacteria. Under FA stress, more extracellular polymeric substances (EPS) were secreted, and the glnA gene abundance, glutamine synthase concentration, and glutamine concentration in cell and EPS significantly increased, indicating the enhancement of glutamine biosynthesis in PD bacteria for ammonia assimilation played an important role in response to FA stress. Metagenomic sequencing showed that FA stimulated the upregulation of narK (NO3[-]-N/NO2[-]-N antiporter) gene abundance and enhanced uptake of NO3[-]-N and extrusion of NO2[-]-N. Comamonas, unclassified_f__Comamonadaceae and Thauera were highly enriched in biofilm, which played a key role in the stable NO2[-]-N accumulation. Furthermore, a novel two stage PD/A-FBBR was applied to mature landfill leachate treatment, and satisfactory total inorganic nitrogen removal efficiency ranged from 81.38 ± 3.56% to 89.16 ± 1.57% was obtained at relatively low COD/NO3[-]-N of 2.57-2.84. Overall, these findings demonstrated how PD bacteria respond to FA stress and confirmed the feasibility of PD/A process in high FA wastewater treatment.}, } @article {pmid37506257, year = {2024}, author = {Yan, M and Zou, X and Wang, Y and Wang, C and Wang, Y and Liu, Z and Shang, L and Cui, X and Cao, B}, title = {Impact of Metagenomic Next-Generation Sequencing of Bronchoalveolar Lavage Fluid on Antimicrobial Stewardship in Patients With Lower Respiratory Tract Infections: A Retrospective Cohort Study.}, journal = {The Journal of infectious diseases}, volume = {229}, number = {1}, pages = {223-231}, doi = {10.1093/infdis/jiad296}, pmid = {37506257}, issn = {1537-6613}, mesh = {Humans ; Bronchoalveolar Lavage Fluid ; *Antimicrobial Stewardship ; Retrospective Studies ; High-Throughput Nucleotide Sequencing ; *Respiratory Tract Infections/drug therapy ; Anti-Bacterial Agents/therapeutic use ; Dimercaprol ; Metagenomics ; Antiviral Agents ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: The impact of metagenomic next-generation sequencing (mNGS) on antimicrobial stewardship in patients with lower respiratory tract infections (LRTIs) is still unknown.

METHODS: This retrospective cohort study included patients who had LRTIs diagnosed and underwent bronchoalveolar lavage between September 2019 and December 2020. Patients who underwent both mNGS and conventional microbiologic tests were classified as the mNGS group, while those with conventional tests only were included as a control group. A 1:1 propensity score match for baseline variables was conducted, after which changes in antimicrobial stewardship between the 2 groups were assessed.

RESULTS: A total of 681 patients who had an initial diagnosis of LRTIs and underwent bronchoalveolar lavage were evaluated; 306 patients were finally included, with 153 in each group. mNGS was associated with lower rates of antibiotic escalation than in the control group (adjusted odds ratio, 0.466 [95% confidence interval, .237-.919]; P = .02), but there was no association with antibiotic de-escalation. Compared with the control group, more patients discontinued the use of antivirals in the mNGS group.

CONCLUSIONS: The use of mNGS was associated with lower rates of antibiotic escalation and may facilitate the cessation of antivirals, but not contribute to antibiotic de-escalation in patients with LRTIs.}, } @article {pmid37505986, year = {2023}, author = {Shetty, P and Shetty, S and Rai, P and Kumar, BK and Bhat, R}, title = {Role of oral microbiota in irreversible pulpitis - Current strategies and future perspectives.}, journal = {Acta microbiologica et immunologica Hungarica}, volume = {70}, number = {3}, pages = {177-186}, doi = {10.1556/030.2023.02082}, pmid = {37505986}, issn = {1588-2640}, mesh = {Humans ; *Pulpitis/microbiology ; Bacteria/genetics ; *Microbiota ; Inflammation ; }, abstract = {Irreversible pulpitis is an inflammation of the tooth pulp caused by an opportunity-driven invasion of the pulp space by oral microbiota typically prevalent in the oral cavity. Microbial organisms are extensively recognised to be the fundamental cause of endodontic infections and treatment failures. Previously, bacterial species responsible for these infections were largely recognised using conventional microbial culture techniques, lending credence to the widely held belief that anaerobic Gram-negative bacteria frequently enter the pulp space and trigger endodontic infections. The advent of novel technologies grants the advantage of detecting and studying microbial populations via an amalgamation of the modern "Omics" techniques and meticulous bioinformatics analysis, additionally detecting the metatranscriptome, metaproteome and metabolome along with the metagenome. Amongst these analytical strategies, metagenomic analyses are essentially pragmatic for investigating the oral microbiome. Metagenomics favor not only assessment of microbial composition in diseased conditions, but also contributes to detection of novel, potentially pathogenic species inclusive of non-viable bacteria. The present review describes current knowledge of root canal microbiome, including its composition and functional attributes, the novel strategies available for detection of microbiome as well as challenges associated and provides some crucial pointers for areas of future research.}, } @article {pmid37505849, year = {2023}, author = {Gao, J and Liu, C and Yi, J and Shi, Y and Li, H and Liu, H}, title = {Genomic Characteristics of Feline Anelloviruses Isolated from Domestic Cats in Shanghai, China.}, journal = {Veterinary sciences}, volume = {10}, number = {7}, pages = {}, pmid = {37505849}, issn = {2306-7381}, support = {[2022]012; No.2019-3-3//Shanghai Academy of Agricultural Sciences (SAAS) Program for Excellent Research Team-Animal disease prevention and control team; Shanghai Agricultural Applied Technology Development Program/ ; }, abstract = {Viral metagenomics techniques allow the high-throughput discovery of possible pathogens carried by companion animals from their feces and other excreta. In this study, the viral metagenomics of 22 groups of fecal samples from domestic cats revealed a high prevalence of feline anelloviruses (FcTTV) infection in domestic cats in Shanghai, China. Serum samples from 30 cat individuals were further detected by polymerase chain reaction, and an average positive rate of 36.67% (11/30) of FcTTV infection was found. Next, the full-length sequences of five Shanghai FcTTV variants were obtained and submitted to GenBank with access numbers OP186140 to OP186144. Phylogenetic analysis indicates that the Shanghai FcTTV variants have relatively consistent genomic characteristics, with two variants from Zhejiang 2019 and one variant from the Czech Republic 2010. The recombination event analysis of the variants showed that one variant (OP186141_SH-02) had a primary parental sequence derived from a variant (KM229764) from the Czech Republic in 2010, while the secondary parental sequence was derived from OP186140_SH-01. The results revealed that FcTTV infection is prevalent in domestic cats and that the use of viral metagenomics to rapidly identify some infecting viruses whose hosts lack clinical features would be an effective approach.}, } @article {pmid37505829, year = {2023}, author = {Thongma, N and Sivamaruthi, BS and Bharathi, M and Tansrisook, C and Peerajan, S and Tanongpitchayes, K and Chawnan, N and Rashmi, S and Thongkorn, K and Chaiyasut, C}, title = {Influence of Gallic Acid-Containing Mouth Spray on Dental Health and Oral Microbiota of Healthy Dogs: A Pilot Study.}, journal = {Veterinary sciences}, volume = {10}, number = {7}, pages = {}, pmid = {37505829}, issn = {2306-7381}, abstract = {The pilot study aimed to investigate the effects of GAMS on oral microbiota in healthy dog subjects. Thirty-eight dogs were recruited and randomly allocated to the placebo (n = 19) and treatment groups (n = 19). The dogs were treated with mouth spray once daily for 42 days. The changes in the gingival index (GI), plaque index (PI), and calculus index (CI) were measured at baseline (day 0) and end of the study (42nd day). The changes in the oral microbial composition of representative dogs (placebo, n = 7; and treatment, n = 7) were also evaluated at baseline and end of the study. Oral microbial composition was assessed by sequencing. The sequences were annotated using the QIIME 2.0[TM]. The GI, PI, and CI indexes were reduced after the GAMS usage. The abundance of the commensal bacterial phylum Actinobacteria and Chloroflexi, genera Frederiksenia, and Bergeyella was improved after six weeks of GAMS usage. GAMS reduced the pathogenic bacterial species, including Neisseria sp., Desulfobulbus sp., Capnocytophaga canis, and Corynebacterium mustelae. Moreover, some pathogenic bacterial abundances were increased at the end of the study. All the microbial variations were observed within the group. The inter-group analysis revealed that the changes were unrelated to GAMS usage. Further studies need to be carried out using more experimental subjects to confirm the effectiveness of GAMS. More metagenomic data are required to evidence the GMAS impact on the oral microbiome of healthy dogs.}, } @article {pmid37505576, year = {2023}, author = {Pei, Y and Sun, M and Zhang, J and Lei, A and Chen, H and Kang, X and Ni, H and Yang, S}, title = {Comparative Metagenomic and Metatranscriptomic Analyses Reveal the Response of Black Soldier Fly (Hermetia illucens) Larvae Intestinal Microbes and Reduction Mechanisms to High Concentrations of Tetracycline.}, journal = {Toxics}, volume = {11}, number = {7}, pages = {}, pmid = {37505576}, issn = {2305-6304}, support = {2021YFD1700900, 2022YFC3401700//National Key Research and Development Program of China/ ; 2022HYTP041//the Young Elite Scientists Sponsorship Program by the Henan Association for Science and Technology/ ; 232102320103//the Key Technologies R & D Program of Henan Province/ ; }, abstract = {Black soldier fly (Hermetia illucens L) larvae (BSFL) possess remarkable antibiotic degradation abilities due to their robust intestinal microbiota. However, the response mechanism of BSFL intestinal microbes to the high concentration of antibiotic stress remains unclear. In this study, we investigated the shift in BSFL gut microbiome and the functional genes that respond to 1250 mg/kg of tetracycline via metagenomic and metatranscriptomic analysis, respectively. The bio-physiological phenotypes showed that the survival rate of BSFL was not affected by tetracycline, while the biomass and substrate consumption of BSFL was slightly reduced. Natural BSFL achieved a 20% higher tetracycline degradation rate than the germ-free BSFL after 8 days of rearing. Metagenomic and metatranscriptomic sequencing results revealed the differences between the entire and active microbiome. Metatranscriptomic analysis indicated that Enterococcus, Vagococcus, Providencia, and Paenalcaligenes were the active genera that responded to tetracycline. Furthermore, based on the active functional genes that responded to tetracycline pressure, the response mechanisms of BSFL intestinal microbes were speculated as follows: the Tet family that mediates the expression of efflux pumps expel tetracycline out of the microbes, while tetM and tetW release it from the ribosome. Eventually, tetracycline was degraded by deacetylases and novel enzymes. Overall, this study provides novel insights about the active intestinal microbes and their functional genes in insects responding to the high concentration of antibiotics.}, } @article {pmid37504575, year = {2023}, author = {Li, J and Sauers, L and Zhuang, D and Ren, H and Guo, J and Wang, L and Zhuang, M and Guo, Y and Zhang, Z and Wu, J and Yao, J and Yang, H and Huang, J and Wang, C and Lin, Q and Zhang, Z and Sadd, BM}, title = {Divergence and convergence of gut microbiomes of wild insect pollinators.}, journal = {mBio}, volume = {14}, number = {4}, pages = {e0127023}, pmid = {37504575}, issn = {2150-7511}, support = {R15 GM129681/GM/NIGMS NIH HHS/United States ; }, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome/physiology ; Phylogeny ; Insecta/physiology ; *Microbiota ; *Wasps ; Pollination ; }, abstract = {Pollination services provided by wild insect pollinators are critical to natural ecosystems and crops around the world. There is an increasing appreciation that the gut microbiota of these insects influences their health and consequently their services. However, pollinator gut microbiota studies have focused on well-described social bees, but rarely include other, more phylogenetically divergent insect pollinators. To expand our understanding, we explored the insect pollinator microbiomes across three insect orders through two DNA sequencing approaches. First, in an exploratory 16S amplicon sequencing analysis of taxonomic community assemblages, we found lineage-specific divergences of dominant microbial genera and microbiota community composition across divergent insect pollinator genera. However, we found no evidence for a strong broad-scale phylogenetic signal, which we see for community relatedness at finer scales. Subsequently, we utilized metagenomic shotgun sequencing to obtain metagenome-assembled genomes and assess the functionality of the microbiota from pollinating flies and social wasps. We uncover a novel gut microbe from pollinating flies in the family Orbaceae that is closely related to Gilliamella spp. from social bees but with divergent functions. We propose this novel species be named Candidatus Gilliamella eristali. Further metagenomes of dominant fly and wasp microbiome members suggest that they are largely not host-insect adapted and instead may be environmentally derived. Overall, this study suggests selective processes involving ecology or physiology, or neutral processes determining microbe colonization may predominate in the turnover of lineages in insect pollinators broadly, while evolution with hosts may occur only under certain circumstances and on smaller phylogenetic scales. IMPORTANCE Wild insect pollinators provide many key ecosystem services, and the microbes associated with these insect pollinators may influence their health. Therefore, understanding the diversity in microbiota structure and function, along with the potential mechanisms shaping the microbiota across diverse insect pollinators, is critical. Our study expands beyond existing knowledge of well-studied social bees, like honey bees, including members from other bee, wasp, butterfly, and fly pollinators. We infer ecological and evolutionary factors that may influence microbiome structure across diverse insect pollinator hosts and the functions that microbiota members may play. We highlight significant differentiation of microbiomes among diverse pollinators. Closer analysis suggests that dominant members may show varying levels of host association and functions, even in a comparison of closely related microbes found in bees and flies. This work suggests varied importance of ecological, physiological, and non-evolutionary filters in determining structure and function across largely divergent wild insect pollinator microbiomes.}, } @article {pmid37504286, year = {2023}, author = {Marín-Paredes, R and Bolívar-Torres, HH and Coronel-Gaytán, A and Martínez-Romero, E and Servín-Garcidueñas, LE}, title = {A Metagenome from a Steam Vent in Los Azufres Geothermal Field Shows an Abundance of Thermoplasmatales archaea and Bacteria from the Phyla Actinomycetota and Pseudomonadota.}, journal = {Current issues in molecular biology}, volume = {45}, number = {7}, pages = {5849-5864}, pmid = {37504286}, issn = {1467-3045}, support = {IA210617 IA208019//PAPIIT-UNAM/ ; }, abstract = {Los Azufres National Park is a geothermal field that has a wide number of thermal manifestations; nevertheless, the microbial communities in many of these environments remain unknown. In this study, a metagenome from a sediment sample from Los Azufres National Park was sequenced. In this metagenome, we found that the microbial diversity corresponds to bacteria (Actinomycetota, Pseudomonadota), archaea (Thermoplasmatales and Candidatus Micrarchaeota and Candidatus Parvarchaeota), eukarya (Cyanidiaceae), and viruses (Fussellovirus and Caudoviricetes). The functional annotation showed genes related to the carbon fixation pathway, sulfur metabolism, genes involved in heat and cold shock, and heavy-metal resistance. From the sediment, it was possible to recover two metagenome-assembled genomes from Ferrimicrobium and Cuniculiplasma. Our results showed that there are a large number of microorganisms in Los Azufres that deserve to be studied.}, } @article {pmid37503781, year = {2023}, author = {Li, S and Luo, Z and Wang, S and Nan, Q and Ji, G}, title = {Denitrification fractionates N and O isotopes of nitrate following a ratio independent of carbon sources in freshwaters.}, journal = {Environmental microbiology}, volume = {25}, number = {11}, pages = {2404-2415}, doi = {10.1111/1462-2920.16468}, pmid = {37503781}, issn = {1462-2920}, mesh = {*Nitrates/analysis ; Nitrogen Isotopes/analysis ; Denitrification ; Carbon/analysis ; Oxygen Isotopes/analysis ; Nitrogen/analysis ; Organic Chemicals ; Fresh Water ; Environmental Monitoring/methods ; *Water Pollutants, Chemical/analysis ; }, abstract = {The stable isotope technique has been used in tracking nitrogen cycling processes, but the isotopic characteristics are influenced by environmental conditions. To better understand the variability of nitrate isotopes in nature, we investigated the influence of organic carbon sources on isotope fractionation characteristics during microbial denitrification. Denitrifying cultures were inoculated with freshwater samples and enriched with five forms of organic compounds, that is, acetate, citrate, glucose, cellobiose, and leucine. Though the isotope enrichment factors of nitrogen and oxygen ([15] ε and [18] ε) changed with carbon sources, [18] ε/[15] ε always followed a proportionality near 1. Genome-centred metagenomics revealed the enrichment of a few populations, such as Pseudomonas, Enterobacter, and Atlantibacter, most of which contained both NapA- and NarG-type nitrate reductases. Metatranscriptome showed that both NapA and NarG were expressed but to different extents in the enrichments. Furthermore, isotopic data collected from a deep reservoir was analysed. The results showed δ[18] O- and δ[15] N-nitrate did not correlate in the surface water where nitrification was active, but [18] ε/[15] ε followed a proportionality of 1.05 ± 011 in deeper waters (≥ 12 m) where denitrification controlled the nitrate isotope. The independence of [18] ε/[15] ε from carbon sources provides an opportunity to determine heterotrophic denitrification and helps the interpretation of nitrate isotopes in freshwaters.}, } @article {pmid37503282, year = {2023}, author = {Joglekar, P and Conlan, S and Lee-Lin, SQ and Deming, C and Kashaf, SS and , and Kong, HH and Segre, JA}, title = {Integrated genomic and functional analyses of human skin-associated Staphylococcus reveals extensive inter- and intra-species diversity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37503282}, abstract = {Human skin is stably colonized by a distinct microbiota that functions together with epidermal cells to maintain a protective physical barrier. Staphylococcus, a prominent genus of the skin microbiota, participates in colonization resistance, tissue repair, and host immune regulation in strain specific manners. To unlock the potential of engineering skin microbial communities, we aim to fully characterize the functional diversity of this genus within the context of the skin environment. We conducted metagenome and pan-genome analyses of isolates obtained from distinct body sites of healthy volunteers, providing a detailed biogeographic depiction of staphylococcal species that colonize our skin. S. epidermidis, S. capitis, and S. hominis were the most abundant species present in all volunteers and were detected at all body sites. Pan-genome analysis of these three species revealed that the genus-core was dominated by central metabolism genes. Species-specific core genes were enriched in host colonization functions. The majority (~68%) of genes were detected only in a fraction of isolate genomes, underscoring the immense strain-specific gene diversity. Conspecific genomes grouped into phylogenetic clades, exhibiting body site preference. Each clade was enriched for distinct gene-sets that are potentially involved in site tropism. Finally, we conducted gene expression studies of select isolates showing variable growth phenotypes in skin-like medium. In vitro expression revealed extensive intra- and inter-species gene expression variation, substantially expanding the functional diversification within each species. Our study provides an important resource for future ecological and translational studies to examine the role of shared and strain-specific staphylococcal genes within the skin environment.}, } @article {pmid37503260, year = {2023}, author = {Sumboh, JG and Agyenkwa-Mawuli, K and Schwinger, E and Donkor, IO and Akorli, JEB and Dwomoh, D and Ashong, Y and Osabutey, D and Ababio, FO and Koram, KA and Humphries, D and Cappello, M and Kwofie, SK and Wilson, MD}, title = {Investigating Environmental Determinants of Soil-Transmitted Helminths Transmission using GPS Tracking and Metagenomics Technologies.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {37503260}, support = {U19 AI129916/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: The Global Health community aims to eliminate soil-transmitted helminth (STH) infections by 2030. Current preventive methods such as Mass Drug Administration, WASH practices, and health education needs to be complimented to halt transmission. We tracked the movement of hookworm-infected and non-infected persons and investigated soil factors in the places they frequented within an endemic community to further understand the role of human movement and sources of infections.

METHODS: 59 positive and negative participants wore GPS tracking devices for 10 consecutive days and their movement data captured in real time. The data was overlaid on the community map to determine where each group differentially spent most of their time. Soil samples were collected from these identified sites and other communal places. Physical and chemical properties were determined for each sample using standard methods and helminth eggs cultured into larvae using the Baermann technique. Bivariate and multivariate analyses were used to determine associations between larvae counts and soil factors. Helminth species were identified with metagenomic sequencing and their distributions mapped to sampling sites in the community.

RESULTS: The study found that there was no significant difference in the average larvae counts in soil between sites assessed by infected and non-infected participants (P=0.59). However, soil factors, such as pH, carbon and sandy-loamy texture were associated with high larvae counts (P<0.001) while nitrogen and clay content were associated with low counts(P<0.001). The dominant helminth species identified were Panagrolaimus superbus (an anhydrobiotic helminth), Parastrongyloides trichosuri (a parasite of small mammals), Trichuris trichuria (whipworm), and Ancylostoma caninum (dog hookworm). Notably, no Necator americanus was identified in any soil sample.

CONCLUSION: This study provides important insights into the association between soil factors and soil-transmitted helminths. These findings contribute to our understanding of STH epidemiology and support evidence-based decision-making for elimination strategies.}, } @article {pmid37502876, year = {2023}, author = {Ahmed, NM and Joglekar, P and Deming, C and , and Lemon, KP and Kong, HH and Segre, JA and Conlan, S}, title = {Genomic characterization of the C. tuberculostearicum species complex, a ubiquitous member of the human skin microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37502876}, abstract = {Corynebacterium is a predominant genus in the skin microbiome, yet its genetic diversity on skin is incompletely characterized and lacks a comprehensive set of reference genomes. Our work aims to investigate the distribution of Corynebacterium species on the skin, as well as to expand the existing genome reference catalog to enable more complete characterization of skin metagenomes. We used V1-V3 16S rRNA gene sequencing data from 14 body sites of 23 healthy volunteers to characterize Corynebacterium diversity and distribution across healthy human skin. Corynebacterium tuberculostearicum is the predominant species found on human skin and we identified two distinct C. tuberculostearicum ribotypes (A & B) that can be distinguished by variation in the 16S rRNA V1-V3 sequence. One is distributed across all body sites and the other found primarily on the feet. We performed whole genome sequencing of 40 C. tuberculostearicum isolates cultured from the skin of five healthy individuals across seven skin sites. We generated five closed genomes of diverse C. tuberculostearicum which revealed that C. tuberculostearicum isolates are largely syntenic and carry a diversity of methylation patterns, plasmids and CRISPR/Cas systems. The pangenome of C. tuberculostearicum is open with a core genome size of 1806 genes and a pangenome size of 5451 total genes. This expanded pangenome enabled the mapping of 24% more C. tuberculostearicum reads from shotgun metagenomic datasets derived from skin body sites. Finally, while the genomes from this study all fall within a C. tuberculostearicum species complex, the ribotype B isolates may constitute a new species.}, } @article {pmid37502423, year = {2023}, author = {Zhang, M and Zhai, Z and Yang, B and He, L and Wang, J and Dai, W and Xue, L and Yang, X and Feng, Y and Wang, H}, title = {Exploring the alteration of gut microbiota and brain function in gender-specific Parkinson's disease based on metagenomic sequencing.}, journal = {Frontiers in aging neuroscience}, volume = {15}, number = {}, pages = {1148546}, pmid = {37502423}, issn = {1663-4365}, abstract = {BACKGROUND: The role of the microbiota-gut-brain axis in Parkinson's disease (PD) has received increasing attention. Although gender differences are known to an essential role in the epidemiology and clinical course of PD, there are no studies on the sex specificity of the microbiota-gut-brain axis in the development and progression of PD.

METHODS: Fresh fecal samples from 24 PD patients (13 males, 11 females) were collected for metagenomic sequencing. The composition and function of the gut microbiota were analyzed by resting-state functional magnetic resonance imaging (fMRI). Gender-dependent differences in brain ALFF values and their correlation with microbiota were further analyzed.

RESULTS: The relative abundance of Propionivibrio, Thermosediminibacter, and Flavobacteriaceae_noname was increased in male PD patients. LEfse analysis showed that Verrucomicrobial, Akkermansiaceae, and Akkermansia were dominant in the males. In female patients, the relative abundance of Propionicicella was decreased and Escherichia, Escherichia_coli, and Lachnospiraceae were predominant. The expression of the sesquiterpenoid and triterpenoid biosynthesis pathways was increased in male PD patients and was statistically different from females. Compared to the Male PD patients, female patients showed decreased ALFF values in the left inferior parietal regions, and the relative abundance of Propionivibrio was positively correlated with the regional ALFF values.

CONCLUSION: Our study provides novel clinical evidence of the gender-specific relationship between gut microbiota alterations and brain function in PD patients, highlighting the critical role of the microbiota-gut-brain axis in gender differences in PD.}, } @article {pmid37501535, year = {2023}, author = {Pavia, MJ and Finn, D and Macedo-Tafur, F and Tello-Espinoza, R and Penaccio, C and Bouskill, N and Cadillo-Quiroz, H}, title = {Genes and genome-resolved metagenomics reveal the microbial functional make up of Amazon peatlands under geochemical gradients.}, journal = {Environmental microbiology}, volume = {25}, number = {11}, pages = {2388-2403}, doi = {10.1111/1462-2920.16469}, pmid = {37501535}, issn = {1462-2920}, mesh = {*Bacteria/genetics/metabolism ; *Microbiota/genetics ; Metagenome ; Metagenomics ; Soil ; }, abstract = {The Pastaza-Marañón Foreland Basin (PMFB) holds the most extensive tropical peatland area in South America. PMFB peatlands store ~7.07 Gt of organic carbon interacting with multiple microbial heterotrophic, methanogenic, and other aerobic/anaerobic respirations. Little is understood about the contribution of distinct microbial community members inhabiting tropical peatlands. Here, we studied the metagenomes of three geochemically distinct peatlands spanning minerotrophic, mixed, and ombrotrophic conditions. Using gene- and genome-centric approaches, we evaluate the functional potential of the underlying microbial communities. Abundance analyses show significant differences in C, N, P, and S acquisition genes. Furthermore, community interactions mediated by toxin-antitoxin and CRISPR-Cas systems were enriched in oligotrophic soils, suggesting that non-metabolic interactions may exert additional controls in low-nutrient environments. Additionally, we reconstructed 519 metagenome-assembled genomes spanning 28 phyla. Our analyses detail key differences across the geochemical gradient in the predicted microbial populations involved in degradation of organic matter, and the cycling of N and S. Notably, we observed differences in the nitric oxide (NO) reduction strategies between sites with high and low N2 O fluxes and found phyla putatively capable of both NO and sulfate reduction. Our findings detail how gene abundances and microbial populations are influenced by geochemical differences in tropical peatlands.}, } @article {pmid37501370, year = {2023}, author = {Song, B and Ning, W and Wei, D and Jiang, M and Zhu, K and Wang, X and Edwards, D and Odeny, DA and Cheng, S}, title = {Plant genome resequencing and population genomics: Current status and future prospects.}, journal = {Molecular plant}, volume = {16}, number = {8}, pages = {1252-1268}, doi = {10.1016/j.molp.2023.07.009}, pmid = {37501370}, issn = {1752-9867}, mesh = {Humans ; Animals ; *Genome, Plant ; Metagenomics ; Sequence Analysis, DNA ; Genome-Wide Association Study ; Selection, Genetic ; Phylogeny ; Stress, Physiological ; Adaptation, Physiological ; }, abstract = {Advances in DNA sequencing technology have sparked a genomics revolution, driving breakthroughs in plant genetics and crop breeding. Recently, the focus has shifted from cataloging genetic diversity in plants to exploring their functional significance and delivering beneficial alleles for crop improvement. This transformation has been facilitated by the increasing adoption of whole-genome resequencing. In this review, we summarize the current progress of population-based genome resequencing studies and how these studies affect crop breeding. A total of 187 land plants from 163 countries have been resequenced, comprising 54 413 accessions. As part of resequencing efforts 367 traits have been surveyed and 86 genome-wide association studies have been conducted. Economically important crops, particularly cereals, vegetables, and legumes, have dominated the resequencing efforts, leaving a gap in 49 orders, including Lycopodiales, Liliales, Acorales, Austrobaileyales, and Commelinales. The resequenced germplasm is distributed across diverse geographic locations, providing a global perspective on plant genomics. We highlight genes that have been selected during domestication, or associated with agronomic traits, and form a repository of candidate genes for future research and application. Despite the opportunities for cross-species comparative genomics, many population genomic datasets are not accessible, impeding secondary analyses. We call for a more open and collaborative approach to population genomics that promotes data sharing and encourages contribution-based credit policy. The number of plant genome resequencing studies will continue to rise with the decreasing DNA sequencing costs, coupled with advances in analysis and computational technologies. This expansion, in terms of both scale and quality, holds promise for deeper insights into plant trait genetics and breeding design.}, } @article {pmid37501202, year = {2023}, author = {Anzà, S and Schneider, D and Daniel, R and Heistermann, M and Sangmaneedet, S and Ostner, J and Schülke, O}, title = {The long-term gut bacterial signature of a wild primate is associated with a timing effect of pre- and postnatal maternal glucocorticoid levels.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {165}, pmid = {37501202}, issn = {2049-2618}, mesh = {Female ; Animals ; Pregnancy ; Humans ; Glucocorticoids ; *Gastrointestinal Microbiome/physiology ; Cross-Sectional Studies ; Primates ; Bacteria/genetics ; *Prenatal Exposure Delayed Effects/microbiology ; }, abstract = {BACKGROUND: During development, elevated levels of maternal glucocorticoids (GCs) can have detrimental effects on offspring morphology, cognition, and behavior as well as physiology and metabolism. Depending on the timing of exposure, such effects may vary in strength or even reverse in direction, may alleviate with age, or may concern more stable and long-term programming of phenotypic traits. Maternal effects on gut bacterial diversity, composition, and function, and the persistence of such effects into adulthood of long-lived model species in the natural habitats remain underexplored.

RESULTS: In a cross-sectional sample of infant, juvenile, and adult Assamese macaques, the timing of exposure to elevated maternal GCs during ontogeny was associated with the gut bacterial community of the offspring. Specifically, naturally varying maternal GC levels during early but not late gestation or lactation were associated with reduced bacterial richness. The overall effect of maternal GCs during early gestation on the gut bacterial composition and function exacerbated with offspring age and was 10 times stronger than the effect associated with exposure during late prenatal or postnatal periods. Instead, variation in maternal GCs during the late prenatal or postnatal period had less pronounced or less stable statistical effects and therefore a weaker effect on the entire bacterial community composition, particularly in adult individuals. Finally, higher early prenatal GCs were associated with an increase in the relative abundance of several potential pro-inflammatory bacteria and a decrease in the abundance of Bifidobacterium and other anti-inflammatory taxa, an effect that exacerbated with age.

CONCLUSIONS: In primates, the gut microbiota can be shaped by developmental effects with strong timing effects on plasticity and potentially detrimental consequences for adult health. Together with results on other macaque species, this study suggests potential detrimental developmental effects similar to rapid inflammaging, suggesting that prenatal exposure to high maternal GC concentrations is a common cause underlying both phenomena. Our findings await confirmation by metagenomic functional and causal analyses and by longitudinal studies of long-lived, ecologically flexible primates in their natural habitat, including developmental effects that originate before birth. Video Abstract.}, } @article {pmid37500914, year = {2023}, author = {Balaban, M and Jiang, Y and Zhu, Q and McDonald, D and Knight, R and Mirarab, S}, title = {Generation of accurate, expandable phylogenomic trees with uDance.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {37500914}, issn = {1546-1696}, support = {U19 AG063744/AG/NIA NIH HHS/United States ; U24 DK131617/DK/NIDDK NIH HHS/United States ; }, abstract = {Phylogenetic trees provide a framework for organizing evolutionary histories across the tree of life and aid downstream comparative analyses such as metagenomic identification. Methods that rely on single-marker genes such as 16S rRNA have produced trees of limited accuracy with hundreds of thousands of organisms, whereas methods that use genome-wide data are not scalable to large numbers of genomes. We introduce updating trees using divide-and-conquer (uDance), a method that enables updatable genome-wide inference using a divide-and-conquer strategy that refines different parts of the tree independently and can build off of existing trees, with high accuracy and scalability. With uDance, we infer a species tree of roughly 200,000 genomes using 387 marker genes, totaling 42.5 billion amino acid residues.}, } @article {pmid37500913, year = {2023}, author = {McDonald, D and Jiang, Y and Balaban, M and Cantrell, K and Zhu, Q and Gonzalez, A and Morton, JT and Nicolaou, G and Parks, DH and Karst, SM and Albertsen, M and Hugenholtz, P and DeSantis, T and Song, SJ and Bartko, A and Havulinna, AS and Jousilahti, P and Cheng, S and Inouye, M and Niiranen, T and Jain, M and Salomaa, V and Lahti, L and Mirarab, S and Knight, R}, title = {Greengenes2 unifies microbial data in a single reference tree.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {37500913}, issn = {1546-1696}, support = {U19 AG063744/AG/NIA NIH HHS/United States ; U24 DK131617/DK/NIDDK NIH HHS/United States ; }, abstract = {Studies using 16S rRNA and shotgun metagenomics typically yield different results, usually attributed to PCR amplification biases. We introduce Greengenes2, a reference tree that unifies genomic and 16S rRNA databases in a consistent, integrated resource. By inserting sequences into a whole-genome phylogeny, we show that 16S rRNA and shotgun metagenomic data generated from the same samples agree in principal coordinates space, taxonomy and phenotype effect size when analyzed with the same tree.}, } @article {pmid37500801, year = {2023}, author = {Esser, SP and Rahlff, J and Zhao, W and Predl, M and Plewka, J and Sures, K and Wimmer, F and Lee, J and Adam, PS and McGonigle, J and Turzynski, V and Banas, I and Schwank, K and Krupovic, M and Bornemann, TLV and Figueroa-Gonzalez, PA and Jarett, J and Rattei, T and Amano, Y and Blaby, IK and Cheng, JF and Brazelton, WJ and Beisel, CL and Woyke, T and Zhang, Y and Probst, AJ}, title = {A predicted CRISPR-mediated symbiosis between uncultivated archaea.}, journal = {Nature microbiology}, volume = {8}, number = {9}, pages = {1619-1633}, pmid = {37500801}, issn = {2058-5276}, mesh = {*Archaea/genetics/metabolism ; *Symbiosis/genetics ; Genomics ; Plasmids ; DNA/metabolism ; }, abstract = {CRISPR-Cas systems defend prokaryotic cells from invasive DNA of viruses, plasmids and other mobile genetic elements. Here, we show using metagenomics, metatranscriptomics and single-cell genomics that CRISPR systems of widespread, uncultivated archaea can also target chromosomal DNA of archaeal episymbionts of the DPANN superphylum. Using meta-omics datasets from Crystal Geyser and Horonobe Underground Research Laboratory, we find that CRISPR spacers of the hosts Candidatus Altiarchaeum crystalense and Ca. A. horonobense, respectively, match putative essential genes in their episymbionts' genomes of the genus Ca. Huberiarchaeum and that some of these spacers are expressed in situ. Metabolic interaction modelling also reveals complementation between host-episymbiont systems, on the basis of which we propose that episymbionts are either parasitic or mutualistic depending on the genotype of the host. By expanding our analysis to 7,012 archaeal genomes, we suggest that CRISPR-Cas targeting of genomes associated with symbiotic archaea evolved independently in various archaeal lineages.}, } @article {pmid37500759, year = {2023}, author = {Chklovski, A and Parks, DH and Woodcroft, BJ and Tyson, GW}, title = {CheckM2: a rapid, scalable and accurate tool for assessing microbial genome quality using machine learning.}, journal = {Nature methods}, volume = {20}, number = {8}, pages = {1203-1212}, pmid = {37500759}, issn = {1548-7105}, mesh = {*Genome, Microbial ; *Bacteria/genetics ; Metagenome ; Metagenomics/methods ; Machine Learning ; }, abstract = {Advances in sequencing technologies and bioinformatics tools have dramatically increased the recovery rate of microbial genomes from metagenomic data. Assessing the quality of metagenome-assembled genomes (MAGs) is a critical step before downstream analysis. Here, we present CheckM2, an improved method of predicting genome quality of MAGs using machine learning. Using synthetic and experimental data, we demonstrate that CheckM2 outperforms existing tools in both accuracy and computational speed. In addition, CheckM2's database can be rapidly updated with new high-quality reference genomes, including taxa represented only by a single genome. We also show that CheckM2 accurately predicts genome quality for MAGs from novel lineages, even for those with reduced genome size (for example, Patescibacteria and the DPANN superphylum). CheckM2 provides accurate genome quality predictions across bacterial and archaeal lineages, giving increased confidence when inferring biological conclusions from MAGs.}, } @article {pmid37499616, year = {2023}, author = {Xiong, X and Rao, Y and Ma, J and Wang, Z and He, Q and Gong, J and Sheng, W and Xu, J and Zhu, X and Tan, Y and Yang, Y}, title = {A catalog of microbial genes and metagenome-assembled genomes from the quail gut microbiome.}, journal = {Poultry science}, volume = {102}, number = {10}, pages = {102931}, pmid = {37499616}, issn = {1525-3171}, mesh = {Animals ; *Metagenome ; *Gastrointestinal Microbiome ; Quail/genetics ; Chickens/genetics ; Genes, Microbial ; }, abstract = {The gut microbiome plays an important role in quail feed efficiency, immunity, production, and even behavior. Gut microbial gene catalogs and reference genomes are important for understanding the quail gut microbiome. However, quail gut microbes are lacked sequenced genomes and functional information to date. In this study, we report the first catalog of the microbial genes and metagenome-assembled genomes (MAGs) in fecal and cecum luminal content samples from 3 quail breeds using deep metagenomic sequencing. We identified a total of 2,419,425 nonredundant genes in the quail genome catalog, and a total of 473 MAGs were reconstructed through binning analysis. At 95% average nucleotide identity, the 473 MAGs were clustered into 283 species-level genome bins (SGBs), of which 225 SGBs belonged to species without any available genomes in the current database. Based on the quail gene catalog and MAGs, we identified 142 discriminative bacterial species and 244 discriminative MAGs between Chinese yellow quails and Japanese quails. The discriminative MAGs suggested a strain-level difference in the gut microbial composition. Additionally, a total of 25 Kyoto Encyclopedia of Genes and Genomes functional terms and 88 carbohydrate-active enzymes were distinctly enriched between Chinese yellow quails and Japanese quails. Most of the different species and MAGs were significantly interrelated with the shifts in the functional capacities of the quail gut microbiome. Taken together, we constructed a quail gut microbial gene catalog and enlarged the reference of quail gut microbial genomes. The results of this study provide a powerful and invaluable resource for quail gut microbiome-related research.}, } @article {pmid37498401, year = {2023}, author = {Vázquez-Guerrero, E and Reyes-Solís, GC and Cano-Ravell, AE and Machain-Williams, C and Leyva-Gastélum, M and Estrada-de Los Santos, P and Álvarez-Hernández, G and Ibarra, JA}, title = {Detection of Rickettsia amblyommatis and Rickettsia bellii in ticks collected from pet dogs in peri-urban and rural areas in Yucatan, Mexico.}, journal = {Experimental & applied acarology}, volume = {90}, number = {3-4}, pages = {441-453}, pmid = {37498401}, issn = {1572-9702}, support = {2023-0850//Secretaria de Investigación y Posgrado, Instituto Politécnico Nacional/ ; }, mesh = {Animals ; Dogs ; Humans ; *Ticks/microbiology ; Mexico ; *Rickettsia ; Mammals ; *Ixodidae/microbiology ; Brazil/epidemiology ; }, abstract = {Rickettsia species are bacteria that may cause multiple diseases in animals and humans, via transmission through multiple arthropod vectors. Routine surveillance of Rickettsia spp. within vectors is critical to determine their presence and risk to mammalian hosts within human populations. Therefore, to better characterize the circulating Rickettsia species in an understudied region we targeted pet dogs to survey. Ticks were collected from pet dogs in three populations of the Yucatan where we tested for the presence of Rickettsia spp. by PCR in metagenomic DNA. In these ticks removed from pet dogs we detected Rickettsia amblyommatis and Rickettsia bellii in Amblyomma auriculatum, Amblyomma ovale and Amblyomma mixtum ticks obtained in a rural community in the Mexican state of Yucatan. This is the first report detecting both species for this state in Mexico, underpinning the importance of more routine surveillance.}, } @article {pmid37497548, year = {2023}, author = {Dou, Y and Wen, M and Yang, C and Zhao, F and Ren, C and Zhang, N and Liang, Y and Wang, J}, title = {Effects of straw and plastic film mulching on microbial functional genes involved in soil nitrogen cycling.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1205088}, pmid = {37497548}, issn = {1664-302X}, abstract = {INTRODUCTION: Microorganisms regulate soil nitrogen (N) cycling in cropping systems. However, how soil microbial functional genes involved in soil N cycling respond to mulching practices is not well known.

METHODS: We collected soil samples from a spring maize field mulched with crop straw (SM) and plastic film (FM) for 10-year and with no mulching (CK) in the Loess Plateau. Microbial functional genes involved in soil N cycling were quantified using metagenomic sequencing. We collected soil samples from a spring maize field mulched with crop straw (SM) and plastic film (FM) for 10-year and with no mulching (CK) in the Loess Plateau. Microbial functional genes involved in soil N cycling were quantified using metagenomic sequencing.

RESULTS: Compared to that in CK, the total abundance of genes involved in soil N cycling increased in SM but had no significant changes in FM. Specifically, SM increased the abundances of functional genes that involved in dissimilatory nitrate reduction to ammonium (nirB, napA, and nrfA), while FM decreased the abundances of functional genes that involved in ammonification (ureC and ureA) in comparison with CK. Other genes involved in assimilatory nitrate reduction, denitrification, and ammonia assimilation, however, were not significantly changed with mulching practices. The nirB and napA were derived from Proteobacteria (mainly Sorangium), and the ureC was derived from Actinobacteria (mainly Streptomyces). Mental test showed that the abundance of functional genes that involved in dissimilatory nitrate reduction was positively correlated with the contents of soil microbial biomass N, potential N mineralization, particulate organic N, and C fractions, while ammonification related gene abundance was positively correlated with soil pH, microbial biomass C and N, and mineral N contents.

DISCUSSION: Overall, this study showed that SM could improve soil N availability and promote the soil N cycling by increasing the abundance of functional genes that involved in DNRA, while FM reduced the abundance of functional genes that involved in ammonification and inhibited soil N cycling.}, } @article {pmid37497269, year = {2023}, author = {Yang, R and Duan, Y and Wang, D and Liu, Q}, title = {Developing a Preliminary Clinical Prediction Model for Prognosis of Pneumonia Complicated with Heart Failure Based on Metagenomic Sequencing.}, journal = {Critical care research and practice}, volume = {2023}, number = {}, pages = {5930742}, pmid = {37497269}, issn = {2090-1305}, abstract = {BACKGROUND: The predictive factors of prognosis in patients with pneumonia complicated with heart failure (HF) have not been fully investigated yet, especially with the use of next-generation sequencing (NGS) of metagenome.

METHODS: Patients diagnosed with pneumonia complicated with HF were collected and divided into control group and NGS group. Univariate and multivariate logistic regression and LASSO regression analysis were conducted to screen the predictive factors for the prognosis, followed by nomogram construction, ROC curve plot, and internal validation. Data analysis was conducted in SPSS and R software.

RESULTS: The NGS of metagenome detected more microbial species. Univariate and multivariate logistic regression and LASSO regression analysis revealed that Enterococcus (χ[2] = 7.449, P = 0.006), Hb (Wals = 6.289, P = 0.012), and ProBNP (Wals = 4.037, P = 0.045) were screened out as potential predictive factors for the prognosis. Nomogram was constructed with these 3 parameters, and the performance of nomogram was checked in ROC curves (AUC = 0.772). The specificity and sensitivity of this model were calculated as 0.579 and 0.851, respectively, with the threshold of 0.630 in ROC curve. Further internal verification indicated that the predictive value of our constructed model was efficient.

CONCLUSION: This study developed a preliminary clinical prediction model for the prognosis of pneumonia complicated with HF based on NGS of metagenome. More objects will be collected and tested to improve the predictive model in the near future.}, } @article {pmid37497061, year = {2023}, author = {Littlejohn, PT and Bar-Yoseph, H and Edwards, K and Li, H and Ramirez-Contreras, CY and Holani, R and Metcalfe-Roach, A and Fan, YM and Yang, TM and Radisavljevic, N and Hu, X and Johnson, JD and Finlay, BB}, title = {Multiple micronutrient deficiencies alter energy metabolism in host and gut microbiome in an early-life murine model.}, journal = {Frontiers in nutrition}, volume = {10}, number = {}, pages = {1151670}, pmid = {37497061}, issn = {2296-861X}, abstract = {INTRODUCTION: Micronutrients perform a wide range of physiological functions essential for growth and development. However, most people still need to meet the estimated average requirement worldwide. Globally, 2 billion people suffer from micronutrient deficiency, most of which are co-occurring deficiencies in children under age five. Despite decades of research, animal models studying multiple micronutrient deficiencies within the early-life period are lacking, which hinders our complete understanding of the long-term health implications and may contribute to the inefficacy of some nutritional interventions. Evidence supporting the Developmental Origins of Health and Disease (DOHaD) theory demonstrates that early-life nutritional deficiencies carry life-long consequences mediated through various mechanisms such as abnormal metabolic programming, stunting, altered body composition, and the gut microbiome. However, this is largely unexplored in the multiple micronutrient deficient host.

METHODS: we developed a preclinical model to examine undernutrition's metabolic and functional impact on the host and gut microbiome early in life. Three-week-old weanling C57BL/6N male mice were fed a low-micronutrient diet deficient in zinc, folate, iron, vitamin A, and vitamin B12 or a control diet for 4-weeks.

RESULTS: Our results showed that early-life multiple micronutrient deficiencies induced stunting, altered body composition, impaired glucose and insulin tolerance, and altered the levels of other micronutrients not depleted in the diet within the host. In addition, functional metagenomics profiling and a carbohydrate fermentation assay showed an increased microbial preference for simple sugars rather than complex ones, suggestive of a less developed microbiome in the low-micronutrient-fed mice. Moreover, we found that a zinc-only deficient diet was not sufficient to induce these phenotypes, further supporting the importance of studying co-occurring deficiencies.

DISCUSSION: Together, these findings highlight a previously unappreciated role of early-life multiple micronutrient deficiencies in shaping the metabolic phenome of the host and gut microbiome through altered glucose energy metabolism, which may have implications for metabolic disease later in life in micronutrient-deficient survivors.}, } @article {pmid37497030, year = {2023}, author = {Price, C and Russell, JA}, title = {AMAnD: an automated metagenome anomaly detection methodology utilizing DeepSVDD neural networks.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1181911}, pmid = {37497030}, issn = {2296-2565}, mesh = {Humans ; *Metagenome ; *COVID-19/genetics ; Neural Networks, Computer ; Genomics ; Metagenomics/methods ; }, abstract = {The composition of metagenomic communities within the human body often reflects localized medical conditions such as upper respiratory diseases and gastrointestinal diseases. Fast and accurate computational tools to flag anomalous metagenomic samples from typical samples are desirable to understand different phenotypes, especially in contexts where repeated, long-duration temporal sampling is done. Here, we present Automated Metagenome Anomaly Detection (AMAnD), which utilizes two types of Deep Support Vector Data Description (DeepSVDD) models; one trained on taxonomic feature space output by the Pan-Genomics for Infectious Agents (PanGIA) taxonomy classifier and one trained on kmer frequency counts. AMAnD's semi-supervised one-class approach makes no assumptions about what an anomaly may look like, allowing the flagging of potentially novel anomaly types. Three diverse datasets are profiled. The first dataset is hosted on the National Center for Biotechnology Information's (NCBI) Sequence Read Archive (SRA) and contains nasopharyngeal swabs from healthy and COVID-19-positive patients. The second dataset is also hosted on SRA and contains gut microbiome samples from normal controls and from patients with slow transit constipation (STC). AMAnD can learn a typical healthy nasopharyngeal or gut microbiome profile and reliably flag the anomalous COVID+ or STC samples in both feature spaces. The final dataset is a synthetic metagenome created by the Critical Assessment of Metagenome Annotation Simulator (CAMISIM). A control dataset of 50 well-characterized organisms was submitted to CAMISIM to generate 100 synthetic control class samples. The experimental conditions included 12 different spiked-in contaminants that are taxonomically similar to organisms present in the laboratory blank sample ranging from one strain tree branch taxonomic distance away to one family tree branch taxonomic distance away. This experiment was repeated in triplicate at three different coverage levels to probe the dependence on sample coverage. AMAnD was again able to flag the contaminant inserts as anomalous. AMAnD's assumption-free flagging of metagenomic anomalies, the real-time model training update potential of the deep learning approach, and the strong performance even with lightweight models of low sample cardinality would make AMAnD well-suited to a wide array of applied metagenomics biosurveillance use-cases, from environmental to clinical utility.}, } @article {pmid37496895, year = {2023}, author = {Lu, Y and Gao, X and Nan, Y and Mohammed, SAD and Fu, J and Wang, T and Wang, C and Yuan, C and Lu, F and Liu, S}, title = {Acanthopanax senticosus Harms improves Parkinson's disease by regulating gut microbial structure and metabolic disorders.}, journal = {Heliyon}, volume = {9}, number = {7}, pages = {e18045}, pmid = {37496895}, issn = {2405-8440}, abstract = {Parkinson's disease (PD) is the second most common neurodegenerative disease, with an increasing prevalence as the population ages, posing a serious threat to human health, but the pathogenesis remains uncertain. Acanthopanax senticosus (Rupr. et Maxim.) Harms (ASH) (aqueous ethanol extract), a Chinese herbal medicine, provides obvious and noticeable therapeutic effects on PD. To further investigate the ASH's mechanism of action in treating PD, the structural and functional gut microbiota, as well as intestinal metabolite before and after ASH intervention in the PD mice model, were examined utilizing metagenomics and fecal metabolomics analysis. α-syn transgenic mice were randomly divided into a model and ASH groups, with C57BL/6 mice as a control. The ASH group was gavaged with ASH (45.5 mg/kg/d for 20d). The time of pole climbing and autonomous activity were used to assess motor ability. The gut microbiota's structure, composition, and function were evaluated using Illumina sequencing. Fecal metabolites were identified using UHPLC-MS/MS to construct intestinal metabolites. The findings of this experiment demonstrate that ASH may reduce the climbing time of PD model mice while increasing the number of autonomous movements. The results of metagenomics analysis revealed that ASH could up-regulated Firmicutes and down-regulated Actinobacteria at the phylum level, while Clostridium was up-regulated and Akkermansia was down-regulated at the genus level; it could also recall 49 species from the phylum Firmicutes, Actinobacteria, and Tenericutes. Simultaneously, metabolomics analysis revealed that alpha-Linolenic acid metabolism might be a key metabolic pathway for ASH to impact in PD. Furthermore, metagenomics function analysis and metabolic pathway enrichment analysis revealed that ASH might influence unsaturated fatty acid synthesis and purine metabolism pathways. These metabolic pathways are connected to ALA, Palmitic acid, Adenine, and 16 species of Firmicutes, Actinobacteria, and Tenericutes. Finally, these results indicate that ASH may alleviate the movement disorder of the PD model, which may be connected to the regulation of gut microbiota structure and function as well as the modulation of metabolic disorders by ASH.}, } @article {pmid37496083, year = {2023}, author = {Liang, X and Zhang, Z and Wang, H and Lu, X and Li, W and Lu, H and Roy, A and Shen, X and Irwin, DM and Shen, Y}, title = {Early-life prophylactic antibiotic treatment disturbs the stability of the gut microbiota and increases susceptibility to H9N2 AIV in chicks.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {163}, pmid = {37496083}, issn = {2049-2618}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Gastrointestinal Microbiome/genetics ; *Influenza A Virus, H9N2 Subtype/genetics ; Chickens/microbiology ; *Microbiota ; }, abstract = {BACKGROUND: Antibiotics are widely used for prophylactic therapy and for improving the growth performance of chicken. The problem of bacterial drug resistance caused by antibiotic abuse has previously attracted extensive attention; however, the influence of early-day use of prophylactic antibiotics on the gut microflora and on the disease resistance ability in chicks has not been explored. Here, we comprehensively evaluate the growth performance, gut microbial dynamics, level of antibiotic resistance genes (ARGs) in the gut microbial community, and resistance to H9N2 avian influenza virus (AIV) in chickens following long-term and short-term early-day prophylactic antibiotic treatment.

RESULTS: Unexpectedly, long-term prophylactic enrofloxacin treatment slowed the growth rate of chickens, whereas short-term antibiotics treatments were found to increase the growth rate, but these changes were not statistically significant. Strikingly, expansions of Escherichia-Shigella populations were observed in early-life prophylactic antibiotics-treated groups of chickens, which is in contrast to the general perception that antibiotics should control their pathogenicity in chicks. The gut microbiota composition of chickens treated long term with antibiotics or received early-day antibiotics treatment tend to be more dramatically disturbed compared to the gut microbiome of chickens treated with antibiotics for a short term at a later date, especially after H9N2 AIV infection.

CONCLUSIONS: Our data provide evidence that early-day and long-term antibiotic treatments have a more adverse effect on the intestinal microbiome of chickens, compared to short-term late age antibiotic treatment. Furthermore, our metagenomic data reveal that both long-term and short-term antibiotic treatment increase the relative abundance of ARGs. Our findings highlight the adverse effects of prophylactic antibiotic treatment and provide a theoretical basis for the cautious administration of antibiotics in food-producing animal management. Video Abstract.}, } @article {pmid37495988, year = {2023}, author = {Abdou, YT and Saleeb, SM and Abdel-Raouf, KMA and Allam, M and Adel, M and Amleh, A}, title = {Characterization of a novel peptide mined from the Red Sea brine pools and modified to enhance its anticancer activity.}, journal = {BMC cancer}, volume = {23}, number = {1}, pages = {699}, pmid = {37495988}, issn = {1471-2407}, mesh = {Female ; Humans ; HeLa Cells ; Cell Line, Tumor ; Indian Ocean ; *Antimicrobial Cationic Peptides/pharmacology ; *Antineoplastic Agents/pharmacology/chemistry ; Apoptosis ; Cell Proliferation ; }, abstract = {Drug resistance is a major cause of the inefficacy of conventional cancer therapies, and often accompanied by severe side effects. Thus, there is an urgent need to develop novel drugs with low cytotoxicity, high selectivity and minimal acquired chemical resistance. Peptide-based drugs (less than 0.5 kDa) have emerged as a potential approach to address these issues due to their high specificity and potent anticancer activity. In this study, we developed a support vector machine model (SVM) to detect the potential anticancer properties of novel peptides by scanning the American University in Cairo (AUC) Red Sea metagenomics library. We identified a novel 37-mer antimicrobial peptide through SVM pipeline analysis and characterized its anticancer potential through in silico cross-examination. The peptide sequence was further modified to enhance its anticancer activity, analyzed for gene ontology, and subsequently synthesized. To evaluate the anticancer properties of the modified 37-mer peptide, we assessed its effect on the viability and morphology of SNU449, HepG2, SKOV3, and HeLa cells, using an MTT assay. Additionally, we evaluated the migration capabilities of SNU449 and SKOV3 cells using a scratch-wound healing assay. The targeted selectivity of the modified peptide was examined by evaluating its hemolytic activity on human erythrocytes. Treatment with the peptide significantly reduced cell viability and had a critical impact on the morphology of hepatocellular carcinoma (SNU449 and HepG2), and ovarian cancer (SKOV3) cells, with a marginal effect on cervical cancer cell lines (HeLa). The viability of a human fibroblast cell line (1Br-hTERT) was also significantly reduced by peptide treatment, as were the proliferation and migration abilities of SNU449 and SKOV3 cells. The annexin V assay revealed programmed cell death (apoptosis) as one of the potential cellular death pathways in SNU449 cells upon peptide treatment. Finally, the peptide exhibited antimicrobial effects on both gram-positive and gram-negative bacterial strains. The findings presented here suggest the potential of our novel peptide as a potent anticancer and antimicrobial agent.}, } @article {pmid37495676, year = {2023}, author = {Peterson, BD and Poulin, BA and Krabbenhoft, DP and Tate, MT and Baldwin, AK and Naymik, J and Gastelecutto, N and McMahon, KD}, title = {Metabolically diverse microorganisms mediate methylmercury formation under nitrate-reducing conditions in a dynamic hydroelectric reservoir.}, journal = {The ISME journal}, volume = {17}, number = {10}, pages = {1705-1718}, pmid = {37495676}, issn = {1751-7370}, mesh = {Animals ; *Methylmercury Compounds/metabolism ; Nitrates ; Manganese ; *Mercury/metabolism ; Archaea/genetics/metabolism ; *Water Pollutants, Chemical ; }, abstract = {Brownlee Reservoir is a mercury (Hg)-impaired hydroelectric reservoir that exhibits dynamic hydrological and geochemical conditions and is located within the Hells Canyon Complex in Idaho, USA. Methylmercury (MeHg) contamination in fish is a concern in the reservoir. While MeHg production has historically been attributed to sulfate-reducing bacteria and methanogenic archaea, microorganisms carrying the hgcA gene are taxonomically and metabolically diverse and the major biogeochemical cycles driving mercury (Hg) methylation are not well understood. In this study, Hg speciation and redox-active compounds were measured throughout Brownlee Reservoir across the stratified period in four consecutive years (2016-2019) to identify the location where and redox conditions under which MeHg is produced. Metagenomic sequencing was performed on a subset of samples to characterize the microbial community with hgcA and identify possible links between biogeochemical cycles and MeHg production. Biogeochemical profiles suggested in situ water column Hg methylation was the major source of MeHg. These profiles, combined with genome-resolved metagenomics focused on hgcA-carrying microbes, indicated that MeHg production occurs in this system under nitrate- or manganese-reducing conditions, which were previously thought to preclude Hg-methylation. Using this multidisciplinary approach, we identified the cascading effects of interannual variability in hydrology on the redox status, microbial metabolic strategies, abundance and metabolic diversity of Hg methylators, and ultimately MeHg concentrations throughout the reservoir. This work expands the known conditions conducive to producing MeHg and suggests that the Hg-methylation mitigation efforts by nitrate or manganese amendment may be unsuccessful in some locations.}, } @article {pmid37495367, year = {2023}, author = {Lee, SH and Kim, J and Kim, NH and Kim, OH and Shon, CH and Kim, SJ and Jang, Y and Yun, S and Lim, SE and Jung, SY and Yoo, HJ and Heo, SH and Lee, SW}, title = {Gut microbiota composition and metabolite profiling in smokers: a comparative study between emphysema and asymptomatic individuals with therapeutic implications.}, journal = {Thorax}, volume = {78}, number = {11}, pages = {1080-1089}, doi = {10.1136/thorax-2021-217923}, pmid = {37495367}, issn = {1468-3296}, mesh = {Humans ; Animals ; Mice ; Smokers ; *Gastrointestinal Microbiome ; Propionates ; Disease Models, Animal ; *Pulmonary Emphysema ; *Pulmonary Disease, Chronic Obstructive ; Forced Expiratory Volume ; *Emphysema/complications ; Acetates ; }, abstract = {BACKGROUND: Diet has a crucial role in the gut microbiota, and dysbiosis in the gut and lungs has been suggested to be associated with chronic obstructive pulmonary disease. We compared the diet, microbiome and metabolome between asymptomatic smokers and those with emphysema.

METHODS: We enrolled 10 asymptomatic smokers with preserved lung function and 16 smokers with emphysema with severe airflow limitation. Dietary intake information was gathered by a self-reported questionnaire. Sputum and faecal samples were collected for microbial and metabolomics analysis. A murine model of emphysema was used to determine the effect of metabolite supplementation.

RESULTS: Despite having a similar smoking history with emphysema patients, asymptomatic smokers had higher values of body mass index, fibre intake and faecal acetate level. Linear discriminant analysis identified 17 microbial taxonomic members that were relatively enriched in the faeces of asymptomatic smokers. Analysis of similarity results showed dissimilarity between the two groups (r=0.287, p=0.003). Higher acetate level was positively associated with forced expiratory volume in one second in the emphysema group (r=0.628, p=0.012). Asymptomatic smokers had a greater number of species associated with acetate and propionate (r>0.6) than did those with emphysema (30 vs 19). In an emphysema mouse model, supplementation of acetate and propionate reduced alveolar destruction and the production of proinflammatory cytokines, and propionate decreased the CD3[+]CD4[+]IL-17[+] T-cell population in the lung and spleen.

CONCLUSION: Smokers with emphysema showed differences in diet, microbiome and short-chain fatty acids compared with asymptomatic smokers. Acetate and propionate showed therapeutic effects in a smoking-induced murine model of emphysema.}, } @article {pmid37494472, year = {2023}, author = {Thompson, KN and Bonham, KS and Ilott, NE and Britton, GJ and Colmenero, P and Bullers, SJ and McIver, LJ and Ma, S and Nguyen, LH and Filer, A and Brough, I and Pearson, C and Moussa, C and Kumar, V and Lam, LH and Jackson, MA and Pawluk, A and , and Kiriakidis, S and Taylor, PC and Wedderburn, LR and Marsden, B and Young, SP and Littman, DR and Faith, JJ and Pratt, AG and Bowness, P and Raza, K and Powrie, F and Huttenhower, C and , }, title = {Alterations in the gut microbiome implicate key taxa and metabolic pathways across inflammatory arthritis phenotypes.}, journal = {Science translational medicine}, volume = {15}, number = {706}, pages = {eabn4722}, doi = {10.1126/scitranslmed.abn4722}, pmid = {37494472}, issn = {1946-6242}, support = {203141/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; 21226/VAC_/Versus Arthritis/United Kingdom ; 22072/VAC_/Versus Arthritis/United Kingdom ; /DH_/Department of Health/United Kingdom ; 21593/VAC_/Versus Arthritis/United Kingdom ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Arthritis, Rheumatoid ; Inflammation ; *Microbiota ; Phenotype ; Metabolic Networks and Pathways ; }, abstract = {Musculoskeletal diseases affect up to 20% of adults worldwide. The gut microbiome has been implicated in inflammatory conditions, but large-scale metagenomic evaluations have not yet traced the routes by which immunity in the gut affects inflammatory arthritis. To characterize the community structure and associated functional processes driving gut microbial involvement in arthritis, the Inflammatory Arthritis Microbiome Consortium investigated 440 stool shotgun metagenomes comprising 221 adults diagnosed with rheumatoid arthritis, ankylosing spondylitis, or psoriatic arthritis and 219 healthy controls and individuals with joint pain without an underlying inflammatory cause. Diagnosis explained about 2% of gut taxonomic variability, which is comparable in magnitude to inflammatory bowel disease. We identified several candidate microbes with differential carriage patterns in patients with elevated blood markers for inflammation. Our results confirm and extend previous findings of increased carriage of typically oral and inflammatory taxa and decreased abundance and prevalence of typical gut clades, indicating that distal inflammatory conditions, as well as local conditions, correspond to alterations to the gut microbial composition. We identified several differentially encoded pathways in the gut microbiome of patients with inflammatory arthritis, including changes in vitamin B salvage and biosynthesis and enrichment of iron sequestration. Although several of these changes characteristic of inflammation could have causal roles, we hypothesize that they are mainly positive feedback responses to changes in host physiology and immune homeostasis. By connecting taxonomic alternations to functional alterations, this work expands our understanding of the shifts in the gut ecosystem that occur in response to systemic inflammation during arthritis.}, } @article {pmid37494371, year = {2023}, author = {Xie, M and Tsai, CY and McAdams, ZL and Oo, M and Hansen, M and Dougher, M and Sansano, A and Watson, A and LoMauro, K and Antilus-Sainte, R and Ericsson, A and Dartois, V and Gengenbacher, M}, title = {Wild mouse gut microbiota limits initial tuberculosis infection in BALB/c mice.}, journal = {PloS one}, volume = {18}, number = {7}, pages = {e0288290}, pmid = {37494371}, issn = {1932-6203}, support = {T32 GM008396/GM/NIGMS NIH HHS/United States ; U19 AI111143/AI/NIAID NIH HHS/United States ; U19 AI162568/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Mice, Inbred BALB C ; *Tuberculosis ; *Latent Tuberculosis/pathology ; Lung/pathology ; Dysbiosis/pathology ; }, abstract = {Mouse models are critical tools in tuberculosis (TB) research. Recent studies have demonstrated that the wild mouse gut microbiota promotes host fitness and improves disease resistance. Here we examine whether the wild mouse gut microbiota alters the immunopathology of TB in BALB/c mice. Conventional BALB/c mice (LabC) and mice born to germ-free BALB/c mothers reconstituted with the wild mouse gut microbiota (WildR) were used in our studies. WildR mice controlled initial TB infection better than LabC mice. The microbial gut communities of LabC mice and WildR mice had similar richness but significantly different composition prior to infection. TB reduced the gut community richness in both cohorts while differences in community composition remained indicating a general TB-induced dysbiosis. The wild mouse gut microbiota did not alter the typical lung histopathology of TB in the BALB/c model that includes unstructured immune cell infiltrates with infected foamy macrophages invading alveolar spaces. Animals of both cohorts mounted robust T cell responses in lungs and spleen with lower absolute counts of CD4 and CD8 T cells in lungs of WildR mice during acute infection, corresponding with observed differences in pathogen load. In summary, LabC mice and WildR mice showed largely overlapping TB immunopathology and pathogen kinetics, with WildR mice controlling early acute infection better than LabC mice.}, } @article {pmid37493648, year = {2023}, author = {Breusing, C and Xiao, Y and Russell, SL and Corbett-Detig, RB and Li, S and Sun, J and Chen, C and Lan, Y and Qian, PY and Beinart, RA}, title = {Ecological differences among hydrothermal vent symbioses may drive contrasting patterns of symbiont population differentiation.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0028423}, pmid = {37493648}, issn = {2379-5077}, support = {R35 GM128932/GM/NIGMS NIH HHS/United States ; K99 GM135583/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Hydrothermal Vents/microbiology ; *Mytilidae/genetics ; Bacteria/genetics ; Ecosystem ; Geography ; *Gastropoda/microbiology ; }, abstract = {The intra-host composition of horizontally transmitted microbial symbionts can vary across host populations due to interactive effects of host genetics, environmental, and geographic factors. While adaptation to local habitat conditions can drive geographic subdivision of symbiont strains, it is unknown how differences in ecological characteristics among host-symbiont associations influence the genomic structure of symbiont populations. To address this question, we sequenced metagenomes of different populations of the deep-sea mussel Bathymodiolus septemdierum, which are common at Western Pacific deep-sea hydrothermal vents and show characteristic patterns of niche partitioning with sympatric gastropod symbioses. Bathymodiolus septemdierum lives in close symbiotic relationship with sulfur-oxidizing chemosynthetic bacteria but supplements its symbiotrophic diet through filter-feeding, enabling it to occupy ecological niches with little exposure to geochemical reductants. Our analyses indicate that symbiont populations associated with B. septemdierum show structuring by geographic location, but that the dominant symbiont strain is uncorrelated with vent site. These patterns are in contrast to co-occurring Alviniconcha and Ifremeria gastropod symbioses that exhibit greater symbiont nutritional dependence and occupy habitats with higher spatial variability in environmental conditions. Our results suggest that relative habitat homogeneity combined with sufficient symbiont dispersal and genomic mixing might promote persistence of similar symbiont strains across geographic locations, while mixotrophy might decrease selective pressures on the host to affiliate with locally adapted symbiont strains. Overall, these data contribute to our understanding of the potential mechanisms influencing symbiont population structure across a spectrum of marine microbial symbioses that occupy contrasting ecological niches. IMPORTANCE Beneficial relationships between animals and microbial organisms (symbionts) are ubiquitous in nature. In the ocean, microbial symbionts are typically acquired from the environment and their composition across geographic locations is often shaped by adaptation to local habitat conditions. However, it is currently unknown how generalizable these patterns are across symbiotic systems that have contrasting ecological characteristics. To address this question, we compared symbiont population structure between deep-sea hydrothermal vent mussels and co-occurring but ecologically distinct snail species. Our analyses show that mussel symbiont populations are less partitioned by geography and do not demonstrate evidence for environmental adaptation. We posit that the mussel's mixotrophic feeding mode may lower its need to affiliate with locally adapted symbiont strains, while microhabitat stability and symbiont genomic mixing likely favors persistence of symbiont strains across geographic locations. Altogether, these findings further our understanding of the mechanisms shaping symbiont population structure in marine environmentally transmitted symbioses.}, } @article {pmid37493577, year = {2023}, author = {Zhu, J and Song, Y and Xiao, Y and Ma, L and Hu, C and Yang, H and Wang, X and Lyu, W}, title = {Metagenomic reconstructions of caecal microbiome in Landes, Roman and Zhedong White geese.}, journal = {British poultry science}, volume = {64}, number = {5}, pages = {565-576}, doi = {10.1080/00071668.2023.2239172}, pmid = {37493577}, issn = {1466-1799}, mesh = {Animals ; *Geese ; Chickens ; *Microbiota ; Bacteria/genetics ; Cecum ; Carbohydrates ; }, abstract = {1. The caecal microbiota in geese play a crucial role in determining the host's health, disease status and behaviour, as evidenced by extensive epidemiological data. The present investigation conducted 10× metagenomic sequencing of caecal content samples obtained from three distinct goose species, namely Landes geese, Roman geese and Zhedong White geese (n = 5), to explore the contribution of the gut microbiome to carbohydrate metabolism.2. In total, 337GB of Illumina data were generated, which identified 1,048,575 complete genes and construction of 331 metagenomic bins, encompassing 78 species from nine phyla. Firmicutes, Bacteroidetes, Actinobacteria, Proteobacteria and Bacteria were identified as the dominant phyla while Prevotella, Bacteroides, Streptococcus, and Subdoligranulum were the most abundant genera in the caecum of geese.3. The genes were allocated to 375 pathways using the Kyoto Encyclopedia of Genes and Genome (KEGG) analysis. The most abundant classes in the caecum of geese were confirmed to be glycoside hydrolases (GHs), glycosyl transferases (GTs), as identified through the carbohydrate-active enzyme (CAZyme) database mapping. Subdoligranulum variabile and Mediterraneibacter glycyrrhizinilyticus were discovered to potentially facilitate carbohydrate digestion in geese.4. Notwithstanding, further investigation and validation are required to establish a connection between these species and CAZymes. Based on binning analysis, Mediterraneibacter glycyrrhizinilyticus and Ruminococcus sp. CAG:177 are potential species in LD geese that contribute to the production of fatty liver.}, } @article {pmid37493238, year = {2023}, author = {Bell, DT}, title = {Deciphering the potential of plasma cell-free metagenomic next-generation sequencing using the Karius test.}, journal = {Current opinion in infectious diseases}, volume = {36}, number = {5}, pages = {420-425}, doi = {10.1097/QCO.0000000000000942}, pmid = {37493238}, issn = {1473-6527}, mesh = {Humans ; High-Throughput Nucleotide Sequencing ; *Invasive Fungal Infections ; Metagenomics ; *Respiratory Tract Infections ; Sensitivity and Specificity ; Retrospective Studies ; }, abstract = {PURPOSE OF REVIEW: Plasma cell-free metagenomic next-generation sequencing (cf-mNGS) is increasingly employed for the diagnosis of infection, but a consensus for optimal use has not been established. This minireview focuses on the commercially available Karius Test and is aimed at local leaders seeking to understand the complexities of cf-mNGS to make informed test utilization policies and better interpret results.

RECENT FINDINGS: Recent retrospective studies have reported how the Karius Test was applied at their institutions and identified areas of potential patient benefit. In addition, substantive studies have reported how this test performs in specific indications, particularly invasive fungal disease, endovascular infection and lower respiratory infection.

SUMMARY: Successfully integrating plasma cf-mNGS requires careful assessment of performance in the specific applications and patient populations in which it is used. Individual institutions must independently evaluate implementation strategies and determine where diagnostic yields outweigh the potential pitfalls.}, } @article {pmid37492262, year = {2023}, author = {Kakizaki, N and Asai, K and Kuroda, M and Watanabe, R and Kujiraoka, M and Sekizuka, T and Katagiri, M and Moriyama, H and Watanabe, M and Saida, Y}, title = {Rapid identification of bacteria using a multiplex polymerase chain reaction system for acute abdominal infections.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1220651}, pmid = {37492262}, issn = {1664-302X}, abstract = {PURPOSE: Acute abdominal infections can be fatal if the causative organism (s) are misidentified. The spread of antimicrobial-resistant bacteria has become a serious problem worldwide, making antibiotic selection extremely difficult. Using quantitative metagenomic analysis, we evaluated a commercial multiplex polymerase chain reaction (PCR) system (FilmArray™, bioMérieux, Marcy-l'Étoile, France) for the rapid identification of causative bacteria.

METHODS: The cases of 10 patients with acute abdominal infections were enrolled in this retrospective study. There were six cases of perforated peritonitis and four cases of intraabdominal abscess. Fluid collected from the acute surgical abdominal infections were examined.

RESULTS: All specimens tested positive for microorganisms in culture, and six involved two or more microorganisms. Using the multiplex PCR system, nine of ten specimens were found to involve at least one microorganism. One specimen was not included in the multiplex PCR system panel. Nineteen of 21 microorganisms (90.5%) isolated by culture were detected by the multiplex PCR system. Microorganisms with very small numbers of reads (19 reads) were detectable.

CONCLUSION: This multiplex PCR system showed a high detection rate for causative microorganisms in ascites and intraabdominal abscesses. This system may be suitable as an affordable rapid identification system for causative bacteria in these cases.}, } @article {pmid37491404, year = {2023}, author = {Dass, M and Singh, Y and Ghai, M}, title = {A Review on Microbial Species for Forensic Body Fluid Identification in Healthy and Diseased Humans.}, journal = {Current microbiology}, volume = {80}, number = {9}, pages = {299}, pmid = {37491404}, issn = {1432-0991}, mesh = {Humans ; Female ; *Vaginosis, Bacterial/microbiology ; Vagina/microbiology ; *Body Fluids/microbiology ; Gardnerella vaginalis ; Saliva/microbiology ; Bacteria/genetics ; }, abstract = {Microbial communities present in body fluids can assist in distinguishing between types of body fluids. Metagenomic studies have reported bacterial genera which are core to specific body fluids and are greatly influenced by geographical location and ethnicity. Bacteria in body fluids could also be due to bacterial infection; hence, it would be worthwhile taking into consideration bacterial species associated with diseases. The present review reports bacterial species characteristic of diseased and healthy body fluids across geographical locations, and bacteria described in forensic studies, with the aim of collating a set of bacteria to serve as the core species-specific markers for forensic body fluid identification. The most widely reported saliva-specific bacterial species are Streptococcus salivarius, Prevotella melaninogenica, Neisseria flavescens, with Fusobacterium nucleatum associated with increased diseased state. Lactobacillus crispatus and Lactobacillus iners are frequently dominant in the vaginal microbiome of healthy women. Atopobium vaginae, Prevotella bivia, and Gardnerella vaginalis are more prevalent in women with bacterial vaginosis. Semen and urine-specific bacteria at species level have not been reported, and menstrual blood bacteria are indistinguishable from vaginal fluid. Targeting more than one bacterial species is recommended for accurate body fluid identification. Although metagenomic sequencing provides information of a broad microbial profile, the specific bacterial species could be used to design biosensors for rapid body fluid identification. Validation of microbial typing methods and its application in identifying body fluids in a mixed sample would allow regular use of microbial profiling in a forensic workflow.}, } @article {pmid37491386, year = {2023}, author = {Zhang, D and Li, X and Wu, Y and Xu, X and Liu, Y and Shi, B and Peng, Y and Dai, D and Sha, Z and Zheng, J}, title = {Microbe-driven elemental cycling enables microbial adaptation to deep-sea ferromanganese nodule sediment fields.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {160}, pmid = {37491386}, issn = {2049-2618}, mesh = {*Manganese/metabolism ; *Ferric Compounds/metabolism ; Geologic Sediments/microbiology ; Bacteria ; Iron/metabolism ; Archaea ; }, abstract = {BACKGROUND: Ferromanganese nodule-bearing deep-sea sediments cover vast areas of the ocean floor, representing a distinctive habitat in the abyss. These sediments harbor unique conditions characterized by high iron concentration and low degradable nutrient levels, which pose challenges to the survival and growth of most microorganisms. While the microbial diversity in ferromanganese nodule-associated sediments has been surveyed several times, little is known about the functional capacities of the communities adapted to these unique habitats.

RESULTS: Seven sediment samples collected adjacent to ferromanganese nodules from the Clarion-Clipperton Fracture Zone (CCFZ) in the eastern Pacific Ocean were subjected to metagenomic analysis. As a result, 179 high-quality metagenome-assembled genomes (MAGs) were reconstructed and assigned to 21 bacterial phyla and 1 archaeal phylum, with 88.8% of the MAGs remaining unclassified at the species level. The main mechanisms of resistance to heavy metals for microorganisms in sediments included oxidation (Mn), reduction (Cr and Hg), efflux (Pb), synergy of reduction and efflux (As), and synergy of oxidation and efflux (Cu). Iron, which had the highest content among all metallic elements, may occur mainly as Fe(III) that potentially functioned as an electron acceptor. We found that microorganisms with a diverse array of CAZymes did not exhibit higher community abundance. Instead, microorganisms mainly obtained energy from oxidation of metal (e.g., Mn(II)) and sulfur compounds using oxygen or nitrate as an electron acceptor. Chemolithoautotrophic organisms (Thaumarchaeota and Nitrospirota phyla) were found to be potential manganese oxidizers. The functional profile analysis of the dominant microorganisms further indicated that utilization of inorganic nutrients by redox reactions (rather than organic nutrient metabolism) is a major adaptive strategy used by microorganisms to support their survival in the ferromanganese nodule sediments.

CONCLUSIONS: This study provides a comprehensive metagenomic analysis of microbes inhabiting metal-rich ferromanganese nodule sediments. Our results reveal extensive redundancy across taxa for pathways of metal resistance and transformation, the highly diverse mechanisms used by microbes to obtain nutrition, and their participation in various element cycles in these unique environments. Video Abstract.}, } @article {pmid37491320, year = {2023}, author = {Brito, BP and Frost, MJ and Anantanawat, K and Jaya, F and Batterham, T and Djordjevic, SP and Chang, WS and Holmes, EC and Darling, AE and Kirkland, PD}, title = {Expanding the range of the respiratory infectome in Australian feedlot cattle with and without respiratory disease using metatranscriptomics.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {158}, pmid = {37491320}, issn = {2049-2618}, mesh = {Animals ; Cattle ; *Rhinitis ; Australia ; *Respiratory Tract Diseases ; *Viruses/genetics ; *Cattle Diseases/microbiology ; }, abstract = {BACKGROUND: Bovine respiratory disease (BRD) is one of the most common diseases in intensively managed cattle, often resulting in high morbidity and mortality. Although several pathogens have been isolated and extensively studied, the complete infectome of the respiratory complex consists of a more extensive range unrecognised species. Here, we used total RNA sequencing (i.e., metatranscriptomics) of nasal and nasopharyngeal swabs collected from animals with and without BRD from two cattle feedlots in Australia.

RESULTS: A high abundance of bovine nidovirus, influenza D, bovine rhinitis A and bovine coronavirus was found in the samples. Additionally, we obtained the complete or near-complete genome of bovine rhinitis B, enterovirus E1, bovine viral diarrhea virus (sub-genotypes 1a and 1c) and bovine respiratory syncytial virus, and partial sequences of other viruses. A new species of paramyxovirus was also identified. Overall, the most abundant RNA virus, was the bovine nidovirus. Characterisation of bacterial species from the transcriptome revealed a high abundance and diversity of Mollicutes in BRD cases and unaffected control animals. Of the non-Mollicutes species, Histophilus somni was detected, whereas there was a low abundance of Mannheimia haemolytica.

CONCLUSION: This study highlights the use of untargeted sequencing approaches to study the unrecognised range of microorganisms present in healthy or diseased animals and the need to study previously uncultured viral species that may have an important role in cattle respiratory disease. Video Abstract.}, } @article {pmid37491204, year = {2023}, author = {Hess, MK and Zetouni, L and Hess, AS and Budel, J and Dodds, KG and Henry, HM and Brauning, R and McCulloch, AF and Hickey, SM and Johnson, PL and Elmes, S and Wing, J and Bryson, B and Knowler, K and Hyndman, D and Baird, H and McRae, KM and Jonker, A and Janssen, PH and McEwan, JC and Rowe, SJ}, title = {Combining host and rumen metagenome profiling for selection in sheep: prediction of methane, feed efficiency, production, and health traits.}, journal = {Genetics, selection, evolution : GSE}, volume = {55}, number = {1}, pages = {53}, pmid = {37491204}, issn = {1297-9686}, support = {SOW-AGR-GPLER-SP5//Global Research Alliance on Agricultural Livestock Emmissions Research/ ; C10X1306//Ministry of Business, Innovation and Employment/ ; C10X1807//Ministry of Business, Innovation and Employment/ ; }, mesh = {Sheep/genetics ; Animals ; Female ; *Metagenome ; *Methane ; Rumen ; Carbon Dioxide ; RNA, Ribosomal, 16S/genetics ; Phenotype ; Diet/veterinary ; Animal Feed ; }, abstract = {BACKGROUND: Rumen microbes break down complex dietary carbohydrates into energy sources for the host and are increasingly shown to be a key aspect of animal performance. Host genotypes can be combined with microbial DNA sequencing to predict performance traits or traits related to environmental impact, such as enteric methane emissions. Metagenome profiles were generated from 3139 rumen samples, collected from 1200 dual purpose ewes, using restriction enzyme-reduced representation sequencing (RE-RRS). Phenotypes were available for methane (CH4) and carbon dioxide (CO2) emissions, the ratio of CH4 to CH4 plus CO2 (CH4Ratio), feed efficiency (residual feed intake: RFI), liveweight at the time of methane collection (LW), liveweight at 8 months (LW8), fleece weight at 12 months (FW12) and parasite resistance measured by faecal egg count (FEC1). We estimated the proportion of phenotypic variance explained by host genetics and the rumen microbiome, as well as prediction accuracies for each of these traits.

RESULTS: Incorporating metagenome profiles increased the variance explained and prediction accuracy compared to fitting only genomics for all traits except for CO2 emissions when animals were on a grass diet. Combining the metagenome profile with host genotype from lambs explained more than 70% of the variation in methane emissions and residual feed intake. Predictions were generally more accurate when incorporating metagenome profiles compared to genetics alone, even when considering profiles collected at different ages (lamb vs adult), or on different feeds (grass vs lucerne pellet). A reference-free approach to metagenome profiling performed better than metagenome profiles that were restricted to capturing genera from a reference database. We hypothesise that our reference-free approach is likely to outperform other reference-based approaches such as 16S rRNA gene sequencing for use in prediction of individual animal performance.

CONCLUSIONS: This paper shows the potential of using RE-RRS as a low-cost, high-throughput approach for generating metagenome profiles on thousands of animals for improved prediction of economically and environmentally important traits. A reference-free approach using a microbial relationship matrix from log10 proportions of each tag normalized within cohort (i.e., the group of animals sampled at the same time) is recommended for future predictions using RE-RRS metagenome profiles.}, } @article {pmid37491010, year = {2023}, author = {Guo, Y and Li, Z and Dong, S and Si, X and Ta, N and Liang, H and Xu, L}, title = {Multiple infections of zoonotic pathogens in wild Brandt's voles (Lasiopodomys brandtii).}, journal = {Veterinary medicine and science}, volume = {9}, number = {5}, pages = {2201-2211}, pmid = {37491010}, issn = {2053-1095}, mesh = {Humans ; Animals ; Phylogeny ; *Animals, Wild ; *DNA ; Arvicolinae/genetics ; China ; }, abstract = {BACKGROUND: The frequent interactions of rodents with humans make them a common source of zoonotic infections. Brandt's vole is the dominant rodent species of the typical steppe in Inner Mongolia, and it is also an important pest in grassland.

OBJECTIVES: To obtain an initial unbiased measure of the microbial diversity and abundance in the blood and intestinal tracts and to detect the pathogens carried by wild Brandt's voles in Hulun Buir, Inner Mongolia.

METHODS: Twenty wild adult Brandt's voles were trapped using live cages, and 12 intestinal samples were collected for metagenomic analysis and 8 blood samples were collected for meta-transcriptomic analysis. We compared the sequencing data with pathogenic microbiota databases to analyse the phylogenetic characteristics of zoonotic pathogens carried by wild voles.

RESULTS: A total of 122 phyla, 79 classes, 168 orders, 382 families and 1693 genera of bacteria and a total of 32 families of DNA and RNA viruses in Brandt's voles were characterized. We found that each sample carried more than 10 pathogens, whereas some pathogens that were low in abundance were still at risk of transmission to humans.

CONCLUSION: This study improves our understanding of the viral and bacterial diversity in wild Brandt's voles and highlights the multiple viral and bacterial pathogens carried by this rodent. These findings may serve as a basis for developing strategies targeting rodent population control in Hulun Buir and provide a better approach to the surveillance of pathogenic microorganisms in wildlife.}, } @article {pmid37490989, year = {2024}, author = {Deng, Z and Ouyang, Z and Mei, S and Zhang, X and Li, Q and Meng, F and Hu, Y and Dai, X and Zhou, S and Mao, K and Huang, C and Dai, J and Yi, C and Tan, N and Feng, T and Long, H and Tian, X}, title = {Enhancing NKT cell-mediated immunity against hepatocellular carcinoma: Role of XYXD in promoting primary bile acid synthesis and improving gut microbiota.}, journal = {Journal of ethnopharmacology}, volume = {318}, number = {Pt B}, pages = {116945}, doi = {10.1016/j.jep.2023.116945}, pmid = {37490989}, issn = {1872-7573}, mesh = {Animals ; *Carcinoma, Hepatocellular/drug therapy ; *Drugs, Chinese Herbal/pharmacology ; *Gastrointestinal Microbiome ; *Liver Neoplasms/drug therapy ; Bile Acids and Salts ; Immunity, Cellular ; }, abstract = {'Xiayuxue decoction' (XYXD) is a traditional Chinese medicine compound, composing of three natural medicines: Rheum officinale Baill., Prunus persica (L.) Batsch and Eupolyphaga sinensis Walker. It is derived from the famous traditional Chinese medical classics 'Jingui Yaolue' and has been used for thousands of years. In the Guidelines for the Diagnosis and Treatment of Primary liver Cancer issued by China's Health Commission, XYXD was applied in the treatment of primary liver cancer.

AIM OF THE STUDY: To clarify the pharmacodynamic material basis and mechanism of XYXD in the treatment of hepatocellular carcinoma (HCC).

MATERIALS AND METHODS: Firstly, the active components of XYXD and its distribution in vivo were identified by Ultraperformance liquid chromatography coupled with quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF-MS). Then, the effective components and mechanism of XYXD against HCC were explored by network pharmacology combined with cell experiments in vitro. Furthermore, the anti-HCC effect of XYXD was determined by animal experiments in vivo. Metagenomic sequencing was used to detect its effect in gut microbiota, and targeted metabolism was used to detect the changes of bile acids in the liver. Finally, the related targets of NKT cell immune function activation were detected by RT-qPCR and Elisa.

RESULTS: A total of 113 active ingredients in XYXD were identified, and the distribution of active ingredients in blood, liver, tumor, cecum, intestinal contents and feces was clarified. The circulation process and active ingredient group of XYXD were preliminarily clarified. In addition, we found five anti-HCC active ingredients in XYXD through network pharmacology combined with cell experiments in vitro, among which aloe emodin had the most significant effect, and predicted the potential mechanism of XYXD against HCC through NKT cell pathway. Moreover, the inhibitory effect of XYXD on liver tumor growth was clarified by animal experiments in vivo. The mechanism was mainly to promote the production of bile salt hydrolase (BSH) by increasing the abundance of Bacteroides and Lactobacillus, BSH converts conjugated bile acids into primary bile acids, and reduces the conversion of primary bile acids to secondary bile acids by reducing the abundance of Eubacterium, thereby increasing the content of primary bile acids. Primary bile acids trigger NKT cells in the liver to produce interferon-γ to exert anti-HCC immune effects.

CONCLUSION: This study found that the traditional Chinese herbal formula XYXD can trigger the immune effect of NKT cells against HCC by regulating the interaction between gut microbiota and bile acids.}, } @article {pmid37490185, year = {2023}, author = {Perlejewski, K and Radkowski, M and Rydzanicz, M and Dzieciątkowski, T and Silling, S and Wieczorek, M and Makowiecki, M and Horban, A and Laskus, T}, title = {Metagenomic search of viral coinfections in herpes simplex encephalitis patients.}, journal = {Journal of neurovirology}, volume = {29}, number = {5}, pages = {588-597}, pmid = {37490185}, issn = {1538-2443}, support = {2017/25/B/NZ6/01463//Narodowe Centrum Nauki/ ; }, mesh = {Humans ; *Coinfection ; *Encephalitis, Herpes Simplex/diagnosis ; *Virus Diseases ; Polymerase Chain Reaction/methods ; Enterovirus B, Human ; *Central Nervous System Infections ; DNA ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Little is known about concomitant central nervous system (CNS) infections by more than one virus. Current diagnostics are based on molecular tests for particular pathogens making it difficult to identify multi-viral infections. In the present study, we applied DNA- and RNA-based next-generation sequencing metagenomics (mNGS) to detect viruses in cerebrospinal fluids from 20 patients with herpes simplex encephalitis. Coinfection was detected in one patient: sequences in cerebrospinal fluids matched enterovirus A (2.660 reads; 4% of recovered genome) and enterovirus B (1.571 reads; 13% of recovered genome). Subsequent PCR combined with serotyping allowed to identify human echovirus 6, a representative of enterovirus B. Several other mNGS hits (human pegivirus, Merkel cell polyomavirus, human papillomavirus type 5) were not considered to represent a genuine signal as they could not be confirmed by specific RT-PCR/PCR. HSV DNA, while being detectable by PCR in every patient, was detected by mNGS in only one. In conclusion, contaminations and false signals may complicate mNGS interpretation; however, the method can be useful in diagnostics of viral coinfections in CNS, particularly in the case of rare pathogens.}, } @article {pmid37489282, year = {2023}, author = {Thorburn, DJ and Sagonas, K and Binzer-Panchal, M and Chain, FJJ and Feulner, PGD and Bornberg-Bauer, E and Reusch, TBH and Samonte-Padilla, IE and Milinski, M and Lenz, TL and Eizaguirre, C}, title = {Origin matters: Using a local reference genome improves measures in population genomics.}, journal = {Molecular ecology resources}, volume = {23}, number = {7}, pages = {1706-1723}, doi = {10.1111/1755-0998.13838}, pmid = {37489282}, issn = {1755-0998}, support = {EI 841/4-1//Deutsche Forschungsgemeinschaft/ ; EI 841/6-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Animals ; *Metagenomics ; Genome/genetics ; Chromosome Mapping ; Genomics/methods ; Sequence Analysis, DNA/methods ; *Smegmamorpha/genetics ; }, abstract = {Genome sequencing enables answering fundamental questions about the genetic basis of adaptation, population structure and epigenetic mechanisms. Yet, we usually need a suitable reference genome for mapping population-level resequencing data. In some model systems, multiple reference genomes are available, giving the challenging task of determining which reference genome best suits the data. Here, we compared the use of two different reference genomes for the three-spined stickleback (Gasterosteus aculeatus), one novel genome derived from a European gynogenetic individual and the published reference genome of a North American individual. Specifically, we investigated the impact of using a local reference versus one generated from a distinct lineage on several common population genomics analyses. Through mapping genome resequencing data of 60 sticklebacks from across Europe and North America, we demonstrate that genetic distance among samples and the reference genomes impacts downstream analyses. Using a local reference genome increased mapping efficiency and genotyping accuracy, effectively retaining more and better data. Despite comparable distributions of the metrics generated across the genome using SNP data (i.e. π, Tajima's D and FST), window-based statistics using different references resulted in different outlier genes and enriched gene functions. A marker-based analysis of DNA methylation distributions had a comparably high overlap in outlier genes and functions, yet with distinct differences depending on the reference genome. Overall, our results highlight how using a local reference genome decreases reference bias to increase confidence in downstream analyses of the data. Such results have significant implications in all reference-genome-based population genomic analyses.}, } @article {pmid37488386, year = {2023}, author = {Sanusi, IO and Olutona, GO and Wawata, IG and Onohuean, H}, title = {Occurrence, environmental impact and fate of pharmaceuticals in groundwater and surface water: a critical review.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {39}, pages = {90595-90614}, pmid = {37488386}, issn = {1614-7499}, mesh = {Humans ; Chromatography, Liquid ; Wastewater ; Water/analysis ; Tandem Mass Spectrometry ; Ecosystem ; *Groundwater/chemistry ; Sulfamethoxazole/analysis ; Pharmaceutical Preparations ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring/methods ; }, abstract = {In many nations and locations, groundwater serves as the population's primary drinking water supply. However, pharmaceuticals found in groundwater and surface waters may affect aquatic ecosystems and public health. As a result, their existence in natural raw waters are now more widely acknowledged as a concern. This review summarises the evidence of research on pharmaceuticals' occurrence, impact and fate, considering results from different water bodies. Also, various analytical techniques were reviewed to compare different pharmaceuticals' detection frequencies in water bodies. These include liquid chromatography-mass spectrometry (LC-MS), high-performance liquid chromatography (HPLC), ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS), and gas chromatography-mass spectrometry (GC-MS). However, owing to LC-MS's high sensitivity and specification, it is the most reported instrument used for analysis. The PRISMA reviewing methodology was adopted based on relevant literature in order to focus on aim of the review. Among other pharmaceuticals reviewed, sulfamethoxazole was found to be the most frequently detected drug in wastewater (up to 100% detection frequency). The most reported pharmaceutical group in this review is antibiotics, with sulfamethoxazole having the highest concentration among the analysed pharmaceuticals in groundwater and freshwater (up to 5600 ng/L). Despite extensive study and analysis on the occurrence and fate of pharmaceuticals in the environment, appropriate wastewater management and disposal of pharmaceuticals in the water environment are not still monitored regularly. Therefore, there is a need for mainstream studies tailored to the surveillance of pharmaceuticals in water bodies to limit environmental risks to human and aquatic habitats in both mid and low-income nations.}, } @article {pmid37488221, year = {2023}, author = {Sun, J and Germain, A and Kaglan, G and Servant, F and Lelouvier, B and Federici, M and Fernandez-Real, JM and Sala, DT and Neagoe, RM and Bouloumié, A and Burcelin, R}, title = {The visceral adipose tissue bacterial microbiota provides a signature of obesity based on inferred metagenomic functions.}, journal = {International journal of obesity (2005)}, volume = {47}, number = {10}, pages = {1008-1022}, pmid = {37488221}, issn = {1476-5497}, mesh = {Animals ; Humans ; *Intra-Abdominal Fat/metabolism ; Obesity/metabolism ; *Microbiota ; Obesity, Abdominal/metabolism ; Inflammation/metabolism ; Adipose Tissue/metabolism ; }, abstract = {BACKGROUND: Metabolic inflammation mediated obesity requires bacterial molecules to trigger immune and adipose cells leading to inflammation and adipose depot development. In addition to the well-established gut microbiota dysbiosis, a leaky gut has been identified in patients with obesity and animal models, characterized by the presence of a tissue microbiota in the adipose fat pads.

METHODS: To determine its potential role, we sequenced the bacterial 16 S rRNA genes in the visceral adipose depot of patients with obesity. Taking great care (surgical, biochemical, and bioinformatic) to avoid environmental contaminants. We performed statistical discriminant analyses to identify specific signatures and constructed network of interactions between variables.

RESULTS: The data showed that a specific 16SrRNA gene signature was composed of numerous bacterial families discriminating between lean versus patients with obesity and people with severe obesity. The main discriminant families were Burkholderiaceae, Yearsiniaceae, and Xanthomonadaceae, all of which were gram-negative. Interestingly, the Morganellaceae were totally absent from people without obesity while preponderant in all in patients with obesity. To generate hypotheses regarding their potential role, we inferred metabolic pathways from the 16SrRNA gene signatures. We identified several pathways associated with adenosyl-cobalamine previously described to be linked with adipose tissue development. We further identified chorismate biosynthesis, which is involved in aromatic amino-acid metabolism and could play a role in fat pad development. This innovative approach generates novel hypotheses regarding the gut to adipose tissue axis.

CONCLUSIONS: This innovative approach generates novel hypotheses regarding the gut to adipose tissue axis in obesity and notably the potential role of tissue microbiota.}, } @article {pmid37488016, year = {2023}, author = {Lu, H and Liu, S and Wang, A and Yang, H and Liang, X and Chen, X and Li, Q}, title = {Transmission and regulation insights into antibiotic resistance genes in straw-sludge composting system amended with calcium peroxide.}, journal = {Bioresource technology}, volume = {386}, number = {}, pages = {129539}, doi = {10.1016/j.biortech.2023.129539}, pmid = {37488016}, issn = {1873-2976}, mesh = {*Genes, Bacterial/genetics ; Sewage/microbiology ; *Composting ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Manure ; }, abstract = {This study developed a Fenton-like system by adding calcium peroxide (CaO2) to a composting system containing straw and sludge. The objective was to examine the influence of antibiotic resistance genes (ARGs) and the structure of the bacterial community. The findings indicated that the inclusion of CaO2 facilitated the reduction of ARGs. ARGs abundance in the test group (T) with CaO2 was 19.02% lower than that in the control check group (CK) without CaO2, and the abundance of ARGs in both groups after composting was lower than the initial abundance. Additionally, the structure of bacterial community in both groups underwent significant changes. Redundancy analysis (RDA) revealed that the CaO2-induced Fenton-like reaction predominantly affected temperature, pH, and the bacterial community by means of reactive oxygen species (ROS). In conclusion, the addition of CaO2 enhanced the removal of ARGs from sewage-sludge and improved compost quality in the composting.}, } @article {pmid37487417, year = {2023}, author = {Armstrong, AJS and Horton, DB and Andrews, T and Greenberg, P and Roy, J and Gennaro, ML and Carson, JL and Panettieri, RA and Barrett, ES and Blaser, MJ}, title = {Saliva microbiome in relation to SARS-CoV-2 infection in a prospective cohort of healthy US adults.}, journal = {EBioMedicine}, volume = {94}, number = {}, pages = {104731}, pmid = {37487417}, issn = {2352-3964}, support = {R01 AI158911/AI/NIAID NIH HHS/United States ; R33 HD105619/HD/NICHD NIH HHS/United States ; R61 HD105619/HD/NICHD NIH HHS/United States ; UL1 TR003017/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Adult ; *COVID-19 ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; SARS-CoV-2 ; Saliva ; *Microbiota ; }, abstract = {BACKGROUND: The clinical outcomes of SARS-CoV-2 infection vary in severity, potentially influenced by the resident human microbiota. There is limited consensus on conserved microbiome changes in response to SARS-CoV-2 infection, with many studies focusing on severely ill individuals. This study aimed to assess the variation in the upper respiratory tract microbiome using saliva specimens in a cohort of individuals with primarily mild to moderate disease.

METHODS: In early 2020, a cohort of 831 adults without known SARS-CoV-2 infection was followed over a six-month period to assess the occurrence and natural history of SARS-CoV-2 infection. From this cohort, 81 participants with a SARS-CoV-2 infection, along with 57 unexposed counterparts were selected with a total of 748 serial saliva samples were collected for analysis. Total bacterial abundance, composition, population structure, and gene function of the salivary microbiome were measured using 16S rRNA gene and shotgun metagenomic sequencing.

FINDINGS: The salivary microbiome remained stable in unexposed individuals over the six-month study period, as evidenced by all measured metrics. Similarly, participants with mild to moderate SARS-CoV-2 infection showed microbiome stability throughout and after their infection. However, there were significant reductions in microbiome diversity among SARS-CoV-2-positive participants with severe symptoms early after infection. Over time, the microbiome diversity in these participants showed signs of recovery.

INTERPRETATION: These findings demonstrate the resilience of the salivary microbiome in relation to SARS-CoV-2 infection. Mild to moderate infections did not significantly disrupt the stability of the salivary microbiome, suggesting its ability to maintain its composition and function. However, severe SARS-CoV-2 infection was associated with temporary reductions in microbiome diversity, indicating the limits of microbiome resilience in the face of severe infection.

FUNDING: This project was supported in part by Danone North America and grants from the National Institutes of Health, United States.}, } @article {pmid37486790, year = {2023}, author = {Makhsous, N and Goya, S and Avendaño, CC and Rupp, J and Kuypers, J and Jerome, KR and Boeckh, M and Waghmare, A and Greninger, AL}, title = {Within-host rhinovirus evolution in upper and lower respiratory tract highlights capsid variability and mutation-independent compartmentalization.}, journal = {The Journal of infectious diseases}, volume = {}, number = {}, pages = {}, doi = {10.1093/infdis/jiad284}, pmid = {37486790}, issn = {1537-6613}, support = {R01 AI153087/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Rhinovirus (RV) infections can progress from the upper (URT) to lower (LRT) respiratory tract in immunocompromised individuals, causing high rates of fatal pneumonia. Little is known about how RV evolves within hosts during infection.

METHODS: We sequenced RV complete genomes from 12 hematopoietic cell transplant patients with infection for up to 190 days from both URT (nasal wash, NW) and LRT (bronchoalveolar lavage, BAL). Metagenomic (mNGS) and amplicon NGS were used to track the emergence and evolution of intra-host single nucleotide variants (iSNVs).

RESULTS: Identical RV intra-host populations in matched NW and BAL specimens indicated no genetic adaptation is required for RV to progress from URT to LRT. Coding iSNVs were 2.3-fold more prevalent in capsid over non-structural genes. iSNVs modeled were significantly more likely to be found in capsid surface capsid residues, but were not preferentially located in known RV neutralizing antibody epitopes. Newly emergent, genotype-matched iSNV haplotypes from immunocompromised individuals from 2008-2010 could be detected in Seattle-area community RV sequences from 2020-2021.

CONCLUSION: RV infections in immunocompromised hosts can progress from URT to LRT with no specific evolutionary requirement. Capsid proteins carry the highest variability and emergent mutations can be detected in other, including future, RV sequences.}, } @article {pmid37485826, year = {2023}, author = {Jaramillo-Jaramillo, AS and Coulson, TJD and Hofacre, C and Jones, M and O'Neill, L and Nguyen, N and Labbe, A}, title = {Effect of in-water administration of quorum system inhibitors in broilers' productive performance and intestinal microbiome in a mild necrotic enteritis challenge.}, journal = {Avian pathology : journal of the W.V.P.A}, volume = {52}, number = {5}, pages = {309-322}, doi = {10.1080/03079457.2023.2224260}, pmid = {37485826}, issn = {1465-3338}, mesh = {Animals ; *Bacterial Toxins/metabolism ; Enterotoxins/metabolism ; *Clostridium Infections/veterinary/microbiology ; Chickens/microbiology ; *Enteritis/veterinary/microbiology ; *Gastrointestinal Microbiome ; Clostridium perfringens/genetics ; Water/metabolism ; *Poultry Diseases/microbiology ; }, abstract = {The poultry industry has been facing the impact of necrotic enteritis (NE), a disease caused by the bacterium Clostridium perfringens producing the haemolytic toxin NetB. NE severity may vary from mild clinical to prominent enteric signs causing reduced growth rates and affecting feed conversion ratio. NetB production is controlled by the Agr-like quorum-sensing (QS) system, which coordinates virulence gene expression in response to bacterial cell density. In this study, the peptide-containing cell-free spent media (CFSM) from Enterococcus faecium was tested in NE challenged broilers in two battery cage and one floor pen studies. Results showed a significant reduction of NE mortality. Metagenomic sequencing of the jejunum microbiome revealed no impact of the CFSM on the microbial community, and growth of C. perfringens was unaffected by CFSM in vitro. The expression of QS-controlled virulence genes netB, plc and pfoA was found to be significantly repressed by CFSM during the mid-logarithmic stage of C. perfringens growth and this corresponded with a significant decrease in haemolytic activity. Purified fractions of CFSM containing bioactive peptides were found to cause reduced haemolysis. These results showed that bioactive peptides reduce NE mortality in broilers by interfering with the QS system of C. perfringens and reducing bacterial virulence. Furthermore, the microbiome of C. perfringens-challenged broilers is not affected by quorum sensing inhibitor containing CFSM.}, } @article {pmid37485822, year = {2023}, author = {Oda, T}, title = {Improving protein structure prediction with extended sequence similarity searches and deep-learning-based refinement in CASP15.}, journal = {Proteins}, volume = {91}, number = {12}, pages = {1712-1723}, doi = {10.1002/prot.26551}, pmid = {37485822}, issn = {1097-0134}, mesh = {Humans ; *Deep Learning ; Models, Molecular ; Computational Biology/methods ; Proteins/chemistry ; Protein Conformation ; }, abstract = {The human predictor team PEZYFoldings got first place with the assessor's formulae (3rd place with Global Distance Test Total Score [GDT-TS]) in the single-domain category and 10th place in the multimer category in Critical Assessment of Structure Prediction 15. In this paper, I describe the exact method used by PEZYFoldings in the competition. As AlphaFold2 and AlphaFold-Multimer, developed by DeepMind, were state-of-the-art structure prediction tools, it was assumed that enhancing the input and output of the tools was an effective strategy to obtain the highest accuracy for structure prediction. Therefore, I used additional tools and databases to collect evolutionarily related sequences and introduced a deep-learning-based model in the refinement step. In addition to these modifications, manual interventions were performed to address various tasks. Detailed analyses were performed after the competition to identify the main contributors to performance. Comparing the number of evolutionarily related sequences I used with those of the other teams that provided AlphaFold2's baseline predictions revealed that an extensive sequence similarity search was one of the main contributors. Nonetheless, there were specific targets for which I could not identify any evolutionarily related sequences, resulting in my inability to construct accurate structures for these targets. Notably, I noticed that I had gained large Z-scores with the subunits of H1137, for which I performed manual domain parsing considering the interfaces between the subunits. This finding implies that the manual intervention contributed to my performance. The influence of the refinement model on the accuracy of structure prediction was minimal. I could have predicted structures with a similar level of accuracy without employing the refinement model. However, from the perspective of accuracy self-estimate, many structures demonstrated improvement after refinement. This improvement likely had a substantial influence on improving my position in the assessor's formulae rankings. These results highlight the opportunities for improvement in (1) multimer prediction, (2) building of larger and more diverse databases, and (3) developing tools to predict structures from primary sequences alone. In addition, transferring the manual intervention process to automation is a future concern.}, } @article {pmid37485738, year = {2023}, author = {Wuyts, S and Alves, R and Zimmermann-Kogadeeva, M and Nishijima, S and Blasche, S and Driessen, M and Geyer, PE and Hercog, R and Kartal, E and Maier, L and Müller, JB and Garcia Santamarina, S and Schmidt, TSB and Sevin, DC and Telzerow, A and Treit, PV and Wenzel, T and Typas, A and Patil, KR and Mann, M and Kuhn, M and Bork, P}, title = {Consistency across multi-omics layers in a drug-perturbed gut microbial community.}, journal = {Molecular systems biology}, volume = {19}, number = {9}, pages = {e11525}, pmid = {37485738}, issn = {1744-4292}, support = {MC_UU_00025/11/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Multiomics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metabolomics/methods ; Bacteria/genetics ; Metagenomics/methods ; }, abstract = {Multi-omics analyses are used in microbiome studies to understand molecular changes in microbial communities exposed to different conditions. However, it is not always clear how much each omics data type contributes to our understanding and whether they are concordant with each other. Here, we map the molecular response of a synthetic community of 32 human gut bacteria to three non-antibiotic drugs by using five omics layers (16S rRNA gene profiling, metagenomics, metatranscriptomics, metaproteomics and metabolomics). We find that all the omics methods with species resolution are highly consistent in estimating relative species abundances. Furthermore, different omics methods complement each other for capturing functional changes. For example, while nearly all the omics data types captured that the antipsychotic drug chlorpromazine selectively inhibits Bacteroidota representatives in the community, the metatranscriptome and metaproteome suggested that the drug induces stress responses related to protein quality control. Metabolomics revealed a decrease in oligosaccharide uptake, likely caused by Bacteroidota depletion. Our study highlights how multi-omics datasets can be utilized to reveal complex molecular responses to external perturbations in microbial communities.}, } @article {pmid37485720, year = {2023}, author = {Jacques, C and Bacqueville, D and Jamin, EL and Maitre, M and Delsol, C and Simcic-Mori, A and Bianchi, P and Noustens, A and Jouanin, I and Debrauwer, L and Bessou-Touya, S and Stockfleth, E and Duplan, H}, title = {Multi-omics approach to understand the impact of sun exposure on an in vitro skin ecosystem and evaluate a new broad-spectrum sunscreen.}, journal = {Photochemistry and photobiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/php.13841}, pmid = {37485720}, issn = {1751-1097}, abstract = {A reconstructed human epidermal model (RHE) colonized with human microbiota and sebum was developed to reproduce the complexity of the skin ecosystem in vitro. The RHE model was exposed to simulated solar radiation (SSR) with or without SPF50+ sunscreen (with UVB, UVA, long-UVA, and visible light protection). Structural identification of discriminant metabolites was acquired by nuclear magnetic resonance and metabolomic fingerprints were identified using reverse phase-ultra high-performance liquid chromatography-high resolution mass spectrometry, followed by pathway enrichment analysis. Over 50 metabolites were significantly altered by SSR (p < 0.05, log2 values), showing high skin oxidative stress (glutathione and purine pathways, urea cycle) and altered skin microbiota (branched-chain amino acid cycle and tryptophan pathway). 16S and internal transcribed spacer rRNA sequencing showed the relative abundance of various bacteria and fungi altered by SSR. This study identified highly accurate metabolomic fingerprints and metagenomic modifications of sun-exposed skin to help elucidate the interactions between the skin and its microbiota. Application of SPF50+ sunscreen protected the skin ecosystem model from the deleterious effects of SSR and preserved the physiological interactions within the skin ecosystem. These innovative technologies could thus be used to evaluate the effectiveness of sunscreen.}, } @article {pmid37485518, year = {2023}, author = {Kumar, R and Choudhary, JS and Naik, SK and Mondal, S and Mishra, JS and Poonia, SP and Kumar, S and Hans, H and Kumar, S and Das, A and Kumar, V and Bhatt, BP and Chaudhari, SK and Malik, RK and Craufurd, P and McDonald, A and Sherpa, SR}, title = {Influence of conservation agriculture-based production systems on bacterial diversity and soil quality in rice-wheat-greengram cropping system in eastern Indo-Gangetic Plains of India.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1181317}, pmid = {37485518}, issn = {1664-302X}, abstract = {INTRODUCTION: Conservation agriculture (CA) is gaining attention in the South Asia as an environmentally benign and sustainable food production system. The knowledge of the soil bacterial community composition along with other soil properties is essential for evaluating the CA-based management practices for achieving the soil environment sustainability and climate resilience in the rice-wheat-greengram system. The long-term effects of CA-based tillage-cum-crop establishment (TCE) methods on earthworm population, soil parameters as well as microbial diversity have not been well studied.

METHODS: Seven treatments (or scenarios) were laid down with the various tillage (wet, dry, or zero-tillage), establishment method (direct-or drill-seeding or transplantation) and residue management practices (mixed with the soil or kept on the soil surface). The soil samples were collected after 7 years of experimentation and analyzed for the soil quality and bacterial diversity to examine the effect of tillage-cum-crop establishment methods.

RESULTS AND DISCUSSION: Earthworm population (3.6 times), soil organic carbon (11.94%), macro (NPK) (14.50-23.57%) and micronutrients (Mn, and Cu) (13.25 and 29.57%) contents were appreciably higher under CA-based TCE methods than tillage-intensive farming practices. Significantly higher number of OTUs (1,192 ± 50) and Chao1 (1415.65 ± 14.34) values were observed in partial CA-based production system (p ≤ 0.05). Forty-two (42) bacterial phyla were identified across the scenarios, and Proteobacteria, Actinobacteria, and Firmicutes were the most dominant in all the scenarios. The CA-based scenarios harbor a high abundance of Proteobacteria (2-13%), whereas the conventional tillage-based scenarios were dominated by the bacterial phyla Acidobacteria and Chloroflexi and found statistically differed among the scenarios (p ≤ 0.05). Composition of the major phyla, i.e., Proteobacteria, Actinobacteria, and Firmicutes were associated differently with either CA or farmers-based tillage management practices. Overall, the present study indicates the importance of CA-based tillage-cum-crop establishment methods in shaping the bacterial diversity, earthworms population, soil organic carbon, and plant nutrient availability, which are crucial for sustainable agricultural production and resilience in agro-ecosystem.}, } @article {pmid37485515, year = {2023}, author = {Němečková, K and Mareš, J and Procházková, L and Culka, A and Košek, F and Wierzchos, J and Nedbalová, L and Dudák, J and Tymlová, V and Žemlička, J and Kust, A and Zima, J and Nováková, E and Jehlička, J}, title = {Gypsum endolithic phototrophs under moderate climate (Southern Sicily): their diversity and pigment composition.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1175066}, pmid = {37485515}, issn = {1664-302X}, abstract = {In this study, we used microscopic, spectroscopic, and molecular analysis to characterize endolithic colonization in gypsum (selenites and white crystalline gypsum) from several sites in Sicily. Our results showed that the dominant microorganisms in these environments are cyanobacteria, including: Chroococcidiopsis sp., Gloeocapsopsis pleurocapsoides, Gloeocapsa compacta, and Nostoc sp., as well as orange pigmented green microalgae from the Stephanospherinia clade. Single cell and filament sequencing coupled with 16S rRNA amplicon metagenomic profiling provided new insights into the phylogenetic and taxonomic diversity of the endolithic cyanobacteria. These organisms form differently pigmented zones within the gypsum. Our metagenomic profiling also showed differences in the taxonomic composition of endoliths in different gypsum varieties. Raman spectroscopy revealed that carotenoids were the most common pigments present in the samples. Other pigments such as gloeocapsin and scytonemin were also detected in the near-surface areas, suggesting that they play a significant role in the biology of endoliths in this environment. These pigments can be used as biomarkers for basic taxonomic identification, especially in case of cyanobacteria. The findings of this study provide new insights into the diversity and distribution of phototrophic microorganisms and their pigments in gypsum in Southern Sicily. Furthemore, this study highlights the complex nature of endolithic ecosystems and the effects of gypsum varieties on these communities, providing additional information on the general bioreceptivity of these environments.}, } @article {pmid37485444, year = {2023}, author = {Onohuean, H and Onohuean, FE and Ayogu, EE}, title = {Association between hemoglobin variants and laboratory outcomes in patients infected with P. falciparum from South West Uganda.}, journal = {Future science OA}, volume = {9}, number = {7}, pages = {FSO888}, pmid = {37485444}, issn = {2056-5623}, abstract = {AIMS: We assess the relationship between various hemoglobin variants and some hematological parameters packed cell volume, white blood cells (PCV, WBC) and parasitemia level of patients with malaria in the southwestern, Uganda.

METHODS: Patient were enrolled by rapid diagnostic tests (RDTs), confirmed by microscopy, and laboratory outcomes were determined.

RESULTS: Patients positive for malaria RDTs were 155, microscopic-confirmed P. falciparum parasites were 95 (61.29%) having hemoglobin variants HbAA and HbAS; 75 (78.95%) and 13 (13.68%), respectively. The laboratory outcomes showed mean, PCV (32.19 ± 4.83), WBC (5831.66 ± 2888.29) and P. falciparum parasitaemia density (32,605.45 ± 14031), while the hemoglobin variants mean values AA (39,008.85 ± 31,261.56), AC (15908 ± 10173.48), AS (16,561.46 ± 15,380.93), SC (30,524 ± 0.000) and SS(1652 ± 0.000) were significantly different from the total population (34,321.5 ± 21,924.26) parasite-density.

CONCLUSION: Patients with hemoglobin variants HbAA had a significantly higher parasite-carrying capacity and PCV levels.}, } @article {pmid37484860, year = {2023}, author = {Wen, S and Peng, S and Hu, X and Jiang, N and Li, B and Chen, B and Deng, S and Yuan, Y and Wu, Q and Tao, Y and Ma, J and Li, S and Lin, T and Wen, F and Li, Z and Huang, R and Feng, Z and He, C and Wang, W and Liang, X and Shi, W and Xu, L and Liu, S}, title = {Validation of metagenomic next-generation sequencing of bronchoalveolar lavage fluid for diagnosis of suspected pulmonary infections in patients with systemic autoimmune rheumatic diseases receiving immunosuppressant therapy.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1161661}, pmid = {37484860}, issn = {2296-858X}, abstract = {BACKGROUND: The accuracy and sensitivity of conventional microbiological tests (CMTs) are insufficient to identify opportunistic pathogens in patients with systemic autoimmune rheumatic diseases (SARDs). The study aimed to assess the usefulness of metagenomic next-generation sequencing (mNGS) vs. CMTs for the diagnosis of pulmonary infections in patients with SARDs receiving immunosuppressant therapy.

METHODS: The medical records of 40 patients with pulmonary infections and SARDs treated with immunosuppressants or corticosteroids were reviewed retrospectively. Bronchoalveolar lavage fluid (BALF) samples were collected from all patients and examined by mNGS and CMTs. Diagnostic values of the CMTs and mNGS were compared with the clinical composite diagnosis as the reference standard.

RESULTS: Of the 40 patients included for analysis, 37 (92.5%) were diagnosed with pulmonary infections and 3 (7.5%) with non-infectious diseases, of which two were considered primary diseases and one an asthma attack. In total, 15 pathogens (7 bacteria, 5 fungi, and 3 viruses) were detected by CMTs as compared to 58 (36 bacteria, 12 fungi, and 10 viruses) by mNGS. Diagnostic accuracy of mNGS was superior to that of the CMTs for the detection of co-infections with bacteria and fungi (95 vs. 53%, respectively, p < 0.01), and for the detection of single infections with fungi (97.5 vs. 55%, respectively, p < 0.01). Of the 31 patients diagnosed with co-infections, 4 (12.9%) were positive for two pathogens and 27 (87.1%) for three or more. The detection rate of co-infection was significantly higher for mNGS than CMTs (95 vs. 16%, respectively, p < 0.01).

CONCLUSION: The accuracy of mNGS was superior to that of the CMTs for the diagnosis of pulmonary infections in patients with SARDs treated with immunosuppressants. The rapid diagnosis by mNGS can ensure timely adjustment of treatment regimens to improve diagnosis and outcomes.}, } @article {pmid37484494, year = {2023}, author = {Jayasekara, SK and Joni, HD and Jayantha, B and Dissanayake, L and Mandrell, C and Sinharage, MMS and Molitor, R and Jayasekara, T and Sivakumar, P and Jayakody, LN}, title = {Trends in in-silico guided engineering of efficient polyethylene terephthalate (PET) hydrolyzing enzymes to enable bio-recycling and upcycling of PET.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {3513-3521}, pmid = {37484494}, issn = {2001-0370}, abstract = {Polyethylene terephthalate (PET) is the largest produced polyester globally, and less than 30% of all the PET produced globally (∼6 billion pounds annually) is currently recycled into lower-quality products. The major drawbacks in current recycling methods (mechanical and chemical), have inspired the exploration of potentially efficient and sustainable PET depolymerization using biological approaches. Researchers have discovered efficient PET hydrolyzing enzymes in the plastisphere and have demonstrated the selective degradation of PET to original monomers thus enabling biological recycling or upcycling. However, several significant hurdles such as the less efficiency of the hydrolytic reaction, low thermostability of the enzymes, and the inability of the enzyme to depolymerize crystalline PET must be addressed in order to establish techno-economically feasible commercial-scale biological PET recycling or upcycling processes. Researchers leverage a synthetic biology-based design; build, test, and learn (DBTL) methodology to develop commercially applicable efficient PET hydrolyzing enzymes through 1) high-throughput metagenomic and proteomic approaches to discover new PET hydrolyzing enzymes with superior properties: and, 2) enzyme engineering approaches to modify and optimize PET hydrolyzing properties. Recently, in-silico platforms including molecular mechanics and machine learning concepts are emerging as innovative tools for the development of more efficient and effective PET recycling through the exploration of novel mutations in PET hydrolyzing enzymes. In-silico-guided PET hydrolyzing enzyme engineering with DBTL cycles enables the rapid development of efficient variants of enzymes over tedious conventional enzyme engineering methods such as random or directed evolution. This review highlights the potential of in-silico-guided PET degrading enzyme engineering to create more efficient variants, including Ideonella sakaiensis PETase (IsPETase) and leaf-branch compost cutinases (LCC). Furthermore, future research prospects are discussed to enable a sustainable circular economy through the bioconversion of PET to original or high-value platform chemicals.}, } @article {pmid37484369, year = {2023}, author = {Fang, Z and Liu, Q and Tang, W and Yu, H and Zou, M and Zhang, H and Xue, H and Lin, S and Pei, Y and Ai, J and Chen, J}, title = {Experience in the diagnosis and treatment of pneumonia caused by infection with Tropheryma whipplei: A case series.}, journal = {Heliyon}, volume = {9}, number = {6}, pages = {e17132}, pmid = {37484369}, issn = {2405-8440}, abstract = {Tropheryma whipplei (TW) is the root cause of Whipple's disease (WD), a rare infectious illness leading to multi-organ impairment. A prominent feature of WD is acute pneumonia, which can be exceedingly challenging to diagnose clinically due to the pathogen's surreptitious nature. However and significantly, with the advent of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF), it offers clinicians a potent tool at their disposal to detect TW infections. The present study conducted a retrospective analysis of clinical data gleaned from five patients in Hunan Province in China. Findings in this study demonstrated the potential of BALF-mNGS in diagnosing pneumonia caused by TW infection.}, } @article {pmid37484259, year = {2023}, author = {Chhiba, V and Pillay, P and Mtimka, S and Moonsamy, G and Kwezi, L and Pooe, OJ and Tsekoa, TL}, title = {South Africa's indigenous microbial diversity for industrial applications: A review of the current status and opportunities.}, journal = {Heliyon}, volume = {9}, number = {6}, pages = {e16723}, pmid = {37484259}, issn = {2405-8440}, abstract = {The unique metagenomic, metaviromic libraries and indigenous micro diversity within Southern Africa have the potential for global beneficiation in academia and industry. Microorganisms that flourish at high temperatures, adverse pH conditions, and high salinity are likely to have enzyme systems that function efficiently under those conditions. These attributes afford researchers and industries alternative approaches that could replace existing chemical processes. Thus, a better understanding of African microbial/genetic diversity is crucial for the development of "greener" industries. A concerted drive to exploit the potential locked in biological resources has been previously seen with companies such as Diversa Incorporated and Verenium (Badische Anilin-und SodaFabrik-BASF) both building business models that pioneered the production of high-performance specialty enzymes for a variety of different industrial applications. The market potential and accompanying industry offerings have not been fully exploited in South Africa, nor in Africa at large. Utilization of the continent's indigenous microbial repositories could create long-lasting, sustainable growth in various production sectors, providing economic growth in resource-poor regions. By bolstering local manufacture of high-value bio-based products, scientific and engineering discoveries have the potential to generate new industries which in turn would provide employment avenues for many skilled and unskilled laborers. The positive implications of this could play a role in altering the face of business markets on the continent from costly import-driven markets to income-generating export markets. This review focuses on identifying microbially diverse areas located in South Africa while providing a profile for all associated microbial/genetically derived libraries in this country. A comprehensive list of all the relevant researchers and potential key players is presented, mapping out existing research networks for the facilitation of collaboration. The overall aim of this review is to facilitate a coordinated journey of exploration, one which will hopefully realize the value that South Africa's microbial diversity has to offer.}, } @article {pmid37483820, year = {2023}, author = {Yu, X and Huang, T and Huang, Z and Wu, Z and Che, J and Qin, F and Zhang, W}, title = {Effects of six commercially available koji (Chinese Xiaoqu) on the production of ethyl acetate, ethyl lactate, and higher alcohols in Chinese Baijiu (distilled spirit) brewing.}, journal = {Heliyon}, volume = {9}, number = {7}, pages = {e17739}, pmid = {37483820}, issn = {2405-8440}, abstract = {Commercial koji has been increasingly used in Chinese Baijiu brewing; however, there are only few studies comparing different koji and their relationship with key components of Chinese Baijiu such as ethyl acetate, ethyl lactate, and higher alcohols. Here, we studied six commercially available koji and showed that the microbial communities in the individual koji varied in composition, with Rhizopus, Aspergillus, and Bacillus primarily associated with starch hydrolysis and Saccharomyces mainly associated with alcohol production. In the brewing processes using the six koji, Saccharomyces was undoubtedly the most abundant fungus and Weissella, Bacillus, and Acinetobacter were the predominant bacterial groups. The levels of ethyl acetate, ethyl lactate, and higher alcohols in all brewing processes using the koji exhibited rapid increase in the early stages of fermentation, which stabilized in the later stages, followed by substantial increase after distillation. The results of metagenomic and redundancy analyses of samples taken during the brewing processes indicated that Saccharomyces from the koji was closely related to the production of ethyl acetate, ethyl lactate, and higher alcohols. This study provides a basis for the quality improvement and application of commercial koji.}, } @article {pmid37483431, year = {2023}, author = {Wang, N and Gao, Z and He, S and Han, M and Han, W and Liu, X and Cao, H and Jing, M and Sun, T and Xu, J}, title = {Lung abscess by Fusobacterium nucleatum and Streptococcus spp. co-infection by mNGS: A case series.}, journal = {Open life sciences}, volume = {18}, number = {1}, pages = {20220651}, pmid = {37483431}, issn = {2391-5412}, abstract = {A lung abscess is a necrotizing infection caused by microbiomes that lead to the loss of healthy lung tissue. The routine culture is a waste of time and yields false-negative results, and clinicians could only choose empiric therapy or use broad-spectrum antibiotics, which could significantly contribute to the problem of resistance or aggravate the condition. We report three patients with a routine-culture-negative lung abscess. The presenting symptoms included fever, cough, dyspnea, and chest pain, and a computed tomography scan revealed a lesion in the lungs. The bronchoalveolar lavage fluid and pleural fluid were tested for pathogens using metagenome next-generation sequencing (mNGS), and the results revealed Fusobacterium nucleatum and Streptococcus spp. (S. constellatus, S. intermedius) as the most represented microbial pathogens. Our data demonstrated that mNGS could be a promising alternative diagnostic tool for pathogen detection, and the pathogen lists indicate that it will be important to focus on the Streptococcus genus rather than the dominant Streptococcus spp. in terms of co-infection of pathogen determined by shotgun mNGS.}, } @article {pmid37482746, year = {2023}, author = {Jiang, XW and Liang, ZK and Zeng, L and Yuan, YL}, title = {[Results analysis of mNGS applied to infectious diseases].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {57}, number = {7}, pages = {1124-1130}, doi = {10.3760/cma.j.cn112150-20220824-00836}, pmid = {37482746}, issn = {0253-9624}, support = {2022B1111020003//Guangdong Province Key Area R&D Program/ ; }, mesh = {Humans ; *Communicable Diseases ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {The application of metagenomic second-generation sequencing (mNGS) is shifting from research to clinical laboratories due to rapid technological advances and significant cost reductions. Although many studies and case reports have confirmed that the success of mNGS in improving the prevention, diagnosis, treatment and tracking of infectious diseases, there are still some obstacles that must be overcome. The results of mNGS show all the possible pathogens in the sample, however, in the face of thousands of microbes that can infect humans, it remains challenging to accurately identify the key pathogens. So far, there is no unified interpretation standard for mNGS in clinical practice. This article reviews the interpretation of mNGS results for pathogen infection in different systems, the clinical interpretation and application regulations of mNGS results, and the challenges of mNGS interpretation in pathogen diagnosis.}, } @article {pmid37482646, year = {2023}, author = {Liu, K and Guo, Q and Ding, Y and Luo, L and Huang, J and Zhang, Q}, title = {Alterations in nasal microbiota of patients with amyotrophic lateral sclerosis.}, journal = {Chinese medical journal}, volume = {}, number = {}, pages = {}, pmid = {37482646}, issn = {2542-5641}, abstract = {BACKGROUND: Links between alterations in gut microbiota composition and amyotrophic lateral sclerosis (ALS) have previously been reported. This study aimed to examine the microbiota in the nasal cavity of ALS.

METHODS: Sixty-six ALS patients and 40 healthy caregivers who live in close proximity with patients were enrolled. High throughput metagenomic sequencing of the 16S ribosomal deoxyribonucleic acid (rDNA) gene V3-V4 region of nasal microbiota was used to characterize the alpha and beta diversity and relative abundance of bacterial taxa, predict function, and conduct correlation analysis between specific taxa and clinical features.

RESULTS: The nasal microbiome of ALS patients showed lower alpha diversity than that of corresponding healthy family members. Genera Gaiella, Sphingomonas, Polaribacter_1, Lachnospiraceae_NK4A136_group, Klebsiella, and Alistipes were differentially enriched in ALS patients compared to controls. Nasal microbiota composition in ALS patients significantly differed from that in healthy subjects (unweighted UniFrac P = 0.001), while LEfSe analysis indicated that Bacteroidetes and Firmicutes dominated healthy nasal communities at the phylum level, whereas Actinobacteria was the predominant phylum and Thermoleophilia was the predominant class in ALS patients. Genus Faecalibacterium and Alistipes were positively correlated with ALS functional rating scale revised (ALSFRS-R; rs = 0.349, P = 0.020 and rs = 0.393, P = 0.008), while Prevotella-9 and Bacteroides operational taxonomic units (OTUs) were positively associated with lung function (FVC) in ALS patients (rs = 0.304, P = 0.045, and rs = 0.300, P = 0.048, respectively). Prevotella-1 was positively correlated with white blood cell counts (WBC, rs = 0.347, P = 0.021), neutrophil percentage (Neu%, rs = 0.428, P = 0.004), and neutrophil-to-lymphocyte ratio (NLR, rs = 0.411, P = 0.006), but negatively correlated with lymphocyte percentage (Lym%, rs = -0.408, P = 0.006). In contrast, Streptococcus was negatively associated with Neu% (rs = -0.445, P = 0.003) and NLR (rs = -0.436, P = 0.003), while positively associated with Lym% (rs = 0.437, P = 0.003). No significant differences in nasal microbiota richness and evenness were detected among the severe and mild ALS patients.

CONCLUSIONS: ALS is accompanied by altered nasal microbial community composition and diversity. The findings presented here highlight the need to understand how dysbiosis of nasal microbiota may contribute to the development of ALS.}, } @article {pmid37482605, year = {2023}, author = {Li, H and Wu, X and Zeng, H and Chang, B and Cui, Y and Zhang, J and Wang, R and Ding, T}, title = {Unique microbial landscape in the human oropharynx during different types of acute respiratory tract infections.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {157}, pmid = {37482605}, issn = {2049-2618}, mesh = {Humans ; *Influenza, Human ; Dysbiosis/microbiology ; *Respiratory Tract Infections ; *Orthomyxoviridae Infections ; Oropharynx/microbiology ; Bacteria/genetics ; *Influenza A virus ; *Coinfection ; }, abstract = {BACKGROUND: Secondary bacterial infections and pneumonia are major mortality causes of respiratory viruses, and the disruption of the upper respiratory tract (URT) microbiota is a crucial component of this process. However, whether this URT dysbiosis associates with the viral species (in other words, is viral type-specific) is unclear.

RESULTS: Here, we recruited 735 outpatients with upper respiratory symptoms, identified the infectious virus types in 349 participants using multiplex RT-PCR, and profiled their upper respiratory microbiome using the 16S ribosomal RNA gene and metagenomic gene sequencing. Microbial and viral data were subsequently used as inputs for multivariate analysis aimed at revealing viral type-specific disruption of the upper respiratory microbiota. We found that the oropharyngeal microbiota shaped by influenza A virus (FluA), influenza B virus (FluB), respiratory syncytial virus (RSV), and human rhinovirus (HRV) infections exhibited three distinct patterns of dysbiosis, and Veillonella was identified as a prominent biomarker for any type of respiratory viral infections. Influenza virus infections are significantly correlated with increased oropharynx microbiota diversity and enrichment of functional metabolic pathways such as L-arginine biosynthesis and tetracycline resistance gene tetW. We used the GRiD algorithm and found the predicted growth rate of common respiratory pathogens was increased upon influenza virus infection, while commensal bacteria, such as Streptococcus infantis and Streptococcus mitis, may act as a colonization resistance to the overgrowth of these pathogens.

CONCLUSIONS: We found that respiratory viral infections are linked with viral type-specific disruption of the upper respiratory microbiota, particularly, influenza infections uniquely associated with increased microbial diversity and growth rates of specific pathogens in URT. These findings are essential for clarifying the differences and dynamics of respiratory microbiota in healthy participants and acute respiratory viral infections, which contribute to elucidating the pathogenesis of viral-host-bacterial interactions to provide insights into future studies on effective prevention and treatment of respiratory tract infections. Video Abstract.}, } @article {pmid37482039, year = {2023}, author = {Yue, Z and Zhang, J and Zhang, J and Wang, X and Li, L and Yu, H and Liu, B and Li, Q and Zhu, D and Zou, Y}, title = {Combined virome analysis and metagenomic sequencing to reveal the viral communities and risk of virus-associated antibiotic resistance genes during composting.}, journal = {Journal of hazardous materials}, volume = {459}, number = {}, pages = {132088}, doi = {10.1016/j.jhazmat.2023.132088}, pmid = {37482039}, issn = {1873-3336}, mesh = {Humans ; Animals ; Swine ; *Metagenome ; Genes, Bacterial ; Virome ; *Composting/methods ; Anti-Bacterial Agents/pharmacology ; Biofuels ; Drug Resistance, Microbial/genetics ; Manure/microbiology ; }, abstract = {The issue of antibiotic resistance genes (ARGs) pollution in manure has garnered significant attention, with viruses now being recognized as crucial carriers and disseminators of ARGs. However, the virus-associated ARG profiles and potential health risks in composts are still unclear. In this study, the viral communities and associated ARGs in biogas residue and pig faeces composts were profiled by virome analysis. The viral communities were dominated by Caudovirales, and non-thermophilic viruses were inactivated during composting. The diversity and abundance of ARGs were lower in virome than in metagenome, while ARGs' risk was greater in virome than in metagenome. There were six bacterial genera identified as viral hosts at the genomic level, Pseudomonas and Clostridium carried high-risk ARGs. Virus-associated ARGs in viral hosts had a higher risk rank than non-virus-associated ARGs. Composting reduced the diversity, abundance and risk of viral ARGs. The risk of ARGs in biogas residues was significantly lower than that of pig faeces in the initial period of composting, and the two different substracts equally less harmful after composting. These results revealed that viruses play a non-negligible role in spreading ARGs, posing high risk to environmental and human health.}, } @article {pmid37482002, year = {2023}, author = {Hu, Z and Liu, T and Su, Z and Zhao, J and Guo, J and Hu, S and Yuan, Z and Zheng, M}, title = {Adaptation of anammox process for nitrogen removal from acidic nitritation effluent in a low pH moving bed biofilm reactor.}, journal = {Water research}, volume = {243}, number = {}, pages = {120370}, doi = {10.1016/j.watres.2023.120370}, pmid = {37482002}, issn = {1879-2448}, mesh = {*Nitrites ; Denitrification ; Nitrogen ; Anaerobic Ammonia Oxidation ; Oxidation-Reduction ; Bioreactors/microbiology ; *Ammonium Compounds ; Bacteria ; Biofilms ; Hydrogen-Ion Concentration ; Sewage ; }, abstract = {Acidic partial nitritation (PN) has emerged to be a promisingly stable process in wastewater treatment, which can simultaneously achieve nitrite accumulation and about half of ammonium reduction. However, directly applying anaerobic ammonium oxidation (anammox) process to treat the acidic PN effluent (pH 4-5) is susceptible to the inhibition of anammox bacteria. Here, this study demonstrated the adaptation of anammox process to acidic pH in a moving bed biofilm reactor (MBBR). By feeding the laboratory-scale MBBR with acidic PN effluent (pH = 4.6 ± 0.2), the pH of an anammox reactor was self-sustained in the range of pH 5 - 6. Yet, a high total nitrogen removal efficiency of over 80% at a practical loading rate of up to 149.7 ± 3.9 mg N/L/d was achieved. Comprehensive microbial assessment, including amplicon sequencing, metagenomics, cryosection-FISH, and qPCR, identified that Candidatus Brocadia, close to known neutrophilic members, was the dominant anammox bacteria. Anammox bacteria were found present in the inner layer of thick biofilms but barely present in the surface layer of thick biofilms and in thin biofilms. Results from batch tests also showed that the activity of anammox biofilms could be maintained when subjected to pH 5 at a nitrite concentration of 10 mg N/L, whereas the activity was completely inhibited after disturbing the biofilm structure. These results collectively indicate that the anammox bacteria enriched in the present acidic MBBR could not be inherently acid-tolerant. Instead, the achieved stable anammox performance under the acidic condition is likely due to biofilm stratification and protection. This result highlights the biofilm configuration as a useful solution to address nitrogen removal from acidic PN effluent, and also suggests that biofilm may play a critical role in protecting anammox bacteria found in many acidic nature environments.}, } @article {pmid37481999, year = {2023}, author = {Lin, TY and Liu, WT}, title = {Validation of 16S rRNA gene sequencing and metagenomics for evaluating microbial immigration in a methanogenic bioreactor.}, journal = {Water research}, volume = {243}, number = {}, pages = {120358}, doi = {10.1016/j.watres.2023.120358}, pmid = {37481999}, issn = {1879-2448}, mesh = {RNA, Ribosomal, 16S/genetics ; *Metagenomics/methods ; *Emigration and Immigration ; Genes, rRNA ; Bacteria/genetics ; Bioreactors ; Metagenome ; }, abstract = {To quantitatively evaluate the impact of microbial immigration from an upstream community on the microbial assembly of a downstream community, an ecological genomics (ecogenomics)-based mass balance (EGMB) model coupled with 16S rRNA gene sequencing was previously developed. In this study, a mock community was used to further validate the EGMB models and demonstrate the feasibility of using metagenome-based EGMB model to reveal both microbial activity and function. The mock community consisting of Aeromonas, Escherichia, and Pseudomonas was fed into a lab-scale methanogenic bioreactor together with dissolved organic substrate. Using qPCR, 16S rRNA gene, 16S rRNA gene copy number normalization (GCN), and metagenome, results showed highly comparable community profiles in the feed. In the bioreactor, Aeromonas and Pseudomonas exhibited negative growth rates throughout the experiment by all approaches. Escherichia's growth rate was negative by most biomarkers but was slightly positive by 16S rRNA gene. Still, all approaches showed a decreasing trend toward negative in the growth rate of Escherichia as reactor operation time increased. Uncultivated populations of phyla Desulfobacterota, Chloroflexi, Actinobacteriota, and Spirochaetota were observed to increase in abundance, suggesting their contribution in degrading the feed biomass. Based on metabolic reconstruction of metagenomes, these populations possessed functions of hydrolysis, fermentation, fatty acid degradation, or acetate oxidation. Overall results supported the application of both 16S rRNA gene- and metagenome-based EGMB models to measure the growth rate of microbes in the bioreactor, and the latter had advantage in providing insights into the microbial functions of uncultivated populations.}, } @article {pmid37481110, year = {2023}, author = {Fang, X and Lu, K and Sun, S and Zhang, H and Yu, X and Han, W}, title = {Infection caused by Cupriavidus gilardii in a convalescent COVID-19 patient.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {134}, number = {}, pages = {287-289}, doi = {10.1016/j.ijid.2023.07.015}, pmid = {37481110}, issn = {1878-3511}, mesh = {Male ; Humans ; Aged ; *Gram-Negative Bacterial Infections/microbiology ; *COVID-19 ; *Cupriavidus ; Immunocompromised Host ; Bronchoalveolar Lavage Fluid ; }, abstract = {Cupriavidus gilardii is an aerobic, gram-negative bacillus that can opportunistically infect immunocompromised patients or those undergoing invasive procedures. We reported a case caused by C. gilardii in a previously basic healthy 78-year-old male, who had COVID-19 and had used corticosteroids recently. The bacterium was identified as C. gilardii by the metagenomic next-generation sequencing from the patient's bronchoalveolar lavage fluid and blood. In addition, this is the first time that we isolated C. gilardii from bronchoalveolar lavage fluid, which provides clinical experience in rare bacterial infections.}, } @article {pmid37480620, year = {2023}, author = {Lin, Y and Zhang, W and Xiong, Y and Wang, Y and Yu, Q and Ma, Y and Xie, Y}, title = {Comparative performance of microbiological methods for the detection of tuberculous meningitis pathogens in cerebrospinal fluid.}, journal = {Diagnostic microbiology and infectious disease}, volume = {107}, number = {2}, pages = {116025}, doi = {10.1016/j.diagmicrobio.2023.116025}, pmid = {37480620}, issn = {1879-0070}, mesh = {Humans ; *Tuberculosis, Meningeal/diagnosis ; Microbiological Techniques ; *Mycobacterium tuberculosis/genetics ; Biological Assay ; High-Throughput Nucleotide Sequencing ; }, abstract = {The aim of this study was to comprehensively evaluate metagenomic next-generation sequencing (mNGS), Acid-fast bacillus stain (AFB), MGIT960 culture, polymerase-chain-reaction (PCR), and Xpert MTB/RIF in the diagnosis of tuberculous meningitis (TBM). A cohort of 280 patients who presented with suspected TBM (ie, headache or altered mental status with clinical signs of meningism) were analyzed. The sensitivities of the 5 assays for the diagnosis of TBM ranged from 10.0% to 70.0%. The AFB had the lowest sensitivity of 10.0% (0.5-45.9), while mNGS and PCR had the highest sensitivity, both at 70.0% (35.4-91.9). mNGS demonstrated a distinct advantage in identifying a wider array of pathogens, including viruses, in CSF samples. PCR was a cost-effective option with excellent sensitivity and specificity. However, no single method was statistically significantly better than any other in the diagnosis of TBM. New diagnostic techniques are urgently needed for the independent, rapid and accurate detection of Mycobacterium tuberculosis to guide the diagnosis of TBM.}, } @article {pmid37480075, year = {2023}, author = {Tinta, T and Zhao, Z and Bayer, B and Herndl, GJ}, title = {Jellyfish detritus supports niche partitioning and metabolic interactions among pelagic marine bacteria.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {156}, pmid = {37480075}, issn = {2049-2618}, mesh = {Animals ; Aquatic Organisms ; Bacteria/genetics/metabolism ; Carbohydrates ; Ecosystem ; *Gammaproteobacteria ; *Microbiota ; *Scyphozoa/chemistry/microbiology ; }, abstract = {BACKGROUND: Jellyfish blooms represent a significant but largely overlooked source of labile organic matter (jelly-OM) in the ocean, characterized by a high protein content. Decaying jellyfish are important carriers for carbon export to the ocean's interior. To accurately incorporate them into biogeochemical models, the interactions between microbes and jelly-OM have yet to be fully characterized. We conducted jelly-OM enrichment experiments in microcosms to simulate the scenario experienced by the coastal pelagic microbiome after the decay of a jellyfish bloom. We combined metagenomics, endo- and exo-metaproteomic approaches to obtain a mechanistic understanding on the metabolic network operated by the jelly-OM degrading bacterial consortium.

RESULTS: Our analysis revealed that OM released during the decay of jellyfish blooms triggers a rapid shuffling of the taxonomic and functional profile of the pelagic bacterial community, resulting in a significant enrichment of protein/amino acid catabolism-related enzymes in the jelly-OM degrading community dominated by Pseudoalteromonadaceae, Alteromonadaceae and Vibrionaceae, compared to unamended control treatments. In accordance with the proteinaceous character of jelly-OM, Pseudoalteromonadaceae synthesized and excreted enzymes associated with proteolysis, while Alteromonadaceae contributed to extracellular hydrolysis of complex carbohydrates and organophosphorus compounds. In contrast, Vibrionaceae synthesized transporter proteins for peptides, amino acids and carbohydrates, exhibiting a cheater-type lifestyle, i.e. benefiting from public goods released by others. In the late stage of jelly-OM degradation, Rhodobacteraceae and Alteromonadaceae became dominant, growing on jelly-OM left-overs or bacterial debris, potentially contributing to the accumulation of dissolved organic nitrogen compounds and inorganic nutrients, following the decay of jellyfish blooms.

CONCLUSIONS: Our findings indicate that specific chemical and metabolic fingerprints associated with decaying jellyfish blooms are substantially different to those previously associated with decaying phytoplankton blooms, potentially altering the functioning and biogeochemistry of marine systems. We show that decaying jellyfish blooms are associated with the enrichment in extracellular collagenolytic bacterial proteases, which could act as virulence factors in human and marine organisms' disease, with possible implications for marine ecosystem services. Our study also provides novel insights into niche partitioning and metabolic interactions among key jelly-OM degraders operating a complex metabolic network in a temporal cascade of biochemical reactions to degrade pulses of jellyfish-bloom-specific compounds in the water column. Video Abstract.}, } @article {pmid37479827, year = {2023}, author = {Hirata, K and Asahi, T and Kataoka, K}, title = {Spatial and Sexual Divergence of Gut Bacterial Communities in Field Cricket Teleogryllus occipitalis (Orthoptera: Gryllidae).}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2627-2641}, pmid = {37479827}, issn = {1432-184X}, mesh = {Animals ; Female ; Male ; *Gastrointestinal Microbiome ; *Gryllidae ; RNA, Ribosomal, 16S/genetics ; *Cricket Sport ; Bacteria/genetics ; }, abstract = {The insect gut is colonized by microbes that confer a myriad of beneficial services to the host, including nutritional support, immune enhancement, and even influence behavior. Insect gut microbes show dynamic changes due to the gut compartments, sex, and seasonal and geographic influences. Crickets are omnivorous hemimetabolous insects that have sex-specific roles, such as males producing chirping sounds for communication and exhibiting fighting behavior. However, limited information is available on their gut bacterial communities, hampering studies on functional compartmentalization of the gut and sex-specific roles of the gut microbiota in omnivorous insects. Here, we report a metagenomic analysis of the gut bacteriome of the field cricket Teleogryllus occipitalis using 16S rRNA V3-V4 amplicon sequencing to identify sex- and compartment-dependent influences on its diversity and function. The structure of the gut microbiota is strongly influenced by their gut compartments rather than sex. The species richness and diversity analyses revealed large difference in the bacterial communities between the gut compartments while minor differences were observed between the sexes. Analysis of relative abundance and predicted functions revealed that nitrogen- and oxygen-dependent metabolism and amino acid turnover were subjected to functional compartmentalization in the gut. Comparisons between the sexes revealed differences in the gut microbiota, reflecting efficiency in energy use, including glycolytic and carbohydrate metabolism, suggesting a possible involvement in egg production in females. This study provides insights into the gut compartment dependent and sex-specific roles of host-gut symbiont interactions in crickets and the industrial production of crickets.}, } @article {pmid37479750, year = {2023}, author = {Pan, Q and Yu, SJ and Lei, S and Li, SC and Ding, LL and Liu, L and Cheng, LY and Luo, R and Lei, CY and Lou, BH and Cong, L and Liu, HQ and Wang, XF and Ran, C}, title = {Effects of Candidatus Liberibacter asiaticus infection on metagenome of Diaphorina citri gut endosymbiont.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {478}, pmid = {37479750}, issn = {2052-4463}, mesh = {Animals ; *Hemiptera/genetics/microbiology ; Metagenome ; *Rhizobiaceae/genetics ; }, abstract = {Asian citrus psyllid (Diaphorina citri, D. citri) is the important vector of "Candidatus Liberibacter asiaticus" (CLas), associated with Huanglongbing, the most devastating citrus disease worldwide. CLas can affect endosymbiont abundance of D. citri. Here, we generated the high-quality gut endosymbiont metagenomes of Diaphorina citri on the condition of CLas infected and uninfected. The dataset comprised 6616.74 M and 6586.04 M raw reads, on overage, from CLas uninfected and infected psyllid strains, respectively. Taxonomic analysis revealed that a total of 1046 species were annotated with 10 Archaea, 733 Bacteria, 234 Eukaryota, and 69 Viruses. 80 unique genera in CLas infected D. citri were identified. DIAMOND software was used for complement function research against various functional databases, including Nr, KEGG, eggNOG, and CAZy, which annotated 84543 protein-coding genes. These datasets provided an avenue for further study of the interaction mechanism between CLas and D. citri.}, } @article {pmid37479001, year = {2023}, author = {Wang, Y and Sun, Z and Qiang, Z}, title = {Start-up of solid-phase denitrification process for treatment of nitrate-rich water in recirculating mariculture system: Carbon source selection and nitrate removal mechanism.}, journal = {Chemosphere}, volume = {338}, number = {}, pages = {139568}, doi = {10.1016/j.chemosphere.2023.139568}, pmid = {37479001}, issn = {1879-1298}, mesh = {*Nitrates/analysis ; *Denitrification ; Carbon/metabolism ; Water ; Bioreactors ; Polyesters ; Nitrogen ; }, abstract = {Efficient nitrate removal from recirculating mariculture system (RMS) water is of significance since high concentration of nitrate would cause chronic health effects on aquatic organisms and eutrophication. Solid-phase denitrification (SPD) is a safer and more sustainable approach than conventional heterotrophic denitrification by dosing liquid carbon sources. Thus, its application for treating nitrate-rich RMS water was investigated in this study. Poly 3-hydroxybutyrate-co-3-hydroxyvalerate (PHBV) was identified with the best nitrate removal among four kinds of carbon sources. PHBV-filled reactors started with mariculture, municipal and mixing sludges (at the ratio of 1:1) and fed with 200 mg L[-1] nitrate-rich RMS water all achieved over 81% nitrate removals with a HRT of 4 days. The dissolved organic carbon concentrations of the reactors were in the range of 3-9 mg L[-1]. Arcobacter, Halomonas, and Psedomonas were dominant genera responsible for nitrate removal in different reactors. Metagenomic analyses indicate that both denitrification and assimilatory nitrate reduction (ANR) are the main contributors to nitrate removals. Metagenomic results illustrated nirB/D cooperated with nasA may perform ANR pathway, which transformed nitrate to ammonia for biosynthesis. These results indicate that SPD could be a safer alternative for treating nitrate-rich RMS water, and provide new insights into nitrogen metabolism pathways in SPD process.}, } @article {pmid37478939, year = {2023}, author = {Jin, L and Wu, H and Li, G and Yang, S and Wei, R and Huang, Y and Penttinen, P and Deng, W and Chen, J and Han, X and Li, C and Hu, L and Li, T and Zhang, H and Zhao, K and Zou, L}, title = {Gastrointestinal microbiome, resistance genes, and risk assessment of heavy metals in wild giant pandas.}, journal = {The Science of the total environment}, volume = {899}, number = {}, pages = {165671}, doi = {10.1016/j.scitotenv.2023.165671}, pmid = {37478939}, issn = {1879-1026}, mesh = {Animals ; *Ursidae ; *Gastrointestinal Microbiome ; *Metals, Heavy/analysis ; Anti-Bacterial Agents ; Risk Assessment ; Soil ; Genes, Bacterial ; }, abstract = {The gastrointestinal microbiome (GM) of giant panda (GP) plays an important role in food utilization and health and is also an essential reservoir of resistance genes. Currently, little knowledge is available on the GM, acid resistance genes (AcRGs), antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs) in wild GPs. We sampled the gastrointestinal tract of a dead GP and explored the composition and function of GM and resistance genes through cryo-scanning electron microscopy, metagenomic sequencing, and genome-resolved metagenomics. The concentration of metals in the gastrointestinal lumen, feces, bamboo, and soil was measured by inductively coupled plasma mass spectrometry. Results showed that the composition of the microbiota varied in different gastrointestinal regions. Fecal microbiota was highly associated with small intestinal and colonic microbes. The lignocellulosic cross-linked structure of bamboo was destroyed in the stomach initially and destroying degree increased from stomach to anus. Reconstruction of metagenome-assembled-genomes confirmed that core GM, e.g., Streptococcus, Clostridium, Lactococcus, Leuconostoc, and Enterococcus, carried genes encoding the lignocellulose degradation enzyme. There were no significant differences of resistance genes between gastrointestinal and fecal samples, except MGEs. Multidrug and multi-metal resistance genes were predominant in all samples, while the transposase gene tnpA was the major type of MGE. Significant correlations were observed among the abundance of GM, resistance genes, and MGEs. Gastrointestinal and fecal mercury and chromium were the main metals influencing GM and resistance genes. The content of gastrointestinal and fecal metals was significantly associated with the presence of the same metals in bamboo, which could pose a threat to the health of wild GPs. This study characterized the gastrointestinal microbiome of wild GPs, providing new evidence for the role of the gastrointestinal microbiome in degrading lignocellulose from bamboo and highlighting the urgent need to monitor metal levels in soil and bamboo.}, } @article {pmid37478933, year = {2023}, author = {Yan, Q and Xu, Y and Zhong, Z and Xu, Y and Lin, X and Cao, Z and Feng, G}, title = {Insights into antibiotic resistance-related changes in microbial communities, resistome and mobilome in paddy irrigated with reclaimed wastewater.}, journal = {The Science of the total environment}, volume = {900}, number = {}, pages = {165672}, doi = {10.1016/j.scitotenv.2023.165672}, pmid = {37478933}, issn = {1879-1026}, mesh = {*Wastewater ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology/analysis ; Soil ; *Microbiota ; Drug Resistance, Microbial/genetics ; }, abstract = {Reclaimed wastewater (reclaimed wastewater, RWW) from municipal wastewater treatment plants for paddy irrigation is a well-established practice to alleviate water scarcity. However, the reuse may result in the persistent exposure of the paddy to residual antibiotics in RWW. Continuous presence of even low-level antibiotics can exert selective pressure on microbiota, resulting in the proliferation and dissemination of antibiotic resistance genes (ARGs) in paddy. In this study, metagenomic analysis was applied to firstly deciphered the effects of residual antibiotics on microbiome and resistome in constructed mesocosm-scale paddy soils. The diversity and abundance of ARG have remarkably risen with the increasing antibiotic concentration in RWW. Network analysis revealed that 28 genera belonging to six phyla were considered as the potential ARG hosts, and their abundances were enhanced with increasing antibiotic concentrations. A partial least-squares path model indicated that the microbial community was the principal direct driver of the ARG abundance and the resistome alteration in paddy soil under long-term RWW irrigation. Microbes may acquire ARGs via horizontal gene transfer. IntI1 could play an essential role in the propagation and spread of ARGs. Functional analysis suggested that enhanced SOS response and T4SSs (Type IV secretion systems) modules could stimulate horizontal transfer potential and promote the ARG abundance. The obtained results provide a scientific decision for assessing the ecological risk of RWW application.}, } @article {pmid37478721, year = {2023}, author = {Li, J and Lu, H and Wang, A and Wen, X and Huang, Y and Li, Q}, title = {The fates of antibiotic resistance genes and their association with cell membrane permeability in response to peroxydisulfate during composting.}, journal = {Journal of environmental management}, volume = {344}, number = {}, pages = {118659}, doi = {10.1016/j.jenvman.2023.118659}, pmid = {37478721}, issn = {1095-8630}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Composting ; Genes, Bacterial ; Cell Membrane Permeability ; Manure ; Drug Resistance, Microbial/genetics ; }, abstract = {The aims of this study were to use metagenomics to reveal the fates of antibiotic resistance genes (ARGs) during composting under the regulation of peroxydisulfate and clarify the relationship between ARGs and cell membrane permeability. Results showed that peroxydisulfate increased cell membrane permeability by effectively regulating the expression of outer membrane protein and lipopolysaccharide related genes. Besides, it reduced polysaccharides and proteins in extracellular polymer substances by 36% and 58%, respectively, making it easier for intracellular ARGs (i-ARGs) to reach the extracellular environment, among which the absolute intracellular abundance of mphK, Erm(31), and tet(44) decreased to 1.2, 1.0, and 0.89 fold of the control, respectively. Finally, variation partitioning analysis showed that i-ARGs dominated the removal of ARGs. These results revealed that the removal of i-ARGs by activated peroxydisulfate was the key to the removal of ARGs and increased cell membrane permeability played a key role for peroxydisulfate to remove i-ARGs during composting.}, } @article {pmid37478472, year = {2023}, author = {Ke, Y and Sun, W and Chen, X and Zhu, Y and Guo, X and Yan, W and Xie, S}, title = {Seasonality Determines the Variations of Biofilm Microbiome and Antibiotic Resistome in a Pilot-Scale Chlorinated Drinking Water Distribution System Deciphered by Metagenome Assembly.}, journal = {Environmental science & technology}, volume = {57}, number = {31}, pages = {11430-11441}, doi = {10.1021/acs.est.3c01980}, pmid = {37478472}, issn = {1520-5851}, mesh = {Anti-Bacterial Agents/pharmacology ; Metagenome ; *Drinking Water ; Genes, Bacterial ; *Microbiota ; Biofilms ; }, abstract = {Understanding the biofilm microbiome and antibiotic resistome evolution in drinking water distribution systems (DWDSs) is crucial to ensure the safety of drinking water. We explored the 10 month evolution of the microbial community, antibiotic resistance genes (ARGs), mobile gene elements (MGEs) co-existing with ARGs and pathogenic ARG hosts, and the ARG driving factors in DWDS biofilms using metagenomics assembly. Sampling season was critical in determining the microbial community and antibiotic resistome shift. Pseudomonas was the primary biofilm colonizer, and biofilms diversified more as the formation time increased. Most genera tended to cooperate to adapt to an oligotrophic environment with disinfectant stress. Biofilm microbial community and antibiotic resistome assembly were mainly determined by stochastic processes and changed with season. Metagenome assembly provided the occurrence and fates of MGEs co-existing with ARGs and ARG hosts in DWDS biofilms. The abundance of ARG- and MGE-carrying pathogen Stenotrophomonas maltophilia was high in summer. It primarily harbored the aph(3)-IIb, multidrug transporter, smeD, and metallo-beta-lactamase ARGs, which were transferred via recombination. The microbial community was the most crucial factor driving the antibiotic resistance shift. We provide novel insights about the evolution of pathogens and ARGs and their correlations in DWDS biofilms to ensure the safety of drinking water.}, } @article {pmid37478378, year = {2023}, author = {Abe, K and Shimamura, T}, title = {UNMF: a unified nonnegative matrix factorization for multi-dimensional omics data.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {5}, pages = {}, pmid = {37478378}, issn = {1477-4054}, mesh = {*Algorithms ; *Multiomics ; Principal Component Analysis ; Factor Analysis, Statistical ; }, abstract = {Factor analysis, ranging from principal component analysis to nonnegative matrix factorization, represents a foremost approach in analyzing multi-dimensional data to extract valuable patterns, and is increasingly being applied in the context of multi-dimensional omics datasets represented in tensor form. However, traditional analytical methods are heavily dependent on the format and structure of the data itself, and if these change even slightly, the analyst must change their data analysis strategy and techniques and spend a considerable amount of time on data preprocessing. Additionally, many traditional methods cannot be applied as-is in the presence of missing values in the data. We present a new statistical framework, unified nonnegative matrix factorization (UNMF), for finding informative patterns in messy biological data sets. UNMF is designed for tidy data format and structure, making data analysis easier and simplifying the development of data analysis tools. UNMF can handle a wide range of data structures and formats, and works seamlessly with tensor data including missing observations and repeated measurements. The usefulness of UNMF is demonstrated through its application to several multi-dimensional omics data, offering user-friendly and unified features for analysis and integration. Its application holds great potential for the life science community. UNMF is implemented with R and is available from GitHub (https://github.com/abikoushi/moltenNMF).}, } @article {pmid37476667, year = {2023}, author = {Ascandari, A and Aminu, S and Safdi, NEH and El Allali, A and Daoud, R}, title = {A bibliometric analysis of the global impact of metaproteomics research.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1217727}, pmid = {37476667}, issn = {1664-302X}, abstract = {BACKGROUND: Metaproteomics is a subfield in meta-omics that is used to characterize the proteome of a microbial community. Despite its importance and the plethora of publications in different research area, scientists struggle to fully comprehend its functional impact on the study of microbiomes. In this study, bibliometric analyses are used to evaluate the current state of metaproteomic research globally as well as evaluate the specific contribution of Africa to this burgeoning research area. In this study, we use bibliometric analyses to evaluate the current state of metaproteomic research globally, identify research frontiers and hotspots, and further predict future trends in metaproteomics. The specific contribution of Africa to this research area was evaluated.

METHODS: Relevant documents from 2004 to 2022 were extracted from the Scopus database. The documents were subjected to bibliometric analyses and visualization using VOS viewer and Biblioshiny package in R. Factors such as the trends in publication, country and institutional cooperation networks, leading scientific journals, author's productivity, and keywords analyses were conducted. The African publications were ranked using Field-Weighted Citation Impact (FWCI) scores.

RESULTS: A total of 1,138 documents were included and the number of publications increased drastically from 2004 to 2022 with more publications (170) reported in 2021. In terms of publishers, Frontiers in Microbiology had the highest number of total publications (62). The United States of America (USA), Germany, China, and Canada, together with other European countries were the most productive. Institution-wise, the Helmholtz Zentrum für Umweltforschung, Germany had more publications while Max Plank Institute had the highest total collaborative link strength. Jehmlich N. was the most productive author whereas Hettich RL had the highest h-index of 63. Regarding Africa, only 2.2% of the overall publications were from the continent with more publication outputs from South Africa. More than half of the publications from the continent had an FWCI score ≥ 1.

CONCLUSION: The scientific outputs of metaproteomics are rapidly evolving with developed countries leading the way. Although Africa showed prospects for future progress, this could only be accelerated by providing funding, increased collaborations, and mentorship programs.}, } @article {pmid37476093, year = {2023}, author = {Stoy, S and McMillan, A and Ericsson, AC and Brooks, AE}, title = {The effect of physical and psychological stress on the oral microbiome.}, journal = {Frontiers in psychology}, volume = {14}, number = {}, pages = {1166168}, pmid = {37476093}, issn = {1664-1078}, abstract = {BACKGROUND: The oral microbiome is incredibly complex, containing a diverse complement of microbiota that has previously been categorized into 6 broad phyla. While techniques such as next-generation sequencing have contributed to a better understanding of the composition of the oral microbiome, the role it plays in human health and disease is still under investigation. Previous studies have identified that a more diverse microbiome is advantageous for health. Therefore, alterations to the physical or mental health that are of interest in this study, such as stress, are the factors that decrease microbial diversity, leading to the potential for dysbiosis and disease disposition. Intensive Surgical Skills Week (ISSW) is a hyper-realistic simulation training week for military medical students that takes place at the Strategic Operations (STOPS) facility in San Diego, CA. This training week puts students through mass causality simulations and requires them to work through distinct roles within the healthcare team, providing an almost ideal environment to assess the impact of acute stress on oral microbiome diversity. Based on the literature on stress and microbiota, we hypothesized that the high stress simulation events at ISSW will impact the composition and diversity of the oral microbiome.

METHODS: To investigate this hypothesis, thirty-seven (n = 37) second-or third-year medical students who are enlisted in a branch of the military and who attended ISSW in July of 2021 were included in the study. Student participants were divided into 7 teams to complete the hyper-realistic simulations (SIMs) at ISSW. A pilot of sixty-four buccal samples (n = 64) from three of the seven teams were sent for analysis at the University of Missouri Metagenomic Center.

RESULTS: We saw an overall increase in species richness at the end of ISSW when looking at all samples (n = 64). Fourteen significantly different bacteria were identified from the beginning to the end of data collection. Additionally, third year medical students appear to have a greater species richness compared to second year medical students. Further, third year medical students had a statically significant difference in their oral microbiome richness from beginning to end of data collection (p = 0.008).

CONCLUSION: Our preliminary data indicates that physical and psychological stress can impact the composition of the oral microbiome. The analyses in this study show that using the oral microbiome as an indicator of stress is promising and may provide evidence to support stress management practices.}, } @article {pmid37475836, year = {2023}, author = {Claverie, S and Hoareau, M and Chéhida, SB and Filloux, D and Varsani, A and Roumagnac, P and Martin, DP and Lett, JM and Lefeuvre, P}, title = {Metagenomics reveals the structure of Mastrevirus-host interaction network within an agro-ecosystem.}, journal = {Virus evolution}, volume = {9}, number = {2}, pages = {vead043}, pmid = {37475836}, issn = {2057-1577}, abstract = {As highly pervasive parasites that sometimes cause disease, viruses are likely major components of all natural ecosystems. An important step towards both understanding the precise ecological roles of viruses and determining how natural communities of viral species are assembled and evolve is obtaining full descriptions of viral diversity and distributions at ecosystem scales. Here, we focused on obtaining such 'community-scale' data for viruses in a single genus. We chose the genus Mastrevirus (family Geminiviridae), members of which have predominantly been found infecting uncultivated grasses (family Poaceae) throughout the tropical and sub-tropical regions of the world. We sampled over 3 years, 2,884 individual Poaceae plants belonging to thirty different species within a 2-ha plot which included cultivated and uncultivated areas on the island of Reunion. Mastreviruses were found in ∼8 per cent of the samples, of which 96 per cent did not have any discernible disease symptoms. The multitude of host-virus associations that we uncovered reveals both the plant species that most commonly host mastreviruses and the mastrevirus species (such as maize streak virus and maize streak Reunion virus) that have especially large host ranges. Our findings are consistent with the hypothesis that perennial plant species capable of hosting years-long mixed mastrevirus infections likely play a disproportionately important role in the generation of inter-species and inter-strain mastrevirus recombinants.}, } @article {pmid37475130, year = {2023}, author = {Yang, G and Cao, JM and Cui, HL and Zhan, XM and Duan, G and Zhu, YG}, title = {Artificial Sweetener Enhances the Spread of Antibiotic Resistance Genes During Anaerobic Digestion.}, journal = {Environmental science & technology}, volume = {57}, number = {30}, pages = {10919-10928}, doi = {10.1021/acs.est.2c08673}, pmid = {37475130}, issn = {1520-5851}, mesh = {*Genes, Bacterial ; Anaerobiosis ; *Anti-Bacterial Agents/pharmacology ; Sweetening Agents/pharmacology ; Drug Resistance, Microbial/genetics ; }, abstract = {Artificial sweeteners have been frequently detected in the feedstocks of anaerobic digestion. As these sweeteners can lead to the shift of anaerobic microbiota in the gut similar to that caused by antibiotics, we hypothesize that they may have an antibiotic-like impact on antibiotic resistance genes (ARGs) in anaerobic digestion. However, current understanding on this topic is scarce. This investigation aimed to examine the potential impact of acesulfame, a typical artificial sweetener, on ARGs in anaerobic digestion by using metagenomics sequencing and qPCR. It was found that acesulfame increased the number of detected ARG classes and the abundance of ARGs during anaerobic digestion. The abundance of typical mobile genetic elements (MGEs) and the number of potential hosts of ARGs also increased under acesulfame exposure, suggesting the enhanced potential of horizontal gene transfer of ARGs, which was further confirmed by the correlation analysis between absolute abundances of the targeted ARGs and MGEs. The increased horizontal dissemination of ARGs may be associated with the SOS response induced by the increased ROS production, and the increased cellular membrane permeability. These findings indicate that artificial sweeteners may accelerate ARG spread through digestate disposal, thus corresponding strategies should be considered to prevent potential risks in practice.}, } @article {pmid37474971, year = {2023}, author = {Kilic Yildirim, G and Dinleyici, M and Vandenplas, Y and Dinleyici, EC}, title = {Effects of synbiotic supplementation on intestinal microbiota composition in children and adolescents with exogenous obesity: (Probesity-2 trial).}, journal = {Gut pathogens}, volume = {15}, number = {1}, pages = {36}, pmid = {37474971}, issn = {1757-4749}, abstract = {INTRODUCTION: Gut microbiota manipulation may be a potential therapeutic target to reduce host energy storage. There is limited information about the effects of probiotics/synbiotics on intestinal microbiota composition in children and adolescents with obesity. The objective of this randomized double-blind placebo-controlled trial was to test the effects of a multispecies synbiotic on intestinal microbiota composition in children and adolescents with exogenous obesity.

METHOD: Children with exogenous obesity were managed with a standard diet and increased physical activity and were randomly allocated into two groups at a ratio of 1:1; the 1st group received synbiotic supplementation (probiotic mixture including Lactobacillus acidophilus, Lacticaseibacillus. rhamnosus, Bifidobacterium bifidum, Bifidobacterium longum, Enterococcus faecium (total 2.5 × 10[9] CFU/sachet) and fructo-oligosaccharides (FOS; 625 mg/sachet) for 12 weeks; the 2nd group received placebo once daily for 12 weeks. Fecal samples were obtained before and at the end of the 12-week intervention to characterize the changes in the gut microbiota composition. Detailed metagenomic and bioinformatics analyses were performed.

RESULTS: Before the intervention, there were no significant differences in alpha diversity indicators between the synbiotic and placebo groups. After 12 weeks of intervention, the observed taxonomic units and Chao 1 were lower in the synbiotic group than at baseline (p < 0.001 for both). No difference for alpha diversity indicators was observed in the placebo group between baseline and 12 weeks of intervention. At the phylum level, the intestinal microbiota composition of the study groups was similar at baseline. The major phyla in the synbiotic group were Firmicutes (66.7%) and Bacteroidetes (18.8%). In the synbiotic group, the Bacteroidetes phylum was higher after 12 weeks than at baseline (24.0% vs. 18.8%, p < 0.01). In the synbiotic group, the Firmicutes/Bacteroidetes ratio was 3.54 at baseline and 2.75 at 12 weeks of intervention (p < 0.05). In the placebo group, the Firmicutes/Bacteroidetes ratio was 4.70 at baseline and 3.54 at 12 weeks of intervention (p < 0.05). After 12 weeks of intervention, the Firmicutes/Bacteroidetes ratio was also lower in the synbiotic group than in the placebo group (p < 0.05). In the synbiotic group, compared with the baseline, we observed a statistically significant increase in the genera Prevotella (5.28-14.4%, p < 0.001) and Dialister (9.68-13.4%; p < 0.05). Compared to baseline, we observed a statistically significant increase in the genera Prevotella (6.4-12.4%, p < 0.01) and Oscillospira (4.95% vs. 5.70%, p < 0.001) in the placebo group. In the synbiotic group, at the end of the intervention, an increase in Prevotella, Coprococcus, Lachnospiraceae (at the genus level) and Prevotella copri, Coprococcus eutactus, Ruminococcus spp. at the species level compared to baseline (predominance of Eubacterium dolichum, Lactobacillus ruminis, Clostridium ramosum, Bulleidia moorei) was observed. At the end of the 12th week of the study, when the synbiotic and placebo groups were compared, Bacteroides eggerthi species were dominant in the placebo group, while Collinsella stercoris species were dominant in the synbiotic group.

CONCLUSION: This study is the first pediatric obesity study to show that a synbiotic treatment is associated with both changes intestinal microbiota composition and decreases in BMI. Trial identifier: NCT05162209 (www.

CLINICALTRIALS: gov).}, } @article {pmid37474785, year = {2023}, author = {Rosenboom, I and Pust, MM and Pirr, S and Bakker, A and Willers, M and Davenport, CF and Wiehlmann, L and Viemann, D and Tümmler, B}, title = {Longitudinal development of the airway metagenome of preterm very low birth weight infants during the first two years of life.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {75}, pmid = {37474785}, issn = {2730-6151}, support = {ZN3432//Volkswagen Foundation (VolkswagenStiftung)/ ; ZN3432//Volkswagen Foundation (VolkswagenStiftung)/ ; VI 538 6-3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; VI 538 6-3//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; 390874280//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Preterm birth is accompanied with many complications and requires severe therapeutic regimens at the neonatal intensive care unit. The influence of the above-mentioned factors on the premature-born infants' respiratory metagenome or more generally its maturation is unknown. We therefore applied shotgun metagenome sequencing of oropharyngeal swabs to analyze the airway metagenome development of 24 preterm infants from one week postpartum to 15 months of age. Beta diversity analysis revealed a distinct clustering of airway microbial communities from hospitalized preterms and samples after hospital discharge. At nine and 15 months of age, the preterm infants lost their hospital-acquired individual metagenome signatures towards a common taxonomic structure. However, ecological network analysis and Random Forest classification of cross-sectional data revealed that by this age the preterm infants did not succeed in establishing the uniform and stable bacterial community structures that are characteristic for healthy full-term infants.}, } @article {pmid37474642, year = {2023}, author = {Zhang, IH and Sun, X and Jayakumar, A and Fortin, SG and Ward, BB and Babbin, AR}, title = {Partitioning of the denitrification pathway and other nitrite metabolisms within global oxygen deficient zones.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {76}, pmid = {37474642}, issn = {2730-6151}, support = {OCE-2142998//National Science Foundation (NSF)/ ; OCE-2138890//National Science Foundation (NSF)/ ; }, abstract = {Oxygen deficient zones (ODZs) account for about 30% of total oceanic fixed nitrogen loss via processes including denitrification, a microbially mediated pathway proceeding stepwise from NO3[-] to N2. This process may be performed entirely by complete denitrifiers capable of all four enzymatic steps, but many organisms possess only partial denitrification pathways, either producing or consuming key intermediates such as the greenhouse gas N2O. Metagenomics and marker gene surveys have revealed a diversity of denitrification genes within ODZs, but whether these genes co-occur within complete or partial denitrifiers and the identities of denitrifying taxa remain open questions. We assemble genomes from metagenomes spanning the ETNP and Arabian Sea, and map these metagenome-assembled genomes (MAGs) to 56 metagenomes from all three major ODZs to reveal the predominance of partial denitrifiers, particularly single-step denitrifiers. We find niche differentiation among nitrogen-cycling organisms, with communities performing each nitrogen transformation distinct in taxonomic identity and motility traits. Our collection of 962 MAGs presents the largest collection of pelagic ODZ microorganisms and reveals a clearer picture of the nitrogen cycling community within this environment.}, } @article {pmid37474497, year = {2023}, author = {Mirhakkak, MH and Chen, X and Ni, Y and Heinekamp, T and Sae-Ong, T and Xu, LL and Kurzai, O and Barber, AE and Brakhage, AA and Boutin, S and Schäuble, S and Panagiotou, G}, title = {Genome-scale metabolic modeling of Aspergillus fumigatus strains reveals growth dependencies on the lung microbiome.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4369}, pmid = {37474497}, issn = {2041-1723}, mesh = {Male ; Female ; Humans ; Aspergillus fumigatus/genetics ; *Cystic Fibrosis/microbiology ; Lung ; *Microbiota/genetics ; }, abstract = {Aspergillus fumigatus, an opportunistic human pathogen, frequently infects the lungs of people with cystic fibrosis and is one of the most common causes of infectious-disease death in immunocompromised patients. Here, we construct 252 strain-specific, genome-scale metabolic models of this important fungal pathogen to study and better understand the metabolic component of its pathogenic versatility. The models show that 23.1% of A. fumigatus metabolic reactions are not conserved across strains and are mainly associated with amino acid, nucleotide, and nitrogen metabolism. Profiles of non-conserved reactions and growth-supporting reaction fluxes are sufficient to differentiate strains, for example by environmental or clinical origin. In addition, shotgun metagenomics analysis of sputum from 40 cystic fibrosis patients (15 females, 25 males) before and after diagnosis with an A. fumigatus colonization suggests that the fungus shapes the lung microbiome towards a more beneficial fungal growth environment associated with aromatic amino acid availability and the shikimate pathway. Our findings are starting points for the development of drugs or microbiome intervention strategies targeting fungal metabolic needs for survival and colonization in the non-native environment of the human lung.}, } @article {pmid37474466, year = {2023}, author = {Chiu, KH and Sridhar, S and Yuen, KY}, title = {Preparation for the next pandemic: challenges in strengthening surveillance.}, journal = {Emerging microbes & infections}, volume = {12}, number = {2}, pages = {2240441}, pmid = {37474466}, issn = {2222-1751}, mesh = {Animals ; Humans ; *COVID-19/epidemiology ; Pandemics/prevention & control ; Artificial Intelligence ; *Virus Diseases ; *Vaccines ; }, abstract = {The devastating Coronavirus Disease 2019 (COVID-19) pandemic indicates that early detection of candidates with pandemic potential is vital. However, comprehensive metagenomic sequencing of the total microbiome is not practical due to the astronomical and rapidly evolving numbers and species of micro-organisms. Analysis of previous pandemics suggests that an increase in human-animal interactions, changes in animal and arthropod distribution due to climate change and deforestation, continuous mutations and interspecies jumping of RNA viruses, and frequent travels are important factors driving pandemic emergence. Besides measures mitigating these factors, surveillance at human-animal interfaces targeting animals with unusual tolerance to viral infections, sick heathcare workers, and workers at high biosafety level laboratories is crucial. Surveillance of sick travellers is important when alerted by an early warning system of a suspected outbreak due to unknown agents. These samples should be screened by multiplex nucleic acid amplification and subsequent unbiased next-generation sequencing. Novel viruses should be isolated in routine cell cultures, complemented by organoid cultures, and then tested in animal models for interspecies transmission potential. Potential agents are candidates for designing rapid diagnostics, therapeutics, and vaccines. For early detection of outbreaks, there are advantages in using event-based surveillance and artificial intelligence (AI), but high background noise and censorship are possible drawbacks. These systems are likely useful if they channel reliable information from frontline healthcare or veterinary workers and large international gatherings. Furthermore, sufficient regulation of high biosafety level laboratories, and stockpiling of broad spectrum antiviral drugs, vaccines, and personal protective equipment are indicated for pandemic preparedness.}, } @article {pmid37474105, year = {2023}, author = {Kyaw, TS and Upadhyay, V and Tolstykh, I and Van Loon, K and Laffan, A and Stanfield, D and Gempis, D and Kenfield, SA and Chan, JM and Piawah, S and Atreya, CE and Ng, K and Venook, A and Kidder, W and Turnbaugh, PJ and Van Blarigan, EL}, title = {Variety of Fruit and Vegetables and Alcohol Intake are Associated with Gut Microbial Species and Gene Abundance in Colorectal Cancer Survivors.}, journal = {The American journal of clinical nutrition}, volume = {118}, number = {3}, pages = {518-529}, pmid = {37474105}, issn = {1938-3207}, support = {R01 HL122593/HL/NHLBI NIH HHS/United States ; F30 CA257378/CA/NCI NIH HHS/United States ; R01 AT011117/AT/NCCIH NIH HHS/United States ; R01 AR074500/AR/NIAMS NIH HHS/United States ; R37 CA248774/CA/NCI NIH HHS/United States ; R01 DK114034/DK/NIDDK NIH HHS/United States ; R21 CA227232/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Vegetables ; Fruit ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Diet/methods ; Alcohol Drinking ; *Cancer Survivors ; *Colorectal Neoplasms ; }, abstract = {BACKGROUND: Adherence to the American Cancer Society (ACS) guidelines of avoiding obesity, maintaining physical activity, and consuming a diet rich in fruits, vegetables, and whole grains is associated with longer survival in colorectal cancer (CRC) survivors. Dietary components of the ACS guidelines may act in part by changing the microbiome, which is implicated in CRC outcomes.

OBJECTIVES: We conducted a pilot cross-sectional study to explore associations between ACS guidelines and the gut microbiome.

METHODS: Stool samples and questionnaires were collected from 28 CRC survivors at the University of California, San Francisco from 2019 to 2020. ACS scores were calculated based on validated questionnaires. Gut microbial community structure from 16S amplicons and gene/pathway abundances from metagenomics were tested for associations with the ACS score and its components using ANOVA and general linear models.

RESULTS: The overall ACS score was not significantly associated with variations in the fecal microbiota. However, fruit and vegetable intake and alcohol intake accounted for 19% (P = 0.005) and 13% (P = 0.01) of variation in the microbiota, respectively. Fruit/vegetable consumption was associated with increased microbial diversity, increased Firmicutes, decreased Bacteroidota, and changes to multiple genes and metabolic pathways, including enriched pathways for amino acid and short-chain fatty acid biosynthesis and plant-associated sugar degradation. In contrast, alcohol consumption was positively associated with overall microbial diversity, negatively associated with Bacteroidota abundance, and associated with changes to multiple genes and metabolic pathways. The other components of the ACS score were not statistically significantly associated with the fecal microbiota in our sample.

CONCLUSIONS: These results guide future studies examining the impact of changes in the intake of fruits, vegetables, and alcoholic drinks on the gut microbiome of CRC survivors.}, } @article {pmid37474041, year = {2023}, author = {Cai, S and Yang, Y and Zeng, X and Zhu, Z and Wang, F and Zhang, S and Chen, F and Cai, C and Zeng, X and Qiao, S}, title = {Methionine influences the profile of intestinal antibiotic resistome through inhibiting the growth of Escherichia coli.}, journal = {The Science of the total environment}, volume = {899}, number = {}, pages = {165610}, doi = {10.1016/j.scitotenv.2023.165610}, pmid = {37474041}, issn = {1879-1026}, mesh = {Animals ; Swine ; Female ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Escherichia coli/genetics ; Methionine ; Racemethionine ; Intestines ; }, abstract = {Antibiotic resistance genes (ARGs) are a new type of environmental pollutant. However, studies have mainly focused on the distribution characteristics of ARGs in the livestock environment, lacking of studies on the composition of ARGs in the intestinal tract of animals and the effect of nutrients on intestinal ARGs and microbial communities. Reducing antimicrobial resistance and maintaining optimal animal health and performance are urgently needed. Methionine is an essential amino acid which plays a critical role in the growth and reproductive performance of animals. In this study, feeding experiment, in vitro fermentation and bacterial culture experiment were performed to explore the influence of methionine on the intestinal resistome of sows. We found that dietary 0.2 % methionine supplementation decreased the total abundance of intestinal ARGs, which was further confirmed by in vitro fecal microbial fermentation of sows. Metagenome binning analysis identified that Escherichia coli was the major ARG host, which carried 60-113 ARGs and 134-286 virulence factors, indicating that Escherichia coli in the pig intestine is not only a core ARG host, but also an important pathogen. In addition, we found that methionine supplementation inhibited the growth of Escherichia coli, indicating that dietary methionine may reduce the resistome risk in sow intestine by inhibiting core ARG hosts such as Escherichia coli. These findings reveal that dietary methionine application plays a critical role in intestinal antibiotic resistance, providing a new idea for preventing and controlling environmental pollution by antibiotic-resistant microbes.}, } @article {pmid37471465, year = {2024}, author = {Essex, M and Rios Rodriguez, V and Rademacher, J and Proft, F and Löber, U and Markó, L and Pleyer, U and Strowig, T and Marchand, J and Kirwan, JA and Siegmund, B and Forslund, SK and Poddubnyy, D}, title = {Shared and Distinct Gut Microbiota in Spondyloarthritis, Acute Anterior Uveitis, and Crohn's Disease.}, journal = {Arthritis & rheumatology (Hoboken, N.J.)}, volume = {76}, number = {1}, pages = {48-58}, doi = {10.1002/art.42658}, pmid = {37471465}, issn = {2326-5205}, support = {Food allergy and tolerance (FOOD@-Project ID 428046232)//Deutsche Forschungsgemeinschaft/ ; CRC1449//Deutsche Forschungsgemeinschaft/ ; CRC-TRR241//Deutsche Forschungsgemeinschaft/ ; EXC 2155 "RESIST" (Project ID 390874280//Deutsche Forschungsgemeinschaft/ ; //German Research Foundation/ ; //German Federal Ministry for Health and Research (BMBF)/ ; //Novartis/ ; //BIH-Charité Clinician Scientist Program/ ; //Charité-Universitätsmedizin Berlin/ ; }, mesh = {Humans ; *Crohn Disease/drug therapy/complications ; *Gastrointestinal Microbiome/genetics ; *Spondylarthritis/drug therapy/complications ; *Uveitis, Anterior/drug therapy ; *Antirheumatic Agents ; Clostridiales/metabolism ; HLA-B27 Antigen/genetics ; Acute Disease ; }, abstract = {OBJECTIVE: Spondyloarthritis (SpA) is a group of immune-mediated diseases highly concomitant with nonmusculoskeletal inflammatory disorders, such as acute anterior uveitis (AAU) and Crohn's disease (CD). The gut microbiome represents a promising avenue to elucidate shared and distinct underlying pathophysiology.

METHODS: We performed 16S ribosomal RNA sequencing on stool samples of 277 patients (72 CD, 103 AAU, and 102 SpA) included in the German Spondyloarthritis Inception Cohort and 62 back pain controls without any inflammatory disorder. Discriminatory statistical methods were used to disentangle microbial disease signals from one another and a wide range of potential confounders. Patients were naive to or had not received treatment with biological disease-modifying antirheumatic drugs (DMARDs) for >3 months before enrollment, providing a better approximation of a true baseline disease signal.

RESULTS: We identified a shared, immune-mediated disease signal represented by low abundances of Lachnospiraceae taxa relative to controls, most notably Fusicatenibacter, which was most abundant in controls receiving nonsteroidal antiinflammatory drug monotherapy and implied to partially mediate higher serum C-reactive protein. Patients with SpA showed an enrichment of Collinsella, whereas human leukocyte antigen (HLA)-B27+ individuals displayed enriched Faecalibacterium. CD patients had higher abundances of a Ruminococcus taxon, and previous conventional/synthetic DMARD therapy was associated with increased Akkermansia.

CONCLUSION: Our work supports the existence of a common gut dysbiosis in SpA and related inflammatory pathologies. We reveal shared and disease-specific microbial associations and suggest potential mediators of disease activity. Validation studies are needed to clarify the role of Fusicatenibacter in gut-joint inflammation, and metagenomic resolution is needed to understand the relationship between Faecalibacterium commensals and HLA-B27.}, } @article {pmid37471128, year = {2023}, author = {Ring, N and Low, AS and Wee, B and Paterson, GK and Nuttall, T and Gally, D and Mellanby, R and Fitzgerald, JR}, title = {Rapid metagenomic sequencing for diagnosis and antimicrobial sensitivity prediction of canine bacterial infections.}, journal = {Microbial genomics}, volume = {9}, number = {7}, pages = {}, pmid = {37471128}, issn = {2057-5858}, support = {BBS/E/D/20002173/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/D/20002174/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Dogs ; Animals ; Humans ; *Bacterial Infections/diagnosis/veterinary ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Metagenome ; High-Throughput Nucleotide Sequencing ; }, abstract = {Antimicrobial resistance is a major threat to human and animal health. There is an urgent need to ensure that antimicrobials are used appropriately to limit the emergence and impact of resistance. In the human and veterinary healthcare setting, traditional culture and antimicrobial sensitivity testing typically requires 48-72 h to identify appropriate antibiotics for treatment. In the meantime, broad-spectrum antimicrobials are often used, which may be ineffective or impact non-target commensal bacteria. Here, we present a rapid, culture-free, diagnostics pipeline, involving metagenomic nanopore sequencing directly from clinical urine and skin samples of dogs. We have planned this pipeline to be versatile and easily implementable in a clinical setting, with the potential for future adaptation to different sample types and animals. Using our approach, we can identify the bacterial pathogen present within 5 h, in some cases detecting species which are difficult to culture. For urine samples, we can predict antibiotic sensitivity with up to 95 % accuracy. Skin swabs usually have lower bacterial abundance and higher host DNA, confounding antibiotic sensitivity prediction; an additional host depletion step will likely be required during the processing of these, and other types of samples with high levels of host cell contamination. In summary, our pipeline represents an important step towards the design of individually tailored veterinary treatment plans on the same day as presentation, facilitating the effective use of antibiotics and promoting better antimicrobial stewardship.}, } @article {pmid37470847, year = {2023}, author = {Nishida, S and Omae, K and Inoue, M and Sako, Y and Kamikawa, R and Yoshida, T}, title = {Construction of multiple metagenome assembled genomes containing carbon monoxide dehydrogenases from anaerobic carbon monoxide enrichment cultures.}, journal = {Archives of microbiology}, volume = {205}, number = {8}, pages = {292}, pmid = {37470847}, issn = {1432-072X}, support = {JPMJSP2110//JST SPRING/ ; JP16H06381//Japan Society for the Promotion of Science/ ; L-2021-1-002//Institute for Fermentation, Osaka/ ; }, mesh = {*Carbon Monoxide/metabolism ; *Metagenome ; Anaerobiosis ; RNA, Ribosomal, 16S/genetics ; Firmicutes/genetics ; Aldehyde Oxidoreductases/genetics/metabolism ; }, abstract = {Despite its toxicity to many organisms, including most prokaryotes, carbon monoxide (CO) is utilized by some aerobic and anaerobic prokaryotes. Hydrogenogenic CO utilizers employ carbon monoxide dehydrogenase (CODH) and energy-converting hydrogenase (ECH) to oxidize CO and reduce protons to produce H2. Those prokaryotes constitute a rare biosphere and are difficult to detect even with PCR amplification and with metagenomic analyses. In this study, anaerobic CO-enrichment cultures followed by construction of metagenome assembled genomes (MAGs) detected high-quality MAGs from potential hydrogenogenic CO utilizers. Of 32 MAGs constructed, 5 were potential CO utilizer harboring CODH genes. Of the five MAGs, two were classified into the genus Thermolithobacter on the basis of 16S rRNA sequence identity, related to Carboxydocella tharmautotrophica 41, with an average nucleotide identity (ANI) of approximately 72%. Additionally, two were related to Geoglobus acetivorans with ANI values ranging from 75 to 77% to G. acetivorans SBH6, and one MAG was identified as Desulfotomaculum kuznetsovii with an ANI > 96% to D. kuznetsovii DSM 6115. The two Thermolithobacter MAGs identified in this study contained CODH-ECH gene clusters, and were therefore identified as potential hydrogenogenic CO utilizers. However, these MAGs harbored three CODH gene clusters that showed distinct physiological functions in addition to CODH-ECH gene clusters. In total, the five potential CO utilizer MAGs contained sixteen CODH genes. Among those CODHs, four sets did not cluster with any known CODH protein sequences (with an identity of > 90%), and the CODH database was expanded.}, } @article {pmid37470485, year = {2023}, author = {Zhao, R and Le Moine Bauer, S and Babbin, AR}, title = {"Candidatus Subterrananammoxibiaceae," a New Anammox Bacterial Family in Globally Distributed Marine and Terrestrial Subsurfaces.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {8}, pages = {e0080023}, pmid = {37470485}, issn = {1098-5336}, mesh = {Humans ; *Nitrites/metabolism ; Nitrates/metabolism ; Anaerobic Ammonia Oxidation ; Phylogeny ; Geologic Sediments/microbiology ; Bacteria ; *Ammonium Compounds/metabolism ; Oxidoreductases/metabolism ; Nitrite Reductases/genetics ; Oxidation-Reduction ; Nitrogen/metabolism ; Anaerobiosis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bacteria specialized in anaerobic ammonium oxidation (anammox) are widespread in many anoxic habitats and form an important functional guild in the global nitrogen cycle by consuming bio-available nitrogen for energy rather than biomass production. Due to their slow growth rates, cultivation-independent approaches have been used to decipher their diversity across environments. However, their full diversity has not been well recognized. Here, we report a new family of putative anammox bacteria, "Candidatus Subterrananammoxibiaceae," existing in the globally distributed terrestrial and marine subsurface (groundwater and sediments of estuary, deep-sea, and hadal trenches). We recovered a high-quality metagenome-assembled genome of this family, tentatively named "Candidatus Subterrananammoxibius californiae," from a California groundwater site. The "Ca. Subterrananammoxibius californiae" genome not only contains genes for all essential components of anammox metabolism (e.g., hydrazine synthase, hydrazine oxidoreductase, nitrite reductase, and nitrite oxidoreductase) but also has the capacity for urea hydrolysis. In an Arctic ridge sediment core where redox zonation is well resolved, "Ca. Subterrananammoxibiaceae" is confined within the nitrate-ammonium transition zone where the anammox rate maximum occurs, providing environmental proof of the anammox activity of this new family. Phylogenetic analysis of nitrite oxidoreductase suggests that a horizontal transfer facilitated the spreading of the nitrite oxidation capacity between anammox bacteria (in the Planctomycetota phylum) and nitrite-oxidizing bacteria from Nitrospirota and Nitrospinota. By recognizing this new anammox family, we propose that all lineages within the "Ca. Brocadiales" order have anammox capacity. IMPORTANCE Microorganisms called anammox bacteria are efficient in removing bioavailable nitrogen from many natural and human-made environments. They exist in almost every anoxic habitat where both ammonium and nitrate/nitrite are present. However, only a few anammox bacteria have been cultured in laboratory settings, and their full phylogenetic diversity has not been recognized. Here, we present a new bacterial family whose members are present across both the terrestrial and marine subsurface. By reconstructing a high-quality genome from the groundwater environment, we demonstrate that this family has all critical enzymes of anammox metabolism and, notably, also urea utilization. This bacterium family in marine sediments is also preferably present in the niche where the anammox process occurs. These findings suggest that this novel family, named "Candidatus Subterrananammoxibiaceae," is an overlooked group of anammox bacteria, which should have impacts on nitrogen cycling in a range of environments.}, } @article {pmid37470119, year = {2023}, author = {Chen, Q and Ren, R and Sun, Y and Xu, J and Yang, H and Li, X and Xiao, Y and Li, J and Lyu, W}, title = {The combination of metagenome and metabolome to compare the differential effects and mechanisms of fructose and sucrose on the metabolic disorders and gut microbiota in vitro and in vivo.}, journal = {Food & function}, volume = {14}, number = {15}, pages = {7284-7298}, doi = {10.1039/d3fo02246c}, pmid = {37470119}, issn = {2042-650X}, abstract = {Sucrose and fructose are the most commonly used sweeteners in the modern food industry, but there are few comparative studies on the mechanisms by which fructose and sucrose affect host health. The aim of the present study was to explain the different effects of fructose and sucrose on host metabolism from the perspective of gut microbiota. Mice were fed for 16 weeks with normal drinking water (CON), 30% fructose drinking water (CF) and 30% sucrose drinking water (SUC). Compared with fructose treatment, sucrose caused significantly higher weight gain, epididymal fat deposition, hepatic steatosis, and jejunum histological injury. Sucrose increased the abundance of LPS-producing bacteria which was positively correlated with obesity traits, while fructose increased the abundance of Lactobacillus. An in vitro fermentation experiment also showed that fructose increased the abundance of Lactobacillus, while sucrose increased the abundance of Klebsiella and Escherichia. In addition, combined with microbial functional analysis and metabolomics data, fructose led to the enhancement of carbohydrate metabolism and TCA cycle capacity, and increased the production of glutamate. The cross-cooperation network greatly influenced the microbiota (Klebsiella, Lactobacillus), metabolites (glutamate, fructose 1,6-biosphosphate, citric acid), and genes encoding enzymes (pyruvate kinase, 6-phosphofructokinase 1, fructokinase, lactate dehydrogenase, aconitate hydratase, isocitrate dehydrogenase 3), suggesting that they may be the key differential factors in the process of fructose and sucrose catabolism. Therefore, the changes in gut microbiome mediated by fructose and sucrose are important reasons for their differential effects on host health and metabolism.}, } @article {pmid37469600, year = {2023}, author = {Du, R and Feng, Y and Mao, H}, title = {Case report: Diagnosis of Talaromyces marneffei infection in an HIV-negative patient with septic shock and high-titer anti-interferon gamma autoantibodies by metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1163846}, pmid = {37469600}, issn = {2235-2988}, mesh = {Adult ; Female ; Humans ; Antifungal Agents/therapeutic use ; Autoantibodies ; High-Throughput Nucleotide Sequencing ; Interferon-gamma ; Neoplasm Recurrence, Local/drug therapy ; *Sepsis/drug therapy ; *Shock, Septic/diagnosis ; Talaromyces ; HIV Seronegativity ; *Mycoses/diagnosis ; }, abstract = {BACKGROUND: Sepsis is a life-threatening condition caused by a dysfunctional response to infection from the host. Septic shock, a subset of sepsis, caused by Talaromyces marneffei infection (talaromycosis) has rarely been reported. Owing to its slow culture and low yield, talaromycosis is typically misdiagnosed in HIV-negative patients as other infections, such as tuberculosis, bacterial pneumonia, and lung cancer, especially in non-endemic regions. Early and accurate diagnosis as well as efficient treatment options are required to improve prognosis.

METHOD: A 30-year-old HIV-negative Chinese woman from a non-endemic area of T. marneffei was initially misdiagnosed with tuberculosis. She had a poor response to anti-tuberculosis treatment. On July 16, 2022, she was admitted to our hospital; the patient developed septic shock on the third day after hospitalization and was ultimately diagnosed with talaromycosis via metagenomic next-generation sequencing (mNGS).

RESULT: The condition of the patient improved after appropriate treatment with amphotericin B. Furthermore, enzyme-linked immunosorbent assay results confirmed that the patient had a high-titer of anti-interferon gamma (IFN-γ) autoantibodies.

CONCLUSION: HIV-negative individuals with anti-IFN-γ autoantibodies typically have relapsing, refractory, and fatal infections, such as talaromycosis, which is typically misdiagnosed in the initial course of the disease. This can lead to septic shock. Clinicians should be aware that they may encounter HIV-negative patients with T. marneffei infection in non-endemic areas. Thus, mNGS is an effective technology for detecting T. marneffei infection. Additionally, the detection of anti-IFN-γ autoantibodies in these patients would aid in knowing their susceptibility to fatal infections.}, } @article {pmid37469596, year = {2023}, author = {Almas, S and Carpenter, RE and Rowan, C and Tamrakar, VK and Bishop, J and Sharma, R}, title = {Advantage of precision metagenomics for urinary tract infection diagnostics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1221289}, pmid = {37469596}, issn = {2235-2988}, mesh = {Humans ; *Metagenomics/methods ; *Urinary Tract Infections/diagnosis/epidemiology ; Anti-Bacterial Agents/therapeutic use ; Computational Biology ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Urinary tract infections (UTIs) remain a diagnostic challenge and often promote antibiotic overuse. Despite urine culture being the gold standard for UTI diagnosis, some uropathogens may lead to false-negative or inconclusive results. Although PCR testing is fast and highly sensitive, its diagnostic yield is limited to targeted microorganisms. Metagenomic next-generation sequencing (mNGS) is a hypothesis-free approach with potential of deciphering the urobiome. However, clinically relevant information is often buried in the enormous amount of sequencing data.

METHODS: Precision metagenomics (PM) is a hybridization capture-based method with potential of enhanced discovery power and better diagnostic yield without diluting clinically relevant information. We collected 47 urine samples of clinically suspected UTI and in parallel tested each sample by microbial culture, PCR, and PM; then, we comparatively analyzed the results. Next, we phenotypically classified the cumulative microbial population using the Explify® data analysis platform for potential pathogenicity.

RESULTS: Results revealed 100% positive predictive agreement (PPA) with culture results, which identified only 13 different microorganisms, compared to 19 and 62 organisms identified by PCR and PM, respectively. All identified organisms were classified into phenotypic groups (0-3) with increasing pathogenic potential and clinical relevance. This PM can simultaneously quantify and phenotypically classify the organisms readily through bioinformatic platforms like Explify®, essentially providing dissected and quantitative results for timely and accurate empiric UTI treatment.

CONCLUSION: PM offers potential for building effective diagnostic models beyond usual care testing in complex UTI diseases. Future studies should assess the impact of PM-guided UTI management on clinical outcomes.}, } @article {pmid37469430, year = {2023}, author = {Fernandez-Cantos, MV and Garcia-Morena, D and Yi, Y and Liang, L and Gómez-Vázquez, E and Kuipers, OP}, title = {Bioinformatic mining for RiPP biosynthetic gene clusters in Bacteroidales reveals possible new subfamily architectures and novel natural products.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1219272}, pmid = {37469430}, issn = {1664-302X}, abstract = {The Bacteroidales order, widely distributed among diverse human populations, constitutes a key component of the human microbiota. Members of this Gram-negative order have been shown to modulate the host immune system, play a fundamental role in the gut's microbial food webs, or be involved in pathogenesis. Bacteria inhabiting such a complex environment as the human microbiome are expected to display social behaviors and, hence, possess factors that mediate cooperative and competitive interactions. Different types of molecules can mediate interference competition, including non-ribosomal peptides (NRPs), polyketides, and bacteriocins. The present study investigates the potential of Bacteroidales bacteria to biosynthesize class I bacteriocins, which are ribosomally synthesized and post-translationally modified peptides (RiPPs). For this purpose, 1,136 genome-sequenced strains from this order were mined using BAGEL4. A total of 1,340 areas of interest (AOIs) were detected. The most commonly identified enzymes involved in RiPP biosynthesis were radical S-adenosylmethionine (rSAM), either alone or in combination with other biosynthetic enzymes such as YcaO. A more comprehensive analysis of a subset of 9 biosynthetic gene clusters (BGCs) revealed a consistent association in Bacteroidales BGCs between peptidase-containing ATP-binding transporters (PCATs) and precursor peptides with GG-motifs. This finding suggests a possibly shared mechanism for leader peptide cleavage and transport of mature products. Notably, human metagenomic studies showed a high prevalence and abundance of the RiPP BGCs from Phocaeicola vulgatus and Porphyromonas gulae. The mature product of P. gulae BGC is hypothesized to display γ-thioether linkages and a C-terminal backbone amidine, a potential new combination of post-translational modifications (PTM). All these findings highlight the RiPP biosynthetic potential of Bacteroidales bacteria, as a rich source of novel peptide structures of possible relevance in the human microbiome context.}, } @article {pmid37469427, year = {2023}, author = {Wang, J and Weng, X and Weng, Y and Xu, Q and Lu, Y and Mo, Y}, title = {Clinical features and treatment outcomes of Vibrio vulnificus infection in the coastal city of Ningbo, China.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1220526}, pmid = {37469427}, issn = {1664-302X}, abstract = {BACKGROUND: Vibrio vulnificus is a gram-negative, opportunistic pathogen common to warm waters worldwide. Human V. vulnificus infection is rare and typically affects those residing in coastal areas during the summer months, but it causes rapid deterioration and is fatal.

METHODS: The medical records of six patients with sepsis caused by V. vulnificus infection who were treated at the First Affiliated Hospital of Ningbo University from 2020 to 2022 were retrospectively reviewed. The patient demographics, clinical symptoms, laboratory test results, treatments, and outcomes are summarized.

RESULTS: Vibrio vulnificus infection was confirmed by blood or pus culture, 16S ribosomal DNA sequencing, and metagenomic next-generation sequencing. All six patients were male with pre-existing liver diseases and two reported consuming seafood before the onset of symptoms. Of the six patients, four succumbed to the disease, two recovered, and one underwent leg amputation.

CONCLUSION: Vibrio vulnificus infection progresses rapidly and is highly fatal, thus prompt and aggressive treatment is necessary. Vibrio vulnificus infection should be considered in older (>40 years) patients with a history of liver disease and recent consumption of seafood or exposure to seawater, especially those residing in coastal areas during the summer months.}, } @article {pmid37469114, year = {2023}, author = {Woldeyohannis, NN and Desta, AF}, title = {Fate of antimicrobial resistance genes (ARG) and ARG carriers in struvite production process from human urine.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering}, volume = {58}, number = {9}, pages = {783-792}, doi = {10.1080/10934529.2023.2235246}, pmid = {37469114}, issn = {1532-4117}, mesh = {Humans ; Struvite ; *Anti-Bacterial Agents/pharmacology ; *Fertilizers ; Drug Resistance, Bacterial/genetics ; Carbapenems ; }, abstract = {Struvite, a human urine-derived fertilizer types, is characterized by its low water solubility that renders it a slow-releasing eco-friendly fertilizer. Knowing the fate of antibiotic resistance genes in struvite is important since human urine carries microorganisms, viruses and mobilomes. In this study, urine samples were collected and struvite production was done using MgCl2. From the fresh, stored urine and struvite, DNA was extracted and metagenomic sequencing was done using Illumina HiSeqX. Metagenome-derived genome sequence analysis revealed the dominance of phages of Streptococcus, Bacillus and Escherichia, with nearly 50% abundance of streptococcus phage in fresh urine. Increased antibiotic resistance genes were found in the stored urine than in fresh and struvite samples. The top five resistance genes in all the three samples were to aminoglycosides, carbapenem, chloramphenicol, erythromycin and efflux pump, with key carrying pathogens including Acinetobacter, Aeromonas and Enterococcus. The identified families for carbapenem, aminoglycoside resistance and efflux pump were shown persistent in struvite with a shift in gene families. The detection of resistance-gene-laden mobilomes, including the last-resort antibiotics in the struvite sample, requires due attention before the implementation of struvite as fertilizer. Further optimization of the struvite production process with regard to the minimization of mobilomes is recommended.}, } @article {pmid37469005, year = {2023}, author = {Masudi, WL and Titilawo, Y and Keshinro, TA and Cowan, AK}, title = {Isolation of bacteria with plant growth-promoting properties from microalgae-bacterial flocs produced in high-rate oxidation ponds.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-14}, doi = {10.1080/09593330.2023.2238928}, pmid = {37469005}, issn = {1479-487X}, abstract = {Exploring plant growth-promoting (PGP) bacterial activity of microbial components aggregated by wastewater treatment can reduce dependence on fossil fuel-derived fertilisers. This study describes the isolation and identification of bacteria from microalgae-bacteria flocs (MaB-flocs) generated in high-rate algal oxidation ponds (HRAOP) of an integrated algal pond system (IAPS) remediating municipal wastewater. Amplified 16S rRNA gene sequence analysis determined the molecular identity of the individual strains. Genetic relatedness to known PGP rhizobacteria in the NCBI GenBank database was by metagenomics. Isolated strains were screened for the production of indoles (measured as indole-3-acetic acid; IAA) and an ability to mineralise NH4+, PO43-, and K [+] . Of the twelve bacterial strains isolated from HRAOP MaB-flocs, four produced indoles, nine mineralised NH4+, seven solubilised P, and one K. Potential of isolated strains for PGP activity according to one-way ANOVA on ranks was: ECCN 7b > ECCN 4b > ECCN 6b > ECCN 3b = ECCN 10b > ECCN 1b = ECCN 5b > ECCN 8b > ECCN 2b > ECCN 12b > ECCN 9b = ECCN 11b. Further study revealed that cell-free filtrate from indole-producing cultures of Aeromonas strain ECCN 4b, Enterobacter strain ECCN 7b, and Arthrobacter strain ECCN 6b promoted mung bean adventitious root formation suggestive of the presence of auxin-like biological activity.}, } @article {pmid37468912, year = {2023}, author = {Du, L and Zhang, Z and Zhai, L and Xu, S and Yang, W and Huang, C and Lin, C and Zhong, LLD and Bian, Z and Zhao, L}, title = {Altered gut microbiota-host bile acid metabolism in IBS-D patients with liver depression and spleen deficiency pattern.}, journal = {Chinese medicine}, volume = {18}, number = {1}, pages = {87}, pmid = {37468912}, issn = {1749-8546}, support = {82000504//National Natural Science Foundation of China/ ; 81973578//National Natural Science Foundation of China/ ; 82204893//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Dysregulation of gut microbiota-host bile acid (BA) co-metabolism is a critical pathogenic factor of diarrhea-predominant irritable bowel syndrome (IBS-D). Traditional Chinese Medicine (TCM), instructed by pattern differentiation, is effective in treating IBS-D, in which liver depression and spleen deficiency (LDSD) is the most prevalent pattern. Still, it is unclear the linkage between the LDSD pattern and the BA metabolic phenotype.

PURPOSE: This study aimed to uncover the biological basis of the LDSD pattern from the BA metabolic perspective.

METHODS: Patients with IBS-D completed questionnaires regarding the irritable bowel severity scoring system (IBS-SSS), stool frequency, Stool Bristol scale, and Self-Rating Scales of mental health. Fasting blood and morning feces were collected to analyze the gut metagenome and BA-related indices/metabolites.

RESULTS: IBS-D patients with LDSD had a higher incidence of BA overexcretion (41% vs. 23% non-LDSD) with significant elevations in fecal total BAs and serum BA precursor 7α-hydroxy-4-cholesten-3-one levels. Compared to controls or non-LDSD patients, LDSD patients had a featured fecal BA profile, with higher proportions of deoxycholic acid (DCA), 7-ketodeoxycholic acid, and lithocholic acid. It is consistent with the BA-metabolizing genomic changes in the LDSD gut microbiota characterized by overabundances of 7-dehydroxylating bacteria and BA-inducible genes (baiCD/E/H). The score of bowel symptoms (stool frequency and abdominal pain) showing greater severity in the LDSD pattern were positively correlated with bai-expressing bacterial abundances and fecal DCA levels separately.

CONCLUSION: We clarified a differed BA metabolic phenotype in IBS patients with LDSD, which closely correlates with the severity of bowel symptoms. It demonstrates that gut microbiota and host co-metabolism of BAs would provide crucial insight into the biology of the LDSD pattern and its internal relationship with IBS progression.}, } @article {pmid37468867, year = {2023}, author = {Zhang, D and Weng, S and Xia, C and Ren, Y and Liu, Z and Xu, Y and Yang, X and Wu, R and Peng, L and Sun, L and Zhu, J and Liang, X and Jia, Y and Wang, H and Chen, Q and Liu, D and Chen, Y and Guo, H and Han, X and Jin, Z and Chen, C and Yang, X and Li, Z and Huang, H}, title = {Gastrointestinal symptoms of long COVID-19 related to the ectopic colonization of specific bacteria that move between the upper and lower alimentary tract and alterations in serum metabolites.}, journal = {BMC medicine}, volume = {21}, number = {1}, pages = {264}, pmid = {37468867}, issn = {1741-7015}, mesh = {Humans ; *COVID-19 ; Post-Acute COVID-19 Syndrome ; Aftercare ; Quality of Life ; SARS-CoV-2 ; Patient Discharge ; Feces/microbiology ; Bacteria/genetics ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Since the coronavirus disease 2019 (COVID-19) outbreak, many COVID-19 variants have emerged, causing several waves of pandemics and many infections. Long COVID-19, or long-term sequelae after recovery from COVID-19, has aroused worldwide concern because it reduces patient quality of life after rehabilitation. We aimed to characterize the functional differential profile of the oral and gut microbiomes and serum metabolites in patients with gastrointestinal symptoms associated with long COVID-19.

METHODS: We prospectively collected oral, fecal, and serum samples from 983 antibiotic-naïve patients with mild COVID-19 and performed a 3-month follow-up postdischarge. Forty-five fecal and saliva samples, and 25 paired serum samples were collected from patients with gastrointestinal symptoms of long COVID-19 at follow-up and from healthy controls, respectively. Eight fecal and saliva samples were collected without gastrointestinal symptoms of long COVID-19 at follow-up. Shotgun metagenomic sequencing of fecal samples and 2bRAD-M sequencing of saliva samples were performed on these paired samples. Two published COVID-19 gut microbiota cohorts were analyzed for comparison. Paired serum samples were analyzed using widely targeted metabolomics.

RESULTS: Mild COVID-19 patients without gastrointestinal symptoms of long COVID-19 showed little difference in the gut and oral microbiota during hospitalization and at follow-up from healthy controls. The baseline and 3-month samples collected from patients with gastrointestinal symptoms associated with long COVID-19 showed significant differences, and ectopic colonization of the oral cavity by gut microbes including 27 common differentially abundant genera in the Proteobacteria phylum, was observed at the 3-month timepoint. Some of these bacteria, including Neisseria, Lautropia, and Agrobacterium, were highly related to differentially expressed serum metabolites with potential toxicity, such as 4-chlorophenylacetic acid, 5-sulfoxymethylfurfural, and estradiol valerate.

CONCLUSIONS: Our study characterized the changes in and correlations between the oral and gut microbiomes and serum metabolites in patients with gastrointestinal symptoms associated with long COVID-19. Additionally, our findings reveal that ectopically colonized bacteria from the gut to the oral cavity could exist in long COVID-19 patients with gastrointestinal symptoms, with a strong correlation to some potential harmful metabolites in serum.}, } @article {pmid37468677, year = {2023}, author = {Banas, I and Esser, SP and Turzynski, V and Soares, A and Novikova, P and May, P and Moraru, C and Hasenberg, M and Rahlff, J and Wilmes, P and Klingl, A and Probst, AJ}, title = {Spatio-functional organization in virocells of small uncultivated archaea from the deep biosphere.}, journal = {The ISME journal}, volume = {17}, number = {10}, pages = {1789-1792}, pmid = {37468677}, issn = {1751-7370}, support = {863664/ERC_/European Research Council/International ; }, mesh = {*Archaea/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Viruses/genetics ; DNA, Viral/genetics ; }, abstract = {Despite important ecological roles posited for virocells (i.e., cells infected with viruses), studying individual cells in situ is technically challenging. We introduce here a novel correlative microscopic approach to study the ecophysiology of virocells. By conducting concerted virusFISH, 16S rRNA FISH, and scanning electron microscopy interrogations of uncultivated archaea, we linked morphologies of various altiarchaeal cells to corresponding phylogenetic signals and indigenous virus infections. While uninfected cells exhibited moderate separation between fluorescence signals of ribosomes and DNA, virocells displayed complete cellular segregation of chromosomal DNA from viral DNA, the latter co-localizing with host ribosome signals. A similar spatial separation was observed in dividing cells, with viral signals congregating near ribosomes at the septum. These observations suggest that replication of these uncultivated viruses occurs alongside host ribosomes, which are used to generate the required proteins for virion assembly. Heavily infected cells sometimes displayed virus-like particles attached to their surface, which agree with virus structures in cells observed via transmission electron microscopy. Consequently, this approach is the first to link genomes of uncultivated viruses to their respective structures and host cells. Our findings shed new light on the complex ecophysiology of archaeal virocells in deep subsurface biofilms and provide a solid framework for future in situ studies of virocells.}, } @article {pmid37468676, year = {2023}, author = {Neukirchen, S and Pereira, IAC and Sousa, FL}, title = {Stepwise pathway for early evolutionary assembly of dissimilatory sulfite and sulfate reduction.}, journal = {The ISME journal}, volume = {17}, number = {10}, pages = {1680-1692}, pmid = {37468676}, issn = {1751-7370}, support = {803768/ERC_/European Research Council/International ; }, mesh = {Phylogeny ; Oxidation-Reduction ; *Hydrogensulfite Reductase/genetics/metabolism ; *Proteins/metabolism ; Sulfates/metabolism ; Sulfites ; Sulfur/metabolism ; Oxidoreductases Acting on Sulfur Group Donors/genetics ; }, abstract = {Microbial dissimilatory sulfur metabolism utilizing dissimilatory sulfite reductases (Dsr) influenced the biochemical sulfur cycle during Earth's history and the Dsr pathway is thought to be an ancient metabolic process. Here we performed comparative genomics, phylogenetic, and synteny analyses of several Dsr proteins involved in or associated with the Dsr pathway across over 195,000 prokaryotic metagenomes. The results point to an archaeal origin of the minimal DsrABCMK(N) protein set, having as primordial function sulfite reduction. The acquisition of additional Dsr proteins (DsrJOPT) increased the Dsr pathway complexity. Archaeoglobus would originally possess the archaeal-type Dsr pathway and the archaeal DsrAB proteins were replaced with the bacterial reductive-type version, possibly at the same time as the acquisition of the QmoABC and DsrD proteins. Further inventions of two Qmo complex types, which are more spread than previously thought, allowed microorganisms to use sulfate as electron acceptor. The ability to use the Dsr pathway for sulfur oxidation evolved at least twice, with Chlorobi and Proteobacteria being extant descendants of these two independent adaptations.}, } @article {pmid37468551, year = {2023}, author = {Słowakiewicz, M and Perri, E and Tagliasacchi, E and Działak, P and Borkowski, A and Gradziński, M and Kele, S and Tucker, ME}, title = {Viruses participate in the organomineralization of travertines.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {11663}, pmid = {37468551}, issn = {2045-2322}, mesh = {Humans ; Ecosystem ; *Viruses ; *Bacteriophages/genetics ; *Podoviridae/ultrastructure ; *Siphoviridae/genetics/ultrastructure ; }, abstract = {Travertines, which precipitate from high temperature water saturated with calcium carbonate, are generally considered to be dominated by physico-chemical and microbial precipitates. Here, as an additional influence on organomineral formation, metagenomic data and microscopic analyses clearly demonstrate that highly diverse viral, bacterial and archaeal communities occur in the biofilms associated with several modern classic travertine sites in Europe and Asia, along with virus-like particles. Metagenomic analysis reveals that bacteriophages (bacterial viruses) containing icosahedral capsids and belonging to the Siphoviridae, Myoviridae and Podoviridae families are the most abundant of all viral strains, although the bacteriophage distribution does vary across the sampling sites. Icosahedral shapes of capsids are also the most frequently observed under the microscope, occurring as non-mineralized through to mineralized viruses and virus-like particles. Viruses are initially mineralized by Ca-Si amorphous precipitates with subordinate Mg and Al contents; these then alter to nanospheroids composed of Ca carbonate with minor silicate 80-300 nm in diameter. Understanding the roles of bacteriophages in modern carbonate-saturated settings and related organomineralization processes is critical for their broader inclusion in the geological record and ecosystem models.}, } @article {pmid37468299, year = {2023}, author = {Pedrosa, DA and Bruniera Peres Fernandes, G and Filipe de Souza Godoy, L and C Felício, A and Pinho, JR and Mário Doi, A and de Araújo Gleizer, R}, title = {Neurocysticercosis: diagnosis via metagenomic next-generation sequencing.}, journal = {Practical neurology}, volume = {23}, number = {6}, pages = {509-511}, doi = {10.1136/pn-2023-003795}, pmid = {37468299}, issn = {1474-7766}, mesh = {Female ; Humans ; Aged ; *Neurocysticercosis/diagnosis/genetics ; *Meningitis ; Brain/diagnostic imaging ; *Hydrocephalus ; High-Throughput Nucleotide Sequencing ; }, abstract = {A 68-year-old Brazilian woman had 3 months of progressive fatigue, difficulty walking and 18 kg weight loss. On examination, there was gait apraxia and executive dysfunction. MR scan of brain showed communicating hydrocephalus and a cerebrospinal fluid showed 105 white cells/µL (≤5), predominantly lymphocytes, protein of 1.35 g/L (0.15-0.45) and the glucose content of 0.06 mmol/L (3.3-4.4). We suspected an infective cause and used of metagenomic next-generation sequencing to diagnose neurocysticercosis. This case highlights the challenge of diagnosing chronic meningitis and the relevance of genetic approaches in diagnosing neurological infections.}, } @article {pmid37468017, year = {2023}, author = {Li, X and Fan, S and Zhang, Y and Li, D and Su, C and Qi, Z and Liang, H and Gao, S and Chen, M}, title = {Performance and microbial metabolic mechanism of imidacloprid removal in a microbial electrolysis cell-integrated adsorption biological coupling system.}, journal = {Bioresource technology}, volume = {386}, number = {}, pages = {129513}, doi = {10.1016/j.biortech.2023.129513}, pmid = {37468017}, issn = {1873-2976}, mesh = {*Wastewater ; *Waste Disposal, Fluid/methods ; Adsorption ; Electrolysis ; }, abstract = {Coke used as a filler to treat imidacloprid (IMI) wastewater by both adsorption biological coupling and microbial electrolysis cells (MEC)-adsorption biological coupling technologies, the removal efficiencies on pollutions in wastewater containing IMI were investigated, and the key functional genes related to IMI degradation pathways were also revealed. Results showed that the removal rates of COD, ammonia nitrogen, TP, and IMI under the adsorption biological coupling treatment and MEC-adsorption biological coupling treatment were 94.61-95.54%, 93.37-95.79%, 73.69-83.80%, and 100%, respectively. MEC increased the relative abundance of Proteobacteria by 9.01% and transformed the dominant bacteria from Lysobacter and Reyranella to Brevundimonas and Aquincola. Moreover, MEC up-regulated the abundance of the coding genes PK (9.30%), narG (2.26%), pstS (3.63%), and phnD (1.32%), and converted the IMI degradation products to smaller molecular weight C6H8N2 and C6H6ClNO. This study provided an important reference information for efficient treatment of IMI wastewater using the MEC-adsorption biological coupling technology.}, } @article {pmid37467988, year = {2023}, author = {Wu, ZH and Yang, XD and Huang, LY and Li, SL and Xia, FY and Qiu, YZ and Yi, XZ and Jia, P and Liao, B and Liang, JL and Shu, WS and Li, JT}, title = {In situ enrichment of sulphate-reducing microbial communities with different carbon sources stimulating the acid mine drainage sediments.}, journal = {The Science of the total environment}, volume = {898}, number = {}, pages = {165584}, doi = {10.1016/j.scitotenv.2023.165584}, pmid = {37467988}, issn = {1879-1026}, mesh = {*Sulfates ; Phylogeny ; Bacteria/genetics ; Archaea ; *Microbiota ; Acids ; }, abstract = {The applications of sulphate-reducing microorganisms (SRMs) in acid mine drainage (AMD) treatment systems have received extensive attention due to their ability to reduce sulphate and stabilize metal(loid)s. Despite great phylogenetic diversity of SRMs, only a few have been used in AMD treatment bioreactors. In situ enrichment could be an efficient approach to select new effective SRMs for AMD treatment. Here, we performed in situ enrichment of SRMs in highly stratified AMD sediment cores using different kinds of carbon source mixture. The dsrAB (dissimilatory sulfite reductase) genes affiliated with nine phyla (two archaeal and seven bacterial phyla) and 26 genera were enriched. Remarkably, those genes affiliated with Aciduliprofundum and Vulcanisaeta were enriched in situ in AMD-related environments for the first time, and their relative abundances were negatively correlated with pH. Furthermore, 107 dsrAB-containing metagenome-assembled genomes (MAGs) were recovered from metagenomic datasets, with 14 phyla (two archaeal and 12 bacterial phyla) and 15 genera. The relative abundances of MAGs were positively correlated with total carbon and sulphate contents. Our findings expanded the diversity of SRMs that can be enriched in AMD sediment, and revealed the physiochemical properties that might affect the growth of SRMs, which provided guidance for AMD treatment bioreators.}, } @article {pmid37467933, year = {2023}, author = {George, U and George, O and Oguzie, J and Osasona, O and Motayo, B and Kamani, J and Eromon, P and Folarin, O and Happi, A and Komolafe, I and Happi, C}, title = {Genomic characterization of Alphacoronavirus from Mops condylurus bats in Nigeria.}, journal = {Virus research}, volume = {334}, number = {}, pages = {199174}, pmid = {37467933}, issn = {1872-7492}, support = {U01 HG007480/HG/NHGRI NIH HHS/United States ; U01 AI151812/AI/NIAID NIH HHS/United States ; U54 HG007480/HG/NHGRI NIH HHS/United States ; 216,619/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Alphacoronavirus/genetics ; *Chiroptera ; Phylogeny ; Nigeria ; Genome, Viral ; *Coronavirus/genetics ; *Coronavirus Infections/epidemiology/veterinary/genetics ; Genomics ; }, abstract = {Coronaviruses (CoVs) are responsible for sporadic, epidemic and pandemic respiratory diseases worldwide. Bats have been identified as the reservoir for CoVs. To increase the number of complete coronavirus genomes in Africa and to comprehend the molecular epidemiology of bat Alphacoronaviruses (AlphaCoVs), we used deep metagenomics shotgun sequencing to obtain three (3) near-complete genomes of AlphaCoVs from Mops condylurus (Angolan free-tailed) bat in Nigeria. Phylogenetic and pairwise identity analysis of open reading frame 1ab (ORF1ab), spike (S), envelope (E), membrane (M) and nucleocapsid (N) genes of AlphaCoV in this study to previously described AlphaCoVs subgenera showed that the Nigerian AlphaCoVs may be members of potentially unique AlphaCoV subgenera circulating exclusively in bats in the Molossidae bat family. Recombination events were detected, suggesting the evolution of AlphaCoVs within the Molossidae family. The pairwise identity of the S gene in this study and previously published S gene sequences of other AlphaCoVs indicate that the Nigerian strains may have a genetically unique spike protein that is distantly related to other AlphaCoVs. Variations involving non-polar to polar amino acid substitution in both the Heptad Repeat (HR) regions 1 and 2 were observed. Further monitoring of bats to understand the host receptor use requirements of CoVs and interspecies CoV transmission in Africa is necessary to identify and prevent the potential danger that bat CoVs pose to public health.}, } @article {pmid37467722, year = {2023}, author = {D'Adamo, GL and Chonwerawong, M and Gearing, LJ and Marcelino, VR and Gould, JA and Rutten, EL and Solari, SM and Khoo, PWR and Wilson, TJ and Thomason, T and Gulliver, EL and Hertzog, PJ and Giles, EM and Forster, SC}, title = {Bacterial clade-specific analysis identifies distinct epithelial responses in inflammatory bowel disease.}, journal = {Cell reports. Medicine}, volume = {4}, number = {7}, pages = {101124}, pmid = {37467722}, issn = {2666-3791}, mesh = {Humans ; *Inflammatory Bowel Diseases/genetics ; Colon/pathology ; Biopsy ; Intestinal Mucosa/microbiology ; Epithelial Cells/pathology ; }, abstract = {Abnormal immune responses to the resident gut microbiome can drive inflammatory bowel disease (IBD). Here, we combine high-resolution, culture-based shotgun metagenomic sequencing and analysis with matched host transcriptomics across three intestinal sites (terminal ileum, cecum, rectum) from pediatric IBD (PIBD) patients (n = 58) and matched controls (n = 42) to investigate this relationship. Combining our site-specific approach with bacterial culturing, we establish a cohort-specific bacterial culture collection, comprising 6,620 isolates (170 distinct species, 32 putative novel), cultured from 286 mucosal biopsies. Phylogeny-based, clade-specific metagenomic analysis identifies key, functionally distinct Enterococcus clades associated with either IBD or health. Strain-specific in vitro validation demonstrates differences in cell cytotoxicity and inflammatory signaling in intestinal epithelial cells, consistent with the colonic mucosa-specific response measured in patients with IBD. This demonstrates the importance of strain-specific phenotypes and consideration of anatomical sites in exploring the dysregulated host-bacterial interactions in IBD.}, } @article {pmid37467538, year = {2023}, author = {Hu, L and Zhang, S and Chai, S and Lyu, Y and Wang, S and Feng, Z}, title = {Discovery of two bifunctional/multifunctional cellulases by functional metagenomics.}, journal = {Enzyme and microbial technology}, volume = {169}, number = {}, pages = {110288}, doi = {10.1016/j.enzmictec.2023.110288}, pmid = {37467538}, issn = {1879-0909}, mesh = {*Cellulases/genetics/metabolism ; *Cellulase/genetics/metabolism ; Metagenomics ; Phylogeny ; Glucose ; Substrate Specificity ; }, abstract = {Cellulases are widely used in industry, and the usage in bioconversion of biofuels makes cellulases more valuable. In this study, two tandem genes that encoded cellulases ZF994-1 and ZF994-2, respectively, were identified on a cosmid from a soil metagenomic library. Phylogenetic analysis indicated that ZF994-1 and ZF994-2 belonged to glycoside hydrolase family 12 (GH12), and GH3, respectively. Based on the substrate specificity analysis, the recombinant ZF994-1 exhibited weak endoglucanase activity, moderate β-1,3-glucanase and β-1,4-mannanase activities, and strong β-glucosidase activity, while the recombinant ZF994-2 exhibited moderate endoglucanase activity and strong β-glucosidase activity. More than 45% β-glucosidase activity of the recombinant ZF994-1 retained in the buffer containing 3 M glucose, indicating the good tolerance against glucose. The recombinant ZF994-2 showed high activity in the presence of metal ions and organic reagents, exhibiting potential industrial applications.}, } @article {pmid37467522, year = {2023}, author = {Weiss, ZF and Pyden, AD and Jhaveri, TA and Kanjilal, S}, title = {The diagnostic and clinical utility of microbial cell-free DNA sequencing in a real-world setting.}, journal = {Diagnostic microbiology and infectious disease}, volume = {107}, number = {2}, pages = {116004}, doi = {10.1016/j.diagmicrobio.2023.116004}, pmid = {37467522}, issn = {1879-0070}, mesh = {Humans ; *Cell-Free Nucleic Acids ; Retrospective Studies ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {Microbial cell free DNA sequencing is increasingly used for diagnosis of infection but few studies describe its utility in real-world settings. We performed a single-center retrospective case series of microbial cell free DNA testing using the Karius assay from 29 patient samples to define the clinical reasoning and the impact of testing. Indications fell into 3 categories, identifying a causative pathogen in patients with an infectious syndrome and negative microbiologic workup (15/29, 52%), seeking another pathogen when organisms identified by traditional diagnostics failed to explain the clinical presentation (9/29, 31%) and to "rule out" infection in patients with nonspecific symptoms and negative microbiologic workup (5/29, 17%). Clinical impact was positive in 13/29 (45%) and all were for patients with high pretest probability for infection. Impact was negative in 3/29 (10%) cases. There was no impact in 15/29 (52%) cases. Further work is needed to define the optimal timing accounting for test performance, and patient characteristics.}, } @article {pmid37467434, year = {2023}, author = {Huang, L and Levintal, E and Erikson, CB and Coyotl, A and Horwath, WR and Dahlke, HE and Mazza Rodrigues, JL}, title = {Molecular and Dual-Isotopic Profiling of the Microbial Controls on Nitrogen Leaching in Agricultural Soils under Managed Aquifer Recharge.}, journal = {Environmental science & technology}, volume = {57}, number = {30}, pages = {11084-11095}, pmid = {37467434}, issn = {1520-5851}, mesh = {*Nitrogen/analysis ; Soil ; Agriculture ; Isotopes/analysis ; Nitrates/analysis ; *Groundwater ; }, abstract = {Nitrate (NO3[-]) leaching is a serious health and ecological concern in global agroecosystems, particularly those under the application of agricultural-managed aquifer recharge (Ag-MAR); however, there is an absence of information on microbial controls affecting NO3[-] leaching outcomes. We combine natural dual isotopes of NO3[-] ([15]N/[14]N and [18]O/[16]O) with metagenomics, quantitative polymerase chain reaction (PCR), and a threshold indicator taxa analysis (TITAN) to investigate the activities, taxon profiles, and environmental controls of soil microbiome associated with NO3[-] leaching at different depths from Californian vineyards under Ag-MAR application. The isotopic signatures demonstrated a significant priming effect (P < 0.01) of Ag-MAR on denitrification activities in the topsoil (0-10 cm), with a 12-25-fold increase of [15]N-NO3[-] and [18]O-NO3[-] after the first 24 h of flooding, followed by a sharp decrease in the enrichment of both isotopes with ∼80% decline in denitrification activities thereafter. In contrast, deeper soils (60-100 cm) showed minimal or no denitrification activities over the course of Ag-MAR application, thus resulting in 10-20-fold of residual NO3[-] being leached. Metagenomic profiling and laboratory microcosm demonstrated that both nitrifying and denitrifying groups, responsible for controlling NO3[-] leaching, decreased in abundance and potential activity rates with soil depth. TITAN suggested that Nitrosocosmicus and Bradyrhizobium, as the major nitrifier and denitrifier, had the highest and lowest tipping points with regard to the NO3[-] changes (P < 0.05), respectively. Overall, our study provides new insight into specific depth limitations of microbial controls on soil NO3[-] leaching in agroecosystems.}, } @article {pmid37466699, year = {2023}, author = {Su, X and Xu, FQ and Chen, SJ and Gou, F and Shi, YC and Xing, ZL and Peng, RQ and Deng, YY and Zhang, T and Xiong, J and Zhao, TT}, title = {Microecological health assessment of water environment and sediment based on metagenomics: a case study of Guixi River in Chongqing, China.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {8}, pages = {970}, pmid = {37466699}, issn = {1573-2959}, support = {gzlcx20223150//Chongqing University of Technology Graduate Education High Quality Development Project/ ; 2022NSCQ-MSX1077//the Chongqing NSF Project/ ; KJQN202201131//Scientific and Technological Research Program of Chongqing Municipal Education Commission/ ; 2022118//the Research and Demonstration Project on Coordinated Innovation of Good Ecological Background and Ecological Product Value Realization/ ; cstc2021jszx-cylhx0013//the Chongqing Technology Innovation and Application Development Project/ ; }, mesh = {Humans ; *Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; Rivers/chemistry ; Anti-Bacterial Agents/analysis ; Metagenomics ; Geologic Sediments/chemistry ; Nitrogen/analysis ; Phosphorus/analysis ; Drug Resistance, Bacterial ; Macrolides/analysis ; China ; Water/analysis ; }, abstract = {River sediment is vital in containing water pollution and strengthening water remediation. This paper has conducted a study on the microecological health assessment of the sediment and water body of Guixi River in Dianjiang, Chongqing, China, using metagenomics sequencing and microbial biological integrity index (M-IBI) technology. The analysis of physical and chemical characteristics shows that the concentration of TN varies from 2.62 to 9.76 mg/L in each sampling section, and the eutrophication of the water body is relatively severe. The proportion of Cyanobacteria in the sampling section at the sink entrance is higher than that of other sites, where there are outbreaks of water blooms and potential hazards to human health. The dominant functions of each site include carbon metabolism, TCA cycle, and pyruvate metabolism. In addition, the main virulence factors and antibiotic resistance genes in sediment are Type IV pili (VF0082), LOS (CVF494), MymA operon (CVF649), and macrolide resistance genes macB, tetracyclic tetA (58), and novA. Correlation analysis of environmental factors and microorganisms was also performed, and it was discovered that Thiothrix and Acidovorax had obvious gene expression in the nitrogen metabolism pathway, and the Guixi River Basin had a self-purification capacity. Finally, based on the microecological composition of sediment and physical and chemical characteristics of the water body, the health assessment was carried out, indicating that the main pollution area was Dianjiang Middle School and the watershed near the sewage treatment plant. The findings should theoretically support an in-depth assessment of the water environment's microecological health.}, } @article {pmid37466435, year = {2023}, author = {Wang, Z and Song, W and Zhang, X and Zheng, M and Li, H and Yu, K and Guo, F}, title = {Expanding the Diversity of Accumulibacter with a Novel Type and Deciphering the Transcriptional and Morphological Features among Co-Occurring Strains.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {8}, pages = {e0077123}, pmid = {37466435}, issn = {1098-5336}, mesh = {Phylogeny ; In Situ Hybridization, Fluorescence ; *Betaproteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Phosphorus/metabolism ; Bioreactors ; Polyphosphates/metabolism ; Sewage ; }, abstract = {"Candidatus Accumulibacter" is the major polyphosphate-accumulating organism (PAO) in global wastewater treatment systems, and its phylogenetic and functional diversity have expanded in recent years. In addition to the widely recognized type I and II sublineages, we discovered a novel type enriched in laboratory bioreactors. Core gene and machine learning-based gene feature profiling supported the assertion that type III "Ca. Accumulibacter" is a potential PAO with the unique function of using dimethyl sulfoxide as an electron acceptor. Based on the correlation between ppk1 and genome similarity, the species-level richness of Accumulibacter was estimated to be over 100, suggesting that the currently recognized species are only the tip of the iceberg. Meanwhile, the interstrain transcriptional and morphological features of multiple "Ca. Accumulibacter" strains co-occurring in a bioreactor were investigated. Metatranscriptomics of seven co-occurring strains indicated that the expression level and interphasic dynamics of PAO phenotype-related genes had minimal correlation with their phylogeny. In particular, the expression of denitrifying and polyphosphate (poly-P) metabolism genes exhibited higher interstrain and interphasic divergence than expression of glycogen and polyhydroxyalkanoate metabolic genes. A strategy of cloning rRNA genes from different strains based on similar genomic synteny was successfully applied to differentiate their morphology via fluorescence in situ hybridization. Our study further expands the phylogenetic and functional diversity of "Ca. Accumulibacter" and proposes that deciphering the function and capability of certain "Ca. Accumulibacter" should be tailored to the environment and population in question. IMPORTANCE In the last 2 decades, "Ca. Accumulibacter" has garnered significant attention as the core functional but uncultured taxon for enhanced biological phosphorus removal due to its phylogenetic and functional diversity and intragenus niche differentiation. Since 2002, it has been widely known that this genus has two sublineages (type I and II). However, in this study, a metagenomic approach led to the discovery of a novel type (type III) with proposed novel functional features. By comparing the average nucleotide identity of "Ca. Accumulibacter" genomes and the similarity of ppk1, a phylogenetic biomarker largely deposited in databases, the global species-level richness of "Ca. Accumulibacter" was estimated for the first time to be over 100. Furthermore, we observed the co-occurrence of multiple "Ca. Accumulibacter" strains in a single bioreactor and found the simultaneous transcriptional divergence of these strains intriguing with regard to their niche differentiation within a single community. Our results indicated a decoupling feature between transcriptional pattern and phylogeny for co-occurring strains.}, } @article {pmid37466138, year = {2023}, author = {Zhang, YZ and Liu, Y and Bai, Z and Fujimoto, K and Uematsu, S and Imoto, S}, title = {Zero-shot-capable identification of phage-host relationships with whole-genome sequence representation by contrastive learning.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {5}, pages = {}, pmid = {37466138}, issn = {1477-4054}, mesh = {*Bacteriophages/genetics ; Genome, Viral ; Whole Genome Sequencing ; Chromosome Mapping ; }, abstract = {Accurately identifying phage-host relationships from their genome sequences is still challenging, especially for those phages and hosts with less homologous sequences. In this work, focusing on identifying the phage-host relationships at the species and genus level, we propose a contrastive learning based approach to learn whole-genome sequence embeddings that can take account of phage-host interactions (PHIs). Contrastive learning is used to make phages infecting the same hosts close to each other in the new representation space. Specifically, we rephrase whole-genome sequences with frequency chaos game representation (FCGR) and learn latent embeddings that 'encapsulate' phages and host relationships through contrastive learning. The contrastive learning method works well on the imbalanced dataset. Based on the learned embeddings, a proposed pipeline named CL4PHI can predict known hosts and unseen hosts in training. We compare our method with two recently proposed state-of-the-art learning-based methods on their benchmark datasets. The experiment results demonstrate that the proposed method using contrastive learning improves the prediction accuracy on known hosts and demonstrates a zero-shot prediction capability on unseen hosts. In terms of potential applications, the rapid pace of genome sequencing across different species has resulted in a vast amount of whole-genome sequencing data that require efficient computational methods for identifying phage-host interactions. The proposed approach is expected to address this need by efficiently processing whole-genome sequences of phages and prokaryotic hosts and capturing features related to phage-host relationships for genome sequence representation. This approach can be used to accelerate the discovery of phage-host interactions and aid in the development of phage-based therapies for infectious diseases.}, } @article {pmid37465976, year = {2023}, author = {White, MG and Damania, A and Alshenaifi, J and Sahasrabhojane, P and Peacock, O and Losh, J and Wong, MC and Lutter-Berkova, Z and Chang, GJ and Futreal, A and Wargo, JA and Ajami, NJ and Kopetz, S and You, YN}, title = {Young-onset Rectal Cancer: Unique Tumoral Microbiome and Correlation With Response to Neoadjuvant Therapy.}, journal = {Annals of surgery}, volume = {278}, number = {4}, pages = {538-548}, pmid = {37465976}, issn = {1528-1140}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Middle Aged ; Neoadjuvant Therapy ; *Rectal Neoplasms/therapy/pathology ; Biopsy ; *Microbiota ; }, abstract = {OBJECTIVE: External exposures, the host, and the microbiome interact in oncology. We aimed to investigate tumoral microbiomes in young-onset rectal cancers (YORCs) for profiles potentially correlative with disease etiology and biology.

BACKGROUND: YORC is rapidly increasing, with 1 in 4 new rectal cancer cases occurring under the age of 50 years. Its etiology is unknown.

METHODS: YORC (<50 y old) or later-onset rectal cancer (LORC, ≥50 y old) patients underwent pretreatment biopsied of tumor and tumor-adjacent normal (TAN) tissue. After whole genome sequencing, metagenomic analysis quantified microbial communities comparing tumors versus TANs and YORCs versus LORCs, controlling for multiple testing. Response to neoadjuvant therapy (NT) was categorized as major pathological response (MPR, ≤10% residual viable tumor) versus non-MPR.

RESULTS: Our 107 tumors, 75 TANs from 37 (35%) YORCs, and 70 (65%) LORCs recapitulated bacterial species were previously associated with colorectal cancers (all P <0.0001). YORC and LORC tumoral microbiome signatures were distinct. After NT, 13 patients (12.4%) achieved complete pathologic response, whereas MPR occurred in 47 patients (44%). Among YORCs, MPR was associated with Fusobacterium nucleaum , Bacteroides dorei, and Ruminococcus bromii (all P <0.001), but MPR in LORC was associated with R. bromii (P <0.001). Network analysis of non-MPR tumors demonstrated a preponderance of oral bacteria not observed in MPR tumors.

CONCLUSIONS: Microbial signatures were distinct between YORC and LORC. Failure to achieve an MPR was associated with oral bacteria in tumors. These findings urge further studies to decipher correlative versus mechanistic associations but suggest a potential for microbial modulation to augment current treatments.}, } @article {pmid37465762, year = {2023}, author = {Sun, G and Liu, W and Zheng, Q and Shan, Q and Hou, H}, title = {Ratio of procalcitonin/Simpson's dominance index predicted the short-term prognosis of patients with severe bacterial pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1175747}, pmid = {37465762}, issn = {2235-2988}, mesh = {Humans ; Procalcitonin ; *Sepsis/metabolism ; Sensitivity and Specificity ; Retrospective Studies ; C-Reactive Protein ; *Pneumonia, Bacterial/diagnosis ; }, abstract = {OBJECTIVE: The aim of this study was to explore the predictive value of the ratio of procalcitonin (PCT) in serum to Simpson's dominance index (SDI) in bronchoalveolar lavage fluid (BALF), in short-term prognosis of patients with severe bacterial pneumonia (SBP).

METHODS: This is a retrospective review of case materials of 110 patients with SBP who selected BALF metagenomic next-generation sequencing technique in the intensive care unit (ICU) of the Affiliated Hospital of Yangzhou University from January 2019 and July 2022. Based on the acute physiology and chronic health status score II, within 24 h after admission to the ICU, patients were divided into a non-critical group (n = 40) and a critical group (n = 70). Taking death caused by bacterial pneumonia as the endpoint event, the 28-day prognosis was recorded, and the patients were divided into a survival group (n = 76) and a death group (n = 34). The SDI, PCT, C-reactive protein (CRP), PCT/SDI, and CRP/SDI were compared and analyzed.

RESULTS: Compared with the non-critical group, the critical group had a higher PCT level, a greater PCT/SDI ratio, a longer ventilator-assisted ventilation time (VAVT), and more deaths in 28 days. Compared with the survivors, the death group had a higher PCT level, a lower SDI level, and a greater PCT/SDI ratio. The SDI level was significantly negatively correlated with the VAVT (r = -0.675, p < 0.05), while the PCT level, ratio of PCT/SDI, and ratio of CRP/SDI were remarkably positively correlated with VAVT (r = 0.669, 0.749, and 0.718, respectively, p < 0.05). The receiver operating characteristic (ROC) curves analysis showed that the area under ROC curves of PCT/SDI predicting patient death within 28 days was 0.851, followed by PCT + SDI, PCT, SDI, and CRP/SDI (0.845, 0.811, 0.778, and 0.720, respectively). The sensitivity and specificity of PCT/SDI for predicting death were 94.1% and 65.8%, respectively, at the optimal value (11.56). Cox regression analysis displayed that PCT/SDI (HR = 1.562; 95% CI: 1.271 to 1.920; p = 0.039) and PCT (HR = 1.148; 95% CI: 1.105 to 1.314; p = 0.015) were independent predictors of death in patients.

CONCLUSION: The ratio of PCT/SDI was a more valuable marker in predicting the 28-day prognosis in patients with SBP.}, } @article {pmid37465760, year = {2023}, author = {Song, WJ and Gao, J and Huang, JW and Liu, Y and Long, Z and He, LY}, title = {Is type III prostatitis also associated with bacterial infection?.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1189081}, pmid = {37465760}, issn = {2235-2988}, mesh = {Male ; Humans ; *Prostatitis/complications/diagnosis ; RNA, Ribosomal, 16S/genetics ; Chronic Disease ; *Bacterial Infections/complications/microbiology ; Bacteria/genetics ; }, abstract = {OBJECTIVE: To explore whether type III prostatitis is related to bacterial infection by detecting the composition and function of microorganisms in expressed prostatic secretion (EPS) of patients with chronic prostatitis (CP) and healthy people.

METHODS: According to the inclusion and exclusion criteria, 57 subjects were included in our study, divided into the healthy group, type II prostatitis group, and type III prostatitis group. 16s rRNA sequencing technique was used to detect and analyze the microbial composition of EPS in each group. Additionally, the metagenomics sequencing technique was used to further explore the function of different bacteria in the type III prostatitis group. Data analysis was performed by bioinformatics software, and the results were statistically significant when P<0.05.

RESULTS: Many microorganisms exist in EPS in both CP patients and healthy populations. However, the relative abundance of Pseudomonas, Haemophilus, Sneathia, Allobaculum, and Enterococcus in CP patients (including type II and III) were significantly different. Still, the relative abundance of different bacteria in type II prostatitis patients was much higher than in type III. The metagenomics sequencing results for the type III prostatitis group showed that the different bacteria had certain biological functions.

CONCLUSION: Based on our sequencing results and previous studies, we suggest that type III prostatitis may also be caused by bacterial infection.}, } @article {pmid37465353, year = {2023}, author = {Xie, S and Yang, X and Xia, H and Lai, J and Liu, Q and Lu, Z and He, D and Liu, X}, title = {Clinical features of varicella-zoster virus caused neurological diseases detected by metagenomic next-generation sequencing.}, journal = {Open medicine (Warsaw, Poland)}, volume = {18}, number = {1}, pages = {20230744}, pmid = {37465353}, issn = {2391-5463}, abstract = {Clinical presentation of central nervous system (CNS) infections caused by varicella-zoster virus (VZV) is highly sophisticated, making identification challenging. We retrospectively reported 18 cases of VZV neurologic disease confirmed by metagenomic next-generation sequencing (mNGS). The detection rate of mNGS was higher than that of PCR assay (100 vs 66.7%, p < 0.05) and serum IgM antibody (100 vs 68.8%, p < 0.05) measurement. Of the 18 cases, five patients were diagnosed with acute meningitis, three with acute meningitis combined with facial neuritis, three with acute meningitis combined with polycranial neuritis, and the remaining seven with various clinical diagnoses. Typical clinical symptoms included headache (15), fever (9), and rash (11). Cranial or spinal MRI showed abnormalities in 12 patients, and 17 patients had obvious neurological symptoms. The predominant genotype of VZV in this study was genotype J (100%, 10/10). All patients were treated with acyclovir/penciclovir and dexamethasone, 16 recovered and 2 died. Our study highlights the good performance of mNGS in diagnosing CNS infection caused by VZV. It could provide additional diagnostic evidence in patients with diverse clinical spectrum and variable manifestations.}, } @article {pmid37465185, year = {2023}, author = {Nan, X and Yu, J and Liang, Y and Lou, P and Pan, G}, title = {Application of Different Sampling Methods Combined with Metagenomic Next-Generation Sequencing to Detect Pathogens in Children with Severe Pneumonia on Mechanical Ventilation.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {4545-4553}, pmid = {37465185}, issn = {1178-6973}, abstract = {OBJECTIVE: The aim of this study was to explore the value of applying different sampling methods combined with metagenomic next-generation sequencing (mNGS) to detect pathogens in children with severe pneumonia on mechanical ventilation.

METHODS: Forty children with severe pneumonia on mechanical ventilation were selected, and routine endotracheal suctioning and bronchoalveolar lavage fluid (BALF) sampling methods were performed. The diagnostic efficacy of different sampling methods combined with mNGS versus traditional etiological pathogen detection strategies was compared.

RESULTS: The positive rate of mNGS pathogen detection after routine endotracheal suctioning and BALF sampling was higher than that of traditional etiological detection strategies (P < 0.05). There was no significant difference in the positive rates of pathogen detection by routine endotracheal suctioning + mNGS and BALF + mNGS (P > 0.05).

CONCLUSION: Compared with traditional etiological detection strategies, mNGS is more efficient for diagnosing pathogens. In clinical practice, an appropriate sampling method should be selected for mNGS-based detection according to the condition of the patient. These findings could be of great importance in the diagnosis and treatment of severe pneumonia.}, } @article {pmid37465181, year = {2023}, author = {Lin, L and Zhang, R and Zhang, Z and Chang, Y and Lin, R and Dou, H and Wang, H and Wang, Y and Zheng, B}, title = {Clinical Value of Metagenomics Next-Generation Sequencing in Antibiotic Resistance of a Patient with Severe Refractory Mycoplasma pneumoniae Pneumonia: A Case Report.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {4593-4597}, pmid = {37465181}, issn = {1178-6973}, abstract = {BACKGROUND: Mycoplasma pneumoniae is an important infectious pathogen of lower respiratory tract infection in children and adolescents. Macrolide resistant M. pneumoniae (MRMP) has become increasingly prevalent, and identifying pathogen resistance genes is crucial for treatment.

CASE PRESENTATION: We report a patient with severe refractory M. pneumoniae pneumonia (MPP). The failure of initial clinical treatment prompted the re-analysis of metagenomic next-generation sequencing (mNGS) data for macrolide-resistant gene. Macrolide-resistance 23S ribosomal RNA gene was confirmed with read depth of 64 X for the A2063G mutation, which can decrease the affinity of macrolide with M. pneumoniae ribosome resulting in macrolide resistance. Furthermore, antimicrobial susceptibility testing demonstrated that M. pneumoniae was resistant to macrolide. PCR confirmatory test about M. pneumoniae resistance A2063G mutation, clinical treatment course and prognosis with altered treatment strategy, and M. pneumoniae antimicrobial susceptibility confirmed that the severe refractory MPP was due to macrolide resistant M. pneumoniae.

CONCLUSION: As a new molecular level detection, mNGS is an effective method for detecting M. pneumoniae resistance genes. Early recognition of macrolide resistance and suitable antibiotics strategy is of vital importance for the prognosis of severe refractory MPP.}, } @article {pmid37465028, year = {2023}, author = {Thieringer, PH and Boyd, ES and Templeton, AS and Spear, JR}, title = {Metapangenomic investigation provides insight into niche differentiation of methanogenic populations from the subsurface serpentinizing environment, Samail Ophiolite, Oman.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1205558}, pmid = {37465028}, issn = {1664-302X}, abstract = {Serpentinization reactions produce highly reduced waters that have hyperalkaline pH and that can have high concentrations of H2 and CH4. Putatively autotrophic methanogenic archaea have been identified in the subsurface waters of the Samail Ophiolite, Sultanate of Oman, though the strategies to overcome hyperalkaline pH and dissolved inorganic carbon limitation remain to be fully understood. Here, we recovered metagenome assembled genomes (MAGs) and applied a metapangenomic approach to three different Methanobacterium populations to assess habitat-specific functional gene distribution. A Type I population was identified in the fluids with neutral pH, while a Type II and "Mixed" population were identified in the most hyperalkaline fluids (pH 11.63). The core genome of all Methanobacterium populations highlighted potential DNA scavenging techniques to overcome phosphate or nitrogen limitation induced by environmental conditions. With particular emphasis on the Mixed and Type II population found in the most hyperalkaline fluids, the accessory genomes unique to each population reflected adaptation mechanisms suggesting lifestyles that minimize niche overlap. In addition to previously reported metabolic capability to utilize formate as an electron donor and generate intracellular CO2, the Type II population possessed genes relevant to defense against antimicrobials and assimilating potential osmoprotectants to provide cellular stability. The accessory genome of the Mixed population was enriched in genes for multiple glycosyltransferases suggesting reduced energetic costs by adhering to mineral surfaces or to other microorganisms, and fostering a non-motile lifestyle. These results highlight the niche differentiation of distinct Methanobacterium populations to circumvent the challenges of serpentinization impacted fluids through coexistence strategies, supporting our ability to understand controls on methanogenic lifestyles and adaptations within the serpentinizing subsurface fluids of the Samail Ophiolite.}, } @article {pmid37465027, year = {2023}, author = {Wei, L and Zeng, B and Zhang, S and Guo, W and Li, F and Zhao, J and Li, Y}, title = {Hybridization altered the gut microbiota of pigs.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1177947}, pmid = {37465027}, issn = {1664-302X}, abstract = {Mammalian gut microbiota plays an important role in the host's nutrient metabolism, growth, and immune regulation. Hybridization can enable a progeny to acquire superior traits of the parents, resulting in the hybridization advantage. However, studies on the effects of hybridization on the pigs' gut microbiota are lacking. Therefore, this study used multi-omics technologies to compare and analyze the gut microbiota of the primary wild boar and its offspring. The 16S rRNA gene sequencing results revealed that the gut microbiota of F4 exhibited a host-like dominance phenomenon with a significant increase in the abundance of Lactobacillus and Bifidobacterium. The beta diversity of Duroc was significantly different from those of F0, F2, and F4; after the host hybridization, the similarity of the beta diversity in the progeny decreased with the decrease in the similarity of the F0 lineage. The metagenomic sequencing results showed that the significantly enriched metabolic pathways in F4, such as environmental, circulatory system, fatty acid degradation adaptation, and fatty acid biosynthesis, were similar to those in F0. Moreover, it also exhibited similar significantly enriched metabolic pathways as those in Duroc, such as carbohydrate metabolism, starch and sucrose metabolism, starch-degrading CAZymes, lactose-degrading CAZymes, and various amino acid metabolism pathways. However, the alpha-amylase-related KOs, lipid metabolism, and galactose metabolism in F4 were significantly higher than those in Duroc and F0. Non-targeted metabolome technology analysis found that several metabolites, such as docosahexaenoic acid, arachidonic acid, and citric acid were significantly enriched in the F4 pigs as compared to those in F0. Based on Spearman correlation analysis, Lactobacillus and Bifidobacterium were significantly positively correlated with these metabolites. Finally, the combined metagenomic and metabolomic analysis suggested that the metabolic pathways, such as valine, leucine, and isoleucine biosynthesis and alanine aspartate and glutamate metabolism were significantly enriched in F4 pigs. In conclusion, the gut microbiota of F4 showed a similar host "dominance" phenomenon, which provided reference data for the genetics and evolution of microbiota and the theory of microbial-assisted breeding.}, } @article {pmid37465026, year = {2023}, author = {Samad, A and Degenhardt, D and Séguin, A and Morency, MJ and Gagné, P and Martineau, C}, title = {Microbial community structural and functional differentiation in capped thickened oil sands tailings planted with native boreal species.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1168653}, pmid = {37465026}, issn = {1664-302X}, abstract = {The oil sands mining operations in Alberta have produced billions of m[3] of tailings which must be reclaimed and integrated into various mine closure landforms, including terrestrial landforms. Microorganisms play a central role in nutrient cycling during the reclamation of disturbed landscapes, contributing to successful vegetation restoration and long-term sustainability. However, microbial community succession and response in reconstructed and revegetated tailings remain largely unexplored. This study aimed to monitor the structural and functional responses of microbial communities in tailings subjected to different capping and vegetation strategies over two growing seasons (GS). To achieve this, a column-based greenhouse experiment was conducted to investigate microbial communities in tailings that were capped with a layer (10 or 30 cm) of peat-mineral mix (PMM) and planted with either upland or wetland communities. DNA metabarcoding analysis of the bacterial 16S rRNA gene and fungal ITS2 region as well as shotgun metagenomics were used to asses the impact of treatments on microbial taxonomy and functions, respectively. Results showed that tailings microbial diversity and community composition changed considerably after two GS compared to baseline samples, while communities in the PMM capping layer were much more stable. Likewise, several microbial functions were significantly enriched in tailings after two GS. Interestingly, the impact of capping on bacterial communities in tailings varied depending on the plant community, leading to a higher number of differentially abundant taxa and to a decrease in Shannon diversity and evenness in the upland treatment but not in the wetland treatment. Moreover, while capping in the presence of wetland vegetation increased the energy-related metabolic functions (carbon, nitrogen, and sulfur), these functions were depleted by capping in the upland treatment. Fungi represented a small proportion of the microbial community in tailings, but the relative abundance of several taxa changed over time, while the capping treatments favored the growth of some beneficial taxa, notably the root endophyte Serendipita, in both upland and wetland columns. The results suggest that selecting the right combination of capping material and vegetation type may contribute to improve below-ground microbial processes and sustain plant growth in harsh environments such as oil sands tailings.}, } @article {pmid37464937, year = {2023}, author = {Chen, HY and Li, CQ and Chen, SY and Xiao, H}, title = {Metagenomic analysis reveals hidden links between gut microbes and habitat adaptation among cave and surface dwelling Sinocyclocheilus species.}, journal = {Zoological research}, volume = {44}, number = {4}, pages = {793-807}, pmid = {37464937}, issn = {2095-8137}, mesh = {Animals ; Phylogeny ; Caves ; *Gastrointestinal Microbiome ; *Cyprinidae/genetics ; Ecosystem ; }, abstract = {Intestinal microbes are closely related to vital host functions such as digestion and nutrient absorption, which play important roles in enhancing host adaptability. As a natural "laboratory", caves provide an outstanding model for understanding the significance of gut microbes and feeding habits in the habitat adaptability of hosts. However, research on the relationship between gut microbes, feeding habits, and the adaptability of troglobites remains insufficient. In this study, we compared the characteristics of the intestinal microbes of Sinocyclocheilus cavefish and surface fish and further established the relationship between intestinal and habitat microbes. Furthermore, we conducted environmental DNA (eDNA) (metabarcoding) analysis of environmental samples to clarify the composition of potential food resources in the habitats of the Sinocyclocheilus cavefish and surface fish. Results showed that the structure of the Sinocyclocheilus gut microbes was more related to ecological type (habitat type) than phylogenetic relationships. While horizontal transfer of habitat microbes was a source of gut microbes, hosts also showed strong selection for inherent microbes as dominant microorganisms. Differences in the composition and structure of gut microbes, especially dominant microbes, may enhance the adaptability of the two Sinocyclocheilus fish types from the perspectives of food intake, nutrient utilization, and harmful substance metabolism, suggesting that food resources, predation patterns, intestinal flora, digestive and absorptive capacity, and feeding habits and preferences are linked to habitat adaptability. These results should facilitate our understanding of the significance of fish gut microbes to habitat adaptation and provide a new perspective for studying the adaptive mechanisms of cavefish.}, } @article {pmid37464403, year = {2023}, author = {Bargiela, R and Korzhenkov, AA and McIntosh, OA and Toshchakov, SV and Yakimov, MM and Golyshin, PN and Golyshina, OV}, title = {Evolutionary patterns of archaea predominant in acidic environment.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {61}, pmid = {37464403}, issn = {2524-6372}, support = {N 810280//European Regional Development Fund/ ; N 810280//European Regional Development Fund/ ; N 810280//European Regional Development Fund/ ; RPG-2020-190//Leverhulme Trust/ ; RPG-2020-190//Leverhulme Trust/ ; RPG-2020-190//Leverhulme Trust/ ; }, abstract = {BACKGROUND: Archaea of the order Thermoplasmatales are widely distributed in natural acidic areas and are amongst the most acidophilic prokaryotic organisms known so far. These organisms are difficult to culture, with currently only six genera validly published since the discovery of Thermoplasma acidophilum in 1970. Moreover, known great diversity of uncultured Thermoplasmatales represents microbial dark matter and underlines the necessity of efforts in cultivation and study of these archaea. Organisms from the order Thermoplasmatales affiliated with the so-called "alphabet-plasmas", and collectively dubbed "E-plasma", were the focus of this study. These archaea were found predominantly in the hyperacidic site PM4 of Parys Mountain, Wales, UK, making up to 58% of total metagenomic reads. However, these archaea escaped all cultivation attempts.

RESULTS: Their genome-based metabolism revealed its peptidolytic potential, in line with the physiology of the previously studied Thermoplasmatales isolates. Analyses of the genome and evolutionary history reconstruction have shown both the gain and loss of genes, that may have contributed to the success of the "E-plasma" in hyperacidic environment compared to their community neighbours. Notable genes among them are involved in the following molecular processes: signal transduction, stress response and glyoxylate shunt, as well as multiple copies of genes associated with various cellular functions; from energy production and conversion, replication, recombination, and repair, to cell wall/membrane/envelope biogenesis and archaella production. History events reconstruction shows that these genes, acquired by putative common ancestors, may determine the evolutionary and functional divergences of "E-plasma", which is much more developed than other representatives of the order Thermoplasmatales. In addition, the ancestral hereditary reconstruction strongly indicates the placement of Thermogymnomonas acidicola close to the root of the Thermoplasmatales.

CONCLUSIONS: This study has analysed the metagenome-assembled genome of "E-plasma", which denotes the basis of their predominance in Parys Mountain environmental microbiome, their global ubiquity, and points into the right direction of further cultivation attempts. The results suggest distinct evolutionary trajectories of organisms comprising the order Thermoplasmatales, which is important for the understanding of their evolution and lifestyle.}, } @article {pmid37464386, year = {2023}, author = {McGregor, BA and Razmjou, E and Hooshyar, H and Seeger, DR and Golovko, SA and Golovko, MY and Singer, SM and Hur, J and Solaymani-Mohammadi, S}, title = {A shotgun metagenomic analysis of the fecal microbiome in humans infected with Giardia duodenalis.}, journal = {Parasites & vectors}, volume = {16}, number = {1}, pages = {239}, pmid = {37464386}, issn = {1756-3305}, support = {P20 GM113123/GM/NIGMS NIH HHS/United States ; NIH/NIGMSP20GM113123/NH/NIH HHS/United States ; }, mesh = {Humans ; *Giardia lamblia ; *Giardiasis/parasitology ; Phylogeny ; Genotype ; *Microbiota ; Feces/parasitology ; Multilocus Sequence Typing ; }, abstract = {BACKGROUND: The mechanisms underlying the clinical outcome disparity during human infection with Giardia duodenalis are still unclear. In recent years, evidence has pointed to the roles of host factors as well as parasite's genetic heterogeneity as major contributing factors in the development of symptomatic human giardiasis. However, it remains contested as to how only a small fraction of individuals infected with G. duodenalis develop clinical gastrointestinal manifestations, whereas the majority of infected individuals remain asymptomatic. Here, we demonstrate that diversity in the fecal microbiome correlates with the clinical outcome of human giardiasis.

METHODS: The genetic heterogeneity of G. duodenalis clinical isolates from human subjects with asymptomatic and symptomatic giardiasis was determined using a multilocus analysis approach. We also assessed the genetic proximity of G. duodenalis isolates by constructing phylogenetic trees using the maximum likelihood. Total genomic DNA (gDNA) from fecal specimens was utilized to construct DNA libraries, followed by performing paired-end sequencing using the HiSeq X platform. The Kraken2-generated, filtered FASTQ files were assigned to microbial metabolic pathways and functions using HUMAnN 3.04 and the UniRef90 diamond annotated full reference database (version 201901b). Results from HUMAnN for each sample were evaluated for differences among the biological groups using the Kruskal-Wallis non-parametric test with a post hoc Dunn test.

RESULTS: We found that a total of 8/11 (72.73%) human subjects were infected with assemblage A (sub-assemblage AII) of G. duodenalis, whereas 3/11 (27.27%) human subjects in the current study were infected with assemblage B of the parasite. We also found that the parasite's genetic diversity was not associated with the clinical outcome of the infection. Further phylogenetic analysis based on the tpi and gdh loci indicated that those clinical isolates belonging to assemblage A of G. duodenalis subjects clustered compactly together in a monophyletic clade despite being isolated from human subjects with asymptomatic and symptomatic human giardiasis. Using a metagenomic shotgun sequencing approach, we observed that infected individuals with asymptomatic and symptomatic giardiasis represented distinctive microbial diversity profiles, and that both were distinguishable from the profiles of healthy volunteers.

CONCLUSIONS: These findings identify a potential association between host microbiome disparity with the development of clinical disease during human giardiasis, and may provide insights into the mechanisms by which the parasite induces pathological changes in the gut. These observations may also lead to the development of novel selective therapeutic targets for preventing human enteric microbial infections.}, } @article {pmid37464295, year = {2023}, author = {Chen, H and Tang, M and Yao, L and Zhang, D and Zhang, Y and Zhao, Y and Xia, H and Chen, T and Zheng, J}, title = {Early application of metagenomics next-generation sequencing may significantly reduce unnecessary consumption of antibiotics in patients with fever of unknown origin.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {478}, pmid = {37464295}, issn = {1471-2334}, support = {2018JM7146//Natural Science Basic Research Program of Shaanxi Province/ ; }, mesh = {Humans ; *Fever of Unknown Origin/diagnosis/drug therapy ; Metagenomics ; Retrospective Studies ; Inpatients ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/therapeutic use ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a novel nucleic acid method for the detection of unknown and difficult pathogenic microorganisms, and its application in the etiological diagnosis of fever of unknown origin (FUO) is less reported. We aimed to comprehensively assess the value of mNGS in the etiologic diagnosis of FUO by the pathogen spectrum and diagnostic performance, and to investigate whether it is different in the time to diagnosis, length of hospitalization, antibiotic consumption and cost between FUO patients with and without early application of mNGS.

METHODS: A total of 149 FUO inpatients underwent both mNGS and routine pathogen detection was retrospectively analyzed. The diagnostic performance of mNGS, culture and CMTs for the final clinical diagnosis was evaluated by using sensitivity, specificity, positive predictive value, negative predictive value and total conforming rate. Patients were furtherly divided into two groups: the earlier mNGS detection group (sampling time: 0 to 3 days of the admission) and the later mNGS detection group (sampling time: after 3 days of the admission). The length of hospital stay, time spent on diagnosis, cost and consumption of antibiotics were compared between the two groups.

RESULTS: Compared with the conventional microbiological methods, mNGS detected much more species and had the higher negative predictive (67.6%) and total conforming rate (65.1%). Patients with mNGS sampled earlier had a significantly shorter time to diagnosis (6.05+/-6.23 vs. 10.5+/-6.4 days, P < 0.001) and days of hospital stay (13.7+/-20.0 vs. 30.3 +/-26.9, P < 0.001), as well as a significantly less consumption (13.3+/-7.8 vs. 19.5+/-8.0, P < 0.001) and cost (4543+/-7326 vs. 9873 +/- 9958 China Yuan [CNY], P = 0.001) of antibiotics compared with the patients sampled later.

CONCLUSIONS: mNGS could significantly improve the detected pathogen spectrum, clinical conforming rate of pathogens while having good negative predictive value for ruling out infections. Early mNGS detection may shorten the diagnosis time and hospitalization days and reduce unnecessary consumption of antibiotics.}, } @article {pmid37464123, year = {2023}, author = {Kermani, NZ and Adcock, IM and Djukanović, R and Chung, F and Schofield, JPR}, title = {Systems Biology in Asthma.}, journal = {Advances in experimental medicine and biology}, volume = {1426}, number = {}, pages = {215-235}, pmid = {37464123}, issn = {0065-2598}, mesh = {Humans ; Proteomics ; Systems Biology ; *Asthma/diagnosis/genetics ; *Respiration Disorders ; Biomarkers/metabolism ; }, abstract = {The application of mathematical and computational analysis, together with the modelling of biological and physiological processes, is transforming our understanding of the pathophysiology of complex diseases. This systems biology approach incorporates large amounts of genomic, transcriptomic, proteomic, metabolomic, breathomic, metagenomic and imaging data from disease sites together with deep clinical phenotyping, including patient-reported outcomes. Integration of these datasets will provide a greater understanding of the molecular pathways associated with severe asthma in each individual patient and determine their personalised treatment regime. This chapter describes some of the data integration methods used to combine data sets and gives examples of the results obtained using single datasets and merging of multiple datasets (data fusion and data combination) from several consortia including the severe asthma research programme (SARP) and the Unbiased Biomarkers Predictive of Respiratory Disease Outcomes (U-BIOPRED) consortia. These results highlight the involvement of several different immune and inflammatory pathways and factors in distinct subsets of patients with severe asthma. These pathways often overlap in patients with distinct clinical features of asthma, which may explain the incomplete or no response in patients undergoing specific targeted therapy. Collaboration between groups will improve the predictions obtained using a systems medicine approach in severe asthma.}, } @article {pmid37463935, year = {2023}, author = {Ramos-Barbero, MD and Gómez-Gómez, C and Sala-Comorera, L and Rodríguez-Rubio, L and Morales-Cortes, S and Mendoza-Barberá, E and Vique, G and Toribio-Avedillo, D and Blanch, AR and Ballesté, E and Garcia-Aljaro, C and Muniesa, M}, title = {Characterization of crAss-like phage isolates highlights Crassvirales genetic heterogeneity and worldwide distribution.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4295}, pmid = {37463935}, issn = {2041-1723}, mesh = {Humans ; *Bacteriophages ; Genetic Heterogeneity ; Genomics ; Feces ; Metagenome/genetics ; Genome, Viral/genetics ; Phylogeny ; }, abstract = {Crassvirales (crAss-like phages) are an abundant group of human gut-specific bacteriophages discovered in silico. The use of crAss-like phages as human fecal indicators is proposed but the isolation of only seven cultured strains of crAss-like phages to date has greatly hindered their study. Here, we report the isolation and genetic characterization of 25 new crAss-like phages (termed crAssBcn) infecting Bacteroides intestinalis, belonging to the order Crassvirales, genus Kehishuvirus and, based on their genomic variability, classified into six species. CrAssBcn phage genomes are similar to ΦCrAss001 but show genomic and aminoacidic differences when compared to other crAss-like phages of the same family. CrAssBcn phages are detected in fecal metagenomes around the world at a higher frequency than ΦCrAss001. This study increases the known crAss-like phage isolates and their abundance and heterogeneity open the question of what member of the Crassvirales group should be selected as human fecal marker.}, } @article {pmid37463217, year = {2023}, author = {Fokkens, L and Rep, M}, title = {Population genomics reveals meiotic recombination in Fusarium oxysporum.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {30}, pages = {e2309677120}, pmid = {37463217}, issn = {1091-6490}, mesh = {*Metagenomics ; *Fusarium/genetics ; Sequence Analysis, DNA ; Plant Diseases ; }, } @article {pmid37462611, year = {2023}, author = {Hou, R and Zhang, S and Huang, Q and Lin, L and Li, H and Li, J and Liu, S and Sun, C and Xu, X}, title = {Role of Gastrointestinal Microbiota from Crucian Carp in Microbial Transformation and Estrogenicity Modification of Novel Plastic Additives.}, journal = {Environmental science & technology}, volume = {57}, number = {31}, pages = {11476-11488}, doi = {10.1021/acs.est.3c03595}, pmid = {37462611}, issn = {1520-5851}, mesh = {Animals ; *Carps ; *Gastrointestinal Microbiome ; Plastics ; Estrone ; *Environmental Pollutants ; }, abstract = {Ingestion is a major exposure route for hydrophobic organic pollutants in fish, but the microbial transformation and estrogenic modification of the novel plastic additives by the gut microbiota of fish remain obscure. Using an in vitro approach, we provide evidence that structure-related transformation of various plastic additives by the gastric and intestinal (GI) microbiota from crucian carp, with the degradation ratio of bisphenols and triphenyl phosphate faster than those of brominated compounds. The degradation kinetics for these pollutants could be limited by oxygen and cometabolic substrates (i.e., glucose). The fish GI microbiota could utilize the vast majority of carbon sources in a Biolog EcoPlate, suggesting their high metabolic potential and ability to transform various organic compounds. Unique microorganisms associated with transformation of the plastic additives including genera of Citrobacter, Klebsiella, and some unclassified genera in Enterobacteriaceae were identified by combining high-throughput genetic analyses and metagenomic analyses. Through identification of anaerobic transformation products by high-resolution mass spectrometry, alkyl-cleavage was found the common transformation mechanism, and hydrolysis was the major pathway for ester-containing pollutants. After anaerobic incubation, the estrogenic activities of triphenyl phosphate and bisphenols A, F, and AF declined, whereas that of bisphenol AP increased.}, } @article {pmid37462319, year = {2023}, author = {Vidal-Villarejo, M and Freund, F and Hanekamp, H and von Tiedemann, A and Schmid, K}, title = {Population Genomic Evidence for a Repeated Introduction and Rapid Expansion of the Fungal Maize Pathogen Setosphaeria turcica in Europe.}, journal = {Genome biology and evolution}, volume = {15}, number = {8}, pages = {}, pmid = {37462319}, issn = {1759-6653}, mesh = {*Zea mays/genetics ; Metagenomics ; Phylogeny ; *Ascomycota/genetics ; Plant Diseases/microbiology ; }, abstract = {Modern agricultural practices, climate change, and globalization foster the rapid spread of plant pathogens, such as the maize fungal pathogen Setosphaeria turcica, which causes Northern corn leaf blight and expanded into Central Europe during the twentieth century. To investigate the rapid expansion of S. turcica, we sequenced 121 isolates from Europe and Kenya. Population genomic inference revealed a single genetically diverse cluster in Kenya and three clonal lineages with low diversity, as well as one cluster of multiple clonal sublineages in Europe. Phylogenetic dating suggests that all European lineages originated through sexual reproduction outside Europe and were subsequently introgressed multiple times. Unlike isolates from Kenya, European isolates did not show sexual recombination, despite the presence of both MAT1-1 and MAT1-2 mating types. For the clonal lineages, coalescent model selection supported a selectively neutral model with strong exponential population growth, rather than models with pervasive positive selection caused by host defense resistance or environmental adaptation. Within clonal lineages, phenotypic variation in virulence to different monogenic resistances, which defines the pathogen races, suggests that these races may originate from repeated mutations in virulence genes. Association testing based on k-mers did not identify genomic regions linked to pathogen races, but it did uncover strongly differentiated genomic regions between clonal lineages, which harbor genes with putative roles in pathogenicity. In conclusion, the expansion and population growth of S. turcica in Europe are mainly driven by an expansion of the maize cultivation area and not by rapid adaptation.}, } @article {pmid37461605, year = {2023}, author = {Simpson, AC and Sengupta, P and Zhang, F and Hameed, A and Parker, CW and Singh, NK and Miliotis, G and Rekha, PD and Raman, K and Mason, CE and Venkateswaran, K}, title = {Phylogenetic affiliations and genomic characterization of novel bacterial species and their abundance in the International Space Station.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {37461605}, support = {R01 MH117406/MH/NIMH NIH HHS/United States ; }, abstract = {BACKGROUND: With the advent of long-term human habitation in space and on the moon, understanding how the built environment microbiome of space habitats differs from Earth habits, and how microbes survive, proliferate and spread in space conditions, is coming more and more important. The Microbial Tracking mission series has been monitoring the microbiome of the International Space Station (ISS) for almost a decade. During this mission series, six unique strains of Gram-positive bacteria, including two spore-forming and three non-spore-forming species, were isolated from the environmental surfaces of the International Space Station (ISS).

RESULTS: The analysis of their 16S rRNA gene sequences revealed <99% similarities with previously described bacterial species. To further explore their phylogenetic affiliation, whole genome sequencing (WGS) was undertaken. For all strains, the gyrB gene exhibited <93% similarity with closely related species, which proved effective in categorizing these ISS strains as novel species. Average ucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values, when compared to any known bacterial species, were less than <94% and 50% respectively for all species described here. Traditional biochemical tests, fatty acid profiling, polar lipid, and cell wall composition analyses were performed to generate phenotypic characterization of these ISS strains. A study of the shotgun metagenomic reads from the ISS samples, from which the novel species were isolated, showed that only 0.1% of the total reads mapped to the novel species, supporting the idea that these novel species are rare in the ISS environments. In-depth annotation of the genomes unveiled a variety of genes linked to amino acid and derivative synthesis, carbohydrate metabolism, cofactors, vitamins, prosthetic groups, pigments, and protein metabolism. Further analysis of these ISS-isolated organisms revealed that, on average, they contain 46 genes associated with virulence, disease, and defense. The main predicted functions of these genes are: conferring resistance to antibiotics and toxic compounds, and enabling invasion and intracellular resistance. After conducting antiSMASH analysis, it was found that there are roughly 16 cluster types across the six strains, including β-lactone and type III polyketide synthase (T3PKS) clusters.

CONCLUSIONS: Based on these multi-faceted taxonomic methods, it was concluded that these six ISS strains represent five novel species, which we propose to name as follows: Arthrobacter burdickii IIF3SC-B10[T] (=NRRL B-65660[T]), Leifsonia virtsii, F6_8S_P_1A[T] (=NRRL B-65661[T]), Leifsonia williamsii, F6_8S_P_1B[T] (=NRRL B- 65662[T] and DSMZ 115932[T]), Paenibacillus vandeheii, F6_3S_P_1C[T](=NRRL B-65663[T] and DSMZ 115940[T]), and Sporosarcina highlanderae F6_3S_P_2 T(=NRRL B-65664[T] and DSMZ 115943[T]). Identifying and characterizing the genomes and phenotypes of novel microbes found in space habitats, like those explored in this study, is integral for expanding our genomic databases of space-relevant microbes. This approach offers the only reliable method to determine species composition, track microbial dispersion, and anticipate potential threats to human health from monitoring microbes on the surfaces and equipment within space habitats. By unraveling these microbial mysteries, we take a crucial step towards ensuring the safety and success of future space missions.}, } @article {pmid37461534, year = {2023}, author = {Muller, E and Shiryan, I and Borenstein, E}, title = {Multi-view integration of microbiome data for identifying disease-associated modules.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.07.03.547607}, pmid = {37461534}, abstract = {Machine learning (ML) has become a widespread strategy for studying complex microbiome signatures associated with disease. To this end, metagenomics data are often processed into a single "view" of the microbiome, such as its taxonomic (species) or functional (gene) composition, which in turn serves as input to such ML models. When further omics are available, such as metabolomics, these can be analyzed as additional complementary views. Following training and evaluation, the resulting model can be explored to identify informative features, generating hypotheses regarding underlying mechanisms. Importantly, however, using a single view generally offers relatively limited hypotheses, failing to capture simultaneous shifts or dependencies across multiple microbiome layers that likely play a role in microbiome-host interactions. In this work, inspired by the broad domain of multi-view learning , we aimed to investigate the impact of various integration approaches on the ability to predict disease state based on multiple microbiome views, and primarily to generate multifaceted biological hypotheses linking features across views. We first implemented an "early integration" ML pipeline to serve as a baseline for disease predictability and informative features' detection, and compared the resulting multi-view models to naïve single view models. Using a dataset collection of 25 case-control metagenomic studies, we found that multi-view models typically offer prediction accuracy that is comparable to that of the best-performing single view model, yet, further provide a mixed set of informative features from different views while accounting for between-views dependencies. Such early-integration multi-view models, however, are still limited in their ability to provide well-defined disease-associated multi-view modules that can be used to generate mechanistic hypotheses concerning the disease in question. To address this challenge, we developed a novel "intermediate integration" framework termed MintTea, based on sparse generalized canonical correlation analysis (CCA), to identify multi-view modules of features, highlighting shared disease-associated trends in the data expressed by the different views. We showed that this framework identified multiple modules that both are highly predictive of the disease, and exhibit strong within-module associations across features from different views. We further demonstrated that MintTea has significantly lower false discovery rates compared to other CCA-based approaches. We accordingly advocate for using multi-view models to capture multifaceted microbiome signatures that likely better reflect the complex mechanisms underlying microbiome-disease associations.}, } @article {pmid37461353, year = {2023}, author = {Chen, L and Guo, Y and Zhang, S and Ma, W}, title = {Simultaneous denitrification and electricity generation in a methane-powered bioelectrochemical system.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {95}, number = {8}, pages = {e10910}, doi = {10.1002/wer.10910}, pmid = {37461353}, issn = {1554-7531}, support = {21577108//National Natural Science Foundation of China/ ; }, mesh = {*Nitrates ; *Denitrification ; Methane ; Anaerobiosis ; Bacteria/genetics ; Oxidation-Reduction ; Electricity ; Bioreactors/microbiology ; Nitrogen ; }, abstract = {Bioelectrochemical system is a novel method for controlling down nitrate pollution, yet the feasibility of using methane as the electron donors for denitrification in this system remains unknown. In this study, using the effluent from mother BESs as inocula, a denitrifying anaerobic methane oxidation bioelectrochemical system was successfully started up in 92 days. When operated with 50 mmol/L phosphate buffer solution at pH 7 and 30°C, the maximum methane consumption, nitrate, and total nitrogen removal load reached 0.23 ± 0.01 mmol/d, 551.0 ± 22.1 mg N/m[3] /d, and 64.0 ± 18.8 mg N/m[3] /d, respectively. Meanwhile, the peak voltage of 93 ± 4 mV, the anodic coulombic efficiency of 6.99 ± 0.20%, and the maximum power density of 219.86 mW/m[3] were obtained. The metagenomics profiles revealed that the dominant denitrifying bacteria in the cathodic chamber reduced most nitrate to nitrite through denitrification and assimilatory reduction. In the anodic chamber, various archaea including methanotrophs and methanogens converted methane via reverse methanogenesis to form formate (or H2), acetate, and methyl compounds, which were than utilized by electroactive bacteria to generate electricity. PRACTITIONER POINTS: A denitrifying anaerobic methane oxidation BES was successfully started up in 92 d. Simultaneous removal of methane and nitrate was achieved in the DAMO-BES. Functional genes related to AMO and denitrification were detected in the DAMO-BES. Methylocystis can mediate AMO in the anode and denitrification in the cathode.}, } @article {pmid37461084, year = {2023}, author = {Feehan, B and Ran, Q and Dorman, V and Rumback, K and Pogranichniy, S and Ward, K and Goodband, R and Niederwerder, MC and Lee, STM}, title = {Novel complete methanogenic pathways in longitudinal genomic study of monogastric age-associated archaea.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {35}, pmid = {37461084}, issn = {2524-4671}, support = {P30 GM122731/GM/NIGMS NIH HHS/United States ; U54 HD090216/HD/NICHD NIH HHS/United States ; S10 OD021743/OD/NIH HHS/United States ; UL1 TR002366/TR/NCATS NIH HHS/United States ; }, abstract = {BACKGROUND: Archaea perform critical roles in the microbiome system, including utilizing hydrogen to allow for enhanced microbiome member growth and influencing overall host health. With the majority of microbiome research focusing on bacteria, the functions of archaea are largely still under investigation. Understanding methanogenic functions during the host lifetime will add to the limited knowledge on archaeal influence on gut and host health. In our study, we determined lifelong archaea dynamics, including detection and methanogenic functions, while assessing global, temporal and host distribution of our novel archaeal metagenome-assembled genomes (MAGs). We followed 7 monogastric swine throughout their life, from birth to adult (1-156 days of age), and collected feces at 22 time points. The samples underwent gDNA extraction, Illumina sequencing, bioinformatic quality and assembly processes, MAG taxonomic assignment and functional annotation. MAGs were utilized in downstream phylogenetic analysis for global, temporal and host distribution in addition to methanogenic functional potential determination.

RESULTS: We generated 1130 non-redundant MAGs, representing 588 unique taxa at the species level, with 8 classified as methanogenic archaea. The taxonomic classifications were as follows: orders Methanomassiliicoccales (5) and Methanobacteriales (3); genera UBA71 (3), Methanomethylophilus (1), MX-02 (1), and Methanobrevibacter (3). We recovered the first US swine Methanobrevibacter UBA71 sp006954425 and Methanobrevibacter gottschalkii MAGs. The Methanobacteriales MAGs were identified primarily during the young, preweaned host whereas Methanomassiliicoccales primarily in the adult host. Moreover, we identified our methanogens in metagenomic sequences from Chinese swine, US adult humans, Mexican adult humans, Swedish adult humans, and paleontological humans, indicating that methanogens span different hosts, geography and time. We determined complete metabolic pathways for all three methanogenic pathways: hydrogenotrophic, methylotrophic, and acetoclastic. This study provided the first evidence of acetoclastic methanogenesis in archaea of monogastric hosts which indicated a previously unknown capability for acetate utilization in methanogenesis for monogastric methanogens. Overall, we hypothesized that the age-associated detection patterns were due to differential substrate availability via the host diet and microbial metabolism, and that these methanogenic functions are likely crucial to methanogens across hosts. This study provided a comprehensive, genome-centric investigation of monogastric-associated methanogens which will further improve our understanding of microbiome development and functions.}, } @article {pmid37459997, year = {2023}, author = {Liu, M and Wei, Y and Lian, L and Wei, B and Bi, Y and Liu, N and Yang, G and Zhang, Y}, title = {Macrofungi promote SOC decomposition and weaken sequestration by modulating soil microbial function in temperate steppe.}, journal = {The Science of the total environment}, volume = {899}, number = {}, pages = {165556}, doi = {10.1016/j.scitotenv.2023.165556}, pmid = {37459997}, issn = {1879-1026}, mesh = {*Soil/chemistry ; Carbon/metabolism ; Soil Microbiology ; Biomass ; *Microbiota ; Carbon Sequestration ; }, abstract = {Soil organic carbon (SOC) sequestration is a key grassland ecosystem function, and the magnitude of SOC reservoirs depends on microbial involvement, especially that of fungi. Mycelia developed by macrofungi potentially influence carbon (C) fixation and decomposition; however, the mechanisms underlying their effects on SOC storage in grassland ecosystems remain poorly understood. The fairy rings formed by macrofungi in grasslands are natural platform for exploring macrofungal effects on SOC. In this study, we collected topsoil (0-10 cm) from four different fairy ring zones in a temperate steppe to reveal the macrofungal effects on SOC fractions, including particulate organic carbon (POC) and mineral-associated organic carbon (MAOC), and the SOC storage microbial mechanism using metagenomic sequencing technology. Both POC and MAOC decreased after macrofungal passage, resulting in a 7.37 % reduction in SOC. Macrofungal presence reduced microbial biomass carbon (MBC), but significantly enhanced the β-1,4-glucosidase (BG) activity, which increased dissolved organic carbon (DOC). In addition, the abundance of copiotrophs (Proteobacteria and Bacteroidetes) with lower C metabolic rates increased, and that of oligotrophs (Actinobacteria, Acidobacteria, Chloroflexi, and Verrucomicrobia) with higher substrate utilization efficiency decreased in the presence of macrofungi. This may further promote SOC decomposition. Correspondingly, there was a lower abundance of C-fixation genes but more C-degradation genes (especially hemicellulosic degradation genes) during macrofungal passage. Our results indicate that the presence of macrofungi can modulate the soil microbial community and functional genes to reduce SOC storage by inhibiting microbial C sequestration while promoting C decomposition in grassland ecosystems. These findings refine our mechanistic understanding of SOC persistence through the interactions between macrofungi and other microbes.}, } @article {pmid37459963, year = {2023}, author = {Wang, Y and Guo, Z and Li, J and Sui, F and Dai, W and Zhang, W and Du, H}, title = {Unraveling the differential perturbations of species-level functional profiling of gut microbiota among phases of methamphetamine-induced conditioned place preference.}, journal = {Progress in neuro-psychopharmacology & biological psychiatry}, volume = {127}, number = {}, pages = {110828}, doi = {10.1016/j.pnpbp.2023.110828}, pmid = {37459963}, issn = {1878-4216}, mesh = {*Methamphetamine/pharmacology ; *Central Nervous System Stimulants/pharmacology ; *Gastrointestinal Microbiome ; Conditioning, Classical ; Reward ; }, abstract = {The gut microbiome plays a significant role in methamphetamine addiction. Previous studies using short-read amplicon sequencing have described alterations in microbiota at the genus level and predicted function, in which taxonomic resolution is insufficient for accurate functional measurements. To address this limitation, we employed metagenome sequencing to intuitively associate species to functions of gut microbiota in methamphetamine-induced conditioned place preference. We observed differential perturbations of species-level functional profiling of the gut microbiota across phases of METH-induced CPP, with alterations in SCFA metabolism and bacterial motility at the acquisition phase and substance dependence-alcoholism pathway and amino acid metabolism at the extinction phase. Our findings suggest that reduced beneficial bacteria, i.e., Lactobacillus reuteri, contributed to the alteration of SCFA metabolism, while the increased abundance of Akkermansia muciniphila during the extinction phase may be associated with altered phenylalanine, tyrosine, and tryptophan metabolism and substance dependence pathway. Our study further supports the association between specific microbial taxa and METH-induced rewarding.}, } @article {pmid37459723, year = {2023}, author = {Yu, Y and Huang, W and Yu, W and Tang, S and Yin, H}, title = {Metagenomic insights into the mechanisms of triphenyl phosphate degradation by bioaugmentation with Sphingopyxis sp. GY.}, journal = {Ecotoxicology and environmental safety}, volume = {263}, number = {}, pages = {115261}, doi = {10.1016/j.ecoenv.2023.115261}, pmid = {37459723}, issn = {1090-2414}, mesh = {*Flame Retardants/metabolism ; Organophosphates/metabolism ; *Sphingomonadaceae/genetics/metabolism ; Glutathione ; }, abstract = {Biodegradation of triphenyl phosphate (TPHP) by Sphingopyxis sp. GY was investigated, and results demonstrated that TPHP could be completely degraded in 36 h with intracellular enzymes playing a leading role. This study, for the first time, systematically explores the effects of the typical brominated flame retardants, organophosphorus flame retardants, and heavy metals on TPHP degradation. Our findings reveal that TCPs, BDE-47, HBCD, Cd and Cu exhibit inhibitory effects on TPHP degradation. The hydrolysis-, hydroxylated-, monoglucosylated-, methylated products and glutathione (GSH) conjugated derivative were identified and new degradation pathway of TPHP mediated by microorganism was proposed. Moreover, toxicity evaluation experiments indicate a significant reduction in toxicity following treatment with Sphingopyxis sp. GY. To evaluate its potential for environmental remediation, we conducted bioaugmentation experiments using Sphingopyxis sp. GY in a TPHP contaminated water-sediment system, which resulted in excellent remediation efficacy. Twelve intermediate products were detected in the water-sediment system, including the observation of the glutathione (GSH) conjugated derivative, monoglucosylated product, (OH)2-DPHP and CH3-O-DPHP for the first time in microorganism-mediated TPHP transformation. We further identify the active microbial members involved in TPHP degradation within the water-sediment system using metagenomic analysis. Notably, most of these members were found to possess genes related to TPHP degradation. These findings highlight the significant reduction of TPHP achieved through beneficial interactions and cooperation established between the introduced Sphingopyxis sp. GY and the indigenous microbial populations stimulated by the introduced bacteria. Thus, our study provides valuable insights into the mechanisms, co-existed pollutants, transformation pathways, and remediation potential associated with TPHP biodegradation, paving the way for future research and applications in environmental remediation strategies.}, } @article {pmid37459443, year = {2023}, author = {Verschaffelt, P and Tanca, A and Abbondio, M and Van Den Bossche, T and Moortele, TV and Dawyndt, P and Martens, L and Mesuere, B}, title = {Unipept Desktop 2.0: Construction of Targeted Reference Protein Databases for Metaproteogenomics Analyses.}, journal = {Journal of proteome research}, volume = {22}, number = {8}, pages = {2620-2628}, doi = {10.1021/acs.jproteome.3c00091}, pmid = {37459443}, issn = {1535-3907}, mesh = {Humans ; Databases, Protein ; RNA, Ribosomal, 16S ; *Proteins ; *Metagenomics ; }, abstract = {Unipept Desktop 2.0 is the most recent iteration of the Unipept Desktop tool that adds support for the analysis of metaproteogenomics datasets. Unipept Desktop now supports the automatic construction of targeted protein reference databases that only contain proteins (originating from the UniProtKB resource) associated with a predetermined list of taxa. This improves both the taxonomic and functional resolution of a metaproteomic analysis and yields several technical advantages. By limiting the proteins present in a reference database, it is also possible to perform (meta)proteogenomics analyses. Since the protein reference database resides on the user's local machine, they have complete control over the database used during an analysis. Data no longer need to be transmitted over the Internet, decreasing the time required for an analysis and better safeguarding privacy-sensitive data. As a proof of concept, we present a case study in which a human gut metaproteome dataset is analyzed with Unipept Desktop 2.0 using different targeted databases based on matched 16S rRNA gene sequencing data.}, } @article {pmid37459319, year = {2023}, author = {Galván, V and Pascutti, F and Sandoval, NE and Lanfranconi, MP and Lozada, M and Arabolaza, AL and Mac Cormack, WP and Alvarez, HM and Gramajo, HC and Dionisi, HM}, title = {High wax ester and triacylglycerol biosynthesis potential in coastal sediments of Antarctic and Subantarctic environments.}, journal = {PloS one}, volume = {18}, number = {7}, pages = {e0288509}, pmid = {37459319}, issn = {1932-6203}, mesh = {Antarctic Regions ; *Esters/metabolism ; *Diacylglycerol O-Acyltransferase ; Bacteria/metabolism ; Triglycerides ; Geologic Sediments ; }, abstract = {The wax ester (WE) and triacylglycerol (TAG) biosynthetic potential of marine microorganisms is poorly understood at the microbial community level. The goal of this work was to uncover the prevalence and diversity of bacteria with the potential to synthesize these neutral lipids in coastal sediments of two high latitude environments, and to characterize the gene clusters related to this process. Homolog sequences of the key enzyme, the wax ester synthase/acyl-CoA:diacylglycerol acyltransferase (WS/DGAT) were retrieved from 13 metagenomes, including subtidal and intertidal sediments of a Subantarctic environment (Ushuaia Bay, Argentina), and subtidal sediments of an Antarctic environment (Potter Cove, Antarctica). The abundance of WS/DGAT homolog sequences in the sediment metagenomes was 1.23 ± 0.42 times the abundance of 12 single-copy genes encoding ribosomal proteins, higher than in seawater (0.13 ± 0.31 times in 338 metagenomes). Homolog sequences were highly diverse, and were assigned to the Pseudomonadota, Actinomycetota, Bacteroidota and Acidobacteriota phyla. The genomic context of WS/DGAT homologs included sequences related to WE and TAG biosynthesis pathways, as well as to other related pathways such as fatty-acid metabolism, suggesting carbon recycling might drive the flux to neutral lipid synthesis. These results indicate the presence of abundant and taxonomically diverse bacterial populations with the potential to synthesize lipid storage compounds in marine sediments, relating this metabolic process to bacterial survival.}, } @article {pmid37459167, year = {2023}, author = {Cisneros-Martínez, AM and Eguiarte, LE and Souza, V}, title = {Metagenomic comparisons reveal a highly diverse and unique viral community in a seasonally fluctuating hypersaline microbial mat.}, journal = {Microbial genomics}, volume = {9}, number = {7}, pages = {}, pmid = {37459167}, issn = {2057-5858}, support = {BB/P024378/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P024270/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 223743/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Metagenomics ; Seasons ; *Microbiota ; *Virome ; }, abstract = {In spring 2016, a shallow hypersaline pond (50×25 m) was found in the Cuatro Cienegas Basin (CCB). This pond, known as Archaean Domes (AD) because of its elastic microbial mats that form dome-shaped structures due to the production of reducing gases reminiscent of the Archaean eon, such as methane and hydrogen sulfide, harbour a highly diverse microbial community, rich in halophilic and methanogenic archaea. AD is a seasonally fluctuating hypersaline site, with salinity ranging from low hypersaline (5.3%) during the wet season to high hypersaline (saturation) during the dry season. To characterize the viral community and to test whether it resembles those of other hypersaline sites (whose diversity is conditioned by salinity), or if it is similar to other CCB sites (with which it shares a common geological history), we generated 12 metagenomes from different seasons and depths over a 4 year period and compared them to 35 metagenomes from varied environments. Haloarchaeaviruses were detected, but were never dominant (average of 15.37 % of the total viral species), and the viral community structure and diversity were not affected by environmental fluctuations. In fact, unlike other viral communities at hypersaline sites, AD remained more diverse than other environments regardless of season. β-Diversity analyses show that AD is closely related to other CCB sites, although it has a unique viral community that forms a cluster of its own. The similarity of two surface samples to the 30 and 50 cm depth samples, as well as the observed increase in diversity at greater depths, supports the hypothesis that the diversity of CCB has evolved as a result of a long time environmental stability of a deep aquifer that functions as a 'seed bank' of great microbial diversity that is transported to the surface by sporadic groundwater upwelling events.}, } @article {pmid37458723, year = {2023}, author = {Zhang, J and He, Y and He, J and Ying, Y and Zhu, F}, title = {Full annotation of viral metagenomics in different components from Chinese blood donors using next-generation sequencing.}, journal = {Blood transfusion = Trasfusione del sangue}, volume = {}, number = {}, pages = {}, doi = {10.2450/BloodTransfus.451}, pmid = {37458723}, issn = {2385-2070}, abstract = {BACKGROUND: Emerging viruses in the blood of healthy/qualified donors can seriously affect transfusion safety. However, the virus characteristics in different healthy blood donors and blood components are still not fully understood.

MATERIALS AND METHODS: Buffy coat (BC) and plasma specimens were collected from 32 whole blood donors, and platelet (PLT) and BC specimens from 30 apheresis platelet donors to explore the full annotation of viral metagenomics in different blood components from Chinese blood donors using next-generation sequencing technology.

RESULTS: The study detected 56 viruses in the plasma and BC groups of whole blood donors. The plasma group had a significantly higher viral abundance and more types of viruses than the BC group. We detected 20 viruses in the PLT and BC groups of apheresis platelet donors. Viral abundance and types were significantly lower in the BC group than in the PLT group. According to β-diversity analysis, the plasma group had a significantly different community structure and composition than the BC group.

DISCUSSION: Viral nucleic acid is found in the blood of healthy Chinese blood donors, with the highest concentration in plasma, which could explain the distribution of viruses in the blood of healthy individuals.}, } @article {pmid37457982, year = {2023}, author = {Barber, C and Sabater, C and Guarner, F and Margolles, A and Azpiroz, F}, title = {Metabolic response of intestinal microbiota to guar gum consumption.}, journal = {Frontiers in nutrition}, volume = {10}, number = {}, pages = {1160694}, pmid = {37457982}, issn = {2296-861X}, abstract = {BACKGROUND: Guar gum is used extensively as a thickening agent in food, but it remains uncertain whether and to what extent it is fermented by colonic microbiota and whether it has microbiota modulatory properties.

AIM: To determine the metabolic response of intestinal microbiota to guar gum consumption, specifically, the extent of initial fermentation and subsequent adaptation.

METHODS: Single-center, single arm, open label, proof-of-concept study testing the effect of guar gum on microbiota metabolism and adaptation. Healthy male subjects (n = 12) were administered gum guar (8 g/day) for 18 days. Outcomes were measured before, at initial and late administration: (a) anal gas evacuations (number/day); (b) digestive sensations (daily scales); and (c) fecal gut microbiota taxonomy and metabolic functions by shotgun sequencing.

RESULTS: At initial consumption, guar gum induced a transient increase in anal gas evacuations and digestive sensations; gas evacuation completely reverted upon continuous administration, whereas sensations reverted only in part. Guar gum induced moderate changes in human microbiota composition at both taxonomic and functional levels. Positive associations between effects on microbiota (proliferation of Agathobaculum butyriciproducens and Lachnospira pectinoschiza) and hedonic sensations were detected.

CONCLUSION: Guar gum is metabolized by intestinal microbiota, and, upon continuous consumption, induces a selective adaptation of microbial taxonomy and function. These data highlight the potential interest of guar gum for novel prebiotic ingredient formulation.}, } @article {pmid37457869, year = {2023}, author = {Taha, SFM and Bhassu, S and Omar, H and Raju, CS and Rajamanikam, A and Govind, SKP and Mohamad, SB}, title = {Gut microbiota of healthy Asians and their discriminative features revealed by metagenomics approach.}, journal = {3 Biotech}, volume = {13}, number = {8}, pages = {275}, pmid = {37457869}, issn = {2190-572X}, abstract = {UNLABELLED: This study is conducted to identify the microbial architecture and its functional capacity in the Asian population via the whole metagenomics approach. A brief comparison of the Asian countries namely Malaysia, India, China, and Thailand, was conducted, giving a total of 916 taxa under observation. Results show a close representation of the taxonomic diversity in the gut microbiota of Malaysia, India, and China, where Bacteroidetes, Firmicutes, and Actinobacteria were more predominant compared to other phyla. Mainly due to the multi-racial population in Malaysia, which also consists of Malays, Indian, and Chinese, the population tend to share similar dietary preferences, culture, and lifestyle, which are major influences that shapes the structure of the gut microbiota. Moreover, Thailand showed a more distinct diversity in the gut microbiota which was highly dominated by Firmicutes. Meanwhile, functional profiles show 1034 gene families that are common between the four countries. The Malaysia samples are having the most unique gene families with a total of 67,517 gene families, and 51 unique KEGG Orthologs, mainly dominated by the metabolic pathways, followed by microbial metabolism in diverse environments. In conclusion, this study provides some general overview on the structure of the Asian gut microbiota, with some additional highlights on the Malaysian population.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03671-3.}, } @article {pmid37457591, year = {2023}, author = {Deng, Z and Tang, Y and Tu, Y and Liu, M and Cheng, Q and Zhang, J and Liu, F and Li, X}, title = {BALF metagenomic next-generation sequencing analysis in hematological malignancy patients with suspected pulmonary infection: clinical significance of negative results.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1195629}, pmid = {37457591}, issn = {2296-858X}, abstract = {PURPOSE: Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) is gradually being used in hematological malignancy (HM) patients with suspected pulmonary infections. However, negative results are common and the clinical value and interpretation of such results in this patient population require further analysis.

METHODS: Retrospective analysis of 112 HM patients with suspected pulmonary infection who underwent BALF mNGS and conventional microbiological tests. The final diagnosis, imaging findings, laboratory results and treatment regimen of 29 mNGS-negative patients were mainly analyzed.

RESULTS: A total of 83 mNGS positive and 29 negative patients (15 true-negatives and 14 false-negatives) were included in the study. Compared to false-negative patients, true-negative patients showed more thickening of interlobular septa on imaging (p < 0.05); fewer true-negative patients had acute respiratory symptoms such as coughing or sputum production (p < 0.05) clinically; On the aspect of etiology, drug-related interstitial pneumonia (6/15, 40%) was the most common type of lung lesion in true-negative patients; on the aspect of pathogenesis, false-negative patients mainly missed atypical pathogens such as fungi and tuberculosis (8/14, 57.1%). Regarding treatment, delayed anti-infection treatment occurred after pathogen missing in mNGS false-negative patients, with the longest median time delay observed for anti-tuberculosis therapy (13 days), followed by antifungal therapy (7 days), and antibacterial therapy (1.5 days); the delay in anti-tuberculosis therapy was significantly longer than that in antibacterial therapy (p < 0.05).

CONCLUSION: For HMs patients with imaging showing thickening of interlobular septa and no obvious acute respiratory symptoms, lung lesions are more likely caused by drug treatment or the underlying disease, so caution should be exercised when performing BALF mNGS. If BALF mNGS is negative but infection is still suspected, atypical pathogenic infections should be considered.}, } @article {pmid37457549, year = {2023}, author = {Nilendu, D}, title = {Toward Oral Thanatomicrobiology-An Overview of the Forensic Implications of Oral Microflora.}, journal = {Academic forensic pathology}, volume = {13}, number = {2}, pages = {51-60}, pmid = {37457549}, issn = {1925-3621}, abstract = {INTRODUCTION: The oral cavity is home to numerous microorganisms including bacteria, fungi, and viruses which together form the oral microflora. It is the second most diverse microbial site in the human body after the gastrointestinal tract. Microbial degradation is a common phenomenon that occurs after death, with the early and advanced stages of decomposition being closely associated with oral microbial activity.

METHODS: This article reviews the current state of knowledge on the role of the oral microflora in postmortem events, and highlights the growing importance of terms such as forensic microbiology and thanatomicrobiome. This article also discusses next-generation sequencing, metagenomic sequencing studies, and RNA sequencing to study the oral thanatomicrobiome and epinecrotic communities in forensic oral genetics.

RESULTS: The indigenous microorganisms in the oral cavity are among the first to respond to the process of decomposition. DNA/RNA sequencing is a relatively simple, precise, and cost-effective method to estimate biological diversity during various stages of postmortem decomposition. The field of thanatomicrobiology is rapidly evolving into a key area in forensic research.

CONCLUSION: This article briefly narrates oral microflora and its implications in forensic odontology. The role of microbial activity in postmortem events is gaining importance in forensic research, and further studies are needed to fully understand the potential applications of advanced technology in the study of the oral thanatomicrobiome.}, } @article {pmid37457347, year = {2023}, author = {Ferrarezi, JA and Defant, H and de Souza, LF and Azevedo, JL and Hungria, M and Quecine, MC}, title = {Meta-omics integration approach reveals the effect of soil native microbiome diversity in the performance of inoculant Azospirillum brasilense.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1172839}, pmid = {37457347}, issn = {1664-462X}, abstract = {Plant growth promoting bacteria (PGPB) have been used as integrative inputs to minimize the use of chemical fertilizers. However, a holistic comprehension about PGPB-plant-microbiome interactions is still incipient. Furthermore, the interaction among PGPB and the holobiont (host-microbiome association) represent a new frontier to plant breeding programs. We aimed to characterize maize bulk soil and rhizosphere microbiomes in irradiated soil (IS) and a native soil (NS) microbial community gradient (dilution-to-extinction) with Azospirillum brasilense Ab-V5, a PGPB commercial inoculant. Our hypothesis was that plant growth promotion efficiency is a result of PGPB niche occupation and persistence according to the holobiont conditions. The effects of Ab-V5 and NS microbial communities were evaluated in microcosms by a combined approach of microbiomics (species-specific qPCR, 16S rRNA metataxonomics and metagenomics) and plant phenomics (conventional and high-throughput methods). Our results revealed a weak maize growth promoting effect of Ab-V5 inoculation in undiluted NS, contrasting the positive effects of NS dilutions 10[-3], 10[-6], 10[-9] and IS with Ab-V5. Alpha diversity in NS + Ab-V5 soil samples was higher than in all other treatments in a time course of 25 days after sowing (DAS). At 15 DAS, alpha diversity indexes were different between NS and IS, but similar in all NS dilutions in rhizospheric samples. These differences were not persistent at 25 DAS, demonstrating a stabilization process in the rhizobiomes. In NS 10[-3] +Ab-V5 and NS 10[-6] Ab-V5, Ab-V5 persisted in the maize rhizosphere until 15 DAS in higher abundances compared to NS. In NS + Ab-V5, abundance of six taxa were positively correlated with response to (a)biotic stresses in plant-soil interface. Genes involved in bacterial metabolism of riboses and amino acids, and cresol degradation were abundant on NS 10[-3] + Ab-V5, indicating that these pathways can contribute to plant growth promotion and might be a result of Ab-V5 performance as a microbial recruiter of beneficial functions to the plant. Our results demonstrated the effects of holobiont on Ab-V5 performance. The meta-omics integration supported by plant phenomics opens new perspectives to better understanding of inoculants-holobiont interaction and for developing better strategies for optimization in the use of microbial products.}, } @article {pmid37456859, year = {2023}, author = {Real, LM and Sáez, ME and Corma-Gómez, A and Gonzalez-Pérez, A and Thorball, C and Ruiz, R and Jimenez-Leon, MR and Gonzalez-Serna, A and Gasca-Capote, C and Bravo, MJ and Royo, JL and Perez-Gomez, A and Camacho-Sojo, MI and Gallego, I and Vitalle, J and Bachiller, S and Gutierrez-Valencia, A and Vidal, F and Fellay, J and Lichterfeld, M and Ruiz-Mateos, E and , }, title = {A metagenome-wide association study of HIV disease progression in HIV controllers.}, journal = {iScience}, volume = {26}, number = {7}, pages = {107214}, pmid = {37456859}, issn = {2589-0042}, abstract = {Some HIV controllers experience immunologic progression with CD4[+] T cell decline. We aimed to identify genetic factors associated with CD4[+] T cell lost in HIV controllers. A total of 561 HIV controllers were included, 442 and 119 from the International HIV controllers Study Cohort and the Swiss HIV Cohort Study, respectively. No SNP or gene was associated with the long-term non-progressor HIV spontaneous control phenotype in the individual GWAS or in the meta-analysis. However, SNPs previously associated with natural HIV control linked to HLA-B (rs2395029 [p = 0.005; OR = 1.70], rs59440261 [p = 0.003; OR = 1.78]), MICA (rs112243036 [p = 0.011; OR = 1.45]), and PSORS1C1 loci (rs3815087 [p = 0.017; OR = 1.39]) showed nominal association with this phenotype. Genetic factors associated with the long-term HIV controllers without risk of immunologic progression are those previously related to the overall HIV controller phenotype.}, } @article {pmid37455749, year = {2023}, author = {McKindles, KM and Manes, M and Neudeck, M and McKay, RM and Bullerjahn, GS}, title = {Multi-year molecular quantification and 'omics analysis of Planktothrix-specific cyanophage sequences from Sandusky Bay, Lake Erie.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1199641}, pmid = {37455749}, issn = {1664-302X}, abstract = {INTRODUCTION: Planktothrix agardhii is a microcystin-producing cyanobacterium found in Sandusky Bay, a shallow and turbid embayment of Lake Erie. Previous work in other systems has indicated that cyanophages are an important natural control factor of harmful algal blooms. Currently, there are few cyanophages that are known to infect P. agardhii, with the best-known being PaV-LD, a tail-less cyanophage isolated from Lake Donghu, China. Presented here is a molecular characterization of Planktothrix specific cyanophages in Sandusky Bay.

METHODS AND RESULTS: Putative Planktothrix-specific viral sequences from metagenomic data from the bay in 2013, 2018, and 2019 were identified by two approaches: homology to known phage PaV-LD, or through matching CRISPR spacer sequences with Planktothrix host genomes. Several contigs were identified as having viral signatures, either related to PaV-LD or potentially novel sequences. Transcriptomic data from 2015, 2018, and 2019 were also employed for the further identification of cyanophages, as well as gene expression of select viral sequences. Finally, viral quantification was tested using qPCR in 2015-2019 for PaV-LD like cyanophages to identify the relationship between presence and gene expression of these cyanophages. Notably, while PaV-LD like cyanophages were in high abundance over the course of multiple years (qPCR), transcriptomic analysis revealed only low levels of viral gene expression.

DISCUSSION: This work aims to provide a broader understanding of Planktothrix cyanophage diversity with the goals of teasing apart the role of cyanophages in the control and regulation of harmful algal blooms and designing monitoring methodology for potential toxin-releasing lysis events.}, } @article {pmid37455748, year = {2023}, author = {Qi, L and Shi, M and Zhu, FC and Lian, CA and He, LS}, title = {Genomic evidence for the first symbiotic Deferribacterota, a novel gut symbiont from the deep-sea hydrothermal vent shrimp Rimicaris kairei.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1179935}, pmid = {37455748}, issn = {1664-302X}, abstract = {The genus Rimicaris is the dominant organism living in hydrothermal vents. However, little research has been done on the functions of their intestinal flora. Here, we investigated the potential functions of Deferribacterota, which is dominant in the intestine of Rimicaris kairei from the Central Indian Ridge. In total, six metagenome-assembled genomes (MAGs) of Deferribacterota were obtained using the metagenomic approach. The six Deferribacterota MAGs (Def-MAGs) were clustered into a new branch in the phylogenetic tree. The six Def-MAGs were further classified into three species, including one new order and two new genera, based on the results of phylogenetic analysis, relative evolutionary divergence (RED), average nucleotide identity (ANI), average amino acid identity (AAI) and DNA-DNA hybridization (DDH) values. The results of the energy metabolism study showed that these bacteria can use a variety of carbon sources, such as glycogen, sucrose, salicin, arbutin, glucose, cellobiose, and maltose. These bacteria have a type II secretion system and effector proteins that can transport some intracellular toxins to the extracellular compartment and a type V CRISPR-Cas system that can defend against various invasions. In addition, cofactors such as biotin, riboflavin, flavin mononucleotide (FMN), and flavin adenine dinucleotide (FAD) synthesized by R. kairei gut Deferribacterota may also assist their host in surviving under extreme conditions. Taken together, the potential function of Deferribacterota in the hydrothermal R. kairei gut suggests its long-term coevolution with the host.}, } @article {pmid37455745, year = {2023}, author = {Xiao, S and Mi, J and Chen, Y and Feng, K and Mei, L and Liao, X and Wu, Y and Wang, Y}, title = {The abundance and diversity of antibiotic resistance genes in layer chicken ceca is associated with farm enviroment.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1177404}, pmid = {37455745}, issn = {1664-302X}, abstract = {Industrialized layer chicken feedlots harbor complex environmental microbial communities that affect the enrichment and exchange of gut bacteria and antibiotic resistance genes (ARGs). However, the contribution of different environmental sources to the gut ARGs of layer chickens is not clear. Here, layer chicken gut and environmental samples (air, water, feed, cage, feather, maternal hen feces, uropygial glands) were collected during the early 3 month period before the laying of eggs, and the source and characteristics of the gut microorganisms and ARGs were analyzed by performing 16S rRNA and metagenomic sequencing. The results showed that the abundances of Bacteroidetes and Actinobacteria in cecum of layer chickens gradually increased, while that of Proteobacteria decreased with age, and the number and relative abundance of ARGs decreased significantly with age. On day 5, 57% of the layer chicken cecal ARGs were from feather samples, and 30% were from cage samples. Subsequently, the contribution of cage ARGs became progressively more prominent over time. At days 30 and 57, the contribution of cage ARGs to the chick cecal ARGs reached 63.3 and 69.5%, respectively. The bacterial community composition (especially the abundances of Klebsiella pneumoniae and Escherichia coli) was the major factor impacting the ARG profile. K. pneumoniae and E. coli were mainly transmitted from feathers to the layer chicken cecum, and the contribution rates were 32 and 3.4%, respectively. In addition, we observed the transmission of ARG-carrying bacteria (Bacteroides fragilis) from the cage to the gut, with a contribution rate of 11.5%. It is noteworthy that B. fragilis is an opportunistic pathogen that may cause diarrhea in laying hens. These results can provide reference data for the healthy breeding of layer chickens and the prevention and control of ARG pollution.}, } @article {pmid37455717, year = {2023}, author = {He, F and Jin, X and Wang, C and Hu, J and Su, S and Zhao, L and Geng, T and Zhao, Y and Pan, L and Bao, N and Sun, H}, title = {Lactobacillus rhamnosus GG ATCC53103 and Lactobacillus plantarum JL01 improved nitrogen metabolism in weaned piglets by regulating the intestinal flora structure and portal vein metabolites.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1200594}, pmid = {37455717}, issn = {1664-302X}, abstract = {At present, most studies have shown that probiotics have a positive regulatory effect on the nutritional metabolism of the body, but the mechanism is still unclear. Here, 48 piglets were divided into four groups. The control group was not fed probiotics, the Lac group was fed L. Rhamnosus GG ATCC53103, the Rha group was fed L. Plantarum JL01, and the mix group was fed two types of probiotics. Nitrogen metabolism and mRNA levels of mTOR and S6K in skeletal muscle were observed in each group. Then, metagenome and non-targeted metabonomics were used to observe the changes of intestinal microorganisms and plasma metabolites in portal channels after probiotics feeding. Finally, we combined the results of omics analysis to reveal the mechanism of probiotics on nitrogen metabolism in weaned piglets. The results showed that L. Rhmnosus GG ATCC53103 and L. Plantarum JL01 increased nitrogen apparent digestibility, nitrogen deposition rate, and nitrogen utilization rate of weaned piglets (P < 0.05); the relative expression of mTOR and SK6 mRNA in skeletal muscle increased significantly (P < 0.05). When L. rhamnosus GG ATCC53103 and L. plantarum JL01 were combined, we found that Clostridium and Prevotella significantly increased in the jejunum (P < 0.05). The relative abundance of Lactobacillus, Ruminococcus, Streptococcus, and Prevotella in the ileum increased significantly (P < 0.05). Compared with the control group, L-Tryptophan, 3-Phosphonyloxypyruvate, cis-Aconitate, and Carbamoyl phosphate were significantly increased in the mixed group portal vein. The result of the combinatorial analysis showed that the significantly increased microorganisms could encode the enzyme genes for the synthesis of L-Tryptophan, 3-Phosphonooxypyruvate, cis-Aconitate, and Carbamoyl phosphate. In summary, our results demonstrated that L. Rhamnosus GG ATCC53103 and L. Plantarum JL01 could stimulate the expression of skeletal muscle protein synthesis genes of weaned piglets by modulating the structure of the gut microbiota and its metabolites, thereby improving nitrogen metabolism in weaned piglets.}, } @article {pmid37455607, year = {2023}, author = {Hutchins, L and Mc Cartney, A and Graham, N and Gillespie, R and Guzman, A}, title = {Arthropods are kin: Operationalizing Indigenous data sovereignty to respectfully utilize genomic data from Indigenous lands.}, journal = {Molecular ecology resources}, volume = {}, number = {}, pages = {}, doi = {10.1111/1755-0998.13822}, pmid = {37455607}, issn = {1755-0998}, support = {//Berkeley Food Institute Faculty Seed Grant/ ; //National Science Foundation Innovations at the Nexus of Food, Energy, and Water Systems/ ; }, abstract = {Indigenous peoples have cultivated biodiverse agroecosystems since time immemorial. The rise of metagenomics and high-throughput sequencing technologies in biodiversity studies has rapidly expanded the scale of data collection from these lands. A respectful approach to the data life cycle grounded in the sovereignty of indigenous communities is imperative to not perpetuate harm. In this paper, we operationalize an indigenous data sovereignty (IDS) framework to outline realistic considerations for genomic data that span data collection, governance, and communication. As a case study for this framework, we use arthropod genomic data collected from diversified and simplified farm sites close to and far from natural habitats within a historic Kānaka 'Ōiwi (Indigenous Hawaiian) agroecosystem. Diversified sites had the highest Operational Taxonomic Unit (OTU) richness for native and introduced arthropods. There may be a significant spillover effect between forest and farm sites, as farm sites near a natural habitat had higher OTU richness than those farther away. We also provide evidence that management factors such as the number of Polynesian crops cultivated may drive arthropod community composition. Through this case study, we emphasize the context-dependent opportunities and challenges for operationalizing IDS by utilizing participatory research methods, expanding novel data management tools through the Local Contexts Hub, and developing and nurturing community partnerships-all while highlighting the potential of agroecosystems for arthropod conservation. Overall, the workflow and the example presented here can help researchers take tangible steps to achieve IDS, which often seems elusive with the expanding use of genomic data.}, } @article {pmid37455332, year = {2023}, author = {Chang, WS and Wille, M}, title = {Winter is coming-The role of seasonality through the lens of the rodent virome.}, journal = {Molecular ecology}, volume = {32}, number = {17}, pages = {4709-4712}, doi = {10.1111/mec.17078}, pmid = {37455332}, issn = {1365-294X}, mesh = {Animals ; *Virome ; Rodentia ; *Viruses/genetics ; Seasons ; Phylogeny ; Metagenomics ; }, abstract = {Rodent virus communities (viromes) are overrepresented with zoonotic viruses, and as such are a key host system for the study of zoonotic viruses. However, the extent of viral diversity beyond characterized zoonotic viruses, and the factors that modulate the viromes of rodents remain opaque. In this issue of Molecular Ecology, Raghwani et al. (2023) use rodents as a model to understand the role of seasonality in dictating virome abundance and composition-a factor known to play an important role in most animal one-host, one-pathogen systems. These data are not only highly relevant to rodents, but have broad applications across understanding and disentangling animal virome ecology.}, } @article {pmid37454463, year = {2023}, author = {Huang, J and Zhao, W and Ju, J and Liu, S and Ye, J and Long, Y}, title = {The existence of ferric hydroxide links the carbon and nitrogen cycles by promoting nitrite-coupled methane anaerobic oxidation.}, journal = {Water research}, volume = {243}, number = {}, pages = {120192}, doi = {10.1016/j.watres.2023.120192}, pmid = {37454463}, issn = {1879-2448}, mesh = {*Nitrites/metabolism ; Anaerobiosis ; *Methane/metabolism ; Carbon ; Oxidation-Reduction ; Nitrogen Cycle ; Iron ; Nitrogen ; }, abstract = {Microorganism-mediated anaerobic oxidation of methane can efficiently mitigate methane atmospheric emissions and is a key process linking the biogeochemical cycles of carbon, nitrogen, and iron. The results showed that methane oxidation and nitrite removal rates in the CF were 1.12 and 1.28 times higher than those in CK, respectively, suggesting that ferric hydroxide can enhance nitrite-driven AOM. The biochemical process was mediated by the enrichment of methanogens, methanotrophs, and denitrifiers. Methanobacterium and Methanosarcina were positively correlated with Fe[3+] and Fe[2+], whereas Methylocystis and Methylocaldum were positively correlated with methane, and denitrifiers were positively correlated with nitrite. Metagenomic analysis revealed that the genes related to methane oxidation, nitrogen reduction, and heme c-type cytochrome were upregulated in CF, indicating that a synergistic action of bacteria and methanogens drove AOM via diverse metabolic pathways, within which ferric hydroxide played a crucial role. This study provides novel insights into the synergistic mechanism of ferric iron and nitrite-driven AOM.}, } @article {pmid37454444, year = {2023}, author = {Schettini, F and Fontana, A and Gattazzo, F and Strina, C and Milani, M and Cappelletti, MR and Cervoni, V and Morelli, L and Curigliano, G and Iebba, V and Generali, D}, title = {Faecal microbiota composition is related to response to CDK4/6-inhibitors in metastatic breast cancer: A prospective cross-sectional exploratory study.}, journal = {European journal of cancer (Oxford, England : 1990)}, volume = {191}, number = {}, pages = {112948}, doi = {10.1016/j.ejca.2023.112948}, pmid = {37454444}, issn = {1879-0852}, mesh = {Humans ; Female ; *Breast Neoplasms/pathology ; Cross-Sectional Studies ; Prospective Studies ; Progression-Free Survival ; Receptor, ErbB-2/metabolism ; *Microbiota ; Protein Kinase Inhibitors/adverse effects ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; Cyclin-Dependent Kinase 4 ; }, abstract = {BACKGROUND: Cyclin-dependent kinase (CDK)4/6-inhibitors with endocrine therapy represent the standard of treatment of hormone receptor-positive(HR+)/human epidermal growth factor receptor 2 (HER2)-negative metastatic breast cancer (MBC). Gut microbiota seems to predict treatment response in several tumour types, being directly implied in chemotherapy resistance and development of adverse effects. No evidence is available on gut microbiota impact on efficacy of HR+ breast cancer treatment.

PATIENTS AND METHODS: We assessed the potential association among faecal microbiota and therapeutic efficacy of CDK4/6-inhibitors on 14 MBC patients classified as responders (R) and non-responders (NR) according to progression-free survival. A stool sample was collected at baseline and V3-V4 16S targeted sequencing was employed to assess its bacterial composition. Statistical associations with R and NR were studied.

RESULTS: No significant differences were observed between R and NR in terms of α-/β-diversity at the phylum and species level. Machine-learning (ML) algorithms evidenced four bacterial species as a discriminant for R (Bifidobacterium longum, Ruminococcus callidus) and NR (Clostridium innocuum, Schaalia odontolytica), and an area under curve (AUC) of 0.946 after Random Forest modelling. Network analysis evidenced two major clusters of bacterial species, named Species Interacting Groups (SIG)1-2, with SIG1 harbouring 75% of NR-related bacterial species, and SIG2 regrouping 76% of R-related species (p < 0.001). Cross-correlations among several patients' circulating immune cells or biomarkers and bacterial species' relative abundances showed associations with potential prognostic implications.

CONCLUSIONS: Our results provide initial insights into the gut microbiota involvement in sensitivity and/or resistance to CDK4/6-inhibitors + endocrine therapy in MBC. If confirmed in larger trials, several microbiota manipulation strategies might be hypothesised to improve response to CDK4/6-inhibitors.}, } @article {pmid37454234, year = {2023}, author = {Ustick, LJ and Larkin, AA and Martiny, AC}, title = {Global scale phylogeography of functional traits and microdiversity in Prochlorococcus.}, journal = {The ISME journal}, volume = {17}, number = {10}, pages = {1671-1679}, pmid = {37454234}, issn = {1751-7370}, support = {T32 AI141346/AI/NIAID NIH HHS/United States ; }, mesh = {Phylogeography ; Phylogeny ; *Prochlorococcus/genetics ; Seawater ; Ecotype ; }, abstract = {Prochlorococcus is the most numerically abundant photosynthetic organism in the surface ocean. The Prochlorococcus high-light and warm-water adapted ecotype (HLII) is comprised of extensive microdiversity, but specific functional differences between microdiverse sub-clades remain elusive. Here we characterized both functional and phylogenetic diversity within the HLII ecotype using Bio-GO-SHIP metagenomes. We found widespread variation in gene frequency connected to local environmental conditions. Metagenome-assembled marker genes and genomes revealed a globally distributed novel HLII haplotype defined by adaptation to chronically low P conditions (HLII-P). Environmental correlation analysis revealed different factors were driving gene abundances verses phylogenetic differences. An analysis of cultured HLII genomes and metagenome-assembled genomes revealed a subclade within HLII, which corresponded to the novel HLII-P haplotype. This work represents the first global assessment of the HLII ecotype's phylogeography and corresponding functional differences. These findings together expand our understanding of how microdiversity structures functional differences and reveals the importance of nutrients as drivers of microdiversity in Prochlorococcus.}, } @article {pmid37454192, year = {2023}, author = {Zhang, R and Aris-Brosou, S and Storck, V and Liu, J and Abdelhafiz, MA and Feng, X and Meng, B and Poulain, AJ}, title = {Mining-impacted rice paddies select for Archaeal methylators and reveal a putative (Archaeal) regulator of mercury methylation.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {74}, pmid = {37454192}, issn = {2730-6151}, support = {41931297, 42022024, and 41921004//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Methylmercury (MeHg) is a microbially produced neurotoxin derived from inorganic mercury (Hg), which accumulation in rice represents a major health concern to humans. However, the microbial control of MeHg dynamics in the environment remains elusive. Here, leveraging three rice paddy fields with distinct concentrations of Hg (Total Hg (THg): 0.21-513 mg kg[-1] dry wt. soil; MeHg: 1.21-6.82 ng g[-1] dry wt. soil), we resorted to metagenomics to determine the microbial determinants involved in MeHg production under contrasted contamination settings. We show that Hg methylating Archaea, along with methane-cycling genes, were enriched in severely contaminated paddy soils. Metagenome-resolved Genomes of novel putative Hg methylators belonging to Nitrospinota (UBA7883), with poorly resolved taxonomy despite high completeness, showed evidence of facultative anaerobic metabolism and adaptations to fluctuating redox potential. Furthermore, we found evidence of environmental filtering effects that influenced the phylogenies of not only hgcA genes under different THg concentrations, but also of two housekeeping genes, rpoB and glnA, highlighting the need for further experimental validation of whether THg drives the evolution of hgcAB. Finally, assessment of the genomic environment surrounding hgcAB suggests that this gene pair may be regulated by an archaeal toxin-antitoxin (TA) system, instead of the more frequently found arsR-like genes in bacterial methylators. This suggests the presence of distinct hgcAB regulation systems in bacteria and archaea. Our results support the emerging role of Archaea in MeHg cycling under mining-impacted environments and shed light on the differential control of the expression of genes involved in MeHg formation between Archaea and Bacteria.}, } @article {pmid37453509, year = {2023}, author = {Yan, M and Xu, C and Li, C and Feng, Y and Duan, J and Zhao, K and Wu, D and Li, G and Yang, S and Han, X and Xie, Y and Huang, Y and Yu, X and Wu, J and Zou, L}, title = {Effects of environmental disinfection on microbial population and resistance genes: A case study of the microecology within a panda enclosure.}, journal = {Environmental research}, volume = {235}, number = {}, pages = {116662}, doi = {10.1016/j.envres.2023.116662}, pmid = {37453509}, issn = {1096-0953}, mesh = {*Disinfection ; Anti-Bacterial Agents/pharmacology ; *Disinfectants/pharmacology ; Escherichia coli ; Bacteria/genetics ; Soil ; }, abstract = {Widespread use of disinfectants raises concerns over their involvement in altering microbial communities and promoting antimicrobial resistance. This study explores the influence of disinfection protocols on microbial populations and resistance genes within an isolated enclosure environment and in the gut of giant pandas (GPs) held within. Samples of panda feces, air conditioning ducts, soil and bamboo were collected before and after disinfection. High-throughput sequencing characterized the microbial flora of GP gut and environmental microbes inside the artificial habitat. Microbial cultures showed that Escherichia coli (34.6%), Enterococcus (15.4%) and other pathogenic bacteria deposited in feces and the enclosure. Isolates exhibit a consistent resistance to disinfectant, with the greatest resistance shown to cyanuric acid, and the lowest to glutaraldehyde-dodecyl dimethyl ammonium bromide (GD-DDAB) and dodecyl dimethyl ammonium bromide (DDAB). The total number of the culturable bacteria in soil and bamboo were significantly diminished after disinfection but increased in the gut. After disinfection, the richness (Chao1 index) of environment samples increased significantly (P < 0.05), while the richness in gut decreased significantly (P < 0.05). Ten genera showed significant change in feces after disinfection. Metagenome sequencing showed that 126 types of virulence genes were present in feces before disinfection and 37 in soil. After disinfection, 110 virulence genes localized in feces and 53 in soil. Eleven virulence genes including ECP and T2SS increased in feces. A total of 182 antibiotic resistance genes (ARGs) subtypes, potentially conferring resistance to 20 classes of drugs, were detected in the soils and feces, with most belonging to efflux pump protein pathways. After disinfection, the number of resistance genes increased both in gut and soil, which suggests disinfection protocols increase the number of resistance pathways. Our study shows that the use of disinfectants helps to shape the microbial community of GPs and their habitat, and increases populations of resistant strain bacteria.}, } @article {pmid37453490, year = {2023}, author = {Sun, WW and Dong, ZW and Zhou, YM and Jin, F and Liu, HC and Fan, L}, title = {Improving the identification and diagnostic efficiency of Metagenomic Next-Generation Sequencing for mycobacterial granuloma on postoperative formalin-fixed paraffin-embedded specimens.}, journal = {Microbes and infection}, volume = {25}, number = {8}, pages = {105185}, doi = {10.1016/j.micinf.2023.105185}, pmid = {37453490}, issn = {1769-714X}, mesh = {Humans ; Paraffin Embedding ; *Mycobacterium/genetics ; *Tuberculosis/microbiology ; Formaldehyde ; High-Throughput Nucleotide Sequencing ; Granuloma/diagnosis ; *Mycobacterium tuberculosis/genetics ; Retrospective Studies ; Metagenomics ; }, abstract = {OBJECTIVE: Metagenomic Next-Generation Sequencing (mNGS) has been validated to have an important role in the diagnosis of mycobacterium infection. The study aimed to further explore the mycobacteria identification ability of mNGS on formalin-fixed paraffin-embedded（FFPE）tissues from postoperative specimens.

METHODS: Patients who underwent surgical biopsy or resection for clarifying the diagnosis and whose initial postoperative pathology indicated granulomatous lesions were included. Fresh tissues were sent for mycobacterium culture and Xpert MTB/RIF (Xpert) to establish the diagnosis. FFPE specimens were sent for mNGS and molecular pathology，the diagnostic values were compared between the two methods.

RESULTS: A total of 65 cases with definite diagnoses were finally included in the study. 31 cases were confirmed as mycobacterium granuloma using the fresh specimen etiology as diagnostic criteria. The overall sensitivity and specificity of mNGS on FFPE specimens in the diagnosis of mycobacterium granuloma were 100% and 88.24%, respectively. In 19 cases diagnosed as tuberculous granulomas, the sensitivity (100% vs47.37%) and negative predictive value (NPV, 100%vs 82.14%) of mNGS were both significantly higher than that of molecular pathology on the FFPE section（both p 0.00）while the positive predictive value (PPV) and specificity were not significantly different. In 12 cases diagnosed as Non-tuberculous mycobacterium (NTM）granuloma, the sensitivity of mNGS was also significantly higher than that of molecular pathology on FFPE section (100% vs 66.67%, p 0.00) while the specificity, PPV and NPV were all not significantly different.

CONCLUSIONS: The mNGS could be used for one-time detection of pathogens on FFPE sections with high sensitivity. It could be recommended as a supplementary method for the identification of pathogenic bacteria in the diagnosis of postoperative granuloma lesions.}, } @article {pmid37453352, year = {2023}, author = {Li, Y and Shi, X and Tan, W and Ling, Q and Pei, F and Luo, S and Qin, P and Yuan, H and Huang, L and Yu, F}, title = {Metagenomics combined with metabolomics reveals the effect of Enterobacter sp. inoculation on the rhizosphere microenvironment of Bidens pilosa L. in heavy metal contaminated soil.}, journal = {Journal of hazardous materials}, volume = {458}, number = {}, pages = {132033}, doi = {10.1016/j.jhazmat.2023.132033}, pmid = {37453352}, issn = {1873-3336}, mesh = {*Bidens ; Rhizosphere ; Soil/chemistry ; Enterobacter/metabolism ; Metagenomics ; *Soil Pollutants/metabolism ; *Metals, Heavy/metabolism ; Biodegradation, Environmental ; Metabolomics ; Soil Microbiology ; Cadmium/analysis ; }, abstract = {Metagenomics analysis was performed to determine the effects of Enterobacter sp. FM-1 (FM-1) on key genera as well as functional genes in the rhizosphere of Bidens pilosa L. (B. pilosa L.). Moreover, metabolomics was used to reveal the differences among rhizosphere metabolites after FM-1 inoculation. FM-1 inoculation significantly increased the activity of enzymes associated with the carbon cycle in soil; among them, invertase activity increased by 5.52 units compared to a control. Specifically, the relative abundance of beneficial genera increased significantly, such as Lysobacter (0.45-2.58 unit increase) in low-contamination soils (LC) and Pseudomonas (31.17-45.99 unit increase) in high-contamination soils (HC). Comparison of different transformation processes of the C cycle revealed that inoculation of FM-1 increased the abundance of functional genes related to the carbon cycle in LC soil. In contrast, the nitrogen cycling pathway was significantly elevated in both the LC and HC soils. FM-1 inoculation reduced HM resistance gene abundance in the rhizosphere soil of B. pilosa L. in the LC soil. Moreover, FM-1 and B. pilosa L. interactions promoted the secretion of rhizosphere metabolites, in which lipids and amino acids played important roles in the phytoremediation process. Overall, we explored the rhizosphere effects induced by plantmicrobe interactions, providing new insights into the functional microbes and rhizosphere metabolites involved in phytoremediation.}, } @article {pmid37452210, year = {2023}, author = {Najah, H and Edelmuth, RCL and Riascos, MC and Grier, A and Al Asadi, H and Greenberg, JA and Miranda, I and Crawford, CV and Finnerty, BM and Fahey, TJ and Zarnegar, R}, title = {Long-term potassium-competitive acid blockers administration causes microbiota changes in rats.}, journal = {Surgical endoscopy}, volume = {37}, number = {10}, pages = {7980-7990}, pmid = {37452210}, issn = {1432-2218}, mesh = {Rats ; Animals ; *Helicobacter Infections ; Potassium/pharmacology/therapeutic use ; Prospective Studies ; Rats, Wistar ; Anti-Bacterial Agents/therapeutic use ; Pyrroles/pharmacology/therapeutic use ; *Gastrointestinal Microbiome ; *Helicobacter pylori/physiology ; Proton Pump Inhibitors/therapeutic use ; Drug Therapy, Combination ; }, abstract = {BACKGROUND: Vonoprazan is a new potassium-competitive acid blocker (P-CAB) that was recently approved by the FDA. It is associated with a fast onset of action and a longer acid inhibition time. Vonoprazan-containing therapy for helicobacter pylori eradication is highly effective and several studies have demonstrated that a vonoprazan-antibiotic regimen affects gut microbiota. However, the impact of vonoprazan alone on gut microbiota is still unclear.Please check and confirm the authors (Maria Cristina Riascos, Hala Al Asadi) given name and family name are correct. Also, kindly confirm the details in the metadata are correct.Yes they are correct. METHODS: We conducted a prospective randomized 12-week experimental trial with 18 Wistar rats. Rats were randomly assigned to one of 3 groups: (1) drinking water as negative control group, (2) oral vonoprazan (4 mg/kg) for 12 weeks, and (3) oral vonoprazan (4 mg/kg) for 4 weeks, followed by 8 weeks off vonoprazan. To investigate gut microbiota, we carried out a metagenomic shotgun sequencing of fecal samples at week 0 and week 12.Please confirm the inserted city and country name is correct for affiliation 2.Yes it's correct.

RESULTS: For alpha diversity metrics at week 12, both long and short vonoprazan groups had lower Pielou's evenness index than the control group (p = 0.019); however, observed operational taxonomic units (p = 0.332) and Shannon's diversity index (p = 0.070) were not statistically different between groups. Beta diversity was significantly different in the three groups, using Bray-Curtis (p = 0.003) and Jaccard distances (p = 0.002). At week 12, differences in relative abundance were observed at all levels. At phylum level, short vonoprazan group had less of Actinobacteria (log fold change = - 1.88, adjusted p-value = 0.048) and Verrucomicrobia (lfc = - 1.76, p = 0.009).Please check and confirm that the author (Ileana Miranda) and their respective affiliation 3 details have been correctly identified and amend if necessary.Yes it's correct. At the genus level, long vonoprazan group had more Bacteroidales (lfc = 5.01, p = 0.021) and Prevotella (lfc = 7.79, p = 0.001). At family level, long vonoprazan group had more Lactobacillaceae (lfc = 0.97, p = 0.001), Prevotellaceae (lfc = 8.01, p < 0.001), and less Erysipelotrichaceae (lfc = - 2.9, p = 0.029).

CONCLUSION: This study provides evidence that vonoprazan impacts the gut microbiota and permits a precise delineation of the composition and relative abundance of the bacteria at all different taxonomic levels.}, } @article {pmid37452097, year = {2023}, author = {Buchholz, HH and Bolaños, LM and Bell, AG and Michelsen, ML and Allen, MJ and Temperton, B}, title = {Novel pelagiphage isolate Polarivirus skadi is a polar specialist that dominates SAR11-associated bacteriophage communities at high latitudes.}, journal = {The ISME journal}, volume = {17}, number = {10}, pages = {1660-1670}, pmid = {37452097}, issn = {1751-7370}, mesh = {*Bacteriophages ; Seawater ; Specialization ; Phylogeny ; Water ; *Alphaproteobacteria ; }, abstract = {The SAR11 clade are the most abundant members of surface marine bacterioplankton and a critical component of global biogeochemical cycles. Similarly, pelagiphages that infect SAR11 are ubiquitous and highly abundant in the oceans. Pelagiphages are predicted to shape SAR11 community structures and increase carbon turnover throughout the oceans. Yet, ecological drivers of host and niche specificity of pelagiphage populations are poorly understood. Here we report the global distribution of a novel pelagiphage called "Polarivirus skadi", which is the sole representative of a novel genus. P. skadi was isolated from the Western English Channel using a cold-water ecotype of SAR11 as bait. P. skadi is closely related to the globally dominant pelagiphage HTVC010P. Along with other HTVC010P-type viruses, P. skadi belongs to a distinct viral family within the order Caudovirales, for which we propose the name Ubiqueviridae. Metagenomic read recruitment identified P. skadi as one of the most abundant pelagiphages on Earth. P. skadi is a polar specialist, replacing HTVC010P at high latitudes. Experimental evaluation of P. skadi host range against cold- and warm-water SAR11 ecotypes supported cold-water specialism. Relative abundance of P. skadi in marine metagenomes correlated negatively with temperature, and positively with nutrients, available oxygen, and chlorophyll concentrations. In contrast, relative abundance of HTVC010P correlated negatively with oxygen and positively with salinity, with no significant correlation to temperature. The majority of other pelagiphages were scarce in most marine provinces, with a few representatives constrained to discrete ecological niches. Our results suggest that pelagiphage populations persist within a global viral seed bank, with environmental parameters and host availability selecting for a few ecotypes that dominate ocean viromes.}, } @article {pmid37452096, year = {2023}, author = {Buessecker, S and Chadwick, GL and Quan, ME and Hedlund, BP and Dodsworth, JA and Dekas, AE}, title = {Mcr-dependent methanogenesis in Archaeoglobaceae enriched from a terrestrial hot spring.}, journal = {The ISME journal}, volume = {17}, number = {10}, pages = {1649-1659}, pmid = {37452096}, issn = {1751-7370}, support = {Postdoctoral Program/NASA/NASA/United States ; 80NNSC17KO548/NASA/NASA/United States ; 80NSSC19M0150/NASA/NASA/United States ; }, mesh = {Phylogeny ; *Hot Springs ; *Archaeoglobales/metabolism ; Methane/metabolism ; Archaea ; }, abstract = {The preeminent source of biological methane on Earth is methyl coenzyme M reductase (Mcr)-dependent archaeal methanogenesis. A growing body of evidence suggests a diversity of archaea possess Mcr, although experimental validation of hypothesized methane metabolisms has been missing. Here, we provide evidence of a functional Mcr-based methanogenesis pathway in a novel member of the family Archaeoglobaceae, designated Methanoglobus nevadensis, which we enriched from a terrestrial hot spring on the polysaccharide xyloglucan. Our incubation assays demonstrate methane production that is highly sensitive to the Mcr inhibitor bromoethanesulfonate, stimulated by xyloglucan and xyloglucan-derived sugars, concomitant with the consumption of molecular hydrogen, and causing a deuterium fractionation in methane characteristic of hydrogenotrophic and methylotrophic methanogens. Combined with the recovery and analysis of a high-quality M. nevadensis metagenome-assembled genome encoding a divergent Mcr and diverse potential electron and carbon transfer pathways, our observations suggest methanogenesis in M. nevadensis occurs via Mcr and is fueled by the consumption of cross-fed byproducts of xyloglucan fermentation mediated by other community members. Phylogenetic analysis shows close affiliation of the M. nevadensis Mcr with those from Korarchaeota, Nezhaarchaeota, Verstraetearchaeota, and other Archaeoglobales that are divergent from well-characterized Mcr. We propose these archaea likely also use functional Mcr complexes to generate methane on the basis of our experimental validation in M. nevadensis. Thus, divergent Mcr-encoding archaea may be underestimated sources of biological methane in terrestrial and marine hydrothermal environments.}, } @article {pmid37452065, year = {2023}, author = {Pomyen, Y and Chaisaingmongkol, J and Rabibhadana, S and Pupacdi, B and Sripan, D and Chornkrathok, C and Budhu, A and Budhisawasdi, V and Lertprasertsuke, N and Chotirosniramit, A and Pairojkul, C and Auewarakul, CU and Ungtrakul, T and Sricharunrat, T and Phornphutkul, K and Sangrajang, S and Loffredo, CA and Harris, CC and Mahidol, C and Wang, XW and Ruchirawat, M and , }, title = {Gut dysbiosis in Thai intrahepatic cholangiocarcinoma and hepatocellular carcinoma.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {11406}, pmid = {37452065}, issn = {2045-2322}, support = {ZIA BC011870/ImNIH/Intramural NIH HHS/United States ; Z01 BC010877/ImNIH/Intramural NIH HHS/United States ; Z01 BC010876/ImNIH/Intramural NIH HHS/United States ; Z01 BC010313/ImNIH/Intramural NIH HHS/United States ; ZIA BC011870/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Humans ; *Carcinoma, Hepatocellular/pathology ; *Liver Neoplasms/pathology ; Dysbiosis ; Southeast Asian People ; Thailand/epidemiology ; *Bile Duct Neoplasms/pathology ; *Cholangiocarcinoma/pathology ; Bile Ducts, Intrahepatic/pathology ; }, abstract = {Primary liver cancer (PLC), which includes intrahepatic cholangiocarcinoma (iCCA) and hepatocellular carcinoma (HCC), has the highest incidence of all cancer types in Thailand. Known etiological factors, such as viral hepatitis and chronic liver disease do not fully account for the country's unusually high incidence. However, the gut-liver axis, which contributes to carcinogenesis and disease progression, is influenced by the gut microbiome. To investigate this relationship, fecal matter from 44 Thai PLC patients and 76 healthy controls were subjected to whole-genome metagenomic shotgun sequencing and then analyzed by marker gene-based and assembly based methods. Results revealed greater gut microbiome heterogeneity in iCCA compared to HCC and healthy controls. Two Veillonella species were found to be more abundant in iCCA samples and could distinguish iCCA from HCC and healthy controls. Conversely, Ruminococcus gnavus was depleted in iCCA patients and could distinguish HCC from iCCA samples. High Veillonella genus counts in the iCCA group were associated with enriched amino acid biosynthesis and glycolysis pathways, while enriched phospholipid and thiamine metabolism pathways characterized the HCC group with high Blautia genus counts. These findings reveal distinct landscapes of gut dysbiosis among Thai iCCA and HCC patients and warrant further investigation as potential biomarkers.}, } @article {pmid37452041, year = {2023}, author = {Tarracchini, C and Alessandri, G and Fontana, F and Rizzo, SM and Lugli, GA and Bianchi, MG and Mancabelli, L and Longhi, G and Argentini, C and Vergna, LM and Anzalone, R and Viappiani, A and Turroni, F and Taurino, G and Chiu, M and Arboleya, S and Gueimonde, M and Bussolati, O and van Sinderen, D and Milani, C and Ventura, M}, title = {Genetic strategies for sex-biased persistence of gut microbes across human life.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4220}, pmid = {37452041}, issn = {2041-1723}, mesh = {Male ; Humans ; Female ; *Gastrointestinal Microbiome/genetics ; Bifidobacterium/genetics/metabolism ; *Microbiota ; Bacteria/genetics ; }, abstract = {Although compositional variation in the gut microbiome during human development has been extensively investigated, strain-resolved dynamic changes remain to be fully uncovered. In the current study, shotgun metagenomic sequencing data of 12,415 fecal microbiomes from healthy individuals are employed for strain-level tracking of gut microbiota members to elucidate its evolving biodiversity across the human life span. This detailed longitudinal meta-analysis reveals host sex-related persistence of strains belonging to common, maternally-inherited species, such as Bifidobacterium bifidum and Bifidobacterium longum subsp. longum. Comparative genome analyses, coupled with experiments including intimate interaction between microbes and human intestinal cells, show that specific bacterial glycosyl hydrolases related to host-glycan metabolism may contribute to more efficient colonization in females compared to males. These findings point to an intriguing ancient sex-specific host-microbe coevolution driving the selective persistence in women of key microbial taxa that may be vertically passed on to the next generation.}, } @article {pmid37450589, year = {2023}, author = {Shi, B and Zhang, X and Song, Z and Dai, Z and Luo, K and Chen, B and Zhou, Z and Cui, Y and Feng, B and Zhu, Z and Zheng, J and Zhang, H and He, X}, title = {Targeting gut microbiota-derived kynurenine to predict and protect the remodeling of the pressure-overloaded young heart.}, journal = {Science advances}, volume = {9}, number = {28}, pages = {eadg7417}, pmid = {37450589}, issn = {2375-2548}, mesh = {Animals ; Mice ; *Kynurenine/metabolism ; *Gastrointestinal Microbiome ; Heart ; Fibroblasts/metabolism ; Metabolomics ; }, abstract = {Pressure-overloaded left ventricular remodeling in young population is progressive and readily degenerate into heart failure. The aims of this study were to identify a plasma metabolite that predicts and is mechanistically linked to the disease. Untargeted metabolomics determined elevated plasma kynurenine (Kyn) in both the patient cohorts and the mice model, which was correlated with remodeling parameters. In vitro and in vivo evidence, combined with single-nucleus RNA sequencing (snRNA-seq), demonstrated that Kyn affected both cardiomyocytes and cardiac fibroblasts by activating aryl hydrocarbon receptors (AHR) to up-regulate hypertrophy- and fibrosis-related genes. Shotgun metagenomics and fecal microbiota transplantation revealed the existence of the altered gut microbiota-Kyn relationship. Supplementation of selected microbes reconstructed the gut microbiota, reduced plasma Kyn, and alleviated ventricular remodeling. Our data collectively discovered a gut microbiota-derived metabolite to activate AHR and its gene targets in remodeling young heart, a process that could be prevented by specific gut microbiota modulation.}, } @article {pmid37450270, year = {2023}, author = {Salam, LB}, title = {Diverse hydrocarbon degradation genes, heavy metal resistome, and microbiome of a fluorene-enriched animal-charcoal polluted soil.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {37450270}, issn = {1874-9356}, abstract = {Environmental compartments polluted with animal charcoal from the skin and hide cottage industries are rich in toxic heavy metals and diverse hydrocarbon classes, some of which are carcinogenic, mutagenic, and genotoxic, and thus require a bio-based eco-benign decommission strategies. A shotgun metagenomic approach was used to decipher the microbiome, hydrocarbon degradation genes, and heavy metal resistome of a microbial consortium (FN8) from an animal-charcoal polluted site enriched with fluorene. Structurally, the FN8 microbial consortium consists of 26 phyla, 53 classes, 119 orders, 245 families, 620 genera, and 1021 species. The dominant phylum, class, order, family, genus, and species in the consortium are Proteobacteria (51.37%), Gammaproteobacteria (39.01%), Bacillales (18.09%), Microbulbiferaceae (11.65%), Microbulbifer (12.21%), and Microbulbifer sp. A4B17 (19.65%), respectively. The microbial consortium degraded 57.56% (28.78 mg/L) and 87.14% (43.57 mg/L) of the initial fluorene concentration in 14 and 21 days. Functional annotation of the protein sequences (ORFs) of the FN8 metagenome using the KEGG GhostKOALA, KofamKOALA, NCBI's conserved domain database, and BacMet revealed the detection of hydrocarbon degradation genes for benzoate, aminobenzoate, polycyclic aromatic hydrocarbons (PAHs), chlorocyclohexane/chlorobenzene, chloroalkane/chloroalkene, toluene, xylene, styrene, naphthalene, nitrotoluene, and several others. The annotation also revealed putative genes for the transport, uptake, efflux, and regulation of heavy metals such as arsenic, cadmium, chromium, mercury, nickel, copper, zinc, and several others. Findings from this study have established that members of the FN8 consortium are well-adapted and imbued with requisite gene sets and could be a potential bioresource for on-site depuration of animal charcoal polluted sites.}, } @article {pmid37450112, year = {2023}, author = {Ji, X and Ni, S and Tian, G and Zhang, L and Wang, W}, title = {Detection of Microorganisms in Body Fluid Samples.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2695}, number = {}, pages = {73-88}, pmid = {37450112}, issn = {1940-6029}, mesh = {RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA/methods ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; *Body Fluids ; }, abstract = {Next-generation sequencing (NGS) has been widely applied to the identification of microbiome in body fluids. The methodology of 16S rRNA amplicon sequencing is simple, fast, and cost-effective. It overcomes the problem that some microorganisms cannot be isolated or cultured. Low abundant bacteria can also be amplified and sequenced, but the resolution of classification can hardly reach species or sub-species level; moreover, this methodology is mainly used to identify bacterial populations, and other microorganisms like viruses or fungi cannot be sequenced. On the other hand, the microbiome profiling obtained by shotgun metagenomic sequencing is more comprehensive with better resolution, and more accurate classification can be expected due to higher coverage of genomic sequences from microorganisms. By combining the capture-based method with metagenomic sequencing, we can further enrich and detect low abundant microorganisms and identify the viral integration sites in host gDNA at once.}, } @article {pmid37449883, year = {2023}, author = {Olo Ndela, E and Enault, F}, title = {CodingDiv: analyzing SNP-level microdiversity to discriminate between coding and noncoding regions in viral genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {7}, pages = {}, pmid = {37449883}, issn = {1367-4811}, mesh = {*Polymorphism, Single Nucleotide ; *Software ; Databases, Factual ; Genome, Viral ; Metagenomics ; }, abstract = {SUMMARY: Viral genes, that are frequently small genes and/or with large overlaps, are still difficult to predict accurately. To help predict all genes in viral genomes, we provide CodingDiv that detects SNP-level microdiversity of all potential coding regions, using metagenomic reads and/or similar sequences from external databases. Protein coding regions can then be identified as the ones containing more synonymous SNPs than unfavorable nonsynonymous substitutions SNPs.

CodingDiv is released under the GPL license. Source code is available at https://github.com/ericolo/codingDiv. The software can be installed and used through a docker container.}, } @article {pmid37448884, year = {2023}, author = {Liao, H and Zhu, M and Cheng, Z}, title = {Epstein-Barr virus (EBV) induced pneumonitis in a patient with breast cancer receiving neoadjuvant chemotherapy: A case report.}, journal = {Respiratory medicine case reports}, volume = {45}, number = {}, pages = {101849}, pmid = {37448884}, issn = {2213-0071}, abstract = {BACKGROUND: Epstein-Barr virus (EBV) usually leads to latent infection and is reported mostly in infectious mononucleosis, lymphoma, and cancer in adolescents and adults, but pneumonitis due to EBV infection in adults is rare.

CASE PRESENTATION: We hereby reported a case of a 52-year-old woman with breast cancer who developed acute pneumonia during neoadjuvant chemotherapy. Her serologic workup revealed a low CD4[+] count and positive anti-EBV antibodies. Chest computed tomography (CT) shows multiple patchy ground-glass shadows in the bilateral lung. Microscopic examination of stained sputum and bronchoalveolar lavage fluid (BALF) smear specimens did not find any pathogens. Metagenomic next-generation sequencing (mNGS) of BALF indicated a large number of EBV reads, allowing to confirm the diagnosis of EBV induced pneumonitis. The patient was then treated with ganciclovir with subsequent dramatic clinical and radiological improvement.

CONCLUSIONS: This case highlights the combined application of mNGS and traditional tests in the clinical diagnosis of invasive pulmonary infection. In the meanwhile, clinicians should be aware neoadjuvant chemotherapy for breast cancer carries a risk of EBV induced pneumonitis, so that EBV induced pneumonitis could be considered in differential diagnosis while similar patients present, to orchestrate improvements in diagnosis, treatment, and prognosis.}, } @article {pmid37448812, year = {2023}, author = {Chafra, F and Borim Correa, F and Oni, F and Konu Karakayalı, Ö and Stadler, PF and Nunes da Rocha, U}, title = {StandEnA: a customizable workflow for standardized annotation and generating a presence-absence matrix of proteins.}, journal = {Bioinformatics advances}, volume = {3}, number = {1}, pages = {vbad069}, pmid = {37448812}, issn = {2635-0041}, abstract = {MOTIVATION: Several genome annotation tools standardize annotation outputs for comparability. During standardization, these tools do not allow user-friendly customization of annotation databases; limiting their flexibility and applicability in downstream analysis.

RESULTS: StandEnA is a user-friendly command-line tool for Linux that facilitates the generation of custom databases by retrieving protein sequences from multiple databases. Directed by a user-defined list of standard names, StandEnA retrieves synonyms to search for corresponding sequences in a set of public databases. Custom databases are used in prokaryotic genome annotation to generate standardized presence-absence matrices and reference files containing standard database identifiers. To showcase StandEnA, we applied it to six metagenome-assembled genomes to analyze three different pathways.

StandEnA is an open-source software available at https://github.com/mdsufz/StandEnA.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.}, } @article {pmid37448579, year = {2023}, author = {Batool, M and Galloway-Peña, J}, title = {Clinical metagenomics-challenges and future prospects.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1186424}, pmid = {37448579}, issn = {1664-302X}, abstract = {Infections lacking precise diagnosis are often caused by a rare or uncharacterized pathogen, a combination of pathogens, or a known pathogen carrying undocumented or newly acquired genes. Despite medical advances in infectious disease diagnostics, many patients still experience mortality or long-term consequences due to undiagnosed or misdiagnosed infections. Thus, there is a need for an exhaustive and universal diagnostic strategy to reduce the fraction of undocumented infections. Compared to conventional diagnostics, metagenomic next-generation sequencing (mNGS) is a promising, culture-independent sequencing technology that is sensitive to detecting rare, novel, and unexpected pathogens with no preconception. Despite the fact that several studies and case reports have identified the effectiveness of mNGS in improving clinical diagnosis, there are obvious shortcomings in terms of sensitivity, specificity, costs, standardization of bioinformatic pipelines, and interpretation of findings that limit the integration of mNGS into clinical practice. Therefore, physicians must understand the potential benefits and drawbacks of mNGS when applying it to clinical practice. In this review, we will examine the current accomplishments, efficacy, and restrictions of mNGS in relation to conventional diagnostic methods. Furthermore, we will suggest potential approaches to enhance mNGS to its maximum capacity as a clinical diagnostic tool for identifying severe infections.}, } @article {pmid37448101, year = {2023}, author = {Bao, S and Wang, H and Li, W and Wu, H and Lu, C and Yong, L and Zhang, Q and Lu, X and Zhao, M and Lu, J and Liu, J and Ikechukwu, CK and Xu, J and Ni, P and Xiong, Y and Zhang, W and Zhou, C}, title = {Viral metagenomics of the gut virome of diarrheal children with Rotavirus A infection.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2234653}, pmid = {37448101}, issn = {1949-0984}, mesh = {Humans ; Child ; *Rotavirus/genetics ; Metagenomics ; *Gastrointestinal Microbiome ; China/epidemiology ; Diarrhea/epidemiology ; *Rotavirus Infections ; Feces ; }, abstract = {Diarrhea is a leading cause of morbidity and mortality in children worldwide and represents a major dysbiosis event. Rotavirus has been recognized as a global leading pathogen of diarrhea. This study is aimed at investigating differences in the gut virome between diarrheal children and healthy controls. In 2018, 76 diarrheal fecal samples and 27 healthy fecal samples in Shanghai and 40 diarrheal fecal samples and 19 healthy fecal samples in Taizhou were collected to investigate the composition of the gut virome. Viral metagenomic analyses revealed that the alpha diversity of the diarrheal virome was not significantly different from that of the healthy virome, and the beta diversity had a significant difference between diarrheal and healthy children. The diarrheal virome was mainly dominated by the families Adenoviridae, Astroviridae, Caliciviridae, and Picornaviridae. Meanwhile, the healthy virome also contains phages, including Microviridae and Caudovirales. The high prevalence of diverse enteric viruses in all samples and the little abundance of Microviridae and Caudovirales in diarrheal groups were identified. The study introduced a general overview of the gut virome in diarrheal children, revealed the compositional differences in the gut viral community compared to healthy controls, and provided a reference for efficient treatments and prevention of virus-infectious diarrhea in children.}, } @article {pmid37446705, year = {2023}, author = {Padilla-Vaca, F and de la Mora, J and García-Contreras, R and Ramírez-Prado, JH and Alva-Murillo, N and Fonseca-Yepez, S and Serna-Gutiérrez, I and Moreno-Galván, CL and Montufar-Rodríguez, JM and Vicente-Gómez, M and Rangel-Serrano, Á and Vargas-Maya, NI and Franco, B}, title = {Two-Component System Sensor Kinases from Asgardian Archaea May Be Witnesses to Eukaryotic Cell Evolution.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {13}, pages = {}, pmid = {37446705}, issn = {1420-3049}, mesh = {*Archaea/genetics/metabolism ; *Eukaryotic Cells ; Bacteria/genetics ; Eukaryota/genetics ; Prokaryotic Cells ; Evolution, Molecular ; Phylogeny ; }, abstract = {The signal transduction paradigm in bacteria involves two-component systems (TCSs). Asgardarchaeota are archaea that may have originated the current eukaryotic lifeforms. Most research on these archaea has focused on eukaryotic-like features, such as genes involved in phagocytosis, cytoskeleton structure, and vesicle trafficking. However, little attention has been given to specific prokaryotic features. Here, the sequence and predicted structural features of TCS sensor kinases analyzed from two metagenome assemblies and a genomic assembly from cultured Asgardian archaea are presented. The homology of the sensor kinases suggests the grouping of Lokiarchaeum closer to bacterial homologs. In contrast, one group from a Lokiarchaeum and a meta-genome assembly from Candidatus Heimdallarchaeum suggest the presence of a set of kinases separated from the typical bacterial TCS sensor kinases. AtoS and ArcB homologs were found in meta-genome assemblies along with defined domains for other well-characterized sensor kinases, suggesting the close link between these organisms and bacteria that may have resulted in the metabolic link to the establishment of symbiosis. Several kinases are predicted to be cytoplasmic; some contain several PAS domains. The data shown here suggest that TCS kinases in Asgardian bacteria are witnesses to the transition from bacteria to eukaryotic organisms.}, } @article {pmid37446198, year = {2023}, author = {Gu, X and Cao, Z and Zhao, L and Seswita-Zilda, D and Zhang, Q and Fu, L and Li, J}, title = {Metagenomic Insights Reveal the Microbial Diversity and Associated Algal-Polysaccharide-Degrading Enzymes on the Surface of Red Algae among Remote Regions.}, journal = {International journal of molecular sciences}, volume = {24}, number = {13}, pages = {}, pmid = {37446198}, issn = {1422-0067}, support = {RFSOCC2023-2025//Impact and Response of Antarctic Seas to Climate Change/ ; RFSOCC2023-2025//Jiang Li/ ; }, mesh = {Metagenomics ; Bacteria/genetics/metabolism ; *Rhodophyta/genetics ; Metagenome ; *Seaweed ; Polysaccharides/metabolism ; }, abstract = {Macroalgae and macroalgae-associated bacteria together constitute the most efficient metabolic cycling system in the ocean. Their interactions, especially the responses of macroalgae-associated bacteria communities to algae in different geographical locations, are mostly unknown. In this study, metagenomics was used to analyze the microbial diversity and associated algal-polysaccharide-degrading enzymes on the surface of red algae among three remote regions. There were significant differences in the macroalgae-associated bacteria community composition and diversity among the different regions. At the phylum level, Proteobacteria, Bacteroidetes, and Actinobacteria had a significantly high relative abundance among the regions. From the perspective of species diversity, samples from China had the highest macroalgae-associated bacteria diversity, followed by those from Antarctica and Indonesia. In addition, in the functional prediction of the bacterial community, genes associated with amino acid metabolism, carbohydrate metabolism, energy metabolism, metabolism of cofactors and vitamins, and membrane transport had a high relative abundance. Canonical correspondence analysis and redundancy analysis of environmental factors showed that, without considering algae species and composition, pH and temperature were the main environmental factors affecting bacterial community structure. Furthermore, there were significant differences in algal-polysaccharide-degrading enzymes among the regions. Samples from China and Antarctica had high abundances of algal-polysaccharide-degrading enzymes, while those from Indonesia had extremely low abundances. The environmental differences between these three regions may impose a strong geographic differentiation regarding the biodiversity of algal microbiomes and their expressed enzyme genes. This work expands our knowledge of algal microbial ecology, and contributes to an in-depth study of their metabolic characteristics, ecological functions, and applications.}, } @article {pmid37446076, year = {2023}, author = {Xu, J and Molin, G and Davidson, S and Roth, B and Sjöberg, K and Håkansson, Å}, title = {CRP in Outpatients with Inflammatory Bowel Disease Is Linked to the Blood Microbiota.}, journal = {International journal of molecular sciences}, volume = {24}, number = {13}, pages = {}, pmid = {37446076}, issn = {1422-0067}, support = {Dnr 143587//Direktör Albert Påhlssons Stiftelse för Välgörenhet/ ; }, mesh = {Humans ; C-Reactive Protein ; Outpatients ; *Inflammatory Bowel Diseases/microbiology ; *Colitis, Ulcerative/microbiology ; *Crohn Disease/microbiology ; *Microbiota ; }, abstract = {The circulation is a closed system that has been assumed to be free from bacteria, but evidence for the existence of a low-density blood microbiota is accumulating. The present study aimed to map the blood microbiota of outpatients with Crohn's disease (CD) or with ulcerative colitis (UC) by 16S metagenomics. A diverse microbiota was observed in the blood samples. Regardless of the type of disease, the alpha diversity of the microbiota was positively associated with C-reactive protein (CRP). The blood microbiota had a surprisingly high proportion of Proteobacteria in comparison with human oral and colonic microbiotas. There was no clear difference in the overall pattern of the microbiota between CD and UC. A non-template control (NTC) was included in the whole process to control for the potential contamination from the environment and reagents. Certain bacterial taxa were concomitantly detected in both blood samples and NTC. However, Acinetobacter, Lactobacillus, Thermicanus and Paracoccus were found in blood from both CD and UC patients but not in NTC, indicating the existence of a specific blood-borne microbiota in the patients. Achromobacter dominated in all blood samples, but a minor amount was also found in NTC. Micrococcaceae was significantly enriched in CD, but it was also detected in high abundance in NTC. Whether the composition of the blood microbiota could be a marker of a particular phenotype in inflammatory bowel disease (IBD) or whether the blood microbiota could be used for diagnostic or therapeutic purposes deserves further attention.}, } @article {pmid37445967, year = {2023}, author = {He, K and Xiong, J and Yang, W and Zhao, L and Wang, T and Qian, W and Hu, S and Wang, Q and Aleem, MT and Miao, W and Yan, W}, title = {Metagenome of Gut Microbiota Provides a Novel Insight into the Pathogenicity of Balantioides coli in Weaned Piglets.}, journal = {International journal of molecular sciences}, volume = {24}, number = {13}, pages = {}, pmid = {37445967}, issn = {1422-0067}, support = {31772733//National Natural Science Foundation of China/ ; }, mesh = {Swine ; Animals ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Balantidiasis ; Virulence ; Diarrhea/microbiology ; }, abstract = {Balantioides coli plays an important role in the diarrhea of weaned piglets, but its pathogenic potential and interaction with gut microbes remain unclear. To investigate the impact of B. coli colonization on the gut bacterial structure and function of weaned piglets, a metagenomic analysis based on shotgun sequencing was performed on fresh fecal samples collected from ten B. coli-colonized piglets and eight B. coli-free ones in this study. The results showed that decreasing diversity and shifted composition and function of the bacterial community were detected in the weaned piglets infected by B. coli. In contrast to the B. coli-negative group, the relative abundances of some members of the Firmicutes phylum including Clostridium, Ruminococcus species, and Intestinimonas butyriciproducens, which produce short-chain fatty acids, were significantly reduced in the B. coli-positive group. Notably, some species of the Prevotella genus (such as Prevotella sp. CAG:604 and Prevotella stercorea) were significantly increased in abundance in the B. coli-positive piglets. A functional analysis of the gut microbiota demonstrated that the differential gene sets for the metabolism of carbohydrates and amino acids were abundant in both groups, and the more enriched pathways in B. coli-infected piglets were associated with the sugar-specific phosphotransferase system (PTS) and the two-component regulatory system, as well as lipopolysaccharide (LPS) biosynthesis. Furthermore, several species of Prevotella were significantly positively correlated to the synthesis of lipid A, leading to the exporting of endotoxins and, thereby, inducing inflammation in the intestines of weaned piglets. Taken together, these findings revealed that colonization by B. coli was distinctly associated with the dysbiosis of gut bacterial structure and function in weaned piglets. Lower relative abundances of Clostridiaceae and Ruminococcaceae and higher abundances of Prevotella species were biomarkers of B. coli infection in weaned piglets.}, } @article {pmid37445696, year = {2023}, author = {Dobretsov, S and Rittschof, D}, title = {"Omics" Techniques Used in Marine Biofouling Studies.}, journal = {International journal of molecular sciences}, volume = {24}, number = {13}, pages = {}, pmid = {37445696}, issn = {1422-0067}, support = {IG/DVC/CEMB/21/01//Sultan Qaboos University/ ; }, mesh = {Animals ; *Biofouling ; Proteomics ; Bacteria ; *Bryozoa ; Technology ; Aquatic Organisms/genetics ; }, abstract = {Biofouling is the growth of organisms on wet surfaces. Biofouling includes micro- (bacteria and unicellular algae) and macrofouling (mussels, barnacles, tube worms, bryozoans, etc.) and is a major problem for industries. However, the settlement and growth of some biofouling species, like oysters and corals, can be desirable. Thus, it is important to understand the process of biofouling in detail. Modern "omic" techniques, such as metabolomics, metagenomics, transcriptomics, and proteomics, provide unique opportunities to study biofouling organisms and communities and investigate their metabolites and environmental interactions. In this review, we analyze the recent publications that employ metagenomic, metabolomic, and proteomic techniques for the investigation of biofouling and biofouling organisms. Specific emphasis is given to metagenomics, proteomics and publications using combinations of different "omics" techniques. Finally, this review presents the future outlook for the use of "omics" techniques in marine biofouling studies. Like all trans-disciplinary research, environmental "omics" is in its infancy and will advance rapidly as researchers develop the necessary expertise, theory, and technology.}, } @article {pmid37444425, year = {2023}, author = {Gonzalez-Bosquet, J and McDonald, ME and Bender, DP and Smith, BJ and Leslie, KK and Goodheart, MJ and Devor, EJ}, title = {Microbial Communities in Gynecological Cancers and Their Association with Tumor Somatic Variation.}, journal = {Cancers}, volume = {15}, number = {13}, pages = {}, pmid = {37444425}, issn = {2072-6694}, support = {R01 CA99908/NH/NIH HHS/United States ; R01 CA184101/NH/NIH HHS/United States ; }, abstract = {There are strong correlations between the microbiome and human disease, including cancer. However, very little is known about potential mechanisms associated with malignant transformation in microbiome-associated gynecological cancer, except for HPV-induced cervical cancer. Our hypothesis is that differences in bacterial communities in upper genital tract epithelium may lead to selection of specific genomic variation at the cellular level of these tissues that may predispose to their malignant transformation. We first assessed differences in the taxonomic composition of microbial communities and genomic variation between gynecologic cancers and normal samples. Then, we performed a correlation analysis to assess whether differences in microbial communities selected for specific single nucleotide variation (SNV) between normal and gynecological cancers. We validated these results in independent datasets. This is a retrospective nested case-control study that used clinical and genomic information to perform all analyses. Our present study confirms a changing landscape in microbial communities as we progress into the upper genital tract, with more diversity in lower levels of the tract. Some of the different genomic variations between cancer and controls strongly correlated with the changing microbial communities. Pathway analyses including these correlated genes may help understand the basis for how changing bacterial landscapes may lead to these cancers. However, one of the most important implications of our findings is the possibility of cancer prevention in women at risk by detecting altered bacterial communities in the upper genital tract epithelium.}, } @article {pmid37444219, year = {2023}, author = {Bester, A and O'Brien, M and Cotter, PD and Dam, S and Civai, C}, title = {Shotgun Metagenomic Sequencing Revealed the Prebiotic Potential of a Fruit Juice Drink with Fermentable Fibres in Healthy Humans.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {13}, pages = {}, pmid = {37444219}, issn = {2304-8158}, support = {00002//London South Bank University/ ; 00003//European Redevelopment Fund/ ; }, abstract = {Fibre-based dietary interventions are at the forefront of gut microbiome modulation research, with a wealth of 16S rRNA information to demonstrate the prebiotic effects of isolated fibres. However, there is a distinct lack of data relating to the effect of a combination of soluble and insoluble fibres in a convenient-to-consume fruit juice food matrix on gut microbiota structure, diversity, and function. Here, we aimed to determine the impact of the MOJU Prebiotic Shot, an apple, lemon, ginger, and raspberry fruit juice drink blend containing chicory inulin, baobab, golden kiwi, and green banana powders, on gut microbiota structure and function. Healthy adults (n = 20) were included in a randomised, double-blind, placebo-controlled, cross-over study, receiving 60 mL MOJU Prebiotic Shot or placebo (without the fibre mix) for 3 weeks with a 3-week washout period between interventions. Shotgun metagenomics revealed significant between-group differences in alpha and beta diversity. In addition, the relative abundance of the phyla Actinobacteria and Desulfobacteria was significantly increased as a result of the prebiotic intervention. Nine species were observed to be differentially abundant (uncorrected p-value of <0.05) as a result of the prebiotic treatment. Of these, Bifidobacterium adolescentis and CAG-81 sp900066785 (Lachnospiraceae) were present at increased abundance relative to baseline. Additionally, KEGG analysis showed an increased abundance in pathways associated with arginine biosynthesis and phenylacetate degradation during the prebiotic treatment. Our results show the effects of the daily consumption of 60 mL MOJU Prebiotic Shot for 3 weeks and provide insight into the functional potential of B. adolescentis.}, } @article {pmid37444034, year = {2023}, author = {Song, F and Ma, S and Zhang, Y and Yang, X and Zhang, H and Han, Y and Liu, Y and Gao, F and Yuan, Z}, title = {Seasonal Variation in Gut Microbiota of the Wild Daurian Ground Squirrel (Spermophilus dauricus): Metagenomic Insights into Seasonal Breeding.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {13}, pages = {}, pmid = {37444034}, issn = {2076-2615}, abstract = {The Spermophilus dauricus, the wild Daurian ground squirrel, is known to exhibit seasonal breeding behavior. Although the importance of gut microbiota in animal digestion, metabolism, and immunity is well-established, the correlation between gut microbiota and seasonal breeding in this species remains inadequately explored. In the present study, using metagenomic sequencing technology, the compositions and functions of the gut microbiota of wild Daurian ground squirrels in different breeding seasons were explored. The dominant gut microbial phyla were Firmicutes and Bacteroidetes. The Firmicutes were predominant in the breeding season, whereas Bacteroidetes were predominant in the non-breeding season. At the genus level, Lactobacillus accumulated during the breeding season, whereas Odoribacter and Alistipes increased during the non-breeding season. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genome) annotations indicated that genes in gut samples were highly associated with metabolic functions. The differential expression gene analysis showed that genes related to the phosphotransferase system, cysteine, and methionine metabolism were highly expressed during the breeding season, whereas the non-breeding season upregulated genes were enriched in starch and sucrose metabolism and bacterial chemotaxis pathways. In conclusion, this study could provide a reference for investigating gut microbiota in seasonal breeding animals and offer new insight into gut microbial function.}, } @article {pmid37443970, year = {2023}, author = {Cao, G and Yang, S and Wang, H and Zhang, R and Wu, Y and Liu, J and Qiu, K and Dong, Y and Yue, M}, title = {Effects of Bacillus licheniformis on the Growth Performance, Antioxidant Capacity, Ileal Morphology, Intestinal Short Chain Fatty Acids, and Colonic Microflora in Piglets Challenged with Lipopolysaccharide.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {13}, pages = {}, pmid = {37443970}, issn = {2076-2615}, support = {2020R01015//Zhejiang Provincial Leading Innovation and Entrepreneurship Team Project/ ; 2022C02059//Key R&D Projects of Zhejiang Province/ ; 32002195//National Natural Science Foundation of China/ ; }, abstract = {The aim of the present study was to investigate the effects of Bacillus licheniformis (BL) on the growth performance, antioxidant capacity, ileal morphology, intestinal fecal short-chain fatty acids, and microflora of weaned piglets challenged with lipopolysaccharide (LPS). Piglets were assigned into three groups: basal diet (Con), a basal diet with added 10[9] CFU B. licheniformis/kg (BLl), and a basal diet with added 10[10] CFU B. licheniformis/kg (BLh). On day 28, BLh piglets were intraperitoneally injected with LPS (CBL) and sterilized saline water (BL), Con piglets were injected with LPS (LPS) and sterilized saline water (Con), with the injections being administered for three consecutive days. The average daily gain significantly increased from day 1 to day 28 and the feed: gain ratio decreased with BL supplementation compared with the Con group. Supplementation with BLl and BLh reduced the diarrhea rate in piglets. Serum catalase activity increased and malondialdehyde concentration decreased in the CBL treatment group compared with the LPS treatment group. Both BL and CBL treatments increased the ileal villus length/crypt depth ratio compared with Con and LPS treatments. BL administration significantly increased colonic propionic and isobutyric acid concentrations compared with Con treatment. Both BL and CBL piglets had significantly increased fecal acetic, propionic, and butyric acid levels compared with LPS piglets. Analysis of the colonic microbial metagenome showed that Prevotella species were the predominant bacteria in piglets treated with BL and CBL. The CBL-treated piglets had higher scores for lysine biosynthesis, arginine biosynthesis, sulfur relay system, and histidine metabolism. BL-treated piglets had higher scores for glycosaminoglycan biosynthesis-keratan sulfate, oxidative phosphorylation, and pyruvate and carbon metabolism.}, } @article {pmid37443184, year = {2023}, author = {Tataru, C and Peras, M and Rutherford, E and Dunlap, K and Yin, X and Chrisman, BS and DeSantis, TZ and Wall, DP and Iwai, S and David, MM}, title = {Topic modeling for multi-omic integration in the human gut microbiome and implications for Autism.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {11353}, pmid = {37443184}, issn = {2045-2322}, support = {R44 DA043954/DA/NIDA NIH HHS/United States ; }, mesh = {Child ; Humans ; *Gastrointestinal Microbiome/genetics ; Multiomics ; RNA, Ribosomal, 16S/genetics ; *Autistic Disorder ; *Microbiota/genetics ; }, abstract = {While healthy gut microbiomes are critical to human health, pertinent microbial processes remain largely undefined, partially due to differential bias among profiling techniques. By simultaneously integrating multiple profiling methods, multi-omic analysis can define generalizable microbial processes, and is especially useful in understanding complex conditions such as Autism. Challenges with integrating heterogeneous data produced by multiple profiling methods can be overcome using Latent Dirichlet Allocation (LDA), a promising natural language processing technique that identifies topics in heterogeneous documents. In this study, we apply LDA to multi-omic microbial data (16S rRNA amplicon, shotgun metagenomic, shotgun metatranscriptomic, and untargeted metabolomic profiling) from the stool of 81 children with and without Autism. We identify topics, or microbial processes, that summarize complex phenomena occurring within gut microbial communities. We then subset stool samples by topic distribution, and identify metabolites, specifically neurotransmitter precursors and fatty acid derivatives, that differ significantly between children with and without Autism. We identify clusters of topics, deemed "cross-omic topics", which we hypothesize are representative of generalizable microbial processes observable regardless of profiling method. Interpreting topics, we find each represents a particular diet, and we heuristically label each cross-omic topic as: healthy/general function, age-associated function, transcriptional regulation, and opportunistic pathogenesis.}, } @article {pmid37442576, year = {2023}, author = {Grandchamp, A and Kühl, L and Lebherz, M and Brüggemann, K and Parsch, J and Bornberg-Bauer, E}, title = {Population genomics reveals mechanisms and dynamics of de novo expressed open reading frame emergence in Drosophila melanogaster.}, journal = {Genome research}, volume = {33}, number = {6}, pages = {872-890}, pmid = {37442576}, issn = {1549-5469}, mesh = {Animals ; *Drosophila melanogaster/genetics ; Open Reading Frames ; *Metagenomics ; DNA Transposable Elements/genetics ; Biological Evolution ; Evolution, Molecular ; }, abstract = {Novel genes are essential for evolutionary innovations and differ substantially even between closely related species. Recently, multiple studies across many taxa showed that some novel genes arise de novo, that is, from previously noncoding DNA. To characterize the underlying mutations that allowed de novo gene emergence and their order of occurrence, homologous regions must be detected within noncoding sequences in closely related sister genomes. So far, most studies do not detect noncoding homologs of de novo genes because of incomplete assemblies and annotations, and long evolutionary distances separating genomes. Here, we overcome these issues by searching for de novo expressed open reading frames (neORFs), the not-yet fixed precursors of de novo genes that emerged within a single species. We sequenced and assembled genomes with long-read technology and the corresponding transcriptomes from inbred lines of Drosophila melanogaster, derived from seven geographically diverse populations. We found line-specific neORFs in abundance but few neORFs shared by lines, suggesting a rapid turnover. Gain and loss of transcription is more frequent than the creation of ORFs, for example, by forming new start and stop codons. Consequently, the gain of ORFs becomes rate limiting and is frequently the initial step in neORFs emergence. Furthermore, transposable elements (TEs) are major drivers for intragenomic duplications of neORFs, yet TE insertions are less important for the emergence of neORFs. However, highly mutable genomic regions around TEs provide new features that enable gene birth. In conclusion, neORFs have a high birth-death rate, are rapidly purged, but surviving neORFs spread neutrally through populations and within genomes.}, } @article {pmid37442461, year = {2023}, author = {Yang, J and He, J and Jia, L and Gu, H}, title = {Integrating metagenomics and metabolomics to study the response of microbiota in black soil degradation.}, journal = {The Science of the total environment}, volume = {899}, number = {}, pages = {165486}, doi = {10.1016/j.scitotenv.2023.165486}, pmid = {37442461}, issn = {1879-1026}, mesh = {*Soil/chemistry ; Metagenomics ; Soil Microbiology ; Bacteria/metabolism ; *Microbiota ; Metabolomics ; }, abstract = {As the largest commercial food production base and ecological security barrier, land degradation in black soil areas seriously threatens the global food supply and natural ecosystems. Therefore, determining the response of soil microbiota is crucial to restoring degraded soils. This study combined metagenomics and metabolomics to investigate the effect of different degrees of soil degradation on microbial community composition and metabolic function in black soils. It was found that alpha diversity in degraded soils (Shannon: 22.3) was higher than in nondegraded soil (ND) (Shannon: 21.8), and the degree of degradation significantly altered the structure and composition of soil microbial communities. The results of LEfSe analysis obtained 9 (ND), 7 (lightly degraded, LD), 10 (moderately degraded, MD), and 1 (severely degraded, SD) biomarkers in four samples. Bradyrhizobium, Sphingomonas, and Ramlibacter were significantly affected by soil degradation and can be considered biomarkers of ND, MD, and SD, respectively. Soil nutrient and enzyme activities decreased significantly with increasing black soil degradation, soil organic matter (SOM) content decreased from 11.12 % to 1.97 %, and Sucrase decreased from 23.53 to 6.59 mg/g/d. In addition, C was the critical driver affecting microbial community structure, contributing 61.2 % to differences in microbial community distribution, and microbial altering relative abundance which participle in the carbon cycle to respond to soil degradation. Metabolomic analyses indicated that soil degradation significantly modified the soil metabolite spectrum, and the metabolic functions of most microorganisms responding to soil degradation were adversely affected. The combined multi-omics analysis further indicated that biomarkers dominate in accumulating metabolites. These findings confirmed that due to their role in the composition and functioning of these degraded soils, these biomarkers could be employed in strategies for managing and restoring degraded black soils.}, } @article {pmid37442263, year = {2023}, author = {Chen, SH and Li, ZT and Zhao, HP}, title = {Bioelectrochemical system accelerates reductive dechlorination through extracellular electron transfer networks.}, journal = {Environmental research}, volume = {235}, number = {}, pages = {116645}, doi = {10.1016/j.envres.2023.116645}, pmid = {37442263}, issn = {1096-0953}, mesh = {*Electrons ; Oxidation-Reduction ; Electricity ; Electrodes ; *Trichloroethylene/chemistry ; Biodegradation, Environmental ; }, abstract = {Bioelectrochemical system is considered as a promising approach for enhanced bio-dechlorination. However, the mechanism of extracellular electron transfer in the dechlorinating consortium is still a controversial issue. In this study, bioelectrochemical systems were established with cathode potential settings at -0.30 V (vs. SHE) for trichloroethylene reduction. The average dechlorination rate (102.0 μM Cl·d[-1]) of biocathode was 1.36 times higher than that of open circuit (74.7 μM Cl·d[-1]). Electrochemical characterization via cyclic voltammetry illustrated that electrostimulation promoted electrochemical activity for redox reactions. Moreover, bacterial community structure analyses indicated electrical stimulation facilitated the enrichment of electroactive and dechlorinating populations on cathode. Metagenomic and quantitative polymerase chain reaction (qPCR) analyses revealed that direct electron transfer (via electrically conductive pili, multi-heme c-type cytochromes) between Axonexus and Desulfovibrio/cathode and indirect electron transfer (via riboflavin) for Dehalococcoides enhanced dechlorination process in BES. Overall, this study verifies the effectiveness of electrostimulated bio-dechlorination and provides novel insights into the mechanisms of dechlorination process enhancement in bioelectrochemical systems through electron transfer networks.}, } @article {pmid37442053, year = {2023}, author = {Durand, M and Touchette, D and Chen, YJ and Magnuson, E and Wasserscheid, J and Greer, CW and Whyte, LG and Altshuler, I}, title = {Effects of marine diesel on microbial diversity and activity in high Arctic beach sediments.}, journal = {Marine pollution bulletin}, volume = {194}, number = {Pt A}, pages = {115226}, doi = {10.1016/j.marpolbul.2023.115226}, pmid = {37442053}, issn = {1879-3363}, mesh = {RNA, Ribosomal, 16S/genetics ; *Bacteria/metabolism ; Arctic Regions ; *Microbiota ; Hydrocarbons/metabolism ; }, abstract = {Global warming induced sea ice loss increases Arctic maritime traffic, enhancing the risk of ecosystem contamination from fuel spills and nutrient loading. The impact of marine diesel on bacterial metabolic activity and diversity, assessed by colorimetric assay, 16S rRNA and metagenomic sequencing, of Northwest Passage (Arctic Ocean) beach sediments was assessed with nutrient amendment at environmentally relevant temperatures (5 and 15 °C). Higher temperature and nutrients stimulated microbial activity, while diesel reduced it, with metabolism inhibited at and above 0.01 % (without nutrients) and at 1 % (with nutrients) diesel inclusions. Diesel exposure significantly decreased microbial diversity and selected for Psychrobacter genus. Microbial hydrocarbon degradation, organic compound metabolism, and exopolysaccharide production gene abundances increased under higher diesel concentrations. Metagenomic binning recovered nine MAGs/bins with hydrocarbon degradation genes. We demonstrate a nutrients' rescue-type effect in diesel contaminated microbial communities via enrichment of microorganisms with stress response, aromatic compound, and ammonia assimilation metabolisms.}, } @article {pmid37441819, year = {2023}, author = {Ren, Z and Jiang, W and Sun, N and Shi, J and Zhang, D and Zhang, J and Wang, Z and Yang, J and Yu, J and Lv, Z}, title = {Responses of the structure and function of microbes in Yellow River Estuary sediments to different levels of mercury.}, journal = {Marine environmental research}, volume = {190}, number = {}, pages = {106097}, doi = {10.1016/j.marenvres.2023.106097}, pmid = {37441819}, issn = {1879-0291}, mesh = {*Mercury/analysis ; Estuaries ; Rivers/chemistry ; RNA, Ribosomal, 16S/genetics ; Geologic Sediments/chemistry ; *Water Pollutants, Chemical/toxicity/analysis ; *Methylmercury Compounds ; *Metals, Heavy/analysis ; *Microbiota ; Environmental Monitoring ; }, abstract = {The health and stability of the estuary of the Yellow River ecosystem have come under increasing pressure from land-based inputs of heavy metals. While it is known that heavy metals affect the function and health of the microbial community, there remains little knowledge on the responses of the microbial community to heavy metals, particularly highly toxic mercury. The research aimed to characterize the responses of the sediment microbial community of the estuary of the Yellow River to different levels of mercury stress. Estuary sediment samples were collected for microbial community analysis, measurement of mercury [including total mercury (THg) and methylmercury (MeHg)], and measurement of other physicochemical factors, including pH, total organic carbon (TOC), sulfide, iron ratio (Fe[3+]/Fe[2+]), ammonium salt (NH4[+]), and biochemical oxygen demand (BOD). The application of 16S rRNA sequencing identified 60 phyla of bacteria, dominated by Proteobacteria, Firmicutes, and Bacteroidetes. Stations with higher THg or MeHg and lower microbial abundance and diversity were generally distributed further outside of the estuary. Besides mercury, the measured physicochemical factors had impacts on microbial diversities and distribution. Metagenomics assessment of three stations, representative of low, moderate, and high mercury concentrations and measured physicochemical factors, revealed the abundances and functions of predicted genes. The most abundant genes regulating the metabolic pathways were categorized as metabolic, environmental information processing, and genetic information processing, genes. At stations with high levels of mercury, the dominant genes were related to energy metabolism, signal transport, and membrane transport. Functional genes with a mercury-resistance function were generally in the mer system (merA, merC, merT, merR), alkylmercury lyase, and metal-transporting ATPase. These results offer insight into the microbial community structure of the sediments in the Yellow River Estuary and the microbial function of mercury resistance under mercury stress.}, } @article {pmid37441178, year = {2023}, author = {Wu, Y and Sun, XR and Pritchard, HW and Shen, YB and Wu, XQ and Peng, CY}, title = {The metagenomics of soil bacteria and fungi and the release of mechanical dormancy in hard seeds.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1187614}, pmid = {37441178}, issn = {1664-462X}, abstract = {Persistence in the soil is a function of seed physiology, particularly non-germination and inherent lifespan. However, for seeds with mechanical dormancy, non-germination is also a function of the composition and activity of the soil microbiota. We attempted to screen out microorganisms in the soil that can specifically and rapidly decompose the hard fruit pericarps of Tilia miqueliana Maxim., a unique native tree species in China. Using the classical replica plating method, more than 100 different culturable microorganisms that could rapidly erode the pericarp were collected from the surface of pericarps under different culture conditions. At the same time, we successfully extended the concept of metagenomics and applied it to the identification of mixed artificial cultures. The decomposition process of the pericarps in soil was also simulated artificially. The physical and chemical data suggested a potential mechanism of microbial scarification and cracking in pericarp, whilst the embryos inside the eroded fruits retained good viability. Our discoveries could pave the way for the removal of physical and mechanical obstacles that prevent hard coat seeds from germinating. We anticipate that the use of this technology will improve the germination of other hard coat seeds. More research is needed to investigate the impacts on other seeds. The findings of this research can inform the design of experiments on the seed ecology of persistence.}, } @article {pmid37440886, year = {2023}, author = {Nakano, S and Furutani, H and Kato, S and Kouduka, M and Yamazaki, T and Suzuki, Y}, title = {Bullet-shaped magnetosomes and metagenomic-based magnetosome gene profiles in a deep-sea hydrothermal vent chimney.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1174899}, pmid = {37440886}, issn = {1664-302X}, abstract = {Magnetosome-producing microorganisms can sense and move toward the redox gradient and have been extensively studied in terrestrial and shallow marine sediment environments. However, given the difficulty of sampling, magnetotactic bacteria (MTB) are poorly explored in deep-sea hydrothermal fields. In this study, a deep-sea hydrothermal vent chimney from the Southern Mariana Trough was collected using a remotely operated submersible. The mineralogical and geochemical characterization of the vent chimney sample showed an internal iron redox gradient. Additionally, the electron microscopy of particles collected by magnetic separation from the chimney sample revealed MTB cells with bullet-shaped magnetosomes, and there were minor occurrences of cuboctahedral and hexagonal prismatic magnetosomes. Genome-resolved metagenomic analysis was performed to identify microorganisms that formed magnetosomes. A metagenome-assembled genome (MAG) affiliated with Nitrospinae had magnetosome genes such as mamA, mamI, mamM, mamP, and mamQ. Furthermore, a diagnostic feature of MTB genomes, such as magnetosome gene clusters (MGCs), including mamA, mamP, and mamQ, was also confirmed in the Nitrospinae-affiliated MAG. Two lines of evidence support the occurrence of MTB in a deep-sea, inactive hydrothermal vent environment.}, } @article {pmid37440879, year = {2023}, author = {Panah, FM and Nielsen, KD and Simpson, GL and Schönherz, A and Schramm, A and Lauridsen, C and Nielsen, TS and Højberg, O and Fredborg, M and Purup, S and Canibe, N}, title = {Corrigendum: A westernized diet changed the colonic bacterial composition and metabolite concentration in a dextran sulfate sodium pig model for ulcerative colitis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1238157}, doi = {10.3389/fmicb.2023.1238157}, pmid = {37440879}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2023.1018242.].}, } @article {pmid37440597, year = {2023}, author = {de Melo, L and Cruz, IA and Fuess, LT and Maynard Santana, CE and Bharagava, RN and Mulla, SI and Bilal, M and Saratale, GD and Figueiredo, RT and Ferreira, LFR}, title = {Development of a simple biogas analyzer module (BAM) for real-time biogas production monitoring.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-11}, doi = {10.1080/09593330.2023.2235457}, pmid = {37440597}, issn = {1479-487X}, abstract = {ABSTRACTAnaerobic digestion (AD) relies on the cooperation of specific microbial communities, making it susceptible to process disruptions that could impact biogas production. In this regard, this study presents a technological solution based on the Arduino platform, in the form of a simple online monitoring system that can track the produced biogas profile, named as biogas analyzer module (BAM). The applicability of the BAM focused on monitoring the biogas produced from sugarcane vinasse inoculated with sewage sludge biodigestion processed in mesophilic conditions (38 [o]C), in a pH range of 6.5-7.5, and following a three-stage operational model: (i) an adaptation (168 h), (ii) complete mixing (168 h), and (iii) bio-stimulation with glycerol (192 h). Then, the lab-made BAM was used to trace the produced biogas profile, which registered a total biogas volume of 8,719.86 cm[3] and biomethane concentration of 95.79% (vol.), removing 90.8% (vol) of carbon dioxide (CO2) and 65.2% (vol) of hydrogen sulfide (H2S). In conclusion, the results ensured good accuracy and efficiency to the device created by comparisons with established standards (chromatographic and colorimetric methods), as well as the cost reduction. The developed device would likely be six times cheaper than what is available in the market.}, } @article {pmid37440462, year = {2023}, author = {Oumarou Hama, H and Boualam, MA and Levasseur, A and Ardagna, Y and Adalian, P and Chaix, AC and Drancourt, M}, title = {Old World Medieval Treponema pallidum Complex Treponematosis: A Case Report.}, journal = {The Journal of infectious diseases}, volume = {228}, number = {5}, pages = {503-510}, doi = {10.1093/infdis/jiad248}, pmid = {37440462}, issn = {1537-6613}, mesh = {Humans ; *Treponema pallidum/genetics ; *Syphilis/diagnosis ; Phylogeny ; Europe ; France ; }, abstract = {BACKGROUND: Introduction of 1 Treponema pallidum complex pathogen in naive European populations following the return of Christopher Columbus' troops from Central America in 1493 is a central dogma in venereology.

METHODS: Among skeletal elements from the seventh or eighth century uncovered in Roquevaire, France, individual RS-1003 femur macroscopically suspected of having an infectious disease was investigated by means of paleoautoimmunohistochemistry, direct metagenomics, and paleoserology, along with 1 control femur from an apparently healthy individual (R-1003) and experimental negative controls.

RESULTS: RS-1003 femur showed infectious bone; paleoautoimmunohistochemistry of the lesions led to microscopic detection of a T. pallidum complex pathogen. Phylogenetic analyses comprising 71 T. pallidum complex-specific reads covering 2.37% of the T. pallidum subsp. pallidum reference genome sequence revealed an ancestral T. pallidum complex pathogen in the lesion. Paleoserology detecting T. pallidum-specific antigens confirmed positive serological findings in individual RS-1003. Individual R-1003 and the negative controls remained negative.

CONCLUSIONS: This case, predating by 8 centuries previous detections of T. pallidum complex treponematosis in Europe, indicated that European populations were not naive to these pathogens before the 1493 introduction of a Central American T. pallidum complex pathogen overwhelming the T. pallidum ones previously circulating in the Old World. These data break a century-old dogma in medical microbiology.}, } @article {pmid37440367, year = {2023}, author = {Muralitharan, RR and Snelson, M and Meric, G and Coughlan, MT and Marques, FZ}, title = {Guidelines for microbiome studies in renal physiology.}, journal = {American journal of physiology. Renal physiology}, volume = {325}, number = {3}, pages = {F345-F362}, doi = {10.1152/ajprenal.00072.2023}, pmid = {37440367}, issn = {1522-1466}, mesh = {Animals ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; Anti-Bacterial Agents ; }, abstract = {Gut microbiome research has increased dramatically in the last decade, including in renal health and disease. The field is moving from experiments showing mere association to causation using both forward and reverse microbiome approaches, leveraging tools such as germ-free animals, treatment with antibiotics, and fecal microbiota transplantations. However, we are still seeing a gap between discovery and translation that needs to be addressed, so that patients can benefit from microbiome-based therapies. In this guideline paper, we discuss the key considerations that affect the gut microbiome of animals and clinical studies assessing renal function, many of which are often overlooked, resulting in false-positive results. For animal studies, these include suppliers, acclimatization, baseline microbiota and its normalization, littermates and cohort/cage effects, diet, sex differences, age, circadian differences, antibiotics and sweeteners, and models used. Clinical studies have some unique considerations, which include sampling, gut transit time, dietary records, medication, and renal phenotypes. We provide best-practice guidance on sampling, storage, DNA extraction, and methods for microbial DNA sequencing (both 16S rRNA and shotgun metagenome). Finally, we discuss follow-up analyses, including tools available, metrics, and their interpretation, and the key challenges ahead in the microbiome field. By standardizing study designs, methods, and reporting, we will accelerate the findings from discovery to translation and result in new microbiome-based therapies that may improve renal health.}, } @article {pmid37440152, year = {2023}, author = {Li, Y and Xiong, L and Zeng, K and Wei, Y and Li, H and Ji, X}, title = {Microbial-driven carbon fixation in natural wetland.}, journal = {Journal of basic microbiology}, volume = {63}, number = {10}, pages = {1115-1127}, doi = {10.1002/jobm.202300273}, pmid = {37440152}, issn = {1521-4028}, support = {32160294//National Natural Science Foundation of China/ ; 31860147//National Natural Science Foundation of China/ ; }, mesh = {*Wetlands ; *Soil/chemistry ; Ecosystem ; Carbon Cycle ; China ; Carbon/analysis ; }, abstract = {With the development of global industrialization, carbon neutrality has become an issue that we must be paid attention to. Microorganisms not only have an important impact on the carbon chemical cycle between the Earth's biosphere and biogeography but also play a key role in maintaining the global organic carbon balance. Wetlands are the main reservoir of organic carbon in the mainland of China, and wetland carbon sinks are indispensable for China to achieve the goal of "dual carbon," and China has taken the consolidation and improvement of wetland carbon sink capacity as an important part of the carbon peaking action plan. As a unique low-latitude, high-altitude seasonal plateau wetland in China, Napahai shows high research value. However, the role of microbes in maintaining dissolved organic carbon balance in this area has not been reported. In the study, six carbon fixation genes, accA, aclB, acsA, acsB, cbbL, and rbcL, were analyzed based on metagenomics to elucidate the rich genetic diversity, uniqueness and differences in the Napahai plateau wetland. It was found that the microbial diversity in the Napahai plateau wetland was different from other habitats. In addition, the aclB gene, a rare taxon with high genetic diversity and rich species in the Napahai plateau wetland, played a key role in the microbial metabolic pathway. Finally, the construction of a metabolic pathway through the Kyoto encyclopedia for genes and genomes revealed the contribution of microbes to carbon fixation and the role of microbes in maintaining the organic carbon balance of the Napahai plateau wetland.}, } @article {pmid37439951, year = {2023}, author = {Chauhan, S and Yadav, U and Bano, N and Kumar, S and Fatima, T and Anshu, and Dubey, A and Singh, PC}, title = {Carbendazim Modulates the Metabolically Active Bacterial Populations in Soil and Rhizosphere.}, journal = {Current microbiology}, volume = {80}, number = {9}, pages = {280}, pmid = {37439951}, issn = {1432-0991}, mesh = {*Soil/chemistry ; Rhizosphere ; *Fungicides, Industrial/pharmacology ; RNA, Ribosomal, 16S/genetics ; Carbon Dioxide ; Bacteria/genetics ; Soil Microbiology ; Zea mays/microbiology ; }, abstract = {The impact of fungicide residues on non-target soil bacterial communities is relatively unexplained. We hypothesize that the persistence of fungicide residues in the soil will affect the soil bacterial populations. Persistence depends on biotic and abiotic factors, primarily determined by agricultural activities. Activities such as fallow soil (F), farmyard manure (FYM) amendment, rice straw (RS) mulching, and cultivation of maize (Zea mays) and clover (Trifolium alexandrinum) were used as treatments. The soil CO2 efflux showed no effect of Carbendazim on dormant bacteria (unwatered condition). However, in irrigated condition, Carbendazim enhanced the CO2 efflux by 8, 164, 131, 249, and 182% in fallow, FYM, RS, maize, and Trifolium treatments, respectively. However, 16S rRNA metagenome study after 30 days of carbendazim treatment showed that maize rhizosphere microflora was most susceptible, decreasing the Shannon diversity index from 0.321 to 0.165. Diversity indices generally increased in maize and RS treatments, and Proteobacteria was the most prominent bacterial phyla in the maize rhizosphere. The microbial communities separated into distinct groups on the Principal Co-ordinate analysis (PCoA) plot. The separation on scale 1 (35%) and scale 2 (13%) was based, respectively, on microbial activity and carbendazim treatments. Functionally Maize+Carbendazim treatment showed the highest enzyme activities dehydrogenase (82.25%), acid phosphatase (78.10%), alkaline phosphatase (48.26%), β-glucosidase (59.99%), protease (126.65%), and urease (50.66%) compared to fallow soil. Overall, Carbendazim enhanced non-target bacterial activity in metabolically active niches, while it did not affect the dormant microflora. Thus, organic amendments and cultivation of fungicide-contaminated soil may help render the contaminant through bacterial activity.}, } @article {pmid37439894, year = {2023}, author = {Torres Manno, MA and Gizzi, FO and Martín, M and Espariz, M and Magni, C and Blancato, VS}, title = {Metagenomic approach to infer rumen microbiome derived traits of cattle.}, journal = {World journal of microbiology & biotechnology}, volume = {39}, number = {9}, pages = {250}, pmid = {37439894}, issn = {1573-0972}, support = {PICT2019-1771//Agencia Nacional de Promoción Científica y Tecnológica/ ; PICT2015-2361//Agencia Nacional de Promoción Científica y Tecnológica/ ; PICT2014-3482//Agencia Nacional de Promoción Científica y Tecnológica/ ; PIP 11220150100855//Consejo Nacional de Investigaciones Científicas y Técnicas/ ; }, mesh = {Female ; Cattle ; Animals ; *Rumen ; *Microbiota/genetics ; Metagenome ; Bacteria ; Glycoside Hydrolases/genetics/metabolism ; Methane/metabolism ; Animal Feed ; Diet ; }, abstract = {Ruminants enable the conversion of indigestible plant material into animal consumables, including dairy products, meat, and valuable fibers. Microbiome research is gaining popularity in livestock species because it aids in the knowledge of illnesses and efficiency processes in animals. In this study, we use WGS metagenomic data to thoroughly characterize the ruminal ecosystem of cows to infer positive and negative livestock traits determined by the microbiome. The rumen of cows from Argentina were described by combining different gene biomarkers, pathways composition and taxonomic information. Taxonomic characterization indicated that the two major phyla were Bacteroidetes and Firmicutes; in third place, Proteobacteria was highly represented followed by Actinobacteria; Prevotella, and Bacteroides were the most abundant genera. Functional profiling of carbohydrate-active enzymes indicated that members of the Glycoside Hydrolase (GH) class accounted for 52.2 to 55.6% of the total CAZymes detected, among them the most abundant were the oligosaccharide degrading enzymes. The diversity of GH families found suggested efficient hydrolysis of complex biomass. Genes of multidrug, macrolides, polymyxins, beta-lactams, rifamycins, tetracyclines, and bacitracin resistance were found below 0.12% of relative abundance. Furthermore, the clustering analysis of genera and genes that correlated to methane emissions or feed efficiency, suggested that the cows analysed could be regarded as low methane emitters and clustered with high feed efficiency reference animals. Finally, the combination of bioinformatic analyses used in this study can be applied to assess cattle traits difficult to measure and guide enhanced nutrition and breeding methods.}, } @article {pmid37439777, year = {2023}, author = {Holman, DB and Gzyl, KE and Kommadath, A}, title = {The gut microbiome and resistome of conventionally vs. pasture-raised pigs.}, journal = {Microbial genomics}, volume = {9}, number = {7}, pages = {}, pmid = {37439777}, issn = {2057-5858}, mesh = {Animals ; Swine ; *Gastrointestinal Microbiome/genetics ; Drug Resistance, Bacterial/genetics ; Feces/microbiology ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents ; }, abstract = {Conventional swine production typically houses pigs indoors and in large groups, whereas pasture-raised pigs are reared outdoors at lower stocking densities. Antimicrobial use also differs, with conventionally raised pigs often being exposed to antimicrobials directly or indirectly to control and prevent infectious disease. However, antimicrobial use can be associated with the development and persistence of antimicrobial resistance. In this study, we used shotgun metagenomic sequencing to compare the gut microbiomes and resistomes of pigs raised indoors on a conventional farm with those raised outdoors on pasture. The microbial compositions as well as the resistomes of both groups of pigs were significantly different from each other. Bacterial species such as Intestinibaculum porci, Pseudoscardovia radai and Sharpea azabuensis were relatively more abundant in the gut microbiomes of pasture-raised pigs and Hallella faecis and Limosilactobacillus reuteri in the conventionally raised swine. The abundance of antimicrobial resistance genes (ARGs) was significantly higher in the conventionally raised pigs for nearly all antimicrobial classes, including aminoglycosides, beta-lactams, macrolides-lincosamides-streptogramin B, and tetracyclines. Functionally, the gut microbiomes of the two group of pigs also differed significantly based on their carbohydrate-active enzyme (CAZyme) profiles, with certain CAZyme families associated with host mucin degradation enriched in the conventional pig microbiomes. We also recovered 1043 dereplicated strain-level metagenome-assembled genomes (≥90 % completeness and <5 % contamination) to provide taxonomic context for specific ARGs and metabolic functions. Overall, the study provides insights into the differences between the gut microbiomes and resistomes of pigs raised under two very different production systems.}, } @article {pmid37439686, year = {2023}, author = {Park, SY and Chang, EJ and Ledeboer, N and Messacar, K and Lindner, MS and Venkatasubrahmanyam, S and Wilber, JC and Vaughn, ML and Bercovici, S and Perkins, BA and Nolte, FS}, title = {Plasma Microbial Cell-Free DNA Sequencing from over 15,000 Patients Identified a Broad Spectrum of Pathogens.}, journal = {Journal of clinical microbiology}, volume = {61}, number = {8}, pages = {e0185522}, pmid = {37439686}, issn = {1098-660X}, mesh = {Adult ; Humans ; *Fungi/genetics ; Bacteria/genetics ; *Viruses/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics ; Sequence Analysis, DNA ; }, abstract = {Microbial cell-free DNA (mcfDNA) sequencing is an emerging infectious disease diagnostic tool which enables unbiased pathogen detection and quantification from plasma. The Karius Test, a commercial mcfDNA sequencing assay developed by and available since 2017 from Karius, Inc. (Redwood City, CA), detects and quantifies mcfDNA as molecules/μL in plasma. The commercial sample data and results for all tests conducted from April 2018 through mid-September 2021 were evaluated for laboratory quality metrics, reported pathogens, and data from test requisition forms. A total of 18,690 reports were generated from 15,165 patients in a hospital setting among 39 states and the District of Columbia. The median time from sample receipt to reported result was 26 h (interquartile range [IQR] 25 to 28), and 96% of samples had valid test results. Almost two-thirds (65%) of patients were adults, and 29% at the time of diagnostic testing had ICD-10 codes representing a diverse array of clinical scenarios. There were 10,752 (58%) reports that yielded at least one taxon for a total of 22,792 detections spanning 701 unique microbial taxa. The 50 most common taxa detected included 36 bacteria, 9 viruses, and 5 fungi. Opportunistic fungi (374 Aspergillus spp., 258 Pneumocystis jirovecii, 196 Mucorales, and 33 dematiaceous fungi) comprised 861 (4%) of all detections. Additional diagnostically challenging pathogens (247 zoonotic and vector-borne pathogens, 144 Mycobacterium spp., 80 Legionella spp., 78 systemic dimorphic fungi, 69 Nocardia spp., and 57 protozoan parasites) comprised 675 (3%) of all detections. This is the largest reported cohort of patients tested using plasma mcfDNA sequencing and represents the first report of a clinical grade metagenomic test performed at scale. Data reveal new insights into the breadth and complexity of potential pathogens identified.}, } @article {pmid37438876, year = {2023}, author = {Basile, A and Heinken, A and Hertel, J and Smarr, L and Li, W and Treu, L and Valle, G and Campanaro, S and Thiele, I}, title = {Longitudinal flux balance analyses of a patient with episodic colonic inflammation reveals microbiome metabolic dynamics.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2226921}, pmid = {37438876}, issn = {1949-0984}, support = {757922/ERC_/European Research Council/International ; RF1 AG058942/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Male ; *Gastrointestinal Microbiome ; *Microbiota ; Inflammation ; Liver ; Anti-Bacterial Agents ; Escherichia coli ; }, abstract = {We report the first use of constraint-based microbial community modeling on a single individual with episodic inflammation of the gastrointestinal tract, who has a well documented set of colonic inflammatory biomarkers, as well as metagenomically-sequenced fecal time series covering seven dates over 16 months. Between the first two time steps the individual was treated with both steroids and antibiotics. Our methodology enabled us to identify numerous time-correlated microbial species and metabolites. We found that the individual's dynamical microbial ecology in the disease state led to time-varying in silico overproduction, compared to healthy controls, of more than 24 biologically important metabolites, including methane, thiamine, formaldehyde, trimethylamine N-oxide, folic acid, serotonin, histamine, and tryptamine. The microbe-metabolite contribution analysis revealed that some Dialister species changed metabolic pathways according to the inflammation phases. At the first time point, characterized by the highest levels of serum (complex reactive protein) and fecal (calprotectin) inflammation biomarkers, they produced L-serine or formate. The production of the compounds, through a cascade effect, was mediated by the interaction with pathogenic Escherichia coli strains and Desulfovibrio piger. We integrated the microbial community metabolic models of each time point with a male whole-body, organ-resolved model of human metabolism to track the metabolic consequences of dysbiosis at different body sites. The presence of D. piger in the gut microbiome influenced the sulfur metabolism with a domino effect affecting the liver. These results revealed large longitudinal variations in an individual's gut microbiome ecology and metabolite production, potentially impacting other organs in the body. Future simulations with more time points from an individual could permit us to assess how external drivers, such as diet change or medical interventions, drive microbial community dynamics.}, } @article {pmid37438797, year = {2023}, author = {Nguyen, LH and Okin, D and Drew, DA and Battista, VM and Jesudasen, SJ and Kuntz, TM and Bhosle, A and Thompson, KN and Reinicke, T and Lo, CH and Woo, JE and Caraballo, A and Berra, L and Vieira, J and Huang, CY and Das Adhikari, U and Kim, M and Sui, HY and Magicheva-Gupta, M and McIver, L and Goldberg, MB and Kwon, DS and Huttenhower, C and Chan, AT and Lai, PS}, title = {Metagenomic assessment of gut microbial communities and risk of severe COVID-19.}, journal = {Genome medicine}, volume = {15}, number = {1}, pages = {49}, pmid = {37438797}, issn = {1756-994X}, support = {K01 DK120742/DK/NIDDK NIH HHS/United States ; K23 DK125838/DK/NIDDK NIH HHS/United States ; UL1 TR002541/TR/NCATS NIH HHS/United States ; T32 HL116275/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; Post-Acute COVID-19 Syndrome ; *COVID-19 ; *Microbiota ; Metagenome ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure.

METHODS: We profiled 127 hospitalized patients with COVID-19 (n = 79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites.

RESULTS: Forty-eight species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or "long COVID," suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with classifying whether stool was obtained from patients with severe vs. moderate COVID-19, a finding that was externally validated in an independent cohort. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease.

CONCLUSIONS: Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to expand upon these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention.}, } @article {pmid37438354, year = {2023}, author = {Lacunza, E and Fink, V and Salas, ME and Canzoneri, R and Naipauer, J and Williams, S and Coso, O and Sued, O and Cahn, P and Mesri, EA and Abba, MC}, title = {Oral and anal microbiome from HIV-exposed individuals: role of host-associated factors in taxa composition and metabolic pathways.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {48}, pmid = {37438354}, issn = {2055-5008}, support = {U54 CA221208/CA/NCI NIH HHS/United States ; }, mesh = {Male ; Humans ; Female ; *HIV Infections/complications ; Homosexuality, Male ; *Sexual and Gender Minorities ; *Microbiota ; Metabolic Networks and Pathways ; }, abstract = {Evidence indicates that the microbiome plays a significant role in HIV immunopathogenesis and associated complications. This study aimed to characterize the oral and anal microbiome of Men who have Sex with Men (MSM) and Transgender Women (TGW), with and without HIV. One hundred and thirty oral and anal DNA-derived samples were obtained from 78 participants and subjected to shotgun metagenomics sequencing for further microbiome analysis. Significant differences in the microbiome composition were found among subjects associated with HIV infection, gender, sex behavior, CD4+ T-cell counts, antiretroviral therapy (ART), and the presence of HPV-associated precancerous anal lesions. Results confirm the occurrence of oncogenic viromes in this high HIV-risk population. The oral microbiome in HIV-associated cases exhibited an enrichment of bacteria associated with periodontal disease pathogenesis. Conversely, anal bacteria showed a significant decrease in HIV-infected subjects (Coprococcus comes, Finegoldia magna, Blautia obeum, Catenibacterium mitsuokai). TGW showed enrichment in species related to sexual transmission, which concurs that most recruited TGW are or have been sex workers. Prevotella bivia and Fusobacterium gonidiaformans were positively associated with anal precancerous lesions among HIV-infected subjects. The enrichment of Holdemanella biformis and C. comes was associated with detectable viral load and ART-untreated patients. Metabolic pathways were distinctly affected by predominant factors linked to sexual behavior or HIV pathogenesis. Gene family analysis identified bacterial gene signatures as potential prognostic and predictive biomarkers for HIV/AIDS-associated malignancies. Conclusions: Identified microbial features at accessible sites are potential biomarkers for predicting precancerous anal lesions and therapeutic targets for HIV immunopathogenesis.}, } @article {pmid37437635, year = {2023}, author = {Zou, Y and Xiao, Z and Wang, L and Wang, Y and Yin, H and Li, Y}, title = {Prevalence of antibiotic resistance genes and virulence factors in the sediment of WWTP effluent-dominated rivers.}, journal = {The Science of the total environment}, volume = {897}, number = {}, pages = {165441}, doi = {10.1016/j.scitotenv.2023.165441}, pmid = {37437635}, issn = {1879-1026}, mesh = {*Genes, Bacterial ; *Wastewater ; Anti-Bacterial Agents/analysis ; Prevalence ; Drug Resistance, Microbial/genetics ; }, abstract = {In the context of increasing aridity due to climate changes, effluent from wastewater treatment plants (WWTPs) became dominant in some rivers. However, the prevalence of antibiotic resistance genes (ARGs) and virulence factors (VFs) in effluent-dominated rivers was rarely investigated. In this study, the profiles of ARGs and VFs in the sediment of two effluent-dominated rivers were revealed through the metagenomic sequencing technique. In each river, samples from the effluent discharge point (P site) and approximately 500 m downstream (D site) were collected. Results showed that the abundances of ARGs and VFs were both higher in D sites than those in P sites, indicating higher risks in the downstream areas. The compositions of ARGs were similar in the P sites of two rivers while being distinct in the D sites. The same was true for changes in the VFs compositions. Microbial community structure variations were the main driver for the changes in ARGs and VFs. Network analysis revealed that the interaction of ARGs and VF genes (VFGs) in sediment was intense. Two VFGs and eleven ARGs were identified to play important roles in the network. Metagenome-assembled genomes (MAGs) were generated to evaluate the coexistence of ARGs and VFGs at the single genome level. It was found that 38.4 % of the MAGs contained both ARGs and VFGs, and two MAGs were from pathogenic genera. These results suggested that high microbiological risks existed in effluent-dominated rivers, and necessary measures should be taken to prevent the potential threat to public health.}, } @article {pmid37437419, year = {2023}, author = {Gundogdu, A and Nalbantoglu, OU}, title = {The role of the Mediterranean diet in modulating the gut microbiome: A review of current evidence.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {114}, number = {}, pages = {112118}, doi = {10.1016/j.nut.2023.112118}, pmid = {37437419}, issn = {1873-1244}, mesh = {Humans ; *Diet, Mediterranean ; *Gastrointestinal Microbiome ; Nutrients ; Nutritional Status ; Micronutrients ; }, abstract = {The Mediterranean diet (MedDiet) is recognized as one of the United Nations Educational, Scientific and Cultural Organization Intangible Cultural Heritage assets associated with lower rates of cardiometabolic diseases; lower prevalence of cancer, Alzheimer's disease, depression, and onset of inflammatory bowel disease; and more generally low-grade inflammation and mortality risks. Beyond being an input source of beneficial micronutrients, it recently has been discovered that the MedDiet plays a role in a more complex human microbiome-mediated mechanism. An interesting hypothesis suggests a bidirectional relationship between the MedDiet and the gut microbiome, where gut microbiota assembly and biosynthetic capacity are responsive to the diet; in return, the microbiome-reachable nutrients shape and modulate the microbiome toward a characteristic probiotic state. It can be speculated that that primary health benefits of the MedDiet exerted via the gut microbiome are mediated by the bioactive compounds transformed by the microbiome. Furthermore, it is possible that additional probiotic properties of the organisms promoted by diet adherence have secondary benefits. As more detailed omic-based studies take place, more evidence on the MedDiet as a core generic probiotic microbiome modulation strategy surface. However, individual-specific microbiome compositions might impose personal variations on the diet outcome. Therefore, a prospective strategy of a fine-tuned precision nutrition approach might deliver optimized benefits of the MedDiet.}, } @article {pmid37437367, year = {2023}, author = {Lin, Y and Liu, Y and Zhang, Y and Yuan, W and Wang, D and Zhu, W}, title = {Biological and genomic characterization of a polyvalent bacteriophage (S19cd) strongly inhibiting Salmonella enterica serovar Choleraesuis.}, journal = {Veterinary microbiology}, volume = {284}, number = {}, pages = {109822}, doi = {10.1016/j.vetmic.2023.109822}, pmid = {37437367}, issn = {1873-2542}, mesh = {Swine ; Animals ; Mice ; *Bacteriophages/genetics ; Serogroup ; *Salmonella enterica/genetics ; Genomics ; }, abstract = {Bacteriophages are a promising alternative for the control of pathogenic bacteria. In this study, we isolated a virulent bacteriophage, S19cd, from pig gut that could infect both a non-pathogenic bacteria Escherichia coli 44 (EC44) and two pathogenic bacterial strains (ATCC 13312 (SC13312) and CICC 21493 (SC21493)) of Salmonella enterica serovar Choleraesuis (SC). S19cd exhibited strong lytic ability in both SC13312 and SC21493 with an optimal multiplicity of infection (MOI) of 10[-6] and 10[-5], respectively, and inhibited their growth at an MOI of 10[-7] within 24 h. Mice pre-treated with S19cd exhibited protection against the SC13312 challenge. Moreover, S19cd has good heat resistance (80 ℃) and pH tolerance (pH 3-12). Genome analysis revealed that S19cd belongs to the Felixounavirus genus and does not contain any virulence or drug-resistance-related genes. Additionally, S19cd encodes an adenine-specific methyltransferase that has no similarity to methyltransferases from other Felixounavirus phages and shares limited similarity with other methyltransferases in the NCBI protein database. Metagenomic analysis of S19cd genomes from 500 pigs revealed that S19cd-like phages may be widespread in Chinese pig gut. In conclusion, S19cd can be a potential phage therapy targeting SC infections.}, } @article {pmid37437215, year = {2023}, author = {Mascher, T}, title = {Past, Present, and Future of Extracytoplasmic Function σ Factors: Distribution and Regulatory Diversity of the Third Pillar of Bacterial Signal Transduction.}, journal = {Annual review of microbiology}, volume = {77}, number = {}, pages = {625-644}, doi = {10.1146/annurev-micro-032221-024032}, pmid = {37437215}, issn = {1545-3251}, mesh = {*Bacterial Proteins/genetics/metabolism ; *Sigma Factor/genetics/metabolism ; Bacteria/genetics/metabolism ; Signal Transduction ; Gene Expression Regulation, Bacterial ; }, abstract = {Responding to environmental cues is a prerequisite for survival in the microbial world. Extracytoplasmic function σ factors (ECFs) represent the third most abundant and by far the most diverse type of bacterial signal transduction. While archetypal ECFs are controlled by cognate anti-σ factors, comprehensive comparative genomics efforts have revealed a much higher abundance and regulatory diversity of ECF regulation than previously appreciated. They have also uncovered a diverse range of anti-σ factor-independent modes of controlling ECF activity, including fused regulatory domains and phosphorylation-dependent mechanisms. While our understanding of ECF diversity is comprehensive for well-represented and heavily studied bacterial phyla-such as Proteobacteria, Firmicutes, and Actinobacteria (phylum Actinomycetota)-our current knowledge about ECF-dependent signaling in the vast majority of underrepresented phyla is still far from complete. In particular, the dramatic extension of bacterial diversity in the course of metagenomic studies represents both a new challenge and an opportunity in expanding the world of ECF-dependent signal transduction.}, } @article {pmid37436481, year = {2023}, author = {Xing, Y and Bian, C and Xue, H and Song, Y and Men, W and Hou, W and Yang, Y and Cai, Q and Xu, L}, title = {The effect of plant compartment and geographical location on shaping microbiome of Pulsatilla chinensis.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {17}, pages = {5555-5567}, pmid = {37436481}, issn = {1432-0614}, support = {L201942//019 Liaoning Provincial Department of Education Scientific Research Project/ ; XLYC2002004//Liaoning Revitalization Talents Program/ ; 2020-MS-224//Natural Science Foundation of Liaoning Province/ ; }, mesh = {*Pulsatilla ; Rhizosphere ; Soil Microbiology ; Plant Roots/microbiology ; *Microbiota ; Bacteria/genetics ; Soil/chemistry ; *Plants, Medicinal ; }, abstract = {The plant-associated microbiome has an effect on plant growth. Pulsatilla chinensis (Bge.) Regel is an important Chinese medicinal plant. Currently, there is little understanding of the P. chinensis-associated microbiome and its diversity and composition. Here, the core microbiome associated with the root, leaf, and rhizospheric soil compartments of P. chinensis from five geographical locations was analyzed by the metagenomics approach. The alpha and beta diversity analysis showed that the microbiome associated with P. chinensis was shaped by the compartment, especially in the bacterial community. The geographical location had little influence on microbial community diversity associated with root and leaf. Hierarchical clustering distinguished the microbial communities of rhizospheric soil based on their geographical location and among the soil properties, pH was showed the more stronger effect on the diversity of rhizospheric soil microbial communities. Proteobacteria was the most dominant bacterial phylum in the root, leaf, and rhizospheric soil. Ascomycota and Basidiomycota were the most dominant fungal phyla in different compartments. Rhizobacter, Anoxybacillus, and IMCC26256 were the most important marker bacterial species for root, leaf, and rhizospheric soil screened by random forest, respectively. The fungal marker species for root, leaf, and rhizospheric soil were not only different across the compartments but also the geographical locations. Functional analysis showed that P. chinensis-associated microbiome had the similar function which had no obvious relationship with geographical location and compartment. The associated microbiome indicated in this study can be used for identifying microorganisms related to the quality and growth of P. chinensis. KEY POINTS: • Microbiome associated with P. chinensis was shaped by the compartment • Microbiome composition and abundance associated with rhizospheric soil were affected by the geographical location • Compared with fungi, bacterial associated with P. chinensis composition and diversity were more stable in different geographical locations and compartments.}, } @article {pmid37436163, year = {2023}, author = {Tan, Y and Chen, Z and Zeng, Z and Wu, S and Liu, J and Zou, S and Wang, M and Liang, K}, title = {Microbiomes Detected by Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing among HIV-Infected and Uninfected Patients with Pulmonary Infection.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0000523}, pmid = {37436163}, issn = {2165-0497}, mesh = {Humans ; Bronchoalveolar Lavage Fluid ; *Pneumonia ; *HIV Infections ; *Microbiota ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {Comparison of lung microbiomes between HIV-infected and uninfected patients with pulmonary infection by metagenomic next-generation sequencing (mNGS) has not been described in China. The lung microbiomes detected in bronchoalveolar fluid (BALF) by mNGS among HIV-infected and uninfected patients with pulmonary infection were reviewed in the First Hospital of Changsha between January 2019 and June 2022. In total, 476 HIV-infected and 280 uninfected patients with pulmonary infection were enrolled. Compared with HIV-uninfected patients, the proportions of Mycobacterium (P = 0.011), fungi (P < 0.001), and viruses (P < 0.001) were significantly higher in HIV-infected patients. The higher positive rate of Mycobacterium tuberculosis (MTB; P = 0.018), higher positive rates of Pneumocystis jirovecii and Talaromyces marneffei (all P < 0.001), and higher positive rate of cytomegalovirus (P < 0.001) contributed to the increased proportions of Mycobacterium, fungi, and viruses among HIV-infected patients, respectively. The constituent ratios of Streptococcus pneumoniae (P = 0.007) and Tropheryma whipplei (P = 0.002) in the bacteria spectrum were significantly higher, while the constituent ratio of Klebsiella pneumoniae (P = 0.005) was significantly lower in HIV-infected patients than in HIV-uninfected patients. Compared with HIV-uninfected patients, the constituent ratios of P. jirovecii and T. marneffei (all P < 0.001) in the fungal spectrum were significantly higher, while the constituent ratios of Candida and Aspergillus (all P < 0.001) were significantly lower in HIV-infected patients. In comparison to HIV-infected patients without antiretroviral therapy (ART), the proportions of T. whipplei (P = 0.001), MTB (P = 0.024), P. jirovecii (P < 0.001), T. marneffei (P < 0.001), and cytomegalovirus (P = 0.008) were significantly lower in HIV-infected patients on ART. Significant differences in lung microbiomes exist between HIV-infected and uninfected patients with pulmonary infection, and ART influences the lung microbiomes among HIV-infected patients with pulmonary infection. IMPORTANCE A better understanding of lung microorganisms is conducive to early diagnosis and treatment and will improve the prognosis of HIV-infected patients with pulmonary infection. Currently, few studies have systematically described the spectrum of pulmonary infection among HIV-infected patients. This study is the first to provide comprehensive information on the lung microbiomes of HIV-infected patients with pulmonary infection (as assessed by more sensitive metagenomic next-generation sequencing of bronchoalveolar fluid) compared with those from HIV-uninfected patients, which could provide a reference for the etiology of pulmonary infection among HIV-infected patients.}, } @article {pmid37435755, year = {2023}, author = {Sayols-Baixeras, S and Dekkers, KF and Baldanzi, G and Jönsson, D and Hammar, U and Lin, YT and Ahmad, S and Nguyen, D and Varotsis, G and Pita, S and Nielsen, N and Eklund, AC and Holm, JB and Nielsen, HB and Ericson, U and Brunkwall, L and Ottosson, F and Larsson, A and Ericson, D and Klinge, B and Nilsson, PM and Malinovschi, A and Lind, L and Bergström, G and Sundström, J and Ärnlöv, J and Engström, G and Smith, JG and Orho-Melander, M and Fall, T}, title = {Streptococcus Species Abundance in the Gut Is Linked to Subclinical Coronary Atherosclerosis in 8973 Participants From the SCAPIS Cohort.}, journal = {Circulation}, volume = {148}, number = {6}, pages = {459-472}, pmid = {37435755}, issn = {1524-4539}, mesh = {Humans ; Female ; Middle Aged ; Male ; *Coronary Artery Disease/diagnostic imaging/epidemiology ; Cross-Sectional Studies ; Calcium ; *Atherosclerosis/epidemiology ; Streptococcus ; }, abstract = {BACKGROUND: Gut microbiota have been implicated in atherosclerotic disease, but their relation with subclinical coronary atherosclerosis is unclear. This study aimed to identify associations between the gut microbiome and computed tomography-based measures of coronary atherosclerosis and to explore relevant clinical correlates.

METHODS: We conducted a cross-sectional study of 8973 participants (50 to 65 years of age) without overt atherosclerotic disease from the population-based SCAPIS (Swedish Cardiopulmonary Bioimage Study). Coronary atherosclerosis was measured using coronary artery calcium score and coronary computed tomography angiography. Gut microbiota species abundance and functional potential were assessed with shotgun metagenomics sequencing of fecal samples, and associations with coronary atherosclerosis were evaluated with multivariable regression models adjusted for cardiovascular risk factors. Associated species were evaluated for association with inflammatory markers, metabolites, and corresponding species in saliva.

RESULTS: The mean age of the study sample was 57.4 years, and 53.7% were female. Coronary artery calcification was detected in 40.3%, and 5.4% had at least 1 stenosis with >50% occlusion. Sixty-four species were associated with coronary artery calcium score independent of cardiovascular risk factors, with the strongest associations observed for Streptococcus anginosus and Streptococcus oralis subsp oralis (P<1×10[-5]). Associations were largely similar across coronary computed tomography angiography-based measurements. Out of the 64 species, 19 species, including streptococci and other species commonly found in the oral cavity, were associated with high-sensitivity C-reactive protein plasma concentrations, and 16 with neutrophil counts. Gut microbial species that are commonly found in the oral cavity were negatively associated with plasma indole propionate and positively associated with plasma secondary bile acids and imidazole propionate. Five species, including 3 streptococci, correlated with the same species in saliva and were associated with worse dental health in the Malmö Offspring Dental Study. Microbial functional potential of dissimilatory nitrate reduction, anaerobic fatty acid β-oxidation, and amino acid degradation were associated with coronary artery calcium score.

CONCLUSIONS: This study provides evidence of an association of a gut microbiota composition characterized by increased abundance of Streptococcus spp and other species commonly found in the oral cavity with coronary atherosclerosis and systemic inflammation markers. Further longitudinal and experimental studies are warranted to explore the potential implications of a bacterial component in atherogenesis.}, } @article {pmid37435524, year = {2023}, author = {Chang, L and Che, G and Yang, Q and Lai, S and Teng, J and Duan, J and Liu, T and Liu, F}, title = {Leishmania donovani visceral leishmaniasis diagnosed by metagenomics next-generation sequencing in an infant with acute lymphoblastic leukemia: a case report.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1197149}, pmid = {37435524}, issn = {2296-2565}, mesh = {Humans ; Male ; Infant ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/complications ; *Leishmaniasis, Visceral/diagnosis/drug therapy ; *Leishmania donovani/genetics/isolation & purification ; Metagenomics ; High-Throughput Nucleotide Sequencing ; *Amphotericin B/therapeutic use ; Treatment Outcome ; }, abstract = {BACKGROUND: Visceral leishmaniasis (VL) is a neglected vector-borne tropical disease caused by Leishmania donovani (L. donovani) and Leishmania infantum (L. infantum). Due to the very small dimensions of the protozoa impounded within blood cells and reticuloendothelial structure, diagnosing VL remains challenging.

CASE PRESENTATION: Herein, we reported a case of VL in a 17-month-old boy with acute lymphoblastic leukemia (ALL). The patient was admitted to West China Second University Hospital, Sichuan University, due to repeated fever after chemotherapy. After admission, chemotherapy-related bone marrow suppression and infection were suspected based on clinical symptoms and laboratory test results. However, there was no growth in the conventional peripheral blood culture, and the patient was unresponsive to routine antibiotics. Metagenomics next-generation sequencing (mNGS) of peripheral blood identified 196123 L. donovani reads, followed by Leishmania spp amastigotes using cytomorphology examination of the bone marrow specimen. The patient was given pentavalent antimonials as parasite-resistant therapy for 10 days. After the initial treatment, 356 L. donovani reads were still found in peripheral blood by mNGS. Subsequently, the anti-leishmanial drug amphotericin B was administrated as rescue therapy, and the patient was discharged after a clinical cure.

CONCLUSION: Our results indicated that leishmaniasis still exists in China. Unbiased mNGS provided a clinically actionable diagnosis of a specific infectious disease from an uncommon pathogen that eluded conventional testing.}, } @article {pmid37435234, year = {2023}, author = {Li, S and Tong, J and Li, H and Mao, C and Shen, W and Lei, Y and Hu, P}, title = {L. pneumophila Infection Diagnosed by tNGS in a Lady with Lymphadenopathy.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {4435-4442}, pmid = {37435234}, issn = {1178-6973}, abstract = {We report a case of a 34-year-old lady with multiple joint pain. Autoimmune diseases were considered first with a positive result of anti-Ro antibody and her right knee joint cavity effusion. Later, bilateral interstitial changes in her lungs and mediastinal lymphadenopathy were found after chest CT scanning. Empirical quinolone therapy was given although pathological examinations of blood, sputum and bronchoalveolar lavage fluid (BALF) did not find anything. Finally, Legionella pneumophila was identified by target next-generation sequencing (tNGS) detection. This case highlighted the timely use of tNGS, a new tool with fast speed, high accuracy and effective cost, could help to identify atypical infection and start an early therapy.}, } @article {pmid37435170, year = {2023}, author = {Qing, L and Zhao, Y and Zhang, Y and Guan, Y and Lu, G}, title = {Metagenomic next-generation sequencing in a diagnosis of Pneumocystis pneumonia in an X-linked immunodeficient child: a case report.}, journal = {Frontiers in pediatrics}, volume = {11}, number = {}, pages = {1183601}, pmid = {37435170}, issn = {2296-2360}, abstract = {BACKGROUND: The diagnosis of Pneumocystis pneumonia (PCP) remains challenging in certain specific clinical situations. Metagenomic next-generation sequencing (mNGS), as a novel diagnostic method, may help in the diagnosis of PCP.

CASE PRESENTATION: A 6-month-old male child developed acute pneumonia and sepsis. This child had previously suffered from Escherichia coli septicemia and was cured. However, the fever and dyspnea relapsed. Blood tests revealed a low lymphocyte count (0.69 × 10[9]/L) and acute inflammatory markers such as high-level procalcitonin (8.0 ng/ml) and C-reactive protein (19 mg/dl). Chest imaging showed inflammation and decreased translucency in both lungs but no thymus shadow. Various serology tests, the 1,3-beta-D-glucan test, culture, as well as sputum smear failed to detect any pathogens. mNGS with blood helped identify 133 specific nucleic acid sequences of Pneumocystis jirovecii, suggesting an infection with this pathogen. After treatment with trimethoprim-sulfamethoxazole for 5 days, the patient's condition improved, but the child still needed ventilator support. Unfortunately, the child died soon after because of respiratory failure after his parents decided to abandon treatment. The family declined an autopsy on the child, and therefore, an anatomical diagnosis could not be obtained. Whole-exome sequencing suggested X-linked immunodeficiency. A hemizygous mutation of c.865c > t (p.r289*) was detected in the IL2RG gene, which was inherited from the mother (heterozygous state).

CONCLUSION: This case report highlights the value of mNGS in diagnosing PCP when conventional diagnostic methods fail to identify the agent. Early onset of recurrent infectious diseases may indicate the presence of an immunodeficiency disease, for which timely genetic analysis and diagnosis are crucial.}, } @article {pmid37434868, year = {2023}, author = {Martinez-Hernandez, JE and Berrios, P and Santibáñez, R and Cuesta Astroz, Y and Sanchez, C and Martin, AJM and Trombert, AN}, title = {First metagenomic analysis of the Andean condor (Vultur gryphus) gut microbiome reveals microbial diversity and wide resistome.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15235}, pmid = {37434868}, issn = {2167-8359}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; *Falconiformes ; Acclimatization ; Chile ; Clostridium perfringens ; }, abstract = {BACKGROUND: The Andean condor (Vultur gryphus) is the largest scavenger in South America. This predatory bird plays a crucial role in their ecological niche by removing carcasses. We report the first metagenomic analysis of the Andean condor gut microbiome.

METHODS: This work analyzed shotgun metagenomics data from a mixture of fifteen captive Chilean Andean condors. To filter eukaryote contamination, we employed BWA-MEM v0.7. Taxonomy assignment was performed using Kraken2 and MetaPhlAn v2.0 and all filtered reads were assembled using IDBA-UD v1.1.3. The two most abundant species were used to perform a genome reference-guided assembly using MetaCompass. Finally, we performed a gene prediction using Prodigal and each gene predicted was functionally annotated. InterproScan v5.31-70.0 was additionally used to detect homology based on protein domains and KEGG mapper software for reconstructing metabolic pathways.

RESULTS: Our results demonstrate concordance with the other gut microbiome data from New World vultures. In the Andean condor, Firmicutes was the most abundant phylum present, with Clostridium perfringens, a potentially pathogenic bacterium for other animals, as dominating species in the gut microbiome. We assembled all reads corresponding to the top two species found in the condor gut microbiome, finding between 94% to 98% of completeness for Clostridium perfringens and Plesiomonas shigelloides, respectively. Our work highlights the ability of the Andean condor to act as an environmental reservoir and potential vector for critical priority pathogens which contain relevant genetic elements. Among these genetic elements, we found 71 antimicrobial resistance genes and 1,786 virulence factors that we associated with several adaptation processes.}, } @article {pmid37434786, year = {2023}, author = {Liu, Q and Liu, X and Hu, B and Xu, H and Sun, R and Li, P and Zhang, Y and Yang, H and Ma, N and Sun, X}, title = {Diagnostic performance and clinical impact of blood metagenomic next-generation sequencing in ICU patients suspected monomicrobial and polymicrobial bloodstream infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1192931}, pmid = {37434786}, issn = {2235-2988}, mesh = {Humans ; Metagenomics ; Retrospective Studies ; *Sepsis/diagnosis/drug therapy ; *Coinfection/diagnosis ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/therapeutic use ; Intensive Care Units ; }, abstract = {INTRODUCTION: Early and effective application of antimicrobial medication has been evidenced to improve outcomes of patients with bloodstream infection (BSI). However, conventional microbiological tests (CMTs) have a number of limitations that hamper a rapid diagnosis.

METHODS: We retrospectively collected 162 cases suspected BSI from intensive care unit with blood metagenomics next-generation sequencing (mNGS) results, to comparatively evaluate the diagnostic performance and the clinical impact on antibiotics usage of mNGS.

RESULTS AND DISCUSSION: Results showed that compared with blood culture, mNGS detected a greater number of pathogens, especially for Aspergillus spp, and yielded a significantly higher positive rate. With the final clinical diagnosis as the standard, the sensitivity of mNGS (excluding viruses) was 58.06%, significantly higher than that of blood culture (34.68%, P<0.001). Combing blood mNGS and culture results, the sensitivity improved to 72.58%. Forty-six patients had infected by mixed pathogens, among which Klebsiella pneumoniae and Acinetobacter baumannii contributed most. Compared to monomicrobial, cases with polymicrobial BSI exhibited dramatically higher level of SOFA, AST, hospitalized mortality and 90-day mortality (P<0.05). A total of 101 patients underwent antibiotics adjustment, among which 85 were adjusted according to microbiological results, including 45 cases based on the mNGS results (40 cases escalation and 5 cases de-escalation) and 32 cases on blood culture. Collectively, for patients suspected BSI in critical condition, mNGS results can provide valuable diagnostic information and contribute to the optimizing of antibiotic treatment. Combining conventional tests with mNGS may significantly improve the detection rate for pathogens and optimize antibiotic treatment in critically ill patients with BSI.}, } @article {pmid37434780, year = {2023}, author = {Xie, G and Hu, Q and Cao, X and Wu, W and Dai, P and Guo, W and Wang, O and Wei, L and Ren, R and Li, Y}, title = {Clinical identification and microbiota analysis of Chlamydia psittaci- and Chlamydia abortus- pneumonia by metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1157540}, pmid = {37434780}, issn = {2235-2988}, mesh = {Humans ; *Chlamydophila psittaci/genetics ; *Chlamydial Pneumonia/diagnosis ; *Coinfection ; *Chlamydia/genetics ; *Microbiota ; *Pneumonia/diagnosis ; *Chlamydia Infections/diagnosis ; High-Throughput Nucleotide Sequencing ; }, abstract = {INTRODUCTION: Recently, the incidence of chlamydial pneumonia caused by rare pathogens such as C. psittaci or C. abortus has shown a significant upward trend. The non-specific clinical manifestations and the limitations of traditional pathogen identification methods determine that chlamydial pneumonia is likely to be poorly diagnosed or even misdiagnosed, and may further result in delayed treatment or unnecessary antibiotic use. mNGS's non-preference and high sensitivity give us the opportunity to obtain more sensitive detection results than traditional methods for rare pathogens such as C. psittaci or C. abortus.

METHODS: In the present study, we investigated both the pathogenic profile characteristics and the lower respiratory tract microbiota of pneumonia patients with different chlamydial infection patterns using mNGS.

RESULTS: More co-infecting pathogens were found to be detectable in clinical samples from patients infected with C. psittaci compared to C. abortus, suggesting that patients infected with C. psittaci may have a higher risk of mixed infection, which in turn leads to more severe clinical symptoms and a longer disease course cycle. Further, we also used mNGS data to analyze for the first time the characteristic differences in the lower respiratory tract microbiota of patients with and without chlamydial pneumonia, the impact of the pattern of Chlamydia infection on the lower respiratory tract microbiota, and the clinical relevance of these characteristics. Significantly different profiles of lower respiratory tract microbiota and microecological diversity were found among different clinical subgroups, and in particular, mixed infections with C. psittaci and C. abortus resulted in lower lung microbiota diversity, suggesting that chlamydial infections shape the unique lung microbiota pathology, while mixed infections with different Chlamydia may have important effects on the composition and diversity of the lung microbiota.

DISCUSSION: The present study provides possible evidences supporting the close correlation between chlamydial infection, altered microbial diversity in patients' lungs and clinical parameters associated with infection or inflammation in patients, which also provides a new research direction to better understand the pathogenic mechanisms of pulmonary infections caused by Chlamydia.}, } @article {pmid37434715, year = {2023}, author = {Trexler, RV and Van Goethem, MW and Goudeau, D and Nath, N and Malmstrom, RR and Northen, TR and Couradeau, E}, title = {BONCAT-FACS-Seq reveals the active fraction of a biocrust community undergoing a wet-up event.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1176751}, pmid = {37434715}, issn = {1664-302X}, abstract = {Determining which microorganisms are active within soil communities remains a major technical endeavor in microbial ecology research. One promising method to accomplish this is coupling bioorthogonal non-canonical amino acid tagging (BONCAT) with fluorescence activated cell sorting (FACS) which sorts cells based on whether or not they are producing new proteins. Combined with shotgun metagenomic sequencing (Seq), we apply this method to profile the diversity and potential functional capabilities of both active and inactive microorganisms in a biocrust community after being resuscitated by a simulated rain event. We find that BONCAT-FACS-Seq is capable of discerning the pools of active and inactive microorganisms, especially within hours of applying the BONCAT probe. The active and inactive components of the biocrust community differed in species richness and composition at both 4 and 21 h after the wetting event. The active fraction of the biocrust community is marked by taxa commonly observed in other biocrust communities, many of which play important roles in species interactions and nutrient transformations. Among these, 11 families within the Firmicutes are enriched in the active fraction, supporting previous reports indicating that the Firmicutes are key early responders to biocrust wetting. We highlight the apparent inactivity of many Actinobacteria and Proteobacteria through 21 h after wetting, and note that members of the Chitinophagaceae, enriched in the active fraction, may play important ecological roles following wetting. Based on the enrichment of COGs in the active fraction, predation by phage and other bacterial members, as well as scavenging and recycling of labile nutrients, appear to be important ecological processes soon after wetting. To our knowledge, this is the first time BONCAT-FACS-Seq has been applied to biocrust samples, and therefore we discuss the potential advantages and shortcomings of coupling metagenomics to BONCAT to intact soil communities such as biocrust. In all, by pairing BONCAT-FACS and metagenomics, we are capable of highlighting the taxa and potential functions that typifies the microbes actively responding to a rain event.}, } @article {pmid37433843, year = {2023}, author = {Hintikka, JE and Ahtiainen, JP and Permi, P and Jalkanen, S and Lehtonen, M and Pekkala, S}, title = {Aerobic exercise training and gut microbiome-associated metabolic shifts in women with overweight: a multi-omic study.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {11228}, pmid = {37433843}, issn = {2045-2322}, mesh = {Adult ; Humans ; Female ; *Overweight/therapy ; *Gastrointestinal Microbiome ; Multiomics ; Exercise ; Obesity/therapy ; Lecithins ; }, abstract = {Physical activity is essential in weight management, improves overall health, and mitigates obesity-related risk markers. Besides inducing changes in systemic metabolism, habitual exercise may improve gut's microbial diversity and increase the abundance of beneficial taxa in a correlated fashion. Since there is a lack of integrative omics studies on exercise and overweight populations, we studied the metabolomes and gut microbiota associated with programmed exercise in obese individuals. We measured the serum and fecal metabolites of 17 adult women with overweight during a 6-week endurance exercise program. Further, we integrated the exercise-responsive metabolites with variations in the gut microbiome and cardiorespiratory parameters. We found clear correlation with several serum and fecal metabolites, and metabolic pathways, during the exercise period in comparison to the control period, indicating increased lipid oxidation and oxidative stress. Especially, exercise caused co-occurring increase in levels of serum lyso-phosphatidylcholine moieties and fecal glycerophosphocholine. This signature was associated with several microbial metagenome pathways and the abundance of Akkermansia. The study demonstrates that, in the absence of body composition changes, aerobic exercise can induce metabolic shifts that provide substrates for beneficial gut microbiota in overweight individuals.}, } @article {pmid37433373, year = {2023}, author = {Huang, X and Chen, C and Xie, W and Zhou, C and Tian, X and Zhang, Z and Wang, Q and Chang, H and Xiao, W and Zhang, R and Gao, Y}, title = {Metagenomic Analysis of Intratumoral Microbiome Linking to Response to Neoadjuvant Chemoradiotherapy in Rectal Cancer.}, journal = {International journal of radiation oncology, biology, physics}, volume = {117}, number = {5}, pages = {1255-1269}, doi = {10.1016/j.ijrobp.2023.06.2515}, pmid = {37433373}, issn = {1879-355X}, mesh = {Humans ; Neoadjuvant Therapy ; Metagenome ; Chemoradiotherapy/methods ; *Rectal Neoplasms/pathology ; Biomarkers ; *Microbiota ; Butyrates ; Treatment Outcome ; }, abstract = {PURPOSE: To assess taxonomic and functional characteristics of tumor-bearing microbiota and its association with response to neoadjuvant chemoradiation therapy (nCRT) in patients with locally advanced rectal cancer.

METHODS AND MATERIALS: We performed metagenomic sequencing of biopsy tumoral tissues from 73 patients with locally advanced rectal cancer before nCRT. Patients were classified into poor responders (PR) and good responders (GR) according to response to nCRT. Subsequent investigation of network alteration, key community, microbial biomarkers, and function related to nCRT responses were carried out.

RESULTS: The network-driven analysis systematically revealed 2 co-occurring bacteria modules that exhibited opposite relationship with rectal cancer radiosensitivity. In the 2 modules, prominent alteration of global graph properties and community structure was observed between networks of PR and GR group. By quantifying changes in between-group association patterns and abundances, a total of 115 discriminative biomarker species linked to nCRT response were found, and 35 microbial variables were selected to establish the optimal randomForest classifier for nCRT response prediction. It yielded an area under the curve value of 85.5% (95% CI, 73.3%-97.8%) in the training cohort and 88.4% (95% CI, 77.5%-99.4%) in the validation cohort. In a comprehensive consideration, 5 key bacteria showed high relevance with inducing resistance to nCRT, including Streptococcus equinus, Schaalia odontolytica, Clostridium hylemonae, Blautia producta, and Pseudomonas azotoformans. One key hub including several butyrate-formation bacteria involving with driving network alteration from GR to PR indicate that microbiota-derived butyrate may also be involved in reducing the antitumor effects of nCRT, especially Coprococcus. The functional analysis of metagenome linked the nitrate and sulfate-sulfur assimilation, histidine catabolic process, and resistance to cephamycin to the reduced therapeutic response. It also linked to leucine degradation, isoleucine biosynthesis, taurine, and hypotaurine metabolism to the improved response to nCRT.

CONCLUSIONS: Our data offer novel potential microbial factors and shared metagenome function linked to resistance to nCRT.}, } @article {pmid37433210, year = {2023}, author = {Sekizuka, T and Yamaguchi, N and Kanamori, H and Kuroda, M}, title = {Multiplex Hybrid Capture Improves the Deep Detection of Antimicrobial Resistance Genes from Wastewater Treatment Plant Effluents to Assess Environmental Issues.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {29}, number = {11}, pages = {510-515}, doi = {10.1089/mdr.2023.0016}, pmid = {37433210}, issn = {1931-8448}, mesh = {*Anti-Bacterial Agents/pharmacology ; Wastewater ; Angiotensin Receptor Antagonists ; Drug Resistance, Bacterial/genetics ; Microbial Sensitivity Tests ; Angiotensin-Converting Enzyme Inhibitors ; Genes, Bacterial/genetics ; *Water Purification/methods ; }, abstract = {Metagenomic sequencing (mDNA-seq) is one of the best approaches to address antimicrobial resistance (AMR) issues and characterize AMR genes (ARGs) and their host bacteria (ARB); however, the sensitivity provided is insufficient for the overall detection in wastewater treatment plant (WWTP) effluents because the effluent is well treated. This study investigated the multiplex hybrid capture (xHYB) method (QIAseq × HYB AMR Panel) and its potential to increase AMR assessment sensitivity. The mDNA-Seq analysis suggested that the WWTP effluents had an average of 104 reads per kilobase of gene per million (RPKM) for the detection of all targeted ARGs, whereas xHYB significantly improved detection at 601,576 RPKM, indicating an average 5,805-fold increase in sensitivity. For instance, sul1 was detected at 15 and 114,229 RPKM using mDNA-seq and xHYB, respectively. The blaCTX-M, blaKPC, and mcr gene variants were not detected by mDNA-Seq but were detected by xHYB at 67, 20, and 1,010 RPKM, respectively. This study demonstrates that the multiplex xHYB method could be a suitable evaluation standard with high sensitivity and specificity for deep-dive detection, highlighting a broader illustration of ongoing dissemination in the entire community.}, } @article {pmid37432727, year = {2023}, author = {Wang, J and Shi, K and Jing, Z and Ge, Y}, title = {Metagenomic Evidence for Cobamide Producers Driving Prokaryotic Co-occurrence Associations and Potential Function in Wastewater Treatment Plants.}, journal = {Environmental science & technology}, volume = {57}, number = {29}, pages = {10640-10651}, doi = {10.1021/acs.est.3c02181}, pmid = {37432727}, issn = {1520-5851}, mesh = {*Cobamides ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Cobamides are required by most organisms but are only produced by specific prokaryotic taxa. These commonly shared cofactors play significant roles in shaping the microbial community and ecosystem function. Wastewater treatment plants (WWTPs) are the world's most common biotechnological systems; knowledge about sharing of cobamides among microorganisms is predicted to be important to decipher the complex microbial relationships in these systems. Herein, we explored prokaryotic potential cobamide producers in global WWTP systems based on metagenomic analyses. A set of 8253 metagenome-assembled genomes (MAGs) were recovered and 1276 (15.5%) of them were identified as cobamide producers, which could potentially be used for the practical biological manipulation of WWTP systems. Moreover, 8090 of the total recovered MAGs (98.0%) contained at least one enzyme family dependent on cobamides, indicating the sharing of cobamides among microbial members in WWTP systems. Importantly, our results showed that the relative abundance and number of cobamide producers improved the complexity of microbial co-occurrence networks and most nitrogen, sulfur, and phosphorus cycling gene abundances, indicating the significance of cobamides in microbial ecology and their potential function in WWTP systems. These findings enhance the knowledge of cobamide producers and their functions in WWTP systems, which has important implications for improving the efficiency of microbial wastewater treatment processes.}, } @article {pmid37432374, year = {2023}, author = {Silvano, A and Meriggi, N and Renzi, S and Seravalli, V and Torcia, MG and Cavalieri, D and Di Tommaso, M}, title = {Vaginal Microbiome in Pregnant Women with and without Short Cervix.}, journal = {Nutrients}, volume = {15}, number = {9}, pages = {}, pmid = {37432374}, issn = {2072-6643}, support = {B15F21003630007//Ente Cassa di Risparmio di Firenze/ ; }, mesh = {Pregnancy ; Humans ; Female ; *Cervix Uteri ; Pregnant Women ; Vagina ; *Microbiota ; Metagenome ; }, abstract = {Cervical shortening is a recognised risk factor for pre-term birth. The vaginal microbiome plays an essential role in pregnancy and in maternal and foetal outcomes. We studied the vaginal microbiome in 68 women with singleton gestation and a cervical length ≤25 mm and in 29 pregnant women with a cervix >25 mm in the second or early third trimester. Illumina protocol 16S Metagenomic Sequencing Library Preparation was used to detail amplified 16SrRNA gene. Statistical analyses were performed in R environment. Firmicutes was the phylum most represented in all pregnant women. The mean relative abundance of Proteobacteria and Actinobacteriota was higher in women with a short cervix. Bacterial abundance was higher in women with a normal length cervix compared to the group of women with a short cervix. Nonetheless, a significant enrichment in bacterial taxa poorly represented in vaginal microbiome was observed in the group of women with a short cervix. Staphylococcus and Pseudomonas, taxa usually found in aerobic vaginitis, were more common in women with a short cervix compared with the control group, while Lactobacillus iners and Bifidobacterium were associated with a normal cervical length. Lactobacillus jensenii and Gardenerella vaginalis were associated with a short cervix.}, } @article {pmid37432207, year = {2023}, author = {Chen, BY and Li, YL and Lin, WZ and Bi, C and Du, LJ and Liu, Y and Zhou, LJ and Liu, T and Xu, S and Zhang, J and Liu, Y and Zhu, H and Zhang, WC and Zhang, ZY and Duan, SZ}, title = {Integrated Omic Analysis of Human Plasma Metabolites and Microbiota in a Hypertension Cohort.}, journal = {Nutrients}, volume = {15}, number = {9}, pages = {}, pmid = {37432207}, issn = {2072-6643}, support = {81725003, 81991503, 81991500, 81921002//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Gastrointestinal Microbiome ; *Hypertension ; }, abstract = {Hypertension is closely related to metabolic dysregulation, which is associated with microbial dysbiosis and altered host-microbiota interactions. However, plasma metabolite profiles and their relationships to oral/gut microbiota in hypertension have not been evaluated in depth. Plasma, saliva, subgingival plaques, and feces were collected from 52 hypertensive participants and 24 healthy controls in a cross-sectional cohort. Untargeted metabolomic profiling of plasma was performed using high-performance liquid chromatography-mass spectrometry. Microbial profiling of oral and gut samples was determined via 16S rRNA and metagenomic sequencing. Correlations between metabolites and clinic parameters/microbiota were identified using Spearman's correlation analysis. Metabolomic evaluation showed distinct clusters of metabolites in plasma between hypertensive participants and control participants. Hypertensive participants had six significantly increased and thirty-seven significantly decreased plasma metabolites compared to controls. The plasma metabolic similarity significantly correlated with the community similarity of microbiota. Both oral and gut microbial community composition had significant correlations with metabolites such as Sphingosine 1-phosphate, a molecule involved in the regulation of blood pressure. Plasma metabolites had a larger number of significant correlations with bacterial genera than fungal genera. The shared oral/gut bacterial genera had more correlations with metabolites than unique genera but shared fungal genera and metabolites did not show clear clusters. The hypertension group had fewer correlations between plasma metabolites and bacteria/fungi than controls at species level. The integrative analysis of plasma metabolome and oral/gut microbiome identified unreported alterations of plasma metabolites in hypertension and revealed correlations between altered metabolites and oral/gut microbiota. These observations suggested metabolites and microbiota may become valuable targets for therapeutic and preventive interventions of hypertension.}, } @article {pmid37432121, year = {2023}, author = {Valentino, V and De Filippis, F and Sequino, G and Ercolini, D}, title = {Psychrotrophic Bacteria Equipped with Virulence and Colonization Traits Populate the Ice Cream Manufacturing Environment.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {8}, pages = {e0076523}, pmid = {37432121}, issn = {1098-5336}, mesh = {Humans ; *Ice Cream ; Virulence ; Bacteria/genetics ; Food Handling ; Biofilms ; *Anti-Infective Agents ; Food Microbiology ; }, abstract = {Several microbial taxa have been associated with food processing facilities, and they might resist by attaching on tools and equipment even after sanitation procedures, producing biofilms that adhere to the surfaces and might embed other microorganisms, including spoilers and pathogens. There is increasing evidence that these communities can be transferred to the final product. To explore the microbial contamination routes in a facility producing ice creams, we collected foods and environmental swabs from industrial surfaces of equipment and tools and performed taxonomic and functional analyses of the microbial DNA extracted from the environmental samples. Our results suggest that complex communities dominated by psychrotrophic bacteria (e.g., Pseudomonas and Acinetobacter spp.) inhabit the food processing environment, and we demonstrate that these communities might be transferred from the surfaces to the products. Functional analysis performed on environmental samples highlighted the presence of several genes linked to antimicrobial resistance and adherence on abiotic surfaces; such genes were more abundant on food contact (FC) than on other surfaces. Metagenome-assembled genomes (MAGs) of Pseudomonas stutzeri showed genes linked with biofilm formation and motility, which are surely linked to colonizing capabilities in the processing lines. The study highlights clear potential advantages of applying microbiome mapping in the food industry for source tracking of microbial contamination and for planning appropriate ad hoc sanitization strategies. IMPORTANCE Several microbial species might permanently establish in food processing facilities, thus contributing to food loss. In fact, food contact surfaces might transfer microorganisms to intermediates and products, potentially representing a hazard to human health. In this work, we provide evidence of the existence of complex microbial communities overcoming sanitation in an ice cream-producing facility. These communities harbored several genes that could potentially lead to attachment to surfaces and antimicrobial resistance. Also, prediction of routes of contamination showed that several potential spoilage taxa might end up in the final product. Importantly, in this work, we show that mapping the environmental microbiome is a high-resolution technique that might help food business operators ensure food quality and safety through detection of potentially hazardous microorganisms.}, } @article {pmid37432120, year = {2023}, author = {Schmitz, D and Zwagemaker, F and van der Veer, B and Vennema, H and Laros, JFJ and Koopmans, MPG and De Graaf, M and Kroneman, A}, title = {Metagenomic Surveillance of Viral Gastroenteritis in a Public Health Setting.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0502222}, pmid = {37432120}, issn = {2165-0497}, mesh = {Child ; Adult ; Humans ; Infant ; Public Health ; Metagenomics ; RNA, Viral/genetics ; *Gastroenteritis/epidemiology ; *Rotavirus/genetics ; *Viruses/genetics ; *Enteritis ; *Enterovirus Infections ; *Adenoviridae Infections ; *Norovirus/genetics ; Adenoviridae/genetics ; *Adenovirus Infections, Human ; *Sapovirus/genetics ; *Enterovirus/genetics ; Feces ; }, abstract = {Norovirus is the primary cause of viral gastroenteritis (GE). To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets consisting of complete genomes. To investigate the potential of shotgun metagenomic sequencing on the Illumina platform for whole-genome sequencing, 71 reverse transcriptase quantitative PCR (RT-qPCR) norovirus positive-feces (threshold cycle [CT], <30) samples from norovirus surveillance within The Netherlands were subjected to metagenomic sequencing. Data were analyzed through an in-house next-generation sequencing (NGS) analysis workflow. Additionally, we assessed the potential of metagenomic sequencing for the surveillance of off-target viruses that are of importance for public health, e.g., sapovirus, rotavirus A, enterovirus, parechovirus, aichivirus, adenovirus, and bocaparvovirus. A total of 60 complete and 10 partial norovirus genomes were generated, representing 7 genogroup I capsid genotypes and 12 genogroup II capsid genotypes. In addition to the norovirus genomes, the metagenomic approach yielded partial or complete genomes of other viruses for 39% of samples from children and 6.7% of samples from adults, including adenovirus 41 (N = 1); aichivirus 1 (N = 1); coxsackievirus A2 (N = 2), A4 (N = 2), A5 (N = 1), and A16 (N = 1); bocaparvovirus 1 (N = 1) and 3 (N = 1); human parechovirus 1 (N = 2) and 3 (N = 1); Rotavirus A (N = 1); and a sapovirus GI.7 (N = 1). The sapovirus GI.7 was initially not detected through RT-qPCR and warranted an update of the primer and probe set. Metagenomic sequencing on the Illumina platform robustly determines complete norovirus genomes and may be used to broaden gastroenteritis surveillance by capturing off-target enteric viruses. IMPORTANCE Viral gastroenteritis results in significant morbidity and mortality in vulnerable individuals and is primarily caused by norovirus. To investigate norovirus epidemiology, there is a need for whole-genome sequencing and reference sets consisting of full genomes. Using surveillance samples sent to the Dutch National Institute for Public Health and the Environment (RIVM), we compared metagenomics against conventional techniques, such as RT-qPCR and Sanger-sequencing, with norovirus as the target pathogen. We determined that metagenomics is a robust method to generate complete norovirus genomes, in parallel to many off-target pathogenic enteric virus genomes, thereby broadening our surveillance efforts. Moreover, we detected a sapovirus that was not detected by our validated gastroenteritis RT-qPCR panel, which exemplifies the strength of metagenomics. Our study shows that metagenomics can be used for public health gastroenteritis surveillance, the generation of reference-sets for molecular epidemiology, and how it compares to current surveillance strategies.}, } @article {pmid37431863, year = {2023}, author = {Han, B and Lv, X and Liu, G and Li, S and Fan, J and Chen, L and Huang, Z and Lin, G and Xu, X and Huang, Z and Zhan, L and Lv, X}, title = {Gut microbiota-related bile acid metabolism-FXR/TGR5 axis impacts the response to anti-α4β7-integrin therapy in humanized mice with colitis.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2232143}, pmid = {37431863}, issn = {1949-0984}, mesh = {Animals ; Mice ; Humans ; *Gastrointestinal Microbiome ; Caco-2 Cells ; *Colitis/chemically induced/drug therapy ; *Inflammatory Bowel Diseases ; Bile Acids and Salts ; Integrins ; }, abstract = {The gut microbiota and bile acid metabolism are key determinants of the response of inflammatory bowel disease to biologic therapy. However, the molecular mechanisms underlying the interactions between the response to anti-α4β7-integrin therapy and the gut microbiota and bile acid metabolism remain unknown. In this research, we investigated the role of gut microbiota-related bile acid metabolism on the response to anti-α4β7-integrin therapy in a humanized immune system mouse model with colitis induced by 2,4,6-trinitrobenzene sulfonic acid. We found that anti-α4β7-integrin significantly mitigated intestinal inflammation, pathological symptoms, and gut barrier disruption in remission-achieving colitis mice. Whole-genome shotgun metagenomic sequencing demonstrated that employing baseline microbiome profiles to predict remission and the treatment response was a promising strategy. Antibiotic-mediated gut microbiota depletion and fecal microbiome transplantation revealed that the baseline gut microbiota contained common microbes with anti-inflammatory effects and reduced mucosal barrier damage, improving the treatment response. Targeted metabolomics analysis illustrated that bile acids associated with microbial diversity were involved in colitis remission. Furthermore, the activation effects of the microbiome and bile acids on FXR and TGR5 were evaluated in colitis mice and Caco-2 cells. The findings revealed that the production of gastrointestinal bile acids, particularly CDCA and LCA, further directly promoted the stimulation of FXR and TGR5, significantly improving gut barrier function and suppressing the inflammatory process. Taken together, gut microbiota-related bile acid metabolism-FXR/TGR5 axis may be a potential mechanism for impacting the response to anti-α4β7-integrin in experimental colitis. Thus, our research provides novel insights into the treatment response in inflammatory bowel disease.}, } @article {pmid37431553, year = {2023}, author = {Pham, J and Su, LD and Hanson, KE and Hogan, CA}, title = {Sequence-based diagnostics and precision medicine in bacterial and viral infections: from bench to bedside.}, journal = {Current opinion in infectious diseases}, volume = {36}, number = {4}, pages = {228-234}, doi = {10.1097/QCO.0000000000000936}, pmid = {37431553}, issn = {1473-6527}, mesh = {Humans ; Precision Medicine ; *Virus Diseases/diagnosis ; High-Throughput Nucleotide Sequencing ; *Clinical Laboratory Services ; *Communicable Diseases ; }, abstract = {PURPOSE OF REVIEW: Nucleic acid sequence-based organism identification plays an important role in the diagnosis and management of transplant and cancer-associated infectious diseases. Here, we provide a high-level overview of advanced sequencing technologies, discuss test performance, and highlight unmet research needs with a focus on immunocompromised hosts.

RECENT FINDINGS: Next-generation sequencing (NGS) technologies are powerful tools with a growing role in managing immunocompromised patients with suspected infection. Targeted NGS (tNGS) can identify pathogens directly from patient specimens, especially for mixed samples, and has been used to detect resistance mutations in transplant-related viruses (e.g. CMV). Whole-genome sequencing (WGS) is increasingly used for outbreak investigations and infection control. Metagenomic NGS (mNGS) is useful for hypothesis-free testing and can simultaneously assess pathogens and host response to infection.

SUMMARY: NGS testing increases diagnostic yield relative to standard culture and Sanger sequencing but may be limited by high cost, turnaround times, and detection of unexpected organisms or commensals of uncertain significance. Close collaboration with the clinical microbiology laboratory and infectious diseases is recommended when NGS testing is considered. Additional research is required to understand which immunocompromised patients are most likely to benefit from NGS testing, and when testing should ideally be performed.}, } @article {pmid37431054, year = {2022}, author = {Seo, H and Lee, S and Park, H and Jo, S and Kim, S and Rahim, MA and Ul-Haq, A and Barman, I and Lee, Y and Seo, A and Kim, M and Jung, IY and Song, HY}, title = {Characteristics and Microbiome Profiling of Korean Gochang Bokbunja Vinegar by the Fermentation Process.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {20}, pages = {}, pmid = {37431054}, issn = {2304-8158}, support = {2021040D288//Gochang Bokbunja vinegar Research Project/ ; Soonchunhyang University Research Fund//Soonchunhyang University/ ; }, abstract = {As NGS (next-generation sequencing) technology develops, metagenomics-based microbial ecology, that is, microbiome research, has recently led to the science of fermented food. Based on the above technology, a study was conducted to understand the characteristics of vinegar made from bokbunja, a local crop in Gochang-gun, Korea. Physicochemical characteristics of vinegar, organic acid analysis, microbial community analysis, and electronic tongue analysis were explored while fermenting the vinegar for 70 days under eight fermentation conditions according to the concentration of bokbunja liquid (100% or 50%), type of fermenter (porcelain jar or stainless container), and fermentation environment (natural outdoor conditions or temperature/oxygen controlled). As a result, distinct microbial community patterns were found in the stage of acetic acid fermentation and, accordingly, this fermentation of Gochang vinegar is classified into three categories. Vinegar prepared by the traditional method of outdoor fermentation using jars showed characteristics of "Acetobacter (42.1%)/Lactobacillus (56.9%) fusion fermentation". Under conditions where oxygen and temperature were controlled indoors using jars, characteristics of "Komagataeibacter (90.2%) fermentation" were found. "Lactobacillus (92.2%) fermentation" characteristics were discovered under natural outdoor conditions using stainless steel containers. These fermentation pattern differences were related to taxonomic phylogenetic diversity, which was also considered involved in determining organic acid production and taste. These results will be helpful as a scientific basis for understanding the fermentation characteristics of Gochang vinegar and developing high-value-added traditional vinegar products.}, } @article {pmid37431045, year = {2022}, author = {Srinivas, M and O'Sullivan, O and Cotter, PD and Sinderen, DV and Kenny, JG}, title = {The Application of Metagenomics to Study Microbial Communities and Develop Desirable Traits in Fermented Foods.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {20}, pages = {}, pmid = {37431045}, issn = {2304-8158}, support = {12/RC/2273/SFI_/Science Foundation Ireland/Ireland ; }, abstract = {The microbial communities present within fermented foods are diverse and dynamic, producing a variety of metabolites responsible for the fermentation processes, imparting characteristic organoleptic qualities and health-promoting traits, and maintaining microbiological safety of fermented foods. In this context, it is crucial to study these microbial communities to characterise fermented foods and the production processes involved. High Throughput Sequencing (HTS)-based methods such as metagenomics enable microbial community studies through amplicon and shotgun sequencing approaches. As the field constantly develops, sequencing technologies are becoming more accessible, affordable and accurate with a further shift from short read to long read sequencing being observed. Metagenomics is enjoying wide-spread application in fermented food studies and in recent years is also being employed in concert with synthetic biology techniques to help tackle problems with the large amounts of waste generated in the food sector. This review presents an introduction to current sequencing technologies and the benefits of their application in fermented foods.}, } @article {pmid37431044, year = {2022}, author = {Yu, Z and Ma, Y and Guan, Y and Zhu, Y and Wang, K and Wang, Y and Liu, P and Chen, J and Yu, Y}, title = {Metagenomics of Virus Diversities in Solid-State Brewing Process of Traditional Chinese Vinegar.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {20}, pages = {}, pmid = {37431044}, issn = {2304-8158}, support = {32072202//National Natural Science Foundation of China/ ; }, abstract = {Traditional Chinese vinegar offers an exceptional flavor and rich nutrients due to its unique solid-state fermentation process, which is a multiple microbial fermentation system including various bacteria, fungi and viruses. However, few studies on the virus diversities in traditional Chinese vinegar have been reported. In this paper, using Zhenjiang aromatic vinegar as a model system, we systemically explored the viral communities in the solid-state brewing process of traditional Chinese vinegar using bacterial and viral metagenomes. Results showed that the viral diversity in vinegar Pei was extensive and the virus communities varied along with the fermentation process. In addition, there existed some interactions between viral and bacterial communities. Moreover, abundant antibiotic resistance genes were found in viromes, indicating that viruses might protect fermentation bacteria strains from the stress of antibiotics in the fermentation environment. Remarkably, we identified abundant auxiliary carbohydrate metabolic genes (including alcohol oxidases, the key enzymes for acetic acid synthesis) from viromes, implying that viruses might participate in the acetic acid synthesis progress of the host through auxiliary metabolic genes. Taken together, our results indicated the potential roles of viruses in the vinegar brewing process and provided a new perspective for studying the fermentation mechanisms of traditional Chinese vinegar.}, } @article {pmid37430931, year = {2022}, author = {Kim, JH and Lee, ES and Kim, BM and Oh, MH}, title = {Potential Correlation between Microbial Diversity and Volatile Flavor Compounds in Different Types of Korean Dry-Fermented Sausages.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {20}, pages = {}, pmid = {37430931}, issn = {2304-8158}, support = {PJ01594202//Rural Development Administration/ ; }, abstract = {The microbial community in fermented sausages plays an important role in determining their quality characteristics. The objective of this study was to investigate the correlation between microbial diversity and volatile compounds in dry-fermented sausages procured from different regions of Korea. Results from metagenomics analysis showed that Lactobacillus and Staphylococcus were the predominant bacterial genera, and Penicillium, Debaryomyces, and Candida were the predominant fungal genera. Twelve volatile compounds were detected using an electronic nose. Leuconostoc exhibited a positive correlation with esters and volatile flavor, whereas Debaryomyces, Aspergillus, Mucor, and Rhodotorula exhibited a negative correlation with methanethiol, thus revealing the involvement of the microorganisms in flavor formation. The results of this study may help in understanding the microbial diversity of dry-fermented sausages in Korea and provide a rationale and quality control guideline through potential correlation with volatile flavor analysis.}, } @article {pmid37430920, year = {2022}, author = {Daji, GA and Green, E and Abrahams, A and Oyedeji, AB and Masenya, K and Kondiah, K and Adebo, OA}, title = {Physicochemical Properties and Bacterial Community Profiling of Optimal Mahewu (A Fermented Food Product) Prepared Using White and Yellow Maize with Different Inocula.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {20}, pages = {}, pmid = {37430920}, issn = {2304-8158}, support = {121826//National Research Foundation/ ; 2020 Doctoral Fellowship//FoodBev SETA/ ; GES 4.0//University of Johannesburg/ ; }, abstract = {Mahewu is a fermented food product from maize, commonly consumed in Southern Africa. This study investigated the effect of optimizing fermentation (time and temperature) and boiling time of white maize (WM) and yellow maize (YM) mahewu, with the use of the Box-Behnken-response surface methodology (RSM). Fermentation time and temperature as well as boiling time were optimized and pH, total titratable acidity (TTA) and total soluble solids (TSS) determined. Results obtained showed that the processing conditions significantly (p ≤ 0.05) influenced the physicochemical properties. pH values of the mahewu samples ranged between 3.48-5.28 and 3.50-4.20 for YM mahewu and WM mahewu samples, respectively. Reduction in pH values after fermentation coincided with an increase in TTA as well as changes in the TSS values. Using the numerical multi-response optimisation of three investigated responses the optimal fermentation conditions were observed to be 25 °C for 54 h and a boiling time of 19 min for white maize mahewu and 29 °C for 72 h and a boiling time of 13 min for yellow maize mahewu. Thereafter white and yellow maize mahewu were prepared with the optimized conditions using different inocula (sorghum malt flour, wheat flour, millet malt flour or maize malt flour) and the pH, TTA and TSS of the derived mahewu samples determined. Additionally, amplicon sequencing of the 16S rRNA gene was used to characterise the relative abundance of bacterial genera in optimized mahewu samples, malted grains as well as flour samples. Major bacterial genera observed in the mahewu samples included Paenibacillus, Stenotrophomonas, Weissella, Pseudomonas, Lactococcus, Enterococcus, Lactobacillus, Bacillus, Massilia, Clostridium sensu stricto 1, Streptococcus, Staphylococcus, Sanguibacter, Roseococcus, Leuconostoc, Cutibacterium, Brevibacterium, Blastococcus, Sphingomonas and Pediococcus, with variations noted for YM mahewu and WM mahewu. As a result, the variations in physicochemical properties are due to differences in maize type and modification in processing conditions. This study also discovered the existence of variety of bacterial that can be isolated for controlled fermentation of mahewu.}, } @article {pmid37430914, year = {2022}, author = {Tzora, A and Nelli, A and Kritikou, AS and Katsarou, D and Giannenas, I and Lagkouvardos, I and Thomaidis, NS and Skoufos, I}, title = {The "Crosstalk" between Microbiota and Metabolomic Profile of Kefalograviera Cheese after the Innovative Feeding Strategy of Dairy Sheep by Omega-3 Fatty Acids.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {20}, pages = {}, pmid = {37430914}, issn = {2304-8158}, support = {FoodOmicsGR_RI Comprehensive Characterization of Foods" (MIS 5029057)//Operational Programme Competitiveness, Entrepreneurship and Innovation (NSRF 2014-2020) and co-financed by Greece and the European Union (European Regional Development Fund)/ ; }, abstract = {The purpose of this study was to examine the effects of two different feeding systems, a control or a flaxseed and lupin diet (experimental), for a sheep flock, on the microbiota and metabolome of Kefalograviera cheese samples produced by their milk. In particular, the microbiota present in Kefalograviera cheese samples was analyzed using 16S rRNA gene sequencing, while ultra-high performance liquid chromatography coupled to quadrupole time-of-flight mass spectrometry (UHPLC-QTOF-MS) was applied to investigate the chemical profile of the cheeses, considering the different feeding systems applied. The metagenomic profile was found to be altered by the experimental feeding system and significantly correlated to specific cheese metabolites, with Streptococcaceae and Lactobacillaceae establishing positive and negative correlations with the discriminant metabolites. Overall, more than 120 features were annotated and identified with high confidence level across the samples while most of them belonged to specific chemical classes. Characteristic analytes detected in different concentrations in the experimental cheese samples including arabinose, dulcitol, hypoxanthine, itaconic acid, L-arginine, L-glutamine and succinic acid. Therefore, taken together, our results provide an extensive foodomics approach for Kefalograviera cheese samples from different feeding regimes, investigating the metabolomic and metagenomic biomarkers that could be used to foresee, improve, and control cheese ripening outcomes, demonstrating the quality of the experimental Kefalograviera cheese.}, } @article {pmid37430367, year = {2023}, author = {Zhong, J and Liu, Y and Luo, N and Wei, Q and Su, Q and Zou, J and Wu, X and Huang, X and Jiang, Y and Liang, L and Li, H and Lin, J}, title = {Metagenomic next-generation sequencing for rapid detection of pulmonary infection in patients with acquired immunodeficiency syndrome.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {22}, number = {1}, pages = {57}, pmid = {37430367}, issn = {1476-0711}, support = {20203052//the Science and Technology Planning Project of Nanning City/ ; RC20180103//the Youth Science and Technology Talents Cultivation Project of Nanning/ ; }, mesh = {Humans ; *Acquired Immunodeficiency Syndrome/complications ; High-Throughput Nucleotide Sequencing ; Azure Stains ; Hospitalization ; Hospitals ; *Pneumonia ; }, abstract = {BACKGROUND: Acquired immunodeficiency syndrome (AIDS) is associated with a high rate of pulmonary infections (bacteria, fungi, and viruses). To overcome the low sensitivity and long turnaround time of traditional laboratory-based diagnostic strategies, we adopted metagenomic next-generation sequencing (mNGS) technology to identify and classify pathogens.

RESULTS: This study enrolled 75 patients with AIDS and suspected pulmonary infections who were admitted to Nanning Fourth People's Hospital. Specimens were collected for traditional microbiological testing and mNGS-based diagnosis. The diagnostic yields of the two methods were compared to evaluate the diagnostic value (detection rate and turn around time) of mNGS for infections with unknown causative agent. Accordingly, 22 cases (29.3%) had a positive culture and 70 (93.3%) had positive valve mNGS results (P value < 0.0001, Chi-square test). Meanwhile, 15 patients with AIDS showed concordant results between the culture and mNGS, whereas only one 1 patient showed concordant results between Giemsa-stained smear screening and mNGS. In addition, mNGS identified multiple microbial infections (at least three pathogens) in almost 60.0% of patients with AIDS. More importantly, mNGS was able to detect a large variety of pathogens from patient tissue displaying potential infection and colonization, while culture results remained negative. There were 18 members of pathogens which were consistently detected in patients with and without AIDS.

CONCLUSIONS: In conclusion, mNGS analysis provides fast and precise pathogen detection and identification, contributing substantially to the accurate diagnosis, real-time monitoring, and treatment appropriateness of pulmonary infection in patients with AIDS.}, } @article {pmid37430211, year = {2023}, author = {Li, X and Li, Z and Ye, J and Ye, W}, title = {Diagnostic performance of metagenomic next-generation sequencing for Pneumocystis jirovecii pneumonia.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {455}, pmid = {37430211}, issn = {1471-2334}, mesh = {Humans ; Correlation of Data ; High-Throughput Nucleotide Sequencing ; Immunocompromised Host ; Knowledge ; *Pneumonia, Pneumocystis/diagnosis ; }, abstract = {OBJECTIVE: Pneumocystis jirovecii pneumonia (PJP) can be a life-threatening opportunistic infection. We aimed to evaluate the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) for PJP.

METHODS: A comprehensive electronic literature search of Web of Knowledge, PubMed, Cochrane Library, CNKI and Wanfang data was performed. Bivariate analysis was conducted to calculate the pooled sensitivity, specificity, diagnostic odds ratio (DOR), the area under the summary receiver operator characteristic (SROC) curve and the Q-point value (Q*).

RESULTS: The literature search resulted in 9 studies with a total of 1343 patients, including 418 cases diagnosed with PJP and 925 controls. The pooled sensitivity of mNGS for diagnosis of PJP was 0.974 [95% confidence interval (CI), 0.953-0.987]. The pooled specificity was 0.943 (95% CI, 0.926-0.957), the DOR was 431.58 (95% CI, 186.77-997.27), the area under the SROC curve was 0.987, and the Q* was 0.951. The I[2] test indicated no heterogeneity between studies. The Deek funnel test suggested no potential publication bias. Subgroup analyses showed that the area under the SROC curve of mNGS for diagnosis of PJP in immunocompromised and non-HIV patients was 0.9852 and 0.979, respectively.

CONCLUSIONS: Current evidence indicates that mNGS exhibits excellent accuracy for the diagnosis of PJP. The mNGS is a promising tool for assessment of PJP in both immunocompromised and non-HIV patients.}, } @article {pmid37429841, year = {2023}, author = {Tisza, MJ and Smith, DDN and Clark, AE and Youn, JH and , and Khil, PP and Dekker, JP}, title = {Roving methyltransferases generate a mosaic epigenetic landscape and influence evolution in Bacteroides fragilis group.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {4082}, pmid = {37429841}, issn = {2041-1723}, mesh = {Humans ; *Methyltransferases/genetics ; Bacteroides fragilis/genetics ; Epigenomics ; DNA Methylation/genetics ; *Bacteriophages/genetics ; Bacteroides ; Epigenesis, Genetic ; }, abstract = {Three types of DNA methyl modifications have been detected in bacterial genomes, and mechanistic studies have demonstrated roles for DNA methylation in physiological functions ranging from phage defense to transcriptional control of virulence and host-pathogen interactions. Despite the ubiquity of methyltransferases and the immense variety of possible methylation patterns, epigenomic diversity remains unexplored for most bacterial species. Members of the Bacteroides fragilis group (BFG) reside in the human gastrointestinal tract as key players in symbiotic communities but also can establish anaerobic infections that are increasingly multi-drug resistant. In this work, we utilize long-read sequencing technologies to perform pangenomic (n = 383) and panepigenomic (n = 268) analysis of clinical BFG isolates cultured from infections seen at the NIH Clinical Center over four decades. Our analysis reveals that single BFG species harbor hundreds of DNA methylation motifs, with most individual motif combinations occurring uniquely in single isolates, implying immense unsampled methylation diversity within BFG epigenomes. Mining of BFG genomes identified more than 6000 methyltransferase genes, approximately 1000 of which were associated with intact prophages. Network analysis revealed substantial gene flow among disparate phage genomes, implying a role for genetic exchange between BFG phages as one of the ultimate sources driving BFG epigenome diversity.}, } @article {pmid37429573, year = {2023}, author = {Wang, L and Hu, M and Wu, X and Ma, L and Yang, H}, title = {Case Report: Diagnosis and Treatment of Two Clinical Cases of Visceral Leishmaniasis-Related Hemophagocytic Lymphohistiocytosis.}, journal = {The American journal of tropical medicine and hygiene}, volume = {109}, number = {2}, pages = {296-300}, pmid = {37429573}, issn = {1476-1645}, mesh = {Humans ; *Lymphohistiocytosis, Hemophagocytic/complications/diagnosis/drug therapy ; *Leishmaniasis, Visceral/complications/diagnosis/drug therapy ; *Leishmania ; *Pancytopenia ; Bone Marrow ; }, abstract = {Visceral leishmaniasis-related hemophagocytic lymphohistiocytosis (VL-HLH) is a potentially life-threatening secondary hemophagocytic lymphocytic syndrome caused by protozoan parasites of the Leishmania species and transmitted by infected sandflies. Therefore, it is important to be highly vigilant of the infection, particularly the visceral subtype, to share information with the public health system, and to improve the early diagnosis rate so that appropriate treatment can be initiated promptly. We report two isolated cases of VL-HLH. The main clinical manifestations were fever, pancytopenia, splenomegaly, hypofibrinogenemia, and hyperferremia, which meet the HLH-2004 diagnostic criteria. In our experience, anti-HLH treatment was not very effective for either case. No Leishmania organism was found in the first bone marrow smear of either patient. The first patient was diagnosed after identification of Leishmania amastigotes via sternal bone marrow biopsy, rK39 immunochromatography test, and metagenomic next-generation sequencing. The other patient was diagnosed by rK39-rapid diagnostic test and polymerase chain reaction. However, because of the delayed diagnosis in both cases, their conditions continued to deteriorate and both patients eventually died of the disease. Leishmaniasis is a parasitic disease with regional specificity and a low incidence. The occurrence of secondary HLH has a great impact on prognosis. When encountering secondary HLH in clinical practice, leishmaniasis should remain on the list of differential causes. Because of a high mortality rate if diagnosed late, it is crucial to be vigilant of VL-HLH in practice so that early detection, diagnosis, and treatment of the disease can be achieved to reduce adverse patient outcomes.}, } @article {pmid37429473, year = {2023}, author = {Yue, Y and Zhang, H and Deng, P and Tan, M and Chen, C and Tang, B and Li, J and Chen, F and Zhao, Q and Li, L and Hao, R and Wang, H and Luo, Y and Tian, L and Xie, J and Chen, M and Yu, Z and Zhou, Z and Pi, H}, title = {Environmental cadmium exposure facilitates mammary tumorigenesis via reprogramming gut microbiota-mediated glutamine metabolism in MMTV-Erbb2 mice.}, journal = {The Science of the total environment}, volume = {897}, number = {}, pages = {165348}, doi = {10.1016/j.scitotenv.2023.165348}, pmid = {37429473}, issn = {1879-1026}, mesh = {Mice ; Animals ; Cadmium/toxicity ; Glutamine ; *Gastrointestinal Microbiome ; Ki-67 Antigen ; *Mammary Neoplasms, Experimental/chemically induced/metabolism/pathology ; Cell Transformation, Neoplastic/metabolism ; Mice, Transgenic ; Carcinogenesis/chemically induced ; Necrosis ; }, abstract = {Cadmium (Cd) is a heavy metal that has been widely reported to be linked to the onset and progression of breast cancer (BC). However, the mechanism of Cd-induced mammary tumorigenesis remains elusive. In our study, a transgenic mouse model that spontaneously develops tumors through overexpression of wild-type Erbb2 (MMTV-Erbb2) was constructed to investigate the effects of Cd exposure on BC tumorigenesis. The results showed that oral exposure to 3.6 mg/L Cd for 23 weeks dramatically accelerated tumor appearance and growth, increased Ki67 density and enhanced focal necrosis and neovascularization in the tumor tissue of MMTV-Erbb2 mice. Notably, Cd exposure enhanced glutamine (Gln) metabolism in tumor tissue, and 6-diazo-5-oxo-l-norleucine (DON), a Gln metabolism antagonist, inhibited Cd-induced breast carcinogenesis. Then our metagenomic sequencing and mass spectrometry-based metabolomics confirmed that Cd exposure disturbed gut microbiota homeostasis, especially Helicobacter and Campylobacter abundance remodeling, which altered the gut metabolic homeostasis of Gln. Moreover, intratumoral Gln metabolism profoundly increased under Cd-elevated gut permeability. Importantly, depletion of microbiota with an antibiotic cocktail (AbX) treatment led to a significant delay in the appearance of palpable tumors, inhibition of tumor growth, decrease in tumor weight, reduction in Ki67 expression and low-grade pathology in Cd-exposed MMTV-Erbb2 mice. Also, transplantation of Cd-modulated microbiota decreased tumor latency, accelerated tumor growth, increased tumor weight, upregulated Ki67 expression and exacerbated neovascularization as well as focal necrosis in MMTV-Erbb2 mice. In summary, Cd exposure induced gut microbiota dysbiosis, elevated gut permeability and increased intratumoral Gln metabolism, leading to the promotion of mammary tumorigenesis. This study provides novel insights into environmental Cd exposure-mediated carcinogenesis.}, } @article {pmid37428554, year = {2023}, author = {Qiu, S and Zeng, H and Yang, Z and Hung, WL and Wang, B and Yang, A}, title = {Dynamic metagenome-scale metabolic modeling of a yogurt bacterial community.}, journal = {Biotechnology and bioengineering}, volume = {120}, number = {8}, pages = {2186-2198}, doi = {10.1002/bit.28492}, pmid = {37428554}, issn = {1097-0290}, mesh = {Yogurt/microbiology ; Metagenome ; *Lactobacillus delbrueckii/genetics ; Fermentation ; *Lactobacillales ; }, abstract = {Genome-scale metabolic models and flux balance analysis (FBA) have been extensively used for modeling and designing bacterial fermentation. However, FBA-based metabolic models that accurately simulate the dynamics of coculture are still rare, especially for lactic acid bacteria used in yogurt fermentation. To investigate metabolic interactions in yogurt starter culture of Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus, this study built a dynamic metagenome-scale metabolic model which integrated constrained proteome allocation. The accuracy of the model was evaluated by comparing predicted bacterial growth, consumption of lactose and production of lactic acid with reference experimental data. The model was then used to predict the impact of different initial bacterial inoculation ratios on acidification. The dynamic simulation demonstrated the mutual dependence of S. thermophilus and L. d. bulgaricus during the yogurt fermentation process. As the first dynamic metabolic model of the yogurt bacterial community, it provided a foundation for the computer-aided process design and control of the production of fermented dairy products.}, } @article {pmid37428148, year = {2023}, author = {Serghiou, IR and Baker, D and Evans, R and Dalby, MJ and Kiu, R and Trampari, E and Phillips, S and Watt, R and Atkinson, T and Murphy, B and Hall, LJ and Webber, MA}, title = {An efficient method for high molecular weight bacterial DNA extraction suitable for shotgun metagenomics from skin swabs.}, journal = {Microbial genomics}, volume = {9}, number = {7}, pages = {}, pmid = {37428148}, issn = {2057-5858}, support = {BBS/E/F/000PR10349/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 100974/C/13/Z/WT_/Wellcome Trust/United Kingdom ; 220876/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T508974/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T014644/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adult ; Humans ; DNA, Bacterial/genetics ; *Metagenomics/methods ; Molecular Weight ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota/genetics ; DNA ; }, abstract = {The human skin microbiome represents a variety of complex microbial ecosystems that play a key role in host health. Molecular methods to study these communities have been developed but have been largely limited to low-throughput quantification and short amplicon-based sequencing, providing limited functional information about the communities present. Shotgun metagenomic sequencing has emerged as a preferred method for microbiome studies as it provides more comprehensive information about the species/strains present in a niche and the genes they encode. However, the relatively low bacterial biomass of skin, in comparison to other areas such as the gut microbiome, makes obtaining sufficient DNA for shotgun metagenomic sequencing challenging. Here we describe an optimised high-throughput method for extraction of high molecular weight DNA suitable for shotgun metagenomic sequencing. We validated the performance of the extraction method, and analysis pipeline on skin swabs collected from both adults and babies. The pipeline effectively characterised the bacterial skin microbiota with a cost and throughput suitable for larger longitudinal sets of samples. Application of this method will allow greater insights into community compositions and functional capabilities of the skin microbiome.}, } @article {pmid37428087, year = {2023}, author = {Bai, H and Liu, T and Wang, S and Gong, W and Shen, L and Zhang, S and Wang, Z}, title = {Identification of Gut Microbiome and Metabolites Associated with Acute Diarrhea in Cats.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0059023}, pmid = {37428087}, issn = {2165-0497}, mesh = {Cats ; Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Case-Control Studies ; Feces/microbiology ; Diarrhea/veterinary/microbiology ; Firmicutes/genetics ; }, abstract = {Changes in diet and environment can lead to acute diarrhea in companion animals, but the composition and interactions of the gut microbiome during acute diarrhea remain unclear. In this multicenter case-control study, we investigated the relationship between intestinal flora and acute diarrhea in two breeds of cats. Acutely diarrheic American Shorthair (MD, n = 12) and British Shorthair (BD, n = 12) and healthy American Shorthair (MH, n = 12) and British Shorthair (BH, n = 12) cats were recruited. Gut microbial 16S rRNA sequencing, metagenomic sequencing, and untargeted metabolomic analysis were performed. We observed significant differences in beta-diversity (Adonis, P < 0.05) across breeds and disease state cohorts. Profound differences in gut microbial structure and function were found between the two cat breeds. In comparison to healthy British Shorthair cats, Prevotella, Providencia, and Sutterella were enriched while Blautia, Peptoclostridium, and Tyzzerella were reduced in American Shorthair cats. In the case-control cohort, cats with acute diarrhea exhibited an increased abundance of Bacteroidota, Prevotella, and Prevotella copri and a decreased abundance of Bacilli, Erysipelotrichales, and Erysipelatoclostridiaceae (both MD and BD cats, P < 0.05). Metabolomic analysis identified significant changes in the BD intestine, affecting 45 metabolic pathways. Moreover, using a random forest classifier, we successfully predicted the occurrence of acute diarrhea with an area under the curve of 0.95. Our findings indicate a distinct gut microbiome profile that is associated with the presence of acute diarrhea in cats. However, further investigations using larger cohorts of cats with diverse conditions are required to validate and extend these findings. IMPORTANCE Acute diarrhea is common in cats, and our understanding of the gut microbiome variations across breeds and disease states remains unclear. We investigated the gut microbiome of two cat breeds (British Shorthair and American Shorthair) with acute diarrhea. Our study revealed significant effects of breeds and disease states on the structure and function of the gut microbiota in cats. These findings emphasize the need to consider breed-related factors in animal nutrition and research models. Additionally, we observed an altered gut metabolome in cats with acute diarrhea, closely linked to changes in bacterial genera. We identified a panel of microbial biomarkers with high diagnostic accuracy for feline acute diarrhea. These findings provide novel insights into the diagnosis, classification, and treatment of feline gastrointestinal diseases.}, } @article {pmid37427988, year = {2023}, author = {Zhang, P and Zhang, T and Chen, J and Zhang, J and He, Y}, title = {Novel Role of Hematite in Anaerobic Digestion: Manipulating Membrane-Bound Electron Transport Chain by the Construction of Biological Capacitors with Humic Acid.}, journal = {Environmental science & technology}, volume = {57}, number = {29}, pages = {10828-10837}, doi = {10.1021/acs.est.3c01867}, pmid = {37427988}, issn = {1520-5851}, mesh = {*Humic Substances ; Electron Transport ; Ferrosoferric Oxide ; Anaerobiosis ; *Hydrogenase ; Oxidation-Reduction ; Anthraquinones ; Methane ; }, abstract = {Humic acid (HA) has attracted much attention for its electron-competitive effect of quinone groups on anaerobic methanogenesis. This study analyzed the biological "capacitor" to determine how it might effectively reduce electron competition. As biological capacitor-producing additives, three semiconductive materials, including magnetite, hematite, and goethite, were selected. The results showed that hematite and magnetite could significantly alleviate the inhibited methanogenesis caused by the HA model compound anthraquinone-2,6-disulfonate (AQDS). The electrons flowing to methane in hematite-AQDS, magnetite-AQDS, control, sole-AQDS, and goethite-AQDS groups accounted for 81.24, 77.12, 75.42, 70.55, and 56.32% of the total produced electrons, respectively. Hematite addition significantly accelerated the methane production rate (18.97%) compared with sole-AQDS. Electrochemical investigation showed that AQDS might have its oxidation potential reduced by adsorbing on hematite, which results in an energy band bending for hematite and the formation of a biological capacitor. The biological capacitor's integrated electric field helps with the transfer of electrons from reduced AQDS to anaerobic consortia via bulk hematite. Metagenomic and metaproteomic sequencing analyses revealed that the ferredoxin and Mph-reducing hydrogenase in hematite addition increased by 7.16 and 21.91%, respectively, compared to sole-AQDS addition. Accordingly, this research suggested that AH2QDS may re-transfer electrons to methanogens via the biological capacitor and the membrane's Mph-reducing hydrogenase, thus lowering the HA electron competition.}, } @article {pmid37427782, year = {2023}, author = {Tang, X and Shang, J and Ji, Y and Sun, Y}, title = {PLASMe: a tool to identify PLASMid contigs from short-read assemblies using transformer.}, journal = {Nucleic acids research}, volume = {51}, number = {15}, pages = {e83}, pmid = {37427782}, issn = {1362-4962}, mesh = {*Genome, Bacterial ; *Software ; Plasmids/genetics ; Metagenome ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Plasmids are mobile genetic elements that carry important accessory genes. Cataloging plasmids is a fundamental step to elucidate their roles in promoting horizontal gene transfer between bacteria. Next generation sequencing (NGS) is the main source for discovering new plasmids today. However, NGS assembly programs tend to return contigs, making plasmid detection difficult. This problem is particularly grave for metagenomic assemblies, which contain short contigs of heterogeneous origins. Available tools for plasmid contig detection still suffer from some limitations. In particular, alignment-based tools tend to miss diverged plasmids while learning-based tools often have lower precision. In this work, we develop a plasmid detection tool PLASMe that capitalizes on the strength of alignment and learning-based methods. Closely related plasmids can be easily identified using the alignment component in PLASMe while diverged plasmids can be predicted using order-specific Transformer models. By encoding plasmid sequences as a language defined on the protein cluster-based token set, Transformer can learn the importance of proteins and their correlation through positionally token embedding and the attention mechanism. We compared PLASMe and other tools on detecting complete plasmids, plasmid contigs, and contigs assembled from CAMI2 simulated data. PLASMe achieved the highest F1-score. After validating PLASMe on data with known labels, we also tested it on real metagenomic and plasmidome data. The examination of some commonly used marker genes shows that PLASMe exhibits more reliable performance than other tools.}, } @article {pmid37426639, year = {2023}, author = {Gao, R and Yang, F and Yang, C and Zhang, Z and Liu, M and Xiang, C and Hu, H and Luo, X and Li, J and Liu, R}, title = {A case report and literature review of immune checkpoint inhibitor-associated pneumonia caused by penpulimab.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1114994}, pmid = {37426639}, issn = {1664-3224}, mesh = {Humans ; Immune Checkpoint Inhibitors/adverse effects ; *Carcinoma, Non-Small-Cell Lung ; *Pneumonia/diagnosis/drug therapy/etiology ; *Lung Neoplasms ; }, abstract = {OBJECTIVE: From the perspective of intensive care physicians, this paper reviews the diagnosis and treatment of CIP patients, analyzes and refines relevant literature on CIP. To summarize the characteristics of diagnosis and treatment of severe CIP provides the basis and reference for early identification, diagnosis and treatment.

METHODS: A case of severe CIP caused by piamprilizumab and ICI was reviewed and the literature was reviewed.

RESULTS: This was a patient with lung squamous cell carcinoma with lymphoma who had been treated with multiple chemoradiotherapy and immunotherapy with piamprizumab. The patient was admitted to the ICU with respiratory failure. The intensive care physician performs anti-infective, fluid management, hormonal anti-inflammatory, respiratory and nutritional support treatment, and relies on mNGS to exclude severe infection and CIP treatment, thus successfully saving the patient's life and improving discharge.

CONCLUSIONS: The incidence of CIP is very low, and its diagnosis should be combined with clinical manifestations and previous drug use. mNGS can provide certain value in the exclusion of severe infections, so as to provide basis and reference for the early identification, diagnosis and treatment of severe CIP.}, } @article {pmid37426511, year = {2022}, author = {Sharma, MK and Srivastav, VK and Joshi, CK and Kumar, M and Bhat, KM}, title = {Metagenomic analysis of oral microbiota among oral cancer patients and tobacco chewers in Rajasthan, India.}, journal = {Bioinformation}, volume = {18}, number = {9}, pages = {757-763}, pmid = {37426511}, issn = {0973-2063}, abstract = {Data on the microbial composition among tobacco chewers and oral cancer patients in Rajasthan, India is of interest. NGS analysis from tobacco chewers and oral cancer comprised the most abundant and core microbial taxa in the oral cavity. It shows that highly pathogenic phylum consisting of 6% Fusobacteria and 9% Firmicutes are observed in oral cancer samples; whereas, 0.6% Treponema, 34% Firmicutes, 0.02% Mollicutes, and 4% Fusobacteria are seen in tobacco chewers. Thus, data shows that the most abundant and core microbial taxa are found in the oral cavity of tobacco chewers and oral cancer patients in Rajasthan, India.}, } @article {pmid37426218, year = {2023}, author = {Li, Y and Qin, T and Liang, Z and Zheng, C}, title = {Oil Has a Higher Methanogenic Potential than Coal in an Oil-Bearing Coal Seam.}, journal = {ACS omega}, volume = {8}, number = {26}, pages = {23880-23888}, pmid = {37426218}, issn = {2470-1343}, abstract = {The presence of oil in coal seams from coal-oil symbiosis areas poses a serious threat to the safe and efficient mining of coal. However, the information about the application of microbial technology in oil-bearing coal seams was insufficient. In this study, the biological methanogenic potential of coal and oil samples in an oil-bearing coal seam was analyzed by anaerobic incubation experiments. The results showed that the biological methanogenic efficiency of the coal sample increased from 0.74 to 1.06 from day 20 to day 90, and the biological methanogenic potential of the oil sample was about twice as high as that of the coal sample after 40 days of incubation. The Shannon diversity and observed operational taxonomic unit (OTU) number of oil were lower than those in coal. The major genera in coal were Sedimentibacter, Lysinibacillus, Brevibacillus, etc., and the major genera in oil mainly included Enterobacter, Sporolactobacillus, and Bacillus. The methanogenic archaea in coal mainly belonged to the order Methanobacteriales, Methanocellales, Methanococcales, etc., and the methanogenic archaea in oil mainly belonged to the genera Methanobacterium, Methanobrevibacter, Methanoculleus, and Methanosarcina. In addition, metagenome analysis showed that functional genes belonging to processes such as methane metabolism, microbial metabolism in different environments, and benzoate degradation were in a higher abundance in the oil culture system, while genes belonging to sulfur metabolism, biotin metabolism, and glutathione metabolism were in a higher abundance in the coal culture system. The metabolites specific to coal samples mainly belonged to phenylpropanoids, polyketides, lipids, and lipid-like molecules; meanwhile, the metabolites specific to oil were mainly organic acids and their derivatives. In summary, this study has a reference value for the elimination of oil from coal in oil-bearing coal seams and can be used to separate oil from oil-bearing coal seams and reduce the hazard brought by oil for coal seam mining.}, } @article {pmid37426026, year = {2023}, author = {Eggers, S and Midya, V and Bixby, M and Gennings, C and Torres-Olascoaga, LA and Walker, RW and Wright, RO and Arora, M and Téllez-Rojo, MM}, title = {Prenatal lead exposure is negatively associated with the gut microbiome in childhood.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1193919}, pmid = {37426026}, issn = {1664-302X}, support = {R01 ES013744/ES/NIEHS NIH HHS/United States ; }, abstract = {BACKGROUND: Metal exposures are associated with gut microbiome (GM) composition and function, and exposures early in development may be particularly important. Considering the role of the GM in association with many adverse health outcomes, understanding the relationship between prenatal metal exposures and the GM is critically important. However, there is sparse knowledge of the association between prenatal metal exposure and GM later in childhood.

OBJECTIVES: This analysis aims to identify associations between prenatal lead (Pb) exposure and GM composition and function in children 9-11 years old.

METHODS: Data come from the Programming Research in Obesity, Growth, Environment and Social Stressors (PROGRESS) cohort based in Mexico City, Mexico. Prenatal metal concentrations were measured in maternal whole blood drawn during the second and third trimesters of pregnancy. Stool samples collected at 9-11 years old underwent metagenomic sequencing to assess the GM. This analysis uses multiple statistical modeling approaches, including linear regression, permutational analysis of variance, weighted quantile sum regression (WQS), and individual taxa regressions, to estimate the association between maternal blood Pb during pregnancy and multiple aspects of the child GM at 9-11 years old, adjusting for relevant confounders.

RESULTS: Of the 123 child participants in this pilot data analysis, 74 were male and 49 were female. Mean prenatal maternal blood Pb was 33.6 (SE = 2.1) ug/L and 34.9 (SE = 2.1) ug/L at second and third trimesters, respectively. Analysis suggests a consistent negative relationship between prenatal maternal blood Pb and the GM at age 9-11, including measures of alpha and beta diversity, microbiome mixture analysis, and individual taxa. The WQS analysis showed a negative association between prenatal Pb exposure and the gut microbiome, for both second and third trimester exposures (2Tβ = -0.17, 95%CI = [-0.46,0.11]; 3Tβ = -0.17, 95%CI = [-0.44,0.10]). Ruminococcus gnavus, Bifidobacterium longum, Alistipes indistinctus, Bacteroides caccae, and Bifidobacterium bifidum all had weights above the importance threshold from 80% or more of the WQS repeated holdouts in association with both second and third trimester Pb exposure.

DISCUSSION: Pilot data analysis suggests a negative association between prenatal Pb exposure and the gut microbiome later in childhood; however, additional investigation is needed.}, } @article {pmid37425997, year = {2023}, author = {Sun, CC and Zhao, WJ and Yue, WZ and Cheng, H and Sun, FL and Wang, YT and Wu, ML and Engel, A and Wang, YS}, title = {Polymeric carbohydrates utilization separates microbiomes into niches: insights into the diversity of microbial carbohydrate-active enzymes in the inner shelf of the Pearl River Estuary, China.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1180321}, pmid = {37425997}, issn = {1664-302X}, abstract = {Polymeric carbohydrates are abundant and their recycling by microbes is a key process of the ocean carbon cycle. A deeper analysis of carbohydrate-active enzymes (CAZymes) can offer a window into the mechanisms of microbial communities to degrade carbohydrates in the ocean. In this study, metagenomic genes encoding microbial CAZymes and sugar transporter systems were predicted to assess the microbial glycan niches and functional potentials of glycan utilization in the inner shelf of the Pearl River Estuary (PRE). The CAZymes gene compositions were significantly different between in free-living (0.2-3 μm, FL) and particle-associated (>3 μm, PA) bacteria of the water column and between water and surface sediments, reflecting glycan niche separation on size fraction and selective degradation in depth. Proteobacteria and Bacteroidota had the highest abundance and glycan niche width of CAZymes genes, respectively. At the genus level, Alteromonas (Gammaproteobacteria) exhibited the greatest abundance and glycan niche width of CAZymes genes and were marked by a high abundance of periplasmic transporter protein TonB and members of the major facilitator superfamily (MFS). The increasing contribution of genes encoding CAZymes and transporters for Alteromonas in bottom water contrasted to surface water and their metabolism are tightly related with particulate carbohydrates (pectin, alginate, starch, lignin-cellulose, chitin, and peptidoglycan) rather than on the utilization of ambient-water DOC. Candidatus Pelagibacter (Alphaproteobacteria) had a narrow glycan niche and was primarily preferred for nitrogen-containing carbohydrates, while their abundant sugar ABC (ATP binding cassette) transporter supported the scavenging mode for carbohydrate assimilation. Planctomycetota, Verrucomicrobiota, and Bacteroidota had similar potential glycan niches in the consumption of the main component of transparent exopolymer particles (sulfated fucose and rhamnose containing polysaccharide and sulfated-N-glycan), developing considerable niche overlap among these taxa. The most abundant CAZymes and transporter genes as well as the widest glycan niche in the abundant bacterial taxa implied their potential key roles on the organic carbon utilization, and the high degree of glycan niches separation and polysaccharide composition importantly influenced bacterial communities in the coastal waters of PRE. These findings expand the current understanding of the organic carbon biotransformation, underlying the size-fractionated glycan niche separation near the estuarine system.}, } @article {pmid37425996, year = {2023}, author = {Lu, H and Yuan, J and Wu, Z and Wang, L and Wu, S and Chen, Q and Zhang, Z and Chen, Z and Zou, X and Hu, Q and Feng, T and Lu, J and Ji, L and Qiu, S and Xu, S and Jiang, M and Li, Y and Peng, B and Bai, Q and Cai, R and Geng, Y and Shi, X}, title = {Distribution of drug-resistant genes in alveolar lavage fluid from patients with psittacosis and traceability analysis of causative organisms.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1182604}, pmid = {37425996}, issn = {1664-302X}, abstract = {BACKGROUND: Chlamydia psittaci is a small bacterium often found in birds, including poultry, and domesticated mammals, which causes psittacosis (or parrot fever) in humans. Different strains of C. psittaci respond variably to antibiotics, suggesting a possible risk of antibiotic resistance. In general, different genotypes of C. psittaci have relatively stable hosts and different pathogenicity.

METHODS: Macrogenomic sequencing was performed using nucleic acids extracted from psittacosis patients' alveolar lavage fluid samples and analyzed for genetic variability and antibiotic resistance genes. Nucleic acid amplification sequences specific to the core coding region of the C. psittaci ompA gene were used, and a phylogenetic tree was constructed with C. psittaci genotypic sequences from other sources, including Chinese published sources. The C. psittaci found in each patient were genotyped by comparing ompA gene sequences. In addition, to better illustrate the relationship between genotype and host of C. psittaci, 60 bird fecal samples were collected from bird-selling stores for screening and C. psittaci typing.

RESULTS: Macrogenomic sequence alignment revealed the presence of resistance genes in varying abundance in samples from all three patients, including C. psittaci resistance gene sequences from two patients that matched those previously published on NCBI. Based on ompA genotyping, two patients were infected with C. psittaci genotype A and one patient was infected with genotype B. All five C. psittaci-positive samples obtained from bird-selling stores were genotype A. Both genotypes are reported to be infectious to humans. The host origin of the samples and the previously reported main sources of each genotype suggested that all but one of the C. psittaci genotype A in this study were derived from parrots, while genotype B was probably derived from chickens.

CONCLUSION: The presence of bacterial resistance genes in psittacosis patients may affect the efficacy of clinical antibiotic therapy. Focusing on the developmental progression of bacterial resistance genes and differences in the therapeutic efficacy may facilitate effective treatment of clinical bacterial infections. Pathogenicity genotypes (e.g., genotype A and genotype B) are not limited to one animal host, suggesting that monitoring the development and changes of C. psittaci may help prevent transmission to humans.}, } @article {pmid37425956, year = {2023}, author = {Montgomery, TL and Wang, Q and Mirza, A and Dwyer, D and Wu, Q and Dowling, CA and Martens, JW and Yang, J and Krementsov, DN and Mao-Draayer, Y}, title = {Identification of commensal gut microbiota signatures as predictors of clinical severity and disease progression in multiple sclerosis.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.06.26.23291875}, pmid = {37425956}, abstract = {BACKGROUND: Multiple sclerosis (MS) is a chronic autoimmune disease of the central nervous system and a leading cause of neurological disability in young adults. Clinical presentation and disease course are highly heterogeneous. Typically, disease progression occurs over time and is characterized by the gradual accumulation of disability. The risk of developing MS is driven by complex interactions between genetic and environmental factors, including the gut microbiome. How the commensal gut microbiota impacts disease severity and progression over time remains unknown.

METHODS: In a longitudinal study, disability status and associated clinical features in 60 MS patients were tracked over 4.2 ± 0.97 years, and the baseline fecal gut microbiome was characterized via 16S amplicon sequencing. Progressor status, defined as patients with an increase in Expanded Disability Status Scale (EDSS), were correlated with features of the gut microbiome to determine candidate microbiota associated with risk of MS disease progression.

RESULTS: We found no overt differences in microbial community diversity and overall structure between MS patients exhibiting disease progression and non-progressors. However, a total of 45 bacterial species were associated with worsening disease, including a marked depletion in Akkermansia , Lachnospiraceae, and Oscillospiraceae , with an expansion of Alloprevotella , Prevotella-9 , and Rhodospirillales . Analysis of the metabolic potential of the inferred metagenome from taxa associated with progression revealed a significant enrichment in oxidative stress-inducing aerobic respiration at the expense of microbial vitamin K 2 production (linked to Akkermansia), and a depletion in SCFA metabolism (linked to Lachnospiraceae and Oscillospiraceae). Further, statistical modeling demonstrated that microbiota composition and clinical features were sufficient to robustly predict disease progression. Additionally, we found that constipation, a frequent gastrointestinal comorbidity among MS patients, exhibited a divergent microbial signature compared with progressor status.

CONCLUSIONS: These results demonstrate the utility of the gut microbiome for predicting disease progression in MS. Further, analysis of the inferred metagenome revealed that oxidative stress, vitamin K 2 and SCFAs are associated with progression.}, } @article {pmid37425953, year = {2023}, author = {Fromm, A and Hevroni, G and Vincent, F and Schatz, D and Martinez-Gutierrez, CA and Aylward, FO and Vardi, A}, title = {Homing in on the rare virosphere reveals the native host of giant viruses.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37425953}, support = {R35 GM147290/GM/NIGMS NIH HHS/United States ; }, abstract = {Giant viruses (phylum Nucleocytoviricota) are globally distributed in aquatic ecosystems[1,2]. They play major roles as evolutionary drivers of eukaryotic plankton[3] and regulators of global biogeochemical cycles[4]. Recent metagenomic studies have significantly expanded the known diversity of marine giant viruses[1,5-7], but we still lack fundamental knowledge about their native hosts, thereby hindering our understanding of their lifecycle and ecological importance. Here, we aim to discover the native hosts of giant viruses using a novel, sensitive single-cell metatranscriptomic approach. By applying this approach to natural plankton communities, we unraveled an active viral infection of several giant viruses, from multiple lineages, and identified their native hosts. We identify a rare lineage of giant virus (Imitervirales-07) infecting a minute population of protists (class Katablepharidaceae) and revealed the prevalence of highly expressed viral-encoded cell-fate regulation genes in infected cells. Further examination of this host-virus dynamics in a temporal resolution suggested this giant virus controls its host population demise. Our results demonstrate how single-cell metatranscriptomics is a sensitive approach for pairing viruses with their authentic hosts and studying their ecological significance in a culture-independent manner in the marine environment.}, } @article {pmid37425938, year = {2023}, author = {Yue, Y and Read, TD and Fedirko, V and Satten, GA and Hu, YJ}, title = {Integrative analysis of microbial 16S gene and shotgun metagenomic sequencing data improves statistical efficiency.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.06.27.546795}, pmid = {37425938}, abstract = {The most widely used technologies for profiling microbial communities are 16S marker-gene sequencing and shotgun metagenomic sequencing. Interestingly, many microbiome studies have performed both sequencing experiments on the same cohort of samples. The two sequencing datasets often reveal consistent patterns of microbial signatures, highlighting the potential for an integrative analysis to improve power of testing these signatures. However, differential experimental biases, partially overlapping samples, and differential library sizes pose tremendous challenges when combining the two datasets. Currently, researchers either discard one dataset entirely or use different datasets for different objectives. In this article, we introduce the first method of this kind, named Com-2seq, that combines the two sequencing datasets for the objective of testing differential abundance at the genus and community levels while overcoming these difficulties. We demonstrate that Com-2seq substantially improves statistical efficiency over analysis of either dataset alone and works better than two ad hoc approaches.}, } @article {pmid37425079, year = {2023}, author = {Deng, B and Hua, J and Zhou, Y and Zhan, D and Zhu, L and Zhan, Y and Fang, Y and Ji, Y and Li, L}, title = {Legionella pneumonia complicated with rhabdomyolysis and acute kidney injury diagnosed by metagenomic next-generation sequencing: a case report.}, journal = {World journal of emergency medicine}, volume = {14}, number = {4}, pages = {322-324}, pmid = {37425079}, issn = {1920-8642}, } @article {pmid37424777, year = {2023}, author = {Gao, Z and Yu, L and Cao, L and Yang, M and Li, Y and Lan, Y and Tang, R and Huang, Y and Luan, G and Liu, Y and Yu, H and Jian, L and Zha, Y and Fan, Z and Bai, Y and Luo, M and He, M and Deng, S}, title = {Analysis of coexisting pathogens in nasopharyngeal swabs from COVID-19.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1140548}, pmid = {37424777}, issn = {2235-2988}, mesh = {Humans ; *COVID-19 ; SARS-CoV-2/genetics ; *Coinfection/microbiology ; *Superinfection ; *Viruses/genetics ; Bacteria/genetics ; Streptococcus pneumoniae ; Klebsiella pneumoniae ; Nasopharynx/microbiology ; }, abstract = {BACKGROUND: The impact of COVID-19 on the world is still ongoing, and it is currently under regular management. Although most infected people have flu-like symptoms and can cure themselves, coexisting pathogens in COVID-19 patients should not be taken lightly. The present study sought to investigate the coexisting pathogens in SARS-CoV-2 infected patients and identify the variety and abundance of dangerous microbes to guide treatment strategies with a better understanding of the untested factors.

METHODS: We extracted total DNA and RNA in COVID-19 patient specimens from nasopharyngeal swabs to construct a metagenomic library and utilize Next Generation Sequencing (NGS) to discover chief bacteria, fungi, and viruses in the body of patients. High-throughput sequencing data from Illumina Hiseq 4000 were analyzed using Krona taxonomic methodology for species diversity.

RESULTS: We studied 56 samples to detect SARS-CoV-2 and other pathogens and analyzed the species diversity and community composition of these samples after sequencing. Our results showed some threatening pathogens such as Mycoplasma pneumoniae, Klebsiella pneumoniae, Streptococcus pneumoniae, and some previously reported pathogens. SARS-CoV-2 combined with bacterial infection is more common. The results of heat map analysis showed that the abundance of bacteria was mostly more than 1000 and that of viruses was generally less than 500. The pathogens most likely to cause SARS-CoV-2 coinfection or superinfection include Streptococcus pneumoniae, Haemophilus influenzae, Staphylococcus aureus, Klebsiella pneumoniae, and Human gammaherpesvirus 4.

CONCLUSIONS: The current coinfection and superinfection status is not optimistic. Bacteria are the major threat group that increases the risk of complications and death in COVID-19 patients and attention should be paid to the use and control of antibiotics. Our study investigated the main types of respiratory pathogens prone to coexisting or superinfection in COVID-19 patients, which is valuable for identifying and treating SARS-CoV-2.}, } @article {pmid37424707, year = {2023}, author = {Enagbonma, BJ and Babalola, OO}, title = {Metagenomics Reveals the Microbiome Multifunctionalities of Environmental Importance From Termite Mound Soils.}, journal = {Bioinformatics and biology insights}, volume = {17}, number = {}, pages = {11779322231184025}, pmid = {37424707}, issn = {1177-9322}, abstract = {The ecological deterioration caused by the continuous and excessive use of synthetic inputs in agriculture has prompted the search for environmentally favorable resources for crop production. Many have advocated for the use of soils from termite mounds to improve soil and plant health; therefore, the purpose of this study was to characterize the microbiome multifunctionalities that are important for plant health and growth in termite mound soil. The metagenomics of soil from termite mounds revealed taxonomic groups with functional potentials associated with promoting the growth and health of plants in nutrient-poor, virtually dry environments. Analysis of microorganisms revealed that Proteobacteria dominated the soil of termite colonies, while Actinobacteria ranked second. The predominance of Proteobacteria and Actinobacteria, the well-known antibiotic-producing populations, indicates that the termite mound soil microbiome possesses metabolic resistance to biotic stresses. Functions recognized for diverse proteins and genes unveiled that a multi-functional microbiome carry out numerous metabolic functions including virulence, disease, defense, aromatic compound and iron metabolism, secondary metabolite synthesis, and stress response. The abundance of genes in termite mound soils associated with these prominent functions could unquestionably validate the enhancement of plants in abiotic and biotically stressed environments. This study reveals opportunities to revisit the multifunctionalities of termite mound soils in order to establish a connection between taxonomic diversity, targeted functions, and genes that could improve plant yield and health in unfavorable soil conditions.}, } @article {pmid37424544, year = {2023}, author = {Gilroy, R and Adam, ME and Kumar, B and Pallen, MJ}, title = {An initial genomic blueprint of the healthy human oesophageal microbiome.}, journal = {Access microbiology}, volume = {5}, number = {6}, pages = {}, pmid = {37424544}, issn = {2516-8290}, abstract = {BACKGROUND: The oesophageal microbiome is thought to contribute to the pathogenesis of oesophageal cancer. However, investigations using culture and molecular barcodes have provided only a low-resolution view of this important microbial community. We therefore explored the potential of culturomics and metagenomic binning to generate a catalogue of reference genomes from the healthy human oesophageal microbiome, alongside a comparison set from saliva.

RESULTS: Twenty-two distinct colonial morphotypes from healthy oesophageal samples were genome-sequenced. These fell into twelve species clusters, eleven of which represented previously defined species. Two isolates belonged to a novel species, which we have named Rothia gullae. We performed metagenomic binning of reads generated from UK samples from this study alongside reads generated from Australian samples in a recent study. Metagenomic binning generated 136 medium or high-quality metagenome-assembled genomes (MAGs). MAGs were assigned to 56 species clusters, eight representing novel Candidatus species, which we have named Ca. Granulicatella gullae, Ca. Streptococcus gullae, Ca. Nanosynbacter quadramensis, Ca. Nanosynbacter gullae, Ca. Nanosynbacter colneyensis, Ca. Nanosynbacter norwichensis, Ca. Nanosynococcus oralis and Ca. Haemophilus gullae. Five of these novel species belong to the recently described phylum Patescibacteria . Although members of the Patescibacteria are known to inhabit the oral cavity, this is the first report of their presence in the oesophagus. Eighteen of the metagenomic species were, until recently, identified only by hard-to-remember alphanumeric placeholder designations. Here we illustrate the utility of a set of recently published arbitrary Latinate species names in providing user-friendly taxonomic labels for microbiome analyses.Our non-redundant species catalogue contained 63 species derived from cultured isolates or MAGs. Mapping revealed that these species account for around half of the sequences in the oesophageal and saliva metagenomes. Although no species was present in all oesophageal samples, 60 species occurred in at least one oesophageal metagenome from either study, with 50 identified in both cohorts.

CONCLUSIONS: Recovery of genomes and discovery of new species represents an important step forward in our understanding of the oesophageal microbiome. The genes and genomes that we have released into the public domain will provide a base line for future comparative, mechanistic and intervention studies.}, } @article {pmid37424042, year = {2023}, author = {Wang, B and Xu, J and Wang, Y and Stirling, E and Zhao, K and Lu, C and Tan, X and Kong, D and Yan, Q and He, Z and Ruan, Y and Ma, B}, title = {Tackling Soil ARG-Carrying Pathogens with Global-Scale Metagenomics.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {10}, number = {26}, pages = {e2301980}, pmid = {37424042}, issn = {2198-3844}, support = {42090060//National Natural Science Foundation of China/ ; 42277283//National Natural Science Foundation of China/ ; 41991334//National Natural Science Foundation of China/ ; 2023C02004//Key R&D Program of Zhejjiang Province/ ; 2023C02015//Key R&D Program of Zhejjiang Province/ ; }, mesh = {*Soil ; *Metagenomics ; Ecosystem ; Soil Microbiology ; Anti-Bacterial Agents ; }, abstract = {Antibiotic overuse and the subsequent environmental contamination of residual antibiotics poses a public health crisis via an acceleration in the spread of antibiotic resistance genes (ARGs) through horizontal gene transfer. Although the occurrence, distribution, and driving factors of ARGs in soils have been widely investigated, little is known about the antibiotic resistance of soilborne pathogens at a global scale. To explore this gap, contigs from 1643 globally sourced metagnomes are assembled, yielding 407 ARG-carrying pathogens (APs) with at least one ARG; APs are detected in 1443 samples (sample detection rate of 87.8%). The richness of APs is greater in agricultural soils (with a median of 20) than in non-agricultural ecosystems. Agricultural soils possess a high prevalence of clinical APs affiliated with Escherichia, Enterobacter, Streptococcus, and Enterococcus. The APs detected in agricultural soils tend to coexist with multidrug resistance genes and bacA. A global map of soil AP richness is generated, where anthropogenic and climatic factors explained AP hot spots in East Asia, South Asia, and the eastern United States. The results herein advance this understanding of the global distribution of soil APs and determine regions prioritized to control soilborne APs worldwide.}, } @article {pmid37423496, year = {2023}, author = {Rasool, A and Farooq, S and Kumar, S and Kashoo, ZA and Dar, PA and Bhat, MA and Qureshi, S and Hussain, I and Shah, RA and Taku, A and Khan, I and Hassan, MN}, title = {Evidence of novel Treponema phylotypes implicated in contagious ovine digital dermatitis and association of treponemes with major lameness causing foot pathogens.}, journal = {Microbial pathogenesis}, volume = {182}, number = {}, pages = {106214}, doi = {10.1016/j.micpath.2023.106214}, pmid = {37423496}, issn = {1096-1208}, mesh = {Sheep ; Animals ; Cattle ; *Digital Dermatitis/epidemiology/microbiology ; Lameness, Animal ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Treponema/genetics ; Sheep, Domestic/genetics ; *Sheep Diseases/microbiology ; *Cattle Diseases/microbiology ; }, abstract = {In this study 269 swabs collected from 254 ovine foot lesions and 15 apparently healthy ovine feet were screened by PCR for the presence of major lameness causing foot pathogens viz. Treponema species, D. nodosus, F. necrophorum and T. pyogenes with the presumption that ovine foot lesion positive for Treponema species alone or in association with other three pathogens were categorized as contagious ovine digital dermatitis (CODD). While samples positive for D. nodosus alone or its combination with F. necrophorum and T. pyogenes were considered as footrot (FR) and samples in which F. necrophorum or T. pyogenes was found either alone or in combination were considered as interdigital dermatitis (ID). The overall occurrence of Treponema sp. in ovine foot lesions was 48.0%, and ranged from 33 to 58%. In Treponema positive samples D. nodosus, F. necrophorum and T. pyogenes were present in 34 (27.4%), 66 (54.4%) and 84 (68.5%) in contrast to Treponema negative samples in which these were present in 15 (11.1%), 20 (14.12%) and 17 (12.6%) samples, respectively. The data signifies that Treponema sp. are significantly associated with these foot pathogens and their different combinations with Treponema sp. influence the severity of CODD lesion. The identification of Treponema phylotypes was done by sequencing the 16S rRNA gene fragment of ten representative samples. Out of ten sequences, four (Trep-2, Trep-4, Trep-7 and Trep-10) were identical to Treponema sp. phylotype 1 (PT1) that belongs to phylogroup T. refringens-like, one sequence (Trep-1) was genetically close (90% sequence homology) to Treponema brennaborense while five sequences (Trep-3, Trep-5, Trep-6, Trep-8 and Trep-9) matched with uncultured bacterium clones of treponemes forming separate monophyletic group in phylogenetic tree and could represent new digital dermatitis phylogroup presently containing five ovine specific phylotypes. This is the first report on the presence of Treponema phylotypes other than three digital dermatitis (DD) Treponema phylogroups viz. T. phagedenis-like, T. medium/T. vincentii-like, and T. pedis-like that are frequently detected in CODD lesions. Metagenomic analysis of two representative samples revealed the abundance of genus Treponema in CODD lesion while this genus was absent in swab collected from clinically healthy foot suggesting that it might play primary role in producing CODD. These findings may further aid in understanding the etiopathogenesis of CODD and could help to develop appropriate treatment and mitigation strategies to combat the disease.}, } @article {pmid37423191, year = {2023}, author = {Wu, SL and Wei, W and Ngo, HH and Guo, W and Wang, C and Wang, Y and Ni, BJ}, title = {In-situ production of lactate driving the biotransformation of waste activated sludge to medium-chain fatty acid.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118524}, doi = {10.1016/j.jenvman.2023.118524}, pmid = {37423191}, issn = {1095-8630}, mesh = {*Sewage ; *Caproates ; Lactic Acid ; Fatty Acids ; Fermentation ; Biotransformation ; }, abstract = {Medium-chain fatty acids (MCFAs) have drawn great attention due to their high energy density and superior hydrophobicity. Waste activated sludge (WAS) has been documented as a renewable feedstock for MCFAs production via anaerobic fermentation. However, MCFAs production from WAS depends on exogenous addition of electron donor (ED, e.g., lactate) for chain elongation (CE) bioprocess, which results in increased economic cost and limited practical application. In this study, a novel biotechnology was proposed to produce MCFAs from WAS with in-situ self-formed lactate by inoculating Yoghurt starter powder containing with Lactobacillales cultures. The batch experimental results revealed that the lactate was in-situ generated from WAS and the maximum production of MCFAs increased from 1.17 to 3.99 g COD/L with the increased addition of Lactobacillales cultures from 6✕10[7] to 2.3✕10[8] CFU/mL WAS. In continuous long-term test over 97 days, average MCFA production reached up to 3.94 g COD/L with a caproate yield of 82.74% at sludge retention time (SRT) 12 days, and the average MCFA production increased to 5.87 g COD/L with 69.28% caproate and 25.18% caprylate at SRT 15 days. A comprehensive analysis of the metagenome and metatranscriptome demonstrated that the genus of Lactobacillus and Streptococcus were capable of producing lactate from WAS and upgrading to MCFAs. Moreover, another genus, i.e., Candidatus Promineofilum, was firstly revealed that it might be responsible for lactate and MCFAs production. Further investigation of related microbial pathways and enzyme expression suggested that D-lactate dehydrogenase and pyruvate ferredoxin oxidoreductase contributed to lactate and acetyl-CoA production, which were the crucial steps for MCFAs generation and were most actively expressed. This study provides a conceptual framework of MCFAs from WAS with endogenous ED, potentially enhancing the energy recovery from WAS treatment.}, } @article {pmid37422855, year = {2023}, author = {Chen, WY and Wu, JH and Wang, BN}, title = {Intermittent Oxygen Supply Facilitates Codegradation of Trichloroethene and Toluene by Anaerobic Consortia.}, journal = {Environmental science & technology}, volume = {57}, number = {28}, pages = {10252-10262}, doi = {10.1021/acs.est.3c02481}, pmid = {37422855}, issn = {1520-5851}, mesh = {*Chloroflexi/genetics/metabolism ; *Trichloroethylene/metabolism ; Anaerobiosis ; Biodegradation, Environmental ; *Environmental Pollutants ; Oxygen ; }, abstract = {Biodegradation is commonly employed for remediating trichloroethene- or toluene-contaminated sites. However, remediation methods using either anaerobic or aerobic degradation are inefficient for dual pollutants. We developed an anaerobic sequencing batch reactor system with intermittent oxygen supply for the codegradation of trichloroethylene and toluene. Our results showed that oxygen inhibited anaerobic dechlorination of trichloroethene, but dechlorination rates remained comparable to that at dissolved oxygen levels of 0.2 mg/L. Intermittent oxygenation engendered reactor redox fluctuations (-146 to -475 mV) and facilitated rapid codegradation of targeting dual pollutants, with trichloroethene degradation constituting only 27.5% of the noninhibited dechlorination. Amplicon sequencing analysis revealed the predominance of Dehalogenimonas (16.0% ± 3.5%) over Dehalococcoides (0.3% ± 0.2%), with ten times higher transcriptomic activity in Dehalogenimonas. Shotgun metagenomics revealed numerous genes related to reductive dehalogenases and oxidative stress resistance in Dehalogenimonas and Dehalococcoides, as well as the enrichment of diversified facultative populations with functional genes related to trichloroethylene cometabolism and aerobic and anaerobic toluene degradation. These findings suggested that the codegradation of trichloroethylene and toluene may involve multiple biodegradation mechanisms. Overall results of this study demonstrate the effectiveness of intermittent micro-oxygenation in aiding trichloroethene-toluene degradation, suggesting the potential for the bioremediation of sites with similar organic pollutants.}, } @article {pmid37422700, year = {2023}, author = {Chaudhary, PP and Myles, IA and Zeldin, J and Dabdoub, S and Deopujari, V and Baveja, R and Baker, R and Bengtson, S and Sutton, A and Levy, S and Hourigan, SK}, title = {Shotgun metagenomic sequencing on skin microbiome indicates dysbiosis exists prior to the onset of atopic dermatitis.}, journal = {Allergy}, volume = {78}, number = {10}, pages = {2724-2731}, pmid = {37422700}, issn = {1398-9995}, support = {ZIA AI001043/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Child ; Infant, Newborn ; Humans ; *Dermatitis, Atopic/diagnosis/microbiology ; Dysbiosis ; Reproducibility of Results ; Skin/microbiology ; *Microbiota ; }, abstract = {BACKGROUND: While the microbiome is increasingly seen as a targetable contributor to atopic dermatitis (AD), questions remain as to whether the dysbiosis is secondary to diseased skin or if it predates symptom onset. Previous work has evaluated how the skin microbiome changes with age and established the influence of factors like delivery mode and breastfeeding on global microbiome diversity. However, these studies were unable to identify taxa which predict subsequent AD.

METHODS: Skin swab samples were collected from the first week of life for 72 children in the neonatal intensive care unit (NICU) at a single site hospital. Participants were followed for 3 years to determine their health status. We applied shotgun metagenomic sequencing to assess the microbiome differences between 31 children who went on to develop AD and 41 controls.

RESULTS: We identified that subsequent development of AD was associated with differential abundance of several bacterial and fungal taxa as well as several metabolic pathways, each of which have been previously associated with active AD.

CONCLUSIONS: Our work provides evidence of reproducibility for the previously reported dysbiotic signatures predating AD onset while also expanding prior findings through the first use of metagenomic assessment prior to AD onset. While extrapolation of our findings beyond the pre-term, NICU cohort is limited, our findings add to the evidence that the dysbiosis associated with AD pre-dates disease onset rather than reflect a secondary consequence of skin inflammation.}, } @article {pmid37422598, year = {2023}, author = {Priest, T and von Appen, WJ and Oldenburg, E and Popa, O and Torres-Valdés, S and Bienhold, C and Metfies, K and Boulton, W and Mock, T and Fuchs, BM and Amann, R and Boetius, A and Wietz, M}, title = {Atlantic water influx and sea-ice cover drive taxonomic and functional shifts in Arctic marine bacterial communities.}, journal = {The ISME journal}, volume = {17}, number = {10}, pages = {1612-1625}, pmid = {37422598}, issn = {1751-7370}, support = {294757/ERC_/European Research Council/International ; }, mesh = {*Ecosystem ; *Water ; Ice Cover/microbiology ; Food Chain ; Arctic Regions ; Bacteria/genetics ; }, abstract = {The Arctic Ocean is experiencing unprecedented changes because of climate warming, necessitating detailed analyses on the ecology and dynamics of biological communities to understand current and future ecosystem shifts. Here, we generated a four-year, high-resolution amplicon dataset along with one annual cycle of PacBio HiFi read metagenomes from the East Greenland Current (EGC), and combined this with datasets spanning different spatiotemporal scales (Tara Arctic and MOSAiC) to assess the impact of Atlantic water influx and sea-ice cover on bacterial communities in the Arctic Ocean. Densely ice-covered polar waters harboured a temporally stable, resident microbiome. Atlantic water influx and reduced sea-ice cover resulted in the dominance of seasonally fluctuating populations, resembling a process of "replacement" through advection, mixing and environmental sorting. We identified bacterial signature populations of distinct environmental regimes, including polar night and high-ice cover, and assessed their ecological roles. Dynamics of signature populations were consistent across the wider Arctic; e.g. those associated with dense ice cover and winter in the EGC were abundant in the central Arctic Ocean in winter. Population- and community-level analyses revealed metabolic distinctions between bacteria affiliated with Arctic and Atlantic conditions; the former with increased potential to use bacterial- and terrestrial-derived substrates or inorganic compounds. Our evidence on bacterial dynamics over spatiotemporal scales provides novel insights into Arctic ecology and indicates a progressing Biological Atlantification of the warming Arctic Ocean, with consequences for food webs and biogeochemical cycles.}, } @article {pmid37422584, year = {2023}, author = {Jespersen, ML and Munk, P and Johansen, J and Kaas, RS and Webel, H and Vigre, H and Nielsen, HB and Rasmussen, S and Aarestrup, FM}, title = {Global within-species phylogenetics of sewage microbes suggest that local adaptation shapes geographical bacterial clustering.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {700}, pmid = {37422584}, issn = {2399-3642}, mesh = {Phylogeny ; *Sewage/microbiology ; *Bacteria/genetics ; Cluster Analysis ; Geography ; }, abstract = {Most investigations of geographical within-species differences are limited to focusing on a single species. Here, we investigate global differences for multiple bacterial species using a dataset of 757 metagenomics sewage samples from 101 countries worldwide. The within-species variations were determined by performing genome reconstructions, and the analyses were expanded by gene focused approaches. Applying these methods, we recovered 3353 near complete (NC) metagenome assembled genomes (MAGs) encompassing 1439 different MAG species and found that within-species genomic variation was in 36% of the investigated species (12/33) coherent with regional separation. Additionally, we found that variation of organelle genes correlated less with geography compared to metabolic and membrane genes, suggesting that the global differences of these species are caused by regional environmental selection rather than dissemination limitations. From the combination of the large and globally distributed dataset and in-depth analysis, we present a wide investigation of global within-species phylogeny of sewage bacteria. The global differences found here emphasize the need for worldwide data sets when making global conclusions.}, } @article {pmid37422553, year = {2023}, author = {Ruvindy, R and Barua, A and Bolch, CJS and Sarowar, C and Savela, H and Murray, SA}, title = {Genomic copy number variability at the genus, species and population levels impacts in situ ecological analyses of dinoflagellates and harmful algal blooms.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {70}, pmid = {37422553}, issn = {2730-6151}, support = {FT12//Department of Education and Training | Australian Research Council (ARC)/ ; HDR Scholarship//University of Technology Sydney (University of Technology, Sydney)/ ; }, abstract = {The application of meta-barcoding, qPCR, and metagenomics to aquatic eukaryotic microbial communities requires knowledge of genomic copy number variability (CNV). CNV may be particularly relevant to functional genes, impacting dosage and expression, yet little is known of the scale and role of CNV in microbial eukaryotes. Here, we quantify CNV of rRNA and a gene involved in Paralytic Shellfish Toxin (PST) synthesis (sxtA4), in 51 strains of 4 Alexandrium (Dinophyceae) species. Genomes varied up to threefold within species and ~7-fold amongst species, with the largest (A. pacificum, 130 ± 1.3 pg cell[-1] /~127 Gbp) in the largest size category of any eukaryote. Genomic copy numbers (GCN) of rRNA varied by 6 orders of magnitude amongst Alexandrium (10[2]- 10[8] copies cell[-1]) and were significantly related to genome size. Within the population CNV of rRNA was 2 orders of magnitude (10[5] - 10[7] cell[-1]) in 15 isolates from one population, demonstrating that quantitative data based on rRNA genes needs considerable caution in interpretation, even if validated against locally isolated strains. Despite up to 30 years in laboratory culture, rRNA CNV and genome size variability were not correlated with time in culture. Cell volume was only weakly associated with rRNA GCN (20-22% variance explained across dinoflagellates, 4% in Gonyaulacales). GCN of sxtA4 varied from 0-10[2] copies cell[-1], was significantly related to PSTs (ng cell[-1]), displaying a gene dosage effect modulating PST production. Our data indicate that in dinoflagellates, a major marine eukaryotic group, low-copy functional genes are more reliable and informative targets for quantification of ecological processes than unstable rRNA genes.}, } @article {pmid37422083, year = {2023}, author = {Lee, H and Yoon, S and Park, YH and Lee, JS and Rhyu, DY and Kim, KT}, title = {Microbiota dysbiosis associated with type 2 diabetes-like effects caused by chronic exposure to a mixture of chlorinated persistent organic pollutants in zebrafish.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {334}, number = {}, pages = {122108}, doi = {10.1016/j.envpol.2023.122108}, pmid = {37422083}, issn = {1873-6424}, mesh = {Animals ; Male ; Female ; *Diabetes Mellitus, Type 2/metabolism ; Zebrafish/metabolism ; Persistent Organic Pollutants/metabolism/pharmacology ; Dysbiosis/chemically induced/microbiology ; *Gastrointestinal Microbiome ; *Microbiota ; *Environmental Pollutants/metabolism ; }, abstract = {Mixtures of chlorinated persistent organic pollutants (C-POPs-Mix) are chemically related risk factors for type 2 diabetes mellitus (T2DM); however, the effects of chronic exposure to C-POPs-Mix on microbial dysbiosis remain poorly understood. Herein, male and female zebrafish were exposed to C-POPs-Mix at a 1:1 ratio of five organochlorine pesticides and Aroclor 1254 at concentrations of 0.02, 0.1, and 0.5 μg/L for 12 weeks. We measured T2DM indicators in blood and profiled microbial abundance and richness in the gut as well as transcriptomic and metabolomic alterations in the liver. Exposure to C-POPs-Mix significantly increased blood glucose levels while decreasing the abundance and alpha diversity of microbial communities only in females at concentrations of 0.02 and 0.1 μg/L. The majorly identified microbial contributors to microbial dysbiosis were Bosea minatitlanensis, Rhizobium tibeticum, Bifidobacterium catenulatum, Bifidobacterium adolescentis, and Collinsella aerofaciens. PICRUSt results suggested that altered pathways were associated with glucose and lipid production and inflammation, which are linked to changes in the transcriptome and metabolome of the zebrafish liver. Metagenomics outcomes revealed close relationships between intestinal and liver disruptions to T2DM-related molecular pathways. Thus, microbial dysbiosis in T2DM-triggered zebrafish occurred as a result of chronic exposure to C-POPs-Mix, indicating strong host-microbiome interactions.}, } @article {pmid37421863, year = {2023}, author = {Ji, M and Giangeri, G and Yu, F and Sessa, F and Liu, C and Sang, W and Canu, P and Li, F and Treu, L and Campanaro, S}, title = {An integrated metagenomic model to uncover the cooperation between microbes and magnetic biochar during microplastics degradation in paddy soil.}, journal = {Journal of hazardous materials}, volume = {458}, number = {}, pages = {131950}, doi = {10.1016/j.jhazmat.2023.131950}, pmid = {37421863}, issn = {1873-3336}, mesh = {*Soil ; *Microplastics ; Plastics ; Polyvinyl Chloride ; Charcoal ; Magnetic Phenomena ; Polyethylenes ; }, abstract = {The free radicals released from the advanced oxidation processes can enhance microplastics degradation, however, the existence of microbes acting synergistically in this process is still uncertain. In this study, magnetic biochar was used to initiate the advanced oxidation process in flooded soil. paddy soil was contaminated with polyethylene and polyvinyl chloride microplastics in a long-term incubation experiment, and subsequently subjected to bioremediation with biochar or magnetic biochar. After incubation, the total organic matter present in the samples containing polyvinyl chloride or polyethylene, and treated with magnetic biochar, significantly increased compared to the control. In the same samples there was an accumulation of "UVA humic" and "protein/phenol-like" substances. The integrated metagenomic investigation revealed that the relative abundance of some key genes involved in fatty acids degradation and in dehalogenation changed in different treatments. Results from genome-centric investigation suggest that a Nocardioides species can cooperate with magnetic biochar in the degradation of microplastics. In addition, a species assigned to the Rhizobium taxon was identified as a candidate in the dehalogenation and in the benzoate metabolism. Overall, our results suggest that cooperation between magnetic biochar and some microbial species involved in microplastic degradation is relevant in determining the fate of microplastics in soil.}, } @article {pmid37420292, year = {2023}, author = {Schiml, VC and Delogu, F and Kumar, P and Kunath, B and Batut, B and Mehta, S and Johnson, JE and Grüning, B and Pope, PB and Jagtap, PD and Griffin, TJ and Arntzen, MØ}, title = {Integrative meta-omics in Galaxy and beyond.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {56}, pmid = {37420292}, issn = {2524-6372}, support = {SFB 992/1 2012//Collaborative Research Centre 992 Medical Epigenetics/ ; 031 A538A/A538C RBC//Bundesministerium für Bildung und Forschung/ ; NNF20OC0061313//Novo Nordisk Fonden/ ; 295910//Norges Forskningsråd/ ; }, abstract = {BACKGROUND: 'Omics methods have empowered scientists to tackle the complexity of microbial communities on a scale not attainable before. Individually, omics analyses can provide great insight; while combined as "meta-omics", they enhance the understanding of which organisms occupy specific metabolic niches, how they interact, and how they utilize environmental nutrients. Here we present three integrative meta-omics workflows, developed in Galaxy, for enhanced analysis and integration of metagenomics, metatranscriptomics, and metaproteomics, combined with our newly developed web-application, ViMO (Visualizer for Meta-Omics) to analyse metabolisms in complex microbial communities.

RESULTS: In this study, we applied the workflows on a highly efficient cellulose-degrading minimal consortium enriched from a biogas reactor to analyse the key roles of uncultured microorganisms in complex biomass degradation processes. Metagenomic analysis recovered metagenome-assembled genomes (MAGs) for several constituent populations including Hungateiclostridium thermocellum, Thermoclostridium stercorarium and multiple heterogenic strains affiliated to Coprothermobacter proteolyticus. The metagenomics workflow was developed as two modules, one standard, and one optimized for improving the MAG quality in complex samples by implementing a combination of single- and co-assembly, and dereplication after binning. The exploration of the active pathways within the recovered MAGs can be visualized in ViMO, which also provides an overview of the MAG taxonomy and quality (contamination and completeness), and information about carbohydrate-active enzymes (CAZymes), as well as KEGG annotations and pathways, with counts and abundances at both mRNA and protein level. To achieve this, the metatranscriptomic reads and metaproteomic mass-spectrometry spectra are mapped onto predicted genes from the metagenome to analyse the functional potential of MAGs, as well as the actual expressed proteins and functions of the microbiome, all visualized in ViMO.

CONCLUSION: Our three workflows for integrative meta-omics in combination with ViMO presents a progression in the analysis of 'omics data, particularly within Galaxy, but also beyond. The optimized metagenomics workflow allows for detailed reconstruction of microbial community consisting of MAGs with high quality, and thus improves analyses of the metabolism of the microbiome, using the metatranscriptomics and metaproteomics workflows.}, } @article {pmid37419993, year = {2023}, author = {Bei, Q and Reitz, T and Schnabel, B and Eisenhauer, N and Schädler, M and Buscot, F and Heintz-Buschart, A}, title = {Extreme summers impact cropland and grassland soil microbiomes.}, journal = {The ISME journal}, volume = {17}, number = {10}, pages = {1589-1600}, pmid = {37419993}, issn = {1751-7370}, mesh = {*Grassland ; Soil/chemistry ; *Microbiota ; Bacteria ; Droughts ; Crops, Agricultural ; Soil Microbiology ; }, abstract = {The increasing frequency of extreme weather events highlights the need to understand how soil microbiomes respond to such disturbances. Here, metagenomics was used to investigate the effects of future climate scenarios (+0.6 °C warming and altered precipitation) on soil microbiomes during the summers of 2014-2019. Unexpectedly, Central Europe experienced extreme heatwaves and droughts during 2018-2019, causing significant impacts on the structure, assembly, and function of soil microbiomes. Specifically, the relative abundance of Actinobacteria (bacteria), Eurotiales (fungi), and Vilmaviridae (viruses) was significantly increased in both cropland and grassland. The contribution of homogeneous selection to bacterial community assembly increased significantly from 40.0% in normal summers to 51.9% in extreme summers. Moreover, genes associated with microbial antioxidant (Ni-SOD), cell wall biosynthesis (glmSMU, murABCDEF), heat shock proteins (GroES/GroEL, Hsp40), and sporulation (spoIID, spoVK) were identified as potential contributors to drought-enriched taxa, and their expressions were confirmed by metatranscriptomics in 2022. The impact of extreme summers was further evident in the taxonomic profiles of 721 recovered metagenome-assembled genomes (MAGs). Annotation of contigs and MAGs suggested that Actinobacteria may have a competitive advantage in extreme summers due to the biosynthesis of geosmin and 2-methylisoborneol. Future climate scenarios caused a similar pattern of changes in microbial communities as extreme summers, but to a much lesser extent. Soil microbiomes in grassland showed greater resilience to climate change than those in cropland. Overall, this study provides a comprehensive framework for understanding the response of soil microbiomes to extreme summers.}, } @article {pmid37419899, year = {2023}, author = {Kipp, EJ and Lindsey, LL and Khoo, B and Faulk, C and Oliver, JD and Larsen, PA}, title = {Metagenomic surveillance for bacterial tick-borne pathogens using nanopore adaptive sampling.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {10991}, pmid = {37419899}, issn = {2045-2322}, support = {R01 AI155472/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Nanopores ; Bacteria/genetics ; *Ixodes/genetics/microbiology ; Zoonoses ; }, abstract = {Technological and computational advancements in the fields of genomics and bioinformatics are providing exciting new opportunities for pathogen discovery and genomic surveillance. In particular, single-molecule nucleotide sequence data originating from Oxford Nanopore Technologies (ONT) sequencing platforms can be bioinformatically leveraged, in real-time, for enhanced biosurveillance of a vast array of zoonoses. The recently released nanopore adaptive sampling (NAS) strategy facilitates immediate mapping of individual nucleotide molecules to a given reference as each molecule is being sequenced. User-defined thresholds then allow for the retention or rejection of specific molecules, informed by the real-time reference mapping results, as they are physically passing through a given sequencing nanopore. Here, we show how NAS can be used to selectively sequence DNA of multiple bacterial tick-borne pathogens circulating in wild populations of the blacklegged tick vector, Ixodes scapularis.}, } @article {pmid37419696, year = {2023}, author = {Mizusawa, M and Carroll, KC}, title = {Recent updates in the development of molecular assays for the rapid identification and susceptibility testing of MRSA.}, journal = {Expert review of molecular diagnostics}, volume = {23}, number = {8}, pages = {679-699}, doi = {10.1080/14737159.2023.2234823}, pmid = {37419696}, issn = {1744-8352}, mesh = {Humans ; *Methicillin-Resistant Staphylococcus aureus/genetics ; *Staphylococcal Infections/diagnosis ; Microbial Sensitivity Tests ; Anti-Bacterial Agents ; }, abstract = {INTRODUCTION: Methicillin-resistant Staphylococcus aureus (MRSA) is a frequent cause of healthcare- and community-associated infections. Nasal carriage of MRSA is a risk factor for subsequent MRSA infections. Increased morbidity and mortality are associated with MRSA infections and screening and diagnostic tests for MRSA play an important role in clinical management.

AREAS COVERED: A literature search was conducted in PubMed and supplemented by citation searching. In this article, we provide a comprehensive review of molecular-based methods for MRSA screening and diagnostic tests including individual nucleic acid detection assays, syndromic panels, and sequencing technologies with a focus on their analytical performance.

EXPERT OPINION: Molecular based-assays for the detection of MRSA have improved in terms of accuracy and availability. Rapid turnaround enables earlier contact isolation and decolonization for MRSA. The availability of syndromic panel tests that include MRSA as a target has expanded from positive blood cultures to pneumonia and osteoarticular infections. Sequencing technologies allow detailed characterizations of novel methicillin-resistance mechanisms that can be incorporated into future assays. Next generation sequencing is capable of diagnosing MRSA infections that cannot be identified by conventional methods and metagenomic next-generation sequencing (mNGS) assays will likely move closer to implementation as front-line diagnostics in the near future.}, } @article {pmid37418948, year = {2023}, author = {Hawes, IA and Alvarenga, BD and Browne, W and Wapniarski, A and Dandekar, R and Bartley, CM and Sowa, GM and DeRisi, JL and Cinque, P and Dravid, AN and Pleasure, SJ and Gisslen, M and Price, RW and Wilson, MR}, title = {Viral co-infection, autoimmunity, and CSF HIV antibody profiles in HIV central nervous system escape.}, journal = {Journal of neuroimmunology}, volume = {381}, number = {}, pages = {578141}, doi = {10.1016/j.jneuroim.2023.578141}, pmid = {37418948}, issn = {1872-8421}, support = {R01 NS094067/NS/NINDS NIH HHS/United States ; R01 MH122471/MH/NIMH NIH HHS/United States ; K08 NS107619/NS/NINDS NIH HHS/United States ; }, mesh = {Humans ; Autoimmunity ; Case-Control Studies ; *Coinfection ; *Epstein-Barr Virus Infections ; Herpesvirus 4, Human ; Central Nervous System ; *HIV Infections/cerebrospinal fluid ; Autoantigens ; }, abstract = {Antiretroviral therapy (ART) suppresses plasma and cerebrospinal fluid (CSF) HIV replication. Neurosymptomatic (NS) CSF escape is a rare exception in which CNS HIV replication occurs in the setting of neurologic impairment. The origins of NS escape are not fully understood. We performed a case-control study of asymptomatic (AS) escape and NS escape subjects with HIV-negative subjects as controls in which we investigated differential immunoreactivity to self-antigens in the CSF of NS escape by employing neuroanatomic CSF immunostaining and massively multiplexed self-antigen serology (PhIP-Seq). Additionally, we utilized pan-viral serology (VirScan) to deeply profile the CSF anti-viral antibody response and metagenomic next-generation sequencing (mNGS) for pathogen detection. We detected Epstein-Barr virus (EBV) DNA more frequently in the CSF of NS escape subjects than in AS escape subjects. Based on immunostaining and PhIP-Seq, there was evidence for increased immunoreactivity against self-antigens in NS escape CSF. Finally, VirScan revealed several immunodominant epitopes that map to the HIV envelope and gag proteins in the CSF of AS and NS escape subjects. Whether these additional inflammatory markers are byproducts of an HIV-driven process or whether they independently contribute to the neuropathogenesis of NS escape will require further study.}, } @article {pmid37418939, year = {2023}, author = {Raghavan, D and Patinharekkara, SC and Elampilay, ST and Payatatti, VKI and Charles, S and Veeraraghavan, S and Kadiyalath, J and Vandana, S and Purayil, SK and Prasadam, H and Anitha, SJ}, title = {New insights into bacterial Zn homeostasis and molecular architecture of the metal resistome in soil polluted with nano zinc oxide.}, journal = {Ecotoxicology and environmental safety}, volume = {263}, number = {}, pages = {115222}, doi = {10.1016/j.ecoenv.2023.115222}, pmid = {37418939}, issn = {1090-2414}, mesh = {*Zinc Oxide/toxicity ; Soil ; Metals ; Zinc/toxicity/metabolism ; Homeostasis ; *Nanoparticles ; }, abstract = {Accumulation of nano ZnO (nZnO) in soils could be toxic to bacterial communities through disruption of Zn homeostasis. Under such conditions, bacterial communities strive to maintain cellular Zn levels by accentuation of appropriate cellular machinery. In this study, soil was exposed to a gradient (50-1000 mg Zn kg[-1]) of nZnO for evaluating their effects on genes involved in Zn homeostasis (ZHG). The responses were compared with similar levels of its bulk counterpart (bZnO). It was observed that ZnO (as nZnO or bZnO) induced a plethora of influx and efflux transporters as well as metallothioneins (MTs) and metallochaperones mediated by an array of Zn sensitive regulatory proteins. Major influx system identified was the ZnuABC transporter, while important efflux transporters identified were CzcCBA, ZntA, YiiP and the major regulator was Zur. The response of communities was dose- dependent at lower concentrations (<500 mg Zn kg[-1] as nZnO or bZnO). However, at 1000 mg Zn kg[-1], a size-dependent threshold of gene/gene family abundances was evident. Under nZnO, a poor adaptation to toxicity induced anaerobic conditions due to deployment of major influx and secondary detoxifying systems as well as poor chelation of free Zn ions was evident. Moreover, Zn homeostasis related link with biofilm formation and virulence were accentuated under nZnO than bZnO. While these findings were verified by PCoA and Procrustes analysis, Network analysis and taxa vs ZHG associations also substantiated that a stronger Zn shunting mechanism was induced under nZnO due to higher toxicity. Molecular crosstalks with systems governing Cu and Fe homeostasis were also evident. Expression analysis of important resistance genes by qRT-PCR showed good alignment with the predictive metagenome data, thereby validating our findings. From the study it was evident that the induction of detoxifying and resistant genes was greatly lowered under nZnO, which markedly hampered Zn homeostasis among the soil bacterial communities.}, } @article {pmid37418475, year = {2023}, author = {Badr, AA and Fouad, WM}, title = {Comparative study of multiple approaches for identifying cultivable microalgae population diversity from freshwater samples.}, journal = {PloS one}, volume = {18}, number = {7}, pages = {e0285913}, pmid = {37418475}, issn = {1932-6203}, mesh = {*Microalgae/genetics ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; *Rivers/microbiology ; Egypt ; Microbiota ; }, abstract = {The vast diversity of microalgae imposes the challenge of identifying them through the most common and economical identification method, morphological identification, or through using the more recent molecular-level identification tools. Here we report an approach combining enrichment and metagenomic molecular techniques to enhance microalgae identification and identify microalgae diversity from environmental water samples. From this perspective, we aimed to identify the most suitable culturing media and molecular approach (using different primer sets and reference databases) for detecting microalgae diversity. Using this approach, we have analyzed three water samples collected from the River Nile on several enrichment media. A total of 37 microalgae were identified morphologically to the genus level. While sequencing the three-primer sets (16S rRNA V1-V3 and V4-V5 and 18S rRNA V4 region) and aligning them to three reference databases (GG, SILVA, and PR2), a total of 87 microalgae were identified to the genus level. The highest eukaryotic microalgae diversity was identified using the 18S rRNA V4 region and alignment to the SILVA database (43 genera). The two 16S rRNA regions sequenced added to the eukaryotic microalgae identification, 26 eukaryotic microalgae. Cyanobacteria were identified through the two sequenced 16S rRNA regions. Alignment to the SILVA database served to identify 14 cyanobacteria to the genera level, followed by Greengenes, 11 cyanobacteria genera. Our multiple-media, primer, and reference database approach revealed a high microalgae diversity that would have been overlooked if a single approach had been used over the other.}, } @article {pmid37418182, year = {2023}, author = {Zhang, T and Zhang, J and Zhang, P and Wang, J and He, Y}, title = {Electronic Bifurcation: A New Perspective on Fe Bio-Utilization in Anaerobic Digestion of Lactate.}, journal = {Environmental science & technology}, volume = {57}, number = {28}, pages = {10448-10457}, doi = {10.1021/acs.est.3c01367}, pmid = {37418182}, issn = {1520-5851}, mesh = {*Lactic Acid/metabolism ; Anaerobiosis ; *Quinones ; Flavins/metabolism ; Iron ; Methane ; Bioreactors ; }, abstract = {Anaerobic microorganisms use flavin/quinone-based electronic bifurcation (EB) to gain a survival advantage at the thermodynamic limits. However, the contribution of EB to microscopic energy and productivity in the anaerobic digestion (AD) system is unknown. This study demonstrates for the first time that under limited substrate conditions, Fe-driven EB in AD leads to a 40% increase in specific methane production and contributes to 25% ATP accumulation, by analyzing the concentration of EB enzymes such as Etf-Ldh, HdrA2B2C2, and Fd, NADH and actual Gibbs free-energy changes. Differential pulse voltammetry and electron respiratory chain inhibition experiments detected that iron enhanced electron transport in EB by accelerating the activity of flavin, Fe-S clusters, and quinone groups. Other microbial and enzyme genes with EB potential closely related to iron transport have also been found in metagenomes. The potential of EB to accumulate energy and enhance productivity in AD systems was investigated, and metabolic pathways were proposed in the study.}, } @article {pmid37417976, year = {2023}, author = {Santos-Pereira, C and Sousa, J and Costa, ÂMA and Santos, AO and Rito, T and Soares, P and Franco-Duarte, R and Silvério, SC and Rodrigues, LR}, title = {Functional and sequence-based metagenomics to uncover carbohydrate-degrading enzymes from composting samples.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {17}, pages = {5379-5401}, pmid = {37417976}, issn = {1432-0614}, support = {UIDB/04469/2020//Fundação para a Ciência e a Tecnologia/ ; POCI-01-0145-FEDER-029773//Fundação para a Ciência e a Tecnologia/ ; PTDC/BII-BIO/5554/2020//Fundação para a Ciência e a Tecnologia/ ; CPCA/A0/408464/2021//Fundação para a Ciência e a Tecnologia/ ; UMINHO/BID/2021/12//Fundação para a Ciência e a Tecnologia/ ; 2022.11695.BD//Fundação para a Ciência e a Tecnologia/ ; }, mesh = {*Composting ; Metagenomics ; Lignin/metabolism ; Carbohydrates ; *Microbiota ; Bacteria/metabolism ; *Cellulases/metabolism ; }, abstract = {The renewable, abundant , and low-cost nature of lignocellulosic biomass can play an important role in the sustainable production of bioenergy and several added-value bioproducts, thus providing alternative solutions to counteract the global energetic and industrial demands. The efficient conversion of lignocellulosic biomass greatly relies on the catalytic activity of carbohydrate-active enzymes (CAZymes). Finding novel and robust biocatalysts, capable of being active under harsh industrial conditions, is thus imperative to achieve an economically feasible process. In this study, thermophilic compost samples from three Portuguese companies were collected, and their metagenomic DNA was extracted and sequenced through shotgun sequencing. A novel multi-step bioinformatic pipeline was developed to find CAZymes and characterize the taxonomic and functional profiles of the microbial communities, using both reads and metagenome-assembled genomes (MAGs) as input. The samples' microbiome was dominated by bacteria, where the classes Gammaproteobacteria, Alphaproteobacteria, and Balneolia stood out for their higher abundance, indicating that the degradation of compost biomass is mainly driven by bacterial enzymatic activity. Furthermore, the functional studies revealed that our samples are a rich reservoir of glycoside hydrolases (GH), particularly of GH5 and GH9 cellulases, and GH3 oligosaccharide-degrading enzymes. We further constructed metagenomic fosmid libraries with the compost DNA and demonstrated that a great number of clones exhibited β-glucosidase activity. The comparison of our samples with others from the literature showed that, independently of the composition and process conditions, composting is an excellent source of lignocellulose-degrading enzymes. To the best of our knowledge, this is the first comparative study on the CAZyme abundance and taxonomic/functional profiles of Portuguese compost samples. KEY POINTS: • Sequence- and function-based metagenomics were used to find CAZymes in compost samples. • Thermophilic composts proved to be rich in bacterial GH3, GH5, and GH9 enzymes. • Compost-derived fosmid libraries are enriched in clones with β-glucosidase activity.}, } @article {pmid37417747, year = {2023}, author = {Peng, Q and Lin, L and Tu, Q and Wang, X and Zhou, Y and Chen, J and Jiao, N and Zhou, J}, title = {Unraveling the roles of coastal bacterial consortia in degradation of various lignocellulosic substrates.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0128322}, pmid = {37417747}, issn = {2379-5077}, mesh = {*Lignin/metabolism ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Cellulose/metabolism ; }, abstract = {Lignocellulose, as the most abundant natural organic carbon on earth, plays a key role in regulating the global carbon cycle, but there have been only few studies in marine ecosystems. Little information is available about the extant lignin-degrading bacteria in coastal wetlands, limiting our understanding of their ecological roles and traits in lignocellulose degradation. We utilized in situ lignocellulose enrichment experiments coupled with 16S rRNA amplicon and shotgun metagenomics sequencing to identify and characterize bacterial consortia attributed to different lignin/lignocellulosic substrates in the southern-east intertidal zone of East China Sea. We found the consortia enriched on woody lignocellulose showed higher diversity than those on herbaceous substrate. This also revealed substrate-dependent taxonomic groups. A time-dissimilarity pattern with increased alpha diversity over time was observed. Additionally, this study identified a comprehensive set of genes associated with lignin degradation potential, containing 23 gene families involved in lignin depolymerization, and 371 gene families involved in aerobic/anaerobic lignin-derived aromatic compound pathways, challenging the traditional view of lignin recalcitrance within marine ecosystems. In contrast to similar cellulase genes among the lignocellulose substrates, significantly different ligninolytic gene groups were observed between consortia under woody and herbaceous substrates. Importantly, we not only observed synergistic degradation of lignin and hemi-/cellulose, but also pinpointed the potential biological actors at the levels of taxa and functional genes, which indicated that the alternation of aerobic and anaerobic catabolism could facilitate lignocellulose degradation. Our study advances the understanding of coastal bacterial community assembly and metabolic potential for lignocellulose substrates. IMPORTANCE It is essential for the global carbon cycle that microorganisms drive lignocellulose transformation, due to its high abundance. Previous studies were primarily constrained to terrestrial ecosystems, with limited information about the role of microbes in marine ecosystems. Through in situ lignocellulose enrichment experiment coupled with high-throughput sequencing, this study demonstrated different impacts that substrates and exposure times had on long-term bacterial community assembly and pinpointed comprehensive, yet versatile, potential decomposers at the levels of taxa and functional genes in response to different lignocellulose substrates. Moreover, the links between ligninolytic functional traits and taxonomic groups of substrate-specific populations were revealed. It showed that the synergistic effect of lignin and hemi-/cellulose degradation could enhance lignocellulose degradation under alternation of aerobic and anaerobic conditions. This study provides valuable taxonomic and genomic insights into coastal bacterial consortia for lignocellulose degradation.}, } @article {pmid37417735, year = {2023}, author = {Pessi, IS and Popin, RV and Durieu, B and Lara, Y and Tytgat, B and Savaglia, V and Roncero-Ramos, B and Hultman, J and Verleyen, E and Vyverman, W and Wilmotte, A}, title = {Novel diversity of polar Cyanobacteria revealed by genome-resolved metagenomics.}, journal = {Microbial genomics}, volume = {9}, number = {7}, pages = {}, pmid = {37417735}, issn = {2057-5858}, mesh = {*Metagenomics ; *Cyanobacteria/genetics ; Lakes/microbiology ; Metagenome ; Base Sequence ; }, abstract = {Benthic microbial mats dominated by Cyanobacteria are important features of polar lakes. Although culture-independent studies have provided important insights into the diversity of polar Cyanobacteria, only a handful of genomes have been sequenced to date. Here, we applied a genome-resolved metagenomics approach to data obtained from Arctic, sub-Antarctic and Antarctic microbial mats. We recovered 37 metagenome-assembled genomes (MAGs) of Cyanobacteria representing 17 distinct species, most of which are only distantly related to genomes that have been sequenced so far. These include (i) lineages that are common in polar microbial mats such as the filamentous taxa Pseudanabaena, Leptolyngbya, Microcoleus/Tychonema and Phormidium; (ii) the less common taxa Crinalium and Chamaesiphon; (iii) an enigmatic Chroococcales lineage only distantly related to Microcystis; and (iv) an early branching lineage in the order Gloeobacterales that is distributed across the cold biosphere, for which we propose the name Candidatus Sivonenia alaskensis. Our results show that genome-resolved metagenomics is a powerful tool for expanding our understanding of the diversity of Cyanobacteria, especially in understudied remote and extreme environments.}, } @article {pmid37415819, year = {2023}, author = {Dong, L and Li, Y and Yang, C and Gong, J and Zhu, W and Huang, Y and Kong, M and Zhao, L and Wang, F and Lu, S and Pu, J and Yang, J}, title = {Species-level microbiota of ticks and fleas from Marmota himalayana in the Qinghai-Tibet Plateau.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1188155}, pmid = {37415819}, issn = {1664-302X}, abstract = {INTRODUCTION: Ticks and fleas, as blood-sucking arthropods, carry and transmit various zoonotic diseases. In the natural plague foci of China, monitoring of Yersinia pestis has been continuously conducted in Marmota himalayana and other host animals, whereas other pathogens carried by vectors are rarely concerned in the Qinghai-Tibet Plateau.

METHODS: In this study, we investigated the microbiota of ticks and fleas sampling from M. himalayana in the Qinghai-Tibet Plateau, China by metataxonomics combined with metagenomic methods.

RESULTS: By metataxonomic approach based on full-length 16S rDNA amplicon sequencing and operational phylogenetic unit (OPU) analyses, we described the microbiota community of ticks and fleas at the species level, annotated 1,250 OPUs in ticks, including 556 known species and 492 potentially new species, accounting for 48.50% and 41.71% of the total reads in ticks, respectively. A total of 689 OPUs were detected in fleas, consisting of 277 known species (40.62% of the total reads in fleas) and 294 potentially new species (56.88%). At the dominant species categories, we detected the Anaplasma phagocytophilum (OPU 421) and potentially pathogenic new species of Wolbachia, Ehrlichia, Rickettsia, and Bartonella. Using shotgun sequencing, we obtained 10 metagenomic assembled genomes (MAGs) from vector samples, including a known species (Providencia heimbachae DFT2), and six new species affliated to four known genera, i.e., Wolbachia, Mumia, Bartonella, and Anaplasma. By the phylogenetic analyses based on full-length 16S rRNA genes and core genes, we identified that ticks harbored pathogenic A. phagocytophilum. Moreover, these potentially pathogenic novel species were more closely related to Ehrlichia muris, Ehrlichia muris subsp. eauclairensis, Bartonella rochalimae, and Rickettsia limoniae, respectively. The OPU 422 Ehrlichia sp1 was most related to Ehrlichia muris and Ehrlichia muris subsp. eauclairensis. The OPU 230 Bartonella sp1 and Bartonella spp. (DTF8 and DTF9) was clustered with Bartonella rochalimae. The OPU 427 Rickettsia sp1 was clustered with Rickettsia limoniae.

DISCUSSION: The findings of the study have advanced our understanding of the potential pathogen groups of vectors in marmot (Marmota himalayana) in the Qinghai-Tibet Plateau.}, } @article {pmid37415812, year = {2023}, author = {Wang, Z and Dalton, KR and Lee, M and Parks, CG and Beane Freeman, LE and Zhu, Q and González, A and Knight, R and Zhao, S and Motsinger-Reif, AA and London, SJ}, title = {Metagenomics reveals novel microbial signatures of farm exposures in house dust.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1202194}, pmid = {37415812}, issn = {1664-302X}, abstract = {Indoor home dust microbial communities, important contributors to human health, are shaped by environmental factors, including farm-related exposures. Advanced metagenomic whole genome shotgun sequencing (WGS) improves detection and characterization of microbiota in the indoor built-environment dust microbiome, compared to conventional 16S rRNA amplicon sequencing (16S). We hypothesized that the improved characterization of indoor dust microbial communities by WGS will enhance detection of exposure-outcome associations. The objective of this study was to identify novel associations of environmental exposures with the dust microbiome from the homes of 781 farmers and farm spouses enrolled in the Agricultural Lung Health Study. We examined various farm-related exposures, including living on a farm, crop versus animal production, and type of animal production, as well as non-farm exposures, including home cleanliness and indoor pets. We assessed the association of the exposures on within-sample alpha diversity and between-sample beta diversity, and the differential abundance of specific microbes by exposure. Results were compared to previous findings using 16S. We found most farm exposures were significantly positively associated with both alpha and beta diversity. Many microbes exhibited differential abundance related to farm exposures, mainly in the phyla Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. The identification of novel differential taxa associated with farming at the genera level, including Rhodococcus, Bifidobacterium, Corynebacterium, and Pseudomonas, was a benefit of WGS compared to 16S. Our findings indicate that characterization of dust microbiota, an important component of the indoor environment relevant to human health, is heavily influenced by sequencing techniques. WGS is a powerful tool to survey the microbial community that provides novel insights on the impact of environmental exposures on indoor dust microbiota. These findings can inform the design of future studies in environmental health.}, } @article {pmid37414297, year = {2023}, author = {Mu, Y and Wan, L and Liang, Z and Yang, D and Han, H and Yi, J and Dai, X}, title = {Enhanced biological phosphorus removal by high concentration powder carrier bio-fluidized bed (HPB): Phosphorus distribution, cyclone separation, and metagenomics.}, journal = {Chemosphere}, volume = {337}, number = {}, pages = {139353}, doi = {10.1016/j.chemosphere.2023.139353}, pmid = {37414297}, issn = {1879-1298}, mesh = {*Sewage/chemistry ; Powders ; Phosphorus/analysis ; Metagenomics ; *Cyclonic Storms ; Extracellular Polymeric Substance Matrix/chemistry ; Denitrification ; Bioreactors ; Nitrogen/analysis ; Waste Disposal, Fluid/methods ; }, abstract = {This study provides a comparative investigation of phosphorus removal between anaerobic-anoxic-oxic (AAO) and high-concentration powder carrier bio-fluidized bed (HPB) in the same full-scale wastewater treatment plant. The results showed that the total phosphorus removal of HPB was 71.45%-96.71%. Compared with AAO, the total phosphorus removal of HPB can be increased by a maximum of 15.73%. The mechanisms of enhanced phosphorus removal by HPB include the followings. Biological phosphorus removal was significant. The anaerobic phosphorus release capacity of HPB was enhanced and polyphosphate (Poly-P) in the excess sludge of HPB was 1.5 times higher than that of AAO. The relative abundance of Candidatus Accumulibacter was 5 times higher than that of AAO, and oxidative phosphorylation and butanoate metabolism were enhanced. The analysis of phosphorus distribution showed that cyclone separation increased the chemical phosphorus precipitation (Chem-P) in the excess sludge by 16.96% to avoid accumulation in the biochemical tank. The phosphorus adsorbed by extracellular polymeric substance (EPS) in the recycled sludge was stripped, and the EPS bound-P in the excess sludge increased by 1.5 times. This study demonstrated the feasibility of HPB to improve the phosphorus removal efficiency for domestic wastewater.}, } @article {pmid37414290, year = {2023}, author = {Kumar, V and Sharma, N and Sharma, P and Pasrija, R and Kaur, K and Umesh, M and Thazeem, B}, title = {Toxicity analysis of endocrine disrupting pesticides on non-target organisms: A critical analysis on toxicity mechanisms.}, journal = {Toxicology and applied pharmacology}, volume = {474}, number = {}, pages = {116623}, doi = {10.1016/j.taap.2023.116623}, pmid = {37414290}, issn = {1096-0333}, mesh = {*Pesticides/toxicity/metabolism ; *Chlorpyrifos ; Reproduction ; Hormones ; *Endocrine Disruptors/toxicity ; }, abstract = {Endocrine disrupting compounds are the chemicals which mimics the natural endocrine hormones and bind to the receptors made for the hormones. Upon binding they activate the cascade of reaction which leads to permanent activating of the signalling cycle and ultimately leads to uncontrolled growth. Pesticides are one of the endocrine disrupting chemicals which cause cancer, congenital birth defects, and reproductive defects in non-target organisms. Non-target organisms are keen on exposing to these pesticides. Although several studies have reported about the pesticide toxicity. But a critical analysis of pesticide toxicity and its role as endocrine disruptor is lacking. Therefore, the presented review literature is an endeavour to understand the role of the pesticides as endocrine disruptors. In addition, it discusses about the endocrine disruption, neurological disruption, genotoxicity, and ROS induced pesticide toxicity. Moreover, biochemical mechanisms of pesticide toxicity on non-target organisms have been presented. An insight on the chlorpyrifos toxicity on non-target organisms along with species names have been presented.}, } @article {pmid37413963, year = {2023}, author = {Xu, N and Zhou, Z and Chen, B and Zhang, Z and Zhang, J and Li, Y and Lu, T and Sun, L and Peijnenburg, WJGM and Qian, H}, title = {Effect of chlorpyrifos on freshwater microbial community and metabolic capacity of zebrafish.}, journal = {Ecotoxicology and environmental safety}, volume = {262}, number = {}, pages = {115230}, doi = {10.1016/j.ecoenv.2023.115230}, pmid = {37413963}, issn = {1090-2414}, abstract = {Chlorpyrifos is a widely used organophosphorus insecticide because of its high efficiency and overall effectiveness, and it is commonly detected in aquatic ecosystems. However, at present, the impact of chlorpyrifos on the aquatic micro-ecological environment is still poorly understood. Here, we established aquatic microcosm systems treated with 0.2 and 2.0 µg/L chlorpyrifos, and employed omics biotechnology, including metagenomics and 16S rRNA gene sequencing, to investigate the effect of chlorpyrifos on the composition and functional potential of the aquatic and zebrafish intestinal microbiomes after 7 d and 14 d chlorpyrifos treatment. After 14 d chlorpyrifos treatment, the aquatic microbial community was adversely affected in terms of its composition, structure, and stability, while its diversity showed only a slight impact. Most functions, especially capacities for environmental information processing and metabolism, were destroyed by chlorpyrifos treatment for 14 d. We observed that chlorpyrifos increased the number of risky antibiotic resistance genes and aggravated the growth of human pathogens. Although no clear effects on the structure of the zebrafish intestinal microbial community were observed, chlorpyrifos treatment did alter the metabolic capacity of the zebrafish. Our study highlights the ecological risk of chlorpyrifos to the aquatic environment and provides a theoretical basis for the rational use of pesticides in agricultural production.}, } @article {pmid37413912, year = {2023}, author = {Zhu, H and Fu, Y and Yu, J and Jing, W and Zhou, M}, title = {Metagenomic insight on consortium degradation of soil weathered petroleum and its supplement based on gene abundance change.}, journal = {Enzyme and microbial technology}, volume = {169}, number = {}, pages = {110285}, doi = {10.1016/j.enzmictec.2023.110285}, pmid = {37413912}, issn = {1879-0909}, mesh = {*Petroleum/analysis/metabolism ; Soil ; *Soil Pollutants/analysis/metabolism ; Biodegradation, Environmental ; Oxidoreductases ; Hydrogen ; Soil Microbiology ; }, abstract = {Petroleum biodegradation is of importance for the mitigation of secondary pollutants from soil chemical remediation. Describing the gene abundance change of the petroleum degradation emerged as an important practice for success. In this study, an indigenous consortium with targeting-enzyme was utilized to develop a degradative system that was later subjected to metagenomic analysis on the soil microbial community. Centering on ko00625 pathway, abundance change of dehydrogenase gene was firstly found increasing from groups D, DS to DC in turn, just in an opposite direction with that of oxygenase. In addition, gene abundance of responsive mechanism went rising with degradative process as well. This finding sufficiently promoted that equal attention should be paid to both degradative and responsive processes. Hydrogen donor system was innovatively built on the consortium-used soil to satisfy the demand of dehydrogenase gene tendency and to sustain further petroleum degradation. Anaerobic pine-needle soil was supplemented to this system, bi-functionally serving as dehydrogenase substrate with nutrients and hydrogen donor. In doing so, two successive degradations optimally achieved the total removal rate 75.6-78.7% for petroleum hydrocarbon. The conception on the gene abundance changes and its corresponding supplement helps industries of concern to develop geno-tag guided framework.}, } @article {pmid37413798, year = {2023}, author = {Wu, T and Zhong, L and Ding, J and Pang, JW and Sun, HJ and Ding, MQ and Ren, NQ and Yang, SS}, title = {Microplastics perturb nitrogen removal, microbial community and metabolism mechanism in biofilm system.}, journal = {Journal of hazardous materials}, volume = {458}, number = {}, pages = {131971}, doi = {10.1016/j.jhazmat.2023.131971}, pmid = {37413798}, issn = {1873-3336}, mesh = {*Denitrification ; Wastewater ; Microplastics ; Plastics ; Nitrogen/metabolism ; Bioreactors ; *Microbiota ; Biofilms ; Polystyrenes ; }, abstract = {Microplastics (MPs) are a significant component of global pollution and cause widespread concern, particularly in wastewater treatment plants. While understanding the impact of MPs on nutrient removal and potential metabolism in biofilm systems is limited. This work investigated the impact of polystyrene (PS) and polyethylene terephthalate (PET) on the performance of biofilm systems. The results revealed that at concentrations of 100 and 1000 μg/L, both PS and PET had almost no effect on the removal of ammonia nitrogen, phosphorus, and chemical oxygen demand, but reduced the removal of total nitrogen by 7.40-16.6%. PS and PET caused cell and membrane damage, as evidenced by increases in reactive oxygen species and lactate dehydrogenase to 136-355% and 144-207% of the control group. Besides, metagenomic analysis demonstrated both PS and PET changed the microbial structure and caused functional differences. Some important genes in nitrite oxidation (e.g. nxrA), denitrification (e.g. narB, nirABD, norB, and nosZ), and electron production process (e.g. mqo, sdh, and mdh) were restrained, meanwhile, species contribution to nitrogen-conversion genes was altered, therefore disturbing nitrogen-conversion metabolism. This work contributes to evaluating the potential risks of biofilm systems exposed to PS and PET, maintaining high nitrogen removal and system stability.}, } @article {pmid37413727, year = {2023}, author = {Xing, Z and Chen, S and Xu, F and Su, X and Gou, F and Shi, Y and Chen, H and Xiang, J and Li, J and Zhao, T}, title = {Quantitative analysis of TCE biodegradation pathway in landfill cover utilizing continuous monitoring, droplet digital PCR and multi-omics sequencing technology.}, journal = {Journal of environmental management}, volume = {344}, number = {}, pages = {118509}, doi = {10.1016/j.jenvman.2023.118509}, pmid = {37413727}, issn = {1095-8630}, mesh = {*Trichloroethylene/chemistry ; Multiomics ; Biodegradation, Environmental ; Waste Disposal Facilities ; Bacteria/genetics/metabolism ; Soil ; Polymerase Chain Reaction ; Technology ; }, abstract = {The remediation of volatile chlorinated hydrocarbons in the quasi-vadose zone has become a significant challenge. We applied an integrated approach to assess the biodegradability of trichloroethylene to identify the biotransformation mechanism. The formation of the functional zone biochemical layer was assessed by analyzing the distribution of landfill gas, physical and chemical properties of cover soil, spatial-temporal variations of micro-ecology, biodegradability of landfill cover soil and distributional difference metabolic pathway. Real-time online monitoring showed that trichloroethylene continuously undergoes anaerobic dichlorination and simultaneous aerobic/anaerobic conversion-aerobic co-metabolic degradation on the vertical gradient of the landfill cover system and reduction in trans-1,2-dichloroethylene in the anoxic zone but not 1,1-dichloroethylene. PCR and diversity sequencing revealed the abundance and spatial distribution of known dichlorination-related genes within the landfill cover, with 6.61 ± 0.25 × 10[4]-6.78 ± 0.09 × 10[6] and 1.17 ± 0.78 × 10[3]-7.82 ± 0.07 × 10[5] copies per g/soil of pmoA and tceA, respectively. In addition, dominant bacteria and diversity were significantly linked with physicochemical factors, and Mesorhizobium, Pseudoxanthomonas and Gemmatimonas were responsible for biodegradation in the aerobic, anoxic and anaerobic zones. Metagenome sequencing identified 6 degradation pathways of trichloroethylene that may occur in the landfill cover; the main pathway was incomplete dechlorination accompanied by cometabolic degradation. These results indicate that the anoxic zone is important for trichloroethylene degradation.}, } @article {pmid37410704, year = {2023}, author = {Chicco, D and Cumbo, F and Angione, C}, title = {Ten quick tips for avoiding pitfalls in multi-omics data integration analyses.}, journal = {PLoS computational biology}, volume = {19}, number = {7}, pages = {e1011224}, pmid = {37410704}, issn = {1553-7358}, mesh = {Humans ; *Genomics ; *Multiomics ; Proteomics ; Computational Biology ; Metabolomics ; }, abstract = {Data are the most important elements of bioinformatics: Computational analysis of bioinformatics data, in fact, can help researchers infer new knowledge about biology, chemistry, biophysics, and sometimes even medicine, influencing treatments and therapies for patients. Bioinformatics and high-throughput biological data coming from different sources can even be more helpful, because each of these different data chunks can provide alternative, complementary information about a specific biological phenomenon, similar to multiple photos of the same subject taken from different angles. In this context, the integration of bioinformatics and high-throughput biological data gets a pivotal role in running a successful bioinformatics study. In the last decades, data originating from proteomics, metabolomics, metagenomics, phenomics, transcriptomics, and epigenomics have been labelled -omics data, as a unique name to refer to them, and the integration of these omics data has gained importance in all biological areas. Even if this omics data integration is useful and relevant, due to its heterogeneity, it is not uncommon to make mistakes during the integration phases. We therefore decided to present these ten quick tips to perform an omics data integration correctly, avoiding common mistakes we experienced or noticed in published studies in the past. Even if we designed our ten guidelines for beginners, by using a simple language that (we hope) can be understood by anyone, we believe our ten recommendations should be taken into account by all the bioinformaticians performing omics data integration, including experts.}, } @article {pmid37410634, year = {2023}, author = {López-Sánchez, R and Hernández-Oaxaca, D and Escobar-Zepeda, A and Ramos Cerrillo, B and López-Munguía, A and Segovia, L}, title = {Analysing the dynamics of the bacterial community in pozol, a Mexican fermented corn dough.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {7}, pages = {}, pmid = {37410634}, issn = {1465-2080}, mesh = {*Zea mays/microbiology ; Mexico ; *Bacteria/genetics ; Streptococcus/metabolism ; Fermentation ; }, abstract = {Pozol is a traditional prehispanic Mexican beverage made from fermented nixtamal dough; it is still part of everyday life in many communities due to its nutritional properties. It is the product of spontaneous fermentation and has a complex microbiota composed primarily of lactic acid bacteria (LAB). Although this is a beverage that has been used for centuries, the microbial processes that participate in this fermented beverage are not well understood. We fermented corn dough to produce pozol and sampled it at four key times to follow the community and metabolic changes (0, 9 24 and 48 h) by shotgun metagenomic sequencing to determine structural changes in the bacterial community, as well as metabolic genes used for substrate fermentation, nutritional properties and product safety. We found a core of 25 abundant genera throughout the 4 key fermentation times, with the genus Streptococcus being the most prevalent throughout fermentation. We also performed an analysis focused on metagenomic assembled genomes (MAGs) to identify species from the most abundant genera. Genes involving starch, plant cell wall (PCW), fructan and sucrose degradation were found throughout fermentation and in MAGs, indicating the metabolic potential of the pozol microbiota to degrade these carbohydrates. Complete metabolic modules responsible for amino acid and vitamin biosynthesis increased considerably during fermentation, and were also found to be abundant in MAG, highlighting the bacterial contribution to the well-known nutritional properties attributed to pozol. Further, clusters of genes containing CAZymes (CGCs) and essential amino acids and vitamins were found in the reconstructed MAGs for abundant species in pozol. The results of this study contribute to our understanding of the metabolic role of micro-organisms in the transformation of corn to produce this traditional beverage and their contribution to the nutritional impact that pozol has had for centuries in the traditional cuisine of southeast Mexico.}, } @article {pmid37409977, year = {2023}, author = {Fan, Q and Zhang, J and Shi, H and Chang, S and Hou, F}, title = {Metagenomic Profiles of Yak and Cattle Manure Resistomes in Different Feeding Patterns before and after Composting.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0064523}, pmid = {37409977}, issn = {1098-5336}, mesh = {Animals ; Humans ; Cattle ; *Genes, Bacterial ; *Composting ; Manure/microbiology ; Metagenomics ; Drug Resistance, Microbial/genetics ; Metals ; Anti-Bacterial Agents/pharmacology ; Livestock ; }, abstract = {Antibiotic resistance is a global threat to public health, with antibiotic resistance genes (ARGs) being one of the emerging contaminants; furthermore, animal manure is an important reservoir of biocide resistance genes (BRGs) and metal resistance genes (MRGs). However, few studies have reported differences in the abundance and diversity of BRGs and MRGs between different types of animal manure and the changes in BRGs and MRGs before and after composting. This study employed a metagenomics-based approach to investigate ARGs, BRGs, MRGs, and mobile genetic elements (MGEs) of yak and cattle manure before and after composting under grazing and intensive feeding patterns. The total abundances of ARGs, clinical ARGs, BRGs, MRGs, and MGEs were lower in the manure of grazing livestock than in the manure of the intensively fed group. After composting, the total abundances of ARGs, clinical ARGs, and MGEs in intensively fed livestock manure decreased, whereas those of ARGs, clinical ARGs, MRGs, and MGEs increased in grazing livestock manure. The synergy between MGEs mediated horizontal gene transfer and vertical gene transmission via host bacteria proliferation, which was the main driver that altered the abundance and diversity of ARGs, BRGs, and MRGs in livestock manure and compost. Additionally, tetQ, IS91, mdtF, and fabK were potential indicators for estimating the total abundance of clinical ARGs, BRGs, MRGs, and MGEs in livestock manure and compost. These findings suggest that grazing livestock manure can be directly discharged into the fields, whereas intensively fed livestock manure should be composted before returning to the field. IMPORTANCE The recent increase in the prevalence of antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), and metal resistance genes (MRGs) in livestock manure poses risks to human health. Composting is known to be a promising technology for reducing the abundance of resistance genes. This study investigated the differences and changes in the abundances of ARGs, BRGs, and MRGs between yak and cattle manure under grazing and intensive feeding patterns before and after composting. The results indicate that the feeding pattern significantly affected the abundances of resistance genes in livestock manure. Manure in intensive farming should be composted before being discharged into the field, while grazing livestock manure is not suitable for composting due to an increased number of resistance genes.}, } @article {pmid37409950, year = {2023}, author = {Huang, R and Wang, Y and Liu, D and Wang, S and Lv, H and Yan, Z}, title = {Long-Read Metagenomics of Marine Microbes Reveals Diversely Expressed Secondary Metabolites.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0150123}, pmid = {37409950}, issn = {2165-0497}, mesh = {*Metagenomics/methods ; *Bacteria/genetics ; Metagenome ; Archaea/genetics ; Bacteroidetes/genetics ; }, abstract = {Microbial secondary metabolites play crucial roles in microbial competition, communication, resource acquisition, antibiotic production, and a variety of other biotechnological processes. The retrieval of full-length BGC (biosynthetic gene cluster) sequences from uncultivated bacteria is difficult due to the technical constraints of short-read sequencing, making it impossible to determine BGC diversity. Using long-read sequencing and genome mining, 339 mainly full-length BGCs were recovered in this study, illuminating the wide range of BGCs from uncultivated lineages discovered in seawater from Aoshan Bay, Yellow Sea, China. Many extremely diverse BGCs were discovered in bacterial phyla such as Proteobacteria, Bacteroidota, Acidobacteriota, and Verrucomicrobiota as well as the previously uncultured archaeal phylum "Candidatus Thermoplasmatota." The data from metatranscriptomics showed that 30.1% of secondary metabolic genes were being expressed, and they also revealed the expression pattern of BGC core biosynthetic genes and tailoring enzymes. Taken together, our results demonstrate that long-read metagenomic sequencing combined with metatranscriptomic analysis provides a direct view into the functional expression of BGCs in environmental processes. IMPORTANCE Genome mining of metagenomic data has become the preferred method for the bioprospecting of novel compounds by cataloguing secondary metabolite potential. However, the accurate detection of BGCs requires unfragmented genomic assemblies, which have been technically difficult to obtain from metagenomes until recently with new long-read technologies. We used high-quality metagenome-assembled genomes generated from long-read data to determine the biosynthetic potential of microbes found in the surface water of the Yellow Sea. We recovered 339 highly diverse and mostly full-length BGCs from largely uncultured and underexplored bacterial and archaeal phyla. Additionally, we present long-read metagenomic sequencing combined with metatranscriptomic analysis as a potential method for gaining access to the largely underutilized genetic reservoir of specialized metabolite gene clusters in the majority of microbes that are not cultured. The combination of long-read metagenomic and metatranscriptomic analyses is significant because it can more accurately assess the mechanisms of microbial adaptation to the environment through BGC expression based on metatranscriptomic data.}, } @article {pmid37409823, year = {2023}, author = {Mukherjee, A and Tikariha, H and Bandla, A and Pavagadhi, S and Swarup, S}, title = {Global analyses of biosynthetic gene clusters in phytobiomes reveal strong phylogenetic conservation of terpenes and aryl polyenes.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0038723}, pmid = {37409823}, issn = {2379-5077}, mesh = {Phylogeny ; *Terpenes ; Secondary Metabolism/genetics ; *Metagenome/genetics ; Multigene Family/genetics ; }, abstract = {There are gaps in our understandings on how did the evolutionary relationships among members of the phytobiomes shape their ability to produce tremendously complex specialized metabolites under the influence of plant host. To determine these relationships, we investigated the phylogenetic conservation of biosynthetic gene clusters (BGCs) on a global collection of 4,519 high-quality and nonredundant (out of 12,181) bacterial isolates and metagenome-assembled genomes from 47 different plant hosts and soil, by adopting three independent phylogenomic approaches (D-test, Pagel's λ, and consenTRAIT). We report that the BGCs are phylogenetically conserved to varying strengths and depths in their different classes. We show that the ability to produce specialized metabolites qualifies as a complex trait, and the depth of conservation is equivalent to ecologically relevant complex microbial traits. Interestingly, terpene and aryl polyene BGCs had the strongest phylogenetic conservation in the phytobiomes, but not in the soil microbiomes. Furthermore, we showed that terpenes are largely uncharacterized in phytobiomes and pinpointed specific clades that harbor potentially novel terpenes. Taken together, this study sheds light on the evolution of specialized metabolites' biosynthesis potential in phytobiomes under the influence of plant hosts and presents strategies to rationally guide the discovery of potentially novel classes of metabolites. IMPORTANCE This study expands our understandings of the biosynthetic potential of phytobiomes by using such worldwide and extensive collection of microbiomes from plants and soil. Apart from providing such vital resource for the plant microbiome researchers, this study provides fundamental insights into the evolution of biosynthetic gene clusters (BGCs) in phytobiomes under the influence of plant host. Specifically, we report that the strength of phylogenetic conservation in microbiomes varies for different classes of BGCs and is influenced as a result of plant host association. Furthermore, our results indicate that biosynthetic potential of specialized metabolites is deeply conserved equivalent to other complex and ecologically relevant microbial traits. Finally, for the most conserved class of specialized metabolites (terpenes), we identified clades harboring potentially novel class of molecules. Future studies could focus on plant-microbe coevolution and interactions through specialized metabolites building upon these findings.}, } @article {pmid37409242, year = {2023}, author = {Yang, X and Liu, Z and Liu, X and Li, Q and Huang, H and Li, R and He, M}, title = {Chlamydia Psittaci Pneumonia-Induced Myocarditis: A Case Report.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {4259-4264}, pmid = {37409242}, issn = {1178-6973}, abstract = {The incidence of Chlamydia psittaci infection has been reported to increase in recent years. The presentation of psittacosis infection varied widely, from none to severe symptoms. Mainly, psittacosis infection presents with pulmonary manifestations. Here, we report the case of a 60-year-old female patient with Chlamydia psittaci pneumonia complicated by myocarditis. After administering antibiotics, the patient recovered from severe atypical pneumonia and myocarditis. In general, Chlamydia psittaci rarely induces myocarditis. Moreover, the optimal therapeutic strategies remain unclear for such cases, especially with a high troponin T level. Metagenomic Next-Generation Sequencing (mNGS) can provide a quick and effective diagnosis of Chlamydia psittaci pneumonia; early intervention (antibiotic therapy and nutritional supplements for myocarditis) favors a good outcome, although complications may worsen the condition. Therefore, more studies are required to help improve understanding of the disease.}, } @article {pmid37408612, year = {2023}, author = {Sun, H and Chen, R and Li, T and Gao, J and Gu, X and Zhu, X and Jin, L and Shi, Y and Li, Q}, title = {Combination of transbronchial cryobiopsy based clinic-radiologic-pathologic strategy and metagenomic next-generation sequencing for differential diagnosis of rapidly progressive diffuse parenchymal lung diseases.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1204024}, pmid = {37408612}, issn = {2235-2988}, mesh = {Humans ; Male ; Middle Aged ; Retrospective Studies ; Diagnosis, Differential ; Biopsy/methods ; China ; *Lung Diseases, Interstitial/diagnosis/pathology ; High-Throughput Nucleotide Sequencing ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: The complicated spectrum of rapidly progressive diffused parenchymal lung diseases (RP-DPLD) creates obstacles to the precise diagnosis and treatment. We evaluated the differential diagnostic value of transbronchial cryobiopsy (TBCB) based clinic-radiologic-pathologic (CRP) strategy combined with bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) in RP-DPLD patients.

METHODS: RP-DPLD patients who underwent the diagnostic strategy of TBCB-based CRP combined with BALF mNGS at Shanghai East Hospital from May 2020 to Oct 2022 were retrospectively analyzed. Clinical characteristics were summarized, including demographic data, high-resolution computed tomography (HRCT) findings, histopathology of TBCB and microbiological results. Diagnostic value of the combined strategy, as well as the sensitivity, specificity, and positive detection rates of mNGS were evaluated.

RESULTS: A total of 115 RP-DPLD patients were enrolled, with a mean age of 64.4 years old and a male proportion of 54.8%. The pulmonary imaging findings in most patients were complex and diverse, with all patients showing bilateral lung diffuse lesions in HRCT, and progressively aggravated imaging changes within one month. After combining TBCB-based CRP strategy with mNGS, all participants received a corresponding diagnosis with 100% diagnostic yield. In these patients, 58.3% (67/115) were diagnosed with noninfectious RP-DPLD and 41.7% (48/115) with infection-related RP-DPLD. There were 86.1% of cases with known etiology according to the DPLD classification. BALF mNGS and traditional pathogen detection methods were performed in all patients, the positive detection rates were 50.4% (58/115) and 32.2% (37/115), respectively. Meanwhile, the mNGS showed significantly higher sensitivity and negative predictive value than the traditional pathogen detection methods for the diagnosis of infection-related RP-DPLD (100% vs 60.4% (p<0.001), 100% vs 75.6% (p<0.001), respectively). Among noninfectious RP-DPLD patients, the true negative rate of mNGS was 85.1% (57/67). All patients had their treatment regimen modified and the 30-day mortality was 7.0%.

CONCLUSION: The novel strategy of TBCB-based CRP combined with mNGS provided dependable and sufficient evidence for the diagnosis, meanwhile further improved the accuracy of RP-DPLD treatment, as well as the prognosis of patients. Our results highlight the significant value of combined strategy in determining whether the RP-DPLD patients were infection associated or not.}, } @article {pmid37406708, year = {2023}, author = {Zheng, X and Zhong, Z and Xu, Y and Lin, X and Cao, Z and Yan, Q}, title = {Response of heavy-metal and antibiotic resistance genes and their related microbe in rice paddy irrigated with treated municipal wastewaters.}, journal = {The Science of the total environment}, volume = {896}, number = {}, pages = {165249}, doi = {10.1016/j.scitotenv.2023.165249}, pmid = {37406708}, issn = {1879-1026}, mesh = {Humans ; Anti-Bacterial Agents/analysis ; Wastewater ; *Oryza/genetics ; Genes, Bacterial ; *Metals, Heavy/analysis ; Drug Resistance, Microbial/genetics ; Soil ; }, abstract = {Paddy irrigation with secondary effluents from municipal wastewater treatment plants (MWTPs) is a well-established practice to alleviate water scarcity. However, the reuse might lead to more complicated contamination caused by interactions between residual antibiotics in effluents and heavy metals in paddy soil. To date, no information is available for the potential effects of dual stress of heavy metals and antibiotics on heavy-metal resistance genes (MRGs) and antibiotic resistance genes (ARGs). Here, this study investigated the response of heavy metal and antibiotic resistance genes, and related microorganisms to the dual threat of antibiotics and heavy metals under the long-term MWTP effluent irrigation for rice paddy using metagenome. The results showed that there was not a negative effect on rice consumption if MWTP effluent was used to irrigate rice for a long time. The concentration of antibiotics could reshape the ARGs and MRG profiles in rice paddy soil. The findings revealed the co-occurrence of ARGs and MRGs in rice paddy soils, thus highlighting the need for simultaneous elimination of antibiotics and heavy metals to effectively reduce ARGs and MRGs. Acn and sul1 genes encoding Iron and sulfonamides resistance mechanisms are the most abundant MRG and ARG, respectively. Network analysis revealed the possibility that IntI1 plays a role in the co-transmission of MRG and ARG to host microbes, and that Proteobacteria are the most dominant hosts for MRG, ARG, and integrons. The presence of antibiotics in irrigated MWTP effluents has been found to stimulate the proliferation of heavy metal and antibiotic resistances by altering soil microbial communities. This study will enhance our comprehension of the co-selection between ARGs and MRGs, as well as reveal the concealed environmental impacts of combined pollution. The obtained results have important implications for food safety and human health in rice.}, } @article {pmid37406691, year = {2023}, author = {Wang, M and Wang, H and Hu, C and Deng, J and Shi, B}, title = {Phthalate acid esters promoted the enrichment of chlorine dioxide-resistant bacteria and their functions related to human diseases in rural polyvinyl chloride distribution pipes.}, journal = {The Science of the total environment}, volume = {896}, number = {}, pages = {165282}, doi = {10.1016/j.scitotenv.2023.165282}, pmid = {37406691}, issn = {1879-1026}, mesh = {Humans ; *Disinfectants/pharmacology ; Polyvinyl Chloride ; *Drinking Water ; *Chlorine Compounds/pharmacology ; Disinfection/methods ; Bacteria ; Esters ; Chlorine/pharmacology ; }, abstract = {Polyvinyl chloride (PVC) pipes are widely used as drinking water distribution pipes in rural areas of China. However, whether phthalate acid esters (PAEs) released from PVC pipes will affect tap water quality is still unknown. The influence of released PAEs on the water quality was analysed in this study, especially after ClO2 disinfection. The results indicated that ClO2 disinfection could control the growth of total coliforms and heterotrophic bacteria (HPC). However, when the ClO2 residual decreased to below 0.10 mg/L, HPC and opportunistic pathogens, including Mycobacterium avium and Pseudomonas aeruginosa, increased significantly. In addition, after ClO2 disinfection, PAEs concentrations increased from 10.6-22.2 μg/L to 21.2-58.8 μg/L in different sampling cites. Linear discriminant analysis (LDA) effect size (LEfSe) and statistical analysis of metagenomic profiles (Stamp) showed that ClO2 disinfection induced the enrichment of Pseudomonas, Bradyrhizobium, and Mycobacterium and functions related to human diseases, such as pathogenic Escherichia coli infection, shigellosis, Staphylococcus aureus infection, and Vibrio cholerae infection. The released PAEs not only promoted the growth of these ClO2-resistant bacterial genera but also enhanced their functions related to human diseases. Moreover, these PAEs also induced the enrichment of other bacterial genera, such as Blastomonas, Dechloromonas, and Kocuria, and their functions, such as chronic myeloid leukaemia, African trypanosomiasis, leishmaniasis, hepatitis C and human T-cell leukaemia virus 1 infection. The released PAEs enhanced the microbial risk of the drinking water. These results are meaningful for guaranteeing water quality in rural areas of China.}, } @article {pmid37406526, year = {2023}, author = {Meng, J and Li, W and Diao, C and Li, Z and Zhao, J and Haider, G and Zhang, H and Xu, J and Hu, M and Shan, S and Chen, H}, title = {Microplastics drive microbial assembly, their interactions, and metagenomic functions in two soils with distinct pH and heavy metal availability.}, journal = {Journal of hazardous materials}, volume = {458}, number = {}, pages = {131973}, doi = {10.1016/j.jhazmat.2023.131973}, pmid = {37406526}, issn = {1873-3336}, mesh = {Microplastics ; Soil ; Plastics ; *Metals, Heavy/analysis ; Bacteria ; *Microbiota ; Hydrogen-Ion Concentration ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Microplastics (MPs) have emerged as widely existing global environmental concerns in terrestrial ecosystems. However, the mechanisms that how MPs are affecting soil microbes and their metagenomic functioning is currently uncertain. Herein, we investigated the response mechanisms of bacterial and fungal communities as well as the metagenomic functions to the addition of MPs in two soils with distinct pH and heavy metals. In this study, the acidic soil (Xintong) and the neutral soil (Huanshan) contaminated by heavy metals were incubated with Polyvinyl Chloride (PVC) MPs at ratios of 2.5% and 5% on 60 and 120 days. We aimed to evaluate the responding, assembly, and interactions of the metagenomic taxonomy and function. Results showed that only in the acidic soil, PVC MPs significantly increased soil pH and decreased CaCl2-extractable heavy metals, and also reduced bacterial alpha diversity and interaction networks. The relative proportions of Proteobacteria and Bacteroidota in bacteria, and Mortierellomycota in fungi, were increased, but Chloroflexi and Acidobacteriota in bacteria, Ascomycota and Basidiomycota in fungi, were significantly decreased by PVC MPs. Metagenomic functions related to C cycling were repressed but the nutrient cycles were enriched with PVC MPs. In conclusion, our study suggests that the addition of PVC MPs could shift soil microbial community and metagenomic functioning, as well as increasing soil pH and reduced heavy metal availability.}, } @article {pmid37406521, year = {2023}, author = {Zeng, J and Pan, Y and Hu, R and Liu, F and Gu, H and Ding, J and Liu, S and Liu, S and Yang, X and Peng, Y and Tian, Y and He, Q and Wu, Y and Yan, Q and Shu, L and He, Z and Wang, C}, title = {The vertically-stratified resistomes in mangrove sediments was driven by the bacterial diversity.}, journal = {Journal of hazardous materials}, volume = {458}, number = {}, pages = {131974}, doi = {10.1016/j.jhazmat.2023.131974}, pmid = {37406521}, issn = {1873-3336}, mesh = {Humans ; *Genes, Bacterial ; Bacteria/genetics ; Anti-Bacterial Agents ; *Microbiota ; }, abstract = {Early evidence has elucidated that the spread of antibiotic (ARGs) and metal resistance genes (MRGs) are mainly attributed to the selection pressure in human-influenced environments. However, whether and how biotic and abiotic factors mediate the distribution of ARGs and MRGs in mangrove sediments under natural sedimentation is largely unclear. Here, we profiled the abundance and diversity of ARGs and MRGs and their relationships with sedimental microbiomes in 0-100 cm mangrove sediments. Our results identified multidrug-resistance and multimetal-resistance as the most abundant ARG and MRG classes, and their abundances generally decreased with the sediment depth. Instead of abiotic factors such as nutrients and antibiotics, the bacterial diversity was significantly negatively correlated with the abundance and diversity of resistomes. Also, the majority of resistance classes (e.g., multidrug and arsenic) were carried by more diverse bacterial hosts in deep layers with low abundances of resistance genes. Together, our results indicated that bacterial diversity was the most important biotic factor driving the vertical profile of ARGs and MRGs in the mangrove sediment. Given that there is a foreseeable increasing human impact on natural environments, this study emphasizes the important role of biodiversity in driving the abundance and diversity of ARGs and MRGs.}, } @article {pmid37406125, year = {2023}, author = {Hou, J and Wang, Y and Zhu, P and Yang, N and Liang, L and Yu, T and Niu, M and Konhauser, K and Woodcroft, BJ and Wang, F}, title = {Taxonomic and carbon metabolic diversification of Bathyarchaeia during its coevolution history with early Earth surface environment.}, journal = {Science advances}, volume = {9}, number = {27}, pages = {eadf5069}, pmid = {37406125}, issn = {2375-2548}, mesh = {*Carbon/metabolism ; *Metabolic Networks and Pathways ; }, abstract = {Bathyarchaeia, as one of the most abundant microorganisms on Earth, play vital roles in the global carbon cycle. However, our understanding of their origin, evolution, and ecological functions remains poorly constrained. Here, we present the largest dataset of Bathyarchaeia metagenome assembled genome to date and reclassify Bathyarchaeia into eight order-level units corresponding to the former subgroup system. Highly diversified and versatile carbon metabolisms were found among different orders, particularly atypical C1 metabolic pathways, indicating that Bathyarchaeia represent overlooked important methylotrophs. Molecular dating results indicate that Bathyarchaeia diverged at ~3.3 billion years, followed by three major diversifications at ~3.0, ~2.5, and ~1.8 to 1.7 billion years, likely driven by continental emergence, growth, and intensive submarine volcanism, respectively. The lignin-degrading Bathyarchaeia clade emerged at ~300 million years perhaps contributed to the sharply decreased carbon sequestration rate during the Late Carboniferous period. The evolutionary history of Bathyarchaeia potentially has been shaped by geological forces, which, in turn, affected Earth's surface environment.}, } @article {pmid37405923, year = {2023}, author = {Ochkalova, S and Tolstoganov, I and Lapidus, A and Korobeynikov, A}, title = {Protocol for refining metagenomic binning with BinSPreader.}, journal = {STAR protocols}, volume = {4}, number = {3}, pages = {102417}, pmid = {37405923}, issn = {2666-1667}, abstract = {The analysis of metagenomic data obtained via high-throughput DNA sequencing is primarily carried out by a dedicated binning process involving clustering contigs, presumably belonging to the same species. Here, we present a protocol for improving the quality of binning using BinSPreader. We describe steps for typical metagenome assembly and binning workflow. We then detail binning refining, its variants, output, and possible caveats. This protocol optimizes the process of reconstructing more complete genomes of microorganisms that make up the metagenome. For complete details on the use and execution of this protocol, please refer to Tolstoganov et al.[1].}, } @article {pmid37405310, year = {2023}, author = {Valdes, C and Stebliankin, V and Ruiz-Perez, D and Park, JI and Lee, H and Narasimhan, G}, title = {Microbiome maps: Hilbert curve visualizations of metagenomic profiles.}, journal = {Frontiers in bioinformatics}, volume = {3}, number = {}, pages = {1154588}, pmid = {37405310}, issn = {2673-7647}, abstract = {Abundance profiles from metagenomic sequencing data synthesize information from billions of sequenced reads coming from thousands of microbial genomes. Analyzing and understanding these profiles can be a challenge since the data they represent are complex. Particularly challenging is their visualization, as existing techniques are inadequate when the taxa number is in the thousands. We present a technique, and accompanying software, for the visualization of metagenomic abundance profiles using a space-filling curve that transforms a profile into an interactive 2D image. We created Jasper, an easy to use tool for the visualization and exploration of metagenomic profiles from DNA sequencing data. It orders taxa using a space-filling Hilbert curve, and creates a "Microbiome Map", where each position in the image represents the abundance of a single taxon from a reference collection. Jasper can order taxa in multiple ways, and the resulting microbiome maps can highlight "hot spots" of microbes that are dominant in taxonomic clades or biological conditions. We use Jasper to visualize samples from a variety of microbiome studies, and discuss ways in which microbiome maps can be an invaluable tool to visualize spatial, temporal, disease, and differential profiles. Our approach can create detailed microbiome maps involving hundreds of thousands of microbial reference genomes with the potential to unravel latent relationships (taxonomic, spatio-temporal, functional, and other) that could remain hidden using traditional visualization techniques. The maps can also be converted into animated movies that bring to life the dynamicity of microbiomes.}, } @article {pmid37405169, year = {2023}, author = {Røyseth, V and Hurysz, BM and Kaczorowska, AK and Dorawa, S and Fedøy, AE and Arsın, H and Serafim, MSM and Myers, SA and Werbowy, O and Kaczorowski, T and Stokke, R and O'Donoghue, AJ and Steen, IH}, title = {Activation mechanism and activity of globupain, a thermostable C11 protease from the Arctic Mid-Ocean Ridge hydrothermal system.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1199085}, pmid = {37405169}, issn = {1664-302X}, abstract = {Deep-sea hydrothermal vents offer unique habitats for heat tolerant enzymes with potential new enzymatic properties. Here, we present the novel C11 protease globupain, which was prospected from a metagenome-assembled genome of uncultivated Archaeoglobales sampled from the Soria Moria hydrothermal vent system located on the Arctic Mid-Ocean Ridge. Sequence comparisons against the MEROPS-MPRO database showed that globupain has the highest sequence identity to C11-like proteases present in human gut and intestinal bacteria. Successful recombinant expression in Escherichia coli of the wild-type zymogen and 13 mutant substitution variants allowed assessment of residues involved in maturation and activity of the enzyme. For activation, globupain required the addition of DTT and Ca[2+]. When activated, the 52kDa proenzyme was processed at K137 and K144 into a 12kDa light- and 32kDa heavy chain heterodimer. A structurally conserved H132/C185 catalytic dyad was responsible for the proteolytic activity, and the enzyme demonstrated the ability to activate in-trans. Globupain exhibited caseinolytic activity and showed a strong preference for arginine in the P1 position, with Boc-QAR-aminomethylcoumarin (AMC) as the best substrate out of a total of 17 fluorogenic AMC substrates tested. Globupain was thermostable (Tm activated enzyme = 94.51°C ± 0.09°C) with optimal activity at 75°C and pH 7.1. Characterization of globupain has expanded our knowledge of the catalytic properties and activation mechanisms of temperature tolerant marine C11 proteases. The unique combination of features such as elevated thermostability, activity at relatively low pH values, and ability to operate under high reducing conditions makes globupain a potential intriguing candidate for use in diverse industrial and biotechnology sectors.}, } @article {pmid37404664, year = {2023}, author = {Shi, H and Li, H and Zheng, L and Qian, W and Wang, Z and Xie, L and Yang, Z and Zheng, L and Chen, C and Yang, X and Bao, X}, title = {Metagenomic next-generation sequencing for the diagnosis of oral and maxillofacial space infections.}, journal = {Journal of dental sciences}, volume = {18}, number = {3}, pages = {1199-1205}, pmid = {37404664}, issn = {2213-8862}, abstract = {BACKGROUND/PURPOSE: Metagenomic next-generation sequencing (mNGS) has been widely used for the detection of pathogens causing infectious diseases. This study aimed to evaluate the potential ability of mNGS to detect pathogens causing oral and maxillofacial space infection (OMSI) and compare the results with those of the traditional diagnostic microbial culture method.

MATERIALS AND METHODS: We retrospectively reviewed the data of 218 patients diagnosed with OMSI who underwent microbial culture and mNGS at the Department of Oral Surgery, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, from July 2020 to January 2022.

RESULTS: The positivity rate of mNGS (216 cases) was significantly higher than that of microbial culture (123 cases). The most frequently detected bacteria were different between these two detection methods. Streptococcus constellatus (16.05%, 35), Streptococcus anginosus (15.69%, 34) and Klebsiella pneumoniae (6.88%, 15) were the most commonly isolated bacteria by culture. However, Peptostreptococcus stomatis (61.47%, 134), Parvimonas micra (68.35%, 149) and Streptococcus constellatus (57.34%, 125) were the most commonly detected bacteria by mNGS. mNGS also has advantages in diagnosing viral infections. The optimal numbers of diagnostic reads were 1162 and 588 for the diagnosis of Streptococcus anginosus and Streptococcus constellatus infections, respectively. Read numbers were significantly correlated with C-reactive protein (CRP), procalcitonin (PCT), and blood glucose levels and neutrophil percentage (NEUT%).

CONCLUSION: For pathogens causing OMSI, mNGS had a higher rate of microbial pathogen detection and remarkable advantages in identifying coinfections involving viruses and fungi. The read numbers for mNGS are important for diagnostic accuracy and disease severity evaluation.}, } @article {pmid37404554, year = {2023}, author = {Shen, H and Cai, X and Liu, J and Yan, G and Ye, Y and Dong, R and Wu, J and Li, L and Shen, Q and Ma, Y and Ou, Q and Shen, M and Chen, W and Lu, G}, title = {Case report: The clinical utility of metagenomic next-generation sequencing in mucormycosis diagnosis caused by fatal Lichtheimia ramosa infection in pediatric neuroblastoma.}, journal = {Frontiers in pediatrics}, volume = {11}, number = {}, pages = {1130775}, pmid = {37404554}, issn = {2296-2360}, abstract = {Lichtheimia ramosa (L. ramosa) is an opportunistic fungal pathogen of the order Mucorales that may result in a rare but serious mucormycosis infection. Mucormycosis could be angioinvasive, causing thrombosis and necrosis in the nose, brain, digestive tract, and respiratory tract. The infection is highly lethal, especially in immunocompromised hosts, and the incidence has been on the rise. However, due to its relatively low incidence in pediatric population and the challenges with diagnosis, the awareness and management experience for pediatric mucormycosis are extremely limited, which might lead to poor outcomes. In this study, we comprehensively reviewed the course of a fatal rhinocerebral mucormycosis case in a pediatric neuroblastoma patient receiving chemotherapy. Due to a lack of awareness of the infection, the standard care of amphotericin B treatment was delayed and not administered until the identification of L. ramosa by metagenomic next-generation sequencing (mNGS)-based pan-pathogen detection of the patient's peripheral blood sample. We also reviewed the literature on L. ramosa infection cases reported worldwide between 2010 and 2022, with an analysis of clinical manifestation, prognosis, and epidemiological data. Our study not only highlighted the clinical value of comprehensive mNGS in rapid pathogen detection but also raised awareness of recognizing lethal fungal infection early in immunocompromised hosts including pediatric cancer patients.}, } @article {pmid37404190, year = {2023}, author = {Kosmopoulos, JC and Campbell, DE and Whitaker, RJ and Wilbanks, EG}, title = {Horizontal Gene Transfer and CRISPR Targeting Drive Phage-Bacterial Host Interactions and Coevolution in "Pink Berry" Marine Microbial Aggregates.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0017723}, pmid = {37404190}, issn = {1098-5336}, support = {T32 DK077653-29//HHS | National Institutes of Health (NIH)/ ; }, mesh = {Humans ; *Bacteriophages/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats ; Gene Transfer, Horizontal ; Fruit ; Host Microbial Interactions ; }, abstract = {Bacteriophages (phages), which are viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics and host evolution. However, the study of phage-host interactions is hindered by a paucity of model systems from natural environments. Here, we investigate phage-host interactions in the "pink berry" consortia, which are naturally occurring, low-diversity, macroscopic bacterial aggregates that are found in the Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data and a comparative genomics approach to identify eight compete phage genomes, infer their bacterial hosts from host-encoded clustered regularly interspaced short palindromic repeats (CRISPRs), and observe the potential evolutionary consequences of these interactions. Seven of the eight phages identified infect known pink berry symbionts, namely, Desulfofustis sp. PB-SRB1, Thiohalocapsa sp. PB-PSB1, and Rhodobacteraceae sp. A2, and they are largely divergent from known viruses. In contrast to the conserved bacterial community structure of pink berries, the distribution of these phages across aggregates is highly variable. Two phages persisted over a period of seven years with high sequence conservation, allowing us to identify gene gain and loss. Increased nucleotide variation in a conserved phage capsid gene that is commonly targeted by host CRISPR systems suggests that CRISPRs may drive phage evolution in pink berries. Finally, we identified a predicted phage lysin gene that was horizontally transferred to its bacterial host, potentially via a transposon intermediary. Taken together, our results demonstrate that pink berry consortia contain diverse and variable phages as well as provide evidence for phage-host coevolution via multiple mechanisms in a natural microbial system. IMPORTANCE Phages, which are viruses that infect bacteria, are important components of all microbial systems, in which they drive the turnover of organic matter by lysing host cells, facilitate horizontal gene transfer (HGT), and coevolve with their bacterial hosts. Bacteria resist phage infection, which is often costly or lethal, through a diversity of mechanisms. One of these mechanisms is CRISPR systems, which encode arrays of phage-derived sequences from past infections to block subsequent infection with related phages. Here, we investigate the bacteria and phage populations from a simple marine microbial community, known as "pink berries", found in salt marshes of Falmouth, Massachusetts, as a model of phage-host coevolution. We identify eight novel phages and characterize a case of putative CRISPR-driven phage evolution as well as an instance of HGT between a phage and its host, together suggesting that phages have large evolutionary impacts in a naturally occurring microbial community.}, } @article {pmid37404187, year = {2023}, author = {Fu, Y and Xu, R and Yang, B and Wu, Y and Xia, L and Tawfik, A and Meng, F}, title = {Mediation of Bacterial Interactions via a Novel Membrane-Based Segregator to Enhance Biological Nitrogen Removal.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0070923}, pmid = {37404187}, issn = {1098-5336}, mesh = {*Sewage/microbiology ; *Wastewater ; Waste Disposal, Fluid/methods ; Denitrification ; Nitrogen/metabolism ; RNA, Ribosomal, 16S/metabolism ; Bacteria ; Bioreactors/microbiology ; Oxygen/metabolism ; Membranes, Artificial ; }, abstract = {The regulation of microbial subpopulations in wastewater treatment plants (WWTPs) with desired functions can guarantee nutrient removal. In nature, "good fences make good neighbors," which can be applied to engineering microbial consortia. Herein, a membrane-based segregator (MBSR) was proposed, where porous membranes not only promote the diffusion of metabolic products but also isolate incompatible microbes. The MBSR was integrated with an anoxic/aerobic membrane bioreactor (i.e., an experimental MBR). The long-term operation showed that the experimental MBR exhibited higher nitrogen removal (10.45 ± 2.73 mg/L total nitrogen) than the control MBR (21.68 ± 4.23 mg/L) in the effluent. The MBSR resulted in much lower oxygen reduction potential in the anoxic tank of the experimental MBR (-82.00 mV) compared to that of the control MBR (83.25 mV). The lower oxygen reduction potential can inevitably aid in the occurrence of denitrification. The 16S rRNA sequencing showed that the MBSR significantly enriched acidogenic consortia, which yielded considerable volatile fatty acids by fermenting the added carbon sources and allowed efficient transfer of these small molecules to the denitrifying community. Moreover, the sludge communities of the experimental MBR harbored a higher abundance of denitrifying bacteria than those of the control MBR. Metagenomic analysis further corroborated these sequencing results. The spatially structured microbial communities in the experimental MBR system demonstrate the practicability of the MBSR, achieving nitrogen removal efficiency superior to that of mixed populations. Our study provides an engineering method for modulating the assembly and metabolic division of labor of subpopulations in WWTPs. IMPORTANCE This study provides an innovative and applicable method for regulating subpopulations (activated sludge and acidogenic consortia), which contributes to the precise control of the metabolic division of labor in biological wastewater treatment processes.}, } @article {pmid37404184, year = {2023}, author = {Chu, R and Wei, Y and Liu, J and Li, B and Zhang, J and Zhou, Y and Du, Y and Zhang, Y}, title = {A Variant of the Sulfoglycolytic Transketolase Pathway for the Degradation of Sulfoquinovose into Sulfoacetate.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0061723}, pmid = {37404184}, issn = {1098-5336}, mesh = {Humans ; *Transketolase ; *Bacteria/genetics/metabolism ; Alkanesulfonates/metabolism ; Oxidoreductases ; Adenosine Triphosphate ; Sulfur/metabolism ; Ligases ; }, abstract = {Sulfoquinovose (SQ, 6-deoxy-6-sulfo-glucose) constitutes the polar head group of plant sulfolipids and is one of the most abundantly produced organosulfur compounds in nature. Degradation of SQ by bacterial communities contributes to sulfur recycling in many environments. Bacteria have evolved at least four mechanisms for glycolytic degradation of SQ, termed sulfoglycolysis, producing C3 sulfonate (dihydroxypropanesulfonate and sulfolactate) and C2 sulfonate (isethionate) by-products. These sulfonates are further degraded by other bacteria, leading to the mineralization of the sulfonate sulfur. The C2 sulfonate sulfoacetate is widespread in the environment and is also thought to be a product of sulfoglycolysis, although the mechanistic details are yet unknown. Here, we describe a gene cluster in an Acholeplasma sp., from a metagenome derived from deeply circulating subsurface aquifer fluids (GenBank accession no. QZKD01000037), encoding a variant of the recently discovered sulfoglycolytic transketolase (sulfo-TK) pathway that produces sulfoacetate instead of isethionate as a by-product. We report the biochemical characterization of a coenzyme A (CoA)-acylating sulfoacetaldehyde dehydrogenase (SqwD) and an ADP-forming sulfoacetate-CoA ligase (SqwKL), which collectively catalyze the oxidation of the transketolase product sulfoacetaldehyde into sulfoacetate, coupled with ATP formation. A bioinformatics study revealed the presence of this sulfo-TK variant in phylogenetically diverse bacteria, adding to the variety of mechanisms by which bacteria metabolize this ubiquitous sulfo-sugar. IMPORTANCE Many bacteria utilize environmentally widespread C2 sulfonate sulfoacetate as a sulfur source, and the disease-linked human gut sulfate- and sulfite-reducing bacteria can use it as a terminal electron receptor for anaerobic respiration generating toxic H2S. However, the mechanism of sulfoacetate formation is unknown, although it has been proposed that sulfoacetate originates from bacterial degradation of sulfoquinovose (SQ), the polar head group of sulfolipids present in all green plants. Here, we describe a variant of the recently discovered sulfoglycolytic transketolase (sulfo-TK) pathway. Unlike the regular sulfo-TK pathway that produces isethionate, our biochemical assays with recombinant proteins demonstrated that a CoA-acylating sulfoacetaldehyde dehydrogenase (SqwD) and an ADP-forming sulfoacetate-CoA ligase (SqwKL) in this variant pathway collectively catalyze the oxidation of the transketolase product sulfoacetaldehyde into sulfoacetate, coupled with ATP formation. A bioinformatics study revealed the presence of this sulfo-TK variant in phylogenetically diverse bacteria and interpreted the widespread existence of sulfoacetate.}, } @article {pmid37404173, year = {2023}, author = {Kiledal, EA and Shaw, M and Polson, SW and Maresca, JA}, title = {Metagenomic Analysis of a Concrete Bridge Reveals a Microbial Community Dominated by Halophilic Bacteria and Archaea.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0511222}, pmid = {37404173}, issn = {2165-0497}, mesh = {*Archaea/genetics ; *Microbiota/genetics ; Metagenome ; Sewage ; Sequence Analysis, DNA ; Metagenomics/methods ; Bacteria/genetics ; }, abstract = {Concrete hosts a small but diverse microbiome that changes over time. Shotgun metagenomic sequencing would enable assessment of both the diversity and function of the microbial community in concrete, but a number of unique challenges make this difficult for concrete samples. The high concentration of divalent cations in concrete interferes with nucleic acid extraction, and the extremely low biomass in concrete means that DNA from laboratory contamination may be a large fraction of the sequence data. Here, we develop an improved method for DNA extraction from concrete, with higher yield and lower laboratory contamination. To show that this method provides DNA of sufficient quality and quantity to do shotgun metagenomic sequencing, DNA was extracted from a sample of concrete obtained from a road bridge and sequenced with an Illumina MiSeq system. This microbial community was dominated by halophilic Bacteria and Archaea, with enriched functional pathways related to osmotic stress responses. Although this was a pilot-scale effort, we demonstrate that metagenomic sequencing can be used to characterize microbial communities in concrete and that older concrete structures may host different microbes than recently poured concrete. IMPORTANCE Prior work on the microbial communities of concrete focused on the surfaces of concrete structures such as sewage pipes or bridge pilings, where thick biofilms were easy to observe and sample. Because the biomass inside concrete is so low, more recent analyses of the microbial communities inside concrete used amplicon sequencing methods to describe those communities. However, to understand the activity and physiology of microbes in concrete, or to develop living infrastructure, we must develop more direct methods of community analysis. The method developed here for DNA extraction and metagenomic sequencing can be used for analysis of microbial communities inside concrete and can likely be adapted for other cementitious materials.}, } @article {pmid37404032, year = {2023}, author = {Deschênes, T and Tohoundjona, FWE and Plante, PL and Di Marzo, V and Raymond, F}, title = {Gene-based microbiome representation enhances host phenotype classification.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0053123}, pmid = {37404032}, issn = {2379-5077}, mesh = {Humans ; *Diabetes Mellitus, Type 2/genetics ; *Microbiota/genetics ; Metagenome ; *Gastrointestinal Microbiome/genetics ; Phenotype ; }, abstract = {With the concomitant advances in both the microbiome and machine learning fields, the gut microbiome has become of great interest for the potential discovery of biomarkers to be used in the classification of the host health status. Shotgun metagenomics data derived from the human microbiome is composed of a high-dimensional set of microbial features. The use of such complex data for the modeling of host-microbiome interactions remains a challenge as retaining de novo content yields a highly granular set of microbial features. In this study, we compared the prediction performances of machine learning approaches according to different types of data representations derived from shotgun metagenomics. These representations include commonly used taxonomic and functional profiles and the more granular gene cluster approach. For the five case-control datasets used in this study (Type 2 diabetes, obesity, liver cirrhosis, colorectal cancer, and inflammatory bowel disease), gene-based approaches, whether used alone or in combination with reference-based data types, allowed improved or similar classification performances as the taxonomic and functional profiles. In addition, we show that using subsets of gene families from specific functional categories of genes highlight the importance of these functions on the host phenotype. This study demonstrates that both reference-free microbiome representations and curated metagenomic annotations can provide relevant representations for machine learning based on metagenomic data. IMPORTANCE Data representation is an essential part of machine learning performance when using metagenomic data. In this work, we show that different microbiome representations provide varied host phenotype classification performance depending on the dataset. In classification tasks, untargeted microbiome gene content can provide similar or improved classification compared to taxonomical profiling. Feature selection based on biological function also improves classification performance for some pathologies. Function-based feature selection combined with interpretable machine learning algorithms can generate new hypotheses that can potentially be assayed mechanistically. This work thus proposes new approaches to represent microbiome data for machine learning that can potentiate the findings associated with metagenomic data.}, } @article {pmid37404011, year = {2023}, author = {Rooney, AM and Cochrane, K and Fedsin, S and Yao, S and Anwer, S and Dehmiwal, S and Hota, S and Poutanen, S and Allen-Vercoe, E and Coburn, B and , }, title = {A microbial consortium alters intestinal Pseudomonadota and antimicrobial resistance genes in individuals with recurrent Clostridioides difficile infection.}, journal = {mBio}, volume = {14}, number = {4}, pages = {e0348222}, pmid = {37404011}, issn = {2150-7511}, mesh = {Humans ; Microbial Consortia ; Anti-Bacterial Agents/pharmacology ; *Clostridioides difficile ; *Gastrointestinal Microbiome ; Drug Resistance, Bacterial ; Fecal Microbiota Transplantation ; *Clostridium Infections/therapy/microbiology ; Feces/microbiology ; *Microbiota ; Treatment Outcome ; }, abstract = {Intestinal colonization with pathogens and antimicrobial-resistant organisms (AROs) is associated with increased risk of infection. Fecal microbiota transplant (FMT) has successfully been used to cure recurrent Clostridioides difficile infection (rCDI) and to decolonize intestinal AROs. However, FMT has significant practical barriers to safe and broad implementation. Microbial consortia represent a novel strategy for ARO and pathogen decolonization, with practical and safety advantages over FMT. We undertook an investigator-initiated analysis of stool samples collected from previous interventional studies of a microbial consortium, microbial ecosystem therapeutic (MET-2), and FMT for rCDI before and after treatment. Our aim was to assess whether MET-2 was associated with decreased Pseudomonadota (Proteobacteria) and antimicrobial resistance gene (ARG) burden with similar effects to FMT. Participants were selected for inclusion if baseline stool had Pseudomonadota relative abundance ≥10%. Pre- and post-treatment Pseudomonadota relative abundance, total ARGs, and obligate anaerobe and butyrate-producer relative abundances were determined by shotgun metagenomic sequencing. MET-2 administration had similar effects to FMT on microbiome outcomes. The median Pseudomonadota relative abundance decreased by four logs after MET-2 treatment, a greater decrease than that observed after FMT. Total ARGs decreased, while beneficial obligate anaerobe and butyrate-producer relative abundances increased. The observed microbiome response remained stable over 4 months post-administration for all outcomes. IMPORTANCE Overgrowth of intestinal pathogens and AROs is associated with increased risk of infection. With the rise in antimicrobial resistance, new therapeutic strategies that decrease pathogen and ARO colonization in the gut are needed. We evaluated whether a microbial consortium had similar effects to FMT on Pseudomonadota abundances and ARGs as well as obligate anaerobes and beneficial butyrate producers in individuals with high Pseudomonadota relative abundance at baseline. This study provides support for a randomized, controlled clinical trial of microbial consortia (such as MET-2) for ARO decolonization and anaerobe repletion.}, } @article {pmid37403552, year = {2023}, author = {Pioli, S and Clagnan, E and Chowdhury, AA and Bani, A and Borruso, L and Ventura, M and Tonon, G and Brusetti, L}, title = {Structural and functional microbial diversity in deadwood respond to decomposition dynamics.}, journal = {Environmental microbiology}, volume = {25}, number = {11}, pages = {2351-2367}, doi = {10.1111/1462-2920.16459}, pmid = {37403552}, issn = {1462-2920}, mesh = {*Fungi/genetics ; Forests ; Wood/microbiology ; *Microbiota/genetics ; Bacteria/genetics ; Cellulose ; }, abstract = {We investigated the changes in microbial community diversities and functions in natural downed wood at different decay stages in a natural oak forest in the Italian Alps, through metagenomics analysis and in vitro analysis. Alfa diversity of bacterial communities was affected by the decay stage and log characteristics, while beta diversity was mainly driven by log diameter. Fungal and archaeal beta diversities were affected by the size of the sampled wood (log diameter), although, fungi were prominently driven by wood decay stage. The analysis of genes targeting cell wall degradation revealed higher abundances of cellulose and pectin-degrading enzymes in bacteria, while in fungi the enzymes targeting cellulose and hemicellulose were more abundant. The decay class affected the abundance of single enzymes, revealing a shift in complex hydrocarbons degradation pathways along the decay process. Moreover, we found that the genes related to Coenzyme M biosynthesis to be the most abundant especially at early stages of wood decomposition while the overall methanogenesis did not seem to be influenced by the decay stage. Intra- and inter-kingdom interactions between bacteria and fungi revealed complex pattern of community structure in response to decay stage possibly reflecting both direct and indirect interactions.}, } @article {pmid37403381, year = {2023}, author = {Liu, Y and Wang, X and Xu, J and Yang, Q and Zhu, H and Yang, J}, title = {Diagnostic value of metagenomic next-generation sequencing of lower respiratory tract specimen for the diagnosis of suspected Pneumocystis jirovecii pneumonia.}, journal = {Annals of medicine}, volume = {55}, number = {1}, pages = {2232358}, pmid = {37403381}, issn = {1365-2060}, mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis ; *Epstein-Barr Virus Infections ; Sensitivity and Specificity ; Herpesvirus 4, Human ; High-Throughput Nucleotide Sequencing ; Respiratory System ; }, abstract = {AIM: To evaluate diagnostic performance of metagenomic next-generation sequencing (mNGS) for Pneumocystis jirovecii pneumonia (PCP), in comparison with polymerase chain reaction (PCR), Gomori methenamine silver (GMS) staining and serum 1,3-β-d-Glucan (BG) assay.

METHODS: 52 PCP patients and 103 patients with non-pneumocystic jirovecii pneumonia (non-PCP) were enrolled, and comparative analysis was conducted of different diagnostic tests. Clinical features and co-pathogen characteristics were reviewed.

RESULTS: The diagnostic sensitivity (92.3%) and specificity (87.4%) of mNGS did not show significant differences compared with that of PCR while mNGS had the advantage over PCR in the detection of co-pathogens. Despite its excellent specificity, the sensitivity of GMS staining (9.3%) was inferior to that of mNGS (p < .001). The combination of mNGS with serum BG statistically outperformed mNGS or serum BG alone in the areas under the receiver operating characteristic curves (AUCs, p = .0013 and p = .0015, respectively). Notably, all the blood samples showing positive mNGS for Pneumocystis jirovecii came from PCP patients. The leading co-pathogens among patients with PCP were cytomegalovirus, Epstein-Barr virus and Torque teno virus.

CONCLUSIONS: mNGS shows superiority over several common clinical methods in the diagnosis of suspected PCP. Serum BG in conjunction with mNGS further improved the diagnostic efficacy of mNGS.}, } @article {pmid37403035, year = {2023}, author = {Flütsch, S and Wiestner, F and Butticaz, L and Moor, D and Stölting, KN}, title = {Vibrio-Sequins - dPCR-traceable DNA standards for quantitative genomics of Vibrio spp.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {375}, pmid = {37403035}, issn = {1471-2164}, mesh = {Polymerase Chain Reaction/methods ; *DNA/genetics ; *Genomics ; Base Sequence ; }, abstract = {BACKGROUND: Vibrio spp. are a diverse group of ecologically important marine bacteria responsible for several foodborne outbreaks of gastroenteritis around the world. Their detection and characterization are moving away from conventional culture-based methods towards next generation sequencing (NGS)-based approaches. However, genomic methods are relative in nature and suffer from technical biases arising from library preparation and sequencing. Here, we introduce a quantitative NGS-based method that enables the quantitation of Vibrio spp. at the limit of quantification (LOQ) through artificial DNA standards and their absolute quantification via digital PCR (dPCR).

RESULTS: We developed six DNA standards, called Vibrio-Sequins, together with optimized TaqMan assays for their quantification in individually sequenced DNA libraries via dPCR. To enable Vibrio-Sequin quantification, we validated three duplex dPCR methods to quantify the six targets. LOQs were ranging from 20 to 120 cp/µl for the six standards, whereas the limit of detection (LOD) was ~ 10 cp/µl for all six assays. Subsequently, a quantitative genomics approach was applied to quantify Vibrio-DNA in a pooled DNA mixture derived from several Vibrio species in a proof-of-concept study, demonstrating the increased power of our quantitative genomic pipeline through the coupling of NGS and dPCR.

CONCLUSIONS: We significantly advance existing quantitative (meta)genomic methods by ensuring metrological traceability of NGS-based DNA quantification. Our method represents a useful tool for future metagenomic studies aiming at quantifying microbial DNA in an absolute manner. The inclusion of dPCR into sequencing-based methods supports the development of statistical approaches for the estimation of measurement uncertainties (MU) for NGS, which is still in its infancy.}, } @article {pmid37402745, year = {2023}, author = {Amit, G and Bashan, A}, title = {Top-down identification of keystone taxa in the microbiome.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3951}, pmid = {37402745}, issn = {2041-1723}, mesh = {Humans ; Cross-Sectional Studies ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Microbial Interactions ; }, abstract = {Keystone taxa in ecological communities are native taxa that play an especially important role in the stability of their ecosystem. However, we still lack an effective framework for identifying these taxa from the available high-throughput sequencing without the notoriously difficult step of reconstructing the detailed network of inter-specific interactions. In addition, while most microbial interaction models assume pair-wise relationships, it is yet unclear whether pair-wise interactions dominate the system, or whether higher-order interactions are relevant. Here we propose a top-down identification framework, which detects keystones by their total influence on the rest of the taxa. Our method does not assume a priori knowledge of pairwise interactions or any specific underlying dynamics and is appropriate to both perturbation experiments and metagenomic cross-sectional surveys. When applied to real high-throughput sequencing of the human gastrointestinal microbiome, we detect a set of candidate keystones and find that they are often part of a keystone module - multiple candidate keystone species with correlated occurrence. The keystone analysis of single-time-point cross-sectional data is also later verified by the evaluation of two-time-points longitudinal sampling. Our framework represents a necessary advancement towards the reliable identification of these key players of complex, real-world microbial communities.}, } @article {pmid37402668, year = {2023}, author = {Duan, ZM and Shen, ZY and Hu, Y and Wang, KF and Fu, H and Wang, CL and Xie, LX and Xie, F}, title = {[The application value of metagenomic next-generation sequencing technology in diagnosis and treatment of pulmonary infection in immunocompromised patients].}, journal = {Zhonghua yi xue za zhi}, volume = {103}, number = {25}, pages = {1885-1891}, doi = {10.3760/cma.j.cn112137-20221226-02703}, pmid = {37402668}, issn = {0376-2491}, support = {61976223//National Natural Science Foundation of China/ ; BLB20J002//Military Logistics Research Key Project/ ; }, mesh = {Female ; Male ; Humans ; Retrospective Studies ; High-Throughput Nucleotide Sequencing ; *Pneumonia ; *Pneumocystis carinii ; Hospitals, General ; Sensitivity and Specificity ; }, abstract = {Objective: To evaluate the application value of metagenomic next-generation sequencing (mNGS) in the diagnosis and treatment of pulmonary infection in immunocompromised patients. Methods: A total of 78 patients with immunocompromised pulmonary infection [55 males and 23 females, aged (50.3±16.9) years] and 61 patients with non-immunocompromised pulmonary infection [42 males and 19 females, aged (63.6±15.9) years] in the Intensive Care Unit of the First Medical Center of College of the Pulmonary & Critical Care Medicine, Chinese PLA General Hospital from November 2018 to May 2022 were retrospectively selected. Patients in both groups received bronchoalveolar lavage fluid (BALF) mNGS and conventional microbiological tests (CMTs) while clinically diagnosed with pulmonary infection. The diagnostic positive rate, pathogen detection rate and clinical coincidence rate of the two methods were compared. At the same time, the difference of adjustment rate of anti-infective treatment strategy based on the results of mNGS detection was compared between the two groups. Results: The positive rates of mNGS in patients with pulmonary infection were 94.9% (74/78) and 82.0% (50/61) in the immunocompromised group and the non-immunocompromised group, respectively. The positive rates of CMTs in patients with pulmonary infection were 64.1% (50/78) and 75.4% (46/61) in the immunocompromised group and the non-immunocompromised group, respectively. The positive rates of mNGS and CMTs in patients with pulmonary infection in immunocompromised group showed a statistically significant difference (P<0.001). The detection rates of mNGS in the immunocompromised group for pneumocystis jirovecii and cytomegalovirus were 41.0% (32/78) and 37.2% (29/78), respectively, and the detection rates of Klebsiella pneumoniae, chlamydia psittaci and Legionella pneumophila were 16.4% (10/61), 9.8% (6/61) and 8.2% (5/61) in the non-immunocompromised patients, respectively, which were higher than those of CMTs [1.3% (1/78), 7.7% (6/78), 4.9% (3/61), 0 and 0] (all P<0.05). In the immunocompromised group, the clinical coincidence rates of mNGS and CMTs and were 89.7% (70/78) and 43.6% (34/78), respectively, with a statistically significant difference (P<0.001). In the non-immunocompromised group, the clinical coincidence rates of mNGS and CMTs were 83.6% (51/61) and 62.3% (38/61), with a statistically significant difference (P=0.008). In the immunocompromised group, according to the results of the etiology of mNGS, the adjustment rate of anti-infection treatment strategy was 87.2% (68/78), while in the non-immunocompromised group, the adjustment rate of anti-infective treatment strategy was 60.7% (37/61), with a statistically significant difference (P<0.001). Conclusion: In patients with immunocompromised pulmonary infection, mNGS has more advantages than CMTs in diagnostic positive rate, diagnosis rate of mixed infection, pathogen detection rate and guidance of anti-infection treatment strategy adjustment, which is worthy of clinical promotion and application.}, } @article {pmid37402447, year = {2023}, author = {Miguel, M and Kim, SH and Lee, SS and Cho, YI}, title = {Composition and functional diversity of bacterial communities during swine carcass decomposition.}, journal = {Animal bioscience}, volume = {36}, number = {9}, pages = {1453-1464}, pmid = {37402447}, issn = {2765-0189}, support = {//Korea Institute of Planning and Evaluation for Technology in Food, Agriculture and Forestry/ ; 118099-03//Ministry of Agriculture, Food and Rural Affairs/ ; }, abstract = {OBJECTIVE: This study investigated the changes in bacterial communities within decomposing swine microcosms, comparing soil with or without intact microbial communities, and under aerobic and anaerobic conditions.

METHODS: The experimental microcosms consisted of four conditions: UA, unsterilized soil-aerobic condition; SA, sterilized soil-aerobic condition; UAn, unsterilized soil-anaerobic condition; and San, sterilized soil-anaerobic condition. The microcosms were prepared by mixing 112.5 g of soil and 37.5 g of ground carcass, which were then placed in sterile containers. The carcass-soil mixture was sampled at day 0, 5, 10, 30, and 60 of decomposition, and the bacterial communities that formed during carcass decomposition were assessed using Illumina MiSeq sequencing of the 16S rRNA gene.

RESULTS: A total of 1,687 amplicon sequence variants representing 22 phyla and 805 genera were identified in the microcosms. The Chao1 and Shannon diversity indices varied in between microcosms at each period (p<0.05). Metagenomic analysis showed variation in the taxa composition across the burial microcosms during decomposition, with Firmicutes being the dominant phylum, followed by Proteobacteria. At the genus level, Bacillus and Clostridium were the main genera within Firmicutes. Functional prediction revealed that the most abundant Kyoto encyclopedia of genes and genomes metabolic functions were carbohydrate and amino acid metabolisms.

CONCLUSION: This study demonstrated a higher bacteria diversity in UA and UAn microcosms than in SA and SAn microcosms. In addition, the taxonomic composition of the microbial community also exhibited changes, highlighting the impact of soil sterilization and oxygen on carcass decomposition. Furthermore, this study provided insights into the microbial communities associated with decomposing swine carcasses in microcosm.}, } @article {pmid37402375, year = {2023}, author = {Amundson, KK and Roux, S and Shelton, JL and Wilkins, MJ}, title = {Long-term CRISPR locus dynamics and stable host-virus co-existence in subsurface fractured shales.}, journal = {Current biology : CB}, volume = {33}, number = {15}, pages = {3125-3135.e4}, doi = {10.1016/j.cub.2023.06.033}, pmid = {37402375}, issn = {1879-0445}, mesh = {*Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Ecosystem ; *Viruses/genetics ; Colorado ; CRISPR-Cas Systems ; }, abstract = {Viruses are the most ubiquitous biological entities on Earth. Even so, elucidating the impact of viruses on microbial communities and associated ecosystem processes often requires identification of unambiguous host-virus linkages-an undeniable challenge in many ecosystems. Subsurface fractured shales present a unique opportunity to first make these strong linkages via spacers in CRISPR-Cas arrays and subsequently reveal complex long-term host-virus dynamics. Here, we sampled two replicated sets of fractured shale wells for nearly 800 days, resulting in 78 metagenomes from temporal sampling of six wells in the Denver-Julesburg Basin (Colorado, USA). At the community level, there was strong evidence for CRISPR-Cas defense systems being used through time and likely in response to viral interactions. Within our host genomes, represented by 202 unique MAGs, we also saw that CRISPR-Cas systems were widely encoded. Together, spacers from host CRISPR loci facilitated 2,110 CRISPR-based viral linkages across 90 host MAGs spanning 25 phyla. We observed less redundancy in host-viral linkages and fewer spacers associated with hosts from the older, more established wells, possibly reflecting enrichment of more beneficial spacers through time. Leveraging temporal patterns of host-virus linkages across differing well ages, we report how host-virus co-existence dynamics develop and converge through time, possibly reflecting selection for viruses that can evade host CRISPR-Cas systems. Together, our findings shed light on the complexities of host-virus interactions as well as long-term dynamics of CRISPR-Cas defense among diverse microbial populations.}, } @article {pmid37402176, year = {2023}, author = {Wu, J and Zhang, H and Gan, R and Xia, Y and Zhang, F and Wang, D and Fu, J and Barraclough, TG}, title = {CRISPR dynamics during the interaction between bacteria and phage in the first year of life.}, journal = {Microbial genomics}, volume = {9}, number = {7}, pages = {}, pmid = {37402176}, issn = {2057-5858}, mesh = {Humans ; *Bacteriophages/genetics ; Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Bacteria/genetics ; Metagenome ; }, abstract = {Gut microbiomes in infancy have a profound impact on health in adulthood. CRISPRs play an essential role in the interaction between bacteria and phages. However, the dynamics of CRISPRs in gut microbiomes during early life are poorly understood. In this study, using shotgun metagenomic sequencing data from 82 Swedish infants' gut microbiomes, 1882 candidate CRISPRs were identified, and their dynamics were analysed. We found large-scale turnover of CRISPRs and their spacers during the first year of life. As well as changes in relative abundance of the bacteria containing CRISPR, acquisition, loss and mutation of spacers were observed within the same CRISPR array sampled over time. Accordingly, the inferred interaction network of bacteria and phage was distinct at different times. This research underpins CRISPR dynamics and their potential role in the interaction between bacteria and phage in early life.}, } @article {pmid37401755, year = {2023}, author = {Ronkainen, A and Khan, I and Krzyżewska-Dudek, E and Hiippala, K and Freitag, TL and Satokari, R}, title = {In vitro adhesion, pilus expression, and in vivo amelioration of antibiotic-induced microbiota disturbance by Bifidobacterium spp. strains from fecal donors.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2229944}, pmid = {37401755}, issn = {1949-0984}, mesh = {Animals ; Mice ; Anti-Bacterial Agents/pharmacology ; Bifidobacterium ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; *Clostridioides difficile ; Mice, Inbred C57BL ; Feces/microbiology ; Fecal Microbiota Transplantation ; *Microbiota ; *Clostridium Infections/microbiology ; }, abstract = {Fecal microbiota transplantation (FMT) is used routinely to treat recurrent Clostridioides difficile infection (rCDI) and investigated as a treatment for numerous conditions associated with gut microbiota alterations. Metagenomic analyses have indicated that recipient colonization by donor bacteria may be associated with favorable clinical outcomes. Bifidobacteria are abundant gut commensals associated with health. We have previously demonstrated that Bifidobacterium strains transferred in FMT can colonize recipients in long term, at least for a year, and recovered such strains by cultivation. This study addressed in vitro adhesion and pilus gene expression of long-term colonizing Bifidobacterium strains from FMT donors as well as in vivo colonization and capability to ameliorate antibiotic-induced microbiota disturbance. RNA-Seq differential gene expression analysis showed that the strongly adherent B. longum strains DY_pv11 and DX_pv23 expressed tight adherence and sortase-dependent pilus genes, respectively. Two B. longum strains, adherent DX_pv23 and poorly adhering DX_pv18, were selected to address in vivo colonization and efficacy to restore antibiotic-disturbed microbiota in C57BL/6 murine model. DX_pv23 colonized mice transiently with a rate comparable to that of the B. animalis BB-12 used as a reference. Although long-term colonization was not observed with any of the three strains, 16S rRNA gene profiling revealed that oral administration of DX_pv23 enhanced the recovery of antibiotic-disturbed microbiota to the original configuration significantly better than the other strains. The findings suggest that selected strains from FMT donors, such as DX_pv23 in this study, may have therapeutic potential by in vitro expression of colonization factors and boosting endogenous gut microbiota.}, } @article {pmid37401151, year = {2023}, author = {Daga-Quisbert, J and Rajarao, GK and Ugarte, F and van Maris, AJA and Quillaguamán, J}, title = {Analysis of the microbiome of the Bolivian high-altitude Lake Pastos Grandes.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {8}, pages = {}, doi = {10.1093/femsec/fiad073}, pmid = {37401151}, issn = {1574-6941}, mesh = {Humans ; *Lakes/microbiology ; Bolivia ; Altitude ; *Microbiota/genetics ; Sodium Chloride ; Water ; }, abstract = {Lake Pastos Grandes in Bolivia is mainly composed of salt flats, which are sporadically and only partially submerged during the wet season. In the present study, the chemical composition of water samples of the lake and some influent rivers was determined. We found that it is likely that the lake was influenced by the dilution of metals from ancient evaporites. We performed the first metagenomic studies of this lake. Analyses of shotgun metagenomics revealed that the relative abundances of Burkholderiales and Pseudomonadales were noteworthy in the water samples, whereas the archaea belonging to the Halobacteriales and Cyanobacteria from subsection III had high abundances in the salt flat. The eukaryotes Crustacea and Diatomea exhibited the highest abundances in the water samples. We investigated further the potential effect of human activities on the nitrogen cycle mobilization in the lake and the propagation of antimicrobial resistance genes. This is the first report about the cycle in the lake. Additionally, rifamycin resistance genes and genes related to efflux pumps, which are not considered a hazard when identified in metagenomes, had the uppermost relative abundances in all sampling points. We found that Lake Pastos Grandes hitherto does not show an appreciable influence by anthropogenic actions.}, } @article {pmid37400907, year = {2023}, author = {Casto-Rebollo, C and Argente, MJ and García, ML and Pena, RN and Blasco, A and Ibáñez-Escriche, N}, title = {Selection for environmental variance shifted the gut microbiome composition driving animal resilience.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {147}, pmid = {37400907}, issn = {2049-2618}, mesh = {Animals ; Rabbits ; *Gastrointestinal Microbiome/genetics ; Feces ; *Microbiota ; Phenotype ; Metagenome ; }, abstract = {BACKGROUND: Understanding how the host's microbiome shapes phenotypes and participates in the host response to selection is fundamental for evolutionists and animal and plant breeders. Currently, selection for resilience is considered a critical step in improving the sustainability of livestock systems. Environmental variance (V E), the within-individual variance of a trait, has been successfully used as a proxy for animal resilience. Selection for reduced V E could effectively shift gut microbiome composition; reshape the inflammatory response, triglyceride, and cholesterol levels; and drive animal resilience. This study aimed to determine the gut microbiome composition underlying the V E of litter size (LS), for which we performed a metagenomic analysis in two rabbit populations divergently selected for low (n = 36) and high (n = 34) V E of LS. Partial least square-discriminant analysis and alpha- and beta-diversity were computed to determine the differences in gut microbiome composition among the rabbit populations.

RESULTS: We identified 116 KEGG IDs, 164 COG IDs, and 32 species with differences in abundance between the two rabbit populations studied. These variables achieved a classification performance of the V E rabbit populations of over than 80%. Compared to the high V E population, the low V E (resilient) population was characterized by an underrepresentation of Megasphaera sp., Acetatifactor muris, Bacteroidetes rodentium, Ruminococcus bromii, Bacteroidetes togonis, and Eggerthella sp. and greater abundances of Alistipes shahii, Alistipes putredinis, Odoribacter splanchnicus, Limosilactobacillus fermentum, and Sutterella, among others. Differences in abundance were also found in pathways related to biofilm formation, quorum sensing, glutamate, and amino acid aromatic metabolism. All these results suggest differences in gut immunity modulation, closely related to resilience.

CONCLUSIONS: This is the first study to show that selection for V E of LS can shift the gut microbiome composition. The results revealed differences in microbiome composition related to gut immunity modulation, which could contribute to the differences in resilience among rabbit populations. The selection-driven shifts in gut microbiome composition should make a substantial contribution to the remarkable genetic response observed in the V E rabbit populations. Video Abstract.}, } @article {pmid37400632, year = {2023}, author = {Yokoyama, D and Takamura, A and Tsuboi, Y and Kikuchi, J}, title = {Large-scale omics dataset of polymer degradation provides robust interpretation for microbial niche and succession on different plastisphere.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {67}, pmid = {37400632}, issn = {2730-6151}, abstract = {While biodegradable polymers have received increased attention due to the recent marine plastic problem, few studies have compared microbiomes and their degradation processes among biodegradable polymers. In this study, we set up prompt evaluation systems for polymer degradation, allowing us to collect 418 microbiome and 125 metabolome samples to clarify the microbiome and metabolome differences according to degradation progress and polymer material (polycaprolactone [PCL], polybutylene succinate-co-adipate [PBSA], polybutylene succinate [PBS], polybutylene adipate-co-terephthalate [PBAT], and poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) [PHBH]). The microbial community compositions were converged to each polymer material, and the largest differences were observed between PHBH and other polymers. Such gaps were probably formed primarily by the presence of specific hydrolase genes (i.e., 3HB depolymerase, lipase, and cutinase) in the microorganisms. Time-series sampling suggested several steps for microbial succession: (1) initial microbes decrease abruptly after incubation starts; (2) microbes, including polymer degraders, increase soon after the start of incubation and show an intermediate peak; (3) microbes, including biofilm constructers, increase their abundance gradually. Metagenome prediction showed functional changes, where free-swimming microbes with flagella adhered stochastically onto the polymer, and certain microbes started to construct a biofilm. Our large-dataset-based results provide robust interpretations for biodegradable polymer degradation.}, } @article {pmid37400174, year = {2023}, author = {Li, B and Yan, T}, title = {Metagenomic next generation sequencing for studying antibiotic resistance genes in the environment.}, journal = {Advances in applied microbiology}, volume = {123}, number = {}, pages = {41-89}, doi = {10.1016/bs.aambs.2023.05.001}, pmid = {37400174}, issn = {0065-2164}, mesh = {Humans ; *Metagenome ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; High-Throughput Nucleotide Sequencing ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; *Anti-Infective Agents ; Metagenomics/methods ; }, abstract = {Bacterial antimicrobial resistance (AMR) is a persisting and growing threat to human health. Characterization of antibiotic resistance genes (ARGs) in the environment is important to understand and control ARG-associated microbial risks. Numerous challenges exist in monitoring ARGs in the environment, due to the extraordinary diversity of ARGs, low abundance of ARGs with respect to the complex environmental microbiomes, difficulties in linking ARGs with bacterial hosts by molecular methods, difficulties in achieving quantification and high throughput simultaneously, difficulties in assessing mobility potential of ARGs, and difficulties in determining the specific AMR determinant genes. Advances in the next generation sequencing (NGS) technologies and related computational and bioinformatic tools are facilitating rapid identification and characterization ARGs in genomes and metagenomes from environmental samples. This chapter discusses NGS-based strategies, including amplicon-based sequencing, whole genome sequencing, bacterial population-targeted metagenome sequencing, metagenomic NGS, quantitative metagenomic sequencing, and functional/phenotypic metagenomic sequencing. Current bioinformatic tools for analyzing sequencing data for studying environmental ARGs are also discussed.}, } @article {pmid37399995, year = {2023}, author = {Wu, Z and Chen, Z and Wang, H and Liu, H and Wei, Z}, title = {Arsenic removal in flue gas through anaerobic denitrification and sulfate reduction cocoupled arsenic oxidation.}, journal = {Chemosphere}, volume = {337}, number = {}, pages = {139350}, doi = {10.1016/j.chemosphere.2023.139350}, pmid = {37399995}, issn = {1879-1298}, mesh = {Humans ; *Arsenic ; Nitrates ; Anaerobiosis ; Denitrification ; Oxidation-Reduction ; *Arsenicals ; Sulfates ; }, abstract = {Arsenic in flue gas from municipal solid waste incineration can damage to human health and ecological environment. A sulfate-nitrate-reducing bioreactor (SNRBR) for flue gas arsenic removal was investigated. Arsenic removal efficiency attained 89.4%. An integrated metagenomic and metaproteomic investigation showed that three nitrate reductases (NapA, NapB and NarG), three sulfate reductases (Sat, AprAB and DsrAB), and arsenite oxidase (ArxA) regulated nitrate reduction, sulfate reduction and bacterial As(III)-oxidation, respectively. Citrobacter and Desulfobulbus could synthetically regulate the expression of arsenite-oxidizing gene, nitrate reductases and sulfate reducatases, which involved in As(III) oxidation, nitrate and sulfate reduction. A bacterial consortium containing Citrobacter, UG_Enterobacteriaceas, Desulfobulbus and Desulfovibrio could capable of simultaneously arsenic oxidation, sulfate reduction and denitrification. Anaerobic denitrification and sulfate reduction were cocoupled to arsenic oxidation. The biofilm was characterized by FTIR, XPS, XRD, EEM, and SEM. XRD and XPS spectra verified the formation of aarsenic species (As(V)) from flue gas As(III) conversion. Arsenic speciation in biofilms of SNRBR consisted of 77% residual arsenic, 15.9% organic matter-bound arsenic, and 4.3% strongly absorbed arsenic. Flue gas arsenic was bio-stabilized in the form of Fe-As-S and As-EPS through biodeposition, biosorption and biocomplexation. This provides a new way of flue gas arsenic removal using the sulfate-nitrate-reducing bioreactor.}, } @article {pmid37399986, year = {2023}, author = {Magnuson, JT and Monticelli, G and Schlenk, D and Bisesi, JH and Pampanin, DM}, title = {Connecting gut microbiome changes with fish health conditions in juvenile Atlantic cod (Gadus morhua) exposed to dispersed crude oil.}, journal = {Environmental research}, volume = {234}, number = {}, pages = {116516}, doi = {10.1016/j.envres.2023.116516}, pmid = {37399986}, issn = {1096-0953}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Gadus morhua/metabolism ; *Petroleum/analysis/metabolism/toxicity ; Fishes ; *Microbiota/genetics ; *Water Pollutants, Chemical/analysis ; }, abstract = {Polycyclic aromatic hydrocarbons found in crude oil can impair fish health following sublethal exposure. However, the dysbiosis of microbial communities within the fish host and influence it has on the toxic response of fish following exposure has been less characterized, particularly in marine species. To better understand the effect of dispersed crude oil (DCO) on juvenile Atlantic cod (Gadus morhua) microbiota composition and potential targets of exposure within the gut, fish were exposed to 0.05 ppm DCO for 1, 3, 7, or 28 days and 16 S metagenomic and metatranscriptomic sequencing on the gut and RNA sequencing on intestinal content were conducted. In addition to assessing species composition, richness, and diversity from microbial gut community analysis and transcriptomic profiling, the functional capacity of the microbiome was determined. Mycoplasma and Aliivibrio were the two most abundant genera after DCO exposure and Photobacterium the most abundant genus in controls, after 28 days. Metagenomic profiles were only significantly different between treatments after a 28-day exposure. The top identified pathways were involved in energy and the biosynthesis of carbohydrates, fatty acids, amino acids, and cellular structure. Biological processes following fish transcriptomic profiling shared common pathways with microbial functional annotations such as energy, translation, amide biosynthetic process, and proteolysis. There were 58 differently expressed genes determined from metatranscriptomic profiling after 7 days of exposure. Predicted pathways that were altered included those involved in translation, signal transduction, and Wnt signaling. EIF2 signaling was consistently dysregulated following exposure to DCO, regardless of exposure duration, with impairments in IL-22 signaling and spermine and spermidine biosynthesis in fish after 28 days. Data were consistent with predictions of a potentially reduced immune response related to gastrointestinal disease. Herein, transcriptomic-level responses helped explain the relevance of differences in gut microbial communities in fish following DCO exposure.}, } @article {pmid37399960, year = {2023}, author = {Jiang, LX and Guo, L and Shapleigh, JP and Liu, Y and Huang, Y and Lian, JS and Xie, L and Deng, LW and Wang, WG and Wang, L}, title = {The long-term effect of glutaraldehyde on the bacterial community in anaerobic ammonium oxidation reactor.}, journal = {Bioresource technology}, volume = {385}, number = {}, pages = {129448}, doi = {10.1016/j.biortech.2023.129448}, pmid = {37399960}, issn = {1873-2976}, mesh = {Glutaral ; Anaerobiosis ; *Bacteria/metabolism ; Metagenome ; *Ammonium Compounds/metabolism ; Oxidation-Reduction ; Bioreactors/microbiology ; Nitrogen/metabolism ; Sewage/microbiology ; Denitrification ; }, abstract = {A 160-day incubation was performed with two anammox reactors (GA and CK) to investigate the effect of glutaraldehyde. The results indicated that anammox bacteria were very sensitive when glutaraldehyde in GA reactor increased to 40 mg/L, the nitrogen removal efficiency sharply decreased to 11%, only one-quarter of CK. Glutaraldehyde changed spatial distribution of exopolysaccharides, caused anammox bacteria (Brocadia CK_gra75) to disassociate from granules (24.70% of the reads in CK but only 14.09% in GA granules). Metagenome analysis indicated glutaraldehyde led to the denitrifier community succession from strains without nir (nitrite reductase) and nor (nitric oxide reductases) genes to those with them, and the rapid growth of denitrifiers with NodT (an outer membrane factor)-related efflux pumps replacing those with another TolC -related ones. Meanwhile, Brocadia CK_gra75 lacks the NodT proteins. This study provides important insight into community adaptation and potential resistance mechanism in an active anammox community after exposure to disinfectant.}, } @article {pmid37399936, year = {2023}, author = {Zhao, L and Lv, Z and Lin, L and Li, X and Xu, J and Huang, S and Chen, Y and Fu, Y and Peng, C and Cao, T and Ke, Y and Xia, X}, title = {Impact of COVID-19 pandemic on profiles of antibiotic-resistant genes and bacteria in hospital wastewater.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {334}, number = {}, pages = {122133}, doi = {10.1016/j.envpol.2023.122133}, pmid = {37399936}, issn = {1873-6424}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Wastewater ; Pandemics ; Genes, Bacterial ; *COVID-19/epidemiology ; Bacteria/genetics ; Drug Resistance, Bacterial/genetics ; Hospitals ; }, abstract = {The COVID-19 pandemic has severely affected healthcare worldwide and has led to the excessive use of disinfectants and antimicrobial agents. However, the impact of excessive disinfection measures and specific medication prescriptions on the development and dissemination of bacterial drug resistance during the pandemic remains unclear. This study investigated the influence of the pandemic on the composition of antibiotics, antibiotic resistance genes (ARGs), and pathogenic communities in hospital wastewater using ultra-performance liquid chromatography-tandem mass spectrometry and metagenome sequencing. The overall level of antibiotics decreased after the COVID-19 outbreak, whereas the abundance of various ARGs increased in hospital wastewater. After COVID-19 outbreak, blaOXA, sul2, tetX, and qnrS had higher concentrations in winter than in summer. Seasonal factors and the COVID-19 pandemic have affected the microbial structure in wastewater, especially of Klebsiella, Escherichia, Aeromonas, and Acinetobacter. Further analysis revealed the co-existence of qnrS, blaNDM, and blaKPC during the pandemic. Various ARGs significantly correlated with mobile genetic elements, implying their potential mobility. A network analysis revealed that many pathogenic bacteria (Klebsiella, Escherichia, and Vibrio) were correlated with ARGs, indicating the existence of multi-drug resistant pathogens. Although the calculated resistome risk score did not change significantly, our results suggest that the COVID-19 pandemic shifted the composition of residual antibiotics and ARGs in hospital wastewater and contributed to the dissemination of bacterial drug resistance.}, } @article {pmid37399829, year = {2023}, author = {Fuhrmeister, ER and Harvey, AP and Nadimpalli, ML and Gallandat, K and Ambelu, A and Arnold, BF and Brown, J and Cumming, O and Earl, AM and Kang, G and Kariuki, S and Levy, K and Pinto Jimenez, CE and Swarthout, JM and Trueba, G and Tsukayama, P and Worby, CJ and Pickering, AJ}, title = {Evaluating the relationship between community water and sanitation access and the global burden of antibiotic resistance: an ecological study.}, journal = {The Lancet. Microbe}, volume = {4}, number = {8}, pages = {e591-e600}, pmid = {37399829}, issn = {2666-5247}, support = {K01 AI103544/AI/NIAID NIH HHS/United States ; KL2 TR002545/TR/NCATS NIH HHS/United States ; R01 AI099525/AI/NIAID NIH HHS/United States ; INV-006556/GATES/Bill & Melinda Gates Foundation/United States ; R01 AI137679/AI/NIAID NIH HHS/United States ; /WT_/Wellcome Trust/United Kingdom ; U19 AI110818/AI/NIAID NIH HHS/United States ; 215675-Z-19-Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *Drinking Water ; Sanitation ; Water Supply ; Hygiene ; Poverty ; }, abstract = {BACKGROUND: Antibiotic resistance is a leading cause of death, with the highest burden occurring in low-resource settings. There is little evidence on the potential for water, sanitation, and hygiene (WASH) access to reduce antibiotic resistance in humans. We aimed to determine the relationship between the burden of antibiotic resistance in humans and community access to drinking water and sanitation.

METHODS: In this ecological study, we linked publicly available, geospatially tagged human faecal metagenomes (from the US National Center for Biotechnology Information Sequence Read Archive) with georeferenced household survey datasets that reported access to drinking water sources and sanitation facility types. We used generalised linear models with robust SEs to estimate the relationship between the abundance of antibiotic resistance genes (ARGs) in human faecal metagenomes and community-level coverage of improved drinking water and sanitation within a defined radii of faecal metagenome coordinates.

FINDINGS: We identified 1589 metagenomes from 26 countries. The mean abundance of ARGs, in units of log10 ARG fragments per kilobase per million mapped reads classified as bacteria, was highest in Africa compared with Europe (p=0·014), North America (p=0·0032), and the Western Pacific (p=0·011), and second highest in South-East Asia compared with Europe (p=0·047) and North America (p=0·014). Increased access to improved water and sanitation was associated with lower ARG abundance (effect estimate -0·22, [95% CI -0·39 to -0·05]) and the association was stronger in urban (-0·32 [-0·63 to 0·00]) than in rural (-0·16 [-0·38 to 0·07]) areas.

INTERPRETATION: Although additional studies to investigate causal effects are needed, increasing access to water and sanitation could be an effective strategy to curb the proliferation of antibiotic resistance in low-income and middle-income countries.

FUNDING: Bill & Melinda Gates Foundation.}, } @article {pmid37399133, year = {2023}, author = {Beliavskaia, A and Tan, KK and Sinha, A and Husin, NA and Lim, FS and Loong, SK and Bell-Sakyi, L and Carlow, CKS and AbuBakar, S and Darby, AC and Makepeace, BL and Khoo, JJ}, title = {Metagenomics of culture isolates and insect tissue illuminate the evolution of Wolbachia, Rickettsia and Bartonella symbionts in Ctenocephalides spp. fleas.}, journal = {Microbial genomics}, volume = {9}, number = {7}, pages = {}, pmid = {37399133}, issn = {2057-5858}, support = {BB/P024378/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/P024270/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 223743/Z/21/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Rickettsia/genetics ; *Bartonella/genetics ; *Siphonaptera/microbiology ; *Ctenocephalides/microbiology ; *Wolbachia/genetics ; Metagenomics ; Insecta ; }, abstract = {While fleas are often perceived simply as a biting nuisance and a cause of allergic dermatitis, they represent important disease vectors worldwide, especially for bacterial zoonoses such as plague (transmitted by rodent fleas) and some of the rickettsioses and bartonelloses. The cosmopolitan cat (Ctenocephalides felis) and dog (Ctenocephalides canis) fleas, as well as Ctenocephalides orientis (restricted to tropical and subtropical Asia), breed in human dwellings and are vectors of cat-scratch fever (caused by Bartonella spp.) and Rickettsia spp., including Rickettsia felis (agent of flea-borne spotted fever) and Rickettsia asembonensis , a suspected pathogen. These Rickettsia spp. are members of a phylogenetic clade known as the ‘transitional group’, which includes both human pathogens and arthropod-specific endosymbionts. The relatively depauperate flea microbiome can also contain other endosymbionts, including a diverse range of Wolbachia strains. Here, we present circularized genome assemblies for two C. orientis-derived pathogens (Bartonella clarridgeiae and R. asembonensis) from Malaysia, a novel Wolbachia strain (wCori), and the C. orientis mitochondrion; all were obtained by direct metagenomic sequencing of flea tissues. Moreover, we isolated two Wolbachia strains from Malaysian C. felis into tick cell culture and recovered circularized genome assemblies for both, one of which (wCfeF) is newly sequenced. We demonstrate that the three Wolbachia strains are representatives of different major clades (‘supergroups’), two of which appear to be flea-specific. These Wolbachia genomes exhibit unique combinations of features associated with reproductive parasitism or mutualism, including prophage WO, cytoplasmic incompatibility factors and the biotin operon of obligate intracellular microbes. The first circularized assembly for R. asembonensis includes a plasmid with a markedly different structure and gene content compared to the published plasmid; moreover, this novel plasmid was also detected in cat flea metagenomes from the USA. Analysis of loci under positive selection in the transitional group revealed genes involved in host–pathogen interactions that may facilitate host switching. Finally, the first B. clarridgeiae genome from Asia exhibited large-scale genome stability compared to isolates from other continents, except for SNPs in regions predicted to mediate interactions with the vertebrate host. These findings highlight the paucity of data on the genomic diversity of Ctenocephalides-associated bacteria and raise questions regarding how interactions between members of the flea microbiome might influence vector competence.}, } @article {pmid37398675, year = {2023}, author = {Zhang, L and Wang, F and Jia, L and Yan, H and Gao, L and Tian, Y and Su, X and Zhang, X and Lv, C and Ma, Z and Xue, Y and Lin, Q and Wang, K}, title = {Corrigendum: Edwardsiella piscicida infection reshapes the intestinal microbiome and metabolome of big-belly seahorses: mechanistic insights of synergistic actions of virulence factors.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1222662}, doi = {10.3389/fimmu.2023.1222662}, pmid = {37398675}, issn = {1664-3224}, abstract = {[This corrects the article DOI: 10.3389/fimmu.2023.1135588.].}, } @article {pmid37398670, year = {2023}, author = {Park, EJ and Yadav, H and Singh, TP}, title = {Editorial: Microbiota in skin inflammatory diseases.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1235314}, pmid = {37398670}, issn = {1664-3224}, mesh = {Humans ; Skin ; *Skin Diseases ; *Microbiota ; }, } @article {pmid37398549, year = {2023}, author = {Takihara, H and Okuda, S}, title = {Glycan-related genes in human gut microbiota exhibit differential distribution and diversity in carbohydrate degradation and glycan synthesis.}, journal = {Frontiers in molecular biosciences}, volume = {10}, number = {}, pages = {1137303}, pmid = {37398549}, issn = {2296-889X}, abstract = {Interactions between humans and the gut microbiome occur by supplying nutrients to gut epithelial cells via short-chain fatty acids obtained from dietary carbohydrates or mucins and activating immunity via mucins' degradation. The degradation of carbohydrates derived from food is an important function for organisms to obtain energy. However, since humans possess only 17 genes encoding carbohydrate-degrading enzymes, the gut microbiome is responsible for degrading plant-derived polysaccharides. Using the method for extracting glycan-related genes from the metagenomes constructed thus far, we calculated the distribution and abundance of different glycan-related genes in the healthy human gut metagenome. Glycan-related genes showed an abundance of 0.64-11.00, indicating large individual differences. However, the distribution of the classes of glycan-related genes was similar between the samples. In addition, the function of carbohydrate degradation was divided into three clusters, showing high diversity; however, the synthesis function was not divided, indicating low diversity. The substrates of enzymes for carbohydrate degradation between clusters were either plant-derived polysaccharides or biased toward degrading polysaccharides derived from other sources. These functional biases differ depending on the type of microorganism used. Based on these findings, we predicted that 1) diversity will be constant because the influence on the host by the transferase of gut bacteria is a function derived from the genome, and 2) diversity will be high because the influence on the host by the hydrolase of gut bacteria is affected by incoming dietary carbohydrates.}, } @article {pmid37398492, year = {2023}, author = {Minor, NR and Ramuta, MD and Stauss, MR and Harwood, OE and Brakefield, SF and Alberts, A and Vuyk, WC and Bobholz, MJ and Rosinski, JR and Wolf, S and Lund, M and Mussa, M and Beversdorf, LJ and Aliota, MT and O'Connor, SL and O'Connor, DH}, title = {Metagenomic sequencing detects human respiratory and enteric viruses in air samples collected from congregate settings.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {37398492}, support = {R01 AI170737/AI/NIAID NIH HHS/United States ; T32 AI055397/AI/NIAID NIH HHS/United States ; }, abstract = {Innovative methods for evaluating virus risk and spread, independent of test-seeking behavior, are needed to improve routine public health surveillance, outbreak response, and pandemic preparedness. Throughout the COVID-19 pandemic, environmental surveillance strategies, including wastewater and air sampling, have been used alongside widespread individual-based SARS-CoV-2 testing programs to provide population-level data. These environmental surveillance strategies have predominantly relied on pathogen-specific detection methods to monitor viruses through space and time. However, this provides a limited picture of the virome present in an environmental sample, leaving us blind to most circulating viruses. In this study, we explore whether pathogen-agnostic deep sequencing can expand the utility of air sampling to detect many human viruses. We show that sequence-independent single-primer amplification sequencing of nucleic acids from air samples can detect common and unexpected human respiratory and enteric viruses, including influenza virus type A and C, respiratory syncytial virus, human coronaviruses, rhinovirus, SARS-CoV-2, rotavirus, mamastrovirus, and astrovirus.}, } @article {pmid37398369, year = {2023}, author = {Zepeda-Rivera, MA and Eisele, Y and Baryiames, A and Wu, H and LaCourse, KD and Jones, DS and Hauner, H and Dewhirst, FE and Minot, SS and Johnston, CD and Bullman, S}, title = {Fusobacterium sphaericum sp. nov. , isolated from a human colon tumor, is prevalent in various human body sites and induces IL-8 secretion from colorectal cancer cells.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.06.16.545380}, pmid = {37398369}, support = {R01 DE027850/DE/NIDCR NIH HHS/United States ; }, abstract = {Cancerous tissue is a largely unexplored microbial niche that provides a unique environment for the colonization and growth of specific bacterial communities, and with it, the opportunity to identify novel bacterial species. Here, we report distinct features of a novel Fusobacterium species, F. sphaericum sp. nov. (Fs), isolated from primary colon adenocarcinoma tissue. We acquire the complete, closed genome of this organism and phylogenetically confirm its classification into the Fusobacterium genus. Phenotypic and genomic analysis of Fs reveal that this novel organism is of coccoid shape, rare for Fusobacterium members, and has species-distinct gene content. Fs displays a metabolic profile and antibiotic resistance repertoire consistent with other Fusobacterium species. In vitro, Fs has adherent and immunomodulatory capabilities, as it intimately associates with human colon cancer epithelial cells and promotes IL-8 secretion. Analysis of the prevalence and abundance of Fs in ∼1,750 human metagenomic samples shows that it is a moderately prevalent member of the human oral cavity and stool. Intriguingly, analysis of ∼1,270 specimens from patients with colorectal cancer demonstrate that Fs is significantly enriched in colonic and tumor tissue as compared to mucosa or feces. Our study sheds light on a novel bacterial species that is prevalent within the human intestinal microbiota and whose role in human health and disease requires further investigation.}, } @article {pmid37398285, year = {2023}, author = {Bank, NC and Singh, V and Grubb, B and McCourt, B and Burberry, A and Roberts, KD and Rodriguez-Palacios, A}, title = {The basis of antigenic operon fragmentation in Bacteroidota and commensalism.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37398285}, support = {R21 DK118373/DK/NIDDK NIH HHS/United States ; }, abstract = {The causes for variability of pro-inflammatory surface antigens that affect gut commensal/opportunistic dualism within the phylum Bacteroidota remain unclear (1, 2). Using the classical lipopolysaccharide/O-antigen 'rfb operon' in Enterobacteriaceae as a surface antigen model (5-gene-cluster rfbABCDX), and a recent rfbA-typing strategy for strain classification (3), we characterized the architecture/conservancy of the entire rfb operon in Bacteroidota. Analyzing complete genomes, we discovered that most Bacteroidota have the rfb operon fragmented into non-random gene-singlets and/or doublets/triplets, termed 'minioperons'. To reflect global operon integrity, duplication, and fragmentation principles, we propose a five-category (infra/supernumerary) cataloguing system and a Global Operon Profiling System for bacteria. Mechanistically, genomic sequence analyses revealed that operon fragmentation is driven by intra-operon insertions of predominantly Bacteroides-DNA (thetaiotaomicron/fragilis) and likely natural selection in specific micro-niches. Bacteroides-insertions, also detected in other antigenic operons (fimbriae), but not in operons deemed essential (ribosomal), could explain why Bacteroidota have fewer KEGG-pathways despite large genomes (4). DNA insertions overrepresenting DNA-exchange-avid species, impact functional metagenomics by inflating gene-based pathway inference and overestimating 'extra-species' abundance. Using bacteria from inflammatory gut-wall cavernous micro-tracts (CavFT) in Crohn's Disease (5), we illustrate that bacteria with supernumerary-fragmented operons cannot produce O-antigen, and that commensal/CavFT Bacteroidota stimulate macrophages with lower potency than Enterobacteriaceae, and do not induce peritonitis in mice. The impact of 'foreign-DNA' insertions on pro-inflammatory operons, metagenomics, and commensalism offers potential for novel diagnostics and therapeutics.}, } @article {pmid37398257, year = {2023}, author = {Bogdanov, A and Salib, MN and Chase, AB and Hammerlindl, H and Muskat, MN and Luedtke, S and Barbosa da Silva, E and O'Donoghue, AJ and Wu, LF and Altschuler, SJ and Molinski, TF and Jensen, PR}, title = {Small Molecule in situ Resin Capture - A Compound First Approach to Natural Product Discovery.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37398257}, support = {R01 GM085770/GM/NIGMS NIH HHS/United States ; R21 AT010493/AT/NCCIH NIH HHS/United States ; }, abstract = {Microbial natural products remain an important resource for drug discovery. Yet, commonly employed discovery techniques are plagued by the rediscovery of known compounds, the relatively few microbes that can be cultured, and laboratory growth conditions that do not elicit biosynthetic gene expression among myriad other challenges. Here we introduce a culture independent approach to natural product discovery that we call the Small Molecule In situ Resin Capture (SMIRC) technique. SMIRC exploits in situ environmental conditions to elicit compound production and represents a new approach to access poorly explored chemical space by capturing natural products directly from the environments in which they are produced. In contrast to traditional methods, this compound-first approach can capture structurally complex small molecules across all domains of life in a single deployment while relying on Nature to provide the complex and poorly understood environmental cues needed to elicit biosynthetic gene expression. We illustrate the effectiveness of SMIRC in marine habitats with the discovery of numerous new compounds and demonstrate that sufficient compound yields can be obtained for NMR-based structure assignment. Two new compound classes are reported including one novel carbon skeleton that possesses a functional group not previously observed among natural products and a second that possesses potent biological activity. We introduce expanded deployments, in situ cultivation, and metagenomics as methods to facilitate compound discovery, enhance yields, and link compounds to producing organisms. This compound first approach can provide unprecedented access to new natural product chemotypes with broad implications for drug discovery.}, } @article {pmid37398242, year = {2023}, author = {Madi, N and Cato, ET and Sayeed, MA and Creasy-Marrazzo, A and Cuénod, A and Islam, K and Khabir, MIU and Bhuiyan, MTR and Begum, Y and Freeman, E and Vustepalli, A and Brinkley, L and Kamat, and Bailey, LS and Basso, KB and Qadri, F and Khan, AI and Shapiro, BJ and Nelson, EJ}, title = {Phage predation is a biomarker for disease severity and shapes pathogen genetic diversity in cholera patients.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37398242}, support = {R21 TW010182/TW/FIC NIH HHS/United States ; S10 OD021758/OD/NIH HHS/United States ; }, abstract = {A century has passed since the discovery that virulent bacteriophages are associated with improved survival of cholera patients. Despite an increasingly detailed picture of the molecular mechanisms that govern phage-bacterial interactions, we lack an understanding of how these interactions impact disease severity. Here we report a year-long, nation-wide study of diarrheal disease patients in Bangladesh. Among the subset of cholera patients, we quantified Vibrio cholerae (prey) and its virulent phages (predators) using metagenomics and quantitative PCR, while accounting for antibiotic exposure using quantitative mass spectrometry. Virulent phage (ICP1) and antibiotics suppressed V. cholerae to varying degrees and were inversely associated with severe dehydration; aspects of these effects were dependent on resistance mechanisms. In the absence of anti-phage defenses, predation was 'effective' with a high predator to prey ratio that correlated with increased genetic diversity among the prey. In the presence of anti-phage defenses, predation was 'ineffective' with a low predator to prey ratio that correlated with increased genetic diversity among the predators. Our results link phage predation to disease severity, support phage-bacteria coevolution within patients, and suggest the ratio of phage to pathogen can serve as a biomarker for clinical, diagnostic, and epidemiologic applications.}, } @article {pmid37398234, year = {2023}, author = {Van Syoc, E and Nixon, MP and Silverman, JD and Luo, Y and Gonzalez, FJ and Elbere, I and Klovins, J and Patterson, AD and Rogers, CJ and Ganda, E}, title = {Changes in the Type 2 diabetes gut mycobiome associate with metformin treatment across populations.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37398234}, support = {R01 GM148972/GM/NIGMS NIH HHS/United States ; T32 DK120509/DK/NIDDK NIH HHS/United States ; }, abstract = {The human gut teems with a diverse ecosystem of microbes, yet non-bacterial portions of that community are overlooked in studies of metabolic diseases firmly linked to gut bacteria. Type 2 diabetes mellitus (T2D) associates with compositional shifts in the gut bacterial microbiome and fungal mycobiome, but whether T2D and/or pharmaceutical treatments underpin the community change is unresolved. To differentiate these effects, we curated a gut mycobiome cohort to-date spanning 1,000 human samples across 5 countries and a murine experimental model. We use Bayesian multinomial logistic normal models to show that metformin and T2D both associate with shifts in the relative abundance of distinct gut fungi. T2D associates with shifts in the Saccharomycetes and Sordariomycetes fungal classes, while the genera Fusarium and Tetrapisipora most consistently associate with metformin treatment. We confirmed the impact of metformin on individual gut fungi by administering metformin to healthy mice. Thus, metformin and T2D account for subtle, but significant and distinct variation in the gut mycobiome across human populations. This work highlights for the first time that oral pharmaceuticals can confound associations of gut fungi with T2D and warrants the need to consider pharmaceutical interventions in investigations of linkages between metabolic diseases and gut microbial inhabitants.}, } @article {pmid37398010, year = {2023}, author = {Shen, Z and Robert, L and Stolpman, M and Che, Y and Walsh, A and Saffery, R and Allen, KJ and Eckert, J and Young, A and Deming, C and Chen, Q and Conlan, S and Laky, K and Li, JM and Chatman, L and Saheb Kashaf, S and , and , and Kong, HH and Frischmeyer-Guerrerio, PA and Perrett, KP and Segre, JA}, title = {A genome catalog of the early-life human skin microbiome.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37398010}, abstract = {Metagenome-assembled genomes have greatly expanded the reference genomes for skin microbiome. However, the current reference genomes are largely based on samples from adults in North America and lack representation from infants and individuals from other continents. Here we used ultra-deep shotgun metagenomic sequencing to profile the skin microbiota of 215 infants at age 2-3 months and 12 months who were part of the VITALITY trial in Australia as well as 67 maternally-matched samples. Based on the infant samples, we present the Early-Life Skin Genomes (ELSG) catalog, comprising 9,194 bacterial genomes from 1,029 species, 206 fungal genomes from 13 species, and 39 eukaryotic viral sequences. This genome catalog substantially expands the diversity of species previously known to comprise human skin microbiome and improves the classification rate of sequenced data by 25%. The protein catalog derived from these genomes provides insights into the functional elements such as defense mechanisms that distinguish early-life skin microbiome. We also found evidence for vertical transmission at the microbial community, individual skin bacterial species and strain levels between mothers and infants. Overall, the ELSG catalog uncovers the skin microbiome of a previously underrepresented age group and population and provides a comprehensive view of human skin microbiome diversity, function, and transmission in early life.}, } @article {pmid37397737, year = {2023}, author = {Li, M and Wang, J and Yao, Z and Liao, H and Su, S and Yang, X and Xie, M and Zheng, Y}, title = {Metagenomic-based pathogen surveillance for children with severe pneumonia in pediatric intensive care unit.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1177069}, pmid = {37397737}, issn = {2296-2565}, mesh = {Humans ; Child ; Female ; Infant ; Child, Preschool ; Aged ; *Pneumonia ; Intensive Care Units, Pediatric ; *Bacteriophages ; *Coinfection ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Pneumonia is a significant cause of morbidity and mortality in children. Metagenomic next-generation sequencing (mNGS) has the potential to assess the landscape of pathogens responsible for severe pulmonary infection.

METHODS: Bronchoalveolar lavage fluid (BALF) samples of 262 children with suspected pulmonary infections were collected from April 2019 to October 2021 in the Pediatric Intensive Care Unit (PICU) of Guangdong Women and Children Hospital. Both mNGS and conventional tests were utilized for pathogen detection.

RESULTS: A total of 80 underlying pathogens were identified using both mNGS and conventional tests. Respiratory syncytial virus (RSV), Staphylococcus aureus and rhinovirus were the most frequently detected pathogens in this cohort. The incidence rate of co-infection was high (58.96%, 148/251), with bacterial-viral agents most co-detected. RSV was the main pathogen in children younger than 6 months of age, and was also commonly found in older pediatric patients. Rhinovirus was prevalent in children older than 6 months. Adenovirus and Mycoplasma pneumoniae were more prevalent in children older than 3 years than in other age groups. Pneumocystis jirovecii was detected in nearly 15% of children younger than 6 months. Besides, influenza virus and adenovirus were rarely found in 2020 and 2021.

CONCLUSIONS: Our study highlights the importance of using advanced diagnostic techniques like mNGS to improve our understanding of the microbial epidemiology of severe pneumonia in pediatric patients.}, } @article {pmid37397354, year = {2023}, author = {Lu, Z and Kong, L and Ren, S and Aschenbach, JR and Shen, H}, title = {Acid tolerance of lactate-utilizing bacteria of the order Bacteroidales contributes to prevention of ruminal acidosis in goats adapted to a high-concentrate diet.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {14}, number = {}, pages = {130-140}, pmid = {37397354}, issn = {2405-6383}, abstract = {The rapid accumulation of organic acids, particularly lactate, has been suggested as the main cause of ruminal acidosis (RA) for ruminants fed high-concentrate diets. Previous research has shown that a gradual shift from low-to high-concentrate diets within 4 to 5 weeks effectively reduces the risk for RA. However, the mechanisms remain unknown. In this study, 20 goats were randomly allocated into four groups (n = 5) and fed with a diet containing a weekly increasing concentrate portion of 20%, 40%, 60%, and 80% over 28 d. At d 7, 14, 21, and 28, one group (named C20, C40, C60, and C80 according to the last concentrate level that they received) was killed and the ruminal microbiome was collected. Ruminal acidosis was not detected in any of the goats during the experiment. Nonetheless, ruminal pH dropped sharply from 6.2 to 5.7 (P < 0.05) when dietary concentrate increased from 40% to 60%. A combined metagenome and metatranscriptome sequencing approach identified that this was linked to a sharp decrease in the abundance and expression of genes encoding nicotinamide adenine dinucleotide (NAD)-dependent lactate dehydrogenase (nLDH), catalyzing the enzymatic conversion of pyruvate to lactate (P < 0.01), whereas the expression of two genes encoding NAD-independent lactate dehydrogenase (iLDH), catalyzing lactate oxidation to pyruvate, showed no significant concomitant change. Abundance and expression alterations for nLDH- and iLDH-encoding genes were attributable to bacteria from Clostridiales and Bacteroidales, respectively. By analyzing the gene profiles of 9 metagenome bins (MAG) with nLDH-encoding genes and 5 MAG with iLDH-encoding genes, we identified primary and secondary active transporters as being the major types of sugar transporter for lactate-producing bacteria (LPB) and lactate-utilizing bacteria (LUB), respectively. Furthermore, more adenosine triphosphate was required for the phosphorylation of sugars to initiate their catabolic pathways in LPB compared to LUB. Thus, the low dependence of sugar transport systems and catabolic pathways on primary energy sources supports the acid tolerance of LUB from Bacteroidales. It favors ruminal lactate utilization during the adaptation of goats to a high-concentrate diet. This finding has valuable implications for the development of measures to prevent RA.}, } @article {pmid37397142, year = {2023}, author = {Leo, S and Cetiner, OF and Pittet, LF and Messina, NL and Jakob, W and Falquet, L and Curtis, N and Zimmermann, P}, title = {Metagenomics analysis of the neonatal intestinal resistome.}, journal = {Frontiers in pediatrics}, volume = {11}, number = {}, pages = {1169651}, pmid = {37397142}, issn = {2296-2360}, abstract = {INTRODUCTION: The intestinal microbiome forms a major reservoir for antibiotic resistance genes (ARGs). Little is known about the neonatal intestinal resistome.

OBJECTIVE: The objective of this study was to investigate the intestinal resistome and factors that influence the abundance of ARGs in a large cohort of neonates.

METHODS: Shotgun metagenomics was used to analyse the resistome in stool samples collected at 1 week of age from 390 healthy, term-born neonates who did not receive antibiotics.

RESULTS: Overall, 913 ARGs belonging to 27 classes were identified. The most abundant ARGs were those conferring resistance to tetracyclines, quaternary ammonium compounds, and macrolide-lincosamide-streptogramin-B. Phylogenetic composition was strongly associated with the resistome composition. Other factors that were associated with the abundance of ARGs were delivery mode, gestational age, birth weight, feeding method, and antibiotics in the last trimester of pregnancy. Sex, ethnicity, probiotic use during pregnancy, and intrapartum antibiotics had little effect on the abundance of ARGs.

CONCLUSION: Even in the absence of direct antibiotic exposure, the neonatal intestine harbours a high abundance and a variety of ARGs.}, } @article {pmid37397028, year = {2023}, author = {Masrahi, AS}, title = {Effect of long-term influx of tertiary treated wastewater on native bacterial communities in a dry valley topsoil: 16S rRNA gene-based metagenomic analysis of composition and functional profile.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15583}, pmid = {37397028}, issn = {2167-8359}, mesh = {*Wastewater ; RNA, Ribosomal, 16S/genetics ; *Ecosystem ; Genes, rRNA ; Bacteria/genetics ; Soil/chemistry ; }, abstract = {Although dumping treated wastewater into soil might provide nutrients and organic matter, it can also expose the ecosystem to biological and chemical risks. A vital indication of soil health and quality is the soil microbial community. The current work used next-generation 16S rRNA gene amplicon sequencing to evaluate the effects of the long-term influx of tertiary treated wastewater (TWW) into Wadi Uranah, a dry valley in Makkah city, Saudi Arabia, on native topsoil bacterial community composition and predicted functions. The findings demonstrated that neither the compositions of microbial communities nor their predicted functions using PICRUSt2 differed significantly (p > 0.05) between polluted valley soil (PolVS) and unpolluted valley soil (UPVS). Alpha and beta diversity, however, showed that the PolVS samples had a considerably higher level of diversity and variability. Firmicutes, Actinobacteria, Proteobacteria, and Bacteroidetes were the most prevalent phyla in both groups. Noticeable relative variations existed in some metabolic pathways such as cofactor, prosthetic group, electron carrier degradation, aldehyde degradation, and Entner-Doudoroff (ED) pathways. Overall, our findings suggest that because both groups have very similar core microbiomes and functions, the long-term disposal of tertiary TWW into Wadi Uranah may have little to no influence on the composition and function of soil bacterial communities. In addition, the long-term discharge of tertiary TWW after partially treated wastewater's initial disposal may have helped the native soil microbial community recover.}, } @article {pmid37397024, year = {2023}, author = {Gomes, A and Narciso, R and Regalado, L and Pinheiro, MC and Barros, F and Sario, S and Santos, C and Mendes, RJ}, title = {Disclosing the native blueberry rhizosphere community in Portugal-an integrated metagenomic and isolation approach.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15525}, pmid = {37397024}, issn = {2167-8359}, mesh = {*Blueberry Plants/microbiology ; Rhizosphere ; Portugal ; *Mycorrhizae/physiology ; Crops, Agricultural/microbiology ; Bacteria ; }, abstract = {BACKGORUND: The production of red fruits, such as blueberry, has been threatened by several stressors from severe periods of drought, nutrient scarcity, phytopathogens, and costs with fertilization programs with adverse consequences. Thus, there is an urgent need to increase this crop's resilience whilst promoting sustainable agriculture. Plant growth-promoting microorganisms (PGPMs) constitute not only a solution to tackle water and nutrient deficits in soils, but also as a control against phytopathogens and as green compounds for agricultural practices.

METHODS: In this study, a metagenomic approach of the local fungal and bacterial community of the rhizosphere of Vaccinium corymbosum plants was performed. At the same time, both epiphytic and endophytic microorganisms were isolated in order to disclose putative beneficial native organisms.

RESULTS: Results showed a high relative abundance of Archaeorhizomyces and Serendipita genera in the ITS sequencing, and Bradyrhizobium genus in the 16S sequencing. Diversity analysis disclosed that the fungal community presented a higher inter-sample variability than the bacterial community, and beta-diversity analysis further corroborated this result. Trichoderma spp., Bacillus spp., and Mucor moelleri were isolated from the V. corymbosum plants.

DISCUSSION: This work revealed a native microbial community capable of establishing mycorrhizal relationships, and with beneficial physiological traits for blueberry production. It was also possible to isolate several naturally-occurring microorganisms that are known to have plant growth-promoting activity and confer tolerance to hydric stress, a serious climate change threat. Future studies should be performed with these isolates to disclose their efficiency in conferring the needed resilience for this and several crops.}, } @article {pmid37396392, year = {2023}, author = {Cappelli, A and Damiani, C and Capone, A and Bozic, J and Mensah, P and Clementi, E and Spaccapelo, R and Favia, G and Ricci, I}, title = {Tripartite interactions comprising yeast-endobacteria systems in the gut of vector mosquitoes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1157299}, pmid = {37396392}, issn = {1664-302X}, abstract = {It is shown that bacteria use yeast as a niche for survival in stressful conditions, therefore yeasts may act as temporary or permanent bacterial reservoirs. Endobacteria colonise the fungal vacuole of various osmotolerant yeasts which survive and multiply in sugar-rich sources such as plant nectars. Nectar-associated yeasts are present even in the digestive system of insects and often establish mutualistic symbioses with both hosts. Research on insect microbial symbioses is increasing but bacterial-fungal interactions are yet unexplored. Here, we have focused on the endobacteria of Wickerhamomyces anomalus (formerly Pichia anomala and Candida pelliculosa), an osmotolerant yeast associated with sugar sources and the insect gut. Symbiotic strains of W. anomalus influence larval development and contribute digestive processes in adults, in addition to exerting wide antimicrobial properties for host defence in diverse insects including mosquitoes. Antiplasmodial effects of W. anomalus have been shown in the gut of the female malaria vector mosquito Anopheles stephensi. This discovery highlights the potential of utilizing yeast as a promising tool for symbiotic control of mosquito-borne diseases. In the present study, we have carried out a large Next Generation Sequencing (NGS) metagenomics analysis including W. anomalus strains associated with vector mosquitoes Anopheles, Aedes and Culex, which has highlighted wide and heterogeneous EB communities in yeast. Furthermore, we have disclosed a Matryoshka-like association in the gut of A stephensi that comprises different EB in the strain of W. anomalus WaF17.12. Our investigations started with the localization of fast-moving bacteria-like bodies within the yeast vacuole of WaF17.12. Additional microscopy analyses have validated the presence of alive intravacuolar bacteria and 16S rDNA libraries from WaF17.12 have identified a few bacterial targets. Some of these EB have been isolated and tested for lytic properties and capability to re-infect the yeast cell. Moreover, a selective competence to enter yeast cell has been shown comparing different bacteria. We suggested possible tripartite interactions among EB, W. anomalus and the host, opening new knowledge on the vector biology.}, } @article {pmid37396382, year = {2023}, author = {Trutschel, LR and Kruger, BR and Sackett, JD and Chadwick, GL and Rowe, AR}, title = {Determining resident microbial community members and their correlations with geochemistry in a serpentinizing spring.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1182497}, pmid = {37396382}, issn = {1664-302X}, abstract = {Terrestrial serpentinizing systems allow us insight into the realm of alkaliphilic microbial communities driven by geology in a way that is frequently more accessible than their deep subsurface or marine counterparts. However, these systems are also marked by geochemical and microbial community variation due to the interactions of serpentinized fluids with host geology and the surface environment. To separate the transient from the endemic microbes in a hyperalkaline environment, we assessed the Ney Springs terrestrial serpentinizing system microbial community and geochemistry at six time points over the span of a year. Using 16S rRNA gene surveys we observed 93 amplicon sequence variants (ASVs) that were found at every sampling event. This is compared to ~17,000 transient ASVs that were detected only once across the six sampling events. Of the resident community members, 16 of these ASVs were regularly greater than 1% of the community during every sampling period. Additionally, many of these core taxa experienced statistically significant changes in relative abundance with time. Variation in the abundance of some core populations correlated with geochemical variation. For example, members of the Tindallia group, showed a positive correlation with variation in levels of ammonia at the spring. Investigating the metagenome assembled genomes of these microbes revealed evidence of the potential for ammonia generation via Stickland reactions within Tindallia. This observation offers new insight into the origin of high ammonia concentrations (>70 mg/L) seen at this site. Similarly, the abundance of putative sulfur-oxidizing microbes like Thiomicrospira, Halomonas, and a Rhodobacteraceae species could be linked to changes observed in sulfur-oxidation intermediates like tetrathionate and thiosulfate. While these data supports the influence of core microbial community members on a hyperalkaline spring's geochemistry, there is also evidence that subsurface processes affect geochemistry and may impact community dynamics as well. Though the physiology and ecology of these astrobiologically relevant ecosystems are still being uncovered, this work helps identify a stable microbial community that impacts spring geochemistry in ways not previously observed in serpentinizing ecosystems.}, } @article {pmid37396369, year = {2023}, author = {Miao, Y and Bian, J and Dong, G and Dai, T}, title = {DETIRE: a hybrid deep learning model for identifying viral sequences from metagenomes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1169791}, pmid = {37396369}, issn = {1664-302X}, abstract = {A metagenome contains all DNA sequences from an environmental sample, including viruses, bacteria, archaea, and eukaryotes. Since viruses are of huge abundance and have caused vast mortality and morbidity to human society in history as a type of major pathogens, detecting viruses from metagenomes plays a crucial role in analyzing the viral component of samples and is the very first step for clinical diagnosis. However, detecting viral fragments directly from the metagenomes is still a tough issue because of the existence of a huge number of short sequences. In this study a hybrid Deep lEarning model for idenTifying vIral sequences fRom mEtagenomes (DETIRE) is proposed to solve the problem. First, the graph-based nucleotide sequence embedding strategy is utilized to enrich the expression of DNA sequences by training an embedding matrix. Then, the spatial and sequential features are extracted by trained CNN and BiLSTM networks, respectively, to enrich the features of short sequences. Finally, the two sets of features are weighted combined for the final decision. Trained by 220,000 sequences of 500 bp subsampled from the Virus and Host RefSeq genomes, DETIRE identifies more short viral sequences (<1,000 bp) than the three latest methods, such as DeepVirFinder, PPR-Meta, and CHEER. DETIRE is freely available at Github (https://github.com/crazyinter/DETIRE).}, } @article {pmid37396356, year = {2023}, author = {Ye, S and Li, S and Su, C and Shi, Z and Li, H and Hong, J and Wang, S and Zhao, J and Zheng, W and Dong, S and Ye, S and Lou, Y and Zhou, Z and Du, J}, title = {Characterization of microbial community and antibiotic resistome in intra urban water, Wenzhou China.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1169476}, pmid = {37396356}, issn = {1664-302X}, abstract = {The present study investigated the water quality index, microbial composition and antimicrobial resistance genes in urban water habitats. Combined chemicals testing, metagenomic analyses and qualitative PCR (qPCR) were conducted on 20 locations, including rivers from hospital surrounds (n = 7), community surrounds (n = 7), and natural wetlands (n = 6). Results showed that the indexes of total nitrogen, phosphorus, and ammonia nitrogen of hospital waters were 2-3 folds high than that of water from wetlands. Bioinformatics analysis revealed a total of 1,594 bacterial species from 479 genera from the three groups of water samples. The hospital-related samples had the greatest number of unique genera, followed by those from wetlands and communities. The hospital-related samples contained a large number of bacteria associated with the gut microbiome, including Alistipes, Prevotella, Klebsiella, Escherichia, Bacteroides, and Faecalibacterium, which were all significantly enriched compared to samples from the wetlands. Nevertheless, the wetland waters enriched bacteria from Nanopelagicus, Mycolicibacterium and Gemmatimonas, which are typically associated with aquatic environments. The presence of antimicrobial resistance genes (ARGs) that were associated with different species origins in each water sample was observed. The majority of ARGs from hospital-related samples were carried by bacteria from Acinetobacter, Aeromonas and various genera from Enterobacteriaceae, which each was associated with multiple ARGs. In contrast, the ARGs that were exclusively in samples from communities and wetlands were carried by species that encoded only 1 to 2 ARGs each and were not normally associated with human infections. The qPCR showed that water samples of hospital surrounds had higher concentrations of intI1 and antimicrobial resistance genes such as tetA, ermA, ermB, qnrB, sul1, sul2 and other beta-lactam genes. Further genes of functional metabolism reported that the enrichment of genes associated with the degradation/utilization of nitrate and organic phosphodiester were detected in water samples around hospitals and communities compared to those from wetlands. Finally, correlations between the water quality indicators and the number of ARGs were evaluated. The presence of total nitrogen, phosphorus, and ammonia nitrogen were significantly correlated with the presence of ermA and sul1. Furthermore, intI1 exhibited a significant correlation with ermB, sul1, and blaSHV, indicating a prevalence of ARGs in urban water environments might be due to the integron intI1's diffusion-promoting effect. However, the high abundance of ARGs was limited to the waters around the hospital, and we did not observe the geographical transfer of ARGs along with the river flow. This may be related to water purifying capacity of natural riverine wetlands. Taken together, continued surveillance is required to assess the risk of bacterial horizontal transmission and its potential impact on public health in the current region.}, } @article {pmid37396353, year = {2023}, author = {Abdullah, K and Wilkins, D and Ferrari, BC}, title = {Utilization of-Omic technologies in cold climate hydrocarbon bioremediation: a text-mining approach.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1113102}, pmid = {37396353}, issn = {1664-302X}, abstract = {Hydrocarbon spills in cold climates are a prominent and enduring form of anthropogenic contamination. Bioremediation is one of a suite of remediation tools that has emerged as a cost-effective strategy for transforming these contaminants in soil, ideally into less harmful products. However, little is understood about the molecular mechanisms driving these complex, microbially mediated processes. The emergence of -omic technologies has led to a revolution within the sphere of environmental microbiology allowing for the identification and study of so called 'unculturable' organisms. In the last decade, -omic technologies have emerged as a powerful tool in filling this gap in our knowledge on the interactions between these organisms and their environment in vivo. Here, we utilize the text mining software Vosviewer to process meta-data and visualize key trends relating to cold climate bioremediation projects. The results of text mining of the literature revealed a shift over time from optimizing bioremediation experiments on the macro/community level to, in more recent years focusing on individual organisms of interest, interactions within the microbiome and the investigation of novel metabolic degradation pathways. This shift in research focus was made possible in large part by the rise of omics studies allowing research to focus not only what organisms/metabolic pathways are present but those which are functional. However, all is not harmonious, as the development of downstream analytical methods and associated processing tools have outpaced sample preparation methods, especially when dealing with the unique challenges posed when analyzing soil-based samples.}, } @article {pmid37396352, year = {2023}, author = {Xiang, H and Hong, Y and Wu, J and Wang, Y and Ye, F and Ye, J and Lu, J and Long, A}, title = {Denitrification contributes to N2O emission in paddy soils.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1218207}, pmid = {37396352}, issn = {1664-302X}, abstract = {Denitrification is vital to nitrogen removal and N2O release in ecosystems; in this regard, paddy soils exhibit strong denitrifying ability. However, the underlying mechanism of N2O emission from denitrification in paddy soils is yet to be elucidated. In this study, the potential N2O emission rate, enzymatic activity for N2O production and reduction, gene abundance, and community composition during denitrification were investigated using the [15]N isotope tracer technique combined with slurry incubation, enzymatic activity detection, quantitative polymerase chain reaction (qPCR), and metagenomic sequencing. Results of incubation experiments showed that the average potential N2O emission rates were 0.51 ± 0.20 μmol⋅N⋅kg[-1]⋅h[-1], which constituted 2.16 ± 0.85% of the denitrification end-products. The enzymatic activity for N2O production was 2.77-8.94 times than that for N2O reduction, indicating an imbalance between N2O production and reduction. The gene abundance ratio of nir to nosZ from qPCR results further supported the imbalance. Results of metagenomic analysis showed that, although Proteobacteria was the common phylum for denitrification genes, other dominant community compositions varied for different denitrification genes. Gammaproteobacteria and other phyla containing the norB gene without nosZ genes, including Actinobacteria, Planctomycetes, Desulfobacterota, Cyanobacteria, Acidobacteria, Bacteroidetes, and Myxococcus, may contribute to N2O emission from paddy soils. Our results suggest that denitrification is highly modular, with different microbial communities collaborating to complete the denitrification process, thus resulting in an emission estimation of 13.67 ± 5.44 g N2O⋅m[-2]⋅yr[-1] in surface paddy soils.}, } @article {pmid37396350, year = {2023}, author = {Ding, Y and Wan, M and Li, Z and Ma, X and Zhang, W and Xu, M}, title = {Comparison of the gut virus communities between patients with Crohn's disease and healthy individuals.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1190172}, pmid = {37396350}, issn = {1664-302X}, abstract = {INTRODUCTION: The escalating incidence of Crohn's disease (CD), a debilitating ailment that ravages individuals and their families, has become a formidable issue over recent decades.

METHOD: In this study, fecal samples from patients with CD and healthy individuals were investigated by means of viral metagenomics.

RESULTS: The fecal virome was analyzed and some suspected disease-causing viruses were described. A polyomavirus named HuPyV with 5,120 base pairs (bp) was found in the disease group. In a preliminary analysis employing large T region-specific primers, it was found that HuPyV was present in 3.2% (1/31) of healthy samples and 43.2% (16/37) of disease samples. Additionally, two other viruses from the anellovirus and CRESS-DNA virus families were found in fecal samples from CD patients. The complete genome sequences of these two viruses were described respectively, and the phylogenetic trees have been built using the anticipated amino acid sequences of the viral proteins.

DISCUSSION: Further research is required to elucidate the relationship between these viruses and the onset and development of Crohn's disease.}, } @article {pmid37396304, year = {2023}, author = {Zhang, X and Wang, F and Yu, J and Jiang, Z}, title = {Clinical application value of metagenomic second-generation sequencing technology in hematologic diseases with and without transplantation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1135460}, pmid = {37396304}, issn = {2235-2988}, mesh = {Humans ; *Coinfection ; *Epstein-Barr Virus Infections ; Retrospective Studies ; Herpesvirus 4, Human ; *Hematologic Diseases/complications ; High-Throughput Nucleotide Sequencing ; *Klebsiella Infections ; Sensitivity and Specificity ; Metagenomics ; }, abstract = {INTRODUCTION: Hematological patients are at risk of infections. It is unknown whether the pathogenic microbial spectrum differs between HSCT and non-HSCT patients, and whether metagenomic next-generation sequencing (mNGS) of peripheral blood can be used as a substitute test specimen such as alveolar lavage.

METHODS: A retrospective study was conducted to evaluate the clinical application value of mNGS in hematological patients with and without HSCT.

RESULTS: Viruses were prevalent pathogens in both non-HSCT (44%) and HSCT (45%) patients, chiefly human cytomegalovirus and Epstein-Barr virus. In non-HSCT patients, Gram-negative bacilli accounted for 33% (predominantly Klebsiella pneumonia), and Gram-positive cocci accounted for 7% (predominantly Enterococcus faecium) of pathogens. However, in HSCT patients, Gram-negative bacilli accounted for 13% (predominantly Stenotrophomonas maltophilia), and Gram-positive cocci accounted for 24% (predominantly Streptococcus pneumonia) of pathogens. Mucor was the most common fungu s in two groups. The positive rate of pathogens by mNGS was 85.82%, higher than conventional detection (20.47%, P < 0.05). Mixed infection accounted for 67.00%, among which the mixed infection of bacteria and virus (25.99%) was the most common. 78 cases had pulmonary infection, the positive rate of traditional laboratory tests was 42.31% (33/78), and of mNGS in peripheral blood was 73.08% (57/78), showing a statistical difference (P = 0.000). The non-HSCT patients had a higher frequency of Klebsiella pneumonia (OR=0.777, 95% CI, 0.697-0.866, P = 0.01) and Torque teno virus (OR=0.883, 95% CI, 0.820-0.950, P = 0.031) infections than HSCT patients, while the rates of Streptococcus pneumonia (OR=12.828, 95% CI, 1.378-119.367, P = 0.016), Candida pseudosmooth (OR=1.100, 95% CI, 0.987-1.225, P = 0.016), human betaherpesvirus 6B (OR=6.345, 95% CI, 1.105-36.437, P = 0.039) and human polyomavirus 1 (OR=1.100, 95% CI, 0.987-1.225, P = 0.016) infections were lower. Leishmania could be detected by mNGS.

CONCLUSION: mNGS of peripheral blood can be used as a substitute test method for hematological patients with pulmonary infection, the detection rate of mixed infections by mNGS was high, and mNGS has high clinical recognition rate and sensitivity in pathogen detection, and provides a basis for guiding the anti-infective treatment in hematological diseases with symptoms such as fever.}, } @article {pmid37396300, year = {2023}, author = {Kim, H and Hong, JS and Yun, PY and Hwang, KG and Kim, KS and Lee, HJ and Park, KU}, title = {Exploration of the interplay between spatially distinct microbial habitats through comparative analysis.}, journal = {Journal of oral microbiology}, volume = {15}, number = {1}, pages = {2229693}, pmid = {37396300}, issn = {2000-2297}, abstract = {OBJECTIVES: The oral microbiome is closely associated with systemic diseases, indicating the presence of bacteremia and inflammatory mediators in the systemic circulation. Our research aims to investigate the relationship between the oral microbiome and other microbial habitats.

METHODS: We analyzed 180 specimens from 36 patients, including saliva, buccal swab, plaque, stool, and blood samples from a healthy group (Non_PD, n = 18) and a periodontitis group (PD, n = 18). The final analysis included 147 specimens, with varying sample sizes for each group. Metagenomic analysis was performed using prokaryotic 16S rRNA on the MiSeq platform (Illumina).

RESULTS: PD saliva showed significant richness differences (P's < 0.05), similar to plaque. Buccal swabs had slight variations. Microbial network analysis revealed altered microbial interactions in the PD group, with decreased interactions in saliva and buccal swabs, and increased interactions in plaque. In our analysis of nine specimens where all paired habitat samples could be analyzed, microorganisms linked to oral periodontitis were found in sterile blood samples, resembling the oral cavity's composition.

CONCLUSIONS: Microbiome differences should consider overall microbial-environment interactions, alongside diversity and richness. Our data cautiously suggest that disease-related changes in the salivary microbiome may be reflected in blood specimens through the oral-blood axis.}, } @article {pmid37396070, year = {2023}, author = {Zhang, X and Chen, H and Lin, Y and Yang, M and Zhao, H and Hu, J and Han, D}, title = {Diagnosis of Non-Tuberculous Mycobacterial Pulmonary Disease by Metagenomic Next-Generation Sequencing on Bronchoalveolar Lavage Fluid.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {4137-4145}, pmid = {37396070}, issn = {1178-6973}, abstract = {PURPOSE: Metagenomic next-generation sequencing (mNGS) has been extensively used in the diagnosis of infectious diseases but has rarely been applied in non-tuberculous mycobacterial pulmonary disease (NTMPD). This study analyzed the diagnostic performance of mNGS in bronchoalveolar lavage fluid (BALF) samples to identify non-tuberculous mycobacteria (NTM).

PATIENTS AND METHODS: A total of 231 patients with suspected NTMPD were recruited from the First Affiliated Hospital, School of Medicine, Zhejiang University, from March 2021 to October 2022. A total of 118 cases were ultimately included. Of these patients, 61 cases were enrolled in the NTMPD group, 23 cases were enrolled in the suspected-NTMPD group, and 34 cases were enrolled in the non-NTMPD group. The diagnostic performance of traditional culture, acid-fast staining (AFS), and mNGS for NTMPD was assessed.

RESULTS: Patients in the NTMPD group had a higher proportion of bronchiectasis (P=0.007). Among mNGS-positive samples in the NTMPD group, a significantly higher reads number of NTM was observed in AFS-positive patients [61.50 (22.00, 395.00) vs 15.50 (6.00, 36.25), P=0.008]. Meanwhile, mNGS demonstrated a sensitivity of 90.2%, which was far superior to AFS (42.0%) and culture (77.0%) (P<0.001). The specificity of mNGS in detecting NTM was 100%, which was the same as that of traditional culture. The area under the receiver operating characteristic curve of mNGS was 0.951 (95% CI 0.906-0.996), which was higher than that of culture (0.885 [95% CI 0.818-0.953]) and AFS (0.686 [95% CI 0.562-0.810]). In addition to NTM, other pulmonary pathogens were also found by mNGS.

CONCLUSION: mNGS using BALF samples is a rapid and effective diagnostic tool for NTMPD, and mNGS is recommended for patients with suspected NMTPD or NTM coinfected pneumonia.}, } @article {pmid37395658, year = {2023}, author = {Androsiuk, L and Shay, T and Tal, S}, title = {Characterization of the Environmental Plasmidome of the Red Sea.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0040023}, pmid = {37395658}, issn = {2165-0497}, mesh = {Indian Ocean ; Plasmids/genetics ; *Anti-Bacterial Agents ; *Metagenomics ; Metagenome ; }, abstract = {Plasmids contribute to microbial diversity and adaptation, providing microorganisms with the ability to thrive in a wide range of conditions in extreme environments. However, while the number of marine microbiome studies is constantly increasing, very little is known about marine plasmids, and they are very poorly represented in public databases. To extend the repertoire of environmental marine plasmids, we established a pipeline for the de novo assembly of plasmids in the marine environment by analyzing available microbiome metagenomic sequencing data. By applying the pipeline to data from the Red Sea, we identified 362 plasmid candidates. We showed that the distribution of plasmids corresponds to environmental conditions, particularly, depth, temperature, and physical location. At least 7 of the 362 candidates are most probably real plasmids, based on a functional analysis of their open reading frames (ORFs). Only one of the seven has been described previously. Three plasmids were identified in other public marine metagenomic data from different locations all over the world; these plasmids contained different cassettes of functional genes at each location. Analysis of antibiotic and metal resistance genes revealed that the same positions that were enriched with genes encoding resistance to antibiotics were also enriched with resistance to metals, suggesting that plasmids contribute site-dependent phenotypic modules to their ecological niches. Finally, half of the ORFs (50.8%) could not be assigned to a function, emphasizing the untapped potential of the unique marine plasmids to provide proteins with multiple novel functions. IMPORTANCE Marine plasmids are understudied and hence underrepresented in databases. Plasmid functional annotation and characterization is complicated but, if successful, may provide a pool of novel genes and unknown functions. Newly discovered plasmids and their functional repertoire are potentially valuable tools for predicting the dissemination of antimicrobial resistance, providing vectors for molecular cloning and an understanding of plasmid-bacterial interactions in various environments.}, } @article {pmid37394812, year = {2023}, author = {Li, C and Wu, Y and Li, L and Zhao, C and Li, B and Wu, Y and Wang, H and Yan, Z}, title = {Different techniques reveal the difference of community structure and function of fungi from root and rhizosphere of Salvia miltiorrhiza Bunge.}, journal = {Plant biology (Stuttgart, Germany)}, volume = {25}, number = {6}, pages = {848-859}, doi = {10.1111/plb.13556}, pmid = {37394812}, issn = {1438-8677}, support = {81973416//Natural Science Foundation of China/ ; CXTD2018017//Chengdu University of Traditional Chinese Medicine Characteristic Innovative Research Team Project/ ; 2021YJ0113//Sichuan Science and Technology Program/ ; }, mesh = {Rhizosphere ; *Salvia miltiorrhiza/genetics/metabolism/microbiology ; Fungi/genetics ; Soil Microbiology ; Plant Roots/microbiology ; *Cellulases/metabolism ; }, abstract = {Fungi have essential functions in plant health and performance. However, the plant-associated functions of many cultured fungi have not been established in detail. Here, the fungal species diversity in Salvia miltiorrhiza roots and rhizosphere was assessed for the first time using culturomics and high-throughput sequencing. We present a comprehensive functional metagenomic analysis of these fungi and verified activity of cellulase and chitinase predicted in the metagenomic analysis. We first collected and cultured fungi from the root and rhizosphere of S. miltiorrhiza. We found 92 species across 37 families and five phyla, with Ascomycota being dominant. Many rDNA internal transcribed spacer sequences could not be assigned to lower taxonomic levels. There were 19 genera of endophytic fungi and 37 genera of rhizosphere fungi. The culturomics approach had lower taxonomic diversity than high-throughput sequencing, but some fungi were only found in cultures. Structural analyses indicated that the dominant species differed in cultured and non-cultured samples at other levels, apart from the phylum level. Functional analysis mapped 223 carbohydrate enzyme families and 393 pathways in the CAZy and KEGG databases, respectively. The most abundant families were glycoside hydrolases and those involved in carbohydrate metabolism. As predicted by metagenomics, we experimentally verified cellulase and chitinase activity for 29 and 74 fungi, respectively. We provide the first evidence of biomass recycling by fungi that are associated with plants. Culturing is essential to reveal the hidden microbial community and critical functions in plant-microbe interactions.}, } @article {pmid37394467, year = {2023}, author = {Zhu La, AT and Feng, Y and Hu, D and Feng, Y and Jin, X and Liu, D and Guo, Y and Cheng, G and Hu, Y}, title = {Enzymatically prepared alginate oligosaccharides improve broiler chicken growth performance by modulating the gut microbiota and growth hormone signals.}, journal = {Journal of animal science and biotechnology}, volume = {14}, number = {1}, pages = {96}, pmid = {37394467}, issn = {1674-9782}, support = {2021YFD1800400//National Key Research and Development Program of China/ ; 6222032//Beijing Natural Science Foundation/ ; }, abstract = {BACKGROUND: Alginate oligosaccharide (AOS) holds great potential as a novel feed supplement in farm animals. However, the effects of AOS on chicken health and the underlying mechanisms are not fully understood. This study aimed to optimize the enzymatic preparation of AOS by using bacterial alginate lyases expressed in yeast, investigate the effects of the prepared AOS on the growth performance and gut health of broiler chickens, and reveal the underlying mechanisms.

RESULTS: Five alginate lyases from bacteria were cloned into Pichia pastoris GS115 and the alginate lyase PDE9 was expressed at relatively high yield, activity and stability in P. pastoris. Animal trials were carried out using 320 1-day-old male Arbor Acres broilers (four groups; 8 replicates/group × 10 chicks/replicate) receiving either a basal diet or the same diet supplemented with 100, 200 and 400 mg/kg PDE9-prepared AOS for 42 d. The results showed that dietary supplementation of 200 mg/kg AOS displayed the highest activity in promoting the birds' ADG and ADFI (P < 0.05). AOS ameliorated the intestinal morphology, absorption function and barrier function, as indicated by the enhanced (P < 0.05) intestinal villus height, maltase activity, and the expression of PEPT, SGLT1, ZNT1, and occludin. AOS also increased serum insulin-like growth factor-1, ghrelin (P < 0.05), and growth hormone (P < 0.1). Moreover, the concentrations of acetate, isobutyrate, isovalerate, valerate, and total SCFAs in cecum of birds fed AOS were significantly higher than the control birds (P < 0.05). Metagenomic analysis indicated that AOS modulated the chicken gut microbiota structure, function, and microbial interactions and promoted the growth of SCFAs-producing bacteria, for example, Dorea sp. 002160985; SCFAs, especially acetate, were found positively correlated with the chicken growth performance and growth-related hormone signals (P < 0.05). We further verified that AOS can be utilized by Dorea sp. to grow and to produce acetate in vitro.

CONCLUSIONS: We demonstrated that the enzymatically produced AOS effectively promoted broiler chicken growth performance by modulating the chicken gut microbiota structure and function. For the first time, we established the connections among AOS, chicken gut microbiota/SCFAs, growth hormone signals and chicken growth performance.}, } @article {pmid37394189, year = {2023}, author = {Li, X and Wu, Y and Wang, H and Wen, J and Zhu, M}, title = {Effects of microorganisms on the migration and transformation of typical heavy metal (loid)s in mercury-thallium mining waste slag during the combined application of fish manure and natural minerals.}, journal = {Chemosphere}, volume = {337}, number = {}, pages = {139385}, doi = {10.1016/j.chemosphere.2023.139385}, pmid = {37394189}, issn = {1879-1298}, mesh = {Thallium/analysis ; *Mercury ; Manure ; *Metals, Heavy/analysis ; Minerals/analysis ; Phosphorus ; }, abstract = {Mercury-thallium mining waste slag has the characteristics of extremely acidic, low fertility and highly toxic polymetallic composite pollution, making it difficult to be treated. We use nitrogen- and phosphorus-rich natural organic matter (fish manure) and calcium- and phosphorus-rich natural minerals (carbonate and phosphate tailings) individually or in combination to amend the slag, analyze their effects on the migration and transformation of potentially toxic elements (Tl and As) in the waste slag. We set up sterile and non-sterile treatments specifically to further investigate the direct or indirect effect of microorganisms attached to added organic matter on Tl and As. The results showed that addition of fish manure and natural minerals to the non-sterile treatments promoted the release of As and Tl, resulting in an increase in As and Tl concentrations in the tailing lixiviums from 0.57 to 2.38-6.37 μg/L and from 69.92 to 107.51-157.21 μg/L, respectively. Sterile treatments promoted the release of As (from 0.28 to 49.88-104.18 μg/L) and inhibited the release of Tl (from 94.53 to 27.60-34.50 μg/L). Use of fish manure and natural minerals alone or in combination significantly reduced the biotoxicity of the mining waste slag, in which the combination was more efficient. XRD analysis showed that microorganisms in the medium promoted the dissolution of jarosite and other minerals, which indicated that the release and migration of As and Tl in Hg-Tl mining waste slag were closely related to microbial activities. Furthermore, metagenomic sequencing revealed that microorganisms such as Prevotella, Bacteroides, Geobacter, and Azospira, which were abundant in the non-sterile treatments, had remarkable resistance to a variety of highly toxic heavy metals and could affect the dissolution of minerals and the release and migration of heavy metals through redox reactions. Our results may aid in the rapid soilless ecological restoration of related large multi-metal waste slag dumps.}, } @article {pmid37394044, year = {2023}, author = {Du, J and Zhou, X and Yin, Q and Zuo, J and Wu, G}, title = {Revealing impacts of operational modes on anaerobic digestion systems coupling with sulfate reduction.}, journal = {Bioresource technology}, volume = {385}, number = {}, pages = {129431}, doi = {10.1016/j.biortech.2023.129431}, pmid = {37394044}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Bioreactors ; *Wastewater ; Sulfur Oxides ; Sulfates/metabolism ; Ethanol ; Methane/metabolism ; }, abstract = {Anaerobic digestion (AD) is promising for treating high-strength wastewater. However, the effect of operational parameters on microbial communities of AD with sulfate is not yet fully understood. To explore this, four reactors were operated under rapid- and slow-filling modes with different organic carbons. Reactors in the rapid-filling mode generally exhibited a fast kinetic property. For example, the degradation of ethanol was 4.6 times faster in ASBRER than in ASBRES, and the degradation of acetate was 11.2 times faster in ASBRAR than in ASBRAS. Nevertheless, reactors in the slow-filling mode could mitigate propionate accumulation when using ethanol as organic carbon. Taxonomic and functional analysis further supported that rapid- and slow-filling modes were suitable for the growth of r-strategists (e.g., Desulfomicrobium) and K-strategists (e.g., Geobacter), respectively. Overall, this study provides valuable insights into microbial interactions of AD processes with sulfate through the application of the r/K selection theory.}, } @article {pmid37393724, year = {2023}, author = {He, Y and Pan, J and Huang, D and Sanford, RA and Peng, S and Wei, N and Sun, W and Shi, L and Jiang, Z and Jiang, Y and Hu, Y and Li, S and Li, Y and Li, M and Dong, Y}, title = {Distinct microbial structure and metabolic potential shaped by significant environmental gradient impacted by ferrous slag weathering.}, journal = {Environment international}, volume = {178}, number = {}, pages = {108067}, doi = {10.1016/j.envint.2023.108067}, pmid = {37393724}, issn = {1873-6750}, mesh = {Humans ; *Bacteria/genetics ; Metagenome ; *Microbiota ; Weather ; Carbon/metabolism ; }, abstract = {Alkaline ferrous slags pose global environmental issues and long-term risks to ambient environments. To explore the under-investigated microbial structure and biogeochemistry in such unique ecosystems, combined geochemical, microbial, ecological and metagenomic analyses were performed in the areas adjacent to a ferrous slag disposal plant in Sichuan, China. Different levels of exposure to ultrabasic slag leachate had resulted in a significant geochemical gradient of pH (8.0-12.4), electric potential (-126.9 to 437.9 mV), total organic carbon (TOC, 1.5-17.3 mg/L), and total nitrogen (TN, 0.17-1.01 mg/L). Distinct microbial communities were observed depending on their exposure to the strongly alkaline leachate. High pH and Ca[2+] concentrations were associated with low microbial diversity and enrichment of bacterial classes Gamma-proteobacteria and Deinococci in the microbial communities exposed to the leachate. Combined metagenomic analyses of 4 leachate-unimpacted and 2-impacted microbial communities led to the assembly of one Serpentinomonas pangenome and 81 phylogenetically diversified metagenome assembled genomes (MAGs). The prevailing taxa in the leachate-impacted habitats (e.g., Serpentinomonas and Meiothermus spp.) were phylogenetically related to those in active serpentinizing ecosystems, suggesting the analogous processes between the man-made and natural systems. More importantly, they accounted for significant abundance of most functional genes associated with environmental adaptation and major element cycling. Their metabolic potential (e.g., cation/H[+] antiporters, carbon fixation on lithospheric carbon source, and respiration coupling sulfur oxidization and oxygen or nitrate reduction) may support these taxa to survive and prosper in these unique geochemical niches. This study provides fundamental understandings of the adaptive strategies of microorganisms in response to the strong environmental perturbation by alkali tailings. It also contributes to a better comprehension of how to remediate environments affected by alkaline industrial material.}, } @article {pmid37393557, year = {2023}, author = {Madrigal-Trejo, D and Sánchez-Pérez, J and Espinosa-Asuar, L and Valdivia-Anistro, JA and Eguiarte, LE and Souza, V}, title = {A Metagenomic Time-Series Approach to Assess the Ecological Stability of Microbial Mats in a Seasonally Fluctuating Environment.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2252-2270}, pmid = {37393557}, issn = {1432-184X}, support = {IG200319//Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México/ ; 970341//Consejo Nacional de Ciencia y Tecnología (CONACYT)/ ; R20F009//http://dx.doi.org/10.13039/501100020884/ ; }, mesh = {Metagenome ; *Cyanobacteria/genetics ; Archaea/genetics ; *Microbiota ; Bacteroidetes/genetics ; }, abstract = {Microbial mats are complex ecological assemblages that have been present in the rock record since the Precambrian and can still be found in extant marginalized environments. These structures are considered highly stable ecosystems. In this study, we evaluate the ecological stability of dome-forming microbial mats in a modern, water-level fluctuating, hypersaline pond located in the Cuatro Ciénegas Basin, Mexico. We conducted metagenomic sampling of the site from 2016 to 2019 and detected 2250 genera of Bacteria and Archaea, with only <20 belonging to the abundant taxa (>1%). The microbial community was dominated by Proteobacteria, Euryarchaeota, Bacteroidetes, Firmicutes, and Cyanobacteria, and was compositionally sensitive to disturbances, leading to high taxonomic replacement even at the phylum level, with a significant increase in Archaea from [Formula: see text]1-4% to [Formula: see text]33% throughout the 2016-2019 study period. Although a core community represented most of the microbial community (>75%), relative abundances shifted significantly between samples, as demonstrated by changes in the abundance of Coleofasciculus from 10.2% in 2017 to 0.05% in 2019. Although functional differences between seasons were subtle, co-occurrence networks suggest differential ecological interactions between the seasons, with the addition of a new module during the rainy season and the potential shift in hub taxa. Functional composition was slightly more similar between samples, but basic processes such as carbohydrate, amino acid, and nucleic acid metabolisms were widely distributed among samples. Major carbon fixation processes included sulfur oxidation, nitrogen fixation, and photosynthesis (both oxygenic and anoxygenic), as well as the Wood-Ljundgahl and Calvin cycles.}, } @article {pmid37392922, year = {2023}, author = {Tian, F and Zhou, B and Li, X and Zhang, Y and Qi, D and Qi, H and Jiang, H and Zhao, K and Liu, S}, title = {Population genomics analysis to identify ion and water transporter genes involved in the adaptation of Tibetan naked carps to brackish water.}, journal = {International journal of biological macromolecules}, volume = {247}, number = {}, pages = {125605}, doi = {10.1016/j.ijbiomac.2023.125605}, pmid = {37392922}, issn = {1879-0003}, mesh = {*Carps/genetics/physiology ; Animals ; Polymorphism, Single Nucleotide ; *Aquaporin 3/genetics ; *Fish Proteins/genetics ; Adaptation, Physiological ; Salinity ; Metagenomics ; }, abstract = {Understanding how evolutionary processes shape the genetic variations and influence the response of species to environmental alterations is critical for biodiversity conservation and molecular breeding. Gymnocypris przewalskii przewalskii is the only known cyprinid fish that dwells in the brackish water of Lake Qinghai on the Qinghai-Tibetan Plateau. To reveal the genetic basis of its adaptation to high salinity and alkalinity, whole-genome sequencing was performed in G. p. przewalskii and its freshwater relatives Gymnocypris eckloni and Gymnocypris przewalskii ganzihonensis. Compared with freshwater species, lower genetic diversity and higher linkage disequilibrium were observed in G. p. przewalskii. Selective sweep analysis identified 424 core-selective genes enriched in transport activities. Transfection analysis showed that genetic changes in the positively selected gene aquaporin 3 (AQP3) improved cell viability after salt treatment, suggesting its involvement in brackish water adaptation. Our analysis indicates that ion and water transporter genes experienced intensive selection, which might have contributed to the maintenance of high osmolality and ion content in G. p. przewalskii. The current study identified key molecules involved in the adaptation of fish to brackish water, providing valuable genomic resources for the molecular breeding of salt-tolerant fish.}, } @article {pmid37392873, year = {2023}, author = {Li, ZT and Yang, SY and Zhao, HP}, title = {The effects of arsenic on dechlorination of trichloroethene by consortium DH: Microbial response and resistance.}, journal = {The Science of the total environment}, volume = {896}, number = {}, pages = {165219}, doi = {10.1016/j.scitotenv.2023.165219}, pmid = {37392873}, issn = {1879-1026}, mesh = {*Chloroflexi/metabolism ; *Trichloroethylene/metabolism ; *Arsenic/metabolism ; Bacteria/metabolism ; *Microbiota ; Biodegradation, Environmental ; *Vinyl Chloride ; }, abstract = {Inorganic arsenic and organochlorines are frequently co-occurring contaminants in anoxic groundwater environments, and the bioremediation of their composite pollution has long been a rigorous predicament. Currently, the dechlorination behaviors and stress responses of microbial dechlorination consortia to arsenic are not yet fully understood. This study assessed the reductive dechlorination performance of a Dehalococcoides-bearing microcosm DH under gradient concentrations of arsenate [As(V)] or arsenite [As(III)] and investigated the response patterns of different functional microorganisms. Our results demonstrated that although the dechlorination rates declined with increasing arsenic concentrations in both As(III/V) scenarios, the inhibitory impact was more pronounced in As(III)-amended groups compared to As(V)-amended groups. Moreover, the vinyl chloride (VC)-to-ethene step was more susceptible to arsenic exposure compared to the trichloroethene (TCE)-to-dichloroethane (DCE) step, while high levels of arsenic exposure [e.g. As(III) > 75 μM] can induce significant accumulation of VC. Functional gene variations and microbial community analyses revealed that As(III/V) affected reductive dechlorination by directly inhibiting organohalide-respiring bacteria (OHRB) and indirectly inhibiting synergistic populations such as acetogens. Metagenomic results indicated that arsenic metabolic and efflux mechanisms were identical among different Dhc strains, and variations in arsenic uptake pathways were possibly responsible for their differential responses to arsenic exposures. By comparison, fermentative bacteria showed high potential for arsenic resistance due to their inherent advantages in arsenic detoxification and efflux mechanisms. Collectively, our findings expanded the understanding of the response patterns of different functional populations to arsenic stress in the dechlorinating consortium and provided insights into modifying bioremediation strategies at co-contaminated sites for furtherance.}, } @article {pmid37392822, year = {2023}, author = {Rothstein, AP and Jesser, KJ and Feistel, DJ and Konstantinidis, KT and Trueba, G and Levy, K}, title = {Population genomics of diarrheagenic Escherichia coli uncovers high connectivity between urban and rural communities in Ecuador.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {113}, number = {}, pages = {105476}, pmid = {37392822}, issn = {1567-7257}, support = {K01 AI103544/AI/NIAID NIH HHS/United States ; R01 AI137679/AI/NIAID NIH HHS/United States ; T32 ES007032/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Escherichia coli ; *Escherichia coli Infections/epidemiology/microbiology ; Diarrhea/epidemiology ; Rural Population ; Ecuador/epidemiology ; Metagenomics ; Travel ; }, abstract = {Human movement may be an important driver of transmission dynamics for enteric pathogens but has largely been underappreciated except for international 'travelers' diarrhea or cholera. Phylodynamic methods, which combine genomic and epidemiological data, are used to examine rates and dynamics of disease matching underlying evolutionary history and biogeographic distributions, but these methods often are not applied to enteric bacterial pathogens. We used phylodynamics to explore the phylogeographic and evolutionary patterns of diarrheagenic E. coli in northern Ecuador to investigate the role of human travel in the geographic distribution of strains across the country. Using whole genome sequences of diarrheagenic E. coli isolates, we built a core genome phylogeny, reconstructed discrete ancestral states across urban and rural sites, and estimated migration rates between E. coli populations. We found minimal structuring based on site locations, urban vs. rural locality, pathotype, or clinical status. Ancestral states of phylogenomic nodes and tips were inferred to have 51% urban ancestry and 49% rural ancestry. Lack of structuring by location or pathotype E. coli isolates imply highly connected communities and extensive sharing of genomic characteristics across isolates. Using an approximate structured coalescent model, we estimated rates of migration among circulating isolates were 6.7 times larger for urban towards rural populations compared to rural towards urban populations. This suggests increased inferred migration rates of diarrheagenic E. coli from urban populations towards rural populations. Our results indicate that investments in water and sanitation prevention in urban areas could limit the spread of enteric bacterial pathogens among rural populations.}, } @article {pmid37392645, year = {2023}, author = {Sułowicz, S and Borymski, S and Dulski, M and Nowak, A and Bondarczuk, K and Markowicz, A}, title = {Nanopesticide risk assessment based on microbiome profiling - Community structure and functional potential as biomarkers in captan@ZnO35-45 nm and captan@SiO220-30 nm treated orchard soil.}, journal = {Journal of hazardous materials}, volume = {458}, number = {}, pages = {131948}, doi = {10.1016/j.jhazmat.2023.131948}, pmid = {37392645}, issn = {1873-3336}, mesh = {Captan ; Soil/chemistry ; Silicon Dioxide ; *Zinc Oxide ; Phylogeny ; *Pesticides ; *Microbiota ; Biomarkers ; Soil Microbiology ; }, abstract = {Nanoformulation should minimise the usage of pesticides and limit their environmental footprint. The risk assessment of two nanopesticides with fungicide captan as an active organic substance and ZnO35-45 nm or SiO220-30 nm as nanocarriers was evaluated using the non-target soil microorganisms as biomarkers. The first time for that kind of nanopesticides next-generation sequencing (NGS) of bacterial 16 S rRNA and fungal ITS region and metagenomics functional predictions (PICRUST2) was made to study structural and functional biodiversity. During a 100-day microcosm study in soil with pesticide application history, the effect of nanopesticides was compared to pure captan and both nanocarriers. Nanoagrochemicals affected microbial composition, especially Acidobacteria-6 class, and alpha diversity, but the observed effect was generally more substantial for pure captan. As for beta diversity, the negative impact was detected only in response to captan and still observed on day 100. Fungal community in the orchard soil showed only a decrease in phylogenetic diversity in captan set-up since day 30. PICRUST2 analysis confirmed several times lower impact of nanopesticides considering the abundance of functional pathways and genes encoding enzymes. Furthermore, the overall data indicated that using SiO220-30 nm as a nanocarrier speeds up a recovery process compared to ZnO35-45 nm.}, } @article {pmid37392592, year = {2023}, author = {Kumar, M and Chaudhary, DR and Jha, B}, title = {Surface-associated bacterial assemblages on marine anthropogenic litter in the intertidal zone of the Arabian Sea, India.}, journal = {Marine pollution bulletin}, volume = {193}, number = {}, pages = {115211}, doi = {10.1016/j.marpolbul.2023.115211}, pmid = {37392592}, issn = {1879-3363}, mesh = {*Ecosystem ; *Polystyrenes ; Plastics ; Bacteria ; Polyethylene ; }, abstract = {Anthropogenic marine litter (mainly plastic pollution) is a serious concern globally. The interactions between terrestrial and marine ecosystems lead to the accumulation of marine litter in the intertidal zone. The biofilm-forming bacteria tend to colonize on surfaces of marine litter which are composed of diverse bacteria and are less studied. The present study investigated the bacterial community composition using both culturable and non-culturable (Next-generation sequencing (NGS)) approaches associated with the marine litter (polyethylene (PE), styrofoam (SF) and fabric (FB)) at three distinct locations (Alang, Diu and Sikka) of the Arabian Sea, Gujarat, India. Predominant bacteria observed using culturable and NGS techniques belonged to Proteobacteria phyla. Alphaproteobacteria class dominated on polyethylene and styrofoam surfaces in the culturable fraction among the sites while the Bacillus dominated fabric surfaces. In the metagenomics fraction, Gammaproteobacteria dominated the surfaces except for PE and SF surfaces from Sikka and Diu, respectively. The PE surface at Sikka was dominated by Fusobacteriia while SF surface from Diu was dominated by Alphaproteobacteria. Both culture-dependent and NGS approaches identified hydrocarbon-degrading bacteria as well as pathogenic bacteria on the surfaces. The outcome of the present study illustrates diverse bacterial assemblages which occur on marine litter and increases our understanding of the plastisphere community.}, } @article {pmid37392508, year = {2023}, author = {Zhou, L and Sang, S and Li, J and Li, Y and Wang, D and Gan, L and Zhao, Z and Wang, J}, title = {From waste to resource: Metagenomics uncovers the molecular ecological resources for plastic degradation in estuaries of South China.}, journal = {Water research}, volume = {242}, number = {}, pages = {120270}, doi = {10.1016/j.watres.2023.120270}, pmid = {37392508}, issn = {1879-2448}, mesh = {*Estuaries ; Plastics ; Metagenomics ; Phylogeny ; China ; Rivers/chemistry ; Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; }, abstract = {Estuaries are hotspots of plastic pollution due to accumulated waste from surrounding rivers and coasts. However, the molecular ecological resources that possess plastic-degrading traits and their biogeographic distributions in estuarine waters remain to be elucidated. In this study, we mapped the distribution profiles of plastic-degrading genes (PDGs) in 30 subtropical estuaries in China based on metagenomic sequencing. A total of 41 PDG subtypes were observed in these estuaries. The Pearl River Estuary had higher diversity and abundance of PDGs than the east and west region estuaries. Genes for degrading synthetic heterochain and natural plastics were the most diverse and abundant types, respectively. The abundance of synthetic PDGs was significantly higher in estuaries affected by intense anthropogenic activities. Further binning strategies revealed diverse microbes with plastic-degrading ability in these estuaries. Rhodobacteraceae, a dominant plastic-degrading bacterial family, primarily carried PDGs for degrading natural plastics. Pseudomonas veronii carrying diverse PDGs was identified, which may be of value for further technical improvement of plastic degradation. In addition, phylogenetic and structural analyses of 19 putative 3HV dehydrogenases, the most diverse and abundant DPGs, showed inconsistent evolution with their hosts, but different sequences were conserved with consistent key functional amino acids. A potential biodegradation pathway for polyhydroxybutyrate by Rhodobacteraceae was proposed. The result implied that plastic-degrading functions are widely distributed in estuarine waters and metagenomics could be used as a promising screening tool for large-scale profiling of plastic-degrading potential in the natural environment. Our findings have important implications and provide potential molecular ecological resources for developing plastic waste removal technologies.}, } @article {pmid37392346, year = {2023}, author = {Van Borm, S and Roupie, V and Linden, A and Vangeluwe, D and De Waele, V and Lambrecht, B and Steensels, M}, title = {RNA sequencing of avian paramyxovirus (Paramyxoviridae, Avulavirinae) isolates from wild mallards in Belgium, 2021: complete genomes and coinfections.}, journal = {Virus genes}, volume = {59}, number = {5}, pages = {723-731}, pmid = {37392346}, issn = {1572-994X}, mesh = {Animals ; *Avulavirus/genetics ; Paramyxoviridae/genetics ; Belgium ; *Coinfection/veterinary ; Phylogeny ; Ducks ; Poultry ; Newcastle disease virus/genetics ; *Influenza in Birds ; Sequence Analysis, RNA ; RNA ; }, abstract = {We used untargeted RNA sequencing to characterize three Avulavirinae isolates from pooled samples obtained from wild mallards in Belgium in 2021. The complete genome sequences of two avian Orthoavulavirus-1 (AOAV-1) strains and one avian Paraavulavirus-4 (APMV-4) strain were determined confirming hemagglutination inhibition testing of the virus isolates. In addition, the applied sequencing strategy identified an avian influenza virus (AIV) coinfection in all three virus isolates, confirming weak-positive AIV realtime RT-PCR results from the original sample material. In one AOAV-1 isolate, partial sequences covering all genome segments of an AIV of subtype H11N9 could be de novo assembled from the sequencing data. Besides an AIV coinfection, RNA metagenomic data from the APMV-4 isolate also showed evidence of Alpharetrovirus and Megrivirus coinfection. In total, two AOAV-1 of Class II, genotype I.2 and one APMV-4 complete genome sequences were assembled and compared to publicly available sequences, highlighting the importance of surveillance for poultry pathogens in wild birds. Beyond the insights from full genome characterization of virus isolates, untargeted RNA sequencing strategies provide additional insights in the RNA virome of clinical samples as well as their derived virus isolates that are particularly useful when targeting wild avifauna reservoirs of poultry pathogens.}, } @article {pmid37392210, year = {2023}, author = {Coe, GL and Krout, IN and Munro-Ehrlich, M and Beamish, CR and Vorojeikina, D and Colman, DR and Boyd, EJ and Walk, ST and Rand, MD}, title = {Assessing the role of the gut microbiome in methylmercury demethylation and elimination in humans and gnotobiotic mice.}, journal = {Archives of toxicology}, volume = {97}, number = {9}, pages = {2399-2418}, pmid = {37392210}, issn = {1432-0738}, support = {ES030940/ES/NIEHS NIH HHS/United States ; ES001247/ES/NIEHS NIH HHS/United States ; T32 207026/ES/NIEHS NIH HHS/United States ; ES030940/ES/NIEHS NIH HHS/United States ; ES001247/ES/NIEHS NIH HHS/United States ; T32 207026/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; *Methylmercury Compounds/toxicity/metabolism ; *Gastrointestinal Microbiome ; *Microbiota ; Kinetics ; Demethylation ; }, abstract = {The risk of methylmercury (MeHg) toxicity following ingestion of contaminated foodstuffs (e.g., fish) is directly related to the kinetics of MeHg elimination among individuals. Yet, the factors driving the wide range of inter-individual variability in MeHg elimination within a population are poorly understood. Here, we investigated the relationship between MeHg elimination, gut microbiome demethylation activity, and gut microbiome composition using a coordinated human clinical trial and gnotobiotic mouse modeling approach together with metagenomic sequence analysis. We first observed MeHg elimination half-lives (t1/2) ranging from 28 to 90 days across 27 volunteers. Subsequently, we found that ingestion of a prebiotic induced changes in the gut microbiome and mixed effects (increased, decrease, and no effect) on elimination in these same individuals. Nonetheless, elimination rates were found to correlate with MeHg demethylation activity in cultured stool samples. In mice, attempts to remove the microbiome via generation of germ-free (GF) animals or through antibiotic (Abx) treatment both diminished MeHg demethylation to a similar extent. While both conditions substantially slowed elimination, Abx treatment resulted in significantly slower elimination than the GF condition, indicating an additional role for host-derived factors in supporting elimination. Human fecal microbiomes transplanted to GF mice restored elimination rates to that seen in control mice. Metagenomic sequence analysis of human fecal DNA did not identify genes encoding proteins typically involved in demethylation (e.g., merB, organomercury lyase). However, the abundance of several anaerobic taxa, notably Alistipes onderdonkii, were positively correlated with MeHg elimination. Surprisingly, mono-colonization of GF free mice with A. onderdonkii did not restore MeHg elimination to control levels. Collectively, our findings indicate the human gut microbiome uses a non-conventional pathway of demethylation to increase MeHg elimination that relies on yet to be resolved functions encoded by the gut microbes and the hostClinical Trial NCT04060212, prospectively registered 10/1/2019.}, } @article {pmid37391847, year = {2023}, author = {Lv, J and Wang, J and Yu, Y and Zhao, M and Yang, W and Liu, J and Zhao, Y and Yang, Y and Wang, G and Guo, L and Zhao, H}, title = {Alterations of gut microbiota are associated with blood pressure: a cross-sectional clinical trial in Northwestern China.}, journal = {Journal of translational medicine}, volume = {21}, number = {1}, pages = {429}, pmid = {37391847}, issn = {1479-5876}, mesh = {Female ; Humans ; Male ; Blood Pressure ; China ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; *Hypertension ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: The human gut microbiota (GM) is involved in the pathogenesis of hypertension (HTN), and could be affected by various factors, including sex and geography. However, available data directly linking GM to HTN based on sex differences are limited.

METHODS: This study investigated the GM characteristics in HTN subjects in Northwestern China, and evaluate the associations of GM with blood pressure levels based on sex differences. A total of 87 HTN subjects and 45 controls were recruited with demographic and clinical characteristics documented. Fecal samples were collected for 16S rRNA gene sequencing and metagenomic sequencing.

RESULTS: GM diversity was observed higher in females compared to males, and principal coordinate analysis showed an obvious segregation of females and males. Four predominant phyla of fecal GM included Firmicutes, Bacteroidetes, Actinobacteria and Proteobacteria. LEfSe analysis indicated that phylum unidentified_Bacteria was enriched in HTN females, while Leuconostocaceae, Weissella and Weissella_cibaria were enriched in control females (P < 0.05). Functionally, ROC analysis revealed that Cellular Processes (0.796, 95% CI 0.620 ~ 0.916), Human Diseases (0.773, 95% CI 0.595 ~ 0.900), Signal transduction (0.806, 95% CI 0.631 ~ 0.922) and Two-component system (0.806, 95% CI 0.631 ~ 0.922) could differentiate HTN females as effective functional classifiers, which were also positively correlated with systolic blood pressure levels.

CONCLUSIONS: This work provides evidence of fecal GM characteristics in HTN females and males in a northwestern Chinese population, further supporting the notion that GM dysbiosis may participate in the pathogenesis of HTN, and the role of sex differences should be considered. Trial registration Chinese Clinical Trial Registry, ChiCTR1800019191. Registered 30 October 2018 - Retrospectively registered, http://www.chictr.org.cn/ .}, } @article {pmid37391513, year = {2023}, author = {Abel, SM and Hong, Z and Williams, D and Ireri, S and Brown, MQ and Su, T and Hung, KY and Henke, JA and Barton, JP and Le Roch, KG}, title = {Small RNA sequencing of field Culex mosquitoes identifies patterns of viral infection and the mosquito immune response.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {10598}, pmid = {37391513}, issn = {2045-2322}, support = {U01 CK000516/CK/NCEZID CDC HHS/United States ; S10 OD026929/OD/NIH HHS/United States ; }, mesh = {Humans ; Animals ; *Culex ; *Culicidae ; Mosquito Vectors ; *Virus Diseases ; Antiviral Agents ; }, abstract = {Mosquito-borne disease remains a significant burden on global health. In the United States, the major threat posed by mosquitoes is transmission of arboviruses, including West Nile virus by mosquitoes of the Culex genus. Virus metagenomic analysis of mosquito small RNA using deep sequencing and advanced bioinformatic tools enables the rapid detection of viruses and other infecting organisms, both pathogenic and non-pathogenic to humans, without any precedent knowledge. In this study, we sequenced small RNA samples from over 60 pools of Culex mosquitoes from two major areas of Southern California from 2017 to 2019 to elucidate the virome and immune responses of Culex. Our results demonstrated that small RNAs not only allowed the detection of viruses but also revealed distinct patterns of viral infection based on location, Culex species, and time. We also identified miRNAs that are most likely involved in Culex immune responses to viruses and Wolbachia bacteria, and show the utility of using small RNA to detect antiviral immune pathways including piRNAs against some pathogens. Collectively, these findings show that deep sequencing of small RNA can be used for virus discovery and surveillance. One could also conceive that such work could be accomplished in various locations across the world and over time to better understand patterns of mosquito infection and immune response to many vector-borne diseases in field samples.}, } @article {pmid37391160, year = {2023}, author = {Hsiao, TH and Chen, PH and Wang, PH and Brandon-Mong, GJ and Li, CW and Horinouchi, M and Hayashi, T and Ismail, W and Meng, M and Chen, YL and Chiang, YR}, title = {Harnessing microbial phylum-specific molecular markers for assessment of environmental estrogen degradation.}, journal = {The Science of the total environment}, volume = {896}, number = {}, pages = {165152}, doi = {10.1016/j.scitotenv.2023.165152}, pmid = {37391160}, issn = {1879-1026}, mesh = {*Ecosystem ; *Estrogens/metabolism ; Estrone/metabolism ; Biodegradation, Environmental ; Bacteria/metabolism ; Proteobacteria/genetics ; }, abstract = {Steroidal estrogens are ubiquitous contaminants that have garnered attention worldwide due to their endocrine-disrupting and carcinogenic activities at sub-nanomolar concentrations. Microbial degradation is one of the main mechanisms through which estrogens can be removed from the environment. Numerous bacteria have been isolated and identified as estrogen degraders; however, little is known about their contribution to environmental estrogen removal. Here, our global metagenomic analysis indicated that estrogen degradation genes are widely distributed among bacteria, especially among aquatic actinobacterial and proteobacterial species. Thus, by using the Rhodococcus sp. strain B50 as the model organism, we identified three actinobacteria-specific estrogen degradation genes, namely aedGHJ, by performing gene disruption experiments and metabolite profile analysis. Among these genes, the product of aedJ was discovered to mediate the conjugation of coenzyme A with a unique actinobacterial C17 estrogenic metabolite, 5-oxo-4-norestrogenic acid. However, proteobacteria were found to exclusively adopt an α-oxoacid ferredoxin oxidoreductase (i.e., the product of edcC) to degrade a proteobacterial C18 estrogenic metabolite, namely 3-oxo-4,5-seco-estrogenic acid. We employed actinobacterial aedJ and proteobacterial edcC as specific biomarkers for quantitative polymerase chain reaction (qPCR) to elucidate the potential of microbes for estrogen biodegradation in contaminated ecosystems. The results indicated that aedJ was more abundant than edcC in most environmental samples. Our results greatly expand the understanding of environmental estrogen degradation. Moreover, our study suggests that qPCR-based functional assays are a simple, cost-effective, and rapid approach for holistically evaluating estrogen biodegradation in the environment.}, } @article {pmid37390725, year = {2023}, author = {Xiong, W and Yang, J and Zeng, J and Xiao, D and Tong, C and Zeng, Z}, title = {Metagenomic analysis of antimicrobial resistance in ducks, workers, and the environment in duck farms, southern China.}, journal = {Ecotoxicology and environmental safety}, volume = {262}, number = {}, pages = {115191}, doi = {10.1016/j.ecoenv.2023.115191}, pmid = {37390725}, issn = {1090-2414}, abstract = {Duck farms are one of the important reservoirs of antimicrobial resistance genes (ARGs) that spread to humans and the environment. However, few studies have focused on the characteristics of antimicrobial profiles in duck farms. Here we explored the distribution characteristics and potential transmission mechanisms of ARGs in ducks, farm workers, and the environment in duck farms by a metagenomic approach. The results showed that the highest abundance and diversity of ARGs were found in duck manure. The abundance and diversity of ARGs in workers and environmental samples were higher than those in the control group. tet(X) and its variants were prevalent in duck farms, with tet(X10) being the most abundant. The genetic structure "tet(X)-like + α/β hydrolase" was found in ducks, workers, and the environment, implying that tet(X) and its variants have been widely spread in duck farms. Network analysis indicated that ISVsa3 and IS5075 might play an important role in the coexistence of ARGs and metal resistance genes (MRGs). The Mantel tests showed that mobile genetic elements (MGEs) were significantly correlated with ARG profiles. The results suggest that duck manure may be a potential hotspot source of ARGs, including tet(X) variants that spread to the surrounding environment and workers via MGEs. These results help us optimize the antimicrobials strategy and deepen our understanding of ARG spread in duck farms.}, } @article {pmid37390685, year = {2023}, author = {Cheng, Z and Li, X and Palomo, A and Yang, Q and Han, L and Wu, Z and Li, Z and Zhang, M and Chen, L and Zhao, B and Yu, K and Zhang, C and Hou, S and Zheng, Y and Xia, Y}, title = {Virus impacted community adaptation in oligotrophic groundwater environment revealed by Hi-C coupled metagenomic and viromic study.}, journal = {Journal of hazardous materials}, volume = {458}, number = {}, pages = {131944}, doi = {10.1016/j.jhazmat.2023.131944}, pmid = {37390685}, issn = {1873-3336}, mesh = {*Metagenome ; Acclimatization ; Metagenomics ; Genomics ; *Groundwater ; }, abstract = {Viruses play a crucial role in microbial mortality, diversity and biogeochemical cycles. Groundwater is the largest global freshwater and one of the most oligotrophic aquatic systems on Earth, but how microbial and viral communities are shaped in this special habitat is largely unexplored. In this study, we collected groundwater samples from 23 to 60 m aquifers at Yinchuan Plain, China. In total, 1920 non-reductant viral contigs were retrieved from metagenomes and viromes constructed by Illumina and Nanopore hybrid sequencing. Only 3% of them could be clustered with known viruses, most of which were Caudoviricetes. Coupling 1.2 Tb Hi-C sequencing with CRISPR matching and homology search, we connected 469 viruses with their hosts while some viral clusters presented a broad-host-range trait. Meanwhile, a large proportion of biosynthesis related auxiliary metabolism genes were identified. Those characteristics might benefit viruses for a better survival in this special oligotrophic environment. Additionally, the groundwater virome showed genomic features distinct from those of the open ocean and wastewater treatment facilities in GC distribution and unannotated gene compositions. This paper expands the current knowledge of the global viromic records and serves as a foundation for a more thorough understanding of viruses in groundwater.}, } @article {pmid37389218, year = {2023}, author = {, }, title = {Erratum: Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1233180}, doi = {10.3389/fcimb.2023.1233180}, pmid = {37389218}, issn = {2235-2988}, abstract = {[This corrects the article DOI: 10.3389/fcimb.2023.1136588.].}, } @article {pmid37389213, year = {2023}, author = {, }, title = {Erratum: Clinical features and diagnostic value of metagenomic next -generation sequencing in five cases of non-HIV related Pneumocystis jirovecii pneumonia in children.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1233206}, doi = {10.3389/fcimb.2023.1233206}, pmid = {37389213}, issn = {2235-2988}, abstract = {[This corrects the article DOI: 10.3389/fcimb.2023.1132472.].}, } @article {pmid37389044, year = {2023}, author = {Zhuang, Z and Qian, L and Lu, J and Zhang, X and Mahmood, A and Cui, L and Wang, H and Wang, X and Yang, S and Ji, L and Shan, T and Shen, Q and Zhang, W}, title = {Comparison of viral communities in the blood, feces and various tissues of wild brown rats (Rattus norvegicus).}, journal = {Heliyon}, volume = {9}, number = {6}, pages = {e17222}, pmid = {37389044}, issn = {2405-8440}, abstract = {Viral diseases caused by new outbreaks of viral infections pose a serious threat to human health. Wild brown rats (Rattus norvegicus), considered one of the world's largest and most widely distributed rodents, are host to various zoonotic pathogens. To further understand the composition of the virus community in wild brown rats and explore new types of potentially pathogenic viruses, viral metagenomics was conducted to investigate blood, feces, and various tissues of wild brown rats captured from Zhenjiang, China. Results indicated that the composition of the virus community in different samples showed significant differences. In blood and tissue samples, members of the Parvoviridae and Anelloviridae form the main body of the virus community. Picornaviridae, Picobirnaviridae, and Astroviridae made up a large proportion of fecal samples. Several novel genome sequences from members of different families, including Anelloviridae, Parvoviridae, and CRESS DNA viruses, were detected in both blood and other samples, suggesting that they have the potential to spread across organs to cause viremia. These viruses included not only strains closely related to human viruses, but also a potential recombinant virus. Multiple dual-segment picornaviruses were obtained from fecal samples, as well as virus sequences from the Astroviridae and Picornaviridae. Phylogenetic analysis showed that these viruses belonged to different genera, with multiple viruses clustered with other animal viruses. Whether they have pathogenicity and the ability to spread across species needs further study.}, } @article {pmid37389021, year = {2023}, author = {Vankova, OE and Brusnigina, NF and Novikova, NA}, title = {NGS Technology in Monitoring the Genetic Diversity of Cytomegalovirus Strains.}, journal = {Sovremennye tekhnologii v meditsine}, volume = {15}, number = {2}, pages = {41-46}, pmid = {37389021}, issn = {2309-995X}, mesh = {Humans ; *Cytomegalovirus/genetics ; High-Throughput Nucleotide Sequencing ; *Cytomegalovirus Infections/diagnosis/epidemiology ; Technology ; Genetic Variation/genetics ; }, abstract = {UNLABELLED: Modern molecular genetic methods, massive parallel sequencing in particular, allow for genotyping of various pathogens with the aim of their epidemiological marking and improvement of molecular epidemiological surveillance of actual infections, including cytomegalovirus infection. The aim of the study is to evaluate the next-generation sequencing (NGS) technology for genotyping clinical isolates of cytomegalovirus (CMV).

MATERIALS AND METHODS: The object of the study were samples of biological substrates (leukocyte mass, saliva, urine) taken from patients who underwent liver and kidney transplantation. Detection of CMV DNA was carried out by a real-time PCR using commercial diagnostic AmpliSense CMV-FL test systems (Central Research Institute for Epidemiology, Moscow, Russia). DNA extraction was performed using DNA-sorb AM and DNA-sorb V kits (Central Research Institute for Epidemiology) in accordance with manufacturer's manual. The quality of the prepared DNA library for sequencing was assessed by means of the QIAxcel Advanced System capillary gel electrophoresis system (QIAGEN, Germany). Alignment and assembly of nucleotide sequences were carried out using CLC Genomics Workbench 5.5 software (CLC bio, USA). The sequencing results were analyzed using BLAST of NCBI server.

RESULTS: CMV DNA samples were selected for genotyping. The two variable genes, UL55(gB) and UL73(gN), were used for CMV genotype determination, which was performed using NGS technology MiSeq sequencer (Illumina, USA). Based on the exploratory studies and analysis of literature sources, primers for genotyping on the UL55(gB) and UL73(gN) genes have been selected and the optimal conditions for the PCR reaction have been defined. The results of sequencing the UL55(gB) and UL73(gN) gene fragments of CMV clinical isolates from recipients of solid organs made it possible to determine the virus genotypes, among which gB2, gN4c, and gN4b were dominant. In some cases, association of two and three CMV genotypes has been revealed.

CONCLUSION: The application of the NGS technology for genotyping cytomegalovirus strains can become one of the main methods of CMV infection molecular epidemiology, as it allows for obtaining reliable results with a significant reduction in research time.}, } @article {pmid37388445, year = {2023}, author = {Cai, B and Zhong, L and Wang, Q and Xu, W and Li, X and Chen, T}, title = {Curcumin alleviates 1-methyl- 4-phenyl- 1,2,3,6-tetrahydropyridine- induced Parkinson's disease in mice via modulating gut microbiota and short-chain fatty acids.}, journal = {Frontiers in pharmacology}, volume = {14}, number = {}, pages = {1198335}, pmid = {37388445}, issn = {1663-9812}, abstract = {Background: The microbiota-gut-brain axis has been proposed as a potential therapeutic target of PD. The effects of curcumin against Parkinson's disease have been demonstrated; however, its neuroprotective mechanisms remain unknown. Our study investigated the potential mechanisms through which curcumin ameliorates Parkinson's disease via the microbiota-gut-brain axis. Methods: Mice were randomly divided into four groups: control, Curcumin, MPTP, and MPTP + Curcumin. Motor deficits and gastrointestinal dysfunction were assessed using behavioral test, intestinal motility test, and fecal parameter measurement. The loss of dopaminergic neurons and intestinal barrier function was measured using Western blot and immunofluorescence. Shotgun metagenomic sequencing and LC-MS were parallelly performed on mice feces to investigate alterations in microbiota and metabolites. Results: Curcumin alleviated motor deficits and the loss of dopaminergic neurons in MPTP-induced mice. Curcumin ameliorated gastrointestinal and intestinal barrier dysfunctions in MPTP-induced mice. Curcumin reduced gut microbial dysbiosis and modulated carbohydrate metabolism in MPTP-induced mice. Curcumin restored short-chain fatty acid (SCFA) profiles in MPTP-induced mice. Conclusion: Concurrently, these results indicate that curcumin inhibits Parkinson's disease by regulating the gut microbiota and short-chain fatty acids.}, } @article {pmid37388248, year = {2023}, author = {Javan, GT and Finley, SJ and Moretti, M and Visonà, SD and Mezzari, MP and Green, RL}, title = {COVID-19 and brain-heart-lung microbial fingerprints in Italian cadavers.}, journal = {Frontiers in molecular biosciences}, volume = {10}, number = {}, pages = {1196328}, pmid = {37388248}, issn = {2296-889X}, abstract = {Introduction: The fact that SARS-CoV-2, the coronavirus that caused COVID-19, can translocate within days of infection to the brain and heart and that the virus can survive for months is well established. However, studies have not investigated the crosstalk between the brain, heart, and lungs regarding microbiota that simultaneously co-inhabit these organs during COVID-19 illness and subsequent death. Given the significant overlap of cause of death from or with SARS-CoV-2, we investigated the possibility of a microbial fingerprint regarding COVID-19 death. Methods: In the current study, the 16S rRNA V4 region was amplified and sequenced from 20 COVID-19-positive and 20 non-COVID-19 cases. Nonparametric statistics were used to determine the resulting microbiota profile and its association with cadaver characteristics. When comparing non-COVID-19 infected tissues versus those infected by COVID-19, there is statistical differences (p < 0.05) between organs from the infected group only. Results: When comparing the three organs, microbial richness was significantly higher in non-COVID-19-infected tissues than infected. Unifrac distance metrics showed more variance between control and COVID-19 groups in weighted analysis than unweighted; both were statistically different. Unweighted Bray-Curtis principal coordinate analyses revealed a near distinct two-community structure: one for the control and the other for the infected group. Both unweighted and weighted Bray-Curtis showed statistical differences. Deblur analyses demonstrated Firmicutes in all organs from both groups. Discussion: Data obtained from these studies facilitated the defining of microbiome signatures in COVID-19 decedents that could be identified as taxonomic biomarkers effective for predicting the occurrence, the co-infections involved in its dysbiosis, and the evolution of the virus.}, } @article {pmid37388163, year = {2023}, author = {Zhong, H and Yu, W and Wang, M and Lin, B and Sun, X and Zheng, N and Wang, J and Zhao, S}, title = {Sodium butyrate promotes gastrointestinal development of preweaning bull calves via inhibiting inflammation, balancing nutrient metabolism, and optimizing microbial community functions.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {14}, number = {}, pages = {88-100}, pmid = {37388163}, issn = {2405-6383}, abstract = {Butyrate promotes the growth and gastrointestinal development of calves. But, the mechanisms behind its effects on signaling pathways of the gastrointestinal tract and rumen microbiome is unclear. This study aimed to reveal transcriptomic pathways of gastrointestinal epithelium and microbial community in response to butyrate supplementation in calves fed a high fiber starter. Fourteen Holstein bull calves (39.9 ± 3.7 kg, 14 d of age) were assigned to 2 groups (sodium butyrate group, SB; control group, Ctrl). The SB group received 0.5% SB supplementation. At d 51, the calves were slaughtered to obtain samples for analysis of the transcriptome of the rumen and jejunum epithelium as well as ruminal microbial metagenome. Sodium butyrate supplementation resulted in a higher performance in average daily gain and development of jejunum and rumen papillae. In both the rumen and jejunum epithelium, SB down-regulated pathways related to inflammation including NF-κB (PPKCB, CXCL8, CXCL12), interleukin-17 (IL17A, IL17B, MMP9), and chemokine (CXCL12, CCL4, CCL8) and up-regulated immune pathways including the intestinal immune network for immunoglobulin A (IgA) production (CD28). Meanwhile, in the jejunum epithelium, SB regulated pathways related to nutritional metabolism including nitrogen metabolism (CA1, CA2, CA3), synthesis and degradation of ketone bodies (HMGCS2, BDH1, LOC100295719), fat digestion and absorption (PLA2G2F, APOA1, APOA4), and the PPAR signaling pathway (FABP4, FABP6, CYP4A11). The metagenome showed that SB greatly increased the relative abundance of Bacillus subtilis and Eubacterium limosum, activated ruminal microbial carbohydrate metabolism pathways and increased the abundance of carbohydrate hydrolysis enzymes. In conclusion, butyrate exhibited promoting effects on growth and gastrointestinal development by inhibiting inflammation, enhancing immunity and energy harvesting, and activating microbial carbohydrate metabolism. These findings provide new insights into the potential mechanisms behind the beneficial effects of butyrate in calf nutrition.}, } @article {pmid37388087, year = {2023}, author = {And Alternative Medicine, EC}, title = {Retracted: Metagenomic Analysis Reveals Neisseria bacilliformis Variation in the Early Childhood Caries Plaque Microbiome.}, journal = {Evidence-based complementary and alternative medicine : eCAM}, volume = {2023}, number = {}, pages = {9781764}, pmid = {37388087}, issn = {1741-427X}, abstract = {[This retracts the article DOI: 10.1155/2021/2774772.].}, } @article {pmid37387190, year = {2023}, author = {Wei, W and Millward, A and Koslicki, D}, title = {Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L2UniFrac.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {39 Suppl 1}, pages = {i57-i65}, pmid = {37387190}, issn = {1367-4811}, support = {R01 GM146462/GM/NIGMS NIH HHS/United States ; }, mesh = {Phylogeny ; Cluster Analysis ; *Metagenome ; *Metagenomics ; }, abstract = {MOTIVATION: Metagenomic samples have high spatiotemporal variability. Hence, it is useful to summarize and characterize the microbial makeup of a given environment in a way that is biologically reasonable and interpretable. The UniFrac metric has been a robust and widely used metric for measuring the variability between metagenomic samples. We propose that the characterization of metagenomic environments can be improved by finding the average, a.k.a. the barycenter, among the samples with respect to the UniFrac distance. However, it is possible that such a UniFrac-average includes negative entries, making it no longer a valid representation of a metagenomic community.

RESULTS: To overcome this intrinsic issue, we propose a special version of the UniFrac metric, termed L2UniFrac, which inherits the phylogenetic nature of the traditional UniFrac and with respect to which one can easily compute the average, producing biologically meaningful environment-specific "representative samples." We demonstrate the usefulness of such representative samples as well as the extended usage of L2UniFrac in efficient clustering of metagenomic samples, and provide mathematical characterizations and proofs to the desired properties of L2UniFrac.

A prototype implementation is provided at https://github.com/KoslickiLab/L2-UniFrac.git. All figures, data, and analysis can be reproduced at https://github.com/KoslickiLab/L2-UniFrac-Paper.}, } @article {pmid37387171, year = {2023}, author = {Pan, S and Zhao, XM and Coelho, LP}, title = {SemiBin2: self-supervised contrastive learning leads to better MAGs for short- and long-read sequencing.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {39 Suppl 1}, pages = {i21-i29}, pmid = {37387171}, issn = {1367-4811}, mesh = {*Metagenome ; *Algorithms ; Cluster Analysis ; Metagenomics ; Software ; }, abstract = {MOTIVATION: Metagenomic binning methods to reconstruct metagenome-assembled genomes (MAGs) from environmental samples have been widely used in large-scale metagenomic studies. The recently proposed semi-supervised binning method, SemiBin, achieved state-of-the-art binning results in several environments. However, this required annotating contigs, a computationally costly and potentially biased process.

RESULTS: We propose SemiBin2, which uses self-supervised learning to learn feature embeddings from the contigs. In simulated and real datasets, we show that self-supervised learning achieves better results than the semi-supervised learning used in SemiBin1 and that SemiBin2 outperforms other state-of-the-art binners. Compared to SemiBin1, SemiBin2 can reconstruct 8.3-21.5% more high-quality bins and requires only 25% of the running time and 11% of peak memory usage in real short-read sequencing samples. To extend SemiBin2 to long-read data, we also propose ensemble-based DBSCAN clustering algorithm, resulting in 13.1-26.3% more high-quality genomes than the second best binner for long-read data.

SemiBin2 is available as open source software at https://github.com/BigDataBiology/SemiBin/ and the analysis scripts used in the study can be found at https://github.com/BigDataBiology/SemiBin2_benchmark.}, } @article {pmid37387148, year = {2023}, author = {Wang, Q and Nute, M and Treangen, TJ}, title = {Bakdrive: identifying a minimum set of bacterial species driving interactions across multiple microbial communities.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {39 Suppl 1}, pages = {i47-i56}, pmid = {37387148}, issn = {1367-4811}, support = {P01 AI152999/AI/NIAID NIH HHS/United States ; R21 NS106640/NS/NINDS NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; *Gastrointestinal Microbiome ; Metagenome ; Bacteria/genetics ; *Crohn Disease ; }, abstract = {MOTIVATION: Interactions among microbes within microbial communities have been shown to play crucial roles in human health. In spite of recent progress, low-level knowledge of bacteria driving microbial interactions within microbiomes remains unknown, limiting our ability to fully decipher and control microbial communities.

RESULTS: We present a novel approach for identifying species driving interactions within microbiomes. Bakdrive infers ecological networks of given metagenomic sequencing samples and identifies minimum sets of driver species (MDS) using control theory. Bakdrive has three key innovations in this space: (i) it leverages inherent information from metagenomic sequencing samples to identify driver species, (ii) it explicitly takes host-specific variation into consideration, and (iii) it does not require a known ecological network. In extensive simulated data, we demonstrate identifying driver species identified from healthy donor samples and introducing them to the disease samples, we can restore the gut microbiome in recurrent Clostridioides difficile (rCDI) infection patients to a healthy state. We also applied Bakdrive to two real datasets, rCDI and Crohn's disease patients, uncovering driver species consistent with previous work. Bakdrive represents a novel approach for capturing microbial interactions.

Bakdrive is open-source and available at: https://gitlab.com/treangenlab/bakdrive.}, } @article {pmid37387143, year = {2023}, author = {Alanko, JN and Vuohtoniemi, J and Mäklin, T and Puglisi, SJ}, title = {Themisto: a scalable colored k-mer index for sensitive pseudoalignment against hundreds of thousands of bacterial genomes.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {39 Suppl 1}, pages = {i260-i269}, pmid = {37387143}, issn = {1367-4811}, mesh = {*Genome, Bacterial ; Genomics ; Metagenomics ; *Nanopores ; }, abstract = {MOTIVATION: Huge datasets containing whole-genome sequences of bacterial strains are now commonplace and represent a rich and important resource for modern genomic epidemiology and metagenomics. In order to efficiently make use of these datasets, efficient indexing data structures-that are both scalable and provide rapid query throughput-are paramount.

RESULTS: Here, we present Themisto, a scalable colored k-mer index designed for large collections of microbial reference genomes, that works for both short and long read data. Themisto indexes 179 thousand Salmonella enterica genomes in 9 h. The resulting index takes 142 gigabytes. In comparison, the best competing tools Metagraph and Bifrost were only able to index 11 000 genomes in the same time. In pseudoalignment, these other tools were either an order of magnitude slower than Themisto, or used an order of magnitude more memory. Themisto also offers superior pseudoalignment quality, achieving a higher recall than previous methods on Nanopore read sets.

Themisto is available and documented as a C++ package at https://github.com/algbio/themisto available under the GPLv2 license.}, } @article {pmid37387129, year = {2023}, author = {Mikalsen, AJ and Zola, J}, title = {Coriolis: enabling metagenomic classification on lightweight mobile devices.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {39 Suppl 1}, pages = {i66-i75}, pmid = {37387129}, issn = {1367-4811}, mesh = {*Algorithms ; *Computers, Handheld ; Databases, Nucleic Acid ; Metagenome ; Metagenomics ; }, abstract = {MOTIVATION: The introduction of portable DNA sequencers such as the Oxford Nanopore Technologies MinION has enabled real-time and in the field DNA sequencing. However, in the field sequencing is actionable only when coupled with in the field DNA classification. This poses new challenges for metagenomic software since mobile deployments are typically in remote locations with limited network connectivity and without access to capable computing devices.

RESULTS: We propose new strategies to enable in the field metagenomic classification on mobile devices. We first introduce a programming model for expressing metagenomic classifiers that decomposes the classification process into well-defined and manageable abstractions. The model simplifies resource management in mobile setups and enables rapid prototyping of classification algorithms. Next, we introduce the compact string B-tree, a practical data structure for indexing text in external storage, and we demonstrate its viability as a strategy to deploy massive DNA databases on memory-constrained devices. Finally, we combine both solutions into Coriolis, a metagenomic classifier designed specifically to operate on lightweight mobile devices. Through experiments with actual MinION metagenomic reads and a portable supercomputer-on-a-chip, we show that compared with the state-of-the-art solutions Coriolis offers higher throughput and lower resource consumption without sacrificing quality of classification.

Source code and test data are available from http://score-group.org/?id=smarten.}, } @article {pmid37386906, year = {2023}, author = {Lefeuvre, C and Thepot, S and Mercier-Delarue, S and Bouille, T and Michonneau, D and Le Goff, J and Salmona, M}, title = {Adenovirus F41 infection and liver cytolysis in adult hematopoietic stem cell transplant recipients.}, journal = {Journal of medical virology}, volume = {95}, number = {7}, pages = {e28922}, doi = {10.1002/jmv.28922}, pmid = {37386906}, issn = {1096-9071}, mesh = {Child ; Adult ; Humans ; *Epstein-Barr Virus Infections ; Phylogeny ; Herpesvirus 4, Human ; *Adenoviruses, Human ; *Adenoviridae Infections ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Liver ; }, abstract = {Human adenoviruses (HAdVs) of the F species are commonly responsible for acute gastroenteritis. A few cases of systemic infections have been described in adults or children who have received a hematopoietic stem cell transplant (HSCT), but with no report of liver cytolysis. Since January 2022, several countries have reported an increase in cases of acute hepatitis of unknown cause in children. Adenovirus species F type 41 (HAdV-F41) infection was predominantly identified. The objective of this study is to describe HAdV-F41 infections diagnosed since January 2022 in adult HSCT recipients in two French hospitals. All four patients had diarrhea and liver cytolysis at the time of diagnosis of infection. HAdV viremia was observed in three patients (#1, #3, and #4), but no disseminated disease was reported. HAdV whole genome sequencing and metagenomics characterization were performed on stool and blood samples. The complete HAdV-F41 genome sequence was obtained for three patients and phylogenetic analysis showed that the strains consisted of similar lineage (2b). We did not identify any new HAdV-F41 strains. Metagenomics analysis found adeno-associated virus 2 and torque-teno virus infection in patient #1 and Epstein-Barr virus in patient #4. This is the first case series reporting liver cytolysis during HAdV-F41 infection in adult HSCT patients.}, } @article {pmid37386754, year = {2023}, author = {Xu, R and Feng, N and Li, Q and Wang, H and Su, Y and Zhu, W}, title = {Short-Term Supplementation of Pectin Alters Substrate Dynamics and Modulates Microbial Carbohydrate Metabolism in the Gut of a Pig Model.}, journal = {Journal of agricultural and food chemistry}, volume = {71}, number = {27}, pages = {10470-10482}, doi = {10.1021/acs.jafc.3c02562}, pmid = {37386754}, issn = {1520-5118}, mesh = {Humans ; Swine ; Animals ; *Pectins/metabolism ; *Polysaccharides/metabolism ; Feces ; Carbohydrate Metabolism ; Dietary Supplements ; }, abstract = {The interaction of pectin and gut microbiota plays an important role in maintaining animal and human health, but this interaction is not fully understood. Here, the impact of pectin supplementation on substrate dynamics and gut microbiota (in the terminal ileum and feces) was integrally investigated in a fistula pig model. Our results showed that a pectin-supplemented diet (PEC) decreased the concentrations of starch, cellulose, and butyrate in feces but not in the terminal ileum. Metagenomic sequencing revealed that PEC had a low impact on the ileal microbiota but significantly increased plant polysaccharide-degrading genera (e.g., Bacteroides, Alistipes, and Treponema) in feces. Additionally, CAZyme profiling indicated that PEC reduced GH68 and GH8 for oligosaccharide degradation in the ileal microbiome, while it enriched GH5, GH57, and GH106 for degradation of carbohydrate substrates in feces. Metabolomic analysis confirmed that PEC increased metabolites involved in carbohydrate metabolism including glucuronate and aconitate. Collectively, pectin could promote complex carbohydrate substrate degradation in the hindgut via modulating the gut microbiota.}, } @article {pmid37386218, year = {2023}, author = {Noszczyńska, M and Pacwa-Płociniczak, M and Bondarczuk, K and Piotrowska-Seget, Z}, title = {The microbial removal of bisphenols in aquatic microcosms and associated alteration in bacterial community.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {36}, pages = {85292-85304}, pmid = {37386218}, issn = {1614-7499}, mesh = {RNA, Ribosomal, 16S/metabolism ; Biodegradation, Environmental ; *Bacteria/metabolism ; *Benzhydryl Compounds/analysis ; Water/analysis ; }, abstract = {The concept of the study resulted from numerous concerns around bisphenol A (BPA) and bisphenol S (BPS) in aquatic environments. In this study, river water and sediment microcosms highly polluted with bisphenols and bioaugmented with two BPs-removing bacterial strains were constructed. The study aimed to determine the rate of high-concentrated BPA and BPS (BPs) removal from river water and sediment microniches, and the effect of water bioaugmentation with bacterial consortium on the removal rates of these pollutants. Moreover, the impact of introduced strains and exposure to BPs on the structural and functional composition of the autochthonous bacterial communities was elucidated. Our findings indicate that the removal activity of autochthonous bacteria was sufficient for effectively BPA elimination and reducing BPS content in the microcosms. The number of introduced bacterial cells decreased continuously until day 40, and on consecutive sampling days, no bioaugmented cells were detected. Sequencing analysis of the total 16S rRNA genes revealed that the community composition in bioaugmented microcosms amended with BPs differed significantly from those treated either with bacteria or BPs. A metagenomic analysis found an increase in the abundance of proteins responsible for xenobiotics removal in BPs-amended microcosms. This study provides new insights into the effects of bioaugmentation with a bacterial consortium on bacterial diversity and BPs removal in aquatic environments.}, } @article {pmid37386210, year = {2023}, author = {Tang, H and Zhong, Z and Hou, J and You, L and Zhao, Z and Kwok, LY and Bilige, M}, title = {Metagenomic analysis revealed the potential of lactic acid bacteria in improving natural saline-alkali land.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {37386210}, issn = {1618-1905}, abstract = {Management and improving saline-alkali land is necessary for sustainable agricultural development. We conducted a field experiment to investigate the effects of spraying lactic acid bacteria (LAB) on the cucumber and tomato plant soils. Three treatments were designed, including spraying of water, viable or sterilized LAB preparations to the soils of cucumber and tomato plants every 20 days. Spraying sterilized or viable LAB could reduce the soil pH, with a more obvious effect by using viable LAB, particularly after multiple applications. Metagenomic sequencing revealed that the soil microbiota in LAB-treated groups had higher alpha-diversity and more nitrogen-fixing bacteria compared with the water-treated groups. Both viable and sterilized LAB, but not water application, increased the complexity of the soil microbiota interactive network. The LAB-treated subgroups were enriched in some KEGG pathways compared with water or sterilized LAB subgroups, such as environmental information processing-related pathways in cucumber plant; and metabolism-related pathways in tomato plant, respectively. Redundancy analysis revealed association between some soil physico-chemical parameters (namely soil pH and total nitrogen) and bacterial biomarkers (namely Rhodocyclaceae, Pseudomonadaceae, Gemmatimonadaceae, and Nitrosomonadales). Our study demonstrated that LAB is a suitable strategy for decreasing soil pH and improving the microbial communities in saline-alkali land.}, } @article {pmid37386187, year = {2023}, author = {Mattock, J and Watson, M}, title = {A comparison of single-coverage and multi-coverage metagenomic binning reveals extensive hidden contamination.}, journal = {Nature methods}, volume = {20}, number = {8}, pages = {1170-1173}, pmid = {37386187}, issn = {1548-7105}, support = {BB/S006680/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R015023/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/V018450/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/D/30002276/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Sequence Analysis, DNA/methods ; *Metagenome ; *Metagenomics/methods ; Algorithms ; }, abstract = {Metagenomic binning has revolutionized the study of uncultured microorganisms. Here we compare single- and multi-coverage binning on the same set of samples, and demonstrate that multi-coverage binning produces better results than single-coverage binning and identifies contaminant contigs and chimeric bins that other approaches miss. While resource expensive, multi-coverage binning is a superior approach and should always be performed over single-coverage binning.}, } @article {pmid37386075, year = {2023}, author = {Wei, W and Wong, CC and Jia, Z and Liu, W and Liu, C and Ji, F and Pan, Y and Wang, F and Wang, G and Zhao, L and Chu, ESH and Zhang, X and Sung, JJY and Yu, J}, title = {Parabacteroides distasonis uses dietary inulin to suppress NASH via its metabolite pentadecanoic acid.}, journal = {Nature microbiology}, volume = {8}, number = {8}, pages = {1534-1548}, pmid = {37386075}, issn = {2058-5276}, mesh = {Animals ; Mice ; *Non-alcoholic Fatty Liver Disease/prevention & control/metabolism/microbiology ; Inulin ; Fatty Acids/metabolism ; Inflammation ; Dietary Fiber ; }, abstract = {Non-alcoholic steatohepatitis (NASH) is the severe form of non-alcoholic fatty liver disease, and is characterized by liver inflammation and fat accumulation. Dietary interventions, such as fibre, have been shown to alleviate this metabolic disorder in mice via the gut microbiota. Here, we investigated the mechanistic role of the gut microbiota in ameliorating NASH via dietary fibre in mice. Soluble fibre inulin was found to be more effective than insoluble fibre cellulose to suppress NASH progression in mice, as shown by reduced hepatic steatosis, necro-inflammation, ballooning and fibrosis. We employed stable isotope probing to trace the incorporation of [13]C-inulin into gut bacterial genomes and metabolites during NASH progression. Shotgun metagenome sequencing revealed that the commensal Parabacteroides distasonis was enriched by [13]C-inulin. Integration of [13]C-inulin metagenomes and metabolomes suggested that P. distasonis used inulin to produce pentadecanoic acid, an odd-chain fatty acid, which was confirmed in vitro and in germ-free mice. P. distasonis or pentadecanoic acid was protective against NASH in mice. Mechanistically, inulin, P. distasonis or pentadecanoic acid restored gut barrier function in NASH models, which reduced serum lipopolysaccharide and liver pro-inflammatory cytokine expression. Overall this shows that gut microbiota members can use dietary fibre to generate beneficial metabolites to suppress metabolic disease.}, } @article {pmid37385587, year = {2023}, author = {Taniguchi, M and Okumura, R and Matsuzaki, T and Nakatani, A and Sakaki, K and Okamoto, S and Ishibashi, A and Tani, H and Horikiri, M and Kobayashi, N and Yoshikawa, HY and Motooka, D and Okuzaki, D and Nakamura, S and Kida, T and Kameyama, A and Takeda, K}, title = {Sialylation shapes mucus architecture inhibiting bacterial invasion in the colon.}, journal = {Mucosal immunology}, volume = {16}, number = {5}, pages = {624-641}, doi = {10.1016/j.mucimm.2023.06.004}, pmid = {37385587}, issn = {1935-3456}, abstract = {In the intestine, mucin 2 (Muc2) forms a network structure and prevents bacterial invasion. Glycans are indispensable for Muc2 barrier function. Among various glycosylation patterns of Muc2, sialylation inhibits bacteria-dependent Muc2 degradation. However, the mechanisms by which Muc2 creates the network structure and sialylation prevents mucin degradation remain unknown. Here, by focusing on two glycosyltransferases, St6 N-acetylgalactosaminide α-2,6-sialyltransferase 6 (St6galnac6) and β-1,3-galactosyltransferase 5 (B3galt5), mediating the generation of desialylated glycans, we show that sialylation forms the network structure of Muc2 by providing negative charge and hydrophilicity. The colonic mucus of mice lacking St6galnac6 and B3galt5 was less sialylated, thinner, and more permeable to microbiota, resulting in high susceptibility to intestinal inflammation. Mice with a B3galt5 mutation associated with inflammatory bowel disease (IBD) also showed the loss of desialylated glycans of mucus and the high susceptibility to intestinal inflammation, suggesting that the reduced sialylation of Muc2 is associated with the pathogenesis of IBD. In mucins of mice with reduced sialylation, negative charge was reduced, the network structure was disturbed, and many bacteria invaded. Thus, sialylation mediates the negative charging of Muc2 and facilitates the formation of the mucin network structure, thereby inhibiting bacterial invasion in the colon to maintain gut homeostasis.}, } @article {pmid37385198, year = {2023}, author = {Tian, Z and Li, G and Xiong, Y and Cao, X and Pang, H and Tang, W and Liu, Y and Bai, M and Zhu, Q and Du, C and Li, M and Zhang, L}, title = {Step-feeding food waste fermentation liquid as supplementary carbon source for low C/N municipal wastewater treatment: Bench scale performance and response of microbial community.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118434}, doi = {10.1016/j.jenvman.2023.118434}, pmid = {37385198}, issn = {1095-8630}, mesh = {Humans ; Wastewater ; Fermentation ; Food ; Waste Disposal, Fluid/methods ; Carbon ; Sewage ; *Severe Fever with Thrombocytopenia Syndrome ; Bioreactors ; *Refuse Disposal ; *Microbiota ; Nitrogen ; Denitrification ; }, abstract = {Municipal wastewater treatment often lacks carbon source, while carbon-rich organics in food waste are deficiently utilized. In this study, the food waste fermentation liquid (FWFL) was step-fed into a bench-scale step-feed three-stage anoxic/aerobic system (SFTS-A/O), to investigate its performance in nutrients removal and the response of microbial community as a supplementary carbon source. The results showed that the total nitrogen (TN) removal rate increased by 21.8-109.3% after step-feeding FWFL. However, the biomass of the SFTS-A/O system was increased by 14.6% and 11.9% in the two phases of the experiment, respectively. Proteobacteria was found to be the dominant functional phyla induced by FWFL, and the increase of its abundance attributed to the enrichment of denitrifying bacteria and carbohydrate-metabolizing bacteria was responsible for the biomass increase. Azospira belonged to Proteobacteria phylum was the dominant denitrifying genera when step-fed with FWFL, its abundance was increased from 2.7% in series 1 (S1) to 18.6% in series 2 (S2) and became the keystone species in the microbial networks. Metagenomics analysis revealed that step-feeding FWFL enhanced the abundance of denitrification and carbohydrates-metabolism genes, which were encode mainly by Proteobacteria. This study constitutes a key step towards the application of FWFL as a supplementary carbon source for low C/N municipal wastewater treatment.}, } @article {pmid37385196, year = {2023}, author = {Hao, DC and Su, XY and Xie, HT and Bao, XL and Zhang, XD and Wang, LF}, title = {Effects of tillage patterns and stover mulching on N2O production, nitrogen cycling genes and microbial dynamics in black soil.}, journal = {Journal of environmental management}, volume = {345}, number = {}, pages = {118458}, doi = {10.1016/j.jenvman.2023.118458}, pmid = {37385196}, issn = {1095-8630}, mesh = {*Soil/chemistry ; Ammonia/analysis ; Carbon/analysis ; Agriculture ; China ; *Microbiota ; Nitrogen/analysis ; Alkynes/analysis ; Soil Microbiology ; Nitrous Oxide/analysis ; }, abstract = {Stover-covered no-tillage (NT) is of great significance to the rational utilization of stover resources and improvement of cultivated land quality, and also has a profound impact on ensuring groundwater, food and ecosystem security. However, the effects of tillage patterns and stover mulching on soil nitrogen turnover remain elusive. Based on the long-term conservation tillage field experiment in the mollisol area of Northeast China since 2007, the shotgun metagenomic sequencing of soils and microcosm incubation were combined with physical and chemical analyses, alkyne inhibition analysis to elucidate the regulatory mechanisms of NT and stover mulching on the farmland soil nitrogen emissions and microbial nitrogen cycling genes. Compared with conventional tillage (CT), NT stover mulching significantly reduced the emission of N2O instead of CO2, especially when 33% mulching was adopted, and correspondingly the nitrate nitrogen of NT33 was higher than that of other mulching amounts. The stover mulching was associated with higher total nitrogen, soil organic carbon and pH. The abundance of AOB (ammonia-oxidizing bacteria)-amoA (ammonia monooxygenase subunit A) was substantially increased by stover mulching, while the abundance of denitrification genes was reduced in most cases. Under alkyne inhibition, the tillage mode, treatment time, gas condition and interactions between them noticeably influenced the N2O emission and nitrogen transformation. In CT, NT0 (no mulching) and NT100 (full mulching), the relative contribution of AOB to N2O production was markedly higher than that of ammonia oxidizing archaea. Different tillage modes were associated with distinct microbial community composition, albeit NT100 was closer to CT than to NT0. Compared with CT, the co-occurrence network of microbial communities was more complex in NT0 and NT100. Our findings suggest that maintaining a low-quantity stover mulching could regulate soil nitrogen turnover toward proficiently enhancing soil health and regenerative agriculture, and coping with global climate change.}, } @article {pmid37384968, year = {2023}, author = {Huang, M and Gan, J and Xu, Z and Guo, Y and Chen, Z and Gao, GF and Liang, H and Liu, WJ}, title = {A black goat-derived novel genotype of Aichi virus C blurs the boundary between caprine and porcine kobuviruses.}, journal = {Virology}, volume = {585}, number = {}, pages = {215-221}, doi = {10.1016/j.virol.2023.06.014}, pmid = {37384968}, issn = {1096-0341}, mesh = {Animals ; Swine ; *Kobuvirus/genetics ; Goats ; Phylogeny ; *Picornaviridae Infections/epidemiology ; Genotype ; Diarrhea ; Feces ; }, abstract = {Aichi virus C, a species in the genus Kobuvirus, causes diarrhea diseases in pigs and goats and pose health threat and economic loss for stock farming. A nearly complete genome sequence of caprine kobuvirus GCCDC14 was obtained from an anal swab of a black goat died from diarrhea collected in Hubei, China in 2019. Phylogenetic analyses suggested that GCCDC14 is a novel genotype of Aichi virus C, forming a sister branch to other caprine kobuviruses, with P1 and VP0 genes more closely related to porcine kobuviruses and VP3 in an independent branch. Compared to previous caprine kobuviruses, unique amino acid changes in the poly-l-proline type II helix structure of VP0 and VP1 were found, which may affect the cellular machinery of host and pathogenicity. This study indicates the presence of the kobuvirus with continuously evolving features and emphasizes the surveillance and genetic evolution investigation of kobuviruses for safety of husbandry.}, } @article {pmid37384733, year = {2023}, author = {Pinsky, ML and Clark, RD and Bos, JT}, title = {Coral Reef Population Genomics in an Age of Global Change.}, journal = {Annual review of genetics}, volume = {57}, number = {}, pages = {87-115}, doi = {10.1146/annurev-genet-022123-102748}, pmid = {37384733}, issn = {1545-2948}, mesh = {Animals ; Humans ; *Coral Reefs ; *Anthozoa/genetics ; Metagenomics ; Genome/genetics ; Biological Evolution ; Climate Change ; Ecosystem ; }, abstract = {Coral reefs are both exceptionally biodiverse and threatened by climate change and other human activities. Here, we review population genomic processes in coral reef taxa and their importance for understanding responses to global change. Many taxa on coral reefs are characterized by weak genetic drift, extensive gene flow, and strong selection from complex biotic and abiotic environments, which together present a fascinating test of microevolutionary theory. Selection, gene flow, and hybridization have played and will continue to play an important role in the adaptation or extinction of coral reef taxa in the face of rapid environmental change, but research remains exceptionally limited compared to the urgent needs. Critical areas for future investigation include understanding evolutionary potential and the mechanisms of local adaptation, developing historical baselines, and building greater research capacity in the countries where most reef diversity is concentrated.}, } @article {pmid37384730, year = {2023}, author = {Dunay, E and Rukundo, J and Atencia, R and Cole, MF and Cantwell, A and Emery Thompson, M and Rosati, AG and Goldberg, TL}, title = {Viruses in saliva from sanctuary chimpanzees (Pan troglodytes) in Republic of Congo and Uganda.}, journal = {PloS one}, volume = {18}, number = {6}, pages = {e0288007}, pmid = {37384730}, issn = {1932-6203}, mesh = {Animals ; Humans ; *Pan troglodytes ; *Saliva ; Congo ; Uganda ; Zoonoses/epidemiology ; Retroviridae ; }, abstract = {Pathogen surveillance for great ape health monitoring has typically been performed on non-invasive samples, primarily feces, in wild apes and blood in sanctuary-housed apes. However, many important primate pathogens, including known zoonoses, are shed in saliva and transmitted via oral fluids. Using metagenomic methods, we identified viruses in saliva samples from 46 wild-born, sanctuary-housed chimpanzees at two African sanctuaries in Republic of Congo and Uganda. In total, we identified 20 viruses. All but one, an unclassified CRESS DNA virus, are classified in five families: Circoviridae, Herpesviridae, Papillomaviridae, Picobirnaviridae, and Retroviridae. Overall, viral prevalence ranged from 4.2% to 87.5%. Many of these viruses are ubiquitous in primates and known to replicate in the oral cavity (simian foamy viruses, Retroviridae; a cytomegalovirus and lymphocryptovirus; Herpesviridae; and alpha and gamma papillomaviruses, Papillomaviridae). None of the viruses identified have been shown to cause disease in chimpanzees or, to our knowledge, in humans. These data suggest that the risk of zoonotic viral disease from chimpanzee oral fluids in sanctuaries may be lower than commonly assumed.}, } @article {pmid37384659, year = {2023}, author = {Harnpicharnchai, P and Pumkaeo, P and Siriarchawatana, P and Likhitrattanapisal, S and Mayteeworakoon, S and Ingsrisawang, L and Boonsin, W and Eurwilaichitr, L and Ingsriswang, S}, title = {AirDNA sampler: An efficient and simple device enabling high-yield, high-quality airborne environment DNA for metagenomic applications.}, journal = {PloS one}, volume = {18}, number = {6}, pages = {e0287567}, pmid = {37384659}, issn = {1932-6203}, mesh = {*DNA, Environmental/genetics ; Metagenomics ; Airports ; Biomass ; Built Environment ; }, abstract = {Analyzing temporal and spatial distributions of airborne particles of biological origins is vital for the assessment and monitoring of air quality, especially with regard to public health, environmental ecology, and atmospheric chemistry. However, the analysis is frequently impeded by the low levels of biomass in the air, especially with metagenomic DNA analysis to explore diversity and composition of living organisms and their components in the air. To obtain sufficient amounts of metagenomic DNA from bioaerosols, researchers usually need a long sampling time with an expensive high-volume air sampler. This work shows the utilization of an air sampling device containing an economical, high-volume portable ventilation fan in combination with customized multi-sheet filter holders to effectively obtain high yields of genomic DNA in a relatively short time. The device, named 'AirDNA' sampler, performed better than other commercial air samplers, including MD8 Airport and Coriolis compact air samplers. Using the AirDNA sampler, an average DNA yield of 40.49 ng (12.47-23.24 ng at 95% CI) was obtained in only 1 hour of air sampling with a 0.85 probability of obtaining ≥10 ng of genomic DNA. The genomic DNA obtained by the AirDNA system is of suitable quantity and quality to be further used for amplicon metabarcoding sequencing of 16S, 18S, and cytochrome c oxidase I (COI) regions, indicating that it can be used to detect various prokaryotes and eukaryotes. Our results showed the effectiveness of our AirDNA sampling apparatus with a simple setup and affordable devices to obtain metagenomic DNA for short-term or long-term spatiotemporal analysis. The technique is well suited for monitoring air in built environments, especially monitoring bioaerosols for health purposes and for fine-scale spatiotemporal environmental studies.}, } @article {pmid37384524, year = {2023}, author = {Bao, Z and Guo, C and Chen, Y and Li, C and Lei, T and Zhou, S and Qi, D and Xiang, Z}, title = {Fatty acid metabolization and insulin regulation prevent liver injury from lipid accumulation in Himalayan marmots.}, journal = {Cell reports}, volume = {42}, number = {7}, pages = {112718}, doi = {10.1016/j.celrep.2023.112718}, pmid = {37384524}, issn = {2211-1247}, mesh = {Animals ; Marmota/genetics ; Insulin ; Fatty Acids ; *Fatty Liver ; *Hibernation/physiology ; }, abstract = {Fat storage and weight gain are dominant traits for hibernating mammals. However, excessive fat accumulation may cause liver damage. Here, we explore the lipid accumulation and metabolic processes of the Himalayan marmot (Marmota himalayana), a hibernating rodent species. We find that the unsaturated fatty acid (UFA) content in food was consistent with a large increase in the body mass of Himalayan marmots. Metagenomic analysis shows that Firmicutes Bacterium CAG:110 plays a synergistic role by synthesizing UFAs, which is demonstrated by fecal transplantation experiments, indicating that the gut microbiome promotes fat storage in Himalayan marmots for hibernation. Microscopic examination results indicate that the risk of fatty liver appears at maximum weight; however, liver function is not affected. Upregulations of UFA catabolism and insulin-like growth factor binding protein genes provide an entry point for avoiding liver injury.}, } @article {pmid37383793, year = {2023}, author = {Babalola, OO and Olowe, OM and Ayangbenro, AS}, title = {Shotgun metagenomics dataset of Striga hermonthica-infested maize (Zea mays L.) rhizospheric soil microbiome.}, journal = {Data in brief}, volume = {48}, number = {}, pages = {109132}, pmid = {37383793}, issn = {2352-3409}, abstract = {This dataset includes shotgun metagenomics sequencing of the rhizosphere microbiome of maize infested with Striga hermonthica from Mbuzini, South Africa, and Eruwa, Nigeria. The sequences were used for microbial taxonomic classification and functional categories in the infested maize rhizosphere. High throughput sequencing of the complete microbial community's DNA was performed using the Illumina NovaSeq 6000 technology. The average base pair count of the sequences were 5,353,206 bp with G+C content of 67%. The raw sequence data used for analysis is available in NCBI under the BioProject accession numbers PRJNA888840 and PRJNA889583. The taxonomic analysis was performed using Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST). Bacteria had the highest taxonomic representation (98.8%), followed by eukaryotes (0.56%), and archaea (0.45%). This metagenome dataset provide valuable information on microbial communities associated with Striga-infested maize rhizosphere and their functionality. It can also be used for further studies on application of microbial resources for sustainable crop production in this region.}, } @article {pmid37383115, year = {2023}, author = {Zhang, WW and Ai, C and Mao, CT and Liu, DK and Guo, Y}, title = {Prevotella oris-caused meningitis and spinal canal infection: A case report.}, journal = {World journal of clinical cases}, volume = {11}, number = {16}, pages = {3830-3836}, pmid = {37383115}, issn = {2307-8960}, abstract = {BACKGROUND: Prevotella oris-induced meningitis and Prevotella oris-induced meningitis concomitant with spinal canal infection are extremely rare. To the best of our knowledge, only 1 case of Prevotella oris-induced central system infection has been reported. This is the second report on meningitis combined with spinal canal infection due to Prevotella oris.

CASE SUMMARY: We report a case of a 9-year-old boy suffering from meningitis and spinal canal infection. The patient presented to the neurosurgery department with lumbosacral pain for 1 mo and headache and vomiting for 1 d. He had been treated with cephalosporin and nonsteroidal anti-inflammatory drugs for fever, otalgia and pharyngalgia in a local hospital 2 mo prior to this admission. During hospitalization, magnetic resonance imaging suggested meningitis and L3-S1 lumbosacral dural sac infection. The cerebrospinal fluid and blood cultures were negative, but the cerebrospinal fluid specimen indicated the presence of Prevotella oris by metagenomic next-generation sequencing. Previous cases of Prevotella oris infection were retrieved from PubMed to characterize the clinicopathological features and identify the prognostic factors and related antimicrobial treatment of infection due to Prevotella oris.

CONCLUSION: This report shed light on the characteristics of Prevotella oris infection and highlighted the role of metagenomic next-generation sequencing in pathogen detection.}, } @article {pmid37382555, year = {2023}, author = {Yi, S and Zhang, C and Yin, P and Yu, L and Tian, F and Chen, W and Zhai, Q}, title = {Compositional and functional features of the intestinal lactobacilli associated with different long-term diet types.}, journal = {Food & function}, volume = {14}, number = {14}, pages = {6570-6581}, doi = {10.1039/d3fo02182c}, pmid = {37382555}, issn = {2042-650X}, mesh = {Humans ; Lactobacillus/genetics/metabolism ; Diet ; *Gastrointestinal Microbiome ; *Probiotics ; }, abstract = {It is well known that diet is one of the most important factors in shaping the host's intestinal microbiota. Lactobacillus, a common group of probiotic bacteria, is widely distributed in the host gut, and studies have linked changes in lactobacilli in the gut to differences in dietary habits. Different dietary habits may affect not only the structural composition but also the function of lactobacilli in the intestine. Therefore, we dissected 283 metagenomes from samples collected from individuals with different dietary habits, investigating the presence of different species of lactobacilli. We demonstrated that the highest abundance of lactobacilli was found in stool samples from omnivorous populations and that Ligilactobacillus ruminis (L. ruminis) and Lactiplantibacillus plantarum (L. plantarum) were more prevalent in these samples than in vegetarian and vegan samples. In addition, we determined that different dietary structures affected the functional potential of lactobacilli by reconstructing the metagenome-assembled genomes (MAGs) of L. ruminis (highest abundance) in the samples. L. ruminis strains associated with a vegetarian diet had a higher "replication, recombination and repair" functional potential and may also have a greater capacity for glutathione (GSH) synthesis and metabolism. The results of our analysis provide evidence for the possibility of a specific selection of lactobacillus strains for people with different dietary habits.}, } @article {pmid37382438, year = {2023}, author = {Goffredi, SK and Panossian, B and Brzechffa, C and Field, N and King, C and Moggioli, G and Rouse, GW and Martín-Durán, JM and Henry, LM}, title = {A dynamic epibiont community associated with the bone-eating polychaete genus Osedax.}, journal = {mBio}, volume = {14}, number = {4}, pages = {e0314022}, pmid = {37382438}, issn = {2150-7511}, support = {IOS-0923775//National Science Foundation (NSF)/ ; NE/M018016/1//UKRI | Natural Environment Research Council (NERC)/ ; 213981/Z/18/Z//Wellcome Trust (WT)/ ; }, abstract = {Osedax, the deep-sea annelid found at sunken whalefalls, is known to host Oceanospirillales bacterial endosymbionts intracellularly in specialized roots, which help it feed exclusively on vertebrate bones. Past studies, however, have also made mention of external bacteria on their trunks. During a 14-yr study, we reveal a dynamic, yet persistent, shift of Campylobacterales integrated into the epidermis of Osedax, which change over time as the whale carcass degrades on the sea floor. The Campylobacterales associated with seven species of Osedax, which comprise 67% of the bacterial community on the trunk, appear initially dominated by the genus Arcobacter (at early time points <24 mo), the Sulfurospirillum at intermediate stages (~50 mo), and the Sulfurimonas at later stages (>140 mo) of whale carcass decomposition. Metagenome analysis of the epibiont metabolic capabilities suggests potential for a transition from heterotrophy to autotrophy and differences in their capacity to metabolize oxygen, carbon, nitrogen, and sulfur. Compared to free-living relatives, the Osedax epibiont genomes were enriched in transposable elements, implicating genetic exchange on the host surface, and contained numerous secretions systems with eukaryotic-like protein (ELP) domains, suggesting a long evolutionary history with these enigmatic, yet widely distributed deep-sea worms. IMPORTANCE Symbiotic associations are widespread in nature and we can expect to find them in every type of ecological niche. In the last twenty years, the myriad of functions, interactions and species comprising microbe-host associations has fueled a surge of interest and appreciation for symbiosis. During this 14-year study, we reveal a dynamic population of bacterial epibionts, integrated into the epidermis of 7 species of a deep-sea worm group that feeds exclusively on the remains of marine mammals. The bacterial genomes provide clues of a long evolutionary history with these enigmatic worms. On the host surface, they exchange genes and appear to undergo ecological succession, as the whale carcass habitat degrades over time, similar to what is observed for some free-living communities. These, and other annelid worms are important keystone species for diverse deep-sea environments, yet the role of attached external bacteria in supporting host health has received relatively little attention.}, } @article {pmid37382405, year = {2023}, author = {Sun, C and Chen, J and Jin, M and Zhao, X and Li, Y and Dong, Y and Gao, N and Liu, Z and Bork, P and Zhao, XM and Chen, WH}, title = {Long-Read Sequencing Reveals Extensive DNA Methylations in Human Gut Phagenome Contributed by Prevalently Phage-Encoded Methyltransferases.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {10}, number = {25}, pages = {e2302159}, pmid = {37382405}, issn = {2198-3844}, support = {32070660//National Natural Science Foundation of China/ ; T2225015//National Natural Science Foundation of China/ ; 61932008//National Natural Science Foundation of China/ ; 81873969//National Natural Science Foundation of China/ ; 31770132//National Natural Science Foundation of China/ ; 2020YFA0712403//National Key Research and Development Program of China/ ; 2019YFA0905600//National Key Research and Development Program of China/ ; 82161138017//NNSF-VR Sino-Swedish Joint Research Programme/ ; 2018SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; IPM21C008//Greater Bay Area Institute of Precision Medicine/ ; 2020YFA0712403//National Key R&D Program of China/ ; }, mesh = {Humans ; *Bacteriophages/genetics/metabolism ; Methyltransferases/genetics ; DNA Methylation/genetics ; DNA ; Metagenome ; }, abstract = {DNA methylation plays a crucial role in the survival of bacteriophages (phages), yet the understanding of their genome methylation remains limited. In this study, DNA methylation patterns are analyzed in 8848 metagenome-assembled high-quality phages from 104 fecal samples using single-molecule real-time sequencing. The results demonstrate that 97.60% of gut phages exhibit methylation, with certain factors correlating with methylation densities. Phages with higher methylation densities appear to have potential viability advantages. Strikingly, more than one-third of the phages possess their own DNA methyltransferases (MTases). Increased MTase copies are associated with higher genome methylation densities, specific methylation motifs, and elevated prevalence of certain phage groups. Notably, the majority of these MTases share close homology with those encoded by gut bacteria, suggesting their exchange during phage-bacterium interactions. Furthermore, these MTases can be employed to accurately predict phage-host relationships. Overall, the findings indicate the widespread utilization of DNA methylation by gut DNA phages as an evasion mechanism against host defense systems, with a substantial contribution from phage-encoded MTases.}, } @article {pmid37382302, year = {2023}, author = {Puente-Sánchez, F and Hoetzinger, M and Buck, M and Bertilsson, S}, title = {Exploring environmental intra-species diversity through non-redundant pangenome assemblies.}, journal = {Molecular ecology resources}, volume = {23}, number = {7}, pages = {1724-1736}, doi = {10.1111/1755-0998.13826}, pmid = {37382302}, issn = {1755-0998}, support = {892961//H2020 Marie Skłodowska-Curie Actions/ ; 2019-02336//Svenska Forskningsrådet Formas/ ; 2017-04422//Vetenskapsrådet/ ; 2018-05973//Vetenskapsrådet/ ; }, mesh = {Phylogeny ; *Bacteria/genetics ; Metagenome ; Algorithms ; *Microbiota ; Metagenomics/methods ; }, abstract = {At the genome level, microorganisms are highly adaptable both in terms of allele and gene composition. Such heritable traits emerge in response to different environmental niches and can have a profound influence on microbial community dynamics. As a consequence, any individual genome or population will contain merely a fraction of the total genetic diversity of any operationally defined "species", whose ecological potential can thus be only fully understood by studying all of their genomes and the genes therein. This concept, known as the pangenome, is valuable for studying microbial ecology and evolution, as it partitions genomes into core (present in all the genomes from a species, and responsible for housekeeping and species-level niche adaptation among others) and accessory regions (present only in some, and responsible for intra-species differentiation). Here we present SuperPang, an algorithm producing pangenome assemblies from a set of input genomes of varying quality, including metagenome-assembled genomes (MAGs). SuperPang runs in linear time and its results are complete, non-redundant, preserve gene ordering and contain both coding and non-coding regions. Our approach provides a modular view of the pangenome, identifying operons and genomic islands, and allowing to track their prevalence in different populations. We illustrate this by analysing intra-species diversity in Polynucleobacter, a bacterial genus ubiquitous in freshwater ecosystems, characterized by their streamlined genomes and their ecological versatility. We show how SuperPang facilitates the simultaneous analysis of allelic and gene content variation under different environmental pressures, allowing us to study the drivers of microbial diversification at unprecedented resolution.}, } @article {pmid37382183, year = {2023}, author = {Ma, Y and Liu, X and Zhang, X and Yu, Y and Li, Y and Song, M and Wang, J}, title = {Efficient Mining of Anticancer Peptides from Gut Metagenome.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {10}, number = {25}, pages = {e2300107}, pmid = {37382183}, issn = {2198-3844}, support = {202077/WT_/Wellcome Trust/United Kingdom ; 202077/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; Animals ; Mice ; *Antineoplastic Agents/pharmacology/therapeutic use/chemistry ; Metagenome ; Peptides/chemistry ; *Neoplasms/therapy ; Cell Line ; }, abstract = {The gut microbiome plays a crucial role in modulating host health and disease. It serves as a vast reservoir of functional molecules that hold great potential for clinical applications. One specific area of interest is identifying anticancer peptides (ACPs) for innovative cancer therapies. However, ACPs discovery is hindered by a heavy reliance on experimental methodologies. To overcome this limitation, we here employed a novel approach by leveraging the overlap between ACPs and antimicrobial peptides (AMPs). By combining well-established AMP prediction methods with mining techniques in metagenomic cohorts, a total of 40 potential ACPs is identified. Out of the identified ACPs, 39 demonstrated inhibitory effects against at least one cancer cell line, exhibiting significant differences from known ACPs. Moreover, the therapeutic potential of the two most promising peptides in a mouse xenograft cancer model is evaluated. Encouragingly, the peptides exhibit effective tumor inhibition without any detectable toxic effects. Interestingly, both peptides display uncommon secondary structures, highlighting its distinctive characteristics. This findings highlight the efficacy of the multi-center mining approach, which effectively uncovers novel ACPs from the gut microbiome. This approach has significant implications for expanding treatment options not only for CRC, but also for other cancer types.}, } @article {pmid37381590, year = {2023}, author = {Han, Z and Cheng, S and Dai, D and Kou, Y and Zhang, X and Li, F and Yin, X and Ji, J and Zhang, Z and Wang, X and Zhu, N and Zhang, Q and Tan, Y and Guo, X and Shen, L and Peng, Z}, title = {The gut microbiome affects response of treatments in HER2-negative advanced gastric cancer.}, journal = {Clinical and translational medicine}, volume = {13}, number = {7}, pages = {e1312}, pmid = {37381590}, issn = {2001-1326}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; B7-H1 Antigen/genetics ; *Stomach Neoplasms/drug therapy/genetics ; Immune Checkpoint Inhibitors ; Reproducibility of Results ; *Adenocarcinoma ; Lactobacillus ; }, abstract = {BACKGROUND: Common treatments for metastatic/unresectable HER2-negative gastric cancer include chemotherapy, immune checkpoint inhibitor monotherapy and chemotherapy plus immune checkpoint inhibitor. However, significant drug resistance exists regardless of the treatment regimen.

METHODS: Patients with metastatic/unresectable HER2-negative gastric/gastroesophageal junction adenocarcinoma were enrolled. All patients were divided into three groups according to the treatment regimen and were further divided into responders and non-responders according to efficacy evaluation. Metagenomics sequencing were performed to analyze gut microbiome signature of patients receiving different treatments at baseline and throughout treatment.

RESULTS: One hundred seventeen patients with HER2-negative advanced gastric or gastroesophageal junction adenocarcinoma receiving chemotherapy alone, anti PD-1/PD-L1 immunotherapy alone or combined regimen were included in this study. Microbiome signatures related to clinical response are distinct among the three treatment groups. Among which, 14, 8 and 13 species were significantly different between responders and non-responders in immunotherapy, immunotherapy plus chemotherapy and chemotherapy group, respectively. Patients with higher relative abundance of Lactobacillus possessed higher microbiome diversity and significantly better response to anti-PD-1/PD-L1 immunotherapy and had a trend to achieve better progression-free survival. Another cohort of 101 patients has been used as an external validation set to confirm the stability and reliability of these findings.

CONCLUSIONS: Gut microbiome affects response of treatments in HER2-negative advanced gastric cancer in a treatment-specific way, immunotherapy plus chemotherapy did not equal to a simple superposition of immunotherapy and chemotherapy. Lactobacillus is expected to become a novel choice as an adjuvant agent in promoting the efficacy of immunotherapy in gastric cancer.}, } @article {pmid37381163, year = {2023}, author = {Venetz, J and Żygadłowska, OM and Lenstra, WK and van Helmond, NAGM and Nuijten, GHL and Wallenius, AJ and Dalcin Martins, P and Slomp, CP and Jetten, MSM and Veraart, AJ}, title = {Versatile methanotrophs form an active methane biofilter in the oxycline of a seasonally stratified coastal basin.}, journal = {Environmental microbiology}, volume = {25}, number = {11}, pages = {2277-2288}, doi = {10.1111/1462-2920.16448}, pmid = {37381163}, issn = {1462-2920}, mesh = {*Methane/metabolism ; Ecosystem ; RNA, Ribosomal, 16S/genetics/metabolism ; Oxidation-Reduction ; *Methylococcaceae/genetics/metabolism ; Water/metabolism ; Oxygen/metabolism ; Phylogeny ; }, abstract = {The potential and drivers of microbial methane removal in the water column of seasonally stratified coastal ecosystems and the importance of the methanotrophic community composition for ecosystem functioning are not well explored. Here, we combined depth profiles of oxygen and methane with 16S rRNA gene amplicon sequencing, metagenomics and methane oxidation rates at discrete depths in a stratified coastal marine system (Lake Grevelingen, The Netherlands). Three amplicon sequence variants (ASVs) belonging to different genera of aerobic Methylomonadaceae and the corresponding three methanotrophic metagenome-assembled genomes (MOB-MAGs) were retrieved by 16S rRNA sequencing and metagenomic analysis, respectively. The abundances of the different methanotrophic ASVs and MOB-MAGs peaked at different depths along the methane oxygen counter-gradient and the MOB-MAGs show a quite diverse genomic potential regarding oxygen metabolism, partial denitrification and sulphur metabolism. Moreover, potential aerobic methane oxidation rates indicated high methanotrophic activity throughout the methane oxygen counter-gradient, even at depths with low in situ methane or oxygen concentration. This suggests that niche-partitioning with high genomic versatility of the present Methylomonadaceae might contribute to the functional resilience of the methanotrophic community and ultimately the efficiency of methane removal in the stratified water column of a marine basin.}, } @article {pmid37380422, year = {2023}, author = {Fan, YF and Li, ZP and Yu, XJ and Li, Z and Zhou, HJ and Zhang, YL and Gan, XT and Hua, D and Lu, X and Kan, B}, title = {[Study of the urban-impact on microbial communities and their virulence factors and antibiotic resistance genomes in the Nandu River, Haikou].}, journal = {Zhonghua liu xing bing xue za zhi = Zhonghua liuxingbingxue zazhi}, volume = {44}, number = {6}, pages = {974-981}, doi = {10.3760/cma.j.cn112338-20221229-01090}, pmid = {37380422}, issn = {0254-6450}, support = {2020YFE0205700, 2022YFC2303900//National Key Research and Development Program of China/ ; 22193064//National Natural Science Foundation of China/ ; 2018ZX10714002//National Science and Technology Major Project of China/ ; }, mesh = {Humans ; *Rivers ; Virulence Factors/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Anti-Bacterial Agents ; Drug Resistance, Microbial/genetics ; }, abstract = {Objective: To explore the changes in bacterial community structure, antibiotic resistance genome, and pathogen virulence genome in river water before and after the river flowing through Haikou City and their transmission and dispersal patterns and to reveal anthropogenic disturbance's effects on microorganisms and resistance genes in the aquatic environment. Methods: The Nandu River was divided into three study areas: the front, middle and rear sections from the upstream before it flowed through Haikou City to the estuary. Three sampling sites were selected in each area, and six copies of the sample were collected in parallel at each site and mixed for 3 L per sample. Microbial community structure, antibiotic resistance, virulence factors, and mobile genetic elements were analyzed through bioinformatic data obtained by metagenomic sequencing and full-length sequencing of 16S rRNA genes. Variations in the distribution of bacterial communities between samples and correlation of transmission patterns were analyzed by principal co-ordinates analysis, procrustes analysis, and Mantel test. Results: As the river flowed through Haikou City, microbes' alpha diversity gradually decreased. Among them, Proteobacteria dominates in the bacterial community in the front, middle, and rear sections, and the relative abundance of Proteobacteria in the middle and rear sections was higher than that in the front segment. The diversity and abundance of antibiotic resistance genes, virulence factors, and mobile genetic elements were all at low levels in the front section and all increased significantly after flow through Haikou City. At the same time, horizontal transmission mediated by mobile genetic elements played a more significant role in the spread of antibiotic-resistance genes and virulence factors. Conclusions: Urbanization significantly impacts river bacteria and the resistance genes, virulence factors, and mobile genetic elements they carry. The Nandu River in Haikou flows through the city, receiving antibiotic-resistant and pathogen-associated bacteria excreted by the population. In contrast, antibiotic-resistant genes and virulence factors are enriched in bacteria, which indicates a threat to environmental health and public health. Comparison of river microbiomes and antibiotic resistance genomes before and after flow through cities is a valuable early warning indicator for monitoring the spread of antibiotic resistance.}, } @article {pmid37379665, year = {2023}, author = {Wu, C and Song, X and Wang, D and Ma, Y and Ren, X and Hu, H and Shan, Y and Ma, X and Cui, J and Ma, Y}, title = {Effects of long-term microplastic pollution on soil heavy metals and metal resistance genes: Distribution patterns and synergistic effects.}, journal = {Ecotoxicology and environmental safety}, volume = {262}, number = {}, pages = {115180}, doi = {10.1016/j.ecoenv.2023.115180}, pmid = {37379665}, issn = {1090-2414}, abstract = {Heavy metals (HMs) and microplastics (MPs) are two emerging factors threatening global food security. Whether long-term MPs pollution will affect the distribution of HMs and their resistance genes (MRGs) in soil is unknown. Here, metagenomic approach was used to decipher the fate of MRGs in cropland soils with long-term film MPs residues. Similar distribution pattern of MRGs was formed in long-term film MPs contaminated soil. A total of 202 MRG subtypes were detected, with resistance genes for Multimetal, Cu, and As being the most prevalent type of MRGs. MRGs formed a modular distribution of five clusters centered on MRGs including ruvB in long-term film MPs contaminated soil. MRGs also formed tight co-occurrence networks with mobile genetic elements (MGEs: integrons, insertions and plasmids). Redundancy analysis showed that HMs together with microbial communities and MGEs affected the distribution of MRGs in soil. Thirteen genera including Pseudomonas were identified as potential hosts for MRGs and MGEs. The research provides preliminary progress on the synergistic effect of HMs and MPs in affecting soil ecological security. The synergistic effect of MPs and HMs needs to be considered in the remediation of contaminated soils.}, } @article {pmid37379385, year = {2023}, author = {Wang, J and Qu, YN and Evans, PN and Guo, Q and Zhou, F and Nie, M and Jin, Q and Zhang, Y and Zhai, X and Zhou, M and Yu, Z and Fu, QL and Xie, YG and Hedlund, BP and Li, WJ and Hua, ZS and Wang, Z and Wang, Y}, title = {Evidence for nontraditional mcr-containing archaea contributing to biological methanogenesis in geothermal springs.}, journal = {Science advances}, volume = {9}, number = {26}, pages = {eadg6004}, pmid = {37379385}, issn = {2375-2548}, mesh = {*Archaea/genetics/metabolism ; Ecosystem ; *Hot Springs ; Methane/metabolism ; Temperature ; Phylogeny ; }, abstract = {Recent discoveries of methyl-coenzyme M reductase-encoding genes (mcr) in uncultured archaea beyond traditional euryarchaeotal methanogens have reshaped our view of methanogenesis. However, whether any of these nontraditional archaea perform methanogenesis remains elusive. Here, we report field and microcosm experiments based on [13]C-tracer labeling and genome-resolved metagenomics and metatranscriptomics, revealing that nontraditional archaea are predominant active methane producers in two geothermal springs. Archaeoglobales performed methanogenesis from methanol and may exhibit adaptability in using methylotrophic and hydrogenotrophic pathways based on temperature/substrate availability. A five-year field survey found Candidatus Nezhaarchaeota to be the predominant mcr-containing archaea inhabiting the springs; genomic inference and mcr expression under methanogenic conditions strongly suggested that this lineage mediated hydrogenotrophic methanogenesis in situ. Methanogenesis was temperature-sensitive , with a preference for methylotrophic over hydrogenotrophic pathways when incubation temperatures increased from 65° to 75°C. This study demonstrates an anoxic ecosystem wherein methanogenesis is primarily driven by archaea beyond known methanogens, highlighting diverse nontraditional mcr-containing archaea as previously unrecognized methane sources.}, } @article {pmid37379127, year = {2023}, author = {Deek, RA and Li, H}, title = {Inference of microbial covariation networks using copula models with mixture margins.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {7}, pages = {}, pmid = {37379127}, issn = {1367-4811}, support = {R01 GM129781/GM/NIGMS NIH HHS/United States ; GM123056/NH/NIH HHS/United States ; }, mesh = {Likelihood Functions ; RNA, Ribosomal, 16S/genetics ; *Microbial Consortia ; Computer Simulation ; *Metagenome ; }, abstract = {MOTIVATION: Quantification of microbial covariations from 16S rRNA and metagenomic sequencing data is difficult due to their sparse nature. In this article, we propose using copula models with mixed zero-beta margins for the estimation of taxon-taxon covariations using data of normalized microbial relative abundances. Copulas allow for separate modeling of the dependence structure from the margins, marginal covariate adjustment, and uncertainty measurement.

RESULTS: Our method shows that a two-stage maximum-likelihood approach provides accurate estimation of model parameters. A corresponding two-stage likelihood ratio test for the dependence parameter is derived and is used for constructing covariation networks. Simulation studies show that the test is valid, robust, and more powerful than tests based upon Pearson's and rank correlations. Furthermore, we demonstrate that our method can be used to build biologically meaningful microbial networks based on a dataset from the American Gut Project.

R package for implementation is available at https://github.com/rebeccadeek/CoMiCoN.}, } @article {pmid37378328, year = {2023}, author = {Jie, Z and Zhu, Q and Zou, Y and Wu, Q and Qin, M and He, D and Lin, X and Tong, X and Zhang, J and Jie, Z and Luo, W and Xiao, X and Chen, S and Wu, Y and Guo, G and Zheng, S and Li, Y and Lai, W and Yang, H and Wang, J and Xiao, L and Chen, J and Zhang, T and Kristiansen, K and Jia, H and Zhong, S}, title = {A consortium of three-bacteria isolated from human feces inhibits formation of atherosclerotic deposits and lowers lipid levels in a mouse model.}, journal = {iScience}, volume = {26}, number = {6}, pages = {106960}, pmid = {37378328}, issn = {2589-0042}, abstract = {By a survey of metagenome-wide association studies (MWAS), we found a robust depletion of Bacteroides cellulosilyticus, Faecalibacterium prausnitzii, and Roseburia intestinalis in individuals with atherosclerotic cardiovascular disease (ACVD). From an established collection of bacteria isolated from healthy Chinese individuals, we selected B. cellulosilyticus, R. intestinalis, and Faecalibacterium longum, a bacterium related to F. prausnitzii, and tested the effects of these bacteria in an Apoe[/-] atherosclerosis mouse model. We show that administration of these three bacterial species to Apoe[-/-] mice robustly improves cardiac function, reduces plasma lipid levels, and attenuates the formation of atherosclerotic plaques. Comprehensive analysis of gut microbiota, plasma metabolome, and liver transcriptome revealed that the beneficial effects are associated with a modulation of the gut microbiota linked to a 7α-dehydroxylation-lithocholic acid (LCA)-farnesoid X receptor (FXR) pathway. Our study provides insights into transcriptional and metabolic impact whereby specific bacteria may hold promises for prevention/treatment of ACVD.}, } @article {pmid37377762, year = {2023}, author = {Lin, L and Xu, M and Zhang, H}, title = {Assistance of metagenomics next-generation sequencing for diagnosis of adenovirus pericarditis with pericardial effusion in a child: a case report and literature review.}, journal = {Frontiers in pediatrics}, volume = {11}, number = {}, pages = {1174326}, pmid = {37377762}, issn = {2296-2360}, abstract = {Human adenoviruses (HAdVs) can cause infection at any age but are most common in the pediatric population, especially young children and infants, with a peak incidence in infants and children from 6 months to 5 years of age. Adenovirus infection can cause severe pneumonia, but pericarditis from adenovirus infection was rare. This article reports a case of a 2-year-old patient with pericarditis caused by adenovirus infection and a moderate pericardial effusion. We detected positive adenovirus nucleic acid in the patient's blood by polymerase chain reaction assay. In addition, HAdVs were identified by metagenomics next-generation sequencing (mNGS) in blood and pericardial effusion. According to the test results and clinical practice, active symptomatic and supportive treatment was given, and finally the child recovered and was discharged from the hospital. Comprehensive and accurate diagnosis of pathogens is a prerequisite for effective treatment, and mNGS provides an effective means for diagnosing rare adenovirus myocarditis in children.}, } @article {pmid37377650, year = {2023}, author = {Dong, W and Ma, L and Huang, Q and Yang, X and Mei, Z and Kong, M and Sun, Z and Zhang, Z and Li, J and Zou, J and Chen, D and Dai, Y and Zhou, D and Zheng, Y and Kang, L}, title = {Gut microbiome alterations in pulmonary hypertension in highlanders and lowlanders.}, journal = {ERJ open research}, volume = {9}, number = {3}, pages = {}, pmid = {37377650}, issn = {2312-0541}, abstract = {BACKGROUND: Alterations in the gut microbiota have been observed in patients with pulmonary hypertension (PH), though whether the roles of the gut microbiota in PH at different altitudes are the same is unknown. This study aims to evaluate the associations of the gut microbiome with PH in highlanders and lowlanders.

METHODS: PH patients and controls were recruited from those who permanently live on the Tibetan plateau (highlanders) or the plains (lowlanders), and underwent transthoracic echocardiography close to their altitude of residence (at 5070 m for highlanders versus6 m for lowlanders). The gut microbiome was profiled using metagenomic shotgun sequencing.

RESULTS: In total, 13 PH patients (46% highlanders) and 88 controls (70% highlanders) were included. The overall microbial composition was different in PH patients compared to controls (p=0.003). Notably, among lowlanders, a composite microbial score of pro-atherosclerotic trimethylamine-producing species was increased in PH patients compared with that in controls (p=0.028), while among highlanders no such difference was observed (p=0.087). Another composite gut microbial score including eight species of Lactobacillus, which has shown beneficial effects on cardiovascular functions, was higher in highlanders than lowlanders (p<0.01). Furthermore, this score tended to be lower in PH patients than controls among highlanders (p=0.056) but not among lowlanders (p=0.840). In addition, the gut microbiome showed a good performance in distinguishing PH patients from controls in both lowlanders and highlanders.

CONCLUSIONS: Our study reported differently altered gut microbiome profiles between highland and lowland PH patients, highlighting the distinct microbial mechanism in PH in highlanders compared with lowlanders.}, } @article {pmid37377419, year = {2023}, author = {Vyshenska, D and Sampara, P and Singh, K and Tomatsu, A and Kauffman, WB and Nuccio, EE and Blazewicz, SJ and Pett-Ridge, J and Louie, KB and Varghese, N and Kellom, M and Clum, A and Riley, R and Roux, S and Eloe-Fadrosh, EA and Ziels, RM and Malmstrom, RR}, title = {A standardized quantitative analysis strategy for stable isotope probing metagenomics.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0128022}, pmid = {37377419}, issn = {2379-5077}, mesh = {Humans ; *Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; DNA/genetics ; Isotopes ; *Microbiota/genetics ; }, abstract = {Stable isotope probing (SIP) facilitates culture-independent identification of active microbial populations within complex ecosystems through isotopic enrichment of nucleic acids. Many DNA-SIP studies rely on 16S rRNA gene sequences to identify active taxa, but connecting these sequences to specific bacterial genomes is often challenging. Here, we describe a standardized laboratory and analysis framework to quantify isotopic enrichment on a per-genome basis using shotgun metagenomics instead of 16S rRNA gene sequencing. To develop this framework, we explored various sample processing and analysis approaches using a designed microbiome where the identity of labeled genomes and their level of isotopic enrichment were experimentally controlled. With this ground truth dataset, we empirically assessed the accuracy of different analytical models for identifying active taxa and examined how sequencing depth impacts the detection of isotopically labeled genomes. We also demonstrate that using synthetic DNA internal standards to measure absolute genome abundances in SIP density fractions improves estimates of isotopic enrichment. In addition, our study illustrates the utility of internal standards to reveal anomalies in sample handling that could negatively impact SIP metagenomic analyses if left undetected. Finally, we present SIPmg, an R package to facilitate the estimation of absolute abundances and perform statistical analyses for identifying labeled genomes within SIP metagenomic data. This experimentally validated analysis framework strengthens the foundation of DNA-SIP metagenomics as a tool for accurately measuring the in situ activity of environmental microbial populations and assessing their genomic potential. IMPORTANCE Answering the questions, "who is eating what?" and "who is active?" within complex microbial communities is paramount for our ability to model, predict, and modulate microbiomes for improved human and planetary health. These questions can be pursued using stable isotope probing to track the incorporation of labeled compounds into cellular DNA during microbial growth. However, with traditional stable isotope methods, it is challenging to establish links between an active microorganism's taxonomic identity and genome composition while providing quantitative estimates of the microorganism's isotope incorporation rate. Here, we report an experimental and analytical workflow that lays the foundation for improved detection of metabolically active microorganisms and better quantitative estimates of genome-resolved isotope incorporation, which can be used to further refine ecosystem-scale models for carbon and nutrient fluxes within microbiomes.}, } @article {pmid37376698, year = {2023}, author = {Fomsgaard, AS and Tahas, SA and Spiess, K and Polacek, C and Fonager, J and Belsham, GJ}, title = {Unbiased Virus Detection in a Danish Zoo Using a Portable Metagenomic Sequencing System.}, journal = {Viruses}, volume = {15}, number = {6}, pages = {}, pmid = {37376698}, issn = {1999-4915}, mesh = {Animals ; Humans ; *Chickens/genetics ; *Herpesviridae/genetics ; DNA Viruses/genetics ; High-Throughput Nucleotide Sequencing/methods ; RNA ; Denmark ; Metagenomics/methods ; Mammals ; }, abstract = {Metagenomic next-generation sequencing (mNGS) is receiving increased attention for the detection of new viruses and infections occurring at the human-animal interface. The ability to actively transport and relocate this technology enables in situ virus identification, which could reduce response time and enhance disease management. In a previous study, we developed a straightforward mNGS procedure that greatly enhances the detection of RNA and DNA viruses in human clinical samples. In this study, we improved the mNGS protocol with transportable battery-driven equipment for the portable, non-targeted detection of RNA and DNA viruses in animals from a large zoological facility, to simulate a field setting for point-of-incidence virus detection. From the resulting metagenomic data, we detected 13 vertebrate viruses from four major virus groups: (+)ssRNA, (+)ssRNA-RT, dsDNA and (+)ssDNA, including avian leukosis virus in domestic chickens (Gallus gallus), enzootic nasal tumour virus in goats (Capra hircus) and several small, circular, Rep-encoding, ssDNA (CRESS DNA) viruses in several mammal species. More significantly, we demonstrate that the mNGS method is able to detect potentially lethal animal viruses, such as elephant endotheliotropic herpesvirus in Asian elephants (Elephas maximus) and the newly described human-associated gemykibivirus 2, a human-to-animal cross-species virus, in a Linnaeus two-toed sloth (Choloepus didactylus) and its enclosure, for the first time.}, } @article {pmid37376670, year = {2023}, author = {Kosoltanapiwat, N and van der Hoek, L and Kinsella, CM and Tongshoob, J and Prasittichai, L and Klein, M and Jebbink, MF and Deijs, M and Reamtong, O and Boonnak, K and Khongsiri, W and Phadungsombat, J and Tongthainan, D and Tulayakul, P and Yindee, M}, title = {A Novel Simian Adenovirus Associating with Human Adeno-virus Species G Isolated from Long-Tailed Macaque Feces.}, journal = {Viruses}, volume = {15}, number = {6}, pages = {}, pmid = {37376670}, issn = {1999-4915}, mesh = {Animals ; Humans ; Macaca fascicularis ; *Adenoviruses, Simian/genetics ; Thailand/epidemiology ; Macaca mulatta ; Adenoviridae ; *Adenoviridae Infections/veterinary ; *Enterovirus ; *Enterovirus Infections ; Feces ; Phylogeny ; }, abstract = {Metagenomics has demonstrated its capability in outbreak investigations and pathogen surveillance and discovery. With high-throughput and effective bioinformatics, many disease-causing agents, as well as novel viruses of humans and animals, have been identified using metagenomic analysis. In this study, a VIDISCA metagenomics workflow was used to identify potential unknown viruses in 33 fecal samples from asymptomatic long-tailed macaques (Macaca fascicularis) in Ratchaburi Province, Thailand. Putatively novel astroviruses, enteroviruses, and adenoviruses were detected and confirmed by PCR analysis of long-tailed macaque fecal samples collected from areas in four provinces, Ratchaburi, Kanchanaburi, Lopburi, and Prachuap Khiri Khan, where humans and monkeys live in proximity (total n = 187). Astroviruses, enteroviruses, and adenoviruses were present in 3.2%, 7.5%, and 4.8% of macaque fecal samples, respectively. One adenovirus, named AdV-RBR-6-3, was successfully isolated in human cell culture. Whole-genome analysis suggested that it is a new member of the species Human adenovirus G, closely related to Rhesus adenovirus 53, with evidence of genetic recombination and variation in the hexon, fiber, and CR1 genes. Sero-surveillance showed neutralizing antibodies against AdV-RBR-6-3 in 2.9% and 11.2% of monkeys and humans, respectively, suggesting cross-species infection of monkeys and humans. Overall, we reported the use of metagenomics to screen for possible new viruses, as well as the isolation and molecular and serological characterization of the new adenovirus with cross-species transmission potential. The findings emphasize that zoonotic surveillance is important and should be continued, especially in areas where humans and animals interact, to predict and prevent the threat of emerging zoonotic pathogens.}, } @article {pmid37376592, year = {2023}, author = {Jung, SW and Kim, KE and Kim, HJ and Lee, TK}, title = {Metavirome Profiling and Dynamics of the DNA Viral Community in Seawater in Chuuk State, Federated States of Micronesia.}, journal = {Viruses}, volume = {15}, number = {6}, pages = {}, pmid = {37376592}, issn = {1999-4915}, mesh = {Humans ; Seawater ; DNA Viruses/genetics ; *Bacteriophages/genetics ; *Viruses/genetics ; DNA ; Phylogeny ; }, abstract = {Despite their abundance and ecological importance, little is known about the diversity of marine viruses, in part because most cannot be cultured in the laboratory. Here, we used high-throughput viral metagenomics of uncultivated viruses to investigate the dynamics of DNA viruses in tropical seawater sampled from Chuuk State, Federated States of Micronesia, in March, June, and December 2014. Among the identified viruses, 71-79% were bacteriophages belonging to the families Myoviridae, Siphoviridae, and Podoviridae (Caudoviriales), listed in order of abundance at all sampling times. Although the measured environmental factors (temperature, salinity, and pH) remained unchanged in the seawater over time, viral dynamics changed. The proportion of cyanophages (34.7%) was highest in June, whereas the proportion of mimiviruses, phycodnaviruses, and other nucleo-cytoplasmic large DNA viruses (NCLDVs) was higher in March and December. Although host species were not analysed, the dramatic viral community change observed in June was likely due to changes in the abundance of cyanophage-infected cyanobacteria, whereas that in NCLDVs was likely due to the abundance of potential eukaryote-infected hosts. These results serve as a basis for comparative analyses of other marine viral communities, and guide policy-making when considering marine life care in Chuuk State.}, } @article {pmid37376527, year = {2023}, author = {Kende, J and Bonomi, M and Temmam, S and Regnault, B and Pérot, P and Eloit, M and Bigot, T}, title = {Virus Pop-Expanding Viral Databases by Protein Sequence Simulation.}, journal = {Viruses}, volume = {15}, number = {6}, pages = {}, pmid = {37376527}, issn = {1999-4915}, mesh = {Humans ; Phylogeny ; *Computational Biology/methods ; Computer Simulation ; Databases, Factual ; *Viruses/genetics ; Metagenomics/methods ; }, abstract = {The improvement of our knowledge of the virosphere, which includes unknown viruses, is a key area in virology. Metagenomics tools, which perform taxonomic assignation from high throughput sequencing datasets, are generally evaluated with datasets derived from biological samples or in silico spiked samples containing known viral sequences present in public databases, resulting in the inability to evaluate the capacity of these tools to detect novel or distant viruses. Simulating realistic evolutionary directions is therefore key to benchmark and improve these tools. Additionally, expanding current databases with realistic simulated sequences can improve the capacity of alignment-based searching strategies for finding distant viruses, which could lead to a better characterization of the "dark matter" of metagenomics data. Here, we present Virus Pop, a novel pipeline for simulating realistic protein sequences and adding new branches to a protein phylogenetic tree. The tool generates simulated sequences with substitution rate variations that are dependent on protein domains and inferred from the input dataset, allowing for a realistic representation of protein evolution. The pipeline also infers ancestral sequences corresponding to multiple internal nodes of the input data phylogenetic tree, enabling new sequences to be inserted at various points of interest in the group studied. We demonstrated that Virus Pop produces simulated sequences that closely match the structural and functional characteristics of real protein sequences, taking as an example the spike protein of sarbecoviruses. Virus Pop also succeeded at creating sequences that resemble real sequences not included in the databases, which facilitated the identification of a novel pathogenic human circovirus not included in the input database. In conclusion, Virus Pop is helpful for challenging taxonomic assignation tools and could help improve databases to better detect distant viruses.}, } @article {pmid37376182, year = {2023}, author = {Dukaew, N and Thongkumkoon, P and Sirikaew, N and Dissook, S and Sakuludomkan, W and Tongjai, S and Thiennimitr, P and Na Takuathung, M and Benjanuwattra, J and Kongthaweelert, P and Koonrungsesomboon, N}, title = {Gut Microbiota-Mediated Pharmacokinetic Drug-Drug Interactions between Mycophenolic Acid and Trimethoprim-Sulfamethoxazole in Humans.}, journal = {Pharmaceutics}, volume = {15}, number = {6}, pages = {}, pmid = {37376182}, issn = {1999-4923}, support = {64-075//Health Systems Research Institute/ ; 098-2563//Faculty of Medicine, Chiang Mai University/ ; }, abstract = {Mycophenolic acid (MPA) and trimethoprim-sulfamethoxazole (TMP-SMX) are commonly prescribed together in certain groups of patients, including solid organ transplant recipients. However, little is known about the pharmacokinetic drug-drug interactions (DDIs) between these two medications. Therefore, the present study aimed to determine the effects of TMP-SMX on MPA pharmacokinetics in humans and to find out the relationship between MPA pharmacokinetics and gut microbiota alteration. This study enrolled 16 healthy volunteers to take a single oral dose of 1000 mg mycophenolate mofetil (MMF), a prodrug of MPA, administered without and with concurrent use of TMP-SMX (320/1600 mg/day) for five days. The pharmacokinetic parameters of MPA and its glucuronide (MPAG) were measured using high-performance liquid chromatography. The composition of gut microbiota in stool samples was profiled using a 16S rRNA metagenomic sequencing technique during pre- and post-TMP-SMX treatment. Relative abundance, bacterial co-occurrence networks, and correlations between bacterial abundance and pharmacokinetic parameters were investigated. The results showed a significant decrease in systemic MPA exposure when TMP-SMX was coadministered with MMF. Analysis of the gut microbiome revealed altered relative abundance of two enriched genera, namely the genus Bacteroides and Faecalibacterium, following TMP-SMX treatment. The relative abundance of the genera Bacteroides, [Eubacterium] coprostanoligenes group, [Eubacterium] eligens group, and Ruminococcus appeared to be significantly correlated with systemic MPA exposure. Coadministration of TMP-SMX with MMF resulted in a reduction in systemic MPA exposure. The pharmacokinetic DDIs between these two drugs were attributed to the effect of TMP-SMX, a broad-spectrum antibiotic, on gut microbiota-mediated MPA metabolism.}, } @article {pmid37375983, year = {2023}, author = {Liu, Y and Yuan, Y and Yuan, H and Wang, Y and Jin, C and Zhang, H and Tang, J and Hu, Y}, title = {Metagenomic Sequencing to Analyze Composition and Function of Top-Gray Chalky Grain Microorganisms from Hybrid Rice Seeds.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {37375983}, issn = {2223-7747}, support = {kh2201219//the Key Project of Changsha Science and Technology Plan/ ; 2022JJ30312//Hunan Provincial Natural Science Foundation/ ; }, abstract = {The top-gray chalkiness of hybrid rice (Oryza sativa L.) seeds is a typical phenomenon in hybrid rice seeds. The chalky part of the grain is infected and is the inoculum to infect the normal seeds during storage and soaking. These seed-associated microorganisms were cultivated and sequenced using metagenomics shotgun sequencing to obtain more comprehensive information on the seed-associated microorganisms in this experiment. The results showed that fungi could grow well on the rice flour medium, similar to the ingredients of rice seed endosperms. After the assembly of metagenomic data, a gene catalog was established, comprising 250,918 genes. Function analysis showed that glycoside hydrolases were the dominant enzymes, and the genus Rhizopus accounted for the dominant microorganisms. The fungal species R. microspores, R. delemar, and R. oryzae were likely to be the candidate pathogens in the top-gray chalky grains of hybrid rice seeds. These results will provide a reference for improving hybrid rice processing after harvest.}, } @article {pmid37375933, year = {2023}, author = {Virág, E and Kiniczky, M and Kutasy, B and Nagy, Á and Pallos, JP and Laczkó, L and Freytag, C and Hegedűs, G}, title = {Supplementation of the Plant Conditioner ELICE Vakcina[®] Product with β-Aminobutyric Acid and Salicylic Acid May Lead to Trans-Priming Signaling in Barley (Hordeum vulgare).}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {37375933}, issn = {2223-7747}, support = {KFI_16-1-2017-0457//National Research, Development and Innovation Office/ ; }, abstract = {Plant immunological memory, priming, is a defense mechanism that can be triggered by external stimuli, leading to the activation of biochemical pathways and preparing plants for disease resistance. Plant conditioners improve yield and crop quality through nutrient efficiency and abiotic stress tolerance, which is enhanced by the addition of resistance- and priming-induced compounds. Based on this hypothesis, this study aimed to investigate plant responses to priming actives of different natures, including salicylic acid and beta-aminobutyric acid, in combination with the plant conditioning agent ELICE Vakcina[®]. Phytotron experiments and RNA-Seq analyses of differentially expressed genes using the combinations of these three investigated compounds were performed in a barley culture to investigate possible synergistic relationships in the genetic regulatory network. The results indicated a strong regulation of defense responses, which was enhanced by supplemental treatments; however, both synergistic and antagonistic effects were enhanced with one or two components, depending on the supplementation. The overexpressed transcripts were functionally annotated to assess their involvement in jasmonic acid and salicylic acid signaling; however, their determinant genes were highly dependent on the supplemental treatments. Although the effects overlapped, the potential effects of trans-priming the two supplements tested could be largely separated.}, } @article {pmid37375877, year = {2023}, author = {Langa-Lomba, N and Grimplet, J and Sánchez-Hernández, E and Martín-Ramos, P and Casanova-Gascón, J and Julián-Lagunas, C and González-García, V}, title = {Metagenomic Study of Fungal Microbial Communities in Two PDO Somontano Vineyards (Huesca, Spain): Effects of Age, Plant Genotype, and Initial Phytosanitary Status on the Priming and Selection of their Associated Microorganisms.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {37375877}, issn = {2223-7747}, support = {para la transferencia del conocimiento al sector agroalimentario" program//Cátedra Agrobank under the "IV Convocatoria de Ayudas de la Cátedra AgroBank/ ; }, abstract = {The study of microbial communities associated with different plants of agronomic interest has allowed, in recent years, to answer a number of questions related to the role and influence of certain microbes in key aspects of their autoecology, such as improving the adaptability of the plant host to different abiotic or biotic stresses. In this study, we present the results of the characterization, through both high-throughput sequencing and classical microbiological methods, of the fungal microbial communities associated with grapevine plants in two vineyards of different ages and plant genotypes located in the same biogeographical unit. The study is configured as an approximation to the empirical demonstration of the concept of "microbial priming" by analyzing the alpha- and beta-diversity present in plants from two plots subjected to the same bioclimatic regime to detect differences in the structure and taxonomic composition of the populations. The results were compared with the inventories of fungal diversity obtained by culture-dependent methods to establish, where appropriate, correlations between both microbial communities. Metagenomic data showed a differential enrichment of the microbial communities in the two vineyards studied, including the populations of plant pathogens. This is tentatively explained due to factors such as the different time of exposure to microbial infection, different plant genotype, and different starting phytosanitary situation. Thus, results suggest that each plant genotype recruits differential fungal communities and presents different profiles of associated potential microbial antagonists or communities of pathogenic species.}, } @article {pmid37375584, year = {2023}, author = {Fernandes, A and Oliveira, A and Carvalho, AL and Soares, R and Barata, P}, title = {Faecalibacterium prausnitzii in Differentiated Thyroid Cancer Patients Treated with Radioiodine.}, journal = {Nutrients}, volume = {15}, number = {12}, pages = {}, pmid = {37375584}, issn = {2072-6643}, support = {UID/BIM/04293/2019//Fundação para a Ciência e Tecnologia/ ; }, mesh = {Humans ; Faecalibacterium prausnitzii ; Iodine Radioisotopes/therapeutic use ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; Fatty Acids, Volatile ; *Thyroid Neoplasms/radiotherapy ; }, abstract = {BACKGROUND: Faecalibacterium prausnitzii, one of the most important bacteria of the human gut microbiota, produces butyrate (a short-chain fatty acid). Short-chain fatty acids are known to influence thyroid physiology and thyroid cancer's response to treatment. We aimed to analyze the relative abundance of Faecalibacterium prausnitzii on the gut microbiota of differentiated thyroid cancer patients compared to controls and its variation after radioiodine therapy (RAIT).

METHODS: Fecal samples were collected from 37 patients diagnosed with differentiated thyroid cancer before and after radioiodine therapy and from 10 volunteers. The abundance of F. prausnitzii was determined using shotgun metagenomics.

RESULTS: Our study found that the relative abundance of F. prausnitzii is significantly reduced in thyroid cancer patients compared to volunteers. We also found that there was a mixed response to RAIT, with an increase in the relative and absolute abundances of this bacterium in most patients.

CONCLUSIONS: Our study confirms that thyroid cancer patients present a dysbiotic gut microbiota, with a reduction in F. prausnitzii's relative abundance. In our study, radioiodine did not negatively affect F. prausnitzii, quite the opposite, suggesting that this bacterium might play a role in resolving radiation aggression issues.}, } @article {pmid37375310, year = {2023}, author = {Borowik, A and Wyszkowska, J and Zaborowska, M and Kucharski, J}, title = {Microbial Diversity and Enzyme Activity as Indicators of Permethrin-Exposed Soil Health.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {12}, pages = {}, pmid = {37375310}, issn = {1420-3049}, support = {grant No. 30.610.006-110//University of Warmia and Mazury in Olsztyn, Faculty of Agriculture and Forestry, Department of Soil Science and Microbiology/ ; 010/RID/2018/19//Minister of Education and Science in the range of the program entitled "Regional Initiative of Excellence" for the years 2019-2023/ ; }, mesh = {Humans ; Soil/chemistry ; Permethrin/pharmacology ; Bacteria/genetics ; Alkaline Phosphatase ; *Ascomycota ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Owing to their wide range of applications in the control of ticks and insects in horticulture, forestry, agriculture and food production, pyrethroids pose a significant threat to the environment, including a risk to human health. Hence, it is extremely important to gain a sound understanding of the response of plants and changes in the soil microbiome induced by permethrin. The purpose of this study has been to show the diversity of microorganisms, activity of soil enzymes and growth of Zea mays following the application of permethrin. This article presents the results of the identification of microorganisms with the NGS sequencing method, and of isolated colonies of microorganisms on selective microbiological substrates. Furthermore, the activity of several soil enzymes, such as dehydrogenases (Deh), urease (Ure), catalase (Cat), acid phosphatase (Pac), alkaline phosphatase (Pal), β-glucosidase (Glu) and arylsulfatase (Aryl), as well as the growth of Zea mays and its greenness indicators (SPAD), after 60 days of growth following the application of permethrin, were presented. The research results indicate that permethrin does not have a negative effect on the growth of plants. The metagenomic studies showed that the application of permethrin increases the abundance of Proteobacteria, but decreases the counts of Actinobacteria and Ascomycota. The application of permethrin raised to the highest degree the abundance of bacteria of the genera Cellulomonas, Kaistobacter, Pseudomonas, Rhodanobacter and fungi of the genera Penicillium, Humicola, Iodophanus, Meyerozyma. It has been determined that permethrin stimulates the multiplication of organotrophic bacteria and actinomycetes, decreases the counts of fungi and depresses the activity of all soil enzymes in unseeded soil. Zea mays is able to mitigate the effect of permethrin and can therefore be used as an effective phytoremediation plant.}, } @article {pmid37375113, year = {2023}, author = {Hart, B and Patel, J and De Maayer, P and Nweke, EE and Bizos, D}, title = {Metataxonomic Analysis Demonstrates a Shift in Duodenal Microbiota in Patients with Obstructive Jaundice.}, journal = {Microorganisms}, volume = {11}, number = {6}, pages = {}, pmid = {37375113}, issn = {2076-2607}, support = {N/A//School of Clinical Medicine, University of Witwatersrand/ ; }, abstract = {The human gastrointestinal tract (GIT) is home to an abundance of diverse microorganisms, and the balance of this microbiome plays a vital role in maintaining a healthy GIT. The obstruction of the flow of bile into the duodenum, resulting in obstructive jaundice (OJ), has a major impact on the health of the affected individual. This study sought to identify changes in the duodenal microbiota in South African patients with OJ compared to those without this disorder. Mucosal biopsies were taken from the duodenum of nineteen jaundiced patients undergoing endoscopic retrograde cholangiopancreatography (ERCP) and nineteen control participants (non-jaundiced patients) undergoing gastroscopy. DNA extracted from the samples was subjected to 16S rRNA amplicon sequencing using the Ion S5 TM sequencing platform. Diversity metrics and statistical correlation analyses with the clinical data were performed to compare duodenal microbial communities in both groups. Differences in the mean distribution of the microbial communities in the jaundiced and non-jaundiced samples were observed; however, this difference did not reach statistical significance. Of note, there was a statistically significant difference between the mean distributions of bacteria comparing jaundiced patients with cholangitis to those without (p = 0.0026). On further subset analysis, a significant difference was observed between patients with benign (Cholelithiasis) and malignant disease, namely, head of pancreas (HOP) mass (p = 0.01). Beta diversity analyses further revealed a significant difference between patients with stone and non-stone related disease when factoring in the Campylobacter-Like Organisms (CLO) test status (p = 0.048). This study demonstrated a shift in the microbiota in jaundiced patients, especially considering some underlying conditions of the upper GI tract. Future studies should aim to verify these findings in a larger cohort.}, } @article {pmid37375018, year = {2023}, author = {Muratova, A and Golubev, S and Romanova, V and Sungurtseva, I and Nurzhanova, A}, title = {Effect of Heavy-Metal-Resistant PGPR Inoculants on Growth, Rhizosphere Microbiome and Remediation Potential of Miscanthus × giganteus in Zinc-Contaminated Soil.}, journal = {Microorganisms}, volume = {11}, number = {6}, pages = {}, pmid = {37375018}, issn = {2076-2607}, support = {AP09259724//Ministry of Education and Science of the Republic of Kazakhstan/ ; }, abstract = {Microbial-assisted phytoremediation is considered a more effective approach to soil rehabilitation than the sole use of plants. Mycolicibacterium sp. Pb113 and Chitinophaga sp. Zn19, heavy-metal-resistant PGPR strains originally isolated from the rhizosphere of Miscanthus × giganteus, were used as inoculants of the host plant grown in control and zinc-contaminated (1650 mg/kg) soil in a 4-month pot experiment. The diversity and taxonomic structure of the rhizosphere microbiomes, assessed with metagenomic analysis of rhizosphere samples for the 16S rRNA gene, were studied. Principal coordinate analysis showed differences in the formation of the microbiomes, which was affected by zinc rather than by the inoculants. Bacterial taxa affected by zinc and the inoculants, and the taxa potentially involved in the promotion of plant growth as well as in assisted phytoremediation, were identified. Both inoculants promoted miscanthus growth, but only Chitinophaga sp. Zn19 contributed to significant Zn accumulation in the aboveground part of the plant. In this study, the positive effect of miscanthus inoculation with Mycolicibacterium spp. and Chitinophaga spp. was demonstrated for the first time. On the basis of our data, the bacterial strains studied may be recommended to improve the efficiency of M. × giganteus phytoremediation of zinc-contaminated soil.}, } @article {pmid37374982, year = {2023}, author = {Amaral, WZ and Lubach, GR and Rendina, DN and Phillips, GJ and Lyte, M and Coe, CL}, title = {Significant Microbial Changes Are Evident in the Reproductive Tract of Pregnant Rhesus Monkeys at Mid-Gestation but Their Gut Microbiome Does Not Shift until Late Gestation.}, journal = {Microorganisms}, volume = {11}, number = {6}, pages = {}, pmid = {37374982}, issn = {2076-2607}, support = {R21 MH104198/MH/NIMH NIH HHS/United States ; R33 MH104198/MH/NIMH NIH HHS/United States ; T32 MH018931/MH/NIMH NIH HHS/United States ; MH104198/MH/NIMH NIH HHS/United States ; }, abstract = {Vaginal and rectal specimens were obtained from cycling, pregnant, and nursing rhesus monkeys to assess pregnancy-related changes in the commensal bacteria in their reproductive and intestinal tracts. Using 16S rRNA gene amplicon sequencing, significant differences were found only in the vagina at mid-gestation, not in the hindgut. To verify the apparent stability in gut bacterial composition at mid-gestation, the experiment was repeated with additional monkeys, and similar results were found with both 16S rRNA gene amplicon and metagenomic sequencing. A follow-up study investigated if bacterial changes in the hindgut might occur later in pregnancy. Gravid females were assessed closer to term and compared to nonpregnant females. By late pregnancy, significant differences in bacterial composition, including an increased abundance of 4 species of Lactobacillus and Bifidobacterium adolescentis, were detected, but without a shift in the overall community structure. Progesterone levels were assessed as a possible hormone mediator of bacterial change. The relative abundance of only some taxa (e.g., Bifidobacteriaceae) were specifically associated with progesterone. In summary, pregnancy changes the microbial profiles in monkeys, but the bacterial diversity in their lower reproductive tract is different from women, and the composition of their intestinal symbionts remains stable until late gestation when several Firmicutes become more prominent.}, } @article {pmid37374962, year = {2023}, author = {Marín, A and Feijoo, P and de Llanos, R and Carbonetto, B and González-Torres, P and Tena-Medialdea, J and García-March, JR and Gámez-Pérez, J and Cabedo, L}, title = {Microbiological Characterization of the Biofilms Colonizing Bioplastics in Natural Marine Conditions: A Comparison between PHBV and PLA.}, journal = {Microorganisms}, volume = {11}, number = {6}, pages = {}, pmid = {37374962}, issn = {2076-2607}, support = {AICO/2021/045//Generalitat Valenciana/ ; 10.13039/501100011033//MCIN/AEI/ ; UJI-B2022-34//Jaume I University/ ; PID2021-128749OB-C32//FEDER "Una manera de hacer Europa"/ ; }, abstract = {Biodegradable polymers offer a potential solution to marine pollution caused by plastic waste. The marine biofilms that formed on the surfaces of poly(lactide acid) (PLA) and poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) were studied. Bioplastics were exposed for 6 months to marine conditions in the Mediterranean Sea, and the biofilms that formed on their surfaces were assessed. The presence of specific PLA and PHBV degraders was also studied. PHBV showed extensive areas with microbial accumulations and this led to higher microbial surface densities than PLA (4.75 vs. 5.16 log CFU/cm[2]). Both polymers' surfaces showed a wide variety of microbial structures, including bacteria, fungi, unicellular algae and choanoflagellates. A high bacterial diversity was observed, with differences between the two polymers, particularly at the phylum level, with over 70% of bacteria affiliated to three phyla. Differences in metagenome functions were also detected, revealing a higher presence of proteins involved in PHBV biodegradation in PHBV biofilms. Four bacterial isolates belonging to the Proteobacteria class were identified as PHBV degraders, demonstrating the presence of species involved in the biodegradation of this polymer in seawater. No PLA degraders were detected, confirming its low biodegradability in marine environments. This was a pilot study to establish a baseline for further studies aimed at comprehending the marine biodegradation of biopolymers.}, } @article {pmid37374901, year = {2023}, author = {Baláž, A and Kajsik, M and Budiš, J and Szemes, T and Turňa, J}, title = {PHERI-Phage Host ExploRation Pipeline.}, journal = {Microorganisms}, volume = {11}, number = {6}, pages = {}, pmid = {37374901}, issn = {2076-2607}, support = {313011ATR9//Operational Program Integrated Infrastructure/ ; }, abstract = {Antibiotic resistance is becoming a common problem in medicine, food, and industry, with multidrug-resistant bacterial strains occurring in all regions. One of the possible future solutions is the use of bacteriophages. Phages are the most abundant form of life in the biosphere, so we can highly likely purify a specific phage against each target bacterium. The identification and consistent characterization of individual phages was a common form of phage work and included determining bacteriophages' host-specificity. With the advent of new modern sequencing methods, there was a problem with the detailed characterization of phages in the environment identified by metagenome analysis. The solution to this problem may be to use a bioinformatic approach in the form of prediction software capable of determining a bacterial host based on the phage whole-genome sequence. The result of our research is the machine learning algorithm-based tool called PHERI. PHERI predicts the suitable bacterial host genus for the purification of individual viruses from different samples. In addition, it can identify and highlight protein sequences that are important for host selection.}, } @article {pmid37373701, year = {2023}, author = {Villarejo-Campos, P and García-Arranz, M and Qian, S and Jiménez de Los Galanes, S and Domínguez-Prieto, V and Vélez-Pinto, JF and Guijo Castellano, I and Jiménez-Fuertes, M and Guadalajara, H and García-Olmo, D}, title = {Under the Hood: Understanding the Features of Mucin in Pseudomyxoma Peritonei.}, journal = {Journal of clinical medicine}, volume = {12}, number = {12}, pages = {}, pmid = {37373701}, issn = {2077-0383}, support = {PI20/01052 and DTS22/00048).//ISCIII-FEDER (Instituto de Salud Carlos III-Fondo Europeo de Desarrollo Regional), Spanish Ministry of Health/ ; }, abstract = {Pseudomyxoma peritonei (PMP) is a rare malignant growth characterized by the production of mucin and the potential for peritoneal relapse. This study aimed to investigate the immunohistochemical and biological characteristics of mucin in patients with cellular and acellular PMP. We prospectively analyzed mucin specimens obtained from our patient cohort and described the composition and type of mucin present in each sample. A metagenomic analysis of the samples was performed to investigate the bacterial composition of the PMP microbiome. Secreted mucins 2 and 5AC and membrane-associated mucin-1 were the primary components of mucin in both cellular and acellular tumor specimens. The metagenomic study revealed a predominance of the phylum Proteobacteria and the genus Pseudomonas. Notably, Pseudomonas plecoglossicida, a species not previously reported in the human microbiome, was found to be the most abundant organism in the mucin of pseudomyxoma peritonei. Our findings suggest that the presence of MUC-2 and mucin colonization by Pseudomonas are characteristic features of both cellular and acellular disease. These results may have significant implications for the diagnosis and treatment of this rare entity.}, } @article {pmid37373465, year = {2023}, author = {Mullakkalparambil Velayudhan, S and Sejian, V and Devaraj, C and Manjunathareddy, GB and Ruban, W and Kadam, V and König, S and Bhatta, R}, title = {Novel Insights to Assess Climate Resilience in Goats Using a Holistic Approach of Skin-Based Advanced NGS Technologies.}, journal = {International journal of molecular sciences}, volume = {24}, number = {12}, pages = {}, pmid = {37373465}, issn = {1422-0067}, support = {2020//Indian Council of Agricultural Research/ ; }, mesh = {Animals ; *Goats/physiology ; RNA, Ribosomal, 16S ; Skin/metabolism ; Hair/metabolism ; HSP70 Heat-Shock Proteins/metabolism ; *Heat Stress Disorders/metabolism/veterinary ; }, abstract = {A novel study was conducted to elucidate heat-stress responses on a number of hair- and skin-based traits in two indigenous goat breeds using a holistic approach that considered a number of phenotypic and genomic variables. The two goat breeds, Kanni Aadu and Kodi Aadu, were subjected to a simulated heat-stress study using the climate chambers. Four groups consisting of six goats each (KAC, Kaani Aadu control; KAH, Kanni Aadu heat stress; KOC, Kodi Aadu control; and KOH, Kodi Aadu heat stress) were considered for the study. The impact of heat stress on caprine skin tissue along with a comparative assessment of the thermal resilience of the two goat breeds was assessed. The variables considered were hair characteristics, hair cortisol, hair follicle quantitative PCR (qPCR), sweating (sweating rate and active sweat gland measurement), skin histometry, skin-surface infrared thermography (IRT), skin 16S rRNA V3-V4 metagenomics, skin transcriptomics, and skin bisulfite sequencing. Heat stress significantly influenced the hair fiber characteristics (fiber length) and hair follicle qPCR profile (Heat-shock protein 70 (HSP70), HSP90, and HSP110). Significantly higher sweating rate, activated sweat gland number, skin epithelium, and sweat gland number (histometry) were observed in heat stressed goats. The skin microbiota was also observed to be significantly altered due to heat stress, with a relatively higher alteration being noticed in Kanni Aadu goats than in Kodi Aadi goats. Furthermore, the transcriptomics and epigenetics analysis also pointed towards the significant impact of heat stress at the cellular and molecular levels in caprine skin tissue. The higher proportion of differentially expressed genes (DEGs) along with higher differentially methylated regions (DMRs) in Kanni Aadu goats due to heat stress when compared to Kodi Aadu goats pointed towards the better resilience of the latter breed. A number of established skin, adaptation, and immune-response genes were also observed to be significantly expressed/methylated. Additionally, the influence of heat stress at the genomic level was also predicted to result in significant functional alterations. This novel study thereby highlights the impact of heat stress on the caprine skin tissue and also the difference in thermal resilience exhibited by the two indigenous goat breeds, with Kodi Aadu goats being more resilient.}, } @article {pmid37372597, year = {2023}, author = {Ruiz-Barba, JL and Sánchez, AH and López-López, A and Cortés-Delgado, A and Montaño, A}, title = {Microbial and Chemical Characterization of Natural-Style Green Table Olives from the Gordal, Hojiblanca and Manzanilla Cultivars.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {37372597}, issn = {2304-8158}, support = {P20-00071//Regional Government of Andalusia/ ; PID2020-116314RB-I00//Spanish government/ ; }, abstract = {Microbial and biochemical changes in the brine during the spontaneous fermentation of Gordal, Hojiblanca and Manzanilla olive cultivars processed according to the natural style were monitored. The microbial composition was assessed through a metagenomic study. Sugars, ethanol, glycerol, organic acids and phenolic compounds were quantified by standard methods. In addition, the volatile profiles, contents of phenolic compounds in the olives and quality parameters of the final products were compared. Fermentation in Gordal brines was conducted by lactic acid bacteria (mainly Lactobacillus and Pediococcus) and yeasts (mainly Candida boidinii, Candida tropicalis and Wickerhamomyces anomalus). In Hojiblanca and Manzanilla brines, halophilic Gram-negative bacteria (e.g., Halomonas, Allidiomarina and Marinobacter) along with yeasts (mainly, Saccharomyces) were responsible for the fermentation. Higher acidity and lower pH values were reached in Gordal brines compared to Hojiblanca and Manzanilla. After 30 days of fermentation, no sugars were detected in Gordal brine, but residual amounts were found in the brines from Hojiblanca (<0.2 g/L glucose) and Manzanilla (2.9 g/L glucose and 0.2 g/L fructose). Lactic acid was the main acid product in Gordal fermentation, whereas citric acid was the predominant organic acid in the Hojiblanca and Manzanilla brines. Manzanilla brine samples showed a greater concentration of phenolic compounds than Hojiblanca and Gordal brines. After a 6-month fermentation, Gordal olives were superior compared to the Hojiblanca and Manzanilla varieties regarding product safety (lower final pH and absence of Enterobacteriaceae), content of volatile compounds (richer aroma), content of bitter phenolics (lower content of oleuropein, which resulted in less perceived bitterness) and color parameters (more yellow and lighter color, indicating a higher visual appraisal). The results of the present study will contribute to a better understanding of each fermentation process and could help to promote natural-style elaborations using the above-mentioned olive cultivars.}, } @article {pmid37372408, year = {2023}, author = {Veneruso, I and Cariati, F and Alviggi, C and Pastore, L and Tomaiuolo, R and D'Argenio, V}, title = {Metagenomics Reveals Specific Microbial Features in Males with Semen Alterations.}, journal = {Genes}, volume = {14}, number = {6}, pages = {}, pmid = {37372408}, issn = {2073-4425}, mesh = {Humans ; Male ; *Semen ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Infertility, Male/genetics ; Semen Analysis ; }, abstract = {Infertility incidence is rising worldwide, with male infertility accounting for about 50% of cases. To date, several factors have been associated with male infertility; in particular, it has been suggested that semen microbiota may play a role. Here, we report the NGS-based analyses of 20 semen samples collected from men with (Case) and without (Control) semen alterations. Genomic DNA was extracted from each collected sample, and a specific PCR was carried out to amplify the V4-V6 regions of the 16S rRNA. Sequence reactions were carried out on the MiSeq and analyzed by specific bioinformatic tools. We found a reduced richness and evenness in the Case versus the Control group. Moreover, specific genera, the Mannheimia, the Escherichia_Shigella, and the Varibaculum, were significantly increased in the Case compared to the Control group. Finally, we highlighted a correlation between the microbial profile and semen hyperviscosity. Even if further studies are required on larger groups of subjects to confirm these findings and explore mechanistic hypotheses, our results confirm the correlation between semen features and seminal microbiota. These data, in turn, may open the way to the possible use of semen microbiota as an attractive target for developing novel strategies for infertility management.}, } @article {pmid37372086, year = {2023}, author = {González-Reguero, D and Robas-Mora, M and Fernández-Pastrana, VM and Probanza-Lobo, A and Jiménez-Gómez, PA}, title = {Reduced Antibiotic Resistance in the Rhizosphere of Lupinus albus in Mercury-Contaminated Soil Mediated by the Addition of PGPB.}, journal = {Biology}, volume = {12}, number = {6}, pages = {}, pmid = {37372086}, issn = {2079-7737}, abstract = {The emergence of antibiotic resistance (AR) poses a threat to the "One Health" approach. Likewise, mercury (Hg) pollution is a serious environmental and public health problem. Its ability to biomagnify through trophic levels induces numerous pathologies in humans. As well, it is known that Hg-resistance genes and AR genes are co-selected. The use of plant-growth-promoting bacteria (PGPB) can improve plant adaptation, decontamination of toxic compounds and control of AR dispersal. The cenoantibiogram, a technique that allows estimating the minimum inhibitory concentration (MIC) of a microbial community, has been postulated as a tool to effectively evaluate the evolution of a soil. The present study uses the metagenomics of 16S rRNA gene amplicons to understand the distribution of the microbial soil community prior to bacterial inoculation, and the cenoantibiogram technique to evaluate the ability of four PGPB and their consortia to minimize antibiotic resistance in the rhizosphere of Lupinus albus var. Orden Dorado grown in Hg-contaminated soils. Results showed that the addition of A1 strain (Brevibacterium frigoritolerans) and its consortia with A2, B1 and B2 strains reduced the edaphic community´s MIC against cephalosporins, ertapenem and tigecycline. The metagenomic study revealed that the high MIC of non-inoculated soils could be explained by the bacteria which belong to the detected taxa,. showing a high prevalence of Proteobacteria, Cyanobacteria and Actinobacteria.}, } @article {pmid37371960, year = {2023}, author = {Duarte, S and Puchades, A and Jiménez-Hernández, N and Betoret, E and Gosalbes, MJ and Betoret, N}, title = {Almond (Prunus dulcis) Bagasse as a Source of Bioactive Compounds with Antioxidant Properties: An In Vitro Assessment.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {6}, pages = {}, pmid = {37371960}, issn = {2076-3921}, support = {PRTR-C17.I1-AGROALNEXT-2022/039//MCIN with funding from European Union Next Generation EUand by Generalitat Valenciana/ ; }, abstract = {The presence of components of nutritional interest makes fresh almond bagasse an interesting by-product for obtaining functional ingredients. Stabilization through a dehydration process is an interesting option for its integral use, ensuring its conservation and management. Subsequently, it can be turned into powder, facilitating its use as an ingredient. The aim of this paper was to determine the effects of hot air drying at 60 and 70 °C and lyophilization on the release of phenolic components and antiradical capacity in in vitro gastrointestinal digestion and colonic fermentation, as well as on growing microbiota composition by applying high throughput sequencing. The novelty of this study lies in this holistic approach; considering both technological and physiological aspects related to gastrointestinal digestion and colonic fermentation will provide the best conditions for functional foods. The results obtained showed that lyophilization provides a powder with a total phenol content and antiradical capacity higher than hot air drying. Furthermore, in dehydrated samples, both in vitro digestion and colonic fermentation revealed a phenol content and anti-radical capacity superior to those existing in undigested products. In addition, after colonic fermentation, beneficial bacteria species have been identified. Obtaining powders from almond bagasse is presented as an interesting opportunity for the valorization of this by-product.}, } @article {pmid37371491, year = {2023}, author = {Stupak, A and Kwaśniewski, W}, title = {Evaluating Current Molecular Techniques and Evidence in Assessing Microbiome in Placenta-Related Health and Disorders in Pregnancy.}, journal = {Biomolecules}, volume = {13}, number = {6}, pages = {}, pmid = {37371491}, issn = {2218-273X}, mesh = {Infant, Newborn ; Pregnancy ; Female ; Humans ; Placenta ; *Microbiota ; *Gastrointestinal Microbiome ; Pregnancy Trimester, First ; *Pre-Eclampsia ; }, abstract = {The microbiome is of great interest due to its potential influence on the occurrence and treatment of some human illnesses. It may be regarded as disruptions to the delicate equilibrium that humans ordinarily maintain with their microorganisms or the microbiota in their environment. The focus of this review is on the methodologies and current understanding of the functional microbiome in pregnancy outcomes. We present how novel techniques bring new insights to the contemporary field of maternal-fetal medicine with a critical analysis. The maternal microbiome in late pregnancy has been extensively studied, although data on maternal microbial changes during the first trimester are rare. Research has demonstrated that, in healthy pregnancies, the origin of the placental microbiota is oral (gut) rather than vaginal. Implantation, placental development, and maternal adaptation to pregnancy are complex processes in which fetal and maternal cells interact. Microbiome dysbiosis or microbial metabolites are rising as potential moderators of antenatal illnesses related to the placenta, such as fetal growth restriction, preeclampsia, and others, including gestational diabetes and preterm deliveries. However, because of the presence of antimicrobial components, it is likely that the bacteria identified in placental tissue are (fragments of) bacteria that have been destroyed by the placenta's immune cells. Using genomic techniques (metagenomics, metatranscriptomics, and metaproteomics), it may be possible to predict some properties of a microorganism's genome and the biochemical (epigenetic DNA modification) and physical components of the placenta as its environment. Despite the results described in this review, this subject needs further research on some major and crucial aspects. The phases of an in utero translocation of the maternal gut microbiota to the fetus should be explored. With a predictive knowledge of the impacts of the disturbance on microbial communities that influence human health and the environment, genomics may hold the answer to the development of novel therapies for the health of pregnant women.}, } @article {pmid37370879, year = {2023}, author = {Bozan, G and Pérez-Brocal, V and Aslan, K and Kiral, E and Sevketoglu, E and Uysal Yazici, M and Azapagasi, E and Kendirli, T and Emeksiz, S and Dursun, O and Yildizdas, D and Anil, AB and Akcay, N and Kihtir, HS and Havan, M and Ulgen Tekerek, N and Ekinci, F and Kilic, O and Moya, A and Dinleyici, EC}, title = {Analysis of Intestinal and Nasopharyngeal Microbiota of Children with Meningococcemia in Pediatric Intensive Care Unit: INMACS-PICU Study.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {13}, number = {12}, pages = {}, pmid = {37370879}, issn = {2075-4418}, support = {2018/11046//Eskisehir Osmangazi University Scientific Research Grant/ ; }, abstract = {Microbiota composition might play a role in the pathophysiology and course of sepsis, and understanding its dynamics is of clinical interest. Invasive meningococcal disease (IMD) is an important cause of community-acquired serious infection, and there is no information regarding microbiota composition in children with meningococcemia. In this study, we aimed to evaluate the intestinal and nasopharyngeal microbiota composition of children with IMD. Materials and Methods: In this prospective, multi-center study, 10 children with meningococcemia and 10 age-matched healthy controls were included. Nasopharyngeal and fecal samples were obtained at admission to the intensive care unit and on the tenth day of their hospital stay. The V3 and V4 regions of the 16S rRNA gene were amplified following the 16S Metagenomic Sequencing Library Preparation. Results: Regarding the alpha diversity on the day of admission and on the tenth day at the PICU, the Shannon index was significantly lower in the IMD group compared to the control group (p = 0.002 at admission and p = 0.001, on the tenth day of PICU). A statistical difference in the stool samples was found between the IMD group at Day 0 vs. the controls in the results of the Bray-Curtis and Jaccard analyses (p = 0.005 and p = 0.001, respectively). There were differences in the intestinal microbiota composition between the children with IMD at admission and Day 10 and the healthy controls. Regarding the nasopharyngeal microbiota analysis, in the children with IMD at admission, at the genus level, Neisseria was significantly more abundant compared to the healthy children (p < 0.001). In the children with IMD at Day 10, genera Moraxella and Neisseria were decreased compared to the healthy children. In the children with IMD on Day 0, for paired samples, Moraxella, Neisseria, and Haemophilus were significantly more abundant compared to the children with IMD at Day 10. In the children with IMD at Day 10, the Moraxella and Neisseria genera were decreased, and 20 different genera were more abundant compared to Day 0. Conclusions: We first found alterations in the intestinal and nasopharyngeal microbiota composition in the children with IMD. The infection itself or the other care interventions also caused changes to the microbiota composition during the follow-up period. Understanding the interaction of microbiota with pathogens, e.g., N. meningitidis, could give us the opportunity to understand the disease's dynamics.}, } @article {pmid37370232, year = {2023}, author = {Baden, T and Briseño, J and Coffing, G and Cohen-Bodénès, S and Courtney, A and Dickerson, D and Dölen, G and Fiorito, G and Gestal, C and Gustafson, T and Heath-Heckman, E and Hua, Q and Imperadore, P and Kimbara, R and Król, M and Lajbner, Z and Lichilín, N and Macchi, F and McCoy, MJ and Nishiguchi, MK and Nyholm, SV and Otjacques, E and Pérez-Ferrer, PA and Ponte, G and Pungor, JR and Rogers, TF and Rosenthal, JJC and Rouressol, L and Rubas, N and Sanchez, G and Santos, CP and Schultz, DT and Seuntjens, E and Songco-Casey, JO and Stewart, IE and Styfhals, R and Tuanapaya, S and Vijayan, N and Weissenbacher, A and Zifcakova, L and Schulz, G and Weertman, W and Simakov, O and Albertin, CB}, title = {Cephalopod-omics: Emerging Fields and Technologies in Cephalopod Biology.}, journal = {Integrative and comparative biology}, volume = {63}, number = {6}, pages = {1226-1239}, pmid = {37370232}, issn = {1557-7023}, support = {T32 GM007413/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Cephalopoda ; Genomics/methods ; Genome ; Gene Expression Profiling ; Brain ; }, abstract = {Few animal groups can claim the level of wonder that cephalopods instill in the minds of researchers and the general public. Much of cephalopod biology, however, remains unexplored: the largest invertebrate brain, difficult husbandry conditions, and complex (meta-)genomes, among many other things, have hindered progress in addressing key questions. However, recent technological advancements in sequencing, imaging, and genetic manipulation have opened new avenues for exploring the biology of these extraordinary animals. The cephalopod molecular biology community is thus experiencing a large influx of researchers, emerging from different fields, accelerating the pace of research in this clade. In the first post-pandemic event at the Cephalopod International Advisory Council (CIAC) conference in April 2022, over 40 participants from all over the world met and discussed key challenges and perspectives for current cephalopod molecular biology and evolution. Our particular focus was on the fields of comparative and regulatory genomics, gene manipulation, single-cell transcriptomics, metagenomics, and microbial interactions. This article is a result of this joint effort, summarizing the latest insights from these emerging fields, their bottlenecks, and potential solutions. The article highlights the interdisciplinary nature of the cephalopod-omics community and provides an emphasis on continuous consolidation of efforts and collaboration in this rapidly evolving field.}, } @article {pmid37370007, year = {2023}, author = {Rumore, J and Walker, M and Pagotto, F and Forbes, JD and Peterson, CL and Tyler, AD and Graham, M and Van Domselaar, G and Nadon, C and Reimer, A and Knox, N}, title = {Use of a taxon-specific reference database for accurate metagenomics-based pathogen detection of Listeria monocytogenes in turkey deli meat and spinach.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {361}, pmid = {37370007}, issn = {1471-2164}, mesh = {*Listeria monocytogenes/genetics ; Spinacia oleracea ; Food Microbiology ; Metagenomics ; Reproducibility of Results ; Meat ; }, abstract = {BACKGROUND: The reliability of culture-independent pathogen detection in foods using metagenomics is contingent on the quality and composition of the reference database. The inclusion of microbial sequences from a diverse representation of taxonomies in universal reference databases is recommended to maximize classification precision for pathogen detection. However, these sizable databases have high memory requirements that may be out of reach for some users. In this study, we aimed to assess the performance of a foodborne pathogen (FBP)-specific reference database (taxon-specific) relative to a universal reference database (taxon-agnostic). We tested our FBP-specific reference database's performance for detecting Listeria monocytogenes in two complex food matrices-ready-to-eat (RTE) turkey deli meat and prepackaged spinach-using three popular read-based DNA-to-DNA metagenomic classifiers: Centrifuge, Kraken 2 and KrakenUniq.

RESULTS: In silico host sequence removal led to substantially fewer false positive (FP) classifications and higher classification precision in RTE turkey deli meat datasets using the FBP-specific reference database. No considerable improvement in classification precision was observed following host filtering for prepackaged spinach datasets and was likely a consequence of a higher microbe-to-host sequence ratio. All datasets classified with Centrifuge using the FBP-specific reference database had the lowest classification precision compared to Kraken 2 or KrakenUniq. When a confidence-scoring threshold was applied, a nearly equivalent precision to the universal reference database was achieved for Kraken 2 and KrakenUniq. Recall was high for both reference databases across all datasets and classifiers. Substantially fewer computational resources were required for metagenomics-based detection of L. monocytogenes using the FBP-specific reference database, especially when combined with Kraken 2.

CONCLUSIONS: A universal (taxon-agnostic) reference database is not essential for accurate and reliable metagenomics-based pathogen detection of L. monocytogenes in complex food matrices. Equivalent classification performance can be achieved using a taxon-specific reference database when the appropriate quality control measures, classification software, and analysis parameters are applied. This approach is less computationally demanding and more attainable for the broader scientific and food safety communities.}, } @article {pmid37369825, year = {2023}, author = {Österdahl, MF and Whiston, R and Sudre, CH and Asnicar, F and Cheetham, NJ and Blanco Miguez, A and Bowyer, V and Antonelli, M and Snell, O and Dos Santos Canas, L and Hu, C and Wolf, J and Menni, C and Malim, M and Hart, D and Spector, T and Berry, S and Segata, N and Doores, K and Ourselin, S and Duncan, EL and Steves, CJ}, title = {Metabolomic and gut microbiome profiles across the spectrum of community-based COVID and non-COVID disease.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {10407}, pmid = {37369825}, issn = {2045-2322}, support = {MC_PC_20059/MRC_/Medical Research Council/United Kingdom ; 215010/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; /BHF_/British Heart Foundation/United Kingdom ; /DH_/Department of Health/United Kingdom ; MR/T005351/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 203148/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Humans ; *COVID-19 ; SARS-CoV-2 ; *Gastrointestinal Microbiome ; *Pneumonia ; Hospitalization ; }, abstract = {Whilst most individuals with SARS-CoV-2 infection have relatively mild disease, managed in the community, it was noted early in the pandemic that individuals with cardiovascular risk factors were more likely to experience severe acute disease, requiring hospitalisation. As the pandemic has progressed, increasing concern has also developed over long symptom duration in many individuals after SARS-CoV-2 infection, including among the majority who are managed acutely in the community. Risk factors for long symptom duration, including biological variables, are still poorly defined. Here, we examine post-illness metabolomic profiles, using nuclear magnetic resonance (Nightingale Health Oyj), and gut-microbiome profiles, using shotgun metagenomic sequencing (Illumina Inc), in 2561 community-dwelling participants with SARS-CoV-2. Illness duration ranged from asymptomatic (n = 307) to Post-COVID Syndrome (n = 180), and included participants with prolonged non-COVID-19 illnesses (n = 287). We also assess a pre-established metabolomic biomarker score, previously associated with hospitalisation for both acute pneumonia and severe acute COVID-19 illness, for its association with illness duration. We found an atherogenic-dyslipidaemic metabolic profile, including biomarkers such as fatty acids and cholesterol, was associated with longer duration of illness, both in individuals with and without SARS-CoV-2 infection. Greater values of a pre-existing metabolomic biomarker score also associated with longer duration of illness, regardless of SARS-CoV-2 infection. We found no association between illness duration and gut microbiome profiles in convalescence. This highlights the potential role of cardiometabolic dysfunction in relation to the experience of long duration symptoms after symptoms of acute infection, both COVID-19 as well as other illnesses.}, } @article {pmid37369703, year = {2023}, author = {Kneis, D and Lemay-St-Denis, C and Cellier-Goetghebeur, S and Elena, AX and Berendonk, TU and Pelletier, JN and Heß, S}, title = {Trimethoprim resistance in surface and wastewater is mediated by contrasting variants of the dfrB gene.}, journal = {The ISME journal}, volume = {17}, number = {9}, pages = {1455-1466}, pmid = {37369703}, issn = {1751-7370}, mesh = {*Trimethoprim Resistance/genetics ; *Wastewater ; Genes, Bacterial ; Trimethoprim/pharmacology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Trimethoprim (TMP) is a low-cost, widely prescribed antibiotic. Its effectiveness is increasingly challenged by the spread of genes coding for TMP-resistant dihydrofolate reductases: dfrA, and the lesser-known, evolutionarily unrelated dfrB. Despite recent reports of novel variants conferring high level TMP resistance (dfrB10 to dfrB21), the prevalence of dfrB is still unknown due to underreporting, heterogeneity of the analyzed genetic material in terms of isolation sources, and limited bioinformatic processing. In this study, we explored a coherent set of shotgun metagenomic sequences to quantitatively estimate the abundance of dfrB gene variants in aquatic environments. Specifically, we scanned sequences originating from influents and effluents of municipal sewage treatment plants as well as river-borne microbiomes. Our analyses reveal an increased prevalence of dfrB1, dfrB2, dfrB3, dfrB4, dfrB5, and dfrB7 in wastewater microbiomes as compared to freshwater. These gene variants were frequently found in genomic neighborship with other resistance genes, transposable elements, and integrons, indicating their mobility. By contrast, the relative abundances of the more recently discovered variants dfrB9, dfrB10, and dfrB13 were significantly higher in freshwater than in wastewater microbiomes. Moreover, their direct neighborship with other resistance genes or markers of mobile genetic elements was significantly less likely. Our findings suggest that natural freshwater communities form a major reservoir of the recently discovered dfrB gene variants. Their proliferation and mobilization in response to the exposure of freshwater communities to selective TMP concentrations may promote the prevalence of high-level TMP resistance and thus limit the future effectiveness of antimicrobial therapies.}, } @article {pmid37369325, year = {2023}, author = {Thorwall, S and Trivedi, V and Ottum, E and Wheeldon, I}, title = {Population genomics-guided engineering of phenazine biosynthesis in Pseudomonas chlororaphis.}, journal = {Metabolic engineering}, volume = {78}, number = {}, pages = {223-234}, doi = {10.1016/j.ymben.2023.06.008}, pmid = {37369325}, issn = {1096-7184}, mesh = {*Pseudomonas chlororaphis/genetics/metabolism ; Metagenomics ; Genome-Wide Association Study ; Pseudomonas/genetics/metabolism ; Phenazines/metabolism ; Bacterial Proteins/genetics/metabolism ; }, abstract = {The emergence of next-generation sequencing (NGS) technologies has made it possible to not only sequence entire genomes, but also identify metabolic engineering targets across the pangenome of a microbial population. This study leverages NGS data as well as existing molecular biology and bioinformatics tools to identify and validate genomic signatures for improving phenazine biosynthesis in Pseudomonas chlororaphis. We sequenced a diverse collection of 34 Pseudomonas isolates using short- and long-read sequencing techniques and assembled whole genomes using the NGS reads. In addition, we assayed three industrially relevant phenotypes (phenazine production, biofilm formation, and growth temperature) for these isolates in two different media conditions. We then provided the whole genomes and phenazine production data to a unitig-based microbial genome-wide association study (mGWAS) tool to identify novel genomic signatures responsible for phenazine production in P. chlororaphis. Post-processing of the mGWAS analysis results yielded 330 significant hits influencing the biosynthesis of one or more phenazine compounds. Based on a quantitative metric (called the phenotype score), we elucidated the most influential hits for phenazine production and experimentally validated them in vivo in the most optimal phenazine producing strain. Two genes significantly increased phenazine-1-carboxamide (PCN) production: a histidine transporter (ProY_1), and a putative carboxypeptidase (PS__04251). A putative MarR-family transcriptional regulator decreased PCN titer when overexpressed in a high PCN producing isolate. Overall, this work seeks to demonstrate the utility of a population genomics approach as an effective strategy in enabling the identification of targets for metabolic engineering of bioproduction hosts.}, } @article {pmid37369299, year = {2023}, author = {Yeruva, DK and S, VM}, title = {Electrogenic engineered flow through tri-phasic wetland system for azo dye treatment: Microbial dynamics and functional metagenomics.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {334}, number = {}, pages = {122107}, doi = {10.1016/j.envpol.2023.122107}, pmid = {37369299}, issn = {1873-6424}, mesh = {*Azo Compounds/metabolism ; Wetlands ; Metagenomics ; Wastewater ; *Environmental Pollutants ; }, abstract = {Electrogenic engineered flow through tri-phasic wetland (EEFW) system based on nature-based ecological principles was studied by integrating successive biological microenvironments. The potential mechanism of the plant root-based microbial community and its functional diversity with the influence of plant-microbe-electrode synergism towards dye degradation was evaluated. The EEFW system was operated at three varied dye loads of 10, 25 and 50 mg L[-1], where the results from the cumulative outlets revealed a maximum dye removal efficiency of 96%, 96.5% and 93%, respectively. Microbial community analysis depicted synergistic dependence on the plant-microbe-electrode interactions, influencing their functional diversity and metabolism towards detoxification of pollutants. The core microbial taxa enriched against the microenvironment variation were mostly associated with carbon and dye removal viz., Desulfomonile tiedjei and Rhodopseudomonas palustris in Tank 1 and Chloroflexi bacterium and Steroidobacter denitrificans in Tank 2. The degradation of polycyclic aromatic hydrocarbons, chloroalkane/chloroalkene, nitrotoluene, bisphenol, caprolactam and 1,1,1-trichloro-2,2-bis(4-chlorophenyl) ethane (DDT) were observed to be predominant in Tank 1. EEFW system could be one of the option for utilizing nature-based processes for the treatment of wastewater by self-induced bioelectrogenesis to augment process efficiency.}, } @article {pmid37369278, year = {2023}, author = {Hazime, H and Ducasa, GM and Santander, AM and Brito, N and González, EE and Ban, Y and Kaunitz, J and Akiba, Y and Fernández, I and Burgueño, JF and Abreu, MT}, title = {Intestinal Epithelial Inactivity of Dual Oxidase 2 Results in Microbiome-Mediated Metabolic Syndrome.}, journal = {Cellular and molecular gastroenterology and hepatology}, volume = {16}, number = {4}, pages = {557-572}, pmid = {37369278}, issn = {2352-345X}, mesh = {Animals ; Female ; Male ; Mice ; Anti-Bacterial Agents ; Dual Oxidases ; *Gastrointestinal Microbiome ; *Glucose Intolerance ; Hydrogen Peroxide ; Lipopolysaccharides ; *Metabolic Syndrome ; Obesity/metabolism ; }, abstract = {BACKGROUND & AIMS: Metabolic syndrome (MetS) is characterized by obesity, glucose intolerance, and hepatic steatosis. Alterations in the gut microbiome play important roles in the development of MetS. However, the mechanisms by which this occurs are poorly understood. Dual oxidase 2 (DUOX2) is an antimicrobial reduced nicotinamide adenine dinucleotide phosphate oxidase expressed in the gut epithelium. Here, we posit that epithelial DUOX2 activity provides a mechanistic link between the gut microbiome and the development of MetS.

METHODS: Mice carrying an intestinal epithelial-specific deletion of dual oxidase maturation factor 1/2 (DA IEC-KO), and wild-type littermates were fed a standard diet and killed at 24 weeks. Metabolic alterations were determined by glucose tolerance, lipid tests, and body and organ weight measurements. DUOX2 activity was determined by Amplex Red. Intestinal permeability was determined by fluorescein isothiocyanate-dextran, microbial translocation assessments, and portal vein lipopolysaccharide measurements. Metagenomic analysis of the stool microbiome was performed. The role of the microbiome was assessed in antibiotic-treated mice.

RESULTS: DA IEC-KO males showed increased body and organ weights accompanied by glucose intolerance and increased plasma lipid and liver enzyme levels, and increased adiposity in the liver and adipose tissue. Expression of F4/80, CD68, uncoupling protein 1, carbohydrate response element binding protein, leptin, and adiponectin was altered in the liver and adipose tissue of DA IEC-KO males. DA IEC-KO males produced less epithelial H2O2, had altered relative abundance of Akkermansiaceae and Lachnospiraceae in stool, and showed increased portal vein lipopolysaccharides and intestinal permeability. Females were protected from barrier defects and MetS, despite producing less H2O2. Antibiotic depletion abrogated all MetS phenotypes observed.

CONCLUSIONS: Intestinal epithelial inactivity of DUOX2 promotes MetS in a microbiome-dependent manner.}, } @article {pmid37369253, year = {2023}, author = {Rajasekaran, S and Vasudevan, G and Easwaran, M and Devi Ps, N and Anand K S, SV and Muthurajan, R and Tangavel, C and Murugan, C and B T, P and Shetty, AP and Kanna, RM}, title = {"Are we barking up the wrong tree? Too much emphasis on Cutibacterium acnes and ignoring other pathogens"- a study based on next-generation sequencing of normal and diseased discs.}, journal = {The spine journal : official journal of the North American Spine Society}, volume = {23}, number = {10}, pages = {1414-1426}, doi = {10.1016/j.spinee.2023.06.396}, pmid = {37369253}, issn = {1878-1632}, mesh = {Humans ; Case-Control Studies ; *Gram-Positive Bacterial Infections/epidemiology/microbiology/pathology ; *Intervertebral Disc Degeneration/surgery ; Propionibacterium acnes ; High-Throughput Nucleotide Sequencing ; *Intervertebral Disc/pathology ; }, abstract = {BACKGROUND: The majority of literature on bacterial flora in the disc stands disadvantaged in utilizing traditional culture methods and targeting a single bacterium, Cutibacterium acnes.

PURPOSE: Our objective was to document the diversity in the bacterial flora between normal and degenerated discs for shortlisting potential pathogens using next-generation genomic tools.

STUDY DESIGN: Experimental case-control study.

METHODS: Researchers employed 16S metagenome sequencing to profile bacterial diversity in magnetic resonance imaging normal healthy discs from brain-dead organ voluntary donors (n=20) and 40 degenerated disc samples harvested during surgery (Modic [MC]=20 and non-Modic [NMC]=20). The V3-V4 region was amplified using universal bacterial primers 341F and 806R, and the libraries were sequenced using Illumina NovoSeq 6000 platform. Statistical significance was set at bacteria with a minimum of 100 operational taxonomic unit (OTU) and present in at least 70% of the samples. The quality check-filtered reads were processed using the QIIME-2 pipeline. The OTU clustering and taxonomic classification were carried out for the merged reads using the Greengenes/SILVA reference database. Validation was done by identification of bacterial metabolites in samples using the liquid chromatography-mass spectrometry approach.

RESULTS: Abundant bacteria differing widely in diversity, as evidenced by Alfa and Beta diversity analysis, were present in all control and degenerative samples. The number of bacterial genera was 27 (14-gram-positive: 13-gram-negative) in the control group, 23 (10-gram-positive: 11-gram-negative) in the Modic group, and 16 (11-gram-positive: 5-gram-negative) in the non-Modic group. In the Modic group, gram-negative bacteria OTUs were found to be predominant (more than 50% of the total bacteria identified), whereas in control and non-Modic groups the OTUs of gram-positive bacteria were predominant. Species-level analysis revealed an abundance of opportunistic gram-negative pathogens like Pseudomonas aeruginosa, Sphingomonos paucibacillus, and Ochrobactrum quorumnocens in the discs with Modic changes, more than in non-Modic discs. The presence of bacterial metabolites and quorum-sensing molecules like N-decanoyl-L-homoserine lactone, 6-hydroxynicotinic acid, 2-aminoacetophenone, 4-hydroxy-3-polyprenylbenzoate, PE (16:1(9Z)/18:0) and phthalic acid validated the colonization and cell-cell communication of bacteria in disc ruling out contamination theory. Cutibacterium acnes was not the predominant bacteria in any of the three groups of discs and in fact was in the 16th position in the order of abundance in the control discs (0.72%), seventh position in the Modic discs (1.41%), and 12th position (0.53%) in the non-Modic discs.

CONCLUSION: This study identified a predominance of gram-negative bacteria in degenerated discs and highlights that Cutibacterium acnes may not be the only degeneration-causing bacteria. This may be attributed to the environment, diet, and lifestyle habits of the sample population. Though the study does not reveal the exact pathogen, it may pave the way for future studies on the subject.

CLINICAL SIGNIFICANCE: These findings invite further investigation into causal relationships of bacterial profile with disc degeneration phenotypes as well as phenotype-driven clinical treatment protocols.}, } @article {pmid37367861, year = {2023}, author = {Plaza-Diaz, J and Álvarez-Mercado, AI}, title = {The Interplay between Microbiota and Chemotherapy-Derived Metabolites in Breast Cancer.}, journal = {Metabolites}, volume = {13}, number = {6}, pages = {}, pmid = {37367861}, issn = {2218-1989}, abstract = {The most common cancer in women is breast cancer, which is also the second leading cause of death in this group. It is, however, important to note that some women will develop or will not develop breast cancer regardless of whether certain known risk factors are present. On the other hand, certain compounds are produced by bacteria in the gut, such as short-chain fatty acids, secondary bile acids, and other metabolites that may be linked to breast cancer development and mediate the chemotherapy response. Modeling the microbiota through dietary intervention and identifying metabolites directly associated with breast cancer and its complications may be useful to identify actionable targets and improve the effect of antiangiogenic therapies. Metabolomics is therefore a complementary approach to metagenomics for this purpose. As a result of the combination of both techniques, a better understanding of molecular biology and oncogenesis can be obtained. This article reviews recent literature about the influence of bacterial metabolites and chemotherapy metabolites in breast cancer patients, as well as the influence of diet.}, } @article {pmid37367624, year = {2023}, author = {Wijayawardene, NN and Boonyuen, N and Ranaweera, CB and de Zoysa, HKS and Padmathilake, RE and Nifla, F and Dai, DQ and Liu, Y and Suwannarach, N and Kumla, J and Bamunuarachchige, TC and Chen, HH}, title = {OMICS and Other Advanced Technologies in Mycological Applications.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {6}, pages = {}, pmid = {37367624}, issn = {2309-608X}, support = {Young Talents" Program and "High-End Foreign Experts" Program//Yunnan Revitalization Talents Support Plan/ ; CAAS-ASTIP-2015-IAR//Agricultural Science and Technology Innovation Program/ ; }, abstract = {Fungi play many roles in different ecosystems. The precise identification of fungi is important in different aspects. Historically, they were identified based on morphological characteristics, but technological advancements such as polymerase chain reaction (PCR) and DNA sequencing now enable more accurate identification and taxonomy, and higher-level classifications. However, some species, referred to as "dark taxa", lack distinct physical features that makes their identification challenging. High-throughput sequencing and metagenomics of environmental samples provide a solution to identifying new lineages of fungi. This paper discusses different approaches to taxonomy, including PCR amplification and sequencing of rDNA, multi-loci phylogenetic analyses, and the importance of various omics (large-scale molecular) techniques for understanding fungal applications. The use of proteomics, transcriptomics, metatranscriptomics, metabolomics, and interactomics provides a comprehensive understanding of fungi. These advanced technologies are critical for expanding the knowledge of the Kingdom of Fungi, including its impact on food safety and security, edible mushrooms foodomics, fungal secondary metabolites, mycotoxin-producing fungi, and biomedical and therapeutic applications, including antifungal drugs and drug resistance, and fungal omics data for novel drug development. The paper also highlights the importance of exploring fungi from extreme environments and understudied areas to identify novel lineages in the fungal dark taxa.}, } @article {pmid37367195, year = {2023}, author = {Sharma, S and Pannu, J and Chorlton, S and Swett, JL and Ecker, DJ}, title = {Threat Net: A Metagenomic Surveillance Network for Biothreat Detection and Early Warning.}, journal = {Health security}, volume = {21}, number = {5}, pages = {347-357}, doi = {10.1089/hs.2022.0160}, pmid = {37367195}, issn = {2326-5108}, mesh = {Humans ; *Biohazard Release ; Computer Simulation ; *Disease Outbreaks/prevention & control ; Emergency Service, Hospital ; Hospitals ; High-Throughput Nucleotide Sequencing ; Sensitivity and Specificity ; }, abstract = {Early detection of novel pathogens can prevent or substantially mitigate biological incidents, including pandemics. Metagenomic next-generation sequencing (mNGS) of symptomatic clinical samples may enable detection early enough to contain outbreaks, limit international spread, and expedite countermeasure development. In this article, we propose a clinical mNGS architecture we call "Threat Net," which focuses on the hospital emergency department as a high-yield surveillance location. We develop a susceptible-exposed-infected-removed (SEIR) simulation model to estimate the effectiveness of Threat Net in detecting novel respiratory pathogen outbreaks. Our analysis serves to quantify the value of routine clinical mNGS for respiratory pandemic detection by estimating the cost and epidemiological effectiveness at differing degrees of hospital coverage across the United States. We estimate that a biological threat detection network such as Threat Net could be deployed across hospitals covering 30% of the population in the United States. Threat Net would cost between $400 million and $800 million annually and have a 95% chance of detecting a novel respiratory pathogen with traits of SARS-CoV-2 after 10 emergency department presentations and 79 infections across the United States. Our analyses suggest that implementing Threat Net could help prevent or substantially mitigate the spread of a respiratory pandemic pathogen in the United States.}, } @article {pmid37366621, year = {2023}, author = {Ene, A and Banerjee, S and Wolfe, AJ and Putonti, C}, title = {Exploring the genotypic and phenotypic differences distinguishing Lactobacillus jensenii and Lactobacillus mulieris.}, journal = {mSphere}, volume = {8}, number = {4}, pages = {e0056222}, pmid = {37366621}, issn = {2379-5042}, mesh = {Female ; Humans ; *Vagina ; RNA, Ribosomal, 16S/genetics ; *Maltose ; Lactobacillus/genetics ; Genotype ; }, abstract = {Lactobacillus crispatus, Lactobacillus gasseri, Lactobacillus iners, and Lactobacillus jensenii are dominant species of the urogenital microbiota. Prior studies suggest that these Lactobacillus species play a significant role in the urobiome of healthy females. In our prior genomic analysis of all publicly available L. jensenii and Lactobacillus mulieris genomes at the time (n = 43), we identified genes unique to these two closely related species. This motivated our further exploration here into their genotypic differences as well as into their phenotypic differences. First, we expanded genome sequence representatives of both species to 61 strains, including publicly available strains and nine new strains sequenced here. Genomic analyses conducted include phylogenetics of the core genome as well as biosynthetic gene cluster analysis and metabolic pathway analyses. Urinary strains of both species were assayed for their ability to utilize four simple carbohydrates. We found that L. jensenii strains can efficiently catabolize maltose, trehalose, and glucose, but not ribose, and L. mulieris strains can utilize maltose and glucose, but not trehalose and ribose. Metabolic pathway analysis clearly shows the lack of treB within L. mulieris strains, indicative of its inability to catabolize external sources of trehalose. While genotypic and phenotypic observations provide insight into the differences between these two species, we did not find any association with urinary symptom status. Through this genomic and phenotypic investigation, we identify markers that can be leveraged to clearly distinguish these two species in investigations of the female urogenital microbiota. IMPORTANCE We have expanded upon our prior genomic analysis of L. jensenii and L. mulieris strains, including nine new genome sequences. Our bioinformatic analysis finds that L. jensenii and L. mulieris cannot be distinguished by short-read 16S rRNA gene sequencing alone. Thus, to discriminate between these two species, future studies of the female urogenital microbiome should employ metagenomic sequencing and/or sequence species-specific genes, such as those identified here. Our bioinformatic examination also confirmed our prior observations of differences between the two species related to genes associated with carbohydrate utilization, which we tested here. We found that the transport and utilization of trehalose are key distinguishing traits of L. jensenii, which is further supported by our metabolic pathway analysis. In contrast with other urinary Lactobacillus species, we did not find strong evidence for either species, nor particular genotypes, to be associated with lower urinary tract symptoms (or the lack thereof).}, } @article {pmid37365713, year = {2023}, author = {Zhu, J and Liu, S and Zhang, H and Zhao, W and Ding, J and Dai, R and Xu, K and He, C and Liu, J and Yang, L and Meng, H}, title = {Dynamic distribution of gut microbiota during Alzheimer's disease progression in a mice model.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {131}, number = {9}, pages = {480-490}, doi = {10.1111/apm.13339}, pmid = {37365713}, issn = {1600-0463}, mesh = {Humans ; Mice ; Animals ; *Alzheimer Disease/pathology ; *Gastrointestinal Microbiome ; *Neurodegenerative Diseases ; Mice, Transgenic ; *Microbiota ; Disease Models, Animal ; }, abstract = {Alzheimer's disease (AD) is an irreversible neurodegenerative disease that affects more than 44 million people worldwide. The pathogenic mechanisms of AD still remain unclear. Currently, there are numerous studies investigating the microbiota-gut-brain axis in humans and rodents indicated that gut microbiota played a role in neurodegenerative diseases, including AD. However, the underlying relationship between the progress of AD disease and the dynamic distribution of gut microbiota is not well understood. In the present study, APP[swe] /PS1[ΔE9] transgenic mice of different ages and sex were employed. After the evaluation of the AD mice model, gut metagenomic sequencing was conducted to reveal gut microbiota, moreover, probiotics intervention was treated in the AD mice. The results showed that (1) AD mice had reduced microbiota richness and a changed gut microbiota composition, and AD mice gut microbiota richness was correlated with cognitive performance. We have also found some potential AD-related microbes, for example, in AD-prone mice, the genus Mucispirillum was strongly associated with immune inflammation. (2) Probiotics intervention improved cognitive performance and changed gut microbiota richness and composition of AD mice. We revealed the dynamics distribution of gut microbiota and the effect of probiotics on AD in a mice model, which provides an important reference for the pathogenesis of AD, intestinal microbial markers associated with AD, and AD probiotic intervention.}, } @article {pmid37365664, year = {2023}, author = {Zhao, L and Lin, LZ and Zeng, Y and Teng, WK and Chen, MY and Brand, JJ and Zheng, LL and Gan, NQ and Gong, YH and Li, XY and Lv, J and Chen, T and Han, BP and Song, LR and Shu, WS}, title = {The facilitating role of phycospheric heterotrophic bacteria in cyanobacterial phosphonate availability and Microcystis bloom maintenance.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {142}, pmid = {37365664}, issn = {2049-2618}, mesh = {*Microcystis/genetics/metabolism ; Ecosystem ; *Organophosphonates/metabolism ; *Cyanobacteria/genetics ; Phytoplankton ; Lakes/microbiology ; Phosphorus/metabolism ; }, abstract = {BACKGROUND: Phosphonates are the main components in the global phosphorus redox cycle. Little is known about phosphonate metabolism in freshwater ecosystems, although rapid consumption of phosphonates has been observed frequently. Cyanobacteria are often the dominant primary producers in freshwaters; yet, only a few strains of cyanobacteria encode phosphonate-degrading (C-P lyase) gene clusters. The phycosphere is defined as the microenvironment in which extensive phytoplankton and heterotrophic bacteria interactions occur. It has been demonstrated that phytoplankton may recruit phycospheric bacteria based on their own needs. Therefore, the establishment of a phycospheric community rich in phosphonate-degrading-bacteria likely facilitates cyanobacterial proliferation, especially in waters with scarce phosphorus. We characterized the distribution of heterotrophic phosphonate-degrading bacteria in field Microcystis bloom samples and in laboratory cyanobacteria "phycospheres" by qPCR and metagenomic analyses. The role of phosphonate-degrading phycospheric bacteria in cyanobacterial proliferation was determined through coculturing of heterotrophic bacteria with an axenic Microcystis aeruginosa strain and by metatranscriptomic analysis using field Microcystis aggregate samples.

RESULTS: Abundant bacteria that carry C-P lyase clusters were identified in plankton samples from freshwater Lakes Dianchi and Taihu during Microcystis bloom periods. Metagenomic analysis of 162 non-axenic laboratory strains of cyanobacteria (consortia cultures containing heterotrophic bacteria) showed that 20% (128/647) of high-quality bins from eighty of these consortia encode intact C-P lyase clusters, with an abundance ranging up to nearly 13%. Phycospheric bacterial phosphonate catabolism genes were expressed continually across bloom seasons, as demonstrated through metatranscriptomic analysis using sixteen field Microcystis aggregate samples. Coculturing experiments revealed that although Microcystis cultures did not catabolize methylphosphonate when axenic, they demonstrated sustained growth when cocultured with phosphonate-utilizing phycospheric bacteria in medium containing methylphosphonate as the sole source of phosphorus.

CONCLUSIONS: The recruitment of heterotrophic phosphonate-degrading phycospheric bacteria by cyanobacteria is a hedge against phosphorus scarcity by facilitating phosphonate availability. Cyanobacterial consortia are likely primary contributors to aquatic phosphonate mineralization, thereby facilitating sustained cyanobacterial growth, and even bloom maintenance, in phosphate-deficient waters. Video Abstract.}, } @article {pmid37365493, year = {2023}, author = {Huang, Q and Hong, Z and Hong, Q}, title = {Cryptococcal meningoencephalitis with Actinomyces odontolyticus sepsis: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {434}, pmid = {37365493}, issn = {1471-2334}, mesh = {Humans ; Fluconazole/therapeutic use ; Amphotericin B/therapeutic use ; *Cryptococcus neoformans ; *Actinomycosis/diagnosis/drug therapy/microbiology ; Penicillins/therapeutic use ; *Sepsis/diagnosis/drug therapy ; *Meningoencephalitis/diagnosis/drug therapy ; Actinomyces ; *Intracranial Hypertension/drug therapy ; Antifungal Agents/therapeutic use/pharmacology ; *Meningitis, Cryptococcal/diagnosis ; }, abstract = {BACKGROUND: The combined infection of actinomyces odontolyticus sepsis and cryptococcal encephalitis is rare in routine clinical practice. Thus, we presented this case report and literature review to provide clues to improve such patients' diagnoses and treatment processes.

CASE PRESENTATION: The main clinical manifestations of the patient were high fever and intracranial hypertension. Then, we completed the routine cerebrospinal fluid examination, biochemical detection, cytological examination, bacterial culture, and India ink staining. Firstly, the blood culture suggested actinomyces odontolyticus infection, considering the possibility of actinomyces odontolyticus sepsis and intracranial actinomyces odontolyticus infection. Accordingly, the patient was administered penicillin for treatment. Although the fever was slightly relieved, the symptoms of intracranial hypertension did not relieve. After 7 days, the characteristics of brain magnetic resonance imaging and the results of pathogenic metagenomics sequencing and cryptococcal capsular polysaccharide antigen suggested that cryptococcal infection. Based on the above results, the patient was diagnosed with a combined infection of cryptococcal meningoencephalitis and actinomyces odontolyticus sepsis. Anti-infection therapy with 'penicillin, amphotericin, and fluconazole' was provided, improving the clinical manifestations and objective indexes.

CONCLUSION: The combined infection of Actinomyces odontolyticus sepsis and cryptococcal encephalitis is first reported in this case report, and combined antibiotics with 'penicillin, amphotericin, and fluconazole' are effective.}, } @article {pmid37365438, year = {2023}, author = {Thomas, AM and Fidelle, M and Routy, B and Kroemer, G and Wargo, JA and Segata, N and Zitvogel, L}, title = {Gut OncoMicrobiome Signatures (GOMS) as next-generation biomarkers for cancer immunotherapy.}, journal = {Nature reviews. Clinical oncology}, volume = {20}, number = {9}, pages = {583-603}, pmid = {37365438}, issn = {1759-4782}, support = {U01 CA230551/CA/NCI NIH HHS/United States ; R01 CA219896/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Dysbiosis ; Prospective Studies ; *Neoplasms/drug therapy/genetics ; Biomarkers ; Immunotherapy ; }, abstract = {Oncogenesis is associated with intestinal dysbiosis, and stool shotgun metagenomic sequencing in individuals with this condition might constitute a non-invasive approach for the early diagnosis of several cancer types. The prognostic relevance of antibiotic intake and gut microbiota composition urged investigators to develop tools for the detection of intestinal dysbiosis to enable patient stratification and microbiota-centred clinical interventions. Moreover, since the advent of immune-checkpoint inhibitors (ICIs) in oncology, the identification of biomarkers for predicting their efficacy before starting treatment has been an unmet medical need. Many previous studies addressing this question, including a meta-analysis described herein, have led to the description of Gut OncoMicrobiome Signatures (GOMS). In this Review, we discuss how patients with cancer across various subtypes share several GOMS with individuals with seemingly unrelated chronic inflammatory disorders who, in turn, tend to have GOMS different from those of healthy individuals. We discuss findings from the aforementioned meta-analysis of GOMS patterns associated with clinical benefit from or resistance to ICIs across different cancer types (in 808 patients), with a focus on metabolic and immunological surrogate markers of intestinal dysbiosis, and propose practical guidelines to incorporate GOMS in decision-making for prospective clinical trials in immuno-oncology.}, } @article {pmid37365419, year = {2023}, author = {Gryaznova, M and Smirnova, Y and Burakova, I and Syromyatnikov, M and Chizhkov, P and Popov, E and Popov, V}, title = {Changes in the Human Gut Microbiome Caused by the Short-Term Impact of Lactic Acid Bacteria Consumption in Healthy People.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {37365419}, issn = {1867-1314}, support = {FZGW-2020-0001//Ministry of Science and Higher Education of the Russian Federation/ ; FZGW-2020-0001//Ministry of Science and Higher Education of the Russian Federation/ ; FZGW-2020-0001//Ministry of Science and Higher Education of the Russian Federation/ ; FZGW-2020-0001//Ministry of Science and Higher Education of the Russian Federation/ ; FZGW-2020-0001//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {The gut microbiome is one of the main factors affecting human health. It has been proven that probiotics can regulate the metabolism in the host body. A large number of people use probiotics not as medicines, but as a prophylactic supplement. The aim of our study was to evaluate the effect of lactic acid bacteria on the gut microbiome of healthy people using the V3 region of the 16S rRNA gene. Our study showed changes in the generic composition in the gut of healthy people when taking the supplement. There was an increase in the members responsible for the production of short-chain fatty acids in the gut of the host (Blautia, Fusicatenibacter, Eubacterium hallii group, Ruminococcus), as well as bacteria that improve intestinal homeostasis (Dorea and Barnesiella). There was also a decrease in the abundance of bacteria in the genera Catenibacterium, Hungatella, Escherichia-Shigella, and Pseudomonas, associated with an unhealthy profile of the human gut microbiome. An increase in members of the phylum Actinobacteriota was also observed, which has a positive effect on the host organism. Our results indicate that short-term prophylactic use of lactic acid bacteria-based supplements can be effective, as it contributes to a beneficial effect on the gut microbiome of healthy people.}, } @article {pmid37365103, year = {2023}, author = {Ojala, T and Häkkinen, AE and Kankuri, E and Kankainen, M}, title = {Current concepts, advances, and challenges in deciphering the human microbiota with metatranscriptomics.}, journal = {Trends in genetics : TIG}, volume = {39}, number = {9}, pages = {686-702}, doi = {10.1016/j.tig.2023.05.004}, pmid = {37365103}, issn = {0168-9525}, mesh = {Humans ; *Metagenomics ; *Microbiota/genetics ; Transcriptome/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {Metatranscriptomics refers to the analysis of the collective microbial transcriptome of a sample. Its increased utilization for the characterization of human-associated microbial communities has enabled the discovery of many disease-state related microbial activities. Here, we review the principles of metatranscriptomics-based analysis of human-associated microbial samples. We describe strengths and weaknesses of popular sample preparation, sequencing, and bioinformatics approaches and summarize strategies for their use. We then discuss how human-associated microbial communities have recently been examined and how their characterization may change. We conclude that metatranscriptomics insights into human microbiotas under health and disease have not only expanded our knowledge on human health, but also opened avenues for rational antimicrobial drug use and disease management.}, } @article {pmid37364321, year = {2023}, author = {Shangpliang, HNJ and Tamang, JP}, title = {Metagenome-assembled genomes for biomarkers of bio-functionalities in Laal dahi, an Indian ethnic fermented milk product.}, journal = {International journal of food microbiology}, volume = {402}, number = {}, pages = {110300}, doi = {10.1016/j.ijfoodmicro.2023.110300}, pmid = {37364321}, issn = {1879-3460}, mesh = {Animals ; Metagenome ; *Cultured Milk Products/microbiology ; Bacteria ; *Lactococcus lactis ; *Lactobacillus delbrueckii ; Biomarkers ; Milk/microbiology ; Fermentation ; }, abstract = {Laal dahi is a sweetened and soft pudding-like fermented milk product of the Eastern regions of India, which has not been studied for its microbial community structures and health promoting functionality in terms of 'omics' approaches. We applied metagenomic and metagenomes-assembled genomes (MAGs) tools to decipher the biomarkers for genes encoding for different health promoting functionalities in laal dahi. Abundance of bacterial domains was observed with negligible presence of eukaryotes and viruses. Bacillota was the most abundant phylum with different bacterial species viz., Enterococcus italicus, Lactococcus raffinolactis, Lactobacillus helveticus, Bifidobacterium mongoliense, Hafnia alvei, Lactococcus lactis, Acetobacter okinawensis, Streptococcus thermophilus, Thermus thermophilus, Leuconostoc citreum, Leuconostoc pseudomesenteroides, Acetobacter orientalis, Lactobacillus gallinarum, Lactococcus chungangensis and Lactobacillus delbrueckii. Comparison of laal dahi microbiome with that of similar fermented milk products was also carried out after retrieving the metagenomic datasets from public databases. Significant abundance of Lb. helveticus, E. italicus, Lc. raffinolactis and Lc. lactis in laal dahi. Interestingly, Bifidobacterium mongoliense, Lb. gallinarum, Lc. chungangensis and Acetobacter okinawensis were only detected in laal dahi but Streptococcus infantarius, Lacticaseibacillus rhamnosus and Lb. johnsonii were absent. Reconstruction of putative single environment-specific genomes from metagenomes in addition to subsampling of the abundant species resulted in five high-quality MAGs identified as Lactobacillus delbrueckii, Lactobacillus helveticus, Lactococcus chungangensis, Lactococcus lactis and Streptococcus thermophilus. All MAGs showed the presence of various genes with several putative functions corresponding to different probiotic and prebiotic functions, short-chain fatty acids production, immunomodulation, antitumor genes, essential amino acid and vitamin biosynthesis. Genes for γ-Aminobutyric acid (GABA) production were only detected in MAG of Lactococcus lactis. Gene clusters for secondary metabolites (antimicrobial peptides) were detected in all MAGs except Lc. chungangensis. Additionally, detection of clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) elements was observed only in Lactobacillus delbrueckii and Streptococcus thermophilus. Annotation of several genes with potential health beneficial properties in all five MAGs may support the need to explore the culturability of these MAGs for future use in controlled fermentation of functional dairy products.}, } @article {pmid37364294, year = {2023}, author = {Sipriyadi, S and Khairina, Y and Masrukhin, M and Yulandi, A and Wibowo, R and Nisa, D}, title = {Bacterial community structure in the rhizosphere of fungi-infected Amorphophallus titanum.}, journal = {Canadian journal of microbiology}, volume = {69}, number = {11}, pages = {439-448}, doi = {10.1139/cjm-2022-0256}, pmid = {37364294}, issn = {1480-3275}, mesh = {Fungi ; *Microbiota ; *Amorphophallus ; Rhizosphere ; Plant Roots/microbiology ; Soil Microbiology ; Bacteria ; Soil/chemistry ; *Trichoderma ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The rhizosphere is a narrow soil area directly affected by plant root exudates. Microbes inhabiting the rhizosphere have been widely studied for their beneficial effects on plant nutrition, growth, and disease prevention. Many factors affect the rhizosphere microbial composition, including plant pathogen infection. Here, we analyzed the bacterial community structure in the rhizosphere of fungi-infected Amorphophallus titanum. Soil samples were collected from rhizosphere and non-rhizosphere areas of fungi-infected A. titanum. The 16S metagenomic analysis was conducted to investigate the bacterial community of the samples by amplifying the V3-V4 region. The results showed that the phylum Firmicutes was prevalent in the rhizosphere, whereas the phyla Proteobacteria, Acidobacteria, and Actinobacteria were limited. Some major fungal genera were isolated from infected tubers and rhizosphere soil of A. titanum, including Trichoderma sp., Aspergillus sp., Perenniporia sp., and Cerrena sp. The fungal-isolate Aspergillus spp. is a well-known agricultural pest in several reports. While Cerrena sp. was reported to be pathogenic in plants, including the family of Arecaceae. Overall, the data revealed a potential relationship between fungal infections and the dominant bacterial community in the rhizosphere of A. titanum. Additionally, this research may contribute to the development of microbe-based technology to mitigate diseases in A. titanum.}, } @article {pmid37363265, year = {2023}, author = {Low, DHW and Ch'ng, L and Su, YCF and Linster, M and Zhang, R and Zhuang, Y and Kwak, ML and Borthwick, SA and Hitch, AT and Smith, GJD and Mendenhall, IH}, title = {Cencurut virus: A novel Orthonairovirus from Asian house shrews (Suncus murinus) in Singapore.}, journal = {One health (Amsterdam, Netherlands)}, volume = {16}, number = {}, pages = {100529}, pmid = {37363265}, issn = {2352-7714}, abstract = {Orthonairovirus is a genus of viruses in the family Nairoviridae, order Bunyavirales, with a segmented circular RNA genome. They typically infect birds and mammals and are primarily transmitted by ectoparasites such as ticks. Four of nine Orthonairovirus genogroups can infect humans, with Crimean-Congo hemorrhagic fever virus infections displaying case fatality rates up to 40%. Here, we discover and describe a novel Orthonairovirus as Cencurut virus (CENV). CENV was detected in 34 of 37 Asian house shrews (Suncus murinus) sampled in Singapore and in a nymphal Amblyomma helvolum tick collected from an infected shrew. Pairwise comparison of CENV S, M, and L segments had 95.0 to 100% nucleotide and 97.5 to 100% amino acid homology within CENV genomes, suggesting a diverse viral population. Phylogenetic analysis of the individual gene segments showed that CENV is related to Erve, Lamgora, Lamusara, and Thiafora viruses, with only 49.0 to 58.2% nucleotide and 41.7 to 61.1% amino acid homology, which has previously been detected in other shrew species from France, Gabon, and Senegal respectively. The high detection frequency suggests that CENV is endemic among S. murinus populations in Singapore. The discovery of CENV, from a virus family with known zoonotic potential, underlines the importance of surveillance of synanthropic small mammals that are widely distributed across Southeast Asia.}, } @article {pmid37362931, year = {2023}, author = {Huang, Y and Jiao, J and Yao, D and Guo, F and Li, Y}, title = {Altered fecal microbiome and metabolome profiles in rat models of short bowel syndrome.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1185463}, pmid = {37362931}, issn = {1664-302X}, abstract = {INTRODUCTION: Short bowel syndrome (SBS) is featured by impaired nutrients and fluids absorption due to massive small intestine resection. Gut dysbiosis has been implicated in SBS, this study aimed to characterize the metagenomic and metabolomic profiles of SBS and identify potential therapeutic targets.

METHODS: Fecal samples from SBS and Sham rats (n = 8 per group) were collected for high-throughput metagenomic sequencing. Fecal metabolomics was measured by untargeted liquid chromatography-mass spectrometry.

RESULTS: We found that the species-level α-diversity significantly decreased in SBS rats, accompanied by altered microbiome compositions. The beneficial anaerobes from Firmicutes and Bacteroidetes were depleted while microorganisms from Lactobacillus, Escherichia, Enterococcus, and Streptococcus were enriched in faces from SBS rats. LEfSe analysis identified 17 microbial species and 38 KEGG modules that were remarkably distinct between SBS and Sham rats. In total, 1,577 metabolites with known chemical identity were detected from all samples, among them, 276 metabolites were down-regulated and 224 metabolites were up-regulated in SBS group. The typical signatures of SBS fecal metabolome comprised reduced short-chain fatty acids and products of amino acid metabolism (indole derivatives and p-cresol), as well as altered bile acid spectrum. We revealed 215 robust associations between representative differentially abundant microbial species and metabolites, the species with the same changing trend tended to have a similar correlation with some certain metabolites.

CONCLUSION: The fecal microbiome and metabolome significantly altered in SBS. Our findings may lay the foundation for developing new strategies to facilitate intestinal adaptation in SBS patients.}, } @article {pmid37362928, year = {2023}, author = {Yu, S and Li, L and Zhao, H and Liu, M and Jiang, L and Zhao, Y}, title = {Citrus flavonoid extracts alter the profiling of rumen antibiotic resistance genes and virulence factors of dairy cows.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1201262}, pmid = {37362928}, issn = {1664-302X}, abstract = {Citrus flavonoid extracts (CFE) have the potential to reduce rumen inflammation, improve ruminal function, and enhance production performance in ruminants. Our previous studies have investigated the effects of CFE on the structure and function of rumen microbiota in dairy cows. However, it remains unclear whether CFE affects the prevalence of antibiotic resistance genes (ARG) and virulence factors genes (VFG) in the rumen. Therefore, metagenomics was used to identify the rumen ARG and VFG in lactating dairy cows fed with CFE diets. The results showed that CFE significantly reduced the levels of Multidrug and Antiphagocytosis in the rumen (p < 0.05) and increased the levels of Tetracycline, Iron uptake system, and Magnesium uptake system (p < 0.05). Furthermore, the changes were found to have associations with the phylum Lentisphaerae. It was concluded that CFE could be utilized as a natural plant product to regulate virulence factors and antibiotic resistance of rumen microbiota, thereby improving rumen homeostasis and the health of dairy cows.}, } @article {pmid37362918, year = {2023}, author = {Jiao, Y and Zhao, Z and Li, X and Li, L and Xiao, D and Wan, S and Wu, T and Li, T and Li, P and Zhao, R}, title = {Salidroside ameliorates memory impairment following long-term ethanol intake in rats by modulating the altered intestinal microbiota content and hippocampal gene expression.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1172936}, pmid = {37362918}, issn = {1664-302X}, abstract = {BACKGROUND: Salidroside (Sal), the main component of a famous herb Rhodiola rosea L, enhances memory performance and reduces fatigue. Therefore, this study assessed the effect of Sal on memory impairment induced by a long-term intake of ethanol (EtOH) in rats and investigated its relevant mechanisms using gut microbiota metagenomic analysis and hippocampal transcriptomic analysis.

METHODS: Eighteen male SD rats were divided into the normal control group (CON group), EtOH model group (Model group), and Sal treatment group (Sal group). The rats in the Model and Sal groups intragastrically (i.g.) received 2 g/kg EtOH for 30 consecutive days, whereas the CON group was given an equal volume of distilled water. Meanwhile, the rats in the Sal group were administered i.g. 30 mg/kg Sal 60 min after EtOH intake. All rats were tested in the eight-arm maze for their memory function every 3 days. On the 30th day, metagenomic analyses of gut microbiota and transcriptomic analyses of the hippocampus were performed.

RESULTS: Compared with the Model group, Sal treatment reduced the total time to complete the eight-arm maze task, decreased the number of arm entries, and abated the working memory error that was significant from the 9th day. Additionally, Sal intervention improved the gut microbiota composition, such as the increased abundance of Actinobacteria and Bifidobacterium, which was related to the metabolism of amino acids and terpenoid carbohydrate, endocrine function, and signal transduction by neurotransmitters. In the hippocampus, the EtOH intake differentially expressed 68 genes (54 genes increased, whereas 14 genes decreased), compared with the CON group, whereas Sal intervention affected these changes: 15 genes increased whereas 11 genes decreased. And, enrichment analyses revealed these genes were related to the structural components of the ribosome, mRNA splicing process, protein translation, mitochondria function, and immunological reaction. Finally, a correlation analysis found the memory impairment was positively correlated with the abnormal upregulation of Tomm7 but negatively correlated with decreased abundance of gut Alistipes_indistinctus, Lactobacillus_taiwanensis, Lactobacillus_paragasseri, and Lactobacillus johnsonii.

CONCLUSION: Sal improved memory impairment caused by long-term EtOH intake in rats, which may be related to its regulation of gut dysbiosis and hippocampal dysfunction.}, } @article {pmid37362854, year = {2023}, author = {Sengupta, P and Sivabalan, SKM and Mahesh, A and Palanikumar, I and Kuppa Baskaran, DK and Raman, K}, title = {Big Data for a Small World: A Review on Databases and Resources for Studying Microbiomes.}, journal = {Journal of the Indian Institute of Science}, volume = {}, number = {}, pages = {1-17}, pmid = {37362854}, issn = {0970-4140}, abstract = {Microorganisms are ubiquitous in nature and form complex community networks to survive in various environments. This community structure depends on numerous factors like nutrient availability, abiotic factors like temperature and pH as well as microbial composition. Categorising accessible biomes according to their habitats would help in understanding the complexity of the environment-specific communities. Owing to the recent improvements in sequencing facilities, researchers have started to explore diverse microbiomes rapidly and attempts have been made to study microbial crosstalk. However, different metagenomics sampling, preprocessing, and annotation methods make it difficult to compare multiple studies and hinder the recycling of data. Huge datasets originating from these experiments demand systematic computational methods to extract biological information beyond microbial compositions. Further exploration of microbial co-occurring patterns across the biomes could help us in designing cross-biome experiments. In this review, we catalogue databases with system-specific microbiomes, discussing publicly available common databases as well as specialised databases for a range of microbiomes. If the new datasets generated in the future could maintain at least biome-specific annotation, then researchers could use those contemporary tools for relevant and bias-free analysis of complex metagenomics data.}, } @article {pmid37362078, year = {2023}, author = {Duarte, MF and de Andrade, IA and Silva, JMF and de Melo, FL and Machado, AM and Inoue-Nagata, AK and Nagata, T}, title = {Metagenomic analyses of plant virus sequences in sewage water for plant viruses monitoring.}, journal = {Tropical plant pathology}, volume = {}, number = {}, pages = {1-9}, pmid = {37362078}, issn = {1982-5676}, abstract = {UNLABELLED: Frequent monitoring of emerging viruses of agricultural crops is one of the most important missions for plant virologists. A fast and precise identification of potential harmful viruses may prevent the occurrence of serious epidemics. Nowadays, high-throughput sequencing (HTS) technologies became an accessible and powerful tool for this purpose. The major discussion of this strategy resides in the process of sample collection, which is usually laborious, costly and nonrepresentative. In this study, we assessed the use of sewage water samples for monitoring the widespread, numerous, and stable plant viruses using HTS analysis and RT-qPCR. Plant viruses belonged to 12 virus families were found, from which Virgaviridae, Solemoviridae, Tymoviridae, Alphaflexiviridae, Betaflexiviridae, Closteroviridae and Secoviridae were the most abundant ones with more than 20 species. Additionally, we detected one quarantine virus in Brazil and a new tobamovirus species. To assess the importance of the processed foods as virus release origins to sewage, we selected two viruses, the tobamovirus pepper mild mottle virus (PMMoV) and the carlavirus garlic common latent virus (GarCLV), to detect in processed food materials by RT-qPCR. PMMoV was detected in large amount in pepper-based processed foods and in sewage samples, while GarCLV was less frequent in dried and fresh garlic samples, and in the sewage samples. This suggested a high correlation of virus abundance in sewage and processed food sources. The potential use of sewage for a virus survey is discussed in this study.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s40858-023-00575-8.}, } @article {pmid37361935, year = {2023}, author = {Huang, J and Liu, C and Zhou, Z and Xia, H and Zhu, Z and Lu, J and Lin, J and Chen, Z and Ye, Q and Zuo, L}, title = {Extracorporeal Membrane Oxygenation in Severe Acute Respiratory Distress Syndrome Caused by Chlamydia abortus: A Case Report.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {3893-3901}, pmid = {37361935}, issn = {1178-6973}, abstract = {BACKGROUND: Pneumonia infected by Chlamydia abortus (C. abortus) is rare, especially complicated with severe acute respiratory distress syndrome (ARDS) and multiple organ dysfunction syndrome (MODS).

CASE PRESENTATION: We presented the clinical details of a 44-year-old male who was diagnosed with C. abortus pneumonia, which rapidly progressed and ultimately led to ARDS, sepsis and MODS. Although he was initially diagnosed with pneumonia upon admission, no pathogenic bacteria were detected in sputum by conventional tests. Empirical intravenous infusion of meropenem and moxifloxacin was administered, but unfortunately, his condition deteriorated rapidly, especially respiratory status. On Day 2 after extracorporeal membrane oxygenation (ECMO) initiation, metagenomic next-generation sequencing (mNGS) was performed on the patient's bronchoalveolar lavage fluid, which indicated an infection with C. abortus. The patient's antimicrobial therapy was adjusted to oral doxycycline (0.1g every 12h), intravenous azithromycin (0.5g every day), and imipenem and cilastatin sodium (1g every 6h). The patient's condition improved clinically and biologically. However, the patient was discharged due to financial reasons and unfortunately passed away eight hours later.

CONCLUSION: Infections with C. abortus can result in severe ARDS and serious visceral complications which necessitate prompt diagnosis and active intervention by clinicians. The case highlights the significance of mNGS as an essential diagnostic tool for uncommon pathogens. Tetracyclines, macrolides or their combinations are effective choices for treatment of C. abortus pneumonia. Further study is needed to explore the transmission routes of C. abortus pneumonia and establish precise guidelines for antibiotic treatment.}, } @article {pmid37361484, year = {2023}, author = {Takano, Y and Takekoshi, S and Takano, K and Matoba, Y and Mukumoto, M and Shirai, O}, title = {Metagenomic analysis of ready biodegradability tests to ascertain the relationship between microbiota and the biodegradability of test chemicals.}, journal = {Journal of pesticide science}, volume = {48}, number = {2}, pages = {35-46}, pmid = {37361484}, issn = {1348-589X}, abstract = {Ready biodegradability tests conducted in accordance with the Organisation for Economic Co-operation and Development guidelines (test 301C or test 301F) are performed using activated sludge (AS) prepared by the Chemicals Evaluation and Research Institute (AS-CERI) or that taken from a sewage treatment plant (AS-STP). It had been reported that AS-CERI had lower activity than AS-STP in biodegrading test chemicals, and that biodegradation was accelerated by increasing the volume of the test medium. However, these phenomena have not been clarified from the perspective of the microbiota. In this study, using metagenomic analysis, we first showed that the microbiota of AS-CERI was biased in its distribution of phyla, less diverse, and had greater lot-to-lot variability than that of AS-STP. Second, after cultivation for a long period of time, the microbiota of AS-STP and AS-CERI became more similar to each other in terms of community structure. Third, determining degraders of test substances when each substance was actively biodegraded was found to be an effective approach. Finally, we clarified experimentally that a large volume of test medium increased the number of species that could degrade test substances in the condition where the initial concentrations of each substance and AS-STP were kept constant.}, } @article {pmid37361319, year = {2023}, author = {Torres-Morales, J and Mark Welch, JL and Dewhirst, FE and Borisy, GG}, title = {Site-specialization of human oral Gemella species.}, journal = {Journal of oral microbiology}, volume = {15}, number = {1}, pages = {2225261}, pmid = {37361319}, issn = {2000-2297}, abstract = {Gemella species are core members of the human oral microbiome in healthy subjects and are regarded as commensals, although they can cause opportunistic infections. Our objective was to evaluate the site-specialization of Gemella species among various habitats within the mouth by combining pangenomics and metagenomics. With pangenomics, we identified genome relationships and categorized genes as core and accessory to each species. With metagenomics, we identified the primary oral habitat of individual genomes. Our results establish that the genomes of three species, G. haemolysans, G. sanguinis and G. morbillorum, are abundant and prevalent in human mouths at different oral sites: G. haemolysans on buccal mucosa and keratinized gingiva; G. sanguinis on tongue dorsum, throat, and tonsils; and G. morbillorum in dental plaque. The gene-level basis of site-specificity was investigated by identifying genes that were core to Gemella genomes at a specific oral site but absent from other Gemella genomes. The riboflavin biosynthesis pathway was present in G. haemolysans genomes associated with buccal mucosa but absent from the rest of the genomes. Overall, metapangenomics show that Gemella species have clear ecological preferences in the oral cavity of healthy humans and provides an approach to identifying gene-level drivers of site specificity.}, } @article {pmid37361045, year = {2023}, author = {Wang, D and Ren, H}, title = {Microbial community in buckwheat rhizosphere with different nitrogen application rates.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15514}, pmid = {37361045}, issn = {2167-8359}, mesh = {Rhizosphere ; *Fagopyrum/metabolism ; Nitrogen/analysis ; Fertilizers/analysis ; *Neurodegenerative Diseases ; Soil Microbiology ; *Microbiota/genetics ; }, abstract = {Microorganism plays a pivotal role in regulating sustainable development of agriculture. The excessive application of nitrogen fertilizer is considered to affect the microbial structure in many agricultural systems. The present study aimed to assess the impacts of nitrogen application rate on microbial diversity, community and functionality in rhizosphere of Tartary buckwheat in short-time. The nitrogen fertilizer was applied at rates of 90 kg (N90), 120 kg (N120) and 150 kg (N150) urea per hectare, respectively. The soil properties were measured chemical analysis and displayed no difference among treatments. Metagenome analysis results showed that the microbial diversity was not affected, but the microbial community and functionality were affected by the nitrogen application rate. According to the Linear discriminant analysis effect size (LEfSe) analysis, 15 taxa were significantly enriched in the N120 and N150 groups, no taxon was enriched in the N90 group. Kyoto Encyclopaedia of Genes and Genomes (KEGG) annotation results revealed that the genes related to butanoate and beta alanine metabolism were significantly enriched in the N90 group, the genes related to thiamine metabolism, lipopolysaccharide biosynthesis and biofilm formation were significantly enriched in the N120 group, and the genes related to neurodegenerative disease was significantly enriched in the N150 group. In conclusion, short-time nitrogen fertilizer application shifted the microbial community structure and functionality.}, } @article {pmid37358243, year = {2023}, author = {He, Y and Liang, J and Liu, Y and Zhou, X and Peng, C and Long, C and Huang, P and Feng, J and Zhang, Z}, title = {Combined supplementation with Lactobacillus sp. and Bifidobacterium thermacidophilum isolated from Tibetan pigs improves growth performance, immunity, and microbiota composition in weaned piglets.}, journal = {Journal of animal science}, volume = {101}, number = {}, pages = {}, pmid = {37358243}, issn = {1525-3163}, support = {U2002206//National Natural Science Foundation of China/ ; CARS-35//Youth Innovation Promotion Association/ ; KFZDSW-219//Key Research Program of the Chinese Academy of Sciences/ ; 2019QZKK0503//Second Tibetan Plateau Scientific Expedition and Research (STEP) program/ ; 202001BB050001//Major Science and Technology Project in Yunnan Province of China/ ; }, mesh = {Animals ; Swine ; *Lactobacillus ; Prospective Studies ; Tibet ; Dietary Supplements ; *Microbiota ; Bifidobacterium ; Weaning ; }, abstract = {Probiotics, such as Lactobacillus and Bifidobacterium, promote growth in piglets by modulating gut microbiota composition and improving the host immune system. A strain of Lactobacillus sp. and Bifidobacterium thermacidophilum were previously isolated from fresh feces of Tibetan pigs. The effects of these isolated strains on growth performance, intestinal morphology, immunity, microbiota composition, and their metabolites were evaluated in weaned piglets. Thirty crossbred piglets were selected and fed either a basal diet (CON), a basal diet supplemented with aureomycin (ANT), or a basal diet supplemented with Lactobacillus sp. and B. thermacidophilum (LB) for 28 d. The piglets in the ANT and LB groups had significantly higher body weight gain than those in the CON group (P < 0.05). Piglets in the ANT and LB groups had regularly arranged villi and microvilli in the small intestine. Furthermore, they had improved immune function, as indicated by decreased serum concentrations of inflammatory cytokines (P < 0.05), improved components of immune cells in the blood, mesenteric lymph nodes, and spleen. Additionally, metagenomic sequencing indicated a significant shift in cecal bacterial composition and alterations in microbiota functional profiles following Lactobacillus sp. and B. thermacidophilum supplementation. Metabolomic results revealed that the metabolites were also altered, and Kyoto Encyclopedia of Genes and Genomes analysis revealed that several significantly altered metabolites were enriched in glycerophospholipid and cholesterol metabolism (P < 0.05). Furthermore, correlation analysis showed that several bacterial members were closely related to the alterations in metabolites, including Bacteroides sp., which were negatively correlated with triglyceride (16:0/18:0/20:4[5Z,8Z,11Z,14Z]), the metabolite that owned the highest variable importance of projection scores. Collectively, our findings suggest that combined supplementation with Lactobacillus sp. and B. thermacidophilum significantly improved the growth performance, immunity, and microbiota composition in weaned piglets, making them prospective alternatives to antibiotics in swine production.}, } @article {pmid37357866, year = {2023}, author = {Wang, YH and Luan, YX and Luo, JY and Men, Y and Engel, MS and Damgaard, J and Khila, A and Chen, PP and Figueiredo Moreira, FF and Rafael, JA and Xie, Q}, title = {300 Million years of coral treaders (Insecta: Heteroptera: Hermatobatidae) back to the ocean in the phylogenetic context of Arthropoda.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2001}, pages = {20230855}, pmid = {37357866}, issn = {1471-2954}, mesh = {Animals ; Phylogeny ; *Anthozoa/genetics ; Ecosystem ; *Arthropods ; *Heteroptera ; Coral Reefs ; Insecta ; }, abstract = {Among hundreds of insect families, Hermatobatidae (commonly known as coral treaders) is one of the most unique. They are small, wingless predaceous bugs in the suborder Heteroptera. Adults are almost black in colour, measuring about 5 mm in body length and 3 mm in width. Thirteen species are known from tropical coral reefs or rocky shores, but their origin and evolutionary adaptation to their unusual marine habitat were unexplored. We report here the genome and metagenome of Hermatobates lingyangjiaoensis, hitherto known only from its type locality in the South China Sea. We further reconstructed the evolutionary history and origin of these marine bugs in the broader context of Arthropoda. The dated phylogeny indicates that Hexapoda diverged from their marine sister groups approximately 498 Ma and that Hermatobatidae originated 192 Ma, indicating that they returned to an oceanic life some 300 Myr after their ancestors became terrestrial. Their origin is consistent with the recovery of tropical reef ecosystems after the end-Triassic mass extinction, which might have provided new and open niches for them to occupy and thrive. Our analyses also revealed that both the genome changes and the symbiotic bacteria might have contributed to adaptations necessary for life in the sea.}, } @article {pmid37357823, year = {2023}, author = {Spencer, BL and Job, AM and Robertson, CM and Hameed, ZA and Serchejian, C and Wiafe-Kwakye, CS and Mendonça, JC and Apolonio, MA and Nagao, PE and Neely, MN and Korotkova, N and Korotkov, KV and Patras, KA and Doran, KS}, title = {Heterogeneity of the group B streptococcal type VII secretion system and influence on colonization of the female genital tract.}, journal = {Molecular microbiology}, volume = {120}, number = {2}, pages = {258-275}, pmid = {37357823}, issn = {1365-2958}, support = {F32 AI143203/AI/NIAID NIH HHS/United States ; R01 AI153332/AI/NIAID NIH HHS/United States ; R01 NS116716/NS/NINDS NIH HHS/United States ; R21 AI169231/AI/NIAID NIH HHS/United States ; }, mesh = {Infant, Newborn ; Female ; Humans ; Bacterial Proteins/genetics/metabolism ; *Type VII Secretion Systems/genetics ; Virulence ; Operon/genetics ; Genitalia, Female/metabolism ; *Streptococcal Infections/microbiology ; Streptococcus agalactiae/genetics/metabolism ; Vagina/metabolism/microbiology ; }, abstract = {Type VIIb secretion systems (T7SSb) in Gram-positive bacteria facilitate physiology, interbacterial competition, and/or virulence via EssC ATPase-driven secretion of small ɑ-helical proteins and toxins. Recently, we characterized T7SSb in group B Streptococcus (GBS), a leading cause of infection in newborns and immunocompromised adults. GBS T7SS comprises four subtypes based on variation in the C-terminus of EssC and the repertoire of downstream effectors; however, the intraspecies diversity of GBS T7SS and impact on GBS-host interactions remains unknown. Bioinformatic analysis indicates that GBS T7SS loci encode subtype-specific putative effectors, which have low interspecies and inter-subtype homology but contain similar domains/motifs and therefore may serve similar functions. We further identify orphaned GBS WXG100 proteins. Functionally, we show that GBS T7SS subtype I and III strains secrete EsxA in vitro and that in subtype I strain CJB111, esxA1 appears to be differentially transcribed from the T7SS operon. Furthermore, we observe subtype-specific effects of GBS T7SS on host colonization, as CJB111 subtype I but not CNCTC 10/84 subtype III T7SS promotes GBS vaginal colonization. Finally, we observe that T7SS subtypes I and II are the predominant subtypes in clinical GBS isolates. This study highlights the potential impact of T7SS heterogeneity on host-GBS interactions.}, } @article {pmid37356986, year = {2023}, author = {Li, Y and Xiong, YZ and Fan, HH and Jing, LP and Li, JP and Lin, QS and Xu, CH and Li, Y and Ye, L and Jiao, M and Yang, Y and Li, Y and Yang, WR and Peng, GX and Zhou, K and Zhao, X and Zhang, L and Zhang, FK}, title = {[Metagenomic next-generation sequencing of plasma for the identification of bloodstream infectious pathogens in severe aplastic anemia].}, journal = {Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi}, volume = {44}, number = {3}, pages = {236-241}, pmid = {37356986}, issn = {0253-2727}, support = {81900127//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Anemia, Aplastic/complications/diagnosis ; Asian People ; High-Throughput Nucleotide Sequencing ; Plasma/microbiology ; Sensitivity and Specificity ; *Sepsis/microbiology ; }, abstract = {Objective: To analyze the diagnostic value of cell-free plasma metagenomic next-generation sequencing (mNGS) pathogen identification for severe aplastic anemia (SAA) bloodstream infection. Methods: From February 2021 to February 2022, mNGS and conventional detection methods (blood culture, etc.) were used to detect 33 samples from 29 consecutive AA patients admitted to the Anemia Diagnosis and Treatment Center of the Hematology Hospital of the Chinese Academy of Medical Sciences to assess the diagnostic consistency of mNGS and conventional detection, as well as the impact on clinical treatment benefits and clinical accuracy. Results: ①Among the 33 samples evaluated by mNGS and conventional detection methods, 25 cases (75.76%) carried potential pathogenic microorganisms. A total of 72 pathogenic microorganisms were identified from all cases, of which 65 (90.28%) were detected only by mNGS. ②All 33 cases were evaluated for diagnostic consistency, of which 2 cases (6.06%) were Composite, 18 cases (54.55%) were mNGS only, 2 cases (6.06%) were Conventional method only, 1 case (3.03%) was both common compliances (mNGS/Conventional testing) , and 10 cases (30.3%) were completely non-conforming (None) . ③All 33 cases were evaluated for clinical treatment benefit. Among them, 8 cases (24.24%) received Initiation of targeted treatment, 1 case (3.03%) received Treatment de-escalation, 13 cases (39.39%) received Confirmation, and the remaining 11 cases (33.33%) received No clinical benefit. ④ The sensitivity of 80.77%, specificity of 70.00%, positive predictive value of 63.64%, negative predictive value of 84.85%, positive likelihood ratio of 2.692, and negative likelihood ratio of 0.275 distinguished mNGS from conventional detection methods (21/12 vs 5/28, P<0.001) . Conclusion: mNGS can not only contribute to accurately diagnosing bloodstream infection in patients with aplastic anemia, but can also help to guide accurate anti-infection treatment, and the clinical accuracy is high.}, } @article {pmid37356897, year = {2023}, author = {Oberg, N and Zallot, R and Gerlt, JA}, title = {EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools.}, journal = {Journal of molecular biology}, volume = {435}, number = {14}, pages = {168018}, pmid = {37356897}, issn = {1089-8638}, support = {P01 GM118303/GM/NIGMS NIH HHS/United States ; R24 GM141196/GM/NIGMS NIH HHS/United States ; U54 GM093342/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Bacteria/enzymology/genetics ; Genomics ; *Internet ; Metagenome ; *Enzymes/chemistry/genetics ; Archaea/enzymology/genetics ; Fungi/enzymology/genetics ; *Databases, Genetic ; }, abstract = {The Enzyme Function Initiative (EFI) provides a web resource with "genomic enzymology" web tools to leverage the protein (UniProt) and genome (European Nucleotide Archive; ENA; https://www.ebi.ac.uk/ena/) databases to assist the assignment of in vitro enzymatic activities and in vivo metabolic functions to uncharacterized enzymes (https://efi.igb.illinois.edu/). The tools enable (1) exploration of sequence-function space in enzyme families using sequence similarity networks (SSNs; EFI-EST), (2) easy access to genome context for bacterial, archaeal, and fungal proteins in the SSN clusters so that isofunctional families can be identified and their functions inferred from genome context (EFI-GNT); and (3) determination of the abundance of SSN clusters in NIH Human Metagenome Project metagenomes using chemically guided functional profiling (EFI-CGFP). We describe enhancements that enable SSNs to be generated from taxonomy categories, allowing higher resolution analyses of sequence-function space; we provide examples of the generation of taxonomy category-specific SSNs.}, } @article {pmid37356408, year = {2023}, author = {Porcellato, D and Kristiansen, H and Finton, MD and Leanti La Rosa, S and da Silva Duarte, V and Skeie, SB}, title = {Composition and fate of heat-resistant anaerobic spore-formers in the milk powder production line.}, journal = {International journal of food microbiology}, volume = {402}, number = {}, pages = {110281}, doi = {10.1016/j.ijfoodmicro.2023.110281}, pmid = {37356408}, issn = {1879-3460}, mesh = {Animals ; *Milk/microbiology ; Powders ; *Hot Temperature ; Spores, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Anaerobiosis ; }, abstract = {Anaerobic spore-forming bacteria are a continuous threat to the dairy industry due to their ability to withstand processing conditions, such as those during heat treatment. These ubiquitous microorganisms have ample opportunity for multiple entry points into the milk chain, creating food quality and safety issues. Certain spore-formers, namely bacilli and clostridia, are more problematic due to their ability to spoil dairy products and pathogenicity. In this study, we investigated how milk treatment and milk powder production influenced the composition and survival of anaerobic spore-formers. Samples were obtained on three different days (replicate blocks) during the production of dairy powders and examined in a culture-dependent manner using the most probable number method coupled with 16S rRNA amplicon sequencing and metagenomic analysis of the enriched samples. Results revealed that the milk separation greatly affected the spore-former presence and composition which were detected along the entire production line from raw material to milk powders. Throughout the various points of the production line, the occurrence of species belonging to the Bacillus cereus sensu lato was higher than that of clostridia. Sequence variants (SVs) belonging to the anaerobic spore-forming genus Clostridium were taxonomically assigned to two SVs groups and were detected in all three replicate blocks. A total of 19 metagenome-assembled genomes were recovered from nine enrichments. Four near-complete and two medium-quality genomes were found in raw milk/milk powder samples and further assigned as Clostridium tyrobutyricum and Clostridium diolis, which may constitute a problem in the finished dairy product. In conclusion, our findings highlight spore-formers' importance on dairy quality and may aid in their intervention and control in the dairy production line.}, } @article {pmid37356328, year = {2023}, author = {Xu, M and Gao, P and Chen, HQ and Shen, XX and Xu, RZ and Cao, JS}, title = {Metagenomic insight into the prevalence and driving forces of antibiotic resistance genes in the whole process of three full-scale wastewater treatment plants.}, journal = {Journal of environmental management}, volume = {344}, number = {}, pages = {118369}, doi = {10.1016/j.jenvman.2023.118369}, pmid = {37356328}, issn = {1095-8630}, mesh = {*Anti-Bacterial Agents/pharmacology ; Wastewater ; Genes, Bacterial ; Prevalence ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; *Water Purification ; }, abstract = {The spread of antibiotic resistance genes (ARGs) is an emerging global health concern, and wastewater treatment plants (WWTPs), as an essential carrier for the occurrence and transmission of ARGs, deserves more attention. Based on the Illumina NovaSeq high-throughput sequencing platform, this study conducted a metagenomic analysis of 18 samples from three full-scale WWTPs to explore the fate of ARGs in the whole process (influent, biochemical treatment, advanced treatment, and effluent) of wastewater treatment. Total 70 ARG subtypes were detected, among which multidrug, aminoglycoside, tetracycline, and macrolide ARGs were most abundant. The different treatment processes used for three WWTPs were capable of reducing ARG diversity, but did not significantly reduce ARG abundance. Compared to that by denitrification filters, the membrane bioreactor (MBR) process was advantageous in controlling the prevalence of multidrug ARGs in WWTPs. Linear discriminant analysis Effect Size (LEfSe) suggested g_Nitrospira, g_Curvibacter, and g_Mycobacterium as the key bacteria responsible for differential ARG prevalence among different WWTPs. Meanwhile, adeF, sul1, and mtrA were the persistent antibiotic resistance genes (PARGs) and played dominant roles in the prevalence of ARGs. Proteobacteria and Actinobacteria were the host bacteria of majority ARGs in WWTPs, while Pseudomonas and Nitrospira were the most crucial host bacteria influencing the dissemination of critical ARGs (e.g., adeF). In addition, microbial richness was determined to be the decisive factor affecting the diversity and abundance of ARGs in wastewater treatment processes. Overall, regulating the abundance of microorganisms and key host bacteria by selecting processes with microbial interception, such as MBR process, may be beneficial to control the prevalence of ARGs in WWTPs.}, } @article {pmid37356309, year = {2023}, author = {Zhu, Y and Zhang, Y and Yan, S and Chen, X and Xie, S}, title = {Viral community structure and functional potential vary with lifestyle and altitude in soils of Mt. Everest.}, journal = {Environment international}, volume = {178}, number = {}, pages = {108055}, doi = {10.1016/j.envint.2023.108055}, pmid = {37356309}, issn = {1873-6750}, mesh = {*Soil/chemistry ; Altitude ; Bacteria/genetics ; *Viruses/genetics ; Carbon ; Soil Microbiology ; }, abstract = {More and more focus has been placed on the processes by which viruses interact with bacteria to influence the biogeochemical cycles. The intricacy of soil matrix and the incompleteness of databases, however, constrains the investigation on the mechanisms of soil viruses exerting ecological functions. The modification of ICTV classification system in 2021 was also a huge shock to the results of the existing studies on virome. We used viral metagenomes combined with soil properties to investigate the viral community composition and auxiliary metabolic genes (AMGs) profiles of various lifestyles in soils of Mount Everest at different altitudes. Viral lifestyles and soil nutrient levels were found to significantly influence the diversity and composition of viral communities. Temperate virus lifestyle dominated in high-altitude soils with lower level of nutrients because of its stronger survival adaptability, and the structural and functional diversity of viral communities was positively correlated with the contents of nutrients (total carbon and total nitrogen). The primary types of AMGs carried by temperate and virulent viruses differed, while a variety of genes involved in carbon metabolism highlighted the potential importance of viruses in the soil carbon cycle of Mount Everest. Moreover, the abundance of AMGs encoding carbohydrate-active enzymes had a significant and positive correlation with soil C/N ratio. Overall, these findings provide a context for further exploration on the regulatory mechanisms of viruses in carbon cycle via interactions with microorganisms.}, } @article {pmid37355726, year = {2023}, author = {Elie, C and Perret, M and Hage, H and Sentausa, E and Hesketh, A and Louis, K and Fritah-Lafont, A and Leissner, P and Vachon, C and Rostaing, H and Reynier, F and Gervasi, G and Saliou, A}, title = {Comparison of DNA extraction methods for 16S rRNA gene sequencing in the analysis of the human gut microbiome.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {10279}, pmid = {37355726}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; DNA ; *Microbiota/genetics ; }, abstract = {The gut microbiome is widely analyzed using high-throughput sequencing, such as 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing (SMS). DNA extraction is known to have a large impact on the metagenomic analyses. The aim of this study was to compare DNA extraction protocols for 16S sequencing. In that context, four commonly used DNA extraction methods were compared for the analysis of the gut microbiota. Commercial versions were evaluated against modified protocols using a stool preprocessing device (SPD, bioMérieux) upstream DNA extraction. Stool samples from nine healthy volunteers and nine patients with a Clostridium difficile infection were extracted with all protocols and 16S sequenced. Protocols were ranked using wet- and dry-lab criteria, including quality controls of the extracted genomic DNA, alpha-diversity, accuracy using a mock community of known composition and repeatability across technical replicates. SPD improved overall efficiency of three of the four tested protocols compared with their commercial version, in terms of DNA extraction yield, sample alpha-diversity, and recovery of Gram-positive bacteria. The best overall performance was obtained for the S-DQ protocol, SPD combined with the DNeasy PowerLyser PowerSoil protocol from QIAGEN. Based on this evaluation, we strongly believe that the use of such stool preprocessing device improves both the standardization and the quality of the DNA extraction in the human gut microbiome studies.}, } @article {pmid37355707, year = {2023}, author = {Carlton, JD and Langwig, MV and Gong, X and Aguilar-Pine, EJ and Vázquez-Rosas-Landa, M and Seitz, KW and Baker, BJ and De Anda, V}, title = {Expansion of Armatimonadota through marine sediment sequencing describes two classes with unique ecological roles.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {64}, pmid = {37355707}, issn = {2730-6151}, support = {91951202//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42006134//National Natural Science Foundation of China (National Science Foundation of China)/ ; 687165//Simons Foundation/ ; 1817354//National Science Foundation (NSF)/ ; }, abstract = {Marine sediments comprise one of the largest environments on the planet, and their microbial inhabitants are significant players in global carbon and nutrient cycles. Recent studies using metagenomic techniques have shown the complexity of these communities and identified novel microorganisms from the ocean floor. Here, we obtained 77 metagenome-assembled genomes (MAGs) from the bacterial phylum Armatimonadota in the Guaymas Basin, Gulf of California, and the Bohai Sea, China. These MAGs comprise two previously undescribed classes within Armatimonadota, which we propose naming Hebobacteria and Zipacnadia. They are globally distributed in hypoxic and anoxic environments and are dominant members of deep-sea sediments (up to 1.95% of metagenomic raw reads). The classes described here also have unique metabolic capabilities, possessing pathways to reduce carbon dioxide to acetate via the Wood-Ljungdahl pathway (WLP) and generating energy through the oxidative branch of glycolysis using carbon dioxide as an electron sink, maintaining the redox balance using the WLP. Hebobacteria may also be autotrophic, not previously identified in Armatimonadota. Furthermore, these Armatimonadota may play a role in sulfur and nitrogen cycling, using the intermediate compounds hydroxylamine and sulfite. Description of these MAGs enhances our understanding of diversity and metabolic potential within anoxic habitats worldwide.}, } @article {pmid37355675, year = {2023}, author = {Wang, Y and Guo, A and Zou, Y and Mu, W and Zhang, S and Shi, Z and Liu, Z and Cai, X and Zhu, XQ and Wang, S}, title = {Interaction between tissue-dwelling helminth and the gut microbiota drives mucosal immunoregulation.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {43}, pmid = {37355675}, issn = {2055-5008}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Microbiota ; *Colitis/metabolism ; *Helminths ; }, abstract = {Tissue-dwelling helminths affect billions of people around the world. They are potent manipulators of the host immune system, prominently by promoting regulatory T cells (Tregs) and are generally associated with a modified host gut microbiome. However, the role of the gut microbiota in the immunomodulatory processes for these non-intestinal parasites is still unclear. In the present study, we used an extra-intestinal cestode helminth model-larval Echinococcus multilocularis to explore the tripartite partnership (host-helminth-bacteria) in the context of regulating colonic Tregs in Balb/c mice. We showed that larval E. multilocularis infection in the peritoneal cavity attenuated colitis in Balb/c mice and induced a significant expansion of colonic Foxp3[+] Treg populations. Fecal microbiota depletion and transplantation experiments showed that the gut microbiota contributed to increasing Tregs after the helminth infection. Shotgun metagenomic and metabolic analyses revealed that the gut microbiome structure after infection was significantly shifted with a remarkable increase of Lactobacillus reuteri and that the microbial metabolic capability was reprogrammed to produce more Treg cell regulator-short-chain fatty acids in feces. Furthermore, we also prove that the L. reuteri strain elevated in infected mice was sufficient to promote the colonic Treg frequency and its growth was potentially associated with T cell-dependent immunity in larval E. multilocularis infection. Collectively, these findings indicate that the extraintestinal helminth drives expansions of host colonic Tregs through the gut microbes. This study suggests that the gut microbiome serves as a critical component of anti-inflammation effects even for a therapy based on an extraintestinal helminth.}, } @article {pmid37355612, year = {2023}, author = {Lin, X and Qiao, B and Chang, R and Li, Y and Zheng, W and He, Z and Tian, Y}, title = {Characterization of two keystone taxa, sulfur-oxidizing, and nitrate-reducing bacteria, by tracking their role transitions in the benzo[a]pyrene degradative microbiome.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {139}, pmid = {37355612}, issn = {2049-2618}, mesh = {*Nitrates/metabolism ; Benzo(a)pyrene/metabolism ; Bacteria ; *Microbiota/genetics ; Sulfur/metabolism ; Oxidation-Reduction ; }, abstract = {BACKGROUND: Keystone taxa are drivers of microbiome structure and functioning, which may play critical roles in microbiome-level responses to recalcitrant pollution and are a key to bioremediation. However, the characterization and manipulation of such taxa is a major challenge due to the complexity of microbial communities and rapid turnover in both time and space. Here, microcosms were set up with benzo[a]-pyrene (BaP) and/or nitrate based on C-rich, S-rich, and N-limited mangrove sediments as reductive experimental models to trigger and track the turnover of keystone taxa to address this challenge.

RESULTS: Based on microbial co-occurrence network analysis, two keystone taxa, Sulfurovum and Sulfurimonas, were found to exhibit significant role transitions in different microcosms, where these two taxa played nonkeystone roles with neutral relationships in in situ mangrove sediments. However, Sulfurimonas transitioned to be keystone taxa in nitrate-replenished microcosms and formed a keystone guild with Thioalkalispira. Sulfurovum stood out in BaP-added microcosms and mutualized in a densely polycyclic aromatic hydrocarbon (PAH)-degrader-centric keystone guild with Novosphingobium and Robiginitalea, where 63.25% of added BaP was removed. Under the occurrence of nitrate and BaP, they simultaneously played roles as keystone taxa in their respective guilds but exhibited significant competition. Comparative genomics and metagenome-assembled genome (MAG) analysis was then performed to reveal the metabolic potential of those keystone taxa and to empirically deduce their functional role in keystone guilds. Sulfurimonas possesses a better sense system and motility, indicative of its aggressive role in nitrate acquisition and conversion; Sulfurovum exhibited a better ability for oxidation resistance and transporting nutrients and electrons. High-efficiency thermal asymmetric interlaced polymerase reaction (hiTAIL-PCR) and enhanced green fluorescent protein (eGFP)-labeling approaches were employed to capture and label the BaP key degrader to further experimentally verify the roles of keystone taxa Sulfurovum in the keystone guilds. Observations of the enhancement in reactive oxygen species (ROS) removal, cell growth, and degradation efficiency by co-culture of isolated keystone taxa strains experimentally demonstrated that Sulfurovum contributes to the BaP degradative microbiome against BaP toxicity.

CONCLUSIONS: Our findings suggest that the combined use of co-occurrence network analysis, comparative genomics, and co-culture of captured keystone taxa (3C-strategy) in microbial communities whose structure is strongly shaped by changing environmental factors can characterize keystone taxa roles in keystone guilds and may provide targets for manipulation to improve the function of the microbiome. Video Abstract.}, } @article {pmid37355217, year = {2023}, author = {Wanvimonsuk, S and Somboonwiwat, K}, title = {Peroxiredoxin-4 supplementation modulates the immune response, shapes the intestinal microbiome, and enhances AHPND resistance in Penaeus vannamei.}, journal = {Fish & shellfish immunology}, volume = {139}, number = {}, pages = {108915}, doi = {10.1016/j.fsi.2023.108915}, pmid = {37355217}, issn = {1095-9947}, mesh = {Animals ; Immunity, Innate/genetics ; *Penaeidae ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; Dietary Supplements ; Peroxiredoxins ; *Vibrio parahaemolyticus/physiology ; }, abstract = {Peroxiredoxin-4 from Penaeus vannamei (LvPrx4) is considered a damage-associated molecular pattern (DAMP) that can activate the expression of immune-related genes through the Toll pathway. We previously demonstrated that the recombinant LvPrx4 (rLvPrx4) can enhance shrimp resistance against Vibrio parahaemolyticus, causing acute hepatopancreatic necrosis disease (VPAHPND), which causes great production losses in shrimp farming. Herein, we showed that the rLvPrx4 had a thermal tolerance of around 60 °C and that the ionic strength had no noticeable effect on its activity. We discovered that feeding a diet containing rLvPrx4 to shrimp for three weeks increased the expression of the immune-related genes LvPEN4 and LvVago5. Furthermore, pre-treatment with rLvPrx4 feeding could significantly prolong shrimp survival following the VPAHPND challenge. The shrimp intestinal microbiome was then characterized using PCR amplification of the 16S rRNA gene and Illumina sequencing. Three weeks of rLvPrx4 supplementation altered the bacterial community structure (beta diversity) and revealed the induction of differentially abundant families, including Cryomorphaceae, Flavobacteriaceae, Pirellulaceae, Rhodobacteraceae, and Verrucomicrobiaceae, in the rLvPrx4 group. Metagenomic predictions indicated that some amino acid metabolism pathways, such as arginine and proline metabolism, and genetic information processing were significantly elevated in the rLvPrx4 group compared to the control group. This study is the first to describe the potential use of rLvPrx4 supplementation to enhance shrimp resistance to VPAHPND and alter the composition of a beneficial bacterial community in shrimp, making rLvPrx4 a promising feed supplement as an alternative to antibiotics for controlling VPAHPND infection in shrimp aquaculture.}, } @article {pmid37354103, year = {2023}, author = {Qiao, J and Liu, J and Palomo, A and Bostick, BC and Phan, K and Zheng, Y and Li, F}, title = {Prevalence of Methylated Arsenic and Microbial Arsenic Methylation Genes in Paddy Soils of the Mekong Delta.}, journal = {Environmental science & technology}, volume = {57}, number = {26}, pages = {9675-9682}, doi = {10.1021/acs.est.3c00210}, pmid = {37354103}, issn = {1520-5851}, mesh = {*Arsenic ; Methylation ; Soil ; Prevalence ; *Arsenicals/metabolism ; Bacteria/genetics/metabolism ; *Oryza ; *Soil Pollutants ; }, abstract = {Microbially mediated inorganic-methylated arsenic (As) transformation in paddy soil is crucial to rice safety; however, the linkages between the microbial As methylation process and methylated As species remain elusive. Here, 62 paddy soils were collected from the Mekong River delta of Cambodia to profile As-related functional gene composition involved in the As cycle. The soil As concentration ranged from <1 to 16.6 mg kg[-1], with average As contents of approximately 81% as methylated As and 54% as monomethylarsenate (MMAs(V)) in the phosphate- and oxalate-extractable fractions based on As sequential extraction analysis. Quantitative PCR revealed high arsenite-methylating gene (arsM) copy numbers, and metagenomics identified consistently high arsM gene abundance. The abundance of As-related genes was the highest in bacteria, followed by archaea and fungi. Pseudomonas, Bradyrhizobium, Burkholderia, and Anaeromyxobacter were identified as bacteria harboring the most genes related to As biotransformation. Moreover, arsM and arsI (As demethylation) gene-containing operons were identified in the metagenome-assembled genomes (MAGs), implying that arsM and arsI could be transcribed together. The prevalence of methylated As and arsM genes may have been overlooked in tropical paddy fields. The As methylation-demethylation cycle should be considered when manipulating the methylated As pool in paddy fields for rice safety.}, } @article {pmid37353839, year = {2023}, author = {Xu, J and Zhong, L and Shao, H and Wang, Q and Dai, M and Shen, P and Xiong, Y and Zhang, W and Deng, X and Wang, M and Zhu, Y and Reng, X and Jiang, Y and Chen, M and Zhu, C and Fang, X and He, G and Han, Y and Huang, X and He, X and Xu, Y and Cai, H and Huang, L}, title = {Incidence and clinical features of HHV-7 detection in lower respiratory tract in patients with severe pneumonia: a multicenter, retrospective study.}, journal = {Critical care (London, England)}, volume = {27}, number = {1}, pages = {248}, pmid = {37353839}, issn = {1466-609X}, support = {2022KY435//the Medicines Health Research Fund of Zhejiang/ ; 2023C03083//the National Key Research and Development Program of Zhejiang Province/ ; 2022YFC2504501//National Key Research and Development Program of China/ ; 82202356//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Retrospective Studies ; *Herpesvirus 7, Human ; *Epstein-Barr Virus Infections ; Incidence ; Herpesvirus 4, Human ; *Pneumonia/epidemiology ; Lung ; Cytomegalovirus ; }, abstract = {PURPOSE: The significance of detecting human herpesvirus 7 (HHV-7) in the lower respiratory tract of patients with severe pneumonia is unclear. This study aims to evaluate the clinical characteristics and prognosis of detecting HHV-7 in the lower respiratory tract of patients with severe pneumonia.

METHODS: Patients with severe pneumonia requiring invasive mechanical ventilation and underwent commercial metagenomic next-generation sequencing (mNGS) testing of bronchoalveolar lavage fluid from January 2019 to March 2023 were enrolled in 12 medical centers. Clinical data of patients were collected retrospectively, and propensity score matching was used for subgroup analysis and mortality assessment.

RESULTS: In a total number of 721 patients, 45 cases (6.24%) were identified with HHV-7 positive in lower respiratory tract. HHV-7 positive patients were younger (59.2 vs 64.4, p = 0.032) and had a higher rate of co-detection with Cytomegalovirus (42.2% vs 20.7%, p = 0.001) and Epstein-Barr virus (35.6% vs 18.2%, p = 0.008). After propensity score matching for gender, age, SOFA score at ICU admission, and days from ICU admission to mNGS assay, there was no statistically significant difference in the 28-day mortality rate between HHV-7 positive and negative patients (46.2% vs 36.0%, p = 0.395). Multivariate Cox regression analysis adjusting for gender, age, and SOFA score showed that HHV-7 positive was not an independent risk factor for 28-day mortality (HR 1.783, 95%CI 0.936-3.400, p = 0.079).

CONCLUSION: HHV-7 was detected in the lungs of 6.24% of patients with severe pneumonia. The presence of HHV-7 in patients with severe pneumonia requiring invasive mechanical ventilation is associated with a younger age and co-detected of Cytomegalovirus and Epstein-Barr virus. While HHV-7 positivity was not found to be an independent risk factor for mortality in this cohort, this result may have been influenced by the relatively small sample size of the study.}, } @article {pmid37353172, year = {2023}, author = {Devi, A and Verma, M and Saratale, GD and Saratale, RG and Ferreira, LFR and Mulla, SI and Bharagava, RN}, title = {Microalgae: A green eco-friendly agents for bioremediation of tannery wastewater with simultaneous production of value-added products.}, journal = {Chemosphere}, volume = {336}, number = {}, pages = {139192}, doi = {10.1016/j.chemosphere.2023.139192}, pmid = {37353172}, issn = {1879-1298}, mesh = {Wastewater ; *Microalgae/metabolism ; Biodegradation, Environmental ; Biotechnology ; *Environmental Pollutants/metabolism ; Biomass ; Biofuels ; }, abstract = {Tannery wastewater (TWW) has high BOD, COD, TS and variety of pollutants like chromium, formaldehydes, biocides, oils, chlorophenols, detergents and phthalates etc. Besides these pollutants, TWW also rich source of nutrients like nitrogen, phosphorus, carbon and sulphur etc. that can be utilized by microalgae during their growth. Direct disposal of TWW into the environment may lead severe environmental and health threats, therefore it needs to be treated adequately. Microalgae are considered as an efficient microorganisms (fast growing, adaptability and strain robustness, high surface to volume ratio, energy saving) for remediation of wastewaters with simultaneous biomass recovery and generation of value-added products (VAPs) such as biofuels, biohydrogen, biopolymer, biofertilizer, pigments, bioethanol, bioactive compounds, nutraceutical etc. Most microalgae are photosynthetic and use CO2 and light energy to synthesise carbohydrate and reduces the emission of greenhouse gasses. Microalgae are also reported to remove heavy metals and antibiotics from wastewaters by bioaccumulation, biodegradation and biosorption. Microalgal treatment can be an alternative of conventional processes with generation of VAPs. The use of biotechnology in wastewater remediation with simultaneous generation of VAPs is trending. The validation of economic viability and environmental sustainability, life cycle assessment studies and techno-economic analysis is undergoing. Thus, in this review, the characteristics of TWW and microalgae are summarized, which manifest microalgae as potential candidates for wastewater remediation with simultaneous production of VAPs. Further, the treatment mechanisms, various factors (physical, chemical, mechanical and biological etc.) affecting treatment efficiency as well as challenges associated with microalgal remediation are also discussed.}, } @article {pmid37351316, year = {2023}, author = {Jin, X and Zhang, C and Chen, C and Wang, X and Dong, J and He, Y and Zhang, P}, title = {Tropheryma whipplei-induced plastic bronchitis in children: a case report.}, journal = {Frontiers in pediatrics}, volume = {11}, number = {}, pages = {1185519}, pmid = {37351316}, issn = {2296-2360}, abstract = {This article reports a case of a 7-year-old child with severe pneumonia whose chest CT showed pulmonary consolidation, and bronchoscopy revealed plastic bronchitis. The metagenomic Next-Generation Sequencing (NGS) of the pulmonary lavage fluid suggested the infection of Tropheryma whipplei (T whipplei). The patient was treated with bronchial lavage to remove sputum plugs, intravenous azithromycin, and piperacillin-tazobactam and was discharged after eight days of hospitalization without any recurrence during follow-up. This article aims to raise clinical awareness of T whipplei infection and suggests that NGS for rare pathogens should be performed early for unexplained plastic bronchitis.}, } @article {pmid37350971, year = {2023}, author = {Pan, Y and Shang, G and Li, J and Zhang, Y and Liu, J and Ji, Y and Ding, J and Wang, X}, title = {Case Report: A novel IRF2BP2 mutation in an IEI patient with recurrent infections and autoimmune disorders.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {967345}, pmid = {37350971}, issn = {1664-3224}, mesh = {Humans ; *Reinfection ; *Autoimmune Diseases/diagnosis/genetics ; Autoantibodies ; Autoimmunity ; B-Lymphocytes ; DNA-Binding Proteins ; Transcription Factors ; }, abstract = {INTRODUCTION: Inborn errors of immunity (IEI) are a heterogeneous group of disorders characterized by increased risk of infections, autoimmunity, autoinflammatory diseases, malignancy and allergy. Next-generation sequencing has revolutionized the identification of genetic background of these patients and assists in diagnosis and treatment. In this study, we identified a probable unique monogenic cause of IEI, and evaluated the immunological methods and pathogenic detections.

METHODS: A family with a member with a clinical diagnosis of IEI was screened by whole genomic sequencing (WGS). Demographic data, clinical manifestations, medical history, physical examination, laboratory findings and imaging features of the patient were extracted from medical records. Comprehensive immune monitoring methods include a complete blood count with differential, serum levels of cytokines and autoantibodies, T-cell and B-cell subsets analysis and measurement of serum immunoglobulins. In addition, metagenomic sequencing (mNGS) of blood, cerebrospinal fluid and biopsy from small intestine were used to detect potential pathogens.

RESULTS: The patient manifested with recurrent infections and autoimmune disorders, who was eventually diagnosed with IEI. Repetitive mNGS tests of blood, cerebrospinal fluid and biopsy from small intestine didn't detect pathogenic microorganism. Immunological tests showed a slightly decreased level of IgG than normal, elevated levels of tumor necrosis factor and interleukin-6. Lymphocyte flow cytometry showed elevated total B cells and natural killer cells, decreased total T cells and B-cell plasmablasts. WGS of the patient identified a novel heterozygous mutation in IRF2BP2 (c.439_450dup p. Thr147_Pro150dup), which was also confirmed in his father. The mutation was classified as variant of uncertain significance (VUS) according to the American College of Medical Genetics and Genomics guidelines.

CONCLUSION: We identified a novel IRF2BP2 mutation in a family with a member diagnosed with IEI. Immune monitoring and WGS as auxiliary tests are helpful in identifying genetic defects and assisting diagnosis in patients with clinically highly suspected immune abnormalities and deficiencies in inflammation regulation. In addition, mNGS techniques allow a more comprehensive assessment of the pathogenic characteristics of these patients. This report further validates the association of IRF2BP2 deficiency and IEI, and expands IEI phenotypes.}, } @article {pmid37350784, year = {2023}, author = {Fujihara, H and Hirose, J and Suenaga, H}, title = {Evolution of genetic architecture and gene regulation in biphenyl/PCB-degrading bacteria.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1168246}, pmid = {37350784}, issn = {1664-302X}, abstract = {A variety of bacteria in the environment can utilize xenobiotic compounds as a source of carbon and energy. The bacterial strains degrading xenobiotics are suitable models to investigate the adaptation and evolutionary processes of bacteria because they appear to have emerged relatively soon after the release of these compounds into the natural environment. Analyses of bacterial genome sequences indicate that horizontal gene transfer (HGT) is the most important contributor to the bacterial evolution of genetic architecture. Further, host bacteria that can use energy effectively by controlling the expression of organized gene clusters involved in xenobiotic degradation will have a survival advantage in harsh xenobiotic-rich environments. In this review, we summarize the current understanding of evolutionary mechanisms operative in bacteria, with a focus on biphenyl/PCB-degrading bacteria. We then discuss metagenomic approaches that are useful for such investigation.}, } @article {pmid37350694, year = {2023}, author = {Li, JM and Ou, JH and Verpoort, F and Surmpalli, RY and Huang, WY and Kao, CM}, title = {Toxicity evaluation of a heavy-metal-polluted river: Pollution identification and bacterial community assessment.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {95}, number = {7}, pages = {e10904}, doi = {10.1002/wer.10904}, pmid = {37350694}, issn = {1554-7531}, support = {//Taiwan National Science and Technology Council/ ; }, mesh = {Humans ; Wastewater ; Geologic Sediments ; *Water Pollutants, Chemical/toxicity/analysis ; Environmental Monitoring/methods ; *Metals, Heavy/toxicity/analysis ; Proteobacteria ; Risk Assessment ; *Microbiota ; China ; }, abstract = {The Salt River is an important urban river in Kaohsiung, Taiwan. In this study, the source identification and risk and toxicity assessment of the heavy-metal-contaminated sediments in the Salt River were investigated. The geo-accumulation index (Igeo), enrichment factor (EF), sediment quality guidelines (SQGs), potential ecological risk index (RI), pollution load index (PLI), and toxic units (TU) were applied to determine effects of heavy metals on microbial diversities and ecosystems. Results from the ecological and environmental risk assessment show that high concentrations of Zn, Cr, and Ni were detected in the midstream area and the sum of toxic units (ΣTUs) in the midstream (7.2-32.0) is higher than in the downstream (14.0-19.7) and upstream (9.2-17.1). It could be because of the continuous inputs of heavy-metal-contained wastewaters from adjacent industrial parks. Results also inferred that the detected heavy metals in the upstream residential and commercial areas were possibly caused by nearby vehicle emissions, non-point source pollution, and domestic wastewater discharges. Results of metagenomic assays show that the sediments contained significant microbial diversities. Metal-tolerant bacterial phyla (Proteobacteria: 24.4%-46.4%, Bacteroidetes: 1.3%-14.8%, and Actinobacteria: 2.3%-11.1%) and pathogenic bacterial phyla (Chlamydiae: 0.5%-37.6% and Chloroflexi: 5.8%-7.2%) with relatively high abundance were detected. Metal-tolerant bacteria would adsorb metals and cause the increased metal concentrations in sediments. Results indicate that the bacterial composition in sediment environments was affected by anthropogenic pollution and human activities and the heavy-metal-polluted ecosystem caused the variations in bacterial communities. PRACTITIONER POINTS: Microbial community in sediments is highly affected by heavy metal pollution. Wastewaters and vehicle traffic contribute to river sediments pollution by heavy metals. Proteobacteria, Bacteroidota, and Actinobacteria are dominant heavy-metal-tolerant bacterial phyla in sediments. Toxicity assessment is required to study risk levels of heavy-metal contained sediments.}, } @article {pmid37350639, year = {2023}, author = {Lee, EM and Srinivasan, S and Purvine, SO and Fiedler, TL and Leiser, OP and Proll, SC and Minot, SS and Deatherage Kaiser, BL and Fredricks, DN}, title = {Optimizing metaproteomics database construction: lessons from a study of the vaginal microbiome.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0067822}, pmid = {37350639}, issn = {2379-5077}, support = {P41 GM103493/GM/NIGMS NIH HHS/United States ; R01 AI061628/AI/NIAID NIH HHS/United States ; }, mesh = {Female ; Humans ; RNA, Ribosomal, 16S/genetics ; *Proteomics/methods ; *Microbiota/genetics ; Bacterial Proteins/genetics ; Peptides/metabolism ; Bacteria ; }, abstract = {Metaproteomics, a method for untargeted, high-throughput identification of proteins in complex samples, provides functional information about microbial communities and can tie functions to specific taxa. Metaproteomics often generates less data than other omics techniques, but analytical workflows can be improved to increase usable data in metaproteomic outputs. Identification of peptides in the metaproteomic analysis is performed by comparing mass spectra of sample peptides to a reference database of protein sequences. Although these protein databases are an integral part of the metaproteomic analysis, few studies have explored how database composition impacts peptide identification. Here, we used cervicovaginal lavage (CVL) samples from a study of bacterial vaginosis (BV) to compare the performance of databases built using six different strategies. We evaluated broad versus sample-matched databases, as well as databases populated with proteins translated from metagenomic sequencing of the same samples versus sequences from public repositories. Smaller sample-matched databases performed significantly better, driven by the statistical constraints on large databases. Additionally, large databases attributed up to 34% of significant bacterial hits to taxa absent from the sample, as determined orthogonally by 16S rRNA gene sequencing. We also tested a set of hybrid databases which included bacterial proteins from NCBI RefSeq and translated bacterial genes from the samples. These hybrid databases had the best overall performance, identifying 1,068 unique human and 1,418 unique bacterial proteins, ~30% more than a database populated with proteins from typical vaginal bacteria and fungi. Our findings can help guide the optimal identification of proteins while maintaining statistical power for reaching biological conclusions. IMPORTANCE Metaproteomic analysis can provide valuable insights into the functions of microbial and cellular communities by identifying a broad, untargeted set of proteins. The databases used in the analysis of metaproteomic data influence results by defining what proteins can be identified. Moreover, the size of the database impacts the number of identifications after accounting for false discovery rates (FDRs). Few studies have tested the performance of different strategies for building a protein database to identify proteins from metaproteomic data and those that have largely focused on highly diverse microbial communities. We tested a range of databases on CVL samples and found that a hybrid sample-matched approach, using publicly available proteins from organisms present in the samples, as well as proteins translated from metagenomic sequencing of the samples, had the best performance. However, our results also suggest that public sequence databases will continue to improve as more bacterial genomes are published.}, } @article {pmid37350611, year = {2023}, author = {Brennan, C and Salido, RA and Belda-Ferre, P and Bryant, M and Cowart, C and Tiu, MD and González, A and McDonald, D and Tribelhorn, C and Zarrinpar, A and Knight, R}, title = {Maximizing the potential of high-throughput next-generation sequencing through precise normalization based on read count distribution.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0000623}, pmid = {37350611}, issn = {2379-5077}, support = {R01 EB030134/EB/NIBIB NIH HHS/United States ; I01 BX005707/BX/BLRD VA/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R21 CA259921/CA/NCI NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; R01 HL134887/HL/NHLBI NIH HHS/United States ; R01 AI163483/AI/NIAID NIH HHS/United States ; U01 CA265719/CA/NCI NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; R01 HL148801/HL/NHLBI NIH HHS/United States ; }, mesh = {*Genomics/methods ; Sequence Analysis, DNA ; *Software ; Gene Library ; High-Throughput Nucleotide Sequencing ; }, abstract = {Next-generation sequencing technologies have enabled many advances across diverse areas of biology, with many benefiting from increased sample size. Although the cost of running next-generation sequencing instruments has dropped substantially over time, the cost of sample preparation methods has lagged behind. To counter this, researchers have adapted library miniaturization protocols and large sample pools to maximize the number of samples that can be prepared by a certain amount of reagents and sequenced in a single run. However, due to high variability of sample quality, over and underrepresentation of samples in a sequencing run has become a major issue in high-throughput sequencing. This leads to misinterpretation of results due to increased noise, and additional time and cost rerunning underrepresented samples. To overcome this problem, we present a normalization method that uses shallow iSeq sequencing to accurately inform pooling volumes based on read distribution. This method is superior to the widely used fluorometry methods, which cannot specifically target adapter-ligated molecules that contribute to sequencing output. Our normalization method not only quantifies adapter-ligated molecules but also allows normalization of feature space; for example, we can normalize to reads of interest such as non-ribosomal reads. As a result, this normalization method improves the efficiency of high-throughput next-generation sequencing by reducing noise and producing higher average reads per sample with more even sequencing depth. IMPORTANCE High-throughput next generation sequencing (NGS) has significantly contributed to the field of genomics; however, further improvements can maximize the potential of this important tool. Uneven sequencing of samples in a multiplexed run is a common issue that leads to unexpected extra costs or low-quality data. To mitigate this problem, we introduce a normalization method based on read counts rather than library concentration. This method allows for an even distribution of features of interest across samples, improving the statistical power of data sets and preventing the financial loss associated with resequencing libraries. This method optimizes NGS, which already has huge importance across many areas of biology.}, } @article {pmid37350224, year = {2023}, author = {Zhou, W and Fleming, E and Legendre, G and Roux, L and Latreille, J and Gendronneau, G and Forestier, S and Oh, J}, title = {Skin microbiome attributes associate with biophysical skin ageing.}, journal = {Experimental dermatology}, volume = {32}, number = {9}, pages = {1546-1556}, doi = {10.1111/exd.14863}, pmid = {37350224}, issn = {1600-0625}, support = {P30 CA034196/CA/NCI NIH HHS/United States ; R56 AG060746/AG/NIA NIH HHS/United States ; DP2 GM126893/GM/NIGMS NIH HHS/United States ; R01 AR078634/AR/NIAMS NIH HHS/United States ; R21 AR075174/AR/NIAMS NIH HHS/United States ; }, mesh = {*Skin Aging ; *Microbiota/genetics ; Bacteria ; Anti-Bacterial Agents ; Skin/microbiology ; }, abstract = {Two major arms of skin ageing are changes in the skin's biophysical conditions and alterations in the skin microbiome. This work partitioned both arms to study their interaction in detail. Leveraging the resolution provided by shotgun metagenomics, we explored how skin microbial species, strains and gene content interact with the biophysical traits of the skin during ageing. With a dataset well-controlled for confounding factors, we found that skin biophysical traits, especially the collagen diffusion coefficient, are associated with the composition and the functional potential of the skin microbiome, including the abundance of bacterial strains found in nosocomial infections and the abundance of antibiotic resistance genes. Our findings reveal important associations between skin biophysical features and ageing-related changes in the skin microbiome and generate testable hypotheses for the mechanisms of such associations.}, } @article {pmid37349979, year = {2023}, author = {Fan, G and Cao, F and Kuang, T and Yi, H and Zhao, C and Wang, L and Peng, J and Zhuang, Z and Xu, T and Luo, Y and Xie, Y and Li, H and Zhang, K and Zeng, Y and Zhang, X and Peng, S and Qiu, X and Zhou, D and Liang, H and Yang, B and Kang, J and Liu, Y and Zhang, Y}, title = {Alterations in the gut virome are associated with type 2 diabetes and diabetic nephropathy.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2226925}, pmid = {37349979}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diabetic Nephropathies ; Virome ; *Diabetes Mellitus, Type 2/complications/microbiology ; *Bacteriophages/genetics ; Bacteria/genetics ; }, abstract = {Although changes in gut microbiome have been associated with the development of T2D and its complications, the role of the gut virome remains largely unknown. Here, we characterized the gut virome alterations in T2D and its complications diabetic nephropathy (DN) by metagenomic sequencing of fecal viral-like particles. Compared with controls, T2D subjects, especially those with DN, had significantly lower viral richness and diversity. 81 viral species were identified to be significantly altered in T2D subjects, including a decrease in some phages (e.g. Flavobacterium phage and Cellulophaga phaga). DN subjects were depleted of 12 viral species, including Bacteroides phage, Anoxybacillus virus and Brevibacillus phage, and enriched in 2 phages (Shigella phage and Xylella phage). Multiple viral functions, particularly those of phage lysing host bacteria, were markedly reduced in T2D and DN. Strong viral-bacterial interactions in healthy controls were disrupted in both T2D and DN. Moreover, the combined use of gut viral and bacterial markers achieved a powerful diagnostic performance for T2D and DN, with AUC of 99.03% and 98.19%, respectively. Our results suggest that T2D and its complication DN are characterized by a significant decrease in gut viral diversity, changes in specific virus species, loss of multiple viral functions, and disruption of viral-bacterial correlations. The combined gut viral and bacterial markers have diagnostic potential for T2D and DN.}, } @article {pmid37349686, year = {2023}, author = {Li, H and Fu, J and Erlong, N and Li, R and Xu, C and Hao, L and Chen, J and Chai, W}, title = {Characterization of periprosthetic environment microbiome in patients after total joint arthroplasty and its potential correlation with inflammation.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {423}, pmid = {37349686}, issn = {1471-2334}, support = {No.82102585//Youth Project of National Natural Science Foundation of China/ ; No.2020YFC2004900//National Key Research and Development Program of China/ ; }, mesh = {Humans ; *Prosthesis-Related Infections/microbiology ; Prospective Studies ; Arthroplasty/adverse effects ; Inflammation/complications ; *Arthritis, Infectious/etiology ; *Microbiota ; Staphylococcus ; Retrospective Studies ; *Arthroplasty, Replacement, Hip/adverse effects ; Sensitivity and Specificity ; }, abstract = {AIMS: Periprosthetic joint infection (PJI) is one of the most serious complications after total joint arthroplasty (TJA) but the characterization of the periprosthetic environment microbiome after TJA remains unknown. Here, we performed a prospective study based on metagenomic next-generation sequencing to explore the periprosthetic microbiota in patients with suspected PJI.

METHODS: We recruited 28 patients with culture-positive PJI, 14 patients with culture-negative PJI, and 35 patients without PJI, which was followed by joint aspiration, untargeted metagenomic next-generation sequencing (mNGS), and bioinformatics analysis. Our results showed that the periprosthetic environment microbiome was significantly different between the PJI group and the non-PJI group. Then, we built a "typing system" for the periprosthetic microbiota based on the RandomForest Model. After that, the 'typing system' was verified externally.

RESULTS: We found the periprosthetic microbiota can be classified into four types generally: "Staphylococcus type," "Pseudomonas type," "Escherichia type," and "Cutibacterium type." Importantly, these four types of microbiotas had different clinical signatures, and the patients with the former two microbiota types showed obvious inflammatory responses compared to the latter ones. Based on the 2014 Musculoskeletal Infection Society (MSIS) criteria, clinical PJI was more likely to be confirmed when the former two types were encountered. In addition, the Staphylococcus spp. with compositional changes were correlated with C-reactive protein levels, the erythrocyte sedimentation rate, and the synovial fluid white blood cell count and granulocyte percentage.

CONCLUSIONS: Our study shed light on the characterization of the periprosthetic environment microbiome in patients after TJA. Based on the RandomForest model, we established a basic "typing system" for the microbiota in the periprosthetic environment. This work can provide a reference for future studies about the characterization of periprosthetic microbiota in periprosthetic joint infection patients.}, } @article {pmid37349537, year = {2023}, author = {Lin, L and Yi, X and Liu, H and Meng, R and Li, S and Liu, X and Yang, J and Xu, Y and Li, C and Wang, Y and Xiao, N and Li, H and Liu, Z and Xiang, Z and Shu, W and Guan, WJ and Zheng, XY and Sun, J and Wang, Z}, title = {The airway microbiome mediates the interaction between environmental exposure and respiratory health in humans.}, journal = {Nature medicine}, volume = {29}, number = {7}, pages = {1750-1759}, pmid = {37349537}, issn = {1546-170X}, mesh = {Humans ; Respiratory System ; *Pulmonary Disease, Chronic Obstructive/etiology/microbiology ; Environmental Exposure/adverse effects ; *Microbiota ; Sputum/microbiology ; }, abstract = {Exposure to environmental pollution influences respiratory health. The role of the airway microbial ecosystem underlying the interaction of exposure and respiratory health remains unclear. Here, through a province-wide chronic obstructive pulmonary disease surveillance program, we conducted a population-based survey of bacterial (n = 1,651) and fungal (n = 719) taxa and metagenomes (n = 1,128) from induced sputum of 1,651 household members in Guangdong, China. We found that cigarette smoking and higher PM2.5 concentration were associated with lung function impairment through the mediation of bacterial and fungal communities, respectively, and that exposure was associated with an enhanced inter-kingdom microbial interaction resembling the pattern seen in chronic obstructive pulmonary disease. Enrichment of Neisseria was associated with a 2.25-fold increased risk of high respiratory symptom burden, coupled with an elevation in Aspergillus, in association with occupational pollution. We developed an individualized microbiome-based health index, which covaried with exposure, respiratory symptoms and diseases, with potential generalizability to global datasets. Our results may inform environmental risk prevention and guide interventions that harness airway microbiome.}, } @article {pmid37348505, year = {2023}, author = {Carter, MM and Olm, MR and Merrill, BD and Dahan, D and Tripathi, S and Spencer, SP and Yu, FB and Jain, S and Neff, N and Jha, AR and Sonnenburg, ED and Sonnenburg, JL}, title = {Ultra-deep sequencing of Hadza hunter-gatherers recovers vanishing gut microbes.}, journal = {Cell}, volume = {186}, number = {14}, pages = {3111-3124.e13}, pmid = {37348505}, issn = {1097-4172}, support = {DP1 AT009892/AT/NCCIH NIH HHS/United States ; F32 DK128865/DK/NIDDK NIH HHS/United States ; R01 DK085025/DK/NIDDK NIH HHS/United States ; T32 AI007328/AI/NIAID NIH HHS/United States ; T32 DK007056/DK/NIDDK NIH HHS/United States ; K08 DK134856/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Metagenome ; Eukaryota ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {The gut microbiome modulates immune and metabolic health. Human microbiome data are biased toward industrialized populations, limiting our understanding of non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing on 351 fecal samples from the Hadza hunter-gatherers of Tanzania and comparative populations in Nepal and California. We recovered 91,662 genomes of bacteria, archaea, bacteriophages, and eukaryotes, 44% of which are absent from existing unified datasets. We identified 124 gut-resident species vanishing in industrialized populations and highlighted distinct aspects of the Hadza gut microbiome related to in situ replication rates, signatures of selection, and strain sharing. Industrialized gut microbes were found to be enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource, expands our understanding of microbes capable of colonizing the human gut, and clarifies the extensive perturbation induced by the industrialized lifestyle.}, } @article {pmid37348445, year = {2023}, author = {Chigwada, AD and Ogola, HJO and Tekere, M}, title = {Multivariate analysis of enriched landfill soil consortia provide insight on the community structural perturbation and functioning during low-density polyethylene degradation.}, journal = {Microbiological research}, volume = {274}, number = {}, pages = {127425}, doi = {10.1016/j.micres.2023.127425}, pmid = {37348445}, issn = {1618-0623}, mesh = {*Polyethylene/chemistry/metabolism ; *Soil ; Bacteria/genetics/metabolism ; Multivariate Analysis ; Plastics/metabolism ; Biodegradation, Environmental ; Waste Disposal Facilities ; Carbon/metabolism ; }, abstract = {Plastic-enriched sites like landfills have immense potential for discovery of microbial consortia that can efficiently degrade plastics. In this study, we used a combination of culture enrichment, high-throughput PacBio sequencing of 16 S rRNA and the ITS gene, Fourier transform infrared (FTIR), and scanning electron microscopy (SEM) to examine the compositional and diversity perturbations of bacterial and fungal consortia from landfill soils and their impact on low-density polyethylene (LDPE) film biodegradation over a 90-day period. Results showed that enrichment cultures effectively utilized LDPE as a carbon source for cellular growth, resulting in significant weight reduction (22.4% and 55.6%) in the films. SEM analysis revealed marked changes in the micrometric surface characteristics (cracks, fissures, and erosion) and biofilm formation in LDPE films. FTIR analyses suggested structural and functional group modification related to C-H (2831-2943 cm[-1]), and CH2 (1400 cm[-1]) stretching, CO and CC (680-950 cm[-1]) scission, and CO incorporation (3320-3500 cm[-1]) into the carbon backbone, indicative of LDPE polymer biodegradation. Enrichment cultures had lower diversity and richness of microbial taxa compared to soil samples, with LDPE as a carbon source having a direct influence on the structure and functioning of the microbial consortia. A total of 26 bacterial and 12 fungal OTU exhibiting high relative abundance and significant associations (IndVal > 0.7, q < 0.05) were identified in the enrichment culture. Bacterial taxa such as unclassified Parvibaculum FJ375498, Achromobacter xylosoxidans, unclassified Chitinophagaceae PAC002331, unclassified Paludisphaera and unclassified Comamonas JX898122, and six fungal species (Galactomyces candidus, Trichosporon chiropterorum, Aspergillus fumigatus, Penicillium chalabudae, Talaromyces thailandensis, and Penicillium citreosulfuratum) were identified as the putative LDPE degraders in the enrichment microbial consortium cultures. PICRUSt2 metagenomic functional profiling of taxonomic bacterial taxa abundances in both landfill soil and enrichment microbial consortia also revealed differential enrichment of energy production, stress tolerance, surface attachment and motility pathways, and xenobiotic degrading enzymes important for biofilm formation and hydrolytic/oxidative LDPE biodegradation. The findings shed light on the composition and structural changes in landfill soil microbial consortia during enrichment with LDPE as a carbon source and suggest novel LDPE-degrading bacterial and fungal taxa that could be explored for management of polyethylene pollution.}, } @article {pmid37348417, year = {2023}, author = {Peng, Y and Li, L and Yang, P and Liu, H and Ye, W and Xue, Z and Peng, X and Wang, X}, title = {Integrated genome-centric metagenomic and metaproteomic analyses unravel the responses of the microbial community to ammonia stress.}, journal = {Water research}, volume = {242}, number = {}, pages = {120239}, doi = {10.1016/j.watres.2023.120239}, pmid = {37348417}, issn = {1879-2448}, mesh = {*Propionates ; Ammonia/metabolism ; Anaerobiosis ; Metagenome ; Fatty Acids, Volatile/metabolism ; *Microbiota ; Acetates ; Butyrates ; Valerates ; Firmicutes/metabolism ; Methane/metabolism ; Bioreactors/microbiology ; }, abstract = {Ammonia is a major inhibitor in anaerobic digestion of nitrogen-rich organic wastes. In this study, integrated genome-centric metagenomic and metaproteomic analyses were used to identify the key microorganisms and metabolic links causing instability by characterizing the process performance, microbial community, and metabolic responses of key microorganisms during endogenous ammonia accumulation. The identification of 89 metagenome-assembled genomes and analysis of their abundance profile in different operational phases permitted the identification of key taxa (Firmicutes and Proteobacteria) causing poor performance. Metabolic reconstruction indicated that the key taxa had the genetic potential to participate in the metabolism of C2C5 volatile fatty acids (VFAs). Further investigation suggested that during Phase I, the total ammonia nitrogen (TAN) level was maintained below 2000 mg N/L, and the reactor showed a high methane yield (478.30 ± 33.35 mL/g VS) and low VFAs concentration. When the TAN accumulated to > 2000 mg N/L, acid accumulation, mainly of acetate, began to occur, and the methane yield gradually decreased to 330.44 mL/g VS (Phase II). During this phase, the VFA degradation functions of the community were mainly mediated by Firmicutes. Approximately 61.54% of significant differentially expressed proteins (DEPs) related to acetate metabolism in Firmicutes were down-regulated, which led to an increase in acetate concentration to 4897.91 ± 1558.96 mg/L. However, the reactor performance showed spontaneous recovery without any interference (Phase III), during which Firmicutes gradually adapted to the high ammonia conditions. Approximately 75% of the significant DEPs related to acetate metabolism of Proteobacteria were also up-regulated in Phase III compared with Phase II; thus, VFA-related metabolic functions of the community were enhanced, which resulted in a decrease in the total VFA concentration to 195.39 mg/L. When the TAN increased above 4000 mg N/L, the system gradually showed acid accumulation dominated by propionate, accompanied by a second decrease in methane yield (Phase IV). During this phase, the number of up-regulated and down-regulated proteins related to acetate metabolism of Firmicutes and butyrate/valerate metabolism of Proteobacteria was comparable with that of Phase III, indicating that the metabolic functions related to acetate, butyrate, and valerate of the microbial community were not significantly affected. However, for propionate metabolism, the expression activity of fumarate hydratase from Firmicutes and Proteobacteria was severely inhibited by ammonia, as shown by down-regulation ratios of 63.64% and 85.71%, respectively. No protein with the same function that was not inhibited by ammonia could be detected, and the fumarate degradation function of the microbial community was severely damaged, leading to blocked propionate metabolism and irreversible deterioration of reactor performance. This study has provided a new perspective on the microecological mechanisms of ammonia inhibition.}, } @article {pmid37347202, year = {2023}, author = {Osei Sekyere, J and Oyenihi, AB and Trama, J and Adelson, ME}, title = {Species-Specific Analysis of Bacterial Vaginosis-Associated Bacteria.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0467622}, pmid = {37347202}, issn = {2165-0497}, mesh = {Female ; Humans ; *Vaginosis, Bacterial/diagnosis/genetics/microbiology ; Bacteria/genetics ; Vagina/microbiology ; Metagenome ; Polymerase Chain Reaction ; }, abstract = {Vaginal dysbiosis in women reduces the abundance of Lactobacillus species and increases that of anaerobic fastidious bacteria. This dysbiotic condition in the vagina, called bacterial vaginosis (BV), can be symptomatic with odorous vaginal discharges or asymptomatic and affects a third of women of reproductive age. Three unclassified bacterial species designated BV-associated bacteria 1, 2, and 3 (BVAB-1, -2, and -3) in 2005 were found to be highly preponderant in the vagina of females with BV. Here, we used sequence homology and phylogenetics analyses to identify the actual species of BVAB-1, -2, and -3 and found BVAB-1 to be Clostridiales genomosp. BVAB-1, BVAB-2 to be Oscillospiraceae bacterium strain CHIC02, and BVAB-3 to be Mageeibacillus indolicus, respectively. These are anaerobic and uncultured species that can be identified only through metagenomics. Long-read sequencing of BV specimens can also enable a genomic reassembly of these species' genomes from metagenomes. Species-specific identification of these pathogens and the availability of their genomes from assembled metagenomes will advance our understanding of their biology, facilitate the design of sensitive diagnostics and drugs, and enhance the treatment of BV. IMPORTANCE For many years since 2005, BVAB, an important pathogen of the female vaginal tract that is associated with BV, has been identified using PCR without knowing its actual species. Without a full genome of these pathogens, a better understanding of their pathogenicity, treatment, resistance, and diagnostics cannot be reached. In this analysis, we use the DNA of BVAB-1, -2, and -3 to determine their actual species to enhance further research into their pathogenicity, resistance, diagnosis, and treatment.}, } @article {pmid37346030, year = {2023}, author = {Yu, H and Wang, Q and Tang, J and Dong, L and Dai, G and Zhang, T and Zhang, G and Xie, K and Wang, H and Zhao, Z}, title = {Comprehensive analysis of gut microbiome and host transcriptome in chickens after Eimeria tenella infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1191939}, pmid = {37346030}, issn = {2235-2988}, mesh = {Animals ; *Eimeria tenella/genetics ; Chickens/genetics ; *Gastrointestinal Microbiome/genetics ; Transcriptome ; *Poultry Diseases/genetics ; }, abstract = {BACKGROUND: Coccidiosis is an intestinal parasitic disease caused by Eimeria protozoa, which endangers the health and growth of animals, and causes huge economic losses to the poultry industry worldwide every year. Studies have shown that poultry gut microbiota plays an important role in preventing the colonization of pathogens and maintaining the health of the host. Coccidia infection also affects host gene expression. However, the underlying potential relationship between gut microbiome and host transcriptome during E. tenella infection in chickens remain unclear.

METHODS: In this study, metagenomic and transcriptome sequencing were applied to identify microbiota and genes in cecal contents and cecal tissues of infected (JS) and control (JC) chickens on day 4.5 postinfection (pi), respectively.

RESULTS: First, microbial sequencing results of cecal contents showed that the abundance of Lactobacillus, Roseburia sp. and Faecalibacterium sp decreased significantly after E. tenella infection (P < 0.05), while the abundance of Alistipes and Prevotella pectinovora increased significantly (P < 0.05). Second, transcriptome sequencing results showed that a total of 434 differentially expressed mRNAs were identified, including 196 up-regulated and 238 down-regulated genes. These differentially expressed genes related to inflammation and immunity, such as GAMA, FABP1, F2RL1 and RSAD2, may play an important role in the process of host resistance to coccidia infection. Functional studies showed that the enriched pathways of differentially expressed genes included the TGF-beta signaling pathway and the ErbB signaling pathways. Finally, the integrated analysis of gut microbiome and host transcriptome suggested that Prevotella pectinovora associated with FABP1, Butyricicoccus porcorum and Colidextribacter sp. associated with RSAD2 were involved in the immune response upon E. tenella infection.

CONCLUSION: In conclusion, this study provides valuable information on the microbiota and key immune genes after chicken E. tenella infection, with the aim of providing reference for the impact of coccidia infection on cecal microbiome and host.}, } @article {pmid37345931, year = {2023}, author = {Aldeguer-Riquelme, B and Antón, J and Santos, F}, title = {Distribution, abundance, and ecogenomics of the Palauibacterales, a new cosmopolitan thiamine-producing order within the Gemmatimonadota phylum.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0021523}, pmid = {37345931}, issn = {2379-5077}, mesh = {*Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics ; Metagenome/genetics ; Lakes ; }, abstract = {The phylum Gemmatimonadota comprises mainly uncultured microorganisms that inhabit different environments such as soils, freshwater lakes, marine sediments, sponges, or corals. Based on 16S rRNA gene studies, the group PAUC43f is one of the most frequently retrieved Gemmatimonadota in marine samples. However, its physiology and ecological roles are completely unknown since, to date, not a single PAUC43f isolate or metagenome-assembled genome (MAG) has been characterized. Here, we carried out a broad study of the distribution, abundance, ecotaxonomy, and metabolism of PAUC43f, for which we propose the name of Palauibacterales. This group was detected in 4,965 16S rRNA gene amplicon datasets, mainly from marine sediments, sponges, corals, soils, and lakes, reaching up to 34.3% relative abundance, which highlights its cosmopolitan character, mainly salt-related. The potential metabolic capabilities inferred from 52 Palauibacterales MAGs recovered from marine sediments, sponges, and saline soils suggested a facultative aerobic and chemoorganotrophic metabolism, although some members may also oxidize hydrogen. Some Palauibacterales species might also play an environmental role as N2O consumers as well as suppliers of serine and thiamine. When compared to the rest of the Gemmatimonadota phylum, the biosynthesis of thiamine was one of the key features of the Palauibacterales. Finally, we show that polysaccharide utilization loci (PUL) are widely distributed within the Gemmatimonadota so that they are not restricted to Bacteroidetes, as previously thought. Our results expand the knowledge about this cryptic phylum and provide new insights into the ecological roles of the Gemmatimonadota in the environment. IMPORTANCE Despite advances in molecular and sequencing techniques, there is still a plethora of unknown microorganisms with a relevant ecological role. In the last years, the mostly uncultured Gemmatimonadota phylum is attracting scientific interest because of its widespread distribution and abundance, but very little is known about its ecological role in the marine ecosystem. Here we analyze the global distribution and potential metabolism of the marine Gemmatimonadota group PAUC43f, for which we propose the name of Palauibacterales order. This group presents a saline-related character and a chemoorganoheterotrophic and facultatively aerobic metabolism, although some species might oxidize H2. Given that Palauibacterales is potentially able to synthesize thiamine, whose auxotrophy is the second most common in the marine environment, we propose Palauibacterales as a key thiamine supplier to the marine communities. This finding suggests that Gemmatimonadota could have a more relevant role in the marine environment than previously thought.}, } @article {pmid37345922, year = {2023}, author = {Bosch, DE and Abbasian, R and Parajuli, B and Peterson, SB and Mougous, JD}, title = {Structural disruption of Ntox15 nuclease effector domains by immunity proteins protects against type VI secretion system intoxication in Bacteroidales.}, journal = {mBio}, volume = {14}, number = {4}, pages = {e0103923}, pmid = {37345922}, issn = {2150-7511}, support = {K08 AI159619/AI/NIAID NIH HHS/United States ; K08 AI159619/AI/NIAID NIH HHS/United States ; }, abstract = {Bacteroidales use type VI secretion systems (T6SS) to competitively colonize and persist in the colon. We identify a horizontally transferred T6SS with Ntox15 family nuclease effector (Tde1) that mediates interbacterial antagonism among Bacteroidales, including several derived from a single human donor. Expression of cognate (Tdi1) or orphan immunity proteins in acquired interbacterial defense systems protects against Tde1-dependent attack. We find that immunity protein interaction induces a large effector conformational change in Tde nucleases, disrupting the active site and altering the DNA-binding site. Crystallographic snapshots of isolated Tde1, the Tde1/Tdi1 complex, and homologs from Phocaeicola vulgatus (Tde2/Tdi2) illustrate a conserved mechanism of immunity inserting into the central core of Tde, splitting the nuclease fold into two subdomains. The Tde/Tdi interface and immunity mechanism are distinct from all other polymorphic toxin-immunity interactions of known structure. Bacteroidales abundance has been linked to inflammatory bowel disease activity in prior studies, and we demonstrate that Tde and T6SS structural genes are each enriched in fecal metagenomes from ulcerative colitis subjects. Genetically mobile Tde1-encoding T6SS in Bacteroidales mediate competitive growth and may be involved in inflammatory bowel disease. Broad immunity is conferred by Tdi1 homologs through a fold-disrupting mechanism unique among polymorphic effector-immunity pairs of known structure. IMPORTANCE Bacteroidales are related to inflammatory bowel disease severity and progression. We identify type VI secretion system (T6SS) nuclease effectors (Tde) which are enriched in ulcerative colitis and horizontally transferred on mobile genetic elements. Tde-encoding T6SSs mediate interbacterial competition. Orphan and cognate immunity proteins (Tdi) prevent intoxication by multiple Tde through a new mechanism among polymorphic toxin systems. Tdi inserts into the effector central core, splitting Ntox15 into two subdomains and disrupting the active site. This mechanism may allow for evolutionary diversification of the Tde/Tdi interface as observed in colicin nuclease-immunity interactions, promoting broad neutralization of Tde by orphan Tdi. Tde-dependent T6SS interbacterial antagonism may contribute to Bacteroidales diversity in the context of ulcerative colitis.}, } @article {pmid37345698, year = {2023}, author = {Narayanan, S and Espindola, AS and Malayer, J and Cardwell, K and Ramachandran, A}, title = {Development and evaluation of Microbe Finder (MiFi)[®]: a novel in silico diagnostic platform for pathogen detection from metagenomic data.}, journal = {Journal of medical microbiology}, volume = {72}, number = {6}, pages = {}, doi = {10.1099/jmm.0.001720}, pmid = {37345698}, issn = {1473-5644}, mesh = {Animals ; Cattle ; *Metagenome ; *Metagenomics ; Genomics ; Algorithms ; Polymerase Chain Reaction ; }, abstract = {Introduction. With expanding demand for diagnostics, newer methodologies are needed for faster, user-friendly and multiplexed pathogen detection. Metagenome-based diagnostics offer potential solutions to address these needs as sequencing technologies have become affordable. However, the diagnostic utility of sequencing technologies is currently limited since analysis of the large amounts of data generated, are either computationally expensive or carry lower sensitivity and specificity for pathogen detection.Hypothesis/Gap Statement. There is a need for novel, user friendly, and computationally inexpensive platforms for metagenome sequence analysis for diagnostic applications.Methods. In this study, we report the use of MiFi[®] (Microbe Finder), a computationally inexpensive algorithm with a user-friendly online interface, for accurate, rapid and multiplexed pathogen detection from metagenome sequence data. Detection is accomplished based on identification of signature genomic sequence segments of the target pathogen in metagenome sequence data. In this study we used bovine respiratory disease (BRD) complex as a model.Results and Conclusions. Using MiFi[®], multiple target bacteria and a DNA virus were successfully detected in a multiplex format from metagenome sequences acquired from bovine lung tissue. Overall, 51 clinical samples were assessed and MiFi[®] showed 100 % analytical specificity and varying levels of analytical sensitivity (62.5 %-100 %) when compared with other traditional pathogen detection techniques, such as PCR. Consistent detection of bacteria was possible from lung samples artificially spiked with 10[9]-10[4] c.f.u. of Mannheimia haemolytica.}, } @article {pmid37345674, year = {2023}, author = {Feng, K and Zhang, H and Chen, C and Ho, CT and Kang, M and Zhu, S and Xu, J and Deng, X and Huang, Q and Cao, Y}, title = {Heptamethoxyflavone Alleviates Metabolic Syndrome in High-Fat Diet-Fed Mice by Regulating the Composition, Function, and Metabolism of Gut Microbiota.}, journal = {Journal of agricultural and food chemistry}, volume = {71}, number = {26}, pages = {10050-10064}, doi = {10.1021/acs.jafc.3c01881}, pmid = {37345674}, issn = {1520-5118}, mesh = {Mice ; Animals ; *Metabolic Syndrome/drug therapy/genetics ; *Gastrointestinal Microbiome ; Diet, High-Fat/adverse effects ; Lipid Metabolism ; Fatty Acids, Volatile/pharmacology ; Bile Acids and Salts/pharmacology ; Mice, Inbred C57BL ; }, abstract = {3,5,6,7,8,3',4'-Heptamethoxyflavone (HMF) could prevent obesity and hyperlipidemia, but its effects on gut microbiota and fecal metabolites remain unclear. Here, the effect of HMF on metabolic syndrome (MS) was evaluated in high-fat diet (HFD)-fed mice, and its underlying mechanisms were revealed by integrative metagenomic and metabolomic analyses. We demonstrated that HMF could effectively ameliorate HFD-induced MS by alleviating body-weight gain, fat accumulation, hepatic steatosis, and lipid and glucose abnormalities. HMF significantly altered the gut microbiota composition in HFD-fed mice with enrichment of short-chain fatty acid (SCFA)- and bile acid-producing beneficial bacteria and inhibition of harmful bacteria. Also, HMF improved microbial functions by up-regulating bile acid metabolism and down-regulating fatty acid metabolism and inflammatory response-related pathways. Consistent with the gut microbial changes, HMF altered the fecal metabolite profile of HFD-fed mice, mainly characterized by increasing SCFA and several bile acid levels as well as lowering several lysophospholipids and fatty acid levels. Correlation analysis indicated that three key species Faecalibaculum rodentium, Collinsella aerofaciens, and Lactobacillus fermentum and the increase in microbial metabolites, i.e., SCFAs and secondary bile acids, might play a positive role in alleviating MS. Our results suggested that HMF alleviated HFD-induced MS possibly by modulating the composition, function, and metabolism of gut microbiota.}, } @article {pmid37345233, year = {2023}, author = {Shtossel, O and Isakov, H and Turjeman, S and Koren, O and Louzoun, Y}, title = {Ordering taxa in image convolution networks improves microbiome-based machine learning accuracy.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2224474}, pmid = {37345233}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Artificial Intelligence ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Machine Learning ; }, abstract = {The human gut microbiome is associated with a large number of disease etiologies. As such, it is a natural candidate for machine-learning-based biomarker development for multiple diseases and conditions. The microbiome is often analyzed using 16S rRNA gene sequencing or shotgun metagenomics. However, several properties of microbial sequence-based studies hinder machine learning (ML), including non-uniform representation, a small number of samples compared with the dimension of each sample, and sparsity of the data, with the majority of taxa present in a small subset of samples. We show here using a graph representation that the cladogram structure is as informative as the taxa frequency. We then suggest a novel method to combine information from different taxa and improve data representation for ML using microbial taxonomy. iMic (image microbiome) translates the microbiome to images through an iterative ordering scheme, and applies convolutional neural networks to the resulting image. We show that iMic has a higher precision in static microbiome gene sequence-based ML than state-of-the-art methods. iMic also facilitates the interpretation of the classifiers through an explainable artificial intelligence (AI) algorithm to iMic to detect taxa relevant to each condition. iMic is then extended to dynamic microbiome samples by translating them to movies.}, } @article {pmid37345006, year = {2023}, author = {Vadhwana, B and Tarazi, M and Boshier, PR and Hanna, GB}, title = {Evaluation of the Oesophagogastric Cancer-Associated Microbiome: A Systematic Review and Quality Assessment.}, journal = {Cancers}, volume = {15}, number = {10}, pages = {}, pmid = {37345006}, issn = {2072-6694}, abstract = {OBJECTIVE: Oesophagogastric cancer is the fifth most common cancer worldwide, with poor survival outcomes. The role of bacteria in the pathogenesis of oesophagogastric cancer remains poorly understood.

DESIGN: A systematic search identified studies assessing the oesophagogastric cancer microbiome. The primary outcome was to identify bacterial enrichment specific to oesophagogastric cancer. Secondary outcomes included appraisal of the methodology, diagnostic performance of cancer bacteria and the relationship between oral and tissue microbiome.

RESULTS: A total of 9295 articles were identified, and 87 studies were selected for analysis. Five genera were enriched in gastric cancer: Lactobacillus, Streptococcus, Prevotella, Fusobacterium and Veillonella. No clear trends were observed in oesophageal adenocarcinoma. Streptococcus, Prevotella and Fusobacterium were abundant in oesophageal squamous cell carcinoma. Functional analysis supports the role of immune cells, localised inflammation and cancer-specific pathways mediating carcinogenesis. STORMS reporting assessment identified experimental deficiencies, considering batch effects and sources of contamination prevalent in low-biomass samples.

CONCLUSIONS: Functional analysis of cancer pathways can infer tumorigenesis within the cancer-microbe-immune axis. There is evidence that study design, experimental protocols and analytical techniques could be improved to achieve more accurate and representative results. Whole-genome sequencing is recommended to identify key metabolic and functional capabilities of candidate bacteria biomarkers.}, } @article {pmid37344611, year = {2023}, author = {Acar, C and Celik, SK and Ozdemirel, HO and Tuncdemir, BE and Alan, S and Mergen, H}, title = {Composition of the colon microbiota in the individuals with inflammatory bowel disease and colon cancer.}, journal = {Folia microbiologica}, volume = {}, number = {}, pages = {}, pmid = {37344611}, issn = {1874-9356}, support = {FCD-2020-2065//Inönü Üniversitesi/ ; }, abstract = {The human intestine is a habitat for microorganisms and, recently, the composition of the intestinal microbiota has been correlated with the etiology of diseases such as inflammations, sores, and tumors. Although many studies have been conducted to understand the composition of that microbiota, expanding these studies to more samples and different backgrounds will improve our knowledge. In this work, we showed the colon microbiota composition and diversity of healthy subjects, patients with inflammatory bowel disease (IBD), and colon cancer by metagenomic sequencing. Our results indicated that the relative abundance of prokaryotic and eukaryotic microbes differs between the healthy vs. tumor biopsies, tumor vs. IBD biopsies, and fresh vs. paraffin-embedded tumor biopsies. Fusobacterium, Escherichia-Shigella, and Streptococcus genera were relatively abundant in fresh tumor biopsies, while Pseudomonas was significantly elevated in IBD biopsies. Additionally, another opportunist pathogen Malasseziales was revealed as the most abundant fungal clade in IBD biopsies, especially in ulcerative colitis. We also found that, while the Basidiomycota:Ascomycota ratio was slightly lower in tumor biopsies compared to biopsies from healthy subjects, there was a significant increase in IBD biopsies. Our work will contribute to the known diversity of prokaryotic and eukaryotic microbes in the colon biopsies in patients with IBD and colon cancer.}, } @article {pmid37344105, year = {2023}, author = {Rahman Hera, M and Pierce-Ward, NT and Koslicki, D}, title = {Deriving confidence intervals for mutation rates across a wide range of evolutionary distances using FracMinHash.}, journal = {Genome research}, volume = {33}, number = {7}, pages = {1061-1068}, pmid = {37344105}, issn = {1549-5469}, support = {R01 GM146462/GM/NIGMS NIH HHS/United States ; }, mesh = {*Mutation Rate ; Confidence Intervals ; *Biological Evolution ; Metagenome ; Metagenomics/methods ; }, abstract = {Sketching methods offer computational biologists scalable techniques to analyze data sets that continue to grow in size. MinHash is one such technique to estimate set similarity that has enjoyed recent broad application. However, traditional MinHash has previously been shown to perform poorly when applied to sets of very dissimilar sizes. FracMinHash was recently introduced as a modification of MinHash to compensate for this lack of performance when set sizes differ. This approach has been successfully applied to metagenomic taxonomic profiling in the widely used tool sourmash gather. Although experimental evidence has been encouraging, FracMinHash has not yet been analyzed from a theoretical perspective. In this paper, we perform such an analysis to derive various statistics of FracMinHash, and prove that although FracMinHash is not unbiased (in the sense that its expected value is not equal to the quantity it attempts to estimate), this bias is easily corrected for both the containment and Jaccard index versions. Next, we show how FracMinHash can be used to compute point estimates as well as confidence intervals for evolutionary mutation distance between a pair of sequences by assuming a simple mutation model. We also investigate edge cases in which these analyses may fail to effectively warn the users of FracMinHash indicating the likelihood of such cases. Our analyses show that FracMinHash estimates the containment of a genome in a large metagenome more accurately and more precisely compared with traditional MinHash, and the point estimates and confidence intervals perform significantly better in estimating mutation distances.}, } @article {pmid37344007, year = {2023}, author = {Panneerselvam, P and Senapati, A and Chidambaranathan, P and Prabhukarthikeyan, SR and Mitra, D and Pandi Govindharaj, GP and Nayak, AK and Anandan, A}, title = {Long-term impact of pulses crop rotation on soil fungal diversity in aerobic and wetland rice cultivation.}, journal = {Fungal biology}, volume = {127}, number = {6}, pages = {1053-1066}, doi = {10.1016/j.funbio.2023.04.005}, pmid = {37344007}, issn = {1878-6146}, mesh = {Soil ; *Oryza ; Wetlands ; *Ascomycota ; Crop Production ; Soil Microbiology ; }, abstract = {Pulse crop rotation in rice cultivation is a widely accepted agronomic practice. Depending upon the water regime, rice cultivation has been classified into wetland and aerobic practices. However, no studies have been conducted so far to understand the impact of pulse crop rotation and rice mono-cropping on fungal diversity, particularly in aerobic soil. A targeted metagenomic study was conducted to compare the effects of crop rotations (rice-rice and rice-pulse) on fungal diversity in wetland and aerobic rice soils. Out of 445 OTUs, 41.80% was unknown and 58.20% were assigned to six phyla, namely Ascomycota (56.57%), Basidiomycota (1.32%), Zygomycota (0.22%), Chytridiomycota (0.04%), Glomeromycota (0.03%), and Blastocladiomycota (0.02%). Functional trait analysis found wetland rice-pulse rotation increased symbiotrophs (36.7%) and saprotrophs (62.1%) population, whereas higher pathotrophs were found in aerobic rice-rice (62.8%) and rice-pulse (61.4%) cropping system. Certain soil nutrients played a major role in shaping the fungal community; Ca had significant (p < 0.05) positive impact on saprotroph, symbiotroph and endophytes, whereas Cu had significant (p < 0.05) negative impact on pathotrophs. This study showed that rice-pulse crop rotation could enhance the saprophytic and symbiotic fungal diversity in wetland and reduce the population of pathogens in aerobic rice cultivation.}, } @article {pmid37343864, year = {2023}, author = {Zhao, W and Chen, Z and Yang, X and Sheng, L and Mao, H and Zhu, S}, title = {Metagenomics reveal arbuscular mycorrhizal fungi altering functional gene expression of rhizosphere microbial community to enhance Iris tectorum's resistance to Cr stress.}, journal = {The Science of the total environment}, volume = {895}, number = {}, pages = {164970}, doi = {10.1016/j.scitotenv.2023.164970}, pmid = {37343864}, issn = {1879-1026}, mesh = {*Mycorrhizae/physiology ; *Iris Plant ; Chromium/analysis ; Plant Roots/microbiology ; Rhizosphere ; Metagenomics ; *Metals, Heavy/analysis ; Soil/chemistry ; *Microbiota ; Gene Expression ; Soil Microbiology ; Fungi ; }, abstract = {Chromium (Cr) can disrupt a plant's normal physiological and metabolic functions and severely impact the microenvironment. However, limited studies have investigated the impact of arbuscular mycorrhizal fungi (AMF) inoculation on the rhizosphere microorganisms of Iris tectorum under Cr stress, and the mechanisms of how rhizosphere microorganisms interact with hosts and contaminants. In this study, we investigated the effects of AMF inoculation on the growth, absorption of nutrients and heavy metals, and functional genes of the rhizosphere microbial community of I. tectorum under Cr stress in a greenhouse pot experiment. The results showed that AMF significantly increased the biomass and nutrient levels of I. tectorum, while decreasing the content of Cr in soil. Furthermore, metagenome analysis demonstrated significant changes in the structure and composition of the rhizosphere microbial community after AMF formed a mycorrhizal symbiosis system with the I. tectorum. Specifically, the abundance of functional genes related to nutrient cycling (N, P) and heavy metal resistance (chrA and arsB), as well as the abundance of heavy metal transporter family (P-atPase, MIT, CDF, and ABC) in the rhizosphere microbial community were up-regulated and their expression. Additionally, the synergies between rhizosphere microbial communities were regulated, and the complexity and stability of the rhizosphere microbial ecological network were enhanced. This study provides evidence that AMF can regulate rhizosphere microbial communities to improve plant growth and heavy metal stress tolerance, and helps us to understand the potential mechanism of wetland plant remediation of Cr-contaminated soil under AMF symbiosis.}, } @article {pmid37343848, year = {2023}, author = {Xin, Y and Wu, Y and Zhang, H and Li, X and Qu, X}, title = {Soil depth exerts a stronger impact on microbial communities and the sulfur biological cycle than salinity in salinized soils.}, journal = {The Science of the total environment}, volume = {894}, number = {}, pages = {164898}, doi = {10.1016/j.scitotenv.2023.164898}, pmid = {37343848}, issn = {1879-1026}, mesh = {*Soil/chemistry ; Salinity ; Soil Microbiology ; Bacteria/genetics ; *Microbiota ; Sulfur ; Sulfur Compounds ; }, abstract = {The distribution of microbial communities along salinity gradients in the surface layer of salinized soils has been widely studied. However, it is unknown whether microbial communities exhibit similar distribution patterns in surface and deep soils. Additionally, the relationship between soil depth, salinity, and sulfur metabolism remains unclear. Herein, bulk soils in the surface (S, 5-10 cm) and deep (D, 20-25 cm) layers from high- and low-salinity soils were analyzed using metagenomic and physicochemical analyses. Soil depth was significantly correlated to the concentration of sulfur compounds in the soil and exerted a stronger effect than salinity. Non-metric multidimensional scaling analysis revealed significant differences in microbial community structure with varying soil depths and salinities. However, soil depth clearly influenced microbial community abundance, homogeneity, and diversity, while salinity had a limited effect on microbial abundance. Archaea and bacteria were enriched in the surface and deep soils, respectively. Gene abundance analysis revealed significant differences in the abundance of sulfur-related genes at different soil depths. The abundance of sulfur oxidation genes was lower in deep soil than in surface soil, whereas the abundance of other sulfur-related genes showed the opposite trend. Redundancy analysis (RDA) showed that environmental factors and sulfur compounds have a significant impact on sulfur metabolism genes, with sulfide significantly affecting low-salinity soils in the surface and deep layers, whereas salinity and sulfane sulfur had a greater correlation with high-salinity soils. Correlation analysis further showed that Euryarchaeota clustered with Bacteroidetes and Balneolaeota, while Proteobacteria clustered with many phyla, such as Acidobacteria. Various sulfur metabolism genes were widely distributed in both clusters. Our results indicate that microorganisms actively participate in the sulfur cycle in saline soils and that soil depth can affect these processes and the structure of microbial communities to a greater extent than soil salinity.}, } @article {pmid37343443, year = {2023}, author = {Hu, L and Cheng, N and Wang, Y and Zhang, D and Xu, K and Lv, X and Long, Y}, title = {Arsenate microbial reducing behavior regulated by the temperature fields in landfills.}, journal = {Waste management (New York, N.Y.)}, volume = {168}, number = {}, pages = {366-375}, doi = {10.1016/j.wasman.2023.06.020}, pmid = {37343443}, issn = {1879-2456}, mesh = {*Arsenates/metabolism ; Temperature ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Waste Disposal Facilities ; *Arsenic ; }, abstract = {Attention should be paid to the As(V) reducing behavior in landfills under different temperature fields. In this study, microcosm tests were conducted using enrichment culture from a landfill. The results revealed that the reduction rate of As(V) was significantly affected by the temperature field, with the highest reduction rate observed at 50 °C, followed by 35 °C, 25 °C, and 10 °C. Different As cycling pathways were observed under various temperature fields. At room and medium temperatures, As4S4 was detected, indicating that both biomineralization and methylation processes occurred after As(V) reduction. However, only biogenic methylation was observed under high or low temperatures, indicating that the viability and adaptability of microorganisms varied depending on the temperature field and As contents. Pseudomonas was found to be the primary genus and dominant As(V) reduction bacteria (ARB) in all reactors. The study revealed that Pseudomonas accounted for a significant proportion of arsC genes, ranging from 87.29% to 97.59%, while arsCs genes were predominantly found in Bacillales and Closestridiales, with a contribution ranging from 89.17% to 96.59%. Interestingly, Bacillus and Clostridium were found to possess arsA genes in their metagenome-ssembled genome, resulting in a higher As(V) reducing rate under medium and high temperatures. These findings underscore the importance of temperature in modulating As(V) reducing behavior and As cycling, and could have implications for managing As pollution in landfill sites.}, } @article {pmid37343363, year = {2023}, author = {Kang, X and Ng, SK and Liu, C and Lin, Y and Zhou, Y and Kwong, TNY and Ni, Y and Lam, TYT and Wu, WKK and Wei, H and Sung, JJY and Yu, J and Wong, SH}, title = {Altered gut microbiota of obesity subjects promotes colorectal carcinogenesis in mice.}, journal = {EBioMedicine}, volume = {93}, number = {}, pages = {104670}, pmid = {37343363}, issn = {2352-3964}, mesh = {Humans ; Mice ; Animals ; *Gastrointestinal Microbiome ; *Colonic Neoplasms ; Carcinogenesis ; Obesity/complications ; Azoxymethane/toxicity ; *Colorectal Neoplasms/genetics ; Mice, Inbred C57BL ; Disease Models, Animal ; }, abstract = {BACKGROUND: Obesity is a risk factor for colorectal cancer (CRC). The role of gut microbiota in mediating the cancer-promoting effect of obesity is unknown.

METHODS: Azoxymethane (AOM)-treated, Apc[Min/+] and germ-free mice were gavaged with feces from obese individuals and control subjects respectively. The colonic tumor load and number were recorded at the endpoint in two carcinogenic models. The gut microbiota composition and colonic transcriptome were assessed by metagenomic sequencing and RNA sequencing, respectively. The anticancer effects of bacteria depleted in fecal samples of obese individuals were validated.

FINDINGS: Conventional AOM-treated and Apc[Min/+] mice receiving feces from obese individuals showed significantly increased colon tumor formation compared with those receiving feces from control subjects. AOM-treated mice receiving feces from obese individuals showed impaired intestinal barrier function and significant upregulation of pro-inflammatory cytokines and activation of oncogenic Wnt signaling pathway. Consistently, transferring feces from obese individuals to germ-free mice led to increased colonic cell proliferation, intestinal barrier function impairment, and induction of oncogenic and proinflammatory gene expression. Moreover, germ-free mice transplanted with feces from obese human donors had increased abundance of potential pathobiont Alistipes finegoldii, and reduced abundance of commensals Bacteroides vulgatus and Akkermansia muciniphila compared with those receiving feces from human donors with normal body mass index (BMI). Validation experiments showed that B. vulgatus and A. muciniphila demonstrated anti-proliferative effects in CRC, while A. finegoldii promoted CRC tumor growth.

INTERPRETATION: Our results supported the role of obesity-associated microbiota in colorectal carcinogenesis and identified putative bacterial candidates that may mediate its mechanisms. Microbiota modulation in obese individuals may provide new approaches to prevent or treat obesity-related cancers including CRC.

FUNDING: This work was funded by National Key Research and Development Program of China (2020YFA0509200/2020YFA0509203), National Natural Science Foundation of China (81922082), RGC Theme-based Research Scheme Hong Kong (T21-705/20-N), RGC Research Impact Fund Hong Kong (R4632-21F), RGC-CRF Hong Kong (C4039-19GF and C7065-18GF), RGC-GRF Hong Kong (14110819, 14111621), and NTU Start-Up Grant (021337-00001).}, } @article {pmid37343220, year = {2023}, author = {Bradley, JS and Hajama, H and Akong, K and Jordan, M and Stout, D and Rowe, RS and Conrad, DJ and Hingtgen, S and Segall, AM}, title = {Bacteriophage Therapy of Multidrug-resistant Achromobacter in an 11-Year-old Boy With Cystic Fibrosis Assessed by Metagenome Analysis.}, journal = {The Pediatric infectious disease journal}, volume = {42}, number = {9}, pages = {754-759}, doi = {10.1097/INF.0000000000004000}, pmid = {37343220}, issn = {1532-0987}, support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; }, mesh = {Male ; Humans ; Child ; *Cystic Fibrosis/therapy/drug therapy ; Metagenome ; *Phage Therapy ; *Achromobacter/genetics ; Prospective Studies ; Anti-Bacterial Agents/therapeutic use ; Sputum/microbiology ; }, abstract = {BACKGROUND: Cystic fibrosis (CF) is a genetic disease associated with lung disease characterized by chronic pulmonary infection, increasingly caused by multiple drug-resistant pathogens after repeated antibiotic exposure, limiting antibiotic treatment options. Bacteriophages can provide a pathogen-specific bactericidal treatment used with antibiotics to improve microbiologic and clinical outcomes in CF.

METHODS: Achromobacter species isolates from sputum of a chronically infected person with CF, were assessed for susceptibility to bacteriophages: 2 highly active, purified bacteriophages were administered intravenously every 8 hours, in conjunction with a 14-day piperacillin/tazobactam course for CF exacerbation. Sputum and blood were collected for metagenome analysis during treatment, with sputum analysis at 1-month follow-up. Assessments of clinical status, pulmonary status and laboratory evaluation for safety were conducted.

RESULTS: Bacteriophage administration was well-tolerated, with no associated clinical or laboratory adverse events. Metagenome analysis documented an 86% decrease in the relative proportion of Achromobacter DNA sequence reads in sputum and a 92% decrease in blood, compared with other bacterial DNA reads, comparing pretreatment and posttreatment samples. Bacteriophage DNA reads were detected in sputum after intravenous administration during treatment, and at 1-month follow-up. Reversal of antibiotic resistance to multiple antibiotics occurred in some isolates during treatment. Stabilization of lung function was documented at 1-month follow-up.

CONCLUSIONS: Bacteriophage/antibiotic treatment decreased the host pulmonary bacterial burden for Achromobacter assessed by metagenome analysis of sputum and blood, with ongoing bacteriophage replication documented in sputum at 1-month follow-up. Prospective controlled studies are needed to define the dose, route of administration and duration of bacteriophage therapy for both acute and chronic infection in CF.}, } @article {pmid37342884, year = {2023}, author = {Colson, P and Penant, G and Delerce, J and Boschi, C and Wurtz, N and Bedotto, M and Branger, S and Brouqui, P and Parola, P and Lagier, JC and Cassir, N and Tissot-Dupont, H and Million, M and Aherfi, S and La Scola, B}, title = {Sequencing of monkeypox virus from infected patients reveals viral genomes with APOBEC3-like editing, gene inactivation, and bacterial agents of skin superinfection.}, journal = {Journal of medical virology}, volume = {95}, number = {6}, pages = {e28799}, doi = {10.1002/jmv.28799}, pmid = {37342884}, issn = {1096-9071}, mesh = {Humans ; Monkeypox virus/genetics ; *Superinfection ; *Mpox (monkeypox) ; Genome, Viral ; Gene Silencing ; APOBEC Deaminases/genetics ; }, abstract = {A large outbreak of Monkeypox virus (MPXV) infections has arisen in May 2022 in nonendemic countries. Here, we performed DNA metagenomics using next-generation sequencing with Illumina or Nanopore technologies for clinical samples from MPXV-infected patients diagnosed between June and July 2022. Classification of the MPXV genomes and determination of their mutational patterns were performed using Nextclade. Twenty-five samples from 25 patients were studied. A MPXV genome was obtained for 18 patients, essentially from skin lesions and rectal swabbing. All 18 genomes were classified in clade IIb, lineage B.1, and we identified four B.1 sublineages (B.1.1, B.1.10, B.1.12, B.1.14). We detected a high number of mutations (range, 64-73) relatively to a 2018 Nigerian genome (genome GenBank Accession no. NC_063383.1), which were harbored by a large part of a set of 3184 MPXV genomes of lineage B.1 recovered from GenBank and Nextstrain; and we detected 35 mutations relatively to genome ON563414.3 (a B.1 lineage reference genome). Nonsynonymous mutations occurred in genes encoding central proteins, among which transcription factors and core and envelope proteins, and included two mutations that would truncate a RNA polymerase subunit and a phospholipase d-like protein, suggesting an alternative start codon and gene inactivation, respectively. A large majority (94%) of nucleotide substitutions were G > A or C > U, suggesting the action of human APOBEC3 enzymes. Finally, >1000 reads were identified as from Staphylococcus aureus and Streptococcus pyogenes for 3 and 6 samples, respectively. These findings warrant a close genomic monitoring of MPXV to get a better picture of the genetic micro-evolution and mutational patterns of this virus, and a close clinical monitoring of skin bacterial superinfection in monkeypox patients.}, } @article {pmid37342535, year = {2023}, author = {Carrizales-Sánchez, AK and Tamez-Rivera, O and García-Gamboa, R and García-Cayuela, T and Rodríguez-Gutiérrez, NA and Elizondo-Montemayor, L and García-Rivas, G and Pacheco, A and Hernández-Brenes, C and Senés-Guerrero, C}, title = {Gut microbial composition and functionality of school-age Mexican population with metabolic syndrome and type-2 diabetes mellitus using shotgun metagenomic sequencing.}, journal = {Frontiers in pediatrics}, volume = {11}, number = {}, pages = {1193832}, pmid = {37342535}, issn = {2296-2360}, abstract = {Gut metagenome in pediatric subjects with metabolic syndrome (MetS) and type-2 diabetes mellitus (T2DM) has been poorly studied, despite an alarming worldwide increase in the prevalence and incidence of obesity and MetS within this population. The objective of this study was to characterize the gut microbiome taxonomic composition of Mexican pediatric subjects with MetS and T2DM using shotgun metagenomics and analyze the potential relationship with metabolic changes and proinflammatory effects. Paired-end reads of fecal DNA samples were obtained through the Illumina HiSeq X Platform. Statistical analyses and correlational studies were conducted using gut microbiome data and metadata from all individuals. Gut microbial dysbiosis was observed in MetS and T2DM children compared to healthy subjects, which was characterized by an increase in facultative anaerobes (i.e., enteric and lactic acid bacteria) and a decrease in strict anaerobes (i.e., Erysipelatoclostridium, Shaalia, and Actinomyces genera). This may cause a loss of gut hypoxic environment, increased gut microbial nitrogen metabolism, and higher production of pathogen-associated molecular patterns. These metabolic changes may trigger the activation of proinflammatory activity and impair the host's intermediate metabolism, leading to a possible progression of the characteristic risk factors of MetS and T2DM, such as insulin resistance, dyslipidemia, and an increased abdominal circumference. Furthermore, specific viruses (Jiaodavirus genus and Inoviridae family) showed positive correlations with proinflammatory cytokines involved in these metabolic diseases. This study provides novel evidence for the characterization of MetS and T2DM pediatric subjects in which the whole gut microbial composition has been characterized. Additionally, it describes specific gut microorganisms with functional changes that may influence the onset of relevant health risk factors.}, } @article {pmid37342148, year = {2023}, author = {Gugliucci, W and Cirillo, V and Maggio, A and Romano, I and Ventorino, V and Pepe, O}, title = {Valorisation of hydrothermal liquefaction wastewater in agriculture: effects on tobacco plants and rhizosphere microbiota.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1180061}, pmid = {37342148}, issn = {1664-462X}, abstract = {Industrial wastewater obtained from hydrothermal liquefaction (HTL-WW) of food wastes for biofuels production could represent a source of crop nutrients since it is characterized by a high amount of organic and inorganic compounds. In the present work, the potential use of HTL-WW as irrigation water for industrial crops was investigated. The composition of the HTL-WW was rich in nitrogen, phosphorus, and potassium with high level of organic carbon. A pot experiment with Nicotiana tabacum L. plants was conducted using diluted wastewater to reduce the concentration of some chemical elements below the official accepted threshold values. Plants were grown in the greenhouse under controlled conditions for 21 days and irrigated with diluted HTL-WW every 24 hours. Soils and plants were sampled every seven days to evaluate, over time, the effect of wastewater irrigation both on soil microbial populations, through high-throughput sequencing, and plant growth parameters, through the measurement of different biometric indices. Metagenomic results highlighted that, in the HTL-WW treated rhizosphere, the microbial populations shifted via their mechanisms of adaptation to the new environmental conditions, establishing a new balance among bacterial and fungal communities. Identification of microbial taxa occurring in the rhizosphere of tobacco plants during the experiment highlighted that the HTL-WW application improved the growth of Micrococcaceae, Nocardiaceae and Nectriaceae, which included key species for denitrification, organic compounds degradation and plant growth promotion. As a result, irrigation with HTL-WW improved the overall performance of tobacco plants which showed higher leaf greenness and increased number of flowers compared to irrigated control plants. Overall, these results demonstrate the potential feasibility of using of HTL-WW in irrigated agriculture.}, } @article {pmid37341942, year = {2023}, author = {Li, X and Zhang, M and Dang, C and Wu, Z and Xia, Y}, title = {In situ Nanopore sequencing reveals metabolic characteristics of the Qilian glacier meltwater microbiome.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {35}, pages = {84805-84813}, pmid = {37341942}, issn = {1614-7499}, support = {42277103//National Natural Science Foundation of China/ ; 42177357//National Natural Science Foundation of China/ ; }, mesh = {Ice Cover ; *Nanopore Sequencing ; China ; Lakes ; *Microbiota ; }, abstract = {Nanopore metagenomic sequencing enables rapid annotating microbiological ecosystems, and the previous glacier-related sequencing applications (e.g., targeted ice sheets, ice lake, and cryoconite holes) inspire us to explore high-altitude glacier meltwater at Qilian Mountain, China (3000 to 4000 m above sea level, MASL). Our findings suggest that (1) despite only several hundred meters apart, the microbial communities and functionalities are quite different among vertical alpine distributions; (2) the high-altitude Qilian meltwater microbiome serve several main metabolic functions, including sulfur oxidation, selenite decomposing, photosynthesis, energy production, enzymic, and UV tolerant activities. Meanwhile, our Nanopore metagenomic results indicate that the microbial classifications and functionalities (e.g., chaperones, cold-shock, specific tRNA species, oxidative stress, and resistance to toxic compounds) of Qilian meltwater are highly consistent with the other glacial microbiome, emphasizing that only certain microbial species can survive in the cold environment and the molecular adaptions and lifestyles remain stable all over the world. Besides, we have shown Nanopore metagenomic sequencing can provide reliable prokaryotic classifications within or among studies, which therefore can encourage more applications in the field given faster turnaround time. However, we recommend accumulating at least 400 ng nucleic acids (after extraction) and maximizing Nanopore library preparation efficiency before on-site sequencing to obtain better resolutions.}, } @article {pmid37341802, year = {2023}, author = {Bukin, YS and Mikhailov, IS and Petrova, DP and Galachyants, YP and Zakharova, YR and Likhoshway, YV}, title = {The effect of metabarcoding 18S rRNA region choice on diversity of microeukaryotes including phytoplankton.}, journal = {World journal of microbiology & biotechnology}, volume = {39}, number = {9}, pages = {229}, pmid = {37341802}, issn = {1573-0972}, support = {project no. 0279-2021-0009//Ministry of Science and Higher Education of Russian Federation project "Study of the role of selected genes and proteins of Baikal diatoms by methods of bioinformatics and physicochemical biology"/ ; }, mesh = {*Phytoplankton/genetics ; RNA, Ribosomal, 18S/genetics ; *Ecosystem ; Algorithms ; High-Throughput Nucleotide Sequencing ; }, abstract = {Metabarcoding using high throughput sequencing of amplicons of the 18S rRNA gene is one of the widely used methods for assessing the diversity of microeukaryotes in various ecosystems. We investigated the effectiveness of the V4 and V8-V9 regions of the 18S rRNA gene by comparing the results of metabarcoding microeukaryotic communities using the DADA2 (ASV), USEARCH-UNOISE3 (ZOTU), and USEARCH-UPARSE (OTU with 97% similarity) algorithms. Both regions showed similar levels of genetic variability and taxa identification accuracy. Richness for DADA2 datasets of both regions was lower than for UNOISE3 and UPARSE datasets, which is due to more accurate error correction in amplicons. Microeukaryotic communities (autotrophs and heterotrophs) structure identified using both regions showed a significant relationship with phytoplankton (autotrophs) communities structure based on microscopy in a seasonal freshwater sample series. The strongest relationship was found between the phytoplankton species and V8-V9 ASVs produced by DADA2.}, } @article {pmid37340305, year = {2023}, author = {Cannon, A and McMillan, O and Kelley, WV and East, KM and Cochran, ME and Miskell, EL and Moss, IP and Garner-Duckworth, S and Redden, DT and Might, M and Barsh, GS and Korf, BR}, title = {Medical and psychosocial outcomes of state-funded population genomic screening.}, journal = {Clinical genetics}, volume = {104}, number = {4}, pages = {434-442}, doi = {10.1111/cge.14394}, pmid = {37340305}, issn = {1399-0004}, support = {UL1 TR003096/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Humans ; *Metagenomics ; *Genomics ; Genetic Testing ; }, abstract = {As the uptake of population screening expands, assessment of medical and psychosocial outcomes is needed. Through the Alabama Genomic Health Initiative (AGHI), a state-funded genomic research program, individuals received screening for pathogenic or likely pathogenic variants in 59 actionable genes via genotyping. Of the 3874 eligible participants that received screening results, 858 (22%) responded to an outcomes survey. The most commonly reported motivation for seeking testing through AGHI was contribution to genetic research (64%). Participants with positive results reported a higher median number of planned actions (median = 5) due to AGHI results as compared to negative results (median = 3). Interviews were conducted with survey participants with positive screening results. As determined by certified genetic counselors, 50% of interviewees took appropriate medical action based on their result. There were no negative or harmful actions taken. These findings indicate population genomic screening of an unselected adult population is feasible, is not harmful, and may have positive outcomes on participants now and in the future; however, further research is needed in order to assess clinical utility.}, } @article {pmid37340081, year = {2023}, author = {Yang, C and Xu, J and Xu, X and Xu, W and Tong, B and Wang, S and Ji, R and Tan, Y and Zhu, Y}, title = {Characteristics of gut microbiota in patients with metabolic associated fatty liver disease.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {9988}, pmid = {37340081}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Carcinoma, Hepatocellular ; RNA, Ribosomal, 16S/genetics ; *Liver Neoplasms ; *Microbiota ; *Non-alcoholic Fatty Liver Disease ; Bacteroidetes ; Clostridiaceae ; }, abstract = {Metabolic associated fatty liver disease (MAFLD) is rising in incidence and is an increasingly common cause of cirrhosis and hepatocellular carcinoma (HCC). Alterations in the gut microbiota have been shown to correlate with the development and progression of MAFLD. However, little is known regarding differences in the gut microbiomes of MAFLD patients and healthy cohorts, and subgroups at the abnormal activity of hepatic enzymes in China. In this study, we enrolled 81 MAFLD patients and 25 healthy volunteers. The fecal microbiota was assessed using 16S rRNA gene sequencing and metagenomic sequencing. The results suggested that Ruminococcus obeum and Alistipes were most enriched in healthy individuals when compared with MAFLD patients. Microbe-set Enrichment Analysis (MSEA) results showed Dorea, Lactobacillus and Megasphaera are enriched in MAFLD group. We also found that Alistipes has negatively related to serum glucose (GLU), gamma-glutamyl transferase (GGT), and alanine aminotransferase (ALT). Moreover, the abundance of Dorea was found to be significantly overrepresented in the MAFLD patients and the degree of enrichment increased with the increasing abnormal liver enzyme. An increase in Dorea, combined with decreases in Alistipes appears to be characteristic of MAFLD patients. Further study of microbiota may provide a novel insight into the pathogenesis of MAFLD as well as a novel treatment strategy.}, } @article {pmid37339968, year = {2023}, author = {Narat, V and Salmona, M and Kampo, M and Heyer, T and Rachik, AS and Mercier-Delarue, S and Ranger, N and Rupp, S and Ambata, P and Njouom, R and Simon, F and Le Goff, J and Giles-Vernick, T}, title = {Higher convergence of human-great ape enteric eukaryotic viromes in central African forest than in a European zoo: a One Health analysis.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3674}, pmid = {37339968}, issn = {2041-1723}, mesh = {Animals ; Humans ; Eukaryota ; *One Health ; Virome ; *Hominidae ; Gorilla gorilla ; }, abstract = {Human-animal pathogenic transmissions threaten both human and animal health, and the processes catalyzing zoonotic spillover and spillback are complex. Prior field studies offer partial insight into these processes but overlook animal ecologies and human perceptions and practices facilitating human-animal contact. Conducted in Cameroon and a European zoo, this integrative study elucidates these processes, incorporating metagenomic, historical, anthropological and great ape ecological analyses, and real-time evaluation of human-great ape contact types and frequencies. We find more enteric eukaryotic virome sharing between Cameroonian humans and great apes than in the zoo, virome convergence between Cameroonian humans and gorillas, and adenovirus and enterovirus taxa as most frequently shared between Cameroonian humans and great apes. Together with physical contact from hunting, meat handling and fecal exposure, overlapping human cultivation and gorilla pillaging in forest gardens help explain these findings. Our multidisciplinary study identifies environmental co-use as a complementary mechanism for viral sharing.}, } @article {pmid37339742, year = {2023}, author = {Arora, J and Buček, A and Hellemans, S and Beránková, T and Arias, JR and Fisher, BL and Clitheroe, C and Brune, A and Kinjo, Y and Šobotník, J and Bourguignon, T}, title = {Evidence of cospeciation between termites and their gut bacteria on a geological time scale.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {2001}, pages = {20230619}, pmid = {37339742}, issn = {1471-2954}, mesh = {Animals ; *Isoptera ; Phylogeny ; Symbiosis ; Bacteria/genetics ; *Gastrointestinal Microbiome ; Mammals ; }, abstract = {Termites host diverse communities of gut microbes, including many bacterial lineages only found in this habitat. The bacteria endemic to termite guts are transmitted via two routes: a vertical route from parent colonies to daughter colonies and a horizontal route between colonies sometimes belonging to different termite species. The relative importance of both transmission routes in shaping the gut microbiota of termites remains unknown. Using bacterial marker genes derived from the gut metagenomes of 197 termites and one Cryptocercus cockroach, we show that bacteria endemic to termite guts are mostly transferred vertically. We identified 18 lineages of gut bacteria showing cophylogenetic patterns with termites over tens of millions of years. Horizontal transfer rates estimated for 16 bacterial lineages were within the range of those estimated for 15 mitochondrial genes, suggesting that horizontal transfers are uncommon and vertical transfers are the dominant transmission route in these lineages. Some of these associations probably date back more than 150 million years and are an order of magnitude older than the cophylogenetic patterns between mammalian hosts and their gut bacteria. Our results suggest that termites have cospeciated with their gut bacteria since first appearing in the geological record.}, } @article {pmid37339626, year = {2023}, author = {Frioux, C and Ansorge, R and Özkurt, E and Ghassemi Nedjad, C and Fritscher, J and Quince, C and Waszak, SM and Hildebrand, F}, title = {Enterosignatures define common bacterial guilds in the human gut microbiome.}, journal = {Cell host & microbe}, volume = {31}, number = {7}, pages = {1111-1125.e6}, doi = {10.1016/j.chom.2023.05.024}, pmid = {37339626}, issn = {1934-6069}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Bacteria/genetics ; Metagenome ; Firmicutes ; Bacteroides/genetics ; Feces/microbiology ; }, abstract = {The human gut microbiome composition is generally in a stable dynamic equilibrium, but it can deteriorate into dysbiotic states detrimental to host health. To disentangle the inherent complexity and capture the ecological spectrum of microbiome variability, we used 5,230 gut metagenomes to characterize signatures of bacteria commonly co-occurring, termed enterosignatures (ESs). We find five generalizable ESs dominated by either Bacteroides, Firmicutes, Prevotella, Bifidobacterium, or Escherichia. This model confirms key ecological characteristics known from previous enterotype concepts, while enabling the detection of gradual shifts in community structures. Temporal analysis implies that the Bacteroides-associated ES is "core" in the resilience of westernized gut microbiomes, while combinations with other ESs often complement the functional spectrum. The model reliably detects atypical gut microbiomes correlated with adverse host health conditions and/or the presence of pathobionts. ESs provide an interpretable and generic model that enables an intuitive characterization of gut microbiome composition in health and disease.}, } @article {pmid37338708, year = {2023}, author = {Chickering, G and Krause, MJ and Schwarber, A}, title = {Effects of landfill food waste diversion: a focus on microbial populations and methane generation.}, journal = {Biodegradation}, volume = {34}, number = {5}, pages = {477-488}, pmid = {37338708}, issn = {1572-9729}, support = {EPA999999/ImEPA/Intramural EPA/United States ; }, mesh = {*Refuse Disposal ; Methane/analysis ; Food ; Solid Waste/analysis ; Waste Disposal Facilities ; }, abstract = {The early stages of municipal solid waste degradation in landfills are complex harmonies of physical, biological, and chemical interactions that all work in concert to degrade trash into smaller and more stable materials. While many approaches have been taken to understand parts of this process, this new work attempted to simulate the early stages of landfills in controlled laboratory environments while observing the impacts of food waste content at different concentrations. This was completed by operating landfill lysimeters in a laboratory for approximately 1000 days, simulating landfill interior conditions while measuring the gas and liquid byproducts to study the impact of food waste presence in these environments. Metagenomic analysis after the experiment identified over 18,000 individual species and allowed comparison with past studies while also surveying microorganisms present in landfills. Similar populations found in past studies suggested the current experiments successfully replicated landfill conditions. While food waste diversion had a discernable impact on gas production, it did not show a clear and consistent impact on the microbiomes identified in this study.}, } @article {pmid37338686, year = {2023}, author = {Zhang, Y and Li, J and Wu, T and Ma, K and Cheng, Z and Yi, Q and Dai, Y and Wang, B and Chen, Y and Wang, B and Hu, X and Yang, A and Yang, Q and Zhong, X}, title = {Characteristics of antibiotic resistance genes and microbial community distribution in Wanfeng Lake, upper Pearl River, China.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {35}, pages = {83214-83230}, pmid = {37338686}, issn = {1614-7499}, support = {[2020]1Z051//Science and Technology Program of Guizhou Province/ ; QKZYD [2022]4022//Science and Technology Program of Guizhou Province/ ; QKHJC-ZK[2022]YB102//Science and Technology Program of Guizhou Province/ ; }, mesh = {Animals ; Humans ; Anti-Bacterial Agents/pharmacology/analysis ; Lakes/analysis ; Rivers/chemistry ; Drug Resistance, Bacterial/genetics ; Macrolides ; Ofloxacin ; Sulfonamides ; *Quinolones ; China ; Water/analysis ; *Microbiota ; Genes, Bacterial ; }, abstract = {Wanfeng Lake, a highland lake in the upper part of the Pearl River Basin, China, has long been disturbed by aquaculture and human activities, resulting in the accumulation of antibiotics and antibiotic resistance genes (ARGs), which pose a major threat to humans and animals. In this study, 20 antibiotics, 9 ARGs, 2 mobile genetic elements (intl1 and intl2), and microbial community structure were investigated in Wanfeng Lake. The results of the study showed that the total concentration of antibiotics in surface water was 372.72 ng/L, with ofloxacin (OFX) having the highest concentration (169.48 ng/L), posing a high ecological risk to aquatic organisms. The total concentration of antibiotics in sediments was 235.86 ng/g, with flumequine (FLU) having the highest concentration (122.54 ng/g). This indicates that the main type of antibiotics in Wanfeng Lake are quinolones. QPCR analysis results of the relative abundance of ARGs in both surface water and sediments showed that sulfonamide resistance genes > macrolide resistance genes > tetracycline resistance genes > quinolone resistance genes, indicating that sulfonamide resistance genes were the dominant type. The metagenomic results showed that the predominant microorganisms in the sediment under the phylum level were Planctomycetes, Proteobacteria, Euryarchaeota, and Chloroflexi. Pearson's correlation analysis showed a significantly positive correlation between antibiotics and environmental factors with ARGs in Wanfeng Lake and a significant positive correlation between antibiotics and ARGs with microorganisms in sediments. This suggests that there is a potential pressure of antibiotics on ARGs, while microorganisms provide the driving force for the evolution and spread of ARGs. This study provides a basis for further research on the occurrence and spread of antibiotics and ARGs in Wanfeng Lake. A total of 14 antibiotics were detected in surface water and sediments. OFX poses a high ecological risk in all points of surface water. Antibiotics and ARGs were significantly positively correlated in Wanfeng Lake. Antibiotics and ARGs in sediments were positively correlated with microorganisms.}, } @article {pmid37338635, year = {2023}, author = {Salam, LB and Obayori, OS and Ilori, MO and Amund, OO}, title = {Chromium contamination accentuates changes in the microbiome and heavy metal resistome of a tropical agricultural soil.}, journal = {World journal of microbiology & biotechnology}, volume = {39}, number = {9}, pages = {228}, pmid = {37338635}, issn = {1573-0972}, mesh = {Soil/chemistry ; *Soil Pollutants/analysis ; *Metals, Heavy/toxicity/analysis ; Chromium/toxicity/analysis ; Cadmium/analysis ; *Microbiota ; Environmental Monitoring ; China ; }, abstract = {The impacts of hexavalent chromium (Cr) contamination on the microbiome, soil physicochemistry, and heavy metal resistome of a tropical agricultural soil were evaluated for 6 weeks in field-moist microcosms consisting of a Cr-inundated agricultural soil (SL9) and an untreated control (SL7). The physicochemistry of the two microcosms revealed a diminution in the total organic matter content and a significant dip in macronutrients phosphorus, potassium, and nitrogen concentration in the SL9 microcosm. Heavy metals analysis revealed the detection of seven heavy metals (Zn, Cu, Fe, Cd, Se, Pb, Cr) in the agricultural soil (SL7), whose concentrations drastically reduced in the SL9 microcosm. Illumina shotgun sequencing of the DNA extracted from the two microcosms showed the preponderance of the phyla, classes, genera, and species of Actinobacteria (33.11%), Actinobacteria_class (38.20%), Candidatus Saccharimonas (11.67%), and Candidatus Saccharimonas aalborgensis (19.70%) in SL7, and Proteobacteria (47.52%), Betaproteobacteria (22.88%), Staphylococcus (16.18%), Staphylococcus aureus (9.76%) in SL9, respectively. Functional annotation of the two metagenomes for heavy metal resistance genes revealed diverse heavy metal resistomes involved in the uptake, transport, efflux, and detoxification of various heavy metals. It also revealed the exclusive detection in SL9 metagenome of resistance genes for chromium (chrB, chrF, chrR, nfsA, yieF), cadmium (czcB/czrB, czcD), and iron (fbpB, yqjH, rcnA, fetB, bfrA, fecE) not annotated in SL7 metagenome. The findings from this study revealed that Cr contamination induces significant shifts in the soil microbiome and heavy metal resistome, alters the soil physicochemistry, and facilitates the loss of prominent members of the microbiome not adapted to Cr stress.}, } @article {pmid37338413, year = {2023}, author = {Bittleston, LS and Wolock, CJ and Maeda, J and Infante, V and Ané, JM and Pierce, NE and Pringle, A}, title = {Carnivorous Nepenthes Pitchers with Less Acidic Fluid House Nitrogen-Fixing Bacteria.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0081223}, pmid = {37338413}, issn = {1098-5336}, mesh = {Animals ; *Nitrogen-Fixing Bacteria ; RNA, Ribosomal, 16S/genetics ; Insecta ; Bacteria/genetics ; Nitrogen/analysis ; Alkynes ; }, abstract = {Carnivorous pitcher plants are uniquely adapted to nitrogen limitation, using pitfall traps to acquire nutrients from insect prey. Pitcher plants in the genus Sarracenia may also use nitrogen fixed by bacteria inhabiting the aquatic microcosms of their pitchers. Here, we investigated whether species of a convergently evolved pitcher plant genus, Nepenthes, might also use bacterial nitrogen fixation as an alternative strategy for nitrogen capture. First, we constructed predicted metagenomes of pitcher organisms from three species of Singaporean Nepenthes using 16S rRNA sequence data and correlated predicted nifH abundances with metadata. Second, we used gene-specific primers to amplify and quantify the presence or absence of nifH directly from 102 environmental samples and identified potential diazotrophs with significant differential abundance in samples that also had positive nifH PCR tests. Third, we analyzed nifH in eight shotgun metagenomes from four additional Bornean Nepenthes species. Finally, we conducted an acetylene reduction assay using greenhouse-grown Nepenthes pitcher fluids to confirm nitrogen fixation is indeed possible within the pitcher habitat. Results show active acetylene reduction can occur in Nepenthes pitcher fluid. Variation in nifH from wild samples correlates with Nepenthes host species identity and pitcher fluid acidity. Nitrogen-fixing bacteria are associated with more neutral fluid pH, while endogenous Nepenthes digestive enzymes are most active at low fluid pH. We hypothesize Nepenthes species experience a trade-off in nitrogen acquisition; when fluids are acidic, nitrogen is primarily acquired via plant enzymatic degradation of insects, but when fluids are neutral, Nepenthes plants take up more nitrogen via bacterial nitrogen fixation. IMPORTANCE Plants use different strategies to obtain the nutrients that they need to grow. Some plants access their nitrogen directly from the soil, while others rely on microbes to access the nitrogen for them. Carnivorous pitcher plants generally trap and digest insect prey, using plant-derived enzymes to break down insect proteins and generate a large portion of the nitrogen that they subsequently absorb. In this study, we present results suggesting that bacteria living in the fluids formed by Nepenthes pitcher plants can fix nitrogen directly from the atmosphere, providing an alternative pathway for plants to access nitrogen. These nitrogen-fixing bacteria are only likely to be present when pitcher plant fluids are not strongly acidic. Interestingly, the plant's enzymes are known to be more active under strongly acidic conditions. We propose a potential trade-off where pitcher plants sometimes access nitrogen using their own enzymes to digest prey and at other times take advantage of bacterial nitrogen fixation.}, } @article {pmid37338395, year = {2023}, author = {Putman, LI and Schaerer, LG and Wu, R and Kulas, DG and Zolghadr, A and Ong, RG and Shonnard, DR and Techtmann, SM and Arbanas, LG and Bannerman, GG and Cart, B and Cureton, A and Doerr, BP and Jovicevic, Z and Langosch, M and MacLeod, AB and McCloskey, C and McNally, AM and Monkevich, MK and Noecker, A and Norris, D and Pellizzon, VG and Strom, KB and Taylor, EE}, title = {Metagenomic Sequencing of Two Cultures Grown on Chemically Deconstructed Plastic Products.}, journal = {Microbiology resource announcements}, volume = {12}, number = {7}, pages = {e0130422}, pmid = {37338395}, issn = {2576-098X}, support = {HR00112020033//Defense Advanced Research Projects Agency ReSource Program Cooperative Agreement/ ; HR00112020033//Defense Advanced Research Projects Agency ReSource Program Cooperative Agreement/ ; HR00112020033//Defense Advanced Research Projects Agency ReSource Program Cooperative Agreement/ ; }, abstract = {We report the metagenome sequences of two microbial cultures that were grown with chemically deconstructed plastic products as their sole carbon source. These metagenomes will provide insights into the metabolic capabilities of cultures grown on deconstructed plastics and can serve as a starting point for the identification of novel plastic degradation mechanisms.}, } @article {pmid37338379, year = {2023}, author = {Nilsen, M and Rehbinder, EM and Lødrup Carlsen, KC and Haugen, G and Hedlin, G and Jonassen, CM and Killingstad, ME and Nordlund, B and Ormaasen, I and Skjerven, HO and Snipen, L and Staff, AC and Söderhäll, C and Sørensen, R and Vettukattil, R and Wilborn, LM and Rudi, K}, title = {A Globally Distributed Bacteroides caccae Strain Is the Most Prevalent Mother-Child Shared Bacteroidaceae Strain in a Large Scandinavian Cohort.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0078923}, pmid = {37338379}, issn = {1098-5336}, mesh = {Infant ; Humans ; Female ; Pregnancy ; *Cesarean Section ; *Bacteroidaceae ; Infectious Disease Transmission, Vertical ; Bacteroides/genetics ; Feces ; Mother-Child Relations ; }, abstract = {Bacteroides and Phocaeicola, members of the family Bacteroidaceae, are among the first microbes to colonize the human infant gut. While it is known that these microbes can be transmitted from mother to child, our understanding of the specific strains that are shared and potentially transmitted is limited. In this study, we aimed to investigate the shared strains of Bacteroides and Phocaeicola in mothers and their infants. We analyzed fecal samples from pregnant woman recruited at 18 weeks of gestation from the PreventADALL study, as well as offspring samples from early infancy, including skin swab samples taken within 10 min after birth, the first available fecal sample (meconium), and fecal samples at 3 months of age. We screened 464 meconium samples for Bacteroidaceae, with subsequent selection of 144 mother-child pairs for longitudinal analysis, based on the presence of Bacteroidaceae, longitudinal sample availability, and delivery mode. Our results showed that Bacteroidaceae members were mainly detected in samples from vaginally delivered infants. We identified high prevalences of Phocaeicola vulgatus, Phocaeicola dorei, Bacteroides caccae, and Bacteroides thetaiotaomicron in mothers and vaginally born infants. However, at the strain level, we observed high prevalences of only two strains: a B. caccae strain and a P. vulgatus strain. Notably, the B. caccae strain was identified as a novel component of mother-child shared strains, and its high prevalence was also observed in publicly available metagenomes worldwide. Our findings suggest that mode of delivery may play a role in shaping the early colonization of the infant gut microbiota, in particular the colonization of Bacteroidaceae members. IMPORTANCE Our study provides evidence that Bacteroidaceae strains present on infants' skin within 10 min after birth, in meconium samples, and in fecal samples at 3 months of age in vaginally delivered infants are shared with their mothers. Using strain resolution analyses, we identified two strains, belonging to Bacteroides caccae and Phocaeicola vulgatus, as shared between mothers and their infants. Interestingly, the B. caccae strain showed a high prevalence worldwide, while the P. vulgatus strain was less common. Our findings also showed that vaginal delivery was associated with early colonization of Bacteroidaceae members, whereas cesarean section delivery was associated with delayed colonization. Given the potential for these microbes to influence the colonic environment, our results suggest that understanding the bacterial-host relationship at the strain level may have implications for infant health and development later in life.}, } @article {pmid37337895, year = {2023}, author = {Banzragch, M and Sanli, K and Stensvold, CR and Kurt, O and Ari, S}, title = {Metabarcoding of colonic cleansing fluid reveals unique bacterial members of mucosal microbiota associated with Inflammatory Bowel Disease.}, journal = {Scandinavian journal of gastroenterology}, volume = {58}, number = {11}, pages = {1253-1263}, doi = {10.1080/00365521.2023.2223708}, pmid = {37337895}, issn = {1502-7708}, mesh = {Humans ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; *Inflammatory Bowel Diseases/complications ; *Microbiota/genetics ; *Colitis, Ulcerative/complications ; Intestinal Mucosa/microbiology ; Bacteria/genetics ; }, abstract = {BACKGROUND: Inflammatory Bowel Disease (IBD) is a group of chronic idiopathic inflammatory diseases of the gastrointestinal (GI) tract associated with the dysbiosis of gut microbiota. Metabarcoding-based profiling of the gut microbiota of IBD patients is generally based on the stool samples collected from individual patients which rarely represent the mucosa-associated microbiota. The ideal sampling strategy for routine monitoring of the mucosal component of IBD has yet to be determined.

METHODS: We hereby compare the microbiota composition of the colonic cleansing fluid (CCF) collected during colonoscopy with stool samples from IBD patients. The relationship between IBD and gut microbiota was revealed through the application of the 16S rRNA amplicon sequencing-based metabarcoding approach. CCF and stool samples were collected from IBD patients with Crohn's disease and ulcerative colitis.

RESULTS: The present study shows significant differences in the microbial composition of CCF samples, presumably indicating changes in the mucosal microbiota of IBD patients as compared to the control group. Short-chain fatty acid-producing bacteria under the family Lachnospiraceae, the actinobacterial genus Bifidobacterium, the proteobacterial Sutterella and Raoultella are found to contribute to the microbial dysbiosis of the mucosal flora in IBD patients.

CONCLUSIONS: CCF microbiota has the capacity to distinguish IBD patients from healthy controls and, thus, may constitute an alternative analysis strategy for the early diagnosis and disease progression in IBD biomarker research.}, } @article {pmid37336582, year = {2023}, author = {Colston, SM and Barbato, RA and Goodson, MS and Karl, JP and Kokoska, RJ and Leary, DD and Racicot, K and Varaljay, V and Soares, JW}, title = {Current advances in microbiome sciences within the US Department of Defense: part 2 - enabling technologies and environmental microbiomes.}, journal = {BMJ military health}, volume = {}, number = {}, pages = {}, doi = {10.1136/military-2022-002308}, pmid = {37336582}, issn = {2633-3775}, abstract = {Microbiomes involve complex microbial communities wherein the micro-organisms interact with one another as well as their associated hosts or environmental niches. Much of the characterisation of these communities and the associations have been achieved through 'omics' technologies, such as metagenomics, metaproteomics and metametabolomics, and model systems. Recent research in host-associated microbiomes has been aimed at understanding the role microbes may play in host fitness or conversely how host activities/conditions may perturb the microbial community, which can further affect host health. These studies have led to the investigation of detection, intervention or modulation methods, which may serve to provide benefits to the host and advance our understanding of microbiome associations. With the clear implications on human health and disease, the US Department of Defense (DoD) has made microbiome research a priority, with the founding of the Tri-Service Microbiome Consortium (TSMC) to enhance collaboration, coordination,and communication of microbiome research among DoD organisations and partners in academia and industry. DoD microbiome research focuses mainly on the following themes: (1) human health and performance, (2) environmental microbiomes and (3) enabling technologies. This review provides an update of current DoD microbiome research efforts centred on enabling technologies and environmental microbiomes and highlights innovative research being done in academia and industry that can be leveraged by the DoD. These topics were also communicated and further discussed in the Fifth Annual TSMC Symposium. This paper forms part of the special issue of BMJ Military Health dedicated to personalised digital technology for mental health in the Armed Forces.}, } @article {pmid37336455, year = {2023}, author = {Xiao, C and Wan, K and Hu, J and Deng, X and Liu, X and Zhou, F and Yu, J and Chi, R}, title = {Performance changes in the anammox process under the stress of rare-earth element Ce(III) and the evolution of microbial community and functional genes.}, journal = {Bioresource technology}, volume = {384}, number = {}, pages = {129349}, doi = {10.1016/j.biortech.2023.129349}, pmid = {37336455}, issn = {1873-2976}, mesh = {*Anaerobic Ammonia Oxidation ; Oxidation-Reduction ; *Microbiota ; Wastewater ; Bacteria/genetics/metabolism ; Anaerobiosis ; Nitrogen/metabolism ; Bioreactors/microbiology ; Sewage/microbiology ; Denitrification ; }, abstract = {The high Ce(III) content in ionic rare-earth tailings wastewater has hindered the application of anammox process in this field. Here, the effect of Ce(III) on the performance of anammox processes was investigated, and the evolution of microbial communities and functional genes was explored using metagenomic sequencing. The results showed that the reactor nitrogen removal rate decreased when the Ce(III) concentration reached 25 mg/L, although ammonia nitrogen removal (92.31%) and nitrogen removal efficiency (81.33%) remained at a high level; however, both showed a significant decreasing trend. The relative abundance of anammox bacteria increased continuously from P1-P5, reaching 48.81%, whereas the relative abundance of Candidatus jettenia reached 33.71% at P5, which surpassed that of Candidatus brocadia as the most abundant anammox bacteria, and further analysis of functional genes and metabolic pathways revealed that Candidatus brocadia was richer in biochemical metabolic genes, whereas Candidatus jettenia had richer efflux genes.}, } @article {pmid37336182, year = {2023}, author = {Wang, J and Chi, Q and Pan, L and Zhang, R and Mu, Y and Shen, J}, title = {New insights into enhanced biodegradation of 4-bromphenol in a nitrate-reducing system: Process performance and mechanism.}, journal = {Water research}, volume = {242}, number = {}, pages = {120200}, doi = {10.1016/j.watres.2023.120200}, pmid = {37336182}, issn = {1879-2448}, mesh = {*Nitrates ; Biodegradation, Environmental ; *Phenols ; Bacteria ; Bioreactors ; }, abstract = {Due to the recalcitrant nature of halogenated phenol, conventional anaerobic bioprocess is often limited by low removal efficiency and poor process stability. At the presence of electron acceptors such as nitrate, 4-bromophenol (4-BP) removal efficiency is significantly higher than that in the anaerobic control system, but the mechanism involved is still unclear. Therefore, an up-flow nitrate-reducing bioreactor (NRBR) was designed and consecutively performed for 215 days to explore the synergistic mechanism for BPs biodegradation and nitrate reduction. Complete 4-BP biodegradation could be obtained in NRBR at HRT and 4-BP loading rate of 24 h and 0.29 mol m [-] [3]d [-] [1], while the TOC removal and nitrate reduction efficiencies were as high as 91.33±2.11% and 98.31±1.33%, respectively. Population evolution analyses revealed that the microorganisms involved in 4-BP debromination and biodegradation (Candidatus Peregrinibacteria, Denitratisoma, Anaerolineaceae and Ignavibacterium) as well as nitrate reduction (Denitratisoma, Anaerolineaceae, Limnobacter and Ignavibacterium) were significantly enriched in NRBR. Major intermediates during 4-BP biodegradation, including 4-bromocatechol, 4‑bromo-6-oxo-hexanoic acid and succinic acid were identified, while a distinct 4-BP biodegradation pathway via hydration, aromatic-ring cleavage, hydrolysis debromination and oxidation was expounded. Metagenomic analysis indicated that oxidation (had, pht4, boh, butA), hydrolysis debromination ((S)-2-haloacid dehalogenase) and bio-mineralization (gabD, sdhA) of 4-BP were largely enhanced in NRBR. Moreover, carbon, nitrogen, energy and amino acid metabolisms were significantly facilitated with the injection of nitrate in order to provide energy and electron, thus enhanced microbial activities and enzymatic reactions in NRBR. The proposed mechanism provides new insights into our mechanistic understanding of halogenated phenol biodegradation and the development of sustainable bioremediation strategies.}, } @article {pmid37335713, year = {2023}, author = {Zhang, LM and Zhang, HB and Zou, YF and Liu, MW}, title = {Contactin-associated protein-2 and anti-aquaporin-4 antibody positive autoimmune encephalitis secondary to herpes simplex encephalitis: A case report.}, journal = {Medicine}, volume = {102}, number = {20}, pages = {e33767}, pmid = {37335713}, issn = {1536-5964}, mesh = {Male ; Humans ; Adolescent ; *Encephalitis, Herpes Simplex/complications/diagnosis/drug therapy ; Acyclovir ; *Herpes Simplex/complications ; *Autoimmune Diseases of the Nervous System/complications ; }, abstract = {RATIONALE: Recurrent herpes simplex encephalitis (HSE) can easily induce autoimmune encephalitis (AE). However, there are few reports of anti-contactin-associated protein-2 (CASPR2)-related encephalitis, especially with positive anti-aquaporin 4 (AQP4) antibodies.

PATIENT CONCERNS: A 14-year-old boy was admitted to the Department of Neurology of the First Affiliated Hospital of Kunming Medical University for "headache, dizziness, and fever for four days" with positive anti-CASPR2 and anti-AQP4 antibodies in the cerebrospinal fluid.

DIAGNOSES: Cranial MRI showed lesions in the right hippocampus, amygdala, and insular lobe, with local sulcus enhancement in the right insular, temporal, and frontal lobes. The fluid-attenuated inversion recovery was significantly enhanced. Human herpes virus type I was detected by cerebrospinal fluid metagenomic testing. The patient was diagnosed with AE secondary to HSE, with positive anti-CASPR2 and anti-AQP4 antibodies.

INTERVENTIONS: After 2 weeks of immunoglobulin and methylprednisolone immunomodulatory therapy, acyclovir antivirus, mannitol dehydration, reducing intracranial pressure, and other symptomatic support therapy.

OUTCOMES: The patient's symptoms significantly improved, with no complaints of discomfort, and he was discharged for observation. The patient was followed up a month after discharge and had no complaints of discomfort.

LESSONS: CASPR2 and anti-aquaporin-4 antibody-positive AE have not been reported to be positive. This case will raise awareness of CASPR2 and anti-aquaporin-4 antibody-positive AE secondary to HSE, strengthen diagnostic capacities, and provide advice to treat it.}, } @article {pmid37333852, year = {2023}, author = {Xu, Y and Xu, J and Liu, T and Liu, P and Chen, XG}, title = {Metagenomic analysis reveals the virome profiles of Aedes albopictus in Guangzhou, China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1133120}, pmid = {37333852}, issn = {2235-2988}, mesh = {Animals ; *Aedes ; Metagenomics ; Phylogeny ; Virome/genetics ; Mosquito Vectors ; *Viruses/genetics ; }, abstract = {INTRODUCTION: Aedes albopictus is an aggressive invasive mosquito species widely distributed around the world, and it is also a known vector of arboviruses. Virus metagenomics and RNA interference (RNAi) are important in studying the biology and antiviral defense of Ae. albopictus. However, the virome and potential transmission of plant viruses by Ae. albopictus remain understudied.

METHODS: Mosquito samples of Ae. albopictus were collected from Guangzhou, China, and small RNA sequencing was performed. Raw data were filtered, and virus-associated contigs were generated using VirusDetect. The small RNA profiles were analyzed, and maximum-likelihood phylogenetic trees were constructed.

RESULTS: The small RNA sequencing of pooled Ae. albopictus revealed the presence of five known viruses, including Wenzhou sobemo-like virus 4, mosquito nodavirus, Aedes flavivirus, Hubei chryso-like virus 1, and Tobacco rattle virus RNA1. Additionally, 21 new viruses that had not been previously reported were identified. The mapping of reads and contig assembly provided insights into the viral diversity and genomic characteristics of these viruses. Field survey confirmed the detection of the identified viruses in Ae. albopictus collected from Guangzhou.

DISCUSSION: The comprehensive analysis of the virus metagenomics of Ae. albopictus in this study sheds light on the diversity and prevalence of viruses in mosquito populations. The presence of known and novel viruses highlights the need for continued surveillance and investigation into their potential impact on public health. The findings also emphasize the importance of understanding the virome and potential transmission of plant viruses by Ae. albopictus.

CONCLUSION: This study provides valuable insights into the virome of Ae. albopictus and its potential role as a vector for both known and novel viruses. Further research is needed to expand the sample size, explore additional viruses, and investigate the implications for public health.}, } @article {pmid37333647, year = {2023}, author = {Hao, Y and Zhao, Y and Zhang, Y and Liu, Y and Wang, G and He, Z and Cao, W and Han, T and Zhang, X and Zhang, Z and Wang, Y and Gong, C and Hou, J}, title = {Population response of intestinal microbiota to acute Vibrio alginolyticus infection in half-smooth tongue sole (Cynoglossus semilaevis).}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1178575}, pmid = {37333647}, issn = {1664-302X}, abstract = {INTRODUCTION: Vibriosis causes enormous economic losses of marine fish. The present study investigated the intestinal microbial response to acute infection of half-smooth tongue sole with different-dose Vibrio alginolyticus within 72 h by metagenomic sequencing.

METHODS: The inoculation amount of V. alginolyticus for the control, low-dose, moderate-dose, and high-dose groups were 0, 8.5 × 101, 8.5 × 104, and 8.5 × 107 cells/g respectively, the infected fish were farmed in an automatic seawater circulation system under a relatively stable temperature, dissolved oxygen and photoperiod, and 3 ~ 6 intestinal samples per group with high-quality DNA assay were used for metagenomics analysis.

RESULTS: The acute infections with V. alginolyticus at high, medium, and low doses caused the change of different-type leukocytes at 24 h, whereas the joint action of monocytes and neutrophils to cope with the pathogen infection only occurred in the high-dose group at 72 h. The metagenomic results suggest that a high-dose V. alginolyticus infection can significantly alter the intestinal microbiota, decrease the microbial α-diversity, and increase the bacteria from Vibrio and Shewanella, including various potential pathogens at 24 h. High-abundance species of potential pathogens such as V. harveyii, V. parahaemolyticus, V. cholerae, V. vulnificus, and V. scophthalmi exhibited significant positive correlations with V. alginolyticus. The function analysis revealed that the high-dose inflection group could increase the genes closely related to pathogen infection, involved in cell motility, cell wall/ membrane/envelope biogenesis, material transport and metabolism, and the pathways of quorum sensing, biofilm formation, flagellar assembly, bacterial chemotaxis, virulence factors and antibiotic resistances mainly from Vibrios within 72 h.

DISCUSSION: It indicates that the half-smooth tongue sole is highly likely to be a secondary infection with intestinal potential pathogens, especially species from Vibrio and that the disease could become even more complicated because of the accumulation and transfer of antibiotic-resistance genes in intestinal bacteria during the process of V. alginolyticus intensified infection.}, } @article {pmid37333640, year = {2023}, author = {Vizioli, C and Jaime-Lara, R and Daniel, SG and Franks, A and Diallo, AF and Bittinger, K and Tan, TP and Merenstein, DJ and Brooks, B and Joseph, PV and Maki, KA}, title = {Administration of Bifidobacterium animalis subsp. lactis strain BB-12[®] in healthy children: characterization, functional composition, and metabolism of the gut microbiome.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1165771}, pmid = {37333640}, issn = {1664-302X}, abstract = {INTRODUCTION: The consumption of probiotics may influence children's gut microbiome and metabolome, which may reflect shifts in gut microbial diversity composition and metabolism. These potential changes might have a beneficial impact on health. However, there is a lack of evidence investigating the effect of probiotics on the gut microbiome and metabolome of children. We aimed to examine the potential impact of a two (Streptococcus thermophilus and Lactobacillus delbrueckii; S2) vs. three (S2 + Bifidobacterium animalis subsp. lactis strain BB-12) strain-supplemented yogurt.

METHODS: Included in this study were 59 participants, aged one to five years old, recruited to phase I of a double-blinded, randomized controlled trial. Fecal samples were collected at baseline, after the intervention, and at twenty days post-intervention discontinuation, and untargeted metabolomics and shotgun metagenomics were performed.

RESULTS: Shotgun metagenomics and metabolomic analyses showed no global changes in either intervention group's gut microbiome alpha or beta diversity indices, except for a lower microbial diversity in the S2 + BB12 group at Day 30. The relative abundance of the two and three intervention bacteria increased in the S2 and S2 + BB12 groups, respectively, from Day 0 to Day 10. In the S2 + BB12 group, the abundance of several fecal metabolites increased at Day 10, including alanine, glycine, lysine, phenylalanine, serine, and valine. These fecal metabolite changes did not occur in the S2 group.

DISCUSSION: In conclusion, there were were no significant differences in the global metagenomic or metabolomic profiles between healthy children receiving two (S2) vs. three (S2 + BB12) probiotic strains for 10 days. Nevertheless, we observed a significant increase (Day 0 to Day 10) in the relative abundance of the two and three probiotics administered in the S2 and S2 + BB12 groups, respectively, indicating the intervention had a measurable impact on the bacteria of interest in the gut microbiome. Future research using longer probiotic intervention durations and in children at risk for gastrointestinal disorders may elucidate if functional metabolite changes confer a protective gastrointestinal effect.}, } @article {pmid37333442, year = {2023}, author = {Ferreira, C and Otani, S and Aarestrup, FM and Manaia, CM}, title = {Quantitative PCR versus metagenomics for monitoring antibiotic resistance genes: balancing high sensitivity and broad coverage.}, journal = {FEMS microbes}, volume = {4}, number = {}, pages = {xtad008}, pmid = {37333442}, issn = {2633-6685}, abstract = {The widespread occurrence of clinically relevant antibiotic resistance within humans, animals, and environment motivates the development of sensitive and accurate detection and quantification methods. Metagenomics and quantitative PCR (qPCR) are amongst the most used approaches. In this study, we aimed to evaluate and compare the performance of these methods to screen antibiotic resistance genes in animal faecal, wastewater, and water samples. Water and wastewater samples were from hospital effluent, different treatment stages of two treatment plants, and of the receiving river at the discharge point. The animal samples were from pig and chicken faeces. Antibiotic resistance gene coverage, sensitivity, and usefulness of the quantitative information were analyzed and discussed. While both methods were able to distinguish the resistome profiles and detect gradient stepwise mixtures of pig and chicken faeces, qPCR presented higher sensitivity for the detection of a few antibiotic resistance genes in water/wastewater. In addition, the comparison of predicted and observed antibiotic resistance gene quantifications unveiled the higher accuracy of qPCR. Metagenomics analyses, while less sensitive, provided a markedly higher coverage of antibiotic resistance genes compared to qPCR. The complementarity of both methods and the importance of selecting the best method according to the study purpose are discussed.}, } @article {pmid37333201, year = {2023}, author = {Tran, TH and Roberts, AQ and Escapa, IF and Gao, W and Segre, JA and Kong, HH and Conlan, S and Kelly, MS and Lemon, KP}, title = {Metabolic capabilities are highly conserved among human nasal-associated Corynebacterium species in pangenomic analyses.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37333201}, support = {K23 AI135090/AI/NIAID NIH HHS/United States ; R01 GM117174/GM/NIGMS NIH HHS/United States ; R35 GM141806/GM/NIGMS NIH HHS/United States ; }, abstract = {Corynebacterium species are globally ubiquitous in human nasal microbiota across the lifespan. Moreover, nasal microbiota profiles typified by higher relative abundances of Corynebacterium are often positively associated with health. Among the most common human nasal Corynebacterium species are C. propinquum, C. pseudodiphtheriticum, C. accolens, and C. tuberculostearicum. Based on the prevalence of these species, at least two likely coexist in the nasal microbiota of 82% of adults. To gain insight into the functions of these four species, we identified genomic, phylogenomic, and pangenomic properties and estimated the functional protein repertoire and metabolic capabilities of 87 distinct human nasal Corynebacterium strain genomes: 31 from Botswana and 56 from the U.S. C. pseudodiphtheriticum had geographically distinct clades consistent with localized strain circulation, whereas some strains from the other species had wide geographic distribution across Africa and North America. All four species had similar genomic and pangenomic structures. Gene clusters assigned to all COG metabolic categories were overrepresented in the persistent (core) compared to the accessory genome of each species indicating limited strain-level variability in metabolic capacity. Moreover, core metabolic capabilities were highly conserved among the four species indicating limited species-level metabolic variation. Strikingly, strains in the U.S. clade of C. pseudodiphtheriticum lacked genes for assimilatory sulfate reduction present in the Botswanan clade and in the other studied species, indicating a recent, geographically related loss of assimilatory sulfate reduction. Overall, the minimal species and strain variability in metabolic capacity implies coexisting strains might have limited ability to occupy distinct metabolic niches.}, } @article {pmid37333121, year = {2023}, author = {Salamzade, R and Tran, P and Martin, C and Manson, AL and Gilmore, MS and Earl, AM and Anantharaman, K and Kalan, LR}, title = {zol & fai: large-scale targeted detection and evolutionary investigation of gene clusters.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37333121}, support = {R35 GM137828/GM/NIGMS NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; U19 AI142720/AI/NIAID NIH HHS/United States ; }, abstract = {Many universally and conditionally important genes are genomically aggregated within clusters. Here, we introduce fai and zol, which together enable large-scale comparative analysis of different types of gene clusters and mobile-genetic elements (MGEs), such as biosynthetic gene clusters (BGCs) or viruses. Fundamentally, they overcome a current bottleneck to reliably perform comprehensive orthology inference at large scale across broad taxonomic contexts and thousands of genomes. First, fai allows the identification of orthologous or homologous instances of a query gene cluster of interest amongst a database of target genomes. Subsequently, zol enables reliable, context-specific inference of protein-encoding ortholog groups for individual genes across gene cluster instances. In addition, zol performs functional annotation and computes a variety of statistics for each inferred ortholog group. These programs are showcased through application to: (i) longitudinal tracking of a virus in metagenomes, (ii) discovering novel population-genetic insights of two common BGCs in a fungal species, and (iii) uncovering large-scale evolutionary trends of a virulence-associated gene cluster across thousands of genomes from a diverse bacterial genus.}, } @article {pmid37332501, year = {2022}, author = {Pessi, IS and Rutanen, A and Hultman, J}, title = {Candidatus Nitrosopolaris, a genus of putative ammonia-oxidizing archaea with a polar/alpine distribution.}, journal = {FEMS microbes}, volume = {3}, number = {}, pages = {xtac019}, pmid = {37332501}, issn = {2633-6685}, abstract = {Ammonia-oxidizing archaea (AOA) are key players in the nitrogen cycle of polar soils. Here, we analyzed metagenomic data from tundra soils in Rásttigáisá, Norway, and recovered four metagenome-assembled genomes (MAGs) assigned to the genus 'UBA10452', an uncultured lineage of putative AOA in the order Nitrososphaerales ('terrestrial group I.1b'), phylum Thaumarchaeota. Analysis of other eight previously reported MAGs and publicly available amplicon sequencing data revealed that the UBA10452 lineage is predominantly found in acidic polar and alpine soils. In particular, UBA10452 MAGs were more abundant in highly oligotrophic environments such as mineral permafrost than in more nutrient-rich, vegetated tundra soils. UBA10452 MAGs harbour multiple copies of genes related to cold tolerance, particularly genes involved in DNA replication and repair. Based on the phylogenetic, biogeographic, and ecological characteristics of 12 UBA10452 MAGs, which include a high-quality MAG (90.8% complete, 3.9% redundant) with a nearly complete 16S rRNA gene, we propose a novel Candidatus genus, Ca. Nitrosopolaris, with four species representing clear biogeographic/habitat clusters.}, } @article {pmid37332019, year = {2023}, author = {Fan, S and He, X and Zhu, Z and Chen, L and Zou, Y and Chen, Z and Yu, J and Chen, W and Guan, H and Ma, J}, title = {Integrating host transcriptomic signatures for distinguishing autoimmune encephalitis in cerebrospinal fluid by metagenomic sequencing.}, journal = {Cell & bioscience}, volume = {13}, number = {1}, pages = {111}, pmid = {37332019}, issn = {2045-3701}, support = {82161138018//National Natural Science Foundation of China/ ; CIFMS 2021-I2M-1-003//CAMS Innovations Fund for Medical Sciences/ ; }, abstract = {BACKGROUND: The early accurate diagnoses for autoimmune encephalitis (AE) and infectious encephalitis (IE) are essential since the treatments for them are different. This study aims to discover some specific and sensitive biomarkers to distinguish AE from IE at early stage to give specific treatments for good outcomes.

RESULTS: We compared the host gene expression profiles and microbial diversities of cerebrospinal fluid (CSF) from 41 patients with IE and 18 patients with AE through meta-transcriptomic sequencing. Significant differences were found in host gene expression profiles and microbial diversities in CSF between patients with AE and patients with IE. The most significantly upregulated genes in patients with IE were enriched in pathways related with immune response such as neutrophil degranulation, antigen processing and presentation and adaptive immune system. In contrast, those upregulated genes in patients with AE were mainly involved in sensory organ development such as olfactory transduction, as well as synaptic transmission and signaling. Based on the differentially expressed genes, a classifier consisting of 5 host genes showed outstanding performance with an area under the receiver operating characteristic (ROC) curve (AUC) of 0.95.

CONCLUSIONS: This study provides a promising classifier and is the first to investigate transcriptomic signatures for differentiating AE from IE by using meta-transcriptomic next-generation sequencing technology.}, } @article {pmid37331553, year = {2023}, author = {Zhang, T and Ji, Z and Chen, X and Yu, L}, title = {Shotgun metagenomics reveals a diverse mycobiome in the seawater from a High Arctic fjord (Kongsfjorden, Svalbard).}, journal = {Environmental research}, volume = {233}, number = {}, pages = {116437}, doi = {10.1016/j.envres.2023.116437}, pmid = {37331553}, issn = {1096-0953}, mesh = {Humans ; *Mycobiome ; Estuaries ; Ecosystem ; Svalbard ; Metagenomics ; Seawater ; Arctic Regions ; }, abstract = {In the Arctic fjords, the marine mycobiome experiences significant changes under environmental conditions driven by climate change. However, research on the ecological roles and the adaptive mechanisms of marine mycobiome in the Arctic fjord remains insufficiently explored. The present study employed shotgun metagenomics to comprehensively characterize the mycobiome in 24 seawater samples from Kongsfjorden, a High Arctic fjord situated in Svalbard. It revealed the presence of a diverse mycobiome with eight phyla, 34 classes, 71 orders, 152 families, 214 genera, and 293 species. The taxonomic and functional composition of the mycobiome differed significantly among the three layers, i.e., upper layer (depth of 0 m), middle layer (depths of 30-100 m), and lower layer (depths of 150-200 m). Several taxonomic groups (e.g., phylum Ascomycota, class Eurotiomycetes, order Eurotiales, family Aspergillaceae, and genus Aspergillus) and KOs (e.g., K03236/EIF1A, K03306/TC.PIT, K08852/ERN1, and K03119/tauD) were significantly distinct among the three layers. Among the measured environmental parameters, depth, NO2[-], and PO4[3-] were identified as the key factors influencing the mycobiome composition. Conclusively, our findings revealed that the mycobiome was diverse in the Arctic seawater and significantly impacted by the variability of environmental conditions in the High Arctic fjord. These results will assist future studies in exploring the ecological and adaptive responses towards the changes within the Arctic ecosystems.}, } @article {pmid37331548, year = {2024}, author = {Michaelis, L and Berg, L and Maier, L}, title = {Confounder or Confederate? The Interactions Between Drugs and the Gut Microbiome in Psychiatric and Neurological Diseases.}, journal = {Biological psychiatry}, volume = {95}, number = {4}, pages = {361-369}, doi = {10.1016/j.biopsych.2023.06.004}, pmid = {37331548}, issn = {1873-2402}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Nervous System Diseases/drug therapy ; Brain ; Psychotropic Drugs/pharmacology ; }, abstract = {The gut microbiome is emerging as an important factor in signaling along the gut-brain axis. The intimate physiological connection between the gut and the brain allows perturbations in the microbiome to be directly transmitted to the central nervous system and thereby contribute to psychiatric and neurological diseases. Common microbiome perturbations result from the ingestion of xenobiotic compounds including pharmaceuticals such as psychotropic drugs. In recent years, a variety of interactions between these drug classes and the gut microbiome have been reported, ranging from direct inhibitory effects on gut bacteria to microbiome-mediated drug degradation or sequestration. Consequently, the microbiome may play a critical role in influencing the intensity, duration, and onset of therapeutic effects, as well as in influencing the side effects that patients may experience. Furthermore, because the composition of the microbiome varies from person to person, the microbiome may contribute to the frequently observed interpersonal differences in the response to these drugs. In this review, we first summarize the known interactions between xenobiotics and the gut microbiome. Then, for psychopharmaceuticals, we address the question of whether these interactions with gut bacteria are irrelevant for the host (i.e., merely confounding factors in metagenomic analyses) or whether they may even have therapeutic or adverse effects.}, } @article {pmid37331316, year = {2023}, author = {Gu, Q and Lin, T and Wei, X and Zhang, Y and Wu, S and Yang, X and Zhao, H and Wang, C and Wang, J and Ding, Y and Zhang, J and Wu, Q}, title = {Prevalence of antimicrobial resistance in a full-scale drinking water treatment plant.}, journal = {Journal of environmental management}, volume = {344}, number = {}, pages = {118396}, doi = {10.1016/j.jenvman.2023.118396}, pmid = {37331316}, issn = {1095-8630}, mesh = {Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Drinking Water ; Drug Resistance, Bacterial/genetics ; Prevalence ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; *Water Purification/methods ; }, abstract = {Antibiotic resistance in drinking water has received increasing attention in recent years. In this study, the occurrence and abundance of antibiotic resistance genes (ARGs) in a drinking water treatment plant (DWTP) was comprehensively investigated using metagenomics. Bioinformatics analysis showed that 381 ARG subtypes belonging to 15 ARG types were detected, and bacitracin had the highest abundance (from 0.26 × 10[-2] to 0.86 copies/cell), followed by multidrug (from 0.57 × 10[-1] to 0.47 copies/cell) and sulfonamide (from 0.83 × 10[-2] to 0.35 copies/cell). Additionally, 933 ARG-carrying contigs (ACCs) were obtained from the metagenomic data, among which 153 contigs were annotated as pathogens. The most abundant putative ARG host was Staphylococcus (7.9%), which most frequently carried multidrug ARGs (43.2%). Additionally, 38 high-quality metagenome-assembled genomes (MAGs) were recovered, one of which was identified as Staphylococcus aureus (Bin.624) and harboured the largest number of ARGs (n = 16). Using the cultivation technique, 60 isolates were obtained from DWTP samples, and Staphylococcus spp. (n = 11) were found to be dominant in all isolates, followed by Bacillus spp. (n = 17). Antimicrobial susceptibility testing showed that most Staphylococcus spp. were multidrug resistant (MDR). These results deepen our understanding of the distribution profiles of ARGs and antibiotic resistant bacteria (ARB) in DWTPs for potential health risk evaluation. Our study also highlights the need for new and efficient water purification technologies that can be introduced and applied in DWTPs.}, } @article {pmid37331173, year = {2023}, author = {Yadav, R and Rajput, V and Dharne, M}, title = {Corrigendum to "Metagenomic analysis of a mega-city river network reveals microbial compositional heterogeneity among urban and peri-urban river stretch" [Sci. Total Environ. 783 (2021) 146960].}, journal = {The Science of the total environment}, volume = {892}, number = {}, pages = {164740}, doi = {10.1016/j.scitotenv.2023.164740}, pmid = {37331173}, issn = {1879-1026}, } @article {pmid37330554, year = {2023}, author = {Zhang, L and Rahman, J and Chung, M and Lashua, L and Gordon, A and Balmaseda, A and Kuan, G and Bonneau, R and Ghedin, E}, title = {CRISPR arrays as high-resolution markers to track microbial transmission during influenza infection.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {136}, pmid = {37330554}, issn = {2049-2618}, support = {HHSN272201400031C/AI/NIAID NIH HHS/United States ; U01 AI111598/AI/NIAID NIH HHS/United States ; U01 AI088654/AI/NIAID NIH HHS/United States ; HHSN272201400006C/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Clustered Regularly Interspaced Short Palindromic Repeats ; *Influenza, Human/prevention & control ; Bacteria ; Metagenome/genetics ; *Microbiota/genetics ; *Micrococcaceae/genetics ; }, abstract = {BACKGROUND: Disruption of the microbial community in the respiratory tract due to infections, like influenza, could impact transmission of bacterial pathogens. Using samples from a household study, we determined whether metagenomic-type analyses of the microbiome provide the resolution necessary to track transmission of airway bacteria. Microbiome studies have shown that the microbial community across various body sites tends to be more similar between individuals who cohabit in the same household than between individuals from different households. We tested whether there was increased sharing of bacteria from the airways within households with influenza infections as compared to control households with no influenza.

RESULTS: We obtained 221 respiratory samples that were collected from 54 individuals at 4 to 5 time points across 10 households, with and without influenza infection, in Managua, Nicaragua. From these samples, we generated metagenomic (whole genome shotgun sequencing) datasets to profile microbial taxonomy. Overall, specific bacteria and phages were differentially abundant between influenza positive households and control (no influenza infection) households, with bacteria like Rothia, and phages like Staphylococcus P68virus that were significantly enriched in the influenza-positive households. We identified CRISPR spacers detected in the metagenomic sequence reads and used these to track bacteria transmission within and across households. We observed a clear sharing of bacterial commensals and pathobionts, such as Rothia, Neisseria, and Prevotella, within and between households. However, due to the relatively small number of households in our study, we could not determine if there was a correlation between increased bacterial transmission and influenza infection.

CONCLUSION: We observed that airway microbial composition differences across households were associated with what appeared to be different susceptibility to influenza infection. We also demonstrate that CRISPR spacers from the whole microbial community can be used as markers to study bacterial transmission between individuals. Although additional evidence is needed to study transmission of specific bacterial strains, we observed sharing of respiratory commensals and pathobionts within and across households. Video Abstract.}, } @article {pmid37330070, year = {2023}, author = {Liang, J and Chang, J and Zhang, R and Fang, W and Chen, L and Ma, W and Zhang, Y and Yang, W and Li, Y and Zhang, P and Zhang, G}, title = {Metagenomic analysis reveals the efficient digestion mechanism of corn stover in Angus bull rumen: Microbial community succession, CAZyme composition and functional gene expression.}, journal = {Chemosphere}, volume = {336}, number = {}, pages = {139242}, doi = {10.1016/j.chemosphere.2023.139242}, pmid = {37330070}, issn = {1879-1298}, mesh = {Cattle ; Animals ; Male ; *Zea mays ; Rumen/microbiology ; Fermentation ; *Microbiota/genetics ; Bacteria/genetics ; Gene Expression ; Digestion ; }, abstract = {Ruminant rumen is a biological fermentation system that can efficiently degrade lignocellulosic biomass. The knowledge about mechanisms of efficient lignocellulose degradation with rumen microorganisms is still limited. In this study, composition and succession of bacteria and fungi, carbohydrate-active enzymes (CAZymes), and functional genes involved in hydrolysis and acidogenesis were revealed during fermentation in Angus bull rumen via metagenomic sequencing. Results showed that degradation efficiency of hemicellulose and cellulose reached 61.2% and 50.4% at 72 h fermentation, respectively. Main bacterial genera were composed of Prevotella, Butyrivibrio, Ruminococcus, Eubacterium, and Fibrobacter, and main fungal genera were composed of Piromyces, Neocallimastix, Anaeromyces, Aspergillus, and Orpinomyces. Principal coordinates analysis indicated that community structure of bacteria and fungi dynamically changed during 72 h fermentation. Bacterial networks with higher complexity had stronger stability than fungal networks. Most CAZyme families showed a significant decrease trend after 48 h fermentation. Functional genes related to hydrolysis decreased at 72 h, while functional genes involved in acidogenesis did not change significantly. These findings provide a in-depth understanding of mechanisms of lignocellulose degradation in Angus bull rumen, and may guide the construction and enrichment of rumen microorganisms in anaerobic fermentation of waste biomass.}, } @article {pmid37329328, year = {2023}, author = {Lledós, M and Prats-Sánchez, L and Llucià-Carol, L and Cárcel-Márquez, J and Muiño, E and Cullell, N and Gallego-Fabrega, C and Martín-Campos, JM and Aguilera-Simón, A and Guasch-Jiménez, M and Guisado-Alonso, D and Ramos-Pachón, A and Martínez-Domeño, A and Izquierdo, A and Marín, R and Camps-Renom, P and Martí-Fàbregas, J and Fernández-Cadenas, I}, title = {Ischaemic stroke patients present sex differences in gut microbiota.}, journal = {European journal of neurology}, volume = {30}, number = {11}, pages = {3497-3506}, doi = {10.1111/ene.15931}, pmid = {37329328}, issn = {1468-1331}, support = {//Centres de Recerca de Catalunya/ ; //ERA-NET NEURON/ ; //European Regional Development Fund/ ; //Instituto de Salud Carlos III/ ; //NextGeneration EU/ ; //RICORS-ICTUS/ ; }, abstract = {BACKGROUND: Gut microbiota plays a role in the pathophysiology of ischaemic stroke (IS) through the bidirectional gut-brain axis. Nevertheless, little is known about sex-specific microbiota signatures in IS occurrence.

METHODS: A total of 89 IS patients and 12 healthy controls were enrolled. We studied the taxonomic differences of the gut microbiota between men and women with IS by shotgun metagenomic sequencing. To evaluate the causal effect of several bacteria on IS risk, we performed a two-sample Mendelian randomisation (MR) with inverse-variance weighting (IVW) using genome-wide association analysis (GWAS) summary statistics from two cohorts of 5959 subjects with genetic and microbiota data and 1,296,908 subjects with genetic and IS data, respectively.

RESULTS: α-Diversity analysis measured using Observed Species (p = 0.017), Chao1 (p = 0.009) and Abundance-based Coverage Estimator (p = 0.012) indexes revealed that IS men have a higher species richness compared with IS women. Moreover, we found sex-differences in IS patients in relation to the phylum Fusobacteria, class Fusobacteriia, order Fusobacteriales and family Fusobacteriaceae (all Bonferroni-corrected p < 0.001). MR confirmed that increased Fusobacteriaceae levels in the gut are causally associated with an increased risk of IS (IVW p = 0.02, β = 0.32).

CONCLUSIONS: Our study is the first to indicate that there are gut microbiome differences between men and women with IS, identifying high levels of Fusobacteriaceae in women as a specific risk factor for IS. Incorporating sex stratification analysis is important in the design, analysis and interpretation of studies on stroke and the gut microbiota.}, } @article {pmid37328770, year = {2023}, author = {Sannino, C and Qi, W and Rüthi, J and Stierli, B and Frey, B}, title = {Distinct taxonomic and functional profiles of high Arctic and alpine permafrost-affected soil microbiomes.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {54}, pmid = {37328770}, issn = {2524-6372}, support = {Metagenomics 5233.00388.001.01//Swiss Federal Institute for Forest, Snow and Landscape Research/ ; IZLSZ2_170941//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; Polar Access Fund//Swiss Polar Institute/ ; }, abstract = {BACKGROUND: Global warming is affecting all cold environments, including the European Alps and Arctic regions. Here, permafrost may be considered a unique ecosystem harboring a distinct microbiome. The frequent freeze-thaw cycles occurring in permafrost-affected soils, and mainly in the seasonally active top layers, modify microbial communities and consequently ecosystem processes. Although taxonomic responses of the microbiomes in permafrost-affected soils have been widely documented, studies about how the microbial genetic potential, especially pathways involved in C and N cycling, changes between active-layer soils and permafrost soils are rare. Here, we used shotgun metagenomics to analyze the microbial and functional diversity and the metabolic potential of permafrost-affected soil collected from an alpine site (Val Lavirun, Engadin area, Switzerland) and a High Arctic site (Station Nord, Villum Research Station, Greenland). The main goal was to discover the key genes abundant in the active-layer and permafrost soils, with the purpose to highlight the potential role of the functional genes found.

RESULTS: We observed differences between the alpine and High Arctic sites in alpha- and beta-diversity, and in EggNOG, CAZy, and NCyc datasets. In the High Arctic site, the metagenome in permafrost soil had an overrepresentation (relative to that in active-layer soil) of genes involved in lipid transport by fatty acid desaturate and ABC transporters, i.e. genes that are useful in preventing microorganisms from freezing by increasing membrane fluidity, and genes involved in cell defense mechanisms. The majority of CAZy and NCyc genes were overrepresented in permafrost soils relative to active-layer soils in both localities, with genes involved in the degradation of carbon substrates and in the degradation of N compounds indicating high microbial activity in permafrost in response to climate warming.

CONCLUSIONS: Our study on the functional characteristics of permafrost microbiomes underlines the remarkably high functional gene diversity of the High Arctic and temperate mountain permafrost, including a broad range of C- and N-cycling genes, and multiple survival and energetic metabolisms. Their metabolic versatility in using organic materials from ancient soils undergoing microbial degradation determine organic matter decomposition and greenhouse gas emissions upon permafrost thawing. Attention to their functional genes is therefore essential to predict potential soil-climate feedbacks to the future warmer climate.}, } @article {pmid37328571, year = {2023}, author = {Booker, AE and D'Angelo, T and Adams-Beyea, A and Brown, JM and Nigro, O and Rappé, MS and Stepanauskas, R and Orcutt, BN}, title = {Life strategies for Aminicenantia in subseafloor oceanic crust.}, journal = {The ISME journal}, volume = {17}, number = {9}, pages = {1406-1415}, pmid = {37328571}, issn = {1751-7370}, mesh = {*Geologic Sediments/microbiology ; Oceans and Seas ; *Bacteria/genetics/metabolism ; Seawater/microbiology ; Carbon/metabolism ; }, abstract = {After decades studying the microbial "deep biosphere" in subseafloor oceanic crust, the growth and life strategies in this anoxic, low energy habitat remain poorly described. Using both single cell genomics and metagenomics, we reveal the life strategies of two distinct lineages of uncultivated Aminicenantia bacteria from the basaltic subseafloor oceanic crust of the eastern flank of the Juan de Fuca Ridge. Both lineages appear adapted to scavenge organic carbon, as each have genetic potential to catabolize amino acids and fatty acids, aligning with previous Aminicenantia reports. Given the organic carbon limitation in this habitat, seawater recharge and necromass may be important carbon sources for heterotrophic microorganisms inhabiting the ocean crust. Both lineages generate ATP via several mechanisms including substrate-level phosphorylation, anaerobic respiration, and electron bifurcation driving an Rnf ion translocation membrane complex. Genomic comparisons suggest these Aminicenantia transfer electrons extracellularly, perhaps to iron or sulfur oxides consistent with mineralogy of this site. One lineage, called JdFR-78, has small genomes that are basal to the Aminicenantia class and potentially use "primordial" siroheme biosynthetic intermediates for heme synthesis, suggesting this lineage retain characteristics of early evolved life. Lineage JdFR-78 contains CRISPR-Cas defenses to evade viruses, while other lineages contain prophage that may help prevent super-infection or no detectable viral defenses. Overall, genomic evidence points to Aminicenantia being well adapted to oceanic crust environments by taking advantage of simple organic molecules and extracellular electron transport.}, } @article {pmid37328529, year = {2023}, author = {Guan, Y and Zhang, Y and Zhu, Y and Wang, Y}, title = {CXCL10 as a shared specific marker in rheumatoid arthritis and inflammatory bowel disease and a clue involved in the mechanism of intestinal flora in rheumatoid arthritis.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {9754}, pmid = {37328529}, issn = {2045-2322}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Arthritis, Rheumatoid/genetics/metabolism ; Computational Biology ; *Microbiota ; *Inflammatory Bowel Diseases/genetics ; Chemokine CXCL10/genetics ; }, abstract = {This study aimed to identify shared specific genes associated with rheumatoid arthritis (RA) and inflammatory bowel disease (IBD) through bioinformatic analysis and to examine the role of the gut microbiome in RA. The data were extracted from the 3 RA and 1 IBD gene expression datasets and 1 RA gut microbiome metagenomic dataset. Weighted correlation network analysis (WGCNA) and machine learnings was performed to identify candidate genes associated with RA and IBD. Differential analysis and two different machine learning algorithms were used to investigate RA's gut microbiome characteristics. Subsequently, the shared specific genes related to the gut microbiome in RA were identified, and an interaction network was constructed utilizing the gutMGene, STITCH, and STRING databases. We identified 15 candidates shared genes through a joint analysis of the WGCNA for RA and IBD. The candidate gene CXCL10 was identified as the shared hub gene by the interaction network analysis of the corresponding WGCNA module gene to each disease, and CXCL10 was further identified as the shared specific gene by two machine learning algorithms. Additionally, we identified 3 RA-associated characteristic intestinal flora (Prevotella, Ruminococcus, and Ruminococcus bromii) and built a network of interactions between the microbiomes, genes, and pathways. Finally, it was discovered that the gene CXCL10 shared between IBD and RA was associated with the three gut microbiomes mentioned above. This study demonstrates the relationship between RA and IBD and provides a reference for research into the role of the gut microbiome in RA.}, } @article {pmid37327948, year = {2023}, author = {Naz, S and Ali, Z and Minhas, A and Fatima, A and Waseem, S}, title = {Generation of dysbiotic microbiota in cutaneous leishmaniasis and enhancement of skin inflammation.}, journal = {Microbial pathogenesis}, volume = {181}, number = {}, pages = {106202}, doi = {10.1016/j.micpath.2023.106202}, pmid = {37327948}, issn = {1096-1208}, mesh = {Humans ; *Leishmaniasis, Cutaneous ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; Proteobacteria/genetics ; Inflammation/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cutaneous Leishmaniasis (CL) affects millions of people globally and has a significant impact on morbidity and mortality. Innate immune mediators are likely to influence the clinical phenotype of CL through primary responses that restrict or facilitate parasite spread. The aim of this preliminary study was to bring to attention the significance of microbiota in the development of CL and emphasized the necessity of including the role of microbiota in CL while promoting a One Health approach for managing diseases. To achieve this, we used 16S amplicon metagenome sequencing and QIIME2 pipeline to analyze the microbiome composition of CL-infected patients compared to non-infected, healthy subjects. 16S sequencing analysis showed serum microbiome was dominated by Firmicutes, Proteobacteria, Bacteroidota, and Actinobacteria. CL-infected individuals, Proteobacteria were the most prevalent (27.63 ± 9.79), with the relative abundance (10.73 ± 5.33) of Proteobacteria in control. Bacilli class was found to be the most prevalent in healthy controls (30.71 ± 8.44) while (20.57 ± 9.51) in CL-infected individuals. The class Alphaproteobacteria was found to be more in CL-infected individuals (5.47 ± 2.07) as compared to healthy controls (1.85 ± 0.39). The CL-infected individuals had a significantly lower relative abundance of the Clostridia class (p < 0.0001). An altered serum microbiome of CL infection and higher microbial abundance in the serum of healthy individuals was observed.}, } @article {pmid37327856, year = {2023}, author = {Xu, L and Wu, H and Zhou, H and Zhou, X and Sun, Y}, title = {Purulent meningitis and secondary epilepsy caused by Mycobacterium iranicum infection: A case report.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {135}, number = {}, pages = {5-7}, doi = {10.1016/j.ijid.2023.06.002}, pmid = {37327856}, issn = {1878-3511}, mesh = {Male ; Humans ; Middle Aged ; *Mycobacteriaceae ; *Mycobacterium Infections ; *Meningitis, Bacterial/diagnosis/drug therapy/microbiology ; *Epilepsy/diagnosis/drug therapy ; }, abstract = {Mycobacterium iranicum is characterized by rapid growth and orange-pigmented scotochromogenic colonies. However, it is uncommon for M. iranicum to invade the central nervous system. A man nearly 60 years old was referred to our hospital because of a seizure and unconsciousness. After admission, the patient had fever and dizziness without obvious abnormalities in the cerebrospinal fluid, except for an increase in neutrophils. Metagenomic next-generation sequencing and DNA testing were positive for M. iranicum. The patient was treated with imipenem, minocycline, moxifloxacin, and linezolid, and he gradually recovered during follow-up.}, } @article {pmid37327680, year = {2023}, author = {Rosenzweig, AF and Burian, J and Brady, SF}, title = {Present and future outlooks on environmental DNA-based methods for antibiotic discovery.}, journal = {Current opinion in microbiology}, volume = {75}, number = {}, pages = {102335}, doi = {10.1016/j.mib.2023.102335}, pmid = {37327680}, issn = {1879-0364}, support = {R35 GM122559/GM/NIGMS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology ; *DNA, Environmental ; Bacteria/genetics ; Metagenomics ; *Biological Products ; Multigene Family ; }, abstract = {Novel antibiotics are in constant demand to combat a global increase in antibiotic-resistant infections. Bacterial natural products have been a long-standing source of antibiotic compounds, and metagenomic mining of environmental DNA (eDNA) has increasingly provided new antibiotic leads. The metagenomic small-molecule discovery pipeline can be divided into three main steps: surveying eDNA, retrieving a sequence of interest, and accessing the encoded natural product. Improvements in sequencing technology, bioinformatic algorithms, and methods for converting biosynthetic gene clusters into small molecules are steadily increasing our ability to discover metagenomically encoded antibiotics. We predict that, over the next decade, ongoing technological improvements will dramatically increase the rate at which antibiotics are discovered from metagenomes.}, } @article {pmid37327607, year = {2023}, author = {Xu, R and Kolton, M and Tao, W and Sun, X and Su, P and Huang, D and Zhang, M and Yang, Z and Guo, Z and Gao, H and Wang, Q and Li, B and Chen, C and Sun, W}, title = {Anaerobic selenite-reducing bacteria and their metabolic potentials in Se-rich sediment revealed by the combination of DNA-stable isotope probing, metagenomic binning, and metatranscriptomics.}, journal = {Journal of hazardous materials}, volume = {457}, number = {}, pages = {131834}, doi = {10.1016/j.jhazmat.2023.131834}, pmid = {37327607}, issn = {1873-3336}, mesh = {*Metagenome ; *Selenium/metabolism ; Selenious Acid/metabolism ; Metagenomics ; Anaerobiosis ; Bacteria/metabolism ; Isotopes/metabolism ; Bacteria, Anaerobic/metabolism ; DNA/chemistry ; }, abstract = {Microorganisms play a critical role in the biogeochemical cycling of selenium (Se) in aquatic environments, particularly in reducing the toxicity and bioavailability of selenite (Se(IV)). This study aimed to identify putative Se(IV)-reducing bacteria (Se[IV]RB) and investigate the genetic mechanisms underlying Se(IV) reduction in anoxic Se-rich sediment. Initial microcosm incubation confirmed that Se(IV) reduction was driven by heterotrophic microorganisms. DNA stable-isotope probing (DNA-SIP) analysis identified Pseudomonas, Geobacter, Comamonas, and Anaeromyxobacter as putative Se[IV]RB. High-quality metagenome-assembled genomes (MAGs) affiliated with these four putative Se[IV]RB were retrieved. Annotation of functional gene indicated that these MAGs contained putative Se(IV)-reducing genes such as DMSO reductase family, fumarate and sulfite reductases. Metatranscriptomic analysis of active Se(IV)-reducing cultures revealed significantly higher transcriptional levels of genes associated with DMSO reductase (serA/PHGDH), fumarate reductase (sdhCD/frdCD), and sulfite reductase (cysDIH) compared to those in cultures not amended with Se(IV), suggesting that these genes played important roles in Se(IV) reduction. The current study expands our knowledge of the genetic mechanisms involved in less-understood anaerobic Se(IV) bio-reduction. Additinally, the complementary abilities of DNA-SIP, metagenomics, and metatranscriptomics analyses are demonstrated in elucidating the microbial mechanisms of biogeochemical processes in anoxic sediment.}, } @article {pmid37327543, year = {2023}, author = {Yu, K and Chai, B and Zhuo, T and Tang, Q and Gao, X and Wang, J and He, L and Lei, X and Chen, B}, title = {Hydrostatic pressure drives microbe-mediated biodegradation of microplastics in surface sediments of deep reservoirs: Novel findings from hydrostatic pressure simulation experiments.}, journal = {Water research}, volume = {242}, number = {}, pages = {120185}, doi = {10.1016/j.watres.2023.120185}, pmid = {37327543}, issn = {1879-2448}, mesh = {Humans ; *Microplastics ; Plastics/analysis ; Hydrostatic Pressure ; Polyethylene Terephthalates ; Environmental Monitoring ; *Water Pollutants, Chemical/analysis ; Geologic Sediments/chemistry ; }, abstract = {Microplastics originate from the physical, chemical, or biological degradation of plastics in the environment. Once ingested by organisms at the bottom of the food chain, microplastics are passed on to organisms at higher trophic levels, posing a threat to human health. The distribution of microplastics and the metabolic pathways involved in their microbial degradation in surface sediments of drinking water reservoirs are still poorly understood. This study analyzed the occurrence patterns of microplastics and microbial community structure associated with microplastic biodegradation in surface sediments from a deep reservoir at various hydrostatic pressures. Based on the results of Fourier-transform and laser direct infrared spectroscopy, elevating the pressure resulted in altered sizes and shapes of microplastics in sediment samples with the presence of microorganisms. The influence of hydrostatic pressure on small-sized microplastics (20-500 μm) was pronounced. For instance, high pressure accelerated the breakdown of fibers, pellets, and fragments into smaller-sized microplastics. In particular, the mean size of polyethylene terephthalate microplastics decreased from 425.78 μm at atmospheric pressure to 366.62 μm at 0.7 Mpa. Metagenomic analysis revealed an increase in the relative abundances of plastic-degrading genera, such as Rhodococcus, Flavobacterium, and Aspergillus, in response to elevated pressures. Eight functional genes for biodegradation of polystyrene, polyethylene, and polyethylene terephthalate microplastics were annotated, including paaK, ladA, tphA3. Of these, tphA3 gene abundance was negatively influenced by hydrostatic pressure, providing direct evidence for the pathway by which microbial metabolism of polyethylene terephthalate led to decreased microplastic size under high pressure conditions. This study presents novel insights into hydrostatic pressure-driven microbial community structure, functional gene abundance, and key metabolic pathways associated with biodegradation of microplastics in reservoir sediments.}, } @article {pmid37327214, year = {2023}, author = {Potgieter, MG and Nel, AJM and Fortuin, S and Garnett, S and Wendoh, JM and Tabb, DL and Mulder, NJ and Blackburn, JM}, title = {MetaNovo: An open-source pipeline for probabilistic peptide discovery in complex metaproteomic datasets.}, journal = {PLoS computational biology}, volume = {19}, number = {6}, pages = {e1011163}, pmid = {37327214}, issn = {1553-7358}, mesh = {Humans ; *Tandem Mass Spectrometry ; RNA, Ribosomal, 16S/genetics ; Databases, Protein ; Peptides/genetics/analysis ; *Microbiota/genetics ; Bacteria/genetics ; Proteome/genetics ; }, abstract = {BACKGROUND: Microbiome research is providing important new insights into the metabolic interactions of complex microbial ecosystems involved in fields as diverse as the pathogenesis of human diseases, agriculture and climate change. Poor correlations typically observed between RNA and protein expression datasets make it hard to accurately infer microbial protein synthesis from metagenomic data. Additionally, mass spectrometry-based metaproteomic analyses typically rely on focused search sequence databases based on prior knowledge for protein identification that may not represent all the proteins present in a set of samples. Metagenomic 16S rRNA sequencing only targets the bacterial component, while whole genome sequencing is at best an indirect measure of expressed proteomes. Here we describe a novel approach, MetaNovo, that combines existing open-source software tools to perform scalable de novo sequence tag matching with a novel algorithm for probabilistic optimization of the entire UniProt knowledgebase to create tailored sequence databases for target-decoy searches directly at the proteome level, enabling metaproteomic analyses without prior expectation of sample composition or metagenomic data generation and compatible with standard downstream analysis pipelines.

RESULTS: We compared MetaNovo to published results from the MetaPro-IQ pipeline on 8 human mucosal-luminal interface samples, with comparable numbers of peptide and protein identifications, many shared peptide sequences and a similar bacterial taxonomic distribution compared to that found using a matched metagenome sequence database-but simultaneously identified many more non-bacterial peptides than the previous approaches. MetaNovo was also benchmarked on samples of known microbial composition against matched metagenomic and whole genomic sequence database workflows, yielding many more MS/MS identifications for the expected taxa, with improved taxonomic representation, while also highlighting previously described genome sequencing quality concerns for one of the organisms, and identifying an experimental sample contaminant without prior expectation.

CONCLUSIONS: By estimating taxonomic and peptide level information directly on microbiome samples from tandem mass spectrometry data, MetaNovo enables the simultaneous identification of peptides from all domains of life in metaproteome samples, bypassing the need for curated sequence databases to search. We show that the MetaNovo approach to mass spectrometry metaproteomics is more accurate than current gold standard approaches of tailored or matched genomic sequence database searches, can identify sample contaminants without prior expectation and yields insights into previously unidentified metaproteomic signals, building on the potential for complex mass spectrometry metaproteomic data to speak for itself.}, } @article {pmid37325710, year = {2023}, author = {Liu, Y and Zhong, W and Li, X and Shen, F and Ma, X and Yang, Q and Hong, S and Sun, Y}, title = {Diets, Gut Microbiota and Metabolites.}, journal = {Phenomics (Cham, Switzerland)}, volume = {3}, number = {3}, pages = {268-284}, pmid = {37325710}, issn = {2730-5848}, abstract = {The gut microbiota refers to the gross collection of microorganisms, estimated trillions of them, which reside within the gut and play crucial roles in the absorption and digestion of dietary nutrients. In the past decades, the new generation 'omics' (metagenomics, transcriptomics, proteomics, and metabolomics) technologies made it possible to precisely identify microbiota and metabolites and describe their variability between individuals, populations and even different time points within the same subjects. With massive efforts made, it is now generally accepted that the gut microbiota is a dynamically changing population, whose composition is influenced by the hosts' health conditions and lifestyles. Diet is one of the major contributors to shaping the gut microbiota. The components in the diets vary in different countries, religions, and populations. Some special diets have been adopted by people for hundreds of years aiming for better health, while the underlying mechanisms remain largely unknown. Recent studies based on volunteers or diet-treated animals demonstrated that diets can greatly and rapidly change the gut microbiota. The unique pattern of the nutrients from the diets and their metabolites produced by the gut microbiota has been linked with the occurrence of diseases, including obesity, diabetes, nonalcoholic fatty liver disease, cardiovascular disease, neural diseases, and more. This review will summarize the recent progress and current understanding of the effects of different dietary patterns on the composition of gut microbiota, bacterial metabolites, and their effects on the host's metabolism.}, } @article {pmid37325707, year = {2023}, author = {Wang, Y and Zhang, R and Pu, Y and Wang, D and Wang, Y and Wu, X and Pan, Y and Luo, C and Zhao, G and Quan, Z and Zheng, Y}, title = {Sample Collection, DNA Extraction, and Library Construction Protocols of the Human Microbiome Studies in the International Human Phenome Project.}, journal = {Phenomics (Cham, Switzerland)}, volume = {3}, number = {3}, pages = {300-308}, pmid = {37325707}, issn = {2730-5848}, abstract = {UNLABELLED: The human microbiome plays a crucial role in human health. In the past decade, advances in high-throughput sequencing technologies and analytical software have significantly improved our knowledge of the human microbiome. However, most studies concerning the human microbiome did not provide repeatable protocols to guide the sample collection, handling, and processing procedures, which impedes obtaining valid and timely microbial taxonomic and functional results. This protocol provides detailed operation methods of human microbial sample collection, DNA extraction, and library construction for both the amplicon sequencing-based measurements of the microbial samples from the human nasal cavity, oral cavity, and skin, as well as the shotgun metagenomic sequencing-based measurements of the human stool samples among adult participants. This study intends to develop practical procedure standards to improve the reproducibility of microbiota profiling of human samples.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s43657-023-00097-y.}, } @article {pmid37325051, year = {2023}, author = {Kerdreux, M and Edin, S and Löwenmark, T and Bronnec, V and Löfgren-Burström, A and Zingmark, C and Ljuslinder, I and Palmqvist, R and Ling, A}, title = {Porphyromonas gingivalis in Colorectal Cancer and its Association to Patient Prognosis.}, journal = {Journal of Cancer}, volume = {14}, number = {9}, pages = {1479-1485}, pmid = {37325051}, issn = {1837-9664}, abstract = {Microbiota dysbiosis may affect both the development and progression of colorectal cancer (CRC). Large metagenomic studies have highlighted specific oral bacteria linked to CRC including Porphyromonas gingivalis. Few studies have however analysed the implications of this bacterium in CRC progression and survival. In this study, we investigated the intestinal presence of P. gingivalis by qPCR in both faecal and mucosal samples from two different patient cohorts, including patients with precancerous dysplasia or CRC, as well as controls. P. gingivalis was detected in 2.6-5.3% of CRC patients and significantly different levels of P. gingivalis were found in faeces of CRC patients compared to controls (P = 0.028). Furthermore, an association was found between the presence of P. gingivalis in faeces and tumour tissue (P < 0.001). Our findings further suggested a potential link between mucosal P. gingivalis and tumours of MSI subtype (P = 0.040). Last but not least, patients with faecal P. gingivalis were found to have a significantly decreased cancer-specific survival (P = 0.040). In conclusion, P. gingivalis could be linked to patients with CRC and to a worse patient prognosis. Further studies are needed to elucidate the role of P. gingivalis in CRC pathogenesis.}, } @article {pmid37324728, year = {2023}, author = {Zhao, J and Yang, Y and Teng, M and Zheng, J and Wang, B and Mallawaarachchi, V and Lin, Y and Fang, Z and Shen, C and Yu, S and Yang, F and Qiao, L and Wang, L}, title = {Metaproteomics profiling of the microbial communities in fermentation starters (Daqu) during multi-round production of Chinese liquor.}, journal = {Frontiers in nutrition}, volume = {10}, number = {}, pages = {1139836}, pmid = {37324728}, issn = {2296-861X}, abstract = {INTRODUCTION: The special flavor and fragrance of Chinese liquor are closely related to microorganisms in the fermentation starter Daqu. The changes of microbial community can affect the stability of liquor yield and quality.

METHODS: In this study, we used data-independent acquisition mass spectrometry (DIA-MS) for cohort study of the microbial communities of a total of 42 Daqu samples in six production cycles at different times of a year. The DIA MS data were searched against a protein database constructed by metagenomic sequencing.

RESULTS: The microbial composition and its changes across production cycles were revealed. Functional analysis of the differential proteins was carried out and the metabolic pathways related to the differential proteins were explored. These metabolic pathways were related to the saccharification process in liquor fermentation and the synthesis of secondary metabolites to form the unique flavor and aroma in the Chinese liquor.

DISCUSSION: We expect that the metaproteome profiling of Daqu from different production cycles will serve as a guide for the control of fermentation process of Chinese liquor in the future.}, } @article {pmid37324413, year = {2023}, author = {Walters, KA and Mohan, G and Myers, KS and Ingle, AT and Donohue, TJ and Noguera, DR}, title = {A metagenome-level analysis of a microbial community fermenting ultra-filtered milk permeate.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {11}, number = {}, pages = {1173656}, pmid = {37324413}, issn = {2296-4185}, abstract = {Fermentative microbial communities have the potential to serve as biocatalysts for the conversion of low-value dairy coproducts into renewable chemicals, contributing to a more sustainable global economy. To develop predictive tools for the design and operation of industrially relevant strategies that utilize fermentative microbial communities, there is a need to determine the genomic features of community members that are characteristic to the accumulation of different products. To address this knowledge gap, we performed a 282-day bioreactor experiment with a microbial community that was fed ultra-filtered milk permeate, a low-value coproduct from the dairy industry. The bioreactor was inoculated with a microbial community from an acid-phase digester. A metagenomic analysis was used to assess microbial community dynamics, construct metagenome-assembled genomes (MAGs), and evaluate the potential for lactose utilization and fermentation product synthesis of community members represented by the assembled MAGs. This analysis led us to propose that, in this reactor, members of the Actinobacteriota phylum are important in the degradation of lactose, via the Leloir pathway and the bifid shunt, and the production of acetic, lactic, and succinic acids. In addition, members of the Firmicutes phylum contribute to the chain-elongation-mediated production of butyric, hexanoic, and octanoic acids, with different microbes using either lactose, ethanol, or lactic acid as the growth substrate. We conclude that genes encoding carbohydrate utilization pathways, and genes encoding lactic acid transport into the cell, electron confurcating lactate dehydrogenase, and its associated electron transfer flavoproteins, are genomic features whose presence in Firmicutes needs to be established to infer the growth substrate used for chain elongation.}, } @article {pmid37324088, year = {2023}, author = {Zuo, Y and Shen, W and Chen, G and Liu, H and Liu, N and Xu, T and Pu, J}, title = {Prediction of target genes in community-acquired pneumonia based on the bioinformatics method.}, journal = {Journal of thoracic disease}, volume = {15}, number = {5}, pages = {2694-2707}, pmid = {37324088}, issn = {2072-1439}, abstract = {BACKGROUND: To screen the related genes of community-acquired pneumonia (CAP) by bioinformatics technology, and to analyze the clinical value of key genes.

METHODS: Gene chip data sets containing CAP patients and normal controls were screened from the Gene Expression Omnibus (GEO) database. The downregulated differentially expressed genes (DEGs) were screened using a gene expression analysis tool (GEO2R). Simultaneously, gene set enrichment analysis (GSEA) was used to explore the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway and core genes related to CAP. The candidate genes were then intersected with the genes reported in Online Mendelian Inheritance in Man (OMIM), and the clinical value of these candidate genes was examined based on a literature search. Finally, the clinical data of the CAP patients were retrospectively analyzed. Detect the type of pathogenic bacteria in bronchial-alveolar lavage fluid (BALF) using metagenomics next-generation sequencing (mNGS) high throughput sequencing technology, and detect the expression of key genes through liquid based cell immunohistochemistry to analyze the correlation between pathogenic bacteria and key genes.

RESULTS: Through the intersection of Venn diagrams, 175 co-expressed downregulated DEGs related to CAP were identified. A total of 4 candidate genes, including ICOS, IL7R, ITK, and ZAP70, were obtained by constructing the protein mutual aid network and conducting a module analysis of the common differentially expressed genes. The core genes in the GSEA enrichment pathways were intersected with the CAP-related genes reported in the relevant literature retrieved from the OMIM database. In the Venn diagram, two genes that coexist with OMIM include IL7R and PIK3R1. After considering our findings and the relevant literature, we determined that the key gene related to the occurrence and development of CAP was IL7R. The mNGS detected 13 kinds of bacteria, 4 kinds of fungi, and 2 kinds of viruses. Based on immunohistochemical results, it was found that there were relatively more bacteria detected in the IL7R high expression group.

CONCLUSIONS: The identification of the key gene IL7R and the related signaling pathways extend understanding of the pathogenesis of CAP and provide a theoretical basis for clinical targeted therapy research.}, } @article {pmid37323917, year = {2023}, author = {Dukes, HE and Tinker, KA and Ottesen, EA}, title = {Disentangling hindgut metabolism in the American cockroach through single-cell genomics and metatranscriptomics.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1156809}, pmid = {37323917}, issn = {1664-302X}, abstract = {Omnivorous cockroaches host a complex hindgut microbiota comprised of insect-specific lineages related to those found in mammalian omnivores. Many of these organisms have few cultured representatives, thereby limiting our ability to infer the functional capabilities of these microbes. Here we present a unique reference set of 96 high-quality single cell-amplified genomes (SAGs) from bacterial and archaeal cockroach gut symbionts. We additionally generated cockroach hindgut metagenomic and metatranscriptomic sequence libraries and mapped them to our SAGs. By combining these datasets, we are able to perform an in-depth phylogenetic and functional analysis to evaluate the abundance and activities of the taxa in vivo. Recovered lineages include key genera within Bacteroidota, including polysaccharide-degrading taxa from the genera Bacteroides, Dysgonomonas, and Parabacteroides, as well as a group of unclassified insect-associated Bacteroidales. We also recovered a phylogenetically diverse set of Firmicutes exhibiting a wide range of metabolic capabilities, including-but not limited to-polysaccharide and polypeptide degradation. Other functional groups exhibiting high relative activity in the metatranscriptomic dataset include multiple putative sulfate reducers belonging to families in the Desulfobacterota phylum and two groups of methanogenic archaea. Together, this work provides a valuable reference set with new insights into the functional specializations of insect gut symbionts and frames future studies of cockroach hindgut metabolism.}, } @article {pmid37323913, year = {2023}, author = {Huang, W and Hu, S and Zhu, Y and Liu, S and Zhou, X and Fang, Y and Lu, Y and Wang, R}, title = {Metagenomic surveillance and comparative genomic analysis of Chlamydia psittaci in patients with pneumonia.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1157888}, pmid = {37323913}, issn = {1664-302X}, abstract = {Chlamydia psittaci, a strictly intracellular bacterium, is an underestimated etiologic agent leading to infections in a broad range of animals and mild illness or pneumonia in humans. In this study, the metagenomes of bronchoalveolar lavage fluids from the patients with pneumonia were sequenced and highly abundant C. psittaci was found. The target-enriched metagenomic reads were recruited to reconstruct draft genomes with more than 99% completeness. Two C. psittaci strains from novel sequence types were detected and these were closely related to the animal-borne isolates derived from the lineages of ST43 and ST28, indicating the zoonotic transmissions of C. psittaci would benefit its prevalence worldwide. Comparative genomic analysis combined with public isolate genomes revealed that the pan-genome of C. psittaci possessed a more stable gene repertoire than those of other extracellular bacteria, with ~90% of the genes per genome being conserved core genes. Furthermore, the evidence for significantly positive selection was identified in 20 virulence-associated gene products, particularly bacterial membrane-embedded proteins and type three secretion machines, which may play important roles in the pathogen-host interactions. This survey uncovered novel strains of C. psittaci causing pneumonia and the evolutionary analysis characterized prominent gene candidates involved in bacterial adaptation to immune pressures. The metagenomic approach is of significance to the surveillance of difficult-to-culture intracellular pathogens and the research into molecular epidemiology and evolutionary biology of C. psittaci.}, } @article {pmid37323909, year = {2023}, author = {Reva, O and Messina, E and La Cono, V and Crisafi, F and Smedile, F and La Spada, G and Marturano, L and Selivanova, EA and Rohde, M and Krupovic, M and Yakimov, MM}, title = {Functional diversity of nanohaloarchaea within xylan-degrading consortia.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1182464}, pmid = {37323909}, issn = {1664-302X}, abstract = {Extremely halophilic representatives of the phylum Candidatus Nanohaloarchaeota (members of the DPANN superphyla) are obligately associated with extremely halophilic archaea of the phylum Halobacteriota (according to the GTDB taxonomy). Using culture-independent molecular techniques, their presence in various hypersaline ecosystems around the world has been confirmed over the past decade. However, the vast majority of nanohaloarchaea remain uncultivated, and thus their metabolic capabilities and ecophysiology are currently poorly understood. Using the (meta)genomic, transcriptomic, and DNA methylome platforms, the metabolism and functional prediction of the ecophysiology of two novel extremely halophilic symbiotic nanohaloarchaea (Ca. Nanohalococcus occultus and Ca. Nanohalovita haloferacivicina) stably cultivated in the laboratory as members of a xylose-degrading binary culture with a haloarchaeal host, Haloferax lucentense, was determined. Like all known DPANN superphylum nanoorganisms, these new sugar-fermenting nanohaloarchaea lack many fundamental biosynthetic repertoires, making them exclusively dependent on their respective host for survival. In addition, given the cultivability of the new nanohaloarchaea, we managed to discover many unique features in these new organisms that have never been observed in nano-sized archaea both within the phylum Ca. Nanohaloarchaeota and the entire superphylum DPANN. This includes the analysis of the expression of organism-specific non-coding regulatory (nc)RNAs (with an elucidation of their 2D-secondary structures) as well as profiling of DNA methylation. While some ncRNA molecules have been predicted with high confidence as RNAs of an archaeal signal recognition particle involved in delaying protein translation, others resemble the structure of ribosome-associated ncRNAs, although none belong to any known family. Moreover, the new nanohaloarchaea have very complex cellular defense mechanisms. In addition to the defense mechanism provided by the type II restriction-modification system, consisting of Dcm-like DNA methyltransferase and Mrr restriction endonuclease, Ca. Nanohalococcus encodes an active type I-D CRISPR/Cas system, containing 77 spacers divided into two loci. Despite their diminutive genomes and as part of their host interaction mechanism, the genomes of new nanohaloarchaea do encode giant surface proteins, and one of them (9,409 amino acids long) is the largest protein of any sequenced nanohaloarchaea and the largest protein ever discovered in cultivated archaea.}, } @article {pmid37323907, year = {2023}, author = {Wang, S and Zhang, Q and Sun, L and Kumar, A}, title = {Editorial: Exploring the role of microorganisms in silages: species, communities, interactions, and functional characteristics.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1196267}, doi = {10.3389/fmicb.2023.1196267}, pmid = {37323907}, issn = {1664-302X}, } @article {pmid37323901, year = {2023}, author = {Hyams, Y and Rubin-Blum, M and Rosner, A and Brodsky, L and Rinkevich, Y and Rinkevich, B}, title = {Physiological changes during torpor favor association with Endozoicomonas endosymbionts in the urochordate Botrylloides leachii.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1072053}, pmid = {37323901}, issn = {1664-302X}, abstract = {Environmental perturbations evoke down-regulation of metabolism in some multicellular organisms, leading to dormancy, or torpor. Colonies of the urochordate Botrylloides leachii enter torpor in response to changes in seawater temperature and may survive for months as small vasculature remnants that lack feeding and reproductive organs but possess torpor-specific microbiota. Upon returning to milder conditions, the colonies rapidly restore their original morphology, cytology and functionality while harboring re-occurring microbiota, a phenomenon that has not been described in detail to date. Here we investigated the stability of B. leachii microbiome and its functionality in active and dormant colonies, using microscopy, qPCR, in situ hybridization, genomics and transcriptomics. A novel lineage of Endozoicomonas, proposed here as Candidatus Endozoicomonas endoleachii, was dominant in torpor animals (53-79% read abundance), and potentially occupied specific hemocytes found only in torpid animals. Functional analysis of the metagenome-assembled genome and genome-targeted transcriptomics revealed that Endozoicomonas can use various cellular substrates, like amino acids and sugars, potentially producing biotin and thiamine, but also expressing various features involved in autocatalytic symbiosis. Our study suggests that the microbiome can be linked to the metabolic and physiological states of the host, B. leachii, introducing a model organism for the study of symbioses during drastic physiological changes, such as torpor.}, } @article {pmid37323891, year = {2023}, author = {Ergunay, K and Dincer, E and Justi, SA and Bourke, BP and Nelson, SP and Liao, HM and Timurkan, MO and Oguz, B and Sahindokuyucu, I and Gokcecik, OF and Reinbold-Wasson, DD and Jiang, L and Achee, NL and Grieco, JP and Linton, YM}, title = {Impact of nanopore-based metagenome sequencing on tick-borne virus detection.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1177651}, pmid = {37323891}, issn = {1664-302X}, abstract = {INTRODUCTION: We evaluated metagenomic nanopore sequencing (NS) in field-collected ticks and compared findings from amplification-based assays.

METHODS: Forty tick pools collected in Anatolia, Turkey and screened by broad-range or nested polymerase chain reaction (PCR) for Crimean-Congo Hemorrhagic Fever Virus (CCHFV) and Jingmen tick virus (JMTV) were subjected to NS using a standard, cDNA-based metagenome approach.

RESULTS: Eleven viruses from seven genera/species were identified. Miviruses Bole tick virus 3 and Xinjiang mivirus 1 were detected in 82.5 and 2.5% of the pools, respectively. Tick phleboviruses were present in 60% of the pools, with four distinct viral variants. JMTV was identified in 60% of the pools, where only 22.5% were PCR-positive. CCHFV sequences characterized as Aigai virus were detected in 50%, where only 15% were detected by PCR. NS produced a statistically significant increase in detection of these viruses. No correlation of total virus, specific virus, or targeted segment read counts was observed between PCR-positive and PCR-negative samples. NS further enabled the initial description of Quaranjavirus sequences in ticks, where human and avian pathogenicity of particular isolates had been previously documented.

DISCUSSION: NS was observed to surpass broad-range and nested amplification in detection and to generate sufficient genome-wide data for investigating virus diversity. It can be employed for monitoring pathogens in tick vectors or human/animal clinical samples in hot-spot regions for examining zoonotic spillover.}, } @article {pmid37323848, year = {2023}, author = {Soundararajan, S and Selvakumar, J and Maria Joseph, ZM and Gopinath, Y and Saravanan, V and Santhanam, R}, title = {Investigating the modulatory effects of Moringa oleifera on the gut microbiota of chicken model through metagenomic approach.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1153769}, pmid = {37323848}, issn = {2297-1769}, abstract = {INTRODUCTION: This study aimed to assess the effects of supplementing chicken feed with Moringa oleifera leaf powder, a phytobiotic, on the gastrointestinal microbiota. The objective was to examine the microbial changes induced by the supplementation.

METHODS: A total of 40, one-day-old chickens were fed their basal diet for 42 days and then divided into two groups: SG1 (basal diet) and SG2 (basal diet + 10 g/kg Moringa oleifera leaf powder). Metagenomics analysis was conducted to analyze operational taxonomic units (OTUs), species annotation, and biodiversity. Additionally, 16S rRNA sequencing was performed for molecular characterization of isolated gut bacteria, identified as Enterococcus faecium. The isolated bacteria were tested for essential metabolites, demonstrating antibacterial, antioxidant, and anticancer activities.

RESULTS AND DISCUSSION: The analysis revealed variations in the microbial composition between the control group (SG1) and the M. oleifera-treated group (SG2). SG2 showed a 47% increase in Bacteroides and a 30% decrease in Firmicutes, Proteobacteria, Actinobacteria, and Tenericutes compared to SG1. TM7 bacteria were observed exclusively in the M. oleifera-treated group. These findings suggest that Moringa oleifera leaf powder acts as a modulator that enhances chicken gut microbiota, promoting the colonization of beneficial bacteria. PICRUSt analysis supported these findings, showing increased carbohydrate and lipid metabolism in the M.oleifera-treated gut microbiota.

CONCLUSION: This study indicates that supplementing chicken feed with Moringa oleifera leaf powder as a phytobiotic enhances the gut microbiota in chicken models, potentially improving overall health. The observed changes in bacterial composition, increased presence of Bacteroides, and exclusive presence of TM7 bacteria suggest a positive modulation of microbial balance. The essential metabolites from isolated Enterococcus faecium bacteria further support the potential benefits of Moringa oleifera supplementation.}, } @article {pmid37323571, year = {2023}, author = {Chan, AP and Siddique, A and Desplat, Y and Choi, Y and Ranganathan, S and Choudhary, KS and Khalid, MF and Diaz, J and Bezney, J and DeAscanis, D and George, Z and Wong, S and Selleck, W and Bowers, J and Zismann, V and Reining, L and Highlander, S and Brown, K and Armstrong, JR and Hakak, Y and Schork, NJ}, title = {A CRISPR-enhanced metagenomic NGS test to improve pandemic preparedness.}, journal = {Cell reports methods}, volume = {3}, number = {5}, pages = {100463}, pmid = {37323571}, issn = {2667-2375}, mesh = {Humans ; *COVID-19/diagnosis ; SARS-CoV-2/genetics ; Pandemics ; *Communicable Diseases ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {The lack of preparedness for detecting and responding to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pathogen (i.e., COVID-19) has caused enormous harm to public health and the economy. Testing strategies deployed on a population scale at day zero, i.e., the time of the first reported case, would be of significant value. Next-generation sequencing (NGS) has such capabilities; however, it has limited detection sensitivity for low-copy-number pathogens. Here, we leverage the CRISPR-Cas9 system to effectively remove abundant sequences not contributing to pathogen detection and show that NGS detection sensitivity of SARS-CoV-2 approaches that of RT-qPCR. The resulting sequence data can also be used for variant strain typing, co-infection detection, and individual human host response assessment, all in a single molecular and analysis workflow. This NGS work flow is pathogen agnostic and, therefore, has the potential to transform how large-scale pandemic response and focused clinical infectious disease testing are pursued in the future.}, } @article {pmid37322412, year = {2023}, author = {Yang, R and Li, X and Ying, Z and Zhao, Z and Wang, Y and Wang, Q and Shen, B and Peng, W}, title = {Prematurely delivering mothers show reductions of lachnospiraceae in their gut microbiomes.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {169}, pmid = {37322412}, issn = {1471-2180}, mesh = {Infant, Newborn ; Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome ; Mothers ; *Premature Birth ; *Microbiota ; Bacteria/genetics ; Clostridiales ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Preterm birth is the leading cause of perinatal morbidity and mortality. Despite evidence shows that imbalances in the maternal microbiome associates to the risk of preterm birth, the mechanisms underlying the association between a perturbed microbiota and preterm birth remain poorly understood.

METHOD: Applying shotgun metagenomic analysis on 80 gut microbiotas of 43 mothers, we analyzed the taxonomic composition and metabolic function in gut microbial communities between preterm and term mothers.

RESULTS: Gut microbiome of mothers delivering prematurely showed decreased alpha diversity and underwent significant reorganization, especially during pregnancy. SFCA-producing microbiomes, particularly species of Lachnospiraceae, Ruminococcaceae, and Eubacteriaceae, were significantly depleted in preterm mothers. Lachnospiraceae and its species were the main bacteria contributing to species' differences and metabolic pathways.

CONCLUSION: Gut microbiome of mothers delivering prematurely has altered and demonstrates the reduction of Lachnospiraceae.}, } @article {pmid37322285, year = {2023}, author = {López, JL and Fourie, A and Poppeliers, SWM and Pappas, N and Sánchez-Gil, JJ and de Jonge, R and Dutilh, BE}, title = {Growth rate is a dominant factor predicting the rhizosphere effect.}, journal = {The ISME journal}, volume = {17}, number = {9}, pages = {1396-1405}, pmid = {37322285}, issn = {1751-7370}, mesh = {*Rhizosphere ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; Plant Roots/microbiology ; Bacteria ; Soil/chemistry ; Plants/genetics ; }, abstract = {The root microbiome is shaped by plant root activity, which selects specific microbial taxa from the surrounding soil. This influence on the microorganisms and soil chemistry in the immediate vicinity of the roots has been referred to as the rhizosphere effect. Understanding the traits that make bacteria successful in the rhizosphere is critical for developing sustainable agriculture solutions. In this study, we compared the growth rate potential, a complex trait that can be predicted from bacterial genome sequences, to functional traits encoded by proteins. We analyzed 84 paired rhizosphere- and soil-derived 16S rRNA gene amplicon datasets from 18 different plants and soil types, performed differential abundance analysis, and estimated growth rates for each bacterial genus. We found that bacteria with higher growth rate potential consistently dominated the rhizosphere, and this trend was confirmed in different bacterial phyla using genome sequences of 3270 bacterial isolates and 6707 metagenome-assembled genomes (MAGs) from 1121 plant- and soil-associated metagenomes. We then identified which functional traits were enriched in MAGs according to their niche or growth rate status. We found that predicted growth rate potential was the main feature for differentiating rhizosphere and soil bacteria in machine learning models, and we then analyzed the features that were important for achieving faster growth rates, which makes bacteria more competitive in the rhizosphere. As growth rate potential can be predicted from genomic data, this work has implications for understanding bacterial community assembly in the rhizosphere, where many uncultivated bacteria reside.}, } @article {pmid37321733, year = {2023}, author = {Yao, T and Deemer, DG and Chen, MH and Reuhs, BL and Hamaker, BR and Lindemann, SR}, title = {Differences in fine arabinoxylan structures govern microbial selection and competition among human gut microbiota.}, journal = {Carbohydrate polymers}, volume = {316}, number = {}, pages = {121039}, doi = {10.1016/j.carbpol.2023.121039}, pmid = {37321733}, issn = {1879-1344}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Scattering, Small Angle ; X-Ray Diffraction ; *Microbiota ; Feces/microbiology ; Dietary Fiber ; Fermentation ; }, abstract = {Dietary fibers are known to modulate microbiome composition, but it is unclear to what extent minor fiber structural differences impact community assembly, microbial division of labor, and organismal metabolic responses. To test the hypothesis that fine linkage variations afford different ecological niches for distinct communities and metabolism, we employed a 7-day in vitro sequential batch fecal fermentation with four fecal inocula and measured responses using an integrated multi-omics approach. Two sorghum arabinoxylans (SAXs) were fermented, with one (RSAX) having slightly more complex branch linkages than the other (WSAX). Although there were minor glycoysl linkage differences, consortia on RSAX retained much higher species diversity (42 members) than on WSAX (18-23 members) with distinct species-level genomes and metabolic outcomes (e.g., higher short chain fatty acid production from RSAX and more lactic acid produced from WSAX). The major SAX-selected members were from genera of Bacteroides and Bifidobacterium and family Lachnospiraceae. Carbohydrate active enzyme (CAZyme) genes in metagenomes revealed broad AX-related hydrolytic potentials among key members; however, CAZyme genes enriched in different consortia displayed various catabolic domain fusions with diverse accessory motifs that differ among the two SAX types. These results suggest that fine polysaccharide structure exerts deterministic selection effect for distinct fermenting consortia.}, } @article {pmid37321678, year = {2023}, author = {Colston, SM and Barbato, RA and Goodson, MS and Karl, JP and Kokoska, RJ and Leary, DD and Racicot, K and Varaljay, V and Soares, JW}, title = {Current advances in microbiome sciences within the US Department of Defense-part 1: microbiomes for human health and performance.}, journal = {BMJ military health}, volume = {}, number = {}, pages = {}, doi = {10.1136/military-2022-002307}, pmid = {37321678}, issn = {2633-3775}, abstract = {Microbiomes involve complex microbial communities where the microorganisms interact with one another as well as their associated hosts or environmental niches. The characterisation of these communities and associations have largely been achieved through 'omics' technologies, such as metagenomics, metaproteomics and metametabolomics, and model systems. Recent research in host-associated microbiomes have been aimed at understanding the roles microbes may play in host fitness or conversely how host activities/conditions may perturb the microbial community, which can further affect host health. These studies have led to the investigation of detection, intervention or modulation methods, which may serve to provide benefits to the host and advance our understanding of microbiome associations. With the clear implications on human health and disease, the US Department of Defense (DoD) has made microbiome research a priority, with the founding of the Tri-Service Microbiome Consortium (TSMC) to enhance collaboration, coordination and communication of microbiome research among DoD organisations and partners in academia and industry. DoD microbiome research focuses mainly on the following themes: (1) Human health and performance; (2) Environmental microbiomes; and (3) Enabling technologies. This review provides an update of current DoD microbiome research efforts centred on human health and performance and highlights innovative research being done in academia and industry that can be leveraged by the DoD. These topics were also communicated and further discussed during the fifth Annual TSMC Symposium. This paper forms part of the special issue of BMJ Military Health dedicated to Personalised Digital Technology for Mental Health in the Armed Forces.}, } @article {pmid37317863, year = {2023}, author = {Bowman, J and Gull, T and Ulmanis, EG and Ogunbadewa, AJ and Shen, Z and Johnson, GJ and Odemuyiwa, SO}, title = {Metagenomic identification of a novel oomycete cultured from a pyogranulomatous mass on the tail of a domestic cat.}, journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc}, volume = {35}, number = {5}, pages = {507-513}, pmid = {37317863}, issn = {1943-4936}, mesh = {Cats ; Animals ; Phylogeny ; *Pythium/genetics ; Genomics ; }, abstract = {We report here a transiently culturable oomycete pathogen isolated from a pyogranulomatous tail mass in a cat. The organism was morphologically and genetically distinct from Lagenidium and Pythium species. Following next-generation sequencing (NGS) and assembly of contigs, initial phylogenetic analysis using fragments of the cox1 mitochondrial gene identified this specimen as Paralagenidium sp. after nucleotide alignments with sequences obtained from the Barcode of Life Data System (BOLD). However, further analysis of a concatenation of 13 different mitochondrial genes showed that this organism is unique and different from all known oomycetes. A negative PCR result using primers targeting known oomycete pathogens may not be enough to rule out oomycosis in a suspected case. Additionally, the use of a single gene to classify oomycetes may produce misleading results. The advent of metagenomic sequencing and NGS provides a unique opportunity to further explore the diversity of oomycetes as plant and animal pathogens beyond the current capabilities of global barcoding projects that are based on partial genomic sequences.}, } @article {pmid37317330, year = {2023}, author = {Zheng, Y and Zhu, H and Li, Q and Xu, G}, title = {The Effects of Different Feeding Regimes on Body Composition, Gut Microbial Population, and Susceptibility to Pathogenic Infection in Largemouth Bass.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317330}, issn = {2076-2607}, abstract = {This study investigated the effects of dietary commercial feed (n = 50,025 in triplicate, named group PF for soil dike pond, sampling n = 7; n = 15,000 in triplicate, WF for water tank, n = 8), iced fish (n = 50,025 in triplicate, PI, n = 7), and a combination of both (n = 50,025 in triplicate, PFI, n = 8) on different metabolic parameters of the largemouth bass, Micropterus salmoides (0.67 ± 0.09 g, culture period from June 2017 to July 2018). Throughout the experimental period, different areas of water (including input water of the front, middle of the pond, and from the drain off at the back) and their mixed samples were simultaneously analyzed to find the source of the main infectious bacteria. Various feeding strategies may differentially affect body composition and shape the gut microbiota, but the mode of action has not been determined. Results showed that no significant differences were found in the growth performance except for the product yield using a different culture mode (PFI vs. WF). For muscle composition, the higher ∑SFA, ∑MUFA, ∑n-6PUFA, and 18:3n-3/18:2n-6 levels were detected in largemouth bass fed with iced fish, while enrichment in ∑n-3PUFA and ∑HUFA was detected in largemouth bass fed with commercial feed. For the gut microbiota, Fusobacteria, Proteobacteria, and Firmicutes were the most dominant phyla among all the gut samples. The abundance of Firmicutes and Tenericutes significantly decreased and later increased with iced fish feeding. The relative abundance of species from the Clostridia, Mollicutes, Mycoplasmatales, and families (Clostridiaceae and Mycoplasmataceae) significantly increased in the feed plus iced fish (PFI) group relative to that in the iced fish (PI) group. Pathways of carbohydrate metabolism and the digestive system were enriched in the commercial feed group, whereas infectious bacterial disease resistance-related pathways were enriched in the iced fish group, corresponding to the higher rate of death, fatty liver disease, and frequency and duration of cyanobacteria outbreaks. Feeding with iced fish resulted in more activities in the digestive system and energy metabolism, more efficient fatty acid metabolism, had higher ∑MUFA, and simultaneously had the potential for protection against infectious bacteria from the environment through a change in intestinal microbiota in the pond of largemouth bass culturing. Finally, the difference in feed related to the digestive system may contribute to the significant microbiota branch in the fish gut, and the input and outflow of water affects the intestinal flora in the surrounding water and in the gut, which in turn affects growth and disease resistance.}, } @article {pmid37317237, year = {2023}, author = {Stoyancheva, G and Kabaivanova, L and Hubenov, V and Chorukova, E}, title = {Metagenomic Analysis of Bacterial, Archaeal and Fungal Diversity in Two-Stage Anaerobic Biodegradation for Production of Hydrogen and Methane from Corn Steep Liquor.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317237}, issn = {2076-2607}, support = {КП-06-Н46/4//Bulgarian Science Fund/ ; }, abstract = {The main purpose of this study was to identify the microbial communities (bacterial, archaeal and fungal) in a two-stage system of anaerobic bioreactors for the production of hydrogen and methane from the waste substrate-corn steep liquor. Wastes from the food industry are valuable resources with potential in biotechnological production because of their high organic matter contents. In addition, the production of hydrogen and methane, volatile fatty acids, reducing sugars and cellulose content was monitored. Two-stage anaerobic biodegradation processes were performed by microbial populations in the first hydrogen generating bioreactor (working volume of 3 dm[3]) and in the second methane-generating reactor (working volume of 15 dm[3]). Cumulative hydrogen yield reached 2000 cm[3] or 670 cm[3]/L a day, while the methane production reached a maximum quantity of 3300 cm[3] or 220 cm[3]/L a day. Microbial consortia in anaerobic digestion systems play an essential role for process optimization and biofuel production enhancement. The obtained results showed the possibility of conducting two separate processes-the hydrogenic (hydrolysis and acidogenesis) and methanogenic (acetogenesis and methanogenesis)-as two stages of anaerobic digestion to favor energy production under controlled conditions with corn steep liquor. The diversity of microorganisms as main participants in the processes in the bioreactors of the two-stage system was followed using metagenome sequencing and bioinformatics analysis. The obtained metagenomic data showed that the most abundant phylum in both bacterial communities was Firmicutes-58.61% and 36.49% in bioreactors 1 and 2, respectively. Phylum Actinobacteria were found in significant quantities (22.91%) in the microbial community in Bioreactor 1, whereas in Bioreactor 2, they were 2.1%. Bacteroidetes are present in both bioreactors. Phylum Euryarchaeota made up 0.4% of the contents in the first bioreactor and 11.4% in the second. As the dominant genera among methanogenic archaea are Methanothrix (8.03%) and Methanosarcina (3.39%), the main fungal representatives were Saccharomyces cerevisiae. New knowledge of anaerobic digestion mediated by novel microbial consortia could be widely used to convert different wastes to green energy.}, } @article {pmid37317232, year = {2023}, author = {Kamau, E and Yang, S}, title = {Metagenomic Sequencing of Positive Blood Culture Fluid for Accurate Bacterial and Fungal Species Identification: A Pilot Study.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317232}, issn = {2076-2607}, abstract = {With blood stream infections (BSIs) representing a major cause of mortality and morbidity worldwide, blood cultures play a crucial role in diagnosis, but their clinical application is dampened by the long turn-around time and the detection of only culturable pathogens. In this study, we developed and validated a shotgun metagenomics next-generation sequencing (mNGS) test directly from positive blood culture fluid, allowing for the identification of fastidious or slow growing microorganisms more rapidly. The test was built based on previously validated next-generation sequencing tests, which rely on several key marker genes for bacterial and fungal identification. The new test utilizes an open-source metagenomics CZ-ID platform for the initial analysis to generate the most likely candidate species, which is then used as a reference genome for downstream, confirmatory analysis. This approach is innovative because it takes advantage of an open-source software's agnostic taxonomic calling capability while still relying on the more established and previously validated marker gene-based identification scheme, increasing the confidence in the final results. The test showed high accuracy (100%, 30/30) for both bacterial and fungal microorganisms. We further demonstrated its clinical utility especially for anaerobes and mycobacteria that are either fastidious, slow growing, or unusual. Although applicable in only limited settings, the Positive Blood Culture mNGS test provides an incremental improvement in solving the unmet clinical needs for the diagnosis of challenging BSIs.}, } @article {pmid37317217, year = {2023}, author = {Trapani, S and Caporizzi, A and Ricci, S and Indolfi, G}, title = {Human Bocavirus in Childhood: A True Respiratory Pathogen or a "Passenger" Virus? A Comprehensive Review.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317217}, issn = {2076-2607}, abstract = {Recently, human bocavirus (HBoV) has appeared as an emerging pathogen, with an increasing number of cases reported worldwide. HBoV is mainly associated with upper and lower respiratory tract infections in adults and children. However, its role as a respiratory pathogen is still not fully understood. It has been reported both as a co-infectious agent (predominantly with respiratory syncytial virus, rhinovirus, parainfluenza viruses, and adenovirus), and as an isolated viral pathogen during respiratory tract infections. It has also been found in asymptomatic subjects. The authors review the available literature on the epidemiology of HBoV, the underlying risk factors associated with infection, the virus's transmission, and its pathogenicity as a single pathogen and in co-infections, as well as the current hypothesis about the host's immune response. An update on different HBoV detection methods is provided, including the use of quantitative single or multiplex molecular methods (screening panels) on nasopharyngeal swabs or respiratory secretions, tissue biopsies, serum tests, and metagenomic next-generations sequencing in serum and respiratory secretions. The clinical features of infection, mainly regarding the respiratory tract but also, though rarely, the gastrointestinal one, are extensively described. Furthermore, a specific focus is dedicated to severe HBoV infections requiring hospitalization, oxygen therapy, and/or intensive care in the pediatric age; rare fatal cases have also been reported. Data on tissue viral persistence, reactivation, and reinfection are evaluated. A comparison of the clinical characteristics of single infection and viral or bacterial co-infections with high or low HBoV rates is carried out to establish the real burden of HBoV disease in the pediatric population.}, } @article {pmid37317196, year = {2023}, author = {Santiago-Rodriguez, TM and Le François, B and Macklaim, JM and Doukhanine, E and Hollister, EB}, title = {The Skin Microbiome: Current Techniques, Challenges, and Future Directions.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317196}, issn = {2076-2607}, abstract = {Skin acts as a barrier that promotes the colonization of bacteria, fungi, archaea, and viruses whose membership and function may differ depending on the various specialized niches or micro-environments of the skin. The group of microorganisms inhabiting the skin, also known as the skin microbiome, offers protection against pathogens while actively interacting with the host's immune system. Some members of the skin microbiome can also act as opportunistic pathogens. The skin microbiome is influenced by factors such as skin site, birth mode, genetics, environment, skin products, and skin conditions. The association(s) of the skin microbiome with health and disease has (have) been identified and characterized via culture-dependent and culture-independent methods. Culture-independent methods (such as high-throughput sequencing), in particular, have expanded our understanding of the skin microbiome's role in maintaining health or promoting disease. However, the intrinsic challenges associated with the low microbial biomass and high host content of skin microbiome samples have hindered advancements in the field. In addition, the limitations of current collection and extraction methods and biases derived from sample preparation and analysis have significantly influenced the results and conclusions of many skin microbiome studies. Therefore, the present review discusses the technical challenges associated with the collection and processing of skin microbiome samples, the advantages and disadvantages of current sequencing approaches, and potential future areas of focus for the field.}, } @article {pmid37317182, year = {2023}, author = {Li, Y and Chang, L and Xu, K and Zhang, S and Gao, F and Fan, Y}, title = {Research Progresses on the Function and Detection Methods of Insect Gut Microbes.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317182}, issn = {2076-2607}, support = {22078171//Natural Science Foundation of China/ ; 21374301D//Program of Hebei/ ; 2023B08//Scientific Research Foundation of Tangshan Normal University/ ; }, abstract = {The insect gut is home to an extensive array of microbes that play a crucial role in the digestion and absorption of nutrients, as well as in the protection against pathogenic microorganisms. The variety of these gut microbes is impacted by factors such as age, diet, pesticides, antibiotics, sex, and caste. Increasing evidence indicates that disturbances in the gut microbiota can lead to compromised insect health, and that its diversity has a far-reaching impact on the host's health. In recent years, the use of molecular biology techniques to conduct rapid, qualitative, and quantitative research on the host intestinal microbial diversity has become a major focus, thanks to the advancement of metagenomics and bioinformatics technologies. This paper reviews the main functions, influencing factors, and detection methods of insect gut microbes, in order to provide a reference and theoretical basis for better research utilization of gut microbes and management of harmful insects.}, } @article {pmid37317158, year = {2023}, author = {Yang, C and Das, Q and Rehman, MA and Yin, X and Shay, J and Gauthier, M and Lau, CH and Ross, K and Diarra, MS}, title = {Microbiome of Ceca from Broiler Chicken Vaccinated or Not against Coccidiosis and Fed Berry Pomaces.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317158}, issn = {2076-2607}, support = {GRDI-AMR PSS #1858, J-001262//Canadian Federal Genomic Research and Development Initiative on Antimicrobial resistance/ ; AIP CL-02 AGR-10383//Agriculture and Agri-Food Canada through the Organic Science Cluster II program/ ; }, abstract = {American cranberry (Vaccinium macrocarpon) and lowbush/wild blueberry (V. angustifolium) pomace are polyphenol-rich products having potentially beneficial effects in broiler chickens. This study investigated the cecal microbiome of broiler-vaccinated or non-vaccinated birds against coccidiosis. Birds in each of the two groups (vaccinated or non-vaccinated) were fed a basal non-supplemented diet (NC), a basal diet supplemented with bacitracin (BAC), American cranberry (CP), and lowbush blueberry (BP) pomace alone or in combination (CP + BP). At 21 days of age, cecal DNA samples were extracted and analyzed using both whole-metagenome shotgun sequencing and targeted-resistome sequencing approaches. Ceca from vaccinated birds showed a lower abundance of Lactobacillus and a higher abundance of Escherichia coli than non-vaccinated birds (p < 0.05). The highest and lowest abundance of L. crispatus and E. coli, respectively, were observed in birds fed CP, BP, and CP + BP compared to those from NC or BAC treatments (p < 0.05). Coccidiosis vaccination affected the abundance of virulence genes (VGs) related to adherence, flagella, iron utilization, and secretion system. Toxin-related genes were observed in vaccinated birds (p < 0.05) in general, with less prevalence in birds fed CP, BP, and CP + BP than NC and BAC (p < 0.05). More than 75 antimicrobial resistance genes (ARGs) detected by the shotgun metagenomics sequencing were impacted by vaccination. Ceca from birds fed CP, BP, and CP + BP showed the lowest (p < 0.05) abundances of ARGs related to multi-drug efflux pumps, modifying/hydrolyzing enzyme and target-mediated mutation, when compared to ceca from birds fed BAC. Targeted metagenomics showed that resistome from BP treatment was distant to other groups for antimicrobials, such as aminoglycosides (p < 0.05). Significant differences in the richness were observed between the vaccinated and non-vaccinated groups for aminoglycosides, β-lactams, lincosamides, and trimethoprim resistance genes (p < 0.05). Overall, this study demonstrated that dietary berry pomaces and coccidiosis vaccination significantly impacted cecal microbiota, virulome, resistome, and metabolic pathways in broiler chickens.}, } @article {pmid37317157, year = {2023}, author = {Shabbir, S and Hu, Y and He, X and Huang, K and Xu, W}, title = {Toxicity and Impact of Silica Nanoparticles on the Configuration of Gut Microbiota in Immunodeficient Mice.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317157}, issn = {2076-2607}, support = {00109012//The 2115 Talent Training Plan of China Agricultural University (00109012)./ ; }, abstract = {Nanoparticles (NPs), having exceptional physicochemical and electrical characteristics with lower toxicity, have evolved as dynamic drug delivery carriers in living organisms. Potentially, the intragastric gavage of silica nanoparticles (SiNPs) affects gut microbiota profiles in immunodeficient mice. In this study, the impact of SiNPs of variable size and dosage was investigated in cyclophosphamide (Cy)-induced immunodeficient mice, specifically on their immune functions and gut microbiota, through physicochemical and metagenomic analysis. SiNPs of different sizes and doses were gavaged to Cy-induced immunodeficient mice for 12 days at an interval of 24 h to investigate their effects on immunological functions and the gut microbiome of mice. Our results showed that SiNPs had no significant toxicological effects on the cellular and hematological activities of immunodeficient mice. Furthermore, after the administration of different levels of SiNPs, no immune dysfunction was found in the immunosuppressed mice groups. However, gut-microbial studies and comparisons of characteristic bacterial diversity and compositions demonstrated that SiNPs significantly affect the abundance of different bacterial communities. LEfSe analysis revealed that SiNPs significantly increased the abundance of Lactobacillus, Sphingomonas, Sutterella, Akkermansia, and Prevotella, and potentially reduced Ruminococcus and Allobaculum. Thus, SiNPs significantly regulate and modify the configuration of the gut microbiota in immunodeficient mice. These dynamic variations in the intestinal bacterial community, abundance, and diversity provide new insight into the regulation and administration of silica-based NPs. This would be helpful for the further demonstration of the mechanism of action and prediction of the potential effects of SiNPs.}, } @article {pmid37317137, year = {2023}, author = {Schaefer, EAF and Chu, S and Wylie, KM and Wylie, TN and Griffith, OL and Pearce, JW and Johnson, GC and Bryan, JN and Flesner, BK}, title = {Metagenomic Analysis of DNA Viruses with Targeted Sequence Capture of Canine Lobular Orbital Adenomas and Normal Conjunctiva.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317137}, issn = {2076-2607}, support = {VAF2017-01//ACVO Vision for Animals Foundation/ ; }, abstract = {Our study aims are: (1) to evaluate phenotypically normal canine conjunctival and orbital tissue and tissue from canine lobular orbital adenomas (CLOAs) for the presence of viral genomic material and (2) phylogenetically classify detected DNA viruses to determine if a DNA virus is associated with CLOAs. A total of 31 formalin fixed paraffin embedded CLOA tissue samples, 4 papillomas or sarcoid, and 10 fresh clinically normal conjunctival tissues were included in this study. Genomic DNA was isolated from all samples and sequencing libraries were prepared. The libraries were molecularly indexed and pooled and viral DNA was enriched via targeted sequence capture utilizing ViroCap. The libraries were sequenced on the Illumina HiSeq platform and compared to known viral DNA reference genomes to identify viral DNA. Carnivore parvovirus was identified in 6.4% and 20% of CLOA tissue and normal conjunctival samples, respectively. This study showed that conjunctival tissue from healthy dogs and CLOAs uncommonly harbor DNA viruses, and no DNA virus was associated with these tumors. Further studies are needed to evaluate the etiologic cause of CLOAs.}, } @article {pmid37317135, year = {2023}, author = {Devane, ML and Taylor, W and Dupont, PY and Armstrong, B and Weaver, L and Gilpin, BJ}, title = {Exploring the Bacterial Community in Aged Fecal Sources from Dairy Cows: Impacts on Fecal Source Tracking.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317135}, issn = {2076-2607}, support = {C10X1006//Ministry of Business Innovation and Employment, New Zealand Government/ ; SSIF//Strategic Science Internal Funding (SSIF) from Ministry for Business Innovation and Employment/ ; }, abstract = {(1) Background: This paper discusses the impact of agricultural activities on stream health, particularly in relation to dairy cow fecal pollution. The study explores the fecal microbiome of cattle and the potential ecological implications of aging fecal pollution on waterways. (2) Methods: The study examines changes in the bacterial community available for mobilization from in-situ decomposing cowpats and the effects of simulated rainfall. The microbiome of individual cowpats was monitored over 5.5 months. We used 16S rRNA metagenomics and machine learning software, FEAST (Fast Expectation-mAximization for microbial Source Tracking), for bacterial and fecal source assignments. (3) Results: The phyla Bacillota and Bacteroidota are dominant in the fecal microbiota of fresh cow feces but shift to Pseudomonodota, Actinomycetota, and environmental Bacteroidota in aged cowpats. Potential impacts of these bacterial community shifts on inputs to local agricultural streams are discussed in relation to water quality monitoring and aging sources of fecal contamination. We identified taxon orders that are potential indicators of fresh cattle sources (Oscillospirales and Bacteroidales) and aged sources (Peptostreptococcales-Tissierellales) in water bodies. (4) The paper highlights that bacterial metagenomic profiling can inform our understanding of the ecology of microbial communities in aquatic environments and the potential impacts of agricultural activities on ecosystem health.}, } @article {pmid37317121, year = {2023}, author = {Palmieri, O and Castellana, S and Latiano, A and Latiano, T and Gentile, A and Panza, A and Nardella, M and Ciardiello, D and Latiano, TP and Corritore, G and Mazza, T and Perri, F and Biscaglia, G}, title = {Mucosal Microbiota from Colorectal Cancer, Adenoma and Normal Epithelium Reveals the Imprint of Fusobacterium nucleatum in Cancerogenesis.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317121}, issn = {2076-2607}, support = {Ricerca Corrente program 2022-2024 and Reti//Italian Minister of Health/ ; }, abstract = {UNLABELLED: An increasing amount of evidence suggests the emerging role of the gut microbiota in the development of colorectal cancer (CRC). This study aimed to elucidate the architecture of microbial communities within normal and neoplastic colonic mucosa.

METHODS: Microbiota were analyzed by NGS and by an ensemble of metagenomics analysis tools in a total of 69 tissues from 9 patients with synchronous colorectal neoplasia and adenomas (27 specimens: 9 from normal tissues, 9 adenomas, and 9 tumours), 16 patients with only colonic adenomas (32 specimens: 16 from normal tissues and 16 adenomas), and from healthy subjects (10 specimens of normal mucosa).

RESULTS: Weak differences were observed in alpha and beta metrics among the synchronous tissues from CRC and controls. Through pairwise differential abundance analyses of sample groups, an increasing trend of Rikenellaceae, Pseudomonas and Fusobacterium, and decreasing trends of Staphylococcus, Actinobacillus and Gemmiger were observed in CRC, while Staphylococcus and Bifidobacterium were decreased in patients with only adenomas. At RT-qPCR analysis, Fusobacterium nucleatum was significantly enriched in all the tissues of subjects with synchronous colorectal neoplasia.

CONCLUSION: Our findings provide a comprehensive view of the human mucosa-associated gut microbiota, emphasizing global microbial diversity mostly in synchronous lesions and proving the constant presence of Fusobacterium nucleatum, with its ability to drive carcinogenesis.}, } @article {pmid37317119, year = {2023}, author = {Santos, NACD and Carvalho, VR and Souza-Neto, JA and Alonso, DP and Ribolla, PEM and Medeiros, JF and Araujo, MDS}, title = {Bacterial Microbiota from Lab-Reared and Field-Captured Anopheles darlingi Midgut and Salivary Gland.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317119}, issn = {2076-2607}, support = {INV-003970/GATES/Bill & Melinda Gates Foundation/United States ; }, abstract = {Anopheles darlingi is a major malaria vector in the Amazon region and, like other vectors, harbors a community of microorganisms with which it shares a network of interactions. Here, we describe the diversity and bacterial composition from the midguts and salivary glands of lab-reared and field-captured An. darlingi using metagenome sequencing of the 16S rRNA gene. The libraries were built using the amplification of the region V3-V4 16S rRNA gene. The bacterial community from the salivary glands was more diverse and richer than the community from the midguts. However, the salivary glands and midguts only showed dissimilarities in beta diversity between lab-reared mosquitoes. Despite that, intra-variability was observed in the samples. Acinetobacter and Pseudomonas were dominant in the tissues of lab-reared mosquitoes. Sequences of Wolbachia and Asaia were both found in the tissue of lab-reared mosquitoes; however, only Asaia was found in field-captured An. darlingi, but in low abundance. This is the first report on the characterization of microbiota composition from the salivary glands of An. darlingi from lab-reared and field-captured individuals. This study can provide invaluable insights for future investigations regarding mosquito development and interaction between mosquito microbiota and Plasmodium sp.}, } @article {pmid37317090, year = {2023}, author = {Tapio, M and Fischer, D and Mäntysaari, P and Tapio, I}, title = {Rumen Microbiota Predicts Feed Efficiency of Primiparous Nordic Red Dairy Cows.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317090}, issn = {2076-2607}, support = {818368//European Union/ ; }, abstract = {Efficient feed utilization in dairy cows is crucial for economic and environmental reasons. The rumen microbiota plays a significant role in feed efficiency, but studies utilizing microbial data to predict host phenotype are limited. In this study, 87 primiparous Nordic Red dairy cows were ranked for feed efficiency during their early lactation based on residual energy intake, and the rumen liquid microbial ecosystem was subsequently evaluated using 16S rRNA amplicon and metagenome sequencing. The study used amplicon data to build an extreme gradient boosting model, demonstrating that taxonomic microbial variation can predict efficiency (rtest = 0.55). Prediction interpreters and microbial network revealed that predictions were based on microbial consortia and the efficient animals had more of the highly interacting microbes and consortia. Rumen metagenome data was used to evaluate carbohydrate-active enzymes and metabolic pathway differences between efficiency phenotypes. The study showed that an efficient rumen had a higher abundance of glycoside hydrolases, while an inefficient rumen had more glycosyl transferases. Enrichment of metabolic pathways was observed in the inefficient group, while efficient animals emphasized bacterial environmental sensing and motility over microbial growth. The results suggest that inter-kingdom interactions should be further analyzed to understand their association with the feed efficiency of animals.}, } @article {pmid37317072, year = {2023}, author = {Gao, H and Yu, Y and Lv, Y and Wang, D and Li, H and Li, Z and Zhang, Y and Chen, L and Leng, J}, title = {Metagenomic Sequencing Reveals the Taxonomic and Functional Characteristics of Rumen Micro-organisms in Gayals.}, journal = {Microorganisms}, volume = {11}, number = {5}, pages = {}, pmid = {37317072}, issn = {2076-2607}, support = {32260841//National Natural Science Foundation of China/ ; 31672452//National Natural Science Foundation of China/ ; }, abstract = {As a semi-wild breed, Gayals have a strong fiber degradation capacity, which is unique to the microbial structure and function of their rumen. In this study, the unique rumen microbial composition and function of Gayals were investigated by metagenomic sequencing, with the Yunnan yellow cattle as the control. We compared the differences in rumen micro-organisms between Gayals and the Yunnan Yellow cattle, and the results showed that there were differences in bacteria, archaea and fungi between Gayals and the Yunnan Yellow cattle, while no significant abundance changes were observed in the protozoa. In addition, the ratio of Firmicutes to Bacteroidetes (1.06) in Gayals was higher than that of the Yunnan Yellow cattle (0.66). Three enzymes (PTA, ACH and FTHFS) related to the acetate production pathway and five enzymes (BHBD, THL, PTB, BK and BCACT) involved in butyric acid production were annotated in this study. The CAZymes search results showed that the abundance of GH5, GH26, GH94, CBM11 and CBM63 in Gayals was higher than in the Yunnan Yellow cattle (p < 0.05). Furthermore, this research constructed a model of rumen micro-organisms degrading fibers according to the characteristics and differences in the rumen microbiota structures and functions of the two breeds. This study expands our knowledge of the rumen microbiota and the mechanisms of fiber degradation in Gayals.}, } @article {pmid37316519, year = {2023}, author = {Jin, X and Yu, FB and Yan, J and Weakley, AM and Dubinkina, V and Meng, X and Pollard, KS}, title = {Culturing of a complex gut microbial community in mucin-hydrogel carriers reveals strain- and gene-associated spatial organization.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3510}, pmid = {37316519}, issn = {2041-1723}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Hydrogels ; Metagenome ; *Microbiota/genetics ; Mucins ; }, abstract = {Microbial community function depends on both taxonomic composition and spatial organization. While composition of the human gut microbiome has been deeply characterized, less is known about the organization of microbes between regions such as lumen and mucosa and the microbial genes regulating this organization. Using a defined 117 strain community for which we generate high-quality genome assemblies, we model mucosa/lumen organization with in vitro cultures incorporating mucin hydrogel carriers as surfaces for bacterial attachment. Metagenomic tracking of carrier cultures reveals increased diversity and strain-specific spatial organization, with distinct strains enriched on carriers versus liquid supernatant, mirroring mucosa/lumen enrichment in vivo. A comprehensive search for microbial genes associated with this spatial organization identifies candidates with known adhesion-related functions, as well as novel links. These findings demonstrate that carrier cultures of defined communities effectively recapitulate fundamental aspects of gut spatial organization, enabling identification of key microbial strains and genes.}, } @article {pmid37316017, year = {2023}, author = {Yin, P and Zhang, C and Du, T and Yi, S and Yu, L and Tian, F and Chen, W and Zhai, Q}, title = {Meta-analysis reveals different functional characteristics of human gut Bifidobacteria associated with habitual diet.}, journal = {Food research international (Ottawa, Ont.)}, volume = {170}, number = {}, pages = {112981}, doi = {10.1016/j.foodres.2023.112981}, pmid = {37316017}, issn = {1873-7145}, mesh = {Humans ; Bifidobacterium/genetics ; Diet ; *Bifidobacterium longum/genetics ; *Bifidobacterium pseudocatenulatum ; Dietary Fiber ; }, abstract = {Dietary habits contribute to the composition and function of the gut microbiota. Different dietary structures, including vegan, vegetarian, and omnivorous diets, affect intestinal Bifidobacteria; however, the relationship between Bifidobacterial function and host metabolism in subjects with different dietary patterns is unclear. Here, we analyzed five metagenomics studies and six 16S sequencing studies, including 206 vegetarians (VG), 249 omnivores (O), and 270 vegans (V), through an unbiased theme-level meta-analysis framework and discovered that diet significantly affects the composition and functionality of intestinal Bifidobacteria. The relative abundance of Bifidobacterium pseudocatenulatum was significantly higher in V than in O and Bifidobacterium longum, Bifidobacterium adolescentis, and B. pseudocatenulatum differed significantly in carbohydrate transport and metabolism in subjects with different diet types. Diets high in fiber were associated with B. longum with increased capacity for carbohydrate catabolism and genes encoding GH29 and GH43_27 were significantly enriched in V. Bifidobacterium adolescentis and B. pseudocatenulatum, associated with O, had a higher prevalence of the genes related to carbohydrate transport and metabolism, which showed the enrichment of GH26 and GH27 families. The same Bifidobacterium species has different functions in subjects with different diet types, resulting in different physiological significance. The diversification and functionalities of Bifidobacterial species in the gut microbiome can be influenced by the host diet and this aspect should be considered when studying host-microbe associations.}, } @article {pmid37315663, year = {2023}, author = {Xiao, J and Tsim, KWK and Hajisamae, S and Wang, WX}, title = {Chromosome-level genome and population genomics provide novel insights into adaptive divergence in allopatric Eleutheronema tetradactylum.}, journal = {International journal of biological macromolecules}, volume = {244}, number = {}, pages = {125299}, doi = {10.1016/j.ijbiomac.2023.125299}, pmid = {37315663}, issn = {1879-0003}, mesh = {Animals ; *Metagenomics ; *Genome/genetics ; Fishes ; Base Sequence ; Chromosomes ; }, abstract = {Understanding the adaptive ecological divergence provides important information for revealing biodiversity generation and maintenance. Adaptive ecology divergence in populations occurs in various environments and locations, but its genetic underpinnings remain elusive. We generated a chromosome-level genome of Eleutheronema tetradactylum (~582 Mb) and re-sequenced 50 allopatric E. tetradactylum in two independent environmental axes in China and Thailand Coastal waters as well as 11 cultured relatives. A low level of whole genome-wide diversity explained their decreased adaptive potential in the wild environment. Demographic analysis showed evidence of historically high abundance followed by a continuous distinct decline, plus signs of recent inbreeding and accumulation of deleterious mutations. Extensive signals of selective sweeps with signs of local adaptation to environmental differentiation between China and Thailand at genes related to thermal and salinity adaptation were discovered, which might be the driving factors of the geographical divergence of E. tetradactylum. Many genes and pathways subjected to strong selection under artificial breeding were associated with fatty acids and immunity (ELOVL6L, MAPK, p53/NF-kB), likely contributing to the eventual adaptation of artificial selective breeding. Our comprehensive study provided crucial genetic information for E. tetradactylum, with implications for the further conservation efforts of this threatened and ecologically valuable fish.}, } @article {pmid37315622, year = {2023}, author = {Huo, W and Ye, R and Shao, Y and Bao, M and Stegmann, R and Lu, W}, title = {Enhanced ethanol-driven carboxylate chain elongation by Pt@C in simulated sequencing batch reactors: Process and mechanism.}, journal = {Bioresource technology}, volume = {384}, number = {}, pages = {129310}, doi = {10.1016/j.biortech.2023.129310}, pmid = {37315622}, issn = {1873-2976}, mesh = {Fermentation ; *Ethanol/metabolism ; Caproates/metabolism ; *Clostridium kluyveri/metabolism ; }, abstract = {Carboxylate chain elongation can create value-added bioproducts from the organic waste. The effects of Pt@C on chain elongation and associated mechanisms were investigated in simulated sequencing batch reactors. 5.0 g/L of Pt@C greatly increased the synthesis of caproate, with an average yield of 21.5 g COD/L, which was 207.4% higher than the trial without Pt@C. Integrated metagenomic and metaproteomic analyses were used to reveal the mechanism of Pt@C-enhanced chain elongation. Pt@C enriched chain elongators by increasing the relative abundance of dominant species by 115.5%. The expression of functional genes related to chain elongation was promoted in the Pt@C trial. This study also demonstrates that Pt@C may promote overall chain elongation metabolism by enhancing CO2 uptake of Clostridium kluyveri. The study provides insights into the fundamental mechanisms of how chain elongation can perform CO2 metabolism and how it can be enhanced by Pt@C to upgrade bioproducts from organic waste streams.}, } @article {pmid37529739, year = {2022}, author = {Sorokin, AV and Lavlinskaya, MS}, title = {Interaction of the nitrogen-containing carbon backbone polymers with essential α-amino acids.}, journal = {Turkish journal of chemistry}, volume = {46}, number = {5}, pages = {1531-1540}, pmid = {37529739}, issn = {1300-0527}, abstract = {The aim of this work is to research the interactions of water-soluble nitrogen-containing copolymers with essential amino acids in aqueous media. For this, poly(N-vinylformamide-co-N-vinylimidazole) and poly(N-vinylcaprolactam-co-N-vinylimidazole) random copolymers were synthesized by free radical polymerization. The products obtained are characterized by GPC, DLS, and FTIR. The copolymers have a narrow molecular weight distribution and low dispersity. The interactions of the obtained copolymers with histidine, proline, arginine, leucine, phenylalanine, and methionine were researched by UV spectroscopy, FTIR, and TEM. It was found that conjugation of the copolymers with amino acids correlates with the copolymer composition and hydrodynamic radius Rh, and depends on the pH of the medium and amino acid structures. It is shown that chloride anion presence in the polymer-amino acid-water systems affects the mechanism of their interactions. The research shows that the synthesized copolymers can be used for the creation of effective eco-friendly amino acid extraction systems or matrices for enzyme immobilization.}, } @article {pmid37469625, year = {2022}, author = {Krapohl, J and Pickett, BE}, title = {SnakeWRAP: a Snakemake workflow to facilitate automated processing of metagenomic data through the metaWRAP pipeline.}, journal = {F1000Research}, volume = {11}, number = {}, pages = {265}, pmid = {37469625}, issn = {2046-1402}, mesh = {*Metagenomics ; Workflow ; *Software ; Metagenome ; Computing Methodologies ; }, abstract = {Generating high-quality genome assemblies of complex microbial populations from shotgun metagenomics data is often a manually intensive task involving many computational steps. SnakeWRAP is a novel tool, implemented in the Snakemake workflow language, to automate multiple metaWRAP modules. Specifically, it wraps the shell scripts provided within the original metaWRAP software, within Snakemake. This approach enables high-throughput simultaneous assembly and analysis of multiple shotgun metagenomic datasets using the robust modular metaWRAP software. We expect this advancement to be of import in institutions where high-performance computing infrastructure is available, especially in the context of big data. This software tool is publicly available at https://github.com/jkrapohl/SnakeWRAP.}, } @article {pmid37622131, year = {2022}, author = {Jiang, SC and Bischel, HN and Goel, R and Rosso, D and Sherchan, S and Whiteson, KL and Yan, T and Solo-Gabriele, HM}, title = {Integrating Virus Monitoring Strategies for Safe Non-potable Water Reuse.}, journal = {Water}, volume = {14}, number = {8}, pages = {}, pmid = {37622131}, issn = {2073-4441}, support = {R21 AI157434/AI/NIAID NIH HHS/United States ; R840257/EPA/EPA/United States ; U01 DA053941/DA/NIDA NIH HHS/United States ; }, abstract = {Wastewater reclamation and reuse have the potential to supplement water supplies, offering resiliency in times of drought and helping meet increased water demands associated with population growth. Non-potable water reuse represents the largest potential reuse market. Yet economic constraints for new water reuse infrastructure and safety concerns due to microbial water quality, and especially viral pathogen exposure, limit widespread implementation of water reuse. Cost-effective, real-time methods to measure or indicate viral quality of recycled water would do much to instill greater confidence in the practice. This manuscript discusses advancements in monitoring and modeling of viral health risks in the context of water reuse. First, we describe the current wastewater reclamation processes and treatment technologies with an emphasis on virus removal. Second, we review technologies for the measurement of viruses, both culture- and molecular-based, along with their advantages and disadvantages. We introduce promising viral surrogates and specific pathogenic viruses that can serve as indicators of viral risk for water reuse. We suggest metagenomic analyses for viral screening and flow cytometry for quantification of virus-like particles as new approaches to complement more traditional methods. Third, we describe modeling to assess health risks through quantitative microbial risk assessments (QMRAs), the most common strategy to couple data on virus concentrations with human exposure scenarios. We then explore the potential of artificial neural networks (ANNs) to incorporate suites of data from wastewater treatment processes, water quality parameters, and viral surrogates. We recommend ANNs as a means to utilize existing water quality data, alongside new complementary measures of viral quality, to achieve cost-effective strategies to assess risks associated with infectious human viruses in recycled water. Given the review, we conclude that technologies are ready for identifying and implementing viral surrogates for health risk reduction in the next decade. Incorporating modeling with monitoring data would likely result in more robust assessment of water reuse risk.}, } @article {pmid37332506, year = {2022}, author = {Fagernäs, Z and Salazar-García, DC and Haber Uriarte, M and Avilés Fernández, A and Henry, AG and Lomba Maurandi, J and Ozga, AT and Velsko, IM and Warinner, C}, title = {Understanding the microbial biogeography of ancient human dentitions to guide study design and interpretation.}, journal = {FEMS microbes}, volume = {3}, number = {}, pages = {xtac006}, pmid = {37332506}, issn = {2633-6685}, abstract = {The oral cavity is a heterogeneous environment, varying in factors such as pH, oxygen levels, and salivary flow. These factors affect the microbial community composition and distribution of species in dental plaque, but it is not known how well these patterns are reflected in archaeological dental calculus. In most archaeological studies, a single sample of dental calculus is studied per individual and is assumed to represent the entire oral cavity. However, it is not known if this sampling strategy introduces biases into studies of the ancient oral microbiome. Here, we present the results of a shotgun metagenomic study of a dense sampling of dental calculus from four Chalcolithic individuals from the southeast Iberian peninsula (ca. 4500-5000 BP). Interindividual differences in microbial composition are found to be much larger than intraindividual differences, indicating that a single sample can indeed represent an individual in most cases. However, there are minor spatial patterns in species distribution within the oral cavity that should be taken into account when designing a study or interpreting results. Finally, we show that plant DNA identified in the samples is likely of postmortem origin, demonstrating the importance of including environmental controls or additional lines of biomolecular evidence in dietary interpretations.}, } @article {pmid37602140, year = {2022}, author = {Pockrandt, C and Zimin, AV and Salzberg, SL}, title = {Metagenomic classification with KrakenUniq on low-memory computers.}, journal = {Journal of open source software}, volume = {7}, number = {80}, pages = {}, pmid = {37602140}, issn = {2475-9066}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; }, abstract = {UNLABELLED: Kraken and KrakenUniq are widely-used tools for classifying metagenomics sequences. A key requirement for these systems is a database containing all k-mers from all genomes that the users want to be able to detect, where k = 31 by default. This database can be very large, easily exceeding 100 gigabytes (GB) and sometimes 400 GB. Previously, Kraken and KrakenUniq required loading the entire database into main memory (RAM), and if RAM was insufficient, they used memory mapping, which significantly increased the running time for large datasets. We have implemented a new algorithm in KrakenUniq that allows it to load and process the database in chunks, with only a modest increase in running time. This enhancement now makes it feasible to run KrakenUniq on very large datasets and huge databases on virtually any computer, even a laptop, while providing the same very high classification accuracy as the previous system.

STATEMENT OF NEED: The KrakenUniq software classifies reads from metagenomic samples to establish which organisms are present in the samples and estimate their abundance. The software is widely used used by researchers and clinicians in medical diagnostics, microbiome and environmental studies.Typical databases used by KrakenUniq are tens to hundreds of gigabytes in size. The original KrakenUniq code required loading the entire database in RAM, which demanded expensive high-memory servers to run it efficiently. If a user did not have enough physical RAM to load the entire database, KrakenUniq resorted to memory-mapping the database, which significantly increased run times, frequently by a factor of more than 100. The new functionality described in this paper enables users who do not have access to high-memory servers to run KrakenUniq efficiently, with a CPU time performance increase of 3 to 4-fold, down from 100+.}, } @article {pmid37334231, year = {2021}, author = {Chuckran, PF and Hungate, BA and Schwartz, E and Dijkstra, P}, title = {Variation in genomic traits of microbial communities among ecosystems.}, journal = {FEMS microbes}, volume = {2}, number = {}, pages = {xtab020}, pmid = {37334231}, issn = {2633-6685}, abstract = {Free-living bacteria in nutrient limited environments often exhibit traits which may reduce the cost of reproduction, such as smaller genome size, low GC content and fewer sigma (σ) factor and 16S rRNA gene copies. Despite the potential utility of these traits to detect relationships between microbial communities and ecosystem-scale properties, few studies have assessed these traits on a community-scale. Here, we analysed these traits from publicly available metagenomes derived from marine, soil, host-associated and thermophilic communities. In marine and thermophilic communities, genome size and GC content declined in parallel, consistent with genomic streamlining, with GC content in thermophilic communities generally higher than in marine systems. In contrast, soil communities averaging smaller genomes featured higher GC content and were often from low-carbon environments, suggesting unique selection pressures in soil bacteria. The abundance of specific σ-factors varied with average genome size and ecosystem type. In oceans, abundance of fliA, a σ-factor controlling flagella biosynthesis, was positively correlated with community average genome size-reflecting known trade-offs between nutrient conservation and chemotaxis. In soils, a high abundance of the stress response σ-factor gene rpoS was associated with smaller average genome size and often located in harsh and/or carbon-limited environments-a result which tracks features observed in culture and indicates an increased capacity for stress response in nutrient-poor soils. This work shows how ecosystem-specific constraints are associated with trade-offs which are embedded in the genomic features of bacteria in microbial communities, and which can be detected at the community level, highlighting the importance of genomic features in microbial community analysis.}, } @article {pmid37333957, year = {2020}, author = {In 't Zandt, MH and Frank, J and Yilmaz, P and Cremers, G and Jetten, MSM and Welte, CU}, title = {Long-term enriched methanogenic communities from thermokarst lake sediments show species-specific responses to warming.}, journal = {FEMS microbes}, volume = {1}, number = {1}, pages = {xtaa008}, pmid = {37333957}, issn = {2633-6685}, abstract = {Thermokarst lakes are large potential greenhouse gas (GHG) sources in a changing Arctic. In a warming world, an increase in both organic matter availability and temperature is expected to boost methanogenesis and potentially alter the microbial community that controls GHG fluxes. These community shifts are, however, challenging to detect by resolution-limited 16S rRNA gene-based approaches. Here, we applied full metagenome sequencing on long-term thermokarst lake sediment enrichments on acetate and trimethylamine at 4°C and 10°C to unravel species-specific responses to the most likely Arctic climate change scenario. Substrate amendment was used to mimic the increased organic carbon availability upon permafrost thaw. By performing de novo assembly, we reconstructed five high-quality and five medium-quality metagenome-assembled genomes (MAGs) that represented 59% of the aligned metagenome reads. Seven bacterial MAGs belonged to anaerobic fermentative bacteria. Within the Archaea, the enrichment of methanogenic Methanosaetaceae/Methanotrichaceae under acetate amendment and Methanosarcinaceae under trimethylamine (TMA) amendment was not unexpected. Surprisingly, we observed temperature-specific methanogenic (sub)species responses with TMA amendment. These highlighted distinct and potentially functional climate-induced shifts could not be revealed with 16S rRNA gene-based analyses. Unraveling these temperature- and nutrient-controlled species-level responses is essential to better comprehend the mechanisms that underlie GHG production from Arctic lakes in a warming world.}, } @article {pmid37425237, year = {2020}, author = {Dalton, A}, title = {The Role of Nutrition in Promoting Gut Health and Treating Chronic Illness Through the Attenuation of Inflammation.}, journal = {HCA healthcare journal of medicine}, volume = {1}, number = {2}, pages = {65-69}, pmid = {37425237}, issn = {2689-0216}, abstract = {Description Over the millennia, the human body and microorganisms such as bacteria, viruses, archaea, protozoa and parasites have coevolved together forming an intimate relationship. These microorganisms are found on the skin, in the mouth, genitourinary tract and most abundantly in the large intestine of the digestive tract. States of microbial dysbiosis contribute to chronic inflammation, which can lead to the pathogenesis and progression of numerous diseases. Micro- and macro-nutrients as well as dietary patterns like the Mediterranean diet can help improve health outcomes.}, } @article {pmid37383053, year = {2020}, author = {Seok, J and Suk, KT}, title = {Gut-microbiome Taxonomic Profiling as Non-invasive Biomarkers for the Early Detection of Alcoholic Hepatocellular Carcinoma.}, journal = {Journal of liver cancer}, volume = {20}, number = {1}, pages = {32-40}, pmid = {37383053}, issn = {2383-5001}, abstract = {BACKGROUND/AIMS: Hepatocellular carcinoma (HCC) is a prevalent form of primary liver cancer and the fifth leading cause of worldwide cancer mortality. Though early diagnosis of HCC is important, so far lack of effective biomarkers for early diagnosis of HCC has been a problem. In this study, we searched for potential functional biomarkers of alcoholic HCC by using metagenomics approach.

METHODS: Between September 2017 and April 2019, normal control (n=44), alcoholic liver cirrhosis (n=44), and alcoholic HCC (n=13) groups were prospectively enrolled and analyzed. Gut microbiota was analyzed using the 16S-based microbiome taxonomic profiling platform of EzBioCloud Apps and analyzing system.

RESULTS: There was a statistically significant difference among groups in diversity (P<0.05). In the comparison of phylum between cirrhosis and HCC, Proteobacteria were increased and Bacteroidetes were decreased. Firmicutes were not significantly different among the three groups. In the taxonomic profiling, relative abundance of Lactobacillus in the cirrhosis and HCC groups showed richness (P<0.05). In the biomarker analysis between cirrhosis and HCC, obiquinome Fe-S protein 3, global nitrogen regulator, Vesicle-associated membrane protein 7, toxin YoeB, peroxisome-assembly ATPase, and nitrogen oxide reductase regulator were differently expressed (P<0.001).

CONCLUSIONS: Alcoholic HCC showed different expressions in the stool taxonomy and biomarker compared with that of cirrhosis and control. Therefore, new biomarkers using stool analysis for alcoholic HCC are necessary.}, } @article {pmid37314861, year = {2023}, author = {Palacios, N and Wilkinson, J and Bjornevik, K and Schwarzschild, MA and McIver, L and Ascherio, A and Huttenhower, C}, title = {Metagenomics of the Gut Microbiome in Parkinson's Disease: Prodromal Changes.}, journal = {Annals of neurology}, volume = {94}, number = {3}, pages = {486-501}, pmid = {37314861}, issn = {1531-8249}, support = {UM1 CA186107/NH/NIH HHS/United States ; U01 CA167552/CA/NCI NIH HHS/United States ; R01NS097723/NS/NINDS NIH HHS/United States ; U01 CA167552/NH/NIH HHS/United States ; UM1 CA186107/CA/NCI NIH HHS/United States ; R01 NS097723/NS/NINDS NIH HHS/United States ; }, mesh = {Humans ; *Parkinson Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Case-Control Studies ; Metagenomics ; Follow-Up Studies ; Prodromal Symptoms ; }, abstract = {OBJECTIVE: Prior studies on the gut microbiome in Parkinson's disease (PD) have yielded conflicting results, and few studies have focused on prodromal (premotor) PD or used shotgun metagenomic profiling to assess microbial functional potential. We conducted a nested case-control study within 2 large epidemiological cohorts to examine the role of the gut microbiome in PD.

METHODS: We profiled the fecal metagenomes of 420 participants in the Nurses' Health Study and the Health Professionals Follow-up Study with recent onset PD (N = 75), with features of prodromal PD (N = 101), controls with constipation (N = 113), and healthy controls (N = 131) to identify microbial taxonomic and functional features associated with PD and features suggestive of prodromal PD. Omnibus and feature-wise analyses identified bacterial species and pathways associated with prodromal and recently onset PD.

RESULTS: We observed depletion of several strict anaerobes associated with reduced inflammation among participants with PD or features of prodromal PD. A microbiome-based classifier had moderate accuracy (area under the curve [AUC] = 0.76 for species and 0.74 for pathways) to discriminate between recently onset PD cases and controls. These taxonomic shifts corresponded with functional shifts indicative of carbohydrate source preference. Similar, but less marked, changes were observed in participants with features of prodromal PD, in both microbial features and functions.

INTERPRETATION: PD and features of prodromal PD were associated with similar changes in the gut microbiome. These findings suggest that changes in the microbiome could represent novel biomarkers for the earliest phases of PD. ANN NEUROL 2023;94:486-501.}, } @article {pmid37314210, year = {2023}, author = {Nguyen, M and Elmore, Z and Ihle, C and Moen, FS and Slater, AD and Turner, BN and Parrello, B and Best, AA and Davis, JJ}, title = {Predicting variable gene content in Escherichia coli using conserved genes.}, journal = {mSystems}, volume = {8}, number = {4}, pages = {e0005823}, pmid = {37314210}, issn = {2379-5077}, support = {75N93019C00076/AI/NIAID NIH HHS/United States ; }, mesh = {Escherichia coli/genetics ; Genome, Bacterial/genetics ; Plasmids ; *Escherichia coli Proteins/genetics ; *Anti-Infective Agents ; }, abstract = {Having the ability to predict the protein-encoding gene content of an incomplete genome or metagenome-assembled genome is important for a variety of bioinformatic tasks. In this study, as a proof of concept, we built machine learning classifiers for predicting variable gene content in Escherichia coli genomes using only the nucleotide k-mers from a set of 100 conserved genes as features. Protein families were used to define orthologs, and a single classifier was built for predicting the presence or absence of each protein family occurring in 10%-90% of all E. coli genomes. The resulting set of 3,259 extreme gradient boosting classifiers had a per-genome average macro F1 score of 0.944 [0.943-0.945, 95% CI]. We show that the F1 scores are stable across multi-locus sequence types and that the trend can be recapitulated by sampling a smaller number of core genes or diverse input genomes. Surprisingly, the presence or absence of poorly annotated proteins, including "hypothetical proteins" was accurately predicted (F1 = 0.902 [0.898-0.906, 95% CI]). Models for proteins with horizontal gene transfer-related functions had slightly lower F1 scores but were still accurate (F1s = 0.895, 0.872, 0.824, and 0.841 for transposon, phage, plasmid, and antimicrobial resistance-related functions, respectively). Finally, using a holdout set of 419 diverse E. coli genomes that were isolated from freshwater environmental sources, we observed an average per-genome F1 score of 0.880 [0.876-0.883, 95% CI], demonstrating the extensibility of the models. Overall, this study provides a framework for predicting variable gene content using a limited amount of input sequence data. IMPORTANCE Having the ability to predict the protein-encoding gene content of a genome is important for assessing genome quality, binning genomes from shotgun metagenomic assemblies, and assessing risk due to the presence of antimicrobial resistance and other virulence genes. In this study, we built a set of binary classifiers for predicting the presence or absence of variable genes occurring in 10%-90% of all publicly available E. coli genomes. Overall, the results show that a large portion of the E. coli variable gene content can be predicted with high accuracy, including genes with functions relating to horizontal gene transfer. This study offers a strategy for predicting gene content using limited input sequence data.}, } @article {pmid37314057, year = {2023}, author = {Van Etten, J and Stephens, TG and Bhattacharya, D}, title = {A k-mer-Based Approach for Phylogenetic Classification of Taxa in Environmental Genomic Data.}, journal = {Systematic biology}, volume = {72}, number = {5}, pages = {1101-1118}, doi = {10.1093/sysbio/syad037}, pmid = {37314057}, issn = {1076-836X}, support = {80NSSC19K1542/NASA/NASA/United States ; 80NSSC19K0462/NASA/NASA/United States ; }, mesh = {*Metagenomics/methods ; Phylogeny ; *Genome ; Base Sequence ; }, abstract = {In the age of genome sequencing, whole-genome data is readily and frequently generated, leading to a wealth of new information that can be used to advance various fields of research. New approaches, such as alignment-free phylogenetic methods that utilize k-mer-based distance scoring, are becoming increasingly popular given their ability to rapidly generate phylogenetic information from whole-genome data. However, these methods have not yet been tested using environmental data, which often tends to be highly fragmented and incomplete. Here, we compare the results of one alignment-free approach (which utilizes the D2 statistic) to traditional multi-gene maximum likelihood trees in 3 algal groups that have high-quality genome data available. In addition, we simulate lower-quality, fragmented genome data using these algae to test method robustness to genome quality and completeness. Finally, we apply the alignment-free approach to environmental metagenome assembled genome data of unclassified Saccharibacteria and Trebouxiophyte algae, and single-cell amplified data from uncultured marine stramenopiles to demonstrate its utility with real datasets. We find that in all instances, the alignment-free method produces phylogenies that are comparable, and often more informative, than those created using the traditional multi-gene approach. The k-mer-based method performs well even when there are significant missing data that include marker genes traditionally used for tree reconstruction. Our results demonstrate the value of alignment-free approaches for classifying novel, often cryptic or rare, species, that may not be culturable or are difficult to access using single-cell methods, but fill important gaps in the tree of life.}, } @article {pmid37313947, year = {2023}, author = {El Mouzan, MI and Assiri, AA and Al Sarkhy, AA and Alasmi, MM}, title = {Gut virome profile in healthy Saudi children.}, journal = {Saudi journal of gastroenterology : official journal of the Saudi Gastroenterology Association}, volume = {29}, number = {3}, pages = {171-176}, pmid = {37313947}, issn = {1998-4049}, mesh = {Male ; Humans ; Child ; Adolescent ; Female ; *Virome ; Phylogeny ; Saudi Arabia/epidemiology ; *DNA, Viral ; Feces ; }, abstract = {BACKGROUND: The role of viruses is well known in health and disease. The aim of this report was to describe the profile of viruses in the gut of healthy Saudi children.

METHODS: In 20 randomly selected school age children from Riyadh, stool samples were collected in cryovials and stored at -80° C. At the time of analysis, the samples were sent by express mail in a temperature-controlled container to the laboratory in the USA, Viral DNA was isolated and shotgun metagenomic sequencing was performed. The abundance of each organism was expressed as an average relative percentage across the viral phylogenetic tree from phyla to species.

RESULTS: The median age of the children was 11.3 (range 6.8-15.4) years, and 35% were males. Caudovirales were the most abundant bacteriophage order (77%) and Siphoviridae, Myoviridae, and Podoviridae families predominated, accounting for 41%, 25%, and 11%, respectively. Among the viral bacteriophage species, the most abundant were the Enterobacteria phages.

CONCLUSION: The profile and abundance of the gut virome in healthy Saudi children reveal important differences from the literature. Further studies from different populations with larger sample sizes are needed to understand the role of gut viruses in the pathogenesis of disease in general and in the response to fecal microbiota therapy in particular.}, } @article {pmid37313163, year = {2023}, author = {Tizazu, S and Tesfaye, G and Wang, A and Guadie, A and Andualem, B}, title = {Microbial diversity, transformation and toxicity of azo dye biodegradation using thermo-alkaliphilic microbial consortia.}, journal = {Heliyon}, volume = {9}, number = {6}, pages = {e16857}, pmid = {37313163}, issn = {2405-8440}, abstract = {In this research, the transformation and toxicity of Reactive Red 141 and 239 biodegraded under anaerobic-aerobic conditions as well as metagenomic analysis of Reactive Red 239 degrading microbial consortia collected from Shala Hot spring were investigated. Toxicity of dyes before treatment and after treatment on three plants, fish and microorganisms were done. A halotolerant and thermo-alkaliphilic bacterial consortia decolorizing azo dyes (>98% RR 141 and > 96% RR 239 in 7 h) under optimum conditions of salt concentration (0.5%), temperature (55 °C) and pH (9), were used. Toxicity effect of untreated dyes and treated dyes in Tomato > Beetroot > Cabbage plants, while the effect was Leuconostoc mesenteroides > Lactobacillus plantarum > Escherichia coli in microorganisms. Among fishes, the toxicity effect was highest in Oreochromis niloticus followed by Cyprinus carpio and Clarias gariepinus. The three most dominant phyla that could be in charge of decolorizing RR 239 under anaerobic-aerobic systems were Bacteroidota (22.6-29.0%), Proteobacteria (13.5-29.0%), and Chloroflexi (8.8-23.5%). At class level microbial community structure determination, Bacteroidia (18.9-27.2%), Gammaproteobacteria (11.0-15.8%), Alphaproteobacteria (2.5-5.0%) and Anaerolineae (17.0-21.9%) were dominant classes. The transformation of RR 141 and RR 239 into amine compounds were proposed via high performance liquid chromatography-mass spectroscopy (HPLC/MS) and fourier transform infrared spectroscopy (FT-IR). Overall, dye containing wastewaters treated under anaerobic-aerobic systems using thermo-alkaliphilic microbial consortia were found to be safe to agricultural (fishes and vegetables) purposes.}, } @article {pmid37311764, year = {2023}, author = {Ruff, SE and Humez, P and de Angelis, IH and Diao, M and Nightingale, M and Cho, S and Connors, L and Kuloyo, OO and Seltzer, A and Bowman, S and Wankel, SD and McClain, CN and Mayer, B and Strous, M}, title = {Hydrogen and dark oxygen drive microbial productivity in diverse groundwater ecosystems.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3194}, pmid = {37311764}, issn = {2041-1723}, mesh = {Oxygen ; Oxygen Isotopes ; *Groundwater ; Hydrogen ; *Microbiota ; }, abstract = {Around 50% of humankind relies on groundwater as a source of drinking water. Here we investigate the age, geochemistry, and microbiology of 138 groundwater samples from 95 monitoring wells (<250 m depth) located in 14 aquifers in Canada. The geochemistry and microbiology show consistent trends suggesting large-scale aerobic and anaerobic hydrogen, methane, nitrogen, and sulfur cycling carried out by diverse microbial communities. Older groundwaters, especially in aquifers with organic carbon-rich strata, contain on average more cells (up to 1.4 × 10[7] mL[-1]) than younger groundwaters, challenging current estimates of subsurface cell abundances. We observe substantial concentrations of dissolved oxygen (0.52 ± 0.12 mg L[-1] [mean ± SE]; n = 57) in older groundwaters that seem to support aerobic metabolisms in subsurface ecosystems at an unprecedented scale. Metagenomics, oxygen isotope analyses and mixing models indicate that dark oxygen is produced in situ via microbial dismutation. We show that ancient groundwaters sustain productive communities and highlight an overlooked oxygen source in present and past subsurface ecosystems of Earth.}, } @article {pmid37310918, year = {2023}, author = {Chen, NFG and Chaguza, C and Gagne, L and Doucette, M and Smole, S and Buzby, E and Hall, J and Ash, S and Harrington, R and Cofsky, S and Clancy, S and Kapsak, CJ and Sevinsky, J and Libuit, K and Park, DJ and Hemarajata, P and Garrigues, JM and Green, NM and Sierra-Patev, S and Carpenter-Azevedo, K and Huard, RC and Pearson, C and Incekara, K and Nishimura, C and Huang, JP and Gagnon, E and Reever, E and Razeq, J and Muyombwe, A and Borges, V and Ferreira, R and Sobral, D and Duarte, S and Santos, D and Vieira, L and Gomes, JP and Aquino, C and Savino, IM and Felton, K and Bajwa, M and Hayward, N and Miller, H and Naumann, A and Allman, R and Greer, N and Fall, A and Mostafa, HH and McHugh, MP and Maloney, DM and Dewar, R and Kenicer, J and Parker, A and Mathers, K and Wild, J and Cotton, S and Templeton, KE and Churchwell, G and Lee, PA and Pedrosa, M and McGruder, B and Schmedes, S and Plumb, MR and Wang, X and Barcellos, RB and Godinho, FMS and Salvato, RS and Ceniseros, A and Breban, MI and Grubaugh, ND and Gallagher, GR and Vogels, CBF}, title = {Development of an amplicon-based sequencing approach in response to the global emergence of mpox.}, journal = {PLoS biology}, volume = {21}, number = {6}, pages = {e3002151}, pmid = {37310918}, issn = {1545-7885}, support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *COVID-19/epidemiology ; *Mpox (monkeypox) ; Pandemics ; SARS-CoV-2/genetics ; Genomics ; *Zika Virus ; *Zika Virus Infection ; }, abstract = {The 2022 multicountry mpox outbreak concurrent with the ongoing Coronavirus Disease 2019 (COVID-19) pandemic further highlighted the need for genomic surveillance and rapid pathogen whole-genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical specimens that tested presumptively positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (Ct) (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR Ct below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon-based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole-genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.}, } @article {pmid37310875, year = {2023}, author = {Yin, X and Chen, X and Jiang, XT and Yang, Y and Li, B and Shum, MH and Lam, TTY and Leung, GM and Rose, J and Sanchez-Cid, C and Vogel, TM and Walsh, F and Berendonk, TU and Midega, J and Uchea, C and Frigon, D and Wright, GD and Bezuidenhout, C and Picão, RC and Ahammad, SZ and Nielsen, PH and Hugenholtz, P and Ashbolt, NJ and Corno, G and Fatta-Kassinos, D and Bürgmann, H and Schmitt, H and Cha, CJ and Pruden, A and Smalla, K and Cytryn, E and Zhang, Y and Yang, M and Zhu, YG and Dechesne, A and Smets, BF and Graham, DW and Gillings, MR and Gaze, WH and Manaia, CM and van Loosdrecht, MCM and Alvarez, PJJ and Blaser, MJ and Tiedje, JM and Topp, E and Zhang, T}, title = {Toward a Universal Unit for Quantification of Antibiotic Resistance Genes in Environmental Samples.}, journal = {Environmental science & technology}, volume = {57}, number = {26}, pages = {9713-9721}, doi = {10.1021/acs.est.3c00159}, pmid = {37310875}, issn = {1520-5851}, mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Metagenomics/methods ; }, abstract = {Surveillance of antibiotic resistance genes (ARGs) has been increasingly conducted in environmental sectors to complement the surveys in human and animal sectors under the "One-Health" framework. However, there are substantial challenges in comparing and synthesizing the results of multiple studies that employ different test methods and approaches in bioinformatic analysis. In this article, we consider the commonly used quantification units (ARG copy per cell, ARG copy per genome, ARG density, ARG copy per 16S rRNA gene, RPKM, coverage, PPM, etc.) for profiling ARGs and suggest a universal unit (ARG copy per cell) for reporting such biological measurements of samples and improving the comparability of different surveillance efforts.}, } @article {pmid37310259, year = {2023}, author = {Deblais, L and Ojeda, A and Brhane, M and Mummed, B and Hassen, KA and Ahmedo, BU and Weldesenbet, YD and Amin, JK and Ahmed, IA and Usmane, IA and Yusuf, EA and Seran, AJ and Abrahim, FI and Game, HT and Mummed, BA and Usmail, MM and Umer, KA and Dawid, MM and Gebreyes, W and French, N and Hassen, JY and Roba, KT and Mohammed, A and Yimer, G and Saleem, C and Chen, D and Singh, N and Manary, MJ and McKune, SL and Havelaar, AH and Rajashekara, G}, title = {Prevalence and Load of the Campylobacter Genus in Infants and Associated Household Contacts in Rural Eastern Ethiopia: a Longitudinal Study from the Campylobacter Genomics and Environmental Enteric Dysfunction (CAGED) Project.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0042423}, pmid = {37310259}, issn = {1098-5336}, support = {UL1TR001427//HHS | National Institutes of Health (NIH)/ ; }, mesh = {Child ; Female ; Humans ; Infant ; Animals ; Child, Preschool ; Cattle ; Sheep ; *Campylobacter/genetics ; Ethiopia/epidemiology ; Longitudinal Studies ; Prevalence ; *Drinking Water ; *Campylobacter Infections/epidemiology/veterinary ; Chickens/genetics ; Livestock ; Growth Disorders ; Goats ; Feces ; Genomics ; Real-Time Polymerase Chain Reaction ; Soil ; }, abstract = {In our previous cross-sectional study, multiple species of Campylobacter were detected (88%) in stool samples from children (12 to 14 months of age) in rural eastern Ethiopia. This study assessed the temporal fecal carriage of Campylobacter in infants and identified putative reservoirs associated with these infections in infants from the same region. The prevalence and load of Campylobacter were determined using genus-specific real-time PCR. Stool samples from 106 infants (n = 1,073) were collected monthly from birth until 376 days of age (DOA). Human stool samples (mothers and siblings), livestock feces (cattle, chickens, goats, and sheep), and environmental samples (soil and drinking water) from the 106 households were collected twice per household (n = 1,644). Campylobacter was most prevalent in livestock feces (goats, 99%; sheep, 98%; cattle, 99%; chickens, 93%), followed by human stool samples (siblings, 91%; mothers, 83%; infants, 64%) and environmental samples (soil, 58%; drinking water, 43%). The prevalence of Campylobacter in infant stool samples significantly increased with age, from 30% at 27 DOA to 89% at 360 DOA (1% increase/day in the odds of being colonized) (P < 0.001). The Campylobacter load increased linearly (P < 0.001) with age from 2.95 logs at 25 DOA to 4.13 logs at 360 DOA. Within a household, the Campylobacter load in infant stool samples was positively correlated with the load in mother stool samples (r[2] = 0.18) and soil collected inside the house (r[2] = 0.36), which were in turn both correlated with Campylobacter loads in chicken and cattle feces (0.60 < r[2] < 0.63) (P < 0.01). In conclusion, a high proportion of infants are infected with Campylobacter in eastern Ethiopia, and contact with the mother and contaminated soil may be associated with early infections. IMPORTANCE A high Campylobacter prevalence during early childhood has been associated with environmental enteric dysfunction (EED) and stunting, especially in low-resource settings. Our previous study demonstrated that Campylobacter was frequently found (88%) in children from eastern Ethiopia; however, little is known about potential Campylobacter reservoirs and transmission pathways leading to infection of infants by Campylobacter during early growth. In the longitudinal study presented here, Campylobacter was frequently detected in infants within the 106 surveyed households from eastern Ethiopia, and the prevalence was age dependent. Furthermore, preliminary analyses highlighted the potential role of the mother, soil, and livestock in the transmission of Campylobacter to the infant. Further work will explore the species and genetic composition of Campylobacter in infants and putative reservoirs using PCR and whole-genome and metagenomic sequencing. The findings from these studies can lead to the development of interventions to minimize the risk of transmission of Campylobacter to infants and, potentially, EED and stunting.}, } @article {pmid37310220, year = {2023}, author = {Shi, M and Qin, T and Cheng, Z and Zheng, D and Pu, Z and Yang, Z and Lim, KJ and Yang, M and Wang, Z}, title = {Exploring the Core Bacteria and Functional Traits in Pecan (Carya illinoinensis) Rhizosphere.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0011023}, pmid = {37310220}, issn = {2165-0497}, mesh = {*Rhizosphere ; *Carya/microbiology ; Type IV Secretion Systems ; Bacteria/genetics ; Phenotype ; Soil ; Soil Microbiology ; }, abstract = {Pecan (Carya illinoinensis) and Chinese hickory (Carya cathayensis) are important commercially cultivated nut trees. They are phylogenetically closely related plants; however, they exhibit significantly different phenotypes in response to abiotic stress and development. The rhizosphere selects core microorganisms from bulk soil, playing a pivotal role in the plant's resistance to abiotic stress and growth. In this study, we used metagenomic sequencing to compare the selection capabilities of seedling pecan and seedling hickory at taxonomic and functional levels in bulk soil and the rhizosphere. We observed that pecan has a stronger capacity to enrich rhizosphere plant-beneficial microbe bacteria (e.g., Rhizobium, Novosphingobium, Variovorax, Sphingobium, and Sphingomonas) and their associated functional traits than hickory. We also noted that the ABC transporters (e.g., monosaccharide transporter) and bacterial secretion systems (e.g., type IV secretion system) are the core functional traits of pecan rhizosphere bacteria. Rhizobium and Novosphingobium are the main contributors to the core functional traits. These results suggest that monosaccharides may help Rhizobium to efficiently enrich this niche. Novosphingobium may use a type IV secretion system to interact with other bacteria and thereby influence the assembly of pecan rhizosphere microbiomes. Our data provide valuable information to guide core microbial isolation and expand our knowledge of the assembly mechanisms of plant rhizosphere microbes. IMPORTANCE The rhizosphere microbiome has been identified as a fundamental factor in maintaining plant health, helping plants to fight the deleterious effects of diseases and abiotic stresses. However, to date, studies on the nut tree microbiome have been scarce. Here, we observed a significant "rhizosphere effect" on the seedling pecan. We furthermore demonstrated the core rhizosphere microbiome and function in the seedling pecan. Moreover, we deduced possible factors that help the core bacteria, such as Rhizobium, to efficiently enrich the pecan rhizosphere and the importance of the type IV system for the assembly of pecan rhizosphere bacterial communities. Our findings provide information for understanding the mechanism of the rhizosphere microbial community enrichment process.}, } @article {pmid37310219, year = {2023}, author = {Riley, R and Bowers, RM and Camargo, AP and Campbell, A and Egan, R and Eloe-Fadrosh, EA and Foster, B and Hofmeyr, S and Huntemann, M and Kellom, M and Kimbrel, JA and Oliker, L and Yelick, K and Pett-Ridge, J and Salamov, A and Varghese, NJ and Clum, A}, title = {Terabase-Scale Coassembly of a Tropical Soil Microbiome.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0020023}, pmid = {37310219}, issn = {2165-0497}, mesh = {*Soil ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; Genome, Viral ; Metagenomics/methods ; }, abstract = {Petabases of environmental metagenomic data are publicly available, presenting an opportunity to characterize complex environments and discover novel lineages of life. Metagenome coassembly, in which many metagenomic samples from an environment are simultaneously analyzed to infer the underlying genomes' sequences, is an essential tool for achieving this goal. We applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 terabases (Tbp) of metagenome data from a tropical soil in the Luquillo Experimental Forest (LEF), Puerto Rico. The resulting coassembly yielded 39 high-quality (>90% complete, <5% contaminated, with predicted 23S, 16S, and 5S rRNA genes and ≥18 tRNAs) metagenome-assembled genomes (MAGs), including two from the candidate phylum Eremiobacterota. Another 268 medium-quality (≥50% complete, <10% contaminated) MAGs were extracted, including the candidate phyla Dependentiae, Dormibacterota, and Methylomirabilota. In total, 307 medium- or higher-quality MAGs were assigned to 23 phyla, compared to 294 MAGs assigned to nine phyla in the same samples individually assembled. The low-quality (<50% complete, <10% contaminated) MAGs from the coassembly revealed a 49% complete rare biosphere microbe from the candidate phylum FCPU426 among other low-abundance microbes, an 81% complete fungal genome from the phylum Ascomycota, and 30 partial eukaryotic MAGs with ≥10% completeness, possibly representing protist lineages. A total of 22,254 viruses, many of them low abundance, were identified. Estimation of metagenome coverage and diversity indicates that we may have characterized ≥87.5% of the sequence diversity in this humid tropical soil and indicates the value of future terabase-scale sequencing and coassembly of complex environments. IMPORTANCE Petabases of reads are being produced by environmental metagenome sequencing. An essential step in analyzing these data is metagenome assembly, the computational reconstruction of genome sequences from microbial communities. "Coassembly" of metagenomic sequence data, in which multiple samples are assembled together, enables more complete detection of microbial genomes in an environment than "multiassembly," in which samples are assembled individually. To demonstrate the potential for coassembling terabases of metagenome data to drive biological discovery, we applied MetaHipMer2, a distributed metagenome assembler that runs on supercomputing clusters, to coassemble 3.4 Tbp of reads from a humid tropical soil environment. The resulting coassembly, its functional annotation, and analysis are presented here. The coassembly yielded more, and phylogenetically more diverse, microbial, eukaryotic, and viral genomes than the multiassembly of the same data. Our resource may facilitate the discovery of novel microbial biology in tropical soils and demonstrates the value of terabase-scale metagenome sequencing.}, } @article {pmid37309378, year = {2023}, author = {Liu, Y and Zheng, G and Li, J and Yang, N and Li, J and Liu, Z and Han, Q and Zhao, Y and Du, F and He, Y and Yan, T}, title = {A Case Report of Cutaneous Anthrax Diagnosed by Using a Metagenomic Next-Generation Sequencing (mNGS) Approach.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {3601-3606}, pmid = {37309378}, issn = {1178-6973}, abstract = {Anthrax is caused by Bacillus anthracis. Humans are mainly infected through contact with the fur and meat of livestock. The cutaneous form is the most common form. The skin lesions of typical cutaneous anthrax are characterized by shallow ulcers with black crusts, surrounded by small blisters and nonpitting edema of nearby tissues. Metagenomic next-generation sequencing (mNGS) is a new pathogenic detection method which is rapid and unbiased. We reported the first case of cutaneous anthrax diagnosed by mNGS. Ultimately, the man received prompt antibiotic therapy and had a good prognosis. In conclusion, mNGS is proved to be a good method for etiological diagnosis, especially for rare infectious diseases.}, } @article {pmid37308837, year = {2023}, author = {Li, Z and Zhang, S and Liu, M and Ding, H and Wen, Y and Zhu, H and Zeng, H}, title = {Bacterial DNA metabolism analysis by metagenomic next-generation sequencing (mNGS) after treatment of bloodstream infection.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {392}, pmid = {37308837}, issn = {1471-2334}, mesh = {Animals ; Rabbits ; DNA, Bacterial ; Escherichia coli ; *Sepsis ; Bacteria ; High-Throughput Nucleotide Sequencing ; *Cell-Free Nucleic Acids ; }, abstract = {BACKGROUND: With the advent of metagenomic next-generation sequencing (mNGS), the time of DNA metabolism can be explored after bacteria be killed. In this study, we applied mNGS in investigation of the clearance profile of circulating bacteria DNA.

METHODS: All of the rabbits were injected with the inactivated Escherichia coli. Using mNGS, we analyzed serial samples of plasma collected from rabbits to detect clearance profile of circulating E. coli DNA.

RESULTS: In this study, we found that the of E. coli DNA could still be detected 6 h after injecting killed bacteria. The clearance half-lives associated with the 2 phases are 0.37 and 1.81 h. We also explored there is no correlation between the disease severity with the E. coli DNA reads in circulation.

CONCLUSIONS: After the bacteria were completely killed, their DNA could still be detected in the blood circulation. The metabolism of bacterial DNA in the circulation had two phases: fast and slow phases, and there were no correlations between the level of bacteria reads with the severity of patients' disease after the bacteria have been completely killed.}, } @article {pmid37308527, year = {2023}, author = {Kozhakhmetov, S and Meiirmanova, Z and Mukhanbetzhanov, N and Jarmukhanov, Z and Vinogradova, E and Mureyev, S and Kozhakhmetova, S and Morenko, M and Shnaider, K and Duisbayeva, A and Kushugulova, A}, title = {Compositional and functional variability of the gut microbiome in children with infantile colic.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {9530}, pmid = {37308527}, issn = {2045-2322}, mesh = {Infant, Newborn ; Infant ; Humans ; Child ; *Gastrointestinal Microbiome ; *Colic ; *Microbiota ; Amino Acids ; Anxiety ; Bacteroides ; }, abstract = {The inconsolable crying of a child for no apparent reason at an early age is a source of excitement and anxiety for parents. Previous studies have reported that crying may be caused by discomfort associated with the occupation of the intestines of the newborn by microbiota and its vital activity. We conducted a prospective observational study in which 62 newborns and their mothers were recruited. The study comprised two groups, each consisting of 15 infants with colic and 21 controls. Colic and control groups were vaginally born and exclusively breastfed. Fecal samples from children were collected over time from day 1 to 12 months. Full metagenomic sequencing of fecal samples from children and their mothers was carried out. It was determined that the trajectory of the development of the intestinal microbiome of children with colic was different from the group without colic. In the colic group, a depleted relative abundance of Bifidobacterium and enrichment of Bacteroides Clostridiales was found, while the microbial biodiversity in this group was enriched. Metabolic pathway profiling showed that the non-colic group was enriched by amino acid biosynthetic pathways, while the feces microbiome of the colic group was enriched by glycolysis metabolic pathways that correlated with the Bacteroides taxon. This study shows that infantile colic has a definite relationship with the microbiome structure of infants.}, } @article {pmid37307951, year = {2023}, author = {Zhang, X and Li, H and Wang, Y and Kang, Y and Li, Z}, title = {Metagenomic analysis reveals antibiotic resistance profiles in tissue samples from patients with diabetic foot infections.}, journal = {Journal of global antimicrobial resistance}, volume = {34}, number = {}, pages = {202-210}, doi = {10.1016/j.jgar.2023.05.008}, pmid = {37307951}, issn = {2213-7173}, mesh = {Humans ; Genes, Bacterial ; *Diabetic Foot ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Tetracycline ; *Diabetes Mellitus ; }, abstract = {OBJECTIVES: Treating patients with diabetic foot infection (DFI) is challenging because of high rates of antibiotic resistance. Therefore, to administer a suitable antibiotic treatment, it is necessary to know the antibiotic resistance patterns in DFIs.

METHODS: To explore this question, we selected metagenomic data of 36 tissue samples from patients with DFI in the National Center for Biotechnology Information Sequence Read Archive database.

RESULTS: A total of 229 antibiotic-resistant gene (ARG) subtypes belonging to 20 ARG types were detected. The antibiotic resistome of 229 different genes in the tissue samples of patients with DFI comprised 24 core and 205 accessory resistance genes. Among the core antibiotic resistome, multidrug, tetracycline, macrolide-lincosamide-streptogramin, and beta-lactam resistance genes were the dominant categories. Procrustes analysis indicated that both the microbial community composition and mobile genetic elements (MGEs) were determinants of the ARGs. In the network analysis, 29 species were speculated to be potential hosts of 28 ARGs based on the co-occurrence results. Plasmids and transposons were the most common elements that co-occurred with ARGs.

CONCLUSIONS: Our study provided detailed information about antibiotic resistance patterns in DFI, which has practical implications for suggesting a more specific antibiotic choice.}, } @article {pmid37307729, year = {2023}, author = {Li, J and Zhou, Y and Liu, S and Wen, X and Huang, Y and Li, K and Li, Q}, title = {The removal performances and evaluation of heavy metals, antibiotics, and resistomes driven by peroxydisulfate amendment during composting.}, journal = {Journal of hazardous materials}, volume = {457}, number = {}, pages = {131819}, doi = {10.1016/j.jhazmat.2023.131819}, pmid = {37307729}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents ; Genes, Bacterial ; *Composting ; Manure/microbiology ; *Metals, Heavy ; }, abstract = {This study aimed to explore the effect of peroxydisulfate on the removal of heavy metals, antibiotics, heavy metal resistance genes (HMRGs), and antibiotic resistance genes (ARGs) during composting. The results showed that peroxydisulfate achieved the passivation of Fe, Mn, Zn, and Cu by promoting their speciation variations, thus reducing their bioavailability. And the residual antibiotics were better degraded by peroxydisulfate. In addition, metagenomics analysis indicated that the relative abundance of most HMRGs, ARGs, and MGEs was more effectively down-regulated by peroxydisulfate. Network analysis confirmed Thermobifida and Streptomyces were dominant potential host bacteria of HMRGs and ARGs, whose relative abundance was also effectively down-regulated by peroxydisulfate. Finally, mantel test showed the significant effect of the evolution of microbial communities and strong oxidation of peroxydisulfate on the removal of pollutants. These results suggested that heavy metals, antibiotics, HMRGs, and ARGs shared a joint fate of being removed driven by peroxydisulfate during composting.}, } @article {pmid37306708, year = {2023}, author = {Amin, AB and Zhang, L and Zhang, J and Mao, S}, title = {Metagenomics analysis reveals differences in rumen microbiota in cows with low and high milk protein percentage.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {15}, pages = {4887-4902}, pmid = {37306708}, issn = {1432-0614}, support = {2021YFF1000703-01//National key Research and Development program of China/ ; }, mesh = {Female ; Cattle ; Animals ; *Milk Proteins/metabolism ; Lactation ; Rumen/microbiology ; Metagenomics ; Lysine/metabolism ; Diet/veterinary ; *Microbiota ; Carbohydrates ; Nitrogen/metabolism ; Fermentation ; Animal Feed/analysis ; }, abstract = {Variation exists in milk protein concentration of dairy cows of the same breed that are fed and managed in the same environment, and little information was available on this variation which might be attributed to differences in rumen microbial composition as well as their fermentation metabolites. This study is aimed at investigating the difference in the composition and functions of rumen microbiota as well as fermentation metabolites in Holstein cows with high and low milk protein concentrations. In this study, 20 lactating Holstein cows on the same diet were divided into two groups (10 cows each), high degree of milk protein group (HD), and low degree of milk protein (LD) concentrations based on previous milk composition history. Rumen content samples were obtained to explore the rumen fermentation parameters and rumen microbial composition. Shotgun metagenomics sequencing was employed to investigate the rumen microbial composition and sequences were assembled via the metagenomics binning technique. Metagenomics revealed that 6 Archaea genera, 5 Bacteria genera, 7 Eukaryota genera, and 7 virus genera differed significantly between the HD and LD group. The analysis of metagenome-assembled genomes (MAGs) showed that 2 genera (g__Eubacterium_H and g__Dialister) were significantly enriched (P < 0.05, linear discriminant analysis (LDA) > 2) in the HD group. However, the LD group recorded an increased abundance (P < 0.05, LDA > 2) of 8 genera (g__CAG-603, g__UBA2922, g__Ga6A1, g__RUG13091, g__Bradyrhizobium, g__Sediminibacterium, g__UBA6382, and g__Succinivibrio) when compared to the HD group. Furthermore, investigation of the KEGG genes revealed an upregulation in a higher number of genes associated with nitrogen metabolism and lysine biosynthesis pathways in the HD group as compared to the LD group. Therefore, the high milk protein concentration in the HD group could be explained by an increased ammonia synthesis by ruminal microbes which were converted to microbial amino acids and microbial protein (MCP) in presence of an increased energy source made possible by higher activities of carbohydrate-active enzymes (CAZymes). This MCP gets absorbed in the small intestine as amino acids and might be utilized for the synthesis of milk protein. KEY POINTS: • Rumen microbiota and their functions differed between cows with high milk protein % and those with low milk protein %. • The rumen microbiome of cows with high milk protein recorded a higher number of enriched genes linked to the nitrogen metabolism pathway and lysine biosynthesis pathway. • The activities of carbohydrate-active enzymes were found to be higher in the rumen of cows with high milk protein %.}, } @article {pmid37306587, year = {2023}, author = {Cheng, H and Zhang, Y and Guo, Z and He, X and Liu, R and Zhu, XY and Li, J and Liu, J and Zhang, XH}, title = {Microbial Dimethylsulfoniopropionate Cycling in Deep Sediment of the Mariana Trench.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {7}, pages = {e0025123}, pmid = {37306587}, issn = {1098-5336}, mesh = {*Seawater/microbiology ; Bacteria ; Sulfides/metabolism ; *Sulfonium Compounds/metabolism ; }, abstract = {Dimethylsulfoniopropionate (DMSP) and related organic sulfur compounds play key roles in global sulfur cycling. Bacteria have been found to be important DMSP producers in seawater and surface sediments of the aphotic Mariana Trench (MT). However, detailed bacterial DMSP cycling in the Mariana Trench subseafloor remains largely unknown. Here, the bacterial DMSP-cycling potential in a Mariana Trench sediment core (7.5 m in length) obtained at a 10,816-m water depth was investigated using culture-dependent and -independent methods. The DMSP content fluctuated along the sediment depth and reached the highest concentration at 15 to 18 cm below the seafloor (cmbsf). dsyB was the dominant known DMSP synthetic gene, existing in 0.36 to 1.19% of the bacteria, and was identified in the metagenome-assembled genomes (MAGs) of previously unknown bacterial DMSP synthetic groups such as Acidimicrobiia, Phycisphaerae, and Hydrogenedentia. dddP, dmdA, and dddX were the major DMSP catabolic genes. The DMSP catabolic activities of DddP and DddX retrieved from Anaerolineales MAGs were confirmed by heterologous expression, indicating that such anaerobic bacteria might participate in DMSP catabolism. Moreover, genes involved in methanethiol (MeSH) production from methylmercaptopropionate (MMPA) and dimethyl sulfide (DMS), MeSH oxidation, and DMS production were highly abundant, suggesting active conversions between different organic sulfur compounds. Finally, most culturable DMSP synthetic and catabolic isolates possessed no known DMSP synthetic and catabolic genes, and actinomycetes could be important groups involved in both DMSP synthesis and catabolism in Mariana Trench sediment. This study extends the current understanding of DMSP cycling in Mariana Trench sediment and highlights the need to uncover novel DMSP metabolic genes/pathways in extreme environments. IMPORTANCE Dimethylsulfoniopropionate (DMSP) is an abundant organosulfur molecule in the ocean and is the precursor for the climate-active volatile gas dimethyl sulfide. Previous studies focused mainly on bacterial DMSP cycling in seawater, coastal sediment, and surface trench sediment samples, but DMSP metabolism in the Mariana Trench (MT) subseafloor sediments remains unknown. Here, we describe the DMSP content and metabolic bacterial groups in the subseafloor of the MT sediment. We found that the tendency for vertical variation of the DMSP content in the MT was distinct from that of the continent shelf sediment. Although dsyB and dddP were the dominant DMSP synthetic and catabolic genes in the MT sediment, respectively, both metagenomic and culture methods revealed multiple previously unknown DMSP metabolic bacterial groups, especially anaerobic bacteria and actinomycetes. The active conversion of DMSP, DMS, and methanethiol may also occur in the MT sediments. These results provide novel insights for understanding DMSP cycling in the MT.}, } @article {pmid37306468, year = {2023}, author = {Shen, Y and Qu, W and Yu, F and Zhang, D and Zou, Q and Han, D and Xie, M and Chen, X and Yuan, L and Lou, B and Xie, G and Wang, R and Yang, X and Chen, W and Wang, Q and Teng, Y and Dong, Y and Huang, L and Bao, J and Liu, C and Wu, W and Shen, E and Fan, L and Timko, MP and Zheng, S and Chen, Y}, title = {Dynamic associations between the respiratory tract and gut antibiotic resistome of patients with COVID-19 and its prediction power for disease severity.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2223340}, pmid = {37306468}, issn = {1949-0984}, mesh = {Humans ; Anti-Bacterial Agents ; Vancomycin ; Leukocytes, Mononuclear ; *COVID-19 ; *Gastrointestinal Microbiome ; Respiratory System ; Patient Acuity ; }, abstract = {The antibiotic resistome is the collection of all antibiotic resistance genes (ARGs) present in an individual. Whether an individual's susceptibility to infection and the eventual severity of coronavirus disease 2019 (COVID-19) is influenced by their respiratory tract antibiotic resistome is unknown. Additionally, whether a relationship exists between the respiratory tract and gut ARGs composition has not been fully explored. We recruited 66 patients with COVID-19 at three disease stages (admission, progression, and recovery) and conducted a metagenome sequencing analysis of 143 sputum and 97 fecal samples obtained from them. Respiratory tract, gut metagenomes, and peripheral blood mononuclear cell (PBMC) transcriptomes are analyzed to compare the gut and respiratory tract ARGs of intensive care unit (ICU) and non-ICU (nICU) patients and determine relationships between ARGs and immune response. Among the respiratory tract ARGs, we found that Aminoglycoside, Multidrug, and Vancomycin are increased in ICU patients compared with nICU patients. In the gut, we found that Multidrug, Vancomycin, and Fosmidomycin were increased in ICU patients. We discovered that the relative abundances of Multidrug were significantly correlated with clinical indices, and there was a significantly positive correlation between ARGs and microbiota in the respiratory tract and gut. We found that immune-related pathways in PBMC were enhanced, and they were correlated with Multidrug, Vancomycin, and Tetracycline ARGs. Based on the ARG types, we built a respiratory tract-gut ARG combined random-forest classifier to distinguish ICU COVID-19 patients from nICU patients with an AUC of 0.969. Cumulatively, our findings provide some of the first insights into the dynamic alterations of respiratory tract and gut antibiotic resistome in the progression of COVID-19 and disease severity. They also provide a better understanding of how this disease affects different cohorts of patients. As such, these findings should contribute to better diagnosis and treatment scenarios.}, } @article {pmid37306408, year = {2023}, author = {Tang, W and Zheng, H and Xu, S and Li, P and Zhan, L and Luo, X and Dai, Z and Wang, Q and Yu, G}, title = {MMINP: A computational framework of microbe-metabolite interactions-based metabolic profiles predictor based on the O2-PLS algorithm.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2223349}, pmid = {37306408}, issn = {1949-0984}, mesh = {*Gastrointestinal Microbiome ; Least-Squares Analysis ; Algorithms ; Computational Biology ; Metabolome ; }, abstract = {The gut metabolome acts as an intermediary between the gut microbiota and host, and has tremendous diagnostic and therapeutic potential. Several studies have utilized bioinformatic tools to predict metabolites based on the different aspects of the gut microbiome. Although these tools have contributed to a better understanding of the relationship between the gut microbiota and various diseases, most of them have focused on the impact of microbial genes on the metabolites and the relationship between microbial genes. In contrast, relatively little is known regarding the effect of metabolites on the microbial genes or the relationship between these metabolites. In this study, we constructed a computational framework of Microbe-Metabolite INteractions-based metabolic profiles Predictor (MMINP), based on the Two-Way Orthogonal Partial Least Squares (O2-PLS) algorithm to predict the metabolic profiles associated with gut microbiota. We demonstrated the predictive value of MMINP relative to that of similar methods. Additionally, we identified the features that would profoundly impact the prediction performance of data-driven methods (O2-PLS, MMINP, MelonnPan, and ENVIM), including the training sample size, host disease state, and the upstream data processing methods of the different technical platforms. We suggest that when using data-driven methods, similar host disease states and preprocessing methods, and a sufficient number of training samples are necessary to achieve accurate prediction.}, } @article {pmid37305949, year = {2023}, author = {Nandi, D and Parida, S and Sharma, D}, title = {The gut microbiota in breast cancer development and treatment: The good, the bad, and the useful!.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2221452}, pmid = {37305949}, issn = {1949-0984}, mesh = {Female ; Humans ; *Breast Neoplasms/therapy ; *Gastrointestinal Microbiome ; *Microbiota ; Metagenome ; Cognition ; }, abstract = {Regardless of the global progress in early diagnosis and novel therapeutic regimens, breast carcinoma poses a devastating threat, and the advances are somewhat marred by high mortality rates. Breast cancer risk prediction models based on the known risk factors are extremely useful, but a large number of breast cancers develop in women with no/low known risk. The gut microbiome exerts a profound impact on the host health and physiology and has emerged as a pivotal frontier in breast cancer pathogenesis. Progress in metagenomic analysis has enabled the identification of specific changes in the host microbial signature. In this review, we discuss the microbial and metabolomic changes associated with breast cancer initiation and metastatic progression. We summarize the bidirectional impact of various breast cancer-related therapies on gut microbiota and vice-versa. Finally, we discuss the strategies to modulate the gut microbiota toward a more favorable state that confers anticancer effects.}, } @article {pmid37305415, year = {2023}, author = {Song, Z and Zheng, J and Zhao, Y and Yin, J and Zheng, D and Hu, H and Liu, H and Sun, M and Ruan, L and Liu, F}, title = {Population genomics and pathotypic evaluation of the bacterial leaf blight pathogen of rice reveals rapid evolutionary dynamics of a plant pathogen.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1183416}, pmid = {37305415}, issn = {2235-2988}, mesh = {*Oryza ; Metagenomics ; Agriculture ; China ; Disease Management ; }, abstract = {The Xanthomonas oryzae pv. oryzae (Xoo) is a bacterial pathogen causing bacterial blight disease in rice, resulting in significant yield reductions of up to 50% in rice production. Despite its serious threat to food production globally, knowledge of its population structure and virulence evolution is relatively limited. In this study, we employed whole-genome sequencing to explore the diversity and evolution of Xoo in the main rice-growing areas of China over the past 30 years. Using phylogenomic analysis, we revealed six lineages. CX-1 and CX-2 primarily contained Xoo isolates from South China, while CX-3 represented Xoo isolates from North China. Xoo isolates belonging to CX-5 and CX-6 were the most prevalent across all studied areas, persisting as dominant lineages for several decades. Recent sporadic disease outbreaks were primarily caused by Xoo isolates derived from the two major lineages, CX-5 and CX-6, although Xoo isolates from other lineages also contributed to these outbreaks. The lineage and sub-lineage distributions of Xoo isolates were strongly correlated with their geographical origin, which was found to be mainly determined by the planting of the two major rice subspecies, indica and japonica. Moreover, large-scale virulence testing was conducted to evaluate the diversity of pathogenicity for Xoo. We found rapid virulence evolution against rice, and its determinant factors included the genetic background of Xoo, rice resistance genes, and planting environment of rice. This study provides an excellent model for understanding the evolution and dynamics of plant pathogens in the context of their interactions with their hosts, which are shaped by a combination of geographical conditions and farming practices. The findings of this study may have important implications for the development of effective strategies for disease management and crop protection in rice production systems.}, } @article {pmid37304849, year = {2023}, author = {Green, GBH and Williams, MB and Chehade, SB and Flowers, JT and Morrow, CD and Lawrence, AL and Bej, AK and Watts, SA}, title = {Body Metrics and the Gut Microbiome in Response to Macronutrient Limitation in the Zebrafish Danio rerio.}, journal = {Current developments in nutrition}, volume = {7}, number = {4}, pages = {100065}, pmid = {37304849}, issn = {2475-2991}, abstract = {BACKGROUND: Healthy and predictable physiologic homeostasis is paramount in animal models for biomedical research. Proper macronutrient intake is an essential and controllable environmental factor for maintaining animal health and promoting experimental reproducibility.

OBJECTIVE AND METHODS: Evaluate reductions in dietary macronutrient composition on body weight metrics, composition, and gut microbiome in Danio rerio.

METHODS: D. rerio were fed reference diets deficient in either protein or lipid content for 14 weeks.

RESULTS: Diets of reduced-protein or reduced-fat resulted in lower weight gain than the standard reference diet in male and female D. rerio. Females fed the reduced-protein diet had increased total body lipid, suggesting increased adiposity compared with females fed the standard reference diet. In contrast, females fed the reduced-fat diet had decreased total body lipid compared with females fed the standard reference diet. The microbial community in male and female D. rerio fed the standard reference diet displayed high abundances of Aeromonas, Rhodobacteraceae, and Vibrio. In contrast, Vibrio spp. were dominant in male and female D. rerio fed a reduced-protein diet, whereas Pseudomonas displayed heightened abundance when fed the reduced-fat diet. Predicted functional metagenomics of microbial communities (PICRUSt2) revealed a 3- to 4-fold increase in the KEGG (Kyoto Encyclopedia of Genes and Genomes) functional category of steroid hormone biosynthesis in both male and female D. rerio fed a reduced-protein diet. In contrast, an upregulation of secondary bile acid biosynthesis and synthesis and degradation of ketone bodies was concomitant with a downregulation in steroid hormone biosynthesis in females fed a reduced-fat diet.

CONCLUSIONS: These study outcomes provide insight into future investigations to understand nutrient requirements to optimize growth, reproductive, and health demographics to microbial populations and metabolism in the D. rerio gut ecosystem. These evaluations are critical in understanding the maintenance of steady-state physiologic and metabolic homeostasis in D. rerio. Curr Dev Nutr 20xx;x:xx.}, } @article {pmid37303742, year = {2023}, author = {Lin, L and Ju, F}, title = {Evaluation of different 16S rRNA gene hypervariable regions and reference databases for profiling engineered microbiota structure and functional guilds in a swine wastewater treatment plant.}, journal = {Interface focus}, volume = {13}, number = {4}, pages = {20230012}, pmid = {37303742}, issn = {2042-8898}, abstract = {High-throughput 16S rRNA gene amplicon sequencing technology is widely applied for environmental microbiota structure analysis to derive knowledge that informs microbiome-based surveillance and oriented bioengineering. However, it remains elusive how the selection of 16S rRNA gene hypervariable regions and reference databases affects microbiota diversity and structure profiling. This study systematically evaluated the fitness of different frequently used reference databases (i.e. SILVA 138 SSU, GTDB bact120_r207, Greengenes 13_5 and MiDAS 4.8) and primers of 16S rRNA gene in microbiota profiling of anaerobic digestion and activated sludge collected from a full-scale swine wastewater treatment plant (WWTP). The comparative results showed that MiDAS 4.8 achieved the highest levels of taxonomic diversity and species-level assignment rate. For whichever sample groups, microbiota richness captured by different primers decreased in the following order: V4 > V4-V5 > V3-V4 > V6-V8/V1-V3. Using primer-bias-free metagenomic data results as the judging standard, V4 region also best characterized microbiota structure and well represented typical functional guilds (e.g. methanogens, ammonium oxidizers and denitrifiers), while V6-V8 regions largely overestimated the archaeal methanogens (mainly Methanosarcina) by over 30 times. Therefore, MiDAS 4.8 database and V4 region are recommended for best simultaneous analysis of bacterial and archaeal community diversity and structure of the examined swine WWTP.}, } @article {pmid37303219, year = {2023}, author = {Diao, Z and Zhang, Y and Chen, Y and Han, Y and Chang, L and Ma, Y and Feng, L and Huang, T and Zhang, R and Li, J}, title = {Assessing the Quality of Metagenomic Next-Generation Sequencing for Pathogen Detection in Lower Respiratory Infections.}, journal = {Clinical chemistry}, volume = {69}, number = {9}, pages = {1038-1049}, doi = {10.1093/clinchem/hvad072}, pmid = {37303219}, issn = {1530-8561}, mesh = {Humans ; Reproducibility of Results ; *Respiratory Tract Infections/diagnosis ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Biological Assay ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Laboratory-developed metagenomic next-generation sequencing (mNGS) assays are increasingly being used for the diagnosis of infectious disease. To ensure comparable results and advance the quality control for the mNGS assay, we initiated a large-scale multicenter quality assessment to scrutinize the ability of mNGS to detect pathogens in lower respiratory infections.

METHODS: A reference panel containing artificial microbial communities and real clinical samples was used to assess the performance of 122 laboratories. We comprehensively evaluated the reliability, the source of false-positive and false-negative microbes, as well as the ability to interpret the results.

RESULTS: A wide variety of weighted F1-scores was observed across 122 participants, with a range from 0.20 to 0.97. The majority of false positive microbes (68.56%, 399/582) were introduced from "wet lab." The loss of microbial sequence during wet labs was the chief cause (76.18%, 275/361) of false-negative errors. When the human context is 2 × 105 copies/mL, most DNA and RNA viruses at titers above 104 copies/mL could be detected by >80% of the participants, while >90% of the laboratories could detect bacteria and fungi at titers lower than 103 copies/mL. A total of 10.66% (13/122) to 38.52% (47/122) of the participants could detect the target pathogens but failed to reach a correct etiological diagnosis.

CONCLUSIONS: This study clarified the sources of false-positive and false-negative results and evaluated the performance of interpreting the results. This study was valuable for clinical mNGS laboratories to improve method development, avoid erroneous results being reported, and implement regulatory quality controls in the clinic.}, } @article {pmid37303052, year = {2023}, author = {Bao, R and Mei, Q and Yang, T and Zhang, L and Zhu, C and Fan, X and Wang, Y and Tong, F and He, Y and Fang, X and Geng, S and Yang, Y and Sheng, X and Pan, A}, title = {Comparison of endotracheal aspirate and bronchoalveolar lavage fluid metagenomic next-generation sequencing in severe pneumonia: a nested, matched case-control study.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {389}, pmid = {37303052}, issn = {1471-2334}, support = {WK9110000102//the Fundamental Research Funds for the Central Universities/ ; WK9110000102//the Fundamental Research Funds for the Central Universities/ ; WK9110000102//the Fundamental Research Funds for the Central Universities/ ; WK9110000102//the Fundamental Research Funds for the Central Universities/ ; WK9110000102//the Fundamental Research Funds for the Central Universities/ ; WK9110000102//the Fundamental Research Funds for the Central Universities/ ; WK9110000102//the Fundamental Research Funds for the Central Universities/ ; WK9110000102//the Fundamental Research Funds for the Central Universities/ ; WK9110000102//the Fundamental Research Funds for the Central Universities/ ; WK9110000102//the Fundamental Research Funds for the Central Universities/ ; WK9110000102//the Fundamental Research Funds for the Central Universities/ ; WK9110000102//the Fundamental Research Funds for the Central Universities/ ; WK9110000102//the Fundamental Research Funds for the Central Universities/ ; WK9110000102//the Fundamental Research Funds for the Central Universities/ ; 202104j07020043//the Key Research and Development Program of Anhui Province/ ; 202104j07020043//the Key Research and Development Program of Anhui Province/ ; 202104j07020043//the Key Research and Development Program of Anhui Province/ ; 202104j07020043//the Key Research and Development Program of Anhui Province/ ; 202104j07020043//the Key Research and Development Program of Anhui Province/ ; 202104j07020043//the Key Research and Development Program of Anhui Province/ ; 202104j07020043//the Key Research and Development Program of Anhui Province/ ; 202104j07020043//the Key Research and Development Program of Anhui Province/ ; 202104j07020043//the Key Research and Development Program of Anhui Province/ ; 202104j07020043//the Key Research and Development Program of Anhui Province/ ; 202104j07020043//the Key Research and Development Program of Anhui Province/ ; 202104j07020043//the Key Research and Development Program of Anhui Province/ ; 202104j07020043//the Key Research and Development Program of Anhui Province/ ; 202104j07020043//the Key Research and Development Program of Anhui Province/ ; }, mesh = {Humans ; Case-Control Studies ; Retrospective Studies ; Bronchoalveolar Lavage Fluid ; *Pneumonia/diagnosis ; High-Throughput Nucleotide Sequencing ; }, abstract = {OBJECTIVES: To compare clinical outcomes in patients with severe pneumonia according to the diagnostic strategy used.

METHODS: In this retrospective, nested, case-control study, patients with severe pneumonia who had undergone endotracheal aspirate (ETA) metagenomic next-generation sequencing of (mNGS) testing (n = 53) were matched at a ratio of 1 to 2 (n = 106) by sex, age, underlying diseases, immune status, disease severity scores, and type of pneumonia with patients who had undergone bronchoalveolar lavage fluid (BALF) mNGS. The microbiological characteristics and patient's prognosis of the two groups were compared.

RESULTS: An overall comparison between the two groups showed no significant differences in bacterial, fungal, viral, or mixed infections. However, subgroup analysis of 18 patients who received paired ETA and BALF mNGS showed a complete agreement rate for the two specimens of 33.3%. There were more cases for whom targeted treatment was initiated (36.79% vs. 22.64%; P = 0.043) and fewer cases who received no clinical benefit after mNGS (5.66% vs. 15.09%; P = 0.048) in the BALF group. The pneumonia improvement rate in the BALF group was significantly higher than in the ETA group (73.58% vs. 87.74%, P = 0.024). However, there were no significant differences in ICU mortality or 28-day mortality.

CONCLUSIONS: We do not recommend using ETA mNGS as the first-choice method for analyzing airway pathogenic specimens from severe pneumonia patients.}, } @article {pmid37302767, year = {2023}, author = {Zhang, H and Zhang, W and Zhang, SS and Ma, WC and Zhu, L and Li, YP and Pan, Y and Chen, L}, title = {Simultaneous phosphorus recovery from wastewater and sludge by a novel denitrifying phosphorus removal system.}, journal = {Bioresource technology}, volume = {384}, number = {}, pages = {129284}, doi = {10.1016/j.biortech.2023.129284}, pmid = {37302767}, issn = {1873-2976}, mesh = {*Wastewater ; *Sewage ; Phosphorus/metabolism ; Nitrates ; Denitrification ; Bioreactors ; Organic Chemicals ; Nitrogen ; Waste Disposal, Fluid ; }, abstract = {A novel process was proposed for simultaneous denitrification and phosphorus (P) recovery. The increased nitrate concentration facilitated the activity of denitrifying P removal (DPR) in P enrichment, which stimulated P uptake and storage, making P more readily accessible for release into the recirculated stream. The total P content in the biofilm (TPbiofilm) rose to 54.6 ± 3.5 mg/g SS as the nitrate concentration increased from 15.0 to 25.0 mg/L, while the P concentration of the enriched stream reached 172.5 ± 3.5 mg/L. Moreover, the abundance of denitrifying polyphosphate accumulating organisms (DPAOs) increased from 5.6% to 28.0%, and the increased nitrate concentration facilitated the process of carbon, nitrogen, and P metabolism due to the rise in the genes involved in critical functions of metabolism. Acid/alkaline fermentation analysis indicated that the EPS release was the primary P-release pathway. Additionally, pure struvite crystals were obtained from the enriched stream and fermentation supernatant.}, } @article {pmid37302601, year = {2023}, author = {Shi, K and Zhang, Y and Ding, G and Wang, X and Yan, X and Pan, H and Zhao, Y}, title = {Remediation of Cr(VI)-contaminated soil mixed with chromite ore processing residue by ferrous sulfate and enzyme residue.}, journal = {The Science of the total environment}, volume = {892}, number = {}, pages = {164743}, doi = {10.1016/j.scitotenv.2023.164743}, pmid = {37302601}, issn = {1879-1026}, mesh = {*Ferrous Compounds/chemistry ; Chromium/analysis ; Industrial Waste/analysis ; Soil ; *Soil Pollutants/analysis ; }, abstract = {In this study, Cr(VI)-contaminated soil mixed with COPR by using ferrous sulfate (FeSO4), enzyme residue (ER), and their combination under aerobic or anaerobic condition were investigated. The concentration of Cr(VI) decreased from 1498.05 to 104.63 mg kg[-1] after the simultaneous addition of FeSO4 (30 %, w/w as FeSO4·7H2O) and ER (30 %, w/w) at 45 d under the anaerobic condition with a reduction efficiency of 93.02 %, which is higher than that by single FeSO4 (72.39 %) or ER (75.47 %) under the anaerobic condition. XRD, XPS, FTIR, and fluorescence spectroscopy were conducted to characterize soil and ER composition. Metagenomic analysis was performed to reveal the reduction mechanisms of FeSO4 and ER. The anaerobic condition with lower Eh was beneficial for Cr(VI) reduction than aerobic condition, and Eh was the main driver for the evolution of Cr(VI) reduction-related microorganisms. Moreover, the addition of ER enriched the organic matter and microbials in the soil. During the decomposition of organic matter under the anaerobic condition, organic acids were generated, leading to a decrease in pH and promoting the release of Cr(VI) from minerals. They also served as electron donors in Cr(VI) reduction. Additionally, the addition of excess FeSO4 stimulated the growth of iron-reducing bacteria and sulfate-reducing bacteria, facilitating to Cr(VI) reduction. Metagenomic analysis showed that Acinetobacter, related to the nemA and nfsA genes, was the dominant Cr(VI) reduction genus. Thus, the combination of FeSO4 and ER is a promising method for the remediation of Cr(VI)-contaminated soils mixed with COPR.}, } @article {pmid37302501, year = {2023}, author = {Yang, Z and Li, C and Chen, H and Shan, X and Chen, J and Zhang, J and Liu, S and Liu, Q and Wang, X}, title = {Source-oriented ecological and resistome risks associated with geochemical enrichment of heavy metals in river sediments.}, journal = {Chemosphere}, volume = {336}, number = {}, pages = {139119}, doi = {10.1016/j.chemosphere.2023.139119}, pmid = {37302501}, issn = {1879-1298}, mesh = {Rivers/chemistry ; Cadmium/analysis ; Environmental Monitoring/methods ; *Metals, Heavy/analysis ; *Mercury/analysis ; China ; Risk Assessment ; Anti-Bacterial Agents/analysis ; Geologic Sediments/chemistry ; }, abstract = {Heavy metals (HMs) pose ecological and resistome risks to aquatic systems. To efficiently develop targeted risk mitigation strategies, apportioning HM sources and assessing their source-oriented risks are essential. Although many studies have reported risk assessment and source apportionment of HMs, yet few have explored source-specific ecological and resistome risks associated with geochemical enrichment of HMs in aquatic environments. Therefore, this study proposes an integrated technological framework to characterize source-oriented ecological and resistome risks in the sediments of a plain river in China. Several geochemical tools quantitatively showed Cd and Hg had the highest pollution levels in the environment, with 19.7 and 7.5 times higher than their background values, respectively. Positive matrix factorization (PMF) and Unmix were comparatively used to apportion sources of HMs. Essentially, the two models were complementary and identified similar sources including industrial discharges, agricultural activities, atmospheric deposition and natural background, with contributions of 32.3-37.0%, 8.0-9.0%, 12.1-15.9% and 42.8-43.0%, respectively. To analyze source-specific ecological risks, the apportionment results were integratively incorporated into a modified ecological risk index. The results showed anthropogenic sources were the most significant contributors to the ecological risks. Particularly, industrial discharges majorly contributed high- (44%) and extremely high (52%) ecological risk for Cd, while agricultural activities posed a greater percentage of considerable-(36%) and high- (46%) ecological risk for Hg. Furthermore, the high-throughput sequencing metagenomic analysis identified abundant and diverse antibiotic resistance genes (ARGs), including some carbapenem-resistance genes and emerging genes such as mcr-type in the river sediments. Network and statistical analyses displayed significant correlations between ARGs and geochemical enrichment of HMs (ρ > 0.8; P-value <0.01), indicating their important impacts on resistome risks in the environment. This study provides useful insights into risk prevention and pollution control of HMs, and the framework can be made applicable to other rivers facing environmental challenges worldwide.}, } @article {pmid37302051, year = {2023}, author = {Meng, LN and Li, G and Yuan, HX and Feng, XC and Liu, F and Zhang, SL}, title = {Utility of metagenomics next-generation sequencing in the diagnosis and treatment of severe infectious diseases in the intensive care unit.}, journal = {Technology and health care : official journal of the European Society for Engineering and Medicine}, volume = {31}, number = {5}, pages = {1887-1899}, doi = {10.3233/THC-220856}, pmid = {37302051}, issn = {1878-7401}, mesh = {Humans ; Retrospective Studies ; *Communicable Diseases ; *Sepsis/diagnosis/drug therapy ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents ; Intensive Care Units ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a new method that combines high-throughput sequencing and bioinformatics analysis. However, it has not become as popular due to the limited testing equipment and high costs and lack of family awareness with not much relevant intensive care unit (ICU) research data.

OBJECTIVE: To explore the clinical use and value of metagenomics next-generation sequencing (mNGS) in patients with sepsis in the ICU.

METHODS: We conducted a retrospective analysis of 102 patients with sepsis admitted to the ICU of Peking University International Hospital from January 2018 to January 2022. Based on whether mNGS was performed, the identified patients were divided into the observation group (n= 51) and the control group (n= 51), respectively. Routine laboratory tests, including routine blood test, C-reactive protein, procalcitonin, and culture of suspicious lesion specimens were performed in both groups within 2 hours after admission to the ICU, while mNGS tests were performed in the observation group. Patients in both groups were routinely given initial anti-infective, anti-shock, and organ support treatment. Antibiotic regimens were optimized in a timely manner according to the etiological results. Relevant clinical data were collected.

RESULTS: The testing cycle of mNGS was shorter than that of the conventional culture (30.79 ± 4.01 h vs. 85.38 ± 9.94 h, P< 0.001), while the positive rate of mNGS was higher than that of the conventional culture (82.35% vs. 45.1%, P< 0.05), with obvious superiority in the detection of viruses and fungus. There were significant differences in the optimal time of antibiotics (48 h vs.100 h) and length of ICU stay (11 d vs. 16 d) between the observation group and control group (P< 0.01) respectively, with no difference in 28-day mortality (33.3% vs. 41.2%, P> 0.05).

CONCLUSION: mNGS is useful in the detection of sepsis-causing pathogens in the ICU with the advantages of short testing time and high positive rate. There was no difference in the 28-day outcome between the two groups, which may be related to other confounding factors such as small sample size. Additional studies with extended sample size are needed.}, } @article {pmid37301921, year = {2023}, author = {Zhou, Y and Shi, W and Wen, Y and Mao, E and Ni, T}, title = {Comparison of pathogen detection consistency between metagenomic next-generation sequencing and blood culture in patients with suspected bloodstream infection.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {9460}, pmid = {37301921}, issn = {2045-2322}, mesh = {Humans ; *Blood Culture ; Retrospective Studies ; *Sepsis/diagnosis ; Viremia ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {The application of metagenomic next-generation sequencing (mNGS) has gradually been carried out by clinical practitioner. However, few studies have compared it with blood cultures in patients suffering from suspected bloodstream infections. The purpose of this study was to compare the detection of pathogenic microorganisms by these two assays in patients with suspected bloodstream infection. We retrospectively studied patients with fever, chills, antibiotic use for more than 3 days, suspected bloodstream infection, and admission to the emergency department of Ruijin Hospital from January 2020 to June 2022. All patients had blood drawn on the same day for blood mNGS and blood cultures. Clinical and laboratory parameters were collected on the day blood was drawn. The detection of pathogenic microorganisms by the two methods was compared. Risk factors and in-hospital mortality in patients with bloodstream infections were analysed separately for these two assays. In all 99 patients, the pathogenic microorganisms detection rate in blood mNGS was significantly higher than that in blood culture. Blood mNGS was consistent with blood culture in only 12.00% of all positive bacterial and fungal test results. The level of CRP is related to bacteraemia, fungaemia and viraemia detected by blood mNGS. No clear risk factors could be found in patients with a positive blood culture. In critically ill patients, both tests failed to improve patient outcomes. In patients with suspected bloodstream infection, mNGS is not yet a complete replacement for blood cultures.}, } @article {pmid37301875, year = {2023}, author = {Li, L and Wang, T and Ning, Z and Zhang, X and Butcher, J and Serrana, JM and Simopoulos, CMA and Mayne, J and Stintzi, A and Mack, DR and Liu, YY and Figeys, D}, title = {Revealing proteome-level functional redundancy in the human gut microbiome using ultra-deep metaproteomics.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3428}, pmid = {37301875}, issn = {2041-1723}, support = {R01 AI141529/AI/NIAID NIH HHS/United States ; R01 HD093761/HD/NICHD NIH HHS/United States ; RF1 AG067744/AG/NIA NIH HHS/United States ; UH3 OD023268/OD/NIH HHS/United States ; U19 AI095219/AI/NIAID NIH HHS/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Proteome ; Proteomics ; Xenobiotics ; Feces ; *Microbiota ; }, abstract = {Functional redundancy is a key ecosystem property representing the fact that different taxa contribute to an ecosystem in similar ways through the expression of redundant functions. The redundancy of potential functions (or genome-level functional redundancy [Formula: see text]) of human microbiomes has been recently quantified using metagenomics data. Yet, the redundancy of expressed functions in the human microbiome has never been quantitatively explored. Here, we present an approach to quantify the proteome-level functional redundancy [Formula: see text] in the human gut microbiome using metaproteomics. Ultra-deep metaproteomics reveals high proteome-level functional redundancy and high nestedness in the human gut proteomic content networks (i.e., the bipartite graphs connecting taxa to functions). We find that the nested topology of proteomic content networks and relatively small functional distances between proteomes of certain pairs of taxa together contribute to high [Formula: see text] in the human gut microbiome. As a metric comprehensively incorporating the factors of presence/absence of each function, protein abundances of each function and biomass of each taxon, [Formula: see text] outcompetes diversity indices in detecting significant microbiome responses to environmental factors, including individuality, biogeography, xenobiotics, and disease. We show that gut inflammation and exposure to specific xenobiotics can significantly diminish the [Formula: see text] with no significant change in taxonomic diversity.}, } @article {pmid37301793, year = {2023}, author = {Reis, MP and de Paula, RS and E Souza, CC and de Oliveira Júnior, RB and Cardoso, AV}, title = {Linking microbial slime community structure with abiotic factors and antifouling strategy in hydroelectric cooling systems.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {54}, number = {3}, pages = {1547-1557}, pmid = {37301793}, issn = {1678-4405}, mesh = {*Biofouling/prevention & control ; Biofilms ; Bacteria/genetics ; Brazil ; Quorum Sensing ; }, abstract = {Microfouling can have significant economic impacts for hydroelectric power plants. However, knowledge concerning the composition and metabolism of microbial biofilm in cooling systems remains scarce. We examined the metagenome present in a cooling system, comprising a filter (F) and heat exchanger (HE), in the Nova Ponte hydroelectric power plant in Brazil, to identify bacteria and pathways that could be targeted to monitor and control biofilm formation. Our data revealed that the microfouling sample from heat exchanger 1 (HEM1), with porous consistency, presented enriched bacterial members not frequently described as biofilm formers in cooling systems, besides it has been shown to be an autoinducer repression pathway. Furthermore, the microfouling sample from heat exchanger 2 (HEM2), with gelatinous consistency, seemed to be an established biofilm, containing enriched bacterial groups such as Desulfotomaculum and Crenothrix and autoinducers, with biotechnological relevance in industrial biofilms. The results demonstrate that biofilm composition will vary depending on different abiotic conditions and the antifouling strategy used, including type of compound, concentration, and frequency of use. Therefore, all these variables must be evaluated when a power plant is affected by microbial slime in the cooling system. Our findings could help to define strategies for efficient and ecofriendly measures to contain microfouling in power plants.}, } @article {pmid37301376, year = {2023}, author = {Manter, DK and Hamm, AK and Deel, HL}, title = {Community structure and abundance of ACC deaminase containing bacteria in soils with 16S-PICRUSt2 inference or direct acdS gene sequencing.}, journal = {Journal of microbiological methods}, volume = {211}, number = {}, pages = {106740}, doi = {10.1016/j.mimet.2023.106740}, pmid = {37301376}, issn = {1872-8359}, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics ; *Carbon-Carbon Lyases/genetics ; Water ; Soil Microbiology ; }, abstract = {Bacteria containing the enzyme 1-aminocyclopropane-1-carboxylate deaminase (ACCD+) can reduce plant ethylene levels and increase root development and elongation resulting in increased resiliency to drought and other plant stressors. Although these bacteria are ubiquitous in the soil, non-culture-based methods for their enumeration and identification are not well developed. In this study we compare two culture-independent approaches for identifying ACCD+ bacteria. First, quantitative PCR (qPCR) and direct acdS sequencing with newly designed gene-specific primers; and second, phylogenetic construction of 16S rRNA amplicon libraries with the PICRUSt2 tool. Using soils from eastern Colorado, we showed complementary yet differing results in ACCD+ abundance and community structure responding to water availability. Across all sites, gene abundances estimated from qPCR with the acdS gene-specific primers and phylogenetic reconstruction using PICRUSt2 were significantly correlated. However, PICRUSt2 identified members of the Acidobacteria, Proteobacteria, and Bacteroidetes phyla (now known as Acidobacteriota, Pseudomonadota, and Bacteroidota according to the International Code of Nomenclature of Prokaryotes) as ACCD+ bacteria, whereas the acdS primers amplified only members of the Proteobacteria phyla. Despite these differences, both measures showed that bacterial abundance of ACCD+ decreased as soil water content decreased along a potential evapotranspiration (PET) gradient at three sites in eastern Colorado. One major advantage of using 16S sequencing and PICRUSt2 in metagenomic studies is the ability to get a potential functional profile of all known KEGG (Kyoto Encyclopedia of Genes and Genomes) enzymes within the bacterial community of a single soil sample. The 16S-PICRUSt2 method paints a broader picture of the biological and biochemical function of the soil microbiome compared to direct acdS sequencing; however, phylogenetic analysis based on 16S gene relatedness may not reflect that of the functional gene of interest.}, } @article {pmid37301103, year = {2023}, author = {Dou, L and Liu, C and Chen, X and Yang, Z and Hu, G and Zhang, M and Sun, L and Su, L and Zhao, L and Jin, Y}, title = {Supplemental Clostridium butyricum modulates skeletal muscle development and meat quality by shaping the gut microbiota of lambs.}, journal = {Meat science}, volume = {204}, number = {}, pages = {109235}, doi = {10.1016/j.meatsci.2023.109235}, pmid = {37301103}, issn = {1873-4138}, mesh = {Female ; Sheep ; Animals ; *Clostridium butyricum/physiology ; *Gastrointestinal Microbiome ; Dietary Supplements/analysis ; Meat/analysis ; Muscle Development ; Animal Feed/analysis ; Muscle, Skeletal/metabolism ; }, abstract = {This study evaluated the contributions of Clostridium butyricum on skeletal muscle development, gastrointestinal flora and meat quality of lambs. Eighteen Dorper (♂) × Small Tailed Han sheep (♀) crossed ewe lambs of similar weight (27.43 ± 1.94 kg; age, 88 ± 5 days) were divided into two dietary treatments. The control group was fed the basal diet (C group), and the probiotic group was supplemented with C. butyricum on the basis of the C group (2.5 × 10[8] cfu/g, 5 g/day/lamb; P group) for 90 d. The results showed that dietary C. butyricum elevated growth performance, muscle mass, muscle fiber diameter and cross-sectional area, and decreased the shear force value of meat (P < 0.05). Moreover, C. butyricum supplementation accelerated protein synthesis by regulating the gene expression of IGF-1/Akt/mTOR pathway. We identified 54 differentially expressed proteins that regulated skeletal muscle development through different mechanisms by quantitative proteomics. These proteins were associated with ubiquitin-protease, apoptosis, muscle structure, energy metabolism, heat shock, and oxidative stress. The metagenomics sequencing results showed that Petrimonas at the genus level and Prevotella brevis at the species level in the rumen, while Lachnoclostridium, Alloprevotella and Prevotella at the genus level in the feces, were significantly enriched in the P group. Also, butyric acid and valeric acid levels were elevated in both rumen and feces of the P group. Overall, our results support the idea that C. butyricum could change gastrointestinal flora, and affect skeletal muscle development and meat quality of lambs by modulating gut-muscle axis.}, } @article {pmid37299153, year = {2023}, author = {Baeshen, NN and Baz, L and Shami, AY and Ashy, RA and Jalal, RS and Abulfaraj, AA and Refai, M and Majeed, MA and Abuzahrah, SS and Abdelkader, H and Baeshen, NA and Baeshen, MN}, title = {Composition, Abundance, and Diversity of the Soil Microbiome Associated with the Halophytic Plants Tamarix aphylla and Halopeplis perfoliata on Jeddah Seacoast, Saudi Arabia.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, pmid = {37299153}, issn = {2223-7747}, support = {UJ-23-DR-2//University of Jeddah, Jeddah, Saudi Arabia/ ; }, abstract = {The coast of the Red Sea in Jeddah City is home to a unique microbial community that has adapted to extreme environmental conditions. Therefore, it is essential to characterize the microbial community in this unique microbiome to predict how environmental changes will affect it. The aim of this study was to conduct metagenomic sequencing of 16S rRNA and ITS rRNA genes for the taxonomic classification of the microbial community in soil samples associated with the halophytic plants Tamarix aphylla and Halopeplis perfoliata. Fifteen soil samples were collected in triplicate to enhance robustness and minimize sampling bias. Firstly, to identify novel microbial candidates, the gDNAs were isolated from the saline soil samples surrounding each plant, and then bacterial 16S (V3-V4) and fungal ITS1 regions were sequenced utilizing a high-throughput approach (next-generation sequencing; NGS) on an Illumina MiSeq platform. Quality assessment of the constructed amplicon libraries was conducted using Agilent Bioanalyzer and fluorometric quantification methods. The raw data were processed and analyzed using the Pipeline (Nova Lifetech, Singapore) for bioinformatics analysis. Based on the total number of readings, it was determined that the phylum Actinobacteriota was the most prevalent in the soil samples examined, followed by the phylum Proteobacteria. Based on ITS rRNA gene analysis, the alpha and beta fungal diversity in the studied soil samples revealed that the fungal population is structured into various groups according to the crust (c) and/or rhizosphere (r) plant parts. Fungal communities in the soil samples indicated that Ascomycota and Basidiomycota were the two most abundant phyla based on the total amount of sequence reads. Secondly, heat-map analysis of the diversity indices showed that the bacterial alpha diversity, as measured by Shannon, Simpson, and InvSimpson, was associated with soil crust (Hc and Tc enclosing H. perfoliata and T. aphylla, respectively) and that the soil rhizosphere (Hr and Tr) was strongly correlated with bacterial beta diversity. Finally, fungal-associated Tc and Hc samples clustered together, according to observations made using the Fisher and Chao1 methods, and Hr and Tr samples clustered together according to Shannon, Simpson, and InvSimpson analyses. As a result of the soil investigation, potential agents that have been identified could lead to innovative agricultural, medical, and industrial applications.}, } @article {pmid37299118, year = {2023}, author = {Haegeman, A and Foucart, Y and De Jonghe, K and Goedefroit, T and Al Rwahnih, M and Boonham, N and Candresse, T and Gaafar, YZA and Hurtado-Gonzales, OP and Kogej Zwitter, Z and Kutnjak, D and Lamovšek, J and Lefebvre, M and Malapi, M and Mavrič Pleško, I and Önder, S and Reynard, JS and Salavert Pamblanco, F and Schumpp, O and Stevens, K and Pal, C and Tamisier, L and Ulubaş Serçe, Ç and van Duivenbode, I and Waite, DW and Hu, X and Ziebell, H and Massart, S}, title = {Looking beyond Virus Detection in RNA Sequencing Data: Lessons Learned from a Community-Based Effort to Detect Cellular Plant Pathogens and Pests.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, pmid = {37299118}, issn = {2223-7747}, support = {2018-A-289//FPS Health Belgium/ ; P4-0072, L7-2632 and P4-0165//Slovenian Research Agency/ ; }, abstract = {High-throughput sequencing (HTS), more specifically RNA sequencing of plant tissues, has become an indispensable tool for plant virologists to detect and identify plant viruses. During the data analysis step, plant virologists typically compare the obtained sequences to reference virus databases. In this way, they are neglecting sequences without homologies to viruses, which usually represent the majority of sequencing reads. We hypothesized that traces of other pathogens might be detected in this unused sequence data. In the present study, our goal was to investigate whether total RNA-seq data, as generated for plant virus detection, is also suitable for the detection of other plant pathogens and pests. As proof of concept, we first analyzed RNA-seq datasets of plant materials with confirmed infections by cellular pathogens in order to check whether these non-viral pathogens could be easily detected in the data. Next, we set up a community effort to re-analyze existing Illumina RNA-seq datasets used for virus detection to check for the potential presence of non-viral pathogens or pests. In total, 101 datasets from 15 participants derived from 51 different plant species were re-analyzed, of which 37 were selected for subsequent in-depth analyses. In 29 of the 37 selected samples (78%), we found convincing traces of non-viral plant pathogens or pests. The organisms most frequently detected in this way were fungi (15/37 datasets), followed by insects (13/37) and mites (9/37). The presence of some of the detected pathogens was confirmed by independent (q)PCRs analyses. After communicating the results, 6 out of the 15 participants indicated that they were unaware of the possible presence of these pathogens in their sample(s). All participants indicated that they would broaden the scope of their bioinformatic analyses in future studies and thus check for the presence of non-viral pathogens. In conclusion, we show that it is possible to detect non-viral pathogens or pests from total RNA-seq datasets, in this case primarily fungi, insects, and mites. With this study, we hope to raise awareness among plant virologists that their data might be useful for fellow plant pathologists in other disciplines (mycology, entomology, bacteriology) as well.}, } @article {pmid37298563, year = {2023}, author = {Fiutek, N and Couger, MB and Pirro, S and Roy, SW and de la Torre, JR and Connor, EF}, title = {Genomic Assessment of the Contribution of the Wolbachia Endosymbiont of Eurosta solidaginis to Gall Induction.}, journal = {International journal of molecular sciences}, volume = {24}, number = {11}, pages = {}, pmid = {37298563}, issn = {1422-0067}, support = {IRGEN_RG_2021-1345/IRGEN/IRGEN/United States ; }, mesh = {Animals ; *Wolbachia/genetics ; Tryptophan ; *Tephritidae/metabolism ; Insecta/metabolism ; Indoleacetic Acids/metabolism ; Cytokinins ; Genomics ; }, abstract = {We explored the genome of the Wolbachia strain, wEsol, symbiotic with the plant-gall-inducing fly Eurosta solidaginis with the goal of determining if wEsol contributes to gall induction by its insect host. Gall induction by insects has been hypothesized to involve the secretion of the phytohormones cytokinin and auxin and/or proteinaceous effectors to stimulate cell division and growth in the host plant. We sequenced the metagenome of E. solidaginis and wEsol and assembled and annotated the genome of wEsol. The wEsol genome has an assembled length of 1.66 Mbp and contains 1878 protein-coding genes. The wEsol genome is replete with proteins encoded by mobile genetic elements and shows evidence of seven different prophages. We also detected evidence of multiple small insertions of wEsol genes into the genome of the host insect. Our characterization of the genome of wEsol indicates that it is compromised in the synthesis of dimethylallyl pyrophosphate (DMAPP) and S-adenosyl L-methionine (SAM), which are precursors required for the synthesis of cytokinins and methylthiolated cytokinins. wEsol is also incapable of synthesizing tryptophan, and its genome contains no enzymes in any of the known pathways for the synthesis of indole-3-acetic acid (IAA) from tryptophan. wEsol must steal DMAPP and L-methionine from its host and therefore is unlikely to provide cytokinin and auxin to its insect host for use in gall induction. Furthermore, in spite of its large repertoire of predicted Type IV secreted effector proteins, these effectors are more likely to contribute to the acquisition of nutrients and the manipulation of the host's cellular environment to contribute to growth and reproduction of wEsol than to aid E. solidaginis in manipulating its host plant. Combined with earlier work that shows that wEsol is absent from the salivary glands of E. solidaginis, our results suggest that wEsol does not contribute to gall induction by its host.}, } @article {pmid37298483, year = {2023}, author = {Park, S and Zhang, T and Kang, S}, title = {Fecal Microbiota Composition, Their Interactions, and Metagenome Function in US Adults with Type 2 Diabetes According to Enterotypes.}, journal = {International journal of molecular sciences}, volume = {24}, number = {11}, pages = {}, pmid = {37298483}, issn = {1422-0067}, support = {RS-2023-00208567//National Research Foundation of Korea/ ; }, mesh = {Adult ; Humans ; Metagenome ; *Diabetes Mellitus, Type 2/genetics ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Bacteria/genetics ; }, abstract = {T2DM etiology differs among Asians and Caucasians and may be associated with gut microbiota influenced by different diet patterns. However, the association between fecal bacterial composition, enterotypes, and T2DM susceptibility remained controversial. We investigated the fecal bacterial composition, co-abundance network, and metagenome function in US adults with T2DM compared to healthy adults based on enterotypes. We analyzed 1911 fecal bacterial files of 1039 T2DM and 872 healthy US adults from the Human Microbiome Projects. Operational taxonomic units were obtained after filtering and cleaning the files using Qiime2 tools. Machine learning and network analysis identified primary bacteria and their interactions influencing T2DM incidence, clustered into enterotypes, Bacteroidaceae (ET-B), Lachnospiraceae (ET-L), and Prevotellaceae (ET-P). ET-B showed higher T2DM incidence. Alpha-diversity was significantly lower in T2DM in ET-L and ET-P (p < 0.0001), but not in ET-B. Beta-diversity revealed a distinct separation between T2DM and healthy groups across all enterotypes (p < 0.0001). The XGBoost model exhibited high accuracy and sensitivity. Enterocloster bolteae, Facalicatena fissicatena, Clostridium symbiosum, and Facalibacterium prausnitizii were more abundant in the T2DM group than in the healthy group. Bacteroides koreensis, Oscillibacter ruminantium, Bacteroides uniformis, and Blautia wexlerae were lower in the T2DM than in the healthy group regardless of the enterotypes in the XGBoost model (p < 0.0001). However, the patterns of microbial interactions varied among different enterotypes affecting T2DM risk. The interaction between fecal bacteria was more tightly regulated in the ET-L than in the ET-B and ET-P groups (p < 0.001). Metagenomic analysis revealed an inverse association between bacteria abundance in T2DM, energy utility, butanoate and propanoate metabolism, and the insulin signaling pathway (p < 0.0001). In conclusion, fecal bacteria play a role in T2DM pathogenesis, particularly within different enterotypes, providing valuable insights into the link between gut microbiota and T2DM in the US population.}, } @article {pmid37298280, year = {2023}, author = {Ordóñez, CD and Redrejo-Rodríguez, M}, title = {DNA Polymerases for Whole Genome Amplification: Considerations and Future Directions.}, journal = {International journal of molecular sciences}, volume = {24}, number = {11}, pages = {}, pmid = {37298280}, issn = {1422-0067}, support = {PID2021-123403NB-I00//MCIN/AEI/10.13039/501100011033 and ERDF A way of making Europe/ ; }, mesh = {*DNA/metabolism ; *DNA-Directed DNA Polymerase/metabolism ; Nucleic Acid Amplification Techniques/methods ; Polymerase Chain Reaction ; Genome, Viral ; }, abstract = {In the same way that specialized DNA polymerases (DNAPs) replicate cellular and viral genomes, only a handful of dedicated proteins from various natural origins as well as engineered versions are appropriate for competent exponential amplification of whole genomes and metagenomes (WGA). Different applications have led to the development of diverse protocols, based on various DNAPs. Isothermal WGA is currently widely used due to the high performance of Φ29 DNA polymerase, but PCR-based methods are also available and can provide competent amplification of certain samples. Replication fidelity and processivity must be considered when selecting a suitable enzyme for WGA. However, other properties, such as thermostability, capacity to couple replication, and double helix unwinding, or the ability to maintain DNA replication opposite to damaged bases, are also very relevant for some applications. In this review, we provide an overview of the different properties of DNAPs widely used in WGA and discuss their limitations and future research directions.}, } @article {pmid37298198, year = {2023}, author = {Zubeldia-Varela, E and Barker-Tejeda, TC and Mera-Berriatua, L and Bazire, R and Cabrera-Freitag, P and Ubeda, C and Barber, D and Francino, MP and Rojo, D and Ibáñez-Sandín, MD and Pérez-Gordo, M}, title = {Further Insights into the Gut Microbiota of Cow's Milk Allergic Infants: Analysis of Microbial Functionality and Its Correlation with Three Fecal Biomarkers.}, journal = {International journal of molecular sciences}, volume = {24}, number = {11}, pages = {}, pmid = {37298198}, issn = {1422-0067}, support = {PI17/01087//Instituto de Salud Carlos III/ ; FSEAIC_2016//Sociedad Española de Alergia e Inmunología Clínica/ ; ARADyAL RD16/00060015 and RD16/0006/0026//European Regional Development Fund/ ; PI19/00044//Instituto de Salud Carlos III/ ; PI20/01366//Instituto de Salud Carlos III/ ; }, mesh = {Female ; Animals ; Cattle ; Milk/chemistry ; *Gastrointestinal Microbiome ; Lactoferrin/metabolism ; *Milk Hypersensitivity/diagnosis ; Feces/chemistry ; Biomarkers/analysis ; }, abstract = {Cow's milk allergy (CMA) is one of the most prevalent food allergies in children. Several studies have demonstrated that gut microbiota influences the acquisition of oral tolerance to food antigens at initial stages of life. Changes in the gut microbiota composition and/or functionality (i.e., dysbiosis) have been linked to inadequate immune system regulation and the emergence of pathologies. Moreover, omic sciences have become an essential tool for the analysis of the gut microbiota. On the other hand, the use of fecal biomarkers for the diagnosis of CMA has recently been reviewed, with fecal calprotectin, α-1 antitrypsin, and lactoferrin being the most relevant. This study aimed at evaluating functional changes in the gut microbiota in the feces of cow's milk allergic infants (AI) compared to control infants (CI) by metagenomic shotgun sequencing and at correlating these findings with the levels of fecal biomarkers (α-1 antitrypsin, lactoferrin, and calprotectin) by an integrative approach. We have observed differences between AI and CI groups in terms of fecal protein levels and metagenomic analysis. Our findings suggest that AI have altered glycerophospholipid metabolism as well as higher levels of lactoferrin and calprotectin that could be explained by their allergic status.}, } @article {pmid37298073, year = {2023}, author = {Gureeva, MV and Gureev, AP}, title = {Molecular Mechanisms Determining the Role of Bacteria from the Genus Azospirillum in Plant Adaptation to Damaging Environmental Factors.}, journal = {International journal of molecular sciences}, volume = {24}, number = {11}, pages = {}, pmid = {37298073}, issn = {1422-0067}, support = {23-24-00277//Russian Science Foundation/ ; }, mesh = {*Plants/microbiology ; Bacteria ; Plant Growth Regulators/metabolism ; Plant Development ; *Azospirillum ; Plant Roots/metabolism ; }, abstract = {Agricultural plants are continuously exposed to environmental stressors, which can lead to a significant reduction in yield and even the death of plants. One of the ways to mitigate stress impacts is the inoculation of plant growth-promoting rhizobacteria (PGPR), including bacteria from the genus Azospirillum, into the rhizosphere of plants. Different representatives of this genus have different sensitivities or resistances to osmotic stress, pesticides, heavy metals, hydrocarbons, and perchlorate and also have the ability to mitigate the consequences of such stresses for plants. Bacteria from the genus Azospirillum contribute to the bioremediation of polluted soils and induce systemic resistance and have a positive effect on plants under stress by synthesizing siderophores and polysaccharides and modulating the levels of phytohormones, osmolytes, and volatile organic compounds in plants, as well as altering the efficiency of photosynthesis and the antioxidant defense system. In this review, we focus on molecular genetic features that provide bacterial resistance to various stress factors as well as on Azospirillum-related pathways for increasing plant resistance to unfavorable anthropogenic and natural factors.}, } @article {pmid37297454, year = {2023}, author = {de Carvalho, NM and Oliveira, DL and Costa, CM and Pintado, ME and Madureira, AR}, title = {Strategies to Assess the Impact of Sustainable Functional Food Ingredients on Gut Microbiota.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, pmid = {37297454}, issn = {2304-8158}, support = {POCI-01-0247-FEDER-027578//Alchemy project - Capturing high value from industrial fermentation bio products/ ; }, abstract = {Nowadays, it is evident that food ingredients have different roles and distinct health benefits to the consumer. Over the past years, the interest in functional foods, especially those targeting gut health, has grown significantly. The use of industrial byproducts as a source of new functional and sustainable ingredients as a response to such demands has raised interest. However, the properties of these ingredients can be affected once incorporated into different food matrices. Therefore, when searching for the least costly and most suitable, beneficial, and sustainable formulations, it is necessary to understand how such ingredients perform when supplemented in different food matrices and how they impact the host's health. As proposed in this manuscript, the ingredients' properties can be first evaluated using in vitro gastrointestinal tract (GIT) simulation models prior to validation through human clinical trials. In vitro models are powerful tools that mimic the physicochemical and physiological conditions of the GIT, enabling prediction of the potentials of functional ingredients per se and when incorporated into a food matrix. Understanding how newly developed ingredients from undervalued agro-industrial sources behave as supplements supports the development of new and more sustainable functional foods while scientifically backing up health-benefits claims.}, } @article {pmid37297385, year = {2023}, author = {Nam, NN and Do, HDK and Loan Trinh, KT and Lee, NY}, title = {Metagenomics: An Effective Approach for Exploring Microbial Diversity and Functions.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, pmid = {37297385}, issn = {2304-8158}, support = {2021R1A6A1A03038996//Basic Science Research Program through the National Research Foundation of Korea (NRF) funded by the Ministry of Education/ ; 2020R1A6C101A184//Korea Basic Science Institute (National research Facilities and Equipment Center) grant funded by the Ministry of Education/ ; }, abstract = {Various fields have been identified in the "omics" era, such as genomics, proteomics, transcriptomics, metabolomics, phenomics, and metagenomics. Among these, metagenomics has enabled a significant increase in discoveries related to the microbial world. Newly discovered microbiomes in different ecologies provide meaningful information on the diversity and functions of microorganisms on the Earth. Therefore, the results of metagenomic studies have enabled new microbe-based applications in human health, agriculture, and the food industry, among others. This review summarizes the fundamental procedures on recent advances in bioinformatic tools. It also explores up-to-date applications of metagenomics in human health, food study, plant research, environmental sciences, and other fields. Finally, metagenomics is a powerful tool for studying the microbial world, and it still has numerous applications that are currently hidden and awaiting discovery. Therefore, this review also discusses the future perspectives of metagenomics.}, } @article {pmid37297350, year = {2023}, author = {Liu, L and Narrowe, AB and Firrman, JA and Mahalak, KK and Bobokalonov, JT and Lemons, JMS and Bittinger, K and Daniel, S and Tanes, C and Mattei, L and Friedman, ES and Soares, JW and Kobori, M and Zeng, WB and Tomasula, PM}, title = {Lacticaseibacillus rhamnosus Strain GG (LGG) Regulate Gut Microbial Metabolites, an In Vitro Study Using Three Mature Human Gut Microbial Cultures in a Simulator of Human Intestinal Microbial Ecosystem (SHIME).}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, pmid = {37297350}, issn = {2304-8158}, support = {P30 DK050306/DK/NIDDK NIH HHS/United States ; }, abstract = {In the present research, we investigated changes in the gut metabolome that occurred in response to the administration of the Laticaseibacillus rhamnosus strain GG (LGG). The probiotics were added to the ascending colon region of mature microbial communities established in a human intestinal microbial ecosystem simulator. Shotgun metagenomic sequencing and metabolome analysis suggested that the changes in microbial community composition corresponded with changes to metabolic output, and we can infer linkages between some metabolites and microorganisms. The in vitro method permits a spatially-resolved view of metabolic transformations under human physiological conditions. By this method, we found that tryptophan and tyrosine were mainly produced in the ascending colon region, while their derivatives were detected in the transverse and descending regions, revealing sequential amino acid metabolic pathways along with the colonic tract. The addition of LGG appeared to promote the production of indole propionic acid, which is positively associated with human health. Furthermore, the microbial community responsible for the production of indole propionic acid may be broader than is currently known.}, } @article {pmid37297014, year = {2023}, author = {Golčić, M and Simetić, L and Herceg, D and Blažičević, K and Kenđel Jovanović, G and Dražić, I and Belančić, A and Skočibušić, N and Palčevski, D and Rubinić, I and Vlahović-Palčevski, V and Majnarić, T and Dobrila-Dintinjana, R and Pleština, S}, title = {Analysis of the Gut Microbiome and Dietary Habits in Metastatic Melanoma Patients with a Complete and Sustained Response to Immunotherapy.}, journal = {Cancers}, volume = {15}, number = {11}, pages = {}, pmid = {37297014}, issn = {2072-6694}, support = {n/a (Funding for Shotgun Metagenomics)//Croatian Society for Medical Oncology/ ; }, abstract = {Immunotherapy has improved the prognosis of metastatic melanoma patients, although most patients do not achieve a complete response. While specific gut microbiome and dietary habits might influence treatment success, there is a lack of concordance between the studies, potentially due to dichotomizing patients only into responders and non-responders. The aim of this study was to elucidate whether metastatic melanoma patients with complete and sustained response to immunotherapy exhibit differences in gut microbiome composition among themselves, and whether those differences were associated with specific dietary habits. Shotgun metagenomic sequencing revealed that patients who exhibited a complete response after more than 9 months of treatment (late responders) exhibited a significantly higher beta-diversity (p = 0.02), with a higher abundance of Coprococcus comes (LDA 3.548, p = 0.010), Bifidobacterium pseudocatenulatum (LDA 3.392, p = 0.024), and lower abundance of Prevotellaceae (p = 0.04) compared to early responders. Furthermore, late responders exhibited a different diet profile, with a significantly lower intake of proteins and sweets and a higher intake of flavones (p < 0.05). The research showed that metastatic melanoma patients with a complete and sustained response to immunotherapy were a heterogeneous group. Patients with a late complete response exhibited microbiome and dietary habits which were previously associated with an improved response to immunotherapy.}, } @article {pmid37296048, year = {2023}, author = {Wang, Q and Cui, Y and Indugu, N and Loor, JJ and Jiang, Q and Yu, Z and Baker, L and Pitta, D and Deng, Z and Xu, C}, title = {Integrated meta-omics analyses reveal a role of ruminal microorganisms in ketone body accumulation and ketosis in lactating dairy cows.}, journal = {Journal of dairy science}, volume = {106}, number = {7}, pages = {4906-4917}, doi = {10.3168/jds.2022-22282}, pmid = {37296048}, issn = {1525-3198}, mesh = {Female ; Cattle ; Animals ; Lactation/metabolism ; Propionates/metabolism ; Diet/veterinary ; Milk/metabolism ; *Ketosis/veterinary/metabolism ; Butyrates/metabolism ; 3-Hydroxybutyric Acid ; *Cattle Diseases/metabolism ; }, abstract = {The extent to which a nutrition-related disorder such as ketosis alters the ruminal microbiota or whether microbiota composition is related to ketosis and potential associations with host metabolism is unknown. We aimed to evaluate variations occurring in the ruminal microbiota of ketotic and nonketotic cows in the early postpartum period, and how those changes may affect the risk of developing the disease. Data on milk yield, dry matter intake (DMI), body condition score, and blood β-hydroxybutyrate (BHB) concentrations at 21 d postpartum were used to select 27 cows, which were assigned (n = 9 per group) to a clinical ketotic (CK, 4.10 ± 0.72 mmol BHB/L, DMI 11.61 ± 0.49 kg/d, ruminal pH 7.55 ± 0.07), subclinical ketotic (SK, 1.36 ± 0.12 mmol BHB/L, DMI 15.24 ± 0.34 kg/d, ruminal pH 7.58 ± 0.08), or control (NK, 0.88 ± 0.14 mmol BHB/L, DMI 16.74 ± 0.67/d, ruminal pH 7.61 ± 0.03) group. Cows averaged 3.6 ± 0.5 lactations and a body condition score of 3.11 ± 0.34 at the time of sampling. After blood serum collection for metabolomics analysis ([1]H nuclear magnetic resonance spectra), 150 mL of ruminal digesta was collected from each cow using an esophageal tube, paired-end (2 × 300 bp) sequencing of isolated DNA from ruminal digesta was performed via Illumina MiSeq, and sequencing data were analyzed using QIIME2 (v 2020.6) to measure the ruminal microbiota composition and relative abundance. Spearman correlation coefficients were used to evaluate relationships between relative abundance of bacterial genera and concentrations of serum metabolites. There were more than 200 genera, with approximately 30 being significant between NK and CK cows. Succinivibrionaceae UCG 1 taxa decreased in CK compared with NK cows. Christensenellaceae (Spearman correlation coefficient = 0.6), Ruminococcaceae (Spearman correlation coefficient = 0.6), Lachnospiraceae (Spearman correlation coefficient = 0.5), and Prevotellaceae (Spearman correlation coefficient = 0.6) genera were more abundant in the CK group and were highly positively correlated with plasma BHB. Metagenomic analysis indicated a high abundance of predicted functions related to metabolism (37.7%), genetic information processing (33.4%), and Brite hierarchies (16.3%) in the CK group. The 2 most important metabolic pathways for butyrate and propionate production were enriched in CK cows, suggesting increased production of acetyl coenzyme A and butyrate and decreased production of propionate. Overall, the combined data suggested that microbial populations may be related to ketosis by affecting short-chain fatty acid metabolism and BHB accumulation even in cows with adequate feed intake in the early postpartum period.}, } @article {pmid37295406, year = {2023}, author = {Nguyen, CL and Markey, KA and Miltiadous, O and Dai, A and Waters, N and Sadeghi, K and Fei, T and Shouval, R and Taylor, BP and Liao, C and Slingerland, JB and Slingerland, AE and Clurman, AG and Maloy, MA and Bohannon, L and Giardina, PA and Brereton, DG and Armijo, GK and Fontana, E and Gradissimo, A and Gyurkocza, B and Sung, AD and Chao, NJ and Devlin, SM and Taur, Y and Giralt, SA and Perales, MA and Xavier, JB and Pamer, EG and Peled, JU and Gomes, ALC and van den Brink, MRM}, title = {High-resolution analyses of associations between medications, microbiome, and mortality in cancer patients.}, journal = {Cell}, volume = {186}, number = {12}, pages = {2705-2718.e17}, pmid = {37295406}, issn = {1097-4172}, support = {P01 CA023766/CA/NCI NIH HHS/United States ; R01 CA228308/CA/NCI NIH HHS/United States ; U01 AI124275/AI/NIAID NIH HHS/United States ; R56 AI137269/AI/NIAID NIH HHS/United States ; R01 HL125571/HL/NHLBI NIH HHS/United States ; R01 CA228358/CA/NCI NIH HHS/United States ; R01 HL123340/HL/NHLBI NIH HHS/United States ; R21 AG066388/AG/NIA NIH HHS/United States ; R01 HL151365/HL/NHLBI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; P01 AG052359/AG/NIA NIH HHS/United States ; K08 HL143189/HL/NHLBI NIH HHS/United States ; R01 CA203950/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Metagenome ; *Hematopoietic Stem Cell Transplantation ; Anti-Bacterial Agents ; *Neoplasms/drug therapy ; }, abstract = {Discerning the effect of pharmacological exposures on intestinal bacterial communities in cancer patients is challenging. Here, we deconvoluted the relationship between drug exposures and changes in microbial composition by developing and applying a new computational method, PARADIGM (parameters associated with dynamics of gut microbiota), to a large set of longitudinal fecal microbiome profiles with detailed medication-administration records from patients undergoing allogeneic hematopoietic cell transplantation. We observed that several non-antibiotic drugs, including laxatives, antiemetics, and opioids, are associated with increased Enterococcus relative abundance and decreased alpha diversity. Shotgun metagenomic sequencing further demonstrated subspecies competition, leading to increased dominant-strain genetic convergence during allo-HCT that is significantly associated with antibiotic exposures. We integrated drug-microbiome associations to predict clinical outcomes in two validation cohorts on the basis of drug exposures alone, suggesting that this approach can generate biologically and clinically relevant insights into how pharmacological exposures can perturb or preserve microbiota composition. The application of a computational method called PARADIGM to a large dataset of cancer patients' longitudinal fecal specimens and detailed daily medication records reveals associations between drug exposures and the intestinal microbiota that recapitulate in vitro findings and are also predictive of clinical outcomes.}, } @article {pmid37295348, year = {2023}, author = {Grabner, E and Stare, E and Fanedl, L and Zorec, M and Jones, DS and Johnston, CD and Avguštin, G and Accetto, T}, title = {Expanding the rumen Prevotella collection: The description of Prevotella communis, sp. nov. of ovine origin.}, journal = {Systematic and applied microbiology}, volume = {46}, number = {4}, pages = {126437}, doi = {10.1016/j.syapm.2023.126437}, pmid = {37295348}, issn = {1618-0984}, support = {R01 DE027850/DE/NIDCR NIH HHS/United States ; }, mesh = {Sheep ; Animals ; Cattle ; *Rumen/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Prevotella/genetics ; Polysaccharides/metabolism ; }, abstract = {27 strains representing eight new Prevotella species were isolated from rumen of a single sheep in eight weeks interval. One of the putative species encompassing the highest number of isolated strains which also exhibited some genetic variability in preliminary data, was then selected for description of a novel species. We examined six strains in genomic and phenotypic detail, two of which may actually be the same strain isolated nearly three weeks apart. Other strains formed clearly diverged intraspecies lineages as evidenced by core genome phylogeny and phenotypic differences. Strains of the proposed new Prevotella species are strictly saccharolytic as is usual for rumen Prevotella, and use plant cell-wall xylans and pectins for growth. However, the range of cell-wall polysaccharides utilised for growth is rather limited compared to rumen generalists such as Prevotella bryantii or Prevotella ruminicola and this extends also to the inability to utilise starch, which is unexpected for the members of the genus Prevotella. Based on the data obtained, we propose Prevotella communis sp. nov. to accommodate strain E1-9[T] as well as other strains with the similar properties. The proposed species is widespread: two other strains were previously isolated from sheep in Japan and is also common in metagenomic data of cattle and sheep rumen samples from Scotland and New Zealand. It was also found in a collection of metagenome-assembled genomes originating from cattle in Scotland. Thus, it is a ubiquitous bacterium of domesticated ruminants specialising in degradation of a somewhat restricted set of plant cell wall components.}, } @article {pmid37294294, year = {2023}, author = {Sakamoto, N and Laolerd, W and Akeda, Y and Sugawara, Y and Motooka, D and Yamamoto, N and Takeuchi, D and Shanmugakani, RK and Nishi, I and Suzuki, M and Shibayama, K and Iida, T and Santanirand, P and Tomono, K and Hamada, S}, title = {Temporal shifts in the predominant carbapenemase gene types among carbapenemase-producing Klebsiella pneumoniae isolated in Bangkok, Thailand, during 2013-2016.}, journal = {Journal of medical microbiology}, volume = {72}, number = {6}, pages = {}, doi = {10.1099/jmm.0.001711}, pmid = {37294294}, issn = {1473-5644}, mesh = {Humans ; Klebsiella pneumoniae/genetics ; *Carbapenem-Resistant Enterobacteriaceae/genetics ; Thailand/epidemiology ; Phylogeny ; *Enterobacteriaceae Infections/epidemiology ; beta-Lactamases/genetics ; Bacterial Proteins/genetics ; Microbial Sensitivity Tests ; }, abstract = {Introduction. Carbapenemase-producing Enterobacteriaceae (CPE) have emerged as a global threat to public health and clinical practice.Hypothesis/Gap Statement. In Thailand, reports describing CPEs carrying bla NDM and bla OXA-48-like genes have been increasing recently; however, data on detailed plasmid analysis and temporal shift of sequence type and carbapenemase type are limited.Aim. In this study, we analysed whole-genome sequencing (WGS) data of clinically isolated carbapenemase-producing Klebsiella pneumoniae (CPKP) to reveal the molecular epidemiology of CPKP in a tertiary-care hospital in Bangkok, Thailand.Methodology. Seventy-seven non-duplicated CPKP isolates collected during 2013-2016 were examined for their drug-resistance genes, sequence types and phylogenetic relationships.Results. All the tested isolates possessed carbapenemase gene(s), and the major type of carbapenemase gene in 2014-2015 was bla NDM-1, whereas isolates in 2016 harboured more bla OXA-232 than bla NDM-1. Other carbapenemase gene variants, such as bla NDM-4, bla NDM-5, bla OXA-48, bla OXA-181 and bla IMP-14 were detected in some CPKP isolates. Furthermore, this study revealed that CPKP co-harbouring two genes, bla NDM-1 and bla OXA-232 or bla OXA-181, emerged during this period. Notably, such isolates co-carrying the two carbapenemase genes emerged in three different sequence types, even in a single hospital, and then spread clonally. The WGS of CPKP revealed a temporal shift of the predominant carbapenemase genes from bla NDM-1 to bla OXA-232 along with a variation in other carbapenemase gene types within a span of 4 years.Conclusion. Our findings suggest that a substantial change in CPE types occurred in Thailand and potentially in Southeast Asian countries.}, } @article {pmid37293537, year = {2023}, author = {Gong, F and Chen, Z and Chang, J and Liu, J and Wang, X and Mo, W and Tan, M and Jiang, T}, title = {Metagenomic Next-Generation Sequencing Contributes to the Diagnosis of Pneumonia Caused by Chlamydia abortus in a Male Patient: Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {3463-3468}, pmid = {37293537}, issn = {1178-6973}, abstract = {BACKGROUND: Chlamydia abortus is generally considered as the main cause of ruminants abortion, but it rarely causes human infection resulting in abortion or pneumonia.

CASE PRESENTATION: We report a case of male patient with pneumonia caused by Chlamydia abortus. Results of next generation sequencing (NGS) in the bronchoalveolar lavage fluid (BALF) indicated Chlamydia abortus infection. The patient was treated with intravenous infusion of doxycycline. The clinical symptoms of this patient were ameliorated significantly, and all these improvement were indicated by laboratory parameters significantly. Shown as chest computed tomography (CT), most of the inflammation had been absorbed after doxycycline treatment.

CONCLUSION: Chlamydia abortus mainly infects ruminants and occasionally humans. NGS has its own advantages of rapidity, sensitivity and specificity in detecting Chlamydia abortus. Doxycycline exhibits a great therapeutic effect on pneumonia caused by Chlamydia abortus.}, } @article {pmid37293229, year = {2023}, author = {Pargin, E and Roach, MJ and Skye, A and Papudeshi, B and Inglis, LK and Mallawaarachchi, V and Grigson, SR and Harker, C and Edwards, RA and Giles, SK}, title = {The human gut virome: composition, colonization, interactions, and impacts on human health.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {963173}, pmid = {37293229}, issn = {1664-302X}, abstract = {The gut virome is an incredibly complex part of the gut ecosystem. Gut viruses play a role in many disease states, but it is unknown to what extent the gut virome impacts everyday human health. New experimental and bioinformatic approaches are required to address this knowledge gap. Gut virome colonization begins at birth and is considered unique and stable in adulthood. The stable virome is highly specific to each individual and is modulated by varying factors such as age, diet, disease state, and use of antibiotics. The gut virome primarily comprises bacteriophages, predominantly order Crassvirales, also referred to as crAss-like phages, in industrialized populations and other Caudoviricetes (formerly Caudovirales). The stability of the virome's regular constituents is disrupted by disease. Transferring the fecal microbiome, including its viruses, from a healthy individual can restore the functionality of the gut. It can alleviate symptoms of chronic illnesses such as colitis caused by Clostridiodes difficile. Investigation of the virome is a relatively novel field, with new genetic sequences being published at an increasing rate. A large percentage of unknown sequences, termed 'viral dark matter', is one of the significant challenges facing virologists and bioinformaticians. To address this challenge, strategies include mining publicly available viral datasets, untargeted metagenomic approaches, and utilizing cutting-edge bioinformatic tools to quantify and classify viral species. Here, we review the literature surrounding the gut virome, its establishment, its impact on human health, the methods used to investigate it, and the viral dark matter veiling our understanding of the gut virome.}, } @article {pmid37293091, year = {2023}, author = {Midya, V and Lane, JM and Gennings, C and Torres-Olascoaga, LA and Wright, RO and Arora, M and Téllez-Rojo, MM and Eggers, S}, title = {Prenatal Pb exposure is associated with reduced abundance of beneficial gut microbial cliques in late childhood: an investigation using Microbial Co-occurrence Analysis (MiCA).}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {37293091}, support = {K99 ES032884/ES/NIEHS NIH HHS/United States ; P30 ES023515/ES/NIEHS NIH HHS/United States ; R01 ES013744/ES/NIEHS NIH HHS/United States ; }, abstract = {BACKGROUND: Many analytical methods used in gut microbiome research focus on either single bacterial taxa or the whole microbiome, ignoring multi-bacteria relationships (microbial cliques). We present a novel analytical approach to identify multiple bacterial taxa within the gut microbiome of children at 9-11 years associated with prenatal Pb exposure.

METHODS: Data came from a subset of participants (n=123) in the Programming Research in Obesity, Growth, Environment and Social Stressors (PROGRESS) cohort. Pb concentrations were measured in maternal whole blood from the second and third trimesters of pregnancy. Stool samples collected at 9-11 years old underwent metagenomic sequencing to assess the gut microbiome. Using a novel analytical approach, Microbial Co-occurrence Analysis (MiCA), we paired a machine-learning algorithm with randomization-based inference to first identify microbial cliques that were predictive of prenatal Pb exposure and then estimate the association between prenatal Pb exposure and microbial clique abundance.

RESULTS: With second-trimester Pb exposure, we identified a 2-taxa microbial clique that included Bifidobacterium adolescentis and Ruminococcus callidus, and a 3-taxa clique that added Prevotella clara. Increasing second-trimester Pb exposure was associated with significantly increased odds of having the 2-taxa microbial clique below the 50[th] percentile relative abundance (OR=1.03,95%CI[1.01-1.05]). In an analysis of Pb concentration at or above vs. below the United States and Mexico guidelines for child Pb exposure, odds of the 2-taxa clique in low abundance were 3.36(95%CI[1.32-8.51]) and 6.11(95%CI[1.87-19.93]), respectively. Trends were similar with the 3-taxa clique but not statistically significant.

DISCUSSION: Using a novel combination of machine-learning and causal-inference, MiCA identified a significant association between second-trimester Pb exposure and reduced abundance of a probiotic microbial clique within the gut microbiome in late childhood. Pb exposure levels at the guidelines for child Pb poisoning in the United States, and Mexico are not sufficient to protect against the potential loss of probiotic benefits.}, } @article {pmid37293035, year = {2023}, author = {Veseli, I and Chen, YT and Schechter, MS and Vanni, C and Fogarty, EC and Watson, AR and Jabri, B and Blekhman, R and Willis, AD and Yu, MK and Fernàndez-Guerra, A and Füssel, J and Eren, AM}, title = {Microbes with higher metabolic independence are enriched in human gut microbiomes under stress.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37293035}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; R35 GM128716/GM/NIGMS NIH HHS/United States ; }, abstract = {A wide variety of human diseases are associated with loss of microbial diversity in the human gut, inspiring a great interest in the diagnostic or therapeutic potential of the microbiota. However, the ecological forces that drive diversity reduction in disease states remain unclear, rendering it difficult to ascertain the role of the microbiota in disease emergence or severity. One hypothesis to explain this phenomenon is that microbial diversity is diminished as disease states select for microbial populations that are more fit to survive environmental stress caused by inflammation or other host factors. Here, we tested this hypothesis on a large scale, by developing a software framework to quantify the enrichment of microbial metabolisms in complex metagenomes as a function of microbial diversity. We applied this framework to over 400 gut metagenomes from individuals who are healthy or diagnosed with inflammatory bowel disease (IBD). We found that high metabolic independence (HMI) is a distinguishing characteristic of microbial communities associated with individuals diagnosed with IBD. A classifier we trained using the normalized copy numbers of 33 HMI-associated metabolic modules not only distinguished states of health versus IBD, but also tracked the recovery of the gut microbiome following antibiotic treatment, suggesting that HMI is a hallmark of microbial communities in stressed gut environments.}, } @article {pmid37293019, year = {2023}, author = {Yoo, JS and Goh, B and Heo, K and Jung, DJ and Zheng, W and Lee, CC and Geva-Zatorsky, N and Wu, M and Park, SB and Kasper, DL and Oh, SF}, title = {Functional and metagenomic level diversities of human gut symbiont-derived glycolipids.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.05.23.541633}, pmid = {37293019}, support = {K01 DK102771/DK/NIDDK NIH HHS/United States ; R01 AI165987/AI/NIAID NIH HHS/United States ; R01 AT010268/AT/NCCIH NIH HHS/United States ; }, abstract = {Bioactive metabolites produced by symbiotic microbiota causally impact host health and disease, nonetheless, incomplete functional annotation of genes as well as complexities and dynamic nature of microbiota make understanding species-level contribution in production and actions difficult. Alpha-galactosylceramides produced by Bacteroides fragilis (BfaGC) are one of the first modulators of colonic immune development, but biosynthetic pathways and the significance of the single species in the symbiont community still remained elusive. To address these questions at the microbiota level, we have investigated the lipidomic profiles of prominent gut symbionts and the metagenome-level landscape of responsible gene signatures in the human gut. We first elucidated the chemical diversity of sphingolipid biosynthesis pathways of major bacterial species. In addition to commonly shared ceramide backbone synthases showing two distinct intermediates, alpha-galactosyltransferase (agcT), the necessary and sufficient component for BfaGC production and host colonic type I natural killer T (NKT) cell regulation by B. fragilis, was characterized by forward-genetics based targeted metabolomic screenings. Phylogenetic analysis of agcT in human gut symbionts revealed that only a few ceramide producers have agcT and hence can produce aGCs, on the other hand, structurally conserved homologues of agcT are widely distributed among species lacking ceramides. Among them, alpha-glucosyl-diacylglycerol(aGlcDAG)-producing glycosyltransferases with conserved GT4-GT1 domains are one of the most prominent homologs in gut microbiota, represented by Enterococcus bgsB . Of interest, aGlcDAGs produced by bgsB can antagonize BfaGC-mediated activation of NKT cells, showing the opposite, lipid structure-specific actions to regulate host immune responses. Further metagenomic analysis of multiple human cohorts uncovered that the agcT gene signature is almost exclusively contributed by B. fragilis , regardless of age, geographical and health status, where the bgsB signature is contributed by >100 species, of which abundance of individual microbes is highly variable. Our results collectively showcase the diversities of gut microbiota producing biologically relevant metabolites in multiple layers-biosynthetic pathways, host immunomodulatory functions and microbiome-level landscapes in the host.}, } @article {pmid37292648, year = {2023}, author = {Golob, J and Rao, K and Berinstein, J and Chey, W and Owyang, C and Kamada, N and Higgins, P and Young, V and Bishu, S and Lee, A}, title = {The Fecal Microbiome in Quiescent Crohn's Disease with Persistent Gastrointestinal Symptoms Show Enrichment of Oral Microbes But Depletion of Butyrate and Indole Producers.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.05.16.23290065}, pmid = {37292648}, abstract = {BACKGROUND AND AIMS: Even in the absence of inflammation, persistent symptoms in Crohn's disease (CD) are prevalent and negatively impact quality of life. We aimed to determine whether quiescent CD patients with persistent symptoms (qCD+symptoms) have changes in microbial structure and functional potential compared to those without symptoms (qCD-symptoms).

METHODS: We performed a prospective multi-center observational study nested within the SPARC IBD study. CD patients were included if they had evidence of quiescent disease as defined by fecal calprotectin level < 150 mcg/g. Persistent symptoms were defined by the CD-PRO2 questionnaire. Active CD (aCD), diarrhea-predominant irritable bowel syndrome (IBS-D), and healthy controls (HC) were included as controls. Stool samples underwent whole genome shotgun metagenomic sequencing.

RESULTS: A total of 424 patients were analyzed, including 39 qCD+symptoms, 274 qCD-symptoms, 21 aCD, 40 IBS-D, and 50 HC. Patients with qCD+symptoms had a less diverse microbiome, including significant reductions in Shannon diversity (P <.001) and significant differences in microbial community structure (P <.0001), compared with qCD-symptoms, IBS-D, and HC. Further, patients with qCD+symptoms showed significant enrichment of bacterial species that are normal inhabitants of the oral microbiome, including Klebsiella pneumoniae (q=.003) as well as depletion of important butyrate and indole producers, such as Eubacterium rectale (q=.001), Lachnospiraceae spp . (q<.0001), and Faecalibacterium prausnitzii (q<.0001), compared with qCD-symptoms. Finally, qCD+symptoms showed significant reductions in bacterial tnaA genes, which mediate tryptophan metabolism, as well as significant tnaA allelic variation, compared with qCD-symptoms.

CONCLUSION: The microbiome in patients with qCD+symptoms show significant changes in diversity, community profile, and composition compared with qCD-symptoms. Future studies will focus on the functional significance of these changes.

WHAT YOU NEED TO KNOW: Background: Persistent symptoms in quiescent Crohn's disease (CD) are prevalent and lead to worse outcomes. While changes in the microbial community have been implicated, the mechanisms by which altered microbiota may lead to qCD+symptoms remain unclear.Findings: Quiescent CD patients with persistent symptoms demonstrated significant differences in microbial diversity and composition compared to those without persistent symptoms. Specifically, quiescent CD patients with persistent symptoms were enriched in bacterial species that are normal inhabitants of the oral microbiome but depleted in important butyrate and indole producers compared to those without persistent symptoms.Implications for Patient Care: Alterations in the gut microbiome may be a potential mediator of persistent symptoms in quiescent CD. Future studies will determine whether targeting these microbial changes may improve symptoms in quiescent CD.}, } @article {pmid37292198, year = {2023}, author = {Han, X and He, X and Zhan, X and Yao, L and Sun, Z and Gao, X and Wang, S and Wang, Z}, title = {Disturbed microbiota-metabolites-immune interaction network is associated with olfactory dysfunction in patients with chronic rhinosinusitis.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1159112}, pmid = {37292198}, issn = {1664-3224}, mesh = {Humans ; *Rhinitis/diagnosis ; *Olfaction Disorders/diagnosis/etiology ; Smell ; *Sinusitis/diagnosis ; Chronic Disease ; Inflammation/complications ; *Microbiota ; }, abstract = {PURPOSE: Olfactory dysfunction (OD) is a debilitating symptom frequently reported by patients with chronic rhinosinusitis (CRS) and it is associated with a dysregulated sinonasal inflammation. However, little information is available about the effect of the inflammation-related nasal microbiota and related metabolites on the olfactory function in these patients. Therefore, the current study aimed to investigate the nasal microbiota-metabolites-immune interactions and their role in the pathogenesis of OD in CRS patients.

METHODS: 23 and 19 CRS patients with and without OD, respectively, were enrolled in the present study. The "Sniffin' Sticks" was used to measure the olfactory function, while the metagenomic shotgun sequencing and the untargeted metabolite profiling were performed to assess the differences in terms of the nasal microbiome and metabolome between the two groups. The levels of nasal mucus inflammatory mediators were investigated by a multiplex flow Cytometric Bead Array (CBA).

RESULTS: A decreased diversity in the nasal microbiome from the OD group compared to the NOD group was evidenced. The metagenomic analysis revealed a significant enrichment of Acinetobacter johnsonii in the OD group, while Mycoplasma arginini, Aeromonas dhakensis, and Salmonella enterica were significantly less represented (LDA value > 3, p < 0.05). The nasal metabolome profiles were significantly different between the OD and NOD groups (P < 0.05). The purine metabolism was the most significantly enriched metabolic subpathway in OD patients compared with NOD patients (P < 0.001). The expressions of IL-5, IL-8, MIP-1α, MCP-1, and TNF were statistically and significantly increased in the OD group (P < 0.05). All these data, including the dysregulation of the nasal microbiota, differential metabolites, and elevated inflammatory mediators in OD patients demonstrated a clear interaction relationship.

CONCLUSION: The disturbed nasal microbiota-metabolite-immune interaction networks may be implicated in the pathogenesis of OD in CRS patients and the underlying pathophysiological mechanisms need to be further investigated in future studies.}, } @article {pmid37292141, year = {2023}, author = {Liu, J and Zhou, L and Sun, L and Ye, X and Ma, M and Dou, M and Shi, L}, title = {Association Between Intestinal Prevotella copri Abundance and Glycemic Fluctuation in Patients with Brittle Diabetes.}, journal = {Diabetes, metabolic syndrome and obesity : targets and therapy}, volume = {16}, number = {}, pages = {1613-1621}, pmid = {37292141}, issn = {1178-7007}, abstract = {OBJECTIVE: Previous studies have demonstrated an association between gut microbiota composition and non-brittle type 2 diabetes (NBT2DM) pathogenesis. However, little is known about the correlation between the abundance of intestinal Prevotella copri and glycemic fluctuations in patients with brittle diabetes mellitus (BDM). In this context, we conducted a case-control study of BDM patients and patients with NBT2DM, aiming to determine and analyze the relationship between the abundance of intestinal Prevotella copri and glycemic fluctuations in patients with BDM.

RESEARCH DESIGN AND METHODS: We performed a metagenomic analysis of the gut microbiome obtained from fecal samples of 10 BDM patients, and compared their microbial composition and function to NBT2DM patients (1:1 ratio). Then further collected data including age, sex, BMI, glycated hemoglobin (HbA1c), blood lipids, and alpha diversity of the gut microbiota, which were comparable between the BDM and NBT2DM patients by t-test.

RESULTS: A significant difference existed in the beta diversity of the gut microbiota between the two groups (PCoA, R[2] = 0.254, P = 0.0001). The phylum-level abundance of Bacteroidetes in the gut microbiota of the BDM patients was significantly lower, by 24.9% (P = 0.001), than that of the NBT2DM patients. At the gene level, the abundance of Prevotella copri was obviously reduced, Correlation analysis showed that the Prevotella copri abundance was inversely correlated to the standard deviation of blood glucose (SDBG) (r = -0.477, P = 0.034). Quantitative PCR confirmed that the abundance of Prevotella copri in the BDM patients in the validation cohort was significantly lower than that in NBT2DM patients, and was negatively correlated with SDBG (r = -0.318, P = 0.043). Glycemic variability in BDM was inversely correlated with the abundance of intestinal Prevotella copri.

CONCLUSION: The decreased abundance of Prevotella copri in patients with BDM may be associated with glycemic fluctuation.}, } @article {pmid37292038, year = {2023}, author = {Wu, Y and Li, A and Chen, L and Chen, Q and Li, J and Xu, Y and Huo, D}, title = {Correction: Deep Shotgun metagenomic and 16S rRNA analysis revealed the microbial diversity of lactic acid bacteria in traditional fermented foods of eastern Hainan, China.}, journal = {Food & function}, volume = {14}, number = {12}, pages = {5820}, doi = {10.1039/d3fo90047a}, pmid = {37292038}, issn = {2042-650X}, abstract = {Correction for 'Deep Shotgun metagenomic and 16S rRNA analysis revealed the microbial diversity of lactic acid bacteria in traditional fermented foods of eastern Hainan, China' by Yuqing Wu et al., Food Funct., 2022, 13, 12938-12952, https://doi.org/10.1039/D2FO02501A.}, } @article {pmid37291701, year = {2023}, author = {Suarez, C and Hackl, T and Wilen, BM and Persson, F and Hagelia, P and Jetten, MSM and Dalcin Martins, P}, title = {Novel and unusual genes for nitrogen and metal cycling in Planctomycetota- and KSB1-affiliated metagenome-assembled genomes reconstructed from a marine subsea tunnel.}, journal = {FEMS microbiology letters}, volume = {370}, number = {}, pages = {}, pmid = {37291701}, issn = {1574-6968}, mesh = {*Metagenome ; *Planctomycetes ; Nitrogen ; RNA, Ribosomal, 16S/genetics ; Manganese ; Iron ; Oxidation-Reduction ; }, abstract = {The Oslofjord subsea road tunnel is a unique environment in which the typically anoxic marine deep subsurface is exposed to oxygen. Concrete biodeterioration and steel corrosion in the tunnel have been linked to the growth of iron- and manganese-oxidizing biofilms in areas of saline water seepage. Surprisingly, previous 16S rRNA gene surveys of biofilm samples revealed microbial communities dominated by sequences affiliated with nitrogen-cycling microorganisms. This study aimed to identify microbial genomes with metabolic potential for novel nitrogen- and metal-cycling reactions, representing biofilm microorganisms that could link these cycles and play a role in concrete biodeterioration. We reconstructed 33 abundant, novel metagenome-assembled genomes (MAGs) affiliated with the phylum Planctomycetota and the candidate phylum KSB1. We identified novel and unusual genes and gene clusters in these MAGs related to anaerobic ammonium oxidation, nitrite oxidation, and other nitrogen-cycling reactions. Additionally, 26 of 33 MAGs also had the potential for iron, manganese, and arsenite cycling, suggesting that bacteria represented by these genomes might couple these reactions. Our results expand the diversity of microorganisms putatively involved in nitrogen and metal cycling, and contribute to our understanding of potential biofilm impacts on built infrastructure.}, } @article {pmid37290887, year = {2023}, author = {Yancey, CE and Kiledal, EA and Chaganti, SR and Denef, VJ and Errera, RM and Evans, JT and Hart, LN and Isailovic, D and James, WS and Kharbush, JJ and Kimbrel, JA and Li, W and Mayali, X and Nitschky, H and Polik, CA and Powers, MA and Premathilaka, SH and Rappuhn, NA and Reitz, LA and Rivera, SR and Zwiers, CC and Dick, GJ}, title = {The Western Lake Erie culture collection: A promising resource for evaluating the physiological and genetic diversity of Microcystis and its associated microbiome.}, journal = {Harmful algae}, volume = {126}, number = {}, pages = {102440}, doi = {10.1016/j.hal.2023.102440}, pmid = {37290887}, issn = {1878-1470}, mesh = {Humans ; *Microcystis/genetics ; Lakes/microbiology ; *Cyanobacteria/genetics ; *Microbiota ; Genetic Variation ; }, abstract = {Cyanobacterial harmful algal blooms (cyanoHABs) dominated by Microcystis spp. have significant public health and economic implications in freshwater bodies around the world. These blooms are capable of producing a variety of cyanotoxins, including microcystins, that affect fishing and tourism industries, human and environmental health, and access to drinking water. In this study, we isolated and sequenced the genomes of 21 primarily unialgal Microcystis cultures collected from western Lake Erie between 2017 and 2019. While some cultures isolated in different years have a high degree of genetic similarity (genomic Average Nucleotide Identity >99%), genomic data show that these cultures also represent much of the breadth of known Microcystis diversity in natural populations. Only five isolates contained all the genes required for microcystin biosynthesis while two isolates contained a previously described partial mcy operon. Microcystin production within cultures was also assessed using Enzyme-Linked Immunosorbent Assay (ELISA) and supported genomic results with high concentrations (up to 900 μg L[-1]) in cultures with complete mcy operons and no or low toxin detected otherwise. These xenic cultures also contained a substantial diversity of bacteria associated with Microcystis, which has become increasingly recognized as an essential component of cyanoHAB community dynamics. These results highlight the genomic diversity among Microcystis strains and associated bacteria in Lake Erie, and their potential impacts on bloom development, toxin production, and toxin degradation. This culture collection significantly increases the availability of environmentally relevant Microcystis strains from temperate North America.}, } @article {pmid37290656, year = {2023}, author = {Xu, J and Wang, H and Xu, R and Li, Q and Su, Y and Liu, J and Zhu, W}, title = {The diurnal fluctuation of colonic antibiotic resistome is correlated with nutrient substrates in a pig model.}, journal = {The Science of the total environment}, volume = {891}, number = {}, pages = {164692}, doi = {10.1016/j.scitotenv.2023.164692}, pmid = {37290656}, issn = {1879-1026}, mesh = {Swine ; Animals ; *Anti-Bacterial Agents/analysis ; *Genes, Bacterial ; Ammonia ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; }, abstract = {The increasing prevalence of antimicrobial resistance (AMR) poses a significant threat to public health, and the gut microbiota of livestock (e.g., pigs) are considered a crucial reservoir of antibiotic resistance genes (ARGs), contributing to the long-term persistence of AMR. However, there is still a lack of relevant research on the composition and diurnal fluctuation of ARGs, and their correlation with nutrient substrates in the gut of pigs. To address this knowledge gap, we characterized the antibiotic resistome structure, and circadian oscillations in 45 colonic metagenomically sequenced samples, covering 9-time points within 24 h, from growing pigs. We identified 227 unique types of ARGs, which belonged to 35 drug resistance classes. Tetracycline resistance and antibiotic target protection were the most enriched class and mechanism of drug resistance in colon samples, respectively. The relative abundance of ARGs fluctuated over time within 24 h, with the total abundance peaking at T21 (sampling time at 21:00 p.m.) and the total numbers reaching the peak at T15. A total of 70 core ARGs were identified, which contributed to 99 % of all ARGs. Rhythmicity analysis revealed that 50 out of 227 ARGs and 15 of 49 mobile genetic elements (MGEs) exhibited rhythmic patterns. TetW was the most abundant ARG with circadian rhythm frequently found in Limosilactobacillus reuteri. The concentration of ammonia nitrogen in the colon was significantly correlated with the host genera of rhythmic ARGs. Partial least squares path modeling (PLS-PM) analysis indicated that rhythmic ARGs were significantly correlated with bacterial community, MGEs, and colonic ammonia nitrogen. This study provides new insight into the diurnal fluctuation of ARG profiles in the colon of growing pigs, which was likely driven by the dynamic change of the availability of colonic nutrients substrates.}, } @article {pmid37290480, year = {2023}, author = {Gan, J and Chen, J and Ma, RL and Deng, Y and Ding, XS and Zhu, SY and Sun, AJ}, title = {Metagenomics study on taxonomic and functional change of gut microbiota in patients with obesity with PCOS treated with exenatide combination with metformin or metformin alone.}, journal = {Gynecological endocrinology : the official journal of the International Society of Gynecological Endocrinology}, volume = {39}, number = {1}, pages = {2219342}, doi = {10.1080/09513590.2023.2219342}, pmid = {37290480}, issn = {1473-0766}, mesh = {Female ; Humans ; *Metformin ; *Polycystic Ovary Syndrome/complications/drug therapy/metabolism ; Exenatide/therapeutic use ; *Gastrointestinal Microbiome ; Metagenomics ; Obesity/complications/drug therapy/chemically induced ; }, abstract = {OBJECTIVE: To investigate the effect of exenatide treatment on the composition of intestinal flora and metabolic pathways in patients with obesity with polycystic ovary syndrome.

METHODS: Patients with obesity with polycystic ovary syndrome (PCOS) were distributed to two groups: one received exenatide combined with metformin (COM group, n = 14) and the other used metformin alone (MF group, n = 15). Fresh fecal specimens from the participants, including 29 patients with obesity with PCOS and 6 healthy controls, were collected for metagenomic sequencing. The effect of exenatide combination with metformin or metformin alone on the composition and function of intestinal flora in patients with obesity with PCOS were compared by bioinformatics analysis.

RESULTS: The level of BMI, TT, HbA1c, and HDL-c was significantly improved in both groups. The MF and COM groups were abundant in Firmicutes, Bacteroidetes, Uroviricota, Actinobacteria, and Proteobacteria. Abundance of Bacteroidetes, Proteobacteria, Hungatella, and certain probiotics like Phocaeicola and Anaerobutyricum significantly increased in both groups after treatment. Enriched microbial species in the MF and COM group were different. Clostridium, Fusobacterium, and Oxalobacter were the main bacteria in the post-MF group, while Lactococcus_garvieae, Clostridium_perfringens, and Coprococcus_sp_AF16_5 were the main bacteria in the post-COM group. The post-COM group had more probiotic species including Bifidobacterium, Prevotella, and Anaerobutyricum after treatment.

CONCLUSION: Both exenatide combined with metformin and metformin monotherapy can improve metabolic and endocrine markers, and the diversity and abundance of gut microbiota in patients with obesity with PCOS. The effects of the combination and monotherapy agents on intestinal flora were consistent to some extent but also unique respectively.}, } @article {pmid37290356, year = {2023}, author = {Dang, B and Jia, W and Ma, S and Zhang, X and Huang, Y and Huang, W and Han, D and Zhang, K and Zhao, F and Zhang, Y and Xu, Z}, title = {Characterization of a novel nornicotine-degrading strain Mycolicibacterium sp. SMGY-1XX from a nornicotine-degrading consortium and preliminary elucidation of its biodegradation pathway by multi-omics analysis.}, journal = {Journal of hazardous materials}, volume = {457}, number = {}, pages = {131777}, doi = {10.1016/j.jhazmat.2023.131777}, pmid = {37290356}, issn = {1873-3336}, mesh = {*Nicotine ; Phylogeny ; Multiomics ; Proteomics ; Biodegradation, Environmental ; *Alkaloids/metabolism ; Nicotiana/metabolism ; }, abstract = {Nicotine and nornicotine are all toxic alkaloids involved in the formation of carcinogenic tobacco-specific nitrosamines. Microbes play an important role in removing these toxic alkaloids and their derivatives from tobacco-polluted environments. By now, microbial degradation of nicotine has been well studied. However, limited information is available on the microbial catabolism of nornicotine. In the present study, a nornicotine-degrading consortium was enriched from a river sediment sample and characterized by metagenomic sequencing using a combination of Illumina and Nanopore technologies. The metagenomic sequencing analysis demonstrated that Achromobacter, Azospirillum, Mycolicibacterium, Terrimonas, and Mycobacterium were the dominant genera in the nornicotine-degrading consortium. A total of 7 morphologically distinct bacterial strains were isolated from the nornicotine-degrading consortium. These 7 bacterial strains were characterized by whole genome sequencing and examined for their ability to degrade nornicotine. Based on a combination of 16 S rRNA gene similarity comparisons, 16 S rRNA gene-based phylogenetic analysis, and ANI analysis, the accurate taxonomies of these 7 isolated strains were identified. These 7 strains were identified as Mycolicibacterium sp. strain SMGY-1XX, Shinella yambaruensis strain SMGY-2XX, Sphingobacterium soli strain SMGY-3XX, Runella sp. strain SMGY-4XX, Chitinophagaceae sp. strain SMGY-5XX, Terrimonas sp. strain SMGY-6XX, Achromobacter sp. strain SMGY-8XX. Among these 7 strains, Mycolicibacterium sp. strain SMGY-1XX, which has not been reported previously to have the ability to degrade nornicotine or nicotine, was found to be capable of degrading nornicotine, nicotine as well as myosmine. The degradation intermediates of nornicotine and myosmine by Mycolicibacterium sp. strain SMGY-1XX were determined and the nornicotine degradation pathway in strain SMGY-1XX was proposed. Three novel intermediates, myosmine, pseudooxy-nornicotine, and γ-aminobutyrate, were identified during the nornicotine degradation process. Further, the most likely candidate genes responsible for nornicotine degradation in Mycolicibacterium sp. strain SMGY-1XX were identified by integrating genomic analysis, transcriptomic analysis, and proteomic analysis. The findings in this study will help to expand our understanding on the microbial catabolism of nornicotine and nicotine and provide new insights into the nornicotine degradation mechanism by consortia and pure culture, laying a foundation for the application of strain SMGY-1XX for the removal, biotransformation, or detoxification of nornicotine.}, } @article {pmid37290355, year = {2023}, author = {Kim, JJ and Seong, HJ and Johnson, TA and Cha, CJ and Sul, WJ and Chae, JC}, title = {Persistence of antibiotic resistance from animal agricultural effluents to surface water revealed by genome-centric metagenomics.}, journal = {Journal of hazardous materials}, volume = {457}, number = {}, pages = {131761}, doi = {10.1016/j.jhazmat.2023.131761}, pmid = {37290355}, issn = {1873-3336}, mesh = {Animals ; *Wastewater ; *Metagenomics/methods ; Water ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Rivers/microbiology ; }, abstract = {Concerns about antibiotic resistance genes (ARGs) released from wastewaters of livestock or fish farming into the natural environment are increasing, but studies on unculturable bacteria related to the dissemination of antibiotic resistance are limited. Here, we reconstructed 1100 metagenome-assembled genomes (MAGs) to assess the impact of microbial antibiotic resistome and mobilome in wastewaters discharged to Korean rivers. Our results indicate that ARGs harbored in the MAGs were disseminated from wastewater effluents into downstream rivers. Moreover, it was found that ARGs are more commonly co-localized with mobile genetic elements (MGEs) in agricultural wastewater than in river water. Among the effluent-derived phyla, uncultured members of the superphylum Patescibacteria possessed a high number of MGEs, along with co-localized ARGs. Our findings suggest that members of the Patesibacteria are a potential vector for propagating ARGs into the environmental community. Therefore, we propose that the dissemination of ARGs by uncultured bacteria should be further investigated in multiple environments.}, } @article {pmid37290262, year = {2023}, author = {Mokhtari, P and Jambal, P and Metos, JM and Shankar, K and Anandh Babu, PV}, title = {Microbial taxonomic and functional shifts in adolescents with type 1 diabetes are associated with clinical and dietary factors.}, journal = {EBioMedicine}, volume = {93}, number = {}, pages = {104641}, pmid = {37290262}, issn = {2352-3964}, support = {R01 AT010247/AT/NCCIH NIH HHS/United States ; }, mesh = {Humans ; Adolescent ; *Diabetes Mellitus, Type 1 ; Feces/microbiology ; *Microbiota ; Bacteria ; Vitamins/metabolism ; Amino Acids/metabolism ; }, abstract = {BACKGROUND: Evidence indicates a link between the pathogenesis of type 1 diabetes (T1D) and the gut microbiome. However, the regulation of microbial metabolic pathways and the associations of bacterial species with dietary factors in T1D are largely unknown. We investigated whether microbial metagenomic signatures in adolescents with T1D are associated with clinical/dietary factors.

METHODS: Adolescents with T1D (case) and healthy adolescents (control) were recruited, and microbiome profiling in participants' stool samples was performed using shotgun metagenomic sequencing. The bioBakery3 pipeline (Kneaddata, Metaphlan 4 and HUMAnN) was used to assign taxonomy and functional annotations. Clinical (HbA1c) and dietary information (3-day food record) were collected for conducting association analysis using Spearman's correlation.

FINDINGS: Adolescents with T1D exhibited modest changes in taxonomic composition of gut microbiome. Nineteen microbial metabolic pathways were altered in T1D, including downregulation of biosynthesis of vitamins (B2/flavin, B7/biotin and B9/folate), enzyme cofactors (NAD[+] and s-adenosyl methionine) and amino acids (aspartate, asparagine and lysine) with an upregulation in the fermentation pathways. Furthermore, bacterial species associated with dietary and clinical factors differed between healthy adolescents and adolescents with T1D. Supervised models modeling identified taxa predictive of T1D status, and the top features included Coprococcus and Streptococcus.

INTERPRETATION: Our study provides new insight into the alteration of microbial and metabolic signatures in adolescents with T1D, suggesting that microbial biosynthesis of vitamins, enzyme cofactors and amino acids may be potentially altered in T1D.

FUNDING: Research grants from NIH/NCCIH: R01AT010247 and USDA/NIFA: 2019-67017-29253; and Larry & Gail Miller Family Foundation Assistantship.}, } @article {pmid37290195, year = {2023}, author = {Li, W and Zhu, L and Wu, B and Liu, Y and Li, J and Xu, L and Huangfu, X and Shi, D and Gu, L and Chen, C}, title = {Improving mesophilic anaerobic digestion of food waste by side-stream thermophilic reactor: Activation of methanogenic, key enzymes and metabolism.}, journal = {Water research}, volume = {241}, number = {}, pages = {120167}, doi = {10.1016/j.watres.2023.120167}, pmid = {37290195}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Food ; Rivers ; *Refuse Disposal ; Bioreactors ; Methane ; }, abstract = {Anaerobic digestion (AD) is a favorable way to convert organic pollutants, such as food waste (FW), into clean energy through microbial action. This work adopted a side-stream thermophilic anaerobic digestion (STA) strategy to improve a digestive system's efficiency and stability. Results showed that the STA strategy brought higher methane production as well as higher system stability. It quickly adapted to thermal stimulation and increased the specific methane production from 359 mL CH4/g·VS to 439 mL CH4/g·VS, which was also higher than 317 mL CH4/g·VS from single-stage thermophilic anaerobic digestion. Further exploration of the mechanism of STA using metagenomic and metaproteomic analysis revealed enhanced activity of key enzymes. The main metabolic pathway was up-regulated, while the dominant bacteria were concentrated, and the multifunctional Methanosarcina was enriched. These results indicate that STA optimized organic metabolism patterns, comprehensively promoted methane production pathways, and formed various energy conservation mechanisms. Further, the system's limited heating avoided adverse effects from thermal stimulation, and activated enzyme activity and heat shock proteins through circulating slurries, which improved the metabolic process, showing great application potential.}, } @article {pmid37289931, year = {2023}, author = {Yuan, L and Zhu, Q and Chen, Q and Lai, LM and Liu, P and Liu, Y}, title = {The microbiological diagnostic performance of metagenomic next-generation sequencing in patients with infectious diseases.}, journal = {Laboratory medicine}, volume = {}, number = {}, pages = {}, doi = {10.1093/labmed/lmad046}, pmid = {37289931}, issn = {1943-7730}, support = {GJJ190055//Jiangxi Provincial Department of Education/ ; 2021B723//Jiangxi Traditional Chinese Medicine/ ; }, abstract = {OBJECTIVE: Metagenomic next-generation sequencing (mNGS) can be used to detect pathogens in clinical infectious diseases through the sequencing analysis of microbial and host nucleic acids in clinical samples. This study aimed to assess the diagnostic performance of mNGS in patients with infections.

METHODS: In this study, 641 patients with infectious diseases were enrolled. These patients simultaneously underwent pathogen detection by both mNGS and microbial culture. Through statistical analysis, we judged the diagnostic performance of mNGS and microbial culture on different pathogens.

RESULTS: Among 641 patients, 276 cases of bacteria and 95 cases of fungi were detected by mNGS, whereas 108 cases of bacteria and 41 cases of fungi were detected by traditional cultures. Among all mixed infections, combined bacterial and viral infections were the highest (51%, 87/169), followed by combined bacterial with fungal infections (16.57%, 28/169) and mixed bacterial, fungal, and viral infections (13.61%, 23/169). Among all sample types, bronchoalveolar lavage fluid (BALF) samples had the highest positive rate (87.8%, 144/164), followed by sputum (85.4%, 76/89) and blood samples (61.2%, 158/258). For the culture method, sputum samples had the highest positive rate (47.2%, 42/89), followed by BALF (37.2%, 61/164). The positive rate of mNGS was 69.89% (448/641), which was significantly higher than that of traditional cultures (22.31% [143/641]) (P < .05).

CONCLUSIONS: Our results show that mNGS is an effective tool for the rapid diagnosis of infectious diseases. Compared with traditional detection methods, mNGS also showed obvious advantages in mixed infections and infections with uncommon pathogens.}, } @article {pmid37289817, year = {2023}, author = {Li, YL and Gao, L and Yao, YS and Li, XZ and Wu, ZM and Tan, NZ and Luo, ZQ and Xie, WD and Wu, JY and Zhu, JS}, title = {Altered GC- and AT-biased genotypes of Ophiocordyceps sinensis in the stromal fertile portions and ascospores of natural Cordyceps sinensis.}, journal = {PloS one}, volume = {18}, number = {6}, pages = {e0286865}, pmid = {37289817}, issn = {1932-6203}, mesh = {*Cordyceps/genetics ; Polymorphism, Single Nucleotide ; Mass Spectrometry ; Spores, Fungal/genetics ; Genotype ; }, abstract = {OBJECTIVE: To examine multiple genotypes of Ophiocordyceps sinensis in a semi-quantitative manner in the stromal fertile portion (SFP) densely covered with numerous ascocarps and ascospores of natural Cordyceps sinensis and to outline the dynamic alterations of the coexisting O. sinensis genotypes in different developmental phases.

METHODS: Mature Cordyceps sinensis specimens were harvested and continuously cultivated in our laboratory (altitude 2,254 m). The SFPs (with ascocarps) and fully and semi-ejected ascospores were collected for histological and molecular examinations. Biochip-based single nucleotide polymorphism (SNP) MALDI-TOF mass spectrometry (MS) was used to genotype multiple O. sinensis mutants in the SFPs and ascospores.

RESULTS: Microscopic analysis revealed distinct morphologies of the SFPs (with ascocarps) before and after ascospore ejection and SFP of developmental failure, which, along with the fully and semi-ejected ascospores, were subjected to SNP MS genotyping analysis. Mass spectra showed the coexistence of GC- and AT-biased genotypes of O. sinensis that were genetically and phylogenetically distinct in the SFPs before and after ejection and of developmental failure and in fully and semi-ejected ascospores. The intensity ratios of MS peaks were dynamically altered in the SFPs and the fully and semi-ejected ascospores. Mass spectra also showed transversion mutation alleles of unknown upstream and downstream sequences with altered intensities in the SFPs and ascospores. Genotype #5 of AT-biased Cluster-A maintained a high intensity in all SFPs and ascospores. An MS peak with a high intensity containing AT-biased Genotypes #6 and #15 in pre-ejection SFPs was significantly attenuated after ascospore ejection. The abundance of Genotypes #5‒6 and #16 of AT-biased Cluster-A was differentially altered in the fully and semi-ejected ascospores that were collected from the same Cordyceps sinensis specimens.

CONCLUSION: Multiple O. sinensis genotypes coexisted in different combinations with altered abundances in the SFPs prior to and after ejection, the SFP of developmental failure, and the two types of ascospores of Cordyceps sinensis, demonstrating their genomic independence. Metagenomic fungal members present in different combinations and with dynamic alterations play symbiotic roles in different compartments of natural Cordyceps sinensis.}, } @article {pmid37289241, year = {2023}, author = {Poladyan, A and Trchounian, K and Paloyan, A and Minasyan, E and Aghekyan, H and Iskandaryan, M and Khoyetsyan, L and Aghayan, S and Tsaturyan, A and Antranikian, G}, title = {Valorization of whey-based side streams for microbial biomass, molecular hydrogen, and hydrogenase production.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {14}, pages = {4683-4696}, pmid = {37289241}, issn = {1432-0614}, support = {ADVANCE program//Foundation of Armenian Science and Technology (FAST)/ ; 21AG-1F043//Ministry of Education and Science/ ; }, mesh = {Whey/metabolism ; Escherichia coli/metabolism ; *Hydrogenase/genetics/metabolism ; Biomass ; *Cupriavidus necator ; Whey Proteins/metabolism ; Hydrogen/metabolism ; *Cellulases/metabolism ; }, abstract = {Side streams of the dairy industry are a suitable nutrient source for cultivating microorganisms, producing enzymes, and high-value chemical compounds. The heterotrophic Escherichia coli and chemolithoautotroph Ralstonia eutropha are of major biotechnological interest. R. eutropha is a model organism for producing O2-tolerant [NiFe]-hydrogenases (Hyds) (biocatalysts), and E. coli has found widespread use as an expression platform for producing recombinant proteins, molecular hydrogen (H2), and other valuable products. Aiming at developing suitable cultivation media from side streams of the dairy industry, the pre-treatment (filtration, dilution, and pH adjustment) of cheese (sweet) whey (SW) and curd (acid) whey (AW), with and without the use of ß-glucosidase, has been performed. Growth parameters (oxidation-reduction potential (ORP), pH changes, specific growth rate, biomass formation) of E. coli BW25113 and R. eutropha H16 type strains were monitored during cultivation on filtered and non-filtered SW and AW at 37 °C, pH 7.5 and 30 °C, pH 7.0, respectively. Along with microbial growth, measurements of pH and ORP indicated good fermentative growth. Compared to growth on fructose-nitrogen minimal salt medium (control), a maximum cell yield (OD600 4.0) and H2-oxidizing Hyd activity were achieved in the stationary growth phase for R. eutropha. Hyd-3-dependent H2 production by E. coli utilizing whey as a growth substrate was demonstrated. Moreover, good biomass production and prolonged H2 yields of ~ 5 mmol/L and cumulative H2 ~ 94 mL g/L dry whey (DW) (ß-glucosidase-treated) were observed during the cultivation of the engineered E. coli strain. These results open new avenues for effective whey treatment using thermostable β-glucosidase and confirm whey as an economically viable commodity for biomass and biocatalyst production. KEY POINTS: • Archaeal thermostable β-glucosidase isolated from the metagenome of a hydrothermal spring was used for lactose hydrolysis in whey. • Hydrogenase enzyme activity was induced during the growth of Ralstonia eutropha H16 on whey. • Enhanced biomass and H2 production was shown in a genetically modified strain of Escherichia coli.}, } @article {pmid37288587, year = {2023}, author = {Noh, CK and Jung, W and Yang, MJ and Kim, WH and Hwang, JC}, title = {Alteration of the fecal microbiome in patients with cholecystectomy: potential relationship with postcholecystectomy diarrhea - before and after study.}, journal = {International journal of surgery (London, England)}, volume = {109}, number = {9}, pages = {2585-2597}, pmid = {37288587}, issn = {1743-9159}, mesh = {Humans ; *Gallstones ; *Microbiota ; Feces ; Diarrhea/etiology ; Cholecystectomy/adverse effects ; }, abstract = {BACKGROUND: Bile acid (BA) is a crucial determinant of the gut microbiome, and cholecystectomy can alter the physiology of BA. Physiological changes in BA resulting from cholecystectomy can also influence the gut microbiome. We aimed to identify the specific taxa associated with perioperative symptoms, including postcholecystectomy diarrhea (PCD), and to evaluate the effect of cholecystectomy on the microbiome by investigating the fecal microbiome of patients with gallstones.

METHODS: We analyzed the fecal samples of 39 patients with gallstones (GS group) and 26 healthy controls (HC group) to evaluate their gut microbiome. We also collected fecal samples from GS group 3 months postcholecystectomy. Symptoms of patients were evaluated before and after cholecystectomy. Further, 16S ribosomal RNA amplification and sequencing were performed to determine the metagenomic profile of fecal samples.

RESULTS: The microbiome composition of GS differed from that of HC; however, the alpha diversity was not different. No significant microbiome alterations were observed before and after cholecystectomy. Moreover, GS group showed a significantly lower Firmicutes to Bacteroidetes ratio before and after cholecystectomy than the HC group (6.2, P< 0.05). The inter-microbiome relationship was lower in GS than in HC and tended to recover 3 months after surgery. Furthermore, ~28.1% (n =9) of patients developed PCD after surgery. The most prominent species among PCD (+) patients was Phocaeicola vulgatus. Compared with the preoperative state, Sutterellaceae , Phocaeicola , and Bacteroidals were the most dominant taxa among PCD (+) patients.

CONCLUSION: GS group showed a different microbiome from that of HC; however, their microbiomes were not different 3 months after cholecystectomy. Our data revealed taxa-associated PCD, highlighting the possibility of symptom relief by restoring the gut microbiome.}, } @article {pmid37288562, year = {2023}, author = {Zhu, R and Hong, X and Zhang, D and Xiao, Y and Xu, Q and Wu, B and Guo, J and Han, X and Yang, Q and Zhao, Y and Wu, W}, title = {Application of metagenomic sequencing of drainage fluid in rapid and accurate diagnosis of postoperative intra-abdominal infection: a diagnostic study.}, journal = {International journal of surgery (London, England)}, volume = {109}, number = {9}, pages = {2624-2630}, pmid = {37288562}, issn = {1743-9159}, mesh = {Humans ; *Intraabdominal Infections/diagnosis ; *Abdominal Cavity ; Drainage ; Postoperative Complications/diagnosis ; Elective Surgical Procedures ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Postoperative intra-abdominal infection (PIAI) is one of the most serious complications of abdominal surgery, increasing the risk of postoperative morbidity and mortality and prolonging hospital stay. Rapid diagnosis of PIAI is of great clinical value. Unfortunately, the current diagnostic methods of PIAI are not fast and accurate enough.

METHODS: The authors performed an exploratory study to establish a rapid and accurate diagnostic method of PIAI. The authors explored the turnaround time and accuracy of metagenomic next-generation sequencing (mNGS) in diagnosing PIAI. Patients who underwent elective abdominal surgery and routine abdominal drainage with suspected PIAI were enroled in the study. The fresh midstream abdominal drainage fluid was collected for mNGS and culturing.

RESULTS: The authors found that the median sample-to-answer turnaround time of mNGS was dramatically decreased than that of culture-based methods (<24 h vs. 59.5-111 h). The detection coverage of mNGS was much broader than culture-based methods. The authors found 26 species from 15 genera could only be detected by mNGS. The accuracy of mNGS was not inferior to culture-based methods in the 8 most common pathogens detected from abdominal drainage fluid (sensitivity ranged from 75 to 100%, specificity ranged from 83.3 to 100%, and kappa values were higher than 0.5). Moreover, the composition of the microbial spectrum established by mNGS varied between upper and lower gastrointestinal surgery, enhancing the understanding of PIAI pathogenesis.

CONCLUSION: This study preliminarily revealed the clinical value of mNGS in the rapid diagnosis of PIAI and provided a rationale for further research.}, } @article {pmid37288545, year = {2023}, author = {Lu, F and Lei, T and Zhou, J and Liang, H and Cui, P and Zuo, T and Ye, L and Chen, H and Huang, J}, title = {Using gut microbiota as a diagnostic tool for colorectal cancer: machine learning techniques reveal promising results.}, journal = {Journal of medical microbiology}, volume = {72}, number = {6}, pages = {}, doi = {10.1099/jmm.0.001699}, pmid = {37288545}, issn = {1473-5644}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/diagnosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Bayes Theorem ; Feces/microbiology ; Escherichia coli/genetics ; Machine Learning ; Prevotella/genetics ; }, abstract = {Introduction. Increasing evidence suggests a correlation between gut microbiota and colorectal cancer (CRC).Hypothesis/Gap Statement. However, few studies have used gut microbiota as a diagnostic biomarker for CRC.Aim. The objective of this study was to explore whether a machine learning (ML) model based on gut microbiota could be used to diagnose CRC and identify key biomarkers in the model.Methodology. We sequenced the 16S rRNA gene from faecal samples of 38 participants, including 17 healthy subjects and 21 CRC patients. Eight supervised ML algorithms were used to diagnose CRC based on faecal microbiota operational taxonomic units (OTUs), and the models were evaluated in terms of identification, calibration and clinical practicality for optimal modelling parameters. Finally, the key gut microbiota was identified using the random forest (RF) algorithm.Results. We found that CRC was associated with the dysregulation of gut microbiota. Through a comprehensive evaluation of supervised ML algorithms, we found that different algorithms had significantly different prediction performance using faecal microbiomes. Different data screening methods played an important role in optimization of the prediction models. We found that naïve Bayes algorithms [NB, accuracy=0.917, area under the curve (AUC)=0.926], RF (accuracy=0.750, AUC=0.926) and logistic regression (LR, accuracy=0.750, AUC=0.889) had high predictive potential for CRC. Furthermore, important features in the model, namely s__metagenome_g__Lachnospiraceae_ND3007_group (AUC=0.814), s__Escherichia_coli_g__Escherichia-Shigella (AUC=0.784) and s__unclassified_g__Prevotella (AUC=0.750), could each be used as diagnostic biomarkers of CRC.Conclusions. Our results suggested an association between gut microbiota dysregulation and CRC, and demonstrated the feasibility of the gut microbiota to diagnose cancer. The bacteria s__metagenome_g__Lachnospiraceae_ND3007_group, s__Escherichia_coli_g__Escherichia-Shigella and s__unclassified_g__Prevotella were key biomarkers for CRC.}, } @article {pmid37288274, year = {2023}, author = {Yi, SW and Lee, HG and Kim, E and Jung, YH and Bok, EY and Cho, A and Do, YJ and Hur, TY and Oh, SI}, title = {Raw potato starch diet supplement in weaned pigs could reduce Salmonella Typhimurium infection by altering microbiome composition and improving immune status.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1183400}, pmid = {37288274}, issn = {2297-1769}, abstract = {BACKGORUND: Salmonella enterica serovar Typhimurium (ST) is one of the causative agents of gastroenteritis in pigs. Pigs fed a diet supplemented with raw potato starch (RPS) have improved gut health by the alteration of the microbiota composition and production of short-chain fatty acids (SCFAs). This study aimed to evaluate the effects of RPS supplementation in reducing infection severity and fecal shedding in ST-infected pigs.

METHODS: The weaned experimental pigs were divided into two groups: CON (n = 6) fed a corn/soybean-based diet and TRT (n = 6) supplemented with 5% RPS. After 21 d, the pigs were inoculated with ST, and their body weight, clinical signs, and fecal shedding of ST were monitored for 14 d. At 14 d post-inoculation (dpi), the jejunum, cecum, ileum, and colon tissues were collected from euthanized pigs, and histopathological lesions and cytokine gene expression were compared. Additionally, blood samples at 2 dpi were analyzed for gene ontology enrichment. Moreover, the gutmicrobiome was analyzed using 16S rRNA metagenomic sequencing, and the SCFA concentration was measured using gas chromatography.

RESULTS: The average daily weight gain was significantly higher in TRT than in CON during the ST infection period; however, histopathological lesion scores were significantly lower in TRT than in CON. The relative abundance of nine genera of butyrate- and acetate-producing bacteria significantly increased in TRT compared with that of only two acetate-producing bacteria in CON. Among the genes involved in the immune response, IL-18 expression level was significantly lower in the jejunum and colon in TRT than in CON. Furthermore, Reg3γ expression was significantly different in the cecum and colon of both groups.

CONCLUSION: The diet supplemented with RPS in weaned pigs could result in predominance of butyrate- and acetate-producing bacteria, reducing the severity of ST infection by improving the immune status.}, } @article {pmid37286740, year = {2023}, author = {Wirth, R and Bagi, Z and Shetty, P and Szuhaj, M and Cheung, TTS and Kovács, KL and Maróti, G}, title = {Inter-kingdom interactions and stability of methanogens revealed by machine-learning guided multi-omics analysis of industrial-scale biogas plants.}, journal = {The ISME journal}, volume = {17}, number = {8}, pages = {1326-1339}, pmid = {37286740}, issn = {1751-7370}, mesh = {*Biofuels/microbiology ; Bioreactors/microbiology ; Multiomics ; Archaea ; *Euryarchaeota ; Bacteria ; Anaerobiosis ; }, abstract = {Multi-omics analysis is a powerful tool for the detection and study of inter-kingdom interactions, such as those between bacterial and archaeal members of complex biogas-producing microbial communities. In the present study, the microbiomes of three industrial-scale biogas digesters, each fed with different substrates, were analysed using a machine-learning guided genome-centric metagenomics framework complemented with metatranscriptome data. This data permitted us to elucidate the relationship between abundant core methanogenic communities and their syntrophic bacterial partners. In total, we detected 297 high-quality, non-redundant metagenome-assembled genomes (nrMAGs). Moreover, the assembled 16 S rRNA gene profiles of these nrMAGs showed that the phylum Firmicutes possessed the highest copy number, while the representatives of the archaeal domain had the lowest. Further investigation of the three anaerobic microbial communities showed characteristic alterations over time but remained specific to each industrial-scale biogas plant. The relative abundance of various microorganisms as revealed by metagenome data was independent from corresponding metatranscriptome activity data. Archaea showed considerably higher activity than was expected from their abundance. We detected 51 nrMAGs that were present in all three biogas plant microbiomes with different abundances. The core microbiome correlated with the main chemical fermentation parameters, and no individual parameter emerged as a predominant shaper of community composition. Various interspecies H2/electron transfer mechanisms were assigned to hydrogenotrophic methanogens in the biogas plants that ran on agricultural biomass and wastewater. Analysis of metatranscriptome data revealed that methanogenesis pathways were the most active of all main metabolic pathways.}, } @article {pmid37286586, year = {2023}, author = {Leung, H and Xiong, L and Ni, Y and Busch, A and Bauer, M and Press, AT and Panagiotou, G}, title = {Impaired flux of bile acids from the liver to the gut reveals microbiome-immune interactions associated with liver damage.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {35}, pmid = {37286586}, issn = {2055-5008}, mesh = {Mice ; Animals ; Bile Acids and Salts ; Ecosystem ; *Cholestasis/complications/pathology ; *Liver Diseases/complications ; Cytokines ; *Gastrointestinal Microbiome ; }, abstract = {Currently, there is evidence that alteration in the gut ecosystem contributes to the development of liver diseases, however, the complex mechanisms involved are still unclear. We induced cholestasis in mice by bile duct ligation (BDL), mirroring the phenotype of a bile duct obstruction, to understand how gut microbiota alterations caused by an impaired flow of bile acid to the gut contribute to the pathogenesis and progression of liver disease. We performed longitudinal stool, heart, and liver sampling using mice receiving BDL and controls receiving sham operation (ShamOP). Shotgun metagenomics profiling using fecal samples taken before and on day 1, day 3, and day 7 after surgery was performed, and the cytokines and clinical chemistry profiles from heart blood, as well as the liver bile acids profile, were measured. The BDL surgery reshaped the microbiome of mice, resulting in highly distinct characteristics compared to the ShamOP. Our analysis of the microbiome pathways and ECs revealed that BDL reduces the production of hepatoprotective compounds in the gut, such as biotin, spermidine, arginine, and ornithine, which were negatively associated with inflammatory cytokines (IL-6, IL-23, MCP-1). The reduction of the functional potential of the gut microbiota in producing those hepatoprotective compounds is associated with the decrease of beneficial bacteria species from Anaerotruncus, Blautia, Eubacterium, and Lachnoclostridium genera, as well as the increase of disease-associated bacteria e.g., Escherichia coli and Entercoccus faecalis. Our findings advances our knowledge of the gut microbiome-bile acids-liver triangle, which may serve as a potential therapeutic strategy for liver diseases.}, } @article {pmid37286305, year = {2023}, author = {Lo Russo, G and Prelaj, A and Dolezal, J and Beninato, T and Agnelli, L and Triulzi, T and Fabbri, A and Lorenzini, D and Ferrara, R and Brambilla, M and Occhipinti, M and Mazzeo, L and Provenzano, L and Spagnoletti, A and Viscardi, G and Sgambelluri, F and Brich, S and Miskovic, V and Pedrocchi, ALG and Trovo', F and Manglaviti, S and Giani, C and Ambrosini, P and Leporati, R and Franza, A and McCulloch, J and Torelli, T and Anichini, A and Mortarini, R and Trinchieri, G and Pruneri, G and Torri, V and De Braud, F and Proto, C and Ganzinelli, M and Garassino, MC}, title = {PEOPLE (NTC03447678), a phase II trial to test pembrolizumab as first-line treatment in patients with advanced NSCLC with PD-L1 <50%: a multiomics analysis.}, journal = {Journal for immunotherapy of cancer}, volume = {11}, number = {6}, pages = {}, pmid = {37286305}, issn = {2051-1426}, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/drug therapy/genetics ; *Lung Neoplasms/drug therapy/genetics/metabolism ; B7-H1 Antigen/metabolism ; Multiomics ; Prospective Studies ; Biomarkers ; }, abstract = {BACKGROUND: Chemoimmunotherapy represents the standard of care for patients with advanced non-small cell lung cancer (NSCLC) and programmed death-ligand 1 (PD-L1) <50%. Although single-agent pembrolizumab has also demonstrated some activity in this setting, no reliable biomarkers yet exist for selecting patients likely to respond to single-agent immunotherapy. The main purpose of the study was to identify potential new biomarkers associated with progression-free-survival (PFS) within a multiomics analysis.

METHODS: PEOPLE (NTC03447678) was a prospective phase II trial evaluating first-line pembrolizumab in patients with advanced EGFR and ALK wild type treatment-naïve NSCLC with PD-L1 <50%. Circulating immune profiling was performed by determination of absolute cell counts with multiparametric flow cytometry on freshly isolated whole blood samples at baseline and at first radiological evaluation. Gene expression profiling was performed using nCounter PanCancer IO 360 Panel (NanoString) on baseline tissue. Gut bacterial taxonomic abundance was obtained by shotgun metagenomic sequencing of stool samples at baseline. Omics data were analyzed with sequential univariate Cox proportional hazards regression predicting PFS, with Benjamini-Hochberg multiple comparisons correction. Biological features significant with univariate analysis were analyzed with multivariate least absolute shrinkage and selection operator (LASSO).

RESULTS: From May 2018 to October 2020, 65 patients were enrolled. Median follow-up and PFS were 26.4 and 2.9 months, respectively. LASSO integration analysis, with an optimal lambda of 0.28, showed that peripheral blood natural killer cells/CD56dimCD16+ (HR 0.56, 0.41-0.76, p=0.006) abundance at baseline and non-classical CD14dimCD16+monocytes (HR 0.52, 0.36-0.75, p=0.004), eosinophils (CD15+CD16-) (HR 0.62, 0.44-0.89, p=0.03) and lymphocytes (HR 0.32, 0.19-0.56, p=0.001) after first radiologic evaluation correlated with favorable PFS as well as high baseline expression levels of CD244 (HR 0.74, 0.62-0.87, p=0.05) protein tyrosine phosphatase receptor type C (HR 0.55, 0.38-0.81, p=0.098) and killer cell lectin like receptor B1 (HR 0.76, 0.66-0.89, p=0.05). Interferon-responsive factor 9 and cartilage oligomeric matrix protein genes correlated with unfavorable PFS (HR 3.03, 1.52-6.02, p 0.08 and HR 1.22, 1.08-1.37, p=0.06, corrected). No microbiome features were selected.

CONCLUSIONS: This multiomics approach was able to identify immune cell subsets and expression levels of genes associated to PFS in patients with PD-L1 <50% NSCLC treated with first-line pembrolizumab. These preliminary data will be confirmed in the larger multicentric international I3LUNG trial (NCT05537922).

TRIAL REGISTRATION NUMBER: 2017-002841-31.}, } @article {pmid37285993, year = {2023}, author = {Wu, F and Ding, X and Zhang, Y and Gu, JD and Liu, X and Guo, Q and Li, J and Feng, H}, title = {Metagenomic and metaproteomic insights into the microbiome and the key geobiochemical potentials on the sandstone of rock-hewn Beishiku Temple in Northwest China.}, journal = {The Science of the total environment}, volume = {893}, number = {}, pages = {164616}, doi = {10.1016/j.scitotenv.2023.164616}, pmid = {37285993}, issn = {1879-1026}, mesh = {*Metagenome ; Metagenomics/methods ; *Microbiota/physiology ; Bacteria/metabolism ; Sulfur/metabolism ; }, abstract = {Metagenomics and metaproteomics analyses were used to determine the microbial diversity and taxon composition, as well as the biochemical potentials of the microbiome on the sandstone of Beishiku Temple located in Northwest China. Taxonomic annotation of the metagenomic dataset revealed the predominant taxa of the stone microbiome on this cave temple with characteristics of resistance to harsh environmental conditions. Meanwhile, there were also taxa in the microbiome that showed sensitivity to environmental factors. The taxa distribution and the metabolic functional distribution patterns by the metagenome and metaproteome, respectively, showed clear differences. The high abundance of energy metabolism represented in the metaproteome suggested that there were active geomicrobiological cycles of elements within the microbiome. The taxa responsible for reactions in the nitrogen cycle from both metagenome and metaproteome supported a metabolically active nitrogen cycle, and the high activity of Comammox bacteria indicated the strong metabolic activity of ammonia oxidation to nitrate in the outdoor site. The SOX-related taxa involved in the sulfur cycle showed higher activity outdoors than indoors, and on the outdoor ground than at the outdoor cliff, as detected through metaproteomic analysis. The development of petrochemical industry in the vicinity resulting in the deposition of sulfur/oxidized sulfur via atmosphere may stimulate the physiological activity of SOX. Our findings provide metagenomic and metaproteomic evidence for microbially driven geobiochemical cycles that result in the biodeterioration of stone monuments.}, } @article {pmid37285974, year = {2023}, author = {Ya, H and Zhang, T and Xing, Y and Lv, M and Wang, X and Jiang, B}, title = {Co-existence of polyethylene microplastics and tetracycline on soil microbial community and ARGs.}, journal = {Chemosphere}, volume = {335}, number = {}, pages = {139082}, doi = {10.1016/j.chemosphere.2023.139082}, pmid = {37285974}, issn = {1879-1298}, mesh = {Humans ; *Microplastics ; Plastics ; Polyethylene ; Soil/chemistry ; Genes, Bacterial ; Soil Microbiology ; Anti-Bacterial Agents ; Tetracycline/pharmacology ; *Microbiota ; Aminoglycosides ; }, abstract = {Microplastics are plastic particles with particle size less than 5 mm in the environment. As an emerging organic pollutant, the presence of microplastics in the soil environment has been widely noticed. Also, due to the overuse of antibiotics, a large amount of antibiotics that cannot be fully absorbed by humans and livestock enter the soil environment in the form of urine or manure, making the soils suffer from serious antibiotic contamination problems. To address the environmental problems of microplastics and antibiotic contamination in soils, this study was conducted to investigate the effects of PE microplastics on antibiotic degradation, microbial community characteristics and ARGs in tetracycline-contaminated soils. The results showed that the addition of PE microplastics inhibited the degradation of tetracycline, and significantly increased the organic carbon content and decreased the neutral phosphatase activity. The addition of PE microplastics significantly reduced the alpha diversity of soil microbial community. Compared to the single tetracycline contamination. In addition, combined contamination with PE microplastics and tetracycline significantly affected bacterial genera such as Aeromicrobium, Rhodococcus, Mycobacterium and Intrasporangium. Metagenome sequencing studies revealed that the addition of PE microplastics inhibited the dissipation of ARGs in tetracycline-contaminated soils. There were strong positive correlations between Multidrug, Aminoglycoside and Clycopeptide resistance genes and Chloroflexi and Proteobacteria in tetracycline contaminated soils, and there was a strong positive correlation between Aminoglycoside resistance genes and Actinobacteria in combined contamination of PE microplastics and tetracycline. This study will provide some data support for the current environmental risk assessment of the coexistence of multiple contaminants in soil.}, } @article {pmid37285789, year = {2023}, author = {Xing, X and Lyu, L and Yan, Z and Zhang, H and Li, T and Han, M and Li, Z and Zhang, F and Wang, Z and Wang, S and Hong, Y and Hu, C}, title = {Self-purification of actual wastewater via microbial-synergy driving of catalyst-surface microelectronic field: A pilot-scale study.}, journal = {Journal of hazardous materials}, volume = {457}, number = {}, pages = {131744}, doi = {10.1016/j.jhazmat.2023.131744}, pmid = {37285789}, issn = {1873-3336}, abstract = {High energy consumption is impedimental for eliminating refractory organics in wastewater by current technologies. Herein, we develop an efficient self-purification process for actual non-biodegradable dyeing wastewater at pilot scale, using N-doped graphene-like (CN) complexed Cu-Al2O3 supported Al2O3 ceramics (HCLL-S8-M) fixed-bed reactor without additional input. About 36% chemical oxygen demand removal was achieved within 20 min empty bed retention time and maintained stability for almost one year. The HCLL-S8-M structure feature and its interface on microbial community structure, functions, and metabolic pathways were analyzed by density-functional theory calculation, X-ray photoelectron spectroscopy, multiomics analysis of metagenome, macrotranscriptome and macroproteome. On the surface of HCLL-S8-M, a strong microelectronic field (MEF) was formed by the electron-rich/poor area due to Cu-π interaction from the complexation between phenolic hydroxy of CN and Cu species, driving the electrons of the adsorbed dye pollutants to the microorganisms through extracellular polymeric substance and the direct transfer of extracellular electrons, causing their degradation into CO2 and intermediates, which was degraded partly via intracellular metabolism. The lower energy feeding for the microbiome produced less adenosine triphosphate, resulting in little sludge throughout reaction. The MEF from electronic polarization is greatly potential to develop low-energy wastewater treatment technology.}, } @article {pmid37285121, year = {2023}, author = {Tran, PQ and Bachand, SC and Hotvedt, JC and Kieft, K and McDaniel, EA and McMahon, KD and Anantharaman, K}, title = {Physiological and genomic evidence of cysteine degradation and aerobic hydrogen sulfide production in freshwater bacteria.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0020123}, pmid = {37285121}, issn = {2379-5077}, support = {Hatch project 1025641//U.S. Department of Agriculture (USDA)/ ; CSP 394//Joint Genome Institute (JGI)/ ; //Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (NSERC)/ ; }, mesh = {*Hydrogen Sulfide/metabolism ; Cysteine/metabolism ; Ecosystem ; Sulfides/metabolism ; Bacteria/genetics ; Sulfur/metabolism ; Lakes/microbiology ; Oxygen/metabolism ; Genomics ; }, abstract = {The sulfur-containing amino acid cysteine is abundant in the environment, including in freshwater lakes. Biological cysteine degradation can result in hydrogen sulfide (H2S), a toxic and ecologically relevant compound that is a central player in biogeochemical cycling in aquatic environments. Here, we investigated the ecological significance of cysteine in oxic freshwater, using isolated cultures, controlled experiments, and multiomics. We screened bacterial isolates enriched from natural lake water for their ability to produce H2S when provided cysteine. We identified 29 isolates (Bacteroidota, Proteobacteria, and Actinobacteria) that produced H2S. To understand the genomic and genetic basis for cysteine degradation and H2S production, we further characterized three isolates using whole-genome sequencing (using a combination of short-read and long-read sequencing) and tracked cysteine and H2S levels over their growth ranges: Stenotrophomonas maltophilia (Gammaproteobacteria), S. bentonitica (Gammaproteobacteria), and Chryseobacterium piscium (Bacteroidota). Cysteine decreased and H2S increased, and all three genomes had genes involved in cysteine degradation. Finally, to assess the presence of these organisms and genes in the environment, we surveyed a 5-year time series of metagenomic data from the same isolation source (Lake Mendota, Madison, WI, USA) and identified their presence throughout the time series. Overall, our study shows that diverse isolated bacterial strains can use cysteine and produce H2S under oxic conditions, and we show evidence using metagenomic data that this process may occur more broadly in natural freshwater lakes. Future considerations of sulfur cycling and biogeochemistry in oxic environments should account for H2S production from the degradation of organosulfur compounds. IMPORTANCE Hydrogen sulfide (H2S), a naturally occurring gas with both biological and abiotic origins, can be toxic to living organisms. In aquatic environments, H2S production typically originates from anoxic (lacking oxygen) environments, such as sediments, or the bottom layers of thermally stratified lakes. However, the degradation of sulfur-containing amino acids such as cysteine, which all cells and life forms rely on, can be a source of ammonia and H2S in the environment. Unlike other approaches for biological H2S production such as dissimilatory sulfate reduction, cysteine degradation can occur in the presence of oxygen. Yet, little is known about how cysteine degradation influences sulfur availability and cycling in freshwater lakes. In our study, we identified diverse bacteria from a freshwater lake that can produce H2S in the presence of O2. Our study highlights the ecological importance of oxic H2S production in natural ecosystems and necessitates a change in our outlook on sulfur biogeochemistry.}, } @article {pmid37284747, year = {2023}, author = {Ma, ZH and Jiang, Z and Dong, HX and Xu, WH and Yan, S and Ma, XX and Wang, X}, title = {Use of metagenomic next-generation sequencing in diagnosing lung abscesses caused by oral bacteria.}, journal = {Future microbiology}, volume = {18}, number = {}, pages = {465-469}, doi = {10.2217/fmb-2022-0172}, pmid = {37284747}, issn = {1746-0921}, mesh = {Male ; Humans ; Middle Aged ; *Lung Abscess/diagnosis ; Bacteria/genetics ; *Communicable Diseases ; Metagenome ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {Lung abscesses are one of the most common lower respiratory tract infections worldwide and can seriously endanger life. However, pathogens associated with lung abscesses still cannot be detected quickly and accurately with the current microbial detection technology. Here, the case of a 53-year-old male with a lung abscess caused by oral bacteria is reported. After metagenomic next-generation sequencing was applied to identify the pathogenic microorganism, the patient recovered with precision medicine. Metagenomic next-generation sequencing is an important tool for the clinical diagnosis of infectious diseases caused by microorganisms and in guiding precision medicine.}, } @article {pmid37283942, year = {2023}, author = {Si, Z and Li, L and Han, J}, title = {Analysis of Metagenomic Next-Generation Sequencing (mNGS) in the Diagnosis of Herpes Simplex Virus (HSV) Encephalitis with Normal Cerebrospinal Fluid (CSF).}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {3431-3439}, pmid = {37283942}, issn = {1178-6973}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is becoming increasingly extensive in diagnosing herpes simplex encephalitis (HSE). However, many HSE patients with normal cerebrospinal fluid (CSF) diagnosed by mNGS have been found during the clinical application. This study aimed to summarize and analyze the clinical characteristics, supplementary examinations, and prognosis of patients with HSE whose cerebrospinal fluid was confirmed to be normal by mNGS.

METHODS: This retrospective study evaluated the clinical characteristics, auxiliary examinations, and patient prognosis of patients with HSE that were diagnosed by mNGS but had normal CSF. Clinical data collected included baseline information, signs and symptoms upon admission, and risk factors for infection. Auxiliary examinations included indirect immunofluorescence assay (IIF), cell-based assay (CBA), and CSF testing. Prognosis was evaluated based on hospital stay and patient survival.

RESULTS: Seven of the nine patients (77.8%) experienced headaches, and four (44.4%) had a fever of 38°C or higher. The average leukocyte count in the CSF was 2.6 ± 2.3/L. According to the mNGS, the median sequence count of HSV was 2 (1, 16). Magnetic resonance imaging (MRI) revealed one bilateral temporal lobe lesion (11.1%), two isolated bilateral frontal lobe lesions (22.2%), and one bilateral cingulate gyrus lesion (11.1%). One patient (11.1%) was admitted to the intensive care unit and passed away in the hospital. The remaining patients (88.9%) had a positive prognosis upon discharge.

CONCLUSION: Patients with HSE who had normal CSF were typically middle-aged women with normal immune function. They showed typical HSE clinical features, such as fever, headache and epilepsy, that did not differ from those of other HSE patients. A normal CSF result is generally associated with a low viral load and the body's ability to mount an effective immune response. Most of these patients have a favorable prognosis.}, } @article {pmid37283937, year = {2023}, author = {Zhou, Y and Wang, Q and Shen, Y and Shen, B and Zhang, Y and Wang, W and Li, X}, title = {A Case of Critical Japanese Spotted Fever in Zhejiang, China.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {3425-3430}, pmid = {37283937}, issn = {1178-6973}, abstract = {BACKGROUND: Japanese spotted fever (JSF) is a rare disease, caused by Rickettsia japonica; no case has been reported in Zhejiang Province, China.

CASE PRESENTATION: An elderly woman presented to the hospital with abdominal pain and fever. Her condition rapidly worsened with severe complications, such as multiple organ failure and central nervous system damage. The presence of R. japonica was quickly detected by metagenomic next-generation sequencing. On the basis of combined clinical manifestations and laboratory results, critical JSF was diagnosed and treated with doxycycline. The patient showed good prognosis. Typical symptoms (eschar and rash) were not observed in the early stage, consequently increasing the difficulty of clinical diagnosis.

CONCLUSION: The delay of treatment caused by non-specific symptoms is an important factor affecting the progression of JSF. As an emerging pathogen detection method, mNGS has been successfully applied for disease diagnosis and treatment, and can be an important complement for the diagnosis of this disease.}, } @article {pmid37283932, year = {2023}, author = {Cai, Z and Li, P and Zhu, W and Wei, J and Lu, J and Song, X and Li, K and Li, S and Li, M}, title = {Metagenomic analysis reveals gut plasmids as diagnosis markers for colorectal cancer.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1130446}, pmid = {37283932}, issn = {1664-302X}, abstract = {BACKGROUND: Colorectal cancer (CRC) is linked to distinct gut microbiome patterns. The efficacy of gut bacteria as diagnostic biomarkers for CRC has been confirmed. Despite the potential to influence microbiome physiology and evolution, the set of plasmids in the gut microbiome remains understudied.

METHODS: We investigated the essential features of gut plasmid using metagenomic data of 1,242 samples from eight distinct geographic cohorts. We identified 198 plasmid-related sequences that differed in abundance between CRC patients and controls and screened 21 markers for the CRC diagnosis model. We utilize these plasmid markers combined with bacteria to construct a random forest classifier model to diagnose CRC.

RESULTS: The plasmid markers were able to distinguish between the CRC patients and controls [mean area under the receiver operating characteristic curve (AUC = 0.70)] and maintained accuracy in two independent cohorts. In comparison to the bacteria-only model, the performance of the composite panel created by combining plasmid and bacteria features was significantly improved in all training cohorts (mean AUCcomposite = 0.804 and mean AUCbacteria = 0.787) and maintained high accuracy in all independent cohorts (mean AUCcomposite = 0.839 and mean AUCbacteria = 0.821). In comparison to controls, we found that the bacteria-plasmid correlation strength was weaker in CRC patients. Additionally, the KEGG orthology (KO) genes in plasmids that are independent of bacteria or plasmids significantly correlated with CRC.

CONCLUSION: We identified plasmid features associated with CRC and showed how plasmid and bacterial markers could be combined to further enhance CRC diagnosis accuracy.}, } @article {pmid37283894, year = {2023}, author = {Adedayo, AA and Fadiji, AE and Babalola, OO}, title = {Unraveling the functional genes present in rhizosphere microbiomes of Solanum lycopersicum.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15432}, pmid = {37283894}, issn = {2167-8359}, mesh = {*Solanum lycopersicum/genetics ; Rhizosphere ; Soil Microbiology ; *Microbiota/genetics ; Soil/chemistry ; Plants ; }, abstract = {The microbiomes living in the rhizosphere soil of the tomato plant contribute immensely to the state of health of the tomato plant alongside improving sustainable agriculture. With the aid of shotgun metagenomics sequencing, we characterized the putative functional genes (plant-growth-promoting and disease-resistant genes) produced by the microbial communities dwelling in the rhizosphere soil of healthy and powdery mildew-diseased tomato plants. The results identified twenty-one (21) plant growth promotion (PGP) genes in the microbiomes inhabiting the healthy rhizosphere (HR) which are more predomiant as compared to diseased rhizosphere (DR) that has nine (9) genes and four (4) genes in bulk soil (BR). Likewise, we identified some disease-resistant genes which include nucleotide binding genes and antimicrobial genes. Our study revealed fifteen (15) genes in HR which made it greater in comparison to DR that has three (3) genes and three (3) genes in bulk soil. Further studies should be conducted by isolating these microorganisms and introduce them to field experiments for cultivation of tomatoes.}, } @article {pmid37282943, year = {2023}, author = {Li, XZ and Li, YL and Zhu, JS}, title = {[Differential transcription of mating-type genes during sexual reproduction of natural Cordyceps sinensis].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {48}, number = {10}, pages = {2829-2840}, doi = {10.19540/j.cnki.cjcmm.20230213.102}, pmid = {37282943}, issn = {1001-5302}, mesh = {*Cordyceps/genetics ; Genes, Mating Type, Fungal/genetics ; Reproduction/genetics ; }, abstract = {Natural Cordyceps sinensis as an insect-fungal complex, which is developed after Ophiocordyceps sinensis infects a larva of Hepialidae family. Seventeen genotypes of O. sinensis have been identified in natural C. sinensis. This paper summarized the literature reports and GenBank database regarding occurrence and transcription of the mating-type genes of MAT1-1 and MAT1-2 idiomorphs in natural C. sinensis, in Hirsutella sinensis(GC-biased Genotype #1 of O. sinensis), to infer the mating pattern of O. sinensis in the lifecycle of natural C. sinensis. The mating-type genes and transcripts of MAT1-1 and MAT1-2 idiomorphs were identified in the metagenomes and metatranscriptomes of natural C. sinensis. However, their fungal sources are unclear because of co-colonization of several genotypes of O. sinensis and multiple fungal species in natural C. sinensis. The mating-type genes of MAT1-1 and MAT1-2 idiomorphs were differentially present in 237 H. sinensis strains, constituting the genetic control of the O. sinensis reproduction. Transcriptional control of the O. sinensis reproduction includes: differential transcription or silencing of the mating-type genes of MAT1-1 and MAT1-2 idiomorphs, and the MAT1-2-1 transcript with unspliced intron I that contains 3 stop codons. Research on the H. sinensis transcriptome demonstrated differential and complementary transcriptions of the mating-type genes of MAT1-1 and MAT1-2 idiomorphs in Strains L0106 and 1229, which may become mating partners to accomplish physiological heterothallism. The differential occurrence and transcription of the mating-type genes in H. sinensis are inconsistent with the self-fertilization hypothesis under homothallism or pseudohomothallism, but instead indicate the need of mating partners of the same H. sinensis species, either monoecious or dioecious, for physiological heterothallism, or heterospecific species for hybridization. Multiple GC-and AT-biased genotypes of O. sinensis were identified in the stroma, stromal fertile portion(densely covered with numerous ascocarps) and ascospores of natural C. sinensis. It needs to be further explored if the genome-independent O. sinensis genotypes could become mating partners to accomplish sexual reproduction. S. hepiali Strain FENG experienced differential transcription of the mating-type genes with a pattern complementary to that of H. sinensis Strain L0106. Additional evidence is needed to explore a hybridization possibility between S. hepiali and H. sinensis, whether they are able to break the interspecific reproductive isolation. Genotypes #13～14 of O. sinensis feature large DNA segment reciprocal substitutions and genetic material recombination between 2 heterospecific parental fungi, H. sinensis and an AB067719-type fungus, indicating a possibility of hybridization or parasexuality. Our analysis provides important information at the genetic and transcriptional levels regarding the mating-type gene expression and reproduction physiology of O. sinensis in the sexual life of natural C. sinensis and offers crucial reproductive physiology evidence, to assist in the design of the artificial cultivation of C. sinensis to supplement the increasing scarcity of natural resource.}, } @article {pmid37280708, year = {2023}, author = {Rutjens, S and Vereecke, N and Sauer, J and Croubels, S and Devreese, M}, title = {Cefquinome shows a higher impact on the pig gut microbiome and resistome compared to ceftiofur.}, journal = {Veterinary research}, volume = {54}, number = {1}, pages = {45}, pmid = {37280708}, issn = {1297-9716}, mesh = {Swine ; Animals ; Anti-Bacterial Agents/therapeutic use ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Cephalosporins/pharmacology ; Feces/microbiology ; *Anti-Infective Agents/pharmacology ; Escherichia coli/genetics ; }, abstract = {Cephalosporins are licensed for treatment of severe bacterial infections in different species. However, the effect of these antimicrobials on the fecal microbiome and potential spread of resistance-associated genes causes great concern. This highlights the need to understand the impact of cephalosporins on the porcine fecal microbiome and resistome. A combination of long-read 16S rRNA gene and shotgun metagenomic sequencing was applied to investigate the effect of conventional treatment with either ceftiofur (3 mg.kg[-1] intramuscular, 3 consecutive days) or cefquinome (2 mg.kg[-1] intramuscular, 5 consecutive days) on the porcine microbiome and resistome. Fecal samples were collected from 17 pigs (6 ceftiofur treated, 6 cefquinome treated, 5 control pigs) at four different timepoints. Treatment with ceftiofur resulted in an increase in Proteobacteria members on microbiome level, while on resistome level selection in TetQ containing Bacteroides, CfxA6 containing Prevotella and blaTEM-1 containing Escherichia coli was observed. Cefquinome treatment resulted in a decline in overall species richness (α-diversity) and increase in Proteobacteria members. On genus level, administration of cefquinome significantly affected more genera than ceftiofur (18 vs 8). On resistome level, cefquinome resulted in a significant increase of six antimicrobial resistance genes, with no clear correlation with certain genera. For both antimicrobials, the resistome levels returned back to the control levels 21 days post-treatment. Overall, our study provides novel insights on the effect of specific cephalosporins on the porcine gut microbiome and resistome after conventional intramuscular treatment. These results might contribute to better tailoring of the most ideal treatment strategy for some bacterial infections.}, } @article {pmid37280433, year = {2023}, author = {Acharya, SM and Yee, MO and Diamond, S and Andeer, PF and Baig, NF and Aladesanmi, OT and Northen, TR and Banfield, JF and Chakraborty, R}, title = {Fine scale sampling reveals early differentiation of rhizosphere microbiome from bulk soil in young Brachypodium plant roots.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {54}, pmid = {37280433}, issn = {2730-6151}, support = {DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; DE-AC02-05CH11231//U.S. Department of Energy (DOE)/ ; }, abstract = {For a deeper and comprehensive understanding of the composition and function of rhizosphere microbiomes, we need to focus at the scale of individual roots in standardized growth containers. Root exudation patterns are known to vary along distinct parts of the root even in juvenile plants giving rise to spatially distinct microbial niches. To address this, we analyzed the microbial community from two spatially distinct zones of the developing primary root (tip and base) in young Brachypodium distachyon grown in natural soil using standardized fabricated ecosystems known as EcoFABs as well as in more conventional pot and tubes. 16S rRNA based community analysis showed a strong rhizosphere effect resulting in significant enrichment of several OTUs belonging to Actinobacteria, Bacteroidetes, Firmicutes and Proteobacteria. However, microbial community composition did not differ between root tips and root base or across different growth containers. Functional analysis of bulk metagenomics revealed significant differences between root tips and bulk soil. The genes associated with different metabolic pathways and root colonization were enriched in root tips. On the other hand, genes associated with nutrient-limitation and environmental stress were prominent in the bulk soil compared to root tips, implying the absence of easily available, labile carbon and nutrients in bulk soil relative to roots. Such insights into the relationships between developing root and microbial communities are critical for judicious understanding of plant-microbe interactions in early developmental stages of plants.}, } @article {pmid37280372, year = {2023}, author = {Meriggi, C and Mehrshad, M and Johnson, RK and Laugen, AT and Drakare, S}, title = {Challenges in supplying empirical proof for predictions derived from Species Distribution Models (SDMs): the case of an invasive cyanobacterium.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {56}, pmid = {37280372}, issn = {2730-6151}, support = {DO2017-0053//Stiftelsen Oscar och Lili Lamms Minne (Foundation in Memory of Oscar and Lili Lamm)/ ; DO2017-0053//Stiftelsen Oscar och Lili Lamms Minne (Foundation in Memory of Oscar and Lili Lamm)/ ; DO2017-0053//Stiftelsen Oscar och Lili Lamms Minne (Foundation in Memory of Oscar and Lili Lamm)/ ; DO2017-0053//Stiftelsen Oscar och Lili Lamms Minne (Foundation in Memory of Oscar and Lili Lamm)/ ; DO2017-0053//Stiftelsen Oscar och Lili Lamms Minne (Foundation in Memory of Oscar and Lili Lamm)/ ; CTS 16:267//Carl Tryggers Stiftelse för Vetenskaplig Forskning (Carl Trygger Foundation)/ ; CTS 16:267//Carl Tryggers Stiftelse för Vetenskaplig Forskning (Carl Trygger Foundation)/ ; CTS 16:267//Carl Tryggers Stiftelse för Vetenskaplig Forskning (Carl Trygger Foundation)/ ; CTS 16:267//Carl Tryggers Stiftelse för Vetenskaplig Forskning (Carl Trygger Foundation)/ ; CTS 16:267//Carl Tryggers Stiftelse för Vetenskaplig Forskning (Carl Trygger Foundation)/ ; 2018-05973//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/ ; 2018-05973//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/ ; 2018-05973//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/ ; 2018-05973//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/ ; 2018-05973//Svenska Forskningsrådet Formas (Swedish Research Council Formas)/ ; }, abstract = {Species distribution models (SDMs) calibrated with bioclimatic variables revealed a high probability for range expansion of the invasive toxin producing cyanobacterium, Raphidiopsis raciborskii to Sweden, where no reports of its presence have hitherto been recorded. While predictions focused on the importance of climate variables for possible invasion, other barriers to dispersal and successful colonization need to be overcome by the species for successful invasion. In this study, we combine field-based surveys of R. raciborskii (microscopy and molecular analysis using species-specific primers) of 11 Swedish lakes and in-silico screening of environmental DNA using 153 metagenomic datasets from lakes across Europe to validate the SDMs prediction. Field-based studies in lakes with high/low predicted probability of occurrence did not detect the presence of R. raciborskii, and in-silico screening only detected hints of its presence in 5 metagenomes from lakes with probability ranging from 0.059 to 0.825. The inconsistencies between SDMs results and both field-based/in-silico monitoring could be due to either sensitivity of monitoring approaches in detecting early invasions or uncertainties in SDMs that focused solely on climate drivers. However, results highlight the necessity of proactive monitoring with high temporal and spatial frequency.}, } @article {pmid37280111, year = {2023}, author = {Okoye, CO and Wei, Z and Jiang, H and Wu, Y and Wang, Y and Gao, L and Li, X and Jiang, J}, title = {Metagenomics analysis reveals the performance of homo- and heterofermentative lactic acid bacteria in alfalfa silage fermentation, bacterial community, and functional profiles.}, journal = {Journal of animal science}, volume = {101}, number = {}, pages = {}, pmid = {37280111}, issn = {1525-3163}, mesh = {Animals ; *Silage/analysis ; Medicago sativa/metabolism ; *Lactobacillales/genetics/metabolism ; Fermentation ; Metagenomics ; RNA, Ribosomal, 16S/genetics/metabolism ; Bacteria/genetics/metabolism ; }, abstract = {Alfalfa (Medicago sativa L.) is a kind of roughage frequently utilized as an animal feed but challenging to be ensiled due to its low water-soluble carbohydrate (WSC), high water content, and elevated buffering capacity, thus requiring the application of lactic acid bacteria (LAB) to improve its fermentation. This study employed high-throughput metagenomic sequence technology to reveal the effects of homofermentative LAB, Lactobacillus plantarum (Lp), or Pediococcus pentosaceus (Pp), and heterofermentative LAB, L. buchneri (Lb), or their combinations (LbLp or LbPp) (applied at 1.0 × 109 colony forming units (cfu) per kilogram of alfalfa biomass fresh material) on the fermentation, microbial community, and functional profiles of alfalfa silage after 7, 14, 30, and 60 ensiling days. The results indicated a reduction (P < 0.05) in glucose and pH and higher (P < 0.05) beneficial organic acid contents, xylose, crude protein, ammonia nitrogen, and aerobic stability in Lb-, LbPp-, and LbLp-inoculated alfalfa silages after 30 and 60 d. Also, higher (P < 0.05) WSC contents were recorded in LbLp-inoculated alfalfa silages after 30 d (10.84 g/kg dry matter [DM]) and 60 d (10.92 g/kg DM). Besides, LbLp-inoculated alfalfa silages recorded higher (P < 0.05) LAB count (9.92 log10 cfu/g) after 60 d. Furthermore, a positive correlation was found between the combined LAB inoculants in LbLp-inoculated alfalfa silages and dominant LAB genera, Lactobacillus and Pediococcus, with fermentation properties after 30 and 60 d. In addition, the 16S rRNA gene-predicted functional analyses further showed that the L. buchneri PC-C1 and L. plantarum YC1-1-4B combination improved carbohydrate metabolism and facilitated further degradation of polysaccharides in alfalfa after 60 d of ensiling. These findings reveal the significant performance of L. buchneri and L. plantarum in combination with dominant LAB species in suppressing the growth of Clostridia, molds, and yeasts and improving the fermentation characteristics and functional carbohydrate metabolism of alfalfa after 60 d ensiling, thus suggesting the need for further studies to uncover the diverse performance of the LAB combination and their consortium with other natural and artificial inoculants in various kinds of silages.}, } @article {pmid37279941, year = {2023}, author = {Sheikh, S and Pánek, T and Gahura, O and Týč, J and Záhonová, K and Lukeš, J and Eliáš, M and Hashimi, H}, title = {A Novel Group of Dynamin-Related Proteins Shared by Eukaryotes and Giant Viruses Is Able to Remodel Mitochondria From Within the Matrix.}, journal = {Molecular biology and evolution}, volume = {40}, number = {6}, pages = {}, pmid = {37279941}, issn = {1537-1719}, mesh = {*Giant Viruses/genetics/metabolism ; Phylogeny ; Mitochondrial Proteins/genetics/metabolism ; Mitochondria/genetics/metabolism ; Dynamins/genetics/metabolism ; Saccharomyces cerevisiae/genetics ; }, abstract = {The diverse GTPases of the dynamin superfamily play various roles in the cell, as exemplified by the dynamin-related proteins (DRPs) Mgm1 and Opa1, which remodel the mitochondrial inner membrane in fungi and metazoans, respectively. Via an exhaustive search of genomic and metagenomic databases, we found previously unknown DRP types occurring in diverse eukaryotes and giant viruses (phylum Nucleocytoviricota). One novel DRP clade, termed MidX, combined hitherto uncharacterized proteins from giant viruses and six distantly related eukaryote taxa (Stramenopiles, Telonemia, Picozoa, Amoebozoa, Apusomonadida, and Choanoflagellata). MidX stood out because it was not only predicted to be mitochondria-targeted but also to assume a tertiary structure not observed in other DRPs before. To understand how MidX affects mitochondria, we exogenously expressed MidX from Hyperionvirus in the kinetoplastid Trypanosoma brucei, which lacks Mgm1 or Opa1 orthologs. MidX massively affected mitochondrial morphology from inside the matrix, where it closely associates with the inner membrane. This unprecedented mode of action contrasts to those of Mgm1 and Opa1, which mediate inner membrane remodeling in the intermembrane space. We speculate that MidX was acquired in Nucleocytoviricota evolution by horizontal gene transfer from eukaryotes and is used by giant viruses to remodel host mitochondria during infection. MidX's unique structure may be an adaptation for reshaping mitochondria from the inside. Finally, Mgm1 forms a sister group to MidX and not Opa1 in our phylogenetic analysis, throwing into question the long-presumed homology of these DRPs with similar roles in sister lineages.}, } @article {pmid37279907, year = {2023}, author = {Yao, L and Ding, J and Zhang, T and Jia, Y and Dai, J and Zheng, X and Yu, J and Yang, C and Chen, X}, title = {Heterogeneity changes of active bacterial community on cigar filler leaves after fermentation based on metagenome.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {87}, number = {9}, pages = {1056-1067}, doi = {10.1093/bbb/zbad071}, pmid = {37279907}, issn = {1347-6947}, support = {21978074//National Natural Science Foundation of China/ ; 202105FE04//Ministry of Education/ ; D20211404//Hubei Provincial Department of Education/ ; 110202001039(XJ-01)//China National Tobacco Corporation/ ; 027Y2019-003//Hubei Tobacco Corporation/ ; }, mesh = {*Metagenome ; Fermentation ; Bacteria/genetics/metabolism ; *Tobacco Products ; Plant Leaves/microbiology ; }, abstract = {Microorganisms play an important role in cigar fermentation. To further explore the dynamic changes of bacterial community composition, the changes of surface bacterial diversity of cigar filler leaves were investigated in the present study by high-throughput sequencing technology. It was found that the surface bacterial richness was declined after fermentation, and the dominant microorganisms on the surface of cigar filler leaves evolved from Pseudomonas spp. and Sphingomonas spp. before fermentation to Staphylococcus spp. after fermentation. The chemical composition and sensory quality evaluation of cigar filler leaves were closely related to the changes of surface bacterial community. The changes of the dominant surface bacterial community led to the differences of metabolic functions, among which the metabolic pathways such as the synthesis of secondary metabolites, carbon metabolism, and amino acid biosynthesis were significantly different. The results provide a basis for clarifying the roles of bacteria in fermentation of cigar filler leaves.}, } @article {pmid37279783, year = {2023}, author = {Khatri, A and Thakur, A and Lepcha, A and Acharya, V and Kumar, R}, title = {IHM-DB: a curated collection of metagenomics data from the Indian Himalayan Region, and automated pipeline for 16S rRNA amplicon-based analysis (AutoQii2).}, journal = {Database : the journal of biological databases and curation}, volume = {2023}, number = {}, pages = {}, pmid = {37279783}, issn = {1758-0463}, mesh = {*Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Metagenome ; Databases, Factual ; Software ; }, abstract = {Indian Himalayan metagenome database (IHM-DB) is a web-based database consisting of information on metagenomic datasets from various databases and publications that are specifically reported from the Indian Himalayan Region (IHR). The online interface allows users to view or download the dataset-specific information for the respective states, category-wise, or according to the hypervariable region. The IHM-DB also provides an opportunity for the users to access the metagenomic publications from the IHR as well as upload their microbiome information to the website. Additionally, an open-source 16S rRNA amplicon-based automated bioinformatics pipeline, AutoQii2, allows users to analyze the single-end and paired-end raw reads. AutoQii2 provides an automated approach for performing analysis such as quality check, adapter and chimera removal and exploits the latest ribosomal database project classifier for taxonomic assignments. The source code of the AutoQii2 pipeline is available at https://gitlab.com/khatriabhi2319/autoqii2. Database URL https://ham.ihbt.res.in/ihmdb and https://fgcsl.ihbt.res.in/ihmdb.}, } @article {pmid37279755, year = {2023}, author = {Münch, PC and Eberl, C and Woelfel, S and Ring, D and Fritz, A and Herp, S and Lade, I and Geffers, R and Franzosa, EA and Huttenhower, C and McHardy, AC and Stecher, B}, title = {Pulsed antibiotic treatments of gnotobiotic mice manifest in complex bacterial community dynamics and resistance effects.}, journal = {Cell host & microbe}, volume = {31}, number = {6}, pages = {1007-1020.e4}, doi = {10.1016/j.chom.2023.05.013}, pmid = {37279755}, issn = {1934-6069}, mesh = {Animals ; Mice ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Bacteria/genetics ; *Gastrointestinal Microbiome ; Germ-Free Life ; }, abstract = {Bacteria can evolve to withstand a wide range of antibiotics (ABs) by using various resistance mechanisms. How ABs affect the ecology of the gut microbiome is still poorly understood. We investigated strain-specific responses and evolution during repeated AB perturbations by three clinically relevant ABs, using gnotobiotic mice colonized with a synthetic bacterial community (oligo-mouse-microbiota). Over 80 days, we observed resilience effects at the strain and community levels, and we found that they were correlated with modulations of the estimated growth rate and levels of prophage induction as determined from metagenomics data. Moreover, we tracked mutational changes in the bacterial populations, and this uncovered clonal expansion and contraction of haplotypes and selection of putative AB resistance-conferring SNPs. We functionally verified these mutations via reisolation of clones with increased minimum inhibitory concentration (MIC) of ciprofloxacin and tetracycline from evolved communities. This demonstrates that host-associated microbial communities employ various mechanisms to respond to selective pressures that maintain community stability.}, } @article {pmid37279136, year = {2023}, author = {Wassan, JT and Wang, H and Zheng, H}, title = {Developing a New Phylogeny-Driven Random Forest Model for Functional Metagenomics.}, journal = {IEEE transactions on nanobioscience}, volume = {22}, number = {4}, pages = {763-770}, doi = {10.1109/TNB.2023.3283462}, pmid = {37279136}, issn = {1558-2639}, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Random Forest ; Metagenome/genetics ; *Microbiota/genetics ; Metagenomics/methods ; }, abstract = {Metagenomics is an unobtrusive science linking microbial genes to biological functions or environmental states. Classifying microbial genes into their functional repertoire is an important task in the downstream analysis of Metagenomic studies. The task involves Machine Learning (ML) based supervised methods to achieve good classification performance. Random Forest (RF) has been applied rigorously to microbial gene abundance profiles, mapping them to functional phenotypes. The current research targets tuning RF by the evolutionary ancestry of microbial phylogeny, developing a Phylogeny-RF model for functional classification of metagenomes. This method facilitates capturing the effects of phylogenetic relatedness in an ML classifier itself rather than just applying a supervised classifier over the raw abundances of microbial genes. The idea is rooted in the fact that closely related microbes by phylogeny are highly correlated and tend to have similar genetic and phenotypic traits. Such microbes behave similarly; and hence tend to be selected together, or one of these could be dropped from the analysis, to improve the ML process. The proposed Phylogeny-RF algorithm has been compared with state-of-the-art classification methods including RF and the phylogeny-aware methods of MetaPhyl and PhILR, using three real-world 16S rRNA metagenomic datasets. It has been observed that the proposed method not only achieved significantly better performance than the traditional RF model but also performed better than the other phylogeny-driven benchmarks (p < 0.05). For example, Phylogeny-RF attained a highest AUC of 0.949 and Kappa of 0.891 over soil microbiomes in comparison to other benchmarks.}, } @article {pmid37279013, year = {2023}, author = {Medina-Chávez, NO and Viladomat-Jasso, M and Zarza, E and Islas-Robles, A and Valdivia-Anistro, J and Thalasso-Siret, F and Eguiarte, LE and Olmedo-Álvarez, G and Souza, V and De la Torre-Zavala, S}, title = {A Transiently Hypersaline Microbial Mat Harbors a Diverse and Stable Archaeal Community in the Cuatro Cienegas Basin, Mexico.}, journal = {Astrobiology}, volume = {23}, number = {7}, pages = {796-811}, doi = {10.1089/ast.2021.0047}, pmid = {37279013}, issn = {1557-8070}, mesh = {*Archaea/genetics ; Mexico ; Phylogeny ; Bacteria/genetics ; *Microbiota ; Water ; RNA, Ribosomal, 16S/genetics ; Biodiversity ; }, abstract = {Microbial mats are biologically diverse communities that are analogs to some of the earliest ecosystems on Earth. In this study, we describe a unique transiently hypersaline microbial mat uncovered in a shallow pond within the Cuatro Cienegas Basin (CCB) in northern México. The CCB is an endemism-rich site that harbors living stromatolites that have been studied to understand the conditions of the Precambrian Earth. These microbial mats form elastic domes filled with biogenic gas, and the mats have a relatively large and stable subpopulation of archaea. For this reason, this site has been termed archaean domes (AD). The AD microbial community was analyzed by metagenomics over three seasons. The mat exhibited a highly diverse prokaryotic community dominated by bacteria. Bacterial sequences are represented in 37 phyla, mainly Proteobacteria, Firmicutes, and Actinobacteria, that together comprised >50% of the sequences from the mat. Archaea represented up to 5% of the retrieved sequences, with up to 230 different archaeal species that belong to 5 phyla (Euryarchaeota, Crenarchaeota, Thaumarchaeota, Korarchaeota, and Nanoarchaeota). The archaeal taxa showed low variation despite fluctuations in water and nutrient availability. In addition, predicted functions highlight stress responses to extreme conditions present in the AD, including salinity, pH, and water/drought fluctuation. The observed complexity of the AD mat thriving in high pH and fluctuating water and salt conditions within the CCB provides an extant model of great value for evolutionary studies, as well as a suitable analog to the early Earth and Mars.}, } @article {pmid37278524, year = {2023}, author = {Dedrick, S and Warrier, V and Lemon, KP and Momeni, B}, title = {When does a Lotka-Volterra model represent microbial interactions? Insights from in vitro nasal bacterial communities.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0075722}, pmid = {37278524}, issn = {2379-5077}, support = {R35 GM141806/GM/NIGMS NIH HHS/United States ; R01 GM117174/GM/NIGMS NIH HHS/United States ; T32 HL007427/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; Microbial Interactions ; Models, Theoretical ; Models, Biological ; Bacteria ; }, abstract = {To alter microbial community composition for therapeutic purposes, an accurate and reliable modeling framework capable of predicting microbial community outcomes is required. Lotka-Volterra (LV) equations have been utilized to describe a breadth of microbial communities, yet, the conditions in which this modeling framework is successful remain unclear. Here, we propose that a set of simple in vitro experiments-growing each member in cell-free spent medium obtained from other members-can be used as a test to decide whether an LV model is appropriate for describing microbial interactions of interest. We show that for LV to be a good candidate, the ratio of growth rate to carrying capacity of each isolate when grown in the cell-free spent media of other isolates should remain constant. Using an in vitro community of human nasal bacteria as a tractable system, we find that LV can be a good approximation when the environment is low-nutrient (i.e., when growth is limited by the availability of nutrients) and complex (i.e., when multiple resources, rather than a few, determine growth). These findings can help clarify the range of applicability of LV models and reveal when a more complex model may be necessary for predictive modeling of microbial communities. IMPORTANCE Although mathematical modeling can be a powerful tool to draw useful insights in microbial ecology, it is crucial to know when a simplified model adequately represents the interactions of interest. Here, we take advantage of bacterial isolates from the human nasal passages as a tractable model system and conclude that the commonly used Lotka-Volterra model can represent interactions among microbes well when the environment is complex (with many interaction mediators) and low-nutrient. Our work highlights the importance of considering both realism and simplicity when choosing a model to represent microbial interactions.}, } @article {pmid37278203, year = {2023}, author = {Gao, S and Gao, X and Zhu, R and Wu, D and Feng, Z and Jiao, N and Sun, R and Gao, W and He, Q and Liu, Z and Zhu, L}, title = {Microbial genes outperform species and SNVs as diagnostic markers for Crohn's disease on multicohort fecal metagenomes empowered by artificial intelligence.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2221428}, pmid = {37278203}, issn = {1949-0984}, mesh = {Humans ; *Crohn Disease/diagnosis/genetics ; Metagenome ; Artificial Intelligence ; *Gastrointestinal Microbiome/genetics ; Feces ; Genes, Microbial ; Dysbiosis/diagnosis/genetics ; }, abstract = {Dysbiosis of gut microbial community is associated with the pathogenesis of CD and may serve as a promising noninvasive diagnostic tool. We aimed to compare the performances of the microbial markers of different biological levels by conducting a multidimensional analysis on the microbial metagenomes of CD. We collected fecal metagenomic datasets generated from eight cohorts that altogether include 870 CD patients and 548 healthy controls. Microbial alterations in CD patients were assessed at multidimensional levels including species, gene, and SNV level, and then diagnostic models were constructed using artificial intelligence algorithm. A total of 227 species, 1047 microbial genes, and 21,877 microbial SNVs were identified that differed between CD and controls. The species, gene, and SNV models achieved an average AUC of 0.97, 0.95, and 0.77, respectively. Notably, the gene model exhibited superior diagnostic capability, achieving an average AUC of 0.89 and 0.91 for internal and external validations, respectively. Moreover, the gene model was specific for CD against other microbiome-related diseases. Furthermore, we found that phosphotransferase system (PTS) contributed substantially to the diagnostic capability of the gene model. The outstanding performance of PTS was mainly explained by genes celB and manY, which demonstrated high predictabilities for CD with metagenomic datasets and was validated in an independent cohort by qRT-PCR analysis. Our global metagenomic analysis unravels the multidimensional alterations of the microbial communities in CD and identifies microbial genes as robust diagnostic biomarkers across geographically and culturally distinct cohorts.}, } @article {pmid37277984, year = {2023}, author = {Chen, LL and Abbaspour, A and Aspvall, K and Rück, C and Bulik, CM and Pascal, D}, title = {Longitudinal study of gut microbiome in obsessive-compulsive disorder.}, journal = {Brain and behavior}, volume = {13}, number = {8}, pages = {e3115}, pmid = {37277984}, issn = {2162-3279}, mesh = {Humans ; Longitudinal Studies ; *Gastrointestinal Microbiome ; *Obsessive-Compulsive Disorder/diagnosis ; *Cognitive Behavioral Therapy ; Psychiatric Status Rating Scales ; }, abstract = {INTRODUCTION: Patients with obsessive-compulsive disorder (OCD) often have limited exposure to a diverse environment and perform repetitive compulsions such as excessive cleaning and washing, which could lead to altered gut microbiome. Therefore, longitudinal studies that investigate changes in gut microbiome before and after cognitive behavioral therapy based on exposure and response prevention (ERP) are warranted.

METHODS: All study participants (N = 64) underwent a structured psychiatric diagnostic interview prior to inclusion. Nutritional intake was assessed with a comprehensive food frequency questionnaire. Stool samples were collected from OCD patients before ERP (n = 32) and 1 month after completion of ERP (n = 15), as well as from healthy controls (HCs; n = 32). Taxonomic and functional analyses were performed using data from microbiome whole genome sequencing.

RESULTS: Patients with OCD at baseline reported consuming significantly less fiber than HCs (R[2]  = .12, F(2, 59) = 5.2, p ≤ .01). There were no significant differences in α- and β-diversity indices, or taxonomic dissimilarities at the species level between patients with OCD and HCs, or within patients before and after ERP. Functional profiling based on gut microbial gene expression was grouped into 56 gut-brain modules with neuroactive potential. None of the gut-brain modules differed significantly in expression between patients with OCD at baseline and HCs or within patients before and after ERP.

CONCLUSIONS: The diversity, composition, and functional profile of the gut microbiome in patients with OCD did not differ significantly from HCs and remained stable over time, despite behavioral changes.}, } @article {pmid37277534, year = {2023}, author = {Jespersen, M and Wagner, T}, title = {Assimilatory sulfate reduction in the marine methanogen Methanothermococcus thermolithotrophicus.}, journal = {Nature microbiology}, volume = {8}, number = {7}, pages = {1227-1239}, pmid = {37277534}, issn = {2058-5276}, mesh = {*Sulfates/metabolism ; *Methanococcaceae/metabolism ; Sulfites ; }, abstract = {Methanothermococcus thermolithotrophicus is the only known methanogen that grows on sulfate as its sole sulfur source, uniquely uniting methanogenesis and sulfate reduction. Here we use physiological, biochemical and structural analyses to provide a snapshot of the complete sulfate reduction pathway of this methanogenic archaeon. We find that later steps in this pathway are catalysed by atypical enzymes. PAPS (3'-phosphoadenosine 5'-phosphosulfate) released by APS kinase is converted into sulfite and 3'-phosphoadenosine 5'-phosphate (PAP) by a PAPS reductase that is similar to the APS reductases of dissimilatory sulfate reduction. A non-canonical PAP phosphatase then hydrolyses PAP. Finally, the F420-dependent sulfite reductase converts sulfite to sulfide for cellular assimilation. While metagenomic and metatranscriptomic studies suggest that the sulfate reduction pathway is present in several methanogens, the sulfate assimilation pathway in M. thermolithotrophicus is distinct. We propose that this pathway was 'mix-and-matched' through the acquisition of assimilatory and dissimilatory enzymes from other microorganisms and then repurposed to fill a unique metabolic role.}, } @article {pmid37276653, year = {2023}, author = {Huang, S and Zhang, B and Zhao, Z and Yang, C and Zhang, B and Cui, F and Lens, PNL and Shi, W}, title = {Metagenomic analysis reveals the responses of microbial communities and nitrogen metabolic pathways to polystyrene micro(nano)plastics in activated sludge systems.}, journal = {Water research}, volume = {241}, number = {}, pages = {120161}, doi = {10.1016/j.watres.2023.120161}, pmid = {37276653}, issn = {1879-2448}, mesh = {*Sewage/chemistry ; Plastics ; Polystyrenes ; Waste Disposal, Fluid/methods ; Nitrogen/metabolism ; *Microbiota ; Microplastics ; Metabolic Networks and Pathways ; }, abstract = {Microplastics (MPs) and nanoplastics (NPs) are prevalent in sewage and pose a potential threat to nitrogen biotransformation in wastewater treatment systems. However, investigations on how MPs and NPs affect the microbial nitrogen conversion and metabolism of the activated sludge are still scanty. Herein, the responses of microbiomes and functional genes to polystyrene MPs and NPs in activated sludge systems were investigated by metagenomic analysis. Results indicated that 1 mg/L MPs and NPs had marginal impacts on the nitrogen removal performance of the activated sludge systems, whereas high concentrations of MPs and NPs (20 and 100 mg/L) decreased the total nitrogen removal efficiency (13.4%-30.6%) by suppressing the nitrogen transformation processes. Excessive reactive oxygen species induced by MPs and NPs caused cytotoxicity, as evidenced by impaired cytomembranes and decreased bioactivity. Metagenomic analysis revealed that MPs and NPs diminished the abundance of denitrifiers (e.g. Mesorhizobium, Rhodobacter and Thauera), and concurrently reduced the abundance of functional genes (e.g. napA, napB and nirS) encoding for key enzymes involved in the nitrogen transformations, as well as the genes (e.g. mdh) related to the electron donor production, thereby declining the nitrogen removal efficiency. Network analysis further clarified the attenuate association between denitrifiers and denitrification-related genes in the plastic-exposed systems, elucidating that MPs and NPs restrained the nitrogen removal by inhibiting the contributions of microorganisms to nitrogen transformation processes. This study provides vital insights into the responses of the microbial community structure and nitrogen conversion processes to micro(nano)plastics disturbance in activated sludge systems.}, } @article {pmid37276443, year = {2023}, author = {Hua, D and Zou, Q and Wu, Z and Yuan, D and Yang, L and Ye, C}, title = {Application of Metagenomic High-Throughput Sequencing in a Rare Case of Multisite Infection With Two Microorganisms After Total Knee Arthroplasty.}, journal = {Orthopedics}, volume = {}, number = {}, pages = {1-5}, doi = {10.3928/01477447-20230531-04}, pmid = {37276443}, issn = {1938-2367}, abstract = {Postoperative deep infection is usually identified by microbial culture. However, frequent false-negative results have severely limited effective treatment. We report a rare case of intra-articular and paravertebral infection after total knee arthroplasty caused by Mycoplasma hominis and Ureaplasma urealyticum, with multiple negative microbial culture results. Eventually, the pathogens were identified using metagenomic high-throughput sequencing, and the patient was successfully treated with several "old" antibiotics. We analyze the clinical characteristics of this patient and systematically describe the application of high-throughput sequencing and antibiotics. [Orthopedics. 202x;4x(x):xx-xx.].}, } @article {pmid37275646, year = {2023}, author = {Tamarelle, J and Creze, MM and Savathdy, V and Phonekeo, S and Wallenborn, J and Siengsounthone, L and Fink, G and Odermatt, P and Kounnavong, S and Sayasone, S and Vonaesch, P}, title = {Dynamics and consequences of nutrition-related microbial dysbiosis in early life: study protocol of the VITERBI GUT project.}, journal = {Frontiers in nutrition}, volume = {10}, number = {}, pages = {1111478}, pmid = {37275646}, issn = {2296-861X}, abstract = {INTRODUCTION: Early life under- and overnutrition (jointly termed malnutrition) is increasingly recognized as an important risk factor for adult obesity and metabolic syndrome, a diet-related cluster of conditions including high blood sugar, fat and cholesterol. Nevertheless, the exact factors linking early life malnutrition with metabolic syndrome remain poorly characterized. We hypothesize that the microbiota plays a crucial role in this trajectory and that the pathophysiological mechanisms underlying under- and overnutrition are, to some extent, shared. We further hypothesize that a "dysbiotic seed microbiota" is transmitted to children during the birth process, altering the children's microbiota composition and metabolic health. The overall objective of this project is to understand the precise causes and biological mechanisms linking prenatal or early life under- or overnutrition with the predisposition to develop overnutrition and/or metabolic disease in later life, as well as to investigate the possibility of a dysbiotic seed microbiota inheritance in the context of maternal malnutrition.

METHODS/DESIGN: VITERBI GUT is a prospective birth cohort allowing to study the link between early life malnutrition, the microbiota and metabolic health. VITERBI GUT will include 100 undernourished, 100 normally nourished and 100 overnourished pregnant women living in Vientiane, Lao People's Democratic Republic (PDR). Women will be recruited during their third trimester of pregnancy and followed with their child until its second birthday. Anthropometric, clinical, metabolic and nutritional data are collected from both the mother and the child. The microbiota composition of maternal and child's fecal and oral samples as well as maternal vaginal and breast milk samples will be determined using amplicon and shotgun metagenomic sequencing. Epigenetic modifications and lipid profiles will be assessed in the child's blood at 2 years of age. We will investigate for possible associations between metabolic health, epigenetics, and microbial changes.

DISCUSSION: We expect the VITERBI GUT project to contribute to the emerging literature linking the early life microbiota, epigenetic changes and growth/metabolic health. We also expect this project to give new (molecular) insights into the mechanisms linking malnutrition-induced early life dysbiosis and metabolic health in later life, opening new avenues for microbiota-engineering using microbiota-targeted interventions.}, } @article {pmid37275543, year = {2023}, author = {Zheng, K and Dong, Y and Liang, Y and Liu, Y and Zhang, X and Zhang, W and Wang, Z and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M}, title = {Genomic diversity and ecological distribution of marine Pseudoalteromonas phages.}, journal = {Marine life science & technology}, volume = {5}, number = {2}, pages = {271-285}, pmid = {37275543}, issn = {2662-1746}, abstract = {UNLABELLED: Pseudoalteromonas, with a ubiquitous distribution, is one of the most abundant marine bacterial genera. It is especially abundant in the deep sea and polar seas, where it has been found to have a broad metabolic capacity and unique co-existence strategies with other organisms. However, only a few Pseudoalteromonas phages have so far been isolated and investigated and their genomic diversity and distribution patterns are still unclear. Here, the genomes, taxonomic features and distribution patterns of Pseudoalteromonas phages are systematically analyzed, based on the microbial and viral genomes and metagenome datasets. A total of 143 complete or nearly complete Pseudoalteromonas-associated phage genomes (PSAPGs) were identified, including 34 Pseudoalteromonas phage isolates, 24 proviruses, and 85 Pseudoalteromonas-associated uncultured viral genomes (UViGs); these were assigned to 47 viral clusters at the genus level. Many integrated proviruses (n = 24) and filamentous phages were detected (n = 32), suggesting the prevalence of viral lysogenic life cycle in Pseudoalteromonas. PSAPGs encoded 66 types of 249 potential auxiliary metabolic genes (AMGs) relating to peptidases and nucleotide metabolism. They may also participate in marine biogeochemical cycles through the manipulation of the metabolism of their hosts, especially in the phosphorus and sulfur cycles. Siphoviral and filamentous PSAPGs were the predominant viral lineages found in polar areas, while some myoviral and siphoviral PSAPGs encoding transposase were more abundant in the deep sea. This study has expanded our understanding of the taxonomy, phylogenetic and ecological scope of marine Pseudoalteromonas phages and deepens our knowledge of viral impacts on Pseudoalteromonas. It will provide a baseline for the study of interactions between phages and Pseudoalteromonas in the ocean.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-022-00160-z.}, } @article {pmid37275174, year = {2023}, author = {Chen, J and Zhang, T and Sun, L and Liu, Y and Li, D and Leng, X and An, S}, title = {Abundance trade-offs and dominant taxa maintain the stability of the bacterioplankton community underlying Microcystis blooms.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1181341}, pmid = {37275174}, issn = {1664-302X}, abstract = {Microcystis blooms are an intractable global environmental problem that pollute water and compromise ecosystem functioning. Closed-lake management practices keep lakes free of sewage and harmful algae invasions and have succeeded in controlling local Microcystis blooms; however, there is little understanding of how the bacterioplankton communities associated with Microcystis have changed. Here, based on metagenomic sequencing, the phyla, genera, functional genes and metabolic functions of the bacterioplankton communities were compared between open lakes (underlying Microcystis blooms) and closed lakes (no Microcystis blooms). Water properties and zooplankton density were investigated and measured as factors influencing blooms. The results showed that (1) the water quality of closed lakes was improved, and the nitrogen and phosphorus concentrations were significantly reduced. (2) The stability of open vs. closed-managed lakes differed notably at the species and genus levels (p < 0.01), but no significant variations were identified at the phylum and functional genes levels (p > 0.05). (3) The relative abundance of Microcystis (Cyanobacteria) increased dramatically in the open lakes (proportions from 1.44 to 41.76%), whereas the relative abundance of several other dominant genera of Cyanobacteria experienced a trade-off and decreased with increasing Microcystis relative abundance. (4) The main functions of the bacterioplankton communities were primarily related to dominant genera of Proteobacteria and had no significant relationship with Microcystis. Overall, the closed-lake management practices significantly reduced nutrients and prevented Microcystis blooms, but the taxonomic and functional structures of bacterioplankton communities remained stable overall.}, } @article {pmid37275172, year = {2023}, author = {Dutta, A and Connors, E and Trinh, R and Erazo, N and Dasarathy, S and Ducklow, HW and Steinberg, DK and Schofield, OM and Bowman, JS}, title = {Depth drives the distribution of microbial ecological functions in the coastal western Antarctic Peninsula.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1168507}, pmid = {37275172}, issn = {1664-302X}, abstract = {The Antarctic marine environment is a dynamic ecosystem where microorganisms play an important role in key biogeochemical cycles. Despite the role that microbes play in this ecosystem, little is known about the genetic and metabolic diversity of Antarctic marine microbes. In this study we leveraged DNA samples collected by the Palmer Long Term Ecological Research (LTER) project to sequence shotgun metagenomes of 48 key samples collected across the marine ecosystem of the western Antarctic Peninsula (wAP). We developed an in silico metagenomics pipeline (iMAGine) for processing metagenomic data and constructing metagenome-assembled genomes (MAGs), identifying a diverse genomic repertoire related to the carbon, sulfur, and nitrogen cycles. A novel analytical approach based on gene coverage was used to understand the differences in microbial community functions across depth and region. Our results showed that microbial community functions were partitioned based on depth. Bacterial members harbored diverse genes for carbohydrate transformation, indicating the availability of processes to convert complex carbons into simpler bioavailable forms. We generated 137 dereplicated MAGs giving us a new perspective on the role of prokaryotes in the coastal wAP. In particular, the presence of mixotrophic prokaryotes capable of autotrophic and heterotrophic lifestyles indicated a metabolically flexible community, which we hypothesize enables survival under rapidly changing conditions. Overall, the study identified key microbial community functions and created a valuable sequence library collection for future Antarctic genomics research.}, } @article {pmid37275135, year = {2023}, author = {Li, Y and Wang, C and Chang, H and Zhang, Y and Liu, S and He, W}, title = {Metagenomics reveals the effect of long-term fertilization on carbon cycle in the maize rhizosphere.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1170214}, pmid = {37275135}, issn = {1664-302X}, abstract = {Long-term fertilization can result in the changes in carbon (C) cycle in the maize rhizosphere soil. However, there have been few reports on the impacts of microbial regulatory mechanisms on the C cycle in soil. In the study, we analyzed the response of functional genes that regulate the C fixation, decomposition and methane (CH4) metabolism in maize rhizosphere soil to different fertilization treatments using metagenomics analysis. As the dominant C fixation pathway in maize rhizosphere soil, the abundance of the functional genes regulating the reductive citrate cycle (rTCA cycle) including korA, korB, and IHD1 was higher under the chemical nitrogen (N) fertilizer treatments [nitrogen fertilizer (N), compound chemical fertilization (NPK), the combination of compound chemical fertilizer with maize straw (NPKS)] than maize straw return treatments [maize straw return (S), the combination of phosphorus and potassium fertilizer with maize straw (PKS)]. The NPK treatment decreased the abundance of functional genes involved in 3-hydroxypropionate bicycle (3-HP cycle; porA, porB, and porD), which was one of the major C fixation pathways in soil aside from dicarboxylate-hydroxybutyrate (DC/4-HB cycle) and Calvin cycle. The abundance of functional genes related to C degradation was higher in S, PKS and NPKS treatments than N and NPK treatments, and chemical N fertilizer application had a significant effect on C degradation. The dominant Methanaogenesis pathway in maize rhizosphere soil, used acetate as a substrate, and was significantly promoted under chemical N fertilizer application. The functional genes that were related to CH4 oxidation (i.e., pmoA and pmoB) were reduced under N and NPK treatments. Moreover, soil chemical properties had a significant impact on the functional genes related to C fixation and degradation, with SOC (r[2] = 0.79) and NO3[-]-N (r[2] = 0.63) being the main regulators. These results implied that N fertilization rather than maize straw return had a greater influence on the C cycle in maize rhizosphere soil.}, } @article {pmid37275128, year = {2023}, author = {Huang, C and Huang, Y and Wang, Z and Lin, Y and Li, Y and Chen, Y and Chen, X and Zhang, C and Li, W and Zhang, W and Fang, X and Huang, Z}, title = {Multiplex PCR-based next generation sequencing as a novel, targeted and accurate molecular approach for periprosthetic joint infection diagnosis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1181348}, pmid = {37275128}, issn = {1664-302X}, abstract = {OBJECTIVES: Periprosthetic joint infection (PJI) diagnosis remains challenging, and the identification of the causative microorganism is, by far, the most important aspect. Here, we use multiple PCR-based targeted next-generation sequencing (tNGS) to detect pathogens in PJI. To explore 1. the ability of targeted next-generation sequencing (tNGS) to detect pathogens in PJI; 2. the consistency of tNGS, metagenomic NGS (mNGS), and culture results; and 3. the ability of tNGS to detect drug resistance genes in PJI.

METHODS: PJI was diagnosed according to the Musculoskeletal Infection Society (MSIS) criteria. The microorganisms were detected by culture, mNGS and tNGS to compare the diagnostic effectiveness of the three methods for PJI and to compare their consistency in detecting microorganisms. Drug resistance genes were detected using tNGS. The costs and turnaround times of mNGS and tNGS were compared.

RESULTS: Forty-three patients with PJI, 21 patients without PJI and 10 negative control cases were included. The culture, tNGS, and mNGS sensitivities for PJI diagnosis were 74.41%, 88.37%, and 93.02%, respectively, with no significant differences. The specificities were 90.48%, 95.24%, and 95.24%, respectively, with no significant differences. tNGS detected drug resistance genes in 37.5% of culture-positive PJIs. tNGS was superior to mNGS for turnaround time (14.5 h vs. 28 h) and cost ($150 vs. $260).

CONCLUSIONS: tNGS can effectively identify PJI pathogens and may provide drug resistance information, while tNGS is superior to mNGS regarding cost and turnaround time. A multidisciplinary, multi-technology based algorithm to diagnose PJI is appropriate.

HIGHLIGHTS: 298 microorganisms and 86 drug resistance genes were included in the tNGS panel.Diagnostic efficacy of tNGS is not inferior to that of commonly used indicators.tNGS is superior to mNGS in cost and turnaround time.}, } @article {pmid37274727, year = {2023}, author = {Moubareck, CA and Alawlaqi, B and Alhajeri, S}, title = {Characterization of physicochemical parameters and bacterial diversity of composted organic food wastes in Dubai.}, journal = {Heliyon}, volume = {9}, number = {6}, pages = {e16426}, pmid = {37274727}, issn = {2405-8440}, abstract = {Composting favours recycling organic waste and producing an end product with high bioenergy potential and significant nutritional value for the soil. Analysing composted organic waste prepared in Dubai, a region with a desertic climate and a unique environment is essential since environmental conditions can greatly affect the physicochemical and biological soil properties and no studies in the Gulf region have been published yet on that process. This study analysed twelve different compost samples prepared in well ventilated wooden chambers, using home-generated organic wastes following the hot aerobic composting method for a duration of three months. The physicochemical parameters, measured at the end of the study, revealed that organic matter, electrical conductivity and pH were within the standard ranges while moisture content was low. Concerning macronutrients, most of the samples were within the standard range for carbon, potassium and sodium, while they were poor in phosphorous and nitrogen. Metagenomic analysis with Illumina MiSeq revealed the abundance of Firmicutes (30.35%), followed by Bacteroidota (26.69%), Proteobacteria (21.47%), and Actinobacteriota (11.17%). The phylum Planctomycetota, solely detected in compost and known to have a significant impact on soil ecosystem and decomposition of organic matter, was reported at a relatively significant level (2.35%). The Clostridia class, efficient in degrading cellulose, was described at high levels compared to other studies. The composting project succeeded in generating a healthy soil but lengthening the duration will allow the samples to fully decompose and therefore increase the total available nitrogen and phosphorus to meet the criteria of a typical mature compost. Various microbial consortia helped in the decomposition process. The qualitative information collected in this study will help in improving the composting technology to favour its utilization by a larger public in the Gulf region.}, } @article {pmid37274475, year = {2023}, author = {Mo, L and Jiang, J and Shi, J and Yu, Z and Li, L and Huang, D}, title = {T‑lymphoblastic lymphoma in a child diagnosed by metagenomic sequencing: A case report.}, journal = {Oncology letters}, volume = {26}, number = {1}, pages = {289}, pmid = {37274475}, issn = {1792-1082}, abstract = {T-lymphoblastic lymphoma (T-LBL) is a rare subtype of non-Hodgkin's lymphoma with a higher incidence in children than adults. T-LBL often presents with multiple lymph node enlargements or mediastinal masses, which can cause local compression symptoms, and is frequently misdiagnosed as an infectious disease at an early stage. By summarizing a recently experienced case of T-LBL in a patient with a suspected infection, with an analysis of clinical features and diagnostic methods, the aim of the present study was to provide more information on the early diagnosis of tumors in patients suspected to have an infection. An 8-year-old boy presented at a local hospital with abdominal pain, chest tightness and shortness of breath for >5 days, and bilateral pleural, abdominal and pericardial effusion were considered. Following hospitalization without significant improvement under treatment with an anti-infection regimen and closed chest cavity drainage, the patient was transferred to another hospital. Once admitted, ultrasound examination indicated a large amount of pericardial and pleural effusion. Pericardiocentesis and closed chest cavity drainage were performed immediately. The initial pericardial drainage, which was bloody in appearance, gradually changed to a pale-yellow fluid. The patient continued to present with a temperature and remained under active anti-infection treatment. With repeated drainage procedures, it was observed that the volume of fluid obtained from the closed chest cavity exhibited an increasing trend. The cytological and tumor marker analysis of the idiopathic effusion specimens detected no abnormalities. Metagenomic next-generation sequencing (mNGS) of the pericardial drainage fluid was performed to identify the infectious pathogen. No pathogen was detected in the specimens, but the copy number variation (CNV) found in multiple chromosomes was highly suggestive of cancer development and progression. Lung imaging revealed no mediastinal lesions or tumors. The fluid from a subsequent closed chest drainage procedure was evaluated by mNGS for diagnostic purposes, and multiple CNVs were again noted, with similar results to those from the pericardial effusion. To determine the tumor type, immunophenotyping of the fluid was performed using flow cytometry and a diagnosis of T-LBL was confirmed. The patient was subsequently transferred to the hematology department for chemotherapy. The present case indicates that mNGS can not only differentiate between infections and tumors but also rapidly determine disease etiology.}, } @article {pmid37274359, year = {2023}, author = {Jin, Y and Hu, S and Feng, J and Ni, J}, title = {Clinical Value of Metagenomic Next-Generation Sequencing Using Spinal Tissue in the Rapid Diagnosis of Spinal Tuberculosis.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {3305-3313}, pmid = {37274359}, issn = {1178-6973}, abstract = {PURPOSE: To evaluate the accuracy of metagenomic next-generation sequencing (mNGS) for rapid diagnosis of spinal tuberculosis using spinal tissue specimens.

METHODS: Medical data regarding suspected spinal tuberculosis were retrospectively analyzed. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and area under the curve (AUC) of mNGS were calculated to determine its diagnostic efficacy, and these values were compared with culture and composite reference standard (CRS).

RESULTS: Two hundred and three cases of spinal tuberculosis were included for analysis. The sensitivity, specificity, PPV, NPV, and AUC of mNGS compared with culture were all very good. When CRS was used for the comparison, the sensitivity of mNGS and culture were 71.2% and 73.0%; the specificity and PPV were 100% in all cases; the NPV were 74.2% and 75.4%; the AUCs were all 0.86. The sensitivity and NPV of culture were slightly higher than that of mNGS; however, the diagnostic efficacy of mNGS and culture was consistent (P > 0.05).

CONCLUSION: Spinal tissue specimens for mNGS testing had very good accuracy for diagnosing spinal tuberculosis.}, } @article {pmid37274036, year = {2023}, author = {Zhang, YK and Guan, Y and Zhao, J and Wang, LF}, title = {Diagnosis of tuberculous uveitis by the macrogenome of intraocular fluid: A case report and review of the literature.}, journal = {World journal of clinical cases}, volume = {11}, number = {14}, pages = {3248-3255}, pmid = {37274036}, issn = {2307-8960}, abstract = {BACKGROUND: Tuberculous uveitis caused by tuberculosis infection factors is common, but tuberculous uveitis caused by Mycobacterium tuberculosis found in the intraocular fluid is rare. This report describes the use of intraocular fluid in the diagnosis of tuberculous uveitis in a patient and reviews the relevant literature.

CASE SUMMARY: A 24-year-old woman who was 31-wk pregnant visited Hebei Chest Hospital due to intermittent chest pain, fever, and decreased vision for 3 mo. The hydrothorax test suggested "tuberculous pleurisy", and yellow effusion was extracted from the chest tube twice resulting in a total volume of approximately 800 mL. The patient chose to continue the pregnancy without treatment, and was hospitalized again due to high fever. Following 2 mo of anti-tuberculosis treatment, a healthy boy was delivered by cesarean section. Tuberculous uveitis was diagnosed using tuberculosis Xpert, and intraocular infection was detected by second-generation gene sequencing. Following systemic treatment, the patient gradually improved, and the corrected visual acuity of the left eye gradually increased from 0.08 to 1.0.

CONCLUSION: The etiology of uveitis is complex, and it is necessary to assess the patient's general condition and apply molecular biology methods to determine the pathogenesis and guide precise treatment, to improve clinicians' awareness and standardize treatment of the disease.}, } @article {pmid37274035, year = {2023}, author = {Guo, XZ and Gong, LH and Wang, WX and Yang, DS and Zhang, BH and Zhou, ZT and Yu, XH}, title = {Chronic pulmonary mucormycosis caused by rhizopus microsporus mimics lung carcinoma in an immunocompetent adult: A case report.}, journal = {World journal of clinical cases}, volume = {11}, number = {14}, pages = {3295-3303}, pmid = {37274035}, issn = {2307-8960}, abstract = {BACKGROUND: Pulmonary mucormycosis is a rare but life-threatening invasive fungal infection that mostly affects immunocompromised patients. This disease usually develops acutely and progresses rapidly, often leading to a poor clinical prognosis. Chronic pulmonary mucormycosis is highly unusual in immunocompetent patients.

CASE SUMMARY: A 43-year-old man, who was a house improvement worker with a long history of occupational dust exposure, presented with an irritating cough that had lasted for two months. The patient was previously in good health, without dysglycemia or any known immunodeficiencies. Chest computed tomography revealed a mass in the left lower lobe, measuring approximately 6 cm in diameter, which was suspected to be primary lung carcinoma complicated with obstructive pneumonia. Thoracoscopic-assisted left lower lobectomy was performed, and metagenomic next-generation sequencing detection, along with special pathological staining of surgical specimens, suggested Rhizopus microsporus infection. Postoperatively, the patient's respiratory symptoms were relieved, and no signs of recurrence were found during the six-month follow-up.

CONCLUSION: This article reports a rare case of chronic pulmonary mucormycosis caused by Rhizopus microsporus in a middle-aged male without dysglycemia or immunodeficiency. The patient's surgical outcome was excellent, reaffirming that surgery remains the cornerstone of pulmonary mucormycosis treatment.}, } @article {pmid37273853, year = {2023}, author = {Mu, C and Zhao, Q and Zhao, Q and Yang, L and Pang, X and Liu, T and Li, X and Wang, B and Fung, SY and Cao, H}, title = {Multi-omics in Crohn's disease: New insights from inside.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {3054-3072}, pmid = {37273853}, issn = {2001-0370}, abstract = {Crohn's disease (CD) is an inflammatory bowel disease (IBD) with complex clinical manifestations such as chronic diarrhea, weight loss and hematochezia. Despite the increasing incidence worldwide, cure of CD remains extremely difficult. The rapid development of high-throughput sequencing technology with integrated-omics analyses in recent years has provided a new means for exploring the pathogenesis, mining the biomarkers and designing targeted personalized therapeutics of CD. Host genomics and epigenomics unveil heredity-related mechanisms of susceptible individuals, while microbiome and metabolomics map host-microbe interactions in CD patients. Proteomics shows great potential in searching for promising biomarkers. Nonetheless, single omics technology cannot holistically connect the mechanisms with heterogeneity of pathological behavior in CD. The rise of multi-omics analysis integrates genetic/epigenetic profiles with protein/microbial metabolite functionality, providing new hope for comprehensive and in-depth exploration of CD. Herein, we emphasized the different omics features and applications of CD and discussed the current research and limitations of multi-omics in CD. This review will update and deepen our understanding of CD from integration of broad omics spectra and will provide new evidence for targeted individualized therapeutics.}, } @article {pmid37273228, year = {2023}, author = {Liu, F and Li, R and Zhong, Y and Liu, X and Deng, W and Huang, X and Price, M and Li, J}, title = {Age-related alterations in metabolome and microbiome provide insights in dietary transition in giant pandas.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0025223}, pmid = {37273228}, issn = {2379-5077}, support = {KLSFGAGP2020.006//National Forestry and Grassland Administration (NFGA)/ ; }, mesh = {Animals ; *Ursidae/genetics ; RNA, Ribosomal, 16S/genetics ; Chromatography, Liquid ; Tandem Mass Spectrometry ; *Microbiota ; *Carnivora/genetics ; Metabolome ; Diet ; Bacteria/genetics ; Cellulose/metabolism ; }, abstract = {We conducted UPLC-MS-based metabolomics, 16S rRNA, and metagenome sequencing on the fecal samples of 44 captive giant pandas (Ailuropoda melanoleuca) from four age groups (i.e., Cub, Young, Adult, and Old) to comprehensively understand age-related changes in the metabolism and gut microbiota of giant pandas. We characterized the metabolite profiles of giant pandas based on 1,376 identified metabolites, with 152 significantly differential metabolites (SDMs) found across the age groups. We found that the metabolites and the composition/function of the gut microbiota changed in response to the transition from a milk-dominant diet in panda cubs to a bamboo-specific diet in young and adult pandas. Lipid metabolites such as choline and hippuric acid were enriched in the Cub group, and many plant secondary metabolites were significantly higher in the Young and Adult groups, while oxidative stress and inflammatory related metabolites were only found in the Old group. However, there was a decrease in the α-diversity of gut microbiota in adult and old pandas, who exclusively consume bamboo. The abundance of bacteria related to the digestion of cellulose-rich food, such as Firmicutes, Streptococcus, and Clostridium, significantly increased from the Cub to the Adult group, while the abundance of beneficial bacteria such as Faecalibacterium, Sarcina, and Blautia significantly decreased. Notably, several potential pathogenic bacteria had relatively high abundances, especially in the Young group. Metagenomic analysis identified 277 CAZyme genes including cellulose degrading genes, and seven of the CAZymes had abundances that significantly differed between age groups. We also identified 237 antibiotic resistance genes (ARGs) whose number and diversity increased with age. We also found a significant positive correlation between the abundance of bile acids and gut bacteria, especially Lactobacillus and Bifidobacterium. Our results from metabolome, 16S rRNA, and metagenome data highlight the important role of the gut microbiota-bile acid axis in the regulation of age-related metabolism and provide new insights into the lipid metabolism of giant pandas. IMPORTANCE The giant panda is a member of the order Carnivora but is entirely herbivorous. The giant panda's specialized diet and related metabolic mechanisms have not been fully understood. It is therefore crucial to investigate the dynamic changes in metabolites as giant pandas grow and physiologically adapt to their herbivorous diet. This study conducted UPLC-MS-based metabolomics 16S rRNA, and metagenome sequencing on the fecal samples of captive giant pandas from four age groups. We found that metabolites and the composition/function of gut microbiota changed in response to the transition from a milk-dominant diet in cubs to a bamboo-specific diet in young and adult pandas. The metabolome, 16S rRNA, and metagenome results highlight that the gut microbiota-bile acid axis has an important role in the regulation of age-related metabolism, and our study provides new insights into the lipid metabolism of giant pandas.}, } @article {pmid37272920, year = {2023}, author = {McCallum, GE and Rossiter, AE and Quraishi, MN and Iqbal, TH and Kuehne, SA and van Schaik, W}, title = {Noise reduction strategies in metagenomic chromosome confirmation capture to link antibiotic resistance genes to microbial hosts.}, journal = {Microbial genomics}, volume = {9}, number = {6}, pages = {}, pmid = {37272920}, issn = {2057-5858}, support = {MR/N013913/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Phylogeny ; *Genes, Bacterial ; Bacteria ; Drug Resistance, Microbial/genetics ; Chromosomes ; }, abstract = {The gut microbiota is a reservoir for antimicrobial resistance genes (ARGs). With current sequencing methods, it is difficult to assign ARGs to their microbial hosts, particularly if these ARGs are located on plasmids. Metagenomic chromosome conformation capture approaches (meta3C and Hi-C) have recently been developed to link bacterial genes to phylogenetic markers, thus potentially allowing the assignment of ARGs to their hosts on a microbiome-wide scale. Here, we generated a meta3C dataset of a human stool sample and used previously published meta3C and Hi-C datasets to investigate bacterial hosts of ARGs in the human gut microbiome. Sequence reads mapping to repetitive elements were found to cause problematic noise in, and may importantly skew interpretation of, meta3C and Hi-C data. We provide a strategy to improve the signal-to-noise ratio by discarding reads that map to insertion sequence elements and to the end of contigs. We also show the importance of using spike-in controls to quantify whether the cross-linking step in meta3C and Hi-C protocols has been successful. After filtering to remove artefactual links, 87 ARGs were assigned to their bacterial hosts across all datasets, including 27 ARGs in the meta3C dataset we generated. We show that commensal gut bacteria are an important reservoir for ARGs, with genes coding for aminoglycoside and tetracycline resistance being widespread in anaerobic commensals of the human gut.}, } @article {pmid37272861, year = {2023}, author = {Alexander, LM and Aliaga Goltsman, DS and Liu, J and Lin, JL and Temoche-Diaz, MM and Laperriere, SM and Neerincx, A and Bednarski, C and Knyphausen, P and Cohnen, A and Albers, J and Gonzalez-Osorio, L and Fregoso Ocampo, R and Oki, J and Devoto, AE and Castelle, CJ and Lamothe, RC and Cost, GJ and Butterfield, CN and Thomas, BC and Brown, CT}, title = {Novel and Engineered Type II CRISPR Systems from Uncultivated Microbes with Broad Genome Editing Capability.}, journal = {The CRISPR journal}, volume = {6}, number = {3}, pages = {261-277}, pmid = {37272861}, issn = {2573-1602}, support = {S10 OD018174/OD/NIH HHS/United States ; }, mesh = {Animals ; *Gene Editing ; *CRISPR-Cas Systems/genetics ; CRISPR-Associated Protein 9/genetics/metabolism ; Biotechnology ; RNA, Guide, CRISPR-Cas Systems ; Mammals/genetics/metabolism ; }, abstract = {Type II Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 nucleases have been extensively used in biotechnology and therapeutics. However, many applications are not possible owing to the size, targetability, and potential off-target effects associated with currently known systems. In this study, we identified thousands of CRISPR type II effectors by mining an extensive, genome-resolved metagenomics database encompassing hundreds of thousands of microbial genomes. We developed a high-throughput pipeline that enabled us to predict tracrRNA sequences, to design single guide RNAs, and to demonstrate nuclease activity in vitro for 41 newly described subgroups. Active systems represent an extensive diversity of protein sequences and guide RNA structures and require diverse protospacer adjacent motifs (PAMs) that collectively expand the known targeting capability of current systems. Several nucleases showed activity levels comparable to or significantly higher than SpCas9, despite being smaller in size. In addition, top systems exhibited low levels of off-target editing in mammalian cells, and PAM-interacting domain engineered chimeras further expanded their targetability. These newly discovered nucleases are attractive enzymes for translation into many applications, including therapeutics.}, } @article {pmid37272818, year = {2023}, author = {Wang, H and Ren, L and Liang, Y and Zheng, K and Guo, R and Liu, Y and Wang, Z and Han, Y and Zhang, X and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M}, title = {Psychrobacter Phage Encoding an Antibiotics Resistance Gene Represents a Novel Caudoviral Family.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0533522}, pmid = {37272818}, issn = {2165-0497}, mesh = {*Bacteriophages/genetics ; *Psychrobacter/genetics ; Phylogeny ; Phosphoadenosine Phosphosulfate ; DNA, Viral/genetics ; Genome, Viral ; Escherichia coli/genetics ; Open Reading Frames ; }, abstract = {Psychrobacter is an important bacterial genus that is widespread in Antarctic and marine environments. However, to date, only two complete Psychrobacter phage sequences have been deposited in the NCBI database. Here, the novel Psychrobacter phage vB_PmaS_Y8A, infecting Psychrobacter HM08A, was isolated from sewage in the Qingdao area, China. The morphology of vB_PmaS_Y8A was characterized by transmission electron microscopy, revealing an icosahedral head and long tail. The genomic sequence of vB_PmaS_Y8A is linear, double-stranded DNA with a length of 40,226 bp and 44.1% G+C content, and encodes 69 putative open reading frames. Two auxiliary metabolic genes (AMGs) were identified, encoding phosphoadenosine phosphosulfate reductase and MarR protein. The first AMG uses thioredoxin as an electron donor for the reduction of phosphoadenosine phosphosulfate to phosphoadenosine phosphate. MarR regulates multiple antibiotic resistance mechanisms in Escherichia coli and is rarely found in viruses. No tRNA genes were identified and no lysogeny-related feature genes were detected. However, many similar open reading frames (ORFs) were found in the host genome, which may indicate that Y8A also has a lysogenic stage. Phylogenetic analysis based on the amino acid sequences of whole genomes and comparative genomic analysis indicate that vB_PmaS_Y8A contains a novel genomic architecture similar only to that of Psychrobacter phage pOW20-A, although at a low similarity. vB_PmaS_Y8A represents a new family-level virus cluster with 22 metagenomic assembled viral genomes, here named Minviridae. IMPORTANCE Although Psychrobacter is a well-known and important bacterial genus that is widespread in Antarctic and marine environments, genetic characterization of its phages is still rare. This study describes a novel Psychrobacter phage containing an uncharacterized antibiotic resistance gene and representing a new virus family, Minviridae. The characterization provided here will bolster current understanding of genomes, diversity, evolution, and phage-host interactions in Psychrobacter populations.}, } @article {pmid37272792, year = {2023}, author = {Wu, X and Gushgari-Doyle, S and Lui, LM and Hendrickson, AJ and Liu, Y and Jagadamma, S and Nielsen, TN and Justice, NB and Simmons, T and Hess, NJ and Joyner, DC and Hazen, TC and Arkin, AP and Chakraborty, R}, title = {Distinct Depth-Discrete Profiles of Microbial Communities and Geochemical Insights in the Subsurface Critical Zone.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {6}, pages = {e0050023}, pmid = {37272792}, issn = {1098-5336}, mesh = {*Bacteria/metabolism ; *Microbiota ; Carbon/metabolism ; Tennessee ; }, abstract = {Microbial assembly and metabolic potential in the subsurface critical zone (SCZ) are substantially impacted by subsurface geochemistry and hydrogeology, selecting for microbes distinct from those in surficial soils. In this study, we integrated metagenomics and geochemistry to elucidate how microbial composition and metabolic potential are shaped and impacted by vertical variations in geochemistry and hydrogeology in terrestrial subsurface sediment. A sediment core from an uncontaminated, pristine well at Oak Ridge Field Research Center in Oak Ridge, Tennessee, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone, was used in this study. Our results showed that subsurface microbes were highly localized and that communities were rarely interconnected. Microbial community composition as well as metabolic potential in carbon and nitrogen cycling varied even over short vertical distances. Further analyses indicated a strong depth-related covariation of community composition with a subset of 12 environmental variables. An analysis of dissolved organic carbon (DOC) quality via ultrahigh resolution mass spectrometry suggested that the SCZ was generally a low-carbon environment, with the relative portion of labile DOC decreasing and that of recalcitrant DOC increasing along the depth, selecting microbes from copiotrophs to oligotrophs and also impacting the microbial metabolic potential in the carbon cycle. Our study demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolism in the SCZ. IMPORTANCE In this study, we explored the links between geochemical parameters, microbial community structure and metabolic potential across the depth of sediment, including the shallow subsurface, vadose zone, capillary fringe, and saturated zone. Our results revealed that microbes in the terrestrial subsurface can be highly localized, with communities rarely being interconnected along the depth. Overall, our research demonstrates that sediment geochemistry and hydrogeology are vital in the selection of distinct microbial populations and metabolic potential in different depths of subsurface terrestrial sediment. Such studies correlating microbial community analyses and geochemistry analyses, including high resolution mass spectrometry analyses of natural organic carbon, will further the fundamental understanding of microbial ecology and biogeochemistry in subsurface terrestrial ecosystems and will benefit the future development of predictive models on nutrient turnover in these environments.}, } @article {pmid37272726, year = {2023}, author = {Abe, R and Akeda, Y and Sugawara, Y and Matsumoto, Y and Motooka, D and Iida, T and Hamada, S}, title = {Carbapenem triggers dissemination of chromosomally integrated carbapenemase genes via conjugative plasmids in Escherichia coli.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0127522}, pmid = {37272726}, issn = {2379-5077}, support = {//Japan Agency for Medical Research and Development/ ; }, mesh = {*Carbapenems/pharmacology ; *Escherichia coli/genetics ; Meropenem/pharmacology ; Anti-Bacterial Agents/pharmacology ; Plasmids/genetics ; }, abstract = {Epidemiological surveys have shown that carbapenem resistance is mainly transmitted across species by carbapenemase genes located on conjugative plasmids. As chromosomal integration of carbapenemase genes has rarely been identified, only a few studies have investigated their advantages to the carbapenem-resistant bacterial community. Here, we confirmed the increased stability of blaIMP-6 on a chromosome-integrated plasmid in an Escherichia coli isolate compared with that on original plasmids in the absence of antibiotic pressure. Although plasmids carrying carbapenemase genes are supposedly lost in successive generations, we found that the complete plasmid backbone was retained in bacterial cells even after the occasional loss of their antibiotic-resistance cassettes. This backbone structure has been observed worldwide to carry various antimicrobial resistance genes. Although the chromosomally integrated plasmid carrying blaIMP-6 could not be transmitted by conjugation, we found that meropenem treatment for 1 wk allowed the plasmid to be released from the chromosome and spread among E. coli strains that were susceptible to meropenem. The copy number of blaIMP-6 on the plasmid was amplified eight times, resulting in enhanced resistance. Although the carbapenemase producers that carry chromosomal carbapenemase genes comprised of small subpopulations, they functioned as stable, long-term reservoirs of carbapenem resistance that could be disseminated via plasmids with amplified resistance upon meropenem stimulation. Although plasmids occasionally lose their resistance cassettes as a scaffold for the acquisition of another resistance gene, chromosomal integration may contribute to the effective sharing of carbapenem resistance within a population, complicating the development of a strategy to avoid the dissemination of antimicrobial resistance. IMPORTANCE Although carbapenem antibiotics are the last resort for combating multidrug-resistant organisms, global dissemination of carbapenem-resistant Enterobacteriaceae (CRE) threatens public health. Carbapenemases, which are enzymes responsible for carbapenem resistance, are mainly encoded by genes on plasmids that can be transmitted across bacterial species. Owing to the rarity of chromosomally encoded carbapenemase genes, studies investigating their properties in bacterial communities are lacking. In our study, we revealed the stability of carbapenemase genes on chromosomes compared with those on plasmids, which can be lost through the loss of antimicrobial resistance cassettes despite robust retention of plasmid backbones. Following exposure to meropenem, the carbapenemase gene integrated into the chromosome was released as a plasmid, restarting the dissemination of enhanced carbapenem resistance through amplified copy numbers of carbapenemase genes. Chromosomally encoded carbapenemase genes may function as a reservoir of resistance genes within the bacterial community and challenge infection control against CRE dissemination.}, } @article {pmid37272717, year = {2023}, author = {Singh, HW and Creamer, KE and Chase, AB and Klau, LJ and Podell, S and Jensen, PR}, title = {Metagenomic data reveals type I polyketide synthase distributions across biomes.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0001223}, pmid = {37272717}, issn = {2379-5077}, support = {R01 GM085770/GM/NIGMS NIH HHS/United States ; }, mesh = {*Polyketide Synthases/genetics ; Metagenome/genetics ; Phylogeny ; *Polyketides ; Enediynes ; }, abstract = {Microbial polyketide synthase (PKS) genes encode the biosynthesis of many biomedically or otherwise commercially important natural products. Despite extensive discovery efforts, metagenomic analyses suggest that only a small fraction of nature's polyketide biosynthetic potential has been realized. Much of this potential originates from type I PKSs (T1PKSs), which can be further delineated based on their domain organization and the structural features of the compounds they encode. Notably, phylogenetic relationships among ketosynthase (KS) domains provide an effective method to classify the larger and more complex T1PKS genes in which they occur. Increased access to large metagenomic data sets from diverse habitats provides opportunities to assess T1PKS biosynthetic diversity and distributions through their smaller and more tractable KS domain sequences. Here, we used the web tool NaPDoS2 to detect and classify over 35,000 type I KS domains from 137 metagenomic data sets reported from eight diverse, globally distributed biomes. We found biome-specific separation with soils enriched in KSs from modular cis-acetyltransferase (AT) and hybrid cis-AT KSs relative to other biomes and marine sediments enriched in KSs associated with polyunsaturated fatty acid and enediyne biosynthesis. We linked the phylum Actinobacteria to soil-derived enediyne and cis-AT KSs while marine-derived KSs associated with enediyne and monomodular PKSs were linked to phyla from which the compounds produced by these biosynthetic enzymes have not been reported. These KSs were phylogenetically distinct from those associated with experimentally characterized PKSs suggesting they may be associated with novel structures or enzyme functions. Finally, we employed our metagenome-extracted KS domains to evaluate the PCR primers commonly used to amplify type I KSs and identified modifications that could increase the KS sequence diversity recovered from amplicon libraries. IMPORTANCE Polyketides are a crucial source of medicines, agrichemicals, and other commercial products. Advances in our understanding of polyketide biosynthesis, coupled with the increased availability of metagenomic sequence data, provide new opportunities to assess polyketide biosynthetic potential across biomes. Here, we used the web tool NaPDoS2 to assess type I polyketide synthase (PKS) diversity and distributions by detecting and classifying ketosynthase (KS) domains across 137 metagenomes. We show that biomes are differentially enriched in type I KS domains, providing a roadmap for future biodiscovery strategies. Furthermore, KS phylogenies reveal biome-specific clades that do not include biochemically characterized PKSs, highlighting the biosynthetic potential of poorly explored environments. The large metagenome-derived KS data set allowed us to identify regions of commonly used type I KS PCR primers that could be modified to capture a larger extent of environmental KS diversity. These results facilitate both the search for novel polyketides and our understanding of the biogeographical distribution of PKSs across Earth's major biomes.}, } @article {pmid37272702, year = {2023}, author = {Lu, J and Wang, H and Wang, C and Zhao, M and Hou, R and Shen, Q and Yang, S and Ji, L and Liu, Y and Wang, X and Liu, S and Shan, T and Zhang, W}, title = {Gut phageome of the giant panda (Ailuropoda melanoleuca) reveals greater diversity than relative species.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0016123}, pmid = {37272702}, issn = {2379-5077}, support = {2022YFC2603801//MOST | National Key Research and Development Program of China (NKPs)/ ; 2020CPB-C11 and 2021CPB-B11//Chendu Research Base of Giant Panda Breeding/ ; no. 20210467//Donghai People's Hospital-School of Medicine UJS Joint Laboratory Foundation/ ; BE2017693//Jiangsu Provincial Key Research and Development Program (Key Technologies R&D Program of Jiangsu Province)/ ; HUDF2020105//The Youth Doctoral Scientific Research Foundation of Harbin University/ ; }, mesh = {Animals ; *Ursidae/microbiology ; Virome ; Phylogeny ; Metagenome ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages ; }, abstract = {The gut flora is a treasure house of diverse bacteriophages maintaining a harmonious and coexistent relationship with their hosts. The giant panda (Ailuropoda melanoleuca), as a vulnerable endemic species in China, has existed for millions of years and is regarded as a flagship species for biodiversity conservation. And yet, limited studies have analyzed the phage communities in the gut of giant pandas. Using viral metagenomic analysis, the phageomes of giant pandas and other relative species were investigated. Our study explored and compared the composition of phage communities from different animal sources. Giant pandas possessed more diverse and abundant phage communities in the gut compared with other relevant animals. Phylogenetic analyses based on the phage terminase large subunit (TerL) showed that the Caudovirales phages in giant pandas also presented highly genetic diversity. Our study revealed the diversity of phage communities in giant pandas and other relative species, contributing to the health maintenance of giant pandas and laying the groundwork for molecular evolution research of bacteriophages in mammals. IMPORTANCE Gut phageome plays an important role in shaping gut microbiomes by direct interactions with bacteria or indirect influences on the host immune system, potentially regulating host health and disease status. The giant panda (Ailuropoda melanoleuca) is a vulnerable and umbrella species for biodiversity conservation. Our work explored and compared the gut phageome of giant pandas and relative species, contributing to the health maintenance of giant pandas.}, } @article {pmid37272100, year = {2023}, author = {Luo, W and He, Y and Xu, J and Zhang, S and Li, C and Lv, J and Shen, Y and Ou, Z and Dong, H}, title = {Comparison of Third-Generation Sequencing Technology and Traditional Microbiological Detection in Pathogen Diagnosis of Lower Respiratory Tract Infection.}, journal = {Discovery medicine}, volume = {35}, number = {176}, pages = {332-342}, doi = {10.24976/Discov.Med.202335176.34}, pmid = {37272100}, issn = {1944-7930}, mesh = {Humans ; *Tuberculosis, Pulmonary/diagnosis/drug therapy/microbiology ; Retrospective Studies ; *Tuberculosis/diagnosis ; *Mycobacterium tuberculosis/genetics ; *Respiratory Tract Infections/diagnosis ; Sensitivity and Specificity ; Fungi/genetics ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {BACKGROUND: It is common to obtain a low detection rate and unsatisfactory detection results in complex infection or rare pathogen detection. This retrospective study aimed to illustrate the application value and prospect of the third-generation sequencing technology in lower respiratory tract infection disease.

METHODS: This study recruited 70 patients with lower respiratory tract infection (LRTI). Pathogen detection of bronchoalveolar lavage fluid (BALF) from all patients was performed using nanopore metagenomic sequencing technology and traditional culture. BALF culture combined with quantitiative PCR (qPCR) was used as a reference standard to analyze the sensitivity and specificity of nanopore sequencing technology. The current study also collected the examination results of enrolled samples using technical methods sputum culture, tuberculosis DNA (TB-DNA), and Xpert MTB/RIF and analyzed the detection efficiency of nanopore sequencing for Mycobacterium tuberculosis.

RESULTS: The positive rates of pathogens in 70 BALF samples detected by conventional culture and nanopore sequencing were 25.71% and 84.29%, respectively. Among the 59 positive BALF cases using nanopore sequencing, a total of 31 pathogens were identified, of which the proportions of bacteria, fungi, viruses, and other pathogens were 50%, 17%, 32%, and 1%, respectively. Using the results combined with culture and qPCR detection methods as the standard, the pathogen detection of BALF using nanopore sequencing had a sensitivity of 70% and a specificity of 91.7%. Additionally, the positive rate of the detection of M. tuberculosis using nanopore sequencing was 33.3% (6/18). The clinical medication plans of 74.3% (52/70) of the patients were referred to the nanopore sequencing results, of which 31 cases changed their treatment strategy, 21 supported the previous treatment plans, and 90% (47/52) of the patients finally had clinical improvement.

CONCLUSIONS: BALF detection using nanopore sequencing technology improves the process of detecting pathogens in patients with LRTI, especially for M. tuberculosis, fungi, and viruses, by reducing the report time from three days to six hours. The clinical application prospect of nanopore sequencing technology is promising in the pathogen diagnosis of LRTI.}, } @article {pmid37271802, year = {2023}, author = {Rolon, ML and Tan, X and Chung, T and Gonzalez-Escalona, N and Chen, Y and Macarisin, D and LaBorde, LF and Kovac, J}, title = {The composition of environmental microbiota in three tree fruit packing facilities changed over seasons and contained taxa indicative of L. monocytogenes contamination.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {128}, pmid = {37271802}, issn = {2049-2618}, mesh = {Food Microbiology ; Fruit ; Seasons ; Longitudinal Studies ; Cross-Sectional Studies ; *Listeria monocytogenes/genetics ; *Microbiota/genetics ; Food Contamination/analysis ; }, abstract = {BACKGROUND: Listeria monocytogenes can survive in cold and wet environments, such as tree fruit packing facilities and it has been implicated in outbreaks and recalls of tree fruit products. However, little is known about microbiota that co-occurs with L. monocytogenes and its stability over seasons in tree fruit packing environments. In this 2-year longitudinal study, we aimed to characterize spatial and seasonal changes in microbiota composition and identify taxa indicative of L. monocytogenes contamination in wet processing areas of three tree fruit packing facilities (F1, F2, F3).

METHODS: A total of 189 samples were collected during two apple packing seasons from floors under the washing, drying, and waxing areas. The presence of L. monocytogenes was determined using a standard culturing method, and environmental microbiota was characterized using amplicon sequencing. PERMANOVA was used to compare microbiota composition among facilities over two seasons, and abundance-occupancy analysis was used to identify shared and temporal core microbiota. Differential abundance analysis and random forest were applied to detect taxa indicative of L. monocytogenes contamination. Lastly, three L. monocytogenes-positive samples were sequenced using shotgun metagenomics with Nanopore MinION, as a proof-of-concept for direct detection of L. monocytogenes' DNA in environmental samples.

RESULTS: The occurrence of L. monocytogenes significantly increased from 28% in year 1 to 46% in year 2 in F1, and from 41% in year 1 to 92% in year 2 in F3, while all samples collected from F2 were L. monocytogenes-positive in both years. Samples collected from three facilities had a significantly different microbiota composition in both years, but the composition of each facility changed over years. A subset of bacterial taxa including Pseudomonas, Stenotrophomonas, and Microbacterium, and fungal taxa, including Yarrowia, Kurtzmaniella, Cystobasidium, Paraphoma, and Cutaneotrichosporon, were identified as potential indicators of L. monocytogenes within the monitored environments. Lastly, the DNA of L. monocytogenes was detected through direct Nanopore sequencing of metagenomic DNA extracted from environmental samples.

CONCLUSIONS: This study demonstrated that a cross-sectional sampling strategy may not accurately reflect the representative microbiota of food processing facilities. Our findings also suggest that specific microorganisms are indicative of L. monocytogenes, warranting further investigation of their role in the survival and persistence of L. monocytogenes. Video Abstract.}, } @article {pmid37271450, year = {2023}, author = {Zhou, Y and Xu, X and Liu, Y and Wang, A and Luo, Y and Liu, X and Wang, X and Li, W and Yao, X}, title = {Heterogeneous Regulation of StaphylococcusAureus by Different StaphylococcusEpidermidisagr Types in Atopic Dermatitis.}, journal = {The Journal of investigative dermatology}, volume = {143}, number = {12}, pages = {2484-2493.e11}, doi = {10.1016/j.jid.2023.05.014}, pmid = {37271450}, issn = {1523-1747}, mesh = {Animals ; Mice ; Humans ; Child ; *Dermatitis, Atopic/genetics ; Staphylococcus aureus ; Skin ; Epidermis ; Staphylococcus epidermidis/physiology ; Inflammation ; *Staphylococcal Infections ; }, abstract = {The skin commensal Staphylococcus epidermidis exhibits a protective role in skin inflammation; however, the exact functions of S. epidermidis and their mechanisms in atopic dermatitis (AD) are not fully understood. Here, whole-genome sequencing was conducted on strains of S. epidermidis isolated from pediatric patients with AD and revealed significant strain-level heterogeneity in functional genes. Specific sequence analysis of S. epidermidis identified four types of accessory gene regulator (agr) according to locus variations in the agr operon, which was consistent with the metagenomic data of the contextual microbiota. The number of S. epidermidisagr type I was slightly decreased among AD isolates, whereas agr type IV was hardly detected in AD isolates. Functional experiments showed that strains of S. epidermidisagr types I and IV, but not types II and III, inhibited the expression of S. aureusagr-mediated virulence factors in vitro, suppressed S. aureus epidermal colonization, and attenuated skin inflammation in a mouse model. The delineation of genome signatures of S. epidermidis at the strain level in AD and the quorum-sensing interference between S. epidermidisagr type IV and S. aureus provide a foundation for the modulation of the skin microbiota and the treatment of AD.}, } @article {pmid37271194, year = {2024}, author = {Feng, S and Rao, G and Wei, X and Fu, R and Hou, M and Song, Y and Xu, C and Han, P and Gong, B and Chen, X and Wang, Y and Dong, X and Jiang, Z and Wang, J}, title = {Clinical metagenomic sequencing of plasma microbial cell-free DNA for febrile neutropenia in patients with acute leukaemia.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {30}, number = {1}, pages = {107-113}, doi = {10.1016/j.cmi.2023.05.034}, pmid = {37271194}, issn = {1469-0691}, mesh = {Adult ; Humans ; Prospective Studies ; *Leukemia, Myeloid, Acute/complications ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents ; Metagenomics ; *Febrile Neutropenia/diagnosis ; *Cell-Free Nucleic Acids ; Sensitivity and Specificity ; }, abstract = {OBJECTIVES: To evaluate the diagnostic performance and clinical impact of metagenomic next-generation sequencing (mNGS) of plasma microbial cell-free DNA (mcfDNA) in febrile neutropenia (FN).

METHODS: In a 1-year, multicentre, prospective study, we enrolled 442 adult patients with acute leukaemia with FN and investigated the usefulness of mNGS of plasma mcfDNA for identification of infectious pathogens. The results of mNGS were available to clinicians in real time. The performance of mNGS testing was evaluated in comparison with blood culture (BC) and a composite standard that incorporated standard microbiological testing and clinical adjudication.

RESULTS: In comparison with BC, the positive and negative agreements of mNGS were 81.91% (77 of 94) and 60.92% (212 of 348), respectively. By clinical adjudication, mNGS results were categorized by infectious diseases specialists as definite (n = 76), probable (n = 116), possible (n = 26), unlikely (n = 7), and false negative (n = 5). In 225 mNGS-positive cases, 81 patients (36%) underwent antimicrobials adjustment, resulting in positive impact on 79 patients and negative impact on two patients (antibiotics overuse). Further analysis indicated that mNGS was less affected by prior antibiotics exposure than BC.

DISCUSSION: Our results indicate that mNGS of plasma mcfDNA increased the detection of clinically significant pathogens and enabled early optimization of antimicrobial therapy in patients with acute leukaemia with FN.}, } @article {pmid37270585, year = {2023}, author = {Liu, S and Zeng, J and Yu, H and Wang, C and Yang, Y and Wang, J and He, Z and Yan, Q}, title = {Antimony efflux underpins phosphorus cycling and resistance of phosphate-solubilizing bacteria in mining soils.}, journal = {The ISME journal}, volume = {17}, number = {8}, pages = {1278-1289}, pmid = {37270585}, issn = {1751-7370}, mesh = {Antimony/analysis/chemistry ; Soil/chemistry ; Phosphates/analysis ; Phosphorus/analysis ; Phylogeny ; Environmental Monitoring ; *Soil Pollutants/analysis ; *Metals, Heavy/analysis ; Bacteria/genetics ; *Microbiota ; China ; Soil Microbiology ; }, abstract = {Microorganisms play crucial roles in phosphorus (P) turnover and P bioavailability increases in heavy metal-contaminated soils. However, microbially driven P-cycling processes and mechanisms of their resistance to heavy metal contaminants remain poorly understood. Here, we examined the possible survival strategies of P-cycling microorganisms in horizontal and vertical soil samples from the world's largest antimony (Sb) mining site, which is located in Xikuangshan, China. We found that total soil Sb and pH were the primary factors affecting bacterial community diversity, structure and P-cycling traits. Bacteria with the gcd gene, encoding an enzyme responsible for gluconic acid production, largely correlated with inorganic phosphate (Pi) solubilization and significantly enhanced soil P bioavailability. Among the 106 nearly complete bacterial metagenome-assembled genomes (MAGs) recovered, 60.4% carried the gcd gene. Pi transportation systems encoded by pit or pstSCAB were widely present in gcd-harboring bacteria, and 43.8% of the gcd-harboring bacteria also carried the acr3 gene encoding an Sb efflux pump. Phylogenetic and potential horizontal gene transfer (HGT) analyses of acr3 indicated that Sb efflux could be a dominant resistance mechanism, and two gcd-harboring MAGs appeared to acquire acr3 through HGT. The results indicated that Sb efflux could enhance P cycling and heavy metal resistance in Pi-solubilizing bacteria in mining soils. This study provides novel strategies for managing and remediating heavy metal-contaminated ecosystems.}, } @article {pmid37269993, year = {2023}, author = {Zhou, L and Dong, N and Fu, M and Yue, X and Jian, Y and Li, H and Russenberger, M and Zhuang, WQ}, title = {Dissimilatory sulfate reduction in an anaerobic biofilm reactor for tofu processing wastewater treatment: Bacterial community and their functional genes.}, journal = {The Science of the total environment}, volume = {892}, number = {}, pages = {164579}, doi = {10.1016/j.scitotenv.2023.164579}, pmid = {37269993}, issn = {1879-1026}, mesh = {Wastewater ; Anaerobiosis ; *Soy Foods ; Bioreactors/microbiology ; Bacteria/genetics/metabolism ; *Thiobacillus/metabolism ; Sulfates/metabolism ; Sulfides/metabolism ; Oxidation-Reduction ; }, abstract = {Dissimilatory sulfate reduction (DSR) is the key sulfur cycle that transforms sulfate to sulfide. This process leads to odour issues in wastewater treatment. However, few studies have focused on DSR during treating food processing wastewater with high sulfate. This study investigated DSR microbial population and functional genes in an anaerobic biofilm reactor (ABR) treating tofu processing wastewater. The tofu processing wastewater is a common food processing wastewater in Asia. The full-scale ABR was operated for over 120 days in a tofu and tofu-related products manufacturing factory. Mass balance calculations based on the reactor performance indicated that 79.6-85.1 % of the sulfate was transformed into sulfide irrelevant to dissolved oxygen supplementation. Metagenomic analysis revealed 21 metagenome-assembled genomes (MAGs) containing enzymes encoding DSR. The biofilm contained the complete functional genes of DSR pathway in the full-scale ABR, indicating that biofilm could process DSR independently. Comamonadaceae, Thiobacillus, Nitrosomonadales, Desulfatirhabdium butyrativorans, Desulfomonile tiedjei were the dominant DSR species in the ABR biofilm community. Dissolved oxygen supplementation directly inhibited DSR and mitigated HS[-] production. It was also found that Thiobacillus contained all the function genes encoding every necessary enzyme in DSR, and thus Thiobacillus distribution directly correlated to DSR and the ABR performance.}, } @article {pmid37269991, year = {2023}, author = {Peng, K and Liu, YX and Sun, X and Wang, Q and Du, P and Zhang, Y and Wang, M and Wang, Z and Li, R}, title = {Long-read metagenomic sequencing reveals that high-copy small plasmids shape the highly prevalent antibiotic resistance genes in animal fecal microbiome.}, journal = {The Science of the total environment}, volume = {893}, number = {}, pages = {164585}, doi = {10.1016/j.scitotenv.2023.164585}, pmid = {37269991}, issn = {1879-1026}, mesh = {Animals ; Female ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Genes, Bacterial ; Chickens/genetics ; *Microbiota ; Drug Resistance, Multiple, Bacterial ; Plasmids ; }, abstract = {The emergence and prevalence of animal-derived antibiotic resistance genes (ARGs) pose a great threat to public health globally. Long-read metagenomic sequencing is increasingly being used to decipher the fate of environmental ARGs. However, the investigations of the distribution, co-occurrence patterns, and host information of animal-derived environmental ARGs with long-read metagenomic sequencing have received little attention. To cover the gap, we employed a novel QitanTech nanopore long-read metagenomic sequencing method to perform a comprehensive and systematic investigation of the microbial communities and antibiotic resistance profiles, as well as to analyze the host information and genetic structures of ARGs in the feces of laying hens. Our results showed that highly abundant and diverse ARGs were detected in the feces of different ages of laying hens, indicating that feeding animal feces was an important reservoir for the enrichment and maintenance of ARGs. The distribution pattern of chromosomal ARGs was more strongly associated with fecal microbial communities than plasmid-mediated ARGs. Further long-read host tracking analysis revealed that ARGs from Proteobacteria are commonly located on plasmids, whereas in Firmicutes, they are usually carried by chromosomes. Co-occurrence analysis displayed that co-selection phenomena of different ARGs were common occurrences and highly active insertion sequences (ISs) could result in the serious prevalence of many ARGs. Notably, small high-copy plasmids played a significant role in the dissemination of several ARGs, such as floR and tet(L), which could disturb the compositions of fecal ARGs. Overall, our findings significantly expand our knowledge of the comprehensive landscape of feeding animal feces resistome, which is important for the prevention and management of multi-drug resistant bacteria in laying hens.}, } @article {pmid37269627, year = {2023}, author = {You, G and Wang, C and Wang, P and Chen, J and Gao, Y and Li, Y and Xu, Y}, title = {Long-term transformation of nanoscale zero-valent iron explains its biological effects in anaerobic digestion: From ferroptosis-like death to magnetite-enhanced direct electron transfer networks.}, journal = {Water research}, volume = {241}, number = {}, pages = {120115}, doi = {10.1016/j.watres.2023.120115}, pmid = {37269627}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Ferrosoferric Oxide ; Iron ; *Ferroptosis ; Electrons ; }, abstract = {Nanoscale zero-valent iron (nZVI) has been extensively used for environmental remediation and wastewater treatment. However, the biological effects of nZVI remain unclear, which is no doubt a result of the complexity of iron species and the dynamic succession of microbial community during nZVI aging. Here, the aging effects of nZVI on methanogenesis in anaerobic digestion (AD) were consecutively investigated, with an emphasis on deciphering the causal relationships between nZVI aging process and its biological effects. The addition of nZVI in AD led to ferroptosis-like death with hallmarks of iron-dependent lipid peroxidation and glutathione (GSH) depletion, which inhibited CH4 production during the first 12 days of exposure. With prolonged exposure time, a gradual recovery (12-21 days) and even better performance (21-27 days) in AD were observed. The recovery performance of AD was mainly attributed to nZVI-enhanced membrane rigidity via forming siderite and vivianite on the outer surface of cells, protecting anaerobes against nZVI-induced toxicity. At the end of 27-days exposure, the significantly increased amount of conductive magnetite simulated direct interspecies electron transfer among syntrophic partners, improving CH4 production. Metagenomic analysis further revealed that microbial cells gradually adapted to the aging of nZVI by upregulating functional genes related to chemotaxis, flagella, conductive pili and riboflavin biosynthesis, in which electron transfer networks likely thrived and the cooperative behaviors between consortium members were promoted. These results unveiled the significance of nZVI aging on its biological effects toward multiple microbial communities and provided fundamental insights into the long-term fates and risks of nZVI for in situ applications.}, } @article {pmid37269564, year = {2023}, author = {Zhang, M and Liu, J and Hu, N and Fang, Q and Zhang, D and Qiang, Z and Pan, X}, title = {Cascade capture, oxidization and inactivation for removing multi-species pollutants, antimicrobial resistance and pathogenicity from hospital wastewater.}, journal = {Journal of hazardous materials}, volume = {457}, number = {}, pages = {131730}, doi = {10.1016/j.jhazmat.2023.131730}, pmid = {37269564}, issn = {1873-3336}, mesh = {*Wastewater ; Virulence ; Anti-Bacterial Agents/pharmacology ; Ferric Compounds ; Drug Resistance, Bacterial/genetics ; *Ozone ; Hospitals ; }, abstract = {As reservoirs of pathogens, antimicrobial resistant microorganisms and a wide variety of pollutants, hospital wastewaters (HWWs) need to be effectively treated before discharge. This study employed the functionalized colloidal microbubble technology as one-step fast HWW treatment. Inorganic coagulant (monomeric Fe(III)-coagulant or polymeric Al(III)-coagulant) and ozone were used as surface-decorator and gaseous core modifier, respectively. The Fe(III)- or Al(III)-modified colloidal gas (or, ozone) microbubbles (Fe(III)-CCGMBs, Fe(III)-CCOMBs, Al(III)-CCGMBs and Al(III)-CCOMBs) were constructed. Within 3 min, CCOMBs decreased CODCr and fecal coliform concentration to the levels meeting the national discharge standard for medical organization. Regrowth of bacteria was inhibited and biodegradability of organics was increased after the simultaneous oxidation and cell-inactivation process. The metagenomics analysis further reveals that Al(III)-CCOMBs performed best in capturing the virulence genes, antibiotic resistance genes and their potential hosts. The horizontal transfer of those harmful genes could be effectively hampered thanks to the removal of mobile genetic elements. Interestingly, the virulence factors of adherence, micronutrient uptake/acquisition and phase invasion could facilitate the interface-dominated capture. Featured as cascade processes of capture, oxidation and inactivation in the one-step operation, the robust Al(III)-CCOMB treatment is recommended for the HWW treatment and the protection of downstream aquatic environment.}, } @article {pmid37269417, year = {2023}, author = {Jiao, G and Huang, Y and Dai, H and Gou, H and Li, Z and Shi, H and Yang, J and Ni, S}, title = {Responses of rhizosphere microbial community structure and metabolic function to heavy metal coinhibition.}, journal = {Environmental geochemistry and health}, volume = {45}, number = {8}, pages = {6177-6198}, pmid = {37269417}, issn = {1573-2983}, support = {41977289//National Natural Science Foundation of China/ ; 2021YFQ0066//Sichuan Province Science and Technology Support Program/ ; 2020ZF11405//Everest Scientific Research Program/ ; SKLGP2021Z002//State Key Laboratory of Geological Disaster Prevention and Geological Environmental Protection Independent Project/ ; SKLGP2021Z002//State Key Laboratory of Geohazard Prevention and Geoenvironment Protection Independent Research Project/ ; }, mesh = {Humans ; Cadmium/analysis ; Rhizosphere ; *Metals, Heavy/analysis ; *Microbiota ; Soil/chemistry ; Zea mays/metabolism ; *Soil Pollutants/analysis ; Soil Microbiology ; }, abstract = {Metal mineral mining results in releases of large amounts of heavy metals into the environment, and it is necessary to better understand the response of rhizosphere microbial communities to simultaneous stress from multiple heavy metals (HMs), which directly impacts plant growth and human health. In this study, by adding different concentrations of cadmium (Cd) to a soil with high background concentrations of vanadium (V) and chromium (Cr), the growth of maize during the jointing stage was explored under limiting conditions. High-throughput sequencing was used to explore the response and survival strategies of rhizosphere soil microbial communities to complex HM stress. The results showed that complex HMs inhibited the growth of maize at the jointing stage, and the diversity and abundance of maize rhizosphere soil microorganisms were significantly different at different metal enrichment levels. In addition, according to the different stress levels, the maize rhizosphere attracted many tolerant colonizing bacteria, and cooccurrence network analysis showed that these bacteria interacted very closely. The effects of residual heavy metals on beneficial microorganisms (such as Xanthomonas, Sphingomonas, and lysozyme) were significantly stronger than those of bioavailable metals and soil physical and chemical properties. PICRUSt analysis revealed that the different forms of V and Cd had significantly greater effects on microbial metabolic pathways than all forms of Cr. Cr mainly affected the two major metabolic pathways: microbial cell growth and division and environmental information transmission. In addition, significant differences in rhizosphere microbial metabolism under different concentrations were found, and this can serve as a reference for subsequent metagenomic analysis. This study is helpful for exploring the threshold for the growth of crops in toxic HM soils in mining areas and achieving further biological remediation.}, } @article {pmid37268771, year = {2023}, author = {Listmann, L and Peters, C and Rahlff, J and Esser, SP and Schaum, CE}, title = {Seasonality and Strain Specificity Drive Rapid Co-evolution in an Ostreococcus-Virus System from the Western Baltic Sea.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2414-2423}, pmid = {37268771}, issn = {1432-184X}, support = {CLICCS//Exzellenzcluster Ozean der Zukunft/ ; Start up Prof. Dr. Elisa Schaum//University of Hamburg, Germany/ ; RA3432/1-1//DFG/ ; 730984//Assemble Plus/ ; }, mesh = {*Ecosystem ; Phytoplankton/genetics ; *Chlorophyta ; }, abstract = {Marine viruses are a major driver of phytoplankton mortality and thereby influence biogeochemical cycling of carbon and other nutrients. Phytoplankton-targeting viruses are important components of ecosystem dynamics, but broad-scale experimental investigations of host-virus interactions remain scarce. Here, we investigated in detail a picophytoplankton (size 1 µm) host's responses to infections by species-specific viruses from distinct geographical regions and different sampling seasons. Specifically, we used Ostreococcus tauri and O. mediterraneus and their viruses (size ca. 100 nm). Ostreococcus sp. is globally distributed and, like other picoplankton species, play an important role in coastal ecosystems at certain times of the year. Further, Ostreococcus sp. is a model organism, and the Ostreococcus-virus system is well-known in marine biology. However, only few studies have researched its evolutionary biology and the implications thereof for ecosystem dynamics. The Ostreococcus strains used here stem from different regions of the Southwestern Baltic Sea that vary in salinity and temperature and were obtained during several cruises spanning different sampling seasons. Using an experimental cross-infection set-up, we explicitly confirm species and strain specificity in Ostreococcus sp. from the Baltic Sea. Moreover, we found that the timing of virus-host co-existence was a driver of infection patterns as well. In combination, these findings prove that host-virus co-evolution can be rapid in natural systems.}, } @article {pmid37267305, year = {2023}, author = {Rego-Costa, A and Huang, IT and Desai, MM and Gombert, AK}, title = {Yeast population dynamics in Brazilian bioethanol production.}, journal = {G3 (Bethesda, Md.)}, volume = {13}, number = {7}, pages = {}, pmid = {37267305}, issn = {2160-1836}, mesh = {*Saccharomyces cerevisiae/genetics ; Brazil ; Ecosystem ; Industrial Microbiology ; Fermentation ; *Saccharum ; }, abstract = {The large-scale and nonaseptic fermentation of sugarcane feedstocks into fuel ethanol in biorefineries represents a unique ecological niche, in which the yeast Saccharomyces cerevisiae is the predominant organism. Several factors, such as sugarcane variety, process design, and operating and weather conditions, make each of the ∼400 industrial units currently operating in Brazil a unique ecosystem. Here, we track yeast population dynamics in 2 different biorefineries through 2 production seasons (April to November of 2018 and 2019), using a novel statistical framework on a combination of metagenomic and clonal sequencing data. We find that variation from season to season in 1 biorefinery is small compared to the differences between the 2 units. In 1 biorefinery, all lineages present during the entire production period derive from 1 of the starter strains, while in the other, invading lineages took over the population and displaced the starter strain. However, despite the presence of invading lineages and the nonaseptic nature of the process, all yeast clones we isolated are phylogenetically related to other previously sequenced bioethanol yeast strains, indicating a common origin from this industrial niche. Despite the substantial changes observed in yeast populations through time in each biorefinery, key process indicators remained quite stable through both production seasons, suggesting that the process is robust to the details of these population dynamics.}, } @article {pmid37267076, year = {2024}, author = {Gao, J and Zhao, L and Chen, G and Huang, C and Kong, W and Feng, Y and Zhen, G}, title = {The value of metagenomic next-generation sequencing for the diagnosis of pulmonary tuberculosis using bronchoalveolar lavage fluid.}, journal = {Laboratory medicine}, volume = {55}, number = {1}, pages = {96-102}, pmid = {37267076}, issn = {1943-7730}, support = {82170036//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Bronchoalveolar Lavage Fluid/microbiology ; Retrospective Studies ; Sensitivity and Specificity ; *Tuberculosis, Pulmonary/diagnosis/microbiology ; *Mycobacterium tuberculosis/genetics ; High-Throughput Nucleotide Sequencing ; Sputum/microbiology ; }, abstract = {OBJECTIVE: The aim of this study was to compare metagenomic next-generation sequencing (mNGS) with other methods, including Xpert MTB/RIF, Mycobacterium tuberculosis (MTB) culture, and acid-fast bacillus (AFB) staining in the diagnosis of pulmonary tuberculosis (PTB) using bronchoalveolar lavage fluid (BALF).

METHODS: The data of 186 patients with suspected PTB were retrospectively collected from January 2020 to May 2021 at Tongji Hospital. BALF samples were collected from all patients and analyzed using AFB staining, MTB culture, Xpert MTB/RIF, and mNGS.

RESULTS: Of the 186 patients, 38 patients were ultimately diagnosed as PTB. Metagenomic next-generation sequencing exhibited a sensitivity of 78.95%, which was higher than AFB staining (27.59%) and MTB culture (44.12%) but similar to Xpert MTB/RIF (72.73%). Utilization of combined methods demonstrates improvement for PTB diagnosis. In support of this, the area under the receiver operating characteristic curve for the combination of mNGS and MTB culture (0.933, 95% CI: 0.871, 0.995) was larger than those of mNGS, Xpert MTB/RIF, MTB culture, and the combination of Xpert MTB/RIF and MTB culture.

CONCLUSION: The sensitivity of mNGS in the diagnosis of PTB using BALF specimen is similar to Xpert MTB/RIF. Metagenomic next-generation sequencing in combination with MTB culture may further improve the diagnosis of pulmonary tuberculosis.}, } @article {pmid37267060, year = {2023}, author = {Du, B and Xiao, X and Wang, H and Li, W and Xia, Z and Yang, P and Huang, SK and Yuan, R and Liu, J and Han, M and Zou, Y and Zhu, J and He, D and Lyu, J and Jin, X and Xu, X and Wang, J and Yang, H and Xiao, L and Liu, X and Kristiansen, K}, title = {Evaluation of the Impact of BaP Exposure on the Gut Microbiota and Allergic Responses in an OVA-Sensitized Mouse Model.}, journal = {Environmental health perspectives}, volume = {131}, number = {6}, pages = {67004}, pmid = {37267060}, issn = {1552-9924}, mesh = {Humans ; Female ; Animals ; Mice ; *Gastrointestinal Microbiome ; Ovalbumin/pharmacology ; Caco-2 Cells ; *Hypersensitivity ; Inflammation ; Bacteria ; }, abstract = {BACKGROUND: Exposure to environmental pollutants, including benzo[a]pyrene (BaP), has been implicated in allergic diseases and intestinal microbiota homeostasis, but the environment-microbiota-immunity triangular relationship and to what extent BaP-induced remodeling of the gut microbiota contributes to intestinal allergic inflammation remain to be established.

OBJECTIVES: We investigated the impact of BaP on intestinal allergic inflammation and examined the relationship between this effect and gut microbiota dysbiosis. We explored the potential ability of intestinal bacteria to degrade BaP and alleviate cytotoxicity as a detoxification strategy to counteract the effects of BaP exposure.

METHODS: We combined microbiome shotgun metagenomics with animal histological and intestinal allergic inflammatory responses to assess the effects of BaP (50μg/mouse per day) in a 23-d toxicity test in antigen-induced allergic female mice. In addition, genome annotation, quantitative analysis of BaP, and in vitro cytotoxicity-tests using CaCo-2 cells were conducted to infer the role of intestinal bacteria in BaP detoxification.

RESULTS: BaP exposure impacted the taxonomic composition and the functional potential of the gut microbiota and aggravated antigen-induced intestinal allergic inflammatory responses. The level of inflammatory cytokines correlated with the abundance of specific bacterial taxa, including Lachnospiraceae bacterium 28-4 and Alistipes inops. We identified 614 bacteria harboring genes implicated in the degradation of BaP, and 4 of these bacterial strains were shown to significantly reduce the cytotoxicity of BaP to CaCo-2 cells in vitro.

DISCUSSION: Using allergic female mice as a model, we investigated the relationship between BaP, microbiota, and host immune reactions, highlighting the role of gut bacteria in BaP-aggravated allergic reactions. Our findings offer novel insight toward establishing the causal relationship between BaP exposure and the occurrence of allergic disorders. Identifying gut bacteria that degrade BaP may provide new strategies for ameliorating BaP cytotoxicity. https://doi.org/10.1289/EHP11874.}, } @article {pmid37265934, year = {2023}, author = {Kedia, S and Ahuja, V}, title = {Human gut microbiome: A primer for the clinician.}, journal = {JGH open : an open access journal of gastroenterology and hepatology}, volume = {7}, number = {5}, pages = {337-350}, pmid = {37265934}, issn = {2397-9070}, abstract = {The human host gets tremendously influenced by a genetically and phenotypically distinct and heterogeneous constellation of microbial species-the human microbiome-the gut being one of the most densely populated and characterized site for these organisms. Microbiome science has advanced rapidly, technically with respect to the analytical methods and biologically with respect to its mechanistic influence in health and disease states. A clinician conducting a microbiome study should be aware of the nuances related to microbiome research, especially with respect to the technical and biological factors that can influence the interpretation of research outcomes. Hence, this review is an attempt to detail these aspects of the human gut microbiome, with emphasis on its determinants in a healthy state.}, } @article {pmid37265503, year = {2023}, author = {Ponraj, DS and Lund, M and Lange, J and Poehlein, A and Himmelbach, A and Falstie-Jensen, T and Jørgensen, NP and Ravn, C and Brüggemann, H}, title = {Shotgun sequencing of sonication fluid for the diagnosis of orthopaedic implant-associated infections with Cutibacterium acnes as suspected causative agent.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1165017}, pmid = {37265503}, issn = {2235-2988}, mesh = {Humans ; *Prosthesis-Related Infections/diagnosis/microbiology ; *Orthopedics ; Sonication ; *Coinfection ; Pilot Projects ; Propionibacterium acnes/genetics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {Orthopaedic implant-associated infections (OIAIs) due to Cutibacterium acnes can be difficult to diagnose. The aim of this pilot study was to determine if metagenomic next-generation sequencing (mNGS) can provide additional information to improve the diagnosis of C. acnes OIAIs. mNGS was performed on sonication fluid (SF) specimens derived from 24 implants. These were divided into three groups, based on culture results: group I, culture-negative (n = 4); group II, culture-positive for C. acnes (n = 10); and group III, culture-positive for other bacteria (n = 10). In group I, sequence reads from C. acnes were detected in only one SF sample, originating from a suspected case of OIAIs, which was SF and tissue culture-negative. In group II, C. acnes sequences were detected in 7/10 samples. In group III, C. acnes sequence reads were found in 5/10 samples, in addition to sequence reads that matched the bacterial species identified by culture. These samples could represent polymicrobial infections that were missed by culture. Taken together, mNGS was able to detect C. acnes DNA in more samples compared to culture and could be used to identify cases of suspected C. acnes OIAIs, in particular regarding possible polymicrobial infections, where the growth of C. acnes might be compromised due to a fast-growing bacterial species. However, since SF specimens are usually low-biomass samples, mNGS is prone to DNA contamination, possibly introduced during DNA extraction or sequencing procedures. Thus, it is advisable to set a sequence read count threshold, taking into account project- and NGS-specific criteria.}, } @article {pmid37264698, year = {2024}, author = {Bull, K and Davies, G and Jenkins, TP and Peachey, L}, title = {The faecal microbiome of Exmoor ponies shows step-wise compositional changes with increasing levels of management by humans.}, journal = {Equine veterinary journal}, volume = {56}, number = {1}, pages = {159-170}, doi = {10.1111/evj.13961}, pmid = {37264698}, issn = {2042-3306}, support = {//University of Bristol/ ; }, mesh = {Humans ; Horses/genetics ; Animals ; Female ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; *Microbiota ; Feces/chemistry ; Diet/veterinary ; }, abstract = {BACKGROUND: Horses can suffer from gastrointestinal (GI) disease in domestic environments, often precipitated by human-led changes in management. Understanding the consequences of these changes on equine gut microbiota is key to the prevention of such disease episodes.

OBJECTIVE: Profile the faecal microbiota of adult female Exmoor ponies under three management conditions, representing increasing levels of management by humans, encompassing different diets; whilst controlling for age, breed and sex.

STUDY DESIGN: Cross-sectional descriptive.

METHODS: Faecal samples were collected from three populations of Exmoor ponies kept under contrasting management conditions: 29 adult female ponies in groups with low management (LM) (n = 10), medium management (MM) (n = 10) and high management (HM) (n = 9) levels, based on diet, drug use, handling and exercise. Faecal microbial composition was profiled via high-throughput sequencing of the bacterial 16S rRNA gene, and functional metagenome predictions.

RESULTS: We observed profound step-wise changes in microbiome structure in the transition from LM to MM to HM. A relatively high abundance of Proteobacteria and Tenericutes was associated with the HM group; higher abundance of Methanobacteria was observed in the LM group. The MM group had intermediate levels of these taxa and exhibited high 'within group' variation in alpha diversity. Functional predictions revealed increased amino acid and lipid metabolism in HM; energy metabolism in LM and carbohydrate metabolism and immune/metabolic disease pathways in MM.

MAIN LIMITATIONS: Low group sizes, incomplete knowledge of bacterial genomes in equine gut microbiota and it was not possible to assess the relative impact of diet, drug use, handling and exercise on the microbiome as variables were confounded.

CONCLUSIONS: Human-led management factors had profound step-wise effects on faecal microbial composition. Based on functional metagenome predictions, we hypothesise that dietary differences between groups were the major driver of observed differences.}, } @article {pmid37264481, year = {2023}, author = {Liu, Y and Daniel, SG and Kim, HE and Koo, H and Korostoff, J and Teles, F and Bittinger, K and Hwang, G}, title = {Addition of cariogenic pathogens to complex oral microflora drives significant changes in biofilm compositions and functionalities.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {123}, pmid = {37264481}, issn = {2049-2618}, support = {R01 DE027970/DE/NIDCR NIH HHS/United States ; }, mesh = {Child, Preschool ; Humans ; Biofilms ; Candida albicans/genetics ; Cross-Sectional Studies ; *Dental Caries ; *Microbiota ; Streptococcus mutans/genetics ; Sugars/metabolism ; }, abstract = {BACKGROUND: Dental caries is a microbe and sugar-mediated biofilm-dependent oral disease. Of particular significance, a virulent type of dental caries, known as severe early childhood caries (S-ECC), is characterized by the synergistic polymicrobial interaction between the cariogenic bacterium, Streptococcus mutans, and an opportunistic fungal pathogen, Candida albicans. Although cross-sectional studies reveal their important roles in caries development, these exhibit limitations in determining the significance of these microbial interactions in the pathogenesis of the disease. Thus, it remains unclear the mechanism(s) through which the cross-kingdom interaction modulates the composition of the plaque microbiome. Here, we employed a novel ex vivo saliva-derived microcosm biofilm model to assess how exogenous pathogens could impact the structural and functional characteristics of the indigenous native oral microbiota.

RESULTS: Through shotgun whole metagenome sequencing, we observed that saliva-derived biofilm has decreased richness and diversity but increased sugar-related metabolism relative to the planktonic phase. Addition of S. mutans and/or C. albicans to the native microbiome drove significant changes in its bacterial composition. In addition, the effect of the exogenous pathogens on microbiome diversity and taxonomic abundances varied depending on the sugar type. While the addition of S. mutans induced a broader effect on Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog abundances with glucose/fructose, S. mutans-C. albicans combination under sucrose conditions triggered unique and specific changes in microbiota composition/diversity as well as specific effects on KEGG pathways. Finally, we observed the presence of human epithelial cells within the biofilms via confocal microscopy imaging.

CONCLUSIONS: Our data revealed that the presence of S. mutans and C. albicans, alone or in combination, as well as the addition of different sugars, induced unique alterations in both the composition and functional attributes of the biofilms. In particular, the combination of S. mutans and C. albicans seemed to drive the development (and perhaps the severity) of a dysbiotic/cariogenic oral microbiome. Our work provides a unique and pragmatic biofilm model for investigating the functional microbiome in health and disease as well as developing strategies to modulate the microbiome. Video Abstract.}, } @article {pmid37264459, year = {2023}, author = {Leung, MHY and Tong, X and Shen, Z and Du, S and Bastien, P and Appenzeller, BMR and Betts, RJ and Mezzache, S and Bourokba, N and Cavusoglu, N and Aguilar, L and Misra, N and Clavaud, C and Lee, PKH}, title = {Skin microbiome differentiates into distinct cutotypes with unique metabolic functions upon exposure to polycyclic aromatic hydrocarbons.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {124}, pmid = {37264459}, issn = {2049-2618}, mesh = {*Polycyclic Aromatic Hydrocarbons ; Skin/chemistry ; *Air Pollutants/analysis ; Biodegradation, Environmental ; *Microbiota/genetics ; Environmental Monitoring ; }, abstract = {BACKGROUND: The effects of air pollutants, particularly polycyclic aromatic hydrocarbons (PAHs), on the skin microbiome remain poorly understood. Thus, to better understand the interplay between air pollutants, microbiomes, and skin conditions, we applied metagenomics and metabolomics to analyze the effects of PAHs in air pollution on the skin microbiomes of over 120 subjects residing in two cities in China with different levels of air pollution.

RESULTS: The skin microbiomes differentiated into two cutotypes (termed 1 and 2) with distinct taxonomic, functional, resistome, and metabolite compositions as well as skin phenotypes that transcended geography and host factors. High PAH exposure was linked to dry skin and cutotype 2, which was enriched with species with potential biodegradation functions and had reduced correlation network structure integrity. The positive correlations identified between dominant taxa, key functional genes, and metabolites in the arginine biosynthesis pathway in cutotype 1 suggest that arginine from bacteria contributes to the synthesis of filaggrin-derived natural moisturizing factors (NMFs), which provide hydration for the skin, and could explain the normal skin phenotype observed. In contrast, no correlation with the arginine biosynthesis pathway was observed in cutotype 2, which indicates the limited hydration functions of NMFs and explains the observed dry skin phenotype. In addition to dryness, skin associated with cutotype 2 appeared prone to other adverse conditions such as inflammation.

CONCLUSIONS: This study revealed the roles of PAHs in driving skin microbiome differentiation into cutotypes that vary extensively in taxonomy and metabolic functions and may subsequently lead to variations in skin-microbe interactions that affect host skin health. An improved understanding of the roles of microbiomes on skin exposed to air pollutants can aid the development of strategies that harness microbes to prevent undesirable skin conditions. Video Abstract.}, } @article {pmid37264413, year = {2023}, author = {Lu, DC and Wang, FQ and Amann, RI and Teeling, H and Du, ZJ}, title = {Epiphytic common core bacteria in the microbiomes of co-located green (Ulva), brown (Saccharina) and red (Grateloupia, Gelidium) macroalgae.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {126}, pmid = {37264413}, issn = {2049-2618}, mesh = {*Seaweed/microbiology ; *Ulva/genetics/microbiology ; *Laminaria/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria ; *Rhodophyta/genetics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Macroalgal epiphytic microbial communities constitute a rich resource for novel enzymes and compounds, but studies so far largely focused on tag-based microbial diversity analyses or limited metagenome sequencing of single macroalgal species.

RESULTS: We sampled epiphytic bacteria from specimens of Ulva sp. (green algae), Saccharina sp. (brown algae), Grateloupia sp. and Gelidium sp. (both red algae) together with seawater and sediment controls from a coastal reef in Weihai, China, during all seasons. Using 16S rRNA amplicon sequencing, we identified 14 core genera (consistently present on all macroalgae), and 14 dominant genera (consistently present on three of the macroalgae). Core genera represented ~ 0.7% of all genera, yet accounted for on average 51.1% of the bacterial abundances. Plate cultivation from all samples yielded 5,527 strains (macroalgae: 4,426) representing 1,235 species (685 potentially novel). Sequencing of selected strains yielded 820 non-redundant draft genomes (506 potentially novel), and sequencing of 23 sampled metagenomes yielded 1,619 metagenome-assembled genomes (MAGs), representing further 1,183 non-redundant genomes. 230 isolates and 153 genomes were obtained from the 28 core/dominant genera. We analyzed the genomic potential of phycosphere bacteria to degrade algal polysaccharides and to produce bioactive secondary metabolites. We predicted 4,451 polysaccharide utilization loci (PULs) and 8,810 biosynthetic gene clusters (BGCs). These were particularly prevalent in core/dominant genera.

CONCLUSIONS: Our metabolic annotations and analyses of MAGs and genomes provide new insights into novel species of phycosphere bacteria and their ecological niches for an improved understanding of the macroalgal phycosphere microbiome. Video Abstract.}, } @article {pmid37264385, year = {2023}, author = {Singh, NK and Wood, JM and Patane, J and Moura, LMS and Lombardino, J and Setubal, JC and Venkateswaran, K}, title = {Characterization of metagenome-assembled genomes from the International Space Station.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {125}, pmid = {37264385}, issn = {2049-2618}, mesh = {Metagenome ; Phylogeny ; Bacteria ; *Space Flight ; *Gammaproteobacteria/genetics ; *Anti-Infective Agents ; Metagenomics ; }, abstract = {BACKGROUND: Several investigations on the microbial diversity and functional properties of the International Space Station (ISS) environment were carried out to understand the influence of spaceflight conditions on the microbial population. However, metagenome-assembled genomes (MAGs) of ISS samples are yet to be generated and subjected to various genomic analyses, including phylogenetic affiliation, predicted functional pathways, antimicrobial resistance, and virulence characteristics.

RESULTS: In total, 46 MAGs were assembled from 21 ISS environmental metagenomes, in which metaSPAdes yielded 20 MAGs and metaWRAP generated 26 MAGs. Among 46 MAGs retrieved, 18 bacterial species were identified, including one novel genus/species combination (Kalamiella piersonii) and one novel bacterial species (Methylobacterium ajmalii). In addition, four bins exhibited fungal genomes; this is the first-time fungal genomes were assembled from ISS metagenomes. Phylogenetic analyses of five bacterial species showed ISS-specific evolution. The genes pertaining to cell membranes, such as transmembrane transport, cell wall organization, and regulation of cell shape, were enriched. Variations in the antimicrobial-resistant (AMR) and virulence genes of the selected 20 MAGs were characterized to predict the ecology and evolution of biosafety level (BSL) 2 microorganisms in space. Since microbial virulence increases in microgravity, AMR gene sequences of MAGs were compared with genomes of respective ISS isolates and corresponding type strains. Among these 20 MAGs characterized, AMR genes were more prevalent in the Enterobacter bugandensis MAG, which has been predominantly isolated from clinical samples. MAGs were further used to analyze if genes involved in AMR and biofilm formation of viable microbes in ISS have variation due to generational evolution in microgravity and radiation pressure.

CONCLUSIONS: Comparative analyses of MAGs and whole-genome sequences of related ISS isolates and their type strains were characterized to understand the variation related to the microbial evolution under microgravity. The Pantoea/Kalamiella strains have the maximum single-nucleotide polymorphisms found within the ISS strains examined. This may suggest that Pantoea/Kalamiella strains are much more subjective to microgravity changes. The reconstructed genomes will enable researchers to study the evolution of genomes under microgravity and low-dose irradiation compared to the evolution of microbes here on Earth. Video Abstract.}, } @article {pmid37264312, year = {2023}, author = {Huang, LL and Wang, C and Liu, Y and Gu, XY and Wang, WX and Chen, W and Hu, CM}, title = {Resolution of an insidious and migratory Mycobacterium tuberculosis-associated secondary organizing pneumonia: a case report and literature review.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {372}, pmid = {37264312}, issn = {1471-2334}, support = {WSN-160//The Six Talent Peaks Project in Jiangsu Province/ ; }, mesh = {Humans ; Female ; Middle Aged ; *Mycobacterium tuberculosis/genetics ; *Organizing Pneumonia ; Lung/diagnostic imaging/pathology ; *Cryptogenic Organizing Pneumonia/diagnosis/drug therapy/pathology ; *Pneumonia/complications ; *Tuberculosis/complications/diagnosis/drug therapy ; }, abstract = {BACKGROUND: Organizing pneumonia (OP) is a rare interstitial lung disease. Secondary organizing pneumonia (SOP) caused by Mycobacterium tuberculosis (MTB) is extremely rare. Migratory MTB-associated SOP is more deceptive and dangerous. When insidious tuberculosis (TB) is not recognized, SOP would be misdiagnosed as cryptogenic organizing pneumonia (COP). Use of steroid hormone alone leads to the progression of TB foci or even death. Clues of distinguishing atypical TB at the background of OP is urgently needed.

CASE PRESENTATION: A 56-year-old female patient was hospitalized into the local hospital because of cough and expectoration for more than half a month. Her medical history and family history showed no relation to TB or other lung diseases. Community-acquired pneumonia was diagnosed and anti-infection therapy was initialized but invalid. The patient suffered from continuous weigh loss. More puzzling, the lesions were migratory based on the chest computed tomography (CT) images. The patient was then transferred to our hospital. The immunological indexes of infection in blood and pathogenic tests in sputum and the bronchoalveolar lavage fluid were negative. The percutaneous lung puncture biopsy and pathological observation confirmed OP, but without granulomatous lesions. Additionally, pathogen detection of the punctured lung tissues by metagenomics next generation sequencing test (mNGS) were all negative. COP was highly suspected. Fortunately, the targeted next-generation sequencing (tNGS) detected MTB in the punctured lung tissues and MTB-associated SOP was definitely diagnosed. The combined therapy of anti-TB and prednisone was administrated. After treatment for 10 days, the partial lesions were significantly resorbed and the patient was discharged. In the follow-up of half a year, the patient was healthy.

CONCLUSIONS: It is difficult to distinguish SOP from COP in clinical practice. Diagnosis of COP must be very cautious. Transient small nodules and cavities in the early lung image are a clue to consider TB, even though all pathogen tests are negative. tNGS is also a powerful tool to detect pathogen, ensuring prompt diagnosis of TB-related SOP. For clinicians in TB high burden countries, we encourage them to keep TB in mind before making a final diagnosis of COP.}, } @article {pmid37264063, year = {2023}, author = {Veglia, AJ and Bistolas, KSI and Voolstra, CR and Hume, BCC and Ruscheweyh, HJ and Planes, S and Allemand, D and Boissin, E and Wincker, P and Poulain, J and Moulin, C and Bourdin, G and Iwankow, G and Romac, S and Agostini, S and Banaigs, B and Boss, E and Bowler, C and de Vargas, C and Douville, E and Flores, M and Forcioli, D and Furla, P and Galand, PE and Gilson, E and Lombard, F and Pesant, S and Reynaud, S and Sunagawa, S and Thomas, OP and Troublé, R and Zoccola, D and Correa, AMS and Vega Thurber, RL}, title = {Endogenous viral elements reveal associations between a non-retroviral RNA virus and symbiotic dinoflagellate genomes.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {566}, pmid = {37264063}, issn = {2399-3642}, mesh = {Animals ; *Dinoflagellida/genetics ; Genome ; *Anthozoa/genetics ; *RNA Viruses/genetics ; Coral Reefs ; }, abstract = {Endogenous viral elements (EVEs) offer insight into the evolutionary histories and hosts of contemporary viruses. This study leveraged DNA metagenomics and genomics to detect and infer the host of a non-retroviral dinoflagellate-infecting +ssRNA virus (dinoRNAV) common in coral reefs. As part of the Tara Pacific Expedition, this study surveyed 269 newly sequenced cnidarians and their resident symbiotic dinoflagellates (Symbiodiniaceae), associated metabarcodes, and publicly available metagenomes, revealing 178 dinoRNAV EVEs, predominantly among hydrocoral-dinoflagellate metagenomes. Putative associations between Symbiodiniaceae and dinoRNAV EVEs were corroborated by the characterization of dinoRNAV-like sequences in 17 of 18 scaffold-scale and one chromosome-scale dinoflagellate genome assembly, flanked by characteristically cellular sequences and in proximity to retroelements, suggesting potential mechanisms of integration. EVEs were not detected in dinoflagellate-free (aposymbiotic) cnidarian genome assemblies, including stony corals, hydrocorals, jellyfish, or seawater. The pervasive nature of dinoRNAV EVEs within dinoflagellate genomes (especially Symbiodinium), as well as their inconsistent within-genome distribution and fragmented nature, suggest ancestral or recurrent integration of this virus with variable conservation. Broadly, these findings illustrate how +ssRNA viruses may obscure their genomes as members of nested symbioses, with implications for host evolution, exaptation, and immunity in the context of reef health and disease.}, } @article {pmid37264015, year = {2023}, author = {Hochart, C and Paoli, L and Ruscheweyh, HJ and Salazar, G and Boissin, E and Romac, S and Poulain, J and Bourdin, G and Iwankow, G and Moulin, C and Ziegler, M and Porro, B and Armstrong, EJ and Hume, BCC and Aury, JM and Pogoreutz, C and Paz-García, DA and Nugues, MM and Agostini, S and Banaigs, B and Boss, E and Bowler, C and de Vargas, C and Douville, E and Flores, M and Forcioli, D and Furla, P and Gilson, E and Lombard, F and Pesant, S and Reynaud, S and Thomas, OP and Troublé, R and Wincker, P and Zoccola, D and Allemand, D and Planes, S and Thurber, RV and Voolstra, CR and Sunagawa, S and Galand, PE}, title = {Ecology of Endozoicomonadaceae in three coral genera across the Pacific Ocean.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3037}, pmid = {37264015}, issn = {2041-1723}, mesh = {Animals ; *Anthozoa/microbiology ; Pacific Ocean ; Ecology ; *Gammaproteobacteria ; Bacteria ; Coral Reefs ; }, abstract = {Health and resilience of the coral holobiont depend on diverse bacterial communities often dominated by key marine symbionts of the Endozoicomonadaceae family. The factors controlling their distribution and their functional diversity remain, however, poorly known. Here, we study the ecology of Endozoicomonadaceae at an ocean basin-scale by sampling specimens from three coral genera (Pocillopora, Porites, Millepora) on 99 reefs from 32 islands across the Pacific Ocean. The analysis of 2447 metabarcoding and 270 metagenomic samples reveals that each coral genus harbored a distinct new species of Endozoicomonadaceae. These species are composed of nine lineages that have distinct biogeographic patterns. The most common one, found in Pocillopora, appears to be a globally distributed symbiont with distinct metabolic capabilities, including the synthesis of amino acids and vitamins not produced by the host. The other lineages are structured partly by the host genetic lineage in Pocillopora and mainly by the geographic location in Porites. Millepora is more rarely associated to Endozoicomonadaceae. Our results show that different coral genera exhibit distinct strategies of host-Endozoicomonadaceae associations that are defined at the bacteria lineage level.}, } @article {pmid37263438, year = {2023}, author = {Phulpoto, AH and Pirzada, T and Kanhar, NA}, title = {Exploring community dynamics: Cultivable and uncultivable for the microbial-mediated bioremediation of oil-based paints polluted soil from aqueous media by Plackett-Burman statistically designed conditions.}, journal = {The Science of the total environment}, volume = {891}, number = {}, pages = {164505}, doi = {10.1016/j.scitotenv.2023.164505}, pmid = {37263438}, issn = {1879-1026}, mesh = {Biodegradation, Environmental ; RNA, Ribosomal, 16S/genetics ; *Soil ; Soil Microbiology ; Bacteria/metabolism ; *Soil Pollutants/metabolism ; }, abstract = {Oil-based paint seriously threatens biodiversity due to its complex composition and biocide toxicity. Therefore, it alters the microbial diversity abundance and in modern approaches like metagenomic, a powerful tool to get insight into pollutants effect on soil microbial community abundance. Thus, present study aimed at "exploring community dynamics: cultivable and uncultivable for the microbial-mediated bioremediation of oil-based paints polluted soil from aqueous media by Plackett-Burman statistical designed conditions". The total DNA from oil-based paints polluted soil was extracted by PowerSoil DNA Isolation Kit. The 16S rDNA genes were amplified using universal primers and PCR amplicons were sequenced for analysis of metagenomes to determine the bacterial microbiome abundance. A total 133,140 sequence reads, 2857 Operational Taxonomic Units (OTUs) of 16S rRNA genes, and 30 bacterial phyla were retrieved from all the oil-based paints polluted samples (C, R498, B698 and G492) with the significant increase in Firmicutes (18.90 %, 52.39 %, 49.75 %, 44.36 %) and Actinobacteria (26.66 %, 28.93 %, 28.17 %, 14.68 %) whereas a decrease in Proteobacteria (19.53 %, 6.32 %, 9.37 %, 16.21 %), Chloroflexi (16.93 %, 8.71 %, 9.78 %, 18.17 %), and Bacteroidetes (8.96 %, 0.36 %, 0.41 %, 0.11 %) was recorded respectively. Additionally, the 100 % removal of oil-based paints (R498, B698 and G492) was achieved by the cultivable microbial consortia in laboratory settings. On the other hand for the R498 single cultivable pure isolates exhibited biodegradation potential as "PDB20, 91 %", "PDB14, 81 %", and "PDB16, 87 %" while for the blue B698, "PDB4, 86 %", "PDB20, 89 %", "PDB5, and PDB2, 80%". Moreover, in case of G492, maximum % removal was achieved with "PDB20, 93 %", "PDB5, 90 %", "PDB6, 90 %", "PDB16, 88 %", "PDB2, and PDB4, 89%". Conclusively, in comparison to R498 and B698, maximum percent removal was displayed by G492 and this might be attributed due to difference in pigment. Cultivable consortia and individual pure isolates demonstrated >80 % contribution in the % removal of oil-based paints.}, } @article {pmid37263432, year = {2023}, author = {Wu, X and Bei, S and Zhou, X and Luo, Y and He, Z and Song, C and Yuan, H and Pivato, B and Liesack, W and Peng, J}, title = {Metagenomic insights into genetic factors driving bacterial niche differentiation between bulk and rhizosphere soils.}, journal = {The Science of the total environment}, volume = {891}, number = {}, pages = {164221}, doi = {10.1016/j.scitotenv.2023.164221}, pmid = {37263432}, issn = {1879-1026}, mesh = {Humans ; *Metagenome ; *Soil ; Rhizosphere ; Metagenomics ; Soil Microbiology ; Bacteria/metabolism ; Carbohydrates ; }, abstract = {Cellular motility is crucial for effective colonization of the rhizosphere, but it is not yet clear whether bacterial motility is particularly linked to other genetic traits. Here, we applied genome-resolved metagenomics and phylogenomics to investigate the ecological significance of cellular motility for niche differentiation and the links between the genetic makeup of motile bacteria and rhizosphere colonization within a four-decade maize field experiment. Indeed, highly diverse sets of genes encoding cellular motility, including chemotaxis, flagellar assembly and motility proteins, and utilization of polymeric carbon were the important predictors of bacterial niche differentiation between bulk and rhizosphere soils. This is well exemplified by metagenome-assembled genomes encoding high motility capacity (hmc_MAGs). Their collective abundance was, on average, sixfold higher in rhizosphere soil than in bulk soil. All bulk-soil-derived MAGs showed low motility capacities (lmc). The hmc_MAGs were highly enriched in beneficial traits involved in carbohydrate utilization, assimilatory (nasA) and dissimilatory (nirBD) nitrate reduction, inorganic phosphate solubilization (gcd), and organic phosphate mineralization (phoD). Belonging to the families Sphingomonadaceae, Burkholderiaceae and Steroidobacteraceae, the hmc_MAGs showed a ninefold greater enrichment in these traits than proteobacterial lmc_MAGs and a twofold greater enrichment than 264 genomes publicly available for the above three families, thereby substantiating that a specific rhizosphere effect acted on the microbes represented by the hmc_MAGs. The particular link between the genetic capacities for high cellular motility and increased carbohydrate depolymerization as the key determinant for plant-selected rhizosphere colonization was further substantiated by the analysis of public bulk-rhizosphere soil metagenomes retrieved from wheat and cucumber field sites.}, } @article {pmid37263084, year = {2023}, author = {Podosokorskaya, OA and Elcheninov, AG and Novikov, AA and Merkel, AY and Kublanov, IV}, title = {Fontisphaera persica gen. nov., sp. nov., a thermophilic hydrolytic bacterium from a hot spring of Baikal lake region, and proposal of Fontisphaeraceae fam. nov., and Limisphaeraceae fam. nov. within the Limisphaerales ord. nov. (Verrucomicrobiota).}, journal = {Systematic and applied microbiology}, volume = {46}, number = {4}, pages = {126438}, doi = {10.1016/j.syapm.2023.126438}, pmid = {37263084}, issn = {1618-0984}, mesh = {Humans ; *Hot Springs/microbiology ; Phylogeny ; Lakes/microbiology ; RNA, Ribosomal, 16S/genetics ; Fatty Acids/chemistry ; Bacteria, Anaerobic ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; }, abstract = {A novel facultatively anaerobic moderately thermophilic bacterium, strain B-154 [T], was isolated from a terrestrial hot spring in the Baikal lake region (Russian Federation). Gram-negative, motile, spherical cells were present singly, in pairs, or aggregates, and reproduced by binary fission. The strain grew at 30-57 °C and within a pH range of 5.1-8.4 with the optimum at 50 °C and pH 6.8-7.1. Strain B-154 [T] was a chemoorganoheterotroph, growing on mono-, di- and polysaccharides (xylan, starch, galactan, galactomannan, glucomannan, xyloglucan, pullulan, arabinan, lichenan, beta-glucan, pachyman, locust bean gum, xanthan gum). It did not require sodium chloride or yeast extract for growth. Major cellular fatty acids were anteiso-C15:0, iso-C16:0 and iso-C14:0. The respiratory quinone was MK-7. The complete genome of strain B-154 [T] was 4.73 Mbp in size; its G + C content was 61%. According to the phylogenomic analysis strain B-154 [T] forms a separate family-level phylogenetic lineage. Moreover, together with Limisphaera ngatamarikiensis and "Pedosphaera parvula" this strain forms a separate order-level phylogenetic lineage within Verrucomicrobiae class. Hence, we propose a novel order, Limisphaerales ord. nov., with two families Limisphaeraceae fam. nov. and Fontisphaeraceae fam. nov., and a novel genus and species Fontisphaera persica gen. nov., sp. nov. with type strain B-154 [T]. Ecogenomic analysis showed that representatives of the Limisphaerales are widespread in various environments. Although some of them were detected in hot springs the majority of Limisphaerales (54% of the studied metagenome-assembled genomes) were found in marine habitats. This study allowed a better understanding of physiology and ecology of Verrucomicrobiota - a rather understudied bacterial phylum.}, } @article {pmid37263036, year = {2023}, author = {Wu, C and Zhang, G and Zhang, K and Sun, J and Cui, Z and Guo, Y and Liu, H and Xu, W}, title = {Strong variation in sedimental antibiotic resistomes among urban rivers, estuaries and coastal oceans: Evidence from a river-connected coastal water ecosystem in northern China.}, journal = {Journal of environmental management}, volume = {342}, number = {}, pages = {118132}, doi = {10.1016/j.jenvman.2023.118132}, pmid = {37263036}, issn = {1095-8630}, mesh = {*Anti-Bacterial Agents/analysis ; *Estuaries ; Rivers/microbiology ; Genes, Bacterial ; Ecosystem ; Bacteria/genetics ; Oceans and Seas ; China ; Water ; }, abstract = {Sediment is thought to be a vital reservoir to spread antibiotic resistance genes (ARGs) among various natural environments. However, the spatial distribution patterns of the sedimental antibiotic resistomes around the Bohai Bay region, a river-connected coastal water ecosystem, are still poorly understood. The present study conducted a comprehensive investigation of ARGs among urban rivers (UR), estuaries (ES) and Bohai Bay (BHB) by metagenomic sequencing. Overall, a total of 169 unique ARGs conferring resistance to 15 antimicrobial classes were detected across all sediment samples. The Kruskal-Wallis test showed that the diversity and abundance of ARGs in the UR were all significantly higher than those in the ES and BHB (p < 0.05 and p < 0.01), revealing the distance dilution of the sedimental resistomes from the river to the ocean. Multidrug resistance genes contained most of the ARG subtypes, whereas rifamycin resistance genes were the most abundant ARGs in this region. Our study demonstrated that most antimicrobial resistomes were highly accumulated in urban river sediments, whereas beta-lactamase resistance genes (mainly PNGM-1) dramatically increased away from the estuary to the open ocean. The relative abundance of mobile genetic elements (MGEs) also gradually decreased from rivers to the coastal ocean, whereas the difference in pathogenic bacteria was not significant in the three classifications. Among MGEs, plasmids were recognized as the most important carriers to support the horizontal gene transfer of ARGs within and between species. According to co-occurrence networks, pathogenic Proteobacteria, Actinobacteria, and Bacteroidetes were recognized as potential and important hosts of ARGs. Heavy metals, pH and moisture content were all recognized as the vital environmental factors influencing the distribution of ARGs in sediment samples. Overall, the present study may help to understand the distribution patterns of ARGs at a watershed scale, and help to make effective policies to control the emergence, spread and evolution of different ARG subtypes in different habitats.}, } @article {pmid37263034, year = {2023}, author = {Dang, Q and Zhao, X and Xi, B and Zhang, C and He, L}, title = {The key role of denitrification and dissimilatory nitrate reduction in nitrogen pollution along vertical landfill profiles from metagenomic perspective.}, journal = {Journal of environmental management}, volume = {342}, number = {}, pages = {118300}, doi = {10.1016/j.jenvman.2023.118300}, pmid = {37263034}, issn = {1095-8630}, mesh = {*Nitrates ; Denitrification ; Nitrogen ; Waste Disposal Facilities ; *Garbage ; Nitrous Oxide/analysis ; }, abstract = {Landfill are persistent sources of nitrogen (N) pollution even in the decades after closure. However, the biological pathways of N-pollution, particularly N2O and NH4[+], at different landfill depths have received little attention. In this study, metagenomic analysis was conducted on landfill refuse from vertical reservoir profiles in two closed landfills named XT and MT. NH4[+] concentrations were found to be higher in deeper layers of MT, while greater potential for N2O emissions occurred in XT and the shallow layers of MT. Furthermore, the community structure and function of N-metabolizing microbes were more strongly defined by landfill depth than landfill type. Denitrification, involving abundant nirK and norB genes, was identified as the major pathway for N2O production in both XT and MT-shallow, while dissimilatory nitrate reduction with abundant nirBD genes was identified as the major pathway for NH4[+] accumulation. Microbes of norB-type and nirBD-type were positively affected by NO3[-] in XT, whereas negatively affected by contents of organic material and moisture in MT-shallow. The mechanism by which nitrogen fixation, with abundant nifH genes, contributes to NH4[+] accumulation in MT-deep should be further elucidated. These findings can provide a theoretical basis for governing scientific N-pollution control strategies throughout the entire landfill process.}, } @article {pmid37261715, year = {2023}, author = {Andrianjakarivony, FH and Bettarel, Y and Desnues, C}, title = {Searching for a Reliable Viral Indicator of Faecal Pollution in Aquatic Environments.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {61}, number = {6}, pages = {589-602}, pmid = {37261715}, issn = {1976-3794}, mesh = {Humans ; Ecosystem ; Reproducibility of Results ; Water Microbiology ; *Bacteriophages/genetics ; *Viruses/genetics ; Bacteria ; Feces/microbiology ; Environmental Monitoring/methods ; }, abstract = {The disposal of sewage in significant quantities poses a health hazard to aquatic ecosystems. These effluents can contain a wide range of pathogens, making faecal contamination a leading source of waterborne diseases around the world. Yet monitoring bacteria or viruses in aquatic environments is time consuming and expensive. The standard indicators of faecal pollution all have limitations, including difficulty in determining the source due to lack of host specificity, poor connection with the presence of non-bacterial pathogens, or low environmental persistence. Innovative monitoring techniques are sorely needed to provide more accurate and targeted solutions. Viruses are a promising alternative to faecal indicator bacteria for monitoring, as they are more persistent in ambient water, more abundant in faeces, and are extremely host-specific. Given the range of viruses found in diverse contexts, it is not easy to find one "ideal" viral indicator of faecal pollution; however, several are of interest. In parallel, the ongoing development of molecular techniques coupled with metagenomics and bioinformatics should enable improved ways to detect faecal contamination using viruses. This review examines the evolution of faecal contamination monitoring with the following aims (i) to identify the characteristics of the main viral indicators of faecal contamination, including human enteric viruses, bacteriophages, CRESS and plant viruses, (ii) to assess how these have been used to monitor water pollution in recent years, (iii) to evaluate the reliability of recent detection methods of such viruses, and (iv) to tentatively determine which viruses may be most effective as markers of faecal pollution.}, } @article {pmid37261381, year = {2023}, author = {Shao, Z and Shan, X and Jing, L and Wang, W and Li, W and Ren, Z and Zhang, BN and Huang, Y}, title = {Metagenome Investigation of Ocular Microbiota of Cataract Patients With and Without Type 2 Diabetes.}, journal = {Translational vision science & technology}, volume = {12}, number = {6}, pages = {1}, pmid = {37261381}, issn = {2164-2591}, mesh = {Humans ; Bacteria/genetics ; *Cataract/complications/genetics ; Conjunctiva ; *Diabetes Mellitus, Type 2/complications/epidemiology/genetics ; Metagenome/genetics ; *Microbiota/genetics ; Male ; Female ; }, abstract = {PURPOSE: Our objective was to investigate differences in the ocular surface bacterial composition in cataract patients with and without type 2 diabetes (T2D).

METHODS: Twenty-four diabetic patients with cataracts (group D) and 14 sex- and age-matched patients with age-related cataracts (group N) were recruited for this study. All samples underwent DNA extraction, fragmentation, purification, library construction, and metagenomic sequencing.

RESULTS: The overall conjunctival sac bacterial composition was similar between group D and group N, as determined by alpha diversity and beta diversity. Nevertheless, significant differences were observed in the relative abundance of specific bacteria. At the phylum level, group D had a significantly lower abundance of Chlamydiae, Tenericutes, Chloroflexi, Cyanobacteria, Cossaviricota, Chytridiomycota, Artverviricota, Zoopagomycota, Peploviricota, Deinococcus-Thermus, Preplasmiviricota, and Nucleocytoviricota. At the genus level, group D had a significantly lower abundance of Chlamydia, Mycoplasma, Salmonella, Chryseobacterium, Roseovarius, Desulfococcus, Kangiella, Anaerococcus, and Idiomarina but a significantly higher abundance of Parabacteroides, Phocaeicola, and Sphingomonas. Bacteria such as Aquificae, Parabacteroides, Flavobacterium, Austwickia, Aquifex, Tenacibaculum, and Chryseobacterium in group D and Tenericutes, Chlamydiae, Porphyromonas, Mycoplasma, Chlamydia, Kangiella, Idiomarina, Roseovarius, Aliiroseovarius, and Desulfococcus in group N could be used as conjunctival sac biomarkers, according to the linear discriminant analysis effect size. Gene Ontology functional annotation indicated that bacterial catalytic activity, metabolic processes, locomotion, virion, and reproduction were enriched in group D, while immune system processes were enriched in group N. In addition, the top 30 differentially expressed virulence factors (VFs) were all more enriched in group D.

CONCLUSIONS: The bacterial composition was similar between the two groups. Several bacterial strains that were reported beneficial in gut were decreased, and pathogenic bacteria were increased in T2D. Furthermore, group D had more active bacterial terms and increased VF expression, suggesting that the susceptibility of diabetic patients to infection is closely related to functional changes in the ocular surface flora. Our conjunctival microbiota atlas provides a reference for investigating ocular complications related to diabetes.

TRANSLATIONAL RELEVANCE: The altered composition and functional profile of the ocular microbial community in diabetic patients offer evidence for the need to prevent infection during cataract surgery.}, } @article {pmid37260833, year = {2023}, author = {Myers, KS and Ingle, AT and Walters, KA and Fortney, NW and Scarborough, MJ and Donohue, TJ and Noguera, DR}, title = {Comparison of metagenomes from fermentation of various agroindustrial residues suggests a common model of community organization.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {11}, number = {}, pages = {1197175}, pmid = {37260833}, issn = {2296-4185}, abstract = {The liquid residue resulting from various agroindustrial processes is both rich in organic material and an attractive source to produce a variety of chemicals. Using microbial communities to produce chemicals from these liquid residues is an active area of research, but it is unclear how to deploy microbial communities to produce specific products from the different agroindustrial residues. To address this, we fed anaerobic bioreactors one of several agroindustrial residues (carbohydrate-rich lignocellulosic fermentation conversion residue, xylose, dairy manure hydrolysate, ultra-filtered milk permeate, and thin stillage from a starch bioethanol plant) and inoculated them with a microbial community from an acid-phase digester operated at the wastewater treatment plant in Madison, WI, United States. The bioreactors were monitored over a period of months and sampled to assess microbial community composition and extracellular fermentation products. We obtained metagenome assembled genomes (MAGs) from the microbial communities in each bioreactor and performed comparative genomic analyses to identify common microorganisms, as well as any community members that were unique to each reactor. Collectively, we obtained a dataset of 217 non-redundant MAGs from these bioreactors. This metagenome assembled genome dataset was used to evaluate whether a specific microbial ecology model in which medium chain fatty acids (MCFAs) are simultaneously produced from intermediate products (e.g., lactic acid) and carbohydrates could be applicable to all fermentation systems, regardless of the feedstock. MAGs were classified using a multiclass classification machine learning algorithm into three groups, organisms fermenting the carbohydrates to intermediate products, organisms utilizing the intermediate products to produce MCFAs, and organisms producing MCFAs directly from carbohydrates. This analysis revealed common biological functions among the microbial communities in different bioreactors, and although different microorganisms were enriched depending on the agroindustrial residue tested, the results supported the conclusion that the microbial ecology model tested was appropriate to explain the MCFA production potential from all agricultural residues.}, } @article {pmid37260782, year = {2023}, author = {Zhao, X and Ge, Y and Zhang, Y and Zhang, W and Hu, H and Li, L and Sha, T and Zeng, Z and Wu, F and Chen, Z}, title = {Pathogen Diagnosis Value of Nanopore Sequencing in Severe Hospital-Acquired Pneumonia Patients.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {3293-3303}, pmid = {37260782}, issn = {1178-6973}, abstract = {BACKGROUND: Next-generation sequencing of the metagenome (mNGS) is increasingly used in pathogen diagnosis for infectious diseases due to its short detection time. The time for Oxford Nanopore Technologies (ONT) sequencing-based etiology detection is further shortened compared with that of mNGS, but only a few studies have verified the time advantage and accuracy of ONT sequencing for etiology diagnosis. In 2022, a study confirmed that there was no significant difference in sensitivity and specificity between ONT and mNGS in suspected community-acquired pneumonia patients, which there was no clinical study verified in patients with SHAP.

METHODS: From October 24 to November 20, 2022, 10 patients with severe hospital-acquired pneumonia (SHAP) in the Nanfang Hospital intensive care unit (ICU) were prospectively enrolled. Bronchoalveolar lavage fluid (BALF) was collected for ONT sequencing, mNGS, and traditional culture. The differences in pathogen detection time and diagnostic agreement among ONT sequencing, mNGS, traditional culture method, and clinical composite diagnosis were compared.

RESULTS: Compared with mNGS and the traditional culture method, ONT sequencing had a significant advantage in pathogen detection time (9.6±0.7 h versus 24.7±2.7 h versus 132±58 h, P <0.05). The agreement rate between ONT sequencing and the clinical composite diagnosis was 73.3% (kappa value=0.737, P <0.05).

CONCLUSION: ONT sequencing has a potential advantage for rapidly identifying pathogens.}, } @article {pmid37260707, year = {2023}, author = {Li, X and Yi, Y and Wu, T and Chen, N and Gu, X and Xiang, L and Jiang, Z and Li, J and Jin, H}, title = {Integrated microbiome and metabolome analysis reveals the interaction between intestinal flora and serum metabolites as potential biomarkers in hepatocellular carcinoma patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1170748}, pmid = {37260707}, issn = {2235-2988}, mesh = {Humans ; *Carcinoma, Hepatocellular/diagnosis ; *Liver Neoplasms/diagnosis ; *Gastrointestinal Microbiome ; Quality of Life ; Metabolome ; Biomarkers ; Liver Cirrhosis/diagnosis ; Biomarkers, Tumor ; }, abstract = {Globally, liver cancer poses a serious threat to human health and quality of life. Despite numerous studies on the microbial composition of the gut in hepatocellular carcinoma (HCC), little is known about the interactions of the gut microbiota and metabolites and their role in HCC. This study examined the composition of the gut microbiota and serum metabolic profiles in 68 patients with HCC, 33 patients with liver cirrhosis (LC), and 34 healthy individuals (NC) using a combination of metagenome sequencing and liquid chromatography-mass spectrometry (LC-MS). The composition of the serum metabolites and the structure of the intestinal microbiota were found to be significantly altered in HCC patients compared to non-HCC patients. LEfSe and metabolic pathway enrichment analysis were used to identify two key species (Odoribacter splanchnicus and Ruminococcus bicirculans) and five key metabolites (ouabain, taurochenodeoxycholic acid, glycochenodeoxycholate, theophylline, and xanthine) associated with HCC, which then were combined to create panels for HCC diagnosis. The study discovered that the diagnostic performance of the metabolome was superior to that of the microbiome, and a panel comprised of key species and key metabolites outperformed alpha-fetoprotein (AFP) in terms of diagnostic value. Spearman's rank correlation test was used to determine the relationship between the intestinal flora and serum metabolites and their impact on hepatocarcinogenesis and progression. A random forest model was used to assess the diagnostic performance of the different histologies alone and in combination. In summary, this study describes the characteristics of HCC patients' intestinal flora and serum metabolism, demonstrates that HCC is caused by the interaction of intestinal flora and serum metabolites, and suggests that two key species and five key metabolites may be potential markers for the diagnosis of HCC.}, } @article {pmid37260704, year = {2023}, author = {Ma, J and Sabino-Santos, G}, title = {Editorial: Interactions between pathogens and host immune system in patients with immunodeficiency: estimation from high-throughput sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1200638}, pmid = {37260704}, issn = {2235-2988}, mesh = {Humans ; *Immunologic Deficiency Syndromes ; Immune System ; High-Throughput Nucleotide Sequencing ; }, } @article {pmid37260394, year = {2023}, author = {Zhu, Y and Gan, M and Ge, M and Dong, X and Yan, G and Zhou, Q and Yu, H and Wang, X and Cao, Y and Lu, G and Wu, B and Zhou, W}, title = {Diagnostic Performance and Clinical Impact of Metagenomic Next-Generation Sequencing for Pediatric Infectious Diseases.}, journal = {Journal of clinical microbiology}, volume = {61}, number = {6}, pages = {e0011523}, pmid = {37260394}, issn = {1098-660X}, mesh = {Adult ; Humans ; Child ; Retrospective Studies ; *Communicable Diseases/diagnosis ; *Respiratory Tract Infections ; High-Throughput Nucleotide Sequencing ; *Pneumocystis Infections ; Immunosuppressive Agents ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {Metagenomic next-generation sequencing (mNGS) has shown promise in the diagnosis of infectious diseases in adults, while its efficacy in pediatric infections remains uncertain. We performed a retrospective analysis of 1,493 mNGS samples from pediatric patients with blood, central nervous system, and lower respiratory tract infections. The positive percent agreement (PPA) and the negative percent agreement (NPA) of mNGS were compared to conventional microbiological tests (CMT) based on clinical diagnosis. The agreement of mNGS compared to CMT, as well as the clinical impact of mNGS, were valuated. Using the clinical diagnosis as a reference, mNGS demonstrated a significantly higher overall PPA compared to CMT (53.1% [95% CI = 49.7 to 56.6%] versus 25.8% [95% CI = 22.8 to 28.9%]), while maintaining a comparable overall NPA (93.2% [95% CI = 91.3 to 95.1%] versus 97.2% [95% CI = 95.9 to 98.4%]). In septic patients under 6 years of age or with immunosuppressive status, mNGS showed a higher PPA and a comparable NPA compared to CMT. The overall PPA and NPA of mNGS compared to CMT were 75.3 and 75.0%, respectively. The majority of cases of Streptococcus pneumoniae, Streptococcus agalactiae, Mycobacterium tuberculosis complex, and Pneumocystis jirovecii infections were identified by mNGS. A positive clinical impact of 14.0% (206/1,473), a negative impact of 0.8% (11/1,473), a nonimpact of 84.7% (1,248/1,473), and an unknown impact of 0.5% (8/1,473) were observed in the mNGS results. Notably, the positive impact was greater among immunosuppressed patients than among nonimmunosuppressed individuals (67/247, 27.1% versus 139/1,226, 11.3%; P < 0.001). mNGS is valuable for pathogen detection, diagnosis, and clinical management of infections among pediatric patients. mNGS was thus effective for the diagnosis of pediatric infections, which may guide clinical management. Patients with immunosuppressive conditions benefited more from mNGS testing.}, } @article {pmid37260392, year = {2023}, author = {Putman, LI and Schaerer, LG and Wu, R and Kulas, DG and Zolghadr, A and Ong, RG and Shonnard, DR and Techtmann, SM}, title = {Deconstructed Plastic Substrate Preferences of Microbial Populations from the Natural Environment.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0036223}, pmid = {37260392}, issn = {2165-0497}, mesh = {*Plastics/metabolism ; *Polyethylene/metabolism ; RNA, Ribosomal, 16S/genetics ; Polyethylene Terephthalates/metabolism ; Bacteria ; }, abstract = {Over half of the world's plastic waste is landfilled, where it is estimated to take hundreds of years to degrade. Given the continued use and disposal of plastic products, it is vital that we develop fast and effective ways to utilize plastic waste. Here, we explore the potential of tandem chemical and biological processing to process various plastics quickly and effectively. Four samples of compost or sediment were used to set up enrichment cultures grown on mixtures of compounds, including disodium terephthalate and terephthalic acid (monomers of polyethylene terephthalate), compounds derived from the chemical deconstruction of polycarbonate, and pyrolysis oil derived from high-density polyethylene plastics. Established enrichment communities were also grown on individual substrates to investigate the substrate preferences of different taxa. Biomass harvested from the cultures was characterized using 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing. These data reveal low-diversity microbial communities structured by differences in culture inoculum, culture substrate source plastic type, and time. Microbial populations from the classes Alphaproteobacteria, Gammaproteobacteria, Actinobacteria, and Acidobacteriae were significantly enriched when grown on substrates derived from high-density polyethylene and polycarbonate. The metagenomic data contain abundant aromatic and aliphatic hydrocarbon degradation genes relevant to the biodegradation of deconstructed plastic substrates used here. We show that microbial populations from diverse environments are capable of growth on substrates derived from the chemical deconstruction or pyrolysis of multiple plastic types and that paired chemical and biological processing of plastics should be further developed for industrial applications to manage plastic waste. IMPORTANCE The durability and impermeable nature of plastics have made them a popular material for numerous applications, but these same qualities make plastics difficult to dispose of, resulting in massive amounts of accumulated plastic waste in landfills and the natural environment. Since plastic use and disposal are projected to increase in the future, novel methods to effectively break down and dispose of current and future plastic waste are desperately needed. We show that the products of chemical deconstruction or pyrolysis of plastic can successfully sustain the growth of low-diversity microbial communities. These communities were enriched from multiple environmental sources and are capable of degrading complex xenobiotic carbon compounds. This study demonstrates that tandem chemical and biological processing can be used to degrade multiple types of plastics over a relatively short period of time and may be a future avenue for the mitigation of rapidly accumulating plastic waste.}, } @article {pmid37260265, year = {2023}, author = {Hosszu-Fellous, K and Zanella, MC and Kaiser, L and Neofytos, D}, title = {The present and future of blood virome in allogeneic hematopoietic cell transplant recipients.}, journal = {Current opinion in infectious diseases}, volume = {36}, number = {4}, pages = {243-249}, doi = {10.1097/QCO.0000000000000928}, pmid = {37260265}, issn = {1473-6527}, mesh = {Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Transplant Recipients ; Virome ; Immunosuppression Therapy ; }, abstract = {PURPOSE OF REVIEW: Allogeneic hematopoietic cell transplantation (allogeneic HCT) is a highly effective therapy for a broad range of hematological diseases and its use is increasing worldwide. Despite advances in antiviral prophylaxis and treatment, viral infections are still one of the leading causes of post-HCT morbidity and mortality. In this patient population, metagenomic next-generation sequencing (mNGS) revealed a much larger diversity of viruses than previously suspected via the targeted screening approach. In the context of profound immunosuppression, these viral infections may cause transient viremia or protracted replication and potentially be associated with yet unrecognized or unspecific clinical manifestations. On the contrary, by constantly interacting with the immune system, viral infections may have a significant impact on posttransplant outcomes. Here, we review the latest advances in research assessing the role of the blood virome in the development of post-HCT complications.

RECENT FINDINGS: Research efforts are under way to uncover the potential role of several previously undetected viruses in the development of allogeneic HCT complications and their impact on transplant outcomes.

SUMMARY: The identification of viral actors impacting post-HCT morbidity and survival is key to optimize monitoring and infection prevention/treatment strategies.}, } @article {pmid37260140, year = {2023}, author = {Zhang, H and Jin, K and Xiong, K and Jing, W and Pang, Z and Feng, M and Cheng, X}, title = {Disease-associated gut microbiome and critical metabolomic alterations in patients with colorectal cancer.}, journal = {Cancer medicine}, volume = {12}, number = {14}, pages = {15720-15735}, pmid = {37260140}, issn = {2045-7634}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/pathology ; Bacteria/genetics ; *Microbiota/genetics ; Carcinogenesis ; }, abstract = {BACKGROUND: Gut microbiota plays a significant role in the colorectal cancer (CRC) process. Ectopic colonization of multiple oral bacteria is reportedly associated with CRC pathogenesis and progression, but the details remain unclear.

METHODS: We enrolled a cohort of 50 CRC patients and 52 healthy controls from an East China population. Taxonomic and functional analysis of the fecal microbiota were performed using 16S rDNA (50 + 52 samples) and shotgun metagenomic sequencing (8 + 6 samples), respectively, with particular attention paid to gut-colonized oral bacteria.

RESULTS AND CONCLUSIONS: The results showed more detected bacterial species but lower species evenness within the samples from CRC patients. To determine the specific bacteria enriched in each group, we analyzed their possible protective, carcinogenic, or opportunistic roles in the CRC process. Among the ectopic oral bacteria, we observed a significant increase in the abundance of Fusobacterium and decreased abundance of Prevotella and Ruminococcus in the CRC group. Main differences in the functional composition of these two groups were related to energy metabolism and biosynthesis, especially the glycolytic pathway. Furthermore, we validated the colonization of Fusobacterium nucleatum subsp. animalis within CRC tissues and studied its impact on the host intestinal epithelium and tumor cells. With high selectivity for cancerous tissues, this subspecies promoted CRC cell proliferation and induced potential DNA damage.}, } @article {pmid37260063, year = {2023}, author = {Tandale, BV and Narang, R and Vijay Kumar, G and Jain, M and Tomar, SJ and Deshmukh, PS}, title = {Infectious Causes of Acute Encephalitis Syndrome in India - Decadal Change and the Way Forward.}, journal = {Indian pediatrics}, volume = {60}, number = {9}, pages = {709-713}, pmid = {37260063}, issn = {0974-7559}, mesh = {Child ; Adult ; Humans ; Aged ; *Acute Febrile Encephalopathy/diagnosis/epidemiology/etiology ; *Encephalitis, Japanese/diagnosis/epidemiology ; *Encephalitis/diagnosis/epidemiology ; India/epidemiology ; *Communicable Diseases ; }, abstract = {The diagnosis and management of encephalitis were previously largely based on clinical grounds and minimal laboratory investigations. Japanese encephalitis (JE) gets considered as the probable diagnosis in most encephalitis cases. However, reports of JE in adults and the elderly are increasing after the JE vaccine introduction among children in 2006. The Nipah virus (NiV) emerged in 2002 and continues to afflict humans in new geographic areas. Many other infections cause encephalitis, including Chandipura, chikungunya, dengue, and West Nile. Significant advances in diagnostic testing like multiplex testing panels and metagenomic approaches along with sequencing have helped in the detection of new etiologies. Recent years have witnessed an increase in climate-sensitive zoonotic diseases with encephalitis. This highlights the importance of the One Health approach in studying the impact of climate change-associated infectious diseases on human health. The government of India's efforts to develop health research infrastructure would help future responses to emerging infectious disease epidemics.}, } @article {pmid37259758, year = {2023}, author = {Shi, XQ and Tian, L and Huang, ZH and Song, WT and Wu, JB and Chen, LM}, title = {Metagenomic next-generation sequencing vs. conventional detection methods for detecting the pulmonary infections.}, journal = {European review for medical and pharmacological sciences}, volume = {27}, number = {10}, pages = {4752-4763}, doi = {10.26355/eurrev_202305_32486}, pmid = {37259758}, issn = {2284-0729}, mesh = {Humans ; Retrospective Studies ; *Pneumonia ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/therapeutic use ; Bronchoalveolar Lavage Fluid ; Sensitivity and Specificity ; }, abstract = {OBJECTIVE: The absence of proper pathogen treatment in the early stages can result in missing out on treatment chances or the overuse of antibiotics, both of which are the primary factors behind fatalities caused by lung infections. In this study, we aimed to investigate the efficacy of metagenomic next-generation sequencing (mNGS) in comparison to conventional detection methods in detecting infectious pathogens.

PATIENTS AND METHODS: In this retrospective study, the infection pathogens of 104 patients were examined, and 86 bronchoalveolar lavage fluid (BALF), eight pleural effusions, and ten sputum samples were collected. The conventional detection approaches and mNGS analysis were used to determine the infection pathogen profiles and their detection rates were analyzed.

RESULTS: Our study showed that mNGS was more sensitive (89.42%) than the conventional detection methods (56.73%) (p < 0.001), with a 32.69% improvement in sensitivity. The efficacy of mNGS in detecting mixed infections was significantly higher than that of conventional detection methods, with a detection rate of 85.29% compared to 17.65% (p < 0.001). The study demonstrated that mNGS had a higher sensitivity than the conventional detection methods when it came to diagnosing pulmonary infections, making it a potentially useful tool for clinical diagnosis.

CONCLUSIONS: Combining mNGS with other pathogenic detection techniques can be an effective way to increase the rate of detecting pulmonary infections, as well as to provide guidance for treatment adjustments. Furthermore, the timing of sample collection and antibiotic administration can influence the effectiveness of mNGS when used on BALF specimens.}, } @article {pmid37259161, year = {2023}, author = {Mehringer, S and Seiler, E and Droop, F and Darvish, M and Rahn, R and Vingron, M and Reinert, K}, title = {Hierarchical Interleaved Bloom Filter: enabling ultrafast, approximate sequence queries.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {131}, pmid = {37259161}, issn = {1474-760X}, mesh = {*Software ; *Algorithms ; }, abstract = {We present a novel data structure for searching sequences in large databases: the Hierarchical Interleaved Bloom Filter (HIBF). It is extremely fast and space efficient, yet so general that it could serve as the underlying engine for many applications. We show that the HIBF is superior in build time, index size, and search time while achieving a comparable or better accuracy compared to other state-of-the-art tools. The HIBF builds an index up to 211 times faster, using up to 14 times less space, and can answer approximate membership queries faster by a factor of up to 129.}, } @article {pmid37259063, year = {2023}, author = {Ormaasen, I and Rudi, K and Diep, DB and Snipen, L}, title = {Metagenome-mining indicates an association between bacteriocin presence and strain diversity in the infant gut.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {295}, pmid = {37259063}, issn = {1471-2164}, mesh = {*Metagenome ; Humans ; Child, Preschool ; Child ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Aged ; Aged, 80 and over ; Data Mining ; *Gastrointestinal Microbiome/drug effects ; Bacteriocins/pharmacology ; Genome ; }, abstract = {BACKGROUND: Our knowledge about the ecological role of bacterial antimicrobial peptides (bacteriocins) in the human gut is limited, particularly in relation to their role in the diversification of the gut microbiota during early life. The aim of this paper was therefore to address associations between bacteriocins and bacterial diversity in the human gut microbiota. To investigate this, we did an extensive screening of 2564 healthy human gut metagenomes for the presence of predicted bacteriocin-encoding genes, comparing bacteriocin gene presence to strain diversity and age.

RESULTS: We found that the abundance of bacteriocin genes was significantly higher in infant-like metagenomes (< 2 years) compared to adult-like metagenomes (2-107 years). By comparing infant-like metagenomes with and without a given bacteriocin, we found that bacteriocin presence was associated with increased strain diversities.

CONCLUSIONS: Our findings indicate that bacteriocins may play a role in the strain diversification during the infant gut microbiota establishment.}, } @article {pmid37258873, year = {2023}, author = {Coleman, A and Bose, A and Mitra, S}, title = {Metagenomics Data Visualization Using R.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {359-392}, pmid = {37258873}, issn = {1940-6029}, mesh = {*Software ; *Metagenomics ; Data Visualization ; Programming Languages ; }, abstract = {Communicating key finds is a crucial part of the research process. Data visualization is the field of graphically representing data to help communicate key findings. Building on previous chapters around data manipulating using the R programming language this, chapter will explore how to use R to plot data and generate high-quality graphics. It will cover plotting using the base R plotting functionality and introduce the famous ggplot2 package [2] that is widely used for data visualization in R. After this general introduction to data visualization tools, the chapter will explore more specific data visualization techniques for metagenomics data and their use cases using these basic packages.}, } @article {pmid37258872, year = {2023}, author = {Coleman, A and Callaghan, M}, title = {Manipulating and Basic Analysis of Tabular Metagenomics Datasets Using R.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {339-357}, pmid = {37258872}, issn = {1940-6029}, mesh = {*Software ; *Metagenomics ; Programming Languages ; Workflow ; }, abstract = {Handling and manipulating tabular datasets is a critical step in every metagenomics analysis pipeline. The R statistical programming language offers a variety of versatile tools for working with tabular data that allow for the development of computationally efficient and reproducible workflows. Here we outline the basics of the R programming language and showcase a number of tools for data manipulation and basic analysis of metagenomics datasets.}, } @article {pmid37258871, year = {2023}, author = {Mangalea, MR and Keift, K and Duerkop, BA and Anantharaman, K}, title = {Assembly and Annotation of Viral Metagenomes from Short-Read Sequencing Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {317-337}, pmid = {37258871}, issn = {1940-6029}, mesh = {Humans ; Metagenome ; Genomics ; Metagenomics/methods ; *Viruses/genetics ; *Bacteriophages/genetics ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Viral metagenomics enables the detection, characterization, and quantification of viral sequences present in shotgun-sequenced datasets of purified virus-like particles and whole metagenomes. Next generation sequencing (Illumina) derived short single or paired-end read runs are a principal platform for metagenomics, and assembly of short reads allows for the identification of distinguishing viral signatures and complex genomic features for taxonomy and functional annotation. Here we describe the identification and characterization of viral genome sequences, bacteriophages, and eukaryotic viruses, from a cohort of human stool samples, using multiple methods. Following the purification of virus-like particles, sequencing, quality refinement, and genome assembly, we begin the protocol with raw short reads deposited in an open-source nucleotide archive. We highlight the use of VIBRANT, an automated computational tool for the characterization of microbial viruses and their viral community function. Finally, we also describe an alternative assembly-free option of mapping reads to established databases of reference genomes and previously characterized metagenome-assembled viral genomes.}, } @article {pmid37258870, year = {2023}, author = {Yung, PYM and Tan, SM}, title = {Targeted Enrichment of Low-Abundance and Uncharacterized Taxon Members in Complex Microbial Community with Primer-Free FISH Probes Designed from Next Generation Sequencing Dataset.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {303-315}, pmid = {37258870}, issn = {1940-6029}, mesh = {*High-Throughput Nucleotide Sequencing ; In Situ Hybridization, Fluorescence/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Methods to obtain high-quality assembled genomic information of rare and unclassified member species in complex microbial communities remain a high priority in microbial ecology. Additionally, the supplementation of three-dimensional spatial information that highlights the morphology and spatial interaction would provide additional insights to its ecological role in the community. Fluorescent in-situ hybridization (FISH) coupling with fluorescence-activated cell sorting (FACS) is a powerful tool that enables the detection, visualization, and separation of low-abundance microbial members in samples containing complex microbial compositions. Here, we have described the workflow from designing the appropriate FISH probes from metagenomics or metatranscriptomics datasets to the preparation and treatment of samples to be used in FISH-FACS procedures.}, } @article {pmid37258869, year = {2023}, author = {Abdelrazik, E and El-Hadidi, M}, title = {Tracking Antibiotic Resistance from the Environment to Human Health.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {289-301}, pmid = {37258869}, issn = {1940-6029}, mesh = {Humans ; *Bacteria/genetics ; Drug Resistance, Microbial/genetics ; *Anti-Bacterial Agents/pharmacology ; Genome, Bacterial ; Metagenome ; Genes, Bacterial ; Metagenomics ; }, abstract = {Antimicrobial resistance (AMR) is one of the threats to our world according to the World Health Organization (WHO). Resistance is an evolutionary dynamic process where host-associated microbes have to adapt to their stressful environments. AMR could be classified according to the mechanism of resistance or the biome where resistance takes place. Antibiotics are one of the stresses that lead to resistance through antibiotic resistance genes (ARGs). The resistome could be defined as the collection of all ARGs in an organism's genome or metagenome. Currently, there is a growing body of evidence supporting that the environment is the largest source of ARGs, but to what extent the environment does contribute to the antimicrobial resistance evolution is a matter of investigation. Monitoring the ARGs transfer route from the environment to humans and vice versa is a nature-to-nature feedback loop where you cannot set an accurate starting point of the evolutionary event. Thus, tracking resistome evolution and transfer to and from different biomes is crucial for the surveillance and prediction of the next resistance outbreak.Herein, we review the overlap between clinical and environmental resistomes and the available databases and computational analysis tools for resistome analysis through ARGs detection and characterization in bacterial genomes and metagenomes. Till this moment, there is no tool that can predict the resistance evolution and dynamics in a distinct biome. But, hopefully, by understanding the complicated relationship between the environmental and clinical resistome, we could develop tools that track the feedback loop from nature to nature in terms of evolution, mobilization, and transfer of ARGs.}, } @article {pmid37258867, year = {2023}, author = {Callaghan, M}, title = {Cloud Computing for Metagenomics: Building a Personalized Computational Platform for Pipeline Analyses.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {261-279}, pmid = {37258867}, issn = {1940-6029}, mesh = {*Software ; *Metagenomics ; Cloud Computing ; Computers ; Web Browser ; Computational Biology/methods ; }, abstract = {Cloud Computing services such as Microsoft Azure, Amazon Web Services, and Google Cloud provide a range of tools and services that enable scientists to rapidly prototype, build, and deploy platforms for their computational experiments.This chapter describes a protocol to deploy and configure an Ubuntu Linux Virtual Machine in the Microsoft Azure cloud, which includes Minconda Python, a Jupyter Lab server, and the QIIME toolkit configured for access through a web browser to facilitate a typical metagenomics analysis pipeline.}, } @article {pmid37258866, year = {2023}, author = {Arumugam, K and Bessarab, I and Haryono, MAS and Williams, RBH}, title = {Recovery and Analysis of Long-Read Metagenome-Assembled Genomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {235-259}, pmid = {37258866}, issn = {1940-6029}, mesh = {*Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis, DNA/methods ; Base Sequence ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {The development of long-read nucleic acid sequencing is beginning to make very substantive impact on the conduct of metagenome analysis, particularly in relation to the problem of recovering the genomes of member species of complex microbial communities. Here we outline bioinformatics workflows for the recovery and characterization of complete genomes from long-read metagenome data and some complementary procedures for comparison of cognate draft genomes and gene quality obtained from short-read sequencing and long-read sequencing.}, } @article {pmid37258863, year = {2023}, author = {Jadeja, NB and Kapley, A}, title = {Designing Knowledge-Based Bioremediation Strategies Using Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {195-208}, pmid = {37258863}, issn = {1940-6029}, mesh = {Biodegradation, Environmental ; *Metagenomics/methods ; Wastewater ; *Microbiota ; Metagenome ; }, abstract = {Functional capacities for bioremediation are governed by metabolic mechanisms of inhabiting microbial communities at polluted niches. Process fluctuations lead to stress scenarios where microbes evolve continuously to adapt to sustain the harsh conditions. The biological wastewater treatment (WWT) process harbors the potential of these catabolic microbes for the degradation of organic molecules. In a typical biological WWT or soil bioremediation process, several microbial species coexist which code for enzymes that degrade complex compounds.High throughput DNA sequencing techniques for microbiome analysis in bioremediation processes have led to a powerful paradigm revealing the significance of metabolic functions and microbial diversity. The present chapter describes techniques in taxonomy and functional gene analysis for understanding bioremediation potential and novel strategies built on in silico analysis for the improvisation of existing aerobic wastewater treatment methods. Methods explaining comparative metagenomics by Metagenome Analysis server (MG-RAST) are described with successful case studies by focusing on industrial wastewaters and soil bioremediation studies.}, } @article {pmid37258862, year = {2023}, author = {Arumugam, R and Ravichandran, P and Yeap, SK and Sharma, RSK and Zulkifly, SB and Yawah, D and Annavi, G}, title = {Application of High-Throughput Sequencing (HTS) to Enhance the Well-Being of an Endangered Species (Malayan Tapir): Characterization of Gut Microbiome Using MG-RAST.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {175-194}, pmid = {37258862}, issn = {1940-6029}, mesh = {Animals ; *Endangered Species ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Animals, Wild ; High-Throughput Nucleotide Sequencing ; }, abstract = {The Tapirus indicus, also known as Malayan tapir, has been listed as a rapidly declining animal species in the past decades, along with being declared and categorized as an endangered species by the International Union for Conservation of Nature (IUCN) 2016. This tapir species is geographically distributed across several countries in Southeast Asia such as Peninsular Malaysia, Indonesia (Sumatra), South Thailand, and Myanmar. Amongst these countries, the Peninsula Malaysia forest is recorded to contain the highest number of Malayan tapir population. Unfortunately, in the past decades, the population of Malayan tapirs has declined swiftly due to serious deforestation, habitat fragmentation, and heavy vehicle accidents during road crossings at forest routes. Concerned by this predicament, the Department of Wildlife and National Parks (DWNP) Peninsular Malaysia collaborated with a few local universities to conduct various studies aimed at increasing the population number of tapirs in Malaysia. Several studies were conducted with the aim of enhancing the well-being of tapirs in captivity. Veterinarians face problems when it comes to selecting healthy and suitable tapirs for breeding programs at conservation centers. Conventional molecular methods using high-throughput sequencing provides a solution in determining the health condition of Malayan tapirs using the Next-Generation Sequencing (NGS) technology. Unaware by most, gut microbiome plays an important role in determining the health condition of an organism by various aspects: (1) digestion control; (2) benefiting the immune system; and (3) playing a role as a "second brain." Commensal gut bacterial communities (microbiomes) are predicted to influence organism health and disease. Imbalance of unhealthy and healthy microbes in the gut may contribute to weight gain, high blood sugar, high cholesterol, and other disorders. In infancy, neonatal gut microbiomes are colonized with maternal and environmental flora, and mature toward a stable composition in two to three years. Interactions between the microorganism communities and the host allow for the establishment of microbiological roles. Identifying the core microbiome(s) are essential in the prediction of diseases and changes in environmental behavior of microorganisms. The dataset of 16S rRNA amplicon sequencing of Malayan tapir was deposited in the MG-RAST portal. Parameters such as quality control, taxonomic prediction (unknown and predicted), diversity (rarefaction), and diversity (alpha) were analyzed using sequencing approaches (Amplicon sequencing). Comparisons of parameters, according to the type of sequencing, showed significant differences, except for the prediction variable. In the Amplicon sequencing datasets, the parameters Rarefaction and Unknown had the highest correlation, while Alpha and Predicted had the lowest. Firmicutes, Bacteroidetes, Proteobacteria, Bacilli, and Bacteroidia were the most representative genera in Malayan tapir amplicon sequences, which indicated that most of the tapirs were healthy. However, continuous assessment to maintain the well-being of tapir for long term is still required. This chapter focuses on the introduction of 16S rRNA amplicon metagenomics in analyzing Malayan tapir gut microbiome dataset.}, } @article {pmid37258861, year = {2023}, author = {Abdelsalam, NA and Elshora, H and El-Hadidi, M}, title = {Interactive Web-Based Services for Metagenomic Data Analysis and Comparisons.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {133-174}, pmid = {37258861}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; Metagenome ; *Microbiota/genetics ; Ecology ; Computational Biology/methods ; Data Analysis ; }, abstract = {Recently, sequencing technologies have become readily available, and scientists are more motivated to conduct metagenomic research to unveil the potential of a myriad of ecosystems and biomes. Metagenomics studies the composition and functions of microbial communities and paves the way to multiple applications in medicine, industry, and ecology. Nonetheless, the immense amount of sequencing data of metagenomics research and the few user-friendly analysis tools and pipelines carry a new challenge to the data analysis.Web-based bioinformatics tools are now being developed to facilitate the analysis of complex metagenomic data without prior knowledge of any programming languages or special installation. Specialized web tools help answer researchers' main questions on the taxonomic classification, functional capabilities, discrepancies between two ecosystems, and the probable functional correlations between the members of a specific microbial community. With an Internet connection and a few clicks, researchers can conveniently and efficiently analyze the metagenomic datasets, summarize results, and visualize key information on the composition and the functional potential of metagenomic samples under study. This chapter provides a simple guide to a few of the fundamental web-based services used for metagenomic data analyses, such as BV-BRC, RDP, MG-RAST, MicrobiomeAnalyst, METAGENassist, and MGnify.}, } @article {pmid37258860, year = {2023}, author = {Gautam, A and Zeng, W and Huson, DH}, title = {DIAMOND + MEGAN Microbiome Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {107-131}, pmid = {37258860}, issn = {1940-6029}, mesh = {*Software ; *Microbiota/genetics ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; Databases, Factual ; Metagenome ; Algorithms ; }, abstract = {Metagenomics is the study of microbiomes using DNA sequencing technologies. Basic computational tasks are to determine the taxonomic composition (who is out there?), the functional composition (what can they do?), and also to correlate changes of composition to changes in external parameters (how do they compare?). One approach to address these issues is to first align all sequences against a protein reference database such as NCBI-nr and to then perform taxonomic and functional binning of all sequences based on their alignments. The resulting classifications can then be interactively analyzed and compared. Here we illustrate how to pursue this approach using the DIAMOND+MEGAN pipeline, on two different publicly available datasets, one containing short-read samples and other containing long-read samples.}, } @article {pmid37258858, year = {2023}, author = {Wang, D}, title = {Amplicon Sequencing Pipelines in Metagenomics.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {69-83}, pmid = {37258858}, issn = {1940-6029}, mesh = {Sequence Analysis, DNA ; *Metagenomics ; *High-Throughput Nucleotide Sequencing ; Gene Library ; Computational Biology ; Software ; }, abstract = {Taxonomic profiling among a large number of samples is a fundamental task during amplicon sequencing analysis. The heterogeneity and technical noises in the sample handling, library preparation, and sequencing present a major challenge to how the biological conclusions are drawn from the data analysis, and accordingly, many tools have been developed to address specific issues related to each step of the data analysis. Nowadays, several sophisticated computational pipelines with flexible parameters are made available to provide one-stop comprehensive solutions by integrating various tools, which significantly mitigate the burden imposed by the complexity of the metagenomics data analysis. This chapter discusses the best practices related to the data generation and describes bioinformatics approaches to achieving greater accuracy from data processing. It offers two independent stepwise pipelines using mothur and DADA2 in a parallel way, presents the basic principles in the key steps of the analysis, and enables the comparisons between the two pipelines straightforwardly.}, } @article {pmid37258857, year = {2023}, author = {Wang, D}, title = {Metagenomics Databases for Bacteria.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {55-67}, pmid = {37258857}, issn = {1940-6029}, mesh = {Phylogeny ; *Metagenomics ; Bacteria/genetics ; Databases, Genetic ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The booming sequencing technologies have turned metagenomics into a widely used tool for microbe-related studies, especially in the areas of clinical medicine and ecology. Accordingly, the toolkit of metagenomics data analysis is growing stronger to provide multiple approaches for solving various biological questions and understanding the component and function of microbiome. As part of the toolkit, metagenomics databases play a central role in the creation and maintenance of processed data such as definition of taxonomic classifications, annotation of gene functions, sequence alignment, and phylogenetic tree inference. The availability of a large quantity of high-quality bacterial genomic sequences contributes significantly to the construction and update of metagenomics databases, which constitute the core resource for metagenomics data analysis at various scales. This chapter presents the key concepts, technical options, and challenges for metagenomics projects as well as the curation processes and versatile functions for the four representative bacterial metagenomics databases, including Greengenes, SILVA, Ribosomal Database Project (RDP), and Genome Taxonomy Database (GTDB).}, } @article {pmid37258856, year = {2023}, author = {Gihawi, A and Cardenas, R and Hurst, R and Brewer, DS}, title = {Quality Control in Metagenomics Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {21-54}, pmid = {37258856}, issn = {1940-6029}, mesh = {Reproducibility of Results ; *Metagenomics/methods ; Computational Biology/methods ; *Microbiota ; Research Design ; }, abstract = {Experiments involving metagenomics data are become increasingly commonplace. Processing such data requires a unique set of considerations. Quality control of metagenomics data is critical to extracting pertinent insights. In this chapter, we outline some considerations in terms of study design and other confounding factors that can often only be realized at the point of data analysis.In this chapter, we outline some basic principles of quality control in metagenomics, including overall reproducibility and some good practices to follow. The general quality control of sequencing data is then outlined, and we introduce ways to process this data by using bash scripts and developing pipelines in Snakemake (Python).A significant part of quality control in metagenomics is in analyzing the data to ensure you can spot relationships between variables and to identify when they might be confounded. This chapter provides a walkthrough of analyzing some microbiome data (in the R statistical language) and demonstrates a few days to identify overall differences and similarities in microbiome data. The chapter is concluded by discussing remarks about considering taxonomic results in the context of the study and interrogating sequence alignments using the command line.}, } @article {pmid37258855, year = {2023}, author = {Benz, S and Mitra, S}, title = {From Genomics to Metagenomics in the Era of Recent Sequencing Technologies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2649}, number = {}, pages = {1-20}, pmid = {37258855}, issn = {1940-6029}, mesh = {Humans ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Genomics ; *Microbiota/genetics ; Metagenome ; }, abstract = {Metagenomics, also known as environmental genomics, is the study of the genomic content of a sample of organisms obtained from a common habitat. Metagenomics and other "omics" disciplines have captured the attention of researchers for several decades. The effect of microbes in our body is a relevant concern for health studies. Through sampling the sequences of microbial genomes within a certain environment, metagenomics allows study of the functional metabolic capacity of a community as well as its structure based upon distribution and richness of species. Exponentially increasing number of microbiome literatures illustrate the importance of sequencing techniques which have allowed the expansion of microbial research into areas, including the human gut, antibiotics, enzymes, and more. This chapter illustrates how metagenomics field has evolved with the progress of sequencing technologies.Further, from this chapter, researchers will be able to learn about all current options for sequencing techniques and comparison of their cost and read statistics, which will be helpful for planning their own studies.}, } @article {pmid37258543, year = {2023}, author = {Liu, J and Sun, J and Yu, J and Chen, H and Zhang, D and Zhang, T and Ma, Y and Zou, C and Zhang, Z and Ma, L and Yu, X}, title = {Gut microbiome determines therapeutic effects of OCA on NAFLD by modulating bile acid metabolism.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {29}, pmid = {37258543}, issn = {2055-5008}, mesh = {Mice ; Animals ; *Non-alcoholic Fatty Liver Disease/drug therapy/metabolism ; *Gastrointestinal Microbiome ; Chenodeoxycholic Acid/pharmacology/therapeutic use ; Bile Acids and Salts ; }, abstract = {Non-alcoholic fatty liver disease (NAFLD), the most common chronic liver disease, had no approved pharmacological agents yet. Obeticholic acid (OCA), a novel bile acid derivative, was demonstrated to ameliorate NAFLD-related manifestations. Regarding the role of gut-liver axis in liver disease development, this study aimed to explore the potential role of gut microbiota in the treatment of OCA in NAFLD mice induced by the high-fat diet (HFD). Antibiotic-induced microbiome depletion (AIMD) and fecal microbiota transplantation (FMT) confirmed the critical role of gut microbiota in OCA treatment for NAFLD by effectively alleviating histopathological lesions and restoring liver function impaired by HFD. Metagenomic analysis indicated that OCA intervention in HFD mice remarkably increased the abundance of Akkermansia muciniphila, Bifidobacterium spp., Bacteroides spp., Alistipes spp., Lactobacillus spp., Streptococcus thermophilus, and Parasutterella excrementihominis. Targeted metabolomics analysis indicated that OCA could modulate host bile acids pool by reducing levels of serum hydrophobic cholic acid (CA) and chenodeoxycholic acid (CDCA), and increasing levels of serum-conjugated bile acids, such as taurodeoxycholic acid (TDCA) and tauroursodesoxycholic acid (TUDCA) in the HFD-fed mice. Strong correlations were observed between differentially abundant microbes and the shifted bile acids. Furthermore, bacteria enriched by OCA intervention exhibited much greater potential in encoding 7alpha-hydroxysteroid dehydrogenase (7α-HSDs) producing secondary bile acids rather than bile salt hydrolases (BSHs) mainly responsible for primary bile acid deconjugation. In conclusion, this study demonstrated that OCA intervention altered gut microbiota composition with specially enriched gut microbes modulating host bile acids, thus effectively alleviating NAFLD in the mice.}, } @article {pmid37258268, year = {2023}, author = {Lee, M and Hwang, SM and Park, JS and Park, JH and Park, JS}, title = {Lophomonas blattarum-like organism in bronchoalveolar lavage from a pneumonia patient: current diagnostic scheme and polymerase chain reaction can lead to false-positive results.}, journal = {Parasites, hosts and diseases}, volume = {61}, number = {2}, pages = {202-209}, pmid = {37258268}, issn = {2982-6799}, mesh = {Humans ; *Lung Diseases, Parasitic/diagnosis ; *Parabasalidea ; *Protozoan Infections/diagnosis ; Bronchoalveolar Lavage Fluid ; *Pneumonia, Mycoplasma ; }, abstract = {Lophomonas blattarum is an anaerobic protozoan living in the intestine of cockroaches and house dust mites, with ultramicroscopic characteristics such as the presence of a parabasal body, axial filament, and absence of mitochondria. More than 200 cases of Lophomonas infection of the respiratory tract have been reported worldwide. However, the current diagnosis of such infection depends only on light microscopic morphological findings from respiratory secretions. In this study, we attempted to provide more robust evidence of protozoal infection in an immunocompromised patient with atypical pneumonia, positive for Lophomonas-like protozoal cell forms. A direct search of bronchoalveolar lavage fluid via polymerase chain reaction (PCR), transmission electron microscopy (TEM), and metagenomic next-generation sequencing did not prove the presence of protozoal infection. PCR results were not validated with sufficient rigor, while de novo assembly and taxonomic classification results did not confirm the presence of an unidentified pathogen. The TEM results implied that such protozoal forms in light microscopy are actually non-detached ciliated epithelial cells. After ruling out infectious causes, the patient's final diagnosis was drug-induced pneumonitis. These findings underscore the lack of validation in the previously utilized diagnostic methods, and more evidence in the presence of L. blattarum is required to further prove its pathogenicity.}, } @article {pmid37257865, year = {2023}, author = {Favale, N and Farina, R and Carrieri, A and Simonelli, A and Severi, M and Sabbioni, S and Trombelli, L and Scapoli, C}, title = {Functional profile of oral plaque microbiome: Further insight into the bidirectional relationship between type 2 diabetes and periodontitis.}, journal = {Molecular oral microbiology}, volume = {}, number = {}, pages = {}, doi = {10.1111/omi.12418}, pmid = {37257865}, issn = {2041-1014}, support = {//Research Centre for the Study of Periodontal and Peri-implant Diseases, University of Ferrara, Italy/ ; FIR2017//University of Ferrara, Italy/ ; FAR2018-2019//University of Ferrara, Italy/ ; }, abstract = {Increasing evidence support the association between the oral microbiome and human systemic diseases. This association may be attributed to the ability of many oral microbes to influence the inflammatory microenvironment. Herein, we focused our attention on the bidirectional relationship between periodontitis and type 2 diabetes using high-resolution whole metagenomic shotgun analysis to explore the composition and functional profile of the subgingival microbiome in diabetics and non-diabetics subjects with different periodontal conditions. In the present study, the abundance of metabolic pathways encoded by oral microbes was reconstructed from the metagenome, and we identified a set of dysregulated metabolic pathways significantly enriched in the periodontitis and/or diabetic patients. These pathways were mainly involved in branched and aromatic amino acids metabolism, fatty acid biosynthesis and adipocytokine signaling pathways, ferroptosis and iron homeostasis, nucleotide metabolism, and finally in the peptidoglycan and lipopolysaccharides synthesis. Overall, the results of the present study provide evidence in favor of the hypothesis that during the primary inflammatory challenge, regardless of whether it is induced by periodontitis or diabetes, endotoxemia and/or the release of inflammatory cytokines cause a change in precursor and/or in circulating innate immune cells. Dysbiosis and inflammation, also via oral-gut microbiome axis or adipose tissue, reduce the efficacy of the host immune response, while fueling inflammation and can induce that metabolic/epigenetic reprogramming of chromatin accessibility of genes related to the immune response. Moreover, the presence of an enhanced ferroptosis and an imbalance in purine/pyrimidine metabolism provides new insights into the role of ferroptotic death in this comorbidity.}, } @article {pmid37257800, year = {2023}, author = {Knox, MA and Wierenga, J and Biggs, PJ and Gedye, K and Almeida, V and Hall, R and Kalema-Zikusoka, G and Rubanga, S and Ngabirano, A and Valdivia-Granda, W and Hayman, DTS}, title = {Abundant dsRNA picobirnaviruses show little geographic or host association in terrestrial systems.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {112}, number = {}, pages = {105456}, doi = {10.1016/j.meegid.2023.105456}, pmid = {37257800}, issn = {1567-7257}, mesh = {Humans ; Animals ; Cattle ; *Picobirnavirus/genetics ; Phylogeny ; RNA, Double-Stranded/genetics ; Gorilla gorilla ; Animals, Domestic ; }, abstract = {Picobirnaviruses are double-stranded RNA viruses known from a wide range of host species and locations but with unknown pathogenicity and host relationships. Here, we examined the diversity of picobirnaviruses from cattle and gorillas within and around Bwindi Impenetrable Forest National Park (BIFNP), Uganda, where wild and domesticated animals and humans live in relatively close contact. We use metagenomic sequencing with bioinformatic analyses to examine genetic diversity. We compared our findings to global Picobirnavirus diversity using clustering-based analyses. Picobirnavirus diversity at Bwindi was high, with 14 near-complete RdRp and 15 capsid protein sequences, and 497 new partial viral sequences recovered from 44 gorilla samples and 664 from 16 cattle samples. Sequences were distributed throughout a phylogenetic tree of globally derived picobirnaviruses. The relationship with Picobirnavirus diversity and host taxonomy follows a similar pattern to the global dataset, generally lacking pattern with either host or geography.}, } @article {pmid37257591, year = {2023}, author = {Guo, Y and Li, D and Gao, Y and Gao, J and Zhang, S and Bao, F}, title = {The knock-on effects of different wastewater feeding modes: Change in microbial communities versus resistance genes in pilot-scale aerobic sludge granulation reactors.}, journal = {The Science of the total environment}, volume = {892}, number = {}, pages = {164500}, doi = {10.1016/j.scitotenv.2023.164500}, pmid = {37257591}, issn = {1879-1026}, mesh = {*Wastewater ; Sewage/microbiology ; Waste Disposal, Fluid ; Bioreactors/microbiology ; Bacteria/genetics ; *Microbiota ; Anti-Bacterial Agents ; }, abstract = {To explore the effects of wastewater feeding modes on the formation of aerobic granular sludge (AGS) and the complex relationships between resistance genes and bacteria, two pilot-scale sequencing batch reactors (SBRs) were established. The SBR with influent wastewater introduced uniformly through pipes at bottom was designated as BSBR, and the SBR with inlet wastewater flowing directly from top was TSBR. BSBR formed dense AGS due to uniform wastewater feeding at bottom, while TSBR failed to cultivate AGS. Metagenomic sequencing illustrated that rapid growth of AGS in BSBR was accompanied with increase of antibiotic resistance genes (ARGs) abundance, but ARGs diminished when the size of AGS was stable. The ARGs continued to elevate in TSBR, and abundance of metal resistance genes (MRGs) was always higher than that in BSBR. Two reactors had markedly different bacterial community, microbes in BSBR owned stronger activity, conferred greater potential to proliferate. AdeF in two systems had the most complex gene-bacteria relationships which would undergo HGT within bacterial genus. The different feeding modes of wastewater directly led to the changing size of sludge, which caused knock-on effects of variations in the abundance of microbial communities and resistance genes. This study provided promising suggestions for the rapid cultivation of AGS and control of resistance genes at pilot-scale.}, } @article {pmid37257294, year = {2023}, author = {Chen, J and Ke, Y and Zhu, Y and Chen, X and Xie, S}, title = {Deciphering of sulfonamide biodegradation mechanism in wetland sediments: from microbial community and individual populations to pathway and functional genes.}, journal = {Water research}, volume = {240}, number = {}, pages = {120132}, doi = {10.1016/j.watres.2023.120132}, pmid = {37257294}, issn = {1879-2448}, mesh = {Humans ; Biodegradation, Environmental ; *Wetlands ; Anti-Bacterial Agents/metabolism ; Sulfonamides ; Sulfanilamide ; Sulfadiazine ; *Microbiota ; }, abstract = {Figuring out the comprehensive metabolic mechanism of sulfonamide antibiotics (SA) is critical to improve and optimize SA removal in the bioremediation process, but relevant studies are still lacking. Here, an approach integrating metagenomic analysis, degraders' isolation, reverse transcriptional quantification and targeted metabolite determination was used to decipher microbial interactions and functional genes' characteristics in SA-degrading microbial consortia enriched from wetland sediments. The SA-degrading consortia could rapidly catalyze ipso-hydroxylation and subsequent reactions of SA to achieve the complete mineralization of sulfadiazine and partial mineralization of the other two typical SA (sulfamethoxazole and sulfamethazine). Paenarthrobacter, Achromobacter, Pseudomonas and Methylobacterium were identified as the primary participants for the initial transformation of SA. Among them, Methylobacterium could metabolize the heterocyclic intermediate of sulfadiazine (2-aminopyrimidine), and the owning of sadABC genes (SA degradation genes) made Paenarthrobacter have relatively higher SA-degrading activity. Besides, the coexistence of sadABC genes and sul1 gene (SA resistance gene) gave Paenarthrobacter a dual resistance mechanism to SA. The results of reverse transcription quantification further demonstrated that the activity of sadA gene was related to the biodegradation of SA. Additionally, sadABC genes were relatively conserved in a few Microbacteriaceae and Micrococcaceae SA-degraders, but the multiple recombination events caused by densely nested transposase encoding genes resulted in the differential sequence of sadAB genes in Paenarthrobacter genome. These new findings provide valuable information for the selection and construction of engineered microbiomes.}, } @article {pmid37257197, year = {2023}, author = {Seki, K and Galindo, JL and Karim, AS and Jewett, MC}, title = {A Cell-Free Gene Expression Platform for Discovering and Characterizing Stop Codon Suppressing tRNAs.}, journal = {ACS chemical biology}, volume = {18}, number = {6}, pages = {1324-1334}, doi = {10.1021/acschembio.3c00051}, pmid = {37257197}, issn = {1554-8937}, support = {T32 GM105538/GM/NIGMS NIH HHS/United States ; }, mesh = {Codon, Terminator/genetics ; *RNA, Transfer/chemistry ; Amino Acids/chemistry ; *Amino Acyl-tRNA Synthetases/genetics/metabolism ; Green Fluorescent Proteins/genetics ; Gene Expression ; }, abstract = {Non-canonical amino acids (ncAAs) can be incorporated into peptides and proteins to create new properties and functions. Site-specific ncAA incorporation is typically enabled by orthogonal translation systems comprising a stop codon suppressing tRNA (typically UAG), an aminoacyl-tRNA synthetase, and an ncAA of interest. Unfortunately, methods to discover and characterize suppressor tRNAs are limited because of laborious and time-consuming workflows in living cells. In this work, we develop anEscherichia coli crude extract-based cell-free gene expression system to rapidly express and characterize functional suppressor tRNAs. Our approach co-expresses orthogonal tRNAs using endogenous machinery alongside a stop-codon containing superfolder green fluorescent protein (sfGFP) reporter, which can be used as a simple read-out for suppression. As a model, we evaluate the UAG and UAA suppressing activity of several orthogonal tRNAs. Then, we demonstrate that co-transcription of two mutually orthogonal tRNAs can direct the incorporation of two unique ncAAs within a single modified sfGFP. Finally, we show that the cell-free workflow can be used to discover putative UAG-suppressor tRNAs found in metagenomic data, which are nonspecifically recognized by endogenous aminoacyl-tRNA synthetases. We anticipate that our cell-free system will accelerate the development of orthogonal translation systems for synthetic biology.}, } @article {pmid37256128, year = {2023}, author = {Sun, CB and Ma, Z and Liu, Z}, title = {Case Report: Optic neuritis as the initial presentation of Orientia tsutsugamushi infection detected by metagenomic next-generation sequencing.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1129246}, pmid = {37256128}, issn = {1664-3224}, mesh = {Male ; Humans ; *Scrub Typhus/diagnosis/drug therapy ; Doxycycline/therapeutic use ; Fever/etiology ; *Optic Neuritis/diagnosis/drug therapy ; High-Throughput Nucleotide Sequencing ; Immunoglobulin M ; Immunoglobulin G ; Steroids ; }, abstract = {Scrub typhus is an acute febrile illness caused by Orientia tsutsugamushi infection, and typically manifested as fever, eschar, lymphadenopathy, rash, and other flu-like signs. Ocular involvement was not uncommon, and mostly occurred at post-fever or recovery stage in scrub typhus cases. We hereby report a case of scrub typhus presenting as unilateral optic neuritis (ON). A 56-year-old man going wild fishing nearly every day complained of a blurred vision and an inferior visual field defect in the right eye two or three days after an insect-bite like shin induration in his left leg. He was diagnosed as ON, and treated with dexamethasone in the local hospital. Unfortunately, his right eye vision progressively deteriorated during steroid therapy. Three days after steroid therapy ceased, he suffered from a high fever and painful subcutaneous masses in the left groin. Peripheral blood test by metagenomic next-generation sequencing (mNGS) was positive for Orientia tsutsugamushi, but negative for other pathogens. The diagnosis was then revised to scrub typhus and ON. His systemic symptoms rapidly disappeared after oral doxycycline and omadacycline therapy. However, his right eye vision continuously deteriorated to hand motion. Further serum tests for aquaporin 4-IgG antibody and myelin oligodendrocyte glycoprotein-IgG antibody were both negative, but for anticardiolipin IgM and beta-2-glycoprotein-I IgM were both positive. The patient's right eye vision gradually improved after doxycycline combined with steroid pulse therapy. Our case indicates that ON in scrub typhus cases may present as a parainfectious inflammation, and that mNGS is a useful and valuable method for early diagnosis of scrub typhus.}, } @article {pmid37255437, year = {2023}, author = {Dallman, TJ and Neuert, S and Fernandez Turienzo, C and Berin, M and Richardson, E and Fuentes-Utrilla, P and Loman, N and Gharbia, S and Jenkins, C and Behrens, RH and Godbole, G and Brown, M}, title = {Prevalence and Persistence of Antibiotic Resistance Determinants in the Gut of Travelers Returning to the United Kingdom is Associated with Colonization by Pathogenic Escherichia coli.}, journal = {Microbiology spectrum}, volume = {11}, number = {4}, pages = {e0518522}, pmid = {37255437}, issn = {2165-0497}, support = {/DH_/Department of Health/United Kingdom ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Escherichia coli/genetics ; Prevalence ; Phylogeny ; Drug Resistance, Microbial ; Travel ; Diarrhea/epidemiology/drug therapy ; *Respiratory Distress Syndrome ; }, abstract = {The gut microbiota constitutes an ideal environment for the selection, exchange, and carriage of antibiotic resistance determinants (ARDs), and international travel has been identified as a risk factor for acquisition of resistant organisms. Here, we present a longitudinal metagenomic analysis of the gut resistome in travellers to "high-risk" countries (Gutback). Fifty volunteers, recruited at a travel clinic in London, United Kingdom, provided stool samples before (pre-travel), immediately after (post-travel), and 6 months after their return (follow-up) from a high-risk destination. Fecal DNA was extracted, metagenomic sequencing performed and the resistome profiled. An increase in abundance and diversity of resistome was observed after travel. Significant increases in abundance were seen in antimicrobial genes conferring resistance to macrolides, third-generation cephalosporins, aminoglycosides, and sulfonamides. There was a significant association with increased resistome abundance if the participant experienced diarrhea during travel or took antibiotics, but these two variables were co-correlated. The resistome abundance returned to pre-travel levels by the 6-month sample point but there was evidence of persistence of several ARDs. The post-travel samples had an increase in abundance Escherichia coli which was positively associated with many acquired resistant determinants. Virulence and phylogenetic profiling revealed pathogenic E. coli significantly contributed to this increase abundance. In summary, in this study, foreign travel remains a significant risk factor for acquisition of microbes conferring resistance to multiple classes of antibiotics, often associated with symptomatic exposure to diarrhoeagenic E. coli. IMPORTANCE A future where antimicrobial therapy is severely compromised by the increase in resistant organisms is of grave concern. Given the variability in prevalence and diversity of antimicrobial resistance determinants in different geographical settings, international travel is a known risk factor for acquisition of resistant organisms into the gut microbiota. In this study, we show the utility of metagenomic approaches to quantify the levels of acquisition and carriage of resistance determinants after travel to a "high-risk" setting. Significant modulation to the resistome was seen after travel that is largely resolved within 6 months, although evidence of persistence of several ARDs was observed. Risk factors for acquisition included experiencing a diarrheal episode and the use of antibiotics. Colonization by pathogenic Escherichia coli was correlated with an increase in acquisition of antimicrobial resistance determinants, and as such established public health guidance to travelers on food and water safety remain an important message to reduce the spread of antibiotic resistance.}, } @article {pmid37254939, year = {2023}, author = {Gager, Y and Koppe, J and Vogl, I and Gabert, J and Jentsch, H}, title = {Antibiotic resistance genes in the subgingival microbiome and implications for periodontitis therapy.}, journal = {Journal of periodontology}, volume = {94}, number = {11}, pages = {1295-1301}, doi = {10.1002/JPER.22-0696}, pmid = {37254939}, issn = {1943-3670}, support = {//European Regional Development Fund/ ; }, abstract = {BACKGROUND: Antibiotic resistance is emerging as a global public threat. However, it remains poorly investigated in the context of periodontal therapy. The aim of the study was to investigate the complete diversity of antibiotic resistance genes in a German population.

METHODS: Thirty-nine volunteers with periodontitis contributed to the present study with one to four periodontal pockets for a total of 124 subgingival samples. Samples were analyzed using shotgun metagenomics.

RESULTS: A total of 19 antibiotic resistance genes from six antibiotic classes were detected in subgingival biofilm. Two thirds of the volunteers (n = 26/39) showed antibiotic resistance genes for at least one of the antibiotic classes used for periodontal treatment in dental practice or research: beta-lactam, lincosamide, macrolide, nitroimidazole, and tetracycline. Macrolide was the most abundant class detected (21/39 patients).

CONCLUSIONS: Findings from our study suggest a high prevalence of antibiotic resistance genes in periodontal pockets from German volunteers. We recommend the development and broader use of molecular diagnostic tests for antibiotic resistance in dental practice to ensure treatment success and to minimize antibiotic resistance.}, } @article {pmid37254912, year = {2023}, author = {Gonçalves-Brito, AS and Magaldi, M and Farias, BO and Nascimento, APA and Flores, C and Montenegro, KS and Lopes-Carvalho, M and Gimenez, A and Costa, VSC and Assunção, VC and Quidorne, CS and Bianco, K and Clementino, MM}, title = {Environmental genomic surveillance of SARS-CoV-2 in wastewater in Rio de Janeiro, Brazil.}, journal = {Journal of water and health}, volume = {21}, number = {5}, pages = {653-662}, doi = {10.2166/wh.2023.034}, pmid = {37254912}, issn = {1477-8920}, mesh = {Humans ; *Wastewater ; Brazil/epidemiology ; Metagenomics ; SARS-CoV-2/genetics ; *COVID-19/epidemiology ; }, abstract = {Wastewater-based epidemiology can be a complementary approach for monitoring SARS-CoV-2 prevalence, diversity, and geographic distribution. It is a complementary approach regarding its prevalence and diversity, and geographic distribution. The study aimed to evaluate the genetic diversity of SARS-CoV-2 in two wastewater treatment plants (WWTPs) in Rio de Janeiro, Brazil. Samples were collected over a period of January to December 2021 and were concentrated with PEG8000 and the presence of SARS-CoV-2 was detected using E and N1 genes. Partial sequencing of the SARS-CoV-2 genomes resulted in the identification of variants of concern and variants of interest throughout the collection period. It was possible to identify the Mu, Delta, Gamma and Omicron variants in WWTP1; on the contrary, no variants were observed in WWTP2. To the best of our knowledge, we detected the variant Mu (B.1.621) containing characteristic mutations (S:E484K, S:N501Y) from WWTP, for the first time, in Brazil. Another Mu variant detected from clinical surveillance was announced one month after our finding. The detection of SARS-CoV-2 in wastewater can serve as a tool to monitor the prevalence and epidemiology in each community, helping to understand the spread of the virus among the population.}, } @article {pmid37254790, year = {2023}, author = {López-García, P and Moreira, D}, title = {The symbiotic origin of the eukaryotic cell.}, journal = {Comptes rendus biologies}, volume = {346}, number = {}, pages = {55-73}, doi = {10.5802/crbiol.118}, pmid = {37254790}, issn = {1768-3238}, mesh = {*Eukaryotic Cells ; *Symbiosis ; Phylogeny ; Archaea/genetics ; Eukaryota/genetics ; Biological Evolution ; }, abstract = {Eukaryogenesis represented a major evolutionary transition that led to the emergence of complex cells from simpler ancestors. For several decades, the most accepted scenario involved the evolution of an independent lineage of proto-eukaryotes endowed with an endomembrane system, including a nuclear compartment, a developed cytoskeleton and phagocytosis, which engulfed the alphaproteobacterial ancestor of mitochondria. However, the recent discovery by metagenomic and cultural approaches of Asgard archaea, which harbour many genes in common with eukaryotes and are their closest relatives in phylogenomic trees, rather supports scenarios based on the symbiosis of one Asgard-like archaeon and one or more bacteria at the origin of the eukaryotic cell. Here, we review the recent discoveries that led to this conceptual shift, briefly evoking current models of eukaryogenesis and the challenges ahead to discriminate between them and to establish a detailed, plausible scenario that accounts for the evolution of eukaryotic traits from those of their prokaryotic ancestors.}, } @article {pmid37254739, year = {2023}, author = {Wang, Q and Song, Y and Han, D and Cai, H and Yan, Q and Liu, W and Wang, H and Zheng, X and Ding, L and Yuan, X}, title = {The first suspected disseminated Hormographiella aspergillata infection in China, diagnosed using metagenomic next-generation sequencing: a case report and literature review.}, journal = {Emerging microbes & infections}, volume = {12}, number = {1}, pages = {2220581}, pmid = {37254739}, issn = {2222-1751}, mesh = {Humans ; *Lung Diseases, Fungal ; Neoplasm Recurrence, Local ; *Agaricales/genetics ; *Hematologic Neoplasms ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {Hormographiella aspergillata is a rare and emerging cause of invasive mould infections in patients with haematological malignancies, with a mortality rate of approximately 70%. Here, we present the first reported case of suspected disseminated H. aspergillata infection in China. The patient experienced a second relapse of acute myeloid leukaemia and developed neutropenia, fever, discrepant blood pressure between limbs, and cutaneous lesions limited to the left upper extremity. Since lung tissue biopsy was not feasible, metagenomic next-generation sequencing (mNGS) and panfungal polymerase chain reaction (PCR) analysis of bronchoalveolar lavage fluid and blood samples were performed, which indicated probable H. aspergillata pulmonary infection. Histopathology of cutaneous lesions revealed numerous fungal hyphae within dermal blood vessels. mNGS of a skin biopsy sample identified H. aspergillata sequences, and the fungi was subsequently recovered from fungal culture, proving cutaneous H. aspergillata infection. Despite combined antifungal therapy, the patient died owing to disease progression. Additionally, 22 previously reported cases of invasive H. aspergillata infection were reviewed in patients with haematological malignancies. Thus, mNGS is a powerful diagnostic tool for the early and effective detection of invasive H. aspergillata infections, with the advantage of sequencing all potential pathogens, and providing results within 24 h.}, } @article {pmid37254732, year = {2023}, author = {Chittimalli, K and Jahan, J and Sakamuri, A and McAdams, ZL and Ericsson, AC and Jarajapu, YPR}, title = {Restoration of the gut barrier integrity and restructuring of the gut microbiome in aging by angiotensin-(1-7).}, journal = {Clinical science (London, England : 1979)}, volume = {137}, number = {11}, pages = {913-930}, doi = {10.1042/CS20220904}, pmid = {37254732}, issn = {1470-8736}, support = {U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Mice ; Male ; Animals ; *Gastrointestinal Microbiome ; Angiotensin-Converting Enzyme 2 ; Dysbiosis ; Claudin-1 ; Occludin ; Angiotensin I/pharmacology/metabolism ; Peptidyl-Dipeptidase A/metabolism ; Peptide Fragments/pharmacology/metabolism ; Aging ; Angiotensin II/metabolism ; }, abstract = {Compromised barrier function of colon epithelium with aging is largely due to gut microbial dysbiosis. Recent studies implicate an important role for angiotensin converting enzymes, ACE and ACE2, angiotensins, and the receptors, AT1 receptor (AT1R) and Mas receptor (MasR), in the regulation of colon functions. The present study tested the hypothesis that leaky gut in aging is associated with an imbalance in ACE2/ACE and that the treatment with angiotenisn-(1-7) (Ang-(1-7)) will restore gut barrier integrity and microbiome. Studies were carried out in Young (3-4 months) and old (20-24 months) male mice. Ang-(1-7) was administered by using osmotic pumps. Outcome measures included expressions of ACE, ACE2, AT1R, and MasR, intestinal permeability by using FITC-dextran, and immunohistochemistry of claudin 1 and occludin, and intestinal stem cells (ISCs). ACE2 protein and activity were decreased in Old group while that of ACE were unchanged. Increased intestinal permeability and plasma levels of zonulin-1 in the Old group were normalized by Ang-(1-7). Epithelial disintegrity, reduced number of goblet cells and ISCs in the old group were restored by Ang-(1-7). Expression of claudin 1 and occludin in the aging colon was increased by Ang-(1-7). Infiltration of CD11b+ or F4/80+ inflammatory cells in the old colons were decreased by Ang-(1-7). Gut microbial dysbiosis in aging was evident by decreased richness and altered beta diversity that were reversed by Ang-(1-7) with increased abundance of Lactobacillus or Lachnospiraceae. The present study shows that Ang-(1-7) restores gut barrier integrity and reduces inflammation in the aging colon by restoring the layer of ISCs and by restructuring the gut microbiome.}, } @article {pmid37254378, year = {2023}, author = {Park, J and Bae, D and Kim, SA}, title = {Microbial trace investigation throughout the entire chicken supply chain based on metagenomic high-throughput sequencing.}, journal = {Food research international (Ottawa, Ont.)}, volume = {169}, number = {}, pages = {112775}, doi = {10.1016/j.foodres.2023.112775}, pmid = {37254378}, issn = {1873-7145}, mesh = {Animals ; *Chickens/microbiology ; RNA, Ribosomal, 16S/genetics ; *Meat/microbiology ; Poultry/microbiology ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {As poultry possesses a high risk of contamination by various pathogens and has repeatedly been linked to foodborne outbreaks, ensuring microbiological safety throughout the chicken production chain is essential. In this study, bacterial communities in chickens and associated environments (n = 72), including feces, floors, gloves, and worktables, were trace investigated from the broiler farm, slaughterhouse, meat processing plant, and the market by amplicon sequencing of the V4 region of the 16S rRNA. The bacterial composition in live chickens along the production chain significantly changed across the stages, with distinct microbiota noted at each step. Pseudomonas, Shewanella, Acinetobacter, and Psychrobacter were dominant in the final products. Staphylococcus was abundant in live birds originally (36.83 %) but dramatically decreased after slaughter (3.07 %, 0.06 %, and 0.42 % in slaughtered, processed, and market carcasses, respectively), which may be attributed to defeathering. The proportion of Enterobacteriaceae, Acinetobacter, and Pseudomonas increased from 0.95 %, 0.03 %, and 0.04 % before slaughter to 13.57 %, 34.19 %, and 21.90 %, respectively, after slaughter, highlighting the importance of hygiene management in the succeeding steps. Diversity analysis revealed the possibility of bacterial transmission between samples from the processing plant and the market. Source tracking was performed to identify microbial contamination routes in the chicken microbiome; the major bacterial sources in the final products were the samples from the processing plant (such as processed carcasses, gloves, and worktables), accounting for 93.53 % of the total microbial sources. These results suggest that in-depth knowledge of microbial transmission between chickens and their surroundings can facilitate a precise understanding of microbiological concerns across the poultry production system and help establish safety management measures for the poultry industry.}, } @article {pmid37254352, year = {2023}, author = {Busetta, G and Garofalo, G and Barbera, M and Di Trana, A and Claps, S and Lovallo, C and Franciosi, E and Gaglio, R and Settanni, L}, title = {Metagenomic, microbiological, chemical and sensory profiling of Caciocavallo Podolico Lucano cheese.}, journal = {Food research international (Ottawa, Ont.)}, volume = {169}, number = {}, pages = {112926}, doi = {10.1016/j.foodres.2023.112926}, pmid = {37254352}, issn = {1873-7145}, mesh = {*Food Microbiology ; Streptococcus ; Bacteria ; *Lactobacillales ; Lactobacillus ; }, abstract = {In this study, Caciocavallo Podolico Lucano (CPL) cheese was deeply characterized for its bacterial community, chemical composition and sensory aspects. The entire cheese making process (from milk collection to ripened cheese) was performed by strictly applying the traditional protocol for CPL production in four dairy factories (A-D) representative of the production area. The vat made of wood represents the main transformation tool for CPL cheese production and the biofilms hosted onto the internal surfaces of all vats analyzed in this study were dominated by lactic acid bacteria. Total mesophilic microorganisms present in bulk milk (4.7-5.0 log CFU/ml) increased consistently after contact with the wooden vat surfaces (5.4-6.4 log CFU/ml). The application of Illumina sequencing technology identified barely 18 taxonomic groups among processed samples; streptococci and lactobacilli constituted the major groups of the wooden vat biofilms [94.74-99.70 % of relative abundance (RA)], while lactobacilli dominated almost entirely (94.19-100 % of total RA) the bacterial community of ripened cheeses. Except coagulase positive staphylococci, undesirable bacteria were undetectable. Among chemical parameters, significant variations were registered for unsaturated, monounsaturated, polyunsaturated fatty acids and antioxidant properties (significantly lower for CPL cheeses produced in factory B). The cheeses from factories A, C and D were characterized by a higher lactic acid and persistence smell attributes than factory B. This work indicated that the strict application of CPL cheese making protocol harmonized the main microbiological, physicochemical and sensory parameters of the final cheeses produced in the four factories investigated.}, } @article {pmid37254344, year = {2023}, author = {Yao, L and Zhang, J and Lu, J and Chen, D and Song, S and Wang, H and Sun, M and Feng, T}, title = {Revealing the influence of microbiota on the flavor of kombucha during natural fermentation process by metagenomic and GC-MS analysis.}, journal = {Food research international (Ottawa, Ont.)}, volume = {169}, number = {}, pages = {112909}, doi = {10.1016/j.foodres.2023.112909}, pmid = {37254344}, issn = {1873-7145}, mesh = {Fermentation ; Gas Chromatography-Mass Spectrometry ; *Microbiota/genetics ; Metagenome ; Saccharomyces cerevisiae ; Tea/chemistry ; }, abstract = {In this work, raw Pu-erh tea (RAPT) was employed for kombucha preparation, and the microbial composition and volatile flavor compounds of the fermented tea had been investigated during natural fermentation process. The head space-solid phase microextraction-gas chromatograph mass spectrometry (HS-SPME-GC-MS) was performed for volatiles analysis of unfermented tea and kombucha fermented for 3 days (KF-3) and 6 days (KF-6). Meanwhile, the microbial community of KF-3 and KF-6 were evaluated by metagenomic analysis. A total of 72 volatile compounds were identified and obvious changes in volatiles were observed during the fermentation process based on the results of GC-MS and principal component analysis (PCA). Metagenomic sequencing analysis demonstrated that bacterium Komagataeibacter saccharivorans and unclassified-g-komagataeibacter and yeast Saccharomyces cerevisiae and Brettanomyces bruxellensis were the most common microbes contained in the sampled kombucha communities. Furthermore, the relevance among microbial community and volatile compounds was evaluated through correlation heatmap analysis. The results suggested that the main flavor volatiles of kombucha (i.e., acids, esters and terpenes) were closely related to species of genus Komagataeibacter, Gluconacetobacter, Saccharomyces, Brettanomyces, Acetobacter, Novacetimonas and Pichia microorganisms. The obtained results would help to better understand microbial communities and volatile compounds of kombucha, which could provide useful information for enhancing the flavor quality of kombucha products.}, } @article {pmid37254152, year = {2023}, author = {Wang, K and Mehta, RS and Ma, W and Nguyen, LH and Wang, DD and Ghazi, AR and Yan, Y and Al-Shaar, L and Wang, Y and Hang, D and Fu, BC and Ogino, S and Rimm, EB and Hu, FB and Carmody, RN and Garrett, WS and Sun, Q and Chan, AT and Huttenhower, C and Song, M}, title = {The gut microbiome modifies the associations of short- and long-term physical activity with body weight changes.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {121}, pmid = {37254152}, issn = {2049-2618}, support = {K24 DK098311/NH/NIH HHS/United States ; R01 CA137178/CA/NCI NIH HHS/United States ; R35 CA197735/NH/NIH HHS/United States ; R01 NR019992/NR/NINR NIH HHS/United States ; R01 AG077489/AG/NIA NIH HHS/United States ; R00 CA215314/NH/NIH HHS/United States ; P01 CA087969/CA/NCI NIH HHS/United States ; R00 CA215314/CA/NCI NIH HHS/United States ; UM1 CA186107/CA/NCI NIH HHS/United States ; P01 CA055075/CA/NCI NIH HHS/United States ; R00 DK119412/DK/NIDDK NIH HHS/United States ; R01 CA202704/CA/NCI NIH HHS/United States ; U01 CA261961/CA/NCI NIH HHS/United States ; U01 CA176726/CA/NCI NIH HHS/United States ; U01 CA167552/CA/NCI NIH HHS/United States ; R01 CA151993/CA/NCI NIH HHS/United States ; R01 CA263776/CA/NCI NIH HHS/United States ; UM1 CA167552/CA/NCI NIH HHS/United States ; }, mesh = {Female ; Humans ; Male ; Young Adult ; Body Weight ; Exercise/physiology ; Follow-Up Studies ; *Gastrointestinal Microbiome/genetics ; Obesity/metabolism ; Weight Gain ; Aged ; }, abstract = {BACKGROUND: The gut microbiome regulates host energy balance and adiposity-related metabolic consequences, but it remains unknown how the gut microbiome modulates body weight response to physical activity (PA).

METHODS: Nested in the Health Professionals Follow-up Study, a subcohort of 307 healthy men (mean[SD] age, 70[4] years) provided stool and blood samples in 2012-2013. Data from cohort long-term follow-ups and from the accelerometer, doubly labeled water, and plasma biomarker measurements during the time of stool collection were used to assess long-term and short-term associations of PA with adiposity. The gut microbiome was profiled by shotgun metagenomics and metatranscriptomics. A subcohort of 209 healthy women from the Nurses' Health Study II was used for validation.

RESULTS: The microbial species Alistipes putredinis was found to modify the association between PA and body weight. Specifically, in individuals with higher abundance of A. putredinis, each 15-MET-hour/week increment in long-term PA was associated with 2.26 kg (95% CI, 1.53-2.98 kg) less weight gain from age 21 to the time of stool collection, whereas those with lower abundance of A. putredinis only had 1.01 kg (95% CI, 0.41-1.61 kg) less weight gain (pinteraction = 0.019). Consistent modification associated with A. putredinis was observed for short-term PA in relation to BMI, fat mass%, plasma HbA1c, and 6-month weight change. This modification effect might be partly attributable to four metabolic pathways encoded by A. putredinis, including folate transformation, fatty acid β-oxidation, gluconeogenesis, and stearate biosynthesis.

CONCLUSIONS: A greater abundance of A. putredinis may strengthen the beneficial association of PA with body weight change, suggesting the potential of gut microbial intervention to improve the efficacy of PA in body weight management. Video Abstract.}, } @article {pmid37253970, year = {2023}, author = {Li, S and Yang, S and Wei, X and Jiao, S and Luo, W and Chen, W and Wei, G}, title = {Reduced trace gas oxidizers as a response to organic carbon availability linked to oligotrophs in desert fertile islands.}, journal = {The ISME journal}, volume = {17}, number = {8}, pages = {1257-1266}, pmid = {37253970}, issn = {1751-7370}, mesh = {*Carbon/analysis ; *Ecosystem ; Gases/analysis ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Atmospheric trace gases, such as H2 and CO, are important energy sources for microbial growth and maintenance in various ecosystems, especially in arid deserts with little organic substrate. Nonetheless, the impact of soil organic C availability on microbial trace gas oxidation and the underlying mechanisms are unclear at the community level. This study investigated the energy and life-history strategies of soil microbiomes along an organic C gradient inside and out of Hedysarum scoparium islands dispersed in the Mu Us Desert, China. Metagenomic analysis showed that with increasing organic C availability from bare areas into "fertile islands", the abundance of trace gas oxidizers (TGOs) decreased, but that of trace gas nonoxidizers (TGNOs) increased. The variation in their abundance was more related to labile/soluble organic C levels than to stable/insoluble organic C levels. The consumption rates of H2 and CO confirmed that organic C addition, especially soluble organic C addition, inhibited microbial trace gas oxidation. Moreover, microorganisms with distinct energy-acquiring strategies showed different life-history traits. The TGOs had lower 16 S rRNA operon copy numbers, lower predicted maximum growth rates and higher proportions of labile C degradation genes, implying the prevalence of oligotrophs. In contrast, copiotrophs were prevalent in the TGNOs. These results revealed a mechanism for the microbial community to adapt to the highly heterogeneous distribution of C resources by adjusting the abundances of taxa with distinct energy and life-history strategies, which would further affect trace gas consumption and C turnover in desert ecosystems.}, } @article {pmid37253873, year = {2022}, author = {Xu, Q and Wu, C and Zhu, Q and Gao, R and Lu, J and Valles-Colomer, M and Zhu, J and Yin, F and Huang, L and Ding, L and Zhang, X and Zhang, Y and Xiong, X and Bi, M and Chen, X and Zhu, Y and Liu, L and Liu, Y and Chen, Y and Fan, J and Sun, Y and Wang, J and Cao, Z and Fan, C and Ehrlich, SD and Segata, N and Qin, N and Qin, H}, title = {Author Correction: Metagenomic and metabolomic remodeling in nonagenarians and centenarians and its association with genetic and socioeconomic factors.}, journal = {Nature aging}, volume = {2}, number = {7}, pages = {680}, doi = {10.1038/s43587-022-00258-0}, pmid = {37253873}, issn = {2662-8465}, } @article {pmid37253726, year = {2023}, author = {Yang, G and Zheng, Z and Abbott, BW and Olefeldt, D and Knoblauch, C and Song, Y and Kang, L and Qin, S and Peng, Y and Yang, Y}, title = {Characteristics of methane emissions from alpine thermokarst lakes on the Tibetan Plateau.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3121}, pmid = {37253726}, issn = {2041-1723}, support = {31988102 and 31825006//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Understanding methane (CH4) emission from thermokarst lakes is crucial for predicting the impacts of abrupt thaw on the permafrost carbon-climate feedback. However, observational evidence, especially from high-altitude permafrost regions, is still scarce. Here, by combining field surveys, radio- and stable-carbon isotopic analyses, and metagenomic sequencing, we present multiple characteristics of CH4 emissions from 120 thermokarst lakes in 30 clusters along a 1100 km transect on the Tibetan Plateau. We find that thermokarst lakes have high CH4 emissions during the ice-free period (13.4 ± 1.5 mmol m[-2] d[-1]; mean ± standard error) across this alpine permafrost region. Ebullition constitutes 84% of CH4 emissions, which are fueled primarily by young carbon decomposition through the hydrogenotrophic pathway. The relative abundances of methanogenic genes correspond to the observed CH4 fluxes. Overall, multiple parameters obtained in this study provide benchmarks for better predicting the strength of permafrost carbon-climate feedback in high-altitude permafrost regions.}, } @article {pmid37253538, year = {2023}, author = {Mori, H and Kato, T and Ozawa, H and Sakamoto, M and Murakami, T and Taylor, TD and Toyoda, A and Ohkuma, M and Kurokawa, K and Ohno, H}, title = {Assessment of metagenomic workflows using a newly constructed human gut microbiome mock community.}, journal = {DNA research : an international journal for rapid publication of reports on genes and genomes}, volume = {30}, number = {3}, pages = {}, pmid = {37253538}, issn = {1756-1663}, support = {JP19gm6010007//Japan Agency for Medical Research and Development/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Workflow ; *Microbiota/genetics ; Metagenome ; Metagenomics/methods ; }, abstract = {To quantify the biases introduced during human gut microbiome studies, analyzing an artificial mock community as the reference microbiome is indispensable. However, there are still limited resources for a mock community which well represents the human gut microbiome. Here, we constructed a novel mock community comprising the type strains of 18 major bacterial species in the human gut and assessed the influence of experimental and bioinformatics procedures on the 16S rRNA gene and shotgun metagenomic sequencing. We found that DNA extraction methods greatly affected the DNA yields and taxonomic composition of sequenced reads, and that some of the commonly used primers for 16S rRNA genes were prone to underestimate the abundance of some gut commensal taxa such as Erysipelotrichia, Verrucomicrobiota and Methanobacteriota. Binning of the assembled contigs of shotgun metagenomic sequences by MetaBAT2 produced phylogenetically consistent, less-contaminated bins with varied completeness. The ensemble approach of multiple binning tools by MetaWRAP can improve completeness but sometimes increases the contamination rate. Our benchmark study provides an important foundation for the interpretation of human gut microbiome data by providing means for standardization among gut microbiome data obtained with different methodologies and will facilitate further development of analytical methods.}, } @article {pmid37253164, year = {2024}, author = {Xiao, YH and Luo, ZX and Wu, HW and Xu, DR and Zhao, R}, title = {Metagenomic next-generation sequencing for the identification of infections caused by Gram-negative pathogens and the prediction of antimicrobial resistance.}, journal = {Laboratory medicine}, volume = {55}, number = {1}, pages = {71-79}, doi = {10.1093/labmed/lmad039}, pmid = {37253164}, issn = {1943-7730}, support = {82260085//National Natural Science Fund of China/ ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Retrospective Studies ; High-Throughput Nucleotide Sequencing ; Cytokines ; Sensitivity and Specificity ; }, abstract = {OBJECTIVE: The aim of this study was to evaluate the efficacy of metagenomic next-generation sequencing (mNGS) for the identification of Gram-negative bacteria (GNB) infections and the prediction of antimicrobial resistance.

METHODS: A retrospective analysis was conducted on 182 patients with diagnosis of GNB infections who underwent mNGS and conventional microbiological tests (CMTs).

RESULTS: The detection rate of mNGS was 96.15%, higher than CMTs (45.05%) with a significant difference (χ 2 = 114.46, P < .01). The pathogen spectrum identified by mNGS was significantly wider than CMTs. Interestingly, the detection rate of mNGS was substantially higher than that of CMTs (70.33% vs 23.08%, P < .01) in patients with but not without antibiotic exposure. There was a significant positive correlation between mapped reads and pro-inflammatory cytokines (interleukin-6 and interleukin-8). However, mNGS failed to predict antimicrobial resistance in 5 of 12 patients compared to phenotype antimicrobial susceptibility testing results.

CONCLUSIONS: Metagenomic next-generation sequencing has a higher detection rate, a wider pathogen spectrum, and is less affected by prior antibiotic exposure than CMTs in identifying Gram-negative pathogens. The mapped reads may reflect a pro-inflammatory state in GNB-infected patients. Inferring actual resistance phenotypes from metagenomic data remains a great challenge.}, } @article {pmid37252922, year = {2023}, author = {Hassard, F and Vu, M and Rahimzadeh, S and Castro-Gutierrez, V and Stanton, I and Burczynska, B and Wildeboer, D and Baio, G and Brown, MR and Garelick, H and Hofman, J and Kasprzyk-Hordern, B and Majeed, A and Priest, S and Denise, H and Khalifa, M and Bassano, I and Wade, MJ and Grimsley, J and Lundy, L and Singer, AC and Di Cesare, M}, title = {Wastewater monitoring for detection of public health markers during the COVID-19 pandemic: Near-source monitoring of schools in England over an academic year.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0286259}, pmid = {37252922}, issn = {1932-6203}, mesh = {Humans ; *COVID-19/epidemiology ; SARS-CoV-2/genetics ; Wastewater ; Public Health ; Pandemics ; Wastewater-Based Epidemiological Monitoring ; England/epidemiology ; RNA, Viral ; }, abstract = {BACKGROUND: Schools are high-risk settings for infectious disease transmission. Wastewater monitoring for infectious diseases has been used to identify and mitigate outbreaks in many near-source settings during the COVID-19 pandemic, including universities and hospitals but less is known about the technology when applied for school health protection. This study aimed to implement a wastewater surveillance system to detect SARS-CoV-2 and other public health markers from wastewater in schools in England.

METHODS: A total of 855 wastewater samples were collected from 16 schools (10 primary, 5 secondary and 1 post-16 and further education) over 10 months of school term time. Wastewater was analysed for SARS-CoV-2 genomic copies of N1 and E genes by RT-qPCR. A subset of wastewater samples was sent for genomic sequencing, enabling determination of the presence of SARS-CoV-2 and emergence of variant(s) contributing to COVID-19 infections within schools. In total, >280 microbial pathogens and >1200 AMR genes were screened using RT-qPCR and metagenomics to consider the utility of these additional targets to further inform on health threats within the schools.

RESULTS: We report on wastewater-based surveillance for COVID-19 within English primary, secondary and further education schools over a full academic year (October 2020 to July 2021). The highest positivity rate (80.4%) was observed in the week commencing 30th November 2020 during the emergence of the Alpha variant, indicating most schools contained people who were shedding the virus. There was high SARS-CoV-2 amplicon concentration (up to 9.2x106 GC/L) detected over the summer term (8th June - 6th July 2021) during Delta variant prevalence. The summer increase of SARS-CoV-2 in school wastewater was reflected in age-specific clinical COVID-19 cases. Alpha variant and Delta variant were identified in the wastewater by sequencing of samples collected from December to March and June to July, respectively. Lead/lag analysis between SARS-CoV-2 concentrations in school and WWTP data sets show a maximum correlation between the two-time series when school data are lagged by two weeks. Furthermore, wastewater sample enrichment coupled with metagenomic sequencing and rapid informatics enabled the detection of other clinically relevant viral and bacterial pathogens and AMR.

CONCLUSIONS: Passive wastewater monitoring surveillance in schools can identify cases of COVID-19. Samples can be sequenced to monitor for emerging and current variants of concern at the resolution of school catchments. Wastewater based monitoring for SARS-CoV-2 is a useful tool for SARS-CoV-2 passive surveillance and could be applied for case identification and containment, and mitigation in schools and other congregate settings with high risks of transmission. Wastewater monitoring enables public health authorities to develop targeted prevention and education programmes for hygiene measures within undertested communities across a broad range of use cases.}, } @article {pmid37252635, year = {2023}, author = {Feng, Y and Jiang, Y and Zhou, Y and Li, ZH and Yang, QQ and Mo, JF and Wen, YY and Shen, LP}, title = {Combination of BFHY with Cisplatin Relieved Chemotherapy Toxicity and Altered Gut Microbiota in Mice.}, journal = {International journal of genomics}, volume = {2023}, number = {}, pages = {3568416}, pmid = {37252635}, issn = {2314-4378}, abstract = {AIM: We sought to profile gut microbiota's role in combination of Bu Fei Hua Yu (BFHY) with cisplatin treatment.

METHODS: Non-small cell lung cancer (NSCLC) mice model were constructed followed by treatment with cisplatin alone or combined with BFHY. Mice weight and tumor volume were measured during the experiment. And mice cecum were detected by hematoxylin and eosin, cecum contents were collected for Enzyme Linked ImmuneSorbent Assay, and stool were profiled for metagenomic sequencing.

RESULTS: Combination of BFHY with cisplatin treatment decreased the tumor growth and relieved the damage of cecum. Expressions of interleukin-6 (IL-6), interleukin-1β (IL-1β), monocyte chemotactic protein 1 (MCP), and interferon-γ (IFN-γ) were decreased compared with cisplatin treatment alone. Linear discriminant analysis effect size analysis showed that g_Parabacteroides was downregulated and g_Escherichia and g_Blautia were upregulated after cisplatin treatment. After combination with BFHY, g_Bacteroides and g_Helicobacter were decreased. g_Klebsiella, g_Unclssified_Proteobacteria, and g_Unclssified_Clostridiates were increased. Moreover, heatmap results showed that Bacteroides abundance was increased significantly after cisplatin treatment; BFHY combination treatment reversed this state. Function analysis revealed that multiple functions were slightly decreased in cisplatin treatment alone and increased significantly after combination with BFHY.

CONCLUSION: Our study provided evidence of an efficacy of combination of BFHY with cisplatin on treatment of NSCLC and revealed that gut microbiota plays a role in it. The above results provide new ideas on NSCLC treatment.}, } @article {pmid37252382, year = {2023}, author = {Khan, KA and Ganeshprasad, DN and Sachin, HR and Shouche, YS and Ghramh, HA and Sneharani, AH}, title = {Gut microbial diversity in Apis cerana indica and Apis florea colonies: a comparative study.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1149876}, pmid = {37252382}, issn = {2297-1769}, abstract = {INTRODUCTION: Honey bee gut microbiota have an important role in host health, nutrition, host-symbiont interaction, and interaction behavior with the surrounding environment. Recent discoveries of strain-level variation, characteristics of protective and nutritional capabilities, and reports of eco-physiological significance to the microbial community have emphasized the importance of honey bee gut microbiota. Many regions of Asia and Africa are inhabited by the dwarf honey bee, Apis florea. Studying its microflora and potential for pollination is therefore of foremost importance.

METHODS: In the present investigation, we aimed to explore the gut bacteriobiome composition of two distinct honey bee species, Apis florea and Apis cerana indica using high throughput sequencing. Functional predictions of bee gut bacterial communities using PICRUSt2 was carried out.

RESULTS AND DISCUSSION: The phylum Proteobacteria dominated the bacterial community in both A. cerana indica (50.1%) and A. florea (86.7%), followed by Firmicutes (26.29 and 12.81%), Bacteroidetes (23.19 and 0.04%) and Actinobacteria (0.4 and 0.02%) respectively. The gut bacteria of A. cerana indica was more diverse than that of A. florea. The observed variations in bacterial genomic diversity among these critical pollinator species may have been influenced by the apiary management techniques, ecological adaptation factors or habitat size. These variations can have a significant effect in understanding host-symbiont interactions and functioning of gut microbiota highlighting the importance of metagenomic survey in understanding microbial community ecology and evolution. This is the first comparative study on variation in bacterial diversity between two Asian honey bees.}, } @article {pmid37251515, year = {2023}, author = {Cossart, P and Kolter, R and Lemaitre, B and Typas, A}, title = {The New Microbiology: an international lecture course on the island of Spetses.}, journal = {microLife}, volume = {4}, number = {}, pages = {uqac026}, pmid = {37251515}, issn = {2633-6693}, abstract = {In September 2022, an international summer course entitled 'The new microbiology' took place in Greece, on the island of Spetses. The organizers aimed to highlight the spectacular advances and the renaissance occurring in Microbiology, driven by developments in genomics, proteomics, imaging techniques, and bioinformatics. Combinations of these advances allow for single cell analyses, rapid and relatively inexpensive metagenomic and transcriptomic data analyses and comparisons, visualization of previously unsuspected mechanisms, and large-scale studies. A 'New Microbiology' is emerging which allows studies that address the critical roles of microbes in health and disease, in humans, animals, and the environment. The concept of one health is now transforming microbiology. The goal of the course was to discuss all these topics with members of the new generation of microbiologists all of whom were highly motivated and fully receptive.}, } @article {pmid37251223, year = {2023}, author = {Sheikh, Z and Hirsch, LJ}, title = {A practical approach to in-hospital management of new-onset refractory status epilepticus/febrile infection related epilepsy syndrome.}, journal = {Frontiers in neurology}, volume = {14}, number = {}, pages = {1150496}, pmid = {37251223}, issn = {1664-2295}, abstract = {New-onset refractory status epilepticus (NORSE) is "a clinical presentation, not a specific diagnosis, in a patient without active epilepsy or other preexisting relevant neurological disorder, with new onset of refractory status epilepticus without a clear acute or active structural, toxic, or metabolic cause." Febrile infection related epilepsy syndrome (FIRES) is "a subcategory of NORSE that requires a prior febrile infection, with fever starting between 2 weeks and 24 h before the onset of refractory status epilepticus, with or without fever at the onset of status epilepticus." These apply to all ages. Extensive testing of blood and CSF for infectious, rheumatologic, and metabolic conditions, neuroimaging, EEG, autoimmune/paraneoplastic antibody evaluations, malignancy screen, genetic testing, and CSF metagenomics may reveal the etiology in some patients, while a significant proportion of patients' disease remains unexplained, known as NORSE of unknown etiology or cryptogenic NORSE. Seizures are refractory and usually super-refractory (i.e., persist despite 24 h of anesthesia), requiring a prolonged intensive care unit stay, often (but not always) with fair to poor outcomes. Management of seizures in the initial 24-48 h should be like any case of refractory status epilepticus. However, based on the published consensus recommendations, the first-line immunotherapy should begin within 72 h using steroids, intravenous immunoglobulins, or plasmapheresis. If there is no improvement, the ketogenic diet and second-line immunotherapy should start within seven days. Rituximab is recommended as the second-line treatment if there is a strong suggestion or proof of an antibody-mediated disease, while anakinra or tocilizumab are recommended for cryptogenic cases. Intensive motor and cognitive rehab are usually necessary after a prolonged hospital stay. Many patients will have pharmacoresistant epilepsy at discharge, and some may need continued immunologic treatments and an epilepsy surgery evaluation. Extensive research is in progress now via multinational consortia relating to the specific type(s) of inflammation involved, whether age and prior febrile illness affect this, and whether measuring and following serum and/or CSF cytokines can help determine the best treatment.}, } @article {pmid37250842, year = {2023}, author = {Che, X and He, Z and Tung, TH and Xia, H and Lu, Z}, title = {Diagnosis of primary amoebic meningoencephalitis by metagenomic next-generation sequencing: A case report.}, journal = {Open life sciences}, volume = {18}, number = {1}, pages = {20220579}, pmid = {37250842}, issn = {2391-5412}, abstract = {Primary amoebic meningoencephalitis (PAM) caused by Naegleria fowleri is a fatal infection with a mortality rate of more than 95%, despite advances in antimicrobial chemotherapy and supportive care. Initial manifestations of PAM are indistinguishable from bacterial meningitis. Prompt diagnosis and antifungal treatment may help decline the overall mortality. Here we present a case of a 38-year-old man transferred to our hospital due to mild headache, which deteriorated quickly. Severe increased intracranial pressure was found. The cerebrospinal fluid (CSF) was yellowish with significantly increased leukocyte and protein. Smear and culture were negative. The patient was first diagnosed with pyogenic meningoencephalitis. However, the symptoms deteriorated. Metagenomic next-generation sequencing (mNGS) of CSF was applied and finally confirmed N. fowleri as the protist pathogen within 24 h. However, due to the time cost of sampling and transportation (2 days), the diagnosis came too late, and the patient passed away 1 day before. In summary, mNGS is a rapid and accurate diagnostic method for clinical practices, especially for rare central nervous system infections. It should be used as quickly as possible for acute infections, such as PAM. All aspects of patient interrogation and prompt identification should be paramount to ensure appropriate treatment and decline the overall mortality.}, } @article {pmid37250329, year = {2023}, author = {Li, Y and Liu, Z and Luo, G and Lan, H and Chen, P and Du, R and Jing, G and Liu, L and Cui, X and Li, Y and Han, Y and Xu, J and Zhu, H and Ling, S and Li, Y}, title = {Effects of 60 days of 6° head-down bed rest on the composition and function of the human gut microbiota.}, journal = {iScience}, volume = {26}, number = {5}, pages = {106615}, pmid = {37250329}, issn = {2589-0042}, abstract = {Spaceflight is rigorous and dangerous environment which can negatively affect astronauts' health and the entire mission. The 60 days of 6° head-down bed rest (HDBR) experiment provided us with an opportunity to trace the change of gut microbiota under simulated microgravity. The gut microbiota of volunteers was analyzed and characterized by 16S rRNA gene sequencing and metagenomic sequencing. Our results showed that the composition and function of the volunteers' gut microbiota were markedly was affected by 60 days of 6° HDBR. We further confirmed the species and diversity fluctuations. Resistance and virulence genes in the gut microbiota were also affected by 60 days of 6° HDBR, but the species attributions remained stable. The human gut microbiota affected by 60 days of 6° HDBR which was partially consistent with the effect of spaceflight, this implied that HDBR was a simulation of how spaceflight affects the human gut microbiota.}, } @article {pmid37250055, year = {2023}, author = {Wang, X and Wu, Y and Liu, Y and Chen, F and Chen, S and Zhang, F and Li, S and Wang, C and Gong, Y and Huang, R and Hu, M and Ning, Y and Zhao, H and Guo, X}, title = {Altered gut microbiome profile in patients with knee osteoarthritis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1153424}, pmid = {37250055}, issn = {1664-302X}, abstract = {INTRODUCTION: Osteoarthritis (OA) is a kind of chronic, degenerative disorder with unknown causes. In this study, we aimed to improve our understanding of the gut microbiota profile in patients with knee OA.

METHODS: 16S rDNA gene sequencing was performed to detect the gut microbiota in fecal samples collected from the patients with OA (n = 32) and normal control (NC, n = 57). Then the metagenomic sequencing was used to identify the genes or functions linked with gut microbial changes at the species level in the fecal samples from patients with OA and NC groups.

RESULTS: The Proteobacteria was identified as dominant bacteria in OA group. We identified 81 genera resulted significantly different in abundance between OA and NC. The abundance of Agathobacter, Ruminococcus, Roseburia, Subdoligranulum, and Lactobacillus showed significant decrease in the OA compared to the NC. The abundance of genera Prevotella_7, Clostridium, Flavonifractor and Klebsiella were increasing in the OA group, and the families Lactobacillaceae, Christensenellaceae, Clostridiaceae_1 and Acidaminococcaceae were increasing in the NC. The metagenomic sequencing showed that the abundance of Bacteroides stercoris, Bacteroides vulgatus and Bacteroides uniformis at the species level were significantly decreasing in the OA, and the abundance of Escherichia coli, Klebsiella pneumoniae, Shigella flexneri and Streptococcus salivarius were significantly increased in OA.

DISCUSSION: The results of our study interpret a comprehensive profile of the gut microbiota in patients with knee OA and offer the evidence that the cartilage-gut-microbiome axis could play a crucial role in underlying the mechanisms and pathogenesis of OA.}, } @article {pmid37250024, year = {2023}, author = {Vorimore, F and Jaudou, S and Tran, ML and Richard, H and Fach, P and Delannoy, S}, title = {Combination of whole genome sequencing and supervised machine learning provides unambiguous identification of eae-positive Shiga toxin-producing Escherichia coli.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1118158}, pmid = {37250024}, issn = {1664-302X}, abstract = {INTRODUCTION: The objective of this study was to develop, using a genome wide machine learning approach, an unambiguous model to predict the presence of highly pathogenic STEC in E. coli reads assemblies derived from complex samples containing potentially multiple E. coli strains. Our approach has taken into account the high genomic plasticity of E. coli and utilized the stratification of STEC and E. coli pathogroups classification based on the serotype and virulence factors to identify specific combinations of biomarkers for improved characterization of eae-positive STEC (also named EHEC for enterohemorrhagic E.coli) which are associated with bloody diarrhea and hemolytic uremic syndrome (HUS) in human.

METHODS: The Machine Learning (ML) approach was used in this study on a large curated dataset composed of 1,493 E. coli genome sequences and 1,178 Coding Sequences (CDS). Feature selection has been performed using eight classification algorithms, resulting in a reduction of the number of CDS to six. From this reduced dataset, the eight ML models were trained with hyper-parameter tuning and cross-validation steps.

RESULTS AND DISCUSSION: It is remarkable that only using these six genes, EHEC can be clearly identified from E. coli read assemblies obtained from in silico mixtures and complex samples such as milk metagenomes. These various combinations of discriminative biomarkers can be implemented as novel marker genes for the unambiguous EHEC characterization from different E. coli strains mixtures as well as from raw milk metagenomes.}, } @article {pmid37249962, year = {2023}, author = {Wang, D and Zhang, L and Cai, Z and Liu, Y}, title = {Diagnosis of Acute Q Fever in a Patient by Using Metagenomic Next-Generation Sequencing: A Case Report [Response to Letter].}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {3269-3270}, pmid = {37249962}, issn = {1178-6973}, } @article {pmid37249588, year = {2023}, author = {Li, W and Zhao, J and Tian, H and Shen, Y and Wang, Y and Shao, M and Xiong, T and Yao, Y and Zhang, L and Chen, X and Xiao, H and Xiong, Y and Yang, S and Tan, C and Xu, H}, title = {Gut microbiota enhance energy accumulation of black-necked crane to cope with impending migration.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {14}, pages = {4635-4646}, pmid = {37249588}, issn = {1432-0614}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Proteobacteria ; Birds/genetics/microbiology ; Cellulose ; }, abstract = {Less is known about the role of gut microbiota in overwintering environmental adaptation in migratory birds. Here, we performed metagenomic sequencing on fresh fecal samples (n = 24) collected during 4 periods of overwintering (Dec: early; Jan: middle I; Feb: middle II; Mar: late) to characterize gut microbial taxonomic and functional characteristics of black-necked crane (Grus nigricollis). The results demonstrated no significant change in microbial diversity among overwintering periods. Analysis of compositions of microbiomes with bias correction (ANCOM-BC) determined 15 Proteobacteria species enriched in late overwintering period. Based on previous reports, these species are associated with degradation of chitin, cellulose, and lipids. Meanwhile, fatty acid degradation and betalain biosynthesis pathways are enriched in late overwintering period. Furthermore, metagenomic binning obtained 91 high-quality bins (completeness >70% and contamination <10%), 5 of which enriched in late overwintering period. Carnobacterium maltaromaticum, unknown Enterobacteriaceae, and Yersinia frederiksenii have genes for chitin and cellulose degradation, acetate, and glutamate production. Unknown Enterobacteriaceae and Y. frederiksenii hold genes for synthesis of 10 essential amino acids required by birds, and the latter has genes for γ-aminobutyrate production. C. maltaromaticum has genes for pyridoxal synthesis. These results implied the gut microbiota is adapted to the host diet and may help black-necked cranes in pre-migratory energy accumulation by degrading the complex polysaccharide in their diet, supplying essential amino acids and vitamin pyridoxal, and producing acetate, glutamate, and γ-aminobutyrate that could stimulate host feeding. Additionally, enriched Proteobacteria also encoded more carbohydrate-active enzymes (CAZymes) and antibiotic resistance genes (ARGs) in late overwintering period. KEY POINTS: • Differences in gut microbiota function during overwintering period of black-necked cranes depend mainly on changes in core microbiota abundance • Gut microbiota of black-necked crane adapted to the diet during overwintering period • Gut microbiota could help black-necked cranes to accumulate more energy in the late overwintering period.}, } @article {pmid37249547, year = {2023}, author = {Jiang, G and Zhang, J and Zhang, Y and Yang, X and Li, T and Wang, N and Chen, X and Zhao, FJ and Wei, Z and Xu, Y and Shen, Q and Xue, W}, title = {DCiPatho: deep cross-fusion networks for genome scale identification of pathogens.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {4}, pages = {}, pmid = {37249547}, issn = {1477-4054}, mesh = {Humans ; *Algorithms ; *Software ; Neural Networks, Computer ; Genome ; Genomics ; }, abstract = {Pathogen detection from biological and environmental samples is important for global disease control. Despite advances in pathogen detection using deep learning, current algorithms have limitations in processing long genomic sequences. Through the deep cross-fusion of cross, residual and deep neural networks, we developed DCiPatho for accurate pathogen detection based on the integrated frequency features of 3-to-7 k-mers. Compared with the existing state-of-the-art algorithms, DCiPatho can be used to accurately identify distinct pathogenic bacteria infecting humans, animals and plants. We evaluated DCiPatho on both learned and unlearned pathogen species using both genomics and metagenomics datasets. DCiPatho is an effective tool for the genomic-scale identification of pathogens by integrating the frequency of k-mers into deep cross-fusion networks. The source code is publicly available at https://github.com/LorMeBioAI/DCiPatho.}, } @article {pmid37249085, year = {2023}, author = {Ting, HSL and Chen, Z and Chan, JYK}, title = {Systematic review on oral microbial dysbiosis and its clinical associations with head and neck squamous cell carcinoma.}, journal = {Head & neck}, volume = {45}, number = {8}, pages = {2120-2135}, doi = {10.1002/hed.27422}, pmid = {37249085}, issn = {1097-0347}, mesh = {Humans ; Bacteria ; Dysbiosis/diagnosis/microbiology ; *Head and Neck Neoplasms/diagnosis ; *Microbiota/genetics ; Squamous Cell Carcinoma of Head and Neck ; }, abstract = {OBJECTIVES: The relationship between head and neck squamous cell carcinoma (HNSCC) and the oral microbiome has been drawn in various studies. Microbial diversities, microbiome profiles, metagenomic analysis, and host-pathogen interactions were collected from these studies to highlight similarities and account for inconsistencies. We also evaluate the possible clinical applications of the microbiome regarding screening and diagnosis of HNSCC.

METHODS: Systematic analysis of studies regarding HNSCC and the microbiome was done according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statement guidelines. Articles were retrieved from four databases (PubMed, ScienceDirect, CUHK Full-Text Journals, and Cochrane database) and were screened using predefined criteria.

RESULTS: Twenty studies were chosen after screening for full-text review. α-diversity comparison was inconsistent whereas β-diversity between HNSCC and normal samples showed distinct clustering. Microbial dysbiosis characterized by change in the relative abundances of several bacterial species were also seen in HNSCC patients. At a phylum level, inconsistencies were seen between studies using HNSCC tumor tissue samples and saliva samples. At a genus level, Fusobacterium, Peptostreptococcus, Alloprevotella, Capnocytophaga, Catonella, and Prevotella were differentially enriched in HNSCC while Streptococcus, Actinomyces Veillonella, and Rothia were differentially depleted. Co-occurrence network analysis revealed a positive correlation of HNSCC with periodontal pathogens and a negative correlation with commensal bacteria. Metagenomic analysis of microbiota revealed a differential enrichment of pro-inflammatory genomic pathways which was consistent across various studies. Microbial dysbiosis was applied in clinical use as a tool for HNSCC screening. Random-forest analysis was adopted to differentiate between tumor and normal tissue, at 95.7% and 70.0% accuracies respectively in two studies. Microbial dysbiosis index was also used to predict prognosis.

CONCLUSIONS: Oral microbial dysbiosis could be a promising tool for HNSCC screening and diagnosis. However, more research should be conducted pertaining to clinical applications to improve diagnostic accuracy and explore other clinical uses.}, } @article {pmid37249060, year = {2023}, author = {Wolf, M and Schallert, K and Knipper, L and Sickmann, A and Sczyrba, A and Benndorf, D and Heyer, R}, title = {Advances in the clinical use of metaproteomics.}, journal = {Expert review of proteomics}, volume = {20}, number = {4-6}, pages = {71-86}, doi = {10.1080/14789450.2023.2215440}, pmid = {37249060}, issn = {1744-8387}, mesh = {Humans ; *Proteomics/methods ; *Microbiota/genetics ; Bacterial Proteins/metabolism ; Computational Biology/methods ; Obesity ; }, abstract = {INTRODUCTION: Investigating the taxonomic and functional composition of human microbiomes can aid in the understanding of disease etiologies, diagnosis, and therapy monitoring for several diseases, including inflammatory bowel disease or obesity. One method for microbiome monitoring is metaproteomics, which assesses human and microbial proteins and thus enables the study of host-microbiome interactions. This advantage led to increased interest in metaproteome analyses and significant developments to introduce this method into a clinical context.

AREAS COVERED: This review summarizes the recent progress from a technical side and an application-related point of view.

EXPERT OPINION: Numerous publications imply the massive potential of metaproteomics to impact human health care. However, the key challenges of standardization and validation of experimental and bioinformatic workflows and accurate quantification methods must be overcome.}, } @article {pmid37248474, year = {2023}, author = {Stiller, J and Wilson, NG and Rouse, GW}, title = {Range-wide population genomics of common seadragons shows secondary contact over a former barrier and insights on illegal capture.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {129}, pmid = {37248474}, issn = {1741-7007}, mesh = {Humans ; Animals ; Phylogeny ; *Metagenomics ; Biodiversity ; *Smegmamorpha ; Australia ; Genetic Variation ; }, abstract = {BACKGROUND: Common seadragons (Phyllopteryx taeniolatus, Syngnathidae) are an emblem of the diverse endemic fauna of Australia's southern rocky reefs, the newly recognized "Great Southern Reef." A lack of assessments spanning this global biodiversity hotspot in its entirety is currently hampering an understanding of the factors that have contributed to its diversity. The common seadragon has a wide range across Australia's entire temperate south and includes a geogenetic break over a former land bridge, which has called its status as a single species into question. As a popular aquarium display that sells for high prices, common seadragons are also vulnerable to illegal capture.

RESULTS: Here, we provide range-wide nuclear sequences (986 variable Ultraconserved Elements) for 198 individuals and mitochondrial genomes for 140 individuals to assess species status, identify genetic units and their diversity, and trace the source of two poached individuals. Using published data of the other two seadragon species, we found that lineages of common seadragons have diverged relatively recently (< 0.63 Ma). Within common seadragons, we found pronounced genetic structure, falling into three major groups in the western, central, and eastern parts of the range. While populations across the Bassian Isthmus were divergent, there is also evidence for secondary contact since the passage opened. We found a strong cline of genetic diversity from the range center tapering symmetrically towards the range peripheries. Based on their genetic similarities, the poached individuals were inferred to have originated from around Albany in southwestern Australia.

CONCLUSIONS: We conclude that common seadragons constitute a single species with strong geographic structure but coherence through gene flow. The low genetic diversity on the east and west coasts is concerning given that these areas are projected to face fast climate change. Our results suggest that in addition to their life history, geological events and demographic expansions have all played a role in shaping populations in the temperate south. These insights are an important step towards understanding the historical determinants of the diversity of species endemic to the Great Southern Reef.}, } @article {pmid37247730, year = {2023}, author = {Liu, Y and Yan, Y and Fu, L and Li, X}, title = {Metagenomic insights into the response of rhizosphere microbial to precipitation changes in the alpine grasslands of northern Tibet.}, journal = {The Science of the total environment}, volume = {892}, number = {}, pages = {164212}, doi = {10.1016/j.scitotenv.2023.164212}, pmid = {37247730}, issn = {1879-1026}, mesh = {Tibet ; *Ecosystem ; Grassland ; Rhizosphere ; *Microbiota ; Soil Microbiology ; Soil/chemistry ; Water ; }, abstract = {Water changes caused by precipitation may affect the elemental cycle of ecosystems by influencing soil microorganisms. In this study, precipitation control experiment was conducted in semi-arid alpine grasslands in northern Tibet, and plots were set up and divided into increased water (IW) and decreased water (DW) plots. Moreover, the link between functional genes and soil environmental factors, and the responses of the microbial community functions to precipitation-induced water variations were studied using metagenomic sequencing. To clarify the roles of various proteins and metabolites in the semi-arid alpine grasslands of northern Tibet, functional annotations of clusters of orthologous groups of proteins, Kyoto Encyclopedia of Genes and Genomes, and carbohydrate-active enzyme of the sequencing data were conducted. The results showed that the absolute abundance of microbial functional genes in IW was significantly higher than that in the control check (CK, natural precipitation) and DW. However, the absolute abundance did not significantly differ between CK and DW. There was no significant difference among the four plant species (Stipa purpurea, Carex moocroftii, Othropis microphylla, and Artemisia capillaris) considered in this study. These results indicated that microbial functions were mainly affected by water and do not depend on the species, and that the effect of IW was greater than that of DW. Further, we found that soil C, N, K, and other nutrients play vital roles in microbial growth, microbial functional genes were not affected by pH; however, soil C, N, and K nutrients and functional genes were negative correlated. Overall, this study enhances our understanding of the responses of microorganisms to precipitation and can be used as a valuable reference for understanding the drought resistance of soil microorganisms in semi-arid and alpine regions.}, } @article {pmid37247642, year = {2023}, author = {Czapári, D and Váradi, A and Farkas, N and Nyári, G and Márta, K and Váncsa, S and Nagy, R and Teutsch, B and Bunduc, S and Erőss, B and Czakó, L and Vincze, Á and Izbéki, F and Papp, M and Merkely, B and Szentesi, A and Hegyi, P and , }, title = {Detailed Characteristics of Post-discharge Mortality in Acute Pancreatitis.}, journal = {Gastroenterology}, volume = {165}, number = {3}, pages = {682-695}, doi = {10.1053/j.gastro.2023.05.028}, pmid = {37247642}, issn = {1528-0012}, mesh = {Humans ; *Pancreatitis/epidemiology ; Patient Discharge ; Acute Disease ; Aftercare ; Cachexia ; Retrospective Studies ; }, abstract = {BACKGROUND & AIMS: The in-hospital survival of patients suffering from acute pancreatitis (AP) is 95% to 98%. However, there is growing evidence that patients discharged after AP may be at risk of serious morbidity and mortality. Here, we aimed to investigate the risk, causes, and predictors of the most severe consequence of the post-AP period: mortality.

METHODS: A total of 2613 well-characterized patients from 25 centers were included and followed by the Hungarian Pancreatic Study Group between 2012 and 2021. A general and a hospital-based population was used as the control group.

RESULTS: After an AP episode, patients have an approximately threefold higher incidence rate of mortality than the general population (0.0404 vs 0.0130 person-years). First-year mortality after discharge was almost double than in-hospital mortality (5.5% vs 3.5%), with 3.0% occurring in the first 90-day period. Age, comorbidities, and severity were the most significant independent risk factors for death following AP. Furthermore, multivariate analysis identified creatinine, glucose, and pleural fluid on admission as independent risk factors associated with post-discharge mortality. In the first 90-day period, cardiac failure and AP-related sepsis were among the main causes of death following discharge, and cancer-related cachexia and non-AP-related infection were the key causes in the later phase.

CONCLUSION: Almost as many patients in our cohort died in the first 90-day period after discharge as during their hospital stay. Evaluation of cardiovascular status, follow-up of local complications, and cachexia-preventing oncological care should be an essential part of post-AP patient care. Future study protocols in AP must include at least a 90-day follow-up period after discharge.}, } @article {pmid37246448, year = {2024}, author = {Ikechukwu, CK and Qin, K and Zhang, H and Pan, J and Zhang, W}, title = {Novel equid papillomavirus from domestic donkey.}, journal = {Equine veterinary journal}, volume = {56}, number = {1}, pages = {171-177}, doi = {10.1111/evj.13957}, pmid = {37246448}, issn = {2042-3306}, support = {//National Key Research and Development Programs of China No. 2022YFC2603801 and Funding for Kunlun Talented People of Qinghai Province, High-end Innovation and Entrepreneurship Talents-leading Talents No. 202208170046/ ; }, mesh = {Horses/genetics ; Animals ; Humans ; *Equidae ; Phylogeny ; Cross-Sectional Studies ; *Genome, Viral ; Papillomaviridae/genetics ; }, abstract = {BACKGROUND: Papillomaviruses can be of great medical importance as they infect humans and animals such as Equus species, other livestock and pets. They are responsible for several papillomas and benign tumours in their host.

OBJECTIVES: To describe a novel equid papillomavirus detected in oral swab samples collected from donkeys (Equus asinus) found on the Northwest plateau of China.

STUDY DESIGN: Cross-sectional.

METHODS: Swab samples collected from the oral mucosa of 32 donkeys in the Gansu Province of China, were subjected to viral metagenomic analysis to detect the presence of Papillomavirus. After de novo assembly, a novel papillomavirus genome designated as Equus asinus papillomavirus 3 (EaPV3) was identified in the studied samples. Additional bioinformatic analysis of the assembled genome was done using the Geneious prime software (version 2022.0.2).

RESULTS: The complete circular genome of EaPV3 is 7430 bp in length with a GC content of 50.8%. The genome was predicted to contain five ORFs coding for three early proteins (E7, E1, and E2) and two late proteins (L1 and L2). Phylogenic analysis of the nucleotide sequences of the concatenated amino acid sequences of the E1E2L1L2 genes revealed that EaPV3 is most closely related to Equus asinus papillomavirus 1 (EaPV1). The genome analysis of EaPV3 revealed similar genome organisation with other equine papillomavirus and the presence of E7 papillomavirus oncoprotein.

MAIN LIMITATIONS: Since there were no warts in the oral cavity of the donkeys in this study, and no biopsy samples taken, we are unable to conclusively link the novel virus to any clinical condition in the donkeys.

CONCLUSIONS: The Comparative characterisation of EaPV3 and its closest relatives, as well as phylogenetic analysis demonstrated that it is a novel virus specie that clusters within the Dyochipapilloma PV genus.}, } @article {pmid37246304, year = {2023}, author = {Arredondo, A and Àlvarez, G and Isabal, S and Teughels, W and Laleman, I and Contreras, MJ and Isbej, L and Huapaya, E and Mendoza, G and Mor, C and Nart, J and Blanc, V and León, R}, title = {Comparative 16S rRNA gene sequencing study of subgingival microbiota of healthy subjects and patients with periodontitis from four different countries.}, journal = {Journal of clinical periodontology}, volume = {50}, number = {9}, pages = {1176-1187}, doi = {10.1111/jcpe.13827}, pmid = {37246304}, issn = {1600-051X}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; Healthy Volunteers ; *Dental Plaque/microbiology ; *Periodontitis/microbiology ; Bacteria/genetics ; *Microbiota/genetics ; }, abstract = {AIM: To investigate the differences between the subgingival microbiota of healthy subjects (HS) and periodontitis patients (PP) from four different countries through a metagenomic approach.

MATERIALS AND METHODS: Subgingival samples were obtained from subjects from four different countries. Microbial composition was analysed through high-throughput sequencing of the V3-V4 region of the 16S rRNA gene. The country of origin, diagnosis and clinical and demographic variables of the subjects were used to analyse the microbial profiles.

RESULTS: In total, 506 subgingival samples were analysed: 196 from HS and 310 from patients with periodontitis. Differences in richness, diversity and microbial composition were observed when comparing samples pertaining to different countries of origin and different subject diagnoses. Clinical variables, such as bleeding on probing, did not significantly affect the bacterial composition of the samples. A highly conserved core of microbiota associated with periodontitis was detected, while the microbiota associated with periodontally HS was much more diverse.

CONCLUSIONS: Periodontal diagnosis of the subjects was the main variable explaining the composition of the microbiota in the subgingival niche. Nevertheless, the country of origin also had a significant impact on the microbiota and is therefore an important factor to consider when describing subgingival bacterial communities.}, } @article {pmid37245808, year = {2023}, author = {Huang, Y and Shi, W and Fu, Q and Qiu, Y and Zhao, J and Li, J and Lyu, Q and Yang, X and Xiong, J and Wang, W and Chang, R and Yao, Z and Dai, Z and Qiu, Y and Chen, H}, title = {Soil development following glacier retreat shapes metagenomic and metabolomic functioning associated with asynchronous C and N accumulation.}, journal = {The Science of the total environment}, volume = {892}, number = {}, pages = {164405}, doi = {10.1016/j.scitotenv.2023.164405}, pmid = {37245808}, issn = {1879-1026}, mesh = {*Soil/chemistry ; *Ice Cover/microbiology ; Carbon/metabolism ; Soil Microbiology ; Bacteria/genetics/metabolism ; }, abstract = {Glacier retreat caused by global warming may result in the variation of soil organic carbon and nutrient cycling. Yet, the dynamic change of soil microbial functional profiles, especially C metabolism-related, with soil development following glacier retreat are still unclear. In the present study, we investigated the soil microbial communities, metagenomic functioning, and metabolomic profiles along the Hailuogou Glacier forefield representing a 120-year chronosequence. The alpha diversity indices of soil bacteria, protozoa and nifH genes showed an upward trend with increased soil ages, and the beta diversity of soil archaea, bacteria, fungi, protozoa, nifH and nirS genes were significantly correlated with soil ages, in which increasing soil C and P while decreased C/N and pH significantly contributed to the differences of soil microbial communities among the analyzed environmental variables. The metagenomic functional genes related to the metabolisms of Glycogen and Cellulosome, Iron Acquisition and Metabolism were significantly decreased with chronosequence, while the utilization of Xylose and Lactate, Potassium Metabolism, Sulfur Metabolism showing an upward trend with soil ages, in which soil C/N ratios and pH were the most influential factors. In addition, soil C and C/N ratios were also significantly correlated to metabolomic compositions, in which the complexity of the metabolite structure increased with soil ages. Our results indicate that glacier retreat may lead to the asynchronous C and N accumulation along the chronosequence, thereby affecting the metagenomic and metabolomic functioning of soil microbial communities related to C metabolisms during soil development following glacier retreat.}, } @article {pmid37245381, year = {2023}, author = {Yue, XL and Xu, L and Cui, L and Fu, GY and Xu, XW}, title = {Metagenome-based analysis of carbon-fixing microorganisms and their carbon-fixing pathways in deep-sea sediments of the southwestern Indian Ocean.}, journal = {Marine genomics}, volume = {70}, number = {}, pages = {101045}, doi = {10.1016/j.margen.2023.101045}, pmid = {37245381}, issn = {1876-7478}, mesh = {Indian Ocean ; *Metagenome ; Ecosystem ; Carbon ; *Hydrothermal Vents ; Phylogeny ; }, abstract = {Carbon fixation by chemoautotrophic microorganisms in the dark ocean makes a large contribution to oceanic primary production and the global carbon cycle. In contrast to the Calvin cycle-dominated carbon-fixing pathway in the marine euphotic zone, carbon-fixing pathways and their hosts in deep-sea areas are diverse. In this study, four deep-sea sediment samples close to hydrothermal vents in the southwestern Indian Ocean were collected and processed using metagenomic analysis to investigate carbon fixation potential. Functional annotations revealed that all six carbon-fixing pathways had genes to varied degrees present in the samples. The reductive tricarboxylic acid cycle and Calvin cycle genes occurred in all samples, in contrast to the Wood-Ljungdahl pathway, which previous studies found mainly in the hydrothermal area. The annotations also elucidated the chemoautotrophic microbial members associated with the six carbon-fixing pathways, and the majority of them containing key carbon fixation genes belonged to the phyla Pseudomonadota and Desulfobacterota. The binned metagenome-assembled genomes revealed that key genes for the Calvin cycle and the 3-hydroxypropionate/4-hydroxybutyrate cycle were also found in the order Rhodothermales and the family Hyphomicrobiaceae. By identifying the carbon metabolic pathways and microbial populations in the hydrothermal fields of the southwest Indian Ocean, our study sheds light on complex biogeochemical processes in deep-sea environments and lays the foundation for further in-depth investigations of carbon fixation processes in deep-sea ecosystems.}, } @article {pmid37245359, year = {2023}, author = {Chen, JY and Liu, S and Deng, WK and Niu, SH and Liao, XD and Xiang, L and Xing, SC}, title = {The effect of manure-borne doxycycline combined with different types of oversized microplastic contamination layers on carbon and nitrogen metabolism in sandy loam.}, journal = {Journal of hazardous materials}, volume = {456}, number = {}, pages = {131612}, doi = {10.1016/j.jhazmat.2023.131612}, pmid = {37245359}, issn = {1873-3336}, mesh = {*Carbon ; *Doxycycline/toxicity ; Ecosystem ; Manure ; *Microplastics/toxicity ; Nitrogen/metabolism ; Plastics ; Sand ; Soil/chemistry ; *Soil Microbiology ; Anti-Bacterial Agents/toxicity ; *Nitrogen Cycle/drug effects ; }, abstract = {The different forms and properties of microplastics (MPs) have different effects on the elemental cycles in soil ecosystems, and this is further complicated when the soil contains antibiotics; meanwhile, oversized microplastic (OMP) in soil is always ignored in studies of environmental behavior. In the context of antibiotic action, the effects of OMP on soil carbon (C) and nitrogen (N) cycling have rarely been explored. In this study, we created four types of oversized microplastic (thick fibers, thin fibers, large debris, and small debris) composite doxycycline (DOX) contamination layers (5-10 cm) in sandy loam, hoping to reveal the effects on soil C and N cycling and potential microbial mechanisms when exposed to the combination of manure-borne DOX and different types of OMP from the perspective of metagenomics in the longitudinal soil layer (0-30 cm). The results showed that all different forms of OMP, when combined with DOX, reduced the soil C content in each layer, but only reduced the soil N content in the upper layer of the OMP contamination layer. The microbial structure of the surface soil (0-10 cm) was more noteworthy than that of the deeper soil (10-30 cm). The genera Chryseolinea and Ohtaekwangia were key microbes involved in C and N cycling in the surface layer and regulated carbon fixation in photosynthetic organisms (K00134), carbon fixation pathways in prokaryotes (K00031), methane metabolism (K11212 and K14941), assimilatory nitrate reduction (K00367), and denitrification (K00376 and K04561). The present study is the first to reveal the potential microbial mechanism of C and N cycling under OMP combined with DOX in different layers, mainly the OMP contamination layer and its upper layer, and the OMP shape plays an important role in this process.}, } @article {pmid37245312, year = {2023}, author = {Gong, X and Ge, Z and Ma, Z and Li, Y and Huang, D and Zhang, J}, title = {Effect of different size microplastic particles on the construction of algal-bacterial biofilms and microbial communities.}, journal = {Journal of environmental management}, volume = {343}, number = {}, pages = {118246}, doi = {10.1016/j.jenvman.2023.118246}, pmid = {37245312}, issn = {1095-8630}, mesh = {Bacteria/metabolism ; Biofilms ; *Microbiota ; *Microplastics/metabolism/pharmacology ; Plastics ; Sewage ; }, abstract = {Algal-bacterial symbiotic system is a biological purification system that combines sewage treatment with resource utilization and has the dual effects of carbon sequestration and pollution reduction. In this study, an immobilized algal-bacterial biofilm system was constructed for the treatment of natural sewage. Effects of exposure to microplastics (MPs) with different particle diameters (0.065 μm, 0.5 μm and 5 μm) were determined in terms of algal biomass recovery efficiency, the composition of extracellular polymeric substances (EPS) and morphologic characteristics. The impacts of MPs on the bacterial diversity and community structure of biofilms were also examined. The metagenomic analysis of key microorganisms and related metabolism pathways involved in system was further investigated. Results showed that following exposure to 5 μm MP, a maximum algal recovery efficiency of 80% was achieved, with a minimum PSII primary light energy conversion efficiency (Fv/Fm ratio) of 0.513. Furthermore, 5 μm MP caused the highest level of damage to the algal-bacterial biofilm, enhancing the secretion of protein-rich EPS. The biofilm morphology became rough and loose following exposure to 0.5 μm and 5 μm MP. Community diversity and richness were significantly high in biofilms exposed to 5 μm MP. Proteobacteria (15.3-24.1%), Firmicutes (5.0-7.8%) and Actinobacteria (4.2-4.9%) were dominant in all groups, with exposure to 5 μm MP resulting in the highest relative abundance for these species. The addition of MPs promoted the related metabolic functions while inhibited the degradation of harmful substances by algal-bacterial biofilms. The findings have environmental significance for the practical application of algal-bacterial biofilms for sewage treatment, providing novel insights into the potential effects of MPs on immobilized algal-bacterial biofilm systems.}, } @article {pmid37245209, year = {2023}, author = {Zhao, B and Osbelt, L and Lesker, TR and Wende, M and Galvez, EJC and Hönicke, L and Bublitz, A and Greweling-Pils, MC and Grassl, GA and Neumann-Schaal, M and Strowig, T}, title = {Helicobacter spp. are prevalent in wild mice and protect from lethal Citrobacter rodentium infection in the absence of adaptive immunity.}, journal = {Cell reports}, volume = {42}, number = {6}, pages = {112549}, doi = {10.1016/j.celrep.2023.112549}, pmid = {37245209}, issn = {2211-1247}, mesh = {Animals ; Mice ; Citrobacter rodentium ; *Enterobacteriaceae Infections ; Adaptive Immunity ; *Microbiota ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; }, abstract = {Transfer of the gut microbiota from wild to laboratory mice alters the host's immune status and enhances resistance to infectious and metabolic diseases, but understanding of which microbes and how they promote host fitness is only emerging. Our analysis of metagenomic sequencing data reveals that Helicobacter spp. are enriched in wild compared with specific-pathogen-free (SPF) and conventionally housed mice, with multiple species commonly co-colonizing their hosts. We create laboratory mice harboring three non-SPF Helicobacter spp. to evaluate their effect on mucosal immunity and colonization resistance to the enteropathogen Citrobacter rodentium. Our experiments reveal that Helicobacter spp. interfere with C. rodentium colonization and attenuate C. rodentium-induced gut inflammation in wild-type (WT) mice, even preventing lethal infection in Rag2[-/-] SPF mice. Further analyses suggest that Helicobacter spp. interfere with tissue attachment of C. rodentium, putatively by reducing the availability of mucus-derived sugars. These results unveil pivotal protective functions of wild mouse microbiota constituents against intestinal infection.}, } @article {pmid37244920, year = {2023}, author = {Das, AJ and Sarangi, AN and Ravinath, R and Talambedu, U and Krishnareddy, PM and Nijalingappa, R and Middha, SK}, title = {Improved species level bacterial characterization from rhizosphere soil of wilt infected Punica granatum.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8653}, pmid = {37244920}, issn = {2045-2322}, mesh = {*Soil/chemistry ; *Pomegranate ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Bacteria ; Soil Microbiology ; Plant Diseases/microbiology ; }, abstract = {Pomegranate crops are prone to wilt complex disease, which is known to severely hamper the crop yield. There have been limited studies that have explored bacteria-plant-host associations in wilt complex disease affecting pomegranate crops. In the present study, wilt infected rhizosphere soil samples (ISI, ASI) in pomegranate were studied in comparison to a healthy control (HSC). The 16S metagenomics sequencing approach using the MinION platform was employed for screening of bacterial communities and predictive functional pathways. Altered physicochemical properties in the soil samples were recorded showing a comparatively acidic pH in the ISI (6.35) and ASI (6.63) soil samples to the HSC soil (7.66), along with higher electrical conductivity in the ISI (139.5 µS/cm), ASI soil (180 µS/cm), HSC soil sample (123.33 µS/cm). While concentration of micronutrients such as Cl and B were significantly higher in the ISI and ASI soil as compared to the HSC, Cu and Zn were significantly higher in the ASI soil. The effectiveness and accuracy of 16S metagenomics studies in identifying beneficial and pathogenic bacterial communities in multi-pathogen-host systems depend on the completeness and consistency of the available 16S rRNA sequence repositories. Enhancing these repositories could significantly improve the exploratory potential of such studies. Thus, multiple 16S rRNA data repositories (RDP, GTDB, EzBioCloud, SILVA, and GreenGenes) were benchmarked, and the findings indicated that SILVA yields the most reliable matches. Consequently, SILVA was chosen for further analysis at the species level. Relative abundance estimates of bacterial species showed variations of growth promoting bacteria, namely, Staphylococcus epidermidis, Bacillus subtilis, Bacillus megatarium, Pseudomonas aeruginosa, Pseudomonas putida, Pseudomonas stutzeri and Micrococcus luteus. Functional profiling predictions employing PICRUSt2 revealed a number of enriched pathways such as transporter protein families involved in signalling and cellular processes, iron complex transport system substrate binding protein, peptidoglycan biosynthesis II (staphylococci) and TCA cycle VII (acetate-producers). In line with past reports, results suggest that an acidic pH along with the bioavailability of micronutrients such as Fe and Mn could be facilitating the prevalence and virulence of Fusarium oxysporum, a known causative pathogen, against the host and beneficial bacterial communities. This study identifies bacterial communities taking into account the physicochemical and other abiotic soil parameters in wilt-affected pomegranate crops. The insights obtained could be instrumental in developing effective management strategies to enhance crop yield and mitigate the impact of wilt complex disease on pomegranate crops.}, } @article {pmid37244805, year = {2023}, author = {Everhart, J and Henshaw, NG}, title = {Updates in Molecular Diagnostics in Solid Organ Transplantation Recipients.}, journal = {Infectious disease clinics of North America}, volume = {37}, number = {3}, pages = {495-513}, doi = {10.1016/j.idc.2023.04.002}, pmid = {37244805}, issn = {1557-9824}, mesh = {Humans ; *Pathology, Molecular ; Transplant Recipients ; Metagenome ; *Organ Transplantation/adverse effects ; High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; }, abstract = {Advances in molecular diagnostics have the potential to improve patient care among solid organ transplant recipients by reducing time to pathogen identification and informing directed therapy. Although cultures remain the cornerstone of traditional microbiology, advanced molecular diagnostics, such as metagenomic next-generation sequencing (mNGS), may increase detection of pathogens. This is particularly true in the settings of prior antibiotic exposure, and when causative organisms are fastidious. mNGS also offers a hypothesis-free diagnostic method of testing. This is useful in situations whereby the differential is broad or when the infectious agent is unlikely to be detected by routine methods.}, } @article {pmid37244770, year = {2023}, author = {Mincer, TJ and Bos, RP and Zettler, ER and Zhao, S and Asbun, AA and Orsi, WD and Guzzetta, VS and Amaral-Zettler, LA}, title = {Sargasso Sea Vibrio bacteria: Underexplored potential pathovars in a perturbed habitat.}, journal = {Water research}, volume = {242}, number = {}, pages = {120033}, doi = {10.1016/j.watres.2023.120033}, pmid = {37244770}, issn = {1879-2448}, mesh = {Oceans and Seas ; *Seawater/microbiology ; *Vibrio/genetics ; Ecosystem ; Atlantic Ocean ; }, abstract = {We fully sequenced the genomes of 16 Vibrio cultivars isolated from eel larvae, plastic marine debris (PMD), the pelagic brown macroalga Sargassum, and seawater samples collected from the Caribbean and Sargasso Seas of the North Atlantic Ocean. Annotation and mapping of these 16 bacterial genome sequences to a PMD-derived Vibrio metagenome-assembled genome created for this study showcased vertebrate pathogen genes closely-related to cholera and non-cholera pathovars. Phenotype testing of cultivars confirmed rapid biofilm formation, hemolytic, and lipophospholytic activities, consistent with pathogenic potential. Our study illustrates that open ocean vibrios represent a heretofore undescribed group of microbes, some representing potential new species, possessing an amalgam of pathogenic and low nutrient acquisition genes, reflecting their pelagic habitat and the substrates and hosts they colonize.}, } @article {pmid37244571, year = {2023}, author = {Pfennig, A and Lomsadze, A and Borodovsky, M}, title = {MgCod: Gene Prediction in Phage Genomes with Multiple Genetic Codes.}, journal = {Journal of molecular biology}, volume = {435}, number = {14}, pages = {168159}, doi = {10.1016/j.jmb.2023.168159}, pmid = {37244571}, issn = {1089-8638}, support = {R01 GM128145/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Bacteriophages/genetics ; *Codon, Terminator/genetics ; Proteins/genetics ; *Genome, Viral ; Sequence Analysis ; }, abstract = {Massive sequencing of microbiomes has led to the discovery of a large number of phage genomes with intermittent stop codon recoding. We have developed a computational tool, MgCod, that identifies genomic regions (blocks) with distinct stop codon recoding simultaneously with the prediction of protein-coding regions. When MgCod was used to scan a large volume of human metagenomic contigs hundreds of viral contigs with intermittent stop codon recoding were revealed. Many of these contigs originated from genomes of known crAssphages. Further analyses had shown that intermittent recoding was associated with subtle patterns in the organization of protein-coding genes, such as 'single-coding' and 'dual-coding'. The dual-coding genes, clustered into blocks, could be translated by two alternative codes producing nearly identical proteins. It was observed that the dual-coded blocks were enriched with the early-stage phage genes, while the late-stage genes were residing in the single-coded blocks. MgCod can identify types of stop codon recoding in novel genomic sequences in parallel with gene prediction. It is available for download from https://github.com/gatech-genemark/MgCod.}, } @article {pmid37244468, year = {2023}, author = {Hogan, CA and Miller, S and Piantadosi, A and Gaston, DC and Simner, PJ and Nash, S and Babady, NE}, title = {Which trial do we need? Plasma metagenomic next-generation sequencing to diagnose infections in patients with haematological malignancies and febrile neutropenia: proposal for a randomized-controlled trial.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {29}, number = {12}, pages = {1474-1479}, doi = {10.1016/j.cmi.2023.05.024}, pmid = {37244468}, issn = {1469-0691}, mesh = {Humans ; *Febrile Neutropenia/diagnosis ; *Hematologic Neoplasms/complications ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics ; Randomized Controlled Trials as Topic ; }, } @article {pmid37244312, year = {2023}, author = {Zhou, Z and Sun, Y and Fu, L and Zuo, Y and Shao, Y and Wang, L and Zhou, C and An, Y}, title = {Unraveling roles of the intermediate settler in a microaerobic hydrolysis sludge in situ reduction process.}, journal = {Bioresource technology}, volume = {384}, number = {}, pages = {129228}, doi = {10.1016/j.biortech.2023.129228}, pmid = {37244312}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; Hydrolysis ; *Bioreactors ; Fermentation ; Anaerobiosis ; Methane ; Waste Disposal, Fluid ; }, abstract = {The roles of the intermediate settler in the sludge process reduction activated sludge process (SPRAS), and the influences of its hydraulic retention time (HRTST) on pollutant removal and sludge reduction were investigated. Prolonging HRTST from 3.0 to 4.5 and 6.0 h resulted in sludge reduction efficiencies increased from 46.8% to 61.5% and 62.7%. The sludge accumulation in the intermediate settler formed an anaerobic zone but inhibited methane production, and the alternating microaerobic and anaerobic environment in the sludge process reduction (SPR) module increased the microbial diversity and enriched the hydrolytic and fermentative bacteria. Prolonging HRTST accelerated dissolved organic matter release and elevated the degradation of refractory fraction, and improved the sludge properties of the SPRAS. Metagenomic analysis showed that the SPR module enhanced the glycolysis pathway and decoupling metabolism for sludge reduction. The results revealed that the intermediate settler plays dual roles in solid-liquid separation and sludge reduction metabolism.}, } @article {pmid37243505, year = {2023}, author = {Bruggeling, CE and Te Groen, M and Garza, DR and van Heeckeren Tot Overlaer, F and Krekels, JPM and Sulaiman, BC and Karel, D and Rulof, A and Schaaphok, AR and Hornikx, DLAH and Nagtegaal, ID and Dutilh, BE and Hoentjen, F and Boleij, A}, title = {Bacterial Oncotraits Rather than Spatial Organization Are Associated with Dysplasia in Ulcerative Colitis.}, journal = {Journal of Crohn's & colitis}, volume = {17}, number = {11}, pages = {1870-1881}, pmid = {37243505}, issn = {1876-4479}, support = {//Scientific Research 'Veni/ ; //Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; *Colitis, Ulcerative/pathology ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Hyperplasia ; Biomarkers ; }, abstract = {BACKGROUND AND AIMS: Colonic bacterial biofilms are frequently present in ulcerative colitis [UC] and may increase dysplasia risk through pathogens expressing oncotraits. This prospective cohort study aimed to determine [1] the association of oncotraits and longitudinal biofilm presence with dysplasia risk in UC, and [2] the relation of bacterial composition with biofilms and dysplasia risk.

METHODS: Faeces and left- and right-sided colonic biopsies were collected from 80 UC patients and 35 controls. Oncotraits [FadA of Fusobacterium, BFT of Bacteroides fragilis, colibactin [ClbB] and Intimin [Eae] of Escherichia coli] were assessed in faecal DNA with multiplex quantitative polymerase chain reaction [qPCR]. Biopsies were screened for biofilms [n = 873] with 16S rRNA fluorescent in situ hybridiation. Shotgun metagenomic sequencing [n = 265], and ki67-immunohistochemistry were performed. Associations were determined with a mixed-effects regression model.

RESULTS: Biofilms were highly prevalent in UC patients [90.8%] with a median persistence of 3 years (interquartile range [IQR] 2-5 years). Biofilm-positive biopsies showed increased epithelial hypertrophy [p = 0.025] and a reduced Shannon diversity independent of disease status [p = 0.015], but were not significantly associated with dysplasia in UC: adjusted odds ratio [aOR] 1.45, 95% confidence interval [CI] 0.63-3.40. In contrast, ClbB independently associated with dysplasia [aOR 7.16, 95% CI 1.75-29.28], and FadA and Fusobacteriales were associated with a decreased dysplasia risk in UC [aOR 0.23, 95% CI 0.06-0.83, p <0.01].

CONCLUSIONS: Biofilms are a hallmark of UC; however, because of their high prevalence are a poor biomarker for dysplasia. In contrast, colibactin presence and FadA absence independently associate with dysplasia in UC and might therefore be valuable biomarkers for future risk stratification and intervention strategies.}, } @article {pmid37243298, year = {2023}, author = {Latka, A and Aertsen, A and Boeckaerts, D and Blasdel, B and Ceyssens, PJ and Garcia-Pino, A and Gillis, A and Lavigne, R and Lima-Mendez, G and Matthijnssens, J and Onsea, J and Peeters, E and Pirnay, JP and Thiry, D and Vandenheuvel, D and Van Mechelen, E and Venneman, J and Verbeken, G and Wagemans, J and Briers, Y}, title = {Foundation of the Belgian Society for Viruses of Microbes and Meeting Report of Its Inaugural Symposium.}, journal = {Viruses}, volume = {15}, number = {5}, pages = {}, pmid = {37243298}, issn = {1999-4915}, mesh = {Humans ; Belgium ; *Host Microbial Interactions ; *Viruses ; }, abstract = {The Belgian Society for Viruses of Microbes (BSVoM) was founded on 9 June 2022 to capture and enhance the collaborative spirit among the expanding community of microbial virus researchers in Belgium. The sixteen founders are affiliated to fourteen different research entities across academia, industry and government. Its inaugural symposium was held on 23 September 2022 in the Thermotechnical Institute at KU Leuven. The meeting program covered three thematic sessions launched by international keynote speakers: (1) virus-host interactions, (2) viral ecology, evolution and diversity and (3) present and future applications. During the one-day symposium, four invited keynote lectures, ten selected talks and eight student pitches were given along with 41 presented posters. The meeting hosted 155 participants from twelve countries.}, } @article {pmid37243295, year = {2023}, author = {Lee, E and Vansia, R and Phelan, J and Lofano, A and Smith, A and Wang, A and Bilodeau, GJ and Pernal, SF and Guarna, MM and Rott, M and Griffiths, JS}, title = {Area Wide Monitoring of Plant and Honey Bee (Apis mellifera) Viruses in Blueberry (Vaccinium corymbosum) Agroecosystems Facilitated by Honey Bee Pollination.}, journal = {Viruses}, volume = {15}, number = {5}, pages = {}, pmid = {37243295}, issn = {1999-4915}, mesh = {Animals ; Bees ; *Blueberry Plants ; Pollination ; Ecosystem ; Plants ; Pollen ; }, abstract = {Healthy agroecosystems are dependent on a complex web of factors and inter-species interactions. Flowers are hubs for pathogen transmission, including the horizontal or vertical transmission of plant-viruses and the horizontal transmission of bee-viruses. Pollination by the European honey bee (Apis mellifera) is critical for industrial fruit production, but bees can also vector viruses and other pathogens between individuals. Here, we utilized commercial honey bee pollination services in blueberry (Vaccinium corymbosum) farms for a metagenomics-based bee and plant virus monitoring system. Following RNA sequencing, viruses were identified by mapping reads to a reference sequence database through the bioinformatics portal Virtool. In total, 29 unique plant viral species were found at two blueberry farms in British Columbia (BC). Nine viruses were identified at one site in Ontario (ON), five of which were not identified in BC. Ilarviruses blueberry shock virus (BlShV) and prune dwarf virus (PDV) were the most frequently detected viruses in BC but absent in ON, while nepoviruses tomato ringspot virus and tobacco ringspot virus were common in ON but absent in BC. BlShV coat protein (CP) nucleotide sequences were nearly identical in all samples, while PDV CP sequences were more diverse, suggesting multiple strains of PDV circulating at this site. Ten bee-infecting viruses were identified, with black queen cell virus frequently detected in ON and BC. Area-wide bee-mediated pathogen monitoring can provide new insights into the diversity of viruses present in, and the health of, bee-pollination ecosystems. This approach can be limited by a short sampling season, biased towards pollen-transmitted viruses, and the plant material collected by bees can be very diverse. This can obscure the origin of some viruses, but bee-mediated virus monitoring can be an effective preliminary monitoring approach.}, } @article {pmid37243191, year = {2023}, author = {Habili, N and Wu, Q and Rinaldo, A and Constable, F}, title = {A Chronological Study on Grapevine Leafroll-Associated Virus 2 in Australia.}, journal = {Viruses}, volume = {15}, number = {5}, pages = {}, pmid = {37243191}, issn = {1999-4915}, mesh = {Phylogeny ; Plant Diseases ; *Closterovirus ; *Viroids ; *Vitis ; }, abstract = {Grapevine leafroll disease affects the health status of grapevines worldwide. Most studies in Australia have focused on grapevine leafroll-associated viruses 1 and 3, while little attention has been given to other leafroll virus types, in particular, grapevine leafroll-associated virus 2 (GLRaV-2). A chronological record of the temporal occurrence of GLRaV-2 in Australia since 2001 is reported. From a total of 11,257 samples, 313 tested positive, with an overall incidence of 2.7%. This virus has been detected in 18 grapevine varieties and Vitis rootstocks in different regions of Australia. Most varieties were symptomless on their own roots, while Chardonnay showed a decline in virus-sensitive rootstocks. An isolate of GLRaV-2, on own-rooted Vitis vinifera cv. Grenache, clone SA137, was associated with severe leafroll symptoms after veraison with abnormal leaf necrosis. The metagenomic sequencing results of the virus in two plants of this variety confirmed the presence of GLRaV-2, as well as two inert viruses, grapevine rupestris stem pitting-associated virus (GRSPaV) and grapevine rupestris vein feathering virus (GRVFV). No other leafroll-associated viruses were detected. Among the viroids, hop stunt viroid and grapevine yellow speckle viroid 1 were detected. Of the six phylogenetic groups identified in GLRaV-2, we report the presence of four groups in Australia. Three of these groups were detected in two plants of cv. Grenache, without finding any recombination event. The hypersensitive reaction of certain American hybrid rootstocks to GLRaV-2 is discussed. Due to the association of GLRaV-2 with graft incompatibility and vine decline, the risk from this virus in regions where hybrid Vitis rootstocks are used cannot be overlooked.}, } @article {pmid37243173, year = {2023}, author = {Kaiser, FK and de le Roi, M and Jo, WK and Gerhauser, I and Molnár, V and Osterhaus, ADME and Baumgärtner, W and Ludlow, M}, title = {First Report of Skunk Amdoparvovirus (Species Carnivore amdoparvovirus 4) in Europe in a Captive Striped Skunk (Mephitis mephitis).}, journal = {Viruses}, volume = {15}, number = {5}, pages = {}, pmid = {37243173}, issn = {1999-4915}, mesh = {Animals ; *Aleutian Mink Disease ; British Columbia ; Europe/epidemiology ; *Mephitidae ; Mink ; Phylogeny ; }, abstract = {Skunk amdoparvovirus (Carnivore amdoparvovirus 4, SKAV) is closely related to Aleutian mink disease virus (AMDV) and circulates primarily in striped skunks (Mephitis mephitis) in North America. SKAV poses a threat to mustelid species due to reported isolated infections of captive American mink (Neovison vison) in British Columbia, Canada. We detected SKAV in a captive striped skunk in a German zoo by metagenomic sequencing. The pathological findings are dominated by lymphoplasmacellular inflammation and reveal similarities to its relative Carnivore amdoparvovirus 1, the causative agent of Aleutian mink disease. Phylogenetic analysis of the whole genome demonstrated 94.80% nucleotide sequence identity to a sequence from Ontario, Canada. This study is the first case description of a SKAV infection outside of North America.}, } @article {pmid37242607, year = {2023}, author = {Adnan, A and Borman, AM and Tóth, Z and Forgács, L and Kovács, R and Balázsi, D and Balázs, B and Udvarhelyi, G and Kardos, G and Majoros, L}, title = {In Vitro Killing Activities of Anidulafungin and Micafungin with and without Nikkomycin Z against Four Candida auris Clades.}, journal = {Pharmaceutics}, volume = {15}, number = {5}, pages = {}, pmid = {37242607}, issn = {1999-4923}, support = {NKFIH FK138462//Hungarian National Research, Development and Innovation Office/ ; }, abstract = {Candida auris is a multidrug-resistant pathogen against which echinocandins are the drug of choice. However, information on how the chitin synthase inhibitor nikkomycin Z influences the killing activities of echinocandins against C. auris is currently lacking. We determined the killing activities of anidulafungin and micafungin (0.25, 1, 8, 16 and 32 mg/L each) with and without nikkomycin Z (8 mg/L) against 15 isolates representing four C. auris clades (South Asian n = 5; East Asian n = 3; South African n = 3; South American n = 4, two of which were of environmental origin). Two and one isolates from the South Asian clade harbored mutations in the hot-spot 1 (S639Y and S639P) and 2 (R1354H) regions of the FKS1 gene, respectively. The anidulafungin, micafungin and nikkomycin Z MIC ranges were 0.015-4, 0.03-4 and 2->16 mg/L, respectively. Anidulafungin and micafungin alone exerted weak fungistatic activity against wild-type isolates and the isolate with a mutation in the hot-spot 2 region of FKS1 but was ineffective against the isolates with a mutation in the hot-spot 1 region. The nikkomycin Z killing curves were always similar to their respective controls. Twenty-two of sixty (36.7%) anidulafungin plus nikkomycin Z and twenty-four of sixty (40%) micafungin plus nikkomycin Z combinations produced at least 100-fold decreases in the CFUs (synergy), with a 41.7% and 20% fungicidal effect, respectively, against wild-type isolates. Antagonism was never observed. Similar results were found with the isolate with a mutation in hot-spot 2 of FKS1, but the combinations were ineffective against the two isolates with prominent mutations in hot-spot 1 of FKS1. The simultaneous inhibition of β-1,3 glucan and chitin synthases in wild-type C. auris isolates produced significantly greater killing rates than either drug alone. Further studies are warranted to verify the clinical efficacy of echinocandin plus nikkomycin Z combinations against echinocandin susceptible C. auris isolates.}, } @article {pmid37242478, year = {2023}, author = {Chaiyasut, C and Sivamaruthi, BS and Lailerd, N and Sirilun, S and Thangaleela, S and Khongtan, S and Bharathi, M and Kesika, P and Saelee, M and Choeisoongnern, T and Fukngoen, P and Peerajan, S and Sittiprapaporn, P}, title = {Influence of Bifidobacterium breve on the Glycaemic Control, Lipid Profile and Microbiome of Type 2 Diabetic Subjects: A Preliminary Randomized Clinical Trial.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {16}, number = {5}, pages = {}, pmid = {37242478}, issn = {1424-8247}, abstract = {Type 2 diabetes mellitus (T2DM) is one of the most highly prevalent metabolic disorders worldwide. Uncontrolled T2DM can lead to other health threats such as cardiac arrest, lower-limb amputation, blindness, stroke, impaired kidney function, and microvascular and macrovascular complications. Many studies have demonstrated the association between gut microbiota and diabetes development and probiotic supplementation in improving glycemic properties in T2DM. The study aimed to evaluate the influence of Bifidobacterium breve supplementation on glycemic control, lipid profile, and microbiome of T2DM subjects. Forty participants were randomly divided into two groups, and they received probiotics (50 × 10[9] CFU/day) or placebo interventions (corn starch; 10 mg/day) for 12 weeks. The changes in the blood-urea nitrogen (BUN), aspartate aminotransferase (AST), alanine transaminase (ALT), alkaline phosphatase (ALP), fasting blood sugar (FBS), glycated hemoglobin (HbA1c), total cholesterol (TC), triglycerides (TG), high-density lipoprotein (HDL), low-density lipoprotein (LDL), creatinine levels, and other factors such as body-mass index, visceral fat, body fat, and body weight were assessed at baseline and after 12 weeks. B. breve supplementation significantly reduced BUN, creatinine, LDL, TG, and HbA1c levels compared to the placebo group. Significant changes were observed in the microbiome of the probiotic-treated group compared to the placebo group. Firmicutes and proteobacteria were predominant in the placebo and probiotic-treated groups. Genera Streptococcus, Butyricicoccus, and species Eubacterium hallii were significantly reduced in the probiotic-treated group compared to the placebo. Overall results suggested that B. breve supplementation could prevent worsening of representative clinical parameters in T2DM subjects. The current study has limitations, including fewer subjects, a single probiotic strain, and fewer metagenomic samples for microbiome analysis. Therefore, the results of the current study require further validation using more experimental subjects.}, } @article {pmid37242392, year = {2023}, author = {Capozza, P and Buonavoglia, A and Pratelli, A and Martella, V and Decaro, N}, title = {Old and Novel Enteric Parvoviruses of Dogs.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, pmid = {37242392}, issn = {2076-0817}, support = {PE00000007//Parvovirus research was supported by EU funding within the MUR PNRR Extended Partnership Initiative on Emerging Infectious Diseases/ ; }, abstract = {Parvovirus infections have been well known for around 100 years in domestic carnivores. However, the use of molecular assays and metagenomic approaches for virus discovery and characterization has led to the detection of novel parvovirus species and/or variants in dogs. Although some evidence suggests that these emerging canine parvoviruses may act as primary causative agents or as synergistic pathogens in the diseases of domestic carnivores, several aspects regarding epidemiology and virus-host interaction remain to be elucidated.}, } @article {pmid37241797, year = {2023}, author = {Rajkowska, K and Otlewska, A and Broncel, N and Kunicka-Styczyńska, A}, title = {Microbial Diversity and Bioactive Compounds in Dried Lycium barbarum Fruits (Goji): A Comparative Study.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {10}, pages = {}, pmid = {37241797}, issn = {1420-3049}, mesh = {*Antioxidants ; *Lycium ; Fruit ; Polyphenols ; Carotenoids ; }, abstract = {This study compares the microbial diversity and content of bioactive compounds in dried goji berries available on the Polish market to those of the most highly valued goji berries from the Ningxia region in China. The content of phenols, flavonoids, and carotenoids were determined, as well as the antioxidant capacities of the fruits. The quantitative and qualitative composition of the microbiota inhabiting the fruits was assessed using metagenomics by high-throughput sequencing on the Illumina platform. The highest quality was demonstrated by naturally dried fruits from the Ningxia region. These berries were characterized by a high content of polyphenols and high antioxidant activity, as well as high microbial quality. The lowest antioxidant capacity was shown by goji berries cultivated in Poland. However, they contained a high amount of carotenoids. The highest microbial contamination was found in the goji berries available in Poland (>10[6] CFU/g), which is important in terms of consumer safety. Despite the widely accepted benefits of consuming goji berries, both the country of cultivation and the preservation method may influence their composition, bioactivity, and microbial quality.}, } @article {pmid37240180, year = {2023}, author = {Lafleur, S and Bodein, A and Mbuya Malaïka Mutombo, J and Mathieu, A and Joly Beauparlant, C and Minne, X and Chandad, F and Droit, A and Houde, VP}, title = {Multi-Omics Data Integration Reveals Key Variables Contributing to Subgingival Microbiome Dysbiosis-Induced Inflammatory Response in a Hyperglycemic Microenvironment.}, journal = {International journal of molecular sciences}, volume = {24}, number = {10}, pages = {}, pmid = {37240180}, issn = {1422-0067}, support = {Biocodex Microbiota Foundation//Biocodex (France)/ ; }, mesh = {Humans ; Multiomics ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; U937 Cells ; *Periodontitis/microbiology ; *Microbiota/genetics ; Bacteria/metabolism ; Cytokines/metabolism ; RNA-Binding Proteins ; }, abstract = {Subgingival microbiome dysbiosis promotes the development of periodontitis, an irreversible chronic inflammatory disease associated with metabolic diseases. However, studies regarding the effects of a hyperglycemic microenvironment on host-microbiome interactions and host inflammatory response during periodontitis are still scarce. Here, we investigated the impacts of a hyperglycemic microenvironment on the inflammatory response and transcriptome of a gingival coculture model stimulated with dysbiotic subgingival microbiomes. HGF-1 cells overlaid with U937 macrophage-like cells were stimulated with subgingival microbiomes collected from four healthy donors and four patients with periodontitis. Pro-inflammatory cytokines and matrix metalloproteinases were measured while the coculture RNA was submitted to a microarray analysis. Subgingival microbiomes were submitted to 16s rRNA gene sequencing. Data were analyzed using an advanced multi-omics bioinformatic data integration model. Our results show that the genes krt76, krt27, pnma5, mansc4, rab41, thoc6, tm6sf2, and znf506 as well as the pro-inflammatory cytokines IL-1β, GM-CSF, FGF2, IL-10, the metalloproteinases MMP3 and MMP8, and bacteria from the ASV 105, ASV 211, ASV 299, Prevotella, Campylobacter and Fretibacterium genera are key intercorrelated variables contributing to periodontitis-induced inflammatory response in a hyperglycemic microenvironment. In conclusion, our multi-omics integration analysis unveiled the complex interrelationships involved in the regulation of periodontal inflammation in response to a hyperglycemic microenvironment.}, } @article {pmid37239456, year = {2023}, author = {Sun, Q and Zhang, X and Ouyang, Y and Yu, P and Man, Y and Guo, S and Liu, S and Chen, Y and Wang, Y and Tan, X}, title = {Appressoria Formation in Phytopathogenic Fungi Suppressed by Antimicrobial Peptides and Hybrid Peptides from Black Soldier Flies.}, journal = {Genes}, volume = {14}, number = {5}, pages = {}, pmid = {37239456}, issn = {2073-4425}, mesh = {Animals ; *Antifungal Agents/pharmacology ; Antimicrobial Peptides ; Fungi ; Spores, Fungal ; Peptides ; *Diptera ; }, abstract = {Antimicrobial peptides (AMPs) from black solider flies (Hermetia illucens, BSF) exhibiting broad-spectrum antimicrobial activity are the most promising green substitutes for preventing the infection of phytopathogenic fungi; therefore, AMPs have been a focal topic of research. Recently, many studies have focused on the antibacterial activities of BSF AMPs against animal pathogens; however, currently, their antifungal activities against phytopathogenic fungi remain unclear. In this study, 7 AMPs selected from 34 predicted AMPs based on BSF metagenomics were artificially synthesized. When conidia from the hemibiotrophic phytopathogenic fungi Magnaporthe oryzae and Colletotrichum acutatum were treated with the selected AMPs, three selected AMPs-CAD1, CAD5, and CAD7-showed high appressorium formation inhibited by lengthened germ tubes. Additionally, the MIC50 concentrations of the inhibited appressorium formations were 40 μM, 43 μM, and 43 μM for M. oryzae, while 51 μM, 49 μM, and 44 μM were observed for C. acutatum, respectively. A tandem hybrid AMP named CAD-Con comprising CAD1, CAD5, and CAD7 significantly enhanced antifungal activities, and the MIC50 concentrations against M. oryzae and C. acutatum were 15 μM and 22 μM, respectively. In comparison with the wild type, they were both significantly reduced in terms of virulence when infection assays were performed using the treated conidia of M. oryzae or C. acutatum by CAD1, CAD5, CAD7, or CAD-Con. Meanwhile, their expression levels of CAD1, CAD5, and CAD7 could also be activated and significantly increased after the BSF larvae were treated with the conidia of M. oryzae or C. acutatum, respectively. To our knowledge, the antifungal activities of BSF AMPs against plant pathogenic fungi, which help us to seek potential AMPs with antifungal activities, provide proof of the effectiveness of green control strategies for crop production.}, } @article {pmid37239442, year = {2023}, author = {Choudhury, N and Sahu, TK and Rao, AR and Rout, AK and Behera, BK}, title = {An Improved Machine Learning-Based Approach to Assess the Microbial Diversity in Major North Indian River Ecosystems.}, journal = {Genes}, volume = {14}, number = {5}, pages = {}, pmid = {37239442}, issn = {2073-4425}, mesh = {*Rivers ; Software ; Machine Learning ; Metagenome/genetics ; *Microbiota/genetics ; }, abstract = {The rapidly evolving high-throughput sequencing (HTS) technologies generate voluminous genomic and metagenomic sequences, which can help classify the microbial communities with high accuracy in many ecosystems. Conventionally, the rule-based binning techniques are used to classify the contigs or scaffolds based on either sequence composition or sequence similarity. However, the accurate classification of the microbial communities remains a major challenge due to massive data volumes at hand as well as a requirement of efficient binning methods and classification algorithms. Therefore, we attempted here to implement iterative K-Means clustering for the initial binning of metagenomics sequences and applied various machine learning algorithms (MLAs) to classify the newly identified unknown microbes. The cluster annotation was achieved through the BLAST program of NCBI, which resulted in the grouping of assembled scaffolds into five classes, i.e., bacteria, archaea, eukaryota, viruses and others. The annotated cluster sequences were used to train machine learning algorithms (MLAs) to develop prediction models to classify unknown metagenomic sequences. In this study, we used metagenomic datasets of samples collected from the Ganga (Kanpur and Farakka) and the Yamuna (Delhi) rivers in India for clustering and training the MLA models. Further, the performance of MLAs was evaluated by 10-fold cross validation. The results revealed that the developed model based on the Random Forest had a superior performance compared to the other considered learning algorithms. The proposed method can be used for annotating the metagenomic scaffolds/contigs being complementary to existing methods of metagenomic data analysis. An offline predictor source code with the best prediction model is available at (https://github.com/Nalinikanta7/metagenomics).}, } @article {pmid37238082, year = {2023}, author = {Matthews, C and Walsh, AM and Gordon, SV and Markey, B and Cotter, PD and O' Mahony, J}, title = {Differences in Faecal Microbiome Taxonomy, Diversity and Functional Potential in a Bovine Cohort Experimentally Challenged with Mycobacterium avium subsp. paratuberculosis (MAP).}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {10}, pages = {}, pmid = {37238082}, issn = {2076-2615}, support = {15/S/651 (NexusMAP) and 11/S/141 (IconMAP).//Department of Agriculture Food and the Marine/ ; }, abstract = {Mycobacterium avium subspecies paratuberculosis (MAP) is the causative agent of Johne's disease in ruminants, a chronic enteritis which results in emaciation and eventual loss of the animal. Recent advances in metagenomics have allowed a more in-depth study of complex microbiomes, including that of gastrointestinal tracts, and have the potential to provide insights into consequences of the exposure of an animal to MAP or other pathogens. This study aimed to investigate taxonomic diversity and compositional changes of the faecal microbiome of cattle experimentally challenged with MAP compared to an unexposed control group. Faecal swab samples were collected from a total of 55 animals [exposed group (n = 35) and a control group (n = 20)], across three time points (months 3, 6 and 9 post-inoculation). The composition and functional potential of the faecal microbiota differed across time and between the groups (p < 0.05), with the primary differences, from both a taxonomic and functional perspective, occurring at 3 months post inoculation. These included significant differences in the relative abundance of the genera Methanobrevibacter and Bifidobacterium and also of 11 other species (4 at a higher relative abundance in the exposed group and 7 at a higher relative abundance in the control group). Correlations were made between microbiome data and immunopathology measurements and it was noted that changes in the microbial composition correlated with miRNA-155, miR-146b and IFN-ɣ. In summary, this study illustrates the impact of exposure to MAP on the ruminant faecal microbiome with a number of species that may have relevance in veterinary medicine for tracking exposure to MAP.}, } @article {pmid37238063, year = {2023}, author = {Hasan, I and Rimoldi, S and Saroglia, G and Terova, G}, title = {Sustainable Fish Feeds with Insects and Probiotics Positively Affect Freshwater and Marine Fish Gut Microbiota.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {10}, pages = {}, pmid = {37238063}, issn = {2076-2615}, support = {818367//EU Horizon 2020 AquaIMPACT project (Genomic and nutritional innovations for genetically su-perior farmed fish to improve efficiency in European aquaculture)./ ; }, abstract = {Aquaculture is the fastest-growing agricultural industry in the world. Fishmeal is an essential component of commercial fish diets, but its long-term sustainability is a concern. Therefore, it is important to find alternatives to fishmeal that have a similar nutritional value and, at the same time, are affordable and readily available. The search for high-quality alternatives to fishmeal and fish oil has interested researchers worldwide. Over the past 20 years, different insect meals have been studied as a potential alternate source of fishmeal in aquafeeds. On the other hand, probiotics-live microbial strains-are being used as dietary supplements and showing beneficial effects on fish growth and health status. Fish gut microbiota plays a significant role in nutrition metabolism, which affects a number of other physiological functions, including fish growth and development, immune regulation, and pathogen resistance. One of the key reasons for studying fish gut microbiota is the possibility to modify microbial communities that inhabit the intestine to benefit host growth and health. The development of DNA sequencing technologies and advanced bioinformatics tools has made metagenomic analysis a feasible method for researching gut microbes. In this review, we analyze and summarize the current knowledge provided by studies of our research group on using insect meal and probiotic supplements in aquafeed formulations and their effects on different fish gut microbiota. We also highlight future research directions to make insect meals a key source of proteins for sustainable aquaculture and explore the challenges associated with the use of probiotics. Insect meals and probiotics will undoubtedly have a positive effect on the long-term sustainability and profitability of aquaculture.}, } @article {pmid37237835, year = {2023}, author = {Azuma, T and Katagiri, M and Sasaki, N and Kuroda, M and Watanabe, M}, title = {Performance of a Pilot-Scale Continuous Flow Ozone-Based Hospital Wastewater Treatment System.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, pmid = {37237835}, issn = {2079-6382}, support = {JP22fk0108131//Japan Agency for Medical Research and Development/ ; H30 Shinkogyosei-Ippan-002//a grant for research on emerging and reemerging infectious diseases and immunization from the Ministry of Health, Labour and Welfare, Japan/ ; 21HA1002//a grant for research on emerging and reemerging infectious diseases and immunization from the Ministry of Health, Labour and Welfare, Japan/ ; 20H02289//research grants and scholarships from the Ministry of Education, Culture, Sports, Science, and Technology, Japan./ ; }, abstract = {Antimicrobial resistance (AMR) is becoming a global concern. Recently, research has emerged to evaluate the human and environmental health implications of wastewater from medical facilities and to identify acceptable wastewater treatment methods. In this study, a disinfection wastewater treatment system using an ozone-based continuous flow system was installed in a general hospital located in Japan. The effectiveness of antimicrobial-resistant bacteria (ARB) and antimicrobials in mitigating the environmental impact of hospital wastewater was evaluated. Metagenomic analysis was conducted to characterize the microorganisms in the wastewater before and after treatment. The results demonstrated that ozone treatment enables effective inactivation of general gut bacteria, including Bacteroides, Prevotella, Escherichia coli, Klebsiella, DNA molecules, and ARGs, as well as antimicrobials. Azithromycin and doxycycline removal rates were >99% immediately after treatment, and levofloxacin and vancomycin removal rates remained between 90% and 97% for approximately one month. Clarithromycin was more readily removed than the other antimicrobials (81-91%), and no clear removal trend was observed for ampicillin. Our findings provide a better understanding of the environmental management of hospital wastewater and enhance the effectiveness of disinfection wastewater treatment systems at medical facilities for mitigating the discharge of pollutants into aquatic environments.}, } @article {pmid37237590, year = {2023}, author = {Koh, WLC and Poh, SE and Lee, CK and Chan, THM and Yan, G and Kong, KW and Lau, L and Lee, WYT and Cheng, C and Hoon, S and Seow, Y}, title = {Towards a Rapid-Turnaround Low-Depth Unbiased Metagenomics Sequencing Workflow on the Illumina Platforms.}, journal = {Bioengineering (Basel, Switzerland)}, volume = {10}, number = {5}, pages = {}, pmid = {37237590}, issn = {2306-5354}, support = {NA//Accelerate Venture Creation Pte Ltd (subsidiary of Agency for Science, Technoogy and Research (Singapore) and Paths Diagnostics Pte Ltd/ ; }, abstract = {Unbiased metagenomic sequencing is conceptually well-suited for first-line diagnosis as all known and unknown infectious entities can be detected, but costs, turnaround time and human background reads in complex biofluids, such as plasma, hinder widespread deployment. Separate preparations of DNA and RNA also increases costs. In this study, we developed a rapid unbiased metagenomics next-generation sequencing (mNGS) workflow with a human background depletion method (HostEL) and a combined DNA/RNA library preparation kit (AmpRE) to address this issue. We enriched and detected bacterial and fungal standards spiked in plasma at physiological levels with low-depth sequencing (<1 million reads) for analytical validation. Clinical validation also showed 93% of plasma samples agreed with the clinical diagnostic test results when the diagnostic qPCR had a Ct < 33. The effect of different sequencing times was evaluated with the 19 h iSeq 100 paired end run, a more clinically palatable simulated iSeq 100 truncated run and the rapid 7 h MiniSeq platform. Our results demonstrate the ability to detect both DNA and RNA pathogens with low-depth sequencing and that iSeq 100 and MiniSeq platforms are compatible with unbiased low-depth metagenomics identification with the HostEL and AmpRE workflow.}, } @article {pmid37237535, year = {2023}, author = {Kadnikov, VV and Mardanov, AV and Beletsky, AV and Karnachuk, OV and Ravin, NV}, title = {Prokaryotic Life Associated with Coal-Fire Gas Vents Revealed by Metagenomics.}, journal = {Biology}, volume = {12}, number = {5}, pages = {}, pmid = {37237535}, issn = {2079-7737}, support = {21-14-00114//Russian Science Foundation/ ; 22-14-00178//Russian Science Foundation/ ; }, abstract = {The natural combustion of underground coal seams leads to the formation of gas, which contains molecular hydrogen and carbon monoxide. In places where hot coal gases are released to the surface, specific thermal ecosystems are formed. Here, 16S rRNA gene profiling and shotgun metagenome sequencing were employed to characterize the taxonomic diversity and genetic potential of prokaryotic communities of the near-surface ground layer near hot gas vents in an open quarry heated by a subsurface coal fire. The communities were dominated by only a few groups of spore-forming Firmicutes, namely the aerobic heterotroph Candidatus Carbobacillus altaicus, the aerobic chemolitoautotrophs Kyrpidia tusciae and Hydrogenibacillus schlegelii, and the anaerobic chemolithoautotroph Brockia lithotrophica. Genome analysis predicted that these species can obtain energy from the oxidation of hydrogen and/or carbon monoxide in coal gases. We assembled the first complete closed genome of a member of uncultured class-level division DTU015 in the phylum Firmicutes. This bacterium, 'Candidatus Fermentithermobacillus carboniphilus' Bu02, was predicted to be rod-shaped and capable of flagellar motility and sporulation. Genome analysis showed the absence of aerobic and anaerobic respiration and suggested chemoheterotrophic lifestyle with the ability to ferment peptides, amino acids, N-acetylglucosamine, and tricarboxylic acid cycle intermediates. Bu02 bacterium probably plays the role of a scavenger, performing the fermentation of organics formed by autotrophic Firmicutes supported by coal gases. A comparative genome analysis of the DTU015 division revealed that most of its members have a similar lifestyle.}, } @article {pmid37237391, year = {2023}, author = {Wang, Z and Peters, BA and Bryant, M and Hanna, DB and Schwartz, T and Wang, T and Sollecito, CC and Usyk, M and Grassi, E and Wiek, F and Peter, LS and Post, WS and Landay, AL and Hodis, HN and Weber, KM and French, A and Golub, ET and Lazar, J and Gustafson, D and Sharma, A and Anastos, K and Clish, CB and Burk, RD and Kaplan, RC and Knight, R and Qi, Q}, title = {Gut microbiota, circulating inflammatory markers and metabolites, and carotid artery atherosclerosis in HIV infection.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {119}, pmid = {37237391}, issn = {2049-2618}, support = {P30 MH116867/MH/NIMH NIH HHS/United States ; R01 HL126543/HL/NHLBI NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; P30 AI124414/AI/NIAID NIH HHS/United States ; U01 HL146204/HL/NHLBI NIH HHS/United States ; U01 HL146241/HL/NHLBI NIH HHS/United States ; U01 HL146208/HL/NHLBI NIH HHS/United States ; R01HL140976/HL/NHLBI NIH HHS/United States ; R01 HL132794/HL/NHLBI NIH HHS/United States ; P30 AI050410/AI/NIAID NIH HHS/United States ; U01 HL146194/HL/NHLBI NIH HHS/United States ; UL1 TR001881/TR/NCATS NIH HHS/United States ; K01 HL137557/HL/NHLBI NIH HHS/United States ; UL1 TR003098/TR/NCATS NIH HHS/United States ; U01 HL146245/HL/NHLBI NIH HHS/United States ; U01 HL146205/HL/NHLBI NIH HHS/United States ; P30 AI073961/AI/NIAID NIH HHS/United States ; P30 AI027767/AI/NIAID NIH HHS/United States ; U01 HL146333/HL/NHLBI NIH HHS/United States ; R01 HL095140/HL/NHLBI NIH HHS/United States ; U01 HL146240/HL/NHLBI NIH HHS/United States ; R01 HL083760/HL/NHLBI NIH HHS/United States ; U01 HL146242/HL/NHLBI NIH HHS/United States ; U01 HL146192/HL/NHLBI NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; U01 HL146193/HL/NHLBI NIH HHS/United States ; U01 HL146202/HL/NHLBI NIH HHS/United States ; K01 HL160146/HL/NHLBI NIH HHS/United States ; P30 AI050409/AI/NIAID NIH HHS/United States ; U01 HL146201/HL/NHLBI NIH HHS/United States ; U01 HL146203/HL/NHLBI NIH HHS/United States ; P30 CA013330/CA/NCI NIH HHS/United States ; UL1 TR000004/TR/NCATS NIH HHS/United States ; K01 HL129892/HL/NHLBI NIH HHS/United States ; U01 AI035004/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; *HIV Infections/complications/pathology ; *Carotid Stenosis/complications/pathology ; Proteomics ; *Carotid Artery Diseases/complications/pathology ; *Atherosclerosis/complications/pathology ; Carotid Arteries/metabolism/pathology ; Biomarkers/metabolism ; Inflammation/pathology ; }, abstract = {BACKGROUND: Alterations in gut microbiota have been implicated in HIV infection and cardiovascular disease. However, how gut microbial alterations relate to host inflammation and metabolite profiles, and their relationships with atherosclerosis, have not been well-studied, especially in the context of HIV infection. Here, we examined associations of gut microbial species and functional components measured by shotgun metagenomics with carotid artery plaque assessed by B-mode carotid artery ultrasound in 320 women with or at high risk of HIV (65% HIV +) from the Women's Interagency HIV Study. We further integrated plaque-associated microbial features with serum proteomics (74 inflammatory markers measured by the proximity extension assay) and plasma metabolomics (378 metabolites measured by liquid chromatography tandem mass spectrometry) in relation to carotid artery plaque in up to 433 women.

RESULTS: Fusobacterium nucleatum, a potentially pathogenic bacteria, was positively associated with carotid artery plaque, while five microbial species (Roseburia hominis, Roseburia inulinivorans, Johnsonella ignava, Odoribacter splanchnicus, Clostridium saccharolyticum) were inversely associated with plaque. Results were consistent between women with and without HIV. Fusobacterium nucleatum was positively associated with several serum proteomic inflammatory markers (e.g., CXCL9), and the other plaque-related species were inversely associated with proteomic inflammatory markers (e.g., CX3CL1). These microbial-associated proteomic inflammatory markers were also positively associated with plaque. Associations between bacterial species (especially Fusobacterium nucleatum) and plaque were attenuated after further adjustment for proteomic inflammatory markers. Plaque-associated species were correlated with several plasma metabolites, including the microbial metabolite imidazole-propionate (ImP), which was positively associated with plaque and several pro-inflammatory markers. Further analysis identified additional bacterial species and bacterial hutH gene (encoding enzyme histidine ammonia-lyase in ImP production) associated with plasma ImP levels. A gut microbiota score based on these ImP-associated species was positively associated with plaque and several pro-inflammatory markers.

CONCLUSION: Among women living with or at risk of HIV, we identified several gut bacterial species and a microbial metabolite ImP associated with carotid artery atherosclerosis, which might be related to host immune activation and inflammation. Video Abstract.}, } @article {pmid37237317, year = {2023}, author = {Coutinho, FH and Silveira, CB and Sebastián, M and Sánchez, P and Duarte, CM and Vaqué, D and Gasol, JM and Acinas, SG}, title = {Water mass age structures the auxiliary metabolic gene content of free-living and particle-attached deep ocean viral communities.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {118}, pmid = {37237317}, issn = {2049-2618}, mesh = {Seawater/microbiology ; Water ; Genes, Viral ; *Viruses/genetics ; *Microbiota/genetics ; Oceans and Seas ; }, abstract = {BACKGROUND: Viruses play important roles in the ocean's biogeochemical cycles. Yet, deep ocean viruses are one of the most under-explored fractions of the global biosphere. Little is known about the environmental factors that control the composition and functioning of their communities or how they interact with their free-living or particle-attached microbial hosts.

RESULTS: We analysed 58 viral communities associated with size-fractionated free-living (0.2-0.8 μm) and particle-attached (0.8-20 μm) cellular metagenomes from bathypelagic (2150-4018 m deep) microbiomes obtained during the Malaspina expedition. These metagenomes yielded 6631 viral sequences, 91% of which were novel, and 67 represented high-quality genomes. Taxonomic classification assigned 53% of the viral sequences to families of tailed viruses from the order Caudovirales. Computational host prediction associated 886 viral sequences to dominant members of the deep ocean microbiome, such as Alphaproteobacteria (284), Gammaproteobacteria (241), SAR324 (23), Marinisomatota (39), and Chloroflexota (61). Free-living and particle-attached viral communities had markedly distinct taxonomic composition, host prevalence, and auxiliary metabolic gene content, which led to the discovery of novel viral-encoded metabolic genes involved in the folate and nucleotide metabolisms. Water mass age emerged as an important factor driving viral community composition. We postulated this was due to changes in quality and concentration of dissolved organic matter acting on the host communities, leading to an increase of viral auxiliary metabolic genes associated with energy metabolism among older water masses.

CONCLUSIONS: These results shed light on the mechanisms by which environmental gradients of deep ocean ecosystems structure the composition and functioning of free-living and particle-attached viral communities. Video Abstract.}, } @article {pmid37237239, year = {2023}, author = {Huang, H and Shi, J and Zheng, M and Su, S and Chen, W and Ming, J and Ren, T and Qu, D}, title = {Pathogen detection in suspected spinal infection: metagenomic next-generation sequencing versus culture.}, journal = {European spine journal : official publication of the European Spine Society, the European Spinal Deformity Society, and the European Section of the Cervical Spine Research Society}, volume = {32}, number = {12}, pages = {4220-4228}, pmid = {37237239}, issn = {1432-0932}, support = {81272022//National Natural Science Foundation of China/ ; 185. 2019//Guangzhou Research Collaborative Innovation Projects/ ; }, mesh = {Humans ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents ; Biopsy ; *Mycobacterium tuberculosis/genetics ; Sensitivity and Specificity ; }, abstract = {PURPOSE: The aim is to compare the pathogen detection performance of metagenomic next-generation sequencing (mNGS) and the culturing of percutaneous needle biopsy samples obtained from an individual with a suspected spinal infection.

METHODS: A retrospective study of 141 individuals with a suspected spinal infection was conducted, and mNGS was performed. The microbial spectra and detection performance between mNGS and the culturing-based method were compared, and the effects of antibiotic intervention and biopsy on the detection performance were assessed.

RESULTS: The microorganisms isolated most commonly via the culturing-based method were Mycobacterium tuberculosis (n = 21), followed by Staphylococcus epidermidis (n = 13). The most common microorganisms detected via mNGS were Mycobacterium tuberculosis complex (MTBC) (n = 39), followed by Staphylococcus aureus (n = 15). The difference in the type of detected microorganisms between culturing and mNGS was observed only in Mycobacterium (P = 0.001). mNGS helped identify potential pathogens in 80.9% of cases, which was significantly higher than the positivity rate of 59.6% observed for the culturing-based method (P < 0.001). Moreover, mNGS had a sensitivity of 85.7% (95% CI, 78.4% to 91.3%), a specificity of 86.7% (95% CI, 59.5% to 98.3%), and sensitivity gains of 35% (85.7% vs. 50.8%; P < 0.001) during culturing, while no differences were observed in the specificity (86.7% vs. 93.3%; P = 0.543). In addition, antibiotic interventions significantly lowered the positivity rate of the culturing-based method (66.0% vs. 45.5%, P = 0.021) but had no effects on the results of mNGS (82.5% vs. 77.3%, P = 0.467).

CONCLUSION: The use of mNGS could result in a higher detection rate compared to that observed with the culturing-based method in an individual with spinal infection and is particularly valuable for evaluating the effects of a mycobacterial infection or previous antibiotic intervention.}, } @article {pmid37237157, year = {2023}, author = {Aziz, G and Zaidi, A and Sullivan, DJO'}, title = {Insights from metagenome-assembled genomes on the genetic stability and safety of over-the-counter probiotic products.}, journal = {Current genetics}, volume = {69}, number = {4-6}, pages = {213-234}, pmid = {37237157}, issn = {1432-0983}, support = {IRSIP//Higher Education Commision, Pakistan/ ; PSDP "Development of National Probiotics Lab at NIBGE"//Ministry of Planning, Development & Special Initiatives, Government of Pakistan/ ; }, mesh = {Metagenome ; Phylogeny ; Lactobacillus acidophilus/genetics ; Plasmids ; *Bacteriocins/genetics ; *Probiotics ; }, abstract = {The demand for and acceptance of probiotics is determined by their quality and safety. Illumina NGS sequencing and analytics were used to examine eight marketed probiotics. Up to the species level, sequenced DNA was taxonomically identified, and relative abundances were determined using Kaiju. The genomes were constructed using GTDB and validated through PATRICK and TYGS. A FastTree 2 phylogenetic tree was constructed using several type strain sequences from relevant species. Bacteriocin and ribosomally synthesized polypeptide (RiPP) genes were discovered, and a safety check was performed to test for toxins, antibiotic resistance, and genetic drift genes. Except for two products with unclaimed species, the labeling was taxonomically correct. In three product formulations, Lactobacillus acidophilus, Limosilactobacillus reuteri, Lacticaseibacillus paracasei, and Bifidobacterium animalis exhibited two to three genomic alterations, while Streptococcus equinus was found in one. TYGS and GDTB discovered E. faecium and L. paracasei in distinctly different ways. All the bacteria tested had the genetic repertoire to tolerate GIT transit, although some exhibited antibiotic resistance, and one strain had two virulence genes. Except for Bifidobacterium strains, the others revealed a variety of bacteriocins and ribosomally synthesized polypeptides (RiPP), 92% of which were unique and non-homologous to known ones. Plasmids and mobile genetic elements are present in strains of L. reuteri (NPLps01.et_L.r and NPLps02.uf_L.r), Lactobacillus delbrueckii (NPLps01.et_L.d), Streptococcus thermophilus (NPLps06.ab_S.t), and E. faecium (NPLps07.nf_E.f). Our findings support the use of metagenomics to build better and efficient production and post-production practices for probiotic quality and safety assessment.}, } @article {pmid37237073, year = {2023}, author = {Malla, MA and Dubey, A and Kori, RK and Sharma, V and Kumar, A and Yadav, S and Kumari, S}, title = {GC-MS based untargeted metabolomics reveals the metabolic response of earthworm (Eudrilus eugeniae) after chronic combinatorial exposure to three different pesticides.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8583}, pmid = {37237073}, issn = {2045-2322}, support = {129358//National Research Foundation/ ; }, mesh = {Animals ; *Pesticides/pharmacology ; *Oligochaeta/metabolism ; Gas Chromatography-Mass Spectrometry ; Soil ; Metabolomics ; }, abstract = {In this study GC-MS-based untargeted metabolomics was used to identify the metabolic response of earthworm; Eudrilus eugeniae exposed to sub-lethal concentrations of chlorpyrifos-CHL, cypermethrin-CYP, Glyphosate-GLY, and Combined-C (all three pesticides) at the concentrations of 3, 6, and 12 mg/kg. Principal component analysis of the obtained datasets revealed a clear distinction between the control and treatment groups. The mean weight of the worms in the treated groups decreased significantly (p < 0.05). Among the identified metabolites, oleic acid (~ 93.47%), lysine (~ 92.20%), glutamic acid (~ 91.81%), leucine (~ 90.20%), asparagine (~ 94.20%), methionine (~ 92.27%), malic acid (~ 93.37%), turanose (~ 95.04%), maltose (~ 92.36%), cholesta-3,5-diene (~ 86.11%), galactose (~ 93.20%), cholesterol (~ 91.56%), tocopherol (~ 85.09%), decreased significantly (p < 0.05), whereas myoinositol (~ 83%) and isoleucine (78.09%) increased significantly (p < 0.05) upon exposure to the CHL, CYP, GLY, and C. Overall, the findings suggest that earthworms might be a new entry point for the pesticides into the food chain. The present study highlights that metabolomics can be a reliable approach to understand the effect of different xenobiotics including pesticides on the metabolic response of earthworms.}, } @article {pmid37236880, year = {2023}, author = {Malard, LA and Guisan, A}, title = {Into the microbial niche.}, journal = {Trends in ecology & evolution}, volume = {38}, number = {10}, pages = {936-945}, doi = {10.1016/j.tree.2023.04.015}, pmid = {37236880}, issn = {1872-8383}, mesh = {*Ecosystem ; *Metagenomics ; }, abstract = {The environmental niche concept describes the distribution of a taxon in the environment and can be used to understand community dynamics, biological invasions, and the impact of environmental changes. The uses and applications are still restricted in microbial ecology, largely due to the complexity of microbial systems and associated methodological limitations. The development of shotgun metagenomics and metatranscriptomics opens new ways to investigate the microbial niche by focusing on the metabolic niche within the environmental space. Here, we propose the metabolic niche framework, which, by defining the fundamental and realised metabolic niche of microorganisms, has the potential to not only provide novel insights into habitat preferences and the metabolism associated, but also to inform on metabolic plasticity, niche shifts, and microbial invasions.}, } @article {pmid37236370, year = {2023}, author = {Řezanka, T and Kyselová, L and Murphy, DJ}, title = {Archaeal lipids.}, journal = {Progress in lipid research}, volume = {91}, number = {}, pages = {101237}, doi = {10.1016/j.plipres.2023.101237}, pmid = {37236370}, issn = {1873-2194}, mesh = {*Archaea/chemistry/metabolism ; *Membrane Lipids/metabolism ; Bacteria/metabolism ; Terpenes/metabolism ; Ethers/chemistry/metabolism ; }, abstract = {The major archaeal membrane glycerolipids are distinguished from those of bacteria and eukaryotes by the contrasting stereochemistry of their glycerol backbones, and by the use of ether-linked isoprenoid-based alkyl chains rather than ester-linked fatty acyl chains for their hydrophobic moieties. These fascinating compounds play important roles in the extremophile lifestyles of many species, but are also present in the growing numbers of recently discovered mesophilic archaea. The past decade has witnessed significant advances in our understanding of archaea in general and their lipids in particular. Much of the new information has come from the ability to screen large microbial populations via environmental metagenomics, which has revolutionised our understanding of the extent of archaeal biodiversity that is coupled with a strict conservation of their membrane lipid compositions. Significant additional progress has come from new culturing and analytical techniques that are gradually enabling archaeal physiology and biochemistry to be studied in real time. These studies are beginning to shed light on the much-discussed and still-controversial process of eukaryogenesis, which probably involved both bacterial and archaeal progenitors. Puzzlingly, although eukaryotes retain many attributes of their putative archaeal ancestors, their lipid compositions only reflect their bacterial progenitors. Finally, elucidation of archaeal lipids and their metabolic pathways have revealed potentially interesting applications that have opened up new frontiers for biotechnological exploitation of these organisms. This review is concerned with the analysis, structure, function, evolution and biotechnology of archaeal lipids and their associated metabolic pathways.}, } @article {pmid37236002, year = {2023}, author = {Wu, Y and Hu, W and Zheng, X and Liu, Y and Niu, Q and Chen, Y}, title = {Valorization of food waste into short-chain fatty acids via enzymatic pretreatment: Effects of fermentation-pH on acid-producing processes and microbial metabolic functions.}, journal = {Waste management (New York, N.Y.)}, volume = {167}, number = {}, pages = {22-30}, doi = {10.1016/j.wasman.2023.05.016}, pmid = {37236002}, issn = {1879-2456}, mesh = {Fermentation ; *Food ; Sewage/chemistry ; *Refuse Disposal ; Fatty Acids, Volatile/metabolism ; Anaerobiosis ; Hydrogen-Ion Concentration ; }, abstract = {Food waste (FW) has been widely considered as an essential resource for the production of short-chain fatty acids (SCFAs), an important class of chemicals with wide applications and over 20 million tons of annual market demand, by anaerobic fermentation. Although enzymatic pre-treatment could improve the FW biodegradation efficiency, resulting in enhanced efficiency of solubilization and hydrolysis, the influence of fermentation-pH on the SCFAs production and the metabolic functions, have rarely been reported. This study demonstrated that the uncontrolled pH could efficiently lead to an increase in the SCFAs production (33011 mgCOD/L) during long-term fermentation of FW (mainly consisting of 48.8% carbohydrates, 20.6% proteins, and 17.4% lipids) after enzymatic pre-treatment compared to the control (16413 mgCOD/L). Meanwhile, the acid-producing processes (i.e., solubilization, hydrolysis, and acidification) were synchronously enhanced by the enzymatic pre-treatment and no control over fermentation-pH. Metagenomic analysis revealed that the acid-forming microorganisms (i.e., Olsenella sp. and Sporanaerobacter) were significantly accumulated, and the corresponding genetic expressions related to extracellular hydrolysis (i.e., aspB and gltB), membrane transport (i.e., metL and glnH), and intracellular material metabolism (i.e., pfkA and ackA) were evidently stimulated, thereby promoting ultimate SCFAs generation. Although the alkaline conditions could further slightly increase the SCFAs yield slightly (37100 mgCOD/L) and also stimulate the metabolic activities, it might not be suitable for large-scale practical applications due to additional costs associated with alkaline chemical additives.}, } @article {pmid37235682, year = {2023}, author = {Conrey, PE and Denu, L and O'Boyle, KC and Rozich, I and Green, J and Maslanka, J and Lubin, JB and Duranova, T and Haltzman, BL and Gianchetti, L and Oldridge, DA and De Luna, N and Vella, LA and Allman, D and Spergel, JM and Tanes, C and Bittinger, K and Henrickson, SE and Silverman, MA}, title = {IgA deficiency destabilizes homeostasis toward intestinal microbes and increases systemic immune dysregulation.}, journal = {Science immunology}, volume = {8}, number = {83}, pages = {eade2335}, doi = {10.1126/sciimmunol.ade2335}, pmid = {37235682}, issn = {2470-9468}, support = {R21 AI153956/AI/NIAID NIH HHS/United States ; R38 HL143613/HL/NHLBI NIH HHS/United States ; T32 CA009140/CA/NCI NIH HHS/United States ; P30 DK019525/DK/NIDDK NIH HHS/United States ; K08 AI136660/AI/NIAID NIH HHS/United States ; UL1 TR001878/TR/NCATS NIH HHS/United States ; K08 AI135091/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Child ; Mice ; Animals ; *IgA Deficiency ; Immunoglobulin A, Secretory ; Immunoglobulin M ; Homeostasis ; }, abstract = {The ability of most patients with selective immunoglobulin A (IgA) deficiency (SIgAD) to remain apparently healthy has been a persistent clinical conundrum. Compensatory mechanisms, including IgM, have been proposed, yet it remains unclear how secretory IgA and IgM work together in the mucosal system and, on a larger scale, whether the systemic and mucosal anti-commensal responses are redundant or have unique features. To address this gap in knowledge, we developed an integrated host-commensal approach combining microbial flow cytometry and metagenomic sequencing (mFLOW-Seq) to comprehensively define which microbes induce mucosal and systemic antibodies. We coupled this approach with high-dimensional immune profiling to study a cohort of pediatric patients with SIgAD and household control siblings. We found that mucosal and systemic antibody networks cooperate to maintain homeostasis by targeting a common subset of commensal microbes. In IgA-deficiency, we find increased translocation of specific bacterial taxa associated with elevated levels of systemic IgG targeting fecal microbiota. Associated features of immune system dysregulation in IgA-deficient mice and humans included elevated levels of inflammatory cytokines, enhanced follicular CD4 T helper cell frequency and activation, and an altered CD8 T cell activation state. Although SIgAD is clinically defined by the absence of serum IgA, the symptomatology and immune dysregulation were concentrated in the SIgAD participants who were also fecal IgA deficient. These findings reveal that mucosal IgA deficiency leads to aberrant systemic exposures and immune responses to commensal microbes, which increase the likelihood of humoral and cellular immune dysregulation and symptomatic disease in patients with IgA deficiency.}, } @article {pmid37235649, year = {2023}, author = {Jurdzinski, KT and Mehrshad, M and Delgado, LF and Deng, Z and Bertilsson, S and Andersson, AF}, title = {Large-scale phylogenomics of aquatic bacteria reveal molecular mechanisms for adaptation to salinity.}, journal = {Science advances}, volume = {9}, number = {21}, pages = {eadg2059}, pmid = {37235649}, issn = {2375-2548}, mesh = {Phylogeny ; *Salinity ; *Bacteria/genetics ; Ecosystem ; Fresh Water/microbiology ; }, abstract = {The crossing of environmental barriers poses major adaptive challenges. Rareness of freshwater-marine transitions separates the bacterial communities, but how these are related to brackish counterparts remains elusive, as do the molecular adaptations facilitating cross-biome transitions. We conducted large-scale phylogenomic analysis of freshwater, brackish, and marine quality-filtered metagenome-assembled genomes (11,248). Average nucleotide identity analyses showed that bacterial species rarely existed in multiple biomes. In contrast, distinct brackish basins cohosted numerous species, but their intraspecific population structures displayed clear signs of geographic separation. We further identified the most recent cross-biome transitions, which were rare, ancient, and most commonly directed toward the brackish biome. Transitions were accompanied by systematic changes in amino acid composition and isoelectric point distributions of inferred proteomes, which evolved over millions of years, as well as convergent gains or losses of specific gene functions. Therefore, adaptive challenges entailing proteome reorganization and specific changes in gene content constrains the cross-biome transitions, resulting in species-level separation between aquatic biomes.}, } @article {pmid37235235, year = {2023}, author = {Yuan, X and Lv, Z and Zhang, Z and Han, Y and Liu, Z and Zhang, H}, title = {A Review of Antibiotics, Antibiotic Resistant Bacteria, and Resistance Genes in Aquaculture: Occurrence, Contamination, and Transmission.}, journal = {Toxics}, volume = {11}, number = {5}, pages = {}, pmid = {37235235}, issn = {2305-6304}, support = {2021C02048//Key Research & Development project of the Science and Technology Department of Zhejiang Province/ ; LY22C030004//Natural Science Foundation of Zhejiang Province, China/ ; }, abstract = {Antibiotics are commonly used to prevent and control diseases in aquaculture. However, long-term/overuse of antibiotics not only leaves residues but results in the development of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs). Antibiotics, ARB, and ARGs are widespread in aquaculture ecosystems. However, their impacts and interaction mechanisms in biotic and abiotic media remain to be clarified. In this paper, we summarized the detection methods, present status, and transfer mechanisms of antibiotics, ARB, and ARGs in water, sediment, and aquaculture organisms. Currently, the dominant methods of detecting antibiotics, ARB, and ARGs are UPLC-MS/MS, 16S rRNA sequencing, and metagenomics, respectively. Tetracyclines, macrolides, fluoroquinolones, and sulfonamides are most frequently detected in aquaculture. Generally, antibiotic concentrations and ARG abundance in sediment are much higher than those in water. Yet, no obvious patterns in the category of antibiotics or ARB are present in organisms or the environment. The key mechanisms of resistance to antibiotics in bacteria include reducing the cell membrane permeability, enhancing antibiotic efflux, and structural changes in antibiotic target proteins. Moreover, horizontal transfer is a major pathway for ARGs transfer, including conjugation, transformation, transduction, and vesiculation. Identifying, quantifying, and summarizing the interactions and transmission mechanisms of antibiotics, ARGs, and ARB would provide useful information for future disease diagnosis and scientific management in aquaculture.}, } @article {pmid37235042, year = {2023}, author = {Stepanova, N}, title = {The Gut-Peritoneum Axis in Peritoneal Dialysis and Peritoneal Fibrosis.}, journal = {Kidney medicine}, volume = {5}, number = {6}, pages = {100645}, pmid = {37235042}, issn = {2590-0595}, abstract = {Peritoneal fibrosis is an important cause of peritoneal dialysis (PD) discontinuation worldwide and is associated with high morbidity and mortality rate. Although the era of metagenomics has provided new insights into the interactions between the gut microbiota and fibrosis in various organs and tissues, its role in peritoneal fibrosis has rarely been discussed. This review provides a scientific rationale and points out the potential role of gut microbiota in peritoneal fibrosis. In addition, the interaction between the gut, circulatory, and peritoneal microbiota is highlighted, with an emphasis on the relationship to PD outcomes. More research is needed to elucidate the mechanisms underlying the role of gut microbiota in peritoneal fibrosis and potentially unveil new target options for the management of PD technique failure.}, } @article {pmid37234911, year = {2023}, author = {Holm, JB and Carter, KA and Ravel, J and Brotman, RM}, title = {Lactobacillus iners and genital health: molecular clues to an enigmatic vaginal species.}, journal = {Current infectious disease reports}, volume = {25}, number = {4}, pages = {67-75}, pmid = {37234911}, issn = {1523-3847}, support = {K01 AI163413/AI/NIAID NIH HHS/United States ; R01 NR015495/NR/NINR NIH HHS/United States ; R01 AI116799/AI/NIAID NIH HHS/United States ; F32 AI136400/AI/NIAID NIH HHS/United States ; R01 AI119012/AI/NIAID NIH HHS/United States ; }, abstract = {PURPOSE OF REVIEW: Vaginal lactobacilli are recognized as important drivers of genital health including protection against bacterial vaginosis and sexually transmitted infections. Lactobacillus iners is distinct from L. crispatus, L. gasseri, and L. jensenii by its high global prevalence in vaginal microbiomes, relatively small genome, production of only L-lactic acid, and inconsistent associations with genital health outcomes. In this review, we summarize our current understanding of the role of L. iners in the vaginal microbiome, highlight the importance of strain-level consideration for this species, and explain that while marker gene-based characterization of the composition of the vaginal microbiota does not capture strain-level resolution, whole metagenome sequencing can aid in expanding our understanding of this species in genital health.

RECENT FINDINGS: L. iners exists in the vaginal microbiome as a unique combination of strains. The functional repertoires of these strain combinations are likely wide and contribute to the survival of this species in a variety of vaginal microenvironments. In published studies to date, strain-specific effects are aggregated and may yield imprecise estimates of risk associated with this species.

SUMMARY: The worldwide high prevalence of Lactobacillus iners warrants more research into its functional roles in the vaginal microbiome and how it may directly impact susceptibility to infections. By incorporating strain-level resolution into future research endeavors, we may begin to appreciate L. iners more thoroughly and identify novel therapeutic targets for a variety of genital health challenges.}, } @article {pmid37234610, year = {2023}, author = {Kimisto, AK and Muia, AW and Ong'ondo, GO and Ndung'u, KC}, title = {Molecular characterization of microorganisms with industrial potential for methane production in sludge from Kangemi sewage treatment plant, Nyeri county-Kenya.}, journal = {Heliyon}, volume = {9}, number = {5}, pages = {e15715}, pmid = {37234610}, issn = {2405-8440}, abstract = {Microbial consortia under anaerobic conditions are involved in oxidizing organic matter in the sludge to produce methane gas. However, in developing countries like Kenya, these microbes have not been fully identified to target them for the efficient harnessing of biofuel. This study collected wet sludge from two anaerobic digestion lagoons 1 and 2 that were operational during sampling at Kangemi Sewage Treatment Plant, in Nyeri County, Kenya. DNA was extracted from samples using commercially available ZymoBIOMICS™ DNA Miniprep Kit and sequenced using Shotgun metagenomics. Samples were analyzed using MG-RAST software (Project ID: mgp100988), which allowed for identifying microorganisms directly involved in various stages of methanogenesis pathways. The study found hydrogenotrophic methanogens, such as Methanospirillum (32%), Methanobacterium (27%), Methanobrevibacter (27%), and Methanosarcina (32%), being predominant in the lagoon communities, whereas acetoclastic microorganisms such as the Methanoregula (22%) and the acetate oxidazing bacteria such as Clostridia (68%) were the key microbes for that pathway in the sewage digester sludge. Furthermore, Methanothermobacter (18%), Methanosarcina (21%), Methanosaeta (15%), and Methanospirillum (13%) carried out the methylotrophic pathway. In contrast, Methanosarcina (23%),Methanoregula (14%), methanosaeta (13%), and methnanoprevibacter (13%) seemed to play an important role in the final step of methane release. This study concluded that the sludge produced from the Nyeri-Kangemi WWTP harbors microbes with significant potential for biogas production. The study recommends a pilot study to investigate the efficiency of the identified microbes for biogas production.}, } @article {pmid37234538, year = {2023}, author = {Sarrocco, S and Herrera-Estrella, A and Collinge, DB}, title = {Editorial: Plant disease management in the post-genomic era: from functional genomics to genome editing, Volume II.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1203870}, pmid = {37234538}, issn = {1664-302X}, } @article {pmid37234535, year = {2023}, author = {Ghelardi, E and Mazzantini, D and Celandroni, F and Calvigioni, M and Panattoni, A and Lupetti, A and Bois De Fer, B and Perez, M}, title = {Analysis of the microbial content of probiotic products commercialized worldwide and survivability in conditions mimicking the human gut environment.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1127321}, pmid = {37234535}, issn = {1664-302X}, abstract = {INTRODUCTION: Probiotics are living microorganisms that, when administered in adequate amounts, confer a health benefit on the host. Adequate number of living microbes, the presence of specific microorganisms, and their survival in the gastrointestinal (GI) environment are important to achieve desired health benefits of probiotic products. In this in vitro study, 21 leading probiotic formulations commercialized worldwide were evaluated for their microbial content and survivability in simulated GI conditions.

METHODS: Plate-count method was used to determine the amount of living microbes contained in the products. Culture-dependent Matrix-Assisted Laser Desorption/Ionization-Time of Flight Mass Spectrometry and culture-independent metagenomic analysis through 16S and 18S rDNA sequencing were applied in combination for species identification. To estimate the potential survivability of the microorganisms contained in the products in the harsh GI environment, an in vitro model composed of different simulated gastric and intestinal fluids was adopted.

RESULTS: The majority of the tested probiotic products were concordant with the labels in terms of number of viable microbes and contained probiotic species. However, one product included fewer viable microbes than those displayed on the label, one product contained two species that were not declared, and another product lacked one of the labeled probiotic strains. Survivability in simulated acidic and alkaline GI fluids was highly variable depending on the composition of the products. The microorganisms contained in four products survived in both acidic and alkaline environments. For one of these products, microorganisms also appeared to grow in the alkaline environment.

CONCLUSION: This in vitro study demonstrates that most globally commercialized probiotic products are consistent with the claims described on their labels with respect to the number and species of the contained microbes. Evaluated probiotics generally performed well in survivability tests, although viability of microbes in simulated gastric and intestinal environments showed large variability. Although the results obtained in this study indicate a good quality of the tested formulations, it is important to stress that stringent quality controls of probiotic products should always be performed to provide optimal health benefits for the host.}, } @article {pmid37234531, year = {2023}, author = {Zhao, Q and Li, J and Tay, A and Wang, L}, title = {Editorial: Computational predictions, dynamic tracking, and evolutionary analysis of antibiotic resistance through the mining of microbial genomes and metagenomic data, volume II.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1203297}, doi = {10.3389/fmicb.2023.1203297}, pmid = {37234531}, issn = {1664-302X}, } @article {pmid37234526, year = {2023}, author = {Roda-Garcia, JJ and Haro-Moreno, JM and López-Pérez, M}, title = {Evolutionary pathways for deep-sea adaptation in marine planktonic Actinobacteriota.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1159270}, pmid = {37234526}, issn = {1664-302X}, abstract = {The deep ocean, one of the largest ecosystems on earth, is dominated by microorganisms that are keystones in the regulation of biogeochemical cycles. However, the evolutionary pathways underlying the specific adaptations required (e.g., high pressure and low temperature) by this unique niche remain understudied. Here, we analyzed the first representatives belonging to the order Acidimicrobiales, a group of marine planktonic Actinobacteriota, that specifically inhabits the aphotic zone of the oceanic water column (>200 m). Compared with their epipelagic counterparts, deep-sea representatives showed the same evolution in genome architecture with higher GC content, longer intergenic spaces as well as higher nitrogen (N-ARSC) and lower carbon (C-ARSC) content in encoded amino acid residue side chains consistent with the higher nitrogen concentration and lower carbon concentration in deep waters compared to the photic zone. Metagenomic recruitment showed distribution patterns that allowed the description of different ecogenomic units within the three deep water-associated genera defined by our phylogenomic analyses (UBA3125, S20-B6 and UBA9410). The entire genus UBA3125 was found exclusively associated with oxygen minimum zones linked to the acquisition of genes involved in denitrification. Genomospecies of genus S20-B6 recruited in samples from both mesopelagic (200-1,000 m) and bathypelagic (1000-4,000 m) zones, including polar regions. Diversity in the genus UBA9410 was higher, with genomospecies widely distributed in temperate zones, others in polar regions, and the only genomospecies associated with abyssal zones (>4,000 m). At the functional level, groups beyond the epipelagic zone have a more complex transcriptional regulation including in their genomes a unique WhiB paralog. In addition, they showed higher metabolic potential for organic carbon and carbohydrate degradation as well as the ability to accumulate glycogen as a source of carbon and energy. This could compensate for energy metabolism in the absence of rhodopsins, which is only present in genomes associated with the photic zone. The abundance in deep samples of cytochrome P450 monooxygenases associated with the genomes of this order suggests an important role in remineralization of recalcitrant compounds throughout the water column.}, } @article {pmid37234150, year = {2023}, author = {Zhang, Y and Han, S and Xiao, X and Zheng, L and Chen, Y and Zhang, Z and Gao, X and Zhou, S and Yu, K and Huang, L and Fu, J and Hong, Y and Jiang, J and Qian, W and Yang, H and Shen, J}, title = {Integration analysis of tumor metagenome and peripheral immunity data of diffuse large-B cell lymphoma.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1146861}, pmid = {37234150}, issn = {1664-3224}, mesh = {Adult ; Humans ; *Metagenome ; *Lymphoma, Large B-Cell, Diffuse/genetics/drug therapy ; HLA-DR Antigens ; }, abstract = {BACKGROUND/PURPOSE: It has been demonstrated that gut microbes are closely associated with the pathogenesis of lymphoma, but the gut microbe landscape and its association with immune cells in diffuse large B-cell lymphoma (DLBCL) remain largely unknown. In this study, we explored the associations between gut microbiota, clinical features and peripheral blood immune cell subtypes in DLBCL.

METHOD: A total of 87 newly diagnosed DLBCL adults were enrolled in this study. The peripheral blood samples were collected from all patients and then submitted to immune cell subtyping using full-spectral flow cytometry. Metagenomic sequencing was applied to assess the microbiota landscape of 69 of 87 newly diagnosed DLBCL patients. The microbiotas and peripheral blood immune cell subsets with significant differences between different National Comprehensive Center Network-International Prognostic Indexes (NCCN-IPIs) (low-risk, low-intermediate-risk, intermediate-high-risk, high-risk) groups were screened.

RESULTS: A total of 10 bacterial phyla, 31 orders and 455 bacteria species were identified in 69 patients with newly diagnosed DLBCL. The abundances of 6 bacteria, including Blautia sp.CAG 257, Actinomyces sp.S6 Spd3, Streptococcus parasanguinis, Bacteroides salyersiae, Enterococcus faecalls and Streptococcus salivarius were significantly different between the low-risk, low-intermediate-risk, intermediate-high-risk and high-risk groups, among which Streptococcus parasanguinis and Streptococcus salivarius were markedly accumulated in the high-risk group. The different bacteria species were mostly enriched in the Pyridoxal 5'-phosphate biosynthesis I pathway. In addition, we found that 2 of the 6 bacteria showed close associations with the different immune cell subtypes which were also identified from different NCCN-IPIs. In detail, the abundance of Bacteroides salyersiae was negatively correlated with Treg cells, CD38+ nonrescue exhausted T cells, nature killer 3 cells and CD38+CD8+ effector memory T cells, while the abundance of Streptococcus parasanguinis was negatively correlated with HLA-DR+ NK cells, CD4+ Treg cells, HLA-DR+ NKT cells and HLA-DR+CD94+CD159c+ NKT cells.

CONCLUSION: This study first reveals the gut microbiota landscape of patients with newly diagnosed DLBCL and highlights the association between the gut microbiota and immunity, which may provide a new idea for the prognosis assessment and treatment of DLBCL.}, } @article {pmid37234090, year = {2023}, author = {Zhu, X and Yang, P and Xiong, G and Wei, H and Zhang, L and Wang, Z and Ning, K}, title = {Microbial biogeochemical cycling reveals the sustainability of the rice-crayfish co-culture model.}, journal = {iScience}, volume = {26}, number = {5}, pages = {106769}, pmid = {37234090}, issn = {2589-0042}, abstract = {Aquaculture has great potential in nourishing the global growing population, while such staggering yields are coupled with environmental pollution. Rice-crayfish co-culture models (RCFP) have been widely adopted in China due to their eco-friendliness. However, little is known about RCFP's microbiome pattern, which hinders our understanding of its sustainability. This study has conducted metagenomic analysis across aquaculture models and habitats, which revealed aquaculture model-specific biogeochemical cycling pattern (e.g., nitrogen (N), sulfur (S), and carbon (C)): RCFP is advantageous in N-assimilation, N-contamination, and S-pollutants removal, while non-RCFP features N denitrification process and higher S metabolism ability, producing several hazardous pollutants in non-RCFP (e.g., nitric oxide, nitrogen monoxide, and sulfide). Moreover, RCFP has greater capacity for carbohydrate enzyme metabolism compared with non-RCFP in environmental habitats, but not in crayfish gut. Collectively, RCFP plays an indispensable role in balancing aquaculture productivity and environmental protection, which might be applied to the blue transformation of aquaculture.}, } @article {pmid37233731, year = {2023}, author = {D'Agostino, PM}, title = {Highlights of biosynthetic enzymes and natural products from symbiotic cyanobacteria.}, journal = {Natural product reports}, volume = {40}, number = {11}, pages = {1701-1717}, doi = {10.1039/d3np00011g}, pmid = {37233731}, issn = {1460-4752}, mesh = {Animals ; *Biological Products/chemistry ; *Cyanobacteria/genetics/chemistry ; Symbiosis ; Fungi ; *Urochordata ; }, abstract = {Covering: up to 2023Cyanobacteria have long been known for their intriguing repertoire of natural product scaffolds, which are often distinct from other phyla. Cyanobacteria are ecologically significant organisms that form a myriad of different symbioses including with sponges and ascidians in the marine environment or with plants and fungi, in the form of lichens, in terrestrial environments. Whilst there have been several high-profile discoveries of symbiotic cyanobacterial natural products, genomic data is scarce and discovery efforts have remained limited. However, the rise of (meta-)genomic sequencing has improved these efforts, emphasized by a steep increase in publications in recent years. This highlight focuses on selected examples of symbiotic cyanobacterial-derived natural products and their biosyntheses to link chemistry with corresponding biosynthetic logic. Further highlighted are remaining gaps in knowledge for the formation of characteristic structural motifs. It is anticipated that the continued rise of (meta-)genomic next-generation sequencing of symbiontic cyanobacterial systems will lead to many exciting discoveries in the future.}, } @article {pmid37233257, year = {2023}, author = {Ahmad, N and Ritz, M and Calchera, A and Otte, J and Schmitt, I and Brueck, T and Mehlmer, N}, title = {Biosynthetic Potential of Hypogymnia Holobionts: Insights into Secondary Metabolite Pathways.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {5}, pages = {}, pmid = {37233257}, issn = {2309-608X}, support = {031B0824A//Federal Ministry of Education and Research/ ; }, abstract = {Lichens are symbiotic associations consisting of a photobiont (algae or cyanobacteria) and a mycobiont (fungus). They are known to produce a variety of unique secondary metabolites. To access this biosynthetic potential for biotechnological applications, deeper insights into the biosynthetic pathways and corresponding gene clusters are necessary. Here we provide a comprehensive view of the biosynthetic gene clusters of all organisms comprising a lichen thallus: fungi, green algae, and bacteria. We present two high-quality PacBio metagenomes, in which we identified a total of 460 biosynthetic gene clusters. Lichen mycobionts yielded 73-114 clusters, other lichen associated ascomycetes 8-40, green algae of the genus Trebouxia 14-19, and lichen-associated bacteria 101-105 clusters. The mycobionts contained mainly T1PKSs, followed by NRPSs, and terpenes; Trebouxia reads harbored mainly clusters linked to terpenes, followed by NRPSs and T3PKSs. Other lichen-associated ascomycetes and bacteria contained a mix of diverse biosynthetic gene clusters. In this study, we identified for the first time the biosynthetic gene clusters of entire lichen holobionts. The yet untapped biosynthetic potential of two species of the genus Hypogymnia is made accessible for further research.}, } @article {pmid37231976, year = {2023}, author = {Gao, H and Jiang, F and Zhang, J and Chi, X and Song, P and Li, B and Cai, Z and Zhang, T}, title = {Effects of ex situ conservation on diversity and function of the gut microbiota of the Tibetan wild ass (Equus kiang).}, journal = {Integrative zoology}, volume = {18}, number = {6}, pages = {1089-1104}, doi = {10.1111/1749-4877.12726}, pmid = {37231976}, issn = {1749-4877}, support = {XDA23060602//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; XDA2002030302//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; 2021-ZJ-951Q//Qinghai Province Science and Technology Plan/ ; 2019QZKK0501//Second Tibetan Plateau Scientific Expedition and Research Program/ ; 2019-SF-150//Qinghai Key R&D and Transformation Program/ ; LHZX-2020-01//Joint Grant from Chinese Academy of Sciences-People's Government of Qinghai Province on Sanjiangyuan National Park/ ; //Science and Technology Department of Qinghai Province Major Project "Sanjiangyaun National Park Animal Genome Program"/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Tibet ; Bacteria/genetics ; Animals, Wild/microbiology ; Equidae/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Ex situ conservation is the main method for the protection of endangered wildlife. To explore the effect of ex situ conservation on the gut microbiota of the kiang (Equus kiang), metagenomic sequencing combined with bioinformatics analysis was used to investigate the composition and function of the gut microbiota of the kiang. The results showed that ex situ conservation not only protected wildlife, but also affected the composition and function of gut microbiota, as well as the health of animals. In the zoo, the ratio of the relative abundance of Firmicutes to that of Bacteroidetes (F/B) is higher, clusters of potentially pathogenic bacteria (such as Catonella, Catonella, and Mycoplasma) are more numerous, the abundance of resistance genes is higher, and the abundance of metabolic functions is increased. The dynamic changes of the gut microbiota also played an important role in the nutritional absorption, energy metabolism, and environmental adaptation of the kiang. Improving the rearing environment and increasing food diversity play important roles for increasing the diversity of gut microbiota, reducing the spread of potentially pathogenic bacteria, and reducing diseases. In the wild, especially in winter and in food-deficient areas, food supplementation can enhance the gut microbial homeostasis of wild animals and reduce the impact of crises. In depth studies of the gut microbial function of wildlife have important implications for improving ex situ conservation.}, } @article {pmid37231829, year = {2023}, author = {Kawasaki, Y and Kakimoto, K and Tanaka, Y and Shimizu, H and Nishida, K and Numa, K and Kinoshita, N and Tatsumi, Y and Nakazawa, K and Koshiba, R and Hirata, Y and Ota, K and Sakiyama, N and Terazawa, T and Takeuchi, T and Miyazaki, T and Goto, M and Yokota, H and Makizaki, Y and Tanaka, Y and Nakajima, S and Ohno, H and Higuchi, K and Nakamura, S and Nishikawa, H}, title = {Relationship between Chemotherapy-Induced Diarrhea and Intestinal Microbiome Composition.}, journal = {Digestion}, volume = {104}, number = {5}, pages = {357-369}, pmid = {37231829}, issn = {1421-9867}, mesh = {Humans ; *Gastrointestinal Microbiome ; Dysbiosis/chemically induced ; Diarrhea/drug therapy ; Bacteria ; *Antineoplastic Agents/therapeutic use ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND AND AIM: Fluoropyrimidines (FPs) are key drugs in many chemotherapy regimens; however, recipients are often prone to diarrhea due to gastrointestinal toxicity. Disruption of the intestinal epithelial barrier function by FPs leads to dysbiosis, which may exacerbate intestinal epithelial cell damage as a secondary effect and trigger diarrhea. However, despite studies on chemotherapy-induced changes in the intestinal microbiome of humans, the relationship between dysbiosis and diarrhea is unclear. In this study, we aimed to investigate the relationship between chemotherapy-induced diarrhea and the intestinal microbiome.

METHODS: We conducted a single-center prospective observational study. Twenty-three patients who received chemotherapy, including FPs as first-line chemotherapy for colorectal cancer, were included. Stool samples were collected before the start of chemotherapy and after one cycle of treatment to analyze intestinal microbiome composition and perform PICRUSt predictive metagenomic analysis.

RESULTS: Gastrointestinal toxicity was observed in 7 of 23 patients (30.4%), diarrhea was observed in 4 (17.4%), and nausea and anorexia were observed in 3 (13.0%). In 19 patients treated with oral FPs, the α diversity of the microbial community decreased significantly following chemotherapy only in the diarrheal group. At the phylum level, the diarrheal group showed a significant decrease in the abundance of Firmicutes and a significant increase in the abundance of Bacteroidetes with chemotherapy (p = 0.013 and 0.011, respectively). In the same groups, at the genus level, Bifidobacterium abundance was significantly decreased (p = 0.019). In contrast, in the non-diarrheal group, Actinobacteria abundance increased significantly with chemotherapy at the phylum level (p = 0.011). Further, Bifidobacterium, Fusicatenibacter, and Dorea abundance significantly increased at the genus level (p = 0.006, 0.019, and 0.011, respectively). The PICRUSt predictive metagenomic analysis revealed that chemotherapy caused significant differences in membrane transport in KEGG pathway level 2 and in 8 KEGG pathway level 3, including transporters and oxidative phosphorylation in the diarrhea group.

CONCLUSION: Organic-acid-producing bacteria seem to be involved in diarrhea associated with chemotherapy, including FPs.}, } @article {pmid37231629, year = {2023}, author = {Li, S and Liao, Y and Jiang, Z and Ji, G}, title = {Life strategies and metabolic interactions of core microbes during thiosulphate-based denitrification.}, journal = {Environmental microbiology}, volume = {25}, number = {10}, pages = {1925-1939}, doi = {10.1111/1462-2920.16430}, pmid = {37231629}, issn = {1462-2920}, mesh = {*Nitrates/metabolism ; *Thiosulfates ; Denitrification ; Sulfur ; Vitamins ; Amino Acids ; Water ; Bioreactors ; Nitrogen/metabolism ; }, abstract = {Sulphur-driven denitrification is a low-cost process for the treatment of nitrate-contaminated water. However, a comprehensive understanding of core populations and microbial interactions of a sulphur-based denitrifying system is lacking. This study presents results from three replicated denitrifying systems amended with thiosulphate and operated under a low C/N ratio. Amplicon sequencing revealed gradual enrichments of a few abundant denitrifiers. Based on genome-centred metagenomics and metatranscriptomics, a core set of microbes was identified in the systems, with Pseudomonas 1 and Thauera 2 being the most abundant ones. Although the replicates showed different enrichments, generalized observations were summarized. Most core populations conserved energy from denitrification coupled with sulphur. Pseudomonas 1 and Thauera 2 were able to finish complete denitrification. Surprisingly, they were also able to synthesize almost all amino acids and vitamins. In contrast, less abundant members, including Pseudomonas 2, were relatively auxotrophic and required an exogenous supply of amino acids and vitamins. The high expression of enzymes involved in biosynthesis and transport systems indicated their syntrophic relationships. The genomic findings suggested life strategies and interactions of the core thiosulphate-based denitrifying microbiome, with implications for nitrate-polluted water remediation.}, } @article {pmid37231259, year = {2023}, author = {Pinto, Y and Chakraborty, M and Jain, N and Bhatt, AS}, title = {Phage-inclusive profiling of human gut microbiomes with Phanta.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {37231259}, issn = {1546-1696}, support = {R01AI14862302//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AI14375702//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1S10OD02014101//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 5T32HG000044-25//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; n/a//EIF | Stand Up To Cancer (SU2C)/ ; n/a//Alfred P. Sloan Foundation/ ; Dean's Fellowship//SU | School of Medicine, Stanford University (Stanford School of Medicine, Stanford University)/ ; NDSEG fellowship//U.S. Department of Defense (United States Department of Defense)/ ; }, abstract = {Due to technical limitations, most gut microbiome studies have focused on prokaryotes, overlooking viruses. Phanta, a virome-inclusive gut microbiome profiling tool, overcomes the limitations of assembly-based viral profiling methods by using customized k-mer-based classification tools and incorporating recently published catalogs of gut viral genomes. Phanta's optimizations consider the small genome size of viruses, sequence homology with prokaryotes and interactions with other gut microbes. Extensive testing of Phanta on simulated data demonstrates that it quickly and accurately quantifies prokaryotes and viruses. When applied to 245 fecal metagenomes from healthy adults, Phanta identifies ~200 viral species per sample, ~5× more than standard assembly-based methods. We observe a ~2:1 ratio between DNA viruses and bacteria, with higher interindividual variability of the gut virome compared to the gut bacteriome. In another cohort, we observe that Phanta performs equally well on bulk versus virus-enriched metagenomes, making it possible to study prokaryotes and viruses in a single experiment, with a single analysis.}, } @article {pmid37231159, year = {2023}, author = {Irazoqui, JM and Eberhardt, MF and Santiago, GM and Amadio, AF}, title = {Characterization of novel proteases identified by metagenomic analysis from dairy stabilization ponds.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {13}, pages = {4291-4300}, pmid = {37231159}, issn = {1432-0614}, support = {PICT 2017-0191//Fondo para la Investigación Científica y Tecnológica/ ; IO 2017-00172//Agencia santafecina de ciencia tecnologia e innovacion/ ; PD I106//Instituto Nacional de Tecnología Agropecuaria/ ; PD I114//Instituto Nacional de Tecnología Agropecuaria/ ; PD I116//Instituto Nacional de Tecnología Agropecuaria/ ; PD I150//Instituto Nacional de Tecnología Agropecuaria/ ; }, mesh = {Humans ; Whey Proteins/metabolism ; *Peptide Hydrolases/metabolism ; Protein Hydrolysates/analysis ; Ponds ; Whey/metabolism ; Endopeptidases/genetics/metabolism ; *Cheese ; }, abstract = {Cheese whey is the main by-product of dairy industries. It is used as a raw material for other value-added products, like whey protein concentrate. By using enzymes, this product can be further treated to obtain new higher value products, like whey protein hydrolysates. Proteases (EC: 3.4) represent a large segment of industrial enzymes, since they are used in several industries, including food. In this work, we describe three novel enzymes identified using a metagenomic approach. Metagenomic DNA from dairy industry stabilization ponds were sequenced, and the predicted genes were compared against the MEROPS database, focusing on families commercially used to produce whey protein hydrolysates. From a total of 849 candidates, 10 were selected for cloning and expression and three showed activities with both the chromogenic substrate, azocasein, and whey proteins. Particularly, Pr05, an enzyme from the yet uncultured phylum Patescibacteria, showed activity that is comparable to a commercial protease. All these novel enzymes could represent an alternative for dairy industries to produce value-added products from industrial by-products. KEY POINTS: • Over 19,000 proteases were predicted in a sequence-based metagenomic analysis. • Three proteases were successfully expressed and showed activity with whey proteins. • The enzyme Pr05 showed hydrolysis profiles of interest for food industry.}, } @article {pmid37230981, year = {2023}, author = {Feehily, C and O'Neill, IJ and Walsh, CJ and Moore, RL and Killeen, SL and Geraghty, AA and Lawton, EM and Byrne, D and Sanchez-Gallardo, R and Nori, SRC and Nielsen, IB and Wortmann, E and Matthews, E and O'Flaherty, R and Rudd, PM and Groeger, D and Shanahan, F and Saldova, R and McAuliffe, FM and Van Sinderen, D and Cotter, PD}, title = {Detailed mapping of Bifidobacterium strain transmission from mother to infant via a dual culture-based and metagenomic approach.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {3015}, pmid = {37230981}, issn = {2041-1723}, mesh = {Humans ; Infant ; Female ; Pregnancy ; *Bifidobacterium ; Mothers ; *Gastrointestinal Microbiome/genetics ; Metagenome/genetics ; Parturition ; Feces/microbiology ; }, abstract = {A significant proportion of the infant gut microbiome is considered to be acquired from the mother during and after birth. Thus begins a lifelong and dynamic relationship with microbes that has an enduring impact on host health. Based on a cohort of 135 mother-infant (F = 72, M = 63) dyads (MicrobeMom: ISRCTN53023014), we investigated the phenomenon of microbial strain transfer, with a particular emphasis on the use of a combined metagenomic-culture-based approach to determine the frequency of strain transfer involving members of the genus Bifidobacterium, including species/strains present at low relative abundance. From the isolation and genome sequencing of over 449 bifidobacterial strains, we validate and augment metagenomics-based evidence to reveal strain transfer in almost 50% of dyads. Factors important in strain transfer include vaginal birth, spontaneous rupture of amniotic membranes, and avoidance of intrapartum antibiotics. Importantly, we reveal that several transfer events are uniquely detected employing either cultivation or metagenomic sequencing, highlighting the requirement for a dual approach to obtain an in-depth insight into this transfer process.}, } @article {pmid37230923, year = {2023}, author = {Marchand, S and Rodriguez, C and Woerther, PL}, title = {[High-throughput sequencing for infectious disease diagnoses: Example of shotgun metagenomics in central nervous system infections].}, journal = {La Revue de medecine interne}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.revmed.2023.05.002}, pmid = {37230923}, issn = {1768-3122}, abstract = {The advent of high-throughput sequencing in clinical microbiology is opening the way to new diagnostic and prognostic approaches in infectious diseases. Detection, identification and characterisation of pathogenic microorganisms are essential steps in diagnosis and implementation of appropriate antimicrobial therapy. However, standard methods of microbiological diagnosis are failing in some cases. In addition, the emergence of new infections, facilitated by international travel and global warming, requires the implementation of innovative diagnostic methods. Among the different strategies used in clinical microbiology and reviewed in this article, shotgun metagenomics is the only technique that allows today a panpathogenic and unbiased detection of all microorganisms potentially responsible for an infectious disease, including those still unknown. The aims of this article are to present the different possible strategies of high-throughput sequencing used in the microbiological diagnosis of infectious diseases and to highlight the diagnostic contribution of shotgun metagenomics in the field of central nervous system infections.}, } @article {pmid37230382, year = {2023}, author = {Ruan, H and Wang, Y and Zhang, J and Huang, Y and Yang, Y and Wu, C and Guo, M and Luo, J and Yang, M}, title = {Zearalenone-14-glucoside specifically promotes dysplasia of Gut-Associated Lymphoid Tissue: A natural product for constructing intestinal nodular lymphatic hyperplasia model.}, journal = {Journal of advanced research}, volume = {52}, number = {}, pages = {135-150}, pmid = {37230382}, issn = {2090-1224}, mesh = {Rats ; Animals ; *Zearalenone/metabolism/toxicity ; *Biological Products ; Hyperplasia ; Proteomics ; }, abstract = {INTRODUCTION: Zearalenone-14-glucoside (Z14G) is a modified mycotoxin that widely contaminates food across the world. Our preliminary experiment showed that Z14G degrades to zearalenone (ZEN) in the intestine exerting toxicity. Notably, oral administration of Z14G in rats induces intestinal nodular lymphatic hyperplasia.

OBJECTIVES: To investigate the mechanism of Z14G intestinal toxicity and how it differs from ZEN toxicity. We conducted a precise toxicology study on the intestine of rats exposed to Z14G and ZEN using multi-omics technology.

METHODS: Rats were exposed to ZEN (5 mg/kg), Z14G-L (5 mg/kg), Z14G-H (10 mg/kg), and pseudo germ free (PGF)-Z14G-H (10 mg/kg) for 14 days. Histopathological studies were performed on intestines from each group and compared. Metagenomic, metabolomic, and proteomic analyses were performed on rat feces, serum, and intestines, respectively.

RESULTS: Histopathological studies showed that Z14G exposure resulted in dysplasia of gut-associated lymphoid tissue (GALT) compared to ZEN exposure. The elimination of gut microbes in the PGF-Z14G-H group alleviated or eliminated Z14G-induced intestinal toxicity and GALT dysplasia. Metagenomic analysis revealed that Z14G exposure significantly promoted the proliferation of Bifidobacterium and Bacteroides compared to ZEN. Metabolomic analysis showed that Z14G exposure significantly reduced bile acid, while proteomic analysis found that Z14G exposure significantly reduced the expression of C-type lectins compared to ZEN.

CONCLUSIONS: Our experimental results and previous research suggest that Z14G is hydrolyzed to ZEN by Bifidobacterium and Bacteroides promoting their co-trophic proliferation. This leads to inactivation of lectins by hyperproliferative Bacteroides when ZEN caused intestinal involvement, resulting in abnormal lymphocyte homing and ultimately GALT dysplasia. It is noteworthy that Z14G is a promising model drug to establish rat models of intestinal nodular lymphatic hyperplasia (INLH), which is of great significance for studying the pathogenesis, drug screening and clinical application of INLH.}, } @article {pmid37229851, year = {2023}, author = {Guo, H and Jia, W and Chen, Z and Cai, Y and Wang, Y and Zhao, S and Zhao, W}, title = {Analysis on methane production from various coal slime fermentations based on metagenomics.}, journal = {Journal of environmental management}, volume = {343}, number = {}, pages = {118058}, doi = {10.1016/j.jenvman.2023.118058}, pmid = {37229851}, issn = {1095-8630}, mesh = {Fermentation ; *Coal ; *Metagenomics ; Carbon Dioxide ; Methane ; Anaerobiosis ; Acetates ; Bioreactors ; }, abstract = {Metagenomic sequencing technology was applied to evaluate differences in the anaerobic fermentation process of coal slimes by analyzing microbial diversity, functional activity structure, and cooperative relationship during the anaerobic fermentation of coal slimes with different coal ranks. The obtained results showed that the production of biomethane from coal slime was decreased by increasing metamorphism degree. Internal reason was higher abundance of microbial community in low rank coal slimes compared to that in high rank coal which had higher activity in the gene expression of key steps such as hydrolysis and acidification, methanation and the production of hydrogen and acetic acid. Acetic acid decarboxylation and CO2 reduction are two key pathways of methanation process. At the same time, K11261 (formylmethanofuran dehydrogenase subunit) and K01499 (methenyltetrahydromethanopterin cyclohydrolase) genes were further enriched in low rank slime systems, which enhanced the proportion of CO2 reduction in methanation pathway and was beneficial to biomethane production. Research revealed the roles of different coal slime ranks in biomethane production process and is considered as an important reference significance for further exploration of coal slime resource utilization.}, } @article {pmid37228720, year = {2023}, author = {Du, R and Feng, Y and Wang, Y and Huang, J and Tao, Y and Mao, H}, title = {Metagenomic next-generation sequencing confirms the diagnosis of Legionella pneumonia with rhabdomyolysis and acute kidney injury in a limited resource area: a case report and review.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1145733}, pmid = {37228720}, issn = {2296-2565}, mesh = {Male ; Humans ; Middle Aged ; *Legionnaires' Disease/complications/diagnosis/microbiology ; *Acute Kidney Injury/diagnosis/etiology ; *Legionella/genetics ; *Rhabdomyolysis/diagnosis/complications ; *Pneumonia ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Legionella pneumonia, rhabdomyolysis, and acute kidney injury are called the Legionella triad, which is rare and associated with a poor outcome and even death. Early diagnosis and timely treatment are essential for these patients.

CASE PRESENTATION: A 63-year-old man with cough, fever, and fatigue was initially misdiagnosed with common bacterial infection and given beta-lactam monotherapy but failed to respond to it. Conventional methods, including the first Legionella antibody test, sputum smear, and culture of sputum, blood, and bronchoalveolar lavage fluid (BALF) were negative. He was ultimately diagnosed with a severe infection of Legionella pneumophila by metagenomics next-generation sequencing (mNGS). This patient, who had multisystem involvement and manifested with the rare triad of Legionella pneumonia, rhabdomyolysis, and acute kidney injury, finally improved after combined treatment with moxifloxacin, continuous renal replacement therapy, and liver protection therapy.

CONCLUSION: Our results showed the necessity of early diagnosis of pathogens in severe patients, especially in Legionnaires' disease, who manifested with the triad of Legionella pneumonia, rhabdomyolysis, and acute kidney injury. mNGS may be a useful tool for Legionnaires' disease in limited resource areas where urine antigen tests are not available.}, } @article {pmid37228418, year = {2023}, author = {Babalola, OO and Akanmu, AO and Fadiji, AE}, title = {Dataset of shotgun metagenomic evaluation of lettuce (Lactuta sativa L.) rhizosphere microbiome.}, journal = {Data in brief}, volume = {48}, number = {}, pages = {109214}, pmid = {37228418}, issn = {2352-3409}, abstract = {Lettuce (Lactuca sativa L.) is an important vegetable grown and consumed across the world, including South Africa and its rhizosphere constitutes a dynamic community of root associated microbes. Dataset of the microbial community profile of the lettuce rhizospheric soils obtained from Talton, Gauteng Province of South Africa was subjected to metagenomic evaluation using the shotgun approach. The whole DNA isolated from the community was sequenced using NovaSeq 6000 system (Illumina). The raw data obtained consists of 129,063,513.33 sequences with an average length of 200 base pairs and 60.6% Guanine + Cytosine content. The metagenome data has been deposited to the National Centre for Biotechnology Information SRA under the bioproject number PRJNA763048. The downstream analysis alongside taxonomical annotation carried out using an online server MG-RAST, showed the community analysis as being made up of archaea (0.95%), eukaryotes (1.36%), viruses (0.04%), while 97.65% of the sequences were classified as bacteria. A sum of 25 bacteria, 20 eukaryotic and 4 archaea phyla were identified. The predominant genera were Acinetobacter (4.85%), Pseudomonas (3.41%), Streptomyces (2.79%), Candidatus solibacter (1.93%), Burkholderia (1.65%), Bradyrhizobium (1.51%) and Mycobacterium (1.31%). Annotation using Cluster of Orthologous Group (COG) showed 23.91% of the sequenced data were for metabolic function, 33.08% for chemical process and signaling while 6.42% were poorly characterized. Furthermore, the subsystem annotation method showed that sequences were majorly associated with carbohydrates (12.86%), clustering-based subsystems (12.68%), and genes coding for amino acids and derivatives (10.04%), all of which could serve in growth promotion and plant management.}, } @article {pmid37228377, year = {2023}, author = {Yang, C and Zhang, H and Zhao, X and Liu, P and Wang, L and Wang, W}, title = {A functional metagenomics study of soil carbon and nitrogen degradation networks and limiting factors on the Tibetan plateau.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1170806}, pmid = {37228377}, issn = {1664-302X}, abstract = {INTRODUCTION: The Three-River Source Nature Reserve is located in the core area of the Qinghai-Tibetan Plateau, with the alpine swamp, meadow and steppe as the main ecosystem types. However, the microbial communities in these alpine ecosystems, and their carbon and nitrogen degrading metabolic networks and limiting factors remain unclear.

METHODS: We sequenced the diversity of bacteria and fungi in alpine swamps, meadows, steppes, and their degraded and artificially restored ecosystems and analyzed soil environmental conditions.

RESULTS: The results indicated that moisture content had a greater influence on soil microbial community structure compared to degradation and restoration. Proteobacteria dominated in high moisture alpine swamps and alpine meadows, while Actinobacteria dominated in low moisture alpine steppes and artificial grasslands. A metabolic network analysis of carbon and nitrogen degradation and transformation using metagenomic sequencing revealed that plateau microorganisms lacked comprehensive and efficient enzyme systems to degrade organic carbon, nitrogen, and other biological macromolecules, so that the short-term degradation of alpine vegetation had no effect on the basic composition of soil microbial community. Correlation analysis found that nitrogen fixation was strong in meadows with high moisture content, and their key nitrogen-fixing enzymes were significantly related to Sphingomonas. Denitrification metabolism was enhanced in water-deficient habitats, and the key enzyme, nitrous oxide reductase, was significantly related to Phycicoccus and accelerated the loss of nitrogen. Furthermore, Bacillus contained a large number of amylases (GH13 and GH15) and proteases (S8, S11, S26, and M24) which may promote the efficient degradation of organic carbon and nitrogen in artificially restored grasslands.

DISCUSSION: This study illustrated the irrecoverability of meadow degradation and offered fundamental information for altering microbial communities to restore alpine ecosystems.}, } @article {pmid37228371, year = {2023}, author = {Galisteo, C and de la Haba, RR and Sánchez-Porro, C and Ventosa, A}, title = {A step into the rare biosphere: genomic features of the new genus Terrihalobacillus and the new species Aquibacillus salsiterrae from hypersaline soils.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1192059}, pmid = {37228371}, issn = {1664-302X}, abstract = {Hypersaline soils are a source of prokaryotic diversity that has been overlooked until very recently. The phylum Bacillota, which includes the genus Aquibacillus, is one of the 26 phyla that inhabit the heavy metal contaminated soils of the Odiel Saltmarshers Natural Area (Southwest Spain), according to previous research. In this study, we isolated a total of 32 strains closely related to the genus Aquibacillus by the traditional dilution-plating technique. Phylogenetic studies clustered them into two groups, and comparative genomic analyses revealed that one of them represents a new species within the genus Aquibacillus, whereas the other cluster constitutes a novel genus of the family Bacillaceae. We propose the designations Aquibacillus salsiterrae sp. nov. and Terrihalobacillus insolitus gen. nov., sp. nov., respectively, for these two new taxa. Genome mining analysis revealed dissimilitude in the metabolic traits of the isolates and their closest related genera, remarkably the distinctive presence of the well-conserved pathway for the biosynthesis of molybdenum cofactor in the species of the genera Aquibacillus and Terrihalobacillus, along with genes that encode molybdoenzymes and molybdate transporters, scarcely found in metagenomic dataset from this area. In-silico studies of the osmoregulatory strategy revealed a salt-out mechanism in the new species, which harbor the genes for biosynthesis and transport of the compatible solutes ectoine and glycine betaine. Comparative genomics showed genes related to heavy metal resistance, which seem required due to the contamination in the sampling area. The low values in the genome recruitment analysis indicate that the new species of the two genera, Terrihalobacillus and Aquibacillus, belong to the rare biosphere of representative hypersaline environments.}, } @article {pmid37228370, year = {2023}, author = {Thijssen, M and Tacke, F and Van Espen, L and Cassiman, D and Naser Aldine, M and Nevens, F and Van Ranst, M and Matthijnssens, J and Pourkarim, MR}, title = {Plasma virome dynamics in chronic hepatitis B virus infected patients.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1172574}, pmid = {37228370}, issn = {1664-302X}, abstract = {The virome remains an understudied domain of the human microbiome. The role of commensal viruses on the outcome of infections with known pathogens is not well characterized. In this study we aimed to characterize the longitudinal plasma virome dynamics in chronic hepatitis B virus (HBV) infected patients. Eighty-five longitudinal plasma samples were collected from 12 chronic HBV infected individuals that were classified in the four stages of HBV infection. The virome was characterized with an optimized viral extraction protocol and deep-sequenced on a NextSeq 2500 platform. The plasma virome was primarily composed of members of the Anello- Flavi-, and Hepadnaviridae (HBV) families. The virome structure and dynamics did not correlate with the different stages of chronic HBV infection nor with the administration of antiviral therapy. We observed a higher intrapersonal similarity of viral contigs. Genomic analysis of viruses observed in multiple timepoint demonstrated the presence of a dynamic community. This study comprehensively assessed the blood virome structure in chronic HBV infected individuals and provided insights in the longitudinal development of this viral community.}, } @article {pmid37228368, year = {2023}, author = {Wang, L and Lv, WQ and Yang, JT and Lin, X and Liu, HM and Tan, HJ and Quan, RP and Long, PP and Shen, H and Shen, J and Deng, HW and Xiao, HM}, title = {Enteric nervous system damage caused by abnormal intestinal butyrate metabolism may lead to functional constipation.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1117905}, pmid = {37228368}, issn = {1664-302X}, abstract = {Functional constipation (FC) is a high morbidity gastrointestinal disease for which dysfunction in the enteric nervous system is a major pathogenesis mechanism. To enhance our understanding of the involvement of intestinal microbiota and its metabolites in the pathogenesis of FC, we conducted a shotgun metagenomic sequencing analysis of gut microbiota and serum short-chain fatty acids (SCFAs) analysis in 460 Chinese women with different defecation frequencies. We observed that the abundance ofFusobacterium_varium, a butyric acid-producing bacterium, was positively correlated (P = 0.0096) with the frequency of defecation; however, the concentrations of serum butyric acid was negatively correlated (P = 3.51E-05) with defecation frequency. These results were verified in an independent cohort (6 patients with FC and 6 controls). To further study the effects of butyric acid on intestinal nerve cells, we treated mouse intestinal neurons in vitro with various concentrations of butyrate (0.1, 0.5, 1, and 2.5 mM). We found that intestinal neurons treated with 0.5 mM butyrate proliferated better than those in the other treatment groups, with significant differences in cell cycle and oxidative phosphorylation signal pathways. We suggest that the decreased butyrate production resulting from the reduced abundance of Fusobacterium in gut microbiota affects the proliferation of intestinal neurons and the energy supply of intestinal cells. However, with FC disease advancing, the consumption and excretion of butyric acid reduce, leading to its accumulation in the intestine. Moreover, the accumulation of an excessively high amount of butyric acid inhibits the proliferation of nerve cells and subsequently exacerbates the disease.}, } @article {pmid37228141, year = {2023}, author = {Young, BD and Rosales, SM and Enochs, IC and Kolodziej, G and Formel, N and Moura, A and D'Alonso, GL and Traylor-Knowles, N}, title = {Different disease inoculations cause common responses of the host immune system and prokaryotic component of the microbiome in Acropora palmata.}, journal = {PloS one}, volume = {18}, number = {5}, pages = {e0286293}, pmid = {37228141}, issn = {1932-6203}, mesh = {Animals ; Viverridae/genetics ; *Anthozoa/genetics/microbiology ; *Microbiota/genetics ; Gene Expression Profiling ; Serratia marcescens/genetics ; Coral Reefs ; }, abstract = {Reef-building corals contain a complex consortium of organisms, a holobiont, which responds dynamically to disease, making pathogen identification difficult. While coral transcriptomics and microbiome communities have previously been characterized, similarities and differences in their responses to different pathogenic sources has not yet been assessed. In this study, we inoculated four genets of the Caribbean branching coral Acropora palmata with a known coral pathogen (Serratia marcescens) and white band disease. We then characterized the coral's transcriptomic and prokaryotic microbiomes' (prokaryiome) responses to the disease inoculations, as well as how these responses were affected by a short-term heat stress prior to disease inoculation. We found strong commonality in both the transcriptomic and prokaryiomes responses, regardless of disease inoculation. Differences, however, were observed between inoculated corals that either remained healthy or developed active disease signs. Transcriptomic co-expression analysis identified that corals inoculated with disease increased gene expression of immune, wound healing, and fatty acid metabolic processes. Co-abundance analysis of the prokaryiome identified sets of both healthy-and-disease-state bacteria, while co-expression analysis of the prokaryiomes' inferred metagenomic function revealed infected corals' prokaryiomes shifted from free-living to biofilm states, as well as increasing metabolic processes. The short-term heat stress did not increase disease susceptibility for any of the four genets with any of the disease inoculations, and there was only a weak effect captured in the coral hosts' transcriptomic and prokaryiomes response. Genet identity, however, was a major driver of the transcriptomic variance, primarily due to differences in baseline immune gene expression. Despite genotypic differences in baseline gene expression, we have identified a common response for components of the coral holobiont to different disease inoculations. This work has identified genes and prokaryiome members that can be focused on for future coral disease work, specifically, putative disease diagnostic tools.}, } @article {pmid37227602, year = {2023}, author = {Roldán, DM and Menes, RJ}, title = {Characterisation of 'Candidatus Methylobacter titanis' sp. nov., a putative novel species of Methylobacter clade 2 and their distribution in sediments of freshwater lakes in maritime Antarctica.}, journal = {Antonie van Leeuwenhoek}, volume = {116}, number = {7}, pages = {721-738}, pmid = {37227602}, issn = {1572-9699}, support = {Proyecto de Iniciación a la Investigación 2021 -C216-347//CSIC (Comisión Sectorial de Investigación Científica)/ ; }, mesh = {*Lakes/microbiology ; Antarctic Regions ; RNA, Ribosomal, 16S/genetics ; Methane ; Oxidation-Reduction ; DNA ; Phylogeny ; *Methylococcaceae/genetics ; }, abstract = {Global warming has a strong impact on the polar regions, in particular, the Antarctic Peninsula and nearby islands. Methane (CH4) is a major factor in climate change and mitigation of CH4 emissions can be accomplished through microbial oxidation by methanotrophic bacteria. Understanding this biological process is crucial given the shortage of research carried out in this geographical area. The aim of this study was to characterise psychrophilic enrichment cultures of aerobic methanotrophs obtained from lake sediments of the Fildes Peninsula (King George Island, South Shetland Islands) and revealing the distribution of the genus Methylobacter in different lake sediments of the peninsula. Four stable methanotrophic enrichment cultures were obtained and analysed by metagenome-assembled genomes (MAGs). The phylogeny of methanotroph MAGs recovered from these enrichment cultures based on the 16S rRNA gene showed that K-2018 MAG008 and D1-2020 MAG004[Ts] clustered within the Methylobacter clade 2, with high similarity to Methylobacter tundripaludum SV96[T] (97.88 and 98.56% respectively). However, the average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values with M. tundripaludum were < 95% (84.8 and 85.0%, respectively) and < 70% (30.2 and 30.3%, respectively), suggesting that they represent a putative novel species for which the name 'Ca. Methylobacter titanis' is proposed. This is the first species of clade 2 of the genus Methylobacter obtained from Antarctica. The bacterial diversity assessed by 16S rRNA gene sequencing of 21 samples of different lakes (water column and sediments) revealed 54 ASVs associated with methanotrophs and the genus Methylobacter as the most abundant. These results suggest that aerobic methanotrophs belonging to the Methylobacter clade 2 would be the main responsible for CH4 oxidation in these sediments.}, } @article {pmid37227475, year = {2023}, author = {Bou Orm, E and Sauvagère, S and Rocher, J and Benezet, JC and Bayle, S and Siatka, C and Bergeret, A and Malhautier, L}, title = {Estimating the bias related to DNA recovery from hemp stems for retting microbial community investigation.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {14}, pages = {4665-4681}, pmid = {37227475}, issn = {1432-0614}, mesh = {*Cannabis/genetics/metabolism ; DNA/metabolism ; Bacteria/genetics ; *Microbiota ; Soil ; }, abstract = {The industrial hemp plant Cannabis sativa is a source of vegetable fiber for both textiles and biocomposite applications. After harvesting, the plant stems are laid out on the ground and colonized by microorganisms (bacteria and fungi) naturally present in the soil and on the stems. By producing hydrolytic enzymes that degrade the plant wall polymers, the natural cement that binds the fiber bundles together is removed, thus facilitating their dissociation (retting process) which is required for producing high-performant fibers. To investigate temporal dynamics of retting microbial communities (density levels, diversity, and structure), a reliable protocol for extracting genomic DNA from stems is mandatory. However, very little attention has been paid to the methodological aspects of nucleic acid extraction, although they are crucial for the significance of the final result. Three protocols were selected and tested: a commercial kit (FastDNA™ Spin Kit for soil), the Gns-GII procedure, and a custom procedure from the Genosol platform. A comparative analysis was carried out on soil and two different varieties of hemp stem. The efficiency of each method was measured by evaluating both the quantity and quality of the extracted DNA and the abundance and taxonomy of bacterial and fungal populations. The Genosol protocol provides interesting yields in terms of quantity and quality of genomic DNA compared to the other two protocols. However, no major difference was observed in microbial diversity between the two extraction procedures (FastDNA™ SPIN Kit and Genosol protocol). Based on these results, the FastDNA™ SPIN kit or the Genosol procedure seems to be suitable for studying bacterial and fungal communities of the retting process. It should be noted that this work has demonstrated the importance of evaluating biases associated with DNA recovery from hemp stems. KEY POINTS: • Metagenomic DNA was successfully extracted from hemp stem samples using three different protocols. • Further evaluation was performed in terms of DNA yield and purity, abundance level, and microbial community structure. • This work exhibited the crucial importance of DNA recovery bias evaluation.}, } @article {pmid37227439, year = {2023}, author = {Guo, Y and Yang, Z and Mo, C and Li, H and Li, P}, title = {First Report of Banana mild mosaic virus Infecting Banana in China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-03-23-0410-PDN}, pmid = {37227439}, issn = {0191-2917}, abstract = {Banana (Musa spp.) is an important fruit in tropical and subtropical regions and an essential food crop in some developing countries. China has a long history of banana cultivation and ranks second in global banana production, with a planting area exceeding 11 million hectares (FAOSTAT, 2023). Banana mild mosaic virus (BanMMV) is a flexuous filamentous virus infecting bananas and a banmivirus in the Betaflexiviridae family. Its infection often results in symptomless plants of Musa spp., and the virus has a worldwide distribution, which can explain its high prevalence (Kumar et al., 2015). BanMMV infection often causes transitory symptoms, such as mild chlorotic streaks and mosaics, on young leaves (Thomas, 2015). The mixed infection of BanMMV with other banana-infecting viruses such as banana streak viruses (BSV) and cucumber mosaic virus (CMV), can exacerbate the mosaic symptoms of BanMMV (Fidan et al., 2019). In October 2021, we collected twenty-six leaf samples of suspected viral disease of bananas from four cities (Huizhou, Qingyuan, Zhanjiang, and Yangjiang) in Guangdong province, two cities (Hekou and Jinghong) in Yunnan province, two cities (Yulin and Wuming) in Guangxi Zhuang autonomous region. After fully mixing these infected samples, we divided them into two pools and sent them to Shanghai Biotechnology Corporation (China) for metatranscriptome sequencing. Each sample contained about 5 g of leaves in total. Zymo-Seq RiboFree Total RNA Library Prep Kit (Zymo Research, USA) was used for ribosomal RNA depletion and library preparations. Illumina sequencing (Illumina NovaSeq 6000) was carried out by Shanghai Biotechnology Corporation (China). Paired-end (150 bp) sequencing of the RNA library was performed on an Illumina HiSeq 2000/2500 platform. Clean reads were assembled by a metagenomic de novo assembly using the CLC Genomics Workbench (version: 6.0.4). Then the non-redundant protein database in the National Center for Biotechnology Information (NCBI) was used for BLASTx annotation. A total of 79,528 contigs were generated from the clean reads (68,878,162) through de novo assembly. A contig of 7265 nucleotides (nts) showed the highest nucleotide sequence identity (90.08%) to the genome of BanMMV isolate EM4-2 (GenBank accession no. OL826745.1). We designed specific primers according to the BanMMV CP gene (Table S1), tested the twenty-six leaf samples collected from the above-mentioned eight cities, and found that only one sample of Fenjiao (Musa ABB Pisang Awak) in Guangzhou city was infected with this virus. The symptoms of banana leaves containing BanMMV were slight chlorosis and yellowing of leaf edges (Fig. S1). We failed to detect other banana viruses, such as BSV, CMV, and banana bunchy top virus (BBTV) in the BanMMV-infected banana leaves. RNA from the infected leaves was extracted, and the assembled contig was confirmed by overlapping PCR amplification across the whole sequence (Table S1). All ambiguous regions were amplified by PCR and RACE, and the products were subjected to Sanger sequencing. The complete genome of the virus candidate was 7310 nts in length, excluding the poly (A) tail. The sequence was deposited in GenBank under accession number ON227268 (isolate BanMMV-GZ from Guangzhou). A schematic representation of the genome organization of BanMMV-GZ is shown in Fig. S2. Its genome has five open reading frames (ORF) encoding RNA-dependent RNA polymerase (RdRp), three triple gene block proteins necessary for cell-to-cell movement (TGBp1 to TGBp3) and a coat protein (CP), similar to other BanMMV isolates (Kondo et al., 2021). Phylogenetic analyses of the complete nt sequence of the full genome and RdRp gene using the neighbor-joining (NJ) method also clearly placed the BanMMV-GZ firmly within all isolates of BanMMV (Fig. S3). To our knowledge, this is the first report of BanMMV infecting bananas in China, extending the geographical range of this viral disease around the world. Accordingly, larger-scale BanMMV investigations must be conducted to determine the distribution and prevalence of BanMMV in China.}, } @article {pmid37227290, year = {2023}, author = {Wang, Y and Xu, H and Wei, M and Wang, Y and Wang, W and Ju, J and Liu, Y and Wang, X}, title = {Identification of Putative Bacterial Pathogens for Orofacial Granulomatosis Based on 16S rRNA Metagenomic Analysis.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0226622}, pmid = {37227290}, issn = {2165-0497}, mesh = {Animals ; Mice ; *Granulomatosis, Orofacial/drug therapy/etiology/pathology ; RNA, Ribosomal, 16S/genetics ; *Crohn Disease ; Chronic Disease ; Bacteria/genetics ; }, abstract = {Orofacial granulomatosis (OFG) is a chronic inflammatory disease characterized by nontender swelling of the orofacial tissues, the underlying cause of which remains unknown. Our previous study demonstrated that tooth apical periodontitis (AP) is involved in the development of OFG. To characterize the AP bacterial signatures of OFG patients and identify possible pathogenic bacteria that cause OFG, the compositions of the AP microbiotas in OFG patients and controls were compared using 16S rRNA gene sequencing. Pure cultures of putative bacterial pathogens were established by growing bacteria as colonies followed by purification, identification, and enrichment and then were injected into animal models to determine the causative bacteria contributing to OFG. A specific AP microbiota signature in the OFG patients was shown, characterized by the predominance of phyla Firmicutes and Proteobacteria, notably members of the genera Streptococcus, Lactobacillus, and Neisseria, were found. Streptococcus spp., Lactobacillus casei, Neisseria subflava, Veillonella parvula, and Actinomyces spp. from OFG patients were isolated and successfully cultured in vitro and then injected into mice. Ultimately, footpad injection with N. subflava elicited granulomatous inflammation. IMPORTANCE Infectious agents have long been considered to play a role in the initiation of OFG; however, a direct causal relationship between microbes and OFG has not yet been established. In this study, a unique AP microbiota signature was identified in OFG patients. Moreover, we successfully isolated candidate bacteria from AP lesions of OFG patients and assessed their pathogenicity in laboratory mice. Findings from this study may help provide in-depth insights into the role of microbes in OFG development, providing the basis for targeted therapeutic approaches for OFG.}, } @article {pmid37226493, year = {2023}, author = {Knowles, S and Dennis, M and McElwain, A and Leis, E and Richard, J}, title = {Pathology and infectious agents of unionid mussels: A primer for pathologists in disease surveillance and investigation of mortality events.}, journal = {Veterinary pathology}, volume = {60}, number = {5}, pages = {510-528}, doi = {10.1177/03009858231171666}, pmid = {37226493}, issn = {1544-2217}, mesh = {Animals ; Humans ; Pathologists ; *Bivalvia/parasitology/physiology ; *Unionidae ; Fresh Water ; Ecosystem ; }, abstract = {Freshwater mussels are one of the most imperiled groups of organisms in the world, and more than 30 species have gone extinct in the last century. While habitat alteration and destruction have contributed to the declines, the role of disease in mortality events is unclear. In an effort to involve veterinary pathologists in disease surveillance and the investigation of freshwater mussel mortality events, we provide information on the conservation status of unionids, sample collection and processing techniques, and unique and confounding anatomical and physiological differences. We review the published accounts of pathology and infectious agents described in freshwater mussels including neoplasms, viruses, bacteria, fungi, fungal-like agents, ciliated protists, Aspidogastrea, Digenea, Nematoda, Acari, Diptera, and Odonata. Of the identified infectious agents, a single viral disease, Hyriopsis cumingii plague disease, that occurs only in cultured mussels is known to cause high mortality. Parasites including ciliates, trematodes, nematodes, mites, and insects may decrease host fitness, but are not known to cause mortality. Many of the published reports identify infectious agents at the light or ultrastructural microscopy level with no lesion or molecular characterization. Although metagenomic analyses provide sequence information for infectious agents, studies often fail to link the agents to tissue changes at the light or ultrastructural level or confirm their role in disease. Pathologists can bridge this gap between identification of infectious agents and confirmation of disease, participate in disease surveillance to ensure successful propagation programs necessary to restore decimated populations, and investigate mussel mortality events to document pathology and identify causality.}, } @article {pmid37226095, year = {2023}, author = {Li, R and Duan, W and Ran, Z and Chen, X and Yu, H and Fang, L and Guo, L and Zhou, J}, title = {Diversity and correlation analysis of endophytes and metabolites of Panax quinquefolius L. in various tissues.}, journal = {BMC plant biology}, volume = {23}, number = {1}, pages = {275}, pmid = {37226095}, issn = {1471-2229}, support = {81891014//Natural Science Foundation of China/ ; 2020GXRC060//Higher Educational Science and Technology Program of Jinan City under Grant/ ; 2060302//Construction project for sustainable utilization of valuable traditional Chinese medicine resources/ ; XKY2014//Science and Technology Project of University of Jinan/ ; 2021M701404//fellowship of China Postdoctoral Science Fundation/ ; }, mesh = {Chromatography, Liquid ; *Endophytes ; *Tandem Mass Spectrometry ; Amino Acids ; Citric Acid Cycle ; }, abstract = {BACKGROUND: Panax quinquefolius L. (American ginseng) is widely used in medicine due to its wealth of diverse pharmacological effects. Endophytes colonize within P. quinquefolius in multiple tissue types. However, the relationship between endophytes and the production of their active ingredients in different parts of the plant is not clear.

RESULTS: In this study, the relationship of endophytic diversity and the metabolites produced in different plant tissues of P. quinquefolius were analyzed using metagenomic and metabolomic approaches. The results showed relatively similar endophyte composition in roots and fibrils, but obvious differences between endophyte populations in stems and leaves. Species abundance analysis showed that at the phylum level, the dominant bacterial phylum was Cyanobacteria for roots, fibrils, stems and leaves, Ascomycota forroots and fibrils roots, and Basidiomycota for stems and leaves. LC-MS/MS technology was used to quantitatively analyze the metabolites in different tissues of P. quinquefolius. A total of 398 metabolites and 294 differential metaboliteswere identified, mainly organic acids, sugars, amino acids, polyphenols, and saponins. Most of the differential metabolites were enriched in metabolic pathways such as phenylpropane biosynthesis, flavonoid biosynthesis, citric acid cycle, and amino acid biosynthesis. Correlation analysis showed a positive and negative correlation between the endophytes and the differential metabolites. Conexibacter significantly enriched in root and fibril was significantly positively correlated with saponin differential metabolites, while cyberlindnera significantly enriched in stem and leaf was significantly negatively correlated with differential metabolites (p < 0.05).

CONCLUSION: The endophytic communities diversity were relatively similar in the roots and fibrils of P. quinquefolius, while there were greater differences between the stems and leaves. There was significant difference in metabolite content between different tissues of P. quinquefolius. Correlation analysis methods demonstrated a correlation between endophytes and differential metabolism.}, } @article {pmid37225687, year = {2023}, author = {Zhao, F and Yang, L and Zhang, T and Zhuang, D and Wu, Q and Yu, J and Tian, C and Zhang, Z}, title = {Gut microbiome signatures of extreme environment adaption in Tibetan pig.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {27}, pmid = {37225687}, issn = {2055-5008}, mesh = {Swine ; Animals ; *Gastrointestinal Microbiome ; Tibet ; Ultraviolet Rays ; Acclimatization ; Acetic Acid ; Extreme Environments ; Mammals ; }, abstract = {Tibetan pigs (TPs) can adapt to the extreme environments in the Tibetan plateau implicated by their self-genome signals, but little is known about roles of the gut microbiota in the host adaption. Here, we reconstructed 8210 metagenome-assembled genomes from TPs (n = 65) living in high-altitude and low-altitude captive pigs (87 from China-CPs and 200 from Europe-EPs) that were clustered into 1050 species-level genome bins (SGBs) at the threshold of 95% average nucleotide identity. 73.47% of SGBs represented new species. The gut microbial community structure analysis based on 1,048 SGBs showed that TPs was significantly different from low-altitude captive pigs. TP-associated SGBs enabled to digest multiple complex polysaccharides, including cellulose, hemicellulose, chitin and pectin. Especially, we found TPs showed the most common enrichment of phyla Fibrobacterota and Elusimicrobia, which were involved in the productions of short- and medium-chain fatty acids (acetic acid, butanoate and propanoate; octanomic, decanoic and dodecanoic acids), as well as in the biosynthesis of lactate, 20 essential amino acids, multiple B vitamins (B1, B2, B3, B5, B7 and B9) and cofactors. Unexpectedly, Fibrobacterota solely showed powerful metabolic capacity, including the synthesis of acetic acid, alanine, histidine, arginine, tryptophan, serine, threonine, valine, B2, B5, B9, heme and tetrahydrofolate. These metabolites might contribute to host adaptation to high-altitude, such as energy harvesting and resistance against hypoxia and ultraviolet radiation. This study provides insights into understanding the role of gut microbiome played in mammalian high-altitude adaptation and discovers some potential microbes as probiotics for improving animal health.}, } @article {pmid37225100, year = {2023}, author = {Shuai, W and Itzhari, D and Ronen, Z and Hartmann, EM}, title = {Mitigation of antimicrobial resistance genes in greywater treated at household level.}, journal = {The Science of the total environment}, volume = {890}, number = {}, pages = {164136}, doi = {10.1016/j.scitotenv.2023.164136}, pmid = {37225100}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Metagenome ; Water ; Genes, Bacterial ; }, abstract = {Greywater often contains microorganisms carrying antimicrobial resistance genes (ARGs). Reuse of greywater thus potentially facilitates the enrichment and spread of multidrug resistance, posing a possible hazard for communities that use it. As water reuse becomes increasingly necessary, it is imperative to determine how greywater treatment impacts ARGs. In this study, we characterize ARG patterns in greywater microbial communities before and after treatment by a recirculating vertical flow constructed wetland (RVFCW). This greywater recycling method has been adopted by some small communities and households for greywater treatment; however, its ability to remove ARGs is unknown. We examined the taxonomic and ARG compositions of microbial communities in raw and treated greywater from five households using shotgun metagenomic sequencing. Total ARGs decreased in abundance and diversity in greywater treated by the RVFCW. In parallel, the microbial communities decreased in similarity in treated greywater. Potentially pathogenic bacteria associated with antimicrobial resistance and mobile genetic elements were detected in both raw and treated water, with a decreasing trend after treatment. This study indicates that RVFCW systems have the potential to mitigate antimicrobial resistance-related hazards when reusing treated greywater, but further measures need to be taken regarding persistent mobile ARGs and potential pathogens.}, } @article {pmid37224782, year = {2023}, author = {Xu, M and Su, S and Jiang, S and Li, W and Zhang, Z and Zhang, J and Hu, X}, title = {Short-term arecoline exposure affected the systemic health state of mice, in which gut microbes played an important role.}, journal = {Ecotoxicology and environmental safety}, volume = {259}, number = {}, pages = {115055}, doi = {10.1016/j.ecoenv.2023.115055}, pmid = {37224782}, issn = {1090-2414}, mesh = {Animals ; Mice ; *Arecoline/pharmacology/toxicity ; Interleukin-6/metabolism ; *Gastrointestinal Microbiome ; Lipid Metabolism ; Liver ; }, abstract = {Arecoline is a critical bioactive component in areca nuts with toxicity and pharmacological activities. However, its effects on body health remain unclear. Here, we investigated the effects of arecoline on physiologic and biochemical parameters in mouse serum, liver, brain, and intestine. The effect of arecoline on gut microbiota was investigated based on shotgun metagenomic sequencing. The results showed that arecoline promoted lipid metabolism in mice, manifested as significantly reduced serum TC and TG and liver TC levels and a reduction in abdominal fat accumulation. Arecoline intake significantly modulated the neurotransmitters 5-HT and NE levels in the brain. Notably, arecoline intervention significantly increased serum IL-6 and LPS levels, leading to inflammation in the body. High-dose arecoline significantly reduced liver GSH levels and increased MDA levels, which led to oxidative stress in the liver. Arecoline intake promoted the release of intestinal IL-6 and IL-1β, causing intestinal injury. In addition, we observed a significant response of gut microbiota to arecoline intake, reflecting significant changes in diversity and function of the gut microbes. Further mechanistic exploration suggested that arecoline intake can regulate gut microbes and ultimately affect the host's health. This study provided technical help for the pharmacochemical application and toxicity control of arecoline.}, } @article {pmid37224315, year = {2021}, author = {Claro, IM and Ramundo, MS and Coletti, TM and da Silva, CAM and Valenca, IN and Candido, DS and Sales, FCS and Manuli, ER and de Jesus, JG and de Paula, A and Felix, AC and Andrade, PDS and Pinho, MC and Souza, WM and Amorim, MR and Proenca-Modena, JL and Kallas, EG and Levi, JE and Faria, NR and Sabino, EC and Loman, NJ and Quick, J}, title = {Rapid viral metagenomics using SMART-9N amplification and nanopore sequencing.}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {241}, pmid = {37224315}, issn = {2398-502X}, support = {/WT_/Wellcome Trust/United Kingdom ; INV-034540/GATES/Bill & Melinda Gates Foundation/United States ; INV-034652/GATES/Bill & Melinda Gates Foundation/United States ; R24 AI120942/AI/NIAID NIH HHS/United States ; }, abstract = {Emerging and re-emerging viruses are a global health concern. Genome sequencing as an approach for monitoring circulating viruses is currently hampered by complex and expensive methods. Untargeted, metagenomic nanopore sequencing can provide genomic information to identify pathogens, prepare for or even prevent outbreaks. SMART (Switching Mechanism at the 5' end of RNA Template) is a popular approach for RNA-Seq but most current methods rely on oligo-dT priming to target polyadenylated mRNA molecules. We have developed two random primed SMART-Seq approaches, a sequencing agnostic approach 'SMART-9N' and a version compatible rapid adapters available from Oxford Nanopore Technologies 'Rapid SMART-9N'. The methods were developed using viral isolates, clinical samples, and compared to a gold-standard amplicon-based method. From a Zika virus isolate the SMART-9N approach recovered 10kb of the 10.8kb RNA genome in a single nanopore read. We also obtained full genome coverage at a high depth coverage using the Rapid SMART-9N, which takes only 10 minutes and costs up to 45% less than other methods. We found the limits of detection of these methods to be 6 focus forming units (FFU)/mL with 99.02% and 87.58% genome coverage for SMART-9N and Rapid SMART-9N respectively. Yellow fever virus plasma samples and SARS-CoV-2 nasopharyngeal samples previously confirmed by RT-qPCR with a broad range of Ct-values were selected for validation. Both methods produced greater genome coverage when compared to the multiplex PCR approach and we obtained the longest single read of this study (18.5 kb) with a SARS-CoV-2 clinical sample, 60% of the virus genome using the Rapid SMART-9N method. This work demonstrates that SMART-9N and Rapid SMART-9N are sensitive, low input, and long-read compatible alternatives for RNA virus detection and genome sequencing and Rapid SMART-9N improves the cost, time, and complexity of laboratory work.}, } @article {pmid37223792, year = {2023}, author = {Bertola, M and Righetti, L and Gazza, L and Ferrarini, A and Fornasier, F and Cirlini, M and Lolli, V and Galaverna, G and Visioli, G}, title = {Perenniality, more than genotypes, shapes biological and chemical rhizosphere composition of perennial wheat lines.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1172857}, pmid = {37223792}, issn = {1664-462X}, abstract = {Perennial grains provide various ecosystem services compared to the annual counterparts thanks to their extensive root system and permanent soil cover. However, little is known about the evolution and diversification of perennial grains rhizosphere and its ecological functions over time. In this study, a suite of -OMICSs - metagenomics, enzymomics, metabolomics and lipidomics - was used to compare the rhizosphere environment of four perennial wheat lines at the first and fourth year of growth in comparison with an annual durum wheat cultivar and the parental species Thinopyrum intermedium. We hypothesized that wheat perenniality has a greater role in shaping the rhizobiome composition, biomass, diversity, and activity than plant genotypes because perenniality affects the quality and quantity of C input - mainly root exudates - hence modulating the plant-microbes crosstalk. In support of this hypothesis, the continuous supply of sugars in the rhizosphere along the years created a favorable environment for microbial growth which is reflected in a higher microbial biomass and enzymatic activity. Moreover, modification in the rhizosphere metabolome and lipidome over the years led to changes in the microbial community composition favoring the coexistence of more diverse microbial taxa, increasing plant tolerance to biotic and abiotic stresses. Despite the dominance of the perenniality effect, our data underlined that the OK72 line rhizobiome distinguished from the others by the increase in abundance of Pseudomonas spp., most of which are known as potential beneficial microorganisms, identifying this line as a suitable candidate for the study and selection of new perennial wheat lines.}, } @article {pmid37222807, year = {2023}, author = {Broman, E and Abdelgadir, M and Bonaglia, S and Forsberg, SC and Wikström, J and Gunnarsson, JS and Nascimento, FJA and Sjöling, S}, title = {Long-Term Pollution Does Not Inhibit Denitrification and DNRA by Adapted Benthic Microbial Communities.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2357-2372}, pmid = {37222807}, issn = {1432-184X}, support = {3150-3.1.1-2017//Östersjöstiftelsen/ ; 2020-0002//Naturvårdsverket/ ; 1.1-1602-0106//Statens geotekniska institut/ ; }, mesh = {Nitrates ; *Ammonium Compounds ; Denitrification ; Nitrogen ; *Microbiota ; Oxidation-Reduction ; }, abstract = {Denitrification in sediments is a key microbial process that removes excess fixed nitrogen, while dissimilatory nitrate reduction to ammonium (DNRA) converts nitrate to ammonium. Although microorganisms are responsible for essential nitrogen (N) cycling, it is not yet fully understood how these microbially mediated processes respond to toxic hydrophobic organic compounds (HOCs) and metals. In this study, we sampled long-term polluted sediment from the outer harbor of Oskarshamn (Baltic Sea), measured denitrification and DNRA rates, and analyzed taxonomic structure and N-cycling genes of microbial communities using metagenomics. Results showed that denitrification and DNRA rates were within the range of a national reference site and other unpolluted sites in the Baltic Sea, indicating that long-term pollution did not significantly affect these processes. Furthermore, our results indicate an adaptation to metal pollution by the N-cycling microbial community. These findings suggest that denitrification and DNRA rates are affected more by eutrophication and organic enrichment than by historic pollution of metals and organic contaminants.}, } @article {pmid37222803, year = {2023}, author = {Malesevic, M and Stanisavljevic, N and Matijasevic, D and Curcic, J and Tasic, V and Tasic, S and Kojic, M}, title = {Metagenomic Analysis of Bacterial Community and Isolation of Representative Strains from Vranjska Banja Hot Spring, Serbia.}, journal = {Microbial ecology}, volume = {86}, number = {4}, pages = {2344-2356}, pmid = {37222803}, issn = {1432-184X}, support = {451-03-47/2023-01/200042//Ministarstvo Prosvete, Nauke i Tehnološkog Razvoja/ ; }, mesh = {*Hot Springs/microbiology ; Serbia ; Phylogeny ; Bacteria ; Metagenome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The hot spring Vranjska Banja is the hottest spring on the Balkan Peninsula with a water temperature of 63-95 °C and a pH value of 7.1, in situ. According to the physicochemical analysis, Vranjska Banja hot spring belongs to the bicarbonated and sulfated hyperthermal waters. The structures of microbial community of this geothermal spring are still largely unexplored. In order to determine and monitor the diversity of microbiota of the Vranjska Banja hot spring, a comprehensive culture-independent metagenomic analysis was conducted in parallel with a culture-dependent approach for the first time. Microbial profiling using amplicon sequencing analysis revealed the presence of phylogenetically novel taxa, ranging from species to phyla. Cultivation-based methods resulted in the isolation of 17 strains belonging to the genera Anoxybacillus, Bacillus, Geobacillus, and Hydrogenophillus. Whole-genome sequencing of five representative strains was then performed. The genomic characterization and OrthoANI analysis revealed that the Vranjska Banja hot spring harbors phylogenetically novel species of the genus Anoxybacillus, proving its uniqueness. Moreover, these isolates contain stress response genes that enable them to survive in the harsh conditions of the hot springs. The results of the in silico analysis show that most of the sequenced strains have the potential to produce thermostable enzymes (proteases, lipases, amylases, phytase, chitinase, and glucanase) and various antimicrobial molecules that can be of great importance for industrial, agricultural, and biotechnological applications. Finally, this study provides a basis for further research and understanding of the metabolic potential of these microorganisms.}, } @article {pmid37222623, year = {2023}, author = {Ariyadasa, S and Taylor, W and Weaver, L and McGill, E and Billington, C and Pattis, I}, title = {Nonbacterial Microflora in Wastewater Treatment Plants: an Underappreciated Potential Source of Pathogens.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0048123}, pmid = {37222623}, issn = {2165-0497}, mesh = {Humans ; *Wastewater ; Bacteria/genetics ; Archaea/genetics ; High-Throughput Nucleotide Sequencing ; *Water Purification ; Water ; }, abstract = {Wastewater treatment plants (WWTPs) receive and treat large volumes of domestic, industrial, and urban wastewater containing pathogenic and nonpathogenic microorganisms, chemical compounds, heavy metals, and other potentially hazardous substances. WWTPs play an essential role in preserving human, animal, and environmental health by removing many of these toxic and infectious agents, particularly biological hazards. Wastewater contains complex consortiums of bacterial, viral, archaeal, and eukaryotic species, and while bacteria in WWTP have been extensively studied, the temporal and spatial distribution of nonbacterial microflora (viruses, archaea, and eukaryotes) is less understood. In this study, we analyzed the viral, archaeal, and eukaryotic microflora in wastewater throughout a treatment plant (raw influent, effluent, oxidation pond water, and oxidation pond sediment) in Aotearoa (New Zealand) using Illumina shotgun metagenomic sequencing. Our results suggest a similar trend across many taxa, with an increase in relative abundance in oxidation pond samples compared to influent and effluent samples, except for archaea, which had the opposite trend. Additionally, some microbial families, such as Podoviridae bacteriophages and Apicomplexa alveolates, appeared largely unaffected by the treatment process, with their relative abundance remaining stable throughout. Several groups encompassing pathogenic species, such as Leishmania, Plasmodium, Toxoplasma, Apicomplexa, Cryptococcus, Botrytis, and Ustilago, were identified. If present, these potentially pathogenic species could be a threat to human and animal health and agricultural productivity; therefore, further investigation is warranted. These nonbacterial pathogens should be considered when assessing the potential for vector transmission, distribution of biosolids to land, and discharge of treated wastewater to waterways or land. IMPORTANCE Nonbacterial microflora in wastewater remain understudied compared to their bacterial counterparts despite their importance in the wastewater treatment process. In this study, we report the temporal and spatial distributions of DNA viruses, archaea, protozoa, and fungi in raw wastewater influent, effluent, oxidation pond water, and oxidation pond sediments by using shotgun metagenomic sequencing. Our study indicated the presence of groups of nonbacterial taxa which encompass pathogenic species that may have potential to cause disease in humans, animals, and agricultural crops. We also observed higher alpha diversity in viruses, archaea, and fungi in effluent samples than in influent samples. This suggests that the resident microflora in the wastewater treatment plant may be making a greater contribution to the diversity of taxa observed in wastewater effluent than previously thought. This study provides important insights to better understand the potential human, animal, and environmental health impacts of discharged treated wastewater.}, } @article {pmid37222601, year = {2023}, author = {Bösch, Y and Pold, G and Saghaï, A and Karlsson, M and Jones, CM and Hallin, S}, title = {Distribution and Environmental Drivers of Fungal Denitrifiers in Global Soils.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0006123}, pmid = {37222601}, issn = {2165-0497}, mesh = {*Soil/chemistry ; Denitrification ; Ecosystem ; *Greenhouse Gases ; Bacteria/genetics ; Archaea/genetics ; Soil Microbiology ; }, abstract = {The microbial process of denitrification is the primary source of the greenhouse gas nitrous oxide (N2O) from terrestrial ecosystems. Fungal denitrifiers, unlike many bacteria, lack the N2O reductase, and thereby are sources of N2O. Still, their diversity, global distribution, and environmental determinants, as well as their relative importance, compared to bacterial and archaeal denitrifiers, remain unresolved. Employing a phylogenetically informed approach to analyze 1,980 global soil and rhizosphere metagenomes for the denitrification marker gene nirK, which codes for the copper dependent nitrite reductase in denitrification, we show that fungal denitrifiers are sparse, yet cosmopolitan and that they are dominated by saprotrophs and pathogens. Few showed biome-specific distribution patterns, although members of the Fusarium oxysporum species complex, which are known to produce substantial amounts of N2O, were proportionally more abundant and diverse in the rhizosphere than in other biomes. Fungal denitrifiers were most frequently detected in croplands, but they were most abundant in forest soils when normalized to metagenome size. Nevertheless, the overwhelming dominance of bacterial and archaeal denitrifiers suggests a much lower fungal contribution to N2O emissions than was previously estimated. In relative terms, they could play a role in soils that are characterized by a high carbon to nitrogen ratio and a low pH, especially in the tundra as well as in boreal and temperate coniferous forests. Because global warming predicts the proliferation of fungal pathogens, the prevalence of potential plant pathogens among fungal denitrifiers and the cosmopolitan distribution of these organisms suggest that fungal denitrifier abundance may increase in terrestrial ecosystems. IMPORTANCE Fungal denitrifiers, in contrast to their bacterial counterparts, are a poorly studied functional group within the nitrogen cycle, even though they produce the greenhouse gas N2O. To curb soil N2O emissions, a better understanding of their ecology and distribution in soils from different ecosystems is needed. Here, we probed a massive amount of DNA sequences and corresponding soil data from a large number of samples that represented the major soil environments for a broad understanding of fungal denitrifier diversity at the global scale. We show that fungal denitrifiers are predominantly cosmopolitan saprotrophs and opportunistic pathogens. Fungal denitrifiers constituted, on average, 1% of the total denitrifier community. This suggests that earlier estimations of fungal denitrifier abundance, and, thereby, it is also likely that the contributions of fungal denitrifiers to N2O emissions have been overestimated. Nevertheless, with many fungal denitrifiers being plant pathogens, they could become increasingly relevant, as soilborne pathogenic fungi are predicted to increase with ongoing climate change.}, } @article {pmid37222548, year = {2023}, author = {González-Orozco, BD and García-Cano, I and Escobar-Zepeda, A and Jiménez-Flores, R and Álvarez, VB}, title = {Metagenomic analysis and antibacterial activity of kefir microorganisms.}, journal = {Journal of food science}, volume = {88}, number = {7}, pages = {2933-2949}, doi = {10.1111/1750-3841.16614}, pmid = {37222548}, issn = {1750-3841}, support = {P30 CA016058/CA/NCI NIH HHS/United States ; P30 CA016058/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Animals ; *Kefir/microbiology ; Caco-2 Cells ; *Probiotics ; Milk/microbiology ; Anti-Bacterial Agents/pharmacology ; *Cultured Milk Products/microbiology ; }, abstract = {The microbiota composition of kefir grain and milk kefir was assessed via a metagenomic approach. Significant microorganisms were isolated and identified using molecular methods. A safety assessment was conducted based on antibiotic susceptibility and blood hemolysis. Probiotic traits such as resistance to gastric tract conditions, surface characteristics, adhesion to intestinal cells, and antibacterial activity were also assessed. Metagenomic analysis revealed that kefir grains are a more stable community with clear dominant species as compared to milk kefir. Lactobacillus kefiranofaciens BDGO-A1, Lactobacillus helveticus BDGO-AK2, and Lactobacillu kefiri strains showed tolerance to acidic pH and the presence of bile salts, adhesion capability to Caco-2 cells, in vitro antibacterial activity, and the production of antibacterial proteins. In the metagenomic analysis, contigs associated with these species showed the presence of genes involved in exporting polyketide antibiotics and bacteriocin production. To fully exploit the potential probiotic properties of these microorganisms to help human health, further investigation is necessary to elucidate the mechanisms behind the biological activity and the genotypic characteristics of the isolated strains.}, } @article {pmid37222519, year = {2023}, author = {Haro-Moreno, JM and López-Pérez, M and Alekseev, A and Podoliak, E and Kovalev, K and Gordeliy, V and Stepanauskas, R and Rodriguez-Valera, F}, title = {Flotillin-associated rhodopsin (FArhodopsin), a widespread paralog of proteorhodopsin in aquatic bacteria with streamlined genomes.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0000823}, pmid = {37222519}, issn = {2379-5077}, support = {"FLEX3GEN" PID2020-118052GB-I00//Spanish Ministerio de Economía, Industria y Competitividad/ ; 2021/PER/00020//Spanish Ministerio de Universidades and the European Union -- Next Generation EU/ ; 510023//Simons Foundation/ ; 827839//Simons Foundation/ ; EXC 2067/1-390729940//German Research Foundation to Dr. Tobias Moser via the Multiscale Bioimaging - Cluster of Excellence/ ; }, mesh = {*Rhodopsin/chemistry ; *Rhodopsins, Microbial/genetics ; Bacteria/metabolism ; }, abstract = {Microbial rhodopsins are found more than once in a single genome (paralogs) often have different functions. We screened a large dataset of open ocean single-amplified genomes (SAGs) for co-occurrences of multiple rhodopsin genes. Many such cases were found among Pelagibacterales (SAR11), HIMB59, and the Gammaproteobacteria Pseudothioglobus SAGs. These genomes always had a bona fide proteorhodopsin and a separate cluster of genes containing a second rhodopsin associated with a predicted flotillin coding gene and have thus been named flotillin-associated rhodopsins (FArhodopsins). Although they are members of the proteorhodopsin protein family, they form a separate clade within that family and are quite divergent from known proton-pumping proteorhodopsins. They contain either DTT, DTL, or DNI motifs in their key functional amino acids. FArhodopsins are mainly associated with the lower layers of the epipelagic zone. All marine FArhodopsins had the retinal binding lysine, but we found relatives in freshwater metagenomes lacking this key amino acid. AlphaFold predictions of marine FArhodopsins indicate that their retinal pocket might be very reduced or absent, hinting that they are retinal-less. Freshwater FArhodopsins were more diverse than marine ones, but we could not determine if there were other rhodopsins in the genome due to the lack of SAGs or isolates. Although the function of FArhodopsins could not be established, their conserved genomic context indicated involvement in the formation of membrane microdomains. The conservation of FArhodopsins in diverse and globally abundant microorganisms suggests that they may be important in the adaptation to the twilight zone of aquatic environments. IMPORTANCE Rhodopsins have been shown to play a key role in the ecology of aquatic microbes. Here, we describe a group of widespread rhodopsins in aquatic microbes associated with dim light conditions. Their characteristic genomic context found in both marine and freshwater environments indicates a novel potential involvement in membrane microstructure that could be important for the function of the coexisting proteorhodopsin proton pumps. The absence or reduction of the retinal binding pocket points to a drastically different physiological role.}, } @article {pmid37222510, year = {2023}, author = {Baba, H and Kuroda, M and Sekizuka, T and Kanamori, H}, title = {Highly sensitive detection of antimicrobial resistance genes in hospital wastewater using the multiplex hybrid capture target enrichment.}, journal = {mSphere}, volume = {8}, number = {4}, pages = {e0010023}, pmid = {37222510}, issn = {2379-5042}, mesh = {Humans ; *Wastewater ; Anti-Bacterial Agents/pharmacology ; *Methicillin-Resistant Staphylococcus aureus/genetics ; Drug Resistance, Bacterial/genetics ; Wastewater-Based Epidemiological Monitoring ; beta-Lactamases/genetics ; Bacteria/genetics ; Hospitals ; }, abstract = {Wastewater can be useful in monitoring the spread of antimicrobial resistance (AMR) within a hospital. The abundance of antibiotic resistance genes (ARGs) in hospital effluent was assessed using metagenomic sequencing (mDNA-seq) and hybrid capture (xHYB). mDNA-seq analysis and subsequent xHYB targeted enrichment were conducted on two effluent samples per month from November 2018 to May 2021. Reads per kilobase per million (RPKM) values were calculated for all 1,272 ARGs in the constructed database. The monthly numbers of patients with presumed extended-spectrum β-lactamase (ESBL)-producing and metallo-β-lactamase (MBL)-producing bacteria, methicillin-resistant Staphylococcus aureus (MRSA), and vancomycin-resistant enterococci (VRE) were compared with the monthly RPKM values of blaCTX-M, blaIMP, mecA, vanA, and vanB by xHYB. The average RPKM value for all ARGs detected by xHYB was significantly higher than that of mDNA-seq (665, 225, and 328, respectively, and P < 0.05). The average number of patients with ESBL producers and RPKM values of blaCTX-M-1 genes in 2020 were significantly higher than that in 2019 (17 and 13 patients per month and 921 vs 232 per month, respectively, both P < 0.05). The average numbers of patients with MBL-producers, MRSA, and VRE were 1, 28, and 0 per month, respectively, while the average RPKM values of blaIMP, mecA, vanA, and vanB were 6,163, 6, 0, and 126 per month, respectively. Monitoring ARGs in hospital effluent using xHYB was found to be more useful than conventional mDNA-seq in detecting ARGs including blaCTX-M, blaIMP, and vanB, which are important for infection control.IMPORTANCEEnvironmental ARGs play a crucial role in the emergence and spread of AMR that constitutes a significant global health threat. One major source of ARGs is effluent from healthcare facilities, where patients are frequently administered antimicrobials. Culture-independent methods, including metagenomics, can detect environmental ARGs carried by non-culturable bacteria and extracellular ARGs. mDNA-seq is one of the most comprehensive methods for environmental ARG surveillance; however, its sensitivity is insufficient for wastewater surveillance. This study demonstrates that xHYB appropriately monitors ARGs in hospital effluent for sensitive identification of nosocomial AMR dissemination. Correlations were observed between the numbers of inpatients with antibiotic-resistant bacteria and the ARG RPKM values in hospital effluent over time. ARG surveillance in hospital effluent using the highly sensitive and specific xHYB method could improve our understanding of the emergence and spread of AMR within a hospital.}, } @article {pmid37222264, year = {2023}, author = {Carr, RM and Li, Y and Chau, L and Friedman, ES and Lee, JJ and Adorini, L and Erickson, M and Zaru, L and Shringarpure, R and MacConell, L and Bittinger, K and Li, H and Wu, GD}, title = {An integrated analysis of fecal microbiome and metabolomic features distinguish non-cirrhotic NASH from healthy control populations.}, journal = {Hepatology (Baltimore, Md.)}, volume = {78}, number = {6}, pages = {1843-1857}, pmid = {37222264}, issn = {1527-3350}, support = {P30 DK050306/DK/NIDDK NIH HHS/United States ; R01 AA026302/AA/NIAAA NIH HHS/United States ; R01 GM123056/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/complications ; Cross-Sectional Studies ; Liver Cirrhosis/complications ; Fibrosis ; *Gastrointestinal Microbiome ; Bile Acids and Salts ; Feces/microbiology ; Biomarkers ; }, abstract = {BACKGROUND AND AIMS: There is great interest in identifying microbiome features as reliable noninvasive diagnostic and/or prognostic biomarkers for non-cirrhotic NASH fibrosis. Several cross-sectional studies have reported gut microbiome features associated with advanced NASH fibrosis and cirrhosis, where the most prominent features are associated with cirrhosis. However, no large, prospectively collected data exist establishing microbiome features that discern non-cirrhotic NASH fibrosis, integrate the fecal metabolome as disease biomarkers, and are unconfounded by BMI and age.

APPROACH AND RESULTS: Results from shotgun metagenomic sequencing performed on fecal samples prospectively collected from 279 US patients with biopsy-proven NASH (F1-F3 fibrosis) enrolled in the REGENERATE I303 study were compared to those from 3 healthy control cohorts and integrated with the absolute quantification of fecal bile acids. Microbiota beta-diversity was different, and BMI- and age-adjusted logistic regression identified 12 NASH-associated species. Random forest prediction models resulted in an AUC of 0.75-0.81 in a receiver operator characteristic analysis. In addition, specific fecal bile acids were significantly lower in NASH and correlated with plasma C4 levels. Microbial gene abundance analysis revealed 127 genes increased in controls, many involving protein synthesis, whereas 362 genes were increased in NASH many involving bacterial environmental responses (false discovery rate < 0.01). Finally, we provide evidence that fecal bile acid levels may be a better discriminator of non-cirrhotic NASH versus health than either plasma bile acids or gut microbiome features.

CONCLUSIONS: These results may have value as a set of baseline characteristics of non-cirrhotic NASH against which therapeutic interventions to prevent cirrhosis can be compared and microbiome-based diagnostic biomarkers identified.}, } @article {pmid37222046, year = {2023}, author = {Doss, RK and Palmer, M and Mead, DA and Hedlund, BP}, title = {Functional biology and biotechnology of thermophilic viruses.}, journal = {Essays in biochemistry}, volume = {67}, number = {4}, pages = {671-684}, pmid = {37222046}, issn = {1744-1358}, support = {R43 HG012181/HG/NHGRI NIH HHS/United States ; }, mesh = {*Viruses ; *Bacteriophages/genetics ; Bacteria/genetics ; DNA-Directed DNA Polymerase ; Biotechnology ; Ligases ; Biology ; }, abstract = {Viruses have developed sophisticated biochemical and genetic mechanisms to manipulate and exploit their hosts. Enzymes derived from viruses have been essential research tools since the first days of molecular biology. However, most viral enzymes that have been commercialized are derived from a small number of cultivated viruses, which is remarkable considering the extraordinary diversity and abundance of viruses revealed by metagenomic analysis. Given the explosion of new enzymatic reagents derived from thermophilic prokaryotes over the past 40 years, those obtained from thermophilic viruses should be equally potent tools. This review discusses the still-limited state of the art regarding the functional biology and biotechnology of thermophilic viruses with a focus on DNA polymerases, ligases, endolysins, and coat proteins. Functional analysis of DNA polymerases and primase-polymerases from phages infecting Thermus, Aquificaceae, and Nitratiruptor has revealed new clades of enzymes with strong proofreading and reverse transcriptase capabilities. Thermophilic RNA ligase 1 homologs have been characterized from Rhodothermus and Thermus phages, with both commercialized for circularization of single-stranded templates. Endolysins from phages infecting Thermus, Meiothermus, and Geobacillus have shown high stability and unusually broad lytic activity against Gram-negative and Gram-positive bacteria, making them targets for commercialization as antimicrobials. Coat proteins from thermophilic viruses infecting Sulfolobales and Thermus strains have been characterized, with diverse potential applications as molecular shuttles. To gauge the scale of untapped resources for these proteins, we also document over 20,000 genes encoded by uncultivated viral genomes from high-temperature environments that encode DNA polymerase, ligase, endolysin, or coat protein domains.}, } @article {pmid37221274, year = {2023}, author = {Megremis, S and Constantinides, B and Xepapadaki, P and Yap, CF and Sotiropoulos, AG and Bachert, C and Finotto, S and Jartti, T and Tapinos, A and Vuorinen, T and Andreakos, E and Robertson, DL and Papadopoulos, NG}, title = {Respiratory eukaryotic virome expansion and bacteriophage deficiency characterize childhood asthma.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8319}, pmid = {37221274}, issn = {2045-2322}, mesh = {Child ; Humans ; Child, Preschool ; Eukaryota ; *Bacteriophages ; Virome ; Eukaryotic Cells ; *Asthma ; *Anelloviridae ; Asymptomatic Diseases ; }, abstract = {Asthma development and exacerbation is linked to respiratory virus infections. There is limited information regarding the presence of viruses during non-exacerbation/infection periods. We investigated the nasopharyngeal/nasal virome during a period of asymptomatic state, in a subset of 21 healthy and 35 asthmatic preschool children from the Predicta cohort. Using metagenomics, we described the virome ecology and the cross-species interactions within the microbiome. The virome was dominated by eukaryotic viruses, while prokaryotic viruses (bacteriophages) were independently observed with low abundance. Rhinovirus B species consistently dominated the virome in asthma. Anelloviridae were the most abundant and rich family in both health and asthma. However, their richness and alpha diversity were increased in asthma, along with the co-occurrence of different Anellovirus genera. Bacteriophages were richer and more diverse in healthy individuals. Unsupervised clustering identified three virome profiles that were correlated to asthma severity and control and were independent of treatment, suggesting a link between the respiratory virome and asthma. Finally, we observed different cross-species ecological associations in the healthy versus the asthmatic virus-bacterial interactome, and an expanded interactome of eukaryotic viruses in asthma. Upper respiratory virome "dysbiosis" appears to be a novel feature of pre-school asthma during asymptomatic/non-infectious states and merits further investigation.}, } @article {pmid37221272, year = {2023}, author = {Hsia, K and Zhao, N and Chung, M and Algarrahi, K and Montaser Kouhsari, L and Fu, M and Chen, H and Singh, S and Michaud, DS and Jangi, S}, title = {Alterations in the Fungal Microbiome in Ulcerative Colitis.}, journal = {Inflammatory bowel diseases}, volume = {29}, number = {10}, pages = {1613-1621}, pmid = {37221272}, issn = {1536-4844}, support = {KL2 TR002545/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Humans ; *Colitis, Ulcerative/therapy ; *Mycobiome ; Prospective Studies ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/microbiology ; Candida ; *Biological Products ; }, abstract = {BACKGROUND: Although gut fungi have been implicated in the immunopathogenesis of inflammatory bowel disease, the fungal microbiome has not been deeply explored across endohistologic activity and treatment exposure in ulcerative colitis.

METHODS: We analyzed data from the SPARC IBD (Study of a Prospective Adult Research Cohort with Inflammatory Bowel Disease) registry. We evaluated the fungal composition of fecal samples from 98 patients with ulcerative colitis across endoscopic activity (n = 43), endohistologic activity (n = 41), and biologic exposure (n = 82). Across all subgroups, we assessed fungal diversity and differential abundance of taxonomic groups.

RESULTS: We identified 500 unique fungal amplicon sequence variants across the cohort of 82 patients, dominated by phylum Ascomycota. Compared with endoscopic remission, patients with endoscopic activity had increased Saccharomyces (log2 fold change = 4.54; adjusted P < 5 × 10-5) and increased Candida (log2 fold change = 2.56; adjusted P < .03). After adjusting for age, sex, and biologic exposure among patients with endoscopic activity, Saccharomyces (log2 fold change = 7.76; adjusted P < 1 × 10-15) and Candida (log2 fold change = 7.28; adjusted P< 1 × 10-8) remained enriched during endoscopic activity compared with quiescence.

CONCLUSIONS: Endoscopic inflammation in ulcerative colitis is associated with an expansion of Saccharomyces and Candida compared with remission. The role of these fungal taxa as potential biomarkers and targets for personalized approaches to therapeutics in ulcerative colitis should be evaluated.}, } @article {pmid37220973, year = {2023}, author = {Dreher, TW and Matthews, R and Davis, EW and Mueller, RS}, title = {Woronichinia naegeliana: A common nontoxigenic component of temperate freshwater cyanobacterial blooms with 30% of its genome in transposons.}, journal = {Harmful algae}, volume = {125}, number = {}, pages = {102433}, doi = {10.1016/j.hal.2023.102433}, pmid = {37220973}, issn = {1878-1470}, mesh = {*Cyanobacteria ; Lakes ; *Microcystis ; Nitrates ; }, abstract = {Monitoring in the U.S. state of Washington across the period 2007-2019 showed that Woronichinia has been present in many lakes state-wide. This cyanobacterium was commonly dominant or sub-dominant in cyanobacterial blooms in the wet temperate region west of the Cascade Mountains. In these lakes, Woronichinia often co-existed with Microcystis, Dolichospermum and Aphanizomenon flos-aquae and the cyanotoxin microcystin has often been present in those blooms, although it has not been known whether Woronichinia is a toxin producer. We report the first complete genome of Woronichinia naegeliana WA131, assembled from the metagenome of a sample collected from Wiser Lake, Washington, in 2018. The genome contains no genes for cyanotoxin biosynthesis or taste-and-odor compounds, but there are biosynthetic gene clusters for other bioactive peptides, including anabaenopeptins, cyanopeptolins, microginins and ribosomally produced, post-translationally modified peptides. Genes for photosynthesis, nutrient acquisition, vitamin synthesis and buoyancy that are typical of bloom-forming cyanobacteria are present, although nitrate and nitrite reductase genes are conspicuously absent. However, the 7.9 Mbp genome is 3-4 Mbp larger than those of the above-mentioned frequently co-existing cyanobacteria. The increased genome size is largely due to an extraordinary number of insertion sequence elements (transposons), which account for 30.3% of the genome and many of which are present in multiple copies. The genome contains a relatively large number of pseudogenes, 97% of which are transposase genes. W. naegeliana WA131 thus seems to be able to limit the potentially deleterious effects of high rates of recombination and transposition to the mobilome fraction of its genome.}, } @article {pmid37220151, year = {2023}, author = {Rios-Martinez, C and Bhattacharya, N and Amini, AP and Crawford, L and Yang, KK}, title = {Deep self-supervised learning for biosynthetic gene cluster detection and product classification.}, journal = {PLoS computational biology}, volume = {19}, number = {5}, pages = {e1011162}, pmid = {37220151}, issn = {1553-7358}, mesh = {*Genome, Bacterial ; Metagenome ; Multigene Family/genetics ; *Biological Products/metabolism ; Supervised Machine Learning ; }, abstract = {Natural products are chemical compounds that form the basis of many therapeutics used in the pharmaceutical industry. In microbes, natural products are synthesized by groups of colocalized genes called biosynthetic gene clusters (BGCs). With advances in high-throughput sequencing, there has been an increase of complete microbial isolate genomes and metagenomes, from which a vast number of BGCs are undiscovered. Here, we introduce a self-supervised learning approach designed to identify and characterize BGCs from such data. To do this, we represent BGCs as chains of functional protein domains and train a masked language model on these domains. We assess the ability of our approach to detect BGCs and characterize BGC properties in bacterial genomes. We also demonstrate that our model can learn meaningful representations of BGCs and their constituent domains, detect BGCs in microbial genomes, and predict BGC product classes. These results highlight self-supervised neural networks as a promising framework for improving BGC prediction and classification.}, } @article {pmid37219969, year = {2023}, author = {Lamothe, RC and Storlie, MD and Espinosa, DA and Rudlaff, R and Browne, P and Liu, J and Rivas, A and Devoto, A and Oki, J and Khoubyari, A and Goltsman, DSA and Lin, JL and Butterfield, CN and Brown, CT and Thomas, BC and Cost, GJ}, title = {Novel CRISPR-Associated Gene-Editing Systems Discovered in Metagenomic Samples Enable Efficient and Specific Genome Engineering.}, journal = {The CRISPR journal}, volume = {6}, number = {3}, pages = {243-260}, pmid = {37219969}, issn = {2573-1602}, mesh = {Humans ; *Gene Editing ; *CRISPR-Cas Systems/genetics ; T-Lymphocytes/metabolism ; Cell Differentiation ; Receptors, Antigen, T-Cell/genetics/metabolism ; }, abstract = {Development of medicines using gene editing has been hampered by enzymological and immunological impediments. We described previously the discovery and characterization of improved, novel gene-editing systems from metagenomic data. In this study, we substantially advance this work with three such gene-editing systems, demonstrating their utility for cell therapy development. All three systems are capable of reproducible, high-frequency gene editing in primary immune cells. In human T cells, disruption of the T cell receptor (TCR) alpha-chain was induced in >95% of cells, both paralogs of the TCR beta-chain in >90% of cells, and >90% knockout of β2-microglobulin, TIGIT, FAS, and PDCD1. Simultaneous double knockout of TRAC and TRBC was obtained at a frequency equal to that of the single edits. Gene editing with our systems had minimal effect on T cell viability. Furthermore, we integrate a chimeric antigen receptor (CAR) construct into TRAC (up to ∼60% of T cells), and demonstrate CAR expression and cytotoxicity. We next applied our novel gene-editing tools to natural killer (NK) cells, B cells, hematopoietic stem cells, and induced pluripotent stem cells, generating similarly efficient cell-engineering outcomes including the creation of active CAR-NK cells. Interrogation of our gene-editing systems' specificity reveals a profile comparable with or better than Cas9. Finally, our nucleases lack preexisting humoral and T cell-based immunity, consistent with their sourcing from nonhuman pathogens. In all, we show these new gene-editing systems have the activity, specificity, and translatability necessary for use in cell therapy development.}, } @article {pmid37219423, year = {2023}, author = {Xi, Y and Jiang, X and Xie, X and Zhao, M and Zhang, H and Qin, K and Wang, X and Liu, Y and Yang, S and Shen, Q and Ji, L and Shang, P and Zhang, W and Shan, T}, title = {Viromics Reveals the High Diversity of Viruses from Fishes of the Tibet Highland.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0094623}, pmid = {37219423}, issn = {2165-0497}, mesh = {Animals ; Tibet ; Phylogeny ; *Viruses/genetics ; Zoonoses ; Fishes/genetics ; Mammals ; }, abstract = {Aquaculture is important for food security and nutrition. The economy has recently been significantly threatened and the risk of zoonoses significantly increased by aquatic diseases, and the ongoing introduction of new aquatic pathogens, particularly viruses, continues to represent a hazard. Yet, our knowledge of the diversity and abundance of fish viruses is still limited. Here, we conducted a metagenomic survey of different species of healthy fishes caught in the Lhasa River, Tibet, China, and sampled intestinal contents, gills, and tissues. To be more precise, by identifying and analyzing viral genomes, we aim to determine the abundance, diversity, and evolutionary relationships of viruses in fish with other potential hosts. Our analysis identified 28 potentially novel viruses, 22 of which may be associated with vertebrates, across seven viral families. During our research, we found several new strains of viruses in fish, including papillomavirus, hepadnavirus, and hepevirus. Additionally, we discovered two viral families, Circoviridae and Parvoviridae, which were prevalent and closely related to viruses that infect mammals. These findings further expand our understanding of highland fish viruses and highlight the emerging view that fish harbor large, unknown viruses. IMPORTANCE The economy and zoonoses have recently been significantly threatened by aquatic diseases. Yet, our knowledge of the diversity and abundance of fish viruses is still limited. We identified the wide genetic diversity of viruses that these fish were harboring. Since there are currently few studies on the virome of fish living in the Tibet highland, our research adds to the body of knowledge. This discovery lays the groundwork for future studies on the virome of fish species and other highland animals, preserving the ecological equilibrium on the plateau.}, } @article {pmid37219419, year = {2023}, author = {Whidbey, C and Konopaski, AN and Teshome, R and Dhaliwal, S and Peters, MQ and Mejia, ME and Ballard, MB and Patras, KA}, title = {Complete Genome Sequences of 37 Bacteria from the Human Vaginal Tract.}, journal = {Microbiology resource announcements}, volume = {12}, number = {6}, pages = {e0035823}, pmid = {37219419}, issn = {2576-098X}, support = {F31 AI167538/AI/NIAID NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; T32 GM136554/GM/NIGMS NIH HHS/United States ; R01 DK128053/DK/NIDDK NIH HHS/United States ; }, abstract = {Microorganisms colonizing the human vaginal mucosa are associated with healthy states, as well as conditions such as bacterial vaginosis and infection-associated preterm birth. Here, we report complete genome sequences of 37 bacterial isolates from the human vaginal tract.}, } @article {pmid37219409, year = {2023}, author = {Fisher, AM and Airey, G and Liu, Y and Gemmell, M and Thomas, J and Bentley, EG and Whitehead, MA and Paxton, WA and Pollakis, G and Paterson, S and Viney, M}, title = {The ecology of viruses in urban rodents with a focus on SARS-CoV-2.}, journal = {Emerging microbes & infections}, volume = {12}, number = {1}, pages = {2217940}, pmid = {37219409}, issn = {2222-1751}, mesh = {Humans ; Animals ; Rats ; Mice ; SARS-CoV-2 ; *COVID-19 ; Rodentia ; Pandemics ; *Viruses ; Antibodies, Viral ; }, abstract = {Wild animals are naturally infected with a range of viruses, some of which may be zoonotic. During the human COVID pandemic there was also the possibility of rodents acquiring SARS-CoV-2 from people, so-called reverse zoonoses. To investigate this, we sampled rats (Rattus norvegicus) and mice (Apodemus sylvaticus) from urban environments in 2020 during the human COVID-19 pandemic. We metagenomically sequenced lung and gut tissue and faeces for viruses, PCR screened for SARS-CoV-2, and serologically surveyed for anti-SARS-CoV-2 Spike antibodies. We describe the range of viruses that we found in these two rodent species. We found no molecular evidence of SARS-CoV-2 infection, though in rats we found lung antibody responses and evidence of neutralization ability that are consistent with rats being exposed to SARS-CoV-2 and/or exposed to other viruses that result in cross-reactive antibodies.}, } @article {pmid37218009, year = {2023}, author = {Lin, MJ and Su, TH and Chen, CC and Wu, WK and Hsu, SJ and Tseng, TC and Liao, SH and Hong, CM and Yang, HC and Liu, CJ and Wu, MS and Kao, JH}, title = {Diversity and composition of gut microbiota in healthy individuals and patients at different stages of hepatitis B virus-related liver disease.}, journal = {Gut pathogens}, volume = {15}, number = {1}, pages = {24}, pmid = {37218009}, issn = {1757-4749}, support = {110-N01//National Taiwan University Hospital/ ; 111-L1005//National Taiwan University Hospital/ ; 111-L1005//National Taiwan University Hospital/ ; 111-L1005//National Taiwan University Hospital/ ; VN-110-02//National Taiwan University Hospital/ ; MOST 109-2326-B-002-012-MY3//National Science and Technology Council, Taiwan/ ; }, abstract = {BACKGROUND: Hepatitis B virus (HBV) causes chronic hepatitis B (CHB), liver cirrhosis, and hepatocellular carcinoma. The evolution of human gut microbiota during the progression of HBV-related liver diseases remains unclear. Therefore, we prospectively enrolled patients with HBV-related liver diseases and healthy individuals. Through 16S ribosomal RNA amplicon sequencing, we characterized the gut microbiota of the participants and predicted the functions of microbial communities.

RESULTS: We analyzed the gut microbiota of 56 healthy controls and 106 patients with HBV-related liver disease [14 with resolved HBV infection, 58 with CHB, and 34 with advanced liver disease (15 with liver cirrhosis and 19 with hepatocellular carcinoma)]. Patients with HBV-related liver disease exhibited a higher degree of bacterial richness (all P < 0.05) than did healthy controls. Beta diversity analyses revealed a distinct clustering pattern between healthy controls and patients with HBV-related liver disease (all P < 0.05). The composition of bacteria (from the phylum level to the genus level) varied across the stages of liver disease. Linear discriminant analysis effect size revealed multiple taxa that differ significantly in abundance between healthy controls and patients with HBV-related liver disease; however, fewer differences were observed among patients with resolved HBV infection, those with CHB, and those with advanced liver disease. The ratio of Firmicutes to Bacteroidetes was increased in all three patient groups compared with the ratio in healthy controls (all P < 0.001). The analysis of the sequencing data by using PICRUSt2 revealed the changes in microbial functions with disease progression.

CONCLUSIONS: The diversity and composition of gut microbiota appear to vary significantly between healthy controls and patients at different stages of HBV-related liver disease. The understanding of gut microbiota may provide novel therapeutic options in these patients.}, } @article {pmid37217817, year = {2023}, author = {Srivastava, A and Verma, D}, title = {Urbanization led to the abundance of Gram-negative, chemo-organo-heterotrophs, and antibiotic resistance genes in the downstream regions of the Ganga River water of India.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {30}, pages = {75417-75438}, doi = {10.1007/s11356-023-27552-7}, pmid = {37217817}, issn = {1614-7499}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology/analysis ; *Genes, Bacterial ; Urbanization ; RNA, Ribosomal, 16S/genetics ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Water ; }, abstract = {The present investigation assesses the bacterial microbiome and antibiotic resistance genes (ARGs) of the river Ganga from Uttarakhand (upstream region; US group) and Uttar Pradesh (downstream region; DS group) regions using a 16S rRNA amplicon-based metagenomic approach. Gram-negative, aerobic, and chemo-organotrophic bacteria made up the majority of the bacterial genera during the overall analysis. Physicochemical analysis revealed a higher concentration of nitrate and phosphate in the downstream sites of the Ganga River. The prevalence of Gemmatimonas, Flavobacterium, Arenimonas, and Verrucomicrobia in the water of the DS region indicates a high organic load. Pseudomonas and Flavobacterium emerged as the most prevalent genera among the 35 significantly different shared genera (p-value < 0.05) in the US and DS regions, respectively. Overall antibiotic resistance analysis of the samples showed the dominance of β-lactam resistance (33.92%) followed by CAMP (cationic antimicrobial peptide) resistance (27.75%), and multidrug resistance (19.17%), vancomycin resistance (17.84%), and tetracycline resistance (0.77%). While comparing, the DS group exhibited a higher abundance of ARGs over the US group, where the CAMP resistance and β-lactam ARGs were dominant in the respective regions. The correlation (p-value < 0.05) analysis showed that most bacteria exhibit a significant correlation with tetracycline resistance followed by the phenicol antibiotic. The present findings draw attention to the need for regulated disposal of multiform human-derived wastes into the Ganga River to reduce the irrepressible ARGs dissemination.}, } @article {pmid37217593, year = {2023}, author = {Shiozaki, T and Nishimura, Y and Yoshizawa, S and Takami, H and Hamasaki, K and Fujiwara, A and Nishino, S and Harada, N}, title = {Distribution and survival strategies of endemic and cosmopolitan diazotrophs in the Arctic Ocean.}, journal = {The ISME journal}, volume = {17}, number = {8}, pages = {1340-1350}, pmid = {37217593}, issn = {1751-7370}, mesh = {*Seawater/microbiology ; Nitrogen Fixation/physiology ; Ecosystem ; Oceans and Seas ; *Cyanobacteria/genetics ; }, abstract = {Dinitrogen (N2) fixation is the major source of reactive nitrogen in the ocean and has been considered to occur specifically in low-latitude oligotrophic oceans. Recent studies have shown that N2 fixation also occurs in the polar regions and thus is a global process, although the physiological and ecological characteristics of polar diazotrophs are not yet known. Here, we successfully reconstructed diazotroph genomes, including that of cyanobacterium UCYN-A (Candidatus 'Atelocyanobacterium thalassa'), from metagenome data corresponding to 111 samples isolated from the Arctic Ocean. These diazotrophs were highly abundant in the Arctic Ocean (max., 1.28% of the total microbial community), suggesting that they have important roles in the Arctic ecosystem and biogeochemical cycles. Further, we show that diazotrophs within genera Arcobacter, Psychromonas, and Oceanobacter are prevalent in the <0.2 µm fraction in the Arctic Ocean, indicating that current methods cannot capture their N2 fixation. Diazotrophs in the Arctic Ocean were either Arctic-endemic or cosmopolitan species from their global distribution patterns. Arctic-endemic diazotrophs, including Arctic UCYN-A, were similar to low-latitude-endemic and cosmopolitan diazotrophs in genome-wide function, however, they had unique gene sets (e.g., diverse aromatics degradation genes), suggesting adaptations to Arctic-specific conditions. Cosmopolitan diazotrophs were generally non-cyanobacteria and commonly had the gene that encodes the cold-inducible RNA chaperone, which presumably makes their survival possible even in deep, cold waters of global ocean and polar surface waters. This study shows global distribution pattern of diazotrophs with their genomes and provides clues to answering the question of how diazotrophs can inhabit polar waters.}, } @article {pmid37217592, year = {2023}, author = {Waldrop, MP and Chabot, CL and Liebner, S and Holm, S and Snyder, MW and Dillon, M and Dudgeon, SR and Douglas, TA and Leewis, MC and Walter Anthony, KM and McFarland, JW and Arp, CD and Bondurant, AC and Taş, N and Mackelprang, R}, title = {Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients.}, journal = {The ISME journal}, volume = {17}, number = {8}, pages = {1224-1235}, pmid = {37217592}, issn = {1751-7370}, support = {RL5 GM118975/GM/NIGMS NIH HHS/United States ; }, mesh = {*Permafrost/chemistry ; Soil/chemistry ; Soil Microbiology ; *Microbiota/genetics ; Metagenome ; Carbon/metabolism ; }, abstract = {Permafrost underlies approximately one quarter of Northern Hemisphere terrestrial surfaces and contains 25-50% of the global soil carbon (C) pool. Permafrost soils and the C stocks within are vulnerable to ongoing and future projected climate warming. The biogeography of microbial communities inhabiting permafrost has not been examined beyond a small number of sites focused on local-scale variation. Permafrost is different from other soils. Perennially frozen conditions in permafrost dictate that microbial communities do not turn over quickly, thus possibly providing strong linkages to past environments. Thus, the factors structuring the composition and function of microbial communities may differ from patterns observed in other terrestrial environments. Here, we analyzed 133 permafrost metagenomes from North America, Europe, and Asia. Permafrost biodiversity and taxonomic distribution varied in relation to pH, latitude and soil depth. The distribution of genes differed by latitude, soil depth, age, and pH. Genes that were the most highly variable across all sites were associated with energy metabolism and C-assimilation. Specifically, methanogenesis, fermentation, nitrate reduction, and replenishment of citric acid cycle intermediates. This suggests that adaptations to energy acquisition and substrate availability are among some of the strongest selective pressures shaping permafrost microbial communities. The spatial variation in metabolic potential has primed communities for specific biogeochemical processes as soils thaw due to climate change, which could cause regional- to global- scale variation in C and nitrogen processing and greenhouse gas emissions.}, } @article {pmid37217495, year = {2023}, author = {Cho, H and Ren, Z and Divaris, K and Roach, J and Lin, BM and Liu, C and Azcarate-Peril, MA and Simancas-Pallares, MA and Shrestha, P and Orlenko, A and Ginnis, J and North, KE and Zandona, AGF and Ribeiro, AA and Wu, D and Koo, H}, title = {Selenomonas sputigena acts as a pathobiont mediating spatial structure and biofilm virulence in early childhood caries.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2919}, pmid = {37217495}, issn = {2041-1723}, support = {UL1 TR001111/TR/NCATS NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; R90 DE031532/DE/NIDCR NIH HHS/United States ; UL1 TR002489/TR/NCATS NIH HHS/United States ; U01 DE025046/DE/NIDCR NIH HHS/United States ; R03 DE028983/DE/NIDCR NIH HHS/United States ; R01 DE025220/DE/NIDCR NIH HHS/United States ; }, mesh = {Male ; Child ; Female ; Humans ; Child, Preschool ; Virulence ; *Dental Caries Susceptibility ; *Streptococcus mutans/genetics ; Biofilms ; }, abstract = {Streptococcus mutans has been implicated as the primary pathogen in childhood caries (tooth decay). While the role of polymicrobial communities is appreciated, it remains unclear whether other microorganisms are active contributors or interact with pathogens. Here, we integrate multi-omics of supragingival biofilm (dental plaque) from 416 preschool-age children (208 males and 208 females) in a discovery-validation pipeline to identify disease-relevant inter-species interactions. Sixteen taxa associate with childhood caries in metagenomics-metatranscriptomics analyses. Using multiscale/computational imaging and virulence assays, we examine biofilm formation dynamics, spatial arrangement, and metabolic activity of Selenomonas sputigena, Prevotella salivae and Leptotrichia wadei, either individually or with S. mutans. We show that S. sputigena, a flagellated anaerobe with previously unknown role in supragingival biofilm, becomes trapped in streptococcal exoglucans, loses motility but actively proliferates to build a honeycomb-like multicellular-superstructure encapsulating S. mutans, enhancing acidogenesis. Rodent model experiments reveal an unrecognized ability of S. sputigena to colonize supragingival tooth surfaces. While incapable of causing caries on its own, when co-infected with S. mutans, S. sputigena causes extensive tooth enamel lesions and exacerbates disease severity in vivo. In summary, we discover a pathobiont cooperating with a known pathogen to build a unique spatial structure and heighten biofilm virulence in a prevalent human disease.}, } @article {pmid37217150, year = {2023}, author = {Khanthong, K and Kadam, R and Kim, T and Park, J}, title = {Synergetic effects of anaerobic co-digestion of food waste and algae on biogas production.}, journal = {Bioresource technology}, volume = {382}, number = {}, pages = {129208}, doi = {10.1016/j.biortech.2023.129208}, pmid = {37217150}, issn = {1873-2976}, mesh = {*Food ; Anaerobiosis ; Biofuels/analysis ; *Refuse Disposal/methods ; Sewage/microbiology ; Bioreactors/microbiology ; Methane ; Fatty Acids, Volatile ; }, abstract = {Anaerobic co-digestion of food waste and algae was assessed to offset the drawbacks of anaerobic mono-digestion of each substrate. Batch test results indicated that a food waste and algae mixture ratio of 8:2 facilitated the highest CH4 yield (334 mL CH4/g CODInput). This ratio was applied to the anaerobic co-digestion reactor, resulting in a CH4 yield that was twice that of the anaerobic mono-digestion reactors, thereby facilitating high operational stability. In contrast to the anaerobic mono-digestion, anaerobic co-digestion resulted in stable CH4 production by overcoming volatile fatty acid accumulation and a decreased pH, even under a high organic loading rate (3 kg COD/m[3]∙d). Furthermore, a comparative metagenomic analysis revealed that the abundance of volatile fatty acid-oxidizing bacteria and hydrogenotrophic and methylotrophic methanogens was significantly increased in the anaerobic co-digestion reactor. These findings indicate that the anaerobic co-digestion of food waste and algae significantly improves CH4 production and process stability.}, } @article {pmid37217131, year = {2023}, author = {Li, R and Ren, C and Wu, L and Zhang, X and Mao, X and Fan, Z and Cui, W and Zhang, W and Wei, G and Shu, D}, title = {Fertilizing-induced alterations of microbial functional profiles in soil nitrogen cycling closely associate with crop yield.}, journal = {Environmental research}, volume = {231}, number = {Pt 2}, pages = {116194}, doi = {10.1016/j.envres.2023.116194}, pmid = {37217131}, issn = {1096-0953}, mesh = {*Soil ; *Nitrogen/analysis ; Fertilizers/analysis ; Soil Microbiology ; Agriculture ; Bacteria/metabolism ; }, abstract = {Fertilization and rhizosphere selection are key regulators for soil nitrogen (N) cycling and microbiome. Thus, clarifying how the overall N cycling processes and soil microbiome respond to these factors is a prerequisite for understanding the consequences of high inputs of fertilizers, enhancing crop yields, and formulating reasonable nitrogen management strategies under agricultural intensification scenarios. To do this, we applied shotgun metagenomics sequencing to reconstruct N cycling pathways on the basis of abundance and distribution of related gene families, as well as explored the microbial diversity and interaction via high throughput sequencing based on a two-decade fertilization experiment in Loess Plateau of China semiarid area. We found that bacteria and fungi respond divergent to fertilization regimes and rhizosphere selection, in terms of community diversity, niche breadth, and microbial co-occurrence networks. Moreover, organic fertilization decreased the complexity of bacterial networks but increased the complexity and stability of fungal networks. Most importantly, rhizosphere selection exerted more strongly influences on the soil overall nitrogen cycling than the application of fertilizers, accompanied by the increase in the abundance of nifH, NIT-6, and narI genes and the decrease in the abundance of amoC, norC, and gdhA genes in the rhizosphere soil. Furthermore, keystone families screening from soil microbiome (e.g., Sphingomonadaceae, Sporichthyaceae, and Mortierellaceae), which were affected by the edaphic variables, contributed greatly to crop yield. Collectively, our findings emphasize the pivotal roles of rhizosphere selection interacting with fertilization regimes in sustaining soil nitrogen cycling processes in response to decades-long fertilization, as well as the potential importance of keystone taxa in maintaining crop yield. These findings significantly facilitate our understanding of nitrogen cycling in diverse agricultural soils and lay a foundation for manipulating specific microorganisms to regulate N cycling and promote agroecosystem sustainability.}, } @article {pmid37215499, year = {2023}, author = {Cao, X and Yuan, L}, title = {Gemella morbillorum infective endocarditis: A case report and literature review.}, journal = {Open life sciences}, volume = {18}, number = {1}, pages = {20220599}, pmid = {37215499}, issn = {2391-5412}, abstract = {Infective endocarditis (IE) caused by Gemella morbillorum is rare. Consequently, little is known about the natural course of endocarditis caused by this pathogen. This report describes the case of a 37-year-old male patient with G. morbillorum endocarditis. The patient was hospitalized for a fever of unknown origin. He complained of intermittent fever of unknown origin for 2 months. He had also undergone root canal therapy for pulpitis a month ago. After admission, the infectious pathogen G. morbillorum was identified using metagenomic next-generation sequence technology. The anaerobic blood culture bottle showed only Gram-positive cocci. Transthoracic echocardiography showed 10 mm vegetation on the aorta, which met the IE diagnostic Duke's criteria, and the patient was diagnosed with G. morbillorum IE. Because no bacterial colonies were formed on the culture, the drug sensitivity test could not be conducted. Ceftriaxone anti-infective drugs are based on careful consideration of the literature and patient. Six days after antibiotic treatment in our department, the patient was discharged from the hospital in stable condition and had no adverse reactions at 1 week of follow-up. To help clinicians better understand the disease of G. morbillorum IE, we also reviewed and discussed the relevant cases published after 2010 when presenting the report.}, } @article {pmid37215494, year = {2023}, author = {Dan, T and Qin, H and Sun, C and Shen, H and Guo, L}, title = {Detection of V. vulnificus septic shock with ARDS using mNGS.}, journal = {Open life sciences}, volume = {18}, number = {1}, pages = {20220584}, pmid = {37215494}, issn = {2391-5412}, abstract = {The latest surveillance from the Centers for Disease Control and Prevention shows that the annual incidence of V. vulnificus infection is increasing. Unfortunately, in less well-known high-risk groups, this infection is usually excluded from differential diagnosis. Transmitted through wound exposure or ingestion, the mortality rate of foodborne diseases of V. vulnificus is the highest of all V. vulnificus. V. vulnificus is as lethal early diagnosis as Ebola and bubonic plague, so timely treatment is imperative. Sepsis caused by V. vulnificus infection mainly exists in the United States and is rarely reported in Southeast Asia. We report a 78-year-old man who went to the local hospital and complained of swelling in his right hand with severe pain. He ate raw salmon 2 days ago and denied other recognized seafood stab or trauma history and other seafood contact history. He was in septic shock at the time of treatment, so we immediately transferred to the emergency intensive care unit and tested for metagenomic next-generation sequencing (mNGS). The diagnosis was confirmed the second day after admission, and eventually he was cured and discharged from the hospital only after medical treatment, thus avoiding the risk of surgical debridement or even amputation. mNGS is helpful for early clinical diagnosis and effective early intervention for etiology, so that patients can get a good prognosis.}, } @article {pmid37215132, year = {2023}, author = {Zhang, L and Wang, F and Jia, L and Yan, H and Gao, L and Tian, Y and Su, X and Zhang, X and Lv, C and Ma, Z and Xue, Y and Lin, Q and Wang, K}, title = {Edwardsiella piscicida infection reshapes the intestinal microbiome and metabolome of big-belly seahorses: mechanistic insights of synergistic actions of virulence factors.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1135588}, pmid = {37215132}, issn = {1664-3224}, mesh = {Animals ; Virulence Factors/metabolism ; *Gastrointestinal Microbiome ; Virulence ; *Smegmamorpha/metabolism ; Fishes/metabolism ; *Enteritis ; Metabolome ; }, abstract = {Uncovering the mechanism underlying the pathogenesis of Edwardsiella piscicida-induced enteritis is essential for global aquaculture. In the present study, we identified E. piscicida as a lethal pathogen of the big-belly seahorse (Hippocampus abdominalis) and revealed its pathogenic pattern and characteristics by updating our established bacterial enteritis model and evaluation system. Conjoint analysis of metagenomic and metabolomic data showed that 15 core virulence factors could mutually coordinate the remodeling of intestinal microorganisms and host metabolism and induce enteritis in the big-belly seahorse. Specifically, the Flagella, Type IV pili, and Lap could significantly increase the activities of the representative functional pathways of both flagella assembly and bacterial chemotaxis in the intestinal microbiota (P < 0.01) to promote pathogen motility, adherence, and invasion. Legiobactin, IraAB, and Hpt could increase ABC transporter activity (P < 0.01) to compete for host nutrition and promote self-replication. Capsule1, HP-NAP, and FarAB could help the pathogen to avoid phagocytosis. Upon entering epithelial cells and phagocytes, Bsa T3SS and Dot/Icm could significantly increase bacterial secretion system activity (P < 0.01) to promote the intracellular survival and replication of the pathogen and the subsequent invasion of the neighboring tissues. Finally, LPS3 could significantly increase lipopolysaccharide biosynthesis (P < 0.01) to release toxins and kill the host. Throughout the pathogenic process, BopD, PhoP, and BfmRS significantly activated the two-component system (P < 0.01) to coordinate with other VFs to promote deep invasion. In addition, the levels of seven key metabolic biomarkers, Taurine, L-Proline, Uridine, L-Glutamate, Glutathione, Xanthosine, and L-Malic acid, significantly decreased (P < 0.01), and they can be used for characterizing E. piscicida infection. Overall, the present study systematically revealed how a combination of virulence factors mediate E. piscicida-induced enteritis in fish for the first time, providing a theoretical reference for preventing and controlling this disease in the aquaculture of seahorses and other fishes.}, } @article {pmid37215025, year = {2023}, author = {Trinh, P and Roberts, MC and Rabinowitz, PM and Willis, AD}, title = {Differences in gut metagenomes between dairy workers and community controls: a cross-sectional study.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37215025}, support = {R21 AI168679/AI/NIAID NIH HHS/United States ; R35 GM133420/GM/NIGMS NIH HHS/United States ; T32 ES015459/ES/NIEHS NIH HHS/United States ; }, abstract = {BACKGROUND: As a nexus of routine antibiotic use and zoonotic pathogen presence, the livestock farming environment is a potential hotspot for the emergence of zoonotic diseases and antibiotic resistant bacteria. Livestock can further facilitate disease transmission by serving as intermediary hosts for pathogens as they undergo evolution prior to a spillover event. In light of this, we are interested in characterizing the microbiome and resistome of dairy workers, whose exposure to the livestock farming environment places them at risk for facilitating community transmission of antibiotic resistant genes and emerging zoonotic diseases.

RESULTS: Using shotgun sequencing, we investigated differences in the taxonomy, diversity and gene presence of the human gut microbiome of 10 dairy farm workers and 6 community controls, supplementing these samples with additional publicly available gut metagenomes. We observed greater abundance of tetracycline resistance genes and prevalence of cephamycin resistance genes in dairy workers' metagenomes, and lower average gene diversity. We also found evidence of commensal organism association with plasmid-mediated tetracycline resistance genes in both dairy workers and community controls (including Faecalibacterium prausnitzii, Ligilactobacillus animalis, and Simiaoa sunii). However, we did not find significant differences in the prevalence of resistance genes or virulence factors overall, nor differences in the taxonomic composition of dairy worker and community control metagenomes.

CONCLUSIONS: This study presents the first metagenomics analysis of United States dairy workers, providing insights into potential risks of exposure to antibiotics and pathogens in animal farming environments. Previous metagenomic studies of livestock workers in China and Europe have reported increased abundance and carriage of antibiotic resistance genes in livestock workers. While our investigation found no strong evidence for differences in the abundance or carriage of antibiotic resistance genes and virulence factors between dairy worker and community control gut metagenomes, we did observe patterns in the abundance of tetracycline resistance genes and the prevalence of cephamycin resistance genes that is consistent with previous work.}, } @article {pmid37214944, year = {2023}, author = {Fan, J and Singh, NP and Khan, J and Pibiri, GE and Patro, R}, title = {Fulgor: A fast and compact k-mer index for large-scale matching and color queries.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37214944}, abstract = {The problem of sequence identification or matching - determining the subset of references from a given collection that are likely to contain a query nucleotide sequence - is relevant for many important tasks in Computational Biology, such as metagenomics and pan-genome analysis. Due to the complex nature of such analyses and the large scale of the reference collections a resourceefficient solution to this problem is of utmost importance. The reference collection should therefore be pre-processed into an index for fast queries. This poses the threefold challenge of designing an index that is efficient to query, has light memory usage, and scales well to large collections. To solve this problem, we describe how recent advancements in associative, order-preserving, k-mer dictionaries can be combined with a compressed inverted index to implement a fast and compact colored de Bruijn graph data structure. This index takes full advantage of the fact that unitigs in the colored de Bruijn graph are monochromatic (all k-mers in a unitig have the same set of references of origin, or "color"), leveraging the order-preserving property of its dictionary. In fact, k-mers are kept in unitig order by the dictionary, thereby allowing for the encoding of the map from k-mers to their inverted lists in as little as 1+o(1) bits per unitig. Hence, one inverted list per unitig is stored in the index with almost no space/time overhead. By combining this property with simple but effective compression methods for inverted lists, the index achieves very small space. We implement these methods in a tool called Fulgor. Compared to Themisto, the prior state of the art, Fulgor indexes a heterogeneous collection of 30,691 bacterial genomes in 3.8× less space, a collection of 150,000 Salmonella enterica genomes in approximately 2× less space, is at least twice as fast for color queries, and is 2 - 6× faster to construct.}, } @article {pmid37214901, year = {2023}, author = {Eggers, S and Midya, V and Bixby, M and Gennings, C and Torres-Olascoaga, LA and Walker, RW and Wright, RO and Arora, M and Téllez-Rojo, MM}, title = {Prenatal Lead Exposure is Negatively Associated with the Gut Microbiome in Childhood.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {37214901}, support = {K99 ES032884/ES/NIEHS NIH HHS/United States ; P30 ES023515/ES/NIEHS NIH HHS/United States ; R01 ES013744/ES/NIEHS NIH HHS/United States ; }, abstract = {BACKGROUND: Metal exposures are associated with gut microbiome (GM) composition and function, and exposures early in development may be particularly important. Considering the role of the GM in association with many adverse health outcomes, understanding the relationship between prenatal metal exposures and the GM is critically important. However, there is sparse knowledge of the association between prenatal metal exposure and GM later in childhood.

OBJECTIVES: This analysis aims to identify associations between prenatal lead (Pb) exposure and GM composition and function in children 9-11 years old.

METHODS: Data come from the Programming Research in Obesity, Growth, Environment and Social Stressors (PROGRESS) cohort based in Mexico City, Mexico. Prenatal metal concentrations were measured in maternal whole blood drawn during the second and third trimesters of pregnancy. Stool samples collected at 9-11 years old underwent metagenomic sequencing to assess the GM. This analysis uses multiple statistical modeling approaches, including linear regression, permutational analysis of variance, weighted quantile sum regression (WQS), and individual taxa regressions, to estimate the association between maternal blood Pb during pregnancy and multiple aspects of the child GM at 9-11 years old, adjusting for relevant confounders.

RESULTS: Of the 123 child participants in this pilot data analysis, 74 were male and 49 were female. Mean prenatal maternal blood Pb was 33.6(SE=2.1) ug/L and 34.9(SE=2.1) ug/L at second and third trimesters, respectively. Analysis suggests a consistent negative relationship between prenatal maternal blood Pb and the GM at age 9-11, including measures of alpha and beta diversity, microbiome mixture analysis, and individual taxa. The WQS analysis showed a negative association between prenatal Pb exposure and the gut microbiome, for both second and third trimester exposures (2Tβ=-0.17,95%CI=[-0.46,0.11]; 3Tβ=-0.17,95%CI=[-0.44,0.10]). Ruminococcus gnavus, Bifidobacterium longum, Alistipes indistinctus, Bacteroides caccae, and Bifidobacterium bifidum all had weights above the importance threshold from 80% or more of the WQS repeated holdouts in association with both second and third trimester Pb exposure.

DISCUSSION: Pilot data analysis suggests a negative association between prenatal Pb exposure and the gut microbiome later in childhood; however, additional investigation is needed.}, } @article {pmid37214811, year = {2023}, author = {Rojas, CA and Marks, SL and Borras, E and Lesea, H and McCartney, MM and Coil, D and Davis, CE and Eisen, JA}, title = {Characterization of the microbiome and volatile compounds in anal gland secretions from domestic cats (Felis catus) using metagenomics and metabolomics.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {37214811}, support = {P30 ES023513/ES/NIEHS NIH HHS/United States ; }, abstract = {Animals rely on volatile chemical compounds for their communication and behavior. Many of these compounds are sequestered in endocrine and exocrine glands and are synthesized by anaerobic microbes. While the volatile organic compound (VOC) or microbiome composition of glandular secretions has been investigated in several mammalian species, few have linked specific bacterial taxa to the production of volatiles or to specific microbial gene pathways. Here, we use metagenomic sequencing, mass-spectrometry based metabolomics, and culturing to profile the microbial and volatile chemical constituents of anal gland secretions in twenty-three domestic cats (Felis catus), in attempts to identify organisms potentially involved in host odor production. We found that the anal gland microbiome was dominated by bacteria in the genera Corynebacterium, Bacteroides, Proteus, Lactobacillus, and Streptococcus, and showed striking variation among individual cats. Microbiome profiles also varied with host age and obesity. Metabolites such as fatty-acids, ketones, aldehydes and alcohols were detected in glandular secretions. Overall, microbiome and metabolome profiles were modestly correlated (r=0.17), indicating that a relationship exists between the bacteria in the gland and the metabolites produced in the gland. Functional analyses revealed the presence of genes predicted to code for enzymes involved in VOC metabolism such as dehydrogenases, reductases, and decarboxylases. From metagenomic data, we generated 85 high-quality metagenome assembled genomes (MAGs). Of these, four were inferred to have high relative abundance in metagenome profiles and had close relatives that were recovered as cultured isolates. These four MAGs were classified as Corynebacterium frankenforstense, Proteus mirabilis, Lactobacillus johnsonii, and Bacteroides fragilis. They represent strong candidates for further investigation of the mechanisms of volatile synthesis and scent production in the mammalian anal gland.}, } @article {pmid37214809, year = {2023}, author = {Makhsous, N and Goya, S and Avendaño, C and Rupp, J and Kuypers, J and Jerome, KR and Boeckh, M and Waghmare, A and Greninger, AL}, title = {Within-host rhinovirus evolution in upper and lower respiratory tract highlights capsid variability and mutation-independent compartmentalization.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37214809}, support = {K23 AI114844/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Human rhinovirus (HRV) infections can progress from the upper (URT) to lower (LRT) respiratory tract in immunocompromised individuals, causing high rates of fatal pneumonia. Little is known about how HRV evolves within hosts during infection.

METHODS: We sequenced HRV complete genomes from 12 hematopoietic cell transplant patients with prolonged infection for up to 190 days from both URT (nasal wash, NW) and LRT (bronchoalveolar lavage, BAL) specimens. Metagenomic (mNGS) and amplicon-based NGS were used to study the emergence and evolution of intra-host single nucleotide variants (iSNVs).

RESULTS: Identical HRV intra-host populations in matched NW and BAL specimens indicated no genetic adaptation is required for HRV to progress from URT to LRT. Microbial composition between matched NW and BAL confirmed no cross-contamination during sampling procedure. Coding iSNVs were 2.3-fold more prevalent in capsid over non-structural genes, adjusted for length. iSNVs modeled onto HRV capsid structures were significantly more likely to be found in surface residues, but were not preferentially located in known HRV neutralizing antibody epitopes. Newly emergent, serotype-matched iSNV haplotypes from immunocompromised individuals from 2008-2010 could be detected in Seattle-area community HRV sequences from 2020-2021.

CONCLUSION: HRV infections in immunocompromised hosts can progress from URT to LRT with no specific evolutionary requirement. Capsid proteins carry the highest variability and emergent mutations can be detected in other, including future, HRV sequences.}, } @article {pmid37214087, year = {2023}, author = {Fadeyi, TE and Oyedemi, OT and Awe, OO and Ayeni, F}, title = {Antibiotic use in infants within the first year of life is associated with the appearance of antibiotic-resistant genes in their feces.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15015}, pmid = {37214087}, issn = {2167-8359}, mesh = {Humans ; Infant ; *Anti-Bacterial Agents/adverse effects ; Feces/microbiology ; }, abstract = {BACKGROUND: Antibiotic resistance, an increasing challenge, is not only a national threat but also a global threat. Carriage of resistance genes is not limited to adults alone, various microbiota niches present in the body system of children have been found to harbor bacteria carrying resistant genes, especially, their gut microbiota. This study aims to identify selected antibiotic-resistant genes from the fecal samples of infants and the association of antibiotics use with the occurrence of resistant genes in the infant's gut.

METHODS: A total number of 172 metagenomic DNA samples previously extracted from stool samples of 28 Nigerian babies longitudinally within their first year of life were screened for the presence of ESBL genes (blaSHV, blaTEM, and blaCTX-M), PMQR genes (qnrA, qnrB, qnrS, qepA), ribosomal protection protein tetracycline resistance gene, (RPP) β-lactamase (blaZ), macrolide (ermA, ermB, mefA/E), aminoglycoside modifying enzymes gent[R] (aac(6')/aph(2″)) and dfrA genes by PCR. Nineteen (19) of the 28 babies used antibiotics during the study. The association between antibiotic use by the babies within the first year of life and occurrence of resistant genes were analyzed by Spearman rank correlation.

RESULTS: One hundred and twenty-two (122) samples (71%) out of the 172 isolates had antibiotic-resistance genes. PMQR genes were absent in all the samples. Three isolates had blaTEM gene, nine isolates had blaSHV gene, six isolates had blaCTX-M gene and 19 isolates had dfrA gene, 31 samples had tet gene, 29 samples had mef gene, 27 samples had ermB gene, four samples had ermA gene, 13 samples had blaZ gene and 16 samples had aac gene. The babies whose samples had resistant genes used antibiotics in the same months the samples were collected. Interestingly, the 11 babies whose samples had the dfrA gene all used antibiotics in the same months their samples were collected but none of them used trimethoprim/sulfamethoxazole antibiotic. The overall correlation matrix of the babies showed a strong association between antibiotic use (AU) and antibiotic use presence of resistance genes (AUPRG) with a coefficient of 0.89. Antibiotic-resistant genes are present in the gut of infants and their occurrence is strongly connected with antibiotic use by infants.}, } @article {pmid37213867, year = {2023}, author = {Zachariasen, T and Petersen, AØ and Brejnrod, A and Vestergaard, GA and Eklund, A and Nielsen, HB}, title = {Identification of representative species-specific genes for abundance measurements.}, journal = {Bioinformatics advances}, volume = {3}, number = {1}, pages = {vbad060}, pmid = {37213867}, issn = {2635-0041}, abstract = {MOTIVATION: Metagenomic binning facilitates the reconstruction of genomes and identification of Metagenomic Species Pan-genomes or Metagenomic Assembled Genomes. We propose a method for identifying a set of de novo representative genes, termed signature genes, which can be used to measure the relative abundance and used as markers of each metagenomic species with high accuracy.

RESULTS: An initial set of the 100 genes that correlate with the median gene abundance profile of the entity is selected. A variant of the coupon collector's problem was utilized to evaluate the probability of identifying a certain number of unique genes in a sample. This allows us to reject the abundance measurements of strains exhibiting a significantly skewed gene representation. A rank-based negative binomial model is employed to assess the performance of different gene sets across a large set of samples, facilitating identification of an optimal signature gene set for the entity. When benchmarked the method on a synthetic gene catalog, our optimized signature gene sets estimate relative abundance significantly closer to the true relative abundance compared to the starting gene sets extracted from the metagenomic species. The method was able to replicate results from a study with real data and identify around three times as many metagenomic entities.

The code used for the analysis is available on GitHub: https://github.com/trinezac/SG_optimization.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.}, } @article {pmid37213556, year = {2023}, author = {Babalola, OO and Olowe, OM and Ayangbenro, AS}, title = {Corrigendum to "Shotgun metagenomics dataset of Striga hermonthica-infested maize (Zea mays L.) rhizospheric soil microbiome" [Data in Brief, volume 48 (2023) 1-5/109132].}, journal = {Data in brief}, volume = {48}, number = {}, pages = {109191}, doi = {10.1016/j.dib.2023.109191}, pmid = {37213556}, issn = {2352-3409}, abstract = {[This corrects the article DOI: 10.1016/j.dib.2023.109132.].}, } @article {pmid37213515, year = {2023}, author = {Sonke, A and Trembath-Reichert, E}, title = {Expanding the taxonomic and environmental extent of an underexplored carbon metabolism-oxalotrophy.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1161937}, pmid = {37213515}, issn = {1664-302X}, abstract = {Oxalate serves various functions in the biological processes of plants, fungi, bacteria, and animals. It occurs naturally in the minerals weddellite and whewellite (calcium oxalates) or as oxalic acid. The environmental accumulation of oxalate is disproportionately low compared to the prevalence of highly productive oxalogens, namely plants. It is hypothesized that oxalotrophic microbes limit oxalate accumulation by degrading oxalate minerals to carbonates via an under-explored biogeochemical cycle known as the oxalate-carbonate pathway (OCP). Neither the diversity nor the ecology of oxalotrophic bacteria is fully understood. This research investigated the phylogenetic relationships of the bacterial genes oxc, frc, oxdC, and oxlT, which encode key enzymes for oxalotrophy, using bioinformatic approaches and publicly available omics datasets. Phylogenetic trees of oxc and oxdC genes demonstrated grouping by both source environment and taxonomy. All four trees included genes from metagenome-assembled genomes (MAGs) that contained novel lineages and environments for oxalotrophs. In particular, sequences of each gene were recovered from marine environments. These results were supported with marine transcriptome sequences and description of key amino acid residue conservation. Additionally, we investigated the theoretical energy yield from oxalotrophy across marine-relevant pressure and temperature conditions and found similar standard state Gibbs free energy to "low energy" marine sediment metabolisms, such as anaerobic oxidation of methane coupled to sulfate reduction. These findings suggest further need to understand the role of bacterial oxalotrophy in the OCP, particularly in marine environments, and its contribution to global carbon cycling.}, } @article {pmid37213501, year = {2023}, author = {Huang, Y and Jiang, P and Liang, Z and Chen, R and Yue, Z and Xie, X and Guan, C and Fang, X}, title = {Assembly and analytical validation of a metagenomic reference catalog of human gut microbiota based on co-barcoding sequencing.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1145315}, pmid = {37213501}, issn = {1664-302X}, abstract = {Human gut microbiota is associated with human health and disease, and is known to have the second-largest genome in the human body. The microbiota genome is important for their functions and metabolites; however, accurate genomic access to the microbiota of the human gut is hindered due to the difficulty of cultivating and the shortcomings of sequencing technology. Therefore, we applied the stLFR library construction method to assemble the microbiota genomes and demonstrated that assembly property outperformed standard metagenome sequencing. Using the assembled genomes as references, SNP, INDEL, and HGT gene analyses were performed. The results demonstrated significant differences in the number of SNPs and INDELs among different individuals. The individual displayed a unique species variation spectrum, and the similarity of strains within individuals decreased over time. In addition, the coverage depth analysis of the stLFR method shows that a sequencing depth of 60X is sufficient for SNP calling. HGT analysis revealed that the genes involved in replication, recombination and repair, mobilome prophages, and transposons were the most transferred genes among different bacterial species in individuals. A preliminary framework for human gut microbiome studies was established using the stLFR library construction method.}, } @article {pmid37213492, year = {2023}, author = {Zhang, X and Liang, Y and Zheng, K and Wang, Z and Dong, Y and Liu, Y and Ren, L and Wang, H and Han, Y and McMinn, A and Sung, YY and Mok, WJ and Wong, LL and He, J and Wang, M}, title = {Characterization and genomic analysis of phage vB_ValR_NF, representing a new viral family prevalent in the Ulva prolifera blooms.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1161265}, pmid = {37213492}, issn = {1664-302X}, abstract = {INTRODUCTION: Vibrio is an important bacterial genus containing many pathogenic species. Although more and more Vibrio phages were isolated, the genome, ecology and evolution of Vibrio phages and their roles in bacteriophage therapy, have not been fully revealed.

METHODS: Novel Vibrio phage vB_ValR_NF infecting Vibrio alginolyticus was isolated from the coastal waters of Qingdao during the Ulva prolifera blooms, Characterization and genomic feature of phage vB_ValR_NF has been analysed using phage isolation, sequencing and metagenome method.

RESULTS AND DISCUSSION: Phage vB_ValR_NF has a siphoviral morphology (icosahedral head 114±1 nm in diameter; a tail length of 231±1 nm), a short latent period (30 minutes) and a large burst size (113 virions per cell), and the thermal/pH stability study showed that phage vB_ValR_NF was highly tolerant to a range of pHs (4-12) and temperatures (-20 - 45 °C), respectively. Host range analysis suggests that phage vB_ValR_NF not only has a high inhibitory ability against the host strain V. alginolyticus, but also can infect 7 other Vibrio strains. In addition, the phage vB_ValR_NF has a double-stranded 44, 507 bp DNA genome, with 43.10 % GC content and 75 open reading frames. Three auxiliary metabolic genes associated with aldehyde dehydrogenase, serine/threonine protein phosphatase and calcineurin-like phosphoesterase were predicted, might help the host V. alginolyticus occupy the survival advantage, thus improving the survival chance of phage vB_ValR_NF under harsh conditions. This point can be supported by the higher abundance of phage vB_ValR_NF during the U. prolifera blooms than in other marine environments. Further phylogenetic and genomic analysis shows that the viral group represented by Vibrio phage vB_ValR_NF is different from other well-defined reference viruses, and can be classified into a new family, named Ruirongviridae. In general, as a new marine phage infecting V. alginolyticus, phage vB_ValR_NF provides basic information for further molecular research on phage-host interactions and evolution, and may unravel a novel insight into changes in the community structure of organisms during the U. prolifera blooms. At the same time, its high tolerance to extreme conditions and excellent bactericidal ability will become important reference factors when evaluating the potential of phage vB_ValR_NF in bacteriophage therapy in the future.}, } @article {pmid37213047, year = {2023}, author = {Chaudhari, DS and Jain, S and Yata, VK and Mishra, SP and Kumar, A and Fraser, A and Kociolek, J and Dangiolo, M and Smith, A and Golden, A and Masternak, MM and Holland, P and Agronin, M and White-Williams, C and Arikawa, AY and Labyak, CA and Yadav, H}, title = {Unique trans-kingdom microbiome structural and functional signatures predict cognitive decline in older adults.}, journal = {GeroScience}, volume = {45}, number = {5}, pages = {2819-2834}, pmid = {37213047}, issn = {2509-2723}, support = {RF1AG071762/AG/NIA NIH HHS/United States ; R56AG069676/AG/NIA NIH HHS/United States ; R21AG072379/AG/NIA NIH HHS/United States ; R56AG064075/AG/NIA NIH HHS/United States ; U01 AG076928/AG/NIA NIH HHS/United States ; U01AG076928/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Aged ; RNA, Ribosomal, 16S/genetics ; Pilot Projects ; *Microbiota/genetics ; *Cognitive Dysfunction ; Bacteria/genetics ; *Dementia ; }, abstract = {The prevalence of age-related cognitive disorders/dementia is increasing, and effective prevention and treatment interventions are lacking due to an incomplete understanding of aging neuropathophysiology. Emerging evidence suggests that abnormalities in gut microbiome are linked with age-related cognitive decline and getting acceptance as one of the pillars of the Geroscience hypothesis. However, the potential clinical importance of gut microbiome abnormalities in predicting the risk of cognitive decline in older adults is unclear. Till now the majority of clinical studies were done using 16S rRNA sequencing which only accounts for analyzing bacterial abundance, while lacking an understanding of other crucial microbial kingdoms, such as viruses, fungi, archaea, and the functional profiling of the microbiome community. Utilizing data and samples of older adults with mild cognitive impairment (MCI; n = 23) and cognitively healthy controls (n = 25). Our whole-genome metagenomic sequencing revealed that the gut of older adults with MCI harbors a less diverse microbiome with a specific increase in total viruses and a decrease in bacterial abundance compared with controls. The virome, bacteriome, and microbial metabolic signatures were significantly distinct in subjects with MCI versus controls. Selected bacteriome signatures show high predictive potential of cognitive dysfunction than virome signatures while combining virome and metabolic signatures with bacteriome boosts the prediction power. Altogether, the results from our pilot study indicate that trans-kingdom microbiome signatures are significantly distinct in MCI gut compared with controls and may have utility for predicting the risk of developing cognitive decline and dementia- debilitating public health problems in older adults.}, } @article {pmid37212592, year = {2023}, author = {Sisti, LS and Pena-Passos, M and Lishcka Sampaio Mayer, J}, title = {Isolation, Characterization, and Total DNA Extraction to Identify Endophytic Fungi in Mycoheterotrophic Plants.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {195}, pages = {}, doi = {10.3791/65135}, pmid = {37212592}, issn = {1940-087X}, mesh = {*Mycorrhizae ; Fungi/genetics ; Symbiosis ; Plant Roots/microbiology ; Plants/genetics ; DNA ; }, abstract = {Mycoheterotrophic plants present one of the most extreme forms of mycorrhizal dependency, having totally lost their autotrophic capacity. As essential as any other vital resource, the fungi with which these plants intimately associate are essential for them. Hence, some of the most relevant techniques in studying mycoheterotrophic species are the ones that enable the investigation of associated fungi, especially those inhabiting roots and subterranean organs. In this context, techniques for identifying culture-dependent and culture-independent endophytic fungi are commonly applied. Isolating fungal endophytes provides a means for morphologically identifying them, analyzing their diversity, and maintaining inocula for applications in the symbiotic germination of orchid seeds. However, it is known that there is a large variety of non-culturable fungi inhabiting plant tissues. Thus, culture-independent molecular identification techniques offer a broader cover of species diversity and abundance. This article aims to provide the methodological support necessary for starting two investigation procedures: a culture-dependent and an independent one. Regarding the culture-dependent protocol, the processes of collecting and maintaining plant samples from collection sites to laboratory facilities are detailed, along with isolating filamentous fungi from subterranean and aerial organs of mycoheterotrophic plants, keeping a collection of isolates, morphologically characterizing hyphae by slide culture methodology, and molecular identification of fungi by total DNA extraction. Encompassing culture-independent methodologies, the detailed procedures include collecting plant samples for metagenomic analyses and total DNA extraction from achlorophyllous plant organs using a commercial kit. Finally, continuity protocols (e.g., polymerase chain reaction [PCR], sequencing) are also suggested for analyses, and techniques are presented here.}, } @article {pmid37212321, year = {2023}, author = {Ogunbayo, AE and Mogotsi, MT and Sondlane, H and Sabiu, S and Nyaga, MM}, title = {Metagenomics characterization of respiratory viral RNA pathogens in children under five years with severe acute respiratory infection in the Free State, South Africa.}, journal = {Journal of medical virology}, volume = {95}, number = {5}, pages = {e28753}, doi = {10.1002/jmv.28753}, pmid = {37212321}, issn = {1096-9071}, mesh = {Humans ; Child ; Child, Preschool ; RNA, Viral/genetics ; South Africa ; *COVID-19 ; *Viruses/genetics ; *RNA Viruses/genetics ; *Bacterial Infections ; Bacteria/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; }, abstract = {Prompt detection of viral respiratory pathogens is crucial in managing respiratory infection including severe acute respiratory infection (SARI). Metagenomics next-generation sequencing (mNGS) and bioinformatics analyses remain reliable strategies for diagnostic and surveillance purposes. This study evaluated the diagnostic utility of mNGS using multiple analysis tools compared with multiplex real-time PCR for the detection of viral respiratory pathogens in children under 5 years with SARI. Nasopharyngeal swabs collected in viral transport media from 84 children admitted with SARI as per the World Health Organization definition between December 2020 and August 2021 in the Free State Province, South Africa, were used in this study. The obtained specimens were subjected to mNGS using the Illumina MiSeq system, and bioinformatics analysis was performed using three web-based analysis tools; Genome Detective, One Codex and Twist Respiratory Viral Research Panel. With average reads of 211323, mNGS detected viral pathogens in 82 (97.6%) of the 84 patients. Viral aetiologies were established in nine previously undetected/missed cases with an additional bacterial aetiology (Neisseria meningitidis) detected in one patient. Furthermore, mNGS enabled the much needed viral genotypic and subtype differentiation and provided significant information on bacterial co-infection despite enrichment for RNA viruses. Sequences of nonhuman viruses, bacteriophages, and endogenous retrovirus K113 (constituting the respiratory virome) were also uncovered. Notably, mNGS had lower detectability rate for severe acute respiratory syndrome coronavirus 2 (missing 18/32 cases). This study suggests that mNGS, combined with multiple/improved bioinformatics tools, is practically feasible for increased viral and bacterial pathogen detection in SARI, especially in cases where no aetiological agent could be identified by available traditional methods.}, } @article {pmid37212230, year = {2023}, author = {Zhao, Y and Wang, H and Wu, P and Li, Z and Liu, F and Gu, Q and Liu, W and Gao, J and Han, X}, title = {[Engineering the plastic degradation enzyme Ple629 from marine consortium to improve its thermal stability].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {39}, number = {5}, pages = {2040-2052}, doi = {10.13345/j.cjb.221045}, pmid = {37212230}, issn = {1872-2075}, mesh = {*Plastics/metabolism ; *Polyethylene Terephthalates/metabolism ; Biodegradation, Environmental ; Metagenome ; }, abstract = {Petrochemical-derived polyester plastics such as polyethylene terephthalate (PET) and polybutylene adipate terephthalate (PBAT) have been widely used. However, the difficulty to be degraded in nature (PET) or the long biodegradation cycle (PBAT) resulted in serious environmental pollution. In this connection, treating these plastic wastes properly becomes one of the challenges of environment protection. From the perspective of circular economy, biologically depolymerizing the waste of polyester plastics and reusing the depolymerized products is one of the most promising directions. Recent years have seen many reports on polyester plastics degrading organisms and enzymes. Highly efficient degrading enzymes, especially those with better thermal stability, will be conducive to their application. The mesophilic plastic-degrading enzyme Ple629 from the marine microbial metagenome is capable of degrading PET and PBAT at room temperature, but it cannot tolerate high temperature, which hampers its potential application. On the basis of the three-dimensional structure of Ple629 obtained from our previous study, we identified some sites which might be important for its thermal stability by structural comparison and mutation energy analysis. We carried out transformation design, and performed expression, purification and thermal stability determination of the mutants. The melting temperature (Tm) values of mutants V80C and D226C/S281C were increased by 5.2 ℃ and 6.9 ℃, respectively, and the activity of mutant D226C/S281C was also increased by 1.5 times compared with that of the wild-type enzyme. These results provide useful information for future engineering and application of Ple629 in polyester plastic degradation.}, } @article {pmid37212075, year = {2023}, author = {Brown, EL and Essigmann, HT and Hoffman, KL and Alexander, AS and Newmark, M and Jiang, ZD and Suescun, J and Schiess, MC and Hanis, CL and DuPont, HL}, title = {IgA-Biome Profiles Correlate with Clinical Parkinson's Disease Subtypes.}, journal = {Journal of Parkinson's disease}, volume = {13}, number = {4}, pages = {501-513}, pmid = {37212075}, issn = {1877-718X}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Parkinson Disease/complications ; Tremor/etiology ; *Gastrointestinal Microbiome/physiology ; Disease Progression ; Immunoglobulin A ; }, abstract = {BACKGROUND: Parkinson's disease is a heterogeneous neurodegenerative disorder with distinctive gut microbiome patterns suggesting that interventions targeting the gut microbiota may prevent, slow, or reverse disease progression and severity.

OBJECTIVE: Because secretory IgA (SIgA) plays a key role in shaping the gut microbiota, characterization of the IgA-Biome of individuals classified into either the akinetic rigid (AR) or tremor dominant (TD) Parkinson's disease clinical subtypes was used to further define taxa unique to these distinct clinical phenotypes.

METHODS: Flow cytometry was used to separate IgA-coated and -uncoated bacteria from stool samples obtained from AR and TD patients followed by amplification and sequencing of the V4 region of the 16 S rDNA gene on the MiSeq platform (Illumina).

RESULTS: IgA-Biome analyses identified significant alpha and beta diversity differences between the Parkinson's disease phenotypes and the Firmicutes/Bacteroides ratio was significantly higher in those with TD compared to those with AR. In addition, discriminant taxa analyses identified a more pro-inflammatory bacterial profile in the IgA+ fraction of those with the AR clinical subclass compared to IgA-Biome analyses of those with the TD subclass and with the taxa identified in the unsorted control samples.

CONCLUSION: IgA-Biome analyses underscores the importance of the host immune response in shaping the gut microbiome potentially affecting disease progression and presentation. In the present study, IgA-Biome analyses identified a unique proinflammatory microbial signature in the IgA+ fraction of those with AR that would have otherwise been undetected using conventional microbiome analysis approaches.}, } @article {pmid37211850, year = {2023}, author = {Matsushima, N and Batkhishig, D and Enkhbayar, P and Kretsinger, RH}, title = {A Dual Leucine-rich Repeat in Proteins from the Eukaryotic SAR Group.}, journal = {Protein and peptide letters}, volume = {30}, number = {7}, pages = {574-586}, doi = {10.2174/0929866530666230519160439}, pmid = {37211850}, issn = {1875-5305}, mesh = {Leucine/chemistry ; *Eukaryota ; Amino Acid Sequence ; *Proteins/genetics/chemistry ; Protein Domains ; }, abstract = {BACKGROUND: Leucine-rich repeats (LRRs) occurring in tandem are 20-29 amino acids long. Eleven LRR types have been recognized; they include plant-specific (PS) type with the consensus of LxxLxLxxNxL SGxIPxxIxxLxx of 24 residues and SDS22-like type with the consensus of LxxLxLxxNxL xxIxxIxxLxx of 22 residues.

OBJECTIVE: A viral LRR protein in metagenome data indicated that most of the LRRs (5/6 = 0.83) are represented by the consensus of LxxLDLxxTxV SGKLSDLxxLTN of 23 residues. This LRR shows a dual characteristic of PS and SDS22-like LRRs (called PS/SDS22-like LRR). A comprehensive similarity search was performed under the hypothesis that many proteins contain LRR domains consisting of only or mainly PS/SDS22-like LRR.

METHODS: Sequence similarity search by the FASTA and BLAST programs was performed using the sequence of this PS/SDS22-like LRR domain as a query sequence. The presence of PS/SDS22-like LRR was screened within the LRR domains in known structures.

RESULTS: Over 280 LRR proteins were identified from protists, fungi, and bacteria; ~ 40% come from the SAR group (the phyla Alveolate and Stramenopiles). The secondary structure analysis of PS/SDS22-like LRRs occurring sporadically in the known structures indicates three or four type patterns of secondary structures.

CONCLUSION: PS/SDS22-like LRR forms an LRR class with PS, SDS22-like and Leptospira-like LRRs. It appears that PS/SDS22-like LRR is a chameleon-like sequence. A duality of two LRR types brings diversity.}, } @article {pmid37211644, year = {2023}, author = {Urvois, T and Perrier, C and Roques, A and Sauné, L and Courtin, C and Kajimura, H and Hulcr, J and Cognato, AI and Auger-Rozenberg, MA and Kerdelhué, C}, title = {The worldwide invasion history of a pest ambrosia beetle inferred using population genomics.}, journal = {Molecular ecology}, volume = {32}, number = {15}, pages = {4381-4400}, doi = {10.1111/mec.16993}, pmid = {37211644}, issn = {1365-294X}, mesh = {Animals ; *Coleoptera/genetics ; *Weevils ; Ambrosia/genetics ; Metagenomics ; Europe ; Introduced Species ; }, abstract = {Xylosandrus crassiusculus, a fungus-farming wood borer native to Southeastern Asia, is the most rapidly spreading invasive ambrosia species worldwide. Previous studies focusing on its genetic structure suggested the existence of cryptic genetic variation in this species. Yet, these studies used different genetic markers, focused on different geographical areas and did not include Europe. Our first goal was to determine the worldwide genetic structure of this species based on both mitochondrial and genomic markers. Our second goal was to study X. crassiusculus' invasion history on a global level and identify the origins of the invasion in Europe. We used a COI and RAD sequencing design to characterize 188 and 206 specimens worldwide, building the most comprehensive genetic data set for any ambrosia beetle to date. The results were largely consistent between markers. Two differentiated genetic clusters were invasive, albeit in different regions of the world. The markers were inconsistent only for a few specimens found exclusively in Japan. Mainland USA could have acted as a source for further expansion to Canada and Argentina through stepping stone expansion and bridgehead events. We showed that Europe was only colonized by Cluster II through a complex invasion history including several arrivals from multiple origins in the native area, and possibly including bridgehead from the United States. Our results also suggested that Spain was colonized directly from Italy through intracontinental dispersion. It is unclear whether the mutually exclusive allopatric distribution of the two clusters is due to neutral effects or due to different ecological requirements.}, } @article {pmid37211607, year = {2023}, author = {Liu, Y and Wang, H and Qian, X and Gu, J and Chen, W and Shen, X and Tao, S and Jiao, S and Wei, G}, title = {Metagenomics insights into responses of rhizobacteria and their alleviation role in licorice allelopathy.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {109}, pmid = {37211607}, issn = {2049-2618}, mesh = {*Glycyrrhiza/chemistry ; Allelopathy ; Glycyrrhizic Acid ; Metagenomics ; Rhizosphere ; }, abstract = {BACKGROUND: Allelopathy is closely associated with rhizosphere biological processes, and rhizosphere microbial communities are essential for plant development. However, our understanding of rhizobacterial communities under influence of allelochemicals in licorice remains limited. In the present study, the responses and effects of rhizobacterial communities on licorice allelopathy were investigated using a combination of multi-omics sequencing and pot experiments, under allelochemical addition and rhizobacterial inoculation treatments.

RESULTS: Here, we demonstrated that exogenous glycyrrhizin inhibits licorice development, and reshapes and enriches specific rhizobacteria and corresponding functions related to glycyrrhizin degradation. Moreover, the Novosphingobium genus accounted for a relatively high proportion of the enriched taxa and appeared in metagenomic assembly genomes. We further characterized the different capacities of single and synthetic inoculants to degrade glycyrrhizin and elucidated their distinct potency for alleviating licorice allelopathy. Notably, the single replenished N (Novosphingobium resinovorum) inoculant had the greatest allelopathy alleviation effects in licorice seedlings.

CONCLUSIONS: Altogether, the findings highlight that exogenous glycyrrhizin simulates the allelopathic autotoxicity effects of licorice, and indigenous single rhizobacteria had greater effects than synthetic inoculants in protecting licorice growth from allelopathy. The results of the present study enhance our understanding of rhizobacterial community dynamics during licorice allelopathy, with potential implications for resolving continuous cropping obstacle in medicinal plant agriculture using rhizobacterial biofertilizers. Video Abstract.}, } @article {pmid37211250, year = {2023}, author = {Ridlon, JM and Daniel, SL and Gaskins, HR}, title = {The Hylemon-Björkhem pathway of bile acid 7-dehydroxylation: history, biochemistry, and microbiology.}, journal = {Journal of lipid research}, volume = {64}, number = {8}, pages = {100392}, pmid = {37211250}, issn = {1539-7262}, support = {R01 CA204808/CA/NCI NIH HHS/United States ; R01 GM134423/GM/NIGMS NIH HHS/United States ; R01 GM145920/GM/NIGMS NIH HHS/United States ; R03 AI147127/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Bile Acids and Salts/metabolism ; *Clostridium ; Feces ; }, abstract = {Bile acids are detergents derived from cholesterol that function to solubilize dietary lipids, remove cholesterol from the body, and act as nutrient signaling molecules in numerous tissues with functions in the liver and gut being the best understood. Studies in the early 20th century established the structures of bile acids, and by mid-century, the application of gnotobiology to bile acids allowed differentiation of host-derived "primary" bile acids from "secondary" bile acids generated by host-associated microbiota. In 1960, radiolabeling studies in rodent models led to determination of the stereochemistry of the bile acid 7-dehydration reaction. A two-step mechanism was proposed, which we have termed the Samuelsson-Bergström model, to explain the formation of deoxycholic acid. Subsequent studies with humans, rodents, and cell extracts of Clostridium scindens VPI 12708 led to the realization that bile acid 7-dehydroxylation is a result of a multi-step, bifurcating pathway that we have named the Hylemon-Björkhem pathway. Due to the importance of hydrophobic secondary bile acids and the increasing measurement of microbial bai genes encoding the enzymes that produce them in stool metagenome studies, it is important to understand their origin.}, } @article {pmid37211189, year = {2023}, author = {Qin, J and Luo, Z and Wang, Q and Tang, C and Meng, M and Huang, Z and Guo, B and He, Y and Feng, L and Nong, Y and Deng, L and Zhu, D and Guo, H and Liang, Y and Su, Z}, title = {Integrating metabonomics and metagenomics sequencing to study the anti-liver fibrosis effects of palmatine in Corydalis saxicola Bunting.}, journal = {Journal of ethnopharmacology}, volume = {315}, number = {}, pages = {116666}, doi = {10.1016/j.jep.2023.116666}, pmid = {37211189}, issn = {1872-7573}, mesh = {*Corydalis/chemistry ; Metagenomics ; Metabolomics/methods ; Liver Cirrhosis/drug therapy ; Inflammation ; }, abstract = {Corydalis saxicola Bunting (CS), a traditional Chinese folk medicine, has been effectively used for treating liver disease in Zhuang nationality in South China. However, the main anti-liver fibrosis ingredients in CS are incompletely understood.

AIM OF THE STUDY: To elucidate the main anti-liver fibrosis ingredients in CS and its underlying mechanism.

MATERIAL AND METHODS: Firstly, spectrum-effect relationship (SER) strategy was applied to identify the major ingredients against liver fibrosis in CS. Subsequently, [1]H NMR metabonomics and metagenomics sequencing techniques were used to clarify the intervention of palmatine (PAL) on liver fibrosis. Furthermore, the expression of tight junction proteins and the levels of liver inflammation factors were examined, the effect of PAL on microbiota was verified by FMT.

RESULTS: The SER model revealed that PAL was the most important active ingredient in CS. [1]H NMR fecal metabonomics showed that PAL could reserve the abnormal levels of gut microbial-mediated metabolites of liver fibrosis, such as isoleucine, taurine, butyrate, propionate, lactate, glucose, which mainly involved in amino acid metabolism, intestinal flora metabolism and energy metabolism. Metagenomics sequencing found that PAL could callback the abundance of s__Lactobacillus_murinus, s__Lactobacillus_reuteri, s__Lactobacillus_johnsonii, s__Lactobacillus_acidophilus and s__Faecalibaculum_rodentium to varying degree. Furthermore, the intestinal barrier function and the levels of hepatic inflammation factors were significantly ameliorated by PAL. FMT demonstrated that the therapeutic efficiency of PAL was closely associated with gut microbiota.

CONCLUSION: The effects of CS on liver fibrosis were attributed in part to PAL by alleviating metabolic disorders and rebalancing gut microbiota. The SER strategy may be a useful method for the discovery of active constituents in natural plants.}, } @article {pmid37211102, year = {2023}, author = {Fan, Y and Li, Z and Li, B and Ke, B and Zhao, W and Lu, P and Li, Z and Zhang, T and Lu, X and Kan, B}, title = {Metagenomic profiles of planktonic bacteria and resistome along a salinity gradient in the Pearl River Estuary, South China.}, journal = {The Science of the total environment}, volume = {889}, number = {}, pages = {164265}, doi = {10.1016/j.scitotenv.2023.164265}, pmid = {37211102}, issn = {1879-1026}, mesh = {*Estuaries ; *Genes, Bacterial ; Ecosystem ; Salinity ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; China ; }, abstract = {Estuarine ecosystems undergo pronounced and intricate changes due to the mixing of freshwater and saltwater. Additionally, urbanization and population growth in estuarine regions result in shifts in the planktonic bacterial community and the accumulation of antibiotic resistance genes (ARGs). The dynamic changes in bacterial communities, environmental factors, and carriage of ARGs from freshwater to seawater, as well as the complex interrelationships among these factors, have yet to be fully elucidated. Here, we conducted a comprehensive study based on metagenomic sequencing and full-length 16S rRNA sequencing, covering the entire Pearl River Estuary (PRE) in Guangdong, China. The abundance and distribution of the bacterial community, ARGs, mobile genetic elements (MGEs), and bacterial virulence factors (VFs) were analyzed on a site-by-site basis through sampling along the salinity gradient in PRE, from upstream to downstream. The structure of the planktonic bacterial community undergoes continuous changes in response to variations in estuarine salinity, with the phyla Proteobacteria and Cyanobacteria being dominant bacterial throughout the entire region. The diversity and abundance of ARGs and MGEs gradually decreased with the direction of water flow. A large number of ARGs were carried by potentially pathogenic bacteria, especially in Alpha-proteobacteria and Beta-proteobacteria. Multi-drug resistance genes have the highest abundance and subtypes in PRE. In addition, ARGs are more linked to some MGEs than to specific bacterial taxa and disseminate mainly by HGT and not by vertical transfer in the bacterial communities. Various environmental factors, such as salinity and nutrient concentrations, have a significantly impact on the community structure and distribution of bacteria. In conclusion, our results represent a valuable resource for further investigating the intricate interplay between environmental factors and anthropogenic disturbances on bacterial community dynamics. Moreover, they contribute to a better understanding of the relative impact of these factors on the dissemination of ARGs.}, } @article {pmid37210808, year = {2023}, author = {Lamichhane, S and Härkönen, T and Vatanen, T and Hyötyläinen, T and Knip, M and Orešič, M}, title = {Impact of exposure to per- and polyfluoroalkyl substances on fecal microbiota composition in mother-infant dyads.}, journal = {Environment international}, volume = {176}, number = {}, pages = {107965}, doi = {10.1016/j.envint.2023.107965}, pmid = {37210808}, issn = {1873-6750}, support = {DP3 DK094338/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Female ; Humans ; Infant ; Mothers ; *Microbiota ; Maternal Exposure ; Bacteria/genetics ; *Fluorocarbons/toxicity ; *Environmental Pollutants ; *Alkanesulfonic Acids ; }, abstract = {There is growing evidence suggesting that chemical exposure alters gut microbiota composition. However, not much is known about the impact of per- and polyfluoroalkyl substances (PFAS) on the gut microbial community. Here, in a mother-infant study, we set out to identify the gut bacterial species that associate with chemical exposure before (maternal) and after (maternal, infant) birth. Paired serum and stool samples were collected from mother-infant dyads (n = 30) in a longitudinal setting. PFAS were quantified in maternal serum to examine their associations with the microbial compositions (determined by shotgun metagenomic sequencing) in mothers and infants. High maternal exposure to PFAS was consistently associated with increased abundance of Methanobrevibacter smithii in maternal stool. Among individual PFAS compounds, PFOS and PFHpS showed the strongest association with M. smithii. However, maternal total PFAS exposure associated only weakly with the infant microbiome. Our findings suggest that PFAS exposure affects the composition of the adult gut microbiome.}, } @article {pmid37210545, year = {2023}, author = {Du, R and Xiong, W and Xu, L and Xu, Y and Wu, Q}, title = {Metagenomics reveals the habitat specificity of biosynthetic potential of secondary metabolites in global food fermentations.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {115}, pmid = {37210545}, issn = {2049-2618}, mesh = {Humans ; *Metagenomics ; Fermentation ; *Metagenome ; Genome, Bacterial/genetics ; Secondary Metabolism/genetics ; }, abstract = {BACKGROUND: Fermented foods are considered to be beneficial for human health. Secondary metabolites determined by biosynthetic gene clusters (BGCs) are precious bioactive compounds with various biological activities. However, the diversity and distribution of the biosynthetic potential of secondary metabolites in global food fermentations remain largely unknown. In this study, we performed a large-scale and comprehensive investigation for the BGCs in global food fermentations by metagenomics analysis.

RESULTS: We recovered 653 bacterial metagenome-assembled genomes (MAGs) from 367 metagenomic sequencing datasets covering 15 general food fermentation types worldwide. In total, 2334 secondary metabolite BGCs, including 1003 novel BGCs, were identified in these MAGs. Bacillaceae, Streptococcaceae, Streptomycetaceae, Brevibacteriaceae and Lactobacillaceae contained high abundances of novel BGCs (≥ 60 novel BGCs). Among 2334 BGCs, 1655 were habitat-specific, originating from habitat-specific species (80.54%) and habitat-specific genotypes within multi-habitat species (19.46%) in different food fermentation types. Biological activity analysis suggested that 183 BGC-producing secondary metabolites exhibited high probabilities of antibacterial activity (> 80%). These 183 BGCs were distributed across all 15 food fermentation types, and cheese fermentation contained the most BGC number.

CONCLUSIONS: This study demonstrates that food fermentation systems are an untapped reservoir of BGCs and bioactive secondary metabolites, and it provides novel insights into the potential human health benefits of fermented foods. Video Abstract.}, } @article {pmid37210515, year = {2023}, author = {Leleiwi, I and Rodriguez-Ramos, J and Shaffer, M and Sabag-Daigle, A and Kokkinias, K and Flynn, RM and Daly, RA and Kop, LFM and Solden, LM and Ahmer, BMM and Borton, MA and Wrighton, KC}, title = {Exposing new taxonomic variation with inflammation - a murine model-specific genome database for gut microbiome researchers.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {114}, pmid = {37210515}, issn = {2049-2618}, support = {R01 AI143288/AI/NIAID NIH HHS/United States ; T32 GM132057/GM/NIGMS NIH HHS/United States ; R01AI143288/NH/NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; Disease Models, Animal ; Mice, Inbred CBA ; *Microbiota ; Inflammation ; Bacteroidetes ; }, abstract = {BACKGROUND: The murine CBA/J mouse model widely supports immunology and enteric pathogen research. This model has illuminated Salmonella interactions with the gut microbiome since pathogen proliferation does not require disruptive pretreatment of the native microbiota, nor does it become systemic, thereby representing an analog to gastroenteritis disease progression in humans. Despite the value to broad research communities, microbiota in CBA/J mice are not represented in current murine microbiome genome catalogs.

RESULTS: Here we present the first microbial and viral genomic catalog of the CBA/J murine gut microbiome. Using fecal microbial communities from untreated and Salmonella-infected, highly inflamed mice, we performed genomic reconstruction to determine the impacts on gut microbiome membership and functional potential. From high depth whole community sequencing (~ 42.4 Gbps/sample), we reconstructed 2281 bacterial and 4516 viral draft genomes. Salmonella challenge significantly altered gut membership in CBA/J mice, revealing 30 genera and 98 species that were conditionally rare and unsampled in non-inflamed mice. Additionally, inflamed communities were depleted in microbial genes that modulate host anti-inflammatory pathways and enriched in genes for respiratory energy generation. Our findings suggest decreases in butyrate concentrations during Salmonella infection corresponded to reductions in the relative abundance in members of the Alistipes. Strain-level comparison of CBA/J microbial genomes to prominent murine gut microbiome databases identified newly sampled lineages in this resource, while comparisons to human gut microbiomes extended the host relevance of dominant CBA/J inflammation-resistant strains.

CONCLUSIONS: This CBA/J microbiome database provides the first genomic sampling of relevant, uncultivated microorganisms within the gut from this widely used laboratory model. Using this resource, we curated a functional, strain-resolved view on how Salmonella remodels intact murine gut communities, advancing pathobiome understanding beyond inferences from prior amplicon-based approaches. Salmonella-induced inflammation suppressed Alistipes and other dominant members, while rarer commensals like Lactobacillus and Enterococcus endure. The rare and novel species sampled across this inflammation gradient advance the utility of this microbiome resource to benefit the broad research needs of the CBA/J scientific community, and those using murine models for understanding the impact of inflammation on the gut microbiome more generally. Video Abstract.}, } @article {pmid37210404, year = {2023}, author = {Zvi-Kedem, T and Vintila, S and Kleiner, M and Tchernov, D and Rubin-Blum, M}, title = {Metabolic handoffs between multiple symbionts may benefit the deep-sea bathymodioline mussels.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {48}, pmid = {37210404}, issn = {2730-6151}, support = {913/19//Israel Science Foundation (ISF)/ ; 2019055//United States - Israel Binational Science Foundation (BSF)/ ; 2019055//United States - Israel Binational Science Foundation (BSF)/ ; 2003107//NSF | BIO | Division of Integrative Organismal Systems (IOS)/ ; }, abstract = {Bathymodioline mussels rely on thiotrophic and/or methanotrophic chemosynthetic symbionts for nutrition, yet, secondary heterotrophic symbionts are often present and play an unknown role in the fitness of the organism. The bathymodioline Idas mussels that thrive in gas seeps and on sunken wood in the Mediterranean Sea and the Atlantic Ocean, host at least six symbiont lineages that often co-occur. These lineages include the primary symbionts chemosynthetic methane- and sulfur-oxidizing gammaproteobacteria, and the secondary symbionts, Methylophagaceae, Nitrincolaceae and Flavobacteriaceae, whose physiology and metabolism are obscure. Little is known about if and how these symbionts interact or exchange metabolites. Here we curated metagenome-assembled genomes of Idas modiolaeformis symbionts and used genome-centered metatranscriptomics and metaproteomics to assess key symbiont functions. The Methylophagaceae symbiont is a methylotrophic autotroph, as it encoded and expressed the ribulose monophosphate and Calvin-Benson-Bassham cycle enzymes, particularly RuBisCO. The Nitrincolaceae ASP10-02a symbiont likely fuels its metabolism with nitrogen-rich macromolecules and may provide the holobiont with vitamin B12. The Urechidicola (Flavobacteriaceae) symbionts likely degrade glycans and may remove NO. Our findings indicate that these flexible associations allow for expanding the range of substrates and environmental niches, via new metabolic functions and handoffs.}, } @article {pmid37209986, year = {2023}, author = {Zhang, M and Tang, H and Chen, Y and Chen, Z and Xu, Y and Fu, X and Sun, Y and Zhao, Z}, title = {Impact of environmental characteristics on children's gut microbiota - A pilot study in assessing the role of indoor microbiome and metabolites.}, journal = {Environmental research}, volume = {234}, number = {}, pages = {116114}, doi = {10.1016/j.envres.2023.116114}, pmid = {37209986}, issn = {1096-0953}, mesh = {Humans ; Child ; *Gastrointestinal Microbiome/physiology ; Pilot Projects ; Tryptophan/metabolism ; China ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Indoles ; }, abstract = {BACKGROUND: A diverse and balanced human gut microbiota is crucial for maintaining normal human physiological functions. However, the impact of indoor microbiome and metabolites on gut microbiota is not well understood.

METHODS: A self-administered questionnaire was used to collect information on more than 40 personal and environmental characteristics and dietary habits from 56 children in Shanghai, China. Shotgun metagenomics and untargeted liquid chromatography-mass spectrometry (LC-MS) were used to characterize the indoor microbiome and metabolomic/chemical exposure in children's living rooms. PacBio full-length 16 S rRNA sequencing was used to characterize children's gut microbiota. Associations between environmental characteristics and gut microbiota diversity/composition were assessed using PERMANOVA and regression.

RESULTS: In total, 6247 and 318 indoor and gut microbial species and 1442 indoor metabolites were characterized. Age of children (R[2] = 0.033, p = 0.008), age start kindergarten (R[2] = 0.029, p = 0.03), living adjacent to heavy traffic (R[2] = 0.031, p = 0.01) and drinking soft drinks (R[2] = 0.028, p = 0.04) significantly impacted overall gut microbial composition, consistent with previous studies. Having pets/plants and frequent vegetable intake were positively associated with gut microbiota diversity and the Gut Microbiome Health Index (GMHI), while frequent juice and fries intake decreased gut microbiota diversity (p < 0.05). The abundance of indoor Clostridia and Bacilli was positively associated with gut microbial diversity and GMHI (p < 0.01). Total indoor indole derivatives and 6 indole metabolites (L-tryptophan, indole, 3-methylindole, indole-3-acetate, 5-hydroxy-L-tryptophan and indolelactic acid, p < 0.05) were positively associated with the abundance of total protective gut bacteria, suggesting a potential role in promoting gut health. Neural network analysis revealed that these indole derivatives were derived from indoor microorganisms.

CONCLUSIONS: The study is the first to report associations between indoor microbiome/metabolites and gut microbiota, highlighting the potential role of indoor microbiome in shaping human gut microbiota.}, } @article {pmid37209898, year = {2023}, author = {Qi, Z and Jin, S and Guo, X and Tong, H and Ren, N and You, S}, title = {Distribution and transmission of β-lactamase resistance genes in meal-to-milk chain on dairy farm.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {331}, number = {Pt 2}, pages = {121831}, doi = {10.1016/j.envpol.2023.121831}, pmid = {37209898}, issn = {1873-6424}, mesh = {Animals ; Humans ; *Genes, Bacterial ; Farms ; *Milk/chemistry ; Manure/analysis ; beta-Lactam Resistance ; Anti-Bacterial Agents/analysis ; }, abstract = {Antibiotics have been widely used in animal husbandry, which leads to high risk of food-borne transfer of antibiotic resistance genes (ARGs). The present study investigated the distribution of β-lactamase resistance genes (β-RGs) on dairy farm in the Songnen Plain of western Heilongjiang Province, China, to provide mechanistic insights into food-borne transmission of β-RGs through "meal-to-milk" chain under practically relevant circumstances. The results demonstrated that the abundance of β-RGs (91%) was much higher than that of other ARGs in the livestock farms. The blaTEM exhibited the content as high as 94.55% among all ARGs, and higher than 98% blaTEM was detected in meal, water and milk sample. The metagenomic taxonomy analysis indicated that the blaTEM should be carried by tnpA-04 (7.04%) and tnpA-03 (1.48%) hosted in Pseudomonas genus (15.36%) and Pantoea (29.02%) genus. Both tnpA-04 and tnpA-03 in the milk sample were identified to be the key mobile genetic elements (MGEs) responsible for transferring blaTEM along the "meal-manure-soil-surface water-milk" chain. The ARGs transfer across ecological boundaries underscored the need to evaluate potential dissemination of high-risk Proteobacteria and Bacteroidetes carried by humans and animals. They were capable of producing expanded-spectrum β-lactamases (ESBLs) and destroying commonly used antibiotics, leading to possible risk of food-borne horizontal transmission of ARGs. This study not only has important environmental implications for identifying the pathway for ARGs transfer, but also highlights the demand for appropriate policy toward safe regulation of dairy farm and husbandry products.}, } @article {pmid37209750, year = {2023}, author = {Dinesh, R and Sreena, CP and Sheeja, TE and Kumar, IPV and Praveena, R and Charles, S and Srinivasan, V and Jayarajan, K and Sajith, V and Subila, KP and Haritha, P}, title = {Soil polluted with nano ZnO reveals unstable bacterial communities and decoupling of taxonomic and functional diversities.}, journal = {The Science of the total environment}, volume = {889}, number = {}, pages = {164285}, doi = {10.1016/j.scitotenv.2023.164285}, pmid = {37209750}, issn = {1879-1026}, mesh = {*Soil/chemistry ; *Zinc Oxide/toxicity ; Bacteria ; Acidobacteria ; Firmicutes ; Soil Microbiology ; }, abstract = {Due to relentless production and disposal of nano zinc oxide (nZnO), it has become critical to comprehend the serious risks large-scale accumulation of nZnO pose to bacterial communities in soil. The primary objective was to evaluate the changes in bacterial community structure and associated functional pathways through predictive metagenomic profiling and subsequent validation through Quantitative Realtime PCR in soil spiked with nZnO (0, 50, 200, 500 and 1000 mg Zn kg[-1]) and similar levels of bulk ZnO (bZnO). The results revealed that soil microbial biomass-C, -N, -P, soil respiration and enzyme activities decreased markedly at higher ZnO levels. The alpha diversity decreased with increasing ZnO level, with more impact under nZnO, while beta diversity analyses indicated a distinct dose- dependent separation of bacterial communities. The dominant taxa including Proteobacteria, Bacterioidetes, Acidobacteria and Planctomycetes significantly increased in abundance, while Firmicutes, Actinobacteria and Chloroflexi decreased in abundance with elevated nZnO and bZnO levels. Redundancy analysis indicated that changes in bacterial community structure instilled a greater dose- rather than size- specific response on key microbial parameters. Predicted key functions did not show a dose- specific response, and at 1000 mg Zn kg[-1], methane metabolism as well as starch and sucrose metabolism were attenuated, while functions involving two component systems and bacterial secretion systems were enhanced under bZnO indicating better stress avoidance mechanism than under nZnO. Realtime PCR and microbial endpoint assays confirmed the metagenome derived taxonomic and functional data, respectively. Taxa and functions that varied substantially under stress were established as bioindicators to predict nZnO toxicity in soils. Taxon-function decoupling indicated that the soil bacterial communities deployed adaptive mechanisms under high ZnO, with lesser buffering capacity and resilience of communities under nZnO.}, } @article {pmid37209654, year = {2023}, author = {Xiong, X and Xu, J and Yan, X and Wu, S and Ma, J and Wang, Z and He, Q and Gong, J and Rao, Y}, title = {Gut microbiome and serum metabolome analyses identify biomarkers associated with sexual maturity in quails.}, journal = {Poultry science}, volume = {102}, number = {7}, pages = {102762}, pmid = {37209654}, issn = {1525-3171}, mesh = {Animals ; *Gastrointestinal Microbiome ; Chickens ; Metabolome ; Metagenome ; Bacteria ; Biomarkers ; }, abstract = {Increasing evidence indicates that the gut microbiome plays an important role in host aging and sexual maturity. However, the gut microbial taxa associated with sexual maturity in quails are unknown. This study used shotgun metagenomic sequencing to identify bacterial taxa associated with sexual maturity in d 20 and d 70 quails. We found that 17 bacterial species and 67 metagenome-assembled genomes (e.g., Bacteroides spp. and Enterococcus spp.) significantly differed between the d 20 and d 70 groups, including 5 bacterial species (e.g., Enterococcus faecalis) enriched in the d 20 group and 12 bacterial species (e.g., Christensenella massiliensis, Clostridium sp. CAG:217, and Bacteroides neonati) which had high abundances in the d 70 group. The bacterial species enriched in d 20 or d 70 were key biomarkers distinguishing sexual maturity and significantly correlated with the shifts in the functional capacities of the gut microbiome. Untargeted serum metabolome analysis revealed that 5 metabolites (e.g., nicotinamide riboside) were enriched in the d 20 group, and 6 metabolites (e.g., D-ribose, stevioside, and barbituric acid) were enriched in the d 70 group. Furthermore, metabolites with high abundances in the d 20 group were significantly enriched for the KEGG pathways of arginine biosynthesis, nicotinate and nicotinamide metabolism, and lysine degradation. However, glutathione metabolism and valine, leucine and isoleucine biosynthesis were enriched in high-abundance metabolites from the d 70 group. These results provide important insights into the effects of gut microbiome and host metabolism on quail sexual maturity.}, } @article {pmid37209219, year = {2023}, author = {Ma, W and Yu, J and Yang, F and Zhang, X and Zhang, F and Jin, W and Sun, Z and Zhao, Z and Jia, S and Zhong, C and Xue, J}, title = {Metagenomic analysis of the relationship between the microorganisms and the volatiles' development in the wines during spontaneous fermentation from the eastern foothills of the Ningxia Helan mountains in China.}, journal = {Journal of the science of food and agriculture}, volume = {103}, number = {13}, pages = {6429-6439}, doi = {10.1002/jsfa.12718}, pmid = {37209219}, issn = {1097-0010}, support = {2022A02002-2//the Xinjiang Autonomous Region Key Project of Science and Technology/ ; 2019YFD1002500//the National Key Research and Development Project/ ; }, abstract = {BACKGROUND: The natural fermentation of multispecies microbial communities is responsible for unique flavors of winery regions of the eastern foothills of the Ningxia Helan Mountains in China. However, the participation of different microorganisms in the metabolic network for the development of important flavor substances is not clearly defined. Microbial population and diversity on different fermentation phases of Ningxia wine were analyzed by metagenomic sequencing approach.

RESULTS: Gas chromatography-mass spectrometry and ion chromatography were used to identify flavor components, and 13 esters, 13 alcohols, nine aldehydes and seven ketones were detected in volatile substances with odor activity values > 1, and eight organic acids were detected as important flavor components in young wine. Thus, 52 238 predicted protein-coding genes from 24 genera were identified in the Kyoto Encyclopedia of Genes and Genomes level 2 pathways of global and overview maps, and the genes were primarily involved in amino acid metabolism and carbohydrate metabolism. Major microbial genera (Saccharomyces, Tatumella, Hanseniaspora, Lactobacillus, and Lachancea) were closely related to self-characteristic compound metabolism and further contributed to wine flavor.

CONCLUSION: This study clarifies the different metabolic roles of microorganisms in flavor formation during Ningxia wine spontaneous fermentation. Saccharomyces, dominant fungi involved in glycolysis and pyruvate metabolism, produces not only ethanol but also two important precursors, pyruvate and acetyl-CoA, which are necessary for the tricarboxylic acid cycle, fatty acid metabolism, amino acid metabolism, and flavor formation. Lactobacillus and Lachancea, dominant bacteria involved in lactic acid metabolism. Tatumella, dominant bacteria involved in amino acid metabolism, fatty acid metabolism, and acetic acid metabolism to produce esters in the Shizuishan City region samples. These findings provide insights into the use of local functional strains to generate unique flavor formation, as well as improved stability and quality, in wine production. © 2023 Society of Chemical Industry.}, } @article {pmid37208728, year = {2023}, author = {Yu, J and Meng, J and Qin, Z and Yu, Y and Liang, Y and Wang, Y and Min, D}, title = {Dysbiosis of gut microbiota inhibits NMNAT2 to promote neurobehavioral deficits and oxidative stress response in the 6-OHDA-lesioned rat model of Parkinson's disease.}, journal = {Journal of neuroinflammation}, volume = {20}, number = {1}, pages = {117}, pmid = {37208728}, issn = {1742-2094}, support = {NO. 2020-274//Scientific Research Project of Heilongjiang Provincial Health Commission/ ; GXZYB20220437//Project of Guangxi Zhuang Autonomous Region Administration of Traditional Chinese Medicine/ ; }, mesh = {Animals ; Rats ; Dysbiosis/metabolism ; *Gastrointestinal Microbiome/physiology ; NAD ; Oxidative Stress ; Oxidopamine/toxicity ; *Parkinson Disease/metabolism ; *Nicotinamide-Nucleotide Adenylyltransferase/metabolism ; }, abstract = {BACKGROUND: New data are accumulating on gut microbial dysbiosis in Parkinson's disease (PD), while the specific mechanism remains uncharacterized. This study aims to investigate the potential role and pathophysiological mechanism of dysbiosis of gut microbiota in 6-hydroxydopamine (6-OHDA)-induced PD rat models.

METHODS: The shotgun metagenome sequencing data of fecal samples from PD patients and healthy individuals were obtained from the Sequence Read Archive (SRA) database. The diversity, abundance, and functional composition of gut microbiota were further analyzed in these data. After the exploration of the functional pathway-related genes, KEGG and GEO databases were used to obtain PD-related microarray datasets for differential expression analysis. Finally, in vivo experiments were performed to confirm the roles of fecal microbiota transplantation (FMT) and upregulated NMNAT2 in neurobehavioral symptoms and oxidative stress response in 6-OHDA-lesioned rats.

RESULTS: Significant differences were found in the diversity, abundance, and functional composition of gut microbiota between PD patients and healthy individuals. Dysbiosis of gut microbiota could regulate NAD[+] anabolic pathway to affect the occurrence and development of PD. As a NAD[+] anabolic pathway-related gene, NMNAT2 was poorly expressed in the brain tissues of PD patients. More importantly, FMT or overexpression of NMNAT2 alleviated neurobehavioral deficits and reduced oxidative stress in 6-OHDA-lesioned rats.

CONCLUSIONS: Taken together, we demonstrated that dysbiosis of gut microbiota suppressed NMNAT2 expression, thus exacerbating neurobehavioral deficits and oxidative stress response in 6-OHDA-lesioned rats, which could be rescued by FMT or NMNAT2 restoration.}, } @article {pmid37208617, year = {2023}, author = {Liao, F and Qian, J and Yang, R and Gu, W and Li, R and Yang, T and Fu, X and Yuan, B and Zhang, Y}, title = {Metagenomics of gut microbiome for migratory seagulls in Kunming city revealed the potential public risk to human health.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {269}, pmid = {37208617}, issn = {1471-2164}, mesh = {Animals ; Humans ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Viruses/genetics ; Bacteria/genetics ; DNA ; }, abstract = {BACKGROUND: Seagull as a migratory wild bird has become most popular species in southwest China since 1980s. Previously, we analyzed the gut microbiota and intestinal pathogenic bacteria configuration for this species by using 16S rRNA sequencing and culture methods. To continue in-depth research on the gut microbiome of migratory seagulls, the metagenomics, DNA virome and RNA virome were both investigated for their gut microbial communities of abundance and diversity in this study.

RESULTS: The metagenomics results showed 99.72% of total species was bacteria, followed by viruses, fungi, archaea and eukaryota. In particular, Shigella sonnei, Escherichia albertii, Klebsiella pneumonia, Salmonella enterica and Shigella flexneri were the top distributed taxa at species level. PCoA, NMDS, and statistics indicated some drug resistant genes, such as adeL, evgS, tetA, PmrF, and evgA accumulated as time went by from November to January of the next year, and most of these genes were antibiotic efflux. DNA virome composition demonstrated that Caudovirales was the most abundance virus, followed by Cirlivirales, Geplafuvirales, Petitvirales and Piccovirales. Most of these phages corresponded to Enterobacteriaceae and Campylobacteriaceae bacterial hosts respectively. Caliciviridae, Coronaviridae and Picornaviridae were the top distributed RNA virome at family level of this migratory animal. Phylogenetic analysis indicated the sequences of contigs of Gammacoronavirus and Deltacoronavirus had highly similarity with some coronavirus references.

CONCLUSIONS: In general, the characteristics of gut microbiome of migratory seagulls were closely related to human activities, and multiomics still revealed the potential public risk to human health.}, } @article {pmid37208450, year = {2023}, author = {Mo, S and Yan, B and Gao, T and Li, J and Kashif, M and Song, J and Bai, L and Yu, D and Liao, J and Jiang, C}, title = {Sulfur metabolism in subtropical marine mangrove sediments fundamentally differs from other habitats as revealed by SMDB.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {8126}, pmid = {37208450}, issn = {2045-2322}, mesh = {*Microbiota ; Geologic Sediments ; Bacteria ; Archaea/genetics ; Sulfur/metabolism ; Phylogeny ; }, abstract = {Shotgun metagenome sequencing provides the opportunity to recover underexplored rare populations and identify difficult-to-elucidate biochemical pathways. However, information on sulfur genes, including their sequences, is scattered in public databases. Here, we introduce SMDB (https://smdb.gxu.edu.cn/)-a manually curated database of sulfur genes based on an in-depth review of the scientific literature and orthology database. The SMDB contained a total of 175 genes and covered 11 sulfur metabolism processes with 395,737 representative sequences affiliated with 110 phyla and 2340 genera of bacteria/archaea. The SMDB was applied to characterize the sulfur cycle from five habitats and compared the microbial diversity of mangrove sediments with that of other habitats. The structure and composition of microorganism communities and sulfur genes were significantly different among the five habitats. Our results show that microorganism alpha diversity in mangrove sediments was significantly higher than in other habitats. Genes involved in dissimilatory sulfate reduction were abundant in subtropical marine mangroves and deep-sea sediments. The neutral community model results showed that microbial dispersal was higher in the marine mangrove ecosystem than in others habitats. The Flavilitoribacter of sulfur-metabolizing microorganism becomes a reliable biomarker in the five habitats. SMDB will assist researchers to analyze genes of sulfur cycle from the metagenomic efficiently.}, } @article {pmid37208257, year = {2023}, author = {Wang, Q and Wu, S and Ye, X and Tan, S and Huang, F and Su, G and Kijlstra, A and Yang, P}, title = {Gut microbial signatures and their functions in Behcet's uveitis and Vogt-Koyanagi-Harada disease.}, journal = {Journal of autoimmunity}, volume = {137}, number = {}, pages = {103055}, doi = {10.1016/j.jaut.2023.103055}, pmid = {37208257}, issn = {1095-9157}, mesh = {Humans ; *Uveomeningoencephalitic Syndrome ; Leukocytes, Mononuclear ; *Gastrointestinal Microbiome ; *Uveitis/etiology ; *Behcet Syndrome ; }, abstract = {BACKGROUND: A number of public metagenomic studies reveal an association between the gut microbiome and various immune-mediated diseases including Behcet's uveitis (BU) and Vogt-Koyanagi-Harada disease (VKH). Integrated-analysis and subsequent validation of these results could be a potentially powerful way to understand the microbial signatures and their functions in these two uveitis entities.

METHODS: We integrated the sequencing data of our previous metagenomic studies on two major uveitis entities, BU and VKH as well as four other publicly available immune-mediated diseases datasets, including Ankylosing Spondylitis (AS), Rheumatoid Arthritis (RA), Crohn's disease (CD) and Ulcerative Colitis (UC). Alpha-diversity and beta-diversity analysis were used to compare the gut microbiome signatures between both uveitis entities and other immune-mediated diseases and healthy controls. Amino acid homology between microbial proteins and a uveitogenic peptide of the interphotoreceptor retinoid-binding protein (IRBP)161-180 was investigated using a similarity search in the NCBI protein BLAST program (BLASTP). Enzyme-linked Immunosorbent Assay (ELISA) was performed to evaluate the cross-reactive responses of experimental autoimmune uveitis (EAU)-derived lymphocytes and BU patients-derived peripheral blood mononuclear cells (PBMCs) against homologous peptides. The area under the curve (AUC) analysis was used to test the sensitivity and specificity of gut microbial biomarkers.

RESULTS: Depleted Dorea, Blautia, Coprococcus, Erysipelotrichaceae and Lachnospiraceae as well as enriched Bilophila and Stenotrophomonas were identified in BU patients. An enriched Alistipes along with a lower level of Dorea were observed in VKH patients. A peptide antigen (SteTDR) encoded by BU specifically enriched Stenotrophomonas was identified to share homology with IRBP161-180. In vitro experiments showed that lymphocytes from EAU or PBMCs from BU patients reacted to this peptide antigen as shown by the production of IFN-γ and IL-17. Addition of the SteTDR peptide to the classical IRBP immunization protocol exacerbated EAU severity. Gut microbial marker profiles consisted of 24 species and 32 species respectively differentiated BU and VKH from each other as well as from the other four immune-mediated diseases and healthy controls. Protein annotation identified 148 and 119 specific microbial proteins associated with BU and VKH, respectively. For metabolic function analysis, 108 and 178 metabolic pathways were shown to be associated with BU and VKH, respectively.

CONCLUSIONS: Our study revealed specific gut microbial signatures and their potentially functional roles in BU and VKH pathogenesis that differ significantly from other immune-mediated diseases as well as healthy controls.}, } @article {pmid37207327, year = {2023}, author = {Gschwind, R and Ugarcina Perovic, S and Weiss, M and Petitjean, M and Lao, J and Coelho, LP and Ruppé, E}, title = {ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics.}, journal = {Nucleic acids research}, volume = {51}, number = {W1}, pages = {W493-W500}, pmid = {37207327}, issn = {1362-4962}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Metagenomics ; *Databases, Genetic ; Internet ; }, abstract = {Metagenomics can be used to monitor the spread of antibiotic resistance genes (ARGs). ARGs found in databases such as ResFinder and CARD primarily originate from culturable and pathogenic bacteria, while ARGs from non-culturable and non-pathogenic bacteria remain understudied. Functional metagenomics is based on phenotypic gene selection and can identify ARGs from non-culturable bacteria with a potentially low identity shared with known ARGs. In 2016, the ResFinderFG v1.0 database was created to collect ARGs from functional metagenomics studies. Here, we present the second version of the database, ResFinderFG v2.0, which is available on the Center of Genomic Epidemiology web server (https://cge.food.dtu.dk/services/ResFinderFG/). It comprises 3913 ARGs identified by functional metagenomics from 50 carefully curated datasets. We assessed its potential to detect ARGs in comparison to other popular databases in gut, soil and water (marine + freshwater) Global Microbial Gene Catalogues (https://gmgc.embl.de). ResFinderFG v2.0 allowed for the detection of ARGs that were not detected using other databases. These included ARGs conferring resistance to beta-lactams, cycline, phenicol, glycopeptide/cycloserine and trimethoprim/sulfonamide. Thus, ResFinderFG v2.0 can be used to identify ARGs differing from those found in conventional databases and therefore improve the description of resistomes.}, } @article {pmid37207198, year = {2023}, author = {de Medeiros, RM and Valverde-Villegas, JM and Ellwanger, JH}, title = {Editorial: Host-virus interaction at the omics and ecology levels.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1209532}, pmid = {37207198}, issn = {1664-3224}, mesh = {*Host Microbial Interactions ; *Ecology ; Metagenomics ; }, } @article {pmid37207189, year = {2023}, author = {Gamsjäger, L and Cirone, KM and Schluessel, S and Campsall, M and Herik, A and Lahiri, P and Young, D and Dufour, A and Sapountzis, P and Otani, S and Gomez, DE and Windeyer, MC and Cobo, ER}, title = {Host innate immune responses and microbiome profile of neonatal calves challenged with Cryptosporidium parvum and the effect of bovine colostrum supplementation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1165312}, pmid = {37207189}, issn = {2235-2988}, mesh = {Female ; Pregnancy ; Animals ; Cattle ; *Cryptosporidium parvum ; *Cryptosporidiosis/epidemiology ; *Cryptosporidium ; Colostrum ; Proteomics ; Feces ; Diarrhea/veterinary/epidemiology ; Immunity, Innate ; Dietary Supplements ; *Cattle Diseases ; }, abstract = {INTRODUCTION: Calves are highly susceptible to gastrointestinal infection with Cryptosporidium parvum (C. parvum), which can result in watery diarrhea and eventually death or impaired development. With little to no effective therapeutics, understanding the host's microbiota and pathogen interaction at the mucosal immune system has been critical to identify and test novel control strategies.

METHODS: Herein, we used an experimental model of C. parvum challenge in neonatal calves to describe the clinical signs and histological and proteomic profiling of the mucosal innate immunity and microbiota shifts by metagenomics in the ileum and colon during cryptosporidiosis. Also, we investigated the impact of supplemental colostrum feeding on C. parvum infection.

RESULTS: We showed that C. parvum challenged calves experienced clinical signs including pyrexia and diarrhea 5 days post challenge. These calves showed ulcerative neutrophil ileitis with a proteomic signature driven by inflammatory effectors, including reactive oxygen species and myeloperoxidases. Colitis was also noticed with an aggravated mucin barrier depletion and incompletely filled goblet cells. The C. parvum challenged calves also displayed a pronounced dysbiosis with a high prevalence of Clostridium species (spp.) and number of exotoxins, adherence factors, and secretion systems related to Clostridium spp. and other enteropathogens, including Campylobacter spp., Escherichia sp., Shigella spp., and Listeria spp. Daily supplementation with a high-quality bovine colostrum product mitigated some of the clinical signs and modulated the gut immune response and concomitant microbiota to a pattern more similar to that of healthy unchallenged calves.

DISCUSSION: C. parvum infection in neonatal calves provoked severe diarrheic neutrophilic enterocolitis, perhaps augmented due to the lack of fully developed innate gut defenses. Colostrum supplementation showed limited effect mitigating diarrhea but demonstrated some clinical alleviation and specific modulatory influence on host gut immune responses and concomitant microbiota.}, } @article {pmid37207186, year = {2023}, author = {Hao, SR and Zhou, YY and Zhang, X and Jiang, HY}, title = {Gut microbiome profiles may be related to atypical antipsychotic associated overweight in Asian children with psychiatric disorder: a preliminary study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1124846}, pmid = {37207186}, issn = {2235-2988}, mesh = {Humans ; Child ; Overweight/chemically induced/drug therapy/microbiology ; *Gastrointestinal Microbiome/physiology ; *Antipsychotic Agents/adverse effects ; Cross-Sectional Studies ; *Mental Disorders ; Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; }, abstract = {OBJECTIVE: Atypical antipsychotics (APs) modify the gut microbiome, and weight gain in response to AP could be mediated by the gut microbiome. Thus, the present study aimed to explore the changes in the gut bacterial microbiome in AP-exposed children with obesity.

METHODS: To rule out the confounder of AP indication, the gut bacterial microbiome was compared between healthy controls (Con) and AP-exposed individuals with overweight (APO) or normal weight (APN). Fifty-seven AP-treated outpatients (21 APO and 36 APN) and 25 Con were included in this cross-sectional microbiota study.

RESULTS: AP users, regardless of body mass index, exhibited decreased microbial richness and diversity and a distinct metagenomic composition compared to the Con. Although no differences in the microbiota structure were observed between APO and APN groups, the APO group was characterised by a higher abundance of Megamonas and Lachnospira. Additionally, the differences in the microbial functions were observed between APO and APN groups.

CONCLUSIONS: The gut bacterial microbiota of APO children revealed taxonomic and functional differences compared to Con and APN. Further studies are needed to verify these findings and to explore the temporal and causal relationships between these variables.}, } @article {pmid37206897, year = {2023}, author = {Kyritsi, M and Tsiolas, G and Michailidou, S and Koukaras, K and Argiriou, A}, title = {Genomic and 16S metabarcoding data of Holothuria tubulosa Gmelin, 1791.}, journal = {Data in brief}, volume = {48}, number = {}, pages = {109171}, pmid = {37206897}, issn = {2352-3409}, abstract = {Holothuria tubulosa Gmelin, 1791 is an edible sea cucumber species widespread in the Mediterranean Sea with ecological and increasing economic importance. Genome data of holothurian species is limited and the availability of genomic data resources is crucial in understanding their biology and adaptability mechanisms. This dataset presents the raw genome sequence data of H. tubulosa sequenced on an Illumina NextSeq 2000 platform. Genome size estimation was performed based on k-mer frequency approach. Additionally, the bacterial microbiome in the stomach and intestine of H. tubulosa collected from the Strymonian Gulf (North Aegean Sea, Greece) through 16S rRNA amplicon metabarcoding sequencing is reported. Sequencing was performed on an Illumina MiSeq platform. Analysis was conducted using the QIIME2 software package, the DADA2 algorithm and a trained classifier for taxonomy assignment. The datasets presented in this work serve as valuable resources for a comprehensive investigation of H. tubulosa at the genome level and for comparative genomics and echinoderms gut microbial studies.}, } @article {pmid37206333, year = {2023}, author = {Russo, N and Floridia, V and D'Alessandro, E and Lopreiato, V and Pino, A and Chiofalo, V and Caggia, C and Liotta, L and Randazzo, CL}, title = {Influence of olive cake dietary supplementation on fecal microbiota of dairy cows.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1137452}, pmid = {37206333}, issn = {1664-302X}, abstract = {Olive by-products represent a valuable low-price feed supplement for animal nutrition. In the present study, the effect of the dietary destoned olive cake supplementation, on both composition and dynamics of the fecal bacterial biota of cow, was assessed by Illumina MiSeq analysis of the 16S rRNA gene. In addition, metabolic pathways were predicted by using the PICRUSt2 bioinformatic tool. Eighteen lactating cows, according to the body condition score, the days from calving, and the daily milk production were homogeneously allocated into two groups, control or experimental, and subjected to different dietary treatments. In detail, the experimental diet contained, along with the components of the control one, 8% of destoned olive cake. Metagenomics data revealed significant differences in abundance rather than in richness between the two groups. Results showed that Bacteroidota and Firmicutes were identified as the dominant phyla, accounting for over 90% of the total bacterial population. The Desulfobacterota phylum, able to reduce sulfur compounds, was detected only in fecal samples of cows allocated to the experimental diet whereas the Elusimicrobia phylum, a common endosymbiont or ectosymbiont of various flagellated protists, was detected only in cows subjected to the control diet. In addition, both Oscillospiraceae and Ruminococcaceae families were mainly found in the experimental group whereas fecal samples of control cows showed the presence of Rikenellaceae and Bacteroidaceae families, usually associated with the high roughage or low concentrate diet. Based on the PICRUSt2 bioinformatic tool, pathways related to carbohydrate, fatty acid, lipid, and amino acids biosynthesis were mainly up regulated in the experimental group. On the contrary, in the control group, the metabolic pathways detected with the highest occurrence were associated with amino acids biosynthesis and degradation, aromatic compounds degradation, nucleosides and nucleotides biosynthesis. Hence, the present study confirms that the destoned olive cake is a valuable feed supplement able to modulate the fecal microbiota of cows. Further studies will be conducted in order to deepen the inter-relationships between the GIT microbiota and the host.}, } @article {pmid37205512, year = {2023}, author = {Wang, Y and Gallagher, LA and Andrade, PA and Liu, A and Humphreys, IR and Turkarslan, S and Cutler, KJ and Arrieta-Ortiz, ML and Li, Y and Radey, MC and McLean, JS and Cong, Q and Baker, D and Baliga, NS and Peterson, SB and Mougous, JD}, title = {Genetic manipulation of candidate phyla radiation bacteria provides functional insights into microbial dark matter.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37205512}, support = {R01 AI128215/AI/NIAID NIH HHS/United States ; R01 AI141953/AI/NIAID NIH HHS/United States ; R01 DE023810/DE/NIDCR NIH HHS/United States ; }, abstract = {The study of bacteria has yielded fundamental insights into cellular biology and physiology, biotechnological advances and many therapeutics. Yet due to a lack of suitable tools, the significant portion of bacterial diversity held within the candidate phyla radiation (CPR) remains inaccessible to such pursuits. Here we show that CPR bacteria belonging to the phylum Saccharibacteria exhibit natural competence. We exploit this property to develop methods for their genetic manipulation, including the insertion of heterologous sequences and the construction of targeted gene deletions. Imaging of fluorescent protein-labeled Saccharibacteria provides high spatiotemporal resolution of phenomena accompanying epibiotic growth and a transposon insertion sequencing genome-wide screen reveals the contribution of enigmatic Saccharibacterial genes to growth on their Actinobacteria hosts. Finally, we leverage metagenomic data to provide cutting-edge protein structure-based bioinformatic resources that support the strain Southlakia epibionticum and its corresponding host, Actinomyces israelii , as a model system for unlocking the molecular underpinnings of the epibiotic lifestyle.}, } @article {pmid37205374, year = {2023}, author = {Salerno, P and Verster, A and Valls, R and Barrack, K and Price, C and Madan, J and O'Toole, GA and Ross, BD}, title = {Persistent delay in maturation of the developing gut microbiota in infants with cystic fibrosis.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.05.02.539134}, pmid = {37205374}, abstract = {The healthy human infant gut microbiome undergoes stereotypical changes in taxonomic composition between birth and maturation to an adult-like stable state. During this time, extensive communication between microbiota and the host immune system contributes to health status later in life. Although there are many reported associations between microbiota compositional alterations and disease in adults, less is known about how microbiome development is altered in pediatric diseases. One pediatric disease linked to altered gut microbiota composition is cystic fibrosis (CF), a multi-organ genetic disease involving impaired chloride secretion across epithelia and heightened inflammation both in the gut and at other body sites. Here, we use shotgun metagenomics to profile the strain-level composition and developmental dynamics of the infant fecal microbiota from several CF and non-CF longitudinal cohorts spanning from birth to greater than 36 months of life. We identify a set of keystone species whose prevalence and abundance reproducibly define microbiota development in early life in non-CF infants, but are missing or decreased in relative abundance in infants with CF. The consequences of these CF-specific differences in gut microbiota composition and dynamics are a delayed pattern of microbiota maturation, persistent entrenchment in a transitional developmental phase, and subsequent failure to attain an adult-like stable microbiota. We also detect the increased relative abundance of oral-derived bacteria and higher levels of fungi in CF, features that are associated with decreased gut bacterial density in inflammatory bowel diseases. Our results define key differences in the gut microbiota during ontogeny in CF and suggest the potential for directed therapies to overcome developmental delays in microbiota maturation.}, } @article {pmid37204943, year = {2023}, author = {Romashchenko, N and Linard, B and Rivals, E and Pardi, F}, title = {Computing Phylo- k-Mers.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {20}, number = {5}, pages = {2889-2897}, doi = {10.1109/TCBB.2023.3278049}, pmid = {37204943}, issn = {1557-9964}, abstract = {Finding the correct position of new sequences within an established phylogenetic tree is an increasingly relevant problem in evolutionary bioinformatics and metagenomics. Recently, alignment-free approaches for this task have been proposed. One such approach is based on the concept of phylogenetically-informative k-mers or phylo- k-mers for short. In practice, phylo- k-mers are inferred from a set of related reference sequences and are equipped with scores expressing the probability of their appearance in different locations within the input reference phylogeny. Computing phylo- k-mers, however, represents a computational bottleneck to their applicability in real-world problems such as the phylogenetic analysis of metabarcoding reads and the detection of novel recombinant viruses. Here we consider the problem of phylo- k-mer computation: how can we efficiently find all k-mers whose probability lies above a given threshold for a given tree node? We describe and analyze algorithms for this problem, relying on branch-and-bound and divide-and-conquer techniques. We exploit the redundancy of adjacent windows of the alignment to save on computation. Besides computational complexity analyses, we provide an empirical evaluation of the relative performance of their implementations on simulated and real-world data. The divide-and-conquer algorithms are found to surpass the branch-and-bound approach, especially when many phylo- k-mers are found.}, } @article {pmid37204507, year = {2023}, author = {Aktar, N and Mannan, E and Kabir, SMT and Hasan, R and Hossain, MS and Ahmed, R and Ahmed, B and Islam, MS}, title = {Comparative metagenomics and microbial dynamics of jute retting environment.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {}, number = {}, pages = {}, pmid = {37204507}, issn = {1618-1905}, abstract = {Jute, eco-friendly natural fiber, depends on conventional water-based microbial retting process that suffers from the production of low-quality fiber, restricting its diversified applications. The efficiency of water retting of jute depends on plant polysaccharide fermenting pectinolytic microorganisms. Understanding the phase difference in retting microbial community composition is crucial to provide knowledge on the functions of each member of microbiota for the improvement of retting and fiber quality. The retting microbiota profiling of jute was commonly performed previously using only one retting phase with culture-dependent methods which has limited coverage and accuracy. Here, for the first we have analyzed jute retting water through WGS metagenome approach in three phases (pre-retting, aerobic retting, and anaerobic retting phases) and characterized the microbial communities both culturable and non-culturable along with their dynamics with the fluctuation of oxygen availability. Our analysis revealed a total of 25.99 × 10[4] unknown proteins (13.75%), 16.18 × 10[5] annotated proteins (86.08%), and 32.68 × 10[2] ribosomal RNA (0.17%) in the pre-retting phase, 15.12 × 10[4] unknown proteins (8.53%), 16.18 × 10[5] annotated proteins (91.25%), and 38.62 × 10[2] ribosomal RNA (0.22%) in the aerobic retting phase, and 22.68 × 102 ribosomal RNA and 80.14 × 10[4] (99.72%) annotated protein in the anaerobic retting phase. Taxonomically, we identified 53 different phylotypes in the retting environment, with Proteobacteria being the dominant taxa comprising over 60% of the population. We have identified 915 genera from Archaea, Viruses, Bacteria, and Eukaryota in the retting habitat, with anaerobic or facultative anaerobic pectinolytic microflora being enriched in the anoxic, nutrient-rich retting niche, such as Aeromonas (7%), Bacteroides (3%), Clostridium (6%), Desulfovibrio (4%), Acinetobacter (4%), Enterobacter (1%), Prevotella (2%), Acidovorax (3%), Bacillus (1%), Burkholderia (1%), Dechloromonas (2%), Caulobacter (1%) and Pseudomonas (7%). We observed an increase in the expression of 30 different KO functional level 3 pathways in the final retting stage compared to the middle and pre-retting stages. The main functional differences among the retting phases were found to be related to nutrient absorption and bacterial colonization. These findings reveal the bacterial groups that are involved in fiber retting different phases and will facilitate to develop future phase-specific microbial consortia for the improvement of jute retting process.}, } @article {pmid37204286, year = {2023}, author = {Shankar, A and Das, DJ and Nayar, S and Thomas, S}, title = {Deciphering the effect of maternal postpartum antibiotic prophylaxis on the infant gut microbiome: a whole metagenomic analysis.}, journal = {Future microbiology}, volume = {18}, number = {}, pages = {427-441}, doi = {10.2217/fmb-2022-0200}, pmid = {37204286}, issn = {1746-0921}, support = {AC1-250/2018/SPHCL//Department of Health and Family Welfare, Government of Kerala, India/ ; }, mesh = {Female ; Humans ; Infant ; *Gastrointestinal Microbiome ; Antibiotic Prophylaxis ; Mothers ; Milk, Human ; Postpartum Period ; Feces ; }, abstract = {Aim: To analyze the impact of postpartum antibiotic (Ab) prophylaxis on the infant gut microbiome. Materials & methods: Whole metagenomic analysis was performed on breast milk and infant fecal samples collected from mother-infant pairs who belonged to two groups: an Ab group comprising mothers who had received a single course of Abs in the immediate postpartum period and a non-Ab group comprising mothers who had not received Abs. Results: The characteristic presence of Citrobacter werkmanii, an emerging multidrug-resistant uropathogen, and a higher relative abundance of genes encoding resistance to specific Abs were noted in samples from the Ab group compared with those from the non-Ab group. Conclusion: Policies regarding prophylactic Ab prescription across government and private health sectors in the postpartum period need to be strengthened.}, } @article {pmid37204034, year = {2023}, author = {Liu, M and Liu, H and Li, F and Shen, Y and Zhang, L and Wang, G and Wang, H and Qu, C and Chen, G and Zhao, X and Liu, L and Zhou, J}, title = {Metagenomic surveillance in Jinan, China, reveals serum microbiome and biochemistry features in fever of unknown origin (FUO) patients.}, journal = {Letters in applied microbiology}, volume = {76}, number = {6}, pages = {}, doi = {10.1093/lambio/ovad060}, pmid = {37204034}, issn = {1472-765X}, support = {2020-4-113//National Health Commission/ ; 21320061330000//College of Public Health/ ; }, mesh = {Humans ; *Fever of Unknown Origin/diagnosis ; Metagenomics/methods ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; }, abstract = {Here we aim to build up a metagenomics-centered surveillance on the infectious microbiome showing in the fever of unknown origin (FUO) patients. We collected venous blood, bronchoalveolar lavage fluid, cerebrospinal fluid, tissue block, sputum, bone marrow biopsy, and purulent liquid samples from 123 patients. Metagenomic sequencing (mNGS) for both DNA and RNA sequences was performed to profile the total pathogenic microbiome in the samples. A large pool of infectious or conditional infectious bacteria was found, belonging to Enterobacteriaceae, Staphylococcaceae (10.55%), Burkholderiaceae (10.05%), and Comamonadaceae (4.25%). The major virus families detected from mNGS analysis include Adenoviridae, Anelloviridae, Peribunyaviridae, Flaviviridae, and Herpesviridae, showing up in 34.96%, 47.37%, 30.89%, 5.69%, 3.25%, and 1.63% of patients, respectively. Using the Ward clustering method, two clusters of patients were organized: high-variety group and low-variety group. The patients in the high-variety group demonstrated higher levels of immune cells and inflammatory indicators such as lactate dehydrogenase, aspartate aminotransferase, and alanine aminotransferase. The patients in the low-variety group showed higher levels of inflammatory lipids such as 13,14-dihy-15-keto PGE2 (fold > 10, P = 0.021); tetra-PGDM (fold = 5.29, P = 0.037); and 20-HETE (fold > 10, P = 0.02). The mNGS surveillance system demonstrated remarkable potential in preventing infectious diseases using mNGS data.}, } @article {pmid37203688, year = {2023}, author = {Bucholz, JR and Hopper, GW and González, IS and Kelley, TE and Jackson, CR and Garrick, RC and Atkinson, CL and Lozier, JD}, title = {Community-wide correlations between species richness, abundance and population genomic diversity in a freshwater biodiversity hotspot.}, journal = {Molecular ecology}, volume = {32}, number = {22}, pages = {5894-5912}, doi = {10.1111/mec.16991}, pmid = {37203688}, issn = {1365-294X}, support = {1831512//National Science Foundation/ ; 1831531//National Science Foundation/ ; }, mesh = {Humans ; Animals ; Metagenomics ; Biodiversity ; Fresh Water ; Rivers ; *Unionidae ; *Bivalvia/genetics ; Ecosystem ; }, abstract = {Understanding patterns of diversity across macro (e.g. species-level) and micro (e.g. molecular-level) scales can shed light on community function and stability by elucidating the abiotic and biotic drivers of diversity within ecological communities. We examined the relationships among taxonomic and genetic metrics of diversity in freshwater mussels (Bivalvia: Unionidae), an ecologically important and species-rich group in the southeastern United States. Using quantitative community surveys and reduced-representation genome sequencing across 22 sites in seven rivers and two river basins, we surveyed 68 mussel species and sequenced 23 of these species to characterize intrapopulation genetic variation. We tested for the presence of species diversity-abundance correlations (i.e. the more-individuals hypothesis, MIH), species-genetic diversity correlations (SGDCs) and abundance-genetic diversity correlations (AGDCs) across all sites to evaluate relationships between different metrics of diversity. Sites with greater cumulative multispecies density (a standardized metric of abundance) had a greater number of species, consistent with the MIH hypothesis. Intrapopulation genetic diversity was strongly associated with the density of most species, indicating the presence of AGDCs. However, there was no consistent evidence for SGDCs. Although sites with greater overall densities of mussels had greater species richness, sites with higher genetic diversity did not always exhibit positive correlations with species richness, suggesting that there are spatial and evolutionary scales at which the processes influencing community-level diversity and intraspecific diversity differ. Our work reveals the importance of local abundance as indicator (and possibly a driver) of intrapopulation genetic diversity.}, } @article {pmid37203453, year = {2023}, author = {Eckstrand, CD and Torrevillas, BK and Wolking, RM and Bradway, DS and Warg, JV and Clayton, RD and Williams, LB and Pessier, AP and Reno, JL and McMenamin-Snekvik, KM and Thompson, J and Baszler, T and Snekvik, KR}, title = {Investigation of laboratory methods for characterization of aquatic viruses in fish infected experimentally with infectious salmon anemia virus.}, journal = {Journal of veterinary diagnostic investigation : official publication of the American Association of Veterinary Laboratory Diagnosticians, Inc}, volume = {}, number = {}, pages = {10406387231173332}, doi = {10.1177/10406387231173332}, pmid = {37203453}, issn = {1943-4936}, abstract = {Rapid growth in aquaculture has resulted in high-density production systems in ecologically and geographically novel conditions in which the emergence of diseases is inevitable. Well-characterized methods for detection and surveillance of infectious diseases are vital for rapid identification, response, and recovery to protect economic and food security. We implemented a proof-of-concept approach for virus detection using a known high-consequence fish pathogen, infectious salmon anemia virus (ISAV), as the archetypal pathogen. In fish infected with ISAV, we integrated histopathology, virus isolation, whole-genome sequencing (WGS), electron microscopy (EM), in situ hybridization (ISH), and reverse transcription real-time PCR (RT-rtPCR). Fresh-frozen and formalin-fixed tissues were collected from virus-infected, control, and sham-infected Atlantic salmon (Salmo salar). Microscopic differences were not evident between uninfected and infected fish. Viral cytopathic effect was observed in cell cultures inoculated with fresh-frozen tissue homogenates from 3 of 3 ISAV-infected and 0 of 4 uninfected or sham-infected fish. The ISAV genome was detected by shotgun metagenomics in RNA extracted from the medium from 3 of 3 inoculated cell cultures, 3 of 3 infected fish, and 0 of 4 uninfected or sham-infected fish, yielding sufficient coverage for de novo assembly. An ISH probe against ISAV revealed ISAV genome in multiple organs, with abundance in renal hematopoietic tissue. Virus was detected by RT-rtPCR in gill, heart, kidney, liver, and spleen. EM and metagenomic WGS from tissues were challenging and unsuccessful. Our proof-of-concept methodology has promise for detection and characterization of unknown aquatic pathogens and also highlights some associated methodology challenges that require additional investigation.}, } @article {pmid37202853, year = {2023}, author = {Velsko, IM and Gallois, S and Stahl, R and Henry, AG and Warinner, C}, title = {High conservation of the dental plaque microbiome across populations with differing subsistence strategies and levels of market integration.}, journal = {Molecular ecology}, volume = {32}, number = {14}, pages = {3872-3891}, doi = {10.1111/mec.16988}, pmid = {37202853}, issn = {1365-294X}, mesh = {Humans ; *Dental Plaque ; *Microbiota/genetics ; Mouth ; Diet ; North America ; }, abstract = {Industrialization-including urbanization, participation in the global food chain and consumption of heavily processed foods-is thought to drive substantial shifts in the human microbiome. While diet strongly influences stool microbiome composition, the influence of diet on the oral microbiome is largely speculative. Multiple ecologically distinct surfaces in the mouth, each harbouring a unique microbial community, pose a challenge to assessing changes in the oral microbiome in the context of industrialization, as the results depend on the oral site under study. Here, we investigated whether microbial communities of dental plaque, the dense biofilm on non-shedding tooth surfaces, are distinctly different across populations with dissimilar subsistence strategies and degree of industrialized market integration. Using a metagenomic approach, we compared the dental plaque microbiomes of Baka foragers and Nzime subsistence agriculturalists in Cameroon (n = 46) with the dental plaque and calculus microbiomes of highly industrialized populations in North America and Europe (n = 38). We found that differences in microbial taxonomic composition between populations were minimal, with high conservation of abundant microbial taxa and no significant differences in microbial diversity related to dietary practices. Instead, we find that the major source of variation in dental plaque microbial species composition is related to tooth location and oxygen availability, which may be influenced by toothbrushing or other dental hygiene measures. Our results support that dental plaque, in contrast to the stool microbiome, maintains an inherent stability against ecological perturbations in the oral environment.}, } @article {pmid37202810, year = {2023}, author = {Wang, G and Yin, X and Feng, Z and Chen, C and Chen, D and Wu, B and Liu, C and Morel, JL and Jiang, Y and Yu, H and He, H and Chao, Y and Tang, Y and Qiu, R and Wang, S}, title = {Novel biological aqua crust enhances in situ metal(loid) bioremediation driven by phototrophic/diazotrophic biofilm.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {110}, pmid = {37202810}, issn = {2049-2618}, mesh = {*Ecosystem ; Biodegradation, Environmental ; *Environmental Monitoring ; Biofilms ; }, abstract = {BACKGROUND: Understanding the ecological and environmental functions of phototrophic biofilms in the biological crust is crucial for improving metal(loid) (e.g. Cd, As) bioremediation in mining ecosystems. In this study, in combination with metal(loid) monitoring and metagenomic analysis, we systematically evaluated the effect of biofilm in a novel biological aqua crust (biogenic aqua crust-BAC) on in situ metal(loid) bioremediation of a representative Pb/Zn tailing pond.

RESULTS: We observed strong accumulation of potentially bioavailable metal(loid)s and visible phototrophic biofilms in the BAC. Furthermore, dominating taxa Leptolyngbyaceae (10.2-10.4%, Cyanobacteria) and Cytophagales (12.3-22.1%, Bacteroidota) were enriched in biofilm. Along with predominant heterotrophs (e.g. Cytophagales sp.) as well as diazotrophs (e.g. Hyphomonadaceae sp.), autotrophs/diazotrophs (e.g. Leptolyngbyaceae sp.) in phototrophic biofilm enriched the genes encoding extracellular peptidase (e.g. family S9, S1), CAZymes (e.g. CBM50, GT2) and biofilm formation (e.g. OmpR, CRP and LuxS), thus enhancing the capacity of nutrient accumulation and metal(loid) bioremediation in BAC system.

CONCLUSIONS: Our study demonstrated that a phototrophic/diazotrophic biofilm constitutes the structured communities containing specific autotrophs (e.g. Leptolyngbyaceae sp.) and heterotrophs (e.g. Cytophagales sp.), which effectively control metal(loid) and nutrient input using solar energy in aquatic environments. Elucidation of the mechanisms of biofilm formation coupled with metal(loid) immobilization in BAC expands the fundamental understanding of the geochemical fate of metal(loid)s, which may be harnessed to enhance in situ metal(loid) bioremediation in the aquatic ecosystem of the mining area. Video Abstract.}, } @article {pmid37202771, year = {2023}, author = {Ahmed, OY and Rossi, M and Gagie, T and Boucher, C and Langmead, B}, title = {SPUMONI 2: improved classification using a pangenome index of minimizer digests.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {122}, pmid = {37202771}, issn = {1474-760X}, support = {R01 HG011392/HG/NHGRI NIH HHS/United States ; R01HG011392/HG/NHGRI NIH HHS/United States ; }, mesh = {*Algorithms ; *Genomics ; Metagenomics ; Databases, Factual ; Sequence Analysis, DNA ; }, abstract = {Genomics analyses use large reference sequence collections, like pangenomes or taxonomic databases. SPUMONI 2 is an efficient tool for sequence classification of both short and long reads. It performs multi-class classification using a novel sampled document array. By incorporating minimizers, SPUMONI 2's index is 65 times smaller than minimap2's for a mock community pangenome. SPUMONI 2 achieves a speed improvement of 3-fold compared to SPUMONI and 15-fold compared to minimap2. We show SPUMONI 2 achieves an advantageous mix of accuracy and efficiency in practical scenarios such as adaptive sampling, contamination detection and multi-class metagenomics classification.}, } @article {pmid37202728, year = {2023}, author = {Xing, W and Qi, B and Chen, R and Ding, W and Zhang, F}, title = {Metagenomic analysis reveals taxonomic and functional diversity of microbial communities on the deteriorated wall paintings of Qinling Tomb in the Southern Tang Dynasty, China.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {140}, pmid = {37202728}, issn = {1471-2180}, mesh = {*Microbiota ; Metagenome ; *Cyanobacteria ; Proteobacteria ; China ; }, abstract = {The microbial colonization on ancient murals attracts more and more attention since the threaten by microorganisms was first reported in Lascaux, Spain. However, the biodeterioration or biodegradation of mural paintings resulted by microorganisms is not clear yet. Especially the biological function of microbial communities in different conditions remained largely unaddressed. The two mausoleums of the Southern Tang Dynasty are the largest group of emperor mausoleums during the Five Dynasties and Ten Kingdoms period in China, which are of great significance to the study of the architecture, imperial mausoleum systems and art in the Tang and Song Dynasties. To make clear the species composition and metabolic functions of different microbial communities (MID and BK), we analyzed the samples from the wall paintings in one of the two mausoleums of the Southern Tang Dynasty with metagenomics method. The result showed totally 55 phyla and 1729 genera were detected in the mural paintings. The two microbial community structure were similar with the dominance of Proteobacteria, Actinobacteria and Cyanobacteria. However, the species abundance presented a significant difference between two communities at genus level --- MID is Lysobacter, Luteimonas are predominant in MID while Sphingomonas and Streptomyces are popular in BK, which is partially attributed to the different substrate materials of murals. As a result, the two communities presented the different metabolic patterns that MID community was mainly participated in the formation of biofilm as well as the degradation of exogenous pollutants while the BK was predominantly related to the photosynthesis process and biosynthesis of secondary metabolites. Taken together, these findings indicated the effect of environmental factor on the taxonomic composition and functional diversity of the microbial populations. The installation of artificial lighting needs to be considered carefully in the future protection of cultural relics.}, } @article {pmid37202719, year = {2023}, author = {Wang, XY and Meng, JX and Ren, WX and Ma, H and Liu, G and Liu, R and Geng, HL and Zhao, Q and Zhang, XX and Ni, HB}, title = {Amplicon-based metagenomic association analysis of gut microbiota in relation to egg-laying period and breeds of hens.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {138}, pmid = {37202719}, issn = {1471-2180}, mesh = {Animals ; Female ; *Gastrointestinal Microbiome/genetics ; Chickens/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Cyanobacteria/genetics ; }, abstract = {BACKGROUND: The gut microbiota plays an essential role in maintaining gut homeostasis and improving performance, with the composition of microbial communities visibly differing across different laying stages in hens and significantly correlating with egg production. To gain further insights into the association between microbial community characteristics and laying periods in Hy-Line variety brown and Isa brown laying hens, we conducted a 16S rRNA amplicon sequencing survey.

RESULTS: Our result revealed the diversity of bacteria in the early laying period was commonly higher than peak, and in Hy-Line variety brown laying hens were generally higher than Isa brown. Principal coordinate analysis (PCoA) and permutational multivariate analysis of variance (PERMANOVA) revealed that the structure and composition of the gut microbiota of laying hens exhibited significant differences among different groups. Phylum Firmicutes, Bacteroidota, Proteobacteria, and Fusobacteriota were found that dominant in the host's feces. Therein, the abundance of Fusobacteriota was higher in the peak period than in the early period, while the abundance of Cyanobacteria in the early period was higher in two breeds of hens. Furthermore, random forest based on machine learning showed that there were several distinctly abundant genera, which can be used as potential biomarkers to differentiate the different groups of laying periods and breeds. In addition, the prediction of biological function indicated the existing discrepancy in microbial function among the microbiota of four groups.

CONCLUSIONS: Our findings offer new insights into the bacterial diversity and intestinal flora composition of different strains of laying hens during various laying periods, contributing significantly to the improvement of production performance and the prevention of chicken diseases.}, } @article {pmid37202543, year = {2023}, author = {Zeng, N and Wu, F and Lu, J and Li, X and Lin, S and Zhou, L and Wang, Z and Wu, G and Huang, Q and Zheng, D and Gao, J and Wu, S and Chen, X and Chen, M and Meng, F and Shang, H and He, Y and Chen, P and Wei, H and Li, Z and Zhou, H}, title = {High-fat diet impairs gut barrier through intestinal microbiota-derived reactive oxygen species.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {37202543}, issn = {1869-1889}, abstract = {Gut barrier disruption is a key event in bridging gut microbiota dysbiosis and high-fat diet (HFD)-associated metabolic disorders. However, the underlying mechanism remains elusive. In the present study, by comparing HFD- and normal diet (ND)-treated mice, we found that the HFD instantly altered the composition of the gut microbiota and subsequently damaged the integrity of the gut barrier. Metagenomic sequencing revealed that the HFD upregulates gut microbial functions related to redox reactions, as confirmed by the increased reactive oxygen species (ROS) levels in fecal microbiota incubation in vitro and in the lumen, which were detected using in vivo fluorescence imaging. This microbial ROS-producing capability induced by HFD can be transferred through fecal microbiota transplantation (FMT) into germ-free (GF) mice, downregulating the gut barrier tight junctions. Similarly, mono-colonizing GF mice with an Enterococcus strain excelled in ROS production, damaged the gut barrier, induced mitochondrial malfunction and apoptosis of the intestinal epithelial cells, and exacerbated fatty liver, compared with other low-ROS-producing Enterococcus strains. Oral administration of recombinant high-stability-superoxide dismutase (SOD) significantly reduced intestinal ROS, protected the gut barrier, and improved fatty liver against the HFD. In conclusion, our study suggests that extracellular ROS derived from gut microbiota play a pivotal role in HFD-induced gut barrier disruption and is a potential therapeutic target for HFD-associated metabolic diseases.}, } @article {pmid37201703, year = {2023}, author = {Liu, X and Ren, W and Lin, M and Tan, X and Wan, C}, title = {Biomineralization behavior and mechanism of microbial-mediated removal of arsenate from water.}, journal = {Environmental research}, volume = {231}, number = {Pt 1}, pages = {116183}, doi = {10.1016/j.envres.2023.116183}, pmid = {37201703}, issn = {1096-0953}, mesh = {*Arsenates ; *Arsenic/metabolism ; Water/chemistry ; Sewage/microbiology ; Biomineralization ; Sulfates/chemistry ; }, abstract = {The microbial-mediated removal of arsenate by biomineralization received much attention, but the molecular mechanism of Arsenic (As) removal by mixed microbial populations remains to be elucidated. In this study, a process for the arsenate treatment using sulfate-reducing bacteria (SRB) containing sludge was constructed, and the performance of As removal was investigated at different molar ratios of AsO4[3-] to SO4[2-]. It was found that biomineralization mediated by SRB could achieve the simultaneous removal of arsenate and sulfate from wastewater but only occurred when microbial metabolic processes were involved. The reducing ability of the microorganisms for the sulfate and arsenate was equivalent, so the precipitates produced at the molar ratio of AsO4[3-] to SO4[2-]of 2:3 were most significant. X-ray absorption fine structure (XAFS) spectroscopy was the first time used to determine the molecular structure of the precipitates which were confirmed to be orpiment (As2S3). Combined with the metagenomics analysis, the microbial metabolism mechanism of simultaneous removal of sulfate and arsenate by the mixed microbial population containing SRB was revealed, that is, the sulfate and As(V) were reduced by microbial enzymes to produce S[2-] and As(III) to further form As2S3 precipitates. This research provided a reference and theoretical foundation for the simultaneous removal of sulfate and arsenic mediated by SRB-containing sludge in wastewater treatment.}, } @article {pmid37201701, year = {2023}, author = {Wang, X and Zou, Y and Wang, Y and Niu, J and Li, H}, title = {Metabolic insights into the interaction between nitrogen removal and 4-chlorophenol reduction of anammox consortia.}, journal = {Environmental research}, volume = {231}, number = {Pt 2}, pages = {116192}, doi = {10.1016/j.envres.2023.116192}, pmid = {37201701}, issn = {1096-0953}, mesh = {*Denitrification ; *Wastewater ; Anaerobic Ammonia Oxidation ; Nitrogen/metabolism ; Oxidation-Reduction ; Bioreactors/microbiology ; Sewage ; }, abstract = {The response characteristic and performance stabilization of anammox process under the stress of the potential organic pollutants support the application of ammonia-nitrogen wastewater treatment. In the present study, nitrogen removal performance was significantly suppressed with the addition of 4-chlorophenol. The activity of anammox process was inhibited by 14.23% (0.1 mg/L), 20.54% (1 mg/L) and 78.15% (10 mg/L), respectively. Metagenomic analysis revealed a significant decrease in the abundance of KEGG pathways associated with carbohydrate and amino acid metabolism with increasing 4-chlorophenol concentration. Metabolic pathway profiles suggest that putrescine is down-regulated at high 4-chlorophenol stress due to inhibition of nitrogen metabolism processes, while it is up-regulated to reduce oxidative damage. In addition, the presence of 4-chlorophenol induced an enhancement of EPS and bacterial debris decomposition, and a partial conversion of 4-chlorophenol to p-nitrophenol. This study unravels the mechanism of effect on anammox consortia in response to 4-CP, which could provide supplementary to facilitate its full-scale application.}, } @article {pmid37201375, year = {2023}, author = {Huang, DQ and Wu, Q and Yang, JH and Jiang, Y and Li, ZY and Fan, NS and Jin, RC}, title = {Deciphering endogenous and exogenous regulations of anammox consortia in responding to lincomycin by multiomics: quorum sensing and CRISPR system.}, journal = {Water research}, volume = {239}, number = {}, pages = {120061}, doi = {10.1016/j.watres.2023.120061}, pmid = {37201375}, issn = {1879-2448}, mesh = {Animals ; Humans ; *Quorum Sensing ; *CRISPR-Cas Systems ; Lincomycin/pharmacology ; Multiomics ; Anaerobic Ammonia Oxidation ; Anti-Bacterial Agents/pharmacology ; }, abstract = {The widespread use of antibiotics has created an antibiotic resistance genes (ARGs)-enriched environment, which causes high risks on human and animal health. Although antibiotics can be partially adsorbed and degraded in wastewater treatment processes, striving for a complete understanding of the microbial adaptive mechanism to antibiotic stress remains urgent. Combined with metagenomics and metabolomics, this study revealed that anammox consortia could adapt to lincomycin by spontaneously changing the preference for metabolite utilization and establishing interactions with eukaryotes, such as Ascomycota and Basidiomycota. Specifically, quorum sensing (QS) based microbial regulation and the ARGs transfer mediated by clustered regularly interspaced short palindromic repeats (CRISPR) system and global regulatory genes were the principal adaptive strategies. Western blotting results validated that Cas9 and TrfA were mainly responsible for the alteration of ARGs transfer pathway. These findings highlight the potential adaptative mechanism of microbes to antibiotic stress and fill gaps in horizontal gene transfer pathways in the anammox process, further facilitating the ARGs control through molecular and synthetic biology techniques.}, } @article {pmid37201335, year = {2023}, author = {Laragione, T and Harris, C and Azizgolshani, N and Beeton, C and Bongers, G and Gulko, PS}, title = {Magnesium increases numbers of Foxp3+ Treg cells and reduces arthritis severity and joint damage in an IL-10-dependent manner mediated by the intestinal microbiome.}, journal = {EBioMedicine}, volume = {92}, number = {}, pages = {104603}, pmid = {37201335}, issn = {2352-3964}, mesh = {Mice ; Animals ; T-Lymphocytes, Regulatory ; Magnesium/metabolism/pharmacology ; Interleukin-10/genetics/metabolism ; *Gastrointestinal Microbiome ; Cytokines/metabolism ; *Arthritis, Rheumatoid/metabolism ; Mice, Knockout ; Th17 Cells ; Forkhead Transcription Factors/genetics/metabolism ; }, abstract = {BACKGROUND: Rheumatoid arthritis (RA) is a common autoimmune disease with emerging environmental and microbiome risk factors. The western diet is typically deficient in magnesium (Mg), and there is some evidence suggesting that Mg may have anti-inflammatory properties. But the actual role of Mg supplementation in arthritis or in T cell subsets has not been explored.

METHODS: We investigated the role of a high Mg diet in two different mouse models of RA induced with the KRN serum, and collagen-induced arthritis. We also characterized the phenotypes of splenocytes, gene expression, and an extensive intestinal microbiome analyses including fecal material transplantation (FMT).

FINDINGS: The high Mg diet group was significantly protected with reduced arthritis severity and joint damage, and reduced expression of IL-1β, IL-6, and TNFα. The high Mg group also had increased numbers of Foxp3+ Treg cells and IL-10-producing T cells. The high Mg protective effect disappeared in IL-10 knockout mice. FMT from the high Mg diet mice recreated the phenotypes seen in the diet-treated mice, with reduced arthritis severity, increased Foxp3+ Treg, and increased IL-10-producing T cells. Intestinal microbiome analyses using 16S rDNA sequencing revealed diet-specific changes, including reduced levels of RA-associated Prevotella in the high Mg group, while increasing levels of Bacteroides and other bacteria associated with increased production of short-chain fatty acids. Metagenomic analyses implicated additional pathways including L-tryptophan biosynthesis and arginine deiminase.

INTERPRETATION: We describe a new role for Mg in suppressing arthritis, in expanding Foxp3+ T reg cells and in the production of IL-10, and show that these effects are mediated by the intestinal microbiome. Our discoveries suggest a novel strategy for modifying the intestinal microbiome to treat RA and other autoimmune and inflammatory diseases.

FUNDING: None.}, } @article {pmid37201276, year = {2023}, author = {Chen, L and Zheng, X and Zhang, K and Wu, B and Pei, X and Chen, W and Wei, X and Luo, Z and Li, Y and Zhang, Z}, title = {Sustained-release nitrate combined with microbial fuel cell: A novel strategy for PAHs and odor removal from sediment.}, journal = {Journal of hazardous materials}, volume = {455}, number = {}, pages = {131610}, doi = {10.1016/j.jhazmat.2023.131610}, pmid = {37201276}, issn = {1873-3336}, mesh = {Nitrates/metabolism ; *Bioelectric Energy Sources ; *Polycyclic Aromatic Hydrocarbons ; Odorants ; Collodion ; Delayed-Action Preparations ; Denitrification ; Biodegradation, Environmental ; Water ; Sulfides ; }, abstract = {Nitrate addition is a biostimulation technique that can improve both the oxidation of acid volatile sulfide (AVS) through autotrophic denitrification and the biodegradation of polycyclic aromatic hydrocarbons (PAHs) via heterotrophic denitrification. However, during the remediation, parts of the dissolved nitrate in the sediment migrates from the sediment to the overlying water, leading to the loss of effective electron acceptor. To overcome this limitation, a combined approached was proposed, which involved nitrocellulose addition and a microbial fuel cell (MFC). Results indicated the nitrate could be slowly released and maintained at a higher concentration over long term. In the combined system, the removal efficiencies of PAHs and AVS were 71.56% and 89.76%, respectively. Furthermore, the voltage attained for the MFC-nitrocellulose treatment was maintained at 146.1 mV on Day 70, which was 5.37 times higher than that of the MFC-calcium nitrate treatment. Sediments with nitrocellulose resulted in lower levels of nitrate and ammonium in the overlying water. Metagenomic results revealed that the combined technology improved the expression of nitrogen-cycling genes. The introduction of MFC inhibited sulfide regeneration during incubation by suppressing the enzyme activity like EC4.4.1.2. The enhanced biostimulation provided potential for in-situ bioremediation utilizing MFC coupled with slow-released nitrate (i.e., nitrocellulose) treatment.}, } @article {pmid37201116, year = {2023}, author = {Dahdouh, E and Cendejas-Bueno, E and Ruiz-Carrascoso, G and Schüffelmann, C and Lázaro-Perona, F and Castro-Martínez, M and Moreno-Ramos, F and Escosa-García, L and Alguacil-Guillén, M and Mingorance, J}, title = {Intestinal loads of extended-spectrum beta-lactamase and Carbapenemase genes in critically ill pediatric patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1180714}, pmid = {37201116}, issn = {2235-2988}, mesh = {Adult ; Humans ; Child ; *Critical Illness ; *beta-Lactamases/genetics ; Bacterial Proteins/genetics ; Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Gram-Negative Bacteria ; Microbial Sensitivity Tests ; }, abstract = {INTRODUCTION: Intestinal colonization by Multi-Drug Resistant Organisms (MDROs) can pose a threat on the health of critically ill patients. The extent of colonization by these organisms is related to previous antibiotic treatments and their ability to cause infections among adult patients. The aim of this study is to determine the relationship between the intestinal Relative Loads (RLs) of selected antibiotic resistance genes, antibiotic consumption and extra-intestinal spread among critically ill pediatric patients.

METHODS: RLs of bla CTX-M-1-Family, bla OXA-1, bla OXA-48 and bla VIM were determined in 382 rectal swabs obtained from 90 pediatric critically ill patients using qPCRs. The RLs were compared to the patients' demographics, antibiotic consumption, and detection of MDROs from extra-intestinal sites. 16SrDNA metagenomic sequencing was performed for 40 samples and clonality analyses were done for representative isolates.

RESULTS AND DISCUSSION: 76 (74.45%) patients from which 340 (89.01%) rectal swabs were collected had at least one swab that was positive for one of the tested genes. Routine cultures did not identify carbapenemases in 32 (45.1%) and 78 (58.2%) swabs that were positive by PCR for bla OXA-48 and blaVIM, respectively. RLs of above 6.5% were associated with extra-intestinal spread of blaOXA-48-harboring MDROs. Consumption of carbapenems, non-carbapenem β-lactams, and glycopeptides were statistically associated with testing negative for bla CTX-M-1-Family and bla OXA-1 while the consumption of trimethoprim/sulfamethoxazole and aminoglycosides was associated with testing negative for blaOXA-48 (P<0.05). In conclusion, targeted qPCRs can be used to determine the extent of intestinal dominance by antibiotic resistant opportunistic pathogens and their potential to cause extra-intestinal infections among a critically ill pediatric population.}, } @article {pmid37201115, year = {2023}, author = {Fernandez-Garcia, MD and Faye, M and Diez-Fuertes, F and Moreno-Docón, A and Chirlaque-López, MD and Faye, O and Cabrerizo, M}, title = {Metagenomic sequencing, molecular characterization, and Bayesian phylogenetics of imported type 2 vaccine-derived poliovirus, Spain, 2021.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1168355}, pmid = {37201115}, issn = {2235-2988}, mesh = {Humans ; *Poliovirus/genetics ; Phylogeny ; *Poliomyelitis/epidemiology/prevention & control ; Spain/epidemiology ; Bayes Theorem ; Poliovirus Vaccine, Oral ; }, abstract = {INTRODUCTION: In 2021, a type 2 vaccine-derived poliovirus (VDPV2) was isolated from the stool of a patient with acute flaccid paralysis (AFP) admitted to Spain from Senegal. A virological investigation was conducted to characterize and trace the origin of VDPV2.

METHODS: We used an unbiased metagenomic approach for the whole-genome sequencing of VDPV2 from the stool (pre-treated with chloroform) and from the poliovirus-positive supernatant. Phylogenetic analyses and molecular epidemiological analyses relying on the Bayesian Markov Chain Monte Carlo methodology were used to determine the geographical origin and estimate the date of the initiating dose of the oral poliovirus vaccine for the imported VDPV2.

RESULTS: We obtained a high percentage of viral reads per total reads mapped to the poliovirus genome (69.5% for pre-treated stool and 75.8% for isolate) with a great depth of sequencing coverage (5,931 and 11,581, respectively) and complete genome coverage (100%). The two key attenuating mutations in the Sabin 2 strain had reverted (A481G in the 5'UTR and Ile143Thr in VP1). In addition, the genome had a recombinant structure between type-2 poliovirus and an unidentified non-polio enterovirus-C (NPEV-C) strain with a crossover point in the protease-2A genomic region. VP1 phylogenetic analysis revealed that this strain is closely related to VDPV2 strains circulating in Senegal in 2021. According to Bayesian phylogenetics, the most recent common ancestor of the imported VDPV2 could date back 2.6 years (95% HPD: 1.7-3.7) in Senegal. We suggest that all VDPV2s circulating in 2020-21 in Senegal, Guinea, Gambia, and Mauritania have an ancestral origin in Senegal estimated around 2015. All 50 stool samples from healthy case contacts collected in Spain (n = 25) and Senegal (n = 25) and four wastewater samples collected in Spain were poliovirus negative.

DISCUSSION: By using a whole-genome sequencing protocol with unbiased metagenomics from the clinical sample and viral isolate with high sequence coverage, efficiency, and throughput, we confirmed the classification of VDPV as a circulating type. The close genomic linkage with strains from Senegal was consistent with their classification as imported. Given the scarce number of complete genome sequences for NPEV-C in public databases, this protocol could help expand poliovirus and NPEV-C sequencing capacity worldwide.}, } @article {pmid37200913, year = {2023}, author = {Bai, Y and Li, Y and Liu, W and Li, J and Tian, F and Liu, L and Han, X and Tong, Y}, title = {Analysis of the diversity of tick-borne viruses at the border areas in Liaoning Province, China.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1179156}, pmid = {37200913}, issn = {1664-302X}, abstract = {Ticks play a significant role in transmitting arboviruses, which pose a risk to human and animal health. The region of Liaoning Province, China, with abundant plant resources with multiple tick populations, has reported several tick-borne diseases. However, there remains a scarcity of research on the composition and evolution of the tick virome. In this study, we conducted the metagenomic analysis of 561 ticks in the border area of Liaoning Province in China and identified viruses related to known diseases in humans and animals, including severe fever with thrombocytopenia syndrome virus (SFTSV) and nairobi sheep disease virus (NSDV). Moreover, the groups of tick viruses were also closely related to the families of Flaviviridae, Parvoviridae, Phenuiviridae, and Rhabdoviridae. Notably, the Dabieshan tick virus (DBTV) of the family Phenuiviridae was prevalent in these ticks, with the minimum infection rate (MIR) of 9.09%, higher than previously reported in numerous provinces in China. In addition, sequences of tick-borne viruses of the family Rhabdoviridae have first been reported from the border area of Liaoning Province, China, after being described from Hubei Province, China. This research furthered the insight into pathogens carried by ticks in the northeastern border areas of China, offering epidemiological information for possible forthcoming outbreaks of infectious diseases. Meanwhile, we provided an essential reference for assessing the risk of tick bite infection in humans and animals, as well as for exploring into the evolution of the virus and the mechanisms of species transmission.}, } @article {pmid37200912, year = {2023}, author = {Dai, R and Ma, X and Dingkao, R and Huang, C and La, Y and Li, X and Ma, X and Wu, X and Chu, M and Guo, X and Pei, J and Yan, P and Liang, C}, title = {Effects of dietary crude protein levels in the concentrate supplement after grazing on rumen microbiota and metabolites by using metagenomics and metabolomics in Jersey-yak.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1124917}, pmid = {37200912}, issn = {1664-302X}, abstract = {INTRODUCTION: The crude protein level in the diet will affect the fermentation parameters, microflora, and metabolites in the rumen of ruminants. It is of great significance to study the effect of crude protein levels in supplementary diet on microbial community and metabolites for improving animal growth performance. At present, the effects of crude protein level in supplementary diet on rumen fermentation parameters, microbial community, and metabolites of Jersey-Yak (JY) are still unclear.

METHODS: The purpose of this experiment was to study the appropriate crude protein level in the diet of JY. The rumen fermentation indexes (volatile fatty acids and pH) were determined by supplementary diets with crude protein levels of 15.16 and 17.90%, respectively, and the microbial community and metabolites of JYs were analyzed by non-target metabonomics and metagenome sequencing technology, and the changes of rumen fermentation parameters, microbial flora, and metabolites in the three groups and their interactions were studied.

RESULTS AND DISCUSSION: The crude protein level in the supplementary diet had significant effects on pH, valeric acid, and the ratio of acetic acid to propionic acid (p < 0.05). The protein level had no significant effect on the dominant microflora at the phylum level (p > 0.05), and all three groups were Bacteroides and Firmicutes. The results of metabolite analysis showed that the crude protein level of supplementary diet significantly affected the metabolic pathways such as Bile secretion and styrene degradation (p < 0.05), and there were different metabolites between the LP group and HP group, and these different metabolites were related to the dominant microbial to some extent. To sum up, in this experiment, the effects of crude protein level in supplementary diet on rumen microorganisms and metabolites of JY and their relationship were studied, which provided the theoretical basis for formulating a more scientific and reasonable supplementary diet in the future.}, } @article {pmid37200788, year = {2023}, author = {Vassileva, I and Baev, V and Yahubyan, G and Apostolova-Kuzova, E and Angelov, A and Koprinarova, M}, title = {Identification of Bulgarian Sourdough Microbiota by Metagenomic Approach Using Three Commercially Available DNA Extraction Protocols.}, journal = {Food technology and biotechnology}, volume = {61}, number = {1}, pages = {138-147}, pmid = {37200788}, issn = {1330-9862}, abstract = {RESEARCH BACKGROUND: Sourdough is a spontaneously formed, complex microbial ecosystem of various lactic acid bacteria (LAB) and yeast which, by producing specific metabolites, determines the quality of the baked products. In order to design and control the sourdough with preferred nutritional characteristics, it is crucial that the LAB diversity of the product of interest be elucidated.

EXPERIMENTAL APPROACH: Using the opportunities of next-generation sequencing (NGS) of the V1-V3 hypervariable gene region of 16S rRNA, we studied the microbial ecosystem of a whole grain sourdough made of Triticum monococcum, originating from Southwestern Bulgaria. Since the DNA extraction method is considered crucial for the accuracy of the sequencing results, as it can introduce significant differences in the examined microbiota, we used three different commercial kits for DNA isolation and analyzed their impact on the observed bacterial diversity.

RESULTS AND CONCLUSIONS: All three DNA extraction kits provided bacterial DNA which passed quality control and was successfully sequenced on Illumina MiSeq platform. The results received from the different DNA protocols showed variations in the microbial profiles. Alpha diversity indices (ACE, Chao1, Shannon, and Simpson) were also different among the three groups of results. Nevertheless, a strong dominance of phylum Firmicutes, class Bacilli, order Lactobacillales, represented mostly by family Lactobacillaceae, genus Lactobacillus (relative abundance of 63.11-82.28%) and family Leuconostocaceae, genus Weissella (relative abundance of 3.67-36.31%) was observed. Lactiplantibacillus plantarum and Levilactobacillus brevis with relative abundance of 16.15-31.24% and 6.21-16.29% respectively, were the two dominant species identified in all three DNA isolates.

The presented results give insight into the taxonomic composition of bacterial community of a specific Bulgarian sourdough. Having in mind that the sourdough is a difficult matrix for DNA isolation on the one hand, and that there is no standardized DNA extraction protocol for this matrix on the other hand, this pilot study aims to give a small contribution to the future establishment and validation of such a protocol, which will allow accurate assessment of the specific microbiota of sourdough samples.}, } @article {pmid37199998, year = {2023}, author = {Getz, EW and Lanclos, VC and Kojima, CY and Cheng, C and Henson, MW and Schön, ME and Ettema, TJG and Faircloth, BC and Thrash, JC}, title = {The AEGEAN-169 clade of bacterioplankton is synonymous with SAR11 subclade V (HIMB59) and metabolically distinct.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0017923}, pmid = {37199998}, issn = {2379-5077}, support = {Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation/ ; OCE-1945279, EF-2125191//National Science Foundation/ ; }, mesh = {*Seawater/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Aquatic Organisms ; Bacteria/genetics ; *Alphaproteobacteria ; }, abstract = {Bacterioplankton of the SAR11 clade are the most abundant marine microorganisms and consist of numerous subclades spanning order-level divergence (Pelagibacterales). The assignment of the earliest diverging subclade V (a.k.a. HIMB59) to the Pelagibacterales is highly controversial, with multiple recent phylogenetic studies placing them completely separate from SAR11. Other than through phylogenomics, subclade V has not received detailed examination due to limited genomes from this group. Here, we assessed the ecogenomic characteristics of subclade V to better understand the role of this group in comparison to the Pelagibacterales. We used a new isolate genome, recently released single-amplified genomes and metagenome-assembled genomes, and previously established SAR11 genomes to perform a comprehensive comparative genomics analysis. We paired this analysis with the recruitment of metagenomes spanning the open ocean, coastal, and brackish systems. Phylogenomics, average amino acid identity, and 16S rRNA gene phylogeny indicate that SAR11 subclade V is synonymous with the ubiquitous AEGEAN-169 clade and support the contention that this group represents a taxonomic family. AEGEAN-169 shared many bulk genome qualities with SAR11, such as streamlining and low GC content, but genomes were generally larger. AEGEAN-169 had overlapping distributions with SAR11 but was metabolically distinct from SAR11 in its potential to transport and utilize a broader range of sugars as well as in the transport of trace metals and thiamin. Thus, regardless of the ultimate phylogenetic placement of AEGEAN-169, these organisms have distinct metabolic capacities that likely allow them to differentiate their niche from canonical SAR11 taxa. IMPORTANCE One goal of marine microbiologists is to uncover the roles various microorganisms are playing in biogeochemical cycles. Success in this endeavor relies on differentiating groups of microbes and circumscribing their relationships. An early-diverging group (subclade V) of the most abundant bacterioplankton, SAR11, has recently been proposed as a separate lineage that does not share a most recent common ancestor. But beyond phylogenetics, little has been done to evaluate how these organisms compare with SAR11. Our work leverages dozens of new genomes to demonstrate the similarities and differences between subclade V and SAR11. In our analysis, we also establish that subclade V is synonymous with a group of bacteria established from 16S rRNA gene sequences, AEGEAN-169. Subclade V/AEGEAN-169 has clear metabolic distinctions from SAR11 and their shared traits point to remarkable convergent evolution if they do not share a most recent common ancestor.}, } @article {pmid37199989, year = {2023}, author = {Duarte, ASR and Marques, AR and Andersen, VD and Korsgaard, HB and Mordhorst, H and Møller, FD and Petersen, TN and Vigre, H and Hald, T and Aarestrup, FM}, title = {Antimicrobial resistance monitoring in the Danish swine production by phenotypic methods and metagenomics from 1999 to 2018.}, journal = {Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin}, volume = {28}, number = {20}, pages = {}, pmid = {37199989}, issn = {1560-7917}, mesh = {Swine ; Animals ; Female ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Bacterial/genetics ; Metagenomics ; Macrolides ; *Anti-Infective Agents ; Bacteria/genetics ; Escherichia coli/genetics ; Protein Synthesis Inhibitors ; Denmark ; }, abstract = {BackgroundIn Denmark, antimicrobial resistance (AMR) in pigs has been monitored since 1995 by phenotypic approaches using the same indicator bacteria. Emerging methodologies, such as metagenomics, may allow novel surveillance ways.AimThis study aimed to assess the relevance of indicator bacteria (Escherichia coli and Enterococcus faecalis) for AMR surveillance in pigs, and the utility of metagenomics.MethodsWe collated existing data on AMR and antimicrobial use (AMU) from the Danish surveillance programme and performed metagenomics sequencing on caecal samples that had been collected/stored through the programme during 1999-2004 and 2015-2018. We compared phenotypic and metagenomics results regarding AMR, and the correlation of both with AMU.ResultsVia the relative abundance of AMR genes, metagenomics allowed to rank these genes as well as the AMRs they contributed to, by their level of occurrence. Across the two study periods, resistance to aminoglycosides, macrolides, tetracycline, and beta-lactams appeared prominent, while resistance to fosfomycin and quinolones appeared low. In 2015-2018 sulfonamide resistance shifted from a low occurrence category to an intermediate one. Resistance to glycopeptides consistently decreased during the entire study period. Outcomes of both phenotypic and metagenomics approaches appeared to positively correlate with AMU. Metagenomics further allowed to identify multiple time-lagged correlations between AMU and AMR, the most evident being that increased macrolide use in sow/piglets or fatteners led to increased macrolide resistance with a lag of 3-6 months.ConclusionWe validated the long-term usefulness of indicator bacteria and showed that metagenomics is a promising approach for AMR surveillance.}, } @article {pmid37199915, year = {2023}, author = {Begeman, A and Babaian, A and Lewis, SC}, title = {Metatranscriptomic analysis uncovers prevalent viral ORFs compatible with mitochondrial translation.}, journal = {mSystems}, volume = {8}, number = {3}, pages = {e0100222}, pmid = {37199915}, issn = {2379-5077}, support = {R00 GM129456/GM/NIGMS NIH HHS/United States ; R35 GM147218/GM/NIGMS NIH HHS/United States ; T32 GM007232/GM/NIGMS NIH HHS/United States ; R00GM129456/NH/NIH HHS/United States ; }, mesh = {Open Reading Frames ; *RNA Viruses/genetics ; *Viruses/genetics ; Codon ; RNA-Dependent RNA Polymerase/genetics ; }, abstract = {RNA viruses are ubiquitous components of the global virosphere, yet relatively little is known about their genetic diversity or the cellular mechanisms by which they exploit the biology of their diverse eukaryotic hosts. A hallmark of (+)ssRNA (positive single-stranded RNA) viruses is the ability to remodel host endomembranes for their own replication. However, the subcellular interplay between RNA viruses and host organelles that harbor gene expression systems, such as mitochondria, is complex and poorly understood. Here we report the discovery of 763 new virus sequences belonging to the family Mitoviridae by metatranscriptomic analysis, the identification of previously uncharacterized mitovirus clades, and a putative new viral class. With this expanded understanding of the diversity of mitovirus and encoded RNA-dependent RNA polymerases (RdRps), we annotate mitovirus-specific protein motifs and identify hallmarks of mitochondrial translation, including mitochondrion-specific codons. This study expands the known diversity of mitochondrial viruses and provides additional evidence that they co-opt mitochondrial biology for their survival. IMPORTANCE Metatranscriptomic studies have rapidly expanded the cadre of known RNA viruses, yet our understanding of how these viruses navigate the cytoplasmic milieu of their hosts to survive remains poorly characterized. In this study, we identify and assemble 763 new viral sequences belonging to the Mitoviridae, a family of (+)ssRNA viruses thought to interact with and remodel host mitochondria. We exploit this genetic diversity to identify new clades of Mitoviridae, annotate clade-specific sequence motifs that distinguish the mitoviral RdRp, and reveal patterns of RdRp codon usage consistent with translation on host cell mitoribosomes. These results serve as a foundation for understanding how mitoviruses co-opt mitochondrial biology for their proliferation.}, } @article {pmid37199659, year = {2023}, author = {Cebriá-Mendoza, M and Beamud, B and Andreu-Moreno, I and Arbona, C and Larrea, L and Díaz, W and Sanjuán, R and Cuevas, JM}, title = {Human Anelloviruses: Influence of Demographic Factors, Recombination, and Worldwide Diversity.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0492822}, pmid = {37199659}, issn = {2165-0497}, mesh = {Male ; Humans ; Female ; *Anelloviridae/genetics ; *DNA Virus Infections/epidemiology ; *Torque teno virus/genetics ; Demography ; Recombination, Genetic ; DNA, Viral ; }, abstract = {Anelloviruses represent the major and most diverse component of the healthy human virome, referred to as the anellome. In this study, we determined the anellome of 50 blood donors, forming two sex- and age-matched groups. Anelloviruses were detected in 86% of the donors. The number of detected anelloviruses increased with age and was approximately twice as high in men as in women. A total of 349 complete or nearly complete genomes were classified as belonging to torque teno virus (TTV), torque teno mini virus (TTMV), and torque teno midi virus (TTMDV) anellovirus genera (197, 88, and 64 sequences, respectively). Most donors had intergenus (69.8%) or intragenus (72.1%) coinfections. Despite the limited number of sequences, intradonor recombination analysis showed 6 intragenus recombination events in ORF1. As thousands of anellovirus sequences have been described recently, we finally analyzed the global diversity of human anelloviruses. Species richness and diversity were close to saturation in each anellovirus genus. Recombination was found to be the main factor promoting diversity, although its effect was significantly lower in TTV than in TTMV and TTMDV. Overall, our results suggest that differences in diversity between genera may be caused by variations in the relative contribution of recombination. IMPORTANCE Anelloviruses are the most common human infectious viruses and are considered essentially harmless. Compared to other human viruses, they are characterized by enormous diversity, and recombination is suggested to play an important role in their diversification and evolution. Here, by analyzing the composition of the plasma anellome of 50 blood donors, we find that recombination is also a determinant of viral evolution at the intradonor level. On a larger scale, analysis of anellovirus sequences currently available in databases shows that their diversity is close to saturation and differs among the three human anellovirus genera and that recombination is the main factor explaining this intergenus variability. Global characterization of anellovirus diversity could provide clues about possible associations between certain virus variants and pathologies, as well as facilitate the implementation of unbiased PCR-based detection protocols, which may be relevant for using anelloviruses as endogenous markers of immune status.}, } @article {pmid37199657, year = {2023}, author = {Sylvain, FÉ and Bouslama, S and Holland, A and Leroux, N and Mercier, PL and Val, AL and Derome, N}, title = {Bacterioplankton Communities in Dissolved Organic Carbon-Rich Amazonian Black Water.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0479322}, pmid = {37199657}, issn = {2165-0497}, mesh = {*Water ; *Dissolved Organic Matter ; RNA, Ribosomal, 16S/genetics ; Aquatic Organisms ; Carbon/analysis ; }, abstract = {The Amazon River basin sustains dramatic hydrochemical gradients defined by three water types: white, clear, and black waters. In black water, important loads of allochthonous humic dissolved organic matter (DOM) result from the bacterioplankton degradation of plant lignin. However, the bacterial taxa involved in this process remain unknown, since Amazonian bacterioplankton has been poorly studied. Its characterization could lead to a better understanding of the carbon cycle in one of the Earth's most productive hydrological systems. Our study characterized the taxonomic structure and functions of Amazonian bacterioplankton to better understand the interplay between this community and humic DOM. We conducted a field sampling campaign comprising 15 sites distributed across the three main Amazonian water types (representing a gradient of humic DOM), and a 16S rRNA metabarcoding analysis based on bacterioplankton DNA and RNA extracts. Bacterioplankton functions were inferred using 16S rRNA data in combination with a tailored functional database from 90 Amazonian basin shotgun metagenomes from the literature. We discovered that the relative abundances of fluorescent DOM fractions (humic-, fulvic-, and protein-like) were major drivers of bacterioplankton structure. We identified 36 genera for which the relative abundance was significantly correlated with humic DOM. The strongest correlations were found in the Polynucleobacter, Methylobacterium, and Acinetobacter genera, three low abundant but omnipresent taxa that possessed several genes involved in the main steps of the β-aryl ether enzymatic degradation pathway of diaryl humic DOM residues. Overall, this study identified key taxa with DOM degradation genomic potential, the involvement of which in allochthonous Amazonian carbon transformation and sequestration merits further investigation. IMPORTANCE The Amazon basin discharge carries an important load of terrestrially derived dissolved organic matter (DOM) to the ocean. The bacterioplankton from this basin potentially plays important roles in transforming this allochthonous carbon, which has consequences on marine primary productivity and global carbon sequestration. However, the structure and function of Amazonian bacterioplanktonic communities remain poorly studied, and their interactions with DOM are unresolved. In this study, we (i) sampled bacterioplankton in all the main Amazon tributaries, (ii) combined information from the taxonomic structure and functional repertory of Amazonian bacterioplankton communities to understand their dynamics, (iii) identified the main physicochemical parameters shaping bacterioplanktonic communities among a set of >30 measured environmental parameters, and (iv) characterized how bacterioplankton structure varies according to the relative abundance of humic compounds, a by-product from the bacterial degradation process of allochthonous DOM.}, } @article {pmid37199636, year = {2023}, author = {Muzny, CA and Cerca, N and Elnaggar, JH and Taylor, CM and Sobel, JD and Van Der Pol, B}, title = {State of the Art for Diagnosis of Bacterial Vaginosis.}, journal = {Journal of clinical microbiology}, volume = {61}, number = {8}, pages = {e0083722}, pmid = {37199636}, issn = {1098-660X}, support = {R01 AI146065/AI/NIAID NIH HHS/United States ; R21 AI167754/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Female ; *Vaginosis, Bacterial/diagnosis/microbiology ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; Vagina/microbiology ; *Sexually Transmitted Diseases ; }, abstract = {Bacterial vaginosis (BV) is the most common cause of vaginal discharge among reproductive-age women. It is associated with multiple adverse health outcomes, including increased risk of acquisition of HIV and other sexually transmitted infections (STIs), in addition to adverse birth outcomes. While it is known that BV is a vaginal dysbiosis characterized by a shift in the vaginal microbiota from protective Lactobacillus species to an increase in facultative and strict anaerobic bacteria, its exact etiology remains unknown. The purpose of this minireview is to provide an updated overview of the range of tests currently used for the diagnosis of BV in both clinical and research settings. This article is divided into two primary sections: traditional BV diagnostics and molecular diagnostics. Molecular diagnostic assays, particularly 16S rRNA gene sequencing, shotgun metagenomic sequencing, and fluorescence in situ hybridization (FISH), are specifically highlighted, in addition to multiplex nucleic acid amplification tests (NAATs), given their increasing use in clinical practice (NAATs) and research studies (16S rRNA gene sequencing, shotgun metagenomic sequencing, and FISH) regarding the vaginal microbiota and BV pathogenesis. We also provide a discussion of the strengths and weaknesses of current BV diagnostic tests and discuss future challenges in this field of research.}, } @article {pmid37199622, year = {2023}, author = {Kristensen, M and de Koff, EM and Chu, ML and Groendijk, S and Tramper-Stranders, GA and de Winter-de Groot, KM and Janssens, HM and Tiddens, HA and van Westreenen, M and Sanders, EAM and Arets, BHGM and van der Ent, CK and Prevaes, SMPJ and Bogaert, D}, title = {16S rRNA-Based Microbiota Profiling Assists Conventional Culture Analysis of Airway Samples from Pediatric Cystic Fibrosis Patients.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0405722}, pmid = {37199622}, issn = {2165-0497}, mesh = {Infant ; Humans ; Child ; Infant, Newborn ; *Cystic Fibrosis/diagnosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Respiratory System/microbiology ; Bacteria/genetics ; *Microbiota/genetics ; }, abstract = {16S-based sequencing provides broader information on the respiratory microbial community than conventional culturing. However, it (often) lacks species- and strain-level information. To overcome this issue, we used 16S rRNA-based sequencing results from 246 nasopharyngeal samples obtained from 20 infants with cystic fibrosis (CF) and 43 healthy infants, which were all 0 to 6 months old, and compared them to both standard (blind) diagnostic culturing and a 16S-sequencing-informed "targeted" reculturing approach. Using routine culturing, we almost uniquely detected Moraxella catarrhalis, Staphylococcus aureus, and Haemophilus influenzae (42%, 38%, and 33% of samples, respectively). Using the targeted reculturing approach, we were able to reculture 47% of the top-5 operational taxonomical units (OTUs) in the sequencing profiles. In total, we identified 60 species from 30 genera with a median of 3 species per sample (range, 1 to 8). We also identified up to 10 species per identified genus. The success of reculturing the top-5 genera present from the sequencing profile depended on the genus. In the case of Corynebacterium being in the top 5, we recultured them in 79% of samples, whereas for Staphylococcus, this value was only 25%. The success of reculturing was also correlated with the relative abundance of those genera in the corresponding sequencing profile. In conclusion, revisiting samples using 16S-based sequencing profiles to guide a targeted culturing approach led to the detection of more potential pathogens per sample than conventional culturing and may therefore be useful in the identification and, consequently, treatment of bacteria considered relevant for the deterioration or exacerbation of disease in patients like those with CF. IMPORTANCE Early and effective treatment of pulmonary infections in cystic fibrosis is vital to prevent chronic lung damage. Although microbial diagnostics and treatment decisions are still based on conventional culture methods, research is gradually focusing more on microbiome and metagenomic-based approaches. This study compared the results of both methods and proposed a way to combine the best of both worlds. Many species can relatively easily be recultured based on the 16S-based sequencing profile, and it provides more in-depth information about the microbial composition of a sample than that obtained through routine (blind) diagnostic culturing. Still, well-known pathogens can be missed by both routine diagnostic culture methods as well as by targeted reculture methods, sometimes even when they are highly abundant, which may be a consequence of either sample storage conditions or antibiotic treatment at the time of sampling.}, } @article {pmid37199613, year = {2023}, author = {Okoh, GR and Ariel, E and Whitmore, D and Horwood, PF}, title = {Draft Genome Sequence of a Novel Adenovirus Recovered from the Metagenome of Agile Wallabies.}, journal = {Microbiology resource announcements}, volume = {12}, number = {6}, pages = {e0011223}, pmid = {37199613}, issn = {2576-098X}, support = {//Australian Wildlife Society (AWS)/ ; //James Cook University Higher Degree Research Enhancement Scheme Grant/ ; }, abstract = {Here, we report the draft genome sequence of a novel agile wallaby adenovirus that was detected in the fecal metagenome of agile wallabies. The genome is 31,512 bp long, with a G+C content of 34.4%. Currently, the pathogenic and zoonotic potential of this novel virus is unknown.}, } @article {pmid37198283, year = {2023}, author = {Wang, Y and Sun, Y and Li, X and Chen, R and Li, W and Ji, L and Zhao, Q and Ji, L and Yang, S and Zhang, W}, title = {Molecular detection and characterization of three novel parvoviruses belonging to two different subfamilies in zoo birds.}, journal = {Archives of virology}, volume = {168}, number = {6}, pages = {163}, pmid = {37198283}, issn = {1432-8798}, support = {2022YFC2603801//National Key Research and Development Programs of China/ ; 32102682//National Natural Science Foundation of China/ ; 21KJB230006//Science Foundation of Higher Education of Jiangsu Province/ ; 2020CPB-C11//Chengdu Research Base of Giant Panda Breeding/ ; }, mesh = {Animals ; Humans ; Phylogeny ; *Parvovirus/genetics ; *Parvoviridae Infections/epidemiology/veterinary ; Birds ; *Parvovirinae/genetics ; *Viruses ; }, abstract = {Birds carry a large number of viruses that may cause diseases in animals or humans. At present, information about the virome of zoo birds is limited. In this study, using viral metagenomics, we investigated the fecal virome of zoo birds collected from a zoo in Nanjing, Jiangsu Province, China. Three novel parvoviruses were obtained and characterized. The genomes of the three viruses are 5,909, 4,411, and 4,233 nt in length, respectively, and contain four or five ORFs. Phylogenetic analysis showed that these three novel parvoviruses clustered with other strains and formed three different clades. Pairwise comparison of NS1 amino acid sequences showed that Bir-01-1 shared 44.30-74.92% aa sequence identity with other parvoviruses belonging to the genus Aveparvovirus, while Bir-03-1 and Bir-04-1 shared less than 66.87% and 53.09% aa sequence identity, respectively, with other parvoviruses belonging to the genus Chaphamaparvovirus. Each of these three viruses was identified as a member of a novel species based on the species demarcation criteria for parvoviruses. These findings broaden our knowledge of the genetic diversity of parvoviruses and provide epidemiological data regarding potential outbreaks of parvovirus disease in birds.}, } @article {pmid37197440, year = {2023}, author = {Dora, D and Ligeti, B and Kovacs, T and Revisnyei, P and Galffy, G and Dulka, E and Krizsán, D and Kalcsevszki, R and Megyesfalvi, Z and Dome, B and Weiss, GJ and Lohinai, Z}, title = {Non-small cell lung cancer patients treated with Anti-PD1 immunotherapy show distinct microbial signatures and metabolic pathways according to progression-free survival and PD-L1 status.}, journal = {Oncoimmunology}, volume = {12}, number = {1}, pages = {2204746}, pmid = {37197440}, issn = {2162-402X}, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung/drug therapy/pathology ; *Lung Neoplasms/drug therapy/pathology ; Progression-Free Survival ; B7-H1 Antigen ; *Antineoplastic Agents, Immunological/adverse effects ; Immunotherapy ; Metabolic Networks and Pathways ; }, abstract = {Due to the high variance in response rates concerning anti-PD1 immunotherapy (IT), there is an unmet need to discover innovative biomarkers to predict immune checkpoint inhibitor (ICI)-efficacy. Our study included 62 Caucasian advanced-stage non-small cell lung cancer (NSCLC) patients treated with anti-PD1 ICI. Gut bacterial signatures were evaluated by metagenomic sequencing and correlated with progression-free survival (PFS), PD-L1 expression and other clinicopathological parameters. We confirmed the predictive role of PFS-related key bacteria with multivariate statistical models (Lasso- and Cox-regression) and validated on an additional patient cohort (n = 60). We find that alpha-diversity showed no significant difference in any comparison. However, there was a significant difference in beta-diversity between patients with long- (>6 months) vs. short (≤6 months) PFS and between chemotherapy (CHT)-treated vs. CHT-naive cases. Short PFS was associated with increased abundance of Firmicutes (F) and Actinobacteria phyla, whereas elevated abundance of Euryarchaeota was specific for low PD-L1 expression. F/Bacteroides (F/B) ratio was significantly increased in patients with short PFS. Multivariate analysis revealed an association between Alistipes shahii, Alistipes finegoldii, Barnesiella visceriola, and long PFS. In contrast, Streptococcus salivarius, Streptococcus vestibularis, and Bifidobacterium breve were associated with short PFS. Using Random Forest machine learning approach, we find that taxonomic profiles performed superiorly in predicting PFS (AUC = 0.74), while metabolic pathways including Amino Acid Synthesis and Fermentation were better predictors of PD-L1 expression (AUC = 0.87). We conclude that specific metagenomic features of the gut microbiome, including bacterial taxonomy and metabolic pathways might be suggestive of ICI efficacy and PD-L1 expression in NSCLC patients.}, } @article {pmid37197021, year = {2023}, author = {Chaudhari, HG and Prajapati, S and Wardah, ZH and Raol, G and Prajapati, V and Patel, R and Shati, AA and Alfaifi, MY and Elbehairi, SEI and Sayyed, RZ}, title = {Decoding the microbial universe with metagenomics: a brief insight.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1119740}, pmid = {37197021}, issn = {1664-8021}, abstract = {A major part of any biological system on earth involves microorganisms, of which the majority are yet to be cultured. The conventional methods of culturing microbes have given fruitful outcomes yet have limitations. The curiosity for better understanding has led to the development of culture-independent molecular methods that help push aside the roadblocks of earlier methods. Metagenomics unifies the scientific community in search of a better understanding of the functioning of the ecosystem and its component organisms. This approach has opened a new paradigm in advanced research. It has brought to light the vast diversity and novelty among microbial communities and their genomes. This review focuses on the development of this field over time, the techniques and analysis of data generated through sequencing platforms, and its prominent interpretation and representation.}, } @article {pmid37196954, year = {2023}, author = {Zhang, Y and Yang, S and Yang, J and Wu, Z and Liu, H and Nie, Z and Qu, J and Hu, Y and Shao, Y and Liu, J and Liu, F and Hua, D}, title = {Temporal hormetic response of soil microbes to cadmium: A metagenomic perspective.}, journal = {The Science of the total environment}, volume = {891}, number = {}, pages = {164190}, doi = {10.1016/j.scitotenv.2023.164190}, pmid = {37196954}, issn = {1879-1026}, mesh = {Cadmium/analysis ; Hormesis ; Soil/chemistry ; *Soil Pollutants/analysis ; *Metals, Heavy ; Soil Microbiology ; }, abstract = {The hormetic response of microbes to cadmium (Cd) is often observed in soil, but the mechanisms are unclear. In this study, we proposed a novel perspective of hormesis that successfully explained the temporal hermetic response of soil enzymes and microbes, and the variation of soil physicochemical properties. Several soil enzymatic and microbial activities were stimulated by 0.5 mg·kg[-1] exogenous Cd, but inhibited at higher Cd dosages. The phenomena suggested the hormetic response to 0.5 mg·kg[-1] Cd was highly generalizable concerning soil enzymes and microbial activity. However, the response disappeared after incubation for >10 days. Soil respiration was also initially enhanced by exogenous Cd and decreased after consumption of labile soil organic matter. The metagenomic results revealed Cd stimulation of genes involved in labile soil organic matter decomposition. Additionally, Cd enriched the antioxidant enzymatic activity and abundances of the corresponding marker genes, rather than genes involved in the efflux-mediated heavy metal resistance. The microbes enhanced their primary metabolism to make up the energy gaps, with hormesis evident. The hormetic response disappeared after the labile compounds in soil were exhausted. Overall, this study illustrates the dose-dependence and temporal variation of stimulants and provides a novel and feasible strategy for the study of Cd in soil microorganisms.}, } @article {pmid37196884, year = {2023}, author = {Lehman, PC and Cady, N and Ghimire, S and Shahi, SK and Shrode, RL and Lehmler, HJ and Mangalam, AK}, title = {Low-dose glyphosate exposure alters gut microbiota composition and modulates gut homeostasis.}, journal = {Environmental toxicology and pharmacology}, volume = {100}, number = {}, pages = {104149}, pmid = {37196884}, issn = {1872-7077}, support = {T32 AI007485/AI/NIAID NIH HHS/United States ; I01 CX002212/CX/CSRD VA/United States ; R01 AI137075/AI/NIAID NIH HHS/United States ; T90 DE023520/DE/NIDCR NIH HHS/United States ; P30 ES005605/ES/NIEHS NIH HHS/United States ; }, mesh = {Mice ; Humans ; Animals ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; *Herbicides/toxicity ; Homeostasis ; Glyphosate ; }, abstract = {The widespread use of glyphosate, a broad-spectrum herbicide, has resulted in significant human exposure, and recent studies have challenged the notion that glyphosate is safe for humans. Although the link between disease states and glyphosate exposure is increasingly appreciated, the mechanistic links between glyphosate and its toxic effects on human health are poorly understood. Recent studies have suggested that glyphosate may cause toxicity through modulation of the gut microbiome, but evidence for glyphosate-induced gut dysbiosis and its effect on host physiology at doses approximating the U.S. Acceptable Daily Intake (ADI = 1.75 mg/kg body weight) is limited. Here, utilizing shotgun metagenomic sequencing of fecal samples from C57BL/6 J mice, we show that glyphosate exposure at doses approximating the U.S. ADI significantly impacts gut microbiota composition. These gut microbial alterations were associated with effects on gut homeostasis characterized by increased proinflammatory CD4[+]IL17A[+] T cells and Lipocalin-2, a known marker of intestinal inflammation.}, } @article {pmid37196747, year = {2023}, author = {Zhang, Z and Yang, H and Wang, B and Chen, C and Zou, X and Cheng, T and Li, J}, title = {Aerobic co-composting of mature compost with cattle manure: Organic matter conversion and microbial community characterization.}, journal = {Bioresource technology}, volume = {382}, number = {}, pages = {129187}, doi = {10.1016/j.biortech.2023.129187}, pmid = {37196747}, issn = {1873-2976}, mesh = {Cattle ; Animals ; Soil ; Manure ; *Composting ; *Microbiota ; Carbohydrates ; }, abstract = {The production of organic fertilizer by aerobic composting of cattle manure is an important way of its resource utilization. This study evaluated the effects of adding mature compost on the decomposition and microbial communities in the aerobic composting of cattle manure. The addition of mature compost shortens the composting cycle and results in a final lignocellulosic degradation rate of 35%. Metagenomic analysis showed that this was due to the proliferation of thermophilic and organic matter-degrading functional microorganisms, which enhanced the activity of carbohydrate-active enzymes. With the addition of mature compost, the microbial community exhibited stronger metabolic functions, especially carbohydrate and amino acid metabolism, which are the driving forces of organic matter degradation. This study deepens the understanding of organic matter conversion and microbial community metabolic functions when mature compost is used for livestock manure composting and provides a promising technology for livestock manure composting.}, } @article {pmid37196739, year = {2023}, author = {Zhang, W and Yu, C and Yin, S and Chang, X and Chen, K and Xing, Y and Yang, Y}, title = {Transmission and retention of antibiotic resistance genes (ARGs) in chicken and sheep manure composting.}, journal = {Bioresource technology}, volume = {382}, number = {}, pages = {129190}, doi = {10.1016/j.biortech.2023.129190}, pmid = {37196739}, issn = {1873-2976}, mesh = {Animals ; Sheep/genetics ; *Composting ; Chickens/genetics ; Genes, Bacterial/genetics ; Manure/microbiology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; }, abstract = {Transmission of ARGs during composting with different feedstocks (i.e., sheep manure (SM), chicken manure (CM) and mixed manure (MM, SM:CM = 3:1 ratio) was studied by metagenomic sequencing. 53 subtypes of ARGs for 22 types of antibiotics were identified as commonly present in these compost mixes; among them, CM had higher abundance of ARGs, 1.69 times than that in SM, while the whole elimination rate of CM, MM and SM were 55.2%, 54.7% and 42.9%, respectively. More than 50 subtypes of ARGs (with 8.6%, 11.4% and 20.9% abundance in the initial stage in CM, MM and SM composting) were "diehard" ARGs, and their abundance grew significantly to 56.5%, 63.2% and 69.9% at the mature stage. These "diehard" ARGs were transferred from initial hosts of pathogenic and/or probiotic bacteria to final hosts of thermophilic bacteria, by horizontal gene transfer (HGT) via mobile gene elements (MGEs), and became rooted in composting products.}, } @article {pmid37196617, year = {2023}, author = {Wang, Q and Wei, S and Zhou, Y and Mašek, O and Khan, MA and Li, D and Liu, Q and Liu, Y and Lu, W and Su, X and Zhu, Z and Zhao, X and Bai, Y and Li, X and Jin, F and Wang, J and Huang, Q}, title = {Rhizosphere effect on the relationship between dissolved organic matter and functional genes in contaminated soil.}, journal = {Journal of environmental management}, volume = {342}, number = {}, pages = {118118}, doi = {10.1016/j.jenvman.2023.118118}, pmid = {37196617}, issn = {1095-8630}, mesh = {*Arsenic ; Dissolved Organic Matter ; Rhizosphere ; Ecosystem ; Soil ; *Soil Pollutants/analysis ; }, abstract = {Arsenic contamination in a mining area is a potential threat to the local population. In the context of one-health, biological pollution in contaminated soil should be known and understandable. This study was conducted to clarify the effects of amendments on arsenic species and potential threat factors (e.g., arsenic-related genes (AMGs), antibiotic resistance genes (ARGs) and heavy-metal resistance genes (MRGs)). Ten groups (control (CK), T1, T2, T3, T4, T5, T6, T7, T8, and T9) were set up by adding different ratio of organic fertilizer, biochar, hydroxyapatite and plant ash. The maize crop was grown in each treatment. Compared with CK, the bioavailability of arsenic was reduced by 16.2%-71.8% in the rhizosphere soil treatments, and 22.4%-69.2% in the bulk soil treatments, except for T8. The component 2 (C2), component 3 (C3) and component 5 (C5) of dissolved organic matter (DOM) increased by 22.6%-72.6%, 16.8%-38.1%, 18.4%-37.1%, respectively, relative to CK in rhizosphere soil. A total of 17 AMGs, 713 AGRs and 492 MRGs were detected in remediated soil. The humidification of DOM might directly correlate with MRGs in both soils, while it was influenced directly on ARGs in bulk soil. This may be caused by the rhizosphere effect, which affects the interaction between microbial functional genes and DOM. These findings provide a theoretical basis for regulating soil ecosystem function from the perspective of arsenic contaminated soil.}, } @article {pmid37196568, year = {2023}, author = {Xu, Y and Teng, Y and Wang, X and Ren, W and Zhao, L and Luo, Y and Christie, P and Greening, C}, title = {Endogenous biohydrogen from a rhizobium-legume association drives microbial biodegradation of polychlorinated biphenyl in contaminated soil.}, journal = {Environment international}, volume = {176}, number = {}, pages = {107962}, doi = {10.1016/j.envint.2023.107962}, pmid = {37196568}, issn = {1873-6750}, mesh = {*Polychlorinated Biphenyls/analysis ; *Rhizobium/metabolism ; *Fabaceae/metabolism ; Ecosystem ; *Soil Pollutants/analysis ; Biodegradation, Environmental ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Endogenous hydrogen (H2) is produced through rhizobium-legume associations in terrestrial ecosystems worldwide through dinitrogen fixation. In turn, this gas may alter rhizosphere microbial community structure and modulate biogeochemical cycles. However, very little is understood about the role that this H2 leaking to the rhizosphere plays in shaping the persistent organic pollutants degrading microbes in contaminated soils. Here, we combined DNA-stable isotope probing (DNA-SIP) with metagenomics to explore how endogenous H2 from the symbiotic rhizobium-alfalfa association drives the microbial biodegradation of tetrachlorobiphenyl PCB 77 in a contaminated soil. The results showed that PCB77 biodegradation efficiency increased significantly in soils treated with endogenous H2. Based on metagenomes of [13]C-enriched DNA fractions, endogenous H2 selected bacteria harboring PCB degradation genes. Functional gene annotation allowed the reconstruction of several complete pathways for PCB catabolism, with different taxa conducting successive metabolic steps of PCB metabolism. The enrichment through endogenous H2 of hydrogenotrophic Pseudomonas and Magnetospirillum encoding biphenyl oxidation genes drove PCB biodegradation. This study proves that endogenous H2 is a significant energy source for active PCB-degrading communities and suggests that elevated H2 can influence the microbial ecology and biogeochemistry of the legume rhizosphere.}, } @article {pmid37196086, year = {2023}, author = {Maire, J and Tandon, K and Collingro, A and van de Meene, A and Damjanovic, K and Gotze, CR and Stephenson, S and Philip, GK and Horn, M and Cantin, NE and Blackall, LL and van Oppen, MJH}, title = {Colocalization and potential interactions of Endozoicomonas and chlamydiae in microbial aggregates of the coral Pocillopora acuta.}, journal = {Science advances}, volume = {9}, number = {20}, pages = {eadg0773}, doi = {10.1126/sciadv.adg0773}, pmid = {37196086}, issn = {2375-2548}, mesh = {Animals ; *Anthozoa/physiology ; Bacteria/genetics ; Coral Reefs ; *Gammaproteobacteria/genetics ; Metagenome ; }, abstract = {Corals are associated with a variety of bacteria, which occur in the surface mucus layer, gastrovascular cavity, skeleton, and tissues. Some tissue-associated bacteria form clusters, termed cell-associated microbial aggregates (CAMAs), which are poorly studied. Here, we provide a comprehensive characterization of CAMAs in the coral Pocillopora acuta. Combining imaging techniques, laser capture microdissection, and amplicon and metagenome sequencing, we show that (i) CAMAs are located in the tentacle tips and may be intracellular; (ii) CAMAs contain Endozoicomonas (Gammaproteobacteria) and Simkania (Chlamydiota) bacteria; (iii) Endozoicomonas may provide vitamins to its host and use secretion systems and/or pili for colonization and aggregation; (iv) Endozoicomonas and Simkania occur in distinct, but adjacent, CAMAs; and (v) Simkania may receive acetate and heme from neighboring Endozoicomonas. Our study provides detailed insight into coral endosymbionts, thereby improving our understanding of coral physiology and health and providing important knowledge for coral reef conservation in the climate change era.}, } @article {pmid37195657, year = {2023}, author = {Xue, W and Peng, P and Wen, X and Meng, H and Qin, Y and Deng, T and Guo, S and Chen, T and Li, X and Liang, J and Zhang, F and Xie, Z and Jin, M and Liang, Q and Wei, L}, title = {Metagenomic Sequencing Analysis Identifies Cross-Cohort Gut Microbial Signatures Associated With Age-Related Macular Degeneration.}, journal = {Investigative ophthalmology & visual science}, volume = {64}, number = {5}, pages = {11}, pmid = {37195657}, issn = {1552-5783}, mesh = {Humans ; Metagenome ; *Gastrointestinal Microbiome/genetics ; Dysbiosis/microbiology ; Bacteria/genetics/metabolism ; Bacteroidetes ; *Macular Degeneration/genetics ; }, abstract = {PURPOSE: Alterations in the gut microbiota have been associated with age-related macular degeneration (AMD). However, the dysbiosis shared by different ethnicity and geographic groups, which may associate with the disease pathogenesis, remain underexplored. Here, we characterized dysbiosis of the gut microbiota in patients with AMD from Chinese and Swiss cohorts and identified cross-cohort signatures associated with AMD.

METHODS: Shotgun metagenomic sequencing was performed on fecal samples from 30 patients with AMD and 30 healthy subjects. Published datasets with 138 samples from Swiss patients with AMD and healthy subjects were re-analyzed. Comprehensive taxonomic profiling was conducted by matching to the RefSeq genome database, metagenome-assembled genome (MAG) database, and Gut Virome Database (GVD). Functional profiling was performed by reconstruction of the MetaCyc pathways.

RESULTS: The α-diversity of the gut microbiota was decreased in patients with AMD according to taxonomic profiles generated using MAG but not RefSeq database as reference. The Firmicutes/Bacteroidetes ratio was also decreased in patients with AMD. Among AMD-associated bacteria shared between Chinese and Swiss cohorts, Ruminococcus callidus, Lactobacillus gasseri, and Prevotellaceae (f) uSGB 2135 were enriched in patients with AMD, whereas Bacteroidaceae (f) uSGB 1825 was depleted in patients with AMD and was negatively associated with hemorrhage size. Bacteroidaceae was one of the major hosts of phages associated with AMD. Three degradation pathways were reduced in AMD.

CONCLUSIONS: These results demonstrated that dysbiosis of the gut microbiota was associated with AMD. We identified cross-cohort gut microbial signatures involving bacteria, viruses, and metabolic pathways, which potentially serve as promising targets for the prevention or treatment of AMD.}, } @article {pmid37195454, year = {2023}, author = {Robidou, L and Peterlongo, P}, title = {fimpera: drastic improvement of Approximate Membership Query data-structures with counts.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {5}, pages = {}, pmid = {37195454}, issn = {1367-4811}, mesh = {*Software ; Sequence Analysis, DNA/methods ; *Algorithms ; Metagenomics ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {MOTIVATION: High throughput sequencing technologies generate massive amounts of biological sequence datasets as costs fall. One of the current algorithmic challenges for exploiting these data on a global scale consists in providing efficient query engines on these petabyte-scale datasets. Most methods indexing those datasets rely on indexing words of fixed length k, called k-mers. Many applications, such as metagenomics, require the abundance of indexed k-mers as well as their simple presence or absence, but no method scales up to petabyte-scaled datasets. This deficiency is primarily because storing abundance requires explicit storage of the k-mers in order to associate them with their counts. Using counting Approximate Membership Queries (cAMQ) data structures, such as counting Bloom filters, provides a way to index large amounts of k-mers with their abundance, but at the expense of a sensible false positive rate.

RESULTS: We propose a novel algorithm, called fimpera, that enables the improvement of any cAMQ performance. Applied to counting Bloom filters, our proposed algorithm reduces the false positive rate by two orders of magnitude and it improves the precision of the reported abundances. Alternatively, fimpera allows for the reduction of the size of a counting Bloom filter by two orders of magnitude while maintaining the same precision. fimpera does not introduce any memory overhead and may even reduces the query time.

https://github.com/lrobidou/fimpera.}, } @article {pmid37195357, year = {2023}, author = {Wu, HJ and Du, XY and Wu, WJ and Zheng, J and Song, JY and Xie, JC}, title = {Metagenomic analysis reveals specific BTEX degrading microorganisms of a bacterial consortium.}, journal = {AMB Express}, volume = {13}, number = {1}, pages = {48}, pmid = {37195357}, issn = {2191-0855}, support = {2020D-5008//Research on Basic Science and Technology of The Strategic Reserve fund projects of PetroChina Company Limited/ ; 2021DQ03-A4//Research on Basic Science and Technology of The Strategic Reserve fund projects of PetroChina Company Limited/ ; }, abstract = {Petroleum hydrocarbon contamination is of environmental and public health concerns due to its toxic components. Bioremediation utilizes microbial organisms to metabolism and remove these contaminants. The aim of this study was to enrich a microbial community and examine its potential to degrade petroleum hydrocarbon. Through successive enrichment, we obtained a bacterial consortium using crude oil as sole carbon source. The 16 S rRNA gene analysis illustrated the structural characteristics of this community. Metagenomic analysis revealed the specific microbial organisms involved in the degradation of cyclohexane and all the six BTEX components, with a demonstration of the versatile metabolic pathways involved in these reactions. Results showed that our consortium contained the full range of CDSs that could potentially degrade cyclohexane, benzene, toluene, and (o-, m-, p-) xylene completely. Interestingly, a single taxon that possessed all the genes involved in either the activation or the central intermediates degrading pathway was not detected, except for the Novosphingobium which contained all the genes involved in the upper degradation pathway of benzene, indicating the synergistic interactions between different bacterial genera during the hydrocarbon degradation.}, } @article {pmid37195254, year = {2023}, author = {Free, T}, title = {Long-read sequencing for the metagenomic analysis of microbiomes.}, journal = {BioTechniques}, volume = {74}, number = {4}, pages = {153-155}, doi = {10.2144/btn-2023-0028}, pmid = {37195254}, issn = {1940-9818}, mesh = {*High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; Metagenome/genetics ; Sequence Analysis, DNA ; Metagenomics ; }, abstract = {One technology, long-read sequencing, and one research field, microbiome studies, have risen to prominence over the last decade. But how can one be used in the other? What changes are being wrought? And what limitations remain? [Formula: see text].}, } @article {pmid37194694, year = {2023}, author = {Wishart, DS and Han, S and Saha, S and Oler, E and Peters, H and Grant, JR and Stothard, P and Gautam, V}, title = {PHASTEST: faster than PHASTER, better than PHAST.}, journal = {Nucleic acids research}, volume = {51}, number = {W1}, pages = {W443-W450}, pmid = {37194694}, issn = {1362-4962}, support = {//CIHR/Canada ; }, mesh = {*Databases, Nucleic Acid ; Genome, Bacterial ; Molecular Sequence Annotation ; Plasmids ; *Prophages/genetics ; *Search Engine ; *Software ; }, abstract = {PHASTEST (PHAge Search Tool with Enhanced Sequence Translation) is the successor to the PHAST and PHASTER prophage finding web servers. PHASTEST is designed to support the rapid identification, annotation and visualization of prophage sequences within bacterial genomes and plasmids. PHASTEST also supports rapid annotation and interactive visualization of all other genes (protein coding regions, tRNA/tmRNA/rRNA sequences) in bacterial genomes. Given that bacterial genome sequencing has become so routine, the need for fast tools to comprehensively annotate bacterial genomes has become progressively more important. PHASTEST not only offers faster and more accurate prophage annotations than its predecessors, it also provides more complete whole genome annotations and much improved genome visualization capabilities. In standardized tests, we found that PHASTEST is 31% faster and 2-3% more accurate in prophage identification than PHASTER. Specifically, PHASTEST can process a typical bacterial genome in 3.2 min (raw sequence) or in 1.3 min when given a pre-annotated GenBank file. Improvements in PHASTEST's ability to annotate bacterial genomes now make it a particularly powerful tool for whole genome annotation. In addition, PHASTEST now offers a much more modern and responsive visualization interface that allows users to generate, edit, annotate and interactively visualize (via zooming, rotating, dragging, panning, resetting), colourful, publication quality genome maps. PHASTEST continues to offer popular options such as an API for programmatic queries, a Docker image for local installations, support for multiple (metagenomic) queries and the ability to perform automated look-ups against thousands of previously PHAST-annotated bacterial genomes. PHASTEST is available online at https://phastest.ca.}, } @article {pmid37194081, year = {2023}, author = {Gallet, A and Halary, S and Duval, C and Huet, H and Duperron, S and Marie, B}, title = {Disruption of fish gut microbiota composition and holobiont's metabolome during a simulated Microcystis aeruginosa (Cyanobacteria) bloom.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {108}, pmid = {37194081}, issn = {2049-2618}, mesh = {Animals ; *Microcystis/physiology ; *Gastrointestinal Microbiome ; *Cyanobacteria/genetics ; Lakes/microbiology ; Metabolome ; *Oryzias/physiology ; }, abstract = {BACKGROUND: Cyanobacterial blooms are one of the most common stressors encountered by metazoans living in freshwater lentic systems such as lakes and ponds. Blooms reportedly impair fish health, notably through oxygen depletion and production of bioactive compounds including cyanotoxins. However, in the times of the "microbiome revolution", it is surprising that so little is still known regarding the influence of blooms on fish microbiota. In this study, an experimental approach is used to demonstrate that blooms affect fish microbiome composition and functions, as well as the metabolome of holobionts. To this end, the model teleost Oryzias latipes is exposed to simulated Microcystis aeruginosa blooms of various intensities in a microcosm setting, and the response of bacterial gut communities is evaluated in terms of composition and metabolome profiling. Metagenome-encoded functions are compared after 28 days between control individuals and those exposed to highest bloom level.

RESULTS: The gut bacterial community of O. latipes exhibits marked responses to the presence of M. aeruginosa blooms in a dose-dependent manner. Notably, abundant gut-associated Firmicutes almost disappear, while potential opportunists increase. The holobiont's gut metabolome displays major changes, while functions encoded in the metagenome of bacterial partners are more marginally affected. Bacterial communities tend to return to original composition after the end of the bloom and remain sensitive in case of a second bloom, reflecting a highly reactive gut community.

CONCLUSION: Gut-associated bacterial communities and holobiont functioning are affected by both short and long exposure to M. aeruginosa, and show evidence of post-bloom resilience. These findings point to the significance of bloom events to fish health and fitness, including survival and reproduction, through microbiome-related effects. In the context of increasingly frequent and intense blooms worldwide, potential outcomes relevant to conservation biology as well as aquaculture warrant further investigation. Video Abstract.}, } @article {pmid37194043, year = {2023}, author = {Yao, S and Jin, T and Zhang, L and Zhang, Y and Chen, R and Wang, Q and Lv, M and Hu, C and Ma, T and Xia, W}, title = {N/S element transformation modulating lithospheric microbial communities by single-species manipulation.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {107}, pmid = {37194043}, issn = {2049-2618}, mesh = {Nitrates/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Petroleum/metabolism/microbiology ; Sulfur/metabolism ; Nitrogen/metabolism ; Sulfates ; }, abstract = {BACKGROUND: The lithospheric microbiome plays a vital role in global biogeochemical cycling, yet their mutual modulation mechanisms remain largely uncharted. Petroleum reservoirs are important lithosphere ecosystems that provide desirable resources for understanding microbial roles in element cycling. However, the strategy and mechanism of modulating indigenous microbial communities for the optimization of community structures and functions are underexplored, despite its significance in energy recovery and environmental remediation.

RESULTS: Here we proposed a novel selective stimulation of indigenous functional microbes by driving nitrogen and sulfur cycling in petroleum reservoirs using injections of an exogenous heterocycle-degrading strain of Pseudomonas. We defined such bacteria capable of removing and releasing organically bound sulfur and nitrogen from heterocycles as "bioredox triggers". High-throughput 16S rRNA amplicon sequencing, metagenomic, and gene transcription-level analyses of extensive production water and sandstone core samples spanning the whole oil production process clarified the microbiome dynamics following the intervention. These efforts demonstrated the feasibility of in situ N/S element release and electron acceptor generation during heterocycle degradation, shifting microbiome structures and functions and increasing phylogenetic diversity and genera engaged in sulfur and nitrogen cycling, such as Desulfovibrio, Shewanella, and Sulfurospirillum. The metabolic potentials of sulfur- and nitrogen-cycling processes, particularly dissimilatory sulfate reduction and dissimilatory nitrate reduction, were elevated in reservoir microbiomes. The relative expression of genes involved in sulfate reduction (dsrA, dsrB) and nitrate reduction (napA) was upregulated by 85, 28, and 22 folds, respectively. Field trials showed significant improvements in oil properties, with a decline in asphaltenes and aromatics, hetero-element contents, and viscosity, hence facilitating the effective exploitation of heavy oil.

CONCLUSIONS: The interactions between microbiomes and element cycling elucidated in this study will contribute to a better understanding of microbial metabolic involvement in, and response to, biogeochemical processes in the lithosphere. The presented findings demonstrated the immense potential of our microbial modulation strategy for green and enhanced heavy oil recovery. Video Abstract.}, } @article {pmid37194001, year = {2023}, author = {Zhang, Y and Fang, L and Zhou, Y and Zhang, Y and Liang, B and Yan, C and Li, L}, title = {A case report of long-delayed diagnosis of pseudorabies virus encephalitis with endophthalmitis: lessons from metagenomic next generation sequencing.}, journal = {BMC neurology}, volume = {23}, number = {1}, pages = {192}, pmid = {37194001}, issn = {1471-2377}, mesh = {*Pseudorabies/complications/diagnosis/drug therapy ; *Encephalitis, Viral/complications/diagnosis/drug therapy ; *Endophthalmitis/diagnosis/drug therapy/virology ; *Herpesvirus 1, Suid/genetics/isolation & purification ; Metagenomics ; High-Throughput Nucleotide Sequencing ; Delayed Diagnosis ; Humans ; Male ; Middle Aged ; *Aqueous Humor/virology ; Acyclovir/therapeutic use ; Foscarnet/therapeutic use ; Methylprednisolone/therapeutic use ; Antiviral Agents/therapeutic use ; *Blindness/virology ; DNA, Viral/isolation & purification ; }, abstract = {BACKGROUND: Pseudorabies virus (PRV) was thought to only infect animals. Recent studies have shown that it can also infect human.

CASE PRESENTATION: We report a case of pseudorabies virus encephalitis and endophthalmitis, diagnosed 89 days after onset, confirmed with intraocular fluid metagenomic next generation sequencing (mNGS) after the result of two cerebrospinal fluid (CSF) mNGS tests were negative. Although treatment with intravenous acyclovir, foscarnet sodium, and methylprednisolone improved the symptoms of encephalitis, significant diagnostic delay resulted in permanent visual loss.

CONCLUSIONS: This case suggests that pseudorabies virus (PRV) DNA in the intraocular fluid may have a higher positivity than that in the CSF. PRV may persist in the intraocular fluid for an extended period and may thus require extended antiviral therapy. Patients with severe encephalitis and PRV should be examined with the focus on pupil reactivity and light reflex. A fundus examination should be performed in patients with a central nervous system infection, specifically, those in a comatose state, to help reduce eye disability.}, } @article {pmid37193854, year = {2023}, author = {Atsawawaranunt, K and Ewart, KM and Major, RE and Johnson, RN and Santure, AW and Whibley, A}, title = {Tracing the introduction of the invasive common myna using population genomics.}, journal = {Heredity}, volume = {131}, number = {1}, pages = {56-67}, pmid = {37193854}, issn = {1365-2540}, mesh = {Metagenomics ; Animals ; *Introduced Species ; *Starlings/genetics ; Genetic Variation ; }, abstract = {The common myna (Acridotheres tristis) is one of the most invasive bird species in the world, yet its colonisation history is only partly understood. We identified the introduction history and population structure, and quantified the genetic diversity of myna populations from the native range in India and introduced populations in New Zealand, Australia, Fiji, Hawaii, and South Africa, based on thousands of single nucleotide polymorphism markers in 814 individuals. We were able to identify the source population of mynas in several invasive locations: mynas from Fiji and Melbourne, Australia, were likely founded by individuals from a subpopulation in Maharashtra, India, while mynas in Hawaii and South Africa were likely independently founded by individuals from other localities in India. Our findings suggest that New Zealand mynas were founded by individuals from Melbourne, which, in turn, were founded by individuals from Maharashtra. We identified two genetic clusters among New Zealand mynas, divided by New Zealand's North Island's axial mountain ranges, confirming previous observations that mountains and thick forests may form barriers to myna dispersal. Our study provides a foundation for other population and invasion genomic studies and provides useful information for the management of this invasive species.}, } @article {pmid37193765, year = {2023}, author = {Hao, L and Wen, P and Song, W and Zhang, B and Wu, Y and Zhang, Y and Ma, T and Qiu, Y}, title = {Direct detection and identification of periprosthetic joint infection pathogens by metagenomic next-generation sequencing.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {7897}, pmid = {37193765}, issn = {2045-2322}, mesh = {Humans ; *Prosthesis-Related Infections/diagnosis ; Retrospective Studies ; Sensitivity and Specificity ; *Arthritis, Infectious ; *Arthroplasty, Replacement, Hip/adverse effects ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {This study assessed the application of metagenomic next-generation sequencing in pathogen detection of periprosthetic joint infections. A total of 95 cases who previously had undergone hip and knee replacement undergoing revision from January 2018 to January 2021 were included in this study. Specimens of synovial fluid and deep-tissue were collected for culture and metagenomic next-generation sequencing, and patients were retrospectively categorized as infected or aseptic using the Musculoskeletal Infection Society criteria after revision surgery. The sensitivity, specificity, positive and negative predictive values were compared. A total of 36 cases had positive culture results and 59 cases had positive metagenomic next-generation sequencing results. Culture was positive in 34 infected cases (58.6%) and 2 aseptic cases (5.4%). Metagenomic next-generation sequencing was positive in 55 infected cases (94.8%) and 4 aseptic cases (10.8%). Five cases diagnosed with infection had other potential pathogens detected by metagenomic next-generation sequencing. Among the 24 culture-negative periprosthetic joint infections, metagenomic next-generation sequencing was able to identify potential pathogens in 21 cases (87.5%). From sampling to reporting, the average time needed for culture was 5.2 (95% CI 3.1-7.3) days, while that for metagenomic next-generation sequencing was 1.3 (95% CI 0.9-1.7) days. Metagenomic next-generation sequencing is more advantageous in pathogen detection of periprosthetic joint infection after total joint replacement, especially in patients with multiple infections or negative culture results.}, } @article {pmid37193348, year = {2023}, author = {Stockdale, SR and Blanchard, AM and Nayak, A and Husain, A and Nashine, R and Dudani, H and McClure, CP and Tarr, AW and Nag, A and Meena, E and Sinha, V and Shrivastava, SK and Hill, C and Singer, AC and Gomes, RL and Acheampong, E and Chidambaram, SB and Bhatnagar, T and Vetrivel, U and Arora, S and Kashyap, RS and Monaghan, TM}, title = {RNA-Seq of untreated wastewater to assess COVID-19 and emerging and endemic viruses for public health surveillance.}, journal = {The Lancet regional health. Southeast Asia}, volume = {14}, number = {}, pages = {100205}, pmid = {37193348}, issn = {2772-3682}, abstract = {BACKGROUND: The COVID-19 pandemic showcased the power of genomic sequencing to tackle the emergence and spread of infectious diseases. However, metagenomic sequencing of total microbial RNAs in wastewater has the potential to assess multiple infectious diseases simultaneously and has yet to be explored.

METHODS: A retrospective RNA-Seq epidemiological survey of 140 untreated composite wastewater samples was performed across urban (n = 112) and rural (n = 28) areas of Nagpur, Central India. Composite wastewater samples were prepared by pooling 422 individual grab samples collected prospectively from sewer lines of urban municipality zones and open drains of rural areas from 3rd February to 3rd April 2021, during the second COVID-19 wave in India. Samples were pre-processed and total RNA was extracted prior to genomic sequencing.

FINDINGS: This is the first study that has utilised culture and/or probe-independent unbiased RNA-Seq to examine Indian wastewater samples. Our findings reveal the detection of zoonotic viruses including chikungunya, Jingmen tick and rabies viruses, which have not previously been reported in wastewater. SARS-CoV-2 was detectable in 83 locations (59%), with stark abundance variations observed between sampling sites. Hepatitis C virus was the most frequently detected infectious virus, identified in 113 locations and co-occurring 77 times with SARS-CoV-2; and both were more abundantly detected in rural areas than urban zones. Concurrent identification of segmented virus genomic fragments of influenza A virus, norovirus, and rotavirus was observed. Geographical differences were also observed for astrovirus, saffold virus, husavirus, and aichi virus that were more prevalent in urban samples, while the zoonotic viruses chikungunya and rabies, were more abundant in rural environments.

INTERPRETATION: RNA-Seq can effectively detect multiple infectious diseases simultaneously, facilitating geographical and epidemiological surveys of endemic viruses that could help direct healthcare interventions against emergent and pre-existent infectious diseases as well as cost-effectively and qualitatively characterising the health status of the population over time.

FUNDING: UK Research and Innovation (UKRI) Global Challenges Research Fund (GCRF) grant number H54810, as supported by Research England.}, } @article {pmid37193298, year = {2023}, author = {Dany, F and Septima Mariya, S and Noviantari, A}, title = {Diagnosis of Acute Q Fever in a Patient by Using Metagenomic Next-Generation Sequencing: A Case Report [Letter].}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {2921-2922}, pmid = {37193298}, issn = {1178-6973}, } @article {pmid37193127, year = {2023}, author = {Fritch, EJ and Sanders, W and Sims, AC and Herring, LE and Barker, NK and Schepmoes, AA and Weitz, KK and Texier, JR and Dittmer, DP and Graves, LM and Smith, RD and Waters, KM and Moorman, NJ and Baric, RS and Graham, RL}, title = {Metatranscriptomics analysis reveals a novel transcriptional and translational landscape during Middle East respiratory syndrome coronavirus infection.}, journal = {iScience}, volume = {26}, number = {6}, pages = {106780}, pmid = {37193127}, issn = {2589-0042}, abstract = {Among all RNA viruses, coronavirus RNA transcription is the most complex and involves a process termed "discontinuous transcription" that results in the production of a set of 3'-nested, co-terminal genomic and subgenomic RNAs during infection. While the expression of the classic canonical set of subgenomic RNAs depends on the recognition of a 6- to 7-nt transcription regulatory core sequence (TRS), here, we use deep sequence and metagenomics analysis strategies and show that the coronavirus transcriptome is even more vast and more complex than previously appreciated and involves the production of leader-containing transcripts that have canonical and noncanonical leader-body junctions. Moreover, by ribosome protection and proteomics analyses, we show that both positive- and negative-sense transcripts are translationally active. The data support the hypothesis that the coronavirus proteome is much vaster than previously noted in the literature.}, } @article {pmid37192858, year = {2022}, author = {Yang, LZ and Gao, BQ and Huang, Y and Wang, Y and Yang, L and Chen, LL}, title = {Multi-color RNA imaging with CRISPR-Cas13b systems in living cells.}, journal = {Cell insight}, volume = {1}, number = {4}, pages = {100044}, pmid = {37192858}, issn = {2772-8927}, abstract = {Visualizing RNA dynamics is important for understanding RNA function. Catalytically dead (d) CRISPR-Cas13 systems have been established to image and track RNAs in living cells, but efficient dCas13 for RNA imaging is still limited. Here, we analyzed metagenomic and bacterial genomic databases to comprehensively screen Cas13 homologies for their RNA labeling capabilities in living mammalian cells. Among eight previously unreported dCas13 proteins that can be used for RNA labeling, dHgm4Cas13b and dMisCas13b displayed comparable, if not higher, efficiencies to the best-known ones when targeting endogenous MUC4 and NEAT1_2 by single guide (g) RNAs. Further examination of the labeling robustness of different dCas13 systems using the GCN4 repeats revealed that a minimum of 12 GCN4 repeats was required for dHgm4Cas13b and dMisCas13b imaging at the single RNA molecule level, while >24 GCN4 repeats were required for reported dLwaCas13a, dRfxCas13d and dPguCas13b. Importantly, by silencing pre-crRNA processing activity of dMisCas13b (ddMisCas13b) and further incorporating RNA aptamers including PP7, MS2, Pepper or BoxB to individual gRNAs, a CRISPRpalette system was developed to successfully achieve multi-color RNA visualization in living cells.}, } @article {pmid37192670, year = {2023}, author = {Zbinden, ZD and Douglas, MR and Chafin, TK and Douglas, ME}, title = {A community genomics approach to natural hybridization.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1999}, pages = {20230768}, pmid = {37192670}, issn = {1471-2954}, mesh = {Animals ; *Metagenomics ; *Hybridization, Genetic ; Sequence Analysis, DNA ; }, abstract = {Hybridization is a complicated, oft-misunderstood process. Once deemed unnatural and uncommon, hybridization is now recognized as ubiquitous among species. But hybridization rates within and among communities are poorly understood despite the relevance to ecology, evolution and conservation. To clarify, we examined hybridization across 75 freshwater fish communities within the Ozarks of the North American Interior Highlands (USA) by single nucleotide polymorphism (SNP) genotyping 33 species (N = 2865 individuals; double-digest restriction site-associated DNA sequencing (ddRAD)). We found evidence of hybridization (70 putative hybrids; 2.4% of individuals) among 18 species-pairs involving 73% (24/33) of study species, with the majority being concentrated within one family (Leuciscidae/minnows; 15 species; 66 hybrids). Interspecific genetic exchange-or introgression-was evident from 24 backcrossed individuals (10/18 species-pairs). Hybrids occurred within 42 of 75 communities (56%). Four selected environmental variables (species richness, protected area extent, precipitation (May and annually)) exhibited 73-78% accuracy in predicting hybrid occurrence via random forest classification. Our community-level assessment identified hybridization as spatially widespread and environmentally dependent (albeit predominantly within one diverse, omnipresent family). Our approach provides a more holistic survey of natural hybridization by testing a wide range of species-pairs, thus contrasting with more conventional evaluations.}, } @article {pmid37192316, year = {2023}, author = {Li, N and Zhang, R and Zhou, J and Huang, Z}, title = {Structures, Biochemical Characteristics, and Functions of β-Xylosidases.}, journal = {Journal of agricultural and food chemistry}, volume = {71}, number = {21}, pages = {7961-7976}, doi = {10.1021/acs.jafc.3c01425}, pmid = {37192316}, issn = {1520-5118}, mesh = {*Xylosidases/chemistry ; Oligosaccharides ; Xylose/metabolism ; Fungi/genetics/metabolism ; }, abstract = {The complete degradation of abundant xylan derived from plants requires the participation of β-xylosidases to produce the xylose which can be converted to xylitol, ethanol, and other valuable chemicals. Some phytochemicals can also be hydrolyzed by β-xylosidases into bioactive substances, such as ginsenosides, 10-deacetyltaxol, cycloastragenol, and anthocyanidins. On the contrary, some hydroxyl-containing substances such as alcohols, sugars, and phenols can be xylosylated by β-xylosidases into new chemicals such as alkyl xylosides, oligosaccharides, and xylosylated phenols. Thus, β-xylosidases shows great application prospects in food, brewing, and pharmaceutical industries. This review focuses on the molecular structures, biochemical properties, and bioactive substance transformation function of β-xylosidases derived from bacteria, fungi, actinomycetes, and metagenomes. The molecular mechanisms of β-xylosidases related to the properties and functions are also discussed. This review will serve as a reference for the engineering and application of β-xylosidases in food, brewing, and pharmaceutical industries.}, } @article {pmid37192099, year = {2023}, author = {Koonin, EV and Gootenberg, JS and Abudayyeh, OO}, title = {Discovery of Diverse CRISPR-Cas Systems and Expansion of the Genome Engineering Toolbox.}, journal = {Biochemistry}, volume = {62}, number = {24}, pages = {3465-3487}, pmid = {37192099}, issn = {1520-4995}, support = {R01 EB031957/EB/NIBIB NIH HHS/United States ; R21 AI149694/AI/NIAID NIH HHS/United States ; R56 HG011857/HG/NHGRI NIH HHS/United States ; }, mesh = {*CRISPR-Cas Systems ; *Gene Editing/methods ; Bacteria/genetics ; RNA, Bacterial/genetics ; DNA ; }, abstract = {CRISPR systems mediate adaptive immunity in bacteria and archaea through diverse effector mechanisms and have been repurposed for versatile applications in therapeutics and diagnostics thanks to their facile reprogramming with RNA guides. RNA-guided CRISPR-Cas targeting and interference are mediated by effectors that are either components of multisubunit complexes in class 1 systems or multidomain single-effector proteins in class 2. The compact class 2 CRISPR systems have been broadly adopted for multiple applications, especially genome editing, leading to a transformation of the molecular biology and biotechnology toolkit. The diversity of class 2 effector enzymes, initially limited to the Cas9 nuclease, was substantially expanded via computational genome and metagenome mining to include numerous variants of Cas12 and Cas13, providing substrates for the development of versatile, orthogonal molecular tools. Characterization of these diverse CRISPR effectors uncovered many new features, including distinct protospacer adjacent motifs (PAMs) that expand the targeting space, improved editing specificity, RNA rather than DNA targeting, smaller crRNAs, staggered and blunt end cuts, miniature enzymes, promiscuous RNA and DNA cleavage, etc. These unique properties enabled multiple applications, such as harnessing the promiscuous RNase activity of the type VI effector, Cas13, for supersensitive nucleic acid detection. class 1 CRISPR systems have been adopted for genome editing, as well, despite the challenge of expressing and delivering the multiprotein class 1 effectors. The rich diversity of CRISPR enzymes led to rapid maturation of the genome editing toolbox, with capabilities such as gene knockout, base editing, prime editing, gene insertion, DNA imaging, epigenetic modulation, transcriptional modulation, and RNA editing. Combined with rational design and engineering of the effector proteins and associated RNAs, the natural diversity of CRISPR and related bacterial RNA-guided systems provides a vast resource for expanding the repertoire of tools for molecular biology and biotechnology.}, } @article {pmid37191684, year = {2023}, author = {Lu, J and Sha, H and Chen, J and Yi, X and Xiong, J}, title = {Characterizing sediment functional traits and ecological consequences respond to increasing antibiotic pollution.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {12}, pages = {4093-4107}, pmid = {37191684}, issn = {1432-0614}, support = {32071549//National Natural Science Foundation of China/ ; HZ202201//One health Interdisciplinary Research Project, Ningbo University/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; *Microbiota ; Environmental Pollution ; Nitrification ; Sulfates ; }, abstract = {Current studies have shown that the taxonomic structures of ecologically important microbial communities are altered by antibiotic exposure, but the resulting effects on functional potentials and subsequent biogeochemical processes are poorly understood. However, this knowledge is indispensable for developing an accurate projection of nutrient dynamics in the future. Using metagenomic analyses, here we explored the responses of taxonomical and functional structures of a sediment microbial community, and their links with key biogeochemical processes to increasing antibiotic pollution from the pristine inlet to the outfall sites along an aquaculture discharge channel. We identified sharply contrasting sedimentary microbial communities and functional traits along increasing antibiotic pollution. Functional structures exhibited steeper distance-decay relationships than taxonomical structures along both the antibiotic distance and physicochemical distance, revealing higher functional sensitivity. Sediment enzyme activities were significantly and positively coupled with the relative abundances of their coding genes, thus the abundances of genes were indicative of functional potentials. The nitrogen cycling pathways were commonly inhibited by antibiotics, but not for the first step of nitrification, which could synergistically mitigate nitrous oxide emission. However, antibiotic pollution stimulated methanogens and inhibited methanotrophs, thereby promoting methane efflux. Furthermore, microbes could adapt to antibiotic pollution through enriched potential of sulfate uptake. Antibiotics indirectly affected taxonomic structures through alterations in network topological features, which in turn affected sediment functional structures and biogeochemical processes. Notably, only 13 antibiotics concentration-discriminatory genes contributed an overall 95.9% accuracy in diagnosing in situ antibiotic concentrations, in which just two indicators were antibiotic resistance genes. Our study comprehensively integrates sediment compositional and functional traits, biotic interactions, and enzymatic activities, thus generating a better understanding about ecological consequences of increasing antibiotics pollution. KEY POINTS: • Contrasting functional traits respond to increasing antibiotic pollution. • Antibiotics pollution stimulates CH4 efflux, while mitigating N2O emission and may drive an adaptive response of enriched sulfate uptake. • Indicator genes contribute 95.9% accuracy in diagnosing antibiotic concentrations.}, } @article {pmid37191543, year = {2023}, author = {Rizzo, SM and Alessandri, G and Lugli, GA and Fontana, F and Tarracchini, C and Mancabelli, L and Viappiani, A and Bianchi, MG and Bussolati, O and van Sinderen, D and Ventura, M and Turroni, F}, title = {Exploring Molecular Interactions between Human Milk Hormone Insulin and Bifidobacteria.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0066523}, pmid = {37191543}, issn = {2165-0497}, mesh = {Infant ; Humans ; Infant, Newborn ; Female ; Pregnancy ; Milk, Human/metabolism/microbiology ; Bifidobacterium/genetics/metabolism ; Insulin/metabolism ; *Microbiota ; *Gastrointestinal Microbiome ; Feces/microbiology ; }, abstract = {Multiple millennia of human evolution have shaped the chemical composition of breast milk toward an optimal human body fluid for nutrition and protection and for shaping the early gut microbiota of newborns. This biological fluid is composed of water, lipids, simple and complex carbohydrates, proteins, immunoglobulins, and hormones. Potential interactions between hormones present in mother's milk and the microbial community of the newborn are a very fascinating yet unexplored topic. In this context, insulin, in addition to being one of the most prevalent hormones in breast milk, is also involved in a metabolic disease that affects many pregnant women, i.e., gestational diabetes mellitus (GDM). Analysis of 3,620 publicly available metagenomic data sets revealed that the bifidobacterial community varies in relation to the different concentrations of this hormone in breast milk of healthy and diabetic mothers. Starting from this assumption, in this study, we explored possible molecular interactions between this hormone and bifidobacterial strains that represent bifidobacterial species commonly occurring in the infant gut using 'omics' approaches. Our findings revealed that insulin modulates the bifidobacterial community by apparently improving the persistence of the Bifidobacterium bifidum taxon in the infant gut environment compared to other typical infant-associated bifidobacterial species. IMPORTANCE Breast milk is a key factor in modulating the infant's intestinal microbiota composition. Even though the interaction between human milk sugars and bifidobacteria has been extensively studied, there are other bioactive compounds in human milk that may influence the gut microbiota, such as hormones. In this article, the molecular interaction of the human milk hormone insulin and the bifidobacterial communities colonizing the human gut in the early stages of life has been explored. This molecular cross talk was assessed using an in vitro gut microbiota model and then analyzed by various omics approaches, allowing the identification of genes associated with bacterial cell adaptation/colonization in the human intestine. Our findings provide insights into the manner by which assembly of the early gut microbiota may be regulated by host factors such as hormones carried by human milk.}, } @article {pmid37191511, year = {2023}, author = {Zhang, JW and Wang, R and Liang, X and Han, P and Zheng, YL and Li, XF and Gao, DZ and Liu, M and Hou, LJ and Dong, HP}, title = {Novel Gene Clusters for Natural Product Synthesis Are Abundant in the Mangrove Swamp Microbiome.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {6}, pages = {e0010223}, pmid = {37191511}, issn = {1098-5336}, mesh = {*Biological Products ; Wetlands ; Phylogeny ; *Microbiota ; Multigene Family ; }, abstract = {Natural microbial communities produce a diverse array of secondary metabolites with ecologically and biotechnologically relevant activities. Some of them have been used clinically as drugs, and their production pathways have been identified in a few culturable microorganisms. However, since the vast majority of microorganisms in nature have not been cultured, identifying the synthetic pathways of these metabolites and tracking their hosts remain a challenge. The microbial biosynthetic potential of mangrove swamps remains largely unknown. Here, we examined the diversity and novelty of biosynthetic gene clusters in dominant microbial populations in mangrove wetlands by mining 809 newly reconstructed draft genomes and probing the activities and products of these clusters by using metatranscriptomic and metabolomic techniques. A total of 3,740 biosynthetic gene clusters were identified from these genomes, including 1,065 polyketide and nonribosomal peptide gene clusters, 86% of which showed no similarity to known clusters in the Minimum Information about a Biosynthetic Gene Cluster (MIBiG) repository. Of these gene clusters, 59% were harbored by new species or lineages of Desulfobacterota-related phyla and Chloroflexota, whose members are highly abundant in mangrove wetlands and for which few synthetic natural products have been reported. Metatranscriptomics revealed that most of the identified gene clusters were active in field and microcosm samples. Untargeted metabolomics was also used to identify metabolites from the sediment enrichments, and 98% of the mass spectra generated were unrecognizable, further supporting the novelty of these biosynthetic gene clusters. Our study taps into a corner of the microbial metabolite reservoir in mangrove swamps, providing clues for the discovery of new compounds with valuable activities. IMPORTANCE At present, the majority of known clinical drugs originated from cultivated species of a few bacterial lineages. It is vital for the development of new pharmaceuticals to explore the biosynthetic potential of naturally uncultivable microorganisms using new techniques. Based on the large numbers of genomes reconstructed from mangrove wetlands, we identified abundant and diverse biosynthetic gene clusters in previously unsuspected phylogenetic groups. These gene clusters exhibited a variety of organizational architectures, especially for nonribosomal peptide synthetase (NRPS) and polyketide synthase (PKS), implying the presence of new compounds with valuable activities in the mangrove swamp microbiome.}, } @article {pmid37190315, year = {2023}, author = {Nardone, OM and Zammarchi, I and Santacroce, G and Ghosh, S and Iacucci, M}, title = {Inflammation-Driven Colorectal Cancer Associated with Colitis: From Pathogenesis to Changing Therapy.}, journal = {Cancers}, volume = {15}, number = {8}, pages = {}, pmid = {37190315}, issn = {2072-6694}, abstract = {Patients affected by inflammatory bowel disease (IBD) have a two-fold higher risk of developing colorectal cancer (CRC) than the general population. IBD-related CRC follows a different genetic and molecular pathogenic pathway than sporadic CRC and can be considered a complication of chronic intestinal inflammation. Since inflammation is recognised as an independent risk factor for neoplastic progression, clinicians strive to modulate and control disease, often using potent therapy agents to achieve mucosal healing and decrease the risk of colorectal cancer in IBD patients. Improved therapeutic control of inflammation, combined with endoscopic advances and early detection of pre-cancerous lesions through surveillance programs, explains the lower incidence rate of IBD-related CRC. In addition, current research is increasingly focused on translating emerging and advanced knowledge in microbiome and metagenomics into personalised, early, and non-invasive CRC screening tools that guide organ-sparing therapy in IBD patients. This review aims to summarise the existing literature on IBD-associated CRC, focusing on new insights into the alteration of the intestinal barrier and the interactions with the gut microbiome as the initial promoter. In addition, the role of OMIC techniques for precision medicine and the impact of the available IBD therapeutic armamentarium on the evolution to CRC will be discussed.}, } @article {pmid37189387, year = {2023}, author = {Aljuraiban, GS and Alfhili, MA and Aldhwayan, MM and Aljazairy, EA and Al-Musharaf, S}, title = {Metagenomic Shotgun Sequencing Reveals Specific Human Gut Microbiota Associated with Insulin Resistance and Body Fat Distribution in Saudi Women.}, journal = {Biomolecules}, volume = {13}, number = {4}, pages = {}, pmid = {37189387}, issn = {2218-273X}, mesh = {Humans ; Female ; *Insulin Resistance ; Saudi Arabia ; *Gastrointestinal Microbiome/genetics ; Body Fat Distribution ; Obesity ; Insulin ; }, abstract = {(1) Background: Gut microbiota dysbiosis may lead to diseases such as insulin resistance and obesity. We aimed to investigate the relationship between insulin resistance, body fat distribution, and gut microbiota composition. (2) Methods: The present study included 92 Saudi women (18-25 years) with obesity (body mass index (BMI) ≥ 30 kg/m[2], n = 44) and with normal weight (BMI 18.50-24.99 kg/m[2], n = 48). Body composition indices, biochemical data, and stool samples were collected. The whole-genome shotgun sequencing technique was used to analyze the gut microbiota. Participants were divided into subgroups stratified by the homeostatic model assessment for insulin resistance (HOMA-IR) and other adiposity indices. (3) Results: HOMA-IR was inversely correlated with Actinobacteria (r = -0.31, p = 0.003), fasting blood glucose was inversely correlated with Bifidobacterium kashiwanohense (r = -0.22, p = 0.03), and insulin was inversely correlated with Bifidobacterium adolescentis (r = -0.22, p = 0.04). There were significant differences in α- and β-diversities in those with high HOMA-IR and waist-hip ratio (WHR) compared to low HOMA-IR and WHR (p = 0.02, 0.03, respectively). (4) Conclusions: Our findings highlight the relationship between specific gut microbiota at different taxonomic levels and measures of glycemic control in Saudi Arabian women. Future studies are required to determine the role of the identified strains in the development of insulin resistance.}, } @article {pmid37189337, year = {2023}, author = {Dossey, AT and Oppert, B and Chu, FC and Lorenzen, MD and Scheffler, B and Simpson, S and Koren, S and Johnston, JS and Kataoka, K and Ide, K}, title = {Genome and Genetic Engineering of the House Cricket (Acheta domesticus): A Resource for Sustainable Agriculture.}, journal = {Biomolecules}, volume = {13}, number = {4}, pages = {}, pmid = {37189337}, issn = {2218-273X}, mesh = {Animals ; *Gryllidae/genetics/metabolism ; Agriculture ; Crops, Agricultural ; Allergens/metabolism ; Genetic Engineering ; }, abstract = {Background: The house cricket, Acheta domesticus, is one of the most farmed insects worldwide and the foundation of an emerging industry using insects as a sustainable food source. Edible insects present a promising alternative for protein production amid a plethora of reports on climate change and biodiversity loss largely driven by agriculture. As with other crops, genetic resources are needed to improve crickets for food and other applications. Methods: We present the first high quality annotated genome assembly of A. domesticus from long read data and scaffolded to chromosome level, providing information needed for genetic manipulation. Results: Gene groups related to immunity were annotated and will be useful for improving value to insect farmers. Metagenome scaffolds in the A. domesticus assembly, including Invertebrate Iridescent Virus 6 (IIV6), were submitted as host-associated sequences. We demonstrate both CRISPR/Cas9-mediated knock-in and knock-out of A. domesticus and discuss implications for the food, pharmaceutical, and other industries. RNAi was demonstrated to disrupt the function of the vermilion eye-color gene producing a useful white-eye biomarker phenotype. Conclusions: We are utilizing these data to develop technologies for downstream commercial applications, including more nutritious and disease-resistant crickets, as well as lines producing valuable bioproducts, such as vaccines and antibiotics.}, } @article {pmid37189333, year = {2023}, author = {Cres, CM and Tritt, A and Bouchard, KE and Zhang, Y}, title = {DL-TODA: A Deep Learning Tool for Omics Data Analysis.}, journal = {Biomolecules}, volume = {13}, number = {4}, pages = {}, pmid = {37189333}, issn = {2218-273X}, mesh = {Humans ; *Deep Learning ; Neural Networks, Computer ; Bacteria/genetics ; Metagenome ; *Microbiota/genetics ; Algorithms ; }, abstract = {Metagenomics is a technique for genome-wide profiling of microbiomes; this technique generates billions of DNA sequences called reads. Given the multiplication of metagenomic projects, computational tools are necessary to enable the efficient and accurate classification of metagenomic reads without needing to construct a reference database. The program DL-TODA presented here aims to classify metagenomic reads using a deep learning model trained on over 3000 bacterial species. A convolutional neural network architecture originally designed for computer vision was applied for the modeling of species-specific features. Using synthetic testing data simulated with 2454 genomes from 639 species, DL-TODA was shown to classify nearly 75% of the reads with high confidence. The classification accuracy of DL-TODA was over 0.98 at taxonomic ranks above the genus level, making it comparable with Kraken2 and Centrifuge, two state-of-the-art taxonomic classification tools. DL-TODA also achieved an accuracy of 0.97 at the species level, which is higher than 0.93 by Kraken2 and 0.85 by Centrifuge on the same test set. Application of DL-TODA to the human oral and cropland soil metagenomes further demonstrated its use in analyzing microbiomes from diverse environments. Compared to Centrifuge and Kraken2, DL-TODA predicted distinct relative abundance rankings and is less biased toward a single taxon.}, } @article {pmid37189332, year = {2023}, author = {Smith, L and Goldobina, E and Govi, B and Shkoporov, AN}, title = {Bacteriophages of the Order Crassvirales: What Do We Currently Know about This Keystone Component of the Human Gut Virome?.}, journal = {Biomolecules}, volume = {13}, number = {4}, pages = {}, pmid = {37189332}, issn = {2218-273X}, support = {220646/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Humans ; *Bacteriophages/genetics ; Virome ; Metagenomics ; Genomics ; DNA ; Mammals/genetics ; }, abstract = {The order Crassvirales comprises dsDNA bacteriophages infecting bacteria in the phylum Bacteroidetes that are found in a variety of environments but are especially prevalent in the mammalian gut. This review summarises available information on the genomics, diversity, taxonomy, and ecology of this largely uncultured viral taxon. With experimental data available from a handful of cultured representatives, the review highlights key properties of virion morphology, infection, gene expression and replication processes, and phage-host dynamics.}, } @article {pmid37189250, year = {2023}, author = {Tong, CCL and Lin, X and Seckar, T and Koptyra, M and Kohanski, MA and Cohen, NA and Kennedy, DW and Adappa, ND and Papagiannopoulos, P and Kuan, EC and Baranov, E and Jalaly, JB and Feldman, MD and Storm, PB and Resnick, AC and Palmer, JN and Wei, Z and Robertson, ES}, title = {A metagenomic analysis of the virome of inverted papilloma and squamous cell carcinoma.}, journal = {International forum of allergy & rhinology}, volume = {13}, number = {11}, pages = {2055-2062}, doi = {10.1002/alr.23182}, pmid = {37189250}, issn = {2042-6984}, abstract = {INTRODUCTION: Inverted papilloma (IP) is a sinonasal tumor with a well-known potential for malignant transformation. The role of human papillomavirus (HPV) in its pathogenesis has been controversial. The purpose of this study was to determine the virome associated with IP, with progression to carcinoma in situ (CIS), and invasive carcinoma.

METHODS: To determine the HPV-specific types, a metagenomics assay that contains 62,886 probes targeting viral genomes in a microarray format was used. The platform screens DNA and RNA from fixed tissues from eight controls, 16 IP without dysplasia, five IP with CIS, and 13 IP-associated squamous cell carcinoma (IPSCC). Paired with next-generation sequencing, 48 types of HPV with 857 region-specific probes were interrogated against the tumors.

RESULTS: The prevalence of HPV-16 was 14%, 42%, 70%, and 73% in control tissue, IP without dysplasia, IP with CIS, and IPSCC, respectively. The prevalence of HPV-18 had a similar progressive increase in prevalence, with 14%, 27%, 67%, and 74%, respectively. The assay allowed region-specific analysis, which identified the only oncogenic HPV-18 E6 to be statistically significant when compared with control tissue. The prevalence of HPV-18 E6 was 0% in control tissue, 25% in IP without dysplasia, 60% in IP with CIS, and 77% in IPSCC.

CONCLUSIONS: There are over 200 HPV types that infect human epithelial cells, of which only a few are known to be high-risk. Our study demonstrated a trend of increasing prevalence of HPV-18 E6 that correlated with histologic severity, which is novel and supports a potential role for HPV in the pathogenesis of IP.}, } @article {pmid37188815, year = {2023}, author = {Tomofuji, Y and Sonehara, K and Kishikawa, T and Maeda, Y and Ogawa, K and Kawabata, S and Nii, T and Okuno, T and Oguro-Igashira, E and Kinoshita, M and Takagaki, M and Yamamoto, K and Kurakawa, T and Yagita-Sakamaki, M and Hosokawa, A and Motooka, D and Matsumoto, Y and Matsuoka, H and Yoshimura, M and Ohshima, S and Nakamura, S and Inohara, H and Kishima, H and Mochizuki, H and Takeda, K and Kumanogoh, A and Okada, Y}, title = {Reconstruction of the personal information from human genome reads in gut metagenome sequencing data.}, journal = {Nature microbiology}, volume = {8}, number = {6}, pages = {1079-1094}, pmid = {37188815}, issn = {2058-5276}, mesh = {Humans ; *Metagenome ; *Genome, Human ; Feces ; Whole Genome Sequencing ; Genotype ; }, abstract = {Human DNA present in faecal samples can result in a small number of human reads in gut shotgun metagenomic sequencing data. However, it is presently unclear how much personal information can be reconstructed from such reads, and this has not been quantitatively evaluated. Such a quantitative evaluation is necessary to clarify the ethical concerns related to data sharing and to enable efficient use of human genetic information in stool samples, such as for research and forensics. Here we used genomic approaches to reconstruct personal information from the faecal metagenomes of 343 Japanese individuals with associated human genotype data. Genetic sex could be accurately predicted based on the sequencing depth of sex chromosomes for 97.3% of the samples. Individuals could be re-identified from the matched genotype data based on human reads recovered from the faecal metagenomic data with 93.3% sensitivity using a likelihood score-based method. This method also enabled us to predict the ancestries of 98.3% of the samples. Finally, we performed ultra-deep shotgun metagenomic sequencing of five faecal samples as well as whole-genome sequencing of blood samples. Using genotype-calling approaches, we demonstrated that the genotypes of both common and rare variants could be reconstructed from faecal samples. This included clinically relevant variants. Our approach can be used to quantify personal information contained within gut metagenome data.}, } @article {pmid37188814, year = {2023}, author = {Johansen, J and Atarashi, K and Arai, Y and Hirose, N and Sørensen, SJ and Vatanen, T and Knip, M and Honda, K and Xavier, RJ and Rasmussen, S and Plichta, DR}, title = {Centenarians have a diverse gut virome with the potential to modulate metabolism and promote healthy lifespan.}, journal = {Nature microbiology}, volume = {8}, number = {6}, pages = {1064-1078}, pmid = {37188814}, issn = {2058-5276}, support = {DP3 DK094338/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Aged, 80 and over ; Humans ; Longevity ; Virome ; Centenarians ; *Viruses/genetics ; *Microbiota ; *Bacteriophages/genetics ; }, abstract = {Distinct gut microbiome ecology may be implicated in the prevention of aging-related diseases as it influences systemic immune function and resistance to infections. Yet, the viral component of the microbiome throughout different stages in life remains unexplored. Here we present a characterization of the centenarian gut virome using previously published metagenomes from 195 individuals from Japan and Sardinia. Compared with gut viromes of younger adults (>18 yr) and older individuals (>60 yr), centenarians had a more diverse virome including previously undescribed viral genera, such as viruses associated with Clostridia. A population shift towards higher lytic activity was also observed. Finally, we investigated phage-encoded auxiliary functions that influence bacterial physiology, which revealed an enrichment of genes supporting key steps in sulfate metabolic pathways. Phage and bacterial members of the centenarian microbiome displayed an increased potential for converting methionine to homocysteine, sulfate to sulfide and taurine to sulfide. A greater metabolic output of microbial hydrogen sulfide in centenarians may in turn support mucosal integrity and resistance to pathobionts.}, } @article {pmid37188775, year = {2023}, author = {Sandstedt, J and Vukusic, K and Dellgren, G and Jeppsson, A and Mattsson Hultén, L and Rotter Sopasakis, V}, title = {Metagenomic sequencing of human cardiac tissue reveals Microbial RNA which correlates with Toll-like receptor-associated inflammation in patients with heart disease.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {7884}, pmid = {37188775}, issn = {2045-2322}, mesh = {Humans ; *Atrial Fibrillation ; Metagenomics ; *Heart Diseases ; Toll-Like Receptors/genetics ; Inflammation/genetics ; *Heart Valve Prosthesis Implantation ; Treatment Outcome ; RNA ; }, abstract = {Cardiovascular disease (CVD) is strongly associated with chronic low-grade inflammation, involving activated Toll-like receptors and their downstream cellular machinery. Moreover, CVD and other related inflammatory conditions are associated with infiltration of bacteria and viruses originating from distant body sites. Thus, in this study we aimed to map the presence of microbes in the myocardium of patients with heart disease that we previously found to display upregulated Toll-like receptor signaling. We performed metagenomics analysis of atrial cardiac tissue from patients undergoing coronary artery bypass grafting (CABG) or aortic valve replacement (AVR) and compared with atrial cardiac tissue from organ donors. A total of 119 species of bacteria and seven species of virus were detected in the cardiac tissue. RNA expression of five bacterial species were increased in the patient group of which L. kefiranofaciens correlated positively with cardiac Toll-like receptor-associated inflammation. Interaction network analysis revealed four main gene set clusters involving cell growth and proliferation, Notch signaling, G protein signaling and cell communication in association with L. kefiranofaciens RNA expression. Taken together, intracardial expression of L. kefiranofaciens RNA correlates with pro-inflammatory markers in the diseased cardiac atrium and may have an effect on specific signaling processes important for cell growth, proliferation and cell communication.}, } @article {pmid37188713, year = {2023}, author = {Orihara, K and Yahagi, K and Saito, Y and Watanabe, Y and Sasai, T and Hara, T and Tsukuda, N and Oki, K and Fujimoto, J and Matsuki, T}, title = {Characterization of Bifidobacterium kashiwanohense that utilizes both milk- and plant-derived oligosaccharides.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2207455}, pmid = {37188713}, issn = {1949-0984}, mesh = {Infant ; Child ; Humans ; Phylogeny ; *Gastrointestinal Microbiome ; Milk, Human/metabolism ; Oligosaccharides/metabolism ; alpha-L-Fucosidase/metabolism ; }, abstract = {Bifidobacteria are prominent members of the human gut microbiota throughout life. The ability to utilize milk- and plant-derived carbohydrates is important for bifidobacterial colonization of the infant and adult gut. The Bifidobacterium catenulatum subspecies kashiwanohense (B. kashiwanohense) was originally isolated from infant feces. However, only a few strains have been described, and the characteristics of this subspecies have been poorly investigated. Here, we characterized genotypes and phenotypes of 23 B. kashiwanohense-associated strains, including 12 newly sequenced isolates. Genome-based analysis clarified the phylogenetic relationship between these strains, revealing that only 13 strains are genuine B. kashiwanohense. We defined specific marker sequences and investigated the worldwide prevalence of B. kashiwanohense based on metagenome data. This revealed that not only infants but also adults and weaning children harbor this subspecies in the gut. Most B. kashiwanohense strains utilize long-chain xylans and possess genes for extracellular xylanase (GH10), arabinofuranosidase and xylosidase (GH43), and ABC transporters that contribute to the utilization of xylan-derived oligosaccharides. We also confirmed that B. kashiwanohense strains utilize short- and long-chain human milk oligosaccharides and possess genes for fucosidase (GH95 and GH29) and specific ABC transporter substrate-binding proteins that contribute to the utilization of a wide range of human milk oligosaccharides. Collectively, we found that B. kashiwanohense strains utilize both plant- and milk-derived carbohydrates and identified key genetic factors that allow them to assimilate various carbohydrates.}, } @article {pmid37188649, year = {2023}, author = {Chen, S and Hou, C and Kang, Y and Li, D and Rong, J and Li, Z}, title = {Application of metagenomic next-generation sequencing in the diagnosis and resistome analysis of community-acquired pneumonia pathogens from bronchoalveolar lavage samples.}, journal = {Journal of applied microbiology}, volume = {134}, number = {6}, pages = {}, doi = {10.1093/jambio/lxad102}, pmid = {37188649}, issn = {1365-2672}, support = {2021YFC2301001//National Key Research and Development Program of China/ ; 82073624//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Prospective Studies ; Bronchoalveolar Lavage ; Bronchoalveolar Lavage Fluid ; *High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/pharmacology ; Dimercaprol ; Metagenomics ; *Pneumonia/diagnosis ; Sensitivity and Specificity ; }, abstract = {AIMS: To perform a prospective diagnostic study exploring the clinical utility of metagenomic next-generation sequencing (mNGS) in diagnosing community-acquired pneumonia (CAP), and revealing resistome differences in bronchoalveolar lavage fluid (BALF) from CAP patients with varying severity of admission base on Pneumonia Patient Outcomes Research Team (PORT) risk classes.

METHODS AND RESULTS: We compared the diagnostic performances of mNGS and conventional testing for the detection of pathogens in BALF from 59 CAP patients, and performed resistome differences analysis of metagenomic data from 59 BALF samples, namely, 25 from CAP patients with PORT score I (I group), 14 from CAP patients with PORT score II (II group), 12 from CAP patients with PORT score III (III group), and 8 from CAP patients with PORT score IV (IV group). The diagnostic sensitivities of mNGS and conventional testing for the detection of pathogens in BALF in patients with CAP were 96.6% (57/59) and 30.5% (18/59), respectively. There was a significant difference in the overall relative abundance of resistance genes between the four groups (P = 0.014). The results of principal coordinate analysis based on Bray-Curtis dissimilarities showed that there were significant differences in the composition of resistance genes among the I, II, III, and IV groups (P = 0.007). A large number of antibiotic resistance genes, such as those affiliated with multidrug, tetracycline, aminoglycoside, and fosfomycin resistance, were enriched in the IV group.

CONCLUSIONS: In conclusion, mNGS has a high diagnostic value in CAP. There were significant differences present in microbiota resistance to antibiotics in BALF from CAP patients in different PORT risk classes, which should attract enough attention.}, } @article {pmid37188549, year = {2023}, author = {Hosokawa, M and Iwai, N and Arikawa, K and Saeki, T and Endoh, T and Kamata, K and Yoda, T and Tsuda, S and Takeyama, H}, title = {Target enrichment of uncultured human oral bacteria with phage-derived molecules found by single-cell genomics.}, journal = {Journal of bioscience and bioengineering}, volume = {136}, number = {1}, pages = {58-66}, doi = {10.1016/j.jbiosc.2023.04.005}, pmid = {37188549}, issn = {1347-4421}, mesh = {Humans ; *Bacteriophages/genetics ; Bacteria/metabolism ; Genomics ; Metagenomics/methods ; Genome, Bacterial ; }, abstract = {Advances in culture-independent microbial analysis, such as metagenomics and single-cell genomics, have significantly increased our understanding of microbial lineages. While these methods have uncovered a large number of novel microbial taxa, many remain uncultured, and their function and mode of existence in the environment are still unknown. This study aims to explore the use of bacteriophage-derived molecules as probes for detecting and isolating uncultured bacteria. Here, we proposed multiplex single-cell sequencing to obtain massive uncultured oral bacterial genomes and searched prophage sequences from over 450 obtained human oral bacterial single-amplified genomes (SAGs). The focus was on the cell wall binding domain (CBD) in phage endolysin, and fluorescent protein-fused CBDs were generated based on several CBD gene sequences predicted from Streptococcus SAGs. The ability of the Streptococcus prophage-derived CBDs to detect and enrich specific Streptococcus species from human saliva while maintaining cell viability was confirmed by magnetic separation and flow cytometry. The approach to phage-derived molecule generation based on uncultured bacterial SAG is expected to improve the process of designing molecules that selectively capture or detect specific bacteria, notably from uncultured gram-positive bacteria, and will have applications in isolation and in situ detection of beneficial or pathogenic bacteria.}, } @article {pmid37188245, year = {2023}, author = {Mathias, MB and Menezes, FG and Fernandes, GBP and Paes, VR and Silva, GS and Braga-Neto, P and Barbosa, AA and De Oliveira, ACP and Baccin, CE and Dutra, LA}, title = {Neurobrucellosis Mimicking Primary CNS Vasculitis-Should We Perform CSF Metagenomics Before Brain Biopsy?: A Case Report.}, journal = {Neurology. Clinical practice}, volume = {13}, number = {4}, pages = {e200167}, pmid = {37188245}, issn = {2163-0402}, abstract = {OBJECTIVE: To report a patient with neurobrucellosis mimicking primary CNS vasculitis (PCNSV) diagnosed by CSF metagenomic next-generation sequencing (mNGS).

METHODS: A 32-year-old male patient with a prior stroke developed headache, dizziness, fever, and memory complaints in the past 30 days. Physical examination was unremarkable except for slight apathy. He was investigated with brain MRI, cerebral digital angiography, CSF analysis with mNGS, and brain biopsy.

RESULTS: An examination of the brain MRI showed a left nucleocapsular gliosis compatible with prior stroke; MR angiogram showed circular enhancement of distal branches of the middle cerebral arteries. Digital angiogram revealed stenosis of intracranial carotid arteries and the left middle cerebral artery. The CSF disclosed 42 cells/mm[3], 46 mg/dL of glucose, and 82 mg/dL of protein. Brain biopsy showed a chronic leptomeningeal inflammatory process, not fulfilling criteria for PCNSV. mNGS revealed the presence of Brucella sp. genetic material. He was treated with antibiotics with full remission of systemic and neurologic symptoms.

DISCUSSION: Brucellosis is an endemic disease in developing countries and may mimic PCNSV. Our patient fulfilled the criteria for possible PCNSV; however, brain biopsy was inconsistent with PCNSV, and CSF mNGS disclosed neurobrucellosis. This case illustrates the importance of CSF mNGS in the differential diagnosis of CNS vasculitis.}, } @article {pmid37187470, year = {2023}, author = {Wu, C and Yi, H and Hu, Y and Luo, D and Tang, Z and Wen, X and Zhang, Y and Tang, M and Zhang, L and Wu, S and Chen, M}, title = {Effects of second-line anti-tuberculosis drugs on the intestinal microbiota of patients with rifampicin-resistant tuberculosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1127916}, pmid = {37187470}, issn = {2235-2988}, mesh = {Humans ; Antitubercular Agents/pharmacology/therapeutic use ; Rifampin/pharmacology/therapeutic use ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Tryptophan ; *Tuberculosis, Multidrug-Resistant/drug therapy ; *Tuberculosis/drug therapy ; *Mycobacterium tuberculosis ; }, abstract = {OBJECTIVE: To determine the effects of second-line anti-tuberculosis (TB) drugs on the composition and functions of intestinal microbiota in patients with rifampicin-resistant TB (RR-TB).

METHODS: In this cross-sectional study, stool samples and relevant clinical information were collected from patients with RR-TB admitted to the Drug-resistant Specialty Department at Hunan Chest Hospital (Hunan Institute For Tuberculosis Control). The composition and functions of intestinal microbiota were analyzed using metagenomic sequencing and bioinformatics methods.

RESULTS: Altered structural composition of the intestinal microbiota was found when patients from the control, intensive phase treatment, and continuation phase treatment groups were compared (P<0.05). Second-line anti-TB treatment resulted in a decrease in the relative abundance of species, such as Prevotella copri, compared with control treatment. However, the relative abundance of Escherichia coli, Salmonella enterica, and 11 other conditionally pathogenic species increased significantly in the intensive phase treatment group. Based on differential functional analysis, some metabolism-related functions, such as the biosynthesises of phenylalanine, tyrosine, and tryptophan, were significantly inhibited during second-line anti-TB drug treatment, while other functions, such as phenylalanine metabolism, were significantly promoted during the intensive phase of treatment.

CONCLUSION: Second-line anti-TB drug treatment caused changes in the structural composition of the intestinal microbiota in patients with RR-TB. In particular, this treatment induced a significant increase in the relative abundance of 11 conditionally pathogenic species, including Escherichia coli. Functional analysis revealed significantly decreased biosynthesises of phenylalanine, tyrosine, and tryptophan and significantly increased phenylalanine metabolism.}, } @article {pmid37187112, year = {2023}, author = {Bargheet, A and Klingenberg, C and Esaiassen, E and Hjerde, E and Cavanagh, JP and Bengtsson-Palme, J and Pettersen, VK}, title = {Development of early life gut resistome and mobilome across gestational ages and microbiota-modifying treatments.}, journal = {EBioMedicine}, volume = {92}, number = {}, pages = {104613}, pmid = {37187112}, issn = {2352-3964}, mesh = {Infant ; Infant, Newborn ; Humans ; Gestational Age ; *Microbiota ; Gastrointestinal Tract/microbiology ; Infant, Extremely Premature ; Anti-Bacterial Agents/adverse effects ; Feces/microbiology ; *Probiotics/therapeutic use ; }, abstract = {BACKGROUND: Gestational age (GA) and associated level of gastrointestinal tract maturation are major factors driving the initial gut microbiota composition in preterm infants. Besides, compared to term infants, premature infants often receive antibiotics to treat infections and probiotics to restore optimal gut microbiota. How GA, antibiotics, and probiotics modulate the microbiota's core characteristics, gut resistome and mobilome, remains nascent.

METHODS: We analysed metagenomic data from a longitudinal observational study in six Norwegian neonatal intensive care units to describe the bacterial microbiota of infants of varying GA and receiving different treatments. The cohort consisted of probiotic-supplemented and antibiotic-exposed extremely preterm infants (n = 29), antibiotic-exposed very preterm (n = 25), antibiotic-unexposed very preterm (n = 8), and antibiotic-unexposed full-term (n = 10) infants. The stool samples were collected on days of life 7, 28, 120, and 365, and DNA extraction was followed by shotgun metagenome sequencing and bioinformatical analysis.

FINDINGS: The top predictors of microbiota maturation were hospitalisation length and GA. Probiotic administration rendered the gut microbiota and resistome of extremely preterm infants more alike to term infants on day 7 and ameliorated GA-driven loss of microbiota interconnectivity and stability. GA, hospitalisation, and both microbiota-modifying treatments (antibiotics and probiotics) contributed to an elevated carriage of mobile genetic elements in preterm infants compared to term controls. Finally, Escherichia coli was associated with the highest number of antibiotic-resistance genes, followed by Klebsiella pneumoniae and Klebsiella aerogenes.

INTERPRETATION: Prolonged hospitalisation, antibiotics, and probiotic intervention contribute to dynamic alterations in resistome and mobilome, gut microbiota characteristics relevant to infection risk.

FUNDING: Odd-Berg Group, Northern Norway Regional Health Authority.}, } @article {pmid37187058, year = {2023}, author = {Yadav, R and Rajput, V and Dharne, M}, title = {Corrigendum to "Functional metagenomic landscape of polluted river reveals potential genes involved in degradation of xenobiotic pollutants" [Vol 192, 110332].}, journal = {Environmental research}, volume = {231}, number = {Pt 1}, pages = {116128}, doi = {10.1016/j.envres.2023.116128}, pmid = {37187058}, issn = {1096-0953}, } @article {pmid37186513, year = {2023}, author = {Liu, M and Yang, S and Wu, S and Chen, L and Li, S and Li, Z and Zhou, M and Wang, L and Xu, H and Liu, R and Fang, Y and Huang, W and Zhang, M and Guo, W and Dai, Y and Ren, Y and Guo, H and Wu, W}, title = {Detection of pathogens and antimicrobial resistance genes directly from urine samples in patients suspected of urinary tract infection by metagenomics nanopore sequencing: A large-scale multi-centre study.}, journal = {Clinical and translational medicine}, volume = {13}, number = {4}, pages = {e824}, pmid = {37186513}, issn = {2001-1326}, mesh = {Humans ; Anti-Bacterial Agents ; Metagenomics ; *Nanopore Sequencing ; Drug Resistance, Bacterial/genetics ; *Anti-Infective Agents ; *Urinary Tract Infections/diagnosis ; }, } @article {pmid37186335, year = {2023}, author = {Zuo, K and Fang, C and Gao, Y and Fu, Y and Wang, H and Li, J and Zhong, J and Yang, X and Xu, L}, title = {Suppression of the gut microbiota-bile acid-FGF19 axis in patients with atrial fibrillation.}, journal = {Cell proliferation}, volume = {56}, number = {11}, pages = {e13488}, pmid = {37186335}, issn = {1365-2184}, support = {7222068//Beijing Natural Science Foundation/ ; 31771021//National Natural Science Foundation of China/ ; 81670214//National Natural Science Foundation of China/ ; 81770253//National Natural Science Foundation of China/ ; 81970271//National Natural Science Foundation of China/ ; 82100334//National Natural Science Foundation of China/ ; 91849111//National Natural Science Foundation of China/ ; 92168117//National Natural Science Foundation of China/ ; CYJZ202107//the Golden-seed training plan/ ; QML20230316//Beijing Hospitals Authority Youth Programme/ ; }, mesh = {Humans ; Bile Acids and Salts ; *Gastrointestinal Microbiome ; *Atrial Fibrillation ; Cross-Sectional Studies ; Palmitic Acid ; Fibroblast Growth Factors/metabolism ; }, abstract = {This study aimed to investigate the role of the gut microbiota (GM)-bile acid (BA)-fibroblast growth factor (FGF) 19 axis in patients with atrial fibrillation (AF). Gut bacterial metabolisms of BAs were determined in an AF metagenomic dataset. The composition of faecal BAs pools was characterized by targeted metabolomics in an independent AF cross-sectional cohort. Circulating levels of FGF19 were measured by ELISA. In vitro cell experiments were conducted to validate the regulatory role of FGF19 in atrial cardiomyocytes stimulated with palmitic acid. First, metagenomic profiling revealed that gut microbial biotransformation from primary to secondary BAs was dysregulated in AF patients. Second, the proportion of secondary BAs decreased in the faeces of patients with AF. Also, eight BAs were identified as AF-associated BAs, including seven AF-enriched BAs (ursodeoxycholic acid, chenodeoxycholic acid, etc.), and AF-decreased dehydrolithocholic acid. Third, reduced levels of circulating FGF19 were observed in patients with AF. Subsequently, FGF19 was found to protect against palmitic acid-induced lipid accumulation and dysregulated signalling in atrial cardiomyocytes, including attenuated phosphorylation of YAP and Ca[2+] /calmodulin-dependent protein kinases II and secretion of interleukin-1β, mediated via peroxisome proliferator-activated receptor α. Our data found decreased levels of secondary BAs and circulating FGF19, resulting in the impaired protective function of FGF19 against lipid accumulation in atrial cardiomyocytes.}, } @article {pmid37186232, year = {2023}, author = {Sheehy, L and MacDonald-Howard, K and Williams, CD and Weedall, GD and Jones, H and Rae, R}, title = {A parasitic nematode induces dysbiosis in susceptible but not resistant gastropod hosts.}, journal = {MicrobiologyOpen}, volume = {12}, number = {2}, pages = {e1346}, pmid = {37186232}, issn = {2045-8827}, mesh = {Animals ; *Gastropoda ; Dysbiosis ; *Nematoda ; *Rhabditoidea ; Disease Susceptibility ; }, abstract = {Animals' gut microbiomes affect a wide array of biological processes including immunity and protection from pathogens. However, how the microbiome changes due to infection by parasites is still largely unknown, as is how the microbiome changes in hosts that differ in their susceptibility to parasites. To investigate this, we exposed two slug species of differing susceptibility to the parasitic nematode Phasmarhabditis hermaphrodita (Deroceras reticulatum is highly susceptible and Ambigolimax valentianus resistant to the nematode) and profiled the gut microbiota after 7 and 14 days. Before infection, both slug species' microbiota was dominated by similar bacterial genera: Pseudomonas (by far the most abundant), Sphingobacterium, Pedobacter, Chryseobacterium, and Flavobacterium. In the resistant host A. valentianus, there was no significant change in the bacterial genera after infection, but in D. reticulatum, the bacterial profile changed, with a decrease in the abundance of Pseudomonadaceae and an increase in the abundance of Flavobacteriaceae and Sphingobacteriaceae after 7 days postinfection. This suggests nematode infection causes dysbiosis in hosts that are susceptible to infection, but the microbiome of resistant species remains unaltered. In summary, the regulation of the immune system is tightly linked with host survival, and nematode infection can alter the microbiome structure.}, } @article {pmid37186231, year = {2023}, author = {Stach, TL and Sieber, G and Shah, M and Simon, SA and Soares, A and Bornemann, TLV and Plewka, J and Künkel, J and Becker, C and Meyer, F and Boenigk, J and Probst, AJ}, title = {Temporal disturbance of a model stream ecosystem by high microbial diversity from treated wastewater.}, journal = {MicrobiologyOpen}, volume = {12}, number = {2}, pages = {e1347}, pmid = {37186231}, issn = {2045-8827}, mesh = {*Ecosystem ; Rivers/microbiology ; Wastewater ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota/genetics ; }, abstract = {Microbial communities in freshwater streams play an essential role in ecosystem functioning via biogeochemical cycling. Yet, the impacts of treated wastewater influx into stream ecosystems on microbial strain diversity remain mostly unexplored. Here, we coupled full-length 16S ribosomal RNA gene Nanopore sequencing and strain-resolved metagenomics to investigate the impact of treated wastewater on a mesocosm system (AquaFlow) run with restored river water. Over 10 days, community Bray-Curtis dissimilarities between treated and control mesocosm decreased (0.57 ± 0.058 to 0.26 ± 0.046) based on ribosomal protein S3 gene clustering, finally converging to nearly identical communities. Similarly, strain-resolved metagenomics revealed a high diversity of bacteria and viruses after the introduction of treated wastewater; these microbes also decreased over time resulting in the same strain clusters in control and treatment at the end of the experiment. Specifically, 39.2% of viral strains detected in all samples were present after the introduction of treated wastewater only. Although bacteria present at low abundance in the treated wastewater introduced additional antibiotic resistance genes, signals of naturally occurring ARG-encoding organisms resembled the resistome at the endpoint. Our results suggest that the previously stressed freshwater stream and its microbial community are resilient to a substantial introduction of treated wastewater.}, } @article {pmid37186226, year = {2023}, author = {Gill, SP and Snelling, WJ and Dooley, JSG and Ternan, NG and Banat, IM and Arnscheidt, J and Hunter, WR}, title = {Biological and synthetic surfactant exposure increases antimicrobial gene occurrence in a freshwater mixed microbial biofilm environment.}, journal = {MicrobiologyOpen}, volume = {12}, number = {2}, pages = {e1351}, pmid = {37186226}, issn = {2045-8827}, mesh = {RNA, Ribosomal, 16S/genetics ; *Surface-Active Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; Fresh Water ; Biofilms ; }, abstract = {Aquatic habitats are particularly susceptible to chemical pollution, such as antimicrobials, from domestic, agricultural, and industrial sources. This has led to the rapid increase of antimicrobial resistance (AMR) gene prevalence. Alternate approaches to counteract pathogenic bacteria are in development including synthetic and biological surfactants such as sodium dodecyl sulfate (SDS) and rhamnolipids. In the aquatic environment, these surfactants may be present as pollutants with the potential to affect biofilm formation and AMR gene occurrence. We tested the effects of rhamnolipid and SDS on aquatic biofilms in a freshwater stream in Northern Ireland. We grew biofilms on contaminant exposure substrates deployed within the stream over 4 weeks. We then extracted DNA and carried out shotgun sequencing using a MinION portable sequencer to determine microbial community composition, with 16S rRNA analyses (64,678 classifiable reads identified), and AMR gene occurrence (81 instances of AMR genes over 9 AMR gene classes) through a metagenomic analysis. There were no significant changes in community composition within all systems; however, biofilm exposed to rhamnolipid had a greater number of unique taxa as compared to SDS treatments and controls. AMR gene prevalence was higher in surfactant-treated biofilms, although not significant, with biofilm exposed to rhamnolipids having the highest presence of AMR genes and classes compared to the control or SDS treatments. Our results suggest that the presence of rhamnolipid encourages an increase in the prevalence of AMR genes in biofilms produced in mixed-use water bodies.}, } @article {pmid37185621, year = {2023}, author = {Li, J and Liu, T and McIlroy, SJ and Tyson, GW and Guo, J}, title = {Phylogenetic and metabolic diversity of microbial communities performing anaerobic ammonium and methane oxidations under different nitrogen loadings.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {39}, pmid = {37185621}, issn = {2730-6151}, abstract = {The microbial guild coupling anammox and nitrite/nitrate-dependent anaerobic methane oxidation (n-DAMO) is an innovative process to achieve energy-efficient nitrogen removal with the beneficial use of methane in biogas or in anaerobically treated wastewater. Here, metagenomics and metatranscriptomics were used to reveal the microbial ecology of two biofilm systems, which incorporate anammox and n-DAMO for high-level nitrogen removal in low-strength domestic sewage and high-strength sidestream wastewater, respectively. We find that different nitrogen loadings (i.e., 0.1 vs. 1.0 kg N/m[3]/d) lead to different combinations of anammox bacteria and anaerobic methanotrophs ("Candidatus Methanoperedens" and "Candidatus Methylomirabilis"), which play primary roles for carbon and nitrogen transformations therein. Despite methane being the only exogenous organic carbon supplied, heterotrophic populations (e.g., Verrucomicrobiota and Bacteroidota) co-exist and actively perform partial denitrification or dissimilatory nitrate reduction to ammonium (DNRA), likely using organic intermediates from the breakdown of methane and biomass as carbon sources. More importantly, two novel genomes belonging to "Ca. Methylomirabilis" are recovered, while one surprisingly expresses nitrate reductases, which we designate as "Ca. Methylomirabilis nitratireducens" representing its inferred capability in performing nitrate-dependent anaerobic methane oxidation. This finding not only suggests a previously neglected possibility of "Ca. Methylomirabilis" bacteria in performing methane-dependent nitrate reduction, and also challenges the previous understanding that the methane-dependent complete denitrification from nitrate to dinitrogen gas is carried out by the consortium of bacteria and archaea.}, } @article {pmid37184398, year = {2023}, author = {Johnson, MA and Vinatzer, BA and Li, S}, title = {Reference-Free Plant Disease Detection Using Machine Learning and Long-Read Metagenomic Sequencing.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {6}, pages = {e0026023}, pmid = {37184398}, issn = {1098-5336}, mesh = {*Metagenome ; *Metagenomics/methods ; Machine Learning ; Chromosome Mapping ; Plant Diseases ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Surveillance for early disease detection is crucial to reduce the threat of plant diseases to food security. Metagenomic sequencing and taxonomic classification have recently been used to detect and identify plant pathogens. However, for an emerging pathogen, its genome may not be similar enough to any public genome to permit reference-based tools to identify infected samples. Also, in the case of point-of care diagnosis in the field, database access may be limited. Therefore, here we explore reference-free detection of plant pathogens using metagenomic sequencing and machine learning (ML). We used long-read metagenomes from healthy and infected plants as our model system and constructed k-mer frequency tables to test eight different ML models. The accuracy in classifying individual reads as coming from a healthy or infected metagenome were compared. Of all models, random forest (RF) had the best combination of short run-time and high accuracy (over 0.90) using tomato metagenomes. We further evaluated the RF model with a different tomato sample infected with the same pathogen or a different pathogen and a grapevine sample infected with a grapevine pathogen and achieved similar performances. ML models can thus learn features to successfully perform reference-free detection of plant diseases whereby a model trained with one pathogen-host system can also be used to detect different pathogens on different hosts. Potential and challenges of applying ML to metagenomics in plant disease detection are discussed. IMPORTANCE Climate change may lead to the emergence of novel plant diseases caused by yet unknown pathogens. Surveillance for emerging plant diseases is crucial to reduce their threat to food security. However, conventional genomic based methods require knowledge of existing plant pathogens and cannot be applied to detecting newly emerged pathogens. In this work, we explored reference-free, meta-genomic sequencing-based disease detection using machine learning. By sequencing the genomes of all microbial species extracted from an infected plant sample, we were able to train machine learning models to accurately classify individual sequencing reads as coming from a healthy or an infected plant sample. This method has the potential to be integrated into a generic pipeline for a meta-genomic based plant disease surveillance approach but also has limitations that still need to be overcome.}, } @article {pmid37184380, year = {2023}, author = {Castro-Nallar, E and Berríos-Farías, V and Díez, B and Guajardo-Leiva, S}, title = {Spatially and Temporally Explicit Metagenomes and Metagenome-Assembled Genomes from the Comau Fjord (42°S), Patagonia.}, journal = {Microbiology resource announcements}, volume = {12}, number = {6}, pages = {e0005923}, pmid = {37184380}, issn = {2576-098X}, support = {FONDECYT1200834//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; FONDECYT3210547//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; }, abstract = {Microbes play an important role in coastal and estuarine waters. We present 93 metagenomes and 677 metagenome-assembled genomes (MAGs) from Comau Fjord, Patagonia (42°S), to further understand the microbial dynamics and their response to anthropogenic disturbances. These data represent a spatially (35-km transect) and temporally (2016 to 2019) explicit data set.}, } @article {pmid37183784, year = {2023}, author = {Ma, L and Lyu, W and Song, Y and Chen, K and Lv, L and Yang, H and Wang, W and Xiao, Y}, title = {Anti-Inflammatory Effect of Clostridium butyricum-Derived Extracellular Vesicles in Ulcerative Colitis: Impact on Host microRNAs Expressions and Gut Microbiome Profiles.}, journal = {Molecular nutrition & food research}, volume = {67}, number = {13}, pages = {e2200884}, doi = {10.1002/mnfr.202200884}, pmid = {37183784}, issn = {1613-4133}, mesh = {Mice ; Animals ; *Colitis, Ulcerative/chemically induced/drug therapy ; *Clostridium butyricum/genetics ; *Gastrointestinal Microbiome ; *Colitis/drug therapy ; *Inflammatory Bowel Diseases ; Inflammation/drug therapy ; Colon ; *MicroRNAs/genetics ; Anti-Inflammatory Agents ; Dextran Sulfate/toxicity ; Disease Models, Animal ; *Extracellular Vesicles ; }, abstract = {SCORE: Probiotics extracellular vesicles (EVs) have shown potential as EV-based nanomaterials therapy for the treatment of inflammatory bowel disease (IBD). Although probiotic Clostridium butyricum has been reported to be protective in various models of intestinal inflammation, the therapeutic effects of C. butyricum-derived extracellular vesicles (CbEVs) in IBD remain to be demonstrated.

METHODS AND RESULTS: In this study, multi-omics sequencing is combined with an in vitro model of lipopolysaccharide-induced RAW264.7 cells and an in vivo mouse model of dextran sodium sulfate-induced colitis to explore the regulatory impact and mechanism of CbEVs in ulcerative colitis. Through small RNA sequencing, the study finds that microRNA is involved in the alleviation of colonic inflammation under CbEVs treatment. Mechanistically, CbEVs restore miR-199a-3p expression, interacting with map3k4, and thereby suppress proinflammatory MAPK and NF-κB signaling. Additionally, metagenomic sequencing demonstrate that CbEVs alleviate bacterial dysbiosis in colitis mice and significantly reduces the abundance of the bacterial pathogens Escherichia coli and Shigella flexneri. Furthermore, CbEVs regulate the microbial tryptophan metabolites, which further improve intestinal barrier integrity and inhibit the inflammatory response in colitis mice.

CONCLUSION: C. butyricum-derived extracellular vesicles can be a novel agent for the treatment of colitis and miR-199a-3p can be a potential target for IBD treatment.}, } @article {pmid37183345, year = {2023}, author = {Nath, A and Gadratagi, BG and Maurya, RP and Ullah, F and Patil, NB and Adak, T and Govindharaj, GPP and Ray, A and Mahendiran, A and Desneux, N and Chandra Rath, P}, title = {Sublethal phosphine fumigation induces transgenerational hormesis in a factitious host, Corcyra cephalonica.}, journal = {Pest management science}, volume = {79}, number = {10}, pages = {3548-3558}, doi = {10.1002/ps.7542}, pmid = {37183345}, issn = {1526-4998}, support = {//National Rice Research Institute, Indian Council of Agricultural Research/ ; }, mesh = {Animals ; Hormesis ; Fumigation ; *Moths ; Larva ; *Insecticides/pharmacology ; Lipids ; }, abstract = {BACKGROUND: The rice moth, Corcyra cephalonica (Stainton) (Lepidoptera: Pyralidae) is a pest of stored grains and widely used as a factitious host during the mass rearing of several natural enemies of crop pests. Hormesis is well-documented in pest insects, to some extent in natural enemies of pests.

RESULTS: We report transgenerational stimulatory effects of the widely used fumigant, phosphine. The study reports the consequences of sublethal, low lethal and median lethal concentrations (LC5 , LC25 and LC50) and untreated control for two sequential generations of the species (G1 to G2). In this study, we investigated the life-history traits, nutrient reserves (protein, lipid and carbohydrate) and larval gut microbiome (using 16 s rRNA V3-V4 metagenomics sequencing) of C. cephalonica. Stimulatory effects were observed for various biological traits of C. cephalonica, notably adult longevity, emergence and increased egg hatchability when exposed to LC5 of phosphine. The total protein, lipid and carbohydrate contents of C. cephalonica also were found to be significantly increased by LC5 in both generations. The microbial diversity of LC5 treated larval gut was higher and found to be different from the rest of the treatments. This is the first report showing hormesis to a fumigant insecticide.

CONCLUSION: Our findings increase knowledge on the interaction between hormesis, nutrient reserves and gut bacteria in C. cephalonica exposed to insecticides. Overall, the present study establishes phosphine-induced hormesis at LC5 in the host C. cephalonica, which might help improve the quality of mass rearing of various natural enemies. © 2023 Society of Chemical Industry.}, } @article {pmid37182783, year = {2023}, author = {Zhou, T and Xiang, Y and Liu, S and Shao, Z and Liu, Y and Ma, H and He, Q and Chai, H}, title = {Insights into simultaneous nitrogen and phosphorus removal in biofilm: The overlooked comammox Nitrospira and the positive role of glycogen-accumulating organisms.}, journal = {The Science of the total environment}, volume = {887}, number = {}, pages = {164130}, doi = {10.1016/j.scitotenv.2023.164130}, pmid = {37182783}, issn = {1879-1026}, mesh = {*Ammonia ; *Nitrogen ; Nitrites ; Nitrates ; Nitrification ; Phosphorus ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; Oxidation-Reduction ; Bacteria ; Biofilms ; Bioreactors/microbiology ; }, abstract = {Simultaneous nitrogen and phosphorus removal (SNPR) biofilm system is an effective wastewater treatment process. However, the understanding on the mechanism of functional microorganisms driving SNPR is still limited, especially the role of complete ammonia oxidation (comammox) Nitrospira and glycogen-accumulating organisms (GAO). In this study, a sequencing batch biofilm reactor (SBBR) performing SNPR was operated for 249 d. Based on the 16S rRNA gene, comammox amoA amplicon sequencing, metagenomics and batch experiment, we found that comammox Nitrospira was the main ammonia-oxidizing microorganisms (AOM) and provided nitrite for anaerobic ammonia oxidation (anammox) bacteria (AnAOB). Besides, GAO was dominated by the bacteria of genus Defluviicoccus and played a primary role in reducing nitrate rather than nitrite. Fluorescent in situ hybridization (FISH) analysis confirmed that Nitrospira was enriched in the inner layer of the biofilm. Thus, we put forward a novel insight into the mechanism of SNPR biofilm system. Comammox Nitrospira was responsible for nitrite and nitrate production in the inner biofilm, and AnAOB consumed the produced nitrite during the anammox process. While GAO reduced nitrate to nitrite and polyphosphate-accumulating organisms (PAO) converted nitrite to dinitrogen via denitrifying phosphorus removal in the outer biofilm. These findings provide a new understanding in SNPR biofilm system.}, } @article {pmid37182710, year = {2023}, author = {Wang, L and Li, A}, title = {Impact of zero-valent iron on nitrifying granular sludge for 17α-ethinylestradiol removal and its mechanism.}, journal = {Chemosphere}, volume = {333}, number = {}, pages = {138904}, doi = {10.1016/j.chemosphere.2023.138904}, pmid = {37182710}, issn = {1879-1298}, mesh = {*Sewage ; *Ammonia/metabolism ; Iron/metabolism ; Ethinyl Estradiol/metabolism ; Wastewater ; Bacteria/genetics/metabolism ; Bioreactors ; }, abstract = {Aerobic granulation of nitrifying activated sludge could enhance the removal of 17α-ethinylestradiol (EE2) via abiotic nitration induced by reactive nitrogen species, cometabolism by ammonia-oxidizing bacteria and biodegradation by heterotrophic bacteria. Zero-valent iron (ZVI), a promising and low-cost material, has previously been applied to effectively enhance biological wastewater treatment. The impact and the effect mechanism of ZVI on nitrifying granular sludge (NGS) for EE2 removal was investigated in this study. The results showed that the addition of ZVI achieved better EE2 removal, though ZVI was not conducive to the accumulation of nitrite in NGS which reduced the abiotic transformation of EE2. Moreover, ZVI enriched heterotrophic denitrifying bacteria such as Arenimonas, thus changing the EE2 removal pathway and improving the degradation and mineralization of EE2. In addition, ZVI reduced the emission risk of the greenhouse gas N2O and strengthened the stability of the granules. Metagenomic analysis further revealed that the functional genes related to EE2 mineralization, nitrite oxidation, N2O reduction and quorum sensing in NGS were enriched with ZVI addition. This study provides meaningful guidance for ZVI application in the NGS process to achieve efficient and simultaneous removal of ammonia and emerging contaminants.}, } @article {pmid37182682, year = {2023}, author = {He, H and Yang, H and Foo, R and Chan, W and Zhu, F and Liu, Y and Zhou, X and Ma, L and Wang, LF and Zhai, W}, title = {Population genomic analysis reveals distinct demographics and recent adaptation in the black flying fox (Pteropus alecto).}, journal = {Journal of genetics and genomics = Yi chuan xue bao}, volume = {50}, number = {8}, pages = {554-562}, doi = {10.1016/j.jgg.2023.05.002}, pmid = {37182682}, issn = {1673-8527}, mesh = {Animals ; *Chiroptera/genetics ; Metagenomics ; Genomics ; Sequence Analysis, DNA ; Demography ; }, abstract = {As the only mammalian group capable of powered flight, bats have many unique biological traits. Previous comparative genomic studies in bats have focused on long-term evolution. However, the micro-evolutionary processes driving recent evolution are largely under-explored. Using resequencing data from 50 black flying foxes (Pteropus alecto), one of the model species for bats, we find that black flying fox has much higher genetic diversity and lower levels of linkage disequilibrium than most of the mammalian species. Demographic inference reveals strong population fluctuations (>100 fold) coinciding with multiple historical events including the last glacial change and Toba super eruption, suggesting that the black flying fox is a very resilient species with strong recovery abilities. While long-term adaptation in the black flying fox is enriched in metabolic genes, recent adaptation in the black flying fox has a unique landscape where recently selected genes are not strongly enriched in any functional category. The demographic history and mode of adaptation suggest that black flying fox might be a well-adapted species with strong evolutionary resilience. Taken together, this study unravels a vibrant landscape of recent evolution for the black flying fox and sheds light on several unique evolutionary processes for bats comparing to other mammalian groups.}, } @article {pmid37182622, year = {2023}, author = {Bharwad, K and Shekh, S and Singh, NK and Patel, A and Joshi, C}, title = {Heterologous expression and biochemical characterization of novel multifunctional thermostable α-amylase from hot-spring metagenome.}, journal = {International journal of biological macromolecules}, volume = {242}, number = {Pt 2}, pages = {124810}, doi = {10.1016/j.ijbiomac.2023.124810}, pmid = {37182622}, issn = {1879-0003}, mesh = {*alpha-Amylases/chemistry ; *Metagenome ; Enzyme Stability ; India ; Hydrogen-Ion Concentration ; Temperature ; }, abstract = {Hot-springs are regarded as the best source of industrially significant biocules and one of the unique locations for extremophiles. The α-amylase is one of the most important enzymes used in starch consuming industries, where the need of thermostability is paramount. In this study, the full metagenome sequences obtained from the soil of Tuwa hot-spring (Gujarat, India) were examined for the presence of several thermostable enzymes using bioinformatic techniques. The whole gene sequence for α-amylase was found from the metagenome. The α-amylase gene was amplified, cloned, and expressed in Escherichia coli and further characterized in vitro. The rm-α-amylase was found optimally active at 60 °C and at pH 6.0 and showed significantly high activity in 0.1 mM Co[2+] as well as in other heavy metal ions without any effect on its thermostability. Apart from α-amylase activity the purified rm-α-amylase was also shown to hydrolyse agar, xylan, pectin, alginate and cellulose. To our knowledge, this is the first report of a new, multifunctional, thermostable amylase that was discovered from the hot-spring metagenomes. Owing to their multifunctionality, resilience towards high temperature and heavy metal ions, stability with solvents, additives and inhibitors, rm-α-amylase can be exploited for a variety of biotechnological applications.}, } @article {pmid37182146, year = {2023}, author = {Bucher-Johannessen, C and Birkeland, EE and Vinberg, E and Bemanian, V and Hoff, G and Berstad, P and Rounge, TB}, title = {Long-term follow-up of colorectal cancer screening attendees identifies differences in Phascolarctobacterium spp. using 16S rRNA and metagenome sequencing.}, journal = {Frontiers in oncology}, volume = {13}, number = {}, pages = {1183039}, pmid = {37182146}, issn = {2234-943X}, abstract = {BACKGROUND: The microbiome has been implicated in the initiation and progression of colorectal cancer (CRC) in cross-sectional studies. However, there is a lack of studies using prospectively collected samples.

METHODS: From the Norwegian Colorectal Cancer Prevention (NORCCAP) trial, we analyzed 144 archived fecal samples from participants who were diagnosed with CRC or high-risk adenoma (HRA) at screening and from participants who remained cancer-free during 17 years of follow-up. We performed 16S rRNA sequencing of all the samples and metagenome sequencing on a subset of 47 samples. Differences in taxonomy and gene content between outcome groups were assessed for alpha and beta diversity and differential abundance.

RESULTS: Diversity and composition analyses showed no significant differences between CRC, HRA, and healthy controls. Phascolarctobacterium succinatutens was more abundant in CRC compared with healthy controls in both the 16S and metagenome data. The abundance of Bifidobacterium and Lachnospiraceae spp. was associated with time to CRC diagnosis.

CONCLUSION: Using a longitudinal study design, we identified three taxa as being potentially associated with CRC. These should be the focus of further studies of microbial changes occurring prior to CRC diagnosis.}, } @article {pmid37181826, year = {2023}, author = {Deng, S and Cai, K and Pei, C and Zhang, X and Xiao, X and Chen, Y and Chen, Y and Liang, R and Chen, Y and Li, P and Xie, Z and Liao, Q}, title = {16S rRNA and Metagenomics Combined with UPLC-Q/TOF-MS Metabolomics Analysis Reveals the Potential Mechanism of Radix Astragali Against Hyperuricemia in Mice.}, journal = {Drug design, development and therapy}, volume = {17}, number = {}, pages = {1371-1386}, pmid = {37181826}, issn = {1177-8881}, mesh = {Mice ; Animals ; *Hyperuricemia/drug therapy ; RNA, Ribosomal, 16S ; Metagenomics ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Xanthine Oxidase/genetics/metabolism ; }, abstract = {PURPOSE: This study aimed to investigate the underlying treatment mechanism of Radix Astragali (RA) in hyperuricemia from the perspective of microbiota and metabolomics.

METHODS: We used potassium oxyazinate (PO) to induce hyperuricemia mice, and we determined serum alanine aminotransferase/aspartate aminotransferase (ALT/AST), xanthine oxidase (XOD), creatinine (CRE), uric acid (UA), blood urea nitrogen (BUN) levels, liver XOD levels and assessed the kidney tissue histopathology. The therapeutic mechanism of RA in hyperuricemic mice was studied by 16S rRNA, metagenomic sequencing and metabolomics.

RESULTS: Our research showed that RA has therapeutic effect in hyperuricemia mice, such as slow the weight loss, repair kidney damage, and downregulate serum UA, XOD, CRE, ALT/AST, BUN, and liver XOD levels. RA restored the disturbance structure of the microbiota in hyperuricemia mice by increasing the relative abundances of beneficial bacteria (Lactobacillaceae and Lactobacillus murine) but decreasing the relative abundances of pathogenic bacteria (Prevotellaceae, Rikenellaceae and Bacteroidaceae). Meanwhile, we found that RA directly regulated the metabolic pathway (such as linoleic acid metabolism and glycerophospholipid metabolism) and indirectly regulated bile acid metabolism by mediating microbiota to ameliorate metabolic disorders. Subsequently, there was a robust correlation between specific microbiota, metabolites and the disease index.

CONCLUSION: The ability of RA to protect mice against hyperuricemia is strongly linked to the microbiome-metabolite axis, which would provide evidence for RA as a medicine to prevent or treat hyperuricemia.}, } @article {pmid37181218, year = {2023}, author = {Yu, HH and Yi, SH and Lim, SD and Hong, SP}, title = {The Effect of Vacuum Films on Physicochemical and Microbiological Characteristics of Hanwoo (Korean Native Cattle).}, journal = {Food science of animal resources}, volume = {43}, number = {3}, pages = {441-453}, pmid = {37181218}, issn = {2636-0780}, abstract = {The objective of this study was to investigate the physicochemical and microbiological characteristics of round of Hanwoo by vacuum packaging film materials, polyvinylidene chloride (PVDC) and ethylene vinyl alcohol (EVOH). The packaged beef samples were stored in refrigerated conditions (2±1°C) for 12 weeks. Physicochemical analysis with pH, surface color, thiobarbituric acid reactive substances (TBARS) values, and volatile basic nitrogen (VBN) values and microbiological analysis with aerobic plate count (APC) and metagenomic analysis of packaged beef samples were performed. The pH and surface color did not change substantially during the 12 weeks and EVOH-packaged beef tended to be lower than those of PVDC-packaged beef. PVDC- and EVOH-packaged samples showed low TBARS and VBN values below standard limits. APC did not exceed 7 Log CFU/g for both samples during storage. In metagenomic analysis, Firmicutes and Lactobacillaceae were dominant phylum and family of the PVDC- and EVOH-packaged beef. In both packaged samples, Dellaglioa algida was the dominant species during storage, with the notable difference being the presence of Lactococcus piscium. Therefore, this study provided the information on the quality of vacuum-packaged beef according to different vacuum films for long-term refrigerated storage.}, } @article {pmid37180976, year = {2023}, author = {Marchukov, D and Li, J and Juillerat, P and Misselwitz, B and Yilmaz, B}, title = {Benchmarking microbial DNA enrichment protocols from human intestinal biopsies.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1184473}, pmid = {37180976}, issn = {1664-8021}, abstract = {Shotgun metagenomic sequencing is a powerful tool for studying bacterial communities in their natural habitats or sites of infection, without the need for cultivation. However, low microbial signals in metagenomic sequencing can be overwhelmed by host DNA contamination, resulting in decreased sensitivity for microbial read detection. Several commercial kits and other methods have been developed to enrich bacterial sequences; however, these assays have not been tested extensively for human intestinal tissues yet. Therefore, the objective of this study was to assess the effectiveness of various wet-lab and software-based approaches for depleting host DNA from microbiome samples. Four different microbiome DNA enrichment methods, namely the NEBNext Microbiome DNA Enrichment kit, Molzym Ultra-Deep Microbiome Prep, QIAamp DNA Microbiome kit, and Zymo HostZERO microbial DNA kit, were evaluated, along with a software-controlled adaptive sampling (AS) approach by Oxford Nanopore Technologies (ONT) providing microbial signal enrichment by aborting unwanted host DNA sequencing. The NEBNext and QIAamp kits proved to be effective in shotgun metagenomic sequencing studies, as they efficiently reduced host DNA contamination, resulting in 24% and 28% bacterial DNA sequences, respectively, compared to <1% in the AllPrep controls. Additional optimization steps using further detergents and bead-beating steps improved the efficacy of less efficient protocols but not of the QIAamp kit. In contrast, ONT AS increased the overall number of bacterial reads resulting in a better bacterial metagenomic assembly with more bacterial contigs with greater completeness compared to non-AS approaches. Additionally, AS also allowed for the recovery of antimicrobial resistance markers and the identification of plasmids, demonstrating the potential utility of AS for targeted sequencing of microbial signals in complex samples with high amounts of host DNA. However, ONT AS resulted in relevant shifts in the observed bacterial abundance, including 2 to 5 times more Escherichia coli reads. Furthermore, a modest enrichment of Bacteroides fragilis and Bacteroides thetaiotaomicron was also observed with AS. Overall, this study provides insight into the efficacy and limitations of various methods for reducing host DNA contamination in human intestinal samples to improve the utility of metagenomic sequencing.}, } @article {pmid37180934, year = {2023}, author = {Kütt, ML and Orgusaar, K and Stulova, I and Priidik, R and Pismennõi, D and Vaikma, H and Kallastu, A and Zhogoleva, A and Morell, I and Kriščiunaite, T}, title = {Starter culture growth dynamics and sensory properties of fermented oat drink.}, journal = {Heliyon}, volume = {9}, number = {5}, pages = {e15627}, pmid = {37180934}, issn = {2405-8440}, abstract = {In the present study, an oat drink, a plant-based alternative to dairy products, was developed by fermenting the oat base with different vegan starter cultures. The desired pH below 4.2 was achieved in 12 h, regardless of starter culture used. Metagenomic sequencing revealed that S. thermophilus was the dominating species, ranging from 38% to 99% of the total microbial consortia. At lower pH values, population of L. acidophilus, L. plantarum and L. paracasei continued to increase in fermented oat drinks. Lactic acid was produced between 1.6 and 2.8 g/L. The sensory panel showed that all fermented oat drinks had a sour odor and taste. The volatile compounds identified belonged to the ketone, alcohol, aldehyde, acids, and furan classes. The concentration of the most preferred volatile components, such as diacetyl and acetoin, increased during fermentation. However, sensory evaluation showed that all samples were associated with cereals and not dairy in terms of taste and odor. Rheological analysis showed the formation of weak gel-like structures in fermented oat drinks. Overall, fermentation improved flavor and texture of the product. This study provides a broad overview of the oat drink fermentation process from the perspectives of starter culture growth, microbial consortium dynamics, lactic acid bacteria metabolism, and sensory profile formation.}, } @article {pmid37180439, year = {2023}, author = {Niu, C and Tu, Y and Jin, Q and Chen, Z and Yuan, K and Wang, M and Zhang, P and Luo, J and Li, H and Yang, Y and Liu, X and Mao, M and Dong, T and Tan, W and Hu, X and Pan, Y and Hou, L and Ma, R and Huang, Z}, title = {Mapping the human oral and gut fungal microbiota in patients with metabolic dysfunction-associated fatty liver disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1157368}, pmid = {37180439}, issn = {2235-2988}, mesh = {Humans ; *Mycobiome ; Fungi/genetics ; *Gastrointestinal Microbiome ; Feces/microbiology ; Saliva ; *Non-alcoholic Fatty Liver Disease ; }, abstract = {Metabolic dysfunction-associated fatty liver disease (MAFLD) is a phenotype of liver diseases associated with metabolic syndrome. The pathogenesis MAFLD remains unclear. The liver maintains is located near the intestine and is physiologically interdependent with the intestine via metabolic exchange and microbial transmission, underpinning the recently proposed "oral-gut-liver axis" concept. However, little is known about the roles of commensal fungi in the disease development. This study aimed to characterize the alterations of oral and gut mycobiota and their roles in MAFLD. Twenty-one MAFLD participants and 20 healthy controls were enrolled. Metagenomics analyses of saliva, supragingival plaques, and feces revealed significant alterations in the gut fungal composition of MAFLD patients. Although no statistical difference was evident in the oral mycobiome diversity within MAFLD and healthy group, significantly decreased diversities were observed in fecal samples of MAFLD patients. The relative abundance of one salivary species, five supragingival species, and seven fecal species was significantly altered in MAFLD patients. Twenty-two salivary, 23 supragingival, and 22 fecal species were associated with clinical parameters. Concerning the different functions of fungal species, pathways involved in metabolic pathways, biosynthesis of secondary metabolites, microbial metabolism in diverse environments, and carbon metabolism were abundant both in the oral and gut mycobiomes. Moreover, different fungal contributions in core functions were observed between MAFLD patients and the healthy controls, especially in the supragingival plaque and fecal samples. Finally, correlation analysis between oral/gut mycobiome and clinical parameters identified correlations of certain fungal species in both oral and gut niches. Particularly, Mucor ambiguus, which was abundant both in saliva and feces, was positively correlated with body mass index, total cholesterol, low-density lipoprotein, alanine aminotransferase, and aspartate aminotransferase, providing evidence of a possible "oral-gut-liver" axis. The findings illustrate the potential correlation between core mycobiome and the development of MAFLD and could propose potential therapeutic strategies.}, } @article {pmid37180436, year = {2023}, author = {Che, Y and Wang, N and Ma, Q and Liu, J and Xu, Z and Li, Q and Wang, J and Sun, Y}, title = {Microbial characterization of the nasal cavity in patients with allergic rhinitis and non-allergic rhinitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1166389}, pmid = {37180436}, issn = {2235-2988}, mesh = {Humans ; *Rhinitis/diagnosis ; Nasal Cavity ; *Rhinitis, Allergic/diagnosis/metabolism ; Lactobacillus ; }, abstract = {INTRODUCTION: Although recent studies have shown that the human microbiome is involved in the pathogenesis of allergic diseases, the impact of microbiota on allergic rhinitis (AR) and non-allergic rhinitis (nAR) has not been elucidated. The aim of this study was to investigate the differences in the composition of the nasal flora in patients with AR and nAR and their role in the pathogenesis.

METHOD: From February to September 2022, 35 AR patients and 35 nAR patients admitted to Harbin Medical University's Second Affiliated Hospital, as well as 20 healthy subjects who underwent physical examination during the same period, were subjected to 16SrDNA and metagenomic sequencing of nasal flora.

RESULTS: The microbiota composition of the three groups of study subjects differs significantly. The relative abundance of Vibrio vulnificus and Acinetobacter baumanni in the nasal cavity of AR patients was significantly higher when compared to nAR patients, while the relative abundance of Lactobacillus murinus, Lactobacillus iners, Proteobacteria, Pseudomonadales, and Escherichia coli was lower. In addition, Lactobacillus murinus and Lacttobacillus kunkeei were also negatively correlated with IgE, while Lacttobacillus kunkeei was positively correlated with age. The relative distribution of Faecalibacterium was higher in moderate than in severe AR patients. According to KEGG functional enrichment annotation, ICMT(protein-S-isoprenylcysteine O-methyltransferase,ICMT) is an AR microbiota-specific enzyme that plays a role, while glycan biosynthesis and metabolism are more active in AR microbiota. For AR, the model containing Parabacteroides goldstemii, Sutterella-SP-6FBBBBH3, Pseudoalteromonas luteoviolacea, Lachnospiraceae bacterium-615, and Bacteroides coprocola had the highest the area under the curve (AUC), which was 0.9733(95%CI:0.926-1.000) in the constructed random forest prediction model. The largest AUC for nAR is 0.984(95%CI:0.949-1.000) for the model containing Pseudomonas-SP-LTJR-52, Lachnospiraceae bacterium-615, Prevotella corporis, Anaerococcus vaginalis, and Roseburia inulinivorans.

CONCLUSION: In conclusion, patients with AR and nAR had significantly different microbiota profiles compared to healthy controls. The results suggest that the nasal microbiota may play a key role in the pathogenesis and symptoms of AR and nAR, providing us with new ideas for the treatment of AR and nAR.}, } @article {pmid37180266, year = {2023}, author = {Shahid, M and Singh, UB and Khan, MS and Singh, P and Kumar, R and Singh, RN and Kumar, A and Singh, HV}, title = {Bacterial ACC deaminase: Insights into enzymology, biochemistry, genetics, and potential role in amelioration of environmental stress in crop plants.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1132770}, pmid = {37180266}, issn = {1664-302X}, abstract = {Growth and productivity of crop plants worldwide are often adversely affected by anthropogenic and natural stresses. Both biotic and abiotic stresses may impact future food security and sustainability; global climate change will only exacerbate the threat. Nearly all stresses induce ethylene production in plants, which is detrimental to their growth and survival when present at higher concentrations. Consequently, management of ethylene production in plants is becoming an attractive option for countering the stress hormone and its effect on crop yield and productivity. In plants, ACC (1-aminocyclopropane-1-carboxylate) serves as a precursor for ethylene production. Soil microorganisms and root-associated plant growth promoting rhizobacteria (PGPR) that possess ACC deaminase activity regulate growth and development of plants under harsh environmental conditions by limiting ethylene levels in plants; this enzyme is, therefore, often designated as a "stress modulator." TheACC deaminase enzyme, encoded by the AcdS gene, is tightly controlled and regulated depending upon environmental conditions. Gene regulatory components of AcdS are made up of the LRP protein-coding regulatory gene and other regulatory components that are activated via distinct mechanisms under aerobic and anaerobic conditions. ACC deaminase-positive PGPR strains can intensively promote growth and development of crops being cultivated under abiotic stresses including salt stress, water deficit, waterlogging, temperature extremes, and presence of heavy metals, pesticides and other organic contaminants. Strategies for combating environmental stresses in plants, and improving growth by introducing the acdS gene into crop plants via bacteria, have been investigated. In the recent past, some rapid methods and cutting-edge technologies based on molecular biotechnology and omics approaches involving proteomics, transcriptomics, metagenomics, and next generation sequencing (NGS) have been proposed to reveal the variety and potential of ACC deaminase-producing PGPR that thrive under external stresses. Multiple stress-tolerant ACC deaminase-producing PGPR strains have demonstrated great promise in providing plant resistance/tolerance to various stressors and, therefore, it could be advantageous over other soil/plant microbiome that can flourish under stressed environments.}, } @article {pmid37180249, year = {2023}, author = {Schaeffer, J and Desdouits, M and Besnard, A and Le Guyader, FS}, title = {Looking into sewage: how far can metagenomics help to detect human enteric viruses?.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1161674}, pmid = {37180249}, issn = {1664-302X}, abstract = {The impact of human sewage on environmental and food contamination constitutes an important safety issue. Indeed, human sewage reflects the microbiome of the local population, and a variety of human viruses can be detected in wastewater samples. Being able to describe the diversity of viruses present in sewage will provide information on the health of the surrounding population health and will help to prevent further transmission. Metagenomic developments, allowing the description of all the different genomes present in a sample, are very promising tools for virome analysis. However, looking for human enteric viruses with short RNA genomes which are present at low concentrations is challenging. In this study we demonstrate the benefits of performing technical replicates to improve viral identification by increasing contig length, and the set-up of quality criteria to increase confidence in results. Our approach was able to effectively identify some virus sequences and successfully describe the viral diversity. The method yielded full genomes either for norovirus, enterovirus and rotavirus, even if, for these segmented genomes, combining genes remain a difficult issue. Developing reliable viromic methods is important as wastewater sample analysis provides an important tool to prevent further virus transmission by raising alerts in case of viral outbreaks or emergence.}, } @article {pmid37180248, year = {2023}, author = {Ding, JYM and Ho, LS and Ibrahim, J and Teh, CK and Goh, KM}, title = {Impact of sterilization and chemical fertilizer on the microbiota of oil palm seedlings.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1091755}, pmid = {37180248}, issn = {1664-302X}, abstract = {Soil nutrients and microbiota are known as essential components for healthy plant growth and crop productivity. However, limited studies have been conducted on the importance of soil microbiota in the early growth of oil palm seedlings (Elaeis guineensis Jacq.) under the influence of nitrogen, phosphorus and potassium (NPK) compound fertilizer (nitrogen, phosphorus, and potassium). In this study, we analyzed the root microbial community associated with seedlings grown under normal and sterilized soil conditions to ascertain the microbial strains potentially associated with soil, plant health and chemical fertilizer efficiency. Oil palm seedlings were grown under four treatments: (i) fertilized normal soil (+FN), (ii) unfertilized normal soil (-FN), (iii) fertilized sterilized soil (+FS) and (iv) unfertilized sterilized soil (-FS). Our findings revealed that chemical fertilizer promoted the growth of the copiotrophs Pseudomonadota and Bacteroidota in the control +FN, which are known to degrade complex polysaccharides. After autoclaving, the soil macronutrient content did not change, but soil sterilization reduced microbial diversity in the +FS and -FS treatments and altered the soil microbiota composition. Sterilized soil with a depleted microbial population adversely affected crop growth, which was exacerbated by fertilizer use. In the rhizosphere and rhizoplane compartments, a total of 412 and 868 amplicon sequence variances (ASVs) were found depleted in the +FS and -FS treatments, respectively. Several genera were identified in the ASVs with diminished abundance, including Humibacter, Microbacterium, Mycobacterium, 1921-2, HSB OF53-F07, Mucilaginibacter, Bacillus, Paenibacillus, and several unclassified genera, suggesting their possible roles in promoting the plant growth of oil palm seedlings. Soil sterilization might remove these beneficial microbes from the bulk soil pool, affecting the colonization ability in the rhizocompartments as well as their role in nutrient transformation. Therefore, this study provides useful insights concerning the benefits of a soil microbiome survey before making fertilizer recommendations.}, } @article {pmid37180228, year = {2023}, author = {Lu, H and Zhu, X and Wu, L and Lou, X and Pan, X and Liu, B and Zhang, H and Zhu, L and Li, L and Wu, Z}, title = {Alterations in the intestinal microbiome and metabolic profile of patients with cirrhosis supplemented with lactulose, Clostridium butyricum, and Bifidobacterium longum infantis: a randomized placebo-controlled trial.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1169811}, pmid = {37180228}, issn = {1664-302X}, abstract = {BACKGROUND: Liver cirrhosis is commonly accompanied by intestinal dysbiosis and metabolic defects. Many clinical trials have shown microbiota-targeting strategies represent promising interventions for managing cirrhosis and its complications. However, the influences of the intestinal metagenomes and metabolic profiles of patients have not been fully elucidated.

METHODS: We administered lactulose, Clostridium butyricum, and Bifidobacterium longum infantis as a synbiotic and used shotgun metagenomics and non-targeted metabolomics to characterize the results.

RESULTS: Patients treated with the synbiotic for 12 weeks had lower dysbiosis index (DI) scores than placebo-treated patients and patients at baseline (NIP group). We identified 48 bacterial taxa enriched in the various groups, 66 differentially expressed genes, 18 differentially expressed virulence factor genes, 10 differentially expressed carbohydrate-active enzyme genes, and 173 metabolites present at differing concentrations in the Synbiotic versus Placebo group, and the Synbiotic versus NIP group. And Bifidobacteria species, especially B. longum, showed positive associations with many differentially expressed genes in synbiotic-treated patients. Metabolites pathway enrichment analysis showed that synbiotic significantly affected purine metabolism and aminoacyl-tRNA biosynthesis. And the purine metabolism and aminoacyl-tRNA biosynthesis were no longer significant differences in the Synbiotic group versus the healthy controls group. In conclusion, although littles influence on clinical parameters in the early intervention, the synbiotic showed a potential benefit to patients by ameliorating intestinal dysbiosis and metabolic defects; and the DI of intestinal microbiota is useful for the evaluation of the effect of clinical microbiota-targeting strategies on cirrhotic patients.

CLINICAL TRIAL REGISTRATION: https://www.clinicaltrials.gov, identifiers NCT05687409.}, } @article {pmid37180114, year = {2023}, author = {Britto, AMA and Siqueira, JD and Curty, G and Goes, LR and Policarpo, C and Meyrelles, AR and Furtado, Y and Almeida, G and Giannini, ALM and Machado, ES and Soares, MA}, title = {Microbiome analysis of Brazilian women cervix reveals specific bacterial abundance correlation to RIG-like receptor gene expression.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1147950}, pmid = {37180114}, issn = {1664-3224}, mesh = {Female ; Humans ; Cervix Uteri ; *Uterine Cervical Neoplasms/genetics/metabolism ; *Papillomavirus Infections ; Brazil ; Toll-Like Receptor 3/genetics ; Bacteria/genetics ; *Microbiota ; Gene Expression ; }, abstract = {The relationship among microbiome, immunity and cervical cancer has been targeted by several studies, yet many questions remain unanswered. We characterized herein the virome and bacteriome from cervical samples and correlated these findings with innate immunity gene expression in a Brazilian convenience sample of HPV-infected (HPV+) and uninfected (HPV-) women. For this purpose, innate immune gene expression data were correlated to metagenomic information. Correlation analysis showed that interferon (IFN) is able to differentially modulate pattern recognition receptors (PRRs) expression based on HPV status. Virome analysis indicated that HPV infection correlates to the presence of Anellovirus (AV) and seven complete HPV genomes were assembled. Bacteriome results unveiled that vaginal community state types (CST) distribution was independent of HPV or AV status, although bacterial phyla distribution differed between groups. Furthermore, TLR3 and IFNαR2 levels were higher in the Lactobacillus no iners-dominated mucosa and we detected correlations among RIG-like receptors (RLR) associated genes and abundance of specific anaerobic bacteria. Collectively, our data show an intriguing connection between HPV and AV infections that could foster cervical cancer development. Besides that, TLR3 and IFNαR2 seem to create a protective milieu in healthy cervical mucosa (L. no iners-dominated), and RLRs, known to recognize viral RNA, were correlated to anaerobic bacteria suggesting that they might be related to dysbiosis.}, } @article {pmid37179340, year = {2023}, author = {Orellana, LH and Krüger, K and Sidhu, C and Amann, R}, title = {Comparing genomes recovered from time-series metagenomes using long- and short-read sequencing technologies.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {105}, pmid = {37179340}, issn = {2049-2618}, mesh = {*Metagenome/genetics ; RNA, Ribosomal, 16S/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Technology ; Metagenomics/methods ; }, abstract = {BACKGROUND: Over the past years, sequencing technologies have expanded our ability to examine novel microbial metabolisms and diversity previously obscured by isolation approaches. Long-read sequencing promises to revolutionize the metagenomic field and recover less fragmented genomes from environmental samples. Nonetheless, how to best benefit from long-read sequencing and whether long-read sequencing can provide recovered genomes of similar characteristics as short-read approaches remains unclear.

RESULTS: We recovered metagenome-assembled genomes (MAGs) from the free-living fraction at four-time points during a spring bloom in the North Sea. The taxonomic composition of all MAGs recovered was comparable between technologies. However, differences consisted of higher sequencing depth for contigs and higher genome population diversity in short-read compared to long-read metagenomes. When pairing population genomes recovered from both sequencing approaches that shared ≥ 99% average nucleotide identity, long-read MAGs were composed of fewer contigs, a higher N50, and a higher number of predicted genes when compared to short-read MAGs. Moreover, 88% of the total long-read MAGs carried a 16S rRNA gene compared to only 23% of MAGs recovered from short-read metagenomes. Relative abundances for population genomes recovered using both technologies were similar, although disagreements were observed for high and low GC content MAGs.

CONCLUSIONS: Our results highlight that short-read technologies recovered more MAGs and a higher number of species than long-read due to an overall higher sequencing depth. Long-read samples produced higher quality MAGs and similar species composition compared to short-read sequencing. Differences in the GC content recovered by each sequencing technology resulted in divergences in the diversity recovered and relative abundance of MAGs within the GC content boundaries.}, } @article {pmid37179329, year = {2023}, author = {Anderson, AC and von Ohle, C and Frese, C and Boutin, S and Bridson, C and Schoilew, K and Peikert, SA and Hellwig, E and Pelz, K and Wittmer, A and Wolff, D and Al-Ahmad, A}, title = {The oral microbiota is a reservoir for antimicrobial resistance: resistome and phenotypic resistance characteristics of oral biofilm in health, caries, and periodontitis.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {22}, number = {1}, pages = {37}, pmid = {37179329}, issn = {1476-0711}, mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Dental Caries Susceptibility ; *Microbiota/genetics ; *Periodontitis/genetics ; Bacteria ; Genes, Bacterial ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is an ever-growing threat to modern medicine and, according to the latest reports, it causes nearly twice as many deaths globally as AIDS or malaria. Elucidating reservoirs and dissemination routes of antimicrobial resistance genes (ARGs) are essential in fighting AMR. Human commensals represent an important reservoir, which is underexplored for the oral microbiota. Here, we set out to investigate the resistome and phenotypic resistance of oral biofilm microbiota from 179 orally healthy (H), caries active (C), and periodontally diseased (P) individuals (TRN: DRKS00013119, Registration date: 22.10.2022). The samples were analysed using shotgun metagenomic sequencing combined, for the first time, with culture technique. A selection of 997 isolates was tested for resistance to relevant antibiotics.

RESULTS: The shotgun metagenomics sequencing resulted in 2,069,295,923 reads classified into 4856 species-level OTUs. PERMANOVA analysis of beta-diversity revealed significant differences between the groups regarding their microbiota composition and their ARG profile. The samples were clustered into three ecotypes based on their microbial composition. The bacterial composition of H and C samples greatly overlapped and was based on ecotypes 1 and 2 whereas ecotype 3 was only detected in periodontitis. We found 64 ARGs conveying resistance to 36 antibiotics, particularly to tetracycline, macrolide-lincosamide-streptogramin, and beta-lactam antibiotics, and a correspondingly high prevalence of phenotypic resistance. Based on the microbiota composition, these ARGs cluster in different resistotypes, and a higher prevalence is found in healthy and caries active than in periodontally diseased individuals. There was a significant association between the resistotypes and the ecotypes. Although numerous associations were found between specific antibiotic resistance and bacterial taxa, only a few taxa showed matching associations with both genotypic and phenotypic analyses.

CONCLUSIONS: Our findings show the importance of the oral microbiota from different niches within the oral cavity as a reservoir for antibiotic resistance. Additionally, the present study showed the need for using more than one method to reveal antibiotic resistance within the total oral biofilm, as a clear mismatch between the shotgun metagenomics method and the phenotypic resistance characterization was shown.}, } @article {pmid37179169, year = {2023}, author = {Zhang, B and Zhou, W and Liu, Q and Huang, C and Hu, Z and Zheng, M and Xin, Y and Zhao, M and Lu, Q}, title = {Effects of fecal microbiota transplant on DNA methylation in patients with systemic lupus erythematosus.}, journal = {Journal of autoimmunity}, volume = {141}, number = {}, pages = {103047}, doi = {10.1016/j.jaut.2023.103047}, pmid = {37179169}, issn = {1095-9157}, mesh = {Humans ; *DNA Methylation ; Fecal Microbiota Transplantation ; Interferon-Induced Helicase, IFIH1/genetics ; Leukocytes, Mononuclear ; *Lupus Erythematosus, Systemic/genetics/therapy ; }, abstract = {Systemic lupus erythematosus (SLE) is a highly heterogeneous autoimmune disease characterized by multiple organ damage accompanied by the over-production of autoantibodies. Decreased intestinal flora diversity and disruption of homeostasis have been proven to be associated with pathogenesis of SLE. In previous study, a clinical trial was conducted to verify the safety and effectiveness of fecal microbiota transplantation (FMT) in the treatment of SLE. To explore the mechanism of FMT in the treatment of SLE, we included 14 SLE patients participating in clinical trials, including 8 in responders group (Rs) and 6 in non-responders group (NRs), and collected peripheral blood DNA and serum. We found that the serum of S-adenosylmethionine (SAM), methylation group donor, was upregulated after FMT, accompanied by an increase in genome-wide DNA methylation level in Rs. We further showed that the methylation levels in promoter regions of Interferon-γ (IFN-γ), induced Helicase C Domain Containing Protein 1 (IFIH1), endoplasmic reticulum membrane protein complex 8 (EMC8), and Tripartite motif-containing protein 58 (TRIM58) increased after FMT treatment. On the contrary, there was no significant change in the methylation of IFIH1 promoter region in the NRs after FMT, and the methylation level of IFIH1 in the Rs was significantly higher than that in the NRs at week 0. We included 850 K methylation chip sequencing, combining previous data of metagenomic sequencing, and metabolomic sequencing for multi-omics analysis to discuss the relationship between flora-metabolite-methylation in FMT. Finally, we found that hexanoic acid treatment can up-regulate the global methylation of peripheral blood mononuclear cells in SLE patients. Overall, our results delineate changes in methylation level after FMT treatment of SLE and reveal possible mechanisms of FMT treatment in terms of the recovery of abnormal hypomethylation.}, } @article {pmid37178843, year = {2023}, author = {Liu, B and Yu, D and Ge, C and Luo, X and Du, L and Zhang, X and Hui, C}, title = {Combined effects of microplastics and chlortetracycline on the intestinal barrier, gut microbiota, and antibiotic resistome of Muscovy ducks (Cairina moschata).}, journal = {The Science of the total environment}, volume = {887}, number = {}, pages = {164050}, doi = {10.1016/j.scitotenv.2023.164050}, pmid = {37178843}, issn = {1879-1026}, mesh = {Animals ; Microplastics ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome ; Plastics ; Ducks ; Polystyrenes ; *Chlortetracycline/pharmacology ; Intestines ; *Microbiota ; }, abstract = {Antibiotics and microplastics (MPs) have become critical concerns worldwide because of their increasing amount and ecological risks to ecosystems. However, how MPs exposure affects the bioaccumulation and risks of antibiotics in waterfowls remains poorly understood. In this study, Muscovy ducks were exposed to single and combined contamination with polystyrene MPs and chlortetracycline (CTC) for 56 days, and the effects of MPs on CTC bioaccumulation and their risks in duck intestines were investigated. MPs exposure reduced the bioaccumulation of CTC in the intestine and liver of ducks and increased their fecal CTC excretion. MPs exposure caused severe oxidative stress, inflammatory response, and intestinal barrier damages. Microbiome analysis showed that MPs exposure induced microbiota dysbiosis by increasing the abundance of Streptococcus and Helicobacter, the increase of which may exacerbate intestinal damages. Co-exposure to MPs and CTC alleviated the intestinal damage by regulating the gut microbiome. Metagenomic sequencing revealed that the combined exposure to MPs and CTC increased the abundance of Prevotella, Faecalibacterium, and Megamonas and incidence of total antibiotic resistance genes (ARGs), especially tetracycline ARGs subtypes in the gut microbiota. The results obtained herein provide new insights into the potential risks of polystyrene MPs and antibiotics in waterfowls living in aquatic environments.}, } @article {pmid37178839, year = {2023}, author = {Rubin-Blum, M and Harbuzov, Z and Cohen, R and Astrahan, P}, title = {Anthropogenic and natural disturbances along a river and its estuary alter the diversity of pathogens and antibiotic resistance mechanisms.}, journal = {The Science of the total environment}, volume = {887}, number = {}, pages = {164108}, doi = {10.1016/j.scitotenv.2023.164108}, pmid = {37178839}, issn = {1879-1026}, mesh = {Animals ; Humans ; *Rivers/microbiology ; *Genes, Bacterial ; Angiotensin Receptor Antagonists ; Estuaries ; Anti-Bacterial Agents/pharmacology ; Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Microbial/genetics ; }, abstract = {Antibiotic resistance (AMR) in pathogens threatens human health worldwide, and antibiotic-resistant bacteria (ARB) are widespread in the environment. In particular, anthropogenically-disturbed rivers became reservoirs of ARBs and hotspots of antibiotic resistance gene (ARG) transmission. However, the diversity and sources of ARB, and the mechanisms of ARG transmission are not fully known. Here, we used deep metagenomic sequencing to study the dynamics of pathogens and their antibiotic resistance mechanisms along the Alexander River (Israel), affected by sewage and animal farm runoffs. Putative pathogens such as Aeromicrobium marinum and Mycobacterium massilipolynesiensis were enriched in western stations, following the inputs of polluted Nablus River. Aeromonas veronii was dominant in eastern stations in Spring. Several AMR mechanisms showed distinct patterns in Summer-Spring (dry season) and Winter (rainy season). We found low abundance beta-lactamases conferring carbapenem resistance: e.g., OXA-912 was linked to A. veronii in Spring; OXA-119 and OXA-205 to Xanthomonadaceae in Winter. We classified 33 % of ARG-containing contigs as putative plasmid sequences, indicating the high potential for resistome transmission. A limited number of ARGs were linked to putative phages. Our results suggest that this model river is a hotspot for AMR activity and transmission, and highlight the merit of deep sequencing for AMR discovery.}, } @article {pmid37178644, year = {2023}, author = {Wang, M and Qin, Y and Liu, Y and Yang, H and Wang, J and Ru, S and Cui, P}, title = {Short-term exposure to enrofloxacin causes hepatic metabolism disorder associated with intestinal flora dysbiosis in adult marine medaka (Oryzias melastigma).}, journal = {Marine pollution bulletin}, volume = {192}, number = {}, pages = {114966}, doi = {10.1016/j.marpolbul.2023.114966}, pmid = {37178644}, issn = {1879-3363}, mesh = {Animals ; *Oryzias/physiology ; Enrofloxacin ; *Gastrointestinal Microbiome ; Dysbiosis/chemically induced/veterinary ; Metabolomics ; *Water Pollutants, Chemical/toxicity ; }, abstract = {Enrofloxacin (ENR) is a widely used fluoroquinolone antibiotic that is frequently detected in the environment. Our study assessed the impact of short-term ENR exposure on the intestinal and liver health of marine medaka (Oryzias melastigma) using gut metagenomic shotgun sequencing and liver metabolomics. We found that ENR exposure resulted in imbalances of Vibrio and Flavobacteria and enrichments of multiple antibiotic resistance genes. Additionally, we found a potential link between the host's response to ENR exposure and the intestinal microbiota disorder. Liver metabolites, including phosphatidylcholine, lysophosphatidylcholine, taurocholic acid, and cholic acid, in addition to several metabolic pathways in the liver that are closely linked to the imbalance of intestinal flora were severely maladjusted. These findings suggest that ENR exposure has the potential to negatively affect the gut-liver axis as the primary toxicological mechanism. Our findings provide evidence regarding the negative physiological impacts of antibiotics on marine fish.}, } @article {pmid37178462, year = {2023}, author = {Zhang, S and Li, T and Hu, J and Li, K and Liu, D and Li, H and Wang, F and Chen, D and Zhang, Z and Fan, Q and Cui, X and Che, R}, title = {Reforestation substantially changed the soil antibiotic resistome and its relationships with metal resistance genes, mobile genetic elements, and pathogens.}, journal = {Journal of environmental management}, volume = {342}, number = {}, pages = {118037}, doi = {10.1016/j.jenvman.2023.118037}, pmid = {37178462}, issn = {1095-8630}, mesh = {*Soil ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; Soil Microbiology ; Interspersed Repetitive Sequences ; }, abstract = {Revealing the effects of reforestation on soil antibiotic resistome is essential for assessing ecosystem health, yet related studies remain scarce. Here, to determine the responses of the soil antibiotic resistome to reforestation, 30 pairs of cropland and forest soil samples were collected from southwestern China, a region with high environmental heterogeneity. All the forests had been derived from croplands more than one decade ago. The diversity and abundance of soil antibiotic resistance genes (ARGs), metal resistance genes (MRGs), mobile genetic elements (MGEs), and pathogens were determined by metagenomic sequencing and real-time PCR. The results showed that reforestation significantly increased soil microbial abundance and the contents of Cu, total carbon, total nitrogen, total organic carbon, and ammonium nitrogen. Nevertheless, it decreased the contents of soil Zn, Ba, nitrate nitrogen, and available phosphorus. The main soil ARGs identified in this region were vancomycin, multidrug, and bacitracin resistance genes. Reforestation significantly increased the soil ARG abundance by 62.58%, while it decreased the ARG richness by 16.50%. Reforestation exerted no significant effects on the abundance of heavy metal resistance genes and pathogens, but it doubled the abundance of MGEs. Additionally, reforestation substantially decreased the co-occurrence frequencies of ARGs with MRGs and pathogens. In contrast, the correlation between ARGs and MGEs was greatly enhanced by reforestation. Similarly, the correlations between soil ARG abundance and environmental factors were also strengthened by reforestation. These findings suggest that reforestation can substantially affect the soil antibiotic resistome and exerts overall positive effects on soil health by decreasing ARG richness, providing critical information for assessing the effects of "grain for green" project on soil health.}, } @article {pmid37178322, year = {2023}, author = {Pandey, U and Tambat, S and Aich, P}, title = {Postnatal 14D is the Key Window for Mice Intestinal Development- An Insight from Age-Dependent Antibiotic-Mediated Gut Microbial Dysbiosis Study.}, journal = {Advanced biology}, volume = {7}, number = {7}, pages = {e2300089}, doi = {10.1002/adbi.202300089}, pmid = {37178322}, issn = {2701-0198}, mesh = {Mice ; Animals ; *Intestines/microbiology ; Intestinal Mucosa/metabolism ; Anti-Bacterial Agents/pharmacology ; *Gastrointestinal Microbiome ; Dysbiosis/metabolism/microbiology ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {The postnatal period is one of the critical windows for the structure-function development of the gastrointestinal tract and associated mucosal immunity. Along with other constituent members, recent studies suggest the contribution of gut microbiota in maintaining host health, immunity, and development. Although the gut microbiota's role in maintaining barrier integrity is known, its function in early life development still needs to be better understood. To understand the details of gut microbiota's effects on intestinal integrity, epithelium development, and immune profile, the route of antibiotic-mediated perturbation is taken. Mice on days 7(P7D), 14(P14D), 21(P21D) and 28(P28D) are sacrificed and 16S rRNA metagenomic analysis is performed. The barrier integrity, tight junction proteins (TJPs) expression, intestinal epithelial cell (IEC) markers, and inflammatory cytokines are analyzed. Results reveal a postnatal age-related impact of gut microbiota perturbation, with a gradual increase in the relative abundance of Proteobacteria and a reduction in Bacteroidetes and Firmicutes. Significant barrier integrity disruption, reduced TJPs and IECs marker expression, and increased systemic inflammation at P14D of AVNM-treated mice are found. Moreover, the microbiota transplantation shows recolonization of Verrucomicrobia, proving a causal role in barrier functions. The investigation reveals P14D as a critical period for neonatal intestinal development, regulated by specific microbiota composition.}, } @article {pmid37177963, year = {2023}, author = {Luo, ZM and Liu, JX and Hu, YQ and He, L and Zhou, YY and Zheng, QR and Chai, BF}, title = {[Taxonomic and Functional Diversity of Soil Microbial Communities in Subalpine Meadow with Different Degradation Degrees in Mount Wutai].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {44}, number = {5}, pages = {2918-2927}, doi = {10.13227/j.hjkx.202204330}, pmid = {37177963}, issn = {0250-3301}, mesh = {*Ecosystem ; Grassland ; Carbon ; Soil ; Soil Microbiology ; *Microbiota ; Bacteria/genetics ; }, abstract = {Although soil microbes play a key role in grassland ecosystem functioning, the response of their diversity to grassland degradation has not been fully investigated. Here, we used shotgun metagenomic sequencing to analyze the characteristics and influencing factors of soil microbial taxonomic and functional diversity at four different degradation stages[i.e., non-degraded (ND), lightly degraded (LD), moderately degraded (MD), and heavily degraded (HD)]of subalpine meadow in the Mount Wutai. The results showed that there were significant differences in the relative abundances of Actinobacteria, Bacteroidetes, Nitrospirae, and Parcubacteria among the four subalpine grasslands with different degradation degrees (P<0.05).Compared with that in ND, the degraded meadows increased the proportion of genes related to carbon metabolism, biosynthesis of amino acids, pyruvate metabolism, citric acid cycle, propanoate metabolism, butanoate metabolism, and fatty acid metabolism (P<0.05), indicating that the degradation of subalpine grassland changed the metabolic potential of energy metabolism and the nutrient cycle of the soil microbial community. Grassland degradation changed soil microbial taxonomic and functional α diversity, especially in MD and HD.Grassland degradation resulted in significant changes in the taxonomic and functional compositions of the microbial communities. The total nitrogen, pH, and soil organic carbon significantly affected the taxonomic and functional compositions of the microbial communities.The β diversity of the plant community was significantly correlated with the taxonomic and functional β diversity of the microbial community (P<0.05), indicating strong coupling. The results of this study revealed the changes and driving mechanisms of subsurface microbial taxonomic and functional diversity during grassland degradation, which can provide a theoretical basis for subalpine meadow protection and ecological restoration.}, } @article {pmid37177929, year = {2023}, author = {Lu, JW and Xu, CY and Hu, C and Liu, SR and Li, F}, title = {[Occurrence Characteristics of Microplastics and Metal Elements in the Surface Water of Huangpu River and Their Associations with Metal Resistance Genes].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {44}, number = {5}, pages = {2551-2561}, doi = {10.13227/j.hjkx.202206267}, pmid = {37177929}, issn = {0250-3301}, mesh = {*Microplastics ; Genes, Bacterial ; Plastics ; Rivers ; Water ; Metals ; *Mercury ; Anti-Bacterial Agents ; }, abstract = {Urban rivers have been regarded as the "hotspots" for microplastic (MPs) and metal contamination as they play important roles in pollution migration. However, as important sinks and sources of resistance genes, there has been little to no research investigating the associations between MPs, metal contaminations, and metal resistance genes (MRGs). Ten water samples were collected from the Huangpu River in situ; along with metal elements, MPs characteristics analyzed. Metal resistance genes and mobile genetic elements (MGEs) in waters and MPs were detected using metagenomic technology. As a result, the highest metal concentration was that of Sb in surface water (3.16±0.419) μg·L[-1]. The average abundance of MPs was (1.78±0.84) n·L[-1], and the peak levels located in industrial and densely populated areas, which was significantly higher than those in agricultural and low population density areas. Fibrous, small-size (<0.5 mm), and transparent polyethylene terephthalate (PET) were the largest contributors of MPs. Eighteen MRGs were detected in all the samples. The relative abundance of MRGs in water was 1.68±0.21. The most dominant MRGs subtypes were merR and ruvB, which are subtypes resistant to mercury and Multi_metals. Correlation analysis showed that chromium and nickel in waters were significantly positively associated with MRG-Cr, MRG-Ni, and Multi_metals resistance genes. For MPs particles, the relative abundance of MRGs was 1.63±0.53. The most dominant MRGs subtypes were merT-P and copB, which also belong to mercury-resistant and Multi_metals. The Multi_metals resistance gene, ctpC, cueA, czrA, kmtR, etc., had significant positive associations with Ni, Cr, and Sb in waters. Compared with water samples, MPs selectively enriched merT-P, copB, ziaA, sodA, and dmeF. Additionally, the co-occurrence patterns of MRGs and MGEs were explored based on network analysis. In water samples, the transposases (tnpA_1 and tnpA_2), integrase (qacEdelta), and insertion sequence (IS91) were the major contributors of the horizontal gene transfer (HGT) of specific MRGs. Multiple subtypes resistant to copper and Multi_metals resistance genes on MPs were positively associated with IncFIC(FII), Rep7, rep7, and rep13, which were subtypes of plasmids. The presence of MPs exerted a significant impact on HGT of specific MRGs mediated by plasmids.}, } @article {pmid37175775, year = {2023}, author = {Kazakova, P and Abasolo, N and de Cripan, SM and Marquès, E and Cereto-Massagué, A and Garcia, L and Canela, N and Tormo, R and Torrell, H}, title = {Gut Microbiome and Small RNA Integrative-Omic Perspective of Meconium and Milk-FED Infant Stool Samples.}, journal = {International journal of molecular sciences}, volume = {24}, number = {9}, pages = {}, pmid = {37175775}, issn = {1422-0067}, mesh = {Infant, Newborn ; Humans ; Infant ; *Meconium ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Milk, Human ; Bacteria/genetics ; DNA, Viral ; }, abstract = {The human gut microbiome plays an important role in health, and its initial development is conditioned by many factors, such as feeding. It has also been claimed that this colonization is guided by bacterial populations, the dynamic virome, and transkingdom interactions between host and microbial cells, partially mediated by epigenetic signaling. In this article, we characterized the bacteriome, virome, and smallRNome and their interaction in the meconium and stool samples from infants. Bacterial and viral DNA and RNA were extracted from the meconium and stool samples of 2- to 4-month-old milk-fed infants. The bacteriome, DNA and RNA virome, and smallRNome were assessed using 16S rRNA V4 sequencing, viral enrichment sequencing, and small RNA sequencing protocols, respectively. Data pathway analysis and integration were performed using the R package mixOmics. Our findings showed that the bacteriome differed among the three groups, while the virome and smallRNome presented significant differences, mainly between the meconium and stool of milk-fed infants. The gut environment is rapidly acquired after birth, and it is highly adaptable due to the interaction of environmental factors. Additionally, transkingdom interactions between viruses and bacteria can influence host and smallRNome profiles. However, virome characterization has several protocol limitations that must be considered.}, } @article {pmid37175619, year = {2023}, author = {Even, G and Mouray, A and Vandenabeele, N and Martel, S and Merlin, S and Lebrun-Ruer, S and Chabé, M and Audebert, C}, title = {Bact-to-Batch: A Microbiota-Based Tool to Determine Optimal Animal Allocation in Experimental Designs.}, journal = {International journal of molecular sciences}, volume = {24}, number = {9}, pages = {}, pmid = {37175619}, issn = {1422-0067}, mesh = {Mice ; Animals ; *Research Design ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Pilot Projects ; *Microbiota/genetics ; Feces ; }, abstract = {The basis of any animal experimentation begins with the housing of animals that should take into account the need for splitting animals into similar groups. Even if it is generally recommended to use the minimum number of animals necessary to obtain reliable and statistically significant results (3Rs rule), the allocation of animals is currently mostly based on randomness. Since variability in gut microbiota is an important confounding factor in animal experiments, the main objective of this study was to develop a new approach based on 16S rRNA gene sequencing analysis of the gut microbiota of animals participating in an experiment, in order to correctly assign the animals across batches. For this purpose, a pilot study was performed on 20 mouse faecal samples with the aim of establishing two groups of 10 mice as similar as possible in terms of their faecal microbiota fingerprinting assuming that this approach limits future analytical bias and ensures reproducibility. The suggested approach was challenged with previously published data from a third-party study. This new method allows to embrace the unavoidable microbiota variability between animals in order to limit artefacts and to provide an additional assurance for the reproducibility of animal experiments.}, } @article {pmid37174418, year = {2023}, author = {Carminati, D and Bonvini, B and Francolino, S and Ghiglietti, R and Locci, F and Tidona, F and Mariut, M and Abeni, F and Zago, M and Giraffa, G}, title = {Low-Level Clostridial Spores' Milk to Limit the Onset of Late Blowing Defect in Lysozyme-Free, Grana-Type Cheese.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {9}, pages = {}, pmid = {37174418}, issn = {2304-8158}, support = {2015/1341 (CR FOODLAB Project)//Fondazione Cariplo, Regione Lombardia/ ; }, abstract = {The growth of clostridial spores during ripening leads to late blowing (LB), which is the main cause of spoilage in Grana Padano Protected Designation of Origin (PDO) cheese and other hard, long-ripened cheeses such as Provolone, Comté, and similar cheeses. This study aimed to verify the cause-effect relationship between the level of clostridial butyric spores (BCS) in milk and the onset of the LB defect. To this end, experimental Grana-type cheeses were produced without lysozyme, using bulk milk with different average BCS content. The vat milk from the so-called "virtuous" farms (L1) contained average levels of BCS of 1.93 ± 0.61 log most probable number (MPN) L[-1], while the vat milk from farms with the highest load of spores (L2), were in the order of 2.99 ± 0.69 log MPN L[-1]. Cheeses after seven months of ripening evidenced a strong connection between BCS level in vat milk and the occurrence of LB defect. In L2 cheeses, which showed an average BCS content of 3.53 ± 1.44 log MPN g[-1] (range 1.36-5.04 log MPN g[-1]), significantly higher than that found in L1 cheeses (p < 0.01), the defect of LB was always present, with Clostridium tyrobutyricum as the only clostridial species identified by species-specific PCR from MPN-positive samples. The L1 cheeses produced in the cold season (C-L1) were free of defects whereas those produced in the warm season (W-L1) showed textural defects, such as slits and cracks, rather than irregular eyes. A further analysis of the data, considering the subset of the cheesemaking trials (W-L1 and W-L2), carried out in the warm season, confirmed the presence of a climate effect that, often in addition to the BCS load in the respective bulk milks (L1 vs. L2), may contribute to explain the significant differences in the chemical composition and some technological parameters between the two series of cheeses. Metagenomic analysis showed that it is not the overall structure of the microbial community that differentiates L1 from L2 cheeses but rather the relative distribution of the species between them. The results of our trials on experimental cheeses suggest that a low-level BCS in vat milk (<200 L[-1]) could prevent, or limit, the onset of LB in Grana-type and similar cheeses produced without lysozyme.}, } @article {pmid37173859, year = {2023}, author = {Chau, KD and Samad-Zada, F and Kelemen, EP and Rehan, SM}, title = {Integrative population genetics and metagenomics reveals urbanization increases pathogen loads and decreases connectivity in a wild bee.}, journal = {Global change biology}, volume = {29}, number = {15}, pages = {4193-4211}, doi = {10.1111/gcb.16757}, pmid = {37173859}, issn = {1365-2486}, support = {//National Science Foundation/ ; //NSERC/ ; //Weston Family Foundation/ ; }, mesh = {Animals ; Bees/genetics ; Humans ; *Urbanization ; Cities ; *Metagenomics ; Hot Temperature ; Genetics, Population ; Ecosystem ; }, abstract = {As urbanization continues to increase, it is expected that two-thirds of the human population will reside in cities by 2050. Urbanization fragments and degrades natural landscapes, threatening wildlife including economically important species such as bees. In this study, we employ whole genome sequencing to characterize the population genetics, metagenome and microbiome, and environmental stressors of a common wild bee, Ceratina calcarata. Population genomic analyses revealed the presence of low genetic diversity and elevated levels of inbreeding. Through analyses of isolation by distance, resistance, and environment across urban landscapes, we found that green spaces including shrubs and scrub were the most optimal pathways for bee dispersal, and conservation efforts should focus on preserving these land traits to maintain high connectivity across sites for wild bees. Metagenomic analyses revealed landscape sites exhibiting urban heat island effects, such as high temperatures and development but low precipitation and green space, had the highest taxa alpha diversity across all domains even when isolating for potential pathogens. Notably, the integration of population and metagenomic data showed that reduced connectivity in urban areas is not only correlated with lower relatedness among individuals but is also associated with increased pathogen diversity, exposing vulnerable urban bees to more pathogens. Overall, our combined population and metagenomic approach found significant environmental variation in bee microbiomes and nutritional resources even in the absence of genetic differentiation, as well as enabled the potential early detection of stressors to bee health.}, } @article {pmid37173775, year = {2023}, author = {Vigneron, A and Cruaud, P and Lovejoy, C and Vincent, WF}, title = {Genomic insights into cryptic cycles of microbial hydrocarbon production and degradation in contiguous freshwater and marine microbiomes.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {104}, pmid = {37173775}, issn = {2049-2618}, mesh = {Canada ; *Hydrocarbons/metabolism ; *Microbiota/genetics ; Alkanes/metabolism ; Bacteria/genetics ; Genomics ; Water ; Lakes/microbiology ; Oxygen/metabolism ; Sulfur/metabolism ; }, abstract = {BACKGROUND: Cyanobacteria and eukaryotic phytoplankton produce long-chain alkanes and generate around 100 times greater quantities of hydrocarbons in the ocean compared to natural seeps and anthropogenic sources. Yet, these compounds do not accumulate in the water column, suggesting rapid biodegradation by co-localized microbial populations. Despite their ecological importance, the identities of microbes involved in this cryptic hydrocarbon cycle are mostly unknown. Here, we identified genes encoding enzymes involved in the hydrocarbon cycle across the salinity gradient of a remote, vertically stratified, seawater-containing High Arctic lake that is isolated from anthropogenic petroleum sources and natural seeps. Metagenomic analysis revealed diverse hydrocarbon cycling genes and populations, with patterns of variation along gradients of light, salinity, oxygen, and sulfur that are relevant to freshwater, oceanic, hadal, and anoxic deep sea ecosystems.

RESULTS: Analyzing genes and metagenome-assembled genomes down the water column of Lake A in the Canadian High Arctic, we detected microbial hydrocarbon production and degradation pathways at all depths, from surface freshwaters to dark, saline, anoxic waters. In addition to Cyanobacteria, members of the phyla Flavobacteria, Nitrospina, Deltaproteobacteria, Planctomycetes, and Verrucomicrobia had pathways for alkane and alkene production, providing additional sources of biogenic hydrocarbons. Known oil-degrading microorganisms were poorly represented in the system, while long-chain hydrocarbon degradation genes were identified in various freshwater and marine lineages such as Actinobacteria, Schleiferiaceae, and Marinimicrobia. Genes involved in sulfur and nitrogen compound transformations were abundant in hydrocarbon producing and degrading lineages, suggesting strong interconnections with nitrogen and sulfur cycles and a potential for widespread distribution in the ocean.

CONCLUSIONS: Our detailed metagenomic analyses across water column gradients in a remote petroleum-free lake derived from the Arctic Ocean suggest that the current estimation of bacterial hydrocarbon production in the ocean could be substantially underestimated by neglecting non-phototrophic production and by not taking low oxygen zones into account. Our findings also suggest that biogenic hydrocarbons may sustain a large fraction of freshwater and oceanic microbiomes, with global biogeochemical implications for carbon, sulfur, and nitrogen cycles. Video Abstract.}, } @article {pmid37172856, year = {2023}, author = {Zhao, X and Niu, Z and Ma, Y and Zhang, Y and Li, Y}, title = {Metagenomic insights into the potential risks of representative bio/non-degradable plastic and non-plastic debris in the upper and lower reaches of Haihe Estuary, China.}, journal = {The Science of the total environment}, volume = {887}, number = {}, pages = {164026}, doi = {10.1016/j.scitotenv.2023.164026}, pmid = {37172856}, issn = {1879-1026}, mesh = {*Estuaries ; Oceans and Seas ; Drug Resistance, Microbial/genetics ; *Bacteria/genetics ; Genes, Bacterial ; China ; Anti-Bacterial Agents ; }, abstract = {As vectors for microorganisms and genetic elements, vast amounts of solid wastes, including plastics and non-plastics, enter oceans through estuaries globally. The heterogeneity of microbiomes developed on different types of plastic and non-plastic matrices and their potential environmental risks in field estuarine regions have not been fully explored. Here, microbial communities, antibiotic resistance genes (ARGs), virulence factors (VFs), and mobile genetic elements (MGEs) on substrate debris (SD) covering non-biodegradable plastics, biodegradable plastics, and non-plastics were first comprehensively characterized based on metagenomic analyzes (substrate identity). These selected substrates were field-exposed at both ends of the Haihe Estuary, China (geographic location). For substrate identity: conspicuously diverse functional gene profiles on different substrates were obtained; the relative gene copies of ARGs, VFs, and MGEs on non-biodegradable plastics were highest at both locations; non-biodegradable plastic matrices recruited the most abundant unique ARGs from ambient waters; the relative abundance of potential bacterial hosts carrying multiple ARGs and VFs (BH-AV) was much higher on non-biodegradable plastic surfaces than on the other two substrates, especially in the coastal water environment. For geographic locations: more abundant specific ARGs, VFs, and MGEs were significantly enriched on SD from the upper estuary; the average relative abundance of identified BH-AV on SD from the upper estuary was 1.99-7.14 folds from the lower estuary. Finally, the results of the Projection Pursuit Regression model verified the higher comprehensive potential risks arising from non-biodegradable plastics (substrate identity) and SD from the upstream of the estuary (geographic location). Based on comparative analysis, our results alert us to pay particular attention to ecological risks triggered by conventional non-biodegradable plastics in rivers and coastal environments and highlight the microbiological risk from terrestrial solid waste to the downstream marine environment.}, } @article {pmid37172685, year = {2023}, author = {Lyu, C and Li, X and Yu, H and Song, Y and Gao, H and Yuan, P}, title = {Insight into the microbial nitrogen cycle in riparian soils in an agricultural region.}, journal = {Environmental research}, volume = {231}, number = {Pt 1}, pages = {116100}, doi = {10.1016/j.envres.2023.116100}, pmid = {37172685}, issn = {1096-0953}, mesh = {*Denitrification ; *Soil ; Nitrates/analysis ; Nitrogen Cycle ; Nitrification ; Nitrogen ; Soil Microbiology ; }, abstract = {Riparian zones are considered as an effective measure on preventing agricultural non-point source nitrogen (N) pollution. However, the mechanism underlying microbial N removal and the characteristics of N-cycle in riparian soils remain elusive. In this study, we systematically monitored the soil potential nitrification rate (PNR), denitrification potential (DP), as well as net N2O production rate, and further used metagenomic sequencing to elucidate the mechanism underlying microbial N removal. As a whole, the riparian soil had a very strong denitrification, with the DP 3.17 times higher than the PNR and 13.82 times higher than the net N2O production rate. This was closely related to the high soil NO3[-]-N content. In different profiles, due to the influence of extensive agricultural activities, the soil DP, PNR, and net N2O production rate near the farmland edge were relatively low. In terms of N-cycling microbial community composition, the taxa of denitrification, dissimilatory nitrate reduction, and assimilatory nitrate reduction accounted for a large proportion, all related to NO3[-]-N reduction. The N-cycling microbial community in waterside zone showed obvious differences to the landside zone. The abundances of N-fixation and anammox genes were significantly higher in the waterside zone, while the abundances of nitrification (amoA&B&C) and urease genes were significantly higher in the landside zone. Furthermore, the groundwater table was an important biogeochemical hotspot in the waterside zone, the abundance of N-cycle genes near the groundwater table was at a relative higher level. In addition, compared to different soil depths, greater variation in N-cycling microbial community composition was observed between different profiles. These results reveal some characteristics of the soil microbial N-cycle in the riparian zone in an agricultural region and are helpful for restoration and management of the riparian zone.}, } @article {pmid37171295, year = {2023}, author = {Qiu, G and Zhu, L and Chen, S and Li, N and Ye, C and Zhuo, S and Shen, Y}, title = {High-throughput metagenomics analysis in early and precise diagnosis of eosinophilic meningoencephalitis complicated with respiratory failure: A case report.}, journal = {Medicine}, volume = {102}, number = {19}, pages = {e33683}, pmid = {37171295}, issn = {1536-5964}, mesh = {Animals ; Female ; Humans ; Aged ; Albendazole/therapeutic use ; Aftercare ; Metagenomics ; Patient Discharge ; *Meningoencephalitis/complications/diagnosis/drug therapy ; *Angiostrongylus cantonensis ; Antibodies ; *Respiratory Insufficiency/complications ; *Meningitis/diagnosis ; }, abstract = {RATIONALE: Human infection with Angiostrongylus cantonensis is uncommon and has only been sporadically reported in the literature. Patients infected with A cantonensis usually have a delayed diagnosis and sometimes a poor prognosis.

PATIENT CONCERNS: A 70-year-old woman presented to the respiratory department with complaints of headache, chest pain, myalgia, fatigue, and anorexia for 7 days.

DIAGNOSES: Complete blood count showed eosinophilia. The serum was tested showing a positive finding of A cantonensis antibody. Cerebrospinal fluid was tested using high-throughput metagenomics analysis and 16 reads for A cantonensis were mapped. The patient was diagnosed with A cantonensis infection.

INTERVENTIONS: The patient received a 7-day course of albendazole and 4-day course of prednisone.

OUTCOMES: When discharged from the hospital, the patient still suffered from fatigue and poor memory. Aminotransferase levels were high due to albendazole's liver toxicity. In a post-discharge follow-up about 1 month later she had recovered completely both physically and mentally, and peripheral eosinophil count and aminotransferase levels were both normal.

LESSONS: Because the direct identification of parasites is difficult, high-throughput metagenomics analysis may provide a reliable alternative tool for the diagnoses of infection with A cantonensis. When albendazole is prescribed, caution must be taken with respect to its liver toxicity.}, } @article {pmid37171132, year = {2023}, author = {Bellone, R and Lechat, P and Mousson, L and Gilbart, V and Piorkowski, G and Bohers, C and Merits, A and Kornobis, E and Reveillaud, J and Paupy, C and Vazeille, M and Martinet, JP and Madec, Y and De Lamballerie, X and Dauga, C and Failloux, AB}, title = {Climate change and vector-borne diseases: a multi-omics approach of temperature-induced changes in the mosquito.}, journal = {Journal of travel medicine}, volume = {30}, number = {4}, pages = {}, doi = {10.1093/jtm/taad062}, pmid = {37171132}, issn = {1708-8305}, support = {ANR-10-LABX-62-IBEID//Laboratoire d'Excellence 'Integrative Biology of Emerging Infectious Diseases'/ ; 734548//European Union's Horizon/ ; }, mesh = {Animals ; Humans ; Climate Change ; Temperature ; Multiomics ; *Chikungunya Fever/epidemiology ; *Chikungunya virus/genetics ; *Aedes ; }, abstract = {BACKGROUND: Climate change and globalization contribute to the expansion of mosquito vectors and their associated pathogens. Long spared, temperate regions have had to deal with the emergence of arboviruses traditionally confined to tropical regions. Chikungunya virus (CHIKV) was reported for the first time in Europe in 2007, causing a localized outbreak in Italy, which then recurred repeatedly over the years in other European localities. This raises the question of climate effects, particularly temperature, on the dynamics of vector-borne viruses. The objective of this study is to improve the understanding of the molecular mechanisms set up in the vector in response to temperature.

METHODS: We combine three complementary approaches by examining Aedes albopictus mosquito gene expression (transcriptomics), bacterial flora (metagenomics) and CHIKV evolutionary dynamics (genomics) induced by viral infection and temperature changes.

RESULTS: We show that temperature alters profoundly mosquito gene expression, bacterial microbiome and viral population diversity. We observe that (i) CHIKV infection upregulated most genes (mainly in immune and stress-related pathways) at 20°C but not at 28°C, (ii) CHIKV infection significantly increased the abundance of Enterobacteriaceae Serratia marcescens at 28°C and (iii) CHIKV evolutionary dynamics were different according to temperature.

CONCLUSION: The substantial changes detected in the vectorial system (the vector and its bacterial microbiota, and the arbovirus) lead to temperature-specific adjustments to reach the ultimate goal of arbovirus transmission; at 20°C and 28°C, the Asian tiger mosquito Ae. albopictus was able to transmit CHIKV at the same efficiency. Therefore, CHIKV is likely to continue its expansion in the northern regions and could become a public health problem in more countries than those already affected in Europe.}, } @article {pmid37170644, year = {2023}, author = {Wang, R and Li, X and Xu, Y and Zhang, L and Mao, M and Wang, C and Zhang, D and Lang, T}, title = {Disseminated visceral Kaposi's sarcoma after allogeneic hematopoietic stem cell transplantation: a case report.}, journal = {The Journal of international medical research}, volume = {51}, number = {5}, pages = {3000605231172871}, pmid = {37170644}, issn = {1473-2300}, mesh = {Female ; Humans ; Child ; *Sarcoma, Kaposi/diagnosis/etiology ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Immunosuppressive Agents ; }, abstract = {Cases of disseminated visceral Kaposi's sarcoma (KS) after allogenic hematopoietic stem cell transplantation (HSCT) are very rare worldwide, and disseminated visceral KS is often rapidly progressive and life-threatening, especially in paediatric patients. Here, the case of a 6-year-old female patient with disseminated visceral KS after allogeneic HSCT for treating severe aplastic anaemia is presented. The authors encountered difficulties in making the diagnosis due to lack of experience, but the diagnosis was achieved relatively quickly and accurately using metagenomic next-generation sequencing. After tapering and withdrawal of immunosuppressant drugs, the patient's condition was controlled. In conclusion, although HSCT-related KS is very rare, it should be considered during differential diagnosis.}, } @article {pmid37170273, year = {2023}, author = {Walker, J and Joy, AA and Vos, LJ and Stenson, TH and Mackey, JR and Jovel, J and Kao, D and Madsen, KL and Wong, GK}, title = {Chemotherapy-induced weight gain in early-stage breast cancer: a prospective matched cohort study reveals associations with inflammation and gut dysbiosis.}, journal = {BMC medicine}, volume = {21}, number = {1}, pages = {178}, pmid = {37170273}, issn = {1741-7015}, mesh = {Humans ; Female ; *Breast Neoplasms/drug therapy ; Cohort Studies ; Prospective Studies ; Dysbiosis/chemically induced ; Quality of Life ; Proteomics ; Inflammation/chemically induced ; Weight Gain ; Feces/chemistry/microbiology ; *Antineoplastic Agents/adverse effects ; Leukocyte L1 Antigen Complex/analysis/therapeutic use ; }, abstract = {BACKGROUND: Early-stage breast cancer patients treated with chemotherapy risk the development of metabolic disease and weight gain, which can result in increased morbidity and reduced quality of life in survivorship. We aimed to analyze changes within the gastrointestinal microbiome of early-stage breast cancer patients treated with and without chemotherapy to investigate a potential relationship between dysbiosis, a systemic inflammatory response, and resultant anthropomorphic changes.

METHODS: We undertook an a priori analysis of serially collected stool and plasma samples from 40 patients with early-stage breast cancer who underwent adjuvant endocrine therapy only, adjuvant chemotherapy only, or both. Gut microbiota were assessed by metagenomic comparison of stool samples following deep sequencing. Inflammatory biomarkers were evaluated by proteomic analysis of plasma and measurement of fecal calprotectin. Body composition was investigated by dual-energy X-ray absorptiometry to determine biomass indices.

RESULTS: As opposed to treatment with endocrine therapy only, chemotherapy resulted in statistically and clinically significant weight gain and an increase in the android to gynoid ratio of fat distribution. Patients treated with chemotherapy gained an average of 0.15% total mass per month, as opposed to a significantly different loss of 0.19% in those patients who received endocrine-only therapy. Concurrently, a twofold increase in fecal calprotectin occurred after chemotherapy that is indicative of interferon-dependent inflammation and evidence of colonic inflammation. These anthropomorphic and inflammatory changes occurred in concert with a chemotherapy-dependent effect on the gut microbiome as evidenced by a reduction in both the abundance and variety of microbial species.

CONCLUSIONS: We confirm the association of chemotherapy treatment with weight gain and potential deleterious anthropometric changes and suggest that alterations of bacterial flora may contribute to these phenomena through the induction of systemic inflammation. Consequently, the gut microbiome may be a future target for intervention in preventing chemotherapy-dependent anthropometric changes.}, } @article {pmid37170023, year = {2023}, author = {Aksoy, E and Azkur, AK}, title = {Genome characterization of a Turkish bovine rotavirus field isolate by shotgun metagenomics.}, journal = {Archives of virology}, volume = {168}, number = {6}, pages = {159}, pmid = {37170023}, issn = {1432-8798}, support = {BAP 2021/111//KIRIKKALE UNIVERSITY/ ; }, mesh = {Cattle ; Animals ; *Rotavirus/genetics ; *Rotavirus Infections/veterinary ; Turkey ; Genome, Viral ; Phylogeny ; Reassortant Viruses/genetics ; Genotype ; }, abstract = {A bovine rotavirus (BRV) isolate from Kirsehir was isolated from feces of a neonatal calf with diarrhea, identified, and sequenced by shotgun sequencing. Its genotype constellation is G10-P[5]-I2-R2-C2-M2-A3-N2-T6-E2-H3. The structural genes and the non-structural genes NSP1, NSP3, and NSP4 of the Kirsehir isolate were similar in sequence to those of BRVs identified in Turkey. However, VP2, NSP2, NSP4, and NSP5/6 showed similarity to those of rotaviruses from different animal hosts. These findings not only expand our current understanding of the diversity of rotaviruses but also contribute to our understanding of the evolution of rotaviruses at both the national and global levels and reinforce the significance of conducting further research on rotaviruses in Turkey.}, } @article {pmid37169918, year = {2023}, author = {Sanders, JG and Sprockett, DD and Li, Y and Mjungu, D and Lonsdorf, EV and Ndjango, JN and Georgiev, AV and Hart, JA and Sanz, CM and Morgan, DB and Peeters, M and Hahn, BH and Moeller, AH}, title = {Widespread extinctions of co-diversified primate gut bacterial symbionts from humans.}, journal = {Nature microbiology}, volume = {8}, number = {6}, pages = {1039-1050}, pmid = {37169918}, issn = {2058-5276}, support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; R01 AI050529/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Humans ; Phylogeny ; Pan troglodytes ; *Gastrointestinal Microbiome ; Primates ; *Hominidae/microbiology ; Bacteria/genetics ; }, abstract = {Humans and other primates harbour complex gut bacterial communities that influence health and disease, but the evolutionary histories of these symbioses remain unclear. This is partly due to limited information about the microbiota of ancestral primates. Here, using phylogenetic analyses of metagenome-assembled genomes (MAGs), we show that hundreds of gut bacterial clades diversified in parallel (that is, co-diversified) with primate species over millions of years, but that humans have experienced widespread losses of these ancestral symbionts. Analyses of 9,460 human and non-human primate MAGs, including newly generated MAGs from chimpanzees and bonobos, revealed significant co-diversification within ten gut bacterial phyla, including Firmicutes, Actinobacteriota and Bacteroidota. Strikingly, ~44% of the co-diversifying clades detected in African apes were absent from available metagenomic data from humans and ~54% were absent from industrialized human populations. In contrast, only ~3% of non-co-diversifying clades detected in African apes were absent from humans. Co-diversifying clades present in both humans and chimpanzees displayed consistent genomic signatures of natural selection between the two host species but differed in functional content from co-diversifying clades lost from humans, consistent with selection against certain functions. This study discovers host-species-specific bacterial symbionts that predate hominid diversification, many of which have undergone accelerated extinctions from human populations.}, } @article {pmid37169871, year = {2023}, author = {López-García, P and Gutiérrez-Preciado, A and Krupovic, M and Ciobanu, M and Deschamps, P and Jardillier, L and López-Pérez, M and Rodríguez-Valera, F and Moreira, D}, title = {Metagenome-derived virus-microbe ratios across ecosystems.}, journal = {The ISME journal}, volume = {17}, number = {10}, pages = {1552-1563}, pmid = {37169871}, issn = {1751-7370}, mesh = {Animals ; *Ecosystem ; Metagenome ; *Viruses/genetics ; DNA Viruses/genetics ; Seawater ; }, abstract = {It is generally assumed that viruses outnumber cells on Earth by at least tenfold. Virus-to-microbe ratios (VMR) are largely based on counts of fluorescently labelled virus-like particles. However, these exclude intracellular viruses and potentially include false positives (DNA-containing vesicles, gene-transfer agents, unspecifically stained inert particles). Here, we develop a metagenome-based VMR estimate (mVRM) that accounts for DNA viruses across all stages of their replication cycles (virion, intracellular lytic and lysogenic) by using normalised RPKM (reads per kilobase of gene sequence per million of mapped metagenome reads) counts of the major capsid protein (MCP) genes and cellular universal single-copy genes (USCGs) as proxies for virus and cell counts, respectively. After benchmarking this strategy using mock metagenomes with increasing VMR, we inferred mVMR across different biomes. To properly estimate mVMR in aquatic ecosystems, we generated metagenomes from co-occurring cellular and viral fractions (>50 kDa-200 µm size-range) in freshwater, seawater and solar saltern ponds (10 metagenomes, 2 control metaviromes). Viruses outnumbered cells in freshwater by ~13 fold and in plankton from marine and saline waters by ~2-4 fold. However, across an additional set of 121 diverse non-aquatic metagenomes including microbial mats, microbialites, soils, freshwater and marine sediments and metazoan-associated microbiomes, viruses, on average, outnumbered cells by barely two-fold. Although viruses likely are the most diverse biological entities on Earth, their global numbers might be closer to those of cells than previously estimated.}, } @article {pmid37169816, year = {2023}, author = {La Reau, AJ and Strom, NB and Filvaroff, E and Mavrommatis, K and Ward, TL and Knights, D}, title = {Shallow shotgun sequencing reduces technical variation in microbiome analysis.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {7668}, pmid = {37169816}, issn = {2045-2322}, mesh = {Humans ; Reproducibility of Results ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {The microbiome is known to play a role in many human diseases, but identifying key microbes and their functions generally requires large studies due to the vast number of species and genes, and the high levels of intra-individual and inter-individual variation. 16S amplicon sequencing of the rRNA gene is commonly used for large studies due to its comparatively low sequencing cost, but it has poor taxonomic and functional resolution. Deep shotgun sequencing is a more accurate and comprehensive alternative for small studies, but can be cost-prohibitive for biomarker discovery in large populations. Shallow or moderate-depth shotgun metagenomics may serve as a viable alternative to 16S sequencing for large-scale and/or dense longitudinal studies, but only if resolution and reproducibility are comparable. Here we applied both 16S and shallow shotgun stool microbiome sequencing to a cohort of 5 subjects sampled twice daily and weekly, with technical replication at the DNA extraction and the library preparation/sequencing steps, for a total of 80 16S samples and 80 shallow shotgun sequencing samples. We found that shallow shotgun sequencing produced lower technical variation and higher taxonomic resolution than 16S sequencing, at a much lower cost than deep shotgun sequencing. These findings suggest that shallow shotgun sequencing provides a more specific and more reproducible alternative to 16S sequencing for large-scale microbiome studies where costs prohibit deep shotgun sequencing and where bacterial species are expected to have good coverage in whole-genome reference databases.}, } @article {pmid37169786, year = {2023}, author = {Lugli, GA and Mancabelli, L and Milani, C and Fontana, F and Tarracchini, C and Alessandri, G and van Sinderen, D and Turroni, F and Ventura, M}, title = {Comprehensive insights from composition to functional microbe-based biodiversity of the infant human gut microbiota.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {25}, pmid = {37169786}, issn = {2055-5008}, mesh = {Humans ; Infant ; Infant, Newborn ; Adult ; *Gastrointestinal Microbiome ; *Microbiota ; Bacteria/genetics ; Metagenome ; Biodiversity ; }, abstract = {During infancy, gut microbiota development is a crucial process involved in the establishment of microbe-host interactions which may persist throughout adulthood, and which are believed to influence host health. To fully understand the complexities of such interactions, it is essential to assess gut microbiota diversity of newborns and its associated microbial dynamics and relationships pertaining to health and disease. To explore microbial biodiversity during the first 3 years of human life, 10,935 shotgun metagenomic datasets were taxonomically and functionally classified. Microbial species distribution between infants revealed the presence of eight major Infant Community State Types (ICSTs), being dominated by 17 bacterial taxa, whose distribution was shown to correspond to the geographical origin and infant health status. In total, 2390 chromosomal sequences of the predominant taxa were reconstructed from metagenomic data and used in combination with 44,987 publicly available genomes to trace the distribution of microbial Population Subspecies (PS) within the different infant groups, revealing patterns of multistrain coexistence among ICSTs. Finally, implementation of a metagenomic- and metatranscriptomic-based metabolic profiling highlighted different enzymatic expression patterns of the gut microbiota that allowed us to acquire insights into mechanistic aspects of health-gut microbiota interplay in newborns. Comparison between metagenomic and metatranscriptomic data highlights how a complex environment like the human gut must be investigated by employing both sequencing methodologies and possibly supplemented with metabolomics approaches. While metagenomic analyses are very useful for microbial classification aimed at unveiling key players driving microbiota balances, using these data to explain functionalities of the microbiota is not always warranted.}, } @article {pmid37169197, year = {2023}, author = {Wang, Y and Li, Q}, title = {Competition and interaction between DNRA and denitrification in composting ecosystems: Insights from metagenomic analysis.}, journal = {Bioresource technology}, volume = {381}, number = {}, pages = {129140}, doi = {10.1016/j.biortech.2023.129140}, pmid = {37169197}, issn = {1873-2976}, mesh = {Nitrates ; *Ammonium Compounds ; Denitrification ; *Composting ; *Microbiota ; Nitrogen ; Bacteria/genetics ; Oxidation-Reduction ; }, abstract = {This study investigated denitrification and dissimilatory nitrate reduction to ammonium (DNRA) competition for nitrite in composting of sugarcane pith and cow manure. Metagenomic analysis showed that Actinobacteria was the main DNRA microorganism. During heating phase and thermophilic phase, the abundances of denitrification functional genes (nirK and nirS decreased by 40.22% and 98.60%, respectively) and DNRA functional genes (nirB, nirD increased by 195.24% and 176.61%, and nrfA decreased by 45%, respectively) showed different trends. Interestingly, the abundance of nrfA increased by 250% during cooling and maturity phases. Mantel test revealed that competition between denitrification and DNRA microorganisms for NO2[-]-N limited the succession of their respective communities (P < 0.01). Network analysis showed that unclassified Solirubrobacterales, Altererythrobacter and Microbacterium were the key microorganisms in DNRA microbial communities. The results provided new insights into the key microorganisms and their driving factors affecting DNRA and nitrogen management in the composting ecosystems.}, } @article {pmid37169166, year = {2023}, author = {Chen, MM and Wang, P and Xie, XH and Nie, Z and Xu, SX and Zhang, N and Wang, W and Yao, L and Liu, Z}, title = {Young Adults with Major Depression Show Altered Microbiome.}, journal = {Neuroscience}, volume = {522}, number = {}, pages = {23-32}, doi = {10.1016/j.neuroscience.2023.05.002}, pmid = {37169166}, issn = {1873-7544}, mesh = {Humans ; Young Adult ; *Depressive Disorder, Major ; Depression ; Pilot Projects ; *Microbiota ; *Gastrointestinal Microbiome ; }, abstract = {There is growing basic and clinical evidence that major depressive disorder (MDD) is associated with gut microbiome alterations, but clinical studies have tended not to adjust for confounding factors. And few studies on the gut microbiome focused on young adults with MDD. Here we performed a pilot study to compare the gut microbiome of young adults with MDD with healthy controls. Shotgun metagenomic sequencing was performed on stool samples obtained from 40 young adults with MDD and 42 healthy controls. After controlling for confounding factors including sex, age, BMI, alcohol or cigarette consumption, bowel movement quality, exercise or defecation frequency, we compared microbiome diversity between groups, identified differentially abundant taxa, and further compared functional differences through gut-brain and gut-metabolic module analysis. There were no significant differences in overall gut microbiome structure and function in young adults with MDD compared with controls. Abundance of Sutterellaceae and species belonging to Clostridium, Eubacterium, and Ruminococcus were significantly different between groups. The cysteine degradation I pathway was increased in MDD. After controlling for most confounding factors, this pilot study provides new evidence on the specific, often subtle gut dysbiosis affecting young adults with depression.}, } @article {pmid37168414, year = {2023}, author = {Cretu, B and Iordache, S and Cursaru, A and Serban, B and Costache, M and Cirstoiu, C and Spiridonica, R}, title = {Metagenomic Next-Generation Sequencing for Periprosthetic Joint Infections.}, journal = {Cureus}, volume = {15}, number = {5}, pages = {e38726}, pmid = {37168414}, issn = {2168-8184}, abstract = {Periprosthetic joint infection (PJI) after arthroplasty is a major complication, which requires significant resources, resulting in high costs for the medical system. In recent years, significant progress has been made in the diagnosis and treatment of periprosthetic infections, the identification of the pathogen being the central element in the establishment of targeted antibiotic therapy. Next-generation sequencing (NGS) or metagenomic NGS (mNGS) represents a promising, fast alternative, with increased specificity and sensitivity compared to identification methods using conventional culture media, thus enabling an increased rate of identification of pathogenic microorganisms and antibiotic resistance genes (ARG). The purpose of this article was to highlight new molecular diagnostic methods for periprosthetic joint infections and their involvement in treatment efficiency. NGS technologies are cutting-edge techniques that may challenge the PJI diagnostic model.}, } @article {pmid37168393, year = {2023}, author = {Li, X and Liang, S and Zhang, D and He, M and Zhang, H}, title = {The clinical application of metagenomic next-generation sequencing in sepsis of immunocompromised patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1170687}, pmid = {37168393}, issn = {2235-2988}, mesh = {Adult ; Humans ; *Sepsis/diagnosis ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents ; Ascitic Fluid ; Immunocompromised Host ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) was commonly applied given its ability to identify and type all infections without depending upon culture and to retrieve all DNA with unbiasedness. In this study, we strive to compare outcomes of mNGS with conventional culture methods in adults with sepsis, investigate the differences between the immunocompromised and control group, and assess the clinical effects of mNGS.

METHODS: In our study, 308 adult sepsis patients were included. We used both mNGS and conventional culture methods to analyze diagnostic results, pathogens, and sample types. The correlation between some laboratory tests and the frequency of pathogens by groups was also analyzed. Furthermore, the clinical impacts of mNGS were estimated.

RESULTS: 308 samples were assigned to an immunocompromised group (92/308,29.9%) and a control group (216/308,70.1%). There was the sensitivity of mNGS considered greater than that of the culture method in all samples (88.0% vs 26.3%; P <​ 0.001), in the immunocompromised group (91.3% vs 26.1%; P <​ 0.001), and the control group (86.6% vs 26.4%; P <​ 0.001), particularly in all sample types of blood (P <​ 0.001), BALF (P <​ 0.001), CSF (P <​ 0.001), sputum (P <​ 0.001) and ascitic fluid (P = 0.008). When examining the mNGS results between groups, Pneumocystis jirovecii (P < 0.001), Mucoraceae (P = 0.014), and Klebsiella (P = 0.045) all showed significant differences. On the whole, mNGS detected more pathogens than culture methods (111 vs 25), found 89 organisms that were continuously overlooked in entire samples by culture methods, and showed a favorable positive clinical effect in 76.3% (235 of 308) of patients. In 185 (60.1%) patients, mNGS prompted a modification in the course of management, which included antibiotic de-escalation in 61(19.8%) patients.

CONCLUSIONS: The research discovered that mNGS was more sensitive than the culture method, particularly in samples of blood, BALF, CSF, sputum, and ascitic fluid. When examining the mNGS results, Pneumocystis jirovecii and Mucoraceae were the pathogens seen more commonly in immunocompromised patients with sepsis, which required more attention from clinicians. There was a substantial benefit of mNGS in enhancing the diagnosis of sepsis and advancing patient treatment.}, } @article {pmid37166514, year = {2023}, author = {Adeniyi, A and Bello, I and Mukaila, T and Monono, E and Hammed, A}, title = {Developing rumen mimicry process for biological ammonia synthesis.}, journal = {Bioprocess and biosystems engineering}, volume = {46}, number = {7}, pages = {1011-1020}, pmid = {37166514}, issn = {1615-7605}, support = {FAR0034901//North Dakota Soybean Council/ ; }, mesh = {Animals ; *Ammonia/metabolism ; Fermentation ; *Rumen/metabolism/microbiology ; Bacteria/metabolism ; Glycine max/metabolism ; }, abstract = {The ruminant rumen houses hyper-ammonia-producing bacteria (HAB) that produce ammonia with minimal energy use. Here we developed a mimicry process to produce bio-ammonia, a solution of ammonia and ammonium. The rumen microbes were used to ferment soybean (SYB), soybean protein isolate (SPI), and pepsin-hydrolysate (HP) for bio-ammonia production. The maximum bio-ammonia produced from SYB, SPI, and HP were 0.65, 1.2, and 1.1 g/L, respectively. The presence of non-protein in SYB hindered bio-ammonia production and the processing of SYB to SPI and HP significantly (p < 0.05) increased bio-ammonia production. HP was converted to bio-ammonia quicker than SPI suggesting that enzymatic hydrolysis increases bioprocessing efficiency. Metagenomic analysis of a sample culture revealed that the HAB population is predominantly Klebsiella quasivariicola (73%), Escherichia coli (6%), and Enterobacter cloacae (6%). The bioprocessing steps developed would enable industrial ammonia production to achieve a low CO2 footprint.}, } @article {pmid37166358, year = {2023}, author = {Melie, T and Pirro, S and Miller, AN and Smith, SD and Schutz, KS and Quandt, CA}, title = {Comparative genomics and phylogenomic investigation of the class Geoglossomycetes provide insights into ecological specialization and the systematics of Pezizomycotina.}, journal = {Mycologia}, volume = {115}, number = {4}, pages = {499-512}, doi = {10.1080/00275514.2023.2186743}, pmid = {37166358}, issn = {1557-2536}, mesh = {Phylogeny ; *Ascomycota/genetics ; Ecosystem ; *Mycorrhizae/genetics ; Genomics ; }, abstract = {Despite their global presence and ubiquity, members of the class Geoglossomycetes (Pezizomycotina, Ascomycota) are understudied systematically and ecologically. These fungi have long been presumed saprobic due to their occurrence in or near leaf litter and soils. Additionally, they lack an apparent association with other organisms, reinforcing this perception. However, observations of sporocarps near ericaceous shrubs have given rise to an alternative hypothesis that members of Geoglossomycetes may form ericoid mycorrhizae or ectomycorrhizae. This claim, however, has yet to be confirmed via microscopy or amplicon-based studies examining root communities. As a result, our current understanding of their ecology is based on cursory observations. This study presents a comparative analysis of genomic signatures related to ecological niche to investigate the hypothesis of an ericoid mycorrhizal or ectomycorrhizal ecology in the class. We compared the carbohydrate-active enzyme (CAZyme) and secondary metabolite contents of six newly sequenced Geoglossomycetes genomes with those of fungi representing specific ecologies across Pezizomycotina. Our analysis reveals CAZyme and secondary metabolite content patterns consistent with ectomycorrhizal (EcM) members of Pezizomycotina. Specifically, we found a reduction in CAZyme-encoding genes and secondary metabolite clusters that suggests a mutualistic ecology. Our work includes the broadest taxon sampling for a phylogenomic study of Pezizomycotina to date. It represents the first functional genomic and genome-scale phylogenetic study of the class Geoglossomycetes and improves the foundational knowledge of the ecology and evolution of these understudied fungi.}, } @article {pmid37166318, year = {2023}, author = {Chen, Q and Zhang, X and Shi, W and Du, X and Ma, L and Wang, W and Tao, S and Xiao, Y}, title = {Longitudinal Investigation of Enteric Virome Signatures from Parental-Generation to Offspring Pigs.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0002323}, pmid = {37166318}, issn = {2165-0497}, mesh = {Pregnancy ; Swine ; Animals ; Male ; Female ; Longitudinal Studies ; *Virome ; Lactation ; Feces/microbiology ; Bacteria/genetics ; *Enterovirus Infections ; }, abstract = {To date, studies on the swine gut microbiome have focused almost exclusively on bacteria. Despite recent advances in the understanding of the swine gut bacteriome at different growth stages, a comprehensive longitudinal study of the lifetime dynamics of the swine gut virome is lacking. Here, we used metagenomic sequencing combined with bioinformatic analysis techniques to characterize the gut viromes of parental-generation and offspring pigs at different biological classification levels. We collected 54 fecal samples from 36 parental-generation pigs (18 breeding boars [Duroc] and 18 pregnant/lactating sows [Landrace]) and 108 fecal samples from 18 offspring pigs during the lactation (day 3), nursery (days 26, 35, and 49), growing (day 120), and finishing (day 180) stages. Alpha diversity, including community richness (richness index) and diversity (Shannon index), showed an overall increasing trend in offspring pigs. Distinct shifts (beta diversity) in the microbiome structure along different growth stages were observed. The linear discriminant analysis effect size (LEfSe) algorithm revealed 53 viral genus that are stage specific. Host prediction results showed that enteric viruses are probably correlated with carbohydrate decomposition. We identified abundant auxiliary carbohydrate-active enzyme (CAZyme) genes from enteric viruses, most of which are glycoside hydrolase genes and participate in the biolysis of complex polysaccharides. IMPORTANCE This study shows that distinct stage-associated swine gut viromes may be determined by age and/or gut physiology at different growth stages, and enteric viruses probably manipulate carbohydrate decomposition by abundant glycoside hydrolases. These findings fill a gap in the longitudinal pattern of the swine gut virome and lay the foundation for research on the function of swine enteric viruses.}, } @article {pmid37166164, year = {2023}, author = {Sun, H and Lv, B and Zhu, H and Zeng, Z and El-Ashram, S and Li, J and Chao, Y and Wang, J and Wang, Z}, title = {Selenized glucose improves rat semen quality by improving the gut microbiota and serum metabolome.}, journal = {Food & function}, volume = {14}, number = {11}, pages = {5105-5119}, doi = {10.1039/d3fo00692a}, pmid = {37166164}, issn = {2042-650X}, mesh = {Male ; Rats ; Animals ; Semen Analysis ; Semen/metabolism ; *Gastrointestinal Microbiome ; *Selenium/metabolism ; Glucose/metabolism ; Rats, Sprague-Dawley ; Metabolome ; Testosterone ; }, abstract = {Selenium (Se), a well-known antioxidant, is important for male fertility and sperm quality. The gut microbiota is involved in vital activities and cross-talk between reproduction and the gut axis. It is still unclear whether the gut microbiota mediates the impact of selenium on semen quality, and what the underlying mechanisms may be. A selenized glucose (SeGlu) derivative is a novel organic Se compound. After 7 days of acclimation, the Sprague-Dawley (SD) male rats (230 g, 6 weeks) were divided into three drinking groups: deionized water group (CK), SeGlu 0.15 group (0.15 mg Se per L), and SeGlu 0.4 group (0.4 mg Se per L). All animals were euthanized 30 days post-treatment. Serum and intratesticular testosterone and semen parameters were measured. Metagenomic and non-targeted metabolomic approaches were used to study the effects of SeGlu on the gut microbiota and serum metabolites of rats. In both the SeGlu 0.15 Group and the SeGlu 0.4 Group, we found a significant increase in seminiferous epithelium thickness. While the SeGlu 0.4 Group had a tendency to increase with insignificant difference, the SeGlu 0.15 Group significantly improved the sperm viability, survival rate, and seminal plasma fructose. SeGlu had no effect on intratesticular testosterone levels, or abnormal sperm counts. Measured serum testosterone levels using ELISA and LC-MS, which showed a decreasing trend. ELISA did not reveal significant differences, but LC-MS indicated a significant decrease in SeGlu 0.4 group. Meanwhile, the SeGlu 0.15 Group reduced the abundance of harmful bacteria such as Rikenella, Barnesiella, Tenacibaculum, and Aeromonas while increasing the abundance of beneficial microbiota such as Intestinimonas, Christensenella, Coprococcus, and Butyrivibrio. Linear discriminant analysis Effect Size (LEfSe) identified the SeGlu 0.15 group's feature genera as Roseburia, Clostridium, Ruminococcus, and Eubacterium. Serum metabolites showed that the SeGlu 0.15 Group increased 5 beta-androstane-3,17-dione while decreasing estrone and 2-methoxyestradiol (2-MeOE2). In conclusion, the SeGlu 0.15 Group can significantly alter the levels of several sex hormones in serum, improve the quality of rats' sperm, and reduce harmful bacterial colonization. SeGlu 0.15 may be used as an effective dietary supplement.}, } @article {pmid37164563, year = {2023}, author = {Yancey, CE and Mathiesen, O and Dick, GJ}, title = {Transcriptionally active nitrogen fixation and biosynthesis of diverse secondary metabolites by Dolichospermum and Aphanizomenon-like Cyanobacteria in western Lake Erie Microcystis blooms.}, journal = {Harmful algae}, volume = {124}, number = {}, pages = {102408}, doi = {10.1016/j.hal.2023.102408}, pmid = {37164563}, issn = {1878-1470}, mesh = {*Microcystis/genetics/metabolism ; *Aphanizomenon/genetics/metabolism ; Lakes/microbiology ; Nitrogen Fixation ; *Cyanobacteria/metabolism ; Nitrogen/metabolism ; }, abstract = {Cyanobacterial harmful algal blooms (cyanoHABs) in the western basin of Lake Erie are dominated by microcystin producing Microcystis spp., but other cyanobacterial taxa that coexist in these communities may play important roles in production of toxins and shaping bloom dynamics and community function. In this study, we used metagenomic and metatranscriptomic data from the 2014 western Lake Erie cyanoHAB to explore the genetic diversity and biosynthetic potential of cyanobacteria belonging to the Anabaena, Dolichospermum, Aphanizomenon (ADA) clade. We reconstructed two near-complete metagenome-assembled genomes from two distinct ADA clade species, each containing biosynthetic gene clusters that encode novel and known secondary metabolites, including those with toxic and/or known taste and odor properties, that were transcriptionally active. However, neither ADA metagenome-assembled genome contained genes encoding guanitoxins, anatoxins, or saxitoxins, which are known to be produced by ADA. The ADA cyanobacteria accounted for most of the metagenomic and metatranscriptomic reads from nitrogen fixation genes, suggesting they were the dominant N-fixers at the times and stations sampled. Despite their relatively low abundance, our results highlight the possibility that ADA taxa could influence the water quality and ecology of Microcystis blooms, although the extent of these impacts remains to be quantified.}, } @article {pmid37164558, year = {2023}, author = {Valadez-Cano, C and Reyes-Prieto, A and Beach, DG and Rafuse, C and McCarron, P and Lawrence, J}, title = {Genomic characterization of coexisting anatoxin-producing and non-toxigenic Microcoleus subspecies in benthic mats from the Wolastoq, New Brunswick, Canada.}, journal = {Harmful algae}, volume = {124}, number = {}, pages = {102405}, doi = {10.1016/j.hal.2023.102405}, pmid = {37164558}, issn = {1878-1470}, mesh = {Animals ; Dogs ; *Bacterial Toxins/toxicity ; New Brunswick ; Ecosystem ; *Cyanobacteria/genetics ; Canada ; Genomics ; }, abstract = {The presence of toxigenic benthic cyanobacteria in riverine ecosystems is an increasing concern around the world. In 2018, the death of three dogs along the Wolastoq (also known as the Saint John River) in New Brunswick, Canada, was attributed to anatoxin exposure after they ingested benthic microbial mats found along the shore. Here, we shotgun sequenced the DNA of 15 non-axenic cyanobacterial isolates derived from four anatoxin-containing benthic mat samples associated with the dog deaths. Anatoxins were produced by some of the isolates, but not all. We retrieved near-complete Microcoleus metagenome-assembled genomes (MAGs) from the isolates that are closely related to anatoxin-producing Microcoleus from the Cardrona River (New Zealand), although the Microcoleus MAGs from the Wolastoq varied in the presence/absence of the anatoxin-a biosynthesis cluster. Sequence similarity at the genomic level suggests that toxigenic and non-toxigenic Microcoleus MAGs from the Wolastoq belong to the same species but are separate subspecies. The toxigenic and nontoxic Wolastoq Microcoleus subspecies coexisted in the mat samples in similar relative abundance. Overall genomic comparisons revealed that toxigenic Microcoleus MAGs are longer and code for more accessory genes than their non-toxigenic relatives, suggesting a differential responsiveness to changing environments, stress conditions and nutrient availability.}, } @article {pmid37164497, year = {2023}, author = {Stephens, K and Charnock-Jones, DS and Smith, GCS}, title = {Group B Streptococcus and the risk of perinatal morbidity and mortality following term labor.}, journal = {American journal of obstetrics and gynecology}, volume = {228}, number = {5S}, pages = {S1305-S1312}, doi = {10.1016/j.ajog.2022.07.051}, pmid = {37164497}, issn = {1097-6868}, mesh = {Infant, Newborn ; Infant ; Pregnancy ; Female ; Humans ; *Pregnancy Complications, Infectious/diagnosis ; Streptococcus agalactiae ; *Streptococcal Infections/epidemiology/diagnosis ; *Labor, Obstetric ; Antibiotic Prophylaxis/methods ; Infectious Disease Transmission, Vertical/prevention & control ; Morbidity ; }, abstract = {Streptococcus agalactiae (group B Streptococcus) colonizes the genital tract of approximately 20% of pregnant women. In the absence of intervention, approximately 1% of infants born to colonized mothers exhibit a clinical infection. This has led to implementation of screening and intervention in the form of intrapartum antibiotic prophylaxis in many countries, including the United States. However, screening has not been introduced in a substantial minority of other countries because of the absence of supportive level 1 evidence, the very large number needed to treat to prevent 1 case, and concerns about antimicrobial resistance. Optimal screening would involve rapid turnaround (to facilitate intrapartum testing) and report antibiotic sensitivity, but no such method exists. There is significant scope for a personalized medicine approach, targeting intrapartum antibiotic prophylaxis to cases at greatest risk, but the pathogen and host factors determining the risk of invasive disease are incompletely understood. Epidemiologic data have indicated the potential of prelabor invasion of the uterus by group B Streptococcus, and metagenomic analysis revealed the presence of group B Streptococcus in the placenta in approximately 5% of pregnant women at term before onset of labor and membrane rupture. However, the determinants and consequences of prelabor invasion of the uterus by group B Streptococcus remain to be established. The vast majority (98%) of invasive neonatal disease is caused by 6 serotypes, and hexavalent vaccines against these serotypes have completed phase 2 trials. However, an obstacle to phase 3 studies is conducting an adequately powered trial to demonstrate clinical effectiveness given that early-onset disease affects approximately 1 in 1000 births in the absence of vaccination.}, } @article {pmid37164230, year = {2023}, author = {Wen, X and Zhou, Y and Liang, X and Li, J and Huang, Y and Li, Q}, title = {A novel carbon-nitrogen coupled metabolic pathway promotes the recyclability of nitrogen in composting habitats.}, journal = {Bioresource technology}, volume = {381}, number = {}, pages = {129134}, doi = {10.1016/j.biortech.2023.129134}, pmid = {37164230}, issn = {1873-2976}, mesh = {*Carbon/metabolism ; Nitrogen/metabolism ; *Composting ; Bacteria/genetics/metabolism ; Ecosystem ; Metabolic Networks and Pathways ; Soil ; Manure ; }, abstract = {This study revealed a novel carbon-nitrogen coupled metabolic pathway. Results showed that the addition of inorganic carbon sources slowed down the decomposition of urea and conserved more nutrients in composting. Metagenomic analysis showed that the main bacteria involved in this new pathway were Actinobacteria, Proteobacteria and Firmicutes. During the late composting period, the dominant genus Microbacteium involved in denitrification accounted for 22.18% in control (CP) and only 0.12% in treatment group (T). Moreover, ureC, rocF, argF, argI, argG were key genes involved in urea cycle. The abundance of functional gene ureC and denitrification genes decreased in thermophilic and cooling phases, respectively. The genes hao, nosZ, ureA and nifH were more closely associated with Chloroflexi_bacterium and Bacillus_paralichenformis. In conclusion, composting habitats with additional inorganic carbon sources could not only weaken denitrification but also allow more nitrogen to be conserved through slow-release urea to improve resource utilization and decrease the environmental risk.}, } @article {pmid37164227, year = {2023}, author = {Wang, P and Yu, M and Lin, P and Zheng, Y and Ren, L}, title = {Effects of biochar supported nano zero-valent iron with different carbon/iron ratios on two-phase anaerobic digestion of food waste.}, journal = {Bioresource technology}, volume = {382}, number = {}, pages = {129158}, doi = {10.1016/j.biortech.2023.129158}, pmid = {37164227}, issn = {1873-2976}, mesh = {*Iron ; Carbon ; Sewage ; Anaerobiosis ; Food ; *Refuse Disposal ; Charcoal ; Methane/metabolism ; }, abstract = {The promotion effects of biochar supported nano zero-valent iron (BC/nZVI) with different carbon/iron ratios on two-phase anaerobic digestion (AD) of food waste (FW) were studied. Results suggested that when the carbon/iron ratio was 3:1 AD system showed the best performance, with the concentration of volatile fatty acids (VFAs) in acidogenic phase (AP) and the cumulative methane production in methanogenic phase (MP) increased by 31.4% and 24.8%, respectively. Metagenomic analysis demonstrated that BC/nZVI increased the relative abundance of Defluviitoga in AP, and promoted the growth of Methanothrix in MP. Metabolic pathway analysis in AP indicated that BC/nZVI mainly promoted the abundances of acetate kinase and butyrate kinase to enhance acid production. Methane metabolism pathway analysis in MP revealed that BC/nZVI increased methane production by promoting the module of M00357 and activating related enzymes. The results of this sutdy showed that BC/nZVI promoted AD of FW mainly through acetoclastic methanogenic pathway.}, } @article {pmid37163833, year = {2023}, author = {Ni, M and Zhao, Y and Pan, Y and Li, D and Huang, Y and Chen, Z and Li, L and Song, Z}, title = {A new insight in enhancing phosphate enrichment in biofilm process: Comparison of the key metabolic pathways in highly-efficient and dominant PAOs based on metagenomics.}, journal = {Journal of environmental management}, volume = {341}, number = {}, pages = {118114}, doi = {10.1016/j.jenvman.2023.118114}, pmid = {37163833}, issn = {1095-8630}, mesh = {*Phosphates ; *Extracellular Polymeric Substance Matrix ; Biofilms ; Acyl-Butyrolactones ; Carbon ; Metabolic Networks and Pathways ; Bioreactors ; Sewage ; }, abstract = {The formation of dominant phosphate-accumulating organisms (PAOs) is essential for the high enrichment of phosphate in biofilm sequencing batch reactors (BSBR) for phosphorus recovery. The dominant PAOs in the biofilm process have not been isolated and purified, and the key metabolic pathways that promote the formation of dominant PAOs are still unclear. In this study, four strains of highly-efficient PAOs were obtained by an innovative isolation procedure. The relationship between the abundance of highly-efficient and dominant PAOs and the phosphate removal ability was compared. We found that the abundance of PAOs was positively correlated with the phosphate removal efficiency in vitro pure culture and complex biofilm process. Metagenomics analysis revealed that compared with highly-efficient PAOs cultured in vitro, dominant PAOs in biofilms had unique key metabolic pathways, F-ATPases and N-Acyl homoserine lactones (AHLs). F-ATPases are important for maintaining the proton motive force (PMF) required for the uptake of carbon sources by PAOs, and AHLs are participating in phosphate metabolism through quorum sensing (QS) mediated secretion of extracellular polymeric substance (EPS). The formation of dominant PAOs was promoted by optimizing carbon source uptake and phosphate metabolism. This study revealed that the difficult isolation of dominant PAOs was due to the AHLs-mediated QS, and we identified the key pathways regulating the formation of dominant PAOs in biofilms through genomics analysis. Our findings provide insights in enhancing phosphate enrichment in BSBR by modulating the components of microbial community under the low concentration of carbon source consumption.}, } @article {pmid37163652, year = {2023}, author = {Anselmo, A and Veys, P and Fumière, O and Lecrenier, MC and Cordonnier, A and Michez, D and Baeten, V}, title = {Challenges related to the application of analytical methods to control insect meals in the context of European legislation.}, journal = {Food additives & contaminants. Part A, Chemistry, analysis, control, exposure & risk assessment}, volume = {40}, number = {6}, pages = {699-710}, doi = {10.1080/19440049.2023.2211677}, pmid = {37163652}, issn = {1944-0057}, mesh = {Animals ; *Proteins/analysis ; *Animal Feed/analysis ; Insecta ; Microscopy/methods ; Polymerase Chain Reaction ; }, abstract = {Since their approval for use in aquaculture in 2017, processed insect proteins have been extensively studied for their nutritional quality in animal feed. This new type of meal is highly promising but requires, as for other products used in animal feed, strict sanitary control in accordance with European legislation. Within this legal framework, light microscopy and PCR remain the official methods but have some analytical limitations that other methods could overcome. This paper aims to provide an overview of the European legislation concerning use of processed insect proteins, but also to highlight the advantages and disadvantages of the official methods for their analysis. It also points out other analytical methods, which have already proved their worth for the analysis of processed animal proteins, which could be used as complementary methods.}, } @article {pmid37162704, year = {2023}, author = {Li, YQ and Xin, Y and Li, C and Liu, J and Huang, T}, title = {Metagenomics-metabolomics analysis of microbial function and metabolism in petroleum-contaminated soil.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {54}, number = {2}, pages = {935-947}, pmid = {37162704}, issn = {1678-4405}, support = {Grant No. 31760026//National Natural Science Foundation of China (NSFC)/ ; 81260411//National Natural Science Foundation of China (NSFC)/ ; }, mesh = {*Petroleum/analysis ; Metagenomics ; Soil Microbiology ; Biodegradation, Environmental ; *Polycyclic Aromatic Hydrocarbons/metabolism ; Metabolomics ; Soil ; *Soil Pollutants/metabolism ; Hydrocarbons/metabolism ; }, abstract = {Contamination of soil by petroleum is becoming increasingly serious in the world today. However, the research on gene functional characteristics, metabolites and distribution of microbial genomes in oil-contaminated soil is limited. Considering that, metagenomic and metabonomic were used to detect microbes and metabolites in oil-contaminated soil, and the changes of functional pathways were analyzed. We found that oil pollution significantly changed the composition of soil microorganisms and metabolites, and promoted the relative abundance of Pseudoxanthomonas, Pseudomonas, Mycobacterium, Immundisolibacter, etc. The degradation of toluene, xylene, polycyclic aromatic hydrocarbon and fluorobenzoate increased in Xenobiotics biodegradation and metabolism. Key monooxygenases and dioxygenase systems were regulated to promote ring opening and degradation of aromatic hydrocarbons. Metabolite contents of polycyclic aromatic hydrocarbons (PAHs) such as 9-fluoronone and gentisic acid increased significantly. The soil microbiome degraded petroleum pollutants into small molecular substances and promoted the bioremediation of petroleum-contaminated soil. Besides, we discovered the complete degradation pathway of petroleum-contaminated soil microorganisms to generate gentisic acid from the hydroxylation of naphthalene in PAHs by salicylic acid. This study offers important insights into bioremediation of oil-contaminated soil from the aspect of molecular regulation mechanism and provides a theoretical basis for the screening of new oil degrading bacteria.}, } @article {pmid37162353, year = {2023}, author = {Barnes, SJ and Althouse, RC and Costa, BF and Hu, B and Kovalev, M and Kulik, T and Lee, YT and Moore, MC and Peng, E and Pook, JY and Sharma, A and Wood, C and Webb, EA and Sterling, H and Aeppli, C and Thrash, JC}, title = {Metagenome-Assembled Genomes from Photo-Oxidized and Nonoxidized Oil-Degrading Marine Microcosms.}, journal = {Microbiology resource announcements}, volume = {12}, number = {6}, pages = {e0021023}, pmid = {37162353}, issn = {2576-098X}, support = {Gulf Research Program Early Career Fellowship//National Academies of Sciences, Engineering, and Medicine (NASEM)/ ; Gulf Research Program Early Career Fellowship//National Academies of Sciences, Engineering, and Medicine (NASEM)/ ; }, abstract = {We performed deep metagenomic sequencing on hydrocarbon-degrading marine microcosms designed to experimentally determine the effect of photo-oxidation on oil biodegradation dynamics. Assembly, binning, and dereplication yielded 73 unique metagenome-assembled genomes (MAGs) from 6 phyla, of which 61 are predicted to be over 90% complete.}, } @article {pmid37162018, year = {2023}, author = {Garaycochea, S and Altier, NA and Leoni, C and Neal, AL and Romero, H}, title = {Abundance and phylogenetic distribution of eight key enzymes of the phosphorus biogeochemical cycle in grassland soils.}, journal = {Environmental microbiology reports}, volume = {15}, number = {5}, pages = {352-369}, pmid = {37162018}, issn = {1758-2229}, mesh = {Phylogeny ; *Soil/chemistry ; *Phosphorus ; Ecosystem ; Grassland ; Alkaline Phosphatase/genetics ; }, abstract = {Grassland biomes provide valuable ecosystem services, including nutrient cycling. Organic phosphorus (Po) represents more than half of the total P in soils. Soil microorganisms release organic P through enzymatic processes, with alkaline phosphatases, acid phosphatases and phytases being the key P enzymes involved in the cycling of organic P. This study analysed 74 soil metagenomes from 17 different grassland biomes worldwide to evaluate the distribution and abundance of eight key P enzymes (PhoD, PhoX, PhoA, Nsap-A, Nsap-B, Nsap-C, BPP and CPhy) and their relationship with environmental factors. Our analyses showed that alkaline phosphatase phoD was the dataset's most abundant P-enzyme encoding genes, with a wide phylogenetic distribution. Followed by the acid phosphatases Nsap-A and Nsap-C showed similar abundance but a different distribution in their respective phylogenetic trees. Multivariate analyses revealed that pH, Tmax , SOC and soil moisture were associated with the abundance and diversity of all genes studied. PhoD and phoX genes strongly correlated with SOC and clay, and the phoX gene was more common in soils with low to medium SOC and neutral pH. In particular, P-enzyme genes tended to respond in a positively correlated manner among them, suggesting a complex relationship of abundance and diversity among them.}, } @article {pmid37161271, year = {2023}, author = {Chen, B and Zhang, Z and Zhang, Q and Xu, N and Lu, T and Wang, T and Hong, W and Fu, Z and Penuelas, J and Gillings, M and Qian, H}, title = {Antimicrobial Peptides in the Global Microbiome: Biosynthetic Genes and Resistance Determinants.}, journal = {Environmental science & technology}, volume = {57}, number = {20}, pages = {7698-7708}, doi = {10.1021/acs.est.3c01664}, pmid = {37161271}, issn = {1520-5851}, mesh = {Humans ; Antimicrobial Cationic Peptides/genetics/pharmacology/chemistry ; Antimicrobial Peptides ; *Anti-Infective Agents ; *Microbiota ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antimicrobial peptides are a promising new class of antimicrobials that could address the antibiotic resistance crisis, which poses a major threat to human health. These peptides are present in all kingdoms of life, but especially in microorganisms, having multiple origins in diverse taxa. To date, there has been no global study on the diversity of antimicrobial peptides, the hosts in which these occur, and the potential for resistance to these agents. Here, we investigated the diversity and number of antimicrobial peptides in four main habitats (aquatic, terrestrial, human, and engineered) by analyzing 52,515 metagenome-assembled genomes. The number of antimicrobial peptides was higher in the human gut microbiome than in other habitats, and most hosts of antimicrobial peptides were habitat-specific. The relative abundance of genes that confer resistance to antimicrobial peptides varied between habitats and was generally low, except for the built environment and on human skin. The horizontal transfer of potential resistance genes among these habitats was probably constrained by ecological barriers. We systematically quantified the risk of each resistance determinant to human health and found that nearly half of them pose a threat, especially those that confer resistance to multiple AMPs and polymyxin B. Our results help identify the biosynthetic potential of antimicrobial peptides in the global microbiome, further identifying peptides with a low risk of developing resistance.}, } @article {pmid37160893, year = {2023}, author = {Seelbinder, B and Lohinai, Z and Vazquez-Uribe, R and Brunke, S and Chen, X and Mirhakkak, M and Lopez-Escalera, S and Dome, B and Megyesfalvi, Z and Berta, J and Galffy, G and Dulka, E and Wellejus, A and Weiss, GJ and Bauer, M and Hube, B and Sommer, MOA and Panagiotou, G}, title = {Candida expansion in the gut of lung cancer patients associates with an ecological signature that supports growth under dysbiotic conditions.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2673}, pmid = {37160893}, issn = {2041-1723}, mesh = {Humans ; Female ; Male ; *Candida ; Cross-Sectional Studies ; *Lung Neoplasms ; Dysbiosis ; Lactic Acid ; }, abstract = {Candida species overgrowth in the human gut is considered a prerequisite for invasive candidiasis, but our understanding of gut bacteria promoting or restricting this overgrowth is still limited. By integrating cross-sectional mycobiome and shotgun metagenomics data from the stool of 75 male and female cancer patients at risk but without systemic candidiasis, bacterial communities in high Candida samples display higher metabolic flexibility yet lower contributional diversity than those in low Candida samples. We develop machine learning models that use only bacterial taxa or functional relative abundances to predict the levels of Candida genus and species in an external validation cohort with an AUC of 78.6-81.1%. We propose a mechanism for intestinal Candida overgrowth based on an increase in lactate-producing bacteria, which coincides with a decrease in bacteria that regulate short chain fatty acid and oxygen levels. Under these conditions, the ability of Candida to harness lactate as a nutrient source may enable Candida to outcompete other fungi in the gut.}, } @article {pmid37160689, year = {2023}, author = {Hu, J and Mei, H and Su, NY and Sun, WJ and Zhang, DK and Fan, LL and He, P and Pan, J and Wang, XW and Zou, PY and Liu, YX and Guo, Y and Lan, CH}, title = {Eradication rates of Helicobacter pylori in treatment-naive patients following 14-day vonoprazan-amoxicillin dual therapy: A multicenter randomized controlled trial in China.}, journal = {Helicobacter}, volume = {28}, number = {4}, pages = {e12970}, doi = {10.1111/hel.12970}, pmid = {37160689}, issn = {1523-5378}, support = {82072253//The National Science Foundation of China/ ; 2019CXLCB003//The Training Program of Clinical Medical Technology Innovation Ability of the Army Medical Center/ ; }, mesh = {Humans ; Amoxicillin/therapeutic use ; *Helicobacter Infections/drug therapy ; *Helicobacter pylori ; Anti-Bacterial Agents ; Drug Therapy, Combination ; Bismuth/therapeutic use ; Treatment Outcome ; Proton Pump Inhibitors/therapeutic use ; Clarithromycin/therapeutic use ; }, abstract = {BACKGROUND: Potassium-competitive acid blockers (P-CAB) are recommended for the treatment of Helicobacter pylori infections, but dual therapy of P-CAB with amoxicillin has been poorly studied. The current study compared the efficacy, adverse reactions, compliance, and effects on gut microbiota of 14-day vonoprazan-amoxicillin (VA) dual therapy with esomeprazole, bismuth potassium citrate, amoxicillin, and metronidazole (EBAM) quadruple therapy in treatment-naive patients with H. pylori.

MATERIALS AND METHODS: This was a multicenter, open-label, randomized, and controlled, non-inferiority study. Patients (n = 194) enrolled from six centers were randomly divided into either the VA or EBAM group. H. pylori eradication was determined using [13] C urea breath tests (UBT) 4-6 weeks post-treatment. Fecal samples were collected, and gut microbial populations were analyzed by 16S rDNA and metagenomic sequencing technology.

RESULTS: Eradication rates of H. pylori in the VA and EBAM groups were 88.7% and 91.8%, respectively, according to intention-to-treat (ITT) analysis; 95.6% and 96.7% with per-protocol (PP) analysis; and 94.5% and 96.7% with modified ITT (mITT) analysis (all p > 0.05). The incidence of adverse reactions in the VA group was significantly lower compared to the EBAM group, and compliance within both groups was good. There was no difference in α-diversity or microbial composition in the VA and EBAM groups at one-month post-treatment compared to baseline, except for a markedly reduced abundance of Bacteroides in the EBAM group.

CONCLUSION: VA therapy achieved excellent eradication rates with low adverse reactions, good compliance, and little impact on gut microbiota. VA therapy should be recommended as a first-line treatment against H. pylori.}, } @article {pmid37160588, year = {2023}, author = {Hou, X and Dai, P and Song, X and Long, X and Gao, J and Chai, T}, title = {Understanding the Effect of Compound Probiotics on the Health of Rabbits and Its Mechanisms Through Metagenomics.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {37160588}, issn = {1867-1314}, support = {2016GNC110014//Key Technology Research and Development Program of Shandong/ ; }, abstract = {In this study, we investigated the effects of probiotics on growth performance, immunity, intestinal flora, and antioxidant capacity of rabbits. Three hundred New Zealand white rabbits were randomly divided into four groups. Groups A, B, C, and D were the lactobacillus group, compound probiotic group, control group, and antibiotic group, respectively. The results showed compared with the control group, the average weight of groups A, B, and D increased by 14.88%, 12.33%, and 11.97%, respectively. Moreover, the index of immune organs and the IgG and IgM in serum of group B were significantly increased (P < 0.05). Meanwhile, the activities of superoxide dismutase (SOD) in group B and catalase (CAT) in group A were significantly increased (P < 0.05). At week 5, the contents of rabbit cecum were taken for metagenome sequencing, and the results showed probiotics increased the relative abundance of Akkermansia, and decreased the relative abundance of Bacteroides. According to the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, we found probiotics could enrich metabolic pathways such as carbohydrates, amino acids, and lipids. According to the Comprehensive Antibiotic Resistance Database (CARD), we found antibiotic resistance ontology (ARO) in cecum mainly included β-lactamases, macrolide 2'-phosphotransferase II, and plasmid-mediated quinolone resistance protein. Among them, there were 1964, 2105, and 1982 types of ARO in group B, group D, and groups A and C, respectively. These results showed probiotics played a beneficial role in maintaining or enhancing the health and growth of rabbits and could replace antibiotics under certain feeding conditions.}, } @article {pmid37159883, year = {2023}, author = {Deng, F and Lin, Q and Xu, X and Li, C and Xu, J and Nie, H}, title = {A case report of healthcare-associated psittacosis.}, journal = {Journal of infection in developing countries}, volume = {17}, number = {4}, pages = {571-577}, doi = {10.3855/jidc.17241}, pmid = {37159883}, issn = {1972-2680}, mesh = {Animals ; Male ; Humans ; Adult ; *Psittacosis/diagnosis ; Health Facilities ; Intensive Care Units ; Bronchoalveolar Lavage Fluid ; *Cross Infection/diagnosis ; Mammals ; }, abstract = {INTRODUCTION: Psittacosis is a well-recognized zoonotic infectious disorder caused by Chlamydia psittaci (C. psittaci). Human-to-human transmission of C. psittaci has rarely been reported previously, especially in the case of healthcare-associated infections.

CASE REPORT: A 32-year-old man was admitted to the intensive care unit with severe pneumonia. An intensive care unit healthcare worker contracted pneumonia 7 days after performing endotracheal intubation on the patient. The first patient, a duck feeder, had been closely exposed to ducks, while the second patient had not been exposed to any birds, mammals or poultry. C. psittaci sequences were obtained by metagenomic next-generation sequencing analyses of bronchial alveolar lavage fluid of both the patients, and they were diagnosed with psittacosis. Therefore, healthcare-associated human-to-human transmission between both cases took place.

CONCLUSIONS: Our findings have implications for managing patients with suspected psittacosis. stringent protective measures are needed to prevent healthcare-associated human-to-human transmission of C. psittaci.}, } @article {pmid37159830, year = {2023}, author = {Grenier, V and Gonzalez, E and Brereton, NJ and Pitre, FE}, title = {Dynamics of bacterial and archaeal communities during horse bedding and green waste composting.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15239}, pmid = {37159830}, issn = {2167-8359}, mesh = {Horses ; Animals ; *Archaea/genetics ; *Composting ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Bedding and Linens ; }, abstract = {Organic waste decomposition can make up substantial amounts of municipal greenhouse emissions during decomposition. Composting has the potential to reduce these emissions as well as generate sustainable fertilizer. However, our understanding of how complex microbial communities change to drive the chemical and biological processes of composting is still limited. To investigate the microbiota associated with organic waste decomposition, initial composting feedstock (Litter), three composting windrows of 1.5 months (Young phase), 3 months (Middle phase) and 12 months (Aged phase) old, and 24-month-old mature Compost were sampled to assess physicochemical properties, plant cell wall composition and the microbial community using 16S rRNA gene amplification. A total of 2,612 Exact Sequence Variants (ESVs) included 517 annotated as putative species and 694 as genera which together captured 57.7% of the 3,133,873 sequences, with the most abundant species being Thermobifida fusca, Thermomonospora chromogena and Thermobifida bifida. Compost properties changed rapidly over time alongside the diversity of the compost community, which increased as composting progressed, and multivariate analysis indicated significant variation in community composition between each time-point. The abundance of bacteria in the feedstock is strongly correlated with the presence of organic matter and the abundance of plant cell wall components. Temperature and pH are the most strongly correlated parameters with bacterial abundance in the thermophilic and cooling phases/mature compost respectively. Differential abundance analysis revealed 810 ESVs annotated as species significantly varied in relative abundance between Litter and Young phase, 653 between the Young and Middle phases, 1182 between Middle and Aged phases and 663 between Aged phase and mature Compost. These changes indicated that structural carbohydrates and lignin degrading species were abundant at the beginning of the thermophilic phase, especially members of the Firmicute and Actinobacteria phyla. A high diversity of species capable of putative ammonification and denitrification were consistently found throughout the composting phases, whereas a limited number of nitrifying bacteria were identified and were significantly enriched within the later mesophilic composting phases. High microbial community resolution also revealed unexpected species which could be beneficial for agricultural soils enriched with mature compost or for the deployment of environmental and plant biotechnologies. Understanding the dynamics of these microbial communities could lead to improved waste management strategies and the development of input-specific composting protocols to optimize carbon and nitrogen transformation and promote a diverse and functional microflora in mature compost.}, } @article {pmid37159695, year = {2023}, author = {Zhou, L and Lu, X and Zhao, C and Zhang, Y and Ning, S and Zhang, W}, title = {Characterization of a novel picornavirus prevalent in experimental rabbits (Oryctolagus cuniculus).}, journal = {Heliyon}, volume = {9}, number = {5}, pages = {e15702}, pmid = {37159695}, issn = {2405-8440}, abstract = {Here, using viral metagenomic method a novel picornavirus (named UJS-2019picorna, GenBank accession number OP821762) was discovered in fecal and blood samples of experimental rabbits (Oryctolagus cuniculus). The complete genome size of UJS-2019picorna is 7832 bp excluding the poly(A)-tail, with GC content of 44.00% and a nucleotide composition of 28.0% A, 28.0% U, 21.5% G, and 22.5% C. The viral genome has a typical picornavirus organization pattern from the 5'-3' direction: VPg-5' UTR-(L)-P1, (VP4-VP2-VP3-VP1)-P2, (2 A-2B-2C)-P3, (3 A-3B-3C-3D)-3' UTR-poly(A). The P1 region of UJS-2019picorna is related to Erbovirus with amino acid identity of 37.31%, while the P2 and P3 regions are the closest to Bopivirus with amino acid identity of 35.66%-39.53%. According to the Picornaviridae Study Group guidelines, UJS-2019picorna should be presumed to be a new genus belonging to the Picornaviridae family. Epidemiologic study revealed that this novel picornavirus was prevalent in a cohort of experimental rabbits, with prevalence rate of 23.68% (9/38) in feces and 18.4% (7/38) in blood samples. Further work is required to elucidate whether this virus is pathogenic to rabbits and whether it has influence on studies using rabbits as experimental animal.}, } @article {pmid37159524, year = {2023}, author = {Arnoriaga-Rodríguez, M and Leal, Y and Mayneris-Perxachs, J and Pérez-Brocal, V and Moya, A and Ricart, W and Fernández-Balsells, M and Fernández-Real, JM}, title = {Gut Microbiota Composition and Functionality Are Associated With REM Sleep Duration and Continuous Glucose Levels.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {108}, number = {11}, pages = {2931-2939}, doi = {10.1210/clinem/dgad258}, pmid = {37159524}, issn = {1945-7197}, mesh = {Humans ; Middle Aged ; Blood Glucose/metabolism ; Blood Glucose Self-Monitoring ; Case-Control Studies ; Cross-Sectional Studies ; *Gastrointestinal Microbiome ; Glucose ; Obesity ; Prospective Studies ; Sleep Duration ; *Sleep, REM ; Adult ; }, abstract = {CONTEXT: Sleep disruption is associated with worse glucose metabolic control and altered gut microbiota in animal models.

OBJECTIVE: We aimed to evaluate the possible links among rapid eye movement (REM) sleep duration, continuous glucose levels, and gut microbiota composition.

METHODS: This observational, prospective, real-life, cross-sectional case-control study included 118 (60 with obesity), middle-aged (39.1-54.8 years) healthy volunteers recruited at a tertiary hospital. Glucose variability and REM sleep duration were assessed by 10-day continuous glucose monitoring (CGM) (Dexcom G6) and wrist actigraphy (Fitbit Charge 3), respectively. The coefficient of variation (CV), interquartile range (IQR), and SD of glucose variability was assessed and the percentage of time in range (% TIR), at 126-139 mg/dL (TIR2), and 140-199 mg/dL (TIR3) were calculated. Shotgun metagenomics sequencing was applied to study gut microbiota taxonomy and functionality.

RESULTS: Increased glycemic variability (SD, CV, and IQR) was observed among subjects with obesity in parallel to increased % TIR2 and % TIR3. REM sleep duration was independently associated with % TIR3 (β = -.339; P < .001) and glucose variability (SD, β = -.350; P < .001). Microbial taxa from the Christensenellaceae family (Firmicutes phylum) were positively associated with REM sleep and negatively with CGM levels, while bacteria from Enterobacteriacea family and bacterial functions involved in iron metabolism showed opposite associations.

CONCLUSION: Decreased REM sleep duration was independently associated with a worse glucose profile. The associations of species from Christensenellaceae and Enterobacteriaceae families with REM sleep duration and continuous glucose values suggest an integrated picture of metabolic health.}, } @article {pmid37158970, year = {2023}, author = {Hu, J and Chen, J and Xu, X and Hou, Q and Ren, J and Yan, X}, title = {Gut microbiota-derived 3-phenylpropionic acid promotes intestinal epithelial barrier function via AhR signaling.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {102}, pmid = {37158970}, issn = {2049-2618}, mesh = {Animals ; Mice ; Swine ; *Gastrointestinal Microbiome ; Receptors, Aryl Hydrocarbon/genetics ; DNA, Ribosomal ; Fecal Microbiota Transplantation ; }, abstract = {BACKGROUND: The intestinal epithelial barrier confers protection against the intestinal invasion by pathogens and exposure to food antigens and toxins. Growing studies have linked the gut microbiota to the intestinal epithelial barrier function. The mining of the gut microbes that facilitate the function of intestinal epithelial barrier is urgently needed.

RESULTS: Here, we studied a landscape of the gut microbiome of seven pig breeds using metagenomics and 16S rDNA gene amplicon sequencing. The results indicated an obvious difference in the gut microbiome between Congjiang miniature (CM) pigs (a native Chinese breed) and commercial Duroc × [Landrace × Yorkshire] (DLY) pigs. CM finishing pigs had stronger intestinal epithelial barrier function than the DLY finishing pigs. Fecal microbiota transplantation from CM and DLY finishing pigs to germ-free (GF) mice transferred the intestinal epithelial barrier characteristics. By comparing the gut microbiome of the recipient GF mice, we identified and validated Bacteroides fragilis as a microbial species that contributes to the intestinal epithelial barrier. B. fragilis-derived 3-phenylpropionic acid metabolite had an important function on the enhancement of intestinal epithelial barrier. Furthermore, 3-phenylpropionic acid facilitated the intestinal epithelial barrier by activating aryl hydrocarbon receptor (AhR) signaling.

CONCLUSIONS: These findings suggest that manipulation of B. fragilis and 3-phenylpropionic acid is a promising strategy for improving intestinal epithelial barrier. Video Abstract.}, } @article {pmid37158954, year = {2023}, author = {Ettinger, CL and Saunders, M and Selbmann, L and Delgado-Baquerizo, M and Donati, C and Albanese, D and Roux, S and Tringe, S and Pennacchio, C and Del Rio, TG and Stajich, JE and Coleine, C}, title = {Highly diverse and unknown viruses may enhance Antarctic endoliths' adaptability.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {103}, pmid = {37158954}, issn = {2049-2618}, mesh = {Antarctic Regions ; *Acclimatization ; Bicycling ; Climate ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Rock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, and further still, viruses in these communities have been largely unexplored despite important roles related to host metabolism and nutrient cycling. To begin to address this, we present a large-scale viral catalog from Antarctic rock microbial communities.

RESULTS: We performed metagenomic analyses on rocks from across Antarctica representing a broad range of environmental and spatial conditions, and which resulted in a predicted viral catalog comprising > 75,000 viral operational taxonomic units (vOTUS). We found largely undescribed, highly diverse and spatially structured virus communities which had predicted auxiliary metabolic genes (AMGs) with functions indicating that they may be potentially influencing bacterial adaptation and biogeochemistry.

CONCLUSION: This catalog lays the foundation for expanding knowledge of virosphere diversity, function, spatial ecology, and dynamics in extreme environments. This work serves as a step towards exploring adaptability of microbial communities in the face of a changing climate. Video Abstract.}, } @article {pmid37158846, year = {2023}, author = {Guo, X and Zhang, X and Qin, Y and Liu, H and Wang, X}, title = {Endocarditis due to Aggregatibacter Segnis: a rare case report.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {309}, pmid = {37158846}, issn = {1471-2334}, support = {82001685//National Natural Science Foundation of China/ ; }, mesh = {Male ; Humans ; Adult ; Aggregatibacter segnis ; Delayed Diagnosis ; *Endocarditis ; *Endocarditis, Bacterial/diagnosis/drug therapy ; *Heart Failure ; Fever ; }, abstract = {BACKGROUND: As a member of the HACEK group, Aggregatibacter segnis (A. segnis) is a fastidious Gram-negative coccobacillus that resides in the human oropharyngeal flora. Infective endocarditis caused by A. segnis is rarely reported.

CASE PRESENTATION: A 31-year-old male was admitted to our hospital for a 3-month history of intermittent high fever, chills, and chest distress. On presentation, he was febrile and tachycardic but otherwise with stable vital signs. Physical examination revealed systolic murmurs in the aortic and mitral valve areas. Pitting edema was evident in the lower extremities. Transthoracic echocardiography demonstrated multiple vegetations in the mitral and aortic valves. Severe regurgitation of the aortic valve and left heart dysfunction were also detected. With the suspicion of infective endocarditis and heart failure, we immediately performed microbiological tests and arranged the cardiac replacement surgery. Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry and metagenomic next-generation sequencing (mNGS) identified A. segnis from the bloodstream. While the surgical specimen culture was negative, the mNGS was positive for A. segnis. The patient was treated with ceftriaxone for four weeks and discharged. He remained clinically well, with laboratory results restored.

CONCLUSION: This is the first report of A. segnis infective endocarditis that combined MALDI-TOF and metagenomic next-generation sequencing in the diagnosis. The hypothesis-independent molecular techniques can outperform conventional tools to prevent diagnostic delay.}, } @article {pmid37157914, year = {2023}, author = {Whitehouse, LS and Schrider, DR}, title = {Timesweeper: accurately identifying selective sweeps using population genomic time series.}, journal = {Genetics}, volume = {224}, number = {3}, pages = {}, pmid = {37157914}, issn = {1943-2631}, support = {R01 AI153523/AI/NIAID NIH HHS/United States ; R35GM138286/GF/NIH HHS/United States ; }, mesh = {*Metagenomics ; Time Factors ; *Genetics, Population ; Polymorphism, Genetic ; Selection, Genetic ; }, abstract = {Despite decades of research, identifying selective sweeps, the genomic footprints of positive selection, remains a core problem in population genetics. Of the myriad methods that have been developed to tackle this task, few are designed to leverage the potential of genomic time-series data. This is because in most population genetic studies of natural populations, only a single period of time can be sampled. Recent advancements in sequencing technology, including improvements in extracting and sequencing ancient DNA, have made repeated samplings of a population possible, allowing for more direct analysis of recent evolutionary dynamics. Serial sampling of organisms with shorter generation times has also become more feasible due to improvements in the cost and throughput of sequencing. With these advances in mind, here we present Timesweeper, a fast and accurate convolutional neural network-based tool for identifying selective sweeps in data consisting of multiple genomic samplings of a population over time. Timesweeper analyzes population genomic time-series data by first simulating training data under a demographic model appropriate for the data of interest, training a one-dimensional convolutional neural network on said simulations, and inferring which polymorphisms in this serialized data set were the direct target of a completed or ongoing selective sweep. We show that Timesweeper is accurate under multiple simulated demographic and sampling scenarios, identifies selected variants with high resolution, and estimates selection coefficients more accurately than existing methods. In sum, we show that more accurate inferences about natural selection are possible when genomic time-series data are available; such data will continue to proliferate in coming years due to both the sequencing of ancient samples and repeated samplings of extant populations with faster generation times, as well as experimentally evolved populations where time-series data are often generated. Methodological advances such as Timesweeper thus have the potential to help resolve the controversy over the role of positive selection in the genome. We provide Timesweeper as a Python package for use by the community.}, } @article {pmid37157891, year = {2023}, author = {Zhang, R and Debeljak, P and Blain, S and Obernosterer, I}, title = {Seasonal shifts in Fe-acquisition strategies in Southern Ocean microbial communities revealed by metagenomics and autonomous sampling.}, journal = {Environmental microbiology}, volume = {25}, number = {10}, pages = {1816-1829}, doi = {10.1111/1462-2920.16397}, pmid = {37157891}, issn = {1462-2920}, mesh = {Seasons ; *Phytoplankton/genetics ; Carbon/analysis ; *Microbiota ; Oceans and Seas ; Seawater/chemistry ; }, abstract = {Iron (Fe) governs the cycling of organic carbon in large parts of the Southern Ocean. The strategies of diverse microbes to acquire the different chemical forms of Fe under seasonally changing organic carbon regimes remain, however, poorly understood. Here, we report high-resolution seasonal metagenomic observations from the region off Kerguelen Island (Indian Sector of the Southern Ocean) where natural Fe-fertilization induces consecutive spring and summer phytoplankton blooms. Our data illustrate pronounced, but distinct seasonal patterns in the abundance of genes implicated in the transport of different forms of Fe and organic substrates, of siderophore biosynthesis and carbohydrate-active enzymes. The seasonal dynamics suggest a temporal decoupling in the prokaryotic requirements of Fe and organic carbon during the spring phytoplankton bloom and a concerted access to these resources after the summer bloom. Taxonomic assignments revealed differences in the prokaryotic groups harbouring genes of a given Fe-related category and pronounced seasonal successions were observed. Using MAGs we could decipher the respective Fe- and organic substrate-related genes of individual taxa assigned to abundant groups. The ecological strategies related to Fe-acquisition provide insights on how this element could shape microbial community composition with potential implications on organic matter transformations in the Southern Ocean.}, } @article {pmid37157031, year = {2023}, author = {Tian, J and Li, C and Dong, Z and Yang, Y and Xing, J and Yu, P and Xin, Y and Xu, F and Wang, L and Mu, Y and Guo, X and Sun, Q and Zhao, G and Gu, Y and Qin, G and Jiang, W}, title = {Inactivation of the antidiabetic drug acarbose by human intestinal microbial-mediated degradation.}, journal = {Nature metabolism}, volume = {5}, number = {5}, pages = {896-909}, pmid = {37157031}, issn = {2522-5812}, mesh = {*Hypoglycemic Agents/metabolism ; Humans ; *Gastrointestinal Microbiome ; *Acarbose/metabolism ; Klebsiella/genetics/metabolism ; Glycoside Hydrolase Inhibitors/metabolism ; Drug Resistance ; Diabetes Mellitus, Type 2/drug therapy ; Male ; Female ; Middle Aged ; Animals ; Mice ; Mice, Inbred C57BL ; RNA-Seq ; Adolescent ; Young Adult ; Adult ; Aged ; Aged, 80 and over ; }, abstract = {Drugs can be modified or degraded by the gut microbiota, which needs to be considered in personalized therapy. The clinical efficacy of the antidiabetic drug acarbose, an inhibitor of α-glucosidase, varies greatly among individuals for reasons that are largely unknown. Here we identify in the human gut acarbose-degrading bacteria, termed Klebsiella grimontii TD1, whose presence is associated with acarbose resistance in patients. Metagenomic analyses reveal that the abundance of K. grimontii TD1 is higher in patients with a weak response to acarbose and increases over time with acarbose treatment. In male diabetic mice, co-administration of K. grimontii TD1 reduces the hypoglycaemic effect of acarbose. Using induced transcriptome and protein profiling, we further identify an acarbose preferred glucosidase, Apg, in K. grimontii TD1, which can degrade acarbose into small molecules with loss of inhibitor function and is widely distributed in human intestinal microorganisms, especially in Klebsiella. Our results suggest that a comparatively large group of individuals could be at risk of acarbose resistance due to its degradation by intestinal bacteria, which may represent a clinically relevant example of non-antibiotic drug resistance.}, } @article {pmid37157029, year = {2023}, author = {Yoshiba, S and Nakagawa, H and Kuwata, H and Nabuchi, A and Yaso, A and Shirota, T}, title = {Metagenomic analysis of oral plaques and aortic valve tissues reveals oral bacteria associated with aortic stenosis.}, journal = {Clinical oral investigations}, volume = {27}, number = {8}, pages = {4335-4344}, pmid = {37157029}, issn = {1436-3771}, mesh = {Humans ; Aortic Valve/microbiology ; Bacteria/genetics ; Mouth/microbiology ; *Aortic Valve Stenosis/microbiology ; *Microbiota ; }, abstract = {OBJECTIVES: Bacteria derived from the oral cavity enter the bloodstream and cause the onset of various systemic diseases, including heart valve disease. However, information on the oral bacteria involved in aortic stenosis is limited.

MATERIALS AND METHODS: We comprehensively analyzed the microbiota in aortic valve tissues collected from aortic stenosis patients using metagenomic sequencing and investigated the relationships between the valve microbiota, the oral microbiota, and oral cavity conditions.

RESULTS: Metagenomic analysis revealed the presence of 629 bacterial species in five oral plaques and 15 aortic valve clinical specimens. Patients were classified into two groups (A and B) according to their aortic valve microbiota composition using principal coordinate analysis. Examination of the oral conditions of the patients showed no difference in the decayed/missing/filled teeth index. Bacteria in group B tend to be associated with severe disease, and the number of bacteria on the dorsum of the tongue and the positive rate of bleeding during probing were significantly higher in this group than in group A. The pathophysiology of aortic stenosis may be related to the presence of oral bacteria such as Streptococcus oralis and Streptococcus sanguinis following bacteremia.

CONCLUSIONS: Systemic inflammation in severe periodontitis may be driven by the oral microbiota, supporting the indirect (inflammatory) association between oral bacteria and aortic stenosis.

CLINICAL RELEVANCE: Appropriate oral hygiene management may contribute to the prevention and treatment of aortic stenosis.}, } @article {pmid37156688, year = {2023}, author = {Polo, TCF and Lai, MRR and Miot, LDB and Bento, GFC and Silva, MGD and Marques, SA and Miot, HA}, title = {Intestinal microbiome characterization of adult Brazilian men with psoriasis compared to omnivore and vegetarian controls.}, journal = {Anais brasileiros de dermatologia}, volume = {98}, number = {5}, pages = {635-643}, pmid = {37156688}, issn = {1806-4841}, mesh = {Male ; Humans ; Adult ; Diet ; Diet, Vegetarian ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Brazil ; Vegetarians ; Dietary Fiber ; *Psoriasis ; }, abstract = {BACKGROUND: Psoriasis is a chronic inflammatory disease associated with systemic inflammation and comorbidities. Changes in the composition of the intestinal microbiome are involved in the pathogenesis of inflammatory diseases and metabolic syndrome. Characterizing the intestinal microbiome of patients with psoriasis may be relevant for the understanding of its clinical course and comorbidity prevention.

OBJECTIVE: To characterize the intestinal microbiome of men with psoriasis compared to omnivore and vegetarian controls (without psoriasis).

METHOD: Cross-sectional study of 42 adult males: 21 omnivores with psoriasis; and controls: 14 omnivores and 7 vegetarian individuals. The characterization of the intestinal microbiome was performed by metagenomic analysis. Serum levels of lipopolysaccharide-binding protein (LPB) and C-reactive protein (CRP) were evaluated.

RESULTS: The groups differed from each other regarding nutritional aspects and microbiome; individuals with psoriasis had a higher consumption of protein and lower consumption of fibers. Levels of LPB, CRP, and the Firmicutes/Bacteroidetes ratio were higher in the group with psoriasis than in the vegetarian group (p<0.05). The genera Prevotella, Mogibacterium, Dorea, Bifidobacterium and Coprococcus, differed in the group with psoriasis compared to vegetarians; the genera Mogibacterium, Collinsella and Desulfovibrio differed from omnivores. A microbiome pattern linked to psoriasis (plsPSO) was identified, which was associated with higher LPB levels (rho=0.39; p=0.02), and lower dietary fiber intake (rho=-0.71; p<0.01).

STUDY LIMITATIONS: Only adult men were evaluated.

CONCLUSION: A difference was identified in the intestinal microbiome of adult men with psoriasis when compared to healthy omnivores and vegetarian controls. The identified microbiome pattern was correlated with dietary fiber intake and serum levels of LPB.}, } @article {pmid37155986, year = {2023}, author = {Guzauskas, GF and Garbett, S and Zhou, Z and Schildcrout, JS and Graves, JA and Williams, MS and Hao, J and Jones, LK and Spencer, SJ and Jiang, S and Veenstra, DL and Peterson, JF}, title = {Population Genomic Screening for Three Common Hereditary Conditions : A Cost-Effectiveness Analysis.}, journal = {Annals of internal medicine}, volume = {176}, number = {5}, pages = {585-595}, doi = {10.7326/M22-0846}, pmid = {37155986}, issn = {1539-3704}, support = {R01 HG012262/HG/NHGRI NIH HHS/United States ; }, mesh = {Adult ; Humans ; Young Adult ; Middle Aged ; Cost-Effectiveness Analysis ; Cost-Benefit Analysis ; Metagenomics ; *Hyperlipoproteinemia Type II ; *Cardiovascular Diseases ; Quality-Adjusted Life Years ; Mass Screening ; }, abstract = {BACKGROUND: The cost-effectiveness of screening the U.S. population for Centers for Disease Control and Prevention (CDC) Tier 1 genomic conditions is unknown.

OBJECTIVE: To estimate the cost-effectiveness of simultaneous genomic screening for Lynch syndrome (LS), hereditary breast and ovarian cancer syndrome (HBOC), and familial hypercholesterolemia (FH).

DESIGN: Decision analytic Markov model.

DATA SOURCES: Published literature.

TARGET POPULATION: Separate age-based cohorts (ages 20 to 60 years at time of screening) of racially and ethnically representative U.S. adults.

TIME HORIZON: Lifetime.

PERSPECTIVE: U.S. health care payer.

INTERVENTION: Population genomic screening using clinical sequencing with a restricted panel of high-evidence genes, cascade testing of first-degree relatives, and recommended preventive interventions for identified probands.

OUTCOME MEASURES: Incident breast, ovarian, and colorectal cancer cases; incident cardiovascular events; quality-adjusted survival; and costs.

RESULTS OF BASE-CASE ANALYSIS: Screening 100 000 unselected 30-year-olds resulted in 101 (95% uncertainty interval [UI], 77 to 127) fewer overall cancer cases and 15 (95% UI, 4 to 28) fewer cardiovascular events and an increase of 495 quality-adjusted life-years (QALYs) (95% UI, 401 to 757) at an incremental cost of $33.9 million (95% UI, $27.0 million to $41.1 million). The incremental cost-effectiveness ratio was $68 600 per QALY gained (95% UI, $41 800 to $88 900).

Screening 30-, 40-, and 50-year-old cohorts was cost-effective in 99%, 88%, and 19% of probabilistic simulations, respectively, at a $100 000-per-QALY threshold. The test costs at which screening 30-, 40-, and 50-year-olds reached the $100 000-per-QALY threshold were $413, $290, and $166, respectively. Variant prevalence and adherence to preventive interventions were also highly influential parameters.

LIMITATIONS: Population averages for model inputs, which were derived predominantly from European populations, vary across ancestries and health care environments.

CONCLUSION: Population genomic screening with a restricted panel of high-evidence genes associated with 3 CDC Tier 1 conditions is likely to be cost-effective in U.S. adults younger than 40 years if the testing cost is relatively low and probands have access to preventive interventions.

PRIMARY FUNDING SOURCE: National Human Genome Research Institute.}, } @article {pmid37155985, year = {2023}, author = {}, title = {Summary for Patients: Population Genomic Screening for Three Common Hereditary Conditions.}, journal = {Annals of internal medicine}, volume = {176}, number = {5}, pages = {I19}, doi = {10.7326/P23-0002}, pmid = {37155985}, issn = {1539-3704}, mesh = {Humans ; *Metagenomics ; *Genetic Testing ; }, } @article {pmid37155936, year = {2023}, author = {Peng, Y and Jin, M and Li, Z and Li, H and Zhang, L and Yu, S and Zhang, Z and Fan, R and Liu, J and Xu, Q and Wilson, K and Xiao, Y}, title = {Population Genomics Provide Insights into the Evolution and Adaptation of the Asia Corn Borer.}, journal = {Molecular biology and evolution}, volume = {40}, number = {5}, pages = {}, pmid = {37155936}, issn = {1537-1719}, mesh = {Animals ; *Zea mays/genetics ; Metagenomics ; Biodiversity ; Temperature ; *Moths/genetics ; Asia ; }, abstract = {Understanding the genetic basis of pest adaptive evolution and the risk of adaptation in response to climate change is essential for the development of sustainable agricultural practices. However, the genetic basis of climatic adaptation for the Asian corn borer (ACB), Ostrinia furnacalis, the main pest of corn in Asia and Oceania, is poorly understood. Here, we revealed the genomic loci underlying the climatic adaptation and evolution in ACB by integrating population genomic and environmental factors. We assembled a 471-Mb chromosome-scale reference genome of ACB and resequenced 423 individuals covering 27 representative geographic areas. We inferred that the ACB effective population size changes tracked with the global temperature and followed by a recent decline. Based on an integrated analysis of whole-genome selection scans and genome-wide genotype-environment association studies, we revealed the genetic basis of ACB adaption to diverse climates. For diapause traits, we identified a major effect association locus containing a circadian clock gene (period) by analyzing a diapause-segregating population. Moreover, our predictions indicated that the northern populations were more ecologically resilient to climate change than the southern populations. Together, our results revealed the genomic basis for ACB environmental adaptation and provided potential candidate genes for future evolutionary studies and genetic adaptation to climate change, intending to maintain the efficacy and sustainability of novel control techniques.}, } @article {pmid37155494, year = {2023}, author = {Gomez-Alvarez, V and Siponen, S and Kauppinen, A and Hokajärvi, AM and Tiwari, A and Sarekoski, A and Miettinen, IT and Torvinen, E and Pitkänen, T}, title = {A comparative analysis employing a gene- and genome-centric metagenomic approach reveals changes in composition, function, and activity in waterworks with different treatment processes and source water in Finland.}, journal = {Water research}, volume = {229}, number = {}, pages = {119495}, pmid = {37155494}, issn = {1879-2448}, support = {EPA999999/ImEPA/Intramural EPA/United States ; }, mesh = {Metagenome ; *Drinking Water/microbiology ; Finland ; Bacteria/metabolism ; *Microbiota/genetics ; Archaea/genetics ; *Disinfectants ; Metagenomics ; }, abstract = {The emergence and development of next-generation sequencing technologies (NGS) has made the analysis of the water microbiome in drinking water distribution systems (DWDSs) more accessible and opened new perspectives in microbial ecology studies. The current study focused on the characterization of the water microbiome employing a gene- and genome-centric metagenomic approach to five waterworks in Finland with different raw water sources, treatment methods, and disinfectant. The microbial communities exhibit a distribution pattern of a few dominant taxa and a large representation of low-abundance bacterial species. Changes in the community structure may correspond to the presence or absence and type of disinfectant residual which indicates that these conditions exert selective pressure on the microbial community. The Archaea domain represented a small fraction (up to 2.5%) and seemed to be effectively controlled by the disinfection of water. Their role particularly in non-disinfected DWDS may be more important than previously considered. In general, non-disinfected DWDSs harbor higher microbial richness and maintaining disinfectant residual is significantly important for ensuring low microbial numbers and diversity. Metagenomic binning recovered 139 (138 bacterial and 1 archaeal) metagenome-assembled genomes (MAGs) that had a >50% completeness and <10% contamination consisting of 20 class representatives in 12 phyla. The presence and occurrence of nitrite-oxidizing bacteria (NOB)-like microorganisms have significant implications for nitrogen biotransformation in drinking water systems. The metabolic and functional complexity of the microbiome is evident in DWDSs ecosystems. A comparative analysis found a set of differentially abundant taxonomic groups and functional traits in the active community. The broader set of transcribed genes may indicate an active and diverse community regardless of the treatment methods applied to water. The results indicate a highly dynamic and diverse microbial community and confirm that every DWDS is unique, and the community reflects the selection pressures exerted at the community structure, but also at the levels of functional properties and metabolic potential.}, } @article {pmid37154701, year = {2023}, author = {Zhou, B and Li, H}, title = {STEMSIM: a simulator of within-strain short-term evolutionary mutations for longitudinal metagenomic data.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {5}, pages = {}, pmid = {37154701}, issn = {1367-4811}, support = {R01 LM014085/LM/NLM NIH HHS/United States ; 1R01LM014085/LM/NLM NIH HHS/United States ; P20CA252728/CA/NCI NIH HHS/United States ; }, mesh = {*Software ; *Metagenome ; Metagenomics ; Computer Simulation ; Mutation ; }, abstract = {MOTIVATION: As the resolution of metagenomic analysis increases, the evolution of microbial genomes in longitudinal metagenomic data has become a research focus. Some software has been developed for the simulation of complex microbial communities at the strain level. However, the tool for simulating within-strain evolutionary signals in longitudinal samples is still lacking.

RESULTS: In this study, we introduce STEMSIM, a user-friendly command-line simulator of short-term evolutionary mutations for longitudinal metagenomic data. The input is simulated longitudinal raw sequencing reads of microbial communities or single species. The output is the modified reads with within-strain evolutionary mutations and the relevant information of these mutations. STEMSIM will be of great use for the evaluation of analytic tools that detect short-term evolutionary mutations in metagenomic data.

STEMSIM and its tutorial are freely available online at https://github.com/BoyanZhou/STEMSim.}, } @article {pmid37154102, year = {2023}, author = {Sinha, A and Li, Z and Poole, CB and Ettwiller, L and Lima, NF and Ferreira, MU and Fombad, FF and Wanji, S and Carlow, CKS}, title = {Multiple lineages of nematode-Wolbachia symbiosis in supergroup F and convergent loss of bacterioferritin in filarial Wolbachia.}, journal = {Genome biology and evolution}, volume = {15}, number = {5}, pages = {}, pmid = {37154102}, issn = {1759-6653}, abstract = {The intracellular endosymbiotic proteobacteria Wolbachia have evolved across the phyla nematoda and arthropoda. In Wolbachia phylogeny, supergroup F is the only clade known so far with members from both arthropod and filarial nematode hosts and therefore can provide unique insights into their evolution and biology. In this study, 4 new supergroup F Wolbachia genomes have been assembled using a metagenomic assembly and binning approach, wMoz and wMpe from the human filarial parasites Mansonella ozzardi and Mansonella perstans, and wOcae and wMoviF from the blue mason bee Osmia caerulescens and the sheep ked Melophagus ovinus respectively. A comprehensive phylogenomic analysis revealed two distinct lineages of filarial Wolbachia in supergroup F, indicating multiple horizontal transfer events between arthropod and nematode hosts. The analysis also reveals that the evolution of Wolbachia-filaria symbioses is accompanied by a convergent pseudogenization and loss of the bacterioferritin gene, a phenomenon found to be shared by all filarial Wolbachia, even those outside supergroup F. These observations indicate that differences in heme metabolism might be a key feature distinguishing filarial and arthropod Wolbachia. The new genomes provide a valuable resource for further studies on symbiosis, evolution, and the discovery of new antibiotics to treat mansonellosis.}, } @article {pmid37153144, year = {2023}, author = {Wang, YL and Guo, XT and Zhu, MY and Mao, YC and Xu, XB and Hua, Y and Xu, L and Jiang, LH and Zhao, CY and Zhang, X and Sheng, GX and Jiang, PF and Yuan, ZF and Gao, F}, title = {Metagenomic next-generation sequencing and proteomics analysis in pediatric viral encephalitis and meningitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1104858}, pmid = {37153144}, issn = {2235-2988}, mesh = {Humans ; Child ; Proteomics ; *Encephalitis, Viral/diagnosis ; *Viruses/genetics ; *Meningitis, Viral/diagnosis ; *Enterovirus/genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {INTRODUCTION: Early and accurate identification of pathogens is essential for improved outcomes in patients with viral encephalitis (VE) and/or viral meningitis (VM).

METHODS: In our research, Metagenomic next-generation sequencing (mNGS) which can identify viral pathogens unbiasedly was performed on RNA and DNA to identify potential pathogens in cerebrospinal fluid (CSF) samples from 50 pediatric patients with suspected VEs and/or VMs. Then we performed proteomics analysis on the 14 HEV-positive CSF samples and another 12 CSF samples from health controls (HCs). A supervised partial least squaresdiscriminant analysis (PLS-DA) and orthogonal PLS-DA (O-PLS-DA) model was performed using proteomics data.

RESULTS: Ten viruses in 48% patients were identified and the most common pathogen was human enterovirus (HEV) Echo18. 11 proteins overlapping between the top 20 DEPs in terms of P value and FC and the top 20 proteins in PLS-DA VIP lists were acquired.

DISCUSSION: Our result showed mNGS has certain advantages on pathogens identification in VE and VM and our research established a foundation to identify diagnosis biomarker candidates of HEV-positive meningitis based on MS-based proteomics analysis, which could also contribute toward investigating the HEV-specific host response patterns.}, } @article {pmid37152987, year = {2023}, author = {Becerra, CY and Wells, RK and Kunihiro, BP and Lee, RH and Umeda, L and Allan, NP and Rubas, NC and McCracken, TA and Nunokawa, CKL and Lee, MH and Pidlaoan, FGS and Phankitnirondorn, K and Dye, CK and Yamamoto, BY and Peres, R and Juarez, R and Maunakea, AK}, title = {Examining the immunoepigenetic-gut microbiome axis in the context of self-esteem among Native Hawaiians and other Pacific Islanders.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1125217}, pmid = {37152987}, issn = {1664-8021}, support = {R01 MD016593/MD/NIMHD NIH HHS/United States ; R56 MD014630/MD/NIMHD NIH HHS/United States ; }, abstract = {Introduction: Native Hawaiian and other Pacific Islander (NHPI) populations experience higher rates of immunometabolic diseases compared to other racial-ethnic groups in Hawaii. As annual NHPI mortality rates for suicide and type 2 diabetes mellitus (T2DM) exceed those of the state as a whole, understanding the social and biological mechanisms underlying these disparities are urgently needed to enable preventive strategies. Methods: A community-based approach was used to investigate the immunoepigenetic-gut microbiome axis in an NHPI-enriched cohort of Oahu residents (N = 68). Self-esteem (SE) data was collected using a modified Rosenberg self-esteem (SE) assessment as a proxy measure for mental wellbeing in consideration for cultural competency. T2DM status was evaluated using point-of-care A1c (%) tests. Stool samples were collected for 16s-based metagenomic sequencing analyses. Plasma from blood samples were isolated by density-gradient centrifugation. Peripheral blood mononuclear cells (PBMCs) were collected from the same samples and enriched for monocytes using negative selection techniques. Flow-cytometry was used for immunoprofiling assays. Monocyte DNA was extracted for Illumina EPIC array-based methylation analysis. Results: Compared to individuals with normal SE (NSE), those with low SE (LSE) exhibited significantly higher plasma concentrations (pg/ml) of proinflammatory cytokines IL-8 (p = 0.051) and TNF-α (p = 0.011). Metagenomic analysis revealed that the relative abundance (%) of specific gut bacteria significantly differed between SE groups - some of which directly correlated with SE scores. Gene ontology analysis revealed that 104 significantly differentially methylated loci (DML) between SE groups were preferentially located at genes involved in immunometabolic processes. Horvath clock analyses indicated epigenetic age (Epi-Age) deceleration in individuals with LSE and acceleration in individuals with NSE (p = 0.042), yet was not reproduced by other clocks. Discussion: These data reveal novel differences in the immunoepigenetic-gut microbiome axis with respect to SE, warranting further investigation into its relationship to brain activity and mental health in NHPI. Unexpected results from Epi-Age analyses warrant further investigation into the relationship between biological age and disparate health outcomes among the NHPI population. The modifiable component of epigenetic processes and the gut microbiome makes this axis an attractive target for potential therapeutics, biomarker discovery, and novel prevention strategies.}, } @article {pmid37152760, year = {2023}, author = {Jiao, X and Guo, W and Li, X and Yao, F and Zeng, M and Yuan, Y and Guo, X and Wang, M and Xie, QD and Cai, L and Yu, F and Yu, P and Xia, Y}, title = {New insight into the microbiome, resistome, and mobilome on the dental waste water in the context of heavy metal environment.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1106157}, pmid = {37152760}, issn = {1664-302X}, abstract = {OBJECT: Hospital sewage have been associated with incorporation of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) into microbes, which is considered as a key indicator for the spread of antimicrobial resistance (AMR). The compositions of dental waste water (DWW) contain heavy metals, the evolution of AMR and its effects on the water environment in the context of heavy metal environment have not been seriously investigated. Thus, our major aims were to elucidate the evolution of AMR in DWW.

METHODS: DWW samples were collected from a major dental department. The presence of microbial communities, ARGs, and MGEs in untreated and treated (by filter membrane and ozone) samples were analyzed using metagenomics and bioinformatic methods.

RESULTS: DWW-associated resistomes included 1,208 types of ARGs, belonging to 29 antibiotic types/subtypes. The most abundant types/subtypes were ARGs of multidrug resistance and of antibiotics that were frequently used in the clinical practice. Pseudomonas putida, Pseudomonas aeruginosa, Chryseobacterium indologenes, Sphingomonas laterariae were the main bacteria which hosted these ARGs. Mobilomes in DWW consisted of 93 MGE subtypes which belonged to 8 MGE types. Transposases were the most frequently detected MGEs which formed networks of communications. For example, ISCrsp1 and tnpA.5/4/11 were the main transposases located in the central hubs of a network. These significant associations between ARGs and MGEs revealed the strong potential of ARGs transmission towards development of antimicrobial-resistant (AMR) bacteria. On the other hand, treatment of DWW using membranes and ozone was only effective in removing minor species of bacteria and types of ARGs and MGEs.

CONCLUSION: DWW contained abundant ARGs, and MGEs, which contributed to the occurrence and spread of AMR bacteria. Consequently, DWW would seriously increase environmental health concerns which may be different but have been well-documented from hospital waste waters.}, } @article {pmid37152756, year = {2023}, author = {He, J and Zhang, Y and Li, H and Xie, Y and Huang, G and Peng, C and Zhao, P and Wang, Z}, title = {Hybridization alters the gut microbial and metabolic profile concurrent with modifying intestinal functions in Tunchang pigs.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1159653}, pmid = {37152756}, issn = {1664-302X}, abstract = {INTRODUCTION: Hybridization has been widely used among Chinese wild boars to improve their growth performance and maintain meat quality. Most studies have focused on the genetic basis for such variation. However, the differences in the gut environment between hybrid and purebred boars, which can have significant impacts on their health and productivity, have been poorly understood.

METHODS: In the current study, metagenomics was used to detect the gut microbial diversity and composition in hybrid Batun (BT, Berkshire × Tunchang) pigs and purebred Tunchang (TC) pigs. Additionally, untargeted metabolomic analysis was used to detect differences in gut metabolic pathways. Furthermore, multiple molecular experiments were conducted to demonstrate differences in intestinal functions.

RESULTS: As a result of hybridization in TC pigs, a microbial change was observed, especially in Prevotella and Lactobacillus. Significant differences were found in gut metabolites, including fatty acyls, steroids, and steroid derivatives. Furthermore, the function of the intestinal barrier was decreased by hybridization, while the function of nutrient metabolism was increased.

DISCUSSION: Evidences were shown that hybridization changed the gut microbiome, gut metabolome, and intestinal functions of TC pigs. These findings supported our hypothesis that hybridization altered the gut microbial composition, thereby modifying the intestinal functions, even the host phenotypes. Overall, our study highlights the importance of considering the gut microbiome as a key factor in the evaluation of animal health and productivity, particularly in the context of genetic selection and breeding programs.}, } @article {pmid37152736, year = {2023}, author = {Delbeke, H and Casteels, I and Joossens, M}, title = {DNA extraction protocol impacts ocular surface microbiome profile.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1128917}, pmid = {37152736}, issn = {1664-302X}, abstract = {PURPOSE: The aim of this study is to provide a reference frame to allow the comparison and interpretation of currently published studies on 16S ribosomal ribonucleic acid amplicon sequencing of ocular microbiome samples using different DNA extraction protocols. Alongside, the quantitative and qualitative yield and the reproducibility of different protocols has been assessed.

METHODS: Both eyes of 7 eligible volunteers were sampled. Five commercially available DNA extraction protocols were selected based on previous publications in the field of the ocular surface microbiome and 2 host DNA depletion protocols were added based on their reported effective host DNA depletion without significant reduction in bacterial DNA concentration. The V3-V4 region of the 16S rRNA gene was targeted using Illumina MiSeq sequencing. The DADA2 pipeline in R was used to perform the bio-informatic processing and taxonomical assignment was done using the SILVA v132 database. The Vegdist function was used to calculate Bray-Curtis distances and the Galaxy web application was used to identify potential metagenomic biomarkers via linear discriminant analysis Effect Size (LEfSe). The R package Decontam was applied to control for potential contaminants.

RESULTS: Samples analysed with PowerSoil, RNeasy and NucleoSpin had the highest DNA yield. The host DNA depletion kits showed a very low microbial DNA yield; and these samples were pooled per kit before sequencing. Despite pooling, 1 of both failed to construct a library.Looking at the beta-diversity, clear microbial compositional differences - dependent on the extraction protocol used - were observed and remained present after decontamination. Eighteen genera were consistently retrieved from the ocular surface of every volunteer by all non-pooled extraction kits and a comprehensive list of differentially abundant bacteria per extraction method was generated using LefSe analysis.

CONCLUSION: High-quality papers have been published in the field of the ocular surface microbiome but consensus on the importance of the extraction protocol used are lacking. Potential contaminants and discriminative genera per extraction protocol used, were introduced and a reference frame was built to facilitate both the interpretation of currently published papers and to ease future choice - making based on the research question at hand.}, } @article {pmid37152731, year = {2023}, author = {Rempfert, KR and Nothaft, DB and Kraus, EA and Asamoto, CK and Evans, RD and Spear, JR and Matter, JM and Kopf, SH and Templeton, AS}, title = {Subsurface biogeochemical cycling of nitrogen in the actively serpentinizing Samail Ophiolite, Oman.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1139633}, pmid = {37152731}, issn = {1664-302X}, abstract = {Nitrogen (N) is an essential element for life. N compounds such as ammonium (NH 4 +) may act as electron donors, while nitrate (NO 3 -) and nitrite (NO 2 -) may serve as electron acceptors to support energy metabolism. However, little is known regarding the availability and forms of N in subsurface ecosystems, particularly in serpentinite-hosted settings where hydrogen (H2) generated through water-rock reactions promotes habitable conditions for microbial life. Here, we analyzed N and oxygen (O) isotope composition to investigate the source, abundance, and cycling of N species within the Samail Ophiolite of Oman. The dominant dissolved N species was dependent on the fluid type, with Mg[2+]- HCO 3 - type fluids comprised mostly of NO 3 - , and Ca[2+]-OH[-] fluids comprised primarily of ammonia (NH3). We infer that fixed N is introduced to the serpentinite aquifer as NO 3 - . High concentrations of NO 3 - (>100 μM) with a relict meteoric oxygen isotopic composition (δ[18]O ~ 22‰, Δ[17]O ~ 6‰) were observed in shallow aquifer fluids, indicative of NO 3 - sourced from atmospheric deposition (rainwater NO 3 - : δ[18]O of 53.7‰, Δ[17]O of 16.8‰) mixed with NO 3 - produced in situ through nitrification (estimated endmember δ[18]O and Δ[17]O of ~0‰). Conversely, highly reacted hyperalkaline fluids had high concentrations of NH3 (>100 μM) with little NO 3 - detectable. We interpret that NH3 in hyperalkaline fluids is a product of NO 3 - reduction. The proportionality of the O and N isotope fractionation ([18]ε / [15]ε) measured in Samail Ophiolite NO 3 - was close to unity ([18]ε / [15]ε ~ 1), which is consistent with dissimilatory NO 3 - reduction with a membrane-bound reductase (NarG); however, abiotic reduction processes may also be occurring. The presence of genes commonly involved in N reduction processes (narG, napA, nrfA) in the metagenomes of biomass sourced from aquifer fluids supports potential biological involvement in the consumption of NO 3 - . Production of NH 4 + as the end-product of NO 3 - reduction via dissimilatory nitrate reduction to ammonium (DNRA) could retain N in the subsurface and fuel nitrification in the oxygenated near surface. Elevated bioavailable N in all sampled fluids indicates that N is not likely limiting as a nutrient in serpentinites of the Samail Ophiolite.}, } @article {pmid37152122, year = {2023}, author = {Gola, U and Kour, S and Kaur, T and Perveen, K and Bukhari, NA and Alsulami, JA and Maithani, D and Dasila, H and Singh, M and Suyal, DC}, title = {Prokaryotic diversity and community structure in the rhizosphere of Lantana weed (Lantana camara L.).}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1174859}, pmid = {37152122}, issn = {1664-462X}, abstract = {Lantana weed (Lantana camara L.) is among the most noxious weeds in the world. Keeping in mind its invasive behavior and great ecological tolerance, it becomes imperative to analyze the structure and function of associated microbiome. In this perspective, Illumina-based metagenome sequencing was performed to gain a better understanding of prokaryotic diversity and community structure in the rhizosphere soil of L. camara L. The organic carbon, nitrogen, phosphorus, and potassium contents in the rhizosphere soil were 0.91% (± 0.21%); 280 Kg ha[-1] (± 4.02 Kg ha[-1]), 54.5 Kg ha[-1] (± 3.12 Kg ha[-1]), and 189 Kg ha[-1] (± 6.11 Kg ha[-1]), respectively. The metagenome analysis revealed the existence of 41 bacterial and 2 archaeal phyla, with only 12 showing ≥1% abundances. Pseudomonadota was the dominant phylum with 31.3% abundance, followed by Actinomycetota (20.9%). Further, 54 different genera were identified with the highest abundance of Devosia (2.8%). The PICRUSt analysis predicted various functional traits in the soil metagenome, with general cellular functions dominating, followed by stress tolerance. Moreover, 10% of the functions were associated with nitrogen fixation, phosphate solubilization, and potassium mobilization. In conclusion, the present study revealed the existence of diverse prokaryotic communities in the rhizosphere of the L. camara L. which was primarily associated with stress response and plant growth promotion. To the best of our knowledge, this study documents for the first time the L. camara L. microbiome. Furthermore, the identified genera can be explored for agricultural needs in future.}, } @article {pmid37150592, year = {2023}, author = {Okumura, T and Horiba, K and Tetsuka, N and Sato, Y and Sugiyama, Y and Haruta, K and Yamaguchi, M and Suzuki, T and Torii, Y and Kawada, JI and Ogi, T and Hayakawa, M and Ito, Y}, title = {Next-generation sequencing-based detection of Ureaplasma in the gastric fluid of neonates with respiratory distress and chorioamnionitis.}, journal = {The journal of maternal-fetal & neonatal medicine : the official journal of the European Association of Perinatal Medicine, the Federation of Asia and Oceania Perinatal Societies, the International Society of Perinatal Obstetricians}, volume = {36}, number = {1}, pages = {2207113}, doi = {10.1080/14767058.2023.2207113}, pmid = {37150592}, issn = {1476-4954}, mesh = {Pregnancy ; Infant, Newborn ; Female ; Humans ; *Chorioamnionitis/microbiology ; Ureaplasma/genetics ; Anti-Bacterial Agents/therapeutic use ; *Infant, Newborn, Diseases/drug therapy ; High-Throughput Nucleotide Sequencing ; *Respiratory Distress Syndrome, Newborn/diagnosis/drug therapy ; Amniotic Fluid/microbiology ; *Ureaplasma Infections/drug therapy ; }, abstract = {BACKGROUND: Respiratory distress is common in neonates admitted to neonatal intensive care units. Additionally, infectious diseases such as intrauterine infections or vertical transmission are important underlying causes of respiratory failure. However, pathogens often cannot be identified in neonates, and there are many cases in which antibacterial drugs are empirically administered. Next-generation sequencing (NGS) is advantageous in that it can detect trace amounts of bacteria that cannot be detected by culturing or bacteria that are difficult to cultivate. However, there are few reports on the diagnosis of infectious diseases using NGS in the neonatal field, especially those targeting respiratory distress.

OBJECTIVE: The purpose of our study was to investigate the microorganisms associated with neonatal respiratory distress and to determine whether less invasive collection specimens such as plasma and gastric fluid are useful.

METHODS: Neonates were prospectively recruited between January and August 2020 from Nagoya University Hospital. The inclusion criteria were as follows: 1) admission to the neonatal intensive care unit; 2) respiratory distress presentation within 48 h of birth; and 3) suspected infection, collection of blood culture, and administration of antibiotics. Plasma samples and blood cultures were simultaneously collected. Gastric fluid samples were also collected if the patient was not started on enteral nutrition. Information on the patients and their mothers were collected from the medical records. DNA was extracted from 140 µL of plasma and gastric fluid samples. DNA sequencing libraries were prepared, and their quality was analyzed. DNA libraries were sequenced using high-throughput NGS. The NGS data of plasma and gastric fluid samples were analyzed using the metagenomic pipeline PATHDET, which calculated the number of reads assigned to microorganisms and their relative abundance. Putative pathogens were listed.

RESULTS: Overall, 30 plasma samples and 25 gastric fluid samples from 30 neonates were analyzed. Microorganism-derived reads of gastric fluid samples were significantly higher than those of plasma samples. Transient tachypnea of the newborn was the most common cause of respiratory distress with 13 cases (43%), followed by respiratory distress syndrome with 7 cases (23%). There were 8 cases (29%) of chorioamnionitis and 7 cases (25%) of funisitis pathologically diagnosed. All blood cultures were negative, and only two gastric fluid cultures were positive for group B Streptococcus (Patient 15) and Candida albicans (Patient 24). Putative pathogens that met the positive criteria for PATHET were detected in four gastric fluid samples, one of which was group B Streptococcus from Patient 15. In the gastric fluid sample of Patient 24, Candida albicans were detected by NGS but did not meet the positive criteria for PATHDET. Cluster analysis of the plasma samples divided them into two study groups, and the indicator genera of each cluster (Phormidium or Toxoplasma) are shown in Figure 1. Clinical findings did not show any significant differences between the two groups. Cluster analysis of the gastric fluid samples divided them into three study groups, and the indicator genera of each cluster (Ureaplasma, Nostoc, and Streptococcus) are shown in Figure 2. The incidence rate of chorioamnionitis was significantly higher in Ureaplasma group than in the other two groups.

CONCLUSION: Gastric fluid may be useful for assessing neonatal patients with respiratory distress. To the best of our knowledge, this was the first study to reveal that the presence of Ureaplasma in the gastric fluid of neonates with respiratory distress was associated with chorioamnionitis. The early diagnosis of intra-amniotic infections using gastric fluid and its treatment may change the treatment strategy for neonatal respiratory distress. Screening for Ureaplasma in neonates with respiratory distress may reduce the need for empirical antibiotic administration. Further research is required to confirm these findings.}, } @article {pmid37150474, year = {2023}, author = {Premetis, GE and Georgakis, ND and Stathi, A and Labrou, NE}, title = {Metaviromics analysis of marine biofilm reveals a glycoside hydrolase endolysin with high specificity towards Acinetobacter baumannii.}, journal = {Biochimica et biophysica acta. Proteins and proteomics}, volume = {1871}, number = {4}, pages = {140918}, doi = {10.1016/j.bbapap.2023.140918}, pmid = {37150474}, issn = {1878-1454}, mesh = {Humans ; *Acinetobacter baumannii/genetics ; Glycoside Hydrolases/genetics ; Escherichia coli ; *Anti-Infective Agents/pharmacology ; Biofilms ; }, abstract = {Multidrug-resistant (MDR) bacteria are a growing threat to the public health. Among them, the Gram-negative Acinetobacter baumannii is considered today as the most dangerous MDR pathogen. Phage-derived endolysins are peptidoglycan (PG) hydrolytic enzymes that can function as effective tools in the fight against MDR bacteria. In the present work, the viral diversity of a marine environmental sample (biofilm), formed near an industrial zone, was mined for the identification of a putative endolysin (AbLys2) that belongs to the glycoside hydrolase family 24 (GH24, EC 3.2.1.17). The coding sequence of AbLys2 was cloned and expressed in E. coli. The lytic activity and specificity of the recombinant enzyme were evaluated against suspensions of a range of Gram-positive and Gram-negative human pathogens using turbidity assays. AbLys2 displayed enhanced selectivity towards A. baumannii cells, compared to other bacteria. Kinetics analysis was carried out to characterize the dependence of its lytic activity on pH and showed that the enzyme exhibits its maximal activity at pH 5.5. Thermostability analysis showed that AbLys2 displays melting temperature Tm 47.1 °C. Florescence microscopy and cell viability assays established that AbLys2 is active towards live cultures of A. baumannii cells with an inhibitory concentration IC50 3.41 ± 0.09 μM. Molecular modeling allowed the prediction of important amino acid residues involved in catalysis. The results of the present study suggest that AbLys2 provides efficient lytic and antimicrobial activity towards A. baumannii cells and therefore is a promising new antimicrobial against this pathogen.}, } @article {pmid37150100, year = {2023}, author = {Makryniotis, K and Nikolaivits, E and Gkountela, C and Vouyiouka, S and Topakas, E}, title = {Discovery of a polyesterase from Deinococcus maricopensis and comparison to the benchmark LCC[ICCG] suggests high potential for semi-crystalline post-consumer PET degradation.}, journal = {Journal of hazardous materials}, volume = {455}, number = {}, pages = {131574}, doi = {10.1016/j.jhazmat.2023.131574}, pmid = {37150100}, issn = {1873-3336}, mesh = {*Benchmarking ; Hydrolases/metabolism ; *Plastics ; *Polyethylene Terephthalates/chemistry ; *Environmental Pollution ; }, abstract = {Plastic pollution remains a significant environmental challenge, with conventional waste management strategies proving insufficient in addressing the problem. Enzymatic degradation has emerged as a promising alternative, with LCC[ICCG], an engineered metagenome-derived cutinase, being the most effective in degrading polyethylene terephthalate (PET), the most commonly produced and discarded polyester. However, more efficient PET-hydrolases are needed for the upscaling of a PET-waste biorefinery. In this regard, the study reports the characterization of a novel, phylogenetically distinct, thermophilic polyesterase from Deinococcus maricopensis (DmPETase) and its comparison to LCC[ICCG]. DmPETase is capable of degrading various synthetic polymers, including PET, polyurethane, as well as four semi-crystalline aliphatic polyesters. DmPETase was found to be comparable to LCC[ICCG] at 50 °C in degrading semi-crystalline sections of post-consumer PET bottles, but it appeared to be less sensitive to crystallinity degree increase. This property makes DmPETase a new template for protein engineering endeavors to create an efficient biocatalyst to be integrated into the bio-recycling process of PET waste, without the need for amorphization of the materials.}, } @article {pmid37149890, year = {2023}, author = {Jiang, M and Delgado-Baquerizo, M and Yuan, MM and Ding, J and Yergeau, E and Zhou, J and Crowther, TW and Liang, Y}, title = {Home-based microbial solution to boost crop growth in low-fertility soil.}, journal = {The New phytologist}, volume = {239}, number = {2}, pages = {752-765}, doi = {10.1111/nph.18943}, pmid = {37149890}, issn = {1469-8137}, mesh = {*Soil/chemistry ; Soil Microbiology ; Agriculture ; Bacteria ; *Agricultural Inoculants ; Plant Roots/microbiology ; Rhizosphere ; }, abstract = {Soil microbial inoculants are expected to boost crop productivity under climate change and soil degradation. However, the efficiency of native vs commercialized microbial inoculants in soils with different fertility and impacts on resident microbial communities remain unclear. We investigated the differential plant growth responses to native synthetic microbial community (SynCom) and commercial plant growth-promoting rhizobacteria (PGPR). We quantified the microbial colonization and dynamic of niche structure to emphasize the home-field advantages for native microbial inoculants. A native SynCom of 21 bacterial strains, originating from three typical agricultural soils, conferred a special advantage in promoting maize growth under low-fertility conditions. The root : shoot ratio of fresh weight increased by 78-121% with SynCom but only 23-86% with PGPRs. This phenotype correlated with the potential robust colonization of SynCom and positive interactions with the resident community. Niche breadth analysis revealed that SynCom inoculation induced a neutral disturbance to the niche structure. However, even PGPRs failed to colonize the natural soil, they decreased niche breadth and increased niche overlap by 59.2-62.4%, exacerbating competition. These results suggest that the home-field advantage of native microbes may serve as a basis for engineering crop microbiomes to support food production in widely distributed poor soils.}, } @article {pmid37149736, year = {2023}, author = {Liu, Y and Zhong, X and Luo, Z and Meng, X and Li, R and Zhong, W and Yang, L and Wang, H and Wei, D}, title = {The identification of a robust leucine dehydrogenase from a directed soil metagenome for efficient synthesis of L-2-aminobutyric acid.}, journal = {Biotechnology journal}, volume = {18}, number = {8}, pages = {e2200590}, doi = {10.1002/biot.202200590}, pmid = {37149736}, issn = {1860-7314}, mesh = {Leucine Dehydrogenase/genetics/metabolism ; *Metagenome ; *Aminobutyrates/metabolism ; Biotechnology ; Leucine ; }, abstract = {L-2-aminobutyric acid (L-2-ABA) is a chiral precursor for the synthesis of anti-epileptic drug levetiracetam and anti-tuberculosis drug ethambutol. Asymmetric synthesis of L-2-ABA by leucine dehydrogenases has been widely developed. However, the limitations of natural enzymes, such as poor stability, low catalytic efficiency, and inhibition of high-concentration substrates, limit large-scale applications. Herein, by directed screening of a metagenomic library from unnatural amino acid-enriched environments, a robust leucine dehydrogenase, TvLeuDH, was identified, which exhibited high substrate tolerance and excellent enzymatic activity towards 2-oxobutyric acid. In addition, TvLeuDH has strong affinity for NADH. Subsequently, a three-enzyme co-expression system containing L-threonine deaminase, TvLeuDH, and glucose dehydrogenase was established. By optimizing reaction conditions, 1.5 M L-threonine could be converted to L-2-ABA with a 99% molar conversion rate and a space-time yield of 51.5 g·L[-1] ·h[-1] . In this process, no external coenzyme was added. The robustness of TvLeuDH allowed the reaction to be performed without the addition of extra salt as the buffer, demonstrating the simplest reaction system currently reported. These unique properties for the efficient and environmentally friendly production of chiral amino acids make TvLeuDH a particularly promising candidate for industrial applications, which reveals the great potential of directed metagenomics for industrial biotechnology.}, } @article {pmid37149730, year = {2023}, author = {Llewellyn, T and Mian, S and Hill, R and Leitch, IJ and Gaya, E}, title = {First Whole Genome Sequence and Flow Cytometry Genome Size Data for the Lichen-Forming Fungus Ramalina farinacea (Ascomycota).}, journal = {Genome biology and evolution}, volume = {15}, number = {5}, pages = {}, pmid = {37149730}, issn = {1759-6653}, abstract = {Lichen-forming fungi are a diverse and ecologically important group of obligate mutualistic symbionts. Due to difficulties with maintaining them in culture and their extremely slow growth, lichenologists are increasingly opting for metagenomic sequencing followed by symbiont genome separation using bioinformatic pipelines. However, without knowing the true genome size of the lichen-forming fungus, we cannot quantify the completeness of the genome assembly and the efficacy of the bioinformatic filtering. To address this issue, we report here the first whole-genome assembly for the lichen-forming fungus Ramalina farinacea (L.) Ach. sequenced with Oxford Nanopore long-read technology alongside direct measurements of its genome size using flow cytometry. The assembly showed high contiguity (N50 = 1.55 Mbp) and gene set completeness (BUSCO = 95.8%). The highly robust genome size obtained of 33.61 Mbp/1C (CV% = 2.98) showed our assembly covered 97% of the entire genome. Our results demonstrate that accurate genome size measurements can be obtained directly from lichen thalli and used to provide a benchmark for assessing true cytometric completeness of metagenome-derived assemblies.}, } @article {pmid37149537, year = {2023}, author = {Ferrillo, A and Kobel, CM and Vera-Ponce de León, A and La Rosa, SL and Kunath, BJ and Pope, PB and Hagen, LH}, title = {Long-Read Metagenomics and CAZyme Discovery.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2657}, number = {}, pages = {253-284}, pmid = {37149537}, issn = {1940-6029}, mesh = {*Metagenomics/methods ; *Microbiota ; Metagenome ; Carbohydrates ; High-Throughput Nucleotide Sequencing ; }, abstract = {Microorganisms play a primary role in regulating biogeochemical cycles and are a valuable source of enzymes that have biotechnological applications, such as carbohydrate-active enzymes (CAZymes). However, the inability to culture the majority of microorganisms that exist in natural ecosystems restricts access to potentially novel bacteria and beneficial CAZymes. While commonplace molecular-based culture-independent methods such as metagenomics enable researchers to study microbial communities directly from environmental samples, recent progress in long-read sequencing technologies are advancing the field. We outline key methodological stages that are required as well as describe specific protocols that are currently used for long-read metagenomic projects dedicated to CAZyme discovery.}, } @article {pmid37149185, year = {2023}, author = {Palladino, G and Rampelli, S and Scicchitano, D and Nanetti, E and Iuffrida, L and Wathsala, RHGR and Interino, N and Marini, M and Porru, E and Turroni, S and Fiori, J and Franzellitti, S and Candela, M}, title = {Seasonal dynamics of the microbiome-host response to pharmaceuticals and pesticides in Mytilus galloprovincialis farmed in the Northwestern Adriatic Sea.}, journal = {The Science of the total environment}, volume = {887}, number = {}, pages = {163948}, doi = {10.1016/j.scitotenv.2023.163948}, pmid = {37149185}, issn = {1879-1026}, mesh = {Animals ; *Mytilus/metabolism ; Seasons ; *Pesticides/analysis ; Xenobiotics/metabolism ; *Microbiota ; *Water Pollutants, Chemical/analysis ; }, abstract = {Marine mussels, especially Mytilus galloprovincialis, are well-established sentinel species, being naturally resistant to the exposure to multiple xenobiotics of natural and anthropogenic origin. Even if the response to multiple xenobiotic exposure is well known at the host level, the role of the mussel-associated microbiome in the animal response to environmental pollution is poorly explored, despite its potential in xenobiotic detoxification and its important role in host development, protection, and adaptation. Here, we characterized the microbiome-host integrative response of M. galloprovincialis in a real-world setting, involving exposure to a complex pattern of emerging pollutants, as occurs in the Northwestern Adriatic Sea. A total of 387 mussel individuals from 3 commercial farms, spanning about 200 km along the Northwestern Adriatic coast, and in 3 different seasons, were collected. Multiresidue analysis (for quantitative xenobiotic determination), transcriptomics (for host physiological response), and metagenomics (for host-associated microbial taxonomical and functional features) analyses were performed on the digestive glands. According to our findings, M. galloprovincialis responds to the presence of the complex pattern of multiple emerging pollutants - including the antibiotics sulfamethoxazole, erythromycin, and tetracycline, the herbicides atrazine and metolachlor, and the insecticide N,N-diethyl-m-toluamide - integrating host defense mechanisms, e.g., through upregulation of transcripts involved in animal metabolic activity, and microbiome-mediated detoxification functions, including microbial functionalities involved in multidrug or tetracycline resistance. Overall, our data highlight the importance of the mussel-associated microbiome as a strategic player for the orchestration of resistance to the multixenobiotic exposure at the holobiont level, providing strategic functionalities for the detoxification of multiple xenobiotic substances, as occurring in real world exposure settings. Complementing the host with microbiome-dependent xenobiotic degradative and resistance genes, the M. galloprovincialis digestive gland associated microbiome can have an important role in the detoxification of emerging pollutants in a context of high anthropogenic pressure, supporting the relevance of mussel systems as potential animal-based bioremediation tool.}, } @article {pmid37148792, year = {2023}, author = {Wang, Y and Tian, X and Song, T and Jiang, Z and Zhang, G and He, C and Li, P}, title = {Linking DOM characteristics to microbial community: The potential role of DOM mineralization for arsenic release in shallow groundwater.}, journal = {Journal of hazardous materials}, volume = {454}, number = {}, pages = {131566}, doi = {10.1016/j.jhazmat.2023.131566}, pmid = {37148792}, issn = {1873-3336}, mesh = {Dissolved Organic Matter ; *Arsenic/analysis ; *Groundwater/chemistry ; Carbon ; *Microbiota ; Nitrogen/analysis ; }, abstract = {Dissolved organic matter (DOM) play critical roles in arsenic (As) biotransformation in groundwater, but its compositional characteristics and interactions with indigenous microbial communities remain unclear. In this study, DOM signatures coupled with taxonomy and functions of microbial community were characterized in As-enriched groundwater by excitation-emission matrix, Fourier transform ion cyclotron resonance mass spectrometry and metagenomic sequencing. Results showed that As concentrations were significantly positively correlated with DOM humification (r = 0.707, p < 0.01) and the most dominant humic acid-like DOM components (r = 0.789, p < 0.01). Molecular characterization further demonstrated high DOM oxidation degree, with the prevalence of unsaturated oxygen-low aromatics, nitrogen (N1/N2)-containing compounds and unique CHO molecules in high As groundwater. These DOM properties were consistent with microbial composition and functional potentials. Both taxonomy and binning analyses demonstrated the dominance of Pseudomonas stutzeri, Microbacterium and Sphingobium xenophagum in As-enriched groundwater which possessed abundant As-reducing gene, with organic carbon degrading genes capable of labile to recalcitrant compounds degradation and high potentials of organic nitrogen mineralization to generate ammonium. Besides, most assembled bins in high As groundwater presented strong fermentation potentials which could facilitate carbon utilization by heterotrophic microbes. This study provides better insight into the potential role of DOM mineralization for As release in groundwater system.}, } @article {pmid37148309, year = {2023}, author = {Gazulla, CR and Cabello, AM and Sánchez, P and Gasol, JM and Sánchez, O and Ferrera, I}, title = {A Metagenomic and Amplicon Sequencing Combined Approach Reveals the Best Primers to Study Marine Aerobic Anoxygenic Phototrophs.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2161-2172}, pmid = {37148309}, issn = {1432-184X}, support = {CEX2019-000928-S//Severo Ochoa Centre of Excellence/ ; PID2019-110128RB-I00/AEI/10.13039/501100011033//Agencia Estatal de Investigación/ ; }, mesh = {Phylogeny ; Metagenomics ; Bacterial Proteins/genetics ; *Gammaproteobacteria ; *Alphaproteobacteria/genetics ; }, abstract = {Studies based on protein-coding genes are essential to describe the diversity within bacterial functional groups. In the case of aerobic anoxygenic phototrophic (AAP) bacteria, the pufM gene has been established as the genetic marker for this particular functional group, although available primers are known to have amplification biases. We review here the existing primers for pufM gene amplification, design new ones, and evaluate their phylogenetic coverage. We then use samples from contrasting marine environments to evaluate their performance. By comparing the taxonomic composition of communities retrieved with metagenomics and with different amplicon approaches, we show that the commonly used PCR primers are biased towards the Gammaproteobacteria phylum and some Alphaproteobacteria clades. The metagenomic approach, as well as the use of other combinations of the existing and newly designed primers, show that these groups are in fact less abundant than previously observed, and that a great proportion of pufM sequences are affiliated to uncultured representatives, particularly in the open ocean. Altogether, the framework developed here becomes a better alternative for future studies based on the pufM gene and, additionally, serves as a reference for primer evaluation of other functional genes.}, } @article {pmid37147923, year = {2023}, author = {Yeh, TK and Lin, KP and Chuang, YC and Wang, LA and Chen, CJ and Lee, DY and Huang, YT and Liu, PY}, title = {Clinical metagenomics-assisted diagnosis of relapsed HIV-associated cryptococcal meningitis.}, journal = {International journal of STD & AIDS}, volume = {34}, number = {10}, pages = {740-744}, doi = {10.1177/09564624231174179}, pmid = {37147923}, issn = {1758-1052}, mesh = {Humans ; *Meningitis, Cryptococcal/diagnosis/microbiology ; *AIDS-Related Opportunistic Infections/diagnosis ; Metagenomics ; *Cryptococcus neoformans/genetics ; Recurrence ; *HIV Infections/complications ; }, abstract = {To date, the identification of crypotococcal relapse remains clinically challenging as it often has similar manifestation with paradoxical immune reconstitution inflammatory syndrome. This study reports on the use of metagenomics assisted next generation sequencing to aid in diagnosing recurrent cryptococcal meningitis in an person living with HIV experiencing recurring symptoms, despite negative culture results for Cryptococcus neoformans in the cerebrospinal fluid. Although fungal culture was negative, when reads from metagenomic and metatranscriptomic sequencing performed on the Day 308 cerebrospinal fluid sample were mapped onto the genome from the Day 4 isolate, 589 specific reads were identified. NCBI BLAST search also revealed Cryptococcus-specific 18S/25S/28S ribosomal RNA, indicating a relapse of the disease.}, } @article {pmid37146932, year = {2023}, author = {Gao, W and Zhi, S and Chang, CC and Zou, S and Zhang, K}, title = {Different rapid startups for high-solid anaerobic digestion treating pig manure: Metagenomic insights into antibiotic resistance genes fate and microbial metabolic pathway.}, journal = {Environmental research}, volume = {231}, number = {Pt 1}, pages = {116038}, doi = {10.1016/j.envres.2023.116038}, pmid = {37146932}, issn = {1096-0953}, mesh = {Swine ; Animals ; *Anti-Bacterial Agents/pharmacology ; *Manure ; Anaerobiosis ; Biofuels ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Metabolic Networks and Pathways/genetics ; Methane ; }, abstract = {High-solid anaerobic digestion (HSAD), as an emerging disposal technology for swine manure, was commonly hampered by the long lag phase and slow startup, resulting in poor performance. Rapid startups by different leachate reflux forms can solve the problem, but related study was scarcely reported. Therefore, metagenomic analysis was used to exploit the effects of different rapid startups on the biogas performance, antibiotic resistance genes (ARGs) removal and microbial metabolic pathway during HSAD. Compared anaerobic digestion with natural start (T1), three different rapid startups were set, including with autologous leachate reflux (T2), with water reflux (T3) and with exogenous leachate reflux (T4). The results showed that rapid startups (T2-T4) enhanced biogas yield and the cumulative methane yield was increased by 3.7-7.3 times compared with the control. Totally, 922 ARGs were found, most of which belonged to multidrug and MLS ARGs. About 56% of these ARGs could be reduced in T4, while just 32% of ARGs were reduced in T1. Antibiotic efflux pump is the main mechanism of microbial action, which could be decreased largely by these treatments. Moreover, all the rapid startups (T2-T4) made Methanosarcina content (9.59%-75.91%) higher than that in the natural startup of T1 (4.54%-40.27%). This is why these fast-startups helped methane production fast. Network analysis showed that microbial community and environmental factors (pH and VFAs) both contributed to the spread of ARGs. The reconstructed methane metabolic pathway by different identified genes showed that all methanogenesis pathways existed but acetate metabolic pathway was dominant. And the rapid startups made the abundance of acetate metabolic (M00357) higher than the natural startup.}, } @article {pmid37146779, year = {2023}, author = {Abilaji, S and Sathishkumar, K and Narenkumar, J and Alsalhi, MS and Devanesan, S and Parthipan, P and Muthuraj, B and Rajasekar, A}, title = {Sequential photo electro oxidation and biodegradation of textile effluent: Elucidation of degradation mechanism and bacterial diversity.}, journal = {Chemosphere}, volume = {331}, number = {}, pages = {138816}, doi = {10.1016/j.chemosphere.2023.138816}, pmid = {37146779}, issn = {1879-1298}, mesh = {Biodegradation, Environmental ; *Bacteria/genetics/metabolism ; Textiles ; Oxidation-Reduction ; *Actinomycetales/metabolism ; Azo Compounds ; Coloring Agents/metabolism ; Textile Industry ; }, abstract = {Textile effluent contains a highly toxic and refractory azo dyes. Eco-friendly method for efficient decolorization and degradation of textile effluent is essential. In the present study, treatment of textile effluent was carried through sequential electro oxidation (EO) and photo electro oxidation (PEO) using RuO2-IrO2 coated titanium electrode as an anode and cathode followed by biodegradation. The pre-treatment of textile effluent by photo electro oxidation for 14 h exhibited 92% of decolorization. Subsequent biodegradation of the pre-treated textile effluent enhanced the reduction of chemical oxygen demand to 90%. Metagenomics results exhibited that Flavobacterium, Dietzia, Curtobacterium, Mesorhizobium, Sphingobium, Streptococcus, Enterococcus, Prevotellaand Stenotrophomonas bacterial communities majorly involved in the biodegradation of textile effluent. Hence, integrating sequential photo electro oxidation and biodegradation proposed an efficient and eco-friendly approach for treating textile effluent.}, } @article {pmid37146742, year = {2023}, author = {Hao, T and Zheng, W and Wu, Y and Yu, H and Qian, X and Yang, C and Zheng, Z and Zhang, X and Guo, Y and Cui, M and Wang, H and Pan, J and Cui, Y}, title = {Population genomics implies potential public health risk of two non-toxigenic Vibrio cholerae lineages.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {112}, number = {}, pages = {105441}, doi = {10.1016/j.meegid.2023.105441}, pmid = {37146742}, issn = {1567-7257}, mesh = {Humans ; *Vibrio cholerae/genetics ; Cholera Toxin/genetics ; Metagenomics ; Public Health ; Virulence ; *Cholera/epidemiology/microbiology ; }, abstract = {Diarrheal cases caused by non-toxigenic Vibrio cholerae have been reported globally. Lineages L3b and L9, characterized as ctxAB-negative and tcpA-positive (CNTP), pose the highest risk and have caused long-term epidemics in different regions worldwide. From 2001 to 2018, two waves (2001-2012 and 2013-2018) of epidemic caused by non-toxigenic V. cholerae occurred in the developed city of Hangzhou, China. In this study, through the integrated analysis of 207 genomes of Hangzhou isolates from these two waves (119 and 88) and 1573 publicly available genomes, we showed that L3b and L9 lineages together caused the second wave as had happened in the first wave, but the dominant lineage shifted from L3b (first wave: 69%) to L9 (second wave: 50%). We further found that the genotype of a key virulence gene, tcpF, in the L9 lineage during the second wave shifted to type I, which may have enhanced bacterial colonization in humans and potentially promoted the pathogenic lineage shift. Moreover, we found that 21% of L3b and L9 isolates had changed to predicted cholera toxin producers, providing evidence that gain of complete CTXφ-carrying ctxAB genes, rather than ctxAB gain in pre-CTXφ-carrying isolates, led to the transition. Taken together, our findings highlight the possible public health risk associated with L3b and L9 lineages due to their potential to cause long-term epidemics and turn into high-virulent cholera toxin producers, which necessitates a more comprehensive and unbiased sampling in further disease control efforts.}, } @article {pmid37146717, year = {2023}, author = {Yan, Y and Wang, D and Li, Y and Wu, Z and Liu, H and Shi, Y and Lu, X and Liu, D}, title = {Prevalence, variation, and transmission patterns of human respiratory syncytial virus from pediatric patients in Hubei, China during 2020-2021.}, journal = {Virologica Sinica}, volume = {38}, number = {3}, pages = {363-372}, pmid = {37146717}, issn = {1995-820X}, mesh = {Child ; Humans ; Infant ; *Respiratory Syncytial Virus, Human/genetics ; *Respiratory Syncytial Virus Infections/epidemiology ; Prevalence ; Evolution, Molecular ; Phylogeny ; China/epidemiology ; *Respiratory Tract Infections ; Genotype ; }, abstract = {Human respiratory syncytial virus (RSV) is a severe threat to children and a main cause of acute lower respiratory tract infections. Nevertheless, the intra-host evolution and inter-regional diffusion of RSV are little known. In this study, we performed a systematic surveillance in hospitalized children in Hubei during 2020-2021, in which 106 RSV-positive samples were detected both clinically and by metagenomic next generation sequencing (mNGS). RSV-A and RSV-B groups co-circulated during surveillance with RSV-B being predominant. About 46 high-quality genomes were used for further analyses. A total of 163 intra-host nucleotide variation (iSNV) sites distributed in 34 samples were detected, and glycoprotein (G) gene was the most enriched gene for iSNVs, with non-synonymous substitutions more than synonymous substitutions. Evolutionary dynamic analysis showed that the evolutionary rates of G and NS2 genes were higher, and the population size of RSV groups changed over time. We also found evidences of inter-regional diffusion from Europe and Oceania to Hubei for RSV-A and RSV-B, respectively. This study highlighted the intra-host and inter-host evolution of RSV, and provided some evidences for understanding the evolution of RSV.}, } @article {pmid37145848, year = {2023}, author = {Chau, KK and Goodall, T and Bowes, M and Easterbrook, K and Brett, H and Hughes, J and Crook, DW and Read, DS and Walker, AS and Stoesser, N}, title = {High-resolution characterization of short-term temporal variability in the taxonomic and resistome composition of wastewater influent.}, journal = {Microbial genomics}, volume = {9}, number = {5}, pages = {}, pmid = {37145848}, issn = {2057-5858}, support = {MRF_MRF-145-0004-TPG-AVISO/MRF/MRF/United Kingdom ; }, mesh = {Humans ; *Wastewater ; RNA, Ribosomal, 16S/genetics ; *Metagenome ; }, abstract = {Wastewater-based epidemiology (WBE) for population-level surveillance of antimicrobial resistance (AMR) is gaining significant traction, but the impact of wastewater sampling methods on results is unclear. In this study, we characterized taxonomic and resistome differences between single-timepoint-grab and 24 h composites of wastewater influent from a large UK-based wastewater treatment work [WWTW (population equivalent: 223 435)]. We autosampled hourly influent grab samples (n=72) over three consecutive weekdays, and prepared additional 24 h composites (n=3) from respective grabs. For taxonomic profiling, metagenomic DNA was extracted from all samples and 16S rRNA gene sequencing was performed. One composite and six grabs from day 1 underwent metagenomic sequencing for metagenomic dissimilarity estimation and resistome profiling. Taxonomic abundances of phyla varied significantly across hourly grab samples but followed a repeating diurnal pattern for all 3 days. Hierarchical clustering grouped grab samples into four time periods dissimilar in both 16S rRNA gene-based profiles and metagenomic distances. 24H-composites resembled mean daily phyla abundances and showed low variability of taxonomic profiles. Of the 122 AMR gene families (AGFs) identified across all day 1 samples, single grab samples identified a median of six (IQR: 5-8) AGFs not seen in the composite. However, 36/36 of these hits were at lateral coverage <0.5 (median: 0.19; interquartile range: 0.16-0.22) and potential false positives. Conversely, the 24H-composite identified three AGFs not seen in any grab with higher lateral coverage (0.82; 0.55-0.84). Additionally, several clinically significant human AGFs (bla VIM, bla IMP, bla KPC) were intermittently or completely missed by grab sampling but captured by the 24 h composite. Wastewater influent undergoes significant taxonomic and resistome changes on short timescales potentially affecting interpretation of results based on sampling strategy. Grab samples are more convenient and potentially capture low-prevalence/transient targets but are less comprehensive and temporally variable. Therefore, we recommend 24H-composite sampling where feasible. Further validation and optimization of WBE methods is vital for its development into a robust AMR surveillance approach.}, } @article {pmid37145100, year = {2023}, author = {Zhang, Y and Gan, Y and Bao, H and Wang, R}, title = {Perturbations of gut microbiome and metabolome of pigs infected with Mycoplasma hyorhinis.}, journal = {Journal of the science of food and agriculture}, volume = {103}, number = {13}, pages = {6219-6232}, doi = {10.1002/jsfa.12690}, pmid = {37145100}, issn = {1097-0010}, support = {//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; //Jiangsu Province Belt and Road International Cooperation Project/ ; }, mesh = {Swine ; Animals ; *Mycoplasma hyorhinis ; *Mycoplasma Infections ; *Gastrointestinal Microbiome ; *Swine Diseases ; Chromatography, Liquid ; Tandem Mass Spectrometry ; Metabolome ; Amino Acids ; Lipids ; }, abstract = {BACKGROUND: Mycoplasma hyorhinis is a prevalent respiratory pathogen in swine, causing significant economic loss to pig producers. There is growing evidence that respiratory pathogen infections have a large impact on intestinal microecology. To study the effect of M. hyorhinis infection on gut microbial composition and metabolome profile, pigs were infected with M. hyorhinis. Metagenomic sequencing analysis was performed of fecal samples and a liquid chromatography/tandem mass spectrometry (LC-MS/MS) analysis of gut digesta was made.

RESULTS: Pigs infected with M. hyorhinis had enriched Sutterella and Mailhella, and depleted Dechloromonas, Succinatimonas, Campylobacter, Blastocystis, Treponema, and Megasphaera. The pigs infected with M. hyorhinis also had greater abundances of bacterium_0_1xD8_71, Ruminococcus_sp__CAG_353, Firmicutes_bacterium_CAG_194, Firmicutes_bacterium_CAG_534, bacterium_1xD42_87, and lower abundances of Chlamydia_suis, Megasphaera_elsdenii, Treponema_porcinum, Bacteroides_sp__CAG_1060, Faecalibacterium_prausnitzii. Metabolomic analysis revealed that some lipids and lipid-like molecules increased in the small intestine, whereas most lipids and lipid-like molecule metabolites decreased in the large intestine. These altered metabolites induce changes in intestinal sphingolipid metabolism, amino acid metabolism, and thiamine metabolism.

CONCLUSION: These findings demonstrate that infection with M. hyorhinis can alter the gut microbial composition and metabolite structure in pigs, which may further affect amino acid metabolism and lipid metabolism in the intestine. © 2023 Society of Chemical Industry.}, } @article {pmid37145069, year = {2023}, author = {Wu, S and Song, J and Hu, F and Li, H and Tian, Y and Cheng, W and Liang, Y and Luo, Q}, title = {Pneumonia During the COVID-19 Pandemic in Hubei Province, China: a Case Report of Mucormycosis.}, journal = {Clinical laboratory}, volume = {69}, number = {5}, pages = {}, doi = {10.7754/Clin.Lab.2022.220905}, pmid = {37145069}, issn = {1433-6510}, mesh = {Humans ; *Mucormycosis/diagnosis/epidemiology ; *COVID-19 ; Pandemics ; *Pneumonia ; China/epidemiology ; Antiviral Agents ; Bronchoalveolar Lavage Fluid ; High-Throughput Nucleotide Sequencing ; *Invasive Fungal Infections ; }, abstract = {BACKGROUND: Mucor infection cannot be ignored in patients with pulmonary shadowing with cavitation. This paper reports a case of mucormycosis during the COVID-19 pandemic in Hubei Province, China.

METHODS: An anesthesiology doctor was initially diagnosed as COVID-19 due to changes in lung imaging. After anti-infective, anti-viral, and symptomatic supportive treatment, some of symptoms were relieved. But some symptoms -'chest pain and discomfort', accompanied by chest sulking and short breath after activities, did not ease. At last, Lichtheimia ramose was detected later by metagenomic next generation sequencing (mNGS) in the bronchoalveolar lavage fluid (BALF).

RESULTS: After adjusting amphotericin B for anti-infective treatment, the patient's infection lesions were shrunk and the symptoms were significantly relieved.

CONCLUSIONS: The diagnosis of invasive fungal infections is very difficult, and mNGS can make an accurate pathogenic diagnosis of invasive fungal diseases for the clinic and provide a basis for clinical treatment.}, } @article {pmid37143545, year = {2023}, author = {Li, Y and Yao, XW and Tang, L and Dong, WJ and Lan, TL and Fan, J and Liu, FS and Qin, SB}, title = {Corrigendum: Diagnostic efficiency of metagenomic next-generation sequencing for suspected spinal tuberculosis in China: a multicenter prospective study.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1198931}, doi = {10.3389/fmicb.2023.1198931}, pmid = {37143545}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2022.1018938.].}, } @article {pmid37142773, year = {2023}, author = {Ikegame, S and Carmichael, JC and Wells, H and Furler O'Brien, RL and Acklin, JA and Chiu, HP and Oguntuyo, KY and Cox, RM and Patel, AR and Kowdle, S and Stevens, CS and Eckley, M and Zhan, S and Lim, JK and Veit, EC and Evans, MJ and Hashiguchi, T and Durigon, E and Schountz, T and Epstein, JH and Plemper, RK and Daszak, P and Anthony, SJ and Lee, B}, title = {Metagenomics-enabled reverse-genetics assembly and characterization of myotis bat morbillivirus.}, journal = {Nature microbiology}, volume = {8}, number = {6}, pages = {1108-1122}, pmid = {37142773}, issn = {2058-5276}, support = {R01 AI071002/AI/NIAID NIH HHS/United States ; R01 AI153400/AI/NIAID NIH HHS/United States ; F31 HL149295/HL/NHLBI NIH HHS/United States ; F32 HL158173/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Chlorocebus aethiops ; Humans ; Vero Cells ; *Chiroptera ; Zoonoses ; *Morbillivirus/genetics ; Cell Line ; }, abstract = {Morbilliviruses are among the most contagious viral pathogens of mammals. Although previous metagenomic surveys have identified morbillivirus sequences in bats, full-length morbilliviruses from bats are limited. Here we characterize the myotis bat morbillivirus (MBaMV) from a bat surveillance programme in Brazil, whose full genome was recently published. We demonstrate that the fusion and receptor binding protein of MBaMV utilize bat CD150 and not human CD150, as an entry receptor in a mammalian cell line. Using reverse genetics, we produced a clone of MBaMV that infected Vero cells expressing bat CD150. Electron microscopy of MBaMV-infected cells revealed budding of pleomorphic virions, a characteristic morbillivirus feature. MBaMV replication reached 10[3]-10[5] plaque-forming units ml[-1] in human epithelial cell lines and was dependent on nectin-4. Infection of human macrophages also occurred, albeit 2-10-fold less efficiently than measles virus. Importantly, MBaMV is restricted by cross-neutralizing human sera elicited by measles, mumps and rubella vaccination and is inhibited by orally bioavailable polymerase inhibitors in vitro. MBaMV-encoded P/V genes did not antagonize human interferon induction. Finally, we show that MBaMV does not cause disease in Jamaican fruit bats. We conclude that, while zoonotic spillover into humans may theoretically be plausible, MBaMV replication would probably be controlled by the human immune system.}, } @article {pmid37142411, year = {2023}, author = {Nimsi, KA and Manjusha, K and Mohamed Hatha, AA and Kathiresan, K}, title = {Diversity, Distribution and Bioprospecting Potentials of Manglicolous Yeasts: A Review.}, journal = {FEMS microbiology ecology}, volume = {}, number = {}, pages = {}, doi = {10.1093/femsec/fiad044}, pmid = {37142411}, issn = {1574-6941}, abstract = {Manglicolous yeasts are those that inhabit mangroves. Being adapted to survive extreme environmental variations, these yeasts possess traits that are desirable in terms of bioprospecting potential. Yeasts have been successfully isolated from different microhabitats within the mangrove ecosystem, including vegetation, water, sediments, and invertebrates. They have been found to be most abundant in sediments and water. Manglicolous yeasts are highly diverse unlike previously assumed. Yeasts belonging to the phyla Ascomycetes are more common in mangrove ecosystems than Basidiomycetes. Candida, Cryptococcus, Debaryomyces, Geotrichum, Kluyveromyces, Rhodotorula, Saccharomyces, and Pichia were some of the dominant yeast genera which are cosmopolitan in distribution. New species yeasts such as Vishniacozyma changhuana and V.taiwanica are also known from mangroves. A compilation of isolation and identification methods employed for manglicolous yeast culture is provided in this review. Culture-independent approaches to understanding yeast diversities have also been introduced. The bioprospecting potentials of manglicolous yeasts have been highlighted these include enzymes, xylitol, biofuel, single-cell oil, anti-cancer agents, antimicrobials, and biosurfactants. Manglicolous yeast also finds application as biocontrol agents, bio-remediators, single-cell proteins, food and feed, and immunostimulants. Our knowledge of the diversity and economical prospects of manglicolous yeasts is limited and likely to remain so as mangroves are disappearing fast. Therefore, this review is an attempt to give insight into these aspects.}, } @article {pmid37142190, year = {2023}, author = {Moore, RL and Feehily, C and Killeen, SL and Yelverton, CA and Geraghty, AA and Walsh, CJ and O'Neill, IJ and Nielsan, IB and Lawton, EM and Sanchez-Gallardo, R and Nori, SRC and Shanahan, F and Murphy, EF and Van Sinderen, D and Cotter, PD and McAuliffe, FM}, title = {Ability of Bifidobacterium breve 702258 to transfer from mother to infant: the MicrobeMom randomized controlled trial.}, journal = {American journal of obstetrics & gynecology MFM}, volume = {5}, number = {7}, pages = {100994}, doi = {10.1016/j.ajogmf.2023.100994}, pmid = {37142190}, issn = {2589-9333}, mesh = {Infant, Newborn ; Humans ; Infant ; Female ; Pregnancy ; Adult ; *Bifidobacterium breve ; Mothers ; *Probiotics ; Gestational Age ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: The composition of the infant microbiome can have a variety of short- and long-term implications for health. It is unclear if maternal probiotic supplementation in pregnancy can affect the infant gut microbiome.

OBJECTIVE: This study aimed to investigate if maternal supplementation of a formulation of Bifidobacterium breve 702258 from early pregnancy until 3 months postpartum could transfer to the infant gut.

STUDY DESIGN: This was a double-blinded, placebo-controlled, randomized controlled trial of B breve 702258 (minimum 1 × 10[9] colony-forming units) or placebo taken orally from 16 weeks' gestation until 3 months postpartum in healthy pregnant women. The primary outcome was presence of the supplemented strain in infant stool up to 3 months of life, detected by at least 2 of 3 methods: strain-specific polymerase chain reaction, shotgun metagenomic sequencing, or genome sequencing of cultured B breve. A total of 120 individual infants' stool samples were required for 80% power to detect a difference in strain transfer between groups. Rates of detection were compared using the Fisher exact test.

RESULTS: A total of 160 pregnant women with average age of 33.6 (3.9) years and mean body mass index of 24.3 (22.5-26.5) kg/m[2], of whom 43% were nulliparous (n=58), were recruited from September 2016 to July 2019. Neonatal stool samples were obtained from 135 infants (65 in intervention and 70 in control group). The presence of the supplemented strain was detected through at least 2 methods (polymerase chain reaction and culture) in 2 infants in the intervention group (n=2/65; 3.1%) and none in the control group (n=0; 0%; P=.230).

CONCLUSION: Direct mother-to-infant strain transfer of B breve 702258 occurred, albeit infrequently. This study highlights the potential for maternal supplementation to introduce microbial strains into the infant microbiome.}, } @article {pmid37141831, year = {2023}, author = {Nguyen, VH and Wemheuer, B and Song, W and Bennett, H and Webster, N and Thomas, T}, title = {Identification, classification, and functional characterization of novel sponge-associated acidimicrobiial species.}, journal = {Systematic and applied microbiology}, volume = {46}, number = {4}, pages = {126426}, doi = {10.1016/j.syapm.2023.126426}, pmid = {37141831}, issn = {1618-0984}, mesh = {Phylogeny ; *Hedgehog Proteins/genetics/metabolism ; *Symbiosis ; RNA, Ribosomal, 16S/genetics ; Bacteria ; }, abstract = {Sponges are known to harbour an exceptional diversity of uncultured microorganisms, including members of the phylum Actinobacteriota. While members of the actinobacteriotal class Actinomycetia have been studied intensively due to their potential for secondary metabolite production, the sister class of Acidimicrobiia is often more abundant in sponges. However, the taxonomy, functions, and ecological roles of sponge-associated Acidimicrobiia are largely unknown. Here, we reconstructed and characterized 22 metagenome-assembled genomes (MAGs) of Acidimicrobiia from three sponge species. These MAGs represented six novel species, belonging to five genera, four families, and two orders, which are all uncharacterized (except the order Acidimicrobiales) and for which we propose nomenclature. These six uncultured species have either only been found in sponges and/or corals and have varying degrees of specificity to their host species. Functional gene profiling indicated that these six species shared a similar potential to non-symbiotic Acidimicrobiia with respect to amino acid biosynthesis and utilization of sulfur compounds. However, sponge-associated Acidimicrobiia differed from their non-symbiotic counterparts by relying predominantly on organic rather than inorganic sources of energy, and their predicted capacity to synthesise bioactive compounds or their precursors implicated in host defence. Additionally, the species possess the genetic capacity to degrade aromatic compounds that are frequently found in sponges. The novel Acidimicrobiia may also potentially mediate host development by modulating Hedgehog signalling and by the production of serotonin, which can affect host body contractions and digestion. These results highlight unique genomic and metabolic features of six new acidimicrobiial species that potentially support a sponge-associated lifestyle.}, } @article {pmid37141315, year = {2023}, author = {Klapper, M and Hübner, A and Ibrahim, A and Wasmuth, I and Borry, M and Haensch, VG and Zhang, S and Al-Jammal, WK and Suma, H and Fellows Yates, JA and Frangenberg, J and Velsko, IM and Chowdhury, S and Herbst, R and Bratovanov, EV and Dahse, HM and Horch, T and Hertweck, C and González Morales, MR and Straus, LG and Vilotijevic, I and Warinner, C and Stallforth, P}, title = {Natural products from reconstructed bacterial genomes of the Middle and Upper Paleolithic.}, journal = {Science (New York, N.Y.)}, volume = {380}, number = {6645}, pages = {619-624}, doi = {10.1126/science.adf5300}, pmid = {37141315}, issn = {1095-9203}, mesh = {Animals ; Humans ; *Biological Products/metabolism ; *Genome, Bacterial ; *Hominidae/genetics ; Metagenome ; *Neanderthals/genetics ; *Furans/metabolism ; DNA, Ancient ; }, abstract = {Major advances over the past decade in the field of ancient DNA are providing access to past paleogenomic diversity, but the diverse functions and biosynthetic capabilities of this growing paleome remain largely elusive. We investigated the dental calculus of 12 Neanderthals and 52 anatomically modern humans ranging from 100,000 years ago to the present and reconstructed 459 bacterial metagenome-assembled genomes. We identified a biosynthetic gene cluster shared by seven Middle and Upper Paleolithic individuals that allows for the heterologous production of a class of previously unknown metabolites that we name "paleofurans." This paleobiotechnological approach demonstrates that viable biosynthetic machinery can be produced from the preserved genetic material of ancient organisms, allowing access to natural products from the Pleistocene and providing a promising area for natural product exploration.}, } @article {pmid37141170, year = {2023}, author = {Piantadosi, A and Shariatzadeh, N and Bombin, A and Arkun, K and Alexandrescu, S and Kleinschmidt-DeMasters, BK and Solomon, IH}, title = {Double-stranded RNA immunohistochemistry as a screening tool for viral encephalitis.}, journal = {American journal of clinical pathology}, volume = {160}, number = {2}, pages = {210-219}, pmid = {37141170}, issn = {1943-7722}, support = {R21 NS119660/NS/NINDS NIH HHS/United States ; R21NS119660/NH/NIH HHS/United States ; }, mesh = {Horses/genetics ; Animals ; Humans ; Immunohistochemistry ; RNA, Double-Stranded ; *West Nile virus/genetics ; *Encephalitis, Viral ; RNA, Viral/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {OBJECTIVES: Viral infections of the central nervous system can be challenging to diagnose because of the wide range of causative agents and nonspecific histologic features. We sought to determine whether detection of double-stranded RNA (dsRNA), produced during active RNA and DNA viral infections, could be used to select cases for metagenomic next-generation sequencing (mNGS) from formalin-fixed, paraffin-embedded brain tissue.

METHODS: Eight commercially available anti-dsRNA antibodies were optimized for immunohistochemistry (IHC) and the top antibody tested in a series of cases with confirmed viral infections (n = 34) and cases with inflammatory brain lesions of unclear etiology (n = 62).

RESULTS: Among known positives, anti-dsRNA IHC produced a strong cytoplasmic or nuclear staining pattern for Powassan virus, West Nile virus, rabies virus, JC polyoma virus, and adenovirus while failing to detect Eastern equine encephalitis virus, Jamestown Canyon virus, or any herpesvirus. All the unknown cases were negative by anti-dsRNA IHC, while mNGS detected rare viral reads (0.3-1.3 reads per million total reads) in 2 cases (3%), with only 1 having potential clinical significance.

CONCLUSIONS: Anti-dsRNA IHC can effectively identify a subset of clinically relevant viral infections but not all. The absence of staining should not exclude cases from mNGS if sufficient clinical and histologic suspicion exists.}, } @article {pmid37141097, year = {2023}, author = {Manghi, P and Blanco-Míguez, A and Manara, S and NabiNejad, A and Cumbo, F and Beghini, F and Armanini, F and Golzato, D and Huang, KD and Thomas, AM and Piccinno, G and Punčochář, M and Zolfo, M and Lesker, TR and Bredon, M and Planchais, J and Glodt, J and Valles-Colomer, M and Koren, O and Pasolli, E and Asnicar, F and Strowig, T and Sokol, H and Segata, N}, title = {MetaPhlAn 4 profiling of unknown species-level genome bins improves the characterization of diet-associated microbiome changes in mice.}, journal = {Cell reports}, volume = {42}, number = {5}, pages = {112464}, pmid = {37141097}, issn = {2211-1247}, support = {U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Mice ; *Microbiota/genetics ; Metagenome ; *Gastrointestinal Microbiome ; Diet ; Metagenomics/methods ; }, abstract = {Mouse models are key tools for investigating host-microbiome interactions. However, shotgun metagenomics can only profile a limited fraction of the mouse gut microbiome. Here, we employ a metagenomic profiling method, MetaPhlAn 4, which exploits a large catalog of metagenome-assembled genomes (including 22,718 metagenome-assembled genomes from mice) to improve the profiling of the mouse gut microbiome. We combine 622 samples from eight public datasets and an additional cohort of 97 mouse microbiomes, and we assess the potential of MetaPhlAn 4 to better identify diet-related changes in the host microbiome using a meta-analysis approach. We find multiple, strong, and reproducible diet-related microbial biomarkers, largely increasing those identifiable by other available methods relying only on reference information. The strongest drivers of the diet-induced changes are uncharacterized and previously undetected taxa, confirming the importance of adopting metagenomic methods integrating metagenomic assemblies for comprehensive profiling.}, } @article {pmid37140369, year = {2023}, author = {Castañeda, S and Muñoz, M and Hotez, PJ and Bottazzi, ME and Paniz-Mondolfi, AE and Jones, KM and Mejia, R and Poveda, C and Ramírez, JD}, title = {Microbiome Alterations Driven by Trypanosoma cruzi Infection in Two Disjunctive Murine Models.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0019923}, pmid = {37140369}, issn = {2165-0497}, mesh = {Mice ; Animals ; Disease Models, Animal ; Mice, Inbred C57BL ; *Chagas Disease/parasitology ; *Trypanosoma cruzi ; *Microbiota ; }, abstract = {Alterations caused by Trypanosoma cruzi in the composition of gut microbiome may play a vital role in the host-parasite interactions that shapes physiology and immune responses against infection. Thus, a better understanding of this parasite-host-microbiome interaction may yield relevant information in the comprehension of the pathophysiology of the disease and the development of new prophylactic and therapeutic alternatives. Therefore, we implemented a murine model with two mice strains (BALB/c and C57BL/6) to evaluate the impact of Trypanosoma cruzi (Tulahuen strain) infection on the gut microbiome utilizing cytokine profiling and shotgun metagenomics. Higher parasite burdens were observed in cardiac and intestinal tissues, including changes in anti-inflammatory (interleukin-4 [IL-4] and IL-10) and proinflammatory (gamma interferon, tumor necrosis factor alpha, and IL-6) cytokines. Bacterial species such as Bacteroides thetaiotaomicron, Faecalibaculum rodentium, and Lactobacillus johnsonii showed a decrease in relative abundance, while Akkermansia muciniphila and Staphylococcus xylosus increased. Likewise, as infection progressed, there was a decrease in gene abundances related to metabolic processes such as lipid synthesis (including short-chain fatty acids) and amino acid synthesis (including branched-chain amino acids). High-quality metagenomic assembled genomes of L. johnsonii and A. muciniphila among other species were reconstructed, confirming, functional changes associated with metabolic pathways that are directly affected by the loss of abundance of specific bacterial taxa. IMPORTANCE Chagas disease (CD) is caused by the protozoan Trypanosoma cruzi, presenting acute and chronic phases where cardiomyopathy, megaesophagus, and/or megacolon stand out. During the course of its life cycle, the parasite has an important gastrointestinal tract transit that leads to severe forms of CD. The intestinal microbiome plays an essential role in the immunological, physiological, and metabolic homeostasis of the host. Therefore, parasite-host-intestinal microbiome interactions may provide information on certain biological and pathophysiological aspects related to CD. The present study proposes a comprehensive evaluation of the potential effects of this interaction based on metagenomic and immunological data from two mice models with different genetic, immunological, and microbiome backgrounds. Our findings suggest that there are alterations in the immune and microbiome profiles that affect several metabolic pathways that can potentially promote the infection's establishment, progression, and persistence. In addition, this information may prove essential in the research of new prophylactic and therapeutic alternatives for CD.}, } @article {pmid37140125, year = {2023}, author = {Li, M and Liu, J and Zhu, J and Wang, H and Sun, C and Gao, NL and Zhao, XM and Chen, WH}, title = {Performance of Gut Microbiome as an Independent Diagnostic Tool for 20 Diseases: Cross-Cohort Validation of Machine-Learning Classifiers.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2205386}, pmid = {37140125}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Machine Learning ; Research Design ; Metagenome ; Metagenomics/methods ; }, abstract = {Cross-cohort validation is essential for gut-microbiome-based disease stratification but was only performed for limited diseases. Here, we systematically evaluated the cross-cohort performance of gut microbiome-based machine-learning classifiers for 20 diseases. Using single-cohort classifiers, we obtained high predictive accuracies in intra-cohort validation (~0.77 AUC), but low accuracies in cross-cohort validation, except the intestinal diseases (~0.73 AUC). We then built combined-cohort classifiers trained on samples combined from multiple cohorts to improve the validation of non-intestinal diseases, and estimated the required sample size to achieve validation accuracies of >0.7. In addition, we observed higher validation performance for classifiers using metagenomic data than 16S amplicon data in intestinal diseases. We further quantified the cross-cohort marker consistency using a Marker Similarity Index and observed similar trends. Together, our results supported the gut microbiome as an independent diagnostic tool for intestinal diseases and revealed strategies to improve cross-cohort performance based on identified determinants of consistent cross-cohort gut microbiome alterations.}, } @article {pmid37139849, year = {2023}, author = {Barnett, SE and Buckley, DH}, title = {Metagenomic stable isotope probing reveals bacteriophage participation in soil carbon cycling.}, journal = {Environmental microbiology}, volume = {25}, number = {10}, pages = {1785-1795}, doi = {10.1111/1462-2920.16395}, pmid = {37139849}, issn = {1462-2920}, mesh = {*Bacteriophages/genetics ; Soil ; Soil Microbiology ; Carbon/analysis ; Isotopes/analysis ; *Streptomyces ; }, abstract = {Soil viruses are important components of the carbon (C) cycle, yet we still know little about viral ecology in soils. We added diverse [13] C-labelled carbon sources to soil and we used metagenomic-SIP to detect [13] C assimilation by viruses and their putative bacterial hosts. These data allowed us to link a [13] C-labelled bacteriophage to its [13] C-labelled Streptomyces putative host, and we used qPCR to track the dynamics of the putative host and phage in response to C inputs. Following C addition, putative host numbers increased rapidly for 3 days, and then more gradually, reaching maximal abundance on Day 6. Viral abundance and virus:host ratio increased dramatically over 6 days, and remained high thereafter (8.42 ± 2.94). From Days 6 to 30, virus:host ratio remained high, while putative host numbers declined more than 50%. Putative host populations were [13] C-labelled on Days 3-30, while [13] C-labelling of phage was detected on Days 14 and 30. This dynamic suggests rapid growth and [13] C-labelling of the host fueled by new C inputs, followed by extensive host mortality driven by phage lysis. These findings indicate that the viral shunt promotes microbial turnover in soil following new C inputs, thereby altering microbial community dynamics, and facilitating soil organic matter production.}, } @article {pmid37139490, year = {2023}, author = {Zhao, X and Bai, LP and Li, BY and Yue, ZZ and Zhao, YC and Zhao, XY}, title = {Comparison of mNGS and conventional culture in non-organ transplant critically ill patients supported by ECMO: a single-center study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1146088}, pmid = {37139490}, issn = {2235-2988}, mesh = {Humans ; Critical Illness/therapy ; *Extracorporeal Membrane Oxygenation ; High-Throughput Nucleotide Sequencing ; *Acinetobacter baumannii ; Aspergillus flavus ; Retrospective Studies ; }, abstract = {OBJECTIVES: Infection is one of the important causes of death in intensive care unit (ICU) patients. At present, there are few articles focused on the detailed analysis of pathogenic microorganisms detected in different therapy periods of critically ill patients supported by extracorporeal membrane oxygenation (ECMO).

METHODS: From October 2020 to October 2022, ECMO-assisted patients who underwent multiple times of both metagenomic next-generation sequencing (mNGS) test and conventional culture were enrolled continuously in the First Affiliated Hospital of Zhengzhou University. The baseline data, laboratory test results, and pathogenic microorganisms detected by mNGS and traditional culture in different time periods were recorded and analyzed.

RESULTS: In the present study, 62 patients were included finally. According to whether the patients survived at discharge, they were divided into the survivor group (n = 24) and the non-survivor group (n = 38). Then, according to the different types of ECMO support, they were divided into the veno-venous ECMO (VV ECMO) group (n = 43) and the veno-arterial ECMO (VA ECMO) group (n = 19). The summit period of specimens of traditional culture and mNGS detection of ECMO patients was 7 days after admission, and the largest number of specimens of surviving patients appeared after ECMO withdrawal. The total number of traditional culture specimens was 1,249, the positive rate was 30.4% (380/1,249), and the positive rate of mNGS was 79.6% (82/103). A total of 28 kinds of pathogenic microorganisms were cultured from conventional culture, and 58 kinds of pathogenic microorganisms were detected by mNGS, including Mycobacterium, Rickettsia, and Chlamydia psittaci. In conventional culture, the most frequent Gram-negative bacteria, Gram-positive bacteria, and fungi were Klebsiella pneumoniae, Corynebacterium striatum, and Candida glabrata, and those with the highest frequency of occurrence in mNGS detection were Acinetobacter baumannii, Enterococcus faecium, and Aspergillus flavus.

CONCLUSIONS: Throughout the whole treatment process, different kinds of suspicious biological specimens of high-infection-risk ICU patients supported by ECMO should undergo both mNGS detection and traditional culture early and repeatedly.}, } @article {pmid37138853, year = {2023}, author = {Han, S and Zhao, Z and Yang, L and Huang, J and Wang, Y and Feng, J}, title = {The performance of metagenomic next-generation sequencing in diagnosing pulmonary infectious diseases using authentic clinical specimens: The Illumina platform versus the Beijing Genomics Institute platform.}, journal = {Frontiers in pharmacology}, volume = {14}, number = {}, pages = {1164633}, pmid = {37138853}, issn = {1663-9812}, abstract = {Introduction: Metagenomic next-generation sequencing (mNGS) has been increasingly used to detect infectious organisms and is rapidly moving from research to clinical laboratories. Presently, mNGS platforms mainly include those from Illumina and the Beijing Genomics Institute (BGI). Previous studies have reported that various sequencing platforms have similar sensitivity in detecting the reference panel that mimics clinical specimens. However, whether the Illumina and BGI platforms provide the same diagnostic performance using authentic clinical samples remains unclear. Methods: In this prospective study, we compared the performance of the Illumina and BGI platforms in detecting pulmonary pathogens. Forty-six patients with suspected pulmonary infection were enrolled in the final analysis. All patients received bronchoscopy, and the specimens collected were sent for mNGS on the two different sequencing platforms. Results: The diagnostic sensitivity of the Illumina and BGI platforms was notably higher than that of conventional examination (76.9% vs. 38.5%, p < 0.001; 82.1% vs. 38.5%, p < 0.001; respectively). The sensitivity and specificity for pulmonary infection diagnosis were not significantly different between the Illumina and BGI platforms. Furthermore, the pathogenic detection rate of the two platforms were not significantly different. Conclusion: The Illumina and BGI platforms exhibited similar diagnostic performance for pulmonary infectious diseases using clinical specimens, and both are superior to conventional examinations.}, } @article {pmid37138639, year = {2023}, author = {Shehata, HR and Newmaster, SG}, title = {The power of DNA based methods in probiotic authentication.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1158440}, pmid = {37138639}, issn = {1664-302X}, abstract = {INTRODUCTION: The global probiotic market is growing rapidly, and strict quality control measures are required to ensure probiotic product efficacy and safety. Quality assurance of probiotic products involve confirming the presence of specific probiotic strains, determining the viable cell counts, and confirming the absence of contaminant strains. Third-party evaluation of probiotic quality and label accuracy is recommended for probiotic manufacturers. Following this recommendation, multiple batches of a top selling multi-strain probiotic product were evaluated for label accuracy.

METHODS: A total of 55 samples (five multi-strain finished products and 50 single-strain raw ingredients) containing a total of 100 probiotic strains were evaluated using a combination of molecular methods including targeted PCR, non-targeted amplicon-based High Throughput Sequencing (HTS), and non-targeted Shotgun Metagenomic Sequencing (SMS).

RESULTS: Targeted testing using species-specific or strain-specific PCR methods confirmed the identity of all strains/species. While 40 strains were identified to strain level, 60 strains were identified to species level only due to lack of strain-specific identification methods. In amplicon based HTS, two variable regions of 16S rRNA gene were targeted. Based on V5-V8 region data, ~99% of total reads per sample corresponded to target species, and no undeclared species were detected. Based on V3-V4 region data, ~95%-97% of total reads per sample corresponded to target species, while ~2%-3% of reads matched undeclared species (Proteus species), however, attempts to culture Proteus confirmed that all batches were free from viable Proteus species. Reads from SMS assembled to the genomes of all 10 target strains in all five batches of the finished product.

DISCUSSION: While targeted methods enable quick and accurate identification of target taxa in probiotic products, non-targeted methods enable the identification of all species in a product including undeclared species, with the caveats of complexity, high cost, and long time to result.}, } @article {pmid37138617, year = {2023}, author = {Zhang, Z and Wu, Z and Liu, H and Yang, M and Wang, R and Zhao, Y and Chen, F}, title = {Genomic analysis and characterization of phages infecting the marine Roseobacter CHAB-I-5 lineage reveal a globally distributed and abundant phage genus.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1164101}, pmid = {37138617}, issn = {1664-302X}, abstract = {Marine phages play an important role in marine biogeochemical cycles by regulating the death, physiological metabolism, and evolutionary trajectory of bacteria. The Roseobacter group is an abundant and important heterotrophic bacterial group in the ocean, and plays an important role in carbon, nitrogen, sulfur and phosphorus cycling. The CHAB-I-5 lineage is one of the most dominant Roseobacter lineages, but remains largely uncultured. Phages infecting CHAB-I-5 bacteria have not yet been investigated due to the lack of culturable CHAB-I-5 strains. In this study, we isolated and sequenced two new phages (CRP-901 and CRP-902) infecting the CHAB-I-5 strain FZCC0083. We applied metagenomic data mining, comparative genomics, phylogenetic analysis, and metagenomic read-mapping to investigate the diversity, evolution, taxonomy, and biogeography of the phage group represented by the two phages. The two phages are highly similar, with an average nucleotide identity of 89.17%, and sharing 77% of their open reading frames. We identified several genes involved in DNA replication and metabolism, virion structure, DNA packing, and host lysis from their genomes. Metagenomic mining identified 24 metagenomic viral genomes closely related to CRP-901 and CRP-902. Genomic comparison and phylogenetic analysis demonstrated that these phages are distinct from other known viruses, representing a novel genus-level phage group (CRP-901-type). The CRP-901-type phages do not contain DNA primase and DNA polymerase genes, but possess a novel bifunctional DNA primase-polymerase gene with both primase and polymerase activities. Read-mapping analysis showed that the CRP-901-type phages are widespread across the world's oceans and are most abundant in estuarine and polar waters. Their abundance is generally higher than other known roseophages and even higher than most pelagiphages in the polar region. In summary, this study has greatly expanded our understanding of the genetic diversity, evolution, and distribution of roseophages. Our analysis suggests that the CRP-901-type phage is an important and novel marine phage group that plays important roles in the physiology and ecology of roseobacters.}, } @article {pmid37138607, year = {2023}, author = {Panah, FM and Nielsen, KD and Simpson, GL and Schönherz, A and Schramm, A and Lauridsen, C and Nielsen, TS and Højberg, O and Fredborg, M and Purup, S and Canibe, N}, title = {A westernized diet changed the colonic bacterial composition and metabolite concentration in a dextran sulfate sodium pig model for ulcerative colitis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1018242}, pmid = {37138607}, issn = {1664-302X}, abstract = {INTRODUCTION: Ulcerative colitis (UC) is characterized by chronic inflammation in the colonic epithelium and has a blurred etiology. A western diet and microbial dysbiosis in the colon were reported to play a role in UC development. In this study, we investigated the effect of a westernized diet, i.e., increasing fat and protein content by including ground beef, on the colonic bacterial composition in a dextran sulfate sodium (DexSS) challenged pig study.

METHODS: The experiment was carried out in three complete blocks following a 2×2 factorial design including 24 six-week old pigs, fed either a standard diet (CT) or the standard diet substituted with 15% ground beef to simulate a typical westernized diet (WD). Colitis was induced in half of the pigs on each dietary treatment by oral administration of DexSS (DSS and WD+DSS, respectively). Samples from proximal and distal colon and feces were collected.

RESULTS AND DISCUSSION: Bacterial alpha diversity was unaffected by experimental block, and sample type. In proximal colon, WD group had similar alpha diversity to CT group and the WD+DSS group showed the lowest alpha diversity compared to the other treatment groups. There was a significant interaction between western diet and DexSS for beta diversity, based on Bray-Curtis dissimilarly. The westernized diet and DexSS resulted in three and seven differentially abundant phyla, 21 and 65 species, respectively, mainly associated with the Firmicutes and Bacteroidota phyla followed by Spirochaetota, Desulfobacterota, and Proteobacteria. The concentration of short-chain fatty acids (SCFA) was lowest in the distal colon. Treatment had a slight effect on the estimates for microbial metabolites that might have valuable biological relevance for future studies. The concentration of putrescine in the colon and feces and that of total biogenic amines was highest in the WD+DSS group. We conclude that a westernized diet could be a potential risk factor and an exacerbating agent for UC by reducing the abundance of SCFA-producing bacteria, increasing the abundance of pathogens such as Helicobacter trogontum, and by increasing the concentration of microbial proteolytic-derived metabolites in the colon.}, } @article {pmid37138603, year = {2023}, author = {Zhu, J and Tang, S and Cheng, K and Cai, Z and Chen, G and Zhou, J}, title = {Microbial community composition and metabolic potential during a succession of algal blooms from Skeletonema sp. to Phaeocystis sp.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1147187}, pmid = {37138603}, issn = {1664-302X}, abstract = {Elucidating the interactions between algal and microbial communities is essential for understanding the dynamic mechanisms regulating algal blooms in the marine environment. Shifts in bacterial communities when a single species dominates algal blooms have been extensively investigated. However, bacterioplankton community dynamics during bloom succession when one algal species shift to another is still poorly understood. In this study, we used metagenomic analysis to investigate the bacterial community composition and function during algal bloom succession from Skeletonema sp. to Phaeocystis sp. The results revealed that bacterial community structure and function shifted with bloom succession. The dominant group in the Skeletonema bloom was Alphaproteobacteria, while Bacteroidia and Gammaproteobacteria dominated the Phaeocystis bloom. The most noticeable feature during the successions was the change from Rhodobacteraceae to Flavobacteriaceae in the bacterial communities. The Shannon diversity indices were significantly higher in the transitional phase of the two blooms. Metabolic reconstruction of the metagenome-assembled genomes (MAGs) showed that dominant bacteria exhibited some environmental adaptability in both blooms, capable of metabolizing the main organic compounds, and possibly providing inorganic sulfur to the host algae. Moreover, we identified specific metabolic capabilities of cofactor biosynthesis (e.g., B vitamins) in MAGs in the two algal blooms. In the Skeletonema bloom, Rhodobacteraceae family members might participate in synthesizing vitamin B1 and B12 to the host, whereas in the Phaeocystis bloom, Flavobacteriaceae was the potential contributor for synthesizing vitamin B7 to the host. In addition, signal communication (quorum sensing and indole-3-acetic acid molecules) might have also participated in the bacterial response to bloom succession. Bloom-associated microorganisms showed a noticeable response in composition and function to algal succession. The changes in bacterial community structure and function might be an internal driving factor for the bloom succession.}, } @article {pmid37138598, year = {2023}, author = {Contreras, MJ and Núñez-Montero, K and Bruna, P and Zárate, A and Pezo, F and García, M and Leal, K and Barrientos, L}, title = {Mammals' sperm microbiome: current knowledge, challenges, and perspectives on metagenomics of seminal samples.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1167763}, pmid = {37138598}, issn = {1664-302X}, abstract = {Bacterial growth is highly detrimental to sperm quality and functionality. However, during the last few years, using sequencing techniques with a metagenomic approach, it has been possible to deepen the study of bacteria-sperm relationships and describe non-culturable species and synergistic and antagonistic relationships between the different species in mammalian animals. We compile the recent metagenomics studies performed on mammalian semen samples and provide updated evidence to understand the importance of the microbial communities in the results of sperm quality and sperm functionality of males, looking for future perspectives on how these technologies can collaborate in the development of andrological knowledge.}, } @article {pmid37138445, year = {2023}, author = {Fowler, VG and Durack, DT and Selton-Suty, C and Athan, E and Bayer, AS and Chamis, AL and Dahl, A and DiBernardo, L and Durante-Mangoni, E and Duval, X and Fortes, CQ and Fosbøl, E and Hannan, MM and Hasse, B and Hoen, B and Karchmer, AW and Mestres, CA and Petti, CA and Pizzi, MN and Preston, SD and Roque, A and Vandenesch, F and van der Meer, JTM and van der Vaart, TW and Miro, JM}, title = {The 2023 Duke-International Society for Cardiovascular Infectious Diseases Criteria for Infective Endocarditis: Updating the Modified Duke Criteria.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {77}, number = {4}, pages = {518-526}, pmid = {37138445}, issn = {1537-6591}, support = {R01 AI165671/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Endocarditis, Bacterial/microbiology ; *Endocarditis/etiology ; Fluorodeoxyglucose F18 ; Positron-Emission Tomography ; *Heart Valve Prosthesis ; *Communicable Diseases/complications ; }, abstract = {The microbiology, epidemiology, diagnostics, and treatment of infective endocarditis (IE) have changed significantly since the Duke Criteria were published in 1994 and modified in 2000. The International Society for Cardiovascular Infectious Diseases (ISCVID) convened a multidisciplinary Working Group to update the diagnostic criteria for IE. The resulting 2023 Duke-ISCVID IE Criteria propose significant changes, including new microbiology diagnostics (enzyme immunoassay for Bartonella species, polymerase chain reaction, amplicon/metagenomic sequencing, in situ hybridization), imaging (positron emission computed tomography with 18F-fluorodeoxyglucose, cardiac computed tomography), and inclusion of intraoperative inspection as a new Major Clinical Criterion. The list of "typical" microorganisms causing IE was expanded and includes pathogens to be considered as typical only in the presence of intracardiac prostheses. The requirements for timing and separate venipunctures for blood cultures were removed. Last, additional predisposing conditions (transcatheter valve implants, endovascular cardiac implantable electronic devices, prior IE) were clarified. These diagnostic criteria should be updated periodically by making the Duke-ISCVID Criteria available online as a "Living Document."}, } @article {pmid37138077, year = {2023}, author = {Bayfield, OW and Shkoporov, AN and Yutin, N and Khokhlova, EV and Smith, JLR and Hawkins, DEDP and Koonin, EV and Hill, C and Antson, AA}, title = {Structural atlas of a human gut crassvirus.}, journal = {Nature}, volume = {617}, number = {7960}, pages = {409-416}, pmid = {37138077}, issn = {1476-4687}, mesh = {Humans ; Capsid/chemistry/metabolism/ultrastructure ; Cryoelectron Microscopy ; *DNA Viruses/chemistry/classification/isolation & purification/metabolism/ultrastructure ; *Virion/chemistry/metabolism/ultrastructure ; Virus Assembly ; *Intestines/microbiology/virology ; *Viral Proteins/chemistry/metabolism/ultrastructure ; Protein Unfolding ; Protein Folding ; }, abstract = {CrAssphage and related viruses of the order Crassvirales (hereafter referred to as crassviruses) were originally discovered by cross-assembly of metagenomic sequences. They are the most abundant viruses in the human gut, are found in the majority of individual gut viromes, and account for up to 95% of the viral sequences in some individuals[1-4]. Crassviruses are likely to have major roles in shaping the composition and functionality of the human microbiome, but the structures and roles of most of the virally encoded proteins are unknown, with only generic predictions resulting from bioinformatic analyses[4,5]. Here we present a cryo-electron microscopy reconstruction of Bacteroides intestinalis virus ΦcrAss001[6], providing the structural basis for the functional assignment of most of its virion proteins. The muzzle protein forms an assembly about 1 MDa in size at the end of the tail and exhibits a previously unknown fold that we designate the 'crass fold', that is likely to serve as a gatekeeper that controls the ejection of cargos. In addition to packing the approximately 103 kb of virus DNA, the ΦcrAss001 virion has extensive storage space for virally encoded cargo proteins in the capsid and, unusually, within the tail. One of the cargo proteins is present in both the capsid and the tail, suggesting a general mechanism for protein ejection, which involves partial unfolding of proteins during their extrusion through the tail. These findings provide a structural basis for understanding the mechanisms of assembly and infection of these highly abundant crassviruses.}, } @article {pmid37137684, year = {2023}, author = {Ben-Yacov, O and Godneva, A and Rein, M and Shilo, S and Lotan-Pompan, M and Weinberger, A and Segal, E}, title = {Gut microbiome modulates the effects of a personalised postprandial-targeting (PPT) diet on cardiometabolic markers: a diet intervention in pre-diabetes.}, journal = {Gut}, volume = {72}, number = {8}, pages = {1486-1496}, pmid = {37137684}, issn = {1468-3288}, mesh = {Adult ; Humans ; *Prediabetic State ; *Gastrointestinal Microbiome ; Blood Glucose Self-Monitoring ; Blood Glucose/metabolism ; Diet ; *Diet, Mediterranean ; *Cardiovascular Diseases ; }, abstract = {OBJECTIVE: To explore the interplay between dietary modifications, microbiome composition and host metabolic responses in a dietary intervention setting of a personalised postprandial-targeting (PPT) diet versus a Mediterranean (MED) diet in pre-diabetes.

DESIGN: In a 6-month dietary intervention, adults with pre-diabetes were randomly assigned to follow an MED or PPT diet (based on a machine-learning algorithm for predicting postprandial glucose responses). Data collected at baseline and 6 months from 200 participants who completed the intervention included: dietary data from self-recorded logging using a smartphone application, gut microbiome data from shotgun metagenomics sequencing of faecal samples, and clinical data from continuous glucose monitoring, blood biomarkers and anthropometrics.

RESULTS: PPT diet induced more prominent changes to the gut microbiome composition, compared with MED diet, consistent with overall greater dietary modifications observed. Particularly, microbiome alpha-diversity increased significantly in PPT (p=0.007) but not in MED arm (p=0.18). Post hoc analysis of changes in multiple dietary features, including food-categories, nutrients and PPT-adherence score across the cohort, demonstrated significant associations between specific dietary changes and species-level changes in microbiome composition. Furthermore, using causal mediation analysis we detect nine microbial species that partially mediate the association between specific dietary changes and clinical outcomes, including three species (from Bacteroidales, Lachnospiraceae, Oscillospirales orders) that mediate the association between PPT-adherence score and clinical outcomes of hemoglobin A1c (HbA1c), high-density lipoprotein cholesterol (HDL-C) and triglycerides. Finally, using machine-learning models trained on dietary changes and baseline clinical data, we predict personalised metabolic responses to dietary modifications and assess features importance for clinical improvement in cardiometabolic markers of blood lipids, glycaemic control and body weight.

CONCLUSIONS: Our findings support the role of gut microbiome in modulating the effects of dietary modifications on cardiometabolic outcomes, and advance the concept of precision nutrition strategies for reducing comorbidities in pre-diabetes.

TRIAL REGISTRATION NUMBER: NCT03222791.}, } @article {pmid37137447, year = {2023}, author = {Li, L and Bian, D and Wang, Q and Xue, C and Zhang, Q and Zhang, SM}, title = {Performance of anammox enchanced by pulsed electric fields under added organic carbon sources using integrated network and metagenomics analyses.}, journal = {Bioresource technology}, volume = {380}, number = {}, pages = {129116}, doi = {10.1016/j.biortech.2023.129116}, pmid = {37137447}, issn = {1873-2976}, mesh = {*Denitrification ; *Anaerobic Ammonia Oxidation ; Bioreactors/microbiology ; Carbon/analysis ; Metagenomics ; Oxidation-Reduction ; Anaerobiosis ; Nitrogen/analysis ; Sewage/microbiology ; }, abstract = {This paper aims to investigate the function of a pulsed electric field (PEF) in the anaerobic ammonia oxidation (anammox) process after adding certain chemical oxygen demand (COD) through integrated network and metagenomics analyses. The findings showed that the presence of COD was detrimental to anammox, but PEF could significantly reduce the adverse effect. The total nitrogen removal in the reactor for applying PEF was 16.99% higher on average than the reactor for only dosing COD. Additionally, PEF upgraded the abundance of anammox bacteria subordinate to the phylum Planctomycetes by 9.64%. The analysis of molecular ecological networks promulgated that PEF resulted in an increase in network scale and topology complexity, thereby boosting the potential collaboration of the communities. Metagenomics analyses demonstrated that PEF dramatically promoted anammox central metabolism in the presence of COD, specifically enhancing pivotal N functional genes (hzs, hdh, amo, hao, nas, nor and nos).}, } @article {pmid37137392, year = {2023}, author = {Jin, Y and Xiong, W and Liu, D and Wu, Z and Xiao, G and Wang, S and Su, H}, title = {Responses of straw foam-based aerobic granular sludge to atrazine: Insights from metagenomics and microbial community variations.}, journal = {Chemosphere}, volume = {331}, number = {}, pages = {138828}, doi = {10.1016/j.chemosphere.2023.138828}, pmid = {37137392}, issn = {1879-1298}, mesh = {Sewage/chemistry ; Waste Disposal, Fluid/methods ; *Atrazine ; Metagenomics ; Bioreactors/microbiology ; Aerobiosis ; *Microbiota ; Bacteria/genetics ; Nitrogen ; }, abstract = {Atrazine (ATZ) has caused serious environmental pollution, but the biodegradation of ATZ is relatively slow and inefficient. Herein, a straw foam-based aerobic granular sludge (SF-AGS) was developed, the spatially ordered architectures of which could greatly improve the drug tolerance and biodegradation efficiency of ATZ. The results showed that, in the presence of ATZ, chemical oxygen demand (COD), ammonium nitrogen (NH4[+]-N), total phosphorus (TP), and total nitrogen (TN) were effectively removed within 6 h, and the removal efficiencies were as high as 93.37%, 85.33%, 84.7%, and 70%, respectively. Furthermore, ATZ stimulated microbial consortia to secrete three times more extracellular polymers compared to without ATZ. Illumina MiSeq sequencing results showed that bacterial diversity and richness decreased, leading to significant changes in microbial population structure and composition. ATZ-resistant bacteria including Proteobacteria, Actinobacteria, and Burkholderia laid the biological basis for the stability of aerobic particles, efficient removal of pollutants, and degradation of ATZ. The study demonstrated that SF-AGS is feasible for ATZ-laden low-strength wastewater treatment.}, } @article {pmid37137366, year = {2023}, author = {Bu, W and Li, Z and Cao, L and Wang, Y and Zhang, S and Wang, Z and Wan, J and Wang, Y}, title = {Metagenomics insights into gentamicin degradation and the dynamic of antibiotic resistance genes during co-composting of the gentamicin myelial residues with addition of various organic wastes.}, journal = {The Science of the total environment}, volume = {885}, number = {}, pages = {163848}, doi = {10.1016/j.scitotenv.2023.163848}, pmid = {37137366}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Gentamicins/pharmacology ; *Composting ; Ecosystem ; Metagenomics ; Tandem Mass Spectrometry ; Genes, Bacterial ; Manure ; Drug Resistance, Microbial/genetics ; }, abstract = {Increasing antibiotic mycelial residues (AMRs) and related antibiotic resistance genes (ARGs) pose a significant threat to ecosystems and public health. Composting is a crucial method for recycling AMRs. However, the variation in ARGs and gentamicin degradation in the composting process of gentamicin mycelial residues (GMRs) has received little attention on an actual industrial scale. This research investigated the metabolic pathways and functional genes on the gentamicin and ARGs removal during the co-composting of GMRs with addition of various organic wastes (rice chaff, mushroom residue, etc.) under various C/N ratios (15:1, 25:1, 35:1). The results showed that the removal efficiencies of gentamicin and the total ARGs were 98.23 % and 53.20 %, respectively, with the C/N ratio of 25:1. Moreover, metagenomics and LS-MS/MS analysis demonstrated that the acetylation was the primary pathway for gentamicin biodegradation and the corresponding degrading genes were the categories of aac(3) and aac(6'). However, the relative abundance of aminoglycoside resistance genes (AMGs) were increased after 60 days composting. The partial least squares path modeling analysis demonstrated that the AMG abundance was directly influenced by the predominant mobile gene elements intI1 (p < 0.05) which was closely related to the bacterial community composition. Therefore, the ecological environmental risks should be assessed in the future application of GMRs composting products.}, } @article {pmid37134153, year = {2023}, author = {Schwartz, DJ and Shalon, N and Wardenburg, K and DeVeaux, A and Wallace, MA and Hall-Moore, C and Ndao, IM and Sullivan, JE and Radmacher, P and Escobedo, M and Burnham, CD and Warner, BB and Tarr, PI and Dantas, G}, title = {Gut pathogen colonization precedes bloodstream infection in the neonatal intensive care unit.}, journal = {Science translational medicine}, volume = {15}, number = {694}, pages = {eadg5562}, pmid = {37134153}, issn = {1946-6242}, support = {R01 AI155893/AI/NIAID NIH HHS/United States ; UH3 AI083265/AI/NIAID NIH HHS/United States ; 2021081/DDCF/Doris Duke Charitable Foundation/United States ; T32 GM139774/GM/NIGMS NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; K08 AI159384/AI/NIAID NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; }, mesh = {Infant ; Infant, Newborn ; Humans ; Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Intensive Care Units, Neonatal ; Vancomycin/pharmacology/therapeutic use ; *Sepsis/microbiology ; *Bacterial Infections ; Bacteria/genetics ; Gentamicins ; Ampicillin ; }, abstract = {Bacterial bloodstream infections (BSIs) resulting in late-onset sepsis affect up to half of extremely preterm infants and have substantial morbidity and mortality. Bacterial species associated with BSIs in neonatal intensive care units (NICUs) commonly colonize the preterm infant gut microbiome. Accordingly, we hypothesized that the gut microbiome is a reservoir of BSI-causing pathogenic strains that increase in abundance before BSI onset. We analyzed 550 previously published fecal metagenomes from 115 hospitalized neonates and found that recent ampicillin, gentamicin, or vancomycin exposure was associated with increased abundance of Enterobacteriaceae and Enterococcaceae in infant guts. We then performed shotgun metagenomic sequencing on 462 longitudinal fecal samples from 19 preterm infants (cases) with BSI and 37 non-BSI controls, along with whole-genome sequencing of the BSI isolates. Infants with BSI caused by Enterobacteriaceae were more likely than infants with BSI caused by other organisms to have had ampicillin, gentamicin, or vancomycin exposure in the 10 days before BSI. Relative to controls, gut microbiomes of cases had increased relative abundance of the BSI-causing species and clustered by Bray-Curtis dissimilarity according to BSI pathogen. We demonstrated that 11 of 19 (58%) of gut microbiomes before BSI, and 15 of 19 (79%) of gut microbiomes at any time, harbored the BSI isolate with fewer than 20 genomic substitutions. Last, BSI strains from the Enterobacteriaceae and Enterococcaceae families were detected in multiple infants, indicating BSI-strain transmission. Our findings support future studies to evaluate BSI risk prediction strategies based on gut microbiome abundance in hospitalized preterm infants.}, } @article {pmid37134083, year = {2023}, author = {Mwakibete, L and Takahashi, S and Ahyong, V and Black, A and Rek, J and Ssewanyana, I and Kamya, M and Dorsey, G and Jagannathan, P and Rodríguez-Barraquer, I and Tato, CM and Greenhouse, B}, title = {Metagenomic next-generation sequencing to characterize potential etiologies of non-malarial fever in a cohort living in a high malaria burden area of Uganda.}, journal = {PLOS global public health}, volume = {3}, number = {5}, pages = {e0001675}, pmid = {37134083}, issn = {2767-3375}, abstract = {Causes of non-malarial fevers in sub-Saharan Africa remain understudied. We hypothesized that metagenomic next-generation sequencing (mNGS), which allows for broad genomic-level detection of infectious agents in a biological sample, can systematically identify potential causes of non-malarial fevers. The 212 participants in this study were of all ages and were enrolled in a longitudinal malaria cohort in eastern Uganda. Between December 2020 and August 2021, respiratory swabs and plasma samples were collected at 313 study visits where participants presented with fever and were negative for malaria by microscopy. Samples were analyzed using CZ ID, a web-based platform for microbial detection in mNGS data. Overall, viral pathogens were detected at 123 of 313 visits (39%). SARS-CoV-2 was detected at 11 visits, from which full viral genomes were recovered from nine. Other prevalent viruses included Influenza A (14 visits), RSV (12 visits), and three of the four strains of seasonal coronaviruses (6 visits). Notably, 11 influenza cases occurred between May and July 2021, coinciding with when the Delta variant of SARS-CoV-2 was circulating in this population. The primary limitation of this study is that we were unable to estimate the contribution of bacterial microbes to non-malarial fevers, due to the difficulty of distinguishing bacterial microbes that were pathogenic from those that were commensal or contaminants. These results revealed the co-circulation of multiple viral pathogens likely associated with fever in the cohort during this time period. This study illustrates the utility of mNGS in elucidating the multiple potential causes of non-malarial febrile illness. A better understanding of the pathogen landscape in different settings and age groups could aid in informing diagnostics, case management, and public health surveillance systems.}, } @article {pmid37133792, year = {2023}, author = {Das, S and Najar, IN and Sherpa, MT and Kumar, S and Sharma, P and Mondal, K and Tamang, S and Thakur, N}, title = {Baseline metagenome-assembled genome (MAG) data of Sikkim hot springs from Indian Himalayan geothermal belt (IHGB) showcasing its potential CAZymes, and sulfur-nitrogen metabolic activity.}, journal = {World journal of microbiology & biotechnology}, volume = {39}, number = {7}, pages = {179}, pmid = {37133792}, issn = {1573-0972}, mesh = {*Metagenome ; *Hot Springs/microbiology ; Sikkim ; Bacteria/genetics ; Archaea/genetics ; Phylogeny ; }, abstract = {Here we present the construction and characterization of metagenome assembled genomes (MAGs) from two hot springs residing in the vicinity of Indian Himalayan Geothermal Belt (IHGB). A total of 78 and 7 taxonomic bins were obtained for Old Yume Samdong (OYS) and New Yume Samdong (NYS) hot springs respectively. After passing all the criteria only 21 and 4 MAGs were further studied based on the successful prediction of their 16 S rRNA. Various databases were used such as GTDB, Kaiju, EzTaxon, BLAST XY Plot and NCBI BLAST to get the taxonomic classification of various 16 S rRNA predicted MAGs. The bacterial genomes found were from both thermophilic and mesophilic bacteria among which Proteobacteria, Chloroflexi, Bacteroidetes and Firmicutes were the abundant phyla. However, in case of OYS, two genomes belonged to archaeal Methanobacterium and Methanocaldococcus. Functional characterization revealed the richness of CAZymes such as Glycosyl Transferase (GT) (56.7%), Glycoside Hydrolase (GH) (37.4%), Carbohydrate Esterase family (CE) (8.2%), and Polysaccharide Lyase (PL) (1.9%). There were negligible antibiotic resistance genes in the MAGs however, a significant heavy metal tolerance gene was found in the MAGs. Thus, it may be assumed that there is no coexistence of antibiotic and heavy metal resistance genes in these hot spring microbiomes. Since the selected hot springs possess good sulfur content thus, we also checked the presence of genes for sulfur and nitrogen metabolism. It was found that MAGs from both the hot springs possess significant number of genes related to sulfur and nitrogen metabolism.}, } @article {pmid37133655, year = {2023}, author = {Kottuparambil, S and Ashok, A and Barozzi, A and Michoud, G and Cai, C and Daffonchio, D and Duarte, CM and Agusti, S}, title = {Tracking the early signals of crude oil in seawater and plankton after a major oil spill in the Red Sea.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {26}, pages = {69150-69164}, pmid = {37133655}, issn = {1614-7499}, mesh = {*Petroleum Pollution/analysis ; Plankton/metabolism ; *Petroleum/analysis ; Indian Ocean ; Seawater/microbiology ; *Synechococcus ; *Polycyclic Aromatic Hydrocarbons/analysis ; *Water Pollutants, Chemical/analysis ; }, abstract = {Understanding the immediate impacts of oil spills is essential to recognizing their long-term consequences on the marine environment. In this study, we traced the early (within one week) signals of crude oil in seawater and plankton after a major oil spill in October 2019 in the Red Sea. At the time of sampling, the plume had moved eastward, but we detected significant signs of incorporation of oil carbon into the dissolved organic carbon pool, resulting in a 10-20% increase in the ultraviolet (UV) absorption coefficient (a254) of chromophoric dissolved organic matter (CDOM), elevated oil fluorescence emissions, and depletion of the carbon isotope composition (δ[13]C) of the seawater. The abundance of the picophytoplankton Synechococcus was not affected, but the proportion of low nucleic acid (LNA) bacteria was significantly higher. Moreover, specific bacterial genera (Alcanivorax, Salinisphaera, and Oleibacter) were enriched in the seawater microbiome. Metagenome-assembled genomes (MAGs) suggested that such bacteria presented pathways for growing on oil hydrocarbons. Traces of polycyclic aromatic hydrocarbons (PAHs) were also detected in zooplankton tissues, revealing the rapid entry of oil pollutants into the pelagic food web. Our study emphasizes the early signs of short-lived spills as an important aspect of the prediction of long-term impacts of marine oil spills.}, } @article {pmid37133617, year = {2023}, author = {Sun, R and Liu, Y and Li, T and Qian, ZJ and Zhou, C and Hong, P and Sun, S and Li, C}, title = {Plastic wastes and surface antibiotic resistance genes pollution in mangrove environments.}, journal = {Environmental monitoring and assessment}, volume = {195}, number = {6}, pages = {634}, pmid = {37133617}, issn = {1573-2959}, support = {202142//Postgraduate Education Innovation Project of Guangdong Ocean University/ ; 2022B1515020091, 2021A1515010291//Guangdong Basic and Applied Basic Research Foun dation/ ; KCXFZ202002011011057, JCYJ20210324122606017, GJHZ20210705142000003//Shenzhen Science and Technology Program/ ; 21874029//National Natural Science Foundation of China/ ; KJYF202001-06//Special Funds for Science Technology Innovation and Industrial Development of Shenzhen Dapeng, New District/ ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Plastics ; Environmental Monitoring ; Drug Resistance, Microbial/genetics ; }, abstract = {Mangroves are located at the intersection of land and sea and are also heavily affected by plastic wastes. Biofilms of plastic wastes in mangroves are reservoirs for antibiotic resistance genes (ARGs). In this study, plastic wastes and ARG pollution were investigated from three typical mangrove areas in Zhanjiang, South China. Transparent was the dominant colors of plastic wastes in three mangroves. Fragment and film shape accounted for 57.73-88.23% of plastic waste samples in mangroves. In addition, 39.50% of plastic wastes in protected area mangroves are PS. The metagenomic results shows that the 175 ARGs were found on plastic wastes of the three mangroves, the abundance accounting for 91.11% of the total ARGs. The abundance of Vibrio accounted for 2.31% of the total bacteria genera in aquaculture pond area mangrove. Correlation analysis shows that a microbe can carry multiple ARGs that may improve resistance to antibiotics. Microbes are the potential hosts of most ARGs, suggesting that ARGs can be transmitted by microbes. Because the mangroves are closely related to human activities and the high abundance of ARGs on plastic increases the ecological risks, people should improve plastic waste management and prevent the spread of ARGs by reducing plastic pollution.}, } @article {pmid37133495, year = {2023}, author = {Saikrishna, K and Talukdar, D and Das, S and Bakshi, S and Chakravarti, P and Jana, P and Karmakar, S and Wig, N and Das, B and Ray, A}, title = {Study on Effects of Probiotics on Gut Microbiome and Clinical Course in Patients with Critical Care Illnesses.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1814-1828}, pmid = {37133495}, issn = {1432-184X}, support = {5/9/1208/2019-Nut, Dt. 16.09.2019//Indian Council of Medical Research/ ; No. BT/PR30159/MED/15/188/2018//Department of Biotechnology, Ministry of Science and Technology, India/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Probiotics/therapeutic use ; Critical Care ; Disease Progression ; }, abstract = {Ventilator-associated pneumonia (VAP) is a nosocomial infection contracted by ventilator patients in which bacteria colonize the upper digestive tract and contaminated secretions are released into the lower airway. This nosocomial infection increases the morbidity and mortality of the patients as well as the cost of treatment. Probiotic formulations have recently been proposed to prevent the colonization of these pathogenic bacteria. In this prospective observational study, we aimed to investigate the effects of probiotics on gut microbiota and their relation to clinical outcomes in mechanically ventilated patients. For this study, 35 patients were recruited (22 probiotic-treated and 13 without probiotic treatment) from a cohort of 169 patients. Patients in the probiotic group were given a dose of 6 capsules of a commercially available probiotic (VSL#3®:112.5 billion CFU/cap) in three divided doses for 10 days. Sampling was carried out after each dose to monitor the temporal change in the gut microbiota composition. To profile the microbiota, we used a 16S rRNA metagenomic approach, and differences among the groups were computed using multivariate statistical analyses. Differences in gut microbial diversity (Bray Curtis and Jaccard distance, p-value > 0.05) between the probiotic-treated group and the control group were not observed. Furthermore, treatment with probiotics resulted in the enrichment of Lactobacillus and Streptococcus in the gut microbiota of the probiotic-treated groups. Our results demonstrated that probiotics might lead to favorable alterations in gut microbiome characteristics. Future studies should focus on the appropriate dosages and frequency of probiotics, which can lead to improved clinical outcomes.}, } @article {pmid37133385, year = {2023}, author = {Podell, S and Oliver, A and Kelly, LW and Sparagon, WJ and Plominsky, AM and Nelson, RS and Laurens, LML and Augyte, S and Sims, NA and Nelson, CE and Allen, EE}, title = {Herbivorous Fish Microbiome Adaptations to Sulfated Dietary Polysaccharides.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {5}, pages = {e0215422}, pmid = {37133385}, issn = {1098-5336}, support = {R01 ES030316/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Polysaccharides ; Sulfates ; Coral Reefs ; Fishes ; *Microbiota ; *Seaweed ; Bacteria/genetics ; }, abstract = {Marine herbivorous fish that feed primarily on macroalgae, such as those from the genus Kyphosus, are essential for maintaining coral health and abundance on tropical reefs. Here, deep metagenomic sequencing and assembly of gut compartment-specific samples from three sympatric, macroalgivorous Hawaiian kyphosid species have been used to connect host gut microbial taxa with predicted protein functional capacities likely to contribute to efficient macroalgal digestion. Bacterial community compositions, algal dietary sources, and predicted enzyme functionalities were analyzed in parallel for 16 metagenomes spanning the mid- and hindgut digestive regions of wild-caught fishes. Gene colocalization patterns of expanded carbohydrate (CAZy) and sulfatase (SulfAtlas) digestive enzyme families on assembled contigs were used to identify likely polysaccharide utilization locus associations and to visualize potential cooperative networks of extracellularly exported proteins targeting complex sulfated polysaccharides. These insights into the gut microbiota of herbivorous marine fish and their functional capabilities improve our understanding of the enzymes and microorganisms involved in digesting complex macroalgal sulfated polysaccharides. IMPORTANCE This work connects specific uncultured bacterial taxa with distinct polysaccharide digestion capabilities lacking in their marine vertebrate hosts, providing fresh insights into poorly understood processes for deconstructing complex sulfated polysaccharides and potential evolutionary mechanisms for microbial acquisition of expanded macroalgal utilization gene functions. Several thousand new marine-specific candidate enzyme sequences for polysaccharide utilization have been identified. These data provide foundational resources for future investigations into suppression of coral reef macroalgal overgrowth, fish host physiology, the use of macroalgal feedstocks in terrestrial and aquaculture animal feeds, and the bioconversion of macroalgae biomass into value-added commercial fuel and chemical products.}, } @article {pmid37132662, year = {2023}, author = {Bos, RP and Kaul, D and Zettler, ER and Hoffman, JM and Dupont, CL and Amaral-Zettler, LA and Mincer, TJ}, title = {Plastics select for distinct early colonizing microbial populations with reproducible traits across environmental gradients.}, journal = {Environmental microbiology}, volume = {25}, number = {12}, pages = {2761-2775}, doi = {10.1111/1462-2920.16391}, pmid = {37132662}, issn = {1462-2920}, support = {OCE-1155379//NSF/ ; OCE-1155571//NSF/ ; OCE-1155671//NSF/ ; 432343//NSF-EFRI/ ; }, mesh = {*Plastics/chemistry ; Oceans and Seas ; Biofilms ; Metagenome ; *Microbiota ; }, abstract = {Little is known about early plastic biofilm assemblage dynamics and successional changes over time. By incubating virgin microplastics along oceanic transects and comparing adhered microbial communities with those of naturally occurring plastic litter at the same locations, we constructed gene catalogues to contrast the metabolic differences between early and mature biofilm communities. Early colonization incubations were reproducibly dominated by Alteromonadaceae and harboured significantly higher proportions of genes associated with adhesion, biofilm formation, chemotaxis, hydrocarbon degradation and motility. Comparative genomic analyses among the Alteromonadaceae metagenome assembled genomes (MAGs) highlighted the importance of the mannose-sensitive hemagglutinin (MSHA) operon, recognized as a key factor for intestinal colonization, for early colonization of hydrophobic plastic surfaces. Synteny alignments of MSHA also demonstrated positive selection for mshA alleles across all MAGs, suggesting that mshA provides a competitive advantage for surface colonization and nutrient acquisition. Large-scale genomic characteristics of early colonizers varied little, despite environmental variability. Mature plastic biofilms were composed of predominantly Rhodobacteraceae and displayed significantly higher proportions of carbohydrate hydrolysis enzymes and genes for photosynthesis and secondary metabolism. Our metagenomic analyses provide insight into early biofilm formation on plastics in the ocean and how early colonizers self-assemble, compared to mature, phylogenetically and metabolically diverse biofilms.}, } @article {pmid37131968, year = {2023}, author = {Kusumawaty, D and Augustine, SMN and Aryani, A and Effendi, Y and Emran, TB and Tallei, TE}, title = {Configuration of gut bacterial community profile and their potential functionality in the digestive tract of the wild and cultivated Indonesian shortfin elver-phase eels (Anguilla bicolor bicolor McClelland, 1844).}, journal = {3 Biotech}, volume = {13}, number = {5}, pages = {153}, pmid = {37131968}, issn = {2190-572X}, abstract = {This study aimed to explore the bacteria present in the digestive tracts of wild and cultivated Indonesian shortfin eel during the elver phase. The eel has high export potential due to its vitamin and micronutrient content, but slow growth and vulnerability to collapse in farm conditions hinder its cultivation. The microbiota in the eel's digestive tract is crucial for its health, particularly during the elver phase. This study used Next Generation Sequencing to analyze the community structure and diversity of bacteria in the eels' digestive tracts, focusing on the V3-V4 regions of the 16S rRNA gene. Mothur software was used for data analysis and PAST v.3.26 was used to calculate alpha diversity. The results showed that Proteobacteria (64.18%) and Firmicutes (33.55%) were the predominant phyla in the digestive tract of cultivated eels, while Bacteroidetes (54.16%), Firmicutes (14.71%), and Fusobacteria (10.56%) were predominant in wild eels. The most prevalent genera in cultivated and wild elver were Plesiomonas and Cetobacterium, respectively. The microbiota in the digestive tract of cultivated eels was diverse despite uneven distribution. The KEGG database analysis revealed that the primary function of the microbiome was to facilitate the eel's absorption of nutrients by contributing significantly to the metabolism of carbohydrates and amino acids. This study's findings can aid in assessing eel health and improving eel farming conditions.}, } @article {pmid37131762, year = {2023}, author = {Koslicki, D and White, S and Ma, C and Novikov, A}, title = {YACHT: an ANI-based statistical test to detect microbial presence/absence in a metagenomic sample.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37131762}, support = {R01 GM146462/GM/NIGMS NIH HHS/United States ; }, abstract = {In metagenomics, the study of environmentally associated microbial communities from their sampled DNA, one of the most fundamental computational tasks is that of determining which genomes from a reference database are present or absent in a given sample metagenome. While tools exist to answer this question, all existing approaches to date return point estimates, with no associated confidence or uncertainty associated with it. This has led to practitioners experiencing difficulty when interpreting the results from these tools, particularly for low abundance organisms as these often reside in the "noisy tail" of incorrect predictions. Furthermore, no tools to date account for the fact that reference databases are often incomplete and rarely, if ever, contain exact replicas of genomes present in an environmentally derived metagenome. In this work, we present solutions for these issues by introducing the algorithm YACHT: Yes/No Answers to Community membership via Hypothesis Testing. This approach introduces a statistical framework that accounts for sequence divergence between the reference and sample genomes, in terms of average nucleotide identity, as well as incomplete sequencing depth, thus providing a hypothesis test for determining the presence or absence of a reference genome in a sample. After introducing our approach, we quantify its statistical power as well as quantify theoretically how this changes with varying parameters. Subsequently, we perform extensive experiments using both simulated and real data to confirm the accuracy and scalability of this approach. Code implementing this approach, as well as all experiments performed, is available at https://github.com/KoslickiLab/YACHT.}, } @article {pmid37130517, year = {2023}, author = {Lee, JWJ and Plichta, DR and Asher, S and Delsignore, M and Jeong, T and McGoldrick, J and Staller, K and Khalili, H and Xavier, RJ and Chung, DC}, title = {Association of distinct microbial signatures with premalignant colorectal adenomas.}, journal = {Cell host & microbe}, volume = {31}, number = {5}, pages = {827-838.e3}, pmid = {37130517}, issn = {1934-6069}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AG068390/AG/NIA NIH HHS/United States ; R01 AI172147/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Colonic Polyps/pathology ; *Colorectal Neoplasms/pathology ; Colonoscopy ; *Adenoma ; }, abstract = {Environmental exposures are a major risk factor for developing colorectal cancer, and the gut microbiome may serve as an integrator of such environmental risk. To study the microbiome associated with premalignant colon lesions, such as tubular adenomas (TAs) and sessile serrated adenomas (SSAs), we profiled stool samples from 971 participants undergoing colonoscopy and paired these data with dietary and medication history. The microbial signatures associated with either SSA or TA are distinct. SSA associates with multiple microbial antioxidant defense systems, whereas TA associates with a depletion of microbial methanogenesis and mevalonate metabolism. Environmental factors, such as diet and medications, link with the majority of identified microbial species. Mediation analyses found that Flavonifractor plautii and Bacteroides stercoris transmit the protective or carcinogenic effects of these factors to early carcinogenesis. Our findings suggest that the unique dependencies of each premalignant lesion may be exploited therapeutically or through dietary intervention.}, } @article {pmid37129684, year = {2023}, author = {Bhende, RS and Dafale, NA}, title = {Insights into the ubiquity, persistence and microbial intervention of imidacloprid.}, journal = {Archives of microbiology}, volume = {205}, number = {5}, pages = {215}, pmid = {37129684}, issn = {1432-072X}, mesh = {*Insecticides/metabolism ; Neonicotinoids/metabolism ; Nitro Compounds/metabolism ; Agriculture ; Soil/chemistry ; }, abstract = {Imidacloprid, a neonicotinoid pesticide, is employed to increase crop productivity. Meanwhile, its indiscriminate application severely affects the non-target organisms and the environment. As an eco-friendly and economically workable option, the microbial intervention has garnered much attention. This review concisely outlines the toxicity, long-term environmental repercussions, degradation kinetics, biochemical pathways, and interplay of genes implicated in imidacloprid remediation. The studies have highlighted imidacloprid residue persistence in the environment for up to 3000 days. In view of high persistence, effective intervention is highly required. Bacteria-mediated degradation has been established as a viable approach with Bacillus spp. being among the most efficient at 30 ℃ and pH 7. Further, a comparative metagenomic investigation reveals dominant neonicotinoid degradation genes in agriculture compared to forest soils with distinctive microbial communities. Functional metabolism of carbohydrates, amino acids, fatty acids, and lipids demonstrated a significantly superior relative abundance in forest soil, implying its quality and fertility. The CPM, CYP4C71v2, CYP4C72, and CYP6AY3v2 genes that synthesize cyt p450 monooxygenase enzyme play a leading role in imidacloprid degradation. In the future, a systems biology approach incorporating integrated kinetics should be utilized to come up with innovative strategies for moderating the adverse effects of imidacloprid on the environment.}, } @article {pmid37129524, year = {2023}, author = {Li, Y and Ouyang, Q and Li, X and Alolgal, RN and Fan, Y and Sun, Y and Gong, H and Xiao, P and Ma, G}, title = {The Role of Gynostemma pentaphyllum in Regulating Hyperlipidemia.}, journal = {The American journal of Chinese medicine}, volume = {51}, number = {4}, pages = {953-978}, doi = {10.1142/S0192415X23500441}, pmid = {37129524}, issn = {1793-6853}, mesh = {Animals ; Mice ; Body Weight ; Diet, High-Fat/adverse effects ; Gynostemma/chemistry ; *Hyperlipidemias/drug therapy ; Lipids ; Plant Extracts/pharmacology/therapeutic use/chemistry ; Tryptophan ; }, abstract = {Developing effective and safe lipid-lowering drugs is highly urgent. This study aims to investigate the effectiveness and underlying mechanisms of Gynostemma pentaphyllum (GP) in the treatment of hyperlipidemia. First, a meta-analysis was performed to determine the lipid-lowering effects of GP. Thereafter, hyperlipidemia was induced in mice using a high-fat diet (HFD) and was subsequently treated with Gynostemma pentaphyllum extract (GPE) by daily gavage for 12 weeks. The body weight, tissue weight, blood lipid level, and liver lipid level were determined. Additionally, mouse serum samples were subjected to metabolomic profiling and feces were collected at different time points for metagenomic analysis via 16S rDNA sequencing. A total of 15 out of 1520 studies were retrieved from six databases. The pooled results of the meta-analysis showed that GP effectively reduced triglyceride levels and increased high-density lipoprotein cholesterol (both [Formula: see text]). Animal experiments revealed that GPE administration significantly reduced body weight, ameliorated high blood lipid levels, limited lipid deposition, and improved insulin resistance. Furthermore, GPE treatment markedly changed the intestinal microbiota structure and constitution of tryptophan metabolites. In conclusion, our results confirm the lipid-lowering effect of GP, which may be partly attributable to regulation of the intestinal microbiota and tryptophan metabolism.}, } @article {pmid37128855, year = {2023}, author = {Wen, T and Niu, G and Chen, T and Shen, Q and Yuan, J and Liu, YX}, title = {The best practice for microbiome analysis using R.}, journal = {Protein & cell}, volume = {14}, number = {10}, pages = {713-725}, pmid = {37128855}, issn = {1674-8018}, support = {CAAS-ZDRW202308//Agricultural Science and Technology Innovation Program/ ; 42277297//Natural Science Foundation of China/ ; 2022ZB325//Jiangsu Funding Program for Excellent Postdoctoral Talent/ ; //Scientific and Technology Innovation Project/ ; C12021A04115//China Academy of Chinese Medical Sciences/ ; //Fundamental Research Funds/ ; ZZ13-YQ-095//Central Public Welfare Research Institutes/ ; }, mesh = {*Software ; *Microbiota ; Sequence Analysis, DNA ; Language ; }, abstract = {With the gradual maturity of sequencing technology, many microbiome studies have published, driving the emergence and advance of related analysis tools. R language is the widely used platform for microbiome data analysis for powerful functions. However, tens of thousands of R packages and numerous similar analysis tools have brought major challenges for many researchers to explore microbiome data. How to choose suitable, efficient, convenient, and easy-to-learn tools from the numerous R packages has become a problem for many microbiome researchers. We have organized 324 common R packages for microbiome analysis and classified them according to application categories (diversity, difference, biomarker, correlation and network, functional prediction, and others), which could help researchers quickly find relevant R packages for microbiome analysis. Furthermore, we systematically sorted the integrated R packages (phyloseq, microbiome, MicrobiomeAnalystR, Animalcules, microeco, and amplicon) for microbiome analysis, and summarized the advantages and limitations, which will help researchers choose the appropriate tools. Finally, we thoroughly reviewed the R packages for microbiome analysis, summarized most of the common analysis content in the microbiome, and formed the most suitable pipeline for microbiome analysis. This paper is accompanied by hundreds of examples with 10,000 lines codes in GitHub, which can help beginners to learn, also help analysts compare and test different tools. This paper systematically sorts the application of R in microbiome, providing an important theoretical basis and practical reference for the development of better microbiome tools in the future. All the code is available at GitHub github.com/taowenmicro/EasyMicrobiomeR.}, } @article {pmid37126733, year = {2023}, author = {de Siqueira, GMV and Guazzaroni, ME}, title = {Host-Dependent Improvement of GFP Expression in Pseudomonas putida KT2440 Using Terminators of Metagenomic Origin.}, journal = {ACS synthetic biology}, volume = {12}, number = {5}, pages = {1562-1566}, doi = {10.1021/acssynbio.3c00098}, pmid = {37126733}, issn = {2161-5063}, mesh = {*Pseudomonas putida/genetics/metabolism ; }, abstract = {Transcriptional terminators are key players in the flow of genetic information, but are often overlooked in circuit design. In this work, we used the Standard European Vector Architecture (SEVA) as a scaffold to investigate the effects of different terminators in the output of a reporter construct expressed in two bacterial species, and found that replacing the conventional T1 and T0 transcriptional terminators of the SEVA vector format with a set of broad-host metagenomic terminators resulted in a significant improvement in the signal of a fluorescent device in Pseudomonas putida KT2440 but not in Escherichia coli DH10B. Our results suggest that replacing the default set of terminators present in the SEVA specification may be an useful strategy for fine-tuning circuit expression in P. putida, which can be leveraged for the development of new devices with improved performance in this microbial host.}, } @article {pmid37126495, year = {2023}, author = {Mineeva, O and Danciu, D and Schölkopf, B and Ley, RE and Rätsch, G and Youngblut, ND}, title = {ResMiCo: Increasing the quality of metagenome-assembled genomes with deep learning.}, journal = {PLoS computational biology}, volume = {19}, number = {5}, pages = {e1011001}, pmid = {37126495}, issn = {1553-7358}, mesh = {*Metagenome/genetics ; *Deep Learning ; Genomics/methods ; Sequence Analysis, DNA/methods ; Metagenomics ; Software ; }, abstract = {The number of published metagenome assemblies is rapidly growing due to advances in sequencing technologies. However, sequencing errors, variable coverage, repetitive genomic regions, and other factors can produce misassemblies, which are challenging to detect for taxonomically novel genomic data. Assembly errors can affect all downstream analyses of the assemblies. Accuracy for the state of the art in reference-free misassembly prediction does not exceed an AUPRC of 0.57, and it is not clear how well these models generalize to real-world data. Here, we present the Residual neural network for Misassembled Contig identification (ResMiCo), a deep learning approach for reference-free identification of misassembled contigs. To develop ResMiCo, we first generated a training dataset of unprecedented size and complexity that can be used for further benchmarking and developments in the field. Through rigorous validation, we show that ResMiCo is substantially more accurate than the state of the art, and the model is robust to novel taxonomic diversity and varying assembly methods. ResMiCo estimated 7% misassembled contigs per metagenome across multiple real-world datasets. We demonstrate how ResMiCo can be used to optimize metagenome assembly hyperparameters to improve accuracy, instead of optimizing solely for contiguity. The accuracy, robustness, and ease-of-use of ResMiCo make the tool suitable for general quality control of metagenome assemblies and assembly methodology optimization.}, } @article {pmid37125929, year = {2023}, author = {Zhu, RS and Zhou, LH and Cheng, JH and Luo, Y and Qiu, WJ and Huang, JT and Jiang, YK and Zhao, HZ and Wang, X and Chen, ZQ and Zhu, LP}, title = {Diagnostic Laboratory Features and Performance of an Aspergillus IgG Lateral Flow Assay in a Chronic Pulmonary Aspergillosis Cohort.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0026423}, pmid = {37125929}, issn = {2165-0497}, mesh = {Humans ; Retrospective Studies ; *Delayed Diagnosis ; *Pulmonary Aspergillosis/diagnosis ; Aspergillus/genetics ; Immunoglobulin G ; Aspergillus fumigatus ; Persistent Infection ; Antibodies, Fungal ; Chronic Disease ; }, abstract = {Chronic pulmonary aspergillosis (CPA) is a chronic and progressive fungal disease with high morbidity and mortality. Avoiding diagnostic delay and misdiagnosis are concerns for CPA patients. However, diagnostic practice is poorly evaluated, especially in resource-constrained areas where Aspergillus antibody testing tools are lacking. This study aimed to investigate the diagnostic laboratory findings in a retrospective CPA cohort and to evaluate the performance of a novel Aspergillus IgG lateral flow assay (LFA; Era Biology, Tianjin, China). During January 2016 and December 2021, suspected CPA patients were screened at the Center for Infectious Diseases at Huashan Hospital. A total of 126 CPA patients were enrolled. Aspergillus IgG was positive in 72.1% with chronic cavitary pulmonary aspergillosis, 75.0% with chronic necrotizing pulmonary aspergillosis, 41.7% with simple aspergilloma, and 30.3% with Aspergillus nodule(s). The cavitary CPA subtypes had significantly higher levels of Aspergillus IgG. Aspergillus IgG was negative in 52 patients, who were finally diagnosed by histopathology, respiratory culture, and metagenomic next-generation sequencing (mNGS). Sputum culture was positive in 39.3% (42/107) of patients and Aspergillus fumigatus was the most common species (69.0%, 29/42). For CPA cohort versus controls, the sensitivity and specificity of the LFA were 55.6% and 92.7%, respectively. In a subgroup analysis, the LFA was highly sensitive for A. fumigatus-associated chronic cavitary pulmonary aspergillosis (CCPA; 96.2%, 26/27). Given the complexity of the disease, a combination of serological and non-serological tests should be considered to avoid misdiagnosis of CPA. The novel LFA has a satisfactory performance and allows earlier screening and diagnosis of CPA patients. IMPORTANCE There are concerns on avoiding diagnostic delay and misdiagnosis for chronic pulmonary aspergillosis due to its high morbidity and mortality. A proportion of CPA patients test negative for Aspergillus IgG. An optimal diagnostic strategy for CPA requires in-depth investigation based on real-world diagnostic practice, which has been rarely discussed. We summarized the clinical and diagnostic laboratory findings of 126 CPA patients with various CPA subtypes. Aspergillus IgG was the most sensitive test for diagnosing CPA. However, it was negative in 52 patients, who were finally diagnosed by non-serological tests, including biopsy, respiratory culture, and metagenomic next-generation sequencing. We also evaluated a novel Aspergillus IgG lateral flow assay, which showed a satisfactory performance in cavitary CPA patients and was highly specific to Aspergillus fumigatus. This study gives a full picture of the diagnostic practice for CPA patients in Chinese context and calls for early diagnosis of CPA with combined approaches.}, } @article {pmid37125649, year = {2023}, author = {Zheng, J and Ge, Q and Yan, Y and Zhang, X and Huang, L and Yin, Y}, title = {dbCAN3: automated carbohydrate-active enzyme and substrate annotation.}, journal = {Nucleic acids research}, volume = {51}, number = {W1}, pages = {W115-W121}, pmid = {37125649}, issn = {1362-4962}, support = {R01 GM140370/GM/NIGMS NIH HHS/United States ; R21 AI171952/AI/NIAID NIH HHS/United States ; }, mesh = {*Carbohydrates ; Carbohydrate Metabolism/genetics ; Polysaccharides ; Databases, Factual ; *Microbiota ; }, abstract = {Carbohydrate active enzymes (CAZymes) are made by various organisms for complex carbohydrate metabolism. Genome mining of CAZymes has become a routine data analysis in (meta-)genome projects, owing to the importance of CAZymes in bioenergy, microbiome, nutrition, agriculture, and global carbon recycling. In 2012, dbCAN was provided as an online web server for automated CAZyme annotation. dbCAN2 (https://bcb.unl.edu/dbCAN2) was further developed in 2018 as a meta server to combine multiple tools for improved CAZyme annotation. dbCAN2 also included CGC-Finder, a tool for identifying CAZyme gene clusters (CGCs) in (meta-)genomes. We have updated the meta server to dbCAN3 with the following new functions and components: (i) dbCAN-sub as a profile Hidden Markov Model database (HMMdb) for substrate prediction at the CAZyme subfamily level; (ii) searching against experimentally characterized polysaccharide utilization loci (PULs) with known glycan substates of the dbCAN-PUL database for substrate prediction at the CGC level; (iii) a majority voting method to consider all CAZymes with substrate predicted from dbCAN-sub for substrate prediction at the CGC level; (iv) improved data browsing and visualization of substrate prediction results on the website. In summary, dbCAN3 not only inherits all the functions of dbCAN2, but also integrates three new methods for glycan substrate prediction.}, } @article {pmid37125213, year = {2023}, author = {Sheng, Z and Li, J and Chen, C and Xie, J and Xu, Y and Zhou, H and Xie, Q}, title = {Chronic Splenic Melioidosis in a Patient with Fever of Unknown Origin Diagnosed by Metagenomics Next-Generation Sequencing: An Emerging Cause and Literature Review.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {2403-2408}, pmid = {37125213}, issn = {1178-6973}, abstract = {INTRODUCTION: Human melioidosis is an emerging infectious disease in tropical areas of China, and chronic melioidosis can be a rare cause of fever of unknown origin (FUO). Timely diagnosis may improve the prognosis of melioidosis.

CASE PRESENTATION: We report a case of melioidosis with splenic abscesses caused by Burkholderia pseudomallei in a 57-year-old man, who presented with FUO. Positron emission tomography/computed tomography (PET/CT) revealed multiple hypermetabolic lesions in the spleen. The spleen biopsy was conducted and metagenomics next-generation sequencing (mNGS) of the spleen specimen identified the presence of B. pseudomallei, confirming the diagnosis of melioidosis. Antimicrobial treatment was initiated with intravenous meropenem, followed by oral faropenem. During the follow-up, the patient was in good condition except having a low-grade fever occasionally. A splenectomy was performed, and subsequent culture and mNGS of the spleen pus were both positive for B. pseudomallei. Histopathological characteristics of chronic splenic melioidosis were noted.

CONCLUSION: Melioidosis is a serious endemic disease, and it is critical to raise awareness about this disease.}, } @article {pmid37125210, year = {2023}, author = {Rzoska-Smith, E and Stelzer, R and Monterio, M and Cary, SC and Williamson, A}, title = {DNA repair enzymes of the Antarctic Dry Valley metagenome.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1156817}, pmid = {37125210}, issn = {1664-302X}, abstract = {Microbiota inhabiting the Dry Valleys of Antarctica are subjected to multiple stressors that can damage deoxyribonucleic acid (DNA) such as desiccation, high ultraviolet light (UV) and multiple freeze-thaw cycles. To identify novel or highly-divergent DNA-processing enzymes that may enable effective DNA repair, we have sequenced metagenomes from 30 sample-sites which are part of the most extensive Antarctic biodiversity survey undertaken to date. We then used these to construct wide-ranging sequence similarity networks from protein-coding sequences and identified candidate genes involved in specialized repair processes including unique nucleases as well as a diverse range of adenosine triphosphate (ATP) -dependent DNA ligases implicated in stationary-phase DNA repair processes. In one of the first direct investigations of enzyme function from these unique samples, we have heterologously expressed and assayed a number of these enzymes, providing insight into the mechanisms that may enable resident microbes to survive these threats to their genomic integrity.}, } @article {pmid37125200, year = {2023}, author = {Chen, C and Chen, S and Wang, B}, title = {A glance at the gut microbiota and the functional roles of the microbes based on marmot fecal samples.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1035944}, pmid = {37125200}, issn = {1664-302X}, abstract = {Research on the gut microbiota, which involves a large and complex microbial community, is an important part of infectious disease control. In China, few studies have been reported on the diversity of the gut microbiota of wild marmots. To obtain full details of the gut microbiota, including bacteria, fungi, viruses and archaea, in wild marmots, we have sequenced metagenomes from five sample-sites feces on the Hulun Buir Grassland in Inner Mongolia, China. We have created a comprehensive database of bacterial, fungal, viral, and archaeal genomes and aligned metagenomic sequences (determined based on marmot fecal samples) against the database. We delineated the detailed and distinct gut microbiota structures of marmots. A total of 5,891 bacteria, 233 viruses, 236 fungi, and 217 archaea were found. The dominant bacterial phyla were Firmicutes, Proteobacteria, Bacteroidetes, and Actinomycetes. The viral families were Myoviridae, Siphoviridae, Phycodnaviridae, Herpesviridae and Podoviridae. The dominant fungi phyla were Ascomycota, Basidiomycota, and Blastocladiomycota. The dominant archaea were Biobacteria, Omoarchaea, Nanoarchaea, and Microbacteria. Furthermore, the gut microbiota was affected by host species and environment, and environment was the most important factor. There were 36,989 glycoside hydrolase genes in the microbiota, with 365 genes homologous to genes encoding β-glucosidase, cellulase, and cellulose β-1,4-cellobiosidase. Additionally, antibiotic resistance genes such as macB, bcrA, and msbA were abundant. To sum up, the gut microbiota of marmot had population diversity and functional diversity, which provides a basis for further research on the regulatory effects of the gut microbiota on the host. In addition, metagenomics revealed that the gut microbiota of marmots can degrade cellulose and hemicellulose.}, } @article {pmid37125190, year = {2023}, author = {Li, J and Qu, W and Hu, C and Liu, Z and Yan, H}, title = {Antidepressants amitriptyline, fluoxetine, and traditional Chinese medicine Xiaoyaosan caused alterations in gut DNA virome composition and function in rats exposed chronic unpredictable mild stress.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1132403}, pmid = {37125190}, issn = {1664-302X}, abstract = {BACKGROUND: In clinical practice, antidepressant drugs are widely used to treat depression. Previous studies have attention to the impact of antidepressants on the bacterial microbiome, while the role of these drugs in the gut virome is still unclear.

METHODS: In this study, we estimated the effects of antidepressant amitriptyline (Ami), fluoxetine (Flu), and traditional Chinese medicine Xiaoyaosan (XYS) administration on gut viral composition and function in a chronic unpredictable mild stress (CUMS)-induced depression rat model based on shotgun metagenomic sequencing.

RESULTS: The results showed that treatment with Ami, Flu, and XYS significantly changed the gut viral composition compared with the CUMS-induced rats. At the family level, the abundance of f_unclassified_Caudovirales in CUMS rats was remarkably lower than in the HC rats, nevertheless, XYS significantly recovered the abundance of Caudovirales. Meanwhile, the abundance of Podoviridae was expanded in CUMS rats compared with the HC rats, and the profile was then significantly reduced after XYS treatment. Furthermore, both antidepressants and XYS increased the abundance of Siphoviridae compared with the CUMS rats, but only Ami treatments had significant differences. Subsequent function annotation further implied that Ami, Flu, and XYS showed to involve an alteration of the diverse viral functions, such as carbohydrate metabolism, xenobiotics biodegradation and metabolism, community-prokaryotes, translation, and neurodegenerative disease. Additionally, the co-occurrence network displayed that there are complex interactions between viral operational taxonomic units (vOTUs) represented by temperate phages and the majority of bacterial genera in the intestine ecosystem.

CONCLUSION: Our study proved for the first time that depression is characterized by massive alterations and functional distortion of the gut viruses, and after oral administration of Ami, Flu, and XYS could affect disordered gut virome, which could be a novel target in depression.}, } @article {pmid37125170, year = {2023}, author = {Munro-Ehrlich, M and Nothaft, DB and Fones, EM and Matter, JM and Templeton, AS and Boyd, ES}, title = {Parapatric speciation of Meiothermus in serpentinite-hosted aquifers in Oman.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1138656}, pmid = {37125170}, issn = {1664-302X}, abstract = {The factors that control the distribution and evolution of microbial life in subsurface environments remain enigmatic due to challenges associated with sampling fluids from discrete depth intervals via boreholes while avoiding mixing of fluids. Here, using an inflatable packer system, fracture waters were isolated and collected from three discrete depth intervals spanning >130 m in a borehole intersecting an ultramafic rock formation undergoing serpentinization in the Samail Ophiolite, Sultanate of Oman. Near surface aquifer waters were moderately reducing and had alkaline pH while deeper aquifer waters were reduced and had hyperalkaline pH, indicating extensive influence by serpentinization. Metagenomic sequencing and analysis of DNA from filtered biomass collected from discrete depth intervals revealed an abundance of aerobes in near surface waters and a greater proportion of anaerobes at depth. Yet the abundance of the putatively obligate aerobe, Meiothermus, increased with depth, providing an opportunity to evaluate the influence of chemical and spatial variation on its distribution and speciation. Two clades of Meiothermus metagenome assembled genomes (MAGs) were identified that correspond to surface and deep populations termed Types I (S) and II (D), respectively; both clades comprised an apparently Oman-specific lineage indicating a common ancestor. Type II (D) clade MAGs encoded fewer genes and were undergoing slower genome replication as inferred from read mapping. Further, single nucleotide variants (SNVs) and mobile genetic elements identified among MAGs revealed detectable, albeit limited, evidence for gene flow/recombination between spatially segregated Type I (S) and Type II (D) populations. Together, these observations indicate that chemical variation generated by serpentinization, combined with physical barriers that reduce/limit dispersal and gene flow, allowed for the parapatric speciation of Meiothermus in the Samail Ophiolite or a geologic precursor. Further, Meiothermus genomic data suggest that deep and shallow aquifer fluids in the Samail Ophiolite may mix over shorter time scales than has been previously estimated from geochemical data.}, } @article {pmid37125168, year = {2023}, author = {Das, R and Tamang, B and Najar, IN and Thakur, N and Mondal, K}, title = {First report on metagenomics and their predictive functional analysis of fermented bamboo shoot food of Tripura, North East India.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1158411}, pmid = {37125168}, issn = {1664-302X}, abstract = {Moiya pansung, mileye amileye, moiya koshak, and midukeye are naturally fermented bamboo shoot foods of Tripura. The present study aimed to reveal the whole microbial community structure of naturally fermented moiya pangsung, mileye amileye, moiya koshak, and midukeye along with the prediction of microbial functional profiles by shotgun metagenomic sequence analysis. The metataxonomic profile of moiya pangsung, mileye amileye, moiya koshak, and midukeye samples showed different domains, viz., bacteria (97.70%) followed by the virus (0.76%), unclassified (0.09%), eukaryotes (1.46%) and archaea (0.05%). Overall, 49 phyla, 409 families, 841 genera, and 1,799 species were found in all the fermented bamboo shoot samples collected from different places of Tripura. Firmicutes was the most abundant phylum (89.28%) followed by Proteobacteria (5.13%), Bacteroidetes (4.38%), Actinobacteria (1.02%), and Fusobacteria (0.17%). Lactiplantibacillus plantarum was the most abundant species in moiya pangsung, mileye amileye, moiya koshak, and midukeye followed by Lactococcus lactis, Levilactobacillus brevis, Leuconostoc mesenteroides, Weissella paramesenteroides, Leuconostoc kimchii, Pediococcus pentosaceus, Leuconostoc gasicomitatum, and Lacticaseibacillus casei. A few phyla of fungus were found, viz., Ascomycota, Basidiomycota, and Glomeromycota, where Ascomycota was present in high abundance. Functional analysis of moiya pangsung, mileye amileye, moiya koshak, and midukeye metagenome revealed the genes for the synthesis and metabolism of a wide range of bioactive compounds including, various essential amino acids, and conjugated amino acids. The abundance profile and predictive analysis of fermented bamboo shoots revealed a huge plethora of essential microorganisms and KEGG analysis revealed genes for amino acid metabolism, pectin degradation, lipid metabolism, and many other essential pathways that can be essential for the improvement of nutritional and sensory qualities of the fermented bamboo shoot products.}, } @article {pmid37124465, year = {2023}, author = {Cheng, SC and Liu, CB and Yao, XQ and Hu, JY and Yin, TT and Lim, BK and Chen, W and Wang, GD and Zhang, CL and Irwin, DM and Zhang, ZG and Zhang, YP and Yu, L}, title = {Hologenomic insights into mammalian adaptations to myrmecophagy.}, journal = {National science review}, volume = {10}, number = {4}, pages = {nwac174}, pmid = {37124465}, issn = {2053-714X}, abstract = {Highly specialized myrmecophagy (ant- and termite-eating) has independently evolved multiple times in species of various mammalian orders and represents a textbook example of phenotypic evolutionary convergence. We explored the mechanisms involved in this unique dietary adaptation and convergence through multi-omic analyses, including analyses of host genomes and transcriptomes, as well as gut metagenomes, in combination with validating assays of key enzymes' activities, in the species of three mammalian orders (anteaters, echidnas and pangolins of the orders Xenarthra, Monotremata and Pholidota, respectively) and their relatives. We demonstrate the complex and diverse interactions between hosts and their symbiotic microbiota that have provided adaptive solutions for nutritional and detoxification challenges associated with high levels of protein and lipid metabolisms, trehalose degradation, and toxic substance detoxification. Interestingly, we also reveal their spatially complementary cooperation involved in degradation of ants' and termites' chitin exoskeletons. This study contributes new insights into the dietary evolution of mammals and the mechanisms involved in the coordination of physiological functions by animal hosts and their gut commensals.}, } @article {pmid37124420, year = {2023}, author = {Morita, R and Kubota-Koketsu, R and Lu, X and Sasaki, T and Nakayama, EE and Liu, YC and Okuzaki, D and Motooka, D and Wing, JB and Fujikawa, Y and Ichida, Y and Amo, K and Goto, T and Hara, J and Shirano, M and Yamasaki, S and Shioda, T}, title = {COVID-19 relapse associated with SARS-CoV-2 evasion from CD4[+] T-cell recognition in an agammaglobulinemia patient.}, journal = {iScience}, volume = {26}, number = {5}, pages = {106685}, pmid = {37124420}, issn = {2589-0042}, abstract = {A 25-year-old patient with a primary immunodeficiency lacking immunoglobulin production experienced a relapse after a 239-day period of persistent severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Viral genetic sequencing demonstrated that SARS-CoV-2 had evolved during the infection period, with at least five mutations associated with host cellular immune recognition. Among them, the T32I mutation in ORF3a was found to evade recognition by CD4[+] T cells. The virus found after relapse showed an increased proliferative capacity in vitro. SARS-CoV-2 may have evolved to evade recognition by CD4[+] T cells and increased in its proliferative capacity during the persistent infection, likely leading to relapse. These mutations may further affect viral clearance in hosts with similar types of human leukocyte antigens. The early elimination of SARS-CoV-2 in immunocompromised patients is therefore important not only to improve the condition of patients but also to prevent the emergence of mutants that threaten public health.}, } @article {pmid37124058, year = {2023}, author = {Shimoda, M and Morimoto, K and Hosoya, M and Osugi, A and Mitarai, S and Tanaka, Y and Fujiwara, K and Yoshimori, K and Ohta, K}, title = {Causative antigens of humidifier lung in vapor from a humidifier: A case report.}, journal = {Respiratory medicine case reports}, volume = {43}, number = {}, pages = {101851}, pmid = {37124058}, issn = {2213-0071}, abstract = {A 68-year-old man exhibited fever and cough three weeks prior to hospital admission after three months of ultrasonic humidifier usage. Chest computed tomography showed bilateral ground-glass opacities, lymphocyte levels in the bronchoalveolar lavage fluid were elevated (60.8%), and the histological examination of a transbronchial lung biopsy showed lymphocytic alveolitis. He gradually improved without medication after he stopped using the humidifier. Accordingly, humidifier lung was the diagnosis. Humidifier water and vapor collected from the patient's humidifier were investigated. Humidifier vapor was obtained by collecting the condensed moisture. Laboratory examinations exhibited gram-negative rods and a high concentration of endotoxin and (1 → 3)-β-D-glucan in both vapor and water. The serum-precipitating antibodies showed a stronger reaction against humidifier vapor than against humidifier water. 16S rRNA metagenomic analysis revealed a high percentage of sequences of Spirosoma lacussanchae and Sphingomonas spp. in both the humidifier vapor and water. The percentages of sequence reads were lower in humidifier vapor than in water; conversely, sequences of Pseudomonas spp. and Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium were more concentrated in the humidifier vapor than in humidifier water. Although the reason for the different bacterial ratios between humidifier vapor and water is uncertain, the bacteria that were more concentrated in humidifier vapor than in humidifier water might have been the causative antigen underlying the humidifier lung diagnosis. This is the first report to indicate the presence of causative antigens in humidifier vapor.}, } @article {pmid37124044, year = {2023}, author = {Hotta, F and Eguchi, H and Kuwahara, T and Nakayama-Imaohji, H and Shimomura, Y and Kusaka, S}, title = {Disturbances in the ocular surface microbiome by perioperative antimicrobial eye drops.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1172345}, pmid = {37124044}, issn = {2235-2988}, mesh = {Humans ; Aged ; Ophthalmic Solutions/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Eye/microbiology ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Microbiota/genetics ; }, abstract = {We aimed to elucidate the effects of antimicrobial eye drops used in the perioperative period of ophthalmic surgery on the ocular surface microbiome by metagenomic analysis. Twenty-eight eyes from 15 patients (mean age 74.1 years) with no history of eye drop use within 3 months before cataract surgery were included in this study. Gatifloxacin eye drops were used in all patients in the perioperative period. The antimicrobial eye drops were started 3 days before surgery. They were discontinued after conjunctival sac specimen collection for 2 weeks after the surgery. Conjunctival sac specimens were collected to investigate the alterations in the ocular surface microbiome by meta-16S analysis targeting the V3-V4 region of the bacterial 16S rRNA gene. Principal coordinate analysis showed that the bacterial composition tended to be different before and 2 and 4 weeks after surgery. Individual observations on six eyes showed that the bacterial composition at 12 weeks after surgery was closer to that before surgery than to that at 4 weeks after surgery in two eyes, while the bacterial composition in the remaining four eyes was different at various time points. Before surgery, Firmicutes, Proteobacteria, and Bacteroidetes were predominant; however, 2 weeks after surgery, the proportion of Proteobacteria increased and that of Firmicutes decreased. A similar trend was noticed 4 weeks after surgery, although antibacterial eye drops had been discontinued 2 weeks after surgery. The Shannon-Weaver coefficient showed a decreasing trend at 2-, 4-, and 12-weeks post operation compared to that before operation. The diversity of the microbiome decreased significantly at 2- and 4-weeks after surgery when compared to that before surgery (p < 0.05). The ocular surface microbiome is easily disrupted by antimicrobial eye drops, and it needs recovery time. In such cases, the ocular surface microbiome is presumed to contain many antimicrobial-resistant bacteria. In some cases, it may not recover, and a new microbiome is formed.}, } @article {pmid37124032, year = {2023}, author = {Xu, Q and Xi, X and Feng, D and Sang, Q and Sheng, Y and Ding, R and Xu, A}, title = {A case report: Severe disseminated infection caused by Strongyloides stercoralis in an immunocompromised patient by metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1082412}, pmid = {37124032}, issn = {2235-2988}, mesh = {Male ; Animals ; Humans ; Aged ; *Strongyloides stercoralis/genetics ; *Strongyloidiasis/diagnosis ; Sputum ; Immunocompromised Host ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Strongyloides stercoralis (S. stercoralis) is a nematode that is widely distributed in the tropical and subtropical regions of the world and which can cause severe disseminated infection in immunocompromised individuals. However, strongyloidiasis, the disease caused by S. stercoralis, is difficult to diagnose because of its non-specific clinical presentation and the inadequate performance of conventional diagnostic methods.

CASE DESCRIPTION: We report the case of a 75-year-old male patient with severe disseminated infection caused by S. stercoralis. The patient had a medical history of seasonal bronchitis and, as a consequence, had taken prednisone for many years. Initial clinical tests failed to detect any pathogens, but metagenomic next-generation sequencing (mNGS) resulted in the identification of S. stercoralis in the patient's bronchoalveolar lavage fluid (BALF) and blood. Subsequently, routine testing repeatedly detected nematode larvae in the patient's stool and sputum. Through a combination of mNGS results and clinical symptoms, the patient was finally diagnosed with severe disseminated infection caused by S. stercoralis.

CONCLUSION: The clinical manifestations of disease caused by infection with S. stercoralis are not specific; therefore, early and accurate diagnosis is very important. mNGS can detect S. stercoralis even when it is present at only a low level. This case report supports the notion that mNGS is a valuable tool in the diagnosis of severe disseminated infections caused by S. stercoralis in immunocompromised patients.}, } @article {pmid37123618, year = {2023}, author = {Meng, Z and Ma, J and Sun, Z and Yang, C and Leng, J and Zhu, W and Cheng, Y}, title = {Characterization of a novel bifunctional enzyme from buffalo rumen metagenome and its effect on in vitro ruminal fermentation and microbial community composition.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {13}, number = {}, pages = {137-149}, pmid = {37123618}, issn = {2405-6383}, abstract = {To efficiently use lignocellulosic materials in ruminants, it is crucial to explore effective enzymes, especially bifunctional enzymes. In this study, a novel stable bifunctional cellulase-xylanase protein from buffalo rumen metagenome was expressed and characterized, CelXyn2. The enzyme displayed optimal activity at pH 6.0 and 45 °C. The residual endoglucanase and xylanase activities were 90.6% and 86.4% after a 60-min pre-incubation at 55 °C. Hydrolysis of rice straw, wheat straw, sheepgrass and sugar beet pulp by CelXyn2 showed its ability to degrade both cellulose and hemicellulose polymers. Treatment with CelXyn2 improved the hydrolysis of agricultural residues with an evident increase in production of total gas, lactate and volatile fatty acids. The results of 16S rRNA and real-time PCR showed that the effect on in vitro ruminal microbial community depended on fermentation substrates. This study demonstrated that CelXyn2 could strengthen lignocellulose hydrolysis and in vitro ruminal fermentation. These characteristics of CelXyn2 distinguish it as a promising candidate for agricultural application.}, } @article {pmid37122759, year = {2023}, author = {Wang, Y and Xia, X and Zhou, X and Zhan, T and Dai, Q and Zhang, Y and Zhang, W and Shu, Y and Li, W and Xu, H}, title = {Association of gut microbiome and metabolites with onset and treatment response of patients with pemphigus vulgaris.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1114586}, pmid = {37122759}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Pemphigus/therapy ; Glucocorticoids ; Eubacterium/metabolism ; Fatty Acids, Volatile/metabolism ; Bacteria/metabolism ; }, abstract = {BACKGROUND: Gut dysbiosis and gut microbiome-derived metabolites have been implicated in both disease onset and treatment response, but this has been rarely demonstrated in pemphigus vulgaris (PV). Here, we aim to systematically characterize the gut microbiome to assess the specific microbial species and metabolites associated with PV.

METHODS: We enrolled 60 PV patients and 19 matched healthy family members, and collected 100 fecal samples (60 treatment-naïve, 21 matched post-treatment, and 19 controls). Metagenomic shotgun sequencing and subsequent quality control/alignment/annotation were performed to assess the composition and microbial species, in order to establish the association between gut microbiome with PV onset and treatment response. In addition, we evaluated short-chain fatty acids (SCFAs) in PV patients through targeted metabolomics analysis.

RESULTS: The diversity of the gut microbiome in PV patients deviates from the healthy family members but not between responder and non-responder, or before and after glucocorticoid treatment. However, the relative abundance of several microbial species, including the pathogenic bacteria (e.g., Escherichia coli) and some SCFA-producing probiotics (e.g., Eubacterium ventriosum), consistently differed between the two groups in each comparison. Escherichia coli was enriched in PV patients and significantly decreased after treatment in responders. In contrast, Eubacterium ventriosum was enriched in healthy family members and significantly increased particularly in responders after treatment. Consistently, several gut microbiome-derived SCFAs were enriched in healthy family members and significantly increased after treatment (e.g., butyric acid and valeric acid).

CONCLUSIONS: This study supports the association between the gut microbiome and PV onset, possibly through disrupting the balance of gut pathogenic bacteria and probiotics and influencing the level of gut microbiome-derived SCFAs. Furthermore, we revealed the potential relationship between specific microbial species and glucocorticoid treatment.}, } @article {pmid37122075, year = {2023}, author = {Simpson, JB and Sekela, JJ and Carry, BS and Beaty, V and Patel, S and Redinbo, MR}, title = {Diverse but desolate landscape of gut microbial azoreductases: A rationale for idiopathic IBD drug response.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2203963}, pmid = {37122075}, issn = {1949-0984}, support = {P30 CA016086/CA/NCI NIH HHS/United States ; R01 GM135218/GM/NIGMS NIH HHS/United States ; R01 GM137286/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Prodrugs ; *Amlodipine Besylate, Olmesartan Medoxomil Drug Combination ; *Crohn Disease ; *Colitis, Ulcerative ; Mesalamine/therapeutic use ; *Inflammatory Bowel Diseases/drug therapy ; }, abstract = {Prodrugs reliant on microbial activation are widely used but exhibit a range of efficacies that remain poorly understood. The anti-inflammatory compound 5-aminosalicylic acid (5-ASA), which is packaged in a variety of azo-linked prodrugs provided to most Ulcerative Colitis (UC) patients, shows confounding inter-individual variabilities in response. Such prodrugs must be activated by azo-bond reduction to form 5-ASA, a process that has been attributed to both enzymatic and non-enzymatic catalysis. Gut microbial azoreductases (AzoRs) are the first catalysts shown to activate azo-linked drugs and to metabolize toxic azo-chemicals. Here, we chart the scope of the structural and functional diversity of AzoRs in health and in patients with the inflammatory bowel diseases (IBDs) UC and Crohn's Disease (CD). Using structural metagenomics, we define the landscape of gut microbial AzoRs in 413 healthy donor and 1059 IBD patient fecal samples. Firmicutes encode a significantly higher number of unique AzoRs compared to other phyla. However, structural and biochemical analyses of distinct AzoRs from the human microbiome reveal significant differences between prevalent orthologs in the processing of toxic azo-dyes, and their generally poor activation of IBD prodrugs. Furthermore, while individuals with IBD show higher abundances of AzoR-encoding gut microbial taxa than healthy controls, the overall abundance of AzoR-encoding microbes is markedly low in both disease and health. Together, these results establish that gut microbial AzoRs are functionally diverse but sparse in both health and disease, factors that may contribute to non-optimal processing of azo-linked prodrugs and idiopathic IBD drug responses.}, } @article {pmid37121282, year = {2023}, author = {Di Cesare, A and Sabatino, R and Sbaffi, T and Fontaneto, D and Brambilla, D and Beghi, A and Pandolfi, F and Borlandelli, C and Fortino, D and Biccai, G and Genoni, P and Corno, G}, title = {Anthropogenic pollution drives the bacterial resistome in a complex freshwater ecosystem.}, journal = {Chemosphere}, volume = {331}, number = {}, pages = {138800}, doi = {10.1016/j.chemosphere.2023.138800}, pmid = {37121282}, issn = {1879-1298}, mesh = {*Ecosystem ; *Genes, Bacterial ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Lakes/microbiology ; Rivers/microbiology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Aquatic ecosystems in anthropogenically impacted areas are important reservoirs of antibiotic resistance genes (ARGs) of allochthonous origin. However, the dynamics of the different ARGs within the bacterial communities of lakes and rivers, as well as the factors that drive their selection, are not completely understood. In this study, we analysed the fate of the bacterial resistome (total content of ARGs and of metal resistance genes, MRGs) for a period of six months (summer-winter) in a continuum lake-river-lake system (Lake Varese, River Bardello, Lake Maggiore) in Northern Italy, by shotgun metagenomics. The metagenomic data were then compared with chemical, physical and microbiological data, to infer the role of anthropogenic pressure in the different sampling stations. ARGs and MRGs were more abundant and diverse in the River Bardello, characterised by the highest anthropogenic pollution. The date of sampling influenced ARGs and MRGs, with higher abundances in summer (August) than in fall or in winter, when the impact of the treated wastewater discharge in the river was limited by a higher water flow from Lake Varese. ARG and MRG abundances were significantly correlated and they co-occurred in the main network analysis modules with potential pathogenic bacteria. Different levels of anthropogenic impact selectively promoted specific ARGs while others, generally abundant in waters, were not affected by anthropogenic pressure. Reducing the level of anthropogenic pressure resulted in a rapid decrease of most ARGs. From our results, the role of anthropogenic pressure in promoting the spread of specific antibiotic resistances and of potential pathogens in aquatic ecosystem becomes clear. Finally we highlight the strict correlation between ARGs and MRGs suggesting their potential co-selection in stressed aquatic bacterial communities.}, } @article {pmid37121198, year = {2023}, author = {Li, L and Yan, W and Zhang, B and Zhang, H and Geng, R and Sun, S and Guan, X}, title = {Coupling of selenate reduction and pyrrhotite oxidation by indigenous microbial consortium in natural aquifer.}, journal = {Water research}, volume = {238}, number = {}, pages = {119987}, doi = {10.1016/j.watres.2023.119987}, pmid = {37121198}, issn = {1879-2448}, mesh = {Selenic Acid ; *Microbial Consortia ; Ferric Compounds ; Oxidation-Reduction ; Ferrous Compounds ; *Groundwater ; }, abstract = {Pyrrhotite is ubiquitously found in natural environment and involved in diverse (bio)processes. However, the pyrrhotite-driven bioreduction of toxic selenate [Se(VI)] remains largely unknown. This study demonstrates that Se(VI) is successfully bioreduced under anaerobic condition with the participation of pyrrhotite for the first time. Completely removal of Se(VI) was achieved at initial concentration of 10 mg/L Se(VI) and 0.56 mL/min flow rate in continuous column experiment with indigenous microbial consortium and pyrrhotite. Variation in hydrochemistry and hydrodynamics affected Se(VI) removal performance. Se(VI) was reduced to insoluble Se(0) while elements in pyrrhotite were oxidized to Fe(III) and SO4[2-]. Breakthrough study indicated that biotic activity contributed 81.4 ± 1.07% to Se(VI) transformation. Microbial community analysis suggested that chemoautotrophic genera (e.g., Thiobacillus) could realize pyrrhotite oxidation and Se(VI) reduction independently, while heterotrophic genera (e.g., Bacillus, Pseudomonas) contributed to Se(VI) detoxification by utilizing metabolic intermediates generated through Fe(II) and S(-II) oxidation, which were further verified by pure culture tests. Metagenomic and qPCR analyses indicated genes encoding enzymes for Se(VI) reduction (e.g., serA, napA and srdBAC), S oxidation (e.g., soxB) and Fe oxidation (e.g., mtrA) were upregulated. The elevated electron transporters (e.g., nicotinamide adenine dinucleotide, cytochrome c) promoted electron transfer from pyrrhotite to Se(VI). This study gains insights into Se biogeochemistry under the effect of Fe(II)-bearing minerals and provides a sustainable strategy for Se(VI) bioremediation in natural aquifer.}, } @article {pmid37120702, year = {2023}, author = {Bar-Shalom, R and Rozenberg, A and Lahyani, M and Hassanzadeh, B and Sahoo, G and Haber, M and Burgsdorf, I and Tang, X and Squatrito, V and Gomez-Consarnau, L and Béjà, O and Steindler, L}, title = {Rhodopsin-mediated nutrient uptake by cultivated photoheterotrophic Verrucomicrobiota.}, journal = {The ISME journal}, volume = {17}, number = {7}, pages = {1063-1073}, pmid = {37120702}, issn = {1751-7370}, mesh = {*Rhodopsin/genetics/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; *Bacteria/genetics ; Phototrophic Processes ; Biological Transport ; Rhodopsins, Microbial/genetics/metabolism ; Phylogeny ; }, abstract = {Rhodopsin photosystems convert light energy into electrochemical gradients used by the cell to produce ATP, or for other energy-demanding processes. While these photosystems are widespread in the ocean and have been identified in diverse microbial taxonomic groups, their physiological role in vivo has only been studied in few marine bacterial strains. Recent metagenomic studies revealed the presence of rhodopsin genes in the understudied Verrucomicrobiota phylum, yet their distribution within different Verrucomicrobiota lineages, their diversity, and function remain unknown. In this study, we show that more than 7% of Verrucomicrobiota genomes (n = 2916) harbor rhodopsins of different types. Furthermore, we describe the first two cultivated rhodopsin-containing strains, one harboring a proteorhodopsin gene and the other a xanthorhodopsin gene, allowing us to characterize their physiology under laboratory-controlled conditions. The strains were isolated in a previous study from the Eastern Mediterranean Sea and read mapping of 16S rRNA gene amplicons showed the highest abundances of these strains at the deep chlorophyll maximum (source of their inoculum) in winter and spring, with a substantial decrease in summer. Genomic analysis of the isolates suggests that motility and degradation of organic material, both energy demanding functions, may be supported by rhodopsin phototrophy in Verrucomicrobiota. Under culture conditions, we show that rhodopsin phototrophy occurs under carbon starvation, with light-mediated energy generation supporting sugar transport into the cells. Overall, this study suggests that photoheterotrophic Verrucomicrobiota may occupy an ecological niche where energy harvested from light enables bacterial motility toward organic matter and supports nutrient uptake.}, } @article {pmid37120693, year = {2023}, author = {Kuppa Baskaran, DK and Umale, S and Zhou, Z and Raman, K and Anantharaman, K}, title = {Metagenome-based metabolic modelling predicts unique microbial interactions in deep-sea hydrothermal plume microbiomes.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {42}, pmid = {37120693}, issn = {2730-6151}, abstract = {Deep-sea hydrothermal vents are abundant on the ocean floor and play important roles in ocean biogeochemistry. In vent ecosystems such as hydrothermal plumes, microorganisms rely on reduced chemicals and gases in hydrothermal fluids to fuel primary production and form diverse and complex microbial communities. However, microbial interactions that drive these complex microbiomes remain poorly understood. Here, we use microbiomes from the Guaymas Basin hydrothermal system in the Pacific Ocean to shed more light on the key species in these communities and their interactions. We built metabolic models from metagenomically assembled genomes (MAGs) and infer possible metabolic exchanges and horizontal gene transfer (HGT) events within the community. We highlight possible archaea-archaea and archaea-bacteria interactions and their contributions to the robustness of the community. Cellobiose, D-Mannose 1-phosphate, O2, CO2, and H2S were among the most exchanged metabolites. These interactions enhanced the metabolic capabilities of the community by exchange of metabolites that cannot be produced by any other community member. Archaea from the DPANN group stood out as key microbes, benefiting significantly as acceptors in the community. Overall, our study provides key insights into the microbial interactions that drive community structure and organisation in complex hydrothermal plume microbiomes.}, } @article {pmid37120676, year = {2023}, author = {Ha, AD and Moniruzzaman, M and Aylward, FO}, title = {Assessing the biogeography of marine giant viruses in four oceanic transects.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {43}, pmid = {37120676}, issn = {2730-6151}, support = {R35 GM147290/GM/NIGMS NIH HHS/United States ; }, abstract = {Viruses of the phylum Nucleocytoviricota are ubiquitous in ocean waters and play important roles in shaping the dynamics of marine ecosystems. In this study, we leveraged the bioGEOTRACES metagenomic dataset collected across the Atlantic and Pacific Oceans to investigate the biogeography of these viruses in marine environments. We identified 330 viral genomes, including 212 in the order Imitervirales and 54 in the order Algavirales. We found that most viruses appeared to be prevalent in shallow waters (<150 m), and that viruses of the Mesomimiviridae (Imitervirales) and Prasinoviridae (Algavirales) are by far the most abundant and diverse groups in our survey. Five mesomimiviruses and one prasinovirus are particularly widespread in oligotrophic waters; annotation of these genomes revealed common stress response systems, photosynthesis-associated genes, and oxidative stress modulation genes that may be key to their broad distribution in the pelagic ocean. We identified a latitudinal pattern in viral diversity in one cruise that traversed the North and South Atlantic Ocean, with viral diversity peaking at high latitudes of the northern hemisphere. Community analyses revealed three distinct Nucleocytoviricota communities across latitudes, categorized by latitudinal distance towards the equator. Our results contribute to the understanding of the biogeography of these viruses in marine systems.}, } @article {pmid37120327, year = {2023}, author = {Jia, XM and Wu, BX and Chen, BD and Li, KT and Liu, YD and Xu, Y and Wang, J and Zhang, X}, title = {Compositional and functional aberrance of the gut microbiota in treatment-naïve patients with primary Sjögren's syndrome.}, journal = {Journal of autoimmunity}, volume = {141}, number = {}, pages = {103050}, doi = {10.1016/j.jaut.2023.103050}, pmid = {37120327}, issn = {1095-9157}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Sjogren's Syndrome/genetics ; *Lupus Erythematosus, Systemic/complications ; Metagenome ; *Lung Diseases, Interstitial ; }, abstract = {OBJECTIVES: To investigate the compositional and functional characteristics of the gut microbiota in primary Sjögren's syndrome (pSS) and compare them with those in systemic lupus erythematosus (SLE).

METHODS: Stool samples from 78 treatment-naïve pSS patients and 78 matched healthy controls were detected by shotgun metagenomic sequencing and compared with those from 49 treatment-naïve SLE patients. The virulence loads and mimotopes of the gut microbiota were also assessed by sequence alignment.

RESULTS: The gut microbiota of treatment-naïve pSS patients had lower richness and evenness and showed a different community distribution than that of healthy controls. The microbial species enriched in the pSS-associated gut microbiota included Lactobacillus salivarius, Bacteroides fragilis, Ruminococcus gnavus, Clostridium bartlettii, Clostridium bolteae, Veillonella parvula, and Streptococcus parasanguinis. Lactobacillus salivarius was the most discriminating species in the pSS patients, especially in those with interstitial lung disease (ILD). Among the differentiating microbial pathways, the superpathway of l-phenylalanine biosynthesis was also further enriched in pSS complicated with ILD. There were more virulence genes carried by the gut microbiota in pSS patients, most of which encoded peritrichous flagella, fimbriae, or curli fimbriae, three types of bacterial surface organelles involved in bacterial colonization and invasion. Five microbial peptides with the potential to mimic pSS-related autoepitopes were also enriched in the pSS gut. SLE and pSS shared significant gut microbial traits, including community distribution, altered microbial taxonomy and pathways, and enriched virulence genes. However, Ruminococcus torques was depleted in pSS patients but enriched in SLE patients compared to healthy controls.

CONCLUSIONS: The gut microbiota in treatment-naïve pSS patients was disturbed and shared significant similarity with that in SLE patients.}, } @article {pmid37120212, year = {2023}, author = {Ammoun, I and Kothe, CI and Mohellibi, N and Beal, C and Yaacoub, R and Renault, P}, title = {Lebanese fermented goat milk products: From tradition to meta-omics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {168}, number = {}, pages = {112762}, doi = {10.1016/j.foodres.2023.112762}, pmid = {37120212}, issn = {1873-7145}, mesh = {Female ; Animals ; *Cultured Milk Products ; Ecosystem ; *Kefir ; *Lactococcus lactis ; Goats ; }, abstract = {Ambriss, Serdaleh and Labneh El Darff are traditional Lebanese products made from fermented goat's milk. A questionnaire completed by 50 producers of these products showed that they are prepared by periodic percolation either by milk or by Laban in amphora or goat skins during the lactation season. Production is carried out on a small scale and in a limited number of production units, often by elderly people, resulting in a real risk of disappearance of these products and loss of the corresponding microbial resources. In this study, 34 samples from 18 producers were characterized by culture-dependent and -independent analyses. The results obtained from these two methods were radically different, the latter revealing in Ambriss and Serdaleh the co-dominance of Lactobacillus kefiranofaciens, a fastidious-growing species, and Lactococcus lactis in a viable but not culturable state. Overall, their composition is reminiscent of kefir grains. Phylogenomic and functional analyses of the genomes of the key species Lb. kefiranofaciens have revealed differences from those found in kefir, particularly in their polysaccharide genes, which may explain the absence of grains. However, Labneh El Darff displayed a dominance of Lactobacillus delbrueckii, probably due to the addition of Laban. In addition, the study identified several zoonotic pathogens, including Streptococcus parasuis, which dominated in one sample. Metagenome-Assembled Genome (MAG) analysis indicated that this pathogen acquired lactose utilization genes through horizontal gene transfer. The contamination of the herd with Mycoplasmopsis agalactiae in the Chouf region was also revealed by MAG analysis of the Serdaleh samples. Antibiotic resistance genes were detected in most of the samples, particularly in the Serdaleh ones, where the dominant L. lactis strains possessed a plasmid with a multi-resistance island. Finally, this study paves the way for further analyses to shed light on the resilience of these ecosystems established in amphora or in goatskins and to improve hygiene practices for milk production.}, } @article {pmid37119735, year = {2023}, author = {Palmu, J and Börschel, CS and Ortega-Alonso, A and Markó, L and Inouye, M and Jousilahti, P and Salido, RA and Sanders, K and Brennan, C and Humphrey, GC and Sanders, JG and Gutmann, F and Linz, D and Salomaa, V and Havulinna, AS and Forslund, SK and Knight, R and Lahti, L and Niiranen, T and Schnabel, RB}, title = {Gut microbiome and atrial fibrillation-results from a large population-based study.}, journal = {EBioMedicine}, volume = {91}, number = {}, pages = {104583}, pmid = {37119735}, issn = {2352-3964}, mesh = {Humans ; *Atrial Fibrillation/etiology/complications ; *Gastrointestinal Microbiome ; Heart ; Bacteria/genetics ; Aging ; Incidence ; }, abstract = {BACKGROUND: Atrial fibrillation (AF) is an important heart rhythm disorder in aging populations. The gut microbiome composition has been previously related to cardiovascular disease risk factors. Whether the gut microbial profile is also associated with the risk of AF remains unknown.

METHODS: We examined the associations of prevalent and incident AF with gut microbiota in the FINRISK 2002 study, a random population sample of 6763 individuals. We replicated our findings in an independent case-control cohort of 138 individuals in Hamburg, Germany.

FINDINGS: Multivariable-adjusted regression models revealed that prevalent AF (N = 116) was associated with nine microbial genera. Incident AF (N = 539) over a median follow-up of 15 years was associated with eight microbial genera with false discovery rate (FDR)-corrected P < 0.05. Both prevalent and incident AF were associated with the genera Enorma and Bifidobacterium (FDR-corrected P < 0.001). AF was not significantly associated with bacterial diversity measures. Seventy-five percent of top genera (Enorma, Paraprevotella, Odoribacter, Collinsella, Barnesiella, Alistipes) in Cox regression analyses showed a consistent direction of shifted abundance in an independent AF case-control cohort that was used for replication.

INTERPRETATION: Our findings establish the basis for the use of microbiome profiles in AF risk prediction. However, extensive research is still warranted before microbiome sequencing can be used for prevention and targeted treatment of AF.

FUNDING: This study was funded by European Research Council, German Ministry of Research and Education, Academy of Finland, Finnish Medical Foundation, and the Finnish Foundation for Cardiovascular Research, the Emil Aaltonen Foundation, and the Paavo Nurmi Foundation.}, } @article {pmid37119673, year = {2023}, author = {Cui, H and Zhang, C and Zhao, K and Liu, J and Pu, J and Kong, Y and Dong, S and Chen, L and Zhao, Y and Chen, Y and Chen, Z and Zhang, L and Wang, Z and Guo, Z}, title = {Effects of different laying periods on airborne bacterial diversity and antibiotic resistance genes in layer hen houses.}, journal = {International journal of hygiene and environmental health}, volume = {251}, number = {}, pages = {114173}, doi = {10.1016/j.ijheh.2023.114173}, pmid = {37119673}, issn = {1618-131X}, mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Bacteria ; Drug Resistance, Microbial ; Chickens ; Aerosols ; Genes, Bacterial/genetics ; }, abstract = {Poultry farms are a complex environment for close contact between humans and animals. Accumulating evidence has indicated that pathogens and drug resistance genes in chicken houses may pose a serious threat to public health and economic concerns. However, insufficient knowledge of the indoor aerosol microbiome and resistome profiles of layer hen houses hampers the understanding of their health effects. Environmental surveillance of antibiotic resistance may contribute to a better understanding and management of the human exposure risk of bioaerosols under the environmental conditions of chicken houses. In addition, the chicken house has a long operation cycle, and the bacterial diversity and antibiotic resistance genes of aerosols in different periods may be different. In this study, air samples were collected from 18 chicken houses on three farms, including the early laying period (EL), peak laying period (PL), and late laying period (LL). 16S rRNA gene sequencing and metagenomics were used to study the composition of the bacteria and resistome in aerosols of layer hen houses and the results showed that they varied with laying period. The highest alpha diversity of bacteria was observed in PL bioaerosols. The dominant bacterial phyla included Firmicutes, Bacteroidetes and Proteobacteria. Three potential pathogenic bacterial genera (Bacteroides, Corynebacterium and Fusobacterium) were found. The most abundant ARG type was aminoglycosides in all laying periods. In total, 22 possible ARG host genera were detected. ARG subtypes and abundance were both higher in LL. Network analysis also showed higher co-occurrence patterns between the bacteria and resistome in bioaerosols. The laying period plays an important role in the bacterial community and resistome in layer house aerosols.}, } @article {pmid37119661, year = {2023}, author = {Chi, X and Zhao, Z and Han, Q and Yan, H and Ji, B and Chai, Y and Li, S and Liu, K}, title = {Insights into autotrophic carbon fixation strategies through metagonomics in the sediments of seagrass beds.}, journal = {Marine environmental research}, volume = {188}, number = {}, pages = {106002}, doi = {10.1016/j.marenvres.2023.106002}, pmid = {37119661}, issn = {1879-0291}, mesh = {*Carbon Cycle ; Autotrophic Processes ; *Hydroxybutyrates ; Carbon ; Geologic Sediments ; }, abstract = {Seagrass beds contributes up to 10% ocean carbon storage. Carbon fixation in seagrass bed greatly affect global carbon cycle. Currently, six carbon fixation pathways are widely studied: Calvin, reductive tricarboxylic acid (rTCA), Wood-Ljungdahl (WL), 3-hydroxypropionate (3HP), 3-hydroxypropionate/4-hydroxybutyrate (3HP/4HB) and dicarboxylate/4-hydroxybutyrate (DC/4-HB). Despite the knowledges about carbon fixation increase, the carbon fixation strategies in seagrass bed sediment remain unexplored. We collected seagrass bed sediment samples from three sites with different characteristics in Weihai, a city in Shandong, China. The carbon fixation strategies were investigated through metagenomics. The results exhibited that five pathways were present, of which Calvin and WL were the most dominant. The community structure of microorganisms containing the key genes of these pathways were further analyzed, and those dominant microorganisms with carbon fixing potential were revealed. Phosphorus significantly negatively corelated with those microorganisms. This study provides an insight into the strategies of carbon fixation in seagrass bed sediments.}, } @article {pmid37119525, year = {2024}, author = {Wang, Z and Yuan, X and Zhu, Z and Pang, L and Ding, S and Li, X and Kang, Y and Hei, G and Zhang, L and Zhang, X and Wang, S and Jian, X and Li, Z and Zheng, C and Fan, X and Hu, S and Shi, Y and Song, X}, title = {Multiomics Analyses Reveal Microbiome-Gut-Brain Crosstalk Centered on Aberrant Gamma-Aminobutyric Acid and Tryptophan Metabolism in Drug-Naïve Patients with First-Episode Schizophrenia.}, journal = {Schizophrenia bulletin}, volume = {50}, number = {1}, pages = {187-198}, pmid = {37119525}, issn = {1745-1701}, support = {U21A20367//National Natural Science Foundation of China/ ; 2021YFC2702100//National Key R&D Program of China/ ; 32070679//Natural Science Foundation of China/ ; 21IRTSTHN027//Science and Technology Innovation Teams in Universities of Henan Province/ ; 204200510019//Zhong Yuan Technological Innovation Leading Talents/ ; SBGJ201808//Medical Science and Technology Foundation of Health and Family Planning Commission of Henan Province/ ; 2017-BSTDJJ-04//Zhengzhou University/ ; SBGJ202003029//Henan Provincial Health Commission/ ; 2017SHZDZX01//Shanghai Municipal Science and Technology Major Project/ ; tsqn201812153//Taishan Scholar Program of Shandong Province/ ; ZR2019YQ14//Natural Science Foundation of Shandong Province/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Tryptophan ; *Schizophrenia/genetics ; Multiomics ; Brain ; *Microbiota ; gamma-Aminobutyric Acid/metabolism ; Neurotransmitter Agents/metabolism/pharmacology ; }, abstract = {BACKGROUND AND HYPOTHESIS: Schizophrenia (SCZ) is associated with complex crosstalk between the gut microbiota and host metabolism, but the underlying mechanism remains elusive. Investigating the aberrant neurotransmitter processes reflected by alterations identified using multiomics analysis is valuable to fully explain the pathogenesis of SCZ.

STUDY DESIGN: We conducted an integrative analysis of multiomics data, including the serum metabolome, fecal metagenome, single nucleotide polymorphism data, and neuroimaging data obtained from a cohort of 127 drug-naïve, first-episode SCZ patients and 92 healthy controls to characterize the microbiome-gut-brain axis in SCZ patients. We used pathway-based polygenic risk score (PRS) analyses to determine the biological pathways contributing to genetic risk and mediation effect analyses to determine the important neuroimaging features. Additionally, a random forest model was generated for effective SCZ diagnosis.

STUDY RESULTS: We found that the altered metabolome and dysregulated microbiome were associated with neuroactive metabolites, including gamma-aminobutyric acid (GABA), tryptophan, and short-chain fatty acids. Further structural and functional magnetic resonance imaging analyses highlighted that gray matter volume and functional connectivity disturbances mediate the relationships between Ruminococcus_torgues and Collinsella_aerofaciens and symptom severity and the relationships between species Lactobacillus_ruminis and differential metabolites l-2,4-diaminobutyric acid and N-acetylserotonin and cognitive function. Moreover, analyses of the Polygenic Risk Score (PRS) support that alterations in GABA and tryptophan neurotransmitter pathways are associated with SCZ risk, and GABA might be a more dominant contributor.

CONCLUSIONS: This study provides new insights into systematic relationships among genes, metabolism, and the gut microbiota that affect brain functional connectivity, thereby affecting SCZ pathogenesis.}, } @article {pmid37119391, year = {2023}, author = {Di Ciaula, A and Bonfrate, L and Khalil, M and Garruti, G and Portincasa, P}, title = {Contribution of the microbiome for better phenotyping of people living with obesity.}, journal = {Reviews in endocrine & metabolic disorders}, volume = {24}, number = {5}, pages = {839-870}, pmid = {37119391}, issn = {1573-2606}, mesh = {Animals ; Humans ; Overweight/complications ; Obesity/metabolism ; *Microbiota ; *Gastrointestinal Microbiome/physiology ; Diet ; Inflammation/complications ; }, abstract = {Obesity has reached epidemic proportion worldwide and in all ages. Available evidence points to a multifactorial pathogenesis involving gene predisposition and environmental factors. Gut microbiota plays a critical role as a major interface between external factors, i.e., diet, lifestyle, toxic chemicals, and internal mechanisms regulating energy and metabolic homeostasis, fat production and storage. A shift in microbiota composition is linked with overweight and obesity, with pathogenic mechanisms involving bacterial products and metabolites (mainly endocannabinoid-related mediators, short-chain fatty acids, bile acids, catabolites of tryptophan, lipopolysaccharides) and subsequent alterations in gut barrier, altered metabolic homeostasis, insulin resistance and chronic, low-grade inflammation. Although animal studies point to the links between an "obesogenic" microbiota and the development of different obesity phenotypes, the translational value of these results in humans is still limited by the heterogeneity among studies, the high variation of gut microbiota over time and the lack of robust longitudinal studies adequately considering inter-individual confounders. Nevertheless, available evidence underscores the existence of several genera predisposing to obesity or, conversely, to lean and metabolically health phenotype (e.g., Akkermansia muciniphila, species from genera Faecalibacterium, Alistipes, Roseburia). Further longitudinal studies using metagenomics, transcriptomics, proteomics, and metabolomics with exact characterization of confounders are needed in this field. Results must confirm that distinct genera and specific microbial-derived metabolites represent effective and precision interventions against overweight and obesity in the long-term.}, } @article {pmid37118882, year = {2023}, author = {Ceylani, T}, title = {Effect of SCD probiotics supplemented with tauroursodeoxycholic acid (TUDCA) application on the aged rat gut microbiota composition.}, journal = {Journal of applied microbiology}, volume = {134}, number = {5}, pages = {}, doi = {10.1093/jambio/lxad092}, pmid = {37118882}, issn = {1365-2672}, mesh = {Rats ; Animals ; Rats, Sprague-Dawley ; *Gastrointestinal Microbiome ; Taurochenodeoxycholic Acid/pharmacology ; *Probiotics/pharmacology ; }, abstract = {AIMS: In this study, the effects of SCD Probiotics with tauroursodeoxycholic acid (TUDCA) application on the aged rat gut microbiota (GM) composition were investigated.

METHODS AND RESULTS: Twenty-four-month-old Sprague-Dawley rats were given 300 mg/kg of TUDCA along with 3 mL (1 × 108 CFU) of SCD probiotics for 7 days. The bacterial profile was determined by the metagenome applied to the cecum content. TUDCA, SCD probiotics, and TUDCA with SCD probiotics designed GM differently. TUDCA and SCD probiotics have the most different dominant species profiles.

CONCLUSIONS: SCD probiotics and TUDCA have their own unique effects on the species found in GM, and when they are evaluated together, the species found in GM are restructured differently.}, } @article {pmid37118698, year = {2023}, author = {Shon, WJ and Song, JW and Oh, SH and Lee, KH and Seong, H and You, HJ and Seong, JK and Shin, DM}, title = {Gut taste receptor type 1 member 3 is an intrinsic regulator of Western diet-induced intestinal inflammation.}, journal = {BMC medicine}, volume = {21}, number = {1}, pages = {165}, pmid = {37118698}, issn = {1741-7015}, mesh = {Mice ; Animals ; Taste ; Diet, Western/adverse effects ; PPAR gamma ; *Colitis/chemically induced/metabolism ; Inflammation/metabolism ; *Inflammatory Bowel Diseases/pathology ; TOR Serine-Threonine Kinases/adverse effects ; Butyrates/adverse effects ; Mice, Inbred C57BL ; Disease Models, Animal ; }, abstract = {BACKGROUND: Long-term intake of a Western diet (WD), characterized by a high-fat content and sugary drinks, is hypothesized to contribute to the development of inflammatory bowel disease (IBD). Despite the identified clinical association, the molecular mechanisms by which dietary changes contribute to IBD development remain unknown. Therefore, we examined the influence of long-term intake of a WD on intestinal inflammation and the mechanisms by which WD intake affects IBD development.

METHODS: Mice fed normal diet or WD for 10 weeks, and bowel inflammation was evaluated through pathohistological and infiltrated inflammatory cell assessments. To understand the role of intestinal taste receptor type 1 member 3 (TAS1R3) in WD-induced intestinal inflammation, cultured enteroendocrine cells harboring TAS1R3, subjected to RNA interference or antagonist treatment, and Tas1r3-deficient mice were used. RNA-sequencing, flow cytometry, 16S metagenomic sequencing, and bioinformatics analyses were performed to examine the involved mechanisms. To demonstrate their clinical relevance, intestinal biopsies from patients with IBD and mice with dextran sulfate sodium-induced colitis were analyzed.

RESULTS: Our study revealed for the first time that intestinal TAS1R3 is a critical mediator of WD-induced intestinal inflammation. WD-fed mice showed marked TAS1R3 overexpression with hallmarks of serious bowel inflammation. Conversely, mice lacking TAS1R3 failed to exhibit inflammatory responses to WD. Mechanistically, intestinal transcriptome analysis revealed that Tas1r3 deficiency suppressed mTOR signaling, significantly increasing the expression of PPARγ (a major mucosal defense enhancer) and upregulating the expression of PPARγ target-gene (tight junction protein and antimicrobial peptide). The gut microbiota of Tas1r3-deficient mice showed expansion of butyrate-producing Clostridia. Moreover, an increased expression of host PPARγ-signaling pathway proteins was positively correlated with butyrate-producing microbes, suggesting that intestinal TAS1R3 regulates the relationship between host metabolism and gut microflora in response to dietary factors. In cultured intestinal cells, regulation of the TAS1R3-mTOR-PPARγ axis was critical for triggering an inflammatory response via proinflammatory cytokine production and secretion. Abnormal regulation of the axis was observed in patients with IBD.

CONCLUSIONS: Our findings suggest that the TAS1R3-mTOR-PPARγ axis in the gut links Western diet consumption with intestinal inflammation and is a potential therapeutic target for IBD.}, } @article {pmid37118575, year = {2023}, author = {Neal, AL and Barrat, HA and Bacq-Lebreuil, A and Qin, Y and Zhang, X and Takahashi, T and Rubio, V and Hughes, D and Clark, IM and Cárdenas, LM and Gardiner, LJ and Krishna, R and Glendining, ML and Ritz, K and Mooney, SJ and Crawford, JW}, title = {Arable soil nitrogen dynamics reflect organic inputs via the extended composite phenotype.}, journal = {Nature food}, volume = {4}, number = {1}, pages = {51-60}, pmid = {37118575}, issn = {2662-1355}, support = {BBS/E/C/000I0320/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/C/000J0100/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Soil/chemistry ; *Nitrogen/analysis ; Agriculture ; Carbon/chemistry ; Nitrous Oxide/analysis ; }, abstract = {Achieving food security requires resilient agricultural systems with improved nutrient-use efficiency, optimized water and nutrient storage in soils, and reduced gaseous emissions. Success relies on understanding coupled nitrogen and carbon metabolism in soils, their associated influences on soil structure and the processes controlling nitrogen transformations at scales relevant to microbial activity. Here we show that the influence of organic matter on arable soil nitrogen transformations can be decoded by integrating metagenomic data with soil structural parameters. Our approach provides a mechanistic explanation of why organic matter is effective in reducing nitrous oxide losses while supporting system resilience. The relationship between organic carbon, soil-connected porosity and flow rates at scales relevant to microbes suggests that important increases in nutrient-use efficiency could be achieved at lower organic carbon stocks than currently envisaged.}, } @article {pmid37118062, year = {2022}, author = {Xu, Q and Wu, C and Zhu, Q and Gao, R and Lu, J and Valles-Colomer, M and Zhu, J and Yin, F and Huang, L and Ding, L and Zhang, X and Zhang, Y and Xiong, X and Bi, M and Chen, X and Zhu, Y and Liu, L and Liu, Y and Chen, Y and Fan, J and Sun, Y and Wang, J and Cao, Z and Fan, C and Ehrlich, SD and Segata, N and Qin, N and Qin, H}, title = {Metagenomic and metabolomic remodeling in nonagenarians and centenarians and its association with genetic and socioeconomic factors.}, journal = {Nature aging}, volume = {2}, number = {5}, pages = {438-452}, pmid = {37118062}, issn = {2662-8465}, mesh = {Aged, 80 and over ; Child ; Humans ; Aged ; Middle Aged ; *Centenarians ; *Nonagenarians ; Longevity/genetics ; Aging/genetics ; Socioeconomic Factors ; }, abstract = {A better understanding of the biological and environmental variables that contribute to exceptional longevity has the potential to inform the treatment of geriatric diseases and help achieve healthy aging. Here, we compared the gut microbiome and blood metabolome of extremely long-lived individuals (94-105 years old) to that of their children (50-79 years old) in 116 Han Chinese families. We found extensive metagenomic and metabolomic remodeling in advanced age and observed a generational divergence in the correlations with socioeconomic factors. An analysis of quantitative trait loci revealed that genetic associations with metagenomic and metabolomic features were largely generation-specific, but we also found 131 plasma metabolic quantitative trait loci associations that were cross-generational with the genetic variants concentrated in six loci. These included associations between FADS1/2 and arachidonate, PTPA and succinylcarnitine and FLVCR1 and choline. Our characterization of the extensive metagenomic and metabolomic remodeling that occurs in people reaching extreme ages may offer new targets for aging-related interventions.}, } @article {pmid37117202, year = {2023}, author = {Hu, X and Li, Y and Wu, J and Zhang, H and Huang, Y and Tan, X and Wen, L and Zhou, X and Xie, P and Olasunkanmi, OI and Zhou, J and Sun, Z and Liu, M and Zhang, G and Yang, J and Zheng, P and Xie, P}, title = {Changes of gut microbiota reflect the severity of major depressive disorder: a cross sectional study.}, journal = {Translational psychiatry}, volume = {13}, number = {1}, pages = {137}, pmid = {37117202}, issn = {2158-3188}, mesh = {Humans ; *Depressive Disorder, Major/microbiology ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; *Microbiota ; Feces/microbiology ; Bacteria ; }, abstract = {Disturbed gut microbiota is a potential factor in the pathogenesis of major depressive disorder (MDD), yet whether gut microbiota dysbiosis is associated with the severity of MDD remains unclear. Here, we performed shotgun metagenomic profiling of cross-sectional stool samples from MDD (n = 138) and healthy controls (n = 155). The patients with MDD were divided into three groups according to Hamilton Depression Rating Scale 17 (HAMD-17), including mild (n = 24), moderate (n = 72) and severe (n = 42) individuals, respectively. We found that microbial diversity was closely related to the severity of MDD. Compared to HCs, the abundance of Bacteroides was significantly increased in both moderate and severe MDD, while Ruminococcus and Eubacterium depleted mainly in severe group. In addition, we identified 99 bacteria species specific to severity of depression. Furthermore, a panel of microbiota marker comprising of 37 bacteria species enabled to effectively distinguish MDD patients with different severity. Together, we identified different perturbation patterns of gut microbiota in mild-to-severe depression, and identified potential diagnostic and therapeutic targets.}, } @article {pmid37116802, year = {2023}, author = {Castillo, J and Alom, J and Gomez-Arias, A and Cebekhulu, S and Matu, A and Cason, E and Valverde, A}, title = {Bacterial communities shift and influence in an acid mine drainage treatment using barium carbonate disperse alkaline substrate system.}, journal = {The Science of the total environment}, volume = {885}, number = {}, pages = {163526}, doi = {10.1016/j.scitotenv.2023.163526}, pmid = {37116802}, issn = {1879-1026}, mesh = {Humans ; *Ecosystem ; RNA, Ribosomal, 16S/genetics ; *Water Pollutants, Chemical/analysis ; Metals ; Acids ; }, abstract = {Chemical passive treatment systems used to remediate acid mine drainage has been evaluated based mainly on the reactivity of the chemical alkaline reagents, overlooking the activity of the microorganisms that proliferate in these artificial ecosystems. In this study, the bacterial communities of a unique passive treatment system known as BDAS (Barium carbonate Dispersed Alkaline Substrate) were investigated using 16S rRNA gene metagenomic sequencing combined with hydrochemical characterization of the AMD and phenotypic characterization of biogenic precipitates. According to the hydrochemical characterization, the water quality improved as the water progressed through the system, with a drastic increase in the pH (up to alkaline conditions) and total organic carbon, as well as the removal of main contaminants such as Ca[2+], SO4[2-], Fe[3+], Al[3+], and Mn[2+]. These environmental changes resulted in an increase in bacterial diversity (richness) after the inlet and in the shift of the bacterial communities from chemoautotrophs (e.g., Ferrovum and Acidiphilum) to chemoheterotrophs (e.g., Brevundimonas and Geobacter). Some of these taxa harbour potential to immobilize metals, aiding in the treatment of the water. One of the mechanisms involved in the immobilization of metals is microbially induced calcium carbonate precipitation, which seems to occur spontaneously in BDAS. The production of biofilm was also observed in most parts of the system, except in the inlet, helping with the removal of metals. However, in the long run, the build-up of biofilm and precipitation of metals could clog (i.e., biofouling) the pores of the matrix, reducing the treatment efficiency. Potential human pathogens (e.g. Legionella) were also detected in BDAS indicating the need for a treatment step at the end of the system to remove pathogenic microorganisms. These findings present a new perspective of the bacterial communities and their effects (both positively and negatively) in a chemical passive treatment system.}, } @article {pmid37116481, year = {2023}, author = {Manara, S and Selma-Royo, M and Huang, KD and Asnicar, F and Armanini, F and Blanco-Miguez, A and Cumbo, F and Golzato, D and Manghi, P and Pinto, F and Valles-Colomer, M and Amoroso, L and Corrias, MV and Ponzoni, M and Raffaetà, R and Cabrera-Rubio, R and Olcina, M and Pasolli, E and Collado, MC and Segata, N}, title = {Maternal and food microbial sources shape the infant microbiome of a rural Ethiopian population.}, journal = {Current biology : CB}, volume = {33}, number = {10}, pages = {1939-1950.e4}, pmid = {37116481}, issn = {1879-0445}, mesh = {Female ; Humans ; Infant ; Infant, Newborn ; *Microbiota ; Bacteria ; Milk, Human/microbiology ; Mothers ; *Gastrointestinal Microbiome ; Feces/microbiology ; }, abstract = {The human microbiome seeding starts at birth, when pioneer microbes are acquired mainly from the mother. Mode of delivery, antibiotic prophylaxis, and feeding method have been studied as modulators of mother-to-infant microbiome transmission, but other key influencing factors like modern westernized lifestyles with high hygienization, high-calorie diets, and urban settings, compared with non-westernized lifestyles have not been investigated yet. In this study, we explored the mother-infant sharing of characterized and uncharacterized microbiome members via strain-resolved metagenomics in a cohort of Ethiopian mothers and infants, and we compared them with four other cohorts with different lifestyles. The westernized and non-westernized newborns' microbiomes composition overlapped during the first months of life more than later in life, likely reflecting similar initial breast-milk-based diets. Ethiopian and other non-westernized infants shared a smaller fraction of the microbiome with their mothers than did most westernized populations, despite showing a higher microbiome diversity, and uncharacterized species represented a substantial fraction of those shared in the Ethiopian cohort. Moreover, we identified uncharacterized species belonging to the Selenomonadaceae and Prevotellaceae families specifically present and shared only in the Ethiopian cohort, and we showed that a locally produced fermented food, injera, can contribute to the higher diversity observed in the Ethiopian infants' gut with bacteria that are not part of the human microbiome but are acquired through fermented food consumption. Taken together, these findings highlight the fact that lifestyle can impact the gut microbiome composition not only through differences in diet, drug consumption, and environmental factors but also through its effect on mother-infant strain-sharing patterns.}, } @article {pmid37115566, year = {2023}, author = {Wang, D and Zhang, X and Yin, Y and Chen, D and Ye, J}, title = {First report of Ludwigia yellow vein Vietnam virus causing leaf curling on tobacco plants in Hainan province, China.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-01-23-0034-PDN}, pmid = {37115566}, issn = {0191-2917}, abstract = {Cigar tobacco (Nicotiana tabacum L.) has been recently introduced into China for various industrial applications. From March 2022, certain symptoms of begomovirus infection, including leaf curling and thickening of veins, were sporadically (disease incidence was approximately 0.2%) observed in several cigar tobacco plantations in numerous counties in Hainan Province, China (Figure 1A). These typical symptoms of begomovirus infection were similar to those caused by the sida leaf curl virus-Hainan (SiLCV-HN) begomovirus and its associated betasatellite, as reported in our previous study on cigar tobacco plants in the same region (Wang et al. 2022). In order to determine whether these symptoms were caused by SiLCV-HN or other begomoviruses, samples of leaves were collected from the diseased tobacco plants for DNA extraction, and the total DNA was extracted for viral metagenomics using an Illumina Sequencing platform at Tiangen Biotech, Beijing. A total of 65711396 filtered reads were obtained, of which 65362322 (99.47%) reads matched to the genome of tobacco. The remaining unmapped 349074 (0.53%) reads were analyzed by BLASTn against the virus Refseq Database of GenBank and subsequently assembled. A total of 8 (5+2+1) enriched contigs of the complete sequence of ludwigia yellow vein Vietnam virus (LuYVVNV) and 9 (8+1) contigs of ludwigia yellow vein virus-associated DNA beta (LuYVB) were finally obtained (Table 1). LuYVVNV belongs to the Begomovirus genus that infects various weeds, including Ludwigia octovalvis and Impatiens balsamina. As far as we know, it was reported earliest on weed in Vietnam (Ha et al. 2008). GenBank contains data pertaining to previously identified isolates of LuYVVNV, and the data revealed that the virus was discovered in Vietnam and the Yunnan province of China currently. However, there are no reports on the infection of crops by LuYVVNV to date. The findings of the present study indicated that LuYVVNV and LuYVB could be responsible for the aforementioned symptoms observed on cigar tobacco. The complete genomes of LuYVVNV and LuYVB were amplified using primer pairs designed based on sequence assembly for viral metagenomics (Table 2). Indeed, two DNA bands with length 2763 bp of LuYVVNV genome and 1348 bp of LuYVB were amplified from leaf samples of diseased tobacco (Figure 1B). The products of polymerase chain reaction (PCR) amplification were analyzed by Sanger sequencing, and the complete nucleotide sequences of LuYVVNV and its associated betasatellite were obtained. Analysis with the BLASTn tool of NCBI revealed that the genome sequence of LuYVVNV isolated from the Hainan province of China had the highest identity of 96.9% to a different isolate of LuYVVNV (GenBank accession number: MN210347.1). These two isolates belong to the same strain, according to the latest revision of Begomovirus taxonomy (Brown et al. 2015). The isolate of LuYVVNV identified in this study was designated as LuYVVNV, Hainan isolate (LuYVVNV-HN, GenBank accession number: OP948731). BLASTn analysis further revealed that the associated betasatellite had the highest sequence identity of 96.9% with an LuYVB (GenBank accession number: AJ965541.1) of a different viral isolate, according to the classification and nomenclature of DNA betasatellites of begomoviruses (Briddon et al. 2008). The sequence of LuYVB obtained herein was therefore designated as LuYVB, Hainan isolate (LuYVB-HN, GenBank accession number: OP948732). The pathogenicity of LuYVVNV-HN and LuYVB-HN was determined using infectious clones that were constructed by ligating two fragments of LuYVVNV-HN or LuYVB-HN to a binary pCAMBIA1300 expression vector, as previously described (Wang et al. 2019). Infectious clones of LuYVVNV-HN, LuYVB-HN, and LuYVVNV-HN plus LuYVB-HN were separately agroinfiltrated into N. benthamiana for determining viral pathogenicity. The typical symptoms of begomovirus infection were observed in N. benthamiana plants inoculated with LuYVVNV-HN alone or LuYVVNV-HN plus LuYVB-HN, and the emerging leaves were mildly or severely down-curled, respectively, at 7 days post inoculation (dpi), with 100% disease incidence (6/6) (Figure 1C). Positive PCR products of the AV1 gene of LuYVVNV-HN were obtained from N. benthamiana plants inoculated with LuYVVNV-HN alone or LuYVVNV-HN plus LuYVB-HN. The βC1 gene of LuYVB-HN was only obtained from N. benthamiana plants co-infected with LuYVVNV-HN and LuYVB-HN (Figure 1D). No symptoms of viral infection were observed in plants individually inoculated with LuYVB-HN, and the results of PCR were negative (Figure 1C and 1D). These findings indicated that the N. benthamiana plants had been successfully inoculated with LuYVVNV-HN, and that LuYVB-HN was incapable of causing infections on its own, but functioned as a helper and enhanced viral pathogenicity. This report is the first to identify isolates of LuYVVNV and LuYVB from cigar tobacco, which is an economically important crop plant. The findings provide insights into the epidemic threat of begomovirus reservoirs in weeds to crop plants, and emphasize the need for monitoring and controlling whitefly-transmitted viral diseases in tobacco plantations worldwide (Ye et al. 2021).}, } @article {pmid37115265, year = {2023}, author = {Houttu, N and Benchraka, C and Lotankar, M and Muhli, E and Niinikoski, H and Lahti, L and Laitinen, K}, title = {Gut microbiota composition and function in pregnancy as determinants of prediabetes at two-year postpartum.}, journal = {Acta diabetologica}, volume = {60}, number = {8}, pages = {1045-1054}, pmid = {37115265}, issn = {1432-5233}, support = {258606//Academy of Finland/ ; 295741//Academy of Finland/ ; }, mesh = {Pregnancy ; Humans ; Female ; *Prediabetic State ; *Gastrointestinal Microbiome ; *Diabetes, Gestational ; Blood Glucose ; Postpartum Period ; }, abstract = {AIMS: Deep metagenomics offers an advanced tool for examining the relationship between gut microbiota composition and function and the onset of disease; in this case, does the composition and function of gut microbiota during pregnancy differ in women who develop prediabetes and those who do not at two-year postpartum, and whether the gut microbiota composition associates with glycemic traits.

METHODS: In total, 439 women were recruited in early pregnancy. Gut microbiota was assessed by metagenomics analysis in early (13.9 ± 2.0 gestational weeks) and late pregnancy (35.1 ± 1.0 gestational weeks). Prediabetes was determined using American Diabetes Association criteria as fasting plasma glucose 5.6-6.9 mmol/l analyzed by an enzymatic hexokinase method. Of the women, 39 (22.1%) developed prediabetes by two-year postpartum.

RESULTS: The relative abundances of Escherichia unclassified (FDR < 0.05), Clostridiales bacterium 1_7_ 47FAA (FDR < 0.25) and Parabacteroides (FDR < 0.25) were higher, and those of Ruminococcaceae bacterium D16 (FDR < 0.25), Anaerotruncus unclassified (FDR < 0.25) and Ruminococcaceae noname (FDR < 0.25) were lower in early pregnancy in those women who later developed prediabetes. In late pregnancy, Porphyromonas was higher and Ruminococcus sp 5_1_39BFAA was lower in prediabetes (FDR < 0.25). Furthermore, fasting glucose concentrations associated inversely with Anaerotruncus unclassified in early pregnancy and directly with Ruminococcus sp 5_1_39BFAA in late pregnancy (FDR < 0.25). α-Diversity or β-diversity did not differ significantly between the groups. Predictions of community function during pregnancy were not associated with prediabetes.

CONCLUSIONS: Our study shows that some bacterial species during pregnancy contributed to the onset of prediabetes within two-year postpartum. These were attributable primarily to a lower abundance of short-chain fatty acids-producing bacteria.}, } @article {pmid37115189, year = {2023}, author = {Salamzade, R and Cheong, JZA and Sandstrom, S and Swaney, MH and Stubbendieck, RM and Starr, NL and Currie, CR and Singh, AM and Kalan, LR}, title = {Evolutionary investigations of the biosynthetic diversity in the skin microbiome using lsaBGC.}, journal = {Microbial genomics}, volume = {9}, number = {4}, pages = {}, pmid = {37115189}, issn = {2057-5858}, support = {U19 AI142720/AI/NIAID NIH HHS/United States ; R35 GM137828/GM/NIGMS NIH HHS/United States ; }, mesh = {*Microbiota/genetics ; Metagenome ; Biological Evolution ; }, abstract = {Bacterial secondary metabolites, synthesized by enzymes encoded in biosynthetic gene clusters (BGCs), can underlie microbiome homeostasis and serve as commercialized products, which have historically been mined from a select group of taxa. While evolutionary approaches have proven beneficial for prioritizing BGCs for experimental characterization efforts to uncover new natural products, dedicated bioinformatics tools designed for comparative and evolutionary analysis of BGCs within focal taxa are limited. We thus developed lineage specific analysis of BGCs (lsaBGC; https://github.com/Kalan-Lab/lsaBGC) to aid exploration of microdiversity and evolutionary trends across homologous groupings of BGCs, gene cluster families (GCFs), in any bacterial taxa of interest. lsaBGC enables rapid and direct identification of GCFs in genomes, calculates evolutionary statistics and conservation for BGC genes, and builds a framework to allow for base resolution mining of novel variants through metagenomic exploration. Through application of the suite to four genera commonly found in skin microbiomes, we uncover new insights into the evolution and diversity of their BGCs. We show that the BGC of the virulence-associated carotenoid staphyloxanthin in Staphylococcus aureus is ubiquitous across the genus Staphylococcus . While one GCF encoding the biosynthesis of staphyloxanthin showcases evidence for plasmid-mediated horizontal gene transfer (HGT) between species, another GCF appears to be transmitted vertically amongst a sub-clade of skin-associated Staphylococcus . Further, the latter GCF, which is well conserved in S. aureus , has been lost in most Staphylococcus epidermidis , which is the most common Staphylococcus species on human skin and is also regarded as a commensal. We also identify thousands of novel single-nucleotide variants (SNVs) within BGCs from the Corynebacterium tuberculostearicum sp. complex, a narrow, multi-species clade that features the most prevalent Corynebacterium in healthy skin microbiomes. Although novel SNVs were approximately 10 times as likely to correspond to synonymous changes when located in the top five percentile of conserved sites, lsaBGC identified SNVs that defied this trend and are predicted to underlie amino acid changes within functionally key enzymatic domains. Ultimately, beyond supporting evolutionary investigations of BGCs, lsaBGC also provides important functionalities to aid efforts for the discovery or directed modification of natural products.}, } @article {pmid37114640, year = {2023}, author = {Jia, L and Wu, Y and Dong, Y and Chen, J and Chen, WH and Zhao, XM}, title = {A survey on computational strategies for genome-resolved gut metagenomics.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {3}, pages = {}, doi = {10.1093/bib/bbad162}, pmid = {37114640}, issn = {1477-4054}, mesh = {Humans ; *Metagenomics ; Sequence Analysis, DNA ; *Metagenome ; Bacteria/genetics ; Gastrointestinal Tract ; }, abstract = {Recovering high-quality metagenome-assembled genomes (HQ-MAGs) is critical for exploring microbial compositions and microbe-phenotype associations. However, multiple sequencing platforms and computational tools for this purpose may confuse researchers and thus call for extensive evaluation. Here, we systematically evaluated a total of 40 combinations of popular computational tools and sequencing platforms (i.e. strategies), involving eight assemblers, eight metagenomic binners and four sequencing technologies, including short-, long-read and metaHiC sequencing. We identified the best tools for the individual tasks (e.g. the assembly and binning) and combinations (e.g. generating more HQ-MAGs) depending on the availability of the sequencing data. We found that the combination of the hybrid assemblies and metaHiC-based binning performed best, followed by the hybrid and long-read assemblies. More importantly, both long-read and metaHiC sequencings link more mobile elements and antibiotic resistance genes to bacterial hosts and improve the quality of public human gut reference genomes with 32% (34/105) HQ-MAGs that were either of better quality than those in the Unified Human Gastrointestinal Genome catalog version 2 or novel.}, } @article {pmid37114494, year = {2023}, author = {Li, S and Xia, H and Wang, Z and Zhang, X and Song, T and Li, J and Xu, L and Zhang, N and Fan, S and Li, Q and Zhang, Q and Ye, Y and Lv, J and Yue, X and Lv, H and Yu, J and Lu, W}, title = {Intratumoral microbial heterogeneity affected tumor immune microenvironment and determined clinical outcome of HBV-related HCC.}, journal = {Hepatology (Baltimore, Md.)}, volume = {78}, number = {4}, pages = {1079-1091}, pmid = {37114494}, issn = {1527-3350}, mesh = {Humans ; *Carcinoma, Hepatocellular ; Case-Control Studies ; Hepatitis B virus/genetics ; *Liver Neoplasms/etiology ; Tumor Microenvironment ; }, abstract = {BACKGROUND AND AIMS: The intratumoral microbiome has been reported to regulate the development and progression of cancers. We aimed to characterize intratumoral microbial heterogeneity (IMH) and establish microbiome-based molecular subtyping of HBV-related HCC to elucidate the correlation between IMH and HCC tumorigenesis.

APPROACH AND RESULTS: A case-control study was designed to investigate microbial landscape and characteristic microbial signatures of HBV-related HCC tissues adopting metagenomics next-generation sequencing. Microbiome-based molecular subtyping of HCC tissues was established by nonmetric multidimensional scaling. The tumor immune microenvironment of 2 molecular subtypes was characterized by EPIC and CIBERSORT based on RNA-seq and verified by immunohistochemistry. The gene set variation analysis was adopted to explore the crosstalk between the immune and metabolism microenvironment. A prognosis-related gene risk signature between 2 subtypes was constructed by the weighted gene coexpression network analysis and the Cox regression analysis and then verified by the Kaplan-Meier survival curve.IMH demonstrated in HBV-related HCC tissues was comparably lower than that in chronic hepatitis tissues. Two microbiome-based HCC molecular subtypes, defined as bacteria- and virus-dominant subtypes, were established and significantly correlated with discrepant clinical-pathologic features. Higher infiltration of M2 macrophage was detected in the bacteria-dominant subtype with to the virus-dominant subtype, accompanied by multiple upregulated metabolism pathways. Furthermore, a 3-gene risk signature containing CSAG4 , PIP4P2 , and TOMM5 was filtered out, which could predict the clinical prognosis of HCC patients accurately using the Cancer Genome Atlas data.

CONCLUSIONS: Microbiome-based molecular subtyping demonstrated IMH of HBV-related HCC was correlated with a disparity in clinical-pathologic features and tumor microenvironment (TME), which might be proposed as a biomarker for prognosis prediction of HCC.}, } @article {pmid37114253, year = {2022}, author = {Liu, H and Xia, H and Jia, B and Wu, J}, title = {Enzyme-linked immunospot assay and metagenomic sequencing of Mycobacterium tuberculosis, coagulopathy symptoms, and pancytopenia testing for characterization of pulmonary tuberculosis: case report and literature review.}, journal = {Cellular and molecular biology (Noisy-le-Grand, France)}, volume = {68}, number = {10}, pages = {178-181}, doi = {10.14715/cmb/2022.68.10.27}, pmid = {37114253}, issn = {1165-158X}, mesh = {Female ; Humans ; Aged ; *Mycobacterium tuberculosis/genetics ; Enzyme-Linked Immunospot Assay ; *Pancytopenia/diagnosis ; *Tuberculosis, Pulmonary/diagnosis/drug therapy/microbiology ; *Tuberculosis/microbiology ; *Blood Coagulation Disorders ; }, abstract = {Pulmonary Tuberculosis (TB) is common in China, but tuberculosis with coagulation disorders and pancytopenia have rarely been reported in the past. In this report presented, a 70-year-old female was admitted to the hospital with poor appetite, dark urine, nausea, vomiting, fatigue, and bilateral lower limb edema; chest CT suggested diffuse infectious lesions in both lungs, coagulation dysfunction, and complete pancytopenia, which was initially considered to be caused by severe infection. However, the patient's symptoms did not improve by potent empiric antibiotics treatment, and a repeat chest CT showed that the lung lesions deteriorated more than before, and coagulation disorders and pancytopenia did not improve. Finally, the TB patient tested positive for enzyme-linked immunospot assay (ELISPOT) and metagenomic sequencing (mNGS) of Mycobacterium tuberculosis (MTB) using bronchoscopic alveolar lavage. So ati-TB was initiated with HRftELfx (isoniazid, 0.3 g qd; rifapentine, 0.45 g biw; ethambutol, 0.75 g qd; and levofloxacin, 0.5 g qd) regimen. Eventually, the patient's clinical symptoms improved significantly, the pulmonary lesions were absorbed, and the coagulation function and blood cell count returned to normal, which achieved a satisfactory treatment effect.}, } @article {pmid37113662, year = {2023}, author = {Liu, Y and Zhu, W and Jiao, M and Guo, W and Luo, Y}, title = {Clinical application value of metagenomic next-generation sequencing in the diagnosis of central nervous system infections.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {11}, number = {}, pages = {885877}, pmid = {37113662}, issn = {2296-4185}, abstract = {Objectives: The purpose of this study is to evaluate the clinical application value of metagenomic next-generation sequencing (mNGS) in central nervous system (CNS) infections. Methods: Both mNGS and routine examination of cerebrospinal fluid (CSF) samples from patients with CNS infections retrospectively analyzed the efficacy of mNGS in this cohort and were ultimately compared with a clinical diagnosis. Results: A total of 94 cases consistent with CNS infections were included in the analysis. The positive rate for mNGS is 60.6% (57/94), which is significantly higher than 20.2% (19/94; p < 0.01) detected using conventional methods. mNGS detected 21 pathogenic strains that could not be detected by routine testing. Routine tests were positive for two pathogens but negative for mNGS. The sensitivity and specificity of mNGS in the diagnosis of central nervous system infections were 89.5% and 44%, respectively, when compared with traditional tests. At discharge, 20 (21.3%) patients were cured, 55 (58.5%) patients showed improvements, five (5.3%) patients did not recover, and two (2.1%) patients died. Conclusion: mNGS has unique advantages in the diagnosis of central nervous system infections. mNGS tests can be performed when patients are clinically suspected of having a central nervous system infection but no pathogenic evidence.}, } @article {pmid37113527, year = {2023}, author = {Yu, C and Guo, W and Zhang, Z and Ma, Y and Cao, X and Sun, N and Cui, Y and Wang, Y and Cui, W and Xu, Y and Zhan, J}, title = {The Impact of mNGS Technology in the Etiological Diagnosis of Severe Pneumonia in Children During the Epidemic of COVID-19.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {2395-2402}, pmid = {37113527}, issn = {1178-6973}, abstract = {PURPOSE: Metagenomic next-generation sequencing (mNGS) is an emerging technique for pathogen detection. However, most literature on the clinical application of pediatrics generally comprises case reports or small-scale cohort studies.

PATIENTS AND METHODS: A total of 101 children with community-acquired severe pneumonia admitted to Tianjin Children's Hospital from November 2021 to February 2022 were included. Pathogens in bronchoalveolar lavage fluid (BALF) specimens were detected using mNGS. The performances of mNGS and conventional tests on pulmonary infection diagnosis and pathogen identification were compared.

RESULTS: According to our data, mNGS had a broader spectrum for pathogen detection. The mNGS results of BALF showed that the number of children with severe pneumonia hospitalized for mycoplasma pneumoniae infection was more than that for other bacterial infections during the COVID-19 epidemic. In addition, 43 cases (42.6%) had been identified with mixed infection, including 36 cases (35.6%) of Mycoplasma pneumoniae mixed with other pathogenic bacteria. Analytically, the mNGS exhibited significantly enhanced detection in the BALF as compared with the conventional laboratory pathogenic detection approaches (P < 0.05). The Pearson correlation analysis revealed positive correlation between the time of fever during hospitalization and the number of mycoplasma sequences (P < 0.05).

CONCLUSION: Compared with traditional methods, mNGS has a higher etiological detection rate and can comprehensively detect various pathogens of severe pneumonia. Therefore, mNGS of bronchoalveolar lavage fluid should be performed in children with severe pneumonia, which is of great significance for guiding treatment.}, } @article {pmid37113242, year = {2023}, author = {Fujita, H and Ushio, M and Suzuki, K and Abe, MS and Yamamichi, M and Okazaki, Y and Canarini, A and Hayashi, I and Fukushima, K and Fukuda, S and Kiers, ET and Toju, H}, title = {Facilitative interaction networks in experimental microbial community dynamics.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1153952}, pmid = {37113242}, issn = {1664-302X}, abstract = {Facilitative interactions between microbial species are ubiquitous in various types of ecosystems on the Earth. Therefore, inferring how entangled webs of interspecific interactions shift through time in microbial ecosystems is an essential step for understanding ecological processes driving microbiome dynamics. By compiling shotgun metagenomic sequencing data of an experimental microbial community, we examined how the architectural features of facilitative interaction networks could change through time. A metabolic modeling approach for estimating dependence between microbial genomes (species) allowed us to infer the network structure of potential facilitative interactions at 13 time points through the 110-day monitoring of experimental microbiomes. We then found that positive feedback loops, which were theoretically predicted to promote cascade breakdown of ecological communities, existed within the inferred networks of metabolic interactions prior to the drastic community-compositional shift observed in the microbiome time-series. We further applied "directed-graph" analyses to pinpoint potential keystone species located at the "upper stream" positions of such feedback loops. These analyses on facilitative interactions will help us understand key mechanisms causing catastrophic shifts in microbial community structure.}, } @article {pmid37113232, year = {2023}, author = {Selmani, Z and Attard, E and Lauga, B and Barakat, M and Ortet, P and Tulumello, J and Achouak, W and Kaci, Y and Heulin, T}, title = {Culturing the desert microbiota.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1098150}, pmid = {37113232}, issn = {1664-302X}, abstract = {Over the last 30 years, the description of microbial diversity has been mainly based on culture-independent approaches (metabarcoding and metagenomics) allowing an in-depth analysis of microbial diversity that no other approach allows. Bearing in mind that culture-dependent approaches cannot replace culture-independent approaches, we have improved an original method for isolating strains consisting of "culturing" grains of sand directly on Petri dishes (grain-by-grain method). This method allowed to cultivate up to 10% of the bacteria counted on the surface of grains of the three sites studied in the Great Western Erg in Algeria (Timoudi, Béni Abbès, and Taghit), knowing that on average about 10 bacterial cells colonize each grain. The diversity of culturable bacteria (collection of 290 strains) predicted by 16S rRNA gene sequencing revealed that Arthrobacter subterraneus, Arthrobacter tecti, Pseudarthrobacter phenanthrenivorans, Pseudarthrobacter psychrotolerans, and Massilia agri are the dominant species. The comparison of the culture-dependent and -independent (16S rRNA gene metabarcoding) approaches at the Timoudi site revealed 18 bacterial genera common to both approaches with a relative overestimation of the genera Arthrobacter/Pseudarthrobacter and Kocuria, and a relative underestimation of the genera Blastococcus and Domibacillus by the bacterial culturing approach. The bacterial isolates will allow further study on the mechanisms of tolerance to desiccation, especially in Pseudomonadota (Proteobacteria).}, } @article {pmid37113001, year = {2023}, author = {Orf, GS and Olivo, A and Harris, B and Weiss, SL and Achari, A and Yu, G and Federman, S and Mbanya, D and James, L and Mampunza, S and Chiu, CY and Rodgers, MA and Cloherty, GA and Berg, MG}, title = {Metagenomic Detection of Divergent Insect- and Bat-Associated Viruses in Plasma from Two African Individuals Enrolled in Blood-Borne Surveillance.}, journal = {Viruses}, volume = {15}, number = {4}, pages = {}, pmid = {37113001}, issn = {1999-4915}, mesh = {Animals ; *Chiroptera ; Satellite Viruses/genetics ; Metagenomics ; Phylogeny ; *Coinfection ; *Viruses/genetics ; *Virus Diseases ; Retroviridae/genetics ; Hepatitis Viruses/genetics ; Insecta/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {Metagenomic next-generation sequencing (mNGS) has enabled the high-throughput multiplexed identification of sequences from microbes of potential medical relevance. This approach has become indispensable for viral pathogen discovery and broad-based surveillance of emerging or re-emerging pathogens. From 2015 to 2019, plasma was collected from 9586 individuals in Cameroon and the Democratic Republic of the Congo enrolled in a combined hepatitis virus and retrovirus surveillance program. A subset (n = 726) of the patient specimens was analyzed by mNGS to identify viral co-infections. While co-infections from known blood-borne viruses were detected, divergent sequences from nine poorly characterized or previously uncharacterized viruses were also identified in two individuals. These were assigned to the following groups by genomic and phylogenetic analyses: densovirus, nodavirus, jingmenvirus, bastrovirus, dicistrovirus, picornavirus, and cyclovirus. Although of unclear pathogenicity, these viruses were found circulating at high enough concentrations in plasma for genomes to be assembled and were most closely related to those previously associated with bird or bat excrement. Phylogenetic analyses and in silico host predictions suggested that these are invertebrate viruses likely transmitted through feces containing consumed insects or through contaminated shellfish. This study highlights the power of metagenomics and in silico host prediction in characterizing novel viral infections in susceptible individuals, including those who are immunocompromised from hepatitis viruses and retroviruses, or potentially exposed to zoonotic viruses from animal reservoir species.}, } @article {pmid37112986, year = {2023}, author = {Tulloch, RL and Kim, K and Sikazwe, C and Michie, A and Burrell, R and Holmes, EC and Dwyer, DE and Britton, PN and Kok, J and Eden, JS}, title = {RAPIDprep: A Simple, Fast Protocol for RNA Metagenomic Sequencing of Clinical Samples.}, journal = {Viruses}, volume = {15}, number = {4}, pages = {}, pmid = {37112986}, issn = {1999-4915}, mesh = {Humans ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Genomics ; RNA, Viral/genetics ; }, abstract = {Emerging infectious disease threats require rapid response tools to inform diagnostics, treatment, and outbreak control. RNA-based metagenomics offers this; however, most approaches are time-consuming and laborious. Here, we present a simple and fast protocol, the RAPIDprep assay, with the aim of providing a cause-agnostic laboratory diagnosis of infection within 24 h of sample collection by sequencing ribosomal RNA-depleted total RNA. The method is based on the synthesis and amplification of double-stranded cDNA followed by short-read sequencing, with minimal handling and clean-up steps to improve processing time. The approach was optimized and applied to a range of clinical respiratory samples to demonstrate diagnostic and quantitative performance. Our results showed robust depletion of both human and microbial rRNA, and library amplification across different sample types, qualities, and extraction kits using a single workflow without input nucleic-acid quantification or quality assessment. Furthermore, we demonstrated the genomic yield of both known and undiagnosed pathogens with complete genomes recovered in most cases to inform molecular epidemiological investigations and vaccine design. The RAPIDprep assay is a simple and effective tool, and representative of an important shift toward the integration of modern genomic techniques with infectious disease investigations.}, } @article {pmid37112930, year = {2023}, author = {Sáenz, JS and Rios-Galicia, B and Rehkugler, B and Seifert, J}, title = {Dynamic Development of Viral and Bacterial Diversity during Grass Silage Preservation.}, journal = {Viruses}, volume = {15}, number = {4}, pages = {}, pmid = {37112930}, issn = {1999-4915}, mesh = {*Poaceae ; *Silage/analysis/microbiology ; Bacteria/genetics ; Metagenome ; Carbohydrate Metabolism ; }, abstract = {Ensilaging is one of the most common feed preservation processes using lactic acid bacteria to stabilize feed and save feed quality. The silage bacterial community is well known but the role of the virome and its relationship with the bacterial community is scarce. In the present study, metagenomics and amplicon sequencing were used to describe the composition of the bacterial and viral community during a 40-day grass silage preservation. During the first two days, we observed a rapid decrease in the pH and a shift in the bacterial and viral composition. The diversity of the dominant virus operational taxonomic units (vOTUs) decreased throughout the preservation. The changes in the bacterial community resembled the predicted putative host of the recovered vOTUs during each sampling time. Only 10% of the total recovered vOTUs clustered with a reference genome. Different antiviral defense mechanisms were found across the recovered metagenome-assembled genomes (MAGs); however, only a history of bacteriophage infection with Lentilactobacillus and Levilactobacillus was observed. In addition, vOTUs harbored potential auxiliary metabolic genes related to carbohydrate metabolism, organic nitrogen, stress tolerance, and transport. Our data suggest that vOTUs are enriched during grass silage preservation, and they could have a role in the establishment of the bacterial community.}, } @article {pmid37112908, year = {2023}, author = {Zanella, MC and Vu, DL and Hosszu-Fellous, K and Neofytos, D and Van Delden, C and Turin, L and Poncet, A and Simonetta, F and Masouridi-Levrat, S and Chalandon, Y and Cordey, S and Kaiser, L}, title = {Longitudinal Detection of Twenty DNA and RNA Viruses in Allogeneic Hematopoietic Stem Cell Transplant Recipients Plasma.}, journal = {Viruses}, volume = {15}, number = {4}, pages = {}, pmid = {37112908}, issn = {1999-4915}, mesh = {Adult ; Humans ; *Virus Diseases/epidemiology ; DNA, Viral/genetics ; *Torque teno virus/genetics ; *RNA Viruses/genetics ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Merkel cell polyomavirus/genetics ; Transplant Recipients ; }, abstract = {Metagenomics revealed novel and routinely overlooked viruses, representing sources of unrecognized infections after allogeneic hematopoietic stem cell transplantation (allo-HSCT). We aim to describe DNA and RNA virus prevalence and kinetics in allo-HSCT recipients' plasma for one year post HSCT. We included 109 adult patients with first allo-HSCT from 1 March 2017 to 31 January 2019 in this observational cohort study. Seventeen DNA and three RNA viral species were screened with qualitative and/or quantitative r(RT)-PCR assays using plasma samples collected at 0, 1, 3, 6, and 12 months post HSCT. TTV infected 97% of patients, followed by HPgV-1 (prevalence: 26-36%). TTV (median 3.29 × 10[5] copies/mL) and HPgV-1 (median 1.18 × 10[6] copies/mL) viral loads peaked at month 3. At least one Polyomaviridae virus (BKPyV, JCPyV, MCPyV, HPyV6/7) was detected in >10% of patients. HPyV6 and HPyV7 prevalence reached 27% and 12% at month 3; CMV prevalence reached 27%. HSV, VZV, EBV, HHV-7, HAdV and B19V prevalence remained <5%. HPyV9, TSPyV, HBoV, EV and HPg-V2 were never detected. At month 3, 72% of patients had co-infections. TTV and HPgV-1 infections were highly prevalent. BKPyV, MCPyV and HPyV6/7 were frequently detected relative to classical culprits. Further investigation is needed into associations between these viral infections and immune reconstitution or clinical outcomes.}, } @article {pmid37112890, year = {2023}, author = {Turzynski, V and Griesdorn, L and Moraru, C and Soares, AR and Simon, SA and Stach, TL and Rahlff, J and Esser, SP and Probst, AJ}, title = {Virus-Host Dynamics in Archaeal Groundwater Biofilms and the Associated Bacterial Community Composition.}, journal = {Viruses}, volume = {15}, number = {4}, pages = {}, pmid = {37112890}, issn = {1999-4915}, mesh = {Archaea/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Biofilms ; *Groundwater ; *Viruses/genetics ; }, abstract = {Spatial and temporal distribution of lytic viruses in deep groundwater remains unexplored so far. Here, we tackle this gap of knowledge by studying viral infections of Altivir_1_MSI in biofilms dominated by the uncultivated host Candidatus Altiarchaeum hamiconexum sampled from deep anoxic groundwater over a period of four years. Using virus-targeted direct-geneFISH (virusFISH) whose detection efficiency for individual viral particles was 15%, we show a significant and steady increase of virus infections from 2019 to 2022. Based on fluorescence micrographs of individual biofilm flocks, we determined different stages of viral infections in biofilms for single sampling events, demonstrating the progression of infection of biofilms in deep groundwater. Biofilms associated with many host cells undergoing lysis showed a substantial accumulation of filamentous microbes around infected cells probably feeding off host cell debris. Using 16S rRNA gene sequencing across ten individual biofilm flocks from one sampling event, we determined that the associated bacterial community remains relatively constant and was dominated by sulfate-reducing members affiliated with Desulfobacterota. Given the stability of the virus-host interaction in these deep groundwater samples, we postulate that the uncultivated virus-host system described herein represents a suitable model system for studying deep biosphere virus-host interactions in future research endeavors.}, } @article {pmid37112831, year = {2023}, author = {Sánchez, C and Doménech, A and Gomez-Lucia, E and Méndez, JL and Ortiz, JC and Benítez, L}, title = {A Novel Dependoparvovirus Identified in Cloacal Swabs of Monk Parakeet (Myiopsitta monachus) from Urban Areas of Spain.}, journal = {Viruses}, volume = {15}, number = {4}, pages = {}, pmid = {37112831}, issn = {1999-4915}, mesh = {Humans ; Animals ; Parakeets/genetics ; Dependovirus ; Spain ; Phylogeny ; Ecosystem ; *Parrots ; *Parvovirus ; }, abstract = {The introduction of invasive birds into new ecosystems frequently has negative consequences for the resident populations. Accordingly, the increasing population of monk parakeets (Myiopsitta monachus) in Europe may pose a threat because we have little knowledge of the viruses they can transmit to native naïve species. In this study, we describe a new dependoparvovirus detected by metagenomic analysis of cloacal samples from 28 apparently healthy individuals captured in urban areas of Madrid, Spain. The genomic characterization revealed that the genome encoded the NS and VP proteins typical of parvoviruses and was flanked by inverted terminal repeats. No recombination signal was detected. The phylogenetic analysis showed that it was closely related to a parvovirus isolated in a wild psittacid in China. Both viruses share 80% Rep protein sequence identity and only 64% with other dependoparvoviruses identified in Passeriformes, Anseriformes, and Piciformes and are included in a highly supported clade, which could be considered a new species. The prevalence was very low, and none of the additional 73 individuals tested positive by PCR. These results highlight the importance of exploring the viral genome in invasive species to prevent the emergence of novel viral pathogenic species.}, } @article {pmid37111144, year = {2023}, author = {Rehner, J and Schmartz, GP and Kramer, T and Keller, V and Keller, A and Becker, SL}, title = {The Effect of a Planetary Health Diet on the Human Gut Microbiome: A Descriptive Analysis.}, journal = {Nutrients}, volume = {15}, number = {8}, pages = {}, pmid = {37111144}, issn = {2072-6643}, mesh = {Humans ; *Gastrointestinal Microbiome ; Diet, Healthy ; Feces/microbiology ; Diet ; Bacteria/genetics ; }, abstract = {In 2019, researchers from the EAT-Lancet Commission developed the 'Planetary Health (PH) diet'. Specifically, they provided recommendations pertaining to healthy diets derived from sustainable food systems. Thus far, it has not been analysed how such a diet affects the human intestinal microbiome, which is important for health and disease development. Here, we present longitudinal genome-wide metagenomic sequencing and mass spectrometry data on the gut microbiome of healthy volunteers adhering to the PH diet, as opposed to vegetarian or vegan (VV) and omnivorous (OV) diets. We obtained basic epidemiological information from 41 healthy volunteers and collected stool samples at inclusion and after 2, 4, and 12 weeks. Individuals opting to follow the PH diet received detailed instructions and recipes, whereas individuals in the control groups followed their habitual dietary pattern. Whole-genome DNA was extracted from stool specimens and subjected to shotgun metagenomic sequencing (~3 GB per patient). Conventional bacterial stool cultures were performed in parallel and bacterial species were identified with matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) mass spectrometry. We analysed samples from 16 PH, 16 OV, and 9 VV diet patterns. The α-diversity remained relatively stable for all dietary groups. In the PH group, we observed a constant increase from 3.79% at inclusion to 4.9% after 12 weeks in relative abundance of Bifidobacterium adolescentis. Differential PH abundance analysis highlighted a non-significant increase in possible probiotics such as Paraprevotella xylaniphila and Bacteroides clarus. The highest abundance of these bacteria was observed in the VV group. Dietary modifications are associated with rapid alterations to the human gut microbiome, and the PH diet led to a slight increase in probiotic-associated bacteria at ≥4 weeks. Additional research is required to confirm these findings.}, } @article {pmid37110724, year = {2023}, author = {Bhandari, MP and Polaka, I and Vangravs, R and Mezmale, L and Veliks, V and Kirshners, A and Mochalski, P and Dias-Neto, E and Leja, M}, title = {Volatile Markers for Cancer in Exhaled Breath-Could They Be the Signature of the Gut Microbiota?.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {8}, pages = {}, pmid = {37110724}, issn = {1420-3049}, support = {Postdoctoral project number: 1.1.1.2/VIAA/3/19/495 (Activity 1.1.1.2 "Post-doctoral Research Aid")//European Regional Development Fund/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Stomach Neoplasms/diagnosis ; Gas Chromatography-Mass Spectrometry ; *Volatile Organic Compounds/analysis ; Feces/chemistry ; }, abstract = {It has been shown that the gut microbiota plays a central role in human health and disease. A wide range of volatile metabolites present in exhaled breath have been linked with gut microbiota and proposed as a non-invasive marker for monitoring pathological conditions. The aim of this study was to examine the possible correlation between volatile organic compounds (VOCs) in exhaled breath and the fecal microbiome by multivariate statistical analysis in gastric cancer patients (n = 16) and healthy controls (n = 33). Shotgun metagenomic sequencing was used to characterize the fecal microbiota. Breath-VOC profiles in the same participants were identified by an untargeted gas chromatography-mass spectrometry (GC-MS) technique. A multivariate statistical approach involving a canonical correlation analysis (CCA) and sparse principal component analysis identified the significant relationship between the breath VOCs and fecal microbiota. This relation was found to differ between gastric cancer patients and healthy controls. In 16 cancer cases, 14 distinct metabolites identified from the breath belonging to hydrocarbons, alcohols, aromatics, ketones, ethers, and organosulfur compounds were highly correlated with 33 fecal bacterial taxa (correlation of 0.891, p-value 0.045), whereas in 33 healthy controls, 7 volatile metabolites belonging to alcohols, aldehydes, esters, phenols, and benzamide derivatives correlated with 17 bacterial taxa (correlation of 0.871, p-value 0.0007). This study suggested that the correlation between fecal microbiota and breath VOCs was effective in identifying exhaled volatile metabolites and the functional effects of microbiome, thus helping to understand cancer-related changes and improving the survival and life expectancy in gastric cancer patients.}, } @article {pmid37110500, year = {2023}, author = {Dahiya, M and Jovel, J and Monaghan, T and Wong, K and Elhenawy, W and Chui, L and McAlister, F and Kao, D}, title = {In Silico Analysis of Changes in Predicted Metabolic Capabilities of Intestinal Microbiota after Fecal Microbial Transplantation for Treatment of Recurrent Clostridioides difficile Infection.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, pmid = {37110500}, issn = {2076-2607}, abstract = {IMPORTANCE: Although highly effective in treating recurrent Clostridioides difficile infection (RCDI), the mechanisms of action of fecal microbial transplantation (FMT) are not fully understood.

AIM: The aim of this study was to explore microbially derived products or pathways that could contribute to the therapeutic efficacy of FMT.

METHODS: Stool shotgun metagenomic sequencing data from 18 FMT-treated RCDI patients at 4 points in time were used for the taxonomic and functional profiling of their gut microbiome. The abundance of the KEGG orthology (KO) groups was subjected to univariate linear mixed models to assess the significance of the observed differences between 0 (pre-FMT), 1, 4, and 12 weeks after FMT.

RESULTS: Of the 59,987 KO groups identified by shotgun metagenomic sequencing, 27 demonstrated a statistically significant change after FMT. These KO groups are involved in many cellular processes, including iron homeostasis, glycerol metabolism, and arginine regulation, all of which have been implicated to play important roles in bacterial growth and virulence in addition to modulating the intestinal microbial composition.

CONCLUSION: Our findings suggest potential changes in key KO groups post-FMT, which may contribute to FMT efficacy beyond the restored microbial composition/diversity and metabolism of bile acids and short-chain fatty acids. Future larger studies that include a fecal metabolomics analysis combined with animal model validation work are required to further elucidate the molecular mechanisms.}, } @article {pmid37110445, year = {2023}, author = {Taylor, BC and Sheikh Andalibi, M and Wandro, S and Weldon, KC and Sepich-Poore, GD and Carpenter, CS and Fraraccio, S and Franklin, D and Iudicello, JE and Letendre, S and Gianella, S and Grant, I and Ellis, RJ and Heaton, RK and Knight, R and Swafford, AD}, title = {Signatures of HIV and Major Depressive Disorder in the Plasma Microbiome.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, pmid = {37110445}, issn = {2076-2607}, support = {P30 MH062512/MH/NIMH NIH HHS/United States ; T32 GM007198/GM/NIGMS NIH HHS/United States ; R01AG061066./NH/NIH HHS/United States ; }, abstract = {Inter-individual differences in the gut microbiome are linked to alterations in inflammation and blood-brain barrier permeability, which may increase the risk of depression in people with HIV (PWH). The microbiome profile of blood, which is considered by many to be typically sterile, remains largely unexplored. We aimed to characterize the blood plasma microbiome composition and assess its association with major depressive disorder (MDD) in PWH and people without HIV (PWoH). In this cross-sectional, observational cohort, we used shallow-shotgun metagenomic sequencing to characterize the plasma microbiome of 151 participants (84 PWH and 67 PWoH), all of whom underwent a comprehensive neuropsychiatric assessment. The microbial composition did not differ between PWH and PWoH or between participants with MDD and those without it. Using the songbird model, we computed the log ratio of the highest and lowest 30% of the ranked classes associated with HIV and MDD. We found that HIV infection and lifetime MDD were enriched in a set of differentially abundant inflammatory classes, such as Flavobacteria and Nitrospira. Our results suggest that the circulating plasma microbiome may increase the risk of MDD related to dysbiosis-induced inflammation in PWH. If confirmed, these findings may indicate new biological mechanisms that could be targeted to improve treatment of MDD in PWH.}, } @article {pmid37110428, year = {2023}, author = {Farlow, AJ and Rupasinghe, DB and Naji, KM and Capon, RJ and Spiteller, D}, title = {Rosenbergiella meliponini D21B Isolated from Pollen Pots of the Australian Stingless Bee Tetragonula carbonaria.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, pmid = {37110428}, issn = {2076-2607}, abstract = {Rosenbergiella bacteria have been previously isolated predominantly from floral nectar and identified in metagenomic screenings as associated with bees. Here, we isolated three Rosenbergiella strains from the robust Australian stingless bee Tetragonula carbonaria sharing over 99.4% sequence similarity with Rosenbergiella strains isolated from floral nectar. The three Rosenbergiella strains (D21B, D08K, D15G) from T. carbonaria exhibited near-identical 16S rDNA. The genome of strain D21B was sequenced; its draft genome contains 3,294,717 bp, with a GC content of 47.38%. Genome annotation revealed 3236 protein-coding genes. The genome of D21B differs sufficiently from the closest related strain, Rosenbergiella epipactidis 2.1A, to constitute a new species. In contrast to R. epipactidis 2.1A, strain D21B produces the volatile 2-phenylethanol. The D21B genome contains a polyketide/non-ribosomal peptide gene cluster not present in any other Rosenbergiella draft genomes. Moreover, the Rosenbergiella strains isolated from T. carbonaria grew in a minimal medium without thiamine, but R. epipactidis 2.1A was thiamine-dependent. Strain D21B was named R. meliponini D21B, reflecting its origin from stingless bees. Rosenbergiella strains may contribute to the fitness of T. carbonaria.}, } @article {pmid37110411, year = {2023}, author = {Balogun, FO and Abdulsalam, RA and Ojo, AO and Cason, E and Sabiu, S}, title = {Chemical Characterization and Metagenomic Identification of Endophytic Microbiome from South African Sunflower (Helianthus annus) Seeds.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, pmid = {37110411}, issn = {2076-2607}, support = {129494//National Research Foundation, South Africa/ ; 120433//National Research Foundation, South Africa/ ; }, abstract = {Helianthus annus (sunflower) is a globally important oilseed crop whose survival is threatened by various pathogenic diseases. Agrochemical products are used to eradicate these diseases; however, due to their unfriendly environmental consequences, characterizing microorganisms for exploration as biocontrol agents are considered better alternatives against the use of synthetic chemicals. The study assessed the oil contents of 20 sunflower seed cultivars using FAMEs-chromatography and characterized the endophytic fungi and bacteria microbiome using Illumina sequencing of fungi ITS 1 and bacteria 16S (V3-V4) regions of the rRNA operon. The oil contents ranged between 41-52.8%, and 23 fatty acid components (in varied amounts) were found in all the cultivars, with linoleic (53%) and oleic (28%) acids as the most abundant. Ascomycota (fungi) and Proteobacteria (bacteria) dominated the cultivars at the phyla level, while Alternaria and Bacillus at the genus level in varying abundance. AGSUN 5102 and AGSUN 5101 (AGSUN 5270 for bacteria) had the highest fungi diversity structure, which may have been contributed by the high relative abundance of linoleic acid in the fatty acid components. Dominant fungi genera such as Alternaria, Aspergillus, Aureobasidium, Alternariaste, Cladosporium, Penicillium, and bacteria including Bacillus, Staphylococcus, and Lactobacillus are established, providing insight into the fungi and bacteria community structures from the seeds of South Africa sunflower.}, } @article {pmid37110332, year = {2023}, author = {Wilson, A and Bogie, B and Chaaban, H and Burge, K}, title = {The Nonbacterial Microbiome: Fungal and Viral Contributions to the Preterm Infant Gut in Health and Disease.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, pmid = {37110332}, issn = {2076-2607}, support = {P20 GM134973/GM/NIGMS NIH HHS/United States ; 5P20GM134973/NH/NIH HHS/United States ; }, abstract = {The intestinal microbiome is frequently implicated in necrotizing enterocolitis (NEC) pathogenesis. While no particular organism has been associated with NEC development, a general reduction in bacterial diversity and increase in pathobiont abundance has been noted preceding disease onset. However, nearly all evaluations of the preterm infant microbiome focus exclusively on the bacterial constituents, completely ignoring any fungi, protozoa, archaea, and viruses present. The abundance, diversity, and function of these nonbacterial microbes within the preterm intestinal ecosystem are largely unknown. Here, we review findings on the role of fungi and viruses, including bacteriophages, in preterm intestinal development and neonatal intestinal inflammation, with potential roles in NEC pathogenesis yet to be determined. In addition, we highlight the importance of host and environmental influences, interkingdom interactions, and the role of human milk in shaping fungal and viral abundance, diversity, and function within the preterm intestinal ecosystem.}, } @article {pmid37110327, year = {2023}, author = {Guajardo-Leiva, S and Mendez, KN and Meneses, C and Díez, B and Castro-Nallar, E}, title = {A First Insight into the Microbial and Viral Communities of Comau Fjord-A Unique Human-Impacted Ecosystem in Patagonia (42[∘] S).}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, pmid = {37110327}, issn = {2076-2607}, support = {ANID-FONDECYT Regular 1200834//Agencia Nacional de Investigación y Desarrollo/ ; ANID-PIA-Anillo INACH ACT192057//Agencia Nacional de Investigación y Desarrollo/ ; }, abstract = {While progress has been made in surveying the oceans to understand microbial and viral communities, the coastal ocean and, specifically, estuarine waters, where the effects of anthropogenic activity are greatest, remain partially understudied. The coastal waters of Northern Patagonia are of interest since this region experiences high-density salmon farming as well as other disturbances such as maritime transport of humans and cargo. Here, we hypothesized that viral and microbial communities from the Comau Fjord would be distinct from those collected in global surveys yet would have the distinctive features of microbes from coastal and temperate regions. We further hypothesized that microbial communities will be functionally enriched in antibiotic resistance genes (ARGs) in general and in those related to salmon farming in particular. Here, the analysis of metagenomes and viromes obtained for three surface water sites showed that the structure of the microbial communities was distinct in comparison to global surveys such as the Tara Ocean, though their composition converges with that of cosmopolitan marine microbes belonging to Proteobacteria, Bacteroidetes, and Actinobacteria. Similarly, viral communities were also divergent in structure and composition but matched known viral members from North America and the southern oceans. Microbial communities were functionally enriched in ARGs dominated by beta-lactams and tetracyclines, bacitracin, and the group macrolide-lincosamide-streptogramin (MLS) but were not different from other communities from the South Atlantic, South Pacific, and Southern Oceans. Similarly, viral communities were characterized by exhibiting protein clusters similar to those described globally (Tara Oceans Virome); however, Comau Fjord viromes displayed up to 50% uniqueness in their protein content. Altogether, our results indicate that microbial and viral communities from the Comau Fjord are a reservoir of untapped diversity and that, given the increasing anthropogenic impacts in the region, they warrant further study, specifically regarding resilience and resistance against antimicrobials and hydrocarbons.}, } @article {pmid37110300, year = {2023}, author = {Schultz, CR and Johnson, M and Wallace, JG}, title = {Effects of Inbreeding on Microbial Community Diversity of Zea mays.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, pmid = {37110300}, issn = {2076-2607}, support = {#032//Foundation for Food & Agriculture Research/ ; }, abstract = {Heterosis, also known as hybrid vigor, is the basis of modern maize production. The effect of heterosis on maize phenotypes has been studied for decades, but its effect on the maize-associated microbiome is much less characterized. To determine the effect of heterosis on the maize microbiome, we sequenced and compared the bacterial communities of inbred, open pollinated, and hybrid maize. Samples covered three tissue types (stalk, root, and rhizosphere) in two field experiments and one greenhouse experiment. Bacterial diversity was more affected by location and tissue type than genetic background for both within-sample (alpha) and between-sample (beta) diversity. PERMANOVA analysis similarly showed that tissue type and location had significant effects on the overall community structure, whereas the intraspecies genetic background and individual plant genotypes did not. Differential abundance analysis identified only 25 bacterial ASVs that significantly differed between inbred and hybrid maize. Predicted metagenome content was inferred with Picrust2, and it also showed a significantly larger effect of tissue and location than genetic background. Overall, these results indicate that the bacterial communities of inbred and hybrid maize are often more similar than they are different and that non-genetic effects are generally the largest influences on the maize microbiome.}, } @article {pmid37110298, year = {2023}, author = {Greene, G and Koolman, L and Whyte, P and Burgess, C and Bolton, D}, title = {The Gut Microbiota of Broilers Reared with and without Antibiotic Treatment.}, journal = {Microorganisms}, volume = {11}, number = {4}, pages = {}, pmid = {37110298}, issn = {2076-2607}, support = {15F641//Department of Agriculture, Food and the Marine, Ireland/ ; }, abstract = {The aim of this study was to examine the microbiota in broilers reared with and without antibiotics and to investigate differences between the upper, middle and lower sections of the gastrointestinal tract (GIT). One of two commercial flocks was treated with an antibiotic (T) (20 mg trimethoprim and 100 mg sulfamethoxazole per ml in the drinking water for 3 days) and the other was left untreated (UT). The GIT contents of 51 treated and untreated birds were aseptically removed from the upper (U), middle (M) and lower (L) sections. These were pooled in triplicate (n = 17 per section per flock), the DNA extracted and purified, 16S amplicon metagenomic sequencing performed and the resultant data analysed using a range of bioinformatics software. There were significant differences in the microbiota of the upper, middle and lower GIT, and treatment with the antibiotic significantly affected the microbiota in each of these sections. This study provides new data on broiler GIT microbiota and suggests that GIT location is a more important determinant of the constituent bacterial flora rather than the use or otherwise of antimicrobial treatments, at least when applied early in the production cycle.}, } @article {pmid37110188, year = {2023}, author = {Tu, P and Xue, J and Niu, H and Tang, Q and Mo, Z and Zheng, X and Wu, L and Chen, Z and Cai, Y and Wang, X}, title = {Deciphering Gut Microbiome Responses upon Microplastic Exposure via Integrating Metagenomics and Activity-Based Metabolomics.}, journal = {Metabolites}, volume = {13}, number = {4}, pages = {}, pmid = {37110188}, issn = {2218-1989}, support = {2019ZT08L213//the Program for Guangdong Introducing Innovative and Entrepreneurial Teams/ ; 2020B1111380003//the Key-Area Research and Development Program of Guangdong Province/ ; 2019B121203011//the Guangdong Provincial Key Laboratory Project/ ; 42007374//the Natural Science Foundation of China/ ; }, abstract = {Perturbations of the gut microbiome are often intertwined with the onset and development of diverse metabolic diseases. It has been suggested that gut microbiome perturbation could be a potential mechanism through which environmental chemical exposure induces or exacerbates human diseases. Microplastic pollution, an emerging environmental issue, has received ever increasing attention in recent years. However, interactions between microplastic exposure and the gut microbiota remain elusive. This study aimed to decipher the responses of the gut microbiome upon microplastic polystyrene (MP) exposure by integrating 16S rRNA high-throughput sequencing with metabolomic profiling techniques using a C57BL/6 mouse model. The results indicated that MP exposure significantly perturbed aspects of the gut microbiota, including its composition, diversity, and functional pathways that are involved in xenobiotic metabolism. A distinct metabolite profile was observed in mice with MP exposure, which probably resulted from changes in gut bacterial composition. Specifically, untargeted metabolomics revealed that levels of metabolites associated with cholesterol metabolism, primary and secondary bile acid biosynthesis, and taurine and hypotaurine metabolism were changed significantly. Targeted approaches indicated significant perturbation with respect to the levels of short-chain fatty acids derived from the gut microbiota. This study can provide evidence for the missing link in understanding the mechanisms behind the toxic effects of microplastics.}, } @article {pmid37108914, year = {2023}, author = {Hong, Y and Tan, JY and Xue, H and Chow, ML and Ali, M and Ng, A and Leong, A and Yeo, J and Koh, SM and Tang, MSY and Lee, YY and Choong, AMF and Lee, SML and Delli Ponti, R and Chan, PM and Lee, D and Wong, JY and Mutwil, M and Fong, YK}, title = {A Metagenomic Survey of Wood Decay Fungi in the Urban Trees of Singapore.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {4}, pages = {}, pmid = {37108914}, issn = {2309-608X}, support = {NTU REF 2019-1120//Ministry of National Development/ ; }, abstract = {Mature tropical urban trees are susceptible to root and trunk rot caused by pathogenic fungi. A metagenomic survey of such fungi was carried out on 210 soil and tissue samples collected from 134 trees of 14 common species in Singapore. Furthermore, 121 fruiting bodies were collected and barcoded. Out of the 22,067 OTUs (operational taxonomic units) identified, 10,646 OTUs had annotation information, and most were either ascomycetes (63.4%) or basidiomycetes (22.5%). Based on their detection in the diseased tissues and surrounding soils and/or the presence of fruiting bodies, fourteen basidiomycetes (nine Polyporales, four Hymenochaetales, one Boletales) and three ascomycetes (three species of Scytalidium) were strongly associated with the diseased trees. Fulvifomes siamensis affected the largest number of tree species surveyed. The association of three fungi was further supported by in vitro wood decay studies. Genetic heterogeneity was common in the diseased tissues and fruiting bodies (Ganoderma species especially). This survey identified the common pathogenic fungi of tropical urban trees and laid the foundation for early diagnosis and targeted mitigation efforts. It also illustrated the complexity of fungal ecology and pathogenicity.}, } @article {pmid37108829, year = {2023}, author = {Liu, Z and Jiang, W and Kim, C and Peng, X and Fan, C and Wu, Y and Xie, Z and Peng, F}, title = {A Pseudomonas Lysogenic Bacteriophage Crossing the Antarctic and Arctic, Representing a New Genus of Autographiviridae.}, journal = {International journal of molecular sciences}, volume = {24}, number = {8}, pages = {}, pmid = {37108829}, issn = {1422-0067}, support = {2021FY100900//National Science and Technology Fundamental Resources Investigation Program of China/ ; 2022YFC2807501//National Key Research and Development Program of China/ ; Grant No. NIMR-2022-8//R&D Infrastructure and Facility Development Program of the Ministry of Science and Technology of the People's Republic of China/ ; Grant No. 42076230//National Natural Science Foundation of China/ ; IC201706//Chinese Polar Scientific Strategy Research Fund/ ; }, mesh = {*Pseudomonas Phages ; Antarctic Regions ; Phylogeny ; *Bacteriophages ; Pseudomonas/genetics ; Genome, Viral ; }, abstract = {Polar regions tend to support simple food webs, which are vulnerable to phage-induced gene transfer or microbial death. To further investigate phage-host interactions in polar regions and the potential linkage of phage communities between the two poles, we induced the release of a lysogenic phage, vB_PaeM-G11, from Pseudomonas sp. D3 isolated from the Antarctic, which formed clear phage plaques on the lawn of Pseudomonas sp. G11 isolated from the Arctic. From permafrost metagenomic data of the Arctic tundra, we found the genome with high-similarity to that of vB_PaeM-G11, demonstrating that vB_PaeM-G11 may have a distribution in both the Antarctic and Arctic. Phylogenetic analysis indicated that vB_PaeM-G11 is homologous to five uncultured viruses, and that they may represent a new genus in the Autographiviridae family, named Fildesvirus here. vB_PaeM-G11 was stable in a temperature range (4-40 °C) and pH (4-11), with latent and rise periods of about 40 and 10 min, respectively. This study is the first isolation and characterization study of a Pseudomonas phage distributed in both the Antarctic and Arctic, identifying its lysogenic host and lysis host, and thus provides essential information for further understanding the interaction between polar phages and their hosts and the ecological functions of phages in polar regions.}, } @article {pmid37108499, year = {2023}, author = {Bučko, M and Kaniaková, K and Hronská, H and Gemeiner, P and Rosenberg, M}, title = {Epoxide Hydrolases: Multipotential Biocatalysts.}, journal = {International journal of molecular sciences}, volume = {24}, number = {8}, pages = {}, pmid = {37108499}, issn = {1422-0067}, support = {APVV-20-0272//Slovak Research and Development Agency/ ; VEGA 2/0130/20//Slovak Grant Agency for Science/ ; ITMS2014+: 313011V358//The European Regional Development Fund/ ; }, mesh = {*Epoxide Hydrolases/genetics/chemistry ; Catalysis ; *Epoxy Compounds/chemistry ; Hydrolysis ; Genetic Techniques ; Stereoisomerism ; }, abstract = {Epoxide hydrolases are attractive and industrially important biocatalysts. They can catalyze the enantioselective hydrolysis of epoxides to the corresponding diols as chiral building blocks for bioactive compounds and drugs. In this review article, we discuss the state of the art and development potential of epoxide hydrolases as biocatalysts based on the most recent approaches and techniques. The review covers new approaches to discover epoxide hydrolases using genome mining and enzyme metagenomics, as well as improving enzyme activity, enantioselectivity, enantioconvergence, and thermostability by directed evolution and a rational design. Further improvements in operational and storage stabilization, reusability, pH stabilization, and thermal stabilization by immobilization techniques are discussed in this study. New possibilities for expanding the synthetic capabilities of epoxide hydrolases by their involvement in non-natural enzyme cascade reactions are described.}, } @article {pmid37108418, year = {2023}, author = {Chalenko, YM and Slonova, DA and Kechko, OI and Kalinin, EV and Mitkevich, VA and Ermolaeva, SA}, title = {Natural Isoforms of Listeria monocytogenes Virulence Factor Inlb Differ in c-Met Binding Efficiency and Differently Affect Uptake and Survival Listeria in Macrophage.}, journal = {International journal of molecular sciences}, volume = {24}, number = {8}, pages = {}, pmid = {37108418}, issn = {1422-0067}, support = {No. 21-74-00105//Russian Science Foundation/ ; }, mesh = {Humans ; Bacterial Proteins/metabolism ; Carrier Proteins/metabolism ; *Listeria ; *Listeria monocytogenes ; *Listeriosis ; Macrophages/metabolism ; Membrane Proteins/metabolism ; Protein Isoforms/metabolism ; Virulence Factors/metabolism ; Proto-Oncogene Proteins c-met/metabolism ; }, abstract = {Listeria monocytogenes virulence factor InlB specifically interacts with the receptors c-Met and gC1q-R. Both receptors are present in non-professional and professional phagocytes, including macrophages. Phylogenetically defined InlB isoforms differently support invasion into non-professional phagocytes. This work deals with the effects of InlB isoforms on L. monocytogenes uptake and intracellular proliferation in human macrophages. Three isoforms of the receptor binding domain (idInlB) were derived from phylogenetically distinct L. monocytogenes strains belonging to the highly virulent CC1 (idInlBCC1), medium-virulence CC7 (idInlBCC7), and low-virulence CC9 (idInlBCC9) clonal complexes. The constant dissociation increased in the order idInlBCC1 << idInlBCC7 < idInlBCC9 for interactions with c-Met, and idInlBCC1 ≈ idInlBCC7 < idInlBCC9 for interactions with gC1q-R. The comparison of uptake and intracellular proliferation of isogenic recombinant strains which expressed full-length InlBs revealed that the strain expressing idInlBCC1 proliferated in macrophages twice as efficiently as other strains. Macrophage pretreatment with idInlBCC1 followed by recombinant L. monocytogenes infection disturbed macrophage functions decreasing pathogen uptake and improving its intracellular multiplication. Similar pretreatment with idInlBCC7 decreased bacterial uptake but also impaired intracellular multiplication. The obtained results demonstrated that InlB impaired macrophage functions in an idInlB isoform-dependent manner. These data suggest a novel InlB function in L. monocytogenes virulence.}, } @article {pmid37107615, year = {2023}, author = {Boccuto, L and Tack, J and Ianiro, G and Abenavoli, L and Scarpellini, E}, title = {Human Genes Involved in the Interaction between Host and Gut Microbiome: Regulation and Pathogenic Mechanisms.}, journal = {Genes}, volume = {14}, number = {4}, pages = {}, pmid = {37107615}, issn = {2073-4425}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Artificial Intelligence ; *Microbiota ; Immune System ; Biological Evolution ; }, abstract = {INTRODUCTION: The umbrella term "human gut microbiota" describes the complex ecosystem harboring our gut. It includes bacteria, viruses, protozoa, archaea, fungi, and yeasts. This taxonomic classification does not describe its functions, which encompass nutrients digestion and absorption, immune system regulation, and host metabolism. "Gut microbiome" indicates instead the genome belonging to these "microbes" actively involved in these functions. However, the interaction between the host genome and the microbial ones determines the fine functioning of our organism.

METHODS: We reviewed the data available in the scientific literature on the definition of gut microbiota, gut microbiome, and the data on human genes involved in the interaction with the latter. We consulted the main medical databases using the following keywords, acronyms, and their associations: gut microbiota, gut microbiome, human genes, immune function, and metabolism.

RESULTS: Candidate human genes encoding enzymes, inflammatory cytokines, and proteins show similarity with those included in the gut microbiome. These findings have become available through newer artificial intelligence (AI) algorithms allowing big data analysis. From an evolutionary point of view, these pieces of evidence explain the strict and sophisticated interaction at the basis of human metabolism and immunity regulation in humans. They unravel more and more physiopathologic pathways included in human health and disease.

DISCUSSION: Several lines of evidence also obtained through big data analysis support the bi-directional role of gut microbiome and human genome in host metabolism and immune system regulation.}, } @article {pmid37107570, year = {2023}, author = {Becker, B and Pushkareva, E}, title = {Metagenomics Provides a Deeper Assessment of the Diversity of Bacterial Communities in Polar Soils Than Metabarcoding.}, journal = {Genes}, volume = {14}, number = {4}, pages = {}, pmid = {37107570}, issn = {2073-4425}, mesh = {*Metagenomics/methods ; *Soil ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; DNA ; }, abstract = {The diversity of soil bacteria was analyzed via metabarcoding and metagenomic approaches using DNA samples isolated from the biocrusts of 12 different Arctic and Antarctic sites. For the metabarcoding approach, the V3-4 region of the 16S rRNA was targeted. Our results showed that nearly all operational taxonomic units (OTUs = taxa) found in metabarcoding analyses were recovered in metagenomic analyses. In contrast, metagenomics identified a large number of additional OTUs absent in metabarcoding analyses. In addition, we found huge differences in the abundance of OTUs between the two methods. The reasons for these differences seem to be (1) the higher sequencing depth in metagenomics studies, which allows the detection of low-abundance community members in metagenomics, and (2) bias of primer pairs used to amplify the targeted sequence in metabarcoding, which can change the community composition dramatically even at the lower taxonomic levels. We strongly recommend using only metagenomic approaches when establishing the taxonomic profiles of whole biological communities.}, } @article {pmid37107373, year = {2023}, author = {Guo, Y and Liu, M and Liu, X and Zheng, M and Xu, X and Liu, X and Gong, J and Liu, H and Liu, J}, title = {Metagenomic and Untargeted Metabolomic Analysis of the Effect of Sporisorium reilianum Polysaccharide on Improving Obesity.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {8}, pages = {}, pmid = {37107373}, issn = {2304-8158}, support = {2022YFF1100205//National Key Research and Development Program of China/ ; 20210509026RQ//Scientific and Technological Innovation Team Project for the Outstanding Young and Middle-Aged of Jilin Province/ ; 2016YFD0400700//National Key Research and Development Program of China/ ; 2016YFD0400702//National Key Research and Development Program of China/ ; }, abstract = {Gut microbiota plays an important role in the pathophysiology of obesity. Fungal polysaccharide can improve obesity, but the potential mechanism needs further study. This experiment studied the potential mechanism of polysaccharides from Sporisorium reilianum (SRP) to improve obesity in male Sprague Dawley (SD) rats fed with a high-fat diet (HFD) using metagenomics and untargeted metabolomics. After 8 weeks of SRP (100, 200, and 400 mg/kg/day) intervention, we analyzed the related index of obesity, gut microbiota, and untargeted metabolomics of rats. The obesity and serum lipid levels of rats treated with SRP were reduced, and lipid accumulation in the liver and adipocyte hypertrophy was improved, especially in rats treated with a high dose of SRP. SRP improved the composition and function of gut microbiota in rats fed with a high-fat diet, and decreased the ratio of Firmicutes to Bacteroides at the phylum level. At the genus level, the abundance of Lactobacillus increased and that of Bacteroides decreased. At the species level, the abundance of Lactobacillus crispatus, Lactobacillus helveticus, and Lactobacillus acidophilus increased, while the abundance of Lactobacillus reuteri and Staphylococcus xylosus decreased. The function of gut microbiota mainly regulated lipid metabolism and amino acid metabolism. The untargeted metabolomics indicated that 36 metabolites were related to the anti-obesity effect of SRP. Furthermore, linoleic acid metabolism, phenylalanine, tyrosine, and tryptophan biosynthesis, and the phenylalanine metabolism pathway played a role in improving obesity in those treated with SRP. The study results suggest that SRP significantly alleviated obesity via gut-microbiota-related metabolic pathways, and SRP could be used for the prevention and treatment of obesity.}, } @article {pmid37107344, year = {2023}, author = {Romero-Miguel, D and Casquero-Veiga, M and Fernández, J and Lamanna-Rama, N and Gómez-Rangel, V and Gálvez-Robleño, C and Santa-Marta, C and Villar, CJ and Lombó, F and Abalo, R and Desco, M and Soto-Montenegro, ML}, title = {Maternal Supplementation with N-Acetylcysteine Modulates the Microbiota-Gut-Brain Axis in Offspring of the Poly I:C Rat Model of Schizophrenia.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, pmid = {37107344}, issn = {2076-3921}, support = {project number PI17/01766, and grant number BA21/00030//Ministerio de Ciencia e Innovación, Instituto de Salud Carlos III, co-financed by the European Regional Development Fund (ERDF), "A way to make Europe"/ ; project PID2021-128862OB-I00//MCIN /AEI /10.13039/501100011033 / FEDER, UE/ ; project number CB07/09/0031//CIBER de Salud Mental - Instituto de Salud Carlos III/ ; project numbers 2017/085, 2022/008917//Delegación del Gobierno para el Plan Nacional sobre Drogas/ ; 2016/01//Fundación Alicia Koplowitz/ ; grant, PEJD-2018-PRE/BMD-7899//Consejería de Educación e investigación, Comunidad de Madrid, co-funded by the European Social Fund "Investing in your future"/ ; "Programa Intramural de Impulso a la I+D+I 2019"//Instituto de investigación Sanitaria Gregorio Marañón/ ; PT20/00044//Ministerio de Ciencia e Innovación, Instituto de Salud Carlos III/ ; x//The CNIC is supported by the Instituto de Salud Carlos III (ISCIII), the Ministerio de Ciencia e Innovación (MCIN) and the Pro CNIC Foundation, and is a Severo Ochoa Center of Excellence (SEV-2015-0505)/ ; Contrato Intramural Postdoctoral//FINBA/ ; SV-PA-21-AYUD/2021/51347//Ayudas para grupos de investigación de organismos del Principado de Asturias/ ; }, abstract = {The microbiota-gut-brain axis is a complex interconnected system altered in schizophrenia. The antioxidant N-acetylcysteine (NAC) has been proposed as an adjunctive therapy to antipsychotics in clinical trials, but its role in the microbiota-gut-brain axis has not been sufficiently explored. We aimed to describe the effect of NAC administration during pregnancy on the gut-brain axis in the offspring from the maternal immune stimulation (MIS) animal model of schizophrenia. Pregnant Wistar rats were treated with PolyI:C/Saline. Six groups of animals were studied according to the study factors: phenotype (Saline, MIS) and treatment (no NAC, NAC 7 days, NAC 21 days). Offspring were subjected to the novel object recognition test and were scanned using MRI. Caecum contents were used for metagenomics 16S rRNA sequencing. NAC treatment prevented hippocampal volume reduction and long-term memory deficits in MIS-offspring. In addition, MIS-animals showed lower bacterial richness, which was prevented by NAC. Moreover, NAC7/NAC21 treatments resulted in a reduction of proinflammatory taxons in MIS-animals and an increase in taxa known to produce anti-inflammatory metabolites. Early approaches, like this one, with anti-inflammatory/anti-oxidative compounds, especially in neurodevelopmental disorders with an inflammatory/oxidative basis, may be useful in modulating bacterial microbiota, hippocampal size, as well as hippocampal-based memory impairments.}, } @article {pmid37107222, year = {2023}, author = {Pierański, MK and Kosiński, JG and Szymczak, K and Sadowski, P and Grinholc, M}, title = {Antimicrobial Photodynamic Inactivation: An Alternative for Group B Streptococcus Vaginal Colonization in a Murine Experimental Model.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, pmid = {37107222}, issn = {2076-3921}, support = {NCN 2016/23/B/NZ7/03236//National Science Center/ ; 531-N119-D098-23//University of Gdańsk/ ; }, abstract = {BACKGROUND: Streptococcus agalactiae, referred to as Group B Streptococcus (GBS), is a prominent bacterium causing life-threatening neonatal infections. Although antibiotics are efficient against GBS, growing antibiotic resistance forces the search for alternative treatments and/or prevention approaches. Antimicrobial photodynamic inactivation (aPDI) appears to be a potent alternative non-antibiotic strategy against GBS.

METHODS: The effect of rose bengal aPDI on various GBS serotypes, Lactobacillus species, human eukaryotic cell lines and microbial vaginal flora composition was evaluated.

RESULTS: RB-mediated aPDI was evidenced to exert high bactericidal efficacy towards S. agalactiae in vitro (>4 log10 units of viability reduction for planktonic and >2 log10 units for multispecies biofilm culture) and in vivo (ca. 2 log10 units of viability reduction in mice vaginal GBS colonization model) in microbiological and metagenomic analyses. At the same time, RB-mediated aPDI was evidenced to be not mutagenic and safe for human vaginal cells, as well as capable of maintaining the balance and viability of vaginal microbial flora.

CONCLUSIONS: aPDI can efficiently kill GBS and serve as an alternative approach against GBS vaginal colonization and/or infections.}, } @article {pmid37107193, year = {2023}, author = {Caballano-Infantes, E and Ho-Plágaro, A and López-Gómez, C and Martín-Reyes, F and Rodríguez-Pacheco, F and Taminiau, B and Daube, G and Garrido-Sánchez, L and Alcaín-Martínez, G and Andrade, RJ and García-Cortés, M and Lucena, MI and García-Fuentes, E and Rodríguez-Díaz, C}, title = {Membrane Vesicles of Toxigenic Clostridioides difficile Affect the Metabolism of Liver HepG2 Cells.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, pmid = {37107193}, issn = {2076-3921}, support = {PI18/01652, PI19/00883 and PI21/01248//Instituto de Salud Carlos III/ ; PI18-RT-3364 and UMA18-FEDERJA-194//Consejería de Economía, Conocimiento, Empresas y Universidad, Junta de Andalucia (Spain)/ ; }, abstract = {Clostridioides difficile infection (CDI) appears to be associated with different liver diseases. C. difficile secretes membrane vesicles (MVs), which may be involved in the development of nonalcoholic fatty liver disease (NALFD) and drug-induced liver injury (DILI). In this study, we investigated the presence of C. difficile-derived MVs in patients with and without CDI, and analyzed their effects on pathways related to NAFLD and DILI in HepG2 cells. Fecal extracellular vesicles from CDI patients showed an increase of Clostridioides MVs. C. difficile-derived MVs that were internalized by HepG2 cells. Toxigenic C. difficile-derived MVs decreased mitochondrial membrane potential and increased intracellular ROS compared to non-toxigenic C. difficile-derived MVs. In addition, toxigenic C. difficile-derived MVs upregulated the expression of genes related to mitochondrial fission (FIS1 and DRP1), antioxidant status (GPX1), apoptosis (CASP3), glycolysis (HK2, PDK1, LDHA and PKM2) and β-oxidation (CPT1A), as well as anti- and pro-inflammatory genes (IL-6 and IL-10). However, non-toxigenic C. difficile-derived MVs did not produce changes in the expression of these genes, except for CPT1A, which was also increased. In conclusion, the metabolic and mitochondrial changes produced by MVs obtained from toxigenic C. difficile present in CDI feces are common pathophysiological features observed in the NAFLD spectrum and DILI.}, } @article {pmid37106331, year = {2023}, author = {Deng, J and Wu, L and Wei, S and Zhang, X}, title = {Atypical anti-GQ1b antibody syndrome presenting with vomiting as the initial symptom: a case report and literature review.}, journal = {BMC neurology}, volume = {23}, number = {1}, pages = {170}, pmid = {37106331}, issn = {1471-2377}, mesh = {Child ; Humans ; *Miller Fisher Syndrome ; *Guillain-Barre Syndrome/complications ; Immunoglobulins, Intravenous/therapeutic use ; *Ophthalmoplegia/diagnosis/etiology ; Vomiting/complications ; Gangliosides ; }, abstract = {BACKGROUND: Anti-GQ1b antibody syndrome is a rare autoimmune neuropathy, and atypical cases are even more rare, only a few cases have been reported. Anti-GQ1b antibody syndrome is difficult in early diagnosis and prone to misdiagnosis. Generally,in children with anti-GQ1b antibody syndrome,extraocular muscle paralysis is the initial symptom. However, anti-GQ1b antibody syndrome with vomiting as the initial symptom followed by abnormal gait has not been reported.

CASE PRESENTATION: We reported a case of anti-GQ1b antibody syndrome with vomiting as the initial symptom, followed by abnormal gait. One day after vomiting, the child developed abnormal gait, which primarily manifested as a slight tilt of the upper body during walking as well as an opening and swaying of the legs at fast walking paces,then progressively aggravated, and finally he could not stand on his own.In the auxiliary examination, cerebrospinal fluid routine,biochemical and metagenomic Next-Generation Sequencing (DNA and RNA), brain + spinal cord contrast magnetic resonance imaging (MRI),magnetic Resonance angiography (MRA) and diffusion-weighted image (DWI), hip and knee joint ultrasound showed normal results. Anti-GQ1b antibody syndrome was not confirmed until the positive anti-GQ1b IgG antibody was detected in the serum. After treatment with intravenous immunoglobulin (IVIG) and glucocorticoid, the child recovered well, and a 3-month outpatient follow-up showed that the child was able to walk normally.

CONCLUSIONS: There are no previous reports of anti-GQ1b antibody syndrome with vomiting as the initial symptom, followed by abnormal gait. Therefore, this valuable case contributes to expanding the database of clinical manifestation of anti-GQ1b antibody syndrome, so as to improve pediatricians' awareness about such rare diseases and reduce misdiagnosis.}, } @article {pmid37106322, year = {2023}, author = {Zhang, S and Ou, J and Tan, Y and Yang, B and Wu, Y and Liu, L}, title = {Metagenomic next-generation sequencing for pulmonary infections diagnosis in patients with diabetes.}, journal = {BMC pulmonary medicine}, volume = {23}, number = {1}, pages = {142}, pmid = {37106322}, issn = {1471-2466}, support = {ZK[2022]254//Guizhou Province Science and Technology Project/ ; gzwkj2021-088//Science and Technology foundation of Guizhou Health Commission/ ; }, mesh = {Humans ; Retrospective Studies ; *Diabetes Mellitus ; High-Throughput Nucleotide Sequencing ; Bronchoalveolar Lavage Fluid ; Klebsiella pneumoniae/genetics ; *Pneumonia ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Diabetes mellitus is a major cause of high mortality and poor prognosis in patients with pulmonary infections. However, limited data on the application of metagenomic next-generation sequencing (mNGS) are available for diabetic patients. This study aimed to evaluate the diagnostic performance of mNGS in diabetic patients with pulmonary infections.

METHODS: We retrospectively reviewed 184 hospitalized patients with pulmonary infections at Guizhou Provincial People's Hospital between January 2020 to October 2021. All patients were subjected to both mNGS analysis of bronchoalveolar lavage fluid (BALF) and conventional testing. Positive rate by mNGS and the consistency between mNGS and conventional testing results were evaluated for diabetic and non-diabetic patients.

RESULTS: A total of 184 patients with pulmonary infections were enrolled, including 43 diabetic patients and 141 non-diabetic patients. For diabetic patients, the microbial positive rate by mNGS was significantly higher than that detected by conventional testing methods, primarily driven by bacterial detection (microbes: 95.3% vs. 67.4%, P = 0.001; bacteria: 72.1% vs. 37.2%, P = 0.001). mNGS and traditional tests had similar positive rates with regard to fungal and viral detection in diabetic patients. Klebsiella pneumoniae was the most common pathogen identified by mNGS in patients with diabetes. Moreover, mNGS identified pathogens in 92.9% (13/14) of diabetic patients who were reported negative by conventional testing. No significant difference was found in the consistency of the two tests between diabetic and non-diabetic groups.

CONCLUSIONS: mNGS is superior to conventional microbiological tests for bacterial detection in diabetic patients with pulmonary infections. mNGS is a valuable tool for etiological diagnosis of pulmonary infections in diabetic patients.}, } @article {pmid37106038, year = {2023}, author = {Maghini, DG and Dvorak, M and Dahlen, A and Roos, M and Kuersten, S and Bhatt, AS}, title = {Quantifying bias introduced by sample collection in relative and absolute microbiome measurements.}, journal = {Nature biotechnology}, volume = {}, number = {}, pages = {}, pmid = {37106038}, issn = {1546-1696}, support = {Lieberman Fellowship//Stanford University (SU)/ ; T32GM007276//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P30CA124435//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 1S10OD02014101//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AI14862302//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; R01AI14375702//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; }, abstract = {To gain insight into the accuracy of microbial measurements, it is important to evaluate sources of bias related to sample condition, preservative method and bioinformatic analyses. There is increasing evidence that measurement of the total count and concentration of microbes in the gut, or 'absolute abundance', provides a richer source of information than relative abundance and can correct some conclusions drawn from relative abundance data. However, little is known about how preservative choice can affect these measurements. In this study, we investigated how two common preservatives and short-term storage conditions impact relative and absolute microbial measurements. OMNIgene GUT OMR-200 yields lower metagenomic taxonomic variation between different storage temperatures, whereas Zymo DNA/RNA Shield yields lower metatranscriptomic taxonomic variation. Absolute abundance quantification reveals two different causes of variable Bacteroidetes:Firmicutes ratios across preservatives. Based on these results, we recommend OMNIgene GUT OMR-200 preservative for field studies and Zymo DNA/RNA Shield for metatranscriptomics studies, and we strongly encourage absolute quantification for microbial measurements.}, } @article {pmid37105768, year = {2022}, author = {Kumar, R and Kumar, R and Brar, SK and Kaur, G}, title = {Next-generation -omics approaches to drive carboxylate production by acidogenic fermentation of food waste: a review.}, journal = {Bioengineered}, volume = {13}, number = {7-12}, pages = {14987-15002}, pmid = {37105768}, issn = {2165-5987}, mesh = {Fermentation ; *Food ; *Refuse Disposal ; Carbohydrate Metabolism ; Acids ; Fatty Acids, Volatile/metabolism ; Carboxylic Acids ; Bioreactors ; Hydrogen-Ion Concentration ; Sewage ; }, abstract = {Acidogenic fermentation of food waste using mixed microbial cultures can produce carboxylates [or volatile fatty acids (VFA)] as high-valued bioproducts via a complex interplay of microorganisms during different stages of this process. However, the present fermentation systems are incapable of reaching the industrially relevant VFA production yields of ≥50 g/L primarly due to the complex process operation, competitive metabolic pathways, and limited understanding of microbial interplays. Recent reports have demonstrated the significant roles played by microbial communities from different phyla, which work together to control the process kinetics of various stages underlying acidogenic fermentation. In order to fully delineate the abundance, structure, and functionality of these microbial communities, next-generation high-throughput meta-omics technologies are required. In this article, we review the potential of metagenomics and metatranscriptomics approaches to enable microbial community engineering. Specifically, a deeper analysis of taxonomic relationships, shifts in microbial communities, and differences in the genetic expression of key pathway enzymes under varying operational and environmental parameters of acidogenic fermentation could lead to the identification of species-level functionalities for both cultivable and non-cultivable microbial fractions. Furthermore, it could also be used for successful gene sequence-guided microbial isolation and consortium development for bioaugmentation to allow VFA production with high concentrations and purity. Such highly controlled and engineered microbial systems could pave the way for tailored and high-yielding VFA synthesis, thereby creating a petrochemically competitive waste-to-value chain and promoting the circular bioeconomy.Research HighlightsMixed microbial mediated acidogenic fermentation of food waste.Metagenomics and metatranscriptomics based microbial community analysis.Omics derived function-associated microbial isolation and consortium engineering.High-valued sustainable carboxylate bio-products, i.e. volatile fatty acids.}, } @article {pmid37105465, year = {2023}, author = {Guo, Y and Cheng, S and Fang, H and Yang, Y and Li, Y and Shi, F and Zhou, Y}, title = {Copper and cadmium co-contamination affects soil bacterial taxonomic and functional attributes in paddy soils.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {329}, number = {}, pages = {121724}, doi = {10.1016/j.envpol.2023.121724}, pmid = {37105465}, issn = {1873-6424}, mesh = {Cadmium/analysis ; Copper/analysis ; Soil ; *Metals, Heavy/analysis ; Bacteria ; China ; *Soil Pollutants/analysis ; *Oryza/metabolism ; }, abstract = {Microorganisms inhabiting heavy metal-contaminated soils have evolved specific metabolic capabilities to survive, which has the potential for effective bioremediation. However, the ecological consequence of copper (Cu) and cadmium (Cd) on bacterial taxonomic and functional attributes of rice field remains unclear. Here, we selected paddy soils along a polluted river in southern China to evaluate the role of Cu and Cd contaminant fractions in regulating bacterial co-occurrence patterns. We also assessed the effects of these heavy metal fractions on the relative abundance of functional genes using shotgun metagenomic analysis. Soil Cu and Cd concentrations in paddy soils gradually decreased from upstream to downstream of the river, and had a greater impact on bacterial communities and metabolic potentials than soil general properties. Soil Cu and Cd contamination led to drastic changes in the cumulative relative abundance of ecological modules in bacterial co-occurrence networks. Bacteria associated with AD3, HSB_OF53-F07 (both belonging to Chloroflexi), Rokubacteriales, and Nitrospira were identified as tolerant to Cu and Cd contamination. The Cu and Cd contaminant fractions were positively correlated with the genes involved in metal resistance, carbon (C) fixation, nitrification, and denitrification, but negatively correlated with the genes related to nitrogen (N) fixation. These results indicated that soil Cu and Cd pollution not only enriched metal resistant genes, but also affected genes related to microbial C and N cycling. This is critical for facilitating microbiome bioremediation of metal-contaminated paddy soils.}, } @article {pmid37105293, year = {2023}, author = {Chai, F and Li, L and Wang, W and Xue, S and Liu, J}, title = {Electro-stimulated anaerobic oxidation of methane with synergistic denitrification by adding AQS: Electron transfer mode and mechanism.}, journal = {Environmental research}, volume = {229}, number = {}, pages = {115997}, doi = {10.1016/j.envres.2023.115997}, pmid = {37105293}, issn = {1096-0953}, mesh = {Electron Transport ; Anaerobiosis ; *Methane ; *Denitrification ; Electrons ; Oxidation-Reduction ; Bioreactors/microbiology ; Nitrites/metabolism ; Nitrogen/metabolism ; }, abstract = {Denitrifying anaerobic methane-oxidizing (DAMO) processes, which link anaerobic methane oxidation (AMO) and denitrification, have a promising prospect in anaerobic wastewater treatment. In bioelectrochemical systems (BES), DAMO consortium presented potent metabolic activity. However, the extracellular electron transfer (EET) in BES was poorly understood. This study investigated the EET mechanisms and modes of electron transport in BES dominated by anaerobic methanotrophic bacteria. In the bioreactors with the auxiliary voltage of 0.5 and 1.1 V, named EMN-0.5 and EMN-1.1, respectively, biological voltages of 0.198 and 0.329 V were generated with power densities of 0.6 and 1.20 mW/m[2], after removing the voltage. High throughput and metagenome analyses demonstrated that main methanotrophs were DAMO bacteria and Methylocystis sp. The electroactive bacteria detected were Pseudomonas sp., Hypomicrobium sp., Thiobacillus sp, and Rhodococcus sp. The pil, cytochrome c, hdr, and he/fp genes related to EET were present on the electrode surfaces. Carbon 13 isotope tracing and chemicals analysis by GC-MS exhibited that methanol was an intermediate product released to extracellular environment and acted as the electronic carrier to drive the EET in methane oxidation. Extracellular electron transfer was achieved through the collaboration of DAMO bacteria, Methylocystis sp., and Pseudomonas sp. Anthraquinone 2-sulfonic acid ester (AQS) could improve the rate of electron transfer to the extracellular space, especially in the EMN-0.5 reaction system. This study provides a new understanding of AMO consortium metabolism in BES and may provide a scientific basis for developing methane control technology.}, } @article {pmid37105269, year = {2023}, author = {Togawa, A and Chikamatsu, K and Takaki, A and Matsumoto, Y and Yoshimura, M and Tsuchiya, S and Nakamura, S and Mitarai, S}, title = {Multiple mutations of Mycobacterium intracellulare subsp. chimaera causing false-negative reaction to the transcription-reverse transcription concerted method for pathogen detection.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {133}, number = {}, pages = {14-17}, doi = {10.1016/j.ijid.2023.04.406}, pmid = {37105269}, issn = {1878-3511}, mesh = {Humans ; *Mycobacterium avium Complex ; RNA, Ribosomal, 16S/genetics ; Reverse Transcription ; *Mycobacterium ; Mutation ; }, abstract = {OBJECTIVES: To report an isolate of Mycobacterium intracellulare subsp. chimaera with multiple mutations in 16S ribosomal RNA (rRNA) gene, resulting in the false-negative reaction to the transcription-reverse transcription concerted (TRC) method for Mycobacterium avium-intracellulare complex.

METHODS: We used TRC, polymerase chain reaction (PCR), and Matrix-assisted laser desorption/ionization Time-of-Flight/Mass Spectrometry (MALDI-TOF/MS) methods to identify a clinical isolate in 2021. Due to the discordant results between TRC and PCR or MALDI-TOF MS methods, 16S rRNA sequencing, whole-genome shotgun (WGS) sequencing, and average nucleotide identity (ANI) analysis were employed to identify the isolate.

RESULTS: A mycobacterial isolate from a sputum sample gave negative results for the detection of Mycobacterium tuberculosis complex or M. avium-intracellulare complex by the TRC method. However, the isolate was identified as M. intracellulare by both PCR method and MALDI-TOF MS method. WGS sequencing of 16S rRNA genome revealed eight substitution mutations and one insertion mutation within the region, which could hamper the correct reaction to TRC method. Subsequent ANI analysis between the isolate and various species of nontuberculosis mycobacteria revealed that the isolate could be identified as M. intracellulare subsp. chimaera.

CONCLUSION: Rare mutations within the 16S rRNA genome resulted in the false-negative identification of Mycobacterium chimaera by the TRC method. WGS sequencing and ANI analysis was necessary to identify the isolate.}, } @article {pmid37105180, year = {2023}, author = {McGuire, PM and Butkevich, N and Saksena, AV and Walter, MT and Shapleigh, JP and Reid, MC}, title = {Oxic-anoxic cycling promotes coupling between complex carbon metabolism and denitrification in woodchip bioreactors.}, journal = {Environmental microbiology}, volume = {25}, number = {9}, pages = {1696-1712}, doi = {10.1111/1462-2920.16387}, pmid = {37105180}, issn = {1462-2920}, mesh = {Bioreactors ; *Wood/microbiology ; Carbon ; Denitrification ; Oxidation-Reduction ; *Fungi/classification/genetics/isolation & purification ; *Bacteria/classification/genetics/isolation & purification ; Archaea/classification/genetics/isolation & purification ; }, abstract = {Denitrifying woodchip bioreactors (WBRs) are increasingly used to manage the release of non-point source nitrogen (N) by stimulating microbial denitrification. Woodchips serve as a renewable organic carbon (C) source, yet the recalcitrance of organic C in lignocellulosic biomass causes many WBRs to be C-limited. Prior studies have observed that oxic-anoxic cycling increased the mobilization of organic C, increased nitrate (NO3 [-]) removal rates, and attenuated production of nitrous oxide (N2 O). Here, we use multi-omics approaches and amplicon sequencing of fungal 5.8S-ITS2 and prokaryotic 16S rRNA genes to elucidate the microbial drivers for enhanced NO3 [-] removal and attenuated N2 O production under redox-dynamic conditions. Transient oxic periods stimulated the expression of fungal ligninolytic enzymes, increasing the bioavailability of woodchip-derived C and stimulating the expression of denitrification genes. Nitrous oxide reductase (nosZ) genes were primarily clade II, and the ratio of clade II/clade I nosZ transcripts during the oxic-anoxic transition was strongly correlated with the N2 O yield. Analysis of metagenome-assembled genomes revealed that many of the denitrifying microorganisms also have a genotypic ability to degrade complex polysaccharides like cellulose and hemicellulose, highlighting the adaptation of the WBR microbiome to the ecophysiological niche of the woodchip matrix.}, } @article {pmid37104181, year = {2023}, author = {Jin, J and Zhang, C and Ren, X and Tai, B and Xing, F}, title = {Metagenome Analysis Identifies Microbial Shifts upon Deoxynivalenol Exposure and Post-Exposure Recovery in the Mouse Gut.}, journal = {Toxins}, volume = {15}, number = {4}, pages = {}, pmid = {37104181}, issn = {2072-6651}, mesh = {Mice ; Humans ; Animals ; Metagenome ; Inulin ; *Trichothecenes/toxicity ; *Microbiota ; Prebiotics ; *Lactobacillales ; }, abstract = {Deoxynivalenol (DON) is one of the most prevalent food-associated mycotoxins, and is known to cause a variety of adverse health effects on human and animals. Upon oral exposure, the intestine is the main target organ of DON. The current study unraveled that DON exposure (2 mg/kg bw/day or 5 mg/kg bw/day) can significantly reshape the gut microbiota in a mouse model. The study characterized the specific gut microbial strains and genes changed after DON exposure and also investigated the recovery of the microbiota upon either 2 weeks daily prebiotic inulin administration or 2 weeks recovery without intervention after termination of DON exposure (spontaneous recovery). The results obtained reveal that DON exposure causes a shift in gut microorganisms, increasing the relative abundance of Akkermansia muciniphila, Bacteroides vulgatus, Hungatella hathewayi, and Lachnospiraceae bacterium 28-4, while the relative abundance of Mucispirillum schaedleri, Pseudoflavonifractor sp. An85, Faecalibacterium prausnitzii, Firmicutes bacterium ASF500, Flavonifractor plautii, Oscillibacter sp. 1-3, and uncultured Flavonifractor sp. decreased. Notably, DON exposure enhanced the prevalence of A. muciniphila, a species considered as a potential prebiotic in previous studies. Most of the gut microbiome altered by DON in the low- and high-dose exposure groups recovered after 2 weeks of spontaneous recovery. Inulin administration appeared to promote the recovery of the gut microbiome and functional genes after low-dose DON exposure, but not after high-dose exposure, at which changes were exacerbated by inulin-supplemented recovery. The results obtained help to better understand the effect of DON on the gut microbiome, and the gut microbiota's recovery upon termination of DON exposure.}, } @article {pmid37104016, year = {2023}, author = {Alemán-Duarte, MI and Aguilar-Uscanga, BR and García-Robles, G and Ramírez-Salazar, FJ and Benítez-García, I and Balcázar-López, E and Solís-Pacheco, JR}, title = {Improvement and Validation of a Genomic DNA Extraction Method for Human Breastmilk.}, journal = {Methods and protocols}, volume = {6}, number = {2}, pages = {}, pmid = {37104016}, issn = {2409-9279}, support = {298887//Consejo Nacional de Ciencia y Tecnología/ ; }, abstract = {The human milk microbiota (HMM) of healthy women can vary substantially, as demonstrated by recent advances in DNA sequencing technology. However, the method used to extract genomic DNA (gDNA) from these samples may impact the observed variations and potentially bias the microbiological reconstruction. Therefore, it is important to use a DNA extraction method that is able to effectively isolate gDNA from a diverse range of microorganisms. In this study, we improved and compared a DNA extraction method for gDNA isolation from human milk (HM) samples to commercial and standard protocols. We evaluated the extracted gDNA using spectrophotometric measurements, gel electrophoresis, and PCR amplifications to assess its quantity, quality, and amplifiability. Additionally, we tested the improved method's ability to isolate amplifiable gDNA from fungi, Gram-positive and Gram-negative bacteria to validate its potential for reconstructing microbiological profiles. The improved DNA extraction method resulted in a higher quality and quantity of the extracted gDNA compared to the commercial and standard protocols and allowed for polymerase chain reaction (PCR) amplification of the V3-V4 regions of the 16S ribosomal gene in all the samples and the ITS-1 region of the fungal 18S ribosomal gene in 95% of the samples. These results suggest that the improved DNA extraction method demonstrates better performance for gDNA extraction from complex samples such as HM.}, } @article {pmid37103739, year = {2023}, author = {Balakrishnan, K and Krishnaa, D and Balakrishnan, G and Manickam, M and Abdulkader, AM and Dharumadurai, D}, title = {Association of Bacterial Communities with Psychedelic Mushroom and Soil as Revealed in 16S rRNA Gene Sequencing.}, journal = {Applied biochemistry and biotechnology}, volume = {}, number = {}, pages = {}, pmid = {37103739}, issn = {1559-0291}, abstract = {Microbial communities' resident in the mushroom fruiting body and the soil around it play critical roles in the growth and propagation of the mushroom. Among the microbial communities associated with psychedelic mushrooms and the rhizosphere soil, bacterial communities are considered vital since their presence greatly influences the health of the mushrooms. The present study aimed at finding the microbiota present in the psychedelic mushroom Psilocybe cubensis and the soil the mushroom inhabits. The study was conducted at two different locations in Kodaikanal, Tamil Nadu, India. The composition and structure of microbial communities in the mushroom fruiting body and the soil were deciphered. The genomes of the microbial communities were directly assessed. High-throughput amplicon sequencing revealed distinct microbial diversity in the mushroom and the related soil. The interaction of environmental and anthropogenic factors appeared to have a significant impact on the mushroom and soil microbiome. The most abundant bacterial genera were Ochrobactrum, Stenotrophomonas, Achromobacter, and Brevundimonas. Thus, the study advances the knowledge of the composition of the microbiome and microbial ecology of a psychedelic mushroom, and paves the way for in-depth investigation of the influence of microbiota on the mushroom, with special emphasis on the impact of bacterial communities on mushroom growth. Further studies are required for a deeper understanding of the microbial communities that influence the growth of P. cubensis mushroom.}, } @article {pmid37103117, year = {2023}, author = {Huang, YT and Yang, MY and Mao, YC and Lee, DY and Kuo, YL and Tseng, CH and Liu, CW and Fu, YC and Liu, PY}, title = {Identification of Cutibacterium modestum in Spondylitis by Metagenomics Analysis.}, journal = {In vivo (Athens, Greece)}, volume = {37}, number = {3}, pages = {1384-1388}, pmid = {37103117}, issn = {1791-7549}, mesh = {Male ; Humans ; Aged ; *Diskectomy, Percutaneous ; Lumbar Vertebrae ; *Intervertebral Disc Displacement ; *Spondylitis/diagnosis ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {BACKGROUND/AIM: Identifying pathogens with culture-negative pyogenic spondylitis is difficult. Shotgun metagenomic sequencing is an unbiased and culture-free approach in the diagnosis of infectious diseases. There are, however, a variety of contaminating factors that can confound the precision of metagenomic sequencing.

CASE REPORT: In a 65-year-old man suffering from culture-negative L3-5 spondylitis, metagenomics was applied to facilitate the diagnosis. The patient underwent percutaneous endoscopic lumbar discectomy. We applied metagenomic sequencing with a robust contamination-free protocol to the bone biopsy. By comparing the abundance for each taxon between the replicates and negative controls, we reliably identified Cutibacterium modestum as having a statistically higher abundance in all replicates. The patient's antibiotic therapy was switched to penicillin and doxycycline based upon the resistome analysis; the patient fully recovered.

CONCLUSION: This application of next-generation sequencing provides a new perspective in the clinical approach to spinal osteomyelitis and illustrates the potential of this technique in rapid etiological diagnosis.}, } @article {pmid37102874, year = {2023}, author = {Colbert, JF and Kirsch, JM and Erzen, CL and Langouët-Astrié, CJ and Thompson, GE and McMurtry, SA and Kofonow, JM and Robertson, CE and Kovacs, EJ and Sullivan, RC and Hippensteel, JA and Sawant, NV and De Nisco, NJ and McCollister, BD and Schwartz, RS and Horswill, AR and Frank, DN and Duerkop, BA and Schmidt, EP}, title = {Aging-Associated Augmentation of Gut Microbiome Virulence Capability Drives Sepsis Severity.}, journal = {mBio}, volume = {14}, number = {3}, pages = {e0005223}, pmid = {37102874}, issn = {2150-7511}, support = {R01 AI141479/AI/NIAID NIH HHS/United States ; K08 AG061144/AG/NIA NIH HHS/United States ; R03 AG056353/AG/NIA NIH HHS/United States ; R01 GM125095/GM/NIGMS NIH HHS/United States ; R01 AI141479/AI/NIAID NIH HHS/United States ; T32 AI052066/AI/NIAID NIH HHS/United States ; R01 AG018859/AG/NIA NIH HHS/United States ; R01 DK131267/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; Aged ; *Gastrointestinal Microbiome/physiology ; Virulence ; Bacteria/genetics ; Aging ; *Sepsis/microbiology ; }, abstract = {Prior research has focused on host factors as mediators of exaggerated sepsis-associated morbidity and mortality in older adults. This focus on the host, however, has failed to identify therapies that improve sepsis outcomes in the elderly. We hypothesized that the increased susceptibility of the aging population to sepsis is not only a function of the host but also reflects longevity-associated changes in the virulence of gut pathobionts. We utilized two complementary models of gut microbiota-induced experimental sepsis to establish the aged gut microbiome as a key pathophysiologic driver of heightened disease severity. Further murine and human investigations into these polymicrobial bacterial communities demonstrated that age was associated with only subtle shifts in ecological composition but also an overabundance of genomic virulence factors that have functional consequence on host immune evasion. IMPORTANCE Older adults suffer more frequent and worse outcomes from sepsis, a critical illness secondary to infection. The reasons underlying this unique susceptibility are incompletely understood. Prior work in this area has focused on how the immune response changes with age. The current study, however, focuses instead on alterations in the community of bacteria that humans live with within their gut (i.e., the gut microbiome). The central concept of this paper is that the bacteria in our gut evolve along with the host and "age," making them more efficient at causing sepsis.}, } @article {pmid37102867, year = {2023}, author = {Zhang, W and Fan, X and Shi, H and Li, J and Zhang, M and Zhao, J and Su, X}, title = {Comprehensive Assessment of 16S rRNA Gene Amplicon Sequencing for Microbiome Profiling across Multiple Habitats.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0056323}, pmid = {37102867}, issn = {2165-0497}, mesh = {RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; Phylogeny ; *Microbiota/genetics ; Metagenome ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {The 16S rRNA gene works as a rapid and effective marker for the identification of microorganisms in complex communities; hence, a huge number of microbiomes have been surveyed by 16S amplicon-based sequencing. The resolution of the 16S rRNA gene is always considered only at the genus level; however, it has not been verified on a wide range of microbes yet. To fully explore the ability and potential of the 16S rRNA gene in microbial profiling, here, we propose Qscore, a comprehensive method to evaluate the performance of amplicons by integrating the amplification rate, multitier taxonomic annotation, sequence type, and length. Our in silico assessment by a "global view" of 35,889 microbe species across multiple reference databases summarizes the optimal sequencing strategy for 16S short reads. On the other hand, since microbes are unevenly distributed according to their habitats, we also provide the recommended configuration for 16 typical ecosystems based on the Qscores of 157,390 microbiomes in the Microbiome Search Engine (MSE). Detailed data simulation further proves that the 16S amplicons produced with Qscore-suggested parameters exhibit high precision in microbiome profiling, which is close to that of shotgun metagenomes under CAMI metrics. Therefore, by reconsidering the precision of 16S-based microbiome profiling, our work not only enables the high-quality reusability of massive sequence legacy that has already been produced but is also significant for guiding microbiome studies in the future. We have implemented the Qscore as an online service at http://qscore.single-cell.cn to parse the recommended sequencing strategy for specific habitats or expected microbial structures. IMPORTANCE 16S rRNA has long been used as a biomarker to identify distinct microbes from complex communities. However, due to the influence of the amplification region, sequencing type, sequence processing, and reference database, the accuracy of 16S rRNA has not been fully verified on a global range. More importantly, the microbial composition of different habitats varies greatly, and it is necessary to adopt different strategies according to the corresponding target microbes to achieve optimal analytical performance. Here, we developed Qscore, which evaluates the comprehensive performance of 16S amplicons from multiple perspectives, thus providing the best sequencing strategies for common ecological environments by using big data.}, } @article {pmid37102710, year = {2023}, author = {Green, SJ and Torok, T and Allen, JE and Eloe-Fadrosh, E and Jackson, SA and Jiang, SC and Levine, SS and Levy, S and Schriml, LM and Thomas, WK and Wood, JM and Tighe, SW}, title = {Metagenomic Methods for Addressing NASA's Planetary Protection Policy Requirements on Future Missions: A Workshop Report.}, journal = {Astrobiology}, volume = {23}, number = {8}, pages = {897-907}, pmid = {37102710}, issn = {1557-8070}, mesh = {United States ; Humans ; *Planets ; *Space Flight ; Extraterrestrial Environment ; Metagenomics ; United States National Aeronautics and Space Administration ; Spacecraft ; Policy ; }, abstract = {Molecular biology methods and technologies have advanced substantially over the past decade. These new molecular methods should be incorporated among the standard tools of planetary protection (PP) and could be validated for incorporation by 2026. To address the feasibility of applying modern molecular techniques to such an application, NASA conducted a technology workshop with private industry partners, academics, and government agency stakeholders, along with NASA staff and contractors. The technical discussions and presentations of the Multi-Mission Metagenomics Technology Development Workshop focused on modernizing and supplementing the current PP assays. The goals of the workshop were to assess the state of metagenomics and other advanced molecular techniques in the context of providing a validated framework to supplement the bacterial endospore-based NASA Standard Assay and to identify knowledge and technology gaps. In particular, workshop participants were tasked with discussing metagenomics as a stand-alone technology to provide rapid and comprehensive analysis of total nucleic acids and viable microorganisms on spacecraft surfaces, thereby allowing for the development of tailored and cost-effective microbial reduction plans for each hardware item on a spacecraft. Workshop participants recommended metagenomics approaches as the only data source that can adequately feed into quantitative microbial risk assessment models for evaluating the risk of forward (exploring extraterrestrial planet) and back (Earth harmful biological) contamination. Participants were unanimous that a metagenomics workflow, in tandem with rapid targeted quantitative (digital) PCR, represents a revolutionary advance over existing methods for the assessment of microbial bioburden on spacecraft surfaces. The workshop highlighted low biomass sampling, reagent contamination, and inconsistent bioinformatics data analysis as key areas for technology development. Finally, it was concluded that implementing metagenomics as an additional workflow for addressing concerns of NASA's robotic mission will represent a dramatic improvement in technology advancement for PP and will benefit future missions where mission success is affected by backward and forward contamination.}, } @article {pmid37101508, year = {2023}, author = {Levitan, O and Ma, L and Giovannelli, D and Burleson, DB and McCaffrey, P and Vala, A and Johnson, DA}, title = {The gut microbiome-Does stool represent right?.}, journal = {Heliyon}, volume = {9}, number = {3}, pages = {e13602}, pmid = {37101508}, issn = {2405-8440}, abstract = {Many stool-based gut microbiome studies have highlighted the importance of the microbiome. However, we hypothesized that stool is a poor proxy for the inner-colonic microbiome and that studying stool samples may be inadequate to capture the true inner-colonic microbiome. To test this hypothesis, we conducted prospective clinical studies with up to 20 patients undergoing an FDA-cleared gravity-fed colonic lavage without oral purgative pre-consumption. The objective of this study was to present the analysis of inner-colonic microbiota obtained non-invasively during the lavage and how these results differ from stool samples. The inner-colonic samples represented the descending, transverse, and ascending colon. All samples were analyzed for 16S rRNA and shotgun metagenomic sequences. The taxonomic, phylogenetic, and biosynthetic gene cluster analyses showed a distinctive biogeographic gradient and revealed differences between the sample types, especially in the proximal colon. The high percentage of unique information found only in the inner-colonic effluent highlights the importance of these samples and likewise the importance of collecting them using a method that can preserve these distinctive signatures. We proposed that these samples are imperative for developing future biomarkers, targeted therapeutics, and personalized medicine.}, } @article {pmid37101488, year = {2023}, author = {Decsi, K and Kutasy, B and Hegedűs, G and Alföldi, ZP and Kálmán, N and Nagy, Á and Virág, E}, title = {Corrigendum to "Natural immunity stimulation using ELICE16INDURES® plant conditioner in field culture of soybean" [Heliyon 9 (1), (January 2023) Article e12907].}, journal = {Heliyon}, volume = {9}, number = {3}, pages = {e13954}, doi = {10.1016/j.heliyon.2023.e13954}, pmid = {37101488}, issn = {2405-8440}, abstract = {[This corrects the article DOI: 10.1016/j.heliyon.2023.e12907.].}, } @article {pmid37101458, year = {2022}, author = {Li, Y and Gao, P and Sun, X and Li, B and Guo, L and Yang, R and Su, X and Gao, W and Xu, Z and Yan, G and Wang, Q and Sun, W}, title = {Primary Succession Changes the Composition and Functioning of the Protist Community on Mine Tailings, Especially Phototrophic Protists.}, journal = {ACS environmental Au}, volume = {2}, number = {5}, pages = {396-408}, pmid = {37101458}, issn = {2694-2518}, abstract = {Primary succession in mine tailings is a prerequisite for tailing vegetation. Microorganisms, including bacteria, fungi, and protists, play an important role in this process in the driving force for improving the nutritional status. Compared to bacteria and fungi, protist populations have rarely been investigated regarding their role in mine tailings, especially for those inhabiting tailings associated with primary succession. Protists are the primary consumers of fungi and bacteria, and their predatory actions promote the release of nutrients immobilized in the microbial biomass, as well as the uptake and turnover of nutrients, affecting the functions of the wider ecosystems. In this study, three different types of mine tailings associated with three successional stages (original tailings, biological crusts, and Miscanthus sinensis grasslands) were selected to characterize the protistan community diversity, structure, and function during primary succession. Some members classified as consumers dominated the network of microbial communities in the tailings, especially in the original bare land tailings. The keystone phototrophs of Chlorophyceae and Trebouxiophyceae showed the highest relative abundance in the biological crusts and grassland rhizosphere, respectively. In addition, the co-occurrences between protist and bacterial taxa demonstrated that the proportion of protistan phototrophs gradually increased during primary succession. Further, the metagenomic analysis of protistan metabolic potential showed that abundances of many functional genes associated with photosynthesis increased during the primary succession of tailings. Overall, these results suggest that the primary succession of mine tailings drives the changes observed in the protistan community, and in turn, the protistan phototrophs facilitate the primary succession of tailings. This research offers an initial insight into the changes in biodiversity, structure, and function of the protistan community during ecological succession on tailings.}, } @article {pmid37101246, year = {2023}, author = {Zhang, D and Zhang, J and Kalimuthu, S and Liu, J and Song, ZM and He, BB and Cai, P and Zhong, Z and Feng, C and Neelakantan, P and Li, YX}, title = {A systematically biosynthetic investigation of lactic acid bacteria reveals diverse antagonistic bacteriocins that potentially shape the human microbiome.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {91}, pmid = {37101246}, issn = {2049-2618}, mesh = {Female ; Humans ; *Bacteriocins/genetics ; *Lactobacillales/genetics ; *Microbiota/genetics ; Metagenome ; Anti-Bacterial Agents/pharmacology ; }, abstract = {BACKGROUND: Lactic acid bacteria (LAB) produce various bioactive secondary metabolites (SMs), which endow LAB with a protective role for the host. However, the biosynthetic potentials of LAB-derived SMs remain elusive, particularly in their diversity, abundance, and distribution in the human microbiome. Thus, it is still unknown to what extent LAB-derived SMs are involved in microbiome homeostasis.

RESULTS: Here, we systematically investigate the biosynthetic potential of LAB from 31,977 LAB genomes, identifying 130,051 secondary metabolite biosynthetic gene clusters (BGCs) of 2,849 gene cluster families (GCFs). Most of these GCFs are species-specific or even strain-specific and uncharacterized yet. Analyzing 748 human-associated metagenomes, we gain an insight into the profile of LAB BGCs, which are highly diverse and niche-specific in the human microbiome. We discover that most LAB BGCs may encode bacteriocins with pervasive antagonistic activities predicted by machine learning models, potentially playing protective roles in the human microbiome. Class II bacteriocins, one of the most abundant and diverse LAB SMs, are particularly enriched and predominant in the vaginal microbiome. We utilized metagenomic and metatranscriptomic analyses to guide our discovery of functional class II bacteriocins. Our findings suggest that these antibacterial bacteriocins have the potential to regulate microbial communities in the vagina, thereby contributing to the maintenance of microbiome homeostasis.

CONCLUSIONS: Our study systematically investigates LAB biosynthetic potential and their profiles in the human microbiome, linking them to the antagonistic contributions to microbiome homeostasis via omics analysis. These discoveries of the diverse and prevalent antagonistic SMs are expected to stimulate the mechanism study of LAB's protective roles for the microbiome and host, highlighting the potential of LAB and their bacteriocins as therapeutic alternatives. Video Abstract.}, } @article {pmid37100380, year = {2023}, author = {Tang, H and Zhou, T and Jin, W and Zong, S and Mamtimin, T and Salama, ES and Jeon, BH and Liu, P and Han, H and Li, X}, title = {Tumor-targeting engineered probiotic Escherichia coli Nissle 1917 inhibits colorectal tumorigenesis and modulates gut microbiota homeostasis in mice.}, journal = {Life sciences}, volume = {324}, number = {}, pages = {121709}, doi = {10.1016/j.lfs.2023.121709}, pmid = {37100380}, issn = {1879-0631}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Azurin/adverse effects ; Carcinogenesis ; Cell Transformation, Neoplastic ; *Probiotics/therapeutic use ; *Colorectal Neoplasms/metabolism ; Escherichia coli/genetics ; Dextran Sulfate/pharmacology ; Disease Models, Animal ; *Colitis/chemically induced ; }, abstract = {AIMS: Preliminary studies have identified the use of probiotics as a potential treatment strategy against colorectal cancer (CRC). However, natural probiotics lack direct tumor-targeting and tumor-killing activity in the intestine. This study aimed to construct a tumor-targeting engineered probiotic to combat CRC.

MAIN METHODS: Standard adhesion assay was performed to analyze the adherence ability of tumor-binding protein HlpA to CT26 cells. CCK-8 assay, Hoechst 33258 staining and flow cytometry analysis were used for examining cytotoxicity of tumoricidal protein azurin toward CT26 cells. An engineered probiotic Ep-AH harboring azurin and hlpA genes was developed using Escherichia coli Nissle 1917 (EcN) chassis. Antitumor effects of Ep-AH were evaluated in the azoxymethane (AOM) and dextran sodium sulfate salt (DSS)-induced CRC mice. Moreover, analysis of gut microbiota was conducted via fecal 16S rRNA gene sequencing and shotgun metagenomic sequencing.

KEY FINDINGS: Azurin caused a dose-dependent increase of apoptosis in CT26 cells. Ep-AH treatment reversed weight loss (p < 0.001), fecal occult blood (p < 0.01), and shortening of colon length (p < 0.001) than model group, as well as reducing tumorigenesis by 36 % (p < 0.001). Both Ep-H and Ep-A (EcN expressing HlpA or azurin) were less effective than Ep-AH. Furthermore, Ep-AH enriched the members of beneficial bacteria (e.g., Blautia and Bifidobacterium) and reversed abnormal changes of genes associated with several metabolic pathways (e.g., lipopolysaccharide biosynthesis).

SIGNIFICANCE: These results demonstrated that Ep-AH had excellent therapeutic benefits on cancer remission and gut microbiota modulation. Our study provides an effective strategy for anti-CRC treatment.}, } @article {pmid37100126, year = {2023}, author = {Du, X and Li, X and Cheng, K and Zhao, W and Cai, Z and Chen, G and Zhou, J}, title = {Virome reveals effect of Ulva prolifera green tide on the structural and functional profiles of virus communities in coastal environments.}, journal = {The Science of the total environment}, volume = {883}, number = {}, pages = {163609}, doi = {10.1016/j.scitotenv.2023.163609}, pmid = {37100126}, issn = {1879-1026}, mesh = {Ecosystem ; Virome ; *Ulva ; Bacteria ; Eutrophication ; *Viruses ; China ; }, abstract = {Viruses are widely distributed in marine environments, where they influence the transformation of matter and energy by modulating host metabolism. Driven by eutrophication, green tides are a rising concern in Chinese coastal areas, and are a serious ecological disaster that negatively affects coastal ecosystems and disrupts biogeochemical cycles. Although the composition of bacterial communities in green algae has been investigated, the diversity and roles of viruses in green algal blooms are largely unexplored. Therefore, the diversity, abundance, lifestyle, and metabolic potential of viruses in a natural bloom in Qingdao coastal area were investigated at three different stages (pre-bloom, during-bloom, and post-bloom) by metagenomics analysis. The dsDNA viruses, Siphoviridae, Myoviridae, Podoviridae, and Phycodnaviridae, were found to dominate the viral community. The viral dynamics exhibited distinct temporal patterns across different stages. The composition of the viral community varied during the bloom, especially in populations with low abundance. The lytic cycle was most predominant, and the abundance of lytic viruses increased slightly in the post-bloom stage. The diversity and richness of the viral communities varied distinctly during the green tide, and the post-bloom stage favored viral diversity and richness. The total organic carbon, dissolved oxygen, NO[3-], NO[2-], PO4[3-], chlorophyll-a contents, and temperature variably co-influenced the viral communities. The primary hosts included bacteria, algae, and other microplankton. Network analysis revealed the closer links between the viral communities as the bloom progressed. Functional prediction revealed that the viruses possibly influenced the biodegradation of microbial hydrocarbons and carbon by metabolic augmentation via auxiliary metabolic genes. The composition, structure, metabolic potential, and interaction taxonomy of the viromes differed significantly across the different stages of the green tide. The study demonstrated that the ecological event shaped the viral communities during algal bloom, and the viral communities played a significant role in phycospheric microecology.}, } @article {pmid37099155, year = {2023}, author = {Wang, B and Qi, M and Ma, Y and Zhang, B and Hu, Y}, title = {Microbiome Diversity and Cellulose Decomposition Processes by Microorganisms on the Ancient Wooden Seawall of Qiantang River of Hangzhou, China.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2109-2119}, pmid = {37099155}, issn = {1432-184X}, mesh = {Humans ; *Cellulose/metabolism ; Rivers ; *Microbiota/genetics ; Fungi/genetics ; Bacteria/genetics ; Wood/microbiology ; }, abstract = {Archaeological wood, also known as wooden cultural relics, refers to ancient wood that has been worked by humans. Further insights into the decomposition mechanism of archaeological wood are needed for its preventive conservation. In this study, we assessed the microbiome diversity and cellulose decomposition processes on a 200-year-old ancient wooden seawall - the Qiantang River of Hangzhou, China. We used high-throughput sequencing (HTS) to deduce the metagenomic functions, particularly the cellulose-decomposing pathway of the microbial communities, through bioinformatical approaches. The predominant cellulose-decomposing microorganisms were then verified with traditional isolation, culture, and identification method. The results showed that the excavation of archaeological wood significantly altered the environment, accelerating the deterioration process of the archaeological wood through the carbohydrate metabolism and the xenobiotic biodegradation and metabolism pathways, under the comprehensive metabolism of complex ecosystem formed by bacteria, archaea, fungi, microfauna, plants, and algae. Bacteroidetes, Proteobacteria, Firmicutes, and Actinobacteria were found to be the predominant source of bacterial cellulose-decomposing enzymes. Accordingly, we suggest relocating the wooden seawall to an indoor environment with controllable conditions to better preserve it. In addition, these results provide further evidence for our viewpoints that HTS techniques, combined with rational bioinformatical data interpretation approaches, can serve as powerful tools for the preventive protection of cultural heritage.}, } @article {pmid37099000, year = {2023}, author = {Guo, W and Cui, S and Tang, X and Yan, Y and Xiong, F and Zhang, Q and Zhao, J and Mao, B and Zhang, H}, title = {Intestinal microbiomics and hepatic metabolomics insights into the potential mechanisms of probiotic Bifidobacterium pseudolongum CCFM1253 preventing acute liver injury in mice.}, journal = {Journal of the science of food and agriculture}, volume = {103}, number = {12}, pages = {5958-5969}, doi = {10.1002/jsfa.12665}, pmid = {37099000}, issn = {1097-0010}, support = {//Collaborative Innovation Center of Food Safety and Quality Control in Jiangsu Province/ ; //Yongjiang Talent Introduction Programme/ ; }, mesh = {Humans ; Animals ; Mice ; Catalase/metabolism ; Lipopolysaccharides ; Bifidobacterium/metabolism ; *Probiotics ; Antioxidants/metabolism ; Liver/metabolism ; Metabolomics ; Superoxide Dismutase/metabolism ; Inflammation/metabolism ; *Chemical and Drug Induced Liver Injury/metabolism ; Mammals/metabolism ; }, abstract = {BACKGROUND: Bifidobacterium pseudolongum is widely exists in mammal gut and its abundance is associated with human and animal health. The present study aimed to investigate the potential mechanisms of B. pseudolongum CCFM1253 on protecting against lipopolysaccharide (LPS)-induced acute liver injury (ALI) by metagenomic analysis and liver metabolomic profiles.

RESULTS: Bifidobacterium pseudolongum CCFM1253 preintervention remarkably attenuated the influence of LPS on serum alanine transaminase and aspartate amino transferase activities. B. pseudolongum CCFM1253 preintervention remarkably attenuated the inflammation responses (tumor necrosis factor-α, interleukin-1β, and interleukin-6) and elevated antioxidative enzymes activities [total antioxidant capacity, superoxide dismutase, catalase, and glutathione peroxidase] in ALI mice by intervening in the Nf-kβ and Nrf2 pathways, respectively. Bifidobacterium pseudolongum CCFM1253 treatment elevated the proportion of Alistipes and Bifidobacterium, and decreased the proportion of uncultured Bacteroidales bacterium, Muribaculum, Parasutterella and Ruminococcaceae UCG-010 in ALI mice, which were strongly correlated with the inhibition of inflammation responses and oxidative stress. Untargeted liver metabolomics exhibited that the hepatoprotective efficacy of B. pseudolongum CCFM1253 might be achieved by altering liver metabolites-related riboflavin metabolism, phenylalanine metabolism, alanine, citrate cycle (tricarboxylic acid cycle), and so on. Furthermore, riboflavin exposure could control the contents of malondialdehyde, superoxide dismutase, and catalase in hydrogen peroxide-treated HepG2 cells.

CONCLUSION: Bifidobacterium pseudolongum CCFM1253 can effectively alleviate inflammatory response and oxidative stress, and regulate the intestinal microbiota composition and liver metabolism, and elevate the liver riboflavin content in LPS-treated mice. Therefore, B. pseudolongum CCFM1253 could serves as a potential probiotic to ameliorate the host health. © 2023 Society of Chemical Industry.}, } @article {pmid37098974, year = {2023}, author = {Chen, X and Molenda, O and Brown, CT and Toth, CRA and Guo, S and Luo, F and Howe, J and Nesbø, CL and He, C and Montabana, EA and Cate, JHD and Banfield, JF and Edwards, EA}, title = {"Candidatus Nealsonbacteria" Are Likely Biomass Recycling Ectosymbionts of Methanogenic Archaea in a Stable Benzene-Degrading Enrichment Culture.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {5}, pages = {e0002523}, pmid = {37098974}, issn = {1098-5336}, support = {P01 GM051487/GM/NIGMS NIH HHS/United States ; R01 GM065050/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaea/metabolism ; Benzene/metabolism ; Phylogeny ; Biomass ; RNA, Ribosomal, 16S/genetics/metabolism ; In Situ Hybridization, Fluorescence ; Bacteria/genetics ; *Euryarchaeota/metabolism ; }, abstract = {The Candidate Phyla Radiation (CPR), also referred to as superphylum Patescibacteria, is a very large group of bacteria with no pure culture representatives discovered by 16S rRNA sequencing or genome-resolved metagenomic analyses of environmental samples. Within the CPR, candidate phylum Parcubacteria, previously referred to as OD1, is prevalent in anoxic sediments and groundwater. Previously, we had identified a specific member of the Parcubacteria (referred to as DGGOD1a) as an important member of a methanogenic benzene-degrading consortium. Phylogenetic analyses herein place DGGOD1a within the clade "Candidatus Nealsonbacteria." Because of its persistence over many years, we hypothesized that "Ca. Nealsonbacteria" DGGOD1a must play an important role in sustaining anaerobic benzene metabolism in the consortium. To try to identify its growth substrate, we amended the culture with a variety of defined compounds (pyruvate, acetate, hydrogen, DNA, and phospholipid), as well as crude culture lysate and three subfractions thereof. We observed the greatest (10-fold) increase in the absolute abundance of "Ca. Nealsonbacteria" DGGOD1a only when the consortium was amended with crude cell lysate. These results implicate "Ca. Nealsonbacteria" in biomass recycling. Fluorescence in situ hybridization and cryogenic transmission electron microscope images revealed that "Ca. Nealsonbacteria" DGGOD1a cells were attached to larger archaeal Methanothrix cells. This apparent epibiont lifestyle was supported by metabolic predictions from a manually curated complete genome. This is one of the first examples of bacterial-archaeal episymbiosis and may be a feature of other "Ca. Nealsonbacteria" found in anoxic environments. IMPORTANCE An anaerobic microbial enrichment culture was used to study members of candidate phyla that are difficult to grow in the lab. We were able to visualize tiny "Candidatus Nealsonbacteria" cells attached to a large Methanothrix cell, revealing a novel episymbiosis.}, } @article {pmid37098916, year = {2023}, author = {Toth, CRA and Molenda, O and Nesbø, C and Luo, F and Devine, C and Guo, S and Chen, X and Edwards, EA}, title = {Metagenomic and Genomic Sequences from a Methanogenic Benzene-Degrading Consortium.}, journal = {Microbiology resource announcements}, volume = {12}, number = {5}, pages = {e0134222}, pmid = {37098916}, issn = {2576-098X}, support = {OGI-102//Ontario Genomics (OG)/ ; }, abstract = {Draft and complete metagenome assembled genomes (MAGs) were created from multiple metagenomic assemblies of DGG-B, a strictly anaerobic, stable mixed microbial consortium that degrades benzene completely to methane and CO2. Our objective was to obtain closed genome sequences of benzene-fermenting bacteria to enable the elucidation of their elusive anaerobic benzene degradation pathway.}, } @article {pmid37098485, year = {2023}, author = {Park, HM and Won, J and Park, Y and Anzaku, ET and Vankerschaver, J and Van Messem, A and De Neve, W and Shim, H}, title = {CRISPR-Cas-Docker: web-based in silico docking and machine learning-based classification of crRNAs with Cas proteins.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {167}, pmid = {37098485}, issn = {1471-2105}, mesh = {*CRISPR-Cas Systems ; *RNA/genetics ; Internet ; }, abstract = {BACKGROUND: CRISPR-Cas-Docker is a web server for in silico docking experiments with CRISPR RNAs (crRNAs) and Cas proteins. This web server aims at providing experimentalists with the optimal crRNA-Cas pair predicted computationally when prokaryotic genomes have multiple CRISPR arrays and Cas systems, as frequently observed in metagenomic data.

RESULTS: CRISPR-Cas-Docker provides two methods to predict the optimal Cas protein given a particular crRNA sequence: a structure-based method (in silico docking) and a sequence-based method (machine learning classification). For the structure-based method, users can either provide experimentally determined 3D structures of these macromolecules or use an integrated pipeline to generate 3D-predicted structures for in silico docking experiments.

CONCLUSION: CRISPR-Cas-Docker addresses the need of the CRISPR-Cas community to predict RNA-protein interactions in silico by optimizing multiple stages of computation and evaluation, specifically for CRISPR-Cas systems. CRISPR-Cas-Docker is available at www.crisprcasdocker.org as a web server, and at https://github.com/hshimlab/CRISPR-Cas-Docker as an open-source tool.}, } @article {pmid37098438, year = {2023}, author = {López-García, E and Benítez-Cabello, A and Vilches, N and Garrido-Fernández, A and Martín-Arranz, V and Arroyo-López, FN}, title = {Delving into the study of lactic acid bacteria and yeasts distribution in table olive biofilms using a non-destructive procedure.}, journal = {Food microbiology}, volume = {113}, number = {}, pages = {104250}, doi = {10.1016/j.fm.2023.104250}, pmid = {37098438}, issn = {1095-9998}, mesh = {*Lactobacillales/genetics ; *Olea/microbiology ; Yeasts/genetics ; Lactobacillaceae/genetics ; Biofilms ; Saccharomyces cerevisiae ; Fermentation ; Food Microbiology ; }, abstract = {To turn table olives into appropriate carriers of beneficial bacteria and yeasts to consumers, it is essential to have reliable methods for analysing microorganisms in biofilms. This work validates the application of a non-destructive procedure to study the lactic acid bacteria and yeasts distribution in fruits during Spanish-style green table olive fermentations. Laboratory-scale fermentations were inoculated simultaneously with three Lactiplantibacillus pentosus strains (LPG1, 119, and 13B4) and two yeasts (Wickerhamomyces anomalus Y12 and Saccharomyces cerevisiae Y30), all of them natives of table olive fermentations. Data showed that L. pentosus LPG1 and yeasts W. anomalus Y12 were quite prone to colonise olive biofilms, but only the Lactiplantibacillus strain also can penetrate the epidermis of the fruit and colonise the flesh. Applying a non-destructive treatment consisting in shelling the fruits with glass beads led to obtaining similar lactic acid bacteria and yeast recovery than the classical stomacher destructive method. However, the glass bead procedure improved the quality of the metagenomics analysis (especially when using 16 S rRNA gene-based sequencing). Results show the great utility of procedures that do not destroy the fruit for studying fermented vegetable biofilms.}, } @article {pmid37098427, year = {2023}, author = {Ruiz-Barba, JL and Sánchez, AH and López-López, A and Cortés-Delgado, A and Montaño, A}, title = {Microbial community and volatilome changes in brines along the spontaneous fermentation of Spanish-style and natural-style green table olives (Manzanilla cultivar).}, journal = {Food microbiology}, volume = {113}, number = {}, pages = {104286}, doi = {10.1016/j.fm.2023.104286}, pmid = {37098427}, issn = {1095-9998}, mesh = {Fermentation ; *Olea/microbiology ; Food Microbiology ; Yeasts ; *Microbiota ; }, abstract = {Microbial community and volatilome of brines were monitored during the spontaneous fermentations of Spanish-style and Natural-style green table olives from Manzanilla cultivar. Fermentation of olives in the Spanish style was carried out by lactic acid bacteria (LAB) and yeasts, whereas halophilic Gram-negative bacteria and archaea, along with yeasts, drove the fermentation in the Natural style. Clear differences between the two olive fermentations regarding physicochemical and biochemical features were found. Lactobacillus, Pichia, and Saccharomyces were the dominant microbial communities in the Spanish style, whereas Allidiomarina, Halomonas, Saccharomyces, Pichia, and Nakazawaea predominated in the Natural style. Numerous qualitative and quantitative differences in individual volatiles between both fermentations were found. The final products mainly differed in total amounts of volatile acids and carbonyl compounds. In addition, in each olive style, strong positive correlations were found between the dominant microbial communities and various volatile compounds, some of them previously reported as aroma-active compounds in table olives. The findings from this study provide a better understanding of each fermentation process and may help the development of controlled fermentations using starter cultures of bacteria and/or yeasts for the production of high-quality green table olives from Manzanilla cultivar.}, } @article {pmid37098420, year = {2023}, author = {Brandl, MT and Mammel, MK and Simko, I and Richter, TKS and Gebru, ST and Leonard, SR}, title = {Weather factors, soil microbiome, and bacteria-fungi interactions as drivers of the epiphytic phyllosphere communities of romaine lettuce.}, journal = {Food microbiology}, volume = {113}, number = {}, pages = {104260}, doi = {10.1016/j.fm.2023.104260}, pmid = {37098420}, issn = {1095-9998}, mesh = {Lactuca/microbiology ; Soil ; Weather ; Bacteria/genetics ; *Microbiota ; *Shiga-Toxigenic Escherichia coli ; Fungi/genetics ; Plant Leaves/microbiology ; }, abstract = {Lettuce is associated with seasonal outbreaks of Shiga toxin-producing Escherichia coli (STEC) infections. Little is known about how various biotic and abiotic factors affect the lettuce microbiome, which in turn impacts STEC colonization. We characterized the lettuce phyllosphere and surface soil bacterial, fungal, and oomycete communities at harvest in late-spring and -fall in California using metagenomics. Harvest season and field type, but not cultivar, significantly influenced the microbiome composition of leaves and surface soil near plants. Phyllosphere and soil microbiome compositions were correlated with specific weather factors. The relative abundance of Enterobacteriaceae, but not E. coli, was enriched on leaves (5.2%) compared to soil (0.4%) and correlated positively with minimum air temperature and wind speed. Co-occurrence networks revealed seasonal trends in fungi-bacteria interactions on leaves. These associations represented 39%-44% of the correlations between species. All significant E. coli co-occurrences with fungi were positive, while all negative associations were with bacteria. A large proportion of the leaf bacterial species was shared with those in soil, indicating microbiome transmission from the soil surface to the canopy. Our findings provide new insight into factors that shape lettuce microbial communities and the microbial context of foodborne pathogen immigration events in the lettuce phyllosphere.}, } @article {pmid37098397, year = {2023}, author = {Xing, BS and Chang, XL and Cao, S and Wu, D and Zhang, Y and Tang, XF and Li, YY and Wang, XC and Chen, R}, title = {Long-term in-situ starvation and reactivation of co-digestion with food waste and corn straw in a continuous AnDMBR: Performance, sludge characteristics, and microorganism community.}, journal = {The Science of the total environment}, volume = {882}, number = {}, pages = {163673}, doi = {10.1016/j.scitotenv.2023.163673}, pmid = {37098397}, issn = {1879-1026}, mesh = {*Sewage/microbiology ; Anaerobiosis ; Zea mays ; *Refuse Disposal ; Food ; Bioreactors/microbiology ; Methane ; Digestion ; }, abstract = {To explore the effects of in-situ starvation and reactivation in a continuous anaerobic dynamic membrane reactor (AnDMBR), the anaerobic co-digestion system of food waste and corn straw was firstly start-up and stability operated, and then stopped feeding substrate approximately 70 days. After long-term in-situ starvation, the continuous AnDMBR was reactivated using the same operation conditions and organic loading rate as the continuous AnDMBR used before in-situ starvation. Results shown that the anaerobic co-digestion of corn straw and food waste in the continuous AnDMBR can resume stable operation within 5 days, and the corresponding methane production of 1.38 ± 0.26 L/L/d was completely returned to the methane production before in-situ starvation (1.32 ± 0.10 L/L/d). Through analysis of the specific methanogenic activity and key enzyme activity of the digestate sludge, only the acetic acid degradation activity of methanogenic archaea can be partially recovered, however, the activities of lignocellulose enzyme (lignin peroxidase, laccase, and endoglucanase), hydrolase (α-glucosidase) and acidogenic enzyme (acetate kinas, butyrate kinase, and CoA-transferase) can be fully recovered. Analysis of microorganism community structure using metagenomic sequencing technology showed that starvation decreased the abundance of hydrolytic bacteria (Bacteroidetes and Firmicutes) and increased the abundance of small molecule-utilizing bacteria (Proteobacteria and Chloroflexi) due to lack of substrate during the long-term in-situ starvation stage. Furthermore, the microbial community structure and key functional microorganism still maintained and similar with that of starvation final stage even after long-term continuous reactivation. The reactor performance and sludge enzymes activity in the continuous AnDMBR co-digestion of food waste and corn straw can be well reactivated after long-term in-situ starvation, even though the microbial community structure can not be recovered to the initiating stage.}, } @article {pmid37098287, year = {2023}, author = {Nõlvak, H and Truu, M and Tiirik, K and Devarajan, AK and Peeb, A and Truu, J}, title = {The effect of synthetic silver nanoparticles on the antibiotic resistome and the removal efficiency of antibiotic resistance genes in a hybrid filter system treating municipal wastewater.}, journal = {Water research}, volume = {237}, number = {}, pages = {119986}, doi = {10.1016/j.watres.2023.119986}, pmid = {37098287}, issn = {1879-2448}, mesh = {*Wastewater ; Anti-Bacterial Agents/pharmacology/analysis ; Silver/analysis ; *Metal Nanoparticles ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Integrases/genetics ; Waste Disposal, Fluid/methods ; }, abstract = {Engineered nanoparticles, including silver nanoparticles (AgNPs), are released into the environment mainly through wastewater treatment systems. Knowledge of the impact of AgNPs on the abundance and removal efficiency of antibiotic resistance genes (ARGs) in wastewater treatment facilities, including constructed wetlands (CWs), is essential in the context of public health. This study evaluated the effect of increased (100-fold) collargol (protein-coated AgNPs) and ionic Ag[+] in municipal wastewater on the structure, abundance, and removal efficiency of the antibiotic resistome, integron-integrase genes, and pathogens in a hybrid CW using quantitative PCR and metagenomic approaches. The abundance of ARGs in wastewater and the removal efficiency of ARGs in the hybrid system were significantly affected by higher Ag concentrations, especially with collargol treatment, resulting in an elevated ARG discharge of system effluent into the environment. The accumulated Ag in the filters had a more profound effect on the absolute and relative abundance of ARGs in the treated water than the Ag content in the water. This study recorded significantly enhanced relative abundance values for tetracycline (tetA, tetC, tetQ), sulfonamide (sul1, sul2), and aminoglycoside (aadA) resistance genes, which are frequently found on mobile genetic elements in collargol- and, to a lesser extent, AgNO3-treated subsystems. Elevated plasmid and integron-integrase gene levels, especially intI1, in response to collargol presence indicated the substantial role of AgNPs in promoting horizontal gene transfer in the treatment system. The pathogenic segment of the prokaryotic community was similar to a typical sewage community, and strong correlations between pathogen and ARG proportions were recorded in vertical subsurface flow filters. Furthermore, the proportion of Salmonella enterica was positively related to the Ag content in these filter effluents. The effect of AgNPs on the nature and characteristics of prominent resistance genes carried by mobile genetic elements in CWs requires further investigation.}, } @article {pmid37097839, year = {2023}, author = {Prakash, O and Dodsworth, JA and Dong, X and Ferry, JG and L'Haridon, S and Imachi, H and Kamagata, Y and Rhee, SK and Sagar, I and Shcherbakova, V and Wagner, D and Whitman, WB}, title = {Proposed minimal standards for description of methanogenic archaea.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {73}, number = {4}, pages = {}, doi = {10.1099/ijsem.0.005500}, pmid = {37097839}, issn = {1466-5034}, mesh = {*Archaea/genetics ; Phylogeny ; Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; Base Composition ; Bacterial Typing Techniques/methods ; DNA, Bacterial/genetics ; Fatty Acids/chemistry ; *Euryarchaeota/genetics ; Methane/metabolism ; }, abstract = {Methanogenic archaea are a diverse, polyphyletic group of strictly anaerobic prokaryotes capable of producing methane as their primary metabolic product. It has been over three decades since minimal standards for their taxonomic description have been proposed. In light of advancements in technology and amendments in systematic microbiology, revision of the older criteria for taxonomic description is essential. Most of the previously recommended minimum standards regarding phenotypic characterization of pure cultures are maintained. Electron microscopy and chemotaxonomic methods like whole-cell protein and lipid analysis are desirable but not required. Because of advancements in DNA sequencing technologies, obtaining a complete or draft whole genome sequence for type strains and its deposition in a public database are now mandatory. Genomic data should be used for rigorous comparison to close relatives using overall genome related indices such as average nucleotide identity and digital DNA-DNA hybridization. Phylogenetic analysis of the 16S rRNA gene is also required and can be supplemented by phylogenies of the mcrA gene and phylogenomic analysis using multiple conserved, single-copy marker genes. Additionally, it is now established that culture purity is not essential for studying prokaryotes, and description of Candidatus methanogenic taxa using single-cell or metagenomics along with other appropriate criteria is a viable alternative. The revisions to the minimal criteria proposed here by the members of the Subcommittee on the Taxonomy of Methanogenic Archaea of the International Committee on Systematics of Prokaryotes should allow for rigorous yet practical taxonomic description of these important and diverse microbes.}, } @article {pmid37097198, year = {2023}, author = {Yan, N and Yue, H and Liu, Q and Wang, G and Tang, C and Liao, M}, title = {Isolation and Characteristics of a Novel Aichivirus D from Yak.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0009923}, pmid = {37097198}, issn = {2165-0497}, mesh = {Chlorocebus aethiops ; Cattle ; Animals ; Sheep ; Phylogeny ; *Kobuvirus/genetics ; Vero Cells ; Diarrhea/epidemiology/veterinary ; Inflammation ; }, abstract = {Aichivirus D (AiV-D) is a newly emerging Kobuvirus detected in bovine and sheep, and information is limited regarding its biological significance and prevalence. This study aimed to explore both the prevalence and characteristics of AiV-D in yaks. From May to August 2021, 117 fecal samples were collected from yaks with diarrhea in three provinces of China's Qinghai-Tibet Plateau, 15 of which were selected and pooled for metagenomic analysis. A high abundance of AiV-D sequences was obtained. Of the 117 diarrhea samples, 29 (24.8%) tested AiV-D-positive, including 33.3% (14/42) from Sichuan, 21.1% (8/38) from Qinghai, and 18.9% (7/37) from Tibet, respectively, suggesting a wide geographical distribution of the AiV-D in yaks in the Qinghai-Tibet Plateau. Furthermore, three AiV-D strains were successfully isolated using Vero cells. Significantly, the AiV-D strain could cause diarrhea, intestinal bleeding, and inflammation in yak calves via oral inoculation. The virus was distributed in the ileum, jejunum, duodenum, colon, cecum, and rectum. Based on phylogenetic analysis of the genome and capsid protein P1 (VP0, VP3, and VP1 genes), the yak AiV-D strains likely represent a novel genotype of AiV-D. On the whole, this study identified a novel genotype of AiV-D from yaks, which was successfully isolated, and confirmed that this virus is a diarrhea pathogen in yaks and has a wide geographical distribution in the Qinghai-Tibet Plateau. Our results expand the host range of AiV-D and the pathogen spectrum of yaks and have significant implications for diagnosing and controlling diarrhea in yaks. IMPORTANCE In this study, we identified and successfully isolated a novel genotype of AiV-D from yaks. Animal infection confirmed that this virus can cause diarrhea, intestinal bleeding, and inflammation in yak calves via oral inoculation. The virus was distributed in the ileum, jejunum, cecum, duodenum, colon, and rectum. All of these results have significant implications for diagnosing and controlling diarrhea in yaks. These novel AiV-D strains have a wide geographical distribution in yaks from the Qinghai-Tibet Plateau in China. In addition to expanding the host range of AiV-D and the pathogen spectrum of yaks, these findings can increase knowledge of the prevalence and diversity of AiV-D.}, } @article {pmid37097179, year = {2023}, author = {Jin, Y and Lu, Y}, title = {Syntrophic Propionate Oxidation: One of the Rate-Limiting Steps of Organic Matter Decomposition in Anoxic Environments.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {5}, pages = {e0038423}, pmid = {37097179}, issn = {1098-5336}, mesh = {*Propionates/metabolism ; Phylogeny ; Oxidation-Reduction ; *Bacteria ; DNA/metabolism ; Methane/metabolism ; Anaerobiosis ; }, abstract = {Syntrophic propionate oxidation is one of the rate-limiting steps during anaerobic decomposition of organic matter in anoxic environments. Syntrophic propionate-oxidizing bacteria (SPOB) are members of the "rare biosphere" living at the edge of the thermodynamic limit in most natural habitats. Hitherto, only 10 bacterial species capable of syntrophic propionate oxidization have been identified. SPOB employ different metabolisms for propionate oxidation (e.g., methylmalonyl-CoA pathway and C6 dismutation pathway) and show diverse life strategies (e.g., obligately and facultatively syntrophic lifestyle). The flavin-based electron bifurcation/confurcation (FBEB/C) systems have been proposed to help solve the thermodynamic dilemma during the formation of the low-potential products H2 and formate. Molecular ecological approaches, such as DNA stable isotope probing (DNA-SIP) and metagenomics, have been used to detect SPOB in natural environments. Furthermore, the biogeographical pattern of SPOB has been recently described in paddy soils. A comprehensive understanding of SPOB is essential for better predicting and managing organic matter decomposition and carbon cycling in anoxic environments. In this review, we described the critical role of syntrophic propionate oxidation in anaerobic decomposition of organic matter, phylogenetic and metabolic diversity, life strategies and ecophysiology, composition of syntrophic partners, and pattern of biogeographic distribution of SPOB in natural environments. We ended up with a few perspectives for future research.}, } @article {pmid37097162, year = {2023}, author = {Masasa, M and Kushmaro, A and Nguyen, D and Chernova, H and Shashar, N and Guttman, L}, title = {Spatial Succession Underlies Microbial Contribution to Food Digestion in the Gut of an Algivorous Sea Urchin.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0051423}, pmid = {37097162}, issn = {2165-0497}, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics ; *Sea Urchins/genetics ; Seafood ; Digestion ; Sulfates ; }, abstract = {Dietary influence on the microbiome in algivorous sea urchins such as Tripneustes gratilla elatensis suggests a bacterial contribution to the digestion of fiber-rich seaweed. An ecological insight into the spatial arrangement in the gut bacterial community will improve our knowledge of host-microbe relations concerning the involved taxa, their metabolic repertoire, and the niches of activity. Toward this goal, we investigated the bacterial communities in the esophagus, stomach, and intestine of Ulva-fed sea urchins through 16S rRNA amplicon sequencing, followed by the prediction of their functional genes. We revealed communities with distinct features, especially those in the esophagus and intestine. The esophageal community was less diverse and was poor in food digestive or fermentation genes. In contrast, bacteria that can contribute to the digestion of the dietary Ulva were common in the stomach and intestine and consisted of genes for carbohydrate decomposition, fermentation, synthesis of short-chain fatty acids, and various ways of N and S metabolism. Bacteroidetes and Firmicutes were found as the main phyla in the gut and are presumably also necessary in food digestion. The abundant sulfate-reducing bacteria in the stomach and intestine from the genera Desulfotalea, Desulfitispora, and Defluviitalea may aid in removing the excess sulfate from the decomposition of the algal polysaccharides. Although these sea urchins were fed with Ulva, genes for the degradation of polysaccharides of other algae and plants were present in this sea urchin gut microbiome. We conclude that the succession of microbial communities along the gut obtained supports the hypothesis on bacterial contribution to food digestion. IMPORTANCE Alga grazing by the sea urchin Tripneustes gratilla elatensis is vital for nutrient recycling and constructing new reefs. This research was driven by the need to expand the knowledge of bacteria that may aid this host in alga digestion and their phylogeny, roles, and activity niches. We hypothesized alterations in the bacterial compositional structure along the gut and their association with the potential contribution to food digestion. The current spatial insight into the sea urchin's gut microbiome ecology is novel and reveals how distinct bacterial communities are when distant from each other in this organ. It points to keynote bacteria with genes that may aid the host in the digestion of the complex sulfated polysaccharides in dietary Ulva by removing the released sulfates and fermentation to provide energy. The gut bacteria's genomic arsenal may also help to gain energy from diets of other algae and plants.}, } @article {pmid37097160, year = {2023}, author = {Esquerra-Ruvira, B and Baquedano, I and Ruiz, R and Fernandez, A and Montoliu, L and Mojica, FJM}, title = {Identification of the EH CRISPR-Cas9 system on a metagenome and its application to genome engineering.}, journal = {Microbial biotechnology}, volume = {16}, number = {7}, pages = {1505-1523}, pmid = {37097160}, issn = {1751-7915}, mesh = {*CRISPR-Cas Systems ; *Metagenome ; CRISPR-Associated Protein 9 ; Gene Editing ; DNA/genetics ; }, abstract = {Non-coding RNAs (crRNAs) produced from clustered regularly interspaced short palindromic repeats (CRISPR) loci and CRISPR-associated (Cas) proteins of the prokaryotic CRISPR-Cas systems form complexes that interfere with the spread of transmissible genetic elements through Cas-catalysed cleavage of foreign genetic material matching the guide crRNA sequences. The easily programmable targeting of nucleic acids enabled by these ribonucleoproteins has facilitated the implementation of CRISPR-based molecular biology tools for in vivo and in vitro modification of DNA and RNA targets. Despite the diversity of DNA-targeting Cas nucleases so far identified, native and engineered derivatives of the Streptococcus pyogenes SpCas9 are the most widely used for genome engineering, at least in part due to their catalytic robustness and the requirement of an exceptionally short motif (5'-NGG-3' PAM) flanking the target sequence. However, the large size of the SpCas9 variants impairs the delivery of the tool to eukaryotic cells and smaller alternatives are desirable. Here, we identify in a metagenome a new CRISPR-Cas9 system associated with a smaller Cas9 protein (EHCas9) that targets DNA sequences flanked by 5'-NGG-3' PAMs. We develop a simplified EHCas9 tool that specifically cleaves DNA targets and is functional for genome editing applications in prokaryotes and eukaryotic cells.}, } @article {pmid37097110, year = {2023}, author = {Zhang, Y and Su, JQ and Liao, H and Breed, MF and Yao, H and Shangguan, H and Li, HZ and Sun, X and Zhu, YG}, title = {Increasing Antimicrobial Resistance and Potential Human Bacterial Pathogens in an Invasive Land Snail Driven by Urbanization.}, journal = {Environmental science & technology}, volume = {57}, number = {18}, pages = {7273-7284}, doi = {10.1021/acs.est.3c01233}, pmid = {37097110}, issn = {1520-5851}, mesh = {Humans ; *Urbanization ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Genes, Bacterial ; Soil ; }, abstract = {Our understanding of the role urbanization has in augmenting invasive species that carry human bacterial pathogens and antimicrobial resistance (AMR) remains poorly understood. Here, we investigated the gut bacterial communities, antibiotic resistance genes (ARGs) and potential antibiotic-resistant pathogens in giant African snails (Achatina fulica) collected across an urbanization gradient in Xiamen, China (n = 108). There was a lack of correlation between the microbial profiles of giant African snails and the soils of their habitats, and the resistome and human-associated bacteria were significantly higher than those of native snails as well as soils. We observed high diversity (601 ARG subtypes) and abundance (1.5 copies per 16S rRNA gene) of giant African snail gut resistome. Moreover, giant African snails in more urban areas had greater diversity and abundance of high-risk ARGs and potential human bacterial pathogens (e.g., ESKAPE pathogens). We highlight that urbanization significantly impacted the gut microbiomes and resistomes of these invasive snails, indicating that they harbor greater biological contaminants such as ARGs and potential human bacterial pathogens than native snails and soils. This study advances our understanding of the effect of urbanization on human bacterial pathogens and AMR in a problematic invasive snail and should help combat risks associated with invasive species under the One Health framework.}, } @article {pmid37097050, year = {2023}, author = {Gupton, M and Burns, J}, title = {Metagenomic next-generation sequencing in osteoarticular infections with a focus on pediatrics: current concepts and clinical applications.}, journal = {EFORT open reviews}, volume = {8}, number = {4}, pages = {199-212}, pmid = {37097050}, issn = {2058-5241}, abstract = {Osteoarticular infections (OAI) are a significant cause of morbidity and mortality. Cultures and serology are some of the gold standards for identifying infection but are often unable to provide a timely diagnosis or a diagnosis at all. Genetic testing offers capabilities that other modalities lack. Polymerase chain reaction has multiple versions with various costs and turnaround times. This technology has become implemented in multiple pediatric center OAI diagnostic protocols. There is sufficient literature documenting effectiveness in certain clinical situations, especially with fastidious organism diagnosis, but significant limitation still exists. Metagenomic next-generation sequencing is an unbiased or hypothesis-free modality with the capability to detect the genetic material of bacteria, viruses, parasites, fungi, and humans from a single sample. Potential benefits include pathogen identification unaffected by antimicrobial administration, detection of fastidious organisms more quickly, delineation of pathogens in polymicrobial infections, antimicrobial susceptibility, and avoidance of invasive procedures. It is a resource-intensive modality with little standardization of the complex processes. Appropriate use and definitive clinical impact have yet to be determined.}, } @article {pmid37096395, year = {2023}, author = {Bajagai, YS and Yeoh, YK and Li, X and Zhang, D and Dennis, PG and Ouwerkerk, D and Dart, PJ and Klieve, AV and Bryden, WL}, title = {Enhanced meat chicken productivity in response to the probiotic Bacillus amyloliquefaciens H57 is associated with the enrichment of microbial amino acid and vitamin biosynthesis pathways.}, journal = {Journal of applied microbiology}, volume = {134}, number = {5}, pages = {}, doi = {10.1093/jambio/lxad085}, pmid = {37096395}, issn = {1365-2672}, support = {LP120200837//Australian Research Council/ ; }, mesh = {Animals ; *Bacillus amyloliquefaciens/genetics ; Chickens ; Amino Acids ; *Probiotics/pharmacology ; Dietary Supplements ; Diet/veterinary ; Anti-Bacterial Agents/pharmacology ; Vitamins ; Meat/analysis ; Animal Feed/analysis ; }, abstract = {AIMS: Sub-therapeutic use of antibiotics as a growth promoter in animal diets has either been banned or voluntarily withdrawn from use in many countries to help curb the emergence of antibiotic-resistant pathogens. Probiotics may be an alternative to antibiotics as a growth promoter. We investigated the effects of a novel probiotic strain, Bacillus amyloliquefaciens H57 (H57) on the performance and microbiome-associated metabolic potential.

METHODS AND RESULTS: Broiler chickens were fed either sorghum- or wheat-based diets supplemented with the probiotic H57. The growth rate, feed intake, and feed conversion in supplemented birds were compared with those in non-supplemented control. Caecal microbial metabolic functions were studied with shotgun metagenomic sequencing. H57 supplementation significantly increased the growth rate and daily feed intake of meat chickens relative to the non-supplemented controls without any effect on feed conversion ratio. In addition, relative to the non-supplemented controls, gene-centric metagenomics revealed that H57 significantly altered the functional capacity of the caecal microbiome, with amino acid and vitamin synthesis pathways being positively associated with H57 supplementation.

CONCLUSIONS: Bacillus amyloliquefaciens H57 improves the performance of meat chickens or broilers and significantly modifies the functional potential of their caecal microbiomes, with enhanced potential capacity for amino acid and vitamin biosynthesis.}, } @article {pmid37095530, year = {2023}, author = {Hao, Z and Meng, C and Li, L and Feng, S and Zhu, Y and Yang, J and Han, L and Sun, L and Lv, W and Figeys, D and Liu, H}, title = {Positive mood-related gut microbiota in a long-term closed environment: a multiomics study based on the "Lunar Palace 365" experiment.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {88}, pmid = {37095530}, issn = {2049-2618}, mesh = {Animals ; Humans ; *Gastrointestinal Microbiome ; Moon ; Multiomics ; Tryptophan ; Glutamates ; Mammals ; }, abstract = {BACKGROUND: Psychological health risk is one of the most severe and complex risks in manned deep-space exploration and long-term closed environments. Recently, with the in-depth research of the microbiota-gut-brain axis, gut microbiota has been considered a new approach to maintain and improve psychological health. However, the correlation between gut microbiota and psychological changes inside long-term closed environments is still poorly understood. Herein, we used the "Lunar Palace 365" mission, a 1-year-long isolation study in the Lunar Palace 1 (a closed manned Bioregenerative Life Support System facility with excellent performance), to investigate the correlation between gut microbiota and psychological changes, in order to find some new potential psychobiotics to maintain and improve the psychological health of crew members.

RESULTS: We report some altered gut microbiota that were associated with psychological changes in the long-term closed environment. Four potential psychobiotics (Bacteroides uniformis, Roseburia inulinivorans, Eubacterium rectale, and Faecalibacterium prausnitzii) were identified. On the basis of metagenomic, metaproteomic, and metabolomic analyses, the four potential psychobiotics improved mood mainly through three pathways related to nervous system functions: first, by fermenting dietary fibers, they may produce short-chain fatty acids, such as butyric and propionic acids; second, they may regulate amino acid metabolism pathways of aspartic acid, glutamic acid, tryptophan, etc. (e.g., converting glutamic acid to gamma-aminobutyric acid; converting tryptophan to serotonin, kynurenic acid, or tryptamine); and third, they may regulate other pathways, such as taurine and cortisol metabolism. Furthermore, the results of animal experiments confirmed the positive regulatory effect and mechanism of these potential psychobiotics on mood.

CONCLUSIONS: These observations reveal that gut microbiota contributed to a robust effect on the maintenance and improvement of mental health in a long-term closed environment. Our findings represent a key step towards a better understanding the role of the gut microbiome in mammalian mental health during space flight and provide a basis for future efforts to develop microbiota-based countermeasures that mitigate risks to crew mental health during future long-term human space expeditions on the moon or Mars. This study also provides an essential reference for future applications of psychobiotics to neuropsychiatric treatments. Video Abstract.}, } @article {pmid37095175, year = {2023}, author = {Baltar, F and Martínez-Pérez, C and Amano, C and Vial, M and Robaina-Estévez, S and Reinthaler, T and Herndl, GJ and Zhao, Z and Logares, R and Morales, SE and González, JM}, title = {A ubiquitous gammaproteobacterial clade dominates expression of sulfur oxidation genes across the mesopelagic ocean.}, journal = {Nature microbiology}, volume = {8}, number = {6}, pages = {1137-1148}, pmid = {37095175}, issn = {2058-5276}, mesh = {Oceans and Seas ; *Genomics ; *Ecosystem ; Metagenomics ; Sulfur/metabolism ; }, abstract = {The deep ocean (>200 m depth) is the largest habitat on Earth. Recent evidence suggests sulfur oxidation could be a major energy source for deep ocean microbes. However, the global relevance and the identity of the major players in sulfur oxidation in the oxygenated deep-water column remain elusive. Here we combined single-cell genomics, community metagenomics, metatranscriptomics and single-cell activity measurements on samples collected beneath the Ross Ice Shelf in Antarctica to characterize a ubiquitous mixotrophic bacterial group (UBA868) that dominates expression of RuBisCO genes and of key sulfur oxidation genes. Further analyses of the gene libraries from the 'Tara Oceans' and 'Malaspina' expeditions confirmed the ubiquitous distribution and global relevance of this enigmatic group in the expression of sulfur oxidation and dissolved inorganic carbon fixation genes across the global mesopelagic ocean. Our study also underscores the unrecognized importance of mixotrophic microbes in the biogeochemical cycles of the deep ocean.}, } @article {pmid37094914, year = {2023}, author = {Brunetto, MR and Salvati, A and Petralli, G and Bonino, F}, title = {Nutritional intervention in the management of non-alcoholic fatty liver disease.}, journal = {Best practice & research. Clinical gastroenterology}, volume = {62-63}, number = {}, pages = {101830}, doi = {10.1016/j.bpg.2023.101830}, pmid = {37094914}, issn = {1532-1916}, mesh = {Animals ; Humans ; *Non-alcoholic Fatty Liver Disease/pathology ; Diet ; Nutritional Status ; Life Style ; *Microbiota ; Liver/metabolism/pathology ; }, abstract = {Lifestyle modification is the primary intervention to control NAFLD progression, but despite evidence-based effectiveness it is difficult to distinguish the benefits of nutrition from physical activity and the optimal diet composition is not established. Macronutrients as saturated fatty acids, sugars and animal proteins are harmful in NAFLD and the Mediterranean Diet reducing sugar, red meat and refined carbohydrates and increasing unsaturated-fatty-acids was reported to be beneficial. However one size cannot fit all since NAFLD is a multifaceted syndrome encompassing many diseases of unknown etiologies, different clinical severity and outcomes. Studies of the intestinal metagenome, provided new insights into the physio-pathological interplay between intestinal microbiota and NAFLD. How much the microbiota heterogeneity can influence response to diet remains unknown. New knowledge indicates that AI guided personalized nutrition based on clinic-pathologic and genetic data combined with pre/post nutritional intervention gut metagenomics/metabolomics will be part of the future management of NAFLD.}, } @article {pmid37094681, year = {2023}, author = {Xue, Z and Tian, W and Han, Y and Feng, Z and Wang, Y and Zhang, W}, title = {The hidden diversity of microbes in ballast water and sediments revealed by metagenomic sequencing.}, journal = {The Science of the total environment}, volume = {882}, number = {}, pages = {163666}, doi = {10.1016/j.scitotenv.2023.163666}, pmid = {37094681}, issn = {1879-1026}, mesh = {*Water ; *Bacteria/genetics ; Enterococcus ; Metagenome ; Archaea/genetics ; Ships ; Geologic Sediments/microbiology ; }, abstract = {With the rapid globalization of trade, the worldwide spread of pathogens through ballast water is becoming a major concern. Although the international maritime organization (IMO) convention has been adopted to prevent the spread of harmful pathogens, the limited species resolution of the current microbe-monitoring methods challenged the ballast water and sediments management (BWSM). In this study, we explored metagenomic sequencing to investigate the species composition of microbial communities in four international vessels for BWSM. Our results showed the largest species diversity (14,403) in ballast water and sediments, including bacteria (11,710), eukaryotes (1007), archaea (829), and viruses (790). A total of 129 phyla were detected, among which the Proteobacteria, followed by Bacteroidetes, and Actinobacteria were the most abundant. Notably, 422 pathogens that are potentially harmful to marine environments and aquaculture were identified. The co-occurrence network analysis showed that most of these pathogens were positively correlated with the commonly used indicator bacteria Vibrio cholerae, Escherichia coli, and intestinal Enterococci species, validating the D-2 standard in BWSM. The functional profile showed prominent pathways of methane and sulfur metabolism, indicating that the microbial community in the severe tank environment still utilizes the energy to sustain such a high level of microbe diversity. In conclusion, metagenomic sequencing provides novel information for BWSM.}, } @article {pmid37094669, year = {2023}, author = {Hu, Z and Yang, L and Liu, Z and Han, J and Zhao, Y and Jin, Y and Sheng, Y and Zhu, L and Hu, B}, title = {Excessive disinfection aggravated the environmental prevalence of antimicrobial resistance during COVID-19 pandemic.}, journal = {The Science of the total environment}, volume = {882}, number = {}, pages = {163598}, pmid = {37094669}, issn = {1879-1026}, mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; Disinfection ; Pandemics ; Prevalence ; Drug Resistance, Bacterial/genetics ; *COVID-19 ; *Disinfectants/pharmacology ; Quaternary Ammonium Compounds ; Genes, Bacterial ; }, abstract = {During COVID-19 pandemic, chemicals from excessive consumption of pharmaceuticals and disinfectants i.e., antibiotics, quaternary ammonium compounds (QACs), and trihalomethanes (THMs), flowed into the urban environment, imposing unprecedented selective pressure to antimicrobial resistance (AMR). To decipher the obscure character pandemic-related chemicals portrayed in altering environmental AMR, 40 environmental samples covering water and soil matrix from surroundings of Wuhan designated hospitals were collected on March 2020 and June 2020. Chemical concentrations and antibiotic resistance gene (ARG) profiles were revealed by ultra-high-performance liquid chromatography-tandem mass spectrometry and metagenomics. Selective pressure from pandemic-related chemicals ascended by 1.4-5.8 times in March 2020 and then declined to normal level of pre-pandemic period in June 2020. Correspondingly, the relative abundance of ARGs under increasing selective pressure was 20.1 times that under normal selective pressure. Moreover, effect from QACs and THMs in aggravating the prevalence of AMR was elaborated by null model, variation partition and co-occurrence network analyses. Pandemic-related chemicals, of which QACs and THMs respectively displayed close interaction with efflux pump genes and mobile genetic elements, contributed >50 % in shaping ARG profile. QACs bolstered the cross resistance effectuated by qacEΔ1 and cmeB to 3.0 times higher while THMs boosted horizon ARG transfer by 7.9 times for initiating microbial response to oxidative stress. Under ascending selective pressure, qepA encoding quinolone efflux pump and oxa-20 encoding β-lactamases were identified as priority ARGs with potential human health risk. Collectively, this research validated the synergistic effect of QACs and THMs in exacerbating environmental AMR, appealing for the rational usage of disinfectants and the attention for environmental microbes in one-health perspective.}, } @article {pmid37094620, year = {2023}, author = {Cao, J and Duan, G and Lin, A and Zhou, Y and You, S and Wong, JWC and Yang, G}, title = {Metagenomic insights into the inhibitory mechanisms of Cu on fermentative hydrogen production.}, journal = {Bioresource technology}, volume = {380}, number = {}, pages = {129080}, doi = {10.1016/j.biortech.2023.129080}, pmid = {37094620}, issn = {1873-2976}, mesh = {Fermentation ; *Bioreactors/microbiology ; *Metagenomics ; Hydrogen ; Glucose ; }, abstract = {Cu is widely present in the feedstocks of dark fermentation, which can inhibit H2 production efficiency of the process. However, current understanding on the inhibitory mechanisms of Cu, especially the microbiological mechanism, is still lacking. This study investigated the inhibitory mechanisms of Cu[2+] on fermentative hydrogen production by metagenomics sequencing. Results showed that the exposure to Cu[2+] reduced the abundances of high-yielding hydrogen-producing genera (e.g. Clostridium sensu stricto), and remarkably down-regulated the genes involved in substrate membrane transport (e.g., gtsA, gtsB and gtsC), glycolysis (e.g. PK, ppgK and pgi-pmi), and hydrogen formation (e.g. pflA, fdoG, por and E1.12.7.2), leading to significant inhibition on the process performances. The H2 yield was reduced from 1.49 mol H2/mol-glucose to 0.59 and 0.05 mol H2/mol-glucose upon exposure to 500 and 1000 mg/L of Cu[2+], respectively. High concentrations of Cu[2+] also reduced the rate of H2 production and prolonged the H2-producing lag phase.}, } @article {pmid37093913, year = {2023}, author = {Keum, GB and Kim, ES and Cho, J and Song, M and Oh, KK and Cho, JH and Kim, S and Kim, H and Kwak, J and Doo, H and Pandey, S and Kim, HB and Lee, JH}, title = {Analysis of antibiotic resistance genes in pig feces during the weaning transition using whole metagenome shotgun sequencing.}, journal = {Journal of animal science and technology}, volume = {65}, number = {1}, pages = {175-182}, pmid = {37093913}, issn = {2055-0391}, abstract = {Antibiotics have been used in livestock production for not only treatment but also for increasing the effectiveness of animal feed, aiding animal growth, and preventing infectious diseases at the time when immunity is lowered due to stress. South Korea and the EU are among the countries that have prohibited the use of antibiotics for growth promotion in order to prevent indiscriminate use of antibiotics, as previous studies have shown that it may lead to increase in cases of antibiotic-resistant bacteria. Therefore, this study evaluated the number of antibiotic resistance genes in piglets staging from pre-weaning to weaning. Fecal samples were collected from 8 piglets just prior to weaning (21 d of age) and again one week after weaning (28 d of age). Total DNA was extracted from the 200 mg of feces collected from the 8 piglets. Whole metagenome shotgun sequencing was carried out using the Illumina Hi-Seq 2000 platform and raw sequence data were imported to Metagenomics Rapid Annotation using Subsystem Technology (MG-RAST) pipeline for microbial functional analysis. The results of this study did not show an increase in antibiotic-resistant bacteria although confirmed an increase in antibiotic-resistant genes as the consequence of changes in diet and environment during the experiment.}, } @article {pmid37093508, year = {2023}, author = {Wijdeveld, M and van Olst, N and van der Vossen, EWJ and de Brauw, M and Acherman, YIZ and de Goffau, MC and Gerdes, VEA and Nieuwdorp, M}, title = {Identifying Gut Microbiota associated with Gastrointestinal Symptoms upon Roux-en-Y Gastric Bypass.}, journal = {Obesity surgery}, volume = {33}, number = {6}, pages = {1635-1645}, pmid = {37093508}, issn = {1708-0428}, mesh = {Humans ; *Gastric Bypass/adverse effects ; *Gastrointestinal Microbiome ; *Obesity, Morbid/surgery ; Quality of Life ; *Microbiota ; }, abstract = {PURPOSE: Roux-en-Y gastric bypasses (RYGB) are frequently accompanied by long-term gastrointestinal (GI) symptoms. Direct mechanistic insight into the causation of these symptoms is lacking, but changes in the intestinal microbiome have been proposed to play a role. With this study, we aimed to investigate whether a microbial predisposition exists before RYGB which is associated with GI symptoms during follow-up and to evaluate which microbial groups are involved.

MATERIALS AND METHODS: In total, 67 RYGB patients were included. Shotgun metagenomic sequencing was performed on fecal samples obtained just before and 1 year after surgery. To assess GI symptoms, patients filled out Gastrointestinal Quality of Life Index (GIQLI) questionnaires and were divided into groups based on their total GIQLI score and change in score (postsurgery versus baseline). Extremely randomized tree predictor models were used to identify the most distinctive microbial species associated with postoperative GI symptoms.

RESULTS: Beta diversity differed significantly between baseline and 1-year post-surgery samples, with the post-surgery microbiome resembling a more dysbiotic profile. The most predictive species regarding total GIQLI (AUC 0.77) or delta GIQLI score (AUC 0.83) were identified. Many of these species are known butyrate producers or species known to support them and/or species with anti-inflammatory properties, including Coprococcus eutactus, Faecalibacterium prausnitzii, and Ruminococcus callidus.

CONCLUSION: Beneficial commensal gut microbiota related to a high GI score were associated to adequate intestinal fermentative capacity, suggesting these species might have protective properties against postoperative GI malfunctioning.}, } @article {pmid37093231, year = {2023}, author = {Ichige, R and Urabe, J}, title = {Divergence of the Host-Associated Microbiota with the Genetic Distance of Host Individuals Within a Parthenogenetic Daphnia Species.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2097-2108}, pmid = {37093231}, issn = {1432-184X}, support = {JPMJSP2114//Japan Science and Technology Agency/ ; KAKENHI:20H03315//Japan Society for the Promotion of Science Grant-in-Aid for Scientific Research/ ; }, mesh = {Animals ; *Daphnia/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Genotype ; }, abstract = {The taxonomic composition of the microbiota in the gut and epidermis of animals is known to vary among genetically and physiologically different host individuals within the same species. However, it is not clear whether the taxonomic composition diverges with increasing genetic distance of the host individuals. To unveil this uncertainty, we compared the host-associated microbiota among the genotypes within and between genetically distant lineages of parthenogenetic Daphnia cf. pulex across different physiological states, namely, well-fed, starved, and dead. Metagenomic analysis with 16S rRNA showed that, regardless of the host genotypes, diversity of the host-associated microbiota was high when the host individuals were fed food and gradually decreased when they were starved until they died. However, the difference in the host-associated microbiota, that is, β-diversity, was significant among the genotypes within and between the host lineages when they were fed. Although some bacteria in the microbiota, such as Limnohabitans, Rhodococcus, and Aeromicrobium, were found abundantly and commonly in all host genotypes; others, such as those of Holosoporacea, were found only in the genotypes of a specific lineage. Accordingly, the β-diversity tended to increase with increasing genetic distance of the host individuals. These results support an idea that the host-associated microbiota diverged with genetic divergence in the host species and that at least some bacteria are highly dependent on the genetically specific metabolites produced by the host individuals.}, } @article {pmid37093167, year = {2023}, author = {Schoen, R and de Koning, PPM and de Krom, C and Oplaat, C and Westenberg, M and Massart, S and Temple, C and De Jonghe, K and Blouin, AG and Botermans, M}, title = {First report of lettuce ring necrosis virus in chili pepper and tomato in Belgium and The Netherlands.}, journal = {Plant disease}, volume = {}, number = {}, pages = {}, doi = {10.1094/PDIS-01-23-0036-PDN}, pmid = {37093167}, issn = {0191-2917}, abstract = {Lettuce ring necrosis virus (LRNV), genus Ophiovirus, was detected by the Netherlands Institute for Vectors, Invasive plants and Plant health (NIVIP) in June and November of 2021 in two samples of chili pepper fruits (Capsicum spp.), both in mixed infection with other viruses. The first sample originated from a production site in Belgium (Sample ID: 40009704) and the second from a production site in the Netherlands (Sample ID: 41115269). One of the fruits of 40009704 showed a light purple circular pattern, while fruits from 41115269 showed colored (ring)spots. The samples were analyzed using Illumina sequencing on a NovaSeq 6000 platform (PE 150) as described previously (Hammond et al., 2021), obtaining 39.9M and 22.8M total reads for 40009704 and 41115269. The corresponding sequence read archives (SRA) were deposited in the NCBI SRA database under BioProject accession number PRJNA917231. From both samples, the nearly complete genome of LRNV (RNA1-4) was obtained and deposited in GenBank (40009704, OQ160823- OQ160826 (7616, 1799, 1502, 1382 nt, mapped reads: 40K, 12K, 114K, 12K , average read coverage (ARC): 0.8K, 0.9K, 11.3K and 1.1K); 41115269, OQ160827- OQ160830 (7616, 1801, 1518, 1389 nt, mapped reads: 112K, 7K, 357K, 55K reads, ARC: 2.2K, 0.6K, 34K and 5.8K)). The shared sequence identities with the Genbank reference sequence of LRNV (NC_006051-NC_006051) were 99.2 and 99.2% (RNA1), 99.1 and 99.1% (RNA2), 98.3 and 98.8% (RNA3), 99.0 and 98.9% (RNA4) for 40009704 and 41115269 respectively. The shared sequence identities between 40009704 and 41115269 were 99.9 (RNA1), 99.0 (RNA2), 99.1 (RNA3) and 99.5% (RNA4). In addition to LRNV, the ophiovirus ranunculus white mottle virus (RWMV) was detected in both samples (OQ160831-OQ160834; OQ160835-OQ160838), while the tobamovirus pepper mild mottle virus (PMMoV) was present in the fruits of 41115269 (OQ160839). Since RWMV has been associated with leaf symptoms in pepper (Gambley et al., 2019; Rivarez et al., 2022) and the colored (ring)spots of 41115269 were very similar to reported symptoms of PMMoV-infected pepper fruits (Martínez-Ochoa et al., 2003), it remains unclear whether LRNV contributed to the observed symptoms. Additionally, LRNV was detected in tomato (Solanum lycopersicum) in Belgium in 2020. In the frame of a metagenomic survey using Virion-Associated Nucleic Acids (VANA)-based protocol (Maclot et al., 2021) on a Nextseq 500 platform (PE 150), partial genome sequences of LRNV were detected in two pools of tomato plants. One pool was made of 44 asymptomatic cultivars from a non-commercial grower (one sample per cultivar) yielding 118K total reads of which 84, 59, 335, and 18 reads mapped on RNA1, 2, 3, and 4, covering 35%, 69%, 100% and 55% of the genome, respectively. The other pool consisted of 15 plants from one cultivar from a production site yielding 3.1M total reads of which 6 and 5 reads mapped on RNA3 and 4, respectively. The detection of LRNV was confirmed for both pooled samples using the real-time RT-PCR method, targeting the CP gene, as described by Maachi et al. (2021). To our knowledge this is the first report of LRNV in pepper anywhere in the world. Additionally, although the disease lettuce ring necrosis in lettuce (Lactuca sativa) has been described in Belgium and the Netherlands before the causal agent was identified (Bos & Huijberts, 1996), this is the first official report of this virus in Belgium and the Netherlands. This publication resulted from pre-publication data sharing of sequences and biological data among plant virologists to provide more context to two independent findings (Hammond et al., 2021).}, } @article {pmid37093042, year = {2023}, author = {Gundamraj, V and Hasbun, R}, title = {Viral meningitis and encephalitis: an update.}, journal = {Current opinion in infectious diseases}, volume = {36}, number = {3}, pages = {177-185}, doi = {10.1097/QCO.0000000000000922}, pmid = {37093042}, issn = {1473-6527}, mesh = {Humans ; *Influenza, Human ; *COVID-19/epidemiology ; SARS-CoV-2 ; *Meningitis, Viral ; *Viruses ; *Encephalitis ; Herpesvirus 3, Human ; *Herpesvirus 1, Human ; *Zika Virus ; *Zika Virus Infection ; }, abstract = {PURPOSE OF REVIEW: The most common infectious etiologies of meningitis and encephalitis are viruses. In this review, we will discuss current epidemiology, prevention, diagnosis, and treatment of the most common causes of viral meningitis and encephalitis worldwide.

RECENT FINDINGS: Viral meningitis and encephalitis are increasingly diagnosed as molecular diagnostic techniques and serologies have become more readily available worldwide but recent progress in novel antiviral therapies remains limited. Emerging and re-emerging viruses that have caused endemic or worldwide outbreaks or epidemics are arboviruses (e.g., West Nile virus, Japanese encephalitis, Tick borne encephalitis, Dengue, Zika, Toscana), enteroviruses (e.g., Enterovirus 71, Enterovirus D68), Parechoviruses, respiratory viruses [e.g., severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), influenza, metapneumoviruses, measles, mumps], and herpes viruses [e.g., herpes simplex virus (HSV) type 1 (HSV-1), HSV-2, human herpes (HV) 6, varicella zoster virus (VZV)]. Future efforts should concentrate in increasing availability for those viruses with effective vaccination [e.g., Japanese encephalitis, Tick borne encephalitis, varicella zoster viruses, SARS-CoV-2, influenza], prompt initiation of those with encephalitis with treatable viruses (e.g., HSV-1, VZV), increasing the diagnostic yield by using novel techniques such as metagenomic sequencing and avoiding unnecessary antibiotics in those with viral meningitis or encephalitis.

SUMMARY: We review the current epidemiology, clinical presentation, diagnosis, and treatment of the common causative agents of viral meningitis and encephalitis worldwide.}, } @article {pmid37093039, year = {2023}, author = {Dithugoe, CD and Bezuidt, OKI and Cavan, EL and Froneman, WP and Thomalla, SJ and Makhalanyane, TP}, title = {Bacteria and Archaea Regulate Particulate Organic Matter Export in Suspended and Sinking Marine Particle Fractions.}, journal = {mSphere}, volume = {8}, number = {3}, pages = {e0042022}, pmid = {37093039}, issn = {2379-5042}, support = {0182/2017//Department of Science and Technology, Republic of South Africa (DST)/ ; 110729//National Research Foundation (NRF)/ ; 148867//National Research Foundation (NRF)/ ; }, mesh = {*Archaea/genetics/metabolism ; *Seawater/microbiology ; Particulate Matter/metabolism ; Bacteria/genetics/metabolism ; Dissolved Organic Matter ; Carbon/metabolism ; }, abstract = {The biological carbon pump (BCP) in the Southern Ocean is driven by phytoplankton productivity and is a significant organic matter sink. However, the role of particle-attached (PA) and free-living (FL) prokaryotes (bacteria and archaea) and their diversity in influencing the efficiency of the BCP is still unclear. To investigate this, we analyzed the metagenomes linked to suspended and sinking marine particles from the Sub-Antarctic Southern Ocean Time Series (SOTS) by deploying a Marine Snow Catcher (MSC), obtaining suspended and sinking particulate material, determining organic carbon and nitrogen flux, and constructing metagenome-assembled genomes (MAGs). The suspended and sinking particle-pools were dominated by bacteria with the potential to degrade organic carbon. Bacterial communities associated with the sinking fraction had more genes related to the degradation of complex organic carbon than those in the suspended fraction. Archaea had the potential to drive nitrogen metabolism via nitrite and ammonia oxidation, altering organic nitrogen concentration. The data revealed several pathways for chemoautotrophy and the secretion of recalcitrant dissolved organic carbon (RDOC) from CO2, with bacteria and archaea potentially sequestering particulate organic matter (POM) via the production of RDOC. These findings provide insights into the diversity and function of prokaryotes in suspended and sinking particles and their role in organic carbon/nitrogen export in the Southern Ocean. IMPORTANCE The biological carbon pump is crucial for the export of particulate organic matter in the ocean. Recent studies on marine microbes have shown the profound influence of bacteria and archaea as regulators of particulate organic matter export. Yet, despite the importance of the Southern Ocean as a carbon sink, we lack comparable insights regarding microbial contributions. This study provides the first insights regarding prokaryotic contributions to particulate organic matter export in the Southern Ocean. We reveal evidence that prokaryotic communities in suspended and sinking particle fractions harbor widespread genomic potential for mediating particulate organic matter export. The results substantially enhance our understanding of the role played by microorganisms in regulating particulate organic matter export in suspended and sinking marine fractions in the Southern Ocean.}, } @article {pmid37092383, year = {2023}, author = {Lv, H and Zhou, JH and Guo, Y and Chen, H and Xu, JZ and Zhang, ZR and Zhang, ZH}, title = {Mycobacterium Avium Complex Infection of the Spine in a Patient Without Acquired Immune Deficiency Syndrome: A Case Report and Literature Review.}, journal = {Orthopaedic surgery}, volume = {15}, number = {6}, pages = {1707-1715}, pmid = {37092383}, issn = {1757-7861}, mesh = {Humans ; Middle Aged ; Mycobacterium avium Complex ; *Mycobacterium avium-intracellulare Infection/diagnosis/drug therapy/microbiology ; *Acquired Immunodeficiency Syndrome/drug therapy ; Clarithromycin/therapeutic use ; Rifampin/therapeutic use ; Drug Therapy, Combination ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {A 52-year-old patient misdiagnosed with spinal tuberculosis was successfully diagnosed with Mycobacterium avium infection using metagenomic next-generation sequencing and cured with four-drug combination protocol chemotherapy (amikacin, rifampicin, clarithromycin, ethambutol) and spinal fixation.}, } @article {pmid37092330, year = {2023}, author = {Castillo, DF and Denson, LA and Haslam, DB and Hommel, KA and Ollberding, NJ and Sahay, R and Santucci, NR}, title = {The microbiome in adolescents with irritable bowel syndrome and changes with percutaneous electrical nerve field stimulation.}, journal = {Neurogastroenterology and motility}, volume = {35}, number = {7}, pages = {e14573}, pmid = {37092330}, issn = {1365-2982}, support = {K23 DK135797/DK/NIDDK NIH HHS/United States ; P30 DK078392/DK/NIDDK NIH HHS/United States ; T32 DK007727/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Female ; Adolescent ; Child ; *Irritable Bowel Syndrome/diagnosis ; *Microbiota ; Abdominal Pain/complications ; Catastrophization ; Carbohydrates ; }, abstract = {BACKGROUND: Irritable bowel syndrome (IBS), a disorder of the gut-brain axis, is affected by the microbiome. Microbial studies in pediatric IBS, especially for centrally mediated treatments, are lacking. We compared the microbiome between pediatric IBS patients and healthy controls (HC), in relation to symptom severity, and with percutaneous electrical nerve field stimulation (PENFS), a non-invasive treatment targeting central pain pathways.

METHODS: We collected a stool sample, questionnaires and a 1-2 week stool and pain diary from 11 to 18 years patients with IBS. A patient subset completed 4 weeks of PENFS and repeated data collection immediately after and/or 3 months after treatment. Stool samples were collected from HC. Samples underwent metagenomic sequencing to evaluate diversity, composition, and abundance of species and MetaCyc pathways.

KEY RESULTS: We included 27 cases (15.4 ± 2.5 year) and 34 HC (14.2 ± 2.9 year). Twelve species including Firmicutes spp., and carbohydrate degradation/long-chain fatty acid (LCFA) synthesis pathways, were increased in IBS but not statistically significantly associated with symptom severity. Seventeen participants (female) who completed PENFS showed improvements in pain (p = 0.012), disability (p = 0.007), and catastrophizing (p = 0.003). Carbohydrate degradation and LCFA synthesis pathways decreased post-treatment and at follow-up (FDR p-value <0.1).

CONCLUSIONS AND INFERENCES: Firmicutes, including Clostridiaceae spp., and LCFA synthesis pathways were increased in IBS patients suggesting pain-potentiating effects. PENFS led to marked improvements in abdominal pain, functioning, and catastrophizing, while Clostridial species and LCFA microbial pathways decreased with treatment, suggesting these as potential targets for IBS centrally mediated treatments.}, } @article {pmid37092136, year = {2023}, author = {Xu, Y and Lian, QY and Chen, A and Zhang, JH and Xu, X and Huang, DX and He, JX and Ju, CR}, title = {Clinical characteristics and treatment strategy of nocardiosis in lung transplant recipients: A single-center experience.}, journal = {IDCases}, volume = {32}, number = {}, pages = {e01758}, pmid = {37092136}, issn = {2214-2509}, abstract = {OBJECTIVE: Nocardia are infrequent pathogens that disproportionately afflict organ transplant recipients. The present study aimed to summarize the clinical manifestations, diagnostic approaches, and treatment strategies of nocardiosis in lung transplant recipients.

METHODS: This retrospective study reviewed the clinical data of adult lung transplant recipients who were complicated with nocardiosis between January 2018 and December 2021 at the largest lung transplant center in South China.

RESULTS: The incidence of nocardiosis was 4.2% (13/316), including 9 cases of pulmonary nocardiosis and 4 disseminated nocardiosis (blood, pulmonary and intracranial). The accuracy in diagnosing nocardiosis was 77.8% by culture and 100% by metagenomic next-generation sequencing (mNGS). Nocardia farcinica was the most common causative pathogen. Trimethoprim-sulfamethoxazole-based combination therapy was administered initially, followed by a single antibiotic as the maintained therapy, lasting for 4-8 months.

CONCLUSIONS: mNGS is more accurate than culture in diagnosing nocardiosis. Most patients responded well to the antibiotic therapy with combined antibiotics at the initial stage followed by a single antibiotic treatment.}, } @article {pmid37091676, year = {2023}, author = {Lv, M and Zhu, C and Zhu, C and Yao, J and Xie, L and Zhang, C and Huang, J and Du, X and Feng, G}, title = {Clinical values of metagenomic next-generation sequencing in patients with severe pneumonia: a systematic review and meta-analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1106859}, pmid = {37091676}, issn = {2235-2988}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; Hospitals ; Metagenome ; Metagenomics ; *Pneumonia/diagnosis ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Clinical values of metagenomic next-generation sequencing (mNGS) in patients with severe pneumonia remain controversial. Therefore, we conduct this meta-analysis to evaluate the diagnostic performance of mNGS for pathogen detection and its role in the prognosis of severe pneumonia.

METHODS: We systematically searched the literature published in PubMed, Embase, Cochrane Library, Web of Science, Clinical Trials.gov, CNKI, Wanfang Data, and CBM from the inception to the 28th September 2022. Relevant trials comparing mNGS with conventional methods applied to patients with severe pneumonia were included. The primary outcomes of this study were the pathogen-positive rate, the 28-day mortality, and the 90-day mortality; secondary outcomes included the duration of mechanical ventilation, the length of hospital stay, and the length of stay in the ICU.

RESULTS: Totally, 24 publications with 3220 patients met the inclusion criteria and were enrolled in this study. Compared with conventional methods (45.78%, 705/1540), mNGS (80.48%, 1233/1532) significantly increased the positive rate of pathogen detection [OR = 6.81, 95% CI (4.59, 10.11, P < 0.001]. The pooled 28-day and 90-day mortality in mNGS group were 15.08% (38/252) and 22.36% (36/161), respectively, which were significantly lower than those in conventional methods group 33.05% (117/354) [OR = 0.35, 95% CI (0.23, 0.55), P < 0.001, I[2] = 0%] and 43.43%(109/251) [OR = 0.34, 95% CI (0.21, 0.54), P < 0.001]. Meanwhile, adjusted treatment based on the results of mNGS shortened the length of hospital stay [MD = -2.76, 95% CI (- 3.56, - 1.96), P < 0.001] and the length of stay in ICU [MD = -4.11, 95% CI (- 5.35, - 2.87), P < 0.001].

CONCLUSION: The pathogen detection positive rate of mNGS was much higher than that of conventional methods. Adjusted treatment based on mNGS results can reduce the 28-day and 90-day mortality of patients with severe pneumonia, and shorten the length of hospital and ICU stay. Therefore, mNGS advised to be applied to severe pneumonia patients as early as possible in addition to conventional methods to improve the prognosis and reduce the length of hospital stay.}, } @article {pmid37091672, year = {2023}, author = {Xiang, C and Wu, X and Wei, Y and Li, T and Tang, X and Wang, Y and Zhang, X and Huang, X and Wang, Y}, title = {First report on severe septic shock associated with human Parvovirus B19 infection after cardiac surgery.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1064760}, pmid = {37091672}, issn = {2235-2988}, mesh = {Female ; Humans ; Middle Aged ; *Erythema Infectiosum/complications ; *Shock, Septic/etiology/complications ; *Parvovirus B19, Human/genetics ; *Cardiac Surgical Procedures ; Antibodies, Viral ; }, abstract = {BACKGROUND: Human Parvovirus B19 (PB19) is a single-stranded DNA virus. Septic shock from viremia is rare with PB19; however, this infection can progress to life-threatening conditions. We report the first case of severe septic shock associated with a PB19 infection after cardiac surgery.

CASE PRESENTATION: A 50-year-old Chinese woman received elective double metal valve replacement, including the aortic valve and the mitral valve, under cardiopulmonary bypass (CPB) and suffered severe septic shock on postoperative day (PD) 30. Through the detection of PB19-specific nucleic acids in blister fluid and serum samples via metagenomic next-generation sequencing (mNGS), positive serum PB19 IgM and no other proven infection, acute PB19 infection was confirmed. After five days of combined treatment, no further fever or abdominal discomfort was noted, and the patient's circulation gradually became stable without vasoactive medications.

CONCLUSION: PB19 may be an unrecognized cause of septic shock, rash, fever of unknown origin or multiple systemic signs and symptoms, especially in immunosuppressed and immunocompetent critically ill patients. Investigations for viral aetiology are needed.}, } @article {pmid37091249, year = {2023}, author = {Harusato, A and Seo, W and Abo, H and Nakanishi, Y and Nishikawa, H and Itoh, Y}, title = {Impact of particulate microplastics generated from polyethylene terephthalate on gut pathology and immune microenvironments.}, journal = {iScience}, volume = {26}, number = {4}, pages = {106474}, pmid = {37091249}, issn = {2589-0042}, abstract = {Environmental microplastics have emerged as a critical issue in maintaining the planetary ecosystem. In this study, we generated particulate microplastics from polyethylene terephthalate (PM-PET) and investigated their impact in the gut by using mouse models and implementing histological examinations, as well as multi-omics analysis for colonic immune cells and microbiota. As a result, histological approaches showed that chronic and physiological low dose exposure of PM-PET did not affect intestinal pathology and mucin barriers, respectively. Moreover, immunohistochemical analysis demonstrated that the numbers of T cells, B cells, macrophages, and granulocytes were not affected by the exposure to PM-PET. However, RNA-seq analysis revealed that PM-PET had a substantial impact on the transcriptome in gut immune cells and their metabolisms, while 16s rRNA metagenomic analysis showed that the composition of microbiota was modestly affected. These results suggest an unexpected role played by the PM-PET in affecting gut immune homeostasis without detectable inflammation.}, } @article {pmid37090719, year = {2023}, author = {Meng, JX and Wei, XY and Guo, H and Chen, Y and Wang, W and Geng, HL and Yang, X and Jiang, J and Zhang, XX}, title = {Metagenomic insights into the composition and function of the gut microbiota of mice infected with Toxoplasma gondii.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1156397}, pmid = {37090719}, issn = {1664-3224}, mesh = {Animals ; Mice ; *Toxoplasma ; *Gastrointestinal Microbiome ; Persistent Infection ; Dysbiosis ; *Toxoplasmosis ; Inflammation ; }, abstract = {INTRODUCTION: Despite Toxoplasma gondii infection leading to dysbiosis and enteritis, the function of gut microbiota in toxoplasmosis has not been explored.

METHODS: Here, shotgun metagenomics was employed to characterize the composition and function of mouse microbial community during acute and chronic T. gondii infection, respectively.

RESULTS: The results revealed that the diversity of gut bacteria was decreased immediately after T. gondii infection, and was increased with the duration of infection. In addition, T. gondii infection led to gut microbiota dysbiosis both in acute and chronic infection periods. Therein, several signatures, including depression of Firmicutes to Bacteroidetes ratio and infection-enriched Proteobacteria, were observed in the chronic period, which may contribute to aggravated gut inflammation and disease severity. Functional analysis showed that a large amount of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and carbohydrate-active enzymes (CAZy) family displayed distinct variation in abundance between infected and healthy mice. The lipopolysaccharide biosynthesis related pathways were activated in the chronic infection period, which might lead to immune system imbalance and involve in intestinal inflammation. Moreover, microbial and functional spectrums were more disordered in chronic than acute infection periods, thus implying gut microbiota was more likely to participate in disease process in the chronically infected mice, even exacerbated immunologic derangement and disease progression.

DISCUSSION: Our data indicate that the gut microbiota plays a potentially important role in protecting mice from T. gondii infection, and contributes to better understand the association between gut microbiota and toxoplasmosis.}, } @article {pmid37090637, year = {2023}, author = {Wang, Z and Dalton, KR and Lee, M and Parks, CG and Beane Freeman, LE and Zhu, Q and González, A and Knight, R and Zhao, S and Motsinger-Reif, AA and London, SJ}, title = {Metagenomics reveals novel microbial signatures of farm exposures in house dust.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {37090637}, support = {Z01 CP010119/ImNIH/Intramural NIH HHS/United States ; Z01 ES049030/ImNIH/Intramural NIH HHS/United States ; }, abstract = {Indoor home dust microbial communities, important contributors to human health outcomes, are shaped by environmental factors, including farm-related exposures. Detection and characterization of microbiota are influenced by sequencing methodology; however, it is unknown if advanced metagenomic whole genome shotgun sequencing (WGS) can detect novel associations between environmental exposures and the indoor built-environment dust microbiome, compared to conventional 16S rRNA amplicon sequencing (16S). This study aimed to better depict indoor dust microbial communities using WGS to investigate novel associations with environmental risk factors from the homes of 781 farmers and farm spouses enrolled in the Agricultural Lung Health Study. We examined various farm-related exposures, including living on a farm, crop versus animal production, and type of animal production, as well as non-farm exposures, including home cleanliness and indoor pets. We assessed the association of the exposures on within-sample alpha diversity and between-sample beta diversity, and the differential abundance of specific microbes by exposure. Results were compared to previous findings using 16S. We found most farm exposures were significantly positively associated with both alpha and beta diversity. Many microbes exhibited differential abundance related to farm exposures, mainly in the phyla Actinobacteria, Bacteroidetes, Firmicutes , and Proteobacteria . The identification of novel differential taxa associated with farming at the genera level, including Rhodococcus, Bifidobacterium, Corynebacterium , and Pseudomonas , was a benefit of WGS compared to 16S. Our findings indicate that characterization of dust microbiota, an important component of the indoor environment relevant to human health, is heavily influenced by sequencing techniques. WGS is a powerful tool to survey the microbial community that provides novel insights on the impact of environmental exposures on indoor dust microbiota, and should be an important consideration in designing future studies in environmental health.}, } @article {pmid37089648, year = {2023}, author = {Aswini, K and Suman, A and Sharma, P and Singh, PK and Gond, S and Pathak, D}, title = {Seed endophytic bacterial profiling from wheat varieties of contrasting heat sensitivity.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1101818}, pmid = {37089648}, issn = {1664-462X}, abstract = {Wheat yield can be limited by many biotic and abiotic factors. Heat stress at the grain filling stage is a factor that reduces wheat production tremendously. The potential role of endophytic microorganisms in mitigating plant stress through various biomolecules like enzymes and growth hormones and also by improving plant nutrition has led to a more in-depth exploration of the plant microbiome for such functions. Hence, we devised this study to investigate the abundance and diversity of wheat seed endophytic bacteria (WSEB) from heat[S] (heat susceptible, GW322) and heat[T] (heat tolerant, HD3298 and HD3271) varieties by culturable and unculturable approaches. The results evidenced that the culturable diversity was higher in the heat[S] variety than in the heat[T] variety and Bacillus was found to be dominant among the 10 different bacterial genera identified. Though the WSEB population was higher in the heat[S] variety, a greater number of isolates from the heat[T] variety showed tolerance to higher temperatures (up to 55°C) along with PGP activities such as indole acetic acid (IAA) production and nutrient acquisition. Additionally, the metagenomic analysis of seed microbiota unveiled higher bacterial diversity, with a predominance of the phyla Proteobacteria covering >50% of OTUs, followed by Firmicutes and Actinobacteria. There were considerable variations in the abundance and diversity between heat sensitivity contrasting varieties, where notably more thermophilic bacterial OTUs were observed in the heat[T] samples, which could be attributed to conferring tolerance against heat stress. Furthermore, exploring the functional characteristics of culturable and unculturable microbiomes would provide more comprehensive information on improving plant growth and productivity for sustainable agriculture.}, } @article {pmid37089560, year = {2023}, author = {Hammer, TJ and Kueneman, J and Argueta-Guzmán, M and McFrederick, QS and Grant, L and Wcislo, W and Buchmann, S and Danforth, BN}, title = {Bee breweries: The unusually fermentative, lactobacilli-dominated brood cell microbiomes of cellophane bees.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1114849}, pmid = {37089560}, issn = {1664-302X}, abstract = {Pathogens and parasites of solitary bees have been studied for decades, but the microbiome as a whole is poorly understood for most taxa. Comparative analyses of microbiome features such as composition, abundance, and specificity, can shed light on bee ecology and the evolution of host-microbe interactions. Here we study microbiomes of ground-nesting cellophane bees (Colletidae: Diphaglossinae). From a microbial point of view, the diphaglossine genus Ptiloglossa is particularly remarkable: their larval provisions are liquid and smell consistently of fermentation. We sampled larval provisions and various life stages from wild nests of Ptiloglossa arizonensis and two species of closely related genera: Caupolicana yarrowi and Crawfordapis luctuosa. We also sampled nectar collected by P. arizonensis. Using 16S rRNA gene sequencing, we find that larval provisions of all three bee species are near-monocultures of lactobacilli. Nectar communities are more diverse, suggesting ecological filtering. Shotgun metagenomic and phylogenetic data indicate that Ptiloglossa culture multiple species and strains of Apilactobacillus, which circulate among bees and flowers. Larval lactobacilli disappear before pupation, and hence are likely not vertically transmitted, but rather reacquired from flowers as adults. Thus, brood cell microbiomes are qualitatively similar between diphaglossine bees and other solitary bees: lactobacilli-dominated, environmentally acquired, and non-species-specific. However, shotgun metagenomes provide evidence of a shift in bacterial abundance. As compared with several other bee species, Ptiloglossa have much higher ratios of bacterial to plant biomass in larval provisions, matching the unusually fermentative smell of their brood cells. Overall, Ptiloglossa illustrate a path by which hosts can evolve quantitatively novel symbioses: not by acquiring or domesticating novel symbionts, but by altering the microenvironment to favor growth of already widespread and generalist microbes.}, } @article {pmid37089545, year = {2023}, author = {Montero, I and Barrientos, D and Hidalgo-Cantabrana, C and Martínez-Álvarez, N}, title = {GutAlive[®] enables DNA-based microbiome analysis without disrupting the original composition and diversity.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1118291}, pmid = {37089545}, issn = {1664-302X}, abstract = {INTRODUCTION: A precise fecal microbiome analysis requires normalized methods for microbiome sampling, transport and manipulation in order to obtain a representative snapshot of the microbial community. GutAlive[®] is the unique stool collection kit that generates an anaerobic atmosphere enabling oxygen sensitive bacteria to survive, maintaining the original microbiome composition and diversity.

METHODS: Five stool samples from different donors were collected using two different sampling devices, GutAlive[®] and Zymo DNA/RNA Shield[®], and processed at four different time points. Shotgun metagenomics was used to evaluate the influence of the device and the processing timing on the microbial populations to unravel the potential fluctuations on the composition and diversity of the fecal microbiome and the metabolic pathways profiling. Additionally, RT-qPCR was used to quantify bacterial cell viability for downstream applications of microbiota samples beyond metagenomics.

RESULTS: Our results show that GutAlive[®] enables bacterial cell viability overtime preserving DNA integrity, obtaining high-quantity and high-quality DNA to perform microbiome analysis using shotgun metagenomics. Based on the taxonomic profiling, metabolic pathways analysis, phylogeny and metagenome-assembled genomes, GutAlive[®] displayed greater performance without significant variability over time, showcasing the stabilization of the microbiome preserving the original composition and diversity. Indeed, this DNA stabilization is enabled with the preservation of bacterial viability on an anaerobic environment inside of the sampling device, without the addition of any reagents that interact directly with sample.

CONCLUSION: All the above makes GutAlive[®] an user-friendly kit for self-collection of biological samples, suitable for microbiome analysis, diagnostics, fecal microbiota transplant and bacterial isolation, maintaining the stability and bacterial viability over time, preserving the original composition and diversity of the microbiome.}, } @article {pmid37089532, year = {2023}, author = {Yang, BY and Zhao, FZ and Li, XH and Zhao, MS and Lv, JC and Shi, MJ and Li, J and Zhou, ZY and Wang, JJ and Song, J}, title = {Alteration of pro-carcinogenic gut microbiota is associated with clear cell renal cell carcinoma tumorigenesis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1133782}, pmid = {37089532}, issn = {1664-302X}, abstract = {OBJECTIVE: Increasing evidence suggests that gut microbiota is involved in the occurrence and progression of urinary system diseases such as clear cell renal cell carcinoma (ccRCC). However, the mechanism of how alteration of gut metagenome promotes ccRCC remains unclear. Here we aim to elucidate the association of specific gut bacteria and their metabolites with ccRCC.

METHODS: In a pilot case-control study among 30 ccRCC patients (RCC group) and 30 healthy controls (Control group), 16S ribosomal RNA (rRNA) gene sequencing were analyzed from fecal samples collected prior to surgery or hospitalization. Alpha diversity and beta diversity analysis of the gut microbiota were performed, and differential taxa were identified by multivariate statistics. Meanwhile, serum metabolism was measured by UHPLC-MS, and differential genes were identified based on the TCGA database.

RESULTS: Alpha diversity found there were no significant microbial diversity differences of gut microbiota between the RCC group and the Control group. However, beta diversity analysis showed that the overall structures of the two groups were significantly separated (p = 0.008). Random Forests revealed the relative abundances of 20 species differed significantly between the RCC group and the Control group, among which nine species were enriched in the RCC group such as Desulfovibrionaceae, and 11 species were less abundant such as four kinds of Lactobacillus. Concomitantly, serum level of taurine, which was considered to be consumed by Desulfovibrionaceae and released by Lactobacillus, has decreased in the RCC group. In addition, macrophage-related genes such as Gabbr1 was upregulated in ccRCC patients.

CONCLUSION: Reduction of protective bacteria, proliferation of sulfide-degrading bacteria Desulfovibrionaceae, reduction of taurine, and enrichment of macrophage related genes might be the risk predictors of ccRCC.}, } @article {pmid37089304, year = {2023}, author = {Wang, D and Ma, Q and Lin, H and Zhou, J and Yuan, S and Ma, B and Bai, Y and Qu, J}, title = {Enhancement of micropollutant biotransformation by adding manganese sand in constructed wetlands.}, journal = {Heliyon}, volume = {9}, number = {4}, pages = {e15092}, pmid = {37089304}, issn = {2405-8440}, abstract = {Recent investigations have shown that the addition of manganese (Mn) sand to constructed wetlands (i.e., Mn-amended CWs) can improve the performance of organic micropollutants (MPs) removal. In addition to the direct oxidation and adsorption of Mn oxides, the indirect role of Mn oxides in MP biotransformation is crucial to the removal of MPs but has seldom been referred to. Herein, we constructed lab-scale CWs with or without the addition of natural Mn sand (∼35% Mn oxides) to decipher the influence of Mn oxides on the biotransformation of the six selected MPs which commonly existed in the wastewater. The experimental results showed that the addition of Mn sand to CWs can improve the removal of MPs (8.48% atrazine, 13.16% atenolol, and 6.27% sulfamethoxazole [pairwise Wilcoxon test p < 0.05]). Combining the detection of transformation products and metagenomic sequencing, we found that the enhanced removal of atrazine in the Mn-amended CWs was mainly due to the bioaugmented hydroxylation process. The enrichment of biotransformation-related genes and associated microbes of atenolol and sulfamethoxazole in Mn-amended CWs indicated that the addition of Mn sand to CWs can strengthen the biotransformation of MPs. Furthermore, we found that these MP-biodegrading microbes were widely present in the full-scale CWs. Overall, our research provides fundamental information and insights for further application of Mn-amended CWs in MP removal.}, } @article {pmid37089205, year = {2023}, author = {Nguyen, TH and Tran, DM}, title = {Root endophytic microbiome dataset of sugarcane (Saccharum officinarum L.) cultivated in the Central Highlands, Vietnam, established by the 16S rRNA metagenomics.}, journal = {Data in brief}, volume = {48}, number = {}, pages = {109103}, pmid = {37089205}, issn = {2352-3409}, abstract = {Sugarcane (Saccharum officinarum L.) is one of the main annual crops grown in the Central Highlands of Vietnam. By understanding the taxonomic and functional profiles of root endophytic microbiome, we can develop a new cultivation technique for the sustainable production of this plant. In this work, a representative sample was obtained by mixing the roots collected from five different sugarcane fields in Dak Lak Province, the Central Highlands, in 2021. The genomic DNA of the endophytic bacteria was extracted using the DNeasy Powersoil kit, and the V1-V9 regions of the 16S rRNA genes were amplified by PCR. Libraries of 16S rRNA gene amplicons were prepared using the Swift amplicon 16S plus ITS panel kit. Finally, the Illumina MiSeq platform was used to sequence the 16S rRNA gene amplicons library. The raw data of the endophytic microbiome were uploaded to the National Center for Biotechnology Information (NCBI) with Bioproject PRJNA923851 and can be retrieved at https://www.ncbi.nlm.nih.gov/Traces/study/?acc=%20PRJNA923851. The obtained data provide basic information on the root endophytic microbiome of sugarcane cultivated in the Central Highlands of Vietnam. The data can also be useful for further developing a new technique for sustainable sugarcane production based on indigenous microorganisms. This work is the first report on the endophytic microbiome of sugarcane cultivated in this region.}, } @article {pmid37088586, year = {2023}, author = {Takaori, A and Hashimoto, D and Ikeura, T and Ito, T and Nakamaru, K and Masuda, M and Nakayama, S and Yamaki, S and Yamamoto, T and Fujimoto, K and Matsuo, Y and Akagawa, S and Ishida, M and Yamaguchi, K and Imoto, S and Hirota, K and Uematsu, S and Satoi, S and Sekimoto, M and Naganuma, M}, title = {Impact of neoadjuvant therapy on gut microbiome in patients with resectable/borderline resectable pancreatic ductal adenocarcinoma.}, journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]}, volume = {23}, number = {4}, pages = {367-376}, doi = {10.1016/j.pan.2023.04.001}, pmid = {37088586}, issn = {1424-3911}, mesh = {Humans ; Neoadjuvant Therapy ; *Gastrointestinal Microbiome ; *Carcinoma, Pancreatic Ductal/drug therapy/surgery ; Deoxycytidine/therapeutic use ; RNA, Ribosomal, 16S ; Antineoplastic Combined Chemotherapy Protocols/therapeutic use ; *Pancreatic Neoplasms/drug therapy/surgery ; Fluorouracil/therapeutic use ; Leucovorin/therapeutic use ; }, abstract = {BACKGROUND: /Objectives: Effects of chemotherapy on gut microbiota have been reported in various carcinomas. The current study aimed to evaluate the changes in the gut microbiota before and after neoadjuvant chemotherapy (NAC) in patients with resectable (R) and borderline resectable (BR) pancreatic ductal adenocarcinoma (PDAC) and understand their clinical implications.

METHODS: Twenty patients diagnosed with R/BR-PDAC were included in this study. Stool samples were collected at two points, before and after NAC, for microbiota analysis using 16S ribosomal RNA (16S rRNA) gene sequences.

RESULTS: Of the 20 patients, 18 (90%) were treated with gemcitabine plus S-1 as NAC, and the remaining patients received gemcitabine plus nab-paclitaxel and a fluorouracil, leucovorin, irinotecan, and oxaliplatin combination. No significant differences were observed in the α- and β-diversity before and after NAC. Bacterial diversity was not associated with Evans classification (histological grade of tumor destruction by NAC) or postoperative complications. The relative abundance of Actinobacteria phylum after NAC was significantly lower than that before NAC (P = 0.02). At the genus level, the relative abundance of Bifidobacterium before NAC in patients with Evans grade 2 disease was significantly higher than that in patients with Evans grade 1 disease (P = 0.03). Patients with Evans grade 2 lost significantly more Bifidobacterium than patients with Evans grade 1 (P = 0.01).

CONCLUSIONS: The diversity of gut microbiota was neither decreased by NAC for R/BR-PDAC nor associated with postoperative complications. Lower incidence of Bifidobacterium genus before NAC may be associated with a lower pathological response to NAC.}, } @article {pmid37088208, year = {2023}, author = {Kuo, HD and Zure, D and Lin, CR}, title = {Occurrences of similar viral diversity in campus wastewater and reclaimed water of a university dormitory.}, journal = {Chemosphere}, volume = {330}, number = {}, pages = {138713}, doi = {10.1016/j.chemosphere.2023.138713}, pmid = {37088208}, issn = {1879-1298}, mesh = {Humans ; Wastewater ; Universities ; *Norovirus ; Water Quality ; *Disinfectants ; }, abstract = {Water reuse from wastewater sources still remain some critical safety concerns associated with treacherous contaminants like pathogenic viruses. In this study, viral diversities in campus wastewater (CWW) and its reclaimed water (RCW) recycled for toilet flushing and garden irrigation of a university dormitory were assessed using metagenomic sequencing for acquisition of more background data. Results suggested majority (>80%) of gene sequences within assembled contigs predicted by open reading frame (ORF) finder were no-hit yet believed to be novel/unrevealed viral genomic information whereas hits matched bacteriophages (i.e., mainly Myoviridae, Podoviridae, and Siphoviridae families) were predominant in both CWW and RCW samples. Moreover, few pathogenic viruses (<1%) related to infections of human skin (e.g., Molluscum contagiosum virus, MCV), digestion system (e.g., hepatitis C virus, HCV), and gastrointestinal tract (e.g., human norovirus, HuNoV) were also noticed raising safety concerns about application of reclaimed waters. Low-affinity interactions of particular viral exterior proteins (e.g., envelope glycoproteins or spike proteins) for disinfectant ligand (e.g., chlorite) elucidated treatment limitations of current sewage processing systems even with membrane bioreactor and disinfectant contactor. Revolutionary disinfection approaches together with routine monitoring and new regulations are prerequisite to secure pathogen-correlated water quality for safer reuse of reclaimed waters.}, } @article {pmid37087889, year = {2023}, author = {Wang, Y and Yang, X and Li, H and Zhu, L and Wang, H}, title = {Steel slag assists potassium ferrate to improve SCFAs production from anaerobic sludge fermentation.}, journal = {Journal of environmental management}, volume = {340}, number = {}, pages = {117996}, doi = {10.1016/j.jenvman.2023.117996}, pmid = {37087889}, issn = {1095-8630}, mesh = {Fermentation ; *Sewage/chemistry ; *Steel ; Anaerobiosis ; Fatty Acids, Volatile ; Hydrogen-Ion Concentration ; }, abstract = {Potassium ferrate (PF) pretreatment in anaerobic sludge and its potential influence mechanisms have received widely attention. This study investigated the coupling effect of PF loading on steel slag (SS) on excess sludge anaerobic fermentation. Results showed that SS loading increase the treatment performance of PF on short chain volatile fatty acids (SCFAs) production from anaerobic fermented sludge. It was showed that the modified PF loaded SS (MPF-SS) promoted the dissolution and release of organic substrates from intracellular to extracellular. Further exploration showed the promotion of PF and MPF-SS exposure to acid production microorganisms was much more than that to acid consumption microorganisms. MPF-SS addition can also effectively reinforce the carbohydrate transport, amino acid metabolism and the key enhanced genes associated with fatty acid biosynthesis pathways. This study fills the knowledge gap about modified PF on sludge treatment and also expands a new perspective for its application for sludge resource recovery.}, } @article {pmid37087535, year = {2023}, author = {Raza, S and Koh, Y and Yoon, SS and Woo, SY and Ahn, KS and Kim, HL and Kim, HN}, title = {Identification of novel Carnobacterium maltaromaticum strains in bone marrow samples of patients with acute myeloid leukemia using a metagenomic binning approach.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {26}, number = {4}, pages = {1033-1040}, pmid = {37087535}, issn = {1618-1905}, mesh = {Humans ; *Metagenome ; Bone Marrow ; Carnobacterium/genetics/metabolism ; *Leukemia, Myeloid, Acute/genetics ; }, abstract = {The aim of this study aimed to examine the existence of a bacterial metagenome in the bone marrow of patients with acute myeloid leukemia (AML). We re-examined whole-genome sequencing data from the bone marrow samples of seven patients with AML, four of whom were remitted after treatment, for metagenomic analysis. After the removal of human reads, unmapped reads were used to profile the species-level composition. We used the metagenomic binning approach to confirm whether the identified taxon was a complete genome of known or novel strains. We observed a unique and novel microbial signature in which Carnobacterium maltaromaticum was the most abundant species in five patients with AML or remission. The complete genome of C. maltaromaticum "BMAML_KR01," which was observed in all samples, was 100% complete with 8.5% contamination and closely clustered with C. maltaromaticum strains DSM20730 and SF668 based on single nucleotide polymorphism variations. We identified five unique proteins that could contribute to cancer progression and 104 virulent factor proteins in the BMAML_KR01 genome. To our knowledge, this is the first report of a new strain of C. maltaromaticum in patients with AML. The presence of C. maltaromaticum and its new strain in patients indicates an urgent need to validate the existence of this bacterium and evaluate its pathophysiological role.}, } @article {pmid37087457, year = {2023}, author = {Gu, F and Zhu, S and Hou, J and Tang, Y and Liu, JX and Xu, Q and Sun, HZ}, title = {The hindgut microbiome contributes to host oxidative stress in postpartum dairy cows by affecting glutathione synthesis process.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {87}, pmid = {37087457}, issn = {2049-2618}, mesh = {Animals ; Cattle ; Female ; Mice ; Cysteine ; Glutamates ; *Glutamine ; Glutathione ; *Microbiota ; Oxidative Stress ; Postpartum Period ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Dairy cows are susceptible to postpartum systemic oxidative stress (OS), which leads to significant production loss and metabolic disorders. The gut microbiota has been linked to host health and stress levels. However, to what extent the gut microbiota is associated with postpartum OS remains unknown. In this study, the contribution of the fecal microbiota to postpartum systemic OS and its underlying mechanisms were investigated by integrating 16S rRNA gene sequencing, metagenomics, and metabolomics in postpartum dairy cattle and by transplanting fecal microbiota from cattle to mice.

RESULTS: A strong link was found between fecal microbial composition and postpartum OS, with an explainability of 43.1%. A total of 17 significantly differential bacterial genera and 19 species were identified between cows with high (HOS) and low OS (LOS). Among them, 9 genera and 16 species showed significant negative correlations with OS, and Marasmitruncus and Ruminococcus_sp._CAG:724 had the strongest correlations. The microbial functional analysis showed that the fecal microbial metabolism of glutamine, glutamate, glycine, and cysteine involved in glutathione synthesis was lower in HOS cows. Moreover, 58 significantly different metabolites were identified between HOS and LOS cows, and of these metabolites, 19 were produced from microbiota or cometabolism of microbiota and host. Furthermore, these microbial metabolites were enriched in the metabolism of glutamine, glutamate, glycine, and cysteine. The mice gavaged with HOS fecal microbiota had significantly higher OS and lower plasma glutathione peroxidase and glutathione content than those orally administered saline or LOS fecal microbiota.

CONCLUSIONS: Integrated results suggest that the fecal microbiota is responsible for OS and that lower glutathione production plays a causative role in HOS. These findings provide novel insights into the mechanisms of postpartum OS and potential regulatory strategies to alleviate OS in dairy cows. Video Abstract.}, } @article {pmid37087286, year = {2023}, author = {Li, X and Tan, G and Chen, P and Cai, K and Dong, W and Peng, N and Zhao, S}, title = {Uncovering acid resistance genes in lactic acid bacteria and impact of non-viable bacteria on bacterial community during Chinese strong-flavor baijiu fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {167}, number = {}, pages = {112741}, doi = {10.1016/j.foodres.2023.112741}, pmid = {37087286}, issn = {1873-7145}, mesh = {Fermentation ; *Lactobacillales/genetics ; Alcoholic Beverages/analysis ; Bacteria/genetics/metabolism ; *Microbiota/genetics ; Lactobacillus/genetics ; }, abstract = {Chinese strong-flavor baijiu (CSFB) brewing is a spontaneously solid-state fermentation process for approximately 60 days. Numerous microorganisms grow, die, and spark a series of metabolic reactions during fermentation. In this study, the microbial community and structure between total and viable bacteria in zaopei from the 5- and 20-year pits of CSFB are revealed by amplicon sequencing. Metagenome sequencing was applied to investigate acid resistance genes in Lactobacillus and predict carbohydrate active enzyme in zaopei. Besides, SourceTracker was conducted to expose bacterial sources. Results revealed that there was no significant difference in the bacterial community and structure between the total and viable bacteria; Lactobacillus was the most dominant bacterium in zaopei of two types of pits. Meanwhile, acid resistance genes argR, aspA, ilvE, gshA, DnaK, and cfa were genes that sustained Lactobacillus survival in the late stages of fermentation with high contents of acid and ethanol, and glycosyltransferases were identified as the predominated enzymes during the CSFB fermentation which catalyzed the process of lactic acid generation via Embden-Meyerhof-Parnas pathway and Hexose Monophosphate Pathway. Moreover, the environment contributed most bacteria to zaopei of the 5- and 20-year pits. These findings will provide a deeper understanding of the microbial community structure of viable and total bacteria and the reason for the dominance of Lactobacillus in the later stages of CSFB fermentation.}, } @article {pmid37087092, year = {2023}, author = {Lee, MR and Kim, JC and Park, SE and Kim, WJ and Kim, JS}, title = {Detection of viral genes in Metarhizium anisopliae JEF-290-infected longhorned tick, Haemaphysalis longicornis using transcriptome analysis.}, journal = {Journal of invertebrate pathology}, volume = {198}, number = {}, pages = {107926}, doi = {10.1016/j.jip.2023.107926}, pmid = {37087092}, issn = {1096-0805}, mesh = {Humans ; Animals ; *Ticks ; *Metarhizium/genetics ; Phylogeny ; *Ixodidae/genetics/microbiology ; Genes, Viral ; Gene Expression Profiling ; }, abstract = {Ticks are carriers of viruses that can cause disease in humans and animals. The longhorned ticks (Haemaphysalis longicornis; LHT), for example, mediates the severe fever with thrombocytopenia syndrome virus (SFTSV) in humans, and the population of ticks is growing due to increases in temperature caused by climate change. As ticks carry primarily RNA viruses, there is a need to study the possibility of detecting new viruses through tick virome analysis. In this study, viruses in LHTs collected in Korea were investigated and virus titers in ticks exposed to the entomopathogenic fungus Metarhizium anisopliae JEF-290 were analyzed. Total RNA was extracted from the collected ticks, and short reads were obtained from Illumina sequencing. A total of 50,024 contigs with coding capacity were obtained after de novo assembly of the reads in the metaSPAdes genome assembler. A series of BLAST-based analyses using the GenBank database was performed to screen viral contigs, and three putative virus species were identified from the tick meta-transcriptome, such as Alongshan virus (ALSV), Denso virus and Taggert virus. Measurements of virus-expression levels of infected and non-infected LHTs failed to detect substantial differences in expression levels. However, we suggest that LHT can spread not only SFTSV, but also various other disease-causing viruses over large areas of the world. From the phylogenetic analysis of ALSV glycoproteins, genetic differences in the ALSV could be due to host differences as well as regional differences. Viral metagenome analysis can be used as a tool to manage future outbreaks of disease caused by ticks by detecting unknown viruses.}, } @article {pmid37086993, year = {2023}, author = {Yang, J and Yu, Q and Su, W and Wang, S and Wang, X and Han, Q and Qu, J and Li, H}, title = {Metagenomics reveals elevated temperature causes nitrogen accumulation mainly by inhibiting nitrate reduction process in polluted water.}, journal = {The Science of the total environment}, volume = {882}, number = {}, pages = {163631}, doi = {10.1016/j.scitotenv.2023.163631}, pmid = {37086993}, issn = {1879-1026}, mesh = {Animals ; *Nitrates ; Temperature ; Nitrogen/metabolism ; Metagenomics ; *Microbiota ; Water ; Glutamates ; Denitrification ; }, abstract = {Determining the response of functional genes and microbiota involved in the nitrogen (N) cycle to warming in the face of global climate change is a hotpot topic. However, whether and how elevated temperature affects the N-cycle genes in polluted water remains unclear. Based on metagenomics, we investigated the responses of the whole N-cycling genes and their microbial communities to the temperature gradients (23, 26, 29, 32, and 35 °C) using animal cadavers as an N-pollution model. We found that the abundance of gene families involved in glutamate metabolism, assimilatory nitrate reduction to nitrite (ANRN), and denitrification pathways decreased with temperature. Moreover, warming reduced the diversity of N-cycling microbial communities. Ecological network analysis indicated that elevated temperature intensified the mutual competition of N-cycle genes. The partial least squares path model (PLS-PM) showed that warming directly suppressed most N-cycle pathways, especially glutamate metabolism, denitrification, and ANRN pathways. Corpse decay also indirectly inhibited N-cycling via regulating N content and microbial communities. Our results highlight warming leads to N accumulation by inhibiting the ANRN and denitrification pathways, which may jeopardize ecological environment security. Our study is expected to provide valuable insights into the complex N-cycle process and N-pollution in warmer aquatic ecosystems.}, } @article {pmid37086990, year = {2023}, author = {Liu, Q and Li, C and Fan, J and Peng, Y and Du, R}, title = {Evaluation of sludge anaerobic fermentation driving partial denitrification capability: In view of kinetics and metagenomic mechanisms.}, journal = {The Science of the total environment}, volume = {884}, number = {}, pages = {163581}, doi = {10.1016/j.scitotenv.2023.163581}, pmid = {37086990}, issn = {1879-1026}, mesh = {*Sewage ; Fermentation ; *Nitrites/metabolism ; Nitrates/metabolism ; Wastewater ; Denitrification ; Anaerobiosis ; Kinetics ; Nitrogen Dioxide ; Bioreactors ; Nitrogen ; Carbon/metabolism ; Oxidation-Reduction ; }, abstract = {Partial denitrification (PD) provides a promising approach of efficient and stable nitrite (NO2[-]-N) generation for annamox. In this study, the feasibility of short-term sludge anaerobic fermentation driving PD was evaluated. It was found that a higher NO2[-]-N accumulation in nitrate (NO3[-]-N) reduction was obtained with the 5-days fermented sludge compared to 8 and 15-days fermentation. Moreover, compared to acetate as carbon source, sludge fermentation products (SFPs) induced the higher NO2[-]-N production with nitrate-to-nitrite transformation ratio (NTR) nearly 100 %. Denitrification activity of fermented sludge were obviously improved with SFPs as electron donor. Metagenomic analysis revealed that Thauera was the dominant bacteria, which was assumed to be the key contributor to PD performance by harboring the highest narGHI and napAB but much lower nirS and nirK. Under the conditions of SFPs and fermented sludge, Thauera was speculated to have higher resistance than other denitrifiers attributed to versatile carbon metabolic capabilities utilizing SFPs with the significantly improved genes for metabolism of complex organic carbon via glycolysis after anaerobic fermentation. A novel integration of sludge fermentation driving PD and anammox for mainstream wastewater treatment and sidestream polishing was proposed to offer a promising application with reduced commercial carbon source consumption and waste sludge reduction.}, } @article {pmid37086884, year = {2023}, author = {Gharechahi, J and Vahidi, MF and Sharifi, G and Ariaeenejad, S and Ding, XZ and Han, JL and Salekdeh, GH}, title = {Lignocellulose degradation by rumen bacterial communities: New insights from metagenome analyses.}, journal = {Environmental research}, volume = {229}, number = {}, pages = {115925}, doi = {10.1016/j.envres.2023.115925}, pmid = {37086884}, issn = {1096-0953}, mesh = {Animals ; *Metagenome ; *Rumen/metabolism/microbiology ; Lignin ; Bacteria/genetics/metabolism ; Polysaccharides/metabolism ; Bacteroidetes/genetics/metabolism ; }, abstract = {Ruminant animals house a dense and diverse community of microorganisms in their rumen, an enlarged compartment in their stomach, which provides a supportive environment for the storage and microbial fermentation of ingested feeds dominated by plant materials. The rumen microbiota has acquired diverse and functionally overlapped enzymes for the degradation of plant cell wall polysaccharides. In rumen Bacteroidetes, enzymes involved in degradation are clustered into polysaccharide utilization loci to facilitate coordinated expression when target polysaccharides are available. Firmicutes use free enzymes and cellulosomes to degrade the polysaccharides. Fibrobacters either aggregate lignocellulose-degrading enzymes on their cell surface or release them into the extracellular medium in membrane vesicles, a mechanism that has proven extremely effective in the breakdown of recalcitrant cellulose. Based on current metagenomic analyses, rumen Bacteroidetes and Firmicutes are categorized as generalist microbes that can degrade a wide range of polysaccharides, while other members adapted toward specific polysaccharides. Particularly, there is ample evidence that Verrucomicrobia and Spirochaetes have evolved enzyme systems for the breakdown of complex polysaccharides such as xyloglucans, peptidoglycans, and pectin. It is concluded that diversity in degradation mechanisms is required to ensure that every component in feeds is efficiently degraded, which is key to harvesting maximum energy by host animals.}, } @article {pmid37086432, year = {2023}, author = {Ji, Y and Shang, J and Tang, X and Sun, Y}, title = {HOTSPOT: hierarchical host prediction for assembled plasmid contigs with transformer.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {5}, pages = {}, pmid = {37086432}, issn = {1367-4811}, mesh = {Phylogeny ; Plasmids/genetics ; *Software ; *Metagenome ; Metagenomics/methods ; Bacteria/genetics ; }, abstract = {MOTIVATION: As prevalent extrachromosomal replicons in many bacteria, plasmids play an essential role in their hosts' evolution and adaptation. The host range of a plasmid refers to the taxonomic range of bacteria in which it can replicate and thrive. Understanding host ranges of plasmids sheds light on studying the roles of plasmids in bacterial evolution and adaptation. Metagenomic sequencing has become a major means to obtain new plasmids and derive their hosts. However, host prediction for assembled plasmid contigs still needs to tackle several challenges: different sequence compositions and copy numbers between plasmids and the hosts, high diversity in plasmids, and limited plasmid annotations. Existing tools have not yet achieved an ideal tradeoff between sensitivity and precision on metagenomic assembled contigs.

RESULTS: In this work, we construct a hierarchical classification tool named HOTSPOT, whose backbone is a phylogenetic tree of the bacterial hosts from phylum to species. By incorporating the state-of-the-art language model, Transformer, in each node's taxon classifier, the top-down tree search achieves an accurate host taxonomy prediction for the input plasmid contigs. We rigorously tested HOTSPOT on multiple datasets, including RefSeq complete plasmids, artificial contigs, simulated metagenomic data, mock metagenomic data, the Hi-C dataset, and the CAMI2 marine dataset. All experiments show that HOTSPOT outperforms other popular methods.

The source code of HOTSPOT is available via: https://github.com/Orin-beep/HOTSPOT.}, } @article {pmid37086309, year = {2023}, author = {Sasaki, T and Matsumoto, Y and Murakami, K and Endo, S and Toyozumi, T and Otsuka, R and Kinoshita, K and Hu, J and Iida, S and Morishita, H and Nishioka, Y and Nakano, A and Uesato, M and Matsubara, H}, title = {Gut microbiome can predict chemoradiotherapy efficacy in patients with esophageal squamous cell carcinoma.}, journal = {Esophagus : official journal of the Japan Esophageal Society}, volume = {20}, number = {4}, pages = {691-703}, pmid = {37086309}, issn = {1612-9067}, mesh = {Humans ; *Esophageal Squamous Cell Carcinoma/therapy ; *Esophageal Neoplasms/therapy/pathology ; *Carcinoma, Squamous Cell/therapy/pathology ; *Gastrointestinal Microbiome ; Chemoradiotherapy ; }, abstract = {PURPOSE: The gut microbiome plays an important role in cancer pathogenesis and therapy. Some studies have reported that specific bacteria in tumor tissues may contribute to the prognosis and treatment of esophageal squamous cell carcinoma (ESCC). However, there is limited evidence that the gut microbiome is associated with ESCC. This study assessed the utility of the gut microbiome as a predictive marker of the therapeutic effect in patients with ESCC undergoing chemo-radiotherapy (CRT).

PATIENTS AND METHODS: Fecal samples were collected from 51 patients with ESCC who had never undergone treatment between April 2021 and May 2022 in the Department of Frontier Surgery, Chiba University. The gut microbiome was analyzed using 16S metagenomics sequencing. The association between the gut microbiome composition and stage according to the TNM classification (American Joint Committee on Cancer 7.0) and CRT response according to the RECIST criteria was evaluated.

RESULTS: The relative abundance of Fusobacteriaceae was enriched in cStage III-IVb group. Among the 27 patients who received CRT, the relative abundance of Lactobacillaceae was enriched in those with a partial and complete response. Lactobacillaceae also did not correlate with any clinical data, but the high Lactobacillales group had a higher LMR (P = 0.032) and lower PLR (P = 0.045) than in the low Lactobacillales group.

CONCLUSIONS: In conclusion, we found that the relative abundance of Lactobacillaceae was enriched in patients with a partial or complete response among CRT those with ESCC, thus suggesting that the relative abundance of Lactobacillaceae can predict the effect of CRT.}, } @article {pmid37085932, year = {2023}, author = {Singh, S and Aghdam, SA and Lahowetz, RM and Brown, AMV}, title = {Metapangenomics of wild and cultivated banana microbiome reveals a plethora of host-associated protective functions.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {36}, pmid = {37085932}, issn = {2524-6372}, abstract = {BACKGROUND: Microbiomes are critical to plants, promoting growth, elevating stress tolerance, and expanding the plant's metabolic repertoire with novel defense pathways. However, generally microbiomes within plant tissues, which intimately interact with their hosts, remain poorly characterized. These endospheres have become a focus in banana (Musa spp.)-an important plant for study of microbiome-based disease protection. Banana is important to global food security, while also being critically threatened by pandemic diseases. Domestication and clonal propagation are thought to have depleted protective microbiomes, whereas wild relatives may hold promise for new microbiome-based biological controls. The goal was to compare metapangenomes enriched from 7 Musa genotypes, including wild and cultivated varieties grown in sympatry, to assess the host associations with root and leaf endosphere functional profiles.

RESULTS: Density gradients successfully generated culture-free microbial enrichment, dominated by bacteria, with all together 24,325 species or strains distinguished, and 1.7 million metagenomic scaffolds harboring 559,108 predicted gene clusters. About 20% of sequence reads did not match any taxon databases and ~ 62% of gene clusters could not be annotated to function. Most taxa and gene clusters were unshared between Musa genotypes. Root and corm tissues had significantly richer endosphere communities that were significantly different from leaf communities. Agrobacterium and Rhizobium were the most abundant in all samples while Chitinophagia and Actinomycetia were more abundant in roots and Flavobacteria in leaves. At the bacterial strain level, there were > 2000 taxa unique to each of M. acuminata (AAA genotype) and M. balbisiana (B-genotype), with the latter 'wild' relatives having richer taxa and functions. Gene ontology functional enrichment showed core beneficial functions aligned with those of other plants but also many specialized prospective beneficial functions not reported previously. Some gene clusters with plant-protective functions showed signatures of phylosymbiosis, suggesting long-standing associations or heritable microbiomes in Musa.

CONCLUSIONS: Metapangenomics revealed key taxa and protective functions that appeared to be driven by genotype, perhaps contributing to host resistance differences. The recovery of rich novel taxa and gene clusters provides a baseline dataset for future experiments in planta or in vivo bacterization or engineering of wild host endophytes.}, } @article {pmid37085924, year = {2023}, author = {Ho, SFS and Wheeler, NE and Millard, AD and van Schaik, W}, title = {Gauge your phage: benchmarking of bacteriophage identification tools in metagenomic sequencing data.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {84}, pmid = {37085924}, issn = {2049-2618}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; 215154/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; BB/S017941/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Bacteriophages/genetics ; Benchmarking ; Sequence Analysis, DNA/methods ; Metagenome/genetics ; *Microbiota ; Metagenomics/methods ; }, abstract = {BACKGROUND: The prediction of bacteriophage sequences in metagenomic datasets has become a topic of considerable interest, leading to the development of many novel bioinformatic tools. A comparative analysis of ten state-of-the-art phage identification tools was performed to inform their usage in microbiome research.

METHODS: Artificial contigs generated from complete RefSeq genomes representing phages, plasmids, and chromosomes, and a previously sequenced mock community containing four phage species, were used to evaluate the precision, recall, and F1 scores of the tools. We also generated a dataset of randomly shuffled sequences to quantify false-positive calls. In addition, a set of previously simulated viromes was used to assess diversity bias in each tool's output.

RESULTS: VIBRANT and VirSorter2 achieved the highest F1 scores (0.93) in the RefSeq artificial contigs dataset, with several other tools also performing well. Kraken2 had the highest F1 score (0.86) in the mock community benchmark by a large margin (0.3 higher than DeepVirFinder in second place), mainly due to its high precision (0.96). Generally, k-mer-based tools performed better than reference similarity tools and gene-based methods. Several tools, most notably PPR-Meta, called a high number of false positives in the randomly shuffled sequences. When analysing the diversity of the genomes that each tool predicted from a virome set, most tools produced a viral genome set that had similar alpha- and beta-diversity patterns to the original population, with Seeker being a notable exception.

CONCLUSIONS: This study provides key metrics used to assess performance of phage detection tools, offers a framework for further comparison of additional viral discovery tools, and discusses optimal strategies for using these tools. We highlight that the choice of tool for identification of phages in metagenomic datasets, as well as their parameters, can bias the results and provide pointers for different use case scenarios. We have also made our benchmarking dataset available for download in order to facilitate future comparisons of phage identification tools. Video Abstract.}, } @article {pmid37085819, year = {2023}, author = {Oosterlinck, B and Ceuleers, H and Arras, W and De Man, JG and Geboes, K and De Schepper, H and Peeters, M and Lebeer, S and Skieceviciene, J and Hold, GL and Kupcinskas, J and Link, A and De Winter, BY and Smet, A}, title = {Mucin-microbiome signatures shape the tumor microenvironment in gastric cancer.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {86}, pmid = {37085819}, issn = {2049-2618}, mesh = {Humans ; *Stomach Neoplasms/genetics/metabolism/pathology ; Mucin-2/genetics ; Tumor Microenvironment ; RNA, Ribosomal, 16S/genetics ; Mucin-6/genetics ; *Adenocarcinoma ; *Microbiota ; Phenotype ; }, abstract = {BACKGROUND AND AIMS: We aimed to identify mucin-microbiome signatures shaping the tumor microenvironment in gastric adenocarcinomas and clinical outcomes.

METHODS: We performed high-throughput profiling of the mucin phenotypes present in 108 gastric adenocarcinomas and 20 functional dyspepsia cases using validated mucin-based RT-qPCRs with subsequent immunohistochemistry validation and correlated the data with clinical outcome parameters. The gastric microbiota was assessed by 16S rRNA gene sequencing, taxonomy, and community composition determined, microbial networks analyzed, and the metagenome inferred in association with mucin phenotypes and expression.

RESULTS: Gastric adenocarcinomas with an intestinal mucin environment or high-level MUC13 expression are associated with poor survival. On the contrary, gastric MUC5AC or MUC6 abundance was associated with a more favorable outcome. The oral taxa Neisseria, Prevotella, and Veillonella had centralities in tumors with intestinal and mixed phenotypes and were associated with MUC13 overexpression, highlighting their role as potential drivers in MUC13 signaling in GC. Furthermore, dense bacterial networks were observed in intestinal and mixed mucin phenotype tumors whereas the lowest community complexity was shown in null mucin phenotype tumors due to higher Helicobacter abundance resulting in a more decreased diversity. Enrichment of oral or intestinal microbes was mucin phenotype dependent. More specifically, intestinal mucin phenotype tumors favored the establishment of pro-inflammatory oral taxa forming strong co-occurrence networks.

CONCLUSIONS: Our results emphasize key roles for mucins in gastric cancer prognosis and shaping microbial networks in the tumor microenvironment. Specifically, the enriched oral taxa associated with aberrant MUC13 expression can be potential biomarkers in predicting disease outcomes. Video Abstract.}, } @article {pmid37085482, year = {2023}, author = {Li, Q and Fei, HL and Luo, ZH and Gao, SM and Wang, PD and Lan, LY and Zhao, XF and Huang, LN and Fan, PF}, title = {Gut microbiome responds compositionally and functionally to the seasonal diet variations in wild gibbons.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {21}, pmid = {37085482}, issn = {2055-5008}, mesh = {Animals ; *Hylobates ; *Gastrointestinal Microbiome ; Seasons ; RNA, Ribosomal, 16S/genetics ; Longitudinal Studies ; China ; Diet ; }, abstract = {Wild animals may encounter multiple challenges especially food shortage and altered diet composition in their suboptimal ranges. Yet, how the gut microbiome responds to dietary changes remains poorly understood. Prior studies on wild animal microbiomes have typically leaned upon relatively coarse dietary records and individually unresolved fecal samples. Here, we conducted a longitudinal study integrating 514 time-series individually recognized fecal samples with parallel fine-grained dietary data from two Skywalker hoolock gibbon (Hoolock tianxing) groups populating high-altitude mountainous forests in western Yunnan Province, China. 16S rRNA gene amplicon sequencing showed a remarkable seasonal fluctuation in the gibbons' gut microbial community structure both across individuals and between the social groups, especially driven by the relative abundances of Lanchnospiraceae and Oscillospiraceae associated with fluctuating consumption of leaf. Metagenomic functional profiling revealed that diverse metabolisms associated with cellulose degradation and short-chain fatty acids (SCFAs) production were enriched in the high-leaf periods possibly to compensate for energy intake. Genome-resolved metagenomics further enabled the resolving metabolic capacities associated with carbohydrate breakdown among community members which exhibited a high degree of functional redundancy. Our results highlight a taxonomically and functionally sensitive gut microbiome actively responding to the seasonally shifting diet, facilitating the survival and reproduction of the endangered gibbon species in their suboptimal habitats.}, } @article {pmid37085283, year = {2023}, author = {Rofael, SAD and Brown, J and Lipman, MCI and Lowe, DM and Spratt, D and Quaderi, S and Hurst, JR and McHugh, TD}, title = {Impact of prophylactic and 'rescue pack' antibiotics on the airway microbiome in chronic lung disease.}, journal = {BMJ open respiratory research}, volume = {10}, number = {1}, pages = {}, pmid = {37085283}, issn = {2052-4439}, mesh = {Humans ; Anti-Bacterial Agents/therapeutic use ; Quality of Life ; Phylogeny ; *Pulmonary Disease, Chronic Obstructive/genetics ; *Microbiota ; }, abstract = {UNLABELLED: The management of many chronic lung diseases involves multiple antibiotic prescriptions either to treat acute exacerbations or as prophylactic therapy to reduce the frequency of exacerbations and improve patients' quality of life.

AIM: To investigate the effects of antibiotics on the homeostasis of bacterial communities in the airways, and how this may contribute to antimicrobial resistance (AMR) among respiratory pathogens and microbiota.

METHODS: Within an observational cohort study, sputum was collected from 84 patients with chronic obstructive pulmonary disease and/or bronchiectasis at stable state: 47 were receiving antibiotic prophylaxis therapy. V3-V4 16S-rRNA sequencing on Illumina MiSeq, quantitative PCR for typical respiratory pathogens, bacteriology cultures and antimicrobial susceptibility testing of sputum isolates, resistome analysis on a subset of 17 sputum samples using MinION metagenomics sequencing were performed.

FINDING: The phylogenetic α-diversity and the total bacterial density in sputum were significantly lower in patients receiving prophylactic antibiotics (p=0.014 and 0.029, respectively). Antibiotic prophylaxis was associated with significantly lower relative abundance of respiratory pathogens such as Pseudomonas aeruginosa, Moraxella catarrhalis and members of family Enterobacteriaceae in the airway microbiome, but not Haemophilus influenzae and Streptococcus pneumoniae. No major definite directional shifts in the microbiota composition were identified with prophylactic antibiotic use at the cohort level. Surveillance of AMR and resistome analysis revealed a high frequency of resistance to macrolide and tetracycline in the cohort. AMR expressed by pathogenic bacterial isolates was associated with antibiotics prescribed as 'rescue packs' for prompt initiation of self-treatment of exacerbations (Spearman's rho=0.408, p=0.02).

CONCLUSIONS: Antibiotic prophylactic therapy suppresses recognised pathogenic bacteria in the sputum of patients with chronic lung disease. The use of antibiotic rescue packs may be driving AMR in this cohort rather than prophylactic antibiotics.}, } @article {pmid37085110, year = {2023}, author = {Rolton, A and Webb, SC and López-Sanmartín, M and Hutson, KS}, title = {Bivalve digestive epithelial virosis (DEV): A cause of disease or a natural process?.}, journal = {Journal of invertebrate pathology}, volume = {198}, number = {}, pages = {107924}, doi = {10.1016/j.jip.2023.107924}, pmid = {37085110}, issn = {1096-0805}, mesh = {Animals ; Hyperplasia ; *Bivalvia ; New Zealand ; }, abstract = {Epithelial hyperplasia and sloughing of the digestive gland in bivalve mollusks are a global phenomenon and occur in species of commercial interest and cultural significance to indigenous peoples. Where hemocytosis, hyperplasia, and necrosis of digestive tubule cells have been observed associated with electron-dense uncoated virus-like particles (VLPs) 25-45 nm in diameter, the condition has been named digestive epithelial virosis (DEV). This condition has been associated with mortalities of some bivalve species in New Zealand. Similar digestive gland alterations, but without detection of associated VLPs, have been reported in other bivalve species worldwide and are termed "DEV-like" since no virus link has been demonstrated. It remains unclear if DEV is an infectious condition and whether associated VLPs are the cause, a contributor, or simply associated with the observed condition. It is also unclear whether DEV or DEV-like conditions pose a biosecurity or economic threat, or alternatively, whether they reflect a natural cyclic event that does not require disease management. In this mini-review, we summarize the history of digestive epithelial alteration with VLPs (i.e., DEV) or without observation of VLPs (i.e., DEV-like), and we examine the evidence for and against viral-like particles as the cause of DEV in bivalves. We also explore other viral afflictions of bivalves and non-infectious agents, such as harmful algae and xenotoxins, that could elicit similar tissue alterations. Future recommendations for approaches to identify key risk factors that lead to the development of digestive epithelial alterations such as DEV include histological characterization of the digestive gland of marine mollusks; the use of metagenome analysis to design primers that could be used for detection of VLPs and to study host microbiota; disease challenges demonstrating that DEV causes pathology and the relationship between DEV intensity and morbidity/mortality.}, } @article {pmid37084618, year = {2023}, author = {Liu, MK and Tang, YM and Liu, CY and Tian, XH and Zhang, JW and Fan, XL and Jiang, KF and Ni, XL and Zhang, XY}, title = {Variation in microbiological heterogeneity in Chinese strong-flavor Baijiu fermentation for four representative varieties of sorghum.}, journal = {International journal of food microbiology}, volume = {397}, number = {}, pages = {110212}, doi = {10.1016/j.ijfoodmicro.2023.110212}, pmid = {37084618}, issn = {1879-3460}, mesh = {Fermentation ; *Sorghum ; Alcoholic Beverages/microbiology ; Carbohydrate Metabolism ; Bacteria/genetics/metabolism ; Edible Grain ; }, abstract = {The quality and composition of strong-flavor Baijiu (SFB), a type of Chinese liquor, depends on the variety of sorghum used in fermentation. However, comprehensive in situ studies measuring the effects sorghum varieties on the fermentation are lacking and the underlying microbial mechanisms remains poorly understood. We studied the in situ fermentation of SFB by using metagenomic, metaproteomic, and metabolomic techniques across four sorghum varieties. Sensory characteristics were best for SFB made from glutinous variety Luzhouhong, followed by glutinous hybrid Jinnuoliang and Jinuoliang, and those made with non-glutinous Dongzajiao. In agreement with sensory evaluations, the volatile composition of SFB samples differed between sorghum varieties (P < 0.05). Fermentation of different sorghum varieties varied in microbial diversity, structure, volatile compounds, and physicochemical properties (pH, temperature, starch, reducing sugar, and moisture) (P < 0.05), with most changes occurring within the first 21 days. Additionally, the microbial interactions and their relationship with volatiles, as well as the physicochemical factors that govern microbial succession, differed between varieties of sorghum. The number of physicochemical factors affecting bacterial communities outweighed those affecting fungal communities, suggesting that bacteria were less resilient to the brewing conditions. This correlates with the finding that bacteria play a major role in the differences in microbial communities and metabolic functions during fermentation with the different varieties of sorghum. Metagenomic function analysis revealed differences in amino acid and carbohydrate metabolism between sorghum varieties throughout most of the brewing process. Metaproteomics further indicated most differential proteins were found in these two pathways, related to differences in volatiles between sorghum varieties of Baijiu and originating from Lactobacillus. These results provide insight into the microbial principles underlying Baijiu production and can be used to improve the quality of Baijiu by selecting the appropriate raw materials and optimizing fermentation parameters.}, } @article {pmid37084583, year = {2023}, author = {El Samak, M and Zakeer, S and Hanora, A and Solyman, SM}, title = {Metagenomic and metatranscriptomic exploration of the Egyptian Red Sea sponge Theonella sp. associated microbial community.}, journal = {Marine genomics}, volume = {70}, number = {}, pages = {101032}, doi = {10.1016/j.margen.2023.101032}, pmid = {37084583}, issn = {1876-7478}, mesh = {Animals ; *Porifera/genetics ; *Theonella/microbiology ; Metagenomics ; Indian Ocean ; Egypt ; Phylogeny ; Bacteria/genetics ; *Microbiota ; }, abstract = {Marine sponges associated microorganisms are considered to be prolific source of bioactive natural products. Omics-based techniques such as metagenomics and metatranscriptomics have been used as effective tools to discover natural products. In this study, we used integrated metagenomic and metatranscriptomic analysis of three samples of the Egyptian Red Sea sponge Theonella sp. microbiome to obtain a complete picture of its biosynthetic activity to produce bioactive compounds. Our data revealed high biodiversity of the Egyptian sponge microbiota represented by 38 bacterial phyla with Candidate Phylum Poribacteria as the most abundant phyla with an average of 27.5% of the microbial community. The analysis also revealed high biosynthetic activity of the sponge microbiome through detecting different types of biosynthetic gene clusters (BGCs) with predicted antibacterial, cytotoxic and inhibitory bioactivity and the majority of these clusters were found to be actively transcribed. The complete BGCs of the cytotoxic theonellamide and misakinolide were detected and found to be actively transcribed. The majority of the detected BGCs were predicted to be novel as they did not show any similarity with any known cluster in the MIBiG database.}, } @article {pmid37083735, year = {2023}, author = {Roux, S and Camargo, AP and Coutinho, FH and Dabdoub, SM and Dutilh, BE and Nayfach, S and Tritt, A}, title = {iPHoP: An integrated machine learning framework to maximize host prediction for metagenome-derived viruses of archaea and bacteria.}, journal = {PLoS biology}, volume = {21}, number = {4}, pages = {e3002083}, pmid = {37083735}, issn = {1545-7885}, mesh = {*Archaea/genetics ; Metagenome/genetics ; *Viruses/genetics ; Bacteria/genetics ; Metagenomics/methods ; Machine Learning ; Genome, Viral/genetics ; }, abstract = {The extraordinary diversity of viruses infecting bacteria and archaea is now primarily studied through metagenomics. While metagenomes enable high-throughput exploration of the viral sequence space, metagenome-derived sequences lack key information compared to isolated viruses, in particular host association. Different computational approaches are available to predict the host(s) of uncultivated viruses based on their genome sequences, but thus far individual approaches are limited either in precision or in recall, i.e., for a number of viruses they yield erroneous predictions or no prediction at all. Here, we describe iPHoP, a two-step framework that integrates multiple methods to reliably predict host taxonomy at the genus rank for a broad range of viruses infecting bacteria and archaea, while retaining a low false discovery rate. Based on a large dataset of metagenome-derived virus genomes from the IMG/VR database, we illustrate how iPHoP can provide extensive host prediction and guide further characterization of uncultivated viruses.}, } @article {pmid37083597, year = {2023}, author = {Wang, YM and Abdullah, S and Luebbering, N and Langenberg, L and Duell, A and Lake, K and Lane, A and Hils, B and Vazquez Silva, O and Trapp, M and Nalapareddy, K and Koo, J and Denson, LA and Jodele, S and Haslam, DB and Faubion, WA and Davies, SM and Khandelwal, P}, title = {Intestinal permeability in patients undergoing stem cell transplantation correlates with systemic acute phase responses and dysbiosis.}, journal = {Blood advances}, volume = {7}, number = {17}, pages = {5137-5151}, pmid = {37083597}, issn = {2473-9537}, mesh = {Young Adult ; Humans ; Child ; *Lactulose/metabolism ; Rhamnose ; Acute-Phase Reaction ; Dysbiosis ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Permeability ; }, abstract = {Intestinal permeability may correlate with adverse outcomes during hematopoietic stem cell transplantation (HSCT), but longitudinal quantification with traditional oral mannitol and lactulose is not feasible in HSCT recipients because of mucositis and diarrhea. A modified lactulose:rhamnose (LR) assay is validated in children with environmental enteritis. Our study objective was to quantify peri-HSCT intestinal permeability changes using the modified LR assay. The LR assay was administered before transplant, at day +7 and +30 to 80 pediatric and young adult patients who received allogeneic HSCT. Lactulose and rhamnose were detected using urine mass spectrometry and expressed as an L:R ratio. Metagenomic shotgun sequencing of stool for microbiome analyses and enzyme-linked immunosorbent assay analyses of plasma lipopolysaccharide binding protein (LBP), ST2, REG3α, claudin1, occludin, and intestinal alkaline phosphatase were performed at the same timepoints. L:R ratios were increased at day +7 but returned to baseline at day +30 in most patients (P = .014). Conditioning regimen intensity did not affect the trajectory of L:R (P = .39). Baseline L:R ratios did not vary with diagnosis. L:R correlated with LBP levels (r2 = 0.208; P = .0014). High L:R ratios were associated with lower microbiome diversity (P = .035), loss of anaerobic organisms (P = .020), and higher plasma LBP (P = .0014). No adverse gastrointestinal effects occurred because of LR. Intestinal permeability as measured through L:R ratios after allogeneic HSCT correlates with intestinal dysbiosis and elevated plasma LBP. The LR assay is well-tolerated and may identify transplant recipients who are more likely to experience adverse outcomes.}, } @article {pmid37082183, year = {2023}, author = {Lv, M and Zhang, J and Deng, J and Hu, J and Zhong, Q and Su, M and Lin, D and Xu, T and Bai, X and Li, J and Guo, X}, title = {Analysis of the relationship between the gut microbiota enterotypes and colorectal adenoma.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1097892}, pmid = {37082183}, issn = {1664-302X}, abstract = {INTRODUCTION: The essence of enterotypes is to stratify the entire human gut microbiota, and dysregulation of gut microbiota is closely related to the development of colorectal adenoma. Enterotypes may therefore be a useful target for the prevention of colorectal adenoma. However, the relationship between gut microbiota and colorectal adenoma has not been fully elucidated. In this study, we aimed to analyze the differences in gut microbiome composition between adenoma and control populations.

METHODS: We recruited 31 patients with colorectal adenoma and 71 non-adenoma controls. Patient demographics, risk factors, fecal samples from each subject were collected and metagenomic sequencing was performed. LEfSe analysis was used to reveal differences in intestinal microbiome composition. Multiple logistic regression analysis was used to determine the association between enterotypes and colorectal adenoma.

RESULTS: The results showed that Prevotella enterotype (enterotype 4) is only present in adenoma group. Logistic regression analysis showed that Prevotella enterotype was an independent risk factor for colorectal adenoma.

DISCUSSION: The Prevotella enterotype may increase the occurrence of colorectal adenoma through inflammatory association and interference with glucose and lipid metabolism in human body. In conclusion, the differences we observed between different enterotypes add a new potential factor to the development of colorectal adenoma.}, } @article {pmid37081873, year = {2023}, author = {Chen, Y and Knight, R and Gallo, RL}, title = {Evolving approaches to profiling the microbiome in skin disease.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1151527}, pmid = {37081873}, issn = {1664-3224}, support = {R01 DK128787/DK/NIDDK NIH HHS/United States ; R37 AI052453/AI/NIAID NIH HHS/United States ; R01 AR076082/AR/NIAMS NIH HHS/United States ; P50 AR080594/AR/NIAMS NIH HHS/United States ; U01 AI152038/AI/NIAID NIH HHS/United States ; R01 AI153185/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Dysbiosis ; RNA, Ribosomal, 16S/genetics ; Skin/microbiology ; *Microbiota/genetics ; *Psoriasis ; Bacteria/genetics ; }, abstract = {Despite its harsh and dry environment, human skin is home to diverse microbes, including bacteria, fungi, viruses, and microscopic mites. These microbes form communities that may exist at the skin surface, deeper skin layers, and within microhabitats such as the hair follicle and sweat glands, allowing complex interactions with the host immune system. Imbalances in the skin microbiome, known as dysbiosis, have been linked to various inflammatory skin disorders, including atopic dermatitis, acne, and psoriasis. The roles of abundant commensal bacteria belonging to Staphylococcus and Cutibacterium taxa and the fungi Malassezia, where particular species or strains can benefit the host or cause disease, are increasingly appreciated in skin disorders. Furthermore, recent research suggests that the interactions between microorganisms and the host's immune system on the skin can have distant and systemic effects on the body, such as on the gut and brain, known as the "skin-gut" or "skin-brain" axes. Studies on the microbiome in skin disease have typically relied on 16S rRNA gene sequencing methods, which cannot provide accurate information about species or strains of microorganisms on the skin. However, advancing technologies, including metagenomics and other functional 'omic' approaches, have great potential to provide more comprehensive and detailed information about the skin microbiome in health and disease. Additionally, inter-species and multi-kingdom interactions can cause cascading shifts towards dysbiosis and are crucial but yet-to-be-explored aspects of many skin disorders. Better understanding these complex dynamics will require meta-omic studies complemented with experiments and clinical trials to confirm function. Evolving how we profile the skin microbiome alongside technological advances is essential to exploring such relationships. This review presents the current and emerging methods and their findings for profiling skin microbes to advance our understanding of the microbiome in skin disease.}, } @article {pmid37081594, year = {2023}, author = {Rodriguez, C and Boizeau, L and Soulier, A and N'Debi, M and Demontant, V and Trawinski, E and Seng, S and Fontaine, H and Woerther, PL and Marchand, S and Fourati, S and Chevaliez, S and Cappy, P and Pol, S and Pawlotsky, JM}, title = {Unknown Circovirus in Immunosuppressed Patient with Hepatitis, France, 2022.}, journal = {Emerging infectious diseases}, volume = {29}, number = {5}, pages = {1051-1054}, pmid = {37081594}, issn = {1080-6059}, mesh = {Humans ; *Circoviridae Infections/diagnosis ; *Circovirus/genetics ; France/epidemiology ; *Hepatitis ; *Hepatitis A ; Metagenome ; *Viruses ; Immunocompromised Host ; }, abstract = {Hepatitis of undetermined origin can be caused by a wide variety of pathogens, sometimes emerging pathogens. We report the discovery, by means of routine shotgun metagenomics, of a new virus belonging to the family Circoviridae, genus Circovirus, in a patient in France who had acute hepatitis of unknown origin.}, } @article {pmid37081583, year = {2023}, author = {Li, Y and Zhang, P and Ye, M and Tian, RR and Li, N and Cao, L and Ma, Y and Liu, FL and Zheng, YT and Zhang, C}, title = {Novel Circovirus in Blood from Intravenous Drug Users, Yunnan, China.}, journal = {Emerging infectious diseases}, volume = {29}, number = {5}, pages = {1015-1019}, pmid = {37081583}, issn = {1080-6059}, mesh = {Animals ; Swine ; Humans ; *Drug Users ; *Circovirus/genetics ; *Substance Abuse, Intravenous/complications/epidemiology ; China/epidemiology ; Hepacivirus ; Phylogeny ; *Swine Diseases/epidemiology ; }, abstract = {We identified a novel circovirus (human-associated circovirus 2 [HuCV2]) from the blood of 2 intravenous drug users in China who were infected with HIV-1, hepatitis C virus, or both. HuCV2 is most closely related to porcine circovirus 3. Our findings underscore the risk for HuCV2 and other emerging viruses among this population.}, } @article {pmid37081531, year = {2023}, author = {Zhang, D and Yu, H and Yang, Y and Liu, F and Li, M and Huang, J and Yu, Y and Wang, C and Jiang, F and He, Z and Yan, Q}, title = {Ecological interactions and the underlying mechanism of anammox and denitrification across the anammox enrichment with eutrophic lake sediments.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {82}, pmid = {37081531}, issn = {2049-2618}, mesh = {*Lakes/microbiology ; *Denitrification ; Anaerobic Ammonia Oxidation ; Oxidation-Reduction ; Bacteria/genetics/metabolism ; Bioreactors/microbiology ; }, abstract = {BACKGROUND: Increasing attention has recently been devoted to the anaerobic ammonium oxidation (anammox) in eutrophic lakes due to its potential key functions in nitrogen (N) removal for eutrophication control. However, successful enrichment of anammox bacteria from lake sediments is still challenging, partly due to the ecological interactions between anammox and denitrifying bacteria across such enrichment with lake sediments remain unclear.

RESULTS: This study thus designed to fill such knowledge gaps using bioreactors to enrich anammox bacteria with eutrophic lake sediments for more than 365 days. We continuously monitored the influent and effluent water, measured the anammox and denitrification efficiencies, quantified the anammox and denitrifying bacteria, as well as the related N cycling genes. We found that the maximum removal efficiencies of NH4[+] and NO2[-] reached up to 85.92% and 95.34%, respectively. Accordingly, the diversity of anammox and denitrifying bacteria decreased significantly across the enrichment, and the relative dominant anammox (e.g., Candidatus Jettenia) and denitrifying bacteria (e.g., Thauera, Afipia) shifted considerably. The ecological cooperation between anammox and denitrifying bacteria tended to increase the microbial community stability, indicating a potential coupling between anammox and denitrifying bacteria. Moreover, the nirS-type denitrifiers showed stronger coupling with anammox bacteria than that of nirK-type denitrifiers during the enrichment. Functional potentials as depicted by metagenome sequencing confirmed the ecological interactions between anammox and denitrification. Metagenome-assembled genomes-based ecological model indicated that the most dominant denitrifiers could provide various materials such as amino acid, cofactors, and vitamin for anammox bacteria. Cross-feeding in anammox and denitrifying bacteria highlights the importance of microbial interactions for increasing the anammox N removal in eutrophic lakes.

CONCLUSIONS: This study greatly expands our understanding of cooperation mechanisms among anammox and denitrifying bacteria during the anammox enrichment with eutrophic lake sediments, which sheds new insights into N removal for controlling lake eutrophication. Video Abstract.}, } @article {pmid37081504, year = {2023}, author = {Yu, T and Wu, W and Liang, W and Wang, Y and Hou, J and Chen, Y and Elvert, M and Hinrichs, KU and Wang, F}, title = {Anaerobic degradation of organic carbon supports uncultured microbial populations in estuarine sediments.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {81}, pmid = {37081504}, issn = {2049-2618}, mesh = {*Carbon/metabolism ; Lignin/metabolism ; Anaerobiosis ; Caseins/genetics/metabolism ; *Cellulase/genetics/metabolism ; Bacteria/genetics/metabolism ; Peptide Hydrolases/genetics ; Geologic Sediments/microbiology ; Phylogeny ; }, abstract = {BACKGROUND: A large proportion of prokaryotic microbes in marine sediments remains uncultured, hindering our understanding of their ecological functions and metabolic features. Recent environmental metagenomic studies suggested that many of these uncultured microbes contribute to the degradation of organic matter, accompanied by acetogenesis, but the supporting experimental evidence is limited.

RESULTS: Estuarine sediments were incubated with different types of organic matters under anaerobic conditions, and the increase of uncultured bacterial populations was monitored. We found that (1) lignin stimulated the increase of uncultured bacteria within the class Dehalococcoidia. Their ability to metabolize lignin was further supported by the presence of genes associated with a nearly complete degradation pathway of phenolic monomers in the Dehalococcoidia metagenome-assembled genomes (MAGs). (2) The addition of cellulose stimulated the increase of bacteria in the phylum Ca. Fermentibacterota and family Fibrobacterales, a high copy number of genes encoding extracellular endoglucanase or/and 1,4-beta-cellobiosidase for cellulose decomposition and multiple sugar transporters were present in their MAGs. (3) Uncultured lineages in the order Bacteroidales and the family Leptospiraceae were enriched by the addition of casein and oleic acid, respectively, a high copy number of genes encoding extracellular peptidases, and the complete β-oxidation pathway were found in those MAGs of Bacteroidales and Leptospiraceae, respectively. (4) The growth of unclassified bacteria of the order Clostridiales was found after the addition of both casein and cellulose. Their MAGs contained multiple copies of genes for extracellular peptidases and endoglucanase. Additionally, [13]C-labeled acetate was produced in the incubations when [13]C-labeled dissolved inorganic carbon was provided.

CONCLUSIONS: Our results provide new insights into the roles of microorganisms during organic carbon degradation in anaerobic estuarine sediments and suggest that these macro and single molecular organic carbons support the persistence and increase of uncultivated bacteria. Acetogenesis is an additional important microbial process alongside organic carbon degradation. Video Abstract.}, } @article {pmid37081217, year = {2023}, author = {Gao, FZ and He, LY and Chen, X and Chen, JL and Yi, X and He, LX and Huang, XY and Chen, ZY and Bai, H and Zhang, M and Liu, YS and Ying, GG}, title = {Swine farm groundwater is a hidden hotspot for antibiotic-resistant pathogenic Acinetobacter.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {34}, pmid = {37081217}, issn = {2730-6151}, abstract = {Acinetobacter is present in the livestock environment, but little is known about their antibiotic resistance and pathogenic species in the farm groundwater. Here we investigated antibiotic resistance of Acinetobacter in the swine farm groundwater (JZPG) and residential groundwater (JZG) of a swine farming village, in comparison to a nearby (3.5 km) non-farming village (WTG) using metagenomic and culture-based approaches. Results showed that the abundance of antibiotic resistome in some JZG and all JZPG (~3.4 copies/16S rRNA gene) was higher than that in WTG (~0.7 copies/16S rRNA gene), indicating the influence of farming activities on both groundwater types. Acinetobacter accounted for ~95.7% of the bacteria in JZG and JZPG, but only ~8.0% in WTG. They were potential hosts of ~95.6% of the resistome in farm affected groundwater, which includes 99 ARG subtypes against 23 antibiotic classes. These ARGs were associated with diverse intrinsic and acquired resistance mechanisms, and the predominant ARGs were tetracyclines and fluoroquinolones resistance genes. Metagenomic binning analysis elucidated that non-baumannii Acinetobacter including A. oleivorans, A. beijerinckii, A. seifertii, A. bereziniae and A. modestus might pose environmental risks because of multidrug resistance, pathogenicity and massive existence in the groundwater. Antibiotic susceptibility tests showed that the isolated strains were resistant to multiple antibiotics including sulfamethoxazole (resistance ratio: 96.2%), levofloxacin (42.5%), gatifloxacin (39.0%), ciprofloxacin (32.6%), tetracycline (32.0%), doxycycline (29.0%) and ampicillin (12.0%) as well as last-resort polymyxin B (31.7%), colistin (24.1%) and tigecycline (4.1%). The findings highlight potential prevalence of groundwater-borne antibiotic-resistant pathogenic Acinetobacter in the livestock environment.}, } @article {pmid37081077, year = {2023}, author = {Zorz, J and Li, C and Chakraborty, A and Gittins, DA and Surcon, T and Morrison, N and Bennett, R and MacDonald, A and Hubert, CRJ}, title = {SituSeq: an offline protocol for rapid and remote Nanopore 16S rRNA amplicon sequence analysis.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {33}, pmid = {37081077}, issn = {2730-6151}, abstract = {Microbiome analysis through 16S rRNA gene sequencing is a crucial tool for understanding the microbial ecology of any habitat or ecosystem. However, workflows require large equipment, stable internet, and extensive computing power such that most of the work is performed far away from sample collection in both space and time. Performing amplicon sequencing and analysis at sample collection would have positive implications in many instances including remote fieldwork and point-of-care medical diagnoses. Here we present SituSeq, an offline and portable workflow for the sequencing and analysis of 16S rRNA gene amplicons using Nanopore sequencing and a standard laptop computer. SituSeq was validated by comparing Nanopore 16S rRNA gene amplicons, Illumina 16S rRNA gene amplicons, and Illumina metagenomes, sequenced using the same environmental DNA. Comparisons revealed consistent community composition, ecological trends, and sequence identity across platforms. Correlation between the abundance of taxa in each taxonomic level in Illumina and Nanopore data sets was high (Pearson's r > 0.9), and over 70% of Illumina 16S rRNA gene sequences matched a Nanopore sequence with greater than 97% sequence identity. On board a research vessel on the open ocean, SituSeq was used to analyze amplicon sequences from deep sea sediments less than 2 h after sequencing, and 8 h after sample collection. The rapidly available results informed decisions about subsequent sampling in near real-time while the offshore expedition was still underway. SituSeq is a portable and user-friendly workflow that helps to bring the power of microbial genomics and diagnostics to many more researchers and situations.}, } @article {pmid37081021, year = {2023}, author = {Zhao, J and Yao, Y and Li, D and Zhu, W and Xiao, H and Xie, M and Xiong, Y and Wu, J and Ni, Q and Zhang, M and Xu, H}, title = {Metagenome and metabolome insights into the energy compensation and exogenous toxin degradation of gut microbiota in high-altitude rhesus macaques (Macaca mulatta).}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {20}, pmid = {37081021}, issn = {2055-5008}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Macaca mulatta/genetics/microbiology ; Metagenome ; Altitude ; Acetyl Coenzyme A/genetics ; Metabolome ; }, abstract = {There have been many reports on the genetic mechanism in rhesus macaques (RMs) for environmental adaptation to high altitudes, but the synergistic involvement of gut microbiota in this adaptation remains unclear. Here we performed fecal metagenomic and metabolomic studies on samples from high- and low-altitude populations to assess the synergistic role of gut microbiota in the adaptation of RMs to high-altitude environments. Microbiota taxonomic annotation yielded 7471 microbiota species. There were 37 bacterial species whose abundance was significantly enriched in the high-altitude populations, 16 of which were previously reported to be related to the host's dietary digestion and energy metabolism. Further functional gene enrichment found a stronger potential for gut microbiota to synthesize energy substrate acetyl-CoA using CO2 and energy substrate pyruvate using oxaloacetate, as well as a stronger potential to transform acetyl-CoA to energy substrate acetate in high-altitude populations. Interestingly, there were no apparent differences between low-altitude and high-altitude populations in terms of genes enriched in the main pathways by which the microbiota consumed the three energy substrates, and none of the three energy substrates were detected in the fecal metabolites. These results strongly suggest that gut microbiota plays an important energy compensatory role that helps RMs to adapt to high-altitude environments. Further functional enrichment after metabolite source analysis indicated the abundance of metabolites related to the degradation of exogenous toxins was also significantly higher in high-altitude populations, which suggested a contributory role of gut microbiota to the degradation of exogenous toxins in wild RMs adapted to high-altitude environments.}, } @article {pmid37080313, year = {2023}, author = {Ovis-Sánchez, JO and Perera-Pérez, VD and Buitrón, G and Quintela-Baluja, M and Graham, DW and Morales-Espinosa, R and Carrillo-Reyes, J}, title = {Exploring resistomes and microbiomes in pilot-scale microalgae-bacteria wastewater treatment systems for use in low-resource settings.}, journal = {The Science of the total environment}, volume = {882}, number = {}, pages = {163545}, doi = {10.1016/j.scitotenv.2023.163545}, pmid = {37080313}, issn = {1879-1026}, mesh = {Humans ; Waste Disposal, Fluid ; *Microalgae/metabolism ; Wastewater ; Bacteria/genetics ; Anti-Bacterial Agents/metabolism ; *Water Purification ; *Microbiota ; Genes, Bacterial ; }, abstract = {Antibiotic resistance genes (ARGs) released into the environment are an emerging human and environmental health concern, including ARGs spread in wastewater treatment effluents. In low-to-middle income countries (LMICs), an alternate wastewater treatment option instead of conventional systems are low-energy, high-rate algal ponds (HRAP) that use microalgae-bacteria aggregates (MABA) for waste degradation. Here we studied the robustness of ARG removal in MABA-based pilot-scale outdoor systems for 140 days of continuous operation. The HRAP system successfully removed 73 to 88 % chemical oxygen demand and up to 97.4 % ammonia, with aggregate size increasing over operating time. Fourteen ARG classes were identified in the HRAP influent, MABA, and effluent using metagenomics, with the HRAP process reducing total ARG abundances by up to 5-fold from influent to effluent. Parallel qPCR analyses showed the HRAP system significantly reduced exemplar ARGs (p < 0.05), with 1.2 to 4.9, 2.7 to 6.3, 0 to 1.5, and 1.2 to 4.8 log-removals for sul1, tetQ, blaKPC, and intl1 genes, respectively. Sequencing of influent, effluent and MABAs samples showed associated microbial communities differed significantly, with influent communities by Enterobacteriales (clinically relevant ARGs carrying bacteria), which were less evident in MABA and effluent. In this sense, such bacteria might be excluded from MABA due to their good settling properties and the presence of antimicrobial peptides. Microalgae-bacteria treatment systems steadily reduced ARGs from wastewater during operation time, using sunlight as the energetic driver, making them ideal for use in LMIC wastewater treatment applications.}, } @article {pmid37080303, year = {2023}, author = {Yang, JT and Xiao, DY and Zhang, LJ and Chen, HX and Zheng, XR and Xu, XL and Jiang, HX}, title = {Antimicrobial resistome during the transition from an integrated to a monoculture aquaculture farm in southern China.}, journal = {The Science of the total environment}, volume = {882}, number = {}, pages = {163511}, doi = {10.1016/j.scitotenv.2023.163511}, pmid = {37080303}, issn = {1879-1026}, mesh = {Animals ; Humans ; *Genes, Bacterial ; *Angiotensin Receptor Antagonists/analysis ; Drug Resistance, Microbial/genetics ; Angiotensin-Converting Enzyme Inhibitors/analysis ; Bacteria/genetics ; Aquaculture/methods ; Anti-Bacterial Agents/analysis ; Water/analysis ; China ; }, abstract = {Integrated and monoculture freshwater aquaculture systems are often regarded as important reservoirs for antimicrobial resistance genes (ARGs) and antimicrobial resistance bacteria (ARBs), yet only a few studies have assessed differences in the antimicrobial resistome and antibiotic residues between aquaculture modes. In this study, a metagenomic approach was used to comprehensively explore the dynamic patterns and potential transmission mechanisms of ARGs in ducks, human workers, fish, water and sediments during the transition from an integrated to a monoculture freshwater aquaculture mode and to investigate the associations of ARGs with potential hosts in microbial communities using network analysis and a binning approach. The results showed that the abundance and diversity of ARGs were higher under integrated fish-duck farming than in single fish ponds. During the transition from an integrated to a monoculture aquaculture farm, ARGs in workers and sediments were not easily removed. However, ARGs in the aquatic environment underwent regular changes. In addition, duck manure was probably the most dominant source of ARGs in the duck farm environment. Network analysis indicated that Escherichia spp. were the most dominant hosts of ARGs. Variation partitioning analysis (VPA) showed that in water samples, the bacterial community played an important role in the ARG profile. In addition, we identified a potential risk of the presence of highly virulent and antimicrobial-resistant Klebsiella pneumoniae in workers. These results help assess the risk of ARG transmission in integrated and monoculture aquaculture farms and suggest that we should strengthen the monitoring of long-term resistance in integrated aquaculture environments.}, } @article {pmid37080265, year = {2023}, author = {Wu, YL and Hu, SF and Zhang, XL and Wang, HM and Pan, HY and Liu, GH and Deng, YP}, title = {Complete bacterial profile and potential pathogens of cat fleas Ctenocephalides felis.}, journal = {Acta tropica}, volume = {243}, number = {}, pages = {106923}, doi = {10.1016/j.actatropica.2023.106923}, pmid = {37080265}, issn = {1873-6254}, mesh = {Animals ; Humans ; Mice ; Cats ; *Ctenocephalides/genetics ; *Flea Infestations/veterinary/parasitology ; *Rickettsia felis/genetics ; *Siphonaptera ; Bacteria/genetics ; *Felis ; *Cat Diseases ; }, abstract = {Fleas are important ectoparasites and vectors associated with a wide range of pathogenic diseases, posing threats to public health concerns, especially cat fleas that spread worldwide. Understanding the microbial components is essential due to cat fleas are capable of transmitting pathogens to humans, causing diseases like plague and murine typhus. In the present study, metagenomic next-generation sequencing was applied to obtain the complete microbiota and related functions in the gut of Ctenocephalides felis. A total of 1,870 species was taxonomically recognized including 1,407 bacteria, 365 eukaryotes, 69 viruses, and 29 archaea. Proteobacteria was the dominant phylum among the six samples. Pathogens Rickettsia felis, Acinetobacter baumannii, Coxiella burnetii, and Anaplasma phagocytophilum were taxonomically identified and had high abundances in all samples. The resistance gene MexD was predominant in microbial communities of all cat fleas. We also performed epidemiological surveys of pathogens R. felis, A. baumannii, C. burnetii, and A. phagocytophilum among 165 cat fleas collected from seven provinces in China, while only the DNAs of R. felis (38/165, 23.03%) and C. burnetii (2/165, 1.21%) were obtained. The data provide new insight and understanding of flea intestinal microbiota and support novel information for preventing and controlling fleas and their transmitted diseases.}, } @article {pmid37080086, year = {2023}, author = {Usié, A and Leão, C and Gaspar, D and Monteiro, H and Tábuas, L and Bettencourt, E and Caetano, P and Padre, L and Carolino, N and Ramos, AM and de Matos, C and Branco, S}, title = {A metagenomics approach to characterize the footrot microbiome in Merino sheep.}, journal = {Veterinary microbiology}, volume = {281}, number = {}, pages = {109745}, doi = {10.1016/j.vetmic.2023.109745}, pmid = {37080086}, issn = {1873-2542}, mesh = {Animals ; Sheep ; *Sheep Diseases/microbiology ; *Foot Rot/microbiology ; Fusobacterium necrophorum ; *Dichelobacter nodosus/genetics ; Bacteria/genetics ; Sheep, Domestic ; *Microbiota/genetics ; *Gram-Negative Bacterial Infections/microbiology/veterinary ; }, abstract = {In the Portuguese Alentejo region, Merino sheep breed is the most common breed, reared for the production of meat, dairy, and wool. Footrot is responsible for lameness, decreased animal welfare, and higher production losses, generating a negative economic impact. The disease is caused by Dichelobacter nodosus that interacts with the sheep foot microbiome, to date largely uncharacterized. In fact, Dichelobacter nodosus is not able to induce footrot by itself being required the presence of a second pathogen known as Fusobacterium necrophorum. To understand and characterize the footrot microbiome dynamics of different footrot lesion scores, a whole metagenome sequencing (WMGS) approach was used. Foot tissue samples were collected from 212 animals with different degrees of footrot lesion scores, ranging from 0 to 5. Distinct bacterial communities were associated with feet with different footrot scores identifying a total of 63 phyla and 504 families. As the severity of footrot infection increases the microorganisms' diversity decreases triggering a shift in the composition of the microbiome from a dominant gram-positive in mild stages to a dominant gram-negative in the severe stages. Several species previously associated with footrot and other polymicrobial diseases affecting the epidermis and provoking inflammatory responses such as Treponema spp., Staphylococcus spp., Streptococcus spp. and Campylobacter spp. were identified proliferating along with the lesions' severity. Although these bacteria are not able to initiate footrot, several evidences have been described supporting their association with the severity and incidence increase of footrot lesions caused by Dichelobacter nodosus and Fusobacterium necrophorum. Further investigation is required to establish the roles of particular taxa and identify which of them play a role in the disease process and which are opportunistic pathogens.}, } @article {pmid37079883, year = {2023}, author = {Gollnisch, R and Wallenius, J and Gribble, KE and Ahrén, D and Rengefors, K}, title = {SAG-RAD: A Method for Single-Cell Population Genomics of Unicellular Eukaryotes.}, journal = {Molecular biology and evolution}, volume = {40}, number = {5}, pages = {}, pmid = {37079883}, issn = {1537-1719}, mesh = {*Metagenomics ; *Eukaryota/genetics ; Genomics/methods ; Genome ; Sequence Analysis, DNA/methods ; }, abstract = {Sequencing of reduced representation libraries enables genotyping of many individuals for population genomic studies. However, high amounts of DNA are required, and the method cannot be applied directly on single cells, preventing its use on most microbes. We developed and implemented the analysis of single amplified genomes followed by restriction-site-associated DNA sequencing to bypass labor-intensive culturing and to avoid culturing bias in population genomic studies of unicellular eukaryotes. This method thus opens the way for addressing important questions about the genetic diversity, gene flow, adaptation, dispersal, and biogeography of hitherto unexplored species.}, } @article {pmid37079385, year = {2023}, author = {Vadaq, N and Zhang, Y and Vos, WA and Groenendijk, AL and Blaauw, MJ and van Eekeren, LE and Jacobs-Cleophas, M and van de Wijer, L and Dos Santos, JC and Gasem, MH and Joosten, LA and Netea, MG and de Mast, Q and Fu, J and van der Ven, AJ and Matzaraki, V}, title = {High-throughput proteomic analysis reveals systemic dysregulation in virally suppressed people living with HIV.}, journal = {JCI insight}, volume = {8}, number = {11}, pages = {}, pmid = {37079385}, issn = {2379-3708}, mesh = {Humans ; Proteomics ; *HIV Infections/complications/drug therapy ; Inflammation/complications ; C-Reactive Protein ; *Cardiovascular Diseases ; }, abstract = {BACKGROUNDPeople living with HIV (PLHIV) receiving antiretroviral therapy (ART) exhibit persistent immune dysregulation and microbial dysbiosis, leading to development of cardiovascular diseases (CVDs). We initially compared plasma proteomic profiles between 205 PLHIV and 120 healthy control participants (HCs) and validated the results in an independent cohort of 639 PLHIV and 99 HCs. Differentially expressed proteins (DEPs) were then associated to microbiome data. Finally, we assessed which proteins were linked with CVD development in PLHIV.METHODSProximity extension assay technology was used to measure 1,472 plasma proteins. Markers of systemic inflammation (C-reactive protein, D-dimer, IL-6, soluble CD14, and soluble CD163) and microbial translocation (IFABP) were measured by ELISA, and gut bacterial species were identified using shotgun metagenomic sequencing. Baseline CVD data were available for all PLHIV, and 205 PLHIV were recorded for development of CVD during a 5-year follow-up.RESULTSPLHIV receiving ART had systemic dysregulation of protein concentrations, compared with HCs. Most of the DEPs originated from the intestine and lymphoid tissues and were enriched in immune- and lipid metabolism-related pathways. DEPs originating from the intestine were associated with specific gut bacterial species. Finally, we identified upregulated proteins in PLHIV (GDF15, PLAUR, RELT, NEFL, COL6A3, and EDA2R), unlike most markers of systemic inflammation, associated with the presence and risk of developing CVD during 5-year follow-up.CONCLUSIONOur findings suggest a systemic dysregulation of protein concentrations in PLHIV; some proteins were associated with CVD development. Most DEPs originated from the gut and were related to specific gut bacterial species.TRIAL REGISTRATIONClinicalTrials.gov NCT03994835.FUNDINGAIDS-fonds (P-29001), ViiV healthcare grant (A18-1052), Spinoza Prize (NWO SPI94-212), European Research Council (ERC) Advanced grant (grant 833247), and Indonesia Endowment Fund for Education.}, } @article {pmid37079280, year = {2023}, author = {Thompson, TP and Gilmore, BF}, title = {Exploring halophilic environments as a source of new antibiotics.}, journal = {Critical reviews in microbiology}, volume = {}, number = {}, pages = {1-30}, doi = {10.1080/1040841X.2023.2197491}, pmid = {37079280}, issn = {1549-7828}, abstract = {Microbial natural products from microbes in extreme environments, including haloarchaea, and halophilic bacteria, possess a huge capacity to produce novel antibiotics. Additionally, enhanced isolation techniques and improved tools for genomic mining have expanded the efficiencies in the antibiotic discovery process. This review article provides a detailed overview of known antimicrobial compounds produced by halophiles from all three domains of life. We summarize that while halophilic bacteria, in particular actinomycetes, contribute the vast majority of these compounds the importance of understudied halophiles from other domains of life requires additional consideration. Finally, we conclude by discussing upcoming technologies- enhanced isolation and metagenomic screening, as tools that will be required to overcome the barriers to antimicrobial drug discovery. This review highlights the potential of these microbes from extreme environments, and their importance to the wider scientific community, with the hope of provoking discussion and collaborations within halophile biodiscovery. Importantly, we emphasize the importance of bioprospecting from communities of lesser-studied halophilic and halotolerant microorganisms as sources of novel therapeutically relevant chemical diversity to combat the high rediscovery rates. The complexity of halophiles will necessitate a multitude of scientific disciplines to unravel their potential and therefore this review reflects these research communities.}, } @article {pmid37078655, year = {2023}, author = {Yong, HYF and Pastula, DM and Kapadia, RK}, title = {Diagnosing viral encephalitis and emerging concepts.}, journal = {Current opinion in neurology}, volume = {36}, number = {3}, pages = {175-184}, doi = {10.1097/WCO.0000000000001155}, pmid = {37078655}, issn = {1473-6551}, mesh = {Humans ; *COVID-19 ; COVID-19 Testing ; *Encephalitis, Viral/diagnosis ; *Nervous System Diseases ; }, abstract = {PURPOSE OF REVIEW: This review offers a contemporary clinical approach to the diagnosis of viral encephalitis and discusses recent advances in the field. The neurologic effects of coronaviruses, including COVID-19, as well as management of encephalitis are not covered in this review.

RECENT FINDINGS: The diagnostic tools for evaluating patients with viral encephalitis are evolving quickly. Multiplex PCR panels are now in widespread use and allow for rapid pathogen detection and potentially reduce empiric antimicrobial exposure in certain patients, while metagenomic next-generation sequencing holds great promise in diagnosing challenging and rarer causes of viral encephalitis. We also review topical and emerging infections pertinent to neuroinfectious disease practice, including emerging arboviruses, monkeypox virus (mpox), and measles.

SUMMARY: Although etiological diagnosis remains challenging in viral encephalitis, recent advances may soon provide the clinician with additional tools. Environmental changes, host factors (such as ubiquitous use of immunosuppression), and societal trends (re-emergence of vaccine preventable diseases) are likely to change the landscape of neurologic infections that are considered and treated in clinical practice.}, } @article {pmid37078608, year = {2023}, author = {Fourgeaud, J and Lecuit, MM and Pérot, P and Bruneau, J and Regnault, B and Da Rocha, N and Bessaud, M and Picard, C and Jeziorski, É and Fournier, B and Levy, R and Marçais, A and Blanche, S and Frange, P and Fischer, A and Cavazzana, M and Ferroni, A and Jamet, A and Leruez-Ville, M and Eloit, M and Neven, B}, title = {Chronic Aichi Virus Infection As a Cause of Long-Lasting Multiorgan Involvement in Patients With Primary Immune Deficiencies.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {77}, number = {4}, pages = {620-628}, doi = {10.1093/cid/ciad237}, pmid = {37078608}, issn = {1537-6591}, mesh = {Humans ; *Kobuvirus/genetics ; Phylogeny ; Patients ; *Primary Immunodeficiency Diseases ; *Virus Diseases ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) was used to assess patients with primary or secondary immune deficiencies (PIDs and SIDs) who presented with immunopathological conditions related to immunodysregulation.

METHODS: Thirty patients with PIDs or SIDs who presented with symptoms related to immunodysregulation and 59 asymptomatic patients with similar PIDs or SIDs were enrolled. mNGS was performed on organ biopsy. Specific Aichi virus (AiV) reverse-transcription polymerase chain reaction (RT-PCR) was used to confirm AiV infection and screen the other patients. In situ hybridization (ISH) assay was done on AiV-infected organs to identify infected cells. Virus genotype was determined by phylogenetic analysis.

RESULTS: AiV sequences were detected using mNGS in tissue samples of 5 patients and by RT-PCR in peripheral samples of another patient, all of whom presented with PID and long-lasting multiorgan involvement, including hepatitis, splenomegaly, and nephritis in 4 patients. CD8+ T-cell infiltration was a hallmark of the disease. RT-PCR detected intermittent low viral loads in urine and plasma from infected patients but not from uninfected patients. Viral detection stopped after immune reconstitution obtained by hematopoietic stem cell transplantation. ISH demonstrated the presence of AiV RNA in hepatocytes (n = 1) and spleen tissue (n = 2). AiV belonged to genotype A (n = 2) or B (n = 3).

CONCLUSIONS: The similarity of the clinical presentation, the detection of AiV in a subgroup of patients suffering from immunodysregulation, the absence of AiV in asymptomatic patients, the detection of viral genome in infected organs by ISH, and the reversibility of symptoms after treatment argue for AiV causality.}, } @article {pmid37078491, year = {2023}, author = {Rehman, A and Pham, V and Seifert, N and Richard, N and Sybesma, W and Steinert, RE}, title = {The Polyunsaturated Fatty Acids Eicosapentaenoic Acid and Docosahexaenoic Acid, and Vitamin K1 Modulate the Gut Microbiome: A Study Using an In Vitro Shime Model.}, journal = {Journal of dietary supplements}, volume = {}, number = {}, pages = {1-19}, doi = {10.1080/19390211.2023.2198007}, pmid = {37078491}, issn = {1939-022X}, abstract = {Omega-3 polyunsaturated fatty acids (PUFAs) and vitamins exert multiple beneficial effects on host health, some of which may be mediated through the gut microbiome. We investigated the prebiotic potential of eicosapentaenoic acid (EPA), docosahexaenoic acid (DHA) and lipid-soluble phylloquinone (vitamin K1), each at 0.2x, 1x and 5x using the simulator of the human intestinal microbial ecosystem (SHIME®) to exclude in vivo systemic effects and host-microbe interactions.Microbial community composition and, diversity [shotgun metagenomic sequencing] and microbial activity [pH, gas pressure, and production of short-chain fatty acids (SCFAs)] were measured over a period of 48 h. Fermentations supernatants were used to investigate the effect on gut barrier integrity using a Caco-2/goblet cell co-culture model.We found that EPA, DHA and vitamin K1 increased alpha-diversity at 24 h when compared with control. Moreover, there was an effect on beta-diversity with changes in gut microbial composition, such as an increase in the Firmicutes/Bacteroidetes (F/B) ratio and a consistent increase in Veillonella and Dialister abundances with all treatments. DHA, EPA, and vitamin K1 also modulated metabolic activity of the gut microbiome by increasing total SCFAs which was related mainly to an increase in propionate (highest with EPA and vitamin K1 at 0.2x). Finally, we found that EPA and DHA increased gut barrier integrity with DHA at 1x and EPA at 5x (p < 0.05, respectively). In conclusion, our in vitro data further establish a role of PUFAs and vitamin K to modulate the gut microbiome with effects on the production of SCFAs and barrier integrity.}, } @article {pmid37078124, year = {2023}, author = {Vázquez, L and Cabrera-Rubio, R and Tamames, J and Mayo, B and Flórez, AB}, title = {Assessment of short-read shotgun sequencing and microbiome analysis of faecal samples to discriminate between equol producers and non-producers.}, journal = {Beneficial microbes}, volume = {}, number = {}, pages = {1-14}, doi = {10.3920/BM2022.0027}, pmid = {37078124}, issn = {1876-2891}, abstract = {Among the isoflavones and isoflavone-derived metabolites, equol, which in the human gut is synthesised from daidzein by minority bacterial populations, shows the strongest estrogenic and antioxidant activity. The beneficial effects on human health of isoflavone consumption might be partially or indeed totally attributable to this equol. Although some of the bacterial strains involved in its formation have been identified, the interplay between the composition and functionality of the gut microbiota and equol producer phenotype has hardly been studied. In this study, after shotgun metagenomic sequencing, different pipelines for the taxonomic and functional annotation of sequencing data were used in the search for similarities and differences in the faecal metagenome of equol-producing (n=3) and non-producing (n=2) women, with special focus on equol-producing taxa and their equol-associated genes. The taxonomic profiles of the samples differed significantly depending on the analytical method followed, although the microbial diversity detected by each tool was very similar at the phylum, genus and species levels. Equol-producing taxa were detected in both equol producers and non-producers, but no correlation between the abundance of equol-producing taxa and the equol producing/non-producing phenotype was found. Indeed, functional metagenomic analysis was unable to identify the genes involved in equol production, even in samples from equol producers. By aligning equol operons with the collected metagenomics data, a small number of reads mapping to equol-associated sequences were recognised in samples from both equol producers and equol non-producers, but only two reads mapping onto equol reductase-encoding genes in a sample from an equol producer. In conclusion, the taxonomic analysis of metagenomic data might not be suitable for detecting and quantifying equol-producing microbes in human faeces. Functional analysis of the data might provide an alternative. However, to detect the genetic makeup of the minority gut populations, more extensive sequencing than that achieved in the present study might be required.}, } @article {pmid37077687, year = {2023}, author = {Guzmán-Armenteros, TM and Ramos-Guerrero, LA and Guerra, LS and Weckx, S and Ruales, J}, title = {Optimization of cacao beans fermentation by native species and electromagnetic fields.}, journal = {Heliyon}, volume = {9}, number = {4}, pages = {e15065}, pmid = {37077687}, issn = {2405-8440}, abstract = {Acid and bitter notes of the cocoa clone Cacao Castro Naranjal 51 (CCN 51) negatively affect the final quality of the chocolate. Thence, the fermentative process of cocoa beans using native species and electromagnetic fields (EMF) was carried out to evaluate the effect on the yield and quality of CCN 51 cocoa beans. The variables magnetic field density (D), exposure time (T), and inoculum concentration (IC) were optimized through response surface methodology to obtain two statistically validated second-order models, explaining 88.39% and 92.51% of the variability in the yield and quality of the beans, respectively. In the coordinate: 5 mT(D), 22.5 min (T), and 1.6% (CI), yield and bean quality improved to 110% and 120% above the control (without magnetic field). The metagenomic analysis showed that the changes in the microbial communities favored the aroma profile at low and intermediate field densities (5-42 mT) with high yields and floral, fruity, and nutty notes. Conversely, field densities (80 mT) were evaluated with low yields and undesirable notes of acidity and bitterness. The findings revealed that EMF effectively improves the yield and quality of CCN 51 cocoa beans with future applications in the development and quality of chocolate products.}, } @article {pmid37077683, year = {2023}, author = {Alves, LF and Bortolucci, J and Reginato, V and Guazzaroni, ME and Mussatto, SI}, title = {Improving Saccharomyces cerevisiae acid and oxidative stress resistance using a prokaryotic gene identified by functional metagenomics.}, journal = {Heliyon}, volume = {9}, number = {4}, pages = {e14838}, pmid = {37077683}, issn = {2405-8440}, abstract = {Innovations in obtaining products from lignocellulosic biomass have been largely based on the improvement of microorganisms and enzymes capable of degrading these materials. To complete the whole process, microorganisms must be able to ferment the resulting sugars and tolerate high concentrations of product, osmotic pressure, ion toxicity, temperature, toxic compounds from lignocellulose pretreatment, low pH, and oxidative stress. In this work, we engineered laboratory and industrial Saccharomyces cerevisiae strains by combining a gene (hu) recovered from a metagenomic approach with different native and synthetic promoters to obtain improved acid and oxidative stress resistance. Laboratorial strains harboring hu gene under the control of the synthetic stress responsive PCCW14v5 showed increased survival rates after 2 h exposure to pH 1.5. The hu gene was also able to significantly enhance the tolerance of the industrial strain to high concentrations of H2O2 when combined with PTEF1, PYGP1 or PYGP1v7 after 3 h exposure.}, } @article {pmid37077253, year = {2023}, author = {He, Y and Wang, S and Deng, J and Pu, Q and Chen, H and Huang, L}, title = {Chlamydia psittaci Pneumonia Complicated with Lower Extremity Atherosclerotic Occlusive Disease.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {2141-2145}, pmid = {37077253}, issn = {1178-6973}, abstract = {Chlamydia is a zoonotic pathogen that mainly infects poultry and pet birds. This Gram-negative obligate intracellular parasite also causes human psittacosis, the severity of which varies from mild flu-like symptoms to life-threatening severe pneumonia, including sepsis, acute respiratory distress syndrome, and multiple organ failure. Inhalation of aerosols from contaminated bird excreta through the respiratory tract is the main route of transmission to humans. Here, we present a case of Chlamydia psittaci pneumonia accompanied by lower extremity atherosclerotic occlusive disease. A 48-year-old man was admitted to the emergency department with a four-day history of cough and dyspnea. A detailed history revealed his contact with domestic pigeons. The results of metagenomic next-generation sequencing of bronchoalveolar lavage fluid suggested C. psittaci infection. Antibacterial agents were switched to targeted doxycycline, but in the next week, skin examination revealed acrocyanosis of both lower extremities, and the remarkable palpable purpura progressively worsened. Re-examination of the lower extremity vascular ultrasound suggested left dorsalis pedis artery occlusion and right peroneal vein thrombosis, which resulted in the amputation of both legs. This case is the first report of C. psittaci pneumonia combined with arterioocclusive sclerosis of both lower extremities.}, } @article {pmid37076818, year = {2023}, author = {Gao, P and Zhang, X and Huang, X and Chen, Z and Marietou, A and Holmkvist, L and Qu, L and Finster, K and Gong, X}, title = {Genomic insight of sulfate reducing bacterial genus Desulfofaba reveals their metabolic versatility in biogeochemical cycling.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {209}, pmid = {37076818}, issn = {1471-2164}, support = {42006134//National Natural Science Foundation of China/ ; 42106153//National Natural Science Foundation of China/ ; 91951202//National Natural Science Foundation of China/ ; }, mesh = {*Sulfates/metabolism ; Phylogeny ; *Carbon Dioxide/metabolism ; Bacteria/genetics ; Genomics ; Oxidation-Reduction ; Carbon/metabolism ; }, abstract = {BACKGROUND: Sulfate-reducing bacteria (SRB) drive the ocean sulfur and carbon cycling. They constitute a diverse phylogenetic and physiological group and are widely distributed in anoxic marine environments. From a physiological viewpoint, SRB's can be categorized as complete or incomplete oxidizers, meaning that they either oxidize their carbon substrate completely to CO2 or to a stoichiometric mix of CO2 and acetate. Members of Desulfofabaceae family are incomplete oxidizers, and within that family, Desulfofaba is the only genus with three isolates that are classified into three species. Previous physiological experiments revealed their capability of respiring oxygen.

RESULTS: Here, we sequenced the genomes of three isolates in Desulfofaba genus and reported on a genomic comparison of the three species to reveal their metabolic potentials. Based on their genomic contents, they all could oxidize propionate to acetate and CO2. We confirmed their phylogenetic position as incomplete oxidizers based on dissimilatory sulfate reductase (DsrAB) phylogeny. We found the complete pathway for dissimilatory sulfate reduction, but also different key genes for nitrogen cycling, including nitrogen fixation, assimilatory nitrate/nitrite reduction, and hydroxylamine reduction to nitrous oxide. Their genomes also contain genes that allow them to cope with oxygen and oxidative stress. They have genes that encode for diverse central metabolisms for utilizing different substrates with the potential for more strains to be isolated in the future, yet their distribution is limited.

CONCLUSIONS: Results based on marker gene search and curated metagenome assembled genomes search suggest a limited environmental distribution of this genus. Our results reveal a large metabolic versatility within the Desulfofaba genus which establishes their importance in biogeochemical cycling of carbon in their respective habitats, as well as in the support of the entire microbial community through releasing easily degraded organic matters.}, } @article {pmid37076623, year = {2023}, author = {Gaïa, M and Meng, L and Pelletier, E and Forterre, P and Vanni, C and Fernandez-Guerra, A and Jaillon, O and Wincker, P and Ogata, H and Krupovic, M and Delmont, TO}, title = {Mirusviruses link herpesviruses to giant viruses.}, journal = {Nature}, volume = {616}, number = {7958}, pages = {783-789}, pmid = {37076623}, issn = {1476-4687}, mesh = {Animals ; Ecosystem ; Eukaryota/virology ; Genome, Viral/genetics ; *Giant Viruses/classification/genetics ; *Herpesviridae/classification/genetics ; *Phylogeny ; *Plankton/virology ; Metagenomics ; Metagenome ; Sunlight ; *Oceans and Seas ; Transcription, Genetic/genetics ; *Aquatic Organisms/virology ; }, abstract = {DNA viruses have a major influence on the ecology and evolution of cellular organisms[1-4], but their overall diversity and evolutionary trajectories remain elusive[5]. Here we carried out a phylogeny-guided genome-resolved metagenomic survey of the sunlit oceans and discovered plankton-infecting relatives of herpesviruses that form a putative new phylum dubbed Mirusviricota. The virion morphogenesis module of this large monophyletic clade is typical of viruses from the realm Duplodnaviria[6], with multiple components strongly indicating a common ancestry with animal-infecting Herpesvirales. Yet, a substantial fraction of mirusvirus genes, including hallmark transcription machinery genes missing in herpesviruses, are closely related homologues of giant eukaryotic DNA viruses from another viral realm, Varidnaviria. These remarkable chimaeric attributes connecting Mirusviricota to herpesviruses and giant eukaryotic viruses are supported by more than 100 environmental mirusvirus genomes, including a near-complete contiguous genome of 432 kilobases. Moreover, mirusviruses are among the most abundant and active eukaryotic viruses characterized in the sunlit oceans, encoding a diverse array of functions used during the infection of microbial eukaryotes from pole to pole. The prevalence, functional activity, diversification and atypical chimaeric attributes of mirusviruses point to a lasting role of Mirusviricota in the ecology of marine ecosystems and in the evolution of eukaryotic DNA viruses.}, } @article {pmid37075861, year = {2023}, author = {He, T and Jin, M and Cui, P and Sun, X and He, X and Huang, Y and Xiao, X and Zhang, T and Zhang, X}, title = {Environmental viromes reveal the global distribution signatures of deep-sea DNA viruses.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2023.04.009}, pmid = {37075861}, issn = {2090-1224}, abstract = {INTRODUCTION: Viruses are abundant and ecologically significant in marine ecosystems. However, the virome of deep-sea sediments is not extensively investigated.

OBJECTIVES: To explore the distribution pattern of deep-sea viruses on a global scale, the viromes of DNA viruses isolated from 138 sediments of 5 deep-sea ecosystems were characterized.

METHODS: The viral particles were purified from each sediment sample. Then the viral DNAs were extracted and subjected to viral metagenomic analysis.

RESULTS: Here, we constructed a global deep-sea environmental virome dataset by analyzing the viral DNA of 138 sediment samples. A total of 347,737 viral operational taxonomic units (vOTUs) were identified, of which 84.94% were hitherto unknown, indicating that deep sea was a reservoir of novel DNA viruses. Furthermore, circular viral genome analysis revealed 98,581 complete genomes. The classified vOTUs included eukaryotic (44.55%) and prokaryotic (25.75%) viruses, and were taxonomically assigned to 63 viral families. The composition and abundance of the deep-sea sediment viromes were dependent on the deep-sea ecosystem as opposed to geographical region. Further analysis revealed that the viral community differentiation in different deep-sea ecosystems was driven by the virus-mediated energy metabolism.

CONCLUSION: Our findings showed that deep-sea ecosystems are a reservoir of novel DNA viruses and the viral community is shaped by the environmental characteristics of deep-sea ecosystems, thus presenting critical information for determining the ecological significance of viruses in global deep-sea ecosystems.}, } @article {pmid37075636, year = {2023}, author = {Wang, R and An, Z and Fan, L and Zhou, Y and Su, X and Zhu, J and Zhang, Q and Chen, C and Lin, H and Sun, F}, title = {Effect of quorum quenching on biofouling control and microbial community in membrane bioreactors by Brucella sp. ZJ1.}, journal = {Journal of environmental management}, volume = {339}, number = {}, pages = {117961}, doi = {10.1016/j.jenvman.2023.117961}, pmid = {37075636}, issn = {1095-8630}, mesh = {Quorum Sensing ; *Biofouling/prevention & control ; Extracellular Polymeric Substance Matrix ; *Brucella ; Bioreactors/microbiology ; *Microbiota ; Membranes, Artificial ; }, abstract = {Quorum quenching (QQ) has been demonstrated to be a novel technique for controlling biofouling in membrane bioreactors (MBRs), as it can significantly inhibit biofilm formation by disrupting quorum sensing (QS). The exploration of new QQ bacterial strains and the evaluation of their performance in mitigating membrane fouling in MBR systems is significant. In this study, an efficient QQ strain, Brucella sp. ZJ1 was encapsulated in alginate beads and evaluated for its ability to mitigate biofouling. The findings revealed that MBR with QQ beads extended the operation time by 2-3 times without affecting pollutant degradation. QQ beads maintained approximately 50% QQ activity after more than 50 days operation, indicating a long-lasting and endurable QQ effect. The QQ effect reduced extracellular polymeric substance (EPS) production especially in terms of polysaccharide and protein by more than 40%. QQ beads in the MBR also reduced the cake resistance and the irreversible resistance of membrane biofouling. Metagenomic sequencing suggests that QQ beads suppressed the QS effect and increased the abundance of QQ enzyme genes, ultimately inducing efficient membrane biofouling control.}, } @article {pmid37075471, year = {2023}, author = {Che Lah, EF and Ahamad, M and Dmitry, A and Md-Zain, BM and Yaakop, S}, title = {Metagenomic profile of the bacterial communities associated with Ixodes granulatus (Acari: Ixodidae): a potential vector of tick-borne diseases.}, journal = {Journal of medical entomology}, volume = {60}, number = {4}, pages = {753-768}, doi = {10.1093/jme/tjad044}, pmid = {37075471}, issn = {1938-2928}, mesh = {Humans ; Female ; Animals ; *Ixodes/microbiology ; *Ixodidae/microbiology ; Rickettsiales ; Ehrlichia ; *Rickettsia/genetics ; *Borrelia/genetics ; *Tick-Borne Diseases/microbiology ; }, abstract = {Ixodes granulatus Supino, 1897 (Acari: Ixodida) is one of Malaysia's most common hard ticks and is a potential vector for tick-borne diseases (TBDs). Despite its great public health importance, research on I. granulatus microbial communities remains largely unexplored. Therefore, this study aimed to investigate the bacterial communities of on-host I. granulatus collected from three different recreational areas on the East Coast of Peninsular Malaysia using high throughput Next Generation Sequencing (NGS). A total of 9 females on-host I. granulatus were subjected to metabarcoding analysis targeting V3-V4 regions of 16S ribosomal RNA (rRNA) using the Illumina MiSeq platform. This study identified 15 bacterial phyla corresponding to 19 classes, 54 orders, and 90 families from 435 amplicon sequence variants (ASVs), revealing a diverse bacterial community profile. Together with 130 genera assigned, local I. granulatus harbored 4 genera of pathogens, i.e., Rickettsia da Rocha Lima, 1916 (Rickettsiales: Rickettsiaceae) (58.6%), Borrelia Swellengrebel 1907 (Spirochaetales: Borreliaceae) (31.6%), Borreliella Adeolu and Gupta 2015 (Spirochaetales: Borreliaceae) (0.6%), and Ehrlichia Cowdria Moshkovski 1947 (Rickettsiales: Ehrlichiaceae) (39.9%). Some endosymbiont bacteria, such as Coxiella (Philip, 1943) (Legionellales: Coxiellaceae), Wolbachia Hertig 1936 (Rickettsiales: Ehrlichiaceae), and Rickettsiella Philip, 1956 (Legionellales: Coxiellaceae), were also detected at very low abundance. Interestingly, this study reported the co-infection of Borrelia and Ehrlichia for the first time, instilling potential health concerns in the context of co-transmission to humans, especially in areas with a high population of I. granulatus. This study successfully characterized the tick microbiome and provided the first baseline data of I. granulatus bacterial communities in Malaysia. These results support the need for way-forward research on tick-associated bacteria using NGS, focusing on medically important species toward TBD prevention.}, } @article {pmid37074549, year = {2023}, author = {Gureev, AP and Silachev, DN and Sadovnikova, IS and Krutskikh, EP and Chernyshova, EV and Volodina, DE and Samoylova, NA and Potanina, DV and Burakova, IY and Smirnova, YD and Popov, VN and Plotnikov, EY}, title = {The Ketogenic Diet but not Hydroxycitric Acid Keeps Brain Mitochondria Quality Control and mtDNA Integrity Under Focal Stroke.}, journal = {Molecular neurobiology}, volume = {60}, number = {8}, pages = {4288-4303}, pmid = {37074549}, issn = {1559-1182}, support = {21-75-30009//Russian science foundation/ ; }, mesh = {Mice ; Animals ; *DNA, Mitochondrial/genetics/metabolism ; *Diet, Ketogenic ; Mitochondria/metabolism ; Brain/metabolism ; Liver/metabolism ; }, abstract = {Mitochondrial dysfunction in the ischemic brain is one of the hallmarks of stroke. Dietary interventions such as the ketogenic diet and hydroxycitric acid supplementation (a caloric restriction mimetic) may potentially protect neurons from mitochondrial damage induced by focal stroke in mice. We showed that in control mice, the ketogenic diet and the hydroxycitric acid did not impact significantly on the mtDNA integrity and expression of genes involved in the maintenance of mitochondrial quality control in the brain, liver, and kidney. The ketogenic diet changed the bacterial composition of the gut microbiome, which via the gut-brain axis may affect the increase in anxiety behavior and reduce mice mobility. The hydroxycitric acid causes mortality and suppresses mitochondrial biogenesis in the liver. Focal stroke modelling caused a significant decrease in the mtDNA copy number in both ipsilateral and contralateral brain cortex and increased the levels of mtDNA damage in the ipsilateral hemisphere. These alterations were accompanied by a decrease in the expression of some of the genes involved in maintaining mitochondrial quality control. The ketogenic diet consumption before stroke protects mtDNA in the ipsilateral cortex, probably via activation of the Nrf2 signaling. The hydroxycitric acid, on the contrary, increased stroke-induced injury. Thus, the ketogenic diet is the most preferred variant of dietetic intervention for stroke protection compared with the hydroxycitric acid supplementation. Our data confirm some reports about hydroxycitric acid toxicity, not only for the liver but also for the brain under stroke condition.}, } @article {pmid37074327, year = {2023}, author = {Elnaggar, JH and Lammons, JW and Taylor, CM and Toh, E and Ardizzone, CM and Dong, A and Aaron, KJ and Luo, M and Tamhane, A and Lefkowitz, EJ and Quayle, AJ and Nelson, DE and Muzny, CA}, title = {Characterization of Vaginal Microbial Community Dynamics in the Pathogenesis of Incident Bacterial Vaginosis, a Pilot Study.}, journal = {Sexually transmitted diseases}, volume = {50}, number = {8}, pages = {523-530}, pmid = {37074327}, issn = {1537-4521}, support = {UL1 TR003096/TR/NCATS NIH HHS/United States ; K23 AI106957/AI/NIAID NIH HHS/United States ; R01 AI118860/AI/NIAID NIH HHS/United States ; R01 AI146065/AI/NIAID NIH HHS/United States ; P20 GM103424/GM/NIGMS NIH HHS/United States ; }, mesh = {Female ; Humans ; *Vaginosis, Bacterial/diagnosis ; Pilot Projects ; Vagina/microbiology ; Gardnerella vaginalis/genetics ; *Microbiota ; Bacteria/genetics ; Lactobacillus/genetics ; }, abstract = {BACKGROUND: Despite more than 60 years of research, the etiology of bacterial vaginosis (BV) remains controversial. In this pilot study, we used shotgun metagenomic sequencing to characterize vaginal microbial community changes before the development of incident BV (iBV).

METHODS: A cohort of African American women with a baseline healthy vaginal microbiome (no Amsel criteria, Nugent score 0-3 with no Gardnerella vaginalis morphotypes) were followed for 90 days with daily self-collected vaginal specimens for iBV (≥2 consecutive days of a Nugent score of 7-10). Shotgun metagenomic sequencing was performed on select vaginal specimens from 4 women, every other day for 12 days before iBV diagnosis. Sequencing data were analyzed through Kraken2 and bioBakery 3 workflows, and specimens were classified into community state types. Quantitative polymerase chain reaction was performed to compare the correlation of read counts with bacterial abundance.

RESULTS: Common BV-associated bacteria such as G. vaginalis , Prevotella bivia , and Fannyhessea vaginae were increasingly identified in the participants before iBV. Linear modeling indicated significant increases in G. vaginalis and F . vaginae relative abundance before iBV, whereas the relative abundance of Lactobacillus species declined over time. The Lactobacillus species decline correlated with the presence of Lactobacillus phages. We observed enrichment in bacterial adhesion factor genes on days before iBV. There were also significant correlations between bacterial read counts and abundances measured by quantitative polymerase chain reaction.

CONCLUSIONS: This pilot study characterizes vaginal community dynamics before iBV and identifies key bacterial taxa and mechanisms potentially involved in the pathogenesis of iBV.}, } @article {pmid37074196, year = {2023}, author = {Hu, G and Jiang, F and Luo, Q and Zong, K and Dong, L and Mei, G and Du, H and Dong, H and Song, Q and Song, J and Xia, Z and Gao, C and Han, J}, title = {Diversity Analysis of Tick-Borne Viruses from Hedgehogs and Hares in Qingdao, China.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0534022}, pmid = {37074196}, issn = {2165-0497}, mesh = {Animals ; *Hares ; Hedgehogs ; Phylogeny ; *Ticks ; *Ixodidae ; *Viruses ; *RNA Viruses/genetics ; }, abstract = {Tick-borne viruses (TBVs) have attracted increasingly global public health attention. In this study, the viral compositions of five tick species, Haemaphysalis flava, Rhipicephalus sanguineus, Dermacentor sinicus, Haemaphysalis longicornis, and Haemaphysalis campanulata, from hedgehogs and hares in Qingdao, China, were profiled via metagenomic sequencing. Thirty-six strains of 10 RNA viruses belonging to 4 viral families, including 3 viruses of Iflaviridae, 4 viruses of Phenuiviridae, 2 viruses of Nairoviridae, and 1 virus of Chuviridae, were identified in five tick species. Three novel viruses of two families, namely, Qingdao tick iflavirus (QDTIFV) of the family of Iflaviridae and Qingdao tick phlebovirus (QDTPV) and Qingdao tick uukuvirus (QDTUV) of the family of Phenuiviridae, were found in this study. This study shows that ticks from hares and hedgehogs in Qingdao harbored diverse viruses, including some that can cause emerging infectious diseases, such as Dabie bandavirus. Phylogenetic analysis revealed that these tick-borne viruses were genetically related to viral strains isolated previously in Japan. These findings shed new light on the cross-sea transmission of tick-borne viruses between China and Japan. IMPORTANCE Thirty-six strains of 10 RNA viruses belonging to 4 viral families, including 3 viruses of Iflaviridae, 4 viruses of Phenuiviridae, 2 viruses of Nairoviridae, and 1 virus of Chuviridae, were identified from five tick species in Qingdao, China. A diversity of tick-borne viruses from hares and hedgehogs in Qingdao was found in this study. Phylogenetic analysis showed that most of these TBVs were genetically related to Japanese strains. These findings indicate the possibility of the cross-sea transmission of TBVs between China and Japan.}, } @article {pmid37074059, year = {2023}, author = {Zhang, D and You, F and He, Y and Te, SH and Gin, KY}, title = {Corrected and Republished from: "Isolation and Characterization of the First Freshwater Cyanophage Infecting Pseudanabaena".}, journal = {Journal of virology}, volume = {97}, number = {5}, pages = {e0040523}, pmid = {37074059}, issn = {1098-5514}, support = {Karina Yew-Hoong Gin E2S2-CREATE Phase 2//National Research Foundation Singapore (NRF)/ ; }, abstract = {Cyanobacteria are the major primary producers in both freshwater and marine environments. However, the majority of freshwater cyanophages remain unknown due to the limited number of cyanophage isolates. In this study, we present a novel lytic freshwater cyanophage, PA-SR01, which was isolated from the Singapore Serangoon Reservoir. To our knowledge, this is the first isolate of a cyanophage that has been found to infect the cyanobacterium Pseudanabaena. PA-SR01 has a narrow host range, a short latent period, and is chloroform sensitive. PA-SR01 is a member of Siphoviridae with a long noncontractile tail. It is a double-stranded DNA virus with a 137,012-bp genome. Functional annotation for the predicted open reading frames (ORFs) of the PA-SR01 genome identified genes with putative functions related to DNA metabolism, structural proteins, lysis, host-derived metabolic genes, and DNA packaging. Out of 166 predicted ORFs, only 17 ORFs have homology with genes with known function. Phylogenetic analysis of the major capsid protein and terminase large subunit further suggests that phage PA-SR01 is evolutionary distinct from known cyanophages. Metagenomics sequence recruitment onto the PA-SR01 genome indicates that PA-SR01 represents a new evolutionary lineage of phage which shares considerable genetic similarities with phage sequences in aquatic environments and could play key ecological roles. IMPORTANCE This study presents the isolation of the very first freshwater cyanophage, PA-SR01, that infects Pseudanabaena, and fills an important knowledge gap on freshwater cyanophages as well as cyanophages infecting Pseudanabaena.}, } @article {pmid37073121, year = {2023}, author = {Sanchez-Cid, C and Keuschnig, C and Vogel, TM and Larose, C}, title = {Impact of in situ solar irradiation on snow bacterial communities and functional potential.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {6}, pages = {}, doi = {10.1093/femsec/fiad042}, pmid = {37073121}, issn = {1574-6941}, mesh = {*Snow/microbiology ; *Cold Climate ; Bacteria/genetics ; Svalbard ; }, abstract = {Polar regions are increasingly exposed to ultraviolet light due to ozone depletion. Snowpacks contain photochemically active particles that, when irradiated, can lead to the production and accumulation of reactive species that can induce oxidative stress on snow microorganisms. This could generate a selective pressure on snowpack bacteria. In this study, snow microcosms were buried in a snowpack at Ny-Ålesund (Svalbard), either exposed to solar irradiation or incubated in the dark for 10 days, and the bacterial response to solar irradiation was evaluated in situ using a metagenomics approach. Solar irradiation induced a significant decrease in bacterial abundance and richness. Genes involved in glutathione synthesis, sulphur metabolism, and multidrug efflux were significantly enriched in the light, whereas genes related to cell wall assembly and nutrient uptake were more abundant in the dark. This is the first study demonstrating the response of snow bacterial communities to solar irradiation in situ and providing insights into the mechanisms involved. Our research shows that polar sun irradiation is sufficiently intense to impose a selective pressure on snow bacteria and supports the concern that increased ultraviolet exposure due to anthropogenic activities and climatic change could drive critical changes in the structure and functioning of snow bacterial communities.}, } @article {pmid37073087, year = {2023}, author = {Xu, B and Zhang, W and Li, D and Jin, Y and Rong, X and Xu, Y and Wang, R}, title = {Characterization of a salt-resistant isocitrate lyase gene from mangrove wetland using shotgun metagenomic sequencing.}, journal = {Letters in applied microbiology}, volume = {76}, number = {4}, pages = {}, doi = {10.1093/lambio/ovad044}, pmid = {37073087}, issn = {1472-765X}, support = {//Academician Stations of Hainan Province/ ; YSPTZX202130//Innovation Platform for Academicians of Hainan Province/ ; Hnky2020-23//Education Department of Hainan Province/ ; }, mesh = {*Isocitrate Lyase/chemistry/genetics/metabolism ; *Wetlands ; Escherichia coli/genetics ; Base Sequence ; Recombinant Proteins/genetics ; }, abstract = {Isocitrate lyase (ICL), as the key enzyme in the glyoxylate metabolic pathway, plays an important role in metabolic adaptation to environmental changes. In this study, metagenomic DNA from the soil and water microorganism collected from the Dongzhai Harbor Mangroves (DHM) reserve, in Haikou City, China, was high-throughput sequenced using an Illumina HiSeq 4000 platform. The icl121 gene, encoding an ICL with the highly conserved catalytic pattern IENQVSDEKQCGHQD was identified. Then, this gene was subcloned into the pET-30a vector and overexpressed in Escherichia coli BL21 (DE3) cells. The maximum enzymatic activity of the recombinant ICL121 protein is 9.47 × 102 U/mg occurring at pH 7.5 and 37°C. Furthermore, as a metalo-enzyme, ICL121 can utilize the appropriate concentrations of Mg2+, Mn2+, and Na+ ion as cofactors to exhibit high enzymatic activity. In particular, the novel metagenomic-derived icl121 gene displayed distinct salt tolerance (NaCl) and might be useful for generating salt-tolerant crops in the future.}, } @article {pmid37072776, year = {2023}, author = {Hernández, M and Roy, S and Keevil, CW and Dumont, MG}, title = {Identification of diverse antibiotic resistant bacteria in agricultural soil with H2[18]O stable isotope probing combined with high-throughput sequencing.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {34}, pmid = {37072776}, issn = {2524-6372}, support = {NE/N02026X/1//Natural Environment Research Council/ ; NE/N02026X/1//Natural Environment Research Council/ ; }, abstract = {BACKGROUND: We aimed to identify bacteria able to grow in the presence of several antibiotics including the ultra-broad-spectrum antibiotic meropenem in a British agricultural soil by combining DNA stable isotope probing (SIP) with high throughput sequencing. Soil was incubated with cefotaxime, meropenem, ciprofloxacin and trimethoprim in [18]O-water. Metagenomes and the V4 region of the 16S rRNA gene from the labelled "heavy" and the unlabelled "light" SIP fractions were sequenced.

RESULTS: An increase of the 16S rRNA copy numbers in the "heavy" fractions of the treatments with [18]O-water compared with their controls was detected. The treatments resulted in differences in the community composition of bacteria. Members of the phyla Acidobacteriota (formally Acidobacteria) were highly abundant after two days of incubation with antibiotics. Pseudomonadota (formally Proteobacteria) including Stenotrophomonas were prominent after four days of incubation. Furthermore, a metagenome-assembled genome (MAG-1) from the genus Stenotrophomonas (90.7% complete) was retrieved from the heavy fraction. Finally, 11 antimicrobial resistance genes (ARGs) were identified in the unbinned-assembled heavy fractions, and 10 ARGs were identified in MAG-1. In comparison, only two ARGs from the unbinned-assembled light fractions were identified.

CONCLUSIONS: The results indicate that both non-pathogenic soil-dwelling bacteria as well as potential clinical pathogens are present in this agricultural soil and several ARGs were identified from the labelled communities, but it is still unclear if horizontal gene transfer between these groups can occur.}, } @article {pmid37072710, year = {2023}, author = {Liu, J and Zhang, W and Wu, S and Zeng, T and Luo, F and Jiang, Q and Yang, R}, title = {A clinical case report of Balamuthia granulomatous amoebic encephalitis in a non-immunocompromised patient and literature review.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {245}, pmid = {37072710}, issn = {1471-2334}, mesh = {Male ; Humans ; Middle Aged ; *Encephalitis/diagnosis ; *Central Nervous System Protozoal Infections/diagnosis/parasitology ; *Infectious Encephalitis ; *Amebiasis/diagnosis/parasitology/pathology ; Brain/pathology ; *Central Nervous System Parasitic Infections/pathology ; Granuloma/pathology ; Fatal Outcome ; }, abstract = {BACKGROUND: Balamuthia granulomatous amoebic encephalitis (GAE) is a peculiar parasitic infectious disease of the central nervous system, about 39% of the infected Balamuthia GAE patients were found to be immunocompromised and is extremely rare clinically. The presence of trophozoites in diseased tissue is an important basis for pathological diagnosis of GAE. Balamuthia GAE is a rare and highly fatal infection for which there is no effective treatment plan in clinical practice.

CASE PRESENTATION: This paper reports clinical data from a patient with Balamuthia GAE to improve physician understanding of the disease and diagnostic accuracy of imaging and reduce misdiagnosis. A 61-year-old male poultry farmer presented with moderate swelling pain in the right frontoparietal region without obvious inducement three weeks ago. Head computed tomography(CT) and magnetic resonance imaging(MRI) revealed a space-occupying lesion in the right frontal lobe. Intially clinical imaging diagnosed it as a high-grade astrocytoma. The pathological diagnosis of the lesion was inflammatory granulomatous lesions with extensive necrosis, suggesting amoeba infection. The pathogen detected by metagenomic next-generation sequencing (mNGS) is Balamuthia mandrillaris, the final pathological diagnosis was Balamuthia GAE.

CONCLUSION: When a head MRI shows irregular or annular enhancement, clinicians should not blindly diagnose common diseases such as brain tumors. Although Balamuthia GAE accounts for only a small proportion of intracranial infections, it should be considered in the differential diagnosis.}, } @article {pmid37072468, year = {2023}, author = {Khachatryan, L and Xiang, Y and Ivanov, A and Glaab, E and Graham, G and Granata, I and Giordano, M and Maddalena, L and Piccirillo, M and Manipur, I and Baruzzo, G and Cappellato, M and Avot, B and Stan, A and Battey, J and Lo Sasso, G and Boue, S and Ivanov, NV and Peitsch, MC and Hoeng, J and Falquet, L and Di Camillo, B and Guarracino, MR and Ulyantsev, V and Sierro, N and Poussin, C}, title = {Results and lessons learned from the sbv IMPROVER metagenomics diagnostics for inflammatory bowel disease challenge.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {6303}, pmid = {37072468}, issn = {2045-2322}, mesh = {Humans ; *Inflammatory Bowel Diseases/diagnosis/genetics ; *Colitis, Ulcerative/diagnosis ; *Crohn Disease/diagnosis/genetics ; Metagenomics ; *Gastrointestinal Microbiome/genetics ; }, abstract = {A growing body of evidence links gut microbiota changes with inflammatory bowel disease (IBD), raising the potential benefit of exploiting metagenomics data for non-invasive IBD diagnostics. The sbv IMPROVER metagenomics diagnosis for inflammatory bowel disease challenge investigated computational metagenomics methods for discriminating IBD and nonIBD subjects. Participants in this challenge were given independent training and test metagenomics data from IBD and nonIBD subjects, which could be wither either raw read data (sub-challenge 1, SC1) or processed Taxonomy- and Function-based profiles (sub-challenge 2, SC2). A total of 81 anonymized submissions were received between September 2019 and March 2020. Most participants' predictions performed better than random predictions in classifying IBD versus nonIBD, Ulcerative Colitis (UC) versus nonIBD, and Crohn's Disease (CD) versus nonIBD. However, discrimination between UC and CD remains challenging, with the classification quality similar to the set of random predictions. We analyzed the class prediction accuracy, the metagenomics features by the teams, and computational methods used. These results will be openly shared with the scientific community to help advance IBD research and illustrate the application of a range of computational methodologies for effective metagenomic classification.}, } @article {pmid37072090, year = {2023}, author = {Cheng, M and Zhang, Y and Yan, J and Huang, Y and Wang, M and Zhai, Z and Liu, G and Liu, C and Li, J and Zhang, Y and Xiao, Y and Wang, C and Ban, C and Ren, Z and Song, L}, title = {Inhibiting virus replication and excessive inflammatory response: Mechanism of combined prescription of Ma-Xing-Shi-Gan decoction and Xiao-Chai-Hu decoction against influenza virus.}, journal = {Journal of ethnopharmacology}, volume = {313}, number = {}, pages = {116481}, doi = {10.1016/j.jep.2023.116481}, pmid = {37072090}, issn = {1872-7573}, mesh = {Mice ; Animals ; Mice, Inbred C57BL ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Lung ; *Orthomyxoviridae Infections ; Cytokines/metabolism ; *Orthomyxoviridae/metabolism ; Virus Replication ; Weight Loss ; }, abstract = {The combined prescription of two classical decoctions (Ma-Xing-Shi-Gan decoction with Xiao-Chai-Hu decoction), named as San-Yang-He-Zhi (SYHZ) decoction, has been widely used for the treatment of influenza virus (IFV) infections for decades.

AIM OF THE STUDY: This study aimed to evaluate the anti-influenza effect of SYHZ decoction and explore the underlying mechanism.

MATERIALS AND METHODS: The ingredients of SYHZ decoction were analyzed by mass spectrometry. An animal model of IFV infection was established by challenging C57BL/6J mice with PR8 virus. Three groups of mice were infected with lethal or non-lethal doses of IFV, then followed by oral administration of phosphate-buffered saline (PBS), or SYHZ, or oseltamir; blank control mice (without IFV infection) were treated with PBS. Survival rate, Lung index, colon length, body weight loss and IFV viral load were measured 7 days post infection; histology and electron-microscopy examinations of lung tissue were performed; cytokine and chemokine levels in lung and serum were measured; and the intestinal metagenome, the cecum metabolome, and the lung transcriptome were analyzed.

RESULTS: SYHZ treatment significantly improved survival rate compared with PBS (40% vs 0%); improved lung index, colon length, and body weight loss; and alleviated lung histological damage and viral load. SYHZ-treated mice had significantly lower levels of IL-1β, TNF-α, IL-6, CCL2, CXCL10 in lung and serum, and increased levels of multiple bioactive components in cecum. Pro-inflammatory cytokines, Toll- and NOD-like receptors, pro-apoptosis molecules, and lung-injury-related proteins were downregulated in SYHZ mice, whereas surfactant protein and mucin were upregulated. The NOD-like receptor pathway, Toll-like receptor pathway, and NF-κB pathway were downregulated by SYHZ treatment.

CONCLUSIONS: SYHZ decoction alleviated IFV infection in a mouse model. Multiple bioactive ingredients of SYHZ may inhibit replication of IFV and suppress excessive immune response.}, } @article {pmid37071646, year = {2023}, author = {Poudel, SK and Padmanabhan, R and Dave, H and Guinta, K and Stevens, T and Sanaka, MR and Chahal, P and Sohal, DPS and Khorana, AA and Eng, C}, title = {Microbiomic profiles of bile in patients with benign and malignant pancreaticobiliary disease.}, journal = {PloS one}, volume = {18}, number = {4}, pages = {e0283021}, pmid = {37071646}, issn = {1932-6203}, mesh = {Humans ; Bile ; RNA, Ribosomal, 16S/genetics ; Cholangiopancreatography, Endoscopic Retrograde ; *Pancreatic Neoplasms/genetics/pathology ; *Cholangiocarcinoma/genetics/pathology ; *Bile Duct Neoplasms/pathology ; Bile Ducts, Intrahepatic/pathology ; Pancreatic Ducts/pathology ; }, abstract = {BACKGROUND: The prognostic and pathophysiologic significance of the biliary microbiota in pancreaticobiliary malignancies is little understood. Our goal was to find malignancy-related microbiomic fingerprints in bile samples taken from patients with benign and malignant pancreaticobiliary diseases.

METHODS: Bile specimens were collected from consenting patients during routine endoscopic retrograde cholangiopancreatography. We used PowerViral RNA/DNA Isolation kit to extract DNA from bile specimens. The Illumina 16S Metagenomic Sequencing Library Preparation guide was used to amplify the bacterial 16S rRNA gene and create libraries. QIIME (Quantitative Insights Into Microbial Ecology), Bioconductor phyloseq, microbiomeSeq, and mixMC packages were used for post-sequencing analysis.

RESULTS: Of 46 enrolled patients, 32 patients had pancreatic cancers, 6 had cholangiocarcinoma and 1 had gallbladder cancer. Rest of the patients had benign diseases including gallstones, and acute and chronic pancreatitis. We used multivariate approach in mixMC to classify Operational Taxonomic Units (OTUs). Doing this, we found a predominance of genera Dickeya (p = 0.00008), [Eubacterium] hallii group (p = 0.0004), Bacteroides (p = 0.0006), Faecalibacterium (p = 0.006), Escherichia-Shigella (p = 0.008), and Ruminococcus 1 (p = 0.008) in bile samples from pancreaticobiliary cancers as compared to benign diseases. Additionally, bile samples from patients with pancreatic cancer exhibited a predominance of genus Rothia (p = 0.008) as compared to those with cholangiocarcinoma, whereas bile samples from patients with cholangiocarcinoma exhibited a predominance of genera Akkermansia (p = 0.031) and Achromobacter (p = 0.031) as compared to those with pancreatic cancers.

CONCLUSIONS: Both benign and malignant pancreaticobiliary diseases have distinct microbiomic fingerprints. The relative abundance of OTUs in bile samples varies between patients with benign and malignant pancreaticobiliary diseases, as well as between cholangiocarcinoma and pancreatic cancer. Our data suggest that either these OTUs play a role in carcinogenesis or that benign disease-specific microenvironmental changes differ from cancer-specific microenvironmental changes, resulting to a clear separation of OTU clusters. We need more research to confirm and expand on our findings.}, } @article {pmid37071644, year = {2023}, author = {Ishizuka, TK and Cordeiro, EMG and Alves-Pereira, A and de Araújo Batista, CE and Murúa, MG and Pinheiro, JB and Sethi, A and Nagoshi, RN and Foresti, J and Zucchi, MI}, title = {Population genomics of fall armyworm by genotyping-by-sequencing: Implications for pest management.}, journal = {PloS one}, volume = {18}, number = {4}, pages = {e0284587}, pmid = {37071644}, issn = {1932-6203}, mesh = {Animals ; Spodoptera/genetics ; Genotype ; *Metagenomics ; *Pest Control ; Brazil ; Zea mays/genetics ; }, abstract = {The fall armyworm (FAW), Spodoptera frugiperda, is a significant pest of many crops in the world and it is native to the Americas, where the species has shown the ability to rapidly evolve resistance to insecticides and transgenic plants. Despite the importance of this species, there is a gap in the knowledge regarding the genetic structure of FAW in South America. Here, we examined the genetic diversity of FAW populations across a wide agricultural area of Brazil and Argentina using a Genotyping-by-Sequencing (GBS) approach. We also characterized samples by their host strain based on mitochondrial and Z-linked genetic markers. The GBS methodology enabled us to discover 3309 SNPs, including neutral and outlier markers. Data showed significant genetic structure between Brazil and Argentina populations, and also among the Argentinian ecoregions. Populations inside Brazil showed little genetic differentiation indicating high gene flow among locations and confirming that structure is related to the presence of corn and rice strains. Outlier analysis indicated 456 loci putatively under selection, including genes possibly related to resistance evolution. This study provides clarification of the population genetic structure of FAW in South America and highlights the importance of genomic research to understand the risks of spread of resistance genes.}, } @article {pmid37071008, year = {2023}, author = {Vassallo, A and Modi, A and Quagliariello, A and Bacci, G and Faddetta, T and Gallo, M and Provenzano, A and La Barbera, A and Lombardo, G and Maggini, V and Firenzuoli, F and Zaccaroni, M and Gallo, G and Caramelli, D and Aleo Nero, C and Baldi, F and Fani, R and Palumbo Piccionello, A and Pucciarelli, S and Puglia, AM and Sineo, L}, title = {Novel Sources of Biodiversity and Biomolecules from Bacteria Isolated from a High Middle Ages Soil Sample in Palermo (Sicily, Italy).}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0437422}, pmid = {37071008}, issn = {2165-0497}, mesh = {Animals ; Humans ; Sicily ; *Bacteria ; *Biodiversity ; Anti-Bacterial Agents ; Soil/chemistry ; }, abstract = {The urban plan of Palermo (Sicily, Italy) has evolved throughout Punic, Roman, Byzantine, Arab, and Norman ages until it stabilized within the borders that correspond to the current historic center. During the 2012 to 2013 excavation campaign, new remains of the Arab settlement, directly implanted above the structures of the Roman age, were found. The materials investigated in this study derived from the so-called Survey No 3, which consists of a rock cavity of subcylindrical shape covered with calcarenite blocks: it was probably used to dispose of garbage during the Arabic age and its content, derived from daily activities, included grape seeds, scales and bones of fish, small animal bones, and charcoals. Radiocarbon dating confirmed the medieval origin of this site. The composition of the bacterial community was characterized through a culture-dependent and a culture-independent approach. Culturable bacteria were isolated under aerobic and anaerobic conditions and the total bacterial community was characterized through metagenomic sequencing. Bacterial isolates were tested for the production of compounds with antibiotic activity: a Streptomyces strain, whose genome was sequenced, was of particular interest because of its inhibitory activity, which was due to the Type I polyketide aureothin. Moreover, all strains were tested for the production of secreted proteases, with those belonging to the genus Nocardioides having the most active enzymes. Finally, protocols commonly used for ancient DNA studies were applied to evaluate the antiquity of isolated bacterial strains. Altogether these results show how paleomicrobiology might represent an innovative and unexplored source of novel biodiversity and new biotechnological tools. IMPORTANCE One of the goals of paleomicrobiology is the characterization of the microbial community present in archaeological sites. These analyses can usually provide valuable information about past events, such as occurrence of human and animal infectious diseases, ancient human activities, and environmental changes. However, in this work, investigations about the composition of the bacterial community of an ancient soil sample (harvested in Palermo, Italy) were carried out aiming to screen ancient culturable strains with biotechnological potential, such as the ability to produce bioactive molecules and secreted hydrolytic enzymes. Besides showing the biotechnological relevance of paleomicrobiology, this work reports a case of germination of putatively ancient bacterial spores recovered from soil rather than extreme environments. Moreover, in the case of spore-forming species, these results raise questions about the accuracy of techniques usually applied to estimate antiquity of DNA, as they could lead to its underestimation.}, } @article {pmid37070981, year = {2023}, author = {Yancey, CE and Yu, F and Tripathi, A and Sherman, DH and Dick, GJ}, title = {Expression of Microcystis Biosynthetic Gene Clusters in Natural Populations Suggests Temporally Dynamic Synthesis of Novel and Known Secondary Metabolites in Western Lake Erie.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {5}, pages = {e0209222}, pmid = {37070981}, issn = {1098-5336}, support = {P01 ES028939/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Microcystis/genetics ; Lakes/microbiology ; Ecosystem ; *Cyanobacteria/genetics ; Harmful Algal Bloom ; Multigene Family ; }, abstract = {Microcystis spp. produce diverse secondary metabolites within freshwater cyanobacterial harmful algal blooms (cyanoHABs) around the world. In addition to the biosynthetic gene clusters (BGCs) encoding known compounds, Microcystis genomes harbor numerous BGCs of unknown function, indicating a poorly understood chemical repertoire. While recent studies show that Microcystis produces several metabolites in the lab and field, little work has focused on analyzing the abundance and expression of its broader suite of BGCs during cyanoHAB events. Here, we use metagenomic and metatranscriptomic approaches to track the relative abundance of Microcystis BGCs and their transcripts throughout the 2014 western Lake Erie cyanoHAB. The results indicate the presence of several transcriptionally active BGCs that are predicted to synthesize both known and novel secondary metabolites. The abundance and expression of these BGCs shifted throughout the bloom, with transcript abundance levels correlating with temperature, nitrate, and phosphorus concentrations and the abundance of co-occurring predatory and competitive eukaryotic microorganisms, suggesting the importance of both abiotic and biotic controls in regulating expression. This work highlights the need for understanding the chemical ecology and potential risks to human and environmental health posed by secondary metabolites that are produced but often unmonitored. It also indicates the prospects for identifying pharmaceutical-like molecules from cyanoHAB-derived BGCs. IMPORTANCE Microcystis spp. dominate cyanobacterial harmful algal blooms (cyanoHABs) worldwide and pose significant threats to water quality through the production of secondary metabolites, many of which are toxic. While the toxicity and biochemistry of microcystins and several other compounds have been studied, the broader suite of secondary metabolites produced by Microcystis remains poorly understood, leaving gaps in our understanding of their impacts on human and ecosystem health. We used community DNA and RNA sequences to track the diversity of genes encoding synthesis of secondary metabolites in natural Microcystis populations and assess patterns of transcription in western Lake Erie cyanoHABs. Our results reveal the presence of both known gene clusters that encode toxic secondary metabolites as well as novel ones that may encode cryptic compounds. This research highlights the need for targeted studies of the secondary metabolite diversity in western Lake Erie, a vital freshwater source to the United States and Canada.}, } @article {pmid37070075, year = {2023}, author = {Li, M and Wang, B and Liu, P and Wang, H and Zhu, J}, title = {Prostatitis as initial manifestation of Chlamydia psittaci pneumonia diagnosed by metagenome next-generation sequencing: A case report.}, journal = {Open life sciences}, volume = {18}, number = {1}, pages = {20220596}, pmid = {37070075}, issn = {2391-5412}, abstract = {Chlamydia psittaci (C. psittaci) pneumonia is a zoonotic infectious disease caused by C. psittaci, which is often underdiagnosed. The application of metagenomic next-generation sequencing (mNGS) provides an unbiased method for the detection of unknown pathogens. A 46-year-old man received empirical treatment with piperacillin-tazobactam and moxifloxacin after an initial diagnosis of prostatitis and pneumonia. However, he experienced recurrent symptoms and a cough, and a chest computed tomography (CT) showed aggravated pulmonary inflammation. Upon further questioning, the patient recalled a history of contact with pigeons, and a bronchoscope alveolar lavage fluid analysis with mNGS suggested C. psittaci infection. Following treatment with doxycycline, the patient's symptoms were rapidly alleviated, and chest CT showed pulmonary lesions absorption. The patient was followed up for 1 month without any discomfort. This case highlights that initial manifestations of C. psittaci pneumonia may present with atypical symptoms such as prostatitis. Furthermore, mNGS can be a useful tool for the detection of rare or unknown pathogens such as C. psittaci.}, } @article {pmid37069671, year = {2023}, author = {Sidhu, C and Kirstein, IV and Meunier, CL and Rick, J and Fofonova, V and Wiltshire, KH and Steinke, N and Vidal-Melgosa, S and Hehemann, JH and Huettel, B and Schweder, T and Fuchs, BM and Amann, RI and Teeling, H}, title = {Dissolved storage glycans shaped the community composition of abundant bacterioplankton clades during a North Sea spring phytoplankton bloom.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {77}, pmid = {37069671}, issn = {2049-2618}, mesh = {*Phytoplankton/genetics/metabolism ; North Sea ; *Eutrophication ; Plankton/genetics ; Polysaccharides/metabolism ; Bacteria/genetics/metabolism ; }, abstract = {BACKGROUND: Blooms of marine microalgae play a pivotal role in global carbon cycling. Such blooms entail successive blooms of specialized clades of planktonic bacteria that collectively remineralize gigatons of algal biomass on a global scale. This biomass is largely composed of distinct polysaccharides, and the microbial decomposition of these polysaccharides is therefore a process of prime importance.

RESULTS: In 2020, we sampled a complete biphasic spring bloom in the German Bight over a 90-day period. Bacterioplankton metagenomes from 30 time points allowed reconstruction of 251 metagenome-assembled genomes (MAGs). Corresponding metatranscriptomes highlighted 50 particularly active MAGs of the most abundant clades, including many polysaccharide degraders. Saccharide measurements together with bacterial polysaccharide utilization loci (PUL) expression data identified β-glucans (diatom laminarin) and α-glucans as the most prominent and actively metabolized dissolved polysaccharide substrates. Both substrates were consumed throughout the bloom, with α-glucan PUL expression peaking at the beginning of the second bloom phase shortly after a peak in flagellate and the nadir in bacterial total cell counts.

CONCLUSIONS: We show that the amounts and composition of dissolved polysaccharides, in particular abundant storage polysaccharides, have a pronounced influence on the composition of abundant bacterioplankton members during phytoplankton blooms, some of which compete for similar polysaccharide niches. We hypothesize that besides the release of algal glycans, also recycling of bacterial glycans as a result of increased bacterial cell mortality can have a significant influence on bacterioplankton composition during phytoplankton blooms. Video Abstract.}, } @article {pmid37069665, year = {2023}, author = {Watson, AR and Füssel, J and Veseli, I and DeLongchamp, JZ and Silva, M and Trigodet, F and Lolans, K and Shaiber, A and Fogarty, E and Runde, JM and Quince, C and Yu, MK and Söylev, A and Morrison, HG and Lee, STM and Kao, D and Rubin, DT and Jabri, B and Louie, T and Eren, AM}, title = {Metabolic independence drives gut microbial colonization and resilience in health and disease.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {78}, pmid = {37069665}, issn = {1474-760X}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; P30 CA014599/CA/NCI NIH HHS/United States ; RC2 DK122394/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Fecal Microbiota Transplantation ; *Microbiota ; Metagenomics ; Amino Acids ; Feces ; }, abstract = {BACKGROUND: Changes in microbial community composition as a function of human health and disease states have sparked remarkable interest in the human gut microbiome. However, establishing reproducible insights into the determinants of microbial succession in disease has been a formidable challenge.

RESULTS: Here we use fecal microbiota transplantation (FMT) as an in natura experimental model to investigate the association between metabolic independence and resilience in stressed gut environments. Our genome-resolved metagenomics survey suggests that FMT serves as an environmental filter that favors populations with higher metabolic independence, the genomes of which encode complete metabolic modules to synthesize critical metabolites, including amino acids, nucleotides, and vitamins. Interestingly, we observe higher completion of the same biosynthetic pathways in microbes enriched in IBD patients.

CONCLUSIONS: These observations suggest a general mechanism that underlies changes in diversity in perturbed gut environments and reveal taxon-independent markers of "dysbiosis" that may explain why widespread yet typically low-abundance members of healthy gut microbiomes can dominate under inflammatory conditions without any causal association with disease.}, } @article {pmid37069598, year = {2023}, author = {Wang, C and Wu, DD and Yuan, YH and Yao, MC and Han, JL and Wu, YJ and Shan, F and Li, WP and Zhai, JQ and Huang, M and Peng, SM and Cai, QH and Yu, JY and Liu, QX and Liu, ZY and Li, LX and Teng, MS and Huang, W and Zhou, JY and Zhang, C and Chen, W and Tu, XL}, title = {Population genomic analysis provides evidence of the past success and future potential of South China tiger captive conservation.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {64}, pmid = {37069598}, issn = {1741-7007}, mesh = {Animals ; Female ; Male ; *Tigers/genetics ; Metagenomics ; Genome ; Genomics ; China ; Conservation of Natural Resources ; }, abstract = {BACKGROUND: Among six extant tiger subspecies, the South China tiger (Panthera tigris amoyensis) once was widely distributed but is now the rarest one and extinct in the wild. All living South China tigers are descendants of only two male and four female wild-caught tigers and they survive solely in zoos after 60 years of effective conservation efforts. Inbreeding depression and hybridization with other tiger subspecies were believed to have occurred within the small, captive South China tiger population. It is therefore urgently needed to examine the genomic landscape of existing genetic variation among the South China tigers.

RESULTS: In this study, we assembled a high-quality chromosome-level genome using long-read sequences and re-sequenced 29 high-depth genomes of the South China tigers. By combining and comparing our data with the other 40 genomes of six tiger subspecies, we identified two significantly differentiated genomic lineages among the South China tigers, which harbored some rare genetic variants introgressed from other tiger subspecies and thus maintained a moderate genetic diversity. We noticed that the South China tiger had higher FROH values for longer runs of homozygosity (ROH > 1 Mb), an indication of recent inbreeding/founder events. We also observed that the South China tiger had the least frequent homozygous genotypes of both high- and moderate-impact deleterious mutations, and lower mutation loads than both Amur and Sumatran tigers. Altogether, our analyses indicated an effective genetic purging of deleterious mutations in homozygous states from the South China tiger, following its population contraction with a controlled increase in inbreeding based on its pedigree records.

CONCLUSIONS: The identification of two unique founder/genomic lineages coupled with active genetic purging of deleterious mutations in homozygous states and the genomic resources generated in our study pave the way for a genomics-informed conservation, following the real-time monitoring and rational exchange of reproductive South China tigers among zoos.}, } @article {pmid37069515, year = {2023}, author = {Xie, S and Lai, Z and Xia, H and Tang, M and Lai, J and Liu, Q and Lu, Z and He, D and Qi, J and Liu, X}, title = {A case report of brainstem hemorrhage due to Rhizopus delemar-induced encephalitis diagnosed by metagenomic next-generation sequencing (mNGS).}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {235}, pmid = {37069515}, issn = {1471-2334}, support = {21RGSF0013//Science and Technology Project of Xi'an/ ; z211100002921063//Central Government Funds of Beijing Municipal Science & Technology Commission/ ; }, mesh = {Male ; Humans ; Middle Aged ; *Diabetes Mellitus, Type 2 ; *Encephalitis/diagnosis ; Anti-Bacterial Agents ; High-Throughput Nucleotide Sequencing/methods ; Brain Stem ; Hemorrhage ; }, abstract = {BACKGROUND: Rhizopus delemar is an invasive fungal pathogen that can cause fatal mucormycosis in immunodeficient individuals. Encephalitis caused by R. delemar is rare and difficult to diagnose early. Clinical detection methods for R. delemar include blood fungal culture, direct microscopic examination, and histopathological examination, but the detection is often inadequate for clinical diagnosis and can easily lead to missed diagnosis with delayed treatment.

CASE PRESENTATION: We report a case of a 47-year-old male with brainstem hemorrhage caused by encephalitis due to R. delemar. The patient had a history of hypertension, type 2 diabetes, and irregular medication. No pathogens were detected in cerebrospinal fluid (CSF) and nasopharyngeal secretion cultures. R. delemar was identified by metagenomic next-generation sequencing (mNGS) in CSF, and in combination with the patient's clinical characteristics, encephalitis caused by R. delemar was diagnosed. Antibiotic treatment using amphotericin B liposome in combination with posaconazole was given immediately. However, due to progressive aggravation of the patient's symptoms, he later died due to brainstem hemorrhage after giving up treatment.

CONCLUSIONS: mNGS technique is a potential approach for the early diagnosis of infections, which can help clinicians provide appropriate antibiotic treatments, thus reducing the mortality and disability rate of patients.}, } @article {pmid37069399, year = {2023}, author = {Fan, Y and Støving, RK and Berreira Ibraim, S and Hyötyläinen, T and Thirion, F and Arora, T and Lyu, L and Stankevic, E and Hansen, TH and Déchelotte, P and Sinioja, T and Ragnarsdottir, O and Pons, N and Galleron, N and Quinquis, B and Levenez, F and Roume, H and Falony, G and Vieira-Silva, S and Raes, J and Clausen, L and Telléus, GK and Bäckhed, F and Oresic, M and Ehrlich, SD and Pedersen, O}, title = {The gut microbiota contributes to the pathogenesis of anorexia nervosa in humans and mice.}, journal = {Nature microbiology}, volume = {8}, number = {5}, pages = {787-802}, pmid = {37069399}, issn = {2058-5276}, mesh = {Humans ; Female ; Animals ; Mice ; Male ; *Gastrointestinal Microbiome ; *Anorexia Nervosa/microbiology ; Metabolomics ; Feces/microbiology ; Feeding Behavior ; Bacteria/genetics ; }, abstract = {Anorexia nervosa (AN) is an eating disorder with a high mortality. About 95% of cases are women and it has a population prevalence of about 1%, but evidence-based treatment is lacking. The pathogenesis of AN probably involves genetics and various environmental factors, and an altered gut microbiota has been observed in individuals with AN using amplicon sequencing and relatively small cohorts. Here we investigated whether a disrupted gut microbiota contributes to AN pathogenesis. Shotgun metagenomics and metabolomics were performed on faecal and serum samples, respectively, from a cohort of 77 females with AN and 70 healthy females. Multiple bacterial taxa (for example, Clostridium species) were altered in AN and correlated with estimates of eating behaviour and mental health. The gut virome was also altered in AN including a reduction in viral-bacterial interactions. Bacterial functional modules associated with the degradation of neurotransmitters were enriched in AN and various structural variants in bacteria were linked to metabolic features of AN. Serum metabolomics revealed an increase in metabolites associated with reduced food intake (for example, indole-3-propionic acid). Causal inference analyses implied that serum bacterial metabolites are potentially mediating the impact of an altered gut microbiota on AN behaviour. Further, we performed faecal microbiota transplantation from AN cases to germ-free mice under energy-restricted feeding to mirror AN eating behaviour. We found that the reduced weight gain and induced hypothalamic and adipose tissue gene expression were related to aberrant energy metabolism and eating behaviour. Our 'omics' and mechanistic studies imply that a disruptive gut microbiome may contribute to AN pathogenesis.}, } @article {pmid37069235, year = {2023}, author = {Zhang, Y and Liu, T and Li, MM and Hua, ZS and Evans, P and Qu, Y and Tan, S and Zheng, M and Lu, H and Jiao, JY and Lücker, S and Daims, H and Li, WJ and Guo, J}, title = {Hot spring distribution and survival mechanisms of thermophilic comammox Nitrospira.}, journal = {The ISME journal}, volume = {17}, number = {7}, pages = {993-1003}, pmid = {37069235}, issn = {1751-7370}, support = {P 30570/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Ammonia/metabolism ; Ecosystem ; *Hot Springs ; Oxidation-Reduction ; Bacteria/genetics/metabolism ; Nitrification ; *Ammonium Compounds/metabolism ; Nitrates/metabolism ; Phylogeny ; Archaea/genetics ; }, abstract = {The recent discovery of Nitrospira species capable of complete ammonia oxidation (comammox) in non-marine natural and engineered ecosystems under mesothermal conditions has changed our understanding of microbial nitrification. However, little is known about the occurrence of comammox bacteria or their ability to survive in moderately thermal and/or hyperthermal habitats. Here, we report the wide distribution of comammox Nitrospira in five terrestrial hot springs at temperatures ranging from 36 to 80°C and provide metagenome-assembled genomes of 11 new comammox strains. Interestingly, the identification of dissimilatory nitrate reduction to ammonium (DNRA) in thermophilic comammox Nitrospira lineages suggests that they have versatile ecological functions as both sinks and sources of ammonia, in contrast to the described mesophilic comammox lineages, which lack the DNRA pathway. Furthermore, the in situ expression of key genes associated with nitrogen metabolism, thermal adaptation, and oxidative stress confirmed their ability to survive in the studied hot springs and their contribution to nitrification in these environments. Additionally, the smaller genome size and higher GC content, less polar and more charged amino acids in usage profiles, and the expression of a large number of heat shock proteins compared to mesophilic comammox strains presumably confer tolerance to thermal stress. These novel insights into the occurrence, metabolic activity, and adaptation of comammox Nitrospira in thermal habitats further expand our understanding of the global distribution of comammox Nitrospira and have significant implications for how these unique microorganisms have evolved thermal tolerance strategies.}, } @article {pmid37069233, year = {2023}, author = {Xia, R and Sun, M and Balcázar, JL and Yu, P and Hu, F and Alvarez, PJJ}, title = {Benzo[a]pyrene stress impacts adaptive strategies and ecological functions of earthworm intestinal viromes.}, journal = {The ISME journal}, volume = {17}, number = {7}, pages = {1004-1014}, pmid = {37069233}, issn = {1751-7370}, mesh = {Animals ; Benzo(a)pyrene/toxicity ; *Oligochaeta ; Virome ; *Bacteriophages/genetics ; Prophages/genetics ; }, abstract = {The earthworm gut virome influences the structure and function of the gut microbiome, which in turn influences worm health and ecological functions. However, despite its ecological and soil quality implications, it remains elusive how earthworm intestinal phages respond to different environmental stress, such as soil pollution. Here we used metagenomics and metatranscriptomics to investigate interactions between the worm intestinal phages and their bacteria under different benzo[a]pyrene (BaP) concentrations. Low-level BaP (0.1 mg kg[-1]) stress stimulated microbial metabolism (1.74-fold to control), and enhanced the antiphage defense system (n = 75) against infection (8 phage-host pairs). Low-level BaP exposure resulted in the highest proportion of lysogenic phages (88%), and prophages expressed auxiliary metabolic genes (AMGs) associated with nutrient transformation (e.g., amino acid metabolism). In contrast, high-level BaP exposure (200 mg kg[-1]) disrupted microbial metabolism and suppressed the antiphage systems (n = 29), leading to the increase in phage-bacterium association (37 phage-host pairs) and conversion of lysogenic to lytic phages (lysogenic ratio declined to 43%). Despite fluctuating phage-bacterium interactions, phage-encoded AMGs related to microbial antioxidant and pollutant degradation were enriched, apparently to alleviate pollution stress. Overall, these findings expand our knowledge of complex phage-bacterium interactions in pollution-stressed worm guts, and deepen our understanding of the ecological and evolutionary roles of phages.}, } @article {pmid37069161, year = {2023}, author = {Wang, L and Yao, H and Morgan, DC and Lau, KS and Leung, SY and Ho, JWK and Leung, WK}, title = {Altered human gut virome in patients undergoing antibiotics therapy for Helicobacter pylori.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2196}, pmid = {37069161}, issn = {2041-1723}, mesh = {Humans ; *Helicobacter pylori/genetics ; *Helicobacter Infections/microbiology ; Virome ; Anti-Bacterial Agents/adverse effects ; Drug Therapy, Combination ; }, abstract = {Transient gut microbiota alterations have been reported after antibiotic therapy for Helicobacter pylori. However, alteration in the gut virome after H. pylori eradication remains uncertain. Here, we apply metagenomic sequencing to fecal samples of 44 H. pylori-infected patients at baseline, 6-week (N = 44), and 6-month (N = 33) after treatment. Following H. pylori eradication, we discover contraction of the gut virome diversity, separation of virome community with increased community difference, and shifting towards a higher proportion of core virus. While the gut microbiota is altered at 6-week and restored at 6-month, the virome community shows contraction till 6-month after the treatment with enhanced phage-bacteria interactions at 6-week. Multiple courses of antibiotic treatments further lead to lower virus community diversity when compared with treatment naive patients. Our results demonstrate that H. pylori eradication therapies not only result in transient alteration in gut microbiota but also significantly alter the previously less known gut virome community.}, } @article {pmid37069152, year = {2023}, author = {Njaci, I and Waweru, B and Kamal, N and Muktar, MS and Fisher, D and Gundlach, H and Muli, C and Muthui, L and Maranga, M and Kiambi, D and Maass, BL and Emmrich, PMF and Domelevo Entfellner, JB and Spannagl, M and Chapman, MA and Shorinola, O and Jones, CS}, title = {Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1915}, pmid = {37069152}, issn = {2041-1723}, mesh = {*Metagenomics ; Plant Breeding ; Crops, Agricultural/genetics ; Genome, Plant/genetics ; *Fabaceae/genetics ; Chromosomes ; }, abstract = {Under-utilised orphan crops hold the key to diversified and climate-resilient food systems. Here, we report on orphan crop genomics using the case of Lablab purpureus (L.) Sweet (lablab) - a legume native to Africa and cultivated throughout the tropics for food and forage. Our Africa-led plant genome collaboration produces a high-quality chromosome-scale assembly of the lablab genome. Our assembly highlights the genome organisation of the trypsin inhibitor genes - an important anti-nutritional factor in lablab. We also re-sequence cultivated and wild lablab accessions from Africa confirming two domestication events. Finally, we examine the genetic and phenotypic diversity in a comprehensive lablab germplasm collection and identify genomic loci underlying variation of important agronomic traits in lablab. The genomic data generated here provide a valuable resource for lablab improvement. Our inclusive collaborative approach also presents an example that can be explored by other researchers sequencing indigenous crops, particularly from low and middle-income countries (LMIC).}, } @article {pmid37068733, year = {2023}, author = {Teng, T and Clarke, G and Wu, J and Wu, Q and Maes, M and Wang, J and Wu, H and Yin, B and Jiang, Y and Li, X and Liu, X and Han, Y and Song, J and Jin, X and Ji, P and Guo, Y and Zhou, X and Xie, P}, title = {Disturbances of purine and lipid metabolism in the microbiota-gut-brain axis in male adolescent nonhuman primates with depressive-like behaviors.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2023.04.010}, pmid = {37068733}, issn = {2090-1224}, abstract = {INTRODUCTION: Major depressive disorder (MDD) in adolescents is a widespread and growing global public health concern with unique characteristics and pathophysiological mechanisms that are distinct from MDD in adults.

OBJECTIVE: The purpose of our work was to address this knowledge gap about the unique characteristics and pathophysiological mechanisms of adolescent depression from a microbiota-gut-brain (MGB) axis perspective.

METHOD: Ten healthy male cynomolgus macaques (Macaca fascicularis) were paired into five pairs based on age and body weight, and two cynomolgus macaques from each pair were randomly allocated to chronic unpredictable mild stress group, or unstressed control group. At endpoint, microbe composition from cecum, ascending colon, transverse colon, and descending colon were analyzed by metagenome sequencing, and the metabolite profiles of MGB axis including central (prefrontal cortex, hippocampus and amygdala) and peripheral (plasma, gut and feces of cecum, ascending colon, transverse colon and descending colon) samples were analyzed by metabolomic profiling. Then, we compare the gut microbiome and metabolic signatures in MGB axis between adolescent and adult depressed macaques.

RESULTS: The microbial composition and gut-brain metabolic signatures were widely divergent between adolescent and adult depressed macaques, though the phylum Firmicutes and lipid metabolism pathways were persistently altered in both populations. Purine and arginine biosynthesis metabolism were a specific hallmark of adolescent depressed macaques, while fatty acyl metabolism was specially altered in adult. These differential metabolic pathways in adolescent and adult depressed macaques were mainly mapped into the prefrontal cortex and hippocampus, respectively. Notably, the genus Clostridium and Haemophilus, characteristically disturbed in adolescent depressed macaques but not in adult, were also significantly associated with the majority of purine metabolites in MGB axis.

CONCLUSION: These findings provide a new framework describing divergent pathophysiological mechanisms between adolescent and adult depression, and may open new windows for more effective treatment strategies of adolescent depression.}, } @article {pmid37068263, year = {2023}, author = {Vagefi, MR and Idowu, OO and Miller, A and Doan, T and Chen, C and Hinterwirth, A and Zhong, L and Ahmad, M and Ashraf, DC and Grob, SR and Kersten, RC and Winn, BJ}, title = {Metagenomic Deep Sequencing for Orbital Inflammatory Disease.}, journal = {Ocular immunology and inflammation}, volume = {}, number = {}, pages = {1-4}, pmid = {37068263}, issn = {1744-5078}, support = {P30 EY002162/EY/NEI NIH HHS/United States ; }, abstract = {PURPOSE: Orbital inflammatory disease (OID) is a heterogeneous group of immunologic disorders whose etiology is often non-specific despite routine investigation. In this proof-of-concept study, metagenomic deep sequencing (MDS) is applied to examine host gene expression in two subtypes of OID.

METHODS: Prospectively collected lacrimal gland tissue from patients with OID was processed for MDS. Differential gene expression analysis was performed to evaluate for host transcriptome signatures. Proof-of-concept comparison was made between histologically confirmed samples of idiopathic dacryoadenitis and IgG4-related disease (IgG4-RD).

RESULTS: Twelve genes were identified to be differentially expressed between idiopathic dacryoadenitis and IgG4-RD. Differences in innate humoral immunity gene expression were observed. Several additional genes of interests were also found to be upregulated in idiopathic dacryoadenitis.

CONCLUSIONS: A unique transcriptome signature was found when comparing idiopathic dacryoadenitis to IgG4-RD. This suggests that MDS can identify differentially expressed genes in OID. Such insight could potentially provide a better understanding of host gene expression and the inflammatory pathways involved in OID.}, } @article {pmid37068005, year = {2023}, author = {Wen, L and Yang, L and Chen, C and Li, J and Fu, J and Liu, G and Kan, Q and Ho, CT and Huang, Q and Lan, Y and Cao, Y}, title = {Applications of multi-omics techniques to unravel the fermentation process and the flavor formation mechanism in fermented foods.}, journal = {Critical reviews in food science and nutrition}, volume = {}, number = {}, pages = {1-17}, doi = {10.1080/10408398.2023.2199425}, pmid = {37068005}, issn = {1549-7852}, abstract = {Fermented foods are important components of the human diet. There is increasing awareness of abundant nutritional and functional properties present in fermented foods that arise from the transformation of substrates by microbial communities. Thus, it is significant to unravel the microbial communities and mechanisms of characteristic flavor formation occurring during fermentation. There has been rapid development of high-throughput and other omics technologies, such as metaproteomics and metabolomics, and as a result, there is growing recognition of the importance of integrating these approaches. The successful applications of multi-omics approaches and bioinformatics analyses have provided a solid foundation for exploring the fermentation process. Compared with single-omics, multi-omics analyses more accurately delineate microbial and molecular features, thus they are more apt to reveal the mechanisms of fermentation. This review introduces fermented foods and an overview of single-omics technologies - including metagenomics, metatranscriptomics, metaproteomics, and metabolomics. We also discuss integrated multi-omics and bioinformatic analyses and their role in recent research progress related to fermented foods, as well as summarize the main potential pathways involved in certain fermented foods. In the future, multilayered analyses of multi-omics data should be conducted to enable better understanding of flavor formation mechanisms in fermented foods.}, } @article {pmid37067654, year = {2023}, author = {Yuan, T and Qazi, IH and Yang, P and Zhang, X and Li, J and Liu, J}, title = {Analysis of endophytic bacterial flora of mulberry cultivars susceptible and resistant to bacterial wilt using metagenomic sequencing and culture-dependent approach.}, journal = {World journal of microbiology & biotechnology}, volume = {39}, number = {6}, pages = {163}, pmid = {37067654}, issn = {1573-0972}, support = {CARS-18-ZJ0304//China Agriculture Research System/ ; }, mesh = {*Morus/microbiology ; Bacteria/genetics ; Proteobacteria ; Firmicutes ; Endophytes/genetics ; }, abstract = {Endophytes have a wide range of potential in maintaining plant health and sustainable agricultural environmental conditions. In this study, we analysed the diversity of endophytic bacteria in four mulberry cultivars with different resistance capacity against bacterial wilt using metagenomic sequencing and culture-dependent approaches. We further assessed the role of 11 shared genera in the control of bacterial wilt of mulberry. The results of the present study showed that Actinobacteria, Firmicutes, and Proteobacteria were the three dominant phyla in all communities, with the representative genera Acinetobacter and Pseudomonas. The diversity analysis showed that the communities of the highly and moderately resistant varieties were more diverse compared to those of the weakly resistant and susceptible varieties. The control tests of mulberry bacterial wilt showed that Pantoea, Atlantibacter, Stenotrophomonas, and Acinetobacter were effective, with a control rate of over 80%. Microbacterium and Kosakonia were moderately effective, with a control rate between 50 and 80%. At the same time, Escherichia, Lysinibacillus, Pseudomonas, and Rhizobium were found to be less effective, with a control rate of less than 40%. In conclusion, this study provides a reasonable experimental reference data for the control of bacterial wilt of mulberry.}, } @article {pmid37067438, year = {2023}, author = {Pu, J and Yang, J and Lu, S and Jin, D and Luo, X and Xiong, Y and Bai, X and Zhu, W and Huang, Y and Wu, S and Niu, L and Liu, L and Xu, J}, title = {Species-Level Taxonomic Characterization of Uncultured Core Gut Microbiota of Plateau Pika.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0349522}, pmid = {37067438}, issn = {2165-0497}, mesh = {Animals ; Humans ; Ecosystem ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Lagomorpha/genetics/microbiology ; }, abstract = {Rarely has the vast diversity of bacteria on Earth been profiled, particularly on inaccessible plateaus. These uncultured microbes, which are also known as "microbial dark matter," may play crucial roles in maintaining the ecosystem and are linked to human health, regarding pathogenicity and prebioticity. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is a keystone species in the maintenance of ecological balance. We used a combination of full-length 16S rRNA amplicon sequencing, shotgun metagenomics, and metabolomics to elucidate the species-level community structure and the metabolic potential of the gut microbiota of the plateau pika. Using a full-length 16S rRNA metataxonomic approach, we clustered 618 (166 ± 35 per sample) operational phylogenetic units (OPUs) from 105 plateau pika samples and assigned them to 215 known species, 226 potentially new species, and 177 higher hierarchical taxa. Notably, 39 abundant OPUs (over 60% total relative abundance) are found in over 90% of the samples, thereby representing a "core microbiota." They are all classified as novel microbial lineages, from the class to the species level. Using metagenomic reads, we independently assembled and binned 109 high-quality, species-level genome bins (SGBs). Then, a precise taxonomic assignment was performed to clarify the phylogenetic consistency of the SGBs and the 16S rRNA amplicons. Thus, the majority of the core microbes possess their genomes. SGBs belonging to the genus Treponema, the families Muribaculaceae, Lachnospiraceae, and Oscillospiraceae, and the order Eubacteriales are abundant in the metagenomic samples. In addition, multiple CAZymes are detected in these SGBs, indicating their efficient utilization of plant biomass. As the most widely connected metabolite with the core microbiota, tryptophan may relate to host environmental adaptation. Our investigation allows for a greater comprehension of the composition and functional capacity of the gut microbiota of the plateau pika. IMPORTANCE The great majority of microbial species remain uncultured, severely limiting their taxonomic characterization and biological understanding. The plateau pika (Ochotona curzoniae) is a small burrowing steppe lagomorph that is endemic to the Qinghai-Tibetan Plateau and is considered to be the keystone species in the maintenance of ecological stability. We comprehensively investigated the gut microbiota of the plateau pika via a multiomics endeavor. Combining full-length 16S rRNA metataxonomics, shotgun metagenomics, and metabolomics, we elucidated the species-level taxonomic assignment of the core uncultured intestinal microbiota of the plateau pika and revealed their correlation to host nutritional metabolism and adaptation. Our findings provide insights into the microbial diversity and biological significance of alpine animals.}, } @article {pmid37067419, year = {2023}, author = {Bhattacharyya, C and Barman, D and Tripathi, D and Dutta, S and Bhattacharya, C and Alam, M and Choudhury, P and Devi, U and Mahanta, J and Rasaily, R and Basu, A and Paine, SK}, title = {Influence of Maternal Breast Milk and Vaginal Microbiome on Neonatal Gut Microbiome: a Longitudinal Study during the First Year.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0496722}, pmid = {37067419}, issn = {2165-0497}, mesh = {Infant ; Infant, Newborn ; Adult ; Humans ; Pregnancy ; Female ; Cesarean Section ; *Gastrointestinal Microbiome ; Milk, Human ; Longitudinal Studies ; *Microbiota ; }, abstract = {It is believed that establishment of the gut microbiome starts very early in life and is crucial for growth, immunity, and long-term metabolic health. In this longitudinal study, we recruited 25 mothers in their third trimester, of whom 15 had vaginal delivery while 10 had an unplanned cesarean section (C-section). The mother-neonate pairs were followed for 1 year, and we generated 16S metagenomic data to study the neonatal gut microbiome along with mother's breast milk and vaginal microbiomes through 12 months after delivery, at 1, 3, 6, and 12 months. We inferred (i) mode of delivery is an important factor influencing both composition and entropy of the neonatal gut microbiome, and the genus Streptococcus plays an important role in the temporal differentiation. (ii) Microbial diversity monotonically increases with age, irrespective of the mode of delivery, and it is significantly altered once exclusive breastfeeding is stopped. (iii) We found little evidence in favor of the microflora of mother's breast milk and a vaginal swab being directly reflected in the offspring's gut microbiome; however, some distinction could be made in the gut microbiome of neonates whose mothers were classified as community state type III (CSTIII) and CSTIV, based on their vaginal microbiomes. (iv) A lot of the mature gut microbiome is possibly acquired from the environment, as the genera Prevotella and Faecalibacterium, two of the most abundant flora in the neonatal gut microbiome, are introduced after initiation of solidified food. The distinction between the gut microbiome of babies born by vaginal delivery and babies born by C-section becomes blurred after introduction of solid food, although the diversity in the gut microbiota drastically increases in both cases. IMPORTANCE Gut microbiome architecture seems to have a potential impact on host metabolism, health, and nutrition. Early life gut microbiome development is considered a crucial phenomenon for neonatal health as well as adulthood metabolic complications. In this longitudinal study, we examined the association of neonatal gut microbiome entropy and its temporal variation. The study revealed that adult-like gut microbiome architecture starts taking shape after initiation of solidified food. Further, we also observed that the difference of microbial diversity was reduced between vaginally delivered and C-section babies compared to exclusive breastfeeding tenure. We found evidence in favor of the inheritance of the microflora of mother's posterior vaginal wall to the offspring's gut microbiome.}, } @article {pmid37067403, year = {2023}, author = {Guajardo-Leiva, S and Berríos-Farías, V and Bermúdez, FG and Castro-Nallar, E}, title = {Fecal Metagenomes and Metagenome-Assembled Genomes from the South American Sea Lion (Otaria flavescens) from the Comau Fjord (42°S), Patagonia.}, journal = {Microbiology resource announcements}, volume = {12}, number = {5}, pages = {e0018323}, pmid = {37067403}, issn = {2576-098X}, support = {FONDECYT1200834//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; FONDECYT Postdoctoral 3210547//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; }, abstract = {Environmental disturbances can be monitored using sentinel species. We present 30 temporally explicit metagenomes and 166 metagenome-assembled genomes (MAGs) from the gut of the South American sea lion (Otaria flavescens) to further understanding of whether variations in the gut microbiome composition and gene content might reflect environmental disturbances from salmon farming.}, } @article {pmid37067276, year = {2023}, author = {Zhang, F and Blackburn, D and Hosea, CN and Assié, A and Samuel, BS}, title = {Application of Flow Vermimetry for Quantification and Analysis of the Caenorhabditis elegans Gut Microbiome.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {193}, pages = {}, doi = {10.3791/64605}, pmid = {37067276}, issn = {1940-087X}, support = {DP2 DK116645/DK/NIDDK NIH HHS/United States ; S10 OD025251/OD/NIH HHS/United States ; P40 OD010440/OD/NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Caenorhabditis elegans ; *Microbiota ; }, abstract = {The composition of the gut microbiome can have a dramatic impact on host physiology throughout the development and the life of the animal. Measuring compositional changes in the microbiome is crucial in identifying the functional relationships between these physiological changes. Caenorhabditis elegans has emerged as a powerful host system to examine the molecular drivers of host-microbiome interactions. With its transparent body plan and fluorescent-tagged natural microbes, the relative levels of microbes within the gut microbiome of an individual C. elegans animal can be easily quantified using a large particle sorter. Here we describe the procedures for the experimental setup of a microbiome, collection, and analysis of C. elegans populations in the desired life stage, operation, and maintenance of the sorter, and statistical analyses of the resulting datasets. We also discuss considerations for optimizing sorter settings based on the microbes of interest, the development of effective gating strategies for C. elegans life stages, and how to utilize sorter capabilities to enrich animal populations based on gut microbiome composition. Examples of potential applications will be presented as part of the protocol, including the potential for scalability to high-throughput applications.}, } @article {pmid37067110, year = {2023}, author = {Gu, A and Jiang, J and Ma, F and Zhang, L}, title = {Metagenomic next-generation sequencing for the aetiological diagnosis of Mycobacterium marinum infections: A pilot study.}, journal = {Indian journal of dermatology, venereology and leprology}, volume = {89}, number = {5}, pages = {745-748}, doi = {10.25259/IJDVL_768_2022}, pmid = {37067110}, issn = {0973-3922}, mesh = {Humans ; *Mycobacterium marinum/genetics ; Pilot Projects ; *Mycobacterium Infections, Nontuberculous/diagnosis ; High-Throughput Nucleotide Sequencing ; }, } @article {pmid37066413, year = {2023}, author = {Rodríguez-Ramos, J and Oliverio, A and Borton, MA and Danczak, R and Mueller, BM and Schulz, H and Ellenbogen, J and Flynn, RM and Daly, RA and Schopflin, L and Shaffer, M and Goldman, A and Lewandowski, J and Stegen, JC and Wrighton, KC}, title = {Spatial and temporal metagenomics of river compartments reveals viral community dynamics in an urban impacted stream.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.04.04.535500}, pmid = {37066413}, abstract = {Although river ecosystems comprise less than 1% of Earth's total non-glaciated area, they are critical modulators of microbially and virally orchestrated global biogeochemical cycles. However, most studies either use data that is not spatially resolved or is collected at timepoints that do not reflect the short life cycles of microorganisms. As a result, the relevance of microbiome interactions and the impacts they have over time on biogeochemical cycles are poorly understood. To assess how viral and microbial communities change over time, we sampled surface water and pore water compartments of the wastewater-impacted River Erpe in Germany every 3 hours over a 48-hour period resulting in 32 metagenomes paired to geochemical and metabolite measurements. We reconstructed 6,500 viral and 1,033 microbial genomes and found distinct communities associated with each river compartment. We show that 17% of our vMAGs clustered to viruses from other ecosystems like wastewater treatment plants and rivers. Our results also indicated that 70% of the viral community was persistent in surface waters, whereas only 13% were persistent in the pore waters taken from the hyporheic zone. Finally, we predicted linkages between 73 viral genomes and 38 microbial genomes. These putatively linked hosts included members of the Competibacteraceae, which we suggest are potential contributors to carbon and nitrogen cycling. Together, these findings demonstrate that microbial and viral communities in surface waters of this urban river can exist as stable communities along a flowing river; and raise important considerations for ecosystem models attempting to constrain dynamics of river biogeochemical cycles.}, } @article {pmid37066400, year = {2023}, author = {Røyseth, V and Hurysz, BM and Kaczorowska, A and Dorawa, S and Fedøy, AE and Arsin, H and Serafim, M and Werbowy, O and Kaczorowski, T and Stokke, R and O'Donoghue, AJ and Helene Steen, I}, title = {Activation mechanism and activity of globupain, a thermostable C11 protease from the Arctic Mid-Ocean Ridge hydrothermal system.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37066400}, support = {T32 GM007752/GM/NIGMS NIH HHS/United States ; }, abstract = {Deep-sea hydrothermal vent systems with prevailing extreme thermal conditions for life offer unique habitats to source heat tolearant enzymes with potential new enzymatic properties. Here, we present the novel C11 protease globupain , prospected from a metagenome-assembled genome of uncultivated Archaeoglobales sampled from the Soria Moria hydrothermal vent system located on the Arctic Mid- Ocean Ridges. By sequence comparisons against the MEROPS-MPRO database, globupain showed highest sequence identity to C11-like proteases present in human gut and intestinal bacteria,. Successful recombinant expression in Escherichia coli of the active zymogen and 13 mutant substitution variants allowed assesment of residues involved in maturation and activity of the enzyme. For activation, globupain required the addition of DTT and Ca[2+]. When activated, the 52 kDa proenzyme was processed at Lys 137 and Lys 144 into a 12 kDa light- and 32 kDa heavy chain heterodimer. A structurally conserved His 132 /Cys 185 catalytic dyad was responsible for the proteolytic activity, and the enzyme demonstrated the ability to activate in-trans . Globupain exhibited caseinolytic activity and showed a strong preference for arginine in the P1 position, with Boc-QAR- aminomethylcoumarin (AMC) as the best substrate out of a total of 17 fluorogenic AMC substrates tested. Globupain was thermostable (T m activated enzyme = 94.51 ± 0.09°C) with optimal activity at 75 °C and pH 7.1. By characterizing globupain, our knowledge of the catalytic properties and activation mechanisms of temperature tolerant marine C11 proteases have been expanded. The unique combination of features such as elevated thermostability, activity at relatively low pH values, and ability to operate under high reducing conditions makes globupain a potential intriguing candidate for use in diverse industrial and biotechnology sectors.}, } @article {pmid37066369, year = {2023}, author = {Mallawaarachchi, V and Roach, MJ and Decewicz, P and Papudeshi, B and Giles, SK and Grigson, SR and Bouras, G and Hesse, RD and Inglis, LK and Hutton, ALK and Dinsdale, EA and Edwards, RA}, title = {Phables: from fragmented assemblies to high-quality bacteriophage genomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37066369}, abstract = {Microbial communities influence both human health and different environments. Viruses infecting bacteria, known as bacteriophages or phages, play a key role in modulating bacterial communities within environments. High-quality phage genome sequences are essential for advancing our understanding of phage biology, enabling comparative genomics studies, and developing phage-based diagnostic tools. Most available viral identification tools consider individual sequences to determine whether they are of viral origin. As a result of the challenges in viral assembly, fragmentation of genomes can occur, leading to the need for new approaches in viral identification. Therefore, the identification and characterisation of novel phages remain a challenge. We introduce Phables, a new computational method to resolve phage genomes from fragmented viral metagenome assemblies. Phables identifies phage-like components in the assembly graph, models each component as a flow network, and uses graph algorithms and flow decomposition techniques to identify genomic paths. Experimental results of viral metagenomic samples obtained from different environments show that Phables recovers on average over 49% more high-quality phage genomes compared to existing viral identification tools. Furthermore, Phables can resolve variant phage genomes with over 99% average nucleotide identity, a distinction that existing tools are unable to make. Phables is available on GitHub at https://github.com/Vini2/phables.}, } @article {pmid37066359, year = {2023}, author = {Mak, L and Tierney, B and Ronkowski, C and Toomey, M and Martinez, JSA and Zimmerman, S and Fu, C and Kopbayeva, M and Noyvert, A and Farthing, B and Tang, S and Mason, C and Hajirasouliha, I}, title = {A modular metagenomics analysis system for integrated multi-step data exploration.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {37066359}, support = {R35 GM138152/GM/NIGMS NIH HHS/United States ; }, abstract = {MOTIVATION: Computational analysis of large-scale metagenomics sequencing datasets has proved to be both incredibly valuable for extracting isolate-level taxonomic and functional insights from complex microbial communities. However, thanks to an ever-expanding ecosystem of metagenomics-specific algorithms and file formats, designing studies, implementing seamless and scalable end-to-end workflows, and exploring the massive amounts of output data have become studies unto themselves. Furthermore, there is little inter-communication between output data of different analytic purposes, such as short-read classification and metagenome assembled genomes (MAG) reconstruction. One-click pipelines have helped to organize these tools into targeted workflows, but they suffer from general compatibility and maintainability issues.

RESULTS: To address the gap in easily extensible yet robustly distributable metagenomics workflows, we have developed a module-based metagenomics analysis system written in Snakemake, a popular workflow management system, along with a standardized module and working directory architecture. Each module can be run independently or conjointly with a series of others to produce the target data format (ex. short-read preprocessing alone, or short-read preprocessing followed by de novo assembly), and outputs aggregated summary statistics reports and semi-guided Jupyter notebook-based visualizations, The module system is a bioinformatics-optimzied scaffold designed to be rapidly iterated upon by the research community at large.

AVAILABILITY: The module template as well as the modules described below can be found at https://github.com/MetaSUB-CAMP.}, } @article {pmid37066122, year = {2023}, author = {Xiang, B and Zhao, L and Zhang, M}, title = {Unitig level assembly graph based metagenome-assembled genome refiner (UGMAGrefiner): A tool to increase completeness and resolution of metagenome-assembled genomes.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {2394-2404}, pmid = {37066122}, issn = {2001-0370}, abstract = {De novo assembly of next generation metagenomic reads is widely used to provide taxonomic and functional information of genomes in a microbial community. As strains are functionally specific, recovery of strain-resolved genomes is important but still a challenge. Unitigs and assembly graphs are mid-products generated during the assembly of reads into contigs, and they provide higher resolution for sequences connection information. In this study, we propose a new approach UGMAGrefiner (a unitig level assembly graph-based metagenome-assembled Genome refiner), which uses the connection and coverage information from unitig level assembly graphs to recruit unbinned unitigs to MAGs, adjust binning result, and infer unitigs shared by multiple MAGs. In two simulated datasets (Simdata and CAMI data) and one real dataset (GD02), it outperforms two state-of-the-art assembly graph-based binning refine tools in the refinement of MAGs' quality by stably increasing the completeness of genomes. UGMAGrefiner can identify genome specific clusters of genomes with below 99% average nucleotide identity for homologous sequences. For MAGs mixed with 99% similarity genome clusters, it could distinguish 8 out of 9 genomes in Simdata and 8 out of 12 genomes in CAMI data. In GD02 data, it could identify 16 new unitig clusters representing genome specific regions of mixed genomes and 4 unitig clusters representing new genomes from total 135 MAGs for further functional analysis. UGMAGrefiner provides an efficient way to obtain more complete MAGs and study genome specific functions. It will be useful to improve taxonomic and functional information of genomes after de novo assembly.}, } @article {pmid37065800, year = {2023}, author = {Ting, A and Abidin, CMRZ and Hamid, NH and Azzam, G and Salim, H}, title = {Uncovering the Microbiota of Bagworm Metisa plana (Lepidoptera: Psychidae) in Oil Palm Plantations in Malaysia.}, journal = {Tropical life sciences research}, volume = {34}, number = {1}, pages = {185-218}, pmid = {37065800}, issn = {1985-3718}, abstract = {Bagworm Metisa plana is one of the major pests in Malaysia's oil palm plantation, with infestation resulting in huge economical loss. Currently, the microbial profile of the bagworm has yet to be study. Understanding the biology of the pest such as the bacterial community is crucial as bacteria associated with insects often provide benefits to the insect, giving the insect host a better chance of survival. Here, 16S amplicon sequencing was used to identify the bacteria community of M. plana. Additionally, two comparisons were made, the bacterial communities between two larval stages (early instar stage and late instar stage) from outbreak area; the bacterial communities of late instar stage larvae from non-outbreak between outbreak areas. From this study, it was found that the bacterial community of M. plana consisted of Proteobacteria, Actinobacteria, Bacterioidetes, Firmicutes and other minor phyla, with Proteobacteria being the most dominant phylum. Furthermore, bacterial genera of M. plana consisted of Pantoea, Curtobacterium, Pseudomonas, Massilia and other minor genera, with Pantoea being the most dominant. It was also found that the alpha and beta diversity in both comparisons were not significantly different. We present our data as a first insight towards the bacterial community of M. plana, paving a way towards understanding the biology of the bagworm M. plana.}, } @article {pmid37065754, year = {2023}, author = {Chen, XH and Liu, HQ and Nie, Q and Wang, H and Xiang, T}, title = {Causal relationship between type 1 diabetes mellitus and six high-frequency infectious diseases: A two-sample mendelian randomization study.}, journal = {Frontiers in endocrinology}, volume = {14}, number = {}, pages = {1135726}, pmid = {37065754}, issn = {1664-2392}, mesh = {Humans ; Causality ; *Communicable Diseases/epidemiology ; *Diabetes Mellitus, Type 1/epidemiology/genetics ; Glycated Hemoglobin ; Mendelian Randomization Analysis ; Respiratory Tract Infections ; Sepsis ; }, abstract = {PURPOSE: Type 1 diabetes mellitus (T1DM) is associated with different types of infections; however, studies on the causal relationship between T1DM and infectious diseases are lacking. Therefore, our study aimed to explore the causalities between T1DM and six high-frequency infections using a Mendelian randomization (MR) approach.

METHODS: Two-sample MR studies were conducted to explore the causalities between T1DM and six high-frequency infections: sepsis, acute lower respiratory infections (ALRIs), intestinal infections (IIs), infections of the genitourinary tract (GUTIs) in pregnancy, infections of the skin and subcutaneous tissues (SSTIs), and urinary tract infections (UTIs). Data on summary statistics for T1DM and infections were obtained from the European Bioinformatics Institute database, the United Kingdom Biobank, FinnGen biobank, and Medical Research Council Integrative Epidemiology Unit. All data obtained for summary statistics were from European countries. The inverse-variance weighted (IVW) method was employed as the main analysis. Considering the multiple comparisons, statistical significance was set at p< 0.008. If univariate MR analyses found a significant causal association, multivariable MR (MVMR) analyses were performed to adjust body mass index (BMI) and glycated hemoglobin (HbA1c). MVMR-IVW was performed as the primary analysis, and the least absolute shrinkage and selection operator (LASSO) regression and MVMR-Robust were performed as complementary analyses.

RESULTS: MR analysis showed that susceptibility to IIs increased in patients with T1DM by 6.09% using the IVW-fixed method [odds ratio (OR)=1.0609; 95% confidence interval (CI): 1.0281-1.0947, p=0.0002]. Results were still significant after multiple testing. Sensitivity analyses did not show any significant horizontal pleiotropy or heterogeneity. After adjusting for BMI and HbA1c, MVMR-IVW (OR=1.0942; 95% CI: 1.0666-1.1224, p<0.0001) showed significant outcomes that were consistent with those of LASSO regression and MVMR-Robust. However, no significant causal relationship was found between T1DM and sepsis susceptibility, ALRI susceptibility, GUTI susceptibility in pregnancy, SSTI susceptibility, and UTI susceptibility.

CONCLUSIONS: Our MR analysis genetically predicted increased susceptibility to IIs in T1DM. However, no causality between T1DM and sepsis, ALRIs, GUTIs in pregnancy, SSTIs, or UTIs was found. Larger epidemiological and metagenomic studies are required to further investigate the observed associations between the susceptibility of certain infectious diseases with T1DM.}, } @article {pmid37065150, year = {2023}, author = {von Fricken, ME and Melendrez, MC and Linton, YM and Takhampunya, R}, title = {Editorial: Metagenomics for epidemiological surveillance in One Health.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1191946}, pmid = {37065150}, issn = {1664-302X}, } @article {pmid37065146, year = {2023}, author = {Vannier, P and Farrant, GK and Klonowski, A and Gaidos, E and Thorsteinsson, T and Marteinsson, VÞ}, title = {Metagenomic analyses of a microbial assemblage in a subglacial lake beneath the Vatnajökull ice cap, Iceland.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1122184}, pmid = {37065146}, issn = {1664-302X}, abstract = {Skaftárkatlar are two subglacial lakes located beneath the Vatnajökull ice cap in Iceland associated with geothermal and volcanic activity. Previous studies of these lakes with ribosomal gene (16S rDNA) tag sequencing revealed a limited diversity of bacteria adapted to cold, dark, and nutrient-poor waters. In this study, we present analyses of metagenomes from the lake which give new insights into its microbial ecology. Analyses of the 16S rDNA genes in the metagenomes confirmed the existence of a low-diversity core microbial assemblage in the lake and insights into the potential metabolisms of the dominant members. Seven taxonomic genera, Sulfuricurvum, Sulfurospirillum, Acetobacterium, Pelobacter/Geobacter, Saccharibacteria, Caldisericum, and an unclassified member of Prolixibacteraceae, comprised more than 98% of the rDNA reads in the library. Functional characterisation of the lake metagenomes revealed complete metabolic pathways for sulphur cycling, nitrogen metabolism, carbon fixation via the reverse Krebs cycle, and acetogenesis. These results show that chemolithoautotrophy constitutes the main metabolism in this subglacial ecosystem. This assemblage and its metabolisms are not reflected in enrichment cultures, demonstrating the importance of in situ investigations of this environment.}, } @article {pmid37065129, year = {2023}, author = {Li, M and Zhang, G and Cui, L and Zhang, L and Zhou, Q and Mu, C and Chi, R and Zhang, N and Ma, G}, title = {Dynamic changes in gut microbiota during pregnancy among Chinese women and influencing factors: A prospective cohort study.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1114228}, pmid = {37065129}, issn = {1664-302X}, abstract = {Gut microbiota (GM) dynamics during pregnancy vary among different populations and are affected by many factors, such as living environments and diet. This study aims to observe and evaluate the changes in the structure and function of the GM from the first to the third trimester of pregnancy in Chinese women, and to explore the main factors affecting the changes in intestinal microecology. Fifty-five Chinese pregnant women were recruited for this study and their fecal samples were collected during the first (P1), second (P2), and third trimesters (P3) of pregnancy. We exploited metagenomic sequencing to compare the composition and function of the GM in different pregnancy periods. Bioinformatic analysis revealed that there were differences in the composition of the GM among P1, P2, and P3, as indicated by the increase in α-diversity and β-diversity of the GM and the differences in the relative abundances of distinct bacterial phyla. Gestational diabetes mellitus (GDM) was the main factor (P < 0.05) that affected the changes in GM at various stages of pregnancy. There were also disparities in the structure of the GM between the GDM group and non-GDM group in the P1, P2, and P3. The GDM group exhibited increased abundances in Ruminococcus_gnavus, Akkermansia_muciniphila, Alistipes_shahii, Blautia_obeum, and Roseburia_intestinalis; while, the abundances of Bacteroides coprocola, Bacteroides plebeius, Erysipelatoclostridium ramosum, and Prevotella copri were increased in the non-GDM group. Three of the four species enriched in the non-GDM group manifestied significantly negative correlations with the insulin-signaling pathway and lipopolysaccharide biosynthesis (r ≤ -0.3, adjusted P < 0.05). In the GDM group, Bacteroides vulgatus and Ruminococcus gnavus were significantly and positively correlated with insulin signaling pathway and lipopolysaccharide biosynthesis (r ≤ -0.3, adjusted P < 0.05) among the species enriched from early pregnancy. Virtually all of the species enriched in P2 and P3 were positively correlated with steroid hormone biosynthesis. These results suggest a potential role for the GM in the development of GDM, enabling the potential prevention of GDM by targeting the GM.}, } @article {pmid37065124, year = {2023}, author = {Yavari-Bafghi, M and Rezaei Somee, M and Amoozegar, MA and Dastgheib, SMM and Shavandi, M}, title = {Genome-resolved analyses of oligotrophic groundwater microbial communities along phenol pollution in a continuous-flow biodegradation model system.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1147162}, pmid = {37065124}, issn = {1664-302X}, abstract = {Groundwater pollution is one of the major environmental concerns. The entrance of pollutants into the oligotrophic groundwater ecosystems alters native microbial community structure and metabolism. This study investigated the application of innovative Small Bioreactor Chambers and CaO2 nanoparticles for phenol removal within continuous-flow sand-packed columns for 6 months. Scanning electron microscopy and confocal laser scanning microscopy analysis were conducted to indicate the impact of attached biofilm on sand surfaces in bioremediation columns. Then, the influence of each method on the microbial biodiversity of the column's groundwater was investigated by next-generation sequencing of the 16S rRNA gene. The results indicated that the simultaneous application of biostimulation and bioaugmentation completely eliminated phenol during the first 42 days. However, 80.2% of phenol remained in the natural bioremediation column at the end of the experiment. Microbial diversity was decreased by CaO2 injection while order-level groups known for phenol degradation such as Rhodobacterales and Xanthomonadales dominated in biostimulation columns. Genome-resolved comparative analyses of oligotrophic groundwater prokaryotic communities revealed that Burkholderiales, Micrococcales, and Cytophagales were the dominant members of the pristine groundwater. Six-month exposure of groundwater to phenol shifted the microbial population towards increasing the heterotrophic members of Desulfobacterales, Pseudomonadales, and Xanthomonadales with the degradation potential of phenol and other hydrocarbons.}, } @article {pmid37065117, year = {2023}, author = {Li, Y and Jiang, X and Chen, J and Hu, Y and Bai, Y and Xu, W and He, L and Wang, Y and Chen, C and Chen, J}, title = {Evaluation of the contribution of gut microbiome dysbiosis to cardiac surgery-associated acute kidney injury by comparative metagenome analysis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1119959}, pmid = {37065117}, issn = {1664-302X}, abstract = {INTRODUCTION: Cardiac surgery-associated acute kidney injury (CSA-AKI) is a common hospital-acquired AKI that carries a grave disease burden. Recently, gut-kidney crosstalk has greatly changed our understanding of the pathogenesis of kidney diseases. However, the relationship between gut microbial dysbiosis and CSA-AKI remains unclear. The purpose of this study was to investigate the possible contributions of gut microbiota alterations in CSA-AKI patients.

METHODS: Patients undergoing cardiac surgery were enrolled and divided into acute kidney injury (AKI) and Non_AKI groups. Faecal samples were collected before the operation. Shotgun metagenomic sequencing was performed to identify the taxonomic composition of the intestinal microbiome. All groups were statistically compared with alpha- and beta-diversity analysis, and linear discriminant analysis effect size (LEfSe) analysis was performed.

RESULTS: A total of 70 individuals comprising 35 AKI and 35 Non_AKI were enrolled in the study. There was no significant difference between the AKI and Non_AKI groups with respect to the alpha-and beta-diversity of the Shannon index, Simpson or Chao1 index values except with respect to functional pathways (p < 0.05). However, the relative abundance of top 10 gut microbiota in CSA-AKI was different from the Non_AKI group. Interestingly, both LEfSe and multivariate analysis confirmed that the species Escherichia coli, Rothia mucilaginosa, and Clostridium innocuum were associated with CSA-AKI. Moreover, correlation heat map indicated that altered pathways and disrupted function could be attributed to disturbances of gut microbiota involving Escherichia coli.

CONCLUSION: Dysbiosis of the intestinal microbiota in preoperative stool affects susceptibility to CSA-AKI, indicating the crucial role of key microbial players in the development of CSA-AKI. This work provides valuable knowledge for further study of the contribution of gut microbiota in CSA-AKI.}, } @article {pmid37065115, year = {2023}, author = {Yuan, H and Wang, Z and Wang, Z and Zhang, F and Guan, D and Zhao, R}, title = {Trends in forensic microbiology: From classical methods to deep learning.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1163741}, pmid = {37065115}, issn = {1664-302X}, abstract = {Forensic microbiology has been widely used in the diagnosis of causes and manner of death, identification of individuals, detection of crime locations, and estimation of postmortem interval. However, the traditional method, microbial culture, has low efficiency, high consumption, and a low degree of quantitative analysis. With the development of high-throughput sequencing technology, advanced bioinformatics, and fast-evolving artificial intelligence, numerous machine learning models, such as RF, SVM, ANN, DNN, regression, PLS, ANOSIM, and ANOVA, have been established with the advancement of the microbiome and metagenomic studies. Recently, deep learning models, including the convolutional neural network (CNN) model and CNN-derived models, improve the accuracy of forensic prognosis using object detection techniques in microorganism image analysis. This review summarizes the application and development of forensic microbiology, as well as the research progress of machine learning (ML) and deep learning (DL) based on microbial genome sequencing and microbial images, and provided a future outlook on forensic microbiology.}, } @article {pmid37065114, year = {2023}, author = {Wang, Y and Wu, Y and Cao, C and Han, S and Zhao, W and Li, Q and Liu, X and Kong, L}, title = {Effects of fertilizer reduction coupled with straw returning on soil fertility, wheat root endophytic bacteria, and the occurrence of wheat crown rot.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1143480}, pmid = {37065114}, issn = {1664-302X}, abstract = {Excessive fertilization is associated with nutrient loss, soil compaction, and weak plant resistance. Straw returning can increase soil fertility with a consequent reduction in fertilizer, but the effects of fertilizer reduction coupled with straw returning on crop endophytic microbes and crop disease are poorly understood. Therefore, using metagenomic sequencing methods we investigated the responses of soil fertility, diversity, the function of root endophytic bacteria, and the occurrence of wheat crown rot due to the application of fertilizer (no, moderate and excessive fertilizer) coupled with or without straw returning after 7 years of treatments. The results showed that, after excessive fertilization, the wheat crown rot became severe, registering a disease index of 23. Compared with excessive fertilization, moderate fertilization coupled with straw returning significantly reduced the incidence of wheat crown rot, the disease index was reduced by 38.50%, and the richness and diversity of endophytic bacteria were increased by 61.20 and 11.93%, respectively, but the soil fertility was not significantly affected. In addition, moderate fertilization coupled with straw returning changed the community structure of endophytic bacteria and increased the relative abundance of carbohydrate metabolism and nitrogen fixation-related genes by 4.72 and 9.32%, respectively. Our results indicated that fertilizer reduction coupled with straw returning reduced the occurrence of wheat crown rot, increased the diversity of endophytic bacteria, and changed the community structure and function of endophytic bacteria, which will provide a better understanding of the interaction of fertilization coupled with straw returning, endophytic bacteria and wheat crown rot.}, } @article {pmid37064368, year = {2023}, author = {Wu, J and Pan, J and Han, C and Liu, C and Huang, J and Yan, J and Zhang, K and Chen, YC}, title = {Clinical and CT diagnosis of 50 cases of Chlamydia psittaci pneumonia.}, journal = {Quantitative imaging in medicine and surgery}, volume = {13}, number = {4}, pages = {2053-2064}, pmid = {37064368}, issn = {2223-4292}, abstract = {BACKGROUND: This is a retrospective cross-sectional study aiming to explore the clinical and imaging manifestations of Chlamydia psittaci pneumonia (CPP), thus improving its diagnosis, guiding its early clinical treatment, and reducing its mortality rate.

METHODS: Fifty cases of CPP diagnosed by hospitals across the country with metagenomics next-generation sequencing (mNGS) from January 2019 to March 2021 were collected. Its clinical symptoms, laboratory test results, and computed tomography (CT) features were discussed.

RESULTS: Forty patients had a history of poultry exposure; 37 experienced respiratory symptoms, 48 had a fever, 14 experienced gastrointestinal symptoms, and 12 experienced neurological symptoms; 34 patients had normal blood cell counts, 49 patients had elevated C-reactive protein, and 24 showed decreased serum sodium. Imaging manifestations: (I) Distribution: lesions were limited to a single lung in 31 patients, lesions were distributed in bilateral lungs in 19 patients; (II) Signs: 37 patients developed the "fine mesh sign". Necrosis, cavity and "tree-in-bud" were not observed. Pleural effusion occurred in 33 patients, mediastinal lymphadenopathy in 18, and splenomegaly in 15 patients.

CONCLUSIONS: Patients with CPP often have a history of poultry exposure and present with fever and increased C-reactive protein. White blood cells may be slightly increased or completely normal. Hyponatremia may occur in some patients, and multiple systems may be clinically involved. The imaging can show lesions with unilateral or bilateral lung distribution and a rapid progression. Both the lung parenchyma and the interstitium are involved. Fine mesh sign is the most common sign. Necrosis, cavitation, and tree-in-bud signs are not observed. In conclusion, imaging examinations are helpful for the early diagnosis of this disease and the evaluation of the treatment effect.}, } @article {pmid37063855, year = {2023}, author = {Li, C and Zhang, Y and Yan, Q and Guo, R and Chen, C and Li, S and Zhang, Y and Meng, J and Ma, J and You, W and Wu, Z and Sun, W}, title = {Alterations in the gut virome in patients with ankylosing spondylitis.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1154380}, pmid = {37063855}, issn = {1664-3224}, mesh = {Humans ; *Spondylitis, Ankylosing ; Virome ; *Gastrointestinal Microbiome ; *Viruses ; *Bacteriophages/genetics ; *Autoimmune Diseases ; }, abstract = {INTRODUCTION: Ankylosing spondylitis (AS), a chronic autoimmune disease, has been linked to the gut bacteriome.

METHODS: To investigate the characteristics of the gut virome in AS, we profiled the gut viral community of 193 AS patients and 59 healthy subjects based on a metagenome-wide analysis of fecal metagenomes from two publicly available datasets.

RESULTS: AS patients revealed a significant decrease in gut viral richness and a considerable alteration of the overall viral structure. At the family level, AS patients had an increased abundance of Gratiaviridae and Quimbyviridae and a decreased abundance of Drexlerviridae and Schitoviridae. We identified 1,004 differentially abundant viral operational taxonomic units (vOTUs) between patients and controls, including a higher proportion of AS-enriched Myoviridae viruses and control-enriched Siphoviridae viruses. Moreover, the AS-enriched vOTUs were more likely to infect bacteria such as Flavonifractor, Achromobacter, and Eggerthellaceae, whereas the control-enriched vOTUs were more likely to be Blautia, Ruminococcus, Collinsella, Prevotella, and Faecalibacterium bacteriophages. Additionally, some viral functional orthologs differed significantly in frequency between the AS-enriched and control-enriched vOTUs, suggesting the functional role of these AS-associated viruses. Moreover, we trained classification models based on gut viral signatures to discriminate AS patients from healthy controls, with an optimal area under the receiver operator characteristic curve (AUC) up to 0.936, suggesting the clinical potential of the gut virome for diagnosing AS.

DISCUSSION: This work provides novel insight into the AS gut virome, and the findings may guide future mechanistic and therapeutic studies for other autoimmune diseases.}, } @article {pmid37063829, year = {2023}, author = {Elnaggar, JH and Huynh, VO and Lin, D and Hillman, RT and Abana, CO and El Alam, MB and Tomasic, KC and Karpinets, TV and Kouzy, R and Phan, JL and Wargo, J and Holliday, EB and Das, P and Mezzari, MP and Ajami, NJ and Lynn, EJ and Minsky, BD and Morris, VK and Milbourne, A and Messick, CA and Klopp, AH and Futreal, PA and Taniguchi, CM and Schmeler, KM and Colbert, LE}, title = {HPV-related anal cancer is associated with changes in the anorectal microbiome during cancer development.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1051431}, pmid = {37063829}, issn = {1664-3224}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; T32 CA101642/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Female ; *Papillomavirus Infections ; Prospective Studies ; Cross-Sectional Studies ; *Anus Neoplasms ; *Carcinoma, Squamous Cell/complications ; *Microbiota ; Tumor Microenvironment ; }, abstract = {BACKGROUND: Squamous cell carcinoma of the anus (SCCA) is a rare gastrointestinal cancer. Factors associated with progression of HPV infection to anal dysplasia and cancer are unclear and screening guidelines and approaches for anal dysplasia are less clear than for cervical dysplasia. One potential contributing factor is the anorectal microbiome. In this study, we aimed to identify differences in anal microbiome composition in the settings of HPV infection, anal dysplasia, and anal cancer in this rare disease.

METHODS: Patients were enrolled in two prospective studies. Patients with anal dysplasia were part of a cross-sectional cohort that enrolled women with high-grade lower genital tract dysplasia. Anorectal tumor swabs were prospectively collected from patients with biopsy-confirmed locally advanced SCCA prior to receiving standard-of-care chemoradiotherapy (CRT). Patients with high-grade lower genital tract dysplasia without anal dysplasia were considered high-risk (HR Normal). 16S V4 rRNA Microbiome sequencing was performed for anal swabs. Alpha and Beta Diversity and composition were compared for HR Normal, anal dysplasia, and anal cancer.

RESULTS: 60 patients with high-grade lower genital tract dysplasia were initially enrolled. Seven patients had concurrent anal dysplasia and 44 patients were considered HR Normal. Anorectal swabs from 21 patients with localized SCCA were included, sequenced, and analyzed in the study. Analysis of weighted and unweighted UniFrac distances demonstrated significant differences in microbial community composition between anal cancer and HR normal (p=0.018). LEfSe identified that all three groups exhibited differential enrichment of specific taxa. Peptoniphilus (p=0.028), Fusobacteria (p=0.0295), Porphyromonas (p=0.034), and Prevotella (p=0.029) were enriched in anal cancer specimens when compared to HR normal.

CONCLUSION: Although alpha diversity was similar between HR Normal, dysplasia and cancer patients, composition differed significantly between the three groups. Increased anorectal Peptoniphilus, Fusobacteria, Porphyromonas, and Prevotella abundance were associated with anal cancer. These organisms have been reported in various gastrointestinal cancers with roles in facilitating the proinflammatory microenvironment and neoplasia progression. Future work should investigate a potential role of microbiome analysis in screening for anal dysplasia and investigation into potential mechanisms of how these microbial imbalances influence the immune system and anal carcinogenesis.}, } @article {pmid37063664, year = {2023}, author = {Agudelo-Pérez, S and Fernández-Sarmiento, J and Rivera León, D and Peláez, RG}, title = {Metagenomics by next-generation sequencing (mNGS) in the etiological characterization of neonatal and pediatric sepsis: A systematic review.}, journal = {Frontiers in pediatrics}, volume = {11}, number = {}, pages = {1011723}, pmid = {37063664}, issn = {2296-2360}, abstract = {INTRODUCTION: Pediatric and neonatal sepsis is one of the main causes of mortality and morbidity in these age groups. Accurate and early etiological identification is essential for guiding antibiotic treatment, improving survival, and reducing complications and sequelae. Currently, the identification is based on culture-dependent methods, which has many limitations for its use in clinical practice, and obtaining its results is delayed. Next-generation sequencing enables rapid, accurate, and unbiased identification of multiple microorganisms in biological samples at the same time. The objective of this study was to characterize the etiology of neonatal and pediatric sepsis by metagenomic techniques.

METHODS: A systematic review of the literature was carried out using the PRISMA-2020 guide. Observational, descriptive, and case report studies on pediatric patients were included, with a diagnostic evaluation by clinical criteria of sepsis based on the systemic inflammatory response, in sterile and non-sterile biofluid samples. The risk of bias assessment of the observational studies was carried out with the STROBE-metagenomics instrument and the CARE checklist for case reports.

RESULTS AND DISCUSSION: Five studies with a total of 462 patients were included. Due to the data obtained from the studies, it was not possible to perform a quantitative synthesis (meta-analysis). Based on the data from the included studies, the result identified that mNGS improves the etiological identification in neonatal and pediatric sepsis, especially in the context of negative cultures and in the identification of unusual microorganisms (bacteria that are difficult to grow in culture, viruses, fungi, and parasites). The number of investigations is currently limited, and the studies are at high risk of bias. Further research using this technology would have the potential to improve the rational use of antibiotics.}, } @article {pmid37063260, year = {2023}, author = {Shi, J and Chen, J and Xie, X and Li, Y and Ye, W and Yao, J and Zhang, X and Zhang, T and Gao, J}, title = {Baicalein-corrected gut microbiota may underlie the amelioration of memory and cognitive deficits in APP/PS1 mice.}, journal = {Frontiers in pharmacology}, volume = {14}, number = {}, pages = {1132857}, pmid = {37063260}, issn = {1663-9812}, abstract = {Background: Baicalein is an active ingredient extracted from the root of S. baicalensis Georgi, which exhibits cardiovascular protection, anti-inflammatory, and anti-microbial properties. Our previous study showed that chronic treatment of Baicalein ameliorated cognitive dysfunction in a mouse model of Alzheimer's disease (AD). However, it remains unknown whether Baicalein ameliorates cognitive deficits in AD mouse models by altering gut microbiota and its metabolites. Methods: Behavioral tests, metagenomic and untargeted metabolomics analyses were used to evaluate the effects of Baicalein on the APP/PS1 mice. Results: Our research showed that treatment of Baicalein for 2 weeks ameliorated cognition and memory in a dose-dependent manner, as indicated by the significant increases in the Discrimination index and Number of crossings and decrease in latency to the previous platform location in 8-month of age APP/PS1 mice in novel object recognition and water maze tests. The metagenomic analysis showed the abundance of the dominant phyla in all groups, including Bacteroidetes (14.59%-67.02%) and Firmicutes (20.19%-61.39%). LEfSe analysis of metagenomics identified three species such as s__Roseburia_sp_1XD42_69, s__Muribaculaceae_bacterium_Isolate_104_HZI, s__Muribaculaceae_bacterium_Isolate_110_HZI as Baicalein-treated potential biomarkers. Metabolite analysis revealed the increment of metabolites, including glutamate, thymine and hexanoyl-CoA. Conclusion: The effects of Baicalein on memory and cognition may relate to the metabolism of nucleotides, lipids and glucose.}, } @article {pmid37062947, year = {2023}, author = {Váncsa, S and Sipos, Z and Váradi, A and Nagy, R and Ocskay, K and Juhász, FM and Márta, K and Teutsch, B and Mikó, A and Hegyi, PJ and Vincze, Á and Izbéki, F and Czakó, L and Papp, M and Hamvas, J and Varga, M and Török, I and Mickevicius, A and Erőss, B and Párniczky, A and Szentesi, A and Pár, G and Hegyi, P and , }, title = {Metabolic-associated fatty liver disease is associated with acute pancreatitis with more severe course: Post hoc analysis of a prospectively collected international registry.}, journal = {United European gastroenterology journal}, volume = {11}, number = {4}, pages = {371-382}, pmid = {37062947}, issn = {2050-6414}, mesh = {Humans ; *Pancreatitis/diagnosis/epidemiology/etiology ; *Non-alcoholic Fatty Liver Disease/complications/diagnosis/epidemiology ; Acute Disease ; Prospective Studies ; Registries ; }, abstract = {INTRODUCTION: Non-alcoholic fatty liver disease (NAFLD) is a proven risk factor for acute pancreatitis (AP). However, NAFLD has recently been redefined as metabolic-associated fatty liver disease (MAFLD). In this post hoc analysis, we quantified the effect of MAFLD on the outcomes of AP.

METHODS: We identified our patients from the multicentric, prospective International Acute Pancreatitis Registry of the Hungarian Pancreatic Study Group. Next, we compared AP patients with and without MAFLD and the individual components of MAFLD regarding in-hospital mortality and AP severity based on the revised Atlanta classification. Lastly, we calculated odds ratios (ORs) with 95% confidence intervals (CIs) using multivariate logistic regression analysis.

RESULTS: MAFLD had a high prevalence in AP, 39% (801/2053). MAFLD increased the odds of moderate-to-severe AP (OR = 1.43, CI: 1.09-1.89). However, the odds of in-hospital mortality (OR = 0.89, CI: 0.42-1.89) and severe AP (OR = 1.70, CI: 0.97-3.01) were not higher in the MAFLD group. Out of the three diagnostic criteria of MAFLD, the highest odds of severe AP was in the group based on metabolic risk abnormalities (OR = 2.68, CI: 1.39-5.09). In addition, the presence of one, two, and three diagnostic criteria dose-dependently increased the odds of moderate-to-severe AP (OR = 1.23, CI: 0.88-1.70, OR = 1.38, CI: 0.93-2.04, and OR = 3.04, CI: 1.63-5.70, respectively) and severe AP (OR = 1.13, CI: 0.54-2.27, OR = 2.08, CI: 0.97-4.35, and OR = 4.76, CI: 1.50-15.4, respectively). Furthermore, in patients with alcohol abuse and aged ≥60 years, the effect of MAFLD became insignificant.

CONCLUSIONS: MAFLD is associated with AP severity, which varies based on the components of its diagnostic criteria. Furthermore, MAFLD shows a dose-dependent effect on the outcomes of AP.}, } @article {pmid37061654, year = {2023}, author = {Elbehery, AHA and Beason, E and Siam, R}, title = {Metagenomic profiling of antibiotic resistance genes in Red Sea brine pools.}, journal = {Archives of microbiology}, volume = {205}, number = {5}, pages = {195}, pmid = {37061654}, issn = {1432-072X}, support = {Faculty (Research) Support Grant//The American University in Cairo/ ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Indian Ocean ; *Drug Resistance, Bacterial/genetics ; Macrolides ; Genes, Bacterial ; }, abstract = {Antibiotic resistance (AR) is an alarming global health concern, causing an annual death rate of more than 35,000 deaths in the US. AR is a natural phenomenon, reported in several pristine environments. In this study, we report AR in pristine Red Sea deep brine pools. Antimicrobial resistance genes (ARGs) were detected for several drug classes with tetracycline and macrolide resistance being the most abundant. As expected, ARGs abundance increased in accordance with the level of human impact with pristine Red Sea samples having the lowest mean ARG level followed by estuary samples, while activated sludge samples showed a significantly higher ARG level. ARG hierarchical clustering grouped drug classes for which resistance was detected in Atlantis II Deep brine pool independent of the rest of the samples. ARG abundance was significantly lower in the Discovery Deep brine pool. A correlation between integrons and ARGs abundance in brine pristine samples could be detected, while insertion sequences and plasmids showed a correlation with ARGs abundance in human-impacted samples not seen in brine pristine samples. This suggests different roles of distinct mobile genetic elements (MGEs) in ARG distribution in pristine versus human-impacted sites. Additionally, we showed the presence of mobile antibiotic resistance genes in the Atlantis II brine pool as evidenced by the co-existence of integrases and plasmid replication proteins on the same contigs harboring predicted multidrug-resistant efflux pumps. This study addresses the role of non-pathogenic environmental bacteria as a silent reservoir for ARGs, and the possible horizontal gene transfer mechanism mediating ARG acquisition.}, } @article {pmid37060877, year = {2023}, author = {Zhou, S and Yang, Z and Zhang, S and Gao, Y and Tang, Z and Duan, Y and Zhang, Y and Wang, Y}, title = {Metagenomic insights into the distribution, mobility, and hosts of extracellular antibiotic resistance genes in activated sludge under starvation stress.}, journal = {Water research}, volume = {236}, number = {}, pages = {119953}, doi = {10.1016/j.watres.2023.119953}, pmid = {37060877}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; *Wastewater ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Carbon ; }, abstract = {Extracellular antibiotic resistance genes (eARGs) are important emerging environmental pollutants in wastewater treatment plants (WWTPs). Nutritional substrate deficiency (i.e., starvation) frequently occurs in WWTPs owing to annual maintenance, water quality fluctuation, and sludge storage; and it can greatly alter the antibiotic resistance and extracellular DNA content of bacteria. However, the fate and corresponding transmission risk of eARGs in activated sludge under starvation stress remain largely unknown. Herein, we used metagenomic sequencing to explore the effects of starvation scenarios (carbon, nitrogen, and/or phosphorus deficiency) and environmental conditions (alternating anaerobic-aerobic, anaerobic, anoxic, and aerobic) on the distribution, mobility, and hosts of eARGs in activated sludge. The results showed that 30 days of starvation reduced the absolute abundances of eARGs by 40.9%-88.2%, but high-risk dual and multidrug resistance genes persisted. Starvation, particularly the simultaneous lack of carbon, nitrogen, and phosphorus under aerobic conditions, effectively alleviated eARGs by reducing the abundance of extracellular mobile genetic elements (eMGEs). Starvation also altered the profile of bacterial hosts of eARGs and the bacterial community composition, the latter of which had an indirect positive effect on eARGs via changing eMGEs. Our findings shed light on the response patterns and mechanisms of eARGs in activated sludge under starvation conditions and highlight starvation as a potential strategy to mitigate the risk of previously neglected eARGs in WWTPs.}, } @article {pmid37060793, year = {2023}, author = {Phua, YH and Tejeda, J and Roy, MC and Husnik, F and Wakeman, KC}, title = {Bacterial communities and toxin profiles of Ostreopsis (Dinophyceae) from the Pacific island of Okinawa, Japan.}, journal = {European journal of protistology}, volume = {89}, number = {}, pages = {125976}, doi = {10.1016/j.ejop.2023.125976}, pmid = {37060793}, issn = {1618-0429}, mesh = {Japan ; Pacific Islands ; Phylogeny ; *Dinoflagellida/genetics/metabolism ; Bacteria ; }, abstract = {Variations in toxicity of the benthic dinoflagellate Ostreopsis Schmidt 1901 have been attributed to specific molecular clades, biogeography of isolated strains, and the associated bacterial community. Here, we attempted to better understand the biodiversity and the basic biology influencing toxin production of Ostreopsis. Nine clonal cultures were established from Okinawa, Japan, and identified using phylogenetic analysis of the ITS-5.8S rRNA and 28S rRNA genes. Morphological analysis suggests that the apical pore complex L/W ratio could be a feature for differentiating Ostreopsis sp. 2 from the O. ovata species complex. We analyzed the toxicity and bacterial communities using liquid chromatography-mass spectrometry, and PCR-free metagenomic sequencing. Ovatoxin was detected in three of the seven strains of O. cf. ovata extracts, highlighting intraspecies variation in toxin production. Additionally, two new potential analogs of ovatoxin-a and ostreocin-A were identified. Commonly associated bacteria clades of Ostreopsis were identified from the established cultures. While some of these bacteria groups may be common to Ostreopsis (Rhodobacterales, Flavobacteria-Sphingobacteria, and Enterobacterales), it was not clear from our analysis if any one or more of these plays a role in toxin biosynthesis. Further examination of biosynthetic pathways in metagenomic data and additional experiments isolating specific bacteria from Ostreopsis would aid these efforts.}, } @article {pmid37060751, year = {2023}, author = {Vaccari, F and Zhang, L and Giuberti, G and Grasso, A and Bandini, F and García-Pérez, P and Copat, C and Lucini, L and Dall'Asta, M and Ferrante, M and Puglisi, E}, title = {The impact of metallic nanoparticles on gut fermentation processes: An integrated metabolomics and metagenomics approach following an in vitro digestion and fecal fermentation model.}, journal = {Journal of hazardous materials}, volume = {453}, number = {}, pages = {131331}, doi = {10.1016/j.jhazmat.2023.131331}, pmid = {37060751}, issn = {1873-3336}, mesh = {Humans ; *Zinc Oxide/toxicity ; Metagenomics ; Fermentation ; *Metal Nanoparticles/toxicity ; Titanium ; Metabolomics ; Escherichia coli ; Digestion ; }, abstract = {Metallic nanoparticles (MNPs) are becoming widespread environmental contaminants. They are currently added to several food preparations and cause a fast-growing concern for human health. The present work aims to assess the impact of zinc oxide (ZnO), titanium dioxide (TiO2), and silver (Ag) nanoparticles (NPs) on the human gut metabolome and microbiome. Water samples spiked with two different concentrations of each MNPs were subjected to in-vitro gastrointestinal digestion and in-vitro large intestine fermentation. The effects of the treatments were determined through 16 S amplicon sequencing and untargeted metabolomics. Multi-omics data integration was then applied to correlate the two datasets. MNPs treatments modulated the microbial genera Bifidobacterium, Sutterella, Escherichia and Bacteroides. The treatments, especially the lower concentrations of Ag and ZnO, caused modulation of indole derivatives, peptides, and metabolites related to protein metabolism in the large intestine. Notably, these metabolites are implicated in ulcerative colitis and inflammatory bowel disease. TiO2 NPs treatment in all concentrations increased E.coli relative abundance and decreased the abundance of B. longum. Moreover, for TiO2, an enrichment in proinflammatory lipid mediators of arachidonic acid metabolites, such as prostaglandin E2 and leukotrienes B4, was detected. For all metals except TiO2, low NP concentrations promoted differentiated profiles, thus suggesting that MNPs aggregation can limit adverse effects on living cells.}, } @article {pmid37060094, year = {2023}, author = {Qu, A and Duan, B and Wang, Y and Cui, Z and Zhang, N and Wu, D}, title = {Children with autism show differences in the gut DNA virome compared to non-autistic children: a case control study.}, journal = {BMC pediatrics}, volume = {23}, number = {1}, pages = {174}, pmid = {37060094}, issn = {1471-2431}, mesh = {Humans ; *Autism Spectrum Disorder/genetics ; *Autistic Disorder ; Case-Control Studies ; Virome ; DNA ; }, abstract = {BACKGROUND: Several previous studies have identified a potential role that the gut microbiome can play in autism spectrum disorder (ASD) in children, but little is known about how variations in the virome may be involved in ASD. We aimed to understand the changes in the gut DNA virome of children with ASD.

METHODS: A case-control study was presented, in which 13 two-children families were observed while considering the age, mode of birth, history of antibiotic use, and vaccination history to minimize the influence of confounding factors. DNA viral metagenomic sequencing was successfully performed on stool samples from 11 children with ASD and 12 healthy non-ASD children. The basic composition and gene function of the participants' fecal DNA virome were detected and analyzed. Finally, the abundance and diversity of the DNA virome of children with ASD and their healthy siblings were compared.

RESULTS: The gut DNA virome in children aged 3-11 years was found to be dominated by the Siphoviridae family of Caudovirales. The proteins encoded by the DNA genes mainly carry out the functions of genetic information transmission and metabolism. Compared the gut DNA virome of ASD and healthy non-ASD children, their abundance of Caudovirales and Petitvirales both showed a significant negative correlation (r = -0.902, P < 0.01), there was no statistically significant difference in the relative abundance of viruses at the order and family levels, and a difference in the relative abundance at the genus level for Skunavirus (Ζ = -2.157, P = 0.031). Viral α diversity was reduced in children with ASD, but α diversity and β diversity did not differ statistically between groups.

CONCLUSIONS: This study indicates that elevated Skunavirus abundance and decreased α diversity in the gut DNA virulence group of children with ASD, but no statistically significant difference in the change in alpha and beta diversity. This provides preliminary cumulative information on virological aspects of the relationship between the microbiome and ASD, and should benefit future multi-omics and large sample studies on the gut microbes in children with ASD.}, } @article {pmid37060052, year = {2023}, author = {Liu, Y and Wang, M and Li, W and Gao, Y and Li, H and Cao, N and Hao, W and Zhao, L}, title = {Differences in gut microbiota and its metabolic function among different fasting plasma glucose groups in Mongolian population of China.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {102}, pmid = {37060052}, issn = {1471-2180}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2 ; Blood Glucose ; Diet ; Bacteria/genetics ; Fasting ; }, abstract = {BACKGROUND: Many studies reported the association between gut microbiota and type 2 diabetes mellitus (T2D), but it is still unclear which bacterial genus plays a key role and how the metabolic function of gut microbiota changes in the occurrence and development of T2D. Besides, there is a high diabetic prevalence in Mongolian population, which may be partly affected by their high calorie diet. This study identified the main bacterial genus influencing T2D in Mongolian population, and analyzed the changes of metabolic function of gut microbiome. The association between dietary factors and the relative abundance of main bacterial genus and its metabolic function was also studied.

METHODS: Dietary surveys and gut microbiota test were performed on 24 Mongolian volunteers that were divided into T2D (6 cases), PRET2D (6 cases) and Control group (12 cases) according to fasting plasma glucose (FPG) values. The relative abundance and metabolic function of gut microbiome from their fecal samples were measured by metagenomic analysis. Statistic method was used to evaluate the association between dietary factors and the relative abundance of the main bacterial genus or its metabolic function.

RESULTS: This study found that the Clostridium genus may be one of the key bacterial genera affecting the process of T2D. First, the relative abundance of Clostridium genus was significantly different among the three groups. Second, there was a higher relative abundance of metabolic enzymes of gut bacteria in PRET2D and T2D group than that in Control group. Third, a strong correlation between Clostridium genus and many metabolic enzymes was uncovered, many of which may be produced by the Clostridium. Last, carotene intake daily was negatively correlated with the Clostridium but positively correlated with tagaturonate reductase catalyzing interconversions of pentose and glucuronate.

CONCLUSIONS: The gut Clostridium genus may play an important role in the development of T2D and it could be a potential biomarker for T2D in Mongolian population. Meanwhile, the metabolic function of gut bacteria has changed during the early stage of T2D and the changes in carbohydrate, amino acid, lipid or energy metabolism of Clostridium genus may play a critical role. In addition, the carotene intake may affect reproduction and metabolic function of Clostridium genus.}, } @article {pmid37059533, year = {2023}, author = {Ge, YM and Zhang, Y and Yang, JS and Ye, WY and Gao, HM and Liu, JZ and Bao, QB and Jiang, W}, title = {Facile preparation of a novel iminodisuccinate modified chitin and its excellent properties as a silver bioadsorbent and antibacterial agent.}, journal = {Carbohydrate polymers}, volume = {312}, number = {}, pages = {120793}, doi = {10.1016/j.carbpol.2023.120793}, pmid = {37059533}, issn = {1879-1344}, mesh = {*Chitin/pharmacology ; *Metal Nanoparticles/chemistry ; Silver/pharmacology/chemistry ; Anti-Bacterial Agents/pharmacology/chemistry ; }, abstract = {A novel iminodisuccinate modified chitin (ICH) was prepared using crab shells via a one-step facile procedure. The ICH with grafting degree of 1.46 and deacetylation degree of 47.68 % possessed maximum adsorption capacity of 2572.41 mg/g for silver ions (Ag(I)).The ICH also exhibited good selectivity and reusability. The adsorption followed better with the Freundlich isotherm model, while fitted well with both the Pseudo-first-order and Pseudo-second-order kinetics models. The characteristical results showed that the excellent Ag(I) adsorption capability of ICH should be attributed to both looser porous microstructure as well as additional functional groups-grafting molecular. Moreover, the Ag-loaded ICH (ICH-Ag) showed remarkable antibacterial properties against six typical pathogenic bacteria strains (Escherichia coli, Pseudomonas aeruginosa, Enterobacter aerogenes, Salmonella typhimurium, Staphylococcus aureus, and Listeria monocytogenes), with the corresponding 90 % minimal inhibitory concentrations ranged 0.426-0.685 mg/mL. Further study on the silver release, microcell morphology, and metagenomic analysis suggested that many Ag nanoparticles were formed after the Ag(I) adsorption, and the antibacterial mechanisms of the ICH-Ag involved both cell membranes destruction and intracellular metabolism disturbing. This research presented a coupling solution of crab shell wastes treatment with chitin-based bioadsorbents preparation, metal removal and recovery, as well as antibacterial agent production.}, } @article {pmid37059172, year = {2023}, author = {Jiménez-Volkerink, SN and Jordán, M and Singleton, DR and Grifoll, M and Vila, J}, title = {Bacterial benz(a)anthracene catabolic networks in contaminated soils and their modulation by other co-occurring HMW-PAHs.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {328}, number = {}, pages = {121624}, doi = {10.1016/j.envpol.2023.121624}, pmid = {37059172}, issn = {1873-6424}, mesh = {*Polycyclic Aromatic Hydrocarbons/metabolism ; Molecular Weight ; Biodegradation, Environmental ; *Sphingomonadaceae/genetics/metabolism ; Benz(a)Anthracenes/metabolism ; Soil ; *Soil Pollutants/metabolism ; Soil Microbiology ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are major environmental pollutants in a number of point source contaminated sites, where they are found embedded in complex mixtures containing different polyaromatic compounds. The application of bioremediation technologies is often constrained by unpredictable end-point concentrations enriched in recalcitrant high molecular weight (HMW)-PAHs. The aim of this study was to elucidate the microbial populations and potential interactions involved in the biodegradation of benz(a)anthracene (BaA) in PAH-contaminated soils. The combination of DNA stable isotope probing (DNA-SIP) and shotgun metagenomics of [13]C-labeled DNA identified a member of the recently described genus Immundisolibacter as the key BaA-degrading population. Analysis of the corresponding metagenome assembled genome (MAG) revealed a highly conserved and unique genetic organization in this genus, including novel aromatic ring-hydroxylating dioxygenases (RHD). The influence of other HMW-PAHs on BaA degradation was ascertained in soil microcosms spiked with BaA and fluoranthene (FT), pyrene (PY) or chrysene (CHY) in binary mixtures. The co-occurrence of PAHs resulted in a significant delay in the removal of PAHs that were more resistant to biodegradation, and this delay was associated with relevant microbial interactions. Members of Immundisolibacter, associated with the biodegradation of BaA and CHY, were outcompeted by Sphingobium and Mycobacterium, triggered by the presence of FT and PY, respectively. Our findings highlight that interacting microbial populations modulate the fate of PAHs during the biodegradation of contaminant mixtures in soils.}, } @article {pmid37058886, year = {2023}, author = {Russo, E and Gloria, LD and Nannini, G and Meoni, G and Niccolai, E and Ringressi, MN and Baldi, S and Fani, R and Tenori, L and Taddei, A and Ramazzotti, M and Amedei, A}, title = {From adenoma to CRC stages: the oral-gut microbiome axis as a source of potential microbial and metabolic biomarkers of malignancy.}, journal = {Neoplasia (New York, N.Y.)}, volume = {40}, number = {}, pages = {100901}, pmid = {37058886}, issn = {1476-5586}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/pathology ; *Adenoma/diagnosis ; *Microbiota ; Bacteria ; *Rectal Neoplasms ; Biomarkers ; }, abstract = {BACKGROUND: Approximately 95% of Colorectal cancers (CRC) consist of adenocarcinomas originating from colonic Adenomatous polyps (AP). Increasing importance in CRC occurrence and progression has been attributed to the gut microbiota; however, a huge proportion of microorganisms inhabit the human digestive system. So, to comprehensively study the microbial spatial variations and their role in CRC progression, from AP to the different CRC phases, a holistic vision is imperative, including the simultaneous evaluation of multiple niches from the gastrointestinal system. Through an integrated approach, we identified potential microbial and metabolic biomarkers, able to discriminate human CRC from AP and/or also the different Tumor node metastasis (TNM) staging. In addition, as the microbiota contributes to the production of essential metabolic products detectable in fecal samples, we analysed and compared metabolites obtained from CRC and AP patients by using a Nuclear magnetic resonance (NMR) approach.

METHODS: In this observational study, saliva, tissue and stool samples from 61 patients, have been collected, including 46 CRC and 15 AP patients, age and sex-matched, undergoing surgery in 2018 at the Careggi University Hospital (Florence, Italy). First, the microbiota in the three-district between CRC and AP patients has been characterized, as well as in different CRC TNM stages. Subsequently, proton NMR spectroscopy has been used in combination with multivariate and univariate statistical approaches, to define the fecal metabolic profile of a restricted group of CRC and AP patients.

RESULTS: CRC patients display a different profile of tissue and fecal microbiota with respect to AP patients. Significant differences have been observed in CRC tissue microbial clades, with a rise of the Fusobacterium genus. In addition, significant taxa increase at the genus level has been observed in stool samples of CRC patients. Furthermore, Fusobacterium found in intestinal tissue has been positively correlated with fecal Parvimonas, for the first time. Moreover, as predicted by metagenomics pathway analysis, a significant increase of lactate (p=0.037) has been observed in the CRC fecal metabolic profiles, and positively correlated with Bifidobacterium (p=0.036). Finally, minor bacterial differences in CRC patients at stage T2 (TNM classification) have been detected, with a raise of the Spirochaetota phylum in CRC samples, with a slight increase of the Alphaproteobacteria class in fecal samples.

CONCLUSION: Our results suggest the importance of microbiota communities and oncometabolites in CRC development. Further studies on CRC/AP management with a focus on CRC assessment are needed to investigate novel microbial-related diagnostic tools aimed to improve therapeutic interventions.}, } @article {pmid37058056, year = {2023}, author = {Ma, H and Wang, Y and Liu, J and Du, L and Wang, X and Wang, Y}, title = {Systemic lupus erythematosus complicated with cryptococcal meningitis: A case report.}, journal = {Medicine}, volume = {102}, number = {15}, pages = {e33541}, pmid = {37058056}, issn = {1536-5964}, mesh = {Female ; Humans ; Adult ; *Meningitis, Cryptococcal/complications/diagnosis/drug therapy ; Amphotericin B/therapeutic use ; Flucytosine/therapeutic use ; *Lupus Erythematosus, Systemic/drug therapy ; Antifungal Agents/therapeutic use ; *Cryptococcus neoformans ; }, abstract = {RATIONALE: Patients with systemic lupus erythematosus (SLE) complicated with cryptococcal meningitis (CM) are easy to be misdiagnosed as neuropsychiatric lupus or tuberculous meningitis due to the lack of specificity of clinical symptoms, which may delay treatment. Through this case, we considered early improvement of India ink stain of cerebrospinal fluid (CSF) and metagenomic next generation sequences to determine whether there is microbial infection, and gave the idea of empirical anti-infection therapy, so as to make early diagnosis and slow down the progression of the disease.

PATIENT CONCERNS: We report the case of a 40-year-old female with SLE for 10 years. Five days ago she came down with a fever and a headache.

India ink stain of CSF in patients with SLE shows Cryptococcus neoformans growth. Combined with imaging findings, the patient was diagnosed with CM. The patient improved after 3 weeks of antifungal therapy with amphotericin B 42 mg/d and flucytosine 6000 mg/d.

LESSONS: The possibility of CM should be considered when SLE patients have sudden headache and fever. India ink stain of CSF and metagenomic next generation sequences should be actively improved in the early stage of the disease to identify whether there is microbial infection, and early empirical anti-infection treatment should be given to reduce mortality.}, } @article {pmid37057308, year = {2023}, author = {Ķimsis, J and Pokšāne, A and Kazarina, A and Vilcāne, A and Petersone-Gordina, E and Zayakin, P and Gerhards, G and Ranka, R}, title = {Tracing microbial communities associated with archaeological human samples in Latvia, 7-11th centuries AD.}, journal = {Environmental microbiology reports}, volume = {15}, number = {5}, pages = {383-391}, pmid = {37057308}, issn = {1758-2229}, mesh = {Animals ; Humans ; Latvia ; *Microbiota/genetics ; DNA ; Burial ; }, abstract = {In the grave environment, microorganisms are major ecological participants in the successional decomposition of vertebrates and could infiltrate the skeleton/skeletal material during taphonomic processes. The diversity of archaeological skeleton-associated microbial assemblages and the impact of various factors are poorly understood. This study aimed to evaluate the taxonomic microbial composition of archaeological human bone and teeth samples from the 7th to 11th centuries AD from two burial sites in Latvia. Samples were analysed by a shotgun metagenomics-based approach. The results showed a strong presence of the environmental DNA in the samples, and variability in microbial community structure between individual samples. Differences in microbial composition were observed between bone and tooth samples, as well as between different burial sites. Furthermore, the presence of endogenous ancient DNA (aDNA) in tooth samples was detected. Overall, compositions of microbial communities associated with archaeological human remains in Latvia dated 7-11th century AD were influenced by the sample type and burial location. These findings indicate that, while the content of historical DNA in archaeological samples is low, the comparison of archaeological skeleton-associated microbial assemblages across time and space, along with aDNA damage profile analysis, is important and could help to reveal putative ancient microorganisms.}, } @article {pmid37057090, year = {2023}, author = {Lee, JH and Dixey, P and Bhavsar, P and Raby, K and Kermani, N and Chadeau-Hyam, M and Adcock, IM and Song, WJ and Kwon, HS and Lee, SW and Sook Cho, Y and Fan Chung, K and Kim, TB}, title = {Precision Medicine Intervention in Severe Asthma (PRISM) study: molecular phenotyping of patients with severe asthma and response to biologics.}, journal = {ERJ open research}, volume = {9}, number = {2}, pages = {}, pmid = {37057090}, issn = {2312-0541}, abstract = {Severe asthma represents an important clinical unmet need despite the introduction of biologic agents. Although advanced omics technologies have aided researchers in identifying clinically relevant molecular pathways, there is a lack of an integrated omics approach in severe asthma particularly in terms of its evolution over time. The collaborative Korea-UK research project Precision Medicine Intervention in Severe Asthma (PRISM) was launched in 2020 with the aim of identifying molecular phenotypes of severe asthma by analysing multi-omics data encompassing genomics, epigenomics, transcriptomics, proteomics, metagenomics and metabolomics. PRISM is a prospective, observational, multicentre study involving patients with severe asthma attending severe asthma clinics in Korea and the UK. Data including patient demographics, inflammatory phenotype, medication, lung function and control status of asthma will be collected along with biological samples (blood, sputum, urine, nasal epithelial cells and exhaled breath condensate) for omics analyses. Follow-up evaluations will be performed at baseline, 1 month, 4-6 months and 10-12 months to assess the stability of phenotype and treatment responses for those patients who have newly begun biologic therapy. Standalone and integrated omics data will be generated from the patient samples at each visit, paired with clinical information. By analysing these data, we will identify the molecular pathways that drive lung function, asthma control status, acute exacerbations and the requirement for daily oral corticosteroids, and that are involved in the therapeutic response to biological therapy. PRISM will establish a large multi-omics dataset of severe asthma to identify potential key pathophysiological pathways of severe asthma.}, } @article {pmid37056746, year = {2023}, author = {Zhang, H and Rehman, MU and Chang, YF and Zhaoxin, T}, title = {Editorial: The potential role of gut microbiome in animal gut-linked diseases.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1179481}, pmid = {37056746}, issn = {1664-302X}, } @article {pmid37056740, year = {2023}, author = {Zhang, L and Yang, Z and Yang, F and Wang, G and Zeng, M and Zhang, Z and Yang, M and Wang, Z and Li, Z}, title = {Gut microbiota of two invasive fishes respond differently to temperature.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1087777}, pmid = {37056740}, issn = {1664-302X}, abstract = {Temperature variation structures the composition and diversity of gut microbiomes in ectothermic animals, key regulators of host physiology, with potential benefit to host or lead to converse results (i.e., negative). So, the significance of either effect may largely depend on the length of time exposed to extreme temperatures and how rapidly the gut microbiota can be altered by change in temperature. However, the temporal effects of temperature on gut microbiota have rarely been clarified. To understand this issue, we exposed two juvenile fishes (Cyprinus carpio and Micropterus salmoides), which both ranked among the 100 worst invasive alien species in the world, to increased environmental temperature and sampled of the gut microbiota at multiple time points after exposure so as to determine when differences in these communities become detectable. Further, how temperature affects the composition and function of microbiota was examined by comparing predicted metagenomic profiles of gut microbiota between treatment groups at the final time point of the experiment. The gut microbiota of C. carpio was more plastic than those of M. salmoides. Specifically, communities of C. carpio were greatly altered by increased temperature within 1 week, while communities of M. salmoides exhibit no significant changes. Further, we identified 10 predicted bacterial functional pathways in C. carpio that were temperature-dependent, while none functional pathways in M. salmoides was found to be temperature-dependent. Thus, the gut microbiota of C. carpio was more sensitive to temperature changes and their functional pathways were significantly changed after temperature treatment. These results showed the gut microbiota of the two invasive fishes differ in response to temperature change, which may indicate that they differ in colonization modes. Broadly, we have confirmed that the increased short-term fluctuations in temperatures are always expected to alter the gut microbiota of ectothermic vertebrates when facing global climate change.}, } @article {pmid37056706, year = {2023}, author = {Chen, L and Peng, W and Lan, G and Long, G and Yang, H and Xu, Y and Fu, A and Yi, H and Wan, Q}, title = {The application of metagenomic next-generation sequencing in patients with infection or colonization caused by Lichtheimia species.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1103626}, pmid = {37056706}, issn = {2235-2988}, mesh = {Humans ; *Mucormycosis/diagnosis/drug therapy/microbiology ; *Mucorales/genetics ; *Invasive Fungal Infections ; Early Diagnosis ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Mucormycosis is considered the fourth most common invasive fungal disease after candidiasis, aspergillosis and cryptococcosis. Lichtheimia species accounted for 5%-29% of all mucormycosis. However, available data on species-specific analysis of Lichtheimia infections are limited.

METHODS: This study included nine patients hospitalized in five hospitals in two cities in south China with mucormycosis or colonization caused by Lichtheimia species, diagnosed mainly by metagenomic next-generation sequencing (mNGS). The corresponding medical records were reviewed, and the clinical data analyzed included demographic characteristics, site of infection, host factors and type of underlying disease, diagnosis, clinical course, management, and prognosis.

RESULTS: In this study, nine patients with Lichtheimia infections or colonization had a recent history of haematological malignancy (33.3%), solid organ transplants (33.3%), pulmonary disease (22.2%), and trauma (11.1%) and were categorized as 11.1% (one case) proven, 66.7% (six cases) probable mucormycosis and 22.2% (two cases) colonization. Pulmonary mucormycosis or colonization was the predominant presentation in 77.8% of cases and mucormycosis caused by Lichtheimia resulted in death in four out of seven patients (57.1%).

CONCLUSION: These cases highlight the importance of early diagnosis and combined therapy for these sporadic yet life-threatening infections. Further studies on the diagnosis and control of Lichtheimia infection in China are required.}, } @article {pmid37056463, year = {2022}, author = {Liu, Y and Wang, H and Li, Y and Yu, Z}, title = {Clinical application of metagenomic next-generation sequencing in tuberculosis diagnosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {984753}, pmid = {37056463}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *Tuberculosis/diagnosis ; *Latent Tuberculosis ; High-Throughput Nucleotide Sequencing ; *Mycobacterium tuberculosis/genetics ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {OBJECTIVE: The purpose of this study was to evaluate the clinical diagnostic value of metagenomic next-generation sequencing (mNGS) for tuberculosis (TB).

METHODS: This retrospective study included 52 patients with suspected TB infection. mNGS, targeted PCR, acid-fast staining and, T-SPOT.TB assay were performed on the specimen. The positive rate of mNGS and traditional detection methods was statistically analyzed. Pathological tests were performed when necessary.

RESULTS: In total, 52 patients with suspected of TB in this study were included in the analysis, and 31 patients were finally diagnosed with TB. Among 52 patients, 14 (26.9%) cases were positive for acid-fast staining. The positive rate of T-SPOT.TB assay in 52 patients was 73.1% (38/52). Among 52 patients, 39 (75%) were detected positive for Mycobacterium tuberculosis (MTB) by mNGS. Regarding the detection rate of MTB, mNGS were as high as 75% (39/52), whereas acid-resistant staining was only 26.9% (14/52), which showed a statistically significant difference (p<0.05). The positive rates of T-SPOT.TB assay and mNGS were not statistically significant (p>0.05). Of the 52 suspected TB patients, 24 had targeted PCR, of which 18 were PCR positive. In 24 patients, the positive rate of PCR was 75%, and the positive rate of mNGS was 100%, with statistical difference between them (p<0.05).

CONCLUSIONS: The detection rate of MTB by mNGS was higher than that by conventional acid-fast staining and PCR, but not statistically significant compared with T-SPOT.TB assay. As an adjunctive diagnostic technology, mNGS can be combined with traditional detection methods to play a guiding role in the diagnosis and treatment of TB.}, } @article {pmid37055994, year = {2023}, author = {Li, B and Jeon, MK and Li, X and Yan, T}, title = {Differential impacts of salinity on antibiotic resistance genes during cattle manure stockpiling are linked to mobility potentials revealed by metagenomic sequencing.}, journal = {Journal of hazardous materials}, volume = {445}, number = {}, pages = {130590}, doi = {10.1016/j.jhazmat.2022.130590}, pmid = {37055994}, issn = {1873-3336}, mesh = {Cattle ; Animals ; *Anti-Bacterial Agents/pharmacology ; *Manure/analysis ; Genes, Bacterial ; Salinity ; Drug Resistance, Microbial/genetics ; }, abstract = {Livestock manure is an important source of antibiotic resistance genes (ARGs), and its salinity level can change during stockpiling. To understand how the salinity changes affect the fate of ARGs, cattle manure was adjusted of salinity and stockpiled in laboratory microcosms at low (0.3% salt), moderate (3.0%) and high salinity levels (10.0%) for 44 days. Amongst the five ARGs (tetO, blaTEM, sul1, tetM, and ermB) and the first-class integrase (intI1) monitored by qPCR, the relative abundance of tetO and blaTEM exhibited no clear trend in response to salinity levels, while that of sul1, tetM, ermB and intI1 showed clear downward trends over time at the lower salinity levels (0.3% and 3%) but not at the high salinity level (10%). Metagenomic contig construction of cattle manure samples revealed that sul1, tetM and ermB genes were more likely to associate with mobile genetic elements (MGEs) than tetO and blaTEM, suggesting that their slower decay at higher salinity levels was either caused by horizontal gene transfer or co-selection of ARGs and osmotic stress resistant determinants. Further analysis of metagenomic contigs showed that osmotic stress resistance can also be located on MGEs or in conjunction with ARGs.}, } @article {pmid37055869, year = {2023}, author = {Wu, X and Almatari, AL and Cyr, WA and Williams, DE and Pfiffner, SM and Rivkina, EM and Lloyd, KG and Vishnivetskaya, TA}, title = {Microbial life in 25-m-deep boreholes in ancient permafrost illuminated by metagenomics.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {33}, pmid = {37055869}, issn = {2524-6372}, abstract = {This study describes the composition and potential metabolic adaptation of microbial communities in northeastern Siberia, a repository of the oldest permafrost in the Northern Hemisphere. Samples of contrasting depth (1.75 to 25.1 m below surface), age (from ~ 10 kyr to 1.1 Myr) and salinity (from low 0.1-0.2 ppt and brackish 0.3-1.3 ppt to saline 6.1 ppt) were collected from freshwater permafrost (FP) of borehole AL1_15 on the Alazeya River, and coastal brackish permafrost (BP) overlying marine permafrost (MP) of borehole CH1_17 on the East Siberian Sea coast. To avoid the limited view provided with culturing work, we used 16S rRNA gene sequencing to show that the biodiversity decreased dramatically with permafrost age. Nonmetric multidimensional scaling (NMDS) analysis placed the samples into three groups: FP and BP together (10-100 kyr old), MP (105-120 kyr old), and FP (> 900 kyr old). Younger FP/BP deposits were distinguished by the presence of Acidobacteriota, Bacteroidota, Chloroflexota_A, and Gemmatimonadota, older FP deposits had a higher proportion of Gammaproteobacteria, and older MP deposits had much more uncultured groups within Asgardarchaeota, Crenarchaeota, Chloroflexota, Patescibacteria, and unassigned archaea. The 60 recovered metagenome-assembled genomes and un-binned metagenomic assemblies suggested that despite the large taxonomic differences between samples, they all had a wide range of taxa capable of fermentation coupled to nitrate utilization, with the exception of sulfur reduction present only in old MP deposits.}, } @article {pmid37055720, year = {2023}, author = {Chen, X and Zhu, J and Liu, Z and Ye, J and Yang, L and Zhang, Z}, title = {Mixed infection of three nontuberculous mycobacteria species identified by metagenomic next-generation sequencing in a patient with peritoneal dialysis-associated peritonitis: a rare case report and literature review.}, journal = {BMC nephrology}, volume = {24}, number = {1}, pages = {95}, pmid = {37055720}, issn = {1471-2369}, mesh = {Humans ; Nontuberculous Mycobacteria/genetics ; *Coinfection/complications ; *Peritonitis/etiology ; *Peritoneal Dialysis/adverse effects ; High-Throughput Nucleotide Sequencing ; *Mycobacterium Infections, Nontuberculous/complications ; }, abstract = {BACKGROUND: Peritonitis caused by nontuberculous mycobacteria (NTM) is an infrequent but important complication in patients undergoing peritoneal dialysis (PD). There has been no report of mixed infections with multiple NTM. Peritoneal dialysis-associated peritonitis (PDAP) caused by Mycobacterium abscessus is more common than that caused by M. smegmatis and M. goodii.

CASE PRESENTATION: This case concerns a patient with PDAP caused by gram-positive bacilli, which could not be identified at the species level in successive detections of initial peritoneal effluent. Later, M. smegmatis was detected with no sensitivity results in bacterial culture. However, metagenomic next-generation sequencing (mNGS) and first whole-genome sequences indicated that there were three species coexisting in the culture, including M. smegmatis (24,708 reads), M. abscessus (9224 reads), and M. goodii (8305 reads). This is the first case of PDAP with specific evidence that conventional detection methods isolated a poorly pathogenic NTM, whereas mNGS and first whole-genome sequences identified multiple NTM. Pathogenic bacteria might not be detected using conventional methods due to their lower abundance. This case report is the first description of mixed infections with more than two species of NTM during PDAP.

CONCLUSIONS: PDAP caused by multiple NTM is rare, and the diagnosis is difficult. When NTM are isolated by conventional tests in patients who are suspected of infection, clinicians should be vigilant, and further tests should be performed to determine the presence of rare or even previously unknown bacteria, for which the quantity is relatively low, but the pathogenicity is high. The rare pathogen may be a primary agent in causing such complications.}, } @article {pmid37055228, year = {2023}, author = {Xiong, YF and Cai, Z and Li, SC and Song, YJ and Hu, XM and Zheng, L}, title = {[Bioinformatics analysis in metagenomic next-generation sequencing of pathogenic microorganisms: current status and challenges].}, journal = {Zhonghua yi xue za zhi}, volume = {103}, number = {15}, pages = {1098-1102}, doi = {10.3760/cma.j.cn112137-20221208-02598}, pmid = {37055228}, issn = {0376-2491}, support = {81601819//National Natural Science Foundation of China/ ; }, mesh = {*High-Throughput Nucleotide Sequencing ; *Ambulatory Care Facilities ; Computational Biology ; Data Analysis ; Head ; Sensitivity and Specificity ; }, abstract = {The clinical application of metagenomic next-generation sequencing (mNGS) in the diagnosis of unknown pathogenic infections and critical infections has become increasingly valuable. Due to the huge volume of mNGS data and the complexity of clinical diagnosis and treatment, mNGS has difficulties in data analysis and interpretation in practical application. Therefore, in the process of clinical practice, it is crucial to grasp the key points of bioinformatics analysis and establish a standardized bioinformatics analysis process, which is an important step in the transformation of mNGS from laboratory to clinic. At present, bioinformatics analysis of mNGS has made great progress, but with the high requirements of clinical standardization of bioinformatics analysis and the development of computer technology, bioinformatics analysis of mNGS is also facing new challenges. This article mainly elaborates on quality control, and identification and visualization of pathogenic bacteria.}, } @article {pmid37055227, year = {2023}, author = {Zhang, D and Yang, QW}, title = {[Construction and quality assurance of metagenomic next-generation sequencing platform in pathogen detection].}, journal = {Zhonghua yi xue za zhi}, volume = {103}, number = {15}, pages = {1092-1097}, doi = {10.3760/cma.j.cn112137-20220825-01801}, pmid = {37055227}, issn = {0376-2491}, support = {82072318//National Natural Science Foundation of China/ ; 2018YFE0101800, 2021YFC2301002//National Key Research and Development Program of China/ ; ZK201000//Beijing Key Clinical Specialty for Laboratory Medicine-Excellent Project/ ; }, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Hospitals ; Laboratories ; Metagenome ; Quality Control ; Sensitivity and Specificity ; }, abstract = {Early diagnosis remains the key to prevent and control infectious diseases. In recent years, metagenomic next-generation sequencing (mNGS) technology breaks through the limitations of conventional culture methods or targeted molecular detection methods. It improves the diagnosis and treatment level of difficult and rare infectious pathogens through the shotgun high-throughput sequencing to conduct unbiased and rapid detection of microorganisms in clinical samples, which has been widely recognized in clinical practice. Due to the complex detection process of mNGS, there are no uniform specifications and requirements at present. Meanwhile, most laboratories lack of relevant talents at the initial stage of platform establishment, which poses severe challenges to the construction and quality control of the mNGS platform. Based on the practical experience in the construction and operation of the mNGS laboratory of Peking Union Medical College Hospital, the current article summarizes the hardware requirements for the establishment of the mNGS laboratory, the establishment and evaluation methods of the mNGS testing system and the quality assurance after the clinical application, and comprehensively introduces the suggestions for the standardized construction and operation of the mNGS testing platform and quality management system.}, } @article {pmid37054879, year = {2023}, author = {Zhang, X and Wan, H and Jin, M and Huang, L and Zhang, X}, title = {Environmental viromes reveal global virosphere of deep-sea sediment RNA viruses.}, journal = {Journal of advanced research}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.jare.2023.04.003}, pmid = {37054879}, issn = {2090-1224}, abstract = {INTRODUCTION: Viruses are the most abundant and diverse life forms on the earth. Both DNA viruses and RNA viruses play important roles in marine ecosystems via regulating biogeochemical cycles.

OBJECTIVES: However, the virome of marine RNA viruses has been rarely explored so far. In this study, therefore, the environmental viromes of deep-sea sediment RNA viruses were characterized on a global scale to reveal the global virosphere of deep-sea RNA viruses.

METHODS: The viral particles were purified from each of 133 deep-sea sediment samples and then characterized based on metagenomes of RNA viruses.

RESULTS: In this study, we established the global virome dataset of deep-sea RNA viruses purified from 133 sediment samples that were collected from typical deep-sea ecosystems of three oceans. A total of 85,059 viral operational taxonomic units (vOTUs) were identified, of which only 1.72% were hitherto known, indicating that the deep-sea sediment is a repository of novel RNA viruses. These vOTUs were classified into 20 viral families, including prokaryotic (7.09%) and eukaryotic (65.81%) RNA viruses. Furthermore, 1,463 deep-sea RNA viruses with complete genomes were obtained. The differentiation of RNA viral communities was driven by the deep-sea ecosystems as opposed to geographical region. Specifically, the virus-encoded metabolic genes took great effects on the differentiation of RNA viral communities by mediating the energy metabolism in the deep-sea ecosystems.

CONCLUSIONS: Therefore, our findings indicate that the deep sea is a vast reservoir of novel RNA viruses for the first time, and the differentiation of RNA viral communities is driven by the deep-sea ecosystems through energy metabolism.}, } @article {pmid37054839, year = {2023}, author = {Chunxiao, D and Ma, F and Wu, W and Li, S and Yang, J and Chen, Z and Lian, S and Qu, Y}, title = {Metagenomic analysis reveals indole signaling effect on microbial community in sequencing batch reactors: Quorum sensing inhibition and antibiotic resistance enrichment.}, journal = {Environmental research}, volume = {229}, number = {}, pages = {115897}, doi = {10.1016/j.envres.2023.115897}, pmid = {37054839}, issn = {1096-0953}, mesh = {*Quorum Sensing/physiology ; Drug Resistance, Microbial ; Lactones/pharmacology ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Indoles/pharmacology ; }, abstract = {Indole is an essential signal molecule in microbial studies. However, its ecological role in biological wastewater treatments remains enigmatic. This study explores the links between indole and complex microbial communities using sequencing batch reactors exposed to 0, 15, and 150 mg/L indole concentrations. A concentration of 150 mg/L indole enriched indole degrader Burkholderiales, while pathogens, such as Giardia, Plasmodium, and Besnoitia were inhibited at 15 mg/L indole concentration. At the same time, indole reduced the abundance of predicted genes in the "signaling transduction mechanisms" pathway via the Non-supervised Orthologous Groups distributions analysis. Indole significantly decreased the concentration of homoserine lactones, especially C14-HSL. Furthermore, the quorum-sensing signaling acceptors containing LuxR, the dCACHE domain, and RpfC showed negative distributions with indole and indole oxygenase genes. Signaling acceptors' potential origins were mainly Burkholderiales, Actinobacteria, and Xanthomonadales. Meanwhile, concentrated indole (150 mg/L) increased the total abundance of antibiotic resistance genes by 3.52 folds, especially on aminoglycoside, multidrug, tetracycline, and sulfonamide. Based on Spearman's correlation analysis, the homoserine lactone degradation genes which were significantly impacted by indole negatively correlated with the antibiotic resistance gene abundance. This study brings new insights into the effect of indole signaling on in biological wastewater treatment plants.}, } @article {pmid37054678, year = {2023}, author = {Saheb Kashaf, S and Harkins, CP and Deming, C and Joglekar, P and Conlan, S and Holmes, CJ and , and Almeida, A and Finn, RD and Segre, JA and Kong, HH}, title = {Staphylococcal diversity in atopic dermatitis from an individual to a global scale.}, journal = {Cell host & microbe}, volume = {31}, number = {4}, pages = {578-592.e6}, pmid = {37054678}, issn = {1934-6069}, support = {ZIA AR041217/ImNIH/Intramural NIH HHS/United States ; ZIA HG000180/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Humans ; *Dermatitis, Atopic/genetics ; Staphylococcus aureus/genetics ; Prospective Studies ; Staphylococcus/genetics ; Skin ; *Staphylococcal Infections ; Staphylococcus epidermidis/genetics ; }, abstract = {Atopic dermatitis (AD) is a multifactorial, chronic relapsing disease associated with genetic and environmental factors. Among skin microbes, Staphylococcus aureus and Staphylococcus epidermidis are associated with AD, but how genetic variability and staphylococcal strains shape the disease remains unclear. We investigated the skin microbiome of an AD cohort (n = 54) as part of a prospective natural history study using shotgun metagenomic and whole genome sequencing, which we analyzed alongside publicly available data (n = 473). AD status and global geographical regions exhibited associations with strains and genomic loci of S. aureus and S. epidermidis. In addition, antibiotic prescribing patterns and within-household transmission between siblings shaped colonizing strains. Comparative genomics determined that S. aureus AD strains were enriched in virulence factors, whereas S. epidermidis AD strains varied in genes involved in interspecies interactions and metabolism. In both species, staphylococcal interspecies genetic transfer shaped gene content. These findings reflect the staphylococcal genomic diversity and dynamics associated with AD.}, } @article {pmid37054579, year = {2023}, author = {Mahmoud, E and Hanora, A and Abdalla, S and Abdelrahman Ahmed, AA and Zakeer, S}, title = {Shotgun metagenomic analysis of bacterial symbionts associated with "Chromodoris quadricolor" mantle.}, journal = {Marine genomics}, volume = {69}, number = {}, pages = {101030}, doi = {10.1016/j.margen.2023.101030}, pmid = {37054579}, issn = {1876-7478}, mesh = {Animals ; *Ecosystem ; *Gastropoda/genetics ; Bacteria/genetics ; Metagenome ; Symbiosis ; Phylogeny ; }, abstract = {Nudibranchs are colorful marine invertebrates having a diverse group of understudied animals. Recently, some nudibranch members have acquired some attention while others still have not. Chromodoris quadricolor is a member of the Red Sea nudibranch, which did not have the chance to get significant attention. Unlike various invertebrates, it lacks a shell suggesting that it must defend itself in other ways. Therefore, in the present study, we were concerned about the mantle-associated bacterial communities. Being essential partners of this dorid nudibranch system, we investigated their taxonomic and functional profiles. We performed a whole metagenomic shotgun approach for the mantle bacterial cells after a differential pelleting procedure. In this procedure, we separated most of the prokaryotic cells from the eukaryotic host cells. Our findings showed that the mantle-body part holds a diverse group of bacterial species relating mainly to Proteobacteria and Tenericutes phyla. There were novel findings regarding the bacterial members associated with the nudibranch mollusks group. Various species were not previously recorded as bacterial symbionts with nudibranchs. Those members were Bathymodiolus brooksi thiotrophic gill symbiont (23.2%), Mycoplasma marinum (7.4%), Mycoplasma todarodis (5%), and Solemya velum gill symbiont (2.6%). The presence of these bacterial species assumed a nutritional role to the host. However, some of these species were present in a high abundance, suggesting their important symbiosis with Chromodoris quadricolor. In addition, exploring the bacterial ability to produce valuable products resulted in the prediction of 2088 biosynthetic gene clusters (BGCs). We identified different gene cluster classes. Polyketide BGC class was the most represented. Others were related to fatty acid BGCs, RiPP, saccharide, terpene, and NRP BGC classes. Prediction of the activity of these gene clusters resulted in, mainly, an antibacterial activity. In addition, different antimicrobial secondary metabolites were also detected. These secondary metabolites are considered key components regulating the bacterial species interactions in their ecosystem. This suggested the significant contribution of these bacterial symbionts to protect the nudibranch host against predators and pathogens. Globally, it is the first detailed study concerned with both the taxonomic diversity and functional potentials of the bacterial symbionts associated with Chromodoris quadricolor mantle.}, } @article {pmid37054443, year = {2023}, author = {Palermo, CN and Fulthorpe, RR and Saati, R and Short, SM}, title = {Analysis of bacterioplankton genes in an impaired Great Lakes harbour reveals seasonal metabolic shifts and a previously undetected cyanobacterium.}, journal = {Canadian journal of microbiology}, volume = {69}, number = {8}, pages = {281-295}, doi = {10.1139/cjm-2022-0252}, pmid = {37054443}, issn = {1480-3275}, mesh = {*Lakes/microbiology ; Seasons ; *Cyanobacteria/genetics ; Aquatic Organisms ; Ontario ; }, abstract = {Hamilton Harbour is an impaired embayment of Lake Ontario that experiences seasonal algal blooms despite decades of remedial efforts. To study the harbour's cyanobacterial and heterotrophic bacterial communities, we extracted and sequenced community DNA from surface water samples collected biweekly from different sites during summer and fall. Assembled contigs were annotated at the phylum level, and Cyanobacteria were further characterized at order and species levels. Actinobacteria were most abundant in early summer, while Cyanobacteria were dominant in mid-summer. Microcystis aeruginosa and Limnoraphis robusta were most abundant throughout the sampling period, expanding the documented diversity of Cyanobacteria in Hamilton Harbour. Functional annotations were performed using the MG-RAST pipeline and SEED database, revealing that genes for photosynthesis, nitrogen metabolism, and aromatic compound metabolism varied in relative abundances over the season, while phosphorus metabolism was consistent, suggesting that these genes remained essential despite fluctuating environmental conditions and community succession. We observed seasonal shifts from anoxygenic to oxygenic phototrophy, and from ammonia assimilation to nitrogen fixation, coupled with decreasing heterotrophic bacteria and increasing Cyanobacteria relative abundances. Our data contribute important insights into bacterial taxa and functional potentials in Hamilton Harbour, revealing seasonal and spatial dynamics that can be used to inform ongoing remediation efforts.}, } @article {pmid37052633, year = {2023}, author = {Nagar, S and Bharti, M and Negi, RK}, title = {Genome-resolved metagenomics revealed metal-resistance, geochemical cycles in a Himalayan hot spring.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {10}, pages = {3273-3289}, pmid = {37052633}, issn = {1432-0614}, mesh = {*Hot Springs/microbiology ; Metagenomics ; Bacteria/genetics/metabolism ; Archaea/genetics/metabolism ; Metagenome ; *Microbiota ; Metals/metabolism ; Sulfur/metabolism ; Nitrogen/metabolism ; Phylogeny ; }, abstract = {The hot spring microbiome is a complex assemblage of micro- and macro-organisms; however, the understanding and projection of enzymatic repertoire that access earth's integral ecosystem processes remains ambivalent. Here, the Khirganga hot spring characterized with white microbial mat and ions rich in sulfate, chlorine, sodium, and magnesium ions is investigated and displayed the examination of 41 high and medium qualified metagenome-assembled genomes (MAGs) belonged to at least 12 bacterial and 2 archaeal phyla which aids to drive sulfur, oxygen, iron, and nitrogen cycles with metabolic mechanisms involved in heavy metal tolerance. These MAGs possess over 1749 genes putatively involved in crucial metabolism of elements viz. nitrogen, phosphorus, and sulfur and 598 genes encoding enzymes for czc efflux system, chromium, arsenic, and copper heavy metals resistance. The MAGs also constitute 229 biosynthetic gene clusters classified abundantly as bacteriocins and terpenes. The metabolic roles possibly involved in altering linkages in nitrogen biogeochemical cycles and explored a discerned rate of carbon fixation exclusively in archaeal member Methanospirillum hungatei inhabited in microbial mat. Higher Pfam entropy scores of biogeochemical cycling in Proteobacteria members assuring their major contribution in assimilation of ammonia and sequestration of nitrate and sulfate components as electron acceptors. This study will readily improve the understanding of the composite relationship between bacterial species owning metal resistance genes (MRGs) and underline the exploration of adaptive mechanism of these MAGs in multi-metal contaminated environment. KEY POINTS: • Identification of 41 novel bacterial and archaeal species in habitats of hot spring • Genome-resolved metagenomics revealed MRGs (n = 598) against Cr, Co, Zn, Cd, As, and Cu • Highest entropies of N (0.48) and Fe (0.44) cycles were detected within the MAGs.}, } @article {pmid37052498, year = {2023}, author = {Hu, X and Dong, R and Huang, S and Zeng, Y and Zhan, W and Gao, X and Tian, D and Peng, J and Xu, J and Wang, T and Zhang, Y and Wang, X and Zhang, X and Liu, J and Guang, B and Yang, T}, title = {CDBN-YGXZ, a Novel Small-Molecule Drug, Shows Efficacy against Clostridioides difficile Infection and Recurrence in Mouse and Hamster Infection Models.}, journal = {Antimicrobial agents and chemotherapy}, volume = {67}, number = {5}, pages = {e0170422}, pmid = {37052498}, issn = {1098-6596}, mesh = {Cricetinae ; Animals ; Mice ; Vancomycin/pharmacology ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Clostridioides difficile ; *Clostridium Infections/drug therapy/prevention & control ; Recurrence ; }, abstract = {Clostridioides difficile infection (CDI) causes severe diarrhea and colitis, leading to significant morbidity, mortality, and high medical costs worldwide. Oral vancomycin, a first-line treatment for CDI, is associated with a high risk of recurrence, necessitating novel therapies for primary and recurrent CDI. A novel small-molecule compound, CDBN-YGXZ, was synthesized by modifying the benzene ring of nitazoxanide with lauric acid. The mechanism of action of CDBN-YGXZ was validated using a pyruvate:ferredoxin/flavodoxin oxidoreductase (PFOR) inhibition assay. The efficacy of CDBN-YGXZ was evaluated using the MIC test and CDI infection model in mice and hamsters. Furthermore, metagenomics was used to reveal the underlying reasons for the effective reduction or prevention of CDI after CDBN-YGXZ treatment. The inhibitory activity against PFOR induced by CDBN-YGXZ. MIC tests showed that the in vitro activity of CDBN-YGXZ against C. difficile ranging from 0.1 to 1.5 μg/mL. In the mouse and hamster CDI models, CDBN-YGXZ provided protection during both treatment and relapse, while vancomycin treatment resulted in severe relapse and significant clinical scores. Compared with global effects on the indigenous gut microbiota induced by vancomycin, CDBN-YGXZ treatment had a mild influence on gut microbes, thus resulting in the disappearance or reduction of CDI recurrence. CDBN-YGXZ displayed potent activity against C. difficile in vitro and in vivo, reducing or preventing relapse in infected animals, which could merit further development as a potential drug candidate for treating CDI.}, } @article {pmid37052495, year = {2023}, author = {Morgan, SJ and Chaston, JM}, title = {Flagellar Genes Are Associated with the Colonization Persistence Phenotype of the Drosophila melanogaster Microbiota.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0458522}, pmid = {37052495}, issn = {2165-0497}, support = {R15 GM140388/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Drosophila melanogaster/genetics/microbiology ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Bacteria/genetics ; Phenotype ; }, abstract = {In this work, we use Drosophila melanogaster as a model to identify bacterial genes necessary for bacteria to colonize their hosts independent of the bulk flow of diet. Early work on this model system established that dietary replenishment drives the composition of the D. melanogaster gut microbiota, and subsequent research has shown that some bacterial strains can stably colonize, or persist within, the fly independent of dietary replenishment. Here, we reveal transposon insertions in specific bacterial genes that influence the bacterial colonization persistence phenotype by using a gene association approach. We initially established that different bacterial strains persist at various levels, independent of dietary replenishment. We then repeated the analysis with an expanded panel of bacterial strains and performed a metagenome-wide association (MGWA) study to identify distinct bacterial genes that are significantly correlated with the level of colonization by persistent bacterial strains. Based on the MGWA study, we tested if 44 bacterial transposon insertion mutants from 6 gene categories affect bacterial persistence within the flies. We identified that transposon insertions in four flagellar genes, one urea carboxylase gene, one phosphatidylinositol gene, one bacterial secretion gene, and one antimicrobial peptide (AMP) resistance gene each significantly influenced the colonization of D. melanogaster by an Acetobacter fabarum strain. Follow-up experiments revealed that each flagellar mutant was nonmotile, even though the wild-type strain was motile. Taken together, these results reveal that transposon insertions in specific bacterial genes, including motility genes, are necessary for at least one member of the fly microbiota to persistently colonize the fly. IMPORTANCE Despite the growing body of research on the microbiota, the mechanisms by which the microbiota colonizes a host can still be further elucidated. This study identifies bacterial genes that are associated with the colonization persistence phenotype of the microbiota in Drosophila melanogaster, which reveals specific bacterial factors that influence the establishment of the microbiota within its host. The identification of specific genes that affect persistence can help inform how the microbiota colonizes a host. Furthermore, a deeper understanding of the genetic mechanisms of the establishment of the microbiota could aid in the further development of the Drosophila microbiota as a model for microbiome research.}, } @article {pmid37052402, year = {2023}, author = {Cuff, C and Lin, LD and Mahurkar-Joshi, S and Jacobs, JP and Lagishetty, V and Jaffe, N and Smith, J and Dong, T and Sohn, J and Chang, L}, title = {Randomized controlled pilot study assessing fructose tolerance during fructose reintroduction in non-constipated irritable bowel syndrome patients successfully treated with a low FODMAP diet.}, journal = {Neurogastroenterology and motility}, volume = {35}, number = {7}, pages = {e14575}, doi = {10.1111/nmo.14575}, pmid = {37052402}, issn = {1365-2982}, support = {IK2 CX001717/CX/CSRD VA/United States ; }, mesh = {Humans ; Female ; Adult ; Male ; *Irritable Bowel Syndrome/diagnosis ; Disaccharides ; Oligosaccharides ; Fructose ; Pilot Projects ; FODMAP Diet ; Fermentation ; Glucose ; Diet ; }, abstract = {BACKGROUND: Limited data exist to guide FODMAP (fermentable oligo-, di-, monosaccharides, and polyols) reintroduction to assess tolerance following a low FODMAP diet (LFD). Fructose reintroduction is often stepwise up to 7.5 g fructose (e.g., three tsp of honey). We aimed to determine the fructose tolerance threshold in non-constipated, LFD-responsive patients with irritable bowel syndrome (IBS) and assess whether stool microbiome predicted LFD response or fructose tolerance.

METHODS: Thirty-nine non-constipated IBS patients (51% women, mean age 33.7 years) completed a 4-week LFD. LFD responders were defined as those who reported adequate relief of IBS symptoms following the LFD. Responders were randomized to one of the three solution groups (100% fructose, 56% fructose/44% glucose, or 100% glucose) and received four doses (2.5, 5, 10, 15 g) for 3 days each. Patients reached their tolerance dose if their mean daily IBS symptom severity (visual analog scale [VAS], 0-100 mm) was >20 mm higher than post-LFD VAS. Stool samples before and after LFD were analyzed using shotgun metagenomics.

RESULTS: Seventy-nine percent of patients were LFD responders. Most responders tolerated the 15 g sugar dose. There was no significant difference in mean dose tolerated between solution groups (p = 0.56). Compared to baseline, microbiome composition (beta diversity) significantly shifted and six bacterial genes in fructose and mannose metabolism pathways decreased after LFD, irrespective of LFD response or the solution group.

CONCLUSIONS: Non-constipated, LFD-responsive IBS patients should be reintroduced to fructose in higher doses than 15 g to assess tolerance. LFD is associated with significant changes in microbial composition and bacterial genes involved in FODMAP metabolism.}, } @article {pmid37052201, year = {2023}, author = {Jansen, D and Falony, G and Vieira-Silva, S and Simsek, C and Marcelis, T and Caenepeel, C and Machiels, K and Raes, J and Vermeire, S and Matthijnssens, J}, title = {Community Types of the Human Gut Virome are Associated with Endoscopic Outcome in Ulcerative Colitis.}, journal = {Journal of Crohn's & colitis}, volume = {17}, number = {9}, pages = {1504-1513}, pmid = {37052201}, issn = {1876-4479}, support = {1S78021N//Fonds Wetenschappelijk Onderzoek/ ; }, abstract = {BACKGROUND: Inflammatory bowel disease [IBD] is a major debilitating disease. Recently, the gut microbiota has gained attention as an important factor involved in the pathophysiology of IBD. As a complement to the established bacterial 'enterotypes' associated with IBD, we focused here on viruses. We investigated the intestinal virome of IBD patients undergoing biological therapy for the presence of virome configurations associated with IBD, and to uncover how those configurations are associated with therapeutic success.

METHODS: Viral-like particle enrichment followed by deep sequencing was performed on 432 faecal samples from 181 IBD patients starting biological therapy. Redundancy analysis and Dirichlet Multinomial Mixtures were applied to determine covariates of the virome composition and to condense the gut virota into 'viral community types', respectively.

RESULTS: Patients were stratified based on unsupervised clustering into two viral community types. Community type CA showed a low α-diversity and a high relative abundance of Caudoviricetes [non-CrAss] phages and was associated with the dysbiotic Bact2-enterotype. Community type CrM showed a high α-diversity and a high relative abundance of Crassvirales and Malgrandaviricetes phages. During post-interventional analysis, endoscopic outcome was associated with gut virome composition. Remitting UC patients had a high percentage of community type CrM, a high Shannon diversity and a low lysogenic potential. Pre-interventional analyses also identified five novel phages associated with treatment success.

CONCLUSIONS: This study proposed two gut virome configurations that may be involved in the pathophysiology of IBD. Interestingly, those viral configurations are further associated with therapeutic success, suggesting a potential clinical relevance.}, } @article {pmid37051624, year = {2023}, author = {Zhou, K and Peng, M and Tan, Z and Xiao, N}, title = {Diarrhea Caused by High-Fat and High-Protein Diet Was Associated With Intestinal Lactase-Producing Bacteria.}, journal = {The Turkish journal of gastroenterology : the official journal of Turkish Society of Gastroenterology}, volume = {34}, number = {7}, pages = {691-699}, pmid = {37051624}, issn = {2148-5607}, mesh = {Animals ; Male ; Mice ; Bacteria/genetics/metabolism ; Diarrhea/microbiology ; *Diet, High-Protein ; *Lactase/genetics/metabolism ; }, abstract = {BACKGROUND/AIMS: This study aimed to investigate the effect of diarrhea induced by a high-fat and high-protein diet on lactase-producing bacteria in the intestinal contents of mice from the perspective of diarrhea-related genes.

MATERIALS AND METHODS: Ten specific pathogen-free Kunming male mice were chosen and randomly divided into the normal group and model group. The mice in the normal group were fed with high-fat and high-protein diet plus gavage of vegetable oil, while those in the model group were fed with general diet plus gavage of distilled water. After successful modeling, the distribution and diversity of lactase-producing bacteria in the intestinal contents were characterized by metagenomic sequencing technology.

RESULTS: After high-fat and high-protein diet intervention, Chao1, observed species index, and operational taxonomic units number decreased in the model group (P > .05), while the Shannon, Simpson, Pielou's evenness, and Goods coverage indices increased (P > .05). The principal coordinate analysis showed that the composition of lactase-producing bacteria differed between the normal group and model group (P < .05). The lactase-producing bacterial source in the intestinal contents of mice was Actinobacteria, Firmicutes, and Proteobacteria, of which Actinobacteria was the most abundant phylum. At the genus level, both groups had their unique genera, respectively. Compared to the normal group, the abundance of Bifidobacterium, Rhizobium, and Sphingobium increased, while Lachnoclostridium, Lactobacillus, Saccharopolyspora, and Sinorhizobium decreased in the model group.

CONCLUSION: High-fat and high-protein diet altered the structure of lactase-producing bacteria in the intestinal contents, elevating the abundance of dominant lactase-producing bacteria, while decreasing the richness of lactase-producing bacteria, which may further induce the occurrence of diarrhea.}, } @article {pmid37051301, year = {2023}, author = {Zhao, X and Duan, MX and Lu, YY and Bai, LP and Zhao, XY}, title = {Short-term prognostic analysis of patients with systemic lupus erythematosus co-infection and comparison of mNGS and conventional microbiological test results.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1131258}, pmid = {37051301}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; Prognosis ; *Coinfection/diagnosis ; *Lupus Erythematosus, Systemic/complications/diagnosis ; High-Throughput Nucleotide Sequencing ; }, abstract = {OBJECTIVES: Infection is one of the major causes of morbidity and mortality in patients with systemic lupus erythematosus (SLE), and as a new diagnostic technique, metagenomic next-generation sequencing (mNGS) is increasingly used for the pathogenetic detection of co-infected SLE patients. However, conventional microbiological testing (CMT) is still the gold standard for pathogenic diagnosis, and the specific diagnostic efficacy of mNGS versus CMT in such patients is not known. In addition, there are few studies on the short-term prognosis of co-infected SLE patients.

METHODS: This study retrospectively included 58 SLE patients with co-infection admitted to the First Affiliated Hospital of Zhengzhou University from October 2020 to August 2022. Patients were divided into a survivors (n=27) and a non-survivors (n=31) according to their discharge status. Baseline characteristics and etiological data were collected and statistically analyzed for all patients during their hospitalization. The sequential organ failure assessment (SOFA) score, acute physiology and chronic health evaluation (APACHE) II and systemic lupus erythematosus disease activity index (SLEDAI) were calculated for each patient to assess the predictive ability of the 3 scores on the short-term prognosis of SLE patients. The mNGS and CMT culture results were also compared to clarify the flora characteristics of patients with SLE infection.

RESULTS: More patients in the non-survivors had renal impairment, neurological manifestations, multiplasmatic cavity effusion and gastrointestinal manifestations compared to the survivors (p < 0.05). The SOFA score, APACHE II and SLEDAI were significantly higher in the non-survivors than in the survivors (p < 0.01). There were also significant differences between the two groups in several tests such as hemoglobin, platelets, albumin, total bilirubin, C-reactive protein (CRP), procalcitonin (PCT), and complement C3 (p < 0.05). In addition, the absolute values of T lymphocytes, CD4+ T cells and CD8+ T cells were smaller in the non-survivors than in the survivors (p < 0.05). The most common type of infection in this study was pulmonary infection, followed by bloodstream infection. mNGS and CMT positivity rates were not significantly different among patients in the non-survivors, but were significantly different among patients in the survivors (p=0.029). In-hospital survival of patients with SLE infection could be predicted based on the SOFA score in relation to 6. For patients with SOFA <6, we recommend earlier mNGS testing to identify the pathogen and improve patient prognosis.

CONCLUSIONS: For SLE patients with co-infection, in-hospital survival can be predicted based on SOFA score. For patients with SOFA <6, advising them to complete mNGS testing as early as possible may improve the prognosis to some extent.}, } @article {pmid37051296, year = {2023}, author = {Zhang, Y and Cheng, S and Zou, H and Han, Z and Xie, T and Zhang, B and Dai, D and Yin, X and Liang, Y and Kou, Y and Tan, Y and Shen, L and Peng, Z}, title = {Correlation of the gut microbiome and immune-related adverse events in gastrointestinal cancer patients treated with immune checkpoint inhibitors.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1099063}, pmid = {37051296}, issn = {2235-2988}, mesh = {Humans ; Immune Checkpoint Inhibitors/adverse effects ; *Gastrointestinal Microbiome ; Prospective Studies ; *Neoplasms/drug therapy ; *Gastrointestinal Neoplasms/drug therapy/etiology ; *Colonic Neoplasms ; Immunotherapy/adverse effects/methods ; }, abstract = {INTRODUCTION: The wide application of immune checkpoint inhibitors has significantly improved the survival expectation of cancer patients. While immunotherapy brings benefits to patients, it also results in a series of immune-related adverse events (irAEs). Increasing evidence suggests that the gut microbiome is critical for immunotherapy response and the development of irAEs.

METHODS: In this prospective study, we recruited 95 patients with advanced/unresectable gastrointestinal cancers treated with immunotherapy and report a comprehensive analysis of the association of the gut microbiome with irAEs. Metagenome sequencing was used to analyze the differences in bacterial composition and metabolic pathways of baseline fecal samples.

RESULTS: In summary, we identified bacterial species and metabolic pathways that might be associated with the occurrence of irAEs in gastric, esophageal, and colon cancers. Ruminococcus callidus and Bacteroides xylanisolvens were enriched in patients without severe irAEs. Several microbial metabolic pathways involved in the urea cycle, including citrulline and arginine biosynthesis, were associated with irAEs. We also found that irAEs in different cancer types and toxicity in specific organs and the endocrine system were associated with different gut microbiota profiles. These findings provide the basis for future mechanistic exploration.}, } @article {pmid37049841, year = {2023}, author = {Chudan, S and Ishibashi, R and Nishikawa, M and Tabuchi, Y and Nagai, Y and Ikushiro, S and Furusawa, Y}, title = {Effect of Wheat-Derived Arabinoxylan on the Gut Microbiota Composition and Colonic Regulatory T Cells.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {7}, pages = {}, pmid = {37049841}, issn = {1420-3049}, support = {20K05929//Japan Society for the Promotion of Science/ ; n/a//LOTTE Foundation/ ; n/a//Tamura Science and Technology Foundation/ ; n/a//Takeda Science Foundation/ ; n/a//Kanamori Foundation/ ; n/a//Tojuro Iijima Foundation for Food Science and Technology/ ; }, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; T-Lymphocytes, Regulatory ; Triticum ; *Colitis/chemically induced/drug therapy/metabolism ; Butyrates/pharmacology ; Mice, Inbred C57BL ; }, abstract = {The health benefits of wheat-derived arabinoxylan, a commonly consumed dietary fiber, have been studied for decades. However, its effect on the gut microenvironment and inflammatory bowel disease remains unclear. The objective of this study was to understand the effect of wheat-derived arabinoxylan on gut microbiota, colonic regulatory T cells (Tregs), and experimental colitis. In this study, healthy and chronic colitis model mice were fed chow containing cellulose or wheat-derived arabinoxylan for 2-6 weeks and subjected to subsequent analysis. A 16S-based metagenomic analysis of the fecal DNA revealed that Lachnospiraceae, comprising butyrate-producing and Treg-inducing bacteria, were overrepresented in arabinoxylan-fed mice. In line with the changes in the gut microbiota, both the fecal butyrate concentration and the colonic Treg population were elevated in the arabinoxylan-fed mice. In a T cell transfer model of chronic colitis, wheat-derived arabinoxylan ameliorated body weight loss and colonic tissue inflammation, which may, in part, be mediated by Treg induction. Moreover, wheat-derived arabinoxylan suppressed TNFα production from type 1 helper T cells in this colitis model. In conclusion, wheat-derived arabinoxylans, by altering the gut microenvironment, may be a promising prebiotic for the prevention of colitis.}, } @article {pmid37049820, year = {2023}, author = {Kacsir, I and Sipos, A and Major, E and Bajusz, N and Bényei, A and Buglyó, P and Somsák, L and Kardos, G and Bai, P and Bokor, É}, title = {Half-Sandwich Type Platinum-Group Metal Complexes of C-Glucosaminyl Azines: Synthesis and Antineoplastic and Antimicrobial Activities.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {7}, pages = {}, pmid = {37049820}, issn = {1420-3049}, support = {K142141//National Research, Development and Innovation Office/ ; FK125067//National Research, Development and Innovation Office/ ; TKP2020-IKA-04//National Research, Development and Innovation Office/ ; TKP2021-EGA-19//National Research, Development and Innovation Office/ ; TKP2021-EGA-20//National Research, Development and Innovation Office/ ; POST-COVID2021-33//Hungarian Academy of Sciences/ ; NKM2022-30//Hungarian Academy of Sciences/ ; }, mesh = {Humans ; Female ; *Coordination Complexes/chemistry ; *Cytostatic Agents/therapeutic use ; Cell Line, Tumor ; *Ovarian Neoplasms/drug therapy ; *Antineoplastic Agents/chemistry ; Metals ; Azo Compounds/therapeutic use ; *Quinolines/therapeutic use ; Pyridines/pharmacology/therapeutic use ; *Anti-Infective Agents/pharmacology/therapeutic use ; *Ruthenium/chemistry ; }, abstract = {While platinum-based compounds such as cisplatin form the backbone of chemotherapy, the use of these compounds is limited by resistance and toxicity, driving the development of novel complexes with cytostatic properties. In this study, we synthesized a set of half-sandwich complexes of platinum-group metal ions (Ru(II), Os(II), Ir(III) and Rh(III)) with an N,N-bidentate ligand comprising a C-glucosaminyl group and a heterocycle, such as pyridine, pyridazine, pyrimidine, pyrazine or quinoline. The sugar-containing ligands themselves are unknown compounds and were obtained by nucleophilic additions of lithiated heterocycles to O-perbenzylated 2-nitro-glucal. Reduction of the adducts and, where necessary, subsequent protecting group manipulations furnished the above C-glucosaminyl heterocycles in their O-perbenzylated, O-perbenzoylated and O-unprotected forms. The derived complexes were tested on A2780 ovarian cancer cells. Pyridine, pyrazine and pyridazine-containing complexes proved to be cytostatic and cytotoxic on A2780 cells, while pyrimidine and quinoline derivatives were inactive. The best complexes contained pyridine as the heterocycle. The metal ion with polyhapto arene/arenyl moiety also impacted on the biological activity of the complexes. Ruthenium complexes with p-cymene and iridium complexes with Cp* had the best performance in ovarian cancer cells, followed by osmium complexes with p-cymene and rhodium complexes with Cp*. Finally, the chemical nature of the protective groups on the hydroxyl groups of the carbohydrate moiety were also key determinants of bioactivity; in particular, O-benzyl groups were superior to O-benzoyl groups. The IC50 values of the complexes were in the low micromolar range, and, importantly, the complexes were less active against primary, untransformed human dermal fibroblasts; however, the anticipated therapeutic window is narrow. The bioactive complexes exerted cytostasis on a set of carcinomas such as cell models of glioblastoma, as well as breast and pancreatic cancers. Furthermore, the same complexes exhibited bacteriostatic properties against multiresistant Gram-positive Staphylococcus aureus and Enterococcus clinical isolates in the low micromolar range.}, } @article {pmid37049587, year = {2023}, author = {Dai, A and Hoffman, K and Xu, AA and Gurwara, S and White, DL and Kanwal, F and Jang, A and El-Serag, HB and Petrosino, JF and Jiao, L}, title = {The Association between Caffeine Intake and the Colonic Mucosa-Associated Gut Microbiota in Humans-A Preliminary Investigation.}, journal = {Nutrients}, volume = {15}, number = {7}, pages = {}, pmid = {37049587}, issn = {2072-6643}, support = {RP#140767//Cancer Prevention and Research Institute of Texas/ ; 000//Gillson Longenbaugh Foundation/ ; 000//Golfers against cancer organization/ ; DK56338/NH/NIH HHS/United States ; CX001430/VA/VA/United States ; }, mesh = {Adult ; Humans ; *Caffeine ; Coffee ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Intestinal Mucosa/microbiology ; Risk Factors ; }, abstract = {We examined the association between caffeine and coffee intake and the community composition and structure of colonic microbiota. A total of 34 polyp-free adults donated 97 colonic biopsies. Microbial DNA was sequenced for the 16S rRNA gene V4 region. The amplicon sequence variant was assigned using DADA2 and SILVA. Food consumption was ascertained using a food frequency questionnaire. We compared the relative abundance of taxonomies by low (<82.9 mg) vs. high (≥82.9 mg) caffeine intake and by never or <2 cups vs. 2 cups vs. ≥3 cups coffee intake. False discovery rate-adjusted p values (q values) <0.05 indicated statistical significance. Multivariable negative binomial regression models were used to estimate the incidence rate ratio and its 95% confidence interval of having a non-zero count of certain bacteria by intake level. Higher caffeine and coffee intake was related to higher alpha diversity (Shannon index p < 0.001), higher relative abundance of Faecalibacterium and Alistipes, and lower relative abundance of Erysipelatoclostridium (q values < 0.05). After adjustment of vitamin B2 in multivariate analysis, the significant inverse association between Erysipelatoclostridium count and caffeine intake remained statistically significant. Our preliminary study could not evaluate other prebiotics in coffee.}, } @article {pmid37049457, year = {2023}, author = {Wang, Z and Li, J and Ma, L and Liu, X and Wei, H and Xiao, Y and Tao, S}, title = {Metagenomic Sequencing Identified Specific Bacteriophage Signature Discriminating between Healthy and Diarrheal Neonatal Piglets.}, journal = {Nutrients}, volume = {15}, number = {7}, pages = {}, pmid = {37049457}, issn = {2072-6643}, support = {32272898//National Nature Science Foundation of China/ ; 2021CFB436//Natural Science Foundation of Hubei Province/ ; 2021CFA018//Natural Science Foundation of Hubei Province/ ; 31902189//National Nature Science Foundation of China/ ; 2022020801020230//Knowledge Innovation Program of Wuhan-Shuguang Project/ ; 2662022YJ003//Fundamental Research Funds for the Central Universities/ ; 2662020DKQD004//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Animals ; Swine ; Infant, Newborn ; Humans ; *Escherichia coli ; *Bacteriophages/genetics ; Diarrhea/veterinary/microbiology ; Bacteria ; Feces/microbiology ; }, abstract = {Neonatal diarrhea is one of the most severe diseases in human beings and pigs, leading to high mortality and growth faltering. Gut microbiome-related studies mostly focus on the relationship between bacteria and neonatal diarrhea onset, and no research study has investigated the role of the gut virome in neonatal diarrhea. Here, using metagenomic sequencing, we characterized the fecal viral community of diarrheal and healthy neonatal piglets. We found that the viral community of diarrheal piglets showed higher individual heterogeneity and elevated abundance of Myoviridae. By predicting the bacterial host of the identified viral genomes, phages infecting Proteobacteria, especially E. coli, were the dominant taxa in neonatal diarrheal piglets. Consistent with this, the antibiotic resistance gene of E. coli origin was also enriched in neonatal diarrheal piglets. Finally, we established a random forest model to accurately discriminate between neonatal diarrheal piglets and healthy controls and identified genus E. coli- and genus listeria-infecting bacteriophages, including psa and C5 viruses, as key biomarkers. In conclusion, we provide the first glance of viral community and function characteristics in diarrheal and healthy neonatal piglets. These findings expand our understanding of the relationship among phages, bacteria and diarrhea, and may facilitate the development of therapeutics for the prevention and treatment of neonatal diarrhea.}, } @article {pmid37047647, year = {2023}, author = {Cisek, AA and Dolka, B and Bąk, I and Cukrowska, B}, title = {Microorganisms Involved in Hydrogen Sink in the Gastrointestinal Tract of Chickens.}, journal = {International journal of molecular sciences}, volume = {24}, number = {7}, pages = {}, pmid = {37047647}, issn = {1422-0067}, support = {2017/25/N/NZ7/02905//National Science Center/ ; }, mesh = {Animals ; Chickens/genetics ; *Hydrogenase/genetics ; Hydrogen/metabolism ; RNA, Ribosomal, 16S/genetics ; Gastrointestinal Tract/metabolism ; Cecum/metabolism ; *Euryarchaeota/genetics ; }, abstract = {Hydrogen sink is a beneficial process, which has never been properly examined in chickens. Therefore, the aim of this study was to assess the quantity and quality of microbiota involved in hydrogen uptake with the use of real-time PCR and metagenome sequencing. Analyses were carried out in 50 free-range chickens, 50 commercial broilers, and 54 experimental chickens isolated from external factors. The median values of acetogens, methanogens, sulfate-reducing bacteria (SRB), and [NiFe]-hydrogenase utilizers measured in the cecum were approx. 7.6, 0, 0, and 3.2 log10/gram of wet weight, respectively. For the excreta samples, these values were 5.9, 4.8, 4, and 3 log10/gram of wet weight, respectively. Our results showed that the acetogens were dominant over the other tested groups of hydrogen consumers. The quantities of methanogens, SRB, and the [NiFe]-hydrogenase utilizers were dependent on the overall rearing conditions, being the result of diet, environment, agrotechnical measures, and other factors combined. By sequencing of the 16S rRNA gene, archaea of the genus Methanomassiliicoccus (Candidatus Methanomassiliicoccus) were discovered in chickens for the first time. This study provides some indication that in chickens, acetogenesis may be the main metabolic pathway responsible for hydrogen sink.}, } @article {pmid37047594, year = {2023}, author = {Laterza, L and Putignani, L and Settanni, CR and Petito, V and Varca, S and De Maio, F and Macari, G and Guarrasi, V and Gremese, E and Tolusso, B and Wlderk, G and Pirro, MA and Fanali, C and Scaldaferri, F and Turchini, L and Amatucci, V and Sanguinetti, M and Gasbarrini, A}, title = {Ecology and Machine Learning-Based Classification Models of Gut Microbiota and Inflammatory Markers May Evaluate the Effects of Probiotic Supplementation in Patients Recently Recovered from COVID-19.}, journal = {International journal of molecular sciences}, volume = {24}, number = {7}, pages = {}, pmid = {37047594}, issn = {1422-0067}, support = {na//Actial Farmaceutica/ ; na//Fondazione Roma/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Citrulline ; *COVID-19 ; *Probiotics/therapeutic use/pharmacology ; Cytokines ; Bifidobacterium ; Machine Learning ; }, abstract = {Gut microbiota (GM) modulation can be investigated as possible solution to enhance recovery after COVID-19. An open-label, single-center, single-arm, pilot, interventional study was performed by enrolling twenty patients recently recovered from COVID-19 to investigate the role of a mixed probiotic, containing Lactobacilli, Bifidobacteria and Streptococcus thermophilus, on gastrointestinal symptoms, local and systemic inflammation, intestinal barrier integrity and GM profile. Gastrointestinal Symptom Rating Scale, cytokines, inflammatory, gut permeability, and integrity markers were evaluated before (T0) and after 8 weeks (T1) of probiotic supplementation. GM profiling was based on 16S-rRNA targeted-metagenomics and QIIME 2.0, LEfSe and PICRUSt computational algorithms. Multiple machine learning (ML) models were trained to classify GM at T0 and T1. A statistically significant reduction of IL-6 (p < 0.001), TNF-α (p < 0.001) and IL-12RA (p < 0.02), citrulline (p value < 0.001) was reported at T1. GM global distribution and microbial biomarkers strictly reflected probiotic composition, with a general increase in Bifidobacteria at T1. Twelve unique KEGG orthologs were associated only to T0, including tetracycline resistance cassettes. ML classified the GM at T1 with 100% score at phylum level. Bifidobacteriaceae and Bifidobacterium spp. inversely correlated to reduction of citrulline and inflammatory cytokines. Probiotic supplementation during post-COVID-19 may trigger anti-inflammatory effects though Bifidobacteria and related-metabolism enhancement.}, } @article {pmid37047542, year = {2023}, author = {Choy, CT and Chan, UK and Siu, PLK and Zhou, J and Wong, CH and Lee, YW and Chan, HW and Tsui, JCC and Loo, SKF and Tsui, SKW}, title = {A Novel E3 Probiotics Formula Restored Gut Dysbiosis and Remodelled Gut Microbial Network and Microbiome Dysbiosis Index (MDI) in Southern Chinese Adult Psoriasis Patients.}, journal = {International journal of molecular sciences}, volume = {24}, number = {7}, pages = {}, pmid = {37047542}, issn = {1422-0067}, support = {Nil//Hong Kong Society of Gut Microbiome/ ; }, mesh = {Adult ; Humans ; *Dysbiosis/complications/drug therapy ; East Asian People ; *Gastrointestinal Microbiome/drug effects/physiology ; *Probiotics/pharmacology/therapeutic use ; *Psoriasis/complications/drug therapy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Psoriasis is a common chronic immune-mediated inflammatory skin disease with the association of various comorbidities. Despite the introduction of highly effective biologic therapies over the past few decades, the exact trigger for an immune reaction in psoriasis is unclear. With the majority of immune cells residing in the gut, the effect of gut microbiome dysbiosis goes beyond the gastrointestinal site and may exacerbate inflammation and regulate the immune system elsewhere, including but not limited to the skin via the gut-skin axis. In order to delineate the role of the gut microbiome in Southern Chinese psoriasis patients, we performed targeted 16S rRNA sequencing and comprehensive bioinformatic analysis to compare the gut microbiome profile of 58 psoriasis patients against 49 healthy local subjects presumably with similar lifestyles. Blautia wexlerae and Parabacteroides distasonis were found to be enriched in psoriasis patients and in some of the healthy subjects, respectively. Metabolic functional pathways were predicted to be differentially abundant, with a clear shift toward SCFA synthesis in healthy subjects. The alteration of the co-occurrence network was also evident in the psoriasis group. In addition, we also profiled the gut microbiome in 52 of the 58 recruited psoriasis patients after taking 8 weeks of an orally administrated novel E3 probiotics formula (with prebiotics, probiotics and postbiotics). The Dermatological Life Quality Index (p = 0.009) and Psoriasis Area and Severity Index (p < 0.001) were significantly improved after taking 8 weeks of probiotics with no adverse effect observed. We showed that probiotics could at least partly restore gut dysbiosis via the modulation of the gut microbiome. Here, we also report the potential application of a machine learning-derived gut dysbiosis index based on a quantitative PCR panel (AUC = 0.88) to monitor gut dysbiosis in psoriasis patients. To sum up, our study suggests the gut microbial landscape differed in psoriasis patients at the genera, species, functional and network levels. Additionally, the dysbiosis index could be a cost-effective and rapid tool to monitor probiotics use in psoriasis patients.}, } @article {pmid37047466, year = {2023}, author = {Lu, J and Shu, Y and Zhang, H and Zhang, S and Zhu, C and Ding, W and Zhang, W}, title = {The Landscape of Global Ocean Microbiome: From Bacterioplankton to Biofilms.}, journal = {International journal of molecular sciences}, volume = {24}, number = {7}, pages = {}, pmid = {37047466}, issn = {1422-0067}, mesh = {*Aquatic Organisms ; Oceans and Seas ; *Microbiota ; Plankton ; Metagenomics ; Biofilms ; }, abstract = {The development of metagenomics has opened up a new era in the study of marine microbiota, which play important roles in biogeochemical cycles. In recent years, the global ocean sampling expeditions have spurred this research field toward a deeper understanding of the microbial diversities and functions spanning various lifestyles, planktonic (free-living) or sessile (biofilm-associated). In this review, we deliver a comprehensive summary of marine microbiome datasets generated in global ocean expeditions conducted over the last 20 years, including the Sorcerer II GOS Expedition, the Tara Oceans project, the bioGEOTRACES project, the Micro B3 project, the Bio-GO-SHIP project, and the Marine Biofilms. These datasets have revealed unprecedented insights into the microscopic life in our oceans and led to the publication of world-leading research. We also note the progress of metatranscriptomics and metaproteomics, which are confined to local marine microbiota. Furthermore, approaches to transforming the global ocean microbiome datasets are highlighted, and the state-of-the-art techniques that can be combined with data analyses, which can present fresh perspectives on marine molecular ecology and microbiology, are proposed.}, } @article {pmid37047311, year = {2023}, author = {Kimeklis, AK and Gladkov, GV and Orlova, OV and Afonin, AM and Gribchenko, ES and Aksenova, TS and Kichko, AA and Pinaev, AG and Andronov, EE}, title = {The Succession of the Cellulolytic Microbial Community from the Soil during Oat Straw Decomposition.}, journal = {International journal of molecular sciences}, volume = {24}, number = {7}, pages = {}, pmid = {37047311}, issn = {1422-0067}, support = {18-16-00073//Russian Science Foundation/ ; }, mesh = {Soil/chemistry ; Avena ; *Microbiota ; Bacteria/genetics/metabolism ; *Ascomycota ; Glycoside Hydrolases/metabolism ; Soil Microbiology ; }, abstract = {The process of straw decomposition is dynamic and is accompanied by the succession of the microbial decomposing community, which is driven by poorly understood interactions between microorganisms. Soil is a complex ecological niche, and the soil microbiome can serve as a source of potentially active cellulolytic microorganisms. Here, we performed an experiment on the de novo colonization of oat straw by the soil microbial community by placing nylon bags with sterilized oat straw in the pots filled with chernozem soil and incubating them for 6 months. The aim was to investigate the changes in decomposer microbiota during this process using conventional sequencing techniques. The bacterial succession during straw decomposition occurred in three phases: the early phase (first month) was characterized by high microbial activity and low diversity, the middle phase (second to third month) was characterized by low activity and low diversity, and the late phase (fourth to sixth months) was characterized by low activity and high diversity. Analysis of amplicon sequencing data revealed three groups of co-changing phylotypes corresponding to these phases. The early active phase was abundant in the cellulolytic members from Pseudomonadota, Bacteroidota, Bacillota, and Actinobacteriota for bacteria and Ascomycota for fungi, and most of the primary phylotypes were gone by the end of the phase. The second intermediate phase was marked by the set of phylotypes from the same phyla persisting in the community. In the mature community of the late phase, apart from the core phylotypes, non-cellulolytic members from Bdellovibrionota, Myxococcota, Chloroflexota, and Thermoproteota appeared. Full metagenome sequencing of the microbial community from the end of the middle phase confirmed that major bacterial and fungal members of this consortium had genes of glycoside hydrolases (GH) connected to cellulose and chitin degradation. The real-time analysis of the selection of these genes showed that their representation varied between phases, and this occurred under the influence of the host, and not the GH family factor. Our findings demonstrate that soil microbial community may act as an efficient source of cellulolytic microorganisms and that colonization of the cellulolytic substrate occurs in several phases, each characterized by its own taxonomic and functional profile.}, } @article {pmid37047089, year = {2023}, author = {Samoylova, NA and Gureev, AP and Popov, VN}, title = {Methylene Blue Induces Antioxidant Defense and Reparation of Mitochondrial DNA in a Nrf2-Dependent Manner during Cisplatin-Induced Renal Toxicity.}, journal = {International journal of molecular sciences}, volume = {24}, number = {7}, pages = {}, pmid = {37047089}, issn = {1422-0067}, support = {SP-2802.2021.4//the President of the Russian Federation for young scientists and PhD students/ ; NSh-1375.2022.5//the President grant for support of leading scientific school/ ; }, mesh = {*Cisplatin/toxicity/metabolism ; Antioxidants/pharmacology/metabolism ; NF-E2-Related Factor 2/genetics/metabolism ; Methylene Blue/pharmacology ; DNA, Mitochondrial/metabolism ; Hydrogen Peroxide/metabolism ; *Antineoplastic Agents/toxicity ; Mitochondria/metabolism ; Oxidative Stress ; }, abstract = {Cisplatin is a platinum-based cytostatic drug that is widely used for cancer treatment. Mitochondria and mtDNA are important targets for platinum-based cytostatics, which mediates its nephrotoxicity. It is important to develop therapeutic approaches to protect the kidneys from cisplatin during chemotherapy. We showed that the exposure of mitochondria to cisplatin increased the level of lipid peroxidation products in the in vitro experiment. Cisplatin caused strong damage to renal mtDNA, both in the in vivo and in vitro experiments. Cisplatin injections induced oxidative stress by depleting renal antioxidants at the transcriptome level but did not increase the rate of H2O2 production in isolated mitochondria. Methylene blue, on the contrary, induced mitochondrial H2O2 production. We supposed that methylene blue-induced H2O2 production led to activation of the Nrf2/ARE signaling pathway. The consequences of activation of this signaling pathway were manifested in an increase in the expression of some antioxidant genes, which likely caused a decrease in the amount of mtDNA damage. Methylene blue treatment induced an increase in the expression of genes that were involved in the base excision repair (BER) pathway: the main pathway for mtDNA reparation. It is known that the expression of these genes can also be regulated by the Nrf2/ARE signaling pathway. We can assume that the protective effect of methylene blue is related to the activation of Nrf2/ARE signaling pathways, which can activate the expression of genes related to antioxidant defense and mtDNA reparation. Thus, the protection of kidney mitochondria from cisplatin-induced damage using methylene blue can significantly expand its application in medicine.}, } @article {pmid37046762, year = {2023}, author = {Kiousi, DE and Kouroutzidou, AZ and Neanidis, K and Karavanis, E and Matthaios, D and Pappa, A and Galanis, A}, title = {The Role of the Gut Microbiome in Cancer Immunotherapy: Current Knowledge and Future Directions.}, journal = {Cancers}, volume = {15}, number = {7}, pages = {}, pmid = {37046762}, issn = {2072-6694}, support = {5047285//European Regional Development Fund/ ; }, abstract = {Cancer immunotherapy is a treatment modality that aims to stimulate the anti-tumor immunity of the host to elicit favorable clinical outcomes. Immune checkpoint inhibitors (ICIs) gained traction due to the lasting effects and better tolerance in patients carrying solid tumors in comparison to conventional treatment. However, a significant portion of patients may present primary or acquired resistance (non-responders), and thus, they may have limited therapeutic outcomes. Resistance to ICIs can be derived from host-related, tumor-intrinsic, or environmental factors. Recent studies suggest a correlation of gut microbiota with resistance and response to immunotherapy as well as with the incidence of adverse events. Currently, preclinical and clinical studies aim to elucidate the unique microbial signatures related to ICI response and anti-tumor immunity, employing metagenomics and/or multi-omics. Decoding this complex relationship can provide the basis for manipulating the malleable structure of the gut microbiota to enhance therapeutic success. Here, we delve into the factors affecting resistance to ICIs, focusing on the intricate gut microbiome-immunity interplay. Additionally, we review clinical studies and discuss future trends and directions in this promising field.}, } @article {pmid37044345, year = {2023}, author = {Sánchez-Reyes, A and Gaytán, I and Pulido-García, J and Burelo, M and Vargas-Suárez, M and Cruz-Gómez, MJ and Loza-Tavera, H}, title = {Genetic basis for the biodegradation of a polyether-polyurethane-acrylic copolymer by a landfill microbial community inferred by metagenomic deconvolution analysis.}, journal = {The Science of the total environment}, volume = {881}, number = {}, pages = {163367}, doi = {10.1016/j.scitotenv.2023.163367}, pmid = {37044345}, issn = {1879-1026}, mesh = {*Polyurethanes/chemistry ; Metagenome ; Plastics ; *Microbiota ; Biodegradation, Environmental ; Waste Disposal Facilities ; }, abstract = {Plastic accumulation in the world amounts to approximately 8300 million tons. Polyurethanes (PU) account for 7.7 % of total plastics production worldwide, and their diverse chemical composition makes them highly recalcitrant to biodegradation. Several works have reported polyurethane-degrading microbial communities. However, it is still necessary to learn more about the chemical, biochemical, and genetic bases linked to the polyurethanolytic phenotype and the microbial taxonomic determinants responsible for metabolizing the PU polymer and its associated chemical additives. To shed light on this problem, we applied physical, chemical, biochemical, metagenomic, and bioinformatic analyses to explore the biodegradation capability and related biochemical and genetic determinants of the BP6 microbial community that can grow in PolyLack, a commercial coating containing a polyether polyurethane acrylate (PE-PU-A) copolymer and several additives, as sole carbon source. We observed complete additives (isopropanol, N-methyl-2-pyrrolidone, 2-butoxyethanol, alkyl glycol ethers) biodegradation and the appearance of released polymer components (toluene diisocyanate (TDI) and methylene diphenyl diisocyanate (MDI) derivatives), and multiple degradation products since early cultivation times. The Hi-C metagenomic analysis identified a complex microbiome with 35 deconvolved Metagenome-Assembled Genomes (MAGs) - several new species - and biodegradation markers that suggest the coexistence of hydrolytic, oxidative, and reductive metabolic strategies for degrading the additives and the PU copolymer. This work also provides evidence of the metabolic capability the BP6 community has for biodegrading polyether polyurethane foams. Based on these analyses, we propose a novel metabolic pathway for 4,4'-methylenedianiline (MDA), an initial biodegradation intermediate of MDI-based PU, encoded in the complex BP6 community metagenome and suggest that this community is a potential biotechnological tool for PU bio-recycling.}, } @article {pmid37043060, year = {2023}, author = {Achudhan, AB and Kannan, P and Saleena, LM}, title = {CRISPR detection in metagenome-assembled genomes (MAGs) of coal mine.}, journal = {Functional & integrative genomics}, volume = {23}, number = {2}, pages = {122}, pmid = {37043060}, issn = {1438-7948}, mesh = {Metagenome ; *Burkholderia/genetics ; *Bacteriophages/genetics ; Coal ; Metagenomics ; }, abstract = {Bacterial and archaeal CRISPR-Cas systems provide adaptive immune protection against foreign mobile genetic elements. When viruses infect bacteria, a small portion of the viral DNA is inserted into the bacterial DNA in a specific pattern to produce segments known as CRISPR arrays. Metagenome assembled genomes (MAGs) were used in our study to identify the CRISPR sequence for determining the interacted phage. Metagenomic data from a coal mine was used to perform a computational study. From raw reads, 206151 contigs were assembled. Then contigs were clustered into 150 Metagenome assembled genomes from which 78 non-redundant MAGs were selected. Using the CHECKM standard, seven MAGs were found to have >80 completeness and <20 contaminations. Those MAGs were analyzed for the presence of CRISPR elements. Out of seven MAGs, four MAGs have the CRISPR elements and are searched against the VIROblast database. CRISPR arrays have 4, 1, 3, and 7 spacer sequences in the MAGs of Burkholderia, Acinetobacter, Oxalobacteraceae, and Burkholderia multivorans respectively. The uncultured Caudovirales phage genomic regions were present in the genomes of Burkholderia, Oxalobacteriaceae, and Burkholderia multivorans. This study follows the unconventional metagenomics workflow to provide a better understanding of bacteria and phage interactions.}, } @article {pmid37042774, year = {2023}, author = {Ley, Y and Cheng, XY and Ying, ZY and Zhou, NY and Xu, Y}, title = {Characterization of Two Marine Lignin-Degrading Consortia and the Potential Microbial Lignin Degradation Network in Nearshore Regions.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0442422}, pmid = {37042774}, issn = {2165-0497}, mesh = {*Lignin/metabolism ; *Microbial Consortia ; Biodegradation, Environmental ; Bacteria/metabolism ; Alkalies ; Carbon/metabolism ; }, abstract = {Terrestrial organic carbon such as lignin is an important component of the global marine carbon. However, the structural complexity and recalcitrant nature of lignin are deemed challenging for biodegradation. It has been speculated that bacteria play important roles in lignin degradation in the marine system. However, the extent of the involvement of marine microorganisms in lignin degradation and their contribution to the oceanic carbon cycle remains elusive. In this study, two bacterial consortia capable of degrading alkali lignin (a model compound of lignin), designated LIG-B and LIG-S, were enriched from the nearshore sediments of the East and South China Seas. Consortia LIG-B and LIG-S mainly comprised of the Proteobacteria phylum with Nitratireductor sp. (71.6%) and Halomonas sp. (91.6%), respectively. Lignin degradation was found more favorable in consortium LIG-B (max 57%) than in LIG-S (max 18%). Ligninolytic enzymes laccase (Lac), manganese peroxidase (MnP), and lignin peroxidase (LiP) capable of decomposing lignin into smaller fragments were all active in both consortia. The newly emerged low-molecular-weight aromatics, organic acids, and other lignin-derived compounds in biotreated alkali lignin also evidently showed the depolymerization of lignin by both consortia. The lignin degradation pathways reconstructed from consortium LIG-S were found to be more comprehensive compared to consortium LIG-B. It was further revealed that catabolic genes, involved in the degradation of lignin and its derivatives through multiple pathways via protocatechuate and catechol, are present not only in lignin-degrading consortia LIG-B and LIG-S but also in 783 publicly available metagenomic-assembled genomes from nine nearshore regions. IMPORTANCE Numerous terrigenous lignin-containing plant materials are constantly discharged from rivers and estuaries into the marine system. However, only low levels of terrigenous organic carbon, especially lignin, are detected in the global marine system due to the abundance of active heterotrophic microorganisms driving the carbon cycle. Simultaneously, the lack of knowledge on lignin biodegradation has hindered our understanding of the oceanic carbon cycle. Moreover, bacteria have been speculated to play important roles in the marine lignin biodegradation. Here, we enriched two bacterial consortia from nearshore sediments capable of utilizing alkali lignin for cell growth while degrading it into smaller molecules and reconstructed the lignin degradation network. In particular, this study highlights that marine microorganisms in nearshore regions mostly undergo similar pathways using protocatechuate and catechol as ring-cleavage substrates to drive lignin degradation as part of the oceanic carbon cycle, regardless of whether they are in sediments or water column.}, } @article {pmid37042768, year = {2023}, author = {Zhang, P and Zhang, Y and Cao, L and Li, J and Wu, C and Tian, M and Zhang, Z and Zhang, C and Zhang, W and Li, Y}, title = {A Diverse Virome Is Identified in Parasitic Flatworms of Domestic Animals in Xinjiang, China.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0070223}, pmid = {37042768}, issn = {2165-0497}, mesh = {Adult ; Animals ; Dogs ; Humans ; Animals, Domestic ; Phylogeny ; Virome ; *Viruses/genetics ; *RNA Viruses ; Metagenome ; *Platyhelminths ; }, abstract = {Parasitic flatworms infect diverse vertebrates and are major threats to animal and even human health; however, little is known about the virome of these lower life forms. Using viral metagenomic sequencing, we characterized the virome of the parasitic flatworms collected from major domestic animals, including Dicrocoelium lanceatum and Taenia hydatigena, Echinococcus granulosus sensu stricto and Echinococcus multilocularis. Seven and three different viruses were discovered from D. lanceatum and T. hydatigena, respectively, and no viral sequences were found in adult tapeworms and protoscoleces of E. granulosus sensu stricto and E. multilocularis. Two out of the five parasitic flatworm species carry viruses, showing a host specificity of these viruses. These viruses belong to the Parvoviridae, Circoviridae, unclassified circular, Rep-encoding single-stranded (CRESS) DNA virus, Rhabdoviridae, Endornaviridae, and unclassified RNA viruses. The presence of multiple highly divergent RNA viruses, especially those that cluster with viruses found in marine animals, implies a deep evolutionary history of parasite-associated viruses. In addition, we found viruses with high identity to common pathogens in dogs, including canine circovirus and canine parvovirus 2. The presence of these viruses in the parasites implies that they may infect parasitic flatworms but does not completely exclude the possibility of contamination from host intestinal contents. Furthermore, we demonstrated that certain viruses, such as CRESS DNA virus may integrate into the genome of their host. Our results expand the knowledge of viral diversity in parasites of important domestic animals, highlighting the need for further investigations of their prevalence among other parasites of key animals. IMPORTANCE Characterizing the virome of parasites is important for unveiling the viral diversity, evolution, and ecology and will help to understand the "Russian doll" pattern among viruses, parasites, and host animals. Our data indicate that diverse viruses are present in specific parasitic flatworms, including viruses that may have an ancient evolutionary history and viruses currently circulating in parasite-infected host animals. These data also raise the question of whether parasitic flatworms acquire and/or carry some viruses that may have transmission potential to animals. In addition, through the study of virus-parasite-host interactions, including the influence of viral infection on the life cycle of the parasite, as well as its fitness and pathogenicity to the host, we could find new strategies to prevent and control parasitic diseases.}, } @article {pmid37042763, year = {2023}, author = {Marquis, B and Ardissone, S and Greub, G}, title = {Temperature Affects the Host Range of Rhabdochlamydia porcellionis.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {5}, pages = {e0030923}, pmid = {37042763}, issn = {1098-5336}, mesh = {Animals ; *Host Specificity ; RNA, Ribosomal, 16S/genetics ; Temperature ; Cell Line ; *Arthropods ; Mammals ; }, abstract = {The Rhabdochlamydiaceae family is a recent addition to the Chlamydiae phylum. Its members were discovered in cockroaches and woodlice, but recent metagenomics surveys demonstrated the widespread distribution of this family in the environment. It was, moreover, estimated to be the largest family of the Chlamydiae phylum based on the diversity of its 16S rRNA encoding gene. Unlike most Chlamydia-like organisms, no Rhabdochlamydiaceae member could be cultivated in amoebae, and its host range remains unknown. We tested the permissivity of various mammalian and arthropod cell lines to determine the host range of Rhabdochlamydia porcellionis, the only cultured representative of this family. While growth could initially be obtained only in the Sf9 cell line, lowering the incubation temperature of the mammalian cells from 37°C to 28°C allowed the growth of R. porcellionis. Furthermore, a 6-h exposure to 37°C was sufficient to irreversibly block the replication of R. porcellionis, suggesting that this bacterium either lost or never acquired the ability to grow at 37°C. We next sought to determine if temperature would also affect the infectivity of elementary bodies. Although we could not purify enough bacteria to reach a conclusive result for R. porcellionis, our experiment showed that the elementary bodies of Chlamydia trachomatis and Waddlia chondrophila lose their infectivity faster at 37°C than at room temperature. Our results demonstrate that members of the Chlamydiae phylum adapt to the temperature of their host organism and that this adaptation can in turn restrict their host range. IMPORTANCE The Rhabdochlamydiaceae family is part of the Chlamydiae, a phylum of bacteria that includes obligate intracellular bacteria sharing the same biphasic developmental cycle. This family has been shown to be highly prevalent in the environment, particularly in freshwater and soil, and despite being estimated to be the largest family in the Chlamydiae phylum is only poorly studied. Members of the Rhabdochlamydiaceae have been detected in various arthropods like ticks, spiders, cockroaches, and woodlice, but the full host range of this family is currently unknown. In this study, we showed that R. porcellionis, the only cultured representative of the Rhabdochlamydiaceae family, cannot grow at 37°C and is quickly inactivated at this temperature. A similar temperature sensitivity was also observed for elementary bodies of chlamydial species adapted to mammals. Our work demonstrates that chlamydiae adapt to the temperature of their reservoir, making a jump between species with different body temperatures unlikely.}, } @article {pmid37042671, year = {2023}, author = {Schwartz, DA and Rodríguez-Ramos, JA and Shaffer, M and Flynn, RM and Daly, RA and Wrighton, KC and Lennon, JT}, title = {Human-Gut Phages Harbor Sporulation Genes.}, journal = {mBio}, volume = {14}, number = {3}, pages = {e0018223}, pmid = {37042671}, issn = {2150-7511}, mesh = {Animals ; Humans ; *Bacteriophages/genetics ; Gene Regulatory Networks ; Bacteria/genetics ; Spores, Bacterial ; Transcription Factors/genetics ; Mammals/genetics ; }, abstract = {Spore-forming bacteria are prevalent in mammalian guts and have implications for host health and nutrition. The production of dormant spores is thought to play an important role in the colonization, persistence, and transmission of these bacteria. Spore formation also modifies interactions among microorganisms such as infection by phages. Recent studies suggest that phages may counter dormancy-mediated defense through the expression of phage-carried sporulation genes during infection, which can alter the transitions between active and inactive states. By mining genomes and gut-derived metagenomes, we identified sporulation genes that are preferentially carried by phages that infect spore-forming bacteria. These included genes involved in chromosome partitioning, DNA damage repair, and cell wall-associated functions. In addition, phages contained homologs of sporulation-specific transcription factors, notably spo0A, the master regulator of sporulation, which could allow phages to control the complex genetic network responsible for spore development. Our findings suggest that phages could influence the formation of bacterial spores with implications for the health of the human gut microbiome, as well as bacterial communities in other environments. IMPORTANCE Phages acquire bacterial genes and use them to alter host metabolism in ways that enhance phage fitness. To date, most auxiliary genes replace or modulate enzymes that are used by the host for nutrition or energy production. However, phage fitness is affected by all aspects of host physiology, including decisions that reduce the metabolic activity of the cell. Here, we focus on endosporulation, a complex and ancient form of dormancy found among the Bacillota that involves hundreds of genes. By coupling homology searches with host classification, we identified 31 phage-carried homologs of sporulation genes that are mostly limited to phages infecting spore-forming bacteria. Nearly one-third of the homologs recovered were regulatory genes, suggesting that phages may manipulate host genetic networks by tapping into their control elements. Our findings also suggest a mechanism by which phages can overcome the defensive strategy of dormancy, which may be involved in coevolutionary dynamics of spore-forming bacteria.}, } @article {pmid37041201, year = {2023}, author = {Ding, W and Wang, S and Qin, P and Fan, S and Su, X and Cai, P and Lu, J and Cui, H and Wang, M and Shu, Y and Wang, Y and Fu, HH and Zhang, YZ and Li, YX and Zhang, W}, title = {Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2033}, pmid = {37041201}, issn = {2041-1723}, mesh = {*Thiosulfates/metabolism ; *Roseobacter/genetics/metabolism ; Anaerobiosis ; Proteomics ; Biofilms ; }, abstract = {Thiosulfate oxidation by microbes has a major impact on global sulfur cycling. Here, we provide evidence that bacteria within various Roseobacter lineages are important for thiosulfate oxidation in marine biofilms. We isolate and sequence the genomes of 54 biofilm-associated Roseobacter strains, finding conserved sox gene clusters for thiosulfate oxidation and plasmids, pointing to a niche-specific lifestyle. Analysis of global ocean metagenomic data suggests that Roseobacter strains are abundant in biofilms and mats on various substrates, including stones, artificial surfaces, plant roots, and hydrothermal vent chimneys. Metatranscriptomic analysis indicates that the majority of active sox genes in biofilms belong to Roseobacter strains. Furthermore, we show that Roseobacter strains can grow and oxidize thiosulfate to sulfate under both aerobic and anaerobic conditions. Transcriptomic and membrane proteomic analyses of biofilms formed by a representative strain indicate that thiosulfate induces sox gene expression and alterations in cell membrane protein composition, and promotes biofilm formation and anaerobic respiration. We propose that bacteria of the Roseobacter group are major thiosulfate-oxidizers in marine biofilms, where anaerobic thiosulfate metabolism is preferred.}, } @article {pmid37041035, year = {2023}, author = {Sun, Y and Cheng, Z and Li, X and Yang, Q and Zhao, B and Wu, Z and Xia, Y}, title = {Genome enrichment of rare and unknown species from complicated microbiomes by nanopore selective sequencing.}, journal = {Genome research}, volume = {33}, number = {4}, pages = {612-621}, pmid = {37041035}, issn = {1549-5469}, mesh = {Humans ; *Nanopores ; *Microbiota/genetics ; Metagenome ; Metagenomics ; }, abstract = {Rare species are vital members of a microbial community, but retrieving their genomes is difficult because of their low abundance. The ReadUntil (RU) approach allows nanopore devices to sequence specific DNA molecules selectively in real time, which provides an opportunity for enriching rare species. Despite the robustness of enriching rare species by reducing the sequencing depth of known host sequences, such as the human genome, there is still a gap in RU-based enriching of rare species in environmental samples whose community composition is unclear, and many rare species have poor or incomplete reference genomes in public databases. Therefore, here we present metaRUpore to overcome this challenge. When we applied metaRUpore to a thermophilic anaerobic digester (TAD) community and human gut microbial community, it reduced coverage of the high-abundance populations and modestly increased (∼2×) the genome coverage of the rare taxa, facilitating successful recovery of near-finished metagenome-assembled genomes (nf-MAGs) of rare species. The simplicity and robustness of the approach make it accessible for laboratories with moderate computational resources, and hold the potential to become the standard practice in future metagenomic sequencing of complicated microbiomes.}, } @article {pmid37041031, year = {2023}, author = {Miścicka, A and Lu, K and Abaeva, IS and Pestova, TV and Hellen, CUT}, title = {Initiation of translation on nedicistrovirus and related intergenic region IRESs by their factor-independent binding to the P site of 80S ribosomes.}, journal = {RNA (New York, N.Y.)}, volume = {29}, number = {7}, pages = {1051-1068}, pmid = {37041031}, issn = {1469-9001}, support = {R01 AI123406/AI/NIAID NIH HHS/United States ; R01 GM097014/GM/NIGMS NIH HHS/United States ; R35 GM122602/GM/NIGMS NIH HHS/United States ; }, mesh = {*Internal Ribosome Entry Sites/genetics ; DNA, Intergenic/genetics/metabolism ; *Ribosomes/metabolism ; Peptide Initiation Factors ; RNA, Transfer/chemistry ; RNA, Viral/genetics/chemistry ; Protein Biosynthesis ; }, abstract = {Initiation of translation on many viral mRNAs occurs by noncanonical mechanisms that involve 5' end-independent binding of ribosomes to an internal ribosome entry site (IRES). The ∼190-nt-long intergenic region (IGR) IRES of dicistroviruses such as cricket paralysis virus (CrPV) initiates translation without Met-tRNAi [Met] or initiation factors. Advances in metagenomics have revealed numerous dicistrovirus-like genomes with shorter, structurally distinct IGRs, such as nedicistrovirus (NediV) and Antarctic picorna-like virus 1 (APLV1). Like canonical IGR IRESs, the ∼165-nt-long NediV-like IGRs comprise three domains, but they lack key canonical motifs, including L1.1a/L1.1b loops (which bind to the L1 stalk of the ribosomal 60S subunit) and the apex of stem-loop V (SLV) (which binds to the head of the 40S subunit). Domain 2 consists of a compact, highly conserved pseudoknot (PKIII) that contains a UACUA loop motif and a protruding CrPV-like stem--loop SLIV. In vitro reconstitution experiments showed that NediV-like IRESs initiate translation from a non-AUG codon and form elongation-competent 80S ribosomal complexes in the absence of initiation factors and Met-tRNAi [Met] Unlike canonical IGR IRESs, NediV-like IRESs bind directly to the peptidyl (P) site of ribosomes leaving the aminoacyl (A) site accessible for decoding. The related structures of NediV-like IRESs and their common mechanism of action indicate that they exemplify a distinct class of IGR IRES.}, } @article {pmid37040763, year = {2023}, author = {Qu, P and Rom, O and Li, K and Jia, L and Gao, X and Liu, Z and Ding, S and Zhao, M and Wang, H and Chen, S and Xiong, X and Zhao, Y and Xue, C and Zhao, Y and Chu, C and Wen, B and Finney, AC and Zheng, Z and Cao, W and Zhao, J and Bai, L and Zhao, S and Sun, D and Zeng, R and Lin, J and Liu, W and Zheng, L and Zhang, J and Liu, E and Chen, YE}, title = {DT-109 ameliorates nonalcoholic steatohepatitis in nonhuman primates.}, journal = {Cell metabolism}, volume = {35}, number = {5}, pages = {742-757.e10}, doi = {10.1016/j.cmet.2023.03.013}, pmid = {37040763}, issn = {1932-7420}, mesh = {Humans ; Mice ; Animals ; *Non-alcoholic Fatty Liver Disease/metabolism ; Liver/metabolism ; Fibrosis ; Lipid Metabolism ; Primates ; }, abstract = {Nonalcoholic steatohepatitis (NASH) prevalence is rising with no pharmacotherapy approved. A major hurdle in NASH drug development is the poor translatability of preclinical studies to safe/effective clinical outcomes, and recent failures highlight a need to identify new targetable pathways. Dysregulated glycine metabolism has emerged as a causative factor and therapeutic target in NASH. Here, we report that the tripeptide DT-109 (Gly-Gly-Leu) dose-dependently attenuates steatohepatitis and fibrosis in mice. To enhance the probability of successful translation, we developed a nonhuman primate model that histologically and transcriptionally mimics human NASH. Applying a multiomics approach combining transcriptomics, proteomics, metabolomics, and metagenomics, we found that DT-109 reverses hepatic steatosis and prevents fibrosis progression in nonhuman primates, not only by stimulating fatty acid degradation and glutathione formation, as found in mice, but also by modulating microbial bile acid metabolism. Our studies describe a highly translatable NASH model and highlight the need for clinical evaluation of DT-109.}, } @article {pmid37040073, year = {2023}, author = {Wurm, P and Stampfer, L and Greimel, T and Leitner, E and Zechner, EL and Bauchinger, S and Hauer, AC and Gorkiewicz, G and Högenauer, C and Hoffmann, KM}, title = {Gut Microbiota Dysbiosis in Suspected Food Protein Induced Proctocolitis-A Prospective Comparative Cohort Trial.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {77}, number = {1}, pages = {31-38}, doi = {10.1097/MPG.0000000000003789}, pmid = {37040073}, issn = {1536-4801}, mesh = {Humans ; Infant ; Bifidobacterium ; Dysbiosis ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Proctocolitis ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVES: In infants with suspected food protein induced proctocolitis (sFPIP) only a minority of patients are finally diagnosed with the disease following diagnostic dietary intervention (DDI). There is a need for a pathophysiological explanation for the cause of hematochezia in the majority of sFPIP infants.

METHODS: We prospectively recruited infants with sFPIP and healthy controls. Fecal samples were collected at inclusion, week 4 (end of DDI in sFPIP), and week 8. For 16S rRNA sequencing (515F/806R) we used Illumina MiSeq sequencing system. Amplicon sequence variants were generated using Qiime2 and DADA2. Qiime diversity alpha and beta group comparisons and linear discriminant analysis effect size analysis was performed. For shotgun metagenomic analysis on species level we used KneadData and MetaPhlAn2.

RESULTS: Fourteen sFPIP infants were compared to 55 healthy infants. At inclusion overall microbial composition of sFPIP infants differed significantly from controls (weighted UniFrac; Pairwise PERMANOVA, P = 0.002, pseudo- F = 5.008). On genus level healthy infant microbiota was significantly enriched with Bifidobacterium (B) compared to sFPIP patients (linear discriminant analysis [LDA] = 5.5, P < 0.001, 31.3% vs 12.1%). sFPIP stool was significantly enriched by Clostridium sensu stricto 1 over controls (LDA = 5.3, P = 0.003, 3.5% vs 18.3%). DDI caused a significant and sustained increase of Bifidobacterium (LDA = 5.4, P = 0.048, 27.9%) in sFPIP infants. Species level analysis revealed significant reduction of abundance of B longum in sFPIP patients, which after DDI was reversed by B. species other than B longum .

CONCLUSIONS: We revealed a gut microbiota dysbiosis phenomenon in sFPIP infants. DDI induces a microbiota composition comparable to that of healthy infants. In most sFPIP infants hematochezia might be triggered by a gut microbiota dysbiosis phenomenon.}, } @article {pmid37039875, year = {2023}, author = {Chen, Y and Li, X and Yu, C and Wang, E and Luo, C and Jin, Y and Zhang, L and Ma, Y and Jin, Y and Yang, L and Sun, B and Qiao, J and Zhou, X and Rasche, L and Einsele, H and Song, J and Bai, T and Hou, X}, title = {Gut microbiome alterations in patients with COVID-19-related coagulopathy.}, journal = {Annals of hematology}, volume = {102}, number = {6}, pages = {1589-1598}, pmid = {37039875}, issn = {1432-0584}, support = {XGFY2020000027//Department of Science and Technology, Hubei Provincial People's Government/ ; YFYB2020001694//Department of Science and Technology, Hubei Provincial People's Government/ ; 2020FCA014//Department of Science and Technology, Hubei Provincial People's Government/ ; 2020BHB017//Department of Science and Technology, Hubei Provincial People's Government/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; *COVID-19/complications ; *Blood Coagulation Disorders/etiology ; *Microbiota ; }, abstract = {COVID-19 is characterized by a predominantly prothrombotic state, which underlies severe disease and poor outcomes. Imbalances of the gut microbiome have been linked with abnormal hemostatic processes. Understanding the relationship between the gut microbiome and abnormal coagulation parameters in COVID-19 could provide a novel framework for the diagnosis and management of COVID-related coagulopathies (CRC). This cross-sectional study used shotgun metagenomic sequencing to examine the gut microbiota of patients with CRC (n = 66) and compared it to COVID control (CCs) (n = 27) and non-COVID control (NCs) (n = 22) groups. Three, 1, and 3 taxa were found enriched in CRCs, CCs, and NCs. Next, random forest models using 7 microbial biomarkers and differential clinical characteristics were constructed and achieved strong diagnostic potential in distinguishing CRC. Specifically, the most promising biomarker species for CRC were Streptococcus thermophilus, Enterococcus faecium, and Citrobacter portucalensis. Conversely, Enterobacteriaceae family and Fusicatenibacter genus are potentially protective against CRC in COVID patients. We further identified 4 species contributing to 20 MetaCyc pathways that were differentially abundant among groups, with S. thermophilus as the main coding species in CRCs. Our findings suggest that the alterations of gut microbiota compositional and functional profiles may influence the pathogenesis of CRC and that microbiota-based diagnosis and treatment could potentially benefit COVID patients in preventing and alleviating thrombosis-related clinical outcomes.}, } @article {pmid37039637, year = {2023}, author = {Gemler, BT and Mukherjee, C and Howland, C and Fullerton, PA and Spurbeck, RR and Catlin, LA and Smith, A and Minard-Smith, AT and Bartling, C}, title = {UltraSEQ, a Universal Bioinformatic Platform for Information-Based Clinical Metagenomics and Beyond.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0416022}, pmid = {37039637}, issn = {2165-0497}, support = {75D30121C11398//HHS | Centers for Disease Control and Prevention (CDC)/ ; }, mesh = {Humans ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; Metagenome ; Computational Biology/methods ; }, abstract = {Applied metagenomics is a powerful emerging capability enabling the untargeted detection of pathogens, and its application in clinical diagnostics promises to alleviate the limitations of current targeted assays. While metagenomics offers a hypothesis-free approach to identify any pathogen, including unculturable and potentially novel pathogens, its application in clinical diagnostics has so far been limited by workflow-specific requirements, computational constraints, and lengthy expert review requirements. To address these challenges, we developed UltraSEQ, a first-of-its-kind accurate and scalable metagenomic bioinformatic tool for potential clinical diagnostics and biosurveillance utility. Here, we present the results of the evaluation of our novel UltraSEQ pipeline using an in silico-synthesized metagenome, mock microbial community data sets, and publicly available clinical data sets from samples of different infection types, including both short-read and long-read sequencing data. Our results show that UltraSEQ successfully detected all expected species across the tree of life in the in silico sample and detected all 10 bacterial and fungal species in the mock microbial community data set. For clinical data sets, even without requiring data set-specific configuration setting changes, background sample subtraction, or prior sample information, UltraSEQ achieved an overall accuracy of 91%. Furthermore, as an initial demonstration with a limited patient sample set, we show UltraSEQ's ability to provide antibiotic resistance and virulence factor genotypes that are consistent with phenotypic results. Taken together, the above-described results demonstrate that the UltraSEQ platform offers a transformative approach for microbial and metagenomic sample characterization, employing a biologically informed detection logic, deep metadata, and a flexible system architecture for the classification and characterization of taxonomic origin, gene function, and user-defined functions, including disease-causing infections. IMPORTANCE Traditional clinical microbiology-based diagnostic tests rely on targeted methods that can detect only one to a few preselected organisms or slow, culture-based methods. Although widely used today, these methods have several limitations, resulting in rates of cases of an unknown etiology of infection of >50% for several disease types. Massive developments in sequencing technologies have made it possible to apply metagenomic methods to clinical diagnostics, but current offerings are limited to a specific disease type or sequencer workflow and/or require laboratory-specific controls. The limitations associated with current clinical metagenomic offerings result from the fact that the backend bioinformatic pipelines are optimized for the specific parameters described above, resulting in an excess of unmaintained, redundant, and niche tools that lack standardization and explainable outputs. In this paper, we demonstrate that UltraSEQ uses a novel, information-based approach that enables accurate, evidence-based predictions for diagnosis as well as the functional characterization of a sample.}, } @article {pmid37039269, year = {2023}, author = {Riveros Escalona, MA and Poloni, JF and Krause, MJ and Dorn, M}, title = {Meta-analyses of host metagenomes from colorectal cancer patients reveal strong relationship between colorectal cancer-associated species.}, journal = {Molecular omics}, volume = {19}, number = {5}, pages = {429-444}, doi = {10.1039/d3mo00021d}, pmid = {37039269}, issn = {2515-4184}, mesh = {Humans ; Metagenome ; *Colorectal Neoplasms ; *Gastrointestinal Microbiome ; Cell Transformation, Neoplastic ; Carcinogenesis ; }, abstract = {Colorectal cancer (CRC) is one of the most common types of cancer, with many studies associating its development with changes in the gut microbiota. Recent developments in sequencing technologies and subsequent meta-analyses of gut metagenome provided a better understanding of species related to CRC tumorigenesis. Still, the importance of high-importance taxonomic singletons (i.e. species highly associated with a given condition but observed only in the minority of datasets) and the species interactions and co-occurrence across cohorts need further exploration. It has been shown that the gut metagenome presents a high functional redundancy, meaning that species interactions could mitigate the absence of any given species. In a CRC framework, this implies that species co-occurrence could play a role in tumorigenesis, even if CRC-associated species show low abundance. We propose to evaluate the prevalence of microbial species in tumor by initially analyzing each dataset individually and subsequently intersecting the results for differentially abundant species between CRC and healthy samples. We then identify metabolic pathways from these species based on KEGG orthologs, highlighting metabolic pathways associated with CRC. Our results indicate seven species with high prevalence across all projects and with high association to CRC, including the genus Bacteroides, Enterocloster and Prevotella. Finally, we show that CRC is also characterized by the co-occurrence of species that do not present significant differential abundance, but have been described in the literature as potential CRC biomarkers. These results indicate that between-species interactions could also play a role in CRC tumorigenesis.}, } @article {pmid37037972, year = {2023}, author = {Zeng, C and Ma, YS and Zhou, JY and Xue, CB and Xiong, Y and Zhou, W and Zhou, LH and Li, JG and Ye, SJ and Ye, QF}, title = {Donor-Derived Transmission of Scedosporiosis in Kidney Transplant Recipients from a Systemic lupus erythematosus donor.}, journal = {Current medical science}, volume = {43}, number = {2}, pages = {417-420}, pmid = {37037972}, issn = {2523-899X}, mesh = {Humans ; *Kidney Transplantation/adverse effects ; Voriconazole/therapeutic use ; *Invasive Fungal Infections ; *Lupus Erythematosus, Systemic/drug therapy ; }, abstract = {Donor-derived infection (DDI) associated with Scedosporium spp is extremely rare, and results in a very poor prognosis. The present study reports a probable DDI due to Scedosporium boydii (S. boydii) from a donor with neuropsychiatric systemic lupus erythematosus. Two recipients developed Scedosporiosis after kidney transplantation from the same donor. Recipient 1 died of central nervous system infection due to S. boydii based on the clinical presentations, and the positive metagenomic next-generation sequencing (mNGS) and culture results for the cerebrospinal fluid. The other recipient with urinary tract obstruction due to S. boydii, which was identified through the positive culture and mNGS results of the removed stents, was successfully treated by stent replacement and voriconazole administration. Undiagnosed disseminated donor infection and the transmission of S. boydii should be given attention, particularly when the donor and recipients have primary immunodeficiency disease. The screening of donors and recipients for S. boydii using mNGS may be helpful in guiding antifungal prophylaxis and treatment recipients, due to its higher sensitivity and shorter diagnostic time relative to other traditional techniques.}, } @article {pmid37037946, year = {2023}, author = {Yang, P and Zhu, X and Ning, K}, title = {Microbiome-based enrichment pattern mining has enabled a deeper understanding of the biome-species-function relationship.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {391}, pmid = {37037946}, issn = {2399-3642}, mesh = {*Copper ; Biological Evolution ; *Microbiota/genetics ; Soil ; Metagenome ; }, abstract = {Microbes live in diverse habitats (i.e. biomes), yet their species and genes were biome-specific, forming enrichment patterns. These enrichment patterns have mirrored the biome-species-function relationship, which is shaped by ecological and evolutionary principles. However, a grand picture of these enrichment patterns, as well as the roles of external and internal factors in driving these enrichment patterns, remain largely unexamined. In this work, we have examined the enrichment patterns based on 1705 microbiome samples from four representative biomes (Engineered, Gut, Freshwater, and Soil). Moreover, an "enrichment sphere" model was constructed to elucidate the regulatory principles behind these patterns. The driving factors for this model were revealed based on two case studies: (1) The copper-resistance genes were enriched in Soil biomes, owing to the copper contamination and horizontal gene transfer. (2) The flagellum-related genes were enriched in the Freshwater biome, due to high fluidity and vertical gene accumulation. Furthermore, this enrichment sphere model has valuable applications, such as in biome identification for metagenome samples, and in guiding 3D structure modeling of proteins. In summary, the enrichment sphere model aims towards creating a bluebook of the biome-species-function relationships and be applied in many fields.}, } @article {pmid37037943, year = {2023}, author = {Shah, SA and Deng, L and Thorsen, J and Pedersen, AG and Dion, MB and Castro-Mejía, JL and Silins, R and Romme, FO and Sausset, R and Jessen, LE and Ndela, EO and Hjelmsø, M and Rasmussen, MA and Redgwell, TA and Leal Rodríguez, C and Vestergaard, G and Zhang, Y and Chawes, B and Bønnelykke, K and Sørensen, SJ and Bisgaard, H and Enault, F and Stokholm, J and Moineau, S and Petit, MA and Nielsen, DS}, title = {Expanding known viral diversity in the healthy infant gut.}, journal = {Nature microbiology}, volume = {8}, number = {5}, pages = {986-998}, pmid = {37037943}, issn = {2058-5276}, support = {143924//CIHR/Canada ; }, mesh = {Infant ; Humans ; Prospective Studies ; *Bacteriophages/genetics ; Lysogeny ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; }, abstract = {The gut microbiome is shaped through infancy and impacts the maturation of the immune system, thus protecting against chronic disease later in life. Phages, or viruses that infect bacteria, modulate bacterial growth by lysis and lysogeny, with the latter being especially prominent in the infant gut. Viral metagenomes (viromes) are difficult to analyse because they span uncharted viral diversity, lacking marker genes and standardized detection methods. Here we systematically resolved the viral diversity in faecal viromes from 647 1-year-olds belonging to Copenhagen Prospective Studies on Asthma in Childhood 2010, an unselected Danish cohort of healthy mother-child pairs. By assembly and curation we uncovered 10,000 viral species from 248 virus family-level clades (VFCs). Most (232 VFCs) were previously unknown, belonging to the Caudoviricetes viral class. Hosts were determined for 79% of phage using clustered regularly interspaced short palindromic repeat spacers within bacterial metagenomes from the same children. Typical Bacteroides-infecting crAssphages were outnumbered by undescribed phage families infecting Clostridiales and Bifidobacterium. Phage lifestyles were conserved at the viral family level, with 33 virulent and 118 temperate phage families. Virulent phages were more abundant, while temperate ones were more prevalent and diverse. Together, the viral families found in this study expand existing phage taxonomy and provide a resource aiding future infant gut virome research.}, } @article {pmid37037821, year = {2023}, author = {Whaley-Martin, KJ and Chen, LX and Nelson, TC and Gordon, J and Kantor, R and Twible, LE and Marshall, S and McGarry, S and Rossi, L and Bessette, B and Baron, C and Apte, S and Banfield, JF and Warren, LA}, title = {O2 partitioning of sulfur oxidizing bacteria drives acidity and thiosulfate distributions in mining waters.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {2006}, pmid = {37037821}, issn = {2041-1723}, mesh = {*Thiosulfates/metabolism ; Oxidation-Reduction ; *Bacteria/genetics/metabolism ; Sulfur/metabolism ; Sulfur Compounds/metabolism ; Water/metabolism ; }, abstract = {The acidification of water in mining areas is a global environmental issue primarily catalyzed by sulfur-oxidizing bacteria (SOB). Little is known about microbial sulfur cycling in circumneutral pH mine tailing impoundment waters. Here we investigate biological sulfur oxidation over four years in a mine tailings impoundment water cap, integrating aqueous sulfur geochemistry, genome-resolved metagenomics and metatranscriptomics. The microbial community is consistently dominated by neutrophilic, chemolithoautotrophic SOB (relative abundances of ~76% in 2015, ~55% in 2016/2017 and ~60% in 2018). Results reveal two SOB strategies alternately dominate across the four years, influencing acid generation and sulfur speciation. Under oxic conditions, novel Halothiobacillus drive lower pH conditions (as low as 4.3) and lower [S2O3[2-]] via the complete Sox pathway coupled to O2. Under anoxic conditions, Thiobacillus spp. dominate in activity, via the incomplete Sox and rDSR pathways coupled to NO3[-], resulting in higher [S2O3[2-]] and no net significant acidity generation. This study provides genomic evidence explaining acidity generation and thiosulfate accumulation patterns in a circumneutral mine tailing impoundment and has significant environmental applications in preventing the discharge of sulfur compounds that can impact downstream environments. These insights illuminate opportunities for in situ biotreatment of reduced sulfur compounds and prediction of acidification events using gene-based monitoring and in situ RNA detection.}, } @article {pmid37037471, year = {2022}, author = {Jeong, J and Oh, Y and Jeon, J and Baek, DH and Kim, DH and Srikulnath, K and Han, K}, title = {Effective microbial molecular diagnosis of periodontitis-related pathogen Porphyromonas gingivalis from salivary samples using rgpA gene.}, journal = {Genomics & informatics}, volume = {21}, number = {1}, pages = {e13}, pmid = {37037471}, issn = {1598-866X}, abstract = {Importance of accurate molecular diagnosis and quantification of particular disease-related pathogenic microorganisms is highlighted as an introductory step to prevent and care for diseases. In this study, we designed a primer/probe set for quantitative real-time polymerase chain reaction (qRT-PCR) targeting rgpA gene, known as the specific virulence factor of periodontitis-related pathogenic bacteria 'Porphyromonas gingivalis', and evaluated its diagnostic efficiency by detecting and quantifying relative bacterial load of P. gingivalis within saliva samples collected from clinical subjects. As a result of qRT-PCR, we confirmed that relative bacterial load of P. gingivalis was detected and quantified within all samples of positive control and periodontitis groups. On the contrary, negative results were confirmed in both negative control and healthy groups. Additionally, as a result of comparison with next-generation sequencing (NGS)-based 16S metagenome profiling data, we confirmed relative bacterial load of P. gingivalis, which was not identified on bacterial classification table created through 16S microbiome analysis, in qRT-PCR results. It showed that an approach to quantifying specific microorganisms by applying qRT-PCR method could solve microbial misclassification issues at species level of an NGS-based 16S microbiome study. In this respect, we suggest that P. gingivalis-specific primer/probe set introduced in present study has efficient applicability in various oral healthcare industries, including periodontitis-related microbial molecular diagnosis field.}, } @article {pmid37037356, year = {2023}, author = {Li, Y and Cui, Z and Luan, X and Bian, X and Li, G and Hao, T and Liu, J and Feng, K and Song, Y}, title = {Degradation potential and pathways of methylcyclohexane by bacteria derived from Antarctic surface water.}, journal = {Chemosphere}, volume = {329}, number = {}, pages = {138647}, doi = {10.1016/j.chemosphere.2023.138647}, pmid = {37037356}, issn = {1879-1298}, mesh = {Water/metabolism ; *Cycloparaffins/metabolism ; Antarctic Regions ; *Water Pollutants, Chemical/analysis ; Bacteria/genetics/metabolism ; *Petroleum/metabolism ; Hydrocarbons/metabolism ; Seawater/microbiology ; Biodegradation, Environmental ; RNA, Ribosomal, 16S/metabolism ; }, abstract = {Cycloalkanes pose a tremendous environmental risk due to their high concentration in petroleum hydrocarbons and hazardous effects to organisms. Numerous studies have documented the biodegradation of acyclic alkanes and aromatic hydrocarbons. However, insufficient attention has been paid to studies on the microbial degradation of cycloalkanes, which might be closely linked to psychrophilic microbes derived from low-temperature habitats. Here we show that endemic methylcyclohexane (MCH, an abundant cycloalkane species in oil) consumers proliferated in seawater samples derived from the Antarctic surface water (AASW). The MCH-consuming bacterial communities derived from AASW exhibited a distinct species composition compared with their counterparts derived from other cold-water habitats. We also probed Colwellia and Roseovarius as the key active players in cycloalkane degradation by dilution-to-extinction-based incubation with MCH as sole source of carbon and energy. Furthermore, we propose two nearly complete MCH degradation pathways, lactone formation and aromatization, concurrently in the high-quality metagenome-assembled genomes of key MCH consumer Roseovarius. Overall, we revealed that these Antarctic microbes might have strong interactions that enhance the decomposition of more refractory hydrocarbons through complementary degradation pathways.}, } @article {pmid37037312, year = {2023}, author = {Wang, H and Min, C and Xia, F and Xia, Y and Tang, M and Li, J and Hu, Y and Zou, M}, title = {Metagenomic analysis reveals the short-term influences on conjugation of blaNDM-1 and microbiome in hospital wastewater by silver nanoparticles at environmental-related concentration.}, journal = {Environmental research}, volume = {228}, number = {}, pages = {115866}, doi = {10.1016/j.envres.2023.115866}, pmid = {37037312}, issn = {1096-0953}, mesh = {Wastewater ; Silver ; Metagenome ; *Metal Nanoparticles ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Microbiota ; Hospitals ; }, abstract = {Hospital wastewater contains large amounts of antibiotic-resistant bacteria and serves as an important reservoir for horizontal gene transfer (HGT). However, the response of the microbiome in hospital wastewater to silver remains unclear. In this study, the short-term impacts of silver on the microbiome in hospital wastewater were investigated by metagenome next-generation sequencing. The influence of silver on the conjugation of plasmid carrying blaNDM-1 was further examined. Our results showed that in hospital wastewater, high abundances of antibiotic resistance genes (ARGs) were detected. The distribution tendencies of certain ARG types on chromosomes or plasmids were different. Clinically important ARGs were identified in phage-like contigs, indicating potential transmission via transduction. Pseudomonadales, Enterobacterales, and Bacteroidales were the major ARG hosts. Mobile genetic elements were mainly detected in plasmids and associated with various types of ARGs. The binning approach identified 29 bins that were assigned to three phyla. Various ARGs and virulence factors were identified in 14 and 11 bins, respectively. MetaCHIP identified 49 HGT events. The transferred genes were annotated as ARGs, mobile genetic elements, and functional genes, and they mainly originated from donors belonging to Bacteroides and Pseudomonadales. In addition, 20 nm AgNPs reduced microbial diversity and enhanced the relative abundance of Acinetobacter. The changes induced by 20 nm AgNPs included increases in the abundances of ARGs and genes involved lipid metabolism pathway. Conjugation experiments showed that Ag[+] and 20 nm AgNPs caused 2.38-, 3.31-, 4.72-, and 4.57-fold and 1.46-, 1.61-, 3.86-, and 2.16-fold increases in conjugation frequencies of plasmid with blaNDM-1 at 0.1, 1, 10, and 100 μg/L, respectively. Our findings provide insight into the response of the microbiome in hospital wastewater to silver, emphasize the adaptation capability of Acinetobacter inhabiting hospitals against adverse environments, and highlight the promotion of silver for antibiotic resistance.}, } @article {pmid37036967, year = {2023}, author = {Bellas, C and Hackl, T and Plakolb, MS and Koslová, A and Fischer, MG and Sommaruga, R}, title = {Large-scale invasion of unicellular eukaryotic genomes by integrating DNA viruses.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {16}, pages = {e2300465120}, pmid = {37036967}, issn = {1091-6490}, support = {FWF P-34620//Austrian Science Fund (FWF)/ ; }, mesh = {Animals ; *Eukaryota/genetics ; DNA Viruses/genetics ; *Viruses/genetics ; Virophages ; Genome, Viral/genetics ; Phylogeny ; }, abstract = {Eukaryotic genomes contain a variety of endogenous viral elements (EVEs), which are mostly derived from RNA and ssDNA viruses that are no longer functional and are considered to be "genomic fossils." Genomic surveys of EVEs, however, are strongly biased toward animals and plants, whereas protists, which represent the majority of eukaryotic diversity, remain poorly represented. Here, we show that protist genomes harbor tens to thousands of diverse, ~14 to 40 kbp long dsDNA viruses. These EVEs, composed of virophages, Polinton-like viruses, and related entities, have remained hitherto hidden owing to poor sequence conservation between virus groups and their repetitive nature that precluded accurate short-read assembly. We show that long-read sequencing technology is ideal for resolving virus insertions. Many protist EVEs appear intact, and most encode integrases, which suggests that they have actively colonized hosts across the tree of eukaryotes. We also found evidence for gene expression in host transcriptomes and that closely related virophage and Polinton-like virus genomes are abundant in viral metagenomes, indicating that many EVEs are probably functional viruses.}, } @article {pmid37036103, year = {2022}, author = {Cornet, L and Durieu, B and Baert, F and D'hooge, E and Colignon, D and Meunier, L and Lupo, V and Cleenwerck, I and Daniel, HM and Rigouts, L and Sirjacobs, D and Declerck, S and Vandamme, P and Wilmotte, A and Baurain, D and Becker, P}, title = {The GEN-ERA toolbox: unified and reproducible workflows for research in microbial genomics.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {37036103}, issn = {2047-217X}, mesh = {Workflow ; Reproducibility of Results ; *Genomics/methods ; *Computational Biology/methods ; Genome, Microbial ; Phylogeny ; }, abstract = {BACKGROUND: Microbial culture collections play a key role in taxonomy by studying the diversity of their strains and providing well-characterized biological material to the scientific community for fundamental and applied research. These microbial resource centers thus need to implement new standards in species delineation, including whole-genome sequencing and phylogenomics. In this context, the genomic needs of the Belgian Coordinated Collections of Microorganisms were studied, resulting in the GEN-ERA toolbox. The latter is a unified cluster of bioinformatic workflows dedicated to both bacteria and small eukaryotes (e.g., yeasts).

FINDINGS: This public toolbox allows researchers without a specific training in bioinformatics to perform robust phylogenomic analyses. Hence, it facilitates all steps from genome downloading and quality assessment, including genomic contamination estimation, to tree reconstruction. It also offers workflows for average nucleotide identity comparisons and metabolic modeling.

TECHNICAL DETAILS: Nextflow workflows are launched by a single command and are available on the GEN-ERA GitHub repository (https://github.com/Lcornet/GENERA). All the workflows are based on Singularity containers to increase reproducibility.

TESTING: The toolbox was developed for a diversity of microorganisms, including bacteria and fungi. It was further tested on an empirical dataset of 18 (meta)genomes of early branching Cyanobacteria, providing the most up-to-date phylogenomic analysis of the Gloeobacterales order, the first group to diverge in the evolutionary tree of Cyanobacteria.

CONCLUSION: The GEN-ERA toolbox can be used to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. Although designed for routine bioinformatics of culture collections, it can also be used by all researchers interested in microbial taxonomy, as exemplified by our case study on Gloeobacterales.}, } @article {pmid37035670, year = {2023}, author = {Zhong, JG and Lan, WT and Feng, YQ and Li, YH and Shen, YY and Gong, JH and Zou, Z and Hou, X}, title = {Associations between dysbiosis gut microbiota and changes of neurotransmitters and short-chain fatty acids in valproic acid model rats.}, journal = {Frontiers in physiology}, volume = {14}, number = {}, pages = {1077821}, pmid = {37035670}, issn = {1664-042X}, abstract = {Introduction: The microbiota-gut-brain axis plays an important role in the pathophysiology of autism spectrum disorder, but its specific mechanisms remain unclear. This study aimed to explore the associations of changes in neurotransmitters and short-chain fatty acids with alterations in gut microbiota in valproic acid model rats. Methods: The autism model rats were established by prenatal exposure to valproic acid (VPA). The Morris water maze test, open field test, and three-chamber test were conducted to assess the behaviors of rats. 16S rRNA gene sequences extracted from fecal samples were used to assess the gut microbial composition. Gas and liquid chromatography-mass spectroscopy was used to identify short-chain fatty acids in fecal samples and neurotransmitters in the prefrontal cortex (PFC). Results: The results showed that 28 bacterial taxa between valproic acid model rats and control rats were identified, and the most differential bacterial taxa in valproic acid model rats and control rats belonged to metagenomic species and Lactobacillus intestinalis. Acetic acid, butyric acid, valeric acid, isobutyric acid, and isovaleric acid were significantly decreased in the valproic acid model rats compared to those in control rats. Five neurotransmitters (threonine, kynurenine, tryptophan, 5-hydroxyindoleacetic acid, denoted as 5-HIAA, and betaine aldehyde chloride, denoted as BAC) were significantly decreased, whereas betaine was increased in the prefrontal cortex of valproic acid model rats compared to control rats. A variety of neurotransmitters (≥4) were correlated with Pseudomonas, Collisella, and Streptococcus at the genus level, and they were also related to the decrease of short-chain fatty acids. Discussion: According to this study, we can preliminarily infer that gut microbiota or their metabolic productions (such as SCFAs) may influence central neurotransmitter metabolism through related pathways of the gut-brain axis. These results provide microbial and short-chain fatty acid (SCFA) frameworks for understanding the role of the microbiota-gut-brain axis in autism spectrum disorder and shed new light on autism spectrum disorder treatment.}, } @article {pmid37035219, year = {2023}, author = {Zhao, JD and Sun, M and Li, Y and Yu, CJ and Cheng, RD and Wang, SH and Du, X and Fang, ZH}, title = {Characterization of gut microbial and metabolite alterations in faeces of Goto Kakizaki rats using metagenomic and untargeted metabolomic approach.}, journal = {World journal of diabetes}, volume = {14}, number = {3}, pages = {255-270}, pmid = {37035219}, issn = {1948-9358}, abstract = {BACKGROUND: In recent years, the incidence of type 2 diabetes (T2DM) has shown a rapid growth trend. Goto Kakizaki (GK) rats are a valuable model for the study of T2DM and share common glucose metabolism features with human T2DM patients. A series of studies have indicated that T2DM is associated with the gut microbiota composition and gut metabolites. We aimed to systematically characterize the faecal gut microbes and metabolites of GK rats and analyse the relationship between glucose and insulin resistance.

AIM: To evaluate the gut microbial and metabolite alterations in GK rat faeces based on metagenomics and untargeted metabolomics.

METHODS: Ten GK rats (model group) and Wistar rats (control group) were observed for 10 wk, and various glucose-related indexes, mainly including weight, fasting blood glucose (FBG) and insulin levels, homeostasis model assessment of insulin resistance (HOMA-IR) and homeostasis model assessment of β cell (HOMA-β) were assessed. The faecal gut microbiota was sequenced by metagenomics, and faecal metabolites were analysed by untargeted metabolomics. Multiple metabolic pathways were evaluated based on the differential metabolites identified, and the correlations between blood glucose and the gut microbiota and metabolites were analysed.

RESULTS: The model group displayed significant differences in weight, FBG and insulin levels, HOMA-IR and HOMA-β indexes (P < 0.05, P < 0.01) and a shift in the gut microbiota structure compared with the control group. The results demonstrated significantly decreased abundances of Prevotella sp. CAG:604 and Lactobacillus murinus (P < 0.05) and a significantly increased abundance of Allobaculum stercoricanis (P < 0.01) in the model group. A correlation analysis indicated that FBG and HOMA-IR were positively correlated with Allobaculum stercoricanis and negatively correlated with Lactobacillus murinus. An orthogonal partial least squares discriminant analysis suggested that the faecal metabolic profiles differed between the model and control groups. Fourteen potential metabolic biomarkers, including glycochenodeoxycholic acid, uric acid, 13(S)-hydroxyoctadecadienoic acid (HODE), N-acetylaspartate, β-sitostenone, sphinganine, 4-pyridoxic acid, and linoleic acid, were identified. Moreover, FBG and HOMA-IR were found to be positively correlated with glutathione, 13(S)-HODE, uric acid, 4-pyridoxic acid and allantoic acid and ne-gatively correlated with 3-α, 7-α, chenodeoxycholic acid glycine conjugate and 26-trihydroxy-5-β-cholestane (P < 0.05, P < 0.01). Allobaculum stercoricanis was positively correlated with linoleic acid and sphinganine (P < 0.01), and 2-methyl-3-hydroxy-5-formylpyridine-4-carboxylate was negatively associated with Prevotella sp. CAG:604 (P < 0.01). The metabolic pathways showing the largest differences were arginine biosynthesis; primary bile acid biosynthesis; purine metabolism; linoleic acid metabolism; alanine, aspartate and glutamate metabolism; and nitrogen metabolism.

CONCLUSION: Metagenomics and untargeted metabolomics indicated that disordered compositions of gut microbes and metabolites may be common defects in GK rats.}, } @article {pmid37034501, year = {2023}, author = {Chen, Q and Zhang, Y and Zhang, L and Xian, S and Huang, L and Ding, X and Wu, H and Xia, H and Yang, X and Cai, X}, title = {Liver abscess complicated with multiple organ invasive infection caused by hematogenous disseminated hypervirulent Klebsiella pneumoniae: A case report.}, journal = {Open medicine (Warsaw, Poland)}, volume = {18}, number = {1}, pages = {20230694}, pmid = {37034501}, issn = {2391-5463}, abstract = {Hypervirulent Klebsiella pneumoniae (hvKp) causes increasing infections in healthy individuals from the community. In severe cases, it can cause multiple organ infection with invasive metastasis of blood sources, seriously threatening the patients' life. Rapid and accurate diagnosis of the pathogen becomes the key to timely antibiotic treatment to improve the prognosis. This article reports a case of liver abscess complicated with multiple organ invasive infection caused by hematogenous-disseminated hvKp. K. pneumoniae was identified by culture and metagenomic next-generation sequencing (mNGS) using blood and liver abscess drainage fluid. The isolates from the two samples were subsequently identified with high homology (99.999%) by whole genome sequencing. In addition, multiple virulence genes were detected in the two isolates and the string test was positive, indicating hvKp with hypermucoviscosity phenotype. Multiple antibiotic treatments were given. The conditions of the patient were stable but the temperature remained high. Surgical drainage treatment was performed, and the patient's body temperature immediately dropped to normal. He finally recovered after 6 months of follow-up. mNGS using body fluids can facilitate the rapid diagnosis of pathogens. For hvKp infection, choosing a better antibiotic therapy and receiving surgical drainage can significantly improve the prognosis of the patient.}, } @article {pmid37033728, year = {2023}, author = {Hauck, LL and Atkinson, CL and Homyack, JA and Penaluna, BE and Mangum, C and Coble, AA and Nettles, J and Thornton-Frost, JE and Fix, MJ}, title = {Molecular identity crisis: environmental DNA metabarcoding meets traditional taxonomy-assessing biodiversity and freshwater mussel populations (Unionidae) in Alabama.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e15127}, pmid = {37033728}, issn = {2167-8359}, mesh = {Animals ; *DNA, Environmental/genetics ; Ecosystem ; DNA Barcoding, Taxonomic/methods ; Phylogeny ; Alabama ; Identity Crisis ; Fresh Water ; Biodiversity ; *Bivalvia/genetics ; *Unionidae/genetics ; Fishes ; }, abstract = {The use of environmental DNA (eDNA) to assess aquatic biodiversity is a growing field with great potential for monitoring and managing threatened species, like freshwater mussel (Unionidae) populations. Freshwater mussels are globally imperiled and serve essential roles in aquatic systems as a food source and as a natural water filter making their management essential for ecosystem health. Unfortunately, mussel populations are often understudied, and challenges exist to accurately and efficiently describe the full suite of species present. Multispecies eDNA approaches may also be more challenging where freshwater mussel populations are most diverse due to ongoing and significant taxonomic restructuring that has been further complicated by molecular phylogenies using mitochondrial genes. For this study, we developed a microfluidic metabarcoding array that targets a wide range of species, from invertebrates to fishes, with an emphasis on detecting unionid mussels known to be present in the Sipsey River, Alabama. We compared mussel species diversity across six sites with well-studied mussel assemblages using eDNA surveys and traditional quadrat surveys in 2016. We examined how factors such as mussel population density, biomass and location in the river substrate impacted our ability to detect certain species; and investigated unexpected eDNA detections through phylogenetic analysis. Our eDNA results for fish and mussel species were broadly consistent with the data from traditional electrofishing and quadrat-based field surveys, although both community eDNA and conventional sampling detected species unique to that method. Our phylogenetic analysis agreed with other studies that treat Pleurobema decisum and P. chattanoogaense as synonymous species; however, they are still listed as unique species in molecular databases which complicates their identity in a metabarcoding assay. We also found that Fusconaia flava and F. cerina are indistinguishable from one another using a portion of the NADH dehydrogenase Subunit 1 (ND1) marker, which may warrant further investigation into whether or not they are synonymous. Our results show that many factors impacted our ability to detect and correctly identify Unionidae mussel species. Here we describe the obstacles we faced, including the murky phylogeny of Unionidae mussels and turbid river conditions, and our development of a potentially impactful freshwater mussel monitoring eDNA assay.}, } @article {pmid37033478, year = {2023}, author = {Li, W and Li, C and Ren, C and Zhou, S and Cheng, H and Chen, Y and Han, X and Zhong, Y and Zhou, L and Xie, D and Liu, H and Xie, J}, title = {Bidirectional effects of oral anticoagulants on gut microbiota in patients with atrial fibrillation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1038472}, pmid = {37033478}, issn = {2235-2988}, mesh = {Humans ; *Atrial Fibrillation/complications/drug therapy/chemically induced ; *Gastrointestinal Microbiome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Stroke ; Risk Factors ; Anticoagulants/therapeutic use ; Hemorrhage/chemically induced/complications ; Administration, Oral ; Risk Assessment ; }, abstract = {BACKGROUND: The imbalance of gut microbiota (GM) is associated with a higher risk of thrombosis in patients with atrial fibrillation (AF). Oral anticoagulants (OACs) have been found to significantly reduce the risk of thromboembolism and increase the risk of bleeding. However, the OAC-induced alterations in gut microbiota in patients with AF remain elusive.

METHODS: In this study, the microbial composition in 42 AF patients who received long-term OAC treatment (AF-OAC group), 47 AF patients who did not (AF group), and 40 volunteers with the risk of AF (control group) were analyzed by 16S rRNA gene sequencing of fecal bacterial DNA. The metagenomic functional prediction of major bacterial taxa was performed using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) software package.

RESULTS: The gut microbiota differed between the AF-OAC and AF groups. The abundance of Bifidobacterium and Lactobacillus decreased in the two disease groups at the genus level, but OACs treatment mitigated the decreasing tendency and increased beneficial bacterial genera, such as Megamonas. In addition, OACs reduced the abundance of pro-inflammatory taxa on the genus Ruminococcus but increased certain potential pathogenic taxa, such as genera Streptococcus, Escherichia-Shigella, and Klebsiella. The Subgroup Linear discriminant analysis effect size (LEfSe) analyses revealed that Bacteroidetes, Brucella, and Ochrobactrum were more abundant in the anticoagulated bleeding AF patients, Akkermansia and Faecalibacterium were more abundant in the non-anticoagulated-bleeding-AF patients. The neutrophil-to-lymphocyte ratio (NLR) was lower in the AF-OAC group compared with the AF group (P < 0.05). Ruminococcus was positively correlated with the NLR and negatively correlated with the CHA2DS2-VASc score (P < 0.05), and the OACs-enriched species (Megamonas and Actinobacteria) was positively correlated with the prothrombin time (PT) (P < 0.05). Ruminococcus and Roseburia were negatively associated with bleeding events (P < 0.05).

CONCLUSIONS: Our study suggested that OACs might benefit AF patients by reducing the inflammatory response and modulating the composition and abundance of gut microbiota. In particular, OACs increased the abundance of some gut microbiota involved in bleeding and gastrointestinal dysfunction indicating that the exogenous supplementation with Faecalibacterium and Akkermansia might be a prophylactic strategy for AF-OAC patients to lower the risk of bleeding after anticoagulation.}, } @article {pmid37033411, year = {2023}, author = {Maddah, R and Goodarzi, V and Asadi-Yousefabad, SL and Abbasluo, M and Shariati, P and Shafiei Kafraj, A}, title = {Evaluation of the gut microbiome associated with COVID-19.}, journal = {Informatics in medicine unlocked}, volume = {38}, number = {}, pages = {101239}, pmid = {37033411}, issn = {2352-9148}, abstract = {INTRODUCTION: In 2019, a new virus from the coronavirus family called SARS-CoV-2, infected populations throughout the world. Coronavirus disease 2019 (COVID-19), an illness induced by this virus, attacks vital organs in the body, such as the respiratory system and the gastrointestinal tract. Recent studies have confirmed changes in the gut microbiome caused by the COVID-19 disease. We examined the alteration of the gut microbiome in COVID-19 patients compared to healthy individuals.

MATERIALS AND METHODS: in this study, the 16s metagenomics dataset, publicly available in the Sequence Read Archive (SRA) database, was used for analysis (accession number PRJNA636824). The analysis processes were performed using the CLC Microbial Genomics Module 20.1.1 (Qiagen). At first, the sequence reads of samples were trimmed and classified into operational taxonomic units (OTUs) with 97% similarity and then assigned to the Greengenes reference database (v138). Differential abundance analysis was used to determine statistically significant differences in OTUs between COVID-19 and healthy groups. Next, biodiversity analyses including the alpha diversity (intragroup diversity) and beta diversity (intergroup diversity) using defined indexes were estimated. Then, the co-occurrence network at the species level was constructed using the Pearson correlation coefficient calculation between pairs of OTUs in R software and visualized using Cytoscape software. Ultimately, the hub OTUs at the species level were identified using the cytoHubba plugin of Cytoscape based on Maximal Clique Centrality (MCC) algorithm.

RESULTS: The results of the metagenomic analysis revealed that the intestinal microbiome in healthy individuals has a higher biodiversity compared to COVID-19 patients. Indeed, healthy people also have a higher percentage of beneficial bacteria such as bifidobacteria adolescentis compared to COVID-19 patients; in contrast, COVID-19 patients have higher levels of opportunistic and pathogenic bacteria such as Streptococcus anginosus than healthy people. Also, by constructing a co-occurrence network at the species level, Bifidobacterium longum in the healthy group and Veillonella parvulain the COVID-19 group were found as hub species.

CONCLUSION: The results of this study shed light on the relationship between the gut microbiome and COVID-19. These results could be helpful for understanding the pathogenesis, clinical features, and treatment of COVID-9.}, } @article {pmid37032874, year = {2023}, author = {Wang, J and Zhang, Y and Liu, Y and Xie, Z and Cao, J and Zhang, H and Liu, J and Bao, T and Sun, C and Liu, B and Wei, Y and Fang, J}, title = {The phylogeny and metabolic potentials of an n-alkane-degrading Venatorbacter bacterium isolated from deep-sea sediment of the Mariana Trench.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1108651}, pmid = {37032874}, issn = {1664-302X}, abstract = {Recently, several reports showed that n-alkanes were abundant in the hadal zone, suggesting that n-alkanes could be an important source of nutrients for microorganisms in hadal ecosystems. To date, most of the published studies on the microbial capacity to degrade hydrocarbons were conducted only at atmospheric temperature and pressure (0.1 MPa), and little is known about whether and which microbes could utilize n-alkanes at in situ environmental conditions in the hadal zone, including low temperature and high hydrostatic pressure (especially >30 MPa). In this study, a piezotolerant bacterium, strain C2-1, was isolated from a Mariana Trench sediment at depth of 5,800 m. Strain C2-1 was able to grow at in situ temperature (4°C) and pressure (58 MPa) with n-alkanes as the sole carbon source. Phylogenetically, strain C2-1 and related strains (TMPB967, ST750PaO-4, IMCC1826, and TTBP476) should be classified into the genus Venatorbacter. Metagenomic analysis using ~5,000 publicly available datasets showed that Venatorbacter has a wide environmental distribution in seawater (38), marine sediments (3), hydrothermal vent plumes (2), Antarctic ice (1), groundwater (13), and marine sponge ecosystems (1). Most Venatorbacter species are non-obligate n-alkane degraders that could utilize, at a minimal, C16-C18 n-alkanes, as well as other different types of carbon substrates, including carbohydrates, amino acids, peptides, and phospholipids. The type II secretion system, extracellular proteases, phospholipase, and endonuclease of Venatorbacter species were robustly expressed in the metatranscriptomes of deep-sea hydrothermal vents, suggesting their important contribution to secondary productivity by degrading extracellular macromolecules. The identification of denitrifying genes suggested a genus-specific ecological potential that allowed Venatorbacter species to be active in anoxic environments, e.g., the oxygen-minimal zone (OMZ) and the deeply buried marine sediments. Our results show that Venatorbacter species are responsible for the degradation of hydrocarbon and extracellular macromolecules, suggesting that they may play an important role in the biogeochemistry process in the Trench ecosystems.}, } @article {pmid37032869, year = {2023}, author = {Reinoso-Peláez, EL and Saura, M and González-Recio, Ó and González, C and Fernández, A and Peiro-Pastor, R and López-García, A and Saborío-Montero, A and Calvo, JH and Ramón, M and Serrano, M}, title = {Impact of oestrus synchronization devices on ewes vaginal microbiota and artificial insemination outcome.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1063807}, pmid = {37032869}, issn = {1664-302X}, abstract = {INTRODUCTION: The low pregnancy rate by artificial insemination in sheep represents a fundamental challenge for breeding programs. In this species, oestrus synchronization is carried out by manipulating hormonal regimens through the insertion of progestogen intravaginal devices. This reproductive strategy may alter the vaginal microbiota affecting the artificial insemination outcome.

METHODS: In this study, we analyzed the vaginal microbiome of 94 vaginal swabs collected from 47 ewes with alternative treatments applied to the progesterone-releasing intravaginal devices (probiotic, maltodextrin, antibiotic and control), in two sample periods (before placing and after removing the devices). To our knowledge, this is the first study using nanopore-based metagenome sequencing for vaginal microbiome characterization in livestock.

RESULTS: Our results revealed a significant lower abundance of the genera Oenococcus (Firmicutes) and Neisseria (Proteobacteria) in pregnant compared to non-pregnant ewes. We also detected a significant lower abundance of Campylobacter in the group of samples treated with the probiotic.

DISCUSSION: Although the use of probiotics represents a promising practice to improve insemination results, the election of the suitable species and concentration requires further investigation. In addition, the use of progestogen in the synchronization devices seemed to increase the alpha-diversity and decrease the abundance of harmful microorganisms belonging to Gammaproteobacteria and Fusobacteriia classes, suggesting a beneficial effect of their use.}, } @article {pmid37032859, year = {2023}, author = {Ning, Q and Chen, L and Li, F and Zhou, G and Zhang, C and Ma, D and Zhang, J}, title = {Tradeoffs of microbial life history strategies drive the turnover of microbial-derived organic carbon in coastal saline soils.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1141436}, pmid = {37032859}, issn = {1664-302X}, abstract = {Stable soil organic carbon (SOC) formation in coastal saline soils is important to improve arable land quality and mitigate greenhouse gas emissions. However, how microbial life-history strategies and metabolic traits regulate SOC turnover in coastal saline soils remains unknown. Here, we investigated the effects of microbial life history strategy tradeoffs on microbial carbon use efficiency (CUE) and microbial-derived SOC formation using metagenomic sequencing technology in different salinity soils. The results showed that high-salinity is detrimental to microbial CUE and microbial-derived SOC formation. Moreover, the regulation of nutrients stoichiometry could not mitigate adverse effects of salt stress on microbial CUE, which indicated that microbial-derived SOC formation is independent of stoichiometry in high-salinity soil. Low-salinity soil is dominated by a high growth yield (Y) strategy, such as higher microbial biomass carbon and metabolic traits which are related to amino acid metabolism, carbohydrate metabolism, and cell processes. However, high-salinity soil is dominated by stress tolerance (S) (e.g., higher metabolic functions of homologous recombination, base excision repair, biofilm formation, extracellular polysaccharide biosynthesis, and osmolytes production) and resource acquisition (A) strategies (e.g., higher alkaline phosphatase activity, transporters, and flagellar assembly). These trade-offs of strategies implied that resource reallocation took place. The high-salinity soil microbes diverted investments away from growth yield to microbial survival and resource capture, thereby decreasing biomass turnover efficiency and impeding microbial-derived SOC formation. Moreover, altering the stoichiometry in low-salinity soil caused more investment in the A-strategy, such as the production of more β-glucosidase and β-N-acetyl-glucosaminidase, and increasing bacterial chemotaxis, which thereby reduced microbial-derived SOC formation. Our research reveals that shift the microbial community from S- and A- strategies to the Y-strategy is important to increase the microbial CUE, and thus enhance SOC turnover in coastal saline soils.}, } @article {pmid37032854, year = {2023}, author = {Merges, D and Dal Grande, F and Valim, H and Singh, G and Schmitt, I}, title = {Gene abundance linked to climate zone: Parallel evolution of gene content along elevation gradients in lichenized fungi.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1097787}, pmid = {37032854}, issn = {1664-302X}, abstract = {INTRODUCTION: Intraspecific genomic variability affects a species' adaptive potential toward climatic conditions. Variation in gene content across populations and environments may point at genomic adaptations to specific environments. The lichen symbiosis, a stable association of fungal and photobiont partners, offers an excellent system to study environmentally driven gene content variation. Many of these species have remarkable environmental tolerances, and often form populations across different climate zones. Here, we combine comparative and population genomics to assess the presence and absence of genes in high and low elevation genomes of two lichenized fungi of the genus Umbilicaria.

METHODS: The two species have non-overlapping ranges, but occupy similar climatic niches in North America (U. phaea) and Europe (U. pustulata): high elevation populations are located in the cold temperate zone and low elevation populations in the Mediterranean zone. We assessed gene content variation along replicated elevation gradients in each of the two species, based on a total of 2050 individuals across 26 populations. Specifically, we assessed shared orthologs across species within the same climate zone, and tracked, which genes increase or decrease in abundance within populations along elevation.

RESULTS: In total, we found 16 orthogroups with shared orthologous genes in genomes at low elevation and 13 at high elevation. Coverage analysis revealed one ortholog that is exclusive to genomes at low elevation. Conserved domain search revealed domains common to the protein kinase superfamily. We traced the discovered ortholog in populations along five replicated elevation gradients on both continents and found that the number of this protein kinase gene linearly declined in abundance with increasing elevation, and was absent in the highest populations.

DISCUSSION: We consider the parallel loss of an ortholog in two species and in two geographic settings a rare find, and a step forward in understanding the genomic underpinnings of climatic tolerances in lichenized fungi. In addition, the tracking of gene content variation provides a widely applicable framework for retrieving biogeographical determinants of gene presence/absence patterns. Our work provides insights into gene content variation of lichenized fungi in relation to climatic gradients, suggesting a new research direction with implications for understanding evolutionary trajectories of complex symbioses in relation to climatic change.}, } @article {pmid37032561, year = {2023}, author = {Blum, LN and Colman, DR and Eloe-Fadrosh, EA and Kellom, M and Boyd, ES and Zhaxybayeva, O and Leavitt, WD}, title = {Distribution and abundance of tetraether lipid cyclization genes in terrestrial hot springs reflect pH.}, journal = {Environmental microbiology}, volume = {25}, number = {9}, pages = {1644-1658}, doi = {10.1111/1462-2920.16375}, pmid = {37032561}, issn = {1462-2920}, mesh = {*Hot Springs ; Glycerol ; Cyclization ; Glyceryl Ethers/chemistry ; Archaea/genetics/chemistry ; Membrane Lipids/chemistry ; Hydrogen-Ion Concentration ; }, abstract = {Many Archaea produce membrane-spanning lipids that enable life in extreme environments. These isoprenoid glycerol dibiphytanyl glycerol tetraethers (GDGTs) may contain up to eight cyclopentyl and one cyclohexyl ring, where higher degrees of cyclization are associated with more acidic, hotter or energy-limited conditions. Recently, the genes encoding GDGT ring synthases, grsAB, were identified in two Sulfolobaceae; however, the distribution and abundance of grs homologs across environments inhabited by these and related organisms remain a mystery. To address this, we examined the distribution of grs homologs in relation to environmental temperature and pH, from thermal springs across Earth, where sequences derive from metagenomes, metatranscriptomes, single-cell and cultivar genomes. The abundance of grs homologs shows a strong negative correlation to pH, but a weak positive correlation to temperature. Archaeal genomes and metagenome-assembled genomes (MAGs) that carry two or more grs copies are more abundant in low pH springs. We also find grs in 12 archaeal classes, with the most representatives in Thermoproteia, followed by MAGs of the uncultured Korarchaeia, Bathyarchaeia and Hadarchaeia, while several Nitrososphaeria encodes >3 copies. Our findings highlight the key role of grs-catalysed lipid cyclization in archaeal diversification across hot and acidic environments.}, } @article {pmid37032329, year = {2023}, author = {Bazant, W and Blevins, AS and Crouch, K and Beiting, DP}, title = {Improved eukaryotic detection compatible with large-scale automated analysis of metagenomes.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {72}, pmid = {37032329}, issn = {2049-2618}, support = {INV-016988/GATES/Bill & Melinda Gates Foundation/United States ; }, mesh = {Humans ; *Metagenome/genetics ; Eukaryota/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Archaea/genetics ; Metagenomics/methods ; }, abstract = {BACKGROUND: Eukaryotes such as fungi and protists frequently accompany bacteria and archaea in microbial communities. Unfortunately, their presence is difficult to study with "shotgun" metagenomic sequencing since prokaryotic signals dominate in most environments. Recent methods for eukaryotic detection use eukaryote-specific marker genes, but they do not incorporate strategies to handle the presence of eukaryotes that are not represented in the reference marker gene set, and they are not compatible with web-based tools for downstream analysis.

RESULTS: Here, we present CORRAL (for Clustering Of Related Reference ALignments), a tool for the identification of eukaryotes in shotgun metagenomic data based on alignments to eukaryote-specific marker genes and Markov clustering. Using a combination of simulated datasets, mock community standards, and large publicly available human microbiome studies, we demonstrate that our method is not only sensitive and accurate but is also capable of inferring the presence of eukaryotes not included in the marker gene reference, such as novel strains. Finally, we deploy CORRAL on our MicrobiomeDB.org resource, producing an atlas of eukaryotes present in various environments of the human body and linking their presence to study covariates.

CONCLUSIONS: CORRAL allows eukaryotic detection to be automated and carried out at scale. Implementation of CORRAL in MicrobiomeDB.org creates a running atlas of microbial eukaryotes in metagenomic studies. Since our approach is independent of the reference used, it may be applicable to other contexts where shotgun metagenomic reads are matched against redundant but non-exhaustive databases, such as the identification of bacterial virulence genes or taxonomic classification of viral reads. Video Abstract.}, } @article {pmid37031921, year = {2023}, author = {Mukhopadhyay, A and Choudhury, S and Kumar, M}, title = {Metaviromic analyses of DNA virus community from sediments of the N-Choe stream, North India.}, journal = {Virus research}, volume = {330}, number = {}, pages = {199110}, pmid = {37031921}, issn = {1872-7492}, mesh = {Rivers ; Ecosystem ; DNA Viruses/genetics ; *Viruses/genetics ; *Bacteriophages/genetics ; Metagenomics ; }, abstract = {Virome exploration from the freshwater stream ecosystem is less explored. We deciphered the DNA virome from sediments of the N-Choe stream in Chandigarh, India. This study utilized the long-read nanopore sequencing data analyzed by assembly-free and assembly-based approaches to study the viral community structure and its genetic potential. In the classified fraction of the virome, we observed the dominance of the ssDNA viruses. The prominent ssDNA virus families were Microviridae, Circoviridae, and Genomoviridae. The majority of dsDNA viruses were bacteriophages belonging to class Caudoviricetes. We also recovered metagenome-assembled viruses of Microviridae, CRESS DNA viruses, and viral-like circular molecules. We identified the structural and functional gene repertoire of the viromes and their gene ontology. Furthermore, we detected auxiliary metabolic genes (AMGs) involved in pathways such as pyrimidine synthesis, organosulfur metabolism indicating the functional importance of viruses in the ecosystem. The antibiotic resistance genes (ARGs), metal resistance genes (MRGs), and mobile genetic elements (MGEs) present in the viromes and their co-occurrence were studied. ARGs of the glycopeptide, macrolide, lincosamide, streptogramin (MLS), and mupirocin categories were well represented. Among the reads containing ARGs, a few reads were also classified as viruses, indicating that environmental viruses act as reservoirs of ARGs.}, } @article {pmid37031818, year = {2023}, author = {Du, M and Wei, L and Yuan, M and Zou, R and Xu, Y and Wang, X and Wang, W and Li, F}, title = {Enzymatic comparison of two homologous enzymes reveals N-terminal domain of chondroitinase ABC I regulates substrate selection and product generation.}, journal = {The Journal of biological chemistry}, volume = {299}, number = {5}, pages = {104692}, pmid = {37031818}, issn = {1083-351X}, mesh = {Animals ; Mice ; Bacteria/enzymology ; *Chondroitin ABC Lyase/chemistry ; *Chondroitin Sulfates/metabolism ; Dermatan Sulfate/chemistry ; Disaccharides/chemistry ; Peptides ; Substrate Specificity ; }, abstract = {Chondroitinase ABC-type I (CSase ABC I), which can digest both chondroitin sulfate (CS) and dermatan sulfate (DS) in an endolytic manner, is an essential tool in structural and functional studies of CS/DS. Although a few CSase ABC I have been identified from bacteria, the substrate-degrading pattern and regulatory mechanisms of them have rarely been investigated. Herein, two CSase ABC I, IM3796 and IM1634, were identified from the intestinal metagenome of CS-fed mice. They show high sequence homology (query coverage: 88.00%, percent identity: 90.10%) except for an extra peptide (Met[1]-His[109]) at the N-terminus in IM1634, but their enzymatic properties are very different. IM3796 prefers to degrade 6-O-sulfated GalNAc residue-enriched CS into tetra- and disaccharides. In contrast, IM1634 exhibits nearly a thousand times more activity than IM3796 and can completely digest CS/DS with various sulfation patterns to produce disaccharides, unlike most CSase ABC I. Structure modeling showed that IM3796 did not contain an N-terminal domain composed of two β-sheets, which is found in IM1634 and other CSase ABC I. Furthermore, deletion of the N-terminal domain (Met[1]-His[109]) from IM1634 caused the enzymatic properties of the variant IM1634-T109 to be similar to those of IM3796, and conversely, grafting this domain to IM3796 increased the similarity of the variant IM3796-A109 to IM1634. In conclusion, the comparative study of the new CSase ABC I provides two unique tools for CS/DS-related studies and applications and, more importantly, reveals the critical role of the N-terminal domain in regulating the substrate binding and degradation of these enzymes.}, } @article {pmid37031672, year = {2023}, author = {Senthil Kumar, R and Koner, S and Tsai, HC and Chen, JS and Huang, SW and Hsu, BM}, title = {Deciphering endemic rhizosphere microbiome community's structure towards the host-derived heavy metals tolerance and plant growth promotion functions in serpentine geo-ecosystem.}, journal = {Journal of hazardous materials}, volume = {452}, number = {}, pages = {131359}, doi = {10.1016/j.jhazmat.2023.131359}, pmid = {37031672}, issn = {1873-3336}, mesh = {Nickel/analysis ; Rhizosphere ; RNA, Ribosomal, 16S/genetics/analysis ; *Metals, Heavy/toxicity/analysis ; *Microbiota ; Flavobacterium ; Soil/chemistry ; Plants ; Chromium/toxicity/analysis ; Soil Microbiology ; Plant Roots/microbiology ; }, abstract = {Environmental microbes in rhizosphere soil and surrounding plants have the potential to alter ecosystem functions. We investigated the microbial communities inhabiting the rhizosphere soils of both serpentine and non-serpentine rhizosphere zones to evaluate their heavy metal tolerance and ability to promote plant growth, utilizing 16S rRNA metabarcoding. The Biolog-EcoPlate technique was employed to determine how abiotic stress factors affect carbon utilization capacity by rhizospheric microbial communities in the serpentine geo-ecosystem. The phyla Proteobacteria, Acidobacteria, Bacteroidetes, and Nitrospirae colonized in the roots of Miscanthus sp., Biden sp., and Oryza sp. showed noticeable differences in different rhizosphere zones. The PICRUSt2-based analysis identified chromium/iron resistance genes (ceuE, chrA) and arsenic resistance genes (arsR, acr3, arsC) abundant in all the studied rhizosphere soils. Notably, nickel resistance genes (nikA, nikD, nikE, and nikR) from Arthrobacter, Microbacterium, and Streptomyces strongly correlate with functions related to solubilization of nickel and an increase in siderophore and IAA production. The abundance of Arthrobacter, Clostridium, Geobacter, Dechloromonas, Pseudomonas, and Flavobacterium was positively correlated with chromium and nickel but negatively correlated with the calcium/magnesium ratio. Our results contribute to a better understanding of the functions of plant-tolerant PGPR interaction in the heavy metal-contaminated rhizosphere and eco-physiological responses from long-term biological weathering.}, } @article {pmid37031568, year = {2023}, author = {Behling, AH and Wilson, BC and Ho, D and Virta, M and O'Sullivan, JM and Vatanen, T}, title = {Addressing antibiotic resistance: computational answers to a biological problem?.}, journal = {Current opinion in microbiology}, volume = {74}, number = {}, pages = {102305}, doi = {10.1016/j.mib.2023.102305}, pmid = {37031568}, issn = {1879-0364}, mesh = {*Artificial Intelligence ; *Bacteria/metabolism ; Drug Resistance, Microbial ; Anti-Bacterial Agents/pharmacology/metabolism ; }, abstract = {The increasing prevalence of infections caused by antibiotic-resistant bacteria is a global healthcare crisis. Understanding the spread of resistance is predicated on the surveillance of antibiotic resistance genes within an environment. Bioinformatics and artificial intelligence (AI) methods applied to metagenomic sequencing data offer the capacity to detect known and infer yet-unknown resistance mechanisms, and predict future outbreaks of antibiotic-resistant infections. Machine learning methods, in particular, could revive the waning antibiotic discovery pipeline by helping to predict the molecular structure and function of antibiotic resistance compounds, and optimising their interactions with target proteins. Consequently, AI has the capacity to play a central role in guiding antibiotic stewardship and future clinical decision-making around antibiotic resistance.}, } @article {pmid37031344, year = {2023}, author = {Liao, H and Liu, C and Ai, C and Gao, T and Yang, QE and Yu, Z and Gao, S and Zhou, S and Friman, VP}, title = {Mesophilic and thermophilic viruses are associated with nutrient cycling during hyperthermophilic composting.}, journal = {The ISME journal}, volume = {17}, number = {6}, pages = {916-930}, pmid = {37031344}, issn = {1751-7370}, mesh = {*Composting ; *Viruses/genetics ; Archaea ; Bacteria/genetics ; *Microbiota/genetics ; Nutrients ; }, abstract = {While decomposition of organic matter by bacteria plays a major role in nutrient cycling in terrestrial ecosystems, the significance of viruses remains poorly understood. Here we combined metagenomics and metatranscriptomics with temporal sampling to study the significance of mesophilic and thermophilic bacteria and their viruses on nutrient cycling during industrial-scale hyperthermophilic composting (HTC). Our results show that virus-bacteria density dynamics and activity are tightly coupled, where viruses specific to mesophilic and thermophilic bacteria track their host densities, triggering microbial community succession via top-down control during HTC. Moreover, viruses specific to mesophilic bacteria encoded and expressed several auxiliary metabolic genes (AMGs) linked to carbon cycling, impacting nutrient turnover alongside bacteria. Nutrient turnover correlated positively with virus-host ratio, indicative of a positive relationship between ecosystem functioning, viral abundances, and viral activity. These effects were predominantly driven by DNA viruses as most detected RNA viruses were associated with eukaryotes and not associated with nutrient cycling during the thermophilic phase of composting. Our findings suggest that DNA viruses could drive nutrient cycling during HTC by recycling bacterial biomass through cell lysis and by expressing key AMGs. Viruses could hence potentially be used as indicators of microbial ecosystem functioning to optimize productivity of biotechnological and agricultural systems.}, } @article {pmid37031343, year = {2023}, author = {Saini, JS and Manni, M and Hassler, C and Cable, RN and Duhaime, MB and Zdobnov, EM}, title = {Genomic insights into the coupling of a Chlorella-like microeukaryote and sulfur bacteria in the chemocline of permanently stratified Lake Cadagno.}, journal = {The ISME journal}, volume = {17}, number = {6}, pages = {903-915}, pmid = {37031343}, issn = {1751-7370}, support = {PP00P2-138955/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {*Lakes/microbiology ; *Chlorella/genetics ; Phylogeny ; Bacteria/metabolism ; Genomics ; Sulfur/metabolism ; }, abstract = {Meromictic Lake Cadagno is a permanently stratified system with a persistent microbial bloom within the oxic-anoxic boundary called the chemocline. The association between oxygenic and anoxygenic photosynthesis within the chemocline has been known for at least two decades. Although anoxygenic purple and green sulfur bacteria have been well studied, reports on oxygenic phytoplankton have remained sparse since their discovery in the 1920s. Nearly a century later, this study presents the first near-complete genome of a photosynthetic microbial eukaryote from the chemocline of Lake Cadagno, provisionally named Chlorella-like MAG. The 18.9 Mbp nuclear genome displays a high GC content (71.5%), and the phylogenetic placement suggests that it is a novel species of the genus Chlorella of Chlorophytes. Functional annotation of the Chlorella-like metagenome-assembled genome predicted 10,732 protein-coding genes, with an approximate 0.6% proportion potentially involved in carbon, sulfur, and nitrogen (C, N, and S) metabolism. In addition to C4 photosynthesis, this study detected genes for heat shock proteins (HSPs) in the Chlorella-like algae, consistent with the other Chlorella species. Altogether, the genomic insights in this study suggest the cooperation of photosynthetic algae with phototrophic sulfur bacteria via C, N, and S metabolism, which may aid their collective persistence in the Lake Cadagno chemocline. Furthermore, this work additionally presents the chloroplast genome of Cryptomonas-like species, which was likely to be presumed as cyanobacteria in previous studies because of the presence of phycobilisomes.}, } @article {pmid37031232, year = {2023}, author = {Strike, LT and Hansell, NK and Chuang, KH and Miller, JL and de Zubicaray, GI and Thompson, PM and McMahon, KL and Wright, MJ}, title = {The Queensland Twin Adolescent Brain Project, a longitudinal study of adolescent brain development.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {195}, pmid = {37031232}, issn = {2052-4463}, support = {1078756//Department of Health | National Health and Medical Research Council (NHMRC)/ ; }, mesh = {Adolescent ; Child ; Humans ; *Brain/diagnostic imaging/physiology ; Longitudinal Studies ; Magnetic Resonance Imaging ; Queensland ; Twins ; *Adolescent Development ; }, abstract = {We describe the Queensland Twin Adolescent Brain (QTAB) dataset and provide a detailed methodology and technical validation to facilitate data usage. The QTAB dataset comprises multimodal neuroimaging, as well as cognitive and mental health data collected in adolescent twins over two sessions (session 1: N = 422, age 9-14 years; session 2: N = 304, 10-16 years). The MRI protocol consisted of T1-weighted (MP2RAGE), T2-weighted, FLAIR, high-resolution TSE, SWI, resting-state fMRI, DWI, and ASL scans. Two fMRI tasks were added in session 2: an emotional conflict task and a passive movie-watching task. Outside of the scanner, we assessed cognitive function using standardised tests. We also obtained self-reports of symptoms for anxiety and depression, perceived stress, sleepiness, pubertal development measures, and risk and protective factors. We additionally collected several biological samples for genomic and metagenomic analysis. The QTAB project was established to promote health-related research in adolescence.}, } @article {pmid37030000, year = {2023}, author = {Lefebvre, MJM and Daron, J and Legrand, E and Fontaine, MC and Rougeron, V and Prugnolle, F}, title = {Population Genomic Evidence of Adaptive Response during the Invasion History of Plasmodium falciparum in the Americas.}, journal = {Molecular biology and evolution}, volume = {40}, number = {5}, pages = {}, pmid = {37030000}, issn = {1537-1719}, mesh = {Humans ; Animals ; *Plasmodium falciparum/genetics ; Metagenomics ; *Malaria, Falciparum/genetics ; Americas ; Polymorphism, Genetic ; }, abstract = {Plasmodium falciparum, the most virulent agent of human malaria, spread from Africa to all continents following the out-of-Africa human migrations. During the transatlantic slave trade between the 16th and 19th centuries, it was introduced twice independently to the Americas where it adapted to new environmental conditions (new human populations and mosquito species). Here, we analyzed the genome-wide polymorphisms of 2,635 isolates across the current P. falciparum distribution range in Africa, Asia, Oceania, and the Americas to investigate its genetic structure, invasion history, and selective pressures associated with its adaptation to the American environment. We confirmed that American populations originated from Africa with at least two independent introductions that led to two genetically distinct clusters, one in the North (Haiti and Colombia) and one in the South (French Guiana and Brazil), and an admixed Peruvian group. Genome scans revealed recent and more ancient signals of positive selection in the American populations. Particularly, we detected positive selection signals in genes involved in interactions with hosts (human and mosquito) cells and in genes involved in resistance to malaria drugs in both clusters. Analyses suggested that for five genes, adaptive introgression between clusters or selection on standing variation was at the origin of this repeated evolution. This study provides new genetic evidence on P. falciparum colonization history and on its local adaptation in the Americas.}, } @article {pmid37029352, year = {2023}, author = {Wu, J and He, D and Yu, F and Huang, Y and Bian, M and Yu, C and Liu, J and Cai, Z and Zhao, Y}, title = {Mycoplasma infection mimicking a malignancy in a waldenstrom macroglobulinemia patient.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {219}, pmid = {37029352}, issn = {1471-2334}, support = {LY22H080004//Zhejiang Provincial Natural Science Foundation of China/ ; 2021KY143//Medical and Health Science and Technology Project of Zhejiang Province/ ; }, mesh = {Humans ; Fluorodeoxyglucose F18 ; Positron Emission Tomography Computed Tomography/methods ; Positron-Emission Tomography ; Radiopharmaceuticals ; *Urinary Bladder Neoplasms ; *Waldenstrom Macroglobulinemia/diagnosis ; Diagnosis, Differential ; Neoplasms ; }, abstract = {BACKGROUND: Mycoplasma hominis infection is common in urinary tract. [18]F-FDG-PET/CT is a valuable tool for tumor and infection diagnosis. Few studies have shown the [18]F-FDG-PET/CT images after mycoplasma infection.

CASE PRESENTATION: Here we described a case of Waldenstrom macroglobulinemia with thickened bladder wall. The [18]F-FDG-PET/CT showed the SUVmax up to 36.1 mimicking bladder cancer. The results of histopathological examination and metagenomic sequencing of the blood and urinary revealed the Mycoplasma hominis infection.

CONCLUSION: The full consideration should be given to the possibility of infection besides tumor in lesions with high SUV value in [18]F-FDG-PET/CT, especially in immunodeficiency patients.}, } @article {pmid37029236, year = {2023}, author = {Dreisbach, C and Prescott, S and Siega-Riz, AM and McCulloch, J and Habermeyer, L and Dudley, D and Trinchieri, G and Kelsey, C and Alhusen, J}, title = {Composition of the maternal gastrointestinal microbiome as a predictor of neonatal birth weight.}, journal = {Pediatric research}, volume = {94}, number = {3}, pages = {1158-1165}, pmid = {37029236}, issn = {1530-0447}, support = {F31 NR017821/NR/NINR NIH HHS/United States ; }, mesh = {Infant, Newborn ; Pregnancy ; Female ; Humans ; Birth Weight ; *Gastrointestinal Microbiome ; Blood Glucose ; Retrospective Studies ; Cross-Sectional Studies ; Body Mass Index ; }, abstract = {BACKGROUND: The biological mechanism by which the maternal gastrointestinal microbiota contributes to fetal growth and neonatal birth weight is currently unknown. The purpose of this study was to explore how the composition of the maternal microbiome in varying pre-gravid body mass index (BMI) groups are associated with neonatal birth weight adjusted for gestational age.

METHODS: Retrospective, cross-sectional metagenomic analysis of bio-banked fecal swab biospecimens (n = 102) self-collected by participants in the late second trimester of pregnancy.

RESULTS: Through high-dimensional regression analysis using principal components (PC) of the microbiome, we found that the best performing multivariate model explained 22.9% of the variation in neonatal weight adjusted for gestational age. Pre-gravid BMI (p = 0.05), PC3 (p = 0.03), and the interaction of the maternal microbiome with maternal blood glucose on the glucose challenge test (p = 0.01) were significant predictors of neonatal birth weight after adjusting for potential confounders including maternal antibiotic use during gestation and total gestational weight gain.

CONCLUSIONS: Our results indicate a significant association between the maternal gastrointestinal microbiome in the late second trimester and neonatal birth weight adjusted for gestational age. Moderated by blood glucose at the time of the universal glucose screening, the gastrointestinal microbiome may have a role in the regulation of fetal growth.

IMPACT: Maternal blood glucose in the late second trimester significantly moderates the relationship between the maternal gastrointestinal microbiome and neonatal size adjusted for gestational age. Our findings provide preliminary evidence for fetal programming of neonatal birth weight through the maternal gastrointestinal microbiome during pregnancy.}, } @article {pmid37029135, year = {2023}, author = {Hu, X and Xia, K and Dai, M and Han, X and Yuan, P and Liu, J and Liu, S and Jia, F and Chen, J and Jiang, F and Yu, J and Yang, H and Wang, J and Xu, X and Jin, X and Kristiansen, K and Xiao, L and Chen, W and Han, M and Duan, S}, title = {Intermittent fasting modulates the intestinal microbiota and improves obesity and host energy metabolism.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {19}, pmid = {37029135}, issn = {2055-5008}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Intermittent Fasting ; Obesity ; Metagenome ; }, abstract = {Intermittent fasting (IF) is a promising paradigm for weight loss which has been shown to modulate the gut microbiota based on 16S rRNA gene amplicon sequencing. Here, 72 Chinese volunteers with a wide range of body mass index (BMI) participated in a three-week IF program during which an average loss of 3.67 kg body weight accompanied with improved clinical parameters was observed irrespective of initial anthropometric and gut microbiota status. Fecal samples were collected before and after the intervention and subjected to shotgun metagenomic sequencing. De novo assembly yielded 2934 metagenome-assembled genomes (MAGs). Profiling revealed significant enrichment of Parabacteroides distasonis and Bacteroides thetaiotaomicron after the intervention, with inverse correlations between their relative abundances and parameters related to obesity and atherosclerotic cardiovascular diseases (ASCVD). MAGs enriched after the intervention showed high richness and diversity of carbohydrate-active enzymes, with an increased relative abundances of genes related to succinate production and glutamate fermentation.}, } @article {pmid37028791, year = {2023}, author = {Xie, X and Yuan, K and Chen, X and Zhao, Z and Huang, Y and Hu, L and Liu, H and Luan, T and Chen, B}, title = {Characterization of metal resistance genes carried by waterborne free-living and particle-attached bacteria in the Pearl River Estuary.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {327}, number = {}, pages = {121547}, doi = {10.1016/j.envpol.2023.121547}, pmid = {37028791}, issn = {1873-6424}, mesh = {*Rivers/microbiology ; Estuaries ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Metals, Heavy/toxicity/analysis ; Genes, Bacterial ; Water ; }, abstract = {Toxic metals can substantially change the bacterial community and functions thereof in aquatic environments. Herein, metal resistance genes (MRGs) are the core genetic foundation for microbial responses to the threats of toxic metals. In this study, waterborne bacteria collected from the Pearl River Estuary (PRE) were separated into the free-living bacteria (FLB) and particle-attached bacteria (PAB), and analyzed using metagenomic approaches. MRGs were ubiquitous in the PRE water and mainly related to Cu, Cr, Zn, Cd and Hg. The levels of PAB MRGs in the PRE water ranged from 8.11 × 10[9] to 9.93 × 10[12] copies/kg, which were significantly higher than those of the FLB (p < 0.01). It could be attributed to a large bacterial population attached on the suspended particulate matters (SPMs), which was evidenced by a significant correlation between the PAB MRGs and 16S rRNA gene levels in the PRE water (p < 0.05). Moreover, the total levels of PAB MRGs were also significantly correlated with those of FLB MRGs in the PRE water. The spatial pattern of MRGs of both FLB and PAB exhibited a declining trend from the low reaches of the PR to the PRE and on to the coastal areas, which was closely related to metal pollution degree. MRGs likely carried by plasmids were also enriched on the SPMs with a range from to 3.85 × 10[8] to 3.08 × 10[12] copies/kg. MRG profiles and taxonomic composition of the predicted MRG hosts were significantly different between the FLB and PAB in the PRE water. Our results suggested that FLB and PAB could behave differential response to heavy metals in the aquatic environments from the perspective of MRGs.}, } @article {pmid37027945, year = {2023}, author = {Zheng, S and Qi, J and Fu, T and Chen, Y and Qiu, X}, title = {Novel mechanisms of cadmium tolerance and Cd-induced fungal stress in wheat: Transcriptomic and metagenomic insights.}, journal = {Ecotoxicology and environmental safety}, volume = {256}, number = {}, pages = {114842}, doi = {10.1016/j.ecoenv.2023.114842}, pmid = {37027945}, issn = {1090-2414}, mesh = {*Cadmium/metabolism ; Transcriptome ; Triticum/metabolism ; Gene Expression Profiling ; Soil ; *Soil Pollutants/analysis ; }, abstract = {Although several studies on the effects of cadmium (Cd) on wheat have been reported, the gene expression profiles of different wheat tissues in response to gradient concentrations of Cd, and whether soil microorganisms are involved in the damage to wheat remain to be discovered. To gain further insight into the molecular mechanisms of Cd-resistance in wheat, we sowed bread wheat (Triticum aestivum) in artificially Cd-contaminated soil and investigated the transcriptomic response of the wheat roots, stems, and leaves to gradient concentrations of Cd, as well as the alteration of the soil microbiome. Results indicated that the root bioaccumulation factors increased with Cd when concentrations were < 10 mg/kg, but at even higher concentrations, the bioaccumulation factors decreased, which is consistent with the overexpression of metal transporters and other genes related to Cd tolerance. In the Cd-contaminated soil, the abundance of fungal pathogens increased, and the antimicrobial response in wheat root was observed. Most of the differentially expressed genes (DEGs) of wheat changed significantly when the Cd concentration increased above 10 mg/kg, and the transcriptional response is much greater in roots than in stems and leaves. The DEGs are mainly involved in Cd transport and chelation, antioxidative stress, antimicrobial responses, and growth regulation. COPT3 and ZnT1 were identified for the first time as the major transporters responding to Cd in wheat. Overexpression of the nicotianamine synthase and pectinesterase genes suggested that nicotianamine and pectin are the key chelators in Cd detoxification. endochitinase, chitinase, and snakin2 were involved in the anti-fungal stress caused by Cd-induced cell damage. Several phytohormone-related DEGs are involved in the root's growth and repair. Overall, this study presents the novel Cd tolerance mechanisms in wheat and the changes in soil fungal pathogens that increase plant damage.}, } @article {pmid37027929, year = {2023}, author = {Gao, G and Shen, S and Zhang, T and Zhang, J and Huang, S and Sun, Z and Zhang, H}, title = {Lacticaseibacillus rhamnosus Probio-M9 enhanced the antitumor response to anti-PD-1 therapy by modulating intestinal metabolites.}, journal = {EBioMedicine}, volume = {91}, number = {}, pages = {104533}, pmid = {37027929}, issn = {2352-3964}, mesh = {Animals ; Mice ; Dietary Supplements ; Lacticaseibacillus ; *Lacticaseibacillus rhamnosus ; *Neoplasms/drug therapy ; *Probiotics/therapeutic use ; Tumor Microenvironment ; *Immune Checkpoint Inhibitors/therapeutic use ; }, abstract = {BACKGROUND: Probiotics have been increasingly proposed for enhancing immune checkpoint blockade (ICB) treatments against cancer. However, its causal relationship with immunotherapeutic efficacy remains unclear, which promoted us to explore if and how probiotic Lacticaseibacillus rhamnosus Probio-M9 manipulates gut microbiome for expected outcomes.

METHODS: We evaluated the effects of Probio-M9 on the anti-PD-1 treatment against colorectal cancer in mice via a multi-omics approach. We defined the mechanisms of Probio-M9-mediated antitumor immunity by comprehensive analyses of metagenome and metabolites of commensal gut microbes as well as the immunologic factors and serum metabolome of the host.

FINDINGS: The results indicated that Probio-M9 intervention strengthened the anti-PD-1-based tumor inhibition. Both prophylactic and therapeutic administration of Probio-M9 showed conspicuous performance in controlling tumor growth with ICB treatment. The supplement of Probio-M9 modulated enhanced immunotherapy response through promoting beneficial microbes (e.g., Lactobacillus and Bifidobacterium animalis), producing beneficial metabolites including butyric acids in the gut, and accumulating blood-derived α-ketoglutaric acid, N-acetyl-l-glutamic acid and pyridoxine in particular, which promoted the infiltration and activation of cytotoxic T lymphocytes (CTLs) and suppressing the function of regulatory T cells (Tregs) in the tumor microenvironment (TME). Subsequently, we found that enhanced immunotherapeutic response was transmissible by transplanting either post-probiotic-treatment gut microbes or intestinal metabolites to new tumor-bearing mice.

INTERPRETATION: This study offered valuable insight into the causal role of Probio-M9 in correcting the defects in gut microbiota that compromised anti-PD-1 therapeutic efficacy, which can be used as an alternative synergetic agent with ICB for clinical cancer treatment.

FUNDING: This research was supported by Research Fund for the National Key R&D Program of China (2022YFD2100702), Inner Mongolia Science and Technology Major Projects (2021ZD0014), and China Agriculture Research System of MOF and MARA.}, } @article {pmid37027361, year = {2023}, author = {Xu, R and Rajeev, S and Salvador, LCM}, title = {The selection of software and database for metagenomics sequence analysis impacts the outcome of microbial profiling and pathogen detection.}, journal = {PloS one}, volume = {18}, number = {4}, pages = {e0284031}, pmid = {37027361}, issn = {1932-6203}, mesh = {Animals ; Mice ; *Metagenomics/methods ; Software ; *Microbiota/genetics ; Algorithms ; Metagenome ; Sequence Analysis, DNA/methods ; }, abstract = {Shotgun metagenomic sequencing analysis is widely used for microbial profiling of biological specimens and pathogen detection. However, very little is known about the technical biases caused by the choice of analysis software and databases on the biological specimen. In this study, we evaluated different direct read shotgun metagenomics taxonomic profiling software to characterize the microbial compositions of simulated mice gut microbiome samples and of biological samples collected from wild rodents across multiple taxonomic levels. Using ten of the most widely used metagenomics software and four different databases, we demonstrated that obtaining an accurate species-level microbial profile using the current direct read metagenomics profiling software is still a challenging task. We also showed that the discrepancies in results when different databases and software were used could lead to significant variations in the distinct microbial taxa classified, in the characterizations of the microbial communities, and in the differentially abundant taxa identified. Differences in database contents and read profiling algorithms are the main contributors for these discrepancies. The inclusion of host genomes and of genomes of the interested taxa in the databases is important for increasing the accuracy of profiling. Our analysis also showed that software included in this study differed in their ability to detect the presence of Leptospira, a major zoonotic pathogen of one health importance, especially at the species level resolution. We concluded that using different databases and software combinations can result in confounding biological conclusions in microbial profiling. Our study warrants that software and database selection must be based on the purpose of the study.}, } @article {pmid37026960, year = {2023}, author = {Shen, XD and Pan, XD and Shi, SS and Xu, T and Xue, SL and Wang, J and Wan, CL and Yao, YT and Lei, W and Tao, T}, title = {Metagenomic next-generation sequencing performed on blood samples for the early recognition of severe Pneumocystis pneumonia in critical hematological patients.}, journal = {Medicine}, volume = {102}, number = {14}, pages = {e33399}, pmid = {37026960}, issn = {1536-5964}, mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis ; Prospective Studies ; High-Throughput Nucleotide Sequencing ; Caspofungin ; Death ; *Pneumocystis carinii/genetics ; *Respiratory Distress Syndrome/diagnosis ; }, abstract = {Severe Pneumocystis pneumonia (PCP) has a poor prognosis, and its early and precise diagnosis is difficult in immunocompromised individuals. Therefore, this study explored the diagnostic value of metagenomic next-generation sequencing (mNGS) of peripheral blood in diagnosing severe PCP in patients with hematological diseases. This prospective study analyzed the clinical manifestations, mNGS results (from the peripheral blood), traditional pathogen detection results, laboratory test results, chest computed tomography (CT) images, treatments, and outcomes of severe PCP in hematological patients who were hospitalized in the 2 centers of the Affiliated Hospital of Soochow University between September 2019 and October 2021. A total of 31 cases of hematological diseases complicated with pulmonary infections, including 7 cases of severe PCP diagnosed by mNGS performed on peripheral blood samples, were analyzed. Traditional pathogen detection methods for PCP cannot be used. In contrast, the laboratory readings for Pneumocystis jirovecii (Pj) detected within 48 hours of symptom onset by mNGS on the 7 blood samples ranged from 12 to 5873, with a median value of 43. Under the guidance of the mNGS results, preemptive antimicrobial therapy with trimethoprim/sulfamethoxazole alone or in combination with caspofungin was administered to treat Pj. After treatment, 4 patients recovered, and 3 patients died of acute respiratory failure and acute respiratory distress syndrome (ARDS). MNGS performed on peripheral blood samples is optional but can provide early recognition of severe PCP and help guide empirical treatment in critical hematological patients.}, } @article {pmid37026945, year = {2023}, author = {Tao, T and Chen, J and Long, K and Zhi, L and Zhang, S and Liu, S and Ma, Y and Yan, H and Lv, L and Xu, Y and Wu, L and Zhao, L and Gao, P}, title = {Severe varicella-zoster virus meningoencephalomyelitis coexisting with visceral disseminated varicella-zoster virus infection in a patient with lupus nephritis: A case report.}, journal = {Medicine}, volume = {102}, number = {14}, pages = {e33459}, pmid = {37026945}, issn = {1536-5964}, mesh = {Male ; Humans ; Young Adult ; Adult ; Herpesvirus 3, Human ; *Lupus Nephritis/drug therapy ; *Herpes Zoster/drug therapy ; *Varicella Zoster Virus Infection/complications ; *Chickenpox ; Acyclovir/therapeutic use ; *Encephalomyelitis ; }, abstract = {RATIONALE: Meningoencephalomyelitis and visceral dissemination infection are rare but life-threatening complications of either the primary infection or reactivation of varicella-zoster virus (VZV) in immunocompromised patients. To date, few studies have reported the co-existence of VZV meningoencephalomyelitis and the visceral dissemination of VZV infection.

PATIENT CONCERNS: A 23-year-old male was diagnosed with lupus nephritis class III and was being treated with oral prednisone and tacrolimus. The patient exhibited herpes zoster 21-day after the initiation of therapy and experienced unbearable abdominal pain and generalized seizures 11 days after the onset of a zoster rash. Magnetic resonance imaging showed progressive lesions in the cerebrum, brainstem, and cerebellum, as well as meningeal thickening and thoracic myelitis. Computed tomography showed pulmonary interstitial infiltration, partial intestinal dilatation, and effusion. Metagenomic next-generation sequencing revealed 198,269 and 152,222 VZV-specific reads in the cerebrospinal fluid and bronchoalveolar lavage fluid, respectively.

DIAGNOSES: Based on the clinical and genetic findings, this patient was finally diagnosed with VZV meningoencephalomyelitis and visceral disseminated VZV infection.

INTERVENTIONS: The patient received intravenous acyclovir (0.5 g every 8 hours) combined with plasma exchange and intravenous immunoglobulin. Treatment against secondary bacterial and fungal infections, organ support therapy and rehabilitation training were given simultaneously.

OUTCOME: The patient's peripheral muscle strength did not improve and repeated metagenomic next-generation sequencing showed the persistence of VZV-specific reads in the cerebrospinal fluid. The patient finally abandoned therapy due to financial constraints at the 1-month follow-up.

LESSONS: Patients with autoimmune diseases receiving immunosuppressive therapy should be warned about the possibility of developing serious neurological infections and visceral disseminated VZV infections as side effects. Early diagnosis and the early initiation of intravenous acyclovir therapy are important for such cases.}, } @article {pmid37026934, year = {2023}, author = {Peng, R and Peng, Z and Mou, M and Wang, Q and Huang, M and Zou, J}, title = {Gastrointestinal Talaromyces marneffei infection in a man with AIDS: A case report.}, journal = {Medicine}, volume = {102}, number = {14}, pages = {e33424}, pmid = {37026934}, issn = {1536-5964}, mesh = {Male ; Humans ; Middle Aged ; Antifungal Agents/therapeutic use/pharmacology ; Itraconazole/therapeutic use ; *HIV Infections/drug therapy ; Ulcer/drug therapy ; Proton Pump Inhibitors ; *Helicobacter Infections/drug therapy ; *Acquired Immunodeficiency Syndrome/complications/drug therapy ; *Helicobacter pylori ; }, abstract = {RATIONALE: Reports of intestinal Talaromyces marneffei infection have increased year by year, but those of gastric infection remain rare. Here, we report disseminated talaromycosis with gastric and intestinal ulcers in an AIDS patient who was treated by antifungal agents and a proton pump inhibitor and achieved a satisfactory outcome.

PATIENT CONCERNS: A 49-year-old man developed a gastrointestinal illness with main abdominal distension, poor appetite and a positive HIV infection to our AIDS clinical treatment center.

DIAGNOSES: Electronic gastrointestinal endoscopy showed that the patient had multiple ulcers in the gastric angle, gastric antrum and large intestine. Gastric Helicobacter pylori infection was ruled out by paraulcerative histopathological analysis and a C14 urea breath test. The diagnosis was confirmed by gastroenteroscopic biopsy and metagenomic next-generation sequencing of gastric ulcer tissue.

INTERVENTIONS: Symptomatic and supportive treatments [a proton pump inhibitor and gastrointestinal motility promotion] were initiated. The patient was prescribed sequential antifungal therapy with amphotericin B (0.5 mg/kg·d, 2 weeks) and itraconazole (200 mg, q12h, 10 weeks), and then followed with itraconazole for long-term secondary prevention (200 mg, qd).

OUTCOMES: The combined use of antifungal agents and a proton pump inhibitor improved the patient's condition, and he was discharged home 20 days later. He had no gastrointestinal symptom during 1 year of telephone-based follow-up.

LESSONS: In endemic areas, clinicians should be alert to the possibility of Talaromyces marneffei infection presenting with gastric ulcers in patients with AIDS, after excluding Helicobacter pylori infection.}, } @article {pmid37026145, year = {2023}, author = {Clark, JR and Terwilliger, A and Avadhanula, V and Tisza, M and Cormier, J and Javornik-Cregeen, S and Ross, MC and Hoffman, KL and Troisi, C and Hanson, B and Petrosino, J and Balliew, J and Piedra, PA and Rios, J and Deegan, J and Bauer, C and Wu, F and Mena, KD and Boerwinkle, E and Maresso, AW}, title = {Wastewater pandemic preparedness: Toward an end-to-end pathogen monitoring program.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1137881}, pmid = {37026145}, issn = {2296-2565}, mesh = {Humans ; *Wastewater ; SARS-CoV-2 ; *COVID-19/epidemiology ; Pandemics ; Public Health ; }, abstract = {Molecular analysis of public wastewater has great potential as a harbinger for community health and health threats. Long-used to monitor the presence of enteric viruses, in particular polio, recent successes of wastewater as a reliable lead indicator for trends in SARS-CoV-2 levels and hospital admissions has generated optimism and emerging evidence that similar science can be applied to other pathogens of pandemic potential (PPPs), especially respiratory viruses and their variants of concern (VOC). However, there are substantial challenges associated with implementation of this ideal, namely that multiple and distinct fields of inquiry must be bridged and coordinated. These include engineering, molecular sciences, temporal-geospatial analytics, epidemiology and medical, and governmental and public health messaging, all of which present their own caveats. Here, we outline a framework for an integrated, state-wide, end-to-end human pathogen monitoring program using wastewater to track viral PPPs.}, } @article {pmid37025626, year = {2023}, author = {Meynadier, A and Marie-Etancelin, C and Palevich, N}, title = {Editorial: Host genome and metagenome interactions for improved ruminant health and performance.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1160074}, doi = {10.3389/fmicb.2023.1160074}, pmid = {37025626}, issn = {1664-302X}, } @article {pmid37025192, year = {2023}, author = {Wang, D and Zhang, L and Cai, Z and Liu, Y}, title = {Diagnosis of Acute Q Fever in a Patient by Using Metagenomic Next-Generation Sequencing: A Case Report.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {1923-1930}, pmid = {37025192}, issn = {1178-6973}, abstract = {BACKGROUND: Q fever is a zoonotic disease caused by Coxiella burnetii infection, with domestic ruminants as the main source of infection and tick bites as one of the transmission vectors. The clinical manifestations of Q fever are varied and atypical. For the reason that C. burnetii is a strictly intracellular pathogen, it is difficult to be diagnosed by traditional culture methods. Additionally, serological and molecular diagnostic methods to assist in the diagnosis of Q fever are not routinely performed in most clinical laboratories. Therefore, early and rapid diagnosis of Q fever is a challenge.

CASE PRESENTATION: In the present study, a 34-year-old male patient presented with an acute onset and symptoms such as high fever, lethargy, pulmonary infection, and liver damage. In addition, he had a history of tick bites. Despite conducting relevant laboratory and radiological examinations, the etiology remained unknown. Subsequently, we detected the sequence reads of C. burnetii in a venous blood sample using metagenomic next-generation sequencing (mNGS), and the symptoms of patients were significantly improved after timely treatment with the special drug tetracycline. To our knowledge, this is the first report of Q fever associated with C. burnetii detected directly from venous blood sample in Wuhan, China.

CONCLUSION: Metagenomic next-generation sequencing is a new diagnostic technology that provides rapid and accurate detection of unexplained infections, including Q fever. Its application plays a crucial role in clinical diagnosis for identifying elusive pathogens.}, } @article {pmid37025159, year = {2023}, author = {Orf, GS and Perez, LJ and Meyer, TV and Luk, KC and Forberg, K and Rodgers, MA and Hadji, A and James, L and Mampunza, S and Achari, A and Yu, G and Federman, S and Chiu, CY and McArthur, CA and Cloherty, GA and Berg, MG}, title = {Purifying selection decreases the potential for Bangui orthobunyavirus outbreaks in humans.}, journal = {Virus evolution}, volume = {9}, number = {1}, pages = {vead018}, pmid = {37025159}, issn = {2057-1577}, abstract = {Pathogens carried by insects, such as bunyaviruses, are frequently transmitted into human populations and cause diseases. Knowing which spillover events represent a public health threat remains a challenge. Metagenomic next-generation sequencing (mNGS) can support infectious disease diagnostics by enabling the detection of any pathogen from clinical specimens. mNGS was performed on blood samples to identify potential viral coinfections in human immunodeficiency virus (HIV)-positive individuals from Kinshasa, the Democratic Republic of the Congo (DRC), participating in an HIV diversity cohort study. Time-resolved phylogenetics and molecular assay development assisted in viral characterization. The nearly complete genome of a novel orthobunyavirus related to Nyangole virus, a virus previously identified in neighboring Uganda, was assembled from a hepatitis B virus-positive patient. A quantitative polymerase chain reaction assay was designed and used to screen >2,500 plasma samples from Cameroon, the DRC, and Uganda, failing to identify any additional cases. The recent sequencing of a US Center for Disease Control Arbovirus Reference Collection revealed that this same virus, now named Bangui virus, was first isolated in 1970 from an individual in the Central African Republic. Time-scaled phylogenetic analyses of Bangui with the related Anopheles and Tanga serogroup complexes indicate that this virus emerged nearly 10,000 years ago. Pervasive and episodic models further suggest that this virus is under purifying selection and that only distant common ancestors were subject to positive selection events. This study represents only the second identification of a Bangui virus infection in over 50 years. The presumed rarity of Bangui virus infections in humans can be explained by its constraint to an avian host and insect vector, precluding efficient transmission into the human population. Our results demonstrate that molecular phylogenetic analyses can provide insights into the threat posed by novel or re-emergent viruses identified by mNGS.}, } @article {pmid37024971, year = {2023}, author = {Louisson, Z and Hermans, SM and Buckley, HL and Case, BS and Taylor, M and Curran-Cournane, F and Lear, G}, title = {Land use modification causes slow, but predictable, change in soil microbial community composition and functional potential.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {30}, pmid = {37024971}, issn = {2524-6372}, abstract = {BACKGROUND: Bacterial communities are critical to ecosystem functioning and sensitive to their surrounding physiochemical environment. However, the impact of land use change on microbial communities remains understudied. We used 16S rRNA gene amplicon sequencing and shotgun metagenomics to assess soil microbial communities' taxonomic and functional responses to land use change. We compared data from long-term grassland, exotic forest and horticulture reference sites to data from sites that transitioned from (i) Grassland to exotic forest or horticulture and from (ii) Exotic forest to grassland.

RESULTS: Community taxonomic and functional profiles of the transitional sites significantly differed from those within reference sites representing both their historic and current land uses (P < 0.001). The bacterial communities in sites that transitioned more recently were compositionally more similar to those representing their historic land uses. In contrast, the composition of communities from sites exposed to older conversion events had shifted towards the compositions at reference sites representing their current land use.

CONCLUSIONS: Our study indicates that microbial communities respond in a somewhat predictable way after a land use conversion event by shifting from communities reflecting their former land use towards those reflecting their current land use. Our findings help us to better understand the legacy effects of land use change on soil microbial communities and implications for their role in soil health and ecosystem functioning. Understanding the responsiveness of microbial communities to environmental disturbances will aid us in incorporating biotic variables into soil health monitoring techniques in the future.}, } @article {pmid37024789, year = {2023}, author = {Wang, Z and Xia, H and Fan, F and Zhang, J and Liu, H and Cao, J}, title = {Survival of community-acquired Bacillus cereus sepsis with venous sinus thrombosis in an immunocompetent adult man - a case report and literature review.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {213}, pmid = {37024789}, issn = {1471-2334}, support = {201801D121332//Natural Science Foundation of Shanxi Province/ ; 20220039//Shanxi Provincial Scholarship Council Foundation/ ; }, mesh = {Humans ; Male ; Adult ; Young Adult ; *Subarachnoid Hemorrhage/etiology ; Bacillus cereus ; *Sepsis/complications/diagnosis/drug therapy ; *Sinus Thrombosis, Intracranial/complications ; }, abstract = {BACKGROUND: Bacillus cereus infections in immunocompetent patients are uncommon and mainly observed in fragile patients. It can cause lethal infections with multiple organ dysfunction syndrome (MODS). However, a patient presenting as venous sinus thrombosis and survival without sequela has not been reported.

CASE PRESENTATION: A 20-year-old previously healthy male developed gastroenteritis after a meal, followed by fever, convulsions, and severe disturbance of consciousness. The patient had significant leukocytosis with a mildly elevated D-dimer, creatinine level, and respiratory failure. The CT(computed tomography) revealed fatal brain edema and subarachnoid hemorrhage. Previous blood culture in a local hospital revealed B. cereus, which was confirmed by mNGS(metagenomic next-generation sequencing) using blood and urine in our hospital. Accordingly, B. cereus sepsis with MODS were considered. Later, cerebral venous sinus thrombosis was proved. After anti-infection (linezolid 0.6 g, Q12h; and meropenem 1.0 g, Q8h), anti-coagulant (enoxaparin 6000U, Q12h), and other symptomatic treatments, the patient recovered completely without sequela at the 6-month follow-up.

CONCLUSIONS: This case suggests that in immunocompetent adults, there is still a risk of infection with B. cereus, causing severe MODS. Special attention should be paid to venous sinus thrombosis and subarachnoid hemorrhage in such cases, while, anti-coagulant is essential therapy.}, } @article {pmid37024618, year = {2023}, author = {Hwang, Y and Roux, S and Coclet, C and Krause, SJE and Girguis, PR}, title = {Viruses interact with hosts that span distantly related microbial domains in dense hydrothermal mats.}, journal = {Nature microbiology}, volume = {8}, number = {5}, pages = {946-957}, pmid = {37024618}, issn = {2058-5276}, mesh = {*Bacteria/genetics ; Ecosystem ; *Viruses/genetics ; DNA ; Microbial Interactions ; }, abstract = {Many microbes in nature reside in dense, metabolically interdependent communities. We investigated the nature and extent of microbe-virus interactions in relation to microbial density and syntrophy by examining microbe-virus interactions in a biomass dense, deep-sea hydrothermal mat. Using metagenomic sequencing, we find numerous instances where phylogenetically distant (up to domain level) microbes encode CRISPR-based immunity against the same viruses in the mat. Evidence of viral interactions with hosts cross-cutting microbial domains is particularly striking between known syntrophic partners, for example those engaged in anaerobic methanotrophy. These patterns are corroborated by proximity-ligation-based (Hi-C) inference. Surveys of public datasets reveal additional viruses interacting with hosts across domains in diverse ecosystems known to harbour syntrophic biofilms. We propose that the entry of viral particles and/or DNA to non-primary host cells may be a common phenomenon in densely populated ecosystems, with eco-evolutionary implications for syntrophic microbes and CRISPR-mediated inter-population augmentation of resilience against viruses.}, } @article {pmid37024272, year = {2023}, author = {Nievas, S and Coniglio, A and Takahashi, WY and López, GA and Larama, G and Torres, D and Rosas, S and Etto, RM and Galvão, CW and Mora, V and Cassán, F}, title = {Unraveling Azospirillum's colonization ability through microbiological and molecular evidence.}, journal = {Journal of applied microbiology}, volume = {134}, number = {4}, pages = {}, doi = {10.1093/jambio/lxad071}, pmid = {37024272}, issn = {1365-2672}, mesh = {RNA, Ribosomal, 16S/genetics/metabolism ; *Azospirillum/genetics/metabolism ; Plant Growth Regulators/metabolism ; Plants/microbiology ; Signal Transduction ; Rhizosphere ; Plant Roots/microbiology ; Soil Microbiology ; }, abstract = {It is known that members of the bacterial genus Azospirillum can promote the growth of a great variety of plants, an ability harnessed by the industry to create bioproducts aimed to enhance the yield of economically relevant crops. Its versatile metabolism allows this bacterium to adapt to numerous environments, from optimal to extreme or highly polluted. The fact of having been isolated from soil and rhizosphere samples collected worldwide and many other habitats proves its remarkable ubiquity. Azospirillum rhizospheric and endophytic lifestyles are governed by several mechanisms, leading to efficient niche colonization. These mechanisms include cell aggregation and biofilm formation, motility, chemotaxis, phytohormone and other signaling molecules production, and cell-to-cell communication, in turn, involved in regulating Azospirillum interactions with the surrounding microbial community. Despite being infrequently mentioned in metagenomics studies after its introduction as an inoculant, an increasing number of studies detected Azospirillum through molecular tools (mostly 16S rRNA sequencing) as part of diverse, even unexpected, microbiomes. This review focuses on Azospirillum traceability and the performance of the available methods, both classical and molecular. An overview of Azospirillum occurrence in diverse microbiomes and the less-known features explaining its notorious ability to colonize niches and prevail in multiple environments is provided.}, } @article {pmid37024036, year = {2023}, author = {Yue, J and Han, X and Jin, Y and Yu, J}, title = {Potential of direct granulation and organic loading rate tolerance of aerobic granular sludge in ultra-hypersaline environment.}, journal = {Environmental research}, volume = {228}, number = {}, pages = {115831}, doi = {10.1016/j.envres.2023.115831}, pmid = {37024036}, issn = {1096-0953}, mesh = {*Sewage/microbiology ; *Waste Disposal, Fluid ; Aerobiosis ; Bioreactors/microbiology ; Wastewater ; Nitrogen ; }, abstract = {Salt-tolerant aerobic granular sludge (SAGS) technology has shown potentials in the treatment of ultra-hypersaline high-strength organic wastewater. However, the long granulation period and salt-tolerance acclimation period are still bottlenecks that hinder SAGS applications. In this study, "one-step" development strategy was used to try to directly cultivate SAGS under 9% salinity, and the fastest cultivation process was obtained under such high salinity compared to the previous papers with the inoculum of municipal activated sludge without bioaugmentation. Briefly, the inoculated municipal activated sludge was almost discharged on Day 1-10, then fungal pellets appeared and it gradually transitioned to mature SAGS (particle size of ∼4156 μm and SVI30 of 57.8 mL/g) from Day 11 to Day 47 without fragmentation. Metagenomic revealed that fungus Fusarium played key roles in the transition process probably because it functioned as structural backbone. RRNPP and AHL-mediated systems might be the main QS regulation systems of bacteria. TOC and NH4[+]-N removal efficiencies maintained at ∼93.9% (after Day 11) and ∼68.5% (after Day 33), respectively. Subsequently, the influent organic loading rate (OLR) was stepwise increased from 1.8 to 11.7 kg COD/m[3]·d. It was found that SAGS could maintain intact structure and low SVI30 (< 55 mL/g) under 9% salinity and the OLR of 1.8-9.9 kg COD/m[3]·d with adjustment of air velocity. TOC and NH4[+]-N (TN) removal efficiencies could maintain at ∼95.4% (below OLR of 8.1 kg COD/m[3]·d) and ∼84.1% (below nitrogen loading rate of 0.40 kg N/m[3]·d) in ultra-hypersaline environment. Halomonas dominated the SAGS under 9% salinity and varied OLR. This study confirmed the feasibility of direct aerobic granulation in ultra-hypersaline environment and verified the upper OLR boundary of SAGS in ultra-hypersaline high-strength organic wastewater treatment.}, } @article {pmid37023405, year = {2023}, author = {Cavattoni, M and Comin, M}, title = {ClassGraph: Improving Metagenomic Read Classification with Overlap Graphs.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {30}, number = {6}, pages = {633-647}, doi = {10.1089/cmb.2022.0208}, pmid = {37023405}, issn = {1557-8666}, mesh = {*Algorithms ; Sequence Analysis, DNA ; Metagenome ; *Microbiota ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; }, abstract = {Current technologies allow the sequencing of microbial communities directly from the environment without prior culturing. One of the major problems when analyzing a microbial sample is to taxonomically annotate its reads to identify the species it contains. Most methods that are currently available focus on the classification of reads using a set of reference genomes and their k-mers. While in terms of precision these methods have reached percentages of correctness close to perfection, in terms of sensitivity (the actual number of classified reads), the performance is often poor. One reason is that the reads in a sample can be very different from the corresponding reference genomes; for example, viral genomes are usually highly mutated. To address this issue, in this article, we propose ClassGraph, a new taxonomic classification method that makes use of the read overlap graph and applies a label propagation algorithm to refine the results of existing tools. We evaluated its performance on simulated and real datasets with several taxonomic classification tools, and the results showed an improved sensitivity and F-measure, while maintaining high precision. ClassGraph is capable of improving the classification accuracy, especially in difficult cases such as virus and real datasets, where traditional tools can classify <40% of reads.}, } @article {pmid37022443, year = {2023}, author = {Stentz, R and Cheema, J and Philo, M and Carding, SR}, title = {A Possible Aquatic Origin of the Thiaminase TenA of the Human Gut Symbiont Bacteroides thetaiotaomicron.}, journal = {Journal of molecular evolution}, volume = {91}, number = {4}, pages = {482-491}, pmid = {37022443}, issn = {1432-1432}, support = {BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; Animals ; *Bacteroides thetaiotaomicron/metabolism ; Phylogeny ; Australia ; Thiamine/metabolism ; }, abstract = {TenA thiamin-degrading enzymes are commonly found in prokaryotes, plants, fungi and algae and are involved in the thiamin salvage pathway. The gut symbiont Bacteroides thetaiotaomicron (Bt) produces a TenA protein (BtTenA) which is packaged into its extracellular vesicles. An alignment of BtTenA protein sequence with proteins from different databases using the basic local alignment search tool (BLAST) and the generation of a phylogenetic tree revealed that BtTenA is related to TenA-like proteins not only found in a small number of intestinal bacterial species but also in some aquatic bacteria, aquatic invertebrates, and freshwater fish. This is, to our knowledge, the first report describing the presence of TenA-encoding genes in the genome of members of the animal kingdom. By searching metagenomic databases of diverse host-associated microbial communities, we found that BtTenA homologues were mostly represented in biofilms present on the surface of macroalgae found in Australian coral reefs. We also confirmed the ability of a recombinant BtTenA to degrade thiamin. Our study shows that BttenA-like genes which encode a novel sub-class of TenA proteins are sparingly distributed across two kingdoms of life, a feature of accessory genes known for their ability to spread between species through horizontal gene transfer.}, } @article {pmid37022232, year = {2023}, author = {Zimmerman, S and Tierney, BT and Patel, CJ and Kostic, AD}, title = {Quantifying Shared and Unique Gene Content across 17 Microbial Ecosystems.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0011823}, pmid = {37022232}, issn = {2379-5077}, support = {P30 DK036836/DK/NIDDK NIH HHS/United States ; R01 AI127250/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; Metagenome/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Genome, Bacterial ; }, abstract = {Measuring microbial diversity is traditionally based on microbe taxonomy. Here, in contrast, we aimed to quantify heterogeneity in microbial gene content across 14,183 metagenomic samples spanning 17 ecologies, including 6 human associated, 7 nonhuman host associated, and 4 in other nonhuman host environments. In total, we identified 117,629,181 nonredundant genes. The vast majority of genes (66%) occurred in only one sample (i.e., "singletons"). In contrast, we found 1,864 sequences present in every metagenome, but not necessarily every bacterial genome. Additionally, we report data sets of other ecology-associated genes (e.g., abundant in only gut ecosystems) and simultaneously demonstrated that prior microbiome gene catalogs are both incomplete and inaccurately cluster microbial genetic life (e.g., at gene sequence identities that are too restrictive). We provide our results and the sets of environmentally differentiating genes described above at http://www.microbial-genes.bio. IMPORTANCE The amount of shared genetic elements has not been quantified between the human microbiome and other host- and non-host-associated microbiomes. Here, we made a gene catalog of 17 different microbial ecosystems and compared them. We show that most species shared between environment and human gut microbiomes are pathogens and that prior gene catalogs described as "nearly complete" are far from it. Additionally, over two-thirds of all genes only appear in a single sample, and only 1,864 genes (0.001%) are found in all types of metagenomes. These results highlight the large diversity between metagenomes and reveal a new, rare class of genes, those found in every type of metagenome, but not every microbial genome.}, } @article {pmid37022183, year = {2023}, author = {Wang, Q and Wang, D and Agathokleous, E and Cheng, C and Shang, B and Feng, Z}, title = {Soil Microbial Community Involved in Nitrogen Cycling in Rice Fields Treated with Antiozonant under Ambient Ozone.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {4}, pages = {e0018023}, pmid = {37022183}, issn = {1098-5336}, mesh = {Soil/chemistry ; *Oryza ; *Ozone/pharmacology ; *Microbiota ; Soil Microbiology ; Nitrogen ; }, abstract = {Ethylenediurea (EDU) can effectively mitigate the crop yield loss caused by ozone (O3), a major, phytotoxic air pollutant. However, the relevant mechanisms are poorly understood, and the effect of EDU on soil ecosystems has not been comprehensively examined. In this study, a hybrid rice variety (Shenyou 63) was cultivated under ambient O3 and sprayed with 450 ppm EDU or water every 10 days. Real time quantitative polymerase chain reaction (RT-qPCR) showed that EDU had no significant effect on the microbial abundance in either rhizospheric or bulk soils. By applying both metagenomic sequencing and the direct assembly of nitrogen (N)-cycling genes, EDU was found to decrease the abundance of functional genes related to nitrification and denitrification processes. Moreover, EDU increased the abundance of genes involved in N-fixing. Although the abundance of some functional genes did not change significantly, nonmetric multidimensional scaling (NMDS) and a principal coordinates analysis (PCoA) suggested that the microbial community structure involved in N cycling was altered by EDU. The relative abundances of nifH-and norB-harboring microbial genera in the rhizosphere responded differently to EDU, suggesting the existence of functional redundancy, which may play a key role in sustaining microbially mediated N-cycling under ambient O3. IMPORTANCE Ethylenediurea (EDU) is hitherto the most efficient phytoprotectant agent against O3 stress. However, the underlying biological mechanisms of its mode of action are not clear, and the effects of EDU on the environment are still unknown, limiting its large-scale application in agriculture. Due to its sensitivity to environmental changes, the microbial community can be used as an indicator to assess the environmental impacts of agricultural practices on soil quality. This study aimed to unravel the effects of EDU spray on the abundance, community structure, and ecological functions of microbial communities in the rhizosphere of rice plants. Our study provides a deep insight into the impact of EDU spray on microbial-mediated N cycling and the structure of N-cycling microbial communities. Our findings help to elucidate the mode of action of EDU in alleviating O3 stress in crops from the perspective of regulating the structure and function of the rhizospheric soil microbial community.}, } @article {pmid37022167, year = {2023}, author = {Hu, X and Zhao, Y and Han, P and Liu, S and Liu, W and Mai, C and Deng, Q and Ren, J and Luo, J and Chen, F and Jia, X and Zhang, J and Rao, G and Gu, B}, title = {Novel Clinical mNGS-Based Machine Learning Model for Rapid Antimicrobial Susceptibility Testing of Acinetobacter baumannii.}, journal = {Journal of clinical microbiology}, volume = {61}, number = {5}, pages = {e0180522}, pmid = {37022167}, issn = {1098-660X}, mesh = {*Acinetobacter baumannii ; Retrospective Studies ; Cefepime ; Ceftazidime ; Prospective Studies ; Anti-Bacterial Agents/pharmacology ; Imipenem ; Ciprofloxacin ; *Anti-Infective Agents ; Drug Resistance, Multiple, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Microbial Sensitivity Tests ; }, abstract = {Multidrug-resistant (MDR) bacteria are important public health problems. Antibiotic susceptibility testing (AST) currently uses time-consuming culture-based procedures, which cause treatment delays and increased mortality. We developed a machine learning model using Acinetobacter baumannii as an example to explore a fast AST approach using metagenomic next-generation sequencing (mNGS) data. The key genetic characteristics associated with antimicrobial resistance (AMR) were selected through a least absolute shrinkage and selection operator (LASSO) regression model based on 1,942 A. baumannii genomes. The mNGS-AST prediction model was accordingly established, validated, and optimized using read simulation sequences of clinical isolates. Clinical specimens were collected to evaluate the performance of the model retrospectively and prospectively. We identified 20, 31, 24, and 3 AMR signatures of A. baumannii for imipenem, ceftazidime, cefepime, and ciprofloxacin, respectively. Four mNGS-AST models had a positive predictive value (PPV) greater than 0.97 for 230 retrospective samples, with negative predictive values (NPVs) of 100% (imipenem), 86.67% (ceftazidime), 86.67% (cefepime), and 90.91% (ciprofloxacin). Our method classified antibacterial phenotypes with an accuracy of 97.65% for imipenem, 96.57% for ceftazidime, 97.64% for cefepime, and 98.36% for ciprofloxacin. The average reporting time of mNGS-based AST was 19.1 h, in contrast to the 63.3 h for culture-based AST, thus yielding a significant reduction of 44.3 h. mNGS-AST prediction results coincided 100% with the phenotypic AST results when testing 50 prospective samples. The mNGS-based model could be used as a rapid genotypic AST approach to identify A. baumannii and predict resistance and susceptibility to antibacterials and could be applicable to other pathogens and facilitate rational antimicrobial usage.}, } @article {pmid37021604, year = {2023}, author = {Qi, L and Zheng, Y and Hou, L and Liu, B and Zhou, J and An, Z and Wu, L and Chen, F and Lin, Z and Yin, G and Dong, H and Li, X and Liang, X and Liu, M}, title = {Potential response of dark carbon fixation to global warming in estuarine and coastal waters.}, journal = {Global change biology}, volume = {29}, number = {13}, pages = {3821-3832}, doi = {10.1111/gcb.16702}, pmid = {37021604}, issn = {1365-2486}, support = {2016YFA0600904//Chinese National Key Programs for Fundamental Research and Development/ ; KLGIS2022C03//Director's Fund of Key Laboratory of Geographic Information Science (Ministry of Education), East China Normal University/ ; 41725002//National Natural Science Foundation of China/ ; 41730646//National Natural Science Foundation of China/ ; 41971105//National Natural Science Foundation of China/ ; 42030411//National Natural Science Foundation of China/ ; 42222605//National Natural Science Foundation of China/ ; 42230505//National Natural Science Foundation of China/ ; }, mesh = {*Global Warming ; *Ecosystem ; Carbon Cycle ; Seasons ; Carbon/metabolism ; }, abstract = {Dark carbon fixation (DCF), through which chemoautotrophs convert inorganic carbon to organic carbon, is recognized as a vital process of global carbon biogeochemical cycle. However, little is known about the response of DCF processes in estuarine and coastal waters to global warming. Using radiocarbon labelling method, the effects of temperature on the activity of chemoautotrophs were investigated in benthic water of the Yangtze estuarine and coastal areas. A dome-shaped thermal response pattern was observed for DCF rates (i.e., reduced rates at lower or higher temperatures), with the optimum temperature (Topt) varying from about 21.9 to 32.0°C. Offshore sites showed lower Topt values and were more vulnerable to global warming compared with nearshore sites. Based on temperature seasonality of the study area, it was estimated that warming would accelerate DCF rate in winter and spring but inhibit DCF activity in summer and fall. However, at an annual scale, warming showed an overall promoting effect on DCF rates. Metagenomic analysis revealed that the dominant chemoautotrophic carbon fixation pathways in the nearshore area were Calvin-Benson-Bassham (CBB) cycle, while the offshore sites were co-dominated by CBB and 3-hydroxypropionate/4-hydroxybutyrate cycles, which may explain the differential temperature response of DCF along the estuarine and coastal gradients. Our findings highlight the importance of incorporating DCF thermal response into biogeochemical models to accurately estimate the carbon sink potential of estuarine and coastal ecosystems in the context of global warming.}, } @article {pmid37020798, year = {2023}, author = {Deng, W and Jiang, Y and Qin, J and Chen, G and Lv, Y and Lei, Y and Luo, J and Hong, K and Huang, B and Qin, L and Tang, X and Ye, L and Dang, Y and Wang, C and Long, F and Wang, K and Kong, J}, title = {Metagenomic Next-Generation Sequencing Assists in the Diagnosis of Mediastinal Aspergillus fumigatus Abscess in an Immunocompetent Patient: A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {1865-1874}, pmid = {37020798}, issn = {1178-6973}, abstract = {BACKGROUND: Aspergillus fumigatus is an opportunistic fungal pathogen, which is commonly found in lungs and rarely causes infections in mediastinum. Mediastinal Aspergillus abscess is a serious infectious condition, and is characterized by difficult diagnosis due to its clinical manifestations being nonspecific.

CASE PRESENTATION: Here, we report a case of a mediastinal Aspergillus fumigatus abscess in an immunocompetent patient. The patient was a 45-year-old woman who presented with a 20-day history of sore throat without any underlying diseases. Chest computed tomography (CT) showed a mass in the anterior superior mediastinum. Metagenomic next-generation sequencing (mNGS) identified Aspergillus fumigatus sequences in endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA) tissue, indicating the mediastinal Aspergillus fumigatus infection of this patient. The following mediastinal biopsy histological analysis and tissue fungi culture also suggested Aspergillus fumigatus infection, confirming the mNGS detection. The patient was diagnosed with mediastinal aspergillosis caused by Aspergillus fumigatus. After timely voriconazole treatment, the patient was discharged with good condition.

CONCLUSION: Our study presented a rare case with mediastinal Aspergillus fumigatus abscess in an immunocompetent patient. As a new clinical diagnostic method, mNGS could assist timely diagnosis and precise treatment of Aspergillus infection.}, } @article {pmid37020716, year = {2023}, author = {Campos, PM and Miska, KB and Jenkins, MC and Yan, X and Proszkowiec-Weglarz, M}, title = {Effects of Eimeria acervulina infection on the luminal and mucosal microbiota of the duodenum and jejunum in broiler chickens.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1147579}, pmid = {37020716}, issn = {1664-302X}, abstract = {The intestinal disease coccidiosis, caused by Eimeria parasites, impacts nutrient absorption in broiler chickens, leading to weight gain depression and major losses in the poultry industry. To develop alternatives to antibiotics for treating infected chickens, the gut microbiota has been researched because of its association with health factors such as nutrient exchange, immune system modulation, digestive system physiology, and pathogen exclusion. The aim of this study was to determine the effect of Eimeria acervulina infection on the luminal and mucosal microbiota of both the duodenum (DuoL and DuoM) and jejunum (JejL and JejM) at multiple time points (days 3, 5, 7, 10, and 14) post-infection. 16S rRNA amplicon sequencing was utilized to characterize the microbiota and analyze differences in alpha and beta diversity between infected (IF) and control (C) birds at each time point. Alpha diversity differed between IF and C birds in DuoM and JejM microbiota. Combined with beta diversity results, DuoM microbiota appeared to be affected by infection in the longer-term, while JejM microbiota were affected in the shorter-term. Relative abundances of bacterial taxa known for short-chain fatty acid (SCFA) production, such as Lachnospiraceae, Subdoligranulum, and Peptostreptococcaceae, tended to be lower in IF birds for all four microbiota. Moreover, predicted functional abundances showed MetaCyc pathways related to SCFA production, especially butyrate, may be influenced by these differences in bacterial relative abundance. Our findings expand understanding of how Eimeria infection affects luminal and mucosal microbiota in the duodenum and jejunum, and further research on metagenomic function may provide insights on the degree of influence duodenal and jejunal bacteria have on chicken health.}, } @article {pmid37020647, year = {2023}, author = {Rahman, T and Sarwar, PF and Potter, C and Comstock, SS and Klepac-Ceraj, V}, title = {Role of human milk oligosaccharide metabolizing bacteria in the development of atopic dermatitis/eczema.}, journal = {Frontiers in pediatrics}, volume = {11}, number = {}, pages = {1090048}, pmid = {37020647}, issn = {2296-2360}, support = {R15 AI160139/AI/NIAID NIH HHS/United States ; }, abstract = {Despite affecting up to 20% of infants in the United States, there is no cure for atopic dermatitis (AD), also known as eczema. Atopy usually manifests during the first six months of an infant's life and is one predictor of later allergic health problems. A diet of human milk may offer protection against developing atopic dermatitis. One milk component, human milk oligosaccharides (HMOs), plays an important role as a prebiotic in establishing the infant gut microbiome and has immunomodulatory effects on the infant immune system. The purpose of this review is to summarize the available information about bacterial members of the intestinal microbiota capable of metabolizing HMOs, the bacterial genes or metabolic products present in the intestinal tract during early life, and the relationship of these genes and metabolic products to the development of AD/eczema in infants. We find that specific HMO metabolism gene sets and the metabolites produced by HMO metabolizing bacteria may enable the protective role of human milk against the development of atopy because of interactions with the immune system. We also identify areas for additional research to further elucidate the relationship between the human milk metabolizing bacteria and atopy. Detailed metagenomic studies of the infant gut microbiota and its associated metabolomes are essential for characterizing the potential impact of human milk-feeding on the development of atopic dermatitis.}, } @article {pmid37020239, year = {2023}, author = {Qian, L and Yu, X and Gu, H and Liu, F and Fan, Y and Wang, C and He, Q and Tian, Y and Peng, Y and Shu, L and Wang, S and Huang, Z and Yan, Q and He, J and Liu, G and Tu, Q and He, Z}, title = {Vertically stratified methane, nitrogen and sulphur cycling and coupling mechanisms in mangrove sediment microbiomes.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {71}, pmid = {37020239}, issn = {2049-2618}, mesh = {Methane/metabolism ; Nitrogen/metabolism ; *Microbiota ; *Desulfovibrio ; Sulfur/metabolism ; Sulfides ; Geologic Sediments/microbiology ; }, abstract = {BACKGROUND: Mangrove ecosystems are considered as hot spots of biogeochemical cycling, yet the diversity, function and coupling mechanism of microbially driven biogeochemical cycling along the sediment depth of mangrove wetlands remain elusive. Here we investigated the vertical profile of methane (CH4), nitrogen (N) and sulphur (S) cycling genes/pathways and their potential coupling mechanisms using metagenome sequencing approaches.

RESULTS: Our results showed that the metabolic pathways involved in CH4, N and S cycling were mainly shaped by pH and acid volatile sulphide (AVS) along a sediment depth, and AVS was a critical electron donor impacting mangrove sediment S oxidation and denitrification. Gene families involved in S oxidation and denitrification significantly (P < 0.05) decreased along the sediment depth and could be coupled by S-driven denitrifiers, such as Burkholderiaceae and Sulfurifustis in the surface sediment (0-15 cm). Interestingly, all S-driven denitrifier metagenome-assembled genomes (MAGs) appeared to be incomplete denitrifiers with nitrate/nitrite/nitric oxide reductases (Nar/Nir/Nor) but without nitrous oxide reductase (Nos), suggesting such sulphide-utilizing groups might be an important contributor to N2O production in the surface mangrove sediment. Gene families involved in methanogenesis and S reduction significantly (P < 0.05) increased along the sediment depth. Based on both network and MAG analyses, sulphate-reducing bacteria (SRB) might develop syntrophic relationships with anaerobic CH4 oxidizers (ANMEs) by direct electron transfer or zero-valent sulphur, which would pull forward the co-existence of methanogens and SRB in the middle and deep layer sediments.

CONCLUSIONS: In addition to offering a perspective on the vertical distribution of microbially driven CH4, N and S cycling genes/pathways, this study emphasizes the important role of S-driven denitrifiers on N2O emissions and various possible coupling mechanisms of ANMEs and SRB along the mangrove sediment depth. The exploration of potential coupling mechanisms provides novel insights into future synthetic microbial community construction and analysis. This study also has important implications for predicting ecosystem functions within the context of environmental and global change. Video Abstract.}, } @article {pmid37019943, year = {2023}, author = {Akhtar, A and Lata, M and Sunsunwal, S and Yadav, A and Lnu, K and Subramanian, S and Ramya, TNC}, title = {New carbohydrate binding domains identified by phage display based functional metagenomic screens of human gut microbiota.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {371}, pmid = {37019943}, issn = {2399-3642}, support = {P41 GM103694/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Genomics ; Carbohydrates ; *Bacteriophages ; }, abstract = {Uncultured microbes represent a huge untapped biological resource of novel genes and gene products. Although recent genomic and metagenomic sequencing efforts have led to the identification of numerous genes that are homologous to existing annotated genes, there remains, yet, an enormous pool of unannotated genes that do not find significant sequence homology to existing annotated genes. Functional metagenomics offers a way to identify and annotate novel gene products. Here, we use functional metagenomics to mine novel carbohydrate binding domains that might aid human gut commensals in adherence, gut colonization, and metabolism of complex carbohydrates. We report the construction and functional screening of a metagenomic phage display library from healthy human fecal samples against dietary, microbial and host polysaccharides/glycoconjugates. We identify several protein sequences that do not find a hit to any known protein domain but are predicted to contain carbohydrate binding module-like folds. We heterologously express, purify and biochemically characterize some of these protein domains and demonstrate their carbohydrate-binding function. Our study reveals several previously unannotated carbohydrate-binding domains, including a levan binding domain and four complex N-glycan binding domains that might be useful for the labeling, visualization, and isolation of these glycans.}, } @article {pmid37019924, year = {2023}, author = {Richter, PK and Blázquez-Sánchez, P and Zhao, Z and Engelberger, F and Wiebeler, C and Künze, G and Frank, R and Krinke, D and Frezzotti, E and Lihanova, Y and Falkenstein, P and Matysik, J and Zimmermann, W and Sträter, N and Sonnendecker, C}, title = {Structure and function of the metagenomic plastic-degrading polyester hydrolase PHL7 bound to its product.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1905}, pmid = {37019924}, issn = {2041-1723}, mesh = {*Hydrolases/metabolism ; Plastics ; *Phthalic Acids ; Polyethylene Terephthalates/chemistry ; }, abstract = {The recently discovered metagenomic-derived polyester hydrolase PHL7 is able to efficiently degrade amorphous polyethylene terephthalate (PET) in post-consumer plastic waste. We present the cocrystal structure of this hydrolase with its hydrolysis product terephthalic acid and elucidate the influence of 17 single mutations on the PET-hydrolytic activity and thermal stability of PHL7. The substrate-binding mode of terephthalic acid is similar to that of the thermophilic polyester hydrolase LCC and deviates from the mesophilic IsPETase. The subsite I modifications L93F and Q95Y, derived from LCC, increased the thermal stability, while exchange of H185S, derived from IsPETase, reduced the stability of PHL7. The subsite II residue H130 is suggested to represent an adaptation for high thermal stability, whereas L210 emerged as the main contributor to the observed high PET-hydrolytic activity. Variant L210T showed significantly higher activity, achieving a degradation rate of 20 µm h[-1] with amorphous PET films.}, } @article {pmid37019260, year = {2023}, author = {Wang, X and Zhang, G and Ding, A and Zheng, L and Xie, E and Yuan, D and Tan, Q and Xing, Y and Wu, H}, title = {Nitrite-resistance mechanisms on wastewater treatment in denitrifying phosphorus removal process revealed by machine learning, co-occurrence, and metagenomics analysis.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {327}, number = {}, pages = {121549}, doi = {10.1016/j.envpol.2023.121549}, pmid = {37019260}, issn = {1873-6424}, mesh = {*Nitrites/analysis ; Phosphorus/metabolism ; Denitrification ; Wastewater ; Metagenomics ; RNA, Ribosomal, 16S ; Bioreactors ; Nitrification ; *Water Purification ; Machine Learning ; Nitrogen/analysis ; Sewage ; Waste Disposal, Fluid/methods ; }, abstract = {Nitrite is a key intermediate in nitrogen metabolism that determines microbial transformations of N and P, greenhouse gas (N2O) emissions, and system nutrient removal efficiency. However, nitrite also exerts toxic effects on microorganisms. A lack of understanding of high nitrite-resistance mechanisms at community- and genome-scale resolutions hinders the optimization for robustness of wastewater treatment systems. Here, we established nitrite-dependent denitrifying and phosphorus removal (DPR) systems under a gradient concentration of nitrite (0, 5, 10, 15, 20, and 25 mg N/L), relying on 16S rRNA gene amplicon and metagenomics to explore high nitrite-resistance mechanism. The results demonstrated that specific taxa were adopted to change the metabolic relationship of the community through phenotypic evolution to resist toxic nitrite contributing to the enhancement of denitrification and inhibition of nitrification and phosphorus removal. The key specific species, Thauera enhanced denitrification, whereas Candidatus Nitrotoga decreased in abundance to maintain partial nitrification. The extinction of Candidatus Nitrotoga induced a simpler restructuring-community, forcing high nitrite-stimulating microbiome to establish a more focused denitrification rather than nitrification or P metabolism in response to nitrite toxicity. Our work provides insights for understanding microbiome adaptation to toxic nitrite and giving theoretical support for operation strategy of nitrite-based wastewater treatment technology.}, } @article {pmid37019259, year = {2023}, author = {Sun, J and Yuan, Y and Cai, L and Zeng, M and Li, X and Yao, F and Chen, W and Huang, Y and Shafiq, M and Xie, Q and Zhang, Q and Wong, N and Wang, Z and Jiao, X}, title = {Metagenomic evidence for antibiotics-driven co-evolution of microbial community, resistome and mobilome in hospital sewage.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {327}, number = {}, pages = {121539}, doi = {10.1016/j.envpol.2023.121539}, pmid = {37019259}, issn = {1873-6424}, mesh = {Angiotensin Receptor Antagonists/pharmacology ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Genes, Bacterial ; *Microbiota ; *Sewage/microbiology ; Metagenome ; }, abstract = {Overconsumption of antibiotics is an immediate cause for the emergence of antimicrobial resistance (AMR) and antibiotic resistant bacteria (ARB), though its environmental impact remains inadequately clarified. There is an urgent need to dissect the complex links underpinning the dynamic co-evolution of ARB and their resistome and mobilome in hospital sewage. Metagenomic and bioinformatic methods were employed to analyze the microbial community, resistome and mobilome in hospital sewage, in relation to data on clinical antibiotic use collected from a tertiary-care hospital. In this study, resistome (1,568 antibiotic resistance genes, ARGs, corresponding to 29 antibiotic types/subtypes) and mobilome (247 types of mobile genetic elements, MGEs) were identified. Networks connecting co-occurring ARGs with MGEs encompass 176 nodes and 578 edges, in which over 19 types of ARGs had significant correlations with MGEs. Prescribed dosage and time-dependent antibiotic consumption were associated with the abundance and distributions of ARGs, and conjugative transfer of ARGs via MGEs. Variation partitioning analyses show that effects of conjugative transfer were most likely the main contributors to transient propagation and persistence of AMR. We have presented the first evidence supporting idea that use of clinical antibiotics is a potent driving force for the development of co-evolving resistome and mobilome, which in turn supports the growth and evolution of ARB in hospital sewage. The use of clinical antibiotics calls for greater attention in antibiotic stewardship and management.}, } @article {pmid37019240, year = {2023}, author = {Wu, Y and Gong, Z and Wang, S and Song, L}, title = {Occurrence and prevalence of antibiotic resistance genes and pathogens in an industrial park wastewater treatment plant.}, journal = {The Science of the total environment}, volume = {880}, number = {}, pages = {163278}, doi = {10.1016/j.scitotenv.2023.163278}, pmid = {37019240}, issn = {1879-1026}, mesh = {Humans ; *Sewage ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Prevalence ; Ecosystem ; Drug Resistance, Microbial/genetics ; }, abstract = {Antibiotic resistance genes (ARGs) and pathogens are emerging environmental pollutants that pose a threat to human health and ecosystem. Industrial park wastewater treatment plants (WWTPs) treat large amounts of comprehensive wastewater derived from industrial production and park human activity, which is possible a source of ARGs and pathogens. Therefore, this study investigated the occurrence and prevalence of ARGs, ARGs hosts and pathogens and assesses the ARGs health risk in the biological treatment process in a large-sale industrial park WWTP using metagenomic analysis and omics-based framework, respectively. Results show that the major ARG subtypes are multidrug resistance genes (MDRGs), macB, tetA(58), evgS, novA, msbA and bcrA and the ARGs main hosts were genus Acidovorax, Pseudomonas, Mesorhizobium. In particular, all determined ARGs genus level hosts are pathogens. The total removal percentage of ARGs, MDRGs and pathogens were 12.77 %, 12.96 % and 25.71 % respectively, suggesting that the present treatment could not efficiently remove these pollutants. The relative abundance of ARGs, MDRGs and pathogens varied along biological treatment process that ARGs and MDRGs were enriched in activated sludge and pathogens were enriched in both secondary sedimentation tank and activated sludge. Among 980 known ARGs, 23 ARGs (e.g., ermB, gadX and tetM) were assigned into risk Rank I with characters of enrichment in the human-associated environment, gene mobility and pathogenicity. The results indicate that industrial park WWTPs might serve as an important source of ARGs, MDRGs, and pathogens. These observations invite further study of the origination, development, dissemination and risk assessment of industrial park WWTPs ARGs and pathogens.}, } @article {pmid37019193, year = {2023}, author = {Ma, T and Yang, N and Xie, Y and Li, Y and Xiao, Q and Li, Q and Jin, H and Zheng, L and Sun, Z and Zuo, K and Kwok, LY and Zhang, H and Lu, N and Liu, W}, title = {Effect of the probiotic strain, Lactiplantibacillus plantarum P9, on chronic constipation: A randomized, double-blind, placebo-controlled study.}, journal = {Pharmacological research}, volume = {191}, number = {}, pages = {106755}, doi = {10.1016/j.phrs.2023.106755}, pmid = {37019193}, issn = {1096-1186}, mesh = {Humans ; Quality of Life ; Constipation/drug therapy/microbiology ; *Gastrointestinal Diseases ; Feces/microbiology ; Double-Blind Method ; *Probiotics/therapeutic use ; *Lactobacillales ; Treatment Outcome ; }, abstract = {Chronic constipation (CC) is a common gastrointestinal condition associated with intestinal inflammation, and the condition considerably impairs patients' quality of life. We conducted a large-scale 42-day randomized, double-blind, placebo-controlled trial to investigate the effect of probiotics in alleviating CC. 163 patients diagnosed with CC (following Rome IV criteria) were randomly divided into probiotic (n = 78; received Lactiplantibacillus plantarum P9 [P9]; 1 ×10[11] CFU/day) and placebo (n = 85; received placebo material) groups. Ingesting P9 significantly improved the weekly mean frequency of complete spontaneous bowel movements (CSBMs) and spontaneous bowel movements (SBMs), while significantly reducing the level of worries and concerns (WO; P < 0.05). Comparing with the placebo group, P9 group was significantly enriched in potentially beneficial bacteria (Lactiplantibacillus plantarum and Ruminococcus_B gnavus), while depriving of several bacterial and phage taxa (Oscillospiraceae sp., Lachnospiraceae sp., and Herelleviridae; P < 0.05). Interesting significant correlations were also observed between some clinical parameters and subjects' gut microbiome, including: negative correlation between Oscillospiraceae sp. and SBMs; positive correlation between WO and Oscillospiraceae sp., Lachnospiraceae sp. Additionally, P9 group had significantly (P < 0.05) more predicted gut microbial bioactive potential involved in the metabolism of amino acids (L-asparagine, L-pipecolinic acid), short-/medium-chain fatty acids (valeric acid and caprylic acid). Furthermore, several metabolites (p-cresol, methylamine, trimethylamine) related to the intestinal barrier and transit decreased significantly after P9 administration (P < 0.05). In short, the constipation relief effect of P9 intervention was accompanied by desirable changes in the fecal metagenome and metabolome. Our findings support the notion of applying probiotics in managing CC.}, } @article {pmid37019075, year = {2023}, author = {Pietruska, A and Bortoluzzi, C and Hauck, R}, title = {A meta-analysis of the effect of Eimeria spp. and/or Clostridium perfringens infection on the microbiota of broiler chickens.}, journal = {Poultry science}, volume = {102}, number = {6}, pages = {102652}, pmid = {37019075}, issn = {1525-3171}, mesh = {Animals ; *Eimeria ; Chickens/microbiology ; *Enteritis/veterinary ; *Poultry Diseases/microbiology ; *Clostridium Infections/veterinary/microbiology ; *Coccidiosis/veterinary/microbiology ; Clostridium perfringens ; *Microbiota ; }, abstract = {Coccidiosis in chickens is caused by Eimeria spp. The infection provides a growth advantage to Clostridium perfringens (CP), frequently leading to necrotic enteritis. One approach to alleviate the negative impacts of the diseases is to improve the bacterial composition in chickens, and many experiments investigating chicken enteric health in recent years include the characterization of the bacterial microbiota. This meta-analysis synthesized the data of studies investigating the intestinal microbiota after infection with coccidia and/or CP to provide a basis for future research. Inclusion criteria were that experiments contained a group infected with one or both pathogens and an uninfected control group, the use of 16SrRNA Illumina sequencing and the availability of raw data. A total of 17 studies could be included. Meta-analyses of 3 different data sets were performed: 1 on data of 9 experiments on chickens infected with coccidia only; the second on data of 4 studies on chickens infected with CP only; the third on raw data of 8 experiments with chickens infected with coccidia and CP. The meta-analysis of relative abundance and alpha diversity of the data sets was performed in R using the SIAMCAT and metafor packages. The number of families of interest identified by the analyses of experiments with infection with coccidia only, CP only and the combined infection were 23, 2, and 29, respectively. There was an overlap of 13 families identified by analyses of experiments with infection with coccidia only and of experiments with the combined infections. Machine learning was not able to find a model to predict changes of the microbiota in either 1 of the 3 analyses. Meta-analyses of functional profiles showed a more uniform reaction to the infections with the relative abundance of many pathways significantly altered. Alpha diversity was not affected by infection with either pathogen or the combination. In conclusion, the heterogeneity of these microbiota studies makes recognizing common trends difficult, although it seems that coccidia infection affects the microbiota more than an infection with CP. Future studies should focus on the bacterial functions that are changed due to these infections using metagenome techniques.}, } @article {pmid37018898, year = {2023}, author = {Rasmussen, JA and Chua, PYS}, title = {Genome-resolving metagenomics reveals wild western capercaillies (Tetrao urogallus) as avian hosts for antibiotic-resistance bacteria and their interactions with the gut-virome community.}, journal = {Microbiological research}, volume = {271}, number = {}, pages = {127372}, doi = {10.1016/j.micres.2023.127372}, pmid = {37018898}, issn = {1618-0623}, mesh = {Animals ; Humans ; *Virome ; *Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Birds/genetics ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Metagenome ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; }, abstract = {The gut microbiome is a critical component of avian health, influencing nutrient uptake and immune functions. While the gut microbiomes of agriculturally important birds have been studied, the microbiomes of wild birds still need to be explored. Filling this knowledge gap could have implications for the microbial rewilding of captive birds and managing avian hosts for antibiotic-resistant bacteria (ARB). Using genome-resolved metagenomics, we recovered 112 metagenome-assembled genomes (MAGs) from the faeces of wild and captive western capercaillies (Tetrao urogallus) (n = 8). Comparisons of bacterial diversity between the wild and captive capercaillies suggest that the reduced diversity in the captive individual could be due to differences in diet. This was further substantiated through the analyses of 517,657 clusters of orthologous groups (COGs), which revealed that gene functions related to amino acids and carbohydrate metabolisms were more abundant in wild capercaillies. Metagenomics mining of resistome identified 751 antibiotic resistance genes (ARGs), of which 40.7 % were specific to wild capercaillies suggesting that capercaillies could be potential reservoirs for hosting ARG-associated bacteria. Additionally, the core resistome shared between wild and captive capercaillies indicates that birds can acquire these ARG-associated bacteria naturally from the environment (43.1 % of ARGs). The association of 26 MAGs with 120 ARGs and 378 virus operational taxonomic units (vOTUs) also suggests a possible interplay between these elements, where putative phages could have roles in modulating the gut microbiota of avian hosts. These findings can have important implications for conservation and human health, such as avian gut microbiota rewilding, identifying the emerging threats or opportunities due to phage-microbe interactions, and monitoring the potential spread of ARG-associated bacteria from wild avian populations.}, } @article {pmid37017810, year = {2023}, author = {Carbo, EC and Mourik, K and Boers, SA and Munnink, BO and Nieuwenhuijse, D and Jonges, M and Welkers, MRA and Matamoros, S and van Harinxma Thoe Slooten, J and Kraakman, MEM and Karelioti, E and van der Meer, D and Veldkamp, KE and Kroes, ACM and Sidorov, I and de Vries, JJC}, title = {A comparison of five Illumina, Ion Torrent, and nanopore sequencing technology-based approaches for whole genome sequencing of SARS-CoV-2.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {42}, number = {6}, pages = {701-713}, pmid = {37017810}, issn = {1435-4373}, mesh = {Humans ; SARS-CoV-2/genetics ; *COVID-19/diagnosis ; *Nanopore Sequencing ; Phylogeny ; Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; Whole Genome Sequencing/methods ; }, abstract = {Rapid identification of the rise and spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern remains critical for monitoring of the efficacy of diagnostics, therapeutics, vaccines, and control strategies. A wide range of SARS-CoV-2 next-generation sequencing (NGS) methods have been developed over the last years, but cross-sequence technology benchmarking studies have been scarce. In the current study, 26 clinical samples were sequenced using five protocols: AmpliSeq SARS-CoV-2 (Illumina), EasySeq RC-PCR SARS-CoV-2 (Illumina/NimaGen), Ion AmpliSeq SARS-CoV-2 (Thermo Fisher), custom primer sets (Oxford Nanopore Technologies (ONT)), and capture probe-based viral metagenomics (Roche/Illumina). Studied parameters included genome coverage, depth of coverage, amplicon distribution, and variant calling. The median SARS-CoV-2 genome coverage of samples with cycle threshold (Ct) values of 30 and lower ranged from 81.6 to 99.8% for, respectively, the ONT protocol and Illumina AmpliSeq protocol. Correlation of coverage with PCR Ct values varied per protocol. Amplicon distribution signatures differed across the methods, with peak differences of up to 4 log10 at disbalanced positions in samples with high viral loads (Ct values ≤ 23). Phylogenetic analyses of consensus sequences showed clustering independent of the workflow used. The proportion of SARS-CoV-2 reads in relation to background sequences, as a (cost-)efficiency metric, was the highest for the EasySeq protocol. The hands-on time was the lowest when using EasySeq and ONT protocols, with the latter additionally having the shortest sequence runtime. In conclusion, the studied protocols differed on a variety of the studied metrics. This study provides data that assist laboratories when selecting protocols for their specific setting.}, } @article {pmid37017718, year = {2023}, author = {Thompson, CC and Tschoeke, D and Coutinho, FH and Leomil, L and Garcia, GD and Otsuki, K and Turcq, BJ and Moreira, LS and Turcq, PFM and Cordeiro, RC and Asp, NE and Thompson, FL}, title = {Diversity of Microbiomes Across a 13,000-Year-Old Amazon Sediment.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2202-2209}, pmid = {37017718}, issn = {1432-184X}, mesh = {*Microbiota/genetics ; Bacteria ; Metagenome ; Rivers/microbiology ; Lakes/microbiology ; Geologic Sediments/microbiology ; }, abstract = {The microbiome is fundamental for understanding bacterial activities in sediments. However, only a limited number of studies have addressed the microbial diversity of Amazonian sediments. Here, we studied the microbiome of sediments from a 13,000-year BP core retrieved in a floodplain lake in Amazonia using metagenomics and biogeochemistry. Our aim was to evaluate the possible environmental influence over a river to a lake transition using a core sample. To this end, we sampled a core in the Airo Lake, a floodplain lake in the Negro River basin. The Negro River is the largest tributary of the Amazon River. The obtained core was divided into three strata: (i) surface, almost complete separation of the Airo Lake from the Negro River when the environment becomes more lentic with greater deposition of organic matter (black-colored sediment); (ii) transitional environment (reddish brown); and (iii) deep, environment with a tendency for greater past influence of the Negro River (brown color). The deepest sample possibly had the greatest influence of the Negro River as it represented the bottom of this river in the past, while the surface sample is the current Airo Lake bottom. In total, six metagenomes were obtained from the three different depth strata (total number of reads: 10.560.701; sequence length: 538 ± 24, mean ± standard deviation). The older (deeper) sediment strata contained a higher abundance of Burkholderia, Chitinophaga, Mucilaginibacter, and Geobacter, which represented ~ 25% of the metagenomic sequences. On the other hand, the more recent sediment strata had mainly Thermococcus, Termophilum, Sulfolobus, Archaeoglobus, and Methanosarcina (in total 11% of the metagenomic sequences). The sequence data were binned into metagenome-assembled genomes (MAGs). The majority of the obtained MAGs (n = 16) corresponded to unknown taxa, suggesting they may belong to new species. The older strata sediment microbiome was enriched with sulfur cycle genes, TCA cycle, YgfZ, and ATP-dependent proteolysis in bacteria. Meanwhile, serine-glyoxylate cycle, stress response genes, bacterial cell division, cell division-ribosomal stress protein cluster, and oxidative stress increased in the younger strata. Metal resistance and antimicrobial resistance genes were found across the entire core, including genes coding for fluoroquinolones, polymyxin, vancomycin, and multidrug resistance transporters. These findings depict the possible microbial diversity during the depositional past events and provided clues of the past microbial metabolism throughout time.}, } @article {pmid37017243, year = {2023}, author = {Dilmore, AH and Martino, C and Neth, BJ and West, KA and Zemlin, J and Rahman, G and Panitchpakdi, M and Meehan, MJ and Weldon, KC and Blach, C and Schimmel, L and Kaddurah-Daouk, R and Dorrestein, PC and Knight, R and Craft, S and , }, title = {Effects of a ketogenic and low-fat diet on the human metabolome, microbiome, and foodome in adults at risk for Alzheimer's disease.}, journal = {Alzheimer's & dementia : the journal of the Alzheimer's Association}, volume = {19}, number = {11}, pages = {4805-4816}, pmid = {37017243}, issn = {1552-5279}, support = {R01 AG046171/AG/NIA NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; RF1 AG059093/AG/NIA NIH HHS/United States ; /NH/NIH HHS/United States ; U01 AG061359/AG/NIA NIH HHS/United States ; RF1 AG057452/AG/NIA NIH HHS/United States ; P30 AG072947/AG/NIA NIH HHS/United States ; RF1 AG051550/AG/NIA NIH HHS/United States ; RF1 AG0151550/AG/NIA NIH HHS/United States ; /NH/NIH HHS/United States ; RF1 AG0151550/AG/NIA NIH HHS/United States ; }, mesh = {United States ; Humans ; Adult ; *Alzheimer Disease/metabolism ; Diet, Fat-Restricted ; *Microbiota ; Metabolome/physiology ; Seizures ; Ketone Bodies ; gamma-Aminobutyric Acid/metabolism ; }, abstract = {INTRODUCTION: The ketogenic diet (KD) is an intriguing therapeutic candidate for Alzheimer's disease (AD) given its protective effects against metabolic dysregulation and seizures. Gut microbiota are essential for KD-mediated neuroprotection against seizures as well as modulation of bile acids, which play a major role in cholesterol metabolism. These relationships motivated our analysis of gut microbiota and metabolites related to cognitive status following a controlled KD intervention compared with a low-fat-diet intervention.

METHODS: Prediabetic adults, either with mild cognitive impairment (MCI) or cognitively normal (CN), were placed on either a low-fat American Heart Association diet or high-fat modified Mediterranean KD (MMKD) for 6 weeks; then, after a 6-week washout period, they crossed over to the alternate diet. We collected stool samples for shotgun metagenomics and untargeted metabolomics at five time points to investigate individuals' microbiome and metabolome throughout the dietary interventions.

RESULTS: Participants with MCI on the MMKD had lower levels of GABA-producing microbes Alistipes sp. CAG:514 and GABA, and higher levels of GABA-regulating microbes Akkermansia muciniphila. MCI individuals with curcumin in their diet had lower levels of bile salt hydrolase-containing microbes and an altered bile acid pool, suggesting reduced gut motility.

DISCUSSION: Our results suggest that the MMKD may benefit adults with MCI through modulation of GABA levels and gut-transit time.}, } @article {pmid37017239, year = {2023}, author = {Yu, H and Li, J and Liu, X and Chen, Z and Li, D and Wei, Y}, title = {Helicobacter pylori bacteremia presenting as seizure and unconsciousness: The brief case.}, journal = {Helicobacter}, volume = {28}, number = {3}, pages = {e12973}, doi = {10.1111/hel.12973}, pmid = {37017239}, issn = {1523-5378}, mesh = {Humans ; Female ; Adult ; *Helicobacter pylori ; *Helicobacter ; *Helicobacter Infections/complications/diagnosis ; *Bacteremia/diagnosis ; Seizures/complications ; Unconsciousness/complications ; }, abstract = {BACKGROUND: Helicobacter pylori bacteremia is rare and difficult to make a definite diagnosis.

CASE PRESENTATION: This is a 40-year-old woman represented as fever and unconsciousness accompanied by tics. She was diagnosed as Helicobacter pylori bacteremia and received emergency endotracheal intubation and antibiotics. Her symptoms resolved and she was discharged from ICU at the sixth day.

CONCLUSIONS: Helicobacter pylori bacteremia is rare and hard to identify. Varied clinical manifestations leading to more difficult to make a definite diagnosis.}, } @article {pmid37017219, year = {2023}, author = {Dindhoria, K and Manyapu, V and Ali, A and Kumar, R}, title = {Unveiling the role of emerging metagenomics for the examination of hypersaline environments.}, journal = {Biotechnology & genetic engineering reviews}, volume = {}, number = {}, pages = {1-39}, doi = {10.1080/02648725.2023.2197717}, pmid = {37017219}, issn = {2046-5556}, abstract = {Hypersaline ecosystems are distributed all over the globe. They are subjected to poly-extreme stresses and are inhabited by halophilic microorganisms possessing multiple adaptations. The halophiles have many biotechnological applications such as nutrient supplements, antioxidant synthesis, salt tolerant enzyme production, osmolyte synthesis, biofuel production, electricity generation etc. However, halophiles are still underexplored in terms of complex ecological interactions and functions as compared to other niches. The advent of metagenomics and the recent advancement of next-generation sequencing tools have made it feasible to investigate the microflora of an ecosystem, its interactions and functions. Both target gene and shotgun metagenomic approaches are commonly employed for the taxonomic, phylogenetic, and functional analyses of the hypersaline microbial communities. This review discusses different types of hypersaline niches, their residential microflora, and an overview of the metagenomic approaches used to investigate them. Various applications, hurdles and the recent advancements in metagenomic approaches have also been focused on here for their better understanding and utilization in the study of hypersaline microbiome.}, } @article {pmid37016727, year = {2023}, author = {Tilves, C and Tanaka, T and Differding, MK and Spira, AP and Chia, CW and Ferrucci, L and Mueller, NT}, title = {The gut microbiome and regional fat distribution: Findings from the Baltimore Longitudinal Study of Aging.}, journal = {Obesity (Silver Spring, Md.)}, volume = {31}, number = {5}, pages = {1425-1435}, pmid = {37016727}, issn = {1930-739X}, support = {K01 HL141589/HL/NHLBI NIH HHS/United States ; T32 HL007024/HL/NHLBI NIH HHS/United States ; R01 AG050507/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Female ; Male ; Body Mass Index ; Longitudinal Studies ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Baltimore ; Aging ; Absorptiometry, Photon ; }, abstract = {OBJECTIVE: The aim of this study was to examine associations of gut microbiome diversity and composition with directly measured regional fat distribution, including central fat, in a large community-based cohort.

METHODS: A cross-sectional investigation was conducted in the Baltimore Longitudinal Study of Aging (N = 815, 55.2% female, 65.9% White). The fecal microbiome was assessed using whole-genome shotgun metagenomic sequencing, and trunk and leg fat was measured using dual x-ray absorptiometry. Multivariable-adjusted associations of regional fat measures, BMI, or waist circumference with microbiome alpha diversity metrics, microbiome beta diversity metrics, and species differential abundance (verified using two compositional statistical approaches) were examined.

RESULTS: Trunk fat, leg fat, BMI, and waist circumference all significantly explained similar amounts of variance in microbiome structure. Differential abundance testing identified 11 bacterial species significantly associated with at least one measure of body composition or anthropometry. Ruminococcus gnavus was strongly and consistently associated with trunk fat mass, which is congruent with prior literature.

CONCLUSIONS: Microbiome diversity and composition, in particular higher abundance of Ruminococcus gnavus, were associated with greater trunk fat, in addition to other measures of obesity. Longitudinal studies are needed to replicate these findings, and if replicated, randomized trials are needed to determine whether interventions targeting microbiome features such as abundance of Ruminococcus gnavus can lead to reductions in trunk fat and its metabolic sequelae.}, } @article {pmid37016686, year = {2023}, author = {Nguyen, NTH and Huang, MB and Liu, FY and Huang, WL and Tran, HT and Hsu, TW and Huang, CL and Chiang, TY}, title = {Deciphering microbial community dynamics along the fermentation course of soy sauce under different temperatures using metagenomic analysis.}, journal = {Bioscience of microbiota, food and health}, volume = {42}, number = {2}, pages = {104-113}, pmid = {37016686}, issn = {2186-6953}, abstract = {Fermented soy sauce consists of microorganisms that exert beneficial effects. However, the microbial community dynamics during the fermentation course is poorly characterized. Soy sauce production is classified into the stages of mash fermentation with koji (S0), brine addition (S1), microbial transformation (S2), flavor creation (S3), and fermentation completion (S4). In this study, microbial succession was investigated across stages at different temperatures using metagenomics analyses. During mash fermentation, Aspergillus dominated the fungal microbiota in all stages, while the bacterial composition was dominated by Bacillus at room temperature and by a diverse composition of enriched lactic acid bacteria (LAB) at a controlled temperature. Compared with a stable fungal composition, bacterial dynamics were mostly attributable to fluctuations of LAB, which break down carbohydrates into lactic acid. After adding brine, increased levels of Enterococcus and decreased levels of Lactococcus from S1 to S4 may reflect differences in salinity tolerance. Staphylococcus, as a fermentation starter at S0, stayed predominant throughout fermentation and hydrolyzed soybean proteins. Meanwhile, Rhizopus and Penicillium may improve the flavor. The acidification of soy sauce was likely attributable to production of organic acids by Bacillus and LAB under room temperature and controlled temperature conditions, respectively. Metagenomic analysis revealed that microbial succession was associated with the fermentation efficiency and flavor enhancement. Controlled temperature nurture more LAB than uncontrolled temperatures and may ensure the production of lactic acid for the development of soy sauce flavor.}, } @article {pmid37016633, year = {2023}, author = {Xiao, YH and Liu, MF and Wu, H and Xu, DR and Zhao, R}, title = {Clinical Efficacy and Diagnostic Value of Metagenomic Next-Generation Sequencing for Pathogen Detection in Patients with Suspected Infectious Diseases: A Retrospective Study from a Large Tertiary Hospital.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {1815-1828}, pmid = {37016633}, issn = {1178-6973}, abstract = {PURPOSE: Metagenomic next-generation sequencing (mNGS) is a powerful yet unbiased method to identify pathogens in suspected infections. However, little is known about its clinical effectiveness. The present study aimed to assess the efficacy of mNGS in routine clinical practice.

PATIENTS AND METHODS: In this single-center retrospective cohort study, 518 patients with suspected infectious diseases were assessed for inclusion. Among them, each patient had undergone mNGS testing; 407 patients had undergone both microbial culture and mNGS testing. The result of mNGS testing was compared to microbial culture performed concurrently. The diagnostic performance of mNGS was evaluated using the comprehensive clinical diagnosis as the reference standard.

RESULTS: There was a significant difference in the positive detection rates of pathogens between mNGS and culture (331/407, 81.3% vs 79/407, 19.4%, P < 0.001). The sensitivity of mNGS was much higher than the culture method (79.5% vs 21.3%, P < 0.001), especially in sample types of sputum and bronchoalveolar lavage fluid (BALF). Notably, the sensitivity of blood mNGS was relatively lower than other sample types (67.4% vs 88.9-93.8%). Pathogen cfDNA load based on standardized stringently mapped read number at the species level of microorganisms (SDSMRN) was significantly lower in blood than in other sample types from the same patient (P = 0.0003). Importantly, mNGS directly led to a change of treatment regimen in 142 (27.4%) cases, including antibiotic escalation (15.3%), antibiotic de-escalation (9.1%), and early definitive diagnosis to initiate appropriate treatment (3.1%).

CONCLUSION: Our in-house mNGS platform significantly improved the sensitivity for the diagnosis of infectious diseases. mNGS has the potential to improve clinical outcomes by optimizing antimicrobial therapy.}, } @article {pmid37016075, year = {2023}, author = {Weeraphan, T and Somphong, A and Poengsungnoen, V and Buaruang, K and Harunari, E and Igarashi, Y and Tanasupawat, S and Phongsopitanun, W}, title = {Bacterial microbiome in tropical lichens and the effect of the isolation method on culturable lichen-derived actinobacteria.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {5483}, pmid = {37016075}, issn = {2045-2322}, mesh = {*Actinobacteria ; *Lichens/microbiology ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota/genetics ; *Actinomycetales ; Phylogeny ; Biodiversity ; }, abstract = {Ten samples of tropical lichens collected from Doi Inthanon, Thailand, were explored for the diversity of their bacterial microbiomes through 16S rRNA-based metagenomics analysis. The five predominant lichen-associated bacteria belonged to the phyla Proteobacteria (31.84%), Planctomycetota (17.08%), Actinobacteriota (15.37%), Verrucomicrobiota (12.17%), and Acidobacteriota (7.87%). The diversity analysis metric showed that Heterodermia contained the highest bacterial species richness. Within the lichens, Ramalina conduplicans and Cladonia rappii showed a distinct bacterial community from the other lichen species. The community of lichen-associated actinobacteria was investigated as a potential source of synthesized biologically active compounds. From the total Operational Taxonomic Units (OTUs) found across the ten different lichen samples, 13.21% were identified as actinobacteria, including the rare actinobacterial genera that are not commonly found, such as Pseudonocardia, Kineosporia, Dactylosporangium, Amycolatopsis, Actinoplanes, and Streptosporangium. Evaluation of the pretreatment method (heat, air-drying, phenol, and flooding) and isolation media used for the culture-dependent actinobacterial isolation revealed that the different pretreatments combined with different isolation media were effective in obtaining several species of actinobacteria. However, metagenomics analyses revealed that there were still several strains, including rare actinobacterial species, that were not isolated. This research strongly suggests that lichens appear to be a promising source for obtaining actinobacteria.}, } @article {pmid37015877, year = {2023}, author = {Mahatmanto, T and Sunarharum, WB and Putri, FA and Susanto, CA and Davian, AO and Murdiyatmo, U}, title = {The microbiology of arabica and robusta coffee cherries: a comparative study of indigenous bacteria with presumptive impact on coffee quality.}, journal = {FEMS microbiology letters}, volume = {370}, number = {}, pages = {}, doi = {10.1093/femsle/fnad024}, pmid = {37015877}, issn = {1574-6968}, mesh = {*Seeds/microbiology ; *Coffea/microbiology ; Bacteria ; Enterobacteriaceae ; Food Handling ; }, abstract = {Arabica and robusta are the two major coffee beans being sold worldwide. It is well recognized that coffee quality is influenced by their origin and the microbiological activities that drive their fermentation. However, in many coffee plantations, information about the natural diversity of bacteria that inhabit the arabica and robusta coffee cherries is limited. Here, we sampled arabica and robusta coffee cherries from Malang, East Java, Indonesia, then sequenced and analysed their bacterial composition. We found that: (a) arabica cherries contained bacteria with less diversity and abundance compared with robusta; (b) both coffee cherries were heavily populated by extremophiles, presumably dispersed from volcanic activities; (c) groups known to be involved in coffee fermentation such as lactic acid bacteria, acetic acid bacteria, Enterobacteria, and soil-associated bacteria were present in both arabica and robusta coffee cherries, and (d) arabica cherries were dominated by Leuconostoc pseudomesenteroides. These findings highlight that coffee cherry bacteria are highly diverse, the majority of which might come from the environment, with some potentially beneficial or detrimental to coffee quality. Knowledge of the natural microbial diversity of coffee cherries may be useful for the development of coffee fermentation technologies to yield coffee beans with consistent quality.}, } @article {pmid37015876, year = {2023}, author = {Crost, EH and Coletto, E and Bell, A and Juge, N}, title = {Ruminococcus gnavus: friend or foe for human health.}, journal = {FEMS microbiology reviews}, volume = {47}, number = {2}, pages = {}, pmid = {37015876}, issn = {1574-6976}, support = {BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Adult ; Humans ; *Gastrointestinal Microbiome ; Gastrointestinal Tract ; *Ruminococcus/physiology ; }, abstract = {Ruminococcus gnavus was first identified in 1974 as a strict anaerobe in the gut of healthy individuals, and for several decades, its study has been limited to specific enzymes or bacteriocins. With the advent of metagenomics, R. gnavus has been associated both positively and negatively with an increasing number of intestinal and extraintestinal diseases from inflammatory bowel diseases to neurological disorders. This prompted renewed interest in understanding the adaptation mechanisms of R. gnavus to the gut, and the molecular mediators affecting its association with health and disease. From ca. 250 publications citing R. gnavus since 1990, 94% were published in the last 10 years. In this review, we describe the biological characterization of R. gnavus, its occurrence in the infant and adult gut microbiota and the factors influencing its colonization of the gastrointestinal tract; we also discuss the current state of our knowledge on its role in host health and disease. We highlight gaps in knowledge and discuss the hypothesis that differential health outcomes associated with R. gnavus in the gut are strain and niche specific.}, } @article {pmid37014908, year = {2023}, author = {Cumsille, A and Durán, RE and Rodríguez-Delherbe, A and Saona-Urmeneta, V and Cámara, B and Seeger, M and Araya, M and Jara, N and Buil-Aranda, C}, title = {GenoVi, an open-source automated circular genome visualizer for bacteria and archaea.}, journal = {PLoS computational biology}, volume = {19}, number = {4}, pages = {e1010998}, pmid = {37014908}, issn = {1553-7358}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Genomics/methods ; Software ; Genome, Microbial ; }, abstract = {The increase in microbial sequenced genomes from pure cultures and metagenomic samples reflects the current attainability of whole-genome and shotgun sequencing methods. However, software for genome visualization still lacks automation, integration of different analyses, and customizable options for non-experienced users. In this study, we introduce GenoVi, a Python command-line tool able to create custom circular genome representations for the analysis and visualization of microbial genomes and sequence elements. It is designed to work with complete or draft genomes, featuring customizable options including 25 different built-in color palettes (including 5 color-blind safe palettes), text formatting options, and automatic scaling for complete genomes or sequence elements with more than one replicon/sequence. Using a Genbank format file as the input file or multiple files within a directory, GenoVi (i) visualizes genomic features from the GenBank annotation file, (ii) integrates a Cluster of Orthologs Group (COG) categories analysis using DeepNOG, (iii) automatically scales the visualization of each replicon of complete genomes or multiple sequence elements, (iv) and generates COG histograms, COG frequency heatmaps and output tables including general stats of each replicon or contig processed. GenoVi's potential was assessed by analyzing single and multiple genomes of Bacteria and Archaea. Paraburkholderia genomes were analyzed to obtain a fast classification of replicons in large multipartite genomes. GenoVi works as an easy-to-use command-line tool and provides customizable options to automatically generate genomic maps for scientific publications, educational resources, and outreach activities. GenoVi is freely available and can be downloaded from https://github.com/robotoD/GenoVi.}, } @article {pmid37014230, year = {2023}, author = {García-Roldán, A and de la Haba, RR and Vera-Gargallo, B and Sánchez-Porro, C and Ventosa, A}, title = {Metagenomes of a Crystallizer Pond from Isla Cristina Saltern in Spain.}, journal = {Microbiology resource announcements}, volume = {12}, number = {5}, pages = {e0003923}, pmid = {37014230}, issn = {2576-098X}, support = {PID2020-118136GB-I00 funded by MCIN/AEI/10.13039/501100011033//Ministerio de Ciencia e Innovación (MCIN)/ ; P20_01066//Consejería de Economía, Innovación, Ciencia y Empleo, Junta de Andalucía (Ministry of Economy, Innovation, Science and Employment, Government of Andalucia)/ ; }, abstract = {The metagenomic sequences of the prokaryotic microbiota from the brine of a crystallizer pond with 42% (wt/vol) salinity of a saltern located in Isla Cristina, Huelva, southwest Spain, were obtained by Illumina. Haloarchaea and members of the bacterial genus Salinibacter were the most abundant prokaryotes.}, } @article {pmid37014227, year = {2023}, author = {Taş, N and Conejo, N and Salmon, VG}, title = {Metagenomes and Metagenome-Assembled Genome Sequences from Nitrogen-Fixing Alder Nodules.}, journal = {Microbiology resource announcements}, volume = {12}, number = {5}, pages = {e0126622}, pmid = {37014227}, issn = {2576-098X}, support = {NGEE Arctic//U.S. Department of Energy (DOE)/ ; }, abstract = {Bacterial nitrogen (N) fixation in alder nodules is a key process providing nitrogen to nutrient-limited arctic biomes. Here, 45 prokaryotic metagenome-assembled genome (MAG) sequences from root nodules of arctic alder are reported.}, } @article {pmid37014219, year = {2023}, author = {Williams, C and Macalady, J and Grettenberger, C}, title = {Metagenome-Assembled Genomes from Appalachian Acid Mine Drainage Sites.}, journal = {Microbiology resource announcements}, volume = {12}, number = {5}, pages = {e0128022}, pmid = {37014219}, issn = {2576-098X}, support = {S11AC20005//U.S. Office of Surface Mining and Reclamation and Enforcement/ ; //Geological Society of America Graduate Student Research Grant/ ; }, abstract = {Here, we report 7 metagenome-assembled genomes (MAGs) isolated from acid mine drainage sites in the eastern United States. Three genomes are Archaea, including two from the phylum Thermoproteota and one from Euryarchaeota. Four genomes are bacterial, with one from the phylum Candidatus Eremiobacteraeota (formerly WPS-2), one from Acidimicrobiales (Actinobacteria), and two from Gallionellaceae (Proteobacteria).}, } @article {pmid37013357, year = {2023}, author = {Mills, DA and German, JB and Lebrilla, CB and Underwood, MA}, title = {Translating neonatal microbiome science into commercial innovation: metabolism of human milk oligosaccharides as a basis for probiotic efficacy in breast-fed infants.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2192458}, pmid = {37013357}, issn = {1949-0984}, support = {R21 AT006180/AT/NCCIH NIH HHS/United States ; R01 AT007079/AT/NCCIH NIH HHS/United States ; R01 AT008759/AT/NCCIH NIH HHS/United States ; R01 HD061923/HD/NICHD NIH HHS/United States ; R01 HD065122/HD/NICHD NIH HHS/United States ; U01 CA179582/CA/NCI NIH HHS/United States ; F32 HD093185/HD/NICHD NIH HHS/United States ; F32 AT006642/AT/NCCIH NIH HHS/United States ; F32 AT008533/AT/NCCIH NIH HHS/United States ; }, mesh = {Infant, Newborn ; Female ; Infant ; Humans ; Milk, Human/metabolism ; *Gastrointestinal Microbiome ; Bifidobacterium/metabolism ; *Probiotics ; Feces/microbiology ; *Microbiota ; Oligosaccharides/metabolism ; }, abstract = {For over a century, physicians have witnessed a common enrichment of bifidobacteria in the feces of breast-fed infants that was readily associated with infant health status. Recent advances in bacterial genomics, metagenomics, and glycomics have helped explain the nature of this unique enrichment and enabled the tailored use of probiotic supplementation to restore missing bifidobacterial functions in at-risk infants. This review documents a 20-year span of discoveries that set the stage for the current use of human milk oligosaccharide-consuming bifidobacteria to beneficially colonize, modulate, and protect the intestines of at-risk, human milk-fed, neonates. This review also presents a model for probiotic applications wherein bifidobacterial functions, in the form of colonization and HMO-related catabolic activity in situ, represent measurable metabolic outcomes by which probiotic efficacy can be scored toward improving infant health.}, } @article {pmid37013046, year = {2023}, author = {Nguyen, ADD and Shanteau-Jackson, M and LaFramboise, T}, title = {Metagenomic markings of myeloid malignancies.}, journal = {Genes & diseases}, volume = {10}, number = {1}, pages = {4-6}, pmid = {37013046}, issn = {2352-3042}, } @article {pmid37012285, year = {2023}, author = {Yang, X and Zhang, M and Zhang, Y and Wei, H and Guan, Q and Dong, C and Deng, S and Tun, HM and Xia, Y}, title = {Ecological change of the gut microbiota during pregnancy and progression to dyslipidemia.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {14}, pmid = {37012285}, issn = {2055-5008}, mesh = {Humans ; Pregnancy ; Female ; *Gastrointestinal Microbiome/physiology ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; *Microbiota ; Bacteroidetes ; Lipids ; }, abstract = {The composition of the gut microbiome was previously found to be associated with clinical responses to dyslipidemia, but there is limited consensus on the dynamic change of the gut microbiota during pregnancy and the specific microbiome characteristics linked to dyslipidemia in pregnant women. We collected fecal samples from 513 pregnant women at multiple time points during pregnancy in a prospective cohort. Taxonomic composition and functional annotations were determined by 16S rRNA amplicon sequencing and shotgun metagenomic sequencing. The predictive potential of gut microbiota on the risk of dyslipidemia was determined. The gut microbiome underwent dynamic changes during pregnancy, with significantly lower alpha diversity observed in dyslipidemic patients compared to their healthy counterparts. Several genera, including Bacteroides, Paraprevotella, Alistipes, Christensenellaceae R7 group, Clostridia UCG-014, and UCG-002 were negatively associated with lipid profiles and dyslipidemia. Further metagenomic analysis recognized a common set of pathways involved in gastrointestinal inflammation, where disease-specific microbes played an important role. Machine learning analysis confirmed the link between the microbiome and its progression to dyslipidemia, with a micro-averaged AUC of 0.824 (95% CI: 0.782-0.855) combined with blood biochemical data. Overall, the human gut microbiome, including Alistipes and Bacteroides, was associated with the lipid profile and maternal dyslipidemia during pregnancy by perturbing inflammatory functional pathways. Gut microbiota combined with blood biochemical data at the mid-pregnancy stage could predict the risk of dyslipidemia in late pregnancy. Therefore, the gut microbiota may represent a potential noninvasive diagnostic and therapeutic strategy for preventing dyslipidemia in pregnancy.}, } @article {pmid37011852, year = {2023}, author = {Guo, F and Luo, Y and Nie, W and Xiong, Z and Yang, X and Yan, J and Liu, T and Chen, M and Chen, Y}, title = {Biochar boosts nitrate removal in constructed wetlands for secondary effluent treatment: Linking nitrate removal to the metabolic pathway of denitrification and biochar properties.}, journal = {Bioresource technology}, volume = {379}, number = {}, pages = {129000}, doi = {10.1016/j.biortech.2023.129000}, pmid = {37011852}, issn = {1873-2976}, mesh = {*Nitrates ; *Denitrification ; Wetlands ; Charcoal ; Nitrogen ; Metabolic Networks and Pathways ; Waste Disposal, Fluid/methods ; }, abstract = {Constructed wetlands (CWs) amended with biochar have attracted much attention for nitrate removal treating secondary effluent. However, little is acknowledged about the linkage among the nitrate removal performance, microbial metabolic pathway of nitrate, and biochar properties. Herein, biochars pyrolyzed under 300 °C, 500 °C, and 700 °C (BC300, BC500, and BC700, respectively) were used in CWs to reveal the relationship. Results showed that CWs amended with BC300 (59.73%), BC500 (53.27%), and BC700 (49.07%) achieved higher nitrogen removal efficiency, compared with the control (39.51%). Metagenomic analysis showed that biochars could enrich the genes, which encoded key enzymes (adenosine triphosphate production, and electrons generation, transportation, and consumption) involved in carbon and nitrate metabolism. Further, biochar pyrolyzed under lower temperature, with higher oxygen content, molar O/C ratio, and the electron donating capacity, in CWs could obtain higher nitrate removal efficiency. Overall, this research offers new understandings for the promotion of denitrification in CWs amended with biochar.}, } @article {pmid37011797, year = {2023}, author = {Wang, L and Zhu, M and Li, Y and Zhao, Z}, title = {Assessing the effects of aquaculture on tidal flat ecological status using multi-metrics interaction-based index of biotic integrity (Mt-IBI).}, journal = {Environmental research}, volume = {228}, number = {}, pages = {115789}, doi = {10.1016/j.envres.2023.115789}, pmid = {37011797}, issn = {1096-0953}, mesh = {Humans ; *Ecosystem ; Benchmarking ; Environmental Monitoring/methods ; *Microbiota ; Nitrogen ; Aquaculture ; Rivers ; China ; }, abstract = {Given tidal flat special environmental conditions and the degree of pollution caused by human activities, there is an urgent need to quantitatively assess their ecological status. Bioindication has become an indispensable part of environmental quality monitoring on account of its sensitivity to environmental disturbance. Thus, this study used bio-indicators to establish a multi-metrics-based index of biotic integrity (Mt-IBI) to evaluate the ecological status of the tidal flats with/without aquaculture through metagenomic sequencing. Four core indexes that were significantly correlated to other indexes with redundancy (p < 0.05), including Escherichia, beta-lactam antibiotic resistance genes, cellulase and xyloglucanases and the keystone species with 21° in the network, were selected after the screening processes. By implementing Mt-IBI in the tidal flats, the ecological health of the sampling sites was categorized into three levels, with Mt-IBI values of 2.01-2.63 (severe level), 2.81-2.93 (moderate level) and 3.23-4.18 (mild level), respectively. Through SEM analysis, water chemical oxygen demand and antibiotics were determined to be the primary controlling factors of the ecological status of tidal flat regions influenced by aquaculture, followed by salinity and total nitrogen. It is worth noting that the alteration of microbial communities impacted ecological status through the mediation of antibiotics. It is hoped that the results of our study will provide a theoretical basis for coastal environment restoration and that the use of Mt-IBI to assess ecosystem status in different aquatic environments will be further popularized in the future.}, } @article {pmid37223356, year = {2022}, author = {Rigou, S and Christo-Foroux, E and Santini, S and Goncharov, A and Strauss, J and Grosse, G and Fedorov, AN and Labadie, K and Abergel, C and Claverie, JM}, title = {Metagenomic survey of the microbiome of ancient Siberian permafrost and modern Kamchatkan cryosols.}, journal = {microLife}, volume = {3}, number = {}, pages = {uqac003}, pmid = {37223356}, issn = {2633-6693}, abstract = {In the context of global warming, the melting of Arctic permafrost raises the threat of a reemergence of microorganisms some of which were shown to remain viable in ancient frozen soils for up to half a million years. In order to evaluate this risk, it is of interest to acquire a better knowledge of the composition of the microbial communities found in this understudied environment. Here, we present a metagenomic analysis of 12 soil samples from Russian Arctic and subarctic pristine areas: Chukotka, Yakutia and Kamchatka, including nine permafrost samples collected at various depths. These large datasets (9.2 × 10[11] total bp) were assembled (525 313 contigs > 5 kb), their encoded protein contents predicted, and then used to perform taxonomical assignments of bacterial, archaeal and eukaryotic organisms, as well as DNA viruses. The various samples exhibited variable DNA contents and highly diverse taxonomic profiles showing no obvious relationship with their locations, depths or deposit ages. Bacteria represented the largely dominant DNA fraction (95%) in all samples, followed by archaea (3.2%), surprisingly little eukaryotes (0.5%), and viruses (0.4%). Although no common taxonomic pattern was identified, the samples shared unexpected high frequencies of β-lactamase genes, almost 0.9 copy/bacterial genome. In addition to known environmental threats, the particularly intense warming of the Arctic might thus enhance the spread of bacterial antibiotic resistances, today's major challenge in public health. β-Lactamases were also observed at high frequency in other types of soils, suggesting their general role in the regulation of bacterial populations.}, } @article {pmid37124355, year = {2023}, author = {Thirion, F and Speyer, H and Hansen, TH and Nielsen, T and Fan, Y and Le Chatelier, E and Fromentin, S and Berland, M and Plaza Oñate, F and Pons, N and Galleron, N and Levenez, F and Markó, L and Birkner, T and Jørgensen, T and Forslund, SK and Vestergaard, H and Hansen, T and Nordentoft, M and Mors, O and Benros, ME and Pedersen, O and Ehrlich, SD}, title = {Alteration of Gut Microbiome in Patients With Schizophrenia Indicates Links Between Bacterial Tyrosine Biosynthesis and Cognitive Dysfunction.}, journal = {Biological psychiatry global open science}, volume = {3}, number = {2}, pages = {283-291}, pmid = {37124355}, issn = {2667-1743}, abstract = {BACKGROUND: Schizophrenia (SCZ) is a heterogeneous neuropsychiatric disorder for which current treatment has insufficient efficacy and severe adverse effects. The modifiable gut microbiome might be a potential target for intervention to improve neurobiological functions through the gut-microbiome-brain axis.

METHODS: In this case-control study, gut microbiota of 132 patients with SCZ and increased waist circumference were compared with gut microbiota of two age- and sex-matched control groups, composed of 132 healthy individuals and 132 individuals with metabolic syndrome. Shotgun sequencing was used to characterize fecal samples at the taxonomic and functional levels. Cognition of the patients with SCZ was evaluated using the Brief Assessment of Cognition instrument.

RESULTS: SCZ gut microbiota differed significantly from those of healthy control subjects and individuals with metabolic syndrome in terms of richness and global composition. SCZ gut microbiota were notably enriched in Flavonifractor plautii, Collinsella aerofaciens, Bilophila wadsworthia, and Sellimonas intestinalis, while depleted in Faecalibacterium prausnitzii, Ruminococcus lactaris, Ruminococcus bicirculans, and Veillonella rogosae. Functional potential of the gut microbiota accounted for 11% of cognition variability. In particular, the bacterial functional module for synthesizing tyrosine, a precursor for dopamine, was in SCZ cases positively associated with cognitive score (ρ = 0.34, q ≤ .1).

CONCLUSIONS: Overall, this study shows that the gut microbiome of patients with SCZ differs greatly from that of healthy control subjects or individuals with metabolic syndrome. Cognitive function of patients with SCZ is associated with the potential for gut bacterial biosynthesis of tyrosine, a precursor for dopamine, suggesting that gut microbiota might be an intervention target for alleviation of cognitive dysfunction in SCZ.}, } @article {pmid37073225, year = {2022}, author = {Chen, H and Li, DH and Jiang, AJ and Li, XG and Wu, SJ and Chen, JW and Qu, MJ and Qi, XQ and Dai, J and Zhao, R and Zhang, WJ and Liu, SS and Wu, LF}, title = {Metagenomic analysis reveals wide distribution of phototrophic bacteria in hydrothermal vents on the ultraslow-spreading Southwest Indian Ridge.}, journal = {Marine life science & technology}, volume = {4}, number = {2}, pages = {255-267}, pmid = {37073225}, issn = {2662-1746}, abstract = {UNLABELLED: Deep-sea hydrothermal vents are known as chemosynthetic ecosystems. However, high temperature vents emit light that hypothetically can drive photosynthesis in this habitat. Metagenomic studies have sporadically reported the occurrence of phototrophic populations such as cyanobacteria in hydrothermal vents. To determine how geographically and taxonomically widespread phototrophs are in deep-sea hydrothermal vents, we collected samples from three niches in a hydrothermal vent on the Southwest Indian Ridge and carried out an integrated metagenomic analysis. We determined the typical community structures of microorganisms found in active venting fields and identified populations of known potential chlorophototrophs and retinalophototrophs. Complete chlorophyll biosynthetic pathways were identified in all samples. By contrast, proteorhodopsins were only found in active beehive smoker diffusers. Taxonomic groups possessing potential phototrophy dependent on semiconductors present in hydrothermal vents were also found in these samples. This systematic comparative metagenomic study reveals the widespread distribution of phototrophic bacteria in hydrothermal vent fields. Our results support the hypothesis that the ocean is a seed bank of diverse microorganisms. Geothermal vent light may provide energy and confer a competitive advantage on phototrophs to proliferate in hydrothermal vent ecosystems.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-021-00121-y.}, } @article {pmid37073226, year = {2022}, author = {Xie, ZX and Yan, KQ and Kong, LF and Gai, YB and Jin, T and He, YB and Wang, YY and Chen, F and Lin, L and Lin, ZL and Xu, HK and Shao, ZZ and Liu, SQ and Wang, DZ}, title = {Metabolic tuning of a stable microbial community in the surface oligotrophic Indian Ocean revealed by integrated meta-omics.}, journal = {Marine life science & technology}, volume = {4}, number = {2}, pages = {277-290}, pmid = {37073226}, issn = {2662-1746}, abstract = {UNLABELLED: Understanding the mechanisms, structuring microbial communities in oligotrophic ocean surface waters remains a major ecological endeavor. Functional redundancy and metabolic tuning are two mechanisms that have been proposed to shape microbial response to environmental forcing. However, little is known about their roles in the oligotrophic surface ocean due to less integrative characterization of community taxonomy and function. Here, we applied an integrated meta-omics-based approach, from genes to proteins, to investigate the microbial community of the oligotrophic northern Indian Ocean. Insignificant spatial variabilities of both genomic and proteomic compositions indicated a stable microbial community that was dominated by Prochlorococcus, Synechococcus, and SAR11. However, fine tuning of some metabolic functions that are mainly driven by salinity and temperature was observed. Intriguingly, a tuning divergence occurred between metabolic potential and activity in response to different environmental perturbations. Our results indicate that metabolic tuning is an important mechanism for sustaining the stability of microbial communities in oligotrophic oceans. In addition, integrated meta-omics provides a powerful tool to comprehensively understand microbial behavior and function in the ocean.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-021-00119-6.}, } @article {pmid37124704, year = {2021}, author = {Chiba, Y and Oiki, S and Zhao, Y and Nagano, Y and Urayama, SI and Hagiwara, D}, title = {Splitting of RNA-dependent RNA polymerase is common in Narnaviridae: Identification of a type II divided RdRp from deep-sea fungal isolates.}, journal = {Virus evolution}, volume = {7}, number = {2}, pages = {veab095}, pmid = {37124704}, issn = {2057-1577}, abstract = {Until recently, it was accepted that RNA-dependent RNA polymerase (RdRp) is the only essential gene for non-retro RNA viruses and is encoded by a single open reading frame (ORF) in their genomes. However, divided RdRps that are coded by two ORFs were discovered in fungal RNA viruses in a few independent reports. This discovery showed higher plasticity of viral RdRp than was expected. Among these divided RdRps, the division site was common; specifically, the first part of the RdRp contains motifs F, A, and B, whereas the latter part possesses motifs C and D. These RdRps are designated as type I divided RdRp and have been limited to viruses in a specific clade of Narnaviridae. In this study, to further understand the plasticity of RdRp, we explored viruses from deep sea-derived fungal strains as an untapped resource with a focus on Aspergillus section Versicolores. Seven strains were found to be infected by a total of 13 viruses, and the viral RNA genomes were determined by fragmented and primer-ligated double-stranded RNA sequencing technology. Among them, six strains belong to Narnaviridae. One of the strains, Aspergillus tennesseensis narnavirus 1, which infects an Aspergillus tennesseensis, has a divided RdRp with a new division site (referred to as type II divided RdRp). A couple of sequences for possible type II divided RdRps were also detected in public metagenomic data sets. Our findings reveal that different types of divisions in RdRp are present in the virosphere, and two types of RdRp splitting occurred independently within Narnaviridae.}, } @article {pmid37073260, year = {2021}, author = {Wang, B and Zheng, X and Zhang, H and Yu, X and Lian, Y and Yang, X and Yu, H and Hu, R and He, Z and Xiao, F and Yan, Q}, title = {Metagenomic insights into the effects of submerged plants on functional potential of microbial communities in wetland sediments.}, journal = {Marine life science & technology}, volume = {3}, number = {4}, pages = {405-415}, pmid = {37073260}, issn = {2662-1746}, abstract = {UNLABELLED: Submerged plants in wetlands play important roles as ecosystem engineers to improve self-purification and promote elemental cycling. However, their effects on the functional capacity of microbial communities in wetland sediments remain poorly understood. Here, we provide detailed metagenomic insights into the biogeochemical potential of microbial communities in wetland sediments with and without submerged plants (i.e., Vallisneria natans). A large number of functional genes involved in carbon (C), nitrogen (N) and sulfur (S) cycling were detected in the wetland sediments. However, most functional genes showed higher abundance in sediments with submerged plants than in those without plants. Based on the comparison of annotated functional genes in the N and S cycling databases (i.e., NCycDB and SCycDB), we found that genes involved in nitrogen fixation (e.g., nifD/H/K/W), assimilatory nitrate reduction (e.g., nasA and nirA), denitrification (e.g., nirK/S and nosZ), assimilatory sulfate reduction (e.g., cysD/H/J/N/Q and sir), and sulfur oxidation (e.g., glpE, soeA, sqr and sseA) were significantly higher (corrected p < 0.05) in vegetated vs. unvegetated sediments. This could be mainly driven by environmental factors including total phosphorus, total nitrogen, and C:N ratio. The binning of metagenomes further revealed that some archaeal taxa could have the potential of methane metabolism including hydrogenotrophic, acetoclastic, and methylotrophic methanogenesis, which are crucial to the wetland methane budget and carbon cycling. This study opens a new avenue for linking submerged plants with microbial functions, and has further implications for understanding global carbon, nitrogen and sulfur cycling in wetland ecosystems.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-021-00100-3.}, } @article {pmid37073219, year = {2022}, author = {Lu, X and Wang, K and Mou, X}, title = {Metagenomes of polyamine-transforming bacterioplankton along a nearshore-open ocean transect.}, journal = {Marine life science & technology}, volume = {4}, number = {2}, pages = {268-276}, pmid = {37073219}, issn = {2662-1746}, abstract = {UNLABELLED: Short-chained aliphatic polyamines (PAs) have recently been recognized as an important carbon, nitrogen, and/or energy source for marine bacterioplankton. To study the genes and taxa involved in the transformations of different PA compounds and their potential variations among marine systems, we collected surface bacterioplankton from nearshore, offshore, and open ocean stations in the Gulf of Mexico and examined their metagenomic responses to additions of single PA model compounds (putrescine, spermidine, or spermine). Genes affiliated with PA uptake and all three known PA degradation pathways, i.e., transamination, γ-glutamylation, and spermidine cleavage, were significantly enriched in most PA-treated metagenomes. In addition, identified PA-transforming taxa were mostly the alpha and gamma classes of Proteobacteria, with less important contributions from members of Betaproteobacteria, Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and Planctomycetes. These findings suggest that PA transformations are ubiquitous, have diverse pathways, and are carried out by a broad range of the bacterioplankton taxa in the Gulf of Mexico. Identified PA-transforming bacterial genes and taxa were different among nearshore, offshore, and open ocean sites, but were little different among individual compound-amended metagenomes at any specific site. These observations further indicate that PA-transforming taxa and genes are site-specific and with high similarities among PA compounds.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-021-00114-x.}, } @article {pmid37284285, year = {2021}, author = {Ma, Y and Fort, T and Marais, A and Lefebvre, M and Theil, S and Vacher, C and Candresse, T}, title = {Leaf-associated fungal and viral communities of wild plant populations differ between cultivated and natural ecosystems.}, journal = {Plant-environment interactions (Hoboken, N.J.)}, volume = {2}, number = {2}, pages = {87-99}, pmid = {37284285}, issn = {2575-6265}, abstract = {Plants are colonized by diverse fungal and viral communities that influence their growth and survival as well as ecosystem functioning. Viruses interact with both plants and the fungi they host. Our understanding of plant-fungi-virus interactions is very limited, especially in wild plants. Combining metagenomic and culturomic approaches, we assessed the richness, diversity, and composition of leaf-associated fungal and viral communities from pools of herbaceous wild plants representative of four sites corresponding to cultivated or natural ecosystems. We identified 161 fungal families and 18 viral families comprising 249 RNA-dependent RNA polymerase-based operational taxonomic units (RdRp OTUs) from leaves. Fungal culturomics captured 12.3% of the fungal diversity recovered with metagenomic approaches and, unexpectedly, retrieved viral OTUs that were almost entirely different from those recovered by leaf metagenomics. Ecosystem management had a significant influence on both leaf mycobiome and virome, with a higher fungal community richness in natural ecosystems and a higher viral family richness in cultivated ecosystems, suggesting that leaf-associated fungal and viral communities are under the influence of different ecological drivers. Both the leaf-associated fungal and viral community compositions showed a strong site-specificity. Further research is needed to confirm these trends and unravel the factors structuring plant-fungi-virus interactions in wild plant populations.}, } @article {pmid37073339, year = {2021}, author = {Hu, H and Natarajan, VP and Wang, F}, title = {Towards enriching and isolation of uncultivated archaea from marine sediments using a refined combination of conventional microbial cultivation methods.}, journal = {Marine life science & technology}, volume = {3}, number = {2}, pages = {231-242}, pmid = {37073339}, issn = {2662-1746}, abstract = {UNLABELLED: The archaea that can be readily cultivated in the laboratory are only a small fraction of the total diversity that exists in nature. Although molecular ecology methods, such as metagenomic sequencing, can provide valuable information independent of cell cultivation, it is only through cultivation-based experiments that they may be fully characterized, both for their physiological and ecological properties. Here, we report our efforts towards enriching and isolation of uncultivated archaea from marine sediments using a refined combination of conventional microbial cultivation methods. Initially, cells were retrieved from the sediment samples through a cell extraction procedure and the sediment-free mixed cells were then divided into different size-range fractions by successive filtration through 0.8 µm, 0.6 µm and 0.2 µm membranes. Archaeal 16S rRNA gene analyses indicated noticeable retention of different archaeal groups in different fractions. For each fraction, supplementation with a variety of defined substrates (e.g., methane, sulfate, and lignin) and stepwise dilutions led to highly active enrichment cultures of several archaeal groups with Bathyarchaeota most prominently enriched. Finally, using a roll-bottle technique, three co-cultures consisting of Bathyarchaeota (subgroup-8) and a bacterial species affiliated with either Pseudomonas or Glutamicibacter were obtained. Our results demonstrate that a combination of cell extraction, size fractionation, and roll-bottle isolation methods could be a useful protocol for the successful enrichment and isolation of numerous slow-growing archaeal groups from marine sediments.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s42995-021-00092-0.}, } @article {pmid37073293, year = {2021}, author = {Ding, W and Wang, R and Liang, Z and Zhang, R and Qian, PY and Zhang, W}, title = {Expanding our understanding of marine viral diversity through metagenomic analyses of biofilms.}, journal = {Marine life science & technology}, volume = {3}, number = {3}, pages = {395-404}, pmid = {37073293}, issn = {2662-1746}, abstract = {Recent metagenomics surveys have provided insights into the marine virosphere. However, these surveys have focused solely on viruses in seawater, neglecting those associated with biofilms. By analyzing 1.75 terabases of biofilm metagenomic data, 3974 viral sequences were identified from eight locations around the world. Over 90% of these viral sequences were not found in previously reported datasets. Comparisons between biofilm and seawater metagenomes identified viruses that are endemic to the biofilm niche. Analysis of viral sequences integrated within biofilm-derived microbial genomes revealed potential functional genes for trimeric autotransporter adhesin and polysaccharide metabolism, which may contribute to biofilm formation by the bacterial hosts. However, more than 70% of the genes could not be annotated. These findings show marine biofilms to be a reservoir of novel viruses and have enhanced our understanding of natural virus-bacteria ecosystems.}, } @article {pmid37118004, year = {2021}, author = {Zhang, X and Zhong, H and Li, Y and Shi, Z and Ren, H and Zhang, Z and Zhou, X and Tang, S and Han, X and Lin, Y and Yang, F and Wang, D and Fang, C and Fu, Z and Wang, L and Zhu, S and Hou, Y and Xu, X and Yang, H and Wang, J and Kristiansen, K and Li, J and Ji, L}, title = {Sex- and age-related trajectories of the adult human gut microbiota shared across populations of different ethnicities.}, journal = {Nature aging}, volume = {1}, number = {1}, pages = {87-100}, pmid = {37118004}, issn = {2662-8465}, mesh = {Humans ; Female ; Adult ; Male ; *Gastrointestinal Microbiome/genetics ; Feces ; *Microbiota ; Ethnicity ; Metagenomics ; }, abstract = {Lifelong sex- and age-related trajectories of the human gut microbiota remain largely unexplored. Using metagenomics, we derived the gut microbial composition of 2,338 adults (26-76 years) from a Han Chinese population-based cohort where metabolic health, hormone levels and aspects of their lifestyles were also recorded. In this cohort, and in three independent cohorts distributed across China, Israel and the Netherlands, we observed sex differences in the gut microbial composition and a shared age-related decrease in sex-dependent differences in gut microbiota. Compared to men, the gut microbiota of premenopausal women exhibited higher microbial diversity and higher abundances of multiple species known to have beneficial effects on host metabolism. We also found consistent sex-independent, age-related gut microbial characteristics across all populations, with the presence of members of the oral microbiota being the strongest indicator of older chronological age. Our findings highlight the existence of sex- and age-related trajectories in the human gut microbiota that are shared between populations of different ethnicities and emphasize the pivotal links between sex hormones, gut microbiota and host metabolism.}, } @article {pmid37128079, year = {2020}, author = {Walsh, AM and Macori, G and Kilcawley, KN and Cotter, PD}, title = {Meta-analysis of cheese microbiomes highlights contributions to multiple aspects of quality.}, journal = {Nature food}, volume = {1}, number = {8}, pages = {500-510}, pmid = {37128079}, issn = {2662-1355}, support = {12/RC/2273//Science Foundation Ireland (SFI)/ ; 12/RC/2273//Science Foundation Ireland (SFI)/ ; 12/RC/2273//Science Foundation Ireland (SFI)/ ; 12/RC/2273//Science Foundation Ireland (SFI)/ ; 16/RC/3835//Science Foundation Ireland (SFI)/ ; 818368//EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)/ ; }, abstract = {A detailed understanding of the cheese microbiome is key to the optimization of flavour, appearance, quality and safety. Accordingly, we conducted a high-resolution meta-analysis of cheese microbiomes and corresponding volatilomes. Using 77 new samples from 55 artisanal cheeses from 27 Irish producers combined with 107 publicly available cheese metagenomes, we recovered 328 metagenome-assembled genomes, including 47 putative new species that could influence taste or colour through the secretion of volatiles or biosynthesis of pigments. Additionally, from a subset of samples, we found that differences in the abundances of strains corresponded with levels of volatiles. Genes encoding bacteriocins and other antimicrobials, such as pseudoalterin, were common, potentially contributing to the control of undesirable microorganisms. Although antibiotic-resistance genes were detected, evidence suggested they are not of major concern with respect to dissemination to other microbiomes. Phages, a potential cause of fermentation failure, were abundant and evidence for phage-mediated gene transfer was detected. The anti-phage defence mechanism CRISPR was widespread and analysis thereof, and of anti-CRISPR proteins, revealed a complex interaction between phages and bacteria. Overall, our results provide new and substantial technological and ecological insights into the cheese microbiome that can be applied to further improve cheese production.}, } @article {pmid37011532, year = {2023}, author = {Raj, A and Dubey, A and Malla, MA and Kumar, A}, title = {Pesticide pestilence: Global scenario and recent advances in detection and degradation methods.}, journal = {Journal of environmental management}, volume = {338}, number = {}, pages = {117680}, doi = {10.1016/j.jenvman.2023.117680}, pmid = {37011532}, issn = {1095-8630}, mesh = {Humans ; *Pesticides/analysis ; Ecosystem ; Agriculture ; Soil/chemistry ; Environmental Pollution ; }, abstract = {Increased anthropogenic activities are confronted as the main cause for rising environmental and health concerns globally, presenting an indisputable threat to both environment and human well-being. Modern-day industrialization has given rise to a cascade of concurrent environmental and health challenges. The global human population is growing at an alarming rate, posing tremendous pressure on future food security, and healthy and environmentally sustainable diets for all. To feed all, the global food production needs to increase by 50% by 2050, but this increase has to occur from the limited arable land, and under the present-day climate variabilities. Pesticides have become an integral component of contemporary agricultural system, safeguarding crops from pests and diseases and their use must be reduce to fulfill the SDG (Sustainable Development Goals) agenda . However, their indiscriminate use, lengthy half-lives, and high persistence in soil and aquatic ecosystems have impacted global sustainability, overshot the planetary boundaries and damaged the pure sources of life with severe and negative impacts on environmental and human health. Here in this review, we have provided an overview of the background of pesticide use and pollution status and action strategies of top pesticide-using nations. Additionally, we have summarized biosensor-based methodologies for the rapid detection of pesticide residue. Finally, omics-based approaches and their role in pesticide mitigation and sustainable development have been discussed qualitatively. The main aim of this review is to provide the scientific facts for pesticide management and application and to provide a clean, green, and sustainable environment for future generations.}, } @article {pmid37010966, year = {2023}, author = {Serbanescu, MA and Apple, CG and Fernandez-Moure, JS}, title = {Role of Resident Microbial Communities in Biofilm-Related Implant Infections: Recent Insights and Implications.}, journal = {Surgical infections}, volume = {24}, number = {3}, pages = {258-264}, doi = {10.1089/sur.2023.009}, pmid = {37010966}, issn = {1557-8674}, mesh = {Humans ; *Staphylococcal Infections ; Biofilms ; Postoperative Complications ; *Microbiota ; Prostheses and Implants/adverse effects ; }, abstract = {The use of medical implants continues to grow as the population ages. Biofilm-related implant infection is the leading cause of medical implant failure and remains difficult to diagnose and treat. Recent technologies have enhanced our understanding of the composition and complex functions of microbiota occupying various body site niches. In this review, we leverage data from molecular sequencing technologies to explore how silent changes in microbial communities from various sites can influence the development of biofilm-related infections. Specifically, we address biofilm formation and recent insights of the organisms involved in biofilm-related implant infections; how composition of microbiomes from skin, nasopharyngeal, and nearby tissue can impact biofilm-formation, and infection; the role of the gut microbiome in implant-related biofilm formation; and therapeutic strategies to mitigate implant colonization.}, } @article {pmid37010699, year = {2023}, author = {Gao, P and Fan, K}, title = {Sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) in oil reservoir and biological control of SRB: a review.}, journal = {Archives of microbiology}, volume = {205}, number = {5}, pages = {162}, pmid = {37010699}, issn = {1432-072X}, support = {No.31500414//National Natural Science Foundation of China/ ; }, mesh = {*Oil and Gas Fields ; Oxidation-Reduction ; Sulfates/metabolism ; *Desulfovibrio/metabolism ; Bacteria/genetics/metabolism ; Sulfur/metabolism ; }, abstract = {Sulfur-oxidizing bacteria (SOB) and sulfate-reducing bacteria (SRB) inhabit oilfield production systems. Sulfur oxidation driven by SOB and dissimilatory sulfate reduction driven by SRB play important roles in sulfur cycle of oil reservoirs. More importantly, hydrogen sulfide produced by SRB is an acidic, flammable, and smelly toxic gas associated with reservoir souring, corrosion of oil-production facilities, and personnel safety. Effective control of SRB is urgently needed for the oil industry. This depends on an in-depth understanding of the microbial species that drive sulfur cycle and other related microorganisms in oil reservoir environments. Here, we identified SOB and SRB in produced brines of Qizhong block (Xinjiang Oilfield, China) from metagenome sequencing data based on reported SOB and SRB, reviewed metabolic pathways of sulfur oxidation and dissimilatory sulfate reduction, and ways for SRB control. The existing issues and future research of microbial sulfur cycle and SRB control are also discussed. Knowledge of the distribution of the microbial populations, their metabolic characteristics and interactions can help to develop an effective process to harness these microorganisms for oilfield production.}, } @article {pmid37010293, year = {2023}, author = {Maranga, M and Szczerbiak, P and Bezshapkin, V and Gligorijevic, V and Chandler, C and Bonneau, R and Xavier, RJ and Vatanen, T and Kosciolek, T}, title = {Comprehensive Functional Annotation of Metagenomes and Microbial Genomes Using a Deep Learning-Based Method.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0117822}, pmid = {37010293}, issn = {2379-5077}, mesh = {Humans ; Metagenome/genetics ; *Deep Learning ; Molecular Sequence Annotation ; *Microbiota/genetics ; Genome, Microbial ; }, abstract = {Comprehensive protein function annotation is essential for understanding microbiome-related disease mechanisms in the host organisms. However, a large portion of human gut microbial proteins lack functional annotation. Here, we have developed a new metagenome analysis workflow integrating de novo genome reconstruction, taxonomic profiling, and deep learning-based functional annotations from DeepFRI. This is the first approach to apply deep learning-based functional annotations in metagenomics. We validate DeepFRI functional annotations by comparing them to orthology-based annotations from eggNOG on a set of 1,070 infant metagenomes from the DIABIMMUNE cohort. Using this workflow, we generated a sequence catalogue of 1.9 million nonredundant microbial genes. The functional annotations revealed 70% concordance between Gene Ontology annotations predicted by DeepFRI and eggNOG. DeepFRI improved the annotation coverage, with 99% of the gene catalogue obtaining Gene Ontology molecular function annotations, although they are less specific than those from eggNOG. Additionally, we constructed pangenomes in a reference-free manner using high-quality metagenome-assembled genomes (MAGs) and analyzed the associated annotations. eggNOG annotated more genes on well-studied organisms, such as Escherichia coli, while DeepFRI was less sensitive to taxa. Further, we show that DeepFRI provides additional annotations in comparison to the previous DIABIMMUNE studies. This workflow will contribute to novel understanding of the functional signature of the human gut microbiome in health and disease as well as guiding future metagenomics studies. IMPORTANCE The past decade has seen advancement in high-throughput sequencing technologies resulting in rapid accumulation of genomic data from microbial communities. While this growth in sequence data and gene discovery is impressive, the majority of microbial gene functions remain uncharacterized. The coverage of functional information coming from either experimental sources or inferences is low. To solve these challenges, we have developed a new workflow to computationally assemble microbial genomes and annotate the genes using a deep learning-based model DeepFRI. This improved microbial gene annotation coverage to 1.9 million metagenome-assembled genes, representing 99% of the assembled genes, which is a significant improvement compared to 12% Gene Ontology term annotation coverage by commonly used orthology-based approaches. Importantly, the workflow supports pangenome reconstruction in a reference-free manner, allowing us to analyze the functional potential of individual bacterial species. We therefore propose this alternative approach combining deep-learning functional predictions with the commonly used orthology-based annotations as one that could help us uncover novel functions observed in metagenomic microbiome studies.}, } @article {pmid37009964, year = {2023}, author = {Glidden, CK and Karakoç, C and Duan, C and Jiang, Y and Beechler, B and Jabbar, A and Jolles, AE}, title = {Distinct life history strategies underpin clear patterns of succession in microparasite communities infecting a wild mammalian host.}, journal = {Molecular ecology}, volume = {32}, number = {13}, pages = {3733-3746}, pmid = {37009964}, issn = {1365-294X}, support = {R01 GM126549/GM/NIGMS NIH HHS/United States ; R35 GM133439/GM/NIGMS NIH HHS/United States ; BB/L011085/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Biological Evolution ; Biota ; *Host-Parasite Interactions ; *Life History Traits ; Mammals ; *Parasites ; }, abstract = {Individual animals in natural populations tend to host diverse parasite species concurrently over their lifetimes. In free-living ecological communities, organismal life histories shape interactions with their environment, which ultimately forms the basis of ecological succession. However, the structure and dynamics of mammalian parasite communities have not been contextualized in terms of primary ecological succession, in part because few datasets track occupancy and abundance of multiple parasites in wild hosts starting at birth. Here, we studied community dynamics of 12 subtypes of protozoan microparasites (Theileria spp.) in a herd of African buffalo. We show that Theileria communities followed predictable patterns of succession underpinned by four different parasite life history strategies. However, in contrast to many free-living communities, network complexity decreased with host age. Examining parasite communities through the lens of succession may better inform the effect of complex within host eco-evolutionary dynamics on infection outcomes, including parasite co-existence through the lifetime of the host.}, } @article {pmid37009923, year = {2023}, author = {Chapman, R and Jones, L and D'Angelo, A and Suliman, A and Anwar, M and Bagby, S}, title = {Nanopore-Based Metagenomic Sequencing in Respiratory Tract Infection: A Developing Diagnostic Platform.}, journal = {Lung}, volume = {201}, number = {2}, pages = {171-179}, pmid = {37009923}, issn = {1432-1750}, mesh = {Humans ; *Nanopore Sequencing ; *Nanopores ; *Respiratory Tract Infections/diagnosis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; Metagenomics/methods ; }, abstract = {Respiratory tract infection (RTI) remains a significant cause of morbidity and mortality across the globe. The optimal management of RTI relies upon timely pathogen identification via evaluation of respiratory samples, a process which utilises traditional culture-based methods to identify offending microorganisms. This process can be slow and often prolongs the use of broad-spectrum antimicrobial therapy, whilst also delaying the introduction of targeted therapy as a result. Nanopore sequencing (NPS) of respiratory samples has recently emerged as a potential diagnostic tool in RTI. NPS can identify pathogens and antimicrobial resistance profiles with greater speed and efficiency than traditional sputum culture-based methods. Increased speed to pathogen identification can improve antimicrobial stewardship by reducing the use of broad-spectrum antibiotic therapy, as well as improving overall clinical outcomes. This new technology is becoming more affordable and accessible, with some NPS platforms requiring minimal sample preparation and laboratory infrastructure. However, questions regarding clinical utility and how best to implement NPS technology within RTI diagnostic pathways remain unanswered. In this review, we introduce NPS as a technology and as a diagnostic tool in RTI in various settings, before discussing the advantages and limitations of NPS, and finally what the future might hold for NPS platforms in RTI diagnostics.}, } @article {pmid37009900, year = {2023}, author = {Mick, E and Tsitsiklis, A and Kamm, J and Kalantar, KL and Caldera, S and Lyden, A and Tan, M and Detweiler, AM and Neff, N and Osborne, CM and Williamson, KM and Soesanto, V and Leroue, M and Maddux, AB and Simões, EA and Carpenter, TC and Wagner, BD and DeRisi, JL and Ambroggio, L and Mourani, PM and Langelier, CR}, title = {Integrated host/microbe metagenomics enables accurate lower respiratory tract infection diagnosis in critically ill children.}, journal = {The Journal of clinical investigation}, volume = {133}, number = {7}, pages = {}, pmid = {37009900}, issn = {1558-8238}, support = {K23 HL138461/HL/NHLBI NIH HHS/United States ; R01 HL155418/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; Child ; Metagenomics ; Critical Illness ; *Respiratory Tract Infections/diagnosis/microbiology ; Lung ; *Microbiota ; }, abstract = {BACKGROUNDLower respiratory tract infection (LRTI) is a leading cause of death in children worldwide. LRTI diagnosis is challenging because noninfectious respiratory illnesses appear clinically similar and because existing microbiologic tests are often falsely negative or detect incidentally carried microbes, resulting in antimicrobial overuse and adverse outcomes. Lower airway metagenomics has the potential to detect host and microbial signatures of LRTI. Whether it can be applied at scale and in a pediatric population to enable improved diagnosis and treatment remains unclear.METHODSWe used tracheal aspirate RNA-Seq to profile host gene expression and respiratory microbiota in 261 children with acute respiratory failure. We developed a gene expression classifier for LRTI by training on patients with an established diagnosis of LRTI (n = 117) or of noninfectious respiratory failure (n = 50). We then developed a classifier that integrates the host LRTI probability, abundance of respiratory viruses, and dominance in the lung microbiome of bacteria/fungi considered pathogenic by a rules-based algorithm.RESULTSThe host classifier achieved a median AUC of 0.967 by cross-validation, driven by activation markers of T cells, alveolar macrophages, and the interferon response. The integrated classifier achieved a median AUC of 0.986 and increased the confidence of patient classifications. When applied to patients with an uncertain diagnosis (n = 94), the integrated classifier indicated LRTI in 52% of cases and nominated likely causal pathogens in 98% of those.CONCLUSIONLower airway metagenomics enables accurate LRTI diagnosis and pathogen identification in a heterogeneous cohort of critically ill children through integration of host, pathogen, and microbiome features.FUNDINGSupport for this study was provided by the Eunice Kennedy Shriver National Institute of Child Health and Human Development and the National Heart, Lung, and Blood Institute (UG1HD083171, 1R01HL124103, UG1HD049983, UG01HD049934, UG1HD083170, UG1HD050096, UG1HD63108, UG1HD083116, UG1HD083166, UG1HD049981, K23HL138461, and 5R01HL155418) as well as by the Chan Zuckerberg Biohub.}, } @article {pmid37009568, year = {2023}, author = {Simpson, S and Bettauer, V and Ramachandran, A and Kraemer, S and Mahon, S and Medina, M and Vallès, Y and Dumeaux, V and Vallès, H and Walsh, D and Hallett, MT}, title = {A metagenomic-based study of two sites from the Barbadian reef system.}, journal = {Coral reefs (Online)}, volume = {42}, number = {2}, pages = {359-366}, pmid = {37009568}, issn = {1432-0975}, abstract = {UNLABELLED: We study the microbiome of sea water collected from two locations of the Barbadian coral reefs. The two sites differ in several environmental and ecological variables including their endogenous benthic community and their proximity to urban development and runoffs from inland watersheds. The composition of the microbial communities was estimated using whole genome DNA shotgun sequencing with adjuvant measurements of chemical and environmental qualities. Although both sites exhibit a similar degree of richness, the less urbanized site (Maycocks reef at Hangman's Bay) has a strong concentration of phototrophs whereas the more urbanized location (Bellairs reef at Folkstone) is enriched for copiotrophs, macroalgal symbionts and marine-related disease-bearing organisms from taxa scattered across the tree of life. Our results are concordant with previous profiles of warm ocean surface waters, suggesting our approach captures the state of each coral reef site, setting the stage for longitudinal studies of marine microbiome dynamics in Barbados.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00338-022-02330-y.}, } @article {pmid37009509, year = {2023}, author = {Lin, T and Tu, X and Zhao, J and Huang, L and Dai, X and Chen, X and Xu, Y and Li, W and Wang, Y and Lou, J and Wu, S and Zhang, H}, title = {Microbiological diagnostic performance of metagenomic next-generation sequencing compared with conventional culture for patients with community-acquired pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1136588}, pmid = {37009509}, issn = {2235-2988}, mesh = {Humans ; *Pneumonia/diagnosis ; High-Throughput Nucleotide Sequencing ; Bronchoalveolar Lavage Fluid ; *Community-Acquired Infections/diagnosis ; Dietary Supplements ; Escherichia coli ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Community-acquired pneumonia (CAP) is an extraordinarily heterogeneous illness, both in the range of responsible pathogens and the host response. Metagenomic next-generation sequencing (mNGS) is a promising technology for pathogen detection. However, the clinical application of mNGS for pathogen detection remains challenging.

METHODS: A total of 205 patients with CAP admitted to the intensive care unit were recruited, and broncho alveolar lavage fluids (BALFs) from 83 patients, sputum samples from 33 cases, and blood from 89 cases were collected for pathogen detection by mNGS. At the same time, multiple samples of each patient were tested by culture. The diagnostic performance was compared between mNGS and culture for pathogen detection.

RESULTS: The positive rate of pathogen detection by mNGS in BALF and sputum samples was 89.2% and 97.0%, which was significantly higher (P < 0.001) than that (67.4%) of blood samples. The positive rate of mNGS was significantly higher than that of culture (81.0% vs. 56.1%, P = 1.052e-07). A group of pathogens including Mycobacterium abscessus, Chlamydia psittaci, Pneumocystis jirovecii, Orientia tsutsugamushi, and all viruses were only detected by mNGS. Based on mNGS results, Escherichia coli was the most common pathogen (15/61, 24.59%) of non-severe patients with CAP, and Mycobacterium tuberculosis was the most common pathogen (21/144, 14.58%) leading to severe pneumonia. Pneumocystis jirovecii was the most common pathogen (26.09%) in severe CAP patients with an immunocompromised status, which was all detected by mNGS only.

CONCLUSION: mNGS has higher overall sensitivity for pathogen detection than culture, BALF, and sputum mNGS are more sensitive than blood mNGS. mNGS is a necessary supplement of conventional microbiological tests for the pathogen detection of pulmonary infection.}, } @article {pmid37009508, year = {2023}, author = {Niu, J and Wang, J and Jia, P and Zhang, M and Wei, E}, title = {Clinical features and diagnostic value of metagenomic next -generation sequencing in five cases of non-HIV related Pneumocystis jirovecii pneumonia in children.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1132472}, pmid = {37009508}, issn = {2235-2988}, mesh = {Humans ; Male ; Child ; Infant ; *Pneumonia, Pneumocystis/diagnosis/drug therapy/microbiology ; Retrospective Studies ; Cough/complications ; *Pneumocystis carinii/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Pneumocystis jirovecii (PJ) is an opportunistic pathogenic fungus, and PJ pneumonia (PJP) is a commonly problem in HIV-positive patients. While PJP is not caused by HIV, it generally advances rapidly and can quickly lead to severe respiratory failure. To improve pediatricians' understanding of the condition and aid early accurate diagnoses and therapy, we examined the clinical characteristics of five instances of non-HIV related PJP (NH-PJP) in children and the efficacy of metagenomic next-generation sequencing (mNGS) in its diagnosis.

METHODS: From January 2020 to June 2022, five children with NH-PJP were admitted to the PICU of the First Affiliated Hospital of Zhengzhou University. We retrospectively summarize the clinical presentation, previous histories, routine laboratory findings, treatment, outcome of regression, and results of mNGS in these five children.

RESULTS: Five male children between the ages of 11 months and 14 years had an acute onset on NH-PJP, three of the children had chest tightness after activity, shortness of breath and paroxysmal dry cough, - and two had high fever and dry cough. All five of the children had several flocculent high-density pictures in both lungs at the beginning of the disease, and lung auscultation revealed coarse breath sounds in both lungs, one of which was accompanied by a modest quantity of dry rales. PJ nuclear sequences were found in one patient and four patients' blood and alveolar lavage fluid. All five children were treated with Trimethoprim-sulfamethoxazole (TMP-SMX) in combination with Caspofungin and corresponding symptomatic treatment. Four patients were cured and one patient died.

CONCLUSION: Children commonly encounter an initial exposure to NH-PJP, which manifests as a high fever, dry cough, chest discomfort, dyspnea that worsens over time, fast disease progression, and a high death rate. The clinical presentation of children with PJ infection should be taken into consideration along with the results for diagnose. mNGS has higher sensitivity and a shorter detection period compared to identification of PJP.}, } @article {pmid37009495, year = {2023}, author = {Zhang, C and Liu, T and Wang, Y and Chen, W and Liu, J and Tao, J and Zhang, Z and Zhu, X and Zhang, Z and Ming, M and Wang, M and Lu, G and Yan, G}, title = {Metagenomic next-generation sequencing of bronchoalveolar lavage fluid from children with severe pneumonia in pediatric intensive care unit.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1082925}, pmid = {37009495}, issn = {2235-2988}, mesh = {Humans ; Child ; Bronchoalveolar Lavage Fluid ; *Coinfection ; *Epstein-Barr Virus Infections ; Herpesvirus 4, Human ; *Pneumonia/diagnosis ; *Respiratory Tract Infections ; High-Throughput Nucleotide Sequencing ; Intensive Care Units, Pediatric ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Severe pneumonia due to lower respiratory tract infections (LRTIs) is a significant cause of morbidity and mortality in children. Noninfectious respiratory syndromes resembling LRTIs can complicate the diagnosis and may also make targeted therapy difficult because of the difficulty of identifying LRTI pathogens. In the present study, a highly sensitive metagenomic next-generation sequencing (mNGS) approach was used to characterize the microbiome of bronchoalveolar lavage fluid (BALF) in children with severe lower pneumonia and identify pathogenic microorganisms that may cause severe pneumonia. The purpose of this study was to use mNGS to explore the potential microbiomes of children with severe pneumonia in a PICU.

METHODS: We enrolled patients meeting diagnostic criteria for severe pneumonia admitted at PICU of the Children's Hospital of Fudan University, China, from February 2018 to February 2020. In total, 126 BALF samples were collected, and mNGS was performed at the DNA and/or RNA level. The pathogenic microorganisms in BALF were identified and correlated with serological inflammatory indicators, lymphocyte subtypes, and clinical symptoms.

RESULTS: mNGS of BALF identified potentially pathogenic bacteria in children with severe pneumonia in the PICU. An increased BALF bacterial diversity index was positively correlated with serum inflammatory indicators and lymphocyte subtypes. Children with severe pneumonia in the PICU had the potential for coinfection with viruses including Epstein-Barr virus, Cytomegalovirus, and Human betaherpesvirus 6B, the abundance of which was positively correlated with immunodeficiency and pneumonia severity, suggesting that the virus may be reactivated in children in the PICU. There was also the potential for coinfection with fungal pathogens including Pneumocystis jirovecii and Aspergillus fumigatus in children with severe pneumonia in the PICU, and an increase in potentially pathogenic eukaryotic diversity in BALF was positively associated with the occurrence of death and sepsis.

CONCLUSIONS: mNGS can be used for clinical microbiological testing of BALF samples from children in the PICU. Bacterial combined with viral or fungal infections may be present in the BALF of patients with severe pneumonia in the PICU. Viral or fungal infections are associated with greater disease severity and death.}, } @article {pmid37009327, year = {2023}, author = {Jeyaraman, M and Nallakumarasamy, A and Jain, VK}, title = {Gut Microbiome - Should we treat the gut and not the bones?.}, journal = {Journal of clinical orthopaedics and trauma}, volume = {39}, number = {}, pages = {102149}, pmid = {37009327}, issn = {0976-5662}, abstract = {Gut microbiome (GM) forms an integral part of homeostasis of an individual. Due to the recent development of metagenomics, the plausibility of sequencing GM and its therapeutic ability for various diseases has been explored. Dysbiosis or disequilibrium or pertubations of GM leads to disruption of intercommunication signaling among gut-bone axis, gut-bone-brain axis, and gut-disc axis resulting in the progression of various chronic diseases. The therapeutic interventions to restore the GM like prebiotics and probiotics, bacteriophage therapy, fecal microbiota transplantation, and physical biomodulation have been identified. This review throw the lime light on the effect of gut dysbiosis in musculoskeletal diseases.}, } @article {pmid37009095, year = {2023}, author = {Al Bataineh, MT and Künstner, A and Dash, NR and Abdulsalam, RM and Al-Kayyali, RZA and Adi, MB and Alsafar, HS and Busch, H and Ibrahim, SM}, title = {Corrigendum: Altered composition of the oral microbiota in depression among cigarette smokers: A pilot study.}, journal = {Frontiers in psychiatry}, volume = {14}, number = {}, pages = {1175044}, doi = {10.3389/fpsyt.2023.1175044}, pmid = {37009095}, issn = {1664-0640}, abstract = {[This corrects the article DOI: 10.3389/fpsyt.2022.902433.].}, } @article {pmid37008505, year = {2023}, author = {Wang, S and Zhang, X and Li, X and Shen, J and Sun, L and Zaman, S and Wang, Y and Ding, Z}, title = {Different changes of bacterial diversity and soil metabolites in tea plants-legume intercropping systems.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1110623}, pmid = {37008505}, issn = {1664-462X}, abstract = {As an essential agroforestry, intercropping legumes can improve the physical, chemical, and biological fertility of the soil in tea plantations. However, the effects of intercropping different legume species on soil properties, bacterial communities, and metabolites remain elusive. In this study, the 0-20 cm and 20-40 cm soils of three planting patterns (T1: tea plants/mung bean intercropping, T2: tea plants/adzuki bean intercropping, T3: tea plants/mung bean and adzuki bean intercropping) were sampled to explore the diversity of the bacterial community and soil metabolites. The findings showed that, as compared to monocropping, intercropping systems had greater concentrations of organic matter (OM) and dissolved organic carbon (DOC). Notably, pH values were significantly lower, and soil nutrients increased in intercropping systems compared with monoculture in 20-40 cm soils, especially in T3. In addition, intercropping resulted in an increased relative abundance of Proteobacteria but a decreased relative abundance of Actinobacteria. 4-methyl-Tetradecane, acetamide, and diethyl carbamic acid were key metabolites mediating the root-microbe interactions, especially in tea plants/adzuki intercropping and tea plants/mung bean, adzuki bean mixed intercropping soils. Co-occurrence network analysis showed that arabinofuranose, abundant in tea plants and adzuki bean intercropping soils, showed the most remarkable correlation with the soil bacterial taxa. Our findings demonstrate that intercropping with adzuki beans is better at enhancing the diversity of soil bacteria and soil metabolites and is more weed-suppressing than other tea plants/legume intercropping systems.}, } @article {pmid37007969, year = {2023}, author = {Deng, S and Rao, S and Wang, AR and Shi, W}, title = {Case report: Rubella virus-induced cutaneous granulomas in a girl with atypical SCID caused by DCLRE1C gene mutations.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {1115027}, pmid = {37007969}, issn = {1664-8021}, abstract = {Here, we report a case of rubella virus-induced granulomatous dermatitis in a young girl with immunodeficiency caused by DCLRE1C gene mutations. The patient was a 6-year-old girl who presented with multiple erythematous plaques on the face and limbs. Biopsies of the lesions revealed tuberculoid necrotizing granulomas. No pathogens could be identified on extensive special stains, tissue cultures, or PCR-based microbiology assays. Metagenomic next-generation sequencing analysis revealed the rubella virus. Underlying atypical severe combined immunodeficiency was recognized based on the patient's history of repetitive infections since birth, low T-cell, B-cell, and NK cell counts, and abnormal immunoglobulins and complements. Whole-exome sequencing revealed the genetic abnormality of the atypical severe combined immunodeficiency (SCID), and compound heterozygous mutations of the DCLRE1C gene were detected. This report highlights the diagnostic values of metagenomic next-generation sequencing in identifying rare pathogens causing cutaneous granulomas in patients with atypical SCID.}, } @article {pmid37007711, year = {2023}, author = {Keller, LM and Colman, DR and Boyd, ES}, title = {An active microbiome in Old Faithful geyser.}, journal = {PNAS nexus}, volume = {2}, number = {3}, pages = {pgad066}, pmid = {37007711}, issn = {2752-6542}, abstract = {Natural thermal geysers are hot springs that periodically erupt liquid water, steam, and gas. They are found in only a few locations worldwide, with nearly half located in Yellowstone National Park (YNP). Old Faithful geyser (OFG) is the most iconic in YNP and attracts millions of visitors annually. Despite extensive geophysical and hydrological study of geysers, including OFG, far less is known of the microbiology of geysed waters. Here, we report geochemical and microbiological data from geysed vent water and vent water that collects in a splash pool adjacent to OFG during eruptions. Both waters contained microbial cells, and radiotracer studies showed that they fixed carbon dioxide (CO2) when incubated at 70°C and 90°C. Shorter lag times in CO2 fixation activity were observed in vent and splash pool waters incubated at 90°C than 70°C, suggesting cells are better adapted or acclimated to temperatures like those in the OFG vent (∼92-93°C). 16S rDNA and metagenomic sequence data indicated that both communities are dominated by the autotroph Thermocrinis, which likely fuels productivity through the aerobic oxidation of sulfide/thiosulfate in erupted waters or steam. Dominant OFG populations, including Thermocrinis and subdominant Thermus and Pyrobaculum strains, exhibited high-strain level genomic diversity (putative ecotypes) relative to populations from nongeysing YNP hot springs that is attributed to the temporal chemical and temperature dynamics caused by eruptions. These findings show that OFG is habitable and that its eruption dynamics promote genomic diversity, while highlighting the need to further research the extent of life in geyser systems such as OFG.}, } @article {pmid37007517, year = {2023}, author = {Zhang, Y and Pan, D and Xiao, P and Xu, Q and Geng, F and Zhang, X and Zhou, X and Xu, H}, title = {A novel lytic polysaccharide monooxygenase from enrichment microbiota and its application for shrimp shell powder biodegradation.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1097492}, pmid = {37007517}, issn = {1664-302X}, abstract = {Lytic polysaccharide monooxygenases (LPMO) are expected to change the current status of chitin resource utilization. This study reports that targeted enrichment of the microbiota was performed with chitin by the selective gradient culture technique, and a novel LPMO (M2822) was identified from the enrichment microbiota metagenome. First, soil samples were screened based on soil bacterial species and chitinase biodiversity. Then gradient enrichment culture with different chitin concentrations was carried out. The efficiency of chitin powder degradation was increased by 10.67 times through enrichment, and chitin degradation species Chitiniphilus and Chitinolyticbacter were enriched significantly. A novel LPMO (M2822) was found in the metagenome of the enriched microbiota. Phylogenetic analysis showed that M2822 had a unique phylogenetic position in auxiliary activity (AA) 10 family. The analysis of enzymatic hydrolysate showed that M2822 had chitin activity. When M2822 synergized with commercial chitinase to degrade chitin, the yield of N-acetyl glycosamine was 83.6% higher than chitinase alone. The optimum temperature and pH for M2822 activity were 35°C and 6.0. The synergistic action of M2822 and chitin-degrading enzymes secreted by Chitiniphilus sp. LZ32 could efficiently hydrolyze shrimp shell powder. After 12 h of enzymatic hydrolysis, chitin oligosaccharides (COS) yield reached 4,724 μg/mL. To our knowledge, this work is the first study to mine chitin activity LPMO in the metagenome of enriched microbiota. The obtained M2822 showed application prospects in the efficient production of COS.}, } @article {pmid37007506, year = {2023}, author = {Fang, B and Lai, J and Liu, Y and Yu, TT and Yu, X and Li, X and Dong, L and Zhang, X and Yang, W and Yan, Q and Sun, L and Liu, LL}, title = {Genetic characterization of human adenoviruses in patients using metagenomic next-generation sequencing in Hubei, China, from 2018 to 2019.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1153728}, pmid = {37007506}, issn = {1664-302X}, abstract = {OBJECTIVES: This study aimed to characterize the genomic epidemiology of human adenoviruses (HAdVs) in Hubei, China, using metagenomic next-generation sequencing (mNGS).

METHODS: In total, 25 HAdV-positive samples collected from 21 pediatric patients were sequenced and subjected to mNGS using the NextSeq 550 and GenoLab M sequencing platforms. The metagenomic data were assembled de novo for molecular typing, phylogenetic and recombination analyzes.

RESULTS: We assembled 50 HAdV genomes, 88% (22/25) genomes from GenoLab M, and 84% (21/25) genomes from NextSeq 550 have perfect alignments to reference genomes with greater than 90%. The most fully assembled 25 genomes were categorized into 7 HAdV genotypes, the most abundant of which were HAdV-B3 (9/25) and HAdV-C2 (6/25). Phylogenetic analyzes revealed that the newly isolated HAdV-B3 strains diverged into separate clusters according to their genotypes. Vigilance is needed that HAdV-B3 isolates have begun to form new distinct clusters. High nucleotide identity was observed in the whole genome level within the same HAdV genotypes, while marked differences of three capsid genes across HAdV genotypes were noted. The high nucleotide diversity regions were concordant with the reported hypervariable regions. Further, three recombinant strains were identified: S64 and S71 originated from the parental strains HAdV-B14 and HAdV-B11, and S28 originated from HAdV-C1, HAdV-C5, and HAdV-CBJ113. GenoLab M and NextSeq 550 showed comparable performance with respect to data yield, duplication rate, human ratio, and assembly completeness.

CONCLUSION: The sequencing quality and assembly accuracy showed that mNGS assembled genomes can be used for subsequently HAdV genotyping and genomic characterization. The high nucleotide diversity of capsid genes and high frequency of recombination events has highlighted the necessity for HAdV epidemiological surveillance in China.}, } @article {pmid37007500, year = {2023}, author = {Kuang, L and Li, T and Wang, B and Peng, J and Li, J and Li, P and Jiang, J}, title = {Diseased-induced multifaceted variations in community assembly and functions of plant-associated microbiomes.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1141585}, pmid = {37007500}, issn = {1664-302X}, abstract = {Plant-associated microorganisms are believed to be part of the so-called extended plant phenotypes, affecting plant growth and health. Understanding how plant-associated microorganisms respond to pathogen invasion is crucial to controlling plant diseases through microbiome manipulation. In this study, healthy and diseased (bacterial wilt disease, BWD) tomato (Solanum lycopersicum L.) plants were harvested, and variations in the rhizosphere and root endosphere microbial communities were subsequently investigated using amplicon and shotgun metagenome sequencing. BWD led to a significant increase in rhizosphere bacterial diversity in the rhizosphere but reduced bacterial diversity in the root endosphere. The ecological null model indicated that BWD enhanced the bacterial deterministic processes in both the rhizosphere and root endosphere. Network analysis showed that microbial co-occurrence complexity was increased in BWD-infected plants. Moreover, higher universal ecological dynamics of microbial communities were observed in the diseased rhizosphere. Metagenomic analysis revealed the enrichment of more functional gene pathways in the infected rhizosphere. More importantly, when tomato plants were infected with BWD, some plant-harmful pathways such as quorum sensing were significantly enriched, while some plant-beneficial pathways such as streptomycin biosynthesis were depleted. These findings broaden the understanding of plant-microbiome interactions and provide new clues to the underlying mechanism behind the interaction between the plant microbiome and BWD.}, } @article {pmid37007478, year = {2023}, author = {Liu, H and Li, FY and Liu, J and Shi, C and Tang, K and Yang, Q and Liu, Y and Fu, Q and Gao, X and Wang, N and Guo, W}, title = {The reciprocal changes in dominant species with complete metabolic functions explain the decoupling phenomenon of microbial taxonomic and functional composition in a grassland.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1113157}, pmid = {37007478}, issn = {1664-302X}, abstract = {The decoupling of microbial functional and taxonomic components refers to the phenomenon that a drastic change in microbial taxonomic composition leads to no or only a gentle change in functional composition. Although many studies have identified this phenomenon, the mechanisms underlying it are still unclear. Here we demonstrate, using metagenomics data from a steppe grassland soil under different grazing and phosphorus addition treatments, that there is no "decoupling" in the variation of taxonomic and metabolic functional composition of the microbial community within functional groups at species level. In contrast, the high consistency and complementarity between the abundance and functional gene diversity of two dominant species made metabolic functions unaffected by grazing and phosphorus addition. This complementarity between the two dominant species shapes a bistability pattern that differs from functional redundancy in that only two species cannot form observable redundancy in a large microbial community. In other words, the "monopoly" of metabolic functions by the two most abundant species leads to the disappearance of functional redundancy. Our findings imply that for soil microbial communities, the impact of species identity on metabolic functions is much greater than that of species diversity, and it is more important to monitor the dynamics of key dominant microorganisms for accurately predicting the changes in the metabolic functions of the ecosystems.}, } @article {pmid37007475, year = {2023}, author = {Pesantes, N and Barberá, A and Pérez-Rocher, B and Artacho, A and Vargas, SL and Moya, A and Ruiz-Ruiz, S}, title = {Influence of mental health medication on microbiota in the elderly population in the Valencian region.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1094071}, pmid = {37007475}, issn = {1664-302X}, abstract = {Spain has an aging population; 19.93% of the Spanish population is over 65. Aging is accompanied by several health issues, including mental health disorders and changes in the gut microbiota. The gut-brain axis is a bidirectional network linking the central nervous system with gastrointestinal tract functions, and therefore, the gut microbiota can influence an individual's mental health. Furthermore, aging-related physiological changes affect the gut microbiota, with differences in taxa and their associated metabolic functions between younger and older people. Here, we took a case-control approach to study the interplay between gut microbiota and mental health of elderly people. Fecal and saliva samples from 101 healthy volunteers over 65 were collected, of which 28 (EE|MH group) reported using antidepressants or medication for anxiety or insomnia at the time of sampling. The rest of the volunteers (EE|NOMH group) were the control group. 16S rRNA gene sequencing and metagenomic sequencing were applied to determine the differences between intestinal and oral microbiota. Significant differences in genera were found, specifically eight in the gut microbiota, and five in the oral microbiota. Functional analysis of fecal samples showed differences in five orthologous genes related to tryptophan metabolism, the precursor of serotonin and melatonin, and in six categories related to serine metabolism, a precursor of tryptophan. Moreover, we found 29 metabolic pathways with significant inter-group differences, including pathways regulating longevity, the dopaminergic synapse, the serotoninergic synapse, and two amino acids.}, } @article {pmid37007468, year = {2023}, author = {Dopson, M and González-Rosales, C and Holmes, DS and Mykytczuk, N}, title = {Eurypsychrophilic acidophiles: From (meta)genomes to low-temperature biotechnologies.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1149903}, pmid = {37007468}, issn = {1664-302X}, abstract = {Low temperature and acidic environments encompass natural milieus such as acid rock drainage in Antarctica and anthropogenic sites including drained sulfidic sediments in Scandinavia. The microorganisms inhabiting these environments include polyextremophiles that are both extreme acidophiles (defined as having an optimum growth pH < 3), and eurypsychrophiles that grow at low temperatures down to approximately 4°C but have an optimum temperature for growth above 15°C. Eurypsychrophilic acidophiles have important roles in natural biogeochemical cycling on earth and potentially on other planetary bodies and moons along with biotechnological applications in, for instance, low-temperature metal dissolution from metal sulfides. Five low-temperature acidophiles are characterized, namely, Acidithiobacillus ferriphilus, Acidithiobacillus ferrivorans, Acidithiobacillus ferrooxidans, "Ferrovum myxofaciens," and Alicyclobacillus disulfidooxidans, and their characteristics are reviewed. Our understanding of characterized and environmental eurypsychrophilic acidophiles has been accelerated by the application of "omics" techniques that have aided in revealing adaptations to low pH and temperature that can be synergistic, while other adaptations are potentially antagonistic. The lack of known acidophiles that exclusively grow below 15°C may be due to the antagonistic nature of adaptations in this polyextremophile. In conclusion, this review summarizes the knowledge of eurypsychrophilic acidophiles and places the information in evolutionary, environmental, biotechnological, and exobiology perspectives.}, } @article {pmid37007083, year = {2023}, author = {Jiang, H and Wang, J and Deng, W}, title = {Pathologic complete response to chemoimmunotherapy of an advanced gastric cancer patient with high PD-L1 expression, dMMR, and unique gut microbiota composition: A case report.}, journal = {Frontiers in oncology}, volume = {13}, number = {}, pages = {1150931}, pmid = {37007083}, issn = {2234-943X}, abstract = {BACKGROUND: Advanced gastric cancer (AGC) is a malignant disease with limited therapeutic options and a poor prognosis. Recently, immune checkpoint inhibitors (ICIs), represented by inhibitors of programmed cell death 1 (PD-1)/programmed death-ligand 1 (PD-L1), have emerged as a potential gastric cancer (GC) therapy.

CASE PRESENTATION: This case study aimed to reveal the tumor response to neoadjuvant chemotherapy combined with camrelizumab in a patient with AGC based on the characteristics of the clinical pathology, genomics variation, and gut microbiome. Samples from a 59-year-old male patient diagnosed with locally advanced unresectable GC (cT4bN2M0, high grade) presenting PD-L1-positive, deficient mismatch repair (dMMR), and highly specific gut microbiota enrichment were subjected to target region sequencing, metagenomic sequencing, and immunohistochemistry staining. The patient received neoadjuvant therapy, including camrelizumab, apatinib, S-1, and abraxane, which eventually promoted dramatic tumor shrinkage without serious adverse effects and allowed subsequent radical gastrectomy and lymphadenectomy. Finally, the patient achieved pathologic complete response (pCR), and the recurrence-free survival time was 19 months at the last follow-up in April 2021.

CONCLUSIONS: The patient with PD-L1-positive, dMMR, and a highly specific gut microbiota enrichment exhibited a pCR to neoadjuvant chemoimmunotherapy.}, } @article {pmid37006881, year = {2023}, author = {Zhang, X and Qin, Y and Lei, W and Huang, JA}, title = {Metagenomic next‑generation sequencing of BALF for the clinical diagnosis of severe community‑acquired pneumonia in immunocompromised patients: A single‑center study.}, journal = {Experimental and therapeutic medicine}, volume = {25}, number = {4}, pages = {178}, pmid = {37006881}, issn = {1792-1015}, abstract = {The diagnostic methods of conventional microbiological tests (CMTs) for severe community-acquired pneumonia (SCAP) may be too complicated or impossible to use in polymicrobial infections, and it may be difficult to identify unexpected pathogens. CMTs are also limited due to the early application of broad-spectrum or prophylactic antimicrobial drugs and the fastidious or slow-growing pathogenic microorganisms. The present study aimed to investigate the value of mNGS compared with CMTs in the clinical diagnosis of SCAP in immunocompromised individuals. Therefore, 37 patients diagnosed with SCAP in immunocompromised adult patients were enrolled from the Respiratory Intensive Care Unit of the First Affiliated Hospital of Soochow University (Soochow, China) between May 1, 2019, and March 30, 2022. A bronchoalveolar lavage fluid sample from each individual was divided in half. Half was sent to the microbiology laboratory directly for examination, and the other one was sent for DNA extraction and sequencing. In addition, other relevant specimens (such as blood) were sent for CMTs, including culture or smear, T-spot, acid-fast stain, antigen detection, multiplex PCR and direct microscopic examination. Based on a composite reference standard, the diagnostic outcomes were compared between CMTs and mNGS. Among the enrolled patients, 31 patients were diagnosed with microbiologically confirmed pneumonia, with 16 (43.2%) having monomicrobial infections, while 15 (40.5%) had polymicrobial infections. Fungi were the most common etiologic pathogens in immunosuppressive individuals. Pneumocystis jirovecii (45.9%) and Aspergillus spp. (18.9%) were the most common etiologic pathogens. Initial screening test validity of mNGS [sensitivity=96.8%; specificity=33.3%; positive predictive value (PPV)=88.2%; negative predictive value (NPV)=66.6%; likelihood ratio (LR)+, 1.45; LR-, 0.10) was higher compared with that of CMTs (sensitivity=38.7%; specificity=82.3; PPV=92.3%; NPV=20.8%; LR+, 2.3; LR-, 0.74). The total diagnostic accuracy of mNGS was superior to CMTs and it was statistically significantly different [86.5% (32/37) vs. 45.9% (17/37); P<0.001]. In conclusion, the total diagnostic accuracy of mNGS was superior to CMTs for SCAP in immunocompromised patients as an important diagnostic method.}, } @article {pmid37006617, year = {2023}, author = {Achudhan, AB and Kannan, P and Saleena, LM}, title = {Functional metagenomics uncovers nitrile-hydrolysing enzymes in a coal metagenome.}, journal = {Frontiers in molecular biosciences}, volume = {10}, number = {}, pages = {1123902}, pmid = {37006617}, issn = {2296-889X}, abstract = {Introduction: Nitriles are the most toxic compounds that can lead to serious human illness through inhalation and consumption due to environmental pollution. Nitrilases can highly degrade nitriles isolated from the natural ecosystem. In the current study, we focused on the discovery of novel nitrilases from a coal metagenome using in silico mining. Methods: Coal metagenomic DNA was isolated and sequenced on the Illumina platform. Quality reads were assembled using MEGAHIT, and statistics were checked using QUAST. Annotation was performed using the automated tool SqueezeMeta. The annotated amino acid sequences were mined for nitrilase from the unclassified organism. Sequence alignment and phylogenetic analyses were carried out using ClustalW and MEGA11. Conserved regions of the amino acid sequences were identified using InterProScan and NCBI-CDD servers. The physicochemical properties of the amino acids were measured using ExPASy's ProtParam. Furthermore, NetSurfP was used for 2D structure prediction, while AlphaFold2 in Chimera X 1.4 was used for 3D structure prediction. To check the solvation of the predicted protein, a dynamic simulation was conducted on the WebGRO server. Ligands were extracted from the Protein Data Bank (PDB) for molecular docking upon active site prediction using the CASTp server. Results and discussion: In silico mining of annotated metagenomic data revealed nitrilase from unclassified Alphaproteobacteria. By using the artificial intelligence program AlphaFold2, the 3D structure was predicted with a per-residue confidence statistic score of about 95.8%, and the stability of the predicted model was verified with molecular dynamics for a 100-ns simulation. Molecular docking analysis determined the binding affinity of a novel nitrilase with nitriles. The binding scores produced by the novel nitrilase were approximately similar to those of the other prokaryotic nitrilase crystal structures, with a deviation of ±0.5.}, } @article {pmid37004854, year = {2023}, author = {Jiao, P and Tian, Q and Wolfgang, S and Dong, X and Wu, Y}, title = {Cold-resistant performance and the promoted development of functional community with flexible metabolic patterns in a Biofilm Bio-Nutrient Removal (BBNR) system amended with supplementary carbon source for phosphorus recovery.}, journal = {Environmental research}, volume = {227}, number = {}, pages = {115807}, doi = {10.1016/j.envres.2023.115807}, pmid = {37004854}, issn = {1096-0953}, mesh = {*Phosphorus ; *Bioreactors ; Carbon/metabolism ; Extracellular Polymeric Substance Matrix/metabolism ; Nutrients ; Biofilms ; Nitrogen/analysis ; Sewage ; Waste Disposal, Fluid/methods ; }, abstract = {The need for recovery of phosphorus (P) from wastewater has accelerated the retrofitting of existing bio-nutrient removal (BNR) processes into bio-nutrient removal-phosphorus recovery processes (BNR-PR). A periodical carbon source supplement is needed to facilitate the P-recovery. But the impact of this amendment on the cold resistances of the reactor and the functional microorganisms (for nitrogen and phosphorus (P) removal/recovery) are still unknown. This study presents the performances of a biofilm BNR process with a carbon source regulated the P recovery (BBNR-CPR) process operating at different temperatures. When the temperature was decreased from 25 ± 1 °C to 6 ± 1 °C, the system total nitrogen and total phosphorus removals and the corresponding kinetic coefficients decreased moderately. The indicative genes of the phosphorus-accumulating organisms (e.g., Thauera spp. and Candidatus Accumulibacter spp.) increased significantly. An increase of Nitrosomonas spp. genes aligned to polyhydroxyalkanoates (PHAs), glycine, and extracellular polymeric substance synthesis were observed, which was probably related to cold resistance. The results provide a new vision for understanding the advantages of P recovery-targeted carbon source supplementation for constructing a new type of cold-resistant BBNR-CPR processes.}, } @article {pmid37004750, year = {2023}, author = {Lattanzi, G and Strati, F and Díaz-Basabe, A and Perillo, F and Amoroso, C and Protti, G and Rita Giuffrè, M and Iachini, L and Baeri, A and Baldari, L and Cassinotti, E and Ghidini, M and Galassi, B and Lopez, G and Noviello, D and Porretti, L and Trombetta, E and Messuti, E and Mazzarella, L and Iezzi, G and Nicassio, F and Granucci, F and Vecchi, M and Caprioli, F and Facciotti, F}, title = {iNKT cell-neutrophil crosstalk promotes colorectal cancer pathogenesis.}, journal = {Mucosal immunology}, volume = {16}, number = {3}, pages = {326-340}, doi = {10.1016/j.mucimm.2023.03.006}, pmid = {37004750}, issn = {1935-3456}, mesh = {Mice ; Animals ; *Natural Killer T-Cells ; Neutrophils ; *Antineoplastic Agents/pharmacology ; Immunotherapy ; *Colorectal Neoplasms/pathology ; Tumor Microenvironment ; }, abstract = {iNKT cells account for a relevant fraction of effector T-cells in the intestine and are considered an attractive platform for cancer immunotherapy. Although iNKT cells are cytotoxic lymphocytes, their functional role in colorectal cancer (CRC) is still controversial, limiting their therapeutic use. Thus, we examined the immune cell composition and iNKT cell phenotype of CRC lesions in patients (n = 118) and different murine models. High-dimensional single-cell flow-cytometry, metagenomics, and RNA sequencing experiments revealed that iNKT cells are enriched in tumor lesions. The tumor-associated pathobiont Fusobacterium nucleatum induces IL-17 and Granulocyte-macrophage colony-stimulating factor (GM-CSF) expression in iNKT cells without affecting their cytotoxic capability but promoting iNKT-mediated recruitment of neutrophils with polymorphonuclear myeloid-derived suppressor cells-like phenotype and functions. The lack of iNKT cells reduced the tumor burden and recruitment of immune suppressive neutrophils. iNKT cells in-vivo activation with α-galactosylceramide restored their anti-tumor function, suggesting that iNKT cells can be modulated to overcome CRC-associated immune evasion. Tumor co-infiltration by iNKT cells and neutrophils correlates with negative clinical outcomes, highlighting the importance of iNKT cells in the pathophysiology of CRC. Our results reveal a functional plasticity of iNKT cells in CRC, suggesting a pivotal role of iNKT cells in shaping the tumor microenvironment, with relevant implications for treatment.}, } @article {pmid37004601, year = {2023}, author = {do Socorro Fôro Ramos, E and Bahia, SL and de Oliveira Ribeiro, G and Villanova, F and de Pádua Milagres, FA and Brustulin, R and Pandey, RP and Deng, X and Delwart, E and da Costa, AC and Leal, É}, title = {Characterization of Phietavirus Henu 2 in the virome of individuals with acute gastroenteritis.}, journal = {Virus genes}, volume = {59}, number = {3}, pages = {464-472}, pmid = {37004601}, issn = {1572-994X}, support = {302677/2019-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Humans ; *Methicillin-Resistant Staphylococcus aureus ; Virome ; *Bacteriophages ; *Siphoviridae ; *Gastroenteritis ; *Staphylococcal Infections/microbiology ; }, abstract = {There is a growing interest in phages as potential biotechnological tools in human health owing to the antibacterial activity of these viruses. In this study, we characterized a new member (named PhiV_005_BRA/2016) of the recently identified phage species Phietavirus Henu 2. PhiV_005_BRA/2016 was detected through metagenomic analysis of stool samples of individuals with acute gastroenteritis. PhiV_005_BRA/2016 contains double-stranded linear DNA (dsDNA), it has a genome of 43,513 base pairs (bp), with a high identity score (99%) with phage of the genus Phietavirus, species of Phietavirus Henu 2. Life style prediction indicated that PhiV_005_BRA/2016 is a lysogenic phage whose the main host is methicillin-resistant Staphylococcus aureus (MRSA). Indeed, we found PhiV_005_BRA/2016 partially integrated in the genome of distinct MRSA strains. Our findings highlights the importance of large-scale screening of bacteriophages to better understand the emergence of multi-drug resistant bacterial.}, } @article {pmid37004105, year = {2023}, author = {Yue, H and Yue, W and Jiao, S and Kim, H and Lee, YH and Wei, G and Song, W and Shu, D}, title = {Plant domestication shapes rhizosphere microbiome assembly and metabolic functions.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {70}, pmid = {37004105}, issn = {2049-2618}, mesh = {Domestication ; Rhizosphere ; Plant Roots/microbiology ; *Microbiota/genetics ; *Mycobiome ; Plants ; Bacteria/genetics ; Soil Microbiology ; }, abstract = {BACKGROUND: The rhizosphere microbiome, which is shaped by host genotypes, root exudates, and plant domestication, is crucial for sustaining agricultural plant growth. Despite its importance, how plant domestication builds up specific rhizosphere microbiomes and metabolic functions, as well as the importance of these affected rhizobiomes and relevant root exudates in maintaining plant growth, is not well understood. Here, we firstly investigated the rhizosphere bacterial and fungal communities of domestication and wild accessions of tetraploid wheat using amplicon sequencing (16S and ITS) after 9 years of domestication process at the main production sites in China. We then explored the ecological roles of root exudation in shaping rhizosphere microbiome functions by integrating metagenomics and metabolic genomics approaches. Furthermore, we established evident linkages between root morphology traits and keystone taxa based on microbial culture and plant inoculation experiments.

RESULTS: Our results suggested that plant rhizosphere microbiomes were co-shaped by both host genotypes and domestication status. The wheat genomes contributed more variation in the microbial diversity and composition of rhizosphere bacterial communities than fungal communities, whereas plant domestication status exerted much stronger influences on the fungal communities. In terms of microbial interkingdom association networks, domestication destabilized microbial network and depleted the abundance of keystone fungal taxa. Moreover, we found that domestication shifted the rhizosphere microbiome from slow growing and fungi dominated to fast growing and bacteria dominated, thereby resulting in a shift from fungi-dominated membership with enrichment of carbon fixation genes to bacteria-dominated membership with enrichment of carbon degradation genes. Metagenomics analyses further indicated that wild cultivars of wheat possess higher microbial function diversity than domesticated cultivars. Notably, we found that wild cultivar is able to harness rhizosphere microorganism carrying N transformation (i.e., nitrification, denitrification) and P mineralization pathway, whereas rhizobiomes carrying inorganic N fixation, organic N ammonification, and inorganic P solubilization genes are recruited by the releasing of root exudates from domesticated wheat. More importantly, our metabolite-wide association study indicated that the contrasting functional roles of root exudates and the harnessed keystone microbial taxa with different nutrient acquisition strategies jointly determined the aboveground plant phenotypes. Furthermore, we observed that although domesticated and wild wheats recruited distinct microbial taxa and relevant functions, domestication-induced recruitment of keystone taxa led to a consistent growth regulation of root regardless of wheat domestication status.

CONCLUSIONS: Our results indicate that plant domestication profoundly influences rhizosphere microbiome assembly and metabolic functions and provide evidence that host plants are able to harness a differentiated ecological role of root-associated keystone microbiomes through the release of root exudates to sustain belowground multi-nutrient cycles and plant growth. These findings provide valuable insights into the mechanisms underlying plant-microbiome interactions and how to harness the rhizosphere microbiome for crop improvement in sustainable agriculture. Video Abstract.}, } @article {pmid37003965, year = {2023}, author = {Syama, K and Jothi, JAA and Khanna, N}, title = {Automatic disease prediction from human gut metagenomic data using boosting GraphSAGE.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {126}, pmid = {37003965}, issn = {1471-2105}, mesh = {Humans ; Metagenome ; *Microbiota/genetics ; Machine Learning ; Metagenomics/methods ; *Inflammatory Bowel Diseases/genetics ; *Colorectal Neoplasms/genetics ; }, abstract = {BACKGROUND: The human microbiome plays a critical role in maintaining human health. Due to the recent advances in high-throughput sequencing technologies, the microbiome profiles present in the human body have become publicly available. Hence, many works have been done to analyze human microbiome profiles. These works have identified that different microbiome profiles are present in healthy and sick individuals for different diseases. Recently, several computational methods have utilized the microbiome profiles to automatically diagnose and classify the host phenotype.

RESULTS: In this work, a novel deep learning framework based on boosting GraphSAGE is proposed for automatic prediction of diseases from metagenomic data. The proposed framework has two main components, (a). Metagenomic Disease graph (MD-graph) construction module, (b). Disease prediction Network (DP-Net) module. The graph construction module constructs a graph by considering each metagenomic sample as a node in the graph. The graph captures the relationship between the samples using a proximity measure. The DP-Net consists of a boosting GraphSAGE model which predicts the status of a sample as sick or healthy. The effectiveness of the proposed method is verified using real and synthetic datasets corresponding to diseases like inflammatory bowel disease and colorectal cancer. The proposed model achieved a highest AUC of 93%, Accuracy of 95%, F1-score of 95%, AUPRC of 95% for the real inflammatory bowel disease dataset and a best AUC of 90%, Accuracy of 91%, F1-score of 87% and AUPRC of 93% for the real colorectal cancer dataset.

CONCLUSION: The proposed framework outperforms other machine learning and deep learning models in terms of classification accuracy, AUC, F1-score and AUPRC for both synthetic and real metagenomic data.}, } @article {pmid37003554, year = {2023}, author = {Zhao, X and Qi, G and Feng, Y and Du, C}, title = {Application of nematicide avermectin enriched antibiotic-resistant bacteria and antibiotic resistance genes in farmland soil.}, journal = {Environmental research}, volume = {227}, number = {}, pages = {115802}, doi = {10.1016/j.envres.2023.115802}, pmid = {37003554}, issn = {1096-0953}, mesh = {Humans ; *Soil ; Farms ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Manure ; }, abstract = {The extensive use of antibiotics in medicine and agriculture has resulted in the accumulation of antibiotic-resistant microorganisms and antibiotic resistance genes (ARGs) in environments, which threaten human health and contaminate environment. Nematicide avermectin is widely applied to control root-knot nematodes. The effect of five-years application of avermectin on rhizosphere microbiome and resistome of sick tobacco plants in farmland were investigated in present study. The environmental risks of avermectin was assessed adequately. Metagenomic method was used to analyze antibiotic-resistant bacteria and antibiotic resistance genes in the avermectin-treated soil. The abundance and distribution of antibiotic-resistant bacteria and their antibiotic resistance genes were affected by avermectin application. The antibiotic resistant Proteobacteria occupied the highest percentage (36%) in rhizosphere soil and carried 530 ARGs. Opportunistic human pathogens carrying antibiotic resistance genes were enriched in the avermectin-treated soil. Avermectin application increased the counts of many types of antibiotic resistance genes. The relative abundances of genes adeF, BahA, fusH, ileS, and tlrB in the avermectin-treated soil were significantly greater than in the untreated control soil. Different resistance mechanisms were revealed in the avermectin-treated soil. The efflux of antibiotic (670 ARGs), inactivation of antibiotic (475 ARGs), and alteration of antibiotic target (267 ARGs) were the main resistance mechanisms. Rigid control the avermectin dose and use frequency and other pesticides can decrease soil antibiotic resistance genes and protect agricultural products' safety and public health. Overall, application of nematicide avermectin enriched antibiotic-resistant bacteria and antibiotic resistance genes in farmland soil, which should be on the alert for environment protection.}, } @article {pmid37003141, year = {2023}, author = {Roveta, C and Calcinai, B and Girolametti, F and Fernandes Couceiro, J and Puce, S and Annibaldi, A and Costa, R}, title = {The prokaryotic community of Chondrosia reniformis Nardo, 1847: from diversity to mercury detection.}, journal = {Zoology (Jena, Germany)}, volume = {158}, number = {}, pages = {126091}, doi = {10.1016/j.zool.2023.126091}, pmid = {37003141}, issn = {1873-2720}, mesh = {Animals ; *Mercury ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Archaea/genetics ; *Porifera/genetics ; *Ammonium Compounds ; Phylogeny ; Seawater ; }, abstract = {Microbial communities inhabiting sponges are known to take part in many metabolic pathways, including nutrient cycles, and possibly also in the bioaccumulation of trace elements (TEs). Here, we used high-throughput, Illumina sequencing of 16S rRNA genes to characterize the prokaryotic communities present in the cortex and choanosome, respectively the external and internal body region of Chondrosia reniformis, and in the surrounding seawater. Furthermore, we estimated the total mercury content (THg) in these body regions of the sponge and in the corresponding microbial cell pellets. Fifteen prokaryotic phyla were detected in association with C. reniformis, 13 belonging to the domain Bacteria and two to the Archaea. No significant differences between the prokaryotic community composition of the two regions were found. Three lineages of ammonium-oxidizing organisms (Cenarchaeum symbiosum, Nitrosopumilus maritimus, and Nitrosococcus sp.) co-dominated the prokaryotic community, suggesting ammonium oxidation/nitrification as a key metabolic pathway within the microbiome of C. reniformis. In the sponge fractions, higher THg levels were found in the choanosome compared to the cortex. In contrast, comparable THg levels found in the microbial pellets obtained from both regions were significantly lower than those observed in the corresponding sponge fractions. Our work provides new insights into the prokaryotic communities and TEs distribution in different body parts of a model organism relevant for marine conservation and biotechnology. In this sense, this study paves the way for scientists to deepen the possible application of sponges not only as bioindicators, but also as bioremediation tools of metal polluted environments.}, } @article {pmid37003055, year = {2023}, author = {Jamal, R and Messaoudene, M and de Figuieredo, M and Routy, B}, title = {Future indications and clinical management for fecal microbiota transplantation (FMT) in immuno-oncology.}, journal = {Seminars in immunology}, volume = {67}, number = {}, pages = {101754}, doi = {10.1016/j.smim.2023.101754}, pmid = {37003055}, issn = {1096-3618}, support = {//CIHR/Canada ; }, mesh = {Humans ; Animals ; Mice ; Fecal Microbiota Transplantation/adverse effects ; Immune Checkpoint Inhibitors ; Treatment Outcome ; *Microbiota ; *Neoplasms/therapy/etiology ; }, abstract = {The gut microbiota has rapidly emerged as one of the "hallmarks of cancers" and a key contributor to cancer immunotherapy. Metagenomics profiling has established the link between microbiota compositions and immune checkpoint inhibitors response and toxicity, while murine experiments demonstrating the synergistic benefits of microbiota modification with immune checkpoint inhibitors (ICIs) pave a clear path for translation. Fecal microbiota transplantation (FMT) is one of the most effective treatments for patients with Clostridioides difficile, but its utility in other disease contexts has been limited. Nonetheless, promising data from the first trials combining FMT with ICIs have provided strong clinical rationale to pursue this strategy as a novel therapeutic avenue. In addition to the safety considerations surrounding new and emerging pathogens potentially transmissible by FMT, several other challenges must be overcome in order to validate the use of FMT as a therapeutic option in oncology. In this review, we will explore how the lessons learned from FMT in other specialties will help shape the design and development of FMT in the immuno-oncology arena.}, } @article {pmid37002975, year = {2023}, author = {Stockdale, SR and Hill, C}, title = {Incorporating plasmid biology and metagenomics into a holistic model of the human gut microbiome.}, journal = {Current opinion in microbiology}, volume = {73}, number = {}, pages = {102307}, doi = {10.1016/j.mib.2023.102307}, pmid = {37002975}, issn = {1879-0364}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Plasmids/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Metagenomics ; }, abstract = {The human gut microbiome is often described as the collection of bacteria, archaea, fungi, protists, and viruses associated with an individual, with no acknowledgement of the plasmid constituents. However, like viruses, plasmids are autonomous intracellular replicating entities that can influence the genotype and phenotype of their host and mediate trans-kingdom interactions. Plasmids are frequently noted as vehicles for horizontal gene transfer and for spreading antibiotic resistance, yet their multifaceted contribution to mutualistic and antagonistic interactions within the human microbiome and impact on human health is overlooked. In this review, we highlight the importance of plasmids and their biological properties as overlooked components of microbiomes. Subsequent human microbiome studies should include dedicated analyses of plasmids, particularly as a holistic understanding of human-microbial interactions is required before effective and safe interventions can be implemented to improve human well-being.}, } @article {pmid37002784, year = {2023}, author = {Honap, TP and Monroe, CR and Johnson, SJ and Jacobson, DK and Abin, CA and Austin, RM and Sandberg, P and Levine, M and Sankaranarayanan, K and Lewis, CM}, title = {Oral metagenomes from Native American Ancestors reveal distinct microbial lineages in the pre-contact era.}, journal = {American journal of biological anthropology}, volume = {182}, number = {4}, pages = {542-556}, doi = {10.1002/ajpa.24735}, pmid = {37002784}, issn = {2692-7691}, support = {NSF BCS-2045308//National Science Foundation/ ; }, mesh = {Humans ; *American Indian or Alaska Native ; Calculi/genetics ; Chloroflexi/genetics ; DNA, Bacterial/analysis ; *Metagenome/genetics ; Periodontitis/microbiology ; Treponema denticola/genetics ; *Mouth/microbiology ; }, abstract = {OBJECTIVES: Limited studies have focused on how European contact and colonialism impacted Native American oral microbiomes, specifically, the diversity of commensal or opportunistically pathogenic oral microbes, which may be associated with oral diseases. Here, we studied the oral microbiomes of pre-contact Wichita Ancestors, in partnership with the Descendant community, The Wichita and Affiliated Tribes, Oklahoma, USA.

MATERIALS AND METHODS: Skeletal remains of 28 Wichita Ancestors from 20 archeological sites (dating approximately to 1250-1450 CE) were paleopathologically assessed for presence of dental calculus and oral disease. DNA was extracted from calculus, and partial uracil deglycosylase-treated double-stranded DNA libraries were shotgun-sequenced using Illumina technology. DNA preservation was assessed, the microbial community was taxonomically profiled, and phylogenomic analyzes were conducted.

RESULTS: Paleopathological analysis revealed signs of oral diseases such as caries and periodontitis. Calculus samples from 26 Ancestors yielded oral microbiomes with minimal extraneous contamination. Anaerolineaceae bacterium oral taxon 439 was found to be the most abundant bacterial species. Several Ancestors showed high abundance of bacteria typically associated with periodontitis such as Tannerella forsythia and Treponema denticola. Phylogenomic analyzes of Anaerolineaceae bacterium oral taxon 439 and T. forsythia revealed biogeographic structuring; strains present in the Wichita Ancestors clustered with strains from other pre-contact Native Americans and were distinct from European and/or post-contact American strains.

DISCUSSION: We present the largest oral metagenome dataset from a pre-contact Native American population and demonstrate the presence of distinct lineages of oral microbes specific to the pre-contact Americas.}, } @article {pmid37002710, year = {2023}, author = {Sandoval-Quintana, E and Stangl, C and Huang, L and Renkens, I and Duran, R and van Haaften, G and Monroe, G and Lauga, B and Cagnon, C}, title = {CRISPR-Cas9 enrichment, a new strategy in microbial metagenomics to investigate complex genomic regions: The case of an environmental integron.}, journal = {Molecular ecology resources}, volume = {23}, number = {6}, pages = {1288-1298}, doi = {10.1111/1755-0998.13798}, pmid = {37002710}, issn = {1755-0998}, support = {06SEST09//Agence Nationale de la Recherche/ ; CESA-2011-006 01//Agence Nationale de la Recherche/ ; //E2S-UPPA/ ; STF-8420//European Molecular Biology Organization/ ; //Ministère de l'Enseignement Supérieur et de la Recherche Scientifique/ ; 184.034.019//The Netherlands X-omics Initiative/ ; }, mesh = {*Integrons/genetics ; *Metagenomics ; CRISPR-Cas Systems ; Bacteria/genetics ; Integrases/genetics ; }, abstract = {Environmental integrons are ubiquitous in natural microbial communities, but they are mostly uncharacterized and their role remains elusive. Thus far, research has been hindered by methodological limitations. Here, we successfully used an innovative approach combining CRISPR-Cas9 enrichment with long-read nanopore sequencing to target, in a complex microbial community, a putative adaptive environmental integron, InOPS, and to unravel its complete structure and genetic context. A contig of 20 kb was recovered containing the complete integron from the microbial metagenome of oil-contaminated coastal sediments. InOPS exhibited typical integron features. The integrase, closely related to integrases of marine Desulfobacterota, possessed all the elements of a functional integron integrase. The gene cassettes harboured mostly unknown functions hampering inferences about their ecological importance. Moreover, the putative InOPS host, likely a hydrocarbonoclastic marine bacteria, raises questions as to the adaptive potential of InOPS in response to oil contamination. Finally, several mobile genetic elements were intertwined with InOPS highlighting likely genomic plasticity, and providing a source of genetic novelty. This case study showed the power of CRISPR-Cas9 enrichment to elucidate the structure and context of specific DNA regions for which only a short sequence is known. This method is a new tool for environmental microbiologists working with complex microbial communities to target low abundant, large or repetitive genetic structures that are difficult to obtain by classical metagenomics. More precisely, here, it offers new perspectives to comprehensively assess the eco-evolutionary significance of environmental integrons.}, } @article {pmid37002522, year = {2023}, author = {Wagh, MS and Sivarajan, S and Osborne, WJ}, title = {A new paradigm in the bioremoval of lead, nickel, and cadmium using a cocktail of biosystems: a metagenomic approach.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {20}, pages = {58967-58985}, pmid = {37002522}, issn = {1614-7499}, mesh = {Animals ; Cadmium/analysis ; Nickel/analysis ; Lead/analysis ; RNA, Ribosomal, 16S ; *Metals, Heavy/analysis ; Biodegradation, Environmental ; *Microbiota ; Bacteria ; Soil/chemistry ; *Oligochaeta ; *Soil Pollutants/analysis ; }, abstract = {Lead (Pb), nickel (Ni), and cadmium (Cd) are known for its harmful effects on the environment. Microbial community related to soil plays a pivotal role in configuring several properties of the ecosystem. Thus, remediation of such heavy metals using multiple biosystems had shown excellent bioremoval potential. The current study demonstrates the integrated approach of Chrysopogon zizanioides in combination with earthworm Eisenia fetida augmented with VITMSJ3 potent strain for the uptake of metals like Pb, Ni, and Cd from the contaminated soil. For the uptake of heavy metals, Pb, Ni, and Cd with the concentrations of 50, 100, and 150 mg kg[-1] were supplemented in pots with plants and earthworms. C. zizanioides was used for bioremoval due to their massive fibrous root system which can absorb heavy metals. A substantial increase of 70-80% Pb, Ni, and Cd was found for VITMSJ3 augmented setup. A total of 12 earthworms were introduced in each setup and were tested for the toxicity and damages in the various internal structures. Reduction in malondialdehyde (MDA) content was observed in the earthworms with VITMSJ3 strain proving less toxicity and damages. Metagenomic analysis of the soil associated bacterial diversity was assessed by amplifying the V3V4 region of the 16S rRNA gene and the annotations were studied. Firmicutes were found to be the predominant genus with 56.65% abundance in the bioaugmented soil R (60) proving the detoxification of metals in the bioaugmented soil. Our study proved that a synergistic effect of plant and earthworm in association with potent bacterial strain had higher uptake of Pb, Ni, and Cd. Metagenomic analysis revealed the changes in microbial abundance in the soil before and after treatment.}, } @article {pmid37002338, year = {2023}, author = {Su, J and Lui, WW and Lee, Y and Zheng, Z and Siu, GK and Ng, TT and Zhang, T and Lam, TT and Lao, HY and Yam, WC and Tam, KK and Leung, KS and Lam, TW and Leung, AW and Luo, R}, title = {Evaluation of Mycobacterium tuberculosis enrichment in metagenomic samples using ONT adaptive sequencing and amplicon sequencing for identification and variant calling.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {5237}, pmid = {37002338}, issn = {2045-2322}, mesh = {Humans ; *Mycobacterium tuberculosis/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Metagenome ; Computer Simulation ; Sequence Analysis, DNA ; *Nanopores ; }, abstract = {Sensitive detection of Mycobacterium tuberculosis (TB) in small percentages in metagenomic samples is essential for microbial classification and drug resistance prediction. However, traditional methods, such as bacterial culture and microscopy, are time-consuming and sometimes have limited TB detection sensitivity. Oxford nanopore technologies (ONT) MinION sequencing allows rapid and simple sample preparation for sequencing. Its recently developed adaptive sequencing selects reads from targets while allowing real-time base-calling to achieve sequence enrichment or depletion during sequencing. Another common enrichment method is PCR amplification of the target TB genes. In this study, we compared both methods using ONT MinION sequencing for TB detection and variant calling in metagenomic samples using both simulation runs and those with synthetic and patient samples. We found that both methods effectively enrich TB reads from a high percentage of human (95%) and other microbial DNA. Adaptive sequencing with readfish and UNCALLDE achieved a 3.9-fold and 2.2-fold enrichment compared to the control run. We provide a simple automatic analysis framework to support the detection of TB for clinical use, openly available at https://github.com/HKU-BAL/ONT-TB-NF . Depending on the patient's medical condition and sample type, we recommend users evaluate and optimize their workflow for different clinical specimens to improve the detection limit.}, } @article {pmid37001916, year = {2023}, author = {Magner, C and Jenkins, D and Koc, F and Tan, MH and O'Toole, M and Boyle, J and Maguire, N and Duignan, S and Murphy, K and Ross, P and Stanton, C and McMahon, CJ}, title = {Protocol for a prospective cohort study exploring the gut microbiota of infants with congenital heart disease undergoing cardiopulmonary bypass (the GuMiBear study).}, journal = {BMJ open}, volume = {13}, number = {3}, pages = {e067016}, pmid = {37001916}, issn = {2044-6055}, mesh = {Infant, Newborn ; Infant ; Humans ; Child ; *Gastrointestinal Microbiome ; Cardiopulmonary Bypass ; Prospective Studies ; *Heart Defects, Congenital/surgery ; *Cardiac Surgical Procedures ; }, abstract = {INTRODUCTION: The gut microbiota develops from birth and matures significantly during the first 24 months of life, playing a major role in infant health and development. The composition of the gut microbiota is influenced by several factors including mode of delivery, gestational age, feed type and treatment with antibiotics. Alterations in the pattern of gut microbiota development and composition can be associated with illness and compromised health outcomes.Infants diagnosed with 'congenital heart disease' (CHD) often require surgery involving cardiopulmonary bypass (CPB) early in life. The impact of this type of surgery on the integrity of the gut microbiome is poorly understood. In addition, these infants are at significant risk of developing the potentially devastating intestinal condition necrotising enterocolitis.

METHODS AND ANALYSIS: This study will employ a prospective cohort study methodology to investigate the gut microbiota and urine metabolome of infants with CHD undergoing surgery involving CPB. Stool and urine samples, demographic and clinical data will be collected from eligible infants based at the National Centre for Paediatric Cardiac Surgery in Ireland. Shotgun metagenome sequencing will be performed on stool samples and urine metabolomic analysis will identify metabolic biomarkers. The impact of the underlying diagnosis, surgery involving CPB, and the influence of environmental factors will be explored. Data from healthy age-matched infants from the INFANTMET study will serve as a control for this study.

ETHICS AND DISSEMINATION: This study has received full ethical approval from the Clinical Research Ethics Committee of Children's Health Ireland, GEN/826/20.}, } @article {pmid37001571, year = {2023}, author = {Song, C and Ma, Y and Wang, Y and Li, P and Chen, Y and Liu, H and Zhang, Z}, title = {Diosgenin reduces bone loss through the regulation of gut microbiota in ovariectomized rats.}, journal = {Gene}, volume = {869}, number = {}, pages = {147383}, doi = {10.1016/j.gene.2023.147383}, pmid = {37001571}, issn = {1879-0038}, mesh = {Female ; Rats ; Animals ; Humans ; Rats, Sprague-Dawley ; Bone Density ; *Gastrointestinal Microbiome ; *Diosgenin/pharmacology/therapeutic use ; *Bone Diseases, Metabolic ; *Osteoporosis/drug therapy/metabolism ; Estradiol/pharmacology ; Ovariectomy ; }, abstract = {Diosgenin (DIO) is an aglycone of steroid saponins acquired from plants, including Dioscorea alata, Smilax China, and Trigonella foenum graecum, acting as an anti-osteoporosis, anti-diabetic, anti-hyperlipidemic, anti-inflammatory. Recent studies have demonstrated that DIO reduces bone loss. This study aimed to investigate the effects of DIO on the gut microbiota (GM) of ovariectomized (OVX) osteoporotic rats. Female Sprague-Dawley rats were randomly divided into sham operation (sham + vehicle group) or ovariectomy. For 12 weeks, OVX rats were treated using a vehicle (OVX + vehicle group) and DIO (OVX + DIO group). Subsequently, ELISA was conducted to determine serum estradiol levels, micro-CT scanning was performed to evaluate bone quality, and feces were collected for metagenomics sequencing to examine the structure and function of GM. Raw reads were filtered to remove chimera sequences. Operational taxonomic units (OTUs) were clustered in the filtered reads. A Venn diagram analysis was conducted to study the common and unique OTUs in the sham + vehicle, OVX + vehicle, and OVX + DIO groups. LEfSe analysis was conducted to evaluate the specific GM of the three groups. The GM functions were analyzed using the KEGG and CAZy databases. After a 12-week treatment, DIO administration prevented OVX-induced weight gain and increased the estradiol levels. DIO treatment improved the bone microstructure and structural parameters of rat tibias. Metagenomics sequencing results identified 1139, 1207, and 1235 operational taxonomic units (OTUs) in the sham + vehicle, OVX + vehicle, and OVX + DIO groups, respectively. The percentage of common OTUs was 41.2%. Treatment with DIO restored the composition of GM in OVX rats by increasing the abundance of Coriobacteriia Adlercreutzia, Romboutsia, and Romboutsia_idealis and reducing the abundance of Betaproteobacteria, Gammaproteobacteria, Methanobacteria, Bacteroides, Phocaeicola, Alistipes, Bacteroids_uniformis, Bacteroids_xylanisolvens. The anti-osteoporosis effect of DIO can be regulated through environmental information processing, organismal Systems, Cellular Processes, human diseases, metabolism, and genetic information processing. Meanwhile, treatment with DIO improved GM homeostasis by increasing the metabolism of carbohydrates, other amino acids, and glycans and reducing translation, energy metabolism, and nucleotide metabolism. DIO can reduce bone loss by regulating the structural composition and function of GM, a novel strategy for preventing osteoporosis.}, } @article {pmid37001227, year = {2023}, author = {Gao, L and Yang, T and Zhang, X and Lei, W and Huang, JA}, title = {Rapid detection of pulmonary nocardiosis by metagenomic next generation sequencing.}, journal = {Diagnostic microbiology and infectious disease}, volume = {106}, number = {2}, pages = {115928}, doi = {10.1016/j.diagmicrobio.2023.115928}, pmid = {37001227}, issn = {1879-0070}, mesh = {Humans ; High-Throughput Nucleotide Sequencing ; Retrospective Studies ; *Nocardia Infections/diagnosis ; *Nocardia/genetics ; Biological Assay ; Metagenomics ; }, abstract = {We retrospectively analyzed 3 cases of pulmonary nocardiosis. Patients were identified by metagenomic next generation sequencing (mNGS) in the First Affiliated Hospital of Soochow University, from January 2019 to April 2022. All patients had underlying diseases, and were in immunocompromised state, with membranous nephropathy, acute lymphoblastic leukemia (ALL), and systemic lupus erythematosus (SLE), respectively. Symptoms common to all cases included fever, cough and expectoration. Chest computed tomography (CT) presented patchy shadows or nodules, with or without cavitation lesions, or pleural effusion. mNGS detected Nocardia spp. via bronchoalveolar lavage fluid (BALF) or blood samples from patients. All the patients were discharged with recovery after using the trimethoprim-sulfamethoxazole (TMP-SMX) and remained without evidence of disease during regular follow-ups. mNGS may be a tool for rapid and accurate detection and identification of pulmonary nocardiosis, but interpreting the mNGS results should be more cautious because the mNGS assay can also detect colonization.}, } @article {pmid37000853, year = {2023}, author = {Guo, A and Salzberg, SL and Zimin, AV}, title = {JASPER: A fast genome polishing tool that improves accuracy of genome assemblies.}, journal = {PLoS computational biology}, volume = {19}, number = {3}, pages = {e1011032}, pmid = {37000853}, issn = {1553-7358}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Sequence Analysis, DNA ; *High-Throughput Nucleotide Sequencing ; Genome, Human/genetics ; Metagenomics ; *Nanopores ; }, abstract = {Advances in long-read sequencing technologies have dramatically improved the contiguity and completeness of genome assemblies. Using the latest nanopore-based sequencers, we can generate enough data for the assembly of a human genome from a single flow cell. With the long-read data from these sequences, we can now routinely produce de novo genome assemblies in which half or more of a genome is contained in megabase-scale contigs. Assemblies produced from nanopore data alone, though, have relatively high error rates and can benefit from a process called polishing, in which more-accurate reads are used to correct errors in the consensus sequence. In this manuscript, we present a novel tool for genome polishing called JASPER (Jellyfish-based Assembly Sequence Polisher for Error Reduction). In contrast to many other polishing methods, JASPER gains efficiency by avoiding the alignment of reads to the assembly. Instead, JASPER uses a database of k-mer counts that it creates from the reads to detect and correct errors in the consensus. Our experiments demonstrate that JASPER is faster than alignment-based polishers, and both faster and more accurate than other k-mer based polishing methods. We also introduce the idea of using a polishing tool to create population-specific reference genomes, and illustrate this idea using sequence data from multiple individuals from Tokyo, Japan.}, } @article {pmid37000389, year = {2023}, author = {Ganesan, R and Gupta, H and Jeong, JJ and Sharma, SP and Won, SM and Oh, KK and Yoon, SJ and Han, SH and Yang, YJ and Baik, GH and Bang, CS and Kim, DJ and Suk, KT}, title = {Characteristics of microbiome-derived metabolomics according to the progression of alcoholic liver disease.}, journal = {Hepatology international}, volume = {}, number = {}, pages = {}, pmid = {37000389}, issn = {1936-0541}, support = {NRF-2018M3A9F3020956//Ministry of National Defense/ ; NRF-2019R1I1A3A01060447//Ministry of National Defense/ ; NRF-2020R1A6A1A03043026//Ministry of National Defense/ ; P0020622//Korea Institute for Advancement of Technology/ ; }, abstract = {BACKGROUND AND AIM: The prevalence and severity of alcoholic liver disease (ALD) are increasing. The incidence of alcohol-related cirrhosis has risen up to 2.5%. This study aimed to identify novel metabolite mechanisms involved in the development of ALD in patients. The use of gut microbiome-derived metabolites is increasing in targeted therapies. Identifying metabolic compounds is challenging due to the complex patterns that have long-term effects on ALD. We investigated the specific metabolite signatures in ALD patients.

METHODS: This study included 247 patients (heathy control, HC: n = 62, alcoholic fatty liver, AFL; n = 25, alcoholic hepatitis, AH; n = 80, and alcoholic cirrhosis, AC, n = 80) identified, and stool samples were collected. 16S rRNA sequencing and metabolomics were performed with MiSeq sequencer and liquid chromatography coupled to time-of-flight-mass spectrometry (LC-TOF-MS), respectively. The untargeted metabolites in AFL, AH, and AC samples were evaluated by multivariate statistical analysis and metabolic pathotypic expression. Metabolic network classifiers were used to predict the pathway expression of the AFL, AH, and AC stages.

RESULTS: The relative abundance of Proteobacteria was increased and the abundance of Bacteroides was decreased in ALD samples (p = 0.001) compared with that in HC samples. Fusobacteria levels were higher in AH samples (p = 0.0001) than in HC samples. Untargeted metabolomics was applied to quantitatively screen 103 metabolites from each stool sample. Indole-3-propionic acid levels are significantly lower in AH and AC (vs. HC, p = 0.001). Indole-3-lactic acid (ILA: p = 0.04) levels were increased in AC samples. AC group showed an increase in indole-3-lactic acid (vs. HC, p = 0.040) level. Compared with that in HC samples, the levels of short-chain fatty acids (SCFAs: acetic acid, butyric acid, propionic acid, iso-butyric acid, and iso-valeric acid) and bile acids (lithocholic acids) were significantly decreased in AC. The pathways of linoleic acid metabolism, indole compounds, histidine metabolism, fatty acid degradation, and glutamate metabolism were closely associated with ALD metabolism.

CONCLUSIONS: This study identified that microbial metabolic dysbiosis is associated with ALD-related metabolic dysfunction. The SCFAs, bile acids, and indole compounds were depleted during ALD progression.

CLINICAL TRIAL: Clinicaltrials.gov, number NCT04339725.}, } @article {pmid36999249, year = {2023}, author = {D'Alò, F and Zucconi, L and Onofri, S and Canini, F and Cannone, N and Malfasi, F and Morais, DK and Starke, R}, title = {Effects of 5-year experimental warming in the Alpine belt on soil Archaea: Multi-omics approaches and prospects.}, journal = {Environmental microbiology reports}, volume = {15}, number = {4}, pages = {291-297}, pmid = {36999249}, issn = {1758-2229}, mesh = {*Archaea/genetics ; *Soil/chemistry ; Multiomics ; Climate Change ; Italy ; Soil Microbiology ; }, abstract = {We currently lack a predictive understanding of how soil archaeal communities may respond to climate change, particularly in Alpine areas where warming is far exceeding the global average. Here, we characterized the abundance, structure, and function of total (by metagenomics) and active soil archaea (by metatranscriptomics) after 5-year experimental field warming (+1°C) in Italian Alpine grasslands and snowbeds. Our multi-omics approach unveiled an increasing abundance of Archaea during warming in snowbeds, which was negatively correlated with the abundance of fungi (by qPCR) and micronutrients (Ca and Mg), but positively correlated with soil water content. In the snowbeds transcripts, warming resulted in the enrichment of abundances of transcription and nucleotide biosynthesis. Our study provides novel insights into possible changes in soil Archaea composition and function in the climate change scenario.}, } @article {pmid36998409, year = {2023}, author = {González Plaza, JJ and Hradecký, J}, title = {The tropical cookbook: Termite diet and phylogenetics-Over geographical origin-Drive the microbiome and functional genetic structure of nests.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1089525}, pmid = {36998409}, issn = {1664-302X}, abstract = {Termites are key decomposers of dead plant material involved in the organic matter recycling process in warm terrestrial ecosystems. Due to their prominent role as urban pests of timber, research efforts have been directed toward biocontrol strategies aimed to use pathogens in their nest. However, one of the most fascinating aspects of termites is their defense strategies that prevent the growth of detrimental microbiological strains in their nests. One of the controlling factors is the nest allied microbiome. Understanding how allied microbial strains protect termites from pathogen load could provide us with an enhanced repertoire for fighting antimicrobial-resistant strains or mining for genes for bioremediation purposes. However, a necessary first step is to characterize these microbial communities. To gain a deeper understanding of the termite nest microbiome, we used a multi-omics approach for dissecting the nest microbiome in a wide range of termite species. These cover several feeding habits and three geographical locations on two tropical sides of the Atlantic Ocean known to host hyper-diverse communities. Our experimental approach included untargeted volatile metabolomics, targeted evaluation of volatile naphthalene, a taxonomical profile for bacteria and fungi through amplicon sequencing, and further diving into the genetic repertoire through a metagenomic sequencing approach. Naphthalene was present in species belonging to the genera Nasutitermes and Cubitermes. We investigated the apparent differences in terms of bacterial community structure and discovered that feeding habits and phylogenetic relatedness had a greater influence than geographical location. The phylogenetic relatedness among nests' hosts influences primarily bacterial communities, while diet influences fungi. Finally, our metagenomic analysis revealed that the gene content provided both soil-feeding genera with similar functional profiles, while the wood-feeding genus showed a different one. Our results indicate that the nest functional profile is largely influenced by diet and phylogenetic relatedness, irrespective of geographical location.}, } @article {pmid36998393, year = {2023}, author = {Wang, C and Liang, Q and Liu, J and Zhou, R and Lang, X and Xu, S and Li, X and Gong, A and Mu, Y and Fang, H and Yang, KQ}, title = {Impact of intercropping grass on the soil rhizosphere microbial community and soil ecosystem function in a walnut orchard.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1137590}, pmid = {36998393}, issn = {1664-302X}, abstract = {The intercropping of grass in orchards has beneficial effects on soil properties and soil microbial communities and is an important soil management measure for improving orchard productivity and land-use efficiency. However, few studies have explored the effects of grass intercropping on rhizosphere microorganisms in walnut orchards. In this study, we explored the microbial communities of clear tillage (CT), walnut/ryegrass (Lolium perenne L.) (Lp), and walnut/hairy vetch (Vicia villosa Roth.) (Vv) intercropping system using MiSeq sequencing and metagenomic sequencing. The results revealed that the composition and structure of the soil bacterial community changed significantly with walnut/Vv intercropping compared to CT and walnut/Lp intercropping. Moreover, the walnut/hairy vetch intercropping system had the most complex connections between bacterial taxa. In addition, we found that the soil microorganisms of walnut/Vv intercropping had a higher potential for nitrogen cycling and carbohydrate metabolism, which may be related to the functions of Burkholderia, Rhodopseudomonas, Pseudomonas, Agrobacterium, Paraburkholderia, and Flavobacterium. Overall, this study provided a theoretical basis for understanding the microbial communities associated with grass intercropping in walnut orchards, providing better guidance for the management of walnut orchards.}, } @article {pmid36998174, year = {2023}, author = {Ru, J and Khan Mirzaei, M and Xue, J and Peng, X and Deng, L}, title = {ViroProfiler: a containerized bioinformatics pipeline for viral metagenomic data analysis.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2192522}, pmid = {36998174}, issn = {1949-0984}, mesh = {Software ; *Gastrointestinal Microbiome ; Reproducibility of Results ; Metagenome ; *Microbiota ; Metagenomics/methods ; Computational Biology/methods ; Data Analysis ; }, abstract = {Bacteriophages play central roles in the maintenance and function of most ecosystems by regulating bacterial communities. Yet, our understanding of their diversity remains limited due to the lack of robust bioinformatics standards. Here we present ViroProfiler, an in-silico workflow for analyzing shotgun viral metagenomic data. ViroProfiler can be executed on a local Linux computer or cloud computing environments. It uses the containerization technique to ensure computational reproducibility and facilitate collaborative research. ViroProfiler is freely available at https://github.com/deng-lab/viroprofiler.}, } @article {pmid36998097, year = {2023}, author = {Nelkner, J and Huang, L and Lin, TW and Schulz, A and Osterholz, B and Henke, C and Blom, J and Pühler, A and Sczyrba, A and Schlüter, A}, title = {Abundance, classification and genetic potential of Thaumarchaeota in metagenomes of European agricultural soils: a meta-analysis.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {26}, pmid = {36998097}, issn = {2524-6372}, support = {031A532B, 031A533A, 031A533B, 031A534A, 031A535A, 031A537A, 031A537B, 031A537C, 031A537D, 031A538A//Bundesministerium für Bildung und Forschung/ ; 031A532B, 031A533A, 031A533B, 031A534A, 031A535A, 031A537A, 031A537B, 031A537C, 031A537D, 031A538A//Bundesministerium für Bildung und Forschung/ ; 818431//Horizon 2020 Framework Programme/ ; 818431//Horizon 2020 Framework Programme/ ; 818431//Horizon 2020 Framework Programme/ ; 818431//Horizon 2020 Framework Programme/ ; }, abstract = {BACKGROUND: For a sustainable production of food, research on agricultural soil microbial communities is inevitable. Due to its immense complexity, soil is still some kind of black box. Soil study designs for identifying microbiome members of relevance have various scopes and focus on particular environmental factors. To identify common features of soil microbiomes, data from multiple studies should be compiled and processed. Taxonomic compositions and functional capabilities of microbial communities associated with soils and plants have been identified and characterized in the past few decades. From a fertile Loess-Chernozem-type soil located in Germany, metagenomically assembled genomes (MAGs) classified as members of the phylum Thaumarchaeota/Thermoproteota were obtained. These possibly represent keystone agricultural soil community members encoding functions of relevance for soil fertility and plant health. Their importance for the analyzed microbiomes is corroborated by the fact that they were predicted to contribute to the cycling of nitrogen, feature the genetic potential to fix carbon dioxide and possess genes with predicted functions in plant-growth-promotion (PGP). To expand the knowledge on soil community members belonging to the phylum Thaumarchaeota, we conducted a meta-analysis integrating primary studies on European agricultural soil microbiomes.

RESULTS: Taxonomic classification of the selected soil metagenomes revealed the shared agricultural soil core microbiome of European soils from 19 locations. Metadata reporting was heterogeneous between the different studies. According to the available metadata, we separated the data into 68 treatments. The phylum Thaumarchaeota is part of the core microbiome and represents a major constituent of the archaeal subcommunities in all European agricultural soils. At a higher taxonomic resolution, 2074 genera constituted the core microbiome. We observed that viral genera strongly contribute to variation in taxonomic profiles. By binning of metagenomically assembled contigs, Thaumarchaeota MAGs could be recovered from several European soil metagenomes. Notably, many of them were classified as members of the family Nitrososphaeraceae, highlighting the importance of this family for agricultural soils. The specific Loess-Chernozem Thaumarchaeota MAGs were most abundant in their original soil, but also seem to be of importance in other agricultural soil microbial communities. Metabolic reconstruction of Switzerland_1_MAG_2 revealed its genetic potential i.a. regarding carbon dioxide (CO[Formula: see text]) fixation, ammonia oxidation, exopolysaccharide production and a beneficial effect on plant growth. Similar genetic features were also present in other reconstructed MAGs. Three Nitrososphaeraceae MAGs are all most likely members of a so far unknown genus.

CONCLUSIONS: On a broad view, European agricultural soil microbiomes are similarly structured. Differences in community structure were observable, although analysis was complicated by heterogeneity in metadata recording. Our study highlights the need for standardized metadata reporting and the benefits of networking open data. Future soil sequencing studies should also consider high sequencing depths in order to enable reconstruction of genome bins. Intriguingly, the family Nitrososphaeraceae commonly seems to be of importance in agricultural microbiomes.}, } @article {pmid36997838, year = {2023}, author = {Jacky, D and Bibi, C and Meng, LMC and Jason, F and Gwendoline, T and Jeremy, L and Wie, CC}, title = {Effects of OsomeFood Clean Label plant-based meals on the gut microbiome.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {88}, pmid = {36997838}, issn = {1471-2180}, mesh = {Humans ; *Gastrointestinal Microbiome ; Overweight ; Feces/microbiology ; Diet ; Meals ; }, abstract = {BACKGROUND: Plant-based diets offer more beneficial microbes and can modulate gut microbiomes to improve human health. We evaluated the effects of the plant-based OsomeFood Clean Label meal range ('AWE' diet), on the human gut microbiome.

METHODS: Over 21 days, ten healthy participants consumed OsomeFood meals for five consecutive weekday lunches and dinners and resumed their regular diets for other days/meals. On follow-up days, participants completed questionnaires to record satiety, energy and health, and provided stool samples. To document microbiome variations and identify associations, species and functional pathway annotations were analyzed by shotgun sequencing. Shannon diversity and regular diet calorie intake subsets were also assessed.

RESULTS: Overweight participants gained more species and functional pathway diversity than normal BMI participants. Nineteen disease-associated species were suppressed in moderate-responders without gaining diversity, and in strong-responders with diversity gains along with health-associated species. All participants reported improved short-chain fatty acids production, insulin and γ-aminobutyric acid signaling. Moreover, fullness correlated positively with Bacteroides eggerthii; energetic status with B. uniformis, B. longum, Phascolarctobacterium succinatutens, and Eubacterium eligens; healthy status with Faecalibacterium prausnitzii, Prevotella CAG 5226, Roseburia hominis, and Roseburia sp. CAG 182; and overall response with E. eligens and Corprococcus eutactus. Fiber consumption was negatively associated with pathogenic species.

CONCLUSION: Although the AWE diet was consumed for only five days a week, all participants, especially overweight ones, experienced improved fullness, health status, energy and overall responses. The AWE diet benefits all individuals, especially those of higher BMI or low-fiber consumption.}, } @article {pmid36997767, year = {2023}, author = {Zhang, X and Chen, H and Han, D and Wu, W}, title = {Clinical usefulness of metagenomic next-generation sequencing for Rickettsia and Coxiella burnetii diagnosis.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {42}, number = {6}, pages = {681-689}, pmid = {36997767}, issn = {1435-4373}, mesh = {Humans ; *Rickettsia/genetics ; *Coxiella burnetii/genetics ; *Q Fever/diagnosis ; Retrospective Studies ; *Rickettsia Infections/diagnosis ; High-Throughput Nucleotide Sequencing ; }, abstract = {Rickettsia and Coxiella burnetii are zoonotic tick-borne pathogens that cause febrile illnesses in humans. Metagenomic next-generation sequencing (mNGS) is a new technology used to diagnose infectious diseases. However, clinical experience with applying the test to rickettsioses and Q fever is relatively limited. Therefore, this study aimed to explore the diagnostic performance of mNGS in detecting Rickettsia and C. burnetii. We retrospectively studied patients with rickettsioses or Q fever between August 2021 and July 2022. Peripheral blood mNGS and polymerase chain reaction (PCR) were performed for all patients. Clinical data were retrieved for analysis. Thirteen patients were included in this study (eleven confirmed cases and two suspected cases). Signs and symptoms included fever (13, 100%), rash (7, 53.8%), muscle soreness (5, 38.5%), headache (4, 30.8%), skin eschar (3, 23.1%), and disturbance of consciousness (2, 15.4%). In addition, eight patients (61.6%) had thrombocytopenia, ten (76.9%) had liver function impairment, and two (15.4%) had renal function impairment. The results of mNGS revealed seven patients with R. japonica (53.8%), five with C. burneti (38.5%), two with R. heilongjiangensis (15.4%), and one with R. honei (7.7%). PCR results were positive in 11 patients (84.6%). After receiving doxycycline-based treatment, 12 (92.3%) patients returned to a normal temperature within 72 h. All patients were discharged in better health. Therefore, mNGS can help diagnose Rickettsia and C. burnetii and shorten the diagnosis time, especially for patients with atypical clinical manifestations and unclear epidemiologic evidence of a tick bite or exposure.}, } @article {pmid36996985, year = {2023}, author = {Yan, S and Zhang, Z and Wang, J and Xia, Y and Chen, S and Xie, S}, title = {River sediment microbial community composition and function impacted by thallium spill.}, journal = {The Science of the total environment}, volume = {880}, number = {}, pages = {163101}, doi = {10.1016/j.scitotenv.2023.163101}, pmid = {36996985}, issn = {1879-1026}, mesh = {Humans ; *Thallium/analysis ; Rivers ; Metals/analysis ; *Microbiota ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Anti-Bacterial Agents ; }, abstract = {Thallium (Tl) is widely used in various industries, which increases the risk of leakage into the environment. Since Tl is highly toxic, it can do a great harm to human health and ecosystem. In order to explore the response of freshwater sediment microorganisms to sudden Tl spill, metagenomic technique was used to elucidate the changes of microbial community composition and functional genes in river sediments. Tl pollution could have profound impacts on microbial community composition and function. Proteobacteria remained the dominance in contaminated szediments, indicating that it had a strong resistance to Tl contamination, and Cyanobacteria also showed a certain resistance. Tl pollution also had a certain screening effect on resistance genes and affected the abundance of resistance genes. Metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) were enriched at the site near the spill site, where Tl concentration was relatively low among polluted sites. When Tl concentration was higher, the screening effect was not obvious and the resistance genes even became lower. Moreover, there was a significant correlation between MRGs and ARGs. In addition, co-occurrence network analysis showed that Sphingopyxis had the most links with resistance genes, indicating that it was the biggest potential host of resistance genes. This study provided new insight towards the shifts in the composition and function of microbial communities after sudden serious Tl contamination.}, } @article {pmid36996924, year = {2023}, author = {Wang, X and Chen, D and Zhou, Y and Yu, M and Niu, J}, title = {Degradation performance and potential protection mechanism of the anammox consortia in response to capecitabine.}, journal = {Chemosphere}, volume = {327}, number = {}, pages = {138539}, doi = {10.1016/j.chemosphere.2023.138539}, pmid = {36996924}, issn = {1879-1298}, mesh = {*Wastewater ; Capecitabine ; *Anaerobic Ammonia Oxidation ; N-Acetylneuraminic Acid/metabolism ; Oxidation-Reduction ; Bacteria/genetics/metabolism ; Nitrogen/metabolism ; Bioreactors/microbiology ; Denitrification ; Sewage ; }, abstract = {The potential risks of anti-cancer drugs such as capecitabine have attracted considerable attention due to their continuous release. Understanding the response of removal performance and protective mechanism to the presence of emerging contaminants is crucial for the application of anammox techniques in wastewater treatment. Capecitabine affected the nitrogen removal performance slightly in the activity experiment. Due to bio-adsorption and biodegradation, up to 64-70% of the capecitabine can be removed effectively. However, 10 mg/L of capecitabine significantly decreased the removal efficiency of capecitabine and total nitrogen at repeated load of capecitabine. Metabolomic analysis revealed the metabolites 5'-deoxy-5-fluorocytidine and alpha-fluoro-beta-alanine, while metagenomic analysis confirmed the biodegradation pathway and underlying gene distribution. The potentially protective mechanisms of the system against capecitabine were the increased heterotrophic bacteria and secretion of sialic acid. Blast analysis confirmed the presence of potential genes involved in the complete biosynthesis pathway of sialic acid in anammox bacteria, some of which are also found in Nitrosomonas, Thauera, and Candidatus Promineofilum.}, } @article {pmid36996871, year = {2023}, author = {Servellita, V and Sotomayor Gonzalez, A and Lamson, DM and Foresythe, A and Huh, HJ and Bazinet, AL and Bergman, NH and Bull, RL and Garcia, KY and Goodrich, JS and Lovett, SP and Parker, K and Radune, D and Hatada, A and Pan, CY and Rizzo, K and Bertumen, JB and Morales, C and Oluniyi, PE and Nguyen, J and Tan, J and Stryke, D and Jaber, R and Leslie, MT and Lyons, Z and Hedman, HD and Parashar, U and Sullivan, M and Wroblewski, K and Oberste, MS and Tate, JE and Baker, JM and Sugerman, D and Potts, C and Lu, X and Chhabra, P and , and Ingram, LA and Shiau, H and Britt, W and Gutierrez Sanchez, LH and Ciric, C and Rostad, CA and Vinjé, J and Kirking, HL and Wadford, DA and Raborn, RT and St George, K and Chiu, CY}, title = {Adeno-associated virus type 2 in US children with acute severe hepatitis.}, journal = {Nature}, volume = {617}, number = {7961}, pages = {574-580}, pmid = {36996871}, issn = {1476-4687}, support = {R33 HD105618/HD/NICHD NIH HHS/United States ; R61 HD105618/HD/NICHD NIH HHS/United States ; }, mesh = {Child ; Humans ; Acute Disease ; *Adenovirus Infections, Human/epidemiology/virology ; *Coinfection/epidemiology/virology ; *Dependovirus/genetics/isolation & purification ; Epstein-Barr Virus Infections/epidemiology/virology ; *Hepatitis/epidemiology/virology ; Herpesvirus 4, Human/isolation & purification ; Herpesvirus 6, Human/isolation & purification ; Enterovirus A, Human/isolation & purification ; Helper Viruses/isolation & purification ; }, abstract = {As of August 2022, clusters of acute severe hepatitis of unknown aetiology in children have been reported from 35 countries, including the USA[1,2]. Previous studies have found human adenoviruses (HAdVs) in the blood from patients in Europe and the USA[3-7], although it is unclear whether this virus is causative. Here we used PCR testing, viral enrichment-based sequencing and agnostic metagenomic sequencing to analyse samples from 16 HAdV-positive cases from 1 October 2021 to 22 May 2022, in parallel with 113 controls. In blood from 14 cases, adeno-associated virus type 2 (AAV2) sequences were detected in 93% (13 of 14), compared to 4 (3.5%) of 113 controls (P < 0.001) and to 0 of 30 patients with hepatitis of defined aetiology (P < 0.001). In controls, HAdV type 41 was detected in blood from 9 (39.1%) of the 23 patients with acute gastroenteritis (without hepatitis), including 8 of 9 patients with positive stool HAdV testing, but co-infection with AAV2 was observed in only 3 (13.0%) of these 23 patients versus 93% of cases (P < 0.001). Co-infections by Epstein-Barr virus, human herpesvirus 6 and/or enterovirus A71 were also detected in 12 (85.7%) of 14 cases, with higher herpesvirus detection in cases versus controls (P < 0.001). Our findings suggest that the severity of the disease is related to co-infections involving AAV2 and one or more helper viruses.}, } @article {pmid36996751, year = {2023}, author = {Yin, X and Li, L and Chen, X and Liu, YY and Lam, TT and Topp, E and Zhang, T}, title = {Global environmental resistome: Distinction and connectivity across diverse habitats benchmarked by metagenomic analyses.}, journal = {Water research}, volume = {235}, number = {}, pages = {119875}, doi = {10.1016/j.watres.2023.119875}, pmid = {36996751}, issn = {1879-2448}, mesh = {Humans ; *Metagenome ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Ecosystem ; }, abstract = {The widely distributed antibiotic resistance genes (ARGs) were unevenly proliferated in various habitats. Great endeavors are needed to resolve the resistome features that can differentiate or connect different habitats. This study retrieved a broad spectrum of resistome profiles from 1723 metagenomes categorized into 13 habitats, encompassing industrial, urban, agricultural, and natural environments, and spanning most continents and oceans. The resistome features (ARG types, subtypes, indicator ARGs, and emerging mobilizable ARGs: mcr and tet(X)) in these habitats were benchmarked via a standardized workflow. We found that wastewater and wastewater treatment works were characterized to be reservoirs of more diverse genotypes of ARGs than any other habitats including human and livestock fecal samples, while fecal samples were with higher ARG abundance. Bacterial taxonomy composition was significantly correlated with resistome composition across most habitats. Moreover, the source-sink connectivities were disentangled by developing the resistome-based microbial attribution prediction model. Environmental surveys with standardized bioinformatic workflow proposed in this study will help comprehensively understand the transfer of ARGs in the environment, thus prioritizing the critical environments with high risks for intervention to tackle the problem of ARGs.}, } @article {pmid36996192, year = {2023}, author = {Bruner-Montero, G and Luque, CM and Cesar, CS and Ding, SD and Day, JP and Jiggins, FM}, title = {Hunting Drosophila viruses from wild populations: A novel isolation approach and characterisation of viruses.}, journal = {PLoS pathogens}, volume = {19}, number = {3}, pages = {e1010883}, pmid = {36996192}, issn = {1553-7374}, mesh = {Animals ; Female ; *Drosophila ; Drosophila melanogaster ; Insecta ; *Viruses ; }, abstract = {Metagenomic studies have demonstrated that viruses are extremely diverse and abundant in insects, but the difficulty of isolating them means little is known about the biology of these newly discovered viruses. To overcome this challenge in Drosophila, we created a cell line that was more permissive to infection and detected novel viruses by the presence of double-stranded RNA. We demonstrate the utility of these tools by isolating La Jolla virus (LJV) and Newfield virus (NFV) from several wild Drosophila populations. These viruses have different potential host ranges, with distinct abilities to replicate in five Drosophila species. Similarly, in some species they cause high mortality and in others they are comparatively benign. In three species, NFV but not LJV caused large declines in female fecundity. This sterilization effect was associated with differences in tissue tropism, as NFV but not LJV was able to infect Drosophila melanogaster follicular epithelium and induce follicular degeneration in the ovary. We saw a similar effect in the invasive pest of fruit crops Drosophila suzukii, where oral infection with NFV caused reductions in the fecundity, suggesting it has potential as a biocontrol agent. In conclusion, a simple protocol allowed us to isolate new viruses and demonstrate that viruses identified by metagenomics have a large effect on the fitness of the model organism D. melanogaster and related species.}, } @article {pmid36996123, year = {2023}, author = {Ostenfeld, LJ and Munk, P and Aarestrup, FM and Otani, S}, title = {Detection of specific uncultured bacteriophages by fluorescence in situ hybridisation in pig microbiome.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0283676}, pmid = {36996123}, issn = {1932-6203}, mesh = {Animals ; Bacteria/genetics ; *Bacteriophages/genetics ; Fluorescence ; Metagenome ; *Microbiota ; Swine ; }, abstract = {Microbial communities have huge impacts on their ecosystems and local environments spanning from marine and soil communities to the mammalian gut. Bacteriophages (phages) are important drivers of population control and diversity in the community, but our understanding of complex microbial communities is halted by biased detection techniques. Metagenomics have provided a method of novel phage discovery independent of in vitro culturing techniques and have revealed a large proportion of understudied phages. Here, five jumbophage genomes, that were previously assembled in silico from pig faecal metagenomes, are detected and observed directly in their natural environment using a modified phageFISH approach, and combined with methods to decrease bias against large-sized phages (e.g., jumbophages). These phages are uncultured with unknown hosts. The specific phages were detected by PCR and fluorescent in situ hybridisation in their original faecal samples as well as across other faecal samples. Co-localisation of bacterial signals and phage signals allowed detection of the different stages of phage life cycle. All phages displayed examples of early infection, advanced infection, burst, and free phages. To our knowledge, this is the first detection of jumbophages in faeces, which were investigated independently of culture, host identification, and size, and based solely on the genome sequence. This approach opens up opportunities for characterisation of novel in silico phages in vivo from a broad range of gut microbiomes.}, } @article {pmid36995383, year = {2023}, author = {Nie, S and Jing, Z and Wang, J and Deng, Y and Zhang, Y and Ye, Z and Ge, Y}, title = {The link between increased Desulfovibrio and disease severity in Parkinson's disease.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {9}, pages = {3033-3045}, pmid = {36995383}, issn = {1432-0614}, mesh = {Humans ; *Parkinson Disease/diagnosis ; *Hydrogen Sulfide ; RNA, Ribosomal, 16S/genetics ; *Neurodegenerative Diseases ; Patient Acuity ; *Desulfovibrio/genetics ; Sulfates ; }, abstract = {Parkinson's disease (PD), a progressive and incurable neurodegenerative disease, has taken a huge economic toll and medical burden on our society. Increasing evidence has shown a strong link between PD and the gut microbiome, but studies on the relationship between the gut microbiome and the severity of PD are limited. In this study, 90 fecal samples were collected from newly diagnosed and untreated patients with PD (n = 47) and matched healthy control subjects (n = 43). The 16S rRNA amplicon and shotgun metagenomic sequencing was performed, aiming to uncover the connection between the gut microbiome and disease severity in PD. The results showed that Desulfovibrio was significantly increased in PD compared to healthy controls and positively correlated with disease severity. The increase in Desulfovibrio was mainly driven by enhanced homogeneous selection and weakened drift. Moreover, through metagenome-assembled genomes (MAGs) analysis, a Desulfovibrio MAG (MAG58) was obtained which was also positively correlated with disease severity. MAG58 possesses a complete assimilatory sulfate reduction pathway and a near-complete dissimilatory sulfate reduction pathway to produce hydrogen sulfide which may influence the development of PD. Based on these results, a potential pathogenic mechanism was presented to illustrate how the increased Desulfovibrio accelerates the development of PD by producing excessive hydrogen sulfide. The present study highlighted the vital role of Desulfovibrio in the development of PD, which may provide a new target for the diagnosis and treatment of PD. KEY POINTS: • The evidence for the link between increased Desulfovibrio and disease severity in PD • A Desulfovibrio MAG was obtained which was correlated with PD • A model was presented to illustrate how increased Desulfovibrio causes PD.}, } @article {pmid36995244, year = {2023}, author = {Herviou, P and Balvay, A and Bellet, D and Bobet, S and Maudet, C and Staub, J and Alric, M and Leblond-Bourget, N and Delorme, C and Rabot, S and Denis, S and Payot, S}, title = {Transfer of the Integrative and Conjugative Element ICESt3 of Streptococcus thermophilus in Physiological Conditions Mimicking the Human Digestive Ecosystem.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0466722}, pmid = {36995244}, issn = {2165-0497}, mesh = {Animals ; Mice ; Humans ; *Streptococcus thermophilus/genetics ; Conjugation, Genetic ; Gastrointestinal Tract ; Gene Transfer, Horizontal ; *Microbiota ; }, abstract = {Metagenome analyses of the human microbiome suggest that horizontal gene transfer (HGT) is frequent in these rich and complex microbial communities. However, so far, only a few HGT studies have been conducted in vivo. In this work, three different systems mimicking the physiological conditions encountered in the human digestive tract were tested, including (i) the TNO gastro-Intestinal tract Model 1 (TIM-1) system (for the upper part of the intestine), (ii) the ARtificial COLon (ARCOL) system (to mimic the colon), and (iii) a mouse model. To increase the likelihood of transfer by conjugation of the integrative and conjugative element studied in the artificial digestive systems, bacteria were entrapped in alginate, agar, and chitosan beads before being placed in the different gut compartments. The number of transconjugants detected decreased, while the complexity of the ecosystem increased (many clones in TIM-1 but only one clone in ARCOL). No clone was obtained in a natural digestive environment (germfree mouse model). In the human gut, the richness and diversity of the bacterial community would offer more opportunities for HGT events to occur. In addition, several factors (SOS-inducing agents, microbiota-derived factors) that potentially increase in vivo HGT efficiency were not tested here. Even if HGT events are rare, expansion of the transconjugant clones can happen if ecological success is fostered by selecting conditions or by events that destabilize the microbial community. IMPORTANCE The human gut microbiota plays a key role in maintaining normal host physiology and health, but its homeostasis is fragile. During their transit in the gastrointestinal tract, bacteria conveyed by food can exchange genes with resident bacteria. New traits acquired by HGT (e.g., new catabolic properties, bacteriocins, antibiotic resistance) can impact the gut microbial composition and metabolic potential. We showed here that TIM-1, a system mimicking the upper digestive tract, is a useful tool to evaluate HGT events in conditions closer to the physiological ones. Another important fact pointed out in this work is that Enterococcus faecalis is a good candidate for foreign gene acquisition. Due to its high ability to colonize the gut and acquire mobile genetic elements, this commensal bacterium could serve as an intermediate for HGT in the human gut.}, } @article {pmid36995238, year = {2023}, author = {Zhao, X and Sun, C and Jin, M and Chen, J and Xing, L and Yan, J and Wang, H and Liu, Z and Chen, WH}, title = {Enrichment Culture but Not Metagenomic Sequencing Identified a Highly Prevalent Phage Infecting Lactiplantibacillus plantarum in Human Feces.}, journal = {Microbiology spectrum}, volume = {11}, number = {3}, pages = {e0434022}, pmid = {36995238}, issn = {2165-0497}, mesh = {Humans ; *Bacteriophages/classification/genetics/isolation & purification ; *Feces/microbiology/virology ; *Lactobacillus plantarum/virology ; Metagenomics ; Culture Techniques ; Genome, Viral/genetics ; Biodiversity ; }, abstract = {Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum) is increasingly used as a probiotic to treat human diseases, but its phages in the human gut remain unexplored. Here, we report its first gut phage, Gut-P1, which we systematically screened using metagenomic sequencing, virus-like particle (VLP) sequencing, and enrichment culture from 35 fecal samples. Gut-P1 is virulent, belongs to the Douglaswolinvirus genus, and is highly prevalent in the gut (~11% prevalence); it has a genome of 79,928 bp consisting of 125 protein coding genes and displaying low sequence similarities to public L. plantarum phages. Physiochemical characterization shows that it has a short latent period and adapts to broad ranges of temperatures and pHs. Furthermore, Gut-P1 strongly inhibits the growth of L. plantarum strains at a multiplicity of infection (MOI) of 1e-6. Together, these results indicate that Gut-P1 can greatly impede the application of L. plantarum in humans. Strikingly, Gut-P1 was identified only in the enrichment culture, not in our metagenomic or VLP sequencing data nor in any public human phage databases, indicating the inefficiency of bulk sequencing in recovering low-abundance but highly prevalent phages and pointing to the unexplored hidden diversity of the human gut virome despite recent large-scale sequencing and bioinformatics efforts. IMPORTANCE As Lactiplantibacillus plantarum (previously known as Lactobacillus plantarum) is increasingly used as a probiotic to treat human gut-related diseases, its bacteriophages may pose a certain threat to their further application and should be identified and characterized more often from the human intestine. Here, we isolated and identified the first gut L. plantarum phage that is prevalent in a Chinese population. This phage, Gut-P1, is virulent and can strongly inhibit the growth of multiple L. plantarum strains at low MOIs. Our results also show that bulk sequencing is inefficient at recovering low-abundance but highly prevalent phages such as Gut-P1, suggesting that the hidden diversity of human enteroviruses has not yet been explored. Our results call for innovative approaches to isolate and identify intestinal phages from the human gut and to rethink our current understanding of the enterovirus, particularly its underestimated diversity and overestimated individual specificity.}, } @article {pmid36993673, year = {2023}, author = {Rich, MH and Sharrock, AV and Mulligan, TS and Matthews, F and Brown, AS and Lee-Harwood, HR and Williams, EM and Copp, JN and Little, RF and Francis, JJ and Horvat, CN and Stevenson, LJ and Owen, JG and Saxena, MT and Mumm, JS and Ackerley, DF}, title = {A metagenomic library cloning strategy that promotes high-level expression of captured genes to enable efficient functional screening.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36993673}, support = {P30 EY001765/EY/NEI NIH HHS/United States ; R01 OD020376/OD/NIH HHS/United States ; RF1 MH126731/MH/NIMH NIH HHS/United States ; }, abstract = {Functional screening of environmental DNA (eDNA) libraries is a potentially powerful approach to discover enzymatic "unknown unknowns", but is usually heavily biased toward the tiny subset of genes preferentially transcribed and translated by the screening strain. We have overcome this by preparing an eDNA library via partial digest with restriction enzyme FatI (cuts CATG), causing a substantial proportion of ATG start codons to be precisely aligned with strong plasmid-encoded promoter and ribosome-binding sequences. Whereas we were unable to select nitroreductases from standard metagenome libraries, our FatI strategy yielded 21 nitroreductases spanning eight different enzyme families, each conferring resistance to the nitro-antibiotic niclosamide and sensitivity to the nitro-prodrug metronidazole. We showed expression could be improved by co-expressing rare tRNAs and encoded proteins purified directly using an embedded His6-tag. In a transgenic zebrafish model of metronidazole-mediated targeted cell ablation, our lead MhqN-family nitroreductase proved ~5-fold more effective than the canonical nitroreductase NfsB.}, } @article {pmid36993583, year = {2023}, author = {Holm, JB and France, MT and Gajer, P and Ma, B and Brotman, RM and Shardell, M and Forney, L and Ravel, J}, title = {High-resolution functional description of vaginal microbiomes in health and disease.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36993583}, support = {R01 NR015495/NR/NINR NIH HHS/United States ; U19 AI084044/AI/NIAID NIH HHS/United States ; R01 AI116799/AI/NIAID NIH HHS/United States ; F32 AI136400/AI/NIAID NIH HHS/United States ; K01 AI163413/AI/NIAID NIH HHS/United States ; UH2 AI083264/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: A Lactobacillus-dominated vaginal microbiome provides the first line of defense against numerous adverse genital tract health outcomes. However, there is limited understanding of the mechanisms by which the vaginal microbiome modulates protection, as prior work mostly described its composition through morphologic assessment and marker gene sequencing methods that do not capture functional information. To address this limitation, we developed metagenomic community state types (mgCSTs) which uses metagenomic sequences to describe and define vaginal microbiomes based on both composition and function.

RESULTS: MgCSTs are categories of microbiomes classified using taxonomy and the functional potential encoded in their metagenomes. MgCSTs reflect unique combinations of metagenomic subspecies (mgSs), which are assemblages of bacterial strains of the same species, within a microbiome. We demonstrate that mgCSTs are associated with demographics such as age and race, as well as vaginal pH and Gram stain assessment of vaginal smears. Importantly, these associations varied between mgCSTs predominated by the same bacterial species. A subset of mgCSTs, including three of the six predominated by Gardnerella mgSs, as well as a mgSs of L. iners, were associated with a greater likelihood of Amsel bacterial vaginosis diagnosis. This L. iners mgSs, among other functional features, encoded enhanced genetic capabilities for epithelial cell attachment that could facilitate cytotoxin-mediated cell lysis. Finally, we report a mgSs and mgCST classifier as an easily applied, standardized method for use by the microbiome research community.

CONCLUSIONS: MgCSTs are a novel and easily implemented approach to reducing the dimension of complex metagenomic datasets, while maintaining their functional uniqueness. MgCSTs enable investigation of multiple strains of the same species and the functional diversity in that species. Future investigations of functional diversity may be key to unraveling the pathways by which the vaginal microbiome modulates protection to the genital tract. Importantly, our findings support the hypothesis that functional differences between vaginal microbiomes, including those that may look compositionally similar, are critical considerations in vaginal health. Ultimately, mgCSTs may lead to novel hypotheses concerning the role of the vaginal microbiome in promoting health and disease, and identify targets for novel prognostic, diagnostic, and therapeutic strategies to improve women's genital health.}, } @article {pmid36993556, year = {2023}, author = {Fogarty, EC and Schechter, MS and Lolans, K and Sheahan, ML and Veseli, I and Moore, R and Kiefl, E and Moody, T and Rice, PA and Yu, MK and Mimee, M and Chang, EB and Mclellan, SL and Willis, AD and Comstock, LE and Eren, AM}, title = {A highly conserved and globally prevalent cryptic plasmid is among the most numerous mobile genetic elements in the human gut.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36993556}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; }, abstract = {Plasmids are extrachromosomal genetic elements that often encode fitness enhancing features. However, many bacteria carry 'cryptic' plasmids that do not confer clear beneficial functions. We identified one such cryptic plasmid, pBI143, which is ubiquitous across industrialized gut microbiomes, and is 14 times as numerous as crAssphage, currently established as the most abundant genetic element in the human gut. The majority of mutations in pBI143 accumulate in specific positions across thousands of metagenomes, indicating strong purifying selection. pBI143 is monoclonal in most individuals, likely due to the priority effect of the version first acquired, often from one's mother. pBI143 can transfer between Bacteroidales and although it does not appear to impact bacterial host fitness in vivo, can transiently acquire additional genetic content. We identified important practical applications of pBI143, including its use in identifying human fecal contamination and its potential as an inexpensive alternative for detecting human colonic inflammatory states.}, } @article {pmid36992482, year = {2023}, author = {Wu, Q and Habili, N and Kinoti, WM and Tyerman, SD and Rinaldo, A and Zheng, L and Constable, FE}, title = {A Metagenomic Investigation of the Viruses Associated with Shiraz Disease in Australia.}, journal = {Viruses}, volume = {15}, number = {3}, pages = {}, pmid = {36992482}, issn = {1999-4915}, mesh = {*Vitis ; Plant Diseases ; *Flexiviridae/genetics ; Australia/epidemiology ; Metagenome ; }, abstract = {Shiraz disease (SD) is an economically important virus-associated disease that can significantly reduce yield in sensitive grapevine varieties and has so far only been reported in South Africa and Australia. In this study, RT-PCR and metagenomic high-throughput sequencing was used to study the virome of symptomatic and asymptomatic grapevines within vineyards affected by SD and located in South Australia. Results showed that grapevine virus A (GVA) phylogroup II variants were strongly associated with SD symptoms in Shiraz grapevines that also had mixed infections of viruses including combinations of grapevine leafroll-associated virus 3 (GLRaV-3) and grapevine leafroll-associated virus 4 strains 5, 6 and 9 (GLRaV-4/5, GLRaV-4/6, GLRaV-4/9). GVA phylogroup III variants, on the other hand, were present in both symptomatic and asymptomatic grapevines, suggesting no or decreased virulence of these strains. Similarly, only GVA phylogroup I variants were found in heritage Shiraz grapevines affected by mild leafroll disease, along with GLRaV-1, suggesting this phylogroup may not be associated with SD.}, } @article {pmid36992458, year = {2023}, author = {Chen, Z and Zhao, H and Li, Z and Huang, M and Si, N and Zhao, H and Wei, X and Sun, B and Gao, GF and Xu, Z and Liu, WJ}, title = {First Discovery of Phenuiviruses within Diverse RNA Viromes of Asiatic Toad (Bufo gargarizans) by Metagenomics Sequencing.}, journal = {Viruses}, volume = {15}, number = {3}, pages = {}, pmid = {36992458}, issn = {1999-4915}, mesh = {Animals ; RNA ; Metagenomics ; Phylogeny ; Virome ; *RNA Viruses/genetics ; Bufonidae/genetics ; *Picornaviridae/genetics ; Mammals ; *Astroviridae/genetics ; Rodentia ; Genome, Viral ; }, abstract = {Most zoonotic pathogens originate from mammals and avians, but viral diversity and related biosafety risk assessment in lower vertebrates also need to be explored. Amphibians are an important group of lower vertebrates that played a momentous role in animal evolution. To elucidate the diversity of RNA viruses in one important species of amphibians, the Asiatic toad (Bufo gargarizans), we obtained 44 samples including lung, gut, liver, and kidney tissues from Asiatic toads in Sichuan and Jilin provinces, China, for viral metagenomics sequencing. More than 20 novel RNA viruses derived from the order Bunyavirales and 7 families of Astroviridae, Dicistroviridae, Leviviridae, Partitiviridae, Picornaviridae, Rhabdoviridae, and Virgaviridae were discovered, which were distinct from previously described viruses and formed new clusters, as revealed by phylogenetic analyses. Notably, a novel bastrovirus, AtBastV/GCCDC11/2022, of the family Astroviridae was identified from the gut library, the genome of which contains three open reading frames, with the RNA-dependent RNA polymerase (RdRp) coded by ORF1 closely related to that of hepeviruses, and ORF2 encoding an astrovirus-related capsid protein. Notably, phenuiviruses were discovered for the first time in amphibians. AtPhenV1/GCCDC12/2022 and AtPhenV2/GCCDC13/2022 clustered together and formed a clade with the group of phenuiviruses identified from rodents. Picornaviruses and several invertebrate RNA viruses were also detected. These findings improve our understanding of the high RNA viral diversity in the Asiatic toad and provide new insights in the evolution of RNA viruses in amphibians.}, } @article {pmid36992396, year = {2023}, author = {Wang, H and Li, Z and Li, C and Ma, Y and Sun, Q and Zhang, H and Niu, G and Wei, J and Yao, H and Ma, Z}, title = {Viral Metagenomic Analysis of the Fecal Samples in Domestic Dogs (Canis lupus familiaris).}, journal = {Viruses}, volume = {15}, number = {3}, pages = {}, pmid = {36992396}, issn = {1999-4915}, mesh = {Animals ; Dogs ; *Wolves ; Metagenomics ; Phylogeny ; *Viruses ; *Microviridae ; Diarrhea/veterinary ; Myoviridae ; *Siphoviridae ; *Podoviridae ; Bacteria ; }, abstract = {Canine diarrhea is a common intestinal illness that is usually caused by viruses, bacteria, and parasites, and canine diarrhea may induce morbidity and mortality of domestic dogs if treated improperly. Recently, viral metagenomics was applied to investigate the signatures of the enteric virome in mammals. In this research, the characteristics of the gut virome in healthy dogs and dogs with diarrhea were analyzed and compared using viral metagenomics. The alpha diversity analysis indicated that the richness and diversity of the gut virome in the dogs with diarrhea were much higher than the healthy dogs, while the beta diversity analysis revealed that the gut virome of the two groups was quite different. At the family level, the predominant viruses in the canine gut virome were certified to be Microviridae, Parvoviridae, Siphoviridae, Inoviridae, Podoviridae, Myoviridae, and others. At the genus level, the predominant viruses in the canine gut virome were certified to be Protoparvovirus, Inovirus, Chlamydiamicrovirus, Lambdavirus, Dependoparvovirus, Lightbulbvirus, Kostyavirus, Punavirus, Lederbergvirus, Fibrovirus, Peduovirus, and others. However, the viral communities between the two groups differed significantly. The unique viral taxa identified in the healthy dogs group were Chlamydiamicrovirus and Lightbulbvirus, while the unique viral taxa identified in the dogs with diarrhea group were Inovirus, Protoparvovirus, Lambdavirus, Dependoparvovirus, Kostyavirus, Punavirus, and other viruses. Phylogenetic analysis based on the near-complete genome sequences showed that the CPV strains collected in this study together with other CPV Chinese isolates clustered into a separate branch, while the identified CAV-2 strain D5-8081 and AAV-5 strain AAV-D5 were both the first near-complete genome sequences in China. Moreover, the predicted bacterial hosts of phages were certified to be Campylobacter, Escherichia, Salmonella, Pseudomonas, Acinetobacter, Moraxella, Mediterraneibacter, and other commensal microbiota. In conclusion, the enteric virome of the healthy dogs group and the dogs with diarrhea group was investigated and compared using viral metagenomics, and the viral communities might influence canine health and disease by interacting with the commensal gut microbiome.}, } @article {pmid36992315, year = {2023}, author = {Ramos, EDSF and Abreu, WU and Rodrigues, LRR and Marinho, LF and Morais, VDS and Villanova, F and Pandey, RP and Araújo, ELL and Deng, X and Delwart, E and da Costa, AC and Leal, E}, title = {Novel Chaphamaparvovirus in Insectivorous Molossus molossus Bats, from the Brazilian Amazon Region.}, journal = {Viruses}, volume = {15}, number = {3}, pages = {}, pmid = {36992315}, issn = {1999-4915}, mesh = {Animals ; *Chiroptera ; Phylogeny ; Brazil/epidemiology ; Mammals ; *Parvovirus ; }, abstract = {Chaphamaparvovirus (CHPV) is a recently characterized genus of the Parvoviridae family whose members can infect different hosts, including bats, which constitute the second most diverse order of mammals and are described worldwide as important transmitters of zoonotic diseases. In this study, we identified a new CHPV in bat samples from the municipality of Santarém (Pará state, North Brazil). A total of 18 Molossus molossus bats were analyzed using viral metagenomics. In five animals, we identified CHPVs. These CHPV sequences presented the genome with a size ranging from 3797 to 4284 bp. Phylogenetic analysis-based nucleotide and amino acid sequences of the VP1 and NS1 regions showed that all CHPV sequences are monophyletic. They are also closely related to CHPV sequences previously identified in bats in southern and southeast Brazil. According to the International Committee on Taxonomy of Viruses (ICTV) classification criteria for this species (the CHPV NS1 gene region must have 85% identity to be classified in the same species), our sequences are likely a new specie within the genus Chaphamaparvovirus, since they have less than 80% identity with other CHPV described earlier in bats. We also make some phylogenetic considerations about the interaction between CHPV and their host. We suggest a high level of specificity of CPHV and its hosts. Thus, the findings contribute to improving information about the viral diversity of parvoviruses and show the importance of better investigating bats, considering that they harbor a variety of viruses that may favor zoonotic events.}, } @article {pmid36991496, year = {2023}, author = {Shay, JA and Haniford, LSE and Cooper, A and Carrillo, CD and Blais, BW and Lau, CH}, title = {Exploiting a targeted resistome sequencing approach in assessing antimicrobial resistance in retail foods.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {25}, pmid = {36991496}, issn = {2524-6372}, support = {GRDI-AMR//Government of Canada Genomic Research and Development Initiatives/ ; GRDI-AMR//Government of Canada Genomic Research and Development Initiatives/ ; GRDI-AMR//Government of Canada Genomic Research and Development Initiatives/ ; N-000166//Canadian Food Inspection Agency,Canada/ ; }, abstract = {BACKGROUND: With the escalating risk of antimicrobial resistance (AMR), there are limited analytical options available that can comprehensively assess the burden of AMR carried by clinical/environmental samples. Food can be a potential source of AMR bacteria for humans, but its significance in driving the clinical spread of AMR remains unclear, largely due to the lack of holistic-yet-sensitive tools for surveillance and evaluation. Metagenomics is a culture-independent approach well suited for uncovering genetic determinants of defined microbial traits, such as AMR, present within unknown bacterial communities. Despite its popularity, the conventional approach of non-selectively sequencing a sample's metagenome (namely, shotgun-metagenomics) has several technical drawbacks that lead to uncertainty about its effectiveness for AMR assessment; for instance, the low discovery rate of resistance-associated genes due to their naturally small genomic footprint within the vast metagenome. Here, we describe the development of a targeted resistome sequencing method and demonstrate its application in the characterization of the AMR gene profile of bacteria associated with several retail foods.

RESULT: A targeted-metagenomic sequencing workflow using a customized bait-capture system targeting over 4,000 referenced AMR genes and 263 plasmid replicon sequences was validated against both mock and sample-derived bacterial community preparations. Compared to shotgun-metagenomics, the targeted method consistently provided for improved recovery of resistance gene targets with a much-improved target detection efficiency (> 300-fold). Targeted resistome analyses conducted on 36 retail-acquired food samples (fresh sprouts, n = 10; ground meat, n = 26) and their corresponding bacterial enrichment cultures (n = 36) reveals in-depth features regarding the identity and diversity of AMR genes, most of which were otherwise undetected by the whole-metagenome shotgun sequencing method. Furthermore, our findings suggest that foodborne Gammaproteobacteria could be the major reservoir of food-associated AMR genetic determinants, and that the resistome structure of the selected high-risk food commodities are, to a large extent, dictated by microbiome composition.

CONCLUSIONS: For metagenomic sequencing-based surveillance of AMR, the target-capture method presented herein represents a more sensitive and efficient approach to evaluate the resistome profile of complex food or environmental samples. This study also further implicates retail foods as carriers of diverse resistance-conferring genes indicating a potential impact on the dissemination of AMR.}, } @article {pmid36991491, year = {2023}, author = {Hénaff, E and Najjar, D and Perez, M and Flores, R and Woebken, C and Mason, CE and Slavin, K}, title = {Holobiont Urbanism: sampling urban beehives reveals cities' metagenomes.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {23}, pmid = {36991491}, issn = {2524-6372}, support = {OPP1151054//Bill and Melinda Gates Foundation/ ; 1840275//National Science Foundation/ ; G-2015-13964//Alfred P. Sloan Foundation/ ; 1R01MH117406/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Over half of the world's population lives in urban areas with, according to the United Nations, nearly 70% expected to live in cities by 2050. Our cities are built by and for humans, but are also complex, adaptive biological systems involving a diversity of other living species. The majority of these species are invisible and constitute the city's microbiome. Our design decisions for the built environment shape these invisible populations, and as inhabitants we interact with them on a constant basis. A growing body of evidence shows us that human health and well-being are dependent on these interactions. Indeed, multicellular organisms owe meaningful aspects of their development and phenotype to interactions with the microorganisms-bacteria or fungi-with which they live in continual exchange and symbiosis. Therefore, it is meaningful to establish microbial maps of the cities we inhabit. While the processing and sequencing of environmental microbiome samples can be high-throughput, gathering samples is still labor and time intensive, and can require mobilizing large numbers of volunteers to get a snapshot of the microbial landscape of a city.

RESULTS: Here we postulate that honeybees may be effective collaborators in gathering samples of urban microbiota, as they forage daily within a 2-mile radius of their hive. We describe the results of a pilot study conducted with three rooftop beehives in Brooklyn, NY, where we evaluated the potential of various hive materials (honey, debris, hive swabs, bee bodies) to reveal information as to the surrounding metagenomic landscape, and where we conclude that the bee debris are the richest substrate. Based on these results, we profiled 4 additional cities through collected hive debris: Sydney, Melbourne, Venice and Tokyo. We show that each city displays a unique metagenomic profile as seen by honeybees. These profiles yield information relevant to hive health such as known bee symbionts and pathogens. Additionally, we show that this method can be used for human pathogen surveillance, with a proof-of-concept example in which we recover the majority of virulence factor genes for Rickettsia felis, a pathogen known to be responsible for "cat scratch fever".

CONCLUSIONS: We show that this method yields information relevant to hive health and human health, providing a strategy to monitor environmental microbiomes on a city scale. Here we present the results of this study, and discuss them in terms of architectural implications, as well as the potential of this method for epidemic surveillance.}, } @article {pmid36991068, year = {2023}, author = {Zhang, C and Liu, X and Shi, LD and Li, J and Xiao, X and Shao, Z and Dong, X}, title = {Unexpected genetic and microbial diversity for arsenic cycling in deep sea cold seep sediments.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {13}, pmid = {36991068}, issn = {2055-5008}, mesh = {*Geologic Sediments/chemistry/microbiology ; Seawater/chemistry/microbiology ; *Arsenic/metabolism ; Archaea/genetics ; Hydrocarbons/metabolism ; }, abstract = {Cold seeps, where cold hydrocarbon-rich fluid escapes from the seafloor, show strong enrichment of toxic metalloid arsenic (As). The toxicity and mobility of As can be greatly altered by microbial processes that play an important role in global As biogeochemical cycling. However, a global overview of genes and microbes involved in As transformation at seeps remains to be fully unveiled. Using 87 sediment metagenomes and 33 metatranscriptomes derived from 13 globally distributed cold seeps, we show that As detoxification genes (arsM, arsP, arsC1/arsC2, acr3) were prevalent at seeps and more phylogenetically diverse than previously expected. Asgardarchaeota and a variety of unidentified bacterial phyla (e.g. 4484-113, AABM5-125-24 and RBG-13-66-14) may also function as the key players in As transformation. The abundances of As cycling genes and the compositions of As-associated microbiome shifted across different sediment depths or types of cold seep. The energy-conserving arsenate reduction or arsenite oxidation could impact biogeochemical cycling of carbon and nitrogen, via supporting carbon fixation, hydrocarbon degradation and nitrogen fixation. Overall, this study provides a comprehensive overview of As cycling genes and microbes at As-enriched cold seeps, laying a solid foundation for further studies of As cycling in deep sea microbiome at the enzymatic and processual levels.}, } @article {pmid36990699, year = {2023}, author = {Zhou, H}, title = {[Several issues in interpreting the results of metagenomic next generation sequencing of lower respiratory tract infection].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {46}, number = {4}, pages = {319-321}, doi = {10.3760/cma.j.cn112147-20221117-00903}, pmid = {36990699}, issn = {1001-0939}, mesh = {Humans ; Computational Biology ; *High-Throughput Nucleotide Sequencing ; *Metagenome ; *Respiratory Tract Infections/diagnosis ; Sensitivity and Specificity ; }, abstract = {Metagenome next generation sequencing (mNGS) is an important method for pathogen diagnosis of lower respiratory tract infection, but there are many difficulties in interpreting mNGS reports. The Expert Consensus on Clinical Interpretation Path of mNGS of Lower Respiratory Tract Infection, completed by Chinese Thoracic Society, provides a detailed path and guidance for report interpretation. The expert consensus covers clinical medicine, microbiology, molecular diagnosis and other aspects. On this basis, several important clinical issues need to be highlighted. First, the lower respiratory tract specimens used for mNGS must be obtained in a timely and qualified manner. Second, the correct interpretation of the mNGS report needs to be based on a full understanding of the patients and their conditions. Third, the quality of the report should be analyzed according to the main parameters in the mNGS report. Fourth, an understanding of basic microbiology knowledge is beneficial to identify valuable pathogens in the mNGS report. Fifth, other microbiological methods should be actively used during mNGS detection. Sixth, to seek the help of the team when necessary and organize multidisciplinary discussions are vital. Seventh, it is important to constantly adjust the diagnosis and treatment strategies according to the clinical treatment response to treatment and the evolution of the disease. In a word, the interpretation of mNGS results needs to refer to specimen types and sequencing parameters, to combine with the specific conditions of patients in detail, to collect a variety of microbiological test results, to carefully screen and make judgement according to the treatment effect and disease outcome, and finally to make the diagnosis. The interpretation of mNGS report also requires us to have more knowledge of microbiology, sequencing and bioinformatics analysis, and to pay more attention to the strength of the team to discriminate the truth in multidisciplinary collaboration.}, } @article {pmid36990698, year = {2023}, author = {Lu, BH}, title = {[Basic competence for etiological diagnosis of lower respiratory tract infection after application of metagenomic next-generation sequencing].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {46}, number = {4}, pages = {315-318}, doi = {10.3760/cma.j.cn112147-20221121-00915}, pmid = {36990698}, issn = {1001-0939}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; *Respiratory Tract Infections/diagnosis ; Metagenomics ; Polymerase Chain Reaction ; Sensitivity and Specificity ; }, abstract = {In addition to clinical manifestations, medical history, and imaging, the diagnosis of low respiratory tract infection (LRTI) depends mainly on the ability of the clinical microbiology laboratory to detect the pathogens. However, conventional culture may be time-consuming, the sensitivity of microscopy is low, and nucleic acid-based targeted tests (e.g., PCR) could only cover limited range of pathogens. The use of mNGS technology has improved the diagnostic rate of LRTI, but the conventional microbiology detection has been neglected to some extent. This review addressed the appropriate use of these methods with the aim of strengthening the ability of traditional microbiology methods in LRTI diagnosis after mNGS application.}, } @article {pmid36990697, year = {2023}, author = {Shi, Y and Li, P}, title = {[Diagnostic value and consideration of low sequence pathogens detected by metagenomic next-generation sequencing in lower respiratory tract infection].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {46}, number = {4}, pages = {311-314}, doi = {10.3760/cma.j.cn112147-20221129-00939}, pmid = {36990697}, issn = {1001-0939}, mesh = {Humans ; Reproducibility of Results ; *High-Throughput Nucleotide Sequencing ; *Respiratory Tract Infections/diagnosis ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {Pathogenic diagnosis of lower respiratory tract infection has always been a clinical problem. The widespread application of metagenomic next-generation sequencing(mNGS)provides a rapid and accurate method for pathogenic diagnosis. However, how to interpret the results of mNGS detection, especially whether it has diagnostic value in detecting pathogens with low sequence number, has always puzzled clinicians. This paper discusses the definition of low sequence number (lower reads)detected by mNGS in lower respiratory tract infection, the cause of occurrence, the method to determine the reliability of the results, and how to correctly interpret the low sequence number report in combination with clinical practice. It is hoped that by comprehensively mastering the detection knowledge, the proper clinical analysis thinking can be established to improve the diagnostic ability of pathogens with low sequence number detected by mNGS in lower respiratory tract infection.}, } @article {pmid36990340, year = {2023}, author = {Qin, G and Zhang, Q and Zhang, Z and Chen, Y and Zhu, J and Yang, Y and Peijnenburg, WJGM and Qian, H}, title = {Understanding the ecological effects of the fungicide difenoconazole on soil and Enchytraeus crypticus gut microbiome.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {326}, number = {}, pages = {121518}, doi = {10.1016/j.envpol.2023.121518}, pmid = {36990340}, issn = {1873-6424}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Fungicides, Industrial/pharmacology ; Soil/chemistry ; *Pesticides/toxicity ; Bacteria ; *Oligochaeta ; *Soil Pollutants/analysis ; }, abstract = {Increasing knowledge of the impacts of pesticides on soil ecological communities is fundamental to a comprehensive understanding of the functional changes in the global agroecosystem industry. In this study, we examined microbial community shifts in the gut of the soil-dwelling organism Enchytraeus crypticus and functional shifts in the soil microbiome (bacteria and viruses) after 21 d of exposure to difenoconazole, one of the main fungicides in intensified agriculture. Our results demonstrated reduced body weight and increased oxidative stress levels of E. crypticus under difenoconazole treatment. Meanwhile, difenoconazole not only altered the composition and structure of the gut microbial community, but also interfered with the soil-soil fauna microecology stability by impairing the abundance of beneficial bacteria. Using soil metagenomics, we revealed that bacterial genes encoding detoxification and viruses encoding carbon cycle genes exhibited a dependent enrichment in the toxicity of pesticides via metabolism. Taken together, these findings advance the understanding of the ecotoxicological impact of residual difenoconazole on the soil-soil fauna micro-ecology, and the ecological importance of virus-encoded auxiliary metabolic genes under pesticide stress.}, } @article {pmid36990333, year = {2023}, author = {Su, X and Zhu, XR and Li, J and Wu, L and Li, X and Zhang, Q and Peng, Y}, title = {Determination of partial denitrification kinetic model parameters based on batch tests and metagenomic sequencing.}, journal = {Bioresource technology}, volume = {379}, number = {}, pages = {128977}, doi = {10.1016/j.biortech.2023.128977}, pmid = {36990333}, issn = {1873-2976}, mesh = {*Wastewater ; *Nitrites ; Denitrification ; Bioreactors ; Sewage ; }, abstract = {In this study, a model was developed to investigate the partial denitrification(PD) process. The heterotrophic biomass (XH) proportion in the sludge was determined to be 66.4% based on metagenomic sequencing. The kinetic parameters were first calibrated, then validated using the batch tests results. The results showed rapid decreases in the chemical oxygen demand (COD) and nitrate concentrations and gradual increases in the nitrite concentrations in the first four hours, then remained constant from 4 to 8 h. Anoxic reduction factor (ηNO3 and ηNO2) and half saturation constant (KS1 and KS2) were calibrated at 0.097, 0.13, 89.28 mg COD/L, and 102.29 mg COD/L, respectively. Whereas the simulation results demonstrated that the increase in carbon-to-nitrogen (C/N) ratios and the reduction in XH contributed to the increase in the nitrite transformation rate. This model provides potential strategies for optimizing the PD/A process.}, } @article {pmid36990280, year = {2023}, author = {Pyden, A and Rugwizangoga, B and Solomon, IH and Laga, AC}, title = {Teaching Infectious Disease Pathology and Taking it To Africa.}, journal = {Modern pathology : an official journal of the United States and Canadian Academy of Pathology, Inc}, volume = {36}, number = {5}, pages = {100168}, doi = {10.1016/j.modpat.2023.100168}, pmid = {36990280}, issn = {1530-0285}, mesh = {Humans ; Female ; United States ; *Communicable Diseases ; Curriculum ; Education, Medical, Graduate/methods ; *Pathology, Clinical ; Africa ; *Pathology/education ; }, abstract = {With the advent of increasing emerging infectious diseases, rising antibiotic resistance, and the growing number of immunocompromised patients, there is increasing demand for infectious disease (ID) pathology expertise and microbiology testing. Currently, ID pathology training and emerging molecular microbiology techniques (eg, metagenomic next-generation sequencing and whole genome sequencing) are not included in the most American Council of Graduate Medical Education medical microbiology fellowship curricula, and not surprisingly, many institutions lack anatomical pathologists with expertise in ID pathology and advanced molecular diagnostics. In this article, we describe the curriculum and structure of the Franz von Lichtenberg Fellowship in Infectious Disease and Molecular Microbiology at Brigham and Women's Hospital in Boston, MA. We emphasize the value of a training model that strives to integrate anatomical pathology, clinical pathology, and molecular pathology by providing examples in a case-based format and presenting selected metrics of the potential effect of such integrative ID pathology service and briefly describing opportunities and challenges of our global health efforts in Rwanda.}, } @article {pmid36990236, year = {2023}, author = {Xiang, R and Tian, Z and Zhang, C and Zheng, B and Jia, H}, title = {Characterization of dissolved organic matter content, composition, and source during spring algal bloom in tributaries of the Three Gorges Reservoir.}, journal = {The Science of the total environment}, volume = {879}, number = {}, pages = {163139}, doi = {10.1016/j.scitotenv.2023.163139}, pmid = {36990236}, issn = {1879-1026}, mesh = {*Dissolved Organic Matter ; *Ecosystem ; Chlorophyll A ; Rivers ; Humic Substances/analysis ; Eutrophication ; }, abstract = {Dissolved organic matter (DOM) is a key component of aquatic ecosystem function and biogeochemical processes. The characteristics of DOM in tributaries of the Three Gorges Reservoir (TGR) during the severe spring algal bloom period and their relationship with algal growth are unclear. In this study, the content, composition, and source of DOM in the Pengxi River (PXR) and Ruxi River (RXR) exhibiting typical TGR bloom problems were analyzed using various physicochemical indexes, carbon isotopes, fatty acids, and metagenomics. The results showed that chlorophyll a content increased with rising DOM concentration in the PXR and RXR. The dissolved organic carbon (DOC) and chromophoric dissolved organic matter (CDOM) contents in the two rivers were 4.656-16.560 mg/L and 14.373-50.848 μg/L, respectively, and increased during the bloom period. Four fluorescent components were identified, namely, two humic-like substances, and two protein-like substances. Proteobacteria, bacteroidetes, and actinobacteria were the greatest contributors to DOM content. The carbon fixation pathway of microorganisms increased the DOC concentration in both rivers during the bloom period. Physicochemical parameters (WT, pH, DO, and PAR) affected the DOM concentration by influencing microbial activity and DOM degradation. DOM in both rivers was derived from allochthonous and autogenous sources. Meanwhile, the DOC content was more strongly correlated with allochthonous sources. These findings might provide essential information for improving water environment management and algal bloom control in the TGR.}, } @article {pmid36990166, year = {2023}, author = {Yang, H and Wu, C and Chen, L and Chang, X and Luo, G and Wu, K and Tian, W}, title = {A. macrocephala polysaccharide induces alterations to gut microbiome and serum metabolome in constipated mice.}, journal = {Microbial pathogenesis}, volume = {178}, number = {}, pages = {106084}, doi = {10.1016/j.micpath.2023.106084}, pmid = {36990166}, issn = {1096-1208}, mesh = {Mice ; Animals ; *Gastrointestinal Microbiome ; Tryptophan ; Constipation/metabolism ; Polysaccharides/pharmacology ; Metabolome ; }, abstract = {Atractylodes macrocephala polysaccharide (AC1) is extracted from the root of the Chinese herb Atractylodes Macrocephala and is used in the treatment of constipation due to its effects on strengthening cellular immunity and regulating intestinal function. In this study, Metagenomics and Metabolomic are used to analyze the effects of AC1 on the gut microbiota and host metabolites in mice models of constipation. The results show that the abundance of Lachnospiraceae_bacterium_A4, Bact-oides_vulgatus and Prevotella_sp_CAG:891 increased significantly, indicating that AC1-targeted strain modulation effectively alleviated the dysbiosis of the gut microbiota. Besides, the microbial alterations also influenced the metabolic pathways of the mice, including tryptophan metabolism, unsaturated fatty acid synthesis and bile acid metabolism. The physiological parameters of the mice treated with AC1 are improved, such as tryptophan in the colon, 5-hydroxytryptamine (5-HT) and short-chain fatty acids (SCFAs). In conclusion, AC1 as a probiotic can regulate intestinal flora to normal levels and achieve the effect of treating constipation.}, } @article {pmid36989806, year = {2023}, author = {Yan, Y and Zhang, J and Tian, L and Yan, X and Du, L and Leininger, A and Zhang, M and Li, N and Ren, ZJ and Wang, X}, title = {DIET-like mutualism of Geobacter and methanogens at specific electrode potential boosts production of both methane and hydrogen from propionate.}, journal = {Water research}, volume = {235}, number = {}, pages = {119911}, doi = {10.1016/j.watres.2023.119911}, pmid = {36989806}, issn = {1879-2448}, mesh = {*Propionates ; Symbiosis ; *Geobacter ; Methane ; Hydrogen ; Electron Transport ; Diet ; Bioreactors ; Anaerobiosis ; }, abstract = {Direct interspecies electron transfer (DIET) has been demonstrated to be an efficient type of mutualism in methanogenesis. However, few studies have reported its presence in mixed microbial communities and its trigger mechanism in the natural environment and engineered systems. Here, we reported DIET-like mutualism of Geobacter and methanogens in the planktonic microbiome for the first time in anaerobic electrochemical digestion (AED) fed with propionate, potentially triggered by excessive cathodic hydrogen (56 times higher than the lowest) under the electrochemical condition. In contrast with model prediction without DIET, the highest current density and hydrogen and methane production were concurrently observed at -0.2 V where an abundance of Geobacter (49%) and extracellular electron transfer genes were identified in the planktonic microbiome via metagenomic analysis. Metagenomic assembly genomes annotated to Geobacter anodireducens were identified alongside two methanogens, Methanothrix harundinacea and Methanosarcina mazei, which were previously identified to participate in DIET. This discovery revealed that DIET-like mutualism could be triggered without external conductive materials, highlighting its potentially ubiquitous presence. Such mutualism simultaneously boosted methane and hydrogen production, thereby demonstrating the potential of AED in engineering applications.}, } @article {pmid36989799, year = {2023}, author = {Calderón-Franco, D and Corbera-Rubio, F and Cuesta-Sanz, M and Pieterse, B and de Ridder, D and van Loosdrecht, MCM and van Halem, D and Laureni, M and Weissbrodt, DG}, title = {Microbiome, resistome and mobilome of chlorine-free drinking water treatment systems.}, journal = {Water research}, volume = {235}, number = {}, pages = {119905}, doi = {10.1016/j.watres.2023.119905}, pmid = {36989799}, issn = {1879-2448}, mesh = {*Drinking Water/analysis ; Angiotensin Receptor Antagonists/analysis ; Angiotensin-Converting Enzyme Inhibitors/analysis ; Bacteria/genetics ; Genes, Bacterial ; Anti-Bacterial Agents/analysis ; *Water Purification ; Chlorine/analysis ; *Microbiota ; }, abstract = {Drinking water treatment plants (DWTPs) are designed to remove physical, chemical, and biological contaminants. However, until recently, the role of DWTPs in minimizing the cycling of antibiotic resistance determinants has got limited attention. In particular, the risk of selecting antibiotic-resistant bacteria (ARB) is largely overlooked in chlorine-free DWTPs where biological processes are applied. Here, we combined high-throughput quantitative PCR and metagenomics to analyze the abundance and dynamics of microbial communities, antibiotic resistance genes (ARGs), and mobile genetic elements (MGEs) across the treatment trains of two chlorine-free DWTPs involving dune-based and reservoir-based systems. The microbial diversity of the water increased after all biological unit operations, namely rapid and slow sand filtration (SSF), and granular activated carbon filtration. Both DWTPs reduced the concentration of ARGs and MGEs in the water by circa 2.5 log gene copies mL[-1], despite their relative increase in the disinfection sub-units (SSF in dune-based and UV treatment in reservoir-based DWTPs). The total microbial concentration was also reduced (2.5 log units), and none of the DWTPs enriched for bacteria containing genes linked to antibiotic resistance. Our findings highlight the effectiveness of chlorine-free DWTPs in supplying safe drinking water while reducing the concentration of antibiotic resistance determinants. To the best of our knowledge, this is the first study that monitors the presence and dynamics of antibiotic resistance determinants in chlorine-free DWTPs.}, } @article {pmid36989208, year = {2023}, author = {Rajamanikam, A and Isa, MNM and Samudi, C and Devaraj, S and Govind, SK}, title = {Gut bacteria influence Blastocystis sp. phenotypes and may trigger pathogenicity.}, journal = {PLoS neglected tropical diseases}, volume = {17}, number = {3}, pages = {e0011170}, pmid = {36989208}, issn = {1935-2735}, mesh = {Humans ; *Blastocystis/genetics ; Virulence ; Feces/parasitology ; *Blastocystis Infections/parasitology ; Bacteria ; Phenotype ; }, abstract = {Whilst the influence of intestinal microbiota has been shown in many diseases such as irritable bowel syndrome, colorectal cancer, and aging, investigations are still scarce on its role in altering the nature of other infective organisms. Here we studied the association and interaction of Blastocystis sp. and human intestinal microbiota. In this study, we investigated the gut microbiome of Blastocystis sp.-free and Blastocystis sp. ST3-infected individuals who are symptomatic and asymptomatic. We tested if the expression of phenotype and pathogenic characteristics of Blastocystis sp. ST3 was influenced by the alteration of its accompanying microbiota. Blastocystis sp. ST3 infection alters bacterial composition. Its presence in asymptomatic individuals showed a significant effect on microbial richness compared to symptomatic ones. Inferred metagenomic findings suggest that colonization of Blastocystis sp. ST3 could contribute to the alteration of microbial functions. For the first time, we demonstrate the influence of bacteria on Blastocystis sp. pathogenicity. When Blastocystis sp. isolated from a symptomatic individual was co-cultured with bacterial suspension of Blastocystis sp. from an asymptomatic individual, the parasite demonstrated increased growth and reduced potential pathogenic expressions. This study also reveals that Blastocystis sp. infection could influence microbial functions without much effect on the microbiota diversity itself. Our results also demonstrate evidence on the influential role of gut microbiota in altering the characteristics of the parasite, which becomes the basis for the contradictory findings on the parasite's pathogenic role seen across different studies. Our study provides evidence that asymptomatic Blastocystis sp. in a human gut can be triggered to show pathogenic characteristics when influenced by the intestinal microbiota.}, } @article {pmid36988865, year = {2023}, author = {Xu, J and Zhou, P and Liu, J and Zhao, L and Fu, H and Han, Q and Wang, L and Wu, W and Ou, Q and Ma, Y and He, J}, title = {Utilizing Metagenomic Next-Generation Sequencing (mNGS) for Rapid Pathogen Identification and to Inform Clinical Decision-Making: Results from a Large Real-World Cohort.}, journal = {Infectious diseases and therapy}, volume = {12}, number = {4}, pages = {1175-1187}, pmid = {36988865}, issn = {2193-8229}, support = {BE2019656//Jiangsu Provincial Key Research and Development Program/ ; 82070180//National Natural Science Foundation of China/ ; SZM2021011//Suzhou Science and Technology Planning Project/ ; }, abstract = {INTRODUCTION: Clinical metagenomic next-generation sequencing (mNGS) has proven to be a powerful diagnostic tool in pathogen detection. However, its clinical utility has not been thoroughly evaluated.

METHODS: In this single-center prospective study at the First Affiliated Hospital of Soochow University, a total of 228 samples from 215 patients suspected of having acute or chronic infections between June 2018 and December 2018 were studied. Samples that met the mNGS quality control (QC) criteria (N = 201) were simultaneously analyzed using conventional tests (CTs), including multiple clinical microbiological tests and real-time PCR (if applicable).

RESULTS: Pathogen detection results of mNGS in the 201 QC-passed samples were compared to CTs and exhibited a sensitivity of 98.8%, specificity of 38.5%, and accuracy of 87.1%. Specifically, 109 out of 160 (68.1%) CT+/mNGS+ samples exhibited concordant results at the species/genus level, 25 samples (15.6%) showed overlapping results, while the remaining 26 samples (16.3%) had discordant results between the CT and mNGS assays. In addition, mNGS could identify pathogens at the species level, whereas only the genera of some pathogens could be identified by CT. In this cohort, mNGS results were used to guide treatment plans in 24 out of 41 cases that had available follow-up information, and the symptoms were improved in over 70% (17/24) of them.

CONCLUSION: Our data demonstrated the analytic performance of our mNGS pipeline for pathogen detection using a large clinical cohort and strongly supports the notion that in clinical practice, mNGS represents a valuable supplementary tool to CTs to rapidly determine etiological factors of various types of infection and to guide treatment decision-making.}, } @article {pmid36987093, year = {2023}, author = {Ventimiglia, M and Castellacci, M and Usai, G and Vangelisti, A and Simoni, S and Natali, L and Cavallini, A and Mascagni, F and Giordani, T}, title = {Discovering the Repeatome of Five Species Belonging to the Asteraceae Family: A Computational Study.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {6}, pages = {}, pmid = {36987093}, issn = {2223-7747}, support = {Project Plantomics [grant number 569999_2017]//University of Pisa/ ; }, abstract = {Genome divergence by repeat proliferation and/or loss is a process that plays a crucial role in species evolution. Nevertheless, knowledge of the variability related to repeat proliferation among species of the same family is still limited. Considering the importance of the Asteraceae family, here we present a first contribution towards the metarepeatome of five Asteraceae species. A comprehensive picture of the repetitive components of all genomes was obtained by genome skimming with Illumina sequence reads and by analyzing a pool of full-length long terminal repeat retrotransposons (LTR-REs). Genome skimming allowed us to estimate the abundance and variability of repetitive components. The structure of the metagenome of the selected species was composed of 67% repetitive sequences, of which LTR-REs represented the bulk of annotated clusters. The species essentially shared ribosomal DNA sequences, whereas the other classes of repetitive DNA were highly variable among species. The pool of full-length LTR-REs was retrieved from all the species and their age of insertion was established, showing several lineage-specific proliferation peaks over the last 15-million years. Overall, a large variability of repeat abundance at superfamily, lineage, and sublineage levels was observed, indicating that repeats within individual genomes followed different evolutionary and temporal dynamics, and that different events of amplification or loss of these sequences may have occurred after species differentiation.}, } @article {pmid36985385, year = {2023}, author = {García-Maldonado, JQ and Latisnere-Barragán, H and Escobar-Zepeda, A and Cadena, S and Ramírez-Arenas, PJ and Vázquez-Juárez, R and Rojas-Contreras, M and López-Cortés, A}, title = {Revisiting Microbial Diversity in Hypersaline Microbial Mats from Guerrero Negro for a Better Understanding of Methanogenic Archaeal Communities.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985385}, issn = {2076-2607}, support = {FORDECYT-PRONACES, CF-2019-848287//Consejo Nacional de Ciencia y Tecnología/ ; }, abstract = {Knowledge regarding the diversity of methanogenic archaeal communities in hypersaline environments is limited because of the lack of efficient cultivation efforts as well as their low abundance and metabolic activities. In this study, we explored the microbial communities in hypersaline microbial mats. Bioinformatic analyses showed significant differences among the archaeal community structures for each studied site. Taxonomic assignment based on 16S rRNA and methyl coenzyme-M reductase (mcrA) gene sequences, as well as metagenomic analysis, corroborated the presence of Methanosarcinales. Furthermore, this study also provided evidence for the presence of Methanobacteriales, Methanomicrobiales, Methanomassiliicoccales, Candidatus Methanofastidiosales, Methanocellales, Methanococcales and Methanopyrales, although some of these were found in extremely low relative abundances. Several mcrA environmental sequences were significantly different from those previously reported and did not match with any known methanogenic archaea, suggesting the presence of specific environmental clusters of methanogenic archaea in Guerrero Negro. Based on functional inference and the detection of specific genes in the metagenome, we hypothesised that all four methanogenic pathways were able to occur in these environments. This study allowed the detection of extremely low-abundance methanogenic archaea, which were highly diverse and with unknown physiology, evidencing the presence of all methanogenic metabolic pathways rather than the sheer existence of exclusively methylotrophic methanogenic archaea in hypersaline environments.}, } @article {pmid36985376, year = {2023}, author = {Baev, V and Apostolova, E and Gotcheva, V and Koprinarova, M and Papageorgiou, M and Rocha, JM and Yahubyan, G and Angelov, A}, title = {16S-rRNA-Based Metagenomic Profiling of the Bacterial Communities in Traditional Bulgarian Sourdoughs.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985376}, issn = {2076-2607}, support = {KP-06-N-36/3//Bulgarian National Science Fund, grant number KP-06-N-36/3 (КП-06-Н-36/3)./ ; }, abstract = {Sourdoughs (SDs) are spontaneously formed microbial ecosystems composed of various species of lactic acid bacteria (LAB) and acid-tolerant yeasts in food matrices of cereal flours mixed with water. To date, more than 90 LAB species have been isolated, significantly impacting the organoleptic characteristics, shelf life, and health properties of bakery products. To learn more about the unique bacterial communities involved in creating regional Bulgarian sourdoughs, we examined the metacommunities of five sourdoughs produced by spontaneous fermentation and maintained by backslopping in bakeries from three geographic locations. The 16S rRNA gene amplicon sequencing showed that the former genus Lactobacillus was predominant in the studied sourdoughs (51.0-78.9%). Weissella (0.9-42.8%), Herbaspirillum (1.6-3.8%), Serratia (0.1-11.7%), Pediococcus (0.2-7.5%), Bacteroides (0.1-1.3%), and Sphingomonas (0.1-0.5%) were also found in all 5 samples. Genera Leuconostoc, Enterococcus, Bacillus, and Asaia were sample-specific. It is interesting to note that the genus Weissella was more abundant in wholegrain samples. The greatest diversity at the species level was found in the former genus Lactobacillus, presented in the sourdough samples with 13 species. The UPGMA cluster analysis clearly demonstrated similarity in species' relative abundance between samples from the same location. In addition, we can conclude that the presence of two main clusters-one including samples from mountainous places (the cities of Smolyan and Bansko) and the other including samples from the city of Ruse (the banks of the Danube River)-may indicate the impact of climate and geographic location (e.g., terrain, elevation, land use, and nearby water bodies and their streams) on the abundance of microbiome taxa. As the bacterial population is crucial for bread standardization, we expect the local bakery sector to be interested in the relationship between process variables and their effect on bacterial dynamics described in this research study.}, } @article {pmid36985338, year = {2023}, author = {Xiao, Y and Zhang, P and Zhang, H and Wang, H and Min, G and Wang, H and Wang, Y and Xu, J}, title = {Effects of Resource Availability and Antibiotic Residues on Intestinal Antibiotic Resistance in Bellamya aeruginosa.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985338}, issn = {2076-2607}, abstract = {Widespread and inappropriate use of antibiotics has been shown to increase the spread of antibiotics and antimicrobial resistance genes (ARGs) in aquatic environments and organisms. Antibiotic use for the treatment of human and animal diseases is increasing continuously globally. However, the effects of legal antibiotic concentrations on benthic consumers in freshwater environments remain unclear. In the present study, we tested the growth response of Bellamya aeruginosa to florfenicol (FF) for 84 days under high and low concentrations of sediment organic matter (carbon [C] and nitrogen [N]). We characterized FF and sediment organic matter impact on the bacterial community, ARGs, and metabolic pathways in the intestine using metagenomic sequencing and analysis. The high concentrations of organic matter in the sediment impacted the growth, intestinal bacterial community, intestinal ARGs, and microbiome metabolic pathways of B. aeruginosa. B. aeruginosa growth increased significantly following exposure to high organic matter content sediment. Proteobacteria, at the phylum level, and Aeromonas at the genus level, were enriched in the intestines. In particular, fragments of four opportunistic pathogens enriched in the intestine of high organic matter content sediment groups, Aeromonas hydrophila, Aeromonas caviae, Aeromonas veronii, and Aeromonas salmonicida, carried 14 ARGs. The metabolic pathways of the B. aeruginosa intestine microbiome were activated and showed a significant positive correlation with sediment organic matter concentrations. In addition, genetic information processing and metabolic functions may be inhibited by the combined exposure to sediment C, N, and FF. The findings of the present study suggest that antibiotic resistance dissemination from benthic animals to the upper trophic levels in freshwater lakes should be studied further.}, } @article {pmid36985314, year = {2023}, author = {Lozano, FM and Lledó, B and Morales, R and Cascales, A and Hortal, M and Bernabeu, A and Bernabeu, R}, title = {Characterization of the Endometrial Microbiome in Patients with Recurrent Implantation Failure.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985314}, issn = {2076-2607}, abstract = {An abnormal endometrial microbiota has been associated with implantation failure; therefore, it may be important to evaluate it in order to improve reproductive outcomes in infertile patients. The main objective of our study was to compare the endometrial microbiome of patients with recurrent implantation failure (RIF) and control patients undergoing assisted reproduction treatment (ART). A prospective cohort study including forty-five patients with their own or donated gametes. The endometrial microbiome was analysed by massive sequencing of the bacterial 16S rRNA gene. Different bacterial communities were detected in RIF and control patients. Lactobacillus stands out as the most frequent genus, with 92.27% in RIF patients and 97.96% in control patients, and significant differences were reported between the two groups (p = 0.002). No significant differences were found regarding alpha diversity index. In beta diversity analysis, a significant trend was observed in the separation of the bacterial community between established groups (p < 0.07). Relative abundance analysis identified genera Prevotella (p < 0.001), Streptococcus (p < 0.001), Bifidobacterium (p = 0.002), Lactobacillus (p = 0.002) and Dialister (p = 0.003). Our results demonstrated the existence of an endometrial microbiota characteristic of RIF patients and showed that there might be a relationship between population of the endometrial microbiome and embryo implantation failure, providing us the possibility to improve clinical results in this patients.}, } @article {pmid36985295, year = {2023}, author = {Goma-Tchimbakala, EJCD and Pietrini, I and Goma-Tchimbakala, J and Corgnati, SP}, title = {Use of Shotgun Metagenomics to Assess the Microbial Diversity and Hydrocarbons Degrading Functions of Auto-Mechanic Workshops Soils Polluted with Gasoline and Diesel Fuel.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985295}, issn = {2076-2607}, abstract = {Bioaugmentation is a valuable technique for oil recovery. This study investigates the composition and functions of microbial communities in gasoline- and diesel-contaminated soils of garages Matoko (SGM) and Guy et Paul (SGP) originating from auto mechanic workshops as well as the concentration of soil enzymes β-glucosidase, β-glucosaminidase, and acid phosphatase. The work aimed to evaluate the presence of petroleum-hydrocarbon-degrading bacteria for the development of foreseen bioremediation of oil-contaminated soils. Microbial diversity, as given by shotgun metagenomics, indicated the presence of 16 classes, among which Actinobacteria and Gammaproteobacteria dominated, as well as more than 50 families, including the dominant Gordoniaceae (26.63%) in SGM and Pseudomonadaceae (57.89%) in SGP. The dominant bacterial genera in the two soils were, respectively, Gordonia (26.7%) and Pseudomonas (57.9%). The exploration of the bacterial metabolic abilities using HUMANn2 allowed to detect genes and pathways involved in alkanes and aromatic hydrocarbons in the two contaminated soils. Furthermore, enzymes β-glucosidase, β-glucosaminidase, and acid phosphatase were found in high concentrations ranging between 90.27 ± 5.3 and 804.17 ± 20.5 µg pN/g soil/h, which indicated active microbial metabolism. The high diversity of microorganisms with a hydrocarbon degradation genetic package revealed that the bacteria inhabiting the two soils are likely good candidates for the bioaugmentation of oil-contaminated soils.}, } @article {pmid36985280, year = {2023}, author = {Jamwal, VL and Rather, IA and Ahmed, S and Kumar, A and Gandhi, SG}, title = {Changing Rhizosphere Microbial Community and Metabolites with Developmental Stages of Coleus barbatus.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985280}, issn = {2076-2607}, support = {BSC117 (PMSI)//Council of Scientific and Industrial Research/ ; MLP110006//Council of Scientific and Industrial Research/ ; }, abstract = {Coleus barbatus is a medicinal herb belonging to Lamiaceae. It is the only living organism known to produce forskolin, which is a labdane diterpene and is reported to activate adenylate cyclase. Microbes associated with plants play an important role in maintaining plant health. Recently, the targeted application of beneficial plant-associated microbes and their combinations in abiotic and biotic stress tolerance has gained momentum. In this work, we carried out the rhizosphere metagenome sequencing of C. barbatus at different developmental stages to understand how rhizosphere microflora are affected by and affect the metabolite content in plants. We found that the Kaistobacter genus was abundantly present in the rhizosphere of C. barbatus and its accumulation pattern appears to correlate with the quantities of forskolin in the roots at different developmental stages. Members of the Phoma genus, known for several pathogenic species, were in lower numbers in the C. barbatus rhizosphere in comparison with C. blumei. To our knowledge, this is the first metagenomic study of the rhizospheric microbiome of C. barbatus, which may help to explore and exploit the culturable and non-culturable microbial diversity present in the rhizosphere.}, } @article {pmid36985245, year = {2023}, author = {Cruz-Silva, A and Laureano, G and Pereira, M and Dias, R and Silva, JMD and Oliveira, N and Gouveia, C and Cruz, C and Gama-Carvalho, M and Alagna, F and Duarte, B and Figueiredo, A}, title = {A New Perspective for Vineyard Terroir Identity: Looking for Microbial Indicator Species by Long Read Nanopore Sequencing.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985245}, issn = {2076-2607}, support = {UIDB/04292/2020, UIDP/04292/2020,LA/P/0069/2020,UIDP/04046/2020, CEEC-IND/00511/2017, UI/BD/153050/2022, SFRH/BD/145298/2019, PRIMA/0011/2020//Fundação para a Ciência e Tecnologia/ ; }, abstract = {Grapevine is one of the most important fruit crops worldwide, being Portugal one of the top wine producers. It is well established that wine sensory characteristics from a particular region are defined by the physiological responses of the grapevine to its environment and thus, the concept of terroir in viticulture was established. Among all the factors that contribute to terroir definition, soil microorganisms play a major role from nutrient recycling to a drastic influence on plant fitness (growth and protection) and of course wine production. Soil microbiome from four different terroirs in Quinta dos Murças vineyard was analysed through long-read Oxford Nanopore sequencing. We have developed an analytical pipeline that allows the identification of function, ecologies, and indicator species based on long read sequencing data. The Douro vineyard was used as a case study, and we were able to establish microbiome signatures of each terroir.}, } @article {pmid36985231, year = {2023}, author = {Bandarupalli, VVK and St-Pierre, B}, title = {Metagenomics-Based Analysis of Candidate Lactate Utilizers from the Rumen of Beef Cattle.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985231}, issn = {2076-2607}, support = {SD00H551-15//South Dakota State University Agricultural Experiment Station/ ; }, abstract = {In ruminant livestock production, ruminal acidosis is an unintended consequence of the elevated dietary intake of starch-rich feedstuffs. The transition from a state of subacute acidosis (SARA) to acute acidosis is due in large part to the accumulation of lactate in the rumen, which is a consequence of the inability of lactate utilizers to compensate for the increased production of lactate. In this report, we present the 16S rRNA gene-based identification of two bacterial operational taxonomic units (OTUs), Bt-01708_Bf (89.0% identical to Butyrivibrio fibrisolvens) and Bt-01899_Ap (95.3% identical to Anaerococcus prevotii), that were enriched from rumen fluid cultures in which only lactate was provided as an exogenous substrate. Analyses of in-silico-predicted proteomes from metagenomics-assembled contigs assigned to these candidate ruminal bacterial species (Bt-01708_Bf: 1270 annotated coding sequences, 1365 hypothetical coding sequences; Bt-01899_Ap: 871 annotated coding sequences, 1343 hypothetical coding sequences) revealed genes encoding lactate dehydrogenase, a putative lactate transporter, as well as pathways for the production of short chain fatty acids (formate, acetate and butyrate) and for the synthesis of glycogen. In contrast to these shared functions, each OTU also exhibited distinct features, such as the potential for the utilization of a diversified set of small molecules as substrates (Bt-01708_Bf: malate, quinate, taurine and polyamines) or for the utilization of starch (Bt-01899_Ap: alpha-amylase enzymes). Together, these results will contribute to the continued characterization of ruminal bacterial species that can metabolize lactate into distinct subgroups based on other metabolic capabilities.}, } @article {pmid36985222, year = {2023}, author = {Yongsawas, R and In-On, A and Inta, A and Kampuansai, J and Pandith, H and Suwannarach, N and Lumyong, S and Chitov, T and Disayathanoowat, T}, title = {Bacterial Communities in Lanna Fermented Soybeans from Three Different Ethnolinguistic Groups in Northern Thailand.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985222}, issn = {2076-2607}, abstract = {Northern Thailand, the main part of the Lanna region, is home to a diverse range of ethnic groups, each with their own food and cultural heritage. The bacterial compositions in fermented soybean (FSB) products indigenous to three Lanna ethnolinguistic groups, including Karen, Lawa, and Shan, were investigated in this study. Bacterial DNA was extracted from the FSB samples and subjected to 16S rRNA gene sequencing using the Illumina sequencing platform. Metagenomic data showed that the predominant bacteria in all FSBs were members of the genus Bacillus (49.5-86.8%), and the Lawa FSB had the greatest bacterial diversity. The presence of genera Ignatzschineria, Yaniella, Atopostipes in the Karen and Lawa FSBs and Proteus in the Shan FSB might be indicators of food hygiene problems during processing. The network analysis predicted antagonistic effects of Bacillus against some indicator and pathogenic bacteria. The functional prediction revealed some potential functional properties of these FSBs. The presence of Bacillus in all FSBs and Vagococcus in the Shan FSB suggests that these FSBs could potentially be good sources of beneficial bacteria, and they should be conserved and promoted for health and food security reasons. However, food processing hygiene measures should be introduced and monitored to warrant their properties as health foods.}, } @article {pmid36985129, year = {2023}, author = {Slobodkin, AI and Ratnikova, NM and Slobodkina, GB and Klyukina, AA and Chernyh, NA and Merkel, AY}, title = {Composition and Metabolic Potential of Fe(III)-Reducing Enrichment Cultures of Methanotrophic ANME-2a Archaea and Associated Bacteria.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985129}, issn = {2076-2607}, support = {22-14-00011//Russian Science Foundation/ ; No number//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {The key microbial group involved in anaerobic methane oxidation is anaerobic methanotrophic archaea (ANME). From a terrestrial mud volcano, we enriched a microbial community containing ANME-2a, using methane as an electron donor, Fe(III) oxide (ferrihydrite) as an electron acceptor, and anthraquinone-2,6-disulfonate as an electron shuttle. Ferrihydrite reduction led to the formation of a black, highly magnetic precipitate. A significant relative abundance of ANME-2a in batch cultures was observed over five subsequent transfers. Phylogenetic analysis revealed that, in addition to ANME-2a, two bacterial taxa belonging to uncultured Desulfobulbaceae and Anaerolineaceae were constantly present in all enrichments. Metagenome-assembled genomes (MAGs) of ANME-2a contained a complete set of genes for methanogenesis and numerous genes of multiheme c-type cytochromes (MHC), indicating the capability of methanotrophs to transfer electrons to metal oxides or to a bacterial partner. One of the ANME MAGs encoded respiratory arsenate reductase (Arr), suggesting the potential for a direct coupling of methane oxidation with As(V) reduction in the single microorganism. The same MAG also encoded uptake [NiFe] hydrogenase, which is uncommon for ANME-2. The MAG of uncultured Desulfobulbaceae contained genes of dissimilatory sulfate reduction, a Wood-Ljungdahl pathway for autotrophic CO2 fixation, hydrogenases, and 43 MHC. We hypothesize that uncultured Desulfobulbaceae is a bacterial partner of ANME-2a, which mediates extracellular electron transfer to Fe(III) oxide.}, } @article {pmid36985120, year = {2023}, author = {Guo, Y and Yuan, W and Lyu, N and Pan, Y and Cao, X and Wang, Y and Han, Y and Zhu, B}, title = {Association Studies on Gut and Lung Microbiomes in Patients with Lung Adenocarcinoma.}, journal = {Microorganisms}, volume = {11}, number = {3}, pages = {}, pmid = {36985120}, issn = {2076-2607}, support = {2021YFA1301000//National Key R&D Program of China/ ; JNL-2022013B//Research Project of Jinan Microecological Biomedicine Shandong Laboratory/ ; 32170068//National Natural Science Foundation of China/ ; }, abstract = {Lung adenocarcinoma (LADC) is a prevalent type of lung cancer that is associated with lung and gut microbiota. However, the interactions between these microbiota and cancer development remain unclear. In this study, a microbiome study was performed on paired fecal and bronchoalveolar lavage fluid (BALF) samples from 42 patients with LADC and 64 healthy controls using 16S rRNA gene amplicon and shotgun metagenome sequencing, aiming to correlate the lung and gut microbiota with LADC. Patients with LADC had reduced α-diversity in the gut microbiome and altered β-diversity compared with healthy controls, and the abundances of Flavonifractor, Eggerthella, and Clostridium were higher in the gut microbiome of LADC patients. The increased abundance of microbial species, such as Flavonifractor plautii, was associated with advanced-stage LADC and a higher metastasis rate. Phylogenetically, Haemophilus parainfluenzae was the most frequently shared taxon in the lung and gut microbiota of LADC patients. Gut microbiome functional pathways involving leucine, propanoate, and fatty acids were associated with LADC progression. In conclusion, the low diversity of the gut microbiota and the presence of H. parainfluenzae in gut and lung microbiota were linked to LADC development, while an increased abundance of F. plautii and the enriched metabolic pathways could be associated with the progression of LADC.}, } @article {pmid36984841, year = {2023}, author = {Cohen, CC and Huneault, H and Accardi, CJ and Jones, DP and Liu, K and Maner-Smith, KM and Song, M and Welsh, JA and Ugalde-Nicalo, PA and Schwimmer, JB and Vos, MB}, title = {Metabolome × Microbiome Changes Associated with a Diet-Induced Reduction in Hepatic Fat among Adolescent Boys.}, journal = {Metabolites}, volume = {13}, number = {3}, pages = {}, pmid = {36984841}, issn = {2218-1989}, support = {T32 DK007658/DK/NIDDK NIH HHS/United States ; P20GM113226/GM/NIGMS NIH HHS/United States ; P30ES019776/ES/NIEHS NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; T32DK07658/DK/NIDDK NIH HHS/United States ; R01 NR019083/NR/NINR NIH HHS/United States ; R01DK125701/DK/NIDDK NIH HHS/United States ; UL1TR001442/TR/NCATS NIH HHS/United States ; R01NR019083/NR/NINR NIH HHS/United States ; F32 DK131757/DK/NIDDK NIH HHS/United States ; P20GM103436/GM/NIGMS NIH HHS/United States ; P20GM106396/GM/NIGMS NIH HHS/United States ; F32DK131757/DK/NIDDK NIH HHS/United States ; }, abstract = {Dietary sugar reduction is one therapeutic strategy for improving nonalcoholic fatty liver disease (NAFLD), and the underlying mechanisms for this effect warrant further investigation. Here, we employed metabolomics and metagenomics to examine systemic biological adaptations associated with dietary sugar restriction and (subsequent) hepatic fat reductions in youth with NAFLD. Data/samples were from a randomized controlled trial in adolescent boys (11-16 years, mean ± SD: 13.0 ± 1.9 years) with biopsy-proven NAFLD who were either provided a low free-sugar diet (LFSD) (n = 20) or consumed their usual diet (n = 20) for 8 weeks. Plasma metabolomics was performed on samples from all 40 participants by coupling hydrophilic interaction liquid chromatography (HILIC) and C18 chromatography with mass spectrometry. In a sub-sample (n = 8 LFSD group and n = 10 usual diet group), 16S ribosomal RNA (rRNA) sequencing was performed on stool to examine changes in microbial composition/diversity. The diet treatment was associated with differential expression of 419 HILIC and 205 C18 metabolite features (p < 0.05), which were enriched in amino acid pathways, including methionine/cysteine and serine/glycine/alanine metabolism (p < 0.05), and lipid pathways, including omega-3 and linoleate metabolism (p < 0.05). Quantified metabolites that were differentially changed in the LFSD group, compared to usual diet group, and representative of these enriched metabolic pathways included increased serine (p = 0.001), glycine (p = 0.004), 2-aminobutyric acid (p = 0.012), and 3-hydroxybutyric acid (p = 0.005), and decreased linolenic acid (p = 0.006). Microbiome changes included an increase in richness at the phylum level and changes in a few genera within Firmicutes. In conclusion, the LFSD treatment, compared to usual diet, was associated with metabolome and microbiome changes that may reflect biological mechanisms linking dietary sugar restriction to a therapeutic decrease in hepatic fat. Studies are needed to validate our findings and test the utility of these "omics" changes as response biomarkers.}, } @article {pmid36984783, year = {2023}, author = {Fu, X and Zhang, M and Yuan, Y and Chen, Y and Ou, Z and Hashim, Z and Hashim, JH and Zhang, X and Zhao, Z and Norbäck, D and Sun, Y}, title = {Microbial Virulence Factors, Antimicrobial Resistance Genes, Metabolites, and Synthetic Chemicals in Cabins of Commercial Aircraft.}, journal = {Metabolites}, volume = {13}, number = {3}, pages = {}, pmid = {36984783}, issn = {2218-1989}, support = {2020A1515010845; 2021A1515010492//Natural Science Foundation of Guangdong Province/ ; 202102080362//Science and Technology Program of Guangzhou/ ; }, abstract = {Passengers are at a higher risk of respiratory infections and chronic diseases due to microbial exposure in airline cabins. However, the presence of virulence factors (VFs), antimicrobial resistance genes (ARGs), metabolites, and chemicals are yet to be studied. To address this gap, we collected dust samples from the cabins of two airlines, one with textile seats (TSC) and one with leather seats (LSC), and analyzed the exposure using shotgun metagenomics and LC/MS. Results showed that the abundances of 17 VFs and 11 risk chemicals were significantly higher in TSC than LSC (p < 0.01). The predominant VFs in TSC were related to adherence, biofilm formation, and immune modulation, mainly derived from facultative pathogens such as Haemophilus parainfluenzae and Streptococcus pneumoniae. The predominant risk chemicals in TSC included pesticides/herbicides (carbofuran, bromacil, and propazine) and detergents (triethanolamine, diethanolamine, and diethyl phthalate). The abundances of these VFs and detergents followed the trend of TSC > LSC > school classrooms (p < 0.01), potentially explaining the higher incidence of infectious and chronic inflammatory diseases in aircraft. The level of ARGs in aircraft was similar to that in school environments. This is the first multi-omic survey in commercial aircraft, highlighting that surface material choice is a potential intervention strategy for improving passenger health.}, } @article {pmid36983633, year = {2023}, author = {Kartti, S and Bendani, H and Boumajdi, N and Bouricha, EM and Zarrik, O and El Agouri, H and Fokar, M and Aghlallou, Y and El Jaoudi, R and Belyamani, L and Elkhannoussi, B and Ibrahimi, A}, title = {Metagenomics Analysis of Breast Microbiome Highlights the Abundance of Rothia Genus in Tumor Tissues.}, journal = {Journal of personalized medicine}, volume = {13}, number = {3}, pages = {}, pmid = {36983633}, issn = {2075-4426}, abstract = {Breast cancer is one of the main global priorities in terms of public health. It remains the most frequent cancer in women and is the leading cause of their death. The human microbiome plays various roles in maintaining health by ensuring a dynamic balance with the host or in the appearance of various pathologies including breast cancer. In this study, we performed an analysis of bacterial signature differences between tumor and adjacent tissues of breast cancer patients in Morocco. Using 16S rRNA gene sequencing, we observed that adjacent tissue contained a much higher percentage of the Gammaproteobacteria class (35.7%) while tumor tissue was characterized by a higher percentage of Bacilli and Actinobacteria classes, with about 18.8% and 17.2% average abundance, respectively. Analysis of tumor subtype revealed enrichment of genus Sphingomonodas in TNBC while Sphingomonodas was predominant in HER2. The LEfSe and the genus level heatmap analysis revealed a higher abundance of the Rothia genus in tumor tissues. The identified microbial communities can therefore serve as potential biomarkers for prognosis and diagnosis, while also helping to develop new strategies for the treatment of breast cancer patients.}, } @article {pmid36982690, year = {2023}, author = {Belalov, IS and Sokolov, AA and Letarov, AV}, title = {Diversity-Generating Retroelements in Prokaryotic Immunity.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, pmid = {36982690}, issn = {1422-0067}, mesh = {*Bacteria/genetics ; *Retroelements/genetics ; Prokaryotic Cells ; Proteins/genetics ; CRISPR-Cas Systems ; }, abstract = {Adaptive immunity systems found in different organisms fall into two major types. Prokaryotes possess CRISPR-Cas systems that recognize former invaders using memorized (captured) pieces of their DNA as pathogen signatures. Mammals possess a vast repertoire of antibodies and T-cell receptor variants generated in advance. In this second type of adaptive immunity, a pathogen presentation to the immune system specifically activates the cells that express matching antibodies or receptors. These cells proliferate to fight the infection and form the immune memory. The principle of preemptive production of diverse defense proteins for future use can hypothetically take place in microbes too. We propose a hypothesis that prokaryotes employ diversity-generating retroelements to prepare defense proteins against yet-unknown invaders. In this study, we test this hypothesis with the methods of bioinformatics and identify several candidate defense systems based on diversity-generating retroelements.}, } @article {pmid36982303, year = {2023}, author = {Giuffrè, M and Moretti, R and Tiribelli, C}, title = {Gut Microbes Meet Machine Learning: The Next Step towards Advancing Our Understanding of the Gut Microbiome in Health and Disease.}, journal = {International journal of molecular sciences}, volume = {24}, number = {6}, pages = {}, pmid = {36982303}, issn = {1422-0067}, mesh = {Humans ; *Gastrointestinal Microbiome ; Reproducibility of Results ; *Microbiota ; Metagenomics/methods ; Machine Learning ; }, abstract = {The human gut microbiome plays a crucial role in human health and has been a focus of increasing research in recent years. Omics-based methods, such as metagenomics, metatranscriptomics, and metabolomics, are commonly used to study the gut microbiome because they provide high-throughput and high-resolution data. The vast amount of data generated by these methods has led to the development of computational methods for data processing and analysis, with machine learning becoming a powerful and widely used tool in this field. Despite the promising results of machine learning-based approaches for analyzing the association between microbiota and disease, there are several unmet challenges. Small sample sizes, disproportionate label distribution, inconsistent experimental protocols, or a lack of access to relevant metadata can all contribute to a lack of reproducibility and translational application into everyday clinical practice. These pitfalls can lead to false models, resulting in misinterpretation biases for microbe-disease correlations. Recent efforts to address these challenges include the construction of human gut microbiota data repositories, improved data transparency guidelines, and more accessible machine learning frameworks; implementation of these efforts has facilitated a shift in the field from observational association studies to experimental causal inference and clinical intervention.}, } @article {pmid36981070, year = {2023}, author = {Zhang, T and Yue, Y and Jeong, SJ and Ryu, MS and Wu, X and Yang, HJ and Li, C and Jeong, DY and Park, S}, title = {Improvement of Estrogen Deficiency Symptoms by the Intake of Long-Term Fermented Soybeans (Doenjang) Rich in Bacillus Species through Modulating Gut Microbiota in Estrogen-Deficient Rats.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {6}, pages = {}, pmid = {36981070}, issn = {2304-8158}, support = {2021-10//functional research of fermented soybean food (safety monitoring)" under the Ministry of Agriculture, Food and Rural Affairs/ ; }, abstract = {Traditionally made doenjang (TMD) produced by the long-term fermentation of soybeans with salt may improve symptoms of estrogen deficiency. We aimed to evaluate the effects of four TMD types, containing low and high amounts of Bacillus species and biogenic amines (HBHA, HBLA, LBHA, and LBLA), on energy, glucose, and lipid metabolism, by altering the gut microbiota in estrogen-deficient ovariectomized (OVX) rats. Their mechanisms were also examined. The OVX rats were divided into the control, cooked soybean (CSB), HBHA, LBHA, HBLA, and LBLA groups. Sham-operated rats were the normal control group. Serum 17β-estradiol concentrations were similar among all OVX groups. Tail skin temperatures, which are indicative of hot flashes, were higher in the control than the HBHA and HBLA groups and were similar to the normal control group. Weight gain and visceral fat mass were lower in the TMD and CSB intake groups but not as low as in the normal control group. Lean body mass showed a trend opposite to that of visceral fat in the respective groups. The hepatic triglyceride content decreased with the TMD intake compared to the control and CSB groups. mRNA expressions of the peroxisome proliferator-activated receptor-γ (PPAR-γ) and carnitine palmitoyltransferase-1 in the TMD and CSB groups were as high as in the normal control group, and the PPAR-γ mRNA expression was more elevated in the HBLA group than in the normal control group. The morphology of the intestines improved in the TMD groups compared to the control, and the HBHA and HBLA groups showed an enhanced improvement compared to the CSB group. The HBHA, HBLA, and LBHA groups increased the α-diversity of the cecal microbiota compared to the control. Akkermenia and Lactobacillus were higher in the HBLA and LBLA groups compared to the control. The expression of the estrogen, forkhead box proteins of the class-O subgroup, and insulin-signaling pathways were lower in the control group, and HBHA and HBLA prevented their decrement. In conclusion, long-term treatment with TMD containing high amounts of Bacillus potentially improves estrogen deficiency symptoms more than unfermented soybeans.}, } @article {pmid36980929, year = {2023}, author = {Baeza, JA and Barata, R and Rajapakse, D and Penaloza, J and Harrison, P and Haberski, A}, title = {Mitochondrial Genomes Assembled from Non-Invasive eDNA Metagenomic Scat Samples in Critically Endangered Mammals.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, pmid = {36980929}, issn = {2073-4425}, mesh = {Animals ; *DNA, Environmental ; *Genome, Mitochondrial/genetics ; *Ursidae/genetics ; Endangered Species ; *Metagenome ; Feces ; }, abstract = {The abundance of many large-bodied vertebrates, both in marine and terrestrial environments, has declined substantially due to global and regional climate stressors that define the Anthropocene. The development of genetic tools that can serve to monitor population's health non-intrusively and inform strategies for the recovery of these species is crucial. In this study, we formally evaluate whether whole mitochondrial genomes can be assembled from environmental DNA (eDNA) metagenomics scat samples. Mitogenomes of four different large vertebrates, the panda bear (Ailuropoda melanoleuca), the moon bear (Ursus thibetanus), the Java pangolin (Manis javanica), and the the North Atlantic right whale (Eubalaena glacialis) were assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 12x to 480x in 14 out of 18 different eDNA samples. Partial mitochondrial genomes were retrieved from three other eDNA samples. The complete mitochondrial genomes of the studied species were AT-rich and comprised 13 protein coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative D-loop/control region. Synteny observed in all assembled mitogenomes was identical to that reported for specimens of the same and other closely related species. This study demonstrates that it is possible to assemble accurate whole mitochondrial chromosomes from eDNA samples (scats) using forthright bench and bioinformatics workflows. The retrieval of mitochondrial genomes from eDNA samples represents a tool to support bioprospecting, bio-monitoring, and other non-intrusive conservation strategies in species considered 'vulnerable', 'endangered', and/or 'critically endangered' by the IUCN Red List of Threatened Species.}, } @article {pmid36980906, year = {2023}, author = {Das, R and Rai, A and Mishra, DC}, title = {CNN_FunBar: Advanced Learning Technique for Fungi ITS Region Classification.}, journal = {Genes}, volume = {14}, number = {3}, pages = {}, pmid = {36980906}, issn = {2073-4425}, mesh = {Bayes Theorem ; *Algorithms ; *Software ; Neural Networks, Computer ; Fungi/genetics ; }, abstract = {Fungal species identification from metagenomic data is a highly challenging task. Internal Transcribed Spacer (ITS) region is a potential DNA marker for fungi taxonomy prediction. Computational approaches, especially deep learning algorithms, are highly efficient for better pattern recognition and classification of large datasets compared to in silico techniques such as BLAST and machine learning methods. Here in this study, we present CNN_FunBar, a convolutional neural network-based approach for the classification of fungi ITS sequences from UNITE+INSDC reference datasets. Effects of convolution kernel size, filter numbers, k-mer size, degree of diversity and category-wise frequency of ITS sequences on classification performances of CNN models have been assessed at all taxonomic levels (species, genus, family, order, class and phylum). It is observed that CNN models can produce >93% average accuracy for classifying ITS sequences from balanced datasets with 500 sequences per category and 6-mer frequency features at all levels. The comparative study has revealed that CNN_FunBar can outperform machine learning-based algorithms (SVM, KNN, Naïve-Bayes and Random Forest) as well as existing fungal taxonomy prediction software (funbarRF, Mothur, RDP Classifier and SINTAX). The present study will be helpful for fungal taxonomy classification using large metagenomic datasets.}, } @article {pmid36979819, year = {2023}, author = {Leitao Filho, FS and Monica Peters, C and Sheel, AW and Yang, J and Nislow, C and Lam, S and Leung, JM and Sin, DD}, title = {Characterization of the Lower Airways and Oral Microbiota in Healthy Young Persons in the Community.}, journal = {Biomedicines}, volume = {11}, number = {3}, pages = {}, pmid = {36979819}, issn = {2227-9059}, abstract = {Lower airway dysbiosis contributes to disease pathogenesis in respiratory diseases. However, little is known regarding the microbiota of lower airways or the oral cavity of healthy young persons. To address this gap, 25 healthy persons (24.3 ± 3.3 years; 52% females; no current smokers) underwent bronchoscopy during which bronchial brushing (BB) and bronchoalveolar lavage (BAL) fluid were collected. Prior to the procedure, an oral wash (OW) sample was also obtained. Microbiome analyses (16S rRNA locus) were performed (alpha- and beta-diversity, taxa annotations, and predicted functional metagenomic profiles) according to the airway compartment (BB, BAL, and OW). The greatest microbial richness was observed in OW and the lowest in BB (p < 0.001). Microbial communities differed significantly across compartments (p < 0.001), especially between BB and OW. Taxa analyses showed a significantly higher abundance of Firmicutes (BB: 32.7%; BAL: 31.4%) compared to OW (20.9%) (p < 0.001). Conversely, Proteobacteria predominated in OW (27.9%) as opposed to BB (7.0%) and BAL (12.5%) (p < 0.001), mostly due to a greater abundance of the bacteria in the Haemophilus genus in the OW (p < 0.001). The lower airway microbiota (BB and BAL) is significantly different from the OW microbiota in healthy young persons with respect to microbial diversity, taxa profiles, and predicted function.}, } @article {pmid36979806, year = {2023}, author = {Athanasopoulou, K and Adamopoulos, PG and Scorilas, A}, title = {Unveiling the Human Gastrointestinal Tract Microbiome: The Past, Present, and Future of Metagenomics.}, journal = {Biomedicines}, volume = {11}, number = {3}, pages = {}, pmid = {36979806}, issn = {2227-9059}, abstract = {Over 10[14] symbiotic microorganisms are present in a healthy human body and are responsible for the synthesis of vital vitamins and amino acids, mediating cellular pathways and supporting immunity. However, the deregulation of microbial dynamics can provoke diverse human diseases such as diabetes, human cancers, cardiovascular diseases, and neurological disorders. The human gastrointestinal tract constitutes a hospitable environment in which a plethora of microbes, including diverse species of archaea, bacteria, fungi, and microeukaryotes as well as viruses, inhabit. In particular, the gut microbiome is the largest microbiome community in the human body and has drawn for decades the attention of scientists for its significance in medical microbiology. Revolutions in sequencing techniques, including 16S rRNA and ITS amplicon sequencing and whole genome sequencing, facilitate the detection of microbiomes and have opened new vistas in the study of human microbiota. Especially, the flourishing fields of metagenomics and metatranscriptomics aim to detect all genomes and transcriptomes that are retrieved from environmental and human samples. The present review highlights the complexity of the gastrointestinal tract microbiome and deciphers its implication not only in cellular homeostasis but also in human diseases. Finally, a thorough description of the widely used microbiome detection methods is discussed.}, } @article {pmid36979367, year = {2023}, author = {Saxena, A and Mathur, N and Pathak, P and Tiwari, P and Mathur, SK}, title = {Machine Learning Model Based on Insulin Resistance Metagenes Underpins Genetic Basis of Type 2 Diabetes.}, journal = {Biomolecules}, volume = {13}, number = {3}, pages = {}, pmid = {36979367}, issn = {2218-273X}, mesh = {Humans ; *Diabetes Mellitus, Type 2/genetics/metabolism ; *Insulin Resistance/genetics ; Genome-Wide Association Study ; Phenotype ; Oligonucleotide Array Sequence Analysis ; Insulin/metabolism ; Blood Glucose/metabolism ; }, abstract = {Insulin resistance (IR) is considered the precursor and the key pathophysiological mechanism of type 2 diabetes (T2D) and metabolic syndrome (MetS). However, the pathways that IR shares with T2D are not clearly understood. Meta-analysis of multiple DNA microarray datasets could provide a robust set of metagenes identified across multiple studies. These metagenes would likely include a subset of genes (key metagenes) shared by both IR and T2D, and possibly responsible for the transition between them. In this study, we attempted to find these key metagenes using a feature selection method, LASSO, and then used the expression profiles of these genes to train five machine learning models: LASSO, SVM, XGBoost, Random Forest, and ANN. Among them, ANN performed well, with an area under the curve (AUC) > 95%. It also demonstrated fairly good performance in differentiating diabetics from normal glucose tolerant (NGT) persons in the test dataset, with 73% accuracy across 64 human adipose tissue samples. Furthermore, these core metagenes were also enriched in diabetes-associated terms and were found in previous genome-wide association studies of T2D and its associated glycemic traits HOMA-IR and HOMA-B. Therefore, this metagenome deserves further investigation with regard to the cardinal molecular pathological defects/pathways underlying both IR and T2D.}, } @article {pmid36978958, year = {2023}, author = {Lauritano, C and Montuori, E and De Falco, G and Carrella, S}, title = {In Silico Methodologies to Improve Antioxidants' Characterization from Marine Organisms.}, journal = {Antioxidants (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, pmid = {36978958}, issn = {2076-3921}, abstract = {Marine organisms have been reported to be valuable sources of bioactive molecules that have found applications in different industrial fields. From organism sampling to the identification and bioactivity characterization of a specific compound, different steps are necessary, which are time- and cost-consuming. Thanks to the advent of the -omic era, numerous genome, metagenome, transcriptome, metatranscriptome, proteome and microbiome data have been reported and deposited in public databases. These advancements have been fundamental for the development of in silico strategies for basic and applied research. In silico studies represent a convenient and efficient approach to the bioactivity prediction of known and newly identified marine molecules, reducing the time and costs of "wet-lab" experiments. This review focuses on in silico approaches applied to bioactive molecule discoveries from marine organisms. When available, validation studies reporting a bioactivity assay to confirm the presence of an antioxidant molecule or enzyme are reported, as well. Overall, this review suggests that in silico approaches can offer a valuable alternative to most expensive approaches and proposes them as a little explored field in which to invest.}, } @article {pmid36978337, year = {2023}, author = {Rovira, P}, title = {Short-Term Impact of Oxytetracycline Administration on the Fecal Microbiome, Resistome and Virulome of Grazing Cattle.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, pmid = {36978337}, issn = {2079-6382}, support = {CL 48//Instituto Nacional de Investigación Agropecuaria/ ; }, abstract = {Antimicrobial resistance (AMR) is an important public health concern around the world. Limited information exists about AMR in grasslands-based systems where antibiotics are seldom used in beef cattle. The present study investigated the impacts of oxytetracycline (OTC) on the microbiome, antibiotic resistance genes (ARGs), and virulence factor genes (VFGs) in grazing steers with no previous exposure to antibiotic treatments. Four steers were injected with a single dose of OTC (TREAT), and four steers were kept as control (CONT). The effects of OTC on fecal microbiome, ARGs, and VFGs were assessed for 14 days using 16S rRNA sequencing and shotgun metagenomics. Alpha and beta microbiome diversities were significantly affected by OTC. Following treatment, less than 8% of bacterial genera had differential abundance between CONT and TREAT samples. Seven ARGs conferring resistance to tetracycline (tet32, tet40, tet44, tetO, tetQ, tetW, and tetW/N/W) increased their abundance in the post-TREAT samples compared to CONT samples. In addition, OTC use was associated with the enrichment of macrolide and lincosamide ARGs (mel and lnuC, respectively). The use of OTC had no significant effect on VFGs. In conclusion, OTC induced short-term alterations of the fecal microbiome and enrichment of ARGs in the feces of grazing beef cattle.}, } @article {pmid36977970, year = {2023}, author = {Amin, DH and Nageeb, WM and Elkelish, A and Makharita, RR}, title = {Mining metagenomes reveals diverse antibiotic biosynthetic genes in uncultured microbial communities.}, journal = {Brazilian journal of microbiology : [publication of the Brazilian Society for Microbiology]}, volume = {54}, number = {2}, pages = {983-995}, pmid = {36977970}, issn = {1678-4405}, mesh = {*Metagenome ; Phylogeny ; *Microbiota ; Anti-Bacterial Agents/pharmacology ; Soil ; }, abstract = {Pathogens resistant to antimicrobials form a significant threat to public health worldwide. Tackling multidrug-resistant pathogens via screening metagenomic libraries has become a common approach for the discovery of new antibiotics from uncultured microorganisms. This study focuses on capturing nonribosomal peptide synthase (NRPS) gene clusters implicated in the synthesis of many natural compounds of industrial relevance. A NRPS PCR assay was used to screen 2976 Escherichia coli clones in a soil metagenomic library to target NRPS genes. DNA extracts from 4 clones were sequenced and subjected to bioinformatic analysis to identify NRPS domains, their phylogeny, and substrate specificity.Successfully, 17 NRPS-positive hits with a biosynthetic potential were identified. DNA sequencing and BLAST analysis confirmed that NRPS protein sequences shared similarities with members of the genus Delftia in the Proteobacteria taxonomic position. Multiple alignment and phylogenetic analysis demonstrated that clones no. 15cd35 and 15cd37 shared low bootstrap values (54%) and were distantly far from close phylogenetic neighbors. Additionally, NRPS domain substrate specificity has no hits with the known ones; hence, they are more likely to use different substrates to produce new diverse antimicrobials. Further analysis confirmed that the NRPS hits resemble several transposon elements from other bacterial taxa, confirming its diversity. We confirmed that the analyses of the soil metagenomic library revealed a diverse set of NRPS related to the genus Delftia. An in-depth understanding of those positive NRPS hits is a crucial step for genetic manipulation of NRPS, shedding light on alternative novel antimicrobial compounds that can be used in drug discovery and hence supports the pharmaceutical sector.}, } @article {pmid36977954, year = {2023}, author = {Mahiddine, FY and You, I and Park, H and Kim, MJ}, title = {Management of dog sperm parameters and gut microbiota composition with Lactobacillus rhamnosus supplementation.}, journal = {Veterinary research communications}, volume = {47}, number = {3}, pages = {1629-1640}, pmid = {36977954}, issn = {1573-7446}, mesh = {Male ; Dogs ; Animals ; *Gastrointestinal Microbiome ; *Lacticaseibacillus rhamnosus ; Semen ; Dietary Supplements ; Spermatozoa ; }, abstract = {The effects of probiotics supplementation on the reproductive function have been evaluated in many species, but no study has evaluated the changes in the gut microbiome along with the sperm quality changes simultaneously. This study evaluated the effects of dietary supplementation with probiotics on the gut microbiome, sperm quality and gene expression, along with possible correlations between these parameters in dogs. The dogs were supplemented with Lactobacillus rhamnosus for six weeks, and fecal and semen samples were collected at 0, 3, and 6 weeks. Fecal samples were assessed using 16S Metagenomic Sequencing for gut microbiome analysis; and semen samples were analyzed using computer-assisted sperm analysis, DNA and acrosome integrity assessment, viability and morphology assessment, and real-time PCR. The analyses suggested that probiotic supplementation improved kinematic parameters, viability, DNA and acrosome integrity, and morphology of sperms. The mRNA levels of genes associated with fertility, DNA repair and integrity, and antioxidation were also upregulated. The sperm parameters were positively correlated with the relative abundance of Actinobacteria, Allobaculum, Phascolarctobacterium and Catenibacterium, and negatively correlated with Faecalibacterium and Streptococcus. Taken together, the sperm quality enhancement through the gut-testis axis may be due to a change in the gut microorganisms populations.}, } @article {pmid36977254, year = {2023}, author = {Becker, AAMJ and Munden, S and McCabe, E and Hurley, D and Fanning, S and Chapwanya, A and Butaye, P}, title = {The Endometrial Microbiota-16S rRNA Gene Sequence Signatures in Healthy, Pregnant and Endometritis Dairy Cows.}, journal = {Veterinary sciences}, volume = {10}, number = {3}, pages = {}, pmid = {36977254}, issn = {2306-7381}, support = {42019-2019//Ross University School of Veterinary Medicine/ ; IP/2015/0380//School of Public Health, Physiotherapy & Sports Science (Science Center, Belfield), located in Dublin, Ireland, Enterprise Ireland Innovation Partnership/ ; }, abstract = {Endometritis is one of the most important causes of infertility in dairy cows, resulting in high economic losses in the dairy industry. Though the presence of a commensal uterine microbiota is now well established, the complex role of these bacteria in genital health, fertility, and susceptibility to uterine diseases remains unclear. In this study, we explore the endometrial microbiota through 16S rRNA gene profiling from cytobrush samples taken ex vivo from healthy, pregnant, and endometritis cows. There were no significant differences between healthy and pregnant cows, whose uterine microbiota were dominated by Streptococcus, Pseudomonas, Fusobacterium, Lactococcus and Bacteroides. Compared to pregnant and clinically healthy cows, the uterine bacterial community of endometritis cows was significantly decreased in species diversity (p < 0.05), reflecting uneven community composition in different patterns with either dominance of Escherichia-Shigella, Histophilus, Bacteroides and Porphyromonas or Actinobacteria.}, } @article {pmid36976417, year = {2023}, author = {Zhou, Q and Yu, J and Song, X and Zhang, J and Zhang, B}, title = {The discovery of novel papillomaviruses in cats in Southwest China.}, journal = {Virus genes}, volume = {59}, number = {3}, pages = {484-488}, pmid = {36976417}, issn = {1572-994X}, support = {2020YJ0247//the Applied Basic Research Project of Sichuan Province, China/ ; ZYN2022020//the Fundamental Research Funds for the Central Universities of Southwest Minzu University, China/ ; }, mesh = {Cats ; Animals ; Female ; Dogs ; *DNA, Viral/genetics ; Papillomaviridae/genetics ; China/epidemiology ; *Cat Diseases/epidemiology ; Mammals ; }, abstract = {Feline viral diarrhea is a significant cause of death in kittens. In this study, 12 mammalian viruses were identified by metagenomic sequencing in diarrheal feces in 2019, 2020, and 2021, respectively. Interestingly, a novel of felis catus papillomavirus (FcaPV) was identified for the first time in China. Subsequently, we investigated the prevalence of FcaPV in 252 feline samples, including 168 diarrheal feces and 84 oral swabs, with a total of 57 (22.62%, 57/252) samples detected positive. Of the 57 positive samples, FcaPV genotype 3 (FcaPV-3) was detected at high prevalence rate (68.42%, 39/57), followed by FcaPV-4 (22.8%, 13/57), FcaPV-2 (17.54%, 10/57), and FcaPV-1 (1.75%, 1/55), while no FcaPV-5 and FcaPV-6. In addition, two novel putative FcaPVs were identified, which were the highest similarity to Lambdapillomavirus from Leopardus wiedii or canis familiaris, respectively. Therefore, this study was the first characterization of the viral diversity in feline diarrheal feces and the prevalence of FcaPV in Southwest China.}, } @article {pmid36976214, year = {2023}, author = {Elvheim, AI and Li, C and Landfald, B}, title = {Conservation of Genomic Information in Multiple Displacement Amplified Low-Quantity Metagenomic Material from Marine Invertebrates.}, journal = {Marine drugs}, volume = {21}, number = {3}, pages = {}, pmid = {36976214}, issn = {1660-3397}, support = {282567//The Regional Research Fund of Northern Norway/ ; 390017303//UiT The Arctic University of Norway/ ; }, mesh = {*Metagenome/genetics ; Genomics ; Metagenomics/methods ; *Microbiota ; Bacteria/genetics ; Multigene Family ; }, abstract = {Marine invertebrate microbiomes have been a rich source of bioactive compounds and interesting genomic features. In cases where the achievable amounts of metagenomic DNA are too low for direct sequencing, multiple displacement amplification (MDA) can be used for whole genome amplification. However, MDA has known limitations which can affect the quality of the resulting genomes and metagenomes. In this study, we evaluated the conservation of biosynthetic gene clusters (BGCs) and enzymes in MDA products from low numbers of prokaryotic cells (estimated 2-850). Marine invertebrate microbiomes collected from Arctic and sub-Arctic areas served as source material. The cells were separated from the host tissue, lysed, and directly subjected to MDA. The MDA products were sequenced by Illumina sequencing. Corresponding numbers of bacteria from a set of three reference strains were treated the same way. The study demonstrated that useful information on taxonomic, BGC, and enzyme diversities was obtainable from such marginal quantities of metagenomic material. Although high levels of assembly fragmentation resulted in most BGCs being incomplete, we conclude that this genome mining approach has the potential to reveal interesting BGCs and genes from hard-to-reach biological sources.}, } @article {pmid36975940, year = {2023}, author = {Manee, MM and Alqahtani, FH and Al-Shomrani, BM and El-Shafie, HAF and Dias, GB}, title = {Omics in the Red Palm Weevil Rhynchophorus ferrugineus (Olivier) (Coleoptera: Curculionidae): A Bridge to the Pest.}, journal = {Insects}, volume = {14}, number = {3}, pages = {}, pmid = {36975940}, issn = {2075-4450}, support = {20-0078//King Abdulaziz City for Science and Technology/ ; }, abstract = {The red palm weevil (RPW), Rhynchophorus ferrugineus (Coleoptera: Curculionidae), is the most devastating pest of palm trees worldwide. Mitigation of the economic and biodiversity impact it causes is an international priority that could be greatly aided by a better understanding of its biology and genetics. Despite its relevance, the biology of the RPW remains poorly understood, and research on management strategies often focuses on outdated empirical methods that produce sub-optimal results. With the development of omics approaches in genetic research, new avenues for pest control are becoming increasingly feasible. For example, genetic engineering approaches become available once a species's target genes are well characterized in terms of their sequence, but also population variability, epistatic interactions, and more. In the last few years alone, there have been major advances in omics studies of the RPW. Multiple draft genomes are currently available, along with short and long-read transcriptomes, and metagenomes, which have facilitated the identification of genes of interest to the RPW scientific community. This review describes omics approaches previously applied to RPW research, highlights findings that could be impactful for pest management, and emphasizes future opportunities and challenges in this area of research.}, } @article {pmid36975833, year = {2023}, author = {Xiao, X and Luo, M and Zhang, C and Zhang, T and Yin, X and Wu, X and Zhao, J and Tao, J and Chen, Z and Liang, Q and Dong, X}, title = {Metal-Driven Anaerobic Oxidation of Methane as an Important Methane Sink in Methanic Cold Seep Sediments.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0533722}, pmid = {36975833}, issn = {2165-0497}, abstract = {Anaerobic oxidation of methane (AOM) coupled with reduction of metal oxides is supposed to be a globally important bioprocess in marine sediments. However, the responsible microorganisms and their contributions to methane budget are not clear in deep sea cold seep sediments. Here, we combined geochemistry, muti-omics, and numerical modeling to study metal-dependent AOM in methanic cold seep sediments in the northern continental slope of the South China Sea. Geochemical data based on methane concentrations, carbon stable isotope, solid-phase sediment analysis, and pore water measurements indicate the occurrence of anaerobic methane oxidation coupled to metal oxides reduction in the methanic zone. The 16S rRNA gene and transcript amplicons, along with metagenomic and metatranscriptomic data suggest that diverse anaerobic methanotrophic archaea (ANME) groups actively mediated methane oxidation in the methanic zone either independently or in syntrophy with, e.g., ETH-SRB1, as potential metal reducers. Modeling results suggest that the estimated rates of methane consumption via Fe-AOM and Mn-AOM were both 0.3 μmol cm[-2] year[-1], which account for ~3% of total CH4 removal in sediments. Overall, our results highlight metal-driven anaerobic oxidation of methane as an important methane sink in methanic cold seep sediments. IMPORTANCE Anaerobic oxidation of methane (AOM) coupled with reduction of metal oxides is supposed to be a globally important bioprocess in marine sediments. However, the responsible microorganisms and their contributions to methane budget are not clear in deep sea cold seep sediments. Our findings provide a comprehensive view of metal-dependent AOM in the methanic cold seep sediments and uncovered the potential mechanisms for involved microorganisms. High amounts of buried reactive Fe(III)/Mn(IV) minerals could be an important available electron acceptors for AOM. It is estimated that metal-AOM at least contributes 3% of total methane consumption from methanic sediments to the seep. Therefore, this research paper advances our understanding of the role of metal reduction to the global carbon cycle, especially the methane sink.}, } @article {pmid36975809, year = {2023}, author = {Falardeau, J and Yildiz, E and Yan, Y and Castellarin, SD and Wang, S}, title = {Microbiome and Physicochemical Features Associated with Differential Listeria monocytogenes Growth in Soft, Surface-Ripened Cheeses.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {4}, pages = {e0200422}, pmid = {36975809}, issn = {1098-5336}, mesh = {*Listeria monocytogenes ; Food Microbiology ; *Cheese/microbiology ; RNA, Ribosomal, 16S ; *Microbiota ; Colony Count, Microbial ; }, abstract = {Soft-ripened cheeses (SRCs) are at a higher risk for the growth of the foodborne pathogen Listeria monocytogenes due to favorable moisture content and pH compared to other cheeses. L. monocytogenes growth is not consistent across SRCs, however, and may be affected by physicochemical and/or microbiome characteristics of the cheeses. Therefore, the purpose of this study was to investigate how the physicochemical and microbiome profiles of SRCs may affect L. monocytogenes growth. Forty-three SRCs produced from raw (n = 12) or pasteurized (n = 31) milk were inoculated with L. monocytogenes (10[3] CFU/g), and the pathogen growth was monitored over 12 days at 8°C. In parallel, the pH, water activity (aw), microbial plate counts, and organic acid content of cheeses were measured, and the taxonomic profiles of the cheese microbiomes were measured using 16S rRNA gene targeted amplicon sequencing and shotgun metagenomic sequencing. L. monocytogenes growth differed significantly between cheeses (analysis of variance [ANOVA]; P < 0.001), with increases ranging from 0 to 5.4 log CFU (mean of 2.5 ± 1.2 log CFU), and was negatively correlated with aw. Raw milk cheeses showed significantly lower L. monocytogenes growth than pasteurized-milk cheeses (t test; P = 0.008), possibly due to an increase in microbial competition. L. monocytogenes growth in cheeses was positively correlated with the relative abundance of Streptococcus thermophilus (Spearman correlation; P < 0.0001) and negatively correlated with the relative abundances of Brevibacterium aurantiacum (Spearman correlation; P = 0.0002) and two Lactococcus spp. (Spearman correlation; P < 0.01). These results suggest that the cheese microbiome may influence the food safety in SRCs. IMPORTANCE Previous studies have identified differences in L. monocytogenes growth between SRCs, but no clear mechanism has yet been elucidated. To the best of our knowledge, this is the first study to collect a wide range of SRCs from retail sources and attempt to identify key factors associated with pathogen growth. A key finding in this research was the positive correlation between the relative abundance of S. thermophilus and the growth of L. monocytogenes. The inclusion of S. thermophilus as a starter culture is more common in industrialized SRC production, suggesting that industrial production of SRC may increase the risk of L. monocytogenes growth. Overall, the results of this study further our understanding of the impact of aw and the cheese microbiome on the growth of L. monocytogenes in SRCs, hopefully leading toward the development of SRC starter/ripening cultures that can prevent L. monocytogenes growth.}, } @article {pmid36975807, year = {2023}, author = {Zhang, W and Liu, Y and Zheng, K and Xing, J and Li, Q and Gu, C and Wang, Z and Shao, H and Guo, C and He, H and Wang, H and Sung, YY and Mok, WJ and Wong, LL and Liang, Y and McMinn, A and Wang, M}, title = {Discovery of an Abundant Viral Genus in Polar Regions through the Isolation and Genomic Characterization of a New Virus against Oceanospirillaceae.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {4}, pages = {e0189622}, pmid = {36975807}, issn = {1098-5336}, mesh = {*Oceanospirillaceae ; Phylogeny ; Cold Climate ; Genomics ; *Bacteriophages ; Genome, Viral ; }, abstract = {The marine bacterial family Oceanospirillaceae, is well-known for its ability to degrade hydrocarbons and for its close association with algal blooms. However, only a few Oceanospirillaceae-infecting phages have been reported thus far. Here, we report on a novel Oceanospirillum phage, namely, vB_OsaM_PD0307, which has a 44,421 bp linear dsDNA genome and is the first myovirus infecting Oceanospirillaceae. A genomic analysis demonstrated that vB_OsaM_PD0307 is a variant of current phage isolates from the NCBI data set but that it has similar genomic features to two high-quality, uncultured viral genomes identified from marine metagenomes. Hence, we propose that vB_OsaM_PD0307 can be classified as the type phage of a new genus, designated Oceanospimyovirus. Additionally, metagenomic read mapping results have further shown that Oceanospimyovirus species are widespread in the global ocean, display distinct biogeographic distributions, and are abundant in polar regions. In summary, our findings expand the current understanding of the genomic characteristics, phylogenetic diversity, and distribution of Oceanospimyovirus phages. IMPORTANCE Oceanospirillum phage vB_OsaM_PD0307 is the first myovirus found to infect Oceanospirillaceae, and it represents a novel abundant viral genus in polar regions. This study provides insights into the genomic, phylogenetic, and ecological characteristics of the new viral genus, namely Oceanospimyovirus.}, } @article {pmid36975801, year = {2023}, author = {Carter, KA and Fodor, AA and Balkus, JE and Zhang, A and Serrano, MG and Buck, GA and Engel, SM and Wu, MC and Sun, S}, title = {Vaginal Microbiome Metagenome Inference Accuracy: Differential Measurement Error according to Community Composition.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0100322}, pmid = {36975801}, issn = {2379-5077}, support = {R01 MD011504/MD/NIMHD NIH HHS/United States ; T32 AI007140/AI/NIAID NIH HHS/United States ; P30 ES010126/ES/NIEHS NIH HHS/United States ; }, mesh = {Infant, Newborn ; Pregnancy ; Female ; Humans ; Metagenome/genetics ; RNA, Ribosomal, 16S/genetics ; *Premature Birth/genetics ; *Microbiota/genetics ; Vagina/microbiology ; }, abstract = {Several studies have compared metagenome inference performance in different human body sites; however, none specifically reported on the vaginal microbiome. Findings from other body sites cannot easily be generalized to the vaginal microbiome due to unique features of vaginal microbial ecology, and investigators seeking to use metagenome inference in vaginal microbiome research are "flying blind" with respect to potential bias these methods may introduce into analyses. We compared the performance of PICRUSt2 and Tax4Fun2 using paired 16S rRNA gene amplicon sequencing and whole-metagenome sequencing data from vaginal samples from 72 pregnant individuals enrolled in the Pregnancy, Infection, and Nutrition (PIN) cohort. Participants were selected from those with known birth outcomes and adequate 16S rRNA gene amplicon sequencing data in a case-control design. Cases experienced early preterm birth (<32 weeks of gestation), and controls experienced term birth (37 to 41 weeks of gestation). PICRUSt2 and Tax4Fun2 performed modestly overall (median Spearman correlation coefficients between observed and predicted KEGG ortholog [KO] relative abundances of 0.20 and 0.22, respectively). Both methods performed best among Lactobacillus crispatus-dominated vaginal microbiotas (median Spearman correlation coefficients of 0.24 and 0.25, respectively) and worst among Lactobacillus iners-dominated microbiotas (median Spearman correlation coefficients of 0.06 and 0.11, respectively). The same pattern was observed when evaluating correlations between univariable hypothesis test P values generated with observed and predicted metagenome data. Differential metagenome inference performance across vaginal microbiota community types can be considered differential measurement error, which often causes differential misclassification. As such, metagenome inference will introduce hard-to-predict bias (toward or away from the null) in vaginal microbiome research. IMPORTANCE Compared to taxonomic composition, the functional potential within a bacterial community is more relevant to establishing mechanistic understandings and causal relationships between the microbiome and health outcomes. Metagenome inference attempts to bridge the gap between 16S rRNA gene amplicon sequencing and whole-metagenome sequencing by predicting a microbiome's gene content based on its taxonomic composition and annotated genome sequences of its members. Metagenome inference methods have been evaluated primarily among gut samples, where they appear to perform fairly well. Here, we show that metagenome inference performance is markedly worse for the vaginal microbiome and that performance varies across common vaginal microbiome community types. Because these community types are associated with sexual and reproductive outcomes, differential metagenome inference performance will bias vaginal microbiome studies, obscuring relationships of interest. Results from such studies should be interpreted with substantial caution and the understanding that they may over- or underestimate associations with metagenome content.}, } @article {pmid36975791, year = {2023}, author = {Mejia, ME and Robertson, CM and Patras, KA}, title = {Interspecies Interactions within the Host: the Social Network of Group B Streptococcus.}, journal = {Infection and immunity}, volume = {91}, number = {4}, pages = {e0044022}, pmid = {36975791}, issn = {1098-5522}, support = {AI169231/AI/NIAID NIH HHS/United States ; DK128053/DK/NIDDK NIH HHS/United States ; F31 AI167538/AI/NIAID NIH HHS/United States ; GM136554/GM/NIGMS NIH HHS/United States ; AI167538/AI/NIAID NIH HHS/United States ; T32 GM136554/GM/NIGMS NIH HHS/United States ; R01 DK128053/DK/NIDDK NIH HHS/United States ; R21 AI169231/AI/NIAID NIH HHS/United States ; }, mesh = {Female ; Animals ; Infant, Newborn ; Humans ; Pregnancy ; *Streptococcal Infections/microbiology ; Streptococcus agalactiae ; Anti-Bacterial Agents ; *Infant, Newborn, Diseases ; Social Networking ; *Pregnancy Complications, Infectious/microbiology ; }, abstract = {Group B Streptococcus (GBS) is a pervasive neonatal pathogen accounting for a combined half a million deaths and stillbirths annually. The most common source of fetal or neonatal GBS exposure is the maternal microbiota. GBS asymptomatically colonizes the gastrointestinal and vaginal mucosa of 1 in 5 individuals globally, although its precise role in these niches is not well understood. To prevent vertical transmission, broad-spectrum antibiotics are administered to GBS-positive mothers during labor in many countries. Although antibiotics have significantly reduced GBS early-onset neonatal disease, there are several unintended consequences, including an altered neonatal microbiota and increased risk for other microbial infections. Additionally, the incidence of late-onset GBS neonatal disease remains unaffected and has sparked an emerging hypothesis that GBS-microbe interactions in developing neonatal gut microbiota may be directly involved in this disease process. This review summarizes our current understanding of GBS interactions with other resident microbes at the mucosal surface from multiple angles, including clinical association studies, agriculture and aquaculture observations, and experimental animal model systems. We also include a comprehensive review of in vitro findings of GBS interactions with other bacterial and fungal microbes, both commensal and pathogenic, along with newly established animal models of GBS vaginal colonization and in utero or neonatal infection. Finally, we provide a perspective on emerging areas of research and current strategies to design microbe-targeting prebiotic or probiotic therapeutic intervention strategies to prevent GBS disease in vulnerable populations.}, } @article {pmid36974462, year = {2023}, author = {Zhang, S and Li, S and Huang, J and Ding, X and Qiu, Y and Luo, X and Meng, J and Hu, Y and Zhou, H and Fan, H and Cao, Y and Gao, F and Xue, Y and Zou, M}, title = {Gram-Negative Bacteria and Lipopolysaccharides as Risk Factors for the Occurrence of Diabetic Foot.}, journal = {The Journal of clinical endocrinology and metabolism}, volume = {108}, number = {10}, pages = {2604-2614}, pmid = {36974462}, issn = {1945-7197}, mesh = {Mice ; Animals ; Humans ; *Diabetic Foot/etiology ; Lipopolysaccharides ; Toll-Like Receptor 4 ; Dysbiosis ; Gram-Negative Bacteria/genetics ; Risk Factors ; RNA, Ribosomal, 16S/genetics ; *Diabetes Mellitus ; }, abstract = {CONTEXT: Imbalance of the skin microbial community could impair skin immune homeostasis and thus trigger skin lesions. Dysbiosis of skin microbiome may be involved in the early pathogenesis of diabetic foot (DF). However, the potential mechanism remains unclear.

OBJECTIVE: To investigate the dynamic composition and function of the foot skin microbiome with risk stratification for DF and assess whether dysbiosis of the skin microbiome induces diabetic skin lesions.

METHODS: We enrolled 90 consecutive subjects who were divided into 5 groups based on DF risk stratification: very low, low, moderate, and high risk for ulcers and a healthy control group. Integrated analysis of 16S ribosomal RNA and metagenomic sequencing of cotton swab samples was applied to identify the foot skin microbiome composition and functions in subjects. Then a mouse model of microbiota transplantation was used to evaluate the effects of the skin microbiome on diabetic skin lesions.

RESULTS: The results demonstrated that, with the progression of diabetic complications, the proportion of gram-negative bacteria in plantar skin increased. At the species level, metagenome sequencing analyses showed Moraxella osloensis to be a representative core strain in the high-risk group. The major microbial metabolites affecting diabetic skin lesions were increased amino acid metabolites, and antibiotic resistance genes in microorganisms were abundant. Skin microbiota from high-risk patients induced more inflammatory cell infiltration, similar to the lipopolysaccharide (LPS)-stimulated response, which was inhibited by Toll-like receptor 4 (TLR4) antagonists.

CONCLUSIONS: The skin microbiome in patients with diabetes undergoes dynamic changes at taxonomic and functional levels with the progression of diabetic complications. The increase in gram-negative bacteria on the skin surface through LPS-TLR4 signal transduction could induce inflammatory response in early diabetic skin lesions.}, } @article {pmid36973750, year = {2023}, author = {Rivarez, MPS and Pecman, A and Bačnik, K and Maksimović, O and Vučurović, A and Seljak, G and Mehle, N and Gutiérrez-Aguirre, I and Ravnikar, M and Kutnjak, D}, title = {In-depth study of tomato and weed viromes reveals undiscovered plant virus diversity in an agroecosystem.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {60}, pmid = {36973750}, issn = {2049-2618}, mesh = {*Solanum lycopersicum ; Virome ; *Plant Viruses/genetics ; Plants ; }, abstract = {BACKGROUND: In agroecosystems, viruses are well known to influence crop health and some cause phytosanitary and economic problems, but their diversity in non-crop plants and role outside the disease perspective is less known. Extensive virome explorations that include both crop and diverse weed plants are therefore needed to better understand roles of viruses in agroecosystems. Such unbiased exploration is available through viromics, which could generate biological and ecological insights from immense high-throughput sequencing (HTS) data.

RESULTS: Here, we implemented HTS-based viromics to explore viral diversity in tomatoes and weeds in farming areas at a nation-wide scale. We detected 125 viruses, including 79 novel species, wherein 65 were found exclusively in weeds. This spanned 21 higher-level plant virus taxa dominated by Potyviridae, Rhabdoviridae, and Tombusviridae, and four non-plant virus families. We detected viruses of non-plant hosts and viroid-like sequences and demonstrated infectivity of a novel tobamovirus in plants of Solanaceae family. Diversities of predominant tomato viruses were variable, in some cases, comparable to that of global isolates of the same species. We phylogenetically classified novel viruses and showed links between a subgroup of phylogenetically related rhabdoviruses to their taxonomically related host plants. Ten classified viruses detected in tomatoes were also detected in weeds, which might indicate possible role of weeds as their reservoirs and that these viruses could be exchanged between the two compartments.

CONCLUSIONS: We showed that even in relatively well studied agroecosystems, such as tomato farms, a large part of very diverse plant viromes can still be unknown and is mostly present in understudied non-crop plants. The overlapping presence of viruses in tomatoes and weeds implicate possible presence of virus reservoir and possible exchange between the weed and crop compartments, which may influence weed management decisions. The observed variability and widespread presence of predominant tomato viruses and the infectivity of a novel tobamovirus in solanaceous plants, provided foundation for further investigation of virus disease dynamics and their effect on tomato health. The extensive insights we generated from such in-depth agroecosystem virome exploration will be valuable in anticipating possible emergences of plant virus diseases and would serve as baseline for further post-discovery characterization studies. Video Abstract.}, } @article {pmid36973710, year = {2023}, author = {Li, H and Wang, H and Ju, H and Lv, J and Yang, S and Zhang, W and Lu, H}, title = {Comparison of gut viral communities in children under 5 years old and newborns.}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {52}, pmid = {36973710}, issn = {1743-422X}, mesh = {Infant, Newborn ; Humans ; Child ; Child, Preschool ; *Viruses/genetics ; *Bacteriophages/genetics ; Gastrointestinal Tract ; *Gastrointestinal Microbiome ; Feces ; Metagenomics ; }, abstract = {OBJECTIVES: The gut virome of humans is mainly composed of bacteriophages and their role in shaping the gut microbiome and influencing human health is increasingly recognized. However, little is known about the dynamic changes of the gut virome in children and its role in growth and development. In this study, we collected fecal samples from newborns and children under 5 years old from the same area during the same time period to investigate the gut viral community using viral metagenomic technique.

METHODS: We used viral metagenomics to compare the gut bacteriophage composition between newborns and children under 5 years of age. We collected fecal samples from 45 newborns who were born at the Affiliated Hospital of Jiangsu University and 45 healthy children who were examined at the same hospital. The two groups were classified as the newborn group and the children group.

RESULTS: Our sequencing analysis showed that the number of seqeunce reads of the children group were more than that of the newborn group. The results of alpha diversity and beta diversity both indicated that the diversity of the children group was significantly higher than that of the newborn group and the children group is different from the newborn group. The abundance of gut virome in the children group was also higher than that in the newborn group. The analysis of the genetic characteristics of the viruses showed that the phage genome was scattered and clustered with specificity.

CONCLUSION: Our findings indicate that the gut bacteriophage communities undergo changes over time, presenting diversity and dynamic characteristics. We characterized the composition of gut virome in children and newborns in this region. However, further research is needed to investigate the function of bacteriophages in the ecology of the gastrointestinal tract.}, } @article {pmid36973336, year = {2023}, author = {Rodríguez-Gijón, A and Buck, M and Andersson, AF and Izabel-Shen, D and Nascimento, FJA and Garcia, SL}, title = {Linking prokaryotic genome size variation to metabolic potential and environment.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {25}, pmid = {36973336}, issn = {2730-6151}, abstract = {While theories and models have appeared to explain genome size as a result of evolutionary processes, little work has shown that genome sizes carry ecological signatures. Our work delves into the ecological implications of microbial genome size variation in benthic and pelagic habitats across environmental gradients of the brackish Baltic Sea. While depth is significantly associated with genome size in benthic and pelagic brackish metagenomes, salinity is only correlated to genome size in benthic metagenomes. Overall, we confirm that prokaryotic genome sizes in Baltic sediments (3.47 Mbp) are significantly bigger than in the water column (2.96 Mbp). While benthic genomes have a higher number of functions than pelagic genomes, the smallest genomes coded for a higher number of module steps per Mbp for most of the functions irrespective of their environment. Some examples of this functions are amino acid metabolism and central carbohydrate metabolism. However, we observed that nitrogen metabolism was almost absent in pelagic genomes and was mostly present in benthic genomes. Finally, we also show that Bacteria inhabiting Baltic sediments and water column not only differ in taxonomy, but also in their metabolic potential, such as the Wood-Ljungdahl pathway or the presence of different hydrogenases. Our work shows how microbial genome size is linked to abiotic factors in the environment, metabolic potential and taxonomic identity of Bacteria and Archaea within aquatic ecosystems.}, } @article {pmid36972958, year = {2023}, author = {Muzny, CA and Van Gerwen, OT and Schroeder, JA and Kay-Duncan, ES and Siwakoti, K and Aaron, KJ and Eastlund, IC and Graves, KJ and Elnaggar, JH and Tamhane, A and Long, D and Van Wagoner, N and Toh, E and Taylor, CM}, title = {Impact of testosterone use on the vaginal microbiota of transgender men, including susceptibility to bacterial vaginosis: study protocol for a prospective, observational study.}, journal = {BMJ open}, volume = {13}, number = {3}, pages = {e073068}, pmid = {36972958}, issn = {2044-6055}, support = {R21 AI167754/AI/NIAID NIH HHS/United States ; UL1 TR003096/TR/NCATS NIH HHS/United States ; P20 GM103424/GM/NIGMS NIH HHS/United States ; U19 AG055373/AG/NIA NIH HHS/United States ; R01 AI146065/AI/NIAID NIH HHS/United States ; }, mesh = {Male ; Female ; Humans ; *Vaginosis, Bacterial/drug therapy/microbiology ; Prospective Studies ; *Transgender Persons ; Testosterone ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; Vagina/microbiology ; *Microbiota ; Observational Studies as Topic ; }, abstract = {INTRODUCTION: The effect of testosterone (T) therapy on the vaginal microbiota of transgender men (TGM) is not well characterised, although one cross-sectional study comparing the vaginal microbiota of cisgender women to TGM on T≥1 year found that, in 71% of the TGM, the vaginal microbiota was less likely to be Lactobacillus-dominated and more likely to be enriched with >30 other bacterial species, many associated with bacterial vaginosis (BV). This prospective study aims to investigate changes in the composition of the vaginal microbiota over time in TGM who retain their natal genitalia (ie, vagina) and initiate T. In addition, we will identify changes in the vaginal microbiota preceding incident BV (iBV) in this cohort while investigating behavioural factors, along with hormonal shifts, which may be associated with iBV.

METHODS AND ANALYSIS: T-naïve TGM who have not undergone gender-affirming genital surgery with normal baseline vaginal microbiota (ie, no Amsel criteria, normal Nugent Score with no Gardnerella vaginalis morphotypes) will self-collect daily vaginal specimens for 7 days prior to initiating T and for 90 days thereafter. These specimens will be used for vaginal Gram stain, 16S rRNA gene sequencing and shotgun metagenomic sequencing to characterise shifts in the vaginal microbiota over time, including development of iBV. Participants will complete daily diaries on douching, menses and behavioural factors including sexual activity during the study.

ETHICS AND DISSEMINATION: This protocol is approved through the single Institutional Review Board mechanism by the University of Alabama at Birmingham. External relying sites are the Louisiana State University Health Sciences Center, New Orleans Human Research Protection Program and the Indiana University Human Research Protection Program. Study findings will be presented at scientific conferences and peer-reviewed journals as well as shared with community advisory boards at participating gender health clinics and community-based organisations servicing transgender people.

REGISTRATION DETAILS: Protocol # IRB-300008073.}, } @article {pmid36972812, year = {2023}, author = {Tian, H and Li, Y and Chen, H and Zhang, J and Hui, M and Xu, X and Su, Q and Smets, BF}, title = {Aerobic biodegradation of quinoline under denitrifying conditions in membrane-aerated biofilm reactor.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {326}, number = {}, pages = {121507}, doi = {10.1016/j.envpol.2023.121507}, pmid = {36972812}, issn = {1873-6424}, mesh = {*Wastewater ; Pseudomonas ; Bacteria, Aerobic ; Biofilms ; Bioreactors/microbiology ; *Quinolones ; Nitrogen ; Denitrification ; }, abstract = {Aerobic denitrification is being investigated as a novel biological nitrogen removal process, yet the knowledge on aerobic denitrification is limited to pure culture isolations and its occurrence in bioreactors remains unclear. This study investigated the feasibility and capacity of applying aerobic denitrification in membrane aerated biofilm reactor (MABR) for biological treatment of quinoline-laden wastewater. Stable and efficient removals of quinoline (91.5 ± 5.2%) and nitrate (NO3[-]) (86.5 ± 9.3%) were obtained under different operational conditions. Enhanced formation and function of extracellular polymeric substances (EPS) were observed at increasing quinoline loadings. MABR biofilm was highly enriched with aerobic quinoline-degrading bacteria, with a predominance of Rhodococcus (26.9 ± 3.7%) and secondary abundance of Pseudomonas (1.7 ± 1.2%) and Comamonas (0.94 ± 0.9%). Metagenomic analysis indicated that Rhodococcus contributed significantly to both aromatic degradation (24.5 ± 21.3%) and NO3[-] reduction (4.5 ± 3.9%), indicating its key role in aerobic denitrifying quinoline biodegradation. At increasing quinoline loadings, abundances of aerobic quinoline degradation gene oxoO and denitrifying genes of napA, nirS and nirK increased; there was a significant positive correlation of oxoO with nirS and nirK (p < 0.05). Aerobic quinoline degradation was likely initiated by hydroxylation, encoded by oxoO, followed by stepwise oxidations through 5,6-dihydroxy-1H-2-oxoquinoline or 8-hydroxycoumarin pathway. The results advance our understanding of quinoline degradation during biological nitrogen removal, and highlight the potential implementation of aerobic denitrification driven quinoline biodegradation in MABR for simultaneous removal of nitrogen and recalcitrant organic carbon from coking, coal gasification and pharmaceutical wastewaters.}, } @article {pmid36972309, year = {2023}, author = {Krishnan, S and DeMaere, MZ and Beck, D and Ostrowski, M and Seymour, JR and Darling, AE}, title = {Rhometa: Population recombination rate estimation from metagenomic read datasets.}, journal = {PLoS genetics}, volume = {19}, number = {3}, pages = {e1010683}, pmid = {36972309}, issn = {1553-7404}, mesh = {*Metagenomics/methods ; *Metagenome/genetics ; Sequence Analysis, DNA/methods ; Likelihood Functions ; High-Throughput Nucleotide Sequencing/methods ; Software ; Recombination, Genetic/genetics ; Algorithms ; }, abstract = {Prokaryotic evolution is influenced by the exchange of genetic information between species through a process referred to as recombination. The rate of recombination is a useful measure for the adaptive capacity of a prokaryotic population. We introduce Rhometa (https://github.com/sid-krish/Rhometa), a new software package to determine recombination rates from shotgun sequencing reads of metagenomes. It extends the composite likelihood approach for population recombination rate estimation and enables the analysis of modern short-read datasets. We evaluated Rhometa over a broad range of sequencing depths and complexities, using simulated and real experimental short-read data aligned to external reference genomes. Rhometa offers a comprehensive solution for determining population recombination rates from contemporary metagenomic read datasets. Rhometa extends the capabilities of conventional sequence-based composite likelihood population recombination rate estimators to include modern aligned metagenomic read datasets with diverse sequencing depths, thereby enabling the effective application of these techniques and their high accuracy rates to the field of metagenomics. Using simulated datasets, we show that our method performs well, with its accuracy improving with increasing numbers of genomes. Rhometa was validated on a real S. pneumoniae transformation experiment, where we show that it obtains plausible estimates of the rate of recombination. Finally, the program was also run on ocean surface water metagenomic datasets, through which we demonstrate that the program works on uncultured metagenomic datasets.}, } @article {pmid36971593, year = {2023}, author = {Liu, F and Lu, H and Dong, B and Huang, X and Cheng, H and Qu, R and Hu, Y and Zhong, L and Guo, Z and You, Y and Xu, ZZ}, title = {Systematic Evaluation of the Viable Microbiome in the Human Oral and Gut Samples with Spike-in Gram+/- Bacteria.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0073822}, pmid = {36971593}, issn = {2379-5077}, mesh = {Humans ; *Microbiota/genetics ; DNA ; Feces/microbiology ; DNA, Bacterial/genetics ; Bacteria/genetics ; Firmicutes/genetics ; }, abstract = {PMA (propidium monoazide) is one of the few methods that are compatible with metagenomic sequencing to characterize the live/intact microbiota. However, its efficiency in complex communities such as saliva and feces is still controversial. An effective method for depleting host and dead bacterial DNA in human microbiome samples is lacking. Here, we systematically evaluate the efficiency of osmotic lysis and PMAxx treatment (lyPMAxx) in characterizing the viable microbiome with four live/dead Gram+/Gram- microbial strains in simple synthetic and spiked-in complex communities. We show that lyPMAxx-quantitative PCR (qPCR)/sequencing eliminated more than 95% of the host and heat-killed microbial DNA and had a much smaller effect on the live microbes in both simple mock and spiked-in complex communities. The overall microbial load and the alpha diversity of the salivary and fecal microbiome were decreased by lyPMAxx, and the relative abundances of the microbes were changed. The relative abundances of Actinobacteria, Fusobacteria, and Firmicutes in saliva were decreased by lyPMAxx, as was that of Firmicutes in feces. We also found that the frequently used sample storage method, freezing with glycerol, killed or injured 65% and 94% of the living microbial cells in saliva and feces, respectively, with the Proteobacteria phylum affected most in saliva and the Bacteroidetes and Firmicutes phyla affected most in feces. By comparing the absolute abundance variation of the shared species among different sample types and individuals, we found that sample habitat and personal differences affected the response of microbial species to lyPMAxx and freezing. IMPORTANCE The functions and phenotypes of microbial communities are largely defined by viable microbes. Through advanced nucleic acid sequencing technologies and downstream bioinformatic analyses, we gained an insight into the high-resolution microbial community composition of human saliva and feces, yet we know very little about whether such community DNA sequences represent viable microbes. PMA-qPCR was used to characterize the viable microbes in previous studies. However, its efficiency in complex communities such as saliva and feces is still controversial. By spiking-in four live/dead Gram+/Gram- bacterial strains, we demonstrate that lyPMAxx can effectively discriminate between live and dead microbes in the simple synthetic community and complex human microbial communities (saliva and feces). In addition, freezing storage was found to kill or injure the microbes in saliva and feces significantly, as measured with lyPMAxx-qPCR/sequencing. This method has a promising prospect in the viable/intact microbiota detection of complex human microbial communities.}, } @article {pmid36971577, year = {2023}, author = {Balière, C and Hourdel, V and Kwasiborski, A and Grassin, Q and Feher, M and Hoinard, D and Vanhomwegen, J and Taieb, F and Consigny, PH and Manuguerra, JC and Leclercq, I and Batéjat, C and Caro, V}, title = {Complete Genome Sequences of Monkeypox Virus from a French Clinical Sample and the Corresponding Isolated Strain, Obtained Using Nanopore Sequencing.}, journal = {Microbiology resource announcements}, volume = {12}, number = {4}, pages = {e0000923}, pmid = {36971577}, issn = {2576-098X}, support = {//Institut Pasteur/ ; }, abstract = {We report the whole-genome sequences of a monkeypox virus from the skin lesion of a French patient and the corresponding isolated viral strain. Both viral genomic sequences were successfully obtained by applying shotgun metagenomics using the Oxford Nanopore Technologies sequencing approach.}, } @article {pmid36971547, year = {2023}, author = {Etienne-Mesmin, L and Meslier, V and Uriot, O and Fournier, E and Deschamps, C and Denis, S and David, A and Jegou, S and Morabito, C and Quinquis, B and Thirion, F and Plaza Oñate, F and Le Chatelier, E and Ehrlich, SD and Blanquet-Diot, S and Almeida, M}, title = {In Vitro Modelling of Oral Microbial Invasion in the Human Colon.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0434422}, pmid = {36971547}, issn = {2165-0497}, abstract = {Recent advances in the human microbiome characterization have revealed significant oral microbial detection in stools of dysbiotic patients. However, little is known about the potential interactions of these invasive oral microorganisms with commensal intestinal microbiota and the host. In this proof-of-concept study, we proposed a new model of oral-to-gut invasion by the combined use of an in vitro model simulating both the physicochemical and microbial (lumen- and mucus-associated microbes) parameters of the human colon (M-ARCOL), a salivary enrichment protocol, and whole-metagenome shotgun sequencing. Oral invasion of the intestinal microbiota was simulated by injection of enriched saliva in the in vitro colon model inoculated with a fecal sample from the same healthy adult donor. The mucosal compartment of M-ARCOL was able to retain the highest species richness levels over time, while species richness levels decreased in the luminal compartment. This study also showed that oral microorganisms preferably colonized the mucosal microenvironment, suggesting potential oral-to-intestinal mucosal competitions. This new model of oral-to-gut invasion can provide useful mechanistic insights into the role of oral microbiome in various disease processes. IMPORTANCE Here, we propose a new model of oral-to-gut invasion by the combined use of an in vitro model simulating both the physicochemical and microbial (lumen- and mucus-associated microbes) parameters of the human colon (M-ARCOL), a salivary enrichment protocol, and whole-metagenome shotgun sequencing. Our study revealed the importance of integrating the mucus compartment, which retained higher microbial richness during fermentation, showed the preference of oral microbial invaders for the mucosal resources, and indicated potential oral-to-intestinal mucosal competitions. It also underlined promising opportunities to further understand mechanisms of oral invasion into the human gut microbiome, define microbe-microbe and mucus-microbe interactions in a compartmentalized fashion, and help to better characterize the potential of oral microbial invasion and their persistence in the gut.}, } @article {pmid36970947, year = {2023}, author = {Ermolenko, E and Sitkin, S and Vakhitov, T and Solovyeva, O and Karaseva, A and Morozova, A and Kotyleva, M and Shumikhina, I and Lavrenova, N and Demyanova, E and Dmitriev, A and Suvorov, A}, title = {Evaluation of the effectiveness of personalised therapy for the patients with irritable bowel syndrome.}, journal = {Beneficial microbes}, volume = {14}, number = {2}, pages = {119-129}, doi = {10.3920/BM2022.0053}, pmid = {36970947}, issn = {1876-2891}, mesh = {Humans ; Bacteroidetes/genetics ; Enterococcus/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Gram-Positive Cocci ; *Irritable Bowel Syndrome/microbiology ; *Microbiota ; *Probiotics/therapeutic use ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Intestinal microbiota correction in the therapy of irritable bowel syndrome (IBS) is an important medical problem. We conducted a laboratory and pilot clinical trial to investigate the effect of autoprobiotic bacteria, indigenous bifidobacteria and enterococci isolated from faeces and grown on artificial media to use as personified food additives in IBS treatment. Convincing evidence of the clinical efficacy of autoprobiotic was demonstrated by the disappearance of dyspeptic symptoms. The microbiome of patients with IBS was compared to a group of healthy volunteers and changes in the microbiome after autoprobiotic use were detected by quantitative polymerase chain reaction and 16S rRNA metagenome analysis. The possibility of reducing opportunistic microorganisms in the treatment of IBS with autoprobiotics has been convincingly proven. The quantitative content of enterococci in the intestinal microbiota was higher in IBS patients than in healthy volunteers and increased after therapy. An increase in the relative abundance of genera Coprococcus, Blautia and a decrease in the relative abundance of Paraprevotella spp. were found at the end of therapy. A metabolome study which was performed by gas chromatography and mass spectrometry demonstrated an increase in the content of oxalic acid, a decrease of dodecanoate, lauric acid, and other metabolome components after taking autoprobiotics. Some of these parameters correlated with the relative abundances of Paraprevotella spp., Enterococcus spp., and Coprococcus spp. representative of the microbiome. Apparently, they reflected the peculiarities of metabolic compensation and changes in the microbiota. Therefore, the use of autoprobiotics for treatment of IBS may lead to a stable positive clinical effect, associated with compensatory changes in the intestinal microbiota, and accompanied by corresponding changes in metabolic processes in the organism.}, } @article {pmid36970703, year = {2023}, author = {Pan, J and Zeng, M and Zhao, M and Huang, L}, title = {Research Progress on the detection methods of porcine reproductive and respiratory syndrome virus.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1097905}, pmid = {36970703}, issn = {1664-302X}, abstract = {Porcine reproductive and respiratory syndrome virus (PRRSV) causes clinical syndromes typified as reproductive disorders in sows and respiratory diseases in piglets. PRRSV remains one of the most prevalent pathogens affecting the pig industry, because of its complex infection profile and highly heterogeneous genetic and recombination characteristics. Therefore, a rapid and effective PRRSV detection method is important for the prevention and control of PRRS. With extensive in-depth research on PRRSV detection methods, many detection methods have been improved and promoted. Laboratory methods include techniques based on virus isolation (VI), enzyme-linked immunosorbent assays (ELISA), indirect immunofluorescence assays (IFA), immunoperoxidase monolayer assays (IPMA), polymerase chain reaction (PCR), quantitative real-time PCR (qPCR), digital PCR (dPCR), loop-mediated isothermal amplification (LAMP), recombinase polymerase amplification (RPA), clustered regularly interspaced short palindromic repeats (CRISPR), metagenomic next-generation sequencing (mNGS), and other methods. This study reviews the latest research on improving the main PRRSV detection methods and discusses their advantages and disadvantages.}, } @article {pmid36970696, year = {2023}, author = {Dai, R and Wu, H and Liu, G and Shen, L and Geng, Y and Zhang, S and Zhou, H and Jiang, C and Gong, J and Fan, X and Ji, C}, title = {Investigation of bacterial and fungal population structure on environmental surfaces of three medical institutions during the COVID-19 pandemic.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1089474}, pmid = {36970696}, issn = {1664-302X}, abstract = {OBJECTIVES: To evaluate the population structure of environmental bacteria and fungi in three different types of medical institutions and the potential risks due to antibiotic resistance during the coronavirus disease 2019 (COVID-19) pandemic.

METHODS: One hundred twenty-six environmental surface samples were collected from three medical institutions during the COVID-19 pandemic. A total of 6,093 and 13,514 representative sequences of 16S and ITS ribosomal RNA (rRNA) were obtained by amplicon sequencing analysis. The functional prediction was performed using the Phylogenetic Investigation of Communities by Reconstruction of Unobserved States tool based on the Greengenes database and the FAPROTAX database.

RESULTS: On environmental surfaces in three medical institutions during the COVID-19 pandemic, Firmicutes (51.6%) and Bacteroidetes (25%) were the dominant bacteria, while Ascomycota (39.4%) and Basidiomycota (14.2%) were the dominant fungi. A number of potential bacterial and fungal pathogens were successfully identified by the metagenomic approach. Furthermore, compared with the bacterial results, the fungi showed a generally closer Bray Curtis distance between samples. The overall ratio of Gram-negative bacteria to Gram-positive bacteria was about 3:7. The proportion of stress-tolerant bacteria in medical institutions A, B and C reached 88.9, 93.0 and 93.8%, respectively. Anaerobic bacteria accounted for 39.6% in outdoor environments, 77.7% in public areas, 87.9% in inpatient areas and 79.6% in restricted areas. Finally, the β-Lactam resistance pathway and polymyxin resistance pathway were revealed through functional prediction.

CONCLUSION: We described the microbial population structure changes in three different types of medical institutions using the metagenomic approach during the COVID-19 pandemic. We found that the disinfection measures performed by three healthcare facilities may be effective on the "ESKAPE" pathogens, but less effective on fungal pathogens. Moreover, emphasis should be given to the prevention and control of β-lactam and polymyxin antibiotics resistance bacteria during the COVID-19 pandemic.}, } @article {pmid36970681, year = {2023}, author = {Guo, K and Li, J and Li, X and Huang, J and Zhou, Z}, title = {Emerging trends and focus on the link between gut microbiota and type 1 diabetes: A bibliometric and visualization analysis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1137595}, pmid = {36970681}, issn = {1664-302X}, support = {P30 DK045735/DK/NIDDK NIH HHS/United States ; }, abstract = {OBJECTIVE: To conduct the first thorough bibliometric analysis to evaluate and quantify global research regarding to the gut microbiota and type 1 diabetes (T1D).

METHODS: A literature search for research studies on gut microbiota and T1D was conducted using the Web of Science Core Collection (WoSCC) database on 24 September 2022. VOSviewer software and the packages Bibliometrix R and ggplot used in RStudio were applied to perform the bibliometric and visualization analysis.

RESULTS: A total of 639 publications was extracted using the terms "gut microbiota" and "type 1 diabetes" (and their synonyms in MeSH). Ultimately, 324 articles were included in the bibliometric analysis. The United States and European countries are the main contributors to this field, and the top 10 most influential institutions are all based in the United States, Finland and Denmark. The three most influential researchers in this field are Li Wen, Jorma Ilonen and Mikael Knip. Historical direct citation analysis showed the evolution of the most cited papers in the field of T1D and gut microbiota. Clustering analysis defined seven clusters, covering the current main topics in both basic and clinical research on T1D and gut microbiota. The most commonly found high-frequency keywords in the period from 2018 to 2021 were "metagenomics," "neutrophils" and "machine learning."

CONCLUSION: The application of multi-omics and machine learning approaches will be a necessary future step for better understanding gut microbiota in T1D. Finally, the future outlook for customized therapy toward reshaping gut microbiota of T1D patients remains promising.}, } @article {pmid36970670, year = {2023}, author = {Seyler, LM and Kraus, EA and McLean, C and Spear, JR and Templeton, AS and Schrenk, MO}, title = {An untargeted exometabolomics approach to characterize dissolved organic matter in groundwater of the Samail Ophiolite.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1093372}, pmid = {36970670}, issn = {1664-302X}, abstract = {The process of serpentinization supports life on Earth and gives rise to the habitability of other worlds in our Solar System. While numerous studies have provided clues to the survival strategies of microbial communities in serpentinizing environments on the modern Earth, characterizing microbial activity in such environments remains challenging due to low biomass and extreme conditions. Here, we used an untargeted metabolomics approach to characterize dissolved organic matter in groundwater in the Samail Ophiolite, the largest and best characterized example of actively serpentinizing uplifted ocean crust and mantle. We found that dissolved organic matter composition is strongly correlated with both fluid type and microbial community composition, and that the fluids that were most influenced by serpentinization contained the greatest number of unique compounds, none of which could be identified using the current metabolite databases. Using metabolomics in conjunction with metagenomic data, we detected numerous products and intermediates of microbial metabolic processes and identified potential biosignatures of microbial activity, including pigments, porphyrins, quinones, fatty acids, and metabolites involved in methanogenesis. Metabolomics techniques like the ones used in this study may be used to further our understanding of life in serpentinizing environments, and aid in the identification of biosignatures that can be used to search for life in serpentinizing systems on other worlds.}, } @article {pmid36970663, year = {2023}, author = {Zhong, X and Zhao, Y and Huang, L and Liu, J and Wang, K and Gao, X and Zhao, X and Wang, X}, title = {Remodeling of the gut microbiome by Lactobacillus johnsonii alleviates the development of acute myocardial infarction.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1140498}, pmid = {36970663}, issn = {1664-302X}, abstract = {INTRODUCTION: The gut microbial community, which can be disturbed or repaired by changes in the internal environment, contributes to the development of acute myocardial infarction (AMI). Gut probiotics play a role in microbiome remodeling and nutritional intervention post-AMI. A newly isolated Lactobacillus johnsonii strain EU03 has shown potential as a probiotic. Here, we investigated the cardioprotective function and mechanism of L. johnsonii through gut microbiome remodeling in AMI rats.

METHODS: A rat model of left anterior descending coronary artery ligation (LAD)-mediated AMI was assessed with echocardiography, histology, and serum cardiac biomarkers to evaluate the beneficial effects of L. johnsonii. The immunofluorescence analysis was utilized to visualize the intestinal barrier changes. Antibiotic administration model was used for assessing the gut commensals' function in the improvement of cardiac function post-AMI. The underlying beneficial mechanism through L. johnsonii enrichment was further investigated by metagenomics and metabolomics analysis.

RESULTS: A 28-day treatment with L. johnsonii protected cardiac function, delayed cardiac pathology, suppressed myocardial injury cytokines, and improved gut barrier integrity. The microbiome composition was reprogrammed by enhancing the abundance of L. johnsonii. Microbiome dysbiosis by antibiotics abrogated the improvement of cardiac function post-AMI by L. johnsonii. L. johnsonii enrichment caused remodeling of gut microbiome by increasing the abundance of Muribaculaceae, Lactobacillus, and decreasing Romboutsia, Clostridia UCG-014, which were correlated with cardiac traits and serum metabolic biomarkers 16,16-dimethyl-PGA2, and Lithocholate 3-O-glucuronide.

CONCLUSION: These findings reveal that gut microbiome remodeling by L. johnsonii ameliorates the cardiac function post-AMI and might advance microbiome-targeted nutritional intervention.Graphical Abstract.}, } @article {pmid36970502, year = {2023}, author = {Liu, B and Warnow, T}, title = {WITCH-NG: efficient and accurate alignment of datasets with sequence length heterogeneity.}, journal = {Bioinformatics advances}, volume = {3}, number = {1}, pages = {vbad024}, pmid = {36970502}, issn = {2635-0041}, abstract = {SUMMARY: Multiple sequence alignment is a basic part of many bioinformatics pipelines, including in phylogeny estimation, prediction of structure for both RNAs and proteins, and metagenomic sequence analysis. Yet many sequence datasets exhibit substantial sequence length heterogeneity, both because of large insertions and deletions in the evolutionary history of the sequences and the inclusion of unassembled reads or incompletely assembled sequences in the input. A few methods have been developed that can be highly accurate in aligning datasets with sequence length heterogeneity, with UPP one of the first methods to achieve good accuracy, and WITCH a recent improvement on UPP for accuracy. In this article, we show how we can speed up WITCH. Our improvement includes replacing a critical step in WITCH (currently performed using a heuristic search) by a polynomial time exact algorithm using Smith-Waterman. Our new method, WITCH-NG (i.e. 'next generation WITCH') achieves the same accuracy but is substantially faster. WITCH-NG is available at https://github.com/RuneBlaze/WITCH-NG.

The datasets used in this study are from prior publications and are freely available in public repositories, as indicated in the Supplementary Materials.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.}, } @article {pmid36970243, year = {2023}, author = {Wang, L and Lin, C and Qi, Y}, title = {Gestational psittacosis causes severe pneumonia and miscarriage: A case report and literature review.}, journal = {Radiology case reports}, volume = {18}, number = {5}, pages = {1959-1962}, pmid = {36970243}, issn = {1930-0433}, abstract = {Psittacosis is an uncommon zoonotic illness, and gestational psittacosis is even rarer. The clinical signs and symptoms of psittacosis are varied, often overlooked, and swiftly identified by metagenomic next-generation sequencing. We recorded the case of a 41-year-old pregnant woman with psittacosis where the disease was not detected early on, resulting in severe pneumonia and fetal miscarriage. The clinical symptoms, diagnosis, and treatment of psittacosis in pregnancy are the subject of this case study.}, } @article {pmid36969214, year = {2023}, author = {Feng, R and Zhu, Q and Li, Q and Zhai, Y and Wang, J and Qin, C and Liang, D and Zhang, R and Tian, H and Liu, H and Chen, Y and Fu, Y and Wang, X and Ding, X}, title = {Microbiota-ear-brain interaction is associated with generalized anxiety disorder through activation of inflammatory cytokine responses.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1117726}, pmid = {36969214}, issn = {1664-3224}, mesh = {Humans ; *Cytokines ; RNA, Ribosomal, 16S ; Anxiety Disorders/microbiology ; Brain ; *Microbiota ; Inflammation ; }, abstract = {INTRODUCTION: Generalized anxiety disorder (GAD) is one of the most enduring anxiety disorders, being associated with increased systemic inflammation. However, the trigger and mechanisms underlying the activation of inflammatory cytokine responses in GAD remain poorly understood.

MATERIALS AND METHODS: We characterized the ear canal microbiome in GAD patients through 16S rRNA gene sequencing and metagenomic sequencing and identified the serum inflammatory markers in GAD patients. Spearman correlations were applied to test the relationship between the microbiota changes and systemic inflammation.

RESULTS: Our findings showed the higher microbial diversity, accompanied with the significantly increased abundance of Proteobacteria, and decreased abundance of Firmicutes in the ear canal of GAD participants compared to that of the age- and sex-matched healthy controls (HC). Metagenomic sequencing showed that Pseudomonas aeruginosa were significantly increased at species-level in GAD patients. Furthermore, we observed the relative abundance of Pseudomonas aeruginosa was positively associated with elevated systemic inflammatory markers and the severity of disease, suggesting that these ear canal microbiota alterations might be correlated with GAD by activating the inflammatory response.

CONCLUSIONS: These findings indicate that microbiota-ear-brain interaction via upregulating inflammatory reaction involve in the development of GAD, as well as suggest that ear canal bacterial communities may be a target for therapeutic intervention.}, } @article {pmid36968950, year = {2023}, author = {Brochu, E and Huletsky, A and Boudreau, DK and Raymond, F and Bérubé, È and Ouameur, AA and Frenette, J and Boissinot, M and Corbeil, J and Bergeron, MG}, title = {Characterization of vancomycin-resistance vanD gene clusters in the human intestinal microbiota by metagenomics and culture-enriched metagenomics.}, journal = {JAC-antimicrobial resistance}, volume = {5}, number = {2}, pages = {dlad026}, pmid = {36968950}, issn = {2632-1823}, abstract = {OBJECTIVES: To characterize vancomycin-resistance vanD gene clusters and potential vanD-carrying bacteria in the intestinal microbiota of healthy volunteers exposed or not to β-lactam antibiotics.

METHODS: Stool samples were collected before and after 7 days of cefprozil β-lactam antibiotic exposure of 18 participants and six control participants who were not exposed to the antibiotic at the same time points. Metagenomic sequencing and culture-enriched metagenomic sequencing (with and without β-lactam selection) were used to characterize vanD gene clusters and determine potential vanD-carrying bacteria. Alteration by antimicrobials was also examined.

RESULTS: Culture enrichment allowed detection of vanD genes in a large number of participants (11/24; 46%) compared to direct metagenomics (2/24; 8%). vanD genes were detected in stool cultures only following β-lactam exposure, either after β-lactam treatment of participants or after culture of stools with β-lactam selection. Six types of vanD gene clusters were identified. Two types of vanD cluster highly similar to those of enterococci were found in two participants. Other vanD genes or vanD clusters were nearly identical to those identified in commensal anaerobic bacteria of the families Lachnospiraceae and Oscillospiraceae and/or bordered by genomic sequences similar or related to these anaerobes, suggesting that they are the origin or carriers of vanD.

CONCLUSIONS: This study showed that culture-enriched metagenomics allowed detection of vanD genes not detected by direct metagenomics and revealed collateral enrichment of bacteria containing vancomycin-resistance vanD genes following exposure to β-lactams, with a higher prevalence of the most likely gut commensal anaerobes carrying vanD. These commensal anaerobes could be the reservoir of vanD genes carried by enterococci.}, } @article {pmid36968356, year = {2023}, author = {Zhang, M and Xiao, N and Yang, H and Li, Y and Gao, F and Li, J and Zhang, Z}, title = {The layout measures of micro-sprinkler irrigation under plastic film regulate tomato soil bacterial community and root system.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1136439}, pmid = {36968356}, issn = {1664-462X}, abstract = {INTRODUCTION: The change in rhizosphere soil bacterial community and root system under new water-saving device is not clear.

METHODS: A completely randomized experimental design was used to explore the effects of different micropore group spacing (L1: 30 cm micropore group spacing, L2: 50 cm micropore group spacing) and capillary arrangement density (C1: one pipe for one row, C2: one pipe for two rows, C3: one pipe for three rows) on tomato rhizosphere soil bacteria community, roots and tomato yield under MSPF. The bacteria in tomato rhizosphere soil were sequenced by 16S rRNA gene amplicon metagenomic sequencing technology, the interaction of bacterial community, root system and yield in tomato rhizosphere soil was quantitatively described based on regression analysis.

RESULTS: Results showed that L1 was not only beneficial to the development of tomato root morphology, but also promoted the ACE index of tomato soil bacterial community structure and the abundance of nitrogen and phosphorus metabolism functional genes. The yield and crop water use efficiency (WUE) of spring tomato and autumn tomato in L1 were about 14.15% and 11.27%, 12.64% and 10.35% higher than those in L2. With the decrease of capillary arrangement density, the diversity of bacterial community structure in tomato rhizosphere soil decreased, and the abundance of nitrogen and phosphorus metabolism functional genes of soil bacteria also decreased. The small abundance of soil bacterial functional genes limited the absorption of soil nutrients by tomato roots and roots morphological development. The yield and crop water use efficiency of spring and autumn tomato in C2 were significantly higher than those in C3 about 34.76% and 15.23%, 31.94% and 13.91%, respectively. The positive interaction between soil bacterial community and root morphological development of tomato was promoted by the capillary layout measures of MSPF.

DISCUSSION: The L1C2 treatment had a stable bacterial community structure and good root morphological development, which positively promoted the increase of tomato yield. The interaction between soil microorganisms and roots of tomato was regulated by optimizing the layout measures of MSPF to provide data support for water-saving and yield-increasing of tomato in Northwest China.}, } @article {pmid36968018, year = {2023}, author = {Muñoz-Barrera, A and Ciuffreda, L and Alcoba-Florez, J and Rubio-Rodríguez, LA and Rodríguez-Pérez, H and Gil-Campesino, H and García-Martínez de Artola, D and Salas-Hernández, J and Rodríguez-Núñez, J and Íñigo-Campos, A and García-Olivares, V and Díez-Gil, O and González-Montelongo, R and Valenzuela-Fernández, A and Lorenzo-Salazar, JM and Flores, C}, title = {Bioinformatic approaches to draft the viral genome sequence of Canary Islands cases related to the multicountry mpox virus 2022-outbreak.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {2197-2203}, pmid = {36968018}, issn = {2001-0370}, abstract = {On July 23, 2022, monkeypox disease (mpox) was declared a Public Emergency of International Concern (PHEIC) by the World Health Organization (WHO) due to a multicountry outbreak. In Europe, several cases of mpox virus (MPXV) infection related to this outbreak were detected in the Canary Islands (Spain). Here we describe the combination of viral DNA sequencing and bioinformatic approaches, including methods for de novo genome assembly and short- and long-read technologies, used to reconstruct the first MPXV genome isolated in the Canary Islands on the 31st of May 2022 from a male adult patient with mild symptoms. The same sequencing and bioinformatic approaches were then validated with three other positive cases of MPXV infection from the same mpox outbreak. We obtained the best results using a reference-based approach with short reads, evidencing 46-79 nucleotide variants against viral sequences from the 2018-2019 mpox outbreak and placing the viral sequences in the new B.1 sublineage of clade IIb of the MPXV classification. This study of MPXV demonstrates the potential of metagenomics sequencing for rapid and precise pathogen identification.}, } @article {pmid36967692, year = {2023}, author = {Niu, J and Kong, X and Li, Q and Zhang, Y and Yuan, J and Liu, J and Zhang, Y}, title = {Deciphering different effects of ZVI and NaOH on metabolic characteristics in the process of methanogenesis recovery from VFA suppression.}, journal = {Journal of environmental management}, volume = {336}, number = {}, pages = {117686}, doi = {10.1016/j.jenvman.2023.117686}, pmid = {36967692}, issn = {1095-8630}, mesh = {*Iron ; Anaerobiosis ; Sodium Hydroxide ; *Carbon Dioxide ; Bacteria, Anaerobic/metabolism ; Methane ; Bioreactors/microbiology ; }, abstract = {Dosing zero valent iron (ZVI) or sodium hydroxide (NaOH) is the common method of addressing acidification in anaerobic digestion (AD) systems; however, few studies have discussed and compared their effects on microbial metabolism. In the present study, microbial syntrophy and metabolic pathways under ZVI and NaOH regulation are comparatively analyzed through microbial network analysis and metagenomic/metaproteomic analyses. CH4 yield in the ZVI reactor was 414 mL/gVS, an increase of 23% when compared with that in the reactor with NaOH dosing (336 mL/gVS). The methanogenesis recovery period in the ZVI reactor (37 days) was shorter than that in the NaOH reactor (48 days). Co-occurrence networks indicated that ZVI promoted Methanoculleus and Methanosarcina to establish a complex syntrophic association with SAO bacteria (Syntrophaceticus and Aminobacterium) and syntrophic acetogens (Syntrophomonas), strengthening SAO-hydrogenotrophic methanogenesis (HM) and acetoclastic methanogenesis (AM) pathways simultaneously. Metagenomic analysis showed that the relative abundance of mcrA and fwdB in the ZVI reactor was higher 27% than that in the NaOH reactor. Furthermore, through metaproteomics analysis, much more enzymes related to glucose degradation, bioconversion of butyric acid and pyruvate, conversion of formate and acetate to CO2, and production of CH4 from acetate and CO2 were significantly upregulated under ZVI regulation than under NaOH regulation (fold change relative to control [FC] > 1.5, p < 0.05). The results of the present study enhance our understanding of methanogenic mechanisms under the regulation of ZVI, providing a theoretical basis for its practical application in AD systems experiencing VFA suppression.}, } @article {pmid36967247, year = {2023}, author = {O'Connor, L and Heyderman, R}, title = {The challenges of defining the human nasopharyngeal resistome.}, journal = {Trends in microbiology}, volume = {31}, number = {8}, pages = {816-831}, doi = {10.1016/j.tim.2023.02.008}, pmid = {36967247}, issn = {1878-4380}, support = {/DH_/Department of Health/United Kingdom ; }, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Nasopharynx ; Metagenomics ; }, abstract = {The nasopharynx is an important microbial reservoir for the emergence and spread of antibiotic-resistant organisms. The nasopharyngeal resistome is an extensive, adaptable reservoir of antibiotic-resistance genes (ARGs) within this niche. Metagenomic sequencing decodes the genetic material of all organisms within a sample using next-generation technologies, permitting unbiased discovery of novel ARGs and associated mobile genetic elements (MGEs). The challenges of sequencing a low-biomass bacterial sample have limited exploration of the nasopharyngeal resistome. Here, we explore the current understanding of the nasopharyngeal resistome, particularly the role of MGEs in propagating antimicrobial resistance (AMR), explore the advantages and limitations of metagenomic sequencing technologies and bioinformatic pipelines for nasopharyngeal resistome analysis, and highlight the key outstanding questions for future research.}, } @article {pmid36967003, year = {2023}, author = {Li, J and Xu, X and Chen, C and Xu, L and Du, Z and Gu, L and Xiang, P and Shi, D and Huangfu, X and Liu, F}, title = {Conductive materials enhance microbial salt-tolerance in anaerobic digestion of food waste: Microbial response and metagenomics analysis.}, journal = {Environmental research}, volume = {227}, number = {}, pages = {115779}, doi = {10.1016/j.envres.2023.115779}, pmid = {36967003}, issn = {1096-0953}, mesh = {Ferrosoferric Oxide ; Anaerobiosis ; Food ; Charcoal ; Salt Tolerance ; *Graphite ; Metagenomics ; *Refuse Disposal ; Bioreactors ; Methane ; Sewage ; }, abstract = {Previous studies have shown that high salinity environments can inhibit anaerobic digestion (AD) of food waste (FW). Finding ways to alleviate salt inhibition is important for the disposal of the growing amount of FW. We selected three common conductive materials (powdered activated carbon, magnetite, and graphite) to understand their performance and individual mechanisms that relieve salinity inhibition. Digester performances and related enzyme parameters were compared. Our data revealed that under normal and low salinity stress conditions, the anaerobic digester ran steady without significant inhibitions. Further, the presence of conductive materials promoted conversion rate of methanogenesis. This promotion effect was highest from magnetite > powdered activated carbon (PAC) > graphite. At 1.5% salinity, PAC and magnetite are beneficial in maintaining high methane production efficiency while control and the graphite added digester acidified and failed rapidly. Additionally, metagenomics and binning were used to analyze the metabolic capacity of the microorganisms. Some species enriched by PAC and magnetite possessed higher cation transport capacities and were to accumulate compatible solutes. PAC and magnetite promoted direct interspecies electron transference (DIET) and syntrophic oxidation of butyrate and propionate. Also, the microorganisms had more energy available to cope with salt inhibition in the PAC and magnetite added digesters. Our data imply that the promotion of Na+/H+ antiporter, K+ uptake, and osmoprotectant synthesis or transport by conductive materials may be crucial for their proliferation in highly stressful environments. These findings will help to understand the mechanisms of alleviate salt inhibition by conductive materials and help to recover methane from high-salinity FW.}, } @article {pmid36966989, year = {2023}, author = {Chen, Z and Song, B and Guo, H and Xia, D and Cai, Y and Wang, Y and Zhao, W}, title = {Metagenomic characterization of biomethane transformation by lipid-catalyzed anaerobic fermentation of lignite.}, journal = {Environmental research}, volume = {227}, number = {}, pages = {115777}, doi = {10.1016/j.envres.2023.115777}, pmid = {36966989}, issn = {1096-0953}, mesh = {Fermentation ; Anaerobiosis ; *Fatty Acids/metabolism ; *Methane ; Catalysis ; Bioreactors ; }, abstract = {The present study aims at using lipid in a novel way to improve the efficiency of methane production from lignite anaerobic digestion. The obtained results showed an increase by 3.13 times of the cumulative biomethane content of lignite anaerobic fermentation, when 1.8 g lipid was added. The gene expression of functional metabolic enzymes was also found to be enhanced during the anaerobic fermentation. Moreover, the enzymes related to fatty acid degradation such as long-chain Acyl-CoA synthetase and Acyl-CoA dehydrogenase were increased by 1.72 and 10.48 times, respectively, which consequently, accelerated the conversion of fatty acid. Furthermore, the addition of lipid enhanced the carbon dioxide trophic and acetic acid trophic metabolic pathways. Hence, the addition of lipids was argued to promote the production of methane from lignite anaerobic fermentation, which provided a new insight for the conversion and utilization of lipid waste.}, } @article {pmid36966826, year = {2023}, author = {Zhao, Z and Yu, C and Yang, C and Gao, B and Jiménez, N and Wang, C and Li, F and Ao, Y and Zheng, L and Huang, F and Tomberlin, JK and Ren, Z and Yu, Z and Zhang, J and Cai, M}, title = {Mitigation of antibiotic resistome in swine manure by black soldier fly larval conversion combined with composting.}, journal = {The Science of the total environment}, volume = {879}, number = {}, pages = {163065}, doi = {10.1016/j.scitotenv.2023.163065}, pmid = {36966826}, issn = {1879-1026}, mesh = {Humans ; Swine ; Animals ; Larva ; Manure/microbiology ; *Composting ; Anti-Bacterial Agents/pharmacology ; *Diptera ; Bacteria/genetics ; Genes, Bacterial ; }, abstract = {The increasing prevalence of antibiotic resistance genes (ARGs) in animal manure has attracted considerable attention because of their potential contribution to the development of multidrug resistance worldwide. Insect technology may be a promising alternative for the rapid attenuation of ARGs in manure; however, the underlying mechanism remains unclear. This study aimed to evaluate the effects of black soldier fly (BSF, Hermetia illucens [L.]) larvae conversion combined with composting on ARGs dynamics in swine manure and to uncover the mechanisms through metagenomic analysis. Compared to natural composting (i.e. without BSF), BSFL conversion combined with composting reduced the absolute abundance of ARGs by 93.2 % within 28 days. The rapid degradation of antibiotics and nutrient reformulation during BSFL conversion combined with composting indirectly altered manure bacterial communities, resulting in a lower abundance and richness of ARGs. The number of main antibiotic-resistant bacteria (e.g., Prevotella, Ruminococcus) decreased by 74.9 %, while their potential antagonistic bacteria (e.g., Bacillus, Pseudomonas) increased by 128.7 %. The number of antibiotic-resistant pathogenic bacteria (e.g., Selenomonas, Paenalcaligenes) decreased by 88.3 %, and the average number of ARGs carried by each human pathogenic bacterial genus declined by 55.8 %. BSF larvae gut microbiota (e.g., Clostridium butyricum, C. bornimense) could help reduce the risk of multidrug-resistant pathogens. These results provide insight into a novel approach to mitigate multidrug resistance from the animal industry in the environment by using insect technology combined with composting, in particular in light of the global "One Health" requirements.}, } @article {pmid36966821, year = {2023}, author = {Zhang, H and Gong, W and Xue, Y and Zeng, W and Wang, H and Wang, J and Tang, X and Li, G and Liang, H}, title = {Municipal wastewater contains antibiotic treatment using O2 transfer membrane based biofilm reactor: Interaction between regular pollutants metabolism and sulfamethoxazole degradation.}, journal = {The Science of the total environment}, volume = {879}, number = {}, pages = {163060}, doi = {10.1016/j.scitotenv.2023.163060}, pmid = {36966821}, issn = {1879-1026}, mesh = {*Sulfamethoxazole/metabolism ; *Wastewater ; Bioreactors/microbiology ; Anti-Bacterial Agents ; Biofilms ; }, abstract = {The antibiotic sulfamethoxazole (SMX) is frequently detected in wastewater treatment plant effluents and has attracted significant attention owing to its significant potential environmental effects. We present a novel O2 transfer membrane based biofilm reactor (O2TM-BR) to treat municipal wastewater to eliminate containing SMX. Furthermore, conducting metagenomics analyses, the interactions in biodegradation process between SMX and regular pollutants (NH4[+]-N and COD) were studied. Results suggest that O2TM-BR yields evident advantages in SMX degradation. Increasing SMX concentrations did not affect the efficiency of the system, and the effluent concentration remained consistent at approximately 17.0 μg/L. The interaction experiment showed that heterotrophic bacteria tend to consume easily degradable COD for metabolism, resulting in a delay (>36 h) in complete SMX degradation, which is 3-times longer than without COD. It is worth noting that the taxonomic and functional structure and composition in nitrogen metabolism were significantly shifted upon the SMX. NH4[+]-N removal remained unaffected by SMX in O2TM-BR, and the expression of K10944 and K10535 has no significant difference under the stress of SMX (P > 0.02). However, the K00376 and K02567 required in the nitrate reductase is inhibited by SMX (P < 0.01), which hinders the reduction of NO3[-]-N and hence the accumulation of TN. This study provides a new method for SMX treatment and reveals the interaction between SMX and conventional pollutants in O2TM-BR as well as the microbial community function and assembly mechanism.}, } @article {pmid36966280, year = {2023}, author = {Zhao, Y and Yi, J and Xiang, J and Jia, W and Chen, A and Chen, L and Zheng, L and Zhou, W and Wu, M and Yu, Z and Tang, J}, title = {Exploration of lung mycobiome in the patients with non-small-cell lung cancer.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {81}, pmid = {36966280}, issn = {1471-2180}, mesh = {Humans ; *Mycobiome ; *Carcinoma, Non-Small-Cell Lung ; Fungi/genetics ; *Lung Neoplasms ; Lung ; }, abstract = {As the Human Microbiome Project (HMP) progresses, the relationship between microbes and human health has been receiving increasing attention. A growing number of reports support the correlation between cancer and microbes. However, most studies have focused on bacteria, rather than fungal communities. In this study, we studied the alteration in lung mycobiome in patients with non-small-cell lung cancer (NSCLC) using metagenomic sequencing and qPCR. The higher fungal diversity and more complex network were observed in the patients with NSCLC. In addition, Alternaria arborescens was found as the most relevant fungus to NSCLC, and the enrichment of it in cancerous tissue was also detected. This study proposes that the changes in fungal communities may be closely related to lung cancer, and provides insights into further exploration the relationship between lung cancer and fungi.}, } @article {pmid36966258, year = {2023}, author = {Deng, L and Li, Q and Hu, W and Chen, X and Chen, T and Song, S and Mo, P and Zou, S and Zhang, Y and Gao, S and Chen, L and Zhuang, K and Yang, R and Xiong, Y}, title = {Metagenomic next-generation sequencing versus traditional laboratory methods for the diagnosis of central nervous system opportunistic infections in HIV-infected Chinese adults.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {4921}, pmid = {36966258}, issn = {2045-2322}, mesh = {Humans ; Adult ; East Asian People ; *Central Nervous System Infections/diagnosis ; High-Throughput Nucleotide Sequencing ; Metagenomics ; *Opportunistic Infections ; Central Nervous System ; *HIV Infections/complications ; Sensitivity and Specificity ; }, abstract = {To evaluate clinical value of metagenomic next-generation sequencing (mNGS) in people living with HIV/AIDS (PLWHA) who had CNS disorders. Cerebrospinal fluid (CSF) samples from 48 PLWHA presenting with CNS disorders were sequenced using mNGS and compared with clinical conventional diagnostic methods. In total, 36/48 ss(75%) patients were diagnosed with pathogen(s) infection by mNGS, and the positive detection proportion by mNGS was higher than that by clinical conventional diagnostic methods (75% vs 52.1%, X[2] = 5.441, P = 0.020). Thirteen out of 48 patients (27.1%) were detected with 3-7 pathogens by mNGS. Moreover, 77 pathogen strains were detected, of which 94.8% (73/77) by mNGS and 37.0% (30/77) by clinical conventional methods (X[2] = 54.206, P < 0.001). The sensitivity and specificity of pathogens detection by mNGS were 63.9% (23/36) and 66.7% (8/12), respectively, which were superior to that by clinical conventional methods (23/36 vs 9/25, X[2] = 4.601, P = 0.032; 8/12 vs 5/23, X[2] = 5.029, P = 0.009). The application of mNGS was superior for its ability to detect a variety of unknown pathogens and multiple pathogens infection, and relatively higher sensitivity and specificity in diagnosis of CNS disorders in PLWHA.}, } @article {pmid36966231, year = {2023}, author = {Berglund, F and Ebmeyer, S and Kristiansson, E and Larsson, DGJ}, title = {Evidence for wastewaters as environments where mobile antibiotic resistance genes emerge.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {321}, pmid = {36966231}, issn = {2399-3642}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Wastewater ; Genes, Bacterial ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; }, abstract = {The emergence and spread of mobile antibiotic resistance genes (ARGs) in pathogens have become a serious threat to global health. Still little is known about where ARGs gain mobility in the first place. Here, we aimed to collect evidence indicating where such initial mobilization events of clinically relevant ARGs may have occurred. We found that the majority of previously identified origin species did not carry the mobilizing elements that likely enabled intracellular mobility of the ARGs, suggesting a necessary interplay between different bacteria. Analyses of a broad range of metagenomes revealed that wastewaters and wastewater-impacted environments had by far the highest abundance of both origin species and corresponding mobilizing elements. Most origin species were only occasionally detected in other environments. Co-occurrence of origin species and corresponding mobilizing elements were rare in human microbiota. Our results identify wastewaters and wastewater-impacted environments as plausible arenas for the initial mobilization of resistance genes.}, } @article {pmid36966151, year = {2023}, author = {Lin, X and Hu, T and Chen, J and Liang, H and Zhou, J and Wu, Z and Ye, C and Jin, X and Xu, X and Zhang, W and Jing, X and Yang, T and Wang, J and Yang, H and Kristiansen, K and Xiao, L and Zou, Y}, title = {The genomic landscape of reference genomes of cultivated human gut bacteria.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1663}, pmid = {36966151}, issn = {2041-1723}, mesh = {Humans ; Genome, Bacterial/genetics ; Genomics ; Metagenome/genetics ; *Gastrointestinal Microbiome/genetics ; Bacteria ; Metagenomics ; *Bacteriophages/genetics ; }, abstract = {Culture-independent metagenomic studies have revolutionized our understanding of the gut microbiota. However, the lack of full genomes from cultured species is still a limitation for in-depth studies of the gut microbiota. Here we present a substantially expanded version of our Cultivated Genome Reference (CGR), termed CGR2, providing 3324 high-quality draft genomes from isolates selected from a large-scale cultivation of bacterial isolates from fecal samples of healthy Chinese individuals. The CGR2 classifies 527 species (179 previously unidentified species) from 8 phyla, and uncovers a genomic and functional diversity of Collinsella aerofaciens. The CGR2 genomes match 126 metagenome-assembled genomes without cultured representatives in the Unified Human Gastrointestinal Genome (UHGG) collection and harbor 3767 unidentified secondary metabolite biosynthetic gene clusters, providing a source of natural compounds with pharmaceutical potentials. We uncover accurate phage-bacterium linkages providing information on the evolutionary characteristics of interaction between bacteriophages and bacteria at the strain level.}, } @article {pmid36965360, year = {2023}, author = {Li, Z and Qing, Y and Cui, G and Li, M and Liu, T and Zeng, Y and Zhou, C and Hu, X and Jiang, J and Wang, D and Gao, Y and Zhang, J and Cai, C and Wang, T and Wan, C}, title = {Shotgun metagenomics reveals abnormal short-chain fatty acid-producing bacteria and glucose and lipid metabolism of the gut microbiota in patients with schizophrenia.}, journal = {Schizophrenia research}, volume = {255}, number = {}, pages = {59-66}, doi = {10.1016/j.schres.2023.03.005}, pmid = {36965360}, issn = {1573-2509}, mesh = {Humans ; *Gastrointestinal Microbiome ; Lipid Metabolism ; Metagenomics ; Glucose ; *Schizophrenia ; Bacteria/metabolism ; Fatty Acids, Volatile/metabolism ; }, abstract = {Evidence has shown that the gut microbiota is closely related to the pathogenesis of schizophrenia, but temporal changes in the gut microbiota of patients with schizophrenia (SZ) during treatment remain unclear. Here, to evaluate temporal changes in the gut microbiota in schizophrenia, we performed whole-genome shotgun metagenomics on fecal samples from 36 healthy controls (HCs) and 19 baseline-period patients, and followed up with patients upon treatment. Compared to that in HCs, beta diversity in SZ was significantly distinct. The genera Bacteroides, Prevotella and Clostridium were the top 3 altered genera between SZ and HCs, and the Bacteroides-Prevotella ratio was significantly increased in SZ. Thirty-three percent of differentially abundant species were short-chain fatty acid (SCFA)-producing bacteria. Functional analysis showed that glucose and lipid metabolism of the gut microbiota was decreased in SZ compared with those in HCs. The abundances of two rate-limiting enzymes in glucose and lipid metabolism, phosphofructokinase (PFK) and acetyl-CoA carboxylase (ACC), were significantly decreased in SZ, and differentially abundant metabolism-related enzymes were significantly associated with SCFA-producing bacteria. Next, we found that the abundance of SCFA-producing bacteria also changed after treatment and that Clostridium was significantly negatively correlated with the total positive and negative syndrome scale (PANSS) score in patients. Functional analysis showed that glycoside hydrolase family 30 incrementally increased in abundance during treatment and were significantly associated with SCFA-producing bacteria. Our findings help to provide evidence for the role of gut microbiota in the occurrence and development of schizophrenia.}, } @article {pmid36965294, year = {2023}, author = {Hu, P and Qian, Y and Liu, J and Gao, L and Li, Y and Xu, Y and Wu, J and Hong, Y and Ford, T and Radian, A and Yang, Y and Gu, JD}, title = {Delineation of the complex microbial nitrogen-transformation network in an anammox-driven full-scale wastewater treatment plant.}, journal = {Water research}, volume = {235}, number = {}, pages = {119799}, doi = {10.1016/j.watres.2023.119799}, pmid = {36965294}, issn = {1879-2448}, mesh = {Ammonia/metabolism ; Denitrification ; Wastewater ; Nitrites/metabolism ; Nitrates/metabolism ; Anaerobic Ammonia Oxidation ; Nitrogen/metabolism ; Anaerobiosis ; Oxidation-Reduction ; Bioreactors/microbiology ; *Ammonium Compounds/metabolism ; Bacteria/genetics/metabolism ; *Water Purification/methods ; }, abstract = {Microbial-driven nitrogen removal is a crucial step in modern full-scale wastewater treatment plants (WWTPs), and the complexity of nitrogen transformation is integral to the various wastewater treatment processes. A full understanding of the overall nitrogen cycling networks in WWTPs is therefore a prerequisite for the further enhancement and optimization of wastewater treatment processes. In this study, metagenomics and metatranscriptomics were used to elucidate the microbial nitrogen removal processes in an ammonium-enriched full-scale WWTP, which was configured as an anaerobic-anoxic-anaerobic-oxic system for efficient nitrogen removal (99.63%) on a duck breeding farm. A typical simultaneous nitrification-anammox-denitrification (SNAD) process was established in each tank of this WWTP. Ammonia was oxidized by ammonia-oxidizing bacteria (AOB), archaea (AOA), and nitrite-oxidizing bacteria (NOB), and the produced nitrite and nitrate were further reduced to dinitrogen gas (N2) by anammox and denitrifying bacteria. Visible red anammox biofilms were formed successfully on the sponge carriers submerged in the anoxic tank, and the nitrogen removal rate by anammox reaction was 4.85 times higher than that by denitrification based on [15]N isotope labeling and analysis. This supports the significant accumulation of anammox bacteria on the carriers responsible for efficient nitrogen removal. Two distinct anammox bacteria, named "Ca. Brocadia sp. PF01" and "Ca. Jettenia sp. PF02", were identified from the biofilm in this investigation. By recovering their genomic features and their metabolic capabilities, our results indicate that the highly active core anammox process found in PF01, suggests extending its niche within the plant. With the possible contribution of the dissimilatory nitrate reduction to ammonium (DNRA) reaction, enriching PF02 within the biofilm may also be warranted. Collectively, this study highlights the effective design strategies of a full-scale WWTP with enrichment of anammox bacteria on the carrier materials for nitrogen removal and therefore the biochemical reaction mechanisms of the contributing members.}, } @article {pmid36965279, year = {2023}, author = {Viver, T and Conrad, RE and Lucio, M and Harir, M and Urdiain, M and Gago, JF and Suárez-Suárez, A and Bustos-Caparros, E and Sanchez-Martinez, R and Mayol, E and Fassetta, F and Pang, J and Mădălin Gridan, I and Venter, S and Santos, F and Baxter, B and Llames, ME and Cristea, A and Banciu, HL and Hedlund, BP and Stott, MB and Kämpfer, P and Amann, R and Schmitt-Kopplin, P and Konstantinidis, KT and Rossello-Mora, R}, title = {Description of two cultivated and two uncultivated new Salinibacter species, one named following the rules of the bacteriological code: Salinibacter grassmerensis sp. nov.; and three named following the rules of the SeqCode: Salinibacter pepae sp. nov., Salinibacter abyssi sp. nov., and Salinibacter pampae sp. nov.}, journal = {Systematic and applied microbiology}, volume = {46}, number = {3}, pages = {126416}, doi = {10.1016/j.syapm.2023.126416}, pmid = {36965279}, issn = {1618-0984}, mesh = {RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Phylogeny ; *Bacteroidetes ; *Fatty Acids/analysis ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; }, abstract = {Current -omics methods allow the collection of a large amount of information that helps in describing the microbial diversity in nature. Here, and as a result of a culturomic approach that rendered the collection of thousands of isolates from 5 different hypersaline sites (in Spain, USA and New Zealand), we obtained 21 strains that represent two new Salinibacter species. For these species we propose the names Salinibacter pepae sp. nov. and Salinibacter grassmerensis sp. nov. (showing average nucleotide identity (ANI) values < 95.09% and 87.08% with Sal. ruber M31[T], respectively). Metabolomics revealed species-specific discriminative profiles. Sal. ruber strains were distinguished by a higher percentage of polyunsaturated fatty acids and specific N-functionalized fatty acids; and Sal. altiplanensis was distinguished by an increased number of glycosylated molecules. Based on sequence characteristics and inferred phenotype of metagenome-assembled genomes (MAGs), we describe two new members of the genus Salinibacter. These species dominated in different sites and always coexisted with Sal. ruber and Sal. pepae. Based on the MAGs from three Argentinian lakes in the Pampa region of Argentina and the MAG of the Romanian lake Fără Fund, we describe the species Salinibacter pampae sp. nov. and Salinibacter abyssi sp. nov. respectively (showing ANI values 90.94% and 91.48% with Sal. ruber M31[T], respectively). Sal. grassmerensis sp. nov. name was formed according to the rules of the International Code for Nomenclature of Prokaryotes (ICNP), and Sal. pepae, Sal. pampae sp. nov. and Sal. abyssi sp. nov. are proposed following the rules of the newly published Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode). This work constitutes an example on how classification under ICNP and SeqCode can coexist, and how the official naming a cultivated organism for which the deposit in public repositories is difficult finds an intermediate solution.}, } @article {pmid36965198, year = {2023}, author = {Ceylani, T and Allahverdi, H and Teker, HT}, title = {Role of age-related plasma in the diversity of gut bacteria.}, journal = {Archives of gerontology and geriatrics}, volume = {111}, number = {}, pages = {105003}, doi = {10.1016/j.archger.2023.105003}, pmid = {36965198}, issn = {1872-6976}, mesh = {Rats ; Humans ; Animals ; Feces/microbiology ; *Bacteria/genetics ; *Gastrointestinal Microbiome ; Bacteroidetes ; Plasma ; }, abstract = {Recent studies have demonstrated the efficacy of young blood plasma factors in reversing aging-related deformities. However, the impact of plasma exchange between young and old individuals on gut microbiota remains understudied. To investigate this, we evaluated the effects of plasma exchange between 5-week-old and 24-month-old rats on gut microbiota composition. In this study, old rats were administered 0.5 ml of young plasma, while young rats were administered 0.25 ml of old plasma daily for 30 days. Metagenome analysis was performed on the contents of the cecum after completing plasma transfer. Results showed that transferring young plasma to old rats significantly increased the alpha diversity indices (Shannon and Simpson values), while the Firmicutes to Bacteroidetes ratio decreased significantly. Conversely, transferring aged plasma to young rats led to a significant decrease in Shannon value and F/B ratio but no change in Simpson value. Plasma exchange also caused substantial changes in the top ten dominant genera and species found in the gut microbiota of young and old rats. After young blood plasma transfer, the dominant bacterial profile in the old gut microbiota shifted toward the bacterial profile found in the young control group. Notably, old plasma also altered the gut microbiota structure of young rats toward that of old rats. Our findings suggest that age-related changes in plasma play a crucial role in gut microbiota species diversity and their presence rates.}, } @article {pmid36964623, year = {2023}, author = {Manabe, Y and Ishibashi, T and Asano, R and Tonomura, S and Maeda, Y and Motooka, D and Ueda, J and Yanagawa, M and Edamoto-Taira, Y and Chikaishi-Kirino, T and Masaki, T and Inagaki, T and Nakamura, S and Katada, Y and Okazawa, M and Narazaki, M and Ogo, T and Kumanogoh, A and Nakaoka, Y}, title = {Gut dysbiosis is associated with aortic aneurysm formation and progression in Takayasu arteritis.}, journal = {Arthritis research & therapy}, volume = {25}, number = {1}, pages = {46}, pmid = {36964623}, issn = {1478-6362}, mesh = {Humans ; *Takayasu Arteritis/drug therapy ; Retrospective Studies ; Prospective Studies ; Dysbiosis ; Proton Pump Inhibitors/therapeutic use ; *Aortic Aneurysm/complications ; *Vascular Diseases/complications ; }, abstract = {BACKGROUND: Takayasu arteritis (TAK) is an autoimmune large vessel vasculitis that affects the aorta and its major branches, eventually leading to the development of aortic aneurysm and vascular stenosis or occlusion. This retrospective and prospective study aimed to investigate whether the gut dysbiosis exists in patients with TAK and to identify specific gut microorganisms related to aortic aneurysm formation/progression in TAK.

METHODS: We analysed the faecal microbiome of 76 patients with TAK and 56 healthy controls (HCs) using 16S ribosomal RNA sequencing. We examined the relationship between the composition of the gut microbiota and clinical parameters.

RESULTS: The patients with TAK showed an altered gut microbiota with a higher abundance of oral-derived bacteria, such as Streptococcus and Campylobacter, regardless of the disease activity, than HCs. This increase was significantly associated with the administration of a proton pump inhibitor used for preventing gastric ulcers in patients treated with aspirin and glucocorticoids. Among patients taking a proton pump inhibitor, Campylobacter was more frequently detected in those who underwent vascular surgeries and endovascular therapy for aortic dilatation than in those who did not. Among the genus of Campylobacter, Campylobacter gracilis in the gut microbiome was significantly associated with clinical events related to aortic aneurysm formation/worsening in patients with TAK. In a prospective analysis, patients with a gut microbiome positive for Campylobacter were significantly more likely to require interventions for aortic dilatation than those who were negative for Campylobacter. Furthermore, patients with TAK who were positive for C. gracilis by polymerase chain reaction showed a tendency to have severe aortic aneurysms.

CONCLUSIONS: A specific increase in oral-derived Campylobacter in the gut may be a novel predictor of aortic aneurysm formation/progression in patients with TAK.}, } @article {pmid36964199, year = {2023}, author = {Kavagutti, VS and Chiriac, MC and Ghai, R and Salcher, MM and Haber, M}, title = {Isolation of phages infecting the abundant freshwater Actinobacteriota order 'Ca. Nanopelagicales'.}, journal = {The ISME journal}, volume = {17}, number = {6}, pages = {943-946}, pmid = {36964199}, issn = {1751-7370}, mesh = {*Bacteriophages ; Bacteria/genetics ; Gene Transfer, Horizontal ; Metagenome ; Fresh Water/microbiology ; Genome, Viral ; Phylogeny ; }, abstract = {Low-GC Actinobacteriota of the order 'Ca. Nanopelagicales' (also known as acI or hgcI clade) are abundant in freshwaters around the globe. Extensive predation pressure by phages has been assumed to be the reason for their high levels of microdiversity. So far, however, only a few metagenome-assembled phages have been proposed to infect them and no phages have been isolated. Taking advantage of recent advances in the cultivation of 'Ca. Nanopelagicales' we isolated a novel species of its genus 'Ca. Planktophila'. Using this isolate as bait, we cultivated the first two phages infecting this abundant bacterial order. Both genomes contained a whiB-like transcription factor and a RNA polymerase sigma-70 factor, which might aid in manipulating their host's metabolism. Both phages encoded a glycosyltransferase and one an anti-restriction protein, potential means to evade degradation of their DNA by nucleases present in the host genome. The two phage genomes shared only 6% of their genome with their closest relatives, with whom they form a previously uncultured family of actinophages within the Caudoviricetes. Read recruitment analyses against globally distributed metagenomes revealed the endemic distribution of this group of phages infecting 'Ca. Nanopelagicales'. The recruitment pattern against metagenomes from the isolation site and the modular distribution of shared genes between the two phages indicate high levels of horizontal gene transfer, likely mirroring the microdiversity of their host in the evolutionary arms race between host and phage.}, } @article {pmid36964154, year = {2023}, author = {Zimmermann, HH and Stoof-Leichsenring, KR and Dinkel, V and Harms, L and Schulte, L and Hütt, MT and Nürnberg, D and Tiedemann, R and Herzschuh, U}, title = {Marine ecosystem shifts with deglacial sea-ice loss inferred from ancient DNA shotgun sequencing.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1650}, pmid = {36964154}, issn = {2041-1723}, mesh = {*Ecosystem ; *DNA, Ancient ; Ice Cover ; Climate ; Geologic Sediments ; Arctic Regions ; Oceans and Seas ; }, abstract = {Sea ice is a key factor for the functioning and services provided by polar marine ecosystems. However, ecosystem responses to sea-ice loss are largely unknown because time-series data are lacking. Here, we use shotgun metagenomics of marine sedimentary ancient DNA off Kamchatka (Western Bering Sea) covering the last ~20,000 years. We traced shifts from a sea ice-adapted late-glacial ecosystem, characterized by diatoms, copepods, and codfish to an ice-free Holocene characterized by cyanobacteria, salmon, and herring. By providing information about marine ecosystem dynamics across a broad taxonomic spectrum, our data show that ancient DNA will be an important new tool in identifying long-term ecosystem responses to climate transitions for improvements of ocean and cryosphere risk assessments. We conclude that continuing sea-ice decline on the northern Bering Sea shelf might impact on carbon export and disrupt benthic food supply and could allow for a northward expansion of salmon and Pacific herring.}, } @article {pmid36963658, year = {2023}, author = {Xing, X and Liu, Q and Yuan, W and Zhu, C and Yang, J}, title = {Pulmonary scedosporiosis caused by Lomentospora prolificans in a patient who is immunocompetent: A rare case report.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {130}, number = {}, pages = {208-210}, doi = {10.1016/j.ijid.2023.03.037}, pmid = {36963658}, issn = {1878-3511}, mesh = {Humans ; *Scedosporium ; Antifungal Agents/therapeutic use ; *Invasive Fungal Infections/drug therapy ; *Ascomycota ; *Lung Diseases, Fungal/diagnosis/drug therapy ; }, abstract = {Infections with Scedosporium and Lomentospora species are usually found in patients who are immunodeficient, particularly in the transplant population. However, they are relatively rare in patients who are immunocompetent, which is especially useful in ruling out near-drowning and aspiration situations. Here, we report a case of a patient who is immunocompetent, with clinically suspected community-acquired pneumonia caused by Lomentospora prolificans detected by metagenomics next-generation sequencing (mNGS) and polymerase chain reaction from bronchoalveolar lavage fluid. This case highlights mNGS in the clinical diagnosis of pulmonary invasive fungal disease. mNGS is proposed as an important adjunctive diagnostic approach for rare pathogens.}, } @article {pmid36963586, year = {2023}, author = {Dahiya, S and Mohan, SV}, title = {Co-fermenting lactic acid and glucose towards caproic acid production.}, journal = {Chemosphere}, volume = {328}, number = {}, pages = {138491}, doi = {10.1016/j.chemosphere.2023.138491}, pmid = {36963586}, issn = {1879-1298}, mesh = {*Caproates ; *Lactic Acid ; Bioreactors ; Glucose ; Fatty Acids ; Fermentation ; }, abstract = {The functional role of lactate (HLac), as a co-substrate along with glucose (Glu) as well as an electron donor for the synthesis of caproic acid (HCa), a medium chain fatty acid (MCFAs) was studied. A varied HLac and Glu ratios were thus investigated in fed-batch anaerobic reactors (R1-R5) operated at pH 6 with a heat-treated anaerobic consortium. R1 and R5 were noted as controls and operated with sole Glu and HLac, respectively. Strategically, ethanol (HEth) was additionally supplemented as co-electron donor after the production of short chain carboxylic acids (SCCAs) for chain elongation in all the reactors. The reactor operated with HLac and Glu in a ratio of 0.25:0.75 (1.25 g/L (HLac) and 3.75 g/L (Glu)) showed the highest HCa production of 1.86 g/L. R5 operated with solely HLac yielded propionic acid (HPr) as the major product which further led to the higher valeric acid (HVa) production of 1.1 g/L within the reactor. Butyric acid (HBu) was observed in R1, which used Glu as carbon source alone indicating the importance of HLac as electron co-donor. Clostridium observed as the most dominant genera in shotgun metagenome sequencing in R2 and R3, the reactors that produced the highest HCa in comparison to other studied reactors. The study thus provided insight into the importance of substrate and electron donor and their supplementation strategies during the production of MCFAs.}, } @article {pmid36963164, year = {2023}, author = {Beliaeva, MA and Wilmanns, M and Zimmermann, M}, title = {Decipher enzymes from human microbiota for drug discovery and development.}, journal = {Current opinion in structural biology}, volume = {80}, number = {}, pages = {102567}, doi = {10.1016/j.sbi.2023.102567}, pmid = {36963164}, issn = {1879-033X}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Bacteria/genetics ; Genomics ; Drug Discovery ; }, abstract = {The human microbiota plays an important role in human health and contributes to the metabolism of therapeutic drugs affecting their potency. However, the current knowledge on human gut bacterial metabolism is limited and lacks an understanding of the underlying mechanisms of observed drug biotransformations. Despite the complexity of the gut microbial community, genomic and metagenomic sequencing provides insights into the diversity of chemical reactions that can be carried out by the microbiota and poses new challenges to functionally annotate thousands of bacterial enzymes. Here, we outline methods to systematically address the structural and functional space of the human microbiome, highlighting a combination of in silico and in vitro approaches. Systematic knowledge about microbial enzymes could eventually be applied for personalized therapy, the development of prodrugs and modulators of unwanted bacterial activity, and the further discovery of new antibiotics.}, } @article {pmid36962260, year = {2022}, author = {Muthanje, EM and Kimita, G and Nyataya, J and Njue, W and Mulili, C and Mugweru, J and Mutai, B and Kituyi, SN and Waitumbi, J}, title = {March 2019 dengue fever outbreak at the Kenyan south coast involving dengue virus serotype 3, genotypes III and V.}, journal = {PLOS global public health}, volume = {2}, number = {3}, pages = {e0000122}, pmid = {36962260}, issn = {2767-3375}, abstract = {The first description of a disease resembling dengue fever (DF) was in the 15th century slave trade era by Spanish sailors visiting the Tanzania coast. The disease, then associated with evil spirits is now known to be caused by four serotypes of dengue virus (DENV1-4) that are transmitted by Aedes mosquitoes. Kenya has experienced multiple outbreaks, mostly associated with DENV-2. In this study, plasma samples obtained from 37 febrile patients during a DF outbreak at Kenya's south coast in March 2019 were screened for DENV. Total RNA was extracted and screened for the alpha- and flavi-viruses by real-time polymerase chain reaction (qPCR). DENV-3 was the only virus detected. Shotgun metagenomics and targeted sequencing were used to obtain DENV whole genomes and the complete envelope genes (E gene) respectively. Sequences were used to infer phylogenies and time-scaled genealogies. Following Maximum likelihood and Bayesian phylogenetic analysis, two DENV-3 genotypes (III, n = 15 and V, n = 2) were found. We determined that the two genotypes had been in circulation since 2015, and that both had been introduced independently. Genotype III's origin was estimated to have been from Pakistan. Although the origin of genotype V could not be ascertained due to rarity of these sequences globally, it was most related to a 2006 Brazilian isolate. Unlike genotype III that has been described in East and West Africa multiple times, this was the second description of genotype V in Kenya. Of note, there was marked amino acid variances in the E gene between study samples and the Thailand DENV-3 strain used in the approved Dengvaxia vaccine. It remains to be seen whether these variances negatively impact the efficacy of the Dengvaxia or future vaccines.}, } @article {pmid36961862, year = {2023}, author = {Yan, W and Zhu, Y and Liu, W and Zou, C and Jia, B and Chen, ZQ and Han, Y and Wu, J and Yang, DL and Zhang, Z and Xie, L and Chen, B and Li, R and Ding, SW and Wu, Q and Guo, Z}, title = {Discovery of aphid-transmitted Rice tiller inhibition virus from native plants through metagenomic sequencing.}, journal = {PLoS pathogens}, volume = {19}, number = {3}, pages = {e1011238}, pmid = {36961862}, issn = {1553-7374}, mesh = {Animals ; Humans ; *Oryza/genetics ; *Aphids/genetics ; Gene Expression Profiling ; Plants, Genetically Modified/genetics ; *Viruses/genetics ; Plant Diseases ; }, abstract = {A major threat to rice production is the disease epidemics caused by insect-borne viruses that emerge and re-emerge with undefined origins. It is well known that some human viruses have zoonotic origins from wild animals. However, it remains unknown whether native plants host uncharacterized endemic viruses with spillover potential to rice (Oryza sativa) as emerging pathogens. Here, we discovered rice tiller inhibition virus (RTIV), a novel RNA virus species, from colonies of Asian wild rice (O. rufipogon) in a genetic reserve by metagenomic sequencing. We identified the specific aphid vector that is able to transmit RTIV and found that RTIV would cause low-tillering disease in rice cultivar after transmission. We further demonstrated that an infectious molecular clone of RTIV initiated systemic infection and causes low-tillering disease in an elite rice variety after Agrobacterium-mediated inoculation or stable plant transformation, and RTIV can also be transmitted from transgenic rice plant through its aphid vector to cause disease. Finally, global transcriptome analysis indicated that RTIV may disturb defense and tillering pathway to cause low tillering disease in rice cultivar. Thus, our results show that new rice viral pathogens can emerge from native habitats, and RTIV, a rare aphid-transmitted rice viral pathogen from native wild rice, can threaten the production of rice cultivar after spillover.}, } @article {pmid36961286, year = {2023}, author = {López-Islas, JJ and Méndez-Olvera, ET and Reyes C, T and Martínez-Gómez, D}, title = {Identification of antimicrobial resistance genes in intestinal content from Coyote (Canis latrans).}, journal = {Polish journal of veterinary sciences}, volume = {26}, number = {1}, pages = {143-149}, doi = {10.24425/pjvs.2023.145016}, pmid = {36961286}, issn = {2300-2557}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; *Coyotes/genetics ; Gastrointestinal Contents ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; }, abstract = {Antibiotic resistance has become a global public health concern in the last few years. Given the widespread rate of recurrence, increasing attention is being turned toward environmental pathways that potentially contribute to antibiotic resistance genes (ARGs) dissemination outside the clinical realm. In this study, a metagenome analysis of intestinal virus-like particle fraction (VLPs) from a wild coyote (Canis latrans) revealed for the first time, multiple ARGs, such as B-lactamases and multidrug efflux pumps. Description of ARGs presence in natural environments is critical to understand the emergence of resistant strains.}, } @article {pmid36960290, year = {2023}, author = {Marini, S and Boucher, C and Noyes, N and Prosperi, M}, title = {The K-mer antibiotic resistance gene variant analyzer (KARGVA).}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1060891}, pmid = {36960290}, issn = {1664-302X}, support = {R01 AI141810/AI/NIAID NIH HHS/United States ; }, abstract = {Characterization of antibiotic resistance genes (ARGs) from high-throughput sequencing data of metagenomics and cultured bacterial samples is a challenging task, with the need to account for both computational (e.g., string algorithms) and biological (e.g., gene transfers, rearrangements) aspects. Curated ARG databases exist together with assorted ARG classification approaches (e.g., database alignment, machine learning). Besides ARGs that naturally occur in bacterial strains or are acquired through mobile elements, there are chromosomal genes that can render a bacterium resistant to antibiotics through point mutations, i.e., ARG variants (ARGVs). While ARG repositories also collect ARGVs, there are only a few tools that are able to identify ARGVs from metagenomics and high throughput sequencing data, with a number of limitations (e.g., pre-assembly, a posteriori verification of mutations, or specification of species). In this work we present the k-mer, i.e., strings of fixed length k, ARGV analyzer - KARGVA - an open-source, multi-platform tool that provides: (i) an ad hoc, large ARGV database derived from multiple sources; (ii) input capability for various types of high-throughput sequencing data; (iii) a three-way, hash-based, k-mer search setup to process data efficiently, linking k-mers to ARGVs, k-mers to point mutations, and ARGVs to k-mers, respectively; (iv) a statistical filter on sequence classification to reduce type I and II errors. On semi-synthetic data, KARGVA provides very high accuracy even in presence of high sequencing errors or mutations (99.2 and 86.6% accuracy within 1 and 5% base change rates, respectively), and genome rearrangements (98.2% accuracy), with robust performance on ad hoc false positive sets. On data from the worldwide MetaSUB consortium, comprising 3,700+ metagenomics experiments, KARGVA identifies more ARGVs than Resistance Gene Identifier (4.8x) and PointFinder (6.8x), yet all predictions are below the expected false positive estimates. The prevalence of ARGVs is correlated to ARGs but ecological characteristics do not explain well ARGV variance. KARGVA is publicly available at https://github.com/DataIntellSystLab/KARGVA under MIT license.}, } @article {pmid36960043, year = {2023}, author = {Lin, T}, title = {Editorial: New techniques in microbiome research.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1158392}, doi = {10.3389/fcimb.2023.1158392}, pmid = {36960043}, issn = {2235-2988}, mesh = {*Microbiota ; }, } @article {pmid36959975, year = {2023}, author = {Baltoumas, FA and Karatzas, E and Paez-Espino, D and Venetsianou, NK and Aplakidou, E and Oulas, A and Finn, RD and Ovchinnikov, S and Pafilis, E and Kyrpides, NC and Pavlopoulos, GA}, title = {Exploring microbial functional biodiversity at the protein family level-From metagenomic sequence reads to annotated protein clusters.}, journal = {Frontiers in bioinformatics}, volume = {3}, number = {}, pages = {1157956}, pmid = {36959975}, issn = {2673-7647}, abstract = {Metagenomics has enabled accessing the genetic repertoire of natural microbial communities. Metagenome shotgun sequencing has become the method of choice for studying and classifying microorganisms from various environments. To this end, several methods have been developed to process and analyze the sequence data from raw reads to end-products such as predicted protein sequences or families. In this article, we provide a thorough review to simplify such processes and discuss the alternative methodologies that can be followed in order to explore biodiversity at the protein family level. We provide details for analysis tools and we comment on their scalability as well as their advantages and disadvantages. Finally, we report the available data repositories and recommend various approaches for protein family annotation related to phylogenetic distribution, structure prediction and metadata enrichment.}, } @article {pmid36959686, year = {2023}, author = {Yang, Y and Han, Z and Gao, Z and Chen, J and Song, C and Xu, J and Wang, H and Huang, A and Shi, J and Gu, J}, title = {Metagenomic and targeted metabolomic analyses reveal distinct phenotypes of the gut microbiota in patients with colorectal cancer and type 2 diabetes mellitus.}, journal = {Chinese medical journal}, volume = {136}, number = {23}, pages = {2847-2856}, pmid = {36959686}, issn = {2542-5641}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2 ; *Microbiota ; Bacteria/genetics ; Fatty Acids, Volatile ; *Colorectal Neoplasms/metabolism ; Butyrates ; Feces/microbiology ; }, abstract = {BACKGROUND: Type 2 diabetes mellitus (T2DM) is an independent risk factor for colorectal cancer (CRC), and the patients with CRC and T2DM have worse survival. The human gut microbiota (GM) is linked to the development of CRC and T2DM, respectively. However, the GM characteristics in patients with CRC and T2DM remain unclear.

METHODS: We performed fecal metagenomic and targeted metabolomics studies on 36 samples from CRC patients with T2DM (DCRC group, n = 12), CRC patients without diabetes (CRC group, n = 12), and healthy controls (Health group, n = 12). We analyzed the fecal microbiomes, characterized the composition and function based on the metagenomics of DCRC patients, and detected the short-chain fatty acids (SCFAs) and bile acids (BAs) levels in all fecal samples. Finally, we performed a correlation analysis of the differential bacteria and metabolites between different groups.

RESULTS: Compared with the CRC group, LefSe analysis showed that there is a specific GM community in DCRC group, including an increased abundance of Eggerthella , Hungatella , Peptostreptococcus , and Parvimonas , and decreased Butyricicoccus , Lactobacillus , and Paraprevotella . The metabolomics analysis results revealed that the butyric acid level was lower but the deoxycholic acid and 12-keto-lithocholic acid levels were higher in the DCRC group than other groups (P < 0.05). The correlation analysis showed that the dominant bacterial abundance in the DCRC group (Parvimonas , Desulfurispora , Sebaldella , and Veillonellales , among others) was negatively correlated with butyric acid, hyodeoxycholic acid, ursodeoxycholic acid, glycochenodeoxycholic acid, chenodeoxycholic acid, cholic acid and glycocholate. However, the abundance of mostly inferior bacteria was positively correlated with these metabolic acid levels, including Faecalibacterium , Thermococci , and Cellulophaga .

CONCLUSIONS: Unique fecal microbiome signatures exist in CRC patients with T2DM compared to those with non-diabetic CRC. Alterations in GM composition and SCFAs and secondary BAs levels may promote CRC development.}, } @article {pmid36959175, year = {2023}, author = {Bjerg, JJ and Lustermans, JJM and Marshall, IPG and Mueller, AJ and Brokjær, S and Thorup, CA and Tataru, P and Schmid, M and Wagner, M and Nielsen, LP and Schramm, A}, title = {Cable bacteria with electric connection to oxygen attract flocks of diverse bacteria.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1614}, pmid = {36959175}, issn = {2041-1723}, mesh = {Oxidation-Reduction ; *Oxygen ; Geologic Sediments/microbiology ; *Deltaproteobacteria ; Bacteria/genetics ; Sulfides ; }, abstract = {Cable bacteria are centimeter-long filamentous bacteria that conduct electrons via internal wires, thus coupling sulfide oxidation in deeper, anoxic sediment with oxygen reduction in surface sediment. This activity induces geochemical changes in the sediment, and other bacterial groups appear to benefit from the electrical connection to oxygen. Here, we report that diverse bacteria swim in a tight flock around the anoxic part of oxygen-respiring cable bacteria and disperse immediately when the connection to oxygen is disrupted (by cutting the cable bacteria with a laser). Raman microscopy shows that flocking bacteria are more oxidized when closer to the cable bacteria, but physical contact seems to be rare and brief, which suggests potential transfer of electrons via unidentified soluble intermediates. Metagenomic analysis indicates that most of the flocking bacteria appear to be aerobes, including organotrophs, sulfide oxidizers, and possibly iron oxidizers, which might transfer electrons to cable bacteria for respiration. The association and close interaction with such diverse partners might explain how oxygen via cable bacteria can affect microbial communities and processes far into anoxic environments.}, } @article {pmid36958817, year = {2023}, author = {Vich Vila, A and Hu, S and Andreu-Sánchez, S and Collij, V and Jansen, BH and Augustijn, HE and Bolte, LA and Ruigrok, RAAA and Abu-Ali, G and Giallourakis, C and Schneider, J and Parkinson, J and Al-Garawi, A and Zhernakova, A and Gacesa, R and Fu, J and Weersma, RK}, title = {Faecal metabolome and its determinants in inflammatory bowel disease.}, journal = {Gut}, volume = {72}, number = {8}, pages = {1472-1485}, pmid = {36958817}, issn = {1468-3288}, mesh = {Humans ; Genome-Wide Association Study ; *Inflammatory Bowel Diseases/metabolism ; *Colitis, Ulcerative/metabolism ; Metabolome ; Feces ; *Arylamine N-Acetyltransferase/metabolism ; }, abstract = {OBJECTIVE: Inflammatory bowel disease (IBD) is a multifactorial immune-mediated inflammatory disease of the intestine, comprising Crohn's disease and ulcerative colitis. By characterising metabolites in faeces, combined with faecal metagenomics, host genetics and clinical characteristics, we aimed to unravel metabolic alterations in IBD.

DESIGN: We measured 1684 different faecal metabolites and 8 short-chain and branched-chain fatty acids in stool samples of 424 patients with IBD and 255 non-IBD controls. Regression analyses were used to compare concentrations of metabolites between cases and controls and determine the relationship between metabolites and each participant's lifestyle, clinical characteristics and gut microbiota composition. Moreover, genome-wide association analysis was conducted on faecal metabolite levels.

RESULTS: We identified over 300 molecules that were differentially abundant in the faeces of patients with IBD. The ratio between a sphingolipid and L-urobilin could discriminate between IBD and non-IBD samples (AUC=0.85). We found changes in the bile acid pool in patients with dysbiotic microbial communities and a strong association between faecal metabolome and gut microbiota. For example, the abundance of Ruminococcus gnavus was positively associated with tryptamine levels. In addition, we found 158 associations between metabolites and dietary patterns, and polymorphisms near NAT2 strongly associated with coffee metabolism.

CONCLUSION: In this large-scale analysis, we identified alterations in the metabolome of patients with IBD that are independent of commonly overlooked confounders such as diet and surgical history. Considering the influence of the microbiome on faecal metabolites, our results pave the way for future interventions targeting intestinal inflammation.}, } @article {pmid36958333, year = {2023}, author = {Begg, TJA and Schmidt, A and Kocher, A and Larmuseau, MHD and Runfeldt, G and Maier, PA and Wilson, JD and Barquera, R and Maj, C and Szolek, A and Sager, M and Clayton, S and Peltzer, A and Hui, R and Ronge, J and Reiter, E and Freund, C and Burri, M and Aron, F and Tiliakou, A and Osborn, J and Behar, DM and Boecker, M and Brandt, G and Cleynen, I and Strassburg, C and Prüfer, K and Kühnert, D and Meredith, WR and Nöthen, MM and Attenborough, RD and Kivisild, T and Krause, J}, title = {Genomic analyses of hair from Ludwig van Beethoven.}, journal = {Current biology : CB}, volume = {33}, number = {8}, pages = {1431-1447.e22}, doi = {10.1016/j.cub.2023.02.041}, pmid = {36958333}, issn = {1879-0445}, mesh = {Male ; Humans ; Genetic Predisposition to Disease ; *Famous Persons ; *Deafness ; Genomics ; *Music ; Hair ; }, abstract = {Ludwig van Beethoven (1770-1827) remains among the most influential and popular classical music composers. Health problems significantly impacted his career as a composer and pianist, including progressive hearing loss, recurring gastrointestinal complaints, and liver disease. In 1802, Beethoven requested that following his death, his disease be described and made public. Medical biographers have since proposed numerous hypotheses, including many substantially heritable conditions. Here we attempt a genomic analysis of Beethoven in order to elucidate potential underlying genetic and infectious causes of his illnesses. We incorporated improvements in ancient DNA methods into existing protocols for ancient hair samples, enabling the sequencing of high-coverage genomes from small quantities of historical hair. We analyzed eight independently sourced locks of hair attributed to Beethoven, five of which originated from a single European male. We deemed these matching samples to be almost certainly authentic and sequenced Beethoven's genome to 24-fold genomic coverage. Although we could not identify a genetic explanation for Beethoven's hearing disorder or gastrointestinal problems, we found that Beethoven had a genetic predisposition for liver disease. Metagenomic analyses revealed furthermore that Beethoven had a hepatitis B infection during at least the months prior to his death. Together with the genetic predisposition and his broadly accepted alcohol consumption, these present plausible explanations for Beethoven's severe liver disease, which culminated in his death. Unexpectedly, an analysis of Y chromosomes sequenced from five living members of the Van Beethoven patrilineage revealed the occurrence of an extra-pair paternity event in Ludwig van Beethoven's patrilineal ancestry.}, } @article {pmid36958260, year = {2023}, author = {Sugiyama, Y and Takata, K and Kinoshita, M and Motooka, D and Shiraishi, N and Kihara, K and Murata, H and Beppu, S and Koda, T and Yamashita, K and Namba, A and Fujimoto, K and Kumanogoh, A and Okuno, T and Mochizuki, H}, title = {Food additive succinate exacerbates experimental autoimmune encephalomyelitis accompanied by increased IL-1β production.}, journal = {Biochemical and biophysical research communications}, volume = {656}, number = {}, pages = {97-103}, doi = {10.1016/j.bbrc.2023.03.041}, pmid = {36958260}, issn = {1090-2104}, mesh = {Animals ; Humans ; Mice ; *Encephalomyelitis, Autoimmune, Experimental ; Food Additives ; Succinic Acid ; Signal Transduction ; Mice, Inbred C57BL ; }, } @article {pmid36958034, year = {2023}, author = {Farrington, M and Elenz, J and Ginsberg, M and Chiu, CY and Miller, S and Pangonis, SF}, title = {Powassan Virus Infection Detected by Metagenomic Next-Generation Sequencing, Ohio, USA.}, journal = {Emerging infectious diseases}, volume = {29}, number = {4}, pages = {838-841}, pmid = {36958034}, issn = {1080-6059}, mesh = {Male ; Humans ; Child, Preschool ; *Encephalitis Viruses, Tick-Borne ; *Encephalitis, Tick-Borne/epidemiology ; Ohio/epidemiology ; *Encephalitis ; High-Throughput Nucleotide Sequencing ; }, abstract = {We describe a 4-year-old male patient in Ohio, USA, who had encephalitis caused by Powassan virus lineage 2. Virus was detected by using metagenomic next-generation sequencing and confirmed with IgM and plaque reduction neutralization assays. Clinicians should recognize changing epidemiology of tickborne viruses to enhance encephalitis diagnosis and management.}, } @article {pmid36957994, year = {2023}, author = {Martin, NA and Gonzalez, G and Reynolds, LJ and Bennett, C and Campbell, C and Nolan, TM and Byrne, A and Fennema, S and Holohan, N and Kuntamukkula, SR and Sarwar, N and Sala-Comorera, L and Dean, J and Urtasun-Elizari, JM and Hare, D and Liddy, E and Joyce, E and O'Sullivan, JJ and Cuddihy, JM and McIntyre, AM and Robinson, EP and Dahly, D and Fletcher, NF and Cotter, S and Fitzpatrick, E and Carr, MJ and De Gascun, CF and Meijer, WG}, title = {Adeno-Associated Virus 2 and Human Adenovirus F41 in Wastewater during Outbreak of Severe Acute Hepatitis in Children, Ireland.}, journal = {Emerging infectious diseases}, volume = {29}, number = {4}, pages = {751-760}, pmid = {36957994}, issn = {1080-6059}, mesh = {Humans ; Child ; Wastewater ; Ireland/epidemiology ; *Adenoviruses, Human/genetics ; *Hepatitis/epidemiology ; Disease Outbreaks ; Acute Disease ; *Adenovirus Infections, Human/epidemiology ; Phylogeny ; *Respiratory Tract Infections/epidemiology ; }, abstract = {During April-July 2022, outbreaks of severe acute hepatitis of unknown etiology (SAHUE) were reported in 35 countries. Five percent of cases required liver transplantation, and 22 patients died. Viral metagenomic studies of clinical samples from SAHUE cases showed a correlation with human adenovirus F type 41 (HAdV-F41) and adeno-associated virus type 2 (AAV2). To explore the association between those DNA viruses and SAHUE in children in Ireland, we quantified HAdV-F41 and AAV2 in samples collected from a wastewater treatment plant serving 40% of Ireland's population. We noted a high correlation between HAdV-F41 and AAV2 circulation in the community and SAHUE clinical cases. Next-generation sequencing of the adenovirus hexon in wastewater demonstrated HAdV-F41 was the predominant HAdV type circulating. Our environmental analysis showed increased HAdV-F41 and AAV2 prevalence in the community during the SAHUE outbreak. Our findings highlight how wastewater sampling could aid in surveillance for respiratory adenovirus species.}, } @article {pmid36952228, year = {2023}, author = {Lai, JL and Li, ZG and Wang, Y and Xi, HL and Luo, XG}, title = {Tritium and Carbon-14 Contamination Reshaping the Microbial Community Structure, Metabolic Network, and Element Cycle in the Seawater Environment.}, journal = {Environmental science & technology}, volume = {57}, number = {13}, pages = {5305-5316}, doi = {10.1021/acs.est.3c00422}, pmid = {36952228}, issn = {1520-5851}, mesh = {Carbon Radioisotopes/metabolism ; Tritium/metabolism ; *Bacteria/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Seawater ; Metabolic Networks and Pathways ; Carbon/metabolism ; Nitrogen/metabolism ; Phosphorus/metabolism ; Geologic Sediments/chemistry ; }, abstract = {The potential ecological risks caused by entering radioactive wastewater containing tritium and carbon-14 into the sea require careful evaluation. This study simulated seawater's tritium and carbon-14 pollution and analyzed the effects on the seawater and sediment microenvironments. Tritium and carbon-14 pollution primarily altered nitrogen and phosphorus metabolism in the seawater environment. Analysis by 16S rRNA sequencing showed changes in the relative abundance of microorganisms involved in carbon, nitrogen, and phosphorus metabolism and organic matter degradation in response to tritium and carbon-14 exposure. Metabonomics and metagenomic analysis showed that tritium and carbon-14 exposure interfered with gene expression involving nucleotide and amino acid metabolites, in agreement with the results seen for microbial community structure. Tritium and carbon-14 exposure also modulated the abundance of functional genes involved in carbohydrate, phosphorus, sulfur, and nitrogen metabolic pathways in sediments. Tritium and carbon-14 pollution in seawater adversely affected microbial diversity, metabolic processes, and the abundance of nutrient-cycling genes. These results provide valuable information for further evaluating the risks of tritium and carbon-14 in marine environments.}, } @article {pmid36951567, year = {2023}, author = {Goswami, A and Adkins-Jablonsky, SJ and Barreto Filho, MM and Shilling, MD and Dawson, A and Heiser, S and O'Connor, A and Walker, M and Roberts, Q and Morris, JJ}, title = {Heavy Metal Pollution Impacts Soil Bacterial Community Structure and Antimicrobial Resistance at the Birmingham 35th Avenue Superfund Site.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0242622}, pmid = {36951567}, issn = {2165-0497}, abstract = {Heavy metals (HMs) are known to modify bacterial communities both in the laboratory and in situ. Consequently, soils in HM-contaminated sites such as the U.S. Environmental Protection Agency (EPA) Superfund sites are predicted to have altered ecosystem functioning, with potential ramifications for the health of organisms, including humans, that live nearby. Further, several studies have shown that heavy metal-resistant (HMR) bacteria often also display antimicrobial resistance (AMR), and therefore HM-contaminated soils could potentially act as reservoirs that could disseminate AMR genes into human-associated pathogenic bacteria. To explore this possibility, topsoil samples were collected from six public locations in the zip code 35207 (the home of the North Birmingham 35th Avenue Superfund Site) and in six public areas in the neighboring zip code, 35214. 35027 soils had significantly elevated levels of the HMs As, Mn, Pb, and Zn, and sequencing of the V4 region of the bacterial 16S rRNA gene revealed that elevated HM concentrations correlated with reduced microbial diversity and altered community structure. While there was no difference between zip codes in the proportion of total culturable HMR bacteria, bacterial isolates with HMR almost always also exhibited AMR. Metagenomes inferred using PICRUSt2 also predicted significantly higher mean relative frequencies in 35207 for several AMR genes related to both specific and broad-spectrum AMR phenotypes. Together, these results support the hypothesis that chronic HM pollution alters the soil bacterial community structure in ecologically meaningful ways and may also select for bacteria with increased potential to contribute to AMR in human disease. IMPORTANCE Heavy metals cross-select for antimicrobial resistance in laboratory experiments, but few studies have documented this effect in polluted soils. Moreover, despite decades of awareness of heavy metal contamination at the EPA Superfund site in North Birmingham, Alabama, this is the first analysis of the impact of this pollution on the soil microbiome. Specifically, this work advances the understanding of the relationship between heavy metals, microbial diversity, and patterns of antibiotic resistance in North Birmingham soils. Our results suggest that polluted soils carry a risk of increased exposure to antibiotic-resistant infections in addition to the direct health consequences of heavy metals. Our work provides important information relevant to both political and scientific efforts to advance environmental justice for the communities that call Superfund neighborhoods home.}, } @article {pmid36951557, year = {2023}, author = {Wells, M and Kim, M and Akob, DM and Basu, P and Stolz, JF}, title = {Impact of the Dimethyl Sulfoxide Reductase Superfamily on the Evolution of Biogeochemical Cycles.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0414522}, pmid = {36951557}, issn = {2165-0497}, abstract = {The dimethyl sulfoxide reductase (or MopB) family is a diverse assemblage of enzymes found throughout Bacteria and Archaea. Many of these enzymes are believed to have been present in the last universal common ancestor (LUCA) of all cellular lineages. However, gaps in knowledge remain about how MopB enzymes evolved and how this diversification of functions impacted global biogeochemical cycles through geologic time. In this study, we perform maximum likelihood phylogenetic analyses on manually curated comparative genomic and metagenomic data sets containing over 47,000 distinct MopB homologs. We demonstrate that these enzymes constitute a catalytically and mechanistically diverse superfamily defined not by the molybdopterin- or tungstopterin-containing [molybdopterin or tungstopterin bis(pyranopterin guanine dinucleotide) (Mo/W-bisPGD)] cofactor but rather by the structural fold that binds it in the protein. Our results suggest that major metabolic innovations were the result of the loss of the metal cofactor or the gain or loss of protein domains. Phylogenetic analyses also demonstrated that formate oxidation and CO2 reduction were the ancestral functions of the superfamily, traits that have been vertically inherited from the LUCA. Nearly all of the other families, which drive all other biogeochemical cycles mediated by this superfamily, originated in the bacterial domain. Thus, organisms from Bacteria have been the key drivers of catalytic and biogeochemical innovations within the superfamily. The relative ordination of MopB families and their associated catalytic activities emphasize fundamental mechanisms of evolution in this superfamily. Furthermore, it underscores the importance of prokaryotic adaptability in response to the transition from an anoxic to an oxidized atmosphere. IMPORTANCE The MopB superfamily constitutes a repertoire of metalloenzymes that are central to enduring mysteries in microbiology, from the origin of life and how microorganisms and biogeochemical cycles have coevolved over deep time to how anaerobic life adapted to increasing concentrations of O2 during the transition from an anoxic to an oxic world. Our work emphasizes that phylogenetic analyses can reveal how domain gain or loss events, the acquisition of novel partner subunits, and the loss of metal cofactors can stimulate novel radiations of enzymes that dramatically increase the catalytic versatility of superfamilies. We also contend that the superfamily concept in protein evolution can uncover surprising kinships between enzymes that have remarkably different catalytic and physiological functions.}, } @article {pmid36951555, year = {2023}, author = {Chu, Y and Meng, Q and Yu, J and Zhang, J and Chen, J and Kang, Y}, title = {Strain-Level Dynamics Reveal Regulatory Roles in Atopic Eczema by Gut Bacterial Phages.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0455122}, pmid = {36951555}, issn = {2165-0497}, abstract = {The vast population of bacterial phages or viruses (virome) plays pivotal roles in the ecology of human microbial flora and health conditions. Obstacles, including poor viral sequence inference, strain-sensitive virus-host relationship, and the high diversity among individuals, hinder the in-depth understanding of the human virome. We conducted longitudinal studies of the virome based on constructing a high-quality personal reference metagenome (PRM). By applying long-read sequencing for representative samples, we could build a PRM of high continuity that allows accurate annotation and abundance estimation of viruses and bacterial species in all samples of the same individual by aligning short sequencing reads to the PRM. We applied this approach to a series of fecal samples collected for 6 months from a 2-year-old boy who had experienced a 2-month flare-up of atopic eczema (dermatitis) in this period. We identified 31 viral strains in the patient's gut microbiota and deciphered their strain-level relationship to their bacterial hosts. Among them, a lytic crAssphage developed into a dozen substrains and coordinated downregulation in the catabolism of aromatic amino acids (AAAs) in their host bacteria which govern the production of immune-active AAA derivates. The metabolic alterations confirmed based on metabolomic assays cooccurred with symptom remission. Our PRM-based analysis provides an easy approach for deciphering the dynamics of the strain-level human gut virome in the context of entire microbiota. Close temporal correlations among virome alteration, microbial metabolism, and disease remission suggest a potential mechanism for how bacterial phages in microbiota are intimately related to human health. IMPORTANCE The vast populations of viruses or bacteriophages in human gut flora remain mysterious. However, poor annotation and abundance estimation remain obstacles to strain-level analysis and clarification of their roles in microbiome ecology and metabolism associated with human health and diseases. We demonstrate that a personal reference metagenome (PRM)-based approach provides strain-level resolution for analyzing the gut microbiota-associated virome. When applying such an approach to longitudinal samples collected from a 2-year-old boy who has experienced a 2-month flare-up of atopic eczema, we observed thriving substrains of a lytic crAssphage, showing temporal correlation with downregulated catabolism of aromatic amino acids, lower production of immune-active metabolites, and remission of the disease. The PRM-based approach is practical and powerful for strain-centric analysis of the human gut virome, and the underlying mechanism of how strain-level virome dynamics affect disease deserves further investigation.}, } @article {pmid36950986, year = {2023}, author = {Gao, B and Shi, X and Li, S and Xu, W and Gao, N and Shan, J and Shen, W}, title = {Size-dependent effects of polystyrene microplastics on gut metagenome and antibiotic resistance in C57BL/6 mice.}, journal = {Ecotoxicology and environmental safety}, volume = {254}, number = {}, pages = {114737}, doi = {10.1016/j.ecoenv.2023.114737}, pmid = {36950986}, issn = {1090-2414}, mesh = {Humans ; Animals ; Mice ; *Polystyrenes/toxicity/analysis ; Microplastics/toxicity ; Plastics ; Metagenome ; Ecosystem ; Mice, Inbred C57BL ; Drug Resistance, Microbial ; *Water Pollutants, Chemical/toxicity/analysis ; }, abstract = {Microplastic pollution is an emerging threat for marine and terrestrial ecosystems, which has raised global concerns about its implications for human health. Mounting evidence has shown that the gut microbiota plays a key role in human health and diseases. The gut bacteria could be disturbed by many environmental factors, including the microplastic particles. However, the size effect of polystyrene microplastics on mycobiome, as well as gut functional metagenome has not been well studied. In this study, we performed ITS sequencing to explore the size effect of polystyrene microplastics on the fungal composition, in combination with the shotgun metagenomics sequencing to reveal the size effects of polystyrene on the functional metagenome. We found that polystyrene microplastic particles with 0.05-0.1 µm diameter showed greater impact on the bacterial and fungal composition of gut microbiota as well as the metabolic pathways than the polystyrene microplastic particles with 9-10 µm diameter. Our results suggested that size-depended effects should not be ignored in the health risk assessment of microplastics.}, } @article {pmid36950589, year = {2023}, author = {Fabunmi, BT and Adegaye, AC and Ogunjo, ST}, title = {Identification and characterization of molecular entities differentially expressed in bacteria genome upon treatment with glyphosate shock.}, journal = {Heliyon}, volume = {9}, number = {3}, pages = {e13868}, pmid = {36950589}, issn = {2405-8440}, abstract = {Antimetabolites developed from enzymes in the shikimate pathway are appealing targets. There are, however, certain unidentified molecular entities that show bacterial sensitivity to glyphosate shock. This study aims to identify the expression pattern of such entities following treatment with glyphosate shock and to characterize them structurally and functionally. Understanding such entities' catalytic structure and modulatory role guides the design and development of novel antibiotics. This study's functional profiling of 16S rRNA sequencing data and transcriptome analysis of glyphosate-exposedE. coli revealed that two genes were upregulated and twenty-eight were downregulated after glyphosate shock. We discovered the differential expression of some processes based on functional gene analysis, such as global and overview maps (4.2195 on average), carbohydrate metabolism (0.6858 on average), amino acid metabolism (0.5032 on average), and co-factor and vitamin metabolism (0.5032 on average) (0.2876 on average). After examining the two data sets, we discovered that some unidentified proteins were strongly expressed after glyphosate treatment. After examining the two datasets, we discovered a protein with no unique features expressed when treated with glyphosate. The Ecs2020 model looks to be the most stable in structural modeling investigations, while the catalytic residues sought in drug development are anticipated. Furthermore, biological processes and cellular component enrichment analysis revealed that the differentially expressed genes were strongly related to the trehalose manufacturing process and represented the cell membrane's outer membrane component. To estimate the functional gene content of soil sample metagenomics based on 16S rRNA, predictive functional analysis was done with R using the Tax4Fun2 package. On the other hand, transcriptome analysis was carried out using the R tool GEO2R. The results could be a good starting point for making new antibiotic medicines.}, } @article {pmid36950329, year = {2023}, author = {Han, J and Kong, T and Jiang, J and Zhao, X and Zhao, X and Li, P and Gu, Q}, title = {Characteristic flavor metabolic network of fish sauce microbiota with different fermentation processes based on metagenomics.}, journal = {Frontiers in nutrition}, volume = {10}, number = {}, pages = {1121310}, pmid = {36950329}, issn = {2296-861X}, abstract = {This article purposed to discuss the connection between microbiota and characteristic flavor of different fish sauces (Natural fermentation (WQ), koji outdoor fermentation (YQ), heat preservation with enzyme (BWE), and heat preservation with koji (BWQ)) at the early (3 months) and late stage (7 months). A total of 117 flavor compounds were determined according to SPME-GC-MS analysis. O2PLS-DA and VIP values were used to reveal 15 and 28 flavor markers of different fish sauces at 3 and 7 M of fermentation. Further, the possible flavor formation pathways were analyzed using metagenomic sequencing, and the key microbes associated with flavor formation were identified at the genetic level. The top 10 genera related to flavor generation, such as Lactobacillus, Staphylococcus, Enterobacter, etc., appeared to play a prominent part in the flavor formation of fish sauce. The difference was that only BWQ and BWE groups could produce ethyl-alcohol through amino acid metabolism, while YQ, BWE and BWQ groups could generate phenylacetaldehyde through the transformation of Phe by α-ketoacid decarboxylase and aromatic amino acid transferase. Our research contributes to clarifying the various metabolic roles of microorganisms in the flavor generation of fish sauce.}, } @article {pmid36950183, year = {2023}, author = {Luciola Zanette, D and Andrade Coelho, KBC and de Carvalho, E and Aoki, MN and Nardin, JM and Araújo Lalli, L and Dos Santos Bezerra, R and Giovanetti, M and Simionatto Zucherato, V and Montenegro de Campos, G and de Souza Todão Bernardino, J and Louis Viala, V and Ciccozzi, M and Junior Alcantara, LC and Coccuzzo Sampaio, S and Elias, MC and Kashima, S and Tadeu Covas, D and Nanev Slavov, S}, title = {Metagenomic insights into the plasma virome of Brazilian patients with prostate cancer.}, journal = {Molecular & cellular oncology}, volume = {10}, number = {1}, pages = {2188858}, pmid = {36950183}, issn = {2372-3556}, abstract = {Growing evidence suggests that metavirome changes could be associated increased risk for malignant cell transformation. Considering Viruses have been proposed as factors for prostate cancer induction. The objective of this study was to examine the composition of the plasma metavirome of patients with prostate cancer. Blood samples were obtained from 49 male patients with primary prostate adenocarcinoma. Thirty blood donors were included as a control group. The obtained next-generation sequencing data were analyzed using a bioinformatic pipeline for virus metagenomics. Viral reads with higher abundance were assembled in contigs and analyzed taxonomically. Viral agents of interest were also confirmed by qPCR. Anelloviruses and the Human Pegivirus-1 (HPgV-1) were the most abundant component of plasma metavirome. Clinically important viruses like hepatitis C virus (HCV), cytomegalovirus and human adenovirus type C were also identified. In comparison, the blood donor virome was exclusively composed of torque teno virus types (TTV) types. The performed HPgV-1 and HCV phylogeny revealed that these viruses belong to commonly detected in Brazil genotypes. Our study sheds light on the plasma viral abundance in patients with prostatic cancer. The obtained viral diversity allowed us to separate the patients and controls, probably suggesting that malignant processes may influence virome composition. More complex and multiple approach investigations are necessary to examine the likely causal relationship between metavirome and its nvolvement in prostate cancer.}, } @article {pmid36949817, year = {2023}, author = {Viehweger, A and Marquet, M and Hölzer, M and Dietze, N and Pletz, MW and Brandt, C}, title = {Nanopore-based enrichment of antimicrobial resistance genes - a case-based study.}, journal = {GigaByte (Hong Kong, China)}, volume = {2023}, number = {}, pages = {gigabyte75}, pmid = {36949817}, issn = {2709-4715}, abstract = {Rapid screening of hospital admissions to detect asymptomatic carriers of resistant bacteria can prevent pathogen outbreaks. However, the resulting isolates rarely have their genome sequenced due to cost constraints and long turn-around times to get and process the data, limiting their usefulness to the practitioner. Here we used real-time, on-device target enrichment ("adaptive") sequencing as a highly multiplexed assay covering 1,147 antimicrobial resistance genes. We compared its utility against standard and metagenomic sequencing, focusing on an isolate of Raoultella ornithinolytica harbouring three carbapenemases (NDM, KPC, VIM). Based on this experimental data, we then modelled the influence of several variables on the enrichment results and predicted the large effect of nucleotide identity (higher is better) and read length (shorter is better). Lastly, we showed how all relevant resistance genes are detected using adaptive sequencing on a miniature ("Flongle") flow cell, motivating its use in a clinical setting to monitor similar cases and their surroundings.}, } @article {pmid36949609, year = {2023}, author = {Hagh-Doust, N and Mikryukov, V and Anslan, S and Bahram, M and Puusepp, R and Dulya, O and Tedersoo, L}, title = {Effects of nitrogen deposition on carbon and nutrient cycling along a natural soil acidity gradient as revealed by metagenomics.}, journal = {The New phytologist}, volume = {238}, number = {6}, pages = {2607-2620}, doi = {10.1111/nph.18897}, pmid = {36949609}, issn = {1469-8137}, mesh = {*Ecosystem ; Soil/chemistry ; Nitrogen/metabolism ; Carbon/metabolism ; Forests ; *Microbiota ; Soil Microbiology ; }, abstract = {Nitrogen (N) deposition and soil acidification are environmental challenges affecting ecosystem functioning, health, and biodiversity, but their effects on functional genes are poorly understood. Here, we utilized metabarcoding and metagenomics to investigate the responses of soil functional genes to N deposition along a natural soil pH gradient. Soil N content was uncorrelated with pH, enabling us to investigate their effects separately. Soil acidity strongly and negatively affected the relative abundances of most cluster of orthologous gene categories of the metabolism supercategory. Similarly, soil acidity negatively affected the diversity of functional genes related to carbon and N but not phosphorus cycling. Multivariate analyses showed that soil pH was the most important factor affecting microbial and functional gene composition, while the effects of N deposition were less important. Relative abundance of KEGG functional modules related to different parts of the studied cycles showed variable responses to soil acidity and N deposition. Furthermore, our results suggested that the diversity-function relationship reported for other organisms also applies to soil microbiomes. Since N deposition and soil pH affected microbial taxonomic and functional composition to a different extent, we conclude that N deposition effects might be primarily mediated through soil acidification in forest ecosystems.}, } @article {pmid36949545, year = {2023}, author = {Graham, EH and Tom, WA and Neujahr, AC and Adamowicz, MS and Clarke, JL and Herr, JR and Fernando, SC}, title = {The persistence and stabilization of auxiliary genes in the human skin virome.}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {49}, pmid = {36949545}, issn = {1743-422X}, mesh = {Humans ; Virome ; *Bacteriophages/genetics ; *Viruses/genetics ; *Microbiota ; Metagenome ; Bacteria/genetics ; }, abstract = {BACKGROUND: The human skin contains a diverse microbiome that provides protective functions against environmental pathogens. Studies have demonstrated that bacteriophages modulate bacterial community composition and facilitate the transfer of host-specific genes, potentially influencing host cellular functions. However, little is known about the human skin virome and its role in human health. Especially, how viral-host relationships influence skin microbiome structure and function is poorly understood.

RESULTS: Population dynamics and genetic diversity of bacteriophage communities in viral metagenomic data collected from three anatomical skin locations from 60 subjects at five different time points revealed that cutaneous bacteriophage populations are mainly composed of tailed Caudovirales phages that carry auxiliary genes to help improve metabolic remodeling to increase bacterial host fitness through antimicrobial resistance. Sequence variation in the MRSA associated antimicrobial resistance gene, erm(C) was evaluated using targeted sequencing to further confirm the presence of antimicrobial resistance genes in the human virome and to demonstrate how functionality of such genes may influence persistence and in turn stabilization of bacterial host and their functions.

CONCLUSIONS: This large temporal study of human skin associated viruses indicates that the human skin virome is associated with auxiliary metabolic genes and antimicrobial resistance genes to help increase bacterial host fitness.}, } @article {pmid36949471, year = {2023}, author = {Volmer, JG and Soo, RM and Evans, PN and Hoedt, EC and Astorga Alsina, AL and Woodcroft, BJ and Tyson, GW and Hugenholtz, P and Morrison, M}, title = {Isolation and characterisation of novel Methanocorpusculum species indicates the genus is ancestrally host-associated.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {59}, pmid = {36949471}, issn = {1741-7007}, mesh = {Animals ; Australia ; *Methane/metabolism ; Metagenome ; *Microbiota ; }, abstract = {BACKGROUND: With an increasing interest in the manipulation of methane produced from livestock cultivation, the microbiome of Australian marsupials provides a unique ecological and evolutionary comparison with 'low-methane' emitters. Previously, marsupial species were shown to be enriched for novel lineages of Methanocorpusculum, as well as Methanobrevibacter, Methanosphaera, and Methanomassiliicoccales. Despite sporadic reports of Methanocorpusculum from stool samples of various animal species, there remains little information on the impacts of these methanogens on their hosts.

RESULTS: Here, we characterise novel host-associated species of Methanocorpusculum, to explore unique host-specific genetic factors and their associated metabolic potential. We performed comparative analyses on 176 Methanocorpusculum genomes comprising 130 metagenome-assembled genomes (MAGs) recovered from 20 public animal metagenome datasets and 35 other publicly available Methanocorpusculum MAGs and isolate genomes of host-associated and environmental origin. Nine MAGs were also produced from faecal metagenomes of the common wombat (Vombatus ursinus) and mahogany glider (Petaurus gracilis), along with the cultivation of one axenic isolate from each respective animal; M. vombati (sp. nov.) and M. petauri (sp. nov.).

CONCLUSIONS: Through our analyses, we substantially expand the available genetic information for this genus by describing the phenotypic and genetic characteristics of 23 host-associated species of Methanocorpusculum. These lineages display differential enrichment of genes associated with methanogenesis, amino acid biosynthesis, transport system proteins, phosphonate metabolism, and carbohydrate-active enzymes. These results provide insights into the differential genetic and functional adaptations of these novel host-associated species of Methanocorpusculum and suggest that this genus is ancestrally host-associated.}, } @article {pmid36949342, year = {2023}, author = {Nosalova, L and Kiskova, J and Fecskeova, LK and Piknova, M and Pristas, P}, title = {Bacterial Community Structure of Two Cold Sulfur Springs in Slovakia (Central Europe).}, journal = {Current microbiology}, volume = {80}, number = {5}, pages = {145}, pmid = {36949342}, issn = {1432-0991}, support = {VVGS-PF-2021-1745//Pavol Jozef Safarik University/ ; }, mesh = {Slovakia ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Biodiversity ; Bacteria ; *Hot Springs/microbiology ; Sulfur ; }, abstract = {Sulfur-oxidizing bacteria, especially those from hot springs, have attracted the attention of microbiologists for more than 150 years. In contrast, the microbial diversity of cold sulfur springs remains largely unrecognized. Culture-dependent and culture-independent approaches were used to study the diversity of sulfur-oxidizing bacterial communities in two cold sulfur springs in Slovakia. Geological conditions and resulting spring water chemistry appear to be major factors influencing the composition of the sulfur-oxidizing bacterial community. Bacterial communities in both springs were found to be dominated by Proteobacteria with Epsilonproteobacteria being prevalent in the high-salinity Stankovany spring and Alpha- and Gammaproteobacteria in the low-salinity Jovsa spring. Limited overlap was found between culture-dependent and culture-independent approaches with multiple taxa of cultivated sulfur-oxidizing bacteria not being detected by the culture-independent metagenomics approach. Moreover, four cultivated bacterial isolates could represent novel taxa based on the low similarity of their 16S rRNA gene sequence (similarity lower than 98%) to sequences of known bacteria. Our study supports the current view that multiple approaches are required to assess the bacterial diversity in natural habitats and indicates that sulfur springs in Slovakia harbor unique, yet-undescribed microorganisms.}, } @article {pmid36949220, year = {2023}, author = {Lynes, MM and Krukenberg, V and Jay, ZJ and Kohtz, AJ and Gobrogge, CA and Spietz, RL and Hatzenpichler, R}, title = {Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {22}, pmid = {36949220}, issn = {2730-6151}, support = {DBI-1736255//National Science Foundation (NSF)/ ; DBI-1736255//National Science Foundation (NSF)/ ; DBI-1736255//National Science Foundation (NSF)/ ; DBI-1736255//National Science Foundation (NSF)/ ; DBI-1736255//National Science Foundation (NSF)/ ; DBI-1736255//National Science Foundation (NSF)/ ; DBI-1736255//National Science Foundation (NSF)/ ; }, abstract = {Metagenomic studies on geothermal environments have been central in recent discoveries on the diversity of archaeal methane and alkane metabolism. Here, we investigated methanogenic populations inhabiting terrestrial geothermal features in Yellowstone National Park (YNP) by combining amplicon sequencing with metagenomics and mesocosm experiments. Detection of methyl-coenzyme M reductase subunit A (mcrA) gene amplicons demonstrated a wide diversity of Mcr-encoding archaea inhabit geothermal features with differing physicochemical regimes across YNP. From three selected hot springs we recovered twelve Mcr-encoding metagenome assembled genomes (MAGs) affiliated with lineages of cultured methanogens as well as Candidatus (Ca.) Methanomethylicia, Ca. Hadesarchaeia, and Archaeoglobi. These MAGs encoded the potential for hydrogenotrophic, aceticlastic, hydrogen-dependent methylotrophic methanogenesis, or anaerobic short-chain alkane oxidation. While Mcr-encoding archaea represent minor fractions of the microbial community of hot springs, mesocosm experiments with methanogenic precursors resulted in the stimulation of methanogenic activity and the enrichment of lineages affiliated with Methanosaeta and Methanothermobacter as well as with uncultured Mcr-encoding archaea including Ca. Korarchaeia, Ca. Nezhaarchaeia, and Archaeoglobi. We revealed that diverse Mcr-encoding archaea with the metabolic potential to produce methane from different precursors persist in the geothermal environments of YNP and can be enriched under methanogenic conditions. This study highlights the importance of combining environmental metagenomics with laboratory-based experiments to expand our understanding of uncultured Mcr-encoding archaea and their potential impact on microbial carbon transformations in geothermal environments and beyond.}, } @article {pmid36948449, year = {2023}, author = {Wang, C and Wang, J and Yan, J and Chen, F and Zhang, Y and Hu, X}, title = {Mycoplasma hominis, Ureaplasma parvum, and Ureaplasma urealyticum: hidden pathogens in peritoneal dialysis-associated peritonitis.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {131}, number = {}, pages = {13-15}, doi = {10.1016/j.ijid.2023.03.032}, pmid = {36948449}, issn = {1878-3511}, mesh = {Humans ; Female ; Male ; Ureaplasma urealyticum/genetics ; Ureaplasma ; Mycoplasma hominis/genetics ; *Mycoplasma Infections ; *Peritoneal Dialysis/adverse effects ; }, abstract = {Mycoplasma hominis, Ureaplasma parvum, and Ureaplasma urealyticum commonly colonize the human urogenital tract, which may cause urogenital infections. However, infection by M. hominis, U. parvum, or U. urealyticum is rarely reported in patients with peritoneal dialysis (PD)-associated peritonitis. Herein, we reported four cases of PD-associated peritonitis caused by these pathogens, along with a review of the literature. The four cases were female patients with recurrent "culture-negative" PD-associated peritonitis and were related to menstruation. M. hominis, U. parvum, or U. urealyticum was detected in the PD fluid of the patients by metagenomic next-generation sequencing. All four patients were cured by intraperitoneal tigecycline combined with oral azithromycin or minocycline. M. hominis, U. parvum, and U. urealyticum should be paid more attention in female patients with recurrent culture-negative PD-associated peritonitis, especially when the peritonitis is related to menstruation, sexual intercourse, or urogenital tract operation. Moreover, metagenomic next-generation sequencing can provide a reasonable method to identify the pathogen for culture-negative PD-associated peritonitis.}, } @article {pmid36948151, year = {2023}, author = {Toh, E and Xing, Y and Gao, X and Jordan, SJ and Batteiger, TA and Batteiger, BE and Van Der Pol, B and Muzny, CA and Gebregziabher, N and Williams, JA and Fortenberry, LJ and Fortenberry, JD and Dong, Q and Nelson, DE}, title = {Sexual behavior shapes male genitourinary microbiome composition.}, journal = {Cell reports. Medicine}, volume = {4}, number = {3}, pages = {100981}, pmid = {36948151}, issn = {2666-3791}, support = {K23 AI106957/AI/NIAID NIH HHS/United States ; R01 AI116706/AI/NIAID NIH HHS/United States ; }, mesh = {*Sexual Behavior ; *Urethra/microbiology ; *Microbiota ; Humans ; Male ; }, abstract = {The origin, composition, and significance of the distal male urethral microbiome are unclear, but vaginal microbiome dysbiosis is linked to new sex partners and several urogynecological syndromes. We characterized 110 urethral specimens from men without urethral symptoms, infections, or inflammation using shotgun metagenomics. Most urethral specimens contain characteristic lactic acid bacteria and Corynebacterium spp. In contrast, several bacteria associated with vaginal dysbiosis were present only in specimens from men who reported vaginal intercourse. Sexual behavior, but not other evaluated behavioral, demographic, or clinical variables, strongly associated with inter-specimen variance in urethral microbiome composition. Thus, the male urethra supports a simple core microbiome that is established independent of sexual exposures but can be re-shaped by vaginal sex. Overall, the results suggest that urogenital microbiology and sexual behavior are inexorably intertwined, and show that the male urethra harbors female urogenital pathobionts.}, } @article {pmid36947490, year = {2023}, author = {Highlander, SK and Wood, JM and Gillece, JD and Folkerts, M and Fofanov, V and Furstenau, T and Singh, NK and Guan, L and Seuylemezian, A and Benardini, JN and Engelthaler, DM and Venkateswaran, K and Keim, PS}, title = {Multi-faceted metagenomic analysis of spacecraft associated surfaces reveal planetary protection relevant microbial composition.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0282428}, pmid = {36947490}, issn = {1932-6203}, mesh = {Humans ; *Spacecraft ; *Metagenome ; Bacteria/genetics ; }, abstract = {The National Aeronautics and Space Administration (NASA) has been monitoring the microbial burden of spacecraft since the 1970's Viking missions. Originally culture-based and then focused 16S sequencing techniques were used, but we have now applied whole metagenomic sequencing to a variety of cleanroom samples at the Jet Propulsion Lab (JPL), including the Spacecraft Assembly Facility (SAF) with the goals of taxonomic identification and for functional assignment. Our samples included facility pre-filters, cleanroom vacuum debris, and surface wipes. The taxonomic composition was carried out by three different analysis tools to contrast marker, k-mer, and true alignment approaches. Hierarchical clustering analysis of the data separated vacuum particles from other SAF DNA samples. Vacuum particle samples were the most diverse while DNA samples from the ISO (International Standards Organization) compliant facilities and the SAF were the least diverse; all three were dominated by Proteobacteria. Wipe samples had higher diversity and were predominated by Actinobacteria, including human commensals Cutibacterium acnes and Corynebacterium spp. Taxa identified by the three methods were not identical, supporting the use of multiple methods for metagenome characterization. Likewise, functional annotation was performed using multiple methods. Vacuum particles and SAF samples contained strong signals of the tricarboxylic acid cycle and of amino acid biosynthesis, suggesting that many of the identified microorganisms have the ability to grow in nutrient-limited environments. In total, 18 samples generated high quality metagenome assembled genomes (MAG), which were dominated by Moraxella osloensis or Malassezia restricta. One M. osloensis MAG was assembled into a single circular scaffold and gene annotated. This study includes a rigorous quantitative determination of microbial loads and a qualitative dissection of microbial composition. Assembly of multiple specimens led to greater confidence for the identification of particular species and their predicted functional roles.}, } @article {pmid36947091, year = {2023}, author = {Yuan, L and Ju, F}, title = {Potential Auxiliary Metabolic Capabilities and Activities Reveal Biochemical Impacts of Viruses in Municipal Wastewater Treatment Plants.}, journal = {Environmental science & technology}, volume = {57}, number = {13}, pages = {5485-5498}, doi = {10.1021/acs.est.2c07800}, pmid = {36947091}, issn = {1520-5851}, mesh = {Humans ; Phylogeny ; Sewage ; *Viruses/genetics ; *Water Purification ; Carbon/metabolism ; Sulfur ; }, abstract = {Viruses influence biogeochemical cycles in oceans, freshwater, soil, and human gut through infection and by modulating virocell metabolism through virus-encoded auxiliary metabolic genes (vAMGs). However, the geographical distribution, potential metabolic function, and engineering significance of vAMGs in wastewater treatment plants (WWTPs) remain to be explored. Here, 752 single-contig viral genomes with high confidence, 510 of which belonged to Caudovirales, were recovered from the activated sludge metagenomes of 32 geographically distributed WWTPs. A total of 101 vAMGs involved in various metabolic pathways were identified, the most common of which were the queuosine biosynthesis genes folE, queD, and queE and the sulfur metabolism gene cysH. Phylogenetic analysis and virus-host relationship prediction revealed the probable evolutionary histories of vAMGs involved in carbon (acpP and prsA), nitrogen (amoC), sulfur (cysH), and phosphate (phoH) metabolism, which potentially mediate microbial carbon and nutrient cycling. Notably, 11 of the 38 (28.3%) vAMGs identified in the metagenomes with corresponding metatranscriptomes were transcriptionally expressed, implying an active functional state. This meta-analysis provides the first broad catalog of vAMGs in municipal WWTPs and how they may assist in the basic physiological reactions of their microbial hosts or nutrient cycling in the WWTPs, and therefore, may have important effects on the engineering of wastewater treatment processes.}, } @article {pmid36946737, year = {2023}, author = {Castro-Nallar, E and Berríos-Farías, V and Díez, B and Guajardo-Leiva, S}, title = {Seasonal and Spatially Distributed Viral Metagenomes from Comau Fjord (42°S), Patagonia.}, journal = {Microbiology resource announcements}, volume = {12}, number = {4}, pages = {e0008223}, pmid = {36946737}, issn = {2576-098X}, support = {FONDECYT 1200834//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; FONDECYT Postdoctoral 3210547//Agencia Nacional de Investigación y Desarrollo (ANID)/ ; }, abstract = {Viruses are key players in marine environments, affecting food webs and biogeochemical cycles. We present 48 viral metagenomes and 5,656 viral operational taxonomic units (vOTUs) from Comau Fjord, Patagonia (42°S), to understand viral-mediated processes in coastal and estuarine waters. These data represent a spatial (35-km transect, two depths) and seasonal (winter and fall) data set.}, } @article {pmid36946733, year = {2023}, author = {Han, D and Yu, F and Zhang, D and Yang, Q and Xie, M and Yuan, L and Zheng, J and Wang, J and Zhou, J and Xiao, Y and Zheng, S and Chen, Y}, title = {The Real-World Clinical Impact of Plasma mNGS Testing: an Observational Study.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0398322}, pmid = {36946733}, issn = {2165-0497}, abstract = {Plasma metagenomic next-generation sequencing (mNGS) testing is a promising diagnostic modality for infectious diseases, but its real-world clinical impact is poorly understood. We reviewed patients who had undergone plasma mNGS at a general hospital to evaluate the clinical utility of plasma mNGS testing. A total of 76.9% (113/147) of plasma mNGS tests had a positive result. A total of 196 microorganisms (58) were identified and reported, of which 75.6% (148/196) were clinically relevant. The median stringent mapped read number (SMRN) of clinically relevant organisms was 88 versus 22 for irrelevant organisms (P = 0.04). Based on the clinically adjudicated diagnosis, the positive and negative percent agreements of plasma mNGS testing for identifying a clinically defined infection were 95.2% and 67.4%, respectively. The plasma mNGS results led to a positive impact in 83 (57.1%) patients by diagnosing or ruling out infection and initiating targeted therapy. However, only 32.4% (11/34) of negative mNGS tests showed a positive impact, suggesting that plasma mNGS testing alone may not be a powerful tool to rule out infection in clinical practice. In the subset of 37 patients positive for both plasma mNGS and conventional testing, mNGS identified the pathogen(s) 2 days (IQR = 0.75 to 4.25) earlier than conventional testing. mNGS enables pathogen identification within 24 h, but given that the detection of clinically irrelevant organisms and nearly half of the tests result in no or a negative clinical impact, more clinical practice and studies are required to better understand who and when to test and how to optimally integrate mNGS into the infectious disease diagnostic workup. IMPORTANCE In this study, we show that although plasma mNGS testing significantly improved the detection rate of tested samples, nearly one in four (24.5%, 48/196) mNGS tests reported organisms were not clinically relevant, emphasizing the importance of cautious interpretation and infectious disease consultation. Moreover, based on clinical adjudication, plasma mNGS testing resulted in no or a negative impact in nearly half (43.5%, 64/147) of patients in the current study, indicating that how best to integrate this advanced method into current infectious disease diagnostic frameworks to maximize its clinical utility in real-world practice is an important question. Therefore, recommending plasma mNGS testing as a routine supplement to first-line diagnostic tests for infectious diseases faces great challenges. The decision to conduct mNGS testing should take into account the diagnostic performance, turnaround time and cost-effectiveness of mNGS, as well as the availability of conventional tests.}, } @article {pmid36946722, year = {2023}, author = {Chung, T and Yan, R and Weller, DL and Kovac, J}, title = {Conditional Forest Models Built Using Metagenomic Data Accurately Predicted Salmonella Contamination in Northeastern Streams.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0038123}, pmid = {36946722}, issn = {2165-0497}, abstract = {The use of water contaminated with Salmonella for produce production contributes to foodborne disease burden. To reduce human health risks, there is a need for novel, targeted approaches for assessing the pathogen status of agricultural water. We investigated the utility of water microbiome data for predicting Salmonella contamination of streams used to source water for produce production. Grab samples were collected from 60 New York streams in 2018 and tested for Salmonella. Separately, DNA was extracted from the samples and used for Illumina shotgun metagenomic sequencing. Reads were trimmed and used to assign taxonomy with Kraken2. Conditional forest (CF), regularized random forest (RRF), and support vector machine (SVM) models were implemented to predict Salmonella contamination. Model performance was assessed using 10-fold cross-validation repeated 10 times to quantify area under the curve (AUC) and Kappa score. CF models outperformed the other two algorithms based on AUC (0.86, CF; 0.81, RRF; 0.65, SVM) and Kappa score (0.53, CF; 0.41, RRF; 0.12, SVM). The taxa that were most informative for accurately predicting Salmonella contamination based on CF were compared to taxa identified by ALDEx2 as being differentially abundant between Salmonella-positive and -negative samples. CF and differential abundance tests both identified Aeromonas salmonicida (variable importance [VI] = 0.012) and Aeromonas sp. strain CA23 (VI = 0.025) as the two most informative taxa for predicting Salmonella contamination. Our findings suggest that microbiome-based models may provide an alternative to or complement existing water monitoring strategies. Similarly, the informative taxa identified in this study warrant further investigation as potential indicators of Salmonella contamination of agricultural water. IMPORTANCE Understanding the associations between surface water microbiome composition and the presence of foodborne pathogens, such as Salmonella, can facilitate the identification of novel indicators of Salmonella contamination. This study assessed the utility of microbiome data and three machine learning algorithms for predicting Salmonella contamination of Northeastern streams. The research reported here both expanded the knowledge on the microbiome composition of surface waters and identified putative novel indicators (i.e., Aeromonas species) for Salmonella in Northeastern streams. These putative indicators warrant further research to assess whether they are consistent indicators of Salmonella contamination across regions, waterways, and years not represented in the data set used in this study. Validated indicators identified using microbiome data may be used as targets in the development of rapid (e.g., PCR-based) detection assays for the assessment of microbial safety of agricultural surface waters.}, } @article {pmid36946719, year = {2023}, author = {Fukushima, K and Matsumoto, Y and Matsuki, T and Saito, H and Motooka, D and Komukai, S and Fukui, E and Yamuchi, J and Nitta, T and Niitsu, T and Abe, Y and Nabeshima, H and Nagahama, Y and Nii, T and Tsujino, K and Miki, K and Kitada, S and Kumanogoh, A and Akira, S and Nakamura, S and Kida, H}, title = {MGIT-seq for the Identification of Nontuberculous Mycobacteria and Drug Resistance: a Prospective Study.}, journal = {Journal of clinical microbiology}, volume = {61}, number = {4}, pages = {e0162622}, pmid = {36946719}, issn = {1098-660X}, mesh = {Humans ; *Nontuberculous Mycobacteria ; Prospective Studies ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; Anti-Bacterial Agents/pharmacology ; Amikacin ; Macrolides/pharmacology ; Microbial Sensitivity Tests ; }, abstract = {Because nontuberculous mycobacterial pulmonary disease is a considerable health burden, a simple and clinically applicable analytical protocol enabling the identification of subspecies and drug-resistant disease is required to determine the treatment strategy. We aimed to develop a simplified workflow consisting only of direct sequencing of mycobacterial growth indicator tube cultures (MGIT-seq). In total, 138 patients were prospectively enrolled between April 2021 and May 2022, and culture-positive MGIT broths were subjected to sequencing using MinION, a portable next-generation sequencer. Sequence analysis was conducted to identify species using core genome multilocus sequence typing and to predict macrolide and amikacin (AMK) resistance based on previously reported mutations in rrl, rrs, and erm(41). The results were compared to clinical tests for species identification and drug susceptibility. A total of 116 patients with positive MGIT cultures were included in the analysis. MGIT-seq yielded 99.1% accuracy in species-level identification and identified 98 isolates (84.5%) at the subspecies level. Macrolide and AMK resistance were detected in 19.4% and 1.9% of Mycobacterium avium complex (MAC) and Mycobacterium abscessus isolates. The predicted macrolide and AMK resistance was consistent with the results of conventional drug susceptibility tests, with specificities of 97.6% and 100.0%, respectively. Direct MGIT-seq has achieved comprehensive identification and drug resistance detection of nontuberculous mycobacteria, which could be applicable to determine the treatment strategy by a single test in clinical practice.}, } @article {pmid36946508, year = {2023}, author = {Mannan, A and Hoque, MN and Noyon, SH and Mehedi, HMH and Foysal, MJ and Salauddin, A and Islam, SMR and Sharmen, F and Tanni, AA and Siddiki, AZ and Tay, A and Siddique, MM and Rahman, MS and Galib, SM and Akter, F}, title = {SARS-CoV-2 infection alters the gut microbiome in diabetes patients: A cross-sectional study from Bangladesh.}, journal = {Journal of medical virology}, volume = {95}, number = {4}, pages = {e28691}, doi = {10.1002/jmv.28691}, pmid = {36946508}, issn = {1096-9071}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/complications ; Cross-Sectional Studies ; RNA, Ribosomal, 16S/genetics ; Dysbiosis/microbiology ; Bangladesh/epidemiology ; *COVID-19 ; SARS-CoV-2/genetics ; Bacteria/genetics ; }, abstract = {Populations of different South Asian nations including Bangladesh reportedly have a high risk of developing diabetes in recent years. This study aimed to investigate the differences in the gut microbiome of COVID-19-positive participants with or without type 2 diabetes mellitus (T2DM) compared with healthy control subjects. Microbiome data of 30 participants with T2DM were compared with 22 age-, sex-, and body mass index (BMI)-matched individuals. Clinical features were recorded while fecal samples were collected aseptically from the participants. Amplicon-based (16S rRNA) metagenome analyses were employed to explore the dysbiosis of gut microbiota and its correlation with genomic and functional features in COVID-19 patients with or without T2DM. Comparing the detected bacterial genera across the sample groups, 98 unique genera were identified, of which 9 genera had unique association with COVID-19 T2DM patients. Among different bacterial groups, Shigella (25%), Bacteroides (23.45%), and Megamonas (15.90%) had higher mean relative abundances in COVID-19 patients with T2DM. An elevated gut microbiota dysbiosis in T2DM patients with COVID-19 was observed while some metabolic functional changes correlated with bidirectional microbiome dysbiosis between diabetes and non-diabetes humans gut were also found. These results further highlight the possible association of COVID-19 infection that might be linked with alteration of gut microbiome among T2DM patients.}, } @article {pmid36946498, year = {2023}, author = {da Silva, AS and de Campos, GM and Giovanetti, M and Zucherato, VS and Lima, ARJ and Santos, EV and Haddad, R and Ciccozzi, M and Carlos Júnior Alcantara, L and Elias, MC and Sampaio, SC and Covas, DT and Kashima, S and Slavov, SN}, title = {Viral metagenomics unveils MW (Malawi) polyomavirus infection in Brazilian pediatric patients with acute respiratory disease.}, journal = {Journal of medical virology}, volume = {95}, number = {4}, pages = {e28688}, doi = {10.1002/jmv.28688}, pmid = {36946498}, issn = {1096-9071}, mesh = {Infant ; Child ; Humans ; Metagenomics ; Brazil/epidemiology ; Malawi/epidemiology ; Phylogeny ; SARS-CoV-2 ; *COVID-19 ; *Polyomavirus Infections/epidemiology ; *Polyomavirus/genetics ; *Viruses ; *Respiratory Tract Infections/diagnosis/epidemiology ; }, abstract = {Viral metagenomics has been extensively applied for the identification of emerging or poorly characterized viruses. In this study, we applied metagenomics for the identification of viral infections among pediatric patients with acute respiratory disease, but who tested negative for SARS-CoV-2. Twelve pools composed of eight nasopharyngeal specimens were submitted to viral metagenomics. Surprisingly, in two of the pools, we identified reads belonging to the poorly characterized Malawi polyomavirus (MWPyV). Then, the samples composing the positive pools were individually tested using quantitative polymerase chain reaction for identification of the MWPyV index cases. MWPyV-positive samples were also submitted to respiratory virus panel testing due to the metagenomic identification of different clinically important viruses. Of note, MWPyV-positive samples tested also positive for respiratory syncytial virus types A and B. In this study, we retrieved two complete MWPyV genome sequences from the index samples that were submitted to phylogenetic inference to investigate their viral origin. Our study represents the first molecular and genomic characterization of MWPyV obtained from pediatric patients in South America. The detection of MWPyV in acutely infected infants suggests that this virus might participate (coparticipate) in cases of respiratory symptoms. Nevertheless, future studies based on testing of a larger number of clinical samples and MWPyV complete genomes appear to be necessary to elucidate if this emerging polyomavirus might be clinically important.}, } @article {pmid36946423, year = {2023}, author = {Sivapornnukul, P and Chitcharoen, S and Sawaswong, V and Tachaboon, S and Dinhuzen, J and Srisawat, N and Payungporn, S}, title = {Comparison of circulating bacterial profiles between mild and severe COVID-19 patients.}, journal = {Experimental biology and medicine (Maywood, N.J.)}, volume = {248}, number = {10}, pages = {866-873}, pmid = {36946423}, issn = {1535-3699}, mesh = {Humans ; *COVID-19 ; SARS-CoV-2/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; DNA, Ribosomal ; }, abstract = {Recent reports revealed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)-infected patients can develop bacteremia; however, the circulating bacterial profile is not well studied. Therefore, this study has aimed to investigate circulating bacterial profile in mild (n = 15) and severe (n = 13) SARS-CoV-2-infected patients as well as healthy controls (n = 10), using 16S rDNA (V4) sequencing approach. The alpha diversity indexes and Bray-Curtis dissimilarity matrix revealed that the bacterial profiles between the two conditions are significantly different. Correspondingly, the relative abundance indicates that the predominant bacterial phylum in both conditions was Proteobacteria. At genus level, the dominant bacterial genera in the mild patients belonged to Sphingomonas, Stenotrophomonas, and Achromobacter, while bacterial genera belonging to Enhydrobacter, Comamonas, and Acinetobacter were dominant in the severe patients. Furthermore, Linear discriminant analysis (LDA) Effect Size (LEfSe). revealed that Stenotrophomonas, Delftia, Achromobacter, and Neisseria were enriched in the mild condition, while Agrobacterium, Comamonas, Pseudomonas, Corynebacterium, Alkaliphilus, and Kocuria were enriched in the severe patients. These results revealed a distinct circulating bacterial profile in the mild and severe SARS-CoV-2-infected patients, which may provide an insight for further therapeutic strategy.}, } @article {pmid36945965, year = {2023}, author = {Konak, HE and Erden, A and Armağan, B and Güven, SC and Apaydın, H and Dağlı, PA and Uzun, Y and Kaygısız, M and Küçükşahin, O and Omma, A}, title = {Effects of breast milk on Behçet's disease clinical features.}, journal = {Turkish journal of medical sciences}, volume = {53}, number = {1}, pages = {121-129}, pmid = {36945965}, issn = {1303-6165}, mesh = {Infant, Newborn ; Female ; Humans ; Infant ; *Behcet Syndrome/epidemiology/diagnosis ; Milk, Human ; *Sacroiliitis ; Cross-Sectional Studies ; *Low Back Pain ; }, abstract = {BACKGROUND: The etiology of Behçet's disease (BD) is not clearly known, however, abnormal activity in T helper (Th) 1, Th 17, and regulatory T cells (Treg) has critical importance in pathogenesis. It has been shown that the intestinal microbiome can be effective in the modulation of these immune abnormalities in BD patients. Breastfeeding increases the maturation of the infant's intestinal permeability by affecting the newborn's immature intestinal microbiome and metagenome. We aimed to examine the effects of breastfeeding on disease related symptoms, organ involvements and course of the disease in BD patients.

METHODS: This study was designed as a cross-sectional study in Ankara City Hospital rheumatology clinic between December 2021 and March 2022. Patients who were diagnosed with BD by meeting the criteria of the 'International Study Group' and whose information we could access by agreeing to participate in the study were enrolled. The mothers of the patients were also contacted and asked whether these patients were breastfed, the duration of breastfeeding, and the mode of birth. Demographic and clinical data of the patients, comorbid diseases, and drugs used for BD were collected from the records in the hospital database. The presence of sacroiliitis in patients was evaluated with sacroiliac X-ray and/or magnetic resonance imaging (MRI), which was requested because of low back pain symptoms and only patients with previous sacroiliac imaging for low back pain were included in the study. BD-related organ damage was measured by the Vasculitis Damage Index (VDI) and Behçet's syndrome Overall Damage Index (BODI) scores.

RESULTS: : A total of 304 patients were included in the study. The percentage of patients who were reported to have ever breastfed (median duration (IQR): 12(12) months, 33.5% < 6 months, 66.4% ≥ 6 months, and 59.6% ≥ 12 months) is 92%. When the breastfed and nonbreastfed patients were compared, 6.8% of the breastfed patients needed TNF-i against 18.2% of the nonbreastfed patients (p = 0.052). While the rate of having at least one comorbidity was 26.4% for those who were breastfed, this rate was 50% for those who had never been breastfed. When the organ and system involvements of the patients were compared, the incidence of sacroiliitis was statistically significantly higher in the nonbreastfed group (p = 0.025). Patients who were breastfed for less than 6 months were diagnosed with BD at an earlier age than those who were breastfed for more than 6 months, and those who were breastfed for less than 12 months compared to those who were breastfed for more than 12 months (respectively, p = 0.039, p = 0.035).

DISCUSSION: Our results imply that history of breastfeeding may have some positive effects on the course of the disease in BD patients.}, } @article {pmid36945677, year = {2022}, author = {Fomsgaard, AS and Rasmussen, M and Spiess, K and Fomsgaard, A and Belsham, GJ and Fonager, J}, title = {Improvements in metagenomic virus detection by simple pretreatment methods.}, journal = {Journal of clinical virology plus}, volume = {2}, number = {4}, pages = {100120}, pmid = {36945677}, issn = {2667-0380}, abstract = {Early detection of pathogens at the point of care helps reduce the threats to human and animal health from emerging pathogens. Initially, the disease-causing agent will be unknown and needs to be identified; this often requires specific laboratory facilities. Here we describe the development of an unbiased detection assay for RNA and DNA viruses using metagenomic Nanopore sequencing and simple methods that can be transferred into a field setting. Human clinical samples containing the RNA virus SARS-CoV-2 or the DNA viruses human papillomavirus (HPV) and molluscum contagiosum virus (MCV) were used as a test of concept. Firstly, the virus detection potential was optimized by investigating different pretreatments for reducing non-viral nucleic acid components. DNase I pretreatment followed by filtration increased the proportion of SARS-CoV-2 sequenced reads > 500-fold compared with no pretreatments. This was sufficient to achieve virus detection with high confidence and allowed variant identification. Next, we tested individual SARS-CoV-2 samples with various viral loads (measured as CT-values determined by RT-qPCR). Lastly, we tested the assay on clinical samples containing the DNA virus HPV and co-infection with MCV to show the assay's detection potential for DNA viruses. This protocol is fast (same day results). We hope to apply this method in other settings for point of care detection of virus pathogens, thus eliminating the need for transport of infectious samples, cold storage and a specialized laboratory.}, } @article {pmid36945649, year = {2023}, author = {Danhof, HA and Lee, J and Thapa, A and Britton, RA and Di Rienzi, SC}, title = {Microbial stimulation of oxytocin release from the intestinal epithelium via secretin signaling.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36945649}, abstract = {Intestinal microbes impact the health of the intestine and organs distal to the gut. Limosilactobacillus reuteri is a human intestinal microbe that promotes normal gut transit [1] , the anti-inflammatory immune system [2-4] , wound healing [5-7] , normal social behavior in mice [8-10] , and prevents bone reabsorption [11-17] . Each of these functions is impacted by oxytocin [18-22] , and oxytocin signaling is required for L. reuteri- mediated wound healing [5] and social behavior [9] ; however, the initiating events in the gut that lead to oxytocin stimulation and related beneficial functions remain unknown. Here we found evolutionarily conserved oxytocin production in the intestinal epithelium through analysis of single-cell RNA-Seq datasets and imaging of human and mouse intestinal tissues. Moreover, human intestinal organoids produce oxytocin, demonstrating that the intestinal epithelium is sufficient to produce oxytocin. We subsequently found that L. reuteri facilitates oxytocin secretion directly from human intestinal tissue and human intestinal organoids. Finally, we demonstrate that stimulation of oxytocin secretion by L. reuteri is dependent on the gut hormone secretin, which is produced in enteroendocrine cells [23] , while oxytocin itself is produced in enterocytes. Altogether, this work demonstrates that oxytocin is produced and secreted from enterocytes in the intestinal epithelium in response to secretin stimulated by L. reuteri . This work thereby identifies oxytocin as an intestinal hormone and provides mechanistic insight into avenues by which gut microbes promote host health.}, } @article {pmid36945612, year = {2023}, author = {Wang, Y and Sun, Y and Li, X and Chen, R and Li, W and Ji, L and Zhao, Q and Ji, L and Yang, S and Zhang, W}, title = {Molecular detection and characterization of three novel parvoviruses belonging to two different subfamilies in zoo birds.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {36945612}, abstract = {Birds carry a large number of viruses that may cause diseases in animals or human. At present, virome of zoo birds are limited. In this study, using viral metagenomics method, we investigated the feces virome of zoo birds collected from a zoo of Nanjing, Jiangsu Province, China. Three novel parvoviruses were obtained and characterized. The genome of the three viruses are 5,909 bp, 4,411 bp and 4,233 bp in length respectively which encoded four or five ORFs. Phylogenetic analysis indicated that these three novel parvoviruses clustered with other strains formed three different clades. Pairwise comparison of NS1 amino acid sequences showed that Bir-01-1 shared 44.30%-74.92% aa sequence identity with other parvoviruses belonging to the genus Aveparvovirus, while Bir-03-1 and Bir-04-1 had lower than 66.87% and 53.09% aa sequence identity with other parvoviruses belonging to the genus Chaphamaparvovirus. These three viruses were identified as three novel species of the genus Aveparvovirus and Chaphamaparvovirus respectively basing on the species demarcation criteria of parvovirus. Our findings broaden the knowledge of the genetic diversity of parvovirus and provide epidemiological data for the outbreak of potential bird’s parvovirus disease.}, } @article {pmid36945052, year = {2023}, author = {Wang, Y and Zhang, Y and Hu, Y and Liu, L and Liu, SJ and Zhang, T}, title = {Genome-centric metagenomics reveals the host-driven dynamics and ecological role of CPR bacteria in an activated sludge system.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {56}, pmid = {36945052}, issn = {2049-2618}, mesh = {Humans ; *Sewage/microbiology ; *Bacteria/genetics/metabolism ; Metagenomics ; Metagenome/genetics ; Metabolic Networks and Pathways ; Phylogeny ; }, abstract = {BACKGROUND: Candidate phyla radiation (CPR) constitutes highly diverse bacteria with small cell sizes and are likely obligate intracellular symbionts. Given their distribution and complex associations with bacterial hosts, genetic and biological features of CPR bacteria in low-nutrient environments have received increasing attention. However, CPR bacteria in wastewater treatment systems remain poorly understood. We utilized genome-centric metagenomics to answer how CPR communities shift over 11 years and what kind of ecological roles they act in an activated sludge system.

RESULTS: We found that approximately 9% (135) of the 1,526 non-redundant bacterial and archaeal metagenome-assembled genomes were affiliated with CPR. CPR bacteria were consistently abundant with a relative abundance of up to 7.5% in the studied activated sludge system. The observed striking fluctuations in CPR community compositions and the limited metabolic and biosynthetic capabilities in CPR bacteria collectively revealed the nature that CPR dynamics may be directly determined by the available hosts. Similarity-based network analysis further confirmed the broad bacterial hosts of CPR lineages. The proteome contents of activated sludge-associated CPR had a higher similarity to those of environmental-associated CPR than to those of human-associated ones. Comparative genomic analysis observed significant enrichment of genes for oxygen stress resistance in activated sludge-associated CPR bacteria. Furthermore, genes for carbon cycling and horizontal gene transfer were extensively identified in activated sludge-associated CPR genomes.

CONCLUSIONS: These findings highlight the presence of specific host interactions among CPR lineages in activated sludge systems. Despite the lack of key metabolic pathways, these small, yet abundant bacteria may have significant involvements in biogeochemical cycling and bacterial evolution in activated sludge systems. Video Abstract.}, } @article {pmid36944808, year = {2023}, author = {Schotte, U and Binder, A and Goller, KV and Faulde, M and Ruhl, S and Sauer, S and Schlegel, M and Teifke, JP and Ulrich, RG and Wylezich, C}, title = {Field survey and molecular characterization of apicomplexan parasites in small mammals from military camps in Afghanistan.}, journal = {Parasitology research}, volume = {122}, number = {5}, pages = {1199-1211}, pmid = {36944808}, issn = {1432-1955}, mesh = {Humans ; Animals ; Dogs ; Mice ; *Parasites ; Afghanistan ; Phylogeny ; *Military Personnel ; *Eucoccidiida ; Shrews ; }, abstract = {Small mammals are an important reservoir for causative agents of numerous infectious diseases, including zoonotic and vector-borne diseases. The occurrence of these pathogens represents a regional but permanent threat for humans and animals in general and might especially weaken military personnel and companion animals in abroad missions. In our study, small mammals collected in military camps in Afghanistan (Feyzabad, Mazar-e Sharif, and Kunduz) were investigated for the presence of apicomplexans using histopathology and molecular methods. For this purpose, well-established and newly developed real-time PCR assays were applied. A high prevalence was detected not only in house mice (Mus musculus), but also in shrews (Crocidura cf. suaveolens) and grey dwarf hamsters (Cricetulus migratorius). The molecular characterization based on the 18S rRNA gene revealed a close relationship to a cluster of Hepatozoon sp. detected in voles of the genus Microtus. Hepatozoon canis DNA was detected in one house mouse as well as in two Rhipicephalus ticks from a dog puppy. In addition, around 5% of the house mice were found to be infected with far related adeleorinids showing the highest sequence identity of 91.5% to Klossiella equi, the only published Klossiella sequence at present. For their better phylogenetic characterization, we conducted metagenomics by sequencing of two selected samples. The resulting 18S rRNA gene sequences have a length of about 2400 base pairs including an insertion of about 500 base pairs and are 100% identical to each other. Histopathology together with organ tropism and detection rates verified this sequence as of Klossiella muris. In conclusion, we documented naturally occurring protozoan stages and the additional taxonomic characterization of a well-known commensal in mice by applying a combination of different approaches. The study is of medical, social, and biological importance for ensuring human and animal health in military camps and also stresses the required awareness for the potential risk of zoonoses.}, } @article {pmid36943918, year = {2023}, author = {Kharofa, J and Haslam, D and Wilkinson, R and Weiss, A and Patel, S and Wang, K and Esslinger, H and Olowokure, O and Sohal, D and Wilson, G and Ahmad, S and Apewokin, S}, title = {Analysis of the fecal metagenome in long-term survivors of pancreas cancer.}, journal = {Cancer}, volume = {129}, number = {13}, pages = {1986-1994}, doi = {10.1002/cncr.34748}, pmid = {36943918}, issn = {1097-0142}, support = {K08 CA237735/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Metagenome ; Cross-Sectional Studies ; Verrucomicrobia ; Feces ; *Pancreatic Neoplasms/genetics/therapy ; Survivors ; }, abstract = {BACKGROUND: The 5-year overall survival of pancreas adenocarcinoma (PCa) remains less than 10%. Clinical and tumor genomic characteristics have not differentiated PCa long-term survivors (LTSs) from unselected patients. Preclinical studies using fecal transplant experiments from LTSs of PCa have revealed delayed tumor growth through unknown mechanisms involving the fecal microbiota. However, features of the fecal microbiome in patients with long-term survival are not well described.

METHODS: In this cross-sectional study, comprehensive shotgun metagenomics was performed on stool from PCa patients with long-term survival (n = 16). LTS was defined as >4 years from pancreatectomy and all therapy without recurrence. LTSs were compared to control patients with PCa who completed pancreatectomy and chemotherapy (n = 8). Stool was sequenced using an Illumina NextSeq500. Statistical analyses were performed in R with MicrobiomeSeq and Phyloseq for comparison of LTSs and controls.

RESULTS: All patients underwent pancreatectomy and chemotherapy before sample donation. The median time from pancreatectomy of 6 years (4-14 years) for LTSs without evidence of disease compared to a median disease-free survival of 1.8 years from pancreatectomy in the control group. No differences were observed in overall microbial diversity for LTSs and controls using Shannon/Simpson indexes. Significant enrichment of species relative abundance was observed in LTSs for the Ruminococacceae family specifically Faecalibacterium prausnitzii species as well as Akkermansia muciniphila species.

CONCLUSIONS: Stool from patients cured from PCa has more relative abundance of Faecalibacterium prausnitzii and Akkermansia muciniphila. Additional studies are needed to explore potential mechanisms by which the fecal microbiota may influence survival in PCa.

PLAIN LANGUAGE SUMMARY: Although pancreatic cancer treatments have improved, the number of long-term survivors has remained stagnant with a 5-year overall survival estimate of 9%. Emerging evidence suggests that microbes within the gastrointestinal tract can influence cancer response through activation of the immune system. In this study, we profiled the stool microbiome in long-term survivors of pancreas cancer and controls. Several enriched species previously associated with enhanced tumor immune response were observed including Faecalibacterium prausnitzii and Akkermansia muciniphila. These findings warrant additional study assessing mechanisms by which the fecal microbiota may enhance pancreatic cancer immune response.}, } @article {pmid36943133, year = {2023}, author = {Kronen, M and Vázquez-Campos, X and Wilkins, MR and Lee, M and Manefield, MJ}, title = {Evidence for a Putative Isoprene Reductase in Acetobacterium wieringae.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0011923}, pmid = {36943133}, issn = {2379-5077}, mesh = {*Oxidoreductases/genetics ; *Acetobacterium/genetics ; Butadienes/metabolism ; }, abstract = {Recent discoveries of isoprene-metabolizing microorganisms suggest they might play an important role in the global isoprene budget. Under anoxic conditions, isoprene can be used as an electron acceptor and is reduced to methylbutene. This study describes the proteogenomic profiling of an isoprene-reducing bacterial culture to identify organisms and genes responsible for the isoprene hydrogenation reaction. A metagenome-assembled genome (MAG) of the most abundant (89% relative abundance) lineage in the enrichment, Acetobacterium wieringae, was obtained. Comparative proteogenomics and reverse transcription-PCR (RT-PCR) identified a putative five-gene operon from the A. wieringae MAG upregulated during isoprene reduction. The operon encodes a putative oxidoreductase, three pleiotropic nickel chaperones (2 × HypA, HypB), and one 4Fe-4S ferredoxin. The oxidoreductase is proposed as the putative isoprene reductase with a binding site for NADH, flavin adenine dinucleotide (FAD), two pairs of canonical [4Fe-4S] clusters, and a putative iron-sulfur cluster site in a Cys6-bonding environment. Well-studied Acetobacterium strains, such as A. woodii DSM 1030, A. wieringae DSM 1911, or A. malicum DSM 4132, do not encode the isoprene-regulated operon but encode, like many other bacteria, a homolog of the putative isoprene reductase (~47 to 49% amino acid sequence identity). Uncharacterized homologs of the putative isoprene reductase are observed across the Firmicutes, Spirochaetes, Tenericutes, Actinobacteria, Chloroflexi, Bacteroidetes, and Proteobacteria, suggesting the ability of biohydrogenation of unfunctionalized conjugated doubled bonds in other unsaturated hydrocarbons. IMPORTANCE Isoprene was recently shown to act as an electron acceptor for a homoacetogenic bacterium. The focus of this study is the molecular basis for isoprene reduction. By comparing a genome from our isoprene-reducing enrichment culture, dominated by Acetobacterium wieringae, with genomes of other Acetobacterium lineages that do not reduce isoprene, we shortlisted candidate genes for isoprene reduction. Using comparative proteogenomics and reverse transcription-PCR we have identified a putative five-gene operon encoding an oxidoreductase referred to as putative isoprene reductase.}, } @article {pmid36943059, year = {2023}, author = {Durán-Viseras, A and Sánchez-Porro, C and Viver, T and Konstantinidis, KT and Ventosa, A}, title = {Discovery of the Streamlined Haloarchaeon Halorutilus salinus, Comprising a New Order Widespread in Hypersaline Environments across the World.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0119822}, pmid = {36943059}, issn = {2379-5077}, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Ribulose-Bisphosphate Carboxylase/genetics ; Sequence Analysis, DNA ; *Euryarchaeota/genetics ; *Halobacteriales/genetics ; }, abstract = {The class Halobacteria is one of the most diverse groups within the Euryarchaeota phylum, whose members are ubiquitously distributed in hypersaline environments, where they often constitute the major population. Here, we report the discovery and isolation of a new halophilic archaeon, strain F3-133[T] exhibiting ≤86.3% 16S rRNA gene identity to any previously cultivated archaeon, and, thus, representing a new order. Analysis of available 16S rRNA gene amplicon and metagenomic data sets showed that the new isolate represents an abundant group in intermediate-to-high salinity ecosystems and is widely distributed across the world. The isolate presents a streamlined genome, which probably accounts for its ecological success in nature and its fastidious growth in culture. The predominant osmoprotection mechanism appears to be the typical salt-in strategy used by other haloarchaea. Furthermore, the genome contains the complete gene set for nucleotide monophosphate degradation pathway through archaeal RuBisCO, being within the first halophilic archaea representatives reported to code this enzyme. Genomic comparisons with previously described representatives of the phylum Euryarchaeota were consistent with the 16S rRNA gene data in supporting that our isolate represents a novel order within the class Halobacteria for which we propose the names Halorutilales ord. nov., Halorutilaceae fam. nov., Halorutilus gen. nov. and Halorutilus salinus sp. nov. IMPORTANCE The discovery of the new halophilic archaeon, Halorutilus salinus, representing a novel order, family, genus, and species within the class Halobacteria and phylum Euryarchaeota clearly enables insights into the microbial dark matter, expanding the current taxonomical knowledge of this group of archaea. The in-depth comparative genomic analysis performed on this new taxon revealed one of the first known examples of an Halobacteria representative coding the archaeal RuBisCO gene and with a streamlined genome, being ecologically successful in nature and explaining its previous non-isolation. Altogether, this research brings light into the understanding of the physiology of the Halobacteria class members, their ecological distribution, and capacity to thrive in hypersaline environments.}, } @article {pmid36943058, year = {2023}, author = {Rao, YZ and Li, YX and Li, ZW and Qu, YN and Qi, YL and Jiao, JY and Shu, WS and Hua, ZS and Li, WJ}, title = {Metagenomic Discovery of "Candidatus Parvarchaeales"-Related Lineages Sheds Light on Adaptation and Diversification from Neutral-Thermal to Acidic-Mesothermal Environments.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0125222}, pmid = {36943058}, issn = {2379-5077}, mesh = {*Metagenome/genetics ; Phylogeny ; *Biological Evolution ; Adaptation, Physiological/genetics ; Archaea/genetics ; Acids/metabolism ; Amino Acids/genetics ; }, abstract = {"Candidatus Parvarchaeales" microbes, representing a DPANN archaeal group with limited metabolic potential and reliance on hosts for their growth, were initially found in acid mine drainage (AMD). Due to the lack of representatives, however, their ecological roles and adaptation to extreme habitats such as AMD as well as how they diverge across the lineage remain largely unexplored. By applying genome-resolved metagenomics, 28 Parvarchaeales-associated metagenome-assembled genomes (MAGs) representing two orders and five genera were recovered. Among them, we identified three new genera and proposed the names "Candidatus Jingweiarchaeum," "Candidatus Haiyanarchaeum," and "Candidatus Rehaiarchaeum," with the former two belonging to a new order, "Candidatus Jingweiarchaeales." Further analyses of the metabolic potentials revealed substantial niche differentiation between Jingweiarchaeales and Parvarchaeales. Jingweiarchaeales may rely on fermentation, salvage pathways, partial glycolysis, and the pentose phosphate pathway (PPP) for energy conservation reservation, while the metabolic potentials of Parvarchaeales might be more versatile. Comparative genomic analyses suggested that Jingweiarchaeales favor habitats with higher temperatures and that Parvarchaeales are better adapted to acidic environments. We further revealed that the thermal adaptation of these lineages, especially Haiyanarchaeum, might rely on genomic features such as the usage of specific amino acids, genome streamlining, and hyperthermophile featured genes such as rgy. Notably, the adaptation of Parvarchaeales to acidic environments was possibly driven by horizontal gene transfer (HGT). The reconstruction of ancestral states demonstrated that both may have originated from thermal and neutral environments and later spread to mesothermal and acidic environments. These evolutionary processes may also be accompanied by adaptation to oxygen-rich environments via HGT. IMPORTANCE "Candidatus Parvarchaeales" microbes may represent a lineage uniquely distributed in extreme environments such as AMD and hot springs. However, little is known about the strategies and processes of how they adapted to these extreme environments. By the discovery of potential new order-level lineages, "Ca. Jingweiarchaeales," and in-depth comparative genomic analysis, we unveiled the functional differentiation of these lineages. Furthermore, we show that the adaptation of these lineages to high-temperature and acidic environments was driven by different strategies, with the former relying more on genomic characteristics such as genome streamlining and amino acid compositions and the latter relying more on the acquisition of genes associated with acid tolerance. Finally, by the reconstruction of the ancestral states of the optimal growth temperature (OGT) and isoelectric point (pI), we showed the potential evolutionary process of Parvarchaeales-related lineages with regard to the shift from the high-temperature environment of their common ancestors to low-temperature (potentially acidic) environments.}, } @article {pmid36943045, year = {2023}, author = {Lu, J and Zeng, L and Holford, P and Beattie, GAC and Wang, Y}, title = {Discovery of Brassica Yellows Virus and Porcine Reproductive and Respiratory Syndrome Virus in Diaphorina citri and Changes in Virome Due to Infection with 'Ca. L. asiaticus'.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0499622}, pmid = {36943045}, issn = {2165-0497}, abstract = {Detection of new viruses or new virus hosts is essential for the protection of economically important agroecosystems and human health. Increasingly, metatranscriptomic data are being used to facilitate this process. Such data were obtained from adult Asian citrus psyllids (ACP) (Diaphorina citri Kuwayama) that fed solely on mandarin (Citrus ×aurantium L.) plants grafted with buds infected with 'Candidatus Liberibacter asiaticus' (CLas), a phloem-limited bacterium associated with the severe Asian variant of huanglongbing (HLB), the most destructive disease of citrus. Brassica yellows virus (BrYV), the causative agent of yellowing or leafroll symptoms in brassicaceous plants, and its associated RNA (named as BrYVaRNA) were detected in ACP. In addition, the porcine reproductive and respiratory syndrome virus (PRRSV), which affects pigs and is economically important to pig production, was also found in ACP. These viruses were not detected in insects feeding on plants grafted with CLas-free buds. Changes in the concentrations of insect-specific viruses within the psyllid were caused by coinfection with CLas. IMPORTANCE The cross transmission of pathogenic viruses between different farming systems or plant communities is a major threat to plants and animals and, potentially, human health. The use of metagenomics is an effective approach to discover viruses and vectors. Here, we collected buds from the CLas-infected and CLas-free mandarin (Citrus ×aurantium L. [Rutaceae: Aurantioideae: Aurantieae]) trees from a commercial orchard and grafted them onto CLas-free mandarin plants under laboratory conditions. Through metatranscriptome sequencing, we first identified the Asian citrus psyllids feeding on plants grafted with CLas-infected buds carried the plant pathogen, brassica yellows virus and its associated RNA, and the swine pathogen, porcine reproductive and respiratory syndrome virus. These discoveries indicate that both viruses can be transmitted by grafting and acquired by ACP from CLas+ mandarin seedlings.}, } @article {pmid36941739, year = {2023}, author = {Li, F and Wang, J and Chen, C and Yang, H and Man, R and Yu, S}, title = {Otomastoiditis Caused by Nocardia Farcinica: A Case Report and Literature Review.}, journal = {Ear, nose, & throat journal}, volume = {}, number = {}, pages = {1455613231165166}, doi = {10.1177/01455613231165166}, pmid = {36941739}, issn = {1942-7522}, abstract = {Nocardia farcinica usually infects people with impaired immune status and usually manifests in the lungs. Otomastoiditis caused by Nocardia infection is extremely rare, with only 4 cases reported to date. This report describes a case of otomastoid N. farcinica infection in an immunocompetent patient. The case was a 10-month-old immunocompetent infant who presented with an approximately 3-month history of right ear discharge for which treatment with various antibiotics had not resulted in significant improvement. Multiple cultures of secretions and pathologic examination failed to identify the causative organism. The patient then underwent right mastoidectomy. Finally, metagenomic next-generation sequencing identified the pathogen to be N. farcinica. The patient was infection-free at the 6-month follow-up but had developed labyrinthitis ossificans. Otomastoid Nocardia infection has characteristic clinical features, namely, formation of a large amount of granulation tissue and coexistence of bone destruction and new bone formation. Traditionally, Nocardia is challenging to diagnose. Metagenomic next-generation sequencing of lesions is helpful. Complete local debridement and free drainage are key to treatment.}, } @article {pmid36941650, year = {2023}, author = {Lu, X and Zhu, R and Dai, Z}, title = {Characterization of a novel papillomavirus identified from a whale (Delphinapterus leucas) pharyngeal metagenomic library.}, journal = {Virology journal}, volume = {20}, number = {1}, pages = {48}, pmid = {36941650}, issn = {1743-422X}, mesh = {Animals ; *Beluga Whale/genetics ; Phylogeny ; Viral Proteins/genetics ; Papillomaviridae/genetics ; Metagenomics ; Genome, Viral ; *Papillomavirus Infections/veterinary ; }, abstract = {Here, using viral metagenomic method, a novel whale papillomavirus (temporarily named wPV, GenBank accession number OP856597) was discovered in a whale (Delphinapterus leucas) pharyngeal metagenomic library. The complete genome size of wPV is 7179 bp, with GC content of 54.4% and a nucleotide composition of 23.4% A, 22.3% T, 28.4% G, and 25.9% C. The viral genome has a typical papillomavirus organization pattern, and five ORFs were predicted, including two late genes encoding L1 and L2, and three early genes encoding E1, E2, and E6. Pairwise sequence comparison and phylogenetic analysis based on the L1 gene sequence indicated that wPV may be a novel species within genus Dyodeltapapillomavirus. In addition, the E2 region of wPV was predicted to have a potential recombination event. The discovery of this novel papillomavirus increases our understanding of the viral ecology of marine mammals, providing insights into possible future infectious diseases.}, } @article {pmid36941644, year = {2023}, author = {Neyton, LPA and Langelier, CR and Calfee, CS}, title = {Metagenomic Sequencing in the ICU for Precision Diagnosis of Critical Infectious Illnesses.}, journal = {Critical care (London, England)}, volume = {27}, number = {1}, pages = {90}, pmid = {36941644}, issn = {1466-609X}, support = {K23 HL138461/HL/NHLBI NIH HHS/United States ; R01 HL155418/HL/NHLBI NIH HHS/United States ; R35 HL140026/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; Critical Care ; *Communicable Diseases/diagnosis ; Critical Illness/therapy ; *Emergency Medicine ; Intensive Care Units ; }, abstract = {This article is one of ten reviews selected from the Annual Update in Intensive Care and Emergency Medicine 2023. Other selected articles can be found online at https://www.biomedcentral.com/collections/annualupdate2023 . Further information about the Annual Update in Intensive Care and Emergency Medicine is available from https://link.springer.com/bookseries/8901 .}, } @article {pmid36941307, year = {2023}, author = {Kruasuwan, W and Jenjaroenpun, P and Arigul, T and Chokesajjawatee, N and Leekitcharoenphon, P and Foongladda, S and Wongsurawat, T}, title = {Nanopore Sequencing Discloses Compositional Quality of Commercial Probiotic Feed Supplements.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {4540}, pmid = {36941307}, issn = {2045-2322}, mesh = {Animals ; *Nanopore Sequencing ; *Nanopores ; RNA, Ribosomal, 16S/genetics ; Saccharomyces cerevisiae/genetics ; Reproducibility of Results ; *Probiotics ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; }, abstract = {The market for the application of probiotics as a livestock health improvement supplement has increased in recent years. However, most of the available products are quality-controlled using low-resolution techniques and un-curated databases, resulting in misidentification and incorrect product labels. In this work, we deployed two workflows and compared results obtained by full-length 16S rRNA genes (16S) and metagenomic (Meta) data to investigate their reliability for the microbial composition of both liquid and solid forms of animal probiotic products using Oxford Nanopore long-read-only (without short-read). Our result revealed that 16S amplicon data permits to detect the bacterial microbiota even with the low abundance in the samples. Moreover, the 16S approach has the potential to provide species-level resolution for prokaryotes but not for assessing yeast communities. Whereas, Meta data has more power to recover of high-quality metagenome-assembled genomes that enables detailed exploration of both bacterial and yeast populations, as well as antimicrobial resistance genes, and functional genes in the population. Our findings clearly demonstrate that implementing these workflows with long-read-only monitoring could be applied to assessing the quality and safety of probiotic products for animals and evaluating the quality of probiotic products on the market. This would benefit the sustained growth of the livestock probiotic industry.}, } @article {pmid36940870, year = {2023}, author = {Wang, B and Zhang, L and Shi, J and Su, Y and Wu, D and Xie, B}, title = {Genome-centric metagenomics revealed functional traits in high-solids anaerobic co-digestion of restaurant food waste, household food waste and rice straw.}, journal = {Bioresource technology}, volume = {376}, number = {}, pages = {128926}, doi = {10.1016/j.biortech.2023.128926}, pmid = {36940870}, issn = {1873-2976}, mesh = {*Refuse Disposal/methods ; Anaerobiosis ; *Oryza ; Food ; Restaurants ; Bioreactors ; Methane ; Biofuels ; Sewage ; }, abstract = {High-solids anaerobic co-digestion (HS-AcoD) of food waste (FW) and other organic wastes is an effective option to improve the biogas production and system stability compared to mono-digestion. However, the clean and sustainable HS-AcoD strategy for FW and associated microbial functional traits have not been well explored. Here, HS-AcoD of restaurant food waste (RFW), household food waste (HFW) and rice straw (RS) were performed. Results showed that the maximum synergy index (SI) of 1.28 were achieved when the volatile solids ratio of RFW, HFW and RS was 0.45:0.45:0.1. HS-AcoD alleviated the acidification process by regulating metabolism associated with hydrolysis and volatile fatty acids formation. The synergistic relationship between syntrophic bacteria and Methanothrix sp., and the enhanced metabolic capacity associated with the acetotrophic and hydrogenotrophic pathways dominated by Methanothrix sp., provided a further explanation of the synergistic mechanism. These findings advance the knowledge about microbial mechanisms underlying the synergistic effect of HS-AcoD.}, } @article {pmid36940753, year = {2023}, author = {Stiernborg, M and Debelius, JW and Yang, LL and Skott, E and Millischer, V and Giacobini, M and Melas, PA and Boulund, F and Lavebratt, C}, title = {Bacterial gut microbiome differences in adults with ADHD and in children with ADHD on psychostimulant medication.}, journal = {Brain, behavior, and immunity}, volume = {110}, number = {}, pages = {310-321}, doi = {10.1016/j.bbi.2023.03.012}, pmid = {36940753}, issn = {1090-2139}, mesh = {Humans ; Child ; Adult ; *Attention Deficit Disorder with Hyperactivity/drug therapy ; *Gastrointestinal Microbiome ; *Central Nervous System Stimulants/therapeutic use ; Diet ; Feces ; }, abstract = {Recent evidence suggests that there is a link between neurodevelopmental disorders, such as attention-deficit hyperactivity disorder (ADHD), and the gut microbiome. However, most studies to date have had low sample sizes, have not investigated the impact of psychostimulant medication, and have not adjusted for potential confounders, including body mass index, stool consistency and diet. To this end, we conducted the largest, to our knowledge, fecal shotgun metagenomic sequencing study in ADHD, with 147 well-characterized adult and child patients. For a subset of individuals, plasma levels of inflammatory markers and short-chain fatty acids were also measured. In adult ADHD patients (n = 84), compared to controls (n = 52), we found a significant difference in beta diversity both regarding bacterial strains (taxonomic) and bacterial genes (functional). In children with ADHD (n = 63), we found that those on psychostimulant medication (n = 33 on medication vs. n = 30 not on medication) had (i) significantly different taxonomic beta diversity, (ii) lower functional and taxonomic evenness, (iii) lower abundance of the strain Bacteroides stercoris CL09T03C01 and bacterial genes encoding an enzyme in vitamin B12 synthesis, and (iv) higher plasma levels of vascular inflammatory markers sICAM-1 and sVCAM-1. Our study continues to support a role for the gut microbiome in neurodevelopmental disorders and provides additional insights into the effects of psychostimulant medication. However, additional studies are needed to replicate these findings and examine causal relationships with the disorder.}, } @article {pmid36940534, year = {2023}, author = {Andersen, VD and Møller, FD and Jensen, MS and Aarestrup, FM and Vigre, H}, title = {The quantitative effect of antimicrobial usage in Danish pig farms on the abundance of antimicrobial resistance genes in slaughter pigs.}, journal = {Preventive veterinary medicine}, volume = {214}, number = {}, pages = {105899}, doi = {10.1016/j.prevetmed.2023.105899}, pmid = {36940534}, issn = {1873-1716}, mesh = {Swine ; Animals ; *Anti-Bacterial Agents/pharmacology ; Farms ; Drug Resistance, Bacterial/genetics ; *Anti-Infective Agents/pharmacology ; Denmark ; }, abstract = {Research has long established the connection between antimicrobial use (AMU) and antimicrobial resistance (AMR) in production animals, and shown that the ceasing of AMU reduces AMR. Our previous study of Danish slaughter-pig production found a quantitative relationship between lifetime AMU and abundance of antimicrobial resistance genes (ARGs). This study aimed to generate further quantitative knowledge on how changes in AMU in farms influence the abundance of ARGs both with immediate effect and over time. The study included 83 farms that were visited from 1 to 5 times. From each visit, a pooled faecal sample was produced. The abundance of ARGs was obtained by metagenomics. We used two-level linear mixed models for estimating the effect of AMU on the abundance of ARGs against six antimicrobial classes. The lifetime AMU of each batch was calculated from usage during their three rearing periods; as piglets, weaners and slaughter pigs (rearing pathway). AMU at farm level was estimated as the mean lifetime AMU of the sampled batches from each farm. At batch level, AMU was measured as the deviation between the batch-specific lifetime AMU and the general mean lifetime AMU at the farm. For peroral tetracycline and macrolide use there was a significant quantitative linear effect on the abundance of ARGs in batches within individual farms, indicating an immediate effect of changed AMU from batch to batch within farms. These estimated effects between batches within farms were approximately 1/2-1/3 of the effect estimated between farms. For all antimicrobial classes, the effect of the mean farm-level AMU and the abundance of ARGs present in the faeces of slaughter pigs was significant. This effect was identified only for peroral use, except for lincosamides, where the effect was for parenteral use. The results also indicated that the abundance of ARGs against a specific antimicrobial class also increased by the peroral usage of one or several other antimicrobial classes, except for ARGs against beta-lactams. These effects were generally lower than the AMU effect of the specific antimicrobial class. Overall, the farm peroral mean lifetime AMU affected the abundance of ARGs at antimicrobial class level and abundance of ARGs of other classes. However, the difference of AMU of the slaughter-pig batches affected only the abundance of ARGs at the same antimicrobial class level in the same antimicrobial class. The results do not exclude that parenteral usage of antimicrobials may have an effect on the abundance of ARGs.}, } @article {pmid36939866, year = {2023}, author = {Malard, LA and Bergk-Pinto, B and Layton, R and Vogel, TM and Larose, C and Pearce, DA}, title = {Snow Microorganisms Colonise Arctic Soils Following Snow Melt.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {1661-1675}, pmid = {36939866}, issn = {1432-184X}, support = {675546//H2020 Marie Skłodowska-Curie Actions/ ; 1192//Institut Polaire Français Paul Emile Victor/ ; }, mesh = {*Soil ; *Ecosystem ; Snow ; Arctic Regions ; }, abstract = {Arctic soils are constantly subjected to microbial invasion from either airborne, marine, or animal sources, which may impact local microbial communities and ecosystem functioning. However, in winter, Arctic soils are isolated from outside sources other than snow, which is the sole source of microorganisms. Successful colonisation of soil by snow microorganisms depends on the ability to survive and compete of both, the invading and resident community. Using shallow shotgun metagenome sequencing and amplicon sequencing, this study monitored snow and soil microbial communities throughout snow melt to investigate the colonisation process of Arctic soils. Microbial colonisation likely occurred as all the characteristics of successful colonisation were observed. The colonising microorganisms originating from the snow were already adapted to the local environmental conditions and were subsequently subjected to many similar conditions in the Arctic soil. Furthermore, competition-related genes (e.g. motility and virulence) increased in snow samples as the snow melted. Overall, one hundred potentially successful colonisers were identified in the soil and, thus, demonstrated the deposition and growth of snow microorganisms in soils during melt.}, } @article {pmid36939224, year = {2023}, author = {Ghadigaonkar, D and Rath, A}, title = {Isolation and Identification of Waterborne Antibiotic-Resistant Bacteria and Molecular Characterization of their Antibiotic Resistance Genes.}, journal = {Journal of visualized experiments : JoVE}, volume = {}, number = {193}, pages = {}, doi = {10.3791/63934}, pmid = {36939224}, issn = {1940-087X}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Water ; }, abstract = {The development and spread of antibiotic resistance (AR) through microbiota associated with freshwater bodies is a major global health concern. In the present study, freshwater samples were collected and analyzed with respect to the total bacterial diversity and AR genes (ARGs) using both conventional culture-based techniques and a high-throughput culture-independent metagenomic approach. This paper presents a systematic protocol for the enumeration of the total and antibiotic-resistant culturable bacteria from freshwater samples and the determination of phenotypic and genotypic resistance in the culturable isolates. Further, we report the use of whole metagenomic analysis of the total metagenomic DNA extracted from the freshwater sample for the identification of the overall bacterial diversity, including non-culturable bacteria, and the identification of the total pool of different ARGs (resistome) in the water body. Following these detailed protocols, we observed a high antibiotic-resistant bacteria load in the range of 9.6 × 10[5]-1.2 × 10[9] CFU/mL. Most isolates were resistant to the multiple tested antibiotics, including cefotaxime, ampicillin, levofloxacin, chloramphenicol, ceftriaxone, gentamicin, neomycin, trimethoprim, and ciprofloxacin, with multiple antibiotic resistance (MAR) indexes of ≥0.2, indicating high levels of resistance in the isolates. The 16S rRNA sequencing identified potential human pathogens, such as Klebsiella pneumoniae, and opportunistic bacteria, such as Comamonas spp., Micrococcus spp., Arthrobacter spp., and Aeromonas spp. The molecular characterization of the isolates showed the presence of various ARGs, such as blaTEM, blaCTX-M (β-lactams), aadA, aac (6')-Ib (aminoglycosides), and dfr1 (trimethoprims), which was also confirmed by the whole metagenomic DNA analysis. A high prevalence of other ARGs encoding for antibiotic efflux pumps-mtrA, macB, mdtA, acrD, β-lactamases-SMB-1, VIM-20, ccrA, ampC, blaZ, the chloramphenicol acetyltransferase gene catB10, and the rifampicin resistance gene rphB-was also detected in the metagenomic DNA. With the help of the protocols discussed in this study, we confirmed the presence of waterborne MAR bacteria with diverse AR phenotypic and genotypic traits. Thus, whole metagenomic DNA analysis can be used as a complementary technique to conventional culture-based techniques to determine the overall AR status of a water body.}, } @article {pmid36939007, year = {2023}, author = {Yang, C and Lo, T and Nip, KM and Hafezqorani, S and Warren, RL and Birol, I}, title = {Characterization and simulation of metagenomic nanopore sequencing data with Meta-NanoSim.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {36939007}, issn = {2047-217X}, support = {R01 HG007182/HG/NHGRI NIH HHS/United States ; }, mesh = {Metagenome ; *Nanopore Sequencing/methods ; *Nanopores ; Sequence Analysis, DNA/methods ; Computer Simulation ; Metagenomics/methods ; Software ; Algorithms ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {BACKGROUND: Nanopore sequencing is crucial to metagenomic studies as its kilobase-long reads can contribute to resolving genomic structural differences among microbes. However, sequencing platform-specific challenges, including high base-call error rate, nonuniform read lengths, and the presence of chimeric artifacts, necessitate specifically designed analytical algorithms. The use of simulated datasets with characteristics that are true to the sequencing platform under evaluation is a cost-effective way to assess the performance of bioinformatics tools with the ground truth in a controlled environment.

RESULTS: Here, we present Meta-NanoSim, a fast and versatile utility that characterizes and simulates the unique properties of nanopore metagenomic reads. It improves upon state-of-the-art methods on microbial abundance estimation through a base-level quantification algorithm. Meta-NanoSim can simulate complex microbial communities composed of both linear and circular genomes and can stream reference genomes from online servers directly. Simulated datasets showed high congruence with experimental data in terms of read length, error profiles, and abundance levels. We demonstrate that Meta-NanoSim simulated data can facilitate the development of metagenomic algorithms and guide experimental design through a metagenome assembly benchmarking task.

CONCLUSIONS: The Meta-NanoSim characterization module investigates read features, including chimeric information and abundance levels, while the simulation module simulates large and complex multisample microbial communities with different abundance profiles. All trained models and the software are freely accessible at GitHub: https://github.com/bcgsc/NanoSim.}, } @article {pmid36938368, year = {2023}, author = {Sadasivan, H and Wadden, J and Goliya, K and Ranjan, P and Dickson, RP and Blaauw, D and Das, R and Narayanasamy, S}, title = {Rapid Real-time Squiggle Classification for Read until using RawMap.}, journal = {Archives of clinical and biomedical research}, volume = {7}, number = {1}, pages = {45-57}, pmid = {36938368}, issn = {2572-5017}, support = {K24 HL159247/HL/NHLBI NIH HHS/United States ; R01 HL144125/HL/NHLBI NIH HHS/United States ; R01 HL144599/HL/NHLBI NIH HHS/United States ; }, abstract = {ReadUntil enables Oxford Nanopore Technology's (ONT) sequencers to selectively sequence reads of target species in real-time. This enables efficient microbial enrichment for applications such as microbial abundance estimation and is particularly beneficial for metagenomic samples with a very high fraction of non-target reads (> 99% can be human reads). However, read-until requires a fast and accurate software filter that analyzes a short prefix of a read and determines if it belongs to a microbe of interest (target) or not. The baseline Read Until pipeline uses a deep neural network-based basecaller called Guppy and is slow and inaccurate for this task (~60% of bases sequenced are unclassified). We present RawMap, an efficient CPU-only microbial species-agnostic Read Until classifier for filtering non-target human reads in the squiggle space. RawMap uses a Support Vector Machine (SVM), which is trained to distinguish human from microbe using non-linear and non-stationary characteristics of ONT's squiggle output (continuous electrical signals). Compared to the baseline Read Until pipeline, RawMap is a 1327X faster classifier and significantly improves the sequencing time and cost, and compute time savings. We show that RawMap augmented pipelines reduce sequencing time and cost by ~24% and computing cost by 22%. Additionally, since RawMap is agnostic to microbial species, it can also classify microbial species it is not trained on. We also discuss how RawMap may be used as an alternative to the RT-PCR test for viral load quantification of SARS-CoV-2.}, } @article {pmid36937305, year = {2023}, author = {Rocha, LO and Silva, NCC}, title = {Editorial: Application of omics-based technologies and the impact on food science.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1155757}, pmid = {36937305}, issn = {1664-302X}, } @article {pmid36937300, year = {2023}, author = {Yoon, SJ and Yu, JS and Min, BH and Gupta, H and Won, SM and Park, HJ and Han, SH and Kim, BY and Kim, KH and Kim, BK and Joung, HC and Park, TS and Ham, YL and Lee, DY and Suk, KT}, title = {Bifidobacterium-derived short-chain fatty acids and indole compounds attenuate nonalcoholic fatty liver disease by modulating gut-liver axis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1129904}, pmid = {36937300}, issn = {1664-302X}, abstract = {Emerging evidences about gut-microbial modulation have been accumulated in the treatment of nonalcoholic fatty liver disease (NAFLD). We evaluated the effect of Bifidobacterium breve and Bifidobacterium longum on the NAFLD pathology and explore the molecular mechanisms based on multi-omics approaches. Human stool analysis [healthy subjects (n = 25) and NAFLD patients (n = 32)] was performed to select NAFLD-associated microbiota. Six-week-old male C57BL/6 J mice were fed a normal chow diet (NC), Western diet (WD), and WD with B. breve (BB) or B. longum (BL; 109 CFU/g) for 8 weeks. Liver/body weight ratio, histopathology, serum/tool analysis, 16S rRNA-sequencing, and metabolites were examined and compared. The BB and BL groups showed improved liver histology and function based on liver/body ratios (WD 7.07 ± 0.75, BB 5.27 ± 0.47, and BL 4.86 ± 0.57) and NAFLD activity scores (WD 5.00 ± 0.10, BB 1.89 ± 1.45, and BL 1.90 ± 0.99; p < 0.05). Strain treatment showed ameliorative effects on gut barrier function. Metagenomic analysis showed treatment-specific changes in taxonomic composition. The community was mainly characterized by the significantly higher composition of the Bacteroidetes phylum among the NC and probiotic-feeding groups. Similarly, the gut metabolome was modulated by probiotics treatment. In particular, short-chain fatty acids and tryptophan metabolites were reverted to normal levels by probiotics, whereas bile acids were partially normalized to those of the NC group. The analysis of gene expression related to lipid and glucose metabolism as well as the immune response indicated the coordinative regulation of β-oxidation, lipogenesis, and systemic inflammation by probiotic treatment. BB and BL attenuate NAFLD by improving microbiome-associated factors of the gut-liver axis.}, } @article {pmid36937296, year = {2023}, author = {Tian, X and Li, D and Zhao, X and Xiao, Z and Sun, J and Yuan, T and Wang, Y and Zuo, X and Yang, G and Yu, T}, title = {Dietary grape pomace extract supplementation improved meat quality, antioxidant capacity, and immune performance in finishing pigs.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1116022}, pmid = {36937296}, issn = {1664-302X}, abstract = {In pig production, reducing production costs and improving immunity are important. Grape pomace, a good agricultural by-product, has been thrown away as food waste for a long time. Recently, we found that it could be used as a new source of pig feed. We investigated the effect of grape pomace on inflammation, gut barrier function, meat quality, and growth performance in finishing pigs. Our results indicated that treatment samples showed a significant decrease in water loss, IL-1β, DAO, ROS, and MDA content (p < 0.05). IgA, IgG, IgM, CAT, T-AOC, SOD, and IFN-γ significantly increased compared with those in control samples (p < 0.05). Meanwhile, the relative mRNA expression of the tight junction protein occludin showed a significant difference (p < 0.05). Analysis of metagenomic sequencing indicated that grape pomace significantly decreased the relative abundance of Treponema and Streptococcus (p < 0.05). In summary, our results demonstrated that grape pomace could improve meat quality, alleviate inflammation, and decrease oxidative stress.}, } @article {pmid36937279, year = {2023}, author = {Kerr, EN and Papudeshi, B and Haggerty, M and Wild, N and Goodman, AZ and Lima, LFO and Hesse, RD and Skye, A and Mallawaarachchi, V and Johri, S and Parker, S and Dinsdale, EA}, title = {Stingray epidermal microbiomes are species-specific with local adaptations.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1031711}, pmid = {36937279}, issn = {1664-302X}, abstract = {Marine host-associated microbiomes are affected by a combination of species-specific (e.g., host ancestry, genotype) and habitat-specific features (e.g., environmental physiochemistry and microbial biogeography). The stingray epidermis provides a gradient of characteristics from high dermal denticles coverage with low mucus to reduce dermal denticles and high levels of mucus. Here we investigate the effects of host phylogeny and habitat by comparing the epidermal microbiomes of Myliobatis californica (bat rays) with a mucus rich epidermis, and Urobatis halleri (round rays) with a mucus reduced epidermis from two locations, Los Angeles and San Diego, California (a 150 km distance). We found that host microbiomes are species-specific and distinct from the water column, however composition of M. californica microbiomes showed more variability between individuals compared to U. halleri. The variability in the microbiome of M. californica caused the microbial taxa to be similar across locations, while U. halleri microbiomes were distinct across locations. Despite taxonomic differences, Shannon diversity is the same across the two locations in U. halleri microbiomes suggesting the taxonomic composition are locally adapted, but diversity is maintained by the host. Myliobatis californica and U. halleri microbiomes maintain functional similarity across Los Angeles and San Diego and each ray showed several unique functional genes. Myliobatis californica has a greater relative abundance of RNA Polymerase III-like genes in the microbiome than U. halleri, suggesting specific adaptations to a heavy mucus environment. Construction of Metagenome Assembled Genomes (MAGs) identified novel microbial species within Rhodobacteraceae, Moraxellaceae, Caulobacteraceae, Alcanivoracaceae and Gammaproteobacteria. All MAGs had a high abundance of active RNA processing genes, heavy metal, and antibiotic resistant genes, suggesting the stingray mucus supports high microbial growth rates, which may drive high levels of competition within the microbiomes increasing the antimicrobial properties of the microbes.}, } @article {pmid36937148, year = {2023}, author = {Zheng, L and Kang, Z and Wang, R and Lv, M and Gao, Z and Xu, H and Wang, M}, title = {Evaluation of the Diagnostic Performance of mNGS in Detecting Intra-Abdominal Infections of the Emergency Department Patients.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {1421-1432}, pmid = {36937148}, issn = {1178-6973}, abstract = {PURPOSE: Intra-abdominal infections (IAI) are gradually becoming common in the emergency department, though the incidence is low and the prognosis is fair, as the symptoms are similar to other intra-abdominal diseases, rapid and accurate diagnosis of the causative agents is essential for clinical management. This study aimed to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) in detecting IAI in the emergency department.

PATIENTS AND METHODS: This was a retrospective, single-centered study including patients admitted to the emergency department from January 1st, 2021 to August 31st, 2022 with diagnosis of IAI. The comparison between mNGS and microbial culture using paracentesis fluid samples was performed to evaluate the diagnostic performance of mNGS for IAI. Meanwhile, paracentesis fluid and peripheral blood mNGS were compared to explore the sample specificity. Further, the microbial community structure of the patients with pyogenic liver abscesses (PLA) was analyzed.

RESULTS: Thirty-four IAI patients including 23 with pyogenic liver abscesses (PLA), 3 with parapancreatic abscesses, and 8 with other IAI were included in this study. Compared with the conventional microbial culture of paracentesis fluid, mNGS using paracentesis fluid detected more positive cases of IAI (93.75% vs 81.25%), and identified more species of pathogens, especially in obligate anaerobes and viral pathogens. Peripheral blood mNGS presented a relatively high consistency with the paracentesis fluid mNGS (91% mutual positive). The microbial community structure of PLA patients with diabetes is less diverse than that of those without diabetes. Patients with diabetes are at high risk of PLA caused by Klebsiella pneumonia.

CONCLUSION: mNGS has advantages in detecting IAI in the emergency department, and peripheral blood mNGS can be a non-invasive choice for early diagnosis.}, } @article {pmid36937145, year = {2023}, author = {Cheng, H and Tan, N and Lu, Y and Wu, H and Liu, Z and Zhang, D and Xu, Z and Li, C}, title = {Lumbar Spine Infection with Eikenella corrodens Presented as Abdominal Pain: A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {1407-1417}, pmid = {36937145}, issn = {1178-6973}, abstract = {BACKGROUND: Eikenella corrodens is a part of the inherent flora on the surface of human mucosa. It usually does not cause disease unless the patient has been bitten, injured or surgically infected. Lumbar spine infection caused by Eikenella corrodens usually presents with conventional symptoms such as low back pain and fever. Herein, we report a case of lumbar intervertebral space infection with Eikenella corrodens presented as abdominal pain.

CASE PRESENTATION: A 38-year-old man with no medical history of note presented with abdominal pain. Initially, local doctors suspected that the patient had abdominal disease. However, abdominal diseases were ruled out and only lumbar spine infection was confirmed. Then, the patient was misdiagnosed as lumbar tuberculosis. Finally, anaerobic culture and metagenomic next-generation sequencing confirmed the Eikenella corrodens, which was rarely involved in lumbar intervertebral space infection. The patient recovered after operation and antibiotic therapy.

CONCLUSION: This case indicated a rare symptom of lumbar spine infection, abdominal cramping, which is caused by Eikenella corrodens. Blood culture had low sensitivity as a diagnostic method for Eikenella corrodens, but lesion sample culture or metagenomic next-generation sequencing had high sensitivity for early diagnosis.}, } @article {pmid36937014, year = {2023}, author = {Zhang, L and Shen, H and Zhang, J and Mao, S}, title = {Variety of rumen microbial populations involved in biohydrogenation related to individual milk fat percentage of dairy cows.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1106834}, pmid = {36937014}, issn = {2297-1769}, abstract = {Our objective was to investigate the contribution of the rumen microbiome on the individual milk fat percentage (MFP) of Holstein dairy cows under the same nutritional and management conditions. From 92 early lactation dairy cows, the top 10 with the highest MFP (HF; n = 10) and the last 10 with the lowest MFP (LF; n = 10) were selected for the study. As a result, the milk trans-10, cis-12 C18:2 content was significant lower in the HF group than that in the LF group (P < 0.001). The rumen acetate to propionate ratio was significant higher in the HF group than that in the LF group (P = 0.035). According to the results of 16S rRNA gene sequencing, a minor but significant difference existed between the groups (P = 0.040). Three genera of the family Lachnospiraceae and four genera of the order Bacteroidales were identified to be the biomarkers for the LF group and HF group in the LEfSe analysis, respectively. Three microbial modules enriched by the family Lachnospiraceae were positively related to the milk trans-10, cis-12 C18:2 content (r s > 0.60, P < 0.05). According to the results of shotgun metagenome sequencing, three kinds of linoleic acid (LA) isomerase genes were present in the gene pools of the rumen microbiome. Among them, the relative abundance of Bifidobacterium LA isomerase (BBI) was higher in the HF group than that in the LF group (P = 0.007). Three metagenome-assembled genomes (MAGs) with LA isomerase genes were positively correlated to the milk trans-10, cis-12 C18:2 content (r s > 0.40, P < 0.05). Furthermore, all of these three MAGs were found to be able to produce lactate. Taken together, these results indicate that the increased relative abundance of microbial population with the trans-10 biohydrogenation pathway within the rumen microbiome contributes to the decrease of MFP via the increase of rumen trans-10, cis-12 C18:2 production. This study provides a new perspective for the development of measures for improving the milking performance of dairy cows.}, } @article {pmid36936880, year = {2023}, author = {Morishima, S and Kawada, Y and Fukushima, Y and Takagi, T and Naito, Y and Inoue, R}, title = {A randomized, double-blinded study evaluating effect of matcha green tea on human fecal microbiota.}, journal = {Journal of clinical biochemistry and nutrition}, volume = {72}, number = {2}, pages = {165-170}, pmid = {36936880}, issn = {0912-0009}, abstract = {Matcha green tea is made from powdered green tea leaves. Unlike regular green tea, Matcha green tea is believed to exert beneficial effects on the gut microbiota, as it is richer in nutrients such as tea catechins and insoluble dietary fiber. In the present study, we aimed to investigate the effects of consumption of Matcha green tea on the gut microbiota. Human participants were randomly assigned to a placebo (n = 16) or a Matcha green tea (n = 17) drink group and asked to drink the treatments for two weeks. Feces were collected from the participants pre- and post-treatment and fecal microbiota composition was analyzed by 16S rRNA metagenomic sequencing. The beta-diversity of microbial composition significantly (p<0.05) changed in MGT group but not in placebo group. In addition, the number of unique bacterial genera significantly (p<0.05) changed in the Matcha green tea group was 30, while it was only 3 in the Placebo group. Increase and decrease in abundances of Coprococcus and Fusobacterium, respectively, in the gut microbiota of Matcha green tea group, conferred potential health benefits to the host. The present study was registered in the UMIN Clinical Trial Registry (UMIN000043857).}, } @article {pmid36936777, year = {2023}, author = {Jia, K and Huang, S and Shen, C and Li, H and Zhang, Z and Wang, L and Zhao, G and Wu, Z and Lin, Y and Xia, H and Tang, M and Yang, H and Hu, H}, title = {Enhancing urinary tract infection diagnosis for negative culture patients with metagenomic next-generation sequencing (mNGS).}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1119020}, pmid = {36936777}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *Urinary Tract Infections/diagnosis ; High-Throughput Nucleotide Sequencing ; *Body Fluids ; *Coinfection ; Escherichia coli/genetics ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a promising technology that allows unbiased pathogen detection and is increasingly being used for clinical diagnoses. However, its application in urinary tract infection (UTI) is still scarce.

METHODS: The medical records of 33 patients with suspected UTI who were admitted to the Second Hospital of Tianjin Medical University from March 2021 to July 2022 and received urine mNGS were retrospectively analyzed. The performance of mNGS and conventional urine culture in diagnosing infection and identifying causative organisms was compared, and the treatment effects were evaluated in terms of changes in urinalyses and urinary symptoms.

RESULTS: In the detection of bacteria and fungi, mNGS detected at least one pathogen in 29 (87.9%) cases, including 19 (57.6%) with positive mNGS but negative culture results and 10 (30.3%) with both mNGS and culture positive results. The remaining 4 (12.1%) patients were negative by both tests. Overall, mNGS performed better than culture (87.9% vs. 30.3%, P < 0.001). Within the 10 double-positive patients, mNGS matched culture results exactly in 5 cases, partially in 4 cases, and not at all in 1 case. In addition, mNGS detected a broader pathogen spectrum, detecting 26 species compared to only 5 species found in culture. The most abundant bacteria detected by mNGS was Escherichia coli, detected in 9 (27.2%) patients. All anaerobic bacteria, Mycobacterium Tuberculosis and all mixed pathogens were detected by mNGS. The final clinical diagnosis of UTI was made in 25 cases, and the sensitivity of mNGS was significantly higher than culture (100.0% vs 40.0%; P < 0.001) when using the diagnosis as a reference standard; the positive predictive value, negative predictive value and specificity were 86.2%, 100% and 50.0%, respectively. Importantly, targeted antibiotic therapy based on mNGS resulted in significant improvement in urinalyses and urinary symptoms in patients.

CONCLUSIONS: mNGS is a technology that has shown clear advantages over culture, particularly in the context of mixed infections and UTIs that are difficult to diagnose and treat. It helps to improve the detection of pathogens, guide changes in treatment strategies, and is an effective complement to urine culture.}, } @article {pmid36936762, year = {2023}, author = {Cai, Y and Ding, H and Chen, X and Chen, Y and Huang, C and Zhang, C and Huang, Z and Huang, Y and Li, W and Zhang, W and Fang, X}, title = {Optimization and standardization of mNGS-based procedures for the diagnosis of Mycoplasma periprosthetic joint infection: A novel diagnostic strategy for rare bacterial periprosthetic joint infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1089919}, pmid = {36936762}, issn = {2235-2988}, mesh = {Humans ; *Prosthesis-Related Infections/diagnosis/microbiology ; *Mycoplasma/genetics ; Bacteria ; *Arthritis, Infectious/microbiology ; *Bacterial Infections ; *Mycoplasma Infections/diagnosis ; Sensitivity and Specificity ; Reference Standards ; }, abstract = {INTRODUCTION: The diagnosis of Mycoplasma periprosthetic joint infection (PJI) is rather difficult due to its rarity and difficult in isolation, there are not standardized diagnostic procedure for Mycoplasma PJI presently. This study aimed to reported a metagenomic next-generation sequencing (mNGS)-based diagnostic strategy for Mycoplasma PJI.

METHODS: In the present study, we have reported the largest number of Mycoplasma PJI that were precisely diagnosed by mNGS and verified by optimized microbial culture methods and (or) 16S PCR polymerase chain reaction (PCR).

RESULTS: The positive rate of optimized microbial culture methods and 16S PCR in the detection of Mycoplasma PJI was 57.14% and 71.43%, respectively. The infections were well controlled by targeted treatment in all cases.

CONCLUSION: The standardized and optimized procedure based on mNGS presented in this study is useful for the diagnosis of Mycoplasma PJI, which might also be provided as a novel diagnostic strategy for rare bacterial PJI.}, } @article {pmid36936641, year = {2023}, author = {Taibukahn, N and Ab Majid, AH}, title = {Metagenomic 16S rDNA amplicon data of microbial diversity of Cimex hemipterus (F.) (Hemiptera: Cimicidae) treated with insect growth regulators (IGR).}, journal = {Data in brief}, volume = {47}, number = {}, pages = {109024}, pmid = {36936641}, issn = {2352-3409}, abstract = {The metagenomics dataset presented here is based on bacterial 16S rDNA gene amplicons of DNA extracted from tropical bed bugs (Cimex hemipterus). Amplicon-based sequencing was performed using the Illumina MiSeq platform, and the raw sequence data were analyzed using QIIME (version 2022.8.3). The metagenome sequence comprised ten samples that include C1 (133 511bps), C2 (108 920bps), CH1 (106 562bps), CH2 (101 778bps), P1 (103 618bps), P2 (133 258bps), T1 (113 558bps), T2 (133 952bps), TM1 (125 335bps), and TM2 (118 345bps). The sequence data is readily accessible at the NCBI SRA under bio project PRJNA918835. The most abundant microbial community present in the C. hemipterus is the Proteobacteria, with more than 99% of the abundance.}, } @article {pmid36936223, year = {2023}, author = {Liao, Y and Xiao, J and Fang, F and Zhou, H and Liu, L and Liu, X}, title = {Case report: Acinetobacter baumannii septic arthritis in an immunocompetent infant.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {1135178}, pmid = {36936223}, issn = {2296-858X}, abstract = {Acinetobacter baumannii is a gram-negative coccobacilli, mainly causing nosocomial infections with poor prognosis, especially in patients with prolonged hospitalization or antibiotics administration. A. baumannii pneumonia is the most common clinical form and usually occurs in critically ill patients in the intensive care unit. However, septic arthritis caused by A. baumannii is rarely reported. In this report, we describe a case of A. baumannii septic arthritis combined with incomplete Kawasaki disease in an infant. The child's chief complaint was a 2-week intermittent fever with poor response to antibiotics. Initial physical examination revealed swollen lymph nodes in the neck, pharynx congestion, and the appearance of rashes. Combined with laboratory tests, the diagnosis of incomplete Kawasaki disease was considered. After administration of high-dose intravenous immunoglobulin and corticosteroids, the child's fever improved and periungual desquamation appeared simultaneously. Swelling of the right knee occurred 5 days after the fever improved and imaging tests of MRI and ultrasound suggested the existence of infection. A diagnosis of septic arthritis was established subsequently, and arthroscopy was carried out. A. baumannii was finally identified by metagenomics next-generation sequencing of joint draining fluid for pathogenic microorganisms. Treatment with meropenem was then started. The patient eventually recovered and was discharged from the hospital after 23 days of treatment with meropenem. Although A. baumannii is not a common bacterium of septic arthritis, this rare infection can still occur in infants. Early diagnosis, pathogenic identification, and target antibiotic treatment are important to reduce the occurrence of joint sequelae.}, } @article {pmid36935436, year = {2023}, author = {Kocak, FO and Tanir, SGE and Cetin, AK and Degirmenci, L}, title = {Correction: Simulatenous evaluation of composting experiments and metagenome analyses to illuminate the effect of Streptomyces spp. on organic matter degradation.}, journal = {World journal of microbiology & biotechnology}, volume = {39}, number = {5}, pages = {124}, doi = {10.1007/s11274-023-03523-5}, pmid = {36935436}, issn = {1573-0972}, } @article {pmid36934910, year = {2023}, author = {Greses, S and De Bernardini, N and Treu, L and Campanaro, S and González-Fernández, C}, title = {Genome-centric metagenomics revealed the effect of pH on the microbiome involved in short-chain fatty acids and ethanol production.}, journal = {Bioresource technology}, volume = {377}, number = {}, pages = {128920}, doi = {10.1016/j.biortech.2023.128920}, pmid = {36934910}, issn = {1873-2976}, mesh = {Fatty Acids ; Ethanol ; Food ; Metagenomics ; *Refuse Disposal ; Fermentation ; Bioreactors ; *Microbiota/genetics ; Hydrogen-Ion Concentration ; Anaerobiosis ; }, abstract = {Added-value chemicals production via food waste (FWs) valorization using open-mixed cultures is an emerging approach to replace petrochemical-based compounds. Nevertheless, the effects of operational parameters on the product spectrum remain uncertain given the wide number of co-occurring species and metabolisms. In this study, the identification of 58 metagenome-assembled genomes and their investigation assessed the effect of slight pH variations on microbial dynamics and the corresponding functions when FWs were subjected to anaerobic fermentation (AF) in 1-L continuous stirred tank reactors at 25 °C. The initial pH of 6.5 promoted a microbial community involved in acetate, butyrate and ethanol production, mediated by Bifidobacterium subtile IE007 and Eubacteriaceae IE027 as main species. A slight pH decrease to 6.1 shaped microbial functions that resulted in caproate and H2 production, increasing the relevance of Eubacteriaceae IE037 role. This study elucidated the strong pH effect on product outputs when minimal variations take place in AF.}, } @article {pmid36934538, year = {2023}, author = {Dai, C and Qu, Y and Wu, W and Li, S and Chen, Z and Lian, S and Jing, J}, title = {QSP: An open sequence database for quorum sensing related gene analysis with an automatic annotation pipeline.}, journal = {Water research}, volume = {235}, number = {}, pages = {119814}, doi = {10.1016/j.watres.2023.119814}, pmid = {36934538}, issn = {1879-2448}, mesh = {*Quorum Sensing ; *Bacteria/genetics ; Proteins ; Sewage/microbiology ; Water ; }, abstract = {Quorum sensing (QS) has attracted great attention due to its important role in the bacterial interactions and its relevance to water management. With the development of high-throughput sequencing technology, a specific database for QS-related sequence annotation is urgently needed. Here, Hidden Markov Model (HMM) profiles for 38 types of QS-related proteins were built using a total of 4024 collected seed sequences. Based on both homolog search and keywords confirmation against the non-redundant database, we established a QS-related protein (QSP) database, that includes 809,721 protein sequences and 186,133 nucleotide sequences, downloaded available at: https://github.com/chunxiao-dcx/QSP. The entries were classified into 38 types and 315 subtypes among 91 bacterial phyla. Furthermore, an automatic annotation pipeline, named QSAP, was developed for rapid annotation, classification and abundance quantification of QSP-like sequences from sequencing data. This pipeline provided the two homolog alignment strategies offered by Diamond (Blastp) or HMMER (Hmmscan), as well as a data cleansing function for a subset or union set of the hits. The pipeline was tested using 14 metagenomic samples from various water environments, including activated sludge, deep-sea sediments, estuary water, and reservoir water. The QSAP pipeline is freely available for academic use in the code repository at: https://github.com/chunxiao-dcx/QSAP. The establishment of this database and pipeline, provides a useful tool for QS-related sequence annotation in a wide range of projects, and will increase our understanding of QS communication in aquatic environments.}, } @article {pmid36934439, year = {2023}, author = {Runde, J and Veseli, I and Fogarty, EC and Watson, AR and Clayssen, Q and Yosef, M and Shaiber, A and Verma, R and Quince, C and Gerasimidis, K and Rubin, DT and Eren, AM}, title = {Transient Suppression of Bacterial Populations Associated with Gut Health is Critical in Success of Exclusive Enteral Nutrition for Children with Crohn's Disease.}, journal = {Journal of Crohn's & colitis}, volume = {17}, number = {7}, pages = {1103-1113}, doi = {10.1093/ecco-jcc/jjad031}, pmid = {36934439}, issn = {1876-4479}, mesh = {Humans ; *Crohn Disease ; Enteral Nutrition ; Remission Induction ; Bacteria ; *Microbiota ; }, abstract = {BACKGROUND AND AIMS: Exclusive enteral nutrition [EEN] is a dietary intervention to induce clinical remission in children with active luminal Crohn's disease [CD]. While changes in the gut microbial communities have been implicated in achieving this remission, a precise understanding of the role of microbial ecology in the restoration of gut homeostasis is lacking.

METHODS: Here we reconstructed genomes from the gut metagenomes of 12 paediatric subjects who were sampled before, during and after EEN. We then classified each microbial population into distinct 'phenotypes' or patterns of response based on changes in their relative abundances throughout the therapy on a per-individual basis.

RESULTS: Our data show that children achieving clinical remission during therapy were enriched with microbial populations that were either suppressed or that demonstrated a transient bloom as a function of EEN. In contrast, this ecosystem-level response was not observed in cases of EEN failure. Further analysis revealed that populations that were suppressed during EEN were significantly more prevalent in healthy children and adults across the globe compared with those that bloomed ephemerally during the therapy.

CONCLUSIONS: These observations taken together suggest that successful outcomes of EEN are marked by a temporary emergence of microbial populations that are rare in healthy individuals, and a concomitant reduction in microbes that are commonly associated with gut homeostasis. Our work is a first attempt to highlight individual-specific, complex environmental factors that influence microbial response in EEN. This model offers a novel, alternative viewpoint to traditional taxonomic strategies used to characterize associations with health and disease states.}, } @article {pmid36933736, year = {2023}, author = {Li, M and Wang, K and Zheng, W and Maddela, NR and Xiao, Y and Li, Z and Tawfik, A and Chen, Y and Zhou, Z}, title = {Metagenomics and network analysis decipher profiles and co-occurrence patterns of bacterial taxa in soils amended with biogas slurry.}, journal = {The Science of the total environment}, volume = {877}, number = {}, pages = {162911}, doi = {10.1016/j.scitotenv.2023.162911}, pmid = {36933736}, issn = {1879-1026}, mesh = {Animals ; Swine ; *Soil ; *Biofuels ; Metagenomics ; Bacteria/genetics ; Agriculture ; Fertilizers ; Soil Microbiology ; }, abstract = {Microbial community and interaction play crucial roles in ecological functions of soil including nutrient cycling carbon storage, and water maintenance etc. Numerous studies have shown that the application of fertilizers alters bacterial diversity; However, it remains unknown whether and how the continuous application of biogas slurry from anaerobic digestion affects the spatiotemporal heterogeneity of soil layers, complexity and stability of microbial networks, and functions related to C and N cycling. Here, we investigated the bacterial taxa of purple soils treated with swine biogas slurry for four different periods (0, 1, 3 and 8 years) and five different soil depths (20, 40, 60, 80 and 100 cm). The results showed that the application period of biogas slurry and soil depth were two powerful drivers of bacterial diversity and communities. Biogas slurry input resulted in marked changes in the bacterial diversity and composition at the soil depths of 0-60 cm. The relative abundances of Acidobacteriota, Myxococcot, and Nitrospirota decreased, while Actinobacteria, Chloroflexi, and Gemmatimonadota increased with repeated biogas slurry input. The decreasing complexity and stability of the bacterial network with decreasing nodes, links, robustness, and cohesions were found with increasing years of biogas slurry application, suggesting that the bacterial network of soils treated by the biogas slurry became more vulnerability compared with the control. Also, the linkages between the keystone taxa and soil properties were weakened after biogas slurry input, leading to the cooccurrence patterns being less affected by the keystones in the high level of nutrients. Metagenomic analysis confirmed that biogas slurry input increased the relative abundance of liable-C degradation and denitrification genes, which could highly impact the network properties. Overall, our study could give comprehensive understandings on the impacts of biogas slurry amendment on soils, which could be useful for maintaining sustainable agriculture and soil health with liquid fertilization.}, } @article {pmid36933668, year = {2023}, author = {Rohr, JC and Bourassa, KA and Thompson, DS and Fowler, JC and Frueh, BC and Weinstein, BL and Petrosino, J and Madan, A}, title = {History of childhood physical abuse is associated with gut microbiota diversity among adult psychiatric inpatients.}, journal = {Journal of affective disorders}, volume = {331}, number = {}, pages = {50-56}, pmid = {36933668}, issn = {1573-2517}, support = {P30 ES030285/ES/NIEHS NIH HHS/United States ; R25 GM056929/GM/NIGMS NIH HHS/United States ; R25 GM069234/GM/NIGMS NIH HHS/United States ; U54 HG004973/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; Adult ; Child, Preschool ; *Gastrointestinal Microbiome/genetics ; Inpatients ; RNA, Ribosomal, 16S/genetics ; Physical Abuse ; *Microbiota ; }, abstract = {BACKGROUND: Traumatic life events are associated with the development of psychiatric and chronic medical illnesses. This exploratory study examined the relationship between traumatic life events and the gut microbiota among adult psychiatric inpatients.

METHODS: 105 adult psychiatric inpatients provided clinical data and a single fecal sample shortly after admission. A modified version of the Stressful Life Events Screening Questionnaire was used to quantify history of traumatic life events. 16S rRNA gene sequencing was used to analyze the gut microbial community.

RESULTS: Gut microbiota diversity was not associated with overall trauma score or any of the three trauma factor scores. Upon item-level analysis, history of childhood physical abuse was uniquely associated with beta diversity. Linear Discriminant Analysis Effect Size (LefSe) analyses revealed that childhood physical abuse was associated with abundance of distinct bacterial taxa associated with inflammation.

LIMITATIONS: This study did not account for dietary differences, though diet was highly restricted as all participants were psychiatric inpatients. Absolute variance accounted for by the taxa was small though practically meaningful. The study was not powered for full subgroup analysis based on race and ethnicity.

CONCLUSIONS: This study is among the first to demonstrate a relationship between childhood physical abuse and gut microbiota composition among adult psychiatric patients. These findings suggest that early childhood adverse events may have long-conferred systemic consequences. Future efforts may target the gut microbiota for the prevention and/or treatment of psychiatric and medical risk associated with traumatic life events.}, } @article {pmid36933314, year = {2023}, author = {Su, C and Xian, Y and Qin, R and Zhou, Y and Lu, M and Wan, X and Chen, Z and Chen, M}, title = {Fe(III) enhances Cr(VI) bioreduction in a MFC-granular sludge coupling system: Experimental evidence and metagenomics analysis.}, journal = {Water research}, volume = {235}, number = {}, pages = {119863}, doi = {10.1016/j.watres.2023.119863}, pmid = {36933314}, issn = {1879-2448}, mesh = {*Sewage ; Ferric Compounds ; *Bioelectric Energy Sources ; Metagenomics ; Chromium/metabolism ; Oxidation-Reduction ; Methane ; }, abstract = {The influence of Fe(III) on the bioreduction efficiency of Cr(VI) in a microbial fuel cell (MFC)-granular sludge coupling system using dissolved methane as an electron donor and carbon source was explored, and the mechanism of Fe(III) mediating enhancement in the bioreduction process of Cr(VI) in the coupling system was also investigated. Results showed that the presence of Fe(III) enhanced the ability of the coupling system to reduce Cr(VI). The average removal efficiencies of Cr(VI) in the anaerobic zone in response to 0, 5, and 20 mg/L of Fe(III) were 16.53±2.12%, 24.17±2.10%, and 46.33±4.41%, respectively. Fe(III) improved the reducing ability and output power of the system. In addition, Fe(III) enhanced the electron transport systems activity of the sludge, the polysaccharide and protein content in the anaerobic sludge. Meanwhile, X-ray photoelectron spectrometer (XPS) spectra demonstrated that Cr(VI) was reduced to Cr(III), while Fe2p participated in reducing Cr(VI) in the form of Fe(III) and Fe(II). Proteobacteria, Chloroflexi, and Bacteroidetes were the dominant phylum in the Fe(III)-enhanced MFC-granular sludge coupling system, accounting for 49.7%-81.83% of the microbial community. The relative abundance of Syntrophobacter and Geobacter increased after adding Fe(III), indicating that Fe(III) contributed to the microbial mediated anaerobic oxidation of methane (AOM) and bioreduction of Cr(VI). The genes mcr, hdr, and mtr were highly expressed in the coupling system after the Fe(III) concentration increased. Meanwhile, the relative abundances of coo and aacs genes were up-regulated by 0.014% and 0.075%, respectively. Overall, these findings deepen understanding of the mechanism of the Cr(VI) bioreduction in the MFC-granular sludge coupling system driven by methane under the influence of Fe(III).}, } @article {pmid36933182, year = {2023}, author = {Li, J and Huang, T and Zhang, M and Tong, X and Chen, J and Zhang, Z and Huang, F and Ai, H and Huang, L}, title = {Metagenomic sequencing reveals swine lung microbial communities and metagenome-assembled genomes associated with lung lesions-a pilot study.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {26}, number = {4}, pages = {893-906}, pmid = {36933182}, issn = {1618-1905}, support = {2016YT03H062//Guangdong Sail Plan Introduction of Innovative and Entrepreneurship Research Team Program/ ; nycytx-009//National Swine Industry and Technology System of China/ ; }, mesh = {Swine ; *Metagenome ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Lung/microbiology ; Metagenomics ; }, abstract = {Low microbial biomass in the lungs, high host-DNA contamination and sampling difficulty limit the study on lung microbiome. Therefore, little is still known about lung microbial communities and their functions. Here, we perform a preliminary exploratory study to investigate the composition of swine lung microbial community using shotgun metagenomic sequencing and compare the microbial communities between healthy and severe-lesion lungs. We collected ten lavage-fluid samples from swine lungs (five from healthy lungs and five from severe-lesion lungs), and obtained their metagenomes by shotgun metagenomic sequencing. After filtering host genomic DNA contamination (93.5% ± 1.2%) in the lung metagenomic data, we annotated swine lung microbial communities ranging from four domains to 645 species. Compared with previous taxonomic annotation of the same samples by the 16S rRNA gene amplicon sequencing, it annotated the same number of family taxa but more genera and species. We next performed an association analysis between lung microbiome and host lung-lesion phenotype. We found three species (Mycoplasma hyopneumoniae, Ureaplasma diversum, and Mycoplasma hyorhinis) were associated with lung lesions, suggesting they might be the key species causing swine lung lesions. Furthermore, we successfully reconstructed the metagenome-assembled genomes (MAGs) of these three species using metagenomic binning. This pilot study showed us the feasibility and relevant limitations of shotgun metagenomic sequencing for the characterization of swine lung microbiome using lung lavage-fluid samples. The findings provided an enhanced understanding of the swine lung microbiome and its role in maintaining lung health and/or causing lung lesions.}, } @article {pmid36933058, year = {2023}, author = {Balachandran, KRS and Sankara Subramanianan, SH and Dhassiah, MP and Rengarajan, A and Chandrasekaran, M and Rangamaran, VR and Gopal, D}, title = {Microbial community structure and exploration of bioremediation enzymes: functional metagenomics insight into Arabian Sea sediments.}, journal = {Molecular genetics and genomics : MGG}, volume = {298}, number = {3}, pages = {627-651}, pmid = {36933058}, issn = {1617-4623}, mesh = {*Metagenomics/methods ; Biodegradation, Environmental ; *Microbiota/genetics ; Bacteria/genetics ; Hydrocarbons/metabolism ; }, abstract = {Deep-sea sediments provide important information on oceanic biogeochemical processes mediated by the microbiome and their functional roles which could be unravelled using genomic tools. The present study aimed to delineate microbial taxonomic and functional profiles from Arabian Sea sediment samples through whole metagenome sequencing using Nanopore technology. Arabian Sea is considered as a major microbial reservoir with significant bio-prospecting potential which needs to be explored extensively using recent advances in genomics. Assembly, co-assembly, and binning methods were used to predict Metagenome Assembled Genomes (MAGs) which were further characterized by their completeness and heterogeneity. Nanopore sequencing of Arabian Sea sediment samples generated around 1.73 tera basepairs of data. Proteobacteria (78.32%) was found to be the most dominant phylum followed by Bacteroidetes (9.55%) and Actinobacteria (2.14%) in the sediment metagenome. Further, 35 MAGs from assembled and 38 MAGs of co-assembled reads were generated from long-read sequence dataset with major representations from the genera Marinobacter, Kangiella, and Porticoccus. RemeDB analysis revealed a high representation of pollutant-degrading enzymes involved in hydrocarbon, plastic and dye degradation. Validation of enzymes with long nanopore reads using BlastX resulted in better characterization of complete gene signatures involved in hydrocarbon (6-monooxygenase and 4-hydroxyacetophenone monooxygenase) and dye degradation (Arylsulfatase). Enhancing the cultivability of deep-sea microbes predicted from the uncultured WGS approaches by I-tip method resulted in isolation of facultative extremophiles. This study presents a comprehensive insight into the taxonomic and functional profiles of Arabian Sea sediments, indicating a potential hotspot for bioprospection.}, } @article {pmid36932631, year = {2023}, author = {Wen, T and Ding, Z and Thomashow, LS and Hale, L and Yang, S and Xie, P and Liu, X and Wang, H and Shen, Q and Yuan, J}, title = {Deciphering the mechanism of fungal pathogen-induced disease-suppressive soil.}, journal = {The New phytologist}, volume = {238}, number = {6}, pages = {2634-2650}, doi = {10.1111/nph.18886}, pmid = {36932631}, issn = {1469-8137}, mesh = {Soil ; Reactive Oxygen Species/metabolism ; Soil Microbiology ; *Fusarium ; *Cucumis sativus/microbiology ; Plant Roots/metabolism ; Plant Diseases/microbiology ; }, abstract = {One model of a disease-suppressive soil predicts that the confrontation of plant with a phytopathogen can lead to the recruitment and accumulation of beneficial microorganisms. However, more information needs to be deciphered regarding which beneficial microbes become enriched, and how the disease suppression is achieved. Here, we conditioned soil by continuously growing eight generations of cucumber inoculated with Fusarium oxysporum f.sp. cucumerinum in a split-root system. Disease incidence was found to decrease gradually upon pathogen infection accompanied with higher quantity of reactive oxygen species (ROS mainly OH[•]) in roots and accumulation of Bacillus and Sphingomonas. These key microbes were proven to protect the cucumber from pathogen infection by inducing high ROS level in the roots through enrichment of pathways, including a two-component system, a bacterial secretion system, and flagellar assembly revealed by metagenomics sequencing. Untargeted metabolomics analysis combined with in vitro application assays suggested that threonic acid and lysine were pivotal to recruit Bacillus and Sphingomonas. Collectively, our study deciphered a 'cry for help' case, wherein cucumber releases particular compounds to enrich beneficial microbes that raise the ROS level of host to prevent pathogen attack. More importantly, this may be one of the fundamental mechanisms underpinning disease-suppressive soil formation.}, } @article {pmid36931530, year = {2023}, author = {Li, J and Zhu, S and Wang, Y and Fan, M and Dai, J and Zhu, C and Xu, K and Cui, M and Suo, C and Jin, L and Jiang, Y and Chen, X}, title = {Metagenomic association analysis of cognitive impairment in community-dwelling older adults.}, journal = {Neurobiology of disease}, volume = {180}, number = {}, pages = {106081}, doi = {10.1016/j.nbd.2023.106081}, pmid = {36931530}, issn = {1095-953X}, mesh = {Humans ; Aged ; Independent Living ; *Cognitive Dysfunction ; Cognition ; Bacteria ; *Dementia ; }, abstract = {The gut microbiota is reportedly involved in neurodegenerative disorders, and exploration of differences in the gut microbiota in different cognitive status could provide clues for early detection and intervention in cognitive impairment. Here, we used data from the Taizhou Imaging Study (N = 516), a community-based cohort, to compare the overall structure of the gut microbiota at the species level through metagenomic sequencing, and to explore associations with cognition. Interestingly, bacteria capable of producing short-chain fatty acids (SCFAs), such as Bacteroides massiliensis, Bifidobacterium pseudocatenulatum, Fusicatenibacter saccharivorans and Eggerthella lenta, that can biotransform polyphenols, were positively associated with better cognitive performance (p < 0.05). Although Diallister invisus and Streptococcus gordonii were not obviously related to cognition, the former was dominant in individuals with mild cognitive impairment (MCI), while the later was more abundant in cognitively normal (CN) than MCI groups, and positively associated with cognitive performance (p < 0.05). Functional analysis further supported a potential role of SCFAs and lactic acid in the association between the gut microbiota and cognition. The significant associations persisted after accounting for dietary patterns. Collectively, our results demonstrate an association between the gut microbiota and cognition in the general population, indicating a potential role in cognitive impairment. The findings provide clues for microbiome biomarkers of dementia, and insight for the prevention and treatment of dementia.}, } @article {pmid36931448, year = {2023}, author = {Li, W and Pang, L and Chatzisymeon, E and Yang, P}, title = {Effects of micron-scale zero valent iron on behaviors of antibiotic resistance genes and pathogens in thermophilic anaerobic digestion of waste activated sludge.}, journal = {Bioresource technology}, volume = {376}, number = {}, pages = {128895}, doi = {10.1016/j.biortech.2023.128895}, pmid = {36931448}, issn = {1873-2976}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Sewage/microbiology ; Genes, Bacterial/genetics ; Iron/pharmacology ; Anaerobiosis ; Drug Resistance, Microbial/genetics ; }, abstract = {This work investigated the metagenomics-based behavior and risk of antibiotic resistance genes (ARGs), and their potential hosts during thermophilic anaerobic digestion (TAD) of waste activated sludge, enhanced by micron-scale zero valent iron (mZVI). Tests were conducted with 0, 25, 100, and 250 mg mZVI/g total solids (TS). Results showed that up to 7.3% and 4.8% decrease in ARGs' abundance and diversity, respectively, were achieved with 100 mg mZVI/g TS. At these conditions, ARGs with health risk in abundance and human pathogenic bacteria (HPB) diversity were also decreased by 8.3% and 3.6%, respectively. Additionally, mZVI reduced abundance of 72 potential pathogenic supercarriers for ARGs with high health risk by 2.5%, 5.0%, and 6.1%, as its dosage increased. Overall, mZVI, especially at 100 mg/g TS, can mitigate antibiotic resistance risk in TAD. These findings are important for better understanding risks of ARGs and their pathogenic hosts in ZVI-enhanced TAD of solid wastes.}, } @article {pmid36931374, year = {2023}, author = {Yan, F and Wang, S and Huang, Z and Liu, Y and He, L and Qian, F}, title = {Microbial ecological responses of partial nitritation/anammox granular sludge to real water matrices and its potential application.}, journal = {Environmental research}, volume = {226}, number = {}, pages = {115701}, doi = {10.1016/j.envres.2023.115701}, pmid = {36931374}, issn = {1096-0953}, mesh = {*Sewage/microbiology ; Wastewater ; Water ; Anaerobic Ammonia Oxidation ; Bioreactors/microbiology ; *Ammonium Compounds/chemistry/metabolism ; Bacteria/genetics/metabolism ; Oxidation-Reduction ; Nitrogen/metabolism ; }, abstract = {Granular sludges are commonly microbial aggregates used to apply partial nitritation/anammox (PN/A) processes during efficient biological nitrogen removal from ammonium-rich wastewater. Considering keystone taxa of anammox bacteria (AnAOB) in granules and their sensitivity to unfavorable environments, it is essential to investigate microbial responses of autotrophic PN/A granules to real water matrices containing organic and inorganic pollutants. In this study, tap water, surface water, and biotreated wastewater effluents were fed into a series of continuous PN/A granular reactors, respectively, and the differentiation in functional activity, sludge morphology, microbial community structure, and nitrogen metabolic pathways was analyzed by integrating kinetic batch testing, size characterization, and metagenomic sequencing. The results showed that feeding of biotreated wastewater effluents causes significant decreases in nitrogen removal activity and washout of AnAOB (dominated by Candidatus Kuenenia) from autotrophic PN/A granules due to the accumulation of heavy metals and formation of cavities. Microbial co-occurrence networks and nitrogen cycle-related genes provided evidence for the high dependence of symbiotic heterotrophs (such as Proteobacteria, Chloroflexi, and Bacteroidetes) on anammox metabolism. The enhancement of Nitrosomonas nitritation in the granules would be considered as an important contributor to greenhouse gas (N2O) emissions from real water matrices. In a novel view on the application of microbial responses, we suggest a bioassay of PN/A granules by size characterization of red-color cores in ecological risk assessment of water environments.}, } @article {pmid36931186, year = {2023}, author = {Yang, Y and Deng, Y and Shi, X and Liu, L and Yin, X and Zhao, W and Li, S and Yang, C and Zhang, T}, title = {QMRA of beach water by Nanopore sequencing-based viability-metagenomics absolute quantification.}, journal = {Water research}, volume = {235}, number = {}, pages = {119858}, doi = {10.1016/j.watres.2023.119858}, pmid = {36931186}, issn = {1879-2448}, mesh = {Humans ; Microbial Viability ; *Metagenomics ; Reproducibility of Results ; *Nanopore Sequencing ; Propidium ; Azides ; Risk Assessment ; Bacteria ; Escherichia coli ; }, abstract = {The majority of the current regulatory practices for routine monitoring of beach water quality rely on the culture-based enumeration of faecal indicator bacteria (FIB) to develop criteria for promoting the general public's health. To address the limitations of culture methods and the arguable reliability of FIB in indicating health risks, we developed a Nanopore metagenomic sequencing-based viable cell absolute quantification workflow to rapidly and accurately estimate a broad range of microbes in beach waters by a combination of propidium monoazide (PMA) and cellular spike-ins. Using the simple synthetic bacterial communities mixed with viable and heat-killed cells, we observed near-complete relic DNA removal by PMA with minimal disturbance to the composition of viable cells, demonstrating the feasibility of PMA treatment in profiling viable cells by Nanopore sequencing. On a simple mock community comprised of 15 prokaryotic species, our results showed high accordance between the expected and estimated concentrations, suggesting the accuracy of our method in absolute quantification. We then further assessed the accuracy of our method for counting viable Escherichia coli and Vibrio spp. in beach waters by comparing to culture-based method, which were also in high agreement. Furthermore, we demonstrated that 1 Gb sequences obtained within 2 h would be sufficient to quantify a species having a concentration of ≥ 10 cells/mL in beach waters. Using our viability-resolved quantification workflow to assess the microbial risk of the beach water, we conducted (1) screening-level quantitative microbial risk assessment (QMRA) to investigate human illness risk and site-specific risk patterns that might guide risk management efforts and (2) metagenomics-based resistome risk assessment to evaluate another layer of risk caused by difficult illness treatment due to antimicrobial resistance (AMR). In summary, our metagenomic workflow for the rapid absolute quantification of viable bacteria demonstrated its great potential in paving new avenues toward holistic microbial risk assessment.}, } @article {pmid36931127, year = {2023}, author = {Kugarajah, V and Nisha, KN and Jayakumar, R and Sahabudeen, S and Ramakrishnan, P and Mohamed, SB}, title = {Significance of microbial genome in environmental remediation.}, journal = {Microbiological research}, volume = {271}, number = {}, pages = {127360}, doi = {10.1016/j.micres.2023.127360}, pmid = {36931127}, issn = {1618-0623}, mesh = {*Ecosystem ; Genetic Engineering ; *Environmental Pollutants ; Biodegradation, Environmental ; Genome, Microbial ; }, abstract = {Environmental pollutants seriously threaten the ecosystem and health of various life forms, particularly with the rapid industrialization and emerging population. Conventionally physical and chemical strategies are being opted for the removal of these pollutants. Bioremediation, through several advancements, has been a boon to combat the existing threat faced today. Microbes with enzymes degrade various pollutants and utilize them as a carbon and energy source. With the existing demand and through several research explorations, Genetically Engineered Microorganisms (GEMs) have paved to be a successful approach to abate pollution through bioremediation. The genome of the microbe determines its biodegradative nature. Thus, methods including pure culture techniques and metagenomics are used for analyzing the genome of microbes, which provides information about catabolic genes. The information obtained along with the aid of biotechnology helps to construct GEMs that are cost-effective and safer thereby exhibiting higher degradation of pollutants. The present review focuses on the role of microbes in the degradation of environmental pollutants, role of evolution in habitat and adaptation of microbes, microbial degenerative genes, their pathways, and the efficacy of recombinant DNA (rDNA) technology for creating GEMs for bioremediation. The present review also provides a gist of existing GEMs for bioremediation and their limitations, thereby providing a future scope of implementation of these GEMs for a sustainable environment.}, } @article {pmid36931094, year = {2023}, author = {Correia, GD and Marchesi, JR and MacIntyre, DA}, title = {Moving beyond DNA: towards functional analysis of the vaginal microbiome by non-sequencing-based methods.}, journal = {Current opinion in microbiology}, volume = {73}, number = {}, pages = {102292}, doi = {10.1016/j.mib.2023.102292}, pmid = {36931094}, issn = {1879-0364}, mesh = {Female ; Humans ; *Microbiota/genetics ; Metagenomics/methods ; Host Microbial Interactions ; DNA ; }, abstract = {Over the last two decades, sequencing-based methods have revolutionised our understanding of niche-specific microbial complexity. In the lower female reproductive tract, these approaches have enabled identification of bacterial compositional structures associated with health and disease. Application of metagenomics and metatranscriptomics strategies have provided insight into the putative function of these communities but it is increasingly clear that direct measures of microbial and host cell function are required to understand the contribution of microbe-host interactions to pathophysiology. Here we explore and discuss current methods and approaches, many of which rely upon mass-spectrometry, being used to capture functional insight into the vaginal mucosal interface. In addition to improving mechanistic understanding, these methods offer innovative solutions for the development of diagnostic and therapeutic strategies designed to improve women's health.}, } @article {pmid36930418, year = {2023}, author = {Thakur, N and Nigam, M and Awasthi, G and Shukla, A and Shah, AA and Negi, N and Khan, SA and Casini, R and Elansary, HO}, title = {Synergistic soil-less medium for enhanced yield of crops: a step towards incorporating genomic tools for attaining net zero hunger.}, journal = {Functional & integrative genomics}, volume = {23}, number = {2}, pages = {86}, pmid = {36930418}, issn = {1438-7948}, support = {RSP2023R118//Researchers Supporting Project (RSP2023R118), King Saud University/ ; }, mesh = {Humans ; *CRISPR-Cas Systems ; *Soil ; Proteomics ; Hunger ; Phylogeny ; Genome, Plant ; Plant Breeding/methods ; Crops, Agricultural/genetics ; Genomics ; }, abstract = {Globally, industrial farming endangers crucial ecological mechanisms upon which food production relies, while 815 million people are undernourished and a significant number are malnourished. Zero Hunger aims to concurrently solve global ecological sustainability and food security concerns. Recent breakthroughs in molecular tools and approaches have allowed scientists to detect and comprehend the nature and structure of agro-biodiversity at the molecular and genetic levels, providing us an advantage over traditional methods of crop breeding. These bioinformatics techniques let us optimize our target plants for our soil-less medium and vice versa. Most of the soil-borne and seed-borne diseases are the outcomes of non-treated seed and growth media, which are important factors in low productivity. The farmers do not consider these issues, thereby facing problems growing healthy crops and suffering economic losses. This study is going to help the farmers increase their eco-friendly, chemical residue-free, quality yield of crops and their economic returns. The present invention discloses a synergistic soil-less medium that consists of only four ingredients mixed in optimal ratios by weight: vermicompost (70-80%), vermiculite (10-15%), coco peat (10-15%), and Rhizobium (0-1%). The medium exhibits better physical and chemical characteristics than existing conventional media. The vermiculite to coco peat ratio is reduced, while the vermicompost ratio is increased, with the goals of lowering toxicity, increasing plant and water holding capacity, avoiding drying of the media, and conserving water. The medium provides balanced nutrition and proper ventilation for seed germination and the growth of seedlings. Rhizobium is also used to treat the plastic bags and seeds. The results clearly show that the current synergistic soil-less environment is best for complete plant growth. Securing genetic advantages via sexual recombination, induced random mutations, and transgenic techniques have been essential for the development of improved agricultural varieties. The recent availability of targeted genome-editing technology provides a new path for integrating beneficial genetic modifications into the most significant agricultural species on the planet. Clustered regularly interspaced short palindromic repeats and associated protein 9 (CRISPR/Cas9) has evolved into a potent genome-editing tool for imparting genetic modifications to crop species. In addition, the integration of analytical methods like population genomics, phylogenomics, and metagenomics addresses conservation problems, while whole genome sequencing has opened up a new dimension for explaining the genome architecture and its interactions with other species. The in silico genomic and proteomic investigation was also conducted to forecast future investigations for the growth of French beans on a synergistic soil-less medium with the purpose of studying how a blend of vermicompost, vermiculite, cocopeat, and Rhizobium secrete metal ions, and other chemical compounds into the soil-less medium and affect the development of our target plant as well as several other plants. This interaction was studied using functional and conserved region analysis, phylogenetic analysis, and docking tools.}, } @article {pmid36930078, year = {2023}, author = {Zhang, J and Xu, G and Shen, J and Ye, G}, title = {Pulmonary infection of Schizophyllum commune diagnosed by metagenomic next- generation sequencing: A case report.}, journal = {Medicine}, volume = {102}, number = {11}, pages = {e31465}, pmid = {36930078}, issn = {1536-5964}, mesh = {Female ; Humans ; Adult ; *Schizophyllum/genetics ; *Mycoses/microbiology ; *Pneumonia ; *Lung Diseases, Fungal/diagnosis/drug therapy/microbiology ; High-Throughput Nucleotide Sequencing ; }, abstract = {RATIONALE: Fungal infection is common and difficult to be diagnosed timely in clinical, for its various kinds and similar manifestations. The rare pulmonary fungal infection such as Schizophyllum commune was one of the harder ones and misdiagnosed in usual.

PATIENT CONCERNS: We report a 32-year-old female which was diagnosed with Metagenomic Next-Generation Sequencing (mNGS). She was hospitalized with the complaint of 4 months and more of repeated cough and expectorating. The chest computer tomography revealed left lower lobe pathological changes, but antibiotics were ineffective. No positive results were found in laboratory tests, including sputum culture and the pathology of lung puncture biopsy.

DIAGNOSES: mNGS of lung biopsy was performed and detected the sequence number of Schizophyllum for 11.

INTERVENTIONS: The patient was treated with voriconazole and itraconazole successively.

OUTCOMES: She recovered to health. There was no recurrence during follow-up.

LESSONS: mNGS as a diagnostic method could quickly detect pathogens through the processing of fragment, synthesis, comparison, and analysis of sample genes. It is suitable for detecting especially rare and polymicrobial infections. To our best knowledge, infection of Schizophyllum commune have not been reported in English literature with diagnostic method of mNGS.}, } @article {pmid36929732, year = {2023}, author = {Ma, ZS}, title = {Virome comparison (VC): A novel approach to comparing viromes based on virus species specificity and virome specificity diversity.}, journal = {Journal of medical virology}, volume = {95}, number = {4}, pages = {e28682}, doi = {10.1002/jmv.28682}, pmid = {36929732}, issn = {1096-9071}, mesh = {Humans ; *Virome/genetics ; Species Specificity ; *Viruses/genetics ; Metagenomics ; }, abstract = {The human virome, or the viral communities distributed on or in our body, is estimated to contain about 380 trillion of viruses (individuals), which has far reaching influences on our health and diseases. Obviously, the sheer numbers of viruses alone make the comparisons of two or multiple viromes extremely challenging. In fact, the theory of computation in computer science for so-termed NP-hard problems stipulates that the problem is unsolvable when the size of virome is sufficiently large even with fastest supercomputers. Practically, one has to develop heuristic and approximate algorithms to obtain practically satisfactory solutions for NP-hard problems. Here, we extend the species-specificity and specificity-diversity framework to develop a method for virome comparison (VC). The VC method consists of a pair of metrics: virus species specificity (VS) and virome specificity diversity (VSD) and corresponding pair of random search algorithms. Specifically, the VS and VS permutation (VSP) test can detect unique virus species (US) or enriched virus species (ES) in each virome (treatment), and the VSD and VSD permutation (VSDP) test can further determine holistic differences between two viromes or their subsets (assemblages of viruses). The test with four virome data sets demonstrated that the VC method is effective, efficient, and robust.}, } @article {pmid36929690, year = {2023}, author = {Zhu, N and Zhou, D and Yuan, R and Ruzetuoheti, Y and Li, J and Zhang, X and Li, S}, title = {Identification and comparison of Chlamydia psittaci, Legionella and Mycoplasma pneumonia infection.}, journal = {The clinical respiratory journal}, volume = {17}, number = {5}, pages = {384-393}, pmid = {36929690}, issn = {1752-699X}, support = {81970048//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Pneumonia, Mycoplasma ; *Chlamydophila psittaci/genetics ; *Legionella ; Retrospective Studies ; *Pneumonia ; Albumins ; }, abstract = {INTRODUCTION: Conventional etiological detection and pathogenic antibody methods make it challenging to identify the atypical pathogens among the community-acquired pneumonia (CAP). Metagenomic next-generation sequencing (mNGS) could rapidly detect all potentially infectious diseases and identifies novel or potential pathogens.

METHODS: Eighteen patients diagnosed with atypical CAP were enrolled in this retrospective study, including nine Chlamydia psittaci pneumonia (C. p), four Legionella pneumonia (L. p) and five Mycoplasma pneumonia (M. p). We simultaneously tested bronchoalveolar lavage fluid (BALF) samples for conventional microbiological methods and mNGS, and blood specimens were analysed. We also collected and compared baseline and clinical characteristics and treatment responses.

RESULTS: Patients with C. p and L. p had similar symptoms, including fever, cough, headache, dyspnoea, asthenia, shivering and headache, compared with M. p, whose symptoms were slight. C. p and L. p usually showed multiple lobar distributions with pleural effusion. Serologic testing indicated that L. p had higher levels of white blood cells (WBCs), neutrophils, C-reactive protein (CRP), procalcitonin (PCT), alanine aminotransferase (ALT), lactate dehydrogenase (LDH) and creatinine compared with M. p and L. p (p < 0.05). However, patients with C. p had lower levels of albumin (p < 0.05), and M. p had a minimum risk of cardiac volume loads (p < 0.05). CD4/CD8 ratio, lymphocytes, aspartate aminotransferase (AST), creatine kinase (CK), cell counting of BALF and coagulation had no difference (p < 0.05). Pathogenic IgM assay showed that 4/5 cases were positive for M. p and no positive detection for C. p and L. p infection. We timely adjusted the antibiotics according to the final mNGS results. Eventually, 16/18 patients recovered fully. Conditions of L. p patients were worse than those of C. p patients, and those of M. p patients were the least.

CONCLUSION: Early application of mNGS detection increased the atypical pathogenic identification, improved the prognosis and made up for the deficiency of conventional detection methods.}, } @article {pmid36929191, year = {2023}, author = {Sharma, P and Singh, S and Das, K and Mahant, S and Das, R}, title = {Dysbiosis of gut microbiota due to diet, alcohol intake, body mass index, and gastrointestinal diseases in India.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {7-8}, pages = {2547-2560}, pmid = {36929191}, issn = {1432-0614}, support = {EMR/2016/003676//Department of Science and Technology, India/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Body Mass Index ; RNA, Ribosomal, 16S/genetics ; Dysbiosis ; Diet ; Bacteria/genetics ; Alcohol Drinking ; *Gastrointestinal Diseases ; }, abstract = {The human gut is composed of diverse microflora which is influenced by dietary intake. Body mass index (BMI) and lifestyle patterns also play a vital role in human health to alter gut microbial composition. Our study aims to determine the impact of alcohol intake, BMI, and diet on gut microbiota and its relationship with gastrointestinal disorders. Thirty-nine gastric biopsies were taken from patients with various gastrointestinal (GI) diseases, and all the patient's lifestyle behavior were recorded in a written proforma. 16S rRNA metagenome analysis for V3-V4 regions was used to examine microbial compositions. The richness and diversity of gut microbiota were analyzed by PERMANOVA using the Bray-Curtis dissimilarity index and principal component analysis. The difference in relative abundance was calculated by ANOVA (p < 0.05). Alpha diversity indexes between vegetarians and non-vegetarians showed no significant difference based on BMI, alcohol status, and GI diseases. We found that in overweight vegetarian individuals Faecalibacterium and Rumicococcus might play a role in the control of Helicobacter pylori. Similarly, the increased abundance of Akkermansia muciniphila in non-vegetarian individuals with normal BMI might play a role to decrease the level of harmful bacteria like H. pylori, and Corynebacterium sp. Also, the relative abundance of Corynebacterium sp. among the vegetarians and Streptococcus sp. in the non-vegetarians was increased in alcoholics while H. pylori was increased in non-alcoholics irrespective of diet. There is an increased abundance of Faecalibacterium prausnitzii in vegetarians among all categories; however, we did not find any correlation between disease outcomes. Our study shows that alcohol intake and dietary habits have independent effects on gut microbial composition. The relative abundance of F. prausnitzii was high among vegetarians in all categories. KEY POINTS: • The presence of H. pylori is less among alcoholics. • Good bacteria help to maintain a normal body mass index. • Gut microbiota richness is high in vegetarians and diversity in non-vegetarians.}, } @article {pmid36929080, year = {2023}, author = {Ma, S and Li, H}, title = {Statistical and Computational Methods for Microbial Strain Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2629}, number = {}, pages = {231-245}, pmid = {36929080}, issn = {1940-6029}, mesh = {*Microbiota/genetics ; Metagenome ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; }, abstract = {Microbial strains are interpreted as a lineage derived from a recent ancestor that have not experienced "too many" recombination events and can be successfully retrieved with culture-independent techniques using metagenomic sequencing. Such a strain variability has been increasingly shown to display additional phenotypic heterogeneities that affect host health, such as virulence, transmissibility, and antibiotics resistance. New statistical and computational methods have recently been developed to track the strains in samples based on shotgun metagenomics data either based on reference genome sequences or Metagenome-assembled genomes (MAGs). In this paper, we review some recent statistical methods for strain identifications based on frequency counts at a set of single nucleotide variants (SNVs) within a set of single-copy marker genes. These methods differ in terms of whether reference genome sequences are needed, how SNVs are called, what methods of deconvolution are used and whether the methods can be applied to multiple samples. We conclude our review with areas that require further research.}, } @article {pmid36929079, year = {2023}, author = {Kim, Y}, title = {Bioinformatic and Statistical Analysis of Microbiome Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2629}, number = {}, pages = {183-229}, pmid = {36929079}, issn = {1940-6029}, mesh = {Humans ; Phylogeny ; *Microbiota/genetics ; Biodiversity ; Computational Biology/methods ; RNA, Ribosomal, 16S/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Since advances in next-generation sequencing (NGS) technique enabled to investigate uncultured microbiota and their genomes in unbiased manner, many microbiome researches have been reporting strong evidences for close links of microbiome to human health and disease. Bioinformatic and statistical analysis of NGS-based microbiome data are essential components in those microbiome researches to explore the complex composition of microbial community and understand the functions of community members in relation to host and environment. This chapter introduces bioinformatic analysis methods that generate taxonomy and functional feature count table along with phylogenetic tree from raw NGS microbiome data and then introduce statistical methods and machine learning approaches for analyzing the outputs of the bioinformatic analysis to infer the biodiversity of a microbial community and unravel host-microbiome association. Understanding the advantages and limitations of the analysis methods will help readers use the methods correctly in microbiome data analysis and may give a new opportunity to develop new analytic techniques for microbiome research.}, } @article {pmid36928772, year = {2023}, author = {Zhao, X and Guo, Y and Kang, L and Yin, C and Bi, A and Xu, D and Zhang, Z and Zhang, J and Yang, X and Xu, J and Xu, S and Song, X and Zhang, M and Li, Y and Kear, P and Wang, J and Liu, Z and Fu, X and Lu, F}, title = {Population genomics unravels the Holocene history of bread wheat and its relatives.}, journal = {Nature plants}, volume = {9}, number = {3}, pages = {403-419}, pmid = {36928772}, issn = {2055-0278}, support = {32225038//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31970631//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; Humans ; *Genome, Plant ; *Triticum/genetics ; Metagenomics ; Bread ; Europe ; }, abstract = {Deep knowledge of crop biodiversity is essential to improving global food security. Despite bread wheat serving as a keystone crop worldwide, the population history of bread wheat and its relatives, both cultivated and wild, remains elusive. By analysing whole-genome sequences of 795 wheat accessions, we found that bread wheat originated from the southwest coast of the Caspian Sea and underwent a slow speciation process, lasting ~3,300 yr owing to persistent gene flow from its relatives. Soon after, bread wheat spread across Eurasia and reached Europe, South Asia and East Asia ~7,000 to ~5,000 yr ago, shaping a diversified but occasionally convergent adaptive landscape in novel environments. By contrast, the cultivated relatives of bread wheat experienced a population decline by ~82% over the past ~2,000 yr due to the food choice shift of humans. Further biogeographical modelling predicted a continued population shrinking of many bread wheat relatives in the coming decades because of their vulnerability to the changing climate. These findings will guide future efforts in protecting and utilizing wheat biodiversity to enhance global wheat production.}, } @article {pmid36928747, year = {2023}, author = {Zhang, Y and Liu, F and Liang, H and Gao, D}, title = {Correction to: Mediative Mechanism of Freezing/Thawing on Greenhouse Gas Emissions in an Inland Saline Alkaline Wetland: a Metagenomic Analysis.}, journal = {Microbial ecology}, volume = {86}, number = {3}, pages = {2210}, doi = {10.1007/s00248-023-02205-x}, pmid = {36928747}, issn = {1432-184X}, } @article {pmid36928716, year = {2023}, author = {Wahlen, BD and Wendt, LM and St Germain, CC and Traynor, SM and Barboza, C and Dempster, T and Gerken, H and McGowen, J and You, Y}, title = {Effect of nitrogen management in cultivation on the stability and microbial community of post-harvest Monoraphidium sp. algae biomass.}, journal = {Journal of industrial microbiology & biotechnology}, volume = {50}, number = {1}, pages = {}, pmid = {36928716}, issn = {1476-5535}, support = {//U.S. Department of Energy/ ; DE-AC07-05ID14517//Bioenergy Technologies Office/ ; }, mesh = {Biomass ; *Nitrogen/metabolism ; Follow-Up Studies ; *Microalgae/metabolism ; }, abstract = {Long-term storage is necessary to mitigate for seasonal variation in algae productivity, to preserve biomass quality and to guarantee a constant biomass supply to a conversion facility. While ensiling has shown promise as a solution, biomass attributes for successful storage are poorly understood. Storage studies of Monoraphidium sp. biomass indicate a strong correlation between nitrogen management in algae cultivation and stability of post-harvest algae biomass. Algae cultivated with periodic nitrogen addition were stored poorly (>20% loss, dry basis) compared to biomass from nitrogen depleted cultivation (8% loss, dry basis). A follow-up study compared the post-harvest stability of Monoraphidium biomass cultivated in nitrogen-deplete or nitrogen-replete conditions. Replete biomass experienced the largest degradation (24%, dry basis), while deplete biomass experienced the least (10%, dry basis). Dry matter loss experienced among blends of each correlated positively with nitrogen-replete biomass content. The composition of the post-storage algae microbial community was also affected by cultivation conditions, with Clostridia species being more prevalent in stored biomass obtained from nitrogen-replete cultivations. Nitrogen management has long been known to influence algae biomass productivity and biochemical composition; here, we demonstrate that it also strongly influences the stability of post-harvest algae biomass in anaerobic storage.}, } @article {pmid36928667, year = {2023}, author = {Yokoyama, M and Peto, L and Budgell, EP and Jones, N and Sheridan, E and Liu, J and Walker, AS and Stoesser, N and Gweon, HS and Llewelyn, MJ}, title = {Microbial diversity and antimicrobial resistance in faecal samples from acute medical patients assessed through metagenomic sequencing.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0282584}, pmid = {36928667}, issn = {1932-6203}, support = {RP-PG-0514-20015/DH_/Department of Health/United Kingdom ; }, mesh = {Humans ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Metagenome ; *Clostridioides difficile/genetics ; State Medicine ; Drug Resistance, Bacterial/genetics ; *Anti-Infective Agents/pharmacology ; Metagenomics/methods ; }, abstract = {Antimicrobial resistance (AMR) is a threat to global public health. However, unsatisfactory approaches to directly measuring the AMR burden carried by individuals has hampered efforts to assess interventions aimed at reducing selection for AMR. Metagenomics can provide accurate detection and quantification of AMR genes within an individual person's faecal flora (their gut "resistome"). Using this approach, we aimed to test the hypothesis that differences in antimicrobial use across different hospitals in the United Kingdom will result in observable differences in the resistome of individual patients. Three National Health Service acute Hospital Trusts with markedly different antibiotic use and Clostridioides difficile infection rates collected faecal samples from anonymous patients which were discarded after C. difficile testing over a period of 9 to 15 months. Metagenomic DNA was extracted from these samples and sequenced using an Illumina NovaSeq 6000 platform. The resulting sequencing reads were analysed for taxonomic composition and for the presence of AMR genes. Among 683 faecal metagenomes we found huge variation between individuals in terms of taxonomic diversity (Shannon Index range 0.10-3.99) and carriage of AMR genes (Median 1.50 genes/cell/sample overall). We found no statistically significant differences in diversity (median Shannon index 2.16 (IQR 1.71-2.56), 2.15 (IQR 1.62-2.50) and 2.26 (IQR 1.55-2.51)) or carriage of AMR genes (median 1.37 genes/cell/sample (IQR 0.70-3.24), 1.70 (IQR 0.70-4.52) and 1.43 (IQR 0.55-3.71)) at the three trusts respectively. This was also the case across the sample collection period within the trusts. While we have not demonstrated differences over place or time using metagenomic sequencing of faecal discards, other sampling frameworks may be more suitable to determine whether organisational level differences in antibiotic use are associated with individual-level differences in burden of AMR carriage.}, } @article {pmid36928278, year = {2023}, author = {Okazaki, Y and Nguyen, TT and Nishihara, A and Endo, H and Ogata, H and Nakano, SI and Tamaki, H}, title = {A Fast and Easy Method to Co-extract DNA and RNA from an Environmental Microbial Sample.}, journal = {Microbes and environments}, volume = {38}, number = {1}, pages = {}, pmid = {36928278}, issn = {1347-4405}, mesh = {*RNA/genetics ; *DNA/genetics ; Genomics ; Phenol ; }, abstract = {We herein propose a fast and easy DNA and RNA co-extraction method for environmental microbial samples. It combines bead beating and phenol-chloroform phase separation followed by the separation and purification of DNA and RNA using the Qiagen AllPrep DNA/RNA mini kit. With a handling time of ~3 h, our method simultaneously extracted high-quality DNA (peak size >10-15‍ ‍kb) and RNA (RNA integrity number >6) from lake bacterioplankton filtered samples. The method is also applicable to low-biomass samples (expected DNA or RNA yield <50‍ ‍ng) and eukaryotic microbial samples, providing an easy option for more versatile eco-genomic applications.}, } @article {pmid36927888, year = {2023}, author = {Sadee, W and Wang, D and Hartmann, K and Toland, AE}, title = {Pharmacogenomics: Driving Personalized Medicine.}, journal = {Pharmacological reviews}, volume = {75}, number = {4}, pages = {789-814}, pmid = {36927888}, issn = {1521-0081}, support = {R01 CA215151/CA/NCI NIH HHS/United States ; R35 GM140845/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Pharmacogenetics ; Precision Medicine ; Artificial Intelligence ; *Neoplasms/drug therapy/genetics ; Proteomics ; Pharmaceutical Preparations ; }, abstract = {Personalized medicine tailors therapies, disease prevention, and health maintenance to the individual, with pharmacogenomics serving as a key tool to improve outcomes and prevent adverse effects. Advances in genomics have transformed pharmacogenetics, traditionally focused on single gene-drug pairs, into pharmacogenomics, encompassing all "-omics" fields (e.g., proteomics, transcriptomics, metabolomics, and metagenomics). This review summarizes basic genomics principles relevant to translation into therapies, assessing pharmacogenomics' central role in converging diverse elements of personalized medicine. We discuss genetic variations in pharmacogenes (drug-metabolizing enzymes, drug transporters, and receptors), their clinical relevance as biomarkers, and the legacy of decades of research in pharmacogenetics. All types of therapies, including proteins, nucleic acids, viruses, cells, genes, and irradiation, can benefit from genomics, expanding the role of pharmacogenomics across medicine. Food and Drug Administration approvals of personalized therapeutics involving biomarkers increase rapidly, demonstrating the growing impact of pharmacogenomics. A beacon for all therapeutic approaches, molecularly targeted cancer therapies highlight trends in drug discovery and clinical applications. To account for human complexity, multicomponent biomarker panels encompassing genetic, personal, and environmental factors can guide diagnosis and therapies, increasingly involving artificial intelligence to cope with extreme data complexities. However, clinical application encounters substantial hurdles, such as unknown validity across ethnic groups, underlying bias in health care, and real-world validation. This review address the underlying science and technologies germane to pharmacogenomics and personalized medicine, integrated with economic, ethical, and regulatory issues, providing insights into the current status and future direction of health care. SIGNIFICANCE STATEMENT: Personalized medicine aims to optimize health care for the individual patients with use of predictive biomarkers to improve outcomes and prevent adverse effects. Pharmacogenomics drives biomarker discovery and guides the development of targeted therapeutics. This review addresses basic principles and current trends in pharmacogenomics, with large-scale data repositories accelerating medical advances. The impact of pharmacogenomics is discussed, along with hurdles impeding broad clinical implementation, in the context of clinical care, ethics, economics, and regulatory affairs.}, } @article {pmid36927795, year = {2023}, author = {Yi, X and Huang, C and Huang, C and Zhao, M and Lu, Q}, title = {Fecal microbiota from MRL/lpr mice exacerbates pristane-induced lupus.}, journal = {Arthritis research & therapy}, volume = {25}, number = {1}, pages = {42}, pmid = {36927795}, issn = {1478-6362}, mesh = {Mice ; Animals ; Mice, Inbred MRL lpr ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Feces ; *Lupus Erythematosus, Systemic/chemically induced ; }, abstract = {BACKGROUND: The roles of gut microbiota in the pathogenesis of SLE have been receiving much attention during recent years. However, it remains unknown how fecal microbiota transplantation (FMT) and microbial metabolites affect immune responses and lupus progression.

METHODS: We transferred fecal microbiota from MRL/lpr (Lpr) mice and MRL/Mpj (Mpj) mice or PBS to pristane-induced lupus mice and observed disease development. We also screened gut microbiota and metabolite spectrums of pristane-induced lupus mice with FMT via 16S rRNA sequencing, metagenomic sequencing, and metabolomics, followed by correlation analysis.

RESULTS: FMT from MRL/lpr mice promoted the pathogenesis of pristane-induced lupus and affected immune cell profiles in the intestine, particularly the plasma cells. The structure and composition of microbial communities in the gut of the FMT-Lpr mice were different from those of the FMT-Mpj mice and FMT-PBS mice. The abundances of specific microbes such as prevotella taxa were predominantly elevated in the gut microbiome of the FMT-Lpr mice, which were positively associated with functional pathways such as cyanoamino acid metabolism. Differential metabolites such as valine and L-isoleucine were identified with varied abundances among the three groups. The abundance alterations of the prevotella taxa may affect the phenotypic changes such as proteinuria levels in the pristane-induced lupus mice.

CONCLUSION: These findings further confirm that gut microbiota play an important role in the pathogenesis of lupus. Thus, altering the gut microbiome may provide a novel way to treat lupus.}, } @article {pmid36927601, year = {2023}, author = {Thorn, CS and Maness, RW and Hulke, JM and Delmore, KE and Criscione, CD}, title = {Population genomics of helminth parasites.}, journal = {Journal of helminthology}, volume = {97}, number = {}, pages = {e29}, doi = {10.1017/S0022149X23000123}, pmid = {36927601}, issn = {1475-2697}, support = {DEB-1655147//National Science Foundation/ ; }, mesh = {*Metagenomics ; Host-Parasite Interactions/physiology ; *Helminths/classification/genetics ; Hybridization, Genetic/genetics ; Genetic Variation ; Chromosome Mapping ; Drug Resistance/genetics ; Biological Evolution ; Parasitology/trends ; }, abstract = {Next generation sequencing technologies have facilitated a shift from a few targeted loci in population genetic studies to whole genome approaches. Here, we review the types of questions and inferences regarding the population biology and evolution of parasitic helminths being addressed within the field of population genomics. Topics include parabiome, hybridization, population structure, loci under selection and linkage mapping. We highlight various advances, and note the current trends in the field, particularly a focus on human-related parasites despite the inherent biodiversity of helminth species. We conclude by advocating for a broader application of population genomics to reflect the taxonomic and life history breadth displayed by helminth parasites. As such, our basic knowledge about helminth population biology and evolution would be enhanced while the diversity of helminths in itself would facilitate population genomic comparative studies to address broader ecological and evolutionary concepts.}, } @article {pmid36927099, year = {2023}, author = {Chen, J and Li, Y and Zhong, C and Xu, Z and Lu, G and Jing, H and Liu, H}, title = {Genomic Insights into Niche Partitioning across Sediment Depth among Anaerobic Methane-Oxidizing Archaea in Global Methane Seeps.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0117922}, pmid = {36927099}, issn = {2379-5077}, mesh = {*Archaea/genetics ; Anaerobiosis ; *Methane/metabolism ; Oxidation-Reduction ; Metagenomics ; }, abstract = {Marine sediments are important methane reservoirs. Methane efflux from the seabed is significantly restricted by anaerobic methanotrophic (ANME) archaea through a process known as anaerobic oxidation of methane (AOM). Different clades of ANME archaea occupy distinct niches in methane seeps, but their underlying molecular mechanisms still need to be fully understood. To provide genetic explanations for the niche partitioning of ANME archaea, we applied comparative genomic analysis to ANME archaeal genomes retrieved from global methane seeps. Our results showed that ANME-2 archaea are more prevalent than ANME-1 archaea in shallow sediments because they carry genes that encode a significantly higher number of outer membrane multiheme c-type cytochromes and flagellar proteins. These features make ANME-2 archaea perform direct interspecies electron transfer better and benefit more from electron acceptors in AOM. Besides, ANME-2 archaea carry genes that encode extra peroxidase compared to ANME-1 archaea, which may lead to ANME-2 archaea better tolerating oxygen toxicity. In contrast, ANME-1 archaea are more competitive in deep layers than ANME-2 archaea because they carry extra genes (mtb and mtt) for methylotrophic methanogenesis and a significantly higher number of frh and mvh genes for hydrogenotrophic methanogenesis. Additionally, ANME-1 archaea carry exclusive genes (sqr, TST, and mddA) involved in sulfide detoxification compared to ANME-2 archaea, leading to stronger sulfide tolerance. Overall, this study reveals the genomic mechanisms shaping the niche partitioning among ANME archaea in global methane seeps. IMPORTANCE Anaerobic methanotrophic (ANME) archaea are important methanotrophs in marine sediment, controlling the flux of biologically generated methane, which plays an essential role in the marine carbon cycle and climate change. So far, no strain of this lineage has been isolated in pure culture, which makes metagenomics one of the fundamental approaches to reveal their metabolic potential. Although the niche partitioning of ANME archaea was frequently reported in different studies, whether this pattern was consistent in global methane seeps had yet to be verified, and little was known about the genetic mechanisms underlying it. Here, we reviewed and analyzed the community structure of ANME archaea in global methane seeps and indicated that the niche partitioning of ANME archaea was statistically supported. Our comparative genomic analysis indicated that the capabilities of interspecies electron transfer, methanogenesis, and the resistance of oxygen and hydrogen sulfide could be critical in defining the distribution of ANME archaea in methane seep sediment.}, } @article {pmid36927031, year = {2023}, author = {Lin, Z and Akin, H and Rao, R and Hie, B and Zhu, Z and Lu, W and Smetanin, N and Verkuil, R and Kabeli, O and Shmueli, Y and Dos Santos Costa, A and Fazel-Zarandi, M and Sercu, T and Candido, S and Rives, A}, title = {Evolutionary-scale prediction of atomic-level protein structure with a language model.}, journal = {Science (New York, N.Y.)}, volume = {379}, number = {6637}, pages = {1123-1130}, doi = {10.1126/science.ade2574}, pmid = {36927031}, issn = {1095-9203}, mesh = {Amino Acid Sequence ; *Machine Learning ; *Proteins/chemistry ; *Evolution, Molecular ; Protein Conformation ; *Sequence Analysis, Protein ; }, abstract = {Recent advances in machine learning have leveraged evolutionary information in multiple sequence alignments to predict protein structure. We demonstrate direct inference of full atomic-level protein structure from primary sequence using a large language model. As language models of protein sequences are scaled up to 15 billion parameters, an atomic-resolution picture of protein structure emerges in the learned representations. This results in an order-of-magnitude acceleration of high-resolution structure prediction, which enables large-scale structural characterization of metagenomic proteins. We apply this capability to construct the ESM Metagenomic Atlas by predicting structures for >617 million metagenomic protein sequences, including >225 million that are predicted with high confidence, which gives a view into the vast breadth and diversity of natural proteins.}, } @article {pmid36926893, year = {2023}, author = {Shi, C and Tong, M and Cai, Q and Li, Z and Li, P and Lu, Y and Cao, Z and Liu, H and Zhao, HP and Yuan, S}, title = {Electrokinetic-Enhanced Bioremediation of Trichloroethylene-Contaminated Low-Permeability Soils: Mechanistic Insight from Spatio-Temporal Variations of Indigenous Microbial Community and Biodehalogenation Activity.}, journal = {Environmental science & technology}, volume = {57}, number = {12}, pages = {5046-5055}, doi = {10.1021/acs.est.3c00278}, pmid = {36926893}, issn = {1520-5851}, mesh = {*Trichloroethylene ; Biodegradation, Environmental ; Ferric Compounds ; Bacteria ; *Microbiota ; Soil ; Permeability ; Iron ; }, abstract = {Electrokinetic-enhanced bioremediation (EK-Bio), particularly bioaugmentation with injection of biodehalogenation functional microbes such as Dehalococcoides, has been documented to be effective in treating a low-permeability subsurface matrix contaminated with chlorinated ethenes. However, the spatio-temporal variations of indigenous microbial community and biodehalogenation activity of the background matrix, a fundamental aspect for understanding EK-Bio, remain unclear. To fill this gap, we investigated the variation of trichloroethylene (TCE) biodehalogenation activity in response to indigenous microbial community succession in EK-Bio by both column and batch experiments. For a 195 day EK-Bio column (∼1 V/cm, electrolyte circulation, lactate addition), biodehalogenation activity occurred first near the cathode (<60 days) and then spread to the anode (>90 days), which was controlled by electron acceptor (i.e., Fe(III)) competition and microbe succession. Amplicon sequencing and metagenome analysis revealed that iron-reducing bacteria (Geobacter, Anaeromyxobacter, Geothrix) were enriched within initial 60 d and were gradually replaced by organohalide-respiring bacteria (versatile Geobacter and obligate Dehalobacter) afterward. Iron-reducing bacteria required an initial long time to consume the competitive electron acceptors so that an appropriate reductive condition could be developed for the enrichment of organohalide-respiring bacteria and the enhancement of TCE biodehalogenation activity.}, } @article {pmid36926836, year = {2023}, author = {Severino, R and Moreno-Paz, M and Puente-Sánchez, F and Sánchez-García, L and Risso, VA and Sanchez-Ruiz, JM and Cabrol, N and Parro, V}, title = {Immunoanalytical Approach for Detecting and Identifying Ancestral Peptide Biomarkers in Early Earth Analogue Environments.}, journal = {Analytical chemistry}, volume = {95}, number = {12}, pages = {5323-5330}, pmid = {36926836}, issn = {1520-6882}, mesh = {*Peptides ; *beta-Lactamases ; Biomarkers ; Antibodies ; Epitope Mapping ; Epitopes ; }, abstract = {Several mass spectrometry and spectroscopic techniques have been used in the search for molecular biomarkers on Mars. A major constraint is their capability to detect and identify large and complex compounds such as peptides or other biopolymers. Multiplex immunoassays can detect these compounds, but antibodies must be produced for a large number of sequence-dependent molecular targets. Ancestral Sequence Reconstruction (ASR) followed by protein "resurrection" in the lab can help to narrow the selection of targets. Herein, we propose an immunoanalytical method to identify ancient and universally conserved protein/peptide sequences as targets for identifying ancestral biomarkers in nature. We have developed, tested, and validated this approach by producing antibodies to eight previously described ancestral resurrected proteins (three β-lactamases, three thioredoxins, one Elongation Factor Tu, and one RuBisCO, all of them theoretically dated as Precambrian), and used them as a proxy to search for any potential feature of them that could be present in current natural environments. By fluorescent sandwich microarray immunoassays (FSMI), we have detected positive immunoreactions with antibodies to the oldest β-lactamase and thioredoxin proteins (ca. 4 Ga) in samples from a hydrothermal environment. Fine epitope mapping and inhibitory immunoassays allowed the identification of well-conserved epitope peptide sequences that resulted from ASR and were present in the sample. We corroborated these results by metagenomic sequencing and found several genes encoding analogue proteins with significant matches to the peptide epitopes identified with the antibodies. The results demonstrated that peptides inferred from ASR studies have true counterpart analogues in Nature, which validates and strengthens the well-known ASR/protein resurrection technique and our immunoanalytical approach for investigating ancient environments and metabolisms on Earth and elsewhere.}, } @article {pmid36926398, year = {2023}, author = {Deng, ZF and Tang, YJ and Yan, CY and Qin, ZQ and Yu, N and Zhong, XB}, title = {Pulmonary nocardiosis with bloodstream infection diagnosed by metagenomic next-generation sequencing in a kidney transplant recipient: A case report.}, journal = {World journal of clinical cases}, volume = {11}, number = {7}, pages = {1634-1641}, pmid = {36926398}, issn = {2307-8960}, abstract = {BACKGROUND: Pulmonary nocardiosis is difficult to diagnose by culture and other conventional testing, and is often associated with lethal disseminated infections. This difficulty poses a great challenge to the timeliness and accuracy of clinical detection, especially in susceptible immunosuppressed individuals. Metagenomic next-generation sequencing (mNGS) has transformed the conventional diagnosis pattern by providing a rapid and precise method to assess all microorganisms in a sample.

CASE SUMMARY: A 45-year-old male was hospitalized for cough, chest tightness and fatigue for 3 consecutive days. He had received a kidney transplant 42 d prior to admission. No pathogens were detected at admission. Chest computed tomography showed nodules, streak shadows and fiber lesions in both lung lobes as well as right pleural effusion. Pulmonary tuberculosis with pleural effusion was highly suspected based on the symptoms, imaging and residence in a high tuberculosis-burden area. However, anti-tuberculosis treatment was ineffective, showing no improvement in computed tomography imaging. Pleural effusion and blood samples were subsequently sent for mNGS. The results indicated Nocardia farcinica as the major pathogen. After switching to sulphamethoxazole combined with minocycline for anti-nocardiosis treatment, the patient gradually improved and was finally discharged.

CONCLUSION: A case of pulmonary nocardiosis with an accompanying bloodstream infection was diagnosed and promptly treated before the dissemination of the infection. This report emphasizes the value of mNGS in the diagnosis of nocardiosis. mNGS may be an effective method for facilitating early diagnosis and prompt treatment in infectious diseases, which overcomes the shortcomings of conventional testing.}, } @article {pmid36926275, year = {2023}, author = {Bertoline, LMF and Lima, AN and Krieger, JE and Teixeira, SK}, title = {Before and after AlphaFold2: An overview of protein structure prediction.}, journal = {Frontiers in bioinformatics}, volume = {3}, number = {}, pages = {1120370}, pmid = {36926275}, issn = {2673-7647}, abstract = {Three-dimensional protein structure is directly correlated with its function and its determination is critical to understanding biological processes and addressing human health and life science problems in general. Although new protein structures are experimentally obtained over time, there is still a large difference between the number of protein sequences placed in Uniprot and those with resolved tertiary structure. In this context, studies have emerged to predict protein structures by methods based on a template or free modeling. In the last years, different methods have been combined to overcome their individual limitations, until the emergence of AlphaFold2, which demonstrated that predicting protein structure with high accuracy at unprecedented scale is possible. Despite its current impact in the field, AlphaFold2 has limitations. Recently, new methods based on protein language models have promised to revolutionize the protein structural biology allowing the discovery of protein structure and function only from evolutionary patterns present on protein sequence. Even though these methods do not reach AlphaFold2 accuracy, they already covered some of its limitations, being able to predict with high accuracy more than 200 million proteins from metagenomic databases. In this mini-review, we provide an overview of the breakthroughs in protein structure prediction before and after AlphaFold2 emergence.}, } @article {pmid36925044, year = {2023}, author = {Baldanzi, G and Sayols-Baixeras, S and Theorell-Haglöw, J and Dekkers, KF and Hammar, U and Nguyen, D and Lin, YT and Ahmad, S and Holm, JB and Nielsen, HB and Brunkwall, L and Benedict, C and Cedernaes, J and Koskiniemi, S and Phillipson, M and Lind, L and Sundström, J and Bergström, G and Engström, G and Smith, JG and Orho-Melander, M and Ärnlöv, J and Kennedy, B and Lindberg, E and Fall, T}, title = {OSA Is Associated With the Human Gut Microbiota Composition and Functional Potential in the Population-Based Swedish CardioPulmonary bioImage Study.}, journal = {Chest}, volume = {164}, number = {2}, pages = {503-516}, pmid = {36925044}, issn = {1931-3543}, mesh = {Adult ; Animals ; Humans ; *Sleep Apnea, Obstructive ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; Sweden/epidemiology ; Hypoxia ; }, abstract = {BACKGROUND: OSA is a common sleep-breathing disorder linked to increased risk of cardiovascular disease. Intermittent upper airway obstruction and hypoxia, hallmarks of OSA, have been shown in animal models to induce substantial changes to the gut microbiota composition, and subsequent transplantation of fecal matter to other animals induced changes in BP and glucose metabolism.

RESEARCH QUESTION: Does OSA in adults associate with the composition and functional potential of the human gut microbiota?

STUDY DESIGN AND METHODS: We used respiratory polygraphy data from up to 3,570 individuals 50 to 64 years of age from the population-based Swedish Cardiopulmonary bioimage Study combined with deep shotgun metagenomics of fecal samples to identify cross-sectional associations between three OSA parameters covering apneas and hypopneas, cumulative sleep time in hypoxia, and number of oxygen desaturation events with gut microbiota composition. Data collection about potential confounders was based on questionnaires, onsite anthropometric measurements, plasma metabolomics, and linkage with the Swedish Prescribed Drug Register.

RESULTS: We found that all three OSA parameters were associated with lower diversity of species in the gut. Furthermore, in multivariable-adjusted analysis, the OSA-related hypoxia parameters were associated with the relative abundance of 128 gut bacterial species, including higher abundance of Blautia obeum and Collinsella aerofaciens. The latter species was also independently associated with increased systolic BP. Furthermore, the cumulative time in hypoxia during sleep was associated with the abundance of genes involved in nine gut microbiota metabolic pathways, including propionate production from lactate. Finally, we observed two heterogeneous sets of plasma metabolites with opposite association with species positively and negatively associated with hypoxia parameters, respectively.

INTERPRETATION: OSA-related hypoxia, but not the number of apneas/hypopneas, is associated with specific gut microbiota species and functions. Our findings lay the foundation for future research on the gut microbiota-mediated health effects of OSA.}, } @article {pmid36925017, year = {2023}, author = {Liu, YY and Zhang, YX and Wen, HM and Liu, XL and Fan, XJ}, title = {Cloning and rational modification of a cold-adapted esterase for phthalate esters and parabens degradation.}, journal = {Chemosphere}, volume = {325}, number = {}, pages = {138393}, doi = {10.1016/j.chemosphere.2023.138393}, pmid = {36925017}, issn = {1879-1298}, mesh = {Humans ; *Esterases/metabolism ; Parabens ; Molecular Docking Simulation ; *Phthalic Acids/analysis ; Cloning, Molecular ; Esters/analysis ; Dibutyl Phthalate/analysis ; }, abstract = {Phthalate esters (PAEs) and parabens are environmental pollutants that can be toxic to human health. Herein, a cold-adapted esterase from the Mao-tofu metagenome named Est1260 was screened for its PAE-hydrolyzing potential in cold temperatures. The results showed that purified Est1260 could degrade a variety of PAEs and parabens at temperatures as low as 0 °C. After careful analysis of the structural information and molecular docking, site-saturation mutation was conducted at the identified hotspots. Protein expression of variant A1B6 doubled, and its thermal stability significantly improved (24 times) without sacrificing activity at low temperatures. In addition, Est1260 and its variants were activated by NaCl and demonstrated resistance to high concentrations of saline (up to 5 M), making it a potential biocatalyst for bioremediation of PAE and paraben-polluted environments.}, } @article {pmid36923821, year = {2023}, author = {Homayouni, R and Manda, P and Tan, AC and Qin, ZS}, title = {Editorial: AI and data science in drug development and public health: Highlights from the MCBIOS 2022 conference.}, journal = {Frontiers in big data}, volume = {6}, number = {}, pages = {1156811}, doi = {10.3389/fdata.2023.1156811}, pmid = {36923821}, issn = {2624-909X}, } @article {pmid36923492, year = {2023}, author = {Peng, Y and Chiu, ATG and Li, VWY and Zhang, X and Yeung, WL and Chan, SHS and Tun, HM}, title = {The role of the gut-microbiome-brain axis in metabolic remodeling amongst children with cerebral palsy and epilepsy.}, journal = {Frontiers in neurology}, volume = {14}, number = {}, pages = {1109469}, pmid = {36923492}, issn = {1664-2295}, abstract = {BACKGROUND: Epilepsy-associated dysbiosis in gut microbiota has been previously described, but the mechanistic roles of the gut microbiome in epileptogenesis among children with cerebral palsy (CP) have yet to be illustrated.

METHODS: Using shotgun metagenomic sequencing coupled with untargeted metabolomics analysis, this observational study compared the gut microbiome and metabolome of eight children with non-epileptic cerebral palsy (NECP) to those of 13 children with cerebral palsy with epilepsy (CPE). Among children with CPE, 8 had drug-sensitive epilepsy (DSE) and five had drug-resistant epilepsy (DRE). Characteristics at enrollment, medication history, and 7-day dietary intake were compared between groups.

RESULTS: At the species level, CPE subjects had significantly lower abundances of Bacteroides fragilis and Dialister invisus but higher abundances of Phascolarctobacterium faecium and Eubacterium limosum. By contrast, DRE subjects had a significantly higher colonization of Veillonella parvula. Regarding microbial functional pathways, CPE subjects had decreased abundances of pathways for serine degradation, quinolinic acid degradation, glutamate degradation I, glycerol degradation, sulfate reduction, and nitrate reduction but increased abundances of pathways related to ethanol production. As for metabolites, CPE subjects had higher concentrations of kynurenic acid, 2-oxindole, dopamine, 2-hydroxyphenyalanine, 3,4-dihydroxyphenylglycol, L-tartaric acid, and D-saccharic acid; DRE subjects had increased concentrations of indole and homovanilic acid.

CONCLUSIONS: In this study, we found evidence of gut dysbiosis amongst children with cerebral palsy and epilepsy in terms of gut microbiota species, functional pathways, and metabolites. The combined metagenomic and metabolomic analyses have shed insights on the potential roles of B. fragilis and D. invisus in neuroprotection. The combined analyses have also provided evidence for the involvement of GMBA in the epilepsy-related dysbiosis of kynurenine, serotonin, and dopamine pathways and their complex interplay with neuroimmune and neuroendocrinological pathways.}, } @article {pmid36922970, year = {2023}, author = {Zeng, Y and Cao, S and Yang, H}, title = {Roles of gut microbiome in epilepsy risk: A Mendelian randomization study.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1115014}, pmid = {36922970}, issn = {1664-302X}, abstract = {BACKGROUND: Recent studies have suggested an association between gut microbiomes (GMs) and epilepsy. However, the GM taxa identified in different studies are variable. In addition, observational studies cannot indicate causality. Therefore, our study aimed to explore the causal association of GMs with epilepsy and identify the most influential GM taxa.

METHODS: We conducted a Mendelian randomization (MR) study using summary statistics from genome-wide association studies (GWAS) of 211 GM taxa and epilepsy. The GWAS summary statistics for 211 GM taxa (from phylum to genus level) were generated by the MiBioGen consortium, while the FinnGen consortium provided the GWAS summary statistics for epilepsy. The primary analytical method to assess causality was the inverse-variance weighted (IVW) approach. To complement the IVW method, we also applied four additional MR methods: MR-Egger, weighted median, simple mode, and weighted. In addition, we conducted sensitivity analyses using Cochrane's Q-test, MR-Egger intercept test, MR-PRESSO global test, and leave-one-out analysis.

RESULTS: We evaluated the causal effect of 211 GM taxa (from phylum to genus level) on epilepsy, generalized epilepsy, and focal epilepsy. After using the Bonferroni method for multiple testing correction, Class Betaproteobacteria [odds ratio (OR) = 1.357, 95% confidence interval (CI): 1.126-1.635, p = 0.001] and Order Burkholderiales (OR = 1.336, 95% CI: 1.112-1.606, p = 0.002). In addition, 21 nominally significant causal relationships were also identified. Further, the MR-Egger intercept test and MR-PRESSO global test suggested that our MR analysis was unaffected by horizontal pleiotropy (p > 0.05). Finally, the leave-one-out analysis suggested the robustness of the results.

CONCLUSION: Through the MR study, we analyzed the causal relationship of 211 GM taxa with epilepsy and determined the specific intestinal flora associated with increased epilepsy risk. Our findings may provide helpful biomarkers for disease progression and potential candidate therapeutic targets for epilepsy. In addition, in-depth analysis of large-scale microbiome GWAS datasets based on metagenomics sequencing is necessary for future studies.}, } @article {pmid36922966, year = {2023}, author = {Kalntremtziou, M and Papaioannou, IA and Vangalis, V and Polemis, E and Pappas, KM and Zervakis, GI and Typas, MA}, title = {Evaluation of the lignocellulose degradation potential of Mediterranean forests soil microbial communities through diversity and targeted functional metagenomics.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1121993}, pmid = {36922966}, issn = {1664-302X}, abstract = {The enzymatic arsenal of several soil microorganisms renders them particularly suitable for the degradation of lignocellulose, a process of distinct ecological significance with promising biotechnological implications. In this study, we investigated the spatiotemporal diversity and distribution of bacteria and fungi with 16S and Internally Trascribed Spacer (ITS) ribosomal RNA next-generation-sequencing (NGS), focusing on forest mainland Abies cephalonica and insular Quercus ilex habitats of Greece. We analyzed samples during winter and summer periods, from different soil depths, and we applied optimized and combined targeted meta-omics approaches aiming at the peroxidase-catalase family enzymes to gain insights into the lignocellulose degradation process at the soil microbial community level. The microbial communities recorded showed distinct patterns of response to season, soil depth and vegetation type. Overall, in both forests Proteobacteria, Actinobacteria, Acidobacteria were the most abundant bacteria phyla, while the other phyla and the super-kingdom of Archaea were detected in very low numbers. Members of the orders Agaricales, Russulales, Sebacinales, Gomphales, Geastrales, Hysterangiales, Thelephorales, and Trechisporales (Basidiomycota), and Pezizales, Sordariales, Eurotiales, Pleosporales, Helotiales, and Diaporthales (Ascomycota) were the most abundant for Fungi. By using optimized "universal" PCR primers that targeted the peroxidase-catalase enzyme family, we identified several known and novel sequences from various Basidiomycota, even from taxa appearing at low abundance. The majority of the sequences recovered were manganese peroxidases from several genera of Agaricales, Hysterangiales, Gomphales, Geastrales, Russulales, Hymenochaetales, and Trechisporales, while lignin -and versatile-peroxidases were limited to two to eight species, respectively. Comparisons of the obtained sequences with publicly available data allowed a detailed structural analysis of polymorphisms and functionally relevant amino-acid residues at phylogenetic level. The targeted metagenomics applied here revealed an important role in lignocellulose degradation of hitherto understudied orders of Basidiomycota, such as the Hysterangiales and Gomphales, while it also suggested the auxiliary activity of particular members of Proteobacteria, Actinobacteria, Acidobacteria, Verrucomicrobia, and Gemmatimonadetes. The application of NGS-based metagenomics approaches allows a better understanding of the complex process of lignocellulolysis at the microbial community level as well as the identification of candidate taxa and genes for targeted functional investigations and genetic modifications.}, } @article {pmid36922761, year = {2023}, author = {Marynowska, M and Sillam-Dussès, D and Untereiner, B and Klimek, D and Goux, X and Gawron, P and Roisin, Y and Delfosse, P and Calusinska, M}, title = {A holobiont approach towards polysaccharide degradation by the highly compartmentalised gut system of the soil-feeding higher termite Labiotermes labralis.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {115}, pmid = {36922761}, issn = {1471-2164}, support = {C14/SR/ 8286517//Fonds National de la Recherche Luxembourg/ ; C14/SR/ 8286517//Fonds National de la Recherche Luxembourg/ ; C14/SR/ 8286517//Fonds National de la Recherche Luxembourg/ ; C14/SR/ 8286517//Fonds National de la Recherche Luxembourg/ ; C14/SR/ 8286517//Fonds National de la Recherche Luxembourg/ ; C14/SR/ 8286517//Fonds National de la Recherche Luxembourg/ ; PDR T.0065.15//F.R.S.-FNRS Belgium/ ; }, mesh = {Animals ; *Isoptera/genetics ; Soil ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Cellulose/metabolism ; }, abstract = {BACKGROUND: Termites are among the most successful insects on Earth and can feed on a broad range of organic matter at various stages of decomposition. The termite gut system is often referred to as a micro-reactor and is a complex structure consisting of several components. It includes the host, its gut microbiome and fungal gardens, in the case of fungi-growing higher termites. The digestive tract of soil-feeding higher termites is characterised by radial and axial gradients of physicochemical parameters (e.g. pH, O2 and H2 partial pressure), and also differs in the density and structure of residing microbial communities. Although soil-feeding termites account for 60% of the known termite species, their biomass degradation strategies are far less known compared to their wood-feeding counterparts.

RESULTS: In this work, we applied an integrative multi-omics approach for the first time at the holobiont level to study the highly compartmentalised gut system of the soil-feeding higher termite Labiotermes labralis. We relied on 16S rRNA gene community profiling, metagenomics and (meta)transcriptomics to uncover the distribution of functional roles, in particular those related to carbohydrate hydrolysis, across different gut compartments and among the members of the bacterial community and the host itself. We showed that the Labiotermes gut was dominated by members of the Firmicutes phylum, whose abundance gradually decreased towards the posterior segments of the hindgut, in favour of Bacteroidetes, Proteobacteria and Verrucomicrobia. Contrary to expectations, we observed that L. labralis gut microbes expressed a high diversity of carbohydrate active enzymes involved in cellulose and hemicelluloses degradation, making the soil-feeding termite gut a unique reservoir of lignocellulolytic enzymes with considerable biotechnological potential. We also evidenced that the host cellulases have different phylogenetic origins and structures, which is possibly translated into their different specificities towards cellulose. From an ecological perspective, we could speculate that the capacity to feed on distinct polymorphs of cellulose retained in soil might have enabled this termite species to widely colonise the different habitats of the Amazon basin.

CONCLUSIONS: Our study provides interesting insights into the distribution of the hydrolytic potential of the highly compartmentalised higher termite gut. The large number of expressed enzymes targeting the different lignocellulose components make the Labiotermes worker gut a relevant lignocellulose-valorising model to mimic by biomass conversion industries.}, } @article {pmid36922730, year = {2023}, author = {Omori, M and Kato-Kogoe, N and Sakaguchi, S and Komori, E and Inoue, K and Yamamoto, K and Hamada, W and Hayase, T and Tano, T and Nakamura, S and Nakano, T and Une, H and Ueno, T}, title = {Characterization of Oral Microbiota Following Chemotherapy in Patients With Hematopoietic Malignancies.}, journal = {Integrative cancer therapies}, volume = {22}, number = {}, pages = {15347354231159309}, pmid = {36922730}, issn = {1552-695X}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Stomatitis/chemically induced ; *Microbiota ; *Hematologic Neoplasms/drug therapy ; Bacteria ; }, abstract = {Oral microbiota may be associated with serious local or systemic medical conditions resulting from chemotherapy. This study was conducted to evaluate the changes in the oral microbiota following the initiation of chemotherapy in patients with hematopoietic malignancies and to identify the characteristics of the oral microbiota associated with oral mucositis. Oral samples were collected from 57 patients with hematopoietic malignancies at 2 time points: before the start of chemotherapy and 8 to 20 days after the start of chemotherapy, when chemotherapy-induced oral mucositis often occurs, and 16S rRNA metagenomic analyses were performed. Comparative and linear discriminant analysis effect size (LEfSe) analyses were used to determine the characteristic bacterial groups before and after the initiation of chemotherapy and in those who developed oral mucositis. The alpha and beta diversities of oral microbiota before and after the initiation of chemotherapy differed significantly (operational taxonomic unit index, P < .001; Shannon's index, P < .001; unweighted UniFrac distances, P = .001; and weighted UniFrac distances, P = .001). The LEfSe analysis revealed a group of bacteria whose abundance differed significantly before and after the initiation of chemotherapy. In the group of patients who developed oral mucositis, a characteristic group of bacteria was identified before the start of chemotherapy. In conclusion, we characterized the oral microbiota associated with the initiation of chemotherapy in patients with hematopoietic malignancies. In addition, our findings suggest that oral microbiota composition before the start of chemotherapy may be associated with oral mucositis. The results of this study emphasize the importance of oral management focusing on the oral microbiota during chemotherapy in patients with hematologic malignancies.}, } @article {pmid36922572, year = {2023}, author = {Michishita, R and Shimoda, M and Furukawa, S and Uehara, T}, title = {Inoculation with black soldier fly larvae alters the microbiome and volatile organic compound profile of decomposing food waste.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {4297}, pmid = {36922572}, issn = {2045-2322}, mesh = {Animals ; Larva/metabolism ; Food ; *Volatile Organic Compounds/metabolism ; *Refuse Disposal ; *Diptera/metabolism ; *Microbiota ; }, abstract = {The black soldier fly (BSF; Hermetia illucens) is used in sustainable processing of many types of organic waste. However, organic waste being decomposed by BSF produces strong odors, hindering more widespread application. The odor components and how they are produced have yet to be characterized. We found that digestion of food waste by BSF significantly alters the microbial flora, based on metagenomic analyses, and the odor components generated, as shown by thermal desorption gas chromatography mass spectrometry analysis. Inoculation with BSF significantly decreased production of volatile organic sulfur compounds (dimethyl disulfide and dimethyl trisulfide), which are known to be released during methionine and cysteine metabolism by Lactobacillus and Enterococcus bacteria. BSF inoculation significantly changed the abundance of Lactobacillus and Enterococcus and decreased microbial diversity overall. These findings may help in optimizing use of BSF for deodorization of composting food waste.}, } @article {pmid36922385, year = {2023}, author = {Yang, S and Fan, Z and Li, J and Wang, X and Lan, Y and Yue, B and He, M and Zhang, A and Li, J}, title = {Assembly of novel microbial genomes from gut metagenomes of rhesus macaque (Macaca mulatta).}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2188848}, pmid = {36922385}, issn = {1949-0984}, mesh = {Animals ; Humans ; *Metagenome ; Macaca mulatta/genetics ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; Genome, Microbial ; Diarrhea/microbiology ; Metagenomics/methods ; }, abstract = {Rhesus macaque (RM, Macaca mulatta), as an important model animal, commonly suffers from chronic diarrheal disease, challenging the breeding of RMs. Gut microbiomes play key roles in maintaining intestinal health of RMs. However, it is still unclear about more features of gut microbiome as responsible for intestinal health of RMs. In this study, we performed de novo assembly of metagenome-assembled genomes (MAGs) based on fecal metagenomes from chronic diarrheal RMs and asymptomatic individuals. In total of 731 non-redundant MAGs with at least 80% completeness were reconstructed in this study. More than 97% MAGs were novel genomes compared with more than 250,000 reference genomes. MAGs of Campylobacter and Helicobacteraceae from RM guts mainly carried flagella-associated virulence genes and chemotaxis-associated virulence genes, which might mediate motility and adhesion of bacteria. Comparing to MAGs of Campylobacter from humans, distributions and functions of these MAGs of Campylobacter from RMs exhibited significant differences. Most members of Bacteroidota, Spirochaetota, Helicobacteraceae, Lactobacillaceae and Anaerovibrio significantly decreased in guts of chronic diarrhea RMs. More than 92% MAGs in this study were not contained in 2,985 MAGs previously reported from other 22 non-human primates (NHPs), expanding the microbial diversity in guts of NHPs. The distributions and functions of gut microbiome were prominently influenced by host phylogeny of NHPs. Our results could help to more clearly understand about the diversity and function of RMs gut microbiome.}, } @article {pmid36922214, year = {2023}, author = {Liu, CX and Bai, XH}, title = {[Distribution Characteristics of Antibiotic Resistance Genes on Different Water Supply Pipes].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {44}, number = {3}, pages = {1537-1541}, doi = {10.13227/j.hjkx.202204208}, pmid = {36922214}, issn = {0250-3301}, mesh = {*Anti-Bacterial Agents/pharmacology ; Water Supply ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Biofilms ; Genes, Bacterial ; *Drinking Water/microbiology ; }, abstract = {To study the distribution characteristics and horizontal transfer potential of antibiotic resistance genes in biofilms of water supply pipes made of different materials, the biofilms of 304 and 316 L stainless steel pipes and PPR and PE plastic pipes were analyzed using metagenomic sequencing. The results showed that a total of 146 antibiotic resistance genes belonging to 17 classes were detected in the biofilms. Multidrug resistance genes had the highest abundance and varied a lot in different biofilms, which was the main reason for the differences in antibiotic resistance genes in different biofilms. The total abundance of mobile genetic elements was high in different biofilms, but overall coexistence with antibiotic resistance genes was low, with integrase genes showing a closer relationship with antibiotic resistance genes and possibly playing an important role in the horizontal transfer of antibiotic resistance genes. Different antibiotic resistance genes possessed different genera of potential hosts; highly abundant hosts such as Aquabacterium and Bradyrhizobium were the basis for the presence of a high abundance of multidrug resistance genes. Microbial attachment in different pipe walls was selective, and the primary influence of antibiotic resistance in biofilms was bacterial community composition, followed by the horizontal transfer of genes mediated by mobile genetic elements, community composition, and mobile genetic elements together shaping the distribution characteristics of antibiotic resistance genes.}, } @article {pmid36921777, year = {2023}, author = {Li, P and Chen, CZ and Zhao, XL and Liu, L and Li, ZH}, title = {Metagenomics analysis reveals the effects of norfloxacin on the gut microbiota of juvenile common carp (Cyprinus carpio).}, journal = {Chemosphere}, volume = {325}, number = {}, pages = {138389}, doi = {10.1016/j.chemosphere.2023.138389}, pmid = {36921777}, issn = {1879-1298}, mesh = {Animals ; *Gastrointestinal Microbiome ; Norfloxacin/toxicity ; *Carps ; Metagenomics ; Bacteria/genetics ; Anti-Bacterial Agents/toxicity ; }, abstract = {Norfloxacin (NOR) is an early third-generation quinolone antibiotic that has been widely used in animal husbandry and aquaculture because of its bactericidal properties. As an emerging contaminant, NOR may have toxic effects on fish. This study assessed the chronic toxicity (6 weeks) of 0 (control group), 100 ng/L (environmental concentration), and 1 mg/L NOR to the gut microbiota of juvenile common carp (Cyprinus carpio) based on metagenomic sequencing. Metagenomic analysis revealed that the Proteobacteria, Bacteroidetes, Fusobacteria, Firmicutes, and Actinobacteria were the dominant bacteria in the gut of common carp. The relative abundance of Actinobacteria was highest in the control group. The alpha diversity of the environmental concentration NOR was significantly lower than the control group. Principal coordinates analysis (PCoA) indicated that the bacterial community between the different groups formed clear separate clusters. NOR exposure adversely could affect immune function and some substance metabolic pathways in the gut microbiota of common carp. Furthermore, environmental concentrations of NOR produce antibiotic resistance genes (ARGs) in the gut microbiota, enhancing resistance to drugs. In conclusion, environmental concentrations of NOR could alter the composition, structure, and abundance of ARGs in the gut microbiota, thereby affecting the intestinal health of fish.}, } @article {pmid36921697, year = {2023}, author = {Wong, D and Norman, H and Creedy, TJ and Jordaens, K and Moran, KM and Young, A and Mengual, X and Skevington, JH and Vogler, AP}, title = {The phylogeny and evolutionary ecology of hoverflies (Diptera: Syrphidae) inferred from mitochondrial genomes.}, journal = {Molecular phylogenetics and evolution}, volume = {184}, number = {}, pages = {107759}, doi = {10.1016/j.ympev.2023.107759}, pmid = {36921697}, issn = {1095-9513}, mesh = {Animals ; Phylogeny ; *Genome, Mitochondrial ; *Diptera/genetics ; Bayes Theorem ; Larva ; }, abstract = {Hoverflies (Diptera: Syrphidae) are a diverse group of pollinators and a major research focus in ecology, but their phylogenetic relationships remain incompletely known. Using a genome skimming approach we generated mitochondrial genomes for 91 species, capturing a wide taxonomic diversity of the family. To reduce the required amount of input DNA and overall cost of the library construction, sequencing and assembly was conducted on mixtures of specimens, which raises the problem of chimera formation of mitogenomes. We present a novel chimera detection test based on gene tree incongruence, but identified only a single mitogenome of chimeric origin. Together with existing data for a final set of 127 taxa, phylogenetic analysis on nucleotide and amino acid sequences using Maximum Likelihood and Bayesian Inference revealed a basal split of Microdontinae from all other syrphids. The remainder consists of several deep clades assigned to the subfamily Eristalinae in the current classification, including a clade comprising the subfamily Syrphinae (plus Pipizinae). These findings call for a re-definition of subfamilies, but basal nodes had insufficient support to fully justify such action. Molecular-clock dating placed the origin of the Syrphidae crown group in the mid-Cretaceous while the Eristalinae-Syrphinae clade likely originated near the K/Pg boundary. Transformation of larval life history characters on the tree suggests that Syrphidae initially had sap feeding larvae, which diversified greatly in diet and habitat association during the Eocene and Oligocene, coinciding with the diversification of angiosperms and the evolution of various insect groups used as larval host, prey, or mimicry models. Mitogenomes proved to be a powerful phylogenetic marker for studies of Syrphidae at subfamily and tribe levels, allowing dense taxon sampling that provided insight into the great ecological diversity and rapid evolution of larval life history traits of the hoverflies.}, } @article {pmid36921549, year = {2023}, author = {Bortoluzzi, C and Tamburini, I and Geremia, J}, title = {Microbiome modulation, microbiome protein metabolism index, and growth performance of broilers supplemented with a precision biotic.}, journal = {Poultry science}, volume = {102}, number = {5}, pages = {102595}, pmid = {36921549}, issn = {1525-3171}, mesh = {Animals ; *Chickens ; Diet/veterinary ; Dietary Supplements/analysis ; *Microbiota ; Body Weight ; Animal Feed/analysis ; Animal Nutritional Physiological Phenomena ; }, abstract = {The objectives of the present studies were to evaluate: 1) the in vivo impact of the supplementation with a precision biotic (PB) on the growth performance and microbiome modulation of broiler chickens; 2) the role of PB on the modulation of functional pathways of the microbiome collected from animals with low and high body weight gain, and 3) to develop a Microbiome Protein Metabolism Index (MPMI) derived from gut metagenomic data to link microbial protein metabolism with performance. The in vivo work consisted of 2 experiments with 2 treatments: Control vs. PB at 1.1 kg/MT of PB with 21 or 14 replicates of 40 birds per replicate, in experiments 1 and 2, respectively. Growth performance was evaluated in both experiments, and from experiment 1, cecal samples from one bird/replicate was collected on d 21 and 42 (n = 21/treatment) to evaluate the microbiome through whole genome sequencing. In the ex vivo assay, 6 cecal samples were collected from low body weight (BW) birds (at 10% below average), and 6 samples from high BW birds (at least 10% above average). The samples were incubated in the presence or absence of PB. After incubation, DNA was isolated to develop a functional genomic assay and the supernatant was separated to measure short-chain fatty acid (SCFA) production. The MPMI is the sum of beneficial genes in the pathways related to protein metabolism. In the in vivo grow out experiments, it was observed that the supplementation improved the BW gain by 3% in both studies, and the corrected feed conversion ratio (cFCR) by 3.7 and 3.4% in studies 1 and 2, respectively (P < 0.05). The functional microbiome analysis revealed that the PB shifted the microbiome pathways toward a beneficial increase in protein utilization, as shown by higher MPMI. In the ex vivo experiment, the PB increased the abundance of genes related to the beneficial metabolism of protein (quantitative MPMI), and the concentration of SCFA, regardless of the underline BW of the birds. Taken together, the microbiome metabolic shift observed in the in vivo study and higher MPMI, plus the observations from the ex vivo assay with higher SFCA production, may explain the improvement in growth performance obtained with the supplementation of PB.}, } @article {pmid36921415, year = {2023}, author = {Chen, B and Zhang, Z and Wang, T and Hu, H and Qin, G and Lu, T and Hong, W and Hu, J and Penuelas, J and Qian, H}, title = {Global distribution of marine microplastics and potential for biodegradation.}, journal = {Journal of hazardous materials}, volume = {451}, number = {}, pages = {131198}, doi = {10.1016/j.jhazmat.2023.131198}, pmid = {36921415}, issn = {1873-3336}, mesh = {*Microplastics ; Plastics ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring ; Mediterranean Sea ; Biodegradation, Environmental ; }, abstract = {Microplastics are a growing marine environmental concern globally due to their high abundance and persistent degradation. We created a global map for predicting marine microplastic pollution using a machine-learning model based on 9445 samples and found that microplastics converged in zones of accumulation in subtropical gyres and near polar seas. The predicted global potential for the biodegradation of microplastics in 1112 metagenome-assembled genomes from 485 marine metagenomes indicated high potential in areas of high microplastic pollution, such as the northern Atlantic Ocean and the Mediterranean Sea. However, the limited number of samples hindered our prediction, a priority issue that needs to be addressed in the future. We further identified hosts with microplastic degradation genes (MDGs) and found that Proteobacteria accounted for a high proportion of MDG hosts, mainly Alphaproteobacteria and Gammaproteobacteria, with host-specific patterns. Our study is essential for raising awareness, identifying areas with microplastic pollution, providing a prediction method of machine learning to prioritize surveillance, and identifying the global potential of marine microbiomes to degrade microplastics, providing a reference for selecting bacteria that have the potential to degrade microplastics for further applied research.}, } @article {pmid36920617, year = {2023}, author = {Kumar, R and Yadav, G and Kuddus, M and Ashraf, GM and Singh, R}, title = {Unlocking the microbial studies through computational approaches: how far have we reached?.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {17}, pages = {48929-48947}, pmid = {36920617}, issn = {1614-7499}, mesh = {*Artificial Intelligence ; Metagenomics ; *Microbiota ; Proteomics ; DNA ; }, abstract = {The metagenomics approach accelerated the study of genetic information from uncultured microbes and complex microbial communities. In silico research also facilitated an understanding of protein-DNA interactions, protein-protein interactions, docking between proteins and phyto/biochemicals for drug design, and modeling of the 3D structure of proteins. These in silico approaches provided insight into analyzing pathogenic and nonpathogenic strains that helped in the identification of probable genes for vaccines and antimicrobial agents and comparing whole-genome sequences to microbial evolution. Artificial intelligence, more precisely machine learning (ML) and deep learning (DL), has proven to be a promising approach in the field of microbiology to handle, analyze, and utilize large data that are generated through nucleic acid sequencing and proteomics. This enabled the understanding of the functional and taxonomic diversity of microorganisms. ML and DL have been used in the prediction and forecasting of diseases and applied to trace environmental contaminants and environmental quality. This review presents an in-depth analysis of the recent application of silico approaches in microbial genomics, proteomics, functional diversity, vaccine development, and drug design.}, } @article {pmid36920536, year = {2023}, author = {Kazarina, A and Kuzmicka, J and Bortkevica, S and Zayakin, P and Kimsis, J and Igumnova, V and Sadovska, D and Freimane, L and Kivrane, A and Namina, A and Capligina, V and Poksane, A and Ranka, R}, title = {Oral microbiome variations related to ageing: possible implications beyond oral health.}, journal = {Archives of microbiology}, volume = {205}, number = {4}, pages = {116}, pmid = {36920536}, issn = {1432-072X}, mesh = {Humans ; *Oral Health ; *Microbiota ; Bacteria/genetics ; Aging ; Cluster Analysis ; RNA, Ribosomal, 16S ; }, abstract = {The global population is getting older due to a combination of longer life expectancy and declining birth rates. Growing evidence suggests that the oral microbiota composition and distribution may have a profound effect on how well we age. The purpose of this study was to investigate age-related oral microbiome variations of supragingival plaque and buccal mucosa samples in the general population in Latvia. Our results indicated significant difference between supragingival plaque bacterial profiles of three age groups (20-40; 40-60; 60 + years). Within supragingival plaque samples, age group 20-40 showed the highest bacterial diversity with a decline during the 40-60 age period and uprise again after the age of 60. Among other differences, the important oral commensal Neisseria had declined after the age of 40. Additionally, prevalence of two well-documented opportunistic pathogens Streptococcus anginosus and Gemella sanguinis gradually rose with age within our samples. Furthermore, supragingival plaque and buccal mucosa samples significantly differed in overall bacterial composition.}, } @article {pmid36920238, year = {2023}, author = {Kallner, A and Debelius, J and Schuppe-Koistinen, I and Pereira, M and Engstrand, L}, title = {Effects of Consuming Fermented Fish (Surströmming) on the Fecal Microflora in Healthy Individuals.}, journal = {Journal of medicinal food}, volume = {26}, number = {3}, pages = {185-192}, doi = {10.1089/jmf.2021.0195}, pmid = {36920238}, issn = {1557-7600}, mesh = {Animals ; Male ; Female ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; *Bacteria ; *Gastrointestinal Microbiome/genetics ; }, abstract = {Surströmming, a Swedish fermented fish, loved by some and avoided by others, occurs in many reports on improved or cured gastrointestinal problems even by a single meal. We tested the hypothesis that the microbes of the fermented food might have a potency to modify the gut microbiome. Two groups of voluntary participants (11 male, 8 female; aged 20-80 years) were exposed to a single meal containing the fish. A 7-day dietary intervention was carried out comprising the fish as the main source of protein in a single adult. The microbiome was characterized using 16S rRNA and metagenomic sequencing. Individual community-level changes in the microbiome were compared, as well as the presence of bacteria associated with the fermented fish. We focused on Shannon alpha and UniFrac beta diversity. We did not detect any global changes in the gut microbiome in response to Surströmming, nor were we able to recover and identify any members of Halanaerobium, which were associated with and abundant in the ingested fish, in the stool samples of the participants. Our results suggest that Surströmming consumption does not alter the microbiome of healthy individuals. However, beneficial effects on a diseased gut, impaired gut microbiome, or other effects in disease remain to be studied.}, } @article {pmid36920198, year = {2023}, author = {Muratore, D and Bertagnolli, AD and Bristow, LA and Thamdrup, B and Weitz, JS and Stewart, FJ}, title = {Microbial and Viral Genome and Proteome Nitrogen Demand Varies across Multiple Spatial Scales within a Marine Oxygen Minimum Zone.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0109522}, pmid = {36920198}, issn = {2379-5077}, mesh = {*Seawater/chemistry ; *Proteome/genetics ; Proteomics ; Oxygen/analysis ; Nitrogen/metabolism ; Bacteria/genetics ; Archaea/genetics ; Genome, Viral/genetics ; Amino Acids/genetics ; }, abstract = {Nutrient availability can significantly influence microbial genomic and proteomic streamlining, for example, by selecting for lower nitrogen to carbon ratios. Oligotrophic open ocean microbes have streamlined genomic nitrogen requirements relative to those of their counterparts in nutrient-rich coastal waters. However, steep gradients in nutrient availability occur at meter-level, and even micron-level, spatial scales. It is unclear whether such gradients also structure genomic and proteomic stoichiometry. Focusing on the eastern tropical North Pacific oxygen minimum zone (OMZ), we use comparative metagenomics to examine how nitrogen availability shapes microbial and viral genome properties along the vertical gradient across the OMZ and between two size fractions, distinguishing free-living microbes versus particle-associated microbes. We find a substantial increase in the nitrogen content of encoded proteins in particle-associated over free-living bacteria and archaea across nitrogen availability regimes over depth. Within each size fraction, we find that bacterial and viral genomic nitrogen tends to increase with increasing nitrate concentrations with depth. In contrast to cellular genes, the nitrogen content of virus proteins does not differ between size fractions. We identified arginine as a key amino acid in the modulation of the C:N ratios of core genes for bacteria, archaea, and viruses. Functional analysis reveals that particle-associated bacterial metagenomes are enriched for genes that are involved in arginine metabolism and organic nitrogen compound catabolism. Our results are consistent with nitrogen streamlining in both cellular and viral genomes on spatial scales of meters to microns. These effects are similar in magnitude to those previously reported across scales of thousands of kilometers. IMPORTANCE The genomes of marine microbes can be shaped by nutrient cycles, with ocean-scale gradients in nitrogen availability being known to influence microbial amino acid usage. It is unclear, however, how genomic properties are shaped by nutrient changes over much smaller spatial scales, for example, along the vertical transition into oxygen minimum zones (OMZs) or from the exterior to the interior of detrital particles. Here, we measure protein nitrogen usage by marine bacteria, archaea, and viruses by using metagenomes from the nitracline of the eastern tropical North Pacific OMZ, including both particle-associated and nonassociated biomass. Our results show higher genomic and proteomic nitrogen content in particle-associated microbes and at depths with higher nitrogen availability for cellular and viral genomes. This discovery suggests that stoichiometry influences microbial and viral evolution across multiple scales, including the micrometer to millimeter scale associated with particle-associated versus free-living lifestyles.}, } @article {pmid36918963, year = {2023}, author = {Faist, H and Trognitz, F and Antonielli, L and Symanczik, S and White, PJ and Sessitsch, A}, title = {Potato root-associated microbiomes adapt to combined water and nutrient limitation and have a plant genotype-specific role for plant stress mitigation.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {18}, pmid = {36918963}, issn = {2524-6372}, support = {727247//European Commission/ ; 727247//European Commission/ ; 727247//European Commission/ ; 727247//European Commission/ ; 727247//European Commission/ ; 727247//European Commission/ ; }, abstract = {BACKGROUND: Due to climate change and reduced use of fertilizers combined stress scenarios are becoming increasingly frequent in crop production. In a field experiment we tested the effect of combined water and phosphorus limitation on the growth performance and plant traits of eight tetraploid and two diploid potato varieties as well as on root-associated microbiome diversity and functional potential. Microbiome and metagenome analysis targeted the diversity and potential functions of prokaryotes, fungi, plasmids, and bacteriophages and was linked to plant traits like tuber yield or timing of canopy closure.

RESULTS: The different potato genotypes responded differently to the combined stress and hosted distinct microbiota in the rhizosphere and the root endosphere. Proximity to the root, stress and potato genotype had significant effects on bacteria, whereas fungi were only mildly affected. To address the involvement of microbial functions, we investigated well and poorly performing potato genotypes (Stirling and Desirée, respectively) under stress conditions and executed a metagenome analysis of rhizosphere microbiomes subjected to stress and no stress conditions. Functions like ROS detoxification, aromatic amino acid and terpene metabolism were enriched and in synchrony with the metabolism of stressed plants. In Desirée, Pseudonocardiales had the genetic potential to take up assimilates produced in the fast-growing canopy and to reduce plant stress-sensing by degrading ethylene, but overall yield losses were high. In Stirling, Xanthomonadales had the genetic potential to reduce oxidative stress and to produce biofilms, potentially around roots. Biofilm formation could be involved in drought resilience and nutrient accessibility of Stirling and explain the recorded low yield losses. In the rhizosphere exposed to combined stress, the relative abundance of plasmids was reduced, and the diversity of phages was enriched. Moreover, mobile elements like plasmids and phages were affected by combined stresses in a genotype-specific manner.

CONCLUSION: Our study gives new insights into the interconnectedness of root-associated microbiota and plant stress responses in the field. Functional genes in the metagenome, phylogenetic composition and mobile elements play a role in potato stress adaption. In a poor and a well performing potato genotype grown under stress conditions, distinct functional genes pinpoint to a distinct stress sensing, water availability and compounds in the rhizospheres.}, } @article {pmid36917925, year = {2023}, author = {Wang, J and Wang, C and Chu, YX and Tian, G and He, R}, title = {Characterization of methanotrophic community and activity in landfill cover soils under dimethyl sulfide stress.}, journal = {Waste management (New York, N.Y.)}, volume = {161}, number = {}, pages = {263-274}, doi = {10.1016/j.wasman.2023.02.017}, pmid = {36917925}, issn = {1879-2456}, mesh = {*Soil/chemistry ; Methane/chemistry ; Soil Microbiology ; *Methylococcaceae/genetics/metabolism ; Waste Disposal Facilities ; Sulfur Compounds ; Oxidation-Reduction ; }, abstract = {Landfill cover soil is the environmental interface between landfills and the atmosphere and plays an important role in mitigating CH4 emission from landfills. Here, stable isotope probing microcosms with CH4 or CH4 and dimethyl sulfide (DMS) were carried out to characterize activity and community structure of methanotrophs in landfill cover soils under DMS stress. The CH4 oxidation activity in the landfill cover soils was not obviously influenced at the DMS concentration of 0.05%, while it was inhibited at the DMS concentrations of 0.1% and 0.2%. DMS-S was mainly oxidized to sulfate (SO4[2-]) in the landfill cover soils. In the landfill cover soils, DMS could inhibit the expression of bacteria and decrease the abundances of pmoA and mmoX genes, while it could prompt the expression of pmoA and mmoX genes. γ-Proteobacteria methanotrophs including Methylocaldum, Methylobacter, Crenothrix and unclassified Methylococcaceae and α-Proteobacteria methanotrophs Methylocystis dominated in assimilating CH4 in the landfill cover soils. Of them, Methylobacter and Crenothrix had strong tolerance to DMS or DMS could promote the growth and activity of Methylobacter and Crenothrix, while Methylocaldum had weak tolerance to DMS and showed an inhibitory effect. Metagenomic analyses showed that methanotrophs had the genes of methanethiol oxidation and could metabolize CH4 and methanethiol simultaneously in the landfill cover soils. These findings suggested that methanotrophs might metabolize sulfur compounds in the landfill cover soils, which may provide the potential application in engineering for co-removal of CH4 and sulfur compounds.}, } @article {pmid36917471, year = {2023}, author = {Zhang, Z and Yang, C and Veldsman, WP and Fang, X and Zhang, L}, title = {Benchmarking genome assembly methods on metagenomic sequencing data.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {2}, pages = {}, doi = {10.1093/bib/bbad087}, pmid = {36917471}, issn = {1477-4054}, mesh = {Humans ; *Metagenome ; Benchmarking ; *Microbiota/genetics ; Metagenomics/methods ; Genomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenome assembly is an efficient approach to reconstruct microbial genomes from metagenomic sequencing data. Although short-read sequencing has been widely used for metagenome assembly, linked- and long-read sequencing have shown their advancements in assembly by providing long-range DNA connectedness. Many metagenome assembly tools were developed to simplify the assembly graphs and resolve the repeats in microbial genomes. However, there remains no comprehensive evaluation of metagenomic sequencing technologies, and there is a lack of practical guidance on selecting the appropriate metagenome assembly tools. This paper presents a comprehensive benchmark of 19 commonly used assembly tools applied to metagenomic sequencing datasets obtained from simulation, mock communities or human gut microbiomes. These datasets were generated using mainstream sequencing platforms, such as Illumina and BGISEQ short-read sequencing, 10x Genomics linked-read sequencing, and PacBio and Oxford Nanopore long-read sequencing. The assembly tools were extensively evaluated against many criteria, which revealed that long-read assemblers generated high contig contiguity but failed to reveal some medium- and high-quality metagenome-assembled genomes (MAGs). Linked-read assemblers obtained the highest number of overall near-complete MAGs from the human gut microbiomes. Hybrid assemblers using both short- and long-read sequencing were promising methods to improve both total assembly length and the number of near-complete MAGs. This paper also discussed the running time and peak memory consumption of these assembly tools and provided practical guidance on selecting them.}, } @article {pmid36917216, year = {2023}, author = {Houston, H and Wilson, AJ and Stone, N}, title = {Diagnosis of invasive respiratory mycoses in the immunocompromised host.}, journal = {Current opinion in pulmonary medicine}, volume = {29}, number = {3}, pages = {149-159}, doi = {10.1097/MCP.0000000000000955}, pmid = {36917216}, issn = {1531-6971}, mesh = {Humans ; Biopsy ; *Immunocompromised Host ; *Invasive Fungal Infections/diagnosis/immunology/microbiology ; Mycoses/diagnosis/immunology/microbiology ; *Respiratory Tract Infections/diagnosis/immunology/microbiology ; Bronchoalveolar Lavage ; Bronchoalveolar Lavage Fluid/microbiology ; Lung/microbiology/pathology ; }, abstract = {PURPOSE OF REVIEW: The burden of invasive fungal infection is increasing worldwide, largely due to a growing population at-risk. Most serious human fungal pathogens enter the host via the respiratory tract. Early identification and treatment of invasive fungal respiratory infections (IFRIs) in the immunocompromised host saves lives. However, their accurate diagnosis is a difficult challenge for clinicians and mortality remains high.

RECENT FINDINGS: This article reviews IFRIs, focussing on host susceptibility factors, clinical presentation, and mycological diagnosis. Several new diagnostic tools are coming of age including molecular diagnostics and point-of-care antigen tests. As diagnosis of IFRI relies heavily on invasive procedures like bronchoalveolar lavage and lung biopsy, several novel noninvasive diagnostic techniques are in development, such as metagenomics, 'volatilomics' and advanced imaging technologies.

SUMMARY: Where IFRI cannot be proven, clinicians must employ a 'weights-of-evidence' approach to evaluate host factors, clinical and mycological data. Implementation studies are needed to understand how new diagnostic tools can be best applied within clinical pathways. Differentiating invasive infection from colonization and identifying antifungal resistance remain key challenges. As our diagnostic arsenal expands, centralized clinical mycology laboratories and efforts to ensure access to new diagnostics in low-resource settings will become increasingly important.}, } @article {pmid36917170, year = {2023}, author = {Wang, X and Wang, T and Xie, Z and Zhang, Y and Xia, S and Sun, R and He, X and Xiang, R and Zheng, Q and Liu, Z and Wang, J and Wu, H and Jin, X and Chen, W and Li, D and He, Z}, title = {GPMeta: a GPU-accelerated method for ultrarapid pathogen identification from metagenomic sequences.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {2}, pages = {}, doi = {10.1093/bib/bbad092}, pmid = {36917170}, issn = {1477-4054}, mesh = {*Metagenome ; *Microbiota ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Sensitivity and Specificity ; }, abstract = {Metagenomic sequencing (mNGS) is a powerful diagnostic tool to detect causative pathogens in clinical microbiological testing owing to its unbiasedness and substantially reduced costs. Rapid and accurate classification of metagenomic sequences is a critical procedure for pathogen identification in dry-lab step of mNGS test. However, clinical practices of the testing technology are hampered by the challenge of classifying sequences within a clinically relevant timeframe. Here, we present GPMeta, a novel GPU-accelerated approach to ultrarapid pathogen identification from complex mNGS data, allowing users to bypass this limitation. Using mock microbial community datasets and public real metagenomic sequencing datasets from clinical samples, we show that GPMeta has not only higher accuracy but also significantly higher speed than existing state-of-the-art tools such as Bowtie2, Bwa, Kraken2 and Centrifuge. Furthermore, GPMeta offers GPMetaC clustering algorithm, a statistical model for clustering and rescoring ambiguous alignments to improve the discrimination of highly homologous sequences from microbial genomes with average nucleotide identity >95%. GPMetaC exhibits higher precision and recall rate than others. GPMeta underlines its key role in the development of the mNGS test in infectious diseases that require rapid turnaround times. Further study will discern how to best and easily integrate GPMeta into routine clinical practices. GPMeta is freely accessible to non-commercial users at https://github.com/Bgi-LUSH/GPMeta.}, } @article {pmid36916946, year = {2023}, author = {Li, SH and Kang, I and Cho, JC}, title = {Metabolic Versatility of the Family Halieaceae Revealed by the Genomics of Novel Cultured Isolates.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0387922}, pmid = {36916946}, issn = {2165-0497}, abstract = {The family Halieaceae (OM60/NOR5 clade) is a gammaproteobacterial group abundant and cosmopolitan in coastal seawaters and plays an important role in response to phytoplankton blooms. However, the ecophysiology of this family remains understudied because of the vast gap between phylogenetic diversity and cultured representatives. Here, using six pure cultured strains isolated from coastal seawaters, we performed in-depth genomic analyses to provide an overview of the phylogeny and metabolic capabilities of this family. The combined analyses of 16S rRNA genes, genome sequences, and functional genes relevant to taxonomy demonstrated that each strain represents a novel species. Notably, two strains belonged to the hitherto-uncultured NOR5-4 and NOR5-12 subclades. Metabolic reconstructions revealed that the six strains likely have aerobic chemo- or photoheterotrophic lifestyles; five of them possess genes for proteorhodopsin or aerobic anoxygenic phototrophy. The presence of blue- or green-tuned proteorhodopsin in Halieaceae suggested their ability to adapt to light conditions varying with depth or coastal-to-open ocean transition. In addition to the genes of anaplerotic CO2 fixation, genes encoding a complete reductive glycine pathway for CO2 fixation were found in three strains. Putative polysaccharide utilization loci were detected in three strains, suggesting the association with phytoplankton blooms. Read mapping of various metagenomes and metatranscriptomes showed that the six strains are widely distributed and transcriptionally active in marine environments. Overall, the six strains genomically characterized in this study expand the phylogenetic and metabolic diversity of Halieaceae and likely serve as a culture resource for investigating the ecophysiological features of this environmentally relevant bacterial group. IMPORTANCE Although the family Halieaceae (OM60/NOR5 clade) is an abundant and cosmopolitan clade widely found in coastal seas and involved in interactions with phytoplankton, a limited number of cultured isolates are available. In this study, we isolated six pure cultured Halieaceae strains from coastal seawaters and performed a comparative physiological and genomic analysis to give insights into the phylogeny and metabolic potential of this family. The cultured strains exhibited diverse metabolic potential by harboring genes for anaplerotic CO2 fixation, proteorhodopsin, and aerobic anoxygenic phototrophy. Polysaccharide utilization loci detected in some of these strains also indicated an association with phytoplankton blooms. The cultivation of novel strains of Halieaceae and their genomic characteristics largely expanded the phylogenetic and metabolic diversity, which is important for future ecophysiological studies.}, } @article {pmid36916761, year = {2023}, author = {Zamfir, AD and Babalola, BM and Fraile, A and McLeish, MJ and García-Arenal, F}, title = {Tobamoviruses Show Broad Host Ranges and Little Genetic Diversity Among Four Habitat Types of a Heterogeneous Ecosystem.}, journal = {Phytopathology}, volume = {113}, number = {9}, pages = {1697-1707}, doi = {10.1094/PHYTO-11-22-0439-V}, pmid = {36916761}, issn = {0031-949X}, mesh = {Humans ; Host Specificity ; Ecosystem ; Plant Diseases ; *Tobamovirus/genetics ; *Tobacco Mosaic Virus/genetics ; Plants ; Genetic Variation ; }, abstract = {Host ranges of plant viruses are poorly known, as studies have focused on pathogenic viruses in crops and adjacent wild plants. High-throughput sequencing (HTS) avoids the bias toward plant-virus interactions that result in disease. Here we study the host ranges of tobamoviruses, important pathogens of crops, using HTS analyses of an extensive sample of plant communities in four habitats of a heterogeneous ecosystem. Sequences of 17 virus operational taxonomic units (OTUs) matched references in the Tobamovirus genus, eight had narrow host ranges, and five had wide host ranges. Regardless of host range, the OTU hosts belonged to taxonomically distant families, suggesting no phylogenetic constraints in host use associated with virus adaptation, and that tobamoviruses may be host generalists. The OTUs identified as tobacco mild green mosaic virus (TMGMV), tobacco mosaic virus (TMV), pepper mild mottle virus, and Youcai mosaic virus had the largest realized host ranges that occurred across habitats and exhibited host use unrelated to the degree of human intervention. This result is at odds with assumptions that contact-transmitted viruses would be more abundant in crops than in wild plant communities and could be explained by effective seed-, contact-, or pollinator-mediated transmission or by survival in the soil. TMGMV and TMV had low genetic diversity that was not structured according to habitat or host plant taxonomy, which indicated that phenotypic plasticity allows virus genotypes to infect new hosts with no need for adaptive evolution. Our results underscore the relevance of ecological factors in host range evolution, in addition to the more often studied genetic factors. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.}, } @article {pmid36916558, year = {2023}, author = {Aditya, A and Tabashsum, Z and Alvarado Martinez, Z and Wei Tung, C and Suh, G and Nguyen, P and Biswas, D}, title = {Diarrheagenic Escherichia coli and Their Antibiotic Resistance Patterns in Dairy Farms and Their Microbial Ecosystems.}, journal = {Journal of food protection}, volume = {86}, number = {3}, pages = {100051}, doi = {10.1016/j.jfp.2023.100051}, pmid = {36916558}, issn = {1944-9097}, mesh = {Humans ; *Escherichia coli ; Farms ; *Ecosystem ; Longitudinal Studies ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial ; Feces/microbiology ; Bacteria ; Soil ; Dairying ; }, abstract = {Ruminants are the largest reservoir for all types of Escherichia coli, including the pathogenic ones, which can potentially be transmitted to humans via the food chain and environment. A longitudinal study was performed to estimate the prevalence and antibiotic-resistant pattern of pathogenic E. coli (pE.coli) strains in dairy farm environments. A total of 846 environmental samples (water, lagoon slurry, bedding, feed, feces, soil, and compost) were collected in summer over two years from five dairy farms in Maryland, USA. An additional 40 soil samples were collected in winter and summer seasons for evaluating microbiome composition. Collected environmental samples were screened for the presence of pE.coli, which was isolated using a selective culture medium, for later confirmation and virotyping using PCR with specific primers. The overall prevalence of pE.coli in dairy farms was 8.93% (71/846), with the most common virotype identified in isolates being ETEC, followed by STEC. The highest pE.coli prevalence were recorded in lagoon slurry (21.57%) while the lowest was in compost heap (2.99%). Among isolates, 95.87% of the virotypes were resistant to 9 classes of antibiotics whereas only 4.12% were sensitive. The highest proportion (68.04%) of resistance was found for quinolones (e.g., ciprofloxacin). The resulting metagenomic analysis at the phylum and genus levels of the grazing land soil suggests that climatic conditions actively influence the abundance of bacteria. Proteobacteria, which contains many Gram-negative foodborne pathogens (including pE.coli), was the most predominant phylum, accounting for 26.70% and 24.93% of soil bacteria in summer and winter, respectively. In addition to relative abundance, there was no significant difference in species diversity between seasons when calculated via Simpson (D) and Shannon (H) index. This study suggests that antibiotic-resistant E. coli virotypes are present in the dairy farm environment, and proper steps are warranted to control its transmission irrespective of seasonality.}, } @article {pmid36916422, year = {2023}, author = {Wang, AJ and Song, D and Hong, YM and Liu, NN}, title = {Multi-omics insights into the interplay between gut microbiota and colorectal cancer in the "microworld" age.}, journal = {Molecular omics}, volume = {19}, number = {4}, pages = {283-296}, doi = {10.1039/d2mo00288d}, pmid = {36916422}, issn = {2515-4184}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Multiomics ; *Microbiota ; Metabolomics/methods ; *Colorectal Neoplasms/genetics ; }, abstract = {Colorectal cancer (CRC) is a multifactorial heterogeneous disease largely due to both genetic predisposition and environmental factors including the gut microbiota, a dynamic microbial ecosystem inhabiting the gastrointestinal tract. Elucidation of the molecular mechanisms by which the gut microbiota interacts with the host may contribute to the pathogenesis, diagnosis, and promotion of CRC. However, deciphering the influence of genetic variants and interactions with the gut microbial ecosystem is rather challenging. Despite recent advancements in single omics analysis, the application of multi-omics approaches to integrate multiple layers of information in the microbiome and host to introduce effective prevention, diagnosis, and treatment strategies is still in its infancy. Here, we integrate host- and microbe-based multi-omics studies, respectively, to provide a strategy to explore potential causal relationships between gut microbiota and colorectal cancer. Specifically, we summarize the recent multi-omics studies such as metagenomics combined with metabolomics and metagenomics combined with genomics. Meanwhile, the sample size and sample types commonly used in multi-omics research, as well as the methods of data analysis, were also generalized. We highlight multiple layers of information from multi-omics that need to be verified by different types of models. Together, this review provides new insights into the clinical diagnosis and treatment of colorectal cancer patients.}, } @article {pmid36915639, year = {2023}, author = {Roslund, MI and Parajuli, A and Hui, N and Puhakka, R and Grönroos, M and Soininen, L and Nurminen, N and Oikarinen, S and Cinek, O and Kramná, L and Schroderus, AM and Laitinen, OH and Kinnunen, T and Hyöty, H and Sinkkonen, A}, title = {Skin, gut, and sand metagenomic data on placebo-controlled sandbox biodiversity intervention study.}, journal = {Data in brief}, volume = {47}, number = {}, pages = {109003}, pmid = {36915639}, issn = {2352-3409}, abstract = {The metagenomic data presented in this article are related to the published research of "A Placebo-controlled double-blinded test of the biodiversity hypothesis of immune-mediated diseases: Environmental microbial diversity elicits changes in cytokines and increase in T regulatory cells in young children" This database contains 16S ribosomal RNA (rRNA) metagenomics of sandbox sand and skin and gut microbiota of children in the intervention and placebo daycares. In intervention daycares, children aged 3-5 years were exposed to playground sand enriched with microbially diverse soil. In placebo daycares, children were exposed to visually similar as in intervention daycares, but microbially poor sand colored with peat. Sand, skin and gut metagenomics were analyzed at baseline and after 14 and 28 days of intervention by high throughput sequencing of bacterial 16S rRNA gene on the Illumina MiSeq platform. This dataset shows how skin bacterial community composition, including classes Gammaproteobacteria and Bacilli, changed, and how the relative abundance of over 30 bacterial genera shifted on the skin of children in the intervention treatment, while no shifts occurred in the placebo group.}, } @article {pmid36915549, year = {2023}, author = {Qin, J and Ji, B and Ma, Y and Liu, X and Wang, T and Liu, G and Li, B and Wang, G and Gao, P}, title = {Diversity and potential function of pig gut DNA viruses.}, journal = {Heliyon}, volume = {9}, number = {3}, pages = {e14020}, pmid = {36915549}, issn = {2405-8440}, abstract = {Viruses are ubiquitous in the gut of animals and play an important role in the ecology of the gut microbiome. The potential effects of these substances on the growth and development of the body are not fully known. Little is known about the effects of breeding environment on pig gut virome. Here, there are 3584 viral operational taxonomic units (vOTUs) longer than 5 kb identified by virus-enriched metagenome sequencing from 25 pig fecal samples. Only a small minority of vOTUs (11.16%) can be classified at the family level, and ∼50% of the genes could be annotated, supporting the concept of pig gut as reservoirs of substantial undescribed viral genetic diversity. The composition of pig gut virome in the six regions may be related to geography. There are only 20 viral clusters (VCs) shared among pig gut virome in six regions of Shanxi Province. These viruses rarely carry antibiotic resistance genes (ARGs). At the same time, they possess abundant auxiliary metabolic genes (AMGs) potentially involved in carbon, sulfur metabolism and cofactor biosynthesis, etc. This study has revealed the unique characteristics and potential function of pig gut DNA virome and established a foundation for the recognition of the viral roles in gut environment.}, } @article {pmid36915411, year = {2023}, author = {Thippabhotla, S and Liu, B and Podgorny, A and Yooseph, S and Yang, Y and Zhang, J and Zhong, C}, title = {Integrated de novo gene prediction and peptide assembly of metagenomic sequencing data.}, journal = {NAR genomics and bioinformatics}, volume = {5}, number = {1}, pages = {lqad023}, pmid = {36915411}, issn = {2631-9268}, abstract = {Metagenomics is the study of all genomic content contained in given microbial communities. Metagenomic functional analysis aims to quantify protein families and reconstruct metabolic pathways from the metagenome. It plays a central role in understanding the interaction between the microbial community and its host or environment. De novo functional analysis, which allows the discovery of novel protein families, remains challenging for high-complexity communities. There are currently three main approaches for recovering novel genes or proteins: de novo nucleotide assembly, gene calling and peptide assembly. Unfortunately, their information dependency has been overlooked, and each has been formulated as an independent problem. In this work, we develop a sophisticated workflow called integrated Metagenomic Protein Predictor (iMPP), which leverages the information dependencies for better de novo functional analysis. iMPP contains three novel modules: a hybrid assembly graph generation module, a graph-based gene calling module, and a peptide assembly-based refinement module. iMPP significantly improved the existing gene calling sensitivity on unassembled metagenomic reads, achieving a 92-97% recall rate at a high precision level (>85%). iMPP further allowed for more sensitive and accurate peptide assembly, recovering more reference proteins and delivering more hypothetical protein sequences. The high performance of iMPP can provide a more comprehensive and unbiased view of the microbial communities under investigation. iMPP is freely available from https://github.com/Sirisha-t/iMPP.}, } @article {pmid36915394, year = {2023}, author = {Dai, S and He, Q and Han, Z and Shen, W and Deng, Y and Wang, Y and Qiao, W and Yang, M and Zhang, Y}, title = {Uncovering the diverse hosts of tigecycline resistance gene tet(X4) in anaerobic digestion systems treating swine manure by epicPCR.}, journal = {Water research X}, volume = {19}, number = {}, pages = {100174}, pmid = {36915394}, issn = {2589-9147}, abstract = {The tet(X4) gene is a clinically important tigecycline resistance gene and has shown high persistence in livestock-related environments. However, the bacterial hosts of tet(X4) remain unknown due to the lack of appropriate approaches. Herein, a culture-independent and high-throughput epicPCR (emulsion, paired isolation, and concatenation polymerase chain reaction) method was developed, optimized, and demonstrated for the identification of bacterial hosts carrying tet(X4) from environmental samples. Considering the high sequence similarity between tet(X4) and other tet(X)-variant genes, specific primers and amplification conditions were screened and optimized to identify tet(X4) accurately and link tet(X4) with the 16S rRNA gene, which were further validated using artificially constructed bacterial communities. The epicPCR targeting tet(X4) was applied for the identification of bacterial hosts carrying this resistance gene in anaerobic digestion systems treating swine manure. A total of 19 genera were identified as tet(X4) hosts, which were distributed in the phyla Proteobacteria, Bacteroidota, Firmicutes, and Caldatribacteriota. Sixteen genera and two phyla that were identified have not been previously reported as tet(X4) bacterial hosts. The results indicated that a far more diverse range of bacteria was involved in harboring tet(X4) than previously realized. Compared with the tet(X4) hosts determined by correlation-based network analysis and metagenomic binning, epicPCR revealed a high diversity of tet(X4) hosts even at the phylum level. The epicPCR method developed in this study could be effectively employed to reveal the presence of tet(X4) bacterial hosts from a holistic viewpoint.}, } @article {pmid36915382, year = {2023}, author = {Lo, EKK and Wang, X and Lee, PK and Wong, HC and Lee, JC and Gómez-Gallego, C and Zhao, D and El-Nezami, H and Li, J}, title = {Mechanistic insights into zearalenone-accelerated colorectal cancer in mice using integrative multi-omics approaches.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {1785-1796}, pmid = {36915382}, issn = {2001-0370}, abstract = {Zearalenone (ZEA), a secondary metabolite of Fusarium fungi found in cereal-based foods, promotes the growth of colon, breast, and prostate cancer cells in vitro. However, the lack of animal studies hinders a deeper mechanistic understanding of the cancer-promoting effects of ZEA. This study aimed to determine the effect of ZEA on colon cancer progression and its underlying mechanisms. Through integrative analyses of transcriptomics, metabolomics, metagenomics, and host phenotypes, we investigated the impact of a 4-week ZEA intervention on colorectal cancer in xenograft mice. Our results showed a twofold increase in tumor weight with the 4-week ZEA intervention. ZEA exposure significantly increased the mRNA and protein levels of BEST4, DGKB, and Ki67 and the phosphorylation levels of ERK1/2 and AKT. Serum metabolomic analysis revealed that the levels of amino acids, including histidine, arginine, citrulline, and glycine, decreased significantly in the ZEA group. Furthermore, ZEA lowered the alpha diversity of the gut microbiota and reduced the abundance of nine genera, including Tuzzerella and Rikenella. Further association analysis indicated that Tuzzerella was negatively associated with the expression of BEST4 and DGKB genes, serum uric acid levels, and tumor weight. Additionally, circulatory hippuric acid levels positively correlated with tumor weight and the expression of oncogenic genes, including ROBO3, JAK3, and BEST4. Altogether, our results indicated that ZEA promotes colon cancer progression by enhancing the BEST4/AKT/ERK1/2 pathway, lowering circulatory amino acid concentrations, altering gut microbiota composition, and suppressing short chain fatty acids production.}, } @article {pmid36914646, year = {2023}, author = {Ngugi, DK and Acinas, SG and Sánchez, P and Gasol, JM and Agusti, S and Karl, DM and Duarte, CM}, title = {Abiotic selection of microbial genome size in the global ocean.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1384}, pmid = {36914646}, issn = {2041-1723}, mesh = {Genome Size ; Oceans and Seas ; *Genome, Microbial ; Metagenome/genetics ; *Microbiota ; Seawater ; }, abstract = {Strong purifying selection is considered a major evolutionary force behind small microbial genomes in the resource-poor photic ocean. However, very little is currently known about how the size of prokaryotic genomes evolves in the global ocean and whether patterns reflect shifts in resource availability in the epipelagic and relatively stable deep-sea environmental conditions. Using 364 marine microbial metagenomes, we investigate how the average genome size of uncultured planktonic prokaryotes varies across the tropical and polar oceans to the hadal realm. We find that genome size is highest in the perennially cold polar ocean, reflecting elongation of coding genes and gene dosage effects due to duplications in the interior ocean microbiome. Moreover, the rate of change in genome size due to temperature is 16-fold higher than with depth up to 200 m. Our results demonstrate how environmental factors can influence marine microbial genome size selection and ecological strategies of the microbiome.}, } @article {pmid36914318, year = {2023}, author = {Zhao, Y and Sun, C and Wang, S and Zhang, M and Li, Y and Xue, Q and Guo, Q and Lai, H}, title = {Widely targeted metabolomic, transcriptomic, and metagenomic profiling reveal microbe-plant-metabolic reprogramming patterns mediated by Streptomyces pactum Act12 enhance the fruit quality of Capsicum annuum L.}, journal = {Food research international (Ottawa, Ont.)}, volume = {166}, number = {}, pages = {112587}, doi = {10.1016/j.foodres.2023.112587}, pmid = {36914318}, issn = {1873-7145}, mesh = {*Capsicum/chemistry ; Fruit/chemistry ; Transcriptome ; Soil/chemistry ; }, abstract = {Plant growth-promoting rhizobacteria, such as Streptomyces pactum Act12, promote crop growth and stress resistance, but their contribution to fruit quality is still poorly understood. Herein we conducted a field experiment to ascertain the effects of S. pactum Act12-mediated metabolic reprogramming and underlying mechanisms in pepper (Capsicum annuum L.) fruit based on widely targeted metabolomic and transcriptomic profiling. We additionally performed metagenomic analysis to elucidate the potential relationship between S. pactum Act12-mediated reshaping of rhizosphere microbial communities and pepper fruit quality. Soil inoculation with S. pactum Act12 considerably increased the accumulation of capsaicinoids, carbohydrates, organic acids, flavonoids, anthraquinones, unsaturated fatty acids, vitamins, and phenolic acids in pepper fruit samples. Consequently, fruit flavor, taste, and color were modified, accompanied by elevated contents of nutrients and bioactive compounds. Increased microbial diversity and recruitment of potentially beneficial taxa were observed in inoculated soil samples, with crosstalk between microbial gene functions and pepper fruit metabolism. The reformed structure and function of rhizosphere microbial communities were closely associated with pepper fruit quality. Our findings indicate that S. pactum Act12-mediated interactions between rhizosphere microbial communities and pepper plants are responsible for intricate fruit metabolic reprogramming patterns, which enhance not only overall fruit quality but also consumer acceptability.}, } @article {pmid36913841, year = {2023}, author = {Vermote, L and De Roos, J and Cnockaert, M and Vandamme, P and Weckx, S and De Vuyst, L}, title = {New insights into the role of key microorganisms and wooden barrels during lambic beer fermentation and maturation.}, journal = {International journal of food microbiology}, volume = {394}, number = {}, pages = {110163}, doi = {10.1016/j.ijfoodmicro.2023.110163}, pmid = {36913841}, issn = {1879-3460}, mesh = {*Beer/microbiology ; Fermentation ; Bacteria/genetics ; Plasmids ; *Microbiota ; }, abstract = {Belgian lambic beers are still produced through traditional craftsmanship. They rely on a spontaneous fermentation and maturation process that is entirely carried out in wooden barrels. The latter are used repetitively and may introduce some batch-to-batch variability. The present systematic and multiphasic study dealt with two parallel lambic beer productions carried out in nearly identical wooden barrels making use of the same cooled wort. It encompassed a microbiological and metabolomic approach. Further, a taxonomic classification and metagenome-assembled genome (MAG) investigation was based on shotgun metagenomics. These investigations provided new insights into the role of these wooden barrels and key microorganisms for this process. Indeed, besides their role in traditionality, the wooden barrels likely helped in establishing the stable microbial ecosystem of lambic beer fermentation and maturation by acting as an inoculation source of the necessary microorganisms, thereby minimizing batch-to-batch variations. They further provided a microaerobic environment, which aided in achieving the desirable succession of the different microbial communities for a successful lambic beer production process. Moreover, these conditions prevented excessive growth of acetic acid bacteria and, therefore, uncontrolled production of acetic acid and acetoin, which may lead to flavor deviations in lambic beer. Concerning the role of less studied key microorganisms for lambic beer production, it was shown that the Acetobacter lambici MAG contained several acid tolerance mechanisms toward the harsh environment of maturing lambic beer, whereas genes related to sucrose and maltose/maltooligosaccharide consumption and the glyoxylate shunt were absent. Further, a Pediococcus damnosus MAG possessed a gene encoding ferulic acid decarboxylase, possibly contributing to 4-vinyl compound production, as well as several genes, likely plasmid-based, related to hop resistance and biogenic amine production. Finally, contigs related to Dekkera bruxellensis and Brettanomyces custersianus did not possess genes involved in glycerol production, emphasizing the need for alternative external electron acceptors for redox balancing.}, } @article {pmid36913533, year = {2023}, author = {Vilardi, K and Cotto, I and Bachmann, M and Parsons, M and Klaus, S and Wilson, C and Bott, CB and Pieper, KJ and Pinto, AJ}, title = {Co-Occurrence and Cooperation between Comammox and Anammox Bacteria in a Full-Scale Attached Growth Municipal Wastewater Treatment Process.}, journal = {Environmental science & technology}, volume = {57}, number = {12}, pages = {5013-5023}, pmid = {36913533}, issn = {1520-5851}, mesh = {*Ammonia ; Anaerobic Ammonia Oxidation ; Bioreactors/microbiology ; Oxidation-Reduction ; Bacteria ; Nitrification ; Sewage/microbiology ; *Water Purification/methods ; Nitrogen ; Denitrification ; }, abstract = {Cooperation between comammox and anammox bacteria for nitrogen removal has been recently reported in laboratory-scale systems, including synthetic community constructs; however, there are no reports of full-scale municipal wastewater treatment systems with such cooperation. Here, we report intrinsic and extant kinetics as well as genome-resolved community characterization of a full-scale integrated fixed film activated sludge (IFAS) system where comammox and anammox bacteria co-occur and appear to drive nitrogen loss. Intrinsic batch kinetic assays indicated that majority of the aerobic ammonia oxidation was driven by comammox bacteria (1.75 ± 0.08 mg-N/g TS-h) in the attached growth phase, with minimal contribution by ammonia-oxidizing bacteria. Interestingly, a portion of total inorganic nitrogen (∼8%) was consistently lost during these aerobic assays. Aerobic nitrite oxidation assays eliminated the possibility of denitrification as a cause of nitrogen loss, while anaerobic ammonia oxidation assays resulted in rates consistent with anammox stoichiometry. Full-scale experiments at different dissolved oxygen (DO = 2 - 6 mg/L) setpoints indicated persistent nitrogen loss that was partly sensitive to DO concentrations. Genome-resolved metagenomics confirmed the high abundance (relative abundance 6.53 ± 0.34%) of two Brocadia-like anammox populations, while comammox bacteria within the Ca. Nitrospira nitrosa cluster were lower in abundance (0.37 ± 0.03%) and Nitrosomonas-like ammonia oxidizers were even lower (0.12 ± 0.02%). Collectively, our study reports for the first time the co-occurrence and cooperation of comammox and anammox bacteria in a full-scale municipal wastewater treatment system.}, } @article {pmid36913445, year = {2023}, author = {Strobel, KM and Del Vecchio, G and Devaskar, SU and Calkins, KL}, title = {Gut Microbes and Circulating Cytokines in Preterm Infants with Growth Failure.}, journal = {The Journal of nutrition}, volume = {153}, number = {1}, pages = {120-130}, pmid = {36913445}, issn = {1541-6100}, support = {R01 HD081206/HD/NICHD NIH HHS/United States ; T32 DK007180/DK/NIDDK NIH HHS/United States ; KL2 TR000122/TR/NCATS NIH HHS/United States ; }, mesh = {Infant ; Humans ; Infant, Newborn ; *Infant, Premature ; *Gastrointestinal Microbiome/genetics ; Cytokines/genetics ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Birth Weight ; }, abstract = {BACKGROUND: Growth failure (GF) is a multifactorial problem in preterm infants. The intestinal microbiome and inflammation may contribute to GF.

OBJECTIVES: This study's objective was to compare the gut microbiome and plasma cytokines in preterm infants with and without GF.

METHODS: This was a prospective cohort study of infants with birth weights of <1750 g. Infants with a weight or length z-score change from birth to discharge or death that was less than or equal to -0.8 (GF group) were compared with infants without GF [control (CON) group]. The primary outcome was the gut microbiome (at weeks 1-4 of age), assessed by 16S rRNA gene sequencing using Deseq2. Secondary outcomes included inferred metagenomic function and plasma cytokines. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States determined metagenomic function, which was compared using ANOVA. Cytokines were measured by 2-multiplexed immunometric assays and compared using Wilcoxon tests and linear mixed models.

RESULTS: GF (n = 14) and CON group (n = 13) had similar median (IQR) birth weight (1380 [780-1578] g vs. 1275 [1013-1580] g) and gestational age (29 [25-31] weeks vs. 30 [29-32] weeks). Compared with the CON group, the GF group had a greater abundance of Escherichia/Shigella in weeks 2 and 3, Staphylococcus in week 4, and Veillonella in weeks 3 and 4 (P-adjusted < 0.001 for all). Plasma cytokine concentrations did not differ significantly between the cohorts. When all time points are combined, fewer microbes were involved in TCA cycle activity in the GF group compared with the CON group (P = 0.023).

CONCLUSIONS: In this study, when compared with CON infants, GF infants had a distinct microbial signature with increased Escherichia/Shigella and Firmicutes and fewer microbes associated with energy production at later weeks of hospitalization. These findings may suggest a mechanism for aberrant growth.}, } @article {pmid36913444, year = {2023}, author = {Larke, JA and Bacalzo, N and Castillo, JJ and Couture, G and Chen, Y and Xue, Z and Alkan, Z and Kable, ME and Lebrilla, CB and Stephensen, CB and Lemay, DG}, title = {Dietary Intake of Monosaccharides from Foods is Associated with Characteristics of the Gut Microbiota and Gastrointestinal Inflammation in Healthy US Adults.}, journal = {The Journal of nutrition}, volume = {153}, number = {1}, pages = {106-119}, pmid = {36913444}, issn = {1541-6100}, support = {R01 DK124193/DK/NIDDK NIH HHS/United States ; }, mesh = {Male ; Female ; Adult ; Humans ; *Gastrointestinal Microbiome ; Monosaccharides ; Cross-Sectional Studies ; Dietary Fiber ; Eating ; Diet ; Feces/chemistry ; Inflammation ; }, abstract = {BACKGROUND: Current assessment of dietary carbohydrates does not adequately reflect the nutritional properties and effects on gut microbial structure and function. Deeper characterization of food carbohydrate composition can serve to strengthen the link between diet and gastrointestinal health outcomes.

OBJECTIVES: The present study aims to characterize the monosaccharide composition of diets in a healthy US adult cohort and use these features to assess the relationship between monosaccharide intake, diet quality, characteristics of the gut microbiota, and gastrointestinal inflammation.

METHODS: This observational, cross-sectional study enrolled males and females across age (18-33 y, 34-49 y, and 50-65 y) and body mass index (normal, 18.5-24.99 kg/m[2]; overweight, 25-29.99 kg/m[2]; and obese, 30-44 kg/m[2]) categories. Recent dietary intake was assessed by the automated self-administered 24-h dietary recall system, and gut microbiota were assessed with shotgun metagenome sequencing. Dietary recalls were mapped to the Davis Food Glycopedia to estimate monosaccharide intake. Participants with >75% of carbohydrate intake mappable to the glycopedia were included (N = 180).

RESULTS: Diversity of monosaccharide intake was positively associated with the total Healthy Eating Index score (Pearson's r = 0.520, P = 1.2 × 10[-13]) and negatively associated with fecal neopterin (Pearson's r = -0.247, P = 3.0 × 10[-3]). Comparing high with low intake of specific monosaccharides revealed differentially abundant taxa (Wald test, P < 0.05), which was associated with the functional capacity to break down these monomers (Wilcoxon rank-sum test, P < 0.05).

CONCLUSIONS: Monosaccharide intake was associated with diet quality, gut microbial diversity, microbial metabolism, and gastrointestinal inflammation in healthy adults. As specific food sources were rich in particular monosaccharides, it may be possible in the future to tailor diets to fine-tune the gut microbiota and gastrointestinal function. This trial is registered at www.

CLINICALTRIALS: gov as NCT02367287.}, } @article {pmid36912817, year = {2023}, author = {Wiegand, T and Wilkinson, R and Santiago-Frangos, A and Lynes, M and Hatzenpichler, R and Wiedenheft, B}, title = {Functional and Phylogenetic Diversity of Cas10 Proteins.}, journal = {The CRISPR journal}, volume = {6}, number = {2}, pages = {152-162}, pmid = {36912817}, issn = {2573-1602}, support = {K99 GM147842/GM/NIGMS NIH HHS/United States ; R35 GM134867/GM/NIGMS NIH HHS/United States ; }, mesh = {*Gene Editing ; CRISPR-Cas Systems/genetics ; *CRISPR-Associated Proteins/metabolism ; Phylogeny ; Bacterial Proteins/genetics/metabolism ; }, abstract = {Cas10 proteins are large subunits of type III CRISPR RNA (crRNA)-guided surveillance complexes, many of which have nuclease and cyclase activities. Here, we use computational and phylogenetic methods to identify and analyze 2014 Cas10 sequences from genomic and metagenomic databases. Cas10 proteins cluster into five distinct clades that mirror previously established CRISPR-Cas subtypes. Most Cas10 proteins (85.0%) have conserved polymerase active-site motifs, while HD-nuclease domains are less well conserved (36.0%). We identify Cas10 variants that are split over multiple genes or genetically fused to nucleases activated by cyclic nucleotides (i.e., NucC) or components of toxin-antitoxin systems (i.e., AbiEii). To clarify the functional diversification of Cas10 proteins, we cloned, expressed, and purified five representatives from three phylogenetically distinct clades. None of the Cas10s are functional cyclases in isolation, and activity assays performed with polymerase domain active site mutants indicate that previously reported Cas10 DNA-polymerase activity may be a result of contamination. Collectively, this work helps clarify the phylogenetic and functional diversity of Cas10 proteins in type III CRISPR systems.}, } @article {pmid36912756, year = {2023}, author = {Jiang, C and Wang, G and Zhang, J and Gu, S and Wang, X and Qin, W and Chen, K and Yuan, D and Chai, X and Yang, M and Zhou, F and Xiong, J and Miao, W}, title = {iGDP: An integrated genome decontamination pipeline for wild ciliated microeukaryotes.}, journal = {Molecular ecology resources}, volume = {23}, number = {5}, pages = {1182-1193}, doi = {10.1111/1755-0998.13782}, pmid = {36912756}, issn = {1755-0998}, support = {32122015, 31872221, 31900339 and 31900316//National Natural Science Foundation of China/ ; }, mesh = {*Decontamination ; *Genomics ; Metagenome ; Phylogeny ; Eukaryota ; }, abstract = {Ciliates are a large group of ubiquitous and highly diverse single-celled eukaryotes that play an essential role in the functioning of microbial food webs. However, their genomic diversity is far from clear due to the need to develop cultivation methods for most species, so most research is based on wild organisms that almost invariably contain contaminants. Here we establish an integrated Genome Decontamination Pipeline (iGDP) that combines homology search, telomere reads-assisted and clustering approaches to filter contaminated ciliate genome assemblies from wild specimens. We benchmarked the performance of iGDP using genomic data from a contaminated ciliate culture and the results showed that iGDP could recall 91.9% of the target sequences with 96.9% precision. We also used a synthetic dataset to offer guidelines for the application of iGDP in the removal of various groups of contaminants. Compared with several popular metagenome binning tools, iGDP could show better performance. To further validate the effectiveness of iGDP on real-world data, we applied it to decontaminate genome assemblies of three wild ciliate specimens and obtained their genomes with high quality comparable to that of previously well-studied model ciliate genomes. It is anticipated that the newly generated genomes and the established iGDP method will be valuable community resources for detailed studies on ciliate biodiversity, phylogeny, ecology and evolution. The pipeline (https://github.com/GWang2022/iGDP) can be implemented automatically to reduce manual filtering and classification and may be further developed to apply to other microeukaryotes.}, } @article {pmid36912690, year = {2023}, author = {Shekarriz, E and Chen, J and Xu, Z and Liu, H}, title = {Disentangling the Functional Role of Fungi in Cold Seep Sediment.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0197822}, pmid = {36912690}, issn = {2165-0497}, abstract = {Cold seeps are biological oases of the deep sea fueled by methane, sulfates, nitrates, and other inorganic sources of energy. Chemolithoautotrophic bacteria and archaea dominate seep sediment, and their diversity and biogeochemical functions are well established. Fungi are likewise diverse, metabolically versatile, and known for their ability to capture and oxidize methane. Still, no study has ever explored the functional role of the mycobiota in the cold seep biome. To assess the complex role of fungi and fill in the gaps, we performed network analysis on 147 samples to disentangle fungal-prokaryotic interactions (fungal 18S and prokaryotic 16S) in the Haima cold seep region. We demonstrated that fungi are central species with high connectivity at the epicenter of prokaryotic networks, reduce their random-attack vulnerability by 60%, and enhance information transfer efficiency by 15%. We then scavenged a global metagenomic and metatranscriptomic data set from 10 cold seep regions for fungal genes of interest (hydrophobins, cytochrome P450s, and ligninolytic family of enzymes); this is the first study to report active transcription of 2,500+ fungal genes in the cold seep sediment. The genera Fusarium and Moniliella were of notable importance and directly correlated with high methane abundance in the sulfate-methane transition zone (SMTZ), likely due to their ability to degrade and solubilize methane and oils. Overall, our results highlight the essential yet overlooked contribution of fungi to cold seep biological networks and the role of fungi in regulating cold seep biogeochemistry. IMPORTANCE The challenges we face when analyzing eukaryotic metagenomic and metatranscriptomic data sets have hindered our understanding of cold seep fungi and microbial eukaryotes. This fact does not make the mycobiota any less critical in mediating cold seep biogeochemistry. On the contrary, many fungal genera can oxidize and solubilize methane, produce methane, and play a unique role in nutrient recycling via saprotrophic enzymatic activity. In this study, we used network analysis to uncover key fungal-prokaryotic interactions that can mediate methane biogeochemistry and metagenomics and metatranscriptomics to report that fungi are transcriptionally active in the cold seep sediment. With concerns over rising methane levels and cold seeps being a pivotal source of global methane input, our holistic understanding of methane biogeochemistry with all domains of life is essential. We ultimately encourage scientists to utilize state-of-the-art tools and multifaceted approaches to uncover the role of microeukaryotic organisms in understudied systems.}, } @article {pmid36912656, year = {2023}, author = {Kao, S and Kao, CF and Chang, W and Ku, C}, title = {Widespread Distribution and Evolution of Poxviral Entry-Fusion Complex Proteins in Giant Viruses.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0494422}, pmid = {36912656}, issn = {2165-0497}, abstract = {Poxviruses are known to encode a set of proteins that form an entry-fusion complex (EFC) to mediate virus entry. However, the diversity, evolution, and origin of these EFC proteins remain poorly understood. Here, we identify the EFC protein homologs in poxviruses and other giant viruses of the phylum Nucleocytoviricota. The 11 EFC genes are present in almost all poxviruses, with the two smallest, G3 and O3, being absent in Entomopoxvirinae and basal lineages of Chordopoxvirinae. Five of the EFC genes are further grouped into two families, A16/G9/J5 and F9/L1, which are widely distributed across other major lineages of Nucleocytoviricota, including metagenome-assembled genomes, but are generally absent in viruses infecting algae or nonamoebozoan heterotrophic protists. The A16/G9/J5 and F9/L1 families cooccur, mostly as single copies, in 93% of the non-Poxviridae giant viruses that have at least one of them. Distribution and phylogenetic patterns suggest that both families originated in the ancestor of Nucleocytoviricota. In addition to the Poxviridae genes, homologs from each of the other Nucleocytoviricota families are largely clustered together, suggesting their ancient presence and vertical inheritance. Despite deep sequence divergences, we observed noticeable conservation of cysteine residues and predicted structures between EFC proteins of Poxviridae and other families. Overall, our study reveals widespread distribution of these EFC protein homologs beyond poxviruses, implies the existence of a conserved membrane fusion mechanism, and sheds light on host range and ancient evolution of Nucleocytoviricota. IMPORTANCE Fusion between virus and host membranes is critical for viruses to release genetic materials and to initiate infection. Whereas most viruses use a single protein for membrane fusion, poxviruses employ a multiprotein entry-fusion complex (EFC). We report that two major families of the EFC proteins are widely distributed within the virus phylum Nucleocytoviricota, which includes poxviruses and other double-stranded (dsDNA) giant viruses that infect animals, amoebozoans, algae, and various microbial eukaryotes. Each of these two protein families is structurally conserved, traces its origin to the root of Nucleocytoviricota, was passed down to the major subclades of Nucleocytoviricota, and is retained in most giant viruses known to infect animals and amoebozoans. The EFC proteins therefore represent a potential mechanism for virus entry in diverse giant viruses. We hypothesize that they may have facilitated the infection of an animal/amoebozoan-like host by the last Nucleocytoviricota common ancestor.}, } @article {pmid36912626, year = {2023}, author = {Li, D and Ren, Z and Zhou, Y and Jiang, L and Zheng, M and Liu, G}, title = {Comammox Nitrospira and Ammonia-Oxidizing Archaea Are Dominant Ammonia Oxidizers in Sediments of an Acid Mine Lake Containing High Ammonium Concentrations.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {3}, pages = {e0004723}, pmid = {36912626}, issn = {1098-5336}, mesh = {Humans ; Archaea/metabolism ; Ammonia/metabolism ; *Ammonium Compounds/metabolism ; Lakes ; RNA, Ribosomal, 16S/genetics/metabolism ; Oxidation-Reduction ; Bacteria ; Nitrification ; Phylogeny ; *Leukemia, Myeloid, Acute ; }, abstract = {Exploring nitrifiers in extreme environments is vital to expanding our understanding of nitrogen cycle and microbial diversity. This study presents that complete ammonia oxidation (comammox) Nitrospira, together with acidophilic ammonia-oxidizing archaea (AOA), dominate in the nitrifying guild in sediments of an acid mine lake (AML). The lake water was characterized by acidic pH below 5 with a high ammonium concentration of 175 mg-N/liter, which is rare on the earth. Nitrification was active in sediments with a maximum nitrate production potential of 70.5 μg-N/(g-dry weight [dw] day) for mixed sediments. Quantitative PCR assays determined that in AML sediments, comammox Nitrospira and AOA amoA genes had relative abundances of 52% and 41%, respectively, among the total amoA genes. Further assays with 16S rRNA and amoA gene amplicon sequencing and metagenomics confirmed their dominance and revealed that the comammox Nitrospira found in sediments belonged to comammox Nitrospira clade A.2. Metagenomic binning retrieved a metagenome-assembled genome (MAG) of the comammox Nitrospira from sediments (completeness = 96.76%), and phylogenomic analysis suggested that it was a novel comammox Nitrospira. Comparative genomic investigation revealed that this comammox Nitrospira contained diverse metal resistance genes and an acidophile-affiliated F-type ATPase. Moreover, it had a more diverse genomic characteristic on nitrogen metabolism than the AOA in sediments and canonical AOB did. The results suggest that comammox Nitrospira is a versatile nitrifier that can adapt to acidic environments even with high ammonium concentrations. IMPORTANCE Ammonia-oxidizing archaea (AOA) was previously considered the sole dominant ammonia oxidizer in acidic environments. This study, however, found that complete ammonia oxidation (comammox) Nitrospira was also a dominant ammonia oxidizer in the sediments of an acidic mine lake, which had an acidic pH < 5 and a high ammonium concentration of 175 mg-N/liter. In combination with average nucleotide identity analysis, phylogenomic analysis suggested it is a novel strain of comammox Nitrospira. Moreover, the adaption of comammox Nitrospira to the acidic lake had been comprehensively investigated based on genome-centric metagenomic approaches. The outcomes of this study significantly expand our understanding of the diversity and adaptability of ammonia oxidizers in the acidic environments.}, } @article {pmid36912232, year = {2023}, author = {Labourel, A and Parrou, JL and Deraison, C and Mercier-Bonin, M and Lajus, S and Potocki-Veronese, G}, title = {O-Mucin-degrading carbohydrate-active enzymes and their possible implication in inflammatory bowel diseases.}, journal = {Essays in biochemistry}, volume = {67}, number = {3}, pages = {331-344}, pmid = {36912232}, issn = {1744-1358}, mesh = {Humans ; *Mucins/metabolism ; Intestinal Mucosa/metabolism/microbiology ; *Inflammatory Bowel Diseases/metabolism ; Carbohydrates ; Polysaccharides/metabolism ; Bacteria/metabolism ; }, abstract = {Inflammatory bowel diseases (IBD) are modern diseases, with incidence rising around the world. They are associated with perturbation of the intestinal microbiota, and with alteration and crossing of the mucus barrier by the commensal bacteria that feed on it. In the process of mucus catabolism and invasion by gut bacteria, carbohydrate-active enzymes (CAZymes) play a critical role since mucus is mainly made up by O- and N-glycans. Moreover, the occurrence of IBD seems to be associated with low-fiber diets. Conversely, supplementation with oligosaccharides, such as human milk oligosaccharides (HMOs), which are structurally similar to intestinal mucins and could thus compete with them towards bacterial mucus-degrading CAZymes, has been suggested to prevent inflammation. In this mini-review, we will establish the current state of knowledge regarding the identification and characterization of mucus-degrading enzymes from both cultured and uncultured species of gut commensals and enteropathogens, with a particular focus on the present technological opportunities available to further the discovery of mucus-degrading CAZymes within the entire gut microbiome, by coupling microfluidics with metagenomics and culturomics. Finally, we will discuss the challenges to overcome to better assess how CAZymes targeting specific functional oligosaccharides could be involved in the modulation of the mucus-driven cross-talk between gut bacteria and their host in the context of IBD.}, } @article {pmid36911308, year = {2023}, author = {Martinez, ND}, title = {Predicting ecosystem metaphenome from community metagenome: A grand challenge for environmental biology.}, journal = {Ecology and evolution}, volume = {13}, number = {3}, pages = {e9872}, pmid = {36911308}, issn = {2045-7758}, abstract = {Elucidating how an organism's characteristics emerge from its DNA sequence has been one of the great triumphs of biology. This triumph has cumulated in sophisticated computational models that successfully predict how an organism's detailed phenotype emerges from its specific genotype. Inspired by that effort's vision and empowered by its methodologies, a grand challenge is described here that aims to predict the biotic characteristics of an ecosystem, its metaphenome, from nucleic acid sequences of all the species in its community, its metagenome. Meeting this challenge would integrate rapidly advancing abilities of environmental nucleic acids (eDNA and eRNA) to identify organisms, their ecological interactions, and their evolutionary relationships with advances in mechanistic models of complex ecosystems. Addressing the challenge would help integrate ecology and evolutionary biology into a more unified and successfully predictive science that can better help describe and manage ecosystems and the services they provide to humanity.}, } @article {pmid36910237, year = {2023}, author = {Zhang, C and Shi, X and Zhang, J and Zhang, Y and Wang, W}, title = {Dynamics of soil microbiome throughout the cultivation life cycle of morel (Morchella sextelata).}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {979835}, pmid = {36910237}, issn = {1664-302X}, abstract = {Although Morchella sextelata (morel) is a well-known, edible, and medicinal fungus widely cultivated in China, the dynamics and roles of its soil microbiome during cultivation are unclear. Using rhizosphere soil samples collected throughout the M. sextelata cultivation life cycle, we conducted a high-throughput metagenomic sequencing analysis, with an emphasis on variations in soil microbial composition, characteristic biomarkers, and ecological functions. We found that microbial relative abundance, alpha diversity, and structure varied significantly among fungal growth stages. A total of 47 stage-associated biomarkers were identified through a linear discriminant analysis of effect size. In addition, horizontal comparison of soil microbiomes exhibiting successful and failed primordium formation further confirmed primordium-associated microbes with possible key roles in primordium formation. A microbial function analysis revealed that nutrient metabolism-related pathways were enriched during mycelium and fruiting body stages, whereas the signal transduction pathway was enriched during the primordium stage. This result indicates that diverse microbes are required at different growth stages of M. sextelata. Our research has revealed the dynamic scenario of the soil microbiome throughout the cultivation life cycle of M. sextelata. The high-resolution microbial profiles uncovered in the present study provide novel insights that should contribute to the improvement of morel cultivation using microbial inoculants.}, } @article {pmid36910224, year = {2023}, author = {Coskun, ÖK and Gomez-Saez, GV and Beren, M and Ozcan, D and Hosgormez, H and Einsiedl, F and Orsi, WD}, title = {Carbon metabolism and biogeography of candidate phylum "Candidatus Bipolaricaulota" in geothermal environments of Biga Peninsula, Turkey.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1063139}, pmid = {36910224}, issn = {1664-302X}, abstract = {Terrestrial hydrothermal springs and aquifers are excellent sites to study microbial biogeography because of their high physicochemical heterogeneity across relatively limited geographic regions. In this study, we performed 16S rRNA gene sequencing and metagenomic analyses of the microbial diversity of 11 different geothermal aquifers and springs across the tectonically active Biga Peninsula (Turkey). Across geothermal settings ranging in temperature from 43 to 79°C, one of the most highly represented groups in both 16S rRNA gene and metagenomic datasets was affiliated with the uncultivated phylum "Candidatus Bipolaricaulota" (former "Ca. Acetothermia" and OP1 division). The highest relative abundance of "Ca. Bipolaricaulota" was observed in a 68°C geothermal brine sediment, where it dominated the microbial community, representing 91% of all detectable 16S rRNA genes. Correlation analysis of "Ca. Bipolaricaulota" operational taxonomic units (OTUs) with physicochemical parameters indicated that salinity was the strongest environmental factor measured associated with the distribution of this novel group in geothermal fluids. Correspondingly, analysis of 23 metagenome-assembled genomes (MAGs) revealed two distinct groups of "Ca. Bipolaricaulota" MAGs based on the differences in carbon metabolism: one group encoding the bacterial Wood-Ljungdahl pathway (WLP) for H2 dependent CO2 fixation is selected for at lower salinities, and a second heterotrophic clade that lacks the WLP that was selected for under hypersaline conditions in the geothermal brine sediment. In conclusion, our results highlight that the biogeography of "Ca. Bipolaricaulota" taxa is strongly correlated with salinity in hydrothermal ecosystems, which coincides with key differences in carbon acquisition strategies. The exceptionally high relative abundance of apparently heterotrophic representatives of this novel candidate Phylum in geothermal brine sediment observed here may help to guide future enrichment experiments to obtain representatives in pure culture.}, } @article {pmid36910183, year = {2023}, author = {Xi, M and Deyett, E and Stajich, JE and El-Kereamy, A and Roper, MC and Rolshausen, PE}, title = {Microbiome diversity, composition and assembly in a California citrus orchard.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1100590}, pmid = {36910183}, issn = {1664-302X}, abstract = {The citrus root and rhizosphere microbiomes have been relatively well described in the literature, especially in the context of Huanglonbing disease. Yet questions addressing the assembly of root microbial endophytes have remained unanswered. In the above ground tree tissues, leaves and stems have been the research focus point, while flush and flower microbiomes, two important tissues in the vegetative and reproductive cycles of the tree, are not well described. In this study, the fungal and bacterial taxa in five biocompartments (bulk soil, rhizosphere, root endosphere, flower and flush) of citrus trees grown in a single California orchard were profiled using an amplicon-based metagenomic Illumina sequencing approach. Trees with no observable signs of abiotic or biotic stresses were sampled for two consecutive years during the floral development phase. The rhizosphere was the most biodiverse compartment compared to bulk soil, root endosphere, flower and flush microbiomes. In addition, the belowground bacteriome was more diverse than the mycobiome. Microbial richness decreased significantly from the root exosphere to the endosphere and was overall low in the above ground tissues. Root endophytic microbial community composition shared strong similarities to the rhizosphere but also contained few taxa from above ground tissues. Our data indicated compartmentalization of the microbiome with distinct profiles between above and below ground microbial communities. However, several taxa were present across all compartments suggesting the existence of a core citrus microbiota. These findings highlight key microbial taxa that could be engineered as biopesticides and biofertilizers for citriculture.}, } @article {pmid36910168, year = {2023}, author = {Hu, B and Wang, J and Li, Y and Ge, J and Pan, J and Li, G and He, Y and Zhong, H and Wang, B and Huang, Y and Han, S and Xing, Y and He, H}, title = {Gut microbiota facilitates adaptation of the plateau zokor (Myospalax baileyi) to the plateau living environment.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1136845}, pmid = {36910168}, issn = {1664-302X}, abstract = {Gut microbiota not only helps the hosts to perform many key physiological functions such as food digestion, energy harvesting and immune regulation, but also influences host ecology and facilitates adaptation of the host to extreme environments. Plateau zokors epitomize successful physiological adaptation to their living environment in the face of the harsh environment characterized by low temperature, low pressure and hypoxia in the Tibetan plateau region and high concentrations of CO2 in their burrows. Therefore, here we used a metagenomic sequencing approach to explore how gut microbiota contributed to the adaptive evolution of the plateau zokor on the Qinghai-Tibet Plateau. Our metagenomic results show that the gut microbiota of plateau zokors on the Tibetan plateau is not only enriched in a large number of species related to energy metabolism and production of short-chain fatty acids (SCFAs), but also significantly enriched the KO terms that involve carbohydrate uptake pathways, which well address energy uptake in plateau zokors while also reducing inflammatory responses due to low pressure, hypoxia and high CO2 concentrations. There was also a significant enrichment of tripeptidyl-peptidase II (TPPII) associated with antigen processing, apoptosis, DNA damage repair and cell division, which may facilitate the immune response and tissue damage repair in plateau zokors under extreme conditions. These results suggest that these gut microbiota and their metabolites together contribute to the physiological adaptation of plateau zokors, providing new insights into the contribution of the microbiome to the evolution of mammalian adaptation.}, } @article {pmid36910167, year = {2023}, author = {Zhao, J and Rodriguez, J and Martens-Habbena, W}, title = {Fine-scale evaluation of two standard 16S rRNA gene amplicon primer pairs for analysis of total prokaryotes and archaeal nitrifiers in differently managed soils.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1140487}, pmid = {36910167}, issn = {1664-302X}, abstract = {The advance of high-throughput molecular biology tools allows in-depth profiling of microbial communities in soils, which possess a high diversity of prokaryotic microorganisms. Amplicon-based sequencing of 16S rRNA genes is the most common approach to studying the richness and composition of soil prokaryotes. To reliably detect different taxonomic lineages of microorganisms in a single soil sample, an adequate pipeline including DNA isolation, primer selection, PCR amplification, library preparation, DNA sequencing, and bioinformatic post-processing is required. Besides DNA sequencing quality and depth, the selection of PCR primers and PCR amplification reactions arguably have the largest influence on the results. This study tested the performance and potential bias of two primer pairs, i.e., 515F (Parada)-806R (Apprill) and 515F (Parada)-926R (Quince) in the standard pipelines of 16S rRNA gene Illumina amplicon sequencing protocol developed by the Earth Microbiome Project (EMP), against shotgun metagenome-based 16S rRNA gene reads. The evaluation was conducted using five differently managed soils. We observed a higher richness of soil total prokaryotes by using reverse primer 806R compared to 926R, contradicting to in silico evaluation results. Both primer pairs revealed various degrees of taxon-specific bias compared to metagenome-derived 16S rRNA gene reads. Nonetheless, we found consistent patterns of microbial community variation associated with different land uses, irrespective of primers used. Total microbial communities, as well as ammonia oxidizing archaea (AOA), the predominant ammonia oxidizers in these soils, shifted along with increased soil pH due to agricultural management. In the unmanaged low pH plot abundance of AOA was dominated by the acid-tolerant NS-Gamma clade, whereas limed agricultural plots were dominated by neutral-alkaliphilic NS-Delta/NS-Alpha clades. This study stresses how primer selection influences community composition and highlights the importance of primer selection for comparative and integrative studies, and that conclusions must be drawn with caution if data from different sequencing pipelines are to be compared.}, } @article {pmid36909846, year = {2022}, author = {Li, H and Zhang, L and Zhang, K and Huang, Y and Liu, Y and Lu, X and Liao, W and Liu, X and Zhang, Q and Pan, W}, title = {Gut microbiota associated with cryptococcal meningitis and dysbiosis caused by anti-fungal treatment.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1086239}, pmid = {36909846}, issn = {1664-302X}, abstract = {The gut microbiota is a dynamic and highly diverse microbial ecosystem that affects many aspects of the host's physiology. An improved understanding of the gut microbiota could lead to better strategies for the diagnosis and therapy of cryptococcal meningitis (CM), but the impact of Cryptococcus infection and anti-fungal treatment on the gut microbiota has rarely been studied. We characterized the diversity and composition of the gut microbiota in CM patients at diagnosis and healthy controls (HCs) using metagenomic sequencing and determined the effects of anti-fungal drugs. We found that CM patients had distinct bacterial and fungal compositions compared with HCs, with eight differentially abundant fungal and 72 differentially abundant bacterial species identified between the two groups. CM patients showed an increased abundance of Enterococcus avium, Leuconostoc mesenteroides, and Weissella cibaria, and a decreased abundance of Prevotella spp. compared with HCs. However, anti-fungal treatment only led to minor changes in the intestinal microbiota. Moreover, both positive and negative correlations existed in fungal, bacterial, and clinical indicators. Our study suggests that the Cryptococcus neoformans infection caused a distinct dysbiosis of the gut microbiota and contributes valuable information implying potential links between the CM and gut microbiota.}, } @article {pmid36909733, year = {2023}, author = {Chang, L and Qiu, L and Lei, N and Zhou, J and Guo, R and Gao, F and Dong, S and Chen, M and Wu, F and Qin, B}, title = {Characterization of fecal microbiota in cervical cancer patients associated with tumor stage and prognosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1145950}, pmid = {36909733}, issn = {2235-2988}, mesh = {Humans ; Female ; *Uterine Cervical Neoplasms ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Feces ; }, abstract = {Cervical cancer (CC) is the fourth most frequent malignancy among women worldwide, and its prevention and treatment are evolving rapidly. The gut microbiota has been reported to play a crucial role both in the preservation of homeostasis and the development of cervical cancer. In this study, we collected fecal samples to investigate the microbial signatures in cervical cancer patients compared with healthy controls using 16S rRNA sequencing analysis and metagenomic next-generation sequencing (mNGS) testing. Our findings demonstrated a substantial difference in the gut microbiota composition of cervical cancer patients and healthy controls. The disease and stage were most significantly negatively correlated with Ruminococcus 2, which might be considered a potential clinically relevant biomarker. Functions of differential microbiomes were also analyzed, indicating significant differences in metabolisms and biosynthesis between the two groups. These findings demonstrate that patients with cervical cancer have certain species of gut microbiota that are exclusive to them and particular species have the potential to be used in the prognosis of cervical cancer.}, } @article {pmid36909730, year = {2023}, author = {MacDonald, T and Dunn, KA and MacDonald, J and Langille, MGI and Van Limbergen, JE and Bielawski, JP and Kulkarni, K}, title = {The gastrointestinal antibiotic resistome in pediatric leukemia and lymphoma patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1102501}, pmid = {36909730}, issn = {2235-2988}, mesh = {Humans ; Child ; Anti-Bacterial Agents ; Vancomycin ; Genes, Bacterial ; Gastrointestinal Tract/microbiology ; beta-Lactams ; *Leukemia/genetics ; *Lymphoma/genetics ; }, abstract = {INTRODUCTION: Most children with leukemia and lymphoma experience febrile neutropenia. These are treated with empiric antibiotics that include β-lactams and/or vancomycin. These are often administered for extended periods, and the effect on the resistome is unknown.

METHODS: We examined the impact of repeated courses and duration of antibiotic use on the resistome of 39 pediatric leukemia and lymphoma patients. Shotgun metagenome sequences from 127 stool samples of pediatric oncology patients were examined for abundance of antibiotic resistance genes (ARGs) in each sample. Abundances were grouped by repeated courses (no antibiotics, 1-2 courses, 3+ courses) and duration (no use, short duration, long and/or mixed durationg) of β-lactams, vancomycin and "any antibiotic" use. We assessed changes in both taxonomic composition and prevalence of ARGs among these groups.

RESULTS: We found that Bacteroidetes taxa and β-lactam resistance genes decreased, while opportunistic Firmicutes and Proteobacteria taxa, along with multidrug resistance genes, increased with repeated courses and/or duration of antibiotics. Efflux pump related genes predominated (92%) among the increased multidrug genes. While we found β-lactam ARGs present in the resistome, the taxa that appear to contain them were kept in check by antibiotic treatment. Multidrug ARGs, mostly efflux pumps or regulators of efflux pump genes, were associated with opportunistic pathogens, and both increased in the resistome with repeated antibiotic use and/or increased duration.

CONCLUSIONS: Given the strong association between opportunistic pathogens and multidrug-related efflux pumps, we suggest that drug efflux capacity might allow the opportunistic pathogens to persist or increase despite repeated courses and/or duration of antibiotics. While drug efflux is the most direct explanation, other mechanisms that enhance the ability of opportunistic pathogens to handle environmental stress, or other aspects of the treatment environment, could also contribute to their ability to flourish within the gut during treatment. Persistence of opportunistic pathogens in an already dysbiotic and weakened gastrointestinal tract could increase the likelihood of life-threatening blood borne infections. Of the 39 patients, 59% experienced at least one gastrointestinal or blood infection and 60% of bacteremia's were bacteria found in stool samples. Antimicrobial stewardship and appropriate use and duration of antibiotics could help reduce morbidity and mortality in this vulnerable population.}, } @article {pmid36909719, year = {2023}, author = {Dai, J and Lian, X and Mo, J and Li, X and Mo, W and Wang, H and Jiang, J}, title = {Case report: A clinical case study of six patients with Chlamydia psittaci pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1084882}, pmid = {36909719}, issn = {2235-2988}, mesh = {Humans ; *Chlamydophila psittaci ; Retrospective Studies ; *Psittacosis ; *Pneumonia ; Lung ; }, abstract = {OBJECTIVE: To investigate the clinical features, diagnosis, and treatment of Chlamydia psittaci (C. psittaci) pneumonia.

METHODS: We retrospectively analyzed the clinical data of six patients with C. psittaci pneumonia who were admitted to the Division of Pulmonary and Critical Care Medicine of the Second Hospital of Jiaxing from December 2021 to September 2022.

RESULTS: All patients reported a fever and other accompanying symptoms, including cough (5/6), chest tightness (1/6), fatigue (2/6), and headache (1/6). Laboratory results showed that all patients had high levels of C-reactive protein (CRP≥70 mg/L), procalcitonin (PCT; 2 patients with PCT levels ≥0.5 ng/L), and erythrocyte sedimentation rate (ESR). Lactate dehydrogenase (LDH) and aspartate aminotransferase (AST) levels were elevated in 3/6 and of 2/6 patients, respectively. Chest computed tomography (CT) of most patients showed patchy, high-density shadows with partial consolidation, accompanied by air bronchogram signs and pleural effusion. Six patients were diagnosed with C. psittaci pneumonia using metagenomic next-generation sequencing (mNGS). They showed favorable outcomes following immediate adjustment of the regimen to doxycycline-based therapy and hydration, nutrition, and other follow-up treatments. In the imaging findings obtained at one-two month, the lesions were completely cleared, suggesting a favorable prognosis.

CONCLUSION: Patients with C. psittaci pneumonia commonly present sepsis and rapidly progressing disease. Early diagnosis is critical for C. psittaci pneumonia using mNGS, which can lead to favorable prognoses via immediate adjustment therapies.}, } @article {pmid36909625, year = {2023}, author = {Verhoeve, VI and Lehman, SS and Driscoll, TP and Beckmann, JF and Gillespie, JJ}, title = {Metagenome diversity illuminates origins of pathogen effectors.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36909625}, support = {R21 AI126108/AI/NIAID NIH HHS/United States ; R21 AI146773/AI/NIAID NIH HHS/United States ; R21 AI156762/AI/NIAID NIH HHS/United States ; R21 AI166832/AI/NIAID NIH HHS/United States ; }, abstract = {Recent metagenome assembled genome (MAG) analyses have profoundly impacted Rickettsiology systematics. Discovery of basal lineages (Mitibacteraceae and Athabascaceae) with predicted extracellular lifestyles reveals an evolutionary timepoint for the transition to host dependency, which occurred independent of mitochondrial evolution. Notably, these basal rickettsiae carry the Rickettsiales vir homolog (rvh) type IV secretion system (T4SS) and purportedly use rvh to kill congener microbes rather than parasitize host cells as described for derived rickettsial pathogens. MAG analysis also substantially increased diversity for genus Rickettsia and delineated a basal lineage (Tisiphia) that stands to inform on the rise of human pathogens from protist and invertebrate endosymbionts. Herein, we probed Rickettsiales MAG and genomic diversity for the distribution of Rickettsia rvh effectors to ascertain their origins. A sparse distribution of most Rickettsia rvh effectors outside of Rickettsiaceae lineages indicates unique rvh evolution from basal extracellular species and other rickettsial families. Remarkably, nearly every effector was found in multiple divergent forms with variable architectures, illuminating profound roles for gene duplication and recombination in shaping effector repertoires in Rickettsia pathogens. Lateral gene transfer plays a prominent role shaping the rvh effector landscape, as evinced by the discover of many effectors on plasmids and conjugative transposons, as well as pervasive effector gene exchange between Rickettsia and Legionella species. Our study exemplifies how MAGs can provide incredible insight on the origins of pathogen effectors and how their architectural modifications become tailored to eukaryotic host cell biology.}, } @article {pmid36908773, year = {2023}, author = {Murray, AK and Zhang, L and Snape, J and Gaze, WH}, title = {Functional metagenomic libraries generated from anthropogenically impacted environments reveal importance of metabolic genes in biocide and antibiotic resistance.}, journal = {Current research in microbial sciences}, volume = {4}, number = {}, pages = {100184}, pmid = {36908773}, issn = {2666-5174}, abstract = {Anthropogenic activities result in the release of antimicrobial resistant bacteria and a cocktail of antimicrobial compounds into the environment that may directly select or indirectly co-select for antimicrobial resistance (AMR). Many studies use metagenome sequencing or qPCR-based approaches to study the environmental resistome but these methods are limited by a priori knowledge. In this study, a functional metagenomic approach was used to explore biocide resistance mechanisms in two contaminated environments and a pristine site, and to identify whether potentially novel genes conferring biocide resistance also conferred resistance or reduced susceptibility to antibiotics. Resistance was predominately mediated through novel mechanisms exclusive of the well-known qac efflux genes. UDP-galactose 4-epimerase (galE) -like genes were identified in both contaminated environments and were shown to confer cross-resistance to biocides and clinically important antibiotics for the first time (to our knowledge), compared to knockout mutants. GalE -like genes were also co-located with transposons, suggesting mobilisation potential. These results show that housekeeping genes may play a significant yet underappreciated role in AMR in environmental microbiomes.}, } @article {pmid36908513, year = {2023}, author = {Ganda, E and Chakrabarti, A and Sardi, MI and Tench, M and Kozlowicz, BK and Norton, SA and Warren, LK and Khafipour, E}, title = {Saccharomyces cerevisiae fermentation product improves robustness of equine gut microbiome upon stress.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1134092}, pmid = {36908513}, issn = {2297-1769}, abstract = {INTRODUCTION: Nutritional and environmental stressors can disturb the gut microbiome of horses which may ultimately decrease their health and performance. We hypothesized that supplementation with a yeast-derived postbiotic (Saccharomyces cerevisiae fermentation product-SCFP) would benefit horses undergoing an established model of stress due to prolonged transportation.

METHODS: Quarter horses (n = 20) were blocked based on sex, age (22 ± 3 mo) and body weight (439 ± 3 kg) and randomized to receive either a basal diet of 60% hay and 40% concentrate (CON) or the basal diet supplemented with 21 g/d Diamond V TruEquine C (SCFP; Diamond V, Cedar Rapids, IA) for 60 days. On day 57, horses were tethered with their heads elevated 35cm above wither height for 12 h to induce mild upper respiratory tract inflammation. Fecal samples were collected at days 0, 28, and 56 before induction of stress, and at 0, 12, 24, and 72 h post-stress and subjected to DNA extraction and Nanopore shotgun metagenomics. Within sample (alpha) diversity was evaluated by fitting a linear model and between sample (beta) diversity was tested with permutational ANOVA.

RESULTS: The SCFP stabilized alpha diversity across all time points, whereas CON horses had more fluctuation (P < 0.05) at 12, 24, and 72 h post-challenge compared to d 56. A significant difference between CON and SCFP was observed at 0 and 12 h. There was no difference in beta-diversity between SCFP and CON on d 56.

DISCUSSION: Taken together, these observations led us to conclude that treatment with SCFP resulted in more robust and stable microbial profiles in horses after stress challenge.}, } @article {pmid36908366, year = {2023}, author = {Pradhan, S and Prabhakar, MR and Karthika Parvathy, KR and Dey, B and Jayaraman, S and Behera, B and Paramasivan, B}, title = {Metagenomic and physicochemical analysis of Kombucha beverage produced from tea waste.}, journal = {Journal of food science and technology}, volume = {60}, number = {3}, pages = {1088-1096}, pmid = {36908366}, issn = {0022-1155}, abstract = {UNLABELLED: Kombucha beverage produced through fermentation of sugared tea using bacteria and yeast has gained attention for its beneficial health benefits. However, the cost linked to the raw materials often increases the upstream process expenses, thereby the overall operating expenditures. Thus, there is a need to explore alternative waste and cost-effective raw materials for Kombucha fermentation. The present study, compared the physico-chemical and microbial growth pattern of Kombucha beverage production using tea waste from the tea processing industries with that of the green/black tea, reporting similar trends irrespective of its type. Further, the amplicon sequencing of 16S rRNA showed dominant presence of Komagataeibacter rhaeticus and high throughput sequencing of ITS1 confirmed the presence of yeast species similar to Brettanomyces bruxellensis in the tea waste based Kombucha beverage. Appreciable amount of carbohydrates (8.5/100 g) and energy (34 kcal/100 g) with appropriate organoleptic properties favourable for human consumption were also observed during the nutritional content and qualitative property assessment. The overall study showed a broad taxonomic and functional diversity existing during Kombucha fermentation process with tea waste to maintain a sustained eco-system to facilitate cost-effective beverage production with desired properties for safe consumption.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13197-022-05476-3.}, } @article {pmid36908212, year = {2023}, author = {Wu, Q and Wu, Y and Zhao, Y and Zhang, Y and Cao, J and Wu, D and Zhou, J and Chen, F}, title = {Adenovirus infection diagnosed by metagenomic next-generation sequencing after haploidentical hematopoietic stem cell transplantation: A multicenter study in China.}, journal = {Transplant infectious disease : an official journal of the Transplantation Society}, volume = {25}, number = {2}, pages = {e14054}, doi = {10.1111/tid.14054}, pmid = {36908212}, issn = {1399-3062}, mesh = {Humans ; Immunoglobulins, Intravenous/therapeutic use ; Retrospective Studies ; *Adenoviridae Infections/diagnosis/drug therapy ; Cidofovir ; *Graft vs Host Disease/etiology ; *Hematopoietic Stem Cell Transplantation/adverse effects/methods ; High-Throughput Nucleotide Sequencing ; }, abstract = {OBJECTIVE: This study aims to observe and analyze the clinical characteristics and prognosis of adenovirus (ADV) infection diagnosed by metagenomic next-generation sequencing (mNGS) after haploidentical hematopoietic stem cell transplantation (Haplo-HSCT), which was performed following Beijing Protocol.

METHODS: The clinical data of patients who developed ADV infection diagnosed by mNGS after Haplo-HSCT between January 2019 and March 2021, recorded in three transplantation centers, were retrospectively analyzed. Potential risk factors for infection and the clinical manifestations of ADV involvement in different end-organs were also studied. Additionally, the patient prognosis regarding the available treatment was observed.

RESULTS: A total of seven patients were diagnosed with ADV infection by the mNGS technique after Haplo-HSCT of 976 patients enrolled. The risk factors for infection included antithymocyte globulin steroid-refractory graft-versus-host disease (GVHD) history, CD25 monoclonal antibody or ruxolitinib treatment history and <300 cells/μL of CD3+ T cells count in peripheral blood. The clinical manifestations of ADV infection included encephalitis, hepatitis, cystitis, and pneumonia. Six patients were treated with cidofovir (CDV) and intravenous immunoglobulin (IVIg), and one with CDV, ribavirin, IVIg, thymosin Alpha-1 for injection and low-dose donor lymphocyte infusion. One case showed negative ADV DNA results with improved conditions; however, the patient died of the relapse of the primary disease in the later stage. The remaining six died of ADV infection.

CONCLUSION: mNGS can provide screening for ADV and information on ADV subtypes, helpful to understand tissue tropism. This technique could be useful in diagnosing patients at high risk for ADV infection. ADV infection can involve multiple organs, has difficulty in early diagnosis, and has a poor prognosis. Currently, effective treatments are inadequate.}, } @article {pmid36907988, year = {2023}, author = {Mannion, A and Sheh, A and Shen, Z and Dzink-Fox, J and Piazuelo, MB and Wilson, KT and Peek, R and Fox, JG}, title = {Shotgun Metagenomics of Gastric Biopsies Reveals Compositional and Functional Microbiome Shifts in High- and Low-Gastric-Cancer-Risk Populations from Colombia, South America.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2186677}, pmid = {36907988}, issn = {1949-0984}, support = {P01 CA028842/CA/NCI NIH HHS/United States ; R01 CA077955/CA/NCI NIH HHS/United States ; P30 DK058404/DK/NIDDK NIH HHS/United States ; R35 CA210088/CA/NCI NIH HHS/United States ; P01 CA116087/CA/NCI NIH HHS/United States ; I01 CX002171/CX/CSRD VA/United States ; P30 ES002109/ES/NIEHS NIH HHS/United States ; R01 DK058587/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Stomach Neoplasms/microbiology ; Colombia ; RNA, Ribosomal, 16S/genetics ; *Helicobacter Infections/microbiology ; *Gastritis/pathology ; *Gastrointestinal Microbiome ; *Helicobacter pylori/genetics ; Biopsy ; Risk Factors ; *Microbiota ; South America ; }, abstract = {Along with Helicobacter pylori infection, the gastric microbiota is hypothesized to modulate stomach cancer risk in susceptible individuals. Whole metagenomic shotgun sequencing (WMS) is a sequencing approach to characterize the microbiome with advantages over traditional culture and 16S rRNA sequencing including identification of bacterial and non-bacterial taxa, species/strain resolution, and functional characterization of the microbiota. In this study, we used WMS to survey the microbiome in extracted DNA from antral gastric biopsy samples from Colombian patients residing in the high-risk gastric cancer town Túquerres (n = 10, H. pylori-positive = 7) and low-risk town of Tumaco (n = 10, H. pylori-positive = 6). Kraken2/Bracken was used for taxonomic classification and abundance. Functional gene profiles were inferred by InterProScan and KEGG analysis of assembled contigs and gene annotation. The most abundant taxa represented bacteria, non-human eukaryota, and viral genera found in skin, oral, food, and plant/soil environments including Staphylococus, Streptococcus, Bacillus, Aspergillus, and Siphoviridae. H. pylori was the predominant taxa present in H. pylori-positive samples. Beta diversity was significantly different based on H. pylori-status, risk group, and sex. WMS detected more bacterial taxa than 16S rRNA sequencing and aerobic, anaerobic, and microaerobic culture performed on the same gastric biopsy samples. WMS identified significant differences in functional profiles found between H. pylori-status, but not risk or sex groups. H. pylori-positive samples were significantly enriched for H. pylori-specific genes including virulence factors such as vacA, cagA, and urease, while carbohydrate and amino acid metabolism genes were enriched in H. pylori-negative samples. This study shows WMS has the potential to characterize the taxonomy and function of the gastric microbiome as risk factors for H. pylori-associated gastric disease. Future studies will be needed to compare and validate WMS versus traditional culture and 16S rRNA sequencing approaches for characterization of the gastric microbiome.}, } @article {pmid36906632, year = {2023}, author = {Xiao, Y and Wang, H and Lan, Y and Zhong, C and Yan, G and Xu, Z and Lu, G and Chen, J and Wei, T and Wong, WC and Kwan, YH and Qian, PY}, title = {Changes in community structures and functions of the gut microbiomes of deep-sea cold seep mussels during in situ transplantation experiment.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {17}, pmid = {36906632}, issn = {2524-4671}, abstract = {BACKGROUND: Many deep-sea invertebrates largely depend on chemoautotrophic symbionts for energy and nutrition, and some of them have reduced functional digestive tracts. By contrast, deep-sea mussels have a complete digestive system although symbionts in their gills play vital roles in nutrient supply. This digestive system remains functional and can utilise available resources, but the roles and associations among gut microbiomes in these mussels remain unknown. Specifically, how the gut microbiome reacts to environmental change is unclear.

RESULTS: The meta-pathway analysis showed the nutritional and metabolic roles of the deep-sea mussel gut microbiome. Comparative analyses of the gut microbiomes of original and transplanted mussels subjected to environmental change revealed shifts in bacterial communities. Gammaproteobacteria were enriched, whereas Bacteroidetes were slightly depleted. The functional response for the shifted communities was attributed to the acquisition of carbon sources and adjusting the utilisation of ammonia and sulphide. Self-protection was observed after transplantation.

CONCLUSION: This study provides the first metagenomic insights into the community structure and function of the gut microbiome in deep-sea chemosymbiotic mussels and their critical mechanisms for adapting to changing environments and meeting of essential nutrient demand.}, } @article {pmid36906612, year = {2023}, author = {Neumann, CJ and Mahnert, A and Kumpitsch, C and Kiu, R and Dalby, MJ and Kujawska, M and Madl, T and Kurath-Koller, S and Urlesberger, B and Resch, B and Hall, LJ and Moissl-Eichinger, C}, title = {Clinical NEC prevention practices drive different microbiome profiles and functional responses in the preterm intestine.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1349}, pmid = {36906612}, issn = {2041-1723}, support = {100974/C/13/Z/WT_/Wellcome Trust/United Kingdom ; 220876/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; BBS/E/F/00044409/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; DOC 31/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Infant ; Infant, Newborn ; Humans ; Female ; *Infant, Premature ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Intestines ; Feces/microbiology ; Bifidobacterium longum subspecies infantis/genetics ; *Gastrointestinal Microbiome ; }, abstract = {Preterm infants with very low birthweight are at serious risk for necrotizing enterocolitis. To functionally analyse the principles of three successful preventive NEC regimens, we characterize fecal samples of 55 infants (<1500 g, n = 383, female = 22) longitudinally (two weeks) with respect to gut microbiome profiles (bacteria, archaea, fungi, viruses; targeted 16S rRNA gene sequencing and shotgun metagenomics), microbial function, virulence factors, antibiotic resistances and metabolic profiles, including human milk oligosaccharides (HMOs) and short-chain fatty acids (German Registry of Clinical Trials, No.: DRKS00009290). Regimens including probiotic Bifidobacterium longum subsp. infantis NCDO 2203 supplementation affect microbiome development globally, pointing toward the genomic potential to convert HMOs. Engraftment of NCDO 2203 is associated with a substantial reduction of microbiome-associated antibiotic resistance as compared to regimens using probiotic Lactobacillus rhamnosus LCR 35 or no supplementation. Crucially, the beneficial effects of Bifidobacterium longum subsp. infantis NCDO 2203 supplementation depends on simultaneous feeding with HMOs. We demonstrate that preventive regimens have the highest impact on development and maturation of the gastrointestinal microbiome, enabling the establishment of a resilient microbial ecosystem that reduces pathogenic threats in at-risk preterm infants.}, } @article {pmid36906058, year = {2023}, author = {Zhou, Y and Wang, Y and Yang, L and Kong, Q and Zhang, H}, title = {Microbial degradation mechanisms of surface petroleum contaminated seawater in a typical oil trading port.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {324}, number = {}, pages = {121420}, doi = {10.1016/j.envpol.2023.121420}, pmid = {36906058}, issn = {1873-6424}, mesh = {*Petroleum/metabolism ; Persistent Organic Pollutants ; Hydrocarbons/metabolism ; Seawater/chemistry ; Biodegradation, Environmental ; *Petroleum Pollution ; }, abstract = {Petroleum hydrocarbons are significant new persistent organic pollutants for marine oil spill risk areas. Oil trading ports, in turn, have become major bearers of the risk of offshore oil pollution. However, studies on the molecular mechanisms of microbial degradation of petroleum pollutants by natural seawater are limited. Here, an in situ microcosm study was conducted. Combined with metagenomics, differences in metabolic pathways and in the gene abundances of total petroleum hydrocarbons (TPH) are revealed under different conditions. About 88% degradation of TPH was shown after 3 weeks of treatment. The positive responders to TPH were concentrated in the genera Cycloclasticus, Marivita and Sulfitobacter of the orders Rhodobacterales and Thiotrichales. The genera Marivita, Roseobacter, Lentibacter and Glaciecola were key degradation species when mixing dispersants with oil, and all of the above are from the Proteobacteria phylum. The analysis showed that the biodegradability of aromatic compounds, polycyclic aromatic hydrocarbon and dioxin were enhanced after the oil spill, and genes with higher abundances of bphAa, bsdC, nahB, doxE and mhpD were found, but the photosynthesis-related mechanism was inhibited. The dispersant treatment effectively stimulated the microbial degradation of TPH and then accelerated the succession of microbial communities. Meanwhile, functions such as bacterial chemotaxis and carbon metabolism (cheA, fadeJ and fadE) were better developed, but the degradation of persistent organic pollutants such as polycyclic aromatic hydrocarbons was weakened. Our study provides insights into the metabolic pathways and specific functional genes for oil degradation by marine microorganisms and will help improve the application and practice of bioremediation.}, } @article {pmid36905873, year = {2023}, author = {Vandamme, P and Peeters, C and Hettiarachchi, A and Cnockaert, M and Carlier, A}, title = {Govania unica gen. nov., sp. nov., a rare biosphere bacterium that represents a novel family in the class Alphaproteobacteria.}, journal = {Systematic and applied microbiology}, volume = {46}, number = {3}, pages = {126405}, doi = {10.1016/j.syapm.2023.126405}, pmid = {36905873}, issn = {1618-0984}, mesh = {*Fatty Acids/chemistry ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Phylogeny ; Bacteria/genetics ; *Alphaproteobacteria ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; Bacterial Typing Techniques ; }, abstract = {Strain LMG 31809 [T] was isolated from a top soil sample of a temperate, mixed deciduous forest in Belgium. Comparison of its 16S rRNA gene sequence with that of type strains of bacteria with validly published names positioned it in the class Alphaproteobacteria and highlighted a major evolutionary divergence from its near neighbor species which represented species of the orders Emcibacterales and Sphingomonadales. 16S rRNA amplicon sequencing of the same soil sample revealed a highly diverse community in which Acidobacteria and Alphaproteobacteria predominated, but failed to yield amplicon sequence variants highly similar to that of strain LMG 31809 [T]. There were no metagenome assembled genomes that corresponded to the same species and a comprehensive analysis of public 16S rRNA amplicon sequencing data sets demonstrated that strain LMG 31809 [T] represents a rare biosphere bacterium that occurs at very low abundances in multiple soil and water-related ecosystems. The genome analysis suggested that this strain is a strictly aerobic heterotroph that is asaccharolytic and uses organic acids and possibly aromatic compounds as growth substrates. We propose to classify LMG 31809 [T] as a novel species within a novel genus, Govania unica gen. nov., sp. nov, within the novel family Govaniaceae of the class Alphaproteobacteria. Its type strain is LMG 31809 [T] (=CECT 30155 [T]). The whole-genome sequence of strain LMG 31809 [T] has a size of 3.21 Mbp. The G + C content is 58.99 mol%. The 16S rRNA gene and whole-genome sequences of strain LMG 31809 [T] are publicly available under accession numbers OQ161091 and JANWOI000000000, respectively.}, } @article {pmid36904265, year = {2023}, author = {Wang, Z and Xu, X and Deji, Y and Gao, S and Wu, C and Song, Q and Shi, Z and Xiang, X and Zang, J and Su, J}, title = {Bifidobacterium as a Potential Biomarker of Sarcopenia in Elderly Women.}, journal = {Nutrients}, volume = {15}, number = {5}, pages = {}, pmid = {36904265}, issn = {2072-6643}, support = {20194Y0443//The young fund of Shanghai municipal health commission/ ; DIC2019-03//Dietary Nutrition Research and Education Foundation of Danone Nutrition Center/ ; GWV-10.3-YQ22//Outstanding young Talents in the three-year Plan of Shanghai municipal public health system (2020-2022)/ ; GWV-10.2-XD18//Academic leader in the three-year Plan of Shanghai municipal public health system (2020-2022)/ ; GWV-10.1-XK11//Key disciplines in the three-year Plan of Shanghai municipal public health system(2020-2022)/ ; }, mesh = {Humans ; Female ; Aged ; Bifidobacterium ; *Sarcopenia ; Case-Control Studies ; *Gastrointestinal Microbiome ; *Bifidobacterium longum ; Biomarkers ; }, abstract = {Gut microbial dysbiosis influences the development of sarcopenia. This case-control study explored the gut microbiota composition in elderly Chinese women with sarcopenia. The information from 50 cases and 50 controls was collected. Grip strength, body weight, body mass index, skeletal muscle mass, energy intake, and total and high-quality protein intake were lower in cases than in controls (p < 0.05). Gut microbiota metagenomic sequencing showed that phylum Bacteroides was significantly reduced in the case group, whereas genus Prevotella was more abundant (p < 0.05). Linear discriminant analysis (LDA) effect size showed that 9 and 13 distinct microbial taxa were enriched in the case and control groups, respectively (LDA > 2, p < 0.05), among which Prevotella copri and Bifidobacterium longum were significantly different (LDA > 4, p < 0.05). The AUC of Bifidobacterium longum was 0.674 (95% CI: 0.539-0.756). Elderly women with sarcopenia exhibited significantly different gut microbiota compositions than healthy controls.}, } @article {pmid36902625, year = {2023}, author = {Mei, J and Hu, H and Zhu, S and Ding, H and Huang, Z and Li, W and Yang, B and Zhang, W and Fang, X}, title = {Diagnostic Role of mNGS in Polymicrobial Periprosthetic Joint Infection.}, journal = {Journal of clinical medicine}, volume = {12}, number = {5}, pages = {}, pmid = {36902625}, issn = {2077-0383}, support = {2019Y9136//Joint Funds for the innovation of science and Technology, Fujian province/ ; 2020CXA038//Medical Innovation Project, Fujian Province/ ; 2022J011432.//Natural Science Fundation of Fujian Province/ ; }, abstract = {OBJECTIVES: The purpose of this study was to explore the clinical value of metagenomic next-generation sequencing (mNGS) in the diagnosis of polymicrobial periprosthetic joint infection (PJI).

METHODS: Patients with complete data who underwent surgery at our hospital between July 2017 and January 2021 for suspected periprosthetic joint infection (PJI), according to the 2018 ICE diagnostic criteria, were enrolled, and all patients underwent microbial culture and mNGS detection, which were performed on the BGISEQ-500 platform. Microbial cultures were performed on two samples of synovial fluid, six samples of tissue, and two samples of prosthetic sonicate fluid for each patient. The mNGS was performed on 10 tissues, 64 synovial fluid samples, and 17 prosthetic sonicate fluid samples. The results of mNGS testing were based on the interpretation of mNGS results in the previous literature and the assertions of microbiologists and orthopedic surgeons. The diagnostic efficacy of mNGS in polymicrobial PJI was assessed by comparing the results of conventional microbial cultures and mNGS.

RESULTS: A total of 91 patients were finally enrolled in this study. The sensitivity, specificity, and accuracy of conventional culture for the diagnosis of PJI were 71.0%, 95.4%, and 76.9%, respectively. The sensitivity, specificity, and accuracy of mNGS for the diagnosis of PJI were 91.3%, 86.3%, and 90.1%, respectively. The sensitivity, specificity, and accuracy of conventional culture for the diagnosis of polymicrobial PJI were 57.1%, 100%, and 91.3%, respectively. mNGS had a sensitivity, specificity, and accuracy of 85.7%, 60.0%, and 65.2%, respectively, for the diagnosis of polymicrobial PJI.

CONCLUSIONS: mNGS can improve the diagnosis efficiency of polymicrobial PJI, and the combination of culture and mNGS is a promising method to diagnose polymicrobial PJI.}, } @article {pmid36902401, year = {2023}, author = {Rodríguez-Díaz, C and Martín-Reyes, F and Taminiau, B and Ho-Plágaro, A and Camargo, R and Fernandez-Garcia, F and Pinazo-Bandera, J and Toro-Ortiz, JP and Gonzalo, M and López-Gómez, C and Rodríguez-Pacheco, F and Rodríguez de Los Ríos, D and Daube, G and Alcain-Martinez, G and García-Fuentes, E}, title = {The Metagenomic Composition and Effects of Fecal-Microbe-Derived Extracellular Vesicles on Intestinal Permeability Depend on the Patient's Disease.}, journal = {International journal of molecular sciences}, volume = {24}, number = {5}, pages = {}, pmid = {36902401}, issn = {1422-0067}, support = {PI18/01652//Instituto de Salud Carlos III/ ; PE-0098-2019//Consejería de Salud y Familias/ ; }, mesh = {Humans ; Caco-2 Cells ; *Obesity, Morbid ; *Crohn Disease/microbiology ; *Extracellular Vesicles ; Feces/microbiology ; Diarrhea ; }, abstract = {The composition and impact of fecal-microbe-derived extracellular vesicles (EVs) present in different diseases has not been analyzed. We determined the metagenomic profiling of feces and fecal-microbe-derived EVs from healthy subjects and patients with different diseases (diarrhea, morbid obesity and Crohn's disease (CD)) and the effect of these fecal EVs on the cellular permeability of Caco-2 cells. The control group presented higher proportions of Pseudomonas and Rikenellaceae_RC9_gut_group and lower proportions of Phascolarctobacterium, Veillonella and Veillonellaceae_ge in EVs when compared with the feces from which these EVs were isolated. In contrast, there were significant differences in 20 genera between the feces and EV compositions in the disease groups. Bacteroidales and Pseudomonas were increased, and Faecalibacterium, Ruminococcus, Clostridium and Subdoligranum were decreased in EVs from control patients compared with the other three groups of patients. Tyzzerella, Verrucomicrobiaceae, Candidatus_Paracaedibacter and Akkermansia were increased in EVs from the CD group compared with the morbid obesity and diarrhea groups. Fecal EVs from the morbid obesity, CD and, mainly, diarrhea induced a significant increase in the permeability of Caco-2 cells. In conclusion, the metagenomic composition of fecal-microbe-derived EVs changes depending on the disease of the patients. The modification of the permeability of Caco-2 cells produced by fecal EVs depends on the disease of the patients.}, } @article {pmid36902349, year = {2023}, author = {Melo, NCO and Cuevas-Sierra, A and Fernández-Cruz, E and de la O, V and Martínez, JA}, title = {Fecal Microbiota Composition as a Metagenomic Biomarker of Dietary Intake.}, journal = {International journal of molecular sciences}, volume = {24}, number = {5}, pages = {}, pmid = {36902349}, issn = {1422-0067}, support = {AC21/00038//Instituto de Salud Carlos III/ ; FELLOWSHIP//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; Y2020/BIO-6600.//Comunidad de Madrid/ ; FACINGLCOVID-CM//European Union/ ; }, mesh = {Feces/microbiology ; *Gastrointestinal Tract/microbiology ; *Gastrointestinal Microbiome ; Eating ; Biomarkers ; }, abstract = {Gut microbiota encompasses the set of microorganisms that colonize the gastrointestinal tract with mutual relationships that are key for host homeostasis. Increasing evidence supports cross intercommunication between the intestinal microbiome and the eubiosis-dysbiosis binomial, indicating a networking role of gut bacteria as potential metabolic health surrogate markers. The abundance and diversity of the fecal microbial community are already recognized to be associated with several disorders, such as obesity, cardiometabolic events, gastrointestinal alterations, and mental diseases, which suggests that intestinal microbes may be a valuable tool as causal or as consequence biomarkers. In this context, the fecal microbiota could also be used as an adequate and informative proxy of the nutritional composition of the food intake and about the adherence to dietary patterns, such as the Mediterranean or Western diets, by displaying specific fecal microbiome signatures. The aim of this review was to discuss the potential use of gut microbial composition as a putative biomarker of food intake and to screen the sensitivity value of fecal microbiota in the evaluation of dietary interventions as a reliable and precise alternative to subjective questionnaires.}, } @article {pmid36902288, year = {2023}, author = {Pekkala, S}, title = {Fecal Metagenomics and Metabolomics Identifying Microbial Signatures in Non-Alcoholic Fatty Liver Disease.}, journal = {International journal of molecular sciences}, volume = {24}, number = {5}, pages = {}, pmid = {36902288}, issn = {1422-0067}, support = {Physical activity through life span (PACTS2)//Academy of Finland/ ; 349264//Academy of Finland/ ; }, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/metabolism ; Diet, High-Fat ; Liver/metabolism ; Obesity/metabolism ; Biomarkers/metabolism ; }, abstract = {The frequency of non-alcoholic fatty liver disease (NAFLD) has intensified, creating diagnostic challenges and increasing the need for reliable non-invasive diagnostic tools. Due to the importance of the gut-liver axis in the progression of NAFLD, studies attempt to reveal microbial signatures in NAFLD, evaluate them as diagnostic biomarkers, and to predict disease progression. The gut microbiome affects human physiology by processing the ingested food into bioactive metabolites. These molecules can penetrate the portal vein and the liver to promote or prevent hepatic fat accumulation. Here, the findings of human fecal metagenomic and metabolomic studies relating to NAFLD are reviewed. The studies present mostly distinct, and even contradictory, findings regarding microbial metabolites and functional genes in NAFLD. The most abundantly reproducing microbial biomarkers include increased lipopolysaccharides and peptidoglycan biosynthesis, enhanced degradation of lysine, increased levels of branched chain amino acids, as well as altered lipid and carbohydrate metabolism. Among other causes, the discrepancies between the studies may be related to the obesity status of the patients and the severity of NAFLD. In none of the studies, except for one, was diet considered, although it is an important factor driving gut microbiota metabolism. Future studies should consider diet in these analyses.}, } @article {pmid36901710, year = {2023}, author = {Sobol, MS and Kaster, AK}, title = {Back to Basics: A Simplified Improvement to Multiple Displacement Amplification for Microbial Single-Cell Genomics.}, journal = {International journal of molecular sciences}, volume = {24}, number = {5}, pages = {}, pmid = {36901710}, issn = {1422-0067}, support = {320579085//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Sequence Analysis, DNA/methods ; *Genome, Bacterial ; *Genomics/methods ; Metagenomics ; Nucleic Acid Amplification Techniques/methods ; DNA ; Single-Cell Analysis/methods ; }, abstract = {Microbial single-cell genomics (SCG) provides access to the genomes of rare and uncultured microorganisms and is a complementary method to metagenomics. Due to the femtogram-levels of DNA in a single microbial cell, sequencing the genome requires whole genome amplification (WGA) as a preliminary step. However, the most common WGA method, multiple displacement amplification (MDA), is known to be costly and biased against specific genomic regions, preventing high-throughput applications and resulting in uneven genome coverage. Thus, obtaining high-quality genomes from many taxa, especially minority members of microbial communities, becomes difficult. Here, we present a volume reduction approach that significantly reduces costs while improving genome coverage and uniformity of DNA amplification products in standard 384-well plates. Our results demonstrate that further volume reduction in specialized and complex setups (e.g., microfluidic chips) is likely unnecessary to obtain higher-quality microbial genomes. This volume reduction method makes SCG more feasible for future studies, thus helping to broaden our knowledge on the diversity and function of understudied and uncharacterized microorganisms in the environment.}, } @article {pmid36900663, year = {2023}, author = {de Paz-Silava, SLM and Tabios, IKB and Tantengco, OAG and Climacosa, FMM and Velayo, CL and Lintao, RCV and Cando, LFT and Perias, GAS and Idolor, MIC and Francisco, AG and Catral, CDM and Chiong, CM and Dalmacio, LMM}, title = {Determinants of Acquisition, Persistence, and Clearance of Oncogenic Cervical Human Papillomavirus Infection in the Philippines Using a Multi-Omics Approach: DEFEAT HPV Study Protocol.}, journal = {Healthcare (Basel, Switzerland)}, volume = {11}, number = {5}, pages = {}, pmid = {36900663}, issn = {2227-9032}, support = {None.//Department of Science and Technology - Philippine Council for Health Research and Development./ ; }, abstract = {HPV infection is one of the most studied risk factors in cervical cancer-the second most common cancer site and cause of death due to cancer in the Philippines. However, there is a lack of population-based epidemiological data on cervical HPV infection in the Philippines. Local reports on co-infections with other lower genital tract pathogens, commonly reported globally, are also lacking, which emphasizes the need to increase efforts in targeting HPV prevalence, genotype, and distribution. Hence, we aim to determine the molecular epidemiology and natural history of HPV infection among reproductive-age Filipino women using a community-based prospective cohort design. Women from rural and urban centers will be screened until the target sample size of 110 HPV-positive women (55 from rural sites and 55 from urban sites) is reached. Cervical and vaginal swabs will be collected from all screened participants. For HPV-positive patients, HPV genotypes will be determined. One hundred ten healthy controls will be selected from previously screened volunteers. The cases and controls will comprise the multi-omics subset of participants and will be followed up after 6 and 12 months for repeat HPV screening. Metagenomic and metabolomic analyses of the vaginal swabs will also be performed at baseline, after 6 months, and after 12 months. The results of this study will update the prevalence and genotypic distribution of cervical HPV infection among Filipino women, determine whether the current vaccines used for HPV vaccination programs capture the most prevalent high-risk HPV genotypes in the country, and identify vaginal community state types and bacterial taxa associated with the natural history of cervical HPV infection. The results of this study will be used as the basis for developing a biomarker that can help predict the risk of developing persistent cervical HPV infection in Filipino women.}, } @article {pmid36900515, year = {2023}, author = {Mancino, W and Carnevali, P and Terzi, V and Pérez, PG and Zhang, L and Giuberti, G and Morelli, L and Patrone, V and Lucini, L}, title = {Hierarchical Effects of Lactic Fermentation and Grain Germination on the Microbial and Metabolomic Profile of Rye Doughs.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, pmid = {36900515}, issn = {2304-8158}, abstract = {A multi-omics approach was adopted to investigate the impact of lactic acid fermentation and seed germination on the composition and physicochemical properties of rye doughs. Doughs were prepared with either native or germinated rye flour and fermented with Saccharomyces cerevisiae, combined or not with a sourdough starter including Limosilactobacillus fermentum, Weissella confusa and Weissella cibaria. LAB fermentation significantly increased total titrable acidity and dough rise regardless of the flour used. Targeted metagenomics revealed a strong impact of germination on the bacterial community profile of sprouted rye flour. Doughs made with germinated rye displayed higher levels of Latilactobacillus curvatus, while native rye doughs were associated with higher proportions of Lactoplantibacillus plantarum. The oligosaccharide profile of rye doughs indicated a lower carbohydrate content in native doughs as compared to the sprouted counterparts. Mixed fermentation promoted a consistent decrease in both monosaccharides and low-polymerization degree (PD)-oligosaccharides, but not in high-PD carbohydrates. Untargeted metabolomic analysis showed that native and germinated rye doughs differed in the relative abundance of phenolic compounds, terpenoids, and phospholipids. Sourdough fermentation promoted the accumulation of terpenoids, phenolic compounds and proteinogenic and non-proteinogenic amino acids. Present findings offer an integrated perspective on rye dough as a multi-constituent system and on cereal-sourced bioactive compounds potentially affecting the functional properties of derived food products.}, } @article {pmid36900508, year = {2023}, author = {Coelho, MC and Malcata, FX and Silva, CCG}, title = {Distinct Bacterial Communities in São Jorge Cheese with Protected Designation of Origin (PDO).}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, pmid = {36900508}, issn = {2304-8158}, support = {UID/CVT/0153/2016//Fundação para a Ciência e Tecnologia/ ; LA/P/0045/2020//Fundação para a Ciência e Tecnologia/ ; UIDB/00511/2020//Fundação para a Ciência e Tecnologia/ ; SFRH/BD/110227/2015//Fundação para a Ciência e Tecnologia/ ; }, abstract = {São Jorge cheese is an iconic product of the Azores, produced from raw cow's milk and natural whey starter (NWS). Although it is produced according to Protected Designation of Origin (PDO) specifications, the granting of the PDO label depends crucially on sensory evaluation by trained tasters. The aim of this work was to characterize the bacterial diversity of this cheese using next-generation sequencing (NGS) and to identify the specific microbiota that contributes most to its uniqueness as a PDO by distinguishing the bacterial communities of PDO and non-PDO cheeses. The NWS and curd microbiota was dominated by Streptococcus and Lactococcus, whereas Lactobacillus and Leuconostoc were also present in the core microbiota of the cheese along with these genera. Significant differences (p < 0.05) in bacterial community composition were found between PDO cheese and non-certified cheese; Leuconostoc was found to play the chief role in this regard. Certified cheeses were richer in Leuconostoc, Lactobacillus and Enterococcus, but had fewer Streptococcus (p < 0.05). A negative correlation was found between contaminating bacteria, e.g., Staphylococcus and Acinetobacter, and the development of PDO-associated bacteria such as Leuconostoc, Lactobacillus and Enterococcus. A reduction in contaminating bacteria was found to be crucial for the development of a bacterial community rich in Leuconostoc and Lactobacillus, thus justifying the PDO seal of quality. This study has helped to clearly distinguish between cheeses with and without PDO based on the composition of the bacterial community. The characterization of the NWS and the cheese microbiota can contribute to a better understanding of the microbial dynamics of this traditional PDO cheese and can help producers interested in maintaining the identity and quality of São Jorge PDO cheese.}, } @article {pmid36899176, year = {2023}, author = {von Takach, B and Sargent, H and Penton, CE and Rick, K and Murphy, BP and Neave, G and Davies, HF and Hill, BM and Banks, SC}, title = {Population genomics and conservation management of the threatened black-footed tree-rat (Mesembriomys gouldii) in northern Australia.}, journal = {Heredity}, volume = {130}, number = {5}, pages = {278-288}, pmid = {36899176}, issn = {1365-2540}, mesh = {Animals ; Rats ; Australia ; *Conservation of Natural Resources ; *Metagenomics ; Biodiversity ; Ecosystem ; }, abstract = {Genomic diversity is a fundamental component of Earth's total biodiversity, and requires explicit consideration in efforts to conserve biodiversity. To conserve genomic diversity, it is necessary to measure its spatial distribution, and quantify the contribution that any intraspecific evolutionary lineages make to overall genomic diversity. Here, we describe the range-wide population genomic structure of a threatened Australian rodent, the black-footed tree-rat (Mesembriomys gouldii), aiming to provide insight into the timing and extent of population declines across a large region with a dearth of long-term monitoring data. By estimating recent trajectories in effective population sizes at four localities, we confirm widespread population decline across the species' range, but find that the population in the peri-urban area of the Darwin region has been more stable. Based on current sampling, the Melville Island population made the greatest contribution to overall allelic richness of the species, and the prioritisation analysis suggested that conservation of the Darwin and Cobourg Peninsula populations would be the most cost-effective scenario to retain more than 90% of all alleles. Our results broadly confirm current sub-specific taxonomy, and provide crucial data on the spatial distribution of genomic diversity to help prioritise limited conservation resources. Along with additional sampling and genomic analysis from the far eastern and western edges of the black-footed tree-rat distribution, we suggest a range of conservation and research priorities that could help improve black-footed tree-rat population trajectories at large and fine spatial scales, including the retention and expansion of structurally complex habitat patches.}, } @article {pmid36898564, year = {2023}, author = {Xu, Y and Meng, X and Song, Y and Lv, X and Sun, Y}, title = {Effects of different concentrations of butyrate on microbial community construction and metabolic pathways in anaerobic digestion.}, journal = {Bioresource technology}, volume = {377}, number = {}, pages = {128845}, doi = {10.1016/j.biortech.2023.128845}, pmid = {36898564}, issn = {1873-2976}, mesh = {Anaerobiosis ; Butyric Acid ; Biofuels ; Bioreactors/microbiology ; *Microbiota ; *Euryarchaeota/metabolism ; Metabolic Networks and Pathways ; Methane ; }, abstract = {Investigating the effect of butyric acid concentration on anaerobic digestion systems in complex systems is important for the efficient degradation of butyric acid and improving the efficiency of anaerobic digestion. In this study, different loadings of butyric acid with 2.8, 3.2, and 3.6 g/(L·d) were added to the anaerobic reactor. At a high organic loading rate of 3.6 g/(L·d), methane was efficiently produced with VBP (Volumetric Biogas Production) of 1.50 L/(L·d) and biogas content between 65% and 75%. VFAs concentration remained below 2000 mg/L. Metagenome sequencing revealed changes in the functional flora within different stages. Methanosarcina, Syntrophomonas, and Lentimicrobium were the main and functional microorganisms. That the relative abundance of methanogens exceeded 35% and methanogenic metabolic pathways were increased indicated the methanogenic capacity of the system significantly improved. The presence of a large number of hydrolytic acid-producing bacteria also indicated the importance of the hydrolytic acid-producing stage in the system.}, } @article {pmid36898310, year = {2023}, author = {Hu, X and Gu, H and Sun, X and Wang, Y and Liu, J and Yu, Z and Li, Y and Jin, J and Wang, G}, title = {Distinct influence of conventional and biodegradable microplastics on microbe-driving nitrogen cycling processes in soils and plastispheres as evaluated by metagenomic analysis.}, journal = {Journal of hazardous materials}, volume = {451}, number = {}, pages = {131097}, doi = {10.1016/j.jhazmat.2023.131097}, pmid = {36898310}, issn = {1873-3336}, mesh = {*Microplastics ; *Soil ; Plastics/toxicity ; Metagenomics ; Soil Microbiology ; Nitrogen ; }, abstract = {Plastic mulching is one of the large contributors to microplastic (MP) accumulation in agricultural landscapes. However, the effects of conventional (PE-MPs) and biodegradable MPs (BMPs) on microbial functional and genomic information encoding nitrogen (N) cycling have yet to be addressed. Here, a soil microcosmic experiment was conducted by adding PE-MPs and BMPs to a Mollisol at dosage of 5% (w/w) followed by incubation for 90 days. The soils and MPs were examined by metagenomics and genome binning methods. The results revealed that BMPs harbored rougher surfaces and induced stronger alterations in microbial functional and taxonomic profiles in the soil and plastisphere than PE-MPs. In comparison to their respective soils, the plastispheres of PE-MPs and BMPs stimulated the processes of N fixation, N degradation and assimilatory nitrate reduction (ANRA) and reduced the gene abundances encoding nitrification and denitrification, in which BMPs induced stronger influences than PE-MPs. Ramlibacter mainly drove the differences in N cycling processes between the soils containing two types of MPs and was further enriched in the BMP plastisphere. Three high-quality genomes were identified as Ramlibacter stains with higher abundances in the plastisphere of BMP than that of PE-MP. These Ramlibacter strains had the metabolic capacities of N fixation, N degradation, ANRA and ammonium transport, which were potentially attributed to their biosynthesis and the accumulation of soil NH4[+]-N. Taken together, our results highlight the genetic mechanisms of soil N bioavailability in the presence of biodegradable MPs, which have important implications for maintaining sustainable agriculture and controlling microplastic risk.}, } @article {pmid36897935, year = {2023}, author = {Carr, VR and Pissis, SP and Mullany, P and Shoaie, S and Gomez-Cabrero, D and Moyes, DL}, title = {Palidis: fast discovery of novel insertion sequences.}, journal = {Microbial genomics}, volume = {9}, number = {3}, pages = {}, pmid = {36897935}, issn = {2057-5858}, support = {BB/M009513/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S016899/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *DNA Transposable Elements ; *Bacteria/genetics ; Computational Biology ; Genome, Microbial ; Metagenomics ; }, abstract = {The diversity of microbial insertion sequences, crucial mobile genetic elements in generating diversity in microbial genomes, needs to be better represented in current microbial databases. Identification of these sequences in microbiome communities presents some significant problems that have led to their underrepresentation. Here, we present a bioinformatics pipeline called Palidis that recognizes insertion sequences in metagenomic sequence data rapidly by identifying inverted terminal repeat regions from mixed microbial community genomes. Applying Palidis to 264 human metagenomes identifies 879 unique insertion sequences, with 519 being novel and not previously characterized. Querying this catalogue against a large database of isolate genomes reveals evidence of horizontal gene transfer events across bacterial classes. We will continue to apply this tool more widely, building the Insertion Sequence Catalogue, a valuable resource for researchers wishing to query their microbial genomes for insertion sequences.}, } @article {pmid36897930, year = {2023}, author = {Davison, HR and Hurst, GDD and Siozios, S}, title = {'Candidatus Megaira' are diverse symbionts of algae and ciliates with the potential for defensive symbiosis.}, journal = {Microbial genomics}, volume = {9}, number = {3}, pages = {}, pmid = {36897930}, issn = {2057-5858}, mesh = {*Symbiosis ; *Ciliophora ; Phylogeny ; }, abstract = {Symbiotic microbes from the genus 'Candidatus Megaira' (Rickettsiales) are known to be common associates of algae and ciliates. However, genomic resources for these bacteria are scarce, limiting our understanding of their diversity and biology. We therefore utilize Sequence Read Archive and metagenomic assemblies to explore the diversity of this genus. We successfully extract four draft 'Ca. Megaira' genomes including one complete scaffold for a 'Ca. Megaira' and identify an additional 14 draft genomes from uncategorized environmental metagenome-assembled genomes. We use this information to resolve the phylogeny for the hyper-diverse 'Ca. Megaira', with hosts broadly spanning ciliates, and micro- and macro-algae, and find that the current single genus designation 'Ca. Megaira' significantly underestimates their diversity. We also evaluate the metabolic potential and diversity of ''Ca. Megaira' from this new genomic data and find no clear evidence of nutritional symbiosis. In contrast, we hypothesize a potential for defensive symbiosis in 'Ca. Megaira'. Intriguingly, one symbiont genome revealed a proliferation of ORFs with ankyrin, tetratricopeptide and leucine-rich repeats such as those observed in the genus Wolbachia where they are considered important for host–symbiont protein–protein interactions. Onward research should investigate the phenotypic interactions between 'Ca. Megaira' and their various potential hosts, including the economically important Nemacystus decipiens, and target acquisition of genomic information to reflect the diversity of this massively variable group.}, } @article {pmid36896778, year = {2023}, author = {Obregon Alvarez, D and Fonseca de Souza, L and Mendes, LW and de Moraes, MT and Tosi, M and Venturini, AM and Meyer, KM and Barbosa de Camargo, P and Bohannan, BJM and Mazza Rodrigues, JL and Dunfield, KE and Tsai, SM}, title = {Shifts in functional traits and interactions patterns of soil methane-cycling communities following forest-to-pasture conversion in the Amazon Basin.}, journal = {Molecular ecology}, volume = {32}, number = {12}, pages = {3257-3275}, doi = {10.1111/mec.16912}, pmid = {36896778}, issn = {1365-294X}, mesh = {*Soil/chemistry ; Methane/metabolism ; Forests ; Genes, Bacterial ; *Microbiota/genetics ; Soil Microbiology ; }, abstract = {Deforestation threatens the integrity of the Amazon biome and the ecosystem services it provides, including greenhouse gas mitigation. Forest-to-pasture conversion has been shown to alter the flux of methane gas (CH4) in Amazonian soils, driving a switch from acting as a sink to a source of atmospheric CH4 . This study aimed to better understand this phenomenon by investigating soil microbial metagenomes, focusing on the taxonomic and functional structure of methane-cycling communities. Metagenomic data from forest and pasture soils were combined with measurements of in situ CH4 fluxes and soil edaphic factors and analysed using multivariate statistical approaches. We found a significantly higher abundance and diversity of methanogens in pasture soils. As inferred by co-occurrence networks, these microorganisms seem to be less interconnected within the soil microbiota in pasture soils. Metabolic traits were also different between land uses, with increased hydrogenotrophic and methylotrophic pathways of methanogenesis in pasture soils. Land-use change also induced shifts in taxonomic and functional traits of methanotrophs, with bacteria harbouring genes encoding the soluble form of methane monooxygenase enzyme (sMMO) depleted in pasture soils. Redundancy analysis and multimodel inference revealed that the shift in methane-cycling communities was associated with high pH, organic matter, soil porosity and micronutrients in pasture soils. These results comprehensively characterize the effect of forest-to-pasture conversion on the microbial communities driving the methane-cycling microorganisms in the Amazon rainforest, which will contribute to the efforts to preserve this important biome.}, } @article {pmid36896590, year = {2023}, author = {Reboud, EL and Nabholz, B and Chevalier, E and Tilak, MK and Bito, D and Condamine, FL}, title = {Genomics, Population Divergence, and Historical Demography of the World's Largest and Endangered Butterfly, The Queen Alexandra's Birdwing.}, journal = {Genome biology and evolution}, volume = {15}, number = {4}, pages = {}, pmid = {36896590}, issn = {1759-6653}, mesh = {Animals ; *Butterflies/genetics ; Metagenomics ; Demography ; Genomics ; Genome ; }, abstract = {The world's largest butterfly is the microendemic Papua New Guinean Ornithoptera alexandrae. Despite years of conservation efforts to protect its habitat and breed this up-to-28-cm butterfly, this species still figures as endangered in the IUCN Red List and is only known from two allopatric populations occupying a total of only ∼140 km[2]. Here we aim at assembling reference genomes for this species to investigate its genomic diversity, historical demography and determine whether the population is structured, which could provide guidance for conservation programs attempting to (inter)breed the two populations. Using a combination of long and short DNA reads and RNA sequencing, we assembled six reference genomes of the tribe Troidini, with four annotated genomes of O. alexandrae and two genomes of related species Ornithoptera priamus and Troides oblongomaculatus. We estimated the genomic diversity of the three species, and we proposed scenarios for the historical population demography using two polymorphism-based methods taking into account the characteristics of low-polymorphic invertebrates. Indeed, chromosome-scale assemblies reveal very low levels of nuclear heterozygosity across Troidini, which appears to be exceptionally low for O. alexandrae (lower than 0.01%). Demographic analyses demonstrate low and steadily declining Ne throughout O. alexandrae history, with a divergence into two distinct populations about 10,000 years ago. These results suggest that O. alexandrae distribution has been microendemic for a long time. It should also make local conservation programs aware of the genomic divergence of the two populations, which should not be ignored if any attempt is made to cross the two populations.}, } @article {pmid36894986, year = {2023}, author = {de Nies, L and Galata, V and Martin-Gallausiaux, C and Despotovic, M and Busi, SB and Snoeck, CJ and Delacour, L and Budagavi, DP and Laczny, CC and Habier, J and Lupu, PC and Halder, R and Fritz, JV and Marques, T and Sandt, E and O'Sullivan, MP and Ghosh, S and Satagopam, V and , and Krüger, R and Fagherazzi, G and Ollert, M and Hefeng, FQ and May, P and Wilmes, P}, title = {Altered infective competence of the human gut microbiome in COVID-19.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {46}, pmid = {36894986}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *COVID-19 ; SARS-CoV-2/genetics ; *Microbiota ; Multiomics ; }, abstract = {BACKGROUND: Infections with SARS-CoV-2 have a pronounced impact on the gastrointestinal tract and its resident microbiome. Clear differences between severe cases of infection and healthy individuals have been reported, including the loss of commensal taxa. We aimed to understand if microbiome alterations including functional shifts are unique to severe cases or a common effect of COVID-19. We used high-resolution systematic multi-omic analyses to profile the gut microbiome in asymptomatic-to-moderate COVID-19 individuals compared to a control group.

RESULTS: We found a striking increase in the overall abundance and expression of both virulence factors and antimicrobial resistance genes in COVID-19. Importantly, these genes are encoded and expressed by commensal taxa from families such as Acidaminococcaceae and Erysipelatoclostridiaceae, which we found to be enriched in COVID-19-positive individuals. We also found an enrichment in the expression of a betaherpesvirus and rotavirus C genes in COVID-19-positive individuals compared to healthy controls.

CONCLUSIONS: Our analyses identified an altered and increased infective competence of the gut microbiome in COVID-19 patients. Video Abstract.}, } @article {pmid36894760, year = {2023}, author = {Sajid, M and Srivastava, S and Yadav, RK and Joshi, L and Bharadwaj, M}, title = {Fungal Community Composition and Function Associated with Loose Smokeless Tobacco Products.}, journal = {Current microbiology}, volume = {80}, number = {4}, pages = {131}, pmid = {36894760}, issn = {1432-0991}, support = {ISRM/14(04)/TF/2018//Indian Council of Medical Research/ ; }, mesh = {*Tobacco, Smokeless/analysis/microbiology ; *Mycobiome ; Chromatography, Liquid ; Tandem Mass Spectrometry ; Nicotiana ; *Mycotoxins ; }, abstract = {Smokeless tobacco products (STPs) contain several microbial communities which are responsible for the formation of carcinogens, like tobacco-specific nitrosamine (TSNAs). A majority of STPs are sold in loose/unpackaged form which can be loaded with a diverse microbial population. Here, the fungal population and mycotoxins level of three popular Indian loose STPs, Dohra, Mainpuri Kapoori (MK), and loose leaf-chewing tobacco (LCT) was examined using metagenomic sequencing of ITS1 DNA segment of the fungal genome and LC-MS/MS, respectively. We observed that Ascomycota was the most abundant phylum and Sterigmatomyces and Pichia were the predominant fungal genera in loose STPs. MK displayed the highest α-diversity being enriched with pathogenic fungi Apiotrichum, Aspergillus, Candida, Fusarium, Trichosporon, and Wallemia. Further, FUNGuild analysis revealed an abundance of saprotrophs in MK, while pathogen-saprotroph-symbiotroph were abundant in Dohra and LCT. The level of a fungal toxin (ochratoxins A) was high in the MK product. This study caution that loose STPs harbor various harmful fungi that can infect their users and deliver fungal toxins or disrupt the oral microbiome of SLT users which can contribute to several oral pathologies.}, } @article {pmid36894632, year = {2023}, author = {Molari, M and Hassenrueck, C and Laso-Pérez, R and Wegener, G and Offre, P and Scilipoti, S and Boetius, A}, title = {A hydrogenotrophic Sulfurimonas is globally abundant in deep-sea oxygen-saturated hydrothermal plumes.}, journal = {Nature microbiology}, volume = {8}, number = {4}, pages = {651-665}, pmid = {36894632}, issn = {2058-5276}, mesh = {*Seawater/microbiology ; Bacteria/genetics ; *Microbiota ; Hydrogen/metabolism ; Oxygen/metabolism ; }, abstract = {Members of the bacterial genus Sulfurimonas (phylum Campylobacterota) dominate microbial communities in marine redoxclines and are important for sulfur and nitrogen cycling. Here we used metagenomics and metabolic analyses to characterize a Sulfurimonas from the Gakkel Ridge in the Central Arctic Ocean and Southwest Indian Ridge, showing that this species is ubiquitous in non-buoyant hydrothermal plumes at Mid Ocean Ridges across the global ocean. One Sulfurimonas species, [U]Sulfurimonas pluma, was found to be globally abundant and active in cold (<0-4 °C), oxygen-saturated and hydrogen-rich hydrothermal plumes. Compared with other Sulfurimonas species, [U]S. pluma has a reduced genome (>17%) and genomic signatures of an aerobic chemolithotrophic metabolism using hydrogen as an energy source, including acquisition of A2-type oxidase and loss of nitrate and nitrite reductases. The dominance and unique niche of [U]S. pluma in hydrothermal plumes suggest an unappreciated biogeochemical role for Sulfurimonas in the deep ocean.}, } @article {pmid36894532, year = {2023}, author = {Sukumar, S and Wang, F and Simpson, CA and Willet, CE and Chew, T and Hughes, TE and Bockmann, MR and Sadsad, R and Martin, FE and Lydecker, HW and Browne, GV and Davis, KM and Bui, M and Martinez, E and Adler, CJ}, title = {Development of the oral resistome during the first decade of life.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1291}, pmid = {36894532}, issn = {2041-1723}, support = {R01 DE029838/DE/NIDCR NIH HHS/United States ; R01 DE019665/DE/NIDCR NIH HHS/United States ; }, mesh = {Male ; Female ; Humans ; Child ; Drug Resistance, Bacterial/genetics ; *Dental Caries/genetics ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Microbiota/genetics ; }, abstract = {Antibiotic overuse has promoted the spread of antimicrobial resistance (AMR) with significant health and economic consequences. Genome sequencing reveals the widespread presence of antimicrobial resistance genes (ARGs) in diverse microbial environments. Hence, surveillance of resistance reservoirs, like the rarely explored oral microbiome, is necessary to combat AMR. Here, we characterise the development of the paediatric oral resistome and investigate its role in dental caries in 221 twin children (124 females and 97 males) sampled at three time points over the first decade of life. From 530 oral metagenomes, we identify 309 ARGs, which significantly cluster by age, with host genetic effects detected from infancy onwards. Our results suggest potential mobilisation of ARGs increases with age as the AMR associated mobile genetic element, Tn916 transposase was co-located with more species and ARGs in older children. We find a depletion of ARGs and species in dental caries compared to health. This trend reverses in restored teeth. Here we show the paediatric oral resistome is an inherent and dynamic component of the oral microbiome, with a potential role in transmission of AMR and dysbiosis.}, } @article {pmid36893594, year = {2023}, author = {Saibu, S and Adebusoye, SA and Oyetibo, GO}, title = {Soil microbiome response to 2-chlorodibenzo-p-dioxin during bioremediation of contaminated tropical soil in a microcosm-based study.}, journal = {Journal of hazardous materials}, volume = {451}, number = {}, pages = {131105}, doi = {10.1016/j.jhazmat.2023.131105}, pmid = {36893594}, issn = {1873-3336}, mesh = {*Dioxins ; Biodegradation, Environmental ; Soil ; *Soil Pollutants/metabolism ; Bacteria/metabolism ; *Bacillus/metabolism ; *Microbiota ; Soil Microbiology ; }, abstract = {A pristine soil was artificially contaminated with 2-chlorodibenzo-p-dioxin (2-CDD) and separated into three portions. Microcosms SSOC and SSCC were seeded with Bacillus sp. SS2 and a three-member bacterial consortium respectively; SSC was untreated, while heat-sterilized contaminated soil served as overall control. Significant degradation of 2-CDD occurred in all microcosms except for the control where the concentration remained unchanged. Degradation of 2-CDD was highest in SSCC (94.9%) compared to SSOC (91.66%) and SCC (85.9%). There was also a notable reduction in the microbial composition complexity both in species richness and evenness following dioxin contamination, a trend that nearly lasted the study period; particularly in setups SSC and SSOC. Irrespective of the bioremediation strategies, the soil microflora was practically dominated by the Firmicutes and at the genus level, the phylotype Bacillus was the most dominant. Other dominant taxa though negatively impacted were Proteobacteria, Actinobacteria, Chloroflexi, and Acidobacteria. Overall, this study demonstrated the feasibility of microbial seeding as an effective strategy to cleanup tropical soil contaminated with dioxins and the importance of metagenomics in elucidating the microbial diversities of contaminated soils. Meanwhile, the seeded organisms, owed their success not only to metabolic competence, but survivability, adaptability and ability to compete favourably with autochthonous microflora.}, } @article {pmid36892439, year = {2023}, author = {Jain, C}, title = {Coverage-preserving sparsification of overlap graphs for long-read assembly.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {3}, pages = {}, pmid = {36892439}, issn = {1367-4811}, mesh = {Humans ; *Algorithms ; Sequence Analysis, DNA/methods ; *Software ; Genome, Human ; Metagenome ; High-Throughput Nucleotide Sequencing ; }, abstract = {MOTIVATION: Read-overlap-based graph data structures play a central role in computing de novo genome assembly. Most long-read assemblers use Myers's string graph model to sparsify overlap graphs. Graph sparsification improves assembly contiguity by removing spurious and redundant connections. However, a graph model must be coverage-preserving, i.e. it must ensure that there exist walks in the graph that spell all chromosomes, given sufficient sequencing coverage. This property becomes even more important for diploid genomes, polyploid genomes, and metagenomes where there is a risk of losing haplotype-specific information.

RESULTS: We develop a novel theoretical framework under which the coverage-preserving properties of a graph model can be analyzed. We first prove that de Bruijn graph and overlap graph models are guaranteed to be coverage-preserving. We next show that the standard string graph model lacks this guarantee. The latter result is consistent with prior work suggesting that removal of contained reads, i.e. the reads that are substrings of other reads, can lead to coverage gaps during string graph construction. Our experiments done using simulated long reads from HG002 human diploid genome show that 50 coverage gaps are introduced on average by ignoring contained reads from nanopore datasets. To remedy this, we propose practical heuristics that are well-supported by our theoretical results and are useful to decide which contained reads should be retained to avoid coverage gaps. Our method retains a small fraction of contained reads (1-2%) and closes majority of the coverage gaps.

Source code is available through GitHub (https://github.com/at-cg/ContainX) and Zenodo with doi: 10.5281/zenodo.7687543.}, } @article {pmid36892308, year = {2023}, author = {Pienkowska, K and Pust, MM and Gessner, M and Gaedcke, S and Thavarasa, A and Rosenboom, I and Morán Losada, P and Minso, R and Arnold, C and Hedtfeld, S and Dorda, M and Wiehlmann, L and Mainz, JG and Klockgether, J and Tümmler, B}, title = {The Cystic Fibrosis Upper and Lower Airway Metagenome.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0363322}, pmid = {36892308}, issn = {2165-0497}, abstract = {The microbial metagenome in cystic fibrosis (CF) airways was investigated by whole-genome shotgun sequencing of total DNA isolated from nasal lavage samples, oropharyngeal swabs, and induced sputum samples collected from 65 individuals with CF aged 7 to 50 years. Each patient harbored a personalized microbial metagenome unique in microbial load and composition, the exception being monocultures of the most common CF pathogens Staphylococcus aureus and Pseudomonas aeruginosa from patients with advanced lung disease. The sampling of the upper airways by nasal lavage uncovered the fungus Malassezia restricta and the bacterium Staphylococcus epidermidis as prominent species. Healthy and CF donors harbored qualitatively and quantitatively different spectra of commensal bacteria in their sputa, even in the absence of any typical CF pathogen. If P. aeruginosa, S. aureus, or Stenotrophomonas maltophilia belonged to the trio of the most abundant species in the CF sputum metagenome, common inhabitants of the respiratory tract of healthy subjects, i.e., Eubacterium sulci, Fusobacterium periodonticum, and Neisseria subflava, were present only in low numbers or not detectable. Random forest analysis identified the numerical ecological parameters of the bacterial community, such as Shannon and Simpson diversity, as the key parameters that globally distinguish sputum samples from CF and healthy donors. IMPORTANCE Cystic fibrosis (CF) is the most common life-limiting monogenetic disease in European populations and is caused by mutations in the CFTR gene. Chronic airway infections with opportunistic pathogens are the major morbidity that determines prognosis and quality of life in most people with CF. We examined the composition of the microbial communities of the oral cavity and upper and lower airways in CF patients across all age groups. From early on, the spectrum of commensals is different in health and CF. Later on, when the common CF pathogens take up residence in the lungs, we observed differential modes of depletion of the commensal microbiota in the presence of S. aureus, P. aeruginosa, S. maltophilia, or combinations thereof. It remains to be seen whether the implementation of lifelong CFTR (cystic fibrosis transmembrane conductance regulator) modulation will change the temporal evolution of the CF airway metagenome.}, } @article {pmid36892203, year = {2023}, author = {Taoka, A and Eguchi, Y and Shimoshige, R and Fukumori, Y}, title = {Recent advances in studies on magnetosome-associated proteins composing the bacterial geomagnetic sensor organelle.}, journal = {Microbiology and immunology}, volume = {67}, number = {5}, pages = {228-238}, doi = {10.1111/1348-0421.13062}, pmid = {36892203}, issn = {1348-0421}, support = {KAKENHI 19H02868//Japan Society for the Promotion of Science/ ; KAKENHI 20K15430//Japan Society for the Promotion of Science/ ; KAKENHI 21K19071//Japan Society for the Promotion of Science/ ; KAKENHI 21KK0126//Japan Society for the Promotion of Science/ ; }, mesh = {*Magnetosomes/chemistry/metabolism/ultrastructure ; Bacterial Proteins/metabolism ; Bacteria/genetics ; Ferrosoferric Oxide/analysis/chemistry/metabolism ; Gram-Negative Bacteria ; }, abstract = {Magnetotactic bacteria (MTB) generate a membrane-enclosed subcellular compartment called magnetosome, which contains a biomineralized magnetite or greigite crystal, an inner membrane-derived lipid bilayer membrane, and a set of specifically targeted associated proteins. Magnetosomes are formed by a group of magnetosome-associated proteins encoded in a genomic region called magnetosome island. Magnetosomes are then arranged in a linear chain-like positioning, and the resulting magnetic dipole of the chain functions as a geomagnetic sensor for magneto-aerotaxis motility. Recent metagenomic analyses of environmental specimens shed light on the sizable phylogenetical diversity of uncultured MTB at the phylum level. These findings have led to a better understanding of the diversity and conservation of magnetosome-associated proteins. This review provides an overview of magnetosomes and magnetosome-associated proteins and introduces recent topics about this fascinating magnetic bacterial organelle.}, } @article {pmid36891384, year = {2023}, author = {Wang, B and Wang, X and Wang, Z and Zhu, K and Wu, W}, title = {Comparative metagenomic analysis reveals rhizosphere microbial community composition and functions help protect grapevines against salt stress.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1102547}, pmid = {36891384}, issn = {1664-302X}, abstract = {INTRODUCTION: Soil salinization is a serious abiotic stress for grapevines. The rhizosphere microbiota of plants can help counter the negative effects caused by salt stress, but the distinction between rhizosphere microbes of salt-tolerant and salt-sensitive varieties remains unclear.

METHODS: This study employed metagenomic sequencing to explore the rhizosphere microbial community of grapevine rootstocks 101-14 (salt tolerant) and 5BB (salt sensitive) with or without salt stress.

RESULTS AND DISCUSSION: Compared to the control (treated with ddH2O), salt stress induced greater changes in the rhizosphere microbiota of 101-14 than in that of 5BB. The relative abundances of more plant growth-promoting bacteria, including Planctomycetes, Bacteroidetes, Verrucomicrobia, Cyanobacteria, Gemmatimonadetes, Chloroflexi, and Firmicutes, were increased in 101-14 under salt stress, whereas only the relative abundances of four phyla (Actinobacteria, Gemmatimonadetes, Chloroflexi, and Cyanobacteria) were increased in 5BB under salt stress while those of three phyla (Acidobacteria, Verrucomicrobia, and Firmicutes) were depleted. The differentially enriched functions (KEGG level 2) in 101-14 were mainly associated with pathways related to cell motility; folding, sorting, and degradation functions; glycan biosynthesis and metabolism; xenobiotics biodegradation and metabolism; and metabolism of cofactors and vitamins, whereas only the translation function was differentially enriched in 5BB. Under salt stress, the rhizosphere microbiota functions of 101-14 and 5BB differed greatly, especially pathways related to metabolism. Further analysis revealed that pathways associated with sulfur and glutathione metabolism as well as bacterial chemotaxis were uniquely enriched in 101-14 under salt stress and therefore might play vital roles in the mitigation of salt stress on grapevines. In addition, the abundance of various sulfur cycle-related genes, including genes involved in assimilatory sulfate reduction (cysNC, cysQ, sat, and sir), sulfur reduction (fsr), SOX systems (soxB), sulfur oxidation (sqr), organic sulfur transformation (tpa, mdh, gdh, and betC), increased significantly in 101-14 after treatment with NaCl; these genes might mitigate the harmful effects of salt on grapevine. In short, the study findings indicate that both the composition and functions of the rhizosphere microbial community contribute to the enhanced tolerance of some grapevines to salt stress.}, } @article {pmid36891307, year = {2023}, author = {Yang, Q and Yu, C and Wu, Y and Cao, K and Li, X and Cao, W and Cao, L and Zhang, S and Ba, Y and Zheng, Y and Zhang, H and Wang, W}, title = {Unusual Talaromyces marneffei and Pneumocystis jirovecii coinfection in a child with a STAT1 mutation: A case report and literature review.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1103184}, pmid = {36891307}, issn = {1664-3224}, mesh = {Male ; Humans ; Child ; Infant ; *Pneumocystis carinii/genetics ; *Coinfection ; *Talaromyces/genetics ; Mutation ; STAT1 Transcription Factor/genetics ; }, abstract = {Talaromyces marneffei and Pneumocystis jirovecii are the common opportunistic pathogens in immunodeficient patients. There have been no reports of T. marneffei and P. jirovecii coinfection in immunodeficient children. Signal transducer and activator of transcription 1 (STAT1) is a key transcription factor in immune responses. STAT1 mutations are predominately associated with chronic mucocutaneous candidiasis and invasive mycosis. We report a 1-year-2-month-old boy diagnosed with severe laryngitis and pneumonia caused by T. marneffei and P. jirovecii coinfection, which was confirmed by smear, culture, polymerase chain reaction and metagenome next-generation sequencing of bronchoalveolar lavage fluid. He has a known STAT1 mutation at amino acid 274 in the coiled-coil domain of STAT1 according to whole exome sequencing. Based on the pathogen results, itraconazole and trimethoprim-sulfamethoxazole were administered. This patient's condition improved, and he was discharged after two weeks of targeted therapy. In the one-year follow-up, the boy remained symptom-free without recurrence.}, } @article {pmid36891192, year = {2023}, author = {Jeong, J and Ahn, K and Mun, S and Yun, K and Kim, YT and Jung, W and Lee, KE and Kim, MY and Ahn, Y and Han, K}, title = {Understanding the bacterial compositional network associations between oral and gut microbiome within healthy Koreans.}, journal = {Journal of oral microbiology}, volume = {15}, number = {1}, pages = {2186591}, pmid = {36891192}, issn = {2000-2297}, abstract = {Oral microbial ecosystem could influence intestinal diseases, but there have been insufficient studies demonstrating the association of microbial composition between the oral cavity and the intestinal system. Thus, we aimed to investigate the compositional network within the oral microbiome related to gut enterotype from saliva and stool samples collected from 112 healthy Korean subjects. Here, we performed bacterial 16S amplicon sequencing from clinical samples. Then, we determined oral microbiome type related to individual's gut enterotype for healthy Korean. The co-occurrence analysis was performed to interactivity prediction of microbiome within saliva samples. As a result, it could be classified into two Korean oral microbiome types (KO) and four oral-gut-associated microbiome types (KOGA) according to distribution and significant differences of oral microflora. The co-occurrence analysis showed various bacterial compositional networks linked around Streptococcus and Haemophilus within healthy subjects. The present study was first approach in healthy Koreans to identify the oral microbiome types related to the gut microbiome and investigate their characteristics. Hence, we suggest that our results could be potential healthy control data for identifying differences in microbial composition between healthy people and oral disease patients and studying microbial association with the gut microbial environment (oral-gut microbiome axis).}, } @article {pmid36891155, year = {2023}, author = {Liu, G and Wang, L and Li, X and Zhang, Y and Long, H and Wang, Y and Gao, H and Xia, H and Qian, S}, title = {The value of next-generation metagenomic sequencing in pathogen detection of pleural effusions and ascites from children with sepsis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1130483}, pmid = {36891155}, issn = {2235-2988}, mesh = {Child ; Humans ; Ascites/diagnosis ; *Pleural Effusion ; Exudates and Transudates ; *Sepsis/diagnosis ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {OBJECTIVE: To investigate the diagnostic value of metagenomic next-generation sequencing (mNGS) using pleural effusion and ascites from children with sepsis.

METHODS: In this study, children with sepsis or severe sepsis and appeared pleural or peritoneal effusions were enrolled, of whom the pleural effusions or ascites and blood samples were conducted pathogen detection using both conventional and mNGS methods. The samples were divided into pathogen-consistent and pathogen-inconsistent groups based on the consistency of mNGS results from different sample types, and into exudate and transudate groups based on their pleural effusion and ascites properties. The pathogen positive rates, pathogen spectrum, consistency between different sample types, and clinical diagnosis consistency were compared between mNGS and conventional pathogen tests.

RESULTS: A total of 42 pleural effusions or ascites and 50 other type samples were collected from 32 children. The pathogen positive rate of the mNGS test was significantly higher than that of traditional methods (78.57% vs. 14.29%, P < 0.001) in pleural effusion and ascites samples, with a consistent rate of 66.67% between the two methods. Nearly 78.79% (26/33) of mNGS positive results of the pleural effusions and ascites samples were consistent with clinical evaluation, and 81.82% (27/33) of these positive samples reported 1-3 pathogens. The pathogen-consistent group outperformed the pathogen-inconsistent group in terms of consistency with respect to clinical evaluation (88.46% vs. 57.14%, P = 0.093), while there was no significant difference between the exudate and transudate groups (66.67% vs. 50.00%, P = 0.483).

CONCLUSION: Compared to conventional methods, mNGS has great advantages in pathogen detection of pleural effusion and ascites samples. Moreover, consistent results of mNGS tests with different sample types provide more reference values in clinical diagnosis.}, } @article {pmid36890606, year = {2023}, author = {Li, X and Zhao, R and Li, D and Wang, G and Bei, S and Ju, X and An, R and Li, L and Kuyper, TW and Christie, P and Bender, FS and Veen, C and van der Heijden, MGA and van der Putten, WH and Zhang, F and Butterbach-Bahl, K and Zhang, J}, title = {Mycorrhiza-mediated recruitment of complete denitrifying Pseudomonas reduces N2O emissions from soil.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {45}, pmid = {36890606}, issn = {2049-2618}, mesh = {*Soil/chemistry ; *Mycorrhizae ; Denitrification ; Nitrous Oxide/analysis/metabolism ; Soil Microbiology ; Bacteria/genetics ; }, abstract = {BACKGROUND: Arbuscular mycorrhizal fungi (AMF) are key soil organisms and their extensive hyphae create a unique hyphosphere associated with microbes actively involved in N cycling. However, the underlying mechanisms how AMF and hyphae-associated microbes may cooperate to influence N2O emissions from "hot spot" residue patches remain unclear. Here we explored the key microbes in the hyphosphere involved in N2O production and consumption using amplicon and shotgun metagenomic sequencing. Chemotaxis, growth and N2O emissions of isolated N2O-reducing bacteria in response to hyphal exudates were tested using in vitro cultures and inoculation experiments.

RESULTS: AMF hyphae reduced denitrification-derived N2O emission (max. 63%) in C- and N-rich residue patches. AMF consistently enhanced the abundance and expression of clade I nosZ gene, and inconsistently increased that of nirS and nirK genes. The reduction of N2O emissions in the hyphosphere was linked to N2O-reducing Pseudomonas specifically enriched by AMF, concurring with the increase in the relative abundance of the key genes involved in bacterial citrate cycle. Phenotypic characterization of the isolated complete denitrifying P. fluorescens strain JL1 (possessing clade I nosZ) indicated that the decline of net N2O emission was a result of upregulated nosZ expression in P. fluorescens following hyphal exudation (e.g. carboxylates). These findings were further validated by re-inoculating sterilized residue patches with P. fluorescens and by an 11-year-long field experiment showing significant positive correlation between hyphal length density with the abundance of clade I nosZ gene.

CONCLUSIONS: The cooperation between AMF and the N2O-reducing Pseudomonas residing on hyphae significantly reduce N2O emissions in the microsites. Carboxylates exuded by hyphae act as attractants in recruiting P. fluorescens and also as stimulants triggering nosZ gene expression. Our discovery indicates that reinforcing synergies between AMF and hyphosphere microbiome may provide unexplored opportunities to stimulate N2O consumption in nutrient-enriched microsites, and consequently reduce N2O emissions from soils. This knowledge opens novel avenues to exploit cross-kingdom microbial interactions for sustainable agriculture and for climate change mitigation. Video Abstract.}, } @article {pmid36890583, year = {2023}, author = {Burks, DJ and Pusadkar, V and Azad, RK}, title = {POSMM: an efficient alignment-free metagenomic profiler that complements alignment-based profiling.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {16}, pmid = {36890583}, issn = {2524-6372}, abstract = {We present here POSMM (pronounced 'Possum'), Python-Optimized Standard Markov Model classifier, which is a new incarnation of the Markov model approach to metagenomic sequence analysis. Built on the top of a rapid Markov model based classification algorithm SMM, POSMM reintroduces high sensitivity associated with alignment-free taxonomic classifiers to probe whole genome or metagenome datasets of increasingly prohibitive sizes. Logistic regression models generated and optimized using the Python sklearn library, transform Markov model probabilities to scores suitable for thresholding. Featuring a dynamic database-free approach, models are generated directly from genome fasta files per run, making POSMM a valuable accompaniment to many other programs. By combining POSMM with ultrafast classifiers such as Kraken2, their complementary strengths can be leveraged to produce higher overall accuracy in metagenomic sequence classification than by either as a standalone classifier. POSMM is a user-friendly and highly adaptable tool designed for broad use by the metagenome scientific community.}, } @article {pmid36890581, year = {2023}, author = {Shi, J and Lei, Y and Wu, J and Li, Z and Zhang, X and Jia, L and Wang, Y and Ma, Y and Zhang, K and Cheng, Q and Zhang, Z and Ma, Y and Lei, Z}, title = {Antimicrobial peptides act on the rumen microbiome and metabolome affecting the performance of castrated bulls.}, journal = {Journal of animal science and biotechnology}, volume = {14}, number = {1}, pages = {31}, pmid = {36890581}, issn = {1674-9782}, support = {GSSYLXM-02//Research and application of corn straw forage and beef cattle high-efficiency and quality production technology/ ; GSA-XMLZ-2021-01//Gansu beef cattle quality fattening project/ ; 2020C-08//Application of Pingliang Red Bull Planting and Breeding Combined with High-efficiency Circular Production System Construction Technology Application/ ; GSSLCSX-2020-1//Local funding/ ; }, abstract = {BACKGROUND: Many countries have already banned the use of antibiotics in animal husbandry, making it extremely difficult to maintain animal health in livestock breeding. In the livestock industry, there is an urgent need to develop alternatives to antibiotics which will not lead to drug resistance on prolonged use. In this study, eighteen castrated bulls were randomly divided into two groups. The control group (CK) was fed the basal diet, while the antimicrobial peptide group (AP) was fed the basal diet supplemented with 8 g of antimicrobial peptides in the basal diet for the experimental period of 270 d. They were then slaughtered to measure production performance, and the ruminal contents were isolated for metagenomic and metabolome sequencing analysis.

RESULT: The results showed that antimicrobial peptides could improve the daily weight, carcass weight, and net meat weight of the experimental animals. Additionally, the rumen papillae diameter and the micropapillary density in the AP were significantly greater than those in the CK. Furthermore, the determination of digestive enzymes and fermentation parameters showed that the contents of protease, xylanase, and β-glucoside in the AP were greater than those in the CK. However, lipase content in the CK was greater than that in the AP. Moreover, the content of acetate, propionate, butyrate, and valerate was found to be greater in AP than those in CK. The metagenomic analysis annotated 1993 differential microorganisms at the species level. The KEGG enrichment of these microorganisms revealed that the enrichment of drug resistance-related pathways was dramatically decreased in the AP, whereas the enrichment of immune-related pathways was significantly increased. There was also a significant reduction in the types of viruses in the AP. 187 probiotics with significant differences were found, 135 of which were higher in AP than in CK. It was also found that the antimicrobial mechanism of the antimicrobial peptides was quite specific. Seven low-abundance microorganisms (Acinetobacter_sp._Ac_1271, Aequorivita soesokkakensis, Bacillus lacisalsi, Haloferax larsenii, Lysinibacillus_sp._3DF0063, Parabacteroides_sp._2_1_7, Streptomyces_sp._So13.3) were found to regulate growth performance of the bull negatively. Metabolome analysis identified 45 differentially differential metabolites that significantly different between the CK and the AP groups. Seven upregulated metabolites (4-pyridoxic acid, Ala-Phe, 3-ureidopropionate, hippuric acid, terephthalic acid, L-alanine, uridine 5-monophosphate) improve the growth performance of the experimental animals. To detect the interactions between the rumen microbiome and metabolism, we associated the rumen microbiome with the metabolome and found that negative regulation between the above 7 microorganisms and 7 metabolites.

CONCLUSIONS: This study shows that antimicrobial peptides can improve the growth performance of animals while resisting viruses and harmful bacteria and are expected to become healthy alternatives to antibiotics. We demonstrated a new antimicrobial peptides pharmacological model. We demonstrated low-abundance microorganisms may play a role by regulating the content of metabolites.}, } @article {pmid36890518, year = {2023}, author = {McDew-White, M and Lee, E and Premadasa, LS and Alvarez, X and Okeoma, CM and Mohan, M}, title = {Cannabinoids modulate the microbiota-gut-brain axis in HIV/SIV infection by reducing neuroinflammation and dysbiosis while concurrently elevating endocannabinoid and indole-3-propionate levels.}, journal = {Journal of neuroinflammation}, volume = {20}, number = {1}, pages = {62}, pmid = {36890518}, issn = {1742-2094}, support = {R01 DA052845/DA/NIDA NIH HHS/United States ; R01 DA042524/DA/NIDA NIH HHS/United States ; R01 DA050169/DA/NIDA NIH HHS/United States ; P51 OD011133/OD/NIH HHS/United States ; P51 RR000164/RR/NCRR NIH HHS/United States ; R01DA050169/NH/NIH HHS/United States ; }, mesh = {Animals ; *Cannabinoids/pharmacology/therapeutic use ; *Simian Acquired Immunodeficiency Syndrome/complications/drug therapy ; Endocannabinoids ; *Simian Immunodeficiency Virus ; Propionates/therapeutic use ; Dronabinol/therapeutic use ; Neuroinflammatory Diseases ; Brain-Gut Axis ; Macaca mulatta ; Dysbiosis ; *HIV Infections/complications ; }, abstract = {BACKGROUND: Although the advent of combination anti-retroviral therapy (cART) has transformed HIV into a manageable chronic disease, an estimated 30-50% of people living with HIV (PLWH) exhibit cognitive and motor deficits collectively known as HIV-associated neurocognitive disorders (HAND). A key driver of HAND neuropathology is chronic neuroinflammation, where proinflammatory mediators produced by activated microglia and macrophages are thought to inflict neuronal injury and loss. Moreover, the dysregulation of the microbiota-gut-brain axis (MGBA) in PLWH, consequent to gastrointestinal dysfunction and dysbiosis, can lead to neuroinflammation and persistent cognitive impairment, which underscores the need for new interventions.

METHODS: We performed RNA-seq and microRNA profiling in basal ganglia (BG), metabolomics (plasma) and shotgun metagenomic sequencing (colon contents) in uninfected and SIV-infected rhesus macaques (RMs) administered vehicle (VEH/SIV) or delta-9-tetrahydrocannabinol (THC) (THC/SIV).

RESULTS: Long-term, low-dose THC reduced neuroinflammation and dysbiosis and significantly increased plasma endocannabinoid, endocannabinoid-like, glycerophospholipid and indole-3-propionate levels in chronically SIV-infected RMs. Chronic THC potently blocked the upregulation of genes associated with type-I interferon responses (NLRC5, CCL2, CXCL10, IRF1, IRF7, STAT2, BST2), excitotoxicity (SLC7A11), and enhanced protein expression of WFS1 (endoplasmic reticulum stress) and CRYM (oxidative stress) in BG. Additionally, THC successfully countered miR-142-3p-mediated suppression of WFS1 protein expression via a cannabinoid receptor-1-mediated mechanism in HCN2 neuronal cells. Most importantly, THC significantly increased the relative abundance of Firmicutes and Clostridia including indole-3-propionate (C. botulinum, C. paraputrificum, and C. cadaveris) and butyrate (C. butyricum, Faecalibacterium prausnitzii and Butyricicoccus pullicaecorum) producers in colonic contents.

CONCLUSION: This study demonstrates the potential of long-term, low-dose THC to positively modulate the MGBA by reducing neuroinflammation, enhancing endocannabinoid levels and promoting the growth of gut bacterial species that produce neuroprotective metabolites, like indole-3-propionate. The findings from this study may benefit not only PLWH on cART, but also those with no access to cART and more importantly, those who fail to suppress the virus under cART.}, } @article {pmid36890285, year = {2023}, author = {de Sousa, LP and Filho, OG and Mondego, JMC}, title = {Age-Related Rhizosphere Analysis of Coffea arabica Plants.}, journal = {Current microbiology}, volume = {80}, number = {4}, pages = {130}, pmid = {36890285}, issn = {1432-0991}, mesh = {*Coffea ; Rhizosphere ; }, abstract = {The analysis of large-scale sequence data has revealed that plants over time recruit certain microbes that are efficient colonizers of the rhizosphere. This enrichment phenomenon is especially seen in annual crops, but we suggest that there could have been some type of enrichment in perennial crops such as coffee plants. To verify this hypothesis, we performed a metagenomic and chemical analysis in rhizosphere with three different plant ages (young, mature, and old) and cultivated on the same farm. We verified that from mature to old plants, there was a decrease in diversity, particularly Fusarium and Plenodomus, while there was an increase in Aspergillus, Cladosporium, Metarhizium, and Pseudomonas. We also detected that the abundance of anti-microbials and ACC-deaminase grows as plants age, although denitrification and carbon fixation had reduced abundances. In summary, we detected an enrichment in the microbial community, especially in the great increase in the participation of Pseudomonas, passing from 50% of the relative abundance as the plants get older. Such enrichment can occur through the dynamics of nutrients such as magnesium and boron.}, } @article {pmid36890125, year = {2023}, author = {Su, CC and Fung, JA and Chang, RJ and Chang, CJ and Jan, FJ and Shih, HT and Chen, J}, title = {TaqMan Quantitative PCR Detection of Xylella taiwanensis in Taiwan.}, journal = {Plant disease}, volume = {107}, number = {10}, pages = {3051-3056}, doi = {10.1094/PDIS-01-23-0064-RE}, pmid = {36890125}, issn = {0191-2917}, mesh = {Taiwan ; RNA, Ribosomal, 16S/genetics ; *RNA, Ribosomal, 23S ; Polymerase Chain Reaction/methods ; }, abstract = {Xylella taiwanensis (Xt) is a nutritionally fastidious bacterial pathogen causing pear leaf scorch disease (PLSD) in Taiwan. The disease causes early defoliation, loss of tree vigor, and reduction in fruit yield and quality. No cure for PLSD is available. The only option for growers to control the disease is to use pathogen-free propagation material, which requires early and accurate detection of Xt. Currently, only one simplex PCR method is available for the diagnosis of PLSD. We developed five Xt-specific TaqMan quantitative PCR (TaqMan qPCR) systems (primers-probe sets) for the detection of Xt. The PCR systems target three conserved genomic loci commonly used in bacterial pathogen detection: the 16S rRNA gene (rrs), the 16S-23S rRNA intergenic transcribed sequence (16S-23S rRNA ITS), and the DNA gyrase gene (gyrB). BLAST analysis using the GenBank nr sequence database, including whole genome sequences of 88 Xanthomonas campestris pv. campestris (Xcc) strains, 147 X. fastidiosa (Xf) strains, and 32 Xt strains, showed that all primer and probe sequences were specific only to Xt. Single nucleotide polymorphisms (SNPs) provided the primer/probe specificity to Xt. The PCR systems were evaluated by using DNA samples from pure cultures of two Xt strains, one Xf strain, one Xcc strain, and 140 plant samples collected from 23 pear orchards in four counties in Taiwan. The two-copy rrs and 16S-23S rRNA ITS-based PCR systems (Xt803-F/R, Xt731-F/R, and Xt16S-F/R) showed higher detection sensitivity than the two single-copy gyrB-based systems (XtgB1-F/R and XtgB2-F/R). A metagenomic analysis of a representative PLSD leaf sample detected the presence of non-Xt proteobacteria and fungal pathogens that should be taken into consideration in PLSD, as they might interfere with diagnosis.}, } @article {pmid36889461, year = {2024}, author = {Chen, H and Zheng, Y and Zhang, X and Liu, S and Yin, Y and Guo, Y and Wang, X and Zhang, Y and Zhao, C and Gai, W and Wang, H}, title = {Clinical evaluation of cell-free and cellular metagenomic next-generation sequencing of infected body fluids.}, journal = {Journal of advanced research}, volume = {55}, number = {}, pages = {119-129}, pmid = {36889461}, issn = {2090-1224}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; *Body Fluids ; High-Throughput Nucleotide Sequencing ; *Cell-Free Nucleic Acids/genetics ; DNA ; }, abstract = {INTRODUCTION: Previous studies have evaluated metagenomic next-generation sequencing (mNGS) of cell-free DNA (cfDNA) for pathogen detection in blood and body fluid samples. However, no study has assessed the diagnostic efficacy of mNGS using cellular DNA.

OBJECTIVES: This is the first study to systematically evaluate the efficacy of cfDNA and cellular DNA mNGS for pathogen detection.

METHODS: A panel of seven microorganisms was used to compare cfDNA and cellular DNA mNGS assays concerning limits of detection (LoD), linearity, robustness to interference, and precision. In total, 248 specimens were collected between December 2020 and December 2021. The medical records of all the patients were reviewed. These specimens were analysed using cfDNA and cellular DNA mNGS assays, and the mNGS results were confirmed using viral qPCR, 16S rRNA, and internal transcribed spacer (ITS) amplicon next-generation sequencing.

RESULTS: The LoD of cfDNA and cellular DNA mNGS was 9.3 to 149 genome equivalents (GE)/mL and 27 to 466 colony-forming units (CFU)/mL, respectively. The intra- and inter-assay reproducibility of cfDNA and cellular DNA mNGS was 100%. Clinical evaluation revealed that cfDNA mNGS was good at detecting the virus in blood samples (receiver operating characteristic (ROC) area under the curve (AUC), 0.9814). In contrast, the performance of cellular DNA mNGS was better than that of cfDNA mNGS in high host background samples. Overall, the diagnostic efficacy of cfDNA combined with cellular DNA mNGS (ROC AUC, 0.8583) was higher than that of cfDNA (ROC AUC, 0.8041) or cellular DNA alone (ROC AUC, 0.7545).

CONCLUSION: Overall, cfDNA mNGS is good for detecting viruses, and cellular DNA mNGS is suitable for high host background samples. The diagnostic efficacy was higher when cfDNA and cellular DNA mNGS were combined.}, } @article {pmid36889095, year = {2023}, author = {Li, B and Tao, Y and Mao, Z and Gu, Q and Han, Y and Hu, B and Wang, H and Lai, A and Xing, P and Wu, QL}, title = {Iron oxides act as an alternative electron acceptor for aerobic methanotrophs in anoxic lake sediments.}, journal = {Water research}, volume = {234}, number = {}, pages = {119833}, doi = {10.1016/j.watres.2023.119833}, pmid = {36889095}, issn = {1879-2448}, mesh = {Humans ; *Lakes/chemistry ; *Electrons ; Oxidation-Reduction ; Oxidants ; Iron ; Hypoxia ; Oxides ; Methane ; Geologic Sediments/chemistry ; }, abstract = {Conventional aerobic CH4-oxidizing bacteria (MOB) are frequently detected in anoxic environments, but their survival strategy and ecological contribution are still enigmatic. Here we explore the role of MOB in enrichment cultures under O2 gradients and an iron-rich lake sediment in situ by combining microbiological and geochemical techniques. We found that enriched MOB consortium used ferric oxides as alternative electron acceptors for oxidizing CH4 with the help of riboflavin when O2 was unavailable. Within the MOB consortium, MOB transformed CH4 to low molecular weight organic matter such as acetate for consortium bacteria as a carbon source, while the latter secrete riboflavin to facilitate extracellular electron transfer (EET). Iron reduction coupled to CH4 oxidation mediated by the MOB consortium was also demonstrated in situ, reducing 40.3% of the CH4 emission in the studied lake sediment. Our study indicates how MOBs survive under anoxia and expands the knowledge of this previously overlooked CH4 sink in iron-rich sediments.}, } @article {pmid36888627, year = {2023}, author = {Leonard, MM and Kenyon, V and Valitutti, F and Pennacchio-Harrington, R and Piemontese, P and Francavilla, R and Norsa, L and Passaro, T and Crocco, M and Baldassarre, M and Trovato, CM and Fasano, A and , }, title = {Cohort profile: Celiac disease genomic, environmental, microbiome and metabolome study; a prospective longitudinal birth cohort study of children at-risk for celiac disease.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0282739}, pmid = {36888627}, issn = {1932-6203}, support = {K23 DK122127/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Child ; Child, Preschool ; *Celiac Disease ; Prospective Studies ; Cohort Studies ; Birth Cohort ; Metabolome ; Genomics ; *Microbiota/genetics ; }, abstract = {The Celiac Disease Genomic, Environmental, Microbiome and Metabolomic (CDGEMM) study is an international prospective birth cohort in children at-risk of developing celiac disease (CD). The CDGEMM study has been designed to take a multi-omic approach to predicting CD onset in at-risk individuals. Participants are required to have a first-degree family member with biopsy diagnosed CD and must be enrolled prior to the introduction of solid food. Participation involves providing blood and stool samples longitudinally over a period of five years as well as answering questionnaires related to the participant, their family, and environment. Recruitment and data collection have been ongoing since 2014. As of 2022 we have a total of 554 participants and the average age of the cohort is 56.4 months. A total of 54 participants have developed positive antibodies for CD and 31 have confirmed CD. Approximately 80% of the 54 participants with CD have developed it by 3 years of age. To date we have identified several microbial strains, pathways, and metabolites occurring in increased abundance and detected before CD onset, which have previously been linked to autoimmune and inflammatory conditions while others occurred in decreased abundance before CD onset and are known to have anti-inflammatory effects. Our ongoing analysis includes expanding our metagenomic and metabolomic analyses, evaluating environmental risk factors linked to CD onset, and mechanistic studies investigating how alterations in the microbiome and metabolites may protect against or contribute to CD development.}, } @article {pmid36882798, year = {2023}, author = {Inda-Díaz, JS and Lund, D and Parras-Moltó, M and Johnning, A and Bengtsson-Palme, J and Kristiansson, E}, title = {Latent antibiotic resistance genes are abundant, diverse, and mobile in human, animal, and environmental microbiomes.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {44}, pmid = {36882798}, issn = {2049-2618}, mesh = {Animals ; Humans ; Drug Resistance, Microbial/genetics ; *Microbiota/genetics ; Metagenome ; Anti-Bacterial Agents/pharmacology ; Databases, Factual ; }, abstract = {BACKGROUND: Bacterial communities in humans, animals, and the external environment maintain a large collection of antibiotic resistance genes (ARGs). However, few of these ARGs are well-characterized and thus established in existing resistance gene databases. In contrast, the remaining latent ARGs are typically unknown and overlooked in most sequencing-based studies. Our view of the resistome and its diversity is therefore incomplete, which hampers our ability to assess risk for promotion and spread of yet undiscovered resistance determinants.

RESULTS: A reference database consisting of both established and latent ARGs (ARGs not present in current resistance gene repositories) was created. By analyzing more than 10,000 metagenomic samples, we showed that latent ARGs were more abundant and diverse than established ARGs in all studied environments, including the human- and animal-associated microbiomes. The pan-resistomes, i.e., all ARGs present in an environment, were heavily dominated by latent ARGs. In comparison, the core-resistome, i.e., ARGs that were commonly encountered, comprised both latent and established ARGs. We identified several latent ARGs shared between environments and/or present in human pathogens. Context analysis of these genes showed that they were located on mobile genetic elements, including conjugative elements. We, furthermore, identified that wastewater microbiomes had a surprisingly large pan- and core-resistome, which makes it a potentially high-risk environment for the mobilization and promotion of latent ARGs.

CONCLUSIONS: Our results show that latent ARGs are ubiquitously present in all environments and constitute a diverse reservoir from which new resistance determinants can be recruited to pathogens. Several latent ARGs already had high mobile potential and were present in human pathogens, suggesting that they may constitute emerging threats to human health. We conclude that the full resistome-including both latent and established ARGs-needs to be considered to properly assess the risks associated with antibiotic selection pressures. Video Abstract.}, } @article {pmid36882742, year = {2023}, author = {Ji, Z and Ma, L}, title = {Controlling taxa abundance improves metatranscriptomics differential analysis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {60}, pmid = {36882742}, issn = {1471-2180}, support = {R01 GM135440/GM/NIGMS NIH HHS/United States ; R01-GM135440/GM/NIGMS NIH HHS/United States ; }, mesh = {Computer Simulation ; *Metagenomics ; *RNA ; }, abstract = {BACKGROUND: A common task in analyzing metatranscriptomics data is to identify microbial metabolic pathways with differential RNA abundances across multiple sample groups. With information from paired metagenomics data, some differential methods control for either DNA or taxa abundances to address their strong correlation with RNA abundance. However, it remains unknown if both factors need to be controlled for simultaneously.

RESULTS: We discovered that when either DNA or taxa abundance is controlled for, RNA abundance still has a strong partial correlation with the other factor. In both simulation studies and a real data analysis, we demonstrated that controlling for both DNA and taxa abundances leads to superior performance compared to only controlling for one factor.

CONCLUSIONS: To fully address the confounding effects in analyzing metatranscriptomics data, both DNA and taxa abundances need to be controlled for in the differential analysis.}, } @article {pmid36882494, year = {2023}, author = {Dittmer, J and Bredon, M and Moumen, B and Raimond, M and Grève, P and Bouchon, D}, title = {The terrestrial isopod symbiont 'Candidatus Hepatincola porcellionum' is a potential nutrient scavenger related to Holosporales symbionts of protists.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {18}, pmid = {36882494}, issn = {2730-6151}, support = {792813//European Commission (EC)/ ; }, abstract = {The order Holosporales (Alphaproteobacteria) encompasses obligate intracellular bacterial symbionts of diverse Eukaryotes. These bacteria have highly streamlined genomes and can have negative fitness effects on the host. Herein, we present a comparative analysis of the first genome sequences of 'Ca. Hepatincola porcellionum', a facultative symbiont occurring extracellularly in the midgut glands of terrestrial isopods. Using a combination of long-read and short-read sequencing, we obtained the complete circular genomes of two Hepatincola strains and an additional metagenome-assembled draft genome. Phylogenomic analysis validated its phylogenetic position as an early-branching family-level clade relative to all other established Holosporales families associated with protists. A 16S rRNA gene survey revealed that this new family encompasses diverse bacteria associated with both marine and terrestrial host species, which expands the host range of Holosporales bacteria from protists to several phyla of the Ecdysozoa (Arthropoda and Priapulida). Hepatincola has a highly streamlined genome with reduced metabolic and biosynthetic capacities as well as a large repertoire of transmembrane transporters. This suggests that this symbiont is rather a nutrient scavenger than a nutrient provider for the host, likely benefitting from a nutrient-rich environment to import all necessary metabolites and precursors. Hepatincola further possesses a different set of bacterial secretion systems compared to protist-associated Holosporales, suggesting different host-symbiont interactions depending on the host organism.}, } @article {pmid36882183, year = {2023}, author = {Wu, J and Liu, Q and Li, M and Xu, J and Wang, C and Zhang, J and Xiao, M and Bin, Y and Xia, J}, title = {PhaGAA: an integrated web server platform for phage genome annotation and analysis.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {3}, pages = {}, pmid = {36882183}, issn = {1367-4811}, support = {2020YFA0908700//National Key Research and Development Program of China/ ; 62072003//National Natural Science Foundation of China/ ; KJ2020A0047//Education Department of Anhui Province/ ; }, mesh = {*Bacteriophages/genetics ; Software ; Computers ; Metagenome ; Genome, Bacterial ; Molecular Sequence Annotation ; }, abstract = {MOTIVATION: Phage genome annotation plays a key role in the design of phage therapy. To date, there have been various genome annotation tools for phages, but most of these tools focus on mono-functional annotation and have complex operational processes. Accordingly, comprehensive and user-friendly platforms for phage genome annotation are needed.

RESULTS: Here, we propose PhaGAA, an online integrated platform for phage genome annotation and analysis. By incorporating several annotation tools, PhaGAA is constructed to annotate the prophage genome at DNA and protein levels and provide the analytical results. Furthermore, PhaGAA could mine and annotate phage genomes from bacterial genome or metagenome. In summary, PhaGAA will be a useful resource for experimental biologists and help advance the phage synthetic biology in basic and application research.

PhaGAA is freely available at http://phage.xialab.info/.}, } @article {pmid36881655, year = {2023}, author = {Watanabe, M and Motooka, D and Yamasaki, S}, title = {The kinetics of signaling through the common FcRγ chain determine cytokine profiles in dendritic cells.}, journal = {Science signaling}, volume = {16}, number = {775}, pages = {eabn9909}, doi = {10.1126/scisignal.abn9909}, pmid = {36881655}, issn = {1937-9145}, mesh = {*Receptors, Fc ; Kinetics ; *Signal Transduction ; Receptors, IgG/genetics ; Cytokines ; Dendritic Cells ; }, abstract = {The common Fc receptor γ (FcRγ) chain is a signaling subunit common to several immune receptors, but cellular responses induced by FcRγ-coupled receptors are diverse. We investigated the mechanisms by which FcRγ generates divergent signals when coupled to Dectin-2 and Mincle, structurally similar C-type lectin receptors that induce the release of different cytokines from dendritic cells. Chronological tracing of transcriptomic and epigenetic changes upon stimulation revealed that Dectin-2 induced early and strong signaling, whereas Mincle-mediated signaling was delayed, which reflects their expression patterns. Generation of early and strong FcRγ-Syk signaling by engineered chimeric receptors was sufficient to recapitulate a Dectin-2-like gene expression profile. Early Syk signaling selectively stimulated the activity of the calcium ion-activated transcription factor NFAT, which rapidly altered the chromatin status and transcription of the Il2 gene. In contrast, proinflammatory cytokines, such as TNF, were induced regardless of FcRγ signaling kinetics. These results suggest that the strength and timing of FcRγ-Syk signaling can alter the quality of cellular responses through kinetics-sensing signaling machineries.}, } @article {pmid36881114, year = {2023}, author = {Anju, VT and Busi, S and Mohan, MS and Salim, SA and Ar, S and Imchen, M and Kumavath, R and Dyavaiah, M and Prasad, R}, title = {Surveillance and mitigation of soil pollution through metagenomic approaches.}, journal = {Biotechnology & genetic engineering reviews}, volume = {}, number = {}, pages = {1-34}, doi = {10.1080/02648725.2023.2186330}, pmid = {36881114}, issn = {2046-5556}, abstract = {Soil pollution is one of the serious global threats causing risk to environment and humans. The major cause of accumulation of pollutants in soil are anthropogenic activities and some natural processes. There are several types of soil pollutants which deteriorate the quality of human life and animal health. They are recalcitrant hydrocarbon compounds, metals, antibiotics, persistent organic compounds, pesticides and different kinds of plastics. Due to the detrimental properties of pollutants present in soil on human life and ecosystem such as carcinogenic, genotoxic and mutagenic effects, alternate and effective methods to degrade the pollutants are recommended. Bioremediation is an effective and inexpensive method of biological degradation of pollutants using plants, microorganisms and fungi. With the advent of new detection methods, the identification and degradation of soil pollutants in different ecosystems were made easy. Metagenomic approaches are a boon for the identification of unculturable microorganisms and to explore the vast bioremediation potential for different pollutants. Metagenomics is a power tool to study the microbial load in polluted or contaminated land and its role in bioremediation. In addition, the negative ecosystem and health effect of pathogens, antibiotic and metal resistant genes found in the polluted area can be studied. Also, the identification of novel compounds/genes/proteins involved in the biotechnology and sustainable agriculture practices can be performed with the integration of metagenomics.}, } @article {pmid36879954, year = {2023}, author = {Wang, C and Hu, J and Gu, Y and Wang, X and Chen, Y and Yuan, W}, title = {Application of next-generation metagenomic sequencing in the diagnosis and treatment of acute spinal infections.}, journal = {Heliyon}, volume = {9}, number = {3}, pages = {e13951}, pmid = {36879954}, issn = {2405-8440}, abstract = {OBJECTIVES: The purpose of this study was to verify the value of metagenomic next-generation sequencing (mNGS) in detecting the pathogens causing acute spinal infection by reviewing the results of mNGS in 114 patients.

METHODS: A total of 114 patients were included from our hospital. Samples (tissue/blood) were sent for mNGS detection, and the remaining samples were sent to the microbiology laboratory for pathogen culture, smear, histopathological analysis, and other tests. Patients' medical records were reviewed to determine their rates of detection, time needed, guidance for antibiotic treatment and clinical outcomes.

RESULTS: mNGS showed a satisfying diagnostic positive percent agreement of 84.91% (95% confidence interval (CI): 6.34%-96.7%), compared to 30.19% (95% CI: 21.85%-39.99%) for culture and 43.40% (95% CI: 31.39%-49.97%) for conventional methods (p < 0.0125), and mNGS was found positive in 46 culture and smear negative samples. The time required for pathogen identification using mNGS ranged from 29 h to 53 h, which showed an advantage over culture (90.88 ± 8.33 h; P < 0.05). mNGS also played an important role in optimizing antibiotic regimens in patients with negative results obtained using conventional methods. The treatment success rate (TSR) of patients using mNGS-guided antibiotic regimens (20/24, 83.33%) was significantly higher than that of patients using empirical antibiotics (13/23, 56.52%) (P < 0.0001).

CONCLUSIONS: mNGS shows promising potential in the pathogenic diagnosis of acute spinal infections and may enable clinicians to make more timely and effective adjustments to antibiotic regimens.}, } @article {pmid36879851, year = {2023}, author = {Yu, Y and Wang, S and Dong, G and Niu, Y}, title = {Diagnostic Performance of Metagenomic Next⁃Generation Sequencing in the Diagnosis of Prosthetic Joint Infection Using Tissue Specimens.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {1193-1201}, pmid = {36879851}, issn = {1178-6973}, abstract = {PURPOSE: The purpose of this study was to evaluate the ability of metagenomic next-generation sequencing (mNGS) diagnosing prosthetic joint infection (PJI) using tissue from hip/knee rapidly and precisely, especially in patients who had received antibiotic treatment within the preceding two weeks.

METHODS: From May 2020 to March 2022, 52 cases with suspected PJI were enrolled. mNGS was performed on surgical tissue samples. The sensitivity and specificity of mNGS in diagnosis was evaluated using culture in conjunction with MSIS criteria. This study also looked at how antibiotic use affected culture and mNGS efficacy.

RESULTS: According to MSIS criteria, 31 of the 44 cases had PJI, and 13 were classified in the aseptic loosening group. Sensitivity, specificity, positive/negative predictive value (PPV/NPV), positive/negative likelihood ratio (PLR/NLR), and area under the curve (AUC) of mNGS assay were 80.6% (71.9-91.8%), 84.6 (73.7-97.9%), 92.6 (84.2-98.7%), 64.7 (58.6-74.7%), 5.241 (4.081-6.693), 0.229 (0.108-0.482) and 0.826 (0.786-0.967), respectively, with MSIS as a reference. When MSIS was used as a reference, the results of culture assay were 45.2% (40.8-51.5%), 100 (100.0-100.0%), 100 (100.0-100.0%), 43.3 (39.1-49.5%), +∞, 0.548 (0.396-0.617) and 0.726 (0.621-0.864), respectively. The AUC values for mNGS and culture were 0.826 and 0.731, respectively, and the differences were insignificant. mNGS demonstrated higher sensitivity than culture in PJI subjects who had previously received antibiotic treatment within 2 weeks (69.5% vs 23.1%, P = 0.03).

CONCLUSION: In our series, mNGS yield a higher sensitivity for diagnosis and pathogen detection of PJI compared to microbiological culture. Additionally, mNGS is less affected by prior antibiotic exposure.}, } @article {pmid36879645, year = {2023}, author = {Feng, L and Chen, J and Luo, Q and Su, M and Chen, P and Lai, R and Shen, C and Zhou, H and Wang, H and Sun, X and Chen, L and Xia, H and Feng, H}, title = {mNGS facilitates the accurate diagnosis and antibiotic treatment of suspicious critical CNS infection in real practice: A retrospective study.}, journal = {Open life sciences}, volume = {18}, number = {1}, pages = {20220578}, pmid = {36879645}, issn = {2391-5412}, abstract = {Whether metagenomic next-generation sequencing (mNGS) could benefit patients with suspected severe central nervous system (CNS) infection in terms of diagnosis and antibiotic treatment remains unknown. We retrospectively analyzed 79 patients with suspected CNS infection and undertook mNGS. The value of mNGS was investigated in terms of identification of pathogen and guidance for the adjustment of antibiotic treatment. The relationship between the time of initiating mNGS since onset and the Glasgow Outcome Scale (GOS) score after 90-day follow-up were analyzed. Fifty out of 79 cases with suspicious severe CNS infection were finally diagnosed. Despite previous routine laboratory tests, mNGS further promoted the accurate identification of pathogens in 23 cases (47.9%). The sensitivity, specificity, and accuracy of mNGS test in this study were 84.0, 79.3, and 82.3%, respectively. Furthermore, mNGS facilitated the adjustment of empirical antibiotic treatments in 38 cases (48.1%). The time of taking mNGS since onset had an insignificant weak positive correlation with GOS after 90-day follow-up (r = -0.73, P = 0.08). mNGS facilitated the accurate identification of pathogens in suspicious severe CNS infections and promoted the accurate antibiotic therapy even empirical antibiotics were administrated. It should be taken as early as possible to improve the clinical outcome of patients with suspicious severe CNS infection.}, } @article {pmid36879606, year = {2023}, author = {Duncan, A and Barry, K and Daum, C and Eloe-Fadrosh, E and Roux, S and Schmidt, K and Tringe, SG and Valentin, KU and Varghese, N and Salamov, A and Grigoriev, IV and Leggett, RM and Moulton, V and Mock, T}, title = {Dataset of 143 metagenome-assembled genomes from the Arctic and Atlantic Oceans, including 21 for eukaryotic organisms.}, journal = {Data in brief}, volume = {47}, number = {}, pages = {108990}, pmid = {36879606}, issn = {2352-3409}, abstract = {This article presents metagenome-assembled genomes (MAGs) for both eukaryotic and prokaryotic organisms originating from the Arctic and Atlantic oceans, along with gene prediction and functional annotation for MAGs from both domains. Eleven samples from the chlorophyll-a maximum layer of the surface ocean were collected during two cruises in 2012; six from the Arctic in June-July on ARK-XXVII/1 (PS80), and five from the Atlantic in November on ANT-XXIX/1 (PS81). Sequencing and assembly was carried out by the Joint Genome Institute (JGI), who provide annotation of the assembled sequences, and 122 MAGs for prokaryotic organisms. A subsequent binning process identified 21 MAGs for eukaryotic organisms, mostly identified as Mamiellophyceae or Bacillariophyceae. The data for each MAG includes sequences in FASTA format, and tables of functional annotation of genes. For eukaryotic MAGs, transcript and protein sequences for predicted genes are available. A spreadsheet is provided summarising quality measures and taxonomic classifications for each MAG. These data provide draft genomes for uncultured marine microbes, including some of the first MAGs for polar eukaryotes, and can provide reference genetic data for these environments, or used in genomics-based comparison between environments.}, } @article {pmid36875992, year = {2022}, author = {Tadrent, N and Dedeine, F and Hervé, V}, title = {SnakeMAGs: a simple, efficient, flexible and scalable workflow to reconstruct prokaryotic genomes from metagenomes.}, journal = {F1000Research}, volume = {11}, number = {}, pages = {1522}, pmid = {36875992}, issn = {2046-1402}, mesh = {*Metagenome ; Workflow ; *Software ; Metagenomics/methods ; Computational Biology ; }, abstract = {Background: Over the last decade, we have observed in microbial ecology a transition from gene-centric to genome-centric analyses. Indeed, the advent of metagenomics combined with binning methods, single-cell genome sequencing as well as high-throughput cultivation methods have contributed to the continuing and exponential increase of available prokaryotic genomes, which in turn has favored the exploration of microbial metabolisms. In the case of metagenomics, data processing, from raw reads to genome reconstruction, involves various steps and software which can represent a major technical obstacle. Methods: To overcome this challenge, we developed SnakeMAGs, a simple workflow that can process Illumina data, from raw reads to metagenome-assembled genomes (MAGs) classification and relative abundance estimate. It integrates state-of-the-art bioinformatic tools to sequentially perform: quality control of the reads (illumina-utils, Trimmomatic), host sequence removal (optional step, using Bowtie2), assembly (MEGAHIT), binning (MetaBAT2), quality filtering of the bins (CheckM, GUNC), classification of the MAGs (GTDB-Tk) and estimate of their relative abundance (CoverM). Developed with the popular Snakemake workflow management system, it can be deployed on various architectures, from single to multicore and from workstation to computer clusters and grids. It is also flexible since users can easily change parameters and/or add new rules. Results: Using termite gut metagenomic datasets, we showed that SnakeMAGs is slower but allowed the recovery of more MAGs encompassing more diverse phyla compared to another similar workflow named ATLAS. Importantly, these additional MAGs showed no significant difference compared to the other ones in terms of completeness, contamination, genome size nor relative abundance. Conclusions: Overall, it should make the reconstruction of MAGs more accessible to microbiologists. SnakeMAGs as well as test files and an extended tutorial are available at https://github.com/Nachida08/SnakeMAGs.}, } @article {pmid36879349, year = {2023}, author = {Li, Z and Zhao, X and Jian, L and Wang, B and Luo, H}, title = {Rumen microbial-driven metabolite from grazing lambs potentially regulates body fatty acid metabolism by lipid-related genes in liver.}, journal = {Journal of animal science and biotechnology}, volume = {14}, number = {1}, pages = {39}, pmid = {36879349}, issn = {1674-9782}, support = {CARS-38//Agriculture Research System of China/ ; 2018BBF02016//Key Subject of Ningxia Province/ ; }, abstract = {BACKGROUND: Lipid metabolism differs significantly between grazing and stall-feeding lambs, affecting the quality of livestock products. As two critical organs of lipid metabolism, the differences between feeding patterns on rumen and liver metabolism remain unclear. In this study, 16S rRNA, metagenomics, transcriptomics, and untargeted metabolomics were utilized to investigate the key rumen microorganisms and metabolites, as well as liver genes and metabolites associated with fatty acid metabolism under indoor feeding (F) and grazing (G).

RESULTS: Compared with grazing, indoor feeding increased ruminal propionate content. Using metagenome sequencing in combination with 16S rRNA amplicon sequencing, the results showed that the abundance of propionate-producing Succiniclasticum and hydrogenating bacteria Tenericutes was enriched in the F group. For rumen metabolism, grazing caused up-regulation of EPA, DHA and oleic acid and down-regulation of decanoic acid, as well as, screening for 2-ketobutyric acid as a vital differential metabolite, which was enriched in the propionate metabolism pathway. In the liver, indoor feeding increased 3-hydroxypropanoate and citric acid content, causing changes in propionate metabolism and citrate cycle, while decreasing the ETA content. Then, the liver transcriptome revealed that 11 lipid-related genes were differentially expressed in the two feeding patterns. Correlation analysis showed that the expression of CYP4A6, FADS1, FADS2, ALDH6A1 and CYP2C23 was significantly associated with the propionate metabolism process, suggesting that propionate metabolism may be an important factor mediating the hepatic lipid metabolism. Besides, the unsaturated fatty acids in muscle, rumen and liver also had a close correlation.

CONCLUSIONS: Overall, our data demonstrated that rumen microbial-driven metabolite from grazing lambs potentially regulates multiple hepatic lipid-related genes, ultimately affecting body fatty acid metabolism.}, } @article {pmid36879316, year = {2023}, author = {Korry, BJ and Belenky, P}, title = {Trophic level and proteobacteria abundance drive antibiotic resistance levels in fish from coastal New England.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {16}, pmid = {36879316}, issn = {2524-4671}, support = {R01 DK125382/DK/NIDDK NIH HHS/United States ; R21 AT010366/AT/NCCIH NIH HHS/United States ; R01DK125382/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: The natural marine environment represents a vast reservoir of antimicrobial resistant bacteria. The wildlife that inhabits this environment plays an important role as the host to these bacteria and in the dissemination of resistance. The relationship between host diet, phylogeny, and trophic level and the microbiome/resistome in marine fish is not fully understood. To further explore this relationship, we utilize shotgun metagenomic sequencing to define the gastrointestinal tract microbiomes of seven different marine vertebrates collected in coastal New England waters.

RESULTS: We identify inter and intraspecies differences in the gut microbiota of these wild marine fish populations. Furthermore, we find an association between antibiotic resistance genes and host dietary guild, which suggests that higher trophic level organisms have a greater abundance of resistance genes. Additionally, we demonstrate that antibiotic resistance gene burden is positively correlated with Proteobacteria abundance in the microbiome. Lastly, we identify dietary signatures within the gut of these fish and find evidence of possible dietary selection for bacteria with specific carbohydrate utilization potential.

CONCLUSIONS: This work establishes a link between host lifestyle/dietary guild, and microbiome composition and the abundance of antibiotic resistance genes within the gastrointestinal tract of marine organisms. We expand the current understanding of marine organism-associated microbial communities and their role as reservoirs of antimicrobial resistance genes.}, } @article {pmid36879274, year = {2023}, author = {Lousada, MB and Edelkamp, J and Lachnit, T and Fehrholz, M and Jimenez, F and Paus, R}, title = {Laser capture microdissection as a method for investigating the human hair follicle microbiome reveals region-specific differences in the bacteriome profile.}, journal = {BMC research notes}, volume = {16}, number = {1}, pages = {29}, pmid = {36879274}, issn = {1756-0500}, support = {Monasterium Laboratory//Monasterium Laboratory/ ; CRC 1182//Deutsche Forschungsgemeinschaft/ ; Giuliani S.p.a//Giuliani S.p.a/ ; }, mesh = {Humans ; Laser Capture Microdissection ; *Hair Follicle ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; }, abstract = {OBJECTIVE: Human hair follicles (HFs) are populated by a rich and diverse microbiome, traditionally evaluated by methods that inadvertently sample the skin microbiome and/or miss microbiota located in deeper HF regions. Thereby, these methods capture the human HF microbiome in a skewed and incomplete manner. This pilot study aimed to use laser-capture microdissection of human scalp HFs, coupled with 16S rRNA gene sequencing to sample the HF microbiome and overcome these methodological limitations.

RESULTS: HFs were laser-capture microdissected (LCM) into three anatomically distinct regions. All main known core HF bacterial colonisers, including Cutibacterium, Corynebacterium and Staphylococcus, were identified, in all three HF regions. Interestingly, region-specific variations in α-diversity and microbial abundance of the core microbiome genera and Reyranella were identified, suggestive of variations in microbiologically relevant microenvironment characteristics. This pilot study therefore shows that LCM-coupled with metagenomics is a powerful tool for analysing the microbiome of defined biological niches. Refining and complementing this method with broader metagenomic techniques will facilitate the mapping of dysbiotic events associated with HF diseases and targeted therapeutic interventions.}, } @article {pmid36878288, year = {2023}, author = {Chai, X and Wen, L and Song, Y and He, X and Yue, J and Wu, J and Chen, X and Cai, Z and Qi, Z}, title = {DEHP exposure elevated cardiovascular risk in obese mice by disturbing the arachidonic acid metabolism of gut microbiota.}, journal = {The Science of the total environment}, volume = {875}, number = {}, pages = {162615}, doi = {10.1016/j.scitotenv.2023.162615}, pmid = {36878288}, issn = {1879-1026}, mesh = {Mice ; Humans ; Animals ; *Diethylhexyl Phthalate/toxicity/metabolism ; *Gastrointestinal Microbiome ; Mice, Obese ; RNA, Ribosomal, 16S ; Arachidonic Acid ; *Cardiovascular Diseases/chemically induced ; Risk Factors ; Obesity/metabolism ; Heart Disease Risk Factors ; }, abstract = {Phthalate esters (PAEs) are one of the significant classes of emerging contaminants that are increasingly detected in environmental and human samples. Nevertheless, the current toxicity studies rarely report how PAEs affect the cardiovascular system, especially in obese individuals. In this study, diet-induced obese mice and corresponding normal mice were exposed to di(2-ethylhexyl) phthalate (DEHP) by oral gavage at environmentally relevant concentrations and key characteristics of cardiovascular risk were examined. The 16S rRNA and high-resolution mass spectrometry were used to investigate the alterations in the gut microbial profile and metabolic homeostasis. The results indicated that the cardiovascular system of fat individuals was more susceptible to DEHP exposure than mice in the lean group. 16S rRNA-based profiling and correlation analysis collectively suggested DEHP-induced gut microbial remodeling in fed a high-fat diet mice, represented by the abundance of the genus Faecalibaculum. Using metagenomic approaches, Faecalibaculum rodentium was identified as the top-ranked candidate bacterium. Additionally, metabolomics data revealed that DEHP exposure altered the gut metabolic homeostasis of arachidonic acid (AA), which is associated with adverse cardiovascular events. Finally, cultures of Faecalibaculum rodentium were treated with AA in vitro to verify the role of Faecalibaculum rodentium in altering AA metabolism. Our findings provide novel insights into DEHP exposure induced cardiovascular damage in obese individuals and suggest that AA could be used as a potential modulator of gut microbiota to prevent related diseases.}, } @article {pmid36877076, year = {2023}, author = {Kim, JE and Nam, H and Park, JI and Cho, H and Lee, J and Kim, HE and Kim, DK and Joo, KW and Kim, YS and Kim, BS and Park, S and Lee, H}, title = {Gut Microbial Genes and Metabolism for Methionine and Branched-Chain Amino Acids in Diabetic Nephropathy.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0234422}, pmid = {36877076}, issn = {2165-0497}, abstract = {Diabetic mellitus nephropathy (DMN) is a serious complication of diabetes and a major health concern. Although the pathophysiology of diabetes mellitus (DM) leading to DMN is uncertain, recent evidence suggests the involvement of the gut microbiome. This study aimed to determine the relationships among gut microbial species, genes, and metabolites in DMN through an integrated clinical, taxonomic, genomic, and metabolomic analysis. Whole-metagenome shotgun sequencing and nuclear magnetic resonance metabolomic analyses were performed on stool samples from 15 patients with DMN and 22 healthy controls. Six bacterial species were identified to be significantly elevated in the DMN patients after adjusting for age, sex, body mass index, and estimated glomerular filtration rate (eGFR). Multivariate analysis found 216 microbial genes and 6 metabolites (higher valine, isoleucine, methionine, valerate, and phenylacetate levels in the DMN group and higher acetate levels in the control group) that were differentially present between the DMN and control groups. Integrated analysis of all of these parameters and clinical data using the random-forest model showed that methionine and branched-chain amino acids (BCAAs) were among the most significant features, next to the eGFR and proteinuria, in differentiating the DMN group from the control group. Metabolic pathway gene analysis of BCAAs and methionine also revealed that many genes involved in the biosynthesis of these metabolites were elevated in the six species that were more abundant in the DMN group. The suggested correlation among taxonomic, genetic, and metabolic features of the gut microbiome would expand our understanding of gut microbial involvement in the pathogenesis of DMN and may provide potential therapeutic targets for DMN. IMPORTANCE Whole metagenomic sequencing uncovered specific members of the gut microbiota associated with DMN. The gene families derived from the discovered species are involved in the metabolic pathways of methionine and branched-chain amino acids. Metabolomic analysis using stool samples showed increased methionine and branched-chain amino acids in DMN. These integrative omics results provide evidence of the gut microbiota-associated pathophysiology of DMN, which can be further studied for disease-modulating effects via prebiotics or probiotics.}, } @article {pmid36877067, year = {2023}, author = {Ong, DRY and Gutiérrez-Rodríguez, A and Garczarek, L and Marie, D and Lopes Dos Santos, A}, title = {Nested PCR Approach for petB Gene Metabarcoding of Marine Synechococcus Populations.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0408622}, pmid = {36877067}, issn = {2165-0497}, abstract = {The molecular diversity of marine picocyanobacterial populations, an important component of phytoplankton communities, is better characterized using high-resolution marker genes than the 16S rRNA gene as they have greater sequence divergence to differentiate between closely related picocyanobacteria groups. Although specific ribosomal primers have been developed, another general disadvantage of bacterial ribosome-based diversity analyses is the variable number of rRNA gene copies. To overcome these issues, the single-copy petB gene, encoding the cytochrome b6 subunit of the cytochrome b6f complex, has been used as a high-resolution marker gene to characterize Synechococcus diversity. We have designed new primers targeting the petB gene and proposed a nested PCR method (termed Ong_2022) for metabarcoding of marine Synechococcus populations obtained by flow cytometry cell sorting. We evaluated the specificity and sensitivity of Ong_2022 against the standard amplification protocol (termed Mazard_2012) using filtered seawater samples. The Ong_2022 approach was also tested on flow cytometry-sorted Synechococcus populations. Samples (filtered and sorted) were obtained in the Southwest Pacific Ocean, from subtropical (ST) and subantarctic (SA) water masses. The two PCR approaches using filtered samples recovered the same dominant subclades, Ia, Ib, IVa, and IVb, with small differences in relative abundance across the distinct samples. For example, subclade IVa was dominant in ST samples with the Mazard_2012 approach, while the same samples processed with Ong_2022 showed similar contributions of subclades IVa and Ib to the total community. The Ong_2022 approach generally captured a higher genetic diversity of Synechococcus subcluster 5.1 than the Mazard_2012 approach while having a lower proportion of incorrectly assigned amplicon sequence variants (ASVs). All flow cytometry-sorted Synechococcus samples could be amplified only by our nested approach. The taxonomic diversity obtained with our primers on both sample types was in agreement with the clade distribution observed by previous studies that applied other marker genes or PCR-free metagenomic approaches under similar environmental conditions. IMPORTANCE The petB gene has been proposed as a high-resolution marker gene to access the diversity of marine Synechococcus populations. A systematic metabarcoding approach based on the petB gene would improve the characterization/assessment of the Synechococcus community structure in marine planktonic ecosystems. We have designed and tested specific primers to be applied in a nested PCR protocol (Ong_2022) for metabarcoding the petB gene. The Ong_2022 protocol can be applied to samples with low DNA content, such as those obtained by flow cytometry cell sorting, allowing the simultaneous assessment of the genetic diversity of Synechococcus populations and cellular properties and activities (e.g., nutrient cell ratios or carbon uptake rates). Our approach will allow future studies using flow cytometry to investigate the link between ecological traits and taxonomic diversity of marine Synechococcus.}, } @article {pmid36877031, year = {2023}, author = {Barnett, SE and Egan, R and Foster, B and Eloe-Fadrosh, EA and Buckley, DH}, title = {Genomic Features Predict Bacterial Life History Strategies in Soil, as Identified by Metagenomic Stable Isotope Probing.}, journal = {mBio}, volume = {14}, number = {2}, pages = {e0358422}, pmid = {36877031}, issn = {2150-7511}, mesh = {*Life History Traits ; Soil/chemistry ; Soil Microbiology ; Bacteria/genetics/metabolism ; Carbon/metabolism ; Isotopes/metabolism ; Metagenomics ; }, abstract = {Bacteria catalyze the formation and destruction of soil organic matter, but the bacterial dynamics in soil that govern carbon (C) cycling are not well understood. Life history strategies explain the complex dynamics of bacterial populations and activities based on trade-offs in energy allocation to growth, resource acquisition, and survival. Such trade-offs influence the fate of soil C, but their genomic basis remains poorly characterized. We used multisubstrate metagenomic DNA stable isotope probing to link genomic features of bacteria to their C acquisition and growth dynamics. We identify several genomic features associated with patterns of bacterial C acquisition and growth, notably genomic investment in resource acquisition and regulatory flexibility. Moreover, we identify genomic trade-offs defined by numbers of transcription factors, membrane transporters, and secreted products, which match predictions from life history theory. We further show that genomic investment in resource acquisition and regulatory flexibility can predict bacterial ecological strategies in soil. IMPORTANCE Soil microbes are major players in the global carbon cycle, yet we still have little understanding of how the carbon cycle operates in soil communities. A major limitation is that carbon metabolism lacks discrete functional genes that define carbon transformations. Instead, carbon transformations are governed by anabolic processes associated with growth, resource acquisition, and survival. We use metagenomic stable isotope probing to link genome information to microbial growth and carbon assimilation dynamics as they occur in soil. From these data, we identify genomic traits that can predict bacterial ecological strategies which define bacterial interactions with soil carbon.}, } @article {pmid36876113, year = {2023}, author = {Anderson, BD and Bisanz, JE}, title = {Challenges and opportunities of strain diversity in gut microbiome research.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1117122}, pmid = {36876113}, issn = {1664-302X}, abstract = {Just because two things are related does not mean they are the same. In analyzing microbiome data, we are often limited to species-level analyses, and even with the ability to resolve strains, we lack comprehensive databases and understanding of the importance of strain-level variation outside of a limited number of model organisms. The bacterial genome is highly plastic with gene gain and loss occurring at rates comparable or higher than de novo mutations. As such, the conserved portion of the genome is often a fraction of the pangenome which gives rise to significant phenotypic variation, particularly in traits which are important in host microbe interactions. In this review, we discuss the mechanisms that give rise to strain variation and methods that can be used to study it. We identify that while strain diversity can act as a major barrier in interpreting and generalizing microbiome data, it can also be a powerful tool for mechanistic research. We then highlight recent examples demonstrating the importance of strain variation in colonization, virulence, and xenobiotic metabolism. Moving past taxonomy and the species concept will be crucial for future mechanistic research to understand microbiome structure and function.}, } @article {pmid36876106, year = {2023}, author = {Zhang, K and Zhang, Y and Deng, M and Wang, P and Yue, X and Wang, P and Li, W}, title = {Monthly dynamics of microbial communities and variation of nitrogen-cycling genes in an industrial-scale expanded granular sludge bed reactor.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1125709}, pmid = {36876106}, issn = {1664-302X}, abstract = {INTRODUCTION: The expanded granular sludge bed (EGSB) is a major form of anaerobic digestion system during wastewater treatment. Yet, the dynamics of microbial and viral communities and members functioning in nitrogen cycling along with monthly changing physicochemical properties have not been well elucidated.

METHODS: Here, by collecting the anaerobic activated sludge samples from a continuously operating industrial-scale EGSB reactor, we conducted 16S rRNA gene amplicon sequencing and metagenome sequencing to reveal the microbial community structure and variation with the ever-changing physicochemical properties along within a year.

RESULTS: We observed a clear monthly variation of microbial community structures, while COD, the ratio of volatile suspended solids (VSS) to total suspended solids (TSS) (VSS/TSS ratio), and temperature were predominant factors in shaping community dissimilarities examined by generalized boosted regression modeling (GBM) analysis. Meanwhile, a significant correlation was found between the changing physicochemical properties and microbial communities (p <0.05). The alpha diversity (Chao1 and Shannon) was significantly higher (p <0.05) in both winter (December, January, and February) and autumn (September, October, and November) with higher organic loading rate (OLR), higher VSS/TSS ratio, and lower temperature, resulting higher biogas production and nutrition removal efficiency. Further, 18 key genes covering nitrate reduction, denitrification, nitrification, and nitrogen fixation pathways were discovered, the total abundance of which was significantly associated with the changing environmental factors (p <0.05). Among these pathways, the dissimilatory nitrate reduction to ammonia (DNRA) and denitrification had the higher abundance contributed by the top highly abundant genes narGH, nrfABCDH, and hcp. The COD, OLR, and temperature were primary factors in affecting DNRA and denitrification by GBM evaluation. Moreover, by metagenome binning, we found the DNRA populations mainly belonged to Proteobacteria, Planctomycetota, and Nitrospirae, while the denitrifying bacteria with complete denitrification performance were all Proteobacteria. Besides, we detected 3,360 non-redundant viral sequences with great novelty, in which Siphoviridae, Podoviridae, and Myoviridae were dominant viral families. Interestingly, viral communities likewise depicted clear monthly variation and had significant associations with the recovered populations (p <0.05).

DISCUSSION: Our work highlights the monthly variation of microbial and viral communities during the continuous operation of EGSB affected by the predominant changing COD, OLR, and temperature, while DNRA and denitrification pathways dominated in this anaerobic system. The results also provide a theoretical basis for the optimization of the engineered system.}, } @article {pmid36876103, year = {2023}, author = {Wang, L and Zhu, ZB and Zhang, L and Li, J and Zhao, Q}, title = {Editorial: Untangle the broad connections and tight interactions between human microbiota and complex diseases through data-driven approaches.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1157579}, pmid = {36876103}, issn = {1664-302X}, } @article {pmid36876097, year = {2023}, author = {Farjana, N and Tu, Z and Furukawa, H and Yumoto, I}, title = {Environmental factors contributing to the convergence of bacterial community structure during indigo reduction.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1097595}, pmid = {36876097}, issn = {1664-302X}, abstract = {Indigo is solubilized through the reducing action of the microbiota that occurs during alkaline fermentation of composted leaves of Polygonum tinctorium L. (sukumo). However, the environmental effects on the microbiota during this treatment, as well as the mechanisms underlying the microbial succession toward stable state remain unknown. In this study, physicochemical analyses and Illumina metagenomic sequencing was used to determine the impact pretreatment conditions on the subsequent initiation of bacterial community transition and their convergence, dyeing capacity and the environmental factors critical for indigo reducing state during aging of sukumo. The initial pretreatment conditions analyzed included 60°C tap water (heat treatment: batch 1), 25°C tap water (control; batch 2), 25°C wood ash extract (high pH; batch 3) and hot wood ash extract (heat and high pH; batch 4), coupled with successive addition of wheat bran from days 5 to 194. High pH had larger impact than heat treatment on the microbiota, producing more rapid transitional changes from days 1 to 2. Although the initial bacterial community composition and dyeing intensity differed during days 2-5, the microbiota appropriately converged to facilitate indigo reduction from day 7 in all the batches, with Alkaliphilus oremalandii, Amphibacillus, Alkalicella caledoniensis, Atopostipes suicloalis and Tissierellaceae core taxa contributing to the improvement of when the dyeing intensity. This convergence is attributed to the continuous maintenance of high pH (day 1 ~) and low redox potential (day 2~), along with the introduction of wheat bran at day 5 (day 5~). PICRUSt2 predictive function profiling revealed the enrichment of phosphotransferease system (PTS) and starch and sucrose metabolism subpathways key toward indigo reduction. Seven NAD(P)-dependent oxidoreductases KEGG orthologs correlating to the dyeing intensity was also identified, with Alkalihalobacillus macyae, Alkalicella caledoniensis, and Atopostipes suicloalis contributing significantly toward the initiation of indigo reduction in batch 3. During the ripening period, the staining intensity was maintained by continuous addition of wheat bran and the successive emergence of indigo-reducing bacteria that also contributed to material circulation in the system. The above results provide insight into the interaction of microbial system and environmental factors in sukumo fermentation.}, } @article {pmid36876060, year = {2023}, author = {Klair, D and Dobhal, S and Ahmad, A and Hassan, ZU and Uyeda, J and Silva, J and Wang, KH and Kim, S and Alvarez, AM and Arif, M}, title = {Exploring taxonomic and functional microbiome of Hawaiian stream and spring irrigation water systems using Illumina and Oxford Nanopore sequencing platforms.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1039292}, pmid = {36876060}, issn = {1664-302X}, abstract = {Irrigation water is a common source of contamination that carries plant and foodborne human pathogens and provides a niche for proliferation and survival of microbes in agricultural settings. Bacterial communities and their functions in irrigation water were investigated by analyzing samples from wetland taro farms on Oahu, Hawaii using different DNA sequencing platforms. Irrigation water samples (stream, spring, and storage tank water) were collected from North, East, and West sides of Oahu and subjected to high quality DNA isolation, library preparation and sequencing of the V3-V4 region, full length 16S rRNA, and shotgun metagenome sequencing using Illumina iSeq100, Oxford Nanopore MinION and Illumina NovaSeq, respectively. Illumina reads provided the most comprehensive taxonomic classification at the phylum level where Proteobacteria was identified as the most abundant phylum in the stream source and associated water samples from wetland taro fields. Cyanobacteria was also a dominant phylum in samples from tank and spring water, whereas Bacteroidetes were most abundant in wetland taro fields irrigated with spring water. However, over 50% of the valid short amplicon reads remained unclassified and inconclusive at the species level. In contrast, Oxford Nanopore MinION was a better choice for microbe classification at the genus and species levels as indicated by samples sequenced for full length 16S rRNA. No reliable taxonomic classification results were obtained while using shotgun metagenome data. In functional analyzes, only 12% of the genes were shared by two consortia and 95 antibiotic resistant genes (ARGs) were detected with variable relative abundance. Full descriptions of microbial communities and their functions are essential for the development of better water management strategies aimed to produce safer fresh produce and to protect plant, animal, human and environmental health. Quantitative comparisons illustrated the importance of selecting the appropriate analytical method depending on the level of taxonomic delineation sought in each microbiome.}, } @article {pmid36875536, year = {2022}, author = {Wahla, AQ and Anwar, S and Fareed, MI and Ikram, W and Ali, L and Alharby, HF and Bamagoos, AA and Almaghamsi, AA and Iqbal, S and Ali, S}, title = {Immobilization of metribuzin-degrading bacteria on biochar: Enhanced soil remediation and bacterial community restoration.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1027284}, pmid = {36875536}, issn = {1664-302X}, abstract = {Metribuzin (MB), a triazinone herbicide is extensively sprayed for weed control in agriculture, has been reported to contaminate soil, groundwater, and surface waters. In soil, MB residues can negatively affect not only the germination of subsequent crops but also disturb soil bacterial community. The present study describes the use of biochar as a carrier material to immobilize MB-degrading bacterial consortium, for remediation of MB-contaminated soil and restoration of soil bacterial community in soil microcosms. The bacterial consortium (MB3R) comprised four bacterial strains, i.e., Rhodococcus rhodochrous AQ1, Bacillus tequilensis AQ2, Bacillus aryabhattai AQ3, and Bacillus safensis AQ4. Significantly higher MB remediation was observed in soil augmented with bacterial consortium immobilized on biochar compared to the soil augmented with un-immobilized bacterial consortium. Immobilization of MB3R on biochar resulted in higher MB degradation rate (0.017 Kd[-1]) and reduced half-life (40 days) compared to 0.010 Kd[-1] degradation rate and 68 day half-life in treatments where un-immobilized bacterial consortium was employed. It is worth mentioning that the MB degradation products metribuzin-desamino (DA), metribuzin-diketo (DK), and metribuzin desamino-diketo (DADK) were detected in the treatments where MB3R was inoculated either alone or in combination with biochar. MB contamination significantly altered the composition of soil bacteria. However, soil bacterial community was conserved in response to augmentation with MB3R immobilized on biochar. Immobilization of the bacterial consortium MB3R on biochar can potentially be exploited for remediation of MB-contaminated soil and protecting its microbiota.}, } @article {pmid36875219, year = {2023}, author = {Shamsuri, QS and Ab Majid, AH}, title = {Metagenomic 16S rRNA amplicon data of gut microbial diversity in three species of subterranean termites (Coptotermes gestroi, Globitermes sulphureus and Macrotermes gilvus).}, journal = {Data in brief}, volume = {47}, number = {}, pages = {108993}, pmid = {36875219}, issn = {2352-3409}, abstract = {In this paper, we present the metagenomic dataset of gut microbial DNA of the lower group of subterranean termites, i.e. Coptotermes gestroi, and the higher groups, i.e. Globitermes sulphureus and Macrotermes gilvus, in Penang, Malaysia. Two replicates of each species were sequenced using Next-Generation Sequencing (Illumina MiSeq) and analysed via QIIME2. The results returned with 210,248 sequences in C. gestroi, 224,972 in G. sulphureus, and 249,549 in M. gilvus. The sequence data were deposited in the NCBI Sequence Read Archive (SRA) under BioProject number of PRJNA896747. The community analysis showed that Bacteroidota is the most abundant phylum in C. gestroi and M. gilvus, while Spirochaetota is prevalent in G. sulphureus.}, } @article {pmid36875193, year = {2023}, author = {Abdullah, B and Idorus, MY and Daud, S and Aazmi, S and Pillai, TK and Zain, ZM}, title = {Gut Microbiota Composition in the First and Third Trimester of Pregnancy among Malay Women is Associated with Body Mass Index: A Pilot Study.}, journal = {The Malaysian journal of medical sciences : MJMS}, volume = {30}, number = {1}, pages = {116-128}, pmid = {36875193}, issn = {1394-195X}, abstract = {BACKGROUND: This study has analysed the pattern of gut microbiota during the first and third trimesters among pregnant Malay women.

METHODS: This was a pilot prospective observational study involving 12 pregnant Malay women without any endocrine disorders and on neither antibiotics nor probiotics. Demographic details and anthropometric measurements were obtained, and the faecal 16S ribosomal ribonucleic acid (rRNA) metagenome microbiota of the first and third trimesters (T1 and T3) were analysed. Univariate and multivariate statistics, partial least squares discriminant analysis (PLSDA) and Kendall rank correlation testing were used to identify key genera and associations with pregnancy trimester and body mass index (BMI).

RESULTS: The most abundant phyla were Bacteroidetes, Firmicutes, Proteobacteria and Actinobacteria, with significant differences in composition at the genus level demonstrated between T1 and T3. Sequencing showed a statistically significant difference in beta diversity between normal and abnormal BMI at all taxonomic ranks (R [2] = 0.60; Q [2] = 0.23) and genus levels (R [2] = 0.57; Q [2] = 0.37). The relative abundances of Akkermansia (P < 0.05; false discovery rate [FDR] < 0.05), Olsenella (P < 0.05; FDR < 0.05) and Oscillospira (P < 0.05; FDR < 0.05) were found to be significantly higher in normal BMI cases by 2.4, 3.4 and 3.1 times, respectively.

CONCLUSION: Three genera (Akkermansia, Olsenella and Oscillospira) were correlated with normal BMI during pregnancy. All three could be promising biotherapeutic targets in body weight regulation during pregnancy, subsequently reducing complications associated with higher BMI.}, } @article {pmid36875075, year = {2023}, author = {Xu, XJ and Lang, JD and Yang, J and Long, B and Liu, XD and Zeng, XF and Tian, G and You, X}, title = {Differences of gut microbiota and behavioral symptoms between two subgroups of autistic children based on γδT cells-derived IFN-γ Levels: A preliminary study.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1100816}, pmid = {36875075}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Autistic Disorder ; Behavioral Symptoms ; Amino Acids ; *Autism Spectrum Disorder ; }, abstract = {BACKGROUND: Autism Spectrum Disorders (ASD) are defined as a group of pervasive neurodevelopmental disorders, and the heterogeneity in the symptomology and etiology of ASD has long been recognized. Altered immune function and gut microbiota have been found in ASD populations. Immune dysfunction has been hypothesized to involve in the pathophysiology of a subtype of ASD.

METHODS: A cohort of 105 ASD children were recruited and grouped based on IFN-γ levels derived from ex vivo stimulated γδT cells. Fecal samples were collected and analyzed with a metagenomic approach. Comparison of autistic symptoms and gut microbiota composition was made between subgroups. Enriched KEGG orthologues markers and pathogen-host interactions based on metagenome were also analyzed to reveal the differences in functional features.

RESULTS: The autistic behavioral symptoms were more severe for children in the IFN-γ-high group, especially in the body and object use, social and self-help, and expressive language performance domains. LEfSe analysis of gut microbiota revealed an overrepresentation of Selenomonadales, Negatiyicutes, Veillonellaceae and Verrucomicrobiaceae and underrepresentation of Bacteroides xylanisolvens and Bifidobacterium longum in children with higher IFN-γ level. Decreased metabolism function of carbohydrate, amino acid and lipid in gut microbiota were found in the IFN-γ-high group. Additional functional profiles analyses revealed significant differences in the abundances of genes encoding carbohydrate-active enzymes between the two groups. And enriched phenotypes related to infection and gastroenteritis and underrepresentation of one gut-brain module associated with histamine degradation were also found in the IFN-γ-High group. Results of multivariate analyses revealed relatively good separation between the two groups.

CONCLUSIONS: Levels of IFN-γ derived from γδT cell could serve as one of the potential candidate biomarkers to subtype ASD individuals to reduce the heterogeneity associated with ASD and produce subgroups which are more likely to share a more similar phenotype and etiology. A better understanding of the associations among immune function, gut microbiota composition and metabolism abnormalities in ASD would facilitate the development of individualized biomedical treatment for this complex neurodevelopmental disorder.}, } @article {pmid36874978, year = {2023}, author = {Fuchsman, CA and Garcia Prieto, D and Hays, MD and Cram, JA}, title = {Associations between picocyanobacterial ecotypes and cyanophage host genes across ocean basins and depth.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14924}, pmid = {36874978}, issn = {2167-8359}, mesh = {*Ecotype ; Phylogeny ; *Genes, Viral ; Genome, Viral ; Cycadopsida ; }, abstract = {BACKGROUND: Cyanophages, viruses that infect cyanobacteria, are globally abundant in the ocean's euphotic zone and are a potentially important cause of mortality for marine picocyanobacteria. Viral host genes are thought to increase viral fitness by either increasing numbers of genes for synthesizing nucleotides for virus replication, or by mitigating direct stresses imposed by the environment. The encoding of host genes in viral genomes through horizontal gene transfer is a form of evolution that links viruses, hosts, and the environment. We previously examined depth profiles of the proportion of cyanophage containing various host genes in the Eastern Tropical North Pacific Oxygen Deficient Zone (ODZ) and at the subtropical North Atlantic (BATS). However, cyanophage host genes have not been previously examined in environmental depth profiles across the oceans.

METHODOLOGY: We examined geographical and depth distributions of picocyanobacterial ecotypes, cyanophage, and their viral-host genes across ocean basins including the North Atlantic, Mediterranean Sea, North Pacific, South Pacific, and Eastern Tropical North and South Pacific ODZs using phylogenetic metagenomic read placement. We determined the proportion of myo and podo-cyanophage containing a range of host genes by comparing to cyanophage single copy core gene terminase (terL). With this large dataset (22 stations), network analysis identified statistical links between 12 of the 14 cyanophage host genes examined here with their picocyanobacteria host ecotypes.

RESULTS: Picyanobacterial ecotypes, and the composition and proportion of cyanophage host genes, shifted dramatically and predictably with depth. For most of the cyanophage host genes examined here, we found that the composition of host ecotypes predicted the proportion of viral host genes harbored by the cyanophage community. Terminase is too conserved to illuminate the myo-cyanophage community structure. Cyanophage cobS was present in almost all myo-cyanophage and did not vary in proportion with depth. We used the composition of cobS phylotypes to track changes in myo-cyanophage composition.

CONCLUSIONS: Picocyanobacteria ecotypes shift with changes in light, temperature, and oxygen and many common cyanophage host genes shift concomitantly. However, cyanophage phosphate transporter gene pstS appeared to instead vary with ocean basin and was most abundant in low phosphate regions. Abundances of cyanophage host genes related to nutrient acquisition may diverge from host ecotype constraints as the same host can live in varying nutrient concentrations. Myo-cyanophage community in the anoxic ODZ had reduced diversity. By comparison to the oxic ocean, we can see which cyanophage host genes are especially abundant (nirA, nirC, and purS) or not abundant (myo psbA) in ODZs, highlighting both the stability of conditions in the ODZ and the importance of nitrite as an N source to ODZ endemic LLV Prochlorococcus.}, } @article {pmid36873548, year = {2023}, author = {Tamayo-Trujillo, R and Guevara-Ramírez, P and Cadena-Ullauri, S and Paz-Cruz, E and Ruiz-Pozo, VA and Zambrano, AK}, title = {Human virome: Implications in cancer.}, journal = {Heliyon}, volume = {9}, number = {3}, pages = {e14086}, pmid = {36873548}, issn = {2405-8440}, abstract = {In recent years, the human virome has gained importance, especially after the SARS-CoV-2 pandemic, due to its possible involvement in autoimmune, inflammatory diseases, and cancer. Characterization of the human virome can be carried out by shotgun next-generation sequencing (metagenomics), which allows the identification of all viral communities in an environmental sample and the discovery of new viral families not previously described. Variations in viral quantity and diversity have been associated with disease development, mainly due to their effect on gut bacterial microbiota. Phages can regulate bacterial flora through lysogeny; this is associated with increased susceptibility to infections, chronic inflammation, or cancer. The virome characterization in different human body ecological niches could help elucidate these particles' role in disease. Hence, it is important to understand the virome's influence on human health and disease. The present review highlights the significance of the human virome and how it is associated with disease, focusing on virome composition, characterization, and its association with cancer.}, } @article {pmid36871871, year = {2023}, author = {Lei, C and Ge, H and Ding, S and Zhou, X and Yang, B and Yang, D and Wang, R and Guo, T and Yu, Y and Luo, H}, title = {Polybacterial infection in patients with stable bronchiectasis revealed by metagenomic next-generation sequencing.}, journal = {The Journal of infection}, volume = {86}, number = {4}, pages = {e81-e83}, doi = {10.1016/j.jinf.2023.02.041}, pmid = {36871871}, issn = {1532-2742}, mesh = {Humans ; *Bronchiectasis/complications ; Metagenome ; High-Throughput Nucleotide Sequencing ; }, } @article {pmid36871385, year = {2023}, author = {Liang, J and Lin, H and Singh, B and Wang, A and Yan, Z}, title = {A global perspective on compositions, risks, and ecological genesis of antibiotic resistance genes in biofilters of drinking water treatment plants.}, journal = {Water research}, volume = {233}, number = {}, pages = {119822}, doi = {10.1016/j.watres.2023.119822}, pmid = {36871385}, issn = {1879-2448}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; *Drinking Water ; beta-Lactams/pharmacology ; Drug Resistance, Microbial/genetics ; }, abstract = {Antibiotic resistance genes (ARGs) in biofilters of drinking water treatment plants (DWTPs) are regarded to be a remarkable potential health risk to human. A global survey on ARGs in biofilters may help evaluate their risk features as a whole. This study aims to explore the compositions, risks, and ecological genesis of ARGs in the biofilters of DWTPs. In total, 98 metagenomes of DWTP biofilters were collected from Sequence Read Archive (SRA) of National center for Biotechnology Information (NCBI), and the main ARG types were recognized, with multidrug, bacitracin, and beta-lactam as the first three types. Source water types (surface water vs. groundwater) were found to significantly influence antibiotic resistome, overpassing biofilter media and locations. Although ARG abundances of surface water biofilters were approximately five times higher than that of groundwater biofilters, the risk pattern of ARGs was highly similar between surface water biofilters and groundwater biofilters, and up to 99.61% of the ARGs on average belong to the least risk and unassessed ranks, and only 0.23% the highest risk rank. Monobactam biosynthesis pathway and prodigiosin biosynthesis pathway, two antibiotics biosynthesis pathways, were observed to be positively correlated with several ARG types and total ARG abundance in samples of surface water and groundwater biofilters, respectively, suggesting their potential roles in ecological genesis of ARGs. Overall, the results of this study would deepen our understanding of the ARG risks in biofilters of DWTPs and shed light on their ecological genesis inside.}, } @article {pmid36871384, year = {2023}, author = {Duan, X and Luo, J and Su, Y and Liu, C and Feng, L and Chen, Y}, title = {Proteomic profiling of robust acetoclastic methanogen in chrysene-altered anaerobic digestion: Global dissection of enzymes.}, journal = {Water research}, volume = {233}, number = {}, pages = {119817}, doi = {10.1016/j.watres.2023.119817}, pmid = {36871384}, issn = {1879-2448}, mesh = {*Sewage ; Anaerobiosis ; *Chrysenes/metabolism ; Nickel ; Proteomics ; Methanosarcina/metabolism ; Methane/metabolism ; Bioreactors ; }, abstract = {Methanogen is a pivotal player in pollution treatment and energy recovery, and emerging pollutants (EPs) frequently occur in methanogen-applied biotechnology such as anaerobic digestion (AD). However, the direct effect and underlying mechanism of EPs on crucial methanogen involved in its application still remain unclear. The positive effect of chrysene (CH) on semi-continuous AD of sludge and the robust methanogen was dissected in this study. The methane yield in the digester with CH (100 mg/kg dry sludge) was 62.1 mL/g VS substrate, much higher than that in the control (46.1 mL/g VS substrate). Both methane production from acetoclastic methanogenesis (AM) and the AM proportion in the methanogenic pathway were improved in CH-shaped AD. Acetoclastic consortia, especially Methanosarcina and functional profiles of AM were enriched by CH in favor of the corresponding methanogenesis. Further, based on pure cultivation exposed to CH, the methanogenic performance, biomass, survivability and activity of typical Methanosarcina (M. barkeri) were boosted. Notably, iTRAQ proteomics revealed that the manufacturing (transcription and translation), expression and biocatalytic activity of acetoclastic metalloenzymes, particularly tetrahydromethanopterin S-methyltransferase and methyl-coenzyme M reductase with cobalt/nickel-cofactor (F430 and cobalamin), and acetyl-CoA decarbonylase/synthase with cobalt/nickel-active site, of M. barkeri were upregulated significantly with fold changes in the range of 1.21-3.20 due to the CH presence. This study shed light on EPs-affecting industrially crucial methanogen at the molecular biology level during AD and had implications in the technical relevance of methanogens.}, } @article {pmid36871383, year = {2023}, author = {Lu, J and Zhang, B and Geng, R and Lian, G and Dong, H}, title = {Independent and synergistic bio-reductions of uranium (VI) driven by zerovalent iron in aquifer.}, journal = {Water research}, volume = {233}, number = {}, pages = {119778}, doi = {10.1016/j.watres.2023.119778}, pmid = {36871383}, issn = {1879-2448}, mesh = {*Iron/metabolism ; *Uranium ; Oxidation-Reduction ; Electron Transport ; Cytochromes c/metabolism ; }, abstract = {Zerovalent iron [Fe(0)] can donate electron for bioprocess, but microbial uranium (VI) [U(VI)] reduction driven by Fe(0) is still poorly understood. In this study, Fe(0) supported U(VI) bio-reduction was steadily achieved in the 160-d continuous-flow biological column. The maximum removal efficiency and capacity of U(VI) were 100% and 46.4 ± 0.52 g/(m[3]·d) respectively, and the longevity of Fe(0) increased by 3.09 times. U(VI) was reduced to solid UO2, while Fe(0) was finally oxidized to Fe(III). Autotrophic Thiobacillus achieved U(VI) reduction coupled to Fe(0) oxidation, verified by pure culture. H2 produced from Fe(0) corrosion was consumed by autotrophic Clostridium for U(VI) reduction. The detected residual organic intermediates were biosynthesized with energy released from Fe(0) oxidation and utilized by heterotrophic Desulfomicrobium, Bacillus and Pseudomonas to reduce U(VI). Metagenomic analysis found the upregulated genes for U(VI) reduction (e.g., dsrA and dsrB) and Fe(II) oxidation (e.g., CYC1 and mtrA). These functional genes were also transcriptionally expressed. Cytochrome c and glutathione responsible for electron transfer also contributed to U(VI) reduction. This study reveals the independent and synergistic pathways for Fe(0)-dependent U(VI) bio-reduction, providing promising remediation strategy for U(VI)-polluted aquifers.}, } @article {pmid36871189, year = {2023}, author = {Peterson, BD and Krabbenhoft, DP and McMahon, KD and Ogorek, JM and Tate, MT and Orem, WH and Poulin, BA}, title = {Environmental formation of methylmercury is controlled by synergy of inorganic mercury bioavailability and microbial mercury-methylation capacity.}, journal = {Environmental microbiology}, volume = {25}, number = {8}, pages = {1409-1423}, doi = {10.1111/1462-2920.16364}, pmid = {36871189}, issn = {1462-2920}, mesh = {*Methylmercury Compounds ; *Mercury ; Methylation ; Biological Availability ; *Microbiota ; *Water Pollutants, Chemical/analysis ; }, abstract = {Methylmercury (MeHg) production is controlled by the bioavailability of inorganic divalent mercury (Hg(II)i) and Hg-methylation capacity of the microbial community (conferred by the hgcAB gene cluster). However, the relative importance of these factors and their interaction in the environment remain poorly understood. Here, metagenomic sequencing and a full-factorial MeHg formation experiment were conducted across a wetland sulfate gradient with different microbial communities and pore water chemistries. From this experiment, the relative importance of each factor on MeHg formation was isolated. Hg(II)i bioavailability correlated with the dissolved organic matter composition, while the microbial Hg-methylation capacity correlated with the abundance of hgcA genes. MeHg formation responded synergistically to both factors. Notably, hgcA sequences were from diverse taxonomic groups, none of which contained genes for dissimilatory sulfate reduction. This work expands our understanding of the geochemical and microbial constraints on MeHg formation in situ and provides an experimental framework for further mechanistic studies.}, } @article {pmid36871069, year = {2023}, author = {Nowinski, B and Feng, X and Preston, CM and Birch, JM and Luo, H and Whitman, WB and Moran, MA}, title = {Ecological divergence of syntopic marine bacterial species is shaped by gene content and expression.}, journal = {The ISME journal}, volume = {17}, number = {6}, pages = {813-822}, pmid = {36871069}, issn = {1751-7370}, mesh = {RNA, Ribosomal, 16S/genetics/analysis ; *Genes, Bacterial ; *Rhodobacteraceae/genetics ; Phytoplankton/genetics ; Genomics ; Phylogeny ; Genome, Bacterial ; Seawater/microbiology ; }, abstract = {Identifying mechanisms by which bacterial species evolve and maintain genomic diversity is particularly challenging for the uncultured lineages that dominate the surface ocean. A longitudinal analysis of bacterial genes, genomes, and transcripts during a coastal phytoplankton bloom revealed two co-occurring, highly related Rhodobacteraceae species from the deeply branching and uncultured NAC11-7 lineage. These have identical 16S rRNA gene amplicon sequences, yet their genome contents assembled from metagenomes and single cells indicate species-level divergence. Moreover, shifts in relative dominance of the species during dynamic bloom conditions over 7 weeks confirmed the syntopic species' divergent responses to the same microenvironment at the same time. Genes unique to each species and genes shared but divergent in per-cell inventories of mRNAs accounted for 5% of the species' pangenome content. These analyses uncover physiological and ecological features that differentiate the species, including capacities for organic carbon utilization, attributes of the cell surface, metal requirements, and vitamin biosynthesis. Such insights into the coexistence of highly related and ecologically similar bacterial species in their shared natural habitat are rare.}, } @article {pmid36871005, year = {2023}, author = {Wu, TT and Sohn, M and Manning, S and Beblavy, R and Gill, S and Quataert, S and Vasani, S and Jang, H and Zeng, Y and Bruno, J and Vazquez, A and Fiscella, K and Xiao, J}, title = {Metagenomic analysis examines oral microbiome changes and interplay with immune response following prenatal total oral rehabilitation.}, journal = {Journal of translational medicine}, volume = {21}, number = {1}, pages = {172}, pmid = {36871005}, issn = {1479-5876}, support = {K23 DE027412/DE/NIDCR NIH HHS/United States ; R01 DE031025/DE/NIDCR NIH HHS/United States ; R01DE031025/DE/NIDCR NIH HHS/United States ; K23DE027412/DE/NIDCR NIH HHS/United States ; }, mesh = {Pregnancy ; Child ; Female ; Humans ; Infant, Newborn ; *Dental Caries ; Prospective Studies ; *Microbiota ; Physical Therapy Modalities ; Family ; }, abstract = {BACKGROUND: Suboptimal maternal oral health during pregnancy is potentially associated with adverse birth outcomes and increased dental caries risks in children. This study aimed to assess the oral microbiome and immune response following an innovative clinical regimen, Prenatal Total Oral Rehabilitation (PTOR), that fully restores women's oral health to a "disease-free status" before delivery.

METHODS: This prospective cohort study assessed 15 pregnant women at baseline and 3 follow-up visits (1 week, 2 weeks, and 2 months) after receiving PTOR. The salivary and supragingival plaque microbiomes were analyzed using metagenomic sequencing. Multiplexed Luminex cytokine assays were performed to examine immune response following PTOR. The association between salivary immune markers and oral microbiome was further examined.

RESULTS: PTOR was associated with a reduction of periodontal pathogens in plaque, for instance, a lower relative abundance of Tannerella forsythia and Treponema denticola at 2 weeks compared to the baseline (p < 0.05). The alpha diversity of plaque microbial community was significantly reduced at the 1-week follow-up (p < 0.05). Furthermore, we observed significant changes in the Actinomyces defective-associated carbohydrate degradation pathway and Streptococcus Gordonii-associated fatty acid biosynthesis pathway. Two immune markers related to adverse birth outcomes significantly differed between baseline and follow-up. ITAC, negatively correlated with preeclampsia severity, significantly increased at 1-week follow-up; MCP-1, positively correlated with gestational age, was elevated at 1-week follow-up. Association modeling between immune markers and microbiome further revealed specific oral microorganisms that are potentially correlated with the host immune response.

CONCLUSIONS: PTOR is associated with alteration of the oral microbiome and immune response among a cohort of underserved US pregnant women. Future randomized clinical trials are warranted to comprehensively assess the impact of PTOR on maternal oral flora, birth outcomes, and their offspring's oral health.}, } @article {pmid36869541, year = {2023}, author = {Herrera-Rocha, F and Fernández-Niño, M and Cala, MP and Duitama, J and Barrios, AFG}, title = {Omics approaches to understand cocoa processing and chocolate flavor development: A review.}, journal = {Food research international (Ottawa, Ont.)}, volume = {165}, number = {}, pages = {112555}, doi = {10.1016/j.foodres.2023.112555}, pmid = {36869541}, issn = {1873-7145}, mesh = {*Chocolate ; *Cacao ; Food ; *Bacillus ; Candida ; }, abstract = {The global market of chocolate has increased worldwide during the last decade and is expected to reach a value of USD 200 billion by 2028. Chocolate is obtained from different varieties of Theobroma cacao L, a plant domesticated more than 4000 years ago in the Amazon rainforest. However, chocolate production is a complex process requiring extensive post-harvesting, mainly involving cocoa bean fermentation, drying, and roasting. These steps have a critical impact on chocolate quality. Standardizing and better understanding cocoa processing is, therefore, a current challenge to boost the global production of high-quality cocoa worldwide. This knowledge can also help cocoa producers improve cocoa processing management and obtain a better chocolate. Several recent studies have been conducted to dissect cocoa processing via omics analysis. A vast amount of data has been produced regarding omics studies of cocoa processing performed worldwide. This review systematically analyzes the current data on cocoa omics using data mining techniques and discusses opportunities and gaps for cocoa processing standardization from this data. First, we observed a recurrent report in metagenomics studies of species of the fungi genus Candida and Pichia as well as bacteria from the genus Lactobacillus, Acetobacter, and Bacillus. Second, our analyzes of the available metabolomics data showed clear differences in the identified metabolites in cocoa and chocolate from different geographical origin, cocoa type, and processing stage. Finally, our analysis of peptidomics data revealed characteristic patterns in the gathered data including higher diversity and lower size distribution of peptides in fine-flavor cocoa. In addition, we discuss the current challenges in cocoa omics research. More research is still required to fill gaps in central matter in chocolate production as starter cultures for cocoa fermentation, flavor evolution of cocoa, and the role of peptides in the development of specific flavor notes. We also offer the most comprehensive collection of multi-omics data in cocoa processing gathered from different research articles.}, } @article {pmid36869370, year = {2023}, author = {Gu, F and Zhu, S and Tang, Y and Liu, X and Jia, M and Malmuthuge, N and Valencak, TG and McFadden, JW and Liu, JX and Sun, HZ}, title = {Gut microbiome is linked to functions of peripheral immune cells in transition cows during excessive lipolysis.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {40}, pmid = {36869370}, issn = {2049-2618}, mesh = {Female ; Animals ; Cattle ; *Gastrointestinal Microbiome ; Lipolysis ; Bacteroides ; Down-Regulation ; Metabolome ; }, abstract = {BACKGROUND: Postpartum dairy cows experiencing excessive lipolysis are prone to severe immunosuppression. Despite the extensive understanding of the gut microbial regulation of host immunity and metabolism, its role during excessive lipolysis in cows is largely unknown. Herein, we investigated the potential links between the gut microbiome and postpartum immunosuppression in periparturient dairy cows with excessive lipolysis using single immune cell transcriptome, 16S amplicon sequencing, metagenomics, and targeted metabolomics.

RESULTS: The use of single-cell RNA sequencing identified 26 clusters that were annotated to 10 different immune cell types. Enrichment of functions of these clusters revealed a downregulation of functions in immune cells isolated from a cow with excessive lipolysis compared to a cow with low/normal lipolysis. The results of metagenomic sequencing and targeted metabolome analysis together revealed that secondary bile acid (SBA) biosynthesis was significantly activated in the cows with excessive lipolysis. Moreover, the relative abundance of gut Bacteroides sp. OF04 - 15BH, Paraprevotella clara, Paraprevotella xylaniphila, and Treponema sp. JC4 was mainly associated with SBA synthesis. The use of an integrated analysis showed that the reduction of plasma glycolithocholic acid and taurolithocholic acid could contribute to the immunosuppression of monocytes (CD14[+]MON) during excessive lipolysis by decreasing the expression of GPBAR1.

CONCLUSIONS: Our results suggest that alterations in the gut microbiota and their functions related to SBA synthesis suppressed the functions of monocytes during excessive lipolysis in transition dairy cows. Therefore, we concluded that altered microbial SBA synthesis during excessive lipolysis could lead to postpartum immunosuppression in transition cows. Video Abstract.}, } @article {pmid36869137, year = {2023}, author = {Rifkin, RF and Vikram, S and Alcorta, J and Ramond, JB and Cowan, DA and Jakobsson, M and Schlebusch, CM and Lombard, M}, title = {Rickettsia felis DNA recovered from a child who lived in southern Africa 2000 years ago.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {240}, pmid = {36869137}, issn = {2399-3642}, support = {NGS-371R-18//National Geographic Society/ ; }, mesh = {Humans ; Child ; *Rickettsia felis ; Africa, Southern ; DNA ; South Africa ; DNA, Ancient ; }, abstract = {The Stone Age record of South Africa provides some of the earliest evidence for the biological and cultural origins of Homo sapiens. While there is extensive genomic evidence for the selection of polymorphisms in response to pathogen-pressure in sub-Saharan Africa, e.g., the sickle cell trait which provides protection against malaria, there is inadequate direct human genomic evidence for ancient human-pathogen infection in the region. Here, we analysed shotgun metagenome libraries derived from the sequencing of a Later Stone Age hunter-gatherer child who lived near Ballito Bay, South Africa, c. 2000 years ago. This resulted in the identification of ancient DNA sequence reads homologous to Rickettsia felis, the causative agent of typhus-like flea-borne rickettsioses, and the reconstruction of an ancient R. felis genome.}, } @article {pmid36868257, year = {2023}, author = {Rubin, DH and Mortimer, TD and Grad, YH}, title = {Neisseria gonorrhoeae diagnostic escape from a gyrA-based test for ciprofloxacin susceptibility and the effect on zoliflodacin resistance: a bacterial genetics and experimental evolution study.}, journal = {The Lancet. Microbe}, volume = {4}, number = {4}, pages = {e247-e254}, pmid = {36868257}, issn = {2666-5247}, support = {R01 AI132606/AI/NIAID NIH HHS/United States ; R01 AI153521/AI/NIAID NIH HHS/United States ; F30 AI160911/AI/NIAID NIH HHS/United States ; F32 AI145157/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Ciprofloxacin/pharmacology ; Neisseria gonorrhoeae/genetics ; *Gonorrhea/epidemiology/genetics/microbiology ; DNA Gyrase/genetics/pharmacology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {BACKGROUND: The aetiological bacterial agent of gonorrhoea, Neisseria gonorrhoeae, has become resistant to each of the first-line antibiotics used to treat it, including ciprofloxacin. One diagnostic approach to identify ciprofloxacin-susceptible isolates is to determine codon 91 in the gene encoding the A subunit of DNA gyrase, gyrA, where coding for the wild-type serine (gyrA[91S]) is associated with ciprofloxacin susceptibility and phenylalanine (gyrA[91F]) with resistance. The aim of this study was to investigate the possibility of diagnostic escape from gyrA susceptibility testing.

METHODS: We used bacterial genetics to introduce pairwise substitutions in GyrA positions 91 (S or F) and 95 (D, G, or N), which is a second site in GyrA associated with ciprofloxacin resistance, into five clinical isolates of N gonorrhoeae. All five isolates encoded GyrA S91F, an additional substitution in GyrA at position 95, substitutions in ParC that are known to cause an increased minimum inhibitory concentration (MIC) to ciprofloxacin, and GyrB 429D, which is associated with susceptibility to zoliflodacin (a spiropyrimidinetrione-class antibiotic in phase 3 trials for treatment of gonorrhoea). We evolved these isolates to assess for the existence of pathways to ciprofloxacin resistance (MIC ≥1 μg/mL) and measured MICs for ciprofloxacin and zoliflodacin. In parallel, we searched metagenomic data for 11 355 N gonorrhoeae clinical isolates with reported ciprofloxacin MICs that were publicly available from the European Nucleotide Archive for strains that would be identified as susceptible by gyrA codon 91-based assays.

FINDINGS: Three clinical isolates of N gonorrhoeae with substitutions in GyrA position 95 associated with resistance (G or N) maintained intermediate ciprofloxacin MICs (0·125-0·5 μg/mL), which has been associated with treatment failure, despite reversion of GyrA position 91 from phenylalanine to serine. From an in-silico analysis of the 11 355 genomes from N gonorrhoeae clinical isolates, we identified 30 isolates with gyrA codon 91 encoding a serine and a ciprofloxacin resistance-associated mutation at codon 95. The reported MICs for these isolates varied from 0·023 μg/mL to 0·25 μg/mL, including four with intermediate ciprofloxacin MICs (associated with substantially increased risk of treatment failure). Finally, through experimental evolution, one clinical isolate of N gonorrhoeae bearing GyrA 91S acquired ciprofloxacin resistance through mutations in the gene encoding for the B subunit of DNA gyrase (gyrB) that also conferred reduced susceptibility to zoliflodacin (ie, MIC ≥2 μg/mL).

INTERPRETATION: Diagnostic escape from gyrA codon 91 diagnostics could occur through either reversion of the gyrA allele or expansion of circulating lineages. N gonorrhoeae genomic surveillance efforts might benefit from including gyrB, given its potential for contributing to ciprofloxacin and zoliflodacin resistance, and diagnostic strategies that reduce the likelihood of escape, such as the incorporation of multiple target sites, should be investigated. Diagnostics that guide antibiotic therapy can have unintended consequences, including novel resistance determinants and antibiotic cross-resistance.

FUNDING: US National Institutes of Health National Institute of Allergy and Infectious Diseases, National Institute of General Medical Sciences, and the Smith Family Foundation.}, } @article {pmid36868119, year = {2023}, author = {Corbera-Rubio, F and Laureni, M and Koudijs, N and Müller, S and van Alen, T and Schoonenberg, F and Lücker, S and Pabst, M and van Loosdrecht, MCM and van Halem, D}, title = {Meta-omics profiling of full-scale groundwater rapid sand filters explains stratification of iron, ammonium and manganese removals.}, journal = {Water research}, volume = {233}, number = {}, pages = {119805}, doi = {10.1016/j.watres.2023.119805}, pmid = {36868119}, issn = {1879-2448}, mesh = {Manganese/chemistry ; Iron ; *Ammonium Compounds/chemistry ; Ammonia ; Quartz ; Ecosystem ; *Groundwater/chemistry ; Filtration/methods ; *Water Purification/methods ; }, abstract = {Rapid sand filters (RSF) are an established and widely applied technology for groundwater treatment. Yet, the underlying interwoven biological and physical-chemical reactions controlling the sequential removal of iron, ammonia and manganese remain poorly understood. To resolve the contribution and interactions between the individual reactions, we studied two full-scale drinking water treatment plant configurations, namely (i) one dual-media (anthracite and quartz sand) filter and (ii) two single-media (quartz sand) filters in series. In situ and ex situ activity tests were combined with mineral coating characterization and metagenome-guided metaproteomics along the depth of each filter. Both plants exhibited comparable performances and process compartmentalization, with most of ammonium and manganese removal occurring only after complete iron depletion. The homogeneity of the media coating and genome-based microbial composition within each compartment highlighted the effect of backwashing, namely the complete vertical mixing of the filter media. In stark contrast to this homogeneity, the removal of the contaminants was strongly stratified within each compartment, and decreased along the filter height. This apparent and longstanding conflict was resolved by quantifying the expressed proteome at different filter heights, revealing a consistent stratification of proteins catalysing ammonia oxidation and protein-based relative abundances of nitrifying genera (up to 2 orders of magnitude difference between top and bottom samples). This implies that microorganisms adapt their protein pool to the available nutrient load at a faster rate than the backwash mixing frequency. Ultimately, these results show the unique and complementary potential of metaproteomics to understand metabolic adaptations and interactions in highly dynamic ecosystems.}, } @article {pmid36868117, year = {2023}, author = {Hu, ZY and Lin, YP and Wang, QT and Zhang, YX and Tang, J and Hong, SD and Dai, K and Wang, S and Lu, YZ and van Loosdrecht, MCM and Wu, J and Zeng, RJ and Zhang, F}, title = {Identification and degradation of structural extracellular polymeric substances in waste activated sludge via a polygalacturonate-degrading consortium.}, journal = {Water research}, volume = {233}, number = {}, pages = {119800}, doi = {10.1016/j.watres.2023.119800}, pmid = {36868117}, issn = {1879-2448}, mesh = {*Sewage/chemistry ; *Waste Disposal, Fluid/methods ; Extracellular Polymeric Substance Matrix ; Methane ; Anaerobiosis ; }, abstract = {By maintaining the cell integrity of waste activated sludge (WAS), structural extracellular polymeric substances (St-EPS) resist WAS anaerobic fermentation. This study investigates the occurrence of polygalacturonate in WAS St-EPS by combining chemical and metagenomic analyses that identify ∼22% of the bacteria, including Ferruginibacter and Zoogloea, that are associated with polygalacturonate production using the key enzyme EC 5.1.3.6. A highly active polygalacturonate-degrading consortium (GDC) was enriched and the potential of this GDC for degrading St-EPS and promoting methane production from WAS was investigated. The percentage of St-EPS degradation increased from 47.6% to 85.2% after inoculation with the GDC. Methane production was also increased by up to 2.3 times over a control group, with WAS destruction increasing from 11.5% to 28.4%. Zeta potential and rheological behavior confirmed the positive effect which GDC has on WAS fermentation. The major genus in the GDC was identified as Clostridium (17.1%). Extracellular pectate lyases (EC 4.2.2.2 and 4.2.2.9), excluding polygalacturonase (EC 3.2.1.15), were observed in the metagenome of the GDC and most likely play a core role in St-EPS hydrolysis. Dosing with GDC provides a good biological method for St-EPS degradation and thereby enhances the conversion of WAS to methane.}, } @article {pmid36868045, year = {2023}, author = {Sagar, P and Aseem, A and Banjara, SK and Veleri, S}, title = {The role of food chain in antimicrobial resistance spread and One Health approach to reduce risks.}, journal = {International journal of food microbiology}, volume = {391-393}, number = {}, pages = {110148}, doi = {10.1016/j.ijfoodmicro.2023.110148}, pmid = {36868045}, issn = {1879-3460}, mesh = {Humans ; *Drug Resistance, Bacterial/genetics ; Anti-Bacterial Agents/pharmacology ; Food Chain ; *One Health ; Metagenomics ; }, abstract = {The incidence of antimicrobial resistance (AMR) is rapidly spreading worldwide. It is depleting the repertoire of antibiotics in use but the pace of development of new antibiotics is stagnant for decades. Annually, millions of people are killed by AMR. This alarming situation urged both scientific and civil bodies to take steps to curb AMR as a top priority. Here we review the various sources of AMR in the environment, especially focusing on the food chain. Food chain inculcates pathogens with AMR genes and serves as a conduit for its transmission. In certain countries, the antibiotics are more used in livestock than in humans. It is also used in agriculture crops of high value products. The indiscriminate use of antibiotics in livestock and agriculture increased rapid emergence of AMR pathogens. In addition, in many countries nosocomial settings are spewing AMR pathogens, which is a serious health hazard. Both the developed and low and middle income countries (LMIC) face the phenomenon of AMR. Therefore, a comprehensive approach for monitoring all sectors of life is required to identify the emerging trend of AMR in environment. AMR genes' mode of action must be understood to develop strategies to reduce risk. The new generation sequencing technologies, metagenomics and bioinformatics capabilities can be resorted to quickly identify and characterize AMR genes. The sampling for AMR monitoring can be done from multiples nodes of the food chain as envisioned and promoted by the WHO, FAO, OIE and UNEP under the One Health approach to overcome threat of AMR pathogens.}, } @article {pmid36867161, year = {2023}, author = {Wright, RJ and Comeau, AM and Langille, MGI}, title = {From defaults to databases: parameter and database choice dramatically impact the performance of metagenomic taxonomic classification tools.}, journal = {Microbial genomics}, volume = {9}, number = {3}, pages = {}, pmid = {36867161}, issn = {2057-5858}, mesh = {Humans ; *Metagenome ; *Microbiota ; Databases, Factual ; Metagenomics ; }, abstract = {In metagenomic analyses of microbiomes, one of the first steps is usually the taxonomic classification of reads by comparison to a database of previously taxonomically classified genomes. While different studies comparing metagenomic taxonomic classification methods have determined that different tools are 'best', there are two tools that have been used the most to-date: Kraken (k-mer-based classification against a user-constructed database) and MetaPhlAn (classification by alignment to clade-specific marker genes), the latest versions of which are Kraken2 and MetaPhlAn 3, respectively. We found large discrepancies in both the proportion of reads that were classified as well as the number of species that were identified when we used both Kraken2 and MetaPhlAn 3 to classify reads within metagenomes from human-associated or environmental datasets. We then investigated which of these tools would give classifications closest to the real composition of metagenomic samples using a range of simulated and mock samples and examined the combined impact of tool-parameter-database choice on the taxonomic classifications given. This revealed that there may not be a one-size-fits-all 'best' choice. While Kraken2 can achieve better overall performance, with higher precision, recall and F1 scores, as well as alpha- and beta-diversity measures closer to the known composition than MetaPhlAn 3, the computational resources required for this may be prohibitive for many researchers, and the default database and parameters should not be used. We therefore conclude that the best tool-parameter-database choice for a particular application depends on the scientific question of interest, which performance metric is most important for this question and the limit of available computational resources.}, } @article {pmid36867151, year = {2023}, author = {Liu, D and Li, G and Hong, Z and Zhang, C and Zhu, N and Tan, Y and Gao, T}, title = {Prevalence of Multidrug-Resistant Organisms in Healthy Adults in Shenzhen, China.}, journal = {Health security}, volume = {21}, number = {2}, pages = {122-129}, doi = {10.1089/hs.2022.0111}, pmid = {36867151}, issn = {2326-5108}, mesh = {Humans ; Adult ; Prevalence ; *Drug Resistance, Multiple, Bacterial/genetics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; Cephalosporins ; China/epidemiology ; }, abstract = {Public health problems caused by the high transmission of multidrug-resistant organisms (MDROs) have attracted widespread international attention. However, studies on healthy adults in this field are scarce. In this article, we report the microbiological screening results of 180 healthy adults recruited from 1,222 participants between 2019 and 2022 in Shenzhen, China. Findings show a high MDRO carriage rate of 26.7% in those individuals who did not use any antibiotics in the past 6 months and had not been hospitalized within the past year. MDROs were mainly extended-spectrum β-lactamase-producing Escherichia coli with high resistance to cephalosporin. With the assistance of metagenomic sequencing technology, we also performed long-term observations of several participants and found that drug-resistant gene fragments were prevalent even when MDROs were not detected by drug sensitivity testing. Based on our findings, we suggest that healthcare regulators limit the medical overuse of antibiotics and enact measures to limit its nonmedical use.}, } @article {pmid36866839, year = {2023}, author = {Li, C and Zhang, Q and Wen, Y}, title = {Intestinal tuberculosis presented as spindle cell pseudotumor in a HIV-positive case.}, journal = {Revista espanola de enfermedades digestivas}, volume = {115}, number = {12}, pages = {723-724}, doi = {10.17235/reed.2023.9533/2023}, pmid = {36866839}, issn = {1130-0108}, mesh = {Male ; Humans ; Adult ; *Tuberculosis, Lymph Node ; *Peritonitis, Tuberculous ; *Tuberculosis, Gastrointestinal/complications/diagnosis ; *HIV Seropositivity ; *Mycobacterium tuberculosis ; }, abstract = {MSP is a rare and atypical form of benign granulomatous inflammation characterised by tumour-like local proliferation of spindle-shaped histiocytes containing acid-fast positive mycobacteria, which should be differentiated from neoplastic lesions. A 26-year-old Chinese man complained an intermittent and mild right lower abdominal pain for 5 months in May 2022.Histopathology of biopsy samples showed Mycobacterial spindle cell pseudotumor (MSP). The test of Mycobacterium tuberculosis detected by polymerase chain reaction using intestinal tissue slice was negative. The metagenomic next-generation sequencing (BGI-Shenzhen) using formalin-fixation and paraffin-embedded intestine samples confirmed Mycobacterium tuberculosis complex (MTBC).}, } @article {pmid36866565, year = {2022}, author = {Arzamasov, AA and Osterman, AL}, title = {Milk glycan metabolism by intestinal bifidobacteria: insights from comparative genomics.}, journal = {Critical reviews in biochemistry and molecular biology}, volume = {57}, number = {5-6}, pages = {562-584}, pmid = {36866565}, issn = {1549-7798}, support = {R01 DK030292/DK/NIDDK NIH HHS/United States ; }, mesh = {Infant ; Infant, Newborn ; Child ; Humans ; *Bifidobacterium/genetics/metabolism ; *Prebiotics/analysis ; Milk, Human/chemistry/metabolism ; Polysaccharides/metabolism ; Carbohydrates/analysis ; Genomics ; }, abstract = {Bifidobacteria are early colonizers of the human neonatal gut and provide multiple health benefits to the infant, including inhibiting the growth of enteropathogens and modulating the immune system. Certain Bifidobacterium species prevail in the gut of breastfed infants due to the ability of these microorganisms to selectively forage glycans present in human milk, specifically human milk oligosaccharides (HMOs) and N-linked glycans. Therefore, these carbohydrates serve as promising prebiotic dietary supplements to stimulate the growth of bifidobacteria in the guts of children suffering from impaired gut microbiota development. However, the rational formulation of milk glycan-based prebiotics requires a detailed understanding of how bifidobacteria metabolize these carbohydrates. Accumulating biochemical and genomic data suggest that HMO and N-glycan assimilation abilities vary remarkably within the Bifidobacterium genus, both at the species and strain levels. This review focuses on the delineation and genome-based comparative analysis of differences in respective biochemical pathways, transport systems, and associated transcriptional regulatory networks, providing a foundation for genomics-based projection of milk glycan utilization capabilities across a rapidly growing number of sequenced bifidobacterial genomes and metagenomic datasets. This analysis also highlights remaining knowledge gaps and suggests directions for future studies to optimize the formulation of milk-glycan-based prebiotics that target bifidobacteria.}, } @article {pmid36865780, year = {2023}, author = {Feng, J and Zhou, L and Zhao, X and Chen, J and Li, Z and Liu, Y and Ou, L and Xie, Z and Wang, M and Yin, X and Zhang, X and Li, Y and Luo, M and Zeng, L and Yan, Q and Xie, L and Sun, L}, title = {Evaluation of environmental factors and microbial community structure in an important drinking-water reservoir across seasons.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1091818}, pmid = {36865780}, issn = {1664-302X}, abstract = {The composition of microbial communities varies in water and sediments, and changes in environmental factors have major effects on microbiomes. Here, we characterized variations in microbial communities and physicochemical factors at two sites in a large subtropical drinking water reservoir in southern China. The microbiomes of all sites, including the diversity and abundance of microbial species, were determined via metagenomics, and the relationships between microbiomes and physicochemical factors were determined via redundancy analysis. The dominant species in sediment and water samples differed; Dinobryon sp. LO226KS and Dinobryon divergens were dominant in sediment samples, whereas Candidatus Fonsibacter ubiquis and Microcystis elabens were dominant in water. The diversity was also significantly different in microbial alpha diversity between water and sediment habitats (p < 0.01). The trophic level index (TLI) was the major factor affecting the microbial community in water samples; Mycolicibacterium litorale and Mycolicibacterium phlei were significantly positively related to TLI. Furthermore, we also studied the distribution of algal toxin-encoding genes and antibiotic-resistant genes (ARGs) in the reservoir. It found that water samples contained more phycotoxin genes, with the cylindrospermopsin gene cluster most abundant. We found three genera highly related to cylindrospermopsin and explored a new cyanobacteria Aphanocapsa montana that may produce cylindrospermopsin based on the correlation through network analysis. The multidrug resistance gene was the most abundant ARG, while the relationship between ARGs and bacteria in sediment samples was more complicated than in water. The results of this study enhance our understanding of the effects of environmental factors on microbiomes. In conclusion, research on the properties, including profiles of algal toxin-encoding genes and ARGs, and microbial communities can aid water quality monitoring and conservation.}, } @article {pmid36865186, year = {2023}, author = {Robitaille, S and Simmons, EL and Verster, AJ and McClure, EA and Royce, DB and Trus, E and Swartz, K and Schultz, D and Nadell, CD and Ross, BD}, title = {Community composition and the environment modulate the population dynamics of type VI secretion in human gut bacteria.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36865186}, support = {P20 GM113132/GM/NIGMS NIH HHS/United States ; P20 GM130454/GM/NIGMS NIH HHS/United States ; R00 GM129874/GM/NIGMS NIH HHS/United States ; R35 GM142685/GM/NIGMS NIH HHS/United States ; }, abstract = {Understanding the relationship between the composition of the human gut microbiota and the ecological forces shaping it is of high importance as progress towards therapeutic modulation of the microbiota advances. However, given the inaccessibility of the gastrointestinal tract, our knowledge of the biogeographical and ecological relationships between physically interacting taxa has been limited to date. It has been suggested that interbacterial antagonism plays an important role in gut community dynamics, but in practice the conditions under which antagonistic behavior is favored or disfavored by selection in the gut environment are not well known. Here, using phylogenomics of bacterial isolate genomes and analysis of infant and adult fecal metagenomes, we show that the contact-dependent type VI secretion system (T6SS) is repeatedly lost from the genomes of Bacteroides fragilis in adults compare to infants. Although this result implies a significant fitness cost to the T6SS, but we could not identify in vitro conditions under which such a cost manifests. Strikingly, however, experiments in mice illustrated that the B. fragilis T6SS can be favored or disfavored in the gut environment, depending on the strains and species in the surrounding community and their susceptibility to T6SS antagonism. We use a variety of ecological modeling techniques to explore the possible local community structuring conditions that could underlie the results of our larger scale phylogenomic and mouse gut experimental approaches. The models illustrate robustly that the pattern of local community structuring in space can modulate the extent of interactions between T6SS-producing, sensitive, and resistant bacteria, which in turn control the balance of fitness costs and benefits of performing contact-dependent antagonistic behavior. Taken together, our genomic analyses, in vivo studies, and ecological theory point toward new integrative models for interrogating the evolutionary dynamics of type VI secretion and other predominant modes of antagonistic interaction in diverse microbiomes.}, } @article {pmid36864882, year = {2023}, author = {Wang, M and Yan, LY and Qiao, CY and Zheng, CC and Niu, CG and Huang, ZW and Pan, YH}, title = {Ecological shifts of salivary microbiota associated with metabolic-associated fatty liver disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1131255}, pmid = {36864882}, issn = {2235-2988}, mesh = {Humans ; Metagenome ; *Microbiota ; *Non-alcoholic Fatty Liver Disease/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; }, abstract = {INTRODUCTION: Metabolic-associated fatty liver disease (MAFLD) is the most common chronic liver disease related to metabolic syndrome. However, ecological shifts in the saliva microbiome in patients with MAFLD remain unknown. This study aimed to investigate the changes to the salivary microbial community in patients with MAFLD and explore the potential function of microbiota.

METHODS: Salivary microbiomes from ten MAFLD patients and ten healthy participants were analyzed by 16S rRNA amplicon sequencing and bioinformatics analysis. Body composition, plasma enzymes, hormones, and blood lipid profiles were assessed with physical examinations and laboratory tests.

RESULTS: The salivary microbiome of MAFLD patients was characterized by increased α-diversity and distinct β-diversity clustering compared with control subjects. Linear discriminant analysis effect size analysis showed a total of 44 taxa significantly differed between the two groups. Genera Neisseria, Filifactor, and Capnocytophaga were identified as differentially enriched genera for comparison of the two groups. Co-occurrence networks suggested that the salivary microbiota from MAFLD patients exhibited more intricate and robust interrelationships. The diagnostic model based on the salivary microbiome achieved a good diagnostic power with an area under the curve of 0.82(95% CI: 0.61-1). Redundancy analysis and spearman correlation analysis revealed that clinical variables related to insulin resistance and obesity were strongly associated with the microbial community. Metagenomic predictions based on Phylogenetic Investigation of Communities by Reconstruction of Unobserved States revealed that pathways related to metabolism were more prevalent in the two groups.

CONCLUSIONS: Patients with MAFLD manifested ecological shifts in the salivary microbiome, and the saliva microbiome-based diagnostic model provides a promising approach for auxiliary MAFLD diagnosis.}, } @article {pmid36864573, year = {2023}, author = {Cheung, MK and Ng, RWY and Lai, CKC and Zhu, C and Au, ETK and Yau, JWK and Li, C and Wong, HC and Wong, BCK and Kwok, KO and Chen, Z and Chan, PKS and Lui, GCY and Ip, M}, title = {Alterations in faecal microbiome and resistome in Chinese international travellers: a metagenomic analysis.}, journal = {Journal of travel medicine}, volume = {30}, number = {6}, pages = {}, pmid = {36864573}, issn = {1708-8305}, support = {//The Chinese University of Hong Kong/ ; //Health and Medical Research Fund/ ; 18170082//Food and Health Bureau of the Hong Kong Special Administrative Region, China/ ; }, mesh = {Adult ; Humans ; Anti-Bacterial Agents/pharmacology ; Antimalarials/pharmacology ; Doxycycline ; East Asian People ; *Microbiota/genetics/physiology ; *Feces/microbiology ; Drug Resistance, Bacterial/genetics ; }, abstract = {BACKGROUND: International travel increases the risk of acquisition of antibiotic-resistant bacteria and antibiotic resistance genes (ARGs). Previous studies have characterized the changes in the gut microbiome and resistome of Western travellers; however, information on non-Western populations and the effects of travel-related risk factors on the gut microbiome and resistome remains limited.

METHODS: We conducted a prospective observational study on a cohort of 90 healthy Chinese adult residents of Hong Kong. We characterized the microbiome and resistome in stools collected from the subjects before and after travelling to diverse international locations using shotgun metagenomic sequencing and examined their associations with travel-related variables.

RESULTS: Our results showed that travel neither significantly changed the taxonomic composition of the faecal microbiota nor altered the alpha (Shannon) or beta diversity of the faecal microbiome or resistome. However, travel significantly increased the number of ARGs. Ten ARGs, including aadA, TEM, mgrB, mphA, qnrS9 and tetR, were significantly enriched in relative abundance after travel, eight of which were detected in metagenomic bins belonging to Escherichia/Shigella flexneri in the post-trip samples. In sum, 30 ARGs significantly increased in prevalence after travel, with the largest changes observed in tetD and a few qnrS variants (qnrS9, qnrS and qnrS8). We found that travel to low- or middle-income countries, or Africa or Southeast Asia, increased the number of ARG subtypes, whereas travel to low- or middle-income countries and the use of alcohol-based hand sanitizer (ABHS) or doxycycline as antimalarial prophylaxis during travel resulted in increased changes in the beta diversity of the faecal resistome.

CONCLUSIONS: Our study highlights travel to low- or middle-income countries, Africa or Southeast Asia, a long travel duration, or the use of ABHS or doxycycline as antimalarial prophylaxis as important risk factors for the acquisition/enrichment of ARGs during international travel.}, } @article {pmid36864529, year = {2023}, author = {Zhang, C and Fang, YX and Yin, X and Lai, H and Kuang, Z and Zhang, T and Xu, XP and Wegener, G and Wang, JH and Dong, X}, title = {The majority of microorganisms in gas hydrate-bearing subseafloor sediments ferment macromolecules.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {37}, pmid = {36864529}, issn = {2049-2618}, mesh = {*Methane ; Alkanes ; Carbon ; China ; *Chloroflexi ; }, abstract = {BACKGROUND: Gas hydrate-bearing subseafloor sediments harbor a large number of microorganisms. Within these sediments, organic matter and upward-migrating methane are important carbon and energy sources fueling a light-independent biosphere. However, the type of metabolism that dominates the deep subseafloor of the gas hydrate zone is poorly constrained. Here we studied the microbial communities in gas hydrate-rich sediments up to 49 m below the seafloor recovered by drilling in the South China Sea. We focused on distinct geochemical conditions and performed metagenomic and metatranscriptomic analyses to characterize microbial communities and their role in carbon mineralization.

RESULTS: Comparative microbial community analysis revealed that samples above and in sulfate-methane interface (SMI) zones were clearly distinguished from those below the SMI. Chloroflexota were most abundant above the SMI, whereas Caldatribacteriota dominated below the SMI. Verrucomicrobiota, Bathyarchaeia, and Hadarchaeota were similarly present in both types of sediment. The genomic inventory and transcriptional activity suggest an important role in the fermentation of macromolecules. In contrast, sulfate reducers and methanogens that catalyze the consumption or production of commonly observed chemical compounds in sediments are rare. Methanotrophs and alkanotrophs that anaerobically grow on alkanes were also identified to be at low abundances. The ANME-1 group actively thrived in or slightly below the current SMI. Members from Heimdallarchaeia were found to encode the potential for anaerobic oxidation of short-chain hydrocarbons.

CONCLUSIONS: These findings indicate that the fermentation of macromolecules is the predominant energy source for microorganisms in deep subseafloor sediments that are experiencing upward methane fluxes. Video Abstract.}, } @article {pmid36864482, year = {2023}, author = {Lou, YC and Hoff, J and Olm, MR and West-Roberts, J and Diamond, S and Firek, BA and Morowitz, MJ and Banfield, JF}, title = {Using strain-resolved analysis to identify contamination in metagenomics data.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {36}, pmid = {36864482}, issn = {2049-2618}, support = {R01 AI092531/AI/NIAID NIH HHS/United States ; RAI092531A/NH/NIH HHS/United States ; }, mesh = {*Metagenomics ; Biomass ; DNA Contamination ; *Microbiota/genetics ; DNA ; }, abstract = {BACKGROUND: Metagenomics analyses can be negatively impacted by DNA contamination. While external sources of contamination such as DNA extraction kits have been widely reported and investigated, contamination originating within the study itself remains underreported.

RESULTS: Here, we applied high-resolution strain-resolved analyses to identify contamination in two large-scale clinical metagenomics datasets. By mapping strain sharing to DNA extraction plates, we identified well-to-well contamination in both negative controls and biological samples in one dataset. Such contamination is more likely to occur among samples that are on the same or adjacent columns or rows of the extraction plate than samples that are far apart. Our strain-resolved workflow also reveals the presence of externally derived contamination, primarily in the other dataset. Overall, in both datasets, contamination is more significant in samples with lower biomass.

CONCLUSION: Our work demonstrates that genome-resolved strain tracking, with its essentially genome-wide nucleotide-level resolution, can be used to detect contamination in sequencing-based microbiome studies. Our results underscore the value of strain-specific methods to detect contamination and the critical importance of looking for contamination beyond negative and positive controls. Video Abstract.}, } @article {pmid36864192, year = {2023}, author = {Katoh, T and Yamada, C and Wallace, MD and Yoshida, A and Gotoh, A and Arai, M and Maeshibu, T and Kashima, T and Hagenbeek, A and Ojima, MN and Takada, H and Sakanaka, M and Shimizu, H and Nishiyama, K and Ashida, H and Hirose, J and Suarez-Diez, M and Nishiyama, M and Kimura, I and Stubbs, KA and Fushinobu, S and Katayama, T}, title = {A bacterial sulfoglycosidase highlights mucin O-glycan breakdown in the gut ecosystem.}, journal = {Nature chemical biology}, volume = {19}, number = {6}, pages = {778-789}, pmid = {36864192}, issn = {1552-4469}, mesh = {*Mucins/metabolism ; *Ecosystem ; Polysaccharides/metabolism ; Bacteria/metabolism ; }, abstract = {Mucinolytic bacteria modulate host-microbiota symbiosis and dysbiosis through their ability to degrade mucin O-glycans. However, how and to what extent bacterial enzymes are involved in the breakdown process remains poorly understood. Here we focus on a glycoside hydrolase family 20 sulfoglycosidase (BbhII) from Bifidobacterium bifidum, which releases N-acetylglucosamine-6-sulfate from sulfated mucins. Glycomic analysis showed that, in addition to sulfatases, sulfoglycosidases are involved in mucin O-glycan breakdown in vivo and that the released N-acetylglucosamine-6-sulfate potentially affects gut microbial metabolism, both of which were also supported by a metagenomic data mining analysis. Enzymatic and structural analysis of BbhII reveals the architecture underlying its specificity and the presence of a GlcNAc-6S-specific carbohydrate-binding module (CBM) 32 with a distinct sugar recognition mode that B. bifidum takes advantage of to degrade mucin O-glycans. Comparative analysis of the genomes of prominent mucinolytic bacteria also highlights a CBM-dependent O-glycan breakdown strategy used by B. bifidum.}, } @article {pmid36864114, year = {2023}, author = {Wang, X and Wang, S and Yang, Y and Tian, H and Jetten, MSM and Song, C and Zhu, G}, title = {Hot moment of N2O emissions in seasonally frozen peatlands.}, journal = {The ISME journal}, volume = {17}, number = {6}, pages = {792-802}, pmid = {36864114}, issn = {1751-7370}, mesh = {*Ecosystem ; Freezing ; *Soil ; Forests ; Seasons ; Nitrous Oxide/analysis ; Agriculture ; }, abstract = {Since the start of the Anthropocene, northern seasonally frozen peatlands have been warming at a rate of 0.6 °C per decade, twice that of the Earth's average rate, thereby triggering increased nitrogen mineralization with subsequent potentially large losses of nitrous oxide (N2O) to the atmosphere. Here we provide evidence that seasonally frozen peatlands are important N2O emission sources in the Northern Hemisphere and the thawing periods are the hot moment of annual N2O emissions. The flux during the hot moment of thawing in spring was 1.20 ± 0.82 mg N2O m[-2] d[-1], significantly higher than that during the other periods (freezing, -0.12 ± 0.02 mg N2O m[-2] d[-1]; frozen, 0.04 ± 0.04 mg N2O m[-2] d[-1]; thawed, 0.09 ± 0.01 mg N2O m[-2] d[-1]) or observed for other ecosystems at the same latitude in previous studies. The observed emission flux is even higher than those of tropical forests, the World's largest natural terrestrial N2O source. Furthermore, based on soil incubation with [15]N and [18]O isotope tracing and differential inhibitors, heterotrophic bacterial and fungal denitrification was revealed as the main source of N2O in peatland profiles (0-200 cm). Metagenomic, metatranscriptomic, and qPCR assays further revealed that seasonally frozen peatlands have high N2O emission potential, but thawing significantly stimulates expression of genes encoding N2O-producing protein complexes (hydroxylamine dehydrogenase (hao) and nitric oxide reductase (nor)), resulting in high N2O emissions during spring. This hot moment converts seasonally frozen peatlands into an important N2O emission source when it is otherwise a sink. Extrapolation of our data to all northern peatland areas reveals that the hot moment emissions could amount to approximately 0.17 Tg of N2O yr[-1]. However, these N2O emissions are still not routinely included in Earth system models and global IPCC assessments.}, } @article {pmid36864029, year = {2023}, author = {Lee, K and Raguideau, S and Sirén, K and Asnicar, F and Cumbo, F and Hildebrand, F and Segata, N and Cha, CJ and Quince, C}, title = {Population-level impacts of antibiotic usage on the human gut microbiome.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1191}, pmid = {36864029}, issn = {2041-1723}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Microbiota ; Metagenome/genetics ; Genome, Human ; }, abstract = {The widespread usage of antimicrobials has driven the evolution of resistance in pathogenic microbes, both increased prevalence of antimicrobial resistance genes (ARGs) and their spread across species by horizontal gene transfer (HGT). However, the impact on the wider community of commensal microbes associated with the human body, the microbiome, is less well understood. Small-scale studies have determined the transient impacts of antibiotic consumption but we conduct an extensive survey of ARGs in 8972 metagenomes to determine the population-level impacts. Focusing on 3096 gut microbiomes from healthy individuals not taking antibiotics we demonstrate highly significant correlations between both the total ARG abundance and diversity and per capita antibiotic usage rates across ten countries spanning three continents. Samples from China were notable outliers. We use a collection of 154,723 human-associated metagenome assembled genomes (MAGs) to link these ARGs to taxa and detect HGT. This reveals that the correlations in ARG abundance are driven by multi-species mobile ARGs shared between pathogens and commensals, within a highly connected central component of the network of MAGs and ARGs. We also observe that individual human gut ARG profiles cluster into two types or resistotypes. The less frequent resistotype has higher overall ARG abundance, is associated with certain classes of resistance, and is linked to species-specific genes in the Proteobacteria on the periphery of the ARG network.}, } @article {pmid36863655, year = {2023}, author = {Wang, G and Qiu, G and Wei, J and Guo, Z and Wang, W and Liu, X and Song, Y}, title = {Activated carbon enhanced traditional activated sludge process for chemical explosion accident wastewater treatment.}, journal = {Environmental research}, volume = {225}, number = {}, pages = {115595}, doi = {10.1016/j.envres.2023.115595}, pmid = {36863655}, issn = {1096-0953}, mesh = {*Sewage/microbiology ; Wastewater ; Charcoal/chemistry ; Waste Disposal, Fluid/methods ; Explosions ; *Water Purification/methods ; Dissolved Organic Matter ; }, abstract = {With the development of industries, explosion accidents occur frequently during production, transportation, usage and storage of hazard chemicals. It remained challenging to efficiently treat the resultant wastewater. As an enhancement of traditional process, the activated carbon-activated sludge (AC-AS) process has a promising potential in treating wastewater with high concentrations of toxic compounds, chemical oxygen demand (COD) and ammonia nitrogen (NH4[+]-N), etc. In this paper, activated carbon (AC), activated sludge (AS) and AC-AS were used to treat the wastewater produced from an explosion accident in the Xiangshui Chemical Industrial Park. The removal efficiency was assessed by the removal performances of COD, dissolved organic carbon (DOC), NH4[+]-N, aniline and nitrobenzene. Increased removal efficiency and shortened treatment time were achieved in the AC-AS system. To achieve the same COD, DOC and aniline removal (90%), the AC-AS system saved 30, 38 and 58 h compared with the AS system, respectively. The enhancement mechanism of AC on the AS was explored by metagenomic analysis and three-dimensional excitation-emission-matrix spectra (3DEEMs). More organics, especially aromatic substances were removed in the AC-AS system. These results showed that the addition of AC promoted the microbial activity in pollutant degradation. Bacteria, such as Pyrinomonas, Acidobacteria and Nitrospira and genes, such as hao, pmoA-amoA, pmoB-amoB and pmoC-amoC, were found in the AC-AS reactor, which might have played important roles in the degradation of pollutants. To sum up, AC might have enhanced the growth of aerobic bacteria which further improved the removal efficiency via the combined effects of adsorption and biodegradation. The successful treatment of Xiangshui accident wastewater using the AC-AS demonstrated the potential universal characteristics of the process for the treatment of wastewater with high concentration of organic matter and toxicity. This study is expected to provide reference and guidance for the treatment of similar accident wastewaters.}, } @article {pmid36863103, year = {2023}, author = {Huang, J and Dai, X and Chen, X and Ali, I and Chen, H and Gou, J and Zhuo, C and Huang, M and Zhu, B and Tang, Y and Liu, J and Xu, Y and Tang, F and Xue, J}, title = {Combined forage grass-microbial for remediation of strontium-contaminated soil.}, journal = {Journal of hazardous materials}, volume = {450}, number = {}, pages = {131013}, doi = {10.1016/j.jhazmat.2023.131013}, pmid = {36863103}, issn = {1873-3336}, mesh = {*Strontium ; *Soil Pollutants/analysis ; Biodegradation, Environmental ; Plants ; Soil ; }, abstract = {Enrichment plants were screened from six forage grasses in this study to establish a complete combined forage grass-microbial remediation system of strontium-contaminated soil, and microbial groups were added to the screened dominant forage grasses. The occurrence states of strontium in forage grasses were explored by the BCR sequential extraction method. The results showed that the annual removal rate of Sudan grass (Sorghum sudanense (Piper) Stapf.) reached 23.05% in soil with a strontium concentration of 500 mg·kg[-1]. Three dominant microbial groups: E, G and H, have shown good facilitation effects in co-remediation with Sudan grass and Gaodan grass (Sorghum bicolor × sudanense), respectively. When compared to the control, the strontium accumulation of forage grasses in kg of soil with microbial groups was increased by 0.5-4 fold. The optimal forage grass-microbial combination can theoretically repair contaminated soil in three years. The microbial group E was found to promote the transfer of the exchangeable state and the reducible state of strontium to the overground part of the forage grass. Metagenomic sequencing results showed that the addition of microbial groups increased Bacillus spp. in rhizosphere soil, enhanced the disease resistance and tolerance of forage grasses, and improved the remediation ability of forage grass-microbial combinations.}, } @article {pmid36863003, year = {2023}, author = {Xu, G and Hou, B and Xue, C and Xu, Q and Qu, L and Hao, X and Liu, Y and Wang, D and Li, Z and Jin, X}, title = {Acute Retinal Necrosis Associated with Pseudorabies Virus Infection: A Case Report and Literature Review.}, journal = {Ocular immunology and inflammation}, volume = {}, number = {}, pages = {1-8}, doi = {10.1080/09273948.2023.2181188}, pmid = {36863003}, issn = {1744-5078}, abstract = {PURPOSE: To analyze a case of acute retinal necrosis (ARN) associated with pseudorabies virus (PRV) infection and discusses the clinical characteristics of PRV-induced ARN (PRV-ARN).

METHODS: Case report and literature review of ocular features in PRV-ARN.

RESULTS: A 52-year-old female diagnosed with encephalitis presented with bilateral vision loss, mild anterior uveitis, vitreous opacity, occlusive retinal vasculitis, and retinal detachment in her left eye. The result of metagenomic next-generation sequencing (mNGS) indicated that both cerebrospinal fluids and vitreous fluid tested positive for PRV.

CONCLUSION: PRV, a zoonosis, can infect both humans and mammals. Patients affected with PRV may experience severe encephalitis and oculopathy, and the infection has been associated with high mortality and disability. ARN is the most common ocular disease, which develops rapidly following encephalitis and is characterized by five figures: bilateral onset, rapid progression, severe visual impairment, poor response to systemic antiviral drugs, and an unfavorable prognosis.}, } @article {pmid36862944, year = {2023}, author = {Amarelle, V and Roldán, DM and Fabiano, E and Guazzaroni, ME}, title = {Synthetic Biology Toolbox for Antarctic Pseudomonas sp. Strains: Toward a Psychrophilic Nonmodel Chassis for Function-Driven Metagenomics.}, journal = {ACS synthetic biology}, volume = {12}, number = {3}, pages = {722-734}, doi = {10.1021/acssynbio.2c00543}, pmid = {36862944}, issn = {2161-5063}, mesh = {*Synthetic Biology ; *Pseudomonas/genetics ; Metagenomics ; Antarctic Regions ; Biotechnology ; }, abstract = {One major limitation of function-driven metagenomics is the ability of the host to express the metagenomic DNA correctly. Differences in the transcriptional, translational, and post-translational machinery between the organism to which the DNA belongs and the host strain are all factors that influence the success of a functional screening. For this reason, the use of alternative hosts is an appropriate approach to favor the identification of enzymatic activities in function-driven metagenomics. To be implemented, appropriate tools should be designed to build the metagenomic libraries in those hosts. Moreover, discovery of new chassis and characterization of synthetic biology toolbox in nonmodel bacteria is an active field of research to expand the potential of these organisms in processes of industrial interest. Here, we assessed the suitability of two Antarctic psychrotolerant Pseudomonas strains as putative alternative hosts for function-driven metagenomics using pSEVA modular vectors as scaffold. We determined a set of synthetic biology tools suitable for these hosts and, as a proof of concept, we demonstrated their fitness for heterologous protein expression. These hosts represent a step forward for the prospection and identification of psychrophilic enzymes of biotechnological interest.}, } @article {pmid36862673, year = {2023}, author = {Lappa, D and Meijnikman, AS and Krautkramer, KA and Olsson, LM and Aydin, Ö and Van Rijswijk, AS and Acherman, YIZ and De Brauw, ML and Tremaroli, V and Olofsson, LE and Lundqvist, A and Hjorth, SA and Ji, B and Gerdes, VEA and Groen, AK and Schwartz, TW and Nieuwdorp, M and Bäckhed, F and Nielsen, J}, title = {Self-organized metabotyping of obese individuals identifies clusters responding differently to bariatric surgery.}, journal = {PloS one}, volume = {18}, number = {3}, pages = {e0279335}, pmid = {36862673}, issn = {1932-6203}, mesh = {Humans ; *Diabetes Mellitus, Type 2/surgery ; Obesity/surgery ; *Bariatric Surgery ; Adipose Tissue ; Algorithms ; }, abstract = {Weight loss through bariatric surgery is efficient for treatment or prevention of obesity related diseases such as type 2 diabetes and cardiovascular disease. Long term weight loss response does, however, vary among patients undergoing surgery. Thus, it is difficult to identify predictive markers while most obese individuals have one or more comorbidities. To overcome such challenges, an in-depth multiple omics analyses including fasting peripheral plasma metabolome, fecal metagenome as well as liver, jejunum, and adipose tissue transcriptome were performed for 106 individuals undergoing bariatric surgery. Machine leaning was applied to explore the metabolic differences in individuals and evaluate if metabolism-based patients' stratification is related to their weight loss responses to bariatric surgery. Using Self-Organizing Maps (SOMs) to analyze the plasma metabolome, we identified five distinct metabotypes, which were differentially enriched for KEGG pathways related to immune functions, fatty acid metabolism, protein-signaling, and obesity pathogenesis. The gut metagenome of the most heavily medicated metabotypes, treated simultaneously for multiple cardiometabolic comorbidities, was significantly enriched in Prevotella and Lactobacillus species. This unbiased stratification into SOM-defined metabotypes identified signatures for each metabolic phenotype and we found that the different metabotypes respond differently to bariatric surgery in terms of weight loss after 12 months. An integrative framework that utilizes SOMs and omics integration was developed for stratifying a heterogeneous bariatric surgery cohort. The multiple omics datasets described in this study reveal that the metabotypes are characterized by a concrete metabolic status and different responses in weight loss and adipose tissue reduction over time. Our study thus opens a path to enable patient stratification and hereby allow for improved clinical treatments.}, } @article {pmid36862079, year = {2023}, author = {Pino, V and Fajardo, M and McBratney, A and Minasny, B and Wilson, N and Baldock, C}, title = {Australian soil microbiome: A first sightseeing regional prediction driven by cycles of soil temperature and pedogenic variations.}, journal = {Molecular ecology}, volume = {32}, number = {23}, pages = {6243-6259}, doi = {10.1111/mec.16911}, pmid = {36862079}, issn = {1365-294X}, support = {//Comisión Nacional de Investigación Científica y Tecnológica/ ; //University of Sydney/ ; }, mesh = {*Soil ; Australia ; Temperature ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; *Microbiota/genetics ; }, abstract = {Declines in soil multifunctionality (e.gsoil capacity to provide food and energy) are closely related to changes in the soil microbiome (e.g., diversity) Determining ecological drivers promoting such microbiome changes is critical knowledge for protecting soil functions. However, soil-microbe interactions are highly variable within environmental gradients and may not be consistent across studies. Here we propose that analysis of community dissimilarity (β-diversity) is a valuable tool for overviewing soil microbiome spatiotemporal changes. Indeed, β-diversity studies at larger scales (modelling and mapping) simplify complex multivariate interactions and refine our understanding of ecological drivers by also giving the possibility of expanding the environmental scenarios. This study represents the first spatial investigation of β-diversity in the soil microbiome of New South Wales (800,642 km[2]), Australia. We used metabarcoding soil data (16S rRNA and ITS genes) as exact sequence variants (ASVs) and UMAP (Uniform Manifold Approximation and Projection) as the distance metric. β-Diversity maps (1000-m resolution)-concordance correlations of 0.91-0.96 and 0.91-0.95 for bacteria and fungi, respectively-showed soil biome dissimilarities driven primarily by soil chemistry-pH and effective cation exchange capacity (ECEC)-and cycles of soil temperature-land surface temperature (LST-phase and LST-amplitude). Regionally, the spatial patterns of microbes parallel the distribution of soil classes (e.g., Vertosols) beyond spatial distances and rainfall, for example. Soil classes can be valuable discriminants for monitoring approaches, for example pedogenons and pedophenons. Ultimately, cultivated soils exhibited lower richness due to declines in rare microbes which might compromise soil functions over time.}, } @article {pmid36861850, year = {2023}, author = {Ordinola-Zapata, R and Costalonga, M and Dietz, M and Lima, BP and Staley, C}, title = {The root canal microbiome diversity and function. A whole-metagenome shotgun analysis.}, journal = {International endodontic journal}, volume = {}, number = {}, pages = {}, doi = {10.1111/iej.13911}, pmid = {36861850}, issn = {1365-2591}, support = {UL1-TR002494/TR/NCATS NIH HHS/United States ; UL1-TR002494/TR/NCATS NIH HHS/United States ; }, abstract = {AIM: To evaluate the root canal microbiome composition and bacterial functional capability in cases of primary and secondary apical periodontitis utilizing whole-metagenome shotgun sequencing.

METHODOLOGY: Twenty-two samples from patients with primary root canal infections, and 18 samples obtained from previously treated teeth currently diagnosed with apical periodontitis were analysed with whole-metagenome shotgun sequencing at a depth of 20 M reads. Taxonomic and functional gene annotations were made using MetaPhlAn3 and HUMAnN3 software. The Shannon and Chao1 indices were utilized to measure alpha diversity. Differences in community composition were evaluated utilizing analysis of similarity (ANOSIM) using Bray-Curtis dissimilarities. The Wilcoxon rank sum test was used to compare differences in taxa and functional genes.

RESULTS: Microbial community variations within a community were significantly lower in secondary relative to primary infections (alpha diversity p = .001). Community composition was significantly different in primary versus secondary infection (R = .11, p = .005). The predominant taxa observed among samples (>2.5%) were Pseudopropionibacterium propionicum, Prevotella oris, Eubacterium infirmum, Tannerella forsythia, Atopobium rimae, Peptostreptococcus stomatis, Bacteroidetes bacterium oral taxon 272, Parvimonas micra, Olsenella profusa, Streptococcus anginosus, Lactobacillus rhamnosus, Porphyromonas endodontalis, Pseudoramibacter alactolyticus, Fusobacterium nucleatum, Eubacterium brachy and Solobacterium moorei. The Wilcoxon rank test revealed no significant differences in relative abundances of functional genes in both groups. Genes with greater relative abundances (top 25) were associated with genetic, signalling and cellular processes including the iron and peptide/nickel transport system. Numerous genes encoding toxins were identified: exfoliative toxin, haemolysins, thiol-activated cytolysin, phospholipase C, cAMP factor, sialidase, and hyaluronic glucosaminidase.

CONCLUSIONS: Despite taxonomic differences between primary and secondary apical periodontitis, the functional capability of the microbiomes was similar.}, } @article {pmid36861357, year = {2023}, author = {Soto, MA and Desai, D and Bannon, C and LaRoche, J and Bertrand, EM}, title = {Cobalamin producers and prokaryotic consumers in the Northwest Atlantic.}, journal = {Environmental microbiology}, volume = {25}, number = {7}, pages = {1300-1313}, doi = {10.1111/1462-2920.16363}, pmid = {36861357}, issn = {1462-2920}, mesh = {Vitamin B 12 ; *Synechococcus ; Archaea/genetics ; *Flavobacteriaceae ; Atlantic Ocean ; *Alphaproteobacteria ; *Gammaproteobacteria ; }, abstract = {Cobalamin availability can influence primary productivity and ecological interactions in marine microbial communities. The characterization of cobalamin sources and sinks is a first step in investigating cobalamin dynamics and its impact on productivity. Here, we identify potential cobalamin sources and sinks on the Scotian Shelf and Slope in the Northwest Atlantic Ocean. Functional and taxonomic annotation of bulk metagenomic reads, combined with analysis of genome bins, were used to identify potential cobalamin sources and sinks. Cobalamin synthesis potential was mainly attributed to Rhodobacteraceae, Thaumarchaeota, and cyanobacteria (Synechococcus and Prochlorococcus). Cobalamin remodelling potential was mainly attributed to Alteromonadales, Pseudomonadales, Rhizobiales, Oceanospirilalles, Rhodobacteraceae, and Verrucomicrobia, while potential cobalamin consumers include Flavobacteriaceae, Actinobacteria, Porticoccaceae, Methylophiliaceae, and Thermoplasmatota. These complementary approaches identified taxa with the potential to be involved in cobalamin cycling on the Scotian Shelf and revealed genomic information required for further characterization. The Cob operon of Rhodobacterales bacterium HTCC2255, a strain with known importance in cobalamin cycling, was similar to a major cobalamin producer bin, suggesting that a related strain may represent a critical cobalamin source in this region. These results enable future inquiries that will enhance our understanding of how cobalamin shapes microbial interdependencies and productivity in this region.}, } @article {pmid36860485, year = {2023}, author = {Li, Y and Yan, Y and Fu, H and Jin, S and He, S and Wang, Z and Dong, G and Li, B and Guo, S}, title = {Does diet or macronutrients intake drive the structure and function of gut microbiota?.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1126189}, pmid = {36860485}, issn = {1664-302X}, abstract = {Shift of ingestive behavior is an important strategy for animals to adapt to change of the environment. We knew that shifts in animal dietary habits lead to changes in the structure of the gut microbiota, but we are not sure about if changes in the composition and function of the gut microbiota respond to changes in the nutrient intake or food items. To investigate how animal feeding strategies affect nutrient intakes and thus alter the composition and digestion function of gut microbiota, we selected a group of wild primate group for the study. We quantified their diet and macronutrients intake in four seasons of a year, and instant fecal samples were analyzed by high-throughput sequencing of 16S rRNA and metagenomics. These results demonstrated that the main reason that causes seasonal shifts of gut microbiota is the macronutrient variation induced by seasonal dietary differences. Gut microbes can help to compensate for insufficient macronutrients intake of the host through microbial metabolic functions. This study contributes to a deeper understanding of the causes of seasonal variation in host-microbial variation in wild primates.}, } @article {pmid36860407, year = {2023}, author = {Nguyen, DH and Chu, NH and Bettarel, Y and Auguet, JC and Bouvier, T and Chu, HH and Bui, VN}, title = {Metagenomic data of bacterial communities associated with Acropora species from Phu Quoc Islands, Vietnam.}, journal = {Data in brief}, volume = {47}, number = {}, pages = {108977}, pmid = {36860407}, issn = {2352-3409}, abstract = {Acropora is one of the most common coral genera found in Phu Quoc Islands, Vietnam. However, the presence of marine snails, such as the coralllivorous gastropod Drupella rugosa, was a potential threat to the survival of many scleractinian species, leading to changes in the health status and bacterial diversity of coral reefs in Phu Quoc Islands. Here, we describe the composition of bacterial communities associated with two species of Acropora (Acropora formosa and Acropora millepora) using the Illumina sequencing technology. This dataset includes 5 coral samples of each status (grazed or healthy), which were collected in Phu Quoc Islands (9°55'20.6″N 104°01'16.4″E) in May 2020. A total of 19 phyla, 34 classes, 98 orders, 216 families and 364 bacterial genera were detected from 10 coral samples. Overall, Proteobacteria and Firmicutes were the two most common bacterial phyla in all samples. Significant differences in the relative abundances of the genera Fusibacter, Halarcobacter, Malaciobacter, and Thalassotalea between grazed and healthy status were observed. However, there was no differences in alpha diversity indices between the two status. Furthermore, the dataset analysis also indicated that Vibrio and Fusibacter were core genera in the grazed samples, whereas Pseudomonas was the core genus in the healthy samples.}, } @article {pmid36860056, year = {2023}, author = {Chen, X and Ke, Y and Zhu, Y and Xu, M and Chen, C and Xie, S}, title = {Enrichment of tetracycline-degrading bacterial consortia: Microbial community succession and degradation characteristics and mechanism.}, journal = {Journal of hazardous materials}, volume = {448}, number = {}, pages = {130984}, doi = {10.1016/j.jhazmat.2023.130984}, pmid = {36860056}, issn = {1873-3336}, mesh = {*Tetracycline ; Anti-Bacterial Agents ; *Microbiota ; Microbial Consortia ; Metagenome ; }, abstract = {Tetracycline (TC) is an antibiotic that is recently found as an emerging pollutant with low biodegradability. Biodegradation shows great potential for TC dissipation. In this study, two TC-degrading microbial consortia (named SL and SI) were respectively enriched from activated sludge and soil. Bacterial diversity decreased in these finally enriched consortia compared with the original microbiota. Moreover, most ARGs quantified during the acclimation process became less abundant in the finally enriched microbial consortia. Microbial compositions of the two consortia as revealed by 16 S rRNA sequencing were similar to some extent, and the dominant genera Pseudomonas, Sphingobacterium, and Achromobacter were identified as the potential TC degraders. In addition, consortia SL and SI were capable of biodegrading TC (initial 50 mg/L) by 82.92% and 86.83% within 7 days, respectively. They could retain high degradation capabilities under a wide pH range (4-10) and at moderate/high temperatures (25-40 °C). Peptone with concentrations of 4-10 g/L could serve as a desirable primary growth substrate for consortia to remove TC through co-metabolism. A total of 16 possible intermediates including a novel biodegradation product TP245 were detected during TC degradation. Peroxidase genes, tetX-like genes and the enriched genes related to aromatic compound degradation as revealed by metagenomic sequencing were likely responsible for TC biodegradation.}, } @article {pmid36860032, year = {2023}, author = {Ge, L and Song, L and Wang, L and Li, Y and Sun, Y and Wang, C and Chen, J and Wu, G and Pan, A and Wu, Y and Quan, Z and Li, P}, title = {Evaluating response mechanisms of soil microbiomes and metabolomes to Bt toxin additions.}, journal = {Journal of hazardous materials}, volume = {448}, number = {}, pages = {130904}, doi = {10.1016/j.jhazmat.2023.130904}, pmid = {36860032}, issn = {1873-3336}, mesh = {*Soil ; Bacillus thuringiensis Toxins ; RNA, Ribosomal, 16S ; Metabolome ; *Microbiota ; }, abstract = {The accumulation and persistence of Bt toxins in soils from Bt plants and Bt biopesticides may result in environmental hazards such as adverse impacts on soil microorganisms. However, the dynamic relationships among exogenous Bt toxins, soil characteristics, and soil microorganisms are not well understood. Cry1Ab is one of the most commonly used Bt toxins and was added to soils in this study to evaluate subsequent changes in soil physiochemical properties, microbial taxa, microbial functional genes, and metabolites profiles via 16S rRNA gene pyrosequencing, high-throughput qPCR, metagenomic shotgun sequencing, and untargeted metabolomics. Higher additions of Bt toxins led to higher concentrations of soil organic matter (SOM), ammonium (NH[+]4-N), and nitrite (NO2[-]-N) compared against controls without addition after 100 days of soil incubation. High-throughput qPCR analysis and shotgun metagenomic sequencing analysis revealed that the 500 ng/g Bt toxin addition significantly affected profiles of soil microbial functional genes involved in soil carbon (C), nitrogen (N), and phosphorus (P) cycling after 100 days of incubation. Furthermore, combined metagenomic and metabolomic analyses indicated that the 500 ng/g Bt toxin addition significantly altered low molecular weight metabolite profiles of soils. Importantly, some of these altered metabolites are involved in soil nutrient cycling, and robust associations were identified among differentially abundant metabolites and microorganisms due to Bt toxin addition treatments. Taken together, these results suggest that higher levels of Bt toxin addition can alter soil nutrients, probably by affecting the activities of Bt toxin-degrading microorganisms. These dynamics would then activate other microorganisms involved in nutrient cycling, finally leading to broad changes in metabolite profiles. Notably, the addition of Bt toxins did not cause the accumulation of potential microbial pathogens in soils, nor did it adversely affect the diversity and stability of microbial communities. This study provides new insights into the putative mechanistic associations among Bt toxins, soil characteristics, and microorganisms, providing new understanding into the ecological impacts of Bt toxins on soil ecosystems.}, } @article {pmid36859706, year = {2023}, author = {Pinheiro, Y and Faria da Mota, F and Peixoto, RS and van Elsas, JD and Lins, U and Mazza Rodrigues, JL and Rosado, AS}, title = {A thermophilic chemolithoautotrophic bacterial consortium suggests a mutual relationship between bacteria in extreme oligotrophic environments.}, journal = {Communications biology}, volume = {6}, number = {1}, pages = {230}, pmid = {36859706}, issn = {2399-3642}, support = {BAS/1/1096-01-01//King Abdullah University of Science and Technology (KAUST)/ ; }, mesh = {*Actinobacteria ; Carbon ; *Extreme Environments ; *Bacillaceae ; *Alphaproteobacteria ; }, abstract = {A thermophilic, chemolithoautotrophic, and aerobic microbial consortium (termed carbonitroflex) growing in a nutrient-poor medium and an atmosphere containing N2, O2, CO2, and CO is investigated as a model to expand our understanding of extreme biological systems. Here we show that the consortium is dominated by Carbonactinospora thermoautotrophica (strain StC), followed by Sphaerobacter thermophilus, Chelatococcus spp., and Geobacillus spp. Metagenomic analysis of the consortium reveals a mutual relationship among bacteria, with C. thermoautotrophica StC exhibiting carboxydotrophy and carbon-dioxide storage capacity. C. thermoautotrophica StC, Chelatococcus spp., and S. thermophilus harbor genes encoding CO dehydrogenase and formate oxidase. No pure cultures were obtained under the original growth conditions, indicating that a tightly regulated interactive metabolism might be required for group survival and growth in this extreme oligotrophic system. The breadwinner hypothesis is proposed to explain the metabolic flux model and highlight the vital role of C. thermoautotrophica StC (the sole keystone species and primary carbon producer) in the survival of all consortium members. Our data may contribute to the investigation of complex interactions in extreme environments, exemplifying the interconnections and dependency within microbial communities.}, } @article {pmid36859551, year = {2023}, author = {Chazan, A and Das, I and Fujiwara, T and Murakoshi, S and Rozenberg, A and Molina-Márquez, A and Sano, FK and Tanaka, T and Gómez-Villegas, P and Larom, S and Pushkarev, A and Malakar, P and Hasegawa, M and Tsukamoto, Y and Ishizuka, T and Konno, M and Nagata, T and Mizuno, Y and Katayama, K and Abe-Yoshizumi, R and Ruhman, S and Inoue, K and Kandori, H and León, R and Shihoya, W and Yoshizawa, S and Sheves, M and Nureki, O and Béjà, O}, title = {Phototrophy by antenna-containing rhodopsin pumps in aquatic environments.}, journal = {Nature}, volume = {615}, number = {7952}, pages = {535-540}, pmid = {36859551}, issn = {1476-4687}, mesh = {*Aquatic Organisms/metabolism/radiation effects ; Bacteria/metabolism/radiation effects ; Carotenoids/metabolism ; Color ; Cyanobacteria/metabolism/radiation effects ; Heterotrophic Processes/radiation effects ; Light ; Oceans and Seas ; *Phototrophic Processes/radiation effects ; *Proton Pumps/metabolism/radiation effects ; *Rhodopsins, Microbial/metabolism/radiation effects ; Zeaxanthins/metabolism/radiation effects ; Lutein/metabolism/radiation effects ; Metagenome ; Lakes ; }, abstract = {Energy transfer from light-harvesting ketocarotenoids to the light-driven proton pump xanthorhodopsins has been previously demonstrated in two unique cases: an extreme halophilic bacterium[1] and a terrestrial cyanobacterium[2]. Attempts to find carotenoids that bind and transfer energy to abundant rhodopsin proton pumps[3] from marine photoheterotrophs have thus far failed[4-6]. Here we detected light energy transfer from the widespread hydroxylated carotenoids zeaxanthin and lutein to the retinal moiety of xanthorhodopsins and proteorhodopsins using functional metagenomics combined with chromophore extraction from the environment. The light-harvesting carotenoids transfer up to 42% of the harvested energy in the violet- or blue-light range to the green-light absorbing retinal chromophore. Our data suggest that these antennas may have a substantial effect on rhodopsin phototrophy in the world's lakes, seas and oceans. However, the functional implications of our findings are yet to be discovered.}, } @article {pmid36857890, year = {2023}, author = {Liu, Z and Wan, X and Zhang, C and Cai, M and Pan, Y and Li, M}, title = {Deep sequencing reveals comprehensive insight into the prevalence, mobility, and hosts of antibiotic resistance genes in mangrove ecosystems.}, journal = {Journal of environmental management}, volume = {335}, number = {}, pages = {117580}, doi = {10.1016/j.jenvman.2023.117580}, pmid = {36857890}, issn = {1095-8630}, mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Ecosystem ; Prevalence ; Drug Resistance, Microbial/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {Mangrove receives aquaculture wastewater and urban sewage, and thus is a potential reservoir for antibiotic resistance genes (ARGs). However, there is a dearth of a comprehensive profile of ARGs in mangrove ecosystems. We used metagenomic techniques to uncover the occurrence, host range, and potential mobility of ARGs in six mangrove ecosystems in southeastern China. Based on deep sequencing data, a total of 348 ARG subtypes were identified. The abundant ARGs were associated with acriflavine, bacitracin, beta-lactam, fluoroquinolone, macrolide-lincosamide-streptogramin, and polymyxin. Resistance genes tetR, aac(6')-Iae, aac(3)-IXa, vanRA, vanRG, and aac(3)-Ig were proposed as ARG indicators in mangrove ecosystems that can be used to evaluate the abundance of 100 other co-occurring ARGs quantitatively. Remarkably, 250 of 348 identified ARG subtypes were annotated as mobile genetic elements-associated ARGs, indicating a high potential risk of propagation of ARGs in mangrove ecosystems. By surveying the distribution of ARGs in 6281 draft genomes, more than 42 bacterial phyla were identified as the putative hosts of the ARGs. Among them, 21.97% were potentially multidrug-resistant hosts, including human and animal opportunistic pathogens. This research adds to our understanding of the distribution and spread of antibiotic resistomes in mangrove ecosystems, helping improve ARG risk assessment and management worldwide.}, } @article {pmid36857575, year = {2023}, author = {Shaffer, M and Borton, MA and Bolduc, B and Faria, JP and Flynn, RM and Ghadermazi, P and Edirisinghe, JN and Wood-Charlson, EM and Miller, CS and Chan, SHJ and Sullivan, MB and Henry, CS and Wrighton, KC}, title = {kb_DRAM: annotation and metabolic profiling of genomes with DRAM in KBase.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {4}, pages = {}, pmid = {36857575}, issn = {1367-4811}, mesh = {Molecular Sequence Annotation ; *Software ; *Bacteria/genetics ; Archaea/genetics ; Metabolomics ; }, abstract = {UNLABELLED: Microbial genome annotation is the process of identifying structural and functional elements in DNA sequences and subsequently attaching biological information to those elements. DRAM is a tool developed to annotate bacterial, archaeal, and viral genomes derived from pure cultures or metagenomes. DRAM goes beyond traditional annotation tools by distilling multiple gene annotations to genome level summaries of functional potential. Despite these benefits, a downside of DRAM is the requirement of large computational resources, which limits its accessibility. Further, it did not integrate with downstream metabolic modeling tools that require genome annotation. To alleviate these constraints, DRAM and the viral counterpart, DRAM-v, are now available and integrated with the freely accessible KBase cyberinfrastructure. With kb_DRAM users can generate DRAM annotations and functional summaries from microbial or viral genomes in a point-and-click interface, as well as generate genome-scale metabolic models from DRAM annotations.

For kb_DRAM users, the kb_DRAM apps on KBase can be found in the catalog at https://narrative.kbase.us/#catalog/modules/kb_DRAM. For kb_DRAM users, a tutorial workflow with all documentation is available at https://narrative.kbase.us/narrative/129480. For kb_DRAM developers, software is available at https://github.com/shafferm/kb_DRAM.}, } @article {pmid36856771, year = {2023}, author = {Shi, ZJ and Nayfach, S and Pollard, KS}, title = {Identifying species-specific k-mers for fast and accurate metagenotyping with Maast and GT-Pro.}, journal = {STAR protocols}, volume = {4}, number = {1}, pages = {101964}, pmid = {36856771}, issn = {2666-1667}, mesh = {*Genome ; *Microbiota/genetics ; Polymorphism, Single Nucleotide/genetics ; }, abstract = {Genotyping single-nucleotide polymorphisms (SNPs) in microbiomes enables strain-level quantification. In this protocol, we describe a computational pipeline that performs fast and accurate SNP genotyping using metagenomic data. We first demonstrate how to use Maast to catalog SNPs from microbial genomes. Then we use GT-Pro to extract unique SNP-covering k-mers, optimize a data structure for storing these k-mers, and finally perform metagenotyping. For proof of concept, the protocol leverages public whole-genome sequences to metagenotype a synthetic community. For complete details on the use and execution of this protocol, please refer to Shi et al. (2022a)[1] and Shi et al. (2022b).[2].}, } @article {pmid36856420, year = {2023}, author = {Newman, MR and Sanchez, D and Acosta, AM and Connors, BJ}, title = {Amplicons, Metagenomes, and Metatranscriptomes from Sediment and Water.}, journal = {Microbiology resource announcements}, volume = {12}, number = {4}, pages = {e0123022}, pmid = {36856420}, issn = {2576-098X}, support = {1950018//National Science Foundation (NSF)/ ; }, abstract = {High fecal indicator bacterium (FIB) counts in water have been found to correlate with high sediment FIB counts. To determine the other bacterial populations in common between the two substrates, sediment and water samples from suburban waters known to be impacted by stormwater runoff were examined using next-generation sequencing.}, } @article {pmid36855809, year = {2023}, author = {Xiong, Q and Li, L and Xiao, Y and He, S and Zhao, J and Lin, X and He, Y and Wang, J and Guo, X and Liang, W and Zuo, X and Ying, C}, title = {The Effect of Inulin-Type Fructans on Plasma Trimethylamine N-Oxide Levels in Peritoneal Dialysis Patients: A Randomized Crossover Trial.}, journal = {Molecular nutrition & food research}, volume = {67}, number = {9}, pages = {e2200531}, doi = {10.1002/mnfr.202200531}, pmid = {36855809}, issn = {1613-4133}, mesh = {Humans ; *Inulin/pharmacology ; Fructans ; Cross-Over Studies ; Methylamines ; Choline ; *Peritoneal Dialysis ; }, abstract = {SCOPE: Trimethylamine N-oxide (TMAO), an important proatherogenic uremic toxin, is oxidized by hepatic-flavin monooxygenases from gut microbiome-generated trimethylamine (TMA). The present study aims to explore whether manipulating the gut microbiota by inulin-type fructans (ITFs) can reduce circulating TMAO levels in peritoneal dialysis patients.

METHODS AND RESULTS: This is a randomized, double-blind, placebo-controlled, crossover trial with 10 g day[-1] ITFs intervention for 3 months in continuous ambulatory peritoneal dialysis patients. The gut microbiome is measured, and TMA-producing gene clusters are annotated using shotgun metagenomic sequencing. Fecal and plasma TMA, plasma TMAO, and daily urine excretion and dialysis removal of TMAO are measured. Finally, 22 participants complete the trial. The daily intake of macronutrients and TMAO precursors is comparable during the prebiotics, washout, and placebo interventions. The ITFs intervention increases the Firmicutes/Bacteroidetes (F/B) ratio (p = 0.049) of gut microbiome. However, no significant influences are observed on fecal TMA content, circulating TMAO levels, or TMA-producing gene clusters, including choline TMA-lyase (CutC/D), carnitine monooxygenase (CntA/B), and betaine reductase (GrdH).

CONCLUSIONS: Intervention with 10 g day[-1] of ITFs for 3 months is not sufficient to reduce plasma TMAO levels in peritoneal dialysis patients, but it improves the gut microbiome composition.}, } @article {pmid36855218, year = {2023}, author = {Kim, MS and Park, EJ}, title = {Composition and variability of core phyllosphere fungal mycobiota on field-grown broccoli.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {15}, pmid = {36855218}, issn = {2524-6372}, support = {2019R1C1C1009664//Ministry of Science and ICT, Republic of Korea/ ; 2020R1A5A8017671//Ministry of Science and ICT, South Korea/ ; 2021R1F1A1064222//Ministry of Science and ICT, South Korea/ ; 2018R1D1A3B07050366//Ministry of Education/ ; }, abstract = {BACKGROUND: Fresh vegetables harbor an assemblage of different microorganisms on their surfaces. The phyllosphere microbiota is important for maintaining plant health and managing crop quality before and after harvest. However, the diversity and ecology of fungal communities are largely unexplored in fresh vegetables. This study investigated the phyllosphere mycobiota of field-grown broccoli florets (n = 66) collected from 22 farms across four regions in Korea, using culturing, amplicon sequencing of the internal transcribed spacer region, and microbial network analysis.

RESULTS: Microbial network analysis identified core genera (Purpureocillium, Filobasidium, Cystofilobasidium, Papiliotrema, Aureobasidium, and unclassified genera of Capnodiales) specific to the broccoli phyllosphere. The composition and network complexity of core and unique populations varied among farming regions, and was associated with local agro-meteorological conditions. The complexity of microbial associations was higher in mature communities than in immature communities, but complexity was lost upon development of plant pathogenic disease. Broccoli mycobiota were classified according to the dominance of Purpurecillium. While Purpurecillium-type microbiota were prevalent in normal samples, Filobasidium-type microbiota were frequently observed in immature, damaged, or postharvest samples.

CONCLUSIONS: Together, fungal communities were important components of phyllosphere microbiota on fresh vegetables, and have substantial potential for exploitation to enhance and stabilize plant health and growth.}, } @article {pmid36853748, year = {2023}, author = {Edgeworth, JD}, title = {Respiratory metagenomics: route to routine service.}, journal = {Current opinion in infectious diseases}, volume = {36}, number = {2}, pages = {115-123}, pmid = {36853748}, issn = {1473-6527}, mesh = {*Healthcare-Associated Pneumonia ; *Community-Acquired Infections ; Humans ; Intensive Care Units ; *Metagenomics ; COVID-19 ; Pandemics ; High-Throughput Nucleotide Sequencing ; }, abstract = {PURPOSE OF REVIEW: The coronavirus disease 2019 pandemic demonstrated broad utility of pathogen sequencing with rapid methodological progress alongside global distribution of sequencing infrastructure. This review considers implications for now moving clinical metagenomics into routine service, with respiratory metagenomics as the exemplar use-case.

RECENT FINDINGS: Respiratory metagenomic workflows have completed proof-of-concept, providing organism identification and many genotypic antimicrobial resistance determinants from clinical samples in <6 h. This enables rapid escalation or de-escalation of empiric therapy for patient benefit and reducing selection of antimicrobial resistance, with genomic-typing available in the same time-frame. Attention is now focussed on demonstrating clinical, health-economic, accreditation, and regulatory requirements. More fundamentally, pathogen sequencing challenges the traditional culture-orientated time frame of microbiology laboratories, which through automation and centralisation risks becoming increasingly separated from the clinical setting. It presents an alternative future where infection experts are brought together around a single genetic output in an acute timeframe, aligning the microbiology target operating model with the wider human genomic and digital strategy.

SUMMARY: Pathogen sequencing is a transformational proposition for microbiology laboratories and their infectious diseases, infection control, and public health partners. Healthcare systems that link output from routine clinical metagenomic sequencing, with pandemic and antimicrobial resistance surveillance, will create valuable tools for protecting their population against future infectious diseases threats.}, } @article {pmid36853049, year = {2023}, author = {Vereecke, N and Zwickl, S and Gumbert, S and Graaf, A and Harder, T and Ritzmann, M and Lillie-Jaschniski, K and Theuns, S and Stadler, J}, title = {Viral and Bacterial Profiles in Endemic Influenza A Virus Infected Swine Herds Using Nanopore Metagenomic Sequencing on Tracheobronchial Swabs.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0009823}, pmid = {36853049}, issn = {2165-0497}, abstract = {Swine influenza A virus (swIAV) plays an important role in porcine respiratory infections. In addition to its ability to cause severe disease by itself, it is important in the multietiological porcine respiratory disease complex. Still, to date, no comprehensive diagnostics with which to study polymicrobial infections in detail have been offered. Hence, veterinary practitioners rely on monospecific and costly diagnostics, such as Reverse Transcription quantitative PCR (RT-qPCR), antigen detection, and serology. This prevents the proper understanding of the entire disease context, thereby hampering effective preventive and therapeutic actions. A new, nanopore-based, metagenomic diagnostic platform was applied to study viral and bacterial profiles across 4 age groups on 25 endemic swIAV-infected German farms with respiratory distress in the nursery. Farms were screened for swIAV using RT-qPCR on nasal and tracheobronchial swabs (TBS). TBS samples were pooled per age, prior to metagenomic characterization. The resulting data showed a correlation between the swIAV loads and the normalized reads, supporting a (semi-)quantitative interpretation of the metagenomic data. Interestingly, an in-depth characterization using beta diversity and PERMANOVA analyses allowed for the observation of an age-dependent interplay of known microbial agents. Also, lesser-known microbes, such as porcine polyoma, parainfluenza, and hemagglutinating encephalomyelitis viruses, were observed. Analyses of swIAV incidence and clinical signs showed differing microbial communities, highlighting age-specific observations of various microbes in porcine respiratory disease. In conclusion, nanopore metagenomics were shown to enable a panoramic view on viral and bacterial profiles as well as putative pathogen dynamics in endemic swIAV-infected herds. The results also highlighted the need for better insights into lesser studied agents that are potentially associated with porcine respiratory disease. IMPORTANCE To date, no comprehensive diagnostics for the study of polymicrobial infections that are associated with porcine respiratory disease have been offered. This precludes the proper understanding of the entire disease landscape, thereby hampering effective preventive and therapeutic actions. Compared to the often-costly diagnostic procedures that are applied for the diagnostics of porcine respiratory disease nowadays, a third-generation nanopore sequencing diagnostics workflow presents a cost-efficient and informative tool. This approach offers a panoramic view of microbial agents and contributes to the in-depth observation and characterization of viral and bacterial profiles within the respiratory disease context. While these data allow for the study of age-associated, swIAV-associated, and clinical symptom-associated observations, it also suggests that more effort should be put toward the investigation of coinfections and lesser-known pathogens (e.g., PHEV and PPIV), along with their potential roles in porcine respiratory disease. Overall, this approach will allow veterinary practitioners to tailor treatment and/or management changes on farms in a quicker, more complete, and cost-efficient way.}, } @article {pmid36853013, year = {2023}, author = {Ren, Y and Hao, L and Liu, J and Wang, P and Ding, Q and Chen, C and Song, Y}, title = {Alterations in the Gut Microbiota in Pregnant Women with Pregestational Type 2 Diabetes Mellitus.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0114622}, pmid = {36853013}, issn = {2379-5077}, mesh = {Infant, Newborn ; Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2/microbiology ; Pregnant Women ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Pregnancy Outcome ; *Hyperglycemia ; }, abstract = {Human gut dysbiosis is associated with type 2 diabetes mellitus (T2DM); however, the gut microbiome in pregnant women with pregestational type 2 diabetes mellitus (PGDM) remains unexplored. We investigated the alterations in the gut microbiota composition in pregnant women with or without PGDM. The gut microbiota was examined using 16S rRNA sequencing data of 234 maternal fecal samples that were collected during the first (T1), second (T2), and third (T3) trimesters. The PGDM group presented a reduction in the number of gut bacteria taxonomies as the pregnancies progressed. Linear discriminant analyses revealed that Megamonas, Bacteroides, and Roseburia intestinalis were enriched in the PGDM group, whereas Bacteroides vulgatus, Faecalibacterium prausnitzii, Eubacterium rectale, Bacteroides uniformis, Eubacterium eligens, Subdoligranulum, Bacteroides fragilis, Dialister, Lachnospiraceae, Christensenellaceae R-7, Roseburia inulinivorans, Streptococcus oralis, Prevotella melaninogenica, Neisseria perflava, Bacteroides ovatus, Bacteroides caccae, Veillonella dispar, and Haemophilus parainfluenzae were overrepresented in the control group. Correlation analyses showed that the PGDM-enriched taxa were correlated with higher blood glucose levels during pregnancy, whereas the taxonomic biomarkers of normoglycemic pregnancies exhibited negative correlations with glycemic traits. The microbial networks in the PGDM group comprised weaker microbial interactions than those in the control group. Our study reveals the distinct characteristics of the gut microbiota composition based on gestational ages between normoglycemic and PGDM pregnancies. Further longitudinal research involving women with T2DM at preconception stages and investigations using shotgun metagenomic sequencing should be performed to elucidate the relationships between specific bacterial functions and PGDM metabolic statuses during pregnancy and to identify potential therapeutic targets. IMPORTANCE The incidence of pregestational type 2 diabetes mellitus (PGDM) is increasing, with high rates of serious adverse maternal and neonatal outcomes that are strongly correlated with hyperglycemia. Recent studies have shown that type 2 diabetes mellitus is associated with gut microbial dysbiosis; however, the gut microbiome composition and its associations with the metabolic features of patients with PGDM remain largely unknown. In this study, we investigated the changes in the gut microbiota composition in pregnant women with and without PGDM. We identified differential taxa that may be correlated with maternal metabolic statuses during pregnancy. Additionally, we observed that the number of taxonomic and microbial networks of gut bacteria were distinctly reduced in women with hyperglycemia as their pregnancies progressed. These results extend our understanding of the associations between the gut microbial composition, PGDM-related metabolic changes, and pregnancy outcomes.}, } @article {pmid36852830, year = {2023}, author = {Oren, A}, title = {Naming new taxa of prokaryotes in the 21st century.}, journal = {Canadian journal of microbiology}, volume = {69}, number = {4}, pages = {151-157}, doi = {10.1139/cjm-2022-0266}, pmid = {36852830}, issn = {1480-3275}, mesh = {*Bacteria/genetics ; *Archaea/genetics ; Genomics ; }, abstract = {The nomenclature of prokaryotes is regulated by the rules of the International Code of Nomenclature of Prokaryotes (ICNP) and is based on the Linnaean binomial system. The current rules of the Code only cover the nomenclature of the cultivated minority. Proposals to incorporate the uncultivated majority of bacteria and archaea under the rules of the Code were recently rejected by the International Committee on Systematics of Prokaryotes. The provisional rank of Candidatus can be used to name uncultivated prokaryotes whose names cannot be validly published under the rules of the ICNP, but their names can now be validated under the Code of Nomenclature of Prokaryotes Described from Sequence Data (the SeqCode), which was recently established to cover the nomenclature of the uncultivated majority. Metagenomics, single-cell genomics, and high-throughput cultivation techniques have led to a flood of new organisms currently waiting to be named. Automated programs such as GAN and Protologger can assist researchers in naming and describing newly discovered prokaryotes, cultivated as well as uncultivated. However, Latin and Greek skills remain indispensable for proper quality control of names that must meet the standards set by the codes of nomenclature.}, } @article {pmid36852763, year = {2022}, author = {Sarwal, V and Brito, J and Mangul, S and Koslicki, D}, title = {TAMPA: interpretable analysis and visualization of metagenomics-based taxon abundance profiles.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {36852763}, issn = {2047-217X}, support = {R01 GM146462/GM/NIGMS NIH HHS/United States ; }, mesh = {*Metagenomics ; *Benchmarking ; Metagenome ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Metagenomic taxonomic profiling aims to predict the identity and relative abundance of taxa in a given whole-genome sequencing metagenomic sample. A recent surge in computational methods that aim to accurately estimate taxonomic profiles, called taxonomic profilers, has motivated community-driven efforts to create standardized benchmarking datasets and platforms, standardized taxonomic profile formats, and a benchmarking platform to assess tool performance. While this standardization is essential, there is currently a lack of tools to visualize the standardized output of the many existing taxonomic profilers. Thus, benchmarking studies rely on a single-value metrics to compare performance of tools and compare to benchmarking datasets. This is one of the major problems in analyzing metagenomic profiling data, since single metrics, such as the F1 score, fail to capture the biological differences between the datasets.

FINDINGS: Here we report the development of TAMPA (Taxonomic metagenome profiling evaluation), a robust and easy-to-use method that allows scientists to easily interpret and interact with taxonomic profiles produced by the many different taxonomic profiler methods beyond the standard metrics used by the scientific community. We demonstrate the unique ability of TAMPA to generate a novel biological hypothesis by highlighting the taxonomic differences between samples otherwise missed by commonly utilized metrics.

CONCLUSION: In this study, we show that TAMPA can help visualize the output of taxonomic profilers, enabling biologists to effectively choose the most appropriate profiling method to use on their metagenomics data. TAMPA is available on GitHub, Bioconda, and Galaxy Toolshed at https://github.com/dkoslicki/TAMPA and is released under the MIT license.}, } @article {pmid36852697, year = {2023}, author = {Saha, A and Gupta, A and Sar, P}, title = {Metagenome based analysis of groundwater from arsenic contaminated sites of West Bengal revealed community diversity and their metabolic potential.}, journal = {Journal of environmental science and health. Part A, Toxic/hazardous substances & environmental engineering}, volume = {58}, number = {2}, pages = {91-106}, doi = {10.1080/10934529.2023.2173919}, pmid = {36852697}, issn = {1532-4117}, mesh = {Metagenome ; *Arsenic/analysis ; *Water Pollutants, Chemical/analysis ; *Groundwater/chemistry ; Carbon/chemistry ; Sulfates/analysis ; RNA, Ribosomal, 16S ; }, abstract = {The study of microbial community in groundwater systems is considered to be essential to improve our understanding of arsenic (As) biogeochemical cycling in aquifers, mainly as it relates to the fate and transport of As. The present study was conducted to determine the microbial community composition and its functional potential using As-contaminated groundwater from part of the Bengal Delta Plain (BDP) in West Bengal, India. Geochemical analyses indicated low to moderate dissolved oxygen (0.42-3.02 mg/L), varying As (2.5-311 µg/L) and Fe (0.19-1.2 mg/L) content, while low concentrations of total organic carbon (TOC), total inorganic carbon (TIC), nitrate, and sulfate were detected. Proteobacteria was the most abundant phylum, while the indiscriminate presence of an array of archaeal phyla, Euryarchaeota, Crenarchaeota, Nanoarchaeota, etc., was noteworthy. The core community members were affiliated to Sideroxydans, Acidovorax, Pseudoxanthomonas, Brevundimonas, etc. However, diversity assessed over multiple seasons indicated a shift from Sideroxydans to Pseudomonas or Brevundimonas dominant community, suggestive of microbial response to seasonally fluctuating geochemical stimuli. Taxonomy-based functional potential showed prospects for As biotransformation, methanogenesis, sulfate respiration, denitrification, etc. Thus, this study strengthened existing reports from this region by capturing the less abundant or difficult-to-culture taxa collectively forming a major fraction of the microbial community.}, } @article {pmid36851800, year = {2023}, author = {Ibañez-Lligoña, M and Colomer-Castell, S and González-Sánchez, A and Gregori, J and Campos, C and Garcia-Cehic, D and Andrés, C and Piñana, M and Pumarola, T and Rodríguez-Frias, F and Antón, A and Quer, J}, title = {Bioinformatic Tools for NGS-Based Metagenomics to Improve the Clinical Diagnosis of Emerging, Re-Emerging and New Viruses.}, journal = {Viruses}, volume = {15}, number = {2}, pages = {}, pmid = {36851800}, issn = {1999-4915}, support = {PERIS//DGRIS/ ; IDI-20200297//Centre for Industrial Technological Development/ ; PI19/00301, PI22/00258//Instituto de Salud Carlos III/ ; FPU21/04150//Ministerio de Universidades/ ; REIPI RD16/0016/0003//Red Espanola de Investigacion en Patologia Infecciosa/ ; GLD21/00006//Gilead Sciences (Spain)/ ; }, mesh = {*Metagenomics ; Antiviral Agents ; Computational Biology ; Pandemics ; *Viruses/genetics ; }, abstract = {Epidemics and pandemics have occurred since the beginning of time, resulting in millions of deaths. Many such disease outbreaks are caused by viruses. Some viruses, particularly RNA viruses, are characterized by their high genetic variability, and this can affect certain phenotypic features: tropism, antigenicity, and susceptibility to antiviral drugs, vaccines, and the host immune response. The best strategy to face the emergence of new infectious genomes is prompt identification. However, currently available diagnostic tests are often limited for detecting new agents. High-throughput next-generation sequencing technologies based on metagenomics may be the solution to detect new infectious genomes and properly diagnose certain diseases. Metagenomic techniques enable the identification and characterization of disease-causing agents, but they require a large amount of genetic material and involve complex bioinformatic analyses. A wide variety of analytical tools can be used in the quality control and pre-processing of metagenomic data, filtering of untargeted sequences, assembly and quality control of reads, and taxonomic profiling of sequences to identify new viruses and ones that have been sequenced and uploaded to dedicated databases. Although there have been huge advances in the field of metagenomics, there is still a lack of consensus about which of the various approaches should be used for specific data analysis tasks. In this review, we provide some background on the study of viral infections, describe the contribution of metagenomics to this field, and place special emphasis on the bioinformatic tools (with their capabilities and limitations) available for use in metagenomic analyses of viral pathogens.}, } @article {pmid36851794, year = {2023}, author = {Dart, E and Fuhrman, JA and Ahlgren, NA}, title = {Diverse Marine T4-like Cyanophage Communities Are Primarily Comprised of Low-Abundance Species Including Species with Distinct Seasonal, Persistent, Occasional, or Sporadic Dynamics.}, journal = {Viruses}, volume = {15}, number = {2}, pages = {}, pmid = {36851794}, issn = {1999-4915}, support = {1R01GM120624-01A1/NH/NIH HHS/United States ; }, mesh = {*Bacteriophages/genetics ; Host Specificity ; Metagenome ; Pacific Ocean ; Seasons ; *Synechococcus ; }, abstract = {Cyanophages exert important top-down controls on their cyanobacteria hosts; however, concurrent analysis of both phage and host populations is needed to better assess phage-host interaction models. We analyzed picocyanobacteria Prochlorococcus and Synechococcus and T4-like cyanophage communities in Pacific Ocean surface waters using five years of monthly viral and cellular fraction metagenomes. Cyanophage communities contained thousands of mostly low-abundance (<2% relative abundance) species with varying temporal dynamics, categorized as seasonally recurring or non-seasonal and occurring persistently, occasionally, or sporadically (detected in ≥85%, 15-85%, or <15% of samples, respectively). Viromes contained mostly seasonal and persistent phages (~40% each), while cellular fraction metagenomes had mostly sporadic species (~50%), reflecting that these sample sets capture different steps of the infection cycle-virions from prior infections or within currently infected cells, respectively. Two groups of seasonal phages correlated to Synechococcus or Prochlorococcus were abundant in spring/summer or fall/winter, respectively. Cyanophages likely have a strong influence on the host community structure, as their communities explained up to 32% of host community variation. These results support how both seasonally recurrent and apparent stochastic processes, likely determined by host availability and different host-range strategies among phages, are critical to phage-host interactions and dynamics, consistent with both the Kill-the-Winner and the Bank models.}, } @article {pmid36851780, year = {2023}, author = {Krasnikov, N and Yuzhakov, A and Aliper, T and Gulyukin, A}, title = {Metagenomic Approach Reveals the Second Subtype of PRRSV-1 in a Pathogen Spectrum during a Clinical Outbreak with High Mortality in Western Siberia, Russia.}, journal = {Viruses}, volume = {15}, number = {2}, pages = {}, pmid = {36851780}, issn = {1999-4915}, mesh = {Animals ; Swine ; Siberia/epidemiology ; *Porcine respiratory and reproductive syndrome virus/genetics ; Russia/epidemiology ; Disease Outbreaks ; Europe, Eastern ; }, abstract = {Porcine reproductive and respiratory syndrome virus (PRRSV) has a significant economic impact on pig farming worldwide by causing reproductive problems and affecting the respiratory systems of swine. In Eastern Europe, PRRSV-1 strains are characterized by high genetic variability, and pathogenicity differs among all known subtypes. This case study describes the detection of a wide pathogen spectrum, including the second subtype PRRSV-1, with a high mortality rate among nursery piglets (23.8%). This study was conducted at a farrow-to-finish farm in the Western Siberia region of Russia. Clinical symptoms included apathy, sneezing, and an elevation in body temperature, and during the autopsy, degenerative lesions in different tissues were observed. Moreover, 1.5 percent of the affected animals displayed clinical signs of the central nervous system and were characterized by polyserositis. Nasal swabs from diseased piglets and various tissue swabs from deceased animals were studied. For diagnostics, the nanopore sequencing method was applied. All the samples tested positive for PRRSV, and a more detailed analysis defined it as a second subtype of PRRSV-1. The results, along with the clinical picture, showed a complex disease etiology with the dominant role of PRRSV-1 and were informative about the high pathogenicity of the subtype in question under field conditions.}, } @article {pmid36851669, year = {2023}, author = {Ambrose, RK and Blakebrough-Hall, C and Gravel, JL and Gonzalez, LA and Mahony, TJ}, title = {Characterisation of the Upper Respiratory Tract Virome of Feedlot Cattle and Its Association with Bovine Respiratory Disease.}, journal = {Viruses}, volume = {15}, number = {2}, pages = {}, pmid = {36851669}, issn = {1999-4915}, mesh = {Animals ; Cattle ; Case-Control Studies ; Virome ; *Respiratory Tract Diseases ; Trachea ; Nose ; *Cattle Diseases ; *Coronavirus, Bovine/genetics ; *Nidovirales ; Mammals ; }, abstract = {Bovine respiratory disease (BRD) is a major health problem within the global cattle industry. This disease has a complex aetiology, with viruses playing an integral role. In this study, metagenomics was used to sequence viral nucleic acids in the nasal swabs of BRD-affected cattle. The viruses detected included those that are well known for their association with BRD in Australia (bovine viral diarrhoea virus 1), as well as viruses known to be present but not fully characterised (bovine coronavirus) and viruses that have not been reported in BRD-affected cattle in Australia (bovine rhinitis, bovine influenza D, and bovine nidovirus). The nasal swabs from a case-control study were subsequently tested for 10 viruses, and the presence of at least one virus was found to be significantly associated with BRD. Some of the more recently detected viruses had inconsistent associations with BRD. Full genome sequences for bovine coronavirus, a virus increasingly associated with BRD, and bovine nidovirus were completed. Both viruses belong to the Coronaviridae family, which are frequently associated with disease in mammals. This study has provided greater insights into the viral pathogens associated with BRD and highlighted the need for further studies to more precisely elucidate the roles viruses play in BRD.}, } @article {pmid36851645, year = {2023}, author = {Plyusnin, I and Vapalahti, O and Sironen, T and Kant, R and Smura, T}, title = {Enhanced Viral Metagenomics with Lazypipe 2.}, journal = {Viruses}, volume = {15}, number = {2}, pages = {}, pmid = {36851645}, issn = {1999-4915}, mesh = {Animals ; Dogs ; Amino Acid Sequence ; *Animals, Wild ; Biological Evolution ; *Communicable Diseases, Emerging ; Nucleotides ; }, abstract = {Viruses are the main agents causing emerging and re-emerging infectious diseases. It is therefore important to screen for and detect them and uncover the evolutionary processes that support their ability to jump species boundaries and establish themselves in new hosts. Metagenomic next-generation sequencing (mNGS) is a high-throughput, impartial technology that has enabled virologists to detect either known or novel, divergent viruses from clinical, animal, wildlife and environmental samples, with little a priori assumptions. mNGS is heavily dependent on bioinformatic analysis, with an emerging demand for integrated bioinformatic workflows. Here, we present Lazypipe 2, an updated mNGS pipeline with, as compared to Lazypipe1, significant improvements in code stability and transparency, with added functionality and support for new software components. We also present extensive benchmarking results, including evaluation of a novel canine simulated metagenome, precision and recall of virus detection at varying sequencing depth, and a low to extremely low proportion of viral genetic material. Additionally, we report accuracy of virus detection with two strategies: homology searches using nucleotide or amino acid sequences. We show that Lazypipe 2 with nucleotide-based annotation approaches near perfect detection for eukaryotic viruses and, in terms of accuracy, outperforms the compared pipelines. We also discuss the importance of homology searches with amino acid sequences for the detection of highly divergent novel viruses.}, } @article {pmid36851634, year = {2023}, author = {Miller-Ensminger, T and Johnson, G and Banerjee, S and Putonti, C}, title = {When Plaquing Is Not Possible: Computational Methods for Detecting Induced Phages.}, journal = {Viruses}, volume = {15}, number = {2}, pages = {}, pmid = {36851634}, issn = {1999-4915}, mesh = {*Bacteriophages/genetics ; Lysogeny ; Prophages/genetics ; Chromosome Mapping ; Genome, Bacterial ; }, abstract = {High-throughput sequencing of microbial communities has uncovered a large, diverse population of phages. Frequently, phages found are integrated into their bacterial host genome. Distinguishing between phages in their integrated (lysogenic) and unintegrated (lytic) stage can provide insight into how phages shape bacterial communities. Here we present the Prophage Induction Estimator (PIE) to identify induced phages in genomic and metagenomic sequences. PIE takes raw sequencing reads and phage sequence predictions, performs read quality control, read assembly, and calculation of phage and non-phage sequence abundance and completeness. The distribution of abundances for non-phage sequences is used to predict induced phages with statistical confidence. In silico tests were conducted to benchmark this tool finding that PIE can detect induction events as well as phages with a relatively small burst size (10×). We then examined isolate genome sequencing data as well as a mock community and urinary metagenome data sets and found instances of induced phages in all three data sets. The flexibility of this software enables users to easily include phage predictions from their preferred tool of choice or phage sequences of interest. Thus, genomic and metagenomic sequencing now not only provides a means for discovering and identifying phage sequences but also the detection of induced prophages.}, } @article {pmid36851611, year = {2023}, author = {Starchevskaya, M and Kamanova, E and Vyatkin, Y and Tregubchak, T and Bauer, T and Bodnev, S and Rotskaya, U and Polenogova, O and Kryukov, V and Antonets, D}, title = {The Metagenomic Analysis of Viral Diversity in Colorado Potato Beetle Public NGS Data.}, journal = {Viruses}, volume = {15}, number = {2}, pages = {}, pmid = {36851611}, issn = {1999-4915}, mesh = {Animals ; *Coleoptera ; *Solanum tuberosum ; *Insecticides ; Metagenome ; *Dicistroviridae ; }, abstract = {The Colorado potato beetle (CPB) is one of the most serious insect pests due to its high ecological plasticity and ability to rapidly develop resistance to insecticides. The use of biological insecticides based on viruses is a promising approach to control insect pests, but the information on viruses which infect leaf feeding beetles is scarce. We performed a metagenomic analysis of 297 CPB genomic and transcriptomic samples from the public National Center for Biotechnology Information Sequence Read Archive (NCBI SRA) database. The reads that were not aligned to the reference genome were assembled with metaSPAdes, and 13314 selected contigs were analyzed with BLAST tools. The contigs and non-aligned reads were also analyzed with Kraken2 software. A total of 3137 virus-positive contigs were attributed to different viruses belonging to 6 types, 17 orders, and 32 families, matching over 97 viral species. The annotated sequences can be divided into several groups: those that are homologous to genetic sequences of insect viruses (Adintoviridae, Ascoviridae, Baculoviridae, Dicistroviridae, Chuviridae, Hytrosaviridae, Iflaviridae, Iridoviridae, Nimaviridae, Nudiviridae, Phasmaviridae, Picornaviridae, Polydnaviriformidae, Xinmoviridae etc.), plant viruses (Betaflexiviridae, Bromoviridae, Kitaviridae, Potyviridae), and endogenous retroviral elements (Retroviridae, Metaviridae). Additionally, the full-length genomes and near-full length genome sequences of several viruses were assembled. We also found sequences belonging to Bracoviriform viruses and, for the first time, experimentally validated the presence of bracoviral genetic fragments in the CPB genome. Our work represents the first attempt to discover the viral genetic material in CPB samples, and we hope that further studies will help to identify new viruses to extend the arsenal of biopesticides against CPB.}, } @article {pmid36850017, year = {2023}, author = {Theelen, MJP and Luiken, REC and Wagenaar, JA and Sloet van Oldruitenborgh-Oosterbaan, MM and Rossen, JWA and Schaafstra, FJWC and van Doorn, DA and Zomer, AL}, title = {Longitudinal study of the short- and long-term effects of hospitalisation and oral trimethoprim-sulfadiazine administration on the equine faecal microbiome and resistome.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {33}, pmid = {36850017}, issn = {2049-2618}, mesh = {Humans ; Horses ; Animals ; *Trimethoprim/pharmacology ; Longitudinal Studies ; RNA, Ribosomal, 16S/genetics ; Hospitalization ; Feces ; *Microbiota/genetics ; }, abstract = {BACKGROUND: Hospitalisation and antimicrobial treatment are common in horses and significantly impact the intestinal microbiota. Antimicrobial treatment might also increase levels of resistant bacteria in faeces, which could spread to other ecological compartments, such as the environment, other animals and humans. In this study, we aimed to characterise the short- and long-term effects of transportation, hospitalisation and trimethoprim-sulfadiazine (TMS) administration on the faecal microbiota and resistome of healthy equids.

METHODS: In a longitudinal experimental study design, in which the ponies served as their own control, faecal samples were collected from six healthy Welsh ponies at the farm (D0-D13-1), immediately following transportation to the hospital (D13-2), during 7 days of hospitalisation without treatment (D14-D21), during 5 days of oral TMS treatment (D22-D26) and after discharge from the hospital up to 6 months later (D27-D211). After DNA extraction, 16S rRNA gene sequencing was performed on all samples. For resistome analysis, shotgun metagenomic sequencing was performed on selected samples.

RESULTS: Hospitalisation without antimicrobial treatment did not significantly affect microbiota composition. Oral TMS treatment reduced alpha-diversity significantly. Kiritimatiellaeota, Fibrobacteres and Verrucomicrobia significantly decreased in relative abundance, whereas Firmicutes increased. The faecal microbiota composition gradually recovered after discontinuation of TMS treatment and discharge from the hospital and, after 2 weeks, was more similar to pre-treatment composition than to composition during TMS treatment. Six months later, however, microbiota composition still differed significantly from that at the start of the study and Spirochaetes and Verrucomicrobia were less abundant. TMS administration led to a significant (up to 32-fold) and rapid increase in the relative abundance of resistance genes sul2, tetQ, ant6-1a, and aph(3")-lb. lnuC significantly decreased directly after treatment. Resistance genes sul2 (15-fold) and tetQ (six-fold) remained significantly increased 6 months later.

CONCLUSIONS: Oral treatment with TMS has a rapid and long-lasting effect on faecal microbiota composition and resistome, making the equine hindgut a reservoir and potential source of resistant bacteria posing a risk to animal and human health through transmission. These findings support the judicious use of antimicrobials to minimise long-term faecal presence, excretion and the spread of antimicrobial resistance in the environment. Video Abstract.}, } @article {pmid36849099, year = {2023}, author = {Qiao, X and Fu, C and Chen, Y and Fang, F and Zhang, Y and Ding, L and Yang, K and Pan, B and Xu, N and Yu, K and Tao, H and Zhang, L}, title = {Molecular insights into enhanced nitrogen removal induced by trace fluoroquinolone antibiotics in an anammox system.}, journal = {Bioresource technology}, volume = {374}, number = {}, pages = {128784}, doi = {10.1016/j.biortech.2023.128784}, pmid = {36849099}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Nitrogen/metabolism ; Denitrification ; Anaerobic Ammonia Oxidation ; Oxidation-Reduction ; Bioreactors/microbiology ; *Ammonium Compounds/metabolism ; Bacteria/metabolism ; Fluoroquinolones/metabolism ; Anti-Bacterial Agents/metabolism ; }, abstract = {It has been widely reported that fluoroquinolones (FQs) can affect the anaerobic ammonium oxidization (anammox) microorganisms, which interferes with the performance of nitrogen removal from wastewater. However, the metabolic mechanism of anammox microorganisms responding to FQs has rarely been explored. In this study, it was found that 20 μg/L FQs promoted the nitrogen removal performance of anammox microorganisms in batch exposure assays, and 36-51% of FQs were removed simultaneously. Combined metabolomics and genome-resolved metagenomic analysis revealed up-regulated carbon fixation in anammox bacteria (AnAOB), while purine and pyrimidine metabolism, protein generation and transmembrane transport were enhanced in AnAOB and symbiotic bacteria by 20 μg/L FQs. Consequently, hydrazine dehydrogenation, nitrite reduction, and ammonium assimilation were bolstered, improving the nitrogen removal efficiency of the anammox system. These results revealed the potential roles of specific microorganisms in response to emerging FQs and provided further information for practical application of anammox technology in wastewater treatment.}, } @article {pmid36848852, year = {2023}, author = {Liang, Y and Zhou, X and Wu, Y and Wu, Y and Zeng, X and Yu, Z and Peng, P}, title = {Meta-omics elucidates key degraders in a bacterial tris(2-butoxyethyl) phosphate (TBOEP)-degrading enrichment culture.}, journal = {Water research}, volume = {233}, number = {}, pages = {119774}, doi = {10.1016/j.watres.2023.119774}, pmid = {36848852}, issn = {1879-2448}, mesh = {*Phosphates ; Esters/chemistry/metabolism ; Organophosphorus Compounds ; Organophosphates/metabolism ; *Flame Retardants/metabolism ; }, abstract = {Organophosphate esters (OPEs) are emerging contaminants of growing concern, and there is limited information about the bacterial transformation of OPEs. In this study, we investigated the biotransformation of tris(2-butoxyethyl) phosphate (TBOEP), a frequently detected alkyl-OPE by a bacterial enrichment culture under aerobic conditions. The enrichment culture degraded 5 mg/L TBOEP following the first-order kinetics with a reaction rate constant of 0.314 h[-1]. TBOEP was mainly degraded via ether bond cleavage, evidenced by the production of bis(2-butoxyethyl) hydroxyethyl phosphate, 2-butoxyethyl bis(2-hydroxyethyl) phosphate, and 2-butoxyethyl (2-hydroxyethyl) hydrogen phosphate. Other transformation pathways include terminal oxidation of the butoxyethyl group and phosphoester bond hydrolysis. Metagenomic sequencing generated 14 metagenome-assembled genomes (MAGs), showing that the enrichment culture primarily consisted of Gammaproteobacteria, Bacteroidota, Myxococcota, and Actinobacteriota. One MAG assigned to Rhodocuccus ruber strain C1 was the most active in the community, showing upregulation of various monooxygenase, dehydrogenase, and phosphoesterase genes throughout the degradation process, and thus was identified as the key degrader of TBOEP and the metabolites. Another MAG affiliated with Ottowia mainly contributed to TBOEP hydroxylation. Our results provided a comprehensive understanding of the bacterial TBOEP degradation at community level.}, } @article {pmid36848210, year = {2023}, author = {Rojas-Gätjens, D and Avey-Arroyo, J and Chaverri, P and Rojas-Jimenez, K and Chavarría, M}, title = {Differences in fungal communities in the fur of two- and three-toed sloths revealed by ITS metabarcoding.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {2}, pages = {}, pmid = {36848210}, issn = {1465-2080}, mesh = {Animals ; *Mycobiome ; *Sloths ; Ecosystem ; Host Specificity ; Metagenomics ; }, abstract = {Sloths have dense fur on which insects, algae, bacteria and fungi coexist. Previous studies using cultivation-dependent methods and 18S rRNA sequencing revealed that the fungal communities in their furs comprise members of the phyla Ascomycota and Basidiomycota. In this note, we increase the resolution and knowledge of the mycobiome inhabiting the fur of the two- (Choloepus hoffmanni) and three-toed (Bradypus variegatus) sloths. Targeted amplicon metagenomic analysis of ITS2 nrDNA sequences obtained from 10 individuals of each species inhabiting the same site revealed significant differences in the structure of their fungal communities and also in the alpha-diversity estimators. The results suggest a specialization by host species and that the host effect is stronger than that of sex, age and animal weight. Capnodiales were the dominant order in sloths' fur and Cladosporium and Neodevriesia were the most abundant genera in Bradypus and Choloepus, respectively. The fungal communities suggest that the green algae that inhabit the fur of sloths possibly live lichenized with Ascomycota fungal species. The data shown in this note offer a more detailed view of the fungal content in the fur of these extraordinary animals and could help explain other mutualistic relationships in this complex ecosystem.}, } @article {pmid36847914, year = {2023}, author = {Jin, X and Wang, JK and Wang, Q}, title = {Microbial β-glucanases: production, properties, and engineering.}, journal = {World journal of microbiology & biotechnology}, volume = {39}, number = {4}, pages = {106}, pmid = {36847914}, issn = {1573-0972}, mesh = {*Engineering ; Biomass ; Cell Membrane ; *Cell Wall ; Cellulose ; }, abstract = {Lignocellulosic biomass, which mainly consists of cellulose and hemicellulose, is the most abundant renewable biopolymer on earth. β-Glucanases are glycoside hydrolases (GHs) that hydrolyze β-glucan, one of the dominant components of the plant cell wall, into cello-oligosaccharides and glucose. Among them, endo-β-1,4-glucanase (EC 3.2.1.4), exo-glucanase/cellobiohydrolase (EC 3.2.1.91), and β-glucosidase (EC 3.2.1.21) play critical roles in the digestion of glucan-like substrates. β-Glucanases have attracted considerable interest within the scientific community due to their applications in the feed, food, and textile industries. In the past decade, there has been considerable progress in the discovery, production, and characterization of novel β-glucanases. Advances in the development of next-generation sequencing techniques, including metagenomics and metatranscriptomics, have unveiled novel β-glucanases isolated from the gastrointestinal microbiota. The study of β-glucanases is beneficial for research and development of commercial products. In this study, we review the classification, properties, and engineering of β-glucanases.}, } @article {pmid36847735, year = {2023}, author = {Saraiva, JP and Bartholomäus, A and Toscan, RB and Baldrian, P and Nunes da Rocha, U}, title = {Recovery of 197 eukaryotic bins reveals major challenges for eukaryote genome reconstruction from terrestrial metagenomes.}, journal = {Molecular ecology resources}, volume = {23}, number = {5}, pages = {1066-1076}, doi = {10.1111/1755-0998.13776}, pmid = {36847735}, issn = {1755-0998}, support = {460129525//Deutsche Forschungsgemeinschaft/ ; VH-NG-1248 Micro' Big Data'//Helmholtz-Gemeinschaft/ ; }, mesh = {*Metagenome ; *Eukaryota/genetics ; Ecosystem ; Genome, Microbial ; Fungi/genetics ; Metagenomics ; }, abstract = {As most eukaryotic genomes are yet to be sequenced, the mechanisms underlying their contribution to different ecosystem processes remain untapped. Although approaches to recovering Prokaryotic genomes have become common in genome biology, few studies have tackled the recovery of eukaryotic genomes from metagenomes. This study assessed the reconstruction of microbial eukaryotic genomes using 6000 metagenomes from terrestrial and some transition environments using the EukRep pipeline. Only 215 metagenomic libraries yielded eukaryotic bins. From a total of 447 eukaryotic bins recovered 197 were classified at the phylum level. Streptophytes and fungi were the most represented clades with 83 and 73 bins, respectively. More than 78% of the obtained eukaryotic bins were recovered from samples whose biomes were classified as host-associated, aquatic, and anthropogenic terrestrial. However, only 93 bins were taxonomically assigned at the genus level and 17 bins at the species level. Completeness and contamination estimates were obtained for a total of 193 bins and consisted of 44.64% (σ = 27.41%) and 3.97% (σ = 6.53%), respectively. Micromonas commoda was the most frequent taxon found while Saccharomyces cerevisiae presented the highest completeness, probably because more reference genomes are available. Current measures of completeness are based on the presence of single-copy genes. However, mapping of the contigs from the recovered eukaryotic bins to the chromosomes of the reference genomes showed many gaps, suggesting that completeness measures should also include chromosome coverage. Recovering eukaryotic genomes will benefit significantly from long-read sequencing, development of tools for dealing with repeat-rich genomes, and improved reference genomes databases.}, } @article {pmid36847620, year = {2023}, author = {Gu, BH and Choi, JP and Park, T and Kim, AS and Jung, HY and Choi, DY and Lee, SJ and Chang, YS and Kim, M and Park, HK}, title = {Adult asthma with symptomatic eosinophilic inflammation is accompanied by alteration in gut microbiome.}, journal = {Allergy}, volume = {78}, number = {7}, pages = {1909-1921}, doi = {10.1111/all.15691}, pmid = {36847620}, issn = {1398-9995}, support = {NRF-2022R1C1C1003256//Korea Government/ ; NRF-2020R1C1C1011678//Korea Government/ ; }, mesh = {Humans ; Adult ; *Gastrointestinal Microbiome ; *Asthma/genetics ; *Pulmonary Eosinophilia ; Inflammation/genetics ; Metagenome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Accumulating evidence suggests that the gut microbiome is associated with asthma. However, altered gut microbiome in adult asthma is not yet well established. We aimed to investigate the gut microbiome profiles of adult asthmatic patients with symptomatic eosinophilic inflammation.

METHODS: The 16 s rRNA gene metagenomic analysis of feces in the symptomatic eosinophilic asthma group (EA, n = 28) was compared with the healthy control (HC, n = 18) and the chronic cough control (CC, n = 13). A correlation analysis between individual taxa and clinical markers was performed within the EA group. Changes in the gut microbiome were examined in patients with significant symptom improvement in the EA group.

RESULTS: The relative abundances of Lachnospiraceae and Oscillospiraceae significantly decreased and Bacteroidetes increased in the EA group. Within EA group, Lachnospiraceae was negatively correlated with indicators of type 2 inflammation and lung function decline. Enterobacteriaceae and Prevotella was positively associated with type 2 inflammation and lung function decline, respectively. The abundance of predicted genes associated with amino acid metabolism and secondary bile acid biosynthesis was diminished in the EA group. These functional gene family alterations could be related to gut permeability, and the serum lipopolysaccharide concentration was actually high in the EA group. EA patients with symptom improvement after 1 month did not show a significant change in the gut microbiome.

CONCLUSIONS: Symptomatic eosinophilic adult asthma patients showed altered the gut microbiome composition. Specifically, a decrease in commensal clostridia was observed, and a decrease in Lachnospiraceae was correlated with blood eosinophilia and lung function decline.}, } @article {pmid36847544, year = {2023}, author = {Mitra, A and Caron, DA and Faure, E and Flynn, KJ and Leles, SG and Hansen, PJ and McManus, GB and Not, F and do Rosario Gomes, H and Santoferrara, LF and Stoecker, DK and Tillmann, U}, title = {The Mixoplankton Database (MDB): Diversity of photo-phago-trophic plankton in form, function, and distribution across the global ocean.}, journal = {The Journal of eukaryotic microbiology}, volume = {70}, number = {4}, pages = {e12972}, doi = {10.1111/jeu.12972}, pmid = {36847544}, issn = {1550-7408}, mesh = {Animals ; *Plankton/physiology ; *Ecosystem ; Eukaryota/physiology ; Phytoplankton ; Zooplankton/physiology ; Food Chain ; Oceans and Seas ; }, abstract = {Protist plankton are major members of open-water marine food webs. Traditionally divided between phototrophic phytoplankton and phagotrophic zooplankton, recent research shows many actually combine phototrophy and phagotrophy in the one cell; these protists are the "mixoplankton." Under the mixoplankton paradigm, "phytoplankton" are incapable of phagotrophy (diatoms being exemplars), while "zooplankton" are incapable of phototrophy. This revision restructures marine food webs, from regional to global levels. Here, we present the first comprehensive database of marine mixoplankton, bringing together extant knowledge of the identity, allometry, physiology, and trophic interactivity of these organisms. This mixoplankton database (MDB) will aid researchers that confront difficulties in characterizing life traits of protist plankton, and it will benefit modelers needing to better appreciate ecology of these organisms with their complex functional and allometric predator-prey interactions. The MDB also identifies knowledge gaps, including the need to better understand, for different mixoplankton functional types, sources of nutrition (use of nitrate, prey types, and nutritional states), and to obtain vital rates (e.g. growth, photosynthesis, ingestion, factors affecting photo' vs. phago' -trophy). It is now possible to revisit and re-classify protistan "phytoplankton" and "zooplankton" in extant databases of plankton life forms so as to clarify their roles in marine ecosystems.}, } @article {pmid36847515, year = {2023}, author = {Gauthier, NPG and Chorlton, SD and Krajden, M and Manges, AR}, title = {Agnostic Sequencing for Detection of Viral Pathogens.}, journal = {Clinical microbiology reviews}, volume = {36}, number = {1}, pages = {e0011922}, pmid = {36847515}, issn = {1098-6618}, mesh = {*Viruses/genetics ; High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics ; Metagenomics/methods ; Genome, Viral/genetics ; }, abstract = {The advent of next-generation sequencing (NGS) technologies has expanded our ability to detect and analyze microbial genomes and has yielded novel molecular approaches for infectious disease diagnostics. While several targeted multiplex PCR and NGS-based assays have been widely used in public health settings in recent years, these targeted approaches are limited in that they still rely on a priori knowledge of a pathogen's genome, and an untargeted or unknown pathogen will not be detected. Recent public health crises have emphasized the need to prepare for a wide and rapid deployment of an agnostic diagnostic assay at the start of an outbreak to ensure an effective response to emerging viral pathogens. Metagenomic techniques can nonspecifically sequence all detectable nucleic acids in a sample and therefore do not rely on prior knowledge of a pathogen's genome. While this technology has been reviewed for bacterial diagnostics and adopted in research settings for the detection and characterization of viruses, viral metagenomics has yet to be widely deployed as a diagnostic tool in clinical laboratories. In this review, we highlight recent improvements to the performance of metagenomic viral sequencing, the current applications of metagenomic sequencing in clinical laboratories, as well as the challenges that impede the widespread adoption of this technology.}, } @article {pmid36846796, year = {2023}, author = {Feng, J and Lin, T and Mihalca, AD and Niu, Q and Oosthuizen, MC}, title = {Editorial: Coinfections of Lyme disease and other tick-borne diseases.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1140545}, doi = {10.3389/fmicb.2023.1140545}, pmid = {36846796}, issn = {1664-302X}, } @article {pmid36846795, year = {2023}, author = {Nan, Q and Ye, Y and Tao, Y and Jiang, X and Miao, Y and Jia, J and Miao, J}, title = {Alterations in metabolome and microbiome signatures provide clues to the role of antimicrobial peptide KT2 in ulcerative colitis.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1027658}, pmid = {36846795}, issn = {1664-302X}, abstract = {INTRODUCTION: Ulcerative colitis (UC) is an inflammatory disease of the intestinal tract with unknown etiology. Both genetic and environmental factors are involved in the occurrence and development of UC. Understanding changes in the microbiome and metabolome of the intestinal tract is crucial for the clinical management and treatment of UC.

METHODS: Here, we performed metabolomic and metagenomic profiling of fecal samples from healthy control mice (HC group), DSS (Dextran Sulfate Sodium Salt) -induced UC mice (DSS group), and KT2-treated UC mice (KT2 group).

RESULTS AND DISCUSSION: In total, 51 metabolites were identified after UC induction, enriched in phenylalanine metabolism, while 27 metabolites were identified after KT2 treatment, enriched in histidine metabolism and bile acid biosynthesis. Fecal microbiome analysis revealed significant differences in nine bacterial species associated with the course of UC, including Bacteroides, Odoribacter, and Burkholderiales, which were correlated with aggravated UC, and Anaerotruncus, Lachnospiraceae, which were correlated with alleviated UC. We also identified a disease-associated network connecting the above bacterial species with UC-associated metabolites, including palmitoyl sphingomyelin, deoxycholic acid, biliverdin, and palmitoleic acid. In conclusion, our results indicated that Anaerotruncus, Lachnospiraceae, and Mucispirillum were protective species against DSS-induced UC in mice. The fecal microbiomes and metabolomes differed significantly among the UC mice and KT2-treated and healthy-control mice, providing potential evidence for the discovery of biomarkers of UC.}, } @article {pmid36846781, year = {2023}, author = {Fu, L and Lai, S and Zhou, Z and Chen, Z and Cheng, L}, title = {Seasonal variation of microbial community and methane metabolism in coalbed water in the Erlian Basin, China.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1114201}, pmid = {36846781}, issn = {1664-302X}, abstract = {Coalbed water is a semi-open system connecting underground coalbeds with the external environment. Microorganisms in coalbed water play an important role in coal biogasification and the carbon cycle. The community assemblages of microorganisms in such a dynamic system are not well understood. Here, we used high-throughput sequencing and metagenomic analysis to investigate microbial community structure and identify the potential functional microorganisms involved in methane metabolism in coalbed water in the Erlian Basin, a preferred low-rank coal bed methane (CBM) exploration and research area in China. The results showed that there were differences in the responses of bacteria and archaea to seasonal variation. Bacterial community structure was affected by seasonal variation but archaea was not. Methane oxidation metabolism dominated by Methylomonas and methanogenesis metabolism dominated by Methanobacterium may exist simultaneously in coalbed water.}, } @article {pmid36846768, year = {2023}, author = {Min, Z and Yang, L and Hu, Y and Huang, R}, title = {Oral microbiota dysbiosis accelerates the development and onset of mucositis and oral ulcers.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1061032}, pmid = {36846768}, issn = {1664-302X}, abstract = {With the rapid development of metagenomic high-throughput sequencing technology, more and more oral mucosal diseases have been proven to be associated with oral microbiota shifts or dysbiosis. The commensal oral microbiota can greatly influence the colonization and resistance of pathogenic microorganisms and induce primary immunity. Once dysbiosis occurs, it can lead to damage to oral mucosal epithelial defense, thus accelerating the pathological process. As common oral mucosal diseases, oral mucositis and ulcers seriously affect patients' prognosis and quality of life. However, from the microbiota perspective, the etiologies, specific alterations of oral flora, pathogenic changes, and therapy for microbiota are still lacking in a comprehensive overview. This review makes a retrospective summary of the above problems, dialectically based on oral microecology, to provide a new perspective on oral mucosal lesions management and aims at improving patients' quality of life.}, } @article {pmid36846760, year = {2023}, author = {Vuillemin, A}, title = {Nitrogen cycling activities during decreased stratification in the coastal oxygen minimum zone off Namibia.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1101902}, pmid = {36846760}, issn = {1664-302X}, abstract = {Productive oxygen minimum zones are regions dominated by heterotrophic denitrification fueled by sinking organic matter. Microbial redox-sensitive transformations therein result in the loss and overall geochemical deficit in inorganic fixed nitrogen in the water column, thereby impacting global climate in terms of nutrient equilibrium and greenhouse gases. Here, geochemical data are combined with metagenomes, metatranscriptomes, and stable-isotope probing incubations from the water column and subseafloor of the Benguela upwelling system. The taxonomic composition of 16S rRNA genes and relative expression of functional marker genes are used to explore metabolic activities by nitrifiers and denitrifiers under decreased stratification and increased lateral ventilation in Namibian coastal waters. Active planktonic nitrifiers were affiliated with Candidatus Nitrosopumilus and Candidatus Nitrosopelagicus among Archaea, and Nitrospina, Nitrosomonas, Nitrosococcus, and Nitrospira among Bacteria. Concurrent evidence from taxonomic and functional marker genes shows that populations of Nitrososphaeria and Nitrospinota were highly active under dysoxic conditions, coupling ammonia and nitrite oxidation with respiratory nitrite reduction, but minor metabolic activity toward mixotrophic use of simple nitrogen compounds. Although active reduction of nitric oxide to nitrous oxide by Nitrospirota, Gammaproteobacteria, and Desulfobacterota was tractable in bottom waters, the produced nitrous oxide was apparently scavenged at the ocean surface by Bacteroidota. Planctomycetota involved in anaerobic ammonia oxidation were identified in dysoxic waters and their underlying sediments, but were not found to be metabolically active due to limited availability of nitrite. Consistent with water column geochemical profiles, metatranscriptomic data demonstrate that nitrifier denitrification is fueled by fixed and organic nitrogen dissolved in dysoxic waters, and prevails over canonical denitrification and anaerobic oxidation of ammonia when the Namibian coastal waters and sediment-water interface on the shelf are ventilated by lateral currents during austral winter.}, } @article {pmid36846759, year = {2023}, author = {Wei, TS and Gao, ZM and Gong, L and Li, QM and Zhou, YL and Chen, HG and He, LS and Wang, Y}, title = {Genome-centric view of the microbiome in a new deep-sea glass sponge species Bathydorus sp.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1078171}, pmid = {36846759}, issn = {1664-302X}, abstract = {Sponges are widely distributed in the global ocean and harbor diverse symbiotic microbes with mutualistic relationships. However, sponge symbionts in the deep sea remain poorly studied at the genome level. Here, we report a new glass sponge species of the genus Bathydorus and provide a genome-centric view of its microbiome. We obtained 14 high-quality prokaryotic metagenome-assembled genomes (MAGs) affiliated with the phyla Nitrososphaerota, Pseudomonadota, Nitrospirota, Bdellovibrionota, SAR324, Bacteroidota, and Patescibacteria. In total, 13 of these MAGs probably represent new species, suggesting the high novelty of the deep-sea glass sponge microbiome. An ammonia-oxidizing Nitrososphaerota MAG B01, which accounted for up to 70% of the metagenome reads, dominated the sponge microbiomes. The B01 genome had a highly complex CRISPR array, which likely represents an advantageous evolution toward a symbiotic lifestyle and forceful ability to defend against phages. A sulfur-oxidizing Gammaproteobacteria species was the second most dominant symbiont, and a nitrite-oxidizing Nitrospirota species could also be detected, but with lower relative abundance. Bdellovibrio species represented by two MAGs, B11 and B12, were first reported as potential predatory symbionts in deep-sea glass sponges and have undergone dramatic genome reduction. Comprehensive functional analysis indicated that most of the sponge symbionts encoded CRISPR-Cas systems and eukaryotic-like proteins for symbiotic interactions with the host. Metabolic reconstruction further illustrated their essential roles in carbon, nitrogen, and sulfur cycles. In addition, diverse putative phages were identified from the sponge metagenomes. Our study expands the knowledge of microbial diversity, evolutionary adaption, and metabolic complementarity in deep-sea glass sponges.}, } @article {pmid36846685, year = {2023}, author = {Rüstemoğlu, M and Erkan, ME and Cengiz, G and Hajyzadeh, M}, title = {Bacterial metagenome profiling of hand-made herby cheese samples utilizing high-throughput sequencing to detect geographical indication and marketing potential.}, journal = {Heliyon}, volume = {9}, number = {2}, pages = {e13334}, pmid = {36846685}, issn = {2405-8440}, abstract = {Food safety has been a major concern for consumers. Origin of food products matter for consumers such that the quality, reputation, or other special characteristics can be attributed essentially to that origin. While a geographical indication informs consumers for the origin of the product, it develops a competitive advantage for the markets. To detect distinguishing features of dairy products, the microbial composition of its microbiota is one of the emerging areas of interest. Utilizing novel approaches such as Next Generation Sequencing (NGS) technology to decipher the genetic code of 16s rRNA genes to characterize the bacterial population is widely applied. The bacterial microbiota of the herby cheese samples which were collected from Şırnak province in the South Eastern region of Turkey was examined by an NGS approach for purpose of finding geographical indication possibilities. In brief, Firmicutes is the dominant phyla where Lactobacillaceae and Streptococcaceae are abundant families across the analyzed herby cheese microbiota. The most prominent species is Companilactobacillus ginsenosidimutans detected as the dominant member of the bacterial consortia in 16 herby cheese samples. Another remarkable finding reported here is the Weissella jogaejeotgali which was detected in 15 cheese samples. Albeit the abundance of Levilactobacillus koreensis is low at the microbiome level it was identified in four herby cheese samples. As expected, lactic acid bacteria such as Lactobacillus delbrueckii, Lactococcus raffinolactis and Tetragenococcus halophilus were also identified. On the other hand, bacterial diversity and microbial composition among cheese samples are not significantly affected by mixing different herbs on the manufacturing of herby cheeses. To the best of our knowledge, C. ginsenosidimutans, W. jogaejeotgali and L. koreensis are identified and reported for the first time in a dairy product and the bacterial richness and evenness of herby cheese are higher than those of most other cheeses. These findings make the cheeses in the geography where the samples were produced more valuable and provide opportunities for them to receive geographical indications. Thus, it will create added value while marketing the products.}, } @article {pmid36846335, year = {2023}, author = {He, L and Yang, H and Liu, S and Liang, W and Zhou, Z and Long, J and Wu, J}, title = {Physiological analysis of severe chlamydia psittaci pneumonia and clinical diagnosis after doxycycline-based treatment.}, journal = {Frontiers in physiology}, volume = {14}, number = {}, pages = {1132724}, pmid = {36846335}, issn = {1664-042X}, abstract = {Objective: To describe the clinical spectrum of severe Chlamydia psittaci pneumonia in order to understand the disease better. Methods: Retrospective analysis was made on 31 patients with severe Chlamydia psittaci pneumonia diagnosed in ICU by next-generation sequencing of metagenome Metagenomic next-generation sequencing(mNGS) from January 2019-November 2022, including clinical characteristics, laboratory examination results, imaging characteristics, treatment, and prognosis. Results: We included 31 patients with severe Chlamydia psittaci pneumonia, 15 of whom had a history of virus exposure. There were 12 cases with multiple bacterial infections, and the common symptoms included fever (31/31,100%), dyspnea (31/31, 100%), cough (22/31, 71.0%), and myalgia (20/31, 64.5%). Laboratory data showed that white blood cells were average or slightly increased, but the levels of C-reactive protein and neutrophils were high. CT findings of the lung were consolidation (19/31, 61.3%) and pleural effusion (11/31, 35.5%). Only one lobe was involved in 11 patients (35.5%). Before diagnosis, 22 patients (71.0%) did not have atypical pathogens in their antimicrobial regimen. After diagnosis, 19 patients (61.3%) received single drug treatment, of which doxycycline or moxifloxacin were the most commonly used drugs. Among 31 patients, three died, nine improved, and nineteen were cured. Conclusion: The clinical manifestations of severe Chlamydia psittaci pneumonia are non-specific. The application of mNGS can improve the diagnostic accuracy of Chlamydia psittaci pneumonia, reduce the unnecessary use of antibiotics, and shorten the course of the disease. Doxycycline-based treatment is effective for severe chlamydia psittaci pneumonia, but it is necessary to understand the secondary bacterial infection and other complications in the course of the disease.}, } @article {pmid36846017, year = {2023}, author = {Huang, Y and Zheng, W and Gan, W and Zhang, T}, title = {Chlamydia psittaci pneumonia: a clinical analysis of 12 patients.}, journal = {Annals of translational medicine}, volume = {11}, number = {3}, pages = {144}, pmid = {36846017}, issn = {2305-5839}, abstract = {BACKGROUND: We conducted a retrospective analysis to explore the clinical characteristics, laboratory examination, imaging features, treatment outcomes, and prognosis of the Chlamydia psittaci (C. psittaci) pneumonia, aiming to improve early diagnosis and treatment.

METHODS: The clinical data of 12 patients with C. psittaci pneumonia diagnosed by metagenomic next-generation sequencing (mNGS) in our hospital were retrospectively analyzed. These data included baseline information, epidemiological history, clinical symptoms and signs, laboratory and chest computed tomography (CT) examination findings, treatment schemes, and prognosis.

RESULTS: The average age of the 12 patients was 58.25±13.27 years, and there were 7 (58.3%) males and 5 (41.7%) females in this cohort. Five patients had clear exposure to poultry or birds. The main clinical manifestations included fever (12/12, 100.0%), cough (12/12, 100.0%), expectoration (10/12, 83.3%), and dyspnea (10/12, 83.3%). Laboratory examination showed marked elevation of the total white blood cell (WBC) count, neutrophil (NEUT) count, C-reactive protein (CRP), procalcitonin (PCT), D-dimer, aspartate aminotransferase (AST), alanine aminotransferase (ALT), serum creatinine, and creatine kinase (CK) levels; as well as decreased hemoglobin (HGB), blood platelet (PLT), and albumin (ALB) levels. Arterial blood gas analysis showed that the average value of the oxygenation index (PO2/FiO2) was 290.9±83.1, which was less than 300 in 6 cases (50.0%). The main chest CT features were patchy or consolidation in the bilateral or unilateral lungs, and the boundary was not clear but showed a bronchial inflation sign. Also, some of the cases were accompanied by pleural effusion. Once the etiology was obtained, the patients were quickly treated with doxycycline combined with other antibiotics. All 12 patients improved and were discharged from the hospital. However, two severe patients were admitted to the intensive care unit (ICU) and received ventilation and monitoring treatment. There were no deaths.

CONCLUSIONS: C. psittaci pneumonia is an atypical community-acquired pneumonia (CAP) caused by C. psittaci infection, with its own laboratory and imaging characteristics. In this study, diagnosis was established based on the application of mNGS owing to the absence of easily available conventional pathogenic evidence. In addition, an aggressive and precise treatment strategy can help achieve a favorable prognosis for patients.}, } @article {pmid36844847, year = {2023}, author = {Shi, Y and Guo, W and Hu, M and Wang, Y and Li, J and Hu, W and Li, X and Xu, K}, title = {A case of severe leptospirosis with Jarisch-Herxheimer reaction presenting as respiratory failure.}, journal = {Frontiers in public health}, volume = {11}, number = {}, pages = {1125306}, pmid = {36844847}, issn = {2296-2565}, mesh = {Humans ; *Leptospirosis/complications/diagnosis/drug therapy ; Penicillins/adverse effects ; Anti-Bacterial Agents/adverse effects ; Tetracycline ; *Respiratory Insufficiency/etiology ; }, abstract = {BACKGROUND: Leptospirosis is a widespread zoonotic disease caused by pathogenic Leptospira spp. The treatment of penicillin or tetracycline can cause a Jarisch-Herxheimer reaction (JHR), which can lead to acute respiratory distress syndrome (ARDS) and multi-organ failure in severe cases. The overall course of evolution and imaging features of a JHR exacerbation of leptospirosis have rarely been reported.

CASE PRESENTATION: We present a case of leptospirosis complicated by pulmonary alveolar hemorrhage and a Jarisch-Herxheimer reaction (JHR) that required respiratory and vasopressor support. This case demonstrates a well-defined course of evolution of JHR and the imaging features.

CONCLUSIONS: Leptospirosis is easily misdiagnosed in some sporadic areas, and JHR complicates its management. Early diagnosis and appropriate treatment can reduce the mortality of severe leptospirosis with JHR.}, } @article {pmid36844675, year = {2023}, author = {Dai, Q and Ding, J and Cui, X and Zhu, Y and Chen, H and Zhu, L}, title = {Beyond bacteria: Reconstructing microorganism connections and deciphering the predicted mutualisms in mammalian gut metagenomes.}, journal = {Ecology and evolution}, volume = {13}, number = {2}, pages = {e9829}, pmid = {36844675}, issn = {2045-7758}, abstract = {Numerous gut microbial studies have focused on bacteria. However, archaea, viruses, fungi, protists, and nematodes are also regular residents of the gut ecosystem. Little is known about the composition and potential interactions among these six kingdoms in the same samples. Here, we unraveled the complex connection among them using approximately 123 gut metagenomes from 42 mammalian species (including carnivores, omnivores, and herbivores). We observed high variation in bacterial and fungal families and relatively low variation in archaea, viruses, protists, and nematodes. We found that some fungi in the mammalian intestine might come from environmental sources (e.g., soil and dietary plants), and some might be native to the intestine (e.g., the occurrence of Neocallimastigomycetes). The Methanobacteriaceae and Plasmodiidae families (archaea and protozoa, respectively) were predominant in these metagenomes, whereas Onchocercidae and Trichuridae were the two most common nematodes, and Siphoviridae and Myoviridae the two most common virus families in these mammalian gut metagenomes. Interestingly, most of the pairwise co-occurrence patterns were significantly positive among these six kingdoms, and significantly negative networks mainly occurred between fungi and prokaryotes (both bacteria and archaea). Our study revealed some inconvenient characteristics in the mammalian gut microorganism ecosystem: (1) the community formed by members of the analyzed kingdoms reflects the life history of the host and the potential threat posed by pathogenic protists and nematodes in mammals; and (2) the networks suggest the existence of predicted mutualism among members of these six kingdoms and of the predicted competition, mainly among fungi and other kingdoms.}, } @article {pmid36844641, year = {2023}, author = {Tashkandi, M and Baz, L}, title = {Function of CAZymes encoded by highly abundant genes in rhizosphere microbiome of Moringa oleifera.}, journal = {Saudi journal of biological sciences}, volume = {30}, number = {3}, pages = {103578}, pmid = {36844641}, issn = {1319-562X}, abstract = {Metagenomic analysis referring to CAZymes (Carbohydrate-Active enZymes) of CAZy classes encoded by the most abundant genes in rhizosphere versus bulk soil microbes of the wild plant Moringa oleifera was conducted. Results indicated that microbiome signatures and corresponding CAZy datasets differ between the two soil types. CAZy class glycoside hydrolases (GH) and its α-amylase family GH13 in rhizobiome were proven to be the most abundant among CAZy classes and families. The most abundant bacteria harboring these CAZymes include phylum Actinobacteria and its genus Streptomyces and phylum Proteobacteria and its genus Microvirga. These CAZymes participate in KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway "Starch and sucrose metabolism" and mainly use the "double displacement catalytic mechanism" in their reactions. We assume that microbiome of the wild plant Moringa oleifera is a good source of industrially important enzymes that act on starch hydrolysis and/or biosynthesis. In addition, metabolic engineering and integration of certain microbes of this microbiomes can also be used in improving growth of domestic plants and their ability to tolerate adverse environmental conditions.}, } @article {pmid36844406, year = {2023}, author = {Stout, MJ and Brar, AK and Herter, BN and Rankin, A and Wylie, KM}, title = {The plasma virome in longitudinal samples from pregnant patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1061230}, pmid = {36844406}, issn = {2235-2988}, mesh = {Infant, Newborn ; Pregnancy ; Female ; Humans ; Virome ; *Premature Birth ; *Virus Diseases/diagnosis ; Plasma ; *Anelloviridae/genetics ; *Herpesviridae ; Metagenomics/methods ; }, abstract = {INTRODUCTION: Nucleic acid from viruses is common in peripheral blood, even in asymptomatic individuals. How physiologic changes of pregnancy impact host-virus dynamics for acute, chronic, and latent viral infections is not well described. Previously we found higher viral diversity in the vagina during pregnancy associated with preterm birth (PTB) and Black race. We hypothesized that higher diversity and viral copy numbers in the plasma would show similar trends.

METHODS: To test this hypothesis, we evaluated longitudinally collected plasma samples from 23 pregnant patients (11 term and 12 preterm) using metagenomic sequencing with ViroCap enrichment to enhance virus detection. Sequence data were analyzed with the ViroMatch pipeline.

RESULTS: We detected nucleic acid from at least 1 virus in at least 1 sample from 87% (20/23) of the maternal subjects. The viruses represented 5 families: Herpesviridae, Poxviridae, Papillomaviridae, Anelloviridae, and Flaviviridae. We analyzed cord plasma from 18 of the babies from those patients and found nucleic acid from viruses in 33% of the samples (6/18) from 3 families: Herpesviridae, Papillomaviridae, and Anelloviridae. Some viral genomes were found in both maternal plasma and cord plasma from maternal-fetal pairs (e.g. cytomegalovirus, anellovirus). We found that Black race associated with higher viral richness (number of different viruses detected) in the maternal blood samples (P=0.003), consistent with our previous observations in vaginal samples. We did not detect associations between viral richness and PTB or the trimester of sampling. We then examined anelloviruses, a group of viruses that is ubiquitous and whose viral copy numbers fluctuate with immunological state. We tested anellovirus copy numbers in plasma from 63 pregnant patients sampled longitudinally using qPCR. Black race associated with higher anellovirus positivity (P<0.001) but not copy numbers (P=0.1). Anellovirus positivity and copy numbers were higher in the PTB group compared to the term group (P<0.01, P=0.003, respectively). Interestingly, these features did not occur at the time of delivery but appeared earlier in pregnancy, suggesting that although anelloviruses were biomarkers for PTB they were not triggering parturition.

DISCUSSION: These results emphasize the importance of longitudinal sampling and diverse cohorts in studies of virome dynamics during pregnancy.}, } @article {pmid36844401, year = {2023}, author = {Zhang, G and Zhang, H and Hu, X and Xu, D and Tang, B and Tang, M and Liu, S and Li, Y and Xu, W and Guo, C and Gao, Q}, title = {Clinical application value of metagenomic next-generation sequencing in the diagnosis of spinal infections and its impact on clinical outcomes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1076525}, pmid = {36844401}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; *Anti-Bacterial Agents/therapeutic use ; C-Reactive Protein ; Hospitals, University ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {This study aimed to evaluate the impact of precise treatment administered according to the results of metagenomic next-generation sequencing (mNGS) on the clinical outcomes of patients with spinal infections. In this multicenter retrospective study, the clinical data of 158 patients with spinal infections who were admitted to Xiangya Hospital Central South University, Xiangya Boai Rehabilitation Hospital, The First Hospital of Changsha, and Hunan Chest Hospital from 2017 to 2022 were reviewed. Among these 158 patients, 80 patients were treated with targeted antibiotics according to the mNGS results and were assigned to the targeted medicine (TM) group. The remaining 78 patients with negative mNGS results and those without mNGS and negative microbial culture results were treated with empirical antibiotics and assigned to the empirical drug (EM) group. The impact of targeted antibiotics based on the mNGS results on the clinical outcomes of patients with spinal infections in the two groups was analyzed. The positive rate of mNGS for diagnosing spinal infections was significantly higher than that of microbiological culture (X [2]=83.92, P<0.001), procalcitonin (X [2]=44.34, P<0.001), white blood cells (X [2]=89.21, P < 0.001), and IGRAs (Interferon-gamma Release Tests) (X [2] = 41.50, P < 0.001). After surgery, C-reactive protein (CRP) and erythrocyte sedimentation rate (ESR) showed a decreasing trend in the patients with spinal infections in both the TM and EM groups. The decrease in CRP was more obvious in the TM group than in the EM group at 7, 14 days, 3, and 6 months after surgery (P<0.05). The decrease in ESR was also significantly obvious in the TM group compared with the EM group at 1 and 6 months after surgery (P<0.05). The time taken for CRP and ESR to return to normal in the TM group was significantly shorter than that in the EM group (P<0.05). There was no significant difference in the incidence of poor postoperative outcomes between the two groups. The positive rate of mNGS for the diagnosis of spinal infection is significantly higher than that of traditional detection methods. The use of targeted antibiotics based on mNGS results could enable patients with spinal infections to achieve a faster clinical cure.}, } @article {pmid36844396, year = {2023}, author = {Qin, C and Zhang, S and Zhao, Y and Ding, X and Yang, F and Zhao, Y}, title = {Diagnostic value of metagenomic next-generation sequencing in sepsis and bloodstream infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1117987}, pmid = {36844396}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *Intensive Care Units ; *Sepsis/diagnosis ; Hospitalization ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {OBJECTIVE: To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) in sepsis and bloodstream infection (BSI).

METHODS: A retrospective analysis of patients diagnosed with sepsis and BSI at the First Affiliated Hospital of Zhengzhou University from January 2020 to February 2022 was conducted. All the patients underwent blood culture and were divided into mNGS group and non-mNGS group according to whether mNGS was performed or not. The mNGS group was further divided into early group (< 1 day), intermediate group (1-3 days), and late group (> 3 days) according to the time of mNGS inspection.

RESULTS: In 194 patients with sepsis and BSI, the positive rate of mNGS for identifying pathogens was significantly higher than that of blood culture (77.7% vs. 47.9%), and the detection period was shorter (1.41 ± 1.01 days vs. 4.82 ± 0.73 days); the difference was statistically significant (p < 0.05). The 28-day mortality rate of the mNGS group (n = 112) was significantly lower than that of the non-mNGS group (n = 82) (47.32% vs. 62.20%, p = 0.043). The total hospitalization time for the mNGS group was longer than that for the non-mNGS group (18 (9, 33) days vs. 13 (6, 23) days, p = 0.005). There was no significant difference in the ICU hospitalization time, mechanical ventilation time, vasoactive drug use time, and 90-day mortality between the two groups (p > 0.05). Sub-group analysis of patients in the mNGS group showed that the total hospitalization time and the ICU hospitalization time in the late group were longer than those in the early group (30 (18, 43) days vs. 10 (6, 26) days, 17 (6, 31) days vs. 6 (2, 10) days), and the ICU hospitalization time in the intermediate group was longer than that in the early group (6 (3, 15) days vs. 6 (2, 10) days); the differences were statistically significant (p < 0.05). The 28-day mortality rate of the early group was higher than that of the late group (70.21% vs. 30.00%), and the difference was statistically significant (p = 0.001).

CONCLUSIONS: mNGS has the advantages of a short detection period and a high positive rate in the diagnosis of pathogens causing BSI and, eventually, sepsis. Routine blood culture combined with mNGS can significantly reduce the mortality of septic patients with BSI. Early detection using mNGS can shorten the total hospitalization time and the ICU hospitalization time of patients with sepsis and BSI.}, } @article {pmid36844226, year = {2023}, author = {Liu, Y and Mo, X and Feng, Y and Willoughby, RE and Weng, X and Wang, Y and Li, X and Gao, J and Tian, J and Peng, J}, title = {Metagenomic next-generation sequencing for the etiological diagnosis of rabies virus in cerebrospinal fluid.}, journal = {Frontiers in medicine}, volume = {10}, number = {}, pages = {982290}, pmid = {36844226}, issn = {2296-858X}, abstract = {BACKGROUND: Rabies is a highly fatal disease. Once symptoms develop, death usually occurs within days. Survivors were occasionally reported in the literatures. Ante-mortem diagnosis remains a challenge in most rabies endemic countries. A novel, accurate diagnostic assay is highly desirable.

METHODS: We used metagenomic next-generation sequencing (mNGS) to examine the cerebrospinal fluid (CSF) samples of a 49-year-old patient with rabies and validated the results by TaqMan PCR and RT-PCR/Sanger sequencing.

RESULTS: Metagenomic next-generation sequencing identified sequence reads uniquely aligned to the rabies virus (RABV). PCR confirmed the presence of the partial RABV N gene in the CSF. Phylogenetic analysis showed that the RABV grouped as an Asian clade, which is the most broadly distributed clade in China.

CONCLUSION: Metagenomic next-generation sequencing may be a useful screening tool for the etiological diagnosis of rabies, especially in the absence of timely rabies laboratory testing or in patients with no exposure history.}, } @article {pmid36843502, year = {2023}, author = {Winder, JC and Braga, LPP and Kuhn, MA and Thompson, LM and Olefeldt, D and Tanentzap, AJ}, title = {Climate warming has direct and indirect effects on microbes associated with carbon cycling in northern lakes.}, journal = {Global change biology}, volume = {29}, number = {11}, pages = {3039-3053}, doi = {10.1111/gcb.16655}, pmid = {36843502}, issn = {1365-2486}, support = {804673//H2020 European Research Council/ ; }, mesh = {*Lakes ; Climate ; *Permafrost/microbiology ; Carbon Cycle ; Archaea/metabolism ; Carbon/metabolism ; }, abstract = {Northern lakes disproportionately influence the global carbon cycle, and may do so more in the future depending on how their microbial communities respond to climate warming. Microbial communities can change because of the direct effects of climate warming on their metabolism and the indirect effects of climate warming on groundwater connectivity from thawing of surrounding permafrost, especially at lower landscape positions. Here we used shotgun metagenomics to compare the taxonomic and functional gene composition of sediment microbes in 19 peatland lakes across a 1600-km permafrost transect in boreal western Canada. We found microbes responded differently to the loss of regional permafrost cover than to increases in local groundwater connectivity. These results suggest that both the direct and indirect effects of climate warming, which were respectively associated with loss of permafrost and subsequent changes in groundwater connectivity interact to change microbial composition and function. Archaeal methanogens and genes involved in all major methanogenesis pathways were more abundant in warmer regions with less permafrost, but higher groundwater connectivity partly offset these effects. Bacterial community composition and methanotrophy genes did not vary with regional permafrost cover, and the latter changed similarly to methanogenesis with groundwater connectivity. Finally, we found an increase in sugar utilization genes in regions with less permafrost, which may further fuel methanogenesis. These results provide the microbial mechanism for observed increases in methane emissions associated with loss of permafrost cover in this region and suggest that future emissions will primarily be controlled by archaeal methanogens over methanotrophic bacteria as northern lakes warm. Our study more generally suggests that future predictions of aquatic carbon cycling will be improved by considering how climate warming exerts both direct effects associated with regional-scale permafrost thaw and indirect effects associated with local hydrology.}, } @article {pmid36843227, year = {2023}, author = {Lynch, LE and Hair, AB and Soni, KG and Yang, H and Gollins, LA and Narvaez-Rivas, M and Setchell, KDR and Preidis, GA}, title = {Cholestasis impairs gut microbiota development and bile salt hydrolase activity in preterm neonates.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2183690}, pmid = {36843227}, issn = {1949-0984}, support = {K08 DK113114/DK/NIDDK NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; T32 GM136554/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Infant, Newborn ; *Gastrointestinal Microbiome ; Case-Control Studies ; Infant, Premature ; *Cholestasis ; Ursodeoxycholic Acid ; Bile Acids and Salts ; }, abstract = {Cholestasis refers to impaired bile flow from the liver to the intestine. In neonates, cholestasis causes poor growth and may progress to liver failure and death. Normal bile flow requires an intact liver-gut-microbiome axis, whereby liver-derived primary bile acids are transformed into secondary bile acids. Microbial bile salt hydrolase (BSH) enzymes are responsible for the first step, deconjugating glycine- and taurine-conjugated primary bile acids. Cholestatic neonates often are treated with the potent choleretic bile acid ursodeoxycholic acid (UDCA), although interactions between UDCA, gut microbes, and other bile acids are poorly understood. To gain insight into how the liver-gut-microbiome axis develops in extreme prematurity and how cholestasis alters this maturation, we conducted a nested case-control study collecting 124 stool samples longitudinally from 24 preterm infants born at mean 27.2 ± 1.8 weeks gestation and 946 ± 249.6 g, half of whom developed physiologic cholestasis. Samples were analyzed by whole metagenomic sequencing, in vitro BSH enzyme activity assays optimized for low biomass fecal samples, and quantitative mass spectrometry to measure the bile acid metabolome. In extremely preterm neonates, acquisition of the secondary bile acid biosynthesis pathway and BSH genes carried by Clostridium perfringens are the most prominent features of early microbiome development. Cholestasis interrupts this developmental pattern. BSH gene abundance and enzyme activity are profoundly reduced in cholestatic neonates, resulting in decreased quantities of unconjugated bile acids. UDCA restores total fecal bile acid levels in cholestatic neonates, but this is due to a 522-fold increase in fecal UDCA. A majority of bile acids in early development are atypical positional and stereo-isomers of bile acids. We report novel associations linking isomeric bile acids and BSH activity to neonatal growth trajectories. These data highlight deconjugation of bile acids as a key microbial function that is acquired in early neonatal development and impaired by cholestasis.}, } @article {pmid36842848, year = {2023}, author = {Ojala, T and Kankuri, E and Kankainen, M}, title = {Understanding human health through metatranscriptomics.}, journal = {Trends in molecular medicine}, volume = {29}, number = {5}, pages = {376-389}, doi = {10.1016/j.molmed.2023.02.002}, pmid = {36842848}, issn = {1471-499X}, mesh = {Humans ; *Metagenomics ; *Microbiota ; }, abstract = {Metatranscriptomics has revolutionized our ability to explore and understand transcriptional programs in microbial communities. Moreover, it has enabled us to gain deeper and more specific insight into the microbial activities in human gut, respiratory, oral, and vaginal communities. Perhaps the most important contribution of metatranscriptomics arises, however, from the analyses of disease-associated communities. We review the advantages and disadvantages of metatranscriptomics analyses in understanding human health and disease. We focus on human tissues low in microbial biomass and conditions associated with dysbiotic microbiota. We conclude that a more widespread use of metatranscriptomics and increased knowledge on microbe activities will uncover critical interactions between microbes and host in human health and provide diagnostic basis for culturing-independent, direct functional pathogen identification.}, } @article {pmid36842577, year = {2023}, author = {Wang, F and Zhang, L and Luo, Y and Li, Y and Cheng, X and Cao, J and Wu, J and Huang, H and Luo, J and Su, Y}, title = {Surfactant aggravated the antibiotic's stress on antibiotic resistance genes proliferation by altering antibiotic solubilization and microbial traits in sludge anaerobic fermentation.}, journal = {The Science of the total environment}, volume = {873}, number = {}, pages = {162440}, doi = {10.1016/j.scitotenv.2023.162440}, pmid = {36842577}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/toxicity ; *Sewage/microbiology ; Fermentation ; Surface-Active Agents/toxicity ; Anaerobiosis ; Genes, Bacterial ; Sulfadiazine ; Tetracycline ; Drug Resistance, Microbial/genetics ; Cell Proliferation ; }, abstract = {The excessive application of antibiotics and surfactants resulted in their massive accumulation in waste activated sludge (WAS), but the co-occurrent impacts of antibiotics and surfactants on the antibiotic resistant genes (ARGs) fates have seldom reported. This work mainly revealed the roles and critical mechanisms of sodium dodecyl benzene sulfonate (SDBS) on the sulfadiazine (SDZ) stressing for ARGs distribution during WAS anaerobic fermentation. High-throughput qPCR and metagenomic analysis revealed that SDBS aggravated the SDZ selective pressure, and accelerated the proliferation of ARGs. The total abundance of ARGs was increased from 8.81 × 10[10] in SDZ to 1.17 × 10[11] copies/g TSS in the SDBS/SDZ co-occurrence system. Specifically, the absolute abundances of ermF (MLSB), mefA (MLSB), tetM-01 (tetracycline), tetX (tetracycline), sul2 (sulfonamide) and strB (aminoglycoside) were risen from 4.60 × 10[8]-7.44 × 10[9] copies/g TSS in the SDZ reactor to 1.02 × 10[9]-4.63 × 10[10] copies/g TSS in SDBS/SDZ reactor. SDBS was contributed to the SDZ solubilization and simultaneously effective in disintegrating extracellular polymeric substances and improving cell membrane permeability, which would facilitate the SDZ transport and its interactions with ARGs hosts. Consequently, the microbial community structure was evidently altered, and the typical ARGs hosts (i.e., Saccharimonadales and Ahniella) were greatly enriched. Also, the cell signal transduction systems (i.e., glnL, glrK and pilG), oxidative stress response (i.e., frmA and recA) and bacterial secretion systems (i.e., VirB4), which were related with ARGs propagation, were all provoked in the co-occurred SDBS/SDZ reactor compared with that of sole SDZ. PLS-PM analysis suggested that the bacterial community was the predominant factor that determined the ARGs fates, followed by mobile genetic elements and metabolic pathway. This work demonstrated the interactive effects of surfactants and antibiotics on the ARGs fates in WAS fermentation systems and gave insightful implications on the ecological risks of different exogenous pollutants.}, } @article {pmid36842329, year = {2023}, author = {Zhou, L and Zhao, B and Zhuang, WQ}, title = {Double-edged sword effects of dissimilatory nitrate reduction to ammonium (DNRA) bacteria on anammox bacteria performance in an MBR reactor.}, journal = {Water research}, volume = {233}, number = {}, pages = {119754}, doi = {10.1016/j.watres.2023.119754}, pmid = {36842329}, issn = {1879-2448}, mesh = {*Ammonium Compounds ; Nitrates ; Nitrites ; Anaerobic Ammonia Oxidation ; Nitrogen Dioxide ; Oxidation-Reduction ; Bacteria ; Nitrogen ; Bioreactors/microbiology ; Denitrification ; }, abstract = {Dissimilatory nitrate reduction to ammonium (DNRA) bacteria imposing double-edged sword effects on anammox bacteria were investigated in an anammox-membrane bioreactor (MBR) experiencing an induced crash-recovery event. During the experiment, the anammox-MBR was loaded with NH4[+]-N:NO2[-]-N ratios (RatioNH4[+]-N: NO2[-]-N) of 1.20-1.60. Initially, the anammox-MBR removed over 95% of 100 mg/L NH4[+]-N and 132 mg/L NO2[-]-N (RatioNH4[+]-N: NO2[-]-N = 0.76, the well accepted stoichiometric RatioNH4[+]-N: NO2[-]-N for anammox) in the influent (Stage 0). Then, we induced a system crash-recovery event via nitrite shock loadings to better understand responses from different guilds of bacteria in anammox-MBR, loaded with 1.60 RatioNH4[+]-N: NO2[-]-N with 100 mg/L NO2[-]-N in the influent (Stage 1). Interestingly, the nitrogen removal by anammox bacteria was maintained for about 20 days before starting to decrease significantly. In Stage 2, we further increased influent nitrite concentration to 120 mg/L (1.33 RatioNH4[+]-N: NO2[-]-N) to simulate a high nitrite toxicity scenario for a short period of time. As expected, nitrogen removal efficiency dropped to only 16.8%. After the induced system crash, anammox-MBR performance recovered steadily to 93.2% nitrogen removal with a 1.25 RatioNH4[+]-N:NO2[-]-N and a low nitrite influent concentration of 80 mg/L NO2[-]-N. Metagenomics analysis revealed that a probable causality of the decreasing nitrogen removal efficiency in Stage 1 was the overgrowth of DNRA-capable bacteria. The results showed that the members within the Ignavibacteriales order (21.7%) out competed anammox bacteria (17.0%) in the anammox-MBR with elevated nitrite concentrations in the effluent. High NO2[-]-N loading (120 mg N/L) further caused the predominant Candidatus Kuenenia spp. were replaced by Candidatus Brocadia spp. Therefore, it was evident that DNRA bacteria posed negative effects on anammox with 1.60 RatioNH4[+]-N: NO2[-]-N. Also, when 120 mg/L NO2[-]-N fed to anammox-MBR (RatioNH4[+]-N: NO2[-]-N = 1.33), canonical denitrification became the primary nitrogen sink with both DNRA and anammox activities decreased. They probably fed on lysed microbial cells of anammox and DNRA. In Stage 3, a low RatioNH4[+]-N: NO2[-]-N (1.25) with 80 mg/L NO2[-]-N was used to rescue the system, which effectively promoted DNRA-capable bacteria growth. Although anammox bacteria's abundance was only 7.7% during this stage, they could be responsible for about 90% of the total nitrogen removal during this stage.}, } @article {pmid36841901, year = {2023}, author = {Doré, H and Guyet, U and Leconte, J and Farrant, GK and Alric, B and Ratin, M and Ostrowski, M and Ferrieux, M and Brillet-Guéguen, L and Hoebeke, M and Siltanen, J and Le Corguillé, G and Corre, E and Wincker, P and Scanlan, DJ and Eveillard, D and Partensky, F and Garczarek, L}, title = {Differential global distribution of marine picocyanobacteria gene clusters reveals distinct niche-related adaptive strategies.}, journal = {The ISME journal}, volume = {17}, number = {5}, pages = {720-732}, pmid = {36841901}, issn = {1751-7370}, mesh = {Seawater/microbiology ; Ecosystem ; Ferric Compounds/metabolism ; Oceans and Seas ; *Synechococcus/genetics/metabolism ; Metagenome ; Multigene Family ; Nitrogen/metabolism ; Phosphorus/metabolism ; *Prochlorococcus/genetics ; Phylogeny ; }, abstract = {The ever-increasing number of available microbial genomes and metagenomes provides new opportunities to investigate the links between niche partitioning and genome evolution in the ocean, especially for the abundant and ubiquitous marine picocyanobacteria Prochlorococcus and Synechococcus. Here, by combining metagenome analyses of the Tara Oceans dataset with comparative genomics, including phyletic patterns and genomic context of individual genes from 256 reference genomes, we show that picocyanobacterial communities thriving in different niches possess distinct gene repertoires. We also identify clusters of adjacent genes that display specific distribution patterns in the field (eCAGs) and are thus potentially involved in the same metabolic pathway and may have a key role in niche adaptation. Several eCAGs are likely involved in the uptake or incorporation of complex organic forms of nutrients, such as guanidine, cyanate, cyanide, pyrimidine, or phosphonates, which might be either directly used by cells, for example for the biosynthesis of proteins or DNA, or degraded to inorganic nitrogen and/or phosphorus forms. We also highlight the enrichment of eCAGs involved in polysaccharide capsule biosynthesis in Synechococcus populations thriving in both nitrogen- and phosphorus-depleted areas vs. low-iron (Fe) regions, suggesting that the complexes they encode may be too energy-consuming for picocyanobacteria thriving in the latter areas. In contrast, Prochlorococcus populations thriving in Fe-depleted areas specifically possess an alternative respiratory terminal oxidase, potentially involved in the reduction of Fe(III) to Fe(II). Altogether, this study provides insights into how phytoplankton communities populate oceanic ecosystems, which is relevant to understanding their capacity to respond to ongoing climate change.}, } @article {pmid36840602, year = {2023}, author = {Schildkraut, JA and Coolen, JPM and Severin, H and Koenraad, E and Aalders, N and Melchers, WJG and Hoefsloot, W and Wertheim, HFL and van Ingen, J}, title = {MGIT Enriched Shotgun Metagenomics for Routine Identification of Nontuberculous Mycobacteria: a Route to Personalized Health Care.}, journal = {Journal of clinical microbiology}, volume = {61}, number = {3}, pages = {e0131822}, pmid = {36840602}, issn = {1098-660X}, mesh = {Humans ; Nontuberculous Mycobacteria ; Phylogeny ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; *Mycobacterium ; *Mycobacterium marinum ; }, abstract = {Currently, nontuberculous mycobacteria (NTM) are identified using small genomic regions, and species-level identification is often not possible. We introduce a next-generation sequencing (NGS) workflow that identifies mycobacteria to (sub)species level on the basis of the whole genome extracted from enriched shotgun metagenomic data. This technique is used to study the association between genotypes and clinical manifestations to pave the way to more personalized health care. Two sets of clinical isolates (explorative set [n = 212] and validation set [n = 235]) were included. All data were analyzed using a custom pipeline called MyCodentifier. Sequences were matched against a custom hsp65 database (NGS-hsp65) and whole-genome database (NGS-WG) created based on the phylogeny presented by Tortoli et al. (E. Tortoli, T. Fedrizzi, C. J. Meehan, A. Trovato, et al., Infect Genet Evol 56:19-25, 2017, https://doi.org/10.1016/j.meegid.2017.10.013). Lastly, phylogenetic analysis was performed and correlated with clinical manifestation. In the explorative set, we observed 98.6% agreement between the line probe assay and the NGS-hsp65 database. In the validation set, 99.1% agreement between the NGS-WG and NGS-hsp65 databases was seen on the complex level. We identified a cluster of Mycobacterium marinum isolates not represented by the Tortoli et al. phylogeny. Phylogenetic analysis of M. avium complex isolates confirmed misclassification of M. timonense and M. bouchedurhonense and identified subclusters within M. avium although no correlation with clinical manifestation was observed. We performed routine NGS to identify NTM from MGIT enriched shotgun metagenomic data. Phylogenetic analyses identified subtypes of M. avium, but in our set of isolates no correlation with clinical manifestation was found. However, this NGS workflow paves a way for more personalized health care in the future.}, } @article {pmid36840579, year = {2023}, author = {Rix, GD and Sims, LP and Dawson, RA and Williamson, G and Bryant, Y and Crombie, AT and Murrell, JC}, title = {Analysis of Essential Isoprene Metabolic Pathway Proteins in Variovorax sp. Strain WS11.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {3}, pages = {e0212222}, pmid = {36840579}, issn = {1098-5336}, mesh = {*Mixed Function Oxygenases/metabolism ; Oxidation-Reduction ; *Hemiterpenes/metabolism ; Bacteria/metabolism ; Aldehyde Dehydrogenase/metabolism ; Metabolic Networks and Pathways/genetics ; }, abstract = {Isoprene monooxygenase (IsoMO, encoded by isoABCDEF) initiates the oxidation of the climate-active gas isoprene, with the genes isoGHIJ and aldH nearly always found adjacent to isoABCDEF in extant and metagenome-derived isoprene degraders. The roles of isoGHIJ and aldH are uncertain, although each is essential to isoprene degradation. We report here the characterization of these proteins from two model isoprene degraders, Rhodococcus sp. strain AD45 and Variovorax sp. strain WS11. The genes isoHIJ and aldH from Variovorax and aldH from Rhodococcus were expressed individually in Escherichia coli as maltose binding protein fusions to overcome issues of insolubility. The activity of two glutathione S-transferases from Variovorax, IsoI and IsoJ was assessed with model substrates, and the conversion of epoxyisoprene to the intermediate 1-hydroxy-2-glutathionyl-2-methyl-3-butene (HGMB) was demonstrated. The next step of the isoprene metabolic pathway of Variovorax is catalyzed by the dehydrogenase IsoH, resulting in the conversion of HGMB to 2-glutathionyl-2-methyl-3-butenoic acid (GMBA). The aldehyde dehydrogenases (AldH) from Variovorax and Rhodococcus were examined with a variety of aldehydes, with both exhibiting maximum activity with butanal. AldH significantly increased the rate of production of NADH when added to the IsoH-catalyzed conversion of HGMB to GMBA (via GMB), suggesting a synergistic role for AldH in the isoprene metabolic pathway. An in silico analysis of IsoG revealed that this protein, which is essential for isoprene metabolism in Variovorax, is an enzyme of the formyl CoA-transferase family and is predicted to catalyze the formation of a GMBA-CoA thioester as an intermediate in the isoprene oxidation pathway. IMPORTANCE Isoprene is a climate-active gas, largely produced by trees, which is released from the biosphere in amounts equivalent to those of methane and all other volatile organic compounds combined. Bacteria found in many environments, including soils and on the surface of leaves of isoprene-producing trees, can grow on isoprene and thus may represent a significant biological sink for this globally significant volatile compound and remove isoprene before it escapes to the atmosphere, thus reducing its potency as a climate-active gas. The initial oxidation of isoprene by bacteria is mediated by isoprene monooxygenase encoded by the genes isoABCDEF. In isoprene-degrading bacteria, a second gene cluster, isoGHIJ, is also present, although the exact role in isoprene degradation by the proteins encoded by these genes is uncertain. This investigation sheds new light on the roles of these proteins in the isoprene oxidation pathway in two model isoprene-degrading bacteria of the genera Rhodococcus and Variovorax.}, } @article {pmid36840260, year = {2023}, author = {Anguita-Maeso, M and Navas-Cortés, JA and Landa, BB}, title = {Insights into the Methodological, Biotic and Abiotic Factors Influencing the Characterization of Xylem-Inhabiting Microbial Communities of Olive Trees.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, pmid = {36840260}, issn = {2223-7747}, support = {AGL2016-75606-R and PID2020-114917RB-I00//Programa Estatal de I+D Orientado a los Retos de la Sociedad from Spanish Government, the Spanish State Research Agency and FEDER-EU/ ; TED2021-130110B-C41//Proyectos Orientados a la Transición Ecológica y a la Transición Digital-Plan de Recuperación, Transformación y Resiliencia from Spanish Government, the Spanish State Research Agency/ ; grant 727987//XF-ACTORS (Xylella fastidiosa Active Containment Through a Multidisciplinary Oriented Research Strategy; from the European Union's Horizon 2020 Framework Research Programme/ ; }, abstract = {Vascular pathogens are the causal agents of some of the most devastating plant diseases in the world, which can cause, under specific conditions, the destruction of entire crops. These plant pathogens activate a range of physiological and immune reactions in the host plant following infection, which may trigger the proliferation of a specific microbiome to combat them by, among others, inhibiting their growth and/or competing for space. Nowadays, it has been demonstrated that the plant microbiome can be modified by transplanting specific members of the microbiome, with exciting results for the control of plant diseases. However, its practical application in agriculture for the control of vascular plant pathogens is hampered by the limited knowledge of the plant endosphere, and, in particular, of the xylem niche. In this review, we present a comprehensive overview of how research on the plant microbiome has evolved during the last decades to unravel the factors and complex interactions that affect the associated microbial communities and their surrounding environment, focusing on the microbial communities inhabiting the xylem vessels of olive trees (Olea europaea subsp. europaea), the most ancient and important woody crop in the Mediterranean Basin. For that purpose, we have highlighted the role of xylem composition and its associated microorganisms in plants by describing the methodological approaches explored to study xylem microbiota, starting from the methods used to extract xylem microbial communities to their assessment by culture-dependent and next-generation sequencing approaches. Additionally, we have categorized some of the key biotic and abiotic factors, such as the host plant niche and genotype, the environment and the infection with vascular pathogens, that can be potential determinants to critically affect olive physiology and health status in a holobiont context (host and its associated organisms). Finally, we have outlined future directions and challenges for xylem microbiome studies based on the recent advances in molecular biology, focusing on metagenomics and culturomics, and bioinformatics network analysis. A better understanding of the xylem olive microbiome will contribute to facilitate the exploration and selection of specific keystone microorganisms that can live in close association with olives under a range of environmental/agronomic conditions. These microorganisms could be ideal targets for the design of microbial consortia that can be applied by endotherapy treatments to prevent or control diseases caused by vascular pathogens or modify the physiology and growth of olive trees.}, } @article {pmid36840091, year = {2023}, author = {Kutasy, B and Kiniczky, M and Decsi, K and Kálmán, N and Hegedűs, G and Alföldi, ZP and Virág, E}, title = {'Garlic-lipo'4Plants: Liposome-Encapsulated Garlic Extract Stimulates ABA Pathway and PR Genes in Wheat (Triticum aestivum).}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {4}, pages = {}, pmid = {36840091}, issn = {2223-7747}, support = {KFI_16-1-2017-0457//National Research, Development and Innovation Office/ ; }, abstract = {Recently, environmentally friendly crop improvements using next-generation plant biostimulants (PBs) come to the forefront in agriculture, regardless of whether they are used by scientists, farmers, or industries. Various organic and inorganic solutions have been investigated by researchers and producers, focusing on tolerance to abiotic and biotic stresses, crop quality, or nutritional deficiency. Garlic has been considered a universal remedy ever since antiquity. A supercritical carbon dioxide garlic extract encapsulated in nanoscale liposomes composed of plant-derived lipids was examined as a possible PB agent. The present study focused on the characterization of the genes associated with the pathways involved in defense response triggered by the liposome nanoparticles that were loaded with supercritical garlic extracts. This material was applied to Triticum aestivum in greenhouse experiments using foliar spraying. The effects were examined in a large-scale genome-wide transcriptional profiling experiment by collecting the samples four times (0 min, used as a control, and 15 min, 24 h, and 48 h after spraying). Based on a time-course expression analysis, the dynamics of the cellular response were determined by examining differentially expressed genes and applying a cluster analysis. The results suggested an enhanced expression of abscisic acid (ABA) pathway and pathogenesis-related (PR) genes, of which positive regulation was found for the AP2-, C2H2-, HD-ZIP-, and MYB-related transcription factor families.}, } @article {pmid36839335, year = {2023}, author = {Ezzatpour, S and Mondragon Portocarrero, ADC and Cardelle-Cobas, A and Lamas, A and López-Santamarina, A and Miranda, JM and Aguilar, HC}, title = {The Human Gut Virome and Its Relationship with Nontransmissible Chronic Diseases.}, journal = {Nutrients}, volume = {15}, number = {4}, pages = {}, pmid = {36839335}, issn = {2072-6643}, mesh = {Humans ; Virome ; *Viruses/metabolism ; *Bacteriophages ; *Microbiota ; *Gastrointestinal Microbiome ; }, abstract = {The human gastrointestinal tract contains large communities of microorganisms that are in constant interaction with the host, playing an essential role in the regulation of several metabolic processes. Among the gut microbial communities, the gut bacteriome has been most widely studied in recent decades. However, in recent years, there has been increasing interest in studying the influences that other microbial groups can exert on the host. Among them, the gut virome is attracting great interest because viruses can interact with the host immune system and metabolic functions; this is also the case for phages, which interact with the bacterial microbiota. The antecedents of virome-rectification-based therapies among various diseases were also investigated. In the near future, stool metagenomic investigation should include the identification of bacteria and phages, as well as their correlation networks, to better understand gut microbiota activity in metabolic disease progression.}, } @article {pmid36839325, year = {2023}, author = {Halimulati, M and Wang, R and Aihemaitijiang, S and Huang, X and Ye, C and Zhang, Z and Li, L and Zhu, W and Zhang, Z and He, L}, title = {Anti-Hyperuricemic Effect of Anserine Based on the Gut-Kidney Axis: Integrated Analysis of Metagenomics and Metabolomics.}, journal = {Nutrients}, volume = {15}, number = {4}, pages = {}, pmid = {36839325}, issn = {2072-6643}, mesh = {Animals ; Rats ; Anserine/pharmacology ; *Hyperuricemia/drug therapy ; Kidney/metabolism ; Metabolomics ; Uric Acid/metabolism ; Intestines/metabolism ; }, abstract = {Nowadays, developing effective intervention substances for hyperuricemia has become a public health issue. Herein, the therapeutic ability of anserine, a bioactive peptide, was validated through a comprehensive multiomics analysis of a rat model of hyperuricemia. Anserine was observed to improve liver and kidney function and modulate urate-related transporter expressions in the kidneys. Urine metabolomics showed that 15 and 9 metabolites were significantly increased and decreased, respectively, in hyperuricemic rats after the anserine intervention. Key metabolites such as fructose, xylose, methionine, erythronic acid, glucaric acid, pipecolic acid and trans-ferulic acid were associated with ameliorating kidney injury. Additionally, anserine regularly changed the gut microbiota, thereby ameliorating purine metabolism abnormalities and alleviating inflammatory responses. The integrated multiomics analysis indicated that Saccharomyces, Parasutterella excrementihominis and Emergencia timonensis were strongly associated with key differential metabolites. Therefore, we propose that anserine improved hyperuricemia via the gut-kidney axis, highlighting its potential in preventing and treating hyperuricemia.}, } @article {pmid36839205, year = {2023}, author = {Ye, W and Chen, Z and He, Z and Gong, H and Zhang, J and Sun, J and Yuan, S and Deng, J and Liu, Y and Zeng, A}, title = {Lactobacillus plantarum-Derived Postbiotics Ameliorate Acute Alcohol-Induced Liver Injury by Protecting Cells from Oxidative Damage, Improving Lipid Metabolism, and Regulating Intestinal Microbiota.}, journal = {Nutrients}, volume = {15}, number = {4}, pages = {}, pmid = {36839205}, issn = {2072-6643}, support = {LGF21C010002//Zhejiang Provincial Natural Science Foundation/ ; LQ18H020005//Zhejiang Provincial Natural Science Foundation/ ; Y2020218//Science and Technology Plan Project of Wenzhou/ ; QJD2002011//Qianjiang Talent Project of Zhejiang/ ; Y20210108//Science and Technology Plan Project of Wenzhou/ ; }, mesh = {Male ; Humans ; Animals ; Mice ; *Lactobacillus plantarum/physiology ; Lipid Metabolism ; *Gastrointestinal Microbiome/physiology ; *Chemical and Drug Induced Liver Injury, Chronic ; Mice, Inbred C57BL ; Liver/metabolism ; Ethanol/metabolism ; Oxidative Stress ; Superoxide Dismutase/metabolism ; }, abstract = {Here, the aim was to evaluate the protective effect of Lactobacillus plantarum-derived postbiotics, i.e., LP-cs, on acute alcoholic liver injury (ALI). After preincubation with LP-cs, HL7702 human hepatocytes were treated with alcohol, and then the cell survival rate was measured. C57BL/6 male mice were presupplemented with or without LP-cs and LP-cs-loaded calcium alginate hydrogel (LP-cs-Gel) for 3 weeks and given 50% alcohol gavage to establish the mouse model of ALI, LP-cs presupplementation, and LP-cs-Gel presupplementation. The histomorphology of the liver and intestines; the levels of serum AST, ALT, lipid, and SOD activity; liver transcriptomics; and the metagenome of intestinal microbiota were detected in all mouse models. In vitro, LP-cs significantly increased the survival rate of alcohol-treated cells. In vivo, presupplementation with LP-cs and LP-cs-Gel restored the levels of serum AST, ALT, and SOD activity, as well as TC and TG, after acute alcohol intake. In the LP-cs-presupplemented mice, the genes involved in fatty acid metabolic processes were upregulated and the genes involved in steroid biosynthesis were downregulated significantly as compared with the ALI mice. LP-cs significantly increased the abundance of intestinal microbiota, especially Akkermansia muciniphila. In conclusion, LP-cs ameliorates ALI by protecting hepatocytes against oxidative damage, thereby, improving lipid metabolism and regulating the intestinal microbiota. The effect of LP-cs-Gel is similar to that of LP-cs.}, } @article {pmid36838868, year = {2023}, author = {Shao, Y and Wang, W and Hu, Y and Gänzle, MG}, title = {Characterization of the Glucan-Branching Enzyme GlgB Gene from Swine Intestinal Bacteria.}, journal = {Molecules (Basel, Switzerland)}, volume = {28}, number = {4}, pages = {}, pmid = {36838868}, issn = {1420-3049}, support = {Discovery Grant//Natural Sciences and Engineering Research Council/ ; }, mesh = {Animals ; Swine ; *Glucans/metabolism ; Amylose ; *1,4-alpha-Glucan Branching Enzyme/genetics/metabolism ; Starch/metabolism ; Bacteria/metabolism ; }, abstract = {Starch hydrolysis by gut microbiota involves a diverse range of different enzymatic activities. Glucan-branching enzyme GlgB was identified as the most abundant glycosidase in Firmicutes in the swine intestine. GlgB converts α-(1→4)-linked amylose to form α-(1→4,6) branching points. This study aimed to characterize GlgB cloned from a swine intestinal metagenome and to investigate its potential role in formation of α-(1→4,6)-branched α-glucans from starch. The branching activity of purified GlgB was determined with six different starches and pure amylose by quantification of amylose after treatment. GlgB reduced the amylose content of all 6 starches and amylose by more than 85% and displayed a higher preference towards amylose. The observed activity on raw starch indicated a potential role in the primary starch degradation in the large intestine as an enzyme that solubilizes amylose. The oligosaccharide profile showed an increased concentration of oligosaccharide introduced by GlgB that is not hydrolyzed by intestinal enzymes. This corresponded to a reduced in vitro starch digestibility when compared to untreated starch. The study improves our understanding of colonic starch fermentation and may allow starch conversion to produce food products with reduced digestibility and improved quality.}, } @article {pmid36838497, year = {2023}, author = {Habibi, N and Uddin, S and Al-Sarawi, H and Aldhameer, A and Shajan, A and Zakir, F and Abdul Razzack, N and Alam, F}, title = {Metagenomes from Coastal Sediments of Kuwait: Insights into the Microbiome, Metabolic Functions and Resistome.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838497}, issn = {2076-2607}, abstract = {Coastal sediments in the proximity of wastewater and emergency outfalls are often sinks of pharmaceutical compounds and other organic and inorganic contaminants that are likely to affect the microbial community. The metabolites of these contaminants affect microbial diversity and their metabolic processes, resulting in undesirable effects on ecosystem functioning, thus necessitating the need to understand their composition and functions. In the present investigation, we studied the metagenomes of 12 coastal surface sediments through whole genome shot-gun sequencing. Taxonomic binning of the genes predicted about 86% as bacteria, 1% as archaea, >0.001% as viruses and Eukaryota, and 12% as other communities. The dominant bacterial, archaeal, and fungal genera were Woeseia, Nitrosopumilus, and Rhizophagus, respectively. The most prevalent viral families were Myoviridae and Siphoviridae, and the T4 virus was the most dominant bacteriophage. The unigenes further aligned to 26 clusters of orthologous genes (COGs) and five carbohydrate-active enzymes (CAZy) classes. Glycoside hydrolases (GH) and glycoside transferase (GT) were the highest-recorded CAzymes. The Kyoto Encyclopedia of Genes and Genomes (KEGG) level 3 functions were subjugated by purine metabolism > ABC transporters > oxidative phosphorylation > two-component system > pyrimidine metabolism > pyruvate metabolism > quorum sensing > carbon fixation pathways > ribosomes > and glyoxalate and dicarboxylate metabolism. Sequences allying with plasmids, integrons, insertion sequences and antibiotic-resistance genes were also observed. Both the taxonomies and functional abundances exhibited variation in relative abundances, with limited spatial variability (ANOVA p > 0.05; ANOSIM-0.05, p > 0.05). This study underlines the dominant microbial communities and functional genes in the marine sediments of Kuwait as a baseline for future biomonitoring programs.}, } @article {pmid36838473, year = {2023}, author = {Bastos, TS and Souza, CMM and Legendre, H and Richard, N and Pilla, R and Suchodolski, JS and de Oliveira, SG and Lesaux, AA and Félix, AP}, title = {Effect of Yeast Saccharomyces cerevisiae as a Probiotic on Diet Digestibility, Fermentative Metabolites, and Composition and Functional Potential of the Fecal Microbiota of Dogs Submitted to an Abrupt Dietary Change.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838473}, issn = {2076-2607}, abstract = {The aim was to evaluate the effects of yeast probiotic on diet digestibility, fermentative metabolites, and fecal microbiota of dogs submitted to dietary change. Sixteen dogs were divided into two groups of eight dogs each: control, without, and with probiotic, receiving 0.12 g/dog/day of live Saccharomyces cerevisiae yeast. The dogs were fed a lower protein and fiber diet for 21 days and then changed to a higher protein and fiber diet until day 49. Yeast supplementation did not statistically influence diet digestibility. The probiotic group had a lower fecal concentration of total biogenic amines (days 21 and 49), ammonia (day 23), and aromatic compounds and a higher fecal concentration of butyrate (p < 0.05). The probiotic group showed a lower dysbiosis index, a higher abundance (p < 0.05) of Bifidobacterium (days 35 and 49) and Turicibacter, and a lower abundance of Lactobacillus and E. coli (p < 0.05). Beta diversity demonstrated a clear differentiation in the gut microbiota between the control and probiotic groups on day 49. The control group showed upregulation in genes related to virulence factors, antibiotic resistance, and osmotic stress. The results indicated that the live yeast evaluated can have beneficial effects on intestinal functionality of dogs.}, } @article {pmid36838462, year = {2023}, author = {Shi, W and Tang, S and Zhang, S}, title = {Microbiome of High-Rank Coal Reservoirs in the High-Production Areas of the Southern Qinshui Basin.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838462}, issn = {2076-2607}, abstract = {To study the distribution features of microorganisms in distinct hydrological areas of the southern Qinshui Basin, C-N-S microorganisms were studied using 16S RNA sequencing, metagenome sequencing and geochemical technologies, showing the high sensitivity of microorganisms to the hydrodynamic dynamics of coal. The hydrodynamic intensity of the #3 coal gradually decreased from the runoff areas to the stagnant areas. The stagnant zones have higher reservoir pressure, methane content, δ[13]CDIC and TDS and lower SO4[2-], Fe[3+] and NO3[-] concentrations than the runoff areas. C-N-S-cycling microorganisms, including those engaged in methanogenesis, nitrate respiration, fermentation, nitrate reduction, dark oxidation of sulfur compounds, sulfate respiration, iron respiration, chlorate reduction, aromatic compound degradation, denitrification, ammonification and nitrogen fixation, were more abundant in the stagnant areas. The relative abundance of C-N-S functional genes, including genes related to C metabolism (e.g., mcr, mer, mtr, fwd and mtd), N metabolism (e.g., nifDKH, nirK, narGHI, nosZ, amoB, norC and napAB) and sulfur metabolism (e.g., dsrAB and PAPSS), increased in the stagnant zones, indicating that there was active microbiological C-N-S cycling in the stagnant areas. The degradation and fermentation of terrestrial plant organic carbon and coal seam organic matter could provide substrates for methanogens, while nitrogen fixation and nitrification can provide nitrogen for methanogens, which are all favorable factors for stronger methanogenesis in stagnant areas. The coal in the study area is currently in the secondary biogenic gas generation stage because of the rising of the strata, which recharges atmospheric precipitation. The random forest model shows that the abundance of C-N-S microorganisms and genes could be used to distinguish different hydrological zones in coal reservoirs. Since stagnant zones are usually high-gas-bearing zones and high-production areas of CBM exploration, these microbiological indicators can be used as effective parameters to identify high-production-potential zones. In addition, nitrate respiration and sulfate respiration microorganisms consumed NO3[-] and SO4[2-], causing a decrease in the content of these two ions in the stagnant areas.}, } @article {pmid36838449, year = {2023}, author = {Cheatham, CN and Gustafson, KL and McAdams, ZL and Turner, GM and Dorfmeyer, RA and Ericsson, AC}, title = {Standardized Complex Gut Microbiomes Influence Fetal Growth, Food Intake, and Adult Body Weight in Outbred Mice.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838449}, issn = {2076-2607}, support = {T32 GM008396/GM/NIGMS NIH HHS/United States ; T32 OD011126/OD/NIH HHS/United States ; U42 OD010918/OD/NIH HHS/United States ; }, abstract = {Obesity places a tremendous burden on individual health and the healthcare system. The gut microbiome (GM) influences host metabolism and behaviors affecting body weight (BW) such as feeding. The GM of mice varies between suppliers and significantly influences BW. We sought to determine whether GM-associated differences in BW are associated with differences in intake, fecal energy loss, or fetal growth. Pair-housed mice colonized with a low or high microbial richness GM were weighed, and the total and BW-adjusted intake were measured at weaning and adulthood. Pups were weighed at birth to determine the effects of the maternal microbiome on fetal growth. Fecal samples were collected to assess the fecal energy loss and to characterize differences in the microbiome. The results showed that supplier-origin microbiomes were associated with profound differences in fetal growth and excessive BW-adjusted differences in intake during adulthood, with no detected difference in fecal energy loss. Agreement between the features of the maternal microbiome associated with increased birth weight here and in recent human studies supports the value of this model to investigate the mechanisms by which the maternal microbiome regulates offspring growth and food intake.}, } @article {pmid36838393, year = {2023}, author = {Langlois, V and Girard, C and Vincent, WF and Culley, AI}, title = {A Tale of Two Seasons: Distinct Seasonal Viral Communities in a Thermokarst Lake.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838393}, issn = {2076-2607}, abstract = {Thermokarst lakes are important features of subarctic landscapes and are a substantial source of greenhouse gases, although the extent of gas produced varies seasonally. Microbial communities are responsible for the production of methane and CO2 but the "top down" forces that influence microbial dynamics (i.e., grazers and viruses) and how they vary temporally within these lakes are still poorly understood. The aim of this study was to examine viral diversity over time to elucidate the seasonal structure of the viral communities in thermokarst lakes. We produced virus-enriched metagenomes from a subarctic peatland thermokarst lake in the summer and winter over three years. The vast majority of vOTUs assigned to viral families belonged to Caudovirales (Caudoviricetes), notably the morphological groups myovirus, siphovirus and podovirus. We identified two distinct communities: a dynamic, seasonal community in the oxygenated surface layer during the summer and a stable community found in the anoxic water layer at the bottom of the lake in summer and throughout much of the water column in winter. Comparison with other permafrost and northern lake metagenomes highlighted the distinct composition of viral communities in this permafrost thaw lake ecosystem.}, } @article {pmid36838385, year = {2023}, author = {Becker, D and Popp, D and Bonk, F and Kleinsteuber, S and Harms, H and Centler, F}, title = {Metagenomic Analysis of Anaerobic Microbial Communities Degrading Short-Chain Fatty Acids as Sole Carbon Sources.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838385}, issn = {2076-2607}, support = {FKZ 031A317//Federal Ministry of Education and Research/ ; }, abstract = {Analyzing microbial communities using metagenomes is a powerful approach to understand compositional structures and functional connections in anaerobic digestion (AD) microbiomes. Whereas short-read sequencing approaches based on the Illumina platform result in highly fragmented metagenomes, long-read sequencing leads to more contiguous assemblies. To evaluate the performance of a hybrid approach of these two sequencing approaches we compared the metagenome-assembled genomes (MAGs) resulting from five AD microbiome samples. The samples were taken from reactors fed with short-chain fatty acids at different feeding regimes (continuous and discontinuous) and organic loading rates (OLR). Methanothrix showed a high relative abundance at all feeding regimes but was strongly reduced in abundance at higher OLR, when Methanosarcina took over. The bacterial community composition differed strongly between reactors of different feeding regimes and OLRs. However, the functional potential was similar regardless of feeding regime and OLR. The hybrid sequencing approach using Nanopore long-reads and Illumina MiSeq reads improved assembly statistics, including an increase of the N50 value (on average from 32 to 1740 kbp) and an increased length of the longest contig (on average from 94 to 1898 kbp). The hybrid approach also led to a higher share of high-quality MAGs and generated five potentially circular genomes while none were generated using MiSeq-based contigs only. Finally, 27 hybrid MAGs were reconstructed of which 18 represent potentially new species-15 of them bacterial species. During pathway analysis, selected MAGs revealed similar gene patterns of butyrate degradation and might represent new butyrate-degrading bacteria. The demonstrated advantages of adding long reads to metagenomic analyses make the hybrid approach the preferable option when dealing with complex microbiomes.}, } @article {pmid36838375, year = {2023}, author = {Lloyd, AW and Percival, D and Langille, MGI and Yurgel, SN}, title = {Changes to Soil Microbiome Resulting from Synergetic Effects of Fungistatic Compounds Pyrimethanil and Fluopyram in Lowbush Blueberry Agriculture, with Nine Fungicide Products Tested.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838375}, issn = {2076-2607}, support = {2090-21000-003-00D//Agricultural Research Service/ ; RGPIN-2017-04545//Natural Sciences and Engineering Research Council/ ; CRDPJ 507170-16//Natural Sciences and Engineering Research Council/ ; }, abstract = {Lowbush blueberries (Vaccinium spp.) are a crop of economic significance to Atlantic Canada, Quebec, and Maine. The fruit is produced by the management of naturally occurring plant populations. The plants have an intimate relationship with the soil microbiome and depend on it for their health and productivity. Fungicides are an important tool in combatting disease pressure but pose a potential risk to soil health. In this study, amplicon sequencing was used to determine the effects of six fungistatic compounds both alone and in combination via nine commercially available fungicide products on the bacterial and fungal microbiomes associated with lowbush blueberries and to study whether these effects are reflected in crop outcomes and plant phenotypes. One fungicide, Luna Tranquility, a combination of fluopyram and pyrimethanil, was found to impart significant effects to fungal and bacterial community structure, fungal taxonomic abundances, and bacterial functions relative to control. The two fungicides which contained fluopyram and pyrimethanil as single ingredients (Velum Prime and Scala, respectively) did not induce significant changes in any of these regards. These results suggest the possibility that these microbiome changes are the result of the synergistic effect of fluopyram and pyrimethanil on soil microbiomes. While these results suggest a significant disruption to the soil microbiome, no corresponding changes to crop development and outcomes were noted. Ultimately, the majority of the fungicides analysed in this trial did not produce significant changes to the soil microbiome relative to the untreated group (UTG). However, one of the fungicide treatments, Luna Tranquility, did produce significant changes to the soil ecosystem that could have longer-term effects on soil health and its future use may merit additional investigation onto its ecotoxicological properties.}, } @article {pmid36838367, year = {2023}, author = {Lumbreras-Iglesias, P and Sabater, C and Fernández Moreno, A and López de Ugarriza, P and Fernández-Verdugo, A and Margolles, A and Rodicio, MR and Bernal, T and Fernández, J}, title = {Evaluation of a Shotgun Metagenomics Approach for Detection of ESBL- and/or Carbapenemase-Producing Enterobacterales in Culture Negative Patients Recovered from Acute Leukemia.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838367}, issn = {2076-2607}, support = {FIS PI21/01590//Instituto de Salud Carlos III/ ; Independent Scientific Research Grant//Pfizer (Spain)/ ; A Way to Making Europe//European Regional Development Fund of the 229 European Union:/ ; }, abstract = {Patients diagnosed with acute leukemia (AL) have a weakened immune system. Infections acquired by these patients are cause for concern and especially worrisome when Gram-negative multidrug-resistant (MDR) bacteria are involved, as they are difficult to treat, especially in the case of ESBL- and/or carbapenemase-producing Enterobacterales. Culture-based approaches have been relied on over the past decades as the method of choice for the early detection of gut colonization by MDR Gram-negative bacteria. However, various studies have indicated its limited sensitivity, underlining the need for new screening procedures in onco-hematological patients. Here, we evaluated a shotgun metagenomics approach to detect ESBL- and/or carbapenemase-producing Enterobacterales in the gut of 28 patients who had recovered from AL, which were previously colonized by these bacteria but cured at the time of sampling, as judged by culture-based methods. No ESBL or carbapenemase determinants were detected among the many resistance genes found by the metagenomics approach, supporting that patients were truly decolonized, with considerable consequences for their future clinical management. Due to the relatively low number of patients available for the present investigation, further studies should be conducted to support the utility and applicability of metagenomics for the routine screening of MDR bacteria in onco-hematological patients.}, } @article {pmid36838323, year = {2023}, author = {Zhou, X and Ma, Y and Yang, C and Zhao, Z and Ding, Y and Zhang, Y and Wang, P and Zhao, L and Li, C and Su, Z and Wang, X and Ming, W and Zeng, L and Kang, X}, title = {Rumen and Fecal Microbiota Characteristics of Qinchuan Cattle with Divergent Residual Feed Intake.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838323}, issn = {2076-2607}, support = {31760647//National Natural Science Foundation of China/ ; 32160776//National Natural Science Foundation of China/ ; 2021AAC030270//Natural Science Foundation of Ningxia Province/ ; }, abstract = {Residual feed intake (RFI) is one of the indicators of feed efficiency. To investigate the microbial characteristics and differences in the gastrointestinal tract of beef cattle with different RFI, a metagenome methodology was used to explore the characteristics of the rumen and fecal microbiota in 10 Qinchuan cattle (five in each of the extremely high and extremely low RFI groups). The results of taxonomic annotation revealed that Bacteroidetes and Firmicutes were the most dominant phyla in rumen and feces. Prevotella was identified as a potential biomarker in the rumen of the LRFI group by the LEfSe method, while Turicibacter and Prevotella might be potential biomarkers of the HRFI and LRFI group in feces, respectively. Functional annotation revealed that the microbiota in the rumen of the HRFI group had a greater ability to utilize dietary polysaccharides and dietary protein. Association analysis of rumen microbes (genus level) with host genes revealed that microbiota including Prevotella, Paraprevotella, Treponema, Oscillibacter, and Muribaculum, were significantly associated with differentially expressed genes regulating RFI. This study discovered variances in the microbial composition of rumen and feces of beef cattle with different RFIs, demonstrating that differences in microbes may play a critical role in regulating the bovine divergent RFI phenotype variations.}, } @article {pmid36838276, year = {2023}, author = {Petrilli, R and Fabbretti, A and Cerretani, A and Pucci, K and Pagliaretta, G and Picciolini, M and Napolioni, V and Falconi, M}, title = {Selection, Identification and Functional Performance of Ammonia-Degrading Microbial Communities from an Activated Sludge for Landfill Leachate Treatment.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838276}, issn = {2076-2607}, support = {BVC000035-EcoElpidiense//Eco Elpidiense Company , Porto Sant'Elpidio (FM), ITALY/ ; }, abstract = {The increasing amounts of municipal solid waste and their management in landfills caused an increase in the production of leachate, a liquid formed by the percolation of rainwater through the waste. Leachate creates serious problems to municipal wastewater treatment plants; indeed, its high levels of ammonia are toxic for bacterial cells and drastically reduce the biological removal of nitrogen by activated sludge. In the present work, we studied, using a metagenomic approach based on next-generation sequencing (NGS), the microbial composition of sludge in the municipal wastewater treatment plant of Porto Sant'Elpidio (Italy). Through activated sludge enrichment experiments based on the Repetitive Re-Inoculum Assay, we were able to select and identify a minimal bacterial community capable of degrading high concentrations of ammonium (NH4[+]-N ≅ 350 mg/L) present in a leachate-based medium. The analysis of NGS data suggests that seven families of bacteria (Alcaligenaceae, Nitrosomonadaceae, Caulobacteraceae, Xanthomonadaceae, Rhodanobacteraceae, Comamonadaceae and Chitinophagaceae) are mainly responsible for ammonia oxidation. Furthermore, we isolated from the enriched sludge three genera (Klebsiella sp., Castellaniella sp. and Acinetobacter sp.) capable of heterotrophic nitrification coupled with aerobic denitrification. These bacteria released a trace amount of both nitrite and nitrate possibly transforming ammonia into gaseous nitrogen. Our findings represent the starting point to produce an optimized microorganisms's mixture for the biological removal of ammonia contained in leachate.}, } @article {pmid36838234, year = {2023}, author = {Arsyadi, A and Guo, Y and Ebihara, A and Sakagami, N and Sakoda, M and Tago, K and Kamijo, T and Ohta, H and Nishizawa, T}, title = {A Nitrate-Transforming Bacterial Community Dominates in the Miscanthus Rhizosphere on Nitrogen-Deficient Volcanic Deposits of Miyake-jima.}, journal = {Microorganisms}, volume = {11}, number = {2}, pages = {}, pmid = {36838234}, issn = {2076-2607}, support = {16H02932//Japan Society for the Promotion of Science/ ; 19H04315//Japan Society for the Promotion of Science/ ; }, abstract = {The perennial gramineous grass Miscanthus condensatus functions as a major pioneer plant in colonizing acidic volcanic deposits on Miyake-jima, Japan, despite a lack of nitrogen nutrients. The nitrogen cycle in the rhizosphere is important for the vigorous growth of M. condensatus in this unfavorable environment. In the present study, we identified the nitrogen-cycling bacterial community in the M. condensatus rhizosphere on these volcanic deposits using a combination of metagenomics and culture-based analyses. Our results showed a large number of functional genes related to denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in the rhizosphere, indicating that nitrate-transforming bacteria dominated the rhizosphere biome. Furthermore, nitrite reductase genes (i.e., nirK and nirS) related to the denitrification and those genes related to DNRA (i.e., nirB and nrfA) were mainly annotated to the classes Alpha-proteobacteria, Beta-proteobacteria, and Gamma-proteobacteria. A total of 304 nitrate-succinate-stimulated isolates were obtained from the M. condensatus rhizosphere and were classified into 34 operational taxonomic units according to amplified 16S rRNA gene restriction fragment pattern analysis. Additionally, two strains belonging to the genus Cupriavidus in the class Beta-proteobacteria showed a high in vitro denitrifying activity; however, metagenomic results indicated that the DNRA-related rhizobacteria appeared to take a major role in the nitrogen cycle of the M. condensatus rhizosphere in recent Miyake-jima volcanic deposits. This study elucidates the association between the Miscanthus rhizosphere and the nitrate-reducing bacterial community on newly placed volcanic deposits, which furthers our understanding of the transformation of nitrogen nutrition involved in the early development of vegetation.}, } @article {pmid36837868, year = {2023}, author = {Song, F and Xu, Y and Peng, P and Li, H and Zheng, R and Zhang, H and Han, Y and Weng, Q and Yuan, Z}, title = {Seasonal Changes in the Structure and Function of Gut Microbiota in the Muskrat (Ondatra zibethicus).}, journal = {Metabolites}, volume = {13}, number = {2}, pages = {}, pmid = {36837868}, issn = {2218-1989}, support = {32272859//National Natural Science Foundation of China/ ; S202210022048, X202210022057//National Training Program of Innovation and Entrepreneurship for Undergraduates/ ; }, abstract = {The gut microbiota plays a crucial role in the nutrition, metabolism, and immune function of the host animal. The muskrat (Ondatra zibethicus) is a typical seasonal breeding animal. The present study performed a metagenomic analysis of cecum contents from muskrats in the breeding and non-breeding seasons. The results indicated that the breeding muskrats and non-breeding muskrats differed in gut microbiota structure and function. During the breeding season, the relative abundance of phylum Bacteroidetes, genus Prevotella, and genus Alistipes increased, while the relative abundance of phylum Firmicutes and phylum Actinobacteria decreased. The muskrat gut microbiota was enriched in the metabolism-related pathways, especially amino acid and vitamin metabolism, and genetically related metabolites in the breeding season. We presumed that the muskrat gut microbiota might seasonally change to secure reproductive activity and satisfy the metabolic demands of different seasons. This study could explore potential mechanisms by which gut microbiota affects reproduction. Moreover, this study may provide a new theoretical basis for the management of muskrat captive breeding.}, } @article {pmid36836616, year = {2023}, author = {Tarbeeva, S and Kozlova, A and Sarygina, E and Kiseleva, O and Ponomarenko, E and Ilgisonis, E}, title = {Food for Thought: Proteomics for Meat Safety.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, pmid = {36836616}, issn = {2075-1729}, support = {075-15-2020-775//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Foodborne bacteria interconnect food and human health. Despite significant progress in food safety regulation, bacterial contamination is still a serious public health concern and the reason for significant commercial losses. The screening of the microbiome in meals is one of the main aspects of food production safety influencing the health of the end-consumers. Our research provides an overview of proteomics findings in the field of food safety made over the last decade. It was believed that proteomics offered an accurate snapshot of the complex networks of the major biological machines called proteins. The proteomic methods for the detection of pathogens were armed with bioinformatics algorithms, allowing us to map the data onto the genome and transcriptome. The mechanisms of the interaction between bacteria and their environment were elucidated with unprecedented sensitivity, specificity, and depth. Using our web-based tool ScanBious for automated publication analysis, we analyzed over 48,000 scientific articles on antibiotic and disinfectant resistance and highlighted the benefits of proteomics for the food safety field. The most promising approach to studying safety in food production is the combination of classical genomic and metagenomic approaches and the advantages provided by proteomic methods with the use of panoramic and targeted mass spectrometry.}, } @article {pmid36836275, year = {2023}, author = {Singh, G}, title = {Linking Lichen Metabolites to Genes: Emerging Concepts and Lessons from Molecular Biology and Metagenomics.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {2}, pages = {}, pmid = {36836275}, issn = {2309-608X}, abstract = {Lichen secondary metabolites have tremendous pharmaceutical and industrial potential. Although more than 1000 metabolites have been reported from lichens, less than 10 have been linked to the genes coding them. The current biosynthetic research focuses strongly on linking molecules to genes as this is fundamental to adapting the molecule for industrial application. Metagenomic-based gene discovery, which bypasses the challenges associated with culturing an organism, is a promising way forward to link secondary metabolites to genes in non-model, difficult-to-culture organisms. This approach is based on the amalgamation of the knowledge of the evolutionary relationships of the biosynthetic genes, the structure of the target molecule, and the biosynthetic machinery required for its synthesis. So far, metagenomic-based gene discovery is the predominant approach by which lichen metabolites have been linked to their genes. Although the structures of most of the lichen secondary metabolites are well-documented, a comprehensive review of the metabolites linked to their genes, strategies implemented to establish this link, and crucial takeaways from these studies is not available. In this review, I address the following knowledge gaps and, additionally, provide critical insights into the results of these studies, elaborating on the direct and serendipitous lessons that we have learned from them.}, } @article {pmid36835562, year = {2023}, author = {von Eyben, FE and Kristiansen, K and Kapp, DS and Hu, R and Preda, O and Nogales, FF}, title = {Epigenetic Regulation of Driver Genes in Testicular Tumorigenesis.}, journal = {International journal of molecular sciences}, volume = {24}, number = {4}, pages = {}, pmid = {36835562}, issn = {1422-0067}, mesh = {Male ; Humans ; Epigenesis, Genetic ; *Testicular Neoplasms/genetics ; *Neoplasms, Germ Cell and Embryonal/genetics ; *Carcinoma, Embryonal/genetics ; Carcinogenesis/genetics ; Cell Transformation, Neoplastic/genetics ; }, abstract = {In testicular germ cell tumor type II (TGCT), a seminoma subtype expresses an induced pluripotent stem cell (iPSC) panel with four upregulated genes, OCT4/POU5F1, SOX17, KLF4, and MYC, and embryonal carcinoma (EC) has four upregulated genes, OCT4/POU5F1, SOX2, LIN28, and NANOG. The EC panel can reprogram cells into iPSC, and both iPSC and EC can differentiate into teratoma. This review summarizes the literature on epigenetic regulation of the genes. Epigenetic mechanisms, such as methylations of cytosines on the DNA string and methylations and acetylations of histone 3 lysines, regulate expression of these driver genes between the TGCT subtypes. In TGCT, the driver genes contribute to well-known clinical characteristics and the driver genes are also important for aggressive subtypes of many other malignancies. In conclusion, epigenetic regulation of the driver genes are important for TGCT and for oncology in general.}, } @article {pmid36835363, year = {2023}, author = {Smythe, P and Wilkinson, HN}, title = {The Skin Microbiome: Current Landscape and Future Opportunities.}, journal = {International journal of molecular sciences}, volume = {24}, number = {4}, pages = {}, pmid = {36835363}, issn = {1422-0067}, mesh = {Humans ; Dysbiosis ; Skin ; *Microbiota ; *Skin Diseases ; Skin Physiological Phenomena ; }, abstract = {Our skin is the largest organ of the body, serving as an important barrier against the harsh extrinsic environment. Alongside preventing desiccation, chemical damage and hypothermia, this barrier protects the body from invading pathogens through a sophisticated innate immune response and co-adapted consortium of commensal microorganisms, collectively termed the microbiota. These microorganisms inhabit distinct biogeographical regions dictated by skin physiology. Thus, it follows that perturbations to normal skin homeostasis, as occurs with ageing, diabetes and skin disease, can cause microbial dysbiosis and increase infection risk. In this review, we discuss emerging concepts in skin microbiome research, highlighting pertinent links between skin ageing, the microbiome and cutaneous repair. Moreover, we address gaps in current knowledge and highlight key areas requiring further exploration. Future advances in this field could revolutionise the way we treat microbial dysbiosis associated with skin ageing and other pathologies.}, } @article {pmid36834289, year = {2023}, author = {Zhao, F and Wang, B and Huang, K and Yin, J and Ren, X and Wang, Z and Zhang, XX}, title = {Correlations among Antibiotic Resistance Genes, Mobile Genetic Elements and Microbial Communities in Municipal Sewage Treatment Plants Revealed by High-Throughput Sequencing.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {4}, pages = {}, pmid = {36834289}, issn = {1660-4601}, mesh = {*Sewage/microbiology ; Genes, Bacterial ; Angiotensin Receptor Antagonists ; Anti-Bacterial Agents/pharmacology ; Angiotensin-Converting Enzyme Inhibitors/pharmacology ; Drug Resistance, Microbial/genetics ; High-Throughput Nucleotide Sequencing ; *Microbiota ; Interspersed Repetitive Sequences ; }, abstract = {Municipal sewage treatment plants (MSTPs) are environmental pools for antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs), which is cause for growing environmental-health concerns. In this study, the effects of different wastewater treatment processes on microbial antibiotic resistance in four MSTPs were investigated. PCR, q-PCR, and molecular cloning integrally indicated that the tetracycline resistance (tet) genes significantly reduced after activated-sludge treatment. Illumina high-throughput sequencing revealed that the broad-spectrum profile of ARGs and mobile element genes (MGEs) were also greatly decreased by one order of magnitude via activated sludge treatment and were closely associated with each other. Correlations between ARGs and bacterial communities showed that potential ARB, such as Acinetobacter, Bacteroides, and Cloaibacterium, were removed by the activated-sludge process. Sedimentation processes cannot significantly affect the bacterial structure, resulting in the relative abundance of ARGs, MGEs, and ARB in second-clarifier effluent water being similar to activated sludge. A comprehensive study of ARGs associated with MGEs and bacterial structure might be technologically guided for activated sludge design and operation in the MSTPs, to purposefully control ARGs carried by pathogenic hosts and mobility.}, } @article {pmid36833289, year = {2023}, author = {Winder, JC and Boulton, W and Salamov, A and Eggers, SL and Metfies, K and Moulton, V and Mock, T}, title = {Genetic and Structural Diversity of Prokaryotic Ice-Binding Proteins from the Central Arctic Ocean.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, pmid = {36833289}, issn = {2073-4425}, support = {BB/T008717/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Prokaryotic Cells ; *Carrier Proteins ; Protein Domains ; Seawater ; Oceans and Seas ; }, abstract = {Ice-binding proteins (IBPs) are a group of ecologically and biotechnologically relevant enzymes produced by psychrophilic organisms. Although putative IBPs containing the domain of unknown function (DUF) 3494 have been identified in many taxa of polar microbes, our knowledge of their genetic and structural diversity in natural microbial communities is limited. Here, we used samples from sea ice and sea water collected in the central Arctic Ocean as part of the MOSAiC expedition for metagenome sequencing and the subsequent analyses of metagenome-assembled genomes (MAGs). By linking structurally diverse IBPs to particular environments and potential functions, we reveal that IBP sequences are enriched in interior ice, have diverse genomic contexts and cluster taxonomically. Their diverse protein structures may be a consequence of domain shuffling, leading to variable combinations of protein domains in IBPs and probably reflecting the functional versatility required to thrive in the extreme and variable environment of the central Arctic Ocean.}, } @article {pmid36833250, year = {2023}, author = {ZeinEldin, RA and Ahmed, MM and Hassanein, WS and Elshafey, N and Sofy, AR and Hamedo, HA and Elnosary, ME}, title = {Diversity and Distribution Characteristics of Viruses from Soda Lakes.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, pmid = {36833250}, issn = {2073-4425}, mesh = {Humans ; Lakes ; Capsid Proteins/genetics ; *Viruses/genetics ; Myoviridae/genetics ; Biodiversity ; *Siphoviridae ; }, abstract = {Viruses are the most abundant living things and a source of genetic variation. Despite recent research, we know little about their biodiversity and geographic distribution. We used different bioinformatics tools, MG-RAST, genome detective web tools, and GenomeVx, to describe the first metagenomic examination of haloviruses in Wadi Al-Natrun. The discovered viromes had remarkably different taxonomic compositions. Most sequences were derived from double-stranded DNA viruses, especially from Myoviridae, Podoviridae, Siphoviridae, Herpesviridae, Bicaudaviridae, and Phycodnaviridae families; single-stranded DNA viruses, especially from the family Microviridae; and positive-strand RNA viruses, especially from the family Potyviridae. Additionally, our results showed that Myohalovirus chaoS9 has eight Contigs and is annotated to 18 proteins as follows: tail sheath protein, tco, nep, five uncharacterized proteins, HCO, major capsid protein, putative pro head protease protein, putative head assembly protein, CxxC motive protein, terl, HTH domain protein, and terS Exon 2. Additionally, Halorubrum phage CGphi46 has 19 proteins in the brine sample as follows: portal protein, 17 hypothetical proteins, major capsid protein, etc. This study reveals viral lineages, suggesting the Virus's global dispersal more than other microorganisms. Our study clarifies how viral communities are connected and how the global environment changes.}, } @article {pmid36833230, year = {2023}, author = {Wiscovitch-Russo, RA and Santiago-Rodriguez, TM and Toranzos, GA}, title = {Deciphering Diets and Lifestyles of Prehistoric Humans through Paleoparasitology: A Review.}, journal = {Genes}, volume = {14}, number = {2}, pages = {}, pmid = {36833230}, issn = {2073-4425}, mesh = {Animals ; Humans ; *Parasites ; *Parasitic Diseases/parasitology ; Paleopathology/methods ; Diet ; Life Style ; }, abstract = {Parasites have affected and coevolved with humans and animals throughout history. Evidence of ancient parasitic infections, particularly, reside in archeological remains originating from different sources dating to various periods of times. The study of ancient parasites preserved in archaeological remains is known as paleoparasitology, and it initially intended to interpret migration, evolution, and dispersion patterns of ancient parasites, along with their hosts. Recently, paleoparasitology has been used to better understand dietary habits and lifestyles of ancient human societies. Paleoparasitology is increasingly being recognized as an interdisciplinary field within paleopathology that integrates areas such as palynology, archaeobotany, and zooarchaeology. Paleoparasitology also incorporates techniques such as microscopy, immunoassays, PCR, targeted sequencing, and more recently, high-throughput sequencing or shotgun metagenomics to understand ancient parasitic infections and thus interpret migration and evolution patterns, as well as dietary habits and lifestyles. The present review covers the original theories developed in the field of paleoparasitology, as well as the biology of some parasites identified in pre-Columbian cultures. Conclusions, as well as assumptions made during the discovery of the parasites in ancient samples, and how their identification may aid in better understanding part of human history, ancient diet, and lifestyles are discussed.}, } @article {pmid36831166, year = {2023}, author = {Yuan, Q and Wang, X and Li, Z and Guo, W and Cheng, H and Cao, Q}, title = {A Preliminary Study on Microbiota Characteristics of Bronchoalveolar Lavage Fluid in Patients with Pulmonary Nodules Based on Metagenomic Next-Generation Sequencing.}, journal = {Biomedicines}, volume = {11}, number = {2}, pages = {}, pmid = {36831166}, issn = {2227-9059}, abstract = {BACKGROUND: The characteristics and roles of microbes in the occurrence and development of pulmonary nodules are still unclear.

METHODS: We retrospectively analyzed the microbial mNGS results of BALF from 229 patients with pulmonary nodules before surgery, and performed a comparative analysis of lung flora between lung cancer and benign nodules according to postoperative pathology. The analysis also focused on investigating the characteristics of lung microbiota in lung adenocarcinomas with varying histopathology.

RESULTS: There were differences in lung microbiota between lung cancer and benign lung nodules. Bacterial diversity was lower in lung cancer than in benign lung nodules. Four species (Porphyromonas somerae, Corynebacterium accolens, Burkholderia cenocepacia and Streptococcus mitis) were enriched in lung cancer compared with the benign lung nodules. The areas under the ROC curves of these four species were all greater than 0.6, and the AUC of Streptococcus mitis was 0.702, which had the highest diagnostic value for differentiating lung cancer from benign lung diseases. The significantly enriched microbiota varied with the different pathological subtypes of lung adenocarcinoma. Streptococcus mitis, Burkholderia oklahomensis and Burkholderia latens displayed a trend of increasing from the benign lung disease group to the AIS group, MIA group and IAC group, whereas Lactobacillus plantarum showed a downward trend.

CONCLUSION: Changes in the abundance of lung microbiota are closely related to the development of infiltrating adenocarcinoma. Our findings provide new insights into the relationship between the changes in lung microbiota and the development of lung cancer.}, } @article {pmid36830905, year = {2023}, author = {Mańkowska-Wierzbicka, D and Zuraszek, J and Wierzbicka, A and Gabryel, M and Mahadea, D and Baturo, A and Zakerska-Banaszak, O and Slomski, R and Skrzypczak-Zielinska, M and Dobrowolska, A}, title = {Alterations in Gut Microbiota Composition in Patients with COVID-19: A Pilot Study of Whole Hypervariable 16S rRNA Gene Sequencing.}, journal = {Biomedicines}, volume = {11}, number = {2}, pages = {}, pmid = {36830905}, issn = {2227-9059}, abstract = {It is crucial to consider the importance of the microbiome and the gut-lung axis in the context of SARS-CoV-2 infection. This pilot study examined the fecal microbial composition of patients with COVID-19 following a 3-month recovery. Using for the first time metagenomic analysis based on all hypervariable regions (V1-V9) of the 16S rRNA gene, we have identified 561 microbial species; however, 17 were specific only for the COVID-19 group (n = 8). The patients' cohorts revealed significantly greater alpha diversity of the gut microbiota compared to healthy controls (n = 14). This finding has been demonstrated by operational taxonomic units (OTUs) richness (p < 0.001) and Chao1 index (p < 0.01). The abundance of the phylum Verrucomicrobia was 30 times higher in COVID-19 patients compared to healthy subjects. Accordingly, this disproportion was also noted at other taxonomic levels: in the class Verrucomicrobiae, the family Verrucomicrobiaceae, and the genus Akkermansia. Elevated pathobionts such as Escherichia coli, Bilophila wadsworthia, and Parabacteroides distasonis were found in COVID-19 patients. Considering the gut microbiota's ability to disturb the immune response, our findings suggest the importance of the enteric microbiota in the course of SARS-CoV-2 infection. This pilot study shows that the composition of the microbial community may not be fully restored in individuals with SARS-CoV-2 following a 3-month recovery.}, } @article {pmid36830830, year = {2023}, author = {Campbell, C and Kandalgaonkar, MR and Golonka, RM and Yeoh, BS and Vijay-Kumar, M and Saha, P}, title = {Crosstalk between Gut Microbiota and Host Immunity: Impact on Inflammation and Immunotherapy.}, journal = {Biomedicines}, volume = {11}, number = {2}, pages = {}, pmid = {36830830}, issn = {2227-9059}, support = {854385//Crohn's and Colitis Foundation/ ; 855256//American Heart Association (AHA)/ ; }, abstract = {Gut microbes and their metabolites are actively involved in the development and regulation of host immunity, which can influence disease susceptibility. Herein, we review the most recent research advancements in the gut microbiota-immune axis. We discuss in detail how the gut microbiota is a tipping point for neonatal immune development as indicated by newly uncovered phenomenon, such as maternal imprinting, in utero intestinal metabolome, and weaning reaction. We describe how the gut microbiota shapes both innate and adaptive immunity with emphasis on the metabolites short-chain fatty acids and secondary bile acids. We also comprehensively delineate how disruption in the microbiota-immune axis results in immune-mediated diseases, such as gastrointestinal infections, inflammatory bowel diseases, cardiometabolic disorders (e.g., cardiovascular diseases, diabetes, and hypertension), autoimmunity (e.g., rheumatoid arthritis), hypersensitivity (e.g., asthma and allergies), psychological disorders (e.g., anxiety), and cancer (e.g., colorectal and hepatic). We further encompass the role of fecal microbiota transplantation, probiotics, prebiotics, and dietary polyphenols in reshaping the gut microbiota and their therapeutic potential. Continuing, we examine how the gut microbiota modulates immune therapies, including immune checkpoint inhibitors, JAK inhibitors, and anti-TNF therapies. We lastly mention the current challenges in metagenomics, germ-free models, and microbiota recapitulation to a achieve fundamental understanding for how gut microbiota regulates immunity. Altogether, this review proposes improving immunotherapy efficacy from the perspective of microbiome-targeted interventions.}, } @article {pmid36830574, year = {2023}, author = {Roux, S and Fischer, MG and Hackl, T and Katz, LA and Schulz, F and Yutin, N}, title = {Updated Virophage Taxonomy and Distinction from Polinton-like Viruses.}, journal = {Biomolecules}, volume = {13}, number = {2}, pages = {}, pmid = {36830574}, issn = {2218-273X}, support = {DE-AC02-05CH11231//DOE Office of Science User Facility/ ; R15 HG010409/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; *Virophages/genetics ; Phylogeny ; Genome, Viral ; *Viruses/genetics ; Eukaryota/genetics ; }, abstract = {Virophages are small dsDNA viruses that hijack the machinery of giant viruses during the co-infection of a protist (i.e., microeukaryotic) host and represent an exceptional case of "hyperparasitism" in the viral world. While only a handful of virophages have been isolated, a vast diversity of virophage-like sequences have been uncovered from diverse metagenomes. Their wide ecological distribution, idiosyncratic infection and replication strategy, ability to integrate into protist and giant virus genomes and potential role in antiviral defense have made virophages a topic of broad interest. However, one limitation for further studies is the lack of clarity regarding the nomenclature and taxonomy of this group of viruses. Specifically, virophages have been linked in the literature to other "virophage-like" mobile genetic elements and viruses, including polinton-like viruses (PLVs), but there are no formal demarcation criteria and proper nomenclature for either group, i.e., virophage or PLVs. Here, as part of the ICTV Virophage Study Group, we leverage a large set of genomes gathered from published datasets as well as newly generated protist genomes to propose delineation criteria and classification methods at multiple taxonomic ranks for virophages 'sensu stricto', i.e., genomes related to the prototype isolates Sputnik and mavirus. Based on a combination of comparative genomics and phylogenetic analyses, we show that this group of virophages forms a cohesive taxon that we propose to establish at the class level and suggest a subdivision into four orders and seven families with distinctive ecogenomic features. Finally, to illustrate how the proposed delineation criteria and classification method would be used, we apply these to two recently published datasets, which we show include both virophages and other virophage-related elements. Overall, we see this proposed classification as a necessary first step to provide a robust taxonomic framework in this area of the virosphere, which will need to be expanded in the future to cover other virophage-related viruses such as PLVs.}, } @article {pmid36830527, year = {2023}, author = {Christodoulou, C and Mavrommatis, A and Loukovitis, D and Symeon, G and Dotas, V and Kotsampasi, B and Tsiplakou, E}, title = {Effect of Spirulina Dietary Supplementation in Modifying the Rumen Microbiota of Ewes.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {4}, pages = {}, pmid = {36830527}, issn = {2076-2615}, abstract = {Supplementing ruminant diets with microalgae, may prove an effective nutritional strategy to manipulate rumen microbiota. Forty-eight ewes were divided into four homogenous groups (n = 12) according to their fat-corrected milk yield (6%), body weight, age, and days in milk, and were fed individually with concentrate, alfalfa hay, and wheat straw. The concentrate of the control group (CON) had no Spirulina supplementation, while in the treated groups 5 (SP5), 10 (SP10), and 15 g (SP15) of Spirulina were supplemented as an additive in the concentrate. An initial screening using metagenomic next-generation sequencing technology was followed by RT-qPCR analysis for the targeting of specific microbes, which unveiled the main alterations of the rumen microbiota under the Spirulina supplementation levels. The relative abundance of Eubacterium ruminantium and Fibrobacter succinogenes in rumen fluid, as well as Ruminococcus albus in rumen solid fraction, were significantly increased in the SP15 group. Furthermore, the relative abundance of Prevotella brevis was significantly increased in the rumen fluid of the SP5 and SP10 groups. In contrast, the relative abundance of Ruminobacter amylophilus was significantly decreased in the rumen fluid of the SP10 compared to the CON group, while in the solid fraction it was significantly decreased in the SP groups. Moreover, the relative abundance of Selenomonas ruminantium was significantly decreased in the SP5 and SP15 groups, while the relative abundance of Streptococcus bovis was significantly decreased in the SP groups. Consequently, supplementing 15 g Spirulina/ewe/day increased the relative abundance of key cellulolytic species in the rumen, while amylolytic species were reduced only in the solid fraction.}, } @article {pmid36830498, year = {2023}, author = {Hayashi, M and Shinozuka, Y and Kurumisawa, T and Yagisawa, T and Suenaga, N and Shimizu, Y and Suzuki, N and Kawai, K}, title = {Effects of Intramammary Antimicrobial Treatment on the Milk Microbiota Composition in Mild Clinical Bovine Mastitis Caused by Gram-Positive Bacteria.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {4}, pages = {}, pmid = {36830498}, issn = {2076-2615}, abstract = {The purpose of this study was to clarify the effects of antimicrobial treatment for mild mastitis caused by Gram-positive bacteria on the milk microbiota in dairy cattle. Sixteen quarters of sixteen cows with mild clinical mastitis from the same herd were included in the study. On the day of onset (day 0), the cows were randomly allocated to a no-treatment (NT; n = 10) group or an intramammary antimicrobial treatment (AMT) group that received AMT starting on day 0 (AMT-AMT group; n = 6). The next day (day 1), the cows in the NT group were randomly allocated into an NT group (NT-NT group; n = 3) that received no treatment or an AMT group that received AMT starting on day 1 (NT-AMT group; n = 7). Milk samples were collected on days 0, 1, 3 and 7, and the milk microbiota of each sample was comprehensively analyzed via 16S rRNA gene amplicon sequencing of the milk DNA. During the treatment period, the milk microbiota of the NT-NT group did not change, but those of the NT-AMT and AMT-AMT groups changed significantly on days three and seven. Thus, the use of antimicrobials for mild mastitis caused by Gram-positive bacteria changes the milk microbiota composition.}, } @article {pmid36830429, year = {2023}, author = {Tardiolo, G and Romeo, O and Zumbo, A and Di Marsico, M and Sutera, AM and Cigliano, RA and Paytuví, A and D'Alessandro, E}, title = {Characterization of the Nero Siciliano Pig Fecal Microbiota after a Liquid Whey-Supplemented Diet.}, journal = {Animals : an open access journal from MDPI}, volume = {13}, number = {4}, pages = {}, pmid = {36830429}, issn = {2076-2615}, support = {DOT1314842_DR_35_SC_VETER_PON_IND_2//University of Messina/ ; }, abstract = {The utilization of dairy by-products as animal feed, especially in swine production, is a strategy to provide functional ingredients to improve gut health. This study explored the potential effect of a liquid whey-supplemented diet on the fecal microbiota of eleven pigs belonging to the Nero Siciliano breed. Five pigs were assigned to the control group and fed with a standard formulation feed, whereas six pigs were assigned to the experimental group and fed with the same feed supplemented with liquid whey. Fecal samples were collected from each individual before the experimental diet (T0), and one (T1) and two (T2) months after the beginning of the co-feed supplementation. Taxonomic analysis, based on the V3-V4 region of the bacterial 16S rRNA, showed that pig feces were populated by a complex microbial community with a remarkable abundance of Firmicutes, Bacteroidetes, and Spirochaetes phyla and Prevotella, Lactobacillus, Clostridium, and Treponema genera. Alpha and beta diversity values suggested that the experimental diet did not significantly affect the overall fecal microbiota diversity. However, analysis of abundance at different time points revealed significant variation in several bacterial genera, suggesting that the experimental diet potentially affected some genera of the microbial community.}, } @article {pmid36830296, year = {2023}, author = {Dobiáš, R and Stevens, DA and Havlíček, V}, title = {Current and Future Pathways in Aspergillus Diagnosis.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {36830296}, issn = {2079-6382}, support = {22-06771S//Czech Science Foundation/ ; SGS05/LF/2022//Internal Grant Agency of University of Ostrava/ ; }, abstract = {Aspergillus fumigatus has been designated by the World Health Organization as a critical priority fungal pathogen. Some commercially available diagnostics for many forms of aspergillosis rely on fungal metabolites. These encompass intracellular molecules, cell wall components, and extracellular secretomes. This review summarizes the shortcomings of antibody tests compared to tests of fungal products in body fluids and highlights the application of β-d-glucan, galactomannan, and pentraxin 3 in bronchoalveolar lavage fluids. We also discuss the detection of nucleic acids and next-generation sequencing, along with newer studies on Aspergillus metallophores.}, } @article {pmid36830277, year = {2023}, author = {Lüftinger, L and Májek, P and Rattei, T and Beisken, S}, title = {Metagenomic Antimicrobial Susceptibility Testing from Simulated Native Patient Samples.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {36830277}, issn = {2079-6382}, abstract = {Genomic antimicrobial susceptibility testing (AST) has been shown to be accurate for many pathogens and antimicrobials. However, these methods have not been systematically evaluated for clinical metagenomic data. We investigate the performance of in-silico AST from clinical metagenomes (MG-AST). Using isolate sequencing data from a multi-center study on antimicrobial resistance (AMR) as well as shotgun-sequenced septic urine samples, we simulate over 2000 complicated urinary tract infection (cUTI) metagenomes with known resistance phenotype to 5 antimicrobials. Applying rule-based and machine learning-based genomic AST classifiers, we explore the impact of sequencing depth and technology, metagenome complexity, and bioinformatics processing approaches on AST accuracy. By using an optimized metagenomics assembly and binning workflow, MG-AST achieved balanced accuracy within 5.1% of isolate-derived genomic AST. For poly-microbial infections, taxonomic sample complexity and relatedness of taxa in the sample is a key factor influencing metagenomic binning and downstream MG-AST accuracy. We show that the reassignment of putative plasmid contigs by their predicted host range and investigation of whole resistome capabilities improved MG-AST performance on poly-microbial samples. We further demonstrate that machine learning-based methods enable MG-AST with superior accuracy compared to rule-based approaches on simulated native patient samples.}, } @article {pmid36830274, year = {2023}, author = {Olías-Molero, AI and Botías, P and Cuquerella, M and García-Cantalejo, J and Barcia, E and Torrado, S and Torrado, JJ and Alunda, JM}, title = {Effect of Clindamycin on Intestinal Microbiome and Miltefosine Pharmacology in Hamsters Infected with Leishmania infantum.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {36830274}, issn = {2079-6382}, support = {PR87/19-22646//Proyecto Santander/Complutense/ ; }, abstract = {Visceral leishmaniasis (VL), a vector-borne parasitic disease caused by Leishmania donovani and L. infantum (Kinetoplastida), affects humans and dogs, being fatal unless treated. Miltefosine (MIL) is the only oral medication for VL and is considered a first choice drug when resistance to antimonials is present. Comorbidity and comedication are common in many affected patients but the relationship between microbiome composition, drugs administered and their pharmacology is still unknown. To explore the effect of clindamycin on the intestinal microbiome and the availability and distribution of MIL in target organs, Syrian hamsters (120-140 g) were inoculated with L. infantum (10[8] promastigotes/animal). Infection was maintained for 16 weeks, and the animals were treated with MIL (7 days, 5 mg/kg/day), clindamycin (1 mg/kg, single dose) + MIL (7 days, 5 mg/kg/day) or kept untreated. Infection was monitored by ELISA and fecal samples (16 wpi, 18 wpi, end point) were analyzed to determine the 16S metagenomic composition (OTUs) of the microbiome. MIL levels were determined by LC-MS/MS in plasma (24 h after the last treatment; end point) and target organs (spleen, liver) (end point). MIL did not significantly affect the composition of intestinal microbiome, but clindamycin provoked a transient albeit significant modification of the relative abundance of 45% of the genera, including Ruminococcaceae UCG-014, Ruminococcus 2; Bacteroides and (Eubacterium) ruminantium group, besides its effect on less abundant phyla and families. Intestinal dysbiosis in the antibiotic-treated animals was associated with significantly lower levels of MIL in plasma, though not in target organs at the end of the experiment. No clear relationship between microbiome composition (OTUs) and pharmacological parameters was found.}, } @article {pmid36830245, year = {2023}, author = {Ordine, JVW and de Souza, GM and Tamasco, G and Virgilio, S and Fernandes, AFT and Silva-Rocha, R and Guazzaroni, ME}, title = {Metagenomic Insights for Antimicrobial Resistance Surveillance in Soils with Different Land Uses in Brazil.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {36830245}, issn = {2079-6382}, support = {2021/01748-5//São Paulo Research Foundation/ ; 2020/02228-2//São Paulo Research Foundation/ ; 2019/18789-6//São Paulo Research Foundation/ ; 888887.666860/2022-00//Coordenação de Aperfeicoamento de Pessoal de Nível Superior/ ; 302750/2020-7//National Council for Scientific and Technological Development (CNPq)/ ; }, abstract = {Land-use conversion changes soil properties and their microbial communities, which, combined with the overuse of antibiotics in human and animal health, promotes the expansion of the soil resistome. In this context, we aimed to profile the resistome and the microbiota of soils under different land practices. We collected eight soil samples from different locations in the countryside of São Paulo (Brazil), assessed the community profiles based on 16S rRNA sequencing, and analyzed the soil metagenomes based on shotgun sequencing. We found differences in the communities' structures and their dynamics that were correlated with land practices, such as the dominance of Staphylococcus and Bacillus genera in agriculture fields. Additionally, we surveyed the abundance and diversity of antibiotic resistance genes (ARGs) and virulence factors (VFs) across studied soils, observing a higher presence and homogeneity of the vanRO gene in livestock soils. Moreover, three β-lactamases were identified in orchard and urban square soils. Together, our findings reinforce the importance and urgency of AMR surveillance in the environment, especially in soils undergoing deep land-use transformations, providing an initial exploration under the One Health approach of environmental levels of resistance and profiling soil communities.}, } @article {pmid36830206, year = {2023}, author = {Fisher, CR and Patel, R}, title = {Profiling the Immune Response to Periprosthetic Joint Infection and Non-Infectious Arthroplasty Failure.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {36830206}, issn = {2079-6382}, support = {R01 AR056647//National Institute of Allergy and Infectious Diseases/ ; NA//Mayo Clinic Graduate School of Biomedical Sciences/ ; T32 AI07425-25//National Institute of Allergy and Infectious Diseases/ ; }, abstract = {Arthroplasty failure is a major complication of joint replacement surgery. It can be caused by periprosthetic joint infection (PJI) or non-infectious etiologies, and often requires surgical intervention and (in select scenarios) resection and reimplantation of implanted devices. Fast and accurate diagnosis of PJI and non-infectious arthroplasty failure (NIAF) is critical to direct medical and surgical treatment; differentiation of PJI from NIAF may, however, be unclear in some cases. Traditional culture, nucleic acid amplification tests, metagenomic, and metatranscriptomic techniques for microbial detection have had success in differentiating the two entities, although microbiologically negative apparent PJI remains a challenge. Single host biomarkers or, alternatively, more advanced immune response profiling-based approaches may be applied to differentiate PJI from NIAF, overcoming limitations of microbial-based detection methods and possibly, especially with newer approaches, augmenting them. In this review, current approaches to arthroplasty failure diagnosis are briefly overviewed, followed by a review of host-based approaches for differentiation of PJI from NIAF, including exciting futuristic combinational multi-omics methodologies that may both detect pathogens and assess biological responses, illuminating causes of arthroplasty failure.}, } @article {pmid36830128, year = {2023}, author = {Perikleous, EP and Gkentzi, D and Bertzouanis, A and Paraskakis, E and Sovtic, A and Fouzas, S}, title = {Antibiotic Resistance in Patients with Cystic Fibrosis: Past, Present, and Future.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {36830128}, issn = {2079-6382}, abstract = {Patients with cystic fibrosis (CF) are repeatedly exposed to antibiotics, especially during the pulmonary exacerbations of the disease. However, the available therapeutic strategies are frequently inadequate to eradicate the involved pathogens and most importantly, facilitate the development of antimicrobial resistance (AMR). The evaluation of AMR is demanding; conventional culture-based susceptibility-testing techniques cannot account for the lung microenvironment and/or the adaptive mechanisms developed by the pathogens, such as biofilm formation. Moreover, features linked to modified pharmaco-kinetics and pulmonary parenchyma penetration make the dosing of antibiotics even more challenging. In this review, we present the existing knowledge regarding AMR in CF, we shortly review the existing therapeutic strategies, and we discuss the future directions of antimicrobial stewardship. Due to the increasing difficulty in eradicating strains that develop AMR, the appropriate management should rely on targeting the underlying resistance mechanisms; thus, the interest in novel, molecular-based diagnostic tools, such as metagenomic sequencing and next-generation transcriptomics, has increased exponentially. Moreover, since the development of new antibiotics has a slow pace, the design of effective treatment strategies to eradicate persistent infections represents an urgency that requires consorted work. In this regard, both the management and monitoring of antibiotics usage are obligatory and more relevant than ever.}, } @article {pmid36829425, year = {2023}, author = {Fernandes, P and Afonso, IM and Pereira, J and Rocha, R and Rodrigues, AS}, title = {Epiphitic Microbiome of Alvarinho Wine Grapes from Different Geographic Regions in Portugal.}, journal = {Biology}, volume = {12}, number = {2}, pages = {}, pmid = {36829425}, issn = {2079-7737}, support = {POCI-01-0145-FEDER-024328//Fundação para a Ciência e Tecnologia/ ; UIDB/05937/2020//Fundação para a Ciência e Tecnologia/ ; UIDP/05937/2020//Fundação para a Ciência e Tecnologia/ ; }, abstract = {Geographic location and, particularly, soil and climate exert influence on the typicality of a wine from a specific region, which is often justified by the terroir, and these factors also influence the epiphytic flora associated with the surface of the grape berries. In the present study, the microbiome associated with the surface of berries obtained from ten vineyards of the Alvarinho variety located in different geographical locations in mainland Portugal was determined and analyzed. The removal of microbial flora from the surface of the berries was carried out by washing and sonication, after which the extraction and purification of the respective DNA was carried out. High-throughput short amplicon sequencing of the fungal ITS region and the bacterial 16S region was performed, allowing for the determination of the microbial consortium associated with Alvarinho wine grapes. Analysis of α-diversity demonstrated that parcels from the Monção and Melgaço sub-region present a significantly (p < 0.05) lower fungal diversity and species richness when compared to the plots analyzed from other regions/sub-regions. The ubiquitous presence of Metschnikowia spp., a yeast with enologic potential interest in all parcels from Monção and Melgaço, was also observed.}, } @article {pmid36829171, year = {2023}, author = {Huang, L and Xu, S and Huang, Z and Chen, Y and Xu, N and Xie, B}, title = {Risk factors associated with Pneumocystis jirovecii pneumonia in non-HIV immunocompromised patients and co-pathogens analysis by metagenomic next-generation sequencing.}, journal = {BMC pulmonary medicine}, volume = {23}, number = {1}, pages = {72}, pmid = {36829171}, issn = {1471-2466}, mesh = {Male ; Humans ; *Pneumonia, Pneumocystis/diagnosis ; *Pneumocystis carinii ; Risk Factors ; *Cytomegalovirus Infections ; Adrenal Cortex Hormones/therapeutic use ; Immunosuppressive Agents/therapeutic use ; Immunocompromised Host ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) is one of the most common opportunistic infections in immunocompromised patients. However, the accurate prediction of the development of PJP in non-HIV immunocompromised patients is still unclear.

METHODS: Non-HIV immunocompromised patients confirmed diagnosis of PJP by the clinical symptoms, chest computed tomography and etiological results of metagenomic next-generation sequencing (mNGS) were enrolled as observation group. Another group of matched non-HIV immunocompromised patients with non-PJP pneumonia were enrolled to control group. The risk factors for the development of PJP and the co-pathogens in the bronchoalveolar lavage fluid (BALF) detected by mNGS were analyzed.  RESULTS: A total of 67 (33 PJP, 34 non-PJP) participants were enrolled from Fujian Provincial Hospital. The ages, males and underlying illnesses were not significantly different between the two groups. Compared to non-PJP patients, PJP patients were more tends to have the symptoms of fever and dyspnea. The LYM and ALB were significantly lower in PJP patients than in non-PJP patients. Conversely, LDH and serum BDG in PJP patients were significantly higher than in non-PJP controls. For immunological indicators, the levels of immunoglobulin A, G, M and complement C3, C4, the numbers of T, B, and NK cells, had no statistical difference between these two groups. Logistic multivariate analysis showed that concomitant use of corticosteroids and immunosuppressant (OR 14.146, P = 0.004) and the lymphocyte counts < 0.7 × 10[9]/L (OR 6.882, P = 0.011) were risk factors for the development of PJP in non-HIV immunocompromised patients. 81.82% (27/33) and 64.71% (22/34) mixed infections were identified by mNGS in the PJP group and non-PJP group separately. CMV, EBV and Candida were the leading co-pathogens in PJP patients. The percentages of CMV and EBV identified by mNGS in PJP group were significantly higher than those in the control group(p < 0.005).  CONCLUSIONS: Clinicians should pay close attention to the development of PJP in non-HIV immunocompromised patients who possess the risk factors of concomitant use of corticosteroids and immunosuppressant and the lymphocyte counts < 0.7 × 10[9]/L. Prophylaxis for PJP cannot rely solely on CD4[+] T counts in non-HIV immunocompromised patients. Whether CMV infection increases the risk of PJP remains to be further investigated.}, } @article {pmid36828854, year = {2023}, author = {Yu, H and Xiong, L and Li, Y and Wei, Y and Zhang, Q and Li, H and Chen, W and Ji, X}, title = {Genetic diversity of virus auxiliary metabolism genes associated with phosphorus metabolism in Napahai plateau wetland.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {3250}, pmid = {36828854}, issn = {2045-2322}, mesh = {*Wetlands ; Ecosystem ; Phylogeny ; Genes, Viral ; *Viruses ; Genetic Variation ; }, abstract = {Viruses play important roles in ecosystems by interfering with the central metabolic pathways of the host during infection via the expression of auxiliary metabolic genes (AMGs), altering the productivity of ecosystems and thus affecting geochemical cycling. In this study, the genetic diversity of phosphorus metabolism AMGs phoH, phoU and pstS was investigated by phylogenetic analysis, PCoA analysis, and alpha diversity analysis based on metagenomic data. It was found that the majority of the sequences were unique to Napahai plateau wetland. It was shown that the genetic diversity of phoH, phoU and pstS genes was independent of both habitats and host origins. In addition, the metabolic pathway of AMGs associated with the phosphorus cycling was identified based on metagenomic data. When phosphorus is deficient, virus utilizes AMGs to affect the metabolic pathway, contributing to higher phosphorus levels in the host and facilitating virus survival, replication, and propagation in the host cell.}, } @article {pmid36828753, year = {2023}, author = {Mazza Rodrigues, JL and Melotto, M}, title = {Naturally engineered plant microbiomes in resource-limited ecosystems.}, journal = {Trends in microbiology}, volume = {31}, number = {4}, pages = {329-331}, doi = {10.1016/j.tim.2023.02.006}, pmid = {36828753}, issn = {1878-4380}, mesh = {*Ecosystem ; Rhizosphere ; Soil Microbiology ; Plant Roots ; Plants ; *Microbiota/genetics ; }, abstract = {Nature-designed plant microbiomes may offer solutions to improve crop production and ecosystem restoration in less than optimum environments. Through a full exploration of metagenomic data, Camargo et al. showed that a previously unknown microbial diversity enhances nutrient mobilization in stress-adapted plants.}, } @article {pmid36828645, year = {2023}, author = {Ao, Z and Xu, H and Li, M and Liu, H and Deng, M and Liu, Y}, title = {Clinical characteristics, diagnosis, outcomes and lung microbiome analysis of invasive pulmonary aspergillosis in the community-acquired pneumonia patients.}, journal = {BMJ open respiratory research}, volume = {10}, number = {1}, pages = {}, pmid = {36828645}, issn = {2052-4439}, mesh = {Humans ; *Invasive Pulmonary Aspergillosis/complications/diagnosis/microbiology ; Retrospective Studies ; Sensitivity and Specificity ; Bronchoalveolar Lavage Fluid/microbiology ; *Aspergillosis/complications ; Lung ; *Pneumonia/complications ; *Microbiota ; }, abstract = {BACKGROUND: Invasive pulmonary aspergillosis (IPA) remains underestimated in patients with community-acquired pneumonia (CAP). This study aims to describe clinical features and outcomes of IPA in CAP patients, assess diagnostic performance of metagenomic next-generation sequencing (mNGS) for IPA and analyse lung microbiome via mNGS data.

METHODS: This retrospective cohort study included CAP patients from 22 April 2019 to 30 September 2021. Clinical and microbiological data were analysed. Diagnostic performance of mNGS was compared with traditional detection methods. The lung microbiome detected by mNGS was characterised and its association with clinical features was evaluated.

MAIN RESULTS: IPA was diagnosed in 26 (23.4%) of 111 CAP patients. Patients with IPA displayed depressed immunity, higher hospital mortality (30.8% vs 11.8%) and intensive care unit mortality (42.1% vs 17.5%) compared with patients without IPA. The galactomannan (GM) antigen test had the highest sensitivity (57.7%) in detecting the Aspergillus spp, followed by mNGS (42.3%), culture (30.8%) and smear (7.7%). The mNGS, culture and smear had 100% specificity, while GM test had 92.9% specificity. The microbial structure of IPA significantly differed from non-IPA patients (p<0.001; Wilcoxon test). Nineteen different species were significantly correlated with clinical outcomes and laboratory biomarkers, particularly for Streptococcus salivarius, Prevotella timonensis and Human betaherpesvirus 5.

CONCLUSIONS: Our results reveal that patients with Aspergillus infection tend to have a higher early mortality rate. The mNGS may be suggested as a complement to routine microbiological test in diagnosis of patients at risk of Aspergillus infection. The lung microbiota is associated with inflammatory, immune and metabolic conditions of IPA, and thus influences clinical outcomes.}, } @article {pmid36828537, year = {2023}, author = {Parker, K and Wood, H and Russell, JA and Yarmosh, D and Shteyman, A and Bagnoli, J and Knight, B and Aspinwall, JR and Jacobs, J and Werking, K and Winegar, R}, title = {Development and Optimization of an Unbiased, Metagenomics-Based Pathogen Detection Workflow for Infectious Disease and Biosurveillance Applications.}, journal = {Tropical medicine and infectious disease}, volume = {8}, number = {2}, pages = {}, pmid = {36828537}, issn = {2414-6366}, support = {HDTRA1-15-C-0013//the Defense Threat Reduction Agency-Joint Science and Technology Office for Chemical and Biological Defense/ ; }, abstract = {Rapid, specific, and sensitive identification of microbial pathogens is critical to infectious disease diagnosis and surveillance. Classical culture-based methods can be applied to a broad range of pathogens but have long turnaround times. Molecular methods, such as PCR, are time-effective but are not comprehensive and may not detect novel strains. Metagenomic shotgun next-generation sequencing (NGS) promises specific identification and characterization of any pathogen (viruses, bacteria, fungi, and protozoa) in a less biased way. Despite its great potential, NGS has yet to be widely adopted by clinical microbiology laboratories due in part to the absence of standardized workflows. Here, we describe a sample-to-answer workflow called PanGIA (Pan-Genomics for Infectious Agents) that includes simplified, standardized wet-lab procedures and data analysis with an easy-to-use bioinformatics tool. PanGIA is an end-to-end, multi-use workflow that can be used for pathogen detection and related applications, such as biosurveillance and biothreat detection. We performed a comprehensive survey and assessment of current, commercially available wet-lab technologies and open-source bioinformatics tools for each workflow component. The workflow includes total nucleic acid extraction from clinical human whole blood and environmental microbial forensic swabs as sample inputs, host nucleic acid depletion, dual DNA and RNA library preparation, shotgun sequencing on an Illumina MiSeq, and sequencing data analysis. The PanGIA workflow can be completed within 24 h and is currently compatible with bacteria and viruses. Here, we present data from the development and application of the clinical and environmental workflows, enabling the specific detection of pathogens associated with bloodstream infections and environmental biosurveillance, without the need for targeted assay development.}, } @article {pmid36828358, year = {2023}, author = {Sivalingam, P and Sabatino, R and Sbaffi, T and Fontaneto, D and Corno, G and Di Cesare, A}, title = {Extracellular DNA includes an important fraction of high-risk antibiotic resistance genes in treated wastewaters.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {323}, number = {}, pages = {121325}, doi = {10.1016/j.envpol.2023.121325}, pmid = {36828358}, issn = {1873-6424}, mesh = {Humans ; *Wastewater ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; DNA ; Drug Resistance, Microbial/genetics ; }, abstract = {Wastewater treatment plants are among the main hotspots for the release of antibiotic resistance genes (ARGs) into the environment. ARGs in treated wastewater can be found in the intracellular DNA (iDNA) and in the extracellular DNA (eDNA). In this study, we investigated the fate and the distribution (either in eDNA or in iDNA) of ARGs in the treated wastewaters pre and post-disinfection by shotgun metagenomics. The richness of the intracellular resistome was found to be higher than the extracellular one. However, the latter included different high risk ARGs. About 11% of the recovered metagenome assembled genomes (MAGs) from the extracted DNA was positive for at least one ARG and, among them, several were positive for more ARGs. The high-risk ARG bacA was the most frequently detected gene among the MAGs. The disinfection demonstrated to be an important driver of the composition of the antibiotic resistomes. Our results demonstrated that eDNA represents an important fraction of the overall ARGs, including a number of high-risk ARGs, which reach the environment with treated wastewater effluents. The studied disinfections only marginally affect the whole antibiotic resistome but cause important shifts from intracellular to extracellular DNA, potentially threating human health.}, } @article {pmid36828342, year = {2023}, author = {Edridge, A and Namazzi, R and Tebulo, A and Mfizi, A and Deijs, M and Koekkoek, S and de Wever, B and van der Ende, A and Umiwana, J and de Jong, MD and Jans, J and Verhoeven-Duif, N and Titulaer, M and van Karnebeek, C and Seydel, K and Taylor, T and Asiimwe-Kateera, B and van der Hoek, L and Kabayiza, JC and Mallewa, M and Idro, R and Boele van Hensbroek, M and van Woensel, JBM}, title = {Viral, Bacterial, Metabolic, and Autoimmune Causes of Severe Acute Encephalopathy in Sub-Saharan Africa: A Multicenter Cohort Study.}, journal = {The Journal of pediatrics}, volume = {258}, number = {}, pages = {113360}, doi = {10.1016/j.jpeds.2023.02.007}, pmid = {36828342}, issn = {1097-6833}, mesh = {Child ; Humans ; *Brain Diseases/diagnosis/complications ; *Encephalitis/complications/diagnosis/epidemiology ; *Metabolic Diseases ; Cohort Studies ; Malawi ; }, abstract = {OBJECTIVES: To assess whether viral, bacterial, metabolic, and autoimmune diseases are missed by conventional diagnostics among children with severe acute encephalopathy in sub-Saharan Africa.

STUDY DESIGN: One hundred thirty-four children (6 months to 18 years) presenting with nontraumatic coma or convulsive status epilepticus to 1 of 4 medical referral centers in Uganda, Malawi, and Rwanda were enrolled between 2015 and 2016. Locally available diagnostic tests could be supplemented in 117 patients by viral, bacterial, and 16s quantitative polymerase chain reaction testing, metagenomics, untargeted metabolomics, and autoimmune immunohistochemistry screening.

RESULTS: Fourteen (12%) cases of viral encephalopathies, 8 (7%) cases of bacterial central nervous system (CNS) infections, and 4 (4%) cases of inherited metabolic disorders (IMDs) were newly identified by additional diagnostic testing as the most likely cause of encephalopathy. No confirmed cases of autoimmune encephalitis were found. Patients for whom additional diagnostic testing aided causal evaluation (aOR 3.59, 90% CI 1.57-8.36), patients with a viral CNS infection (aOR 7.91, 90% CI 2.49-30.07), and patients with an IMD (aOR 9.10, 90% CI 1.37-110.45) were at increased risk for poor outcome of disease.

CONCLUSIONS: Viral and bacterial CNS infections and IMDs are prevalent causes of severe acute encephalopathy in children in Uganda, Malawi, and Rwanda that are missed by conventional diagnostics and are associated with poor outcome of disease. Improved diagnostic capacity may increase diagnostic yield and might improve outcome of disease.}, } @article {pmid36827814, year = {2023}, author = {Ku, T and Liu, Y and Xie, Y and Hu, J and Hou, Y and Tan, X and Ning, X and Li, G and Sang, N}, title = {Tebuconazole mediates cognitive impairment via the microbe-gut-brain axis (MGBA) in mice.}, journal = {Environment international}, volume = {173}, number = {}, pages = {107821}, doi = {10.1016/j.envint.2023.107821}, pmid = {36827814}, issn = {1873-6750}, mesh = {Mice ; Humans ; Animals ; *Brain-Gut Axis ; *Cognitive Dysfunction ; Triazoles/toxicity ; }, abstract = {Tebuconazole, one of the most widely used triazole fungicides, is reported to potentially pose a risk of inducing neurological disorders in human beings. Considering the increasing exposure, whether it could influence cognitive function remains to be elucidated. Herein, we used a mouse model to evaluate the potential cognitive risks and possible mechanisms from the continuous edible application of tebuconazole at low concentrations. Our study revealed that tebuconazole deteriorated spatial learning and memory and downregulated the expression of glutamate receptor subunits. Importantly, metagenomic analysis indicated that tebuconazole not only led to significant shifts in the composition and diversity of the gut microbiota but also changed intestinal homeostasis. Specifically, after exposure, tebuconazole circulated in the bloodstream and largely entered the gut-brain axis for disruption, including disturbing the Firmicutes/Bacteroidetes ratio, interrelated neurotransmitters and systemic immune factors. Moreover, pretreatment with probiotics improved immune factor expression and restored the deterioration of synaptic function and spatial learning and memory. The current study provides novel insights concerning perturbations of the gut microbiome and its functions as a potential new mechanism by which tebuconazole exposes cognitive function-related human health.}, } @article {pmid36827617, year = {2023}, author = {Gabrielli, M and Dai, Z and Delafont, V and Timmers, PHA and van der Wielen, PWJJ and Antonelli, M and Pinto, AJ}, title = {Identifying Eukaryotes and Factors Influencing Their Biogeography in Drinking Water Metagenomes.}, journal = {Environmental science & technology}, volume = {57}, number = {9}, pages = {3645-3660}, pmid = {36827617}, issn = {1520-5851}, mesh = {*Drinking Water ; Metagenome ; Eukaryota/genetics ; Metagenomics ; }, abstract = {The biogeography of eukaryotes in drinking water systems is poorly understood relative to that of prokaryotes or viruses, limiting the understanding of their role and management. A challenge with studying complex eukaryotic communities is that metagenomic analysis workflows are currently not as mature as those that focus on prokaryotes or viruses. In this study, we benchmarked different strategies to recover eukaryotic sequences and genomes from metagenomic data and applied the best-performing workflow to explore the factors affecting the relative abundance and diversity of eukaryotic communities in drinking water distribution systems (DWDSs). We developed an ensemble approach exploiting k-mer- and reference-based strategies to improve eukaryotic sequence identification and identified MetaBAT2 as the best-performing binning approach for their clustering. Applying this workflow to the DWDS metagenomes showed that eukaryotic sequences typically constituted small proportions (i.e., <1%) of the overall metagenomic data with higher relative abundances in surface water-fed or chlorinated systems with high residuals. The α and β diversities of eukaryotes were correlated with those of prokaryotic and viral communities, highlighting the common role of environmental/management factors. Finally, a co-occurrence analysis highlighted clusters of eukaryotes whose members' presence and abundance in DWDSs were affected by disinfection strategies, climate conditions, and source water types.}, } @article {pmid36827575, year = {2023}, author = {Macocco, I and Glielmo, A and Grilli, J and Laio, A}, title = {Intrinsic Dimension Estimation for Discrete Metrics.}, journal = {Physical review letters}, volume = {130}, number = {6}, pages = {067401}, doi = {10.1103/PhysRevLett.130.067401}, pmid = {36827575}, issn = {1079-7114}, abstract = {Real-world datasets characterized by discrete features are ubiquitous: from categorical surveys to clinical questionnaires, from unweighted networks to DNA sequences. Nevertheless, the most common unsupervised dimensional reduction methods are designed for continuous spaces, and their use for discrete spaces can lead to errors and biases. In this Letter we introduce an algorithm to infer the intrinsic dimension (ID) of datasets embedded in discrete spaces. We demonstrate its accuracy on benchmark datasets, and we apply it to analyze a metagenomic dataset for species fingerprinting, finding a surprisingly small ID, of order 2. This suggests that evolutive pressure acts on a low-dimensional manifold despite the high dimensionality of sequences' space.}, } @article {pmid36827387, year = {2023}, author = {Zhao, M and Zhao, Q and Guan, Z and Liu, Q and Zhou, H and Huang, Q and Huo, B}, title = {Effect of Panax ginseng and Fructus Mume on Intestinal Barrier and Gut Microbiota in Rats with Diarrhea.}, journal = {Journal of medicinal food}, volume = {26}, number = {3}, pages = {165-175}, doi = {10.1089/jmf.2022.K.0069}, pmid = {36827387}, issn = {1557-7600}, mesh = {Rats ; Animals ; NF-kappa B/genetics/metabolism ; *Gastrointestinal Microbiome ; Phosphatidylinositol 3-Kinases/genetics ; Proto-Oncogene Proteins c-akt ; *Panax/chemistry ; Diarrhea/drug therapy ; Tumor Necrosis Factor-alpha ; Tight Junction Proteins/metabolism ; }, abstract = {Panax ginseng and Fructus mume (Renshen Wumei in Chinese, RW) are natural medicines with high nutritional and pharmacological value. They have been widely used together in China to treat gastrointestinal diseases, especially persistent diarrhea, but the potential mechanisms remain elusive. In this study, a diarrhea model was established in rats using a 30% aqueous extract of senna. The therapeutic effects of RW were evaluated by recording the prevalence of loose stools, the diarrhea index, and histopathological changes in colon tissue. The levels of mucins, tight junction (TJ) proteins, inflammatory cytokines, and phosphoinositide 3-kinase/Akt/nuclear factor-κB (PI3K/Akt/NF-κB) signaling pathway proteins were measured. Metagenomic sequencing was used to analyze the gut microbiota. Treatment with RW alleviated injury to the intestinal barrier in rats with diarrhea and also upregulated levels of Muc2 and TJ proteins, such as occludin, zonula occludens-1, and claudin-1. Administration of RW regulated the structure of the gut microbiota in diarrheal rats. Furthermore, RW suppressed levels of interleukin (IL), tumor necrosis factor (TNF)-α, IL-1, PI3K, Akt, and p-NF-κB p65 and also increased IL-4 levels. Our study indicates that P. ginseng and Fructus mume help improve the symptoms of diarrhea, possibly by alleviating the intestinal barrier injury, regulating intestinal flora composition, and inhibiting the PI3K/Akt/NF-κB signaling pathway.}, } @article {pmid36827180, year = {2023}, author = {Qu, YN and Rao, YZ and Qi, YL and Li, YX and Li, A and Palmer, M and Hedlund, BP and Shu, WS and Evans, PN and Nie, GX and Hua, ZS and Li, WJ}, title = {Panguiarchaeum symbiosum, a potential hyperthermophilic symbiont in the TACK superphylum.}, journal = {Cell reports}, volume = {42}, number = {3}, pages = {112158}, doi = {10.1016/j.celrep.2023.112158}, pmid = {36827180}, issn = {2211-1247}, mesh = {*Symbiosis/genetics ; *Hot Springs/microbiology ; Fermentation ; Anaerobiosis ; Amino Acids/metabolism ; Coenzymes/metabolism ; Phylogeography ; Polymorphism, Single Nucleotide/genetics ; Sulfur/metabolism ; Peptides/metabolism ; Proteolysis ; *Archaea/classification/cytology/genetics ; Cell Adhesion/genetics ; Genes, Archaeal ; Gene Expression Regulation, Archaeal ; Genome, Archaeal ; Metagenomics ; Metagenome ; }, abstract = {The biology of Korarchaeia remains elusive due to the lack of genome representatives. Here, we reconstruct 10 closely related metagenome-assembled genomes from hot spring habitats and place them into a single species, proposed herein as Panguiarchaeum symbiosum. Functional investigation suggests that Panguiarchaeum symbiosum is strictly anaerobic and grows exclusively in thermal habitats by fermenting peptides coupled with sulfide and hydrogen production to dispose of electrons. Due to its inability to biosynthesize archaeal membranes, amino acids, and purines, this species likely exists in a symbiotic lifestyle similar to DPANN archaea. Population metagenomics and metatranscriptomic analyses demonstrated that genes associated with amino acid/peptide uptake and cell attachment exhibited positive selection and were highly expressed, supporting the proposed proteolytic catabolism and symbiotic lifestyle. Our study sheds light on the metabolism, evolution, and potential symbiotic lifestyle of Panguiarchaeum symbiosum, which may be a unique host-dependent archaeon within the TACK superphylum.}, } @article {pmid36827117, year = {2023}, author = {Meyer, JL and Gunasekera, SP and Brown, AL and Ding, Y and Miller, S and Teplitski, M and Paul, VJ}, title = {Cryptic Diversity of Black Band Disease Cyanobacteria in Siderastrea siderea Corals Revealed by Chemical Ecology and Comparative Genome-Resolved Metagenomics.}, journal = {Marine drugs}, volume = {21}, number = {2}, pages = {}, pmid = {36827117}, issn = {1660-3397}, support = {R35 GM128742/GM/NIGMS NIH HHS/United States ; GM128742/NH/NIH HHS/United States ; }, mesh = {Animals ; *Anthozoa/microbiology ; *Cyanobacteria/metabolism ; Genomics ; Metagenomics ; }, abstract = {Black band disease is a globally distributed and easily recognizable coral disease. Despite years of study, the etiology of this coral disease, which impacts dozens of stony coral species, is not completely understood. Although black band disease mats are predominantly composed of the cyanobacterial species Roseofilum reptotaenium, other filamentous cyanobacterial strains and bacterial heterotrophs are readily detected. Through chemical ecology and metagenomic sequencing, we uncovered cryptic strains of Roseofilum species from Siderastrea siderea corals that differ from those on other corals in the Caribbean and Pacific. Isolation of metabolites from Siderastrea-derived Roseofilum revealed the prevalence of unique forms of looekeyolides, distinct from previously characterized Roseofilum reptotaenium strains. In addition, comparative genomics of Roseofilum strains showed that only Siderastrea-based Roseofilum strains have the genetic capacity to produce lasso peptides, a family of compounds with diverse biological activity. All nine Roseofilum strains examined here shared the genetic capacity to produce looekeyolides and malyngamides, suggesting these compounds support the ecology of this genus. Similar biosynthetic gene clusters are not found in other cyanobacterial genera associated with black band disease, which may suggest that looekeyolides and malyngamides contribute to disease etiology through yet unknown mechanisms.}, } @article {pmid36827038, year = {2023}, author = {Zhang, H and Wang, X and Xia, H and Liu, Z}, title = {Metagenomics next-generation sequencing assists in the diagnosis of infant pertussis encephalopathy: A case report.}, journal = {Medicine}, volume = {102}, number = {8}, pages = {e33080}, doi = {10.1097/MD.0000000000033080}, pmid = {36827038}, issn = {1536-5964}, mesh = {Infant ; Humans ; Child ; Male ; *Whooping Cough/complications ; Bordetella pertussis/genetics ; *Respiratory Tract Infections/complications ; *Brain Diseases/complications ; High-Throughput Nucleotide Sequencing ; }, abstract = {RATIONALE: Pertussis is an acute respiratory infection that often occurs in the pediatric population, especially in infants under 3 months old. Bordetella pertussis is the causative agent of pertussis, which can lead to pneumonia, encephalopathy, and pulmonary hypertension, causing death in severe cases. Therefore, an accurate and comprehensive diagnosis of the pathogen is essential for effective treatment.

PATIENT CONCERNS: We report a case of 2-month-old male infant admitted to the pediatric intensive care unit of West China Second University due to hoarse cough for 7 days, accompanied by a crowing-like echo, fever and listlessness, occasional nonprojectile vomiting with anorexia, shortness of breath, accelerated heart rate, cyanosis of the lips, and convulsions. B pertussis was identified by metagenomic next-generation sequencing in blood and cerebrospinal fluid and polymerase chain reaction assay using blood.

DIAGNOSES: The infant was diagnosed with pertussis.

INTERVENTIONS: Intravenous infusion of erythromycin (50 mg/kg/d) for anti-infection and dexamethasone for alleviating intracranial inflammatory reaction were given.

OUTCOMES: The patient was eventually recovered and discharged.

LESSONS: This case report emphasized the importance of metagenomic next-generation sequencing using cerebrospinal fluid and blood for early diagnosis of pertussis-associated encephalopathy.}, } @article {pmid36826808, year = {2023}, author = {Tan, TC and Chandrasekaran, L and Leung, YY and Purbojati, R and Pettersson, S and Low, AHL}, title = {Gut microbiome profiling in systemic sclerosis: a metagenomic approach.}, journal = {Clinical and experimental rheumatology}, volume = {41}, number = {8}, pages = {1578-1588}, doi = {10.55563/clinexprheumatol/jof7nx}, pmid = {36826808}, issn = {0392-856X}, mesh = {Adult ; Humans ; Female ; Middle Aged ; *Gastrointestinal Microbiome/genetics ; Feces ; *Scleroderma, Systemic/diagnosis/microbiology ; Bacteria/genetics ; *Scleroderma, Limited ; }, abstract = {OBJECTIVES: The early gastrointestinal (GI) manifestation of systemic sclerosis (SSc) suggests a possible GI microbiota engagement in the pathophysiology and/or progression of SSc. Previous studies have revealed dysbiosis among Caucasian SSc patients. This study extends these findings to Asian SSc patients.

METHODS: Adult SSc patients, stratified according to 1) on immunosuppressive (On-IS) drugs or 2) no immunosuppressive drugs (No-IS), and age-and-sex-matched healthy controls (HC) were recruited. Metagenomic sequencing of stool DNA was compared between SSc patients and HC, and between SSc (On-IS) and (No-IS) patients. Alpha and beta-diversity, taxonomic and functional profiling were evaluated.

RESULTS: Twenty-three female SSc patients (12 On-IS; 11 No-IS; 5 diffuse and 18 limited SSc subtype) and 19 female HC, with median age of 54 years and 56 years, respectively, were recruited. Median SSc disease duration was 3.3 years. Alpha diversity was significantly higher in SSc versus HC (p=0.014) and in SSc (No-IS) versus HC (p=0.006). There was no significant difference in beta diversity between SSc and HC (p=0.307). At the phyla level, there were significantly increased abundance of Firmicutes and Actinobacteria in SSc versus HC, and reduced abundance of Bacteroidetes (all p<0.001). At the species level, there were significantly increased abundance of several Lactobacillus, Bifidobacterium, and Coprococcus species in SSc, and increased abundance of Odoribacter, Bacteroides and Prevotella species in HC. KEGG pathway analysis demonstrated distinct differences between SSc versus HC, and between SSc (No-IS) and SSc (On-IS).

CONCLUSIONS: Using metagenomic sequencing, our study further underlines distinct alterations in microbiota profiling among Asian SSc patients.}, } @article {pmid36826766, year = {2023}, author = {Ji, B and Qin, J and Ma, Y and Liu, X and Wang, T and Liu, G and Li, B and Wang, G and Gao, P}, title = {Metagenomic analysis reveals patterns and hosts of antibiotic resistance in different pig farms.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {18}, pages = {52087-52106}, pmid = {36826766}, issn = {1614-7499}, mesh = {Swine ; Humans ; Animals ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Manure ; Farms ; Macrolides ; Bacteria/genetics ; }, abstract = {In actual production environments, antibiotic-resistant genes (ARGs) are abundant in pig manure, which can form transmission chains through animals, the environment, and humans, thereby threatening human health. Therefore, based on metagenomic analysis methods, ARGs and mobile genetic elements (MGEs) were annotated in pig manure samples from 6 pig farms in 3 regions of Shanxi Province, and the potential hosts of ARGs were analyzed. The results showed that a total of 14 ARG types were detected, including 182 ARG subtypes, among which tetracycline, phenol, aminoglycoside, and macrolide resistance genes were the main ones. ARG profiles, MGE composition, and microbial communities were significantly different in different regions as well as between different pig farms. In addition, Anaerobutyricum, Butyrivibrio, and Turicibacter were significantly associated with multiple ARGs, and bacteria such as Prevotella, Bacteroides, and the family Oscillospiraceae carried multiple ARGs, suggesting that these bacteria are potential ARG hosts in pig manure. Procrustes analysis showed that bacterial communities and MGEs were significantly correlated with ARG profiles. Variation partitioning analysis results indicated that the combined effect of MGEs and bacterial communities accounted for 64.08% of resistance variation and played an important role in ARG profiles. These findings contribute to our understanding of the dissemination and persistence of ARGs in actual production settings, and offer some guidance for the prevention and control of ARGs contamination.}, } @article {pmid36825940, year = {2023}, author = {Almas, S and Carpenter, RE and Singh, A and Rowan, C and Tamrakar, VK and Sharma, R}, title = {Deciphering Microbiota of Acute Upper Respiratory Infections: A Comparative Analysis of PCR and mNGS Methods for Lower Respiratory Trafficking Potential.}, journal = {Advances in respiratory medicine}, volume = {91}, number = {1}, pages = {49-65}, pmid = {36825940}, issn = {2543-6031}, mesh = {Humans ; *Respiratory Tract Infections/diagnosis ; *Microbiota ; Bacteria/genetics ; Polymerase Chain Reaction ; }, abstract = {Although it is clinically important for acute respiratory tract (co)infections to have a rapid and accurate diagnosis, it is critical that respiratory medicine understands the advantages of current laboratory methods. In this study, we tested nasopharyngeal samples (n = 29) with a commercially available PCR assay and compared the results with those of a hybridization-capture-based mNGS workflow. Detection criteria for positive PCR samples was Ct < 35 and for mNGS samples it was >40% target coverage, median depth of 1X and RPKM > 10. A high degree of concordance (98.33% PPA and 100% NPA) was recorded. However, mNGS yielded positively 29 additional microorganisms (23 bacteria, 4 viruses, and 2 fungi) beyond PCR. We then characterized the microorganisms of each method into three phenotypic categories using the IDbyDNA Explify[®] Platform (Illumina[®] Inc, San Diego, CA, USA) for consideration of infectivity and trafficking potential to the lower respiratory region. The findings are significant for providing a comprehensive yet clinically relevant microbiology profile of acute upper respiratory infection, especially important in immunocompromised or immunocompetent with comorbidity respiratory cases or where traditional syndromic approaches fail to identify pathogenicity. Accordingly, this technology can be used to supplement current syndrome-based tests, and data can quickly and effectively be phenotypically characterized for trafficking potential, clinical (co)infection, and comorbid consideration-with promise to reduce morbidity and mortality.}, } @article {pmid36825821, year = {2023}, author = {Gautam, A and Zeng, W and Huson, DH}, title = {MeganServer: facilitating interactive access to metagenomic data on a server.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {3}, pages = {}, pmid = {36825821}, issn = {1367-4811}, mesh = {*Software ; Metagenome ; Computers ; Metagenomics/methods ; *Biochemical Phenomena ; }, abstract = {MOTIVATION: Metagenomic projects often involve large numbers of large sequencing datasets (totaling hundreds of gigabytes of data). Thus, computational preprocessing and analysis are usually performed on a server. The results of such analyses are then usually explored interactively. One approach is to use MEGAN, an interactive program that allows analysis and comparison of metagenomic datasets. Previous releases have required that the user first download the computed data from the server, an increasingly time-consuming process. Here, we present MeganServer, a stand-alone program that serves MEGAN files to the web, using a RESTful API, facilitating interactive analysis in MEGAN, without requiring prior download of the data. We describe a number of different application scenarios.

MeganServer is provided as a stand-alone program tools/megan-server in the MEGAN software suite, available at https://software-ab.cs.uni-tuebingen.de/download/megan6. Source is available at: https://github.com/husonlab/megan-ce/tree/master/src/megan/ms.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36825261, year = {2022}, author = {Ohkusa, T and Nishikawa, Y and Sato, N}, title = {Gastrointestinal disorders and intestinal bacteria: Advances in research and applications in therapy.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {935676}, pmid = {36825261}, issn = {2296-858X}, abstract = {Intestinal bacteria coexist with humans and play a role in suppressing the invasion of pathogens, producing short-chain fatty acids, producing vitamins, and controlling the immune system. Studies have been carried out on culturable bacterial species using bacterial culture methods for many years. However, as metagenomic analysis of bacterial genes has been developed since the 1990s, it has recently revealed that many bacteria in the intestine cannot be cultured and that approximately 1,000 species and 40 trillion bacteria are present in the gut microbiota. Furthermore, the composition of the microbiota is different in each disease state compared with the healthy state, and dysbiosis has received much attention as a cause of various diseases. Regarding gastrointestinal diseases, dysbiosis has been reported to be involved in inflammatory bowel disease, irritable bowel syndrome, and non-alcoholic steatohepatitis. Recent findings have also suggested that dysbiosis is involved in colon cancer, liver cancer, pancreatic cancer, esophageal cancer, and so on. This review focuses on the relationship between the gut microbiota and gastrointestinal/hepatobiliary diseases and also discusses new therapies targeting the gut microbiota.}, } @article {pmid36825092, year = {2023}, author = {Liu, H and Xu, J and Yeung, C and Chen, Q and Li, J}, title = {Effects of hemicellulose on intestinal mucosal barrier integrity, gut microbiota, and metabolomics in a mouse model of type 2 diabetes mellitus.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1096471}, pmid = {36825092}, issn = {1664-302X}, abstract = {BACKGROUND AND OBJECTIVE: Impaired gut barrier contributes to the progression of type 2 diabetes mellitus (T2DM), and the gut microbiota and metabolome play an important role in it. Hemicellulose, a potential prebiotics, how its supplementation impacted the glucose level, the impaired gut barrier, and the gut microbiota and metabolome in T2DM remained unclear.

METHODS: In this study, some mice were arranged randomly into four groups: db/db mice fed by a compositionally defined diet (CDD), db/db mice fed by a CDD with 10% and 20% hemicellulose supplementation, and control mice fed by a CDD. Body weight and fasting blood glucose levels were monitored weekly. The gut barrier was evaluated. Fresh stool samples were analyzed using metagenomic sequencing and liquid chromatography-mass spectrometry to detect gut microbiota and metabolome changes. Systemic and colonic inflammation were evaluated.

RESULTS: Better glycemic control, restoration of the impaired gut barrier, and lowered systemic inflammation levels were observed in db/db mice with the supplementation of 10 or 20% hemicellulose. The gut microbiota showed significant differences in beta diversity among the four groups. Fifteen genera with differential relative abundances and 59 significantly different metabolites were found. In the db/db group, hemicellulose eliminated the redundant Faecalibaculum and Enterorhabdus. The increased succinate and ursodeoxycholic acid (UDCA) after hemicellulose treatment were negatively correlated with Bifidobacterium, Erysipelatoclostridium, and Faecalibaculum. In addition, hemicellulose reduced the colonic expressions of TLR2/4 and TNF-α in db/db mice.

CONCLUSION: Hemicellulose may serve as a potential therapeutic intervention for T2DM by improving impaired intestinal mucosal barrier integrity, modulating gut microbiota composition, and altering the metabolic profile.}, } @article {pmid36824941, year = {2023}, author = {Marinos, G and Hamerich, IK and Debray, R and Obeng, N and Petersen, C and Taubenheim, J and Zimmermann, J and Blackburn, D and Samuel, BS and Dierking, K and Franke, A and Laudes, M and Waschina, S and Schulenburg, H and Kaleta, C}, title = {Metabolic model predictions enable targeted microbiome manipulation through precision prebiotics.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36824941}, abstract = {The microbiome is increasingly receiving attention as an important modulator of host health and disease. However, while numerous mechanisms through which the microbiome influences its host have been identified, there is still a lack of approaches that allow to specifically modulate the abundance of individual microbes or microbial functions of interest. Moreover, current approaches for microbiome manipulation such as fecal transfers often entail a non-specific transfer of entire microbial communities with potentially unwanted side effects. To overcome this limitation, we here propose the concept of precision prebiotics that specifically modulate the abundance of a microbiome member species of interest. In a first step, we show that defining precision prebiotics by compounds that are only taken up by the target species but no other species in a community is usually not possible due to overlapping metabolic niches. Subsequently, we present a metabolic modeling network framework that allows us to define precision prebiotics for a two-member C. elegans microbiome model community comprising the immune-protective Pseudomonas lurida MYb11 and the persistent colonizer Ochrobactrum vermis MYb71. Thus, we predicted compounds that specifically boost the abundance of the host-beneficial MYb11, four of which were experimentally validated in vitro (L-serine, L-threonine, D-mannitol, and γ-aminobutyric acid). L-serine was further assessed in vivo, leading to an increase in MYb11 abundance also in the worm host. Overall, our findings demonstrate that constraint-based metabolic modeling is an effective tool for the design of precision prebiotics as an important cornerstone for future microbiome-targeted therapies.}, } @article {pmid36824891, year = {2023}, author = {Dinic, M and Verpile, R and Meng, J and Marjanovic, J and Burgess, JL and Plano, L and Hower, S and Thaller, SR and Banerjee, S and Lev-Tov, H and Tomic-Canic, M and Pastar, I}, title = {Chronic wound microenvironment mediates selection of biofilm-forming multi drug resistant Staphylococcus epidermidis with capability to impair healing.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {36824891}, support = {F30 DK132806/DK/NIDDK NIH HHS/United States ; }, abstract = {Venous leg ulcers (VLU) are the most common chronic wounds characterized by bacterial biofilms and perturbed microbiome. Staphylococcus epidermidis is primarily known as skin commensal beneficial for the host, however, some strains can form biofilms and cause infections. By employing shotgun metagenomic sequencing we show that genetic signatures of antimicrobial resistance, adhesion and biofilm formation in VLU isolates correlate with in vitro bacterial traits. We demonstrate that the capability of chronic wound isolates to form biofilms and elicit IL-8 and IL-1β expression in human ex vivo wounds, correlates with the non-healing outcomes in patients with VLU. In contrast, commensal strains were incapable of surviving in the human ex vivo wounds. We show that major fitness traits of S. epidermis from VLU involve genes for resistance to methicillin and mupirocin, while the biofilm formation relied on the minimal number of genetic elements responsible for bacterial binding to fibronectin and fibrinogen. This underscores the importance of the emergence of treatment resistant virulent lineages in patients with non-healing wounds.}, } @article {pmid36824686, year = {2023}, author = {Shen, M and Li, Q and Zeng, Z and Han, D and Luo, X}, title = {Mucor indicus caused disseminated infection diagnosed by metagenomic next-generation sequencing in an acute myeloid leukemia patient: A case report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1089196}, pmid = {36824686}, issn = {2235-2988}, mesh = {Animals ; *Mucor/genetics ; Antifungal Agents/therapeutic use ; *Leukemia, Myeloid, Acute/complications/genetics/drug therapy ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Mucormycosis commonly occurs in immunosuppressed patients with hematological diseases, which can be life-threatening. However, many cases are often misdiagnosed due to lack of specific clinical manifestations. Additionally, the traditional blood culture or serological testing, with a high false-negative rate, is time-consuming. Thus, precise and timely diagnosis of infections is essential for the clinical care of infected patients.

CASE PRESENTATION: We report a 29-year-old Chinese man with acute myeloid leukemia (AML) who developed febrile neutropenia after the first course of induction chemotherapy. He received empirical antibiotics, which did not relieve his symptoms. No pathogen was detected by traditional microbiologic assays, while Mucor indicus was identified by metagenomic next-generation sequencing (mNGS) in the blood specimen. Liposomal amphotericin B (LAmB) was used, resulting in the patient's temperature returning to normal. A few days later, abdominal computed tomography (CT) scan showed multiple liver abscesses; fluorescence staining, histopathology, and mNGS identified the causative agent-M. indicus. Posaconazole was combined with LAmB as long-term antifungal treatment. Finally, the patient received allogeneic hematopoietic stem cell transplantation successfully after controlled infection. During follow-up 1 year after transplantation, the number of liver abscesses was reduced to one and remained stable.

CONCLUSION: This report described the first case of an AML patient diagnosed with culture-negative disseminated infections caused by M. indicus leading to rare hepatic manifestations using mNGS of peripheral blood and liver biopsy. LAmB combined with posaconazole was given in time, resulting in a favorable outcome. mNGS is a new method that assists in detecting the probable pathogen and increases the accuracy of identifying an etiology.}, } @article {pmid36824263, year = {2023}, author = {Sheng, S and Li, X and Zhao, S and Zheng, C and Zhang, F}, title = {Effects of levodopa on gut bacterial antibiotic resistance in Parkinson's disease rat.}, journal = {Frontiers in aging neuroscience}, volume = {15}, number = {}, pages = {1122712}, pmid = {36824263}, issn = {1663-4365}, abstract = {The second most prevalent neurodegenerative ailment, Parkinson's disease (PD), is characterized by both motor and non-motor symptoms. Levodopa is the backbone of treatment for PD at the moment. However, levodopa-induced side effects, such as dyskinesia, are commonly seen in PD patients. Recently, several antibiotics were found to present neuroprotective properties against neurodegenerative and neuro-inflammatory processes, which might be developed to effective therapies against PD. In this study, we aimed to identify if levodopa treatment could influence the gut bacterial antibiotic resistance in PD rat. Fecal samples were collected from healthy rats and 6-OHDA induced PD rats treated with different doses of levodopa, metagenomic sequencing data showed that levodopa resulted in gut bacteria composition change, the biomarkers of gut bacteria analyzed by LEfSe changed as well. More interestingly, compared with levodopa (5 mg/kg)-treated or no levodopa-treated PD rats, levodopa (10 mg/kg) caused a significant decrease in the abundance of tetW and vanTG genes in intestinal bacteria, which were related to tetracycline and vancomycin resistance, while the abundance of AAC6-lb-Suzhou gene increased apparently, which was related to aminoglycosides resistance, even though the total quantity of Antibiotic Resistance Gene (ARG) and Antibiotic Resistance Ontology (ARO) among all groups did not significantly differ. Consequently, our results imply that the combination of levodopa and antibiotics, such as tetracycline and vancomycin, in the treatment of PD may decrease the amount of corresponding antibiotic resistance genes in gut bacteria, which would give a theoretical basis for treating PD with levodopa combined with tetracycline and vancomycin in the future.}, } @article {pmid36823673, year = {2023}, author = {Maamary, J and Maddocks, S and Barnett, Y and Wong, S and Rodriguez, M and Hueston, L and Jeoffreys, N and Eden, JS and Dwyer, DE and Floyd, T and Plit, M and Kok, J and Brew, B}, title = {New Detection of Locally Acquired Japanese Encephalitis Virus Using Clinical Metagenomics, New South Wales, Australia.}, journal = {Emerging infectious diseases}, volume = {29}, number = {3}, pages = {627-630}, pmid = {36823673}, issn = {1080-6059}, mesh = {Male ; Humans ; *Encephalitis Virus, Japanese ; New South Wales ; Metagenomics ; Brain ; Australia/epidemiology ; *Encephalitis, Japanese ; }, abstract = {In the context of an emerging Japanese encephalitis outbreak within Australia, we describe a novel locally acquired case in New South Wales. A man in his 70s had rapidly progressive, fatal meningoencephalitis, diagnosed as caused by Japanese encephalitis virus by RNA-based metagenomic next-generation sequencing performed on postmortem brain tissue.}, } @article {pmid36823661, year = {2023}, author = {Haro-Moreno, JM and Cabello-Yeves, PJ and Garcillán-Barcia, MP and Zakharenko, A and Zemskaya, TI and Rodriguez-Valera, F}, title = {A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {12}, pmid = {36823661}, issn = {2524-6372}, abstract = {BACKGROUND: Lake Baikal, the world's deepest freshwater lake, contains important numbers of Candidatus Patescibacteria (formerly CPR) in its deepest reaches. However, previously obtained CPR metagenome-assembled genomes recruited very poorly indicating the potential of other groups being present. Here, we have applied for the first time a long-read (PacBio CCS) metagenomic approach to analyze in depth the Ca. Patescibacteria living in the bathypelagic water column of Lake Baikal at 1600 m.

RESULTS: The retrieval of nearly complete 16S rRNA genes before assembly has allowed us to detect the presence of a novel and a likely endemic group of Ca. Patescibacteria inhabiting bathypelagic Lake Baikal. This novel group seems to possess extremely high intra-clade diversity, precluding complete genomes' assembly. However, read binning and scaffolding indicate that these microbes are similar to other Ca. Patescibacteria (i.e. parasites or symbionts), although they seem to carry more anabolic pathways, likely reflecting the extremely oligotrophic habitat they inhabit. The novel bins have not been found anywhere, but one of the groups appears in small amounts in an oligotrophic and deep alpine Lake Thun. We propose this novel group be named Baikalibacteria.

CONCLUSION: The recovery of 16S rRNA genes via long-read metagenomics plus the use of long-read binning to uncover highly diverse "hidden" groups of prokaryotes are key strategies to move forward in ecogenomic microbiology. The novel group possesses enormous intraclade diversity akin to what happens with Ca. Patescibacteria at the interclade level, which is remarkable in an environment that has changed little in the last 25 million years.}, } @article {pmid36823539, year = {2023}, author = {Ekhlas, D and Argüello, H and Leonard, FC and Manzanilla, EG and Burgess, CM}, title = {Insights on the effects of antimicrobial and heavy metal usage on the antimicrobial resistance profiles of pigs based on culture-independent studies.}, journal = {Veterinary research}, volume = {54}, number = {1}, pages = {14}, pmid = {36823539}, issn = {1297-9716}, support = {2018027//Teagasc/ ; }, mesh = {Humans ; Animals ; Swine ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial ; *Anti-Infective Agents/pharmacology ; *Metals, Heavy/pharmacology ; *Microbiota ; }, abstract = {Antimicrobial resistance is a global threat to human, animal, and environmental health. In pig production, antimicrobials and heavy metals such as zinc oxide are commonly used for treatment and prevention of disease. Nevertheless, the effects of antimicrobials and heavy metals on the porcine resistome composition and the factors influencing this resistance profile are not fully understood. Advances in technologies to determine the presence of antimicrobial resistance genes in diverse sample types have enabled a more complete understanding of the resistome and the factors which influence its composition. The aim of this review is to provide a greater understanding of the influence of antimicrobial and heavy metal usage on the development and transmission of antimicrobial resistance on pig farms. Furthermore, this review aims to identify additional factors that can affect the porcine resistome. Relevant literature that used high-throughput sequencing or quantitative PCR methods to examine links between antimicrobial resistance and antimicrobial and heavy metal use was identified using a systematic approach with PubMed (NCBI), Scopus (Elsevier), and Web of Science (Clarivate Analytics) databases. In total, 247 unique records were found and 28 publications were identified as eligible for inclusion in this review. Based on these, there is clear evidence that antimicrobial and heavy metal use are positively linked with antimicrobial resistance in pigs. Moreover, associations of genes conferring antimicrobial resistance with mobile genetic elements, the microbiome, and the virome were reported, which were further influenced by the host, the environment, or the treatment itself.}, } @article {pmid36823480, year = {2023}, author = {Bai, H and Liu, T and Wang, S and Shen, L and Wang, Z}, title = {Variations in gut microbiome and metabolites of dogs with acute diarrhea in poodles and Labrador retrievers.}, journal = {Archives of microbiology}, volume = {205}, number = {3}, pages = {97}, pmid = {36823480}, issn = {1432-072X}, mesh = {Dogs ; Animals ; *Gastrointestinal Microbiome ; *Microbiota ; Metabolomics ; Metabolome ; Starch/analysis ; Diarrhea ; Feces ; RNA, Ribosomal, 16S ; }, abstract = {For different breeds of dogs with acute diarrhea, the gut microbiota and metabolome profiles are unclear. This prospective observational study analyzed the gut microbiomes of poodles with acute diarrhea and Labrador retrievers with acute diarrhea based on 16S amplicon sequencing, with respective healthy dogs as controls. Fecal non-target metabolomics and metagenomics were performed on poodles with acute diarrhea. This study found that the diversity and structure of the microbial community differed significantly between the two breeds in cohorts of healthy dogs. Two breeds of dogs with acute diarrhea demonstrated different changes in microbial communities and metabolic functions. The metabolism of starch and sucrose was significantly decreased in dogs with acute diarrhea, which may be attributed to the reduced activity of dextran dextrinase. Non-targeted metabolomics identified 21 abnormal metabolic pathways exhibited by dogs with acute diarrhea, including starch, amino acid, bile acid metabolism, etc., and were closely related to specific intestinal flora. This study provided new insights into breed specificity and the development of dietary treatment strategy in canine gastrointestinal disease.}, } @article {pmid36823453, year = {2023}, author = {Webb, EA and Held, NA and Zhao, Y and Graham, ED and Conover, AE and Semones, J and Lee, MD and Feng, Y and Fu, FX and Saito, MA and Hutchins, DA}, title = {Importance of mobile genetic element immunity in numerically abundant Trichodesmium clades.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {15}, pmid = {36823453}, issn = {2730-6151}, support = {1657757//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1851222//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1851222//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1850719//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1850719//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 1850719//NSF | GEO | Division of Ocean Sciences (OCE)/ ; 2125191//NSF | Directorate for Biological Sciences (BIO)/ ; }, abstract = {The colony-forming cyanobacteria Trichodesmium spp. are considered one of the most important nitrogen-fixing genera in the warm, low nutrient ocean. Despite this central biogeochemical role, many questions about their evolution, physiology, and trophic interactions remain unanswered. To address these questions, we describe Trichodesmium pangenomic potential via significantly improved genomic assemblies from two isolates and 15 new >50% complete Trichodesmium metagenome-assembled genomes from hand-picked, Trichodesmium colonies spanning the Atlantic Ocean. Phylogenomics identified ~four N2 fixing clades of Trichodesmium across the transect, with T. thiebautii dominating the colony-specific reads. Pangenomic analyses showed that all T. thiebautii MAGs are enriched in COG defense mechanisms and encode a vertically inherited Type III-B Clustered Regularly Interspaced Short Palindromic Repeats and associated protein-based immunity system (CRISPR-Cas). Surprisingly, this CRISPR-Cas system was absent in all T. erythraeum genomes, vertically inherited by T. thiebautii, and correlated with increased signatures of horizontal gene transfer. Additionally, the system was expressed in metaproteomic and transcriptomic datasets and CRISPR spacer sequences with 100% identical hits to field-assembled, putative phage genome fragments were identified. While the currently CO2-limited T. erythraeum is expected to be a 'winner' of anthropogenic climate change, their genomic dearth of known phage resistance mechanisms, compared to T. thiebautii, could put this outcome in question. Thus, the clear demarcation of T. thiebautii maintaining CRISPR-Cas systems, while T. erythraeum does not, identifies Trichodesmium as an ecologically important CRISPR-Cas model system, and highlights the need for more research on phage-Trichodesmium interactions.}, } @article {pmid36823356, year = {2023}, author = {Blanco-Míguez, A and Beghini, F and Cumbo, F and McIver, LJ and Thompson, KN and Zolfo, M and Manghi, P and Dubois, L and Huang, KD and Thomas, AM and Nickols, WA and Piccinno, G and Piperni, E and Punčochář, M and Valles-Colomer, M and Tett, A and Giordano, F and Davies, R and Wolf, J and Berry, SE and Spector, TD and Franzosa, EA and Pasolli, E and Asnicar, F and Huttenhower, C and Segata, N}, title = {Extending and improving metagenomic taxonomic profiling with uncharacterized species using MetaPhlAn 4.}, journal = {Nature biotechnology}, volume = {41}, number = {11}, pages = {1633-1644}, pmid = {36823356}, issn = {1546-1696}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; U01 CA230551/CA/NCI NIH HHS/United States ; U19 AI110820/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Animals ; Mice ; Metagenome/genetics ; *Microbiota/genetics ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Phylogeny ; }, abstract = {Metagenomic assembly enables new organism discovery from microbial communities, but it can only capture few abundant organisms from most metagenomes. Here we present MetaPhlAn 4, which integrates information from metagenome assemblies and microbial isolate genomes for more comprehensive metagenomic taxonomic profiling. From a curated collection of 1.01 M prokaryotic reference and metagenome-assembled genomes, we define unique marker genes for 26,970 species-level genome bins, 4,992 of them taxonomically unidentified at the species level. MetaPhlAn 4 explains ~20% more reads in most international human gut microbiomes and >40% in less-characterized environments such as the rumen microbiome and proves more accurate than available alternatives on synthetic evaluations while also reliably quantifying organisms with no cultured isolates. Application of the method to >24,500 metagenomes highlights previously undetected species to be strong biomarkers for host conditions and lifestyles in human and mouse microbiomes and shows that even previously uncharacterized species can be genetically profiled at the resolution of single microbial strains.}, } @article {pmid36823301, year = {2023}, author = {Mehta, RS and Mayers, JR and Zhang, Y and Bhosle, A and Glasser, NR and Nguyen, LH and Ma, W and Bae, S and Branck, T and Song, K and Sebastian, L and Pacheco, JA and Seo, HS and Clish, C and Dhe-Paganon, S and Ananthakrishnan, AN and Franzosa, EA and Balskus, EP and Chan, AT and Huttenhower, C}, title = {Gut microbial metabolism of 5-ASA diminishes its clinical efficacy in inflammatory bowel disease.}, journal = {Nature medicine}, volume = {29}, number = {3}, pages = {700-709}, pmid = {36823301}, issn = {1546-170X}, support = {T32 HL007633/HL/NHLBI NIH HHS/United States ; R35 CA253185/CA/NCI NIH HHS/United States ; P30 GM124165/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Mesalamine/therapeutic use ; *Gastrointestinal Microbiome/genetics ; Cross-Sectional Studies ; *Inflammatory Bowel Diseases/drug therapy ; Treatment Outcome ; }, abstract = {For decades, variability in clinical efficacy of the widely used inflammatory bowel disease (IBD) drug 5-aminosalicylic acid (5-ASA) has been attributed, in part, to its acetylation and inactivation by gut microbes. Identification of the responsible microbes and enzyme(s), however, has proved elusive. To uncover the source of this metabolism, we developed a multi-omics workflow combining gut microbiome metagenomics, metatranscriptomics and metabolomics from the longitudinal IBDMDB cohort of 132 controls and patients with IBD. This associated 12 previously uncharacterized microbial acetyltransferases with 5-ASA inactivation, belonging to two protein superfamilies: thiolases and acyl-CoA N-acyltransferases. In vitro characterization of representatives from both families confirmed the ability of these enzymes to acetylate 5-ASA. A cross-sectional analysis within the discovery cohort and subsequent prospective validation within the independent SPARC IBD cohort (n = 208) found three of these microbial thiolases and one acyl-CoA N-acyltransferase to be epidemiologically associated with an increased risk of treatment failure among 5-ASA users. Together, these data address a longstanding challenge in IBD management, outline a method for the discovery of previously uncharacterized gut microbial activities and advance the possibility of microbiome-based personalized medicine.}, } @article {pmid36823282, year = {2023}, author = {Pérez-Cataluña, A and Randazzo, W and Martínez-Blanch, JF and Codoñer, FM and Sánchez, G}, title = {Sample and library preparation approaches for the analysis of the virome of irrigation water.}, journal = {Journal of the science of food and agriculture}, volume = {103}, number = {9}, pages = {4450-4457}, doi = {10.1002/jsfa.12522}, pmid = {36823282}, issn = {1097-0010}, support = {2018CPS10//Center for Produce Safety/ ; APOSTD/2021/292//Generalitat Valenciana/ ; APOTIP/2018/007//Generalitat Valenciana/ ; AGL2017-82909//Ministerio de Ciencia e Innovación/ ; }, mesh = {Humans ; Virome ; *Viruses/genetics ; *Bacteriophages/genetics ; Water ; Metagenomics/methods ; }, abstract = {BACKGROUND: The virome (i.e. community of mainly RNA and DNA eukaryotic viruses and bacteriophages) of waters is yet to be extensively explored. In particular, the virome of waters used for irrigation could therefore potentially carry viral pathogens that can contaminate fresh produce. One problem in obtaining viral sequences from irrigation waters is the relatively low amount of virus particles, as well as the presence of human, bacterial and protozoan cells. The present aimed study was to compare different processing, amplification, and sequencing approaches for virome characterization in irrigation waters.

RESULTS: Our analyses considered percentages of viral reads, values for diversity indices and number of families found in sequencing results. The results obtained suggest that enrichment protocols using two (bezonase and microccocal nuclease) or four enzymes at once (bezonase, microccocal nuclease, DNAse and RNase), regardless of an Amicon filtration step, are more appropriate than separated enzymatic treatments for virome characterization in irrigation water. The NetoVIR protocol combined with the ScriptSeq v2 RNA-Seq Library (P0-L20 protocol) showed the highest percentages of RNA viruses and identified the higher number of families.

CONCLUSION: Although virome characterization applied in irrigation waters is an important tool for protecting public health by informing on circulating human and zoonotic infections, optimized and standardized procedures should be followed to reduce the variability of results related to either the sample itself and the downstream bioinformatics analyses. Our results show that virome characterization can be an important tool in the discovery of pathogenic viruses in the environment and can be used to inform and optimize reference-based detection methods provided that appropriate and rigorous controls are included. © 2023 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.}, } @article {pmid36823152, year = {2023}, author = {Howe, A and Stopnisek, N and Dooley, SK and Yang, F and Grady, KL and Shade, A}, title = {Seasonal activities of the phyllosphere microbiome of perennial crops.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {1039}, pmid = {36823152}, issn = {2041-1723}, mesh = {Seasons ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; *Panicum ; }, abstract = {Understanding the interactions between plants and microorganisms can inform microbiome management to enhance crop productivity and resilience to stress. Here, we apply a genome-centric approach to identify ecologically important leaf microbiome members on replicated plots of field-grown switchgrass and miscanthus, and to quantify their activities over two growing seasons for switchgrass. We use metagenome and metatranscriptome sequencing and curate 40 medium- and high-quality metagenome-assembled-genomes (MAGs). We find that classes represented by these MAGs (Actinomycetia, Alpha- and Gamma- Proteobacteria, and Bacteroidota) are active in the late season, and upregulate transcripts for short-chain dehydrogenase, molybdopterin oxidoreductase, and polyketide cyclase. Stress-associated pathways are expressed for most MAGs, suggesting engagement with the host environment. We also detect seasonally activated biosynthetic pathways for terpenes and various non-ribosomal peptide pathways that are poorly annotated. Our findings support that leaf-associated bacterial populations are seasonally dynamic and responsive to host cues.}, } @article {pmid36823020, year = {2023}, author = {Yan, A and Butcher, J and Schramm, L and Mack, DR and Stintzi, A}, title = {Multiomic spatial analysis reveals a distinct mucosa-associated virome.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2177488}, pmid = {36823020}, issn = {1949-0984}, support = {ECD-144627//CIHR/Canada ; }, mesh = {Humans ; Virome ; Multiomics ; *Gastrointestinal Microbiome/genetics ; *Bacteriophages/genetics ; Metagenomics ; Intestinal Mucosa ; Spatial Analysis ; }, abstract = {The human gut virome has been increasingly explored in recent years. However, nearly all virome-sequencing efforts rely solely on fecal samples and few studies leverage multiomic approaches to investigate phage-host relationships. Here, we combine metagenomics, metaviromics, and metatranscriptomics to study virome-bacteriome interactions at the colonic mucosal-luminal interface in a cohort of three individuals with inflammatory bowel disease; non-IBD controls were not included in this study. We show that the mucosal viral population is distinct from the stool virome and houses abundant crAss-like phages that are undetectable by fecal sampling. Through viral protein prediction and metatranscriptomic analysis, we explore viral gene transcription, prophage activation, and the relationship between the presence of integrase and temperate phages in IBD subjects. We also show the impact of deep sequencing on virus recovery and offer guidelines for selecting optimal sequencing depths in future metaviromic studies. Systems biology approaches such as those presented in this report will enhance our understanding of the human virome and its interactions with our microbiome and our health.}, } @article {pmid36822557, year = {2023}, author = {Pan, W and Ouyang, H and Tan, X and Yan, S and Zhang, R and Deng, R and Gu, L and He, Q}, title = {Effects of biochar addition towards the treatment of blackwater in anaerobic dynamic membrane bioreactor (AnDMBR): Comparison among room temperature, mesophilic and thermophilic conditions.}, journal = {Bioresource technology}, volume = {374}, number = {}, pages = {128776}, doi = {10.1016/j.biortech.2023.128776}, pmid = {36822557}, issn = {1873-2976}, mesh = {Anaerobiosis ; Temperature ; *Bioreactors ; *Methane ; Sewage ; }, abstract = {Effects of biochar addition on the performance of anaerobic dynamic membrane bioreactor (AnDMBR) under different temperatures for blackwater treatment was investigated. When the organic load ratios (OLR) was 1.0 g COD/L·d, the specific methane yield for the three biochar-amended reactors were 125.7, 148.0 and 182.3 mLCH4/g CODremoved, respectively. Compare to those digesters without biochar participation, the methane production in the thermophilic reactor with biochar increased by 12% while the other two digesters increased by 6-10%. An analysis of membrane filtration resistance showed a reduction in total resistance (Rt) of 6.2 × 10[11]-7.3 × 10[11] m[-1] when biochar was added to the three reactors. The thermophilic reactors with biochar increased the relative abundance of Methanothermobacter and promoted gene expression of metabolic pathways related to hydrolysis, acid production and methane production. Overall, biochar showed great potential as an inexpensive conductive material to increase methane production with reduced membrane fouling in AnDMBR systems.}, } @article {pmid36821745, year = {2023}, author = {Sun, S and Peng, K and Sun, S and Wang, M and Shao, Y and Li, L and Xiang, J and Sedjoah, RA and Xin, Z}, title = {Engineering Modular and Highly Sensitive Cell-Based Biosensors for Aromatic Contaminant Monitoring and High-Throughput Enzyme Screening.}, journal = {ACS synthetic biology}, volume = {12}, number = {3}, pages = {877-891}, doi = {10.1021/acssynbio.3c00036}, pmid = {36821745}, issn = {2161-5063}, mesh = {*Bacterial Proteins/genetics ; Escherichia coli/genetics/metabolism ; *Biosensing Techniques/methods ; }, abstract = {Although a variety of whole-cell-based biosensors have been developed for different applications in recent years, most cannot meet practical requirements due to insufficient sensing performance. Here, we constructed two sets of modular genetic circuits by serial and parallel modes capable of significantly amplifying the input/output signal in Escherichia coli. The biosensors are engineered using σ[54]-dependent phenol-responsive regulator DmpR as a sensor and enhanced green fluorescent protein as a reporter. Cells harboring serial and parallel genetic circuits displayed nearly 9- and 16-fold higher sensitivity than the general circuit. The genetic circuits enabled rapid detection of six phenolic contaminants in 12 h and showed the low limit of detection of 2.5 and 2.2 ppb for benzopyrene (BaP) and tetracycline (Tet), with a broad detection range of 0.01-1 and 0.005-5 μM, respectively. Furthermore, the positive rate was as high as 73% when the biosensor was applied to screen intracellular enzymes with ester-hydrolysis activity from soil metagenomic libraries using phenyl acetate as a phenolic substrate. Several novel enzymes were isolated, identified, and biochemically characterized, including serine peptidases and alkaline phosphatase family protein/metalloenzyme. Consequently, this study provides a new signal amplification method for cell-based biosensors that can be widely applied to environmental contaminant assessment and screening of intracellular enzymes.}, } @article {pmid36820999, year = {2023}, author = {Ardanareswari, K and Lowisia, W and Soedarini, B and Liao, JW and Chung, YC}, title = {Jaboticaba (Myrciaria cauliflora) Fruit Extract Suppressed Aberrant Crypt Formation in 1,2-Dimetylhydrazine-Induced Rats.}, journal = {Plant foods for human nutrition (Dordrecht, Netherlands)}, volume = {78}, number = {2}, pages = {286-291}, pmid = {36820999}, issn = {1573-9104}, support = {MOST 110-2320-B-126-003-MY3//Ministry of Science and Technology, R.O.C. Taiwan/ ; }, mesh = {Rats ; Animals ; Fruit ; Gallic Acid ; *Colorectal Neoplasms/prevention & control ; Butyrates ; *Colonic Neoplasms ; 1,2-Dimethylhydrazine/toxicity ; *Aberrant Crypt Foci ; }, abstract = {Early intervention can significantly improve the colorectal cancer survival rate. Foods rich in phenolic compounds, such as jaboticaba (Myrciaria cauliflora), may prevent tumorigenesis. We investigated the effectivity of jaboticaba whole fruit ethanolic extract (FEX) in suppressing aberrant crypt foci (ACF), the earliest lesion of colorectal cancer (CRC), in 1,2-dimethylhydrazine (DMH)-induced rats and the underlying mechanisms related to the gut microbiota composition and short chain fatty acid (SCFA). This study was approved by the Institutional Animal Care and Use Committee (IACUC) of Providence University (Trial Registration Number 20180419A01, registration date: 22 December 2018). The FEX contains gallic acid and an especially high ellagic acid concentration of 54.41 ± 1.80 and 209.79 ± 2.49 mg/100 g FEX. The highest total ACF number (150.00 ± 43.86) was recorded in the DMH control (D) group. After 56 days of oral FEX treatment, the total ACF number in the low FEX dosage (DL) group was significantly lower compared to the D group (p < 0.05). The large-sized ACF (> 5 foci), which has a higher probability of progressing to later stage, was significantly decreased in the high FEX dosage (DH) group. The 16s rDNA metagenomic sequencing of the cecal material revealed that the CRC biomarker Lachnoclostridium was significantly suppressed in the DH group (p < 0.05), whereas some SCFA-producing taxa and the cecal butyrate concentration were significantly elevated in the DL and DH groups (p < 0.05). This study demonstrated the potential of jaboticaba whole fruit in CRC prevention, especially in the initial stage, by shifting gut microbiota composition and improving cecal butyrate level.}, } @article {pmid36820082, year = {2023}, author = {Zhu, Z and Wang, X and Zhao, J and Xie, Z and Yang, C and Li, L and Liu, Y}, title = {Clinical Characteristics of Six Patients with Chlamydia psittaci Infection Diagnosed by Metagenomic Next-Generation Sequencing: A Case Series.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {869-878}, pmid = {36820082}, issn = {1178-6973}, abstract = {The incidence of psittacosis infection has gradually increased in recent years. Metagenomic next-generation sequencing (mNGS) can be used to comprehensively identify the total DNA and RNA content of the microbiome, as well as identify both known and unexpected pathogens within 24 hours. We diagnosed and treated six patients with psittacosis infection using mNGS, two of whom developed severe disease and most of whom presented with pulmonary symptoms. One of the young female patients also presented with irregular vaginal bleeding and myocarditis. Patients with underlying gastric disorders first showed gastrointestinal symptoms, which is a rare manifestation in patients with psittacosis. Older patients with underlying disease usually showed more severe symptoms. However, rare complications can also occur in immunocompetent young people and develop into severe disease. All patients showed significant congestion at bronchial lumen lesions, which may be associated with a severe inflammatory response to mucosal Chlamydia psittaci (C. psittaci) infection. Overall, mNGS is a rapid and effective tool for the clinical diagnosis of psittacosis caused by C. psittaci, and early diagnosis and treatment can prevent psittacosis from developing into a serious illness.}, } @article {pmid36820080, year = {2023}, author = {Wang, L and Li, S and Qin, J and Tang, T and Hong, J and Tung, TH and Xu, C and Yu, S and Qian, J}, title = {Clinical Diagnosis Application of Metagenomic Next-Generation Sequencing of Plasma in Suspected Sepsis.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {891-901}, pmid = {36820080}, issn = {1178-6973}, abstract = {PURPOSE: We analyzed the clinical concordance of mNGS test results from blood samples and improved the clinical efficiency of mNGS in the diagnosis of suspected sepsis pathogens.

PATIENTS AND METHODS: In this study, 99 samples of suspected blood flow infection were included for plasma mNGS, and the correlation between mNGS results and blood culture results, serum inflammatory indices, clinical symptoms and antibiotic treatment was analyzed, as well as the comparison with the detection rate of BALF pathogens, as well as the classification of different pathogens in the mNGS results were analyzed.

RESULTS: The mNGS pathogen detection rate was higher than that of traditional blood culture (83.02% vs 35.82%). The rate of the mNGS results being consistent with the clinical diagnosis was also higher than that of traditional blood culture (58.49% vs 20.75%). This study shows that bacteria and fungi are the main pathogens in sepsis, and viral sepsis is very rare. In this study, 32% of sepsis patients were secondary to pneumonia. Compared with the pathogen detection rate using alveolar lavage fluid, the detection rate from plasma mNGS was 62.5%. Samples were also easy to sample, noninvasive, and more convenient for clinical application.

CONCLUSION: This study shows that compared with blood culture, the detection rate of mNGS pathogen that meets the diagnosis of sepsis is higher. We need a combination of multiple indicators to monitor the early diagnosis and treatment of sepsis.}, } @article {pmid36819695, year = {2023}, author = {Zhan, X and Fletcher, L and Huyben, D and Cai, H and Dingle, S and Qi, N and Huber, LA and Wang, B and Li, J}, title = {Choline supplementation regulates gut microbiome diversity, gut epithelial activity, and the cytokine gene expression in gilts.}, journal = {Frontiers in nutrition}, volume = {10}, number = {}, pages = {1101519}, pmid = {36819695}, issn = {2296-861X}, abstract = {Choline is an essential nutrient that is necessary for both fetal development and maintenance of neural function, while its effect on female ovarian development is largely unexplored. Our previous study demonstrated that choline supplementation promotes ovarian follicular development and ovulation, although its underlying mechanism was unclear. To uncover the potential regulation pathway, eighteen female Yorkshire × Landrace gilts were fed with either standard commercial diet (Control group, n = 9) or choline supplemented diet (Choline group, additional 500 mg/kg of control diet, n = 9) from day 90 of age to day 186. At day 186, feces samples were analyzed for effects on the gut microbiome using 16S ribosomal RNA gene V3-V4 region sequencing with Illumina MiSeq, serum samples were analyzed for trimethylamine (TMA) and trimethylamine-N-oxide (TMAO) using HILIC method, and jejunum tissues were analyzed for immune related gene expression using qRT-PCR. Our results show that choline supplementation did not alter the circulating level of TMA and TMAO (P > 0.05), but rather increased gut microbiome alpha diversity (P < 0.05). Beta diversity analysis results showed that the choline diet mainly increased the abundance of Firmicutes, Proteobacteria, and Actinobacteria, but decreased the abundance of Bacteroidetes, Spirochaetes, and Euryarchaeota at the phyla level. Meta-genomic analysis revealed that choline supplementation activated pathways in the gut microbiota associated with steroid hormone biosynthesis and degradation of infertility-causing environmental pollutants (bisphenol, xylene, and dioxins). To further verify the effect of choline on intestinal activity, a porcine intestine cell line (IPEC-J2) was treated with serial concentrations of choline chloride in vitro. Our data demonstrated that choline promoted the proliferation of IPEC-J2 while inhibiting the apoptotic activity. qRT-PCR results showed that choline significantly increased the expression level of Bcl2 in both IPEC-J2 cells and jejunum tissues. The expression of IL-22, a cytokine that has been shown to impact ovarian function, was increased by choline treatment in vitro. Our findings reveal the beneficial effect of choline supplementation on enhancing the gut microbiome composition and intestinal epithelial activity, and offer insights into how these changes may have contributed to the ovarian development-promoting effect we reported in our previous study.}, } @article {pmid36819069, year = {2023}, author = {Couvillion, SP and Mostoller, KE and Williams, JE and Pace, RM and Stohel, IL and Peterson, HK and Nicora, CD and Nakayasu, ES and Webb-Robertson, BM and McGuire, MA and McGuire, MK and Metz, TO}, title = {Interrogating the role of the milk microbiome in mastitis in the multi-omics era.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1105675}, pmid = {36819069}, issn = {1664-302X}, abstract = {There is growing interest in a functional understanding of milk-associated microbiota as there is ample evidence that host-associated microbial communities play an active role in host health and phenotype. Mastitis, characterized by painful inflammation of the mammary gland, is prevalent among lactating humans and agricultural animals and is associated with significant clinical and economic consequences. The etiology of mastitis is complex and polymicrobial and correlative studies have indicated alterations in milk microbial community composition. Recent evidence is beginning to suggest that a causal relationship may exist between the milk microbiota and host phenotype in mastitis. Multi-omic approaches can be leveraged to gain a mechanistic, molecular level understanding of how the milk microbiome might modulate host physiology, thereby informing strategies to prevent and ameliorate mastitis. In this paper, we review existing studies that have utilized omics approaches to investigate the role of the milk microbiome in mastitis. We also summarize the strengths and challenges associated with the different omics techniques including metagenomics, metatranscriptomics, metaproteomics, metabolomics and lipidomics and provide perspective on the integration of multiple omics technologies for a better functional understanding of the milk microbiome.}, } @article {pmid36819055, year = {2023}, author = {Ugwuanyi, IR and Fogel, ML and Bowden, R and Steele, A and De Natale, G and Troise, C and Somma, R and Piochi, M and Mormone, A and Glamoclija, M}, title = {Comparative metagenomics at Solfatara and Pisciarelli hydrothermal systems in Italy reveal that ecological differences across substrates are not ubiquitous.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1066406}, pmid = {36819055}, issn = {1664-302X}, abstract = {INTRODUCTION: Continental hydrothermal systems (CHSs) are geochemically complex, and they support microbial communities that vary across substrates. However, our understanding of these variations across the complete range of substrates in CHS is limited because many previous studies have focused predominantly on aqueous settings.

METHODS: Here we used metagenomes in the context of their environmental geochemistry to investigate the ecology of different substrates (i.e., water, mud and fumarolic deposits) from Solfatara and Pisciarelli.

RESULTS AND DISCUSSION: Results indicate that both locations are lithologically similar with distinct fluid geochemistry. In particular, all substrates from Solfatara have similar chemistry whereas Pisciarelli substrates have varying chemistry; with water and mud from bubbling pools exhibiting high SO4 [2-] and NH4 [+] concentrations. Species alpha diversity was found to be different between locations but not across substrates, and pH was shown to be the most important driver of both diversity and microbial community composition. Based on cluster analysis, microbial community structure differed significantly between Pisciarelli substrates but not between Solfatara substrates. Pisciarelli mud pools, were dominated by (hyper)thermophilic archaea, and on average, bacteria dominated Pisciarelli fumarolic deposits and all investigated Solfatara environments. Carbon fixation and sulfur oxidation were the most important metabolic pathways fueled by volcanic outgassing at both locations. Together, results demonstrate that ecological differences across substrates are not a widespread phenomenon but specific to the system. Therefore, this study demonstrates the importance of analyzing different substrates of a CHS to understand the full range of microbial ecology to avoid biased ecological assessments.}, } @article {pmid36819012, year = {2023}, author = {Leo, J and Chong, CW and Pribowo, AY and Sutejo, R and Lee, JWJ}, title = {Editorial: Microbiome and human host interactions and their implications on human health.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1135341}, pmid = {36819012}, issn = {1664-302X}, } @article {pmid36818681, year = {2023}, author = {Bhattacharya, S and Abhishek, K and Samiksha, S and Sharma, P}, title = {Occurrence and transport of SARS-CoV-2 in wastewater streams and its detection and remediation by chemical-biological methods.}, journal = {Journal of hazardous materials advances}, volume = {9}, number = {}, pages = {100221}, pmid = {36818681}, issn = {2772-4166}, abstract = {This paper explains the transmission of SARS-CoV and influences of several environmental factors in the transmission process. The article highlighted several methods of collection, sampling and monitoring/estimation as well as surveillance tool for detecting SARS-CoV in wastewater streams. In this context, WBE (Wastewater based epidemiology) is found to be the most effective surveillance tool. Several methods of genomic sequencing are discussed in the paper, which are applied in WBE, like qPCR-based wastewater testing, metagenomics-based analysis, next generation sequencing etc. Additionally, several types of biosensors (colorimetric biosensor, mobile phone-based biosensors, and nanomaterials-based biosensors) showed promising results in sensing SARS-CoV in wastewater. Further, this review paper outlined the gaps in assessing the factors responsible for transmission and challenges in detection and monitoring along with the remediation and disinfection methods of this virus in wastewater. Various methods of disinfection of SARS-CoV-2 in wastewater are discussed (primary, secondary, and tertiary phases) and it is found that a suite of disinfection methods can be used for complete disinfection/removal of the virus. Application of ultraviolet light, ozone and chlorine-based disinfectants are also discussed in the context of treatment methods. This study calls for continuous efforts to gather more information about the virus through continuous monitoring and analyses and to address the existing gaps and identification of the most effective tool/ strategy to prevent SARS-CoV-2 transmission. Wastewater surveillance can be very useful in effective surveillance of future pandemics and epidemics caused by viruses, especially after development of new technologies in detecting and disinfecting viral pathogens more effectively.}, } @article {pmid36818630, year = {2023}, author = {Liu, XP and Mao, CX and Wang, GS and Zhang, MZ}, title = {Metagenomic next-generation sequencing for pleural effusions induced by viral pleurisy: A case report.}, journal = {World journal of clinical cases}, volume = {11}, number = {4}, pages = {844-851}, pmid = {36818630}, issn = {2307-8960}, abstract = {BACKGROUND: Viral pleurisy is a viral infected disease with exudative pleural effusions. It is one of the causes for pleural effusions. Because of the difficult etiology diagnosis, clinically pleural effusions tend to be misdiagnosed as tuberculous pleurisy or idiopathic pleural effusion. Here, we report a case of pleural effusion secondary to viral pleurisy which is driven by infection with epstein-barr virus. Viral infection was identified by metagenomic next-generation sequencing (mNGS).

CASE SUMMARY: A 40-year-old male with a history of dermatomyositis, rheumatoid arthritis, and secondary interstitial pneumonia was administered with long-term oral prednisone. He presented with fever and chest pain after exposure to cold, accompanied by generalized sore and weakness, night sweat, occasional cough, and few sputums. The computed tomography scan showed bilateral pleural effusions and atelectasis of the partial right lower lobe was revealed. The pleural fluids were found to be yellow and slightly turbid after pleural catheterization. Thoracoscopy showed fibrous adhesion and auto-pleurodesis. Combining the results in pleural fluid analysis and mNGS, the patient was diagnosed as viral pleuritis. After receiving Aciclovir, the symptoms and signs of the patient were relieved.

CONCLUSION: Viral infection should be considered in cases of idiopathic pleural effusion unexplained by routine examination. mNGS is helpful for diagnosis.}, } @article {pmid36817979, year = {2023}, author = {Peng, M and Li, W and Li, F and Tang, B and Deng, Y and Peng, S and Chen, L and Dai, Y}, title = {Mycobacterium xenopi related spine infections: A case report and systematic literature review.}, journal = {One health (Amsterdam, Netherlands)}, volume = {16}, number = {}, pages = {100502}, pmid = {36817979}, issn = {2352-7714}, abstract = {BACKGROUND AND PURPOSE: Nontuberculous mycobacteria (NTM) disease is an important infection disease throughout the world. Mycobacterium xenopi (M. xenopi) is a common NTM. Extrapulmonary infections due to M. xenopi, particularly spine infections, are a rare occurrence, but lack of research is cited as a constraint for implementing NTM control in such patients. The purposes of this paper are to describe a case of spondylodiscitis, to review the published literature on cases of M. xenopi spine infections, and to summarize the predisposing factors, diagnosis, and treatment of infection.

METHODS: A case of spondylodiscitis was caused by M. xenopi in a patient with systemic lupus erythematosus (SLE). Research was conducted using the PubMed, ScienceDirect, Embase, Wiley Online Library, and Scopus databases using the following search terms: "Mycobacterium xenopi", "vertebral", "spinal", "spondylodiscitis", "infection", and "osteomyelitis".

RESULTS: We retrieved 14 cases published before August 2022. The risk factors for infection were iatrogenic infections (3/14, 21.43%), SLE (4/14, 28.57%), AIDS (4/14, 28.57%), and immunocompetence without any comorbidities (3/14, 21.43%). The most common sites of infection were thoracic vertebrae (10/14, 71.43%) and lumbar vertebrae (4/14, 28.57%). A total of 14 cases were isolated and identified as M. xenopi from a toad by mycobacterial culture. The identification time was 55.00 ± 7.55 days (the present report identification time of metagenomic next generation sequencing (mNGS) was only 2 days). All patients were treated with antibiotic therapy, and the duration of treatment was 13.18 ± 2.13 months. Clarithromycin-based therapy showed a higher improvement rate (5/6, 83.33%). Surgical intervention was performed in 5 patients. Only 1 patient did not show any improvement after surgical treatment.

CONCLUSION: M. xenopi spine infection in humans presents with atypical clinical symptoms. mNGS identification may be a good choice. M. xenopi may be considered in immunocompromised patients with spinal infection. We recommend a clarithromycin-containing regimen and prolonging the duration of treatment to ensure effectiveness.}, } @article {pmid36817977, year = {2023}, author = {Moonen, JP and Schinkel, M and van der Most, T and Miesen, P and van Rij, RP}, title = {Composition and global distribution of the mosquito virome - A comprehensive database of insect-specific viruses.}, journal = {One health (Amsterdam, Netherlands)}, volume = {16}, number = {}, pages = {100490}, pmid = {36817977}, issn = {2352-7714}, abstract = {Mosquitoes are vectors for emerging and re-emerging infectious viral diseases of humans, livestock and other animals. In addition to these arthropod-borne (arbo)viruses, mosquitoes are host to an array of insect-specific viruses, collectively referred to as the mosquito virome. Mapping the mosquito virome and understanding if and how its composition modulates arbovirus transmission is critical to understand arboviral disease emergence and outbreak dynamics. In recent years, next-generation sequencing as well as PCR and culture-based methods have been extensively used to identify mosquito-associated viruses, providing insights into virus ecology and evolution. Until now, the large amount of mosquito virome data, specifically those acquired by metagenomic sequencing, has not been comprehensively integrated. We have constructed a searchable database of insect-specific viruses associated with vector mosquitoes from 175 studies, published between October 2000 and February 2022. We identify the most frequently detected and widespread viruses of the Culex, Aedes and Anopheles mosquito genera and report their global distribution. In addition, we highlight the challenges of extracting and integrating published virome data and we propose that a standardized reporting format will facilitate data interpretation and re-use by other scientists. We expect our comprehensive database, summarizing mosquito virome data collected over 20 years, to be a useful resource for future studies.}, } @article {pmid36817742, year = {2023}, author = {Ni, Y and Zhong, H and Gu, Y and Liu, L and Zhang, Q and Wang, L and Wan, B and Chen, S and Cao, M and Xu, J and Chen, C and Chen, Y and Sun, S and Ji, L and Sun, W and Wang, C and Yang, J and Lu, X and Shi, B and Feng, C and Su, X}, title = {Clinical Features, Treatment, and Outcome of Psittacosis Pneumonia: A Multicenter Study.}, journal = {Open forum infectious diseases}, volume = {10}, number = {2}, pages = {ofac518}, pmid = {36817742}, issn = {2328-8957}, abstract = {BACKGROUND: We aimed to describe psittacosis pneumonia and risk factors for developing severe pneumonia in this multicenter clinical study.

METHODS: We collected the data of psittacosis pneumonia cases diagnosed with metagenomic next-generation sequencing (mNGS) assay from April 2018 to April 2022 in 15 tertiary hospitals in China.

RESULTS: A total of 122 patients were enrolled; 50.0% had a definite history of bird exposure. In 81.2% of cases, onset happened in autumn or winter. The common symptoms were fever (99.2%), cough (63.1%), fatigue (52.5%), shortness of breath (50.0%), chills (37.7%), central nervous system symptoms (36.9%), myalgia (29.5%), and gastrointestinal tract symptoms (15.6%). Laboratory tests showed that >70% of cases had elevated C-reactive protein, procalcitonin, erythrocyte sedimentation rate, D-dimer, lactate dehydrogenase, and aspartate aminotransferase, and >50% had hyponatremia and hypoproteinemia. The most common imaging finding was consolidation (71.3%), and 42.6% of cases met the criteria for severe pneumonia. Age >65 years and male sex were the risk factors for severe pneumonia. The effective proportion of patients treated with tetracyclines was higher than that of fluoroquinolones (66/69 [95.7%] vs 18/58 [31.0%]; P < .001), and the median defervescence time was shorter. After medication adjustment when the diagnosis was clarified, 119 of 122 (97.5%) patients were finally cured and the other 3 (2.5%) died.

CONCLUSIONS: Psittacosis pneumonia has a high rate of severe disease. Proven diagnosis could be rapidly confirmed by mNGS. Tetracycline therapy had a rapid effect and a high cure rate.}, } @article {pmid36817471, year = {2023}, author = {Meena, AS and Shukla, PK and Rao, R and Canelas, C and Pierre, JF and Rao, R}, title = {TRPV6 deficiency attenuates stress and corticosterone-mediated exacerbation of alcohol-induced gut barrier dysfunction and systemic inflammation.}, journal = {Frontiers in immunology}, volume = {14}, number = {}, pages = {1093584}, pmid = {36817471}, issn = {1664-3224}, support = {R01 AA029270/AA/NIAAA NIH HHS/United States ; }, mesh = {Mice ; Animals ; Corticosterone/metabolism ; *Endotoxemia/metabolism ; Dysbiosis/metabolism ; RNA, Ribosomal, 16S ; Intestinal Mucosa/metabolism ; Ethanol/pharmacology ; *Liver Diseases/metabolism ; Inflammation/metabolism ; Calcium Channels/metabolism ; TRPV Cation Channels/metabolism ; }, abstract = {INTRODUCTION: Chronic stress is co-morbid with alcohol use disorder that feedback on one another, thus impeding recovery from both disorders. Stress and the stress hormone corticosterone aggravate alcohol-induced intestinal permeability and liver damage. However, the mechanisms involved in compounding tissue injury by stress/corticosterone and alcohol are poorly defined. Here we explored the involvement of the TRPV6 channel in stress (or corticosterone) 3and alcohol-induced intestinal epithelial permeability, microbiota dysbiosis, and systemic inflammation.

METHODS: Chronic alcohol feeding was performed on adult wild-type and Trpv6-/- mice with or without corticosterone treatment or chronic restraint stress (CRS). The barrier function was determined by evaluating inulin permeability in vivo and assessing tight junction (TJ) and adherens junction (AJ) integrity by immunofluorescence microscopy. The gut microbiota composition was evaluated by 16S rRNA sequencing and metagenomic analyses. Systemic responses were assessed by evaluating endotoxemia, systemic inflammation, and liver damage.

RESULTS: Corticosterone and CRS disrupted TJ and AJ, increased intestinal mucosal permeability, and caused endotoxemia, systemic inflammation, and liver damage in wild-type but not Trpv6-/- mice. Corticosterone and CRS synergistically potentiated the alcohol-induced breakdown of intestinal epithelial junctions, mucosal barrier impairment, endotoxemia, systemic inflammation, and liver damage in wild-type but not Trpv6-/- mice. TRPV6 deficiency also blocked the effects of CRS and CRS-mediated potentiation of alcohol-induced dysbiosis of gut microbiota.

CONCLUSIONS: These findings indicate an essential role of TRPV6 in stress, corticosterone, and alcohol-induced intestinal permeability, microbiota dysbiosis, endotoxemia, systemic inflammation, and liver injury. This study identifies TRPV6 as a potential therapeutic target for developing treatment strategies for stress and alcohol-associated comorbidity.}, } @article {pmid36816771, year = {2023}, author = {Zhou, LW and May, TW}, title = {Fungal taxonomy: current status and research agendas for the interdisciplinary and globalisation era.}, journal = {Mycology}, volume = {14}, number = {1}, pages = {52-59}, pmid = {36816771}, issn = {2150-1203}, abstract = {Fungal taxonomy is a fundamental discipline that aims to recognise all fungi and their kinships. Approximately 5% of a practical estimate of 2.2-3.8 million species globally are currently known, and consequently the Fungal Tree of Life (FTOL) is very incompletely reconstructed. With the advances of new technologies, mycology is marching into the interdisciplinary and globalisation era. To make fungal taxonomy relevant, innovative sampling methods and phylogenomics analyses should be performed to reconstruct a much more comprehensive FTOL. In association with this densely sampled FTOL, multiomics will reveal what drives fungal species diversification and how fungal traits evolve to adapt to various environments, while metagenomics will facilitate the understanding and protection of the ecological functions of fungi. A coordinated approach to pursuing these research agendas that includes conceiving of and costing a mission to describe all the fungi on the planet will unlock potential of fungi to support sustainable development of our society.}, } @article {pmid36816590, year = {2023}, author = {Liu, T and Chen, YC and Jeng, SL and Chang, JJ and Wang, JY and Lin, CH and Tsai, PF and Ko, NY and Ko, WC and Wang, JL}, title = {Short-term effects of Chlorhexidine mouthwash and Listerine on oral microbiome in hospitalized patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1056534}, pmid = {36816590}, issn = {2235-2988}, mesh = {Humans ; *Chlorhexidine ; Mouthwashes ; Nitrates ; Bacteria ; *Microbiota ; }, abstract = {INTRODUCTION: Chlorhexidine (CHX) and essential oil containing mouthwashes like Listerine[®] can improve oral hygiene via suppressing oral microbes. In hospitalized patients, CHX mouthwash reduces the incidence of ventilator-associated pneumonia. However, CHX use was also associated with increased mortality, which might be related to nitrate-reducing bacteria. Currently, no study determines oral bacteria targeted by essential oils mouthwash in hospitalized patients using a metagenomic approach.

METHODS: We recruited 87 hospitalized patients from a previous randomized control study, and assigned them to three mouthwash groups: CHX, Listerine, and normal saline (control). Before and after gargling the mouthwash twice a day for 5-7 days, oral bacteria were examined using a 16S rDNA approach.

RESULTS: Alpha diversities at the genus level decreased significantly only for the CHX and Listerine groups. Only for the two groups, oral microbiota before and after gargling were significantly different, but not clearly distinct. Paired analysis eliminated the substantial individual differences and revealed eight bacterial genera (including Prevotella, Fusobacterium, and Selenomonas) with a decreased relative abundance, while Rothia increased after gargling the CHX mouthwash. After gargling Listerine, seven genera (including Parvimonas, Eubacterium, and Selenomonas) showed a decreased relative abundance, and the magnitudes were smaller compared to the CHX group. Fewer bacteria targeted by Listerine were reported to be nitrate-reducing compared to the CHX mouthwash.

DISCUSSION: In conclusion, short-term gargling of the CHX mouthwash and Listerine altered oral microbiota in our hospitalized patients. The bacterial genera targeted by the CHX mouthwash and Listerine were largely different and the magnitudes of changes were smaller using Listerine. Functional alterations of gargling CHX and Listerine were also different. These findings can be considered for managing oral hygiene of hospitalized patients.}, } @article {pmid36816587, year = {2023}, author = {Li, SL and Zhao, X and Tao, JZ and Yue, ZZ and Zhao, XY}, title = {Application of metagenomic next-generation sequencing in patients with infective endocarditis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1107170}, pmid = {36816587}, issn = {2235-2988}, mesh = {Humans ; *Endocarditis, Bacterial/complications ; *Endocarditis/diagnosis ; Mitral Valve ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Anti-Bacterial Agents ; }, abstract = {OBJECTIVES: Metagenomic next-generation sequencing (mNGS) technology is helpful for the early diagnosis of infective endocarditis, especially culture-negative infective endocarditis, which may guide clinical treatment. The purpose of this study was to compare the presence of culture-negative infective endocarditis pathogens versus culture-positive ones, and whether mNGS test results could influence treatment regimens for patients with routine culture-negative infective endocarditis.

METHODS: The present study enrolled patients diagnosed with infective endocarditis and tested for mNGS in the First Affiliated Hospital of Zhengzhou University from February 2019 to February 2022 continuously. According to the culture results, patients were divided into culture-negative group (Group CN, n=18) and culture-positive group (Group CP, n=32). The baseline characteristics, clinical data, pathogens, 30 day mortality and treatment regimen of 50 patients with infective endocarditis were recorded and analyzed.

RESULTS: Except for higher levels of PCT in the Group CN [0.33 (0.16-2.74) ng/ml vs. 0.23 (0.12-0.49) ng/ml, P=0.042], there were no significant differences in the basic clinical data and laboratory examinations between the two groups (all P>0.05). The aortic valve and mitral valve were the most involved valves in patients with infective endocarditis (aortic valve involved: Group CN 10, Group CP 16; mitral valve involved: Group CN 8, Group CP 21; P>0.05) while 9 patients had multiple valves involved (Group CN 2, Group CP 7; P>0.05). The detection rate of non-streptococci infections in the Group CN was significantly higher than that in the Group CP (9/18 vs. 3/32, P=0.004). There was no significant difference in patients with heart failure hospitalization and all-cause death at 30 days after discharge (3 in Group CN vs. 4 in Group CP, P>0.05). It is worth noting that 10 patients with culture-negative infective endocarditis had their antibiotic regimen optimized after the blood mNGS.

CONCLUSIONS: Culture-negative infective endocarditis should be tested for mNGS for early diagnosis and to guide clinical antibiotic regimen.}, } @article {pmid36816584, year = {2023}, author = {Xu, L and Chen, X and Yang, X and Jiang, H and Wang, J and Chen, S and Xu, J}, title = {Disseminated Talaromyces marneffei infection after renal transplantation: A case report and literature review.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1115268}, pmid = {36816584}, issn = {2235-2988}, mesh = {Male ; Humans ; Adult ; *Antifungal Agents/therapeutic use ; Amphotericin B ; Voriconazole ; *Kidney Transplantation ; }, abstract = {We reported a 31-year-old man who received renal transplantation for more than 2 years. He was admitted to our hospital on 9 March 2022 due to intermittent diarrhea accompanied by leukopenia for more than 1 month. The patient successively developed high fever, cough, anemia, weight loss, gastrointestinal bleeding, and liver function impairment. Computed tomography (CT) revealed a slight inflammation in the lower lobes of both lungs, enlargement of the lymph nodes in the retroperitoneal and the root of mesenteric areas, and hepatosplenomegaly. Talaromyces marneffei was detected by metagenomics next-generation sequencing (mNGS) in blood and bronchoalveolar lavage fluid, and the pathogen was subsequently verified by blood culture. After endoscopic hemostatic therapy and antifungal therapy with voriconazole and amphotericin B cholesteryl sulfate complex, the patient was successfully discharged. Oral voriconazole was given regularly after discharge. Diarrhea, fever, enlargement of the lymph nodes, and endoscopic evidence of erosion may indicate intestinal T. marneffei infection. Although the mortality of T. marneffei infection after renal transplantation is very high, timely and effective antifungal therapy with amphotericin B cholesteryl sulfate complex is still expected to improve its prognosis.}, } @article {pmid36816581, year = {2023}, author = {Parga, A and Muras, A and Otero-Casal, P and Arredondo, A and Soler-Ollé, A and Àlvarez, G and Alcaraz, LD and Mira, A and Blanc, V and Otero, A}, title = {The quorum quenching enzyme Aii20J modifies in vitro periodontal biofilm formation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1118630}, pmid = {36816581}, issn = {2235-2988}, mesh = {Humans ; *Quorum Sensing ; Biofilms ; Bacteria/metabolism ; Acyl-Butyrolactones/metabolism ; *Periodontal Diseases ; }, abstract = {INTRODUCTION: Recent studies have revealed the presence of N-acyl-homoserine lactones (AHLs) quorum sensing (QS) signals in the oral environment. Yet, their role in oral biofilm development remains scarcely investigated. The use of quorum quenching (QQ) strategies targeting AHLs has been described as efficient for the control of pathogenic biofilms. Here, we evaluate the use of a highly active AHL-targeting QQ enzyme, Aii20J, to modulate oral biofilm formation in vitro.

METHODS: The effect of the QQ enzyme was studied in in vitro multispecies biofilms generated from oral samples taken from healthy donors and patients with periodontal disease. Subgingival samples were used as inocula, aiming to select members of the microbiota of the periodontal pocket niche in the in vitro biofilms. Biofilm formation abilities and microbial composition were studied upon treating the biofilms with the QQ enzyme Aii20J.

RESULTS AND DISCUSSION: The addition of the enzyme resulted in significant biofilm mass reductions in 30 - 60% of the subgingival-derived biofilms, although standard AHLs could not be found in the supernatants of the cultured biofilms. Changes in biofilm mass were not accompanied by significant alterations of bacterial relative abundance at the genus level. The investigation of 125 oral supragingival metagenomes and a synthetic subgingival metagenome revealed a surprisingly high abundance and broad distribution of homologous of the AHL synthase HdtS and several protein families of AHL receptors, as well as an enormous presence of QQ enzymes, pointing to the existence of an intricate signaling network in oral biofilms that has been so far unreported, and should be further investigated. Together, our findings support the use of Aii20J to modulate polymicrobial biofilm formation without changing the microbiome structure of the biofilm. Results in this study suggest that AHLs or AHL-like molecules affect oral biofilm formation, encouraging the application of QQ strategies for oral health improvement, and reinforcing the importance of personalized approaches to oral biofilm control.}, } @article {pmid36815859, year = {2023}, author = {Han, M and Sun, J and Yang, Q and Liang, Y and Jiang, Y and Gao, C and Gu, C and Liu, Q and Chen, X and Liu, G and Shao, H and Guo, C and He, H and Wang, H and Sung, YY and Mok, WJ and Wong, LL and Wang, Z and McMinn, A and Wang, M}, title = {Spatiotemporal Dynamics of Coastal Viral Community Structure and Potential Biogeochemical Roles Affected by an Ulva prolifera Green Tide.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0121122}, pmid = {36815859}, issn = {2379-5077}, mesh = {*Ulva/genetics ; Ecosystem ; Eutrophication ; China ; *Synechococcus ; }, abstract = {The world's largest macroalgal green tide, caused by Ulva prolifera, has resulted in serious consequences for coastal waters of the Yellow Sea, China. Although viruses are considered to be one of the key factors in controlling microalgal bloom demise, understanding of the relationship between viral communities and the macroalgal green tide is still poor. Here, a Qingdao coastal virome (QDCV) time-series data set was constructed based on the metagenomic analysis of 17 DNA viromes along three coastal stations of the Yellow Sea, covering different stages of the green tide from Julian days 165 to 271. A total of 40,076 viral contigs were detected and clustered into 28,058 viral operational taxonomic units (vOTUs). About 84% of the vOTUs could not be classified, and 62% separated from vOTUs in other ecosystems. Green tides significantly influenced the spatiotemporal dynamics of the viral community structure, diversity, and potential functions. For the classified vOTUs, the relative abundance of Pelagibacter phages declined with the arrival of the bloom and rebounded after the bloom, while Synechococcus and Roseobacter phages increased, although with a time lag from the peak of their hosts. More than 80% of the vOTUs reached peaks in abundance at different specific stages, and the viral peaks were correlated with specific hosts at different stages of the green tide. Most of the viral auxiliary metabolic genes (AMGs) were associated with carbon and sulfur metabolism and showed spatiotemporal dynamics relating to the degradation of the large amount of organic matter released by the green tide. IMPORTANCE To the best of our knowledge, this study is the first to investigate the responses of viruses to the world's largest macroalgal green tide. It revealed the spatiotemporal dynamics of the unique viral assemblages and auxiliary metabolic genes (AMGs) following the variation and degradation of Ulva prolifera. These findings demonstrate a tight coupling between viral assemblages, and prokaryotic and eukaryotic abundances were influenced by the green tide.}, } @article {pmid36815495, year = {2023}, author = {Favaro, L and Campanaro, S and Fugaban, JII and Treu, L and Jung, ES and d'Ovidio, L and de Oliveira, DP and Liong, MT and Ivanova, IV and Todorov, SD}, title = {Genomic, metabolomic, and functional characterisation of beneficial properties of Pediococcus pentosaceus ST58, isolated from human oral cavity.}, journal = {Beneficial microbes}, volume = {14}, number = {1}, pages = {57-72}, doi = {10.3920/BM2022.0067}, pmid = {36815495}, issn = {1876-2891}, mesh = {Humans ; Pediococcus pentosaceus/genetics/metabolism ; Random Amplified Polymorphic DNA Technique ; RNA, Ribosomal, 16S/genetics ; Pediococcus/genetics/metabolism ; *Probiotics ; *Bacteriocins/genetics/pharmacology ; Anti-Bacterial Agents/pharmacology ; *Listeria monocytogenes ; Genomics ; }, abstract = {Bacteriocins produced by lactic acid bacteria are proteinaceous antibacterial metabolites that normally exhibit bactericidal or bacteriostatic activity against genetically closely related bacteria. In this work, the bacteriocinogenic potential of Pediococcus pentosaceus strain ST58, isolated from oral cavity of a healthy volunteer was evaluated. To better understand the biological role of this strain, its technological and safety traits were deeply investigated through a combined approach considering physiological, metabolomic and genomic properties. Three out of 14 colonies generating inhibition zones were confirmed to be bacteriocin producers and, according to repPCR and RAPD-PCR, differentiation assays, and 16S rRNA sequencing it was confirmed to be replicates of the same strain, identified as P. pentosaceus, named ST58. Based on multiple isolation of the same strain (P. pentosaceus ST58) over the 26 weeks in screening process for the potential bacteriocinogenic strains from the oral cavity of the same volunteer, strain ST58 can be considered a persistent component of oral cavity microbiota. Genomic analysis of P. pentosaceus ST58 revealed the presence of operons encoding for bacteriocins pediocin PA-1 and penocin A. The produced bacteriocin(s) inhibited the growth of Listeria monocytogenes, Enterococcus spp. and some Lactobacillus spp. used to determine the activity spectrum. The highest levels of production (6400 AU/ml) were recorded against L. monocytogenes strains after 24 h of incubation and the antimicrobial activity was inhibited after treatment of the cell-free supernatants with proteolytic enzymes. Noteworthy, P. pentosaceus ST58 also presented antifungal activity and key metabolites potentially involved in these properties were identified. Overall, this strain can be of great biotechnological interest towards the development of effective bio-preservation cultures as well as potential health promoting microbes.}, } @article {pmid36815276, year = {2023}, author = {Dutoit, L and McCulloch, GA}, title = {Fun in facets: A flexible new tool for population genomics in R.}, journal = {Molecular ecology resources}, volume = {23}, number = {4}, pages = {739-741}, doi = {10.1111/1755-0998.13773}, pmid = {36815276}, issn = {1755-0998}, mesh = {*Metagenomics ; *Genome-Wide Association Study ; Software ; Polymorphism, Single Nucleotide ; }, abstract = {The landscape of analytical tools for population genomics continues to evolve. However, these tools are scattered across programming languages, making them largely inaccessible for many biologists. In this issue of Molecular Ecology Resources, Hemstrom and Jones, 2022 (Mol Ecol Resour; 962) introduce a new R package, snpR. This package combines a large number of existing analyses, to provide a one-stop shop for population genomics. F-statistics, admixture analyses, effective population size inferences, genome-wide association studies (GWAS), and parentage analyses are all implemented natively within the package. A variety of third-party software can also be run without leaving the R environment. The authors pay particular attention to data structure - avoiding redundancy - and allowing analyses to be run across multiple sample or single-nucleotide polymorphism (SNP) groupings. Because of its great accessibility and wide range of analyses, snpR has the potential to become a favourite within the Molecular Ecology community.}, } @article {pmid36814842, year = {2023}, author = {Zampieri, G and Campanaro, S and Angione, C and Treu, L}, title = {Metatranscriptomics-guided genome-scale metabolic modeling of microbial communities.}, journal = {Cell reports methods}, volume = {3}, number = {1}, pages = {100383}, pmid = {36814842}, issn = {2667-2375}, mesh = {Humans ; *Microbiota/genetics ; Metagenome/genetics ; Archaea/genetics ; *Gastrointestinal Microbiome/genetics ; }, abstract = {Multi-omics data integration via mechanistic models of metabolism is a scalable and flexible framework for exploring biological hypotheses in microbial systems. However, although most microorganisms are unculturable, such multi-omics modeling is limited to isolate microbes or simple synthetic communities. Here, we developed an approach for modeling microbial activity and interactions that leverages the reconstruction of metagenome-assembled genomes and associated genome-centric metatranscriptomes. At its core, we designed a method for condition-specific metabolic modeling of microbial communities through the integration of metatranscriptomic data. Using this approach, we explored the behavior of anaerobic digestion consortia driven by hydrogen availability and human gut microbiota dysbiosis associated with Crohn's disease, identifying condition-dependent amino acid requirements in archaeal species and a reduced short-chain fatty acid exchange network associated with disease, respectively. Our approach can be applied to complex microbial communities, allowing a mechanistic contextualization of multi-omics data on a metagenome scale.}, } @article {pmid36814836, year = {2023}, author = {Usyk, M and Peters, BA and Karthikeyan, S and McDonald, D and Sollecito, CC and Vazquez-Baeza, Y and Shaffer, JP and Gellman, MD and Talavera, GA and Daviglus, ML and Thyagarajan, B and Knight, R and Qi, Q and Kaplan, R and Burk, RD}, title = {Comprehensive evaluation of shotgun metagenomics, amplicon sequencing, and harmonization of these platforms for epidemiological studies.}, journal = {Cell reports methods}, volume = {3}, number = {1}, pages = {100391}, pmid = {36814836}, issn = {2667-2375}, support = {N01HC65236/HL/NHLBI NIH HHS/United States ; R01 DK126698/DK/NIDDK NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; N01HC65235/HL/NHLBI NIH HHS/United States ; U01 HL146204/HL/NHLBI NIH HHS/United States ; HHSN261201300005I/CA/NCI NIH HHS/United States ; P30 CA013330/CA/NCI NIH HHS/United States ; HHSN268201000001I/HL/NHLBI NIH HHS/United States ; N01HC65237/HL/NHLBI NIH HHS/United States ; N01HC65234/HL/NHLBI NIH HHS/United States ; HHSN261201300004I/CA/NCI NIH HHS/United States ; R01 MD011389/MD/NIMHD NIH HHS/United States ; N01HC65233/HL/NHLBI NIH HHS/United States ; P30 AI124414/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; Bacteria ; Metagenome ; Sequence Analysis, DNA/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {In a large cohort of 1,772 participants from the Hispanic Community Health Study/Study of Latinos with overlapping 16SV4 rRNA gene (bacterial amplicon), ITS1 (fungal amplicon), and shotgun sequencing data, we demonstrate that 16SV4 amplicon sequencing and shotgun metagenomics offer the same level of taxonomic accuracy for bacteria at the genus level even at shallow sequencing depths. In contrast, for fungal taxa, we did not observe meaningful agreements between shotgun and ITS1 amplicon results. Finally, we show that amplicon and shotgun data can be harmonized and pooled to yield larger microbiome datasets with excellent agreement (<1% effect size variance across three independent outcomes) using pooled amplicon/shotgun data compared to pure shotgun metagenomic analysis. Thus, there are multiple approaches to study the microbiome in epidemiological studies, and we provide a demonstration of a powerful pooling approach that will allow researchers to leverage the massive amount of amplicon sequencing data generated over the last two decades.}, } @article {pmid36814827, year = {2023}, author = {Chen, T and Zhang, L and Huang, W and Zong, H and Li, Q and Zheng, Y and Lv, Q and Kong, D and Ren, Y and Jiang, Y and Li, Y and Liu, P}, title = {Detection of Pathogens and Antimicrobial Resistance Genes in Ventilator-Associated Pneumonia by Metagenomic Next-Generation Sequencing Approach.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {923-936}, pmid = {36814827}, issn = {1178-6973}, abstract = {BACKGROUND: The early identification of pathogens and their antibiotic resistance are essential for the management and treatment of patients affected by ventilator-associated pneumonia (VAP). However, microbiological culture may be time-consuming and has a limited culturability of many potential pathogens. In this study, we developed a rapid nanopore-based metagenomic next-generation sequencing (mNGS) diagnostic assay for detection of VAP pathogens and antimicrobial resistance genes (ARGs).

PATIENTS AND METHODS: Endotracheal aspirate (ETA) samples from 63 patients with suspected VAP were collected between November 2021 and July 2022. Receiver operating characteristic (ROC) curves were established to compare the pathogen identification performance of the target pathogen reads, reads percent of microbes (RPM) and relative abundance (RA). The evaluation of the accuracy of mNGS was performed comparing with the gold standard and the composite standard, respectively. Then, the ARGs were analyzed by mNGS.

RESULTS: ROC curves showed that RA has the highest diagnostic value and the corresponding threshold was 9.93%. The sensitivity and specificity of mNGS test were 91.3% and 78.3%, respectively, based on the gold standard, while the sensitivity and specificity of mNGS test were 97.4% and 100%, respectively, based on the composite standard. A total of 13 patients were virus-positive based on mNGS results, while the coinfection rate increased from 27% to 46% compared to the rate obtained based on clinical findings. The mNGS test also performed well at predicting antimicrobial resistance phenotypes. Patients with a late-onset VAP had a significantly greater proportion of ARGs in their respiratory microbiome compared to those with early-onset VAP (P = 0.041). Moreover, the median turnaround time of mNGS was 4.43 h, while routine culture was 72.00 h.

CONCLUSION: In this study, we developed a workflow that can accurately detect VAP pathogens and enable prediction of antimicrobial resistance phenotypes within 5 h of sample receipt by mNGS.}, } @article {pmid36814618, year = {2023}, author = {DeSantis, TZ and Cardona, C and Narayan, NR and Viswanatham, S and Ravichandar, D and Wee, B and Chow, CE and Iwai, S}, title = {StrainSelect: A novel microbiome reference database that disambiguates all bacterial strains, genome assemblies and extant cultures worldwide.}, journal = {Heliyon}, volume = {9}, number = {2}, pages = {e13314}, pmid = {36814618}, issn = {2405-8440}, abstract = {Motivation: Microbial metagenomic profiling software and databases are advancing rapidly for development of novel disease biomarkers and therapeutics yet three problems impede analyses: 1) the conflation of "genome assembly" and "strain" in reference databases; 2) difficulty connecting DNA biomarkers to a procurable strain for laboratory experimentation; and 3) absence of a comprehensive and unified strain-resolved reference database for integrating both shotgun metagenomics and 16S rRNA gene data. Results: We demarcated 681,087 strains, the largest collection of its kind, by filtering public data into a knowledge graph of vertices representing contiguous DNA sequences, genome assemblies, strain monikers and bio-resource center (BRC) catalog numbers then adding inter-vertex edges only for synonyms or direct derivatives. Surprisingly, for 10,043 important strains, we found replicate RefSeq genome assemblies obstructing interpretation of database searches. We organized each strain into eight taxonomic ranks with bootstrap confidence inversely correlated with genome assembly contamination. The StrainSelect database is suited for applications where a taxonomic, functional or procurement reference is needed for shotgun or amplicon metagenomics since 636,568 strains have at least one 16S rRNA gene, 245,005 have at least one annotated genome assembly, and 36,671 are procurable from at least one BRC. The database overcomes all three aforementioned problems since it disambiguates strains from assemblies, locates strains at BRCs, and unifies a taxonomic reference for both 16S rRNA and shotgun metagenomics. Availability: The StrainSelect database is available in igraph and tabular vertex-edge formats compatible with Neo4J. Dereplicated MinHash and fasta databases are distributed for sourmash and usearch pipelines at http://strainselect.secondgenome.com. Contact:todd.desantis@gmail.com. Supplementary information: Supplementary data are available online.}, } @article {pmid36814567, year = {2023}, author = {Liswadiratanakul, S and Yamamoto, K and Matsutani, M and Wattanadatsaree, V and Kihara, S and Shiwa, Y and Shiwachi, H}, title = {Replacement of water yam (Dioscorea alata L.) indigenous root endophytes and rhizosphere bacterial communities via inoculation with a synthetic bacterial community of dominant nitrogen-fixing bacteria.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1060239}, pmid = {36814567}, issn = {1664-302X}, abstract = {Biofertilizers containing high-density plant growth-promoting bacteria are gaining interest as a sustainable solution to environmental problems caused by eutrophication. However, owing to the limitations of current investigative techniques, the selected microorganisms are not always preferred by the host plant, preventing recruitment into the native microbiota or failing to induce plant growth-promoting effects. To address this, five nitrogen-fixing bacteria previously isolated from water yam (Dioscorea alata L.) plants and showing dominant abundance of 1% or more in the water yam microbiota were selected for analysis of their plant growth-promoting activities when used as a synthetic bacterial inoculant. Water yam cv. A-19 plants were inoculated twice at 10 and 12 weeks after planting under greenhouse conditions. Bacterial communities in root, rhizosphere, and bulk soil samples were characterized using high-throughput 16S rRNA amplicon sequencing. Compared with non-inoculated plants, all bacterial communities were significantly altered by inoculation, mainly at the genus level. The inoculation effects were apparently found in the root communities at 16 weeks after planting, with all inoculated genera showing dominance (in the top 35 genera) compared with the control samples. However, no significant differences in any of the growth parameters or nitrogen contents were observed between treatments. At 20 weeks after planting, the dominance of Stenotrophomonas in the inoculated roots decreased, indicating a decline in the inoculation effects. Interestingly, only the Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium clade was dominant (>1% relative abundance) across all samples, suggesting that bacteria related to this clade are essential core bacteria for water yam growth. This is the first report on addition of a synthetic nitrogen-fixing bacterial community in water yam plants showing that native bacterial communities can be replaced by a synthetic bacterial community, with declining in the effects of Stenotrophomonas on the modified communities several weeks after inoculation.}, } @article {pmid36814443, year = {2023}, author = {Yu, S and Ge, X and Xu, H and Tan, B and Tian, B and Shi, Y and Dai, Y and Li, Y and Hu, S and Qian, J}, title = {Gut microbiome and mycobiome in inflammatory bowel disease patients with Clostridioides difficile infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1129043}, pmid = {36814443}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Mycobiome ; *Clostridioides difficile ; *Inflammatory Bowel Diseases/microbiology ; Bacteria ; *Clostridium Infections/microbiology ; }, abstract = {BACKGROUND: Clostridium difficile infection (CDI) is common in patients with inflammatory bowel disease (IBD) and has been reported as a risk factor for poor outcome. However, gut microbiome and mycobiome of IBD patients with CDI have been barely investigated. This study aimed to assess the gut microbiome and mycobiome in IBD patients with CDI.

METHODS: We collected fecal samples from patients with active IBD and concomitant CDI (IBD-CDI group, n=25), patients with active IBD and no CDI (IBD-only group, n=51), and healthy subjects (HC, n=40). Patients' characteristics including demographic data, disease severity, and medication history were collected. Metagenomic sequencing, taxonomic and functional analysis were carried out in the samples.

RESULTS: We found that the bacterial alpha diversity of the IBD-CDI group was decreased. The bacterial and fungal beta diversity variations between IBD patients and HC were significant, regardless of CDI status. But the IBD-CDI group did not significantly cluster separately from the IBD-only group. Several bacterial taxa, including Enterococcus faecium, Ruminococcus gnavus, and Clostridium innocuum were overrepresented in the IBD-CDI group. Furthermore, IBD patients with CDI were distinguished by several fungal taxa, including overrepresentation of Saccharomyces cerevisiae. We also identified functional differences in IBD patients with CDI include enrichment of peptidoglycan biosynthesis. The network analysis indicated specific interactions between microbial markers in IBD-CDI patients.

CONCLUSION: IBD patients with CDI had pronounced microbial dysbiosis. Gut micro-ecological changes in IBD patients with CDI might provide insight into the pathological process and potential strategies for diagnosis and treatment in this subset of patients.}, } @article {pmid36814349, year = {2023}, author = {Hu, J and Chen, J and Hou, Q and Xu, X and Ren, J and Ma, L and Yan, X}, title = {Core-predominant gut fungus Kazachstania slooffiae promotes intestinal epithelial glycolysis via lysine desuccinylation in pigs.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {31}, pmid = {36814349}, issn = {2049-2618}, mesh = {Animals ; Swine ; *Lysine/metabolism ; *Saccharomycetales ; Glycolysis ; Protein Processing, Post-Translational ; }, abstract = {BACKGROUND: Gut fungi are increasingly recognized as important contributors to host physiology, although most studies have focused on gut bacteria. Post-translational modifications (PTMs) of proteins play vital roles in cell metabolism. However, the contribution of gut fungi to host protein PTMs remains unclear. Mining gut fungi that mediate host protein PTMs and dissecting their mechanism are urgently needed.

RESULTS: We studied the gut fungal communities of 56 weaned piglets and 56 finishing pigs from seven pig breeds using internal transcribed spacer (ITS) gene amplicon sequencing and metagenomics. The results showed that Kazachstania slooffiae was the most abundant gut fungal species in the seven breeds of weaned piglets. K. slooffiae decreased intestinal epithelial lysine succinylation levels, and these proteins were especially enriched in the glycolysis pathway. We demonstrated that K. slooffiae promoted intestinal epithelial glycolysis by decreasing lysine succinylation by activating sirtuin 5 (SIRT5). Furthermore, K. slooffiae-derived 5'-methylthioadenosine metabolite promoted the SIRT5 activity.

CONCLUSIONS: These findings provide a landscape of gut fungal communities of pigs and suggest that K. slooffiae plays a crucial role in intestinal glycolysis metabolism through lysine desuccinylation. Our data also suggest a potential protective strategy for pigs with an insufficient intestinal energy supply. Video Abstract.}, } @article {pmid36813961, year = {2023}, author = {Tintelnot, J and Xu, Y and Lesker, TR and Schönlein, M and Konczalla, L and Giannou, AD and Pelczar, P and Kylies, D and Puelles, VG and Bielecka, AA and Peschka, M and Cortesi, F and Riecken, K and Jung, M and Amend, L and Bröring, TS and Trajkovic-Arsic, M and Siveke, JT and Renné, T and Zhang, D and Boeck, S and Strowig, T and Uzunoglu, FG and Güngör, C and Stein, A and Izbicki, JR and Bokemeyer, C and Sinn, M and Kimmelman, AC and Huber, S and Gagliani, N}, title = {Microbiota-derived 3-IAA influences chemotherapy efficacy in pancreatic cancer.}, journal = {Nature}, volume = {615}, number = {7950}, pages = {168-174}, pmid = {36813961}, issn = {1476-4687}, mesh = {Animals ; Humans ; Mice ; *Carcinoma, Pancreatic Ductal/diet therapy/drug therapy/metabolism/microbiology ; Glutathione Peroxidase/metabolism ; *Microbiota ; *Pancreatic Neoplasms/diet therapy/drug therapy/metabolism/microbiology ; Peroxidase/metabolism ; Reactive Oxygen Species/metabolism ; Tryptophan/metabolism/pharmacology/therapeutic use ; Neutrophils/enzymology ; Autophagy ; Metagenome ; Metabolomics ; Fecal Microbiota Transplantation ; Indoleacetic Acids/pharmacology/therapeutic use ; Disease Models, Animal ; Germ-Free Life ; }, abstract = {Pancreatic ductal adenocarcinoma (PDAC) is expected to be the second most deadly cancer by 2040, owing to the high incidence of metastatic disease and limited responses to treatment[1,2]. Less than half of all patients respond to the primary treatment for PDAC, chemotherapy[3,4], and genetic alterations alone cannot explain this[5]. Diet is an environmental factor that can influence the response to therapies, but its role in PDAC is unclear. Here, using shotgun metagenomic sequencing and metabolomic screening, we show that the microbiota-derived tryptophan metabolite indole-3-acetic acid (3-IAA) is enriched in patients who respond to treatment. Faecal microbiota transplantation, short-term dietary manipulation of tryptophan and oral 3-IAA administration increase the efficacy of chemotherapy in humanized gnotobiotic mouse models of PDAC. Using a combination of loss- and gain-of-function experiments, we show that the efficacy of 3-IAA and chemotherapy is licensed by neutrophil-derived myeloperoxidase. Myeloperoxidase oxidizes 3-IAA, which in combination with chemotherapy induces a downregulation of the reactive oxygen species (ROS)-degrading enzymes glutathione peroxidase 3 and glutathione peroxidase 7. All of this results in the accumulation of ROS and the downregulation of autophagy in cancer cells, which compromises their metabolic fitness and, ultimately, their proliferation. In humans, we observed a significant correlation between the levels of 3-IAA and the efficacy of therapy in two independent PDAC cohorts. In summary, we identify a microbiota-derived metabolite that has clinical implications in the treatment of PDAC, and provide a motivation for considering nutritional interventions during the treatment of patients with cancer.}, } @article {pmid36813851, year = {2023}, author = {Cheng, Z and Zheng, Q and Shi, J and He, Y and Yang, X and Huang, X and Wu, L and Xu, J}, title = {Metagenomic and machine learning-aided identification of biomarkers driving distinctive Cd accumulation features in the root-associated microbiome of two rice cultivars.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {14}, pmid = {36813851}, issn = {2730-6151}, support = {42225705//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Developing low-cadmium (Cd) rice cultivars has emerged as a promising avenue for food safety in Cd-contaminated farmlands. The root-associated microbiomes of rice have been shown to enhance rice growth and alleviate Cd stress. However, the microbial taxon-specific Cd resistance mechanisms underlying different Cd accumulation characteristics between different rice cultivars remain largely unknown. This study compared low-Cd cultivar XS14 and hybrid rice cultivar YY17 for Cd accumulation with five soil amendments. The results showed that XS14 was characterized by more variable community structures and stable co-occurrence networks in the soil-root continuum compared to YY17. The stronger stochastic processes in assembly of the XS14 (~25%) rhizosphere community than that of YY17 (~12%) suggested XS14 may have higher resistance to changes in soil properties. Microbial co-occurrence networks and machine learning models jointly identified keystone indicator microbiota, such as Desulfobacteria in XS14 and Nitrospiraceae in YY17. Meanwhile, genes involved in sulfur cycling and nitrogen cycling were observed among the root-associated microbiome of these two cultivars, respectively. Microbiomes in the rhizosphere and root of XS14 showed a higher diversity in functioning, with the significant enrichment of functional genes related to amino acid and carbohydrate transport and metabolism, and sulfur cycling. Our findings revealed differences and similarities in the microbial communities associated with two rice cultivars, as well as bacterial biomarkers predictive of Cd-accumulation capacity. Thus, we provide new insights into taxon-specific recruitment strategies of two rice cultivars under Cd stress and highlight the utility of biomarkers in offering clues for enhancing crop resilience to Cd stresses in the future.}, } @article {pmid36813387, year = {2023}, author = {Leis, ML}, title = {An Update on the Ocular Surface Bacterial Microbiota in Small Animals.}, journal = {The Veterinary clinics of North America. Small animal practice}, volume = {53}, number = {2}, pages = {299-318}, doi = {10.1016/j.cvsm.2022.10.004}, pmid = {36813387}, issn = {1878-1306}, mesh = {Animals ; *Bacteria/genetics ; *Microbiota ; High-Throughput Nucleotide Sequencing/methods/veterinary ; }, abstract = {High-throughput sequencing (HTS) techniques have revolutionized the way we understand microbial communities in both research and clinical settings and are bringing new insights into what constitutes a healthy ocular surface (and a diseased one). As more diagnostic laboratories incorporate HTS into their technique repertoire, practitioners can expect this technology to become increasingly accessible for clinical practice, potentially becoming the new standard. However, particularly regarding ophthalmic microbiota, considerable research remains to render HTS accessible and applicable.}, } @article {pmid36813198, year = {2023}, author = {Huang, Q and Liu, Z and Guo, Y and Li, B and Yang, Z and Liu, X and Ni, J and Li, X and Zhang, X and Zhou, N and Yin, H and Jiang, C and Hao, L}, title = {Coal-source acid mine drainage reduced the soil multidrug-dominated antibiotic resistome but increased the heavy metal(loid) resistome and energy production-related metabolism.}, journal = {The Science of the total environment}, volume = {873}, number = {}, pages = {162330}, doi = {10.1016/j.scitotenv.2023.162330}, pmid = {36813198}, issn = {1879-1026}, mesh = {*Soil ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; *Metals, Heavy ; Coal ; }, abstract = {A recent global scale study found that mining-impacted environments have multi-antibiotic resistance gene (ARG)-dominated resistomes with an abundance similar to urban sewage but much higher than freshwater sediment. These findings raised concern that mining may increase the risk of ARG environmental proliferation. The current study assessed how typical multimetal(loid)-enriched coal-source acid mine drainage (AMD) contamination affects soil resistomes by comparing with background soils unaffected by AMD. Both contaminated and background soils have multidrug-dominated antibiotic resistomes attributed to the acidic environment. AMD-contaminated soils had a lower relative abundance of ARGs (47.45 ± 23.34 ×/Gb) than background soils (85.47 ± 19.71 ×/Gb) but held high-level heavy metal(loid) resistance genes (MRGs, 133.29 ± 29.36 ×/Gb) and transposase- and insertion sequence-dominated mobile genetic elements (MGEs, 188.51 ± 21.81 ×/Gb), which was 56.26 % and 412.12 % higher than background soils, respectively. Procrustes analysis showed that the microbial community and MGEs exerted more influence on driving heavy metal(loid) resistome variation than antibiotic resistome. The microbial community increased energy production-related metabolism to fulfill the increasing energy needs required by acid and heavy metal(loid) resistance. Horizontal gene transfer (HGT) events primarily exchanged energy- and information-related genes to adapt to the harsh AMD environment. These findings provide new insight into the risk of ARG proliferation in mining environments.}, } @article {pmid36813051, year = {2023}, author = {Hou, Y and He, M and Liu, Y and Wang, Q and Yang, A and Yang, F and Lei, Z and Yi, X and Huang, W}, title = {Biological nitrogen removal mechanisms during anaerobic digestion of swine manure: Effects of biogas circulation and activated carbon addition.}, journal = {Bioresource technology}, volume = {374}, number = {}, pages = {128766}, doi = {10.1016/j.biortech.2023.128766}, pmid = {36813051}, issn = {1873-2976}, mesh = {Animals ; Swine ; *Denitrification ; *Ammonia/metabolism ; Manure ; Biofuels ; Charcoal ; Anaerobiosis ; Nitrogen/metabolism ; Oxidation-Reduction ; Bioreactors/microbiology ; Nitrification ; Bacteria/genetics/metabolism ; }, abstract = {This study investigated the biological nitrogen removal mechanisms during the anaerobic digestion of swine manure and the effects of biogas circulation and activated carbon (AC) addition. Biogas circulation, AC addition, and their combination increased the methane yield by 25.9%, 22.3%, and 44.1%, respectively, when compared to the control. Nitrogen species analysis and metagenomic results indicated that nitrification-denitrification was the dominant ammonia removal pathway in all digesters with little oxygen, while anammox did not occur. Biogas circulation could promote mass transfer and induce air infiltration to enrich nitrification- and denitrification-related bacteria and functional genes. And AC might act as an electron shuttle to facilitate ammonia removal. The combined strategies showed a synergetic effect on the enrichment of nitrification and denitrification bacteria and functional genes, significantly lowering the total ammonia nitrogen by 23.6%. A single digester with biogas circulation and AC addition could enhance methanogenesis and ammonia removal via nitrification and denitrification.}, } @article {pmid36812908, year = {2023}, author = {Li, Z and Yuan, D and Kou, Y and Li, X and Du, C}, title = {Metagenome sequencing to unveil the occurrence and distribution of antibiotic resistome and in a wastewater treatment plant.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-10}, doi = {10.1080/09593330.2022.2158758}, pmid = {36812908}, issn = {1479-487X}, abstract = {The emergence and persistence of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs) has aroused growing public concern for its risk to human health and ecological safety. Moreover, heavy metals concentrated in sewage and sludge could potentially favour co-selection of ARGs and heavy metal resistance genes (HMRGs). In this study, the profile and abundance of antibiotic and metal resistance genes in influent, sludge and effluent were characterized based on the Structured ARG Datebase (SARG) and Antibacterial Biocide and Metal Resistance Gene Datebase (BacMet) by metagenomic analysis. Sequences were aligning against the INTEGRALL, ISFinder, ICEberg and NCBI RefSeq databases to obtain the diversity and abundance of mobile genetic elements (MGEs, e.g.plasmid and transposon). Among them, 20 types of ARGs and 16 types of HMRG were detected in all samples, the influent metagenomes contained many more resistance genes (both ARGs and HMRGs) than the sludge and the influent sample, large reductions in the relatively abundance and diversity of ARG were achieved by biological treatment. ARGs and HMRGs cannot be completely eliminated during the oxidation ditch. A total of 32 species of the potential pathogens were detected, relative abundances of pathogens had no obvious changes. It is suggested that more specific treatments are required to limit their proliferation in the environment. This study can be helpful for further understanding the removal of antibiotic resistance genes in the sewage treatment process via metagenomic sequencing.}, } @article {pmid36812328, year = {2023}, author = {Kiefl, E and Esen, OC and Miller, SE and Kroll, KL and Willis, AD and Rappé, MS and Pan, T and Eren, AM}, title = {Structure-informed microbial population genetics elucidate selective pressures that shape protein evolution.}, journal = {Science advances}, volume = {9}, number = {8}, pages = {eabq4632}, doi = {10.1126/sciadv.abq4632}, pmid = {36812328}, issn = {2375-2548}, support = {R35 GM133420/GM/NIGMS NIH HHS/United States ; }, mesh = {*Genetics, Population ; *Ecology ; Oceans and Seas ; Organic Chemicals ; Base Sequence ; Genetic Variation ; Evolution, Molecular ; }, abstract = {Comprehensive sampling of natural genetic diversity with metagenomics enables highly resolved insights into the interplay between ecology and evolution. However, resolving adaptive, neutral, or purifying processes of evolution from intrapopulation genomic variation remains a challenge, partly due to the sole reliance on gene sequences to interpret variants. Here, we describe an approach to analyze genetic variation in the context of predicted protein structures and apply it to a marine microbial population within the SAR11 subclade 1a.3.V, which dominates low-latitude surface oceans. Our analyses reveal a tight association between genetic variation and protein structure. In a central gene in nitrogen metabolism, we observe decreased occurrence of nonsynonymous variants from ligand-binding sites as a function of nitrate concentrations, revealing genetic targets of distinct evolutionary pressures maintained by nutrient availability. Our work yields insights into the governing principles of evolution and enables structure-aware investigations of microbial population genetics.}, } @article {pmid36812005, year = {2022}, author = {Won, K and Kim, D and Shin, D and Hur, J and Lee, HK and Heo, J and Oh, JD}, title = {High-throughput sequencing-based metagenomic and transcriptomic analysis of intestine in piglets infected with salmonella.}, journal = {Journal of animal science and technology}, volume = {64}, number = {6}, pages = {1144-1172}, pmid = {36812005}, issn = {2055-0391}, abstract = {Salmonella enterica serovar Typhimurium isolate HJL777 is a virulent bacterial strain in pigs. The high rate of salmonella infection are at high risk of non-typhoidal salmonella gastroenteritis development. Salmonellosis is most common in young pigs. We investigated changes in gut microbiota and biological function in piglets infected with salmonella via analysis of rectal fecal metagenome and intestinal transcriptome using 16S rRNA and RNA sequencing. We identified a decrease in Bacteroides and increase in harmful bacteria such as Spirochaetes and Proteobacteria by microbial community analysis. We predicted that reduction of Bacteroides by salmonella infection causes proliferation of salmonella and harmful bacteria that can cause an intestinal inflammatory response. Functional profiling of microbial communities in piglets with salmonella infection showed increasing lipid metabolism associated with proliferation of harmful bacteria and inflammatory responses. Transcriptome analysis identified 31 differentially expressed genes. Using gene ontology and Innate Immune Database analysis, we identified that BGN, DCN, ZFPM2 and BPI genes were involved in extracellular and immune mechanisms, specifically salmonella adhesion to host cells and inflammatory responses during infection. We confirmed alterations in gut microbiota and biological function during salmonella infection in piglets. Our findings will help prevent disease and improve productivity in the swine industry.}, } @article {pmid36810808, year = {2023}, author = {Kunasegaran, T and Balasubramaniam, VRMT and Arasoo, VJT and Palanisamy, UD and Ramadas, A}, title = {Diet Gut Microbiota Axis in Pregnancy: A Systematic Review of Recent Evidence.}, journal = {Current nutrition reports}, volume = {12}, number = {1}, pages = {203-214}, pmid = {36810808}, issn = {2161-3311}, mesh = {Pregnancy ; Female ; Humans ; *Gastrointestinal Microbiome ; Prospective Studies ; Diet ; }, abstract = {PURPOSE OF REVIEW: Although gut microbiota have been associated with the etiology of some diseases, the influence of foods on gut microbiota, especially among pregnant women, remains unclear. Hence, a systematic review was performed to investigate the association between diet and gut microbiota and their influence on metabolic health in pregnant women.

RECENT FINDINGS: We performed the systematic review using the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) 2020 protocol to investigate the association between diet and gut microbiota and their influence on metabolic role in pregnant women. Five databases were searched for relevant peer-reviewed articles published in English since 2011. Two-staged screening of 659 retrieved records resulted in the inclusion of 10 studies. The collated findings suggested associations between nutrient intakes and four key microbes: Collinsella, Lachnospira, Sutterella, Faecalibacterium, and the Firmicutes/Bacteroidetes ratio in pregnant women. Dietary intakes in pregnancy were found to modify the gut microbiota and positively influence the cell metabolism in pregnant women. This review, however, emphasizes the importance of conducting well-designed prospective cohorts to investigate the role of changes in dietary intakes within the pregnancy and the influence of such changes on gut microbiota.}, } @article {pmid36810253, year = {2023}, author = {Li, Z and Zhou, E and Liu, C and Wicks, H and Yildiz, S and Razack, F and Ying, Z and Kooijman, S and Koonen, DPY and Heijink, M and Kostidis, S and Giera, M and Sanders, IMJG and Kuijper, EJ and Smits, WK and van Dijk, KW and Rensen, PCN and Wang, Y}, title = {Dietary butyrate ameliorates metabolic health associated with selective proliferation of gut Lachnospiraceae bacterium 28-4.}, journal = {JCI insight}, volume = {8}, number = {4}, pages = {}, pmid = {36810253}, issn = {2379-3708}, mesh = {Humans ; Animals ; Mice ; *Butyrates/adverse effects ; Obesity/metabolism ; *Metabolic Syndrome ; RNA, Ribosomal, 16S ; Weight Gain ; Cell Proliferation ; }, abstract = {Short-chain fatty acids, including butyrate, have multiple metabolic benefits in individuals who are lean but not in individuals with metabolic syndrome, with the underlying mechanisms still being unclear. We aimed to investigate the role of gut microbiota in the induction of metabolic benefits of dietary butyrate. We performed antibiotic-induced microbiota depletion of the gut and fecal microbiota transplantation (FMT) in APOE*3-Leiden.CETP mice, a well-established translational model for developing human-like metabolic syndrome, and revealed that dietary butyrate reduced appetite and ameliorated high-fat diet-induced (HFD-induced) weight gain dependent on the presence of gut microbiota. FMT from butyrate-treated lean donor mice, but not butyrate-treated obese donor mice, into gut microbiota-depleted recipient mice reduced food intake, attenuated HFD-induced weight gain, and improved insulin resistance. 16S rRNA and metagenomic sequencing on cecal bacterial DNA of recipient mice implied that these effects were accompanied by the selective proliferation of Lachnospiraceae bacterium 28-4 in the gut as induced by butyrate. Collectively, our findings reveal a crucial role of gut microbiota in the beneficial metabolic effects of dietary butyrate as strongly associated with the abundance of Lachnospiraceae bacterium 28-4.}, } @article {pmid36810249, year = {2023}, author = {Sorini, C and Tripathi, KP and Wu, S and Higdon, SM and Wang, J and Cheng, L and Banerjee, S and Reinhardt, A and Kreslavsky, T and Thorell, A and Engstrand, L and Du, J and Villablanca, EJ}, title = {Metagenomic and single-cell RNA-Seq survey of the Helicobacter pylori-infected stomach in asymptomatic individuals.}, journal = {JCI insight}, volume = {8}, number = {4}, pages = {}, pmid = {36810249}, issn = {2379-3708}, mesh = {Humans ; Animals ; Mice ; *Helicobacter pylori ; Immunity, Innate ; Single-Cell Gene Expression Analysis ; Stomach ; Gastric Mucosa ; Plasma Cells ; *Helicobacter Infections ; }, abstract = {Helicobacter pylori colonization of the gastric niche can persist for years in asymptomatic individuals. To deeply characterize the host-microbiota environment in H. pylori-infected (HPI) stomachs, we collected human gastric tissues and performed metagenomic sequencing, single-cell RNA-Seq (scRNA-Seq), flow cytometry, and fluorescent microscopy. HPI asymptomatic individuals had dramatic changes in the composition of gastric microbiome and immune cells compared with noninfected individuals. Metagenomic analysis uncovered pathway alterations related to metabolism and immune response. scRNA-Seq and flow cytometry data revealed that, in contrast to murine stomachs, ILC2s are virtually absent in the human gastric mucosa, whereas ILC3s are the dominant population. Specifically, proportion of NKp44+ ILC3s out of total ILCs were highly increased in the gastric mucosa of asymptomatic HPI individuals, and correlated with the abundance of selected microbial taxa. In addition, CD11c+ myeloid cells and activated CD4+ T cells and B cells were expanded in HPI individuals. B cells of HPI individuals acquired an activated phenotype and progressed into a highly proliferating germinal-center stage and plasmablast maturation, which correlated with the presence of tertiary lymphoid structures within the gastric lamina propria. Our study provides a comprehensive atlas of the gastric mucosa-associated microbiome and immune cell landscape when comparing asymptomatic HPI and uninfected individuals.}, } @article {pmid36809975, year = {2023}, author = {Bovio-Winkler, P and Guerrero, LD and Erijman, L and Oyarzúa, P and Suárez-Ojeda, ME and Cabezas, A and Etchebehere, C}, title = {Genome-centric metagenomic insights into the role of Chloroflexi in anammox, activated sludge and methanogenic reactors.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {45}, pmid = {36809975}, issn = {1471-2180}, mesh = {*Sewage ; *Chloroflexi/genetics/metabolism ; Ecosystem ; In Situ Hybridization, Fluorescence ; Anaerobic Ammonia Oxidation ; Bioreactors ; Anaerobiosis ; Nitrogen/metabolism ; Oxidation-Reduction ; }, abstract = {BACKGROUND: The phylum Chloroflexi is highly abundant in a wide variety of wastewater treatment bioreactors. It has been suggested that they play relevant roles in these ecosystems, particularly in degrading carbon compounds and on structuring flocs or granules. Nevertheless, their function is not yet well understood as most species have not been isolated in axenic cultures. Here we used a metagenomic approach to investigate Chloroflexi diversity and their metabolic potential in three environmentally different bioreactors: a methanogenic full-scale reactor, a full-scale activated sludge reactor and a lab scale anammox reactor.

RESULTS: Differential coverage binning approach was used to assemble the genomes of 17 new Chloroflexi species, two of which are proposed as new Candidatus genus. In addition, we recovered the first representative genome belonging to the genus 'Ca. Villigracilis'. Even though samples analyzed were collected from bioreactors operating under different environmental conditions, the assembled genomes share several metabolic features: anaerobic metabolism, fermentative pathways and several genes coding for hydrolytic enzymes. Interestingly, genome analysis from the anammox reactor indicated a putative role of Chloroflexi in nitrogen conversion. Genes related to adhesiveness and exopolysaccharides production were also detected. Complementing sequencing analysis, filamentous morphology was detected by Fluorescent in situ hybridization.

CONCLUSION: Our results suggest that Chloroflexi participate in organic matter degradation, nitrogen removal and biofilm aggregation, playing different roles according to the environmental conditions.}, } @article {pmid36809918, year = {2023}, author = {Han, H and Kim, DD and Song, MJ and Yun, T and Yoon, H and Lee, HW and Kim, YM and Laureni, M and Yoon, S}, title = {Biotrickling Filtration for the Reduction of N2O Emitted during Wastewater Treatment: Results from a Long-Term In Situ Pilot-Scale Testing.}, journal = {Environmental science & technology}, volume = {57}, number = {9}, pages = {3883-3892}, doi = {10.1021/acs.est.2c08818}, pmid = {36809918}, issn = {1520-5851}, mesh = {*Wastewater ; Nitrous Oxide/analysis ; Bioreactors ; *Water Purification ; Filtration ; Sewage ; }, abstract = {Wastewater treatment plants (WWTPs) are a major source of N2O, a potent greenhouse gas with 300 times higher global warming potential than CO2. Several approaches have been proposed for mitigation of N2O emissions from WWTPs and have shown promising yet only site-specific results. Here, self-sustaining biotrickling filtration, an end-of-the-pipe treatment technology, was tested in situ at a full-scale WWTP under realistic operational conditions. Temporally varying untreated wastewater was used as trickling medium, and no temperature control was applied. The off-gas from the covered WWTP aerated section was conveyed through the pilot-scale reactor, and an average removal efficiency of 57.9 ± 29.1% was achieved during 165 days of operation despite the generally low and largely fluctuating influent N2O concentrations (ranging between 4.8 and 96.4 ppmv). For the following 60-day period, the continuously operated reactor system removed 43.0 ± 21.2% of the periodically augmented N2O, exhibiting elimination capacities as high as 5.25 g N2O m[-3]·h[-1]. Additionally, the bench-scale experiments performed abreast corroborated the resilience of the system to short-term N2O starvations. Our results corroborate the feasibility of biotrickling filtration for mitigating N2O emitted from WWTPs and demonstrate its robustness toward suboptimal field operating conditions and N2O starvation, as also supported by analyses of the microbial compositions and nosZ gene profiles.}, } @article {pmid36809182, year = {2023}, author = {Olekhnovich, EI and Ivanov, AB and Babkina, AA and Sokolov, AA and Ulyantsev, VI and Fedorov, DE and Ilina, EN}, title = {Consistent Stool Metagenomic Biomarkers Associated with the Response To Melanoma Immunotherapy.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0102322}, pmid = {36809182}, issn = {2379-5077}, mesh = {Humans ; Metagenome ; *Melanoma/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Biomarkers ; Immunotherapy/methods ; }, abstract = {The human gut microbiome plays an important role in both health and disease. Recent studies have demonstrated a strong influence of the gut microbiome composition on the efficacy of cancer immunotherapy. However, available studies have not yet succeeded in finding reliable and consistent metagenomic markers that are associated with the response to immunotherapy. Therefore, the reanalysis of the published data may improve our understanding of the association between the composition of the gut microbiome and the treatment response. In this study, we focused on melanoma-related metagenomic data, which are more abundant than are data from other tumor types. We analyzed the metagenomes of 680 stool samples from 7 studies that were published earlier. The taxonomic and functional biomarkers were selected after comparing the metagenomes of patients showing different treatment responses. The list of selected biomarkers was also validated on additional metagenomic data sets that were dedicated to the influence of fecal microbiota transplantation on the response to melanoma immunotherapy. According to our analysis, the resulting cross-study taxonomic biomarkers included three bacterial species: Faecalibacterium prausnitzii, Bifidobacterium adolescentis, and Eubacterium rectale. 101 groups of genes were identified to be functional biomarkers, including those potentially involved in the production of immune-stimulating molecules and metabolites. Moreover, we ranked the microbial species by the number of genes encoding functionally relevant biomarkers that they contained. Thus, we put together a list of potentially the most beneficial bacteria for immunotherapy success. F. prausnitzii, E. rectale, and three species of bifidobacteria stood out as the most beneficial species, even though some useful functions were also present in other bacterial species. IMPORTANCE In this study, we put together a list of potentially the most beneficial bacteria that were associated with a responsiveness to melanoma immunotherapy. Another important result of this study is the list of functional biomarkers of responsiveness to immunotherapy, which are dispersed among different bacterial species. This result possibly explains the existing irregularities between studies regarding the bacterial species that are beneficial to melanoma immunotherapy. Overall, these findings can be utilized to issue recommendations for gut microbiome correction in cancer immunotherapy, and the resulting list of biomarkers might serve as a good stepping stone for the development of a diagnostic test that is aimed at predicting patients' responses to melanoma immunotherapy.}, } @article {pmid36809121, year = {2023}, author = {Hoenigl, M and Egger, M and Price, J and Krause, R and Prattes, J and White, PL}, title = {Metagenomic Next-Generation Sequencing of Plasma for Diagnosis of COVID-19-Associated Pulmonary Aspergillosis.}, journal = {Journal of clinical microbiology}, volume = {61}, number = {3}, pages = {e0185922}, pmid = {36809121}, issn = {1098-660X}, mesh = {*COVID-19/complications ; *Aspergillosis/diagnosis/microbiology ; Humans ; Middle Aged ; Cell-Free Nucleic Acids/isolation & purification ; Male ; Female ; }, abstract = {Timely diagnosis remains an unmet need in non-neutropenic patients at risk for aspergillosis, including those with COVID-19-associated pulmonary aspergillosis (CAPA), which in its early stages is characterized by tissue-invasive growth of the lungs with limited angioinvasion. Currently available mycological tests show limited sensitivity when testing blood specimens. Metagenomic next-generation sequencing (mNGS) to detect microbial cell-free DNA (mcfDNA) in plasma might overcome some of the limitations of conventional diagnostics. A two-center cohort study involving 114 COVID-19 intensive care unit patients evaluated the performance of plasma mcfDNA sequencing for the diagnosis of CAPA. Classification of CAPA was performed using the European Confederation for Medical Mycology (ECMM)/International Society for Human and Animal Mycoses (ISHAM) criteria. A total of 218 plasma samples were collected between April 2020 and June 2021 and tested for mcfDNA (Karius test). Only 6 patients were classified as probable CAPA, and 2 were classified as possible, while 106 patients did not fulfill CAPA criteria. The Karius test detected DNA of mold pathogens in 12 samples from 8 patients, including Aspergillus fumigatus in 10 samples from 6 patients. Mold pathogen DNA was detected in 5 of 6 (83% sensitivity) cases with probable CAPA (A. fumigatus in 8 samples from 4 patients and Rhizopus microsporus in 1 sample), while the test did not detect molds in 103 of 106 (97% specificity) cases without CAPA. The Karius test showed promising performance for diagnosis of CAPA when testing plasma, being highly specific. The test detected molds in all but one patient with probable CAPA, including cases where other mycological tests from blood resulted continuously negative, outlining the need for validation in larger studies.}, } @article {pmid36809109, year = {2023}, author = {Wolff, R and Shoemaker, W and Garud, N}, title = {Ecological Stability Emerges at the Level of Strains in the Human Gut Microbiome.}, journal = {mBio}, volume = {14}, number = {2}, pages = {e0250222}, pmid = {36809109}, issn = {2150-7511}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; *Microbiota ; Models, Theoretical ; }, abstract = {The human gut microbiome harbors substantial ecological diversity at the species level as well as at the strain level within species. In healthy hosts, species abundance fluctuations in the microbiome are thought to be stable, and these fluctuations can be described by macroecological laws. However, it is less clear how strain abundances change over time. An open question is whether individual strains behave like species themselves, exhibiting stability and following the macroecological relationships known to hold at the species level, or whether strains have different dynamics, perhaps due to the relatively close phylogenetic relatedness of cocolonizing lineages. Here, we analyze the daily dynamics of intraspecific genetic variation in the gut microbiomes of four healthy, densely longitudinally sampled hosts. First, we find that the overall genetic diversity of a large majority of species is stationary over time despite short-term fluctuations. Next, we show that fluctuations in abundances in approximately 80% of strains analyzed can be predicted with a stochastic logistic model (SLM), an ecological model of a population experiencing environmental fluctuations around a fixed carrying capacity, which has previously been shown to capture statistical properties of species abundance fluctuations. The success of this model indicates that strain abundances typically fluctuate around a fixed carrying capacity, suggesting that most strains are dynamically stable. Finally, we find that the strain abundances follow several empirical macroecological laws known to hold at the species level. Together, our results suggest that macroecological properties of the human gut microbiome, including its stability, emerge at the level of strains. IMPORTANCE To date, there has been an intense focus on the ecological dynamics of the human gut microbiome at the species level. However, there is considerable genetic diversity within species at the strain level, and these intraspecific differences can have important phenotypic effects on the host, impacting the ability to digest certain foods and metabolize drugs. Thus, to fully understand how the gut microbiome operates in times of health and sickness, its ecological dynamics may need to be quantified at the level of strains. Here, we show that a large majority of strains maintain stable abundances for periods of months to years, exhibiting fluctuations in abundance that can be well described by macroecological laws known to hold at the species level, while a smaller percentage of strains undergo rapid, directional changes in abundance. Overall, our work indicates that strains are an important unit of ecological organization in the human gut microbiome.}, } @article {pmid36809072, year = {2023}, author = {Yuan, S and Friman, VP and Balcazar, JL and Zheng, X and Ye, M and Sun, M and Hu, F}, title = {Viral and Bacterial Communities Collaborate through Complementary Assembly Processes in Soil to Survive Organochlorine Contamination.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {3}, pages = {e0181022}, pmid = {36809072}, issn = {1098-5336}, mesh = {Soil ; Bacteria ; *Microbiota ; Soil Microbiology ; *Viruses ; *Pesticides/metabolism ; *Hydrocarbons, Chlorinated/metabolism ; }, abstract = {The ecological drivers that direct the assembly of viral and host bacterial communities are largely unknown, even though viral-encoded accessory genes help host bacteria survive in polluted environments. To understand the ecological mechanism(s) of viruses and hosts synergistically surviving under organochlorine pesticide (OCP) stress, we investigated the community assembly processes of viruses and bacteria at the taxon and functional gene levels in clean and OCP-contaminated soils in China using a combination of metagenomics/viromics and bioinformatics approaches. We observed a decreased richness of bacterial taxa and functional genes but an increased richness of viral taxa and auxiliary metabolic genes (AMGs) in OCP-contaminated soils (from 0 to 2,617.6 mg · kg[-1]). In OCP-contaminated soils, the assembly of bacterial taxa and genes was dominated by a deterministic process, of which the relative significance was 93.0% and 88.7%, respectively. In contrast, the assembly of viral taxa and AMGs was driven by a stochastic process, which contributed 83.1% and 69.2%, respectively. The virus-host prediction analysis, which indicated Siphoviridae was linked to 75.0% of bacterial phyla, and the higher migration rate of viral taxa and AMGs in OCP-contaminated soil suggested that viruses show promise for the dissemination of functional genes among bacterial communities. Taken together, the results of this study indicated that the stochastic assembly processes of viral taxa and AMGs facilitated bacterial resistance to OCP stress in soils. Moreover, our findings provide a novel avenue for understanding the synergistic interactions between viruses and bacteria from the perspective of microbial ecology, highlighting the significance of viruses in mediating bioremediation of contaminated soils. IMPORTANCE The interaction between viral communities and microbial hosts has been studied extensively, and the viral community affects host community metabolic function through AMGs. Microbial community assembly is the process by which species colonize and interact to establish and maintain communities. This is the first study that aimed to understand the assembly process of bacterial and viral communities under OCP stress. The findings of this study provide information about microbial community responses to OCP stress and reveal the collaborative interactions between viral and bacterial communities to resist pollutant stress. Thereby, we highlight the importance of viruses in soil bioremediation from the perspective of community assembly.}, } @article {pmid36807933, year = {2023}, author = {Moran-Ramos, S and Cerqueda-García, D and López-Contreras, B and Larrieta-Carrasco, E and Villamil-Ramírez, H and Molina-Cruz, S and Torres, N and Sánchez-Tapia, M and Hernández-Pando, R and Aguilar-Salinas, C and Villarreal-Molina, T and Canizales-Quinteros, S}, title = {A metagenomic study identifies a Prevotella copri enriched microbial profile associated with non-alcoholic steatohepatitis in subjects with obesity.}, journal = {Journal of gastroenterology and hepatology}, volume = {38}, number = {5}, pages = {791-799}, doi = {10.1111/jgh.16147}, pmid = {36807933}, issn = {1440-1746}, support = {FOSISS-289699//Mexican National Council for Science and Technology (CONACyT)/ ; //Dirección General de Asuntos de Personal Académico, Universidad Nacional Autónoma de México (DGAPA-UNAM)/ ; }, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease/complications ; Metagenome ; Lipopolysaccharides ; Prevotella/genetics ; Obesity/complications ; Butyrates ; }, abstract = {BACKGROUND AND AIM: Non-alcoholic fatty liver disease (NAFLD) is the most common cause of liver disease. Increasing evidence indicates that the gut microbiota can play an important role in the pathophysiology of NAFLD. Recently, several studies have tested the predictive value of gut microbiome profiles in NAFLD progression; however, comparisons of microbial signatures in NAFLD or non-alcoholic steatohepatitis (NASH) have produced discrepant results, possibly due to ethnic and environmental factors. Thus, we aimed to characterize the gut metagenome composition of patients with fatty liver disease.

METHODS: Gut microbiome of 45 well-characterized patients with obesity and biopsy-proven NAFLD was evaluated using shot-gun sequencing: 11 non-alcoholic fatty liver controls (non-NAFL), 11 with fatty liver, and 23 with NASH.

RESULTS: Our study showed that Parabacteroides distasonis and Alistipes putredenis were enriched in fatty liver but not in NASH patients. Notably, in a hierarchical clustering analysis, microbial profiles were differentially distributed among groups, and membership to a Prevotella copri dominant cluster was associated with a greater risk of developing NASH. Functional analyses showed that although no differences in LPS biosynthesis pathways were observed, Prevotella-dominant subjects had higher circulating levels of LPS and a lower abundance of pathways encoding butyrate production.

CONCLUSIONS: Our findings suggest that a Prevotella copri dominant bacterial community is associated with a greater risk for NAFLD disease progression, probably linked to higher intestinal permeability and lower capacity for butyrate production.}, } @article {pmid36807860, year = {2023}, author = {Kumar, J and Sharma, N and Singh, SP}, title = {Genome-resolved metagenomics inferred novel insights into the microbial community, metabolic pathways, and biomining potential of Malanjkhand acidic copper mine tailings.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {17}, pages = {50864-50882}, pmid = {36807860}, issn = {1614-7499}, mesh = {*Copper/metabolism ; Metagenomics ; Phylogeny ; *Microbiota ; Archaea/metabolism ; Metagenome ; Acidobacteria/genetics ; Metabolic Networks and Pathways ; Soil ; Water/metabolism ; }, abstract = {Mine tailing sites provide profound opportunities to elucidate the microbial mechanisms involved in ecosystem functioning. In the present study, metagenomic analysis of dumping soil and adjacent pond around India's largest copper mine at Malanjkhand has been done. Taxonomic analysis deciphered the abundance of phyla Proteobacteria, Bacteroidetes, Acidobacteria, and Chloroflexi. Genomic signatures of viruses were predicted in the soil metagenome, whereas Archaea and Eukaryotes were noticed in water samples. Mesophilic chemolithotrophs, such as Acidobacteria bacterium, Chloroflexi bacterium, and Verrucomicrobia bacterium, were predominant in soil, whereas, in the water sample, the abundance of Methylobacterium mesophilicum, Pedobacter sp., and Thaumarchaeota archaeon was determined. The functional potential analysis highlighted the abundance of genes related to sulfur, nitrogen, methane, ferrous oxidation, carbon fixation, and carbohydrate metabolisms. The genes for copper, iron, arsenic, mercury, chromium, tellurium, hydrogen peroxide, and selenium resistance were found to be predominant in the metagenomes. Metagenome-assembled genomes (MAGs) were constructed from the sequencing data, indicating novel microbial species genetically related to the phylum predicted through whole genome metagenomics. Phylogenetic analysis, genome annotations, functional potential, and resistome analysis showed the resemblance of assembled novel MAGs with traditional organisms used in bioremediation and biomining applications. Microorganisms harboring adaptive mechanisms, such as detoxification, hydroxyl radical scavenging, and heavy metal resistance, could be the potent benefactions for their utility as bioleaching agents. The genetic information produced in the present investigation provides a foundation for pursuing and understanding the molecular aspects of bioleaching and bioremediation applications.}, } @article {pmid36807446, year = {2023}, author = {Bartuv, R and Berihu, M and Medina, S and Salim, S and Feygenberg, O and Faigenboim-Doron, A and Zhimo, VY and Abdelfattah, A and Piombo, E and Wisniewski, M and Freilich, S and Droby, S}, title = {Functional analysis of the apple fruit microbiome based on shotgun metagenomic sequencing of conventional and organic orchard samples.}, journal = {Environmental microbiology}, volume = {25}, number = {9}, pages = {1728-1746}, doi = {10.1111/1462-2920.16353}, pmid = {36807446}, issn = {1462-2920}, mesh = {*Malus ; Fruit ; Phylogeny ; *Ascomycota ; *Microbiota/genetics ; }, abstract = {Fruits harbour abundant and diverse microbial communities that protect them from post-harvest pathogens. Identification of functional traits associated with a given microbiota can provide a better understanding of their potential influence. Here, we focused on the epiphytic microbiome of apple fruit. We suggest that shotgun metagenomic data can indicate specific functions carried out by different groups and provide information on their potential impact. Samples were collected from the surface of 'Golden Delicious' apples from four orchards that differ in their geographic location and management practice. Approximately 1 million metagenes were predicted based on a high-quality assembly. Functional profiling of the microbiome of fruits from orchards differing in their management practice revealed a functional shift in the microbiota. The organic orchard microbiome was enriched in pathways involved in plant defence activities; the conventional orchard microbiome was enriched in pathways related to the synthesis of antibiotics. The functional significance of the variations was explored using microbial network modelling algorithms to reveal the metabolic role of specific phylogenetic groups. The analysis identified several associations supported by other published studies. For example, the analysis revealed the nutritional dependencies of the Capnodiales group, including the Alternaria pathogen, on aromatic compounds.}, } @article {pmid36807409, year = {2023}, author = {Rasmussen, JA and Kiilerich, P and Madhun, AS and Waagbø, R and Lock, ER and Madsen, L and Gilbert, MTP and Kristiansen, K and Limborg, MT}, title = {Co-diversification of an intestinal Mycoplasma and its salmonid host.}, journal = {The ISME journal}, volume = {17}, number = {5}, pages = {682-692}, pmid = {36807409}, issn = {1751-7370}, mesh = {Animals ; *Salmonidae ; Bacteria ; *Gastrointestinal Microbiome ; *Salmo salar ; }, abstract = {Understanding the evolutionary relationships between a host and its intestinal resident bacteria can transform how we understand adaptive phenotypic traits. The interplay between hosts and their resident bacteria inevitably affects the intestinal environment and, thereby, the living conditions of both the host and the microbiota. Thereby this co-existence likely influences the fitness of both bacteria and host. Whether this co-existence leads to evolutionary co-diversification in animals is largely unexplored, mainly due to the complexity of the environment and microbial communities and the often low host selection. We present the gut metagenome from wild Atlantic salmon (Salmo salar), a new wild organism model with an intestinal microbiota of low complexity and a well-described population structure, making it well-suited for investigating co-evolution. Our data reveal a strong host selection of a core gut microbiota dominated by a single Mycoplasma species. We found a clear co-diversification between the population structure of Atlantic salmon and nucleotide variability of the intestinal Mycoplasma populations conforming to expectations from co-evolution between host and resident bacteria. Our results show that the stable microbiota of Atlantic salmon has evolved with its salmonid host populations while potentially providing adaptive traits to the salmon host populations, including defence mechanisms, biosynthesis of essential amino acids, and metabolism of B vitamins. We highlight Atlantic salmon as a novel model for studying co-evolution between vertebrate hosts and their resident bacteria.}, } @article {pmid36807001, year = {2023}, author = {Ghare, U and Narvekar, S and Lodha, T and Mallebhari, R and Dastager, S and Barvkar, VT and Dhotre, D and Karmalkar, NR and Pable, AA}, title = {Bacterial Communities and Diversity of Western Ghats Soil: A Study of a Biodiversity Hotspot.}, journal = {Current microbiology}, volume = {80}, number = {4}, pages = {108}, pmid = {36807001}, issn = {1432-0991}, mesh = {Animals ; *Soil/chemistry ; Soil Microbiology ; India ; Bacteria/genetics ; Biodiversity ; Proteobacteria ; *Actinobacteria/genetics ; RNA, Ribosomal, 16S/metabolism ; }, abstract = {The Western Ghats is one of India's mega-diversity hotspots and an ecologically and geologically important area for the diversity of endemic plants and animals. The present study provides insights into the aerobic bacterial diversity and composition of the soils of North Western Ghats located in Maharashtra state (NWGM), India. The samples for the culture-dependent study were collected from 6 different locations namely Malshej Ghat, Bhimashankar, Lonavala, Mulshi, Tail-Baila, and Mahabaleshwar. A total of 173 isolates were obtained from the different samples, which belonged to Proteobacteria (43%), Firmicutes (36%), and Actinobacteria (19%). Sequences of 15 strains shared ≤ 98.7% similarity (a species cut-off) which represent potential novel species. Metagenomic analysis revealed the presence of Actinobacteria and Proteobacteria as the most dominant phyla at both MB and MG. However, both sites showed variation in the composition of rare phyla and other dominant phyla. This difference in bacterial community composition could be due to differences in altitude or other physicochemical properties. The functional prediction from the amplicon sequencing showed the abundance of carbohydrate, protein, and lipid metabolism which was corroborated by screening the isolated bacterial strains for the same. The present study has a unique take on microbial diversity and defines the importance of community assembly processes such as drift, dispersal, and selection. Such processes are relatively important in controlling community diversity, distribution, as well as succession. This study has shown that the microbial community of NWGM is a rich source of polysaccharide degrading bacteria having biotechnological potential.}, } @article {pmid36806692, year = {2023}, author = {Gurbich, TA and Almeida, A and Beracochea, M and Burdett, T and Burgin, J and Cochrane, G and Raj, S and Richardson, L and Rogers, AB and Sakharova, E and Salazar, GA and Finn, RD}, title = {MGnify Genomes: A Resource for Biome-specific Microbial Genome Catalogues.}, journal = {Journal of molecular biology}, volume = {435}, number = {14}, pages = {168016}, pmid = {36806692}, issn = {1089-8638}, support = {BB/W002965/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R015228/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/V01868X/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/W016184/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Genome, Microbial ; *Metagenome/genetics ; Metagenomics ; }, abstract = {An increasingly common output arising from the analysis of shotgun metagenomic datasets is the generation of metagenome-assembled genomes (MAGs), with tens of thousands of MAGs now described in the literature. However, the discovery and comparison of these MAG collections is hampered by the lack of uniformity in their generation, annotation and storage. To address this, we have developed MGnify Genomes, a growing collection of biome-specific non-redundant microbial genome catalogues generated using MAGs and publicly available isolate genomes. Genomes within a biome-specific catalogue are organised into species clusters. For species that contain multiple conspecific genomes, the highest quality genome is selected as the representative, always prioritising an isolate genome over a MAG. The species representative sequences and annotations can be visualised on the MGnify website and the full catalogue and associated analysis outputs can be downloaded from MGnify servers. A suite of online search tools is provided allowing users to compare their own sequences, ranging from a gene to sets of genomes, against the catalogues. Seven biomes are available currently, comprising over 300,000 genomes that represent 11,048 non-redundant species, and include 36 taxonomic classes not currently represented by cultured genomes. MGnify Genomes is available at https://www.ebi.ac.uk/metagenomics/browse/genomes/.}, } @article {pmid36805803, year = {2023}, author = {Wei, Y and Zhang, T and Ma, Y and Yan, J and Zhan, J and Zheng, J and Xu, Y}, title = {Clinical Evaluation of Metagenomic Next-Generation Sequencing for the detection of pathogens in BALF in severe community acquired pneumonia.}, journal = {Italian journal of pediatrics}, volume = {49}, number = {1}, pages = {25}, pmid = {36805803}, issn = {1824-7288}, support = {Y2020013//General project of Tianjin Children's Hospital/ ; }, mesh = {Male ; Child ; Female ; Humans ; Bronchoalveolar Lavage Fluid ; *Pneumonia ; High-Throughput Nucleotide Sequencing ; Streptococcus pneumoniae ; Anti-Bacterial Agents ; *Community-Acquired Infections/diagnosis ; Mycoplasma pneumoniae ; }, abstract = {BACKGROUND: Rapid and accurate identification of pathogens is very important for the treatment of Severe community-acquired pneumonia (SCAP) in children. Metagenomic Next-generation sequencing (mNGS) has been applied in the detection of pathogenic bacteria in recent years, while the overall evaluation the application of SCAP in children is lacking.

METHODS: In our study, 84 cases of SCAP were enrolled. Bronchoalveolar lavage fluid (BALF) samples were analysed using mNGS; and sputum, blood, and BALF samples were analysed using conventional technology (CT).

RESULTS: Among the 84 children, 41 were boys, and 43 were girls, with an average age ranging from 2 months to 14 years. The pathogen detection rate of mNGS was higher than that of CT (83.3% [70/84] vs. 63.1% [53/84], P = 0.003). The mNGS was much greater than that of the CT in detecting Streptococcus pneumoniae (89.2% [25/29] vs. 44.8% [13/29], P = 0.001) and Haemophilus influenzae (91.7% [11/12] vs. 33.3% [4/12], P < 0.005). The mNGS also showed superior fungal detection performance compared with that of the CT (81.8% [9/11] vs. 18.2% [2/11], P = 0.004). The mNGS test can detect viruses, such as bocavirus, rhinovirus, and human metapneumovirus, which are not frequently recognised using CT. However, the mNGS detection rate was lower than that of the CT (52.4% [11/21] vs. 95.2% [20/21], P = 0.004) for Mycoplasma pneumoniae (MP). The detection rate of mNGS for mixed infection was greater than that of the CT, although statistical significance was not observed (26.3% [20/39] vs. 21.1% [16/39], P > 0.005). Treatment for 26 (31.0%) children was changed based on mNGS results, and their symptoms were reduced; nine patients had their antibiotic modified, five had antibiotics added, nine had their antifungal medication, and seven had their antiviral medication.

CONCLUSION: mNGS has unique advantages in the detection of SCAP pathogens in children, especially S. pneumoniae, H. influenzae, and fungi. However, the detection rate of MP using mNGS was lower than that of the CT. Additionally, mNGS can detect pathogens that are not generally covered by CT, which is extremely important for the modification of the treatment strategy.}, } @article {pmid36805473, year = {2023}, author = {Jia, Y and Liu, ML and López-Pujol, J and Jia, RW and Kou, YX and Yue, M and Guan, TX and Li, ZH}, title = {The hybridization origin of the Chinese endemic herb genus Notopterygium (Apiaceae): Evidence from population genomics and ecological niche analysis.}, journal = {Molecular phylogenetics and evolution}, volume = {182}, number = {}, pages = {107736}, doi = {10.1016/j.ympev.2023.107736}, pmid = {36805473}, issn = {1095-9513}, mesh = {*Apiaceae/genetics ; Bayes Theorem ; Ecosystem ; Metagenomics ; Phylogeny ; *Hybridization, Genetic ; }, abstract = {Hybridization is recognized as a major force in species evolution and biodiversity formation, generally leading to the origin and differentiation of new species. Multiple hybridization events cannot easily be reconstructed, yet they offer the potential to study a number of evolutionary processes. Here, we used nuclear expressed sequence tag-simple sequence repeat and large-scale single nucleotide polymorphism variation data, combined with niche analysis, to investigate the putative independent hybridization events in Notopterygium, a group of perennial herb plants endemic to China. Population genomic analysis indicated that the four studied species are genetically well-delimited and that N. forrestii and N. oviforme have originated by hybridization. According to Approximate Bayesian Computation, the best-fit model involved the formation of N. forrestii from the crossing of N. franchetii and N. incisum, with N. forrestii further backcrossing to N. franchetii to form N. oviforme. The niche analyses indicated that niche divergence [likely triggered by the regional climate changes, particularly the intensification of East Asian winter monsoon, and tectonic movements (affecting both Qinghai-Tibetan Plateau and Qinling Mountains)] may have promoted and maintained the reproductive isolation among hybrid species. N. forrestii shows ecological specialization with respect to their parental species, whereas N. oviforme has completely shifted its niche. These results suggested that the climate and environmental factors together triggered the two-step hybridization of the East Asia herb plants. Our study also emphasizes the power of genome-wide SNPs for investigating suspected cases of hybridization, particularly unravelling old hybridization events.}, } @article {pmid36804804, year = {2023}, author = {Yorki, S and Shea, T and Cuomo, CA and Walker, BJ and LaRocque, RC and Manson, AL and Earl, AM and Worby, CJ}, title = {Comparison of long- and short-read metagenomic assembly for low-abundance species and resistance genes.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {2}, pages = {}, pmid = {36804804}, issn = {1477-4054}, support = {U01 CK000633/CK/NCEZID CDC HHS/United States ; U01 CK000490/CK/NCEZID CDC HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; }, mesh = {*Metagenome ; Sequence Analysis, DNA/methods ; Escherichia coli/genetics ; *Microbiota/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Recent technological and computational advances have made metagenomic assembly a viable approach to achieving high-resolution views of complex microbial communities. In previous benchmarking, short-read (SR) metagenomic assemblers had the highest accuracy, long-read (LR) assemblers generated the most contiguous sequences and hybrid (HY) assemblers balanced length and accuracy. However, no assessments have specifically compared the performance of these assemblers on low-abundance species, which include clinically relevant organisms in the gut. We generated semi-synthetic LR and SR datasets by spiking small and increasing amounts of Escherichia coli isolate reads into fecal metagenomes and, using different assemblers, examined E. coli contigs and the presence of antibiotic resistance genes (ARGs). For ARG assembly, although SR assemblers recovered more ARGs with high accuracy, even at low coverages, LR assemblies allowed for the placement of ARGs within longer, E. coli-specific contigs, thus pinpointing their taxonomic origin. HY assemblies identified resistance genes with high accuracy and had lower contiguity than LR assemblies. Each assembler type's strengths were maintained even when our isolate was spiked in with a competing strain, which fragmented and reduced the accuracy of all assemblies. For strain characterization and determining gene context, LR assembly is optimal, while for base-accurate gene identification, SR assemblers outperform other options. HY assembly offers contiguity and base accuracy, but requires generating data on multiple platforms, and may suffer high misassembly rates when strain diversity exists. Our results highlight the trade-offs associated with each approach for recovering low-abundance taxa, and that the optimal approach is goal-dependent.}, } @article {pmid36804561, year = {2023}, author = {Wang, F and Zhang, Q and Cui, J and Bao, B and Deng, X and Liu, L and Guo, MY}, title = {Polystyrene microplastics induce endoplasmic reticulum stress, apoptosis and inflammation by disrupting the gut microbiota in carp intestines.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {323}, number = {}, pages = {121233}, doi = {10.1016/j.envpol.2023.121233}, pmid = {36804561}, issn = {1873-6424}, mesh = {Animals ; Microplastics/toxicity ; Polystyrenes ; Plastics ; *Gastrointestinal Microbiome ; *Carps ; Intestines ; Inflammation/chemically induced ; Apoptosis ; Endoplasmic Reticulum Stress ; }, abstract = {Microplastics have been recognized as a widespread new pollutant in nature and have induced an increase in the occurrence of a variety of diseases in carp. An animal model of microplastic ingestion was successfully established in an aqueous environment. The gut microbiota was analysed using a metagenomic approach. The results showed a significant reduction in the relative abundances of Lactococcus garvieae, Bacteroides_paurosaccharolyticus, and Romboutsia_ilealis after PS-MPs treatment. The 16S Silva database was used to predict and analyse the known genes. Intestinal flora disorders related to infectious diseases, cancers, neurodegenerative diseases, endocrine and metabolic diseases, cardiovascular diseases, and other diseases were found. The intake of PS-MPs resulted in damage to carp intestinal tissue and apoptosis of intestinal epithelial cells. The levels of the inflammatory cytokines IL-1β, IL-6, and TNF-α were significantly increased with the intake of PS-MPs. The gene and protein levels of GRP78, Caspase-3, Caspase-7, Caspase-9, Caspase-12, PERK, IRE1, and ATF6 were further examined in PS group. The occurrence of ERS and apoptosis in carp intestines was confirmed. These results suggest that the accumulation of PS-MPs in the aquatic environment can disturb the carp gut microbiota and induce ERS, apoptosis, and inflammation in the intestinal tissue.}, } @article {pmid36804496, year = {2023}, author = {Wei, Z and Lai, Y and Li, W and Cui, X and Zhou, D and Zhang, C and Chen, C and Fang, Y}, title = {Accumulation of nitrite after reclaimed water recharge due to the disinfection byproduct chlorite.}, journal = {Chemosphere}, volume = {321}, number = {}, pages = {138119}, doi = {10.1016/j.chemosphere.2023.138119}, pmid = {36804496}, issn = {1879-1298}, mesh = {Nitrites/analysis ; Disinfection ; *Water Pollutants, Chemical/analysis ; *Drinking Water/analysis ; *Water Purification/methods ; Nitrogen/analysis ; Soil ; }, abstract = {Due to its toxicity, the disinfection byproduct chlorite in drinking water is strictly regulated to be ≤ 1.0 mg/L, but in reclaimed, non-drinking water chlorite is unregulated and rarely considered. However, chlorite is cytotoxic and has a high oxidation potential. Therefore, as reclaimed water infiltrates soil and groundwater, it may alter the soil environment and microbial community, which may affect the degradation of organic matter and the transformation of the N element. In this study, the effects of reclaimed water containing chlorite on soil microorganisms were investigated by simulating subsurface infiltration. It was found that chlorite improved the conversion of nitrate nitrogen to nitrite nitrogen, but inhibited further conversion of nitrite nitrogen. The nitrite nitrogen in the effluent reached 4.61 mg/L when chlorite was present, while only 0.16 mg/L was found in the control system. The chlorite produced obvious oxidative stress reactions in cells, inhibited the EPSs production, in which the contents of polysaccharides and proteins reduced by nearly 41% and 62%, respectively. Besides, chlorite resulted in the enrichment of efflux resistance genes in the microbial community, mainly adeF and cmlB1. Self-protection against chlorite is achieved mainly using efflux pump related genes. Metagenomics data analysis showed that Delftia became the dominant genus when exposed to chlorite, with the greatest abundance at 17.9%. Chlorite also resulted in the upregulated expression of nar genes (by more than 149%) and downregulation of nir gene expression (by more than 62%). This study reveals the effects of the disinfection byproduct chlorite on a soil microecosystem, providing important information for the management and reuse of reclaimed water.}, } @article {pmid36804142, year = {2023}, author = {Prosenkov, A and Cagnon, C and Gallego, JLR and Pelaez, AI}, title = {The microbiome of a brownfield highly polluted with mercury and arsenic.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {323}, number = {}, pages = {121305}, doi = {10.1016/j.envpol.2023.121305}, pmid = {36804142}, issn = {1873-6424}, mesh = {*Mercury/analysis ; *Arsenic/analysis ; Soot/analysis ; *Microbiota ; Eukaryota ; Soil/chemistry ; Soil Microbiology ; *Soil Pollutants/analysis ; *Ascomycota ; }, abstract = {Abandoned brownfields represent a challenge for their recovery. To apply sustainable remediation technologies, such as bioremediation or phytoremediation, indigenous microorganisms are essential agents since they are adapted to the ecology of the soil. Better understanding of microbial communities inhabiting those soils, identification of microorganisms that drive detoxification process and recognising their needs and interactions will significantly improve the outcome of the remediation. With this in mind we have carried out a detailed metagenomic analysis to explore the taxonomic and functional diversity of the prokaryotic and eukaryotic microbial communities in soils, several mineralogically distinct types of pyrometallurgic waste, and groundwater sediments of a former mercury mining and metallurgy site which harbour very high levels of arsenic and mercury pollution. Prokaryotic and eukaryotic communities were identified, which turned out to be more diverse in the surrounding contaminated soils compared to the pyrometallurgic waste. The highest diversity loss was observed in two environments most contaminated with mercury and arsenic (stupp, a solid mercury condenser residue and arsenic-rich soot from arsenic condensers). Interestingly, microbial communities in the stupp were dominated by an overwhelming majority of archaea of the phylum Crenarchaeota, while Ascomycota and Basidiomycota fungi comprised the fungal communities of both stump and soot, results that show the impressive ability of these previously unreported microorganisms to colonize these extreme brownfield environments. Functional predictions for mercury and arsenic resistance/detoxification genes show their increase in environments with higher levels of pollution. Our work establishes the bases to design sustainable remediation methods and, equally important, to study in depth the genetic and functional mechanisms that enable the subsistence of microbial populations in these extremely selective environments.}, } @article {pmid36804134, year = {2023}, author = {Li, Z and Rasic, M and Kwan, M and Sepulveda, M and McIntosh, C and Shastry, V and Chen, L and Finn, P and Perkins, D and Alegre, ML}, title = {Oral administration of the commensal Alistipes onderdonkii prolongs allograft survival.}, journal = {American journal of transplantation : official journal of the American Society of Transplantation and the American Society of Transplant Surgeons}, volume = {23}, number = {2}, pages = {272-277}, pmid = {36804134}, issn = {1600-6143}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; T32 AI007090/AI/NIAID NIH HHS/United States ; P01 AI097113/AI/NIAID NIH HHS/United States ; TL1 DK132769/DK/NIDDK NIH HHS/United States ; U01 AI132898/AI/NIAID NIH HHS/United States ; R01 AI115716/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Mice ; Administration, Oral ; Allografts ; Graft Rejection/drug therapy/etiology/prevention & control ; *Graft Survival ; Mice, Inbred BALB C ; Mice, Inbred C57BL ; *Skin Transplantation ; Transplantation, Homologous ; *Bacteroidetes ; *Probiotics/administration & dosage ; }, abstract = {Intestinal commensals can exert immunomodulatory effects on the host, with beneficial or detrimental consequences depending on underlying diseases. We have previously correlated longer survival of minor mismatched skin grafts in mice with the presence of an intestinal commensal bacterium, Alistipes onderdonkii. In this study, we investigated its sufficiency and mechanism of action. Oral administration of A onderdonkii strain DSM19147 but not DSM108265 was sufficient to prolong minor mismatched skin graft survival through inhibition of tumor necrosis factor production. Through metabolomic and metagenomic comparisons between DSM19147 and DSM108265, we identified candidate gene products associated with the anti-inflammatory effect of DSM19147. A onderdonkii DSM19147 can lower inflammation both at a steady state and after transplantation and may serve as an anti-inflammatory probiotic beneficial for transplant recipients.}, } @article {pmid36803508, year = {2023}, author = {Sjödin, KS and Sjödin, A and Ruszczyński, M and Kristensen, MB and Hernell, O and Szajewska, H and West, CE}, title = {Targeting the gut-lung axis by synbiotic feeding to infants in a randomized controlled trial.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {38}, pmid = {36803508}, issn = {1741-7007}, mesh = {Female ; Humans ; Infant ; *Synbiotics ; RNA, Ribosomal, 16S/genetics ; Prebiotics ; *Probiotics ; Lung ; }, abstract = {BACKGROUND: Formula-fed infants are at increased risk of infections. Due to the cross-talk between the mucosal systems of the gastrointestinal and respiratory tracts, adding synbiotics (prebiotics and probiotics) to infant formula may prevent infections even at distant sites. Infants that were born full term and weaned from breast milk were randomized to prebiotic formula (fructo- and galactooligosaccharides) or the same prebiotic formula with Lactobacillus paracasei ssp. paracasei F19 (synbiotics) from 1 to 6 months of age. The objective was to examine the synbiotic effects on gut microbiota development.

RESULTS: Fecal samples collected at ages 1, 4, 6, and 12 months were analyzed using 16S rRNA gene sequencing and a combination of untargeted gas chromatography-mass spectrometry/liquid chromatography-mass spectrometry. These analyses revealed that the synbiotic group had a lower abundance of Klebsiella, a higher abundance of Bifidobacterium breve compared to the prebiotic group, and increases in the anti-microbial metabolite d-3-phenyllactic acid. We also analyzed the fecal metagenome and antibiotic resistome in the 11 infants that had been diagnosed with lower respiratory tract infection (cases) and 11 matched controls using deep metagenomic sequencing. Cases with lower respiratory tract infection had a higher abundance of Klebsiella species and antimicrobial resistance genes related to Klebsiella pneumoniae, compared to controls. The results obtained using 16S rRNA gene amplicon and metagenomic sequencing were confirmed in silico by successful recovery of the metagenome-assembled genomes of the bacteria of interest.

CONCLUSIONS: This study demonstrates the additional benefit of feeding specific synbiotics to formula-fed infants over prebiotics only. Synbiotic feeding led to the underrepresentation of Klebsiella, enrichment of bifidobacteria, and increases in microbial degradation metabolites implicated in immune signaling and in the gut-lung and gut-skin axes. Our findings support future clinical evaluation of synbiotic formula in the prevention of infections and associated antibiotic treatment as a primary outcome when breastfeeding is not feasible.

TRIAL REGISTRATION: ClinicalTrials.gov NCT01625273 . Retrospectively registered on 21 June 2012.}, } @article {pmid36803415, year = {2023}, author = {Liebhoff, AM and Menden, K and Laschtowitz, A and Franke, A and Schramm, C and Bonn, S}, title = {Pathogen detection in RNA-seq data with Pathonoia.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {53}, pmid = {36803415}, issn = {1471-2105}, support = {CRU306 P-C//Deutsche Forschungsgemeinschaft/ ; LFF 78//Forschungs- und Wissenschaftsstiftung Hamburg/ ; }, mesh = {Humans ; RNA-Seq ; *Algorithms ; Sequence Analysis, RNA/methods ; Base Sequence ; *Bacteria/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {BACKGROUND: Bacterial and viral infections may cause or exacerbate various human diseases and to detect microbes in tissue, one method of choice is RNA sequencing. The detection of specific microbes using RNA sequencing offers good sensitivity and specificity, but untargeted approaches suffer from high false positive rates and a lack of sensitivity for lowly abundant organisms.

RESULTS: We introduce Pathonoia, an algorithm that detects viruses and bacteria in RNA sequencing data with high precision and recall. Pathonoia first applies an established k-mer based method for species identification and then aggregates this evidence over all reads in a sample. In addition, we provide an easy-to-use analysis framework that highlights potential microbe-host interactions by correlating the microbial to the host gene expression. Pathonoia outperforms state-of-the-art methods in microbial detection specificity, both on in silico and real datasets.

CONCLUSION: Two case studies in human liver and brain show how Pathonoia can support novel hypotheses on microbial infection exacerbating disease. The Python package for Pathonoia sample analysis and a guided analysis Jupyter notebook for bulk RNAseq datasets are available on GitHub.}, } @article {pmid36803146, year = {2023}, author = {Li, W and Du, J and Yang, L and Liang, Q and Yang, M and Zhou, X and Du, W}, title = {Chromosome-level genome assembly and population genomics of Mongolian racerunner (Eremias argus) provide insights into high-altitude adaptation in lizards.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {40}, pmid = {36803146}, issn = {1741-7007}, support = {XDB31000000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; }, mesh = {Animals ; *Altitude ; Metagenomics ; *Lizards/genetics ; Biological Evolution ; Adaptation, Physiological/genetics ; Chromosomes ; }, abstract = {BACKGROUND: Although the extreme environmental adaptation of organisms is a hot topic in evolutionary biology, genetic adaptation to high-altitude environment remains poorly characterized in ectothermic animals. Squamates are among the most diverse terrestrial vertebrates, with tremendous ecological plasticity and karyotype diversity, and are a unique model system to investigate the genetic footprints of adaptation.

RESULTS: We report the first chromosome-level assembly of the Mongolian racerunner (Eremias argus) and our comparative genomics analyses found that multiple chromosome fissions/fusions events are unique to lizards. We further sequenced the genomes of 61 Mongolian racerunner individuals that were collected from altitudes ranging from ~ 80 to ~ 2600 m above sea level (m.a.s.l.). Population genomic analyses revealed many novel genomic regions under strong selective sweeps in populations endemic to high altitudes. Genes embedded in those genomic regions are mainly associated with energy metabolism and DNA damage repair pathways. Moreover, we identified and validated two substitutions of PHF14 that may enhance the lizards' tolerance to hypoxia at high altitudes.

CONCLUSIONS: Our study reveals the molecular mechanism of high-altitude adaptation in ectothermic animal using lizard as a research subject and provides a high-quality lizard genomic resource for future research.}, } @article {pmid36802428, year = {2023}, author = {Wilson, K and de Rond, T and Burkhardt, I and Steele, TS and Schäfer, RJB and Podell, S and Allen, EE and Moore, BS}, title = {Terpene biosynthesis in marine sponge animals.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {9}, pages = {e2220934120}, pmid = {36802428}, issn = {1091-6490}, support = {F32 GM129960/GM/NIGMS NIH HHS/United States ; R01 ES030316/ES/NIEHS NIH HHS/United States ; R01 GM085770/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Porifera/genetics ; Aquatic Organisms/genetics ; *Microbiota/genetics ; Metagenome ; *Biological Products ; Phylogeny ; }, abstract = {Sea sponges are the largest marine source of small-molecule natural products described to date. Sponge-derived molecules, such as the chemotherapeutic eribulin, the calcium-channel blocker manoalide, and antimalarial compound kalihinol A, are renowned for their impressive medicinal, chemical, and biological properties. Sponges contain microbiomes that control the production of many natural products isolated from these marine invertebrates. In fact, all genomic studies to date investigating the metabolic origins of sponge-derived small molecules concluded that microbes-not the sponge animal host-are the biosynthetic producers. However, early cell-sorting studies suggested the sponge animal host may play a role particularly in the production of terpenoid molecules. To investigate the genetic underpinnings of sponge terpenoid biosynthesis, we sequenced the metagenome and transcriptome of an isonitrile sesquiterpenoid-containing sponge of the order Bubarida. Using bioinformatic searches and biochemical validation, we identified a group of type I terpene synthases (TSs) from this sponge and multiple other species, the first of this enzyme class characterized from the sponge holobiome. The Bubarida TS-associated contigs consist of intron-containing genes homologous to sponge genes and feature GC percentage and coverage consistent with other eukaryotic sequences. We identified and characterized TS homologs from five different sponge species isolated from geographically distant locations, thereby suggesting a broad distribution amongst sponges. This work sheds light on the role of sponges in secondary metabolite production and speaks to the possibility that other sponge-specific molecules originate from the animal host.}, } @article {pmid36802161, year = {2023}, author = {Liu, H and Cai, X and Luo, K and Chen, S and Su, M and Lu, J}, title = {Microbial Diversity, Community Turnover, and Putative Functions in Submarine Canyon Sediments under the Action of Sedimentary Geology.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0421022}, pmid = {36802161}, issn = {2165-0497}, abstract = {Sampling challenges in deep-sea ecosystems lead to a lack of knowledge about the distribution of microbes in different submarine canyons. To study microbial diversity and community turnover under different ecological processes, we performed 16S/18S rRNA gene amplicon sequencing for sediment samples from a submarine canyon in the South China Sea. Bacteria, archaea, and eukaryotes made up 57.94% (62 phyla), 41.04% (12 phyla), and 1.02% (4 phyla) of the sequences, respectively. Thaumarchaeota, Planctomycetota, Proteobacteria, Nanoarchaeota, and Patescibacteria are the five most abundant phyla. Heterogeneous community composition was mainly observed in vertical profiles rather than horizontal geographic locations, and microbial diversity in the surface layer was much lower than that in deep layers. According to the null model tests, homogeneous selection dominated community assembly within each sediment layer, whereas heterogeneous selection and dispersal limitation dominated community assembly between distant layers. Different sedimentation processes of sediments, i.e., rapid deposition caused by turbidity currents or slow sedimentation, seem to be primarily responsible for these vertical variations. Finally, functional annotation through shotgun-metagenomic sequencing found that glycosyl transferases and glycoside hydrolases are the most abundant carbohydrate-active enzyme categories. The most likely expressed sulfur cycling pathways include assimilatory sulfate reduction, the link between inorganic and organic sulfur transformation, and organic sulfur transformation, while the potentially activated methane cycling pathways include aceticlastic methanogenesis and aerobic and anaerobic oxidation of methane. Overall, our study revealed high levels of microbial diversity and putative functions in canyon sediments and the important influence of sedimentary geology on microbial community turnover between vertical sediment layers. IMPORTANCE Deep-sea microbes have received growing attention due to their contribution to biogeochemical cycles and climate change. However, related research lags due to the difficulty of collecting samples. Based on our previous study, which revealed the formation of sediments under the dual action of turbidity currents and seafloor obstacles in a submarine canyon in the South China Sea, this interdisciplinary research provides new insights into how sedimentary geology influences microbial community assembly in sediments. We proposed some uncommon or new findings, including the following: (i) microbial diversity was much lower on the surface than in deeper layers (ii) archaea and bacteria dominated the surface and deep layers, respectively; (iii) sedimentary geology played key roles in vertical community turnover; and (iv) the microbes have great potential to catalyze sulfur, carbon, and methane cycling. This study may lead to extensive discussion of the assembly and function of deep-sea microbial communities in the context of geology.}, } @article {pmid36801973, year = {2023}, author = {Morgan-Lang, C and Hallam, SJ}, title = {A Guide to Gene-Centric Analysis Using TreeSAPP.}, journal = {Current protocols}, volume = {3}, number = {2}, pages = {e671}, doi = {10.1002/cpz1.671}, pmid = {36801973}, issn = {2691-1299}, support = {//Natural Sciences and Engineering Research Council/ ; //Genome Canada/ ; //Genome British Columbia/ ; //the Digital Research Alliance of Canada/ ; //the G. Unger Vetlesen and Ambrose Monell Foundations/ ; //the U.S. Department of Energy (DOE) Joint Genome Institute (JGI)/ ; //and the Facilities Integrating Collaborations for User Science (FICUS)/ ; }, mesh = {*Software ; Phylogeny ; *Algorithms ; Metagenomics/methods ; Sequence Alignment ; }, abstract = {Gene-centric analysis is commonly used to chart the structure, function, and activity of microbial communities in natural and engineered environments. A common approach is to create custom ad hoc reference marker gene sets, but these come with the typical disadvantages of inaccuracy and limited utility beyond assigning query sequences taxonomic labels. The Tree-based Sensitive and Accurate Phylogenetic Profiler (TreeSAPP) software package standardizes analysis of phylogenetic and functional marker genes and improves predictive performance using a classification algorithm that leverages information-rich reference packages consisting of a multiple sequence alignment, a profile hidden Markov model, taxonomic lineage information, and a phylogenetic tree. Here, we provide a set of protocols that link the various analysis modules in TreeSAPP into a coherent process that both informs and directs the user experience. This workflow, initiated from a collection of candidate reference sequences, progresses through construction and refinement of a reference package to marker identification and normalized relative abundance calculations for homologous sequences in metagenomic and metatranscriptomic datasets. The alpha subunit of methyl-coenzyme M reductase (McrA) involved in biological methane cycling is presented as a use case given its dual role as a phylogenetic and functional marker gene driving an ecologically relevant process. These protocols fill several gaps in prior TreeSAPP documentation and provide best practices for reference package construction and refinement, including manual curation steps from trusted sources in support of reproducible gene-centric analysis. © 2023 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Creating reference packages Support Protocol 1: Installing TreeSAPP Support Protocol 2: Annotating traits within a phylogenetic context Basic Protocol 2: Updating reference packages Basic Protocol 3: Calculating relative abundance of genes in metagenomic and metatranscriptomic datasets.}, } @article {pmid36801799, year = {2023}, author = {Li, J and Lu, H and Yang, H and Wen, X and Huang, Y and Li, Q}, title = {Performances of antibiotic resistance genes profile upon the action of biochar-activated peroxydisulfate in composting.}, journal = {Journal of environmental management}, volume = {334}, number = {}, pages = {117509}, doi = {10.1016/j.jenvman.2023.117509}, pmid = {36801799}, issn = {1095-8630}, mesh = {*Genes, Bacterial ; *Composting/methods ; Anti-Bacterial Agents/pharmacology ; Manure/microbiology ; Drug Resistance, Microbial/genetics ; }, abstract = {In this study, the amendment of biochar-activated peroxydisulfate during composting to remove antibiotic resistance genes (ARGs) by direct (microbial community succession) and indirect methods (physicochemical factors) was analyzed. When implementing indirect methods, the synergistic effect of peroxydisulfate with biochar optimized the physicochemical habitat of compost, maintaining its moisture within a range of 62.95%-65.71%, and a pH of 6.87-7.73, and causing the compost to mature 18 days earlier than the control groups. The direct methods caused the optimized physicochemical habitat to adjust the microbial communities and reduce the abundance of most of the ARG host bacteria (Thermopolyspora, Thermobifida, and Saccharomonospora), thus inhibiting this substance's amplification. Heatmap analysis confirmed the necessary connection between physicochemical factors, microbial communities, and ARGs. Moreover, a mantel test confirmed the direct significant effect of the microbial communities on ARGs and the indirect significant effect of physicochemical factors on ARGs. The results showed that the abundance of more ARGs was down-regulated at the end of composting and regulated by biochar-activated peroxydisulfate, especially for the abundance of AbaF, tet(44), golS, and mryA, which was significantly decreased by 0.87-1.07 fold. These results provide new insights into the removal of ARGs during composting.}, } @article {pmid36801683, year = {2023}, author = {Yan, M and Tian, H and Song, S and Tan, HTW and Lee, JTE and Zhang, J and Sharma, P and Tiong, YW and Tong, YW}, title = {Effects of digestate-encapsulated biochar on plant growth, soil microbiome and nitrogen leaching.}, journal = {Journal of environmental management}, volume = {334}, number = {}, pages = {117481}, doi = {10.1016/j.jenvman.2023.117481}, pmid = {36801683}, issn = {1095-8630}, mesh = {Soil/chemistry ; Fertilizers/analysis ; Food ; Nitrogen/analysis ; *Refuse Disposal ; Charcoal/chemistry ; Minerals ; *Microbiota ; }, abstract = {The increasing amount of food waste and the excessive use of mineral fertilizers have caused detrimental impacts on soil, water, and air quality. Though digestate derived from food waste has been reported to partially replace fertilizer, its efficiency requires further improvement. In this study, the effects of digestate-encapsulated biochar were comprehensively investigated based on growth of an ornamental plant, soil characteristics, nutrient leaching and soil microbiome. Results showed that except for biochar, the tested fertilizers and soil additives, i.e., digestate, compost, commercial fertilizer, digestate-encapsulated biochar had positive effects on plants. Especially, the digestate-encapsulated biochar had the best effectiveness as evidenced by 9-25% increase in chlorophyll content index, fresh weight, leaf area and blossom frequency. For the effects of fertilizers or soil additives on soil characteristics and nutrient retention, the digestate-encapsulated biochar leached least N-nutrients (<8%), while the compost, digestate and mineral fertilizer leached up to 25% N-nutrients. All the treatments had minimal effects on the soil properties of pH and electrical conductivity. According to the microbial analysis, the digestate-encapsulated biochar has the comparable role with compost in improving the soil immune system against pathogen infection. The metagenomics coupling with qPCR analysis suggested that digestate-encapsulated biochar boosted the nitrification process and inhibited the denitrification process. This study provides an extensive understanding into the impacts of the digestate-encapsulated biochar on an ornamental plant and offers practical implications for the choice of sustainable fertilizers or soil additives and food-waste digestate management.}, } @article {pmid36801632, year = {2023}, author = {Wang, L and Liu, J and Yang, H and Peng, L}, title = {Diffuse cystic lung disease caused by tuberculosis infection: Case series.}, journal = {Journal of infection and public health}, volume = {16}, number = {4}, pages = {526-530}, doi = {10.1016/j.jiph.2023.02.013}, pmid = {36801632}, issn = {1876-035X}, mesh = {Humans ; Female ; Middle Aged ; *Lung Diseases ; Lung/diagnostic imaging/pathology ; *Histiocytosis, Langerhans-Cell/diagnosis/pathology ; *Tuberculosis ; *Latent Tuberculosis ; Dyspnea ; *Cysts/pathology ; }, abstract = {Diffuse cystic lung disease (DCLD) is a complex disease that can be caused by various reasons. Although the chest CT scan plays a vital role in suggesting the etiology of DCLD, it is apt to lead to misdiagnosis simply based on the CT image of the lung. Here, we report a rare case of DCLD caused by tuberculosis and misdiagnosed as pulmonary Langerhans cell histiocytosis (PLCH). A 60-year-old female DCLD patient with a long-term smoking history was admitted to the hospital because of a dry cough and dyspnea, and the chest CT scan showed diffuse irregular cysts in both lungs. We considered the patient to be PLCH. To alleviate dyspnea, we chose to give her intravenous glucocorticoids. However, she developed a high fever during the use of glucocorticoids. We performed flexible bronchoscopy and bronchoalveolar lavage. Mycobacterium tuberculosis (specific sequence reads: 30) was detected in BALF. She was finally diagnosed with pulmonary tuberculosis. Tuberculosis infection is one of the rare causes of DCLD. We have discovered thirteen similar cases by searching Pubmed and Web of Science. For DCLD patients, glucocorticoids should not be used blindly unless the existence of a tuberculosis infection is ruled out. TBLB for pathology and bronchoalveolar lavage fluid (BALF) for microbiological detection are helpful for diagnosis.}, } @article {pmid36801373, year = {2023}, author = {Spaulding, F and McLaughlin, JF and Cheek, RG and McCracken, KG and Glenn, TC and Winker, K}, title = {Population genomics indicate three different modes of divergence and speciation with gene flow in the green-winged teal duck complex.}, journal = {Molecular phylogenetics and evolution}, volume = {182}, number = {}, pages = {107733}, pmid = {36801373}, issn = {1095-9513}, support = {P20 GM103395/GM/NIGMS NIH HHS/United States ; RL5 GM118990/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Animals ; *Ducks/genetics ; *Gene Flow ; Phylogeny ; Metagenomics ; DNA, Mitochondrial/genetics ; }, abstract = {The processes leading to divergence and speciation can differ broadly among taxa with different life histories. We examine these processes in a small clade of ducks with historically uncertain relationships and species limits. The green-winged teal (Anas crecca) complex is a Holarctic species of dabbling duck currently categorized as three subspecies (Anas crecca crecca, A. c. nimia, and A. c. carolinensis) with a close relative, the yellow-billed teal (Anas flavirostris) from South America. A. c. crecca and A. c. carolinensis are seasonal migrants, while the other taxa are sedentary. We examined divergence and speciation patterns in this group, determining their phylogenetic relationships and the presence and levels of gene flow among lineages using both mitochondrial and genome-wide nuclear DNA obtained from 1,393 ultraconserved element (UCE) loci. Phylogenetic relationships using nuclear DNA among these taxa showed A. c. crecca, A. c. nimia, and A. c. carolinensis clustering together to form one polytomous clade, with A. flavirostris sister to this clade. This relationship can be summarized as (crecca, nimia, carolinensis)(flavirostris). However, whole mitogenomes revealed a different phylogeny: (crecca, nimia)(carolinensis, flavirostris). The best demographic model for key pairwise comparisons supported divergence with gene flow as the probable speciation mechanism in all three contrasts (crecca-nimia, crecca-carolinensis, and carolinensis-flavirostris). Given prior work, gene flow was expected among the Holarctic taxa, but gene flow between North American carolinensis and South American flavirostris (M ∼0.1-0.4 individuals/generation), albeit low, was not expected. Three geographically oriented modes of divergence are likely involved in the diversification of this complex: heteropatric (crecca-nimia), parapatric (crecca-carolinensis), and (mostly) allopatric (carolinensis-flavirostris). Our study shows that ultraconserved elements are a powerful tool for simultaneously studying systematics and population genomics in systems with historically uncertain relationships and species limits.}, } @article {pmid36801350, year = {2023}, author = {Sammouri, J and Wong, MC and Lynn, EJ and El Alam, MB and Lo, DK and Lin, D and Harris, TH and Karpinets, TV and Court, K and Napravnik, TC and Wu, X and Zhang, J and Klopp, AH and Ajami, NJ and Colbert, LE}, title = {Serial Genotyping of the Human Papillomavirus in Cervical Cancer: An Insight Into Virome Dynamics During Chemoradiation Therapy.}, journal = {International journal of radiation oncology, biology, physics}, volume = {116}, number = {5}, pages = {1043-1054}, doi = {10.1016/j.ijrobp.2023.02.018}, pmid = {36801350}, issn = {1879-355X}, mesh = {Humans ; Female ; *Uterine Cervical Neoplasms/pathology ; Human Papillomavirus Viruses ; *Papillomavirus Infections/complications ; Prospective Studies ; Genotype ; Virome ; Papillomaviridae/genetics ; DNA, Viral/analysis ; }, abstract = {PURPOSE: Human papillomavirus (HPV) is the primary driver of cervical cancer. Although studies in other malignancies correlated peripheral blood DNA clearance with favorable outcomes, research on the prognostic value of HPV clearance in gynecologic cancers using intratumoral HPV is scarce. We aimed to quantify the intratumoral HPV virome in patients undergoing chemoradiation therapy (CRT) and associate this with clinical characteristics and outcomes.

METHODS AND MATERIALS: This prospective study enrolled 79 patients with stage IB-IVB cervical cancer undergoing definitive CRT. Cervical tumor swabs collected at baseline and week 5 (end of intensity modulated radiation therapy) were sent for shotgun metagenome sequencing and processed via VirMAP, a viral genome sequencing and identification tool for all known HPV types. The data were categorized into HPV groups (16, 18, high risk [HR], and low risk [LR]). We used independent t tests and Wilcoxon signed-rank to compare continuous variables and χ[2] and Fisher exact tests to compare categorical variables. Kaplan-Meier survival modeling was performed with log-rank testing. HPV genotyping was verified using quantitative polymerase chain reaction to validate VirMAP results using receiver operating characteristic curve and Cohen's kappa.

RESULTS: At baseline, 42%, 12%, 25%, and 16% of patients were positive for HPV 16, HPV 18, HPV HR, and HPV LR, respectively, and 8% were HPV negative. HPV type was associated with insurance status and CRT response. Patients with HPV 16+ and other HPV HR+ tumors were significantly more likely to have a complete response to CRT versus patients with HPV 18 and HPV LR/HPV-negative tumors. Overall HPV viral loads predominantly decreased throughout CRT, except for HPV LR viral load.

CONCLUSIONS: Rarer, less well-studied HPV types in cervical tumors are clinically significant. HPV 18 and HPV LR/negative tumors are associated with poor CRT response. This feasibility study provides a framework for a larger study of intratumoral HPV profiling to predict outcomes in patients with cervical cancer.}, } @article {pmid36801324, year = {2023}, author = {Li, T and Yu, X and Li, M and Rong, L and Xiao, X and Zou, X}, title = {Ecological insight into antibiotic resistome of ion-adsorption rare earth mining soils from south China by metagenomic analysis.}, journal = {The Science of the total environment}, volume = {872}, number = {}, pages = {162265}, doi = {10.1016/j.scitotenv.2023.162265}, pmid = {36801324}, issn = {1879-1026}, mesh = {*Soil ; Anti-Bacterial Agents ; Adsorption ; Ecosystem ; Genes, Bacterial ; Tetracycline/analysis ; China ; *Metals, Rare Earth/analysis ; Mining ; }, abstract = {Antibiotic resistome has led to growing global threat to public health. Rare earth elements play important roles in modern society and mining activity for them has caused serious impact on soil ecosystems. However, antibiotic resistome in, especially, ion-adsorption rare earth-related soils is still poorly understood. In this work, soils were collected from ion-adsorption rare earth mining areas and adjacent regions of south China and metagenomic analysis was employed for profile, driving factors and ecological assembly of antibiotic resistome in the soils. Results show prevalence of antibiotic resistance genes conferring resistance to tetracycline/fluoroquinolone (adeF), peptide (bcrA), aminoglycoside (rpsL), tetracycline (tet(A)) and mupirocin (mupB) in ion-adsorption rare earth mining soils. Profile of antibiotic resistome is accompanied by its driving factors, i.e., physicochemical properties (La, Ce, Pr, Nd and Y of rare earth elements in 12.50-487.90 mg kg[-1]), taxonomy (Proteobacteria, Actinobacteria) and mobile genetic elements (MGEs, plasmid pYP1, Transposase_20). Variation partitioning analysis and partial least-squares-path modeling demonstrate that taxonomy is the most important individual contributor and pose most direct/indirect effect to antibiotic resistome. Further, null model analysis reveals stochastic processes as dominant ecological assembly of antibiotic resistome. This work advances our knowledge on antibiotic resistome with emphasis on ecological assembly in ion-adsorption rare earth-related soils for ARGs mitigation, mining management and mine restoration.}, } @article {pmid36801274, year = {2023}, author = {Kumar, V and Lakkaboyana, SK and Tsouko, E and Maina, S and Pandey, M and Umesh, M and Singhal, B and Sharma, N and Awasthi, MK and Andler, R and Jayaraj, I and Yuzir, A}, title = {Commercialization potential of agro-based polyhydroxyalkanoates biorefinery: A technical perspective on advances and critical barriers.}, journal = {International journal of biological macromolecules}, volume = {234}, number = {}, pages = {123733}, doi = {10.1016/j.ijbiomac.2023.123733}, pmid = {36801274}, issn = {1879-0003}, mesh = {*Polyhydroxyalkanoates ; Ecosystem ; Biopolymers/chemistry ; Plastics ; *Petroleum ; }, abstract = {The exponential increase in the use and careless discard of synthetic plastics has created an alarming concern over the environmental health due to the detrimental effects of petroleum based synthetic polymeric compounds. Piling up of these plastic commodities on various ecological niches and entry of their fragmented parts into soil and water has clearly affected the quality of these ecosystems in the past few decades. Among the many constructive strategies developed to tackle this global issue, use of biopolymers like polyhydroxyalkanoates as sustainable alternatives for synthetic plastics has gained momentum. Despite their excellent material properties and significant biodegradability, polyhydroxyalkanoates still fails to compete with their synthetic counterparts majorly due to the high cost associated with their production and purification thereby limiting their commercialization. Usage of renewable feedstocks as substrates for polyhydroxyalkanoates production has been the thrust area of research to attain the sustainability tag. This review work attempts to provide insights about the recent developments in the production of polyhydroxyalkanoates using renewable feedstock along with various pretreatment methods used for substrate preparation for polyhydroxyalkanoates production. Further, the application of blends based on polyhydroxyalkanoates, and the challenges associated with the waste valorization based polyhydroxyalkanoates production strategy is elaborated in this review work.}, } @article {pmid36801028, year = {2023}, author = {Yang, H and Xu, M and Wang, L and Wang, X and Jeppesen, E and Zhang, W}, title = {Metagenomic analysis to determine the characteristics of antibiotic resistance genes in typical antibiotic-contaminated sediments.}, journal = {Journal of environmental sciences (China)}, volume = {128}, number = {}, pages = {12-25}, doi = {10.1016/j.jes.2022.08.014}, pmid = {36801028}, issn = {1001-0742}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; China ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; }, abstract = {Comprehensive studies of the effects of various physical and chemical variables (including heavy metals), antibiotics, and microorganisms in the environment on antibiotic resistance genes are rare. We collected sediment samples from the Shatian Lake aquaculture area and surrounding lakes and rivers located in Shanghai, China. The spatial distribution of sediment ARGs was assessed by metagenomic analysis that revealed 26 ARG types (510 subtypes), dominated by Multidrug, β-lactam, Aminoglycoside, Glycopeptides, Fluoroquinolone, and Tetracyline. Redundancy discriminant analysis indicated that antibiotics (SAs and MLs) in the aqueous environment and sediment along with water TN and TP were the key variables affecting the abundance distribution of total ARGs. However, the main environmental drivers and key influences differed among the different ARGs. For total ARGs, the environmental subtypes affecting their structural composition and distribution characteristics were mainly antibiotic residues. Procrustes analysis showed a significant correlation between ARGs and microbial communities in the sediment in the survey area. Network analysis revealed that most of the target ARGs were significantly and positively correlated with microorganisms, and a small number of ARGs (e.g., rpoB, mdtC, and efpA) were highly significantly and positively correlated with microorganisms (e.g., Knoellia, Tetrasphaera, and Gemmatirosa). Potential hosts for the major ARGs included Actinobacteria, Proteobacteria, and Gemmatimonadetes. Our study provides new insight and a comprehensive assessment of the distribution and abundance of ARGs and the drivers of ARG occurrence and transmission.}, } @article {pmid36800400, year = {2023}, author = {Xing, Y and Clark, JR and Chang, JD and Chirman, DM and Green, S and Zulk, JJ and Jelinski, J and Patras, KA and Maresso, AW}, title = {Broad protective vaccination against systemic Escherichia coli with autotransporter antigens.}, journal = {PLoS pathogens}, volume = {19}, number = {2}, pages = {e1011082}, pmid = {36800400}, issn = {1553-7374}, support = {U19 AI157981/AI/NIAID NIH HHS/United States ; U19 AI144297/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Humans ; Mice ; Escherichia coli ; Type V Secretion Systems/genetics ; *Escherichia coli Infections/prevention & control ; *Extraintestinal Pathogenic Escherichia coli/genetics ; Vaccination ; Virulence Factors/genetics ; Vaccines, Synthetic ; *Urinary Tract Infections/prevention & control ; *Bacteremia/prevention & control ; Immunoglobulin G/pharmacology ; }, abstract = {Extraintestinal pathogenic Escherichia coli (ExPEC) is the leading cause of adult life-threatening sepsis and urinary tract infections (UTI). The emergence and spread of multidrug-resistant (MDR) ExPEC strains result in a considerable amount of treatment failure and hospitalization costs, and contribute to the spread of drug resistance amongst the human microbiome. Thus, an effective vaccine against ExPEC would reduce morbidity and mortality and possibly decrease carriage in healthy or diseased populations. A comparative genomic analysis demonstrated a gene encoding an invasin-like protein, termed sinH, annotated as an autotransporter protein, shows high prevalence in various invasive ExPEC phylogroups, especially those associated with systemic bacteremia and UTI. Here, we evaluated the protective efficacy and immunogenicity of a recombinant SinH-based vaccine consisting of either domain-3 or domains-1,2, and 3 of the putative extracellular region of surface-localized SinH. Immunization of a murine host with SinH-based antigens elicited significant protection against various strains of the pandemic ExPEC sequence type 131 (ST131) as well as multiple sequence types in two distinct models of infection (colonization and bacteremia). SinH immunization also provided significant protection against ExPEC colonization in the bladder in an acute UTI model. Immunized cohorts produced significantly higher levels of vaccine-specific serum IgG and urinary IgG and IgA, findings consistent with mucosal protection. Collectively, these results demonstrate that autotransporter antigens such as SinH may constitute promising ExPEC phylogroup-specific and sequence-type effective vaccine targets that reduce E. coli colonization and virulence.}, } @article {pmid36799935, year = {2023}, author = {Cao, L and Dai, Z and Tan, H and Zheng, H and Wang, Y and Chen, J and Kuang, H and Chong, RA and Han, M and Hu, F and Sun, W and Sun, C and Zhang, Z}, title = {Population Structure, Demographic History, and Adaptation of Giant Honeybees in China Revealed by Population Genomic Data.}, journal = {Genome biology and evolution}, volume = {15}, number = {3}, pages = {}, pmid = {36799935}, issn = {1759-6653}, mesh = {Bees/genetics ; Animals ; Humans ; Phylogeny ; *Metagenomics ; *Adaptation, Physiological/genetics ; China ; Demography ; }, abstract = {There have been many population-based genomic studies on human-managed honeybees (Apis mellifera and Apis cerana), but there has been a notable lack of analysis with regard to wild honeybees, particularly in relation to their evolutionary history. Nevertheless, giant honeybees have been found to occupy distinct habitats and display remarkable characteristics, which are attracting an increased amount of attention. In this study, we de novo sequenced and then assembled the draft genome sequence of the Himalayan giant honeybee, Apis laboriosa. Phylogenetic analysis based on genomic information indicated that A. laboriosa and its tropical sister species Apis dorsata diverged ∼2.61 Ma, which supports the speciation hypothesis that links A. laboriosa to geological changes throughout history. Furthermore, we re-sequenced A. laboriosa and A. dorsata samples from five and six regions, respectively, across their population ranges in China. These analyses highlighted major genetic differences for Tibetan A. laboriosa as well as the Hainan Island A. dorsata. The demographic history of most giant honeybee populations has mirrored glacial cycles. More importantly, contrary to what has occurred among human-managed honeybees, the demographic history of these two wild honeybee species indicates a rapid decline in effective population size in the recent past, reflecting their differences in evolutionary histories. Several genes were found to be subject to selection, which may help giant honeybees to adapt to specific local conditions. In summary, our study sheds light on the evolutionary and adaptational characteristics of two wild giant honeybee species, which was useful for giant honeybee conservation.}, } @article {pmid36799744, year = {2023}, author = {Rigou, S and Legendre, M}, title = {[Prehistoric giant viruses identified by metagenomics].}, journal = {Medecine sciences : M/S}, volume = {39}, number = {2}, pages = {107-109}, doi = {10.1051/medsci/2023006}, pmid = {36799744}, issn = {1958-5381}, mesh = {Humans ; *Giant Viruses/genetics ; Metagenomics ; Phylogeny ; Genome, Viral ; }, } @article {pmid36799472, year = {2023}, author = {Renall, N and Lawley, B and Vatanen, T and Merz, B and Douwes, J and Corbin, M and Te Morenga, L and Kruger, R and Breier, BH and Tannock, GW}, title = {The fecal microbiotas of women of Pacific and New Zealand European ethnicities are characterized by distinctive enterotypes that reflect dietary intakes and fecal water content.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2178801}, pmid = {36799472}, issn = {1949-0984}, mesh = {Humans ; Female ; Ethnicity ; *Diabetes Mellitus, Type 2 ; New Zealand ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Microbiota ; Obesity ; Eating ; }, abstract = {Obesity is a complex, multifactorial condition that is an important risk factor for noncommunicable diseases including cardiovascular disease and type 2 diabetes. While prevention and management require a healthy and energy balanced diet and adequate physical activity, the taxonomic composition and functional attributes of the colonic microbiota may have a supplementary role in the development of obesity. The taxonomic composition and metabolic capacity of the fecal microbiota of 286 women, resident in Auckland New Zealand, was determined by metagenomic analysis. Associations with BMI (obese, nonobese), body fat composition, and ethnicity (Pacific, n = 125; NZ European women [NZE], n = 161) were assessed using regression analyses. The fecal microbiotas were characterized by the presence of three distinctive enterotypes, with enterotype 1 represented in both Pacific and NZE women (39 and 61%, respectively), enterotype 2 mainly in Pacific women (84 and 16%) and enterotype 3 mainly in NZE women (13 and 87%). Enterotype 1 was characterized mainly by the relative abundances of butyrate producing species, Eubacterium rectale and Faecalibacterium prausnitzii, enterotype 2 by the relative abundances of lactic acid producing species, Bifidobacterium adolescentis, Bifidobacterium bifidum, and Lactobacillus ruminis, and enterotype 3 by the relative abundances of Subdoligranulum sp., Akkermansia muciniphila, Ruminococcus bromii, and Methanobrevibacter smithii. Enterotypes were also associated with BMI, visceral fat %, and blood cholesterol. Habitual food group intake was estimated using a 5 day nonconsecutive estimated food record and a 30 day, 220 item semi-quantitative Food Frequency Questionnaire. Higher intake of 'egg' and 'dairy' products was associated with enterotype 3, whereas 'non-starchy vegetables', 'nuts and seeds' and 'plant-based fats' were positively associated with enterotype 1. In contrast, these same food groups were inversely associated with enterotype 2. Fecal water content, as a proxy for stool consistency/colonic transit time, was associated with microbiota taxonomic composition and gene pools reflective of particular bacterial biochemical pathways. The fecal microbiotas of women of Pacific and New Zealand European ethnicities are characterized by distinctive enterotypes, most likely due to differential dietary intake and fecal consistency/colonic transit time. These parameters need to be considered in future analyses of human fecal microbiotas.}, } @article {pmid36799223, year = {2023}, author = {Myserlis, EP and Georgakis, MK and Demel, SL and Sekar, P and Chung, J and Malik, R and Hyacinth, HI and Comeau, ME and Falcone, GJ and Langefeld, CD and Rosand, J and Woo, D and Anderson, CD}, title = {A Genomic Risk Score Identifies Individuals at High Risk for Intracerebral Hemorrhage.}, journal = {Stroke}, volume = {54}, number = {4}, pages = {973-982}, pmid = {36799223}, issn = {1524-4628}, support = {P30 AG021342/AG/NIA NIH HHS/United States ; L60 MD013112/MD/NIMHD NIH HHS/United States ; K76 AG059992/AG/NIA NIH HHS/United States ; R03 NS112859/NS/NINDS NIH HHS/United States ; R01 AG072592/AG/NIA NIH HHS/United States ; R01 NS103924/NS/NINDS NIH HHS/United States ; U01 NS069763/NS/NINDS NIH HHS/United States ; }, mesh = {Humans ; *Genome-Wide Association Study ; *Fibrinolytic Agents ; Risk Factors ; Cerebral Hemorrhage/epidemiology/genetics ; Genomics ; }, abstract = {BACKGROUND: Intracerebral hemorrhage (ICH) has an estimated heritability of 29%. We developed a genomic risk score for ICH and determined its predictive power in comparison to standard clinical risk factors.

METHODS: We combined genome-wide association data from individuals of European ancestry for ICH and related traits in a meta-genomic risk score ([metaGRS]; 2.6 million variants). We tested associations with ICH and its predictive performance in addition to clinical risk factors in a held-out validation dataset (842 cases and 796 controls). We tested associations with risk of incident ICH in the population-based UK Biobank cohort (486 784 individuals, 1526 events, median follow-up 11.3 years).

RESULTS: One SD increment in the metaGRS was significantly associated with 31% higher odds for ICH (95% CI, 1.16-1.48) in age-, sex- and clinical risk factor-adjusted models. The metaGRS identified individuals with almost 5-fold higher odds for ICH in the top score percentile (odds ratio, 4.83 [95% CI, 1.56-21.2]). Predictive models for ICH incorporating the metaGRS in addition to clinical predictors showed superior performance compared to the clinical risk factors alone (c-index, 0.695 versus 0.686). The metaGRS showed similar associations for lobar and nonlobar ICH, independent of the known APOE risk locus for lobar ICH. In the UK Biobank, the metaGRS was associated with higher risk of incident ICH (hazard ratio, 1.15 [95% CI, 1.09-1.21]). The associations were significant within both a relatively high-risk population of antithrombotic medications users, as well as among a relatively low-risk population with a good control of vascular risk factors and no use of anticoagulants.

CONCLUSIONS: We developed and validated a genomic risk score that predicts lifetime risk of ICH beyond established clinical risk factors among individuals of European ancestry. Whether implementation of the score in risk prognostication models for high-risk populations, such as patients under antithrombotic treatment, could improve clinical decision making should be explored in future studies.}, } @article {pmid36799010, year = {2023}, author = {He, S and Linz, AM and Stevens, SLR and Tran, PQ and Moya-Flores, F and Oyserman, BO and Dwulit-Smith, JR and Forest, KT and McMahon, KD}, title = {Diversity, distribution, and expression of opsin genes in freshwater lakes.}, journal = {Molecular ecology}, volume = {32}, number = {11}, pages = {2798-2817}, doi = {10.1111/mec.16891}, pmid = {36799010}, issn = {1365-294X}, mesh = {*Lakes/microbiology ; *Opsins/genetics ; Rhodopsin/genetics ; Bacteria/genetics ; Water ; }, abstract = {Microbial rhodopsins are widely distributed in aquatic environments and may significantly contribute to phototrophy and energy budgets in global oceans. However, the study of freshwater rhodopsins has been largely limited. Here, we explored the diversity, ecological distribution, and expression of opsin genes that encode the apoproteins of type I rhodopsins in humic and clearwater lakes with contrasting physicochemical and optical characteristics. Using metagenomes and metagenome-assembled genomes, we recovered opsin genes from a wide range of taxa, mostly predicted to encode green light-absorbing proton pumps. Viral opsin and novel bacterial opsin clades were recovered. Opsin genes occurred more frequently in taxa from clearwater than from humic water, and opsins in some taxa have nontypical ion-pumping motifs that might be associated with physicochemical conditions of these two freshwater types. Analyses of the surface layer of 33 freshwater systems revealed an inverse correlation between opsin gene abundance and lake dissolved organic carbon (DOC). In humic water with high terrestrial DOC and light-absorbing humic substances, opsin gene abundance was low and dramatically declined within the first few meters, whereas the abundance remained relatively high along the bulk water column in clearwater lakes with low DOC, suggesting opsin gene distribution is influenced by lake optical properties and DOC. Gene expression analysis confirmed the significance of rhodopsin-based phototrophy in clearwater lakes and revealed different diel expressional patterns among major phyla. Overall, our analyses revealed freshwater opsin diversity, distribution and expression patterns, and suggested the significance of rhodopsin-based phototrophy in freshwater energy budgets, especially in clearwater lakes.}, } @article {pmid36798948, year = {2023}, author = {Li, N and Fu, J and Zhang, G and Liu, J and Li, Z and Luo, R and Li, L}, title = {Investigating the mechanism of the flavor formation in Sichuan sun vinegar based on flavor-orientation and metagenomics.}, journal = {Current research in food science}, volume = {6}, number = {}, pages = {100460}, pmid = {36798948}, issn = {2665-9271}, abstract = {Fermentation and aging are the key stages of flavor formation in Sichuan sun vinegar (SSV), but the generation mechanisms of the flavor produced by these processes are unknown. However, complex microbial metabolism is critical to the flavor development of SSV. In this study, we analyzed the key flavor compounds present in SSV. Combined with odor activity value (OAV), the main aroma components of SSV were screened, and the relationship between microorganisms and key flavor formation was predicted using metagenomic sequencing technology. The results revealed 38 key flavor compounds in SSV. Lactobacillus, Weissella, Acetobacter, Lichtheimia, Pediococcus, Oenococcus, Brettanomyces, Kazachstania, Pichia, Xanthomonas, Lenconostoc are widely involved in the production of key flavor compounds such as 2,3-butanediol, 2-Furanmethanol, phenylethanol, 3-(Methylthio)-1-propanol, acetic acid, lactic acid, butyric acid, isovaleric acid and other organic acids. Among them, Lichtheimia and Lactobacillus are important genera for the degradation of starch, arabinoxylan and cellulose. The acetaldehyde,4-ethyl-2-methoxy-phenol and 2-methoxy-4-methyl-phenol production pathway may be related to Lactobacillus, Acetobacter and Brettanomyces. This study provides a new understanding of the key flavor-formation stage and flavor compound generation mechanism of SSV and provides a reference for the screening and isolation of functional strains and the reconstruction of microbial communities.}, } @article {pmid36798715, year = {2023}, author = {Khan, A and Singh, AV and Pareek, N and Arya, P and Upadhayay, VK and Kumar Jugran, A and Kumar Mishra, P and Goel, R}, title = {Credibility assessment of cold adaptive Pseudomonas jesenni MP1 and P. palleroniana N26 on growth, rhizosphere dynamics, nutrient status, and yield of the kidney bean cultivated in Indian Central Himalaya.}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1042053}, pmid = {36798715}, issn = {1664-462X}, abstract = {Kidney bean (Phaseolus vulgaris) productivity and nutritional quality are declining due to less nutrient accessibility, poor soil health, and indigent agronomic practices in hilly regions, which collectively led to a fall in farmer's income, and to malnutrition in consumers. Addressing such issues, the present investigation was designed to assess the impact of Pseudomonas jesenii MP1 and Pseudomonas palleroniana N26 treatment on soil health, microbial shift, yield, and nutrient status of the kidney bean in the Harsil and Chakrata locations of Indian Central Himalaya. P. jesenii MP1 and P. palleroniana N26 were characterized as cold adaptive PGPR as they possessed remarkable in vitro plant growth promoting traits. Further, field trial study with PGPR treatments demonstrated remarkable and prolific influence of both strains on yield, kidney bean nutrient status, and soil health at both geographical locations, which was indicated with improved grain yield (11.61%-23.78%), protein (6.13%-24.46%), and zinc content (21.86%-61.17%) over control. The metagenomic study revealed that use of bioinoculants also concentrated the nutrient mobilizing and plant beneficial microorganisms in the rhizosphere of the kidney bean. Moreover, correlation analysis also confirmed that the plant growth-promoting traits of P. jesenii MP1 and P. palleroniana N26 are the basis for improved yield and nutrient status of the kidney bean. Further, cluster and principal component analysis revealed that both P. jesenii MP1 and P. palleroniana N26 exhibited pronounced influence on yield attributes of the kidney bean at both the locations. At the Harsil location, the P. jesenii MP1-treated seed demonstrated highest grain yield over other treatments, whereas at Chakarata, P. jesenii MP1, and P. palleroniana N26 treatment showed almost equal enhancement (~23%) in grain yield over control. The above results revealed that these bioinoculants are efficient plant growth promoters and nutrient mobilizers; they could be used as green technology to improve human health and farmer's income by enhancing soil health, yield, and nutrient status of the kidney bean at hilly regions.}, } @article {pmid36798434, year = {2023}, author = {Sutcliffe, SG and Reyes, A and Maurice, CF}, title = {Bacteriophages playing nice: Lysogenic bacteriophage replication stable in the human gut microbiota.}, journal = {iScience}, volume = {26}, number = {2}, pages = {106007}, pmid = {36798434}, issn = {2589-0042}, abstract = {Bacteriophages, viruses specific to bacteria, coexist with their bacterial hosts with limited diversity fluctuations in the guts of healthy individuals where they replicate mostly via lysogenic replication. This favors 'piggy-back-the-winner' over 'kill-the-winner' dynamics which are driven by lytic bacteriophage replication. Revisiting the deep-viral sequencing data of a healthy individual sampled over 2.4 years, we explore how these dynamics occur. Prophages found in assembled bacterial metagenomes were also found extra-cellularly, as induced phage particles (iPPs), likely derived from prophage activation. These iPPs were diverse and continually present in low abundance, relative to the highly abundant but less diverse lytic phage population. The continuous detection of low levels of iPPs suggests that spontaneous induction regularly occurs in this healthy individual, possibly allowing prophages to maintain their ability to replicate and avoiding degradation and loss from the gut microbiota.}, } @article {pmid36798243, year = {2023}, author = {Vizioli, C and Jaime-Lara, R and Daniel, SG and Franks, A and Diallo, AF and Bittinger, K and Tan, TP and Merenstein, DJ and Brooks, B and Joseph, PV and Maki, KA}, title = {Administration of Bifidobacterium animalis subsp. lactis Strain BB-12 [®] in Healthy Children: Characterization, Functional Composition, and Metabolism of the Gut Microbiome.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {36798243}, abstract = {The consumption of probiotics may influence children's gut microbiome and metabolome, which may reflect shifts in gut microbial diversity composition and metabolism. These potential changes might have a beneficial impact on health. However, there is a lack of evidence investigating the effect of probiotics on the gut microbiome and metabolome of children. We aimed to examine the potential impact of a two (Streptococcus thermophilus and Lactobacillus delbrueckii ; S2) vs . three (S2 + Bifidobacterium animalis subsp. lactis strain BB-12) strain-supplemented yogurt. Included in this study were 59 participants, aged one to five years old, recruited to phase I of a double-blinded, randomized controlled trial. Fecal samples were collected at baseline, after the intervention, and at twenty days post-intervention discontinuation, and untargeted metabolomics and shotgun metagenomics were performed. Shotgun metagenomics and metabolomic analyses showed no global changes in either intervention group's gut microbiome alpha or beta diversity indices. The relative abundance of the two and three intervention bacteria increased in the S2 and S2 + BB12 groups, respectively, from Day 0 to Day 10 . In the S2+BB12 group, the abundance of several fecal metabolites was reduced at Day 10 , including alanine, glycine, lysine, phenylalanine, serine, and valine. These fecal metabolite changes did not occur in the S2 group. Future research using longer probiotic intervention durations and in children at risk for gastrointestinal disorders may elucidate if functional metabolite changes confer a protective gastrointestinal effect.}, } @article {pmid36798240, year = {2023}, author = {Hall, B and Levy, S and Dufault-Thompson, K and Ndjite, GM and Weiss, A and Braccia, D and Jenkins, C and Yang, Y and Arp, G and Abeysinghe, S and Jermain, M and Wu, CH and Jiang, X}, title = {Discovery of the gut microbial enzyme responsible for bilirubin reduction to urobilinogen.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36798240}, abstract = {The degradation of heme and the interplay of its catabolic derivative, bilirubin, between humans and their gut microbiota is an essential facet of human health. However, the hypothesized bacterial enzyme that reduces bilirubin to urobilinogen, a key step that produces the excretable waste products of this pathway, has remained unidentified. In this study, we used a combination of biochemical analyses and comparative genomics to identify a novel enzyme, BilR, that can reduce bilirubin to urobilinogen. We delineated the BilR sequences from other members of the Old Yellow Enzyme family through the identification of key residues in the active site that are critical for bilirubin reduction and found that BilR is predominantly encoded by Firmicutes in the gut microbiome. Our analysis of human gut metagenomes showed that BilR is a common feature of a healthy adult human microbiome but has a decreased prevalence in neonates and IBD patients. This discovery sheds new light on the role of the gut microbiome in bilirubin metabolism and highlights the significance of the gut-liver axis in maintaining bilirubin homeostasis.}, } @article {pmid36798209, year = {2023}, author = {Huss, P and Kieft, K and Meger, A and Nishikawa, K and Anantharaman, K and Raman, S}, title = {Deep metagenomic mining reveals bacteriophage sequence motifs driving host specificity.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.02.07.527309}, pmid = {36798209}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; }, abstract = {Bacteriophages can adapt to new hosts by altering sequence motifs through recombination or convergent evolution. Where such motifs exist and what fitness advantage they confer remains largely unknown. We report a new method, Bacteriophage Library Informed Sequence Scoring (BLISS), to discover sequence motifs in metagenomic datasets governing phage activity. BLISS uses experimental deep mutational scanning data to create sequence profiles to enable deep mining of metagenomes for functional motifs which are otherwise invisible to searches. We experimentally tested 10,073 BLISS-derived sequence motifs for the receptor-binding protein of the T7 phage. The screen revealed hundreds of T7 variants with novel host specificity with functional motifs sourced from distant families besides other major phyla. Position, substitution and location preferences on T7 dictated different specificities. To demonstrate therapeutic utility, we engineered highly active T7 variants against urinary tract pathogens. BLISS is a powerful tool to unlock the functional potential encoded in phage metagenomes.}, } @article {pmid36798152, year = {2023}, author = {Kosmopoulos, JC and Campbell, DE and Whitaker, RJ and Wilbanks, EG}, title = {Horizontal gene transfer and CRISPR targeting drive phage-bacterial host interactions and coevolution in pink berry marine microbial aggregates.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.02.06.527410}, pmid = {36798152}, abstract = {UNLABELLED: Bacteriophages (phages), viruses that infect bacteria, are the most abundant components of microbial communities and play roles in community dynamics and host evolution. The study of phage-host interactions, however, is made difficult by a paucity of model systems from natural environments and known and cultivable phage-host pairs. Here, we investigate phage-host interactions in the "pink berry" consortia, naturally-occurring, low-diversity, macroscopic aggregates of bacteria found in the Sippewissett Salt Marsh (Falmouth, MA, USA). We leverage metagenomic sequence data and a comparative genomics approach to identify eight compete phage genomes, infer their bacterial hosts from host-encoded clustered regularly interspaced short palindromic repeats (CRISPR), and observe the potential evolutionary consequences of these interactions. Seven of the eight phages identified infect the known pink berry symbionts Desulfofustis sp. PB-SRB1, Thiohalocapsa sp. PB-PSB1, and Rhodobacteraceae sp. A2, and belong to entirely novel viral taxa, except for one genome which represents the second member of the Knuthellervirus genus. We further observed increased nucleotide variation over a region of a conserved phage capsid gene that is commonly targeted by host CRISPR systems, suggesting that CRISPRs may drive phage evolution in pink berries. Finally, we identified a predicted phage lysin gene that was horizontally transferred to its bacterial host, potentially via a transposon intermediary, emphasizing the role of phages in bacterial evolution in pink berries. Taken together, our results demonstrate that pink berry consortia contain diverse and variable phages, and provide evidence for phage-host co-evolution via multiple mechanisms in a natural microbial system.

IMPORTANCE: Phages (viruses that infect bacteria) are important components of all microbial systems, where they drive the turnover of organic matter by lysing host cells, facilitate horizontal gene transfer (HGT), and co-evolve with their bacterial hosts. Bacteria resist phage infection, which is often costly or lethal, through a diversity of mechanisms. One of these mechanisms are CRISPR systems, which encode arrays of phage-derived sequences from past infections to block subsequent infection with related phages. Here, we investigate bacteria and phage populations from a simple marine microbial community known as "pink berries" found in salt marshes of Falmouth, Massachusetts, as a model of phage-host co-evolution. We identify eight novel phages, and characterize a case of putative CRISPR-driven phage evolution and an instance of HGT between phage and host, together suggesting that phages have large evolutionary impacts in a naturally-occuring microbial community.}, } @article {pmid36798086, year = {2023}, author = {Wang, Z and Chen, C and Lu, H and Wang, L and Gao, L and Zhang, J and Zhu, C and Du, F and Cui, L and Tan, Y}, title = {Case report: Clinical characteristics of two cases of pneumonia caused with different strains of Chlamydia psittaci.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1086454}, pmid = {36798086}, issn = {2235-2988}, mesh = {Animals ; Male ; Humans ; Aged ; Middle Aged ; *Chlamydophila psittaci/genetics ; Cough ; *Psittacosis/diagnosis/drug therapy/veterinary ; Birds ; Ducks ; *Pneumonia/diagnosis/veterinary ; }, abstract = {BACKGROUND: With the development of metagenomic sequencing technologies, more and more cases of pneumonia caused with Chlamydia psittaci (C. psittaci) have been reported. However, it remains unknown about the characteristics of patients with pneumonia caused by different strains of C. psittaci. Here, we shared the clinical characteristics of two cases of pneumonia caused with C. psittaci strains SZ18-2 and SZ15 which were rarely identified in humans.

CASE PRESENTATION: Case 1: A 69-year-old male farmer who fed ducks presented to hospital for cough, diarrhea and lethargy with the temperature of 39.8°C. Case 2: A 48-year-old male worker who slaughtered ducks was transferred to hospital for high fever, cough, myalgia, diarrhea and loss of appetite. Both patients did not take any protective measures (wearing face masks or gloves) while processing ducks. C. psittaci pneumonia was diagnosed by metagenomic next-generation sequencing and polymerase chain reaction. After treatment with doxycycline and azithromycin individually, they recovered well and discharged from hospital. Through OmpA sequencing, two different strains of SZ18-2 and SZ15 were identified in case 1 and case 2, respectively.

CONCLUSIONS: Patients infected with different strains of C. psittaci may own different clinical manifestations. C. psittaci infection should be suspected when pneumonia appears, accompanied by digestive symptoms and multiple organ dysfunction, especially under the exposure of specific birds.}, } @article {pmid36797830, year = {2023}, author = {Mandal, S and Kim, DH and Hua, X and Li, S and Shi, J}, title = {Estimating the overall fraction of phenotypic variance attributed to high-dimensional predictors measured with error.}, journal = {Biostatistics (Oxford, England)}, volume = {}, number = {}, pages = {}, doi = {10.1093/biostatistics/kxad001}, pmid = {36797830}, issn = {1468-4357}, support = {//NIH/ ; }, abstract = {In prospective genomic studies (e.g., DNA methylation, metagenomics, and transcriptomics), it is crucial to estimate the overall fraction of phenotypic variance (OFPV) attributed to the high-dimensional genomic variables, a concept similar to heritability analyses in genome-wide association studies (GWAS). Unlike genetic variants in GWAS, these genomic variables are typically measured with error due to technical limitation and temporal instability. While the existing methods developed for GWAS can be used, ignoring measurement error may severely underestimate OFPV and mislead the design of future studies. Assuming that measurement error variances are distributed similarly between causal and noncausal variables, we show that the asymptotic attenuation factor equals to the average intraclass correlation coefficients of all genomic variables, which can be estimated based on a pilot study with repeated measurements. We illustrate the method by estimating the contribution of microbiome taxa to body mass index and multiple allergy traits in the American Gut Project. Finally, we show that measurement error does not cause meaningful bias when estimating the correlation of effect sizes for two traits.}, } @article {pmid36797573, year = {2023}, author = {Jiang, MJ and Tang, HN and Tang, LL}, title = {[Research progress of the application of metagenomics technology in female reproductive tract diseases].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {57}, number = {2}, pages = {172-178}, doi = {10.3760/cma.j.cn112150-20220905-00871}, pmid = {36797573}, issn = {0253-9624}, support = {kq2202415//Natural Science Foundation of Changsha City/ ; }, mesh = {Female ; Humans ; *Microbiota/genetics ; Vagina ; Metagenomics/methods ; }, abstract = {In recent years, many studies have found that vaginal microbiota is closely related to female reproductive tract diseases. However, traditional microbial culture technology has the defects of long culture cycle and most microorganisms cannot be cultured. The development of metagenomics technique has broken the limitations of culture technology, and has been gradually applied to the study of vaginal microorganisms with the characteristics of high throughput, short time, identification of microbial population structure and gene function. It also provides technical support for elucidating the relationship between vaginal microbiota and female reproductive tract diseases. This article mainly introduces the metagenomics techniques and their applications in prevention, screening and diagnosis of common female reproductive tract diseases, and discusses their promising development and limitations to be overcome.}, } @article {pmid36797336, year = {2023}, author = {Eisenhofer, R and Odriozola, I and Alberdi, A}, title = {Impact of microbial genome completeness on metagenomic functional inference.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {12}, pmid = {36797336}, issn = {2730-6151}, support = {817729//European Commission (EC)/ ; DNRF143//Danmarks Grundforskningsfond (Danish National Research Foundation)/ ; CF20-0460//Carlsbergfondet (Carlsberg Foundation)/ ; }, abstract = {Inferring the functional capabilities of bacteria from metagenome-assembled genomes (MAGs) is becoming a central process in microbiology. Here we show that the completeness of genomes has a significant impact on the recovered functional signal, spanning all domains of metabolic functions. We identify factors that affect this relationship between genome completeness and function fullness, and provide baseline knowledge to guide efforts to correct for this overlooked bias in metagenomic functional inference.}, } @article {pmid36797305, year = {2023}, author = {Linz, DM and Sienkiewicz, N and Struewing, I and Stelzer, EA and Graham, JL and Lu, J}, title = {Metagenomic mapping of cyanobacteria and potential cyanotoxin producing taxa in large rivers of the United States.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {2806}, pmid = {36797305}, issn = {2045-2322}, mesh = {United States ; *Cyanobacteria/genetics ; *Microcystis ; Rivers/microbiology ; Lakes/microbiology ; Microcystins/genetics ; *Microbiota ; }, abstract = {Cyanobacteria and cyanotoxin producing cyanobacterial blooms are a trending focus of current research. Many studies focus on bloom events in lentic environments such as lakes or ponds. Comparatively few studies have explored lotic environments and fewer still have examined the cyanobacterial communities and potential cyanotoxin producers during ambient, non-bloom conditions. Here we used a metagenomics-based approach to profile non-bloom microbial communities and cyanobacteria in 12 major U.S. rivers at multiple time points during the summer months of 2019. Our data show that U.S. rivers possess microbial communities that are taxonomically rich, yet largely consistent across geographic location and time. Within these communities, cyanobacteria often comprise significant portions and frequently include multiple species with known cyanotoxin producing strains. We further characterized these potential cyanotoxin producing taxa by deep sequencing amplicons of the microcystin E (mcyE) gene. We found that rivers containing the highest levels of potential cyanotoxin producing cyanobacteria consistently possess taxa with the genetic potential for cyanotoxin production and that, among these taxa, the predominant genus of origin for the mcyE gene is Microcystis. Combined, these data provide a unique perspective on cyanobacteria and potential cyanotoxin producing taxa that exist in large rivers across the U.S. and can be used to better understand the ambient conditions that may precede bloom events in lotic freshwater ecosystems.}, } @article {pmid36796678, year = {2023}, author = {Kami, W and Kinjo, T and Hashioka, H and Arakaki, W and Uechi, K and Takahashi, A and Oki, H and Tanaka, K and Motooka, D and Nakamura, S and Nakamatsu, M and Maeda, S and Yamamoto, K and Fujita, J}, title = {Impact of G29179T mutation on two commercial PCR assays for SARS-CoV-2 detection.}, journal = {Journal of virological methods}, volume = {314}, number = {}, pages = {114692}, pmid = {36796678}, issn = {1879-0984}, mesh = {Humans ; *SARS-CoV-2/genetics ; *COVID-19/diagnosis ; COVID-19 Testing ; Clinical Laboratory Techniques/methods ; Nasopharynx ; Sensitivity and Specificity ; Polymerase Chain Reaction ; Nucleic Acid Amplification Techniques ; Mutation ; }, abstract = {Nucleic acid amplification test (NAAT) is the gold standard for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection. However, genetic mutations in the virus can affect the result. Cycle threshold (Ct) values of N genes and their association with mutations using SARS-CoV-2 positive specimens diagnosed by the Xpert Xpress SARS-CoV-2 were examined in this study. In total, 196 nasopharyngeal swab specimens were tested for SARS-CoV-2 infection using the Xpert Xpress SARS-CoV-2, and 34 were positive. WGS was performed for four outlier samples with increased ΔCt identified by Scatterplot analysis as well as seven control samples without increased ΔCt in the Xpert Xpress SARS-CoV-2. The presence of the G29179T mutation was identified as a cause of increased ΔCt. PCR using the Allplex™ SARS-CoV-2 Assay did not show a similar increase in ΔCt. Previous reports focusing on N-gene mutations and their effects on SARS-CoV-2 testing including the Xpert Xpress SARS-CoV-2 were also summarized. While a single mutation that impacts one target of a multiplex NAAT is not a true detection failure, mutation compromising NAAT target region can cause confusion of the results and render the assay susceptible to diagnostic failure.}, } @article {pmid36796613, year = {2023}, author = {Zheng, H and Ji, Y and Li, S and Li, W and Ma, J and Niu, J}, title = {Ecotoxicity and resistance genes induction changing of antibiotic tetracycline degradation products dominated by differential free radicals.}, journal = {Environmental research}, volume = {227}, number = {}, pages = {115427}, doi = {10.1016/j.envres.2023.115427}, pmid = {36796613}, issn = {1096-0953}, mesh = {*Anti-Bacterial Agents/toxicity ; *Tetracycline ; Oxidation-Reduction ; Genes, Bacterial ; Hydroxyl Radical ; }, abstract = {Studying the ecological risks of antibiotics and their degradation products is of great importance to water environment security and advanced oxidation processes (AOPs) development. This work studied the changes and internal influencing mechanisms of ecotoxicity and the capacity for inducing antibiotic resistance genes (ARGs) shown by the tetracycline (TC) degradation products generated in AOPs with differential free radicals. Under the action of superoxide radicals and singlet oxygen in the ozone system, and sulfate and hydroxyl radicals in the thermally activated potassium persulfate system, TC exhibited differential degradation pathways and resulted in the differential growth inhibition trends on the determined strains. Microcosm experiments combined with metagenomics were also performed to analyze the remarkable changes in the TC resistance genes tetA (60), tetT, and otr(B) induced by the degradation products and ARG hosts in the natural water environment. Microcosm experiments exhibited that the microbial community in actual water have changed significantly with the addition of TC and degradation intermediates. Furthermore, the richness of genes related to oxidative stress was investigated to discuss the effect on reactive oxygen species production and SOS response caused by TC and its intermediates.}, } @article {pmid36796520, year = {2023}, author = {Zhao, L and Fu, G and Pang, W and Li, X and Pan, C and Hu, Z}, title = {A novel autotrophic denitrification and nitrification integrated constructed wetland process for marine aquaculture wastewater treatment.}, journal = {Chemosphere}, volume = {321}, number = {}, pages = {138157}, doi = {10.1016/j.chemosphere.2023.138157}, pmid = {36796520}, issn = {1879-1298}, mesh = {Humans ; Nitrification ; Denitrification ; Wetlands ; *Alzheimer Disease ; Autotrophic Processes ; *Water Purification ; Bacteria/metabolism ; Nitrogen/metabolism ; Sulfates ; Bioreactors ; }, abstract = {We undertook a lab-scale evaluation of a novel autotrophic denitrification and nitrification integrated constructed wetland (ADNI-CW) for improved carbon (C), nitrogen (N), and sulfur (S) cycling to treat mariculture wastewater. The process involved an up-flow autotrophic denitrification constructed wetland unit (AD-CW) for sulfate reduction and autotrophic denitrification, and an autotrophic nitrification constructed wetland unit (AN-CW) for nitrification. The 400-day experiment investigated the performance of the AD-CW, AN-CW, and entire ADNI-CW processes under various hydraulic retention times (HRTs), nitrate concentrations, dissolved oxygen levels, and recirculation ratios. Under various HRTs, the AN-CW achieved a nitrification performance exceeding 92%. Correlation analysis of the chemical oxygen demand (COD) revealed that, on average, approximately 96% of COD was removed by sulfate reduction. Under different HRTs, increases in influent NO3[-]-N concentrations caused the amount of sulfide to gradually decrease from sufficient to deficient, and the autotrophic denitrification rate also decreased from 62.18 to 40.93%. In addition, when the NO3[-]-N load rate was above 21.53 g N/m[2]·d, the transformation of organic N by mangrove roots may have increased NO3[-]-N in the top effluent of the AD-CW. The coupling of N and S metabolic processes mediated by various functional microorganisms (Proteobacteria, Chloroflexi, Actinobacteria, Bacteroidetes, and unclassified_d__Bacteria) enhanced N removal. We intensively explored the effects of changing inputs as culture species developed on the physical, chemical, and microbial changes of CW to ensure a consistent and effective management of C, N, and S. This study lays the foundation for green and sustainable mariculture development.}, } @article {pmid36796333, year = {2023}, author = {Venturelli, OS and Wang, HH and Estrela, S and Huang, KC and Ledesma-Amaro, R and Fedorec, AJH and Stecher, B and Lawson, CE and Zarrinpar, A and Guo, CJ and Soyer, OS}, title = {What is the key challenge in engineering microbiomes?.}, journal = {Cell systems}, volume = {14}, number = {2}, pages = {85-90}, doi = {10.1016/j.cels.2023.01.002}, pmid = {36796333}, issn = {2405-4720}, mesh = {*Microbiota ; Engineering ; }, } @article {pmid36796222, year = {2023}, author = {Xie, Z and Jin, Z and Zhang, S and Chen, L}, title = {Biogas utilization without desulfurization pretreatment in a bioelectrochemical system.}, journal = {The Science of the total environment}, volume = {872}, number = {}, pages = {162239}, doi = {10.1016/j.scitotenv.2023.162239}, pmid = {36796222}, issn = {1879-1026}, mesh = {*Biofuels ; *Archaea/metabolism ; Electricity ; Bacteria/metabolism ; Methane/metabolism ; Anaerobiosis ; Bioreactors/microbiology ; }, abstract = {Utilizing biogas as a fuel for heating and power generation usually requires desulfurization pretreatment. In this study, the biogas utilization without desulfurization pretreatment in a bioelectrochemical system (BES) was explored. The results showed that the biogas-fueled BES was successfully started up within 36 d and the presence of hydrogen sulfide promoted both methane consumption and electricity generation. The optimal performance (i.e., a methane consumption of 0.523 ± 0.004 mmol/d, a peak voltage of 577 ± 1 mV, a coulomb production of 37.86 ± 0.43C/d, a coulombic efficiency of 9.37 ± 0.06 % and the maximum power density of 2.070 W/m[3]) was obtained under bicarbonate buffer solution and 40 °C conditions. The addition of 1 mg/L sulfide and 5 mg/L L-cysteine facilitated methane consumption and electricity generation. In the anode biofilm, the dominant bacteria were Sulfurivermis, unclassified_o__Ignavibacteriales and Lentimicrobium, while Methanobacterium, Methanosarcina and Methanothrix were the predominant archaea. Besides, the metagenomics profiles reveal that anaerobic methane oxidation and electricity generation were closely related to sulfur metabolism. These findings provide a novel approach for utilizing biogas without desulfurization pretreatment.}, } @article {pmid36796164, year = {2023}, author = {Liu, WH and Chai, LJ and Wang, HM and Lu, ZM and Zhang, XJ and Xiao, C and Wang, ST and Shen, CH and Shi, JS and Xu, ZH}, title = {Bacteria and filamentous fungi running a relay race in Daqu fermentation enable macromolecular degradation and flavor substance formation.}, journal = {International journal of food microbiology}, volume = {390}, number = {}, pages = {110118}, doi = {10.1016/j.ijfoodmicro.2023.110118}, pmid = {36796164}, issn = {1879-3460}, mesh = {Fermentation ; *Bacteria/genetics/metabolism ; Fungi/genetics ; *Microbiota ; Pichia ; Biodiversity ; Alcoholic Beverages/microbiology ; }, abstract = {As the saccharifying and fermentative agent, medium-temperature Daqu (MT-Daqu) plays an irreplaceable role in the production of strong-flavor Baijiu. Numerous studies have focused on the microbial community structure and potential functional microorganisms, however, little is known about the succession of active microbial community and the formation mechanism of community function during MT-Daqu fermentation. In this study, we presented an integrated analysis of metagenomics, metatranscriptomics, and metabonomics covering the whole fermentation process of MT-Daqu to reveal the active microorganisms and their participations in metabolic networks. The results showed that dynamic of metabolites were time-specific, and the metabolites and co-expressed active unigenes were further classified into four clusters according to their accumulation patterns, with members within each cluster displaying a uniform and clear pattern of abundance across fermentation. Based on KEGG enrichment analysis in co-expression clusters and succession of active microbial community, we revealed that Limosilactobacillus, Staphylococcus, Pichia, Rhizopus, and Lichtheimia were metabolically active members at the early stage, and their metabolic activities were conducive to releasing abundant energy to drive multiple basal metabolisms such as carbohydrates and amino acids. Thereafter, during the high temperature period and at the end of fermentation, multiple heat-resistant filamentous fungi were transcriptionally active populations, and they acted as both the saccharifying agents and flavor compound producers, especially aromatic compounds, suggesting their crucial contribution to enzymatic activity and aroma of mature MT-Daqu. Our findings revealed the succession and metabolic functions of the active microbial community, providing a deeper understanding of their contribution to MT-Daqu ecosystem.}, } @article {pmid36795558, year = {2023}, author = {Guo, LY and Li, Y and Zhu, L and Dong, F and Ji, YQ and Yao, KH and Gang, L}, title = {The First Community-acquired Klebsiella variicola Bacterial Meningitis Identified by Metagenomic Next Generation Sequencing.}, journal = {The Pediatric infectious disease journal}, volume = {42}, number = {5}, pages = {e186-e188}, doi = {10.1097/INF.0000000000003851}, pmid = {36795558}, issn = {1532-0987}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; Klebsiella/genetics ; *Klebsiella Infections/diagnosis/microbiology ; }, } @article {pmid36795181, year = {2023}, author = {Yao, T and Wang, H and Lin, K and Wang, R and Guo, S and Chen, P and Wu, H and Liu, T and Wang, R}, title = {Exercise-induced microbial changes in preventing type 2 diabetes.}, journal = {Science China. Life sciences}, volume = {}, number = {}, pages = {}, pmid = {36795181}, issn = {1869-1889}, abstract = {The metabolic benefits associated with long-term physical activity are well appreciated and growing evidence suggests that it involves the gut microbiota. Here we re-evaluated the link between exercise-induced microbial changes and those associated with prediabetes and diabetes. We found that the relative abundances of substantial amounts of diabetes-associated metagenomic species associated negatively with physical fitness in a Chinese athlete students cohort. We additionally showed that those microbial changes correlated more with handgrip strength, a simple but valuable biomarker suggestive of the diabetes states, than maximum oxygen intake, one of the key surrogates for endurance training. Moreover, the causal relationships among exercise, risks for diabetes, and gut microbiota were explored based on mediation analysis. We propose that the protective roles of exercise against type 2 diabetes are mediated, at least partly, by the gut microbiota.}, } @article {pmid36794943, year = {2023}, author = {Gilbert, NE and LeCleir, GR and Pound, HL and Strzepek, RF and Ellwood, MJ and Twining, BS and Roux, S and Boyd, PW and Wilhelm, SW}, title = {Giant Virus Infection Signatures Are Modulated by Euphotic Zone Depth Strata and Iron Regimes of the Subantarctic Southern Ocean.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0126022}, pmid = {36794943}, issn = {2379-5077}, mesh = {Humans ; *Giant Viruses/genetics ; Iron ; Oceans and Seas ; *Viruses/genetics ; Water ; Eukaryota ; *Virus Diseases ; }, abstract = {Viruses can alter the abundance, evolution, and metabolism of microorganisms in the ocean, playing a key role in water column biogeochemistry and global carbon cycles. Large efforts to measure the contribution of eukaryotic microorganisms (e.g., protists) to the marine food web have been made, yet the in situ activities of the ecologically relevant viruses that infect these organisms are not well characterized. Viruses within the phylum Nucleocytoviricota ("giant viruses") are known to infect a diverse range of ecologically relevant marine protists, yet how these viruses are influenced by environmental conditions remains under-characterized. By employing metatranscriptomic analyses of in situ microbial communities along a temporal and depth-resolved gradient, we describe the diversity of giant viruses at the Southern Ocean Time Series (SOTS), a site within the subpolar Southern Ocean. Using a phylogeny-guided taxonomic assessment of detected giant virus genomes and metagenome-assembled genomes, we observed depth-dependent structuring of divergent giant virus families mirroring dynamic physicochemical gradients in the stratified euphotic zone. Analyses of transcribed metabolic genes from giant viruses suggest viral metabolic reprogramming of hosts from the surface to a 200-m depth. Lastly, using on-deck incubations reflecting a gradient of iron availability, we show that modulating iron regimes influences the activity of giant viruses in the field. Specifically, we show enhanced infection signatures of giant viruses under both iron-replete and iron-limited conditions. Collectively, these results expand our understanding of how the water column's vertical biogeography and chemical surroundings affect an important group of viruses within the Southern Ocean. IMPORTANCE The biology and ecology of marine microbial eukaryotes is known to be constrained by oceanic conditions. In contrast, how viruses that infect this important group of organisms respond to environmental change is less well known, despite viruses being recognized as key microbial community members. Here, we address this gap in our understanding by characterizing the diversity and activity of "giant" viruses within an important region in the sub-Antarctic Southern Ocean. Giant viruses are double-stranded DNA (dsDNA) viruses of the phylum Nucleocytoviricota and are known to infect a wide range of eukaryotic hosts. By employing a metatranscriptomics approach using both in situ samples and microcosm manipulations, we illuminated both the vertical biogeography and how changing iron availability affects this primarily uncultivated group of protist-infecting viruses. These results serve as a foundation for our understanding of how the open ocean water column structures the viral community, which can be used to guide models of the viral impact on marine and global biogeochemical cycling.}, } @article {pmid36794940, year = {2023}, author = {Venkatesan, A and Habis, R and Geocadin, RG}, title = {Approach to acute encephalitis in the intensive care unit.}, journal = {Current opinion in critical care}, volume = {29}, number = {2}, pages = {89-98}, doi = {10.1097/MCC.0000000000001028}, pmid = {36794940}, issn = {1531-7072}, mesh = {Humans ; *Encephalitis/diagnosis/therapy ; Intensive Care Units ; *Hashimoto Disease ; Autoantibodies ; }, abstract = {PURPOSE OF REVIEW: Recent years have seen a dramatic increase in the identification of autoimmune encephalitis (AE) and the emergence of new causes of infectious encephalitis (IE). However, management of these patients remains challenging, with many requiring care in intensive care units. Here, we describe recent advances in the diagnosis and management of acute encephalitis.

RECENT FINDINGS: Advances in the identification of clinical presentations, neuroimaging biomarkers, and electroencephalogram patterns have enabled more rapid diagnosis of encephalitis. Newer modalities such as meningitis/encephalitis multiplex PCR panels, metagenomic next-generation sequencing, and phage display-based assays are being evaluated in an effort to improve detection of autoantibodies and pathogens. Specific advances in the treatment of AE include establishment of a systematic approach to first-line therapies and the development of newer second-line modalities. The role of immunomodulation and its applications in IE are actively being investigated. In the ICU, particular attention to status epilepticus, cerebral edema, and dysautonomia may improve outcomes.

SUMMARY: Substantial diagnostic delays still occur, with many cases left without an identified etiology. Antiviral therapies remain scarce, and optimal treatment regimens for AE still need to be clarified. Nevertheless, our understanding of diagnostic and therapeutic approaches to encephalitis is rapidly evolving.}, } @article {pmid36794928, year = {2023}, author = {Akpudo, YM and Bezuidt, OK and Makhalanyane, TP}, title = {Metagenome-Assembled Genomes of Four Southern Ocean Archaea Harbor Multiple Genes Linked to Polyethylene Terephthalate and Polyhydroxybutyrate Plastic Degradation.}, journal = {Microbiology resource announcements}, volume = {12}, number = {3}, pages = {e0109822}, pmid = {36794928}, issn = {2576-098X}, support = {//National Research Foundation (NRF)/ ; //Technology Innovation Agency/ ; }, abstract = {Here, we present four archaeal metagenome-assembled genomes (MAGs) (three Thaumarchaeota MAGs and one Thermoplasmatota MAG) from a polar upwelling zone in the Southern Ocean. These archaea harbor putative genes encoding enzymes such as polyethylene terephthalate (PET) hydrolases (PETases) and polyhydroxybutyrate (PHB) depolymerases, which are associated with microbial degradation of PET and PHB plastics.}, } @article {pmid36794927, year = {2023}, author = {Chen, G and Tang, X and Shi, M and Sun, Y}, title = {VirBot: an RNA viral contig detector for metagenomic data.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {3}, pages = {}, pmid = {36794927}, issn = {1367-4811}, support = {//Hong Kong Research Grants Council/ ; }, mesh = {*Software ; *RNA Viruses/genetics ; Metagenome ; Metagenomics ; Sequence Analysis, DNA ; }, abstract = {SUMMARY: Without relying on cultivation, metagenomic sequencing greatly accelerated the novel RNA virus detection. However, it is not trivial to accurately identify RNA viral contigs from a mixture of species. The low content of RNA viruses in metagenomic data requires a highly specific detector, while new RNA viruses can exhibit high genetic diversity, posing a challenge for alignment-based tools. In this work, we developed VirBot, a simple yet effective RNA virus identification tool based on the protein families and the corresponding adaptive score cutoffs. We benchmarked it with seven popular tools for virus identification on both simulated and real sequencing data. VirBot shows its high specificity in metagenomic datasets and superior sensitivity in detecting novel RNA viruses.

https://github.com/GreyGuoweiChen/RNA_virus_detector.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36794885, year = {2023}, author = {Adeleke, BS and Muller, D and Babalola, OO}, title = {A metagenomic lens into endosphere microbial communities, promises, and discoveries.}, journal = {Letters in applied microbiology}, volume = {76}, number = {2}, pages = {}, doi = {10.1093/lambio/ovac030}, pmid = {36794885}, issn = {1472-765X}, support = {123634//National Research Foundation/ ; //TWAS/ ; }, mesh = {*Metagenome ; Metagenomics ; *Microbiota/genetics ; Endophytes ; Plants ; }, abstract = {The word endosphere represents the internal tissues of plants harboring diverse microbes capable of producing active biological products for various biotechnological and agricultural applications. The discreet standalone genes and interdependent association of microbial endophytes with plants can be an underlining factor in predicting their ecological functions. Yet-to-be-cultured endophytic microbes have geared the invention of metagenomics in various environmental studies to determine their structural diversity and functional genes with novel attributes. This review presents an overview of the general concept of metagenomics in microbial endophytic studies. First, the endosphere microbial communities were introduced, followed by metagenomic insights in endosphere biology, a promising technology. Also, the major application of metagenomics and a short brief on DNA stable isotope probing in determining functions and metabolic pathways of microbial metagenome were highlighted. Therefore, the use of metagenomics promises to provide answers to yet-to-be-cultured microbes by unraveling their diversity, functional attributes, and metabolic pathways with prospects in integrated and sustainable agriculture.}, } @article {pmid36794865, year = {2023}, author = {Mukherjee, S and Ovchinnikova, G and Stamatis, D and Li, CT and Chen, IA and Kyrpides, NC and Reddy, TBK}, title = {Standardized naming of microbiome samples in Genomes OnLine Database.}, journal = {Database : the journal of biological databases and curation}, volume = {2023}, number = {}, pages = {}, pmid = {36794865}, issn = {1758-0463}, mesh = {*Software ; *Microbiota/genetics ; Metagenome/genetics ; Metagenomics/methods ; Data Management ; }, abstract = {The power of next-generation sequencing has resulted in an explosive growth in the number of projects aiming to understand the metagenomic diversity of complex microbial environments. The interdisciplinary nature of this microbiome research community, along with the absence of reporting standards for microbiome data and samples, poses a significant challenge for follow-up studies. Commonly used names of metagenomes and metatranscriptomes in public databases currently lack the essential information necessary to accurately describe and classify the underlying samples, which makes a comparative analysis difficult to conduct and often results in misclassified sequences in data repositories. The Genomes OnLine Database (GOLD) (https:// gold.jgi.doe.gov/) at the Department of Energy Joint Genome Institute has been at the forefront of addressing this challenge by developing a standardized nomenclature system for naming microbiome samples. GOLD, currently in its twenty-fifth anniversary, continues to enrich the research community with hundreds of thousands of metagenomes and metatranscriptomes with well-curated and easy-to-understand names. Through this manuscript, we describe the overall naming process that can be easily adopted by researchers worldwide. Additionally, we propose the use of this naming system as a best practice for the scientific community to facilitate better interoperability and reusability of microbiome data.}, } @article {pmid36794816, year = {2023}, author = {Derrien, M and Mikulic, N and Uyoga, MA and Chenoll, E and Climent, E and Howard-Varona, A and Nyilima, S and Stoffel, NU and Karanja, S and Kottler, R and Stahl, B and Zimmermann, MB and Bourdet-Sicard, R}, title = {Gut microbiome function and composition in infants from rural Kenya and association with human milk oligosaccharides.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2178793}, pmid = {36794816}, issn = {1949-0984}, mesh = {Humans ; Infant ; *Milk, Human/chemistry ; *Gastrointestinal Microbiome/genetics ; Kenya/epidemiology ; Oligosaccharides ; Bifidobacterium/genetics ; }, abstract = {The gut microbiota evolves rapidly after birth, responding dynamically to environmental factors and playing a key role in short- and long-term health. Lifestyle and rurality have been shown to contribute to differences in the gut microbiome, including Bifidobacterium levels, between infants. We studied the composition, function and variability of the gut microbiomes of 6- to 11-month-old Kenyan infants (n = 105). Shotgun metagenomics showed Bifidobacterium longum to be the dominant species. A pangenomic analysis of B. longum in gut metagenomes revealed a high prevalence of B. longum subsp. infantis (B. infantis) in Kenyan infants (80%), and possible co-existence of this subspecies with B. longum subsp. longum. Stratification of the gut microbiome into community (GMC) types revealed differences in composition and functional features. GMC types with a higher prevalence of B. infantis and abundance of B. breve also had a lower pH and a lower abundance of genes encoding pathogenic features. An analysis of human milk oligosaccharides (HMOs) classified the human milk (HM) samples into four groups defined on the basis of secretor and Lewis polymorphisms revealed a higher prevalence of HM group III (Se+, Le-) (22%) than in most previously studied populations, with an enrichment in 2'-fucosyllactose. Our results show that the gut microbiome of partially breastfed Kenyan infants over the age of six months is enriched in bacteria from the Bifidobacterium community, including B. infantis, and that the high prevalence of a specific HM group may indicate a specific HMO-gut microbiome association. This study sheds light on gut microbiome variation in an understudied population with limited exposure to modern microbiome-altering factors.}, } @article {pmid36794146, year = {2023}, author = {Lin, P and Chen, Y and Xu, J and Huang, X and Wen, W and Zhang, L and Kong, W and Zhao, Z and Ye, Y and Bao, Z and Song, Y and Lin, S and Yu, Z}, title = {A multicenter-retrospective cohort study of chromosome instability in lung cancer: clinical characteristics and prognosis of patients harboring chromosomal instability detected by metagenomic next-generation sequencing.}, journal = {Journal of thoracic disease}, volume = {15}, number = {1}, pages = {112-122}, pmid = {36794146}, issn = {2072-1439}, abstract = {BACKGROUND: The usefulness of metagenomic next-generation sequencing (mNGS) in identifying the prognosis of lung cancer with chromosomal instability (CIN) remains unclear. We aimed to analyze clinical characteristics and prognosis of patients in patients harboring CIN.

METHODS: This retrospective cohort study included 668 patients diagnosed with suspected pulmonary infection or lung cancer whose samples underwent mNGS detection from January 2021 to January 2022. Difference between clinical characteristics were calculated by the Student's t-test and the chi-square test. The subjects were followed-up from registered to September 2022. Survival curves were analyzed by the Kaplan-Meier method.

RESULTS: Of 619 bronchoalveolar lavage fluid (BALF) samples collected by bronchoscopy, 30 CIN-positive samples were confirmed as malignant on histopathology, with a sensitivity of 61.22%, a specificity of 99.65%, and an 83.17% accuracy [cut-off values were established by the receiver operating characteristic (ROC) area under the curve (AUC) =0.804]. In 42 patients with lung cancer, mNGS detected 24 patients as CIN-positive and 18 as CIN-negative. There were no differences between two groups including ages, pathologic types, stage and metastases. In 25 cases, we detected 523 chromosomal copy number variants (CNVs) with forms including duplication (dup), deletion (del), mosaic (mos), and whole chromosome amplification or loss. A total of 243 duplication variants and 192 deletion variants occurred in all chromosomes. Duplications occurred in most chromosomes except for Chr9 and Chr13, in which CNV tended to delete. The median overall survival (OS) in patients with Chr5p15 duplication was 32.4 months [95% confidence interval (CI), 10.35-54.45 months]. The median OS differed significantly between the 5p15dup+ group and the combined group (32.4 vs. 8.63 months, P=0.049). In 29 patients with unresected lung cancer, the median OS of 18 cases in the CIN-positive group was 32.4 months (95% CI, 14.2-50.6 months) and the median OS of 11 cases in the CIN-negative group was 35.63 months (95% CI, 21.64-49.62 months; Wilcoxon, P=0.227).

CONCLUSIONS: Various forms of CIN detected by mNGS may predict prognosis of patients with lung cancer differentially. CIN with duplication or deletion deserves further study to guide clinical treatment.}, } @article {pmid36793764, year = {2023}, author = {Kacsir, I and Sipos, A and Kiss, T and Major, E and Bajusz, N and Tóth, E and Buglyó, P and Somsák, L and Kardos, G and Bai, P and Bokor, É}, title = {Half sandwich-type osmium, ruthenium, iridium and rhodium complexes with bidentate glycosyl heterocyclic ligands induce cytostasis in platinum-resistant ovarian cancer cells and bacteriostasis in Gram-positive multiresistant bacteria.}, journal = {Frontiers in chemistry}, volume = {11}, number = {}, pages = {1086267}, pmid = {36793764}, issn = {2296-2646}, abstract = {The toxicity of and resistance to platinum complexes as cisplatin, oxaliplatin or carboplatin calls for the replacement of these therapeutic agents in clinical settings. We have previously identified a set of half sandwich-type osmium, ruthenium and iridium complexes with bidentate glycosyl heterocyclic ligands exerting specific cytostatic activity on cancer cells but not on non-transformed primary cells. The apolar nature of the complexes, conferred by large, apolar benzoyl protective groups on the hydroxyl groups of the carbohydrate moiety, was the main molecular feature to induce cytostasis. We exchanged the benzoyl protective groups to straight chain alkanoyl groups with varying length (3 to 7 carbon units) that increased the IC50 value as compared to the benzoyl-protected complexes and rendered the complexes toxic. These results suggest a need for aromatic groups in the molecule. The pyridine moiety of the bidentate ligand was exchanged for a quinoline group to enlarge the apolar surface of the molecule. This modification decreased the IC50 value of the complexes. The complexes containing [(η[6]-p-cymene)Ru(II)], [(η[6]-p-cymene)Os(II)] or [(η[5]-Cp*)Ir(III)] were biologically active unlike the complex containing [(η[5]-Cp*)Rh(III)]. The complexes with cytostatic activity were active on ovarian cancer (A2780, ID8), pancreatic adenocarcinoma (Capan2), sarcoma (Saos) and lymphoma cell lines (L428), but not on primary dermal fibroblasts and their activity was dependent on reactive oxygen species production. Importantly, these complexes were cytostatic on cisplatin-resistant A2780 ovarian cancer cells with similar IC50 values as on cisplatin-sensitive A2780 cells. In addition, the quinoline-containing Ru and Os complexes and the short chain alkanoyl-modified complexes (C3 and C4) proved to be bacteriostatic in multiresistant Gram-positive Enterococcus and Staphylococcus aureus isolates. Hereby, we identified a set of complexes with submicromolar to low micromolar inhibitory constants against a wide range of cancer cells, including platinum resistant cells and against multiresistant Gram-positive bacteria.}, } @article {pmid36792209, year = {2023}, author = {Tsuchida, S and Ueda, A and Kakooza, S and Okubo, T and Wampande, EM and Yamada, T and Ushida, K}, title = {The fecal microbiomes analysis of Marabou storks (Leptoptilos crumenifer) reveals their acclimatization to the feeding environment in the Kampala urban areas, Uganda.}, journal = {The Journal of veterinary medical science}, volume = {85}, number = {4}, pages = {450-458}, pmid = {36792209}, issn = {1347-7439}, mesh = {Animals ; Uganda ; RNA, Ribosomal, 16S/genetics ; *Birds ; Acclimatization ; *Microbiota ; Feces ; }, abstract = {The Marabou stork (Leptoptilos crumenifer) is a typical scavenging bird and adapted to the Savannah environment, where they show a carnivorous feeding style. However, Marabou stork recently penetrated into the city areas and acclimatized to the urban environment, where they modified their feeding habits to an omnivorous type toward more carbohydrate. To reveal their adaptation to the variable feeding customs, this study compared the gut microbiomes and chemical compositions of feces of Marabou storks inhabiting two different locations in peri urban Kampala: one is a slaughter house floc that predicted their original carnivorous feeding, and the other is a landfill floc that adapted more to the omnivorous feeding. 16S rRNA gene sequencing analysis revealed more diverse gut microbiome, more enriched Lactobacilli, and less abundant Peptostreptococci in the landfill flock comparing to the slaughter house flock. Isolation work and predicted metagenome analysis confirmed more diverse Lactobacilli and more enriched functions for carbohydrate metabolism in the landfill flock. In addition, chemical composition of feces revealed higher ammonia in the former, which is consisting with higher Peptostreptococci and their practice of carnivorous feeding. These results highlighted their adaptation to the variable feeding environment, which presumably protects their health and ensure survival of species.}, } @article {pmid36792184, year = {2023}, author = {Dong, J and Guan, W and Hu, A and Luo, Q}, title = {Mild Pulmonary Nocardiosis Caused by Nocardia terpenica in an Immunocompetent Patient.}, journal = {Internal medicine (Tokyo, Japan)}, volume = {62}, number = {19}, pages = {2911-2917}, pmid = {36792184}, issn = {1349-7235}, mesh = {Male ; Humans ; Middle Aged ; *Nocardia ; *Nocardia Infections/diagnosis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; }, abstract = {A 53-year-old immunocompetent man was admitted to our hospital because of paroxysmal cough with a low fever for more than 5 months. On admission, chest computed tomography showed multiple plaques and nodules, some with small central cavities, in both lungs and cystic and columnar bronchiectasis of the right middle bronchus. Treatment with various antibiotics was ineffective. Metagenomic next-generation sequencing of the bronchoalveolar lavage fluid showed Nocardia terpenica, and this organism was cultured from bronchoalveolar lavage fluid, resulting in a diagnosis of pulmonary nocardiosis. After administration of trimethoprim-sulfamethoxazole for 5 weeks, chest computed tomography showed a significant reduction in the lung lesions that had been detected on admission. Immunosuppressed patients are particularly prone to nocardiosis infection, which is usually severe. N. terpenica has rarely been detected in clinical samples, and its characteristics require further study with the accumulation of more clinical cases.}, } @article {pmid36791852, year = {2023}, author = {Zhang, L and Guo, H and Gu, J and Hu, T and Wang, X and Sun, Y and Li, H and Sun, W and Qian, X and Song, Z and Xie, J and An, L}, title = {Metagenomic insights into dietary remodeling of gut microbiota and antibiotic resistome in meat rabbits.}, journal = {The Science of the total environment}, volume = {874}, number = {}, pages = {162006}, doi = {10.1016/j.scitotenv.2023.162006}, pmid = {36791852}, issn = {1879-1026}, mesh = {Humans ; Animals ; Rabbits ; Cattle ; Swine ; *Gastrointestinal Microbiome ; Genes, Bacterial ; Manure ; Anti-Bacterial Agents/pharmacology ; Diet/veterinary ; Lactuca ; }, abstract = {The gut microbiota is a repository of antibiotic resistance genes (ARGs), which may affect the health of humans and animals. The intestinal flora is affected by many factors but it is unclear how the intestinal microflora and antibiotic resistome in rabbits might change under dietary intervention. Feeding with lettuce led to the amplification and transfer of exogenous ARGs in the intestinal flora, but there were no significant differences when fed lettuces grown with different manure types. For example, the lsaC of lettuce fed with bovine, chicken and pig manure without adding organic fertilizer increased by 0.143, 0.151, 0.179 and 0.169 logs respectively after 4 weeks, and the efrB also increased by 0.074, 0.068, 0.079 and 0.106 logs respectively. Network analysis showed that Clostridium_ sensu_ stricto_ 18 was a potential host of type 6 virulence factor genes (VFGs). Mantel analysis showed that ARGs were directly influenced by mobile genetic elements (MGEs) and VFGs. Thus, feeding rabbits lettuce grown with different manure types contribute to the transmission of ARGs by remodeling the intestinal microenvironment. In addition, diet may affect exogenous ARGs to change the intestinal antibiotic resistome and possibly threaten health.}, } @article {pmid36790822, year = {2023}, author = {Kirsch-Gerweck, B and Bohnenkämper, L and Henrichs, MT and Alanko, JN and Bannai, H and Cazaux, B and Peterlongo, P and Burger, J and Stoye, J and Diekmann, Y}, title = {HaploBlocks: Efficient Detection of Positive Selection in Large Population Genomic Datasets.}, journal = {Molecular biology and evolution}, volume = {40}, number = {3}, pages = {}, pmid = {36790822}, issn = {1537-1719}, mesh = {*Genetics, Population ; *Metagenomics ; Genomics ; Genome ; Haplotypes ; }, abstract = {Genomic regions under positive selection harbor variation linked for example to adaptation. Most tools for detecting positively selected variants have computational resource requirements rendering them impractical on population genomic datasets with hundreds of thousands of individuals or more. We have developed and implemented an efficient haplotype-based approach able to scan large datasets and accurately detect positive selection. We achieve this by combining a pattern matching approach based on the positional Burrows-Wheeler transform with model-based inference which only requires the evaluation of closed-form expressions. We evaluate our approach with simulations, and find it to be both sensitive and specific. The computational resource requirements quantified using UK Biobank data indicate that our implementation is scalable to population genomic datasets with millions of individuals. Our approach may serve as an algorithmic blueprint for the era of "big data" genomics: a combinatorial core coupled with statistical inference in closed form.}, } @article {pmid36790695, year = {2022}, author = {Rayo, E and Neukamm, J and Tomoum, N and Eppenberger, P and Breidenstein, A and Bouwman, AS and Schuenemann, VJ and Rühli, FJ}, title = {Metagenomic analysis of Ancient Egyptian canopic jars.}, journal = {American journal of biological anthropology}, volume = {179}, number = {2}, pages = {307-313}, pmid = {36790695}, issn = {2692-7691}, mesh = {Humans ; Egypt ; *DNA, Ancient ; *Mummies/pathology ; Lung ; Base Sequence ; }, abstract = {UNLABELLED: Ancient Egyptian remains have been of interest for anthropological research for decades. Despite many investigations, the ritual vessels for the internal organs removed during body preparation-liver, lungs, stomach, and intestines, of Egyptian mummies are rarely used for palaeopathological or medical investigations. These artifacts, commonly referred to as canopic jars, are the perfect combination of cultural and biological material and present an untapped resource for both Egyptological and medical fields. Nevertheless, technical challenges associated with this archeological material have prevented the application of current ancient DNA techniques for both the characterization of human and pathogenic DNA. We present shotgun-sequenced metagenomic profiles and ancient DNA degradation patterns from multiple canopic jars sampled from several European museum collections and enumerate current limitations and possible solutions for the future analysis of similar material. This is the first-ever recorded evidence of ancient human DNA found in Ancient Egyptian canopic jars and the first associated metagenomic description of bacterial taxa in these funerary artifacts.

OBJECTIVES: In this study, our objectives were to characterize the metagenomic profile of the Ancient Egyptian funerary vessels known as canopic jars to retrieve endogenous ancient human DNA, reconstruct ancient microbial communities, and identify possible pathogens that could shed light on disease states of individuals from the past.

METHODS: We applied ancient DNA techniques on 140 canopic jars to extract DNA and generate whole-genome sequencing libraries for the analysis of both human and bacterial DNA. The samples were obtained from museum collections in Berlin (DE), Burgdorf (DE), Leiden (NE), Manchester (UK), Munich (DE), St. Gallen (CH), Turin (IT), and Zagreb (HR).

RESULTS: Here we describe the first isolated DNA from the Egyptian artifacts that hold human viscera. No previous work was ever conducted on such material, which led to the first characterization of human DNA from Ancient Egyptian canopic jars and the profiling of the complex bacterial composition of this highly degraded, challenging, organic material. However, the DNA recovered was not of enough quality to confidently characterize bacterial taxa associated with infectious diseases, nor exclusive bacterial members of the human microbiome.

DISCUSSION: In summary, we present the first genomic survey of the visceral content of Ancient Egyptian funerary artifacts and demonstrate the limitations of current molecular methods to analyze canopic jars, such as the incomplete history of the objects or the presence of uncharacterized compounds that can hamper the recovery of DNA. Our work highlights the main challenges and caveats when working with such complicated archeological material - and offers sampling recommendations for similarly complex future studies, such as incrementing the amount of starting material and sampling from the less exposed parts of the jar content. This is the first-ever recorded evidence of ancient human DNA found in Ancient Egyptian canopic jars, and our results open new avenues in the study of neglected archeological artifacts.}, } @article {pmid36790661, year = {2023}, author = {Mao, B and Guo, W and Liu, X and Cui, S and Zhang, Q and Zhao, J and Tang, X and Zhang, H}, title = {Potential Probiotic Properties of Blautia producta Against Lipopolysaccharide-Induced Acute Liver Injury.}, journal = {Probiotics and antimicrobial proteins}, volume = {15}, number = {3}, pages = {785-796}, pmid = {36790661}, issn = {1867-1314}, mesh = {Mice ; Animals ; Lipopolysaccharides/toxicity ; Interleukin-6 ; Tumor Necrosis Factor-alpha ; *Chemical and Drug Induced Liver Injury ; *Probiotics ; Mammals ; }, abstract = {Blautia is a genus of anaerobic microbe extensively present in the intestine and feces of mammals. This study aims to investigate the influence of Blautia producta to prevent lipopolysaccharide (LPS)-induced acute liver injury (ALI) and elaborate on its hepatoprotective mechanisms. B. producta D4 and DSM2950 pretreatment decreased the activities of serum aspartate transferase (AST), and alanine transaminase (ALT) in mice with LPS treatment significantly decreased the levels of inflammatory tumor necrosis factor-α (TNF-α), interleukin-1β (IL-1β), and interleukin-6 (IL-6) and increased the activities of antioxidative superoxide dismutase (SOD), catalase (CAT), and glutathione peroxidase (GSH-Px). Compared with the model group, B. producta D4 and B. producta DSM2950 pretreatment slightly increased the levels of cecal propionic acid, isobutyric acid, butyric acid, valeric acid, and isovaleric acid (p > 0.05). Metagenomic analysis showed that B. producta D4 and DSM2950 pretreatment remarkably increased the relative abundance of [Eubacterium] xylanophilum group, Lachnospira, Ruminiclostridium, Ruminiclostridium 9, Coprococcus 2, Odoribacter, Roseburia, Alistipes, and Desulfovibrio in ALI mice, and their abundance is negatively related to the levels of inflammatory TNF-α, IL-1β, and IL-6 as revealed by Spearman's correlation analysis. Moreover, transcription and immunohistochemistry analysis revealed that B. producta D4 and B. producta DSM2950 intervention remarkably suppressed the transcription and expression levels of hepatic Tlr4, MyD88, and caspase-3 (p < 0.05). These data indicated that B. producta may be a good candidate for probiotics in the prevention of ALI.}, } @article {pmid36790176, year = {2023}, author = {Lei, Y and Asamizu, S and Ishizuka, T and Onaka, H}, title = {Regulation of Multidrug Efflux Pumps by TetR Family Transcriptional Repressor Negatively Affects Secondary Metabolism in Streptomyces coelicolor A3(2).}, journal = {Applied and environmental microbiology}, volume = {89}, number = {3}, pages = {e0182222}, pmid = {36790176}, issn = {1098-5336}, mesh = {*Streptomyces coelicolor/metabolism ; Secondary Metabolism ; Ecosystem ; Transcription Factors/metabolism ; Anti-Bacterial Agents/pharmacology ; *Streptomyces/metabolism ; ATP-Binding Cassette Transporters/genetics/metabolism ; Adenosine Triphosphate/metabolism ; Gene Expression Regulation, Bacterial ; Bacterial Proteins/metabolism ; }, abstract = {Streptomyces spp. are well-known producers of bioactive secondary metabolites (SMs) that serve as pharmaceutical agents. In addition to their ability to produce SMs, Streptomyces spp. have evolved diverse membrane transport systems to protect cells against antibiotics produced by itself or other microorganisms. We previously screened mutants of Streptomyces coelicolor that show a phenotype of reduced undecylprodigiosin (RED) production in a combined-culture with Tsukamurella pulmonis. Here, we identified a point mutation, which reduced RED production, by performing genome resequencing and genetic complementation. We found that inactivation of the sco1718 gene encoding the TetR family transcriptional regulator (TFR) produced a deficient phenotype for several SMs in Streptomyces coelicolor A3(2). In the genome of S. coelicolor A3(2), two other sets of TFR and two-component ATP-binding cassette (ABC) transporter genes (sco4358-4360 and sco5384-5382) were found which had similar effects on the phenotype for both secondary metabolism and antibiotic resistance. An electrophoretic mobility shift assay and quantitative reverse transcription-PCR experiments demonstrated that TFRs repressed the expression of each adjacent two-component ABC transporter genes by binding to the operator sequence. Notably, the Δsco1718 mutant showed increased resistance to several antibiotics of other actinomycete origin. Our results imply the switching of cell metabolism to direct offense (antibiotic production) or defense (efflux pump activation) using costly and limited quantities of cell energy sources (e.g., ATP) in the soil ecosystem. IMPORTANCE The bacterial metabolic potential to synthesize diverse secondary metabolites in the environment has been revealed by recent (meta)genomics of both unculturable and culturable bacteria. These studies imply that bacteria are continuously exposed to harmful chemical compounds in the environment. Streptomyces spp. contain antibiotic efflux pumps and SM biosynthetic gene clusters. However, the mechanism by which soil bacteria, including Streptomyces, survive against toxic compounds in the environment remains unclear. Here, we identified three sets of TFR-ABC transporter genes in Streptomyces coelicolor A3(2). We found that each TFR controlled the expression of respective ABC transporter, and the expression of all ABC transporters negatively impacted SM production and increased antibiotic resistance. Notably, bioinformatic analysis indicated that these TFR-ABC transporter gene sets are highly conserved and widely distributed in the genome of Streptomyces species, indicating the importance of systematic regulation that directs antibiotic production and xenobiotic excretion.}, } @article {pmid36790127, year = {2023}, author = {Salloum, PM and Jorge, F and Dheilly, NM and Poulin, R}, title = {Eco-evolutionary implications of helminth microbiomes.}, journal = {Journal of helminthology}, volume = {97}, number = {}, pages = {e22}, doi = {10.1017/S0022149X23000056}, pmid = {36790127}, issn = {1475-2697}, mesh = {Animals ; *Helminths/genetics ; *Microbiota ; *Parasites ; Host-Parasite Interactions ; Symbiosis ; }, abstract = {The evolution of helminth parasites has long been seen as an interplay between host resistance to infection and the parasite's capacity to bypass such resistance. However, there has recently been an increasing appreciation of the role of symbiotic microbes in the interaction of helminth parasites and their hosts. It is now clear that helminths have a different microbiome from the organisms they parasitize, and sometimes amid large variability, components of the microbiome are shared among different life stages or among populations of the parasite. Helminths have been shown to acquire microbes from their parent generations (vertical transmission) and from their surroundings (horizontal transmission). In this latter case, natural selection has been strongly linked to the fact that helminth-associated microbiota is not simply a random assemblage of the pool of microbes available from their organismal hosts or environments. Indeed, some helminth parasites and specific microbial taxa have evolved complex ecological relationships, ranging from obligate mutualism to reproductive manipulation of the helminth by associated microbes. However, our understanding is still very elementary regarding the net effect of all microbiome components in the eco-evolution of helminths and their interaction with hosts. In this non-exhaustible review, we focus on the bacterial microbiome associated with helminths (as opposed to the microbiome of their hosts) and highlight relevant concepts and key findings in bacterial transmission, ecological associations, and taxonomic and functional diversity of the bacteriome. We integrate the microbiome dimension in a discussion of the evolution of helminth parasites and identify fundamental knowledge gaps, finally suggesting research avenues for understanding the eco-evolutionary impacts of the microbiome in host-parasite interactions in light of new technological developments.}, } @article {pmid36789238, year = {2023}, author = {Borer, B and Magnúsdóttir, S}, title = {The media composition as a crucial element in high-throughput metabolic network reconstruction.}, journal = {Interface focus}, volume = {13}, number = {2}, pages = {20220070}, pmid = {36789238}, issn = {2042-8898}, abstract = {In recent years, metagenome-assembled genomes (MAGs) have provided glimpses into the intra- and interspecies genetic diversity and interactions that form the bases of complex microbial communities. High-throughput reconstruction of genome-scale metabolic networks (GEMs) from MAGs is a promising avenue to disentangle the myriad trophic interactions stabilizing these communities. However, high-throughput reconstruction of GEMs relies on accurate gap filling of metabolic pathways using automated algorithms. Here, we systematically explore how the composition of the media (specification of the available nutrients and metabolites) during gap filling influences the resulting GEMs concerning predicted auxotrophies for fully sequenced model organisms and environmental isolates. We expand this analysis by using 106 MAGs from the same species with differing quality. We find that although the completeness of MAGs influences the fraction of gap-filled reactions, the composition of the media plays the dominant role in the accurate prediction of auxotrophies that form the basis of myriad community interactions. We propose that constraining the media composition for gap filling through both experimental approaches and computational approaches will increase the reliability of high-throughput reconstruction of genome-scale metabolic models from MAGs and paves the way for culture independent prediction of trophic interactions in complex microbial communities.}, } @article {pmid36789031, year = {2023}, author = {Ji, B and Pi, W and Liu, W and Liu, Y and Cui, Y and Zhang, X and Peng, S}, title = {HyperVR: a hybrid deep ensemble learning approach for simultaneously predicting virulence factors and antibiotic resistance genes.}, journal = {NAR genomics and bioinformatics}, volume = {5}, number = {1}, pages = {lqad012}, pmid = {36789031}, issn = {2631-9268}, abstract = {Infectious diseases emerge unprecedentedly, posing serious challenges to public health and the global economy. Virulence factors (VFs) enable pathogens to adhere, reproduce and cause damage to host cells, and antibiotic resistance genes (ARGs) allow pathogens to evade otherwise curable treatments. Simultaneous identification of VFs and ARGs can save pathogen surveillance time, especially in situ epidemic pathogen detection. However, most tools can only predict either VFs or ARGs. Few tools that predict VFs and ARGs simultaneously usually have high false-negative rates, are sensitive to the cutoff thresholds and can only identify conserved genes. For better simultaneous prediction of VFs and ARGs, we propose a hybrid deep ensemble learning approach called HyperVR. By considering both best hit scores and statistical gene sequence patterns, HyperVR combines classical machine learning and deep learning to simultaneously and accurately predict VFs, ARGs and negative genes (neither VFs nor ARGs). For the prediction of individual VFs and ARGs, in silico spike-in experiment (the VFs and ARGs in real metagenomic data), and pseudo-VFs and -ARGs (gene fragments), HyperVR outperforms the current state-of-the-art prediction tools. HyperVR uses only gene sequence information without strict cutoff thresholds, hence making prediction straightforward and reliable.}, } @article {pmid36788626, year = {2023}, author = {Rieder, J and Kapopoulou, A and Bank, C and Adrian-Kalchhauser, I}, title = {Metagenomics and metabarcoding experimental choices and their impact on microbial community characterization in freshwater recirculating aquaculture systems.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {8}, pmid = {36788626}, issn = {2524-6372}, support = {315230_204838/1//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 315230_204838/1//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 315230_204838/1//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; 315230_204838/1//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung/ ; }, abstract = {BACKGROUND: Microbial communities in recirculating aquaculture systems (RAS) play a role in system success, nutrient cycling, and water quality. Considering the increasing socio-economic role of fish farming, e.g., regarding food security, an in-depth understanding of aquaculture microbial communities is also relevant from a management perspective, especially regarding the growth, development, and welfare of the farmed animal. However, the current data on the composition of microbial communities within RAS is patchy, which is partly attributable to diverging method choices that render comparative analyses challenging. Therefore, there is a need for accurate, standardized, and user-friendly methods to study microbial communities in aquaculture systems.

RESULTS: We compared sequencing approach performances (3 types of 16S short amplicon sequencing, PacBio long-read amplicon sequencing, and amplification-free shotgun metagenomics) in the characterization of microbial communities in two commercial RAS fish farms. Results showed that 16S primer choice and amplicon length affect some values (e.g., diversity measures, number of assigned taxa or distinguishing ASVs) but have no impact on spatio-temporal patterns between sample types, farms and time points. This implies that 16S rRNA approaches are adequate for community studies. The long-read amplicons underperformed regarding the quantitative resolution of spatio-temporal patterns but were suited to identify functional services, e.g., nitrification cycling and the detection of pathogens. Finally, shotgun metagenomics extended the picture to fungi, viruses, and bacteriophages, opening avenues for exploring inter-domain interactions. All sequencing datasets agreed on major prokaryotic players, such as Actinobacteriota, Bacteroidota, Nitrospirota, and Proteobacteria.

CONCLUSION: The different sequencing approaches yielded overlapping and highly complementary results, with each contributing unique data not obtainable with the other approaches. We conclude that a tiered approach constitutes a strategy for obtaining the maximum amount of information on aquaculture microbial communities and can inform basic research on community evolution dynamics. For specific and/or applied questions, single-method approaches are more practical and cost-effective and could lead to better farm management practices.}, } @article {pmid36788222, year = {2023}, author = {Gupta, Y and Ernst, AL and Vorobyev, A and Beltsiou, F and Zillikens, D and Bieber, K and Sanna-Cherchi, S and Christiano, AM and Sadik, CD and Ludwig, RJ and Sezin, T}, title = {Impact of diet and host genetics on the murine intestinal mycobiome.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {834}, pmid = {36788222}, issn = {2041-1723}, mesh = {Male ; Female ; Animals ; Mice ; *Mycobiome/genetics ; Ecosystem ; Diet ; Quantitative Trait Loci ; Bacteria/genetics ; Fungi/genetics ; Mammals/genetics ; }, abstract = {The mammalian gut is home to a diverse microbial ecosystem, whose composition affects various physiological traits of the host. Next-generation sequencing-based metagenomic approaches demonstrated how the interplay of host genetics, bacteria, and environmental factors shape complex traits and clinical outcomes. However, the role of fungi in these complex interactions remains understudied. Here, using 228 males and 363 females from an advanced-intercross mouse line, we provide evidence that fungi are regulated by host genetics. In addition, we map quantitative trait loci associated with various fungal species to single genes in mice using whole genome sequencing and genotyping. Moreover, we show that diet and its' interaction with host genetics alter the composition of fungi in outbred mice, and identify fungal indicator species associated with different dietary regimes. Collectively, in this work, we uncover an association of the intestinal fungal community with host genetics and a regulatory role of diet in this ecological niche.}, } @article {pmid36788215, year = {2023}, author = {Robertson, RC and Edens, TJ and Carr, L and Mutasa, K and Gough, EK and Evans, C and Geum, HM and Baharmand, I and Gill, SK and Ntozini, R and Smith, LE and Chasekwa, B and Majo, FD and Tavengwa, NV and Mutasa, B and Francis, F and Tome, J and Stoltzfus, RJ and Humphrey, JH and Prendergast, AJ and Manges, AR}, title = {The gut microbiome and early-life growth in a population with high prevalence of stunting.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {654}, pmid = {36788215}, issn = {2041-1723}, support = {206455/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; R01 HD060338/HD/NICHD NIH HHS/United States ; }, mesh = {Infant ; Child ; Humans ; Child, Preschool ; *Gastrointestinal Microbiome/genetics ; Prevalence ; *HIV Infections ; Growth Disorders/epidemiology ; Water Supply ; }, abstract = {Stunting affects one-in-five children globally and is associated with greater infectious morbidity, mortality and neurodevelopmental deficits. Recent evidence suggests that the early-life gut microbiome affects child growth through immune, metabolic and endocrine pathways. Using whole metagenomic sequencing, we map the assembly of the gut microbiome in 335 children from rural Zimbabwe from 1-18 months of age who were enrolled in the Sanitation, Hygiene, Infant Nutrition Efficacy Trial (SHINE; NCT01824940), a randomized trial of improved water, sanitation and hygiene (WASH) and infant and young child feeding (IYCF). Here, we show that the early-life gut microbiome undergoes programmed assembly that is unresponsive to the randomized interventions intended to improve linear growth. However, maternal HIV infection is associated with over-diversification and over-maturity of the early-life gut microbiome in their uninfected children, in addition to reduced abundance of Bifidobacterium species. Using machine learning models (XGBoost), we show that taxonomic microbiome features are poorly predictive of child growth, however functional metagenomic features, particularly B-vitamin and nucleotide biosynthesis pathways, moderately predict both attained linear and ponderal growth and growth velocity. New approaches targeting the gut microbiome in early childhood may complement efforts to combat child undernutrition.}, } @article {pmid36787941, year = {2023}, author = {, }, title = {[Consensus of clinical pathways of metagenomic next-generation sequencing test in diagnosis of lower respiratory tract infections in China].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {46}, number = {4}, pages = {322-335}, doi = {10.3760/cma.j.cn112147-20220701-00553}, pmid = {36787941}, issn = {1001-0939}, support = {SQ2022YFA1300137//National Key R&D Program of China/ ; ZYYCXTD-D-202208//Innovation Team and Talents Cultivation Program of National Administration of Traditional Chinese Medicine/ ; }, mesh = {Humans ; *Critical Pathways ; Consensus ; China ; High-Throughput Nucleotide Sequencing ; *Respiratory Tract Infections/diagnosis ; Sensitivity and Specificity ; }, abstract = {Metagenomic next-generation sequencing (mNGS) enables sensitive and unbiased detection of all potential pathogens in lower respiratory tract infection(LRTI). But the lack of consensus and uniformity of applicable clinical scenarios and interpretation of results for mNGS largely limit its utilization. To solve these issues, an expert panel including pulmonary physicians, intensivists and microbiologists is organized by Chinese Thoracic Society. The panel conducted a systematic review of progress and challenges regarding the application of mNGS on etiological diagnosis of LRTI. The panel formulated 17 specific recommendations spanning questions of suitable clinical situations, sample quality control, process of reports interpretation and subsequent medical decisions. Hopefully, this consensus can provide practical guidelines for clinicians and promote the rational application of mNGS in LRTI.}, } @article {pmid36786768, year = {2023}, author = {Yang, R and Shan, S and Shi, J and Li, H and An, N and Li, S and Cui, K and Guo, H and Li, Z}, title = {Coprococcus eutactus, a Potent Probiotic, Alleviates Colitis via Acetate-Mediated IgA Response and Microbiota Restoration.}, journal = {Journal of agricultural and food chemistry}, volume = {}, number = {}, pages = {}, doi = {10.1021/acs.jafc.2c06697}, pmid = {36786768}, issn = {1520-5118}, abstract = {Inflammatory bowel disease (IBD) is a complex disease characterized by relapsing episodes of inflammation of the colonic mucosa. Research into IBD suggests that this disease condition is caused by alterations in resident mucosal bacterial populations. Our previous study showed that Coprococcus was significantly elevated during the improvement of IBD. Human metagenome database GMrepo also indicates Coprococcus, in particular, Coprococcus eutactus (C. eutactus), which was negatively associated with IBD. The current study implied the alleviated effects and mechanisms of C. eutactus on dextran sodium sulfate-induced experimental colitis mice. Gavage with C. eutactus-ameliorated acute colitis, as evidenced, relieved weight loss, decreased concentrations of proinflammatory cytokines TNF-α, IL-1β, and IL-6, and increased anti-inflammatory factors, IL-4, IL-5, and IL-10. In addition, C. eutactus enhanced the maturation of goblet cells and the expressions of mucins and restored the expressions of tight junction proteins such as claudin-1, occludin, and ZO-1. As a short-chain fatty acid-producing bacterium, C. eutactus mainly generates acetic acid. Interestingly, not only high levels of secretory immunoglobulin A (SIgA) but also increased IgA-producing plasma cells were observed in colitis mice during the administration of C. eutactus. Importantly, our data demonstrated that colonic SIgA is specifically coated on pathogens of Enterobacteriaceae. Owing to the selective binding effect of SIgA on microorganisms, the microbial diversity in the intestinal lumen and mucosa of C. eutactus-treated colitis mice was significantly restored, and the microbiota structure was remodeled. These findings provide substantial insight that C. eutactus as a promising probiotic can ameliorate colitis. In conclusion, our findings may deliver a novel approach to the prevention and biotherapy of IBD.}, } @article {pmid36786639, year = {2023}, author = {Talat, A and Blake, KS and Dantas, G and Khan, AU}, title = {Metagenomic Insight into Microbiome and Antibiotic Resistance Genes of High Clinical Concern in Urban and Rural Hospital Wastewater of Northern India Origin: a Major Reservoir of Antimicrobial Resistance.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0410222}, pmid = {36786639}, issn = {2165-0497}, abstract = {India is one of the largest consumers and producers of antibiotics and a hot spot for the emergence and proliferation of antimicrobial resistance genes (ARGs). Indian hospital wastewater (HWW) accumulates ARGs from source hospitals and often merges with urban wastewater, with the potential for environmental and human contamination. Despite its putative clinical importance, there is a lack of high-resolution resistome profiling of Indian hospital wastewater, with most studies either relying on conventional PCR-biased techniques or being limited to one city. In this study, we comprehensively analyzed antibiotic resistomes of wastewater from six Indian hospitals distributed in rural and urban areas of northern India through shotgun metagenomics. Our study revealed the predominance of ARGs against aminoglycoside, macrolide, carbapenem, trimethoprim, and sulfonamide antibiotics in all the samples through both read-based analysis and assembly-based analysis. We detected the mobile colistin resistance gene mcr-5.1 for the first time in Indian hospital sewage. blaNDM-1 was present in 4 out of 6 samples and was carried by Pseudomonas aeruginosa in HWW-2, Klebsiella pneumoniae in HWW-4 and HWW-6, and Acinetobacter baumanii in HWW-5. Most ARGs were plasmid-mediated and hosted by Proteobacteria. We identified virulence factors and transposable elements flanking the ARGs, highlighting the role of horizontal gene transmission of ARGs. IMPORTANCE There is a paucity of research on detailed antibiotic resistome and microbiome diversity of Indian hospital wastewater. This study reports the predominance of clinically concerning ARGs such as the beta-lactamases blaNDM and blaOXA and the colistin resistance gene mcr and their association with the microbiome in six different Indian hospital wastewaters of both urban and rural origin. The abundance of plasmid-mediated ARGs and virulence factors calls for urgent AMR crisis management. The lack of proper wastewater management strategies meeting international standards and open drainage systems further complicates the problem of containing the ARGs at these hospitals. This metagenomic study presents the current AMR profile propagating in hospital settings in India and can be used as a reference for future surveillance and risk management of ARGs in Indian hospitals.}, } @article {pmid36786619, year = {2023}, author = {Murga-Garrido, SM and Ulloa-Pérez, EJ and Díaz-Benítez, CE and Orbe-Orihuela, YC and Cornejo-Granados, F and Ochoa-Leyva, A and Sanchez-Flores, A and Cruz, M and Castañeda-Márquez, AC and Plett-Torres, T and Burguete García, AI and Lagunas-Martínez, A}, title = {Virulence Factors of the Gut Microbiome Are Associated with BMI and Metabolic Blood Parameters in Children with Obesity.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0338222}, pmid = {36786619}, issn = {2165-0497}, abstract = {The development of metabolic diseases is linked to the gut microbiota. A cross-sectional study involving 45 children (6 to 12 years old) was conducted to investigate the relationship between gut microbiota and childhood obesity. Anthropometric and metabolic measurements, food-frequency questionnaires (FFQs), and feces samples were obtained. Using the body mass index (BMI) z-score, we categorized each participant as normal weight (NW), or overweight and obese (OWOB). We determined 2 dietary profiles: one with complex carbohydrates and proteins (pattern 1), and the other with saturated fat and simple carbohydrates (pattern 2). The microbial taxonomic diversity and metabolic capacity were determined using shotgun metagenomics. We found differences between both BMI groups diversity. Taxa contributing to this difference, included Eubacterium sp., Faecalibacterium prausnitzii, Dialister, Monoglobus pectinilyticus, Bifidobacterium pseudocatenulatum, Intestinibacter bartlettii, Bacteroides intestinalis, Bacteroides uniformis, and Methanobrevibacter smithii. Metabolic capacity differences found between NW and OWOB, included the amino acid biosynthesis pathway, the cofactor, carrier, and vitamin biosynthesis pathway, the nucleoside and nucleotide biosynthesis and degradation pathways, the carbohydrate-sugar degradation pathway, and the amine and polyamine biosynthesis pathway. We found significant associations between taxa such as Ruminococcus, Mitsuokella multacida, Klebsiella variicola, and Citrobacter spp., metabolic pathways with the anthropometric, metabolic, and dietary data. We also found the microbiome's lipooligosaccharide (LOS) category as differentially abundant between BMI groups. Metabolic variations emerge during childhood as a result of complex nutritional and microbial interactions, which should be explained in order to prevent metabolic illnesses in adolescence and maturity. IMPORTANCE The alteration of gut microbiome composition has been commonly observed in diseases involving inflammation, such as obesity and metabolic impairment. Inflammatory host response in the gut can be a consequence of dietary driven dysbiosis. This response is conducive to blooms of particular bacterial species, adequate to survive in an inflammatory environment by means of genetical capability of utilizing alternative nutrients. Understanding the genomic and metabolic contribution of microbiota to inflammation, including virulence factor prevalence and functional potential, will contribute to identifying modifiable early life exposures and preventive strategies associated with obesity risk in childhood.}, } @article {pmid36786595, year = {2023}, author = {Szóstak, N and Handschuh, L and Samelak-Czajka, A and Tomela, K and Schmidt, M and Pruss, Ł and Milanowska-Zabel, K and Kozlowski, P and Philips, A}, title = {Host Factors Associated with Gut Mycobiome Structure.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0098622}, pmid = {36786595}, issn = {2379-5077}, mesh = {Humans ; *Mycobiome ; Cohort Studies ; Fungi/genetics ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; Candida ; *Saccharomyces ; Saccharomyces cerevisiae ; }, abstract = {Recent studies revealed a significant role of the gut fungal community in human health. Here, we investigated the content and variation of gut mycobiota among subjects from the European population. We explored the interplay between gut fungi and various host-related sociodemographic, lifestyle, health, and dietary factors. The study included 923 participants. Fecal DNA samples were analyzed by whole-metagenome high-throughput sequencing. Subsequently, fungi taxonomic profiles were determined and accompanied by computational and statistical analyses of the association with 53 host-related factors. Fungal communities were characterized by a high prevalence of Saccharomyces, Candida, and Sporisorium. Ten factors were found to correlate significantly with the overall mycobiota variation. Most were diet related, including the consumption of chips, meat, sodas, sweetening, processed food, and alcohol, followed by age and marital status. Differences in α- and/or β-diversity were also reported for other factors such as body mass index (BMI), job type, autoimmunological diseases, and probiotics. Differential abundance analysis revealed fungal species that exhibited different patterns of changes under specific conditions. The human gut mycobiota is dominated by yeast, including Saccharomyces, Malassezia, and Candida. Although intervolunteer variability was high, several fungal species persisted across most samples, which may be evidence that a core gut mycobiota exists. Moreover, we showed that host-related factors such as diet, age, and marital status influence the variability of gut mycobiota. To our knowledge, this is the first large and comprehensive study of the European cohort in terms of gut mycobiota associations with such an extensive and differentiated host-related set of factors. IMPORTANCE The human gut is inhabited by many organisms, including bacteria and fungi, that may affect human health. However, research on human gut mycobiome is still rare. Moreover, the large European-based cohort study is missing. Here, we analyzed the first large European cohort in terms of gut mycobiota associations with a differentiated host-related set of factors. Our results showed that chips, meat, sodas, sweetening, processed food, beer, alcohol consumption, age, and marital status were associated with the variability of gut mycobiota. Moreover, our analysis revealed changes in abundances at the fungal species level for many investigated factors. Our results can suggest potentially valuable paths for further, narrowly focused research on gut mycobiome and its impact on human health. In the coming era of gut microbiome-based precision medicine, further research into the relationship between different mycobial structures and host-related factors may result in new preventive approaches or therapeutic procedures.}, } @article {pmid36786580, year = {2023}, author = {Gittins, DA and Bhatnagar, S and Hubert, CRJ}, title = {Environmental Selection and Biogeography Shape the Microbiome of Subsurface Petroleum Reservoirs.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0088422}, pmid = {36786580}, issn = {2379-5077}, mesh = {*Petroleum/metabolism ; RNA, Ribosomal, 16S/genetics ; Oil and Gas Fields ; *Microbiota/genetics ; Carbon ; }, abstract = {Petroleum reservoirs within the deep biosphere are extreme environments inhabited by diverse microbial communities and represent biogeochemical hot spots in the subsurface. Despite the ecological and industrial importance of oil reservoir microbiomes, systematic study of core microbial taxa and their associated genomic attributes spanning different environmental conditions is limited. Here, we compile and compare 343 16S rRNA gene amplicon libraries and 25 shotgun metagenomic libraries from oil reservoirs in different parts of the world to test for the presence of core taxa and functions. These oil reservoir libraries do not share any core taxa at the species, genus, family, or order levels, and Gammaproteobacteria was the only taxonomic class detected in all samples. Instead, taxonomic composition varies among reservoirs with different physicochemical characteristics and with geographic distance highlighting environmental selection and biogeography in these deep biosphere habitats. Gene-centric metagenomic analysis reveals a functional core of metabolic pathways including carbon acquisition and energy-yielding strategies consistent with biogeochemical cycling in other subsurface environments. Genes for anaerobic hydrocarbon degradation are observed in a subset of the samples and are therefore not considered to represent core functions in oil reservoirs despite hydrocarbons representing an abundant source of carbon in these deep biosphere settings. Overall, this work reveals common and divergent features of oil reservoir microbiomes that are shaped by and responsive to environmental factors, highlighting controls on subsurface microbial community assembly. IMPORTANCE This comprehensive analysis showcases how environmental selection and geographic distance influence the microbiome of subsurface petroleum reservoirs. We reveal substantial differences in the taxonomy of the inhabiting microbes but shared metabolic function between reservoirs with different in situ temperatures and between reservoirs separated by large distances. The study helps understand and advance the field of deep biosphere science by providing an ecological framework and footing for geologists, chemists, and microbiologists studying these habitats to elucidate major controls on deep biosphere microbial ecology.}, } @article {pmid36785766, year = {2023}, author = {Zeng, G and Lu, J}, title = {Mycobacterium xenopi infection of the kidney and lymph nodes: A case report.}, journal = {Open medicine (Warsaw, Poland)}, volume = {18}, number = {1}, pages = {20230646}, pmid = {36785766}, issn = {2391-5463}, abstract = {The incidence of nontuberculous mycobacterial (NTM) infection has been increasing globally. Further, it has been reported that early NTM infection diagnosis and treatment can considerably improve patient prognosis. However, traditional methods for detecting pathogenic microorganisms are associated with several limitations, and optimal treatment regimens for several NTM infections have not yet been established. Here, we report the case of a 22-year-old woman with renal and lymph node Mycobacterium xenopi infection. This patient presented with repeated fever and systemic lymphadenopathy events for more than 2 years, but the etiology of the disease was unclear. We performed metagenomic next-generation sequencing (mNGS) using tissue sections from the patient's left kidney and successfully identified M. xenopi. Thereafter, the patient's condition was effectively controlled via treatment with rifampicin, clarithromycin, and ethambutol hydrochloride (orally administered after hemodialysis). Further, this case showed that the clinical symptoms of NTM infection are atypical and highly occult, especially for extrapulmonary NTM infections, which are difficult to diagnose. Therefore, mNGS may be a powerful tool for diagnosing NTM infections. The combination therapy used showed efficacy and thus could serve as a reference treatment for kidney and lymph node M. xenopi infection.}, } @article {pmid36782241, year = {2023}, author = {Fontana, F and Longhi, G and Tarracchini, C and Mancabelli, L and Lugli, GA and Alessandri, G and Turroni, F and Milani, C and Ventura, M}, title = {The human gut microbiome of athletes: metagenomic and metabolic insights.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {27}, pmid = {36782241}, issn = {2049-2618}, mesh = {Adult ; Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Metagenome ; Bacteria/genetics ; Athletes ; Feces/microbiology ; Metagenomics ; }, abstract = {BACKGROUND: The correlation between the physical performance of athletes and their gut microbiota has become of growing interest in the past years, since new evidences have emerged regarding the importance of the gut microbiota as a main driver of the health status of athletes. In addition, it has been postulated that the metabolic activity of the microbial population harbored by the large intestine of athletes might influence their physical performances. Here, we analyzed 418 publicly available shotgun metagenomics datasets obtained from fecal samples of healthy athletes and healthy sedentary adults.

RESULTS: This study evidenced how agonistic physical activity and related lifestyle can be associated with the modulation of the gut microbiota composition, inducing modifications of the taxonomic profiles with an enhancement of gut microbes able to produce short-fatty acid (SCFAs). In addition, our analyses revealed a correlation between specific bacterial species and high impact biological synthases (HIBSs) responsible for the generation of a range of microbially driven compounds such vitamin B12, amino acidic derivatives, and other molecules linked to cardiovascular and age-related health-risk reduction.

CONCLUSIONS: Notably, our findings show how subsist an association between competitive athletes, and modulation of the gut microbiota, and how this modulation is reflected in the potential production of microbial metabolites that can lead to beneficial effects on human physical performance and health conditions. Video Abstract.}, } @article {pmid36782173, year = {2023}, author = {Li, K and Wu, J and Chen, J and You, Y}, title = {Glial fibrillary acidic protein astrocytopathy and tuberculous meningoencephalitis occurring in a patient with Legionella pneumonia: a case report.}, journal = {BMC neurology}, volume = {23}, number = {1}, pages = {69}, pmid = {36782173}, issn = {1471-2377}, mesh = {Male ; Humans ; Glial Fibrillary Acidic Protein ; Cough ; *Meningoencephalitis/complications/diagnosis ; Autoantibodies/cerebrospinal fluid ; *Tuberculosis, Meningeal ; Fever ; *Legionella/metabolism ; *Pneumonia ; }, abstract = {BACKGROUND: Autoimmune glial fibrillary acidic protein (GFAP) astrocytopathy is a recently identified recurrent meningoencephalomyelitis with GFAP immunoglobulin G presence in the serum or cerebrospinal fluid (CSF) as a specific biomarker. GFAP astrocytopathy is closely associated with the occurrence of some tumors and often coexists with other antibodies, such as the N-methyl-D-aspartate receptor and aquaporin-4 antibodies. However, GFAP astrocytopathy complicated by central nervous system infection is rare.

CASE PRESENTATION: Here, we present the case of a patient admitted to a local hospital due to a prominent fever and cough. The patient had a 1-month history of headaches before admission that were not considered serious at the time. Metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid revealed a high sequence number of Legionella pneumophila and a few mycobacteria. His cough and fever improved significantly after antibiotic treatment. Still, a slight headache remained. Subsequently, his condition worsened, and he visited our hospital with a disturbance of consciousness. Mycobacterium tuberculosis was detected with mNGS of the CSF, while the CSF and serum were also positive for GFAP antibodies. Following anti-tuberculosis and steroid therapy, the patient's symptoms improved, and he tested negative for the GFAP antibody.

CONCLUSION: This is the first reported case of GFAP astrocytopathy complicated by tuberculous meningoencephalitis. Due to overlaps in the clinical manifestations of the two diseases, GFAP astrocytopathy is sometimes misdiagnosed as tuberculous meningoencephalitis. Therefore, in addition to ensuring careful identification of the two diseases, clinicians need to be aware of their possible co-existence.}, } @article {pmid36782070, year = {2023}, author = {Pascal Andreu, V and Augustijn, HE and Chen, L and Zhernakova, A and Fu, J and Fischbach, MA and Dodd, D and Medema, MH}, title = {gutSMASH predicts specialized primary metabolic pathways from the human gut microbiota.}, journal = {Nature biotechnology}, volume = {41}, number = {10}, pages = {1416-1423}, pmid = {36782070}, issn = {1546-1696}, support = {R01 DK101674/DK/NIDDK NIH HHS/United States ; K08 DK110335/DK/NIDDK NIH HHS/United States ; R35 GM142873/GM/NIGMS NIH HHS/United States ; R01 AT011396/AT/NCCIH NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; DP1 DK113598/DK/NIDDK NIH HHS/United States ; DP1 DK113598/DK/NIDDK NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; K08 DK110335/DK/NIDDK NIH HHS/United States ; R35 GM142873/GM/NIGMS NIH HHS/United States ; R01 AT011396/AT/NCCIH NIH HHS/United States ; }, abstract = {The gut microbiota produce hundreds of small molecules, many of which modulate host physiology. Although efforts have been made to identify biosynthetic genes for secondary metabolites, the chemical output of the gut microbiome consists predominantly of primary metabolites. Here we introduce the gutSMASH algorithm for identification of primary metabolic gene clusters, and we used it to systematically profile gut microbiome metabolism, identifying 19,890 gene clusters in 4,240 high-quality microbial genomes. We found marked differences in pathway distribution among phyla, reflecting distinct strategies for energy capture. These data explain taxonomic differences in short-chain fatty acid production and suggest a characteristic metabolic niche for each taxon. Analysis of 1,135 individuals from a Dutch population-based cohort shows that the level of microbiome-derived metabolites in plasma and feces is almost completely uncorrelated with the metagenomic abundance of corresponding metabolic genes, indicating a crucial role for pathway-specific gene regulation and metabolite flux. This work is a starting point for understanding differences in how bacterial taxa contribute to the chemistry of the microbiome.}, } @article {pmid36781733, year = {2023}, author = {Matsumoto, Y and Nakamura, S}, title = {Rapid and Comprehensive Identification of Nontuberculous Mycobacteria.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2632}, number = {}, pages = {247-255}, pmid = {36781733}, issn = {1940-6029}, mesh = {Humans ; *Nontuberculous Mycobacteria/genetics ; *Mycobacterium Infections, Nontuberculous/diagnosis/microbiology ; Multilocus Sequence Typing ; Prevalence ; }, abstract = {Next-generation sequencing is a powerful tool to accurately identify pathogens. The MinION sequencer is best suited for the rapid identification of bacterial species due to its real-time sequence output. In this chapter, we introduce a method to identify nontuberculous mycobacteria (NTM) in one sequencing analysis from culture isolates using the MinION sequencer. NTM disease is now recognized as a growing global health concern due to its increasing incidence and prevalence. There are over 200 NTM species, of which the major pathogens are further classified into many subspecies showing different antibiotic susceptibilities. Therefore, identifying the pathogens at the subspecies level of NTM is necessary to select an appropriate treatment regimen. The protocol described here includes DNA extraction by lysis using silica beads, library preparation, sequencing by the MinION sequencer, and analysis of multilocus sequence typing using the software "mlstverse" and enables rapid and comprehensive identification of 175 species of NTM at the subspecies level with high sensitivity and accuracy.}, } @article {pmid36781731, year = {2023}, author = {Kryukov, K and Imanishi, T and Nakagawa, S}, title = {Nanopore Sequencing Data Analysis of 16S rRNA Genes Using the GenomeSync-GSTK System.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2632}, number = {}, pages = {215-226}, pmid = {36781731}, issn = {1940-6029}, mesh = {Sequence Analysis, DNA/methods ; RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; *Nanopore Sequencing ; Genomics ; High-Throughput Nucleotide Sequencing/methods ; *Nanopores ; }, abstract = {With the development of nanopore sequencing technology, long reads of DNA sequences can now be determined rapidly from various samples. This protocol introduces the GenomeSync-GSTK system for bacterial species identification in a given sample using nanopore sequencing data of 16S rRNA genes as an example. GenomeSync is a collection of genome sequences designed to provide easy access to genomic data of the species as demanded. GSTK (genome search toolkit) is a set of scripts for managing local homology searches using genomes obtained from the GenomeSync database. Based on this protocol, nanopore sequencing data analyses of metagenomes and amplicons could be efficiently performed. We also noted reanalysis in conjunction with future developments in nanopore sequencing technology and the accumulation of genome sequencing data.}, } @article {pmid36781730, year = {2023}, author = {Matsuo, Y}, title = {Full-Length 16S rRNA Gene Analysis Using Long-Read Nanopore Sequencing for Rapid Identification of Bacteria from Clinical Specimens.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2632}, number = {}, pages = {193-213}, pmid = {36781730}, issn = {1940-6029}, mesh = {RNA, Ribosomal, 16S/genetics ; *Nanopore Sequencing ; Genes, rRNA ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; Bacteria/genetics ; Phylogeny ; }, abstract = {Amplicon sequencing of the 16S ribosomal RNA (rRNA) gene is a practical and reliable measure for taxonomic profiling of bacterial communities. This chapter describes the detailed workflow for full-length 16S rRNA gene amplicon analysis using nanopore sequencing and bioinformatics pipelines to analyze nanopore sequencing data for taxonomic assignment. This approach offers a higher taxonomic resolution for bacterial identification from clinical specimens with a markedly reduced timeframe and improved versatility.}, } @article {pmid36781495, year = {2023}, author = {Pham, DN and Wu, Q and Li, M}, title = {Global profiling of antibiotic resistomes in maize rhizospheres.}, journal = {Archives of microbiology}, volume = {205}, number = {3}, pages = {89}, pmid = {36781495}, issn = {1432-072X}, support = {NIFA-2019-67020-30475//National Institute of Food and Agriculture/ ; CBET-1903597//Division of Chemical, Bioengineering, Environmental, and Transport Systems/ ; }, mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology/analysis ; Bacteria/genetics ; Genes, Bacterial ; Manure/analysis ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; *Zea mays/genetics ; *Drug Resistance, Bacterial/genetics ; }, abstract = {The spreading of antimicrobial resistance (AMR) in crops and food products represents a global concern. In this study, we conducted a survey of resistomes in maize rhizosphere from Michigan, California, the Netherlands, and South Africa, and investigated potential associations with host bacteria and soil management practices in the crop field. For comparison, relative abundance of antibiotic resistance genes (ARGs) is normalized to the size of individual metagenomes. Michigan maize rhizosphere metagenomes showed the highest abundance and diversity of ARGs, with the detection of blaTEM-116, blaACT-4/-6, and FosA2, exhibiting high similarity (≥ 99.0%) to those in animal and human pathogens. This was probably related to the decade-long application of manure/composted manure from antibiotic-treated animals. Moreover, RbpA, vanRO, mtrA, and dfrB were prevalently found across most studied regions, implying their intrinsic origins. Further analysis revealed that RbpA, vanRO, and mtrA are mainly harbored by native Actinobacteria with low mobility since mobile genetic elements were rarely found in their flanking regions. Notably, a group of dfrB genes are adjacent to the recombination binding sites (attC), which together constitute mobile gene cassettes, promoting the transmission from soil bacteria to human pathogens. These results suggest that maize rhizosphere resistomes can be distinctive and affected by many factors, particularly those relevant to agricultural practices.}, } @article {pmid36781145, year = {2023}, author = {Zhang, Y and Bai, J and Zuo, J}, title = {Performance and mechanisms of medium-chain fatty acid production by anaerobic fermentation of food waste without external electron donors.}, journal = {Bioresource technology}, volume = {374}, number = {}, pages = {128735}, doi = {10.1016/j.biortech.2023.128735}, pmid = {36781145}, issn = {1873-2976}, mesh = {Humans ; Fermentation ; Anaerobiosis ; *Food ; Electrons ; *Refuse Disposal ; Fatty Acids ; }, abstract = {This study performed a long-term operation to achieve efficient medium-chain fatty acids (MCFAs) production by anaerobic fermentation of food waste without external electron donors. The results show that total MCFAs reached the highest concentration of 29,886.10 mg COD/L, and n-caproate was the primary product, reaching the current maximum concentration of 28,191.66 mg COD/L. Microbial composition analysis demonstrated Lactobacillus, Bifidobacterium, Sporanaerobacter, and Caproiciproducens constituted the core community throughout the process. Metagenomic analysis suggested that two pathways, reverse β-oxidization (RBO) and fatty acid biosynthesis (FAB), were observed, and the FAB pathway was the main CE pathway. Unclassified_f_Ruminococcaceae and Limosilactobacillus were the main participants in the FAB pathway. This study is expected to provide new insights into MCFAs production from organic waste.}, } @article {pmid36781130, year = {2023}, author = {Ibekwe, AM and Bhattacharjee, AS and Phan, D and Ashworth, D and Schmidt, MP and Murinda, SE and Obayiuwana, A and Murry, MA and Schwartz, G and Lundquist, T and Ma, J and Karathia, H and Fanelli, B and Hasan, NA and Yang, CH}, title = {Potential reservoirs of antimicrobial resistance in livestock waste and treated wastewater that can be disseminated to agricultural land.}, journal = {The Science of the total environment}, volume = {872}, number = {}, pages = {162194}, doi = {10.1016/j.scitotenv.2023.162194}, pmid = {36781130}, issn = {1879-1026}, mesh = {Humans ; Animals ; Swine ; *Wastewater ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Livestock ; Drug Resistance, Bacterial/genetics ; Manure/analysis ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Bacteria ; Soil Microbiology ; beta-Lactams/analysis ; }, abstract = {Livestock manure, dairy lagoon effluent, and treated wastewater are known reservoirs of antibiotic resistance genes (ARGs), antibiotic-resistant bacteria (ARB), and virulence factor genes (VFGs), and their application to agricultural farmland could be a serious public health threat. However, their dissemination to agricultural lands and impact on important geochemical pathways such as the nitrogen (N) cycle have not been jointly explored. In this study, shotgun metagenomic sequencing and analyses were performed to examine the diversity and composition of microbial communities, ARGs, VFGs, and N cycling genes in different livestock manure/lagoon and treated wastewater collected from concentrated animal feeding operations (CAFOs) and a municipal wastewater treatment plant along the west coast of the United States. Multivariate analysis showed that diversity indices of bacterial taxa from the different microbiomes were not significantly different based on InvSimpson (P = 0.05), but differences in ARG mechanisms were observed between swine manure and other microbiome sources. Comparative resistome profiling showed that ARGs in microbiome samples belonged to four core resistance classes: aminoglycosides (40-55 %), tetracyclines (30-45 %), beta-lactam-resistance (20-35 %), macrolides (18-30 %), and >50 % of the VFGs that the 24 microbiomes harbored were phyletically affiliated with two bacteria, Bacteroidetes fragilis and Enterobacter aerogenes. Network analysis based on Spearman correlation showed co-occurrence patterns between several genes such as transporter-gene and regulator, efflux pump and involved-in-polymyxin- resistance, aminoglycoside, beta-lactam, and macrolide with VFGs and bacterial taxa such as Firmicutes, Candidatus Themoplasmatota, Actinobacteria, and Bacteroidetes. Metabolic reconstruction of metagenome-assembled genome (MAGs) analysis showed that the most prevalent drug resistance mechanisms were associated with carbapenem resistance, multidrug resistance (MDR), and efflux pump. Bacteroidales was the main taxa involved in dissimilatory nitrate reduction (DNRA) in dairy lagoon effluent. This study demonstrates that the dissemination of waste from these sources can increase the spread of ARGs, ARB, and VFGs into agricultural lands, negatively impacting both soil and human health.}, } @article {pmid36781125, year = {2023}, author = {Yang, Z and Wang, H and Yang, S and Wang, X and Shen, Q and Ji, L and Zeng, J and Zhang, W and Gong, H and Shan, T}, title = {Virome diversity of ticks feeding on domestic mammals in China.}, journal = {Virologica Sinica}, volume = {38}, number = {2}, pages = {208-221}, pmid = {36781125}, issn = {1995-820X}, mesh = {Animals ; Sheep ; Humans ; *Ticks ; Virome ; Phylogeny ; *Viruses/genetics ; *RNA Viruses/genetics ; Mammals ; *Flaviviridae ; China ; }, abstract = {Ticks are considered the second most common pathogen vectors transmitting a broad range of vital human and veterinary viruses. From 2017 to 2018, 640 ticks were collected in eight different provinces in central and western China. Six species were detected, including H.longicornis, De.everestianus, Rh.microplus, Rh.turanicus, Rh.sanguineous, and Hy.asiaticum. Sixty-four viral metagenomic libraries were constructed on the MiSeq Illumina platform, resulting in 13.44 G (5.88 × 10[7]) of 250-bp-end reads, in which 2,437,941 are viral reads. We found 27 nearly complete genome sequences, including 16 genome sequences encoding entire protein-coding regions (lack of 3' or 5' end non-coding regions) and complete viral genomes, distributed in the arboviral family (Chuviridae, Rhabdoviridae, Nairoviridae, Phenuiviridae, Flaviviridae, Iflaviridae) as well as Parvoviridae and Polyomaviridae that cause disease in mammals and even humans. In addition, 13 virus sequences found in Chuviridae, Nairoviridae, Flaviviridae, Iflaviridae, Hepeviridae, Parvoviridae, and Polyomaviridae were identified as belonging to a new virus species in the identified viral genera. Besides, an epidemiological survey shows a high prevalence (9.38% and 15.63%) of two viruses (Ovine Copiparvovirus and Bovine parvovirus 2) in the tick cohort.}, } @article {pmid36780542, year = {2023}, author = {Plantinga, AM and Kamp, KJ and Wu, Q and Chen, L and Yoo, L and Burr, RL and Cain, KC and Raftery, D and Carnevale Neto, F and Badu, S and So, SY and Savidge, T and Shulman, RJ and Heitkemper, MM}, title = {Exploration of associations among dietary tryptophan, microbiome composition and function, and symptom severity in irritable bowel syndrome.}, journal = {Neurogastroenterology and motility}, volume = {35}, number = {5}, pages = {e14545}, doi = {10.1111/nmo.14545}, pmid = {36780542}, issn = {1365-2982}, support = {P30 DK035816/DK/NIDDK NIH HHS/United States ; K23 NR020044/NR/NINR NIH HHS/United States ; T32 NR016913/NR/NINR NIH HHS/United States ; P01 AI152999/AI/NIAID NIH HHS/United States ; U01 AI042590/AI/NIAID NIH HHS/United States ; R01 NR014479/NR/NINR NIH HHS/United States ; R01 DK130517/DK/NIDDK NIH HHS/United States ; R01 NR013497/NR/NINR NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; }, mesh = {Female ; Humans ; Adult ; *Irritable Bowel Syndrome ; Tryptophan ; Diet ; *Microbiota ; *Gastrointestinal Microbiome ; }, abstract = {BACKGROUND: Imbalance of the tryptophan (TRP) pathway may influence symptoms among patients with irritable bowel syndrome (IBS). This study explored relationships among different components that contribute to TRP metabolism (dietary intake, stool metabolite levels, predicted microbiome metabolic capability) in females with IBS and healthy controls (HCs). Within the IBS group, we also investigated relationships between TRP metabolic determinants, Bifidobacterium abundance, and symptoms of IBS.

METHODS: Participants with IBS (Rome III) and HCs completed a 28-day diary of gastrointestinal symptoms and a 3-day food record for TRP intake. They provided a stool sample for shotgun metagenomics, 16 S rRNA analyses, and quantitative measurement of TRP by mass spectrometry.

RESULTS: Our cohort included 115 females, 69 with IBS and 46 HCs, with a mean age of 28.5 years (SD 7.4). TRP intake (p = 0.71) and stool TRP level (p = 0.27) did not differ between IBS and HC. Bifidobacterium abundance was lower in the IBS group than in HCs (p = 0.004). Predicted TRP metabolism gene content was higher in IBS than HCs (FDR-corrected q = 0.006), whereas predicted biosynthesis gene content was lower (q = 0.045). Within the IBS group, there was no association between symptom severity and TRP intake or stool TRP, but there was a significant interaction between Bifidobacterium abundance and TRP intake (q = 0.029) in predicting stool character.

CONCLUSIONS: Dietary TRP intake, microbiome composition, and differences in TRP metabolism constitute a complex interplay of factors that could modulate IBS symptom severity.}, } @article {pmid36780432, year = {2023}, author = {Simmonds, P and Adriaenssens, EM and Zerbini, FM and Abrescia, NGA and Aiewsakun, P and Alfenas-Zerbini, P and Bao, Y and Barylski, J and Drosten, C and Duffy, S and Duprex, WP and Dutilh, BE and Elena, SF and García, ML and Junglen, S and Katzourakis, A and Koonin, EV and Krupovic, M and Kuhn, JH and Lambert, AJ and Lefkowitz, EJ and Łobocka, M and Lood, C and Mahony, J and Meier-Kolthoff, JP and Mushegian, AR and Oksanen, HM and Poranen, MM and Reyes-Muñoz, A and Robertson, DL and Roux, S and Rubino, L and Sabanadzovic, S and Siddell, S and Skern, T and Smith, DB and Sullivan, MB and Suzuki, N and Turner, D and Van Doorslaer, K and Vandamme, AM and Varsani, A and Vasilakis, N}, title = {Four principles to establish a universal virus taxonomy.}, journal = {PLoS biology}, volume = {21}, number = {2}, pages = {e3001922}, pmid = {36780432}, issn = {1545-7885}, support = {HHSN272201800013C/AI/NIAID NIH HHS/United States ; MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; U24 AI162625/AI/NIAID NIH HHS/United States ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; U01 AI151807/AI/NIAID NIH HHS/United States ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; R24 AI120942/AI/NIAID NIH HHS/United States ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *Bacteriophages ; Metagenomics ; Phylogeny ; *Viruses/genetics ; }, abstract = {A universal taxonomy of viruses is essential for a comprehensive view of the virus world and for communicating the complicated evolutionary relationships among viruses. However, there are major differences in the conceptualisation and approaches to virus classification and nomenclature among virologists, clinicians, agronomists, and other interested parties. Here, we provide recommendations to guide the construction of a coherent and comprehensive virus taxonomy, based on expert scientific consensus. Firstly, assignments of viruses should be congruent with the best attainable reconstruction of their evolutionary histories, i.e., taxa should be monophyletic. This fundamental principle for classification of viruses is currently included in the International Committee on Taxonomy of Viruses (ICTV) code only for the rank of species. Secondly, phenotypic and ecological properties of viruses may inform, but not override, evolutionary relatedness in the placement of ranks. Thirdly, alternative classifications that consider phenotypic attributes, such as being vector-borne (e.g., "arboviruses"), infecting a certain type of host (e.g., "mycoviruses," "bacteriophages") or displaying specific pathogenicity (e.g., "human immunodeficiency viruses"), may serve important clinical and regulatory purposes but often create polyphyletic categories that do not reflect evolutionary relationships. Nevertheless, such classifications ought to be maintained if they serve the needs of specific communities or play a practical clinical or regulatory role. However, they should not be considered or called taxonomies. Finally, while an evolution-based framework enables viruses discovered by metagenomics to be incorporated into the ICTV taxonomy, there are essential requirements for quality control of the sequence data used for these assignments. Combined, these four principles will enable future development and expansion of virus taxonomy as the true evolutionary diversity of viruses becomes apparent.}, } @article {pmid36780083, year = {2023}, author = {Lach, J and Królikowska, K and Baranowska, M and Krupińska, M and Strapagiel, D and Matera-Witkiewicz, A and Stączek, P}, title = {A first insight into the Polish Bochnia Salt Mine metagenome.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {17}, pages = {49551-49566}, pmid = {36780083}, issn = {1614-7499}, support = {POWR.03.02.00-00-I033/16-00//Narodowe Centrum Badań i Rozwoju/ ; WBIOŚ B1811000000038.01//Wydział Biologii i Ochrony Środowiska, Uniwersytet Łódzki/ ; SUB.D250.22.018//Uniwersytet Medyczny im. Piastów Slaskich we Wroclawiu/ ; }, mesh = {Humans ; *Metagenome ; Poland ; RNA, Ribosomal, 16S/genetics ; *Sodium Chloride ; Bacteria/genetics ; Sodium Chloride, Dietary ; Pharmaceutical Preparations ; Metagenomics ; }, abstract = {The Bochnia Salt Mine is one of the oldest mines in Europe. It was established in the thirteenth century, and actively operated until 1990. The mine has been placed on the UNESCO World Heritage List. Previous research describing Polish salt mines has been focused on bioaerosol characteristics and the identification of microorganisms potentially important for human health. The use of Polish salt mines as inhalation chambers for patients of health resorts has also been investigated. Nevertheless, the biodiversity of salt mines associated with biotechnological potential has not been well characterized. The present study paper examines the biodiversity of microorganisms in the Bochnia Salt Mine based on 16S rRNA gene and shotgun sequencing. Biodiversity studies revealed a significantly higher relative abundance of Chlamydiae at the first level of the mine (3.5%) compared to the other levels (< 0.1%). Patescibacteria microorganisms constituted a high percentage (21.6%) in the sample from site RA6. Shotgun sequencing identified 16 unique metagenome-assembled genomes (MAGs). Although one was identified as Halobacterium bonnevillei, the others have not yet been assigned to any species; it is possible that these species may be undescribed. Preliminary analyses of the biotechnological and pharmaceutical potential of microorganisms inhabiting the mine were also performed, and the biosynthetic gene cluster (BGC) profiles and antimicrobial peptide (AMP) coding genes in individual samples were characterized. Hundreds of BGCs and dozens of AMP coding genes were identified in metagenomes. Our findings indicate that Polish salt mines are promising sites for further research aimed at identifying microorganisms that are producers of potentially important substances with biotechnological and pharmaceutical applications.}, } @article {pmid36779794, year = {2023}, author = {Rastegar, K and Kelley, ST and Thackray, VG}, title = {Metagenome-Assembled Genomes from Murine Fecal Microbiomes Dominated by Uncharacterized Bacteria.}, journal = {Microbiology resource announcements}, volume = {12}, number = {3}, pages = {e0116222}, pmid = {36779794}, issn = {2576-098X}, support = {R01 HD095412/HD/NICHD NIH HHS/United States ; HD095412//HHS | NIH | Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD)/ ; }, abstract = {The laboratory mouse gut microbiome has been extensively studied, but our understanding of its diversity remains incomplete. We report the assembly of 51 draft metagenome-assembled genomes (MAGs) from murine fecal samples dominated by uncharacterized bacteria. These MAGs add to our understanding of gut microbial diversity in this critical model organism.}, } @article {pmid36779724, year = {2023}, author = {de Santana, CO and Spealman, P and Gresham, D and Perron, GG}, title = {Metagenomes from Soils along an Agricultural Transect in Ulster County, New York.}, journal = {Microbiology resource announcements}, volume = {12}, number = {3}, pages = {e0101522}, pmid = {36779724}, issn = {2576-098X}, abstract = {Many modern farming practices negatively impact ecosystems on the local and global scales. Here, we assessed the taxonomic structures of 48 soil microbial communities along an agricultural transect using 16S rRNA and internal transcribed spacer (ITS) amplicon sequencing. We further characterized the functional structures of a subsample of 12 microbiomes using whole-genome sequencing.}, } @article {pmid36779262, year = {2023}, author = {Nishimura, H and Kouduka, M and Fukuda, A and Ishimura, T and Amano, Y and Beppu, H and Miyakawa, K and Suzuki, Y}, title = {Anaerobic methane-oxidizing activity in a deep underground borehole dominantly colonized by Ca. Methanoperedenaceae.}, journal = {Environmental microbiology reports}, volume = {15}, number = {3}, pages = {197-205}, pmid = {36779262}, issn = {1758-2229}, mesh = {*Bacteria/genetics ; *Methane ; RNA, Ribosomal, 16S/genetics ; Anaerobiosis ; Ferric Compounds ; Archaea/genetics ; Oxidation-Reduction ; }, abstract = {The family Ca. Methanoperedenaceae archaea mediates the anaerobic oxidation of methane (AOM) in different terrestrial environments. Using a newly developed high-pressure laboratory incubation system, we investigated 214- and 249-m deep groundwater samples at Horonobe Underground Research Laboratory, Japan, where the high and low abundances of Ca. Methanoperedenaceae archaea have been shown by genome-resolved metagenomics, respectively. The groundwater samples amended with [13] C-labelled methane and amorphous Fe(III) were incubated at a pressure of 1.6 MPa. After 3-7 days of incubation, the AOM rate was 45.8 ± 19.8 nM/day in 214-m groundwater. However, almost no activity was detected from 249-m groundwater. Based on the results from 16S rRNA gene analysis, the abundance of Ca. Methanoperedenaceae archaea was high in the 214-m deep groundwater sample, whereas Ca. Methanoperedenaceae archaea was undetected in the 249-m deep groundwater sample. These results support the in situ AOM activity of Ca. Methanoperedenaceae archaea in the 214-m deep subsurface borehole interval. Although the presence of Fe-bearing phyllosilicates was demonstrated in the 214-m deep groundwater, it needs to be determined whether Ca. Methanoperedenaceae archaea use the Fe-bearing phyllosilicates as in situ electron acceptors by high-pressure incubation amended with the Fe-bearing phyllosilicates.}, } @article {pmid36779189, year = {2023}, author = {Zhang, B and Chen, X and Yao, X and Li, M and Li, Z and Liu, B and Liu, S and Liu, Z and Huo, J and Han, Y}, title = {The diagnostic value of blood metagenomic next-generation sequencing in patients with acute hematogenous osteomyelitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1106097}, pmid = {36779189}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *Blood Culture ; High-Throughput Nucleotide Sequencing ; Acute Disease ; Anti-Bacterial Agents ; Metagenomics ; *Osteomyelitis/diagnosis ; Staphylococcus/genetics ; Sensitivity and Specificity ; }, abstract = {AIMS: This study aims to evaluate the diagnostic value of blood metagenomic next-generation sequencing (mNGS) in detecting pathogens from patients clinically diagnosed as acute hematogenous osteomyelitis (AHO).

METHODS: This retrospective study enrolled 66 patients with AHO. The test results of mNGS and bacterial culture on different samples, including blood and puncture fluid samples, from patients with AHO were compared to explore the diagnostic value of blood mNGS. Besides, this study also explored the efficacy of blood mNGS in decision making for antibiotic administration and analyzed the factors associated with the positive result of blood mNGS.

RESULTS: The most common causative pathogens were Staphylococcus and Streptococcus. The sensitivity of blood mNGS (77.3%) was higher than that of blood culture (42.4%) (P<0.001), while the turnaround time of blood mNGS (2.1 ± 0.4 d) is much less than that of blood culture (6.0 ± 2.1 d) (P<0.001). Besides, the sensitivity of blood mNGS tests (77.3%) was slightly lower than that of puncture fluid mNGS (89.4%). Furthermore, detection comparison at pathogen level unravels that blood mNGS might be suitable for diagnosing AHO caused by common pathogens, while puncture fluid mNGS could be considered as preferred examination in diagnosing AHO caused by uncommon pathogens. Finally, three independent factors associated with the true positive result of blood mNGS in patients with AHO were identified, including Gram-positive pathogens (OR=24.4, 95% CI = 1.4-421.0 for Staphylococcus; OR=14.9, 95%CI= 1.6-136.1 for other Gram-positive bacteria), body temperature at sampling time (OR=8.2, 95% CI = 0.6-107.3 for body temperature of >38.5°C; OR=17.2, 95% CI = 2.0-149.1 for patients who were chilling), and no use of antibiotics before sampling (OR=8.9, 95% CI =1.4-59.0).

CONCLUSION: This is the first report on evaluating and emphasizing the importance of blood mNGS in diagnosing AHO. Blood sample might be an alternative sample for puncture fluid for mNGS, and its extensive application in diagnosing AHO could be expected.}, } @article {pmid36779185, year = {2023}, author = {Huang, R and Yuan, Q and Gao, J and Liu, Y and Jin, X and Tang, L and Cao, Y}, title = {Application of metagenomic next-generation sequencing in the diagnosis of urinary tract infection in patients undergoing cutaneous ureterostomy.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {991011}, pmid = {36779185}, issn = {2235-2988}, mesh = {Humans ; Anti-Bacterial Agents/therapeutic use ; Biomarkers ; Case-Control Studies ; *Escherichia coli ; High-Throughput Nucleotide Sequencing ; Interleukin-6 ; Klebsiella pneumoniae ; Sensitivity and Specificity ; Ureterostomy ; *Urinary Tract Infections/diagnosis/microbiology ; }, abstract = {OBJECTIVE: Urinary tract infection (UTI) is an inflammatory response of the urothelium to bacterial invasion and is a common complication in patients with cutaneous ureterostomy (CU). For such patients, accurate and efficient identification of pathogens remains a challenge. The aim of this study included exploring utility of metagenomic next-generation sequencing (mNGS) in assisting microbiological diagnosis of UTI among patients undergoing CU, identifying promising cytokine or microorganism biomarkers, revealing microbiome diversity change and compare virulence factors (VFs) and antibiotic resistance genes (ARGs) after infection.

METHODS: We performed a case-control study of 50 consecutive CU patients from December 2020 to January 2021. According to the clinical diagnostic criteria, samples were divided into infected group and uninfected group and difference of urine culture, cytokines, microorganism, ARGs and VFs were compared between the two groups.

RESULTS: Inflammatory responses were more serious in infected group, as evidenced by a significant increase in IFN-α (p=0.031), IL-1β (0.023) and IL-6 (p=0.018). Clinical culture shows that there is higher positive rate in infected group for most clinical pathogens like Escherichia coli, Klebsiella pneumoniae, Staphylococcus aureus, Candida auris etc. and the top three pathogens with positive frequencies were E. coli, K. pneumoniae, and Enterococcus faecalis. Benchmarking clinical culture, the total sensitivity is 91.4% and specificity is 76.3% for mNGS. As for mNGS, there was no significant difference in microbiome α- diversity between infected and uninfected group. Three species biomarkers including Citrobacter freundii, Klebsiella oxytoca, and Enterobacter cloacae are enriched in infected group based on Lefse. E. cloacae were significantly correlated with IL-6 and IL-10. K. oxytoca were significantly correlated with IL-1β. Besides, the unweighted gene number and weighted gene abundance of VFs or ARGs are significantly higher in infected group. Notablely, ARGs belonging to fluoroquinolones, betalatmas, fosfomycin, phenicol, phenolic compound abundance is significantly higher in infected group which may have bad effect on clinical treatment for patients.

CONCLUSION: mNGS, along with urine culture, will provide comprehensive and efficient reference for the diagnosis of UTI in patients with CU and allow us to monitor microbial changes in urine of these patients. Moreover, cytokines (IL-6, IL-1β, and IFN-a) or microorganisms like C. freundii, K. oxytoca or E. cloacae are promising biomarkers for building effective UTI diagnostic model of patients with CU and seriously the VFs and ARGs abundance increase in infected group may play bad effect on clinical treatment.}, } @article {pmid36779183, year = {2023}, author = {Xie, XH and Huang, YJ and Han, GS and Yu, ZG and Ma, YL}, title = {Microbial characterization based on multifractal analysis of metagenomes.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1117421}, pmid = {36779183}, issn = {2235-2988}, mesh = {Humans ; Infant ; Infant, Newborn ; Metagenome ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Ecology ; }, abstract = {INTRODUCTION: The species diversity of microbiomes is a cutting-edge concept in metagenomic research. In this study, we propose a multifractal analysis for metagenomic research.

METHOD AND RESULTS: Firstly, we visualized the chaotic game representation (CGR) of simulated metagenomes and real metagenomes. We find that metagenomes are visualized with self-similarity. Then we defined and calculated the multifractal dimension for the visualized plot of simulated and real metagenomes, respectively. By analyzing the Pearson correlation coefficients between the multifractal dimension and the traditional species diversity index, we obtain that the correlation coefficients between the multifractal dimension and the species richness index and Shannon diversity index reached the maximum value when q = 0, 1, and the correlation coefficient between the multifractal dimension and the Simpson diversity index reached the maximum value when q = 5. Finally, we apply our method to real metagenomes of the gut microbiota of 100 infants who are newborn and 4 and 12 months old. The results show that the multifractal dimensions of an infant's gut microbiomes can distinguish age differences.

CONCLUSION AND DISCUSSION: There is self-similarity among the CGRs of WGS of metagenomes, and the multifractal spectrum is an important characteristic for metagenomes. The traditional diversity indicators can be unified under the framework of multifractal analysis. These results coincided with similar results in macrobial ecology. The multifractal spectrum of infants' gut microbiomes are related to the development of the infants.}, } @article {pmid36778980, year = {2022}, author = {Sinha, D and Sharma, A and Mishra, DC and Rai, A and Lal, SB and Kumar, S and Farooqi, MS and Chaturvedi, KK}, title = {MetaConClust - Unsupervised Binning of Metagenomics Data using Consensus Clustering.}, journal = {Current genomics}, volume = {23}, number = {2}, pages = {137-146}, pmid = {36778980}, issn = {1389-2029}, abstract = {Background: Binning of metagenomic reads is an active area of research, and many unsupervised machine learning-based techniques have been used for taxonomic independent binning of metagenomic reads. Objective: It is important to find the optimum number of the cluster as well as develop an efficient pipeline for deciphering the complexity of the microbial genome. Methods: Applying unsupervised clustering techniques for binning requires finding the optimal number of clusters beforehand and is observed to be a difficult task. This paper describes a novel method, MetaConClust, using coverage information for grouping of contigs and automatically finding the optimal number of clusters for binning of metagenomics data using a consensus-based clustering approach. The coverage of contigs in a metagenomics sample has been observed to be directly proportional to the abundance of species in the sample and is used for grouping of data in the first phase by MetaConClust. The Partitioning Around Medoid (PAM) method is used for clustering in the second phase for generating bins with the initial number of clusters determined automatically through a consensus-based method. Results: Finally, the quality of the obtained bins is tested using silhouette index, rand Index, recall, precision, and accuracy. Performance of MetaConClust is compared with recent methods and tools using benchmarked low complexity simulated and real metagenomic datasets and is found better for unsupervised and comparable for hybrid methods. Conclusion: This is suggestive of the proposition that the consensus-based clustering approach is a promising method for automatically finding the number of bins for metagenomics data.}, } @article {pmid36778971, year = {2022}, author = {Firrman, J and Liu, L and Mahalak, K and Hu, W and Bittinger, K and Moustafa, A and Jones, SM and Narrowe, A and Tomasula, P}, title = {An in vitro analysis of how lactose modifies the gut microbiota structure and function of adults in a donor-independent manner.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {1040744}, pmid = {36778971}, issn = {2296-861X}, abstract = {INTRODUCTION: Following consumption of milk, lactose, a disaccharide of glucose and galactose, is hydrolyzed and absorbed in the upper gastrointestinal tract. However, hydrolysis and absorption are not always absolute, and some lactose will enter the colon where the gut microbiota is able to hydrolyze lactose and produce metabolic byproducts.

METHODS: Here, the impact of lactose on the gut microbiota of healthy adults was examined, using a short-term, in vitro strategy where fecal samples harvested from 18 donors were cultured anaerobically with and without lactose. The data were compiled to identify donor-independent responses to lactose treatment.

RESULTS AND DISCUSSION: Metagenomic sequencing found that the addition of lactose decreased richness and evenness, while enhancing prevalence of the β-galactosidase gene. Taxonomically, lactose treatment decreased relative abundance of Bacteroidaceae and increased lactic acid bacteria, Lactobacillaceae, Enterococcaceae, and Streptococcaceae, and the probiotic Bifidobacterium. This corresponded with an increased abundance of the lactate utilizers, Veillonellaceae. These structural changes coincided with increased total short-chain fatty acids (SCFAs), specifically acetate, and lactate. These results demonstrated that lactose could mediate the gut microbiota of healthy adults in a donor-independent manner, consistent with other described prebiotics, and provided insight into how dietary milk consumption may promote human health through modifications of the gut microbiome.}, } @article {pmid36778897, year = {2022}, author = {Delmont, TO and Gaia, M and Hinsinger, DD and Frémont, P and Vanni, C and Fernandez-Guerra, A and Eren, AM and Kourlaiev, A and d'Agata, L and Clayssen, Q and Villar, E and Labadie, K and Cruaud, C and Poulain, J and Da Silva, C and Wessner, M and Noel, B and Aury, JM and , and de Vargas, C and Bowler, C and Karsenti, E and Pelletier, E and Wincker, P and Jaillon, O}, title = {Functional repertoire convergence of distantly related eukaryotic plankton lineages abundant in the sunlit ocean.}, journal = {Cell genomics}, volume = {2}, number = {5}, pages = {100123}, pmid = {36778897}, issn = {2666-979X}, abstract = {Marine planktonic eukaryotes play critical roles in global biogeochemical cycles and climate. However, their poor representation in culture collections limits our understanding of the evolutionary history and genomic underpinnings of planktonic ecosystems. Here, we used 280 billion Tara Oceans metagenomic reads from polar, temperate, and tropical sunlit oceans to reconstruct and manually curate more than 700 abundant and widespread eukaryotic environmental genomes ranging from 10 Mbp to 1.3 Gbp. This genomic resource covers a wide range of poorly characterized eukaryotic lineages that complement long-standing contributions from culture collections while better representing plankton in the upper layer of the oceans. We performed the first, to our knowledge, comprehensive genome-wide functional classification of abundant unicellular eukaryotic plankton, revealing four major groups connecting distantly related lineages. Neither trophic modes of plankton nor its vertical evolutionary history could completely explain the functional repertoire convergence of major eukaryotic lineages that coexisted within oceanic currents for millions of years.}, } @article {pmid36778896, year = {2022}, author = {Massana, R and López-Escardó, D}, title = {Metagenome assembled genomes are for eukaryotes too.}, journal = {Cell genomics}, volume = {2}, number = {5}, pages = {100130}, pmid = {36778896}, issn = {2666-979X}, abstract = {Environmental community sequencing is suitable for producing metagenome assembled genomes (MAGs) of prokaryotes, but there is the perception that it cannot work for eukaryotes. In this issue of Cell Genomics, Delmont et al[1] process a massive sequencing dataset from marine plankton to produce 683 eukaryotic MAGs; the study also includes useful functional information.}, } @article {pmid36778888, year = {2023}, author = {Shao, YH and Wu, YW and Naufal, M and Wu, JH}, title = {Genome-centered metagenomics illuminates adaptations of core members to a partial Nitritation-Anammox bioreactor under periodic microaeration.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1046769}, pmid = {36778888}, issn = {1664-302X}, abstract = {The partial nitritation-anaerobic ammonium oxidation (anammox; PN-A) process has been considered a sustainable method for wastewater ammonium removal, with recent attempts to treat low-strength wastewater. However, how microbes adapt to the alternate microaerobic-anoxic operation of the process when treating low ammonium concentrations remains poorly understood. In this study, we applied a metagenomic approach to determine the genomic contents of core members in a PN-A reactor treating inorganic ammonium wastewater at loading as low as 0.0192 kg-N/m[3]/day. The metabolic traits of metagenome-assembled genomes from 18 core species were analyzed. Taxonomically diverse ammonia oxidizers, including two Nitrosomonas species, a comammox Nitrospira species, a novel Chloroflexota-related species, and two anammox bacteria, Ca. Brocadia and Ca. Jettenia, accounted for the PN-A reactions. The characteristics of a series of genes encoding class II ribonucleotide reductase, high-affinity bd-type terminal oxidase, and diverse antioxidant enzymes revealed that comammox Nitrospira has a superior adaptation ability over the competitors, which may confer the privileged partnership with anammox bacteria in the PN-A reactor. This finding is supported by the long-term monitoring experiment, showing the predominance of the comammox Nitrospira in the ammonia-oxidizing community. Metagenomic analysis of seven heterotrophs suggested that nitrate reduction is a common capability in potentially using endogenous carbohydrates and peptides to enhance nitrogen removals. The prevalence of class II ribonucleotide reductase and antioxidant enzymes genes may grant the adaptation to cyclically microaerobic/anoxic environments. The predominant heterotroph is affiliated with Chloroflexota; its genome encodes complete pathways for synthesizing vitamin B6 and methionine. By contrast, other than the two growth factors, Nitrospira and anammox bacteria are complementary to produce various vitamins and amino acids. Besides, the novel Chloroflexota-related ammonia oxidizer lacks corresponding genes for detoxifying the reactive oxygen species and thus requires the aid of co-existing members to alleviate oxidative stress. The analysis results forecast the exchanges of substrates and nutrients as well as the collective alleviation of oxidative stress among the core populations. The new findings of the genomic features and predicted microbial interplay shed light on microbial adaptation to intermittent microaeration specific to the PN-A reactor, which may aid in improving its application to low-strength ammonium wastewater.}, } @article {pmid36778880, year = {2023}, author = {Lan, Q and Lian, Y and Peng, P and Yang, L and Zhao, H and Huang, P and Ma, H and Wei, H and Yin, Y and Liu, M}, title = {Association of gut microbiota and SCFAs with finishing weight of Diannan small ear pigs.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1117965}, pmid = {36778880}, issn = {1664-302X}, abstract = {Finishing weight is a key economic trait in the domestic pig industry. Evidence has linked the gut microbiota and SCFAs to health and production performance in pigs. Nevertheless, for Diannan small ear (DSE) pigs, a specific pig breed in China, the potential effect of gut microbiota and SCFAs on their finishing weight remains unclear. Herein, based on the data of the 16S ribosomal RNA gene and metagenomic sequencing analysis, we found that 13 OTUs could be potential biomarkers and 19 microbial species were associated with finishing weight. Among these, carbohydrate-decomposing bacteria of the families Streptococcaceae, Lactobacillaceae, and Prevotellaceae were positively related to finishing weight, whereas the microbial taxa associated with intestinal inflammation and damage exhibited opposite effects. In addition, interactions of these microbial species were found to be linked with finishing weight for the first time. Gut microbial functional annotation analysis indicated that CAZymes, such as glucosidase and glucanase could significantly affect finishing weight, given their roles in increasing nutrient absorption efficiency. Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthologies (KOs) and KEGG pathways analysis indicated that glycolysis/gluconeogenesis, phosphotransferase system (PTS), secondary bile acid biosynthesis, ABC transporters, sulfur metabolism, and one carbon pool by folate could act as key factors in regulating finishing weight. Additionally, SCFA levels, especially acetate and butyrate, had pivotal impacts on finishing weight. Finishing weight-associated species Prevotella sp. RS2, Ruminococcus sp. AF31-14BH and Lactobacillus pontis showed positive associations with butyrate concentration, and Paraprevotella xylaniphila and Bacteroides sp. OF04-15BH were positively related to acetate level. Taken together, our study provides essential knowledge for manipulating gut microbiomes to improve finishing weight. The underlying mechanisms of how gut microbiome and SCFAs modulate pigs' finishing weight required further elucidation.}, } @article {pmid36778472, year = {2023}, author = {Ha, AD and Moniruzzaman, M and Aylward, FO}, title = {Assessing the biogeography of marine giant viruses in four oceanic transects.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36778472}, abstract = {Viruses of the phylum Nucleocytoviricota are ubiquitous in ocean waters and play important roles in shaping the dynamics of marine ecosystems. In this study, we leveraged the bioGEOTRACES metagenomic dataset collected across the Atlantic and Pacific Oceans to investigate the biogeography of these viruses in marine environments. We identified 330 viral genomes, including 212 in the order Imitervirales and 54 in the order Algavirales . We found that most viruses appeared to be prevalent in shallow waters (<150 meters), and that viruses of the Mesomimiviridae (Imitervirales) and Prasinoviridae (Algavirales) are by far the most abundant and diverse groups in our survey. Five mesomimiviruses and one prasinovirus are particularly widespread in oligotrophic waters; annotation of these genomes revealed common stress response systems, photosynthesis-associated genes, and oxidative stress modulation that may be key to their broad distribution in the pelagic ocean. We identified a latitudinal pattern in viral diversity in one cruise that traversed the North and South Atlantic Ocean, with viral diversity peaking at high latitudes of the northern hemisphere. Community analyses revealed three distinct Nucleocytoviricota communities across latitudes, categorized by latitudinal distance towards the equator. Our results contribute to the understanding of the biogeography of these viruses in marine systems.}, } @article {pmid36778319, year = {2023}, author = {Wright, ML and Podnar, J and Longoria, KD and Nguyen, TC and Lim, S and Garcia, S and Wylie, D}, title = {Comparison of commercial DNA extraction kits for whole metagenome sequencing of human oral, vaginal, and rectal microbiome samples.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36778319}, support = {K01 NR017903/NR/NINR NIH HHS/United States ; }, abstract = {INTRODUCTION: Advancements in DNA extraction and sequencing technologies have been fundamental in deciphering the significance of the microbiome related to human health and pathology. Whole metagenome shotgun sequencing (WMS) is gaining popularity in use compared to its predecessor (i.e., amplicon-based approaches). However, like amplicon-based approaches, WMS is subject to bias from DNA extraction methods that can compromise the integrity of sequencing and subsequent findings. The purpose of this study was to evaluate systematic differences among four commercially available DNA extraction kits frequently used for WMS analysis of the microbiome.

METHODS: Oral, vaginal, and rectal swabs were collected in replicates of four by a healthcare provider from five participants and randomized to one of four DNA extraction kits. Two extraction blanks and three replicate mock community samples were also extracted using each extraction kit. WMS was completed with NovaSeq 6000 for all samples. Sequencing and microbial communities were analyzed using nonmetric multidimensional scaling and compositional bias analysis.

RESULTS: Extraction kits differentially biased the percentage of reads attributed to microbial taxa across samples and body sites. The PowerSoil Pro kit performed best in approximating expected proportions of mock communities. While HostZERO was biased against gram-negative bacteria, the kit outperformed other kits in extracting fungal DNA. In clinical samples, HostZERO yielded a smaller fraction of reads assigned to Homo sapiens across sites and had a higher fraction of reads assigned to bacterial taxa compared to other kits. However, HostZERO appears to bias representation of microbial communities and demonstrated the most dispersion by site, particularly for vaginal and rectal samples.

CONCLUSIONS: Systematic differences exist among four frequently referenced DNA extraction kits when used for WMS analysis of the human microbiome. Consideration of such differences in study design and data interpretation is imperative to safeguard the integrity of microbiome research and reproducibility of results.}, } @article {pmid36778280, year = {2023}, author = {Zhou, Z and Martin, C and Kosmopoulos, JC and Anantharaman, K}, title = {ViWrap: A modular pipeline to identify, bin, classify, and predict viral-host relationships for viruses from metagenomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36778280}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; }, abstract = {Viruses are increasingly being recognized as important components of human and environmental microbiomes. However, viruses in microbiomes remain difficult to study because of difficulty in culturing them and the lack of sufficient model systems. As a result, computational methods for identifying and analyzing uncultivated viral genomes from metagenomes have attracted significant attention. Such bioinformatics approaches facilitate screening of viruses from enormous sequencing datasets originating from various environments. Though many tools and databases have been developed for advancing the study of viruses from metagenomes, there is a lack of integrated tools enabling a comprehensive workflow and analyses platform encompassing all the diverse segments of virus studies. Here, we developed ViWrap, a modular pipeline written in Python. ViWrap combines the power of multiple tools into a single platform to enable various steps of virus analysis including identification, annotation, genome binning, species- and genus-level clustering, assignment of taxonomy, prediction of hosts, characterization of genome quality, comprehensive summaries, and intuitive visualization of results. Overall, ViWrap enables a standardized and reproducible pipeline for both extensive and stringent characterization of viruses from metagenomes, viromes, and microbial genomes. Our approach has flexibility in using various options for diverse applications and scenarios, and its modular structure can be easily amended with additional functions as necessary. ViWrap is designed to be easily and widely used to study viruses in human and environmental systems. ViWrap is publicly available via GitHub (https://github.com/AnantharamanLab/ViWrap). A detailed description of the software, its usage, and interpretation of results can be found on the website.}, } @article {pmid36778267, year = {2023}, author = {Wei, W and Millward, A and Koslicki, D}, title = {Finding phylogeny-aware and biologically meaningful averages of metagenomic samples: L 2 UniFrac.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36778267}, support = {R01 GM146462/GM/NIGMS NIH HHS/United States ; }, abstract = {Metagenomic samples have high spatiotemporal variability. Hence, it is useful to summarize and characterize the microbial makeup of a given environment in a way that is biologically reasonable and interpretable. The UniFrac metric has been a robust and widely-used metric for measuring the variability between metagenomic samples. We propose that the characterization of metagenomic environments can be achieved by finding the average, a.k.a. the barycenter, among the samples with respect to the UniFrac distance. However, it is possible that such a UniFrac-average includes negative entries, making it no longer a valid representation of a metagenomic community. To overcome this intrinsic issue, we propose a special version of the UniFrac metric, termed L 2 UniFrac, which inherits the phylogenetic nature of the traditional UniFrac and with respect to which one can easily compute the average, producing biologically meaningful environment-specific "representative samples". We demonstrate the usefulness of such representative samples as well as the extended usage of L 2 UniFrac in efficient clustering of metagenomic samples, and provide mathematical characterizations and proofs to the desired properties of L 2 UniFrac. A prototype implementation is provided at: https://github.com/KoslickiLab/L2-UniFrac.git .}, } @article {pmid36778191, year = {2022}, author = {Madival, SD and Mishra, DC and Sharma, A and Kumar, S and Maji, AK and Budhlakoti, N and Sinha, D and Rai, A}, title = {A Deep Clustering-based Novel Approach for Binning of Metagenomics Data.}, journal = {Current genomics}, volume = {23}, number = {5}, pages = {353-368}, pmid = {36778191}, issn = {1389-2029}, abstract = {BACKGROUND: One major challenge in binning Metagenomics data is the limited availability of reference datasets, as only 1% of the total microbial population is yet cultured. This has given rise to the efficacy of unsupervised methods for binning in the absence of any reference datasets.

OBJECTIVE: To develop a deep clustering-based binning approach for Metagenomics data and to evaluate results with suitable measures.

METHODS: In this study, a deep learning-based approach has been taken for binning the Metagenomics data. The results are validated on different datasets by considering features such as Tetra-nucleotide frequency (TNF), Hexa-nucleotide frequency (HNF) and GC-Content. Convolutional Autoencoder is used for feature extraction and for binning; the K-means clustering method is used.

RESULTS: In most cases, it has been found that evaluation parameters such as the Silhouette index and Rand index are more than 0.5 and 0.8, respectively, which indicates that the proposed approach is giving satisfactory results. The performance of the developed approach is compared with current methods and tools using benchmarked low complexity simulated and real metagenomic datasets. It is found better for unsupervised and at par with semi-supervised methods.

CONCLUSION: An unsupervised advanced learning-based approach for binning has been proposed, and the developed method shows promising results for various datasets. This is a novel approach for solving the lack of reference data problem of binning in metagenomics.}, } @article {pmid36778052, year = {2022}, author = {Seshadri, R and Roux, S and Huber, KJ and Wu, D and Yu, S and Udwary, D and Call, L and Nayfach, S and Hahnke, RL and Pukall, R and White, JR and Varghese, NJ and Webb, C and Palaniappan, K and Reimer, LC and Sardà, J and Bertsch, J and Mukherjee, S and Reddy, TBK and Hajek, PP and Huntemann, M and Chen, IA and Spunde, A and Clum, A and Shapiro, N and Wu, ZY and Zhao, Z and Zhou, Y and Evtushenko, L and Thijs, S and Stevens, V and Eloe-Fadrosh, EA and Mouncey, NJ and Yoshikuni, Y and Whitman, WB and Klenk, HP and Woyke, T and Göker, M and Kyrpides, NC and Ivanova, NN}, title = {Expanding the genomic encyclopedia of Actinobacteria with 824 isolate reference genomes.}, journal = {Cell genomics}, volume = {2}, number = {12}, pages = {100213}, pmid = {36778052}, issn = {2666-979X}, abstract = {The phylum Actinobacteria includes important human pathogens like Mycobacterium tuberculosis and Corynebacterium diphtheriae and renowned producers of secondary metabolites of commercial interest, yet only a small part of its diversity is represented by sequenced genomes. Here, we present 824 actinobacterial isolate genomes in the context of a phylum-wide analysis of 6,700 genomes including public isolates and metagenome-assembled genomes (MAGs). We estimate that only 30%-50% of projected actinobacterial phylogenetic diversity possesses genomic representation via isolates and MAGs. A comparison of gene functions reveals novel determinants of host-microbe interaction as well as environment-specific adaptations such as potential antimicrobial peptides. We identify plasmids and prophages across isolates and uncover extensive prophage diversity structured mainly by host taxonomy. Analysis of >80,000 biosynthetic gene clusters reveals that horizontal gene transfer and gene loss shape secondary metabolite repertoire across taxa. Our observations illustrate the essential role of and need for high-quality isolate genome sequences.}, } @article {pmid36778050, year = {2022}, author = {Tomofuji, Y and Kishikawa, T and Maeda, Y and Ogawa, K and Otake-Kasamoto, Y and Kawabata, S and Nii, T and Okuno, T and Oguro-Igashira, E and Kinoshita, M and Takagaki, M and Oyama, N and Todo, K and Yamamoto, K and Sonehara, K and Yagita, M and Hosokawa, A and Motooka, D and Matsumoto, Y and Matsuoka, H and Yoshimura, M and Ohshima, S and Shinzaki, S and Nakamura, S and Iijima, H and Inohara, H and Kishima, H and Takehara, T and Mochizuki, H and Takeda, K and Kumanogoh, A and Okada, Y}, title = {Prokaryotic and viral genomes recovered from 787 Japanese gut metagenomes revealed microbial features linked to diets, populations, and diseases.}, journal = {Cell genomics}, volume = {2}, number = {12}, pages = {100219}, pmid = {36778050}, issn = {2666-979X}, abstract = {We reconstructed 19,084 prokaryotic and 31,395 viral genomes from 787 Japanese gut metagenomes as Japanese metagenome-assembled genomes (JMAG) and Japanese Virus Database (JVD), which are large microbial genome datasets for a single population. Population-specific enrichment of the Bacillus subtilis and β-porphyranase among the JMAG could derive from the Japanese traditional food natto (fermented soybeans) and nori (laver), respectively. Dairy-related Enterococcus_B lactis and Streptococcus thermophilus were nominally associated with the East Asian-specific missense variant rs671:G>A in ALDH2, which was associated with dairy consumption. Of the species-level viral genome clusters in the JVD, 62.9% were novel. The β crAss-like phage composition was low among the Japanese but relatively high among African and Oceanian peoples. Evaluations of the association between crAss-like phages and diseases showed significant disease-specific associations. Our large catalog of virus-host pairs identified the positive correlation between the abundance of the viruses and their hosts.}, } @article {pmid36777850, year = {2023}, author = {Lin, K and Zhang, HC and Zhang, Y and Zhou, Y and Fu, ZF and Wang, HY and Zhao, YH and Qiu, C and Fan, MX and Song, JY and Ai, JW and Zhang, WH}, title = {Clinical application and drug-use-guidance value of metagenomic next-generation sequencing in central nervous system infection.}, journal = {American journal of translational research}, volume = {15}, number = {1}, pages = {47-62}, pmid = {36777850}, issn = {1943-8141}, abstract = {OBJECTIVE: Timely and precise etiology diagnosis is crucial for optimized medication regimens and better prognosis in central nervous system infections (CNS infections). We aimed to analyze the impact of mNGS tests on the management of patients with CNS infections.

METHODS: We conducted a single-center retrospective cohort study to analyze the value of mNGS in clinical applications. Three hundred sixty-nine patients with a CNS infection diagnosis were enrolled, and their clinical data were collected. CDI and DDI were defined in our study to describe the intensity of drug use in different groups. We used LOH and mRS to evaluate if the application of mNGS can benefit CNS infected patients.

RESULTS: mNGS reported a 91.67% sensitivity in culture-positive patients and an 88.24% specificity compared with the final diagnoses. Patients who participated with the mNGS test had less drug use, both total (58.77 vs. 81.18) and daily (22.6 vs. 28.12, P < 0.1, McNemar) intensity of drug use, and length of hospitalization (23.14 vs. 24.29). Patients with a consciousness grading 1 and 3 had a decrease in CDI (Grade 1, 86.49 vs. 173.37; Grade 3, 48.18 vs. 68.21), DDI (Grade 1, 1.52 vs. 2.72; Grade 3, 2.3 vs. 2.45), and LOH (Grade 1, 32 vs. 40; Grade 3, 21 vs. 23) with the application of mNGS. Patients infected with bacteria in the CNS had a reduced CDI, DDI, and LOH in the mNGS group. This was compared with the TraE group that had 49% of patients altered medication plans, and 24.7% of patients reduced drug intensity four days after mNGS reports. This was because of the reduction of drug types.

CONCLUSION: mNGS showed its high sensitivity and specificity characteristics. mNGS may assist clinicians with more rational medication regimens and reduce the drug intensity for patients. The primary way of achieving this is to reduce the variety of drugs, especially for severe patients and bacterial infections. mNGS has the ability of improving the prognosis of CNS infected patients.}, } @article {pmid36777666, year = {2023}, author = {Zhao, H and Lv, F and Liu, G and Pang, X and Han, X and Wang, X}, title = {Effects of starters with different NDF/starch ratio on rumen fermentation parameters and rumen microorganisms in lambs.}, journal = {Frontiers in veterinary science}, volume = {10}, number = {}, pages = {1064774}, pmid = {36777666}, issn = {2297-1769}, abstract = {Starch and NDF are the main components in the diets of ruminants worldwide and are the main energy source for rumen microorganisms and hosts. The purpose of this study was to investigate the effects of different NDF/starch ratios on rumen fermentation parameters, rumen development and rumen microbes in lambs and to predict the function of rumen microbes by metagenomic techniques. In this study, 30 lambs with birth weights of (3.0 ± 0.5) kg were selected. The lambs of Hu sheep were randomly divided into two groups, fed starter with an NDF/starch ratio of 0.5 (group A) or 1.0 (group C). Samples of the rumen tissue and contents were collected after slaughter. The results showed that the ADG and ADFI of group A were significantly higher than those of group C (P < 0.05), but there was no significant difference in the FCR (P > 0.05). Therefore, from the perspective of feed-related economic benefits, group C showed greater economic value; the A/P of group C was significantly lower than that of group A (0.05 < P < 0.1), and the TVFA showed no significant difference (P > 0.05); The lengths of the rumen papillae of group C was significantly higher than that of group A (0.05 < P < 0.1). There was no significant difference in the abundance of the top 10 species at the phylum level and genus level (P > 0.05). CAZymes gene enrichment was observed in the rumen microbial community of lambs in group C (P < 0.05). In conclusion, group C, fed with starter with a higher NDF/starch ratio, had a higher feeding value. This study provides comprehensive insights into the composition of NDF and starch in lamb starter.}, } @article {pmid36777525, year = {2023}, author = {Laue, HE and Moroishi, Y and Palys, TJ and Christensen, BC and Criswell, RL and Peterson, LA and Huset, CA and Baker, ER and Karagas, MR and Madan, JC and Romano, ME}, title = {Early-life exposure to per- and polyfluoroalkyl substances and infant gut microbial composition.}, journal = {Environmental epidemiology (Philadelphia, Pa.)}, volume = {7}, number = {1}, pages = {e238}, pmid = {36777525}, issn = {2474-7882}, support = {T32 CA134286/CA/NCI NIH HHS/United States ; }, abstract = {UNLABELLED: Human milk is rich in essential nutrients and immune-activating compounds but is also a source of toxicants including per- and polyfluoroalkyl substances (PFAS). Evidence suggests that immune-related effects of PFAS may, in part, be due to alterations of the microbiome. We aimed to identify the association between milk PFAS exposure and the infant gut microbiome.

METHODS: PFAS [perfluorooctane sulfonic acid (PFOS) and perfluorooctanoate (PFOA)] were quantified in milk from ~6 weeks postpartum using high-performance liquid chromatography with tandem mass spectrometry. A molar sum (ΣPFAS) was calculated. Caregivers collected infant stool samples at 6 weeks (n = 116) and/or 1 year postpartum (n = 119). Stool DNA underwent metagenomic sequencing. We estimated the association of PFAS with diversity and relative abundances of species with linear regression. Single- and multi-PFAS models adjusted for potential confounders in complete case analyses and with imputed missing covariate data for 6-week and 1-year microbiomes separately. We assessed sensitive populations with stratification.

RESULTS: PFOS and PFOA were detected in 94% and 83% of milk samples, respectively. PFOS was associated with increased diversity at 6 weeks among infants fed exclusively human milk [β = 0.24 per PFOS doubling, (95% CI = 0.03, 0.45), P = 0.03] and born to primiparous mothers [β = 0.37 (0.06, 0.67), P = 0.02]. Estimates were strongest in multi-PFAS models and among complete cases. ΣPFAS was associated with Bacteroides vulgatus relative abundance at 1 year [(β = -2.34% per doubling (-3.63, -1.05), FDR q = 0.099].

CONCLUSIONS: PFAS may increase infant gut microbiome diversity and alter the relative abundance of biologically relevant bacteria. Additional analyses may identify related health outcomes.}, } @article {pmid36777162, year = {2022}, author = {Zhang, Y and Zhu, Y and Wan, H}, title = {Case report:Multiple abscesses caused by Porphyromonas gingivalis diagnosed by metagenomic next-generation sequencing.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {1089863}, pmid = {36777162}, issn = {2296-858X}, abstract = {BACKGROUND: Extraoral infection by Porphyromonas gingivalis (P. gingivalis) is extremely rare and challenging to diagnose because the fastidious pathogen is difficult to culture by traditional methods. We report the first case of a patient with multiple abscesses in muscles and the brain with dura empyema due to P. gingivalis, which was diagnosed by metagenomic next-generation sequencing (mNGS).

CASE PRESENTATION: A 65-year-old male patient was admitted to our hospital for multiple lumps in his body. Brain magnetic resonance imaging (MRI) and lower-limb computed tomography (CT) revealed multiple abscesses in the brain and muscles. A diagnosis of P. gingivalis infection was made based on mNGS tests of blood, cerebrospinal fluid (CSF), and pus samples, as the traditional bacterial culture of these samples showed negative results. Target antibiotic therapy with meropenem and metronidazole was administered, and CT-guided percutaneous catheter drainage of abscesses in both thighs was performed. The size of muscle abscesses reduced significantly and neurological function improved. The patient was followed up for 4 months. No abscesses re-appeared, and the remaining abscesses in his backside and both legs were completely absorbed. He can speak fluently and walk around freely without any neurological deficits.

CONCLUSION: Metagenomic next-generation sequencing is helpful for early diagnosis and subsequent treatment of P. gingivalis-associated multiple abscesses.}, } @article {pmid36777031, year = {2022}, author = {Galisteo, C and de la Haba, RR and Sánchez-Porro, C and Ventosa, A}, title = {Biotin pathway in novel Fodinibius salsisoli sp. nov., isolated from hypersaline soils and reclassification of the genus Aliifodinibius as Fodinibius.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1101464}, pmid = {36777031}, issn = {1664-302X}, abstract = {Hypersaline soils are extreme environments that have received little attention until the last few years. Their halophilic prokaryotic population seems to be more diverse than those of well-known aquatic systems. Among those inhabitants, representatives of the family Balneolaceae (phylum Balneolota) have been described to be abundant, but very few members have been isolated and characterized to date. This family comprises the genera Aliifodinibius and Fodinibius along with four others. A novel strain, designated 1BSP15-2V2[T], has been isolated from hypersaline soils located in the Odiel Saltmarshes Natural Area (Southwest Spain), which appears to represent a new species related to the genus Aliifodinibius. However, comparative genomic analyses of members of the family Balneolaceae have revealed that the genera Aliifodinibius and Fodinibius belong to a single genus, hence we propose the reclassification of the species of the genus Aliifodinibius into the genus Fodinibius, which was first described. The novel strain is thus described as Fodinibius salsisoli sp. nov., with 1BSP15-2V2[T] (=CCM 9117[T] = CECT 30246[T]) as the designated type strain. This species and other closely related ones show abundant genomic recruitment within 80-90% identity range when searched against several hypersaline soil metagenomic databases investigated. This might suggest that there are still uncultured, yet abundant closely related representatives to this family present in these environments. In-depth in-silico analysis of the metabolism of Fodinibius showed that the biotin biosynthesis pathway was present in the genomes of strain 1BSP15-2V2[T] and other species of the family Balneolaceae, which could entail major implications in their community role providing this vitamin to other organisms that depend on an exogenous source of this nutrient.}, } @article {pmid36776576, year = {2022}, author = {Zhuo, X and Zhou, Y and Liu, L}, title = {Acute bacterial encephalitis complicated with recurrent nasopharyngeal carcinoma associated with Elizabethkingia miricola infection: A case report.}, journal = {Frontiers in neurology}, volume = {13}, number = {}, pages = {965939}, pmid = {36776576}, issn = {1664-2295}, abstract = {Elizabethkingia miricola (E. miricola) is an extremely rare pathogenic bacterium, which causes serious infections in patients with primary immunodeficiency or tumors, and it is often misdiagnosed. E. miricola has rarely been known to cause a neurologic infection. We describe the first case of acute bacterial encephalitis associated with E. miricola infection in a man with recurrent nasopharyngeal carcinoma, which was successfully cured by antibiotics. The patient initially presented with recurrent episodes of fever and later showed impaired consciousness but these symptoms were alleviated with antibiotic therapy including cefoperazone/sulbactam. This study highlights that rapid and accurate pathogen detection via metagenomic next-generation sequencing and early use of appropriate antibiotics can improve the prognosis of patients with suspected neurologic E. miricola infection. Early treatment for underlying primary diseases can also significantly improve the outcomes of patients.}, } @article {pmid36776009, year = {2023}, author = {Zhang, QY and Jin, B and Feng, Y and Qian, K and Wang, H and Wan, C and Xu, PF and Zhang, M and Jiang, CM}, title = {[Etiological diagnostic value of metagenomic next-generation sequencing in peritoneal dialysis-related peritonitis].}, journal = {Zhonghua gan zang bing za zhi = Zhonghua ganzangbing zazhi = Chinese journal of hepatology}, volume = {39}, number = {1}, pages = {8-12}, doi = {10.3760/cma.j.cn441217-20220729-00748}, pmid = {36776009}, issn = {1007-3418}, support = {YKK21090//Nanjing Healthcare Science and Technology Development Special Fund Project/ ; 2021-LCYJ-PY-12//Fund for Clinical Trials from the Affiliated Drum Tower Hospital, Medical School of Nanjing University/ ; }, mesh = {Female ; Male ; Humans ; Adult ; Middle Aged ; Aged ; Retrospective Studies ; *Peritoneal Dialysis/adverse effects ; High-Throughput Nucleotide Sequencing ; *Peritonitis/diagnosis ; Sensitivity and Specificity ; }, abstract = {Objective: To explore the etiological diagnostic value of metagenomic next-generation sequencing (mNGS) in peritoneal dialysis (PD)-related peritonitis. Methods: The study was a retrospective cohort study. The clinical data of patients with PD-related peritonitis who were treated and underwent microbial cultivation and mNGS test at the same time from June 2020 to July 2021 in the Affiliated Drum Tower Hospital, Medical School of Nanjing University were analyzed. The positive rate, detection time and consistency between mNGS test and traditional microbial culture were compared. Results: A total of 18 patients with age of (50.4±15.4) years old and median dialysis time of 34.0 (12.4, 62.0) months were enrolled in the study, including 11 males and 7 females. Pathogenic microorganisms were isolated in 17 patients by mNGS test, with a positive rate of 17/18, which was higher than 13/18 of microbial culture, but the difference was not statistically significant (P=0.219). Both mNGS test and microbial culture isolated positive pathogenic bacteria in 12 patients, and mNGS test isolated the same types of pathogenic bacteria as microbial cultivation did in 11 patients. In five patients with negative microbial culture, mNGS test also isolated pathogenic microorganisms, including 3 cases of Staphylococcus epidermidis, 1 case of Mycobacterium tuberculosis and 1 case of Ureaplasma urealyticum. In 1 patient, microbial culture isolated pathogenic bacteria (Escherichia coli) whereas mNGS test did not. The detection time of mNGS was 25.0 (24.0, 27.0) h, which was significantly shorter than 89.0 (72.8, 122.0) h of microbial culture (Z=3.726, P<0.001). Conclusions: mNGS test can improve the detection rate of pathogenic microorganisms in PD-related peritonitis and greatly shorten the detection time, and has good consistency with microbial culture. mNGS may provide a new approach for pathogen identification of PD-related peritonitis, especially refractory peritonitis.}, } @article {pmid36775633, year = {2023}, author = {Du, SY and Chen, J and Liu, JW and Guo, XW and Min, W}, title = {[Revealing the Effect of Saline Water Drip Irrigation on Soil Microorganisms in Cotton Fields Based on Metagenomics].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {44}, number = {2}, pages = {1104-1119}, doi = {10.13227/j.hjkx.202204237}, pmid = {36775633}, issn = {0250-3301}, mesh = {*Soil/chemistry ; *Carbon ; Fertilizers ; Bacteria/genetics ; Proteobacteria ; Gossypium ; Acidobacteria ; Saline Waters ; Nitrogen ; Soil Microbiology ; }, abstract = {Saline water irrigation has become an important means to alleviate the shortage of freshwater in arid areas. However, long-term saline water irrigation can cause soil salinity accumulation, affect soil microbial community structure, and then affect soil nutrient transformation. In this study, we used metagenomics to investigate the effects of long-term saline water drip irrigation on soil microbial community structure in a cotton field. In the experiment, the salinity of irrigation water (ECw) was set to two treatments:0.35 dS·m[-1] and 8.04 dS·m[-1] (denoted as FW and SW, respectively), and the nitrogen application rates were 0 kg·hm[-2]and 360 kg·hm[-2] (denoted as N0 and N360, respectively). The results showed that saline water irrigation increased soil water content, salinity, organic carbon, and total nitrogen content and decreased soil pH and available potassium content. Nitrogen fertilizer application increased soil organic carbon, salinity, and total nitrogen content and decreased soil water content, pH, and available potassium content. The dominant bacterial phyla in each treatment were:Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, and Gemmatimonadetes. Saline water irrigation significantly increased the relative abundances of Actinobacteria, Chloroflexi, Gemmatimonadetes, and Firmicutes but significantly decreased the relative abundances of Proteobacteria, Acidobacteria, Cyanobacteria, and Nitrospira. Nitrogen fertilizer application significantly increased the relative abundances of Chloroflexi and Nitrospira but significantly decreased the relative abundances of Acidobacteria, Gemmatimonadetes, Planctomycetes, Cyanobacteria, and Verrucomicrobia. LEfSe analysis showed that saline water irrigation had no significant effect on the number of potential biomarkers, and nitrogen fertilizer application decreased the number of potential biomarkers in soil microbial communities. The correlation network diagram showed that the 20 genera had different degrees of correlation, including 44 positive correlations and 48 negative correlations. The core species in the network diagram were Nocardioides, Streptomyces, Pyrinomonas, Candidatus_Solibacter, and Bradyrhizobium spp. Saline water irrigation increased the relative abundances of the denitrification genes nirK, nirS, nasB, and norC and decreased the relative abundances of the nitrification genes amoB, amoC, and nxrA, whereas nitrogen fertilizer application increased the relative abundances of the nitrification genes amoA, amoB, amoC, hao, and nxrA and decreased the relative abundances of the denitrifying genes narB, napA, nasA, and nosZ. Saline water irrigation could adversely affect soil physicochemical properties; SWC, EC1:5, and BD were the main driving factors affecting soil microbial community structure and function genes; and soil microorganisms adapted to soil salt stress by regulating species composition.}, } @article {pmid36775248, year = {2023}, author = {Li, H and Ge, T and Huang, M and Zhang, W and Li, Z and Xiao, M and Gao, L}, title = {Application of metagenomic next-generation sequencing in bloodstream infection regarding immunosuppression.}, journal = {The Journal of infection}, volume = {86}, number = {5}, pages = {508-512}, doi = {10.1016/j.jinf.2023.02.008}, pmid = {36775248}, issn = {1532-2742}, mesh = {Humans ; *Communicable Diseases ; Metagenome ; *Sepsis/diagnosis ; Immunosuppression Therapy ; High-Throughput Nucleotide Sequencing ; }, } @article {pmid36774796, year = {2023}, author = {Malla, MA and Dubey, A and Kumar, A and Yadav, S and Kumari, S}, title = {Modeling and optimization of chlorpyrifos and glyphosate biodegradation using RSM and ANN: Elucidating their degradation pathways by GC-MS based metabolomics.}, journal = {Ecotoxicology and environmental safety}, volume = {252}, number = {}, pages = {114628}, doi = {10.1016/j.ecoenv.2023.114628}, pmid = {36774796}, issn = {1090-2414}, mesh = {Amino Acids ; Biodegradation, Environmental ; *Chlorpyrifos/metabolism ; Gas Chromatography-Mass Spectrometry ; Neural Networks, Computer ; *Pesticides/metabolism ; Glyphosate ; }, abstract = {Ongoing and extensive use of pesticides negatively impact the environment and human health. Microbe-based remediation bears importance as it is an eco-friendly and cost-effective technique. The present study investigated chlorpyrifos (CHL) and glyphosate (GLY) degrading potential of Bacillus cereus AKAD 3-1, isolated from the soybean rhizosphere. Optimization and validation of different process variables were carried out by response surface methodology (RSM) and artificial neural network (ANN). Critical parameters which affect the degradation process are initial pesticide concentration, pH, and inoculum size. At optimum conditions, the bacterial strain demonstrated 94.52% and 83.58% removal of chlorpyrifos and glyphosate, respectively. Both Central-composite design (CCD-RSM) and ANN approaches proved to perform well in modeling and optimizing the growth conditions. The optimum ANN-GA model resulted in R[2] ≥ 0.99 for chlorpyrifos and glyphosate, while in the case of RSM, the obtained R[2] value was 0.96 and 0.95, respectively. Results indicated that the process variables significantly (p < 0.05) impact chlorpyrifos and glyphosate biodegradation. Moreover, the predicted RSM model had a "lack of fit p-value" of "0.8849" and "0.2502" for chlorpyrifos and glyphosate, respectively. GC-MS analysis revealed that the strain first converted chlorpyrifos into 3,5,6-trichloro pyridin-2-ol & O, O-diethyl O-hydrogen phosphorothiate. Later, these intermediate metabolites were broken and completely mineralized into non-toxic by-products. Similarly, glyphosate was first converted into 2-(methylamino) acetic acid and amino-oxyphosphonic acid, which were further mineralized without any toxic by-products. Taken together, the results of this study clarify the biodegradation pathways and highlights the promising potential of B. cereus AKAD 3-1 in the bioremediation of chlorpyrifos and glyphosate-polluted environments.}, } @article {pmid36774720, year = {2023}, author = {Nguyen, VH and Wemheuer, B and Song, W and Bennett, H and Palladino, G and Burgsdorf, I and Sizikov, S and Steindler, L and Webster, NS and Thomas, T}, title = {Functional characterization and taxonomic classification of novel gammaproteobacterial diversity in sponges.}, journal = {Systematic and applied microbiology}, volume = {46}, number = {2}, pages = {126401}, doi = {10.1016/j.syapm.2023.126401}, pmid = {36774720}, issn = {1618-0984}, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Bacteria ; Metagenome ; *Microbiota ; Sulfur Compounds/metabolism ; }, abstract = {Sponges harbour exceptionally diverse microbial communities, whose members are largely uncultured. The class Gammaproteobacteria often dominates the microbial communities of various sponge species, but most of its diversity remains functional and taxonomically uncharacterised. Here we reconstructed and characterised 32 metagenome-assembled genomes (MAGs) derived from three sponge species. These MAGs represent ten novel species and belong to seven orders, of which one is new. We propose nomenclature for all these taxa. These new species comprise sponge-specific bacteria with varying levels of host specificity. Functional gene profiling highlights significant differences in metabolic capabilities across the ten species, though each also often exhibited a large degree of metabolic diversity involving various nitrogen- and sulfur-based compounds. The genomic features of the ten species suggest they have evolved to form symbiotic interaction with their hosts or are well-adapted to survive within the sponge environment. These Gammaproteobacteria are proposed to scavenge substrates from the host environment, including metabolites or cellular components of the sponge. Their diverse metabolic capabilities may allow for efficient cycling of organic matter in the sponge environment, potentially to the benefit of the host and other symbionts.}, } @article {pmid36774574, year = {2023}, author = {Koirala, S and Myers, B and Shin, GY and Gitaitis, R and Kvitko, BH and Dutta, B}, title = {Evaluating Options to Increase the Efficacy of Biocontrol Agents for the Management of Pantoea spp. Under Field Conditions.}, journal = {Plant disease}, volume = {107}, number = {9}, pages = {2701-2708}, doi = {10.1094/PDIS-11-22-2710-RE}, pmid = {36774574}, issn = {0191-2917}, mesh = {*Pantoea ; Copper ; Plant Diseases/prevention & control ; *Fungicides, Industrial ; Peroxides ; }, abstract = {Center rot of onion is caused by a complex of plant pathogenic Pantoea species, which can lead to significant yield losses in the field and during storage. Conventional growers use foliar protectants such as a mixture of copper bactericides and an ethylene-bis-dithiocarbamate (EBDC) fungicide to manage the disease; however, organic growers have limited management options besides copper-protectants. Biocontrol agents (BCAs) provide an alternative; however, their efficacy could be compromised due in part to their inability to colonize the foliage. We hypothesized that pretreatment with peroxide (OxiDate 2.0: a.i., hydrogen peroxide and peroxyacetic acid) enhances the colonizing ability of the subsequently applied BCAs, leading to effective center rot management. Field trials were conducted in 2020 and 2021 to assess the efficacy of peroxide, BCAs (Serenade ASO: Bacillus subtilis and BlightBan: Pseudomonas fluorescens), and an insecticide program (tank mix of spinosad and neem oil) to manage center rot. We observed no significant difference in foliar area under the disease progress curve (AUDPC) between the peroxide pretreated P. fluorescens plots and only P. fluorescens-treated plots in 2020 and 2021. Peroxide pretreatment before B. subtilis application significantly reduced the foliar AUDPC as compared with the stand-alone B. subtilis treatment in 2020; however, no such difference was observed in 2021. Similarly, peroxide pretreatment before either of the BCAs did not seem to reduce the incidence of bulb rot as compared with the stand-alone BCA treatment in any of the trials (2020 and 2021). Additionally, our foliar microbiome study showed comparatively higher P. fluorescens retention on peroxide pretreated onion foliage; however, at the end of the growing season, P. fluorescens was drastically reduced and was virtually nonexistent (<0.002% of the total reads). Overall, the pretreatment with peroxide had a limited effect in improving the foliar colonizing ability of BCAs and consequently a limited effect in managing center rot.}, } @article {pmid36774423, year = {2023}, author = {Aboshady, HM and Choury, A and Montout, L and Félicité, Y and Godard, X and Bambou, JC}, title = {Metagenome reveals caprine abomasal microbiota diversity at early and late stages of Haemonchus contortus infection.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {2450}, pmid = {36774423}, issn = {2045-2322}, mesh = {Animals ; Sheep ; Metagenome ; *Haemonchus/genetics ; Goats ; *Microbiota/genetics ; Abomasum ; *Haemonchiasis/veterinary/parasitology ; *Sheep Diseases/parasitology ; }, abstract = {Haemonchus contortus is one of the most detrimental gastrointestinal nematode parasites for small ruminants, especially in tropics and subtropics. Gastrointestinal nematode and microbiota share the same microhabitat; thus they interact with each other and their host. Metagenomics tools provide a promising way to examine the alterations in the gastric microbial composition induces by gastrointestinal parasites. In this study, we used metagenomics tools to characterize the impact of H. contortus infection on the caprine abomasal microbiota at early and late stage of infection and compared it with non-infected control. Our results showed that H. contortus infection caused a significant increase in abomasal pH at early (7 days post-infection) and late stage of infection (56 days post-infection). The analysis of alpha and beta diversity showed that the microbiota diversity both in number and in proportion was significantly affected at early and late stage of infection. All microbiota classes are impacted by H. contortus infection but Clostridia and Bacteroidia are more concerned. In infected animals, the genera Prevotella decreased at 7 and 56 days post-infection. Here we showed that the abomasal microbiota was significantly affected early after H. contortus infection, and these changes persist at late stage of the infection.}, } @article {pmid36773904, year = {2023}, author = {Samson, R and Rajput, V and Yadav, R and Shah, M and Dastager, S and Khairnar, K and Dharne, M}, title = {Spatio-temporal variation of the microbiome and resistome repertoire along an anthropogenically dynamic segment of the Ganges River, India.}, journal = {The Science of the total environment}, volume = {872}, number = {}, pages = {162125}, doi = {10.1016/j.scitotenv.2023.162125}, pmid = {36773904}, issn = {1879-1026}, mesh = {*Genes, Bacterial ; Rivers/chemistry ; Bacteria/genetics ; *Microbiota ; India ; Metals ; Anti-Bacterial Agents ; }, abstract = {Aquatic ecosystems are regarded as a hub of antibiotic and metal resistance genes. River Ganges is a unique riverine system in India with socio-cultural and economic significance. However, it remains underexplored for its microbiome and associated resistomes along its anthropogenically impacted course. The present study utilized a nanopore sequencing approach to depict the microbial community structure in the sediments of the river Ganges harboring antibiotic and metal resistance genes (A/MRGs) in lower stretches known for anthropogenic impact. Comprehensive microbiome analyses revealed resistance genes against 23 different types of metals and 28 classes of antibiotics. The most dominant ARG category was multidrug resistance, while the most prevalent MRGs conferred resistance against copper and zinc. Seasonal differences dismally affected the microbiota of the Ganges. However, resistance genes for fosmidomycin and tetracycline varied with season ANOVA, p < 0.05. Interestingly, 333 and 334 ARG subtypes were observed at all the locations in pre-monsoon and post-monsoon, respectively. The taxa associated with the dominant ARGs and MRGs were Pseudomonas and Burkholderia, which are important nosocomial pathogens. A substantial phage diversity for pathogenic and putrefying bacteria at all locations attracts attention for its use to tackle the dissemination of antibiotic and metal-resistant bacteria. This study suggests the accumulation of antibiotics and metals as the driving force for the emergence of resistance genes and the affiliated bacteria trafficking them. The present metagenomic assessment highlights the need for comprehensive, long-term biological and physicochemical monitoring and mitigation strategies toward the contaminants associated with ARGs and MRGs in this nationally important river.}, } @article {pmid36773890, year = {2023}, author = {Wang, G and Long, J and Zhuang, Y and Leng, X and Zhang, Y and Liu, L and Fu, J and Chen, Y and Li, C and Zhou, Y and Huang, B and Feng, C}, title = {Application of metagenomic next-generation sequencing in the detection of pathogens in spinal infections.}, journal = {The spine journal : official journal of the North American Spine Society}, volume = {23}, number = {6}, pages = {859-867}, doi = {10.1016/j.spinee.2023.02.001}, pmid = {36773890}, issn = {1878-1632}, mesh = {Humans ; Retrospective Studies ; *High-Throughput Nucleotide Sequencing ; Antitubercular Agents ; Neutrophils ; *Orthopedics ; Sensitivity and Specificity ; }, abstract = {BACKGROUND CONTEXT: The precise diagnosis and treatment of spinal infections (SI) remains challenging for spine surgeons. Identifying the pathogens of SI through metagenomic next-generation sequencing (mNGS) may be a key approach to addressing this challenge.

PURPOSE: To evaluate the accuracy and applicability of mNGS in determining the etiology of SI.

STUDY DESIGN: Diagnostic test study.

PATIENT SAMPLE: Twenty-five patients who had a clinical suspicion of SI and underwent mNGS testing.

OUTCOME MEASURES: The specificity, sensitivity, and time cost of mNGS and bacterial culture were compared. Clinical outcomes were assessed using the numeric rating scale (NRS) score, Oswestry Disability Index (ODI), and the Japanese Orthopedic Association (JOA) score. Demographic data and laboratory results (blood cell count (WBC), erythrocyte sedimentation rate (ESR), neutrophil percentage (NEUT%), and C-reactive protein level (CRP) were also evaluated.

METHODS: In this retrospective study, samples were obtained from 25 eligible patients via surgery or CT-guided puncture and subjected to histopathological examination, bacterial culture, and mNGS. The sensitivity and specificity of the bacterial cultures and mNGS were calculated with respect to the histopathological results as a reference. Postoperative antibiotics or antituberculosis drugs were administered on the basis of mNGS results, combined with clinical manifestations, imaging examination, and histopathology. The changes of clinical outcomes and laboratory results after treatment were observed.

RESULTS: Of the 25 patients, 21 had a positive pathology, of which 10 showed a tuberculous pathology, and the remaining 11 showed a nontuberculous inflammatory pathology. The sensitivity of mNGS was higher than that of the bacterial culture. However, the difference in specificity between bacterial culture and mNGS was not significant. Moreover, the time needed to perform mNGS was significantly lower than that of bacterial culture and pathology. All patients were followed up for more than three months, and CRP and NEUT% significantly decreased by three months after treatment. There was no significant difference in WBC and ESR. The ODI, NRS and JOA scores were significantly improved after treatment.

CONCLUSION: Metagenomic next-generation sequencing technology can play an important role in the detection of pathogens in SI and should be further investigated and applied in future studies.}, } @article {pmid36773138, year = {2023}, author = {Wang, QS and Ui-Tei, K}, title = {Utilizing Large Functional and Population Genomics Resources for CRISPR/Cas Perturbation Experiment Design.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2637}, number = {}, pages = {63-73}, pmid = {36773138}, issn = {1940-6029}, mesh = {Humans ; *CRISPR-Cas Systems/genetics ; *Metagenomics ; Chromosome Mapping ; Genome, Human ; }, abstract = {Genome sequencing technologies have rapidly evolved in the past decades, enabling us to interpret the human genome through multiple perspectives, ranging from cross-species comparisons, naturally occurring variation in health and disease state to regulatory mechanisms.Although such perspectives are all informative to narrow down the list of genes or variants for perturbation experiments based on specific biological aims, utilizing multiple sources of information is often challenging in practice.In this chapter, we provide an overview of major large-scale functional and population genomics resources, followed by a practical example of selecting target variants for genetic perturbation experiments involving genome engineering techniques such as CRISPR/Cas.}, } @article {pmid36772850, year = {2023}, author = {Kong, C and Liu, G and Kalady, MF and Jin, T and Ma, Y}, title = {Dysbiosis of the stool DNA and RNA virome in Crohn's disease.}, journal = {Journal of medical virology}, volume = {95}, number = {2}, pages = {e28573}, doi = {10.1002/jmv.28573}, pmid = {36772850}, issn = {1096-9071}, mesh = {Humans ; *Crohn Disease/microbiology ; Virome ; Dysbiosis ; DNA Replication ; DNA, Viral/genetics ; Virus Replication ; *Viruses/genetics ; *Bacteriophages/genetics ; Bacteria/genetics ; }, abstract = {Pathogenesis of Crohn's disease (CD) relates to gut microbiome dysbiosis. However, less is known about the viral microbiome, consisting of bacteriophages and eukaryotic viruses, in CD. Here, we profiled the stool virome, viral functions, and viral-bacterial correlations that involved in CD pathogenesis. Metagenomics and metaviromics with novel viral identification and data analysis workflow were performed on stool of non-CD household controls, CD flare and remission patients. Both bacteriome and DNA/RNA virome alterations were characterized and correlated with disease status. There was a decreased diversity and extreme heterogeneity in both DNA and RNA virome in CD. We observed CD-specific dysbiosis in virome, particularly the prominent DNA eukaryotic Torque teno virus (TTV), disease-associated Faecalibacterium phage and Escherichia phage, and RNA tomato diet-related virus in CD, while some diverse prokaryotic viruses were more abundant in healthy subjects. Compared with the remission, inflammation-associated eukaryotic TTV and prokaryotic Staphylococcus phages were predominated in the flare, and displayed a link with complications and multiple therapeutic approaches. Multiple viral functions, particularly functions of viral DNA replication, integration and modification as well as the eukaryotic TTV-related capsid protein, were markedly enriched in CD. Furthermore, the virus-bacteria interactions became more specialized in CD, and the combination of bacteriome and virome composition provided better classification between CD and health. Our study presents a global view of the comprehensive viral component change in the CD patients' gut microbiome, and highlights the great potential of virome biomarkers in pathogenesis and accurate diagnostics of CD risk and disease status.}, } @article {pmid36771951, year = {2023}, author = {Sorokin, AV and Goncharova, SS and Lavlinskaya, MS and Holyavka, MG and Faizullin, DA and Kondratyev, MS and Kannykin, SV and Zuev, YF and Artyukhov, VG}, title = {Carboxymethyl Cellulose-Based Polymers as Promising Matrices for Ficin Immobilization.}, journal = {Polymers}, volume = {15}, number = {3}, pages = {}, pmid = {36771951}, issn = {2073-4360}, support = {МК-2517.2022.1.3//Council on Grants of the President of the Russian Federation for State Support to Young Russian scientists - Candidates of Sciences/ ; Agreement No. 075-15-2021-1351//Ministry of Science and Higher Education of Russia/ ; project No. 21-74-20053//Russian Science Foundation/ ; }, abstract = {The present work is devoted to research on the interaction between carboxymethyl cellulose sodium salt and its derivatives (graft copolymer of carboxymethyl cellulose sodium salt and N,N-dimethyl aminoethyl methacrylate) with cysteine protease (ficin). The interaction was studied by FTIR and by flexible molecular docking, which have shown the conjugates' formation with both matrices. The proteolytic activity assay performed with azocasein demonstrated that the specific activities of all immobilized ficin samples are higher in comparison with those of the native enzyme. This is due to the modulation of the conformation of ficin globule and of the enzyme active site by weak physical interactions involving catalytically valuable amino acids. The results obtained can extend the practical use of ficin in biomedicine and biotechnology.}, } @article {pmid36771611, year = {2023}, author = {Alcalá-Herrera, R and Moreno, B and Aguirrebengoa, M and Winter, S and Robles-Cruz, AB and Ramos-Font, ME and Benítez, E}, title = {Role of Agricultural Management in the Provision of Ecosystem Services in Warm Climate Vineyards: Functional Prediction of Genes Involved in Nutrient Cycling and Carbon Sequestration.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, pmid = {36771611}, issn = {2223-7747}, support = {I 4025/FWF_/Austrian Science Fund FWF/Austria ; }, abstract = {(1) Background: Maintaining soil fertility and crop productivity using natural microbial diversity could be a feasible approach for achieving sustainable development in agriculture. In this study, we compared soils from vineyards under organic and conventional management by predicting functional profiles through metagenomic analysis based on the 16S rRNA gene. (2) Methods: The structure, diversity and predictive functions of soil bacteria related to the biogeochemical cycle of the soil were analyzed, including oxidative and hydrolytic C-cycling enzymes, N-cycling enzymes and P-cycling enzymes. The inter-row spontaneous vegetation in the organic vineyards was also characterized. (3) Results: A clear effect of the farming system (organic vs. conventional) and cover management (herbicides plus tillage, mowing only and mowing plus tillage) on bacterial beta diversity and predicted functions was evidenced. While conventional viticulture increased the potential capacity of the soil to regulate the cycling of inorganic forms of N, organic viticulture in general enhanced those functions involving organic N, P and C substrates. Although the soil bacterial community responded differently to contrasting soil management strategies, nutrient cycling and carbon sequestration functions remained preserved, suggesting a high bacterial functional redundancy in the soil in any case. However, most of the predicted bacterial functions related to soil organic matter turnover were enhanced by organic management. (4) Conclusions: We posit the potential for organic viticulture to adequately address climate change adaptation in the context of sustainable agriculture.}, } @article {pmid36771402, year = {2023}, author = {Leech, SM and Gilbert, MC and Clifton, VL and Kumar, S and Rae, KM and Borg, D and Dekker Nitert, M}, title = {Insufficient Evidence of a Breastmilk Microbiota at Six-Weeks Postpartum: A Pilot Study.}, journal = {Nutrients}, volume = {15}, number = {3}, pages = {}, pmid = {36771402}, issn = {2072-6643}, support = {RTP scholarship//Australian Government Research Training Program/ ; KMR//Mater Foundation and Equity Trustees/ ; RSP fellowship to DJB//University of Queensland/ ; QFC funding//Mater Foundation, The University of Queensland, Giffith University, QUT/ ; 75002_GC_20//The Lott, Golden Casket/ ; 1033//Brisbane Diamantina Health Partners/ ; 2041//Perpetual Impact Funding/ ; 2441//Advance Queensland/ ; equipment support//Qiagen/ ; Equipment support//Microba/ ; }, mesh = {Infant ; Pregnancy ; Humans ; Female ; *Milk, Human/microbiology ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Evidence Gaps ; *Microbiota/genetics ; Postpartum Period ; Mouth ; }, abstract = {Breastmilk is thought to influence the infant gut by supplying prebiotics in the form of human milk oligosaccharides and potentially seeding the gut with breastmilk microbes. However, the presence of a breastmilk microbiota and origins of these microbes are still debated. As a pilot study, we assessed the microbes present in expressed breastmilk at six-weeks postpartum using shotgun metagenomic sequencing in a heterogenous cohort of women who delivered by vaginal (n = 8) and caesarean delivery (n = 8). In addition, we estimated the microbial load of breastmilk at six-weeks post-partum with quantitative PCR targeting the 16S rRNA gene. Breastmilk at six-weeks postpartum had a low microbial mass, comparable with PCR no-template and extraction controls. Microbes identified through metagenomic sequencing were largely consistent with skin and oral microbes, with four samples returning no identifiable bacterial sequences. Our results do not provide convincing evidence for the existence of a breastmilk microbiota at six-weeks postpartum. It is more likely that microbes present in breastmilk are sourced by ejection from the infant's mouth and from surrounding skin, as well as contamination during sampling and processing.}, } @article {pmid36771397, year = {2023}, author = {Seo, H and Yoon, SY and Ul-Haq, A and Jo, S and Kim, S and Rahim, MA and Park, HA and Ghorbanian, F and Kim, MJ and Lee, MY and Kim, KH and Lee, N and Won, JH and Song, HY}, title = {The Effects of Iron Deficiency on the Gut Microbiota in Women of Childbearing Age.}, journal = {Nutrients}, volume = {15}, number = {3}, pages = {}, pmid = {36771397}, issn = {2072-6643}, support = {2021R1G1A1094322//National Research Foundation of Korea/ ; 20018499//Technology Innovation program/ ; Soonchunhyang University Research Fund.//Soonchunhyang University/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome ; *Iron Deficiencies ; *Anemia, Iron-Deficiency/complications/drug therapy ; Iron/therapeutic use ; *Microbiota ; }, abstract = {Iron deficiency anemia (IDA) is the most prevalent and common nutritional deficiency worldwide and is a global health problem with significant risk, particularly among women of reproductive age. Oral iron supplementation is the most widely used and cost-effective treatment for iron deficiency and IDA. However, there are limitations regarding side effects such as enteritis, treatment compliance, and bioavailability. Intestinal microbiome characteristic research has been recently conducted to overcome these issues, but more is needed. Against this background, a metagenomics study on the 16S gene in the feces of young women vulnerable to IDA was conducted. As a result of analyzing 16 normal subjects and 15 IDA patients, significant differences in bacterial community distribution were identified. In particular, a significant decrease in Faecalibacterium was characteristic in IDA patients compared with normal subjects. Furthermore, in the case of patients who recovered from IDA following iron supplementation treatment, it was confirmed that Faecalibacterium significantly recovered to normal levels. However, no significance in beta diversity was seen compared with before treatment. There were also no differences in the beta diversity results between the recovered and normal subjects. Therefore, intestinal dysbiosis during the disease state was considered to be restored as IDA improved. Although the results were derived from a limited number of subjects and additional research is needed, the results of this study are expected to be the basis for developing treatment and prevention strategies based on host-microbiome crosstalk in IDA.}, } @article {pmid36771396, year = {2023}, author = {Gow, ML and Chua, XY and El-Omar, E and Susic, D and Henry, A}, title = {Relationship between Diet Quality and Maternal Stool Microbiota in the MUMS Australian Pregnancy Cohort.}, journal = {Nutrients}, volume = {15}, number = {3}, pages = {}, pmid = {36771396}, issn = {2072-6643}, support = {UNSW RG188959//St George and Sutherland Medical Research Foundation/ ; N/A//The Royal Australian and New Zealand College of Obstetricians and Gynaecologists/ ; APP1158876//National Health and Medical Research Council/ ; }, mesh = {Humans ; Pregnancy ; Female ; Cohort Studies ; Australia ; *Diet ; Postpartum Period ; *Microbiota ; }, abstract = {Dietary intake during pregnancy may influence the antenatal microbiome, which is proposed to impact maternal and infant health during the pregnancy and beyond. The aim of this sub-study was to examine associations between dietary intake and microbiota diversity during pregnancy using whole metagenomic sequencing and examine associations in low-risk versus high-risk pregnancies, as well as complicated versus uncomplicated pregnancies. Pregnancy data were analysed from women participating in the MUMS cohort study in Sydney, Australia (women followed from trimester 1 of pregnancy to 1-year postpartum), who had dietary intake data at either trimester 1 or 3, assessed using the Australian Eating Survey, and a matched stool sample (n = 86). Correlations of microbial alpha diversity with dietary intake data were determined using the repeated-measures correlation, rmcorr, in R. In the combined cohort, no associations were found between diet quality or diet composition and microbial alpha diversity or beta diversity. However, trends in our analysis suggested that dietary intake of specific macro- and micronutrients may influence microbial diversity differently, depending on particular pregnancy conditions. Our findings suggest that dietary intake during pregnancy may have a variable influence on the maternal microbiota, unique to the individual maternal pregnancy phenotype. More research is needed to disentangle these associations.}, } @article {pmid36771360, year = {2023}, author = {Duysburgh, C and Verstrepen, L and Broeck, MVD and Righetto, Z and Perez, M}, title = {Investigation of Enterogermina's Protective and Restorative Mechanisms on the Gut Microbiota with PPI, Using SHIME Technology.}, journal = {Nutrients}, volume = {15}, number = {3}, pages = {}, pmid = {36771360}, issn = {2072-6643}, support = {N/A//Sanofi/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Dysbiosis/chemically induced ; Proton Pump Inhibitors/adverse effects ; *Microbiota ; Feces ; *Probiotics ; }, abstract = {Proton pump inhibitors (PPIs) are commonly prescribed medications associated with changes in the gut microbiome and dysbiosis when used long-term. Probiotics, such as Enterogermina[®] (containing four strains of Bacillus clausii) reduce side effects from triple therapy with PPI+antibiotics. We aim to assess the ability of this probiotic in preventing and/or treating the dysbiosis induced by PPI use. Faecal samples from six healthy donors were used to colonise a Triple-Mucosal-Simulator of the Human Intestinal Microbial Ecosystem[®] model with added ileal compartment. Changes in the microbial community composition and metabolite production were measured for PPI alone (control), PPI+Enterogermina (preventative), and Enterogermina treatment after PPI (curative). Differences were assessed by one-way ANOVA with Tukey's multiple comparisons test. The model was shown to replicate some of the effects of long-term PPI use. There were significant changes in microbial diversity and an increase in butyrate levels in the preventative and curative arms, indicative of a beneficial effect to gut health. Probiotic use countered some of the effects of PPI use: Streptococcus bovis levels increased in the control arm but reduced following probiotic treatment. These results show that probiotic treatment with B. clausii may have beneficial effects on the gut microbiota following PPI treatment.}, } @article {pmid36769278, year = {2023}, author = {Tiew, PY and Meldrum, OW and Chotirmall, SH}, title = {Applying Next-Generation Sequencing and Multi-Omics in Chronic Obstructive Pulmonary Disease.}, journal = {International journal of molecular sciences}, volume = {24}, number = {3}, pages = {}, pmid = {36769278}, issn = {1422-0067}, support = {Clinician Scientist Award (MOH-000710)//Singapore Ministry of Health's National Medical Research Council/ ; Open Fund-Individual Research Grant (MOH-000955)//Singapore Ministry of Health's National Medical Research Council/ ; }, mesh = {Humans ; Multiomics ; *Pulmonary Disease, Chronic Obstructive/diagnosis/genetics/therapy ; *Microbiota/genetics ; Host Microbial Interactions ; High-Throughput Nucleotide Sequencing ; }, abstract = {Microbiomics have significantly advanced over the last decade, driven by the widespread availability of next-generation sequencing (NGS) and multi-omic technologies. Integration of NGS and multi-omic datasets allow for a holistic assessment of endophenotypes across a range of chronic respiratory disease states, including chronic obstructive pulmonary disease (COPD). Valuable insight has been attained into the nature, function, and significance of microbial communities in disease onset, progression, prognosis, and response to treatment in COPD. Moving beyond single-biome assessment, there now exists a growing literature on functional assessment and host-microbe interaction and, in particular, their contribution to disease progression, severity, and outcome. Identifying specific microbes and/or metabolic signatures associated with COPD can open novel avenues for therapeutic intervention and prognosis-related biomarkers. Despite the promise and potential of these approaches, the large amount of data generated by such technologies can be challenging to analyze and interpret, and currently, there remains a lack of standardized methods to address this. This review outlines the current use and proposes future avenues for the application of NGS and multi-omic technologies in the endophenotyping, prognostication, and treatment of COPD.}, } @article {pmid36769093, year = {2023}, author = {Dora, D and Bokhari, SMZ and Aloss, K and Takacs, P and Desnoix, JZ and Szklenárik, G and Hurley, PD and Lohinai, Z}, title = {Implication of the Gut Microbiome and Microbial-Derived Metabolites in Immune-Related Adverse Events: Emergence of Novel Biomarkers for Cancer Immunotherapy.}, journal = {International journal of molecular sciences}, volume = {24}, number = {3}, pages = {}, pmid = {36769093}, issn = {1422-0067}, support = {OTKA #124652; OTKA #129664; OTKA #142287//Hungarian National Research, Development and Innovation Office/ ; }, mesh = {Humans ; *Antineoplastic Agents, Immunological/therapeutic use ; Immune Checkpoint Inhibitors/adverse effects ; *Gastrointestinal Microbiome ; *Neoplasms/drug therapy ; *Melanoma/drug therapy ; *Drug-Related Side Effects and Adverse Reactions/etiology ; Immunotherapy/adverse effects/methods ; Biomarkers ; }, abstract = {Immune checkpoint inhibitors (ICIs) have changed how we think about tumor management. Combinations of anti-programmed death ligand-1 (PD-L1) immunotherapy have become the standard of care in many advanced-stage cancers, including as a first-line therapy. Aside from improved anti-tumor immunity, the mechanism of action of immune checkpoint inhibitors (ICIs) exposes a new toxicity profile known as immune-related adverse effects (irAEs). This novel toxicity can damage any organ, but the skin, digestive and endocrine systems are the most frequently afflicted. Most ICI-attributed toxicity symptoms are mild, but some are severe and necessitate multidisciplinary side effect management. Obtaining knowledge on the various forms of immune-related toxicities and swiftly changing treatment techniques to lower the probability of experiencing severe irAEs has become a priority in oncological care. In recent years, there has been a growing understanding of an intriguing link between the gut microbiome and ICI outcomes. Multiple studies have demonstrated a connection between microbial metagenomic and metatranscriptomic patterns and ICI efficacy in malignant melanoma, lung and colorectal cancer. The immunomodulatory effect of the gut microbiome can have a real effect on the biological background of irAEs as well. Furthermore, specific microbial signatures and metabolites might be associated with the onset and severity of toxicity symptoms. By identifying these biological factors, novel biomarkers can be used in clinical practice to predict and manage potential irAEs. This comprehensive review aims to summarize the clinical aspects and biological background of ICI-related irAEs and their potential association with the gut microbiome and metabolome. We aim to explore the current state of knowledge on the most important and reliable irAE-related biomarkers of microbial origin and discuss the intriguing connection between ICI efficacy and toxicity.}, } @article {pmid36768930, year = {2023}, author = {Eguchi, H and Hotta, F and Kusaka, S}, title = {Applying Metagenomic Analysis Using Nanopore Sequencer (MinION) for Precision Medicine in Bacterial Keratoconjunctivitis: Comprehensive Validation of Molecular Biological and Conventional Examinations.}, journal = {International journal of molecular sciences}, volume = {24}, number = {3}, pages = {}, pmid = {36768930}, issn = {1422-0067}, mesh = {Humans ; *Nanopores ; Precision Medicine ; Sequence Analysis, DNA/methods ; Bacteria/genetics ; *Keratoconjunctivitis/diagnosis ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Smear microscopic examination and culture of the corneal scrapings are the gold standards for the diagnosis of bacterial keratoconjunctivitis. High-sensitivity molecular biological examinations of the ocular surface specimens are used clinically. However, the results require careful interpretation to avoid the unintentional detection of indigenous bacteria. Results of conventional and state-of-the-art examinations require clinical verification for specificity and sensitivity. In this study, smear microscopic examination, culture, and nanopore sequencing using the MinION of ocular surface specimens from eight clinically diagnosed bacterial keratoconjunctivitis cases were performed and compared. Seven of the eight cases (87.5%) were smear positive and five (62.5%) were culture positive. The former showed the same genus in >60% of the classified reads as one specific bacterium inferred from the smear microscopy when sequenced by the MinION. In two of the three culture-negative cases, the smear-positive images were highly reminiscent of the species comprising most of the MinION sequences. Four of the five culture-positive cases were consistent with the most prevalent bacteria in the sequencing results. Probable contamination among specimens processed on the same day were observed. In conclusion, the microscopic examination of the corneal scraping specimens may be more sensitive and specific than the culture examination. Additionally, although metagenomic analysis using the MinION contributes to more precise medication for bacterial keratoconjunctivitis, contamination can affect the results.}, } @article {pmid36768851, year = {2023}, author = {Nunzi, E and Mezzasoma, L and Bellezza, I and Zelante, T and Orvietani, P and Coata, G and Giardina, I and Sagini, K and Manni, G and Di Michele, A and Gargaro, M and Talesa, VN and Di Renzo, GC and Fallarino, F and Romani, R}, title = {Microbiota-Associated HAF-EVs Regulate Monocytes by Triggering or Inhibiting Inflammasome Activation.}, journal = {International journal of molecular sciences}, volume = {24}, number = {3}, pages = {}, pmid = {36768851}, issn = {1422-0067}, support = {GGP17094/TI_/Telethon/Italy ; }, mesh = {Humans ; Female ; Pregnancy ; Monocytes/metabolism ; Inflammasomes/metabolism ; Amniotic Fluid ; Proteomics ; *Extracellular Vesicles/metabolism ; *Microbiota ; Endotoxins/metabolism ; }, abstract = {In pregnancy, human amniotic fluid extracellular vesicles (HAF-EVs) exert anti-inflammatory effects on T cells and on monocytes, supporting their immunoregulatory roles. The specific mechanisms are still not completely defined. The aim of this study was to investigate the ability of HAF-EVs, isolated from pregnant women who underwent amniocentesis and purified by gradient ultracentrifugation, to affect inflammasome activation in the human monocytes. Proteomic studies revealed that HAF-EV samples expressed several immunoregulatory molecules as well as small amounts of endotoxin. Surprisingly, metagenomic analysis shows the presence of specific bacterial strain variants associated with HAF-EVs as potential sources of the endotoxin. Remarkably, we showed that a single treatment of THP-1 cells with HAF-EVs triggered inflammasome activation, whereas the same treatment followed by LPS and ATP sensitization prevented inflammasome activation, a pathway resembling monocyte refractories. A bioinformatics analysis of microbiota-HAF-EVs functional pathways confirmed the presence of enzymes for endotoxin biosynthesis as well as others associated with immunoregulatory functions. Overall, these data suggest that HAF-EVs could serve as a source of the isolation of a specific microbiota during early pregnancy. Moreover, HAF-EVs could act as a novel system to balance immune training and tolerance by modulating the inflammasome in monocytes or other cells.}, } @article {pmid36768793, year = {2023}, author = {Kaplina, A and Kononova, S and Zaikova, E and Pervunina, T and Petrova, N and Sitkin, S}, title = {Necrotizing Enterocolitis: The Role of Hypoxia, Gut Microbiome, and Microbial Metabolites.}, journal = {International journal of molecular sciences}, volume = {24}, number = {3}, pages = {}, pmid = {36768793}, issn = {1422-0067}, support = {22-25-00484//Russian Science Foundation/ ; }, mesh = {Infant ; Pregnancy ; Female ; Infant, Newborn ; Humans ; Infant, Premature ; *Gastrointestinal Microbiome ; *Enterocolitis, Necrotizing/etiology ; *Infant, Newborn, Diseases ; Fetal Growth Retardation ; Hypoxia ; }, abstract = {Necrotizing enterocolitis (NEC) is a life-threatening disease that predominantly affects very low birth weight preterm infants. Development of NEC in preterm infants is accompanied by high mortality. Surgical treatment of NEC can be complicated by short bowel syndrome, intestinal failure, parenteral nutrition-associated liver disease, and neurodevelopmental delay. Issues surrounding pathogenesis, prevention, and treatment of NEC remain unclear. This review summarizes data on prenatal risk factors for NEC, the role of pre-eclampsia, and intrauterine growth retardation in the pathogenesis of NEC. The role of hypoxia in NEC is discussed. Recent data on the role of the intestinal microbiome in the development of NEC, and features of the metabolome that can serve as potential biomarkers, are presented. The Pseudomonadota phylum is known to be associated with NEC in preterm neonates, and the role of other bacteria and their metabolites in NEC pathogenesis is also discussed. The most promising approaches for preventing and treating NEC are summarized.}, } @article {pmid36768705, year = {2023}, author = {Timmers, ER and Swarte, JC and Gacesa, R and Björk, JR and Weersma, RK and Tijssen, MAJ and de Koning, TJ and Harmsen, HJM and Niezen-Koning, KE}, title = {Gut Microbiome Composition in Dystonia Patients.}, journal = {International journal of molecular sciences}, volume = {24}, number = {3}, pages = {}, pmid = {36768705}, issn = {1422-0067}, mesh = {Humans ; *Dystonia ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Mental Disorders ; *Dystonic Disorders ; *Dyskinesias ; }, abstract = {Dystonia is a movement disorder in which patients have involuntary abnormal movements or postures. Non-motor symptoms, such as psychiatric symptoms, sleep problems and fatigue, are common. We hypothesise that the gut microbiome might play a role in the pathophysiology of the (non-)motor symptoms in dystonia via the gut-brain axis. This exploratory study investigates the composition of the gut microbiome in dystonia patients compared to healthy controls. Furthermore, the abundance of neuro-active metabolic pathways, which might be implicated in the (non-)motor symptoms, was investigated. We performed both metagenomic and 16S rRNA sequencing on the stool samples of three subtypes of dystonia (27 cervical dystonia, 20 dopa-responsive dystonia and 24 myoclonus-dystonia patients) and 25 controls. While microbiome alpha and beta diversity was not different between dystonia patients and controls, dystonia patients had higher abundances of Ruminococcus torques and Dorea formicigenerans, and a lower abundance of Butyrivibrio crossotus compared to controls. For those with dystonia, non-motor symptoms and the levels of neurotransmitters in plasma explained the variance in the gut microbiome composition. Several neuro-active metabolic pathways, especially tryptophan degradation, were less abundant in the dystonia patients compared to controls. This suggest that the gut-brain axis might be involved in the pathophysiology of dystonia. Further studies are necessary to confirm our preliminary findings.}, } @article {pmid36768286, year = {2023}, author = {Dionisio, F and Domingues, CPF and Rebelo, JS and Monteiro, F and Nogueira, T}, title = {The Impact of Non-Pathogenic Bacteria on the Spread of Virulence and Resistance Genes.}, journal = {International journal of molecular sciences}, volume = {24}, number = {3}, pages = {}, pmid = {36768286}, issn = {1422-0067}, mesh = {Humans ; Virulence/genetics ; *Bacteria/genetics ; Anti-Bacterial Agents ; *Microbiota/genetics ; }, abstract = {This review discusses the fate of antimicrobial resistance and virulence genes frequently present among microbiomes. A central concept in epidemiology is the mean number of hosts colonized by one infected host in a population of susceptible hosts: R0. It characterizes the disease's epidemic potential because the pathogen continues its propagation through susceptible hosts if it is above one. R0 is proportional to the average duration of infections, but non-pathogenic microorganisms do not cause host death, and hosts do not need to be rid of them. Therefore, commensal bacteria may colonize hosts for prolonged periods, including those harboring drug resistance or even a few virulence genes. Thus, their R0 is likely to be (much) greater than one, with peculiar consequences for the spread of virulence and resistance genes. For example, computer models that simulate the spread of these genes have shown that their diversities should correlate positively throughout microbiomes. Bioinformatics analysis with real data corroborates this expectation. Those simulations also anticipate that, contrary to the common wisdom, human's microbiomes with a higher diversity of both gene types are the ones that took antibiotics longer ago rather than recently. Here, we discuss the mechanisms and robustness behind these predictions and other public health consequences.}, } @article {pmid36768285, year = {2023}, author = {Zaragoza-García, O and Castro-Alarcón, N and Pérez-Rubio, G and Falfán-Valencia, R and Briceño, O and Navarro-Zarza, JE and Parra-Rojas, I and Tello, M and Guzmán-Guzmán, IP}, title = {Serum Levels of IFABP2 and Differences in Lactobacillus and Porphyromonas gingivalis Abundance on Gut Microbiota Are Associated with Poor Therapeutic Response in Rheumatoid Arthritis: A Pilot Study.}, journal = {International journal of molecular sciences}, volume = {24}, number = {3}, pages = {}, pmid = {36768285}, issn = {1422-0067}, mesh = {Female ; Humans ; *Antirheumatic Agents/therapeutic use ; *Arthritis, Rheumatoid/drug therapy/genetics/metabolism ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/genetics/physiology ; Interleukin-17 ; Pilot Projects ; Porphyromonas gingivalis ; Tumor Necrosis Factor-alpha/therapeutic use ; *Lactobacillus ; Intestines/microbiology/physiopathology ; Cell Membrane Permeability ; }, abstract = {Intestinal dysbiosis is related to the physiopathology and clinical manifestation of rheumatoid arthritis (RA) and the response to pharmacologic treatment. The objectives of this study were (1) to analyze the effect of conventional synthetic disease modifying anti-rheumatic drugs (csDMARDs) on the abundance of gut microbiota's bacteria; (2) to evaluate the relationship between the differences in microbial abundance with the serum levels of intestinal fatty-acid binding protein 2 (IFABP2), cytokines, and the response phenotype to csDMARDs therapy in RA. A cross-sectional study was conducted on 23 women diagnosed with RA. The abundance of bacteria in gut microbiota was determined with qPCR. The ELISA technique determined serum levels of IFABP2, TNF-α, IL-10, and IL-17A. We found that the accumulated dose of methotrexate or prednisone is negatively associated with the abundance of Lactobacillus but positively associated with the abundance of Bacteroides fragilis. The Lactobacillus/Porphyromonas gingivalis ratio was associated with the Disease Activity Score-28 for RA with Erythrocyte Sedimentation Rate (DAS28-ESR) (r = 0.778, p = 0.030) and with the levels of IL-17A (r = 0.785, p = 0.027) in the group treated with csDMARD. Moreover, a relation between the serum levels of IFABP2 and TNF-α (r = 0.593, p = 0.035) was observed in the group treated with csDMARD. The serum levels of IFABP2 were higher in patients with secondary non-response to csDMARDs therapy. In conclusion, our results suggest that the ratios of gut microbiota's bacteria and intestinal permeability seems to establish the preamble for therapeutic secondary non-response in RA.}, } @article {pmid36766926, year = {2023}, author = {Al-Khaldy, NS and Al-Musharaf, S and Aljazairy, EA and Hussain, SD and Alnaami, AM and Al-Daghri, N and Aljuraiban, G}, title = {Serum Vitamin D Level and Gut Microbiota in Women.}, journal = {Healthcare (Basel, Switzerland)}, volume = {11}, number = {3}, pages = {}, pmid = {36766926}, issn = {2227-9032}, support = {(IFKSURG-2-932)//Deputyship for Research & Innovation, Ministry of Education in Saudi Arabia/ ; }, abstract = {Obesity and vitamin D deficiency are two major public health concerns. Evidence suggests that alteration in gut microbiota composition is a possible risk factor for obesity. Additionally, altered vitamin D status has a potential role in shaping the gut microbial community. Further, the prevalence of obesity has been rising in the Middle East, especially among women of reproductive age, which is of specific concern due to its adverse effects on the health of their offspring. To date, limited evidence is available on the association between gut microbiota composition and vitamin D levels in Arab women. This study aims to identify the associations between serum vitamin D, gut microbiota, and obesity among Saudi females. The current study is a case-control study including 92 women aged 18 to 25 years, (n = 48) with normal weight and (n = 44) with obesity. Anthropometric, biochemical, lifestyle data, and fecal samples were collected and analyzed. We used shotgun metagenomic sequencing to characterize microbial communities of stool samples. Vitamin D levels were significantly associated with alpha and beta diversities. Serum vitamin D levels were positively associated with bacteria known to regulate immunological responses; Bacteroides thetaiotaomicron in the normal weight group (r = 0.34, p = 0.03) and Bifidobacterium adolescentis in the obesity group (r = 0.33, p = 0.04). In conclusion, the findings suggest that vitamin D status may play a role in regulating the gut microbiota composition by inhibiting the growth of pathogenic bacteria while nourishing the beneficial strains.}, } @article {pmid36766192, year = {2023}, author = {Song, Y and Lu, D and Wang, H and Zhou, Z and Luo, X and Ma, M and Ke, S and Wang, H and Yu, Y and Wei, B}, title = {Metagenomic Insights into the Anti-Obesity Effect of a Polysaccharide from Saccharina japonica.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {3}, pages = {}, pmid = {36766192}, issn = {2304-8158}, support = {No. 81903534, No. 81773628, and No. 81741165//the National Natural Science Foundation of China/ ; No. 2017YFE0103100//the National Key Research and Development Program/ ; }, abstract = {Saccharina japonica polysaccharides exhibit great potential to be developed as anti-obesity and prebiotic health products, but the underlying mechanism has not been adequately addressed. In this study, we investigated the potential mechanism of a S. japonica polysaccharide fraction (SjC) in preventing high-fat-diet (HFD)-induced obesity in mice using 16S rRNA gene and shotgun metagenomic sequencing analysis. SjC was characterized as a 756 kDa sulfated polysaccharide and 16 weeks of SjC supplementation significantly alleviated HFD-induced obesity, insulin resistance, and glucose metabolism disorders. The 16S rRNA and metagenomic sequencing analysis demonstrated that SjC supplementation prevented gut microbiota dysbiosis mainly by regulating the relative abundance of Desulfovibrio and Akkermansia. Metagenomic functional profiling demonstrated that SjC treatment predominantly suppressed the amino acid metabolism of gut microbiota. Linking of 16S rRNA genes with metagenome-assembled genomes indicated that SjC enriched at least 22 gut bacterial species with fucoidan-degrading potential including Desulfovibrio and Akkermansia, which showed significant correlations with bodyweight. In conclusion, our results suggest that SjC exhibits a promising potential as an anti-obesity health product and the interaction between SjC and fucoidan-degrading bacteria may be associated with its anti-obesity effect.}, } @article {pmid36765824, year = {2023}, author = {Pandey, H and Tang, DWT and Wong, SH and Lal, D}, title = {Gut Microbiota in Colorectal Cancer: Biological Role and Therapeutic Opportunities.}, journal = {Cancers}, volume = {15}, number = {3}, pages = {}, pmid = {36765824}, issn = {2072-6694}, support = {021337-00001//NTU Start Up Grant and Wang Lee Wah Memorial Fund/ ; }, abstract = {Colorectal cancer (CRC) is the second-leading cause of cancer-related deaths worldwide. While CRC is thought to be an interplay between genetic and environmental factors, several lines of evidence suggest the involvement of gut microbiota in promoting inflammation and tumor progression. Gut microbiota refer to the ~40 trillion microorganisms that inhabit the human gut. Advances in next-generation sequencing technologies and metagenomics have provided new insights into the gut microbial ecology and have helped in linking gut microbiota to CRC. Many studies carried out in humans and animal models have emphasized the role of certain gut bacteria, such as Fusobacterium nucleatum, enterotoxigenic Bacteroides fragilis, and colibactin-producing Escherichia coli, in the onset and progression of CRC. Metagenomic studies have opened up new avenues for the application of gut microbiota in the diagnosis, prevention, and treatment of CRC. This review article summarizes the role of gut microbiota in CRC development and its use as a biomarker to predict the disease and its potential therapeutic applications.}, } @article {pmid36765767, year = {2023}, author = {Zhang, Y and Wang, W and Zhou, H and Cui, Y}, title = {Urinary Eubacterium sp. CAG:581 Promotes Non-Muscle Invasive Bladder Cancer (NMIBC) Development through the ECM1/MMP9 Pathway.}, journal = {Cancers}, volume = {15}, number = {3}, pages = {}, pmid = {36765767}, issn = {2072-6694}, support = {82204515//National Natural Science Foundation of China/ ; 2022RT04//National High Level Hospital Clinical Research Funding (Research Achievement Transformation Project of Peking University First Hospital)/ ; 2022SF04//Research Seed Fund of Peking University First Hospital/ ; }, abstract = {BACKGROUND: Increasing evidence points to the urinary microbiota as a possible key susceptibility factor for early-stage bladder cancer (BCa) progression. However, the interpretation of its underlying mechanism is often insufficient, given that various environmental conditions have affected the composition of urinary microbiota. Herein, we sought to rule out confounding factors and clarify how urinary Eubacterium sp. CAG:581 promoted non-muscle invasive bladder cancer (NMIBC) development.

METHODS: Differentially abundant urinary microbiota of 51 NMIBC patients and 47 healthy controls (as Cohort 1) were first determined by metagenomics analysis. Then, we modeled the coculture of NMIBC organoids with candidate urinary Eubacterium sp. CAG:581 in anaerobic conditions and explored differentially expressed genes of these NMIBC tissues by RNA-Seq. Furthermore, we dissected the mechanisms involved into Eubacterium sp. CAG:581 by inducing extracellular matrix protein 1 (ECM1) and matrix metalloproteinase 9 (MMP9) upregulation. Finally, we used multivariate Cox modeling to investigate the clinical relevance of urinary Eubacterium sp. CAG:581 16S ribosomal RNA (16SrRNA) levels to the prognosis of 406 NMIBC patients (as Cohort 2).

RESULTS: Eubacterium sp. CAG:581 infection accelerated the proliferation of NMIBC organoids (p < 0.01); ECM1 and MMP9 were the most upregulated genes induced by the increased colony forming units (CFU) gradient of Eubacterium sp. CAG:581 infection via phosphorylating ERK1/2 in NMIBC organoids of Cohort 1. Excluding the favorable impact of potential contributing factors, the ROC curve of Cohort 2 manifested its 3-year AUC value as 0.79 and the cut-off point of Eubacterium sp. CAG:581 16SrRNA as 10.3 (delta CT value).

CONCLUSION: Our evidence suggests that urinary Eubacterium sp. CAG:581 promoted NMIBC progression through the ECM1/MMP9 pathway, which may serve as the promising noninvasive diagnostic biomarker for NMIBC.}, } @article {pmid36764661, year = {2023}, author = {Bornemann, TLV and Esser, SP and Stach, TL and Burg, T and Probst, AJ}, title = {uBin: A manual refining tool for genomes from metagenomes.}, journal = {Environmental microbiology}, volume = {25}, number = {6}, pages = {1077-1083}, doi = {10.1111/1462-2920.16351}, pmid = {36764661}, issn = {1462-2920}, mesh = {*Software ; *Metagenome ; Phylogeny ; Bacteria/classification/genetics ; Archaea/classification/genetics ; Data Curation ; *Genome, Bacterial ; *Genome, Archaeal ; }, abstract = {Resolving bacterial and archaeal genomes from metagenomes has revolutionized our understanding of Earth's biomes yet producing high-quality genomes from assembled fragments has been an ever-standing problem. While automated binning software and their combination produce prokaryotic bins in high throughput, their manual refinement has been slow, sometimes difficult or missing entirely facilitating error propagation in public databases. Here, we present uBin, a GUI-based, standalone bin refiner that runs on all major operating platforms and was additionally designed for educational purposes. When applied to the public CAMI dataset, refinement of bins using GC content, coverage and taxonomy was able to improve 78.9% of bins by decreasing their contamination. We also applied the bin refiner as a standalone binner to public metagenomes from the International Space Station and demonstrate the recovery of near-complete genomes, whose replication indices indicate the active proliferation of microbes in Earth's lower orbit. uBin is an easy to instal software for bin refinement, binning of simple metagenomes and communication of metagenomic results to other scientists and in classrooms. The software and its helper scripts are open source and available under https://github.com/ProbstLab/uBin.}, } @article {pmid36764622, year = {2023}, author = {Liang, Y and Feng, Q and Wei, K and Hou, X and Song, X and Li, Y}, title = {Potential of metagenomic next-generation sequencing in detecting infections of ICU patients.}, journal = {Molecular and cellular probes}, volume = {68}, number = {}, pages = {101898}, doi = {10.1016/j.mcp.2023.101898}, pmid = {36764622}, issn = {1096-1194}, mesh = {Humans ; *Body Fluids ; High-Throughput Nucleotide Sequencing ; Metagenome ; Intensive Care Units ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Due to the limitations of traditional microbiological detection techniques in evaluating complicated infections in ICU patients, it is necessary to explore novel and effective methods to improve the clinical detection of ICU patients' infections.

OBJECTIVE: This study aimed to evaluate the efficiency and specificity of mNGS in screening pathogens in the blood, deep phlegm, urine, and other sample types of ICU patients exploring an effective method for infection detection.

METHODS: A total of 56 ICU patients with 131 samples were included in this study. The sample types included blood, deep phlegm, urine, drainage, anal swabs, and other types. Samples were analyzed by both conventional detection method and mNGS tests. The diagnosis efficiency and consistency of the two methods were compared. The distribution of the identified pathogens was analyzed. Moreover, the clinical features of patients with mNGS-positive or mNGS-negative results were compared.

RESULTS: The positive rate of mNGS was 81.7% (107/131) including 3.1% (4/131) weakly positive, while the positive rate of traditional detection was only 30.5%, including 29 strong positive results and 11 weak positive results. Additionally, there were 41 patients chose to adjust anti-infection strategies according to the results of mNGS, which significantly saved treatment costs. The mNGS-positive patients showed a shorter ICU hospitalization and higher intention to adjust anti-infection strategies than the mNGS-negative patients.

CONCLUSION: mNGS is of great potential for the pathogen detection of ICU patients, and has a higher detection rate than traditional detection methods. Further clinical application investigations can be carried out to expand the application of mNGS.}, } @article {pmid36764616, year = {2023}, author = {Wang, J and Li, L and Chi, B and Shan, J and Yi, X and Liu, Y and Zhou, H}, title = {Metagenomic insights into the effects of benzyl dodecyl dimethyl ammonium bromide (BDAB) shock on bacteria-driven nitrogen removal in a moving-bed biofilm reactor (MBBR).}, journal = {Chemosphere}, volume = {320}, number = {}, pages = {138098}, doi = {10.1016/j.chemosphere.2023.138098}, pmid = {36764616}, issn = {1879-1298}, mesh = {Humans ; Ammonia/analysis ; Bacteria ; Biofilms ; Bioreactors ; *COVID-19 ; Denitrification ; Nitrogen/analysis ; *Quaternary Ammonium Compounds ; SARS-CoV-2 ; Genomics ; }, abstract = {The use of disinfectants made from quaternary ammonium compounds (QACs) has greatly increased since the outbreak of SARS-CoV-2. However, the effect of QACs on wastewater treatment performance is still unclear. In this study, a commonly used QAC, i.e., benzyl dodecyl dimethyl ammonium bromide (BDAB), was added to a moving-bed biofilm reactor (MBBR) to investigate BDAB's effect on nutrient removal. When the BDAB concentration was increased to 50 mg L[-1], the ammonia removal efficiency (ARE) greatly decreased, as did the nitrate production rate constants (NPR). This inhibition was partly recovered by decreasing the BDAB concentration to 30 mg L[-1]. Metagenomic sequencing revealed the functional genera present during different stages of the control (Rc) and BDAB-added reactors (Re). The enriched genera (Rudaea, Nitrosospira, Sphingomonas, and Rhodanobacter) in Rc mainly related to the nitrogen metabolism, while the enriched genera in Re was BDAB-concentration dependent. Functional genes analysis suggested that a lack of ammonia oxidase-encoding genes (amoABC) may have caused a decrease in ARE in Re, while the efflux pump-encoding genes emrE, mdfA, and oprM and a gene encoding BAC oxygenase (oxyBAC) were responsible for BDAB resistance. The increase in the total abundance of antibiotic resistance genes (ARGs) in Re revealed a potential risk arising from BDAB. Overall, this study revealed the potential effect and ecological risks of BDAB introduction in WWTPs.}, } @article {pmid36764550, year = {2023}, author = {Jiang, W and Hu, C and Chen, Y and Li, Y and Sun, X and Wu, H and Yang, R and Tang, Y and Niu, F and Wei, W and Sun, C and Han, T}, title = {Dysregulation of the microbiota-brain axis during long-term exposure to polystyrene nanoplastics in rats and the protective role of dihydrocaffeic acid.}, journal = {The Science of the total environment}, volume = {874}, number = {}, pages = {162101}, doi = {10.1016/j.scitotenv.2023.162101}, pmid = {36764550}, issn = {1879-1026}, mesh = {Rats ; Animals ; Microplastics/metabolism ; Polystyrenes/metabolism ; *Microbiota ; *Drug-Related Side Effects and Adverse Reactions ; *Water Pollutants, Chemical/metabolism ; Brain/metabolism ; *Nanoparticles/chemistry ; Mammals/metabolism ; }, abstract = {Polystyrene nano-plastics (PS-NPs) can be accumulated in the food chain and can penetrate biological barriers to affect multiple physiological functions. However, the adverse effects of nano-plastics on mammals and the underlying mechanism still remain unknown. To fill the gaps, our study administrated low-dose PS-NPs (50 and 100 μg/L) for 24 consecutive weeks in rats. Behavioral and morphological evaluations were performed to assess the neurobehavoirs. A combined analysis of multiple omics was used to evaluate the dysfunctions of the gut-microbe-brain axis. After dihydrochalcone(NHDC) treatment in the PS-NPs rat model, the inflammation response and apoptosis process were assessed and proteomics was used to explore the underlying mechanism. Our results indicated that long-term exposure to low-dose PS-NPs could induce abnormal neurobehaviors and amygdaloid nucleus impairment, and stimulate inflammatory responses and apoptosis. Metagenomics results revealed that four microbial phyla including Proteobacteria, Firmicutes, Defferibacteres, and Bacteroidetes changed significantly compared to the control. Targeted metabolomics analysis in the feces showed alteration of 122 metabolites induced by the PS-NPs exposure, among which the content of dihydrocaffeic acid was significantly associated with the different microbial genera and pivotal differential metabolites in the amygdaloid nucleus. And NHDC treatment significantly alleviated PS-NP-induced neuroinflammation and apoptosis and the cyclic adenosine monophosphate(cAMP)/protein kinase A(PKA)/phosphorylated cAMP-response element binding protein(p-CREB)/plasma membrane calcium-transporting ATPase 2(Atp2b2) signaling pathway was identified in the proteomics. In conclusion, long-term exposure to low-dose PS-NPs has adverse effects on emotion through the dysregulation of the gut-brain axis, and dihydrocaffeic acid can alleviate these effects via the cAMP/PKA/p-CREB/Atp2b2 signaling pathway.}, } @article {pmid36764487, year = {2023}, author = {Nakamura, A and Komatsu, M}, title = {Performance evaluation of whole genome metagenomics sequencing with the MinION nanopore sequencer: Microbial community analysis and antimicrobial resistance gene detection.}, journal = {Journal of microbiological methods}, volume = {206}, number = {}, pages = {106688}, doi = {10.1016/j.mimet.2023.106688}, pmid = {36764487}, issn = {1872-8359}, mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; *Nanopores ; Drug Resistance, Bacterial/genetics ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing ; Sequence Analysis, DNA ; }, abstract = {Recently, the human gut microbiota has been implicated in various diseases such as immunological and neuropsychiatric disorders, and comprehensive gut microbiota analysis by metagenomic analysis using next-generation sequencers has been attracting attention. In this study, we compared microbial communities of 16S rDNA metagenome sequencing (16S-meta) and whole genome metagenome sequencing (WG-meta) using the nanopore sequencer MinION and 16S-meta using the Illumina Miseq sequencer with simulated and fecal samples, and evaluated the ability of WG-meta to detect antimicrobial resistance genes. We used the commercial Microbial Community DNA Standard as the DNA standard and a simulated sample comprising 17 strains of 15 bacterial species. In the detection of antimicrobial resistance genes, we used a simulated sample and spiked fecal samples containing Escherichia coli carrying blaCTX-M-27, Klebsiella pneumoniae carrying blaOXA-48, and Staphylococcus aureus carrying mecA. WG-meta using MinION was superior to 16S-meta and could accurately analyze the microbial communities at the species level, but it underestimated or misidentified the Bacillus subtilis group, Cryptococcus neoformans, Shigella sonnei, and Campylobacter jejuni. WG-meta using MinION could analyze the microbial communities in 5 min, and antimicrobial resistance gene detection using WG-meta could be performed in >30 min in the simulated sample with fewer bacterial counts.}, } @article {pmid36764395, year = {2023}, author = {Van Dijck, C and Laumen, JGE and de Block, T and Abdellati, S and De Baetselier, I and Tsoumanis, A and Malhotra-Kumar, S and Manoharan-Basil, SS and Kenyon, C and Xavier, BB}, title = {The oropharynx of men using HIV pre-exposure prophylaxis is enriched with antibiotic resistance genes: A cross-sectional observational metagenomic study.}, journal = {The Journal of infection}, volume = {86}, number = {4}, pages = {329-337}, doi = {10.1016/j.jinf.2023.02.006}, pmid = {36764395}, issn = {1532-2742}, mesh = {Male ; Humans ; Homosexuality, Male ; Sexual Behavior ; *Pre-Exposure Prophylaxis ; *HIV Infections/prevention & control/epidemiology ; Anti-Bacterial Agents/pharmacology ; Cross-Sectional Studies ; *Sexual and Gender Minorities ; Oropharynx ; Drug Resistance, Microbial ; Fluoroquinolones ; Macrolides ; }, abstract = {BACKGROUND: Phenotypic studies have found high levels of antimicrobial resistance to cephalosporins, macrolides and fluoroquinolones in commensal Neisseria species in the oropharynx of men who have sex with men (MSM) using HIV pre-exposure prophylaxis (PrEP). These species include Neisseria subflava and Neisseria mucosa. This may represent a risk to pathogens like Neisseria gonorrhoeae which tend to take up antibiotic resistance genes (ARGs) from other bacteria. We aimed to explore to what extent the oropharyngeal resistome of MSM using PrEP differed from the general population.

METHODS: We collected oropharyngeal swabs from 32 individuals of the general population and from 64 MSM using PrEP. Thirty-two MSM had consumed antibiotics in the previous six months, whereas none of the other participants had. Samples underwent shotgun metagenomic sequencing. Sequencing reads were mapped against MEGARes 2.0 to estimate ARG abundance. ARG abundance was compared between groups by zero-inflated negative binomial regression.

FINDINGS: ARG abundance was significantly lower in the general population than in MSM (ratio 0.41, 95% CI 0.26-0.65). More specifically, this was the case for fluoroquinolones (0.33, 95% CI 0.15-0.69), macrolides (0.37, 95% CI 0.25-0.56), tetracyclines (0.41, 95% CI 0.25-0.69), and multidrug efflux pumps (0.11, 95% CI 0.03-0.33), but not for beta-lactams (1.38, 95% CI 0.73-2.61). There were no significant differences in ARG abundance between MSM who had used antibiotics and those that had not.

INTERPRETATION: The resistome of MSM using PrEP is enriched with ARGs, independent of recent antibiotic use. Stewardship campaigns should aim to reduce antibiotic consumption in populations at high risk for STIs.}, } @article {pmid36764393, year = {2023}, author = {Zhang, R and Li, Y and Chen, J and Liu, C and Sun, Q and Shu, L and Chen, G and Wang, Z and Wang, S and Li, R}, title = {Population genomic analysis reveals the emergence of high-risk carbapenem-resistant Escherichia coli among ICU patients in China.}, journal = {The Journal of infection}, volume = {86}, number = {4}, pages = {316-328}, doi = {10.1016/j.jinf.2023.02.004}, pmid = {36764393}, issn = {1532-2742}, mesh = {Humans ; *Metagenomics ; Escherichia coli/genetics ; beta-Lactamases/genetics ; *Carbapenem-Resistant Enterobacteriaceae/genetics ; Carbapenems/pharmacology ; Plasmids/genetics ; Genomics ; China/epidemiology ; Intensive Care Units ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; }, abstract = {OBJECTIVES: The increasing incidence of carbapenem-resistant Enterobacterales (CRE) mediated nosocomial infections has caused a significant public health burden globally. Currently, the prevalence and genomic characteristics of carbapenem-resistant Escherichia coli (CREC) in patients admitted to the intensive care unit (ICU) are unknown.

METHODS: Herein, we present a nationwide genomic investigation of CREC isolates among ICU patients in China in 2018 and 2020. In total, 113 CREC isolates were identified from 1105 samples in 25 hospitals, and investigated with phenotyping and genomics approaches.

RESULTS: Carbapenemases were produced in 94.69% (107/113) of CREC isolates, which comprise KPC-2 (n = 53, 49.53%), NDM (n = 51, 47.66%), IMP-4 (n = 2, 1.87%), and OXA-181 (n = 1, 0.93%). Notably, CREC isolates co-carrying mcr-9 and blaNDM-5 or tet(X4) and blaNDM-5 were first identified in clinical settings. The carbapenemase genes of most isolates were located on the plasmids. The blaKPC gene was mainly mediated by IncFII plasmids (n = 37, 69.81%), and blaNDM was located on the IncX3 plasmid (n = 36, 70.59%). CREC isolates belonged to diverse sequence types (STs) of which ST131 was the most prevalent blaKPC-positive CREC isolates (34/113, 30.09%), while blaNDM was associated with ST617 and ST410 isolates, thereby indicating that multiple CREC clones spread in Chinese ICU patients.

CONCLUSIONS: This study highlights the emerging threat of high-risk CREC isolates such as ST131 circulating in the ICU in China. Hence, stringent monitoring of such high-risk clones should be performed.}, } @article {pmid36764254, year = {2023}, author = {Gao, Z and Yi, S and Xue, M and Zhu, K and Yang, R and Wang, T and Sun, H and Zhu, L}, title = {Microbial biotransformation mechanisms of PFPiAs in soil unveiled by metagenomic analysis.}, journal = {Journal of hazardous materials}, volume = {448}, number = {}, pages = {130896}, doi = {10.1016/j.jhazmat.2023.130896}, pmid = {36764254}, issn = {1873-3336}, mesh = {*Phosphinic Acids/metabolism ; Soil ; Half-Life ; Biotransformation ; *Fluorocarbons/analysis ; }, abstract = {As alternatives of long-chain PFASs (Poly- and perfluoroalkyl substances), perfluoroalkyl phosphinic acids (PFPiAs) are increasingly observed in the environment, but their environmental behaviors have not been well understood. Here, the microbial biotransformation of C6/C6 and C8/C8 PFPiA in two soils (Soil N and Y) was investigated. After 252 d and 330 d of incubation with PFPiAs in Soil N and Y respectively, the levels of PFPiAs decreased distinctly, accompanied by the increasing perfluorohexaphosphonic acid (PFHxPA) or perfluorooctanophosphonic acid (PFOPA) formation, magnifying PFPiAs were susceptible to C-P cleavage, which was also confirmed by the density functional theory calculations. The half-lives of the PFPiAs were longer than one year, while generally shorter in Soil N than in Soil Y and that of C6/C6 was shorter than C8/C8 PFPiA (392 d and 746 d in Soil N, and 603 and 1155 d in Soil Y, respectively). Metagenomic sequencing analysis revealed that Proteobacteria as the primary host of the potential functional genes related to CP bond cleavage might be the crucial phyla contributing to the biotransformation of PFPiAs. Meanwhile, the more intensive interactions between the microbes in Soil N consistently contribute to its greater capacity for transforming PFPiAs.}, } @article {pmid36764181, year = {2023}, author = {Lu, Y and Sun, Y and Zhang, L and Zuo, X and Li, X and Yuan, H}, title = {Substance bioconversion, hydrolases activity, and metagenomic analysis to unravel the enhanced biomethanation of corn stover with urea-hydrothermal pretreatment.}, journal = {Journal of environmental management}, volume = {333}, number = {}, pages = {117466}, doi = {10.1016/j.jenvman.2023.117466}, pmid = {36764181}, issn = {1095-8630}, mesh = {Anaerobiosis ; *Zea mays ; *Fatty Acids, Volatile ; Metagenome ; Methane ; Hydrolases ; Bioreactors ; }, abstract = {Corn stover (CS) is a promising feedstock for producing biomethane, that can replace diminishing fossil fuels. However, the recalcitrant structure of CS resulted in low degradability in anaerobic digestion (AD). Numerous studies investigated the pretreatment of CS before AD, but the insight mechanism of biomethanation enhancement is not fully revealed. Therefore, this study advanced low-temperature urea-hydrothermal pretreatment of CS, and the biomethane production, substance bioconversion, hydrolase activity, and metagenomic analysis were conducted to unravel the intrinsic mechanisms of pretreatment for the enhanced biomethanation. The results showed that the pretreatment improved 11.5% of the specific surface area of CS, providing 111.5% higher total volatile fatty acids and 19.9% higher reducing sugars than the control, potentially enriching more anaerobic microorganisms. As a result, the pretreated CS achieved 19.1% higher biomethane yield, 9.1% higher volatile solid removal rate, and 3 days shorter digestion time. The mass balance and microbial community succession analysis indicated that the pretreatment reinforced the biomethane conversion from carbohydrate, which was attributed to the rapid enrichment of hydrolytic acidification bacteria (g__unclassified_o__Bacteroidales) (33.2%) and mixotrophic archaea (Methanosarcina) (72.3%). Meanwhile, the activity of cellulase and xylanase was enhanced up to 23.7% and 66.7%. Metagenomic analysis revealed that the combined pretreatment of CS promoted methanogenesis by enhancing various CAZymes secretion (such as oligosaccharide-degrading enzymes), and functional genes expression of hydrolytic, acidification and acetate-methane pathways at days 1-5. The study indicated that the combined pretreatment could influence microbial composition and function by changing the physicochemical properties of the CS, thereby improving methanogenic performance.}, } @article {pmid36764107, year = {2023}, author = {Liu, R and Li, Z and Han, G and Cun, S and Hou, D and Yu, Z and Xue, K and Liu, X}, title = {Microbial density-dependent viral dynamics and low activity of temperate phages in the activated sludge process.}, journal = {Water research}, volume = {232}, number = {}, pages = {119709}, doi = {10.1016/j.watres.2023.119709}, pmid = {36764107}, issn = {1879-2448}, mesh = {*Bacteriophages ; Sewage ; Lysogeny ; Prophages ; *Microbiota ; }, abstract = {The ecological behavior of bacteriophages (phages), the most abundant biological entity in wastewater treatment systems, is poorly understood, especially that of temperate phages. Here, the temporal dynamics of lytic and temperate phages in a laboratory-scale activated sludge reactor with a sludge bulking issue was investigated using coupled sludge metagenomic and viromic analyses. The lysogenic fragments (prophages) identified were widely distributed in the reconstructed metagenome-assembled genomes (61.7%, n = 227). However, only 12.3% of the identified prophages experienced lysogenic-lytic switching, and the abundance contribution of prophages to free virus communities was only 0.02-0.3%, indicating low activity of temperate phages. Although the sludge community changed dramatically during reactor operation, no massive prophage induction events were detected. Statistical analyses showed strong correlations between sludge concentration and free virus and temperate phage communities, suggesting microbial density-dependent virus dynamics in the sludge microbiota.}, } @article {pmid36763177, year = {2023}, author = {Zhang, D and Wang, Y and He, Y and Ji, L and Zhao, K and Yang, S and Zhang, W}, title = {Identification of avihepadnaviruses and circoviruses in an unexplained death event in farmed ducks.}, journal = {Archives of virology}, volume = {168}, number = {3}, pages = {85}, pmid = {36763177}, issn = {1432-8798}, support = {No.32102682//National Natural Science Foundation of China/ ; No.2022YFC2603801//National Key Research and Development Programs of China/ ; No. 21KJB230006//Science Foundation of Higher Education of Jiangsu Province/ ; No. 2020CPB-C11//Independent Project of Chengdu Research Base of Giant Panda Breeding/ ; }, mesh = {Animals ; Ducks ; *Avihepadnavirus ; Farms ; DNA, Viral ; *Hepatitis B Virus, Duck/genetics ; Liver ; *Hepatitis, Viral, Animal ; }, abstract = {Research into disease pathogens can greatly benefit from viral metagenomics technology. Using this technique, we investigated potential disease pathogens that resulted in the death of many ducks on a duck farm. Two duck circoviruses (DuCV) and one duck hepatitis B virus (DHBV) were detected and identified, and all three strains were closely related to avian-associated viruses. Two duck circoviruses had 81.64%-97.65% genome-wide sequence identity to some reference strains, and duck hepatitis B virus shared 75.85%-98.92% identity with other strains. Clinical characteristics of the diseased ducks, including ruffled feathers, lethargy, and weight loss, were comparable to those observed in cases of DuCV infection. Further research is needed to determine whether coinfection with DHBV leads to liver damage and exacerbation of the disease.}, } @article {pmid36762879, year = {2023}, author = {Xu, Y and Chen, Z and Li, X and Tan, J and Liu, F and Wu, J}, title = {The mechanism of promoting rhizosphere nutrient turnover for arbuscular mycorrhizal fungi attributes to recruited functional bacterial assembly.}, journal = {Molecular ecology}, volume = {32}, number = {9}, pages = {2335-2350}, doi = {10.1111/mec.16880}, pmid = {36762879}, issn = {1365-294X}, mesh = {*Mycorrhizae/genetics ; Rhizosphere ; RNA, Ribosomal, 16S/genetics ; Fungi ; Symbiosis ; Bacteria/genetics ; Soil/chemistry ; Soil Microbiology ; Plant Roots/microbiology ; }, abstract = {Symbiosis with arbuscular mycorrhizal (AM) fungi improves plant nutrient capture from the soil, yet there is limited knowledge about the diversity, structure, functioning, and assembly processes of AM fungi-related microbial communities. Here, 16S rRNA gene sequencing and metagenomic sequencing were used to detect bacteria in the rhizosphere of Lotus japonicus inoculated with and without AM fungi, and the L. japonicus mutant ljcbx (defective in symbiosis) inoculated with AM fungi in southern grassland soil. Our results show that AM symbiosis significantly increased bacterial diversity and promoted deterministic processes of bacterial community construction, suggesting that mycorrhizal symbiosis resulted in the directional enrichment of bacterial communities. AM fungi promoted the enrichment of nine bacteria, including Ohtaekwangia, Niastella, Gemmatimonas, Devosia, Sphingomonas, Novosphingobium, Opitutus, Lysobacter, Brevundimonas, which are positively correlated with NPK-related parameters. Through a functional identification experiment, we found that six of these genera, including Brevundimonas, Lysobacter, Ohtaekwangia, Sphingomonas, Devosia, and Gemmatimonas, demonstrated the ability to mineralize organophosphate and dissolve inorganic phosphorus, nitrogen, and potassium. Our study revealed that AM fungi can regulate rhizosphere bacterial community assembly and attract specific rhizosphere bacteria to promote soil nutrient turnover in southern grasslands.}, } @article {pmid36761901, year = {2023}, author = {Kwon, M and Jung, C and Kil, EJ}, title = {Metagenomic analysis of viromes in honey bee colonies (Apis mellifera; Hymenoptera: Apidae) after mass disappearance in Korea.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1124596}, pmid = {36761901}, issn = {2235-2988}, mesh = {Bees ; Animals ; *Hymenoptera ; Virome ; *Viruses/genetics ; Republic of Korea ; }, abstract = {After the nationwide, massive winter losses of honey bees in Korea during the winter of 2021, samplings were conducted from live honey bees in colonies and dead honey bees nearby colonies in the same bee-farms in six regions in Korea. Each sample was subjected to virome analysis using high-throughput sequencing technology. The number of viral reads was the lowest in the live honey bee group sample with 370,503 reads and the highest in the dead honey bee group sample with 42,659,622 reads. Viral contigs were matched with the viral genomes of the black queen cell virus, deformed wing virus, Israeli acute paralysis virus, and sacbrood virus, all of which have been previously reported in Korea. However, Apis rhabdovirus 5, bee macula-like virus, Varroa orthomyxovirus-1, Hubei partiti-like virus 34, Lake Sinai virus 2, 3, and 4, and the Ditton virus, were also discovered in this study, which are the first records in Korea. Plant viral sequences resembling those of Arabidopsis latent virus 1, and a novel viral sequence was also discovered. In the present study 55 complete viral genome sequences were identified. This study is the first virome analysis of domestic honey bees and provides the latest information on the diversity of honey bee viruses in Korea.}, } @article {pmid36761655, year = {2022}, author = {Song, SL and Yong, HS and Chua, KO and Eamsobhana, P and Lim, PE and Chan, KG}, title = {Core members and differential abundance of chrysomelid microbiota in the life stages of Podontiaaffinis (Galerucinae) and adult Silanafarinosa(Cassidinae, Coleoptera).}, journal = {Biodiversity data journal}, volume = {10}, number = {}, pages = {e87459}, pmid = {36761655}, issn = {1314-2828}, abstract = {The chrysomelid beetlesPodontiaaffinis and Silanafarinosa are members of the subfamilies Galerucinae and Cassidinae, respectively. This study, based on 16S rRNA gene-targeted metagenomics sequencing, reports the core members and differential abundance of bacterial communities in the larvae and adult beetles of P.affinis and the adult S.farinosa. Cyanobacteria/Melainabacteria group was the predominant phylum in the larvae of P.affinis, while Proteobacteria was the predominant phylum in adult P.affinis and S.farinosa. The number of Order, Family, Genus and Species OTUs in the adult stage of P.affinis was higher than that in the larval stage. The bacterial species richness of adult P.affinis was significantly higher than that of adult S.farinosa. Betaproteobacteria was the predominant class in adult P.affinis, Cyanobacteria in the larvae of P.affinis and Gammaproteobacteria in S.farinosa. The larvae and adult beetles of P.affinis and adult S.farinosahad a low number of unique and shared bacterial OTUs (> 5% relative abundance). The differences in the microbiota indicate possible differences in nutrient assimilation, host taxonomy and other stochastic processes. These findings provide new information to our understanding of the bacteria associated with specialist phytophagous chrysomelid beetles and beetles in general.}, } @article {pmid36760646, year = {2023}, author = {Mansotra, R and Ali, T and Bhagat, N and Vakhlu, J}, title = {Injury and not the pathogen is the primary cause of corm rot in Crocus sativus (saffron).}, journal = {Frontiers in plant science}, volume = {14}, number = {}, pages = {1074185}, pmid = {36760646}, issn = {1664-462X}, abstract = {Fusarium oxysporum has been reported to be the most devastating pathogen of Crocus sativus L., a commercially significant crop that yields the saffron spice. However, most of the pathogen isolations have been done from the diseased tissue, mostly from rotten corms, but no study has been conducted on diseased saffron fields. To fill the knowledge gap, the current study was carried out with the intention of recording the diversity of cultivable fungus species from saffron fields and screening them for pathogenicity towards saffron. The three study locations in Jammu and Kashmir, Srinagar (Pampore), Kishtwar, and Ramban, yielded a total of 45 fungal isolates. The internal transcribed spacer (ITS) of rDNA was used for the molecular identification. ITS rDNA-based sequence analysis classified all the operational taxonomic units (OTUs) into two phyla-Ascomycota (88.88%) and Mucoromycota (11.11%). Moreover, Fusarium (57.77%), Geotrichum (17.77%), Mucor (11.11%), Aspergillus (4.44%), Trichoderma (4.44%), Galactomyces (2.22%), and Colletotrichum (2.22%) all had different total abundances at the genus level. It was discovered that the saffron fields in Srinagar have fewer varied fungal species than the other two selected sites. All of the fungal isolates isolated including Fusarium solani, Aspergillus flavus, Trichoderma harzianum, Fusarium neocosmosporiellum, and Mucor circinelloides were pathogenic according to the pathogenicity test; however, injury to the saffron plant was found to be a must. These fungi were pathogenic in addition to F. oxysporum, which is well documented as a major cause of saffron corm rot diseases in Srinagar, but in the present study, injury was a must for F. oxysporum as well. The percentage disease severity index for both saffron roots and corms varied for each fungal isolate.}, } @article {pmid36760592, year = {2023}, author = {Bai, X and Ma, J and Wu, X and Qiu, L and Huang, R and Zhang, H and Huang, H and Chen, X}, title = {Impact of Visceral Obesity on Structural and Functional Alterations of Gut Microbiota in Polycystic Ovary Syndrome (PCOS): A Pilot Study Using Metagenomic Analysis.}, journal = {Diabetes, metabolic syndrome and obesity : targets and therapy}, volume = {16}, number = {}, pages = {1-14}, pmid = {36760592}, issn = {1178-7007}, abstract = {OBJECTIVE: We aimed to identify structural and functional alterations of gut microbiota associated with visceral obesity in adult women with polycystic ovary syndrome (PCOS).

METHODS: Twenty-seven adults with PCOS underwent stool and fasting blood collection, oral glucose tolerance testing, and visceral fat area (VFA) measurement via dual-bioimpedance technique. Metagenomic analysis was used to analyze gut microbiota.

RESULTS: PCOS patients were divided into three groups: visceral obesity group (PCOS-VO, n=9, age 28.33±5.68 years, BMI 37.06±4.27 kg/m[2], VFA 128.67±22.45 cm[2]), non-visceral obesity group (PCOS-NVO, n=10, age 25.40±4.53, BMI 30.74±3.95, VFA 52.00±24.04), normal BMI group (PCOS-NB, n=8, age 27.88±2.53, BMI 21.56±2.20, VFA 27.00±21.18), with no statistical difference in age (P>0.05) and significantly statistical differences in BMI and VFA (P<0.05). The groups showed a significant difference in microbial β-diversity between PCOS-VO and PCOS-NVO (P=0.002) and no difference between PCOS-NVO and PCOS-NB (P=0.177). Bacteroidetes was the phylum with the highest relative abundance among all patients, followed by Firmicutes. Those with visceral obesity had a higher abundance of Prevotella, Megamonas, and Dialister genera, positively correlated with metabolic markers (r>0.4, P<0.05), and lower abundance of Phascolarctobacterium and Neisseria genera, negatively correlated with metabolic markers (r<-0.4, P<0.05). Functional annotation analysis showed significant differences in relative abundance of ribosome pathway, fatty acid biosynthesis pathway, and sphingolipid signaling pathway between groups, affecting lipid homeostasis and visceral fat accumulation.

CONCLUSION: Alteration in β-diversity of gut microbiota exists in PCOS with visceral obesity versus those without visceral obesity and relates to functional differences in ribosomes, fatty acid biosynthesis, and sphingolipid signaling pathways.}, } @article {pmid36760544, year = {2022}, author = {Sun, T and Zou, W and Dong, Q and Huang, O and Tang, D and Yu, H}, title = {Morphology, phylogeny, mitogenomics and metagenomics reveal a new entomopathogenic fungus Ophiocordycepsnujiangensis (Hypocreales, Ophiocordycipitaceae) from Southwestern China.}, journal = {MycoKeys}, volume = {94}, number = {}, pages = {91-108}, pmid = {36760544}, issn = {1314-4049}, abstract = {Ophiocordyceps contains the largest number of Cordyceps sensu lato, various species of which are of great medicinal value. In this study, a new entomopathogenic fungus, Ophiocordycepsnujiangensis, from Yunnan in southwestern China, was described using morphological, phylogenetic, and mitogenomic evidence, and its fungal community composition was identified. It was morphologically characterized by a solitary, woody, and dark brown stromata, smooth-walled and septate hyphae, solitary and gradually tapering conidiogenous cells with plenty of warty protrusions, and oval or fusiform conidia (6.4-11.2 × 3.7-6.4 µm) with mucinous sheath. The phylogenetic location of O.nujiangensis was determined based on the Bayesian inference (BI) and the maximum likelihood (ML) analyses by concatenating nrSSU, nrLSU, tef-1a, rpb1, and rpb2 datasets, and ten mitochondrial protein-coding genes (PCGs) datasets (atp6, atp9, cob, cox2, nad1, nad2, nad3, nad4, nad4L, and nad5). Phylogenetic analyses revealed that O.nujiangensis belonged to the Hirsutellasinensis subclade within the Hirsutella clade of Ophiocordyceps. And O.nujiangensis was phylogenetically clustered with O.karstii, O.liangshanensis, and O.sinensis. Simultaneously, five fungal phyla and 151 fungal genera were recognized in the analysis of the fungal community of O.nujiangensis. The fungal community composition differed from that of O.sinensis, and differences in the microbial community composition of closely related species might be appropriate as further evidence for taxonomy.}, } @article {pmid36760505, year = {2023}, author = {Magnúsdóttir, S and Saraiva, JP and Bartholomäus, A and Soheili, M and Toscan, RB and Zhang, J and Nunes da Rocha, U and , }, title = {Metagenome-assembled genomes indicate that antimicrobial resistance genes are highly prevalent among urban bacteria and multidrug and glycopeptide resistances are ubiquitous in most taxa.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1037845}, pmid = {36760505}, issn = {1664-302X}, abstract = {INTRODUCTION: Every year, millions of deaths are associated with the increased spread of antimicrobial resistance genes (ARGs) in bacteria. With the increasing urbanization of the global population, the spread of ARGs in urban bacteria has become a more severe threat to human health.

METHODS: In this study, we used metagenome-assembled genomes (MAGs) recovered from 1,153 urban metagenomes in multiple urban locations to investigate the fate and occurrence of ARGs in urban bacteria. Additionally, we analyzed the occurrence of these ARGs on plasmids and estimated the virulence of the bacterial species.

RESULTS: Our results showed that multidrug and glycopeptide ARGs are ubiquitous among urban bacteria. Additionally, we analyzed the deterministic effects of phylogeny on the spread of these ARGs and found ARG classes that have a non-random distribution within the phylogeny of our recovered MAGs. However, few ARGs were found on plasmids and most of the recovered MAGs contained few virulence factors.

DISCUSSION: Our results suggest that the observed non-random spreads of ARGs are not due to the transfer of plasmids and that most of the bacteria observed in the study are unlikely to be virulent. Additional research is needed to evaluate whether the ubiquitous and widespread ARG classes will become entirely prevalent among urban bacteria and how they spread among phylogenetically distinct species.}, } @article {pmid36760501, year = {2023}, author = {Schackart, KE and Graham, JB and Ponsero, AJ and Hurwitz, BL}, title = {Evaluation of computational phage detection tools for metagenomic datasets.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1078760}, pmid = {36760501}, issn = {1664-302X}, abstract = {INTRODUCTION: As new computational tools for detecting phage in metagenomes are being rapidly developed, a critical need has emerged to develop systematic benchmarks.

METHODS: In this study, we surveyed 19 metagenomic phage detection tools, 9 of which could be installed and run at scale. Those 9 tools were assessed on several benchmark challenges. Fragmented reference genomes are used to assess the effects of fragment length, low viral content, phage taxonomy, robustness to eukaryotic contamination, and computational resource usage. Simulated metagenomes are used to assess the effects of sequencing and assembly quality on the tool performances. Finally, real human gut metagenomes and viromes are used to assess the differences and similarities in the phage communities predicted by the tools.

RESULTS: We find that the various tools yield strikingly different results. Generally, tools that use a homology approach (VirSorter, MARVEL, viralVerify, VIBRANT, and VirSorter2) demonstrate low false positive rates and robustness to eukaryotic contamination. Conversely, tools that use a sequence composition approach (VirFinder, DeepVirFinder, Seeker), and MetaPhinder, have higher sensitivity, including to phages with less representation in reference databases. These differences led to widely differing predicted phage communities in human gut metagenomes, with nearly 80% of contigs being marked as phage by at least one tool and a maximum overlap of 38.8% between any two tools. While the results were more consistent among the tools on viromes, the differences in results were still significant, with a maximum overlap of 60.65%. Discussion: Importantly, the benchmark datasets developed in this study are publicly available and reusable to enable the future comparability of new tools developed.}, } @article {pmid36760236, year = {2022}, author = {Pan, Y and Zhang, X and Sun, Y and Zhang, Y and Bao, W and Yin, D and Zhang, P and Zhang, M}, title = {Cellular analysis and metagenomic next-generation sequencing of bronchoalveolar lavage fluid in the distinction between pulmonary non-infectious and infectious disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1023978}, pmid = {36760236}, issn = {2235-2988}, mesh = {Humans ; Bronchoalveolar Lavage Fluid ; Retrospective Studies ; *Pneumonia ; *Communicable Diseases ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: The aim of the current study was to investigate the clinical value of cellular analysis and metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in differentiating pulmonary non-infectious and infectious diseases in immunocompetent patients.

METHODS: The present retrospective study was conducted from December 2017 to March 2020, and included immunocompetent patients with suspected pulmonary infection. High-resolution computed tomography, total cell counts and classification of BALF, conventional microbiological tests (CMTs), laboratory tests and mNGS of BALF were performed. Patients were assigned to pulmonary non-infectious disease (PNID) and pulmonary infectious disease (PID) groups based on final diagnoses. PNID-predictive values were analyzed via areas under receiver operating characteristic curves (AUCs). Optimal cutoffs were determined by maximizing the sum of sensitivity and specificity.

RESULTS: A total of 102 patients suspected of pulmonary infection were enrolled in the study, 23 (22.5%) with PNID and 79 (77.5%) with PID. The diagnostic efficiency of BALF mNGS for differentiating PID from PNID was better than that of CMTs. Neutrophil percentage (N%) and the ratio of neutrophils to lymphocytes (N/L) in BALF were significantly lower in the PNID group than in the PID group. The AUCs for distinguishing PNID and PID were 0.739 (95% confidence interval [CI] 0.636-0.825) for BALF N%, 0.727 (95% CI 0.624-0.815) for BALF N/L, and 0.799 (95% CI 0.702-0.876) for BALF mNGS, with respective cutoff values of 6.7%, 0.255, and negative. Joint models of BALF mNGS combined with BALF N/L or BALF N% increased the respective AUCs to 0.872 (95% CI 0.786-0.933) and 0.871 (95% CI 0.784-0.932), which were significantly higher than those for BALF mNGS, BALF N%, and BALF N/L alone.

CONCLUSIONS: BALF N% ≤ 6.7% or BALF N/L ≤ 0.255 combined with a negative BALF mNGS result can effectively distinguish PNID from PID in immunocompetent patients with suspected pulmonary infection. BALF mNGS outperforms CMTs for identifying pathogens in immunocompetent patients, and the combination of mNGS and CMTs may be a better diagnostic strategy.}, } @article {pmid36760234, year = {2022}, author = {Wang, J and Xu, H and Wang, X and Lan, J}, title = {Rapid diagnosis of non-tuberculous mycobacterial pulmonary diseases by metagenomic next-generation sequencing in non-referral hospitals.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1083497}, pmid = {36760234}, issn = {2235-2988}, mesh = {Humans ; Nontuberculous Mycobacteria/genetics ; *Mycobacterium Infections, Nontuberculous/microbiology ; *Lung Diseases ; Retrospective Studies ; Hospitals ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {OBJECTIVES: The incidence of non-tuberculous mycobacterial pulmonary disease (NTM-PD) has increased steadily globally, but the current culture-based diagnosis of NTM-PD is difficult and time-consuming, leading to a high possibility of misdiagnosis. Therefore, new methods should be introduced to improve the processes for clinical diagnosis of this disease.

METHODS: Our retrospective observational study enrolled 12 NTM-PD patients who were identified by way of metagenomic next-generation sequencing (mNGS), as well as the characteristic radiological presentation of slowly progressed, usually concomitant bronchiectasis, small cavitary opacity, and multiple nodules that respond poorly to empirical antibiotic therapy. These patients received the recommended drug regimen based on the identified non-tuberculous mycobacteria (NTM) species. Clinical data, including symptoms, laboratory tests, dynamic computed tomography imaging, treatment, and outcome, were recorded and analyzed.

RESULTS: The results of mNGS were all positive, with the standard specifically mapped read numbers (SDSMRN) of NTM ranging from 1 to 766; this was confirmed in six patients via quantitative polymerase chain reaction (qPCR) analysis. The duration fromsample collection tomNGS results was 1-4 days. Among our 12 patients (except for one lost to follow-up) the CT imaging for 11 patients showed significant absorption of lesions.

CONCLUSIONS: Our results draw attention to NTM infection as a possible cause of community-acquired pneumonia, especially in patients with suggestive radiological presentation and poor responses to empirical antibiotic therapy. Our study also indicated that mNGS represented a potentially effective tool for the rapid identification of NTM in the respiratory sample. Improved clinician awareness combined with the utilization of mNGS could guide earlier diagnosis and targeted treatment, and finally improved the prognoses of patients with NTM-PD.}, } @article {pmid36759770, year = {2023}, author = {Zhang, H and Liu, G and He, L and Zhu, Y and Tu, H and Zhuang, S}, title = {Life-threatening pulmonary coinfection with Mycobacterium tuberculosis and Aspergillus lentulus in a diabetic patient diagnosed by metagenome next-generation sequencing.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {88}, pmid = {36759770}, issn = {1471-2334}, mesh = {Male ; Humans ; Aged ; *Mycobacterium tuberculosis/genetics ; *Coinfection/diagnosis/microbiology ; Metagenome ; *Aspergillosis/microbiology ; *Pneumonia ; *Tuberculosis/complications/diagnosis ; *Diabetes Mellitus ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {BACKGROUND: China has a double burden of diabetes mellitus and tuberculosis. Diabetes mellitus and tuberculosis are both important risk factors for Aspergillus infection. Aspergillus lentulus is an emerging fungal pathogen in China and invasive aspergillosis due to A. lentulus is associated with high mortality.

CASE PRESENTATION: A 79-year-old man was admitted to our hospital, complaining of a 7-day history of fever. Five days before admission, he was diagnosed with pulmonary infection at a local hospital, but his symptoms did not relieve after antibiotic therapy. The patient was diagnosed with diabetes mellitus two months ago. About 20 days ago, he began to present chest tightness and shortness of breath after physical activity. After admission, he developed continuous fever and rapid respiratory deterioration, and finally died after his family abandoned treatment. Pulmonary coinfection with M. tuberculosis and A. lentulus was identified by metagenome next-generation sequencing (mNGS) from bronchoalveolar lavage fluid.

CONCLUSIONS: Clinicians and laboratories should be alert to the emerging A. lentulus infection in China due to its drug-resistance and high mortality. In comparison with conventional methods, mNGS has a great advantage for the diagnosis of mixed pulmonary infection.}, } @article {pmid36759753, year = {2023}, author = {Zhang, Q and Linke, V and Overmyer, KA and Traeger, LL and Kasahara, K and Miller, IJ and Manson, DE and Polaske, TJ and Kerby, RL and Kemis, JH and Trujillo, EA and Reddy, TR and Russell, JD and Schueler, KL and Stapleton, DS and Rabaglia, ME and Seldin, M and Gatti, DM and Keele, GR and Pham, DT and Gerdt, JP and Vivas, EI and Lusis, AJ and Keller, MP and Churchill, GA and Blackwell, HE and Broman, KW and Attie, AD and Coon, JJ and Rey, FE}, title = {Genetic mapping of microbial and host traits reveals production of immunomodulatory lipids by Akkermansia muciniphila in the murine gut.}, journal = {Nature microbiology}, volume = {8}, number = {3}, pages = {424-440}, pmid = {36759753}, issn = {2058-5276}, support = {R01 HL144651/HL/NHLBI NIH HHS/United States ; R01 HL148577/HL/NHLBI NIH HHS/United States ; T15 LM007359/LM/NLM NIH HHS/United States ; R01 DK108259/DK/NIDDK NIH HHS/United States ; R35 GM131817/GM/NIGMS NIH HHS/United States ; R35 GM138376/GM/NIGMS NIH HHS/United States ; P41 GM108538/GM/NIGMS NIH HHS/United States ; R01 GM070683/GM/NIGMS NIH HHS/United States ; T32 GM008505/GM/NIGMS NIH HHS/United States ; R01 DK101573/DK/NIDDK NIH HHS/United States ; T32 HG002760/HG/NHGRI NIH HHS/United States ; RC2 DK125961/DK/NIDDK NIH HHS/United States ; T32 DK007665/DK/NIDDK NIH HHS/United States ; T32 AI055397/AI/NIAID NIH HHS/United States ; }, mesh = {Mice ; Animals ; *Verrucomicrobia/genetics ; *Gastrointestinal Microbiome/genetics ; Akkermansia/genetics ; Phenotype ; }, abstract = {The molecular bases of how host genetic variation impacts the gut microbiome remain largely unknown. Here we used a genetically diverse mouse population and applied systems genetics strategies to identify interactions between host and microbe phenotypes including microbial functions, using faecal metagenomics, small intestinal transcripts and caecal lipids that influence microbe-host dynamics. Quantitative trait locus (QTL) mapping identified murine genomic regions associated with variations in bacterial taxa; bacterial functions including motility, sporulation and lipopolysaccharide production and levels of bacterial- and host-derived lipids. We found overlapping QTL for the abundance of Akkermansia muciniphila and caecal levels of ornithine lipids. Follow-up in vitro and in vivo studies revealed that A. muciniphila is a major source of these lipids in the gut, provided evidence that ornithine lipids have immunomodulatory effects and identified intestinal transcripts co-regulated with these traits including Atf3, which encodes for a transcription factor that plays vital roles in modulating metabolism and immunity. Collectively, these results suggest that ornithine lipids are potentially important for A. muciniphila-host interactions and support the role of host genetics as a determinant of responses to gut microbes.}, } @article {pmid36759752, year = {2023}, author = {Apjok, G and Számel, M and Christodoulou, C and Seregi, V and Vásárhelyi, BM and Stirling, T and Eszenyi, B and Sári, T and Vidovics, F and Nagrand, E and Kovács, D and Szili, P and Lantos, II and Méhi, O and Jangir, PK and Herczeg, R and Gálik, B and Urbán, P and Gyenesei, A and Draskovits, G and Nyerges, Á and Fekete, G and Bodai, L and Zsindely, N and Dénes, B and Yosef, I and Qimron, U and Papp, B and Pál, C and Kintses, B}, title = {Characterization of antibiotic resistomes by reprogrammed bacteriophage-enabled functional metagenomics in clinical strains.}, journal = {Nature microbiology}, volume = {8}, number = {3}, pages = {410-423}, pmid = {36759752}, issn = {2058-5276}, mesh = {*Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Metagenomics ; *Bacteriophages/genetics ; Bacteria/genetics ; }, abstract = {Functional metagenomics is a powerful experimental tool to identify antibiotic resistance genes (ARGs) in the environment, but the range of suitable host bacterial species is limited. This limitation affects both the scope of the identified ARGs and the interpretation of their clinical relevance. Here we present a functional metagenomics pipeline called Reprogrammed Bacteriophage Particle Assisted Multi-species Functional Metagenomics (DEEPMINE). This approach combines and improves the use of T7 bacteriophage with exchanged tail fibres and targeted mutagenesis to expand phage host-specificity and efficiency for functional metagenomics. These modified phage particles were used to introduce large metagenomic plasmid libraries into clinically relevant bacterial pathogens. By screening for ARGs in soil and gut microbiomes and clinical genomes against 13 antibiotics, we demonstrate that this approach substantially expands the list of identified ARGs. Many ARGs have species-specific effects on resistance; they provide a high level of resistance in one bacterial species but yield very limited resistance in a related species. Finally, we identified mobile ARGs against antibiotics that are currently under clinical development or have recently been approved. Overall, DEEPMINE expands the functional metagenomics toolbox for studying microbial communities.}, } @article {pmid36759670, year = {2023}, author = {Popov, IV and Ohlopkova, OV and Donnik, IM and Zolotukhin, PV and Umanets, A and Golovin, SN and Malinovkin, AV and Belanova, AA and Lipilkin, PV and Lipilkina, TA and Popov, IV and Logvinov, AK and Dubovitsky, NA and Stolbunova, KA and Sobolev, IA and Alekseev, AY and Shestopalov, AM and Burkova, VN and Chikindas, ML and Venema, K and Ermakov, AM}, title = {Detection of coronaviruses in insectivorous bats of Fore-Caucasus, 2021.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {2306}, pmid = {36759670}, issn = {2045-2322}, mesh = {Animals ; *Chiroptera ; *Coronavirus/genetics ; *Coronavirus Infections/epidemiology/veterinary/genetics ; Genome, Viral ; Phylogeny ; RNA ; }, abstract = {Coronaviruses (CoVs) pose a huge threat to public health as emerging viruses. Bat-borne CoVs are especially unpredictable in their evolution due to some unique features of bat physiology boosting the rate of mutations in CoVs, which is already high by itself compared to other viruses. Among bats, a meta-analysis of overall CoVs epizootiology identified a nucleic acid observed prevalence of 9.8% (95% CI 8.7-10.9%). The main objectives of our study were to conduct a qPCR screening of CoVs' prevalence in the insectivorous bat population of Fore-Caucasus and perform their characterization based on the metagenomic NGS of samples with detected CoV RNA. According to the qPCR screening, CoV RNA was detected in 5 samples, resulting in a 3.33% (95% CI 1.1-7.6%) prevalence of CoVs in bats from these studied locations. BetaCoVs reads were identified in raw metagenomic NGS data, however, detailed characterization was not possible due to relatively low RNA concentration in samples. Our results correspond to other studies, although a lower prevalence in qPCR studies was observed compared to other regions and countries. Further studies should require deeper metagenomic NGS investigation, as a supplementary method, which will allow detailed CoV characterization.}, } @article {pmid36759614, year = {2023}, author = {Albright, S and Louca, S}, title = {Trait biases in microbial reference genomes.}, journal = {Scientific data}, volume = {10}, number = {1}, pages = {84}, pmid = {36759614}, issn = {2052-4463}, mesh = {Animals ; Archaea/genetics ; *Bacteria/genetics ; *Genome, Microbial ; Metagenome ; Metagenomics/methods ; }, abstract = {Common culturing techniques and priorities bias our discovery towards specific traits that may not be representative of microbial diversity in nature. So far, these biases have not been systematically examined. To address this gap, here we use 116,884 publicly available metagenome-assembled genomes (MAGs, completeness ≥80%) from 203 surveys worldwide as a culture-independent sample of bacterial and archaeal diversity, and compare these MAGs to the popular RefSeq genome database, which heavily relies on cultures. We compare the distribution of 12,454 KEGG gene orthologs (used as trait proxies) in the MAGs and RefSeq genomes, while controlling for environment type (ocean, soil, lake, bioreactor, human, and other animals). Using statistical modeling, we then determine the conditional probabilities that a species is represented in RefSeq depending on its genetic repertoire. We find that the majority of examined genes are significantly biased for or against in RefSeq. Our systematic estimates of gene prevalences across bacteria and archaea in nature and gene-specific biases in reference genomes constitutes a resource for addressing these issues in the future.}, } @article {pmid36759174, year = {2023}, author = {He, Q and Guo, K and Wang, L and Xie, F and Zhao, Q and Jiang, X and He, Z and Wang, P and Li, S and Huang, Y and Zhang, C and Huang, R and Liu, Y and Wang, F and Zhou, X and Niu, R and Zuo, T and Wang, Y and Li, C}, title = {Tannins amount determines whether tannase-containing bacteria are probiotic or pathogenic in IBD.}, journal = {Life science alliance}, volume = {6}, number = {5}, pages = {}, pmid = {36759174}, issn = {2575-1077}, mesh = {Humans ; *Colitis/chemically induced ; Tannins/adverse effects/metabolism ; *Inflammatory Bowel Diseases/chemically induced ; *Probiotics/pharmacology ; Bacteria/metabolism ; }, abstract = {The role of dietary tannin in inflammatory bowel disease (IBD) is still not clear. Therefore, we aim to study the effect of TA in the progression of IBD. Dextran sulphate sodium (DSS)-induced model was used to mimic IBD. Metagenomics and metabolomics were performed to study the alteration of intestinal microbiota and metabolites. NCM460 and THP-1 cells were used for in vitro study. The amount of TA was associated with the outcomes of DSS-induced IBD as evidenced by in vivo and in vitro studies. Metabolomic and metagenomic analyses revealed that TA-induced enrichment of microbial metabolite gallic acid (GA) was responsible for the action of TA. Mechanistically, protective dose of GA promoted colonic mucus secretion to suppress bacterial infection and that it ameliorated DSS-induced epithelial damage by inhibiting p53 signaling, whereas toxic dose of GA directly caused epithelial damage by promoting cell cycle arrest. Therapeutic experiment showed protective dose of GA-promoted recovery of DSS-induced colonic inflammation. The role of tannase-containing bacteria can be transformed under different conditions in IBD progression.}, } @article {pmid36758925, year = {2023}, author = {Osorio, V and Sabater I Mezquita, A and Balcázar, JL}, title = {Comparative metagenomics reveals poultry and swine farming are hotspots for multidrug and tetracycline resistance.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {322}, number = {}, pages = {121239}, doi = {10.1016/j.envpol.2023.121239}, pmid = {36758925}, issn = {1873-6424}, mesh = {Swine ; Humans ; Animals ; Cattle ; *Poultry/microbiology ; *Tetracycline Resistance/genetics ; Manure/microbiology ; Metagenomics ; Anti-Bacterial Agents/toxicity ; Farms ; }, abstract = {Antibiotic misuse in livestock is a major threat to human health, as bacteria are quickly developing resistance to them. We performed a comparative analysis of 25 faecal metagenomes from swine, poultry, cattle, and humans to investigate their resistance profiles. Our analysis revealed that all genes conferring resistance to antibiotic classes assessed except tetracyclines were more prevalent in poultry manure than in the remaining species. We detected clinically relevant antibiotic resistance genes, such as mcr-1 which confers resistance to polymyxins. Among them, extended-spectrum β-lactamase blaCTX-M genes were particularly abundant in all species. Poultry manure was identified as a hotspot for multidrug resistance, which may compromise medical treatment options. Urgent actions in the livestock industry are imperative to hamper the emergence and spread of antibiotic resistance.}, } @article {pmid36758522, year = {2023}, author = {Guo, C and Che, X and Briese, T and Ranjan, A and Allicock, O and Yates, RA and Cheng, A and March, D and Hornig, M and Komaroff, AL and Levine, S and Bateman, L and Vernon, SD and Klimas, NG and Montoya, JG and Peterson, DL and Lipkin, WI and Williams, BL}, title = {Deficient butyrate-producing capacity in the gut microbiome is associated with bacterial network disturbances and fatigue symptoms in ME/CFS.}, journal = {Cell host & microbe}, volume = {31}, number = {2}, pages = {288-304.e8}, pmid = {36758522}, issn = {1934-6069}, support = {R56 AI120724/AI/NIAID NIH HHS/United States ; U54 AI138370/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Fatigue Syndrome, Chronic/metabolism/microbiology ; *Gastrointestinal Microbiome ; Butyrates ; Bacteria/genetics ; Metabolomics ; }, abstract = {Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is characterized by unexplained debilitating fatigue, cognitive dysfunction, gastrointestinal disturbances, and orthostatic intolerance. Here, we report a multi-omic analysis of a geographically diverse cohort of 106 cases and 91 healthy controls that revealed differences in gut microbiome diversity, abundances, functional pathways, and interactions. Faecalibacterium prausnitzii and Eubacterium rectale, which are both recognized as abundant, health-promoting butyrate producers in the human gut, were reduced in ME/CFS. Functional metagenomics, qPCR, and metabolomics of fecal short-chain fatty acids confirmed a deficient microbial capacity for butyrate synthesis. Microbiome-based machine learning classifier models were robust to geographic variation and generalizable in a validation cohort. The abundance of Faecalibacterium prausnitzii was inversely associated with fatigue severity. These findings demonstrate the functional nature of gut dysbiosis and the underlying microbial network disturbance in ME/CFS, providing possible targets for disease classification and therapeutic trials.}, } @article {pmid36758521, year = {2023}, author = {Xiong, R and Gunter, C and Fleming, E and Vernon, SD and Bateman, L and Unutmaz, D and Oh, J}, title = {Multi-'omics of gut microbiome-host interactions in short- and long-term myalgic encephalomyelitis/chronic fatigue syndrome patients.}, journal = {Cell host & microbe}, volume = {31}, number = {2}, pages = {273-287.e5}, pmid = {36758521}, issn = {1934-6069}, support = {R01 AR078634/AR/NIAMS NIH HHS/United States ; U19 AI142733/AI/NIAID NIH HHS/United States ; U54 NS105539/NS/NINDS NIH HHS/United States ; R21 AR075174/AR/NIAMS NIH HHS/United States ; DP2 GM126893/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Fatigue Syndrome, Chronic/metabolism ; *Gastrointestinal Microbiome ; Dysbiosis ; Metabolomics ; Feces ; }, abstract = {Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a complex, debilitating disorder manifesting as severe fatigue and post-exertional malaise. The etiology of ME/CFS remains elusive. Here, we present a deep metagenomic analysis of stool combined with plasma metabolomics and clinical phenotyping of two ME/CFS cohorts with short-term (<4 years, n = 75) or long-term disease (>10 years, n = 79) compared with healthy controls (n = 79). First, we describe microbial and metabolomic dysbiosis in ME/CFS patients. Short-term patients showed significant microbial dysbiosis, while long-term patients had largely resolved microbial dysbiosis but had metabolic and clinical aberrations. Second, we identified phenotypic, microbial, and metabolic biomarkers specific to patient cohorts. These revealed potential functional mechanisms underlying disease onset and duration, including reduced microbial butyrate biosynthesis and a reduction in plasma butyrate, bile acids, and benzoate. In addition to the insights derived, our data represent an important resource to facilitate mechanistic hypotheses of host-microbiome interactions in ME/CFS.}, } @article {pmid36758519, year = {2023}, author = {Walters, WA and Granados, AC and Ley, C and Federman, S and Stryke, D and Santos, Y and Haggerty, T and Sotomayor-Gonzalez, A and Servellita, V and Ley, RE and Parsonnet, J and Chiu, CY}, title = {Longitudinal comparison of the developing gut virome in infants and their mothers.}, journal = {Cell host & microbe}, volume = {31}, number = {2}, pages = {187-198.e3}, pmid = {36758519}, issn = {1934-6069}, support = {R01 HD088837/HD/NICHD NIH HHS/United States ; }, mesh = {Female ; Humans ; Virome/genetics ; *Viruses/genetics ; *Bacteriophages/genetics ; Mothers ; Metagenome ; Metagenomics ; }, abstract = {The human gut virome and its early life development are poorly understood. Prior studies have captured single-point assessments with the evolution of the infant virome remaining largely unexplored. We performed viral metagenomic sequencing on stool samples collected longitudinally from a cohort of 53 infants from age 2 weeks to 3 years (80.7 billion reads), and from their mothers (9.8 billion reads) to examine and compare viromes. The asymptomatic infant virome consisted of bacteriophages, nonhuman dietary/environmental viruses, and human-host viruses, predominantly picornaviruses. In contrast, human-host viruses were largely absent from the maternal virome. Previously undescribed, sequence-divergent vertebrate viruses were detected in the maternal but not infant virome. As infants aged, the phage component evolved to resemble the maternal virome, but by age 3, the human-host component remained dissimilar from the maternal virome. Thus, early life virome development is determined predominantly by dietary, infectious, and environmental factors rather than direct maternal acquisition.}, } @article {pmid36758508, year = {2023}, author = {Ariaeenejad, S and Kavousi, K and Zolfaghari, B and Roy, S and Koshiba, T and Hosseini Salekdeh, G}, title = {Efficient bioconversion of lignocellulosic waste by a novel computationally screened hyperthermostable enzyme from a specialized microbiota.}, journal = {Ecotoxicology and environmental safety}, volume = {252}, number = {}, pages = {114587}, doi = {10.1016/j.ecoenv.2023.114587}, pmid = {36758508}, issn = {1090-2414}, mesh = {Animals ; *Endo-1,4-beta Xylanases/chemistry/metabolism ; Lignin/metabolism ; Temperature ; Hydrolysis ; *Microbiota ; }, abstract = {A large amount of lignocellulosic waste is generated every day in the world, and their accumulation in the agroecosystems, integration in soil compositions, or incineration for energy production has severe environmental pollution effects. Using enzymes as biocatalysts for the biodegradation of lignocellulosic materials, especially in harsh processing conditions, is a practical step towards green energy and environmental biosafety. Hence, the current study focuses on enzyme computationally screened from camel rumen metagenomics data as specialized microbiota that have the capacity to degrade lignocellulosic-rich and recalcitrant materials. The novel hyperthermostable xylanase named PersiXyn10 with the performance at extreme conditions was proper activity within a broad temperature (30-100 ℃) and pH range (4.0-11.0) but showed the maximum xylanolytic activity in severe alkaline and temperature conditions, pH 8.0 and temperature 90 ℃. Also, the enzyme had highly resistant to metals, surfactants, and organic solvents in optimal conditions. The introduced xylanase had unique properties in terms of thermal stability by maintaining over 82% of its activity after 15 days of incubation at 90 ℃. Considering the crucial role of hyperthermostable xylanases in the paper industry, the PersiXyn10 was subjected to biodegradation of paper pulp. The proper performance of hyperthermostable PersiXyn10 on the paper pulp was confirmed by structural analysis (SEM and FTIR) and produced 31.64 g/L of reducing sugar after 144 h hydrolysis. These results proved the applicability of the hyperthermostable xylanase in biobleaching and saccharification of lignocellulosic biomass for declining the environmental hazards.}, } @article {pmid36758494, year = {2023}, author = {Pimentel, AC and Liberato, MV and Franco Cairo, JPL and Tomazetto, G and Gandin, CA and de Oliveira Neto, M and Alvarez, TM and Squina, FM}, title = {Structural and functional insights of the catalytic GH5 and Calx-β domains from the metagenome-derived endoglucanase CelE2.}, journal = {Enzyme and microbial technology}, volume = {165}, number = {}, pages = {110206}, doi = {10.1016/j.enzmictec.2023.110206}, pmid = {36758494}, issn = {1879-0909}, mesh = {*Glycoside Hydrolases/metabolism ; *Cellulase/metabolism ; Metagenome ; Escherichia coli/genetics/metabolism ; Biofuels ; Scattering, Small Angle ; X-Ray Diffraction ; Cellulose/metabolism ; Substrate Specificity ; }, abstract = {Cellulose is the most abundant natural polymer on Earth, representing an attractive feedstock for bioproducts and biofuel production. Cellulases promote the depolymerization of cellulose, generating short oligosaccharides and glucose, which are useful in biotechnological applications. Among the classical cellulases, those from glycoside hydrolase family 5 (GH5) are one of the most abundant in Nature, displaying several modular architectures with other accessory domains attached to its catalytic core, such as carbohydrate-binding modules (CBMs), Ig-like, FN3-like, and Calx-β domains, which can influence the enzyme activity. The metagenome-derived endoglucanase CelE2 has in its modular architecture an N-terminal domain belonging to the GH5 family and a C-terminal domain with a high identity to the Calx-β domain. In this study, the GH5 and the Calx-β domains were subcloned and heterologously expressed in E. coli, to evaluate the structural and functional properties of the individualized domains of CelE2. Thermostability analysis by circular dichroism (CD) revealed a decrease in the denaturation temperature values around 4.6 °C for the catalytic domain (CelE21-381) compared to CelE2 full-length. The CD analyses revealed that the Calx-β domain (CelE2382-477) was unfolded, suggesting that this domain requires to be attached to the catalytic core to become structurally stable. The three-dimensional structure of the catalytic domain CelE21-381 was determined at 2.1 Å resolution, showing a typical (α/β)8-barrel fold and a narrow active site compared to other cellulases from the same family. The biochemical characterization showed that the deletion of the Calx-β domain increased more than 3-fold the activity of the catalytic domain CelE21-381 towards the insoluble substrate Avicel. The main functional properties of CelE2, such as substrate specificity, optimal pH and temperature, thermal stability, and activation by CaCl2, were not altered after the deletion of the accessory domain. Furthermore, the Small Angle X-ray Scattering (SAXS) analyses showed that the addition of CaCl2 was beneficial CelE21-381 protein solvency. This work contributed to fundamental concepts about the structure and function of cellulases, which are useful in applications involving lignocellulosic materials degradation into food and feedstuffs and biofuel production.}, } @article {pmid36758246, year = {2023}, author = {Lee, J and Jeong, H and Kang, HG and Park, J and Choi, EY and Lee, CS and Byeon, SH and Kim, M}, title = {Rapid Pathogen Detection in Infectious Uveitis Using Nanopore Metagenomic Next-Generation Sequencing: A Preliminary Study.}, journal = {Ocular immunology and inflammation}, volume = {}, number = {}, pages = {1-7}, doi = {10.1080/09273948.2023.2173243}, pmid = {36758246}, issn = {1744-5078}, abstract = {PURPOSE: We establish an accurate and rapid diagnostic method for pathogen detection in infectious uveitis using nanopore metagenomic next-generation sequencing (NGS).

METHODS: In eight patients with suspected infectious uveitis, we prospectively compared the accuracy and time taken for pathogen identification between conventional diagnostic methods, such as cultures and PCR, and nanopore metagenomic NGS.

RESULTS: All causative pathogens were identified using nanopore sequencing, while only five of the eight patients were confirmed positive for a specific pathogen using conventional methods. The overall sample-to-answer turnaround time of nanopore sequencing was much shorter than that of conventional methods in the bacterial and fungal infection (mean, 17 h vs. 4d, respectively; P = .028). The pathogens could be detected even when the quantity or quality of DNA was not optimal.

CONCLUSION: Nanopore metagenomic NGS is a promising diagnostic tool that can rapidly and accurately identify the causative pathogen in infectious uveitis.}, } @article {pmid36757364, year = {2023}, author = {Madi, N and Chen, D and Wolff, R and Shapiro, BJ and Garud, NR}, title = {Community diversity is associated with intra-species genetic diversity and gene loss in the human gut microbiome.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {36757364}, issn = {2050-084X}, support = {R25 MH 109172/NH/NIH HHS/United States ; }, mesh = {Humans ; Biodiversity ; *Gastrointestinal Microbiome/genetics ; Genetic Variation ; RNA, Ribosomal, 16S/genetics ; }, abstract = {How the ecological process of community assembly interacts with intra-species diversity and evolutionary change is a longstanding question. Two contrasting hypotheses have been proposed: Diversity Begets Diversity (DBD), in which taxa tend to become more diverse in already diverse communities, and Ecological Controls (EC), in which higher community diversity impedes diversification. Previously, using 16S rRNA gene amplicon data across a range of microbiomes, we showed a generally positive relationship between taxa diversity and community diversity at higher taxonomic levels, consistent with the predictions of DBD (Madi et al., 2020). However, this positive 'diversity slope' plateaus at high levels of community diversity. Here we show that this general pattern holds at much finer genetic resolution, by analyzing intra-species strain and nucleotide variation in static and temporally sampled metagenomes from the human gut microbiome. Consistent with DBD, both intra-species polymorphism and strain number were positively correlated with community Shannon diversity. Shannon diversity is also predictive of increases in polymorphism over time scales up to ~4-6 months, after which the diversity slope flattens and becomes negative - consistent with DBD eventually giving way to EC. Finally, we show that higher community diversity predicts gene loss at a future time point. This observation is broadly consistent with the Black Queen Hypothesis, which posits that genes with functions provided by the community are less likely to be retained in a focal species' genome. Together, our results show that a mixture of DBD, EC, and Black Queen may operate simultaneously in the human gut microbiome, adding to a growing body of evidence that these eco-evolutionary processes are key drivers of biodiversity and ecosystem function.}, } @article {pmid36756615, year = {2023}, author = {Lin, Y and Dai, Y and Zhang, S and Guo, H and Yang, L and Li, J and Wang, K and Ni, M and Hu, Z and Jia, L and Liu, H and Li, P and Song, H}, title = {Application of nanopore adaptive sequencing in pathogen detection of a patient with Chlamydia psittaci infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {13}, number = {}, pages = {1064317}, pmid = {36756615}, issn = {2235-2988}, mesh = {Humans ; *Psittacosis/diagnosis ; *Chlamydophila psittaci/genetics ; *Nanopore Sequencing ; *Nanopores ; High-Throughput Nucleotide Sequencing/methods ; *Chlamydia Infections ; Metagenomics/methods ; }, abstract = {INTRODUCTION: Nanopore sequencing has been widely used in clinical metagenomic sequencing for pathogen detection with high portability and real-time sequencing. Oxford Nanopore Technologies has recently launched an adaptive sequencing function, which can enrich on-target reads through real-time alignment and eject uninteresting reads by reversing the voltage across the nanopore. Here we evaluated the utility of adaptive sequencing in clinical pathogen detection.

METHODS: Nanopore adaptive sequencing and standard sequencing was performed on a same flow cell with a bronchoalveolar lavage fluid sample from a patient with Chlamydia psittacosis infection, and was compared with the previous mNGS results.

RESULTS: Nanopore adaptive sequencing identified 648 on-target stop receiving reads with the longest median read length(688bp), which account for 72.4% of all Chlamydia psittaci reads and 0.03% of total reads in enriched group. The read proportion matched to C. psittaci in the stop receiving group was 99.85%, which was much higher than that of the unblock (<0.01%) and fail to adapt (0.02%) groups. Nanopore adaptive sequencing generated similar data yield of C. psittaci compared with standard nanopore sequencing. The proportion of C. psittaci reads in adaptive sequencing is close to that of standard nanopore sequencing and mNGS, but generated lower genome coverage than mNGS.

DISCUSSION: Nanopore adaptive sequencing can effectively identify target C. psittaci reads in real-time, but how to increase the targeted data of pathogens still needs to be further evaluated.}, } @article {pmid36756612, year = {2023}, author = {Fan, X and Chen, T and Yang, H and Gao, Y and Chen, Y}, title = {Encephalomyelomeningitis Caused by Balamuthia mandrillaris: A Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {727-733}, pmid = {36756612}, issn = {1178-6973}, abstract = {Central nervous system infection by Balamuthia mandrillaris is a rare and severe condition, which has a fatality rate of approximately 95% and often evades timely diagnosis due to its rarity and non-specific clinical manifestations. Here, we report a case of encephalomyelomeningitis caused by B. mandrillaris in a male who presented with transient coma, nausea, and vomiting when working in a garbage dump. Initial magnetic resonance imaging (MRI) of the brain showed normal signals. Despite receiving steroids as well as antibacterial and antiviral treatment, he developed urinary and fecal dysfunction, inability to walk, and deterioration of consciousness. Both brain and spinal cord MRI revealed abnormal findings, and next-generation sequencing of the cerebrospinal fluid showed the presence of B. mandrillaris. A combination of fluconazole and albendazole was administered; however, the patient deteriorated gradually and died 30 days after the onset. We suggest the unbiased metagenomic sequencing of the affected tissues/CSF in patients with CNS infections that are difficult to diagnose or treat, and multiple tests at different stages of the disease may be required.}, } @article {pmid36755857, year = {2022}, author = {Zhu, A and Liu, Y and Li, Z and He, Y and Bai, L and Wu, Y and Zhang, Y and Huang, Y and Jiang, P}, title = {Diagnosis and functional prediction of microbial markers in tumor tissues of sporadic colorectal cancer patients associated with the MLH1 protein phenotype.}, journal = {Frontiers in oncology}, volume = {12}, number = {}, pages = {1116780}, pmid = {36755857}, issn = {2234-943X}, abstract = {OBJECTIVE: Most patients with sporadic colorectal cancer (SCRC) develop microsatellite instability because of defects in mismatch repair (MMR). Moreover, the gut microbiome plays a vital role in the pathogenesis of SCRC. In this study, we assessed the microbial composition and diversity of SCRC tumors with varying MutL protein homolog 1 (MLH1) status, and the effects of functional genes related to bacterial markers and clinical diagnostic prediction.

METHODS: The tumor microbial diversity and composition were profiled using high-throughput sequencing of the 16S ribosomal RNA (rRNA) gene V4 region. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2) software and BugBase tool were used to predict the functional roles of the microbiome. We aimed to construct a high-accuracy model to detect and evaluate the area under the receiver operating characteristic curve with candidate biomarkers.

RESULTS: The study included 23 patients with negative/defective MLH1 (DM group) and 22 patients with positive/intact MLH1 (IM group). Estimation of alpha diversity indices showed that the Shannon index (p = 0.049) was significantly higher in the DM group than in the controls, while the Simpson index (p = 0.025) was significantly lower. At the genus level, we observed a significant difference in beta diversity in the DM group versus the IM group. Moreover, the abundance of Lachnoclostridium spp. and Coprococcus spp. was significantly more enriched in the DM group than in the IM group (q < 0.01 vs. q < 0.001). When predicting metagenomes, there were 18 Kyoto Encyclopedia of Genes and Genomes pathways and one BugBase function difference in both groups (all q < 0.05). On the basis of the model of diagnostic prediction, we built a simplified optimal model through stepwise selection, consisting of the top two bacterial candidate markers (area under the curve = 0.93).

CONCLUSION: In conclusion, the genera Lachnoclostridium and Coprococcus as key species may be crucial biomarkers for non-invasive diagnostic prediction of DM in patients with SCRC in the future.}, } @article {pmid36755852, year = {2022}, author = {Fang, C and Xu, L and Tan, J and Tan, H and Lin, J and Zhao, Z}, title = {Case Report: Chlamydia psittaci pneumonia complicated by Guillain-Barré syndrome detected using metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1070760}, pmid = {36755852}, issn = {2235-2988}, mesh = {Humans ; *Guillain-Barre Syndrome/complications/diagnosis ; *Chlamydophila psittaci/genetics ; *Psittacosis/complications/diagnosis ; Anti-Bacterial Agents/therapeutic use ; *Pneumonia/complications ; Fatigue/complications ; High-Throughput Nucleotide Sequencing ; }, abstract = {Psittacosis and Guillain-Barré syndrome are both rare clinical diseases with low incidence, and their combination has rarely been reported. Here, we report a case of Chlamydia psittaci pneumonia combined with Guillain-Barré syndrome. The patient initially presented with high fever, difficulty breathing, and fatigue. Chest computerised tomography indicated large consolidation opacities in both lungs. Metagenomic next-generation sequencing clearly identified the pathogen as C. psittaci. The patient's fever subsided after targeted antibiotic treatment, but difficulty breathing and fatigue worsened, and the patient developed symmetric limb numbness and weakness. Lumbar puncture, electrophysiological examination, and clinical characteristics were suggestive of Guillain-Barré syndrome, and the symptoms improved after treatment with human immunoglobulin. The results of this study suggest that metagenomic next-generation sequencing is useful for the rapid diagnosis of pulmonary infectious agents. Psittacosis is closely associated with the development of Guillain-Barré syndrome; however, more cases are needed to support this conclusion, and early targeted antibiotic treatment, immunotherapy, and basic supportive treatment are essential for improving outcomes.}, } @article {pmid36755840, year = {2023}, author = {Pardinhas, C and Filipe, R and Vergnaud, P and Grapin, M and Ferrière, E and Jamet, A and Fourgeaud, J and Da Rocha, N and Pérot, P and Boyer, O and Rabant, M and Van Huyen, JD and Isnard, P}, title = {Renal arcuate vein thrombosis-induced acute kidney injury: a rare multiple-Hit-mediated disease.}, journal = {Clinical kidney journal}, volume = {16}, number = {2}, pages = {367-373}, pmid = {36755840}, issn = {2048-8505}, abstract = {BACKGROUND: Renal arcuate vein thrombosis (RAVT) is a rare and recently recognized cause of acute kidney injury (AKI) in young adults. However, the precise incidence and underlying pathophysiologic mechanisms leading to AKI in these patients remain elusive.

METHODS: This study included all patients who underwent a kidney biopsy over a 40-month period sent to the pathology department of Necker-Enfants Malades Hospital, with evidence of RAVT. We performed coagulation tests, genetic testing for thrombophilia, complete urine toxicologic screening and kidney metagenomic sequencing to identify an underlying cause of thrombosis.

RESULTS: We report five pediatric cases of RAVT discovered on kidney biopsy performed in the setting of unexplained AKI. Investigations did not reveal an underlying cause of thrombosis but only a significant nonsteroidal anti-inflammatory drugs (NSAIDs) use was reported in 4/5 patients, supporting a potential link between NSAIDs use and RAVT. By performing metagenomic sequencing on kidney biopsy samples, we detected severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in the kidney of one patient. These results suggest that systemic SARS-CoV-2 infection may also be a key contributing factor of renal thrombosis, particularly by inducing potential endothelial disruption.

CONCLUSIONS: In conclusion, RAVT-induced AKI appears to be a multiple hit-mediated disease in which NSAIDs consumption and viral infection such as SARS-CoV-2 may be crucial contributing factors. These findings may have significant public health implications given the prevalence of NSAIDs use in the general population. Increased awareness and additional study of future cases may lead to a better understanding of this rare cause of AKI in children and young adults.}, } @article {pmid36755570, year = {2023}, author = {Zhou, F and Yang, H and Si, Y and Gan, R and Yu, L and Chen, C and Ren, C and Wu, J and Zhang, F}, title = {PhageTailFinder: A tool for phage tail module detection and annotation.}, journal = {Frontiers in genetics}, volume = {14}, number = {}, pages = {947466}, pmid = {36755570}, issn = {1664-8021}, abstract = {Decades of overconsumption of antimicrobials in the treatment and prevention of bacterial infections have resulted in the increasing emergence of drug-resistant bacteria, which poses a significant challenge to public health, driving the urgent need to find alternatives to conventional antibiotics. Bacteriophages are viruses infecting specific bacterial hosts, often destroying the infected bacterial hosts. Phages attach to and enter their potential hosts using their tail proteins, with the composition of the tail determining the range of potentially infected bacteria. To aid the exploitation of bacteriophages for therapeutic purposes, we developed the PhageTailFinder algorithm to predict tail-related proteins and identify the putative tail module in previously uncharacterized phages. The PhageTailFinder relies on a two-state hidden Markov model (HMM) to predict the probability of a given protein being tail-related. The process takes into account the natural modularity of phage tail-related proteins, rather than simply considering amino acid properties or secondary structures for each protein in isolation. The PhageTailFinder exhibited robust predictive power for phage tail proteins in novel phages due to this sequence-independent operation. The performance of the prediction model was evaluated in 13 extensively studied phages and a sample of 992 complete phages from the NCBI database. The algorithm achieved a high true-positive prediction rate (>80%) in over half (571) of the studied phages, and the ROC value was 0.877 using general models and 0.968 using corresponding morphologic models. It is notable that the median ROC value of 992 complete phages is more than 0.75 even for novel phages, indicating the high accuracy and specificity of the PhageTailFinder. When applied to a dataset containing 189,680 viral genomes derived from 11,810 bulk metagenomic human stool samples, the ROC value was 0.895. In addition, tail protein clusters could be identified for further studies by density-based spatial clustering of applications with the noise algorithm (DBSCAN). The developed PhageTailFinder tool can be accessed either as a web server (http://www.microbiome-bigdata.com/PHISDetector/index/tools/PhageTailFinder) or as a stand-alone program on a standard desktop computer (https://github.com/HIT-ImmunologyLab/PhageTailFinder).}, } @article {pmid36755376, year = {2023}, author = {Roda-Garcia, JJ and Haro-Moreno, JM and Rodriguez-Valera, F and Almagro-Moreno, S and López-Pérez, M}, title = {Single-amplified genomes reveal most streamlined free-living marine bacteria.}, journal = {Environmental microbiology}, volume = {25}, number = {6}, pages = {1136-1154}, doi = {10.1111/1462-2920.16348}, pmid = {36755376}, issn = {1462-2920}, mesh = {Humans ; *Genome, Bacterial/genetics ; *Bacteria/genetics ; Genomics ; Biological Evolution ; Metagenome ; Phylogeny ; }, abstract = {Evolutionary adaptations of prokaryotes to the environment sometimes result in genome reduction. Our knowledge of this phenomenon among free-living bacteria remains scarce. We address the dynamics and limits of genome reduction by examining one of the most abundant bacteria in the ocean, the SAR86 clade. Despite its abundance, comparative genomics has been limited by the absence of pure cultures and the poor representation in metagenome-assembled genomes. We co-assembled multiple previously available single-amplified genomes to obtain the first complete genomes from members of the four families. All families showed a convergent evolutionary trajectory with characteristic features of streamlined genomes, most pronounced in the TMED112 family. This family has a genome size of ca. 1 Mb and only 1 bp as median intergenic distance, exceeding values found in other abundant microbes such as SAR11, OM43 and Prochlorococcus. This genomic simplification led to a reduction in the biosynthesis of essential molecules, DNA repair-related genes, and the ability to sense and respond to environmental factors, which could suggest an evolutionary dependence on other co-occurring microbes for survival (Black Queen hypothesis). Therefore, these reconstructed genomes within the SAR86 clade provide new insights into the limits of genome reduction in free-living marine bacteria.}, } @article {pmid36755207, year = {2023}, author = {Randall, TA and Kurtz, DM}, title = {Assembly of a Draft Genome for the Mouse Ectoparasite Myocoptes musculinus.}, journal = {Journal of the American Association for Laboratory Animal Science : JAALAS}, volume = {62}, number = {1}, pages = {55-63}, pmid = {36755207}, issn = {2769-6677}, mesh = {Animals ; Mice ; *Mite Infestations/diagnosis/veterinary ; *Mites ; Skin ; Polymerase Chain Reaction ; }, abstract = {Myocoptes musculinus is a common ectoparasite of wild mice and is occasionally found on research mice. Infestations of research mice are often subclinical but can cause severe dermatitis. Perhaps more importantly, infestations can cause immunologic reactions that may alter research outcomes, and most animal research facilities strive to prevent or eliminate mites from their mouse colonies. M. musculinus infestations are currently detected by using microscopic evaluation of the fur and skin and PCR assays of pelt swabs targeting the rRNA genes of this mite. In our facility, we encountered multiple, false-positive 18S rRNA PCR results from a closed mouse colony. We could not identify the source of the false positives even after performing PCR analysis of other Myocoptes gene targets using assays developed from the few other target genomic sequences available for M. musculinus or Myocoptes japonensis in public databases. This situation highlighted the limited genetic resources available for development of diagnostic tests specific for this ectoparasite. To expand the available genetic resources, we generated a metagenome of M. musculinus derived by sequencing from fur plucks of an infected mouse. We also determined the completeness of this metagenome and compared it with those of related mites.}, } @article {pmid36752053, year = {2023}, author = {Táncsics, A and Banerjee, S and Soares, A and Bedics, A and Kriszt, B}, title = {Combined Omics Approach Reveals Key Differences between Aerobic and Microaerobic Xylene-Degrading Enrichment Bacterial Communities: Rhodoferax─A Hitherto Unknown Player Emerges from the Microbial Dark Matter.}, journal = {Environmental science & technology}, volume = {57}, number = {7}, pages = {2846-2855}, doi = {10.1021/acs.est.2c09283}, pmid = {36752053}, issn = {1520-5851}, mesh = {Xylenes/analysis/metabolism ; Phylogeny ; *Hydrocarbons, Aromatic/metabolism ; Bacteria/genetics ; *Dioxygenases/genetics/metabolism ; Biodegradation, Environmental ; }, abstract = {Among monoaromatic hydrocarbons, xylenes, especially the ortho and para isomers, are the least biodegradable compounds in oxygen-limited subsurface environments. Although much knowledge has been gained regarding the anaerobic degradation of xylene isomers in the past 2 decades, the diversity of those bacteria which are able to degrade them under microaerobic conditions is still unknown. To overcome this limitation, aerobic and microaerobic xylene-degrading enrichment cultures were established using groundwater taken from a xylene-contaminated site, and the associated bacterial communities were investigated using a polyphasic approach. Our results show that the xylene-degrading bacterial communities were distinctly different between aerobic and microaerobic enrichment conditions. Although members of the genus Pseudomonas were the most dominant in both types of enrichments, the Rhodoferax and Azovibrio lineages were only abundant under microaerobic conditions, while Sphingobium entirely replaced them under aerobic conditions. Analysis of a metagenome-assembled genome of a Rhodoferax-related bacterium revealed aromatic hydrocarbon-degrading ability by identifying two catechol 2,3-dioxygenases in the genome. Moreover, phylogenetic analysis indicated that both enzymes belonged to a newly defined subfamily of type I.2 extradiol dioxygenases (EDOs). Aerobic and microaerobic xylene-degradation experiments were conducted on strains Sphingobium sp. AS12 and Pseudomonas sp. MAP12, isolated from the aerobic and microaerobic enrichments, respectively. The obtained results, together with the whole-genome sequence data of the strains, confirmed the observation that members of the genus Sphingobium are excellent aromatic hydrocarbon degraders but effective only under clear aerobic conditions. Overall, it was concluded that the observed differences between the bacterial communities of aerobic and microaerobic xylene-degrading enrichments were driven primarily by (i) the method of aromatic ring activation (monooxygenation vs dioxygenation), (ii) the type of EDO enzymes, and (iii) the ability of degraders to respire utilizing nitrate.}, } @article {pmid36751856, year = {2023}, author = {Francavilla, A and Ferrero, G and Pardini, B and Tarallo, S and Zanatto, L and Caviglia, GP and Sieri, S and Grioni, S and Francescato, G and Stalla, F and Guiotto, C and Crocella, L and Astegiano, M and Bruno, M and Calvo, PL and Vineis, P and Ribaldone, DG and Naccarati, A}, title = {Gluten-free diet affects fecal small non-coding RNA profiles and microbiome composition in celiac disease supporting a host-gut microbiota crosstalk.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2172955}, pmid = {36751856}, issn = {1949-0984}, mesh = {Adult ; Humans ; Child ; *Celiac Disease/microbiology ; Diet, Gluten-Free ; Glutens/adverse effects ; *Gastrointestinal Microbiome ; *MicroRNAs ; }, abstract = {Current treatment for celiac disease (CD) is adhering to a gluten-free diet (GFD), although its long-term molecular effects are still undescribed. New molecular features detectable in stool may improve and facilitate noninvasive clinical management of CD. For this purpose, fecal small non-coding RNAs (sncRNAs) and gut microbiome profiles were concomitantly explored in CD subjects in relation to strict (or not) GFD adherence over time. In this observational study, we performed small RNA and shotgun metagenomic sequencing in stool from 63 treated CD (tCD) and 3 untreated subjects as well as 66 sex- and age-matched healthy controls. tCD included 51 individuals on strict GFD and with negative transglutaminase (TG) serology (tCD-TG-) and 12 symptomatic with not strict/short-time of GFD adherence and positive TG serology (tCD-TG+). Samples from additional 40 healthy adult individuals and a cohort of 19 untreated pediatric CD subjects and 19 sex/age matched controls were analyzed to further test the outcomes. Several miRNA and microbial profiles were altered in tCD subjects (adj. p < .05). Findings were validated in the external group of adult controls. In tCD-TG-, GFD duration correlated with five miRNA levels (p < .05): for miR-4533-3p and miR-2681-3p, the longer the diet adherence, the less the expression differed from controls. tCD-TG+ and untreated pediatric CD patients showed a similar miRNA dysregulation. Immune-response, trans-membrane transport and cell death pathways were enriched in targets of identified miRNAs. Bifidobacterium longum, Ruminococcus bicirculans, and Haemophilus parainfluenzae abundances shifted (adj. p < .05) with a progressive reduction of denitrification pathways with GFD length. Integrative analysis highlighted 121 miRNA-bacterial relationships (adj. p < .05). Specific molecular patterns in stool characterize CD subjects, reflecting either the long-term GFD effects or the gut inflammatory status, in case of a not strict/short-time adherence. Our findings suggest novel host-microbial interplays and could help the discovery of biomarkers for GFD monitoring over time.}, } @article {pmid36751730, year = {2023}, author = {Nørgaard, JC and Jørgensen, M and Moestrup, KS and Ilett, EE and Zucco, AG and Marandi, RZ and Julian, MN and Paredes, R and Lundgren, JD and Sengeløv, H and MacPherson, C}, title = {Impact of Antibiotic Treatment on the Gut Microbiome and its Resistome in Hematopoietic Stem Cell Transplant Recipients.}, journal = {The Journal of infectious diseases}, volume = {228}, number = {1}, pages = {28-36}, doi = {10.1093/infdis/jiad033}, pmid = {36751730}, issn = {1537-6613}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Anti-Bacterial Agents/adverse effects ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; *Hematopoietic Stem Cell Transplantation/adverse effects ; }, abstract = {Antibiotic-resistant bacterial infections are increasingly an issue in allogenic hematopoietic stem cell transplant patients. How antibiotic treatment impacts antibiotic resistance in the human gut microbiome remains poorly understood in vivo. Here, a total of 577 fecal samples from 233 heavily antibiotic-treated transplant patients were examined using high-resolution prescription data and shotgun metagenomics. The 13 most frequently used antibiotics were significantly associated with 154 (40% of tested associations) microbiome features. Use of broad-spectrum β-lactam antibiotics was most markedly associated with microbial disruption and increase in resistome features. The enterococcal vanA gene was positively associated with 8 of the 13 antibiotics, and in particular piperacillin/tazobactam and vancomycin. Here, we highlight the need for a high-resolution approach in understanding the development of antibiotic resistance in the gut microbiome. Our findings can be used to inform antibiotic stewardship and combat the increasing threat of antibiotic resistance.}, } @article {pmid36749039, year = {2023}, author = {Zang, X and Wang, W and Gu, S and Gu, T and Yang, H and Zheng, E and Xu, Z and Huang, S and Li, Z and Cai, G and Hong, L and Wu, Z}, title = {Interaction between Microbes and Host in Sow Vaginas in Early Pregnancy.}, journal = {mSystems}, volume = {8}, number = {2}, pages = {e0119222}, pmid = {36749039}, issn = {2379-5077}, mesh = {Pregnancy ; Animals ; Female ; Swine ; RNA, Ribosomal, 16S/genetics ; *Vagina/chemistry ; Uterus/chemistry ; *Microbiota/genetics ; Metagenome ; }, abstract = {Extensive research has explored the causes of embryo losses during early pregnancy by analyzing interaction mechanisms in sows' uterus, ignoring the importance of the lower reproductive tract in pregnancy development regulation. Despite recent progress in understanding the diversity of vaginal microbes under different physiological states, the dynamic of sows' vaginal microbiotas during pregnancy and the interaction between vaginal microbes and the host are poorly understood. Here, we performed a comprehensive analysis of sows' vaginal microbial communities in early pregnancy coupled with overall patterns of vaginal mucosal epithelium gene expression. The vaginal microbiota was analyzed by 16s rRNA or metagenome sequencing, and the vaginal mucosal epithelium transcriptome was analyzed by RNA sequencing, followed by integration of the data layers. We found that the sows' vaginal microbiotas in early pregnancy develop dynamically, and there is a homeostasis balance of Firmicutes and Proteobacteria. Subsequently, we identified two pregnancy-specific communities, which play diverse roles. The microbes in the vagina stimulate the epithelial cells, while vaginal epithelium changes its structure and functions in response to stimulation. These changes produce specific inflammation responses to promote pregnancy development. Our findings demonstrate the interaction between microbes and host in the sow vagina in early pregnancy to promote pregnancy development, meanwhile providing a reference data set for the study of targeted therapies of microbial homeostasis dysregulation in the female reproductive tract. IMPORTANCE This work sheds light on the dynamics of the sow vaginal microbiotas in early pregnancy and its roles in pregnancy development. Furthermore, this study provides insight into the functional mechanisms of reproductive tract microbes by outlining vaginal microbe-host interactions, which might identify new research and intervention targets for improving pregnancy development by modulating lower reproductive tract microbiota.}, } @article {pmid36748614, year = {2022}, author = {Durán-Manuel, EM and Loyola-Cruz, MÁ and Cruz-Cruz, C and Ibáñez-Cervantes, G and Gaytán-Cervantes, J and González-Torres, C and Quiroga-Vargas, E and Calzada-Mendoza, CC and Cureño-Díaz, MA and Fernández-Sánchez, V and Castro-Escarpulli, G and Bello-López, JM}, title = {Massive sequencing of the V3-V4 hypervariable region of bronchoalveolar lavage from patients with COVID-19 and VAP reveals the collapse of the pulmonary microbiota.}, journal = {Journal of medical microbiology}, volume = {71}, number = {12}, pages = {}, doi = {10.1099/jmm.0.001634}, pmid = {36748614}, issn = {1473-5644}, mesh = {Humans ; *Pneumonia, Ventilator-Associated/diagnosis/epidemiology ; Anti-Bacterial Agents/therapeutic use ; *COVID-19/diagnosis ; SARS-CoV-2/genetics ; Bronchoalveolar Lavage ; Bacteria/genetics ; *Cross Infection/drug therapy ; *Microbiota ; Intensive Care Units ; }, abstract = {Background. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic is a predisposing factor for the development of healthcare-associated infections, of which ventilator-associated pneumonia (VAP) is one.Hypothesis. VAP is caused by ESKAPE bacteria and other pathogens not detected by microbiological culture.Aim. To elucidate the bacterial pathogens of severe coronavirus disease 2019 (COVID-19) and VAP patients by massive sequencing and to predict their degree of relationship with the age and sex of the patients.Methods. Analysis of ribosomal libraries of the V3-V4 hypervariable region obtained by Illumina sequencing of bronchoalveolar lavages from COVID-19 and VAP (first wave) patients from Hospital Juárez de México.Results. Acinetobacter and Pseudomonas were the main bacterial genera in the bronchoalveolar lavages (BALs) analysed. Other members of the ESKAPE group, such as Enterococcus and Klebsiella, were also identified. Taxonomic composition per patient showed that non-ESKAPE genera were present with significant relative abundances, such as Prevotella, Stenotrophomas, Enterococcus, Mycoplasma, Serratia and Corynebacterium. Kruskal-Wallis analysis proved that VAP acquisition is an adverse event that is not influenced by the sex and age of COVID-19 patients.Discussion. Metagenomic findings in COVID-19/VAP patients highlight the importance of implementing comprehensive microbiological diagnostics by including alternative tools for the detection of the causal agents of healthcare-associated infections (HAIs).Conclusions. Timely identification of bacteria 'not sought' in diagnostic bacteriology laboratories will allow specific and targeted treatments. Implications for the restricted diagnosis of VAP causative agents in COVID-19 patients and the presence of pathogens not detected by classical microbiology are analysed and discussed.}, } @article {pmid36748598, year = {2022}, author = {Berckx, F and Bandong, CM and Wibberg, D and Kalinowski, J and Willemse, J and Brachmann, A and Simbahan, J and Pawlowski, K}, title = {Streptomyces coriariae sp. nov., a novel streptomycete isolated from actinorhizal nodules of Coriaria intermedia.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {12}, pages = {}, doi = {10.1099/ijsem.0.005603}, pmid = {36748598}, issn = {1466-5034}, mesh = {*Fatty Acids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Base Composition ; Philippines ; *Streptomyces ; Phospholipids/chemistry ; Vitamin K 2/chemistry ; }, abstract = {An actinobacterial strain, CMB-FB, was isolated from surface-sterilized root nodules of a Coriaria intermedia plant growing along Halsema Highway in the province of Benguet (Luzon, Philippines). The 16S rRNA gene sequence of CMB-FB showed high sequence similarity to those of the type strains of Streptomyces rishiriensis (99.4 %), Streptomyces humidus (99.1 %), Streptomyces cacaoi subsp. asoensis (99.0 %), and Streptomyces phaeofaciens (98.6 %). The major menaquinones of CMB-FB were composed of MK-9(H4), MK-9(H6) and MK-9(H8), and there was a minor contribution of MK-9(H10). The polar lipid profile consisted of phosphatidylethanolamine, unidentified aminolipids and phospholipids, a glycophospholipid and four unidentified lipids. The diagnostic diamino acid of the peptidoglycan was meso-diaminopimelic acid. The major fatty acids were iso-C16 : 0, anteiso-C15 : 0 and anteiso-C17 : 0. The results of physiological analysis indicated that CMB-FB was mesophilic. The results of phylogenetic, genome-genome distance calculation and average nucleotide identity analysis indicated that the isolated strain represents the type strain of a novel species. On the basis of these results, strain CMB-FB (=DSM 112754[T]=LMG 32457[T]) is proposed as the type strain of the novel species Streptomyces coriariae sp. nov.}, } @article {pmid36748565, year = {2022}, author = {Ghosh, A and Saha, S}, title = {Meta-analysis of sputum microbiome studies identifies airway disease-specific taxonomic and functional signatures.}, journal = {Journal of medical microbiology}, volume = {72}, number = {12}, pages = {}, doi = {10.1099/jmm.0.001617}, pmid = {36748565}, issn = {1473-5644}, mesh = {Humans ; *Cystic Fibrosis/microbiology ; Sputum/microbiology ; *Microbiota/genetics ; *Pulmonary Disease, Chronic Obstructive/microbiology ; *Bronchiectasis/microbiology ; *Asthma/microbiology ; }, abstract = {Introduction. Studying taxonomic and functional signatures of respiratory microbiomes provide a better understanding of airway diseases.Gap Statement. Several human airway metagenomics studies have identified taxonomic and functional features restricted to a single disease condition and the findings are not comparable across airway diseases due to use of different samples, NGS platforms, and bioinformatics databases and tools.Aim. To study the microbial taxonomic and functional components of sputum microbiome across airway diseases and healthy smokers.Methodology. Here, 57 whole metagenome shotgun sequencing (WMSS) runs coming from the sputum of five airway diseases: asthma, bronchiectasis, chronic obstructive pulmonary diseases (COPD), cystic fibrosis (CF), tuberculosis (TB), and healthy smokers as the control were reanalysed using a common WMSS analysis pipeline.Results. Shannon's index (alpha diversity) of the healthy smoker group was the highest among all. The beta diversity showed that the sputum microbiome is distinct in major airway diseases such as asthma, COPD and cystic fibrosis. The microbial composition based on differential analysis showed that there are specific markers for each airway disease like Acinetobacter bereziniae as a marker for COPD and Achromobacter xylosoxidans as a marker of cystic fibrosis. Pathways and metabolites identified from the sputum microbiome of these five diseases and healthy smokers also show specific markers. 'ppGpp biosynthesis' and 'purine ribonucleosides degradation' pathways were identified as differential markers for bronchiectasis and COPD. In this meta-analysis, besides bacteria kingdom, Aspergillus fumigatus was detected in asthma and COPD, and Roseolovirus human betaherpesvirus 7 was detected in COPD. Our analysis showed that the majority of the gene families specific to the drug-resistant associated genes were detected from opportunistic pathogens across all the groups.Conclusion. In summary, the specific species in the sputum of airway diseases along with the microbial features like specific gene families, pathways, and metabolites were identified which can be explored for better diagnosis and therapy.}, } @article {pmid36748564, year = {2023}, author = {Colombi, E and Hill, Y and Lines, R and Sullivan, JT and Kohlmeier, MG and Christophersen, CT and Ronson, CW and Terpolilli, JJ and Ramsay, JP}, title = {Population genomics of Australian indigenous Mesorhizobium reveals diverse nonsymbiotic genospecies capable of nitrogen-fixing symbioses following horizontal gene transfer.}, journal = {Microbial genomics}, volume = {9}, number = {1}, pages = {}, pmid = {36748564}, issn = {2057-5858}, mesh = {Gene Transfer, Horizontal ; *Mesorhizobium/genetics ; Symbiosis/genetics ; Metagenomics ; Nitrogen ; Australia ; *Lotus/microbiology ; Soil ; }, abstract = {Mesorhizobia are soil bacteria that establish nitrogen-fixing symbioses with various legumes. Novel symbiotic mesorhizobia frequently evolve following horizontal transfer of symbiosis-gene-carrying integrative and conjugative elements (ICESyms) to indigenous mesorhizobia in soils. Evolved symbionts exhibit a wide range in symbiotic effectiveness, with some fixing nitrogen poorly or not at all. Little is known about the genetic diversity and symbiotic potential of indigenous soil mesorhizobia prior to ICESym acquisition. Here we sequenced genomes of 144 Mesorhizobium spp. strains cultured directly from cultivated and uncultivated Australian soils. Of these, 126 lacked symbiosis genes. The only isolated symbiotic strains were either exotic strains used previously as legume inoculants, or indigenous mesorhizobia that had acquired exotic ICESyms. No native symbiotic strains were identified. Indigenous nonsymbiotic strains formed 22 genospecies with phylogenomic diversity overlapping the diversity of internationally isolated symbiotic Mesorhizobium spp. The genomes of indigenous mesorhizobia exhibited no evidence of prior involvement in nitrogen-fixing symbiosis, yet their core genomes were similar to symbiotic strains and they generally lacked genes for synthesis of biotin, nicotinate and thiamine. Genomes of nonsymbiotic mesorhizobia harboured similar mobile elements to those of symbiotic mesorhizobia, including ICESym-like elements carrying aforementioned vitamin-synthesis genes but lacking symbiosis genes. Diverse indigenous isolates receiving ICESyms through horizontal gene transfer formed effective symbioses with Lotus and Biserrula legumes, indicating most nonsymbiotic mesorhizobia have an innate capacity for nitrogen-fixing symbiosis following ICESym acquisition. Non-fixing ICESym-harbouring strains were isolated sporadically within species alongside effective symbionts, indicating chromosomal lineage does not predict symbiotic potential. Our observations suggest previously observed genomic diversity amongst symbiotic Mesorhizobium spp. represents a fraction of the extant diversity of nonsymbiotic strains. The overlapping phylogeny of symbiotic and nonsymbiotic clades suggests major clades of Mesorhizobium diverged prior to introduction of symbiosis genes and therefore chromosomal genes involved in symbiosis have evolved largely independent of nitrogen-fixing symbiosis.}, } @article {pmid36748549, year = {2023}, author = {Soares, A and Edwards, A and An, D and Bagnoud, A and Bradley, J and Barnhart, E and Bomberg, M and Budwill, K and Caffrey, SM and Fields, M and Gralnick, J and Kadnikov, V and Momper, L and Osburn, M and Mu, A and Moreau, JW and Moser, D and Purkamo, L and Rassner, SM and Sheik, CS and Sherwood Lollar, B and Toner, BM and Voordouw, G and Wouters, K and Mitchell, AC}, title = {A global perspective on bacterial diversity in the terrestrial deep subsurface.}, journal = {Microbiology (Reading, England)}, volume = {169}, number = {1}, pages = {}, pmid = {36748549}, issn = {1465-2080}, mesh = {Water Microbiology ; Bacteria/genetics ; *Microbiota/genetics ; Biomass ; Metagenomics ; *Gammaproteobacteria ; RNA, Ribosomal, 16S ; }, abstract = {While recent efforts to catalogue Earth's microbial diversity have focused upon surface and marine habitats, 12-20 % of Earth's biomass is suggested to exist in the terrestrial deep subsurface, compared to ~1.8 % in the deep subseafloor. Metagenomic studies of the terrestrial deep subsurface have yielded a trove of divergent and functionally important microbiomes from a range of localities. However, a wider perspective of microbial diversity and its relationship to environmental conditions within the terrestrial deep subsurface is still required. Our meta-analysis reveals that terrestrial deep subsurface microbiota are dominated by Betaproteobacteria, Gammaproteobacteria and Firmicutes, probably as a function of the diverse metabolic strategies of these taxa. Evidence was also found for a common small consortium of prevalent Betaproteobacteria and Gammaproteobacteria operational taxonomic units across the localities. This implies a core terrestrial deep subsurface community, irrespective of aquifer lithology, depth and other variables, that may play an important role in colonizing and sustaining microbial habitats in the deep terrestrial subsurface. An in silico contamination-aware approach to analysing this dataset underscores the importance of downstream methods for assuring that robust conclusions can be reached from deep subsurface-derived sequencing data. Understanding the global panorama of microbial diversity and ecological dynamics in the deep terrestrial subsurface provides a first step towards understanding the role of microbes in global subsurface element and nutrient cycling.}, } @article {pmid36748547, year = {2022}, author = {Stebliankin, V and Sazal, M and Valdes, C and Mathee, K and Narasimhan, G}, title = {A novel approach for combining the metagenome, metaresistome, metareplicome and causal inference to determine the microbes and their antibiotic resistance gene repertoire that contribute to dysbiosis.}, journal = {Microbial genomics}, volume = {8}, number = {12}, pages = {}, pmid = {36748547}, issn = {2057-5858}, support = {R15 AI128714/AI/NIAID NIH HHS/United States ; }, mesh = {Infant ; Infant, Newborn ; Humans ; *Metagenome ; *Infant, Premature ; Anti-Bacterial Agents/pharmacology ; Dysbiosis ; Bayes Theorem ; Bacteria ; Drug Resistance, Bacterial/genetics ; }, abstract = {The use of whole metagenomic data to infer the relative abundance of all its microbes is well established. The same data can be used to determine the replication rate of all eubacterial taxa with circular chromosomes. Despite their availability, the replication rate profiles (metareplicome) have not been fully exploited in microbiome analyses. Another relatively new approach is the application of causal inferencing to analyse microbiome data that goes beyond correlational studies. A novel scalable pipeline called MeRRCI (Metagenome, metaResistome, and metaReplicome for Causal Inferencing) was developed. MeRRCI combines efficient computation of the metagenome (bacterial relative abundance), metaresistome (antimicrobial gene abundance) and metareplicome (replication rates), and integrates environmental variables (metadata) for causality analysis using Bayesian networks. MeRRCI was applied to an infant gut microbiome data set to investigate the microbial community's response to antibiotics. Our analysis suggests that the current treatment stratagem contributes to preterm infant gut dysbiosis, allowing a proliferation of pathobionts. The study highlights the specific antibacterial resistance genes that may contribute to exponential cell division in the presence of antibiotics for various pathogens, namely Klebsiella pneumoniae, Citrobacter freundii, Staphylococcus epidermidis, Veilonella parvula and Clostridium perfringens. These organisms often contribute to the harmful long-term sequelae seen in these young infants.}, } @article {pmid36748522, year = {2022}, author = {Cunningham-Oakes, E and Pointon, T and Murphy, B and Campbell-Lee, S and Connor, TR and Mahenthiralingam, E}, title = {Novel application of metagenomics for the strain-level detection of bacterial contaminants within non-sterile industrial products - a retrospective, real-time analysis.}, journal = {Microbial genomics}, volume = {8}, number = {11}, pages = {}, pmid = {36748522}, issn = {2057-5858}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BB/M009122/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Retrospective Studies ; *Bacteria/genetics ; *Metagenome ; Metagenomics/methods ; Workflow ; }, abstract = {The home and personal care (HPC) industry generally relies on initial cultivation and subsequent biochemical testing for the identification of microorganisms in contaminated products. This process is slow (several days for growth), labour intensive, and misses organisms which fail to revive from the harsh environment of preserved consumer products. Since manufacturing within the HPC industry is high-throughput, the process of identification of microbial contamination could benefit from the multiple cultivation-independent methodologies that have developed for the detection and analysis of microbes. We describe a novel workflow starting with automated DNA extraction directly from a HPC product, and subsequently applying metagenomic methodologies for species and strain-level identification of bacteria. The workflow was validated by application to a historic microbial contamination of a general-purpose cleaner (GPC). A single strain of Pseudomonas oleovorans was detected metagenomically within the product. The metagenome mirrored that of a contaminant isolated in parallel by a traditional cultivation-based approach. Using a dilution series of the incident sample, we also provide evidence to show that the workflow enables detection of contaminant organisms down to 100 CFU/ml of product. To our knowledge, this is the first validated example of metagenomics analysis providing confirmatory evidence of a traditionally isolated contaminant organism, in a HPC product.}, } @article {pmid36748452, year = {2022}, author = {Harris, KA and Brown, JR}, title = {Diagnostic yield of broad-range 16s rRNA gene PCR varies by sample type and is improved by the addition of qPCR panels targeting the most common causative organisms.}, journal = {Journal of medical microbiology}, volume = {71}, number = {12}, pages = {}, doi = {10.1099/jmm.0.001633}, pmid = {36748452}, issn = {1473-5644}, mesh = {Humans ; *Bacteria/genetics ; DNA, Bacterial/genetics/analysis ; Genes, rRNA ; Polymerase Chain Reaction/methods ; Retrospective Studies ; RNA, Ribosomal, 16S/genetics ; *Bacterial Infections/diagnosis ; }, abstract = {Introduction. Molecular techniques are used in the clinical microbiology laboratory to support culture-based diagnosis of infection and are particularly useful for detecting difficult to culture bacteria or following empirical antimicrobial treatment.Hypothesis/Gap Statement. Broad-range 16S rRNA PCR is a valuable tool that detects a wide range of bacterial species. Diagnostic yield is low for some sample types but can be improved with the addition of qPCR panels targeting common bacterial pathogens.Aim. To evaluate the performance of a broad-range 16S rRNA gene PCR and the additional diagnostic yield of targeted qPCR applied to specimens according to a local testing algorithm.Methodology. In total, 6130 primary clinical samples were collected as part of standard clinical practice from patients with suspected infection during a 17 month period. Overall, 5497 samples were tested by broad-range 16S rRNA gene PCR and a panel of targeted real-time qPCR assays were performed on selected samples according to a local testing algorithm. An additional 633 samples were tested by real-time qPCR only. The 16S rRNA gene PCR was performed using two assays targeting different regions of the 16S rRNA gene. Laboratory developed qPCR assays for seven common bacterial pathogens were also performed. Data was extracted retrospectively from Epic Beaker Laboratory Information Management System (LIMS).Results. Broad-range 16S rRNA gene PCR improves diagnostic yield in culture-negative samples and detects a large range of bacterial species. Streptococcus spp., Staphylococcus spp. and the Enterobacteriaceae family are detected the most frequently in samples with a single causative organism, but mixed samples frequently contained anaerobic species. The highest diagnostic yield was obtained from abscess, pus and empyema samples; 44.9 % were positive by 16S and 61 % were positive by the combined 16S and targeted qPCR testing algorithm. Samples with a particularly low diagnostic yield were blood, with 3.3 % of samples positive by 16S and CSF with 4.8 % of samples positive by 16S. The increased diagnostic yield of adding targeted qPCR is largest (~threefold) in these two sample types.Conclusion. Broad-range PCR is a powerful technique that can detect a very large range of bacterial pathogens but has limited diagnostic sensitivity. The data in this report supports a testing strategy that combines broad-range and targeted bacterial PCR assays for maximizing diagnosis of infection in culture-negative specimens. This is particularly justified for blood and CSF samples. Alternative approaches, such as metagenomic sequencing, are needed to provide the breadth of broad-range PCR and the sensitivity of targeted qPCR panels.}, } @article {pmid36748417, year = {2022}, author = {Jaudou, S and Deneke, C and Tran, ML and Schuh, E and Goehler, A and Vorimore, F and Malorny, B and Fach, P and Grützke, J and Delannoy, S}, title = {A step forward for Shiga toxin-producing Escherichia coli identification and characterization in raw milk using long-read metagenomics.}, journal = {Microbial genomics}, volume = {8}, number = {11}, pages = {}, pmid = {36748417}, issn = {2057-5858}, mesh = {Animals ; Food Microbiology ; *Milk/microbiology ; Real-Time Polymerase Chain Reaction ; Shiga Toxin/genetics ; *Shiga-Toxigenic Escherichia coli/isolation & purification ; }, abstract = {Shiga toxin-producing Escherichia coli (STEC) are a cause of severe human illness and are frequently associated with haemolytic uraemic syndrome (HUS) in children. It remains difficult to identify virulence factors for STEC that absolutely predict the potential to cause human disease. In addition to the Shiga-toxin (stx genes), many additional factors have been reported, such as intimin (eae gene), which is clearly an aggravating factor for developing HUS. Current STEC detection methods classically rely on real-time PCR (qPCR) to detect the presence of the key virulence markers (stx and eae). Although qPCR gives an insight into the presence of these virulence markers, it is not appropriate for confirming their presence in the same strain. Therefore, isolation steps are necessary to confirm STEC viability and characterize STEC genomes. While STEC isolation is laborious and time-consuming, metagenomics has the potential to accelerate the STEC characterization process in an isolation-free manner. Recently, short-read sequencing metagenomics have been applied for this purpose, but assembly quality and contiguity suffer from the high proportion of mobile genetic elements occurring in STEC strains. To circumvent this problem, we used long-read sequencing metagenomics for identifying eae-positive STEC strains using raw cow's milk as a causative matrix for STEC food-borne outbreaks. By comparing enrichment conditions, optimizing library preparation for MinION sequencing and generating an easy-to-use STEC characterization pipeline, the direct identification of an eae-positive STEC strain was successful after enrichment of artificially contaminated raw cow's milk samples at a contamination level as low as 5 c.f.u. ml[-1]. Our newly developed method combines optimized enrichment conditions of STEC in raw milk in combination with a complete STEC analysis pipeline from long-read sequencing metagenomics data. This study shows the potential of the innovative methodology for characterizing STEC strains from complex matrices. Further developments will nonetheless be necessary for this method to be applied in STEC surveillance.}, } @article {pmid36747985, year = {2023}, author = {Green, GBH and DePaola, A and Linville, JG and Morrow, CD and Bej, AK}, title = {High-throughput amplicon sequencing datasets of coastal sediments from three locations of the Gulf of Mexico, USA.}, journal = {Data in brief}, volume = {47}, number = {}, pages = {108895}, pmid = {36747985}, issn = {2352-3409}, abstract = {We present high-throughput amplicon sequence (HTS) datasets of the purified microbial metacommunity DNA of coastal surface sediments from Portersville Bay (PVB) (n = 3), Bayou La Batre (BLB) (n = 3), and Mobile Bay (MOB) (n = 3) of the U.S. Gulf of Mexico (U.S. Gulf Coast). The PVB samples were collected from the oyster aquaculture Shellevator™ system; the BLB samples were from locations on the shoreline adjacent to wild oysters attached to rocks and likely polluted from sewage and possibly chemical contamination from boats, shipyards, and seafood processing facilities; and MOB samples were adjacent to aquaculture oysters in bottom cages. The amplicons of the V4 hypervariable segment of the 16S rRNA gene from each sample were sequenced on an Illumina MiSeq to generate these HTS datasets. The raw sequences were quality-checked, demultiplexed into FASTQ files, denoised using DADA2, and subsampled. Then, the FASTA formatted sequences were assigned the taxonomic ids to amplicon sequence variants (ASVs) against the silva-138-99-nb-classifier using the Quantitative Insights Into Microbial Ecology (QIIME2 v2022.2). The applicability of the HTS datasets was confirmed by microbial taxa analysis at the phylum level using the "qiime taxa collapse" command. All HTS datasets are available through the BioSample Submission Portal under the BioProject ID PRJNA876773 (https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA876773).}, } @article {pmid36747826, year = {2023}, author = {Ustick, LJ and Larkin, AA and Martiny, AC}, title = {Global scale phylogeography of functional traits and microdiversity in Prochlorococcus.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.01.24.525399}, pmid = {36747826}, abstract = {Prochlorococcus is the most numerically abundant photosynthetic organism in the surface ocean. The Prochlorococcus high-light and warm-water adapted ecotype (HLII) is comprised of extensive microdiversity, but specific functional differences between microdiverse sub-clades remain elusive. Here we characterized both functional and phylogenetic diversity within the HLII ecotype using Bio-GO-SHIP metagenomes. We found widespread variation in gene frequency connected to local environmental conditions. Metagenomically assembled marker genes and genomes revealed a globally distributed novel HLII haplotype defined by adaptation to chronically low P conditions (HLII-P). Environmental correlation analysis revealed different factors were driving gene abundances verses phylogenetic differences. An analysis of cultured HLII genomes and metagenomically assembled genomes revealed a subclade within HLII, which corresponded to the novel HLII-P haplotype. This work represents the first global assessment of the HLII ecotype’s phylogeography and corresponding functional differences. These findings together expand our understanding of how microdiversity structures functional differences and reveals the importance of nutrients as drivers of microdiversity in Prochlorococcus .}, } @article {pmid36747681, year = {2023}, author = {Spencer, BL and Job, AM and Robertson, CM and Hameed, ZA and Serchejian, C and Wiafe-Kwakye, CS and Mendonça, JC and Apolonio, MA and Nagao, PE and Neely, MN and Korotkova, N and Korotkov, KV and Patras, KA and Doran, KS}, title = {Heterogeneity of the group B streptococcal type VII secretion system and influence on colonization of the female genital tract.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36747681}, abstract = {Type VIIb secretion systems (T7SSb) in Gram-positive bacteria facilitate physiology, interbacterial competition, and/or virulence via EssC ATPase-driven secretion of small ɑ-helical proteins and toxins. Recently, we characterized T7SSb in group B Streptococcus (GBS), a leading cause of infection in newborns and immunocompromised adults. GBS T7SS comprises four subtypes based on variation in the C-terminus of EssC and the repertoire of downstream effectors; however, the intra-species diversity of GBS T7SS and impact on GBS-host interactions remains unknown. Bioinformatic analysis indicates that GBS T7SS loci encode subtype-specific putative effectors, which have low inter-species and inter-subtype homology but contain similar domains/motifs and therefore may serve similar functions. We further identify orphaned GBS WXG100 proteins. Functionally, we show that GBS T7SS subtype I and III strains secrete EsxA in vitro and that in subtype I strain CJB111, esxA1 appears to be differentially transcribed from the T7SS operon. Further, we observe subtype-specific effects of GBS T7SS on host colonization, as subtype I but not subtype III T7SS promotes GBS vaginal persistence. Finally, we observe that T7SS subtypes I and II are the predominant subtypes in clinical GBS isolates. This study highlights the potential impact of T7SS heterogeneity on host-GBS interactions.}, } @article {pmid36747166, year = {2023}, author = {Sarhan, MS and Wurst, C and Tzankov, A and Bircher, AJ and Wittig, H and Briellmann, T and Augsburger, M and Hotz, G and Zink, A and Maixner, F}, title = {A nontuberculous mycobacterium could solve the mystery of the lady from the Franciscan church in Basel, Switzerland.}, journal = {BMC biology}, volume = {21}, number = {1}, pages = {9}, pmid = {36747166}, issn = {1741-7007}, mesh = {Humans ; Female ; Aged ; Nontuberculous Mycobacteria/genetics ; *Mycobacterium Infections, Nontuberculous/diagnosis/epidemiology/microbiology ; Switzerland ; *Syphilis ; Virulence ; }, abstract = {BACKGROUND: In 1975, the mummified body of a female has been found in the Franciscan church in Basel, Switzerland. Molecular and genealogic analyses unveiled her identity as Anna Catharina Bischoff (ACB), a member of the upper class of post-reformed Basel, who died at the age of 68 years, in 1787. The reason behind her death is still a mystery, especially that toxicological analyses revealed high levels of mercury, a common treatment against infections at that time, in different body organs. The computed tomography (CT) and histological analysis showed bone lesions in the femurs, the rib cage, and the skull, which refers to a potential syphilis case.

RESULTS: Although we could not detect any molecular signs of the syphilis-causing pathogen Treponema pallidum subsp. pallidum, we realized high prevalence of a nontuberculous mycobacterium (NTM) species in brain tissue sample. The genome analysis of this NTM displayed richness of virulence genes and toxins, and similarity to other infectious NTM, known to infect immunocompromised patients. In addition, it displayed potential resistance to mercury compounds, which might indicate a selective advantage against the applied treatment. This suggests that ACB might have suffered from an atypical mycobacteriosis during her life, which could explain the mummy's bone lesion and high mercury concentrations.

CONCLUSIONS: The study of this mummy exemplifies the importance of employing differential diagnostic approaches in paleopathological analysis, by combining classical anthropological, radiological, histological, and toxicological observations with molecular analysis. It represents a proof-of-concept for the discovery of not-yet-described ancient pathogens in well-preserved specimens, using de novo metagenomic assembly.}, } @article {pmid36747116, year = {2023}, author = {Lappan, R and Shelley, G and Islam, ZF and Leung, PM and Lockwood, S and Nauer, PA and Jirapanjawat, T and Ni, G and Chen, YJ and Kessler, AJ and Williams, TJ and Cavicchioli, R and Baltar, F and Cook, PLM and Morales, SE and Greening, C}, title = {Molecular hydrogen in seawater supports growth of diverse marine bacteria.}, journal = {Nature microbiology}, volume = {8}, number = {4}, pages = {581-595}, pmid = {36747116}, issn = {2058-5276}, mesh = {*Bacteria/genetics ; *Seawater/microbiology ; Hydrogen ; Oxidation-Reduction ; Oceans and Seas ; }, abstract = {Molecular hydrogen (H2) is an abundant and readily accessible energy source in marine systems, but it remains unknown whether marine microbial communities consume this gas. Here we use a suite of approaches to show that marine bacteria consume H2 to support growth. Genes for H2-uptake hydrogenases are prevalent in global ocean metagenomes, highly expressed in metatranscriptomes and found across eight bacterial phyla. Capacity for H2 oxidation increases with depth and decreases with oxygen concentration, suggesting that H2 is important in environments with low primary production. Biogeochemical measurements of tropical, temperate and subantarctic waters, and axenic cultures show that marine microbes consume H2 supplied at environmentally relevant concentrations, yielding enough cell-specific power to support growth in bacteria with low energy requirements. Conversely, our results indicate that oxidation of carbon monoxide (CO) primarily supports survival. Altogether, H2 is a notable energy source for marine bacteria and may influence oceanic ecology and biogeochemistry.}, } @article {pmid36747011, year = {2023}, author = {Meng, Q and Chandak, S and Zhu, Y and Weissman, T}, title = {Reference-free lossless compression of nanopore sequencing reads using an approximate assembly approach.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {2082}, pmid = {36747011}, issn = {2045-2322}, mesh = {Humans ; Algorithms ; *Nanopore Sequencing ; High-Throughput Nucleotide Sequencing ; *Data Compression ; Software ; Genome, Human ; Sequence Analysis, DNA ; }, abstract = {The amount of data produced by genome sequencing experiments has been growing rapidly over the past several years, making compression important for efficient storage, transfer and analysis of the data. In recent years, nanopore sequencing technologies have seen increasing adoption since they are portable, real-time and provide long reads. However, there has been limited progress on compression of nanopore sequencing reads obtained in FASTQ files since most existing tools are either general-purpose or specialized for short read data. We present NanoSpring, a reference-free compressor for nanopore sequencing reads, relying on an approximate assembly approach. We evaluate NanoSpring on a variety of datasets including bacterial, metagenomic, plant, animal, and human whole genome data. For recently basecalled high quality nanopore datasets, NanoSpring, which focuses only on the base sequences in the FASTQ file, uses just 0.35-0.65 bits per base which is 3-6[Formula: see text] lower than general purpose compressors like gzip. NanoSpring is competitive in compression ratio and compression resource usage with the state-of-the-art tool CoLoRd while being significantly faster at decompression when using multiple threads (> 4[Formula: see text] faster decompression with 20 threads). NanoSpring is available on GitHub at https://github.com/qm2/NanoSpring .}, } @article {pmid36746960, year = {2023}, author = {Geller-McGrath, D and Mara, P and Taylor, GT and Suter, E and Edgcomb, V and Pachiadaki, M}, title = {Diverse secondary metabolites are expressed in particle-associated and free-living microorganisms of the permanently anoxic Cariaco Basin.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {656}, pmid = {36746960}, issn = {2041-1723}, mesh = {*Seawater/microbiology ; Bacteria/metabolism ; Metagenome ; *Microbiota/genetics ; Water/metabolism ; }, abstract = {Secondary metabolites play essential roles in ecological interactions and nutrient acquisition, and are of interest for their potential uses in medicine and biotechnology. Genome mining for biosynthetic gene clusters (BGCs) can be used for the discovery of new compounds. Here, we use metagenomics and metatranscriptomics to analyze BGCs in free-living and particle-associated microbial communities through the stratified water column of the Cariaco Basin, Venezuela. We recovered 565 bacterial and archaeal metagenome-assembled genomes (MAGs) and identified 1154 diverse BGCs. We show that differences in water redox potential and microbial lifestyle (particle-associated vs. free-living) are associated with variations in the predicted composition and production of secondary metabolites. Our results indicate that microbes, including understudied clades such as Planctomycetota, potentially produce a wide range of secondary metabolites in these anoxic/euxinic waters.}, } @article {pmid36746864, year = {2023}, author = {Zheng, M and Ou, H and Dong, F and He, C and Hu, Z and Wang, W}, title = {Mechanism insights into enhanced treatment of wasted activated sludge by hydrogen-mediated anaerobic digestion.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {16}, pages = {47787-47799}, pmid = {36746864}, issn = {1614-7499}, support = {51878232//National Natural Science Foundation of China/ ; 2019YFC0408502//Project of National Key Research and development Program of China/ ; PA2021KCPY0029//Fundamental Research Funds for the Central Universities/ ; JZ2022HGTA0337//Fundamental Research Funds for the Central Universities/ ; JZ2022HGQA0170//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Anaerobiosis ; *Bioreactors ; *Sewage/microbiology ; Hydrogen/metabolism ; Carbon Dioxide ; Methane/metabolism ; }, abstract = {In the current study, different forms of added gas including H2, CO2, and mixed gas (VH2:VCO2 = 4:1), as well as different hydrogen partial pressures (0.10, 0.30, and 0.50 atm) were investigated for the influence on anaerobic performance in waste activated sludge (WAS) treatment. The mixed gas significantly improved methane production by over 20%, which positively correlated with the hydrogen partial pressure. However, pure H2 (0.5 atm) heavily inhibited methane production by 76.5%. Combined with the microbial metabolic activity study, H2 accelerated the hydrolysis process. Afterward, mixing with CO2 accelerated H2 and organic consumption, thus promoting WAS degradation and methane production. Based on the most extra release of organics, the mixed group exerted the superior performance with hydrogen partial pressure at 0.3 atm. The microbial community analysis evidenced that mixed gas enriched proteolytic and homoacetogenic bacteria and hybrid-trophic methanogens. By metagenomics study, hydrolysis, acetogenic, and methanogenesis pathways were all enhanced via the exogenous addition of H2 and CO2, sustainably transforming WAS towards CH4. This study discovered the mechanism of the enhanced conversion from WAS to CH4 by exogenous H2 and provided a promising approach for WAS reduction and energy recovery.}, } @article {pmid36746446, year = {2023}, author = {Wu, HZ and Zhang, X and Cheng, XG and Yu, Q}, title = {[Saliva microbiota and metabolite in individuals with caries or periodontitis].}, journal = {Zhonghua kou qiang yi xue za zhi = Zhonghua kouqiang yixue zazhi = Chinese journal of stomatology}, volume = {58}, number = {2}, pages = {131-142}, doi = {10.3760/cma.j.cn112144-20220829-00464}, pmid = {36746446}, issn = {1002-0098}, support = {82170937, 81870751//National Natural Science Foundation of China/ ; 2022KJXX‑101//Shaanxi Natural Science Basic Research Plan (Innovative Talent Promotion Plan) Youth Science and Technology Star Program/ ; 2021JQ‑353//Shaanxi Natural Science Basic Research Plan Youth Program/ ; 2020cyjhcxg//Air Force Military Medical University Lingyun Project Young Eagle Plan/ ; 2022KJXX-101//Shaanxi Innovation Capability Support Plan/ ; 2021JQ-353//Shaanxi Natural Science Basic Research Plan/ ; 2020cyjhcxg//Air Force Military Medical University Talent Support "Lingyun Project" Plan/ ; }, mesh = {Humans ; Saliva/microbiology ; Dental Caries Susceptibility ; *Periodontitis/microbiology ; *Microbiota/genetics ; Porphyromonas gingivalis/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Objective: To detect and analyze the characteristics of oral microbiota in species composition, function and metabolism among caries, periodontitis and oral healthy individuals, hunting for the microbiome-derived biomarkers with specificity and sensitivity to estimate the occurrence of these two diseases. Methods: Saliva samples were collected from 10 patients with high caries risk [decayed-missing-filled teeth (DMFT)≥6, HC group] in Department of Endodontics, 10 patients with periodontitis of grade Ⅱ A-Ⅲ C (PG group) in Department of Periodontology and 10 oral healthy individuals (HH group) from School of Stomatology, The Fourth Military Medical University during from March 2022 to June 2022. A baseline examination was conducted on all participants, including their oral conditions of caries and periodontal health. Metagenomic sequencing (Illumina PE150 platform) and liquid chromatography-mass spectrometry were used to detect microorganisms and their metabolites in the samples respectively. The sequencing data were analyzed to obtain the information of microbial taxonomic composition, functional genes and metabolites in each group of samples. The basic oral conditions and saliva samples of subjects in each group were evaluated and collected by the same professional endodontist. Results: There were no significant difference in baseline characteristics such as age and sex among the subjects in each group (P>0.05). DMFT in HC group (9.0±1.7) was significantly higher than that in HH group (0) and PG group (0) (F=243.00, P<0.001). Sequencing data analysis showed that the taxonomic compositions of salivary microbiota in each group were mainly Firmicutes, Bacteroidetes, Proteobacteria, Actinobacteria and Fusobacteria at the phylum level, and Streptococcus, Neisseria, Rothia, Prevotella at the genus level. Differential analysis showed that, compared with the HH group, HC group and PG group had significant differences in taxonomic composition (P<0.05), and the most significant among them was Prevotella. At the species level, Prevotella pallens was the most significant change in HC group, and Porphyromonas gingivalis in PG group. Metabolite analysis showed that there were significant differences in metabolites between HC group and PG group. The results showed that, compared with the HH group, the most significant metabolite change was 3-hydroxy-1, 5-diphenylpentan-1-one in HC group (P=0.001) and N1 acetylspermine in PG group (P=0.002) respectively. Compared with the PG group, the metabolite of HC group with the most significant difference is D-glucosamine 6-phosphate (P=0.006). The metabolism gene function analysis showed that, the enrichment of carbohydrate metabolism related genes was highest in HC group, followed with HH group, and it was lowest in PG group. In addition, compared with the HH group, the abundance of functional genes related to glucose metabolism, such as ABC transporter and phosphotransferase system, were significantly decreased in PG group (P<0.05), but significantly increased in HC group (P<0.05). Conclusions: There is a significant correlation between the alternation of carbohydrate metabolism of salivary microbiota with the occurrence of caries and periodontitis. In the future, Prevotella pallens and 3-hydroxy-1, 5-diphenylpentan-1-one may be the potential biomarkers of caries; while Porphyromonas gingivalis and N1 acetylspermine work in the predictions of periodontitis.}, } @article {pmid36746286, year = {2023}, author = {Cui, W and Li, R and Fan, Z and Wu, L and Zhao, X and Wei, G and Shu, D}, title = {Weak environmental adaptation of rare phylotypes sustaining soil multi-element cycles in response to decades-long fertilization.}, journal = {The Science of the total environment}, volume = {871}, number = {}, pages = {162063}, doi = {10.1016/j.scitotenv.2023.162063}, pmid = {36746286}, issn = {1879-1026}, mesh = {*Soil ; Phylogeny ; Soil Microbiology ; *Microbiota ; Bacteria/genetics ; Nitrogen ; }, abstract = {Deciphering the ecological role of soil communities in the maintenance of multiple ecosystem functions is pivotal for the conservation and sustainability of soil biodiversity. However, few studies have investigated niche differentiation of abundant and rare microbiota, as well as their contributions to multiple soil elemental cycles, particularly in agroecosystems that have received decades of intense fertilization. Here, we characterized the environmental thresholds and phylogenetic signals for the environmental adaptation of both abundant and rare microbial subcommunities via amplicon sequencing and metagenomic sequencing and explored their importance in sustaining soil multiple nutrient cycling in agricultural fields that were fertilized for two decades. The results showed that rare taxa exhibited narrower niche breadths and weaker phylogenetic signals than abundant species. The assembly of abundant subcommunity was shaped predominantly by dispersal limitation (explained 71.1 % of the variation in bacteria) and undominated processes (explained 75 % of the variation in fungi), whereas the assembly of rare subcommunity was dominated by homogeneous selection process (explained 100 % of the variation in bacteria and 60 % of the variation in fungi). Soil ammonia nitrogen was the leading factor mediating the balance between stochastic and deterministic processes in both abundant (R[2] = 0.15, P < 0.001) and rare (R[2] = 0.08, P < 0.001) bacterial communities. Notably, the rare biosphere largely contributed to key soil processes such as carbon (R[2]bacteria = 0.03, P < 0.05; R[2]fungi = 0.05, P < 0.05) and nitrogen (R[2]bacteria = 0.03, P < 0.05; R[2]fungi = 0.17, P < 0.001) cycling. Collectively, these findings facilitate our understanding of the maintenance of rhizosphere bacterial and fungal diversity in response to agricultural fertilization and highlight the key role of rare taxa in sustaining agricultural ecosystem functions.}, } @article {pmid36746030, year = {2023}, author = {Liao, Y and Bian, J and Miao, S and Xu, S and Li, R and Liu, R and Liu, H and Qu, J}, title = {Regulation of denitrification performance and microbial topology by lights: Insight into wavelength effects towards microbiota.}, journal = {Water research}, volume = {232}, number = {}, pages = {119434}, doi = {10.1016/j.watres.2022.119434}, pmid = {36746030}, issn = {1879-2448}, mesh = {*Nitrites ; Denitrification ; Oxidation-Reduction ; Bioreactors ; *Microbiota ; Nitrogen ; Sewage ; }, abstract = {The low efficiency of conventional complete denitrification, as well as the unstable nitrite supply for partial-denitrification coupled anammox (PD/A) restrict the efficient removal of nitrogen from industrial wastewaters. Herein, we proposed an optical strategy to bidirectionally regulate denitrification by introducing lights at different wavelengths, and the underlying mechanisms were elucidated accordingly. It turned out that yellow light at wavelength of 590 nm accelerated denitrification by 35.4%, while blue light delayed denitrification with stable nitrite accumulation above 86.9% and high nitrate removal (99.8%). Microbial physiology and viability further supported the positive effects of yellow light on microbial activity. Additionally, despite the sluggish denitrification aroused by blue light, negligible cellular damage was observed. Antioxidant capability divergence, microbial community shifting and metabolic flux redirection contributed to the wavelength-dependent effects. Halomonas and Pseudomonas were identified as high-credit taxonomic biomarkers of yellow and blue light. As revealed by metabolomics, pantothenate and CoA biosynthesis, glutamate metabolism and alkaloid biosynthesis presented high impact values. Co-analysis of metabolomics and metagenomics based on microbial topology further distinguished pivotal metabolic pathways and genes. Oxidative phosphorylation contributed to the divergent denitrification performance through electron transfer chains, whereas glutamate and glutathione metabolism contributed to oxidative stress alleviation and mediated the metabolic flux between peroxisome and nitrogen metabolism. This study shed a light on the application of optical strategy to regulate denitrification performance and achieve either complete denitrification or PD/A.}, } @article {pmid36744984, year = {2023}, author = {Banerjee, P and Sarkar, A and Ghosh, K and Mazumdar, A}, title = {A Metagenomic Based Approach on Abundance and Diversity of Bacterial Communities Across the Life Stages of Culicoides peregrinus (Diptera: Ceratopogonidae) a Vector of Bluetongue Virus.}, journal = {Journal of medical entomology}, volume = {60}, number = {2}, pages = {373-383}, doi = {10.1093/jme/tjad011}, pmid = {36744984}, issn = {1938-2928}, mesh = {Animals ; *Ceratopogonidae ; *Bluetongue virus ; Bacteria/genetics ; Larva ; *Microbiota ; }, abstract = {During larval rearing of Culicoides peregrinus Kieffer (Diptera: Ceratopogonidae) it was obligatory to add a small quantity of mud from larval habitat to nutrient broth in culture plates. This initiated microbial growth in rearing plates which facilitated growth and development of immature. The primary aim was to enumerate gut microbial communities across the different life stages of C. peregrinus. Amplicon sequencing of the V3-V4 hypervariable region (16S rDNA) was done on Illumina Miseq platform to detect gut bacterial communities at different life stages, while ITS regions (18S rRNA) were targeted for fungal communities of the 4th instar larvae. The major findings were: 1) Phylum Proteobacteria and Firmicutes were the most abundant throughout the life stages, along with the highest bacterial alpha diversity in the egg, 2) bacterial compositions were similar to laboratory reared and field collected adults, and 3) abundant fungal phyla associated with the larval gut were Ascomycota and Basidiomycota. Furthermore, analyses of the gut microbiome with METAGENassist might be indicative of their likely function in the natural habitat. Abundant gut-associated bacteria and/or fungal genera detected in the present study could be used as dietary supplements to establish laboratory colonies for further vectorial research. While, individual roles of the bacteria or fungi in paratransgenesis are warned for their possible utilization to frame the management strategy in upcoming works.}, } @article {pmid36744944, year = {2023}, author = {Mafumo, N and Bezuidt, OKI and le Roux, W and Makhalanyane, TP}, title = {CrAssphage May Be Viable Markers of Contamination in Pristine and Contaminated River Water.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0128222}, pmid = {36744944}, issn = {2379-5077}, mesh = {*Rivers ; Ecosystem ; Phylogeny ; Environmental Monitoring ; Water Pollution/analysis ; *Viruses ; Bacteria/genetics ; }, abstract = {Viruses are the most biologically abundant entities and may be ideal indicators of fecal pollutants in water. Anthropogenic activities have triggered drastic ecosystem changes in rivers, leading to substantial shifts in chemical and biological attributes. Here, we evaluate the viability of using the presence of crAssphage as indicators of fecal contamination in South African rivers. Shotgun analysis revealed diverse crAssphage viruses in these rivers, which are impacted by chemical and biological pollution. Overall, the diversity and relative abundances of these viruses was higher in contaminated sites compared to pristine locations. In contrast to fecal coliform counts, crAssphage sequences were detected in pristine rivers, supporting the assertion that the afore mentioned marker may be a more accurate indicator of fecal contamination. Our data demonstrate the presence of diverse putative hosts which includes members of the phyla Bacteroidota, Pseudomonadota, Verrucomicrobiota, and Bacillota. Phylogenetic analysis revealed novel subfamilies, suggesting that rivers potentially harbor distinct and uncharacterized clades of crAssphage. These data provide the first insights regarding the diversity, distribution, and functional roles of crAssphage in rivers. Taken together, the results support the potential application of crAssphage as viable markers for water quality monitoring. IMPORTANCE Rivers support substantial populations and provide important ecosystem services. Despite the application of fecal coliform tests and other markers, we lack rapid and reproducible approaches for determining fecal contamination in rivers. Waterborne viral outbreaks have been reported even after fecal indicator bacteria (FIB) were suggested to be absent or below regulated levels of coliforms. This indicates a need to develop and apply improved indicators of pollutants in aquatic ecosystems. Here, we evaluate the viability of crAssphage as indicators of fecal contamination in two South African rivers. We assess the abundance, distribution, and diversity of these viruses in sites that had been predicted pristine or contaminated by FIB analysis. We show that crAssphage are ideal and sensitive markers for fecal contamination and describe novel clades of crAss-like phages. Known crAss-like subfamilies were unrepresented in our data, suggesting that the diversity of these viruses may reflect geographic locality and dependence.}, } @article {pmid36744910, year = {2023}, author = {Guo, M and Wu, G and Tan, Y and Li, Y and Jin, X and Qi, W and Guo, X and Zhang, C and Zhu, Z and Zhao, L}, title = {Guild-Level Microbiome Signature Associated with COVID-19 Severity and Prognosis.}, journal = {mBio}, volume = {14}, number = {1}, pages = {e0351922}, pmid = {36744910}, issn = {2150-7511}, mesh = {Humans ; *COVID-19 ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; Feces ; Prognosis ; }, abstract = {Coronavirus disease 2019 (COVID-19) severity has been associated with alterations of the gut microbiota. However, the relationship between gut microbiome alterations and COVID-19 prognosis remains elusive. Here, we performed a genome-resolved metagenomic analysis on fecal samples from 300 in-hospital COVID-19 patients, collected at the time of admission. Among the 2,568 high quality metagenome-assembled genomes (HQMAGs), redundancy analysis identified 33 HQMAGs which showed differential distribution among mild, moderate, and severe/critical severity groups. Co-abundance network analysis determined that the 33 HQMAGs were organized as two competing guilds. Guild 1 harbored more genes for short-chain fatty acid biosynthesis, and fewer genes for virulence and antibiotic resistance, compared with Guild 2. Based on average abundance difference between the two guilds, the guild-level microbiome index (GMI) classified patients from different severity groups (average AUROC [area under the receiver operating curve] = 0.83). Moreover, age-adjusted partial Spearman's correlation showed that GMIs at admission were correlated with 8 clinical parameters, which are predictors for COVID-19 prognosis, on day 7 in hospital. In addition, GMI at admission was associated with death/discharge outcome of the critical patients. We further validated that GMI was able to consistently classify patients with different COVID-19 symptom severities in different countries and differentiated COVID-19 patients from healthy subjects and pneumonia controls in four independent data sets. Thus, this genome-based guild-level signature may facilitate early identification of hospitalized COVID-19 patients with high risk of more severe outcomes at time of admission. IMPORTANCE Previous reports on the associations between COVID-19 and gut microbiome have been constrained by taxonomic-level analysis and overlook the interaction between microbes. By applying a genome-resolved, reference-free, guild-based metagenomic analysis, we demonstrated that the relationship between gut microbiota and COVID-19 is genome-specific instead of taxon-specific or even species-specific. Moreover, the COVID-19-associated genomes were not independent but formed two competing guilds, with Guild 1 potentially beneficial and Guild 2 potentially more detrimental to the host based on comparative genomic analysis. The dominance of Guild 2 over Guild 1 at time of admission was associated with hospitalized COVID-19 patients at high risk for more severe outcomes. Moreover, the guild-level microbiome signature is not only correlated with the symptom severity of COVID-19 patients, but also differentiates COVID-19 patients from pneumonia controls and healthy subjects across different studies. Here, we showed the possibility of using genome-resolved and guild-level microbiome signatures to identify hospitalized COVID-19 patients with a high risk of more severe outcomes at the time of admission.}, } @article {pmid36744896, year = {2023}, author = {Zhang, Z and Zhang, L and Zhang, G and Zhao, Z and Wang, H and Ju, F}, title = {Deduplication Improves Cost-Efficiency and Yields of De Novo Assembly and Binning of Shotgun Metagenomes in Microbiome Research.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0428222}, pmid = {36744896}, issn = {2165-0497}, abstract = {In the last decade, metagenomics has greatly revolutionized the study of microbial communities. However, the presence of artificial duplicate reads raised mainly from the preparation of metagenomic DNA sequencing libraries and their impacts on metagenomic assembly and binning have never been brought to attention. Here, we explicitly investigated the effects of duplicate reads on metagenomic assemblies and binning based on analyses of five groups of representative metagenomes with distinct microbiome complexities. Our results showed that deduplication considerably increased the binning yields (by 3.5% to 80%) for most of the metagenomic data sets examined thanks to the improved contig length and coverage profiling of metagenome-assembled contigs, whereas it slightly decreased the binning yields of metagenomes with low complexity (e.g., human gut metagenomes). Specifically, 411 versus 397, 331 versus 317, 104 versus 88, and 9 versus 5 metagenome-assembled genomes (MAGs) were recovered from MEGAHIT assemblies of bioreactor sludge, surface water, lake sediment, and forest soil metagenomes, respectively. Noticeably, deduplication significantly reduced the computational costs of the metagenomic assembly, including the elapsed time (9.0% to 29.9%) and the maximum memory requirement (4.3% to 37.1%). Collectively, we recommend the removal of duplicate reads in metagenomes with high complexity before assembly and binning analyses, for example, the forest soil metagenomes examined in this study. IMPORTANCE Duplicated reads in shotgun metagenomes are usually considered technical artifacts. Their presence in metagenomes would theoretically not only introduce bias into the quantitative analysis but also result in mistakes in the coverage profile, leading to adverse effects on or even failures in metagenomic assembly and binning, as the widely used metagenome assemblers and binners all need coverage information for graph partitioning and assembly binning, respectively. However, this issue was seldom noticed, and its impacts on downstream essential bioinformatic procedures (e.g., assembly and binning) remained unclear. In this study, we comprehensively evaluated for the first time the implications of duplicate reads for the de novo assembly and binning of real metagenomic data sets by comparing the assembly qualities, binning yields, and requirements for computational resources with and without the removal of duplicate reads. It was revealed that deduplication considerably increased the binning yields of metagenomes with high complexity and significantly reduced the computational costs, including the elapsed time and the maximum memory requirement, for most of the metagenomes studied. These results provide empirical references for more cost-efficient metagenomic analyses in microbiome research.}, } @article {pmid36744097, year = {2023}, author = {García-Roldán, A and Durán-Viseras, A and de la Haba, RR and Corral, P and Sánchez-Porro, C and Ventosa, A}, title = {Genomic-based phylogenetic and metabolic analyses of the genus Natronomonas, and description of Natronomonas aquatica sp. nov.}, journal = {Frontiers in microbiology}, volume = {14}, number = {}, pages = {1109549}, pmid = {36744097}, issn = {1664-302X}, abstract = {The genus Natronomonas is classified on the family Haloarculaceae, within the class Halobacteria and currently includes six species isolated from salterns, saline or soda lakes, and salt mines. All are extremely halophilic (optimal growth at 20-25% [w/v] NaCl) and neutrophilic, except Natronomonas pharaonis, the type species of the genus, that is haloalkaliphilic (showing optimal growth at pH 9.0) and possesses distinct phenotypic features, such as a different polar lipid profile than the rest of species of the genus. We have carried out a genome-based study in order to determine the phylogenetic structure of the genus Natronomonas and elucidate its current taxonomic status. Overall genomic relatedness indexes, i.e., OrthoANI (Average Nucleotide Identity), dDDH (digital DNA-DNA hybridization), and AAI (Average Amino acid Identity), were determined with respect to the species of Natronomonas and other representative taxa of the class Halobacteria. Our data show that the six species of Natronomonas constitute a coherent cluster at the genus level. Besides, we have characterized a new haloarchaeon, strain F2-12[T], isolated from the brine of a pond of a saltern in Isla Cristina, Huelva, Spain, and we determined that it constitutes a new species of Natronomonas, for which we propose the name Natronomonas aquatica sp. nov. Besides, the metabolic analysis revealed a heterotrophic lifestyle and a versatile nitrogen metabolism for members of this genus. Finally, metagenomic fragment recruitments from a subset of hypersaline habitats, indicated that the species of Natronomonas are widely distributed in saline lakes and salterns as well as on saline soils. Species of this haloarchaeal genus can be considered as ubiquitous in intermediate to high salinity habitats.}, } @article {pmid36743964, year = {2023}, author = {Li, Y and Jones, FG and Zhang, B and Cui, J and Zhang, W}, title = {The effect of short-term fallowing on the microbial communities in forest soil cultivated with ginseng: Preliminary research.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14758}, pmid = {36743964}, issn = {2167-8359}, mesh = {Soil/chemistry ; *Panax ; *Microbiota/genetics ; *Ascomycota ; Forests ; }, abstract = {BACKGROUND: Continuous cultivation of ginseng crops in fixed plots can lead to disease outbreaks, yield losses and replanting failures. Fallow periods can help restore soil health and increase the sustainability of agricultural systems; however, taking land out of production for extended periods is often not feasible. Short-term fallow periods could restore soil health, but few studies have examined the effects of short-term fallow treatment on the health of soil in ginseng fields.

METHODS: In this preliminary study, we used metagenomic analysis to assess changes in the abundance of major ginseng pathogens and soil health overall following a short-term fallow period in a region in the Changbai Mountains. A sample from a forest plot (Hx0ks), was compared to a sample from a field where ginseng was previously cultivated and then had been left fallow for two years (Hx2), and a sample from a field that had been fallow for two years and was subsequently replanted with ginseng (Clsd).

RESULTS: Soil that was fallow for two years, and then replanted with ginseng, showed reduced nutrient content and lower diversity of soil bacterial and fungal communities than soil that remained fallow. Candidatus Solibacter (5%) and Rhizomicrobium (3%) were the most abudant bacterial genera in Hx2. Rhizomicrobium (4%) and Gemmatimonas (3%) were the most abundant bacterial genera in Clsd. Mortierella (22%) and Peziza (12%) dominated the fungal community in Hx2. Lecanicillium (38%) and Mortierella (13%) dominated the fungal community in Clsd. Fallow periods also increased the functional diversity of soil as predicted by PICRUSt and decreased the relative abundance of the pathogenic fungi.

CONCLUSIONS: Preliminary findings were consistent with the hypothesis that fallow management in ginseng cultivation can improve soil microbial community structure and function and reduces the number of plant pathogens; however, testing this hypothesis will require replicated plots.}, } @article {pmid36743574, year = {2022}, author = {Samal, I and Bhoi, TK and Majhi, PK and Murmu, S and Pradhan, AK and Kumar, D and Saini, V and Paschapur, AU and Raj, MN and Ankur, and Manik, S and Behera, PP and Mahanta, DK and Komal, J and Alam, P and Balawi, TA}, title = {Combatting insects mediated biotic stress through plant associated endophytic entomopathogenic fungi in horticultural crops.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1098673}, pmid = {36743574}, issn = {1664-462X}, abstract = {Horticultural production is a vital catalyst for economic growth, yet insect infestations reduce horticultural crop yield and quality. Pesticides and other pest control methods are used during planting to eliminate pests that cause direct and indirect losses. In such situations, endophytic entomo-pathogenic fungi (EEPF) can act as a potential tools for biological control. They protect plants by boosting growth, nutrition, morpho-physiology and salt or iron tolerance. Antixenosis, antibiosis and plant tolerance change insect performance and preferences. EEPF- plant colonisation slows herbivore development, food consumption, oviposition and larval survival. EEPF changes plant physio-chemical properties like volatile emission profile and secondary metabolite production to regulate insect pest defences. EEPF produces chitinases, laccases, amylases, and cellulases for plant defence. Recent studies focused on EEPF species' significance, isolation, identification and field application. Realizing their full potential is difficult due to insufficient mass production, storage stability and formulation. Genetic-molecular and bioinformatics can help to build EEPF-based biological control systems. Metagenomics helps study microbial EEPF taxonomy and function. Multi-omics and system biology can decode EEPF interactions with host plants and microorganisms. NGS (Next Generation Sequencing), comparative genomics, proteomics, transcriptomics, metabolomics, metatranscriptomics and microarrays are used to evaluate plant-EEPF relationships. IPM requires understanding the abiotic and biotic elements that influence plant-EEPF interaction and the physiological mechanisms of EEPF colonisation. Due to restricted research, there are hundreds of unexplored EEPFs, providing an urgent need to uncover and analyse them.}, } @article {pmid36743335, year = {2023}, author = {Dong, Y and Chen, Q and Tian, B and Li, J and Li, J and Hu, Z}, title = {Advancing Microbe Detection for Lower Respiratory Tract Infection Diagnosis and Management with Metagenomic Next-Generation Sequencing.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {677-694}, pmid = {36743335}, issn = {1178-6973}, abstract = {BACKGROUND: Due to limitations of traditional microbiological methods and the presence of the oropharyngeal normal flora, there are still many pathogens that cause lower respiratory tract infections (LRTIs) cannot be detected. Metagenomic next-generation sequencing (mNGS) has the potential capacity to solve this problem.

METHODS: This retrospective study successively reviewed 77 patients with LRTI and 29 patients without LRTI admitted to Tianjin Medical University General Hospital, China from August 2020 to June 2021. Pathogens in bronchoalveolar lavage fluid (BALF) specimens were detected adopting mNGS and traditional microbiological assays. The diagnostic performance of pathogens was compared between mNGS and BALF culture. The value of mNGS for aetiological and clinical impact investigation in LRTI was also evaluated.

RESULTS: Among 77 patients with LRTI, 22.1%, 40.3%, and 65.0% of cases were detected as definite or probable pathogens by culture, all conventional microbiological tests, and mNGS, respectively. Using the final diagnosis as a gold standard, mNGS exhibited a sensitivity of 76.6% (95% confidence interval [CI], 65.6-85.5%), which was considerably superior to that of BALF culture (76.6% vs 18.2%; P < 0.01); specificity of 79.3% (95% CI, 60.3-92.0%), which was similar (79.3% vs 89.7%; P = 0.38); positive-predictive value of 90.8% (95% CI, 81.0-96.5%), and negative-predictive value of 56.1% (95% CI, 39.7-71.5%). According to our data, mNGS identified potential microorganisms in 66.7% (42/63) of culture-negative samples. Among 59 patients with pathogens identified by mNGS, conventional microbiological methods confirmed pathogenic infections in less than half (28/59) cases. Within the 77 patients, 34 (44.2%) patients received pathogen-directed therapy, 7 (9.1%) patients underwent antibiotic adjustment, and 3 (3.9%) patients stopped using antibiotics due to mNGS results.

CONCLUSION: mNGS exhibits high accuracy in diagnosing LRTI, and combine with traditional microbiological tests, causative pathogens can be detected in approximately 70.0% of cases, thus yields a positive effect on antibiotic application.}, } @article {pmid36742454, year = {2023}, author = {Huang, W and Cai, Q and Huo, Y and Tang, J and Chen, Y and Fang, Y and Lu, Y}, title = {A case of pulmonary embolism with bad warfarin anticoagulant effects caused by E. coli infection.}, journal = {Open life sciences}, volume = {18}, number = {1}, pages = {20220539}, pmid = {36742454}, issn = {2391-5412}, abstract = {Warfarin is an anticoagulant commonly used as an oral drug in preventing and treating thromboembolic diseases. The international normalized ratio (INR) is a clinical monitoring anticoagulation intensity index that adjusts the dose based on important references. In particular, INR value must be strictly monitored when warfarin is used for anticoagulation therapy in infected patients. Herein, we report a 54-year-old female patient diagnosed with pulmonary embolism and venous thrombosis of the lower limbs. After the warfarin administration, the INR was always substandard. The patient did not take other warfarin-interacting drugs or foods during the hospital stay. Metagenome next-generation sequencing suggested a bloodstream infection caused by Escherichia coli, which was further confirmed by blood culture. After meropenem administration for anti-infective treatment, the INR value rose rapidly to a standard level. Considering the lack of relevant reports, this case is the first report of potential interaction between E. coli and warfarin. Further, in patients with thromboembolic diseases complicated by infection, antibiotics should be chosen reasonably with close monitoring of the INR to avoid the interaction of warfarin and antibiotics and to ensure the effectiveness and safety of warfarin treatment.}, } @article {pmid36742174, year = {2023}, author = {Fang, YF and Cao, XH and Yao, LY and Cao, Q}, title = {Pulmonary cryptococcosis after immunomodulator treatment in patients with Crohn's disease: Three case reports.}, journal = {World journal of gastroenterology}, volume = {29}, number = {4}, pages = {758-765}, pmid = {36742174}, issn = {2219-2840}, mesh = {Humans ; *Crohn Disease/pathology ; *Cryptococcosis/diagnosis/drug therapy/pathology ; Immunosuppressive Agents/adverse effects ; }, abstract = {BACKGROUND: Corticosteroids and anti-tumor necrosis factor α mAbs are widely used to treat Crohn's disease (CD). However, one disadvantage of this treatment is impairment of normal immune function, leading to an increased risk of infection. Cryptococcus infection is an opportunistic infection that occurs mainly in immunocompromised patients and poses a significant diagnostic challenge in patients with CD.

CASE SUMMARY: Here, we report three cases of pulmonary cryptococcosis in patients with CD after receiving immunomodulatory treatment. The patients presented with no or mild respiratory symptoms. Chest computed tomography scans revealed pulmonary nodules in the unilateral or bilateral lobes. Diagnoses were made using pathological examination and metagenomic sequencing. The patients were treated with fluconazole 400 mg once daily for 1 to 6 mo, and symptoms were resolved. Literature searches were conducted in PubMed, Web of Science, and Embase to retrieve previously reported cases and summarize patient characteristics.

CONCLUSION: The incidence of cryptococcus infection has increased along with immunomodulator use. Clinical vigilance is required for early identification and standardized treatment.}, } @article {pmid36741899, year = {2022}, author = {Bai, H and Shi, L and Guo, Q and Jiang, Y and Li, X and Geng, D and Wang, C and Bi, Y and Wang, Z and Chen, G and Xue, F and Chang, G}, title = {Metagenomic insights into the relationship between gut microbiota and residual feed intake of small-sized meat ducks.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1075610}, pmid = {36741899}, issn = {1664-302X}, abstract = {INTRODUCTION: The objective of this study was to determine the regulatory effects of gut microbiota on the feed efficiency (FE) of small-sized meat ducks by evaluating correlations between gut microbiota and residual feed intake (RFI).

METHODS: A total of 500 21-day-old healthy male ducks with similar initial body weights (645 ± 15.0 g) were raised contemporaneously in the same experimental facility until slaughter at 56 days of age. In total, nine low-RFI (LR) and nine high-RFI (HR) birds were selected for further gut microbiota composition and functional analyses based on the production performance, and the RFI was calculated from 22 to 56 days of age.

RESULTS: Growth performance results indicated a significantly lower RFI, feed conversion ratio, feed intake, and average daily feed intake in the LR ducks (P < 0.05). Taxonomy results of gut microbiota showed the identification of 19 kinds of phyla and more than 250 kinds of genera in all samples. No significant discrepancies in cecal bacterial α-diversity were discovered between the LR and HR groups, which indicated that the microbial modulatory effects on RFI may be attributed to the bacterial composition, rather than the species diversity. Differential analysis of bacterial communities between the LR and HR groups showed a significant increment of Firmicutes and a significant decline of Bacteroidetes in the LR group (P < 0.05). Specifically, genera of Erysipelatoclostridium, Parasutterella, Fournierella, and Lactococcus significantly proliferated, while Bacteroides significantly decreased in the LR group (P < 0.05). Furthermore, correlation analysis showed that the RFI was significantly correlated with carbohydrate metabolism-related bacteria including Bacteroides, Alistipes, Bifidobacterium, Ruminiclostridium_9, Sellimonas, Oscillibacter, Escherichia-Shigella, Lactococcus, and Streptococcus.

CONCLUSION: In conclusion, the communities related to carbohydrate metabolism had positive regulatory effects on the FE of small-sized meat ducks, promoting it by improving the relative abundance and utilization of these communities. The present study provides valuable insight into the dynamics of gut microbiota underlying the variations in the FE of small-sized meat ducks.}, } @article {pmid36741465, year = {2022}, author = {Cobo-López, S and Gupta, VK and Sung, J and Guimerà, R and Sales-Pardo, M}, title = {Stochastic block models reveal a robust nested pattern in healthy human gut microbiomes.}, journal = {PNAS nexus}, volume = {1}, number = {3}, pages = {pgac055}, pmid = {36741465}, issn = {2752-6542}, abstract = {A key question in human gut microbiome research is what are the robust structural patterns underlying its taxonomic composition. Herein, we use whole metagenomic datasets from healthy human guts to show that such robust patterns do exist, albeit not in the conventional enterotype sense. We first introduce the concept of mixed-membership enterotypes using a network inference approach based on stochastic block models. We find that gut microbiomes across a group of people (hosts) display a nested structure, which has been observed in a number of ecological systems. This finding led us to designate distinct ecological roles to both microbes and hosts: generalists and specialists. Specifically, generalist hosts have microbiomes with most microbial species, while specialist hosts only have generalist microbes. Moreover, specialist microbes are only present in generalist hosts. From the nested structure of microbial taxonomies, we show that these ecological roles of microbes are generally conserved across datasets. Our results show that the taxonomic composition of healthy human gut microbiomes is associated with robustly structured combinations of generalist and specialist species.}, } @article {pmid36741405, year = {2022}, author = {Chen, Z and Yang, H and Fu, H and Wu, L and Liu, M and Jiang, H and Liu, Q and Wang, Y and Xiong, S and Zhou, M and Sun, X and Chen, C and Huang, L}, title = {Gut bacterial species in late trimester of pregnant sows influence the occurrence of stillborn piglet through pro-inflammation response.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1101130}, pmid = {36741405}, issn = {1664-3224}, mesh = {Humans ; Animals ; Swine ; Pregnancy ; Female ; *Stillbirth ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; Lipopolysaccharides ; Bacteria ; Inflammation ; }, abstract = {Maternal gut microbiota is an important regulator for the metabolism and immunity of the fetus during pregnancy. Recent studies have indicated that maternal intestinal microbiota is closely linked to the development of fetus and infant health. Some bacterial metabolites are considered to be directly involved in immunoregulation of fetus during pregnancy. However, the detailed mechanisms are largely unknown. In this study, we exploited the potential correlation between the gut microbiota of pregnant sows and the occurrence of stillborn piglets by combining the 16S rRNA gene and metagenomic sequencing data, and fecal metabolome in different cohorts. The results showed that several bacterial species from Bacteroides, potential pathogens, and LPS-producing bacteria exhibited significantly higher abundances in the gut of sows giving birth to stillborn piglets. Especially, Bacteroides fragilis stood out as the key driver in both tested cohorts and showed the most significant association with the occurrence of stillborn piglets in the DN1 cohort. However, several species producing short-chain fatty acids (SCFAs), such as Prevotella copri, Clostridium butyricum and Faecalibacterium prausnitzii were enriched in the gut of normal sows. Functional capacity analysis of gut microbiome revealed that the pathways associated with infectious diseases and immune diseases were enriched in sows giving birth to stillborn piglets. However, energy metabolism had higher abundance in normal sows. Fecal metabolome profiling analysis found that Lysophosphatidylethanolamine and phosphatidylethanolamine which are the main components of cell membrane of Gram-negative bacteria showed significantly higher concentration in stillbirth sows, while SCFAs had higher concentration in normal sows. These metabolites were significantly associated with the stillborn-associated bacterial species including Bacteroides fragilis. Lipopolysaccharide (LPS), IL-1β, IL-6, FABP2, and zonulin had higher concentration in the serum of stillbirth sows, indicating increased intestinal permeability and pro-inflammatory response. The results from this study suggested that certain sow gut bacterial species in late trimester of pregnancy, e.g., an excess abundance of Bacteroides fragilis, produced high concentration of LPS which induced sow pro-inflammatory response and might cause the death of the relatively weak piglets in a farrow. This study provided novel evidences about the effect of maternal gut microbiota on the fetus development and health.}, } @article {pmid36740746, year = {2023}, author = {Voidaleski, MF and Costa, FF and de Hoog, GS and Gomes, RR and Vicente, VA}, title = {Metagenomics reveals an abundance of black yeast-like fungi in the skin microbiome.}, journal = {Mycoses}, volume = {66}, number = {6}, pages = {488-496}, doi = {10.1111/myc.13574}, pmid = {36740746}, issn = {1439-0507}, support = {//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; //Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, mesh = {Humans ; Saccharomyces cerevisiae ; Metagenomics ; Skin/microbiology ; *Exophiala/genetics ; *Microbiota/genetics ; Fungi/genetics ; }, abstract = {BACKGROUND: The skin is the first line of defence against communities of resident viruses, bacteria and fungi. The composition of the microbiome might change with factors related to the environment and host. The microbiome is dominated by bacteria. Dermatophytes and yeasts are the predominant fungi that are also involved in opportunistic infections of skin, hair and nails. Among environmental fungi, Chaetothyriales (black yeasts and relatives) are enriched by hydrocarbon pollution in domesticated habitats and comprise numerous species that cause mild-to-severe disease.

METHODS: We investigated the presence of black fungi in the skin microbiome by conducting an analysis in the publicly available metagenomic SRA database (NCBI). We focused on the causative agents of chromoblastomycosis and phaeohyphomycosis and used barcodes and padlock probe sequences as diagnostic tools.

RESULTS: A total of 132,159,577 MB was analysed and yielded 18,360 reads that matched with 24 species of black fungi. Exophiala was the most prevalent genus, and Cyphellophora europaea was the most abundant species.

CONCLUSION: This study reveals the abundant presence of Chaetothyriales on the skin without necessarily being associated with infection. Most of the detected causal agents are known from mild skin diseases, while also species were revealed that had been reported from CARD9-deficient patients.}, } @article {pmid36740711, year = {2023}, author = {Meng, Z and Yang, C and Leng, J and Zhu, W and Cheng, Y}, title = {Production, purification, characterization and application of two novel endoglucanases from buffalo rumen metagenome.}, journal = {Journal of animal science and biotechnology}, volume = {14}, number = {1}, pages = {16}, pmid = {36740711}, issn = {1674-9782}, support = {31772627//Natural Science Foundation of China/ ; 32061143034//Natural Science Foundation of China/ ; KYYJ202003//Fundamental Research Funds for the Central Universities/ ; nycytxgxcxtd-2021-21//National Modern Agricultural Industry Technology System Guangxi Dairy Buffalo Innovation Team Project/ ; }, abstract = {BACKGROUND: Lignocellulose biomass is the most abundant and renewable material in nature. The objectives of this study were to characterize two endoglucanases TrepCel3 and TrepCel4, and determine the effect of the combination of them (1.2 mg TrepCel3, 0.8 mg TrepCel4) on in vitro rumen fermentation characteristics. In this study, three nature lignocellulosic substrates (rice straw, RS; wheat straw, WS; leymus chinensis, LC) were evaluated for their in vitro digestibility, gas, NH3-N and volatile fatty acid (VFA) production, and microbial protein (MCP) synthesis by adding enzymatic combination.

METHODS: Two endoglucanases' genes were successfully expressed in Escherichia coli (E. coli) BL21 (DE3), and enzymatic characteristics were further characterized. The combination of TrepCel3 and TrepCel4 was incubated with lignocellulosic substrates to evaluate its hydrolysis ability.

RESULTS: The maximum enzymatic activity of TrepCel3 was determined at pH 5.0 and 40 °C, while TrepCel4 was at pH 6.0 and 50 °C. They were stable over the temperature range of 30 to 60 °C, and active within the pH range of 4.0 to 9.0. The TrepCel3 and TrepCel4 had the highest activity in lichenan 436.9 ± 8.30 and 377.6 ± 6.80 U/mg, respectively. The combination of TrepCel3 and TrepCel4 exhibited the highest efficiency at the ratio of 60:40. Compared to maximum hydrolysis of TrepCel3 or TrepCel4 separately, this combination was shown to have a superior ability to maximize the saccharification yield from lignocellulosic substrates up to 188.4% for RS, 236.7% for wheat straw WS, 222.4% for LC and 131.1% for sugar beet pulp (SBP). Supplemental this combination enhanced the dry matter digestion (DMD), gas, NH3-N and VFA production, and MCP synthesis during in vitro rumen fermentation.

CONCLUSIONS: The TrepCel3 and TrepCel4 exhibited the synergistic relationship (60:40) and significantly increased the saccharification yield of lignocellulosic substrates. The combination of them stimulated in vitro rumen fermentation of lignocellulosic substrates. This combination has the potential to be a feed additive to improve agricultural residues utilization in ruminants. If possible, in the future, experiments in vivo should be carried out to fully evaluate its effect.}, } @article {pmid36740063, year = {2023}, author = {Shi, B and Zhao, R and Su, G and Liu, B and Liu, W and Xu, J and Li, Q and Meng, J}, title = {Metagenomic surveillance of antibiotic resistome in influent and effluent of wastewater treatment plants located on the Qinghai-Tibetan Plateau.}, journal = {The Science of the total environment}, volume = {870}, number = {}, pages = {162031}, doi = {10.1016/j.scitotenv.2023.162031}, pmid = {36740063}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Metagenome ; Tibet ; Wastewater ; Bacteria/genetics ; *Water Purification ; }, abstract = {As hotspots for the dissemination of antibiotic resistance genes (ARGs), wastewater treatment plants (WWTPs) have attracted global attention. However, there lacks a sufficient metagenomic surveillance of antibiotic resistome in the WWTPs located on the Qinghai-Tibet Plateau. Here, metagenomic approaches were used to comprehensively investigate the occurrence, mobility potential, and bacterial hosts of ARGs in influent and effluent of 18 WWTPs located on the Qinghai-Tibet Plateau. The total ARG relative abundances and diversity were significantly decreased from influent to effluent across the WWTPs. Multidrug, bacitracin, sulfonamide, aminoglycoside, and beta-lactam ARGs generally consisted of the main ARG types in effluent samples, which were distinct from influent samples. A group of 72 core ARGs accounting for 61.8-95.8 % of the total ARG abundances were shared by all samples. Clinically relevant ARGs mainly conferring resistance to beta-lactams were detected in influent (277 ARGs) and effluent (178 ARGs). Metagenomic assembly revealed that the genetic location of an ARG on a plasmid or a chromosome was related to its corresponding ARG type, demonstrating the distinction in the mobility potential of different ARG types. The abundance of plasmid-mediated ARGs accounted for a much higher proportion than that of chromosome-mediated ARGs in both influent and effluent. Moreover, the ARGs co-occurring with diverse mobile genetic elements in the effluent exhibited a comparable mobility potential with the influent. Furthermore, 137 metagenome-assembled genomes (MAGs) assigned to 13 bacterial phyla were identified as the ARG hosts, which could be effectively treated in most WWTPs. Notably, 46 MAGs were found to carry multiple ARG types and the potential pathogens frequently exhibited multi-antibiotic resistance. Some ARG types tended to be carried by certain bacteria, showing a specific host-resistance association pattern. This study highlights the necessity for metagenomic surveillance and will facilitate risk assessment and control of antibiotic resistome in WWTPs located on the vulnerable area.}, } @article {pmid36739853, year = {2023}, author = {Yu, Y and Huang, J and Jin, L and Yu, M and Yu, X and Zhu, X and Sun, J and Zhu, L}, title = {Translocation and metabolism of tricresyl phosphate in rice and microbiome system: Isomer-specific processes and overlooked metabolites.}, journal = {Environment international}, volume = {172}, number = {}, pages = {107793}, doi = {10.1016/j.envint.2023.107793}, pmid = {36739853}, issn = {1873-6750}, mesh = {Humans ; *Tritolyl Phosphates ; *Oryza ; Organophosphates ; *Microbiota ; *Flame Retardants/analysis ; Phosphates ; }, abstract = {Tricresyl phosphate (TCP) is extensively used organophosphorus flame retardants and plasticizers that posed risks to organisms and human beings. In this study, the translocation and biotransformation behavior of isomers tri-p-cresyl phosphate (TpCP), tri-m-cresyl phosphate (TmCP), and tri-o-cresyl phosphate (ToCP) in rice and rhizosphere microbiome was explored by hydroponic exposure. TpCP and TmCP were found more liable to be translocated acropetally, compared with ToCP, although they have same molecular weight and similar Kow. Rhizosphere microbiome named microbial consortium GY could reduce the uptake of TpCP, TmCP, and ToCP in rice tissues, and promote rice growth. New metabolites were successfully identified in rice and microbiome, including hydrolysis, hydroxylated, methylated, demethylated, methoxylated, and glucuronide- products. The methylation, demethylation, methoxylation, and glycosylation pathways of TCP isomers were observed for the first time in organisms. What is more important is that the demethylation of TCPs could be an important and overlooked source of triphenyl phosphate (TPHP), which broke the traditional understanding of the only manmade source of toxic TPHP in the environment. Active members of the microbial consortium GY during degradation were revealed and metagenomic analysis indicated that most of active populations contained TCP-degrading genes. It is noteworthy that the strains and function genes in microbial consortium GY that responsible for TCP isomers' transformation were different. These results can improve our understanding of the translocation and transformation of organic pollutant isomers in plants and rhizosphere microbiome.}, } @article {pmid36739716, year = {2023}, author = {Doni, L and Oliveri, C and Lasa, A and Di Cesare, A and Petrin, S and Martinez-Urtaza, J and Coman, F and Richardson, A and Vezzulli, L}, title = {Large-scale impact of the 2016 Marine Heatwave on the plankton-associated microbial communities of the Great Barrier Reef (Australia).}, journal = {Marine pollution bulletin}, volume = {188}, number = {}, pages = {114685}, doi = {10.1016/j.marpolbul.2023.114685}, pmid = {36739716}, issn = {1879-3363}, mesh = {Animals ; Ecosystem ; Coral Reefs ; Plankton ; RNA, Ribosomal, 16S ; *Anthozoa ; Australia ; Bacteria/genetics ; *Microbiota ; }, abstract = {The Great Barrier Reef (GBR) is the world's largest coral ecosystem and is threatened by climate change. This study investigated the impact of the 2016 Marine Heatwave (MHW) on plankton associated microbial communities along a ∼800 km transect in the GBR. 16S rRNA gene metabarcoding of archived plankton samples collected from November 2014 to August 2016 in this region showed a significant increase in Planctomycetes and bacteria belonging to the genus Vibrio and Synechococcus during and after the heatwave. Notably, Droplet Digital PCR and targeted metagenomic analysis applied on samples collected four months after the MHW event revealed the presence of several potential pathogenic Vibrio species previously associated with diseases in aquatic animals. Overall, the 2016 MHW significantly impacted the surface picoplankton community and fostered the spread of potentially pathogenic bacteria across the GBR providing an additional threat for marine biodiversity in this area.}, } @article {pmid36739658, year = {2023}, author = {Li, H and Yu, H and Liang, Y and Zhang, X and Yang, D and Wang, L and Shi, D and Chen, T and Zhou, S and Yin, J and Yang, Z and Li, J and Jin, M}, title = {Extended chloramination significantly enriched intracellular antibiotic resistance genes in drinking water treatment plants.}, journal = {Water research}, volume = {232}, number = {}, pages = {119689}, doi = {10.1016/j.watres.2023.119689}, pmid = {36739658}, issn = {1879-2448}, mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; *Drinking Water/analysis ; Drug Resistance, Microbial/genetics ; *Water Purification/methods ; Bacteria/genetics ; Disinfection/methods ; Genes, Bacterial ; }, abstract = {Chloramination and chlorination are both strong barriers that prevent the transmission of potential pathogens to humans through drinking water. However, the comparative effects of chloramination and chlorination on the occurrence of antibiotic resistance genes (ARGs) in drinking water treatment plants (DWTPs) remain unknown. Herein, the antibiotic resistome in water before and after chloramination or chlorination was analyzed through metagenomic sequencing and then verified through quantitative real-time polymerase chain reaction (qPCR). After the treatment of 90 min, chloramination led to higher enrichment of the total relative abundance of intracellular ARGs (iARGs) in water than chlorination, whereas chlorination facilitated the release of more extracellular ARGs (eARGs) than chloramination. According to redundancy and Pearson's analyses, the total concentration of the observed iARGs in the finished water exhibited a strong positive correlation with ammonium nitrogen (NH4[+]-N) concentration, presenting a linear upward trend with an increase in the NH4[+]-N concentration. This indicated that NH4[+]-N is a crucial driving factor for iARG accumulation during chloramination. iARG enrichment ceases if the duration of chloramination is shortened to 40 min, suggesting that shortening the duration would be a better strategy for controlling iARG enrichment in drinking water. These findings emphasized the potential risk of antibiotic resistance after extended chloramination, shedding light on the control of transmission of antibiotic-resistant bacteria through water by optimizing disinfection procedures in DWTPs.}, } @article {pmid36739288, year = {2023}, author = {Matiasek, K and Pfaff, F and Weissenböck, H and Wylezich, C and Kolodziejek, J and Tengstrand, S and Ecke, F and Nippert, S and Starcky, P and Litz, B and Nessler, J and Wohlsein, P and Baumbach, C and Mundhenk, L and Aebischer, A and Reiche, S and Weidinger, P and Olofsson, KM and Rohdin, C and Weissenbacher-Lang, C and Matt, J and Rosati, M and Flegel, T and Hörnfeldt, B and Höper, D and Ulrich, RG and Nowotny, N and Beer, M and Ley, C and Rubbenstroth, D}, title = {Mystery of fatal 'staggering disease' unravelled: novel rustrela virus causes severe meningoencephalomyelitis in domestic cats.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {624}, pmid = {36739288}, issn = {2041-1723}, mesh = {Humans ; Animals ; Cats ; Mice ; *Encephalomyelitis ; Causality ; Sweden ; Austria ; Germany ; Mammals ; }, abstract = {'Staggering disease' is a neurological disease entity considered a threat to European domestic cats (Felis catus) for almost five decades. However, its aetiology has remained obscure. Rustrela virus (RusV), a relative of rubella virus, has recently been shown to be associated with encephalitis in a broad range of mammalian hosts. Here, we report the detection of RusV RNA and antigen by metagenomic sequencing, RT-qPCR, in-situ hybridization and immunohistochemistry in brain tissues of 27 out of 29 cats with non-suppurative meningoencephalomyelitis and clinical signs compatible with'staggering disease' from Sweden, Austria, and Germany, but not in non-affected control cats. Screening of possible reservoir hosts in Sweden revealed RusV infection in wood mice (Apodemus sylvaticus). Our work indicates that RusV is the long-sought cause of feline 'staggering disease'. Given its reported broad host spectrum and considerable geographic range, RusV may be the aetiological agent of neuropathologies in further mammals, possibly even including humans.}, } @article {pmid36739238, year = {2023}, author = {Carbia, C and Bastiaanssen, TFS and Iannone, LF and García-Cabrerizo, R and Boscaini, S and Berding, K and Strain, CR and Clarke, G and Stanton, C and Dinan, TG and Cryan, JF}, title = {The Microbiome-Gut-Brain axis regulates social cognition & craving in young binge drinkers.}, journal = {EBioMedicine}, volume = {89}, number = {}, pages = {104442}, pmid = {36739238}, issn = {2352-3964}, mesh = {Humans ; Male ; Adolescent ; Young Adult ; Adult ; Craving/physiology ; *Alcoholism ; *Binge Drinking/psychology ; Brain-Gut Axis ; Social Cognition ; Alcohol Drinking/psychology ; Ethanol ; }, abstract = {BACKGROUND: Binge drinking is the consumption of an excessive amount of alcohol in a short period of time. This pattern of consumption is highly prevalent during the crucial developmental period of adolescence. Recently, the severity of alcohol use disorders (AUDs) has been linked with microbiome alterations suggesting a role for the gut microbiome in its development. Furthermore, a strong link has emerged too between microbiome composition and socio-emotional functioning across different disorders including AUD. The aim of this study was to investigate the potential link (and its predictive value) between alcohol-related altered microbial profile, social cognition, impulsivity and craving.

METHODS: Young people (N = 71) aged 18-25 reported their alcohol use and underwent a neuropsychological evaluation. Craving was measured at baseline and three months later. Diet was controlled for. Blood, saliva and hair samples were taken for inflammatory, kynurenine and cortisol analysis. Stool samples were provided for shotgun metagenomic sequencing and short-chain fatty acids (SCFAs) were measured.

FINDINGS: Binge drinking was associated with distinct microbiome alterations and emotional recognition difficulties. Associations were found for several microbiome species with emotional processing and impulsivity. Craving showed a strong link with alterations in microbiome composition and neuroactive potential over time.

INTERPRETATION: In conclusion, this research demonstrates alterations in the gut microbiome of young binge drinkers (BDs) and identifies early biomarkers of craving. Associations between emotional processing and microbiome composition further support the growing literature on the gut microbiome as a regulator of social cognition. These findings are of relevance for new gut-derived interventions directed at improving early alcohol-related alterations during the vulnerability period of adolescence.

FUNDING: C.C. and R.G-C. received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 754535. APC Microbiome Ireland is a research centre funded by Science Foundation Ireland (SFI), through the Irish Government's National Development Plan [grant no. SFI/12/RC/2273_P2]. J.F.C has research support from Cremo, Pharmavite, DuPont and Nutricia. He has spoken at meetings sponsored by food and pharmaceutical companies. G.C. has received honoraria from Janssen, Probi, and Apsen as an invited speaker; is in receipt of research funding from Pharmavite, Fonterra, Nestle and Reckitt; and is a paid consultant for Yakult, Zentiva and Heel pharmaceuticals. All the authors declare no competing interests.}, } @article {pmid36738712, year = {2023}, author = {Yagin, FH and Cicek, İB and Alkhateeb, A and Yagin, B and Colak, C and Azzeh, M and Akbulut, S}, title = {Explainable artificial intelligence model for identifying COVID-19 gene biomarkers.}, journal = {Computers in biology and medicine}, volume = {154}, number = {}, pages = {106619}, pmid = {36738712}, issn = {1879-0534}, mesh = {Humans ; *Artificial Intelligence ; *COVID-19/diagnosis/genetics ; Genetic Markers ; Risk Factors ; Neoplasm Proteins ; }, abstract = {AIM: COVID-19 has revealed the need for fast and reliable methods to assist clinicians in diagnosing the disease. This article presents a model that applies explainable artificial intelligence (XAI) methods based on machine learning techniques on COVID-19 metagenomic next-generation sequencing (mNGS) samples.

METHODS: In the data set used in the study, there are 15,979 gene expressions of 234 patients with COVID-19 negative 141 (60.3%) and COVID-19 positive 93 (39.7%). The least absolute shrinkage and selection operator (LASSO) method was applied to select genes associated with COVID-19. Support Vector Machine - Synthetic Minority Oversampling Technique (SVM-SMOTE) method was used to handle the class imbalance problem. Logistics regression (LR), SVM, random forest (RF), and extreme gradient boosting (XGBoost) methods were constructed to predict COVID-19. An explainable approach based on local interpretable model-agnostic explanations (LIME) and SHAPley Additive exPlanations (SHAP) methods was applied to determine COVID-19- associated biomarker candidate genes and improve the final model's interpretability.

RESULTS: For the diagnosis of COVID-19, the XGBoost (accuracy: 0.930) model outperformed the RF (accuracy: 0.912), SVM (accuracy: 0.877), and LR (accuracy: 0.912) models. As a result of the SHAP, the three most important genes associated with COVID-19 were IFI27, LGR6, and FAM83A. The results of LIME showed that especially the high level of IFI27 gene expression contributed to increasing the probability of positive class.

CONCLUSIONS: The proposed model (XGBoost) was able to predict COVID-19 successfully. The results show that machine learning combined with LIME and SHAP can explain the biomarker prediction for COVID-19 and provide clinicians with an intuitive understanding and interpretability of the impact of risk factors in the model.}, } @article {pmid36737993, year = {2023}, author = {Kuerman, M and Wang, R and Zhou, Y and Tian, X and Cui, Q and Yi, H and Gong, P and Zhang, Z and Lin, K and Liu, T and Zhang, L}, title = {Metagenomic insights into bacterial communities and functional genes associated with texture characteristics of Kazakh artisanal fermented milk Ayran in Xinjiang, China.}, journal = {Food research international (Ottawa, Ont.)}, volume = {164}, number = {}, pages = {112414}, doi = {10.1016/j.foodres.2022.112414}, pmid = {36737993}, issn = {1873-7145}, mesh = {*Cultured Milk Products/microbiology ; Metagenomics ; Bacteria ; *Lactobacillus helveticus ; Peptide Hydrolases/genetics ; }, abstract = {The complex microflora of traditional fermented milk is crucial to milk coagulation mainly through acid and protease production; however, it is still unclear which microbes and proteases significantly influence the texture of Ayran, a Kazakh artisanal fermented milk in Xinjiang, China. In this study, fifty-nine samples of Ayran were collected and investigated on texture properties. Finally, six Ayran samples with different texture features were screened out, and the taxonomic and functional attributes of their microbiota were characterized by metagenomics. The results showed that the hardness of the fermented milk in Yili Kazakh Autonomous Prefecture was significantly higher than that in other pasture areas. Lactobacillus and Lactococcus were the core genera that affected the coagulation quality of milk. Furthermore, we found that the proline iminopeptidase pip (EC 3.4.11.5) gene of Lactobacillus helveticus and Limosilactobacillus fermentum and the dipeptidase E pepE (EC 3.4.13.21) gene of Lactococcus lactis were most associated with the coagulation quality of fermented milk. Furthermore, positive correlations were observed among the hardness of fermented milk, the activity of the proteases, and the corresponding functional gene expressions.}, } @article {pmid36737703, year = {2023}, author = {Zhao, G and Qi, M and Wang, Q and Hu, C and Li, X and Chen, Y and Yang, J and Yu, H and Chen, H and Guo, A}, title = {Gut microbiome variations in Rhinopithecus roxellanae caused by changes in the environment.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {62}, pmid = {36737703}, issn = {1471-2164}, support = {2021CFB118//Nature Science Foundation of Hubei Province/ ; 2013BAD03B01-01//National Science and Technology Infrastructure Program of China/ ; }, mesh = {Animals ; *Presbytini/genetics ; *Gastrointestinal Microbiome/genetics ; *Colobinae/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Endangered Species ; Bacteria/genetics ; Diarrhea ; }, abstract = {BACKGROUND: The snub-nosed monkey (Rhinopithecus roxellanae) is an endangered animal species mainly distributed in China and needs to be protected. Gut microbiome is an important determinant of animal health and population survival as it affects the adaptation of the animals to different foods and environments under kinetic changes of intrinsic and extrinsic factors. Therefore, this study aimed to elucidate gut fecal microbiome profiles of snub-nosed monkeys affected by several extrinsic and intrinsic factors, including raising patterns (captive vs. wild), age, sex, and diarrheal status to provide a reference for making protection strategies.

RESULTS: The 16S rRNA gene sequencing was firstly used to pre-check clustering of 38 fecal samples from the monkeys including 30 wild and 8 captive (5 healthy and 3 diarrheal) from three Regions of Shennongjia Nature Reserve, Hubei Province, China. Then the 24 samples with high-quality DNA from 18 wild and 6 captive (4 healthy and 2 diarrheal) monkeys were subjected to shotgun metagenomic sequencing to characterize bacterial gut microbial communities. We discovered that the raising pattern (captive and wild) rather than age and sex was the predominant factor attributed to gut microbiome structure and proportionality. Wild monkeys had significantly higher bacterial diversity and lower Bacteroidetes/Firmicutes ratios than captive animals. Moreover, the gut microbiomes in wild healthy monkeys were enriched for the genes involved in fatty acid production, while in captive animals, genes were enriched for vitamin biosynthesis and metabolism and amino acid biosynthesis from carbohydrate intermediates. Additionally, a total of 37 antibiotic resistant genes (ARG) types were detected. Unlike the microbiome diversity, the captive monkeys have a higher diversity of ARG than the wild animals.

CONCLUSION: Taken together, we highlight the importance of self-reprogramed metabolism in the snub-nosed monkey gut microbiome to help captive and wild monkeys adapt to different intrinsic and extrinsic environmental change.}, } @article {pmid36736410, year = {2023}, author = {Wang, J and Lou, Y and Ma, D and Feng, K and Chen, C and Zhao, L and Xing, D}, title = {Co-treatment with free nitrous acid and calcium peroxide regulates microbiome and metabolic functions of acidogenesis and methanogenesis in sludge anaerobic digestion.}, journal = {The Science of the total environment}, volume = {870}, number = {}, pages = {161924}, doi = {10.1016/j.scitotenv.2023.161924}, pmid = {36736410}, issn = {1879-1026}, mesh = {*Sewage/chemistry ; Anaerobiosis ; Fermentation ; Nitrous Acid/analysis ; Fatty Acids, Volatile/analysis ; *Microbiota ; Carbon ; }, abstract = {Wasted activated sludge (WAS) is a promising feedstock for carbon management because of its abundance and carbon-neutral features. Currently, the goal is to maximize the energy in WAS and avoid secondary toxic effects or accumulation of harmful substances in the environment. Chemical pretreatment is an effective strategy for enhancing WAS disintegration and production of short chain fatty acids (SCFAs). However, the role of pretreatment in shaping the core microbiome and functional metabolism of anaerobic microorganisms remains obscure. Here, the mechanisms of SCFA synthesis and microbiome response to free nitrous acid (FNA) and calcium peroxide (CaO2) co-treatment during sludge anaerobic digestion (AD) were investigated. The combination of FNA and CaO2 enriched acidogenic Macellibacteroides, Petrimonas, and Sedimentibacter to a relative abundance of 15.0%, 10.3%, and 7.3%, respectively, resulting in an apparent increase in SCFA production. Metagenome analysis indicated that FNA + CaO2 co-treatment facilitated glycolysis, phosphate acetyltransferase-acetate kinase pathway, amino acid metabolism, and acetate transport, but inhibited CO2 reduction and common pathway of methanogenesis compared with the untreated control. This work provides theoretical insights into the functional activity and interaction of microorganisms with ecological factors.}, } @article {pmid36736026, year = {2023}, author = {Du, S and Feng, J and Bi, L and Hu, HW and Hao, X and Huang, Q and Liu, YR}, title = {Tracking soil resistance and virulence genes in rice-crayfish co-culture systems across China.}, journal = {Environment international}, volume = {172}, number = {}, pages = {107789}, doi = {10.1016/j.envint.2023.107789}, pmid = {36736026}, issn = {1873-6750}, mesh = {Animals ; Humans ; *Soil ; Virulence/genetics ; *Oryza ; Astacoidea ; Coculture Techniques ; Genes, Bacterial ; China ; Metals ; Anti-Bacterial Agents ; }, abstract = {Rice-crayfish co-culture (RC) has been widely and rapidly promoted as a sustainable agricultural system in many countries. The accumulation of crayfish residues could enhance soil organic matters; however, impacts of this integrated farming model on the dissemination and pathogenicity of resistance and virulence genes remain poorly understood. Here, we characterized antibiotic resistance genes (ARGs), biocide resistance genes (BRGs), metal resistance genes (MRGs) and virulence factor genes (VFGs) using metagenomic methods in paired RC and rice monoculture (RM) systems across China. The RC model did not increase the abundance of soil ARGs, BRGs, MRGs, or VFGs in comparison to the RM model, but selectively enriched 35 subtypes of these potential resistance and virulence genes. Network analysis revealed that resistance and virulence genes had a higher number of connections with mobile genetic elements (MGEs) in the RC system than that in the RM system, suggesting a higher horizontal transfer potential of these genes. Moreover, the RC model had a higher abundance of human opportunistic pathogens such as Salmonella enterica, Vibrio cholerae, and Shigella dysenteriae which were potential hosts of VFGs such as phoP, fleS, and gspE, suggesting a potential threat to human health. We further unraveled that stochastic process was the main driver of the assembly of resistance and virulence genes in the RC system. The abundance of ARGs and VFGs were primarily associated with microbial community compositions, while the abundance of BRGs and MRGs were mainly associated with that of MGEs. Taken together, our results suggest that the RC model has potential to cause the dissemination and pathogenicity of resistance and virulence genes, which has important implications for the control of soil-borne biological risks and the strategic management of sustainable agriculture.}, } @article {pmid36735785, year = {2023}, author = {Urbelienė, N and Tiškus, M and Tamulaitienė, G and Gasparavičiūtė, R and Lapinskaitė, R and Jauniškis, V and Sūdžius, J and Meškienė, R and Tauraitė, D and Skrodenytė, E and Urbelis, G and Vaitekūnas, J and Meškys, R}, title = {Cytidine deaminases catalyze the conversion of N(S,O)[4]-substituted pyrimidine nucleosides.}, journal = {Science advances}, volume = {9}, number = {5}, pages = {eade4361}, pmid = {36735785}, issn = {2375-2548}, mesh = {*Pyrimidine Nucleosides/metabolism ; Cytidine Deaminase/metabolism ; Uridine/metabolism ; Cytidine ; Deoxycytidine ; }, abstract = {Cytidine deaminases (CDAs) catalyze the hydrolytic deamination of cytidine and 2'-deoxycytidine to uridine and 2'-deoxyuridine. Here, we report that prokaryotic homo-tetrameric CDAs catalyze the nucleophilic substitution at the fourth position of N[4]-acyl-cytidines, N[4]-alkyl-cytidines, and N[4]-alkyloxycarbonyl-cytidines, and S[4]-alkylthio-uridines and O[4]-alkyl-uridines, converting them to uridine and corresponding amide, amine, carbamate, thiol, or alcohol as leaving groups. The x-ray structure of a metagenomic CDA_F14 and the molecular modeling of the CDAs used in this study show a relationship between the bulkiness of a leaving group and the volume of the binding pocket, which is partly determined by the flexible β3α3 loop of CDAs. We propose that CDAs that are active toward a wide range of substrates participate in salvage and/or catabolism of variously modified pyrimidine nucleosides. This identified promiscuity of CDAs expands the knowledge about the cellular turnover of cytidine derivatives, including the pharmacokinetics of pyrimidine-based prodrugs.}, } @article {pmid36735064, year = {2023}, author = {Tessler, M and Cunningham, SW and Ingala, MR and Warring, SD and Brugler, MR}, title = {An Environmental DNA Primer for Microbial and Restoration Ecology.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {796-808}, pmid = {36735064}, issn = {1432-184X}, mesh = {*DNA, Environmental/genetics ; DNA Primers ; DNA Barcoding, Taxonomic/methods ; Ecology ; DNA/genetics ; Environmental Monitoring ; Biodiversity ; }, abstract = {Environmental DNA (eDNA) sequencing-DNA collected from the environment from living cells or shed DNA-was first developed for working with microbes and has greatly benefitted microbial ecologists for decades since. These tools have only become increasingly powerful with the advent of metabarcoding and metagenomics. Most new studies that examine diverse assemblages of bacteria, archaea, protists, fungi, and viruses lean heavily into eDNA using these newer technologies, as the necessary sequencing technology and bioinformatic tools have become increasingly affordable and user friendly. However, eDNA methods are rapidly evolving, and sometimes it can feel overwhelming to simply keep up with the basics. In this review, we provide a starting point for microbial ecologists who are new to DNA-based methods by detailing the eDNA methods that are most pertinent, including study design, sample collection and storage, selecting the right sequencing technology, lab protocols, equipment, and a few bioinformatic tools. Furthermore, we focus on how eDNA work can benefit restoration and what modifications are needed when working in this subfield.}, } @article {pmid36734589, year = {2023}, author = {Chen, X and Shu, X and He, L and Yang, H and Lu, X and Wang, G and Ge, Y}, title = {High prevalence and mortality of Pneumocystis jirovecii pneumonia in anti-MDA5 antibody-positive dermatomyositis.}, journal = {Rheumatology (Oxford, England)}, volume = {62}, number = {10}, pages = {3302-3309}, doi = {10.1093/rheumatology/kead063}, pmid = {36734589}, issn = {1462-0332}, mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis/epidemiology ; *Pneumocystis carinii ; Prevalence ; *Dermatomyositis/complications/epidemiology ; Retrospective Studies ; Trimethoprim, Sulfamethoxazole Drug Combination/therapeutic use ; }, abstract = {OBJECTIVES: To identify potential risk factors and prognostic factors of Pneumocystis jirovecii pneumonia (PJP) infection in anti-melanoma differentiation-associated gene 5 antibody-positive DM (anti-MDA5+ DM) patients, and to evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS).

METHODS: Anti-MDA5+ DM patients who underwent mNGS or real-time PCR for PJP detection were recruited. The potential risk factors for PJP occurrence and death were analysed via Logistic regression and Cox proportional hazards regression, respectively. The diagnostic efficacy of mNGS was compared with the conventional methods.

RESULTS: 91 patients were enrolled and 44 were assigned to PJP+ group. The PJP detection rate was 48.4%. PJP often occurred in the first 3 months (68.2%) of the disease; this period also showed the highest mortality rate (20.5%). Fever and increased lactate dehydrogenase (LDH) were independent risk factors for PJP occurrence, while trimethoprim-sulfamethoxazole (TMP/SMZ) prophylaxis was an independent protective factor (all P < 0.05). Older age and increased LDH were predictors for mortality in patients with anti-MDA5+ DM and PJP (all P < 0.05). In addition, we found that mNGS had a sensitivity of 100.0% and specificity of 90.0% in diagnosing PJP, with the highest area under the curve of 0.95 (P < 0.001).

CONCLUSION: PJP has high prevalence and mortality in anti-MDA5+ DM. It is crucial for clinicians to identify high-risk patients and promptly institute TMP/SMZ to prevent PJP. mNGS is the preferred approach for pathogen detection in anti-MDA5+ DM when PJP is suspected.}, } @article {pmid36734170, year = {2022}, author = {Dai, Z and Wang, H and Wu, H and Zhang, Q and Ji, L and Wang, X and Shen, Q and Yang, S and Ma, X and Shan, T and Zhang, W}, title = {Parvovirus dark matter in the cloaca of wild birds.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {36734170}, issn = {2047-217X}, mesh = {Animals ; Animals, Wild/genetics ; Phylogeny ; Cloaca ; *Parvovirus/genetics ; *Parvoviridae Infections/veterinary ; Birds/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {With the development of viral metagenomics and next-generation sequencing technology, more and more novel parvoviruses have been identified in recent years, including even entirely new lineages. The Parvoviridae family includes a different group of viruses that can infect a wide variety of animals. In this study, systematic analysis was performed to identify the "dark matter" (datasets that cannot be easily attributed to known viruses) of parvoviruses and to explore their genetic diversity from wild birds' cloacal swab samples. We have tentatively defined this parvovirus "dark matter" as a highly divergent lineage in the Parvoviridae family. All parvoviruses showed several characteristics, including 2 major protein-coding genes and similar genome lengths. Moreover, we observed that the novel parvo-like viruses share similar genome organizations to most viruses in Parvoviridae but could not clustered with the established subfamilies in phylogenetic analysis. We also found some new members associated with the Bidnaviridae family, which may be derived from parvovirus. This suggests that systematic analysis of domestic and wild animal samples is necessary to explore the genetic diversity of parvoviruses and to mine for more of this potential dark matter.}, } @article {pmid36733920, year = {2023}, author = {Xie, Y and Dai, B and Zhou, X and Liu, H and Wu, W and Yu, F and Zhu, B}, title = {Diagnostic Value of Metagenomic Next-Generation Sequencing for Multi-Pathogenic Pneumonia in HIV-Infected Patients.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {607-618}, pmid = {36733920}, issn = {1178-6973}, abstract = {BACKGROUND: To evaluate the value and challenges of real-world clinical application of metagenomic next-generation sequencing (mNGS) for bronchoalveolar lavage fluid (BALF) in HIV-infected patients with suspected multi-pathogenic pneumonia.

METHODS: Fifty-seven HIV-infected patients with suspected mixed pneumonia who were agreed to undergo the bronchoscopy were recruited and retrospectively reviewed the results of mNGS and conventional microbiological tests (CMTs) of BALF from July 2020 to June 2022.

RESULTS: 54 patients were diagnosed with pneumonia including 49 patients with definite pathogens and five patients with probable pathogens. mNGS exhibited a higher diagnostic accuracy for fungal detection than CMTs in HIV-infected patients with suspected pulmonary infection. The sensitivity of mNGS in diagnosis of pneumonia in HIV-infected patients was much higher than that of CMTs (79.6% vs 61.1%; P < 0.05). Patients with mixed infection had lower CD4 T-cell count and higher symptom duration before admitting to the hospital than those with single infection. The detection rate of mNGS for mixed infection was significantly higher than that of CMTs and more co-pathogens could be identified by mNGS. The most common pattern of mixed infection observed was fungi-virus (11/29, 37.9%), followed by fungi-virus-bacteria (6/29, 20.7%) coinfection in HIV-infected patients with multi-pathogenic pneumonia.

CONCLUSION: mNGS improved the pathogens detection rate and exhibited advantages in identifying multi-pathogenic pneumonia in HIV-infected patients. Early performance of bronchoscopy and mNGS are recommended in HIV-infected patients with low CD4 T cell counts and long duration of symptoms. The most common pattern of mixed infection observed was fungi-virus, followed by fungi-virus-bacteria coinfection in HIV infected patients with multi-pathogenic pneumonia.}, } @article {pmid36733529, year = {2023}, author = {Barbieri, E and Santoro, N and Umano, GR}, title = {Clinical features and metabolic complications for non-alcoholic fatty liver disease (NAFLD) in youth with obesity.}, journal = {Frontiers in endocrinology}, volume = {14}, number = {}, pages = {1062341}, pmid = {36733529}, issn = {1664-2392}, support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; }, mesh = {Child ; Humans ; Adolescent ; *Non-alcoholic Fatty Liver Disease/complications/epidemiology ; *Insulin Resistance ; *Diabetes Mellitus, Type 2/epidemiology ; *Pediatric Obesity/complications ; }, abstract = {Pediatric obesity has become in the last forty years the most common metabolic disease in children and adolescents affecting about 25% of the pediatric population in the western world. As obesity worsens, a whole-body insulin resistance (IR) occurs. This phenomenon is more pronounced during adolescence, when youth experience a high degree of insulin resistance due the production of growth hormone. As IR progresses, the blunted control of insulin on adipose tissue lipolysis causes an increased flux of fatty acids with FFA deposition in ectopic tissues and organs such as the liver, leading to the development of NAFLD. In this brief review, we will discuss the clinical implications of IR and NAFLD in the context of pediatric obesity. We will review the pathogenesis and the link between these two entities, the major pathophysiologic underpinnings, including the role of genetics and metagenomics, how these two entities lead to the development of type 2 diabetes, and which are the therapeutic options for NAFLD in youth.}, } @article {pmid36732756, year = {2023}, author = {Ge, T and Yang, C and Li, B and Huang, X and Zhao, L and Zhang, X and Tian, L and Zhang, E}, title = {High-energy diet modify rumen microbial composition and microbial energy metabolism pattern in fattening sheep.}, journal = {BMC veterinary research}, volume = {19}, number = {1}, pages = {32}, pmid = {36732756}, issn = {1746-6148}, mesh = {Sheep ; Animals ; *Rumen/metabolism ; *Animal Feed/analysis ; Diet/veterinary ; Butyrates ; Energy Metabolism ; Fermentation ; }, abstract = {Higher dietary energy is often used to achieve better animal performance in mutton sheep production. Notably, changing the diet formula affects rumen fermentation and the microbiota of ruminants. In this study, we investigated the effect of dietary energy on rumen fermentation and ruminal microbiota in fattening sheep. Fifteen 2-month-old white-headed Suffolk sheep (♂) × Hu sheep (♀) crossbred lambs were randomly divided into three treatments based on the dietary energy of the feeds fed: 8.67 MJ/kg (Low energy (LE); n = 5), 10.38 MJ/kg (standard energy (CON); n = 5), and 12.31 MJ/kg (high energy (HE); n = 5) groups. After 70 days of feeding, sheep were slaughtered and the ruminal fluids were collected and analyzed to determine fermentation parameters. Microbiota was determined using metagenomics sequencing. Notably, the microbial cell protein (MCP) and butyric acid concentrations were significantly high in the HE group. Metagenomic sequencing revealed that ACE and Chao indexes of the HE group were significantly decreased. Four genera among the major classified taxa across all the kingdoms differed in relative abundance in the three dietary energy levels. The relative abundances of Prevotella_brevis, Succiniclasticum_ruminis, Prevotellace-ae_bacterium, and Lachnospiraceae_bacterium were significantly correlated with rumen fermentation. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis further revealed that a high-energy diet increased lipid metabolism of microbiota. The Carbohydrate Active enzymes (CAZy) gene, which participates in energy metabolism, was upregulated, while genes regulating plant cell wall degradation were downregulated in the HE group. These results suggest that a high-energy diet had minimal influence on the rumen fermentation pattern but altered the composition of the rumen microbiota, enhancing microbial lipid metabolism and limiting crude fiber metabolism. The findings of this study provide scientific evidence of the effect of dietary energy on ruminant fermentation and fattening sheep production.}, } @article {pmid36732517, year = {2023}, author = {Deng, K and Xu, JJ and Shen, L and Zhao, H and Gou, W and Xu, F and Fu, Y and Jiang, Z and Shuai, M and Li, BY and Hu, W and Zheng, JS and Chen, YM}, title = {Comparison of fecal and blood metabolome reveals inconsistent associations of the gut microbiota with cardiometabolic diseases.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {571}, pmid = {36732517}, issn = {2041-1723}, mesh = {Adult ; Middle Aged ; Aged ; Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 2 ; RNA, Ribosomal, 16S ; Metabolome ; Metabolomics/methods ; Feces ; *Cardiovascular Diseases ; }, abstract = {Blood metabolome is commonly used in human studies to explore the associations of gut microbiota-derived metabolites with cardiometabolic diseases. Here, in a cohort of 1007 middle-aged and elderly adults with matched fecal metagenomic (149 species and 214 pathways) and paired fecal and blood targeted metabolomics data (132 metabolites), we find disparate associations with taxonomic composition and microbial pathways when using fecal or blood metabolites. For example, we observe that fecal, but not blood butyric acid significantly associates with both gut microbiota and prevalent type 2 diabetes. These findings are replicated in an independent validation cohort involving 103 adults. Our results suggest that caution should be taken when inferring microbiome-cardiometabolic disease associations from either blood or fecal metabolome data.}, } @article {pmid36732439, year = {2023}, author = {Evans, T and Ali, U and Anderton, R and Raby, E and Manning, L and Litton, E}, title = {Lower gut dysbiosis and mortality in acute critical illness: a systematic review and meta-analysis.}, journal = {Intensive care medicine experimental}, volume = {11}, number = {1}, pages = {6}, pmid = {36732439}, issn = {2197-425X}, abstract = {BACKGROUND: The human gastrointestinal tract harbours a complex multi-kingdom community known as the microbiome. Dysbiosis refers to its disruption and is reportedly extreme in acute critical illness yet its clinical implications are unresolved. The review systematically evaluates the association between gut dysbiosis and clinical outcomes of patients early in critical illness.

METHODS: Following PRISMA guidelines, a prospectively registered search was undertaken of MEDLINE and Cochrane databases for observational studies undertaking metagenomic sequencing of the lower gastrointestinal tract of critically ill adults and children within 72 h of admission. Eligible studies reported an alpha diversity metric and one or more of the primary outcome, in-hospital mortality, or secondary clinical outcomes. After aggregate data were requested, meta-analysis was performed for four studies with in-hospital mortality stratified to high or low Shannon index.

RESULTS: The search identified 26 studies for systematic review and 4 had suitable data for meta-analysis. No effect of alpha diversity was seen on in-hospital mortality after binary transformation of Shannon index (odds ratio 0.52, CI 0.12-4.98, I[2] = 0.64) however certainty of evidence is low. Pathogen dominance and commensal depletion were each more frequently associated with in-hospital mortality, adverse clinical and ecological sequelae, particularly overabundance of Enterococcus.

CONCLUSIONS: There is a paucity of large, rigorous observational studies in this population. Globally, alpha diversity was dynamically reduced in early ICU admission in adults and children and was not associated with in-hospital mortality. The abundance of taxa such as Enterococcus spp. appears to offer greater predictive capacity for important clinical and ecological outcomes.}, } @article {pmid36731993, year = {2023}, author = {Wang, L}, title = {Diagnostics for Viral Pathogens in Veterinary Diagnostic Laboratories.}, journal = {The Veterinary clinics of North America. Food animal practice}, volume = {39}, number = {1}, pages = {129-140}, doi = {10.1016/j.cvfa.2022.09.002}, pmid = {36731993}, issn = {1558-4240}, mesh = {Animals ; *Laboratories ; Polymerase Chain Reaction/veterinary ; }, abstract = {Laboratory testing is one part of clinical diagnosis, and quick and reliable testing results provide important data to support treatment decision and develop control strategies. Clinical viral testing has been shifting from traditional virus isolation and electron microscopy to molecular polymerase chain reaction and point-of-care antigen tests. This shift in diagnostic methodology also means change from looking for infectious virions or viral particles to hunting viral antigens and genomes. With technological development, it is predicted that metagenomic sequencing will be commonly used in veterinary clinical diagnosis for unveiling the whole picture of microbes involved in diseases in the future.}, } @article {pmid36731660, year = {2023}, author = {Kumar, V and Vangnai, AS and Sharma, N and Kaur, K and Chakraborty, P and Umesh, M and Singhal, B and Utreja, D and Carrasco, EU and Andler, R and Awasthi, MK and Taherzadeh, MJ}, title = {Bioengineering of biowaste to recover bioproducts and bioenergy: A circular economy approach towards sustainable zero-waste environment.}, journal = {Chemosphere}, volume = {319}, number = {}, pages = {138005}, doi = {10.1016/j.chemosphere.2023.138005}, pmid = {36731660}, issn = {1879-1298}, mesh = {*Solid Waste/analysis ; Bioengineering ; Energy-Generating Resources ; *Garbage ; Bioreactors ; Biofuels/analysis ; }, abstract = {The inevitable need for waste valorisation and management has revolutionized the way in which the waste is visualised as a potential biorefinery for various product development rather than offensive trash. Biowaste has emerged as a potential feedstock to produce several value-added products. Bioenergy generation is one of the potential applications originating from the valorisation of biowaste. Bioenergy production requires analysis and optimization of various parameters such as biowaste composition and conversion potential to develop innovative and sustainable technologies for most effective utilization of biowaste with enhanced bioenergy production. In this context, feedstocks, such as food, agriculture, beverage, and municipal solid waste act as promising resources to produce renewable energy. Similarly, the concept of microbial fuel cells employing biowaste has clearly gained research focus in the past few decades. Despite of these potential benefits, the area of bioenergy generation still is in infancy and requires more interdisciplinary research to be sustainable alternatives. This review is aimed at analysing the bioconversion potential of biowaste to renewable energy. The possibility of valorising underutilized biowaste substrates is elaborately presented. In addition, the application and efficiency of microbial fuel cells in utilizing biowaste are described in detail taking into consideration of its great scope. Furthermore, the review addresses the significance bioreactor development for energy production along with major challenges and future prospects in bioenergy production. Based on this review it can be concluded that bioenergy production utilizing biowaste can clearly open new avenues in the field of waste valorisation and energy research. Systematic and strategic developments considering the techno economic feasibilities of this excellent energy generation process will make them a true sustainable alternative for conventional energy sources.}, } @article {pmid36731616, year = {2023}, author = {Li, X and Li, K and Wang, Y and Huang, Y and Yang, H and Zhu, P and Li, Q}, title = {Diversity of lignocellulolytic functional genes and heterogeneity of thermophilic microbes during different wastes composting.}, journal = {Bioresource technology}, volume = {372}, number = {}, pages = {128697}, doi = {10.1016/j.biortech.2023.128697}, pmid = {36731616}, issn = {1873-2976}, mesh = {*Composting ; Manure/microbiology ; Lignin/metabolism ; Bacteria/genetics/metabolism ; Fungi/genetics/metabolism ; *Microbiota ; Soil ; }, abstract = {The goal of this study was to investigate the heterogeneity of thermophilic microorganisms and their lignocellulose-degrading gene diversity during composting. In this study, bagasse pith/dairy manure (BAG) and sawdust/dairy manure (SAW) were used as experimental subjects. The pour plate method indicated that thermophilic bacteria and thermophilic actinobacteria were more culturable than thermophilic fungi. Metagenomics analysis showed that the Actinobacteria, Firmicutes and Proteobacteria were the dominant phyla during composting. In addition, auxiliary activity and glycoside hydrolase families were critical for lignocellulosic degradation, which were found to be more abundant in BAG. As a result, the degradation rates of cellulose, hemicellulose and lignin in BAG (7.36%, 13.99% and 5.68%) were observably higher than those in SAW (6.13%, 12.09% and 2.62%). These findings contribute to understanding how thermophilic microbial communities play a role in the deconstruction of different lignocelluloses and provide a potential strategy to comprehensively utilize the resources of lignocellulosic biomass.}, } @article {pmid36731323, year = {2023}, author = {Huang, Q and Huang, Y and Li, B and Li, X and Guo, Y and Jiang, Z and Liu, X and Yang, Z and Ning, Z and Xiao, T and Jiang, C and Hao, L}, title = {Metagenomic analysis characterizes resistomes of an acidic, multimetal(loid)-enriched coal source mine drainage treatment system.}, journal = {Journal of hazardous materials}, volume = {448}, number = {}, pages = {130898}, doi = {10.1016/j.jhazmat.2023.130898}, pmid = {36731323}, issn = {1873-3336}, mesh = {*Metagenome ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; *Metals, Heavy ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Heavy metal(loid) contaminations caused by mine activities are potential hot spots of antibiotic resistance genes (ARGs) because of heavy metal(loid)-induced co-selection of ARGs and heavy metal(loid) resistance genes (MRGs). This study used high-throughput metagenomic sequencing to analyze the resistome characteristics of a coal source acid mine drainage passive treatment system. The multidrug efflux mechanism dominated the antibiotic resistome, and a highly diverse heavy metal(loid) resistome was dominated by mercury-, iron-, and arsenic--associated resistance. Correlation analysis indicated that mobile gene elements had a greater influence on the dynamic of MRGs than ARGs. Among the metagenome-assembled genomes, six potential pathogens carrying multiple resistance genes resistant to several antibiotics and heavy metal(loid)s were recovered. Pseudomonas spp. contained the highest numbers of resistance genes, with resistance to two types of antibiotics and 12 types of heavy metal(loid)s. Thus, high contents of heavy metal(loid)s drove the co-selection of ARGs and MRGs. The occurrence of potential pathogens containing multiple resistance genes might increase the risk of ARG dissemination in the environment.}, } @article {pmid36731187, year = {2023}, author = {Bai, H and He, LY and Gao, FZ and Wu, DL and Yao, KS and Zhang, M and Jia, WL and He, LX and Zou, HY and Yao, MS and Ying, GG}, title = {Airborne antibiotic resistome and human health risk in railway stations during COVID-19 pandemic.}, journal = {Environment international}, volume = {172}, number = {}, pages = {107784}, pmid = {36731187}, issn = {1873-6750}, mesh = {Humans ; Genes, Bacterial ; Pandemics ; Anti-Bacterial Agents/pharmacology ; Bayes Theorem ; *COVID-19 ; Bacteria/genetics ; *Microbiota ; }, abstract = {Antimicrobial resistance is recognized as one of the greatest public health concerns. It is becoming an increasingly threat during the COVID-19 pandemic due to increasing usage of antimicrobials, such as antibiotics and disinfectants, in healthcare facilities or public spaces. To explore the characteristics of airborne antibiotic resistome in public transport systems, we assessed distribution and health risks of airborne antibiotic resistome and microbiome in railway stations before and after the pandemic outbreak by culture-independent and culture-dependent metagenomic analysis. Results showed that the diversity of airborne antibiotic resistance genes (ARGs) decreased following the pandemic, while the relative abundance of core ARGs increased. A total of 159 horizontally acquired ARGs, predominantly confering resistance to macrolides and aminoglycosides, were identified in the airborne bacteria and dust samples. Meanwhile, the abundance of horizontally acquired ARGs hosted by pathogens increased during the pandemic. A bloom of clinically important antibiotic (tigecycline and meropenem) resistant bacteria was found following the pandemic outbreak. 251 high-quality metagenome-assembled genomes (MAGs) were recovered from 27 metagenomes, and 86 genera and 125 species were classified. Relative abundance of ARG-carrying MAGs, taxonomically assigned to genus of Bacillus, Pseudomonas, Acinetobacter, and Staphylococcus, was found increased during the pandemic. Bayesian source tracking estimated that human skin and anthropogenic activities were presumptive resistome sources for the public transit air. Moreover, risk assessment based on resistome and microbiome data revealed elevated airborne health risks during the pandemic.}, } @article {pmid36730964, year = {2023}, author = {Yu, N and Ye, S and Yang, Z and Chen, Z and Zhang, C}, title = {Disseminated Cunninghamella elegans Infection Diagnosed by mNGS During Induction Therapy in a Child With Intermediate-risk Acute Lymphoblastic Leukemia: A Case Report and Review of Literature.}, journal = {Journal of pediatric hematology/oncology}, volume = {45}, number = {2}, pages = {e266-e271}, doi = {10.1097/MPH.0000000000002577}, pmid = {36730964}, issn = {1536-3678}, mesh = {Female ; Humans ; Child ; Adolescent ; *Cunninghamella ; *Mucormycosis/drug therapy ; Induction Chemotherapy ; Antifungal Agents/therapeutic use ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma/drug therapy ; }, abstract = {We described a 14-year-old girl with acute lymphoblastic leukemia who developed disseminated mucormycosis during induction therapy. Disseminated Cunninghamella elegans infection was confirmed by histopathology, microbiological culture, and metagenomic next-generation sequencing analysis of skin tissue, blood, and cerebrospinal fluid. Subsequently, the patient received a combination of liposomal amphotericin B, posaconazole, and caspofungin for antifungal treatment, but eventually died because of severe fungal pneumonia, respiratory failure, and septic shock. Moreover, case reports of pulmonary mucormycosis in children published since 1959 were reviewed. In summary, metagenomic next-generation sequencing is an effective diagnostic method for Cunninghamella with high speed and sensitivity.}, } @article {pmid36730456, year = {2023}, author = {Satoh, S and Tanaka, R and Yokono, M and Endoh, D and Yabuki, T and Tanaka, A}, title = {Phylogeny analysis of whole protein-coding genes in metagenomic data detected an environmental gradient for the microbiota.}, journal = {PloS one}, volume = {18}, number = {2}, pages = {e0281288}, pmid = {36730456}, issn = {1932-6203}, mesh = {Phylogeny ; *Metagenome ; *Microbiota/genetics ; Japan ; Metagenomics/methods ; }, abstract = {Environmental factors affect the growth of microorganisms and therefore alter the composition of microbiota. Correlative analysis of the relationship between metagenomic composition and the environmental gradient can help elucidate key environmental factors and establishment principles for microbial communities. However, a reasonable method to quantitatively compare whole metagenomic data and identify the primary environmental factors for the establishment of microbiota has not been reported so far. In this study, we developed a method to compare whole proteomes deduced from metagenomic shotgun sequencing data, and quantitatively display their phylogenetic relationships as metagenomic trees. We called this method Metagenomic Phylogeny by Average Sequence Similarity (MPASS). We also compared one of the metagenomic trees with dendrograms of environmental factors using a comparison tool for phylogenetic trees. The MPASS method correctly constructed metagenomic trees of simulated metagenomes and soil and water samples. The topology of the metagenomic tree of samples from the Kirishima hot springs area in Japan was highly similarity to that of the dendrograms based on previously reported environmental factors for this area. The topology of the metagenomic tree also reflected the dynamics of microbiota at the taxonomic and functional levels. Our results strongly suggest that MPASS can successfully classify metagenomic shotgun sequencing data based on the similarity of whole protein-coding sequences, and will be useful for the identification of principal environmental factors for the establishment of microbial communities. Custom Perl script for the MPASS pipeline is available at https://github.com/s0sat/MPASS.}, } @article {pmid36729322, year = {2023}, author = {Valles, SM and Zhao, C and Rivers, AR and Iwata, RL and Oi, DH and Cha, DH and Collignon, RM and Cox, NA and Morton, GJ and Calcaterra, LA}, title = {RNA virus discoveries in the electric ant, Wasmannia auropunctata.}, journal = {Virus genes}, volume = {59}, number = {2}, pages = {276-289}, pmid = {36729322}, issn = {1572-994X}, mesh = {Animals ; *Ants ; *RNA Viruses/genetics ; Genome, Viral/genetics ; Metagenomics ; RNA ; }, abstract = {Despite being one of the most destructive invasive species of ants, only two natural enemies are known currently for Wasmannia auropunctata, commonly known as the electric ant or little fire ant. Because viruses can be effective biological control agents against many insect pests, including ants, a metagenomics/next-generation sequencing approach was used to facilitate discovery of virus sequences from the transcriptomes of W. auropunctata. Five new and complete positive sense, single-stranded RNA virus genomes, and one new negative sense, single-stranded RNA virus genome were identified, sequenced, and characterized from W. auropunctata collected in Argentina by this approach, including a dicistrovirus (Electric ant dicistrovirus), two polycipiviruses (Electric ant polycipivirus 1; Electric ant polycipivirus 2), a solinvivirus (Electric ant solinvivirus), a divergent genome with similarity to an unclassified group in the Picornavirales (Electric ant virus 1), and a rhabdovirus (Electric ant rhabdovirus). An additional virus genome was detected that is likely Solenopsis invicta virus 10 (MH727527). The virus genome sequences were absent from the transcriptomes of W. auropunctata collected in the USA (Hawaii and Florida). Additional limited field surveys corroborated the absence of these viruses in regions where the electric ant is invasive (the USA and Australia). The replicative genome strand of four of the viruses (Electric ant polycipivirus 2, Electric ant solinvivirus, Electric ant virus 1, and Solenopsis invicta virus 10 (in the electric ant) was detected in Argentinean-collected W. auropunctata indicating that the ant is a host for these viruses. These are the first virus discoveries to be made from W. auropunctata.}, } @article {pmid36728456, year = {2023}, author = {Markkanen, MA and Haukka, K and Pärnänen, KMM and Dougnon, VT and Bonkoungou, IJO and Garba, Z and Tinto, H and Sarekoski, A and Karkman, A and Kantele, A and Virta, MPJ}, title = {Metagenomic Analysis of the Abundance and Composition of Antibiotic Resistance Genes in Hospital Wastewater in Benin, Burkina Faso, and Finland.}, journal = {mSphere}, volume = {8}, number = {1}, pages = {e0053822}, pmid = {36728456}, issn = {2379-5042}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Wastewater ; Burkina Faso ; Benin ; Finland ; Drug Resistance, Microbial/genetics ; Hospitals ; }, abstract = {Antibiotic resistance is a global threat to human health, with the most severe effect in low- and middle-income countries. We explored the presence of antibiotic resistance genes (ARGs) in the hospital wastewater (HWW) of nine hospitals in Benin and Burkina Faso, two low-income countries in West Africa, with shotgun metagenomic sequencing. For comparison, we also studied six hospitals in Finland. The highest sum of the relative abundance of ARGs in the 68 HWW samples was detected in Benin and the lowest in Finland. HWW resistomes and mobilomes in Benin and Burkina Faso resembled each other more than those in Finland. Many carbapenemase genes were detected at various abundances, especially in HWW from Burkina Faso and Finland. The blaGES genes, the most widespread carbapenemase gene in the Beninese HWW, were also found in water intended for hand washing and in a puddle at a hospital yard in Benin. mcr genes were detected in the HWW of all three countries, with mcr-5 being the most common mcr gene. These and other mcr genes were observed in very high relative abundances, even in treated wastewater in Burkina Faso and a street gutter in Benin. The results highlight the importance of wastewater treatment, with particular attention to HWW. IMPORTANCE The global emergence and increased spread of antibiotic resistance threaten the effectiveness of antibiotics and, thus, the health of the entire population. Therefore, understanding the resistomes in different geographical locations is crucial in the global fight against the antibiotic resistance crisis. However, this information is scarce in many low- and middle-income countries (LMICs), such as those in West Africa. In this study, we describe the resistomes of hospital wastewater in Benin and Burkina Faso and, as a comparison, Finland. Our results help to understand the hitherto unrevealed resistance in Beninese and Burkinabe hospitals. Furthermore, the results emphasize the importance of wastewater management infrastructure design to minimize exposure events between humans, HWW, and the environment, preventing the circulation of resistant bacteria and ARGs between humans (hospitals and community) and the environment.}, } @article {pmid36728429, year = {2023}, author = {Graffius, S and Garzón, JFG and Zehl, M and Pjevac, P and Kirkegaard, R and Flieder, M and Loy, A and Rattei, T and Ostrovsky, A and Zotchev, SB}, title = {Secondary Metabolite Production Potential in a Microbiome of the Freshwater Sponge Spongilla lacustris.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0435322}, pmid = {36728429}, issn = {2165-0497}, abstract = {Marine and freshwater sponges harbor diverse communities of bacteria with vast potential to produce secondary metabolites that may play an important role in protecting the host from predators and infections. In this work, we initially used cultivation and metagenomics to investigate the microbial community of the freshwater sponge Spongilla lacustris collected in an Austrian lake. Representatives of 41 bacterial genera were isolated from the sponge sample and classified according to their 16S rRNA gene sequences. The genomes of 33 representative isolates and the 20 recovered metagenome-assembled genomes (MAGs) contained in total 306 secondary metabolite biosynthesis gene clusters (BGCs). Comparative 16S rRNA gene and genome analyses showed very little taxon overlap between the recovered isolates and the sponge community as revealed by cultivation-independent methods. Both culture-independent and -dependent analyses suggested high biosynthetic potential of the S. lacustris microbiome, which was confirmed experimentally even at the subspecies level for two Streptomyces isolates. To our knowledge, this is the most thorough description of the secondary metabolite production potential of a freshwater sponge microbiome to date. IMPORTANCE A large body of research is dedicated to marine sponges, filter-feeding animals harboring rich bacterial microbiomes believed to play an important role in protecting the host from predators and infections. Freshwater sponges have received so far much less attention with respect to their microbiomes, members of which may produce bioactive secondary metabolites with potential to be developed into drugs to treat a variety of diseases. In this work, we investigated the potential of bacteria associated with the freshwater sponge Spongilla lacustris to biosynthesize diverse secondary metabolites. Using culture-dependent and -independent methods, we discovered over 300 biosynthetic gene clusters in sponge-associated bacteria and proved production of several compounds by selected isolates using genome mining. Our results illustrate the importance of a complex approach when dealing with microbiomes of multicellular organisms that may contain producers of medically important secondary metabolites.}, } @article {pmid36728425, year = {2023}, author = {Gaston, DC}, title = {Clinical Metagenomics for Infectious Diseases: Progress toward Operational Value.}, journal = {Journal of clinical microbiology}, volume = {61}, number = {2}, pages = {e0126722}, pmid = {36728425}, issn = {1098-660X}, mesh = {Humans ; *Metagenomics/methods ; Pilot Projects ; High-Throughput Nucleotide Sequencing/methods ; *Communicable Diseases ; Metagenome ; }, abstract = {The field of clinical metagenomics for infectious disease diagnostics has advanced to combining questions of technical methodologies with best-use practices due to lowering barriers of implementation. This commentary identifies challenges facing further development of the field and proposes methods for advancement by highlighting a recent prospective pilot study evaluating a targeted metagenomic approach for infectious endocarditis. This commentary introduces the concept of operational value as a method for standardizing results generated by differing clinical metagenomic approaches. Operational value includes assessments of result quality, utility, and cost through incorporating methodological aspects of metagenomics as applied to various infectious syndromes, patient populations, and specimen types. Focus is placed on standardizing outcome-based metrics using an operational value matrix. As ambitions of clinical metagenomics are increasingly realized, new models of study design and collaboration could promote progress toward routine use and positive benefits for patients with infectious diseases.}, } @article {pmid36727292, year = {2023}, author = {Osborne, MG and Molano, G and Simons, AL and Dao, V and Ong, B and Vong, B and Singh, A and Montecinos Arismendi, GJ and Alberto, F and Nuzhdin, SV}, title = {Natural variation of Macrocystis pyrifera gametophyte germplasm culture microbiomes and applications for improving yield in offshore farms.}, journal = {Journal of phycology}, volume = {59}, number = {2}, pages = {402-417}, doi = {10.1111/jpy.13320}, pmid = {36727292}, issn = {1529-8817}, support = {T32-GM118289/NH/NIH HHS/United States ; }, mesh = {*Macrocystis ; Germ Cells, Plant ; Biomass ; *Seaweed ; }, abstract = {With national interest in seaweed-based biofuels as a sustainable alternative to fossil fuels, there is a need for tools that produce high-yield seaweed cultivars and increase the efficiency of offshore farms. Several agricultural studies have demonstrated that the application of microbial inoculants at an early life stage can improve crop yield, and there is an opportunity to use similar techniques in seaweed aquaculture. However, there is a critical knowledge gap regarding host-microbiome associations of macroalgae gametophytes in germplasm cultures. Here, we investigate the microbial community of Macrocystis pyrifera gametophyte germplasm cultures that were used to cultivate an offshore farm in Santa Barbara, California and identify key taxa correlated with increased biomass of mature sporophytes. This work provides a valuable knowledge base for the development of microbial inoculants that produce high-biomass M. pyrifera cultivars to ultimately be used as biofuel feedstocks.}, } @article {pmid36727264, year = {2023}, author = {Gendron, EM and Sevigny, JL and Byiringiro, I and Thomas, WK and Powers, TO and Porazinska, DL}, title = {Nematode mitochondrial metagenomics: A new tool for biodiversity analysis.}, journal = {Molecular ecology resources}, volume = {23}, number = {5}, pages = {975-989}, doi = {10.1111/1755-0998.13761}, pmid = {36727264}, issn = {1755-0998}, support = {AWD07689//National Institute of Food and Agriculture/ ; NH00694//National Institute of Food and Agriculture/ ; }, mesh = {Animals ; Phylogeny ; Metagenomics ; *Nematoda/genetics ; Biodiversity ; DNA ; DNA Barcoding, Taxonomic ; *Genome, Mitochondrial/genetics ; }, abstract = {DNA barcoding approaches have greatly increased our understanding of biodiversity on the planet, and metabarcoding is widely used for classifying members of the phylum Nematoda. However, loci typically utilized in metabarcoding studies are often unable to resolve closely related species or are unable to recover all taxa present in a sample due to inadequate PCR primer binding. Mitochondrial metagenomics (mtMG) is an alternative approach utilizing shotgun sequencing of total DNA to recover the mitochondrial genomes of all species present in samples. However, this approach requires a comprehensive reference database for identification and currently available mitochondrial sequences for nematodes are highly dominated by sequences from the order Rhabditida, and excludes many clades entirely. Here, we analysed the efficacy of mtMG for the recovery of nematode taxa and the generation of mitochondrial genomes. We first developed a curated reference database of nematode mitochondrial sequences and expanded it with 40 newly sequenced taxa. We then tested the mito-metagenomics approach using a series of nematode mock communities consisting of morphologically identified nematode species representing various feeding traits, life stages, and phylogenetic relationships. We were able to identify all but two species through the de novo assembly of COX1 genes. We were also able to recover additional mitochondrial protein coding genes (PCGs) for 23 of the 24 detected species including a full array of 12 PCGs from five of the species. We conclude that mtMG offers a potential for the effective recovery of nematode biodiversity but remains limited by the breadth of the reference database.}, } @article {pmid36726816, year = {2022}, author = {Kulecka, M and Fraczek, B and Balabas, A and Czarnowski, P and Zeber-Lubecka, N and Zapala, B and Baginska, K and Glowienka, M and Szot, M and Skorko, M and Kluska, A and Piatkowska, M and Mikula, M and Ostrowski, J}, title = {Characteristics of the gut microbiome in esports players compared with those in physical education students and professional athletes.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {1092846}, pmid = {36726816}, issn = {2296-861X}, abstract = {INTRODUCTION: Esports is a category of competitive video games that, in many aspects, may be similar to traditional sports; however, the gut microbiota composition of players has not been yet studied.

MATERIALS AND METHODS: Here, we investigated the composition and function of the gut microbiota, as well as short chain fatty acids (SCFAs), and amino acids, in a group of 109 well-characterized Polish male esports players. The results were compared with two reference groups: 25 endurance athletes and 36 healthy students of physical education. DNA and metabolites isolated from fecal samples were analyzed using shotgun metagenomic sequencing and mass spectrometry, respectively. Physical activity and nutritional measures were evaluated by questionnaire.

RESULTS: Although anthropometric, physical activity and nutritional measures differentiated esports players from students, there were no differences in bacterial diversity, the Bacteroidetes/Firmicutes ratio, the composition of enterotype clusters, metagenome functional content, or SCFA concentrations. However, there were significant differences between esports players and students with respect to nine bacterial species and nine amino acids. By contrast, all of the above-mentioned measures differentiated professional athletes from esports players and students, with 45 bacteria differentiating professional athletes from the former and 31 from the latter. The only species differentiating all three experimental groups was Parabacteroides distasonis, showing the lowest and highest abundance in esports players and athletes, respectively.

CONCLUSION: Our study confirms the marked impact of intense exercise training on gut microbial structure and function. Differences in lifestyle and dietary habits between esports players and physical education students appear to not have a major effect on the gut microbiota.}, } @article {pmid36726562, year = {2022}, author = {Liu, Y and Cao, Y and Yohannes Woldemariam, K and Zhong, S and Yu, Q and Wang, J}, title = {Antioxidant effect of yeast on lipid oxidation in salami sausage.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1113848}, pmid = {36726562}, issn = {1664-302X}, abstract = {Salami is a kind of fermented meat product with rich nutrition and unique flavor. Because it is rich in fat, it is easy to oxidize to produce bad flavor. Compared with the way of adding artificial or natural antioxidants to reduce the degree of sausage oxidation, the antioxidant characteristics of developing the starter itself deserve more attention. In this study, firstly the antioxidant activities of 5 strains of yeast were measured in vitro, and then the mixture of yeast and Lactobacillus rhamnosus YL-1 was applied to fermented sausage model. The effect of the starter in the sausage model was investigated through physicochemical parameters, degree of fat oxidation, free fatty acid content, and though volatile flavor compound analysis, sensory evaluation and various indexes after storage were observed. Metagenomics was used to explore metabolic pathways, functional genes and key enzymes related to lipid oxidizing substances in sausage in yeast. The results showed that Wickerhamomyces anomalus Y12-3 and Y12-4 had strong tolerance to H2O2, and had higher SOD and CAT enzyme activities. The addition of yeast effectively reduced the material value of peroxidation value and active thiobarbiturate in salami. In flavor analysis, the content of flavor compounds associated with lipid oxidation, such as hexanal, heptanal, nonanal and (E)-2-decenal were significantly lower with the use of Debaryomyces hansenii Y4-1 and Y12-3. Meanwhile, the possible pathways of yeast metabolism of flavor substances related to lipid oxidation (mainly aldehydes) were discussed with the help of metagenomic techniques. According to the results of metagenomics, fatty acid degradation (ko00071) metabolic pathway was related to the degradation of aldehydes through aldehyde dehydrogenase, which was the potential key enzyme.}, } @article {pmid36725284, year = {2023}, author = {Shinde, PB and Mohite, SV and Yadav, A and Singh, MK and Kedia, S and Ahuja, V and Sharma, KK}, title = {Functional analysis of metalloenzymes from human gut microbiota and their role in ulcerative colitis.}, journal = {Journal of applied microbiology}, volume = {134}, number = {3}, pages = {}, doi = {10.1093/jambio/lxad016}, pmid = {36725284}, issn = {1365-2672}, support = {5/4/8-1/2019-NCD-II//Indian Council of Medical Research/ ; 1196SR/FST/LS-I/2017/4//DST-FIST/ ; }, mesh = {Humans ; *Colitis, Ulcerative/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; }, abstract = {AIM: Metalloenzymes produced by gut microbiota play an essential role in various physiological processes, and maintains homeostasis of gastrointestinal tract. Our study includes functional analysis of microbial metalloenzymes using metagenomics and metatranscriptomics data from Inflammatory Bowel Disease Multiomics Database.

METHODS AND RESULTS: The distance matrix calculated by using metalloenzymes data produced significant results for bacterial taxonomy, with higher variance compared to HMP analysis in both Western and Indian population. Differential gene expression analysis revealed altered expression of ulcerative colitis (UC)-associated enzymes, increased folds changes in Prevotella and Megamonas transcripts; whereas, low transcripts of Alistipes genera. Further, docking and simulation studies performed on screened UC-associated enzymes revealed changes in catalytic efficiency and ligand interacting residues.

CONCLUSION: The β-diversity using microbes containing metalloenzymes suggests considering small group of specific genes or enzymes for understanding the diversity between UC and healthy individuals. The docking and differential gene expression analysis collectively indicate the probable role of metalloenzymes and few UC-associated enzymes in the severity of UC.}, } @article {pmid36725208, year = {2023}, author = {Walsh, AM and Leech, J and Huttenhower, C and Delhomme-Nguyen, H and Crispie, F and Chervaux, C and Cotter, PD}, title = {Integrated molecular approaches for fermented food microbiome research.}, journal = {FEMS microbiology reviews}, volume = {47}, number = {2}, pages = {}, pmid = {36725208}, issn = {1574-6976}, mesh = {Animals ; Humans ; *Microbiota ; Diet ; *Fermented Foods ; Fermentation ; High-Throughput Nucleotide Sequencing ; }, abstract = {Molecular technologies, including high-throughput sequencing, have expanded our perception of the microbial world. Unprecedented insights into the composition and function of microbial communities have generated large interest, with numerous landmark studies published in recent years relating the important roles of microbiomes and the environment-especially diet and nutrition-in human, animal, and global health. As such, food microbiomes represent an important cross-over between the environment and host. This is especially true of fermented food microbiomes, which actively introduce microbial metabolites and, to a lesser extent, live microbes into the human gut. Here, we discuss the history of fermented foods, and examine how molecular approaches have advanced research of these fermented foods over the past decade. We highlight how various molecular approaches have helped us to understand the ways in which microbes shape the qualities of these products, and we summarize the impacts of consuming fermented foods on the gut. Finally, we explore how advances in bioinformatics could be leveraged to enhance our understanding of fermented foods. This review highlights how integrated molecular approaches are changing our understanding of the microbial communities associated with food fermentation, the creation of unique food products, and their influences on the human microbiome and health.}, } @article {pmid36725090, year = {2023}, author = {Verburgt, CM and Dunn, KA and Otley, A and Heyman, MB and Verstraete, S and Sunseri, W and Sylvester, F and de Meij, T and Comeau, A and Langille, M and de Jonge, WJ and Benninga, MA and Van Limbergen, JE}, title = {Personalised azithromycin+metronidazole (PAZAZ), in combination with standard induction therapy, to achieve a faecal microbiome community structure and metagenome changes associated with sustained remission in paediatric Crohn's disease (CD): protocol of a pilot study.}, journal = {BMJ open}, volume = {13}, number = {2}, pages = {e064944}, pmid = {36725090}, issn = {2044-6055}, mesh = {Humans ; Child ; *Crohn Disease/drug therapy ; Azithromycin/therapeutic use ; Metronidazole/therapeutic use ; Pilot Projects ; Induction Chemotherapy/methods ; Metagenome ; Bayes Theorem ; RNA, Ribosomal, 16S ; Anti-Bacterial Agents/therapeutic use ; Remission Induction ; *Microbiota ; Recurrence ; Randomized Controlled Trials as Topic ; Multicenter Studies as Topic ; }, abstract = {INTRODUCTION: Early relapse in Crohn's disease (CD) is associated with a more severe disease course. The microbiome plays a crucial role, yet strategies targeting the microbiome are underrepresented in current guidelines. We hypothesise that early manipulation of the microbiome will improve clinical response to standard-of-care (SOC) induction therapy in patients with a relapse-associated microbiome profile. We describe the protocol of a pilot study assessing feasibility of treatment allocation based on baseline faecal microbiome profiles.

METHODS AND ANALYSIS: This is a 52-week, multicentre, randomised, controlled, open-label, add-on pilot study to test the feasibility of a larger multicontinent trial evaluating the efficacy of adjuvant antibiotic therapy in 20 paediatric patients with mild-to-moderate-CD (10
ETHICS AND DISSEMINATION: This study was approved by METC-AMC and CCMO (Netherlands) and IWK Health Centre (Canada). The first version of this protocol was approved by North Carolina Children's Hospital (USA), Wolfson Medical Centre (Israel). The FDA (USA), Health Canada and Ministry of Health (Israel) have reviewed and approved the protocol. Results will be published in international peer-reviewed journals and summaries will be provided to the funders and participants.

TRIAL REGISTRATION NUMBER: NCT04186247.}, } @article {pmid36724855, year = {2023}, author = {Shen, D and Zhou, B and Shan, M and Li, X and Chu, M and Shen, Y and Zhan, Y and Xu, J and Wu, D and Xu, Y}, title = {Evaluation of the Diagnostic Performance of Plasma Metagenomic Next-Generation Sequencing in Febrile Events in the First 30 Days after Chimeric Antigen Receptor T Cell Infusion.}, journal = {Transplantation and cellular therapy}, volume = {29}, number = {5}, pages = {304.e1-304.e8}, doi = {10.1016/j.jtct.2023.01.024}, pmid = {36724855}, issn = {2666-6367}, mesh = {Humans ; *Receptors, Chimeric Antigen ; Immunotherapy, Adoptive/adverse effects ; High-Throughput Nucleotide Sequencing ; Immunotherapy ; Cytokine Release Syndrome ; Fever/diagnosis/etiology ; }, abstract = {Chimeric antigen receptor-modified T cell (CAR-T) therapy is a promising novel immunotherapy for hematologic malignancies, and the diagnosis of infection after CAR-T infusion (CTI) presents challenges for clinicians. Plasma metagenomic next-generation sequencing (mNGS) has been shown to be a reliable diagnostic approach for infection, especially in immunocompromised patients. We aimed to investigate the diagnostic performance of plasma mNGS for infection in the first 30 days after CTI. A cohort of 153 patients who experienced a total of 170 febrile events during the first 30 days post-CTI were enrolled. Of these events, 51 were evaluated with both mNGS and CDM and 119 were assessed by conventional detection methods (CDM) only. We also explored the epidemiology of infections and differences in infection complications in cases with severe (>2) and moderate (≤2) cytokine release syndrome (CRS). Cases with febrile events were clinically divided into an infection group (IG) (95 of 170; 55.9%) and a noninfection group (NIG) (75 of 170; 44.1%). The sensitivity and specificity of mNGS for the diagnosis of infectious complications in the first 30 days after CTI were 69.2% and 89.2%, respectively, with the sensitivity superior to that of culture (P < .001). More infection cases assessed with both mNGS and CDM than those assessed with CDM only were laboratory-confirmed (63.9% versus 11.9%; P < .001). The serum C-reactive protein level was higher and the IFN-γ level was lower in the IG group, particularly in cases with CRS grade ≤2. Infection is a common complication in the first 30 days after CTI. The addition of mNGS to CDM improved the diagnostic yield, and mNGS showed relatively high sensitivity and specificity in post-CAR-T therapy febrile events.}, } @article {pmid36724220, year = {2023}, author = {Ngugi, DK and Salcher, MM and Andrei, AS and Ghai, R and Klotz, F and Chiriac, MC and Ionescu, D and Büsing, P and Grossart, HP and Xing, P and Priscu, JC and Alymkulov, S and Pester, M}, title = {Postglacial adaptations enabled colonization and quasi-clonal dispersal of ammonia-oxidizing archaea in modern European large lakes.}, journal = {Science advances}, volume = {9}, number = {5}, pages = {eadc9392}, pmid = {36724220}, issn = {2375-2548}, mesh = {*Archaea/genetics ; *Lakes ; Ammonia ; Ecosystem ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Ammonia-oxidizing archaea (AOA) play a key role in the aquatic nitrogen cycle. Their genetic diversity is viewed as the outcome of evolutionary processes that shaped ancestral transition from terrestrial to marine habitats. However, current genome-wide insights into AOA evolution rarely consider brackish and freshwater representatives or provide their divergence timeline in lacustrine systems. An unbiased global assessment of lacustrine AOA diversity is critical for understanding their origins, dispersal mechanisms, and ecosystem roles. Here, we leveraged continental-scale metagenomics to document that AOA species diversity in freshwater systems is remarkably low compared to marine environments. We show that the uncultured freshwater AOA, "Candidatus Nitrosopumilus limneticus," is ubiquitous and genotypically static in various large European lakes where it evolved 13 million years ago. We find that extensive proteome remodeling was a key innovation for freshwater colonization of AOA. These findings reveal the genetic diversity and adaptive mechanisms of a keystone species that has survived clonally in lakes for millennia.}, } @article {pmid36722794, year = {2023}, author = {Guo, W and Ren, K and Ning, R and Li, C and Zhang, Y and Gan, Y and Fu, X and Xiao, C and Pang, Y and Cheng, L and Zhang, S and Li, D and Zhao, J and Dai, M and Li, Y}, title = {Microbial species from multiple maternal body sites shape the developing giant panda (Ailuropoda melanoleuca) cub gut microbiome.}, journal = {Molecular ecology}, volume = {32}, number = {9}, pages = {2271-2286}, doi = {10.1111/mec.16869}, pmid = {36722794}, issn = {1365-294X}, mesh = {Animals ; Female ; Bacteria/genetics ; Diet/veterinary ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Ursidae/genetics ; }, abstract = {The gut microbiome of the giant panda (Ailuropoda melanoleuca) plays a vital role in nutrient acquisition from its specialized bamboo diet. Giant panda cubs harbour significantly different gut microbiota during their growth and development when feeding on milk before switching to bamboo. The fetal gut is sterile, and following birth, mother-to-infant microbial transmission has been implicated as a seeding source for the infant gut microbiota. Details of this transmission in giant pandas remain unclear. In this study, faecal samples were collected from seven panda mother-cub pairs when the cubs were 4-16 months old. Additional samples from the cubs' diet, soil and drinking water, and multiple body sites of the mothers were collected. Bacterial 16S rRNA gene sequencing and shotgun metagenomic sequencing were performed to determine the source and potential transmission routes of the cub gut microbiome. Source tracking analysis showed that maternal vagina, milk and faeces were the primary contributory sources of microbes, shaping the cub gut microbiome. Bacterial species from maternal faeces persisted the longest in the cub gut. Bacterial species in the diet contributed to the microbial community. Metagenomics analysis indicated that the predicted metabolic pathways of the gut microbiome also varied at different growth stages. Gut colonization with bacteria from various body sites of the mothers provides a foundational microbial community that is beneficial in fulfilling the evolving dietary needs of the cubs. This study suggests that mother-to-cub transmission is indispensable in shaping the gut microbiome of the developing panda cub.}, } @article {pmid36722516, year = {2023}, author = {Kwa, WT and Sundarajoo, S and Toh, KY and Lee, J}, title = {Application of emerging technologies for gut microbiome research.}, journal = {Singapore medical journal}, volume = {64}, number = {1}, pages = {45-52}, pmid = {36722516}, issn = {2737-5935}, mesh = {Humans ; *Gastrointestinal Microbiome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Health Status ; }, abstract = {Microbiome is associated with a wide range of diseases. The gut microbiome is also a dynamic reflection of health status, which can be modified, thus representing great potential to exploit the mechanisms that influence human physiology. Recent years have seen a dramatic rise in gut microbiome studies, which has been enabled by the rapidly evolving high-throughput sequencing methods (i.e. 16S rRNA sequencing and shotgun sequencing). As the emerging technologies for microbiome research continue to evolve (i.e. metatranscriptomics, metabolomics, culturomics, synthetic biology), microbiome research has moved beyond phylogenetic descriptions and towards mechanistic analyses. In this review, we highlight different approaches to study the microbiome, in particular, the current limitations and future promise of these techniques. This review aims to provide clinicians with a framework for studying the microbiome, as well as to accelerate the adoption of these techniques in clinical practice.}, } @article {pmid36722204, year = {2023}, author = {Martin, S and Ayling, M and Patrono, L and Caccamo, M and Murcia, P and Leggett, RM}, title = {Capturing variation in metagenomic assembly graphs with MetaCortex.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {1}, pages = {}, pmid = {36722204}, issn = {1367-4811}, support = {BB/CCG1720/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M004805/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MC_UU_12014/9/MRC_/Medical Research Council/United Kingdom ; BB/CSP1720/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Metagenome ; Haplotypes ; *Metagenomics ; Software ; }, abstract = {MOTIVATION: The assembly of contiguous sequence from metagenomic samples presents a particular challenge, due to the presence of multiple species, often closely related, at varying levels of abundance. Capturing diversity within species, for example, viral haplotypes, or bacterial strain-level diversity, is even more challenging.

RESULTS: We present MetaCortex, a metagenome assembler that captures intra-species diversity by searching for signatures of local variation along assembled sequences in the underlying assembly graph and outputting these sequences in sequence graph format. We show that MetaCortex produces accurate assemblies with higher genome coverage and contiguity than other popular metagenomic assemblers on mock viral communities with high levels of strain-level diversity and on simulated communities containing simulated strains.

Source code is freely available to download from https://github.com/SR-Martin/metacortex, is implemented in C and supported on MacOS and Linux. The version used for the results presented in this article is available at doi.org/10.5281/zenodo.7273627.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36722031, year = {2023}, author = {Lilian, M and Rawlynce, B and Charles, G and Felix, K}, title = {Potential role of rumen bacteria in modulating milk production and composition of admixed dairy cows.}, journal = {Letters in applied microbiology}, volume = {76}, number = {2}, pages = {}, doi = {10.1093/lambio/ovad007}, pmid = {36722031}, issn = {1472-765X}, mesh = {Female ; Humans ; Cattle ; Animals ; *Lactation ; RNA, Ribosomal, 16S/genetics ; *Rumen/microbiology ; Animal Feed/analysis ; Bacteria ; Firmicutes/genetics ; Bacteroidetes/genetics ; Diet/veterinary ; Fermentation ; }, abstract = {Cattle milk is an important food for the growing calf and humans because of its concentrated macro and micro nutrients. However, the quantity and quality of milk nutrients vary depending on several factors. This study evaluated the effect of dietary modification on rumen bacteria as well as the potential role of rumen bacteria in modifying milk production and composition profile. Using a 16S rRNA metagenomic approach, the study characterized the rumen bacterial community composition in four dairy cows and their milk production and composition. The results indicated that Bacteroidetes and Firmicutes were the dominant bacteria, totaling ∼83.7% of the rumen bacteria. An increase in concentrate proportion in diet led to an increase in the abundance of Bacteroidetes (P ≤ 0.05) and Proteobacteria while Firmicutes and Fibrobacter decreased. Milk production and composition were highly correlated with the abundance of various rumen bacterial members. Lentispaerae (P = 0.010), and Synergistetes (P = 0.011) exhibited a positive and significant correlation while Tenericutes (P = 0.009) showed a negative correlation with milk protein. Fusobacteria (P = 0.016) showed a negative correlation with milk lactose. Similarly, several genera showed correlations with milk parameters. The correlation between microbes with milk parameters implies that the bacterial community possesses the potential to influence milk production and composition.}, } @article {pmid36721784, year = {2022}, author = {Jun, SC and Kim, YK and Han, KH}, title = {Characterization of Nonaflatoxigenic Aspergillus flavus/oryzae Strains Isolated from Korean Traditional Soybean Meju.}, journal = {Mycobiology}, volume = {50}, number = {6}, pages = {408-419}, pmid = {36721784}, issn = {1229-8093}, abstract = {Filamentous fungi that could be classified into Aspergillus flavus/oryzae were isolated from traditionally fermented meju commercially available in Korea. The samples were analyzed for aflatoxin B1 and ochratoxin A contamination by HPLC; however, no toxin was detected. In addition, fungal and bacterial metagenomic sequencing were performed to analyze the microbial distribution in the samples. The results revealed that the distribution and abundance of fungi and bacteria differed considerably depending on the production regions and fermentation conditions of the meju samples. Through morphological analysis, ITS region sequencing, and assessment of the aflatoxin-producing ability, a total of 32 A. flavus/oryzae strains were identified. PCR analysis of six regions with a high mutation frequency in the aflatoxin gene cluster (AGC) revealed a total of six types of AGC breaking point patterns. The A. flavus/oryzae strains did not exhibit the high amylase activity detected in the commercial yellow koji strain (starter mold). However, their peptidase and lipase activities were generally higher than that of the koji isolates. We verified the safety of the traditionally fermented meju samples by analyzing the AGC breaking point pattern and the enzyme activities of A. flavus/oryzae strains isolated from the samples. The isolated strains could possibly be used as starter molds for soybean fermentation.}, } @article {pmid36721270, year = {2023}, author = {Yang, K and Wang, X and Hou, R and Lu, C and Fan, Z and Li, J and Wang, S and Xu, Y and Shen, Q and Friman, VP and Wei, Z}, title = {Rhizosphere phage communities drive soil suppressiveness to bacterial wilt disease.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {16}, pmid = {36721270}, issn = {2049-2618}, mesh = {Rhizosphere ; Bacteria/genetics ; *Bacteriophages ; *Microbiota ; Soil ; }, abstract = {BACKGROUND: Bacterial viruses, phages, play a key role in nutrient turnover and lysis of bacteria in terrestrial ecosystems. While phages are abundant in soils, their effects on plant pathogens and rhizosphere bacterial communities are poorly understood. Here, we used metagenomics and direct experiments to causally test if differences in rhizosphere phage communities could explain variation in soil suppressiveness and bacterial wilt plant disease outcomes by plant-pathogenic Ralstonia solanacearum bacterium. Specifically, we tested two hypotheses: (1) that healthy plants are associated with stronger top-down pathogen control by R. solanacearum-specific phages (i.e. 'primary phages') and (2) that 'secondary phages' that target pathogen-inhibiting bacteria play a stronger role in diseased plant rhizosphere microbiomes by indirectly 'helping' the pathogen.

RESULTS: Using a repeated sampling of tomato rhizosphere soil in the field, we show that healthy plants are associated with distinct phage communities that contain relatively higher abundances of R. solanacearum-specific phages that exert strong top-down pathogen density control. Moreover, 'secondary phages' that targeted pathogen-inhibiting bacteria were more abundant in the diseased plant microbiomes. The roles of R. solanacearum-specific and 'secondary phages' were directly validated in separate greenhouse experiments where we causally show that phages can reduce soil suppressiveness, both directly and indirectly, via top-down control of pathogen densities and by alleviating interference competition between pathogen-inhibiting bacteria and the pathogen.

CONCLUSIONS: Together, our findings demonstrate that soil suppressiveness, which is most often attributed to bacteria, could be driven by rhizosphere phage communities that regulate R. solanacearum densities and strength of interference competition with pathogen-suppressing bacteria. Rhizosphere phage communities are hence likely to be important in determining bacterial wilt disease outcomes and soil suppressiveness in agricultural fields. Video Abstract.}, } @article {pmid36721059, year = {2023}, author = {Dede, B and Priest, T and Bach, W and Walter, M and Amann, R and Meyerdierks, A}, title = {High abundance of hydrocarbon-degrading Alcanivorax in plumes of hydrothermally active volcanoes in the South Pacific Ocean.}, journal = {The ISME journal}, volume = {17}, number = {4}, pages = {600-610}, pmid = {36721059}, issn = {1751-7370}, mesh = {*Alcanivoraceae/genetics/metabolism ; Pacific Ocean ; In Situ Hybridization, Fluorescence ; RNA, Ribosomal, 16S/genetics ; Hydrocarbons/metabolism ; Phylogeny ; Seawater ; }, abstract = {Species within the genus Alcanivorax are well known hydrocarbon-degraders that propagate quickly in oil spills and natural oil seepage. They are also inhabitants of the deep-sea and have been found in several hydrothermal plumes. However, an in-depth analysis of deep-sea Alcanivorax is currently lacking. In this study, we used multiple culture-independent techniques to analyze the microbial community composition of hydrothermal plumes in the Northern Tonga arc and Northeastern Lau Basin focusing on the autecology of Alcanivorax. The hydrothermal vents feeding the plumes are hosted in an arc volcano (Niua), a rear-arc caldera (Niuatahi) and the Northeast Lau Spreading Centre (Maka). Fluorescence in situ hybridization revealed that Alcanivorax dominated the community at two sites (1210-1565 mbsl), reaching up to 48% relative abundance (3.5 × 10[4] cells/ml). Through 16S rRNA gene and metagenome analyses, we identified that this pattern was driven by two Alcanivorax species in the plumes of Niuatahi and Maka. Despite no indication for hydrocarbon presence in the plumes of these areas, a high expression of genes involved in hydrocarbon-degradation was observed. We hypothesize that the high abundance and gene expression of Alcanivorax is likely due to yet undiscovered hydrocarbon seepage from the seafloor, potentially resulting from recent volcanic activity in the area. Chain-length and complexity of hydrocarbons, and water depth could be driving niche partitioning in Alcanivorax.}, } @article {pmid36720887, year = {2023}, author = {Du, Y and Fuhrman, JA and Sun, F}, title = {ViralCC retrieves complete viral genomes and virus-host pairs from metagenomic Hi-C data.}, journal = {Nature communications}, volume = {14}, number = {1}, pages = {502}, pmid = {36720887}, issn = {2041-1723}, support = {R01 GM131407/GM/NIGMS NIH HHS/United States ; R01 GM120624/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Cattle ; Female ; Humans ; Metagenome/genetics ; Metagenomics ; Wastewater ; Genome, Viral/genetics ; *Microbiota ; *Bacteriophages/genetics ; }, abstract = {The introduction of high-throughput chromosome conformation capture (Hi-C) into metagenomics enables reconstructing high-quality metagenome-assembled genomes (MAGs) from microbial communities. Despite recent advances in recovering eukaryotic, bacterial, and archaeal genomes using Hi-C contact maps, few of Hi-C-based methods are designed to retrieve viral genomes. Here we introduce ViralCC, a publicly available tool to recover complete viral genomes and detect virus-host pairs using Hi-C data. Compared to other Hi-C-based methods, ViralCC leverages the virus-host proximity structure as a complementary information source for the Hi-C interactions. Using mock and real metagenomic Hi-C datasets from several different microbial ecosystems, including the human gut, cow fecal, and wastewater, we demonstrate that ViralCC outperforms existing Hi-C-based binning methods as well as state-of-the-art tools specifically dedicated to metagenomic viral binning. ViralCC can also reveal the taxonomic structure of viruses and virus-host pairs in microbial communities. When applied to a real wastewater metagenomic Hi-C dataset, ViralCC constructs a phage-host network, which is further validated using CRISPR spacer analyses. ViralCC is an open-source pipeline available at https://github.com/dyxstat/ViralCC .}, } @article {pmid36720820, year = {2023}, author = {Bohutínská, M and Vlček, J and Monnahan, P and Kolář, F}, title = {Population Genomic Analysis of Diploid-Autopolyploid Species.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2545}, number = {}, pages = {297-324}, pmid = {36720820}, issn = {1940-6029}, mesh = {*Diploidy ; *Metagenomics ; Genomics ; Ploidies ; Acclimatization ; }, abstract = {This chapter outlines an empirical analysis of genome-wide single-nucleotide polymorphism (SNP) variation and its underlying drivers among multiple natural populations within a diploid-autopolyploid species. The aim is to reconstruct the genetic structure among natural populations of varying ploidy and infer footprints of selection in these populations, framed around specific questions that are typically encountered when analyzing a mixed-ploidy data set,e.g., addressing the relevance of natural whole-genome duplication for speciation and adaptation. We briefly review the options for the analysis of polyploid population genomic data involving variant calling, population structure, demographic history inference, and selection scanning approaches. Further, we provide suggestions for methods and associated software, possible caveats, and examples of their application to mixed-ploidy and autopolyploid data sets.}, } @article {pmid36720819, year = {2023}, author = {Scott, AD and Van de Velde, JD and Novikova, PY}, title = {Inference of Polyploid Origin and Inheritance Mode from Population Genomic Data.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2545}, number = {}, pages = {279-295}, doi = {10.1007/978-1-0716-2561-3_15}, pmid = {36720819}, issn = {1940-6029}, mesh = {Humans ; *Metagenomics ; Phylogeny ; Alleles ; *Inheritance Patterns ; Polyploidy ; }, abstract = {Whole-genome duplications yield varied chromosomal pairing patterns, ranging from strictly bivalent to multivalent, resulting in disomic and polysomic inheritance modes. In the bivalent case, homeologous chromosomes form pairs, where in a multivalent pattern all copies are homologous and are therefore free to pair and recombine. As sufficient sequencing data is more readily available than high-quality cytological assessments of meiotic behavior or population genetic assessment of allelic segregation, especially for non-model organisms, bioinformatics approaches to infer origins and inheritance modes of polyploids using short-read sequencing data are attractive. Here we describe two such approaches, where the first is based on distributions of allelic read depth at heterozygous sites within an individual, as the expectations of such distributions are different for disomic and polysomic inheritance modes. The second approach is more laborious and based on a phylogenetic assessment of partially phased haplotypes of a polyploid in comparison to the closest diploid relatives. We discuss the sources of deviations from expected inheritance patterns, advantages and pitfalls of both methods, effects of mating types on the performance of the methods, and possible future developments.}, } @article {pmid36720814, year = {2023}, author = {Schafran, P and Li, FW and Rothfels, CJ}, title = {PURC Provides Improved Sequence Inference for Polyploid Phylogenetics and Other Manifestations of the Multiple-Copy Problem.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2545}, number = {}, pages = {189-206}, pmid = {36720814}, issn = {1940-6029}, mesh = {Humans ; Phylogeny ; Cluster Analysis ; *Computational Biology ; Consensus Sequence ; *Polyploidy ; }, abstract = {Inferring the true biological sequences from amplicon mixtures remains a difficult bioinformatics problem. The traditional approach is to cluster sequencing reads by similarity thresholds and treat the consensus sequence of each cluster as an "operational taxonomic unit" (OTU). Recently, this approach has been improved by model-based methods that correct PCR and sequencing errors in order to infer "amplicon sequence variants" (ASVs). To date, ASV approaches have been used primarily in metagenomics, but they are also useful for determining homeologs in polyploid organisms. To facilitate the usage of ASV methods among polyploidy researchers, we incorporated ASV inference alongside OTU clustering in PURC v2.0, a major update to PURC (Pipeline for Untangling Reticulate Complexes). In addition, PURC v2.0 features faster demultiplexing than the original version and has been updated to be compatible with Python 3. In this chapter we present results indicating that using the ASV approach is more likely to infer the correct biological sequences in comparison to the earlier OTU-based PURC and describe how to prepare sequencing data, run PURC v2.0 under several different modes, and interpret the output.}, } @article {pmid36719887, year = {2023}, author = {Woo, C and Kumari, P and Eo, KY and Lee, WS and Kimura, J and Yamamoto, N}, title = {Combining vertebrate mitochondrial 12S rRNA gene sequencing and shotgun metagenomic sequencing to investigate the diet of the leopard cat (Prionailurus bengalensis) in Korea.}, journal = {PloS one}, volume = {18}, number = {1}, pages = {e0281245}, pmid = {36719887}, issn = {1932-6203}, mesh = {Cats ; Animals ; Genes, rRNA ; *DNA ; Republic of Korea ; *Diet ; Vertebrates ; Mammals ; }, abstract = {The leopard cat (Prionailurus bengalensis), an endangered species in South Korea, is a small feline widely distributed in Asia. Here, we investigated the diet of leopard cats in the inland areas of Korea by examining their fecal contents using vertebrate mitochondrial 12S rRNA gene sequencing and shotgun metagenomic sequencing. Shotgun metagenomic sequencing revealed that the feces were rich in DNA not only of vertebrates but also of arthropods and plants, but care should be taken when using shotgun metagenomic sequencing to identify vertebrates at low taxonomic levels (e.g., genus level), as it was often erroneous. Meanwhile, vertebrate mitochondrial 12S rRNA gene sequencing was found to be accurate in the genus-level identification, as the genera identified were consistent with the Korean fauna. We found that small mammals such as murids were their main prey. By using these two sequencing methods in combination, this study demonstrated that accurate information about the overall dietary content and vertebrate prey of leopard cats could be obtained. We expect that the continued community efforts to expand the genome database of wildlife, including vertebrates, will alleviate the problem of erroneous identification of prey at low taxonomic levels by shotgun metagenomic sequencing in the near future.}, } @article {pmid36719246, year = {2023}, author = {Santillan, M and Graham, ED and Heidelberg, JF and Webb, EA}, title = {Metagenome-Assembled Genome of an Alphaproteobacterium Isolated from an HetDA Enrichment from the North Pacific Subtropical Gyre.}, journal = {Microbiology resource announcements}, volume = {12}, number = {2}, pages = {e0059522}, pmid = {36719246}, issn = {2576-098X}, abstract = {Here, we present HetDA_MAG_SS10, a metagenome-assembled genome (MAG) from an enrichment of a heterocystous diazotroph originally living in association with Trichodesmium spp. obtained near Station ALOHA in the North Pacific Ocean. HetDA_MAG_SS10, an alphaproteobacterium in the order Micavibrionales, is proposed to be photoheterotrophic via rhodopsin and has the potential for dimethylsulfoniopropionate (DMSP) demethylation.}, } @article {pmid36719237, year = {2023}, author = {Ghimire-Kafle, S and Weaver, ME and Bollmann, A}, title = {Ecophysiological and Genomic Characterization of the Freshwater Complete Ammonia Oxidizer Nitrospira sp. Strain BO4.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {2}, pages = {e0196522}, pmid = {36719237}, issn = {1098-5336}, mesh = {*Ammonia/metabolism ; Nitrites/metabolism ; Nitrates/metabolism ; Bacteria/metabolism ; Archaea/metabolism ; Nitrification ; Oxidation-Reduction ; Genomics ; Fresh Water ; *Ammonium Compounds/metabolism ; Phylogeny ; }, abstract = {Complete ammonia oxidizers (comammox) are a group of ubiquitous chemolithoautotrophic bacteria capable of deriving energy from the oxidation of ammonia to nitrate via nitrite. Here, we present a study characterizing the comammox strain Nitrospira sp. BO4 using a combination of cultivation-dependent and molecular methods. The enrichment culture BO4 was obtained from the sediment of Lake Burr Oak, a mesotrophic lake in eastern Ohio. The metagenome of the enrichment culture was sequenced, and a metagenome-assembled genome (MAG) was constructed for Nitrospira sp. BO4. The closest characterized relative of Nitrospira sp. BO4 was "Candidatus Nitrospira kreftii." All genes for ammonia and nitrite oxidation, reductive tricarboxylic acid (TCA) cycle, and other pathways of the central metabolism were detected. Nitrospira sp. BO4 used ammonia and oxidized it to nitrate with nitrite as the intermediate. The culture grew on initial ammonium concentrations between 0.01 and 3 mM with the highest rates observed at the lowest ammonium concentrations. Blue light completely inhibited the growth of Nitrospira sp. BO4, while white light reduced the growth and red light had no effect on the growth. Nitrospira sp. BO4 did not grow on nitrite as its sole substrate. When supplied with ammonium and nitrite, the culture utilized nitrite after most of the ammonium was consumed. In summary, the genomic information of Nitrospira sp. BO4 coupled with the growth experiments shows that Nitrospira sp. BO4 is a freshwater comammox species. Future research will focus on further characterization of the niches of comammox in freshwater environments. IMPORTANCE Nitrification is a key process in the global nitrogen cycle. Complete ammonia oxidizers (comammox) were discovered recently, and only three enrichment cultures and one pure culture have been characterized with respect to activity and growth under different conditions. The cultivated comammox strains were obtained from engineered systems such as a recirculating aquaculture system and hot water pipes. Here, we present the first study characterizing a comammox strain obtained from a mesotrophic freshwater lake. In freshwater environments, comammox coexist with ammonia-oxidizing archaea (AOA) and ammonia-oxidizing bacteria (AOB). Our results will help elucidate physiological characteristics of comammox and the distribution and niche differentiation of different ammonia oxidizers in freshwater environments.}, } @article {pmid36719236, year = {2023}, author = {Distaso, MA and Chernikova, TN and Bargiela, R and Coscolín, C and Stogios, P and Gonzalez-Alfonso, JL and Lemak, S and Khusnutdinova, AN and Plou, FJ and Evdokimova, E and Savchenko, A and Lunev, EA and Yakimov, MM and Golyshina, OV and Ferrer, M and Yakunin, AF and Golyshin, PN}, title = {Thermophilic Carboxylesterases from Hydrothermal Vents of the Volcanic Island of Ischia Active on Synthetic and Biobased Polymers and Mycotoxins.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {2}, pages = {e0170422}, pmid = {36719236}, issn = {1098-5336}, mesh = {*Carboxylic Ester Hydrolases/metabolism ; Polymers ; *Hydrothermal Vents ; Hydrolases/metabolism ; Polyesters ; Plastics ; Substrate Specificity ; }, abstract = {Hydrothermal vents are geographically widespread and host microorganisms with robust enzymes useful in various industrial applications. We examined microbial communities and carboxylesterases of two terrestrial hydrothermal vents of the volcanic island of Ischia (Italy) predominantly composed of Firmicutes, Proteobacteria, and Bacteroidota. High-temperature enrichment cultures with the polyester plastics polyhydroxybutyrate and polylactic acid (PLA) resulted in an increase of Thermus and Geobacillus species and to some extent Fontimonas and Schleiferia species. The screening at 37 to 70°C of metagenomic fosmid libraries from above enrichment cultures identified three hydrolases (IS10, IS11, and IS12), all derived from yet-uncultured Chloroflexota and showing low sequence identity (33 to 56%) to characterized enzymes. Enzymes expressed in Escherichia coli exhibited maximal esterase activity at 70 to 90°C, with IS11 showing the highest thermostability (90% activity after 20-min incubation at 80°C). IS10 and IS12 were highly substrate promiscuous and hydrolyzed all 51 monoester substrates tested. Enzymes were active with PLA, polyethylene terephthalate model substrate, and mycotoxin T-2 (IS12). IS10 and IS12 had a classical α/β-hydrolase core domain with a serine hydrolase catalytic triad (Ser155, His280, and Asp250) in their hydrophobic active sites. The crystal structure of IS11 resolved at 2.92 Å revealed the presence of a N-terminal β-lactamase-like domain and C-terminal lipocalin domain. The catalytic cleft of IS11 included catalytic Ser68, Lys71, Tyr160, and Asn162, whereas the lipocalin domain enclosed the catalytic cleft like a lid and contributed to substrate binding. Our study identified novel thermotolerant carboxylesterases with a broad substrate range, including polyesters and mycotoxins, for potential applications in biotechnology. IMPORTANCE High-temperature-active microbial enzymes are important biocatalysts for many industrial applications, including recycling of synthetic and biobased polyesters increasingly used in textiles, fibers, coatings and adhesives. Here, we identified three novel thermotolerant carboxylesterases (IS10, IS11, and IS12) from high-temperature enrichment cultures from Ischia hydrothermal vents and incubated with biobased polymers. The identified metagenomic enzymes originated from uncultured Chloroflexota and showed low sequence similarity to known carboxylesterases. Active sites of IS10 and IS12 had the largest effective volumes among the characterized prokaryotic carboxylesterases and exhibited high substrate promiscuity, including hydrolysis of polyesters and mycotoxin T-2 (IS12). Though less promiscuous than IS10 and IS12, IS11 had a higher thermostability with a high temperature optimum (80 to 90°C) for activity and hydrolyzed polyesters, and its crystal structure revealed an unusual lipocalin domain likely involved in substrate binding. The polyesterase activity of these enzymes makes them attractive candidates for further optimization and potential application in plastics recycling.}, } @article {pmid36719226, year = {2023}, author = {Dubinsky, V and Dotan, I and Gophna, U}, title = {Strains Colonizing Different Intestinal Sites within an Individual Are Derived from a Single Founder Population.}, journal = {mBio}, volume = {14}, number = {1}, pages = {e0345622}, pmid = {36719226}, issn = {2150-7511}, mesh = {Adult ; Humans ; *Metagenome ; Bacteria/genetics ; Genome, Bacterial ; Feces/microbiology ; *Inflammatory Bowel Diseases/genetics ; Metagenomics ; }, abstract = {Metagenomics has improved our understanding of commensal bacteria that colonize human intestines yet relies almost exclusively on fecal samples. Thus, spatial information about the niche range of these gut microbes and the level of specialized adaptation that they undergo has been inaccessible to fecal metagenomic studies. Here, we leveraged metagenomic data obtained through colonoscopy aspirates from three intestinal sites of healthy adults, and reconstructed metagenome-assembled genomes of several common gut bacteria to address intestinal site-specific evolution. We show that the genomes of bacterial strains at specific intestinal sites are clearly distinct yet are interrelated and are derived from a single founder strain colonizing multiple sites. We also reveal that within those intestinal sites, purifying selection is the dominant evolutionary force acting on Escherichia coli genomes within human hosts. Importantly, no site-specific adaptations at the level of accessory genes were detected, implying that these commensals are well-adapted to several host microniches and can therefore colonize multiple intestinal sites with high efficiency. Nevertheless, bacterial in situ growth rates differ markedly across different sections of the intestine. Metagenomics of aspirate samples can reveal unique strain- and intestinal tissue-specific genomic information. Such information may be critical for understanding bacterial contribution to gastrointestinal diseases, which involve only a part of the intestine, as is often the case in inflammatory bowel disease. IMPORTANCE By reconstructing bacterial genomes from samples taken from specific sites within the human intestines, via aspiration, we show that strains at specific intestinal sites are genetically distinct yet interrelated and are derived from a single founder population. Organ-specific metagenomic information represents a powerful tool to generate insights into gastrointestinal diseases, which involve only a part of the intestine, such as inflammatory bowel disease.}, } @article {pmid36719194, year = {2023}, author = {Fan, Y and Ju, T and Bhardwaj, T and Korver, DR and Willing, BP}, title = {Week-Old Chicks with High Bacteroides Abundance Have Increased Short-Chain Fatty Acids and Reduced Markers of Gut Inflammation.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0361622}, pmid = {36719194}, issn = {2165-0497}, abstract = {As important commensals in the chicken intestine, Bacteroides are essential complex carbohydrate degraders, and short-chain fatty acid (SCFA) producers that are highly adapted to the distal gut. Previous studies have shown large variation in Bacteroides abundance in young chickens. However, limited information is available regarding how this variation affects the gut microbiome and host immunity. To investigate how elevated or depleted Bacteroides levels affect gut microbial functional capacity and impact host response, we sampled 7-day-old broiler chickens from 14 commercial production flocks. Week-old broiler chickens were screened and birds with low Bacteroides (LB) and high Bacteroides (HB) abundance were identified via 16S rRNA gene amplicon sequencing and quantitative PCR (qPCR) assays. Cecal microbial functionality and SCFA concentration of chickens with distinct cecal Bacteroides abundance were profiled by shotgun metagenomic sequencing and gas chromatography, respectively. The intestinal immune responses of LB and HB chickens were assessed via reverse transcription qPCR. Results showed that the gut microbiota of the LB group had increased abundance of lactic acid bacteria pyruvate fermentation pathway, whereas complex polysaccharide degradation and SCFA production pathways were enriched in the HB group (P < 0.05), which was supported by increased SCFA concentrations in the ceca of HB chickens (P < 0.05). HB chickens also showed decreased expression of interleukin-1β and increased expression of interleukin-10 and tight-junction protein claudin-1 (P < 0.05). Overall, the results indicated that elevated Bacteroides may benefit the 7-day broiler gut and that further work should be done to confirm the causal role of Bacteroides in the observed positive outcomes. IMPORTANCE To date, limited information is available comparing distinct Bacteroides compositions in the chicken gut microbial communities, particularly in the context of microbial functional capacities and host responses. This study showed that possessing a microbiome with elevated Bacteroides in early life may confer beneficial effects to the chicken host, particularly in improving SCFA production and gut health. This study is among the first metagenomic studies focusing on the early life chicken gut microbiota structure, microbial functionality, and host immune responses. We believe that it will offer insights to future studies on broiler gut microbial population and their effects on host health.}, } @article {pmid36719190, year = {2023}, author = {Wang, Z and Liang, L and Liu, L and Wang, Z and Wang, Y and Yu, Z and Wu, B and Chen, Y}, title = {Changes in the Gut Microbiome Associated with Intussusception in Patients with Peutz-Jeghers Syndrome.}, journal = {Microbiology spectrum}, volume = {11}, number = {2}, pages = {e0281922}, pmid = {36719190}, issn = {2165-0497}, abstract = {Peutz-Jeghers syndrome (PJS) is a rare hereditary disorder characterized by intestinal polyposis, and intestinal intussusception is one of the most urgent complications. While it is known that imbalance of the gut microbiota is highly associated with intestinal disorders, the role of the gut microbiome in the pathogenesis of PJS has not been reported. In this study, we performed 16S rRNA sequencing on stools from 168 patients and 68 healthy family members who lived together to determine the gut microbiome composition of PJS patients. Metagenomics sequencing was further performed on the representative samples (61 PJS patients and 27 healthy family members) to analyze the functional changes. We found that the fecal microbiome of patients with PJS showed a greater variation in β-diversity. An enhancement of Escherichia coli and a reduction of Faecalibacterium prausnitzii was identified in PJS patients. Further reduction of Faecalibacterium prausnitzii was the characteristic microbial change observed in patients with intussusception. Functional analysis revealed that the abundance of propanoate metabolism was enriched in PJS patients and further enriched in those with intussusception. Escherichia coli was the major contributor to the enrichment of this metabolism pathway, which was associated with the abnormal expression of methylglyoxal synthase (encoded by mgsA) and phosphate acetyltransferase (encoded by pta). Our findings showed a distinct gut microbiome signature in PJS patients and identified the connection between the gut microbiome and intussusception. Alterations in the gut microbiome might be involved in the pathogenesis of PJS and may serve as biomarkers for gastrointestinal surveillance. IMPORTANCE Recent research has established a link between the gut microbiome and polyps and neoplasia, and antibiotic use influences the microbiome and the development of colorectal polyps. Familial adenomatous polyposis (FAP), which is characterized by the early development of benign precursor lesions (polyps), is associated with enterotoxigenic Bacteroides fragilis and Escherichia coli biofilms. However, the relationship between the gut microbiome and the pathophysiology of PJS has not yet been established. In this study, we found that PJS patients had a distinct microbiome composition, with a greater variation in β-diversity, an increase in Escherichia coli, and a decrease in Faecalibacterium prausnitzii. A further reduction of Faecalibacterium prausnitzii was observed in patients with intussusception. Moreover, PJS involved increased propanoate metabolism as well as abnormal mgsA and pta expression. These findings may contribute to a better understanding of the etiology of PJS and improve disease control strategies.}, } @article {pmid36719089, year = {2023}, author = {Qin, Y and Wang, S and Wang, X and Liu, C and Zhu, G}, title = {Contribution of Ammonium-Induced Nitrifier Denitrification to N2O in Paddy Fields.}, journal = {Environmental science & technology}, volume = {57}, number = {7}, pages = {2970-2980}, doi = {10.1021/acs.est.2c06124}, pmid = {36719089}, issn = {1520-5851}, mesh = {*Ammonium Compounds ; Denitrification ; Ammonia/analysis ; Nitrous Oxide/analysis ; Soil/chemistry ; }, abstract = {Paddy fields are one of the most important sources of nitrous oxide (N2O), but biogeochemical N2O production mechanisms in the soil profile remain unclear. Our study used incubation, dual-isotope ([15]N-[18]O) labeling methods, and molecular techniques to elucidate N2O production characteristics and mechanisms in the soil profile (0-60 cm) during summer fallow, rice cropping, and winter fallow periods. The results pointed out that biotic processes dominated N2O production (72.2-100%) and N2O from the tillage layer accounted for 91.0-98.5% of total N2O in the soil profile. Heterotrophic denitrification (HD) was the main process generating N2O, contributing between 53.4 and 96.6%, the remainder being due to ammonia oxidation pathways, which was further confirmed by metagenomics and quantitative polymerase chain reaction (qPCR) assays. Nitrifier denitrification (ND) was an important N2O production source, contributing 0-46.6% of total N2O production, which showed similar trends with N2O emissions. Among physicochemical and biological factors, ammonium content and the ratio of total organic matter to nitrate were the main driving factors affecting the contribution ratios of the ammonia oxidation pathways and HD pathway, respectively. Moisture content and pH affect norC-carrying Spirochetes and thus the N2O production rate. These findings confirm the importance of ND to N2O production and help to elucidate the impact of anthropogenic activities, including tillage, fertilization, and irrigation, on N2O production.}, } @article {pmid36718144, year = {2023}, author = {Lin, KP and Yeh, TK and Chuang, YC and Wang, LA and Fu, YC and Liu, PY}, title = {Blood Culture Negative Endocarditis: A Review of Laboratory Diagnostic Approaches.}, journal = {International journal of general medicine}, volume = {16}, number = {}, pages = {317-327}, pmid = {36718144}, issn = {1178-7074}, abstract = {Infective endocarditis is a potentially fatal condition, and identifying the pathogen is crucial to optimizing antibiotic treatment. While a blood culture takes time and may yield negative results, it remains the gold standard for diagnosis, blood culture-negative endocarditis, which accounts for up to 20% of infective endocarditis cases, poses a clinical challenge with increasing mortality. To better understand the etiology of blood culture-negative infective endocarditis, we reviewed non-culture-based strategies and compared the results. Serology tests work best in limited pathogens, such as Coxiella burnetii and Bartonella infections. Most of the pathogens identified by broad-range PCR tests are Streptococcus spp, Staphylococcus spp and Propionibacterium spp. adding specific real-time PCR assays to the systematic PCR testing of patients with blood culture-negative endocarditis will increase the efficiency of diagnosis. Recently, metagenomic next-generation sequencing has also shown promising results.}, } @article {pmid36717776, year = {2023}, author = {Champion, C and Neagoe, RM and Effernberger, M and Sala, DT and Servant, F and Christensen, JE and Arnoriaga-Rodriguez, M and Amar, J and Lelouvier, B and Loubieres, P and Azalbert, V and Minty, M and Thomas, C and Blasco-Baque, V and Gamboa, F and Tilg, H and Cardellini, M and Federici, M and Fernández-Real, JM and Loubes, JM and Burcelin, R}, title = {Human liver microbiota modeling strategy at the early onset of fibrosis.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {34}, pmid = {36717776}, issn = {1471-2180}, support = {6869/12.06.2014//VAIOMER SAS/ ; }, mesh = {Humans ; DNA, Bacterial/genetics ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Fibrosis ; *Liver Cirrhosis ; *Microbiota ; }, abstract = {BACKGROUND: Gut microbiota is involved in the development of liver diseases such as fibrosis. We and others identified that selected sets of gut bacterial DNA and bacteria translocate to tissues, notably the liver, to establish a non-infectious tissue microbiota composed of microbial DNA and a low frequency live bacteria. However, the precise set of bacterial DNA, and thereby the corresponding taxa associated with the early stages of fibrosis need to be identified. Furthermore, to overcome the impact of different group size and patient origins we adapted innovative statistical approaches. Liver samples with low liver fibrosis scores (F0, F1, F2), to study the early stages of the disease, were collected from Romania(n = 36), Austria(n = 10), Italy(n = 19), and Spain(n = 17). The 16S rRNA gene was sequenced. We considered the frequency, sparsity, unbalanced sample size between cohorts to identify taxonomic profiles and statistical differences.

RESULTS: Multivariate analyses, including adapted spectral clustering with L1-penalty fair-discriminant strategies, and predicted metagenomics were used to identify that 50% of liver taxa associated with the early stage fibrosis were Enterobacteriaceae, Pseudomonadaceae, Xanthobacteriaceae and Burkholderiaceae. The Flavobacteriaceae and Xanthobacteriaceae discriminated between F0 and F1. Predicted metagenomics analysis identified that the preQ0 biosynthesis and the potential pathways involving glucoryranose and glycogen degradation were negatively associated with liver fibrosis F1-F2 vs F0.

CONCLUSIONS: Without demonstrating causality, our results suggest first a role of bacterial translocation to the liver in the progression of fibrosis, notably at the earliest stages. Second, our statistical approach can identify microbial signatures and overcome issues regarding sample size differences, the impact of environment, and sets of analyses.

TRIAL REGISTRATION: TirguMECCH ROLIVER Prospective Cohort for the Identification of Liver Microbiota, registration 4065/2014. Registered 01 01 2014.}, } @article {pmid36717382, year = {2023}, author = {}, title = {Metagenomic insights into the environmental adaptation and metabolism of Candidatus Halarchaeoplasmatales, one archaeal order thriving in saline lakes.}, journal = {Environmental microbiology}, volume = {25}, number = {2}, pages = {592}, doi = {10.1111/1462-2920.16338}, pmid = {36717382}, issn = {1462-2920}, } @article {pmid36715883, year = {2023}, author = {Song, Y and Sun, M and Ma, F and Xu, D and Mu, G and Jiao, Y and Yu, P and Tuo, Y}, title = {Lactiplantibacillus plantarum DLPT4 Protects Against Cyclophosphamide-Induced Immunosuppression in Mice by Regulating Immune Response and Intestinal Flora.}, journal = {Probiotics and antimicrobial proteins}, volume = {}, number = {}, pages = {}, pmid = {36715883}, issn = {1867-1314}, support = {31571813//National Natural Science Foundation of China/ ; }, abstract = {In this study, the strain Lactiplantibacillus plantarum DLPT4 was investigated for the immunostimulatory activity in cyclophosphamide (CTX)-induced immunosuppressed BALB/c mice. L. plantarum DLPT4 was administered to BALB/c mice by oral gavage for 30 days, and CTX was injected intraperitoneally from the 25th to the 27th days. Intraperitoneal injection of CTX caused damage to the thymic cortex and intestines, and the immune dysfunction of the BALB/c mice. L. plantarum DLPT4 oral administration exerted immunoregulating effects evidenced by increasing serum immunoglobulin (IgA, IgG, and IgM) levels and reducing the genes expression of pro-inflammatory factors (IL-6, IL-1β, and TNF-α) of the CTX-induced immunosuppressed mice. The results of the metagenome-sequencing analysis showed that oral administration of L. plantarum DLPT4 could regulate the intestinal microbial community of the immunosuppressed mice by changing the ratio of Lactiplantibacillus and Bifidobacterium. Meanwhile, the abundance of carbohydrate enzyme (CAZyme), immune diseases metabolic pathways, and AP-1/MAPK signaling pathways were enriched in the mice administrated with L. plantarum DLPT4. In conclusion, oral administration of L. plantarum DLPT4 ameliorated symptoms of CTX-induced immunosuppressed mice by regulating gut microbiota, influencing the abundance of carbohydrate esterase in the intestinal flora, and enhancing immune metabolic activity. L. plantarum DLPT4 could be a potential probiotic to regulate the immune response.}, } @article {pmid36715435, year = {2023}, author = {Liu, J and Ding, H and Yan, C and He, Z and Zhu, H and Ma, KY}, title = {Effect of tea catechins on gut microbiota in high fat diet-induced obese mice.}, journal = {Journal of the science of food and agriculture}, volume = {103}, number = {5}, pages = {2436-2445}, doi = {10.1002/jsfa.12476}, pmid = {36715435}, issn = {1097-0010}, support = {//Joint Laboratory for International Cooperation in Grain Circulation and Security/ ; //Natural Science Foundation of the Higher Education Institutions of Jiangsu Province/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions (PAPD)/ ; //Jiangsu Province/ ; //Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; //International Cooperation/ ; }, mesh = {Mice ; Animals ; Diet, High-Fat ; *Gastrointestinal Microbiome ; Mice, Obese ; *Catechin ; Mice, Inbred C57BL ; Obesity/metabolism ; Tea/chemistry ; }, abstract = {BACKGROUND: Tea catechins have been shown to have beneficial effects on the alleviation of obesity, the prevention of diabetes, and the amelioration of metabolic syndrome. The purpose of the present work is to explore the underlying mechanisms linking the intestinal microbiota and anti-obesity benefits of green tea, oolong tea, and black tea catechins in C57BL/6J mice fed with a high-fat diet (HFD).

RESULTS: The results indicated that, after the dietary intake of three tea catechins, obesity and low-grade inflammation were significantly alleviated. Hepatic steatosis was prevented, and this was accompanied by the upregulation of the mRNA and protein expressions of hepatic peroxisome proliferator-activated receptor α (PPARα). Metagenomic analysis of fecal samples suggested that the three tea catechins similarly changed the microbiota in terms of overall structure, composition, and protein functions by regulating the metabolites, facilitating the generation of short-chain fatty acids (SCFAs), and repressing lipopolysaccharides.

CONCLUSION: The anti-obese properties of three tea catechins were partially mediated by their positive effect on gut microbiota, hepatic steatosis alleviation, and anti-inflammatory activity. © 2023 Society of Chemical Industry.}, } @article {pmid36714834, year = {2022}, author = {Velsko, IM and Semerau, L and Inskip, SA and García-Collado, MI and Ziesemer, K and Ruber, MS and Benítez de Lugo Enrich, L and Molero García, JM and Valle, DG and Peña Ruiz, AC and Salazar-García, DC and Hoogland, MLP and Warinner, C}, title = {Ancient dental calculus preserves signatures of biofilm succession and interindividual variation independent of dental pathology.}, journal = {PNAS nexus}, volume = {1}, number = {4}, pages = {pgac148}, pmid = {36714834}, issn = {2752-6542}, support = {MR/T022302/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Dental calculus preserves oral microbes, enabling comparative studies of the oral microbiome and health through time. However, small sample sizes and limited dental health metadata have hindered health-focused investigations to date. Here, we investigate the relationship between tobacco pipe smoking and dental calculus microbiomes. Dental calculus from 75 individuals from the 19th century Middenbeemster skeletal collection (Netherlands) were analyzed by metagenomics. Demographic and dental health parameters were systematically recorded, including the presence/number of pipe notches. Comparative data sets from European populations before and after the introduction of tobacco were also analyzed. Calculus species profiles were compared with oral pathology to examine associations between microbiome community, smoking behavior, and oral health status. The Middenbeemster individuals exhibited relatively poor oral health, with a high prevalence of periodontal disease, caries, heavy calculus deposits, and antemortem tooth loss. No associations between pipe notches and dental pathologies, or microbial species composition, were found. Calculus samples before and after the introduction of tobacco showed highly similar species profiles. Observed interindividual microbiome differences were consistent with previously described variation in human populations from the Upper Paleolithic to the present. Dental calculus may not preserve microbial indicators of health and disease status as distinctly as dental plaque.}, } @article {pmid36714349, year = {2023}, author = {Huang, PH and Huang, YT and Lee, PH and Tseng, CH and Liu, PY and Liu, CW}, title = {Diagnosis of Legionnaires' Disease Assisted by Next-Generation Sequencing in a Patient with COVID-19.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {355-362}, pmid = {36714349}, issn = {1178-6973}, abstract = {Coinfection in COVID-19 patients is associated with worsening outcome. Among patients with COVID-19, Legionella pneumophila, a common cause of pneumonia, has been reported as a co-occurring respiratory infection. A nonspecific clinical presentation, however, makes an early diagnosis difficult. Bronchoalveolar lavage fluid was collected from a patient suffering from COVID-19 and presenting with pneumonia and sent for metagenomic analysis. Differential abundance analysis was carried out by comparing each taxon reads per million between the bronchoalveolar lavage fluid sample and the negative control. Two replicates of metagenomic sequencing were conducted on bronchoalveolar lavage fluid samples. Within each replicated sequencing, one negative control was sequenced for comparison of taxon abundance in the BALF sample. In both replicates, Legionella pneumophila was the only taxon with significantly higher abundance when compared with the negative control. PCR of the bronchoalveolar further confirmed the presence of L. pneumophila. Several studies have estimated that the incidence of Legionnaires' disease co-infection in patients with COVID-19 infection is approximately 0% to 1.5%. There are some common characteristics of COVID-19 and co-infection with Legionnaires' disease, making it difficult to diagnose bacterial infection early. The diagnosis of these cases is important due to the different treatments used. Current diagnostic tests for Legionnaires' disease include conventional culture, urinary antigen for L. pneumophila serogroup 1, polymerase chain reaction, direct fluorescent antibody stain, and paired serology. The current study demonstrated that metagenomics is a promising approach that facilitated the diagnosis of Legionnaires' disease.}, } @article {pmid36714105, year = {2022}, author = {Liang, Q and Liang, X and Hong, D and Fang, Y and Tang, L and Mu, J and Tan, X and Chen, F}, title = {Case report: Application of metagenomic next-generation sequencing in the diagnosis of visceral leishmaniasis and its treatment evaluation.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {1044043}, pmid = {36714105}, issn = {2296-858X}, abstract = {Visceral leishmaniasis is a vector-borne infection by the Leishmania spp., a parasite. Although the overall incidence of visceral leishmaniasis is low, the disease still occurs frequently in some high-risk areas. In our study, two patients were admitted to the hospital with an unprovoked and recurrent high fever, and the condition was not improved after antibiotics administration. Meanwhile, bone marrow aspiration smears failed to find out any pathogen. Finally, Leishmania-specific nucleic acid sequences were successfully detected in the peripheral blood of two patients through metagenomic next-generation sequencing (mNGS), which was further confirmed by bone marrow smear microscopy and antibody tests. After targeted treatment for visceral leishmaniasis in the patients, mNGS reported a decrease in the reads number of Leishmania sequence. The results indicate the feasibility of mNGS in detecting Leishmania spp. in peripheral blood samples. Its therapeutic effect evaluation may be achieved through a comparative analysis of the number of reads before and after the treatment.}, } @article {pmid36713863, year = {2022}, author = {Qin, T and Shi, M and Zhang, M and Liu, Z and Feng, H and Sun, Y}, title = {Diversity of RNA viruses of three dominant tick species in North China.}, journal = {Frontiers in veterinary science}, volume = {9}, number = {}, pages = {1057977}, pmid = {36713863}, issn = {2297-1769}, abstract = {BACKGROUND: A wide range of bacterial pathogens have been identified in ticks, yet the diversity of viruses in ticks is largely unexplored.

METHODS: Here, we used metagenomic sequencing to characterize the diverse viromes in three principal tick species associated with pathogens, Haemaphysalis concinna, Dermacentor silvarum, and Ixodes persulcatus, in North China.

RESULTS: A total of 28 RNA viruses were identified and belonged to more than 12 viral families, including single-stranded positive-sense RNA viruses (Flaviviridae, Picornaviridae, Luteoviridae, Solemoviridae, and Tetraviridae), negative-sense RNA viruses (Mononegavirales, Bunyavirales, and others) and double-stranded RNA viruses (Totiviridae and Partitiviridae). Of these, Dermacentor pestivirus-likevirus, Chimay-like rhabdovirus, taiga tick nigecruvirus, and Mukawa virus are presented as novel viral species, while Nuomin virus, Scapularis ixovirus, Sara tick-borne phlebovirus, Tacheng uukuvirus, and Beiji orthonairovirus had been established as human pathogens with undetermined natural circulation and pathogenicity. Other viruses include Norway mononegavirus 1, Jilin partitivirus, tick-borne tetravirus, Pico-like virus, Luteo-like virus 2, Luteo-likevirus 3, Vovk virus, Levivirus, Toti-like virus, and Solemo-like virus as well as others with unknown pathogenicity to humans and wild animals.

CONCLUSION: In conclusion, extensive virus diversity frequently occurs in Mononegavirales and Bunyavirales among the three tick species. Comparatively, I. persulcatus ticks had been demonstrated as such a kind of host with a significantly higher diversity of viral species than those of H. concinna and D. silvarum ticks. Our analysis supported that ticks are reservoirs for a wide range of viruses and suggested that the discovery and characterization of tick-borne viruses would have implications for viral taxonomy and provide insights into tick-transmitted viral zoonotic diseases.}, } @article {pmid36713446, year = {2022}, author = {Chen, C and Yan, Q and Yao, X and Li, S and Lv, Q and Wang, G and Zhong, Q and Tang, F and Liu, Z and Huang, Y and An, Y and Zhou, J and Zhang, Q and Zhang, A and Ullah, H and Zhang, Y and Liu, C and Zhu, D and Li, H and Sun, W and Ma, W}, title = {Alterations of the gut virome in patients with systemic lupus erythematosus.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1050895}, pmid = {36713446}, issn = {1664-3224}, mesh = {Humans ; Virome ; *Gastrointestinal Microbiome ; Feces/microbiology ; *Lupus Erythematosus, Systemic/microbiology ; Bacteria/genetics ; *Viruses/genetics ; }, abstract = {BACKGROUND: Systemic lupus erythematosus (SLE) is a systemic autoimmune disease that has been linked to the dysbiosis of the gut microbiome and virome. However, the potential characterization of the gut virome in SLE patients needs to be explored more extensively.

METHODS: Herein, we analyzed the gut viral community of 16 SLE patients and 31 healthy controls using both bulk and virus-like particle (VLP)-based metagenomic sequencing of their fecal samples. A total of 15,999 non-redundant viral operational taxonomic units (vOTUs) were identified from the metagenomic assembled contigs and used for gut virome profiling.

RESULTS: SLE patients exhibited a significant decrease in gut viral diversity in the bulk metagenome dataset, but this change was not significant in the VLP metagenome dataset. Also, considerable alterations of the overall gut virome composition and remarkable changes in the viral family compositions were observed in SLE patients compared with healthy controls, as observed in both two technologies. We identified 408 vOTUs (177 SLE-enriched and 231 control-enriched) with significantly different relative abundances between patients and controls in the bulk virome, and 18 vOTUs (17 SLE-enriched in 1 control-enriched) in the VLP virome. The SLE-enriched vOTUs included numerous Siphoviridae, Microviridae, and crAss-like viruses and were frequently predicted to infect Bacteroides, Parabacteroides, and Ruminococcus_E, while the control-enriched contained numerous members of Siphoviridae and Myoviridae and were predicted to infect Prevotella and Lachnospirales_CAG-274. We explored the correlations between gut viruses and bacteria and found that some Lachnospirales_CAG-274 and Hungatella_A phages may play key roles in the virus-bacterium network. Furthermore, we explored the gut viral signatures for disease discrimination and achieved an area under the receiver operator characteristic curve (AUC) of above 0.95, suggesting the potential of the gut virome in the prediction of SLE.

CONCLUSION: Our findings demonstrated the alterations in viral diversity and taxonomic composition of the gut virome of SLE patients. Further research into the etiology of SLE and the gut viral community will open up new avenues for treating and preventing SLE and other autoimmune diseases.}, } @article {pmid36713194, year = {2022}, author = {Kuang, B and Xiao, R and Hu, Y and Wang, Y and Zhang, L and Wei, Z and Bai, J and Zhang, K and Acuña, JJ and Jorquera, MA and Pan, W}, title = {Metagenomics reveals biogeochemical processes carried out by sediment microbial communities in a shallow eutrophic freshwater lake.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1112669}, pmid = {36713194}, issn = {1664-302X}, abstract = {INTRODUCTION: As the largest shallow freshwater lake in the North China Plain, Baiyangdian lake is essential for maintaining ecosystem functioning in this highly populated region. Sediments are considered to record the impacts of human activities.

METHODS: The abundance, diversity and metabolic pathways of microbial communities in sediments were studied by metagenomic approach to reveal patterns and mechanism of C, N, P and S cycling under the threat of lake eutrophication.

RESULTS: Many genera, with plural genes encoding key enzymes involved in genes, belonging to Proteobacteria and Actinobacteria which were the most main phylum in bacterial community of Baiyangdian sediment were involved in C, N, S, P cycling processes, such as Nocardioides (Actinobacteria), Thiobacillus, Nitrosomonas, Rhodoplanes and Sulfuricaulis (Proteobacteria).For instance, the abundance of Nocardioides were positively correlated to TN, EC, SOC and N/P ratio in pathways of phytase, regulation of phosphate starvation, dissimilatory sulfate reduction and oxidation, assimilatory sulfate reduction, assimilatory nitrate reduction and reductive tricarboxylic acid (rTCA) cycle. Many key genes in C, N, P, S cycling were closely related to the reductive citrate cycle. A complete while weaker sulfur cycle between SO4 [2-] and HS[-] might occur in Baiyangdian lake sediments compared to C fixation and N cycling. In addition, dissimilatory nitrate reduction to ammonia was determined to co-occur with denitrification. Methanogenesis was the main pathway of methane metabolism and the reductive citrate cycle was accounted for the highest proportion of C fixation processes. The abundance of pathways of assimilatory nitrate reduction, denitrification and dissimilatory nitrate reduction of nitrogen cycling in sediments with higher TN content was higher than those with lower TN content. Besides, Nocardioides with plural genes encoding key enzymes involved in nasAB and nirBD gene were involved in these pathways.

DISCUSSION: Nocardioides involved in the processes of assimilatory nitrate reduction, denitrification and dissimilatory nitrate reduction of nitrogen cycling may have important effects on nitrogen transformation.}, } @article {pmid36713193, year = {2022}, author = {Abdelmoneim, TK and Mohamed, MSM and Abdelhamid, IA and Wahdan, SFM and Atia, MAM}, title = {Development of rapid and precise approach for quantification of bacterial taxa correlated with soil health.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1095045}, pmid = {36713193}, issn = {1664-302X}, abstract = {The structure and dynamic of soil bacterial community play a crucial role in soil health and plant productivity. However, there is a gap in studying the un-/or reclaimed soil bacteriome and its impact on future plant performance. The 16S metagenomic analysis is expensive and utilize sophisticated pipelines, making it unfavorable for researchers. Here, we aim to perform (1) in silico and in vitro validation of taxon-specific qPCR primer-panel in the detection of the beneficial soil bacterial community, to ensure its specificity and precision, and (2) multidimensional analysis of three soils/locations in Egypt ('Q', 'B', and 'G' soils) in terms of their physicochemical properties, bacteriome composition, and wheat productivity as a model crop. The in silico results disclosed that almost all tested primers showed high specificity and precision toward the target taxa. Among 17 measured soil properties, the electrical conductivity (EC) value (up to 5 dS/m) of 'Q' soil provided an efficient indicator for soil health among the tested soils. The 16S NGS analysis showed that the soil bacteriome significantly drives future plant performance, especially the abundance of Proteobacteria and Actinobacteria as key indicators. The functional prediction analysis results disclosed a high percentage of N-fixing bacterial taxa in 'Q' soil compared to other soils, which reflects their positive impact on wheat productivity. The taxon-specific qPCR primer-panel results revealed a precise quantification of the targeted taxa compared to the 16S NGS analysis. Moreover, 12 agro-morphological parameters were determined for grown wheat plants, and their results showed a high yield in the 'Q' soil compared to other soils; this could be attributed to the increased abundance of Proteobacteria and Actinobacteria, high enrichment in nutrients (N and K), or increased EC/nutrient availability. Ultimately, the potential use of a taxon-specific qPCR primer-panel as an alternative approach to NGS provides a cheaper, user-friendly setup with high accuracy.}, } @article {pmid36713191, year = {2022}, author = {Xiong, ZR and Sogin, JH and Worobo, RW}, title = {Microbiome analysis of raw honey reveals important factors influencing the bacterial and fungal communities.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1099522}, pmid = {36713191}, issn = {1664-302X}, abstract = {Raw honeys contain diverse microbial communities. Previous studies have focused on isolating bacteria and fungi that are culturable, while missing a large proportion of the microbial community due to culture-based constraints. This study utilized next-generation sequencing (NGS) to analyze the composition of microorganisms in raw honey; these data can reveal environmental and physicochemical variables that are associated with different microbial communities. To examine the microbial composition (bacteria and fungi) of raw honey and analyze its association with physicochemical properties, four types of honey (monofloral, wildflower, manuka, and feral; n total = 36) were analyzed via amplicon metagenomics. The analyzed honey samples had relatively similar bacterial communities but more distinct and diverse fungal communities. Honey type was determined as a significant factor influencing alpha and beta diversity metrics of bacterial and fungal communities. For the bacterial communities, titratable acidity (TA) was associated with community richness and diversity. For the fungal communities, Brix, TA, and color were associated with community richness, while water activity and color were associated with community diversity. Additionally, important bacterial and fungal amplicon sequence variants (ASVs) that influenced the overall community were identified. Results from this study provide important insights into the microbial communities associated with different types of raw honey, which could improve our understanding of microbial dynamics in beehives, improve honey production, and prevent honeybee disease.}, } @article {pmid36712847, year = {2022}, author = {de Flamingh, A and Ishida, Y and Pečnerová, P and Vilchis, S and Siegismund, HR and van Aarde, RJ and Malhi, RS and Roca, AL}, title = {Combining methods for non-invasive fecal DNA enables whole genome and metagenomic analyses in wildlife biology.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {1021004}, pmid = {36712847}, issn = {1664-8021}, abstract = {Non-invasive biological samples benefit studies that investigate rare, elusive, endangered, or dangerous species. Integrating genomic techniques that use non-invasive biological sampling with advances in computational approaches can benefit and inform wildlife conservation and management. Here, we used non-invasive fecal DNA samples to generate low- to medium-coverage genomes (e.g., >90% of the complete nuclear genome at six X-fold coverage) and metagenomic sequences, combining widely available and accessible DNA collection cards with commonly used DNA extraction and library building approaches. DNA preservation cards are easy to transport and can be stored non-refrigerated, avoiding cumbersome or costly sample methods. The genomic library construction and shotgun sequencing approach did not require enrichment or targeted DNA amplification. The utility and potential of the data generated was demonstrated through genome scale and metagenomic analyses of zoo and free-ranging African savanna elephants (Loxodonta africana). Fecal samples collected from free-ranging individuals contained an average of 12.41% (5.54-21.65%) endogenous elephant DNA. Clustering of these elephants with others from the same geographic region was demonstrated by a principal component analysis of genetic variation using nuclear genome-wide SNPs. Metagenomic analyses identified taxa that included Loxodonta, green plants, fungi, arthropods, bacteria, viruses and archaea, showcasing the utility of this approach for addressing complementary questions based on host-associated DNA, e.g., pathogen and parasite identification. The molecular and bioinformatic analyses presented here contributes towards the expansion and application of genomic techniques to conservation science and practice.}, } @article {pmid36712525, year = {2022}, author = {Mahalak, KK and Firrman, J and Narrowe, AB and Hu, W and Jones, SM and Bittinger, K and Moustafa, AM and Liu, L}, title = {Fructooligosaccharides (FOS) differentially modifies the in vitro gut microbiota in an age-dependent manner.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {1058910}, pmid = {36712525}, issn = {2296-861X}, abstract = {INTRODUCTION: Fructooligosaccharides (FOS) are well-known carbohydrates that promote healthy gut microbiota and have been previously demonstrated to enhance levels of Bifidobacterium and Lactobacillus. Its bifidogenic properties are associated with positive health outcomes such as reduced obesity and anti-inflammatory properties, and, therefore, is in use as a prebiotic supplement to support healthy gut microbiota. However, the gut microbiota changes with age, which may lead to differential responses to treatments with prebiotics and other dietary supplements.

METHODS: To address this concern, we implemented a 24-h in vitro culturing method to determine whether FOS treatment in three different adult age groups would have a differential effect. The age groups of interest ranged from 25 to 70 years and were split into young adults, adults, and older adults for the purposes of this analysis. Metagenomics and short-chain fatty acid analysis were performed to determine changes in the structure and function of the microbial communities.

RESULTS: These analyses found that FOS created a bifidogenic response in all age groups, increased overall SCFA levels, decreased alpha diversity, and shifted the communities to be more similar in beta diversity metrics. However, the age groups differed in which taxa were most prevalent or most affected by FOS treatment.

DISCUSSION: Overall, the results of this study demonstrate the positive effects of FOS on the gut microbiome, and importantly, how age may play a role in the effectiveness of this prebiotic.}, } @article {pmid36712370, year = {2022}, author = {Garritano, AN and Song, W and Thomas, T}, title = {Carbon fixation pathways across the bacterial and archaeal tree of life.}, journal = {PNAS nexus}, volume = {1}, number = {5}, pages = {pgac226}, pmid = {36712370}, issn = {2752-6542}, abstract = {Carbon fixation is a critical process for our planet; however, its distribution across the bacterial and archaeal domains of life has not been comprehensively studied. Here, we performed an analysis of 52,515 metagenome-assembled genomes and discover carbon fixation pathways in 1,007 bacteria and archaea. We reveal the genomic potential for carbon fixation through the reverse tricarboxylic acid cycle in previously unrecognized archaeal and bacterial phyla (i.e. Thermoplasmatota and Elusimicrobiota) and show that the 3-hydroxypropionate bi-cycle is not, as previously thought, restricted to the phylum Chloroflexota. The data also substantially expand the phylogenetic breadth for autotrophy through the dicarboxylate/4-hydroxybutyrate cycle and the Calvin-Benson-Bassham cycle. Finally, the genomic potential for carbon fixation through the 3-hydroxypropionate/4-hydroxybutyrate cycle, previously exclusively found in Archaea, was also detected in the Bacteria. Carbon fixation thus appears to be much more widespread than previously known, and this study lays the foundation to better understand the role of archaea and bacteria in global primary production and how they contribute to microbial carbon sinks.}, } @article {pmid36712365, year = {2022}, author = {Espinoza, JL and Torralba, M and Leong, P and Saffery, R and Bockmann, M and Kuelbs, C and Singh, S and Hughes, T and Craig, JM and Nelson, KE and Dupont, CL}, title = {Differential network analysis of oral microbiome metatranscriptomes identifies community scale metabolic restructuring in dental caries.}, journal = {PNAS nexus}, volume = {1}, number = {5}, pages = {pgac239}, pmid = {36712365}, issn = {2752-6542}, support = {R01 AI170111/AI/NIAID NIH HHS/United States ; R01 DE019665/DE/NIDCR NIH HHS/United States ; }, abstract = {Dental caries is a microbial disease and the most common chronic health condition, affecting nearly 3.5 billion people worldwide. In this study, we used a multiomics approach to characterize the supragingival plaque microbiome of 91 Australian children, generating 658 bacterial and 189 viral metagenome-assembled genomes with transcriptional profiling and gene-expression network analysis. We developed a reproducible pipeline for clustering sample-specific genomes to integrate metagenomics and metatranscriptomics analyses regardless of biosample overlap. We introduce novel feature engineering and compositionally-aware ensemble network frameworks while demonstrating their utility for investigating regime shifts associated with caries dysbiosis. These methods can be applied when differential abundance modeling does not capture statistical enrichments or the results from such analysis are not adequate for providing deeper insight into disease. We identified which organisms and metabolic pathways were central in a coexpression network as well as how these networks were rewired between caries and caries-free phenotypes. Our findings provide evidence of a core bacterial microbiome that was transcriptionally active in the supragingival plaque of all participants regardless of phenotype, but also show highly diagnostic changes in the ways that organisms interact. Specifically, many organisms exhibit high connectedness with central carbon metabolism to Cardiobacterium and this shift serves a bridge between phenotypes. Our evidence supports the hypothesis that caries is a multifactorial ecological disease.}, } @article {pmid36712343, year = {2022}, author = {Leão, TF and Wang, M and da Silva, R and Gurevich, A and Bauermeister, A and Gomes, PWP and Brejnrod, A and Glukhov, E and Aron, AT and Louwen, JJR and Kim, HW and Reher, R and Fiore, MF and van der Hooft, JJJ and Gerwick, L and Gerwick, WH and Bandeira, N and Dorrestein, PC}, title = {NPOmix: A machine learning classifier to connect mass spectrometry fragmentation data to biosynthetic gene clusters.}, journal = {PNAS nexus}, volume = {1}, number = {5}, pages = {pgac257}, pmid = {36712343}, issn = {2752-6542}, abstract = {Microbial specialized metabolites are an important source of and inspiration for many pharmaceuticals, biotechnological products and play key roles in ecological processes. Untargeted metabolomics using liquid chromatography coupled with tandem mass spectrometry is an efficient technique to access metabolites from fractions and even environmental crude extracts. Nevertheless, metabolomics is limited in predicting structures or bioactivities for cryptic metabolites. Efficiently linking the biosynthetic potential inferred from (meta)genomics to the specialized metabolome would accelerate drug discovery programs by allowing metabolomics to make use of genetic predictions. Here, we present a k-nearest neighbor classifier to systematically connect mass spectrometry fragmentation spectra to their corresponding biosynthetic gene clusters (independent of their chemical class). Our new pattern-based genome mining pipeline links biosynthetic genes to metabolites that they encode for, as detected via mass spectrometry from bacterial cultures or environmental microbiomes. Using paired datasets that include validated genes-mass spectral links from the Paired Omics Data Platform, we demonstrate this approach by automatically linking 18 previously known mass spectra (17 for which the biosynthesis gene clusters can be found at the MIBiG database plus palmyramide A) to their corresponding previously experimentally validated biosynthetic genes (e.g., via nuclear magnetic resonance or genetic engineering). We illustrated a computational example of how to use our Natural Products Mixed Omics (NPOmix) tool for siderophore mining that can be reproduced by the users. We conclude that NPOmix minimizes the need for culturing (it worked well on microbiomes) and facilitates specialized metabolite prioritization based on integrative omics mining.}, } @article {pmid36712061, year = {2023}, author = {Fei, N and Miyoshi, S and Hermanson, JB and Miyoshi, J and Xie, B and DeLeon, O and Hawkins, M and Charlton, W and D'Souza, M and Hart, J and Sulakhe, D and Martinez-Guryn, KB and Chang, EB and Charlton, MR and Leone, VA}, title = {Imbalanced gut microbiota predicts and drives the progression of nonalcoholic fatty liver disease and nonalcoholic steatohepatitis in a fast-food diet mouse model.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36712061}, support = {P30 DK042086/DK/NIDDK NIH HHS/United States ; }, abstract = {Nonalcoholic fatty liver disease (NAFLD) is multifactorial in nature, affecting over a billion people worldwide. The gut microbiome has emerged as an associative factor in NAFLD, yet mechanistic contributions are unclear. Here, we show fast food (FF) diets containing high fat, added cholesterol, and fructose/glucose drinking water differentially impact short- vs. long-term NAFLD severity and progression in conventionally-raised, but not germ-free mice. Correlation and machine learning analyses independently demonstrate FF diets induce early and specific gut microbiota changes that are predictive of NAFLD indicators, with corresponding microbial community instability relative to control-fed mice. Shotgun metagenomics showed FF diets containing high cholesterol elevate fecal pro-inflammatory effectors over time, relating to a reshaping of host hepatic metabolic and inflammatory transcriptomes. FF diet-induced gut dysbiosis precedes onset and is highly predictive of NAFLD outcomes, providing potential insights into microbially-based pathogenesis and therapeutics.}, } @article {pmid36711990, year = {2023}, author = {Liao, J and Shenhav, L and Urban, JA and Serrano, M and Zhu, B and Buck, GA and Korem, T}, title = {Microdiversity of the Vaginal Microbiome is Associated with Preterm Birth.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36711990}, support = {R01 HD106017/HD/NICHD NIH HHS/United States ; U54 HD080784/HD/NICHD NIH HHS/United States ; }, abstract = {Preterm birth (PTB) is the leading cause of neonatal morbidity and mortality. The vaginal microbiome has been associated with PTB, yet the mechanisms underlying this association are not fully understood. Understanding microbial genetic adaptations to selective pressures, especially those related to the host, may yield new insights into these associations. To this end, we analyzed metagenomic data from 705 vaginal samples collected longitudinally during pregnancy from 40 women who delivered preterm spontaneously and 135 term controls from the Multi-Omic Microbiome Study-Pregnancy Initiative (MOMS-PI). We find that the vaginal microbiome of pregnancies that ended preterm exhibits unique genetic profiles. It is more genetically diverse at the species level, a result which we validate in an additional cohort, and harbors a higher richness and diversity of antimicrobial resistance genes, likely promoted by transduction. Interestingly, we find that Gardnerella species, a group of central vaginal pathobionts, are driving this higher genetic diversity, particularly during the first half of the pregnancy. We further present evidence that Gardnerella spp. undergoes more frequent recombination and stronger purifying selection in genes involved in lipid metabolism. Overall, our results reveal novel associations between the vaginal microbiome and PTB using population genetics analyses, and suggest that evolutionary processes acting on the vaginal microbiome may play a vital role in adverse pregnancy outcomes such as preterm birth.}, } @article {pmid36711755, year = {2023}, author = {Singh, HW and Creamer, KE and Chase, AB and Klau, LJ and Podell, S and Jensen, PR}, title = {Metagenomic Data Reveal Type I Polyketide Synthase Distributions Across Biomes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.01.09.523365}, pmid = {36711755}, abstract = {UNLABELLED: Microbial polyketide synthase (PKS) genes encode the biosynthesis of many biomedically important natural products, yet only a small fraction of nature's polyketide biosynthetic potential has been realized. Much of this potential originates from type I PKSs (T1PKSs), which can be delineated into different classes and subclasses based on domain organization and structural features of the compounds encoded. Notably, phylogenetic relationships among PKS ketosynthase (KS) domains provide a method to classify the larger and more complex genes in which they occur. Increased access to large metagenomic datasets from diverse habitats provides opportunities to assess T1PKS biosynthetic diversity and distributions through the analysis of KS domain sequences. Here, we used the webtool NaPDoS2 to detect and classify over 35,000 type I KS domains from 137 metagenomic data sets reported from eight diverse biomes. We found biome-specific separation with soils enriched in modular cis -AT and hybrid cis -AT KSs relative to other biomes and marine sediments enriched in KSs associated with PUFA and enediyne biosynthesis. By extracting full-length KS domains, we linked the phylum Actinobacteria to soil-specific enediyne and cis -AT clades and identified enediyne and monomodular KSs in phyla from which the associated compound classes have not been reported. These sequences were phylogenetically distinct from those associated with experimentally characterized PKSs suggesting novel structures or enzyme functions remain to be discovered. Lastly, we employed our metagenome-extracted KS domains to evaluate commonly used type I KS PCR primers and identified modifications that could increase the KS sequence diversity recovered from amplicon libraries.

IMPORTANCE: Polyketides are a crucial source of medicines, agrichemicals, and other commercial products. Advances in our understanding of polyketide biosynthesis coupled with the accumulation of metagenomic sequence data provide new opportunities to assess polyketide biosynthetic potential across biomes. Here, we used the webtool NaPDoS2 to assess type I PKS diversity and distributions by detecting and classifying KS domains across 137 metagenomes. We show that biomes are differentially enriched in KS domain classes, providing a roadmap for future biodiscovery strategies. Further, KS phylogenies reveal both biome-specific clades that do not include biochemically characterized PKSs, highlighting the biosynthetic potential of poorly explored environments. The large metagenome-derived KS dataset allowed us to identify regions of commonly used type I KS PCR primers that could be modified to capture a larger extent of KS diversity. These results facilitate both the search for novel polyketides and our understanding of the biogeographical distribution of PKSs across earth's major biomes.}, } @article {pmid36711684, year = {2023}, author = {Wilson, NG and Hernandez-Leyva, A and Schwartz, DJ and Bacharier, LB and Kau, AL}, title = {The gut metagenome harbors metabolic and antibiotic resistance signatures of moderate-to-severe asthma.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36711684}, support = {F30 DK127584/DK/NIDDK NIH HHS/United States ; K08 AI113184/AI/NIAID NIH HHS/United States ; T32 GM007200/GM/NIGMS NIH HHS/United States ; }, abstract = {Asthma is a common allergic airway disease that develops in association with the human microbiome early in life. Both the composition and function of the infant gut microbiota have been linked to asthma risk, but functional alterations in the gut microbiota of older patients with established asthma remain an important knowledge gap. Here, we performed whole metagenomic shotgun sequencing of 95 stool samples from 59 healthy and 36 subjects with moderate-to-severe asthma to characterize the metagenomes of gut microbiota in children and adults 6 years and older. Mapping of functional orthologs revealed that asthma contributes to 2.9% of the variation in metagenomic content even when accounting for other important clinical demographics. Differential abundance analysis showed an enrichment of long-chain fatty acid (LCFA) metabolism pathways which have been previously implicated in airway smooth muscle and immune responses in asthma. We also observed increased richness of antibiotic resistance genes (ARGs) in people with asthma. One differentially abundant ARG was a macrolide resistance marker, ermF, which significantly co-occurred with the Bacteroides fragilis toxin, suggesting a possible relationship between enterotoxigenic B. fragilis, antibiotic resistance, and asthma. Lastly, we found multiple virulence factor (VF) and ARG pairs that co-occurred in both cohorts suggesting that virulence and antibiotic resistance traits are co-selected and maintained in the fecal microbiota of people with asthma. Overall, our results show functional alterations via LCFA biosynthetic genes and increases in antibiotic resistance genes in the gut microbiota of subjects with moderate-to-severe asthma and could have implications for asthma management and treatment.}, } @article {pmid36711562, year = {2023}, author = {Armstrong, DA and Hudson, TR and Hodge, CA and Hampton, TH and Howell, AL and Hayden, MS}, title = {CAS12e (CASX2) CLEAVAGE OF CCR5: IMPACT OF GUIDE RNA LENGTH AND PAM SEQUENCE ON CLEAVAGE ACTIVITY.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36711562}, abstract = {CRISPR/Cas is under development as a therapeutic tool for the cleavage, excision, and/or modification of genes in eukaryotic cells. While much effort has focused on CRISPR/Cas from Streptococcus pyogenes (SpCas9) and Staphylococcus aureus (SaCas9), alternative CRISPR systems have been identified using metagenomic datasets from non-pathogenic microbes, including previously unknown class 2 systems, adding to a diverse toolbox of gene editors. The Cas12e (CasX1, CasX2) endonucleases from non-pathogenic Deltaproteobacteria (DpeCas12e) and Planctomycetes (PlmCas12e) are more compact than SpCas9, have a more selective protospacer adjacent motif (PAM) requirement, and deliver a staggered cleavage cut with 5-7 base overhangs. We investigated varying guide RNA (spacer) lengths and alternative PAM sequences to determine optimal conditions for PlmCas12e cleavage of the cellular gene CCR5 (CC-Chemokine receptor-5). CCR5 encodes one of two chemokine coreceptors required by HIV-1 to infect target cells, and a mutation of CCR5 (delta-32) is responsible for HIV-1 resistance and reported cures following bone marrow transplantation. Consequently, CCR5 has been an important target for gene editing utilizing CRISPR, TALENs, and ZFNs. We determined that CCR5 cleavage activity varied with the target site, guide RNA length, and the terminal nucleotide in the PAM sequence. Our analyses demonstrated a PlmCas12e PAM preference for purines (A, G) over pyrimidines (T, C) in the fourth position of the CasX2 PAM (TTCN). These analyses have contributed to a better understanding of CasX2 cleavage requirements and will position us more favorably to develop a therapeutic that creates the delta-32 mutation in the CCR5 gene in hematopoietic stem cells.}, } @article {pmid36711483, year = {2023}, author = {Sarode, GV and Mazi, TA and Neier, K and Shibata, NM and Jospin, G and Harder, NHO and Heffern, MC and Sharma, AK and More, SK and Dave, M and Schroeder, SM and Wang, L and LaSalle, JM and Lutsenko, S and Medici, V}, title = {The role of intestine in metabolic dysregulation in murine Wilson disease.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, doi = {10.1101/2023.01.13.524009}, pmid = {36711483}, support = {R35 GM133684/GM/NIGMS NIH HHS/United States ; }, abstract = {BACKGROUND AND AIMS: Major clinical manifestations of Wilson disease (WD) are related to copper accumulation in the liver and the brain, and little is known about other tissues involvement in metabolic changes in WD. In vitro studies suggested that the loss of intestinal ATP7B could contribute to metabolic dysregulation in WD. We tested this hypothesis by evaluating gut microbiota and lipidome in two mouse models of WD and by characterizing a new mouse model with a targeted deletion of Atp7b in intestine.

METHODS: Cecal content 16S sequencing and untargeted hepatic and plasma lipidome analyses in the Jackson Laboratory toxic-milk and the Atp7b null global knockout mouse models of WD were profiled and integrated. Intestine-specific Atp7b knockout mice (Atp7b [ΔIEC]) was generated using B6.Cg-Tg(Vil1-cre)997Gum/J mice and Atp7b [Lox/Lox] mice, and characterized using targeted lipidome analysis following a high-fat diet challenge.

RESULTS: Gut microbiota diversity was reduced in animal models of WD. Comparative prediction analysis revealed amino acid, carbohydrate, and lipid metabolism functions to be dysregulated in the WD gut microbial metagenome. Liver and plasma lipidomic profiles showed dysregulated tri- and diglyceride, phospholipid, and sphingolipid metabolism in WD models. When challenged with a high-fat diet, Atp7b [ΔIEC] mice exhibited profound alterations to fatty acid desaturation and sphingolipid metabolism pathways as well as altered APOB48 distribution in intestinal epithelial cells.

CONCLUSION: Coordinated changes of gut microbiome and lipidome analyses underlie systemic metabolic manifestations in murine WD. Intestine-specific ATP7B deficiency affected both intestinal and systemic response to a high-fat challenge. WD is a systemic disease in which intestinal-specific ATP7B loss and diet influence phenotypic presentations.}, } @article {pmid36710980, year = {2022}, author = {Liu, Y and Zhang, R and Yao, B and Yang, J and Ge, H and Zheng, S and Guo, Q and Xing, J}, title = {Metagenomics next-generation sequencing provides insights into the causative pathogens from critically ill patients with pneumonia and improves treatment strategies.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1094518}, pmid = {36710980}, issn = {2235-2988}, mesh = {Humans ; Critical Illness ; Retrospective Studies ; *Pneumonia/diagnosis/drug therapy ; *Mycobacterium tuberculosis ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: The metagenomics next-generation sequencing (mNGS) is a promising technique for pathogens diagnosis. However, whether the application of mNGS in critically ill patients with pneumonia could cause anti-infection treatment adjustment and thereby affect the prognosis of these patients has not been explored.

METHODS: We retrospectively collected the clinical data of patients diagnosed with pulmonary infection in the ICU of the Affiliated Hospital of Qingdao University from January 2018 to January 2021. These patients with pneumonia were divided into mNGS group and no-mNGS group by whether being performed NGS or not. The clinical data, including demographics, illness history, APACHE II score, length of mechanical ventilation, length of stay in the hospital, length of stay in ICU and outcome, were collected. In addition, the data of pathogens and anti-infection treatment before and after NGS were also collected. Propensity score matching was performed to evaluate the mortality and deterioration rate between NGS group and non-NGS group.

RESULTS: A total of 641 patients diagnosed with pneumonia were screened, and 94 patients were excluded based on exclusion criteria. Finally, 547 patients were enrolled, including 160 patients being performed NGS. Among these 160 patients, 142 cases had NGS-positive results. In addition, new pathogens were detected in 132 specimens by NGS, which included 82 cases with virus, 18 cases with fungus, 17 cases with bacteria, 14 cases with mycoplasma, and 1 case with mycobacterium tuberculosis. Anti-infection treatments were adjusted in some patients who performed NGS, including 48 anti-bacterial treatments, 20 antifungal treatments and 20 antiviral treatments. There were no significant differences in the mortality and deterioration rate between NGS and non-NGS group, but it exhibited a trend that the mortality and deterioration rate of NGS group was lower than non-NGS group after the propensity score matching analysis (15.8% vs 24.3%, P=0.173; 25.6% vs 37.8%, P=0.093).

CONCLUSION: NGS could affect the anti-infection treatments and had a trend of reducing the mortality and deterioration rate of critically ill patients with pneumonia.}, } @article {pmid36710967, year = {2022}, author = {Xiao, QY and Ye, TY and Wang, XL and Qi, DM and Cheng, XR}, title = {Effects of Qi-Fu-Yin on aging of APP/PS1 transgenic mice by regulating the intestinal microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1048513}, pmid = {36710967}, issn = {2235-2988}, mesh = {Mice ; Animals ; Mice, Transgenic ; *Gastrointestinal Microbiome ; Amyloid beta-Protein Precursor/genetics ; *Alzheimer Disease ; Aging/metabolism ; Carbohydrates ; Disease Models, Animal ; }, abstract = {INTRODUCTION: Alzheimer's disease is the most common form of dementia and closely related to aging. Qi-Fu-Yin is widely used to treat dementia, but its anti-aging effects is unknown.

METHODS: We used 11-month-old APP/PS1 transgenic mice for behavioral tests to observe the changes in cognitive function and age-related symptoms after Qi-Fu-Yin treatment. Fecal samples were collected for 16sRNA sequencing and metagenomic sequencing. Differences among the groups of intestinal microbiota and the associations with aging and intestinal microbiota were analyzed based on the results.

RESULTS: Here we found that Qi-Fu-Yin improved the ability of motor coordination, raised survival rate and prolonged the survival days under cold stress stimulation in aged APP/ PS1 transgenic mice. Our data from 16sRNA and metagenomic sequencing showed that at the Family level, the intestinal microbiota was significantly different among wild-type mice, APP/PS1 transgenic mice and the Qi-Fu-Yin group by PCA analysis. Importantly, Qi-Fu-Yin improved the functional diversity of the major KEGG pathways, carbohydrate-active enzymes, and major virulence factors in the intestinal flora of APP/PS1 transgenic mice. Among them, the functions of eight carbohydrate-active enzymes (GT2_Glycos_transf_2, GT4, GT41, GH2, CE1, CE10, CE3, and GH24) and the functions of top three virulence factors (defensive virulence factors, offensive virulence factors and nonspecific virulence factors) were significantly and positively correlated with the level of grasping ability. We further indicated that the Qi-Fu-Yin significantly reduced the plasma levels of IL-6.

CONCLUSION: Our results indicated that the effects of Qi-Fu-Yin anti-aging of APP/PS1 transgenic mice might be through the regulation of intestinal flora diversity, species richness and the function of major active enzymes.}, } @article {pmid36710966, year = {2022}, author = {Sopovski, DS and Han, J and Stevens-Riley, M and Wang, Q and Erickson, BD and Oktem, B and Vanlandingham, M and Taylor, CL and Foley, SL}, title = {Investigation of microorganisms in cannabis after heating in a commercial vaporizer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1051272}, pmid = {36710966}, issn = {2235-2988}, mesh = {Humans ; *Cannabis ; Heating ; Nebulizers and Vaporizers ; Hot Temperature ; Temperature ; }, abstract = {INTRODUCTION: There are concerns about microorganisms present on cannabis materials used in clinical settings by individuals whose health status is already compromised and are likely more susceptible to opportunistic infections from microbial populations present on the materials. Most concerning is administration by inhalation where cannabis plant material is heated in a vaporizer, aerosolized, and inhaled to receive the bioactive ingredients. Heating to high temperatures is known to kill microorganisms including bacteria and fungi; however, microbial death is dependent upon exposure time and temperature. It is unknown whether the heating of cannabis at temperatures and times designated by a commercial vaporizer utilized in clinical settings will significantly decrease the microbial loads in cannabis plant material.

METHODS: To assess this question, bulk cannabis plant material supplied by National Institute on Drug Abuse (NIDA) was used to assess the impact of heating by a commercial vaporizer. Initial method development studies using a cannabis placebo spiked with Escherichia coli were performed to optimize culture and recovery parameters. Subsequent studies were carried out using the cannabis placebo, low delta-9 tetrahydrocannabinol (THC) potency and high THC potency cannabis materials exposed to either no heat or heating for 30 or 70 seconds at 190°C. Phosphate-buffered saline was added to the samples and the samples agitated to suspend the microorganism. Microbial growth after no heat or heating was evaluated by plating on growth media and determining the total aerobic microbial counts and total yeast and mold counts.

RESULTS AND DISCUSSION: Overall, while there were trends of reductions in microbial counts with heating, these reductions were not statistically significant, indicating that heating using standard vaporization parameters of 70 seconds at 190°C may not eliminate the existing microbial bioburden, including any opportunistic pathogens. When cultured organisms were identified by DNA sequence analyses, several fungal and bacterial taxa were detected in the different products that have been associated with opportunistic infections or allergic reactions including Enterobacteriaceae, Staphylococcus, Pseudomonas, and Aspergillus.}, } @article {pmid36710917, year = {2023}, author = {John, DV and Purushottam, M}, title = {Metagenomic data reveals microbiome characteristics of culture-negative brain abscess samples.}, journal = {Data in brief}, volume = {46}, number = {}, pages = {108893}, pmid = {36710917}, issn = {2352-3409}, abstract = {A brain abscess is a focal collection of pus in the brain parenchyma surrounded by a well-vascularized collagenous capsule in response to an infection. The microbiome of brain abscesses has been shown to be polymicrobial, dominated by uncultivable and anaerobic organisms of odontogenic origin. The data provided in this article includes the sequences of bacterial 16S rRNA gene from three culture-negative brain abscess samples suspected to have poly-microbial aetiology based on Sanger sequencing. DNA was extracted from brain abscess samples, and targeted-metagenomics sequencing was done by amplifying the full-length bacterial 16S rRNA followed by a nested PCR for V3-V4 regions using universal and specific primers. The barcoded amplicons were sequenced on Illumina MiSeq V2 instrument to generate 0.5M, 250bp paired-end reads/sample. The total sequencing reads were 455966, 345746, and 438658 for samples P32, P49, and P8, respectively. Bioinformatics tools such as FLASH, VSEARCH, and QIIME1 were used to process the reads generated for Operational Taxonomic Unit analysis (OTU). Bacterial species belonging to phyla Firmicutes, Bacteroidetes, and Fusobacteria were abundant in samples P49 and P8, which are mainly anaerobic and microaerophilic bacteria. These are typical of the human oral/gut microbiota and are implicated in brain abscess formation. Sample P32 showed the abundance of bacterial species belonging to phyla Proteobacteria and Actinobacteria, which are commonly found in the environment. Raw data files are available at the Sequence Read Archive (SRA), National Center for Biotechnology Information (NCBI), and data information can be found at the BioProject, PRJNA785100 under the accession numbers SRX13271109, SRX13271110, SRX13295897. The data shows the microbiome constitution, including several anaerobic and unculturable bacterial species from culture-negative brain abscess samples. This dataset will be useful for future research on comparative genomics and management of patients with culture-negative brain abscesses.}, } @article {pmid36709893, year = {2023}, author = {Han, Z and Shao, B and Lei, L and Pang, R and Wu, D and Tai, J and Xie, B and Su, Y}, title = {The role of pretreatments in handling antibiotic resistance genes in anaerobic sludge digestion - A review.}, journal = {The Science of the total environment}, volume = {869}, number = {}, pages = {161799}, doi = {10.1016/j.scitotenv.2023.161799}, pmid = {36709893}, issn = {1879-1026}, mesh = {*Sewage ; *Anti-Bacterial Agents/pharmacology ; Anaerobiosis ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Digestion ; }, abstract = {Sludge is among the most important reservoirs of antibiotic resistance genes (ARGs), which would cause potential environmental risks with the sludge utilization. Currently, anaerobic digestion (AD) is effective to simultaneously realize the resource recovery and pollutants removal, including antibiotic resistance genes (ARGs), and various pretreatments are used to enhance the performance. Recently, plentiful publications have focused on the effects of pretreatment on ARGs removal, but the contradictory results are often obtained, and a comprehensive understanding of the research progress and mechanisms is essential. This study summarizes various pretreatment techniques for improving AD efficiency and ARGs reduction, investigates promising performance in ARGs removal when pretreatments combined with AD, and analyzes the potential mechanisms accounting for ARGs fates. The results showed that although thermal hydrolysis pretreatment showed the best performance in ARGs reduction during the pretreatment process, the significant rebound of ARGs would occur in the subsequent AD process. Conversely, ozone pretreatment and alkali pretreatment had no significant effect on ARGs abundance in the pretreatment stage, but could enhance ARGs removal by 15.6-24.3 % in the subsequent AD. Considering the efficiency and economic effectiveness, free nitrous acid pretreatment would be a promising and feasible option, which could enhance methane yield and ARGs removal by up to 27 % and 74.5 %, respectively. Currently, the factors determining ARGs fates during pretreatment and AD processes included the shift of microbial community, mobile genetic elements (MGEs), and environmental factors. A comprehensive understanding of the relationship between the fate of ARGs and pretreatment technologies could be helpful for systematically evaluating various pretreatments and facilitating the development of emerging and effective pretreatment techniques. Moreover, given the effectiveness, economic efficiency and environmental safety, we called for the applications of modern analysis approaches such as metagenomic and machine learning on the optimization of pretreatment conditions and revealing underlying mechanisms.}, } @article {pmid36709875, year = {2023}, author = {Wang, J and Tian, Y and Wei, J and Lyu, C and Yu, H and Song, Y}, title = {Impacts of dibutyl phthalate on bacterial community composition and carbon and nitrogen metabolic pathways in a municipal wastewater treatment system.}, journal = {Environmental research}, volume = {223}, number = {}, pages = {115378}, doi = {10.1016/j.envres.2023.115378}, pmid = {36709875}, issn = {1096-0953}, mesh = {*Dibutyl Phthalate/toxicity ; Waste Disposal, Fluid ; Nitrogen/metabolism ; Carbon ; RNA, Ribosomal, 16S ; Bacteria/genetics/metabolism ; Metabolic Networks and Pathways ; *Water Purification ; Pharmaceutical Preparations ; Bioreactors/microbiology ; Sewage/microbiology ; }, abstract = {Dibutyl phthalate (DBP) is a typical toxic and hazardous pollutant in pharmaceutical wastewater, affecting the metabolism of microbial flora, leading to decreased treatment efficiency, and deteriorated effluent quality in municipal wastewater treatment plants (WWTPs). This study conducted a long-term experiment with 6 operational stages in a pilot-scale A[2]O-MBR system, analyzing the effect of DBP on the bacterial community and their carbon and nitrogen metabolic pathways. 16S rRNA gene amplicon sequencing analysis and principal components analysis (PCA) showed that DBP at 8 mg/L significantly influenced the structure of bacterial community (P < 0.05), resulting in reduced bacterial community diversity. Metagenomic analysis was used to explore the embedded carbon and nitrogen metabolic pathways. At the presence of DBP, the metabolism of saccharides, lipids, and aromatic compounds were blocked owing to the vanishment of key enzyme (such as acetylaminohexosyltransferase (EC 2.4.1.92) and UDP-sugar pyro phosphorylase (EC 2.7.7.64)) encoding genes, resulting in weakened carbon metabolism, and thus reduced COD removal performance. The resultant deficiency of the genes such as those encoding hydroxyproline dehydrogenase (EC 1.5.5.3) gave rise to interrupted metabolic pathways of amino acid (arginine, proline, tyrosine, and tryptophan), resulting in declined function of nitrogen metabolism and thus reduced TN removal efficiency. The uncovery of the mechanisms by which DBP affects wastewater treatment system efficiency and microbial metabolism is of theoretical importance for the efficient operation of municipal and pharmaceutical wastewater treatment systems.}, } @article {pmid36709348, year = {2023}, author = {Tóth, AG and Farkas, R and Gyurkovszky, M and Krikó, E and Solymosi, N}, title = {First detection of Ixodiphagus hookeri (Hymenoptera: Encyrtidae) in Ixodes ricinus ticks (Acari: Ixodidae) from multiple locations in Hungary.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {1624}, pmid = {36709348}, issn = {2045-2322}, mesh = {Animals ; *Ixodes ; *Ixodidae ; Hungary ; *Wasps ; Europe ; }, abstract = {The parasitoid wasp, Ixodiphagus hookeri (Hymenoptera: Encyrtidae), is the natural enemy of a wide range of hard and soft tick species. While these encyrtid wasps are supposed to be distributed worldwide, only a few studies report on their actual distribution around the globe. Within a shotgun sequencing-based metagenome analysis, the occurrence of I. hookeri was screened at multiple Ixodes ricinus (Acari: Ixodidae) tick sampling points in Hungary to contribute to the assessment of the distribution patterns of the parasitoid wasps in Central Europe. To our knowledge, the first report of the species in Hungary and the description of the southernmost I. hookeri associated geoposition in Central Europe took place within our study. I. hookeri infested I. ricinus nymphs were detected at five sampling points in Hungary. The results show that the exact distribution range of I. hookeri is still barely studied. At the same time, unprecedented public health issues being brought about by climate change might require steps toward the exploitation of the tick biocontrol potential and as an ecological bioindicator role of the parasitoid wasp in the future.}, } @article {pmid36709204, year = {2022}, author = {Wu, YJ and Chen, F and Zhao, Y and Zhang, YM and Cao, JJ and Lin, GQ and Wang, TJ and Xia, J and Tang, XW and Xue, SL and Jin, ZM and Wu, DP}, title = {[A clinical analysis of adenovirus infection diagnosed by metagenomic next-generation sequencing or the diagnosis of adenovirus infection after haploidentical hematopoietic stem cell transplantation clinical analysis of six cases].}, journal = {Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi}, volume = {43}, number = {10}, pages = {869-872}, pmid = {36709204}, issn = {0253-2727}, mesh = {Humans ; *Hematopoietic Stem Cell Transplantation ; *Adenoviridae Infections/diagnosis ; High-Throughput Nucleotide Sequencing ; *Graft vs Host Disease ; Transplantation Conditioning ; }, } @article {pmid36709171, year = {2022}, author = {Hao, SF and Wang, YH and Li, LJ and Wang, HQ and Song, J and Wu, YH and Qu, W and Wang, GJ and Wang, XM and Liu, H and Xing, LM and Guan, J and Shao, ZH and Fu, R}, title = {[Clinical application value of peripheral blood metagenomic next-generation sequencing test for patients with hematological diseases accompanied by fever].}, journal = {Zhonghua xue ye xue za zhi = Zhonghua xueyexue zazhi}, volume = {43}, number = {9}, pages = {766-770}, pmid = {36709171}, issn = {0253-2727}, mesh = {Humans ; Retrospective Studies ; *Hematologic Diseases ; Hematologic Tests ; Fever ; High-Throughput Nucleotide Sequencing ; Sensitivity and Specificity ; }, abstract = {Objective: To investigate the clinical application value of peripheral blood metagenomic next-generation sequencing (mNGS) test for patients with hematological diseases accompanied by fever. Methods: The blood mNGS results and clinical data of inpatients with hematological diseases accompanied by fever treated in the Hematology Department of Tianjin Medical University General Hospital in March 2020 to June 2021were retrospectively analyzed. A total of 90 patients with 98 cases of specimens were included. The pathogen distribution characteristics and mNGS test performance were analyzed. Results: The positive rate of peripheral blood mNGS was significantly higher than that of traditional examination (68.37% vs 37.76%, P<0.001) and blood culture (68.37% vs 9.18%, P<0.001) . Viral, bacterial, and fungal infections accounted for 38.81%, 14.93%, and 2.99% in patients with single-pathogen infections, respectively. Polymicrobial infections accounted for 43.28%, in which viral and bacterial coinfections were the most common type (25.37%) . There were 55 virus-positive cases (82.09%) , 30 bacteria-positive cases (44.78%) , and 14 fungus-positive cases (20.90%) . The clinical approval rate of peripheral blood mNGS was 64.63% (63/98) . The sensitivity, specificity, positive predictive value, and negative predictive value (NPV) of peripheral blood mNGS were 75.68%, 36.07%, 41.79%, and 70.97%, respectively, and the overall consistency rate with traditional examination was 51.02%. Of the 22 pulmonary infection cases with no detectable pathogens by conventional tests, the pathogens were identified by peripheral blood mNGS in 14 cases, 10 of which were clinically approved. Conclusion: The positive rate of peripheral blood mNGS was significantly higher than that of blood culture and traditional laboratory examination. Peripheral blood mNGS had a high clinical recognition rate, sensitivity, and NPV in the detection of pathogens in patients with hematological diseases accompanied by fever.}, } @article {pmid36708142, year = {2023}, author = {Chakraborty, S and Rannala, B}, title = {An efficient exact algorithm for identifying hybrids using population genomic sequences.}, journal = {Genetics}, volume = {223}, number = {4}, pages = {}, pmid = {36708142}, issn = {1943-2631}, support = {GM123306/NH/NIH HHS/United States ; }, mesh = {*Genetics, Population ; *Metagenomics ; Bayes Theorem ; Genomics ; }, abstract = {The identification of individuals that have a recent hybrid ancestry (between populations or species) has been a goal of naturalists for centuries. Since the 1960s, codominant genetic markers have been used with statistical and computational methods to identify F1 hybrids and backcrosses. Existing hybrid inference methods assume that alleles at different loci undergo independent assortment (are unlinked or in population linkage equilibrium). Genomic datasets include thousands of markers that are located on the same chromosome and are in population linkage disequilibrium which violate this assumption. Existing methods may therefore be viewed as composite likelihoods when applied to genomic datasets and their performance in identifying hybrid ancestry (which is a model-choice problem) is unknown. Here, we develop a new program Mongrail that implements a full-likelihood Bayesian hybrid inference method that explicitly models linkage and recombination, generating the posterior probability of different F1 or F2 hybrid, or backcross, genealogical classes. We use simulations to compare the statistical performance of Mongrail with that of an existing composite likelihood method (NewHybrids) and apply the method to analyze genome sequence data for hybridizing species of barred and spotted owls.}, } @article {pmid36708074, year = {2023}, author = {Cody, TT and Kiryu, Y and Bakenhaster, MD and Subramaniam, K and Tabuchi, M and Ahasan, MS and Harris, HE and Landsberg, JH and Waltzek, TB and Fogg, AQ and Shea, C and Pouder, DB and Patterson, WF and Emory, ME and Yanong, RP}, title = {Cutaneous ulcerative lesions of unknown etiology affecting lionfish Pterois spp. in the Gulf of Mexico.}, journal = {Journal of aquatic animal health}, volume = {35}, number = {1}, pages = {20-33}, doi = {10.1002/aah.10174}, pmid = {36708074}, issn = {1548-8667}, mesh = {Animals ; Gulf of Mexico ; *Perciformes/physiology ; Fishes ; }, abstract = {OBJECTIVE: Cutaneous ulcerative skin lesions in a complex of invasive Gulf of Mexico lionfish (Red Lionfish Pterois volitans, Devil Firefish P. miles, and the hybrid Red Lionfish × Devil Firefish) became epizootic beginning in mid-August 2017. Herein, we provide the first pathological descriptions of these lesions and summarize our analyses to elucidate the etiology of the disease.

METHODS: We examined ulcerated and normal fish through gross pathology and histopathology, bacterial sampling, and unbiased metagenomic next-generation sequencing. We tracked prevalence of the disease, and we used biological health indicators (condition factor, splenosomatic and hepatosomatic index) to evaluate impacts to health, while considering sex and age as potential risk factors.

RESULT: Typical ulcerative lesions were deep, exposing skeletal muscle, and were bordered by pale or reddened areas often with some degree of scale loss. Only incidental parasites were found in our examinations. Most fish (86%; n = 50) exhibited wound healing grossly and histologically, confirmed by the presence of granulation tissues. A primary bacterial pathogen was not evident through bacterial culture or histopathology. Metagenomic next-generation sequencing did not reveal a viral pathogen (DNA or RNA) but did provide information about the microbiome of some ulcerated specimens. Compared with clinically healthy fish, ulcerated fish had a significantly lower condition factor and a higher splenosomatic index. Disease prevalence at monitored sites through July 2021 indicated that ulcerated fish were still present but at substantially lower prevalence than observed in 2017.

CONCLUSION: Although some common findings in a number of specimens suggest a potential role for opportunistic bacteria, collectively our suite of diagnostics and analyses did not reveal an intralesional infectious agent, and we must consider the possibility that there was no communicable pathogen.}, } @article {pmid36707995, year = {2023}, author = {Chang, D and Gupta, VK and Hur, B and Cunningham, KY and Sung, J}, title = {GMWI-webtool: a user-friendly browser application for assessing health through metagenomic gut microbiome profiling.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {2}, pages = {}, pmid = {36707995}, issn = {1367-4811}, support = {UL1 TR002494/TR/NCATS NIH HHS/United States ; UL1 TR002377/TR/NCATS NIH HHS/United States ; }, mesh = {*Metagenome ; *Gastrointestinal Microbiome ; Metagenomics/methods ; Feces ; }, abstract = {SUMMARY: We recently introduced the Gut Microbiome Wellness Index (GMWI), a stool metagenome-based indicator for assessing health by determining the likelihood of disease given the state of one's gut microbiome. The calculation of our wellness index depends on the relative abundances of health-prevalent and health-scarce species. Encouragingly, GMWI has already been utilized in various studies focusing on differences in the gut microbiome between cases and controls. Herein, we introduce the GMWI-webtool, a user-friendly browser application that computes GMWI, health-prevalent/-scarce species' relative abundances, and α-diversities from stool shotgun metagenome taxonomic profiles. Users of our interactive online tool can visualize their results and compare them side-by-side with those from our pooled reference dataset of metagenomes, as well as export data in.csv format and high-resolution figures.

GMWI-webtool is freely available here: https://gmwi-webtool.github.io/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36707764, year = {2023}, author = {Pantoja-Feliciano, IG and Karl, JP and Perisin, M and Doherty, LA and McClung, HL and Armstrong, NJ and Renberg, R and Racicot, K and Branck, T and Arcidiacono, S and Soares, JW}, title = {In vitro gut microbiome response to carbohydrate supplementation is acutely affected by a sudden change in diet.}, journal = {BMC microbiology}, volume = {23}, number = {1}, pages = {32}, pmid = {36707764}, issn = {1471-2180}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Diet ; Feces/microbiology ; Carbohydrates ; Starch/metabolism ; Dietary Supplements ; }, abstract = {BACKGROUND: Interactions between diet, stress and the gut microbiome are of interest as a means to modulate health and performance. Here, in vitro fermentation was used to explore the effects of a sudden change in diet, 21 days sole sustenance on the Meal, Ready-to-Eat (MRE) U.S. military combat ration, on inter-species competition and functional potential of the human gut microbiota. Human fecal samples collected before and after MRE intervention or consuming a habitual diet (HAB) were introduced to nutrient-rich media supplemented with starch for in vitro fermentation under ascending colon conditions. 16S rRNA amplicon and Whole-metagenome sequencing (WMS) were used to measure community composition and functional potential. Specific statistical analyses were implemented to detect changes in relative abundance from taxa, genes and pathways.

RESULTS: Differential changes in relative abundance of 11 taxa, Dorea, Lachnospira, Bacteroides fragilis, Akkermansia muciniphila, Bifidobacterium adolescentis, Betaproteobacteria, Enterobacteriaceae, Bacteroides egerthii, Ruminococcus bromii, Prevotella, and Slackia, and nine Carbohydrate-Active Enzymes, specifically GH13_14, over the 24 h fermentation were observed as a function of the diet intervention and correlated to specific taxa of interest.

CONCLUSIONS: These findings suggest that consuming MRE for 21 days acutely effects changes in gut microbiota structure in response to carbohydrate but may induce alterations in metabolic capacity. Additionally, these findings demonstrate the potential of starch as a candidate supplemental strategy to functionally modulate specific gut commensals during stress-induced states.}, } @article {pmid36707341, year = {2023}, author = {Tibayrenc, M}, title = {Towards a general, worldwide, Plasmodium population genomics framework.}, journal = {Trends in parasitology}, volume = {39}, number = {4}, pages = {229-230}, doi = {10.1016/j.pt.2023.01.003}, pmid = {36707341}, issn = {1471-5007}, mesh = {*Metagenomics ; *Plasmodium/genetics ; Genomics ; Genome, Protozoan/genetics ; Plasmodium vivax ; }, } @article {pmid36706527, year = {2023}, author = {Wei, X and Peng, H and Li, Y and Meng, B and Wang, S and Bi, S and Zhao, X}, title = {Pyrethroids exposure alters the community and function of the internal microbiota in Aedes albopictus.}, journal = {Ecotoxicology and environmental safety}, volume = {252}, number = {}, pages = {114579}, doi = {10.1016/j.ecoenv.2023.114579}, pmid = {36706527}, issn = {1090-2414}, mesh = {Animals ; *Insecticides/pharmacology ; Permethrin/toxicity ; *Aedes ; Mosquito Vectors ; *Pyrethrins/pharmacology ; Insecticide Resistance/genetics ; *Microbiota ; }, abstract = {Large amounts of insecticides bring selection pressure and then develop insecticide resistance in Aedes albopictus. This study demonstrated for the first time the effect of pyrethroid exposure on the internal microbiota in Ae. albopictus. 36, 48, 57 strains of virgin adult Ae. albopictus were exposed to the pyrethroids deltamethrin (Dme group), β-cypermethrin (Bcy group), and cis-permethrin (Cper group), respectively, with n-hexane exposure (Hex group) as the controls (n = 36). The internal microbiota community and functions were analyzed based on the metagenomic analysis. The analysis of similarity (ANOSIM) results showed that the Hex/Bcy (p = 0.001), Hex/Cper (p = 0.006), Hex/Dme (p = 0.001) groups were well separated, and the internal microbes of Ae. albopictus vary in the composition and functions depending on the type of pyrethroid insecticide they are applied. Four short chain fatty acid-producing genera, Butyricimonas, Prevotellaceae, Anaerococcus, Pseudorhodobacter were specifically absent in the pyrethroid-exposed mosquitoes. Morganella and Streptomyces were significantly enriched in cis-permethrin-exposed mosquitoes. Wolbachia and Chryseobacterium showed significant enrichment in β-cypermethrin-exposed mosquitoes. Pseudomonas was significantly abundant in deltamethrin-exposed mosquitoes. The significant proliferation of these bacteria may be closely related to insecticide metabolism. Our study recapitulated a specifically enhanced metabolic networks relevant to the exposure to cis-permethrin and β-cypermethrin, respectively. Benzaldehyde dehydrogenase (EC 1.2.1.28), key enzyme in aromatic compounds metabolism, was detected enhanced in cis-permethrin and β-cypermethrin exposed mosquitoes. The internal microbiota metabolism of aromatic compounds may be important influencing factors for pyrethroid resistance. Future work will be needed to elucidate the specific mechanisms by which mosquito microbiota influences host resistance and vector ability.}, } @article {pmid36705908, year = {2023}, author = {Watkins, AM and Das, R}, title = {RNA 3D Modeling with FARFAR2, Online.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2586}, number = {}, pages = {233-249}, pmid = {36705908}, issn = {1940-6029}, support = {R21 CA219847/CA/NCI NIH HHS/United States ; R35 GM122579/GM/NIGMS NIH HHS/United States ; }, mesh = {*RNA/chemistry ; Nucleic Acid Conformation ; Models, Molecular ; *RNA, Catalytic/chemistry ; Algorithms ; }, abstract = {Understanding the three-dimensional structure of an RNA molecule is often essential to understanding its function. Sampling algorithms and energy functions for RNA structure prediction are improving, due to the increasing diversity of structural data available for training statistical potentials and testing structural data, along with a steady supply of blind challenges through the RNA-Puzzles initiative. The recent FARFAR2 algorithm enables near-native structure predictions on fairly complex RNA structures, including automated selection of final candidate models and estimation of model accuracy. Here, we describe the use of a publicly available webserver for RNA modeling for realistic scenarios using FARFAR2, available at https://rosie.rosettacommons.org/farfar2 . We walk through two cases in some detail: a simple model pseudoknot from the frameshifting element of beet western yellows virus modeled using the "basic interface" to the webserver and a replication of RNA-Puzzle 20, a metagenomic twister sister ribozyme, using the "advanced interface." We also describe example runs of FARFAR2 modeling including two kinds of experimental data: a c-di-GMP riboswitch modeled with low-resolution restraints from MOHCA-seq experiments and a tandem GA motif modeled with [1]H NMR chemical shifts.}, } @article {pmid36705037, year = {2023}, author = {Chiu, CY and Chang, KC and Chang, LC and Wang, CJ and Chung, WH and Hsieh, WP and Su, SC}, title = {Phenotype-specific signatures of systems-level gut microbiome associated with childhood airway allergies.}, journal = {Pediatric allergy and immunology : official publication of the European Society of Pediatric Allergy and Immunology}, volume = {34}, number = {1}, pages = {e13905}, doi = {10.1111/pai.13905}, pmid = {36705037}, issn = {1399-3038}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Rhinitis ; *Rhinitis, Allergic ; *Asthma ; Immunoglobulin E/metabolism ; Phenotype ; }, abstract = {BACKGROUND: Perturbation of gut symbiosis has been linked to childhood allergic diseases. However, the underlying host-microbe interaction connected with specific phenotypes is poorly understood.

METHODS: To address this, integrative analyses of stool metagenomic and metabolomic profiles associated with IgE reactions in 56 children with mite-sensitized airway allergies (25 with rhinitis and 31 with asthma) and 28 nonallergic healthy controls were conducted.

RESULTS: We noted a decrease in the number and abundance of gut microbiome-encoded carbohydrate-active enzyme (CAZyme) genes, accompanied with a reduction in species richness, in the asthmatic gut microflora but not in that from allergic rhinitis. Such loss of CAZymes was consistent with the observation that a CAZyme-linked decrease in fecal butyrate was found in asthmatics and negatively correlated with mite-specific IgE responses. Different from the CAZymes, we demonstrated an increase in α diversity at the virulome levels in asthmatic gut microbiota and identified phenotype-specific variations of gut virulome. Moreover, use of fecal metagenomic and metabolomic signatures resulted in distinct effects on differentiating rhinitis and asthma from nonallergic healthy controls.

CONCLUSION: Overall, our integrative analyses reveal several signatures of systems-level gut microbiome in robust associations with fecal metabolites and disease phenotypes, which may be of etiological and diagnostic implications in childhood airway allergies.}, } @article {pmid36704910, year = {2023}, author = {Yuan, X and Zhang, Y and Lin, X and Yang, X and Chen, R}, title = {Association of gut microbiota and glucose metabolism in children with disparate degrees of adiposity.}, journal = {Pediatric obesity}, volume = {18}, number = {4}, pages = {e13009}, doi = {10.1111/ijpo.13009}, pmid = {36704910}, issn = {2047-6310}, mesh = {Male ; Female ; Humans ; Child ; *Gastrointestinal Microbiome ; Blood Glucose ; Adiposity ; *Obesity, Morbid ; Phylogeny ; Obesity/metabolism ; Bacteria ; }, abstract = {OBJECTIVE: To investigate the characteristics of gut microbiota in children with disparate degrees of adiposity, and analyze the association between gut microbiota, glucose metabolism indicators, and inflammatory factors.

METHODS: Clinical data were examined in 89 Chinese children. Children with a body fat percentage ≥ 30% were diagnosed as obese, and ≥ 35% in males and ≥ 40% in females were further defined as severe obesity. The composition of gut microbiota was determined by 16S rDNA-based metagenomics.

RESULTS: The study population (9.75 ± 1.92-year-old) was characterized as normal weight (n = 29), mild obesity (n = 27) and severe obesity (n = 33) groups. Linear discriminant analysis Effect Size (LEfSe) analysis found that compared to the severe obesity group, subjects with mild obesity had more prevalent members of the phylum Fusobacteria, the genus Alistipes, and fewer members of genus Granulicatella and Clostridium (p < 0.05). For subjects with mild obesity, Spearman's correlation analysis revealed that fasting plasma glucose positively correlated with species A. indistinctus, A. putredinis, and negatively correlated with species Ruminococcus gnavus; LBP negatively correlated with species Clostridium hathewayi, and Blautia producta. For subjects with severe obesity, oral glucose tolerance test 2 h plasma glucose (OGTT2HPG) negatively correlated with the phylum Synergistetes, genus Pyramidobacter, species Veillonella parvula, P. piscolens, and positively correlated with species B. producta, INS and HOMA-IR negatively correlated with the genus Haemophilus, species H. parainfluenzae, lipopolysaccharide-binding protein (LBP) negatively correlated with the phylum Actinobacteria, genus Bifidobacterium, Lactobacillus, and species B. longum (all p < 0.05). Phylogenetic investigation of communities by reconstruction of unobserved states 2 (PICRUSt2) analysis discerned that the glucose metabolism pathway, gluconeogenesis I was curtailed in the severe obesity group.

CONCLUSION: The gut microbiota could favourably compensate for glucose metabolism in children with obesity. Genus Haemophilus and Bifidobacterium longum may influence glucose tolerance and insulin resistance in children with severe obesity.}, } @article {pmid36704562, year = {2022}, author = {Xu, LQ and Yang, J and Liang, W and Chen, J and Sun, Z and Zhang, Q and Liu, X and Qiao, F and Li, J}, title = {LDMD: A database of microbes in human lung disease.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1085079}, pmid = {36704562}, issn = {1664-302X}, abstract = {BACKGROUND: Lungs were initially thought to be sterile. However, with the development of sequencing technologies, various commensal microorganisms, especially bacteria, have been observed in the lungs of healthy humans. Several studies have also linked lung microbes to infectious lung diseases. However, few databases have focused on the metagenomics of lungs to provide microbial compositions and corresponding metadata information. Such a database would be handy for researching and treating lung diseases.

METHODS: To provide researchers with a preliminary understanding of lung microbes and their research methods, the LDMD collated nearly 10,000 studies in the literature covering over 30 diseases, gathered basic information such as the sources of lung microbe samples, sequencing methods, and processing software, as well as analyzed the metagenomic sequencing characteristics of lung microbes. Besides, the LDMD also contained data collected in our laboratory.

RESULTS: In this study, we established the Lung Disease Microorganisms Database (LDMD), a comprehensive database of microbes involved in lung disease. The LDMD offered sequence analysis capabilities, allowing users to upload their sequencing results, align them with the data collated in the database, and visually analyze the results.

CONCLUSION: In conclusion, the LDMD possesses various functionalities that provide a convenient and comprehensive resource to study the lung metagenome and treat lung diseases.}, } @article {pmid36704137, year = {2022}, author = {Tang, X and Dai, G and Wang, T and Sun, H and Jiang, W and Chen, Z and Yan, Y}, title = {Comparison of the clinical features of human bocavirus and metapneumovirus lower respiratory tract infections in hospitalized children in Suzhou, China.}, journal = {Frontiers in pediatrics}, volume = {10}, number = {}, pages = {1074484}, pmid = {36704137}, issn = {2296-2360}, abstract = {OBJECTIVE: We compared the clinical data of hospitalized children with lower respiratory tract infections caused by human bocavirus (HBoV) and human metapneumovirus (hMPV).

METHODS: In total, 8,430 children admitted to the Department of Respiration, Children's Hospital of Soochow University for lower respiratory tract infections from January 2017 to October 2021 were enrolled. Seven common respiratory viruses, including respiratory syncytial virus, influenza virus A, influenza virus B, parainfluenza virus (PIV) I, PIV II, PIV III, and adenovirus, were detected by direct immunofluorescence assay, whereas human rhinovirus and hMPV were detected by reverse transcription-polymerase chain reaction. Mycoplasma pneumoniae (MP) and HBoV were detected by real-time fluorescence quantitative polymerase chain reaction. Bacteria was detected in blood, nasopharyngeal secretion, bronchoalveolar lavage specimen or pleural fluid by culture. In parallel, MP was detected by enzyme-linked immunosorbent assay. In addition, we performed metagenomic testing of alveolar lavage fluid from some of the patients in our study.

RESULTS: The detection rate of HBoV was 6.62% (558/8430), whereas that of hMPV was 2.24% (189/ 8430). The detection rate of HBoV was significantly higher in children aged 1 to <3 years than in other age groups, but there were no significant differences in positivity rates for hMPV by age. Before 2020, the incidence of HBoV infection peaked in summer and autumn, whereas that of hMPV peaked in spring. The epidemiology of both HBoV and hMPV has changed because of the impact of the novel coronavirus. Among the positive cases, the HBoV mixed infection rate was 51.6%, which was similar to that for hMPV mixed infection (44.4%). Comparing clinical characteristics between HBoV and hMPV single infection, the median age of children was 17 months in the HBoV group and 11 months in the hMPV group. In the HBoV single infection group, 31 patients (11.5%) had pulse oxygen saturation of less than 92% on admission, 47 (17.4%) had shortness of breath, and 26 (9.6%) presented with dyspnea. Meanwhile, four patients (3.8%) in the hMPV single infection group had pulse oxygen saturation of less than 92% on admission, eight (7.6%) displayed shortness of breath, and three (2.9%) had dyspnea. The proportion of patients requiring mechanical ventilation and the rate of PICU admission were higher in the HBoV group than in the hMPV group.

CONCLUSION: The prevalence of HBoV infection is higher than that of hMPV infection in children with lower respiratory tract infection in Suzhou, and HBoV is more likely to cause severe infection than hMPV. Public health interventions for COVID-19 outbreaks have affected the prevalence of HBoV and hMPV.}, } @article {pmid36704100, year = {2022}, author = {Wu, Z and Zhang, B and Chen, F and Xia, R and Zhu, D and Chen, B and Lin, A and Zheng, C and Hou, D and Li, X and Zhang, S and Chen, Y and Hou, K}, title = {Fecal microbiota transplantation reverses insulin resistance in type 2 diabetes: A randomized, controlled, prospective study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1089991}, pmid = {36704100}, issn = {2235-2988}, mesh = {Humans ; Fecal Microbiota Transplantation/methods ; *Diabetes Mellitus, Type 2/therapy ; *Insulin Resistance ; Prospective Studies ; Blood Glucose/metabolism ; *Metformin/therapeutic use ; Feces/microbiology ; }, abstract = {OBJECTIVES: Recent studies have shown that fecal microbiota transplantation (FMT) improved the metabolic profiles of patients with type 2 diabetes mellitus (T2DM), yet the effectiveness in reversing insulin resistance and increasing metformin sensitivity in T2DM patients have not been reported. In this study, we evaluated the improvements of T2DM patients and their gut microbiota by FMT alone and FMT plus metformin.

METHODS: A total of 31 patients with newly diagnosed T2DM were randomized to intervention by metformin, FMT, or FMT plus metformin in the study. Patients were followed up at baseline and week 4 after treatment. Blood and stool samples were collected and subject to analyze clinical parameters and microbial communities by metagenomic sequencing, respectively.

RESULTS: FMT alone and FMT plus metformin significantly improved the clinical indicators HOMA-IR and BMI in T2DM, besides fasting blood glucose, postprandial blood glucose, and hemoglobin A1c that were also controlled by metformin. Donor microbiota effectively colonized in T2DM with slightly higher colonization ration in FMT than FMT plus metformin within 4 weeks, resulting in increased microbial diversity and community changes from baseline after treatment. A total of 227 species and 441 species were significantly alerted after FMT and FMT plus metformin, respectively. FMT were significantly associated with the clinical parameters. Among them, Chlorobium phaeovibrioides, Bifidibacterium adolescentis and Synechococcus sp.WH8103 were potential due to their significantly negative correlations with HOMA-IR.

CONCLUSIONS: FMT with or without metformin significantly improve insulin resistance and body mass index and gut microbial communities of T2DM patients by colonization of donor-derived microbiota.}, } @article {pmid36703917, year = {2022}, author = {Saproo, S and Sarkar, SS and Gautam, V and Konyak, CW and Dass, G and Karmakar, A and Sharma, M and Ahuja, G and Gupta, A and Tayal, J and Mehta, A and Naidu, S}, title = {Salivary protein kinase C alpha and novel microRNAs as diagnostic and therapeutic resistance markers for oral squamous cell carcinoma in Indian cohorts.}, journal = {Frontiers in molecular biosciences}, volume = {9}, number = {}, pages = {1106963}, pmid = {36703917}, issn = {2296-889X}, abstract = {Oral squamous cell carcinoma (OSCC) is the second leading cause of cancer-related morbidity and mortality in India. Tobacco, alcohol, poor oral hygiene, and socio-economic factors remain causative for this high prevalence. Identification of non-invasive diagnostic markers tailored for Indian population can facilitate mass screening to reduce overall disease burden. Saliva offers non-invasive sampling and hosts a plethora of markers for OSCC diagnosis. Here, to capture the OSCC-specific salivary RNA markers suitable for Indian population, we performed RNA-sequencing of saliva from OSCC patients (n = 9) and normal controls (n = 5). Differential gene expression analysis detected an array of salivary RNAs including mRNAs, long non-coding RNAs, transfer-RNAs, and microRNAs specific to OSCC. Computational analysis and functional predictions identified protein kinase c alpha (PRKCA), miR-6087, miR-449b-5p, miR-3656, miR-326, miR-146b-5p, and miR-497-5p as potential salivary indicators of OSCC. Notably, higher expression of PRKCA, miR-6087 and miR-449b-5p were found to be associated with therapeutic resistance and poor survival, indicating their prognostic potential. In addition, sequencing reads that did not map to the human genome, showed alignments with microbial reference genomes. Metagenomic and statistical analysis of these microbial reads revealed a remarkable microbial dysbiosis between OSCC patients and normal controls. Moreover, the differentially abundant microbial taxa showed a significant association with tumor promoting pathways including inflammation and oxidative stress. Summarily, we provide an integrated landscape of OSCC-specific salivary RNAs relevant to Indian population which can be instrumental in devising non-invasive diagnostics for OSCC.}, } @article {pmid36703900, year = {2022}, author = {Zhang, F and Qin, S and Xia, F and Mao, C and Li, L}, title = {Case report: Streptococcus pneumoniae pneumonia characterized by diffuse centrilobular nodules in both lungs.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {1007160}, pmid = {36703900}, issn = {2296-858X}, abstract = {BACKGROUND: Streptococcus pneumoniae (S. pneumoniae) is the most common pathogen in community-acquired pneumonia (CAP) and takes the form of lobar pneumonia as typical computed tomography (CT) findings. Various patterns of radiological manifestation have also been reported in patients with S. pneumoniae pneumonia; however, the appearance of diffuse centrilobular nodules in both lungs is rarely reported.

CASE PRESENTATION: We report the case of a patient with a history of chronic lymphocytic leukemia (CLL) for 9 years who presented with new-onset fever, cough, excess sputum, and shortness of breath for 1 week. He was given intravenous antibacterial (cephalosporin) treatment for 4 days, but his condition did not improve and dyspnea became more serious. The chest CT indicated diffuse centrilobular nodules in both lungs at admission. Patient's bronchoalveolar (BAL) fluid was sent for metagenomic next-generation sequencing, which only supported a diagnosis of S. pneumoniae infection. His condition improved gradually after antimicrobial treatment (moxifloxacin) and a follow-up CT showed that the diffuse centrilobular nodules in both lungs were absorbed completely.

CONCLUSION: This case highlights a rare CT presentation of S. pneumoniae pneumonia that should alert clinicians, so as to avoid taking unnecessary treatment measures.}, } @article {pmid36702853, year = {2023}, author = {Parida, S and Siddharth, S and Xia, Y and Sharma, D}, title = {Concomitant analyses of intratumoral microbiota and genomic features reveal distinct racial differences in breast cancer.}, journal = {NPJ breast cancer}, volume = {9}, number = {1}, pages = {4}, pmid = {36702853}, issn = {2374-4677}, support = {90047965//Breast Cancer Research Foundation (BCRF)/ ; }, abstract = {Racial disparities are most accentuated among Black women as their lifetime risk of breast cancer incidence is lower than white and Asian women but their breast cancer related mortality is the highest among all races. Black women are more likely to develop triple-negative breast cancer at a younger age and harbor more aggressive tumors. In addition to tumor-centric alterations, tumor growth is also influenced by multiple other tumor microenvironment-related features, including resident immune cells and microbiota. Hence, in this study, we conduct concurrent genomic and metagenomic analyses, and uncover distinctive intratumoral microbial community compositions and tumor immune microenvironment-related traits in breast tumors from Asian, Black and white women. Interestingly, unique racially associated genomic nodes are found in the breast tumors from Asian, Black and white women. Examination of the cellular heterogeneity show differential enrichment of 11 out of 64 immune and stroma cell types in the breast tumors from different racial groups. In terms of microbial diversity, significant differences are revealed in alpha and beta-diversity measures. Intriguingly, potential race-specific microbial biomarkers of breast cancer are identified which significantly correlate with genes involved with tumor aggressiveness, angiogenesis, tumor cell migration and metastasis as well as oncogenic pathways-GLI and Notch. Investigating the metabolic features of intratumoral microbes, we find a significant differential enrichment of environmental information processing pathways, oncogenic pathways, and lipid metabolism pathways. Concomitantly investigating tumor-centric, tumor immune microenvironment-related and microbial alterations, our study provides a comprehensive understanding of racial disparities in breast cancer and warrants further exploration.}, } @article {pmid36702267, year = {2023}, author = {Zhu, Y and Pang, L and Lai, S and Xie, X and Zhang, H and Yu, J and Wu, J and Qi, H and Zhou, Q and Feng, J and Zhang, A}, title = {Deciphering risks of resistomes and pathogens in intensive laying hen production chain.}, journal = {The Science of the total environment}, volume = {869}, number = {}, pages = {161790}, doi = {10.1016/j.scitotenv.2023.161790}, pmid = {36702267}, issn = {1879-1026}, mesh = {Animals ; Female ; Humans ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Chickens/genetics ; Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; *Anti-Infective Agents ; Metagenomics ; }, abstract = {Antimicrobial resistance (AMR) and pathogens derived from food animals and their associated environments have emerged as challenging threats to humans from a health perspective, but our understanding of these risks and their key prevention and control points in the current intensive breeding industry remains poor. By creating an integral composition and risk profile of the resistome and microbiome through metagenomics in feces, flies, dust, sewage, and soil along the four-stage laying hen production chain, we found that the whole production chain is a hotspot for antimicrobial resistance genes (ARGs) with 374 known subtypes and pathogens, including 157 human pathogenic bacteria (HPB). Feces and flies were identified as major risk sources for these contaminations. Also, we confirmed a twin-risk of AMR and pathogenicity prevailing throughout the chain, but with different frequencies in each stage; thus, high-risk ARGs in the young chicken stage and highly prioritized HPB in the chick stage contributed 37.33 % to the total AMR risk and 36.36 % to the pathogenic risks, respectively, thus rendering the two stages to be the key prevention points. Moreover, the prevalence of 112 binned ARG supercarriers (for example, Klebsiella pneumoniae harboring 20 ARGs) was unraveled along the production chain, especially in feces, flies, and dust, and 87 potential hosts exhibited high pathogenic risk, high-risk AMR, or both, with 262 ARGs and 816 virulence factor genes. Overall, this study provides first-hand comprehensive data on high-risk ARGs and their pathogenic hosts in the intensive laying hen production chain, and thus is fundamentally important for developing new measures to help control the global AMR crisis induced through the animal-environment-human pathway.}, } @article {pmid36702020, year = {2023}, author = {Jang, Y and Lee, SH and Kim, NK and Ahn, CH and Rittmann, BE and Park, HD}, title = {Biofilm characteristics for providing resilient denitrification in a hydrogen-based membrane biofilm reactor.}, journal = {Water research}, volume = {231}, number = {}, pages = {119654}, doi = {10.1016/j.watres.2023.119654}, pmid = {36702020}, issn = {1879-2448}, mesh = {*Denitrification ; *Hydrogen ; Bioreactors ; Nitrates/metabolism ; Biofilms ; Nitrogen ; }, abstract = {In a hydrogen-based membrane biofilm reactor (H2-MBfR), the biofilm thickness is considered to be one of the most important factors for denitrification. Thick biofilms in MBfRs are known for low removal fluxes owing to their resistance to substrate transport. In this study, the H2-MBfR was operated under various loading rates of oxyanions, such as NO3-N, SO4-S, and ClO4[-] at an H2 flux of 1.06 e[-] eq/m[2]-d. The experiment was initiated with NO3-N, SO4-S, and ClO4[-] loadings of 0.464, 0.026, and 0.211 e[-] eq/m[2]-d, respectively, at 20 °C. Under the most stressful conditions, the loading rates increased simultaneously to 1.911, 0.869, and 0.108 e[-] eq/m[2]-d, respectively, at 10 °C. We observed improved performance in significantly thicker biofilms (approximately 2.7 cm) compared to previous studies using a denitrifying H2-MBfR for 120 days. Shock oxyanion loadings led to a decrease in total nitrogen (TN) removal by 20 to 30%, but TN removal returned to 100% within a few days. Similarly, complete denitrification was observed, even at 10 °C. The protective function and microbial diversity of the thick biofilm may allow stable denitrification despite stress-imposing conditions. In the microbial community analysis, heterotrophs were dominant and acetogens accounted for 11% of the biofilm. Metagenomic results showed a high abundance of functional genes involved in organic carbon metabolism and homoacetogenesis. Owing to the presence of organic compounds produced by acetogens and autotrophs, heterotrophic denitrification may occur simultaneously with autotrophic denitrification. As a result, the total removal flux of oxyanions (1.84 e[-] eq/m[2]-d) far exceeded the H2 flux (1.06 e[-] eq/m[2]-d). Thus, the large accumulation of biofilms could contribute to good resilience and enhanced removal fluxes.}, } @article {pmid36701053, year = {2023}, author = {Li, Y and He, C and Dong, F and Yuan, S and Hu, Z and Wang, W}, title = {Performance of anaerobic digestion of phenol using exogenous hydrogen and granular activated carbon and analysis of microbial community.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {15}, pages = {45077-45087}, pmid = {36701053}, issn = {1614-7499}, support = {2019YFC0408502//the Project of National Key Research and development Program of China/ ; 51878232//National Science Foundation of China/ ; PA2021KCPY0029//the Fundamental Research Funds for the Central Universities of China/ ; DHSZ202203//Anhui Province Key Laboratory of Industrial Wastewater and Environmental Treatment/ ; }, mesh = {*Phenol ; Anaerobiosis ; Charcoal ; Hydrogen ; Phenols ; *Microbiota ; Methane/metabolism ; Bioreactors ; }, abstract = {Anaerobic conversion rate of phenol to methane was low due to its biological toxicity. In this study, the coupling of granular activated carbon (GAC) and exogenous hydrogen (EH) could enhance greatly methane production of phenol anaerobic digestion, and the metagenomic was firstly used to analyze its potential mechanism. The results indicated that a mass of syntrophic acetate-oxidizing bacteria and hydrogen-utilizing methanogens were enriched on the GAC surface, and SAO-HM pathway has become the dominant pathway. The energy transfer analysis implied that the abundance of adenosine triphosphate (ATP) and nicotinamide adenine dinucleotide (NADH) oxidase increased. Furthermore, direct interspecies electron transfer (DIET) was formed by promoting type IV e-pili between Methanobacterium and Syntrophus, thereby improving the interspecies electron transfer efficiency. The dominant SAO-HM pathway was induced and DIET was formed, which was the internal mechanism of the coupling of GAC and EH to enhance anaerobic biotransformation of phenol.}, } @article {pmid36700636, year = {2023}, author = {Carlson, H and Graham, ED and Heidelberg, JF and Webb, EA}, title = {Metagenome-Assembled Genome HetDA_MAG_MH13 of the Family Devosiaceae, from a Marine N2-fixing Cyanobacterial Enrichment Culture.}, journal = {Microbiology resource announcements}, volume = {12}, number = {2}, pages = {e0045222}, pmid = {36700636}, issn = {2576-098X}, abstract = {Here, we present a draft genome in the order Rhizobiales and family Devosiaceae. This draft genome comes from an enrichment of a heterocystous, cyanobacterial diazotroph (HetDA) that was originally living in association with Trichodesmium species. This Rhizobiales organism is proposed to be an anoxygenic phototroph capable of dissimilatory nitrate reduction to ammonia (DNRA).}, } @article {pmid36699736, year = {2023}, author = {Shen, WX and Chen, YZ}, title = {Toward ordered -omics data science: Researchers on the magic of turning metagenomic chaos into image-like patterns.}, journal = {Patterns (New York, N.Y.)}, volume = {4}, number = {1}, pages = {100673}, pmid = {36699736}, issn = {2666-3899}, abstract = {Wan Xiang Shen, a postdoctoral researcher at National University of Singapore, and Yu Zong Chen, the PI of the Bioinformatics and Drug Design (BIDD) group, have developed an AI pipeline for enhanced deep learning of metagenomic data. Their Patterns paper highlights the advantages of unsupervised data restructuring in microbiome-based disease prediction and biomarker discovery. They talk about their view of data science and the backstory of the article published in Patterns.}, } @article {pmid36699735, year = {2023}, author = {Shen, WX and Liang, SR and Jiang, YY and Chen, YZ}, title = {Enhanced metagenomic deep learning for disease prediction and consistent signature recognition by restructured microbiome 2D representations.}, journal = {Patterns (New York, N.Y.)}, volume = {4}, number = {1}, pages = {100658}, pmid = {36699735}, issn = {2666-3899}, abstract = {Metagenomic analysis has been explored for disease diagnosis and biomarker discovery. Low sample sizes, high dimensionality, and sparsity of metagenomic data challenge metagenomic investigations. Here, an unsupervised microbial embedding, grouping, and mapping algorithm (MEGMA) was developed to transform metagenomic data into individualized multichannel microbiome 2D representation by manifold learning and clustering of microbial profiles (e.g., composition, abundance, hierarchy, and taxonomy). These 2D representations enable enhanced disease prediction by established ConvNet-based AggMapNet models, outperforming the commonly used machine learning and deep learning models in metagenomic benchmark datasets. These 2D representations combined with AggMapNet explainable module robustly identified more reliable and replicable disease-prediction microbes (biomarkers). Employing the MEGMA-AggMapNet pipeline for biomarker identification from 5 disease datasets, 84% of the identified biomarkers have been described in over 74 distinct works as important for these diseases. Moreover, the method also discovered highly consistent sets of biomarkers in cross-cohort colorectal cancer (CRC) patients and microbial shifts in different CRC stages.}, } @article {pmid36699718, year = {2022}, author = {Zhou, L and Guan, Z and Chen, C and Zhu, Q and Qiu, S and Liu, Y and Li, M and Zeng, W and Wang, H and Gao, Y and Yuan, Y and Zhang, H and Ruan, G and Pan, X}, title = {The successful treatment of Enterocytozoon bieneusi Microsporidiosis with nitazoxanide in a patient with B-ALL: A Case Report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1072463}, pmid = {36699718}, issn = {2235-2988}, mesh = {Male ; Humans ; Middle Aged ; *Enterocytozoon/genetics ; Positron Emission Tomography Computed Tomography ; *Microsporidiosis/drug therapy ; *Neoplasms ; Diarrhea ; Feces/microbiology ; }, abstract = {INTRODUCTION: Enterocytozoon bieneusi (E. bieneusi) Microsporidia can cause opportunistic infections in immunocompromised patients and is also an emerging disease in these individuals. Its clinical manifestations are chronic diarrhea and severe wasting syndrome, these can be extremely debilitating and carry a significant risk of death for immunocompromised patients. Often, microsporidia cannot be confirmed immediately by routine examination and culture. Effective and available treatment options are limited for infections caused by E. bieneusi in humans. Such cases are very rare in Chinese Mainland.

CASE PRESENTATION: A 47-year-old male had recurrent, profuse watery diarrhea and abdominal discomfort for more than 7 months, with a fever for 5 days. Two years earlier, he received treatment with a modified BFM-90 protocol for acute B cell lymphoblastic leukemia and is currently in the final stages of maintenance therapy with oral methotrexate and mercaptopurine. The leukemia was assessed as still in remission two months ago. PET/CT showed massive peritoneal fluid accumulation and a high uptake area in the diffused peritoneum (SUVmax 12.57), suggesting tumor invasion or microbial infections. However, broad-spectrum antibacterial therapies were ineffective. Metagenomic sequencing of plasma and peritoneal fluid showed no suggestion of the existence of a tumor but instead showed a high sequence number of DNA and RNA of the Microsporidia. His albendazole treatment failed and subsequent treatment with nitazoxanide successfully resolved the infection.

CONCLUSION: This case shows that we should consider the possibility of atypical pathogen infection in patients with hematologic malignancy who repeatedly develop unexplained diarrhea with wasting. mNGS can help rule out malignant neoplasms and diagnose infections. Our results suggest that nitazoxanide effectively treats E. bieneusi microsporidia infections.}, } @article {pmid36699594, year = {2022}, author = {Vigneron, A and Cruaud, P and Guyoneaud, R and Goñi-Urriza, M}, title = {Into the darkness of the microbial dark matter in situ activities through expression profiles of Patescibacteria populations.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1073483}, pmid = {36699594}, issn = {1664-302X}, abstract = {Patescibacteria form a highly diverse and widespread superphylum of uncultured microorganisms representing a third of the global microbial diversity. Most of our knowledge on Patescibacteria putative physiology relies on metagenomic mining and metagenome-assembled genomes, but the in situ activities and the ecophysiology of these microorganisms have been rarely explored, leaving the role of Patescibacteria in ecosystems elusive. Using a genome-centric metatranscriptomic approach, we analyzed the diel and seasonal gene transcription profiles of 18 Patescibacteria populations in brackish microbial mats to test whether our understanding of Patescibacteria metabolism allows the extrapolation of their in situ activities. Although our results revealed a circadian cycle in Patescibacteria activities, a strong streamlined genetic expression characterized the Patescibacteria populations. This result has a major consequence for the extrapolation of their physiology and environmental function since most transcribed genes were uncharacterized, indicating that the ecophysiology of Patescibacteria cannot be yet reliably predicted from genomic data.}, } @article {pmid36699587, year = {2022}, author = {Jiang, F and Li, Q and Wang, S and Shen, T and Wang, H and Wang, A and Xu, D and Yuan, L and Lei, L and Chen, R and Yang, B and Deng, Y and Fan, W}, title = {Recovery of metagenome-assembled microbial genomes from a full-scale biogas plant of food waste by pacific biosciences high-fidelity sequencing.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1095497}, pmid = {36699587}, issn = {1664-302X}, abstract = {BACKGROUND: Anaerobic digestion (AD) is important in treating of food waste, and thousands of metagenome-assembled genomes (MAGs) have been constructed for the microbiome in AD. However, due to the limitations of the short-read sequencing and assembly technologies, most of these MAGs are grouped from hundreds of short contigs by binning algorithms, and the errors are easily introduced.

RESULTS: In this study, we constructed a total of 60 non-redundant microbial genomes from 64.5 Gb of PacBio high-fidelity (HiFi) long reads, generated from the digestate samples of a full-scale biogas plant fed with food waste. Of the 60 microbial genomes, all genomes have at least one copy of rRNA operons (16S, 23S, and 5S rRNA), 54 have ≥18 types of standard tRNA genes, and 39 are circular complete genomes. In comparison with the published short-read derived MAGs for AD, we found 23 genomes with average nucleotide identity less than 95% to any known MAGs. Besides, our HiFi-derived genomes have much higher average contig N50 size, slightly higher average genome size and lower contamination. GTDB-Tk classification of these genomes revealed two genomes belonging to novel genus and four genomes belonging to novel species, since their 16S rRNA genes have identities lower than 95 and 97% to any known 16S rRNA genes, respectively. Microbial community analysis based on the these assembled genomes reveals the most predominant phylum was Thermotogae (70.5%), followed by Euryarchaeota (6.1%), and Bacteroidetes (4.7%), and the most predominant bacterial and archaeal genera were Defluviitoga (69.1%) and Methanothrix (5.4%), respectively. Analysis of the full-length 16S rRNA genes identified from the HiFi reads gave similar microbial compositions to that derived from the 60 assembled genomes.

CONCLUSION: High-fidelity sequencing not only generated microbial genomes with obviously improved quality but also recovered a substantial portion of novel genomes missed in previous short-read based studies, and the novel genomes will deepen our understanding of the microbial composition in AD of food waste.}, } @article {pmid36699586, year = {2022}, author = {Liu, G and Xu, N and Feng, J}, title = {Metagenomic analysis of gut microbiota and antibiotic-resistant genes in Anser erythropus wintering at Shengjin and Caizi Lakes in China.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1081468}, pmid = {36699586}, issn = {1664-302X}, abstract = {Migratory birds are the primary source and reservoir of antibiotic-resistant genes (ARGs) related to their gut microbes. In this study, we performed metagenomics analysis to study the gut microbial communities and ARGs of Anser erythropus wintering at Shengjin (SJ) and Caizi (CZ) Lakes. The results showed that bacteria, fungi, viruses, and archaea were the dominant gut microbes. Principal component analysis (PCA) indicated that the microbiota compositions significantly differed between the two populations. Diet may be the most crucial driver of the gut microbial communities for A. erythropus. This species fed exclusively on Poaceae spp. at Shengjin Lake and primarily on Carex spp. at Caizi Lake. Tetracycline, macrolide, fluoroquinolone, phenicol, and peptide antibiotics were the dominant resistant types. ARGs had a significantly higher abundance of operational taxonomic units (OTUs) in the Shengjin Lake samples than in Caizi Lake samples. PCA indicated that most Shengjin Lake samples significantly differed in gut microbiota composition from those obtained at Caizi Lake. This difference in gut microbiota composition between the two lakes' samples is attributed to more extensive aquaculture operations and poultry farms surrounding Shengjin Lake than Caizi Lake. ARGs-microbes associations indicated that 24 bacterial species, commonly used as indicators of antibiotic resistance in surveillance efforts, were abundant in wintering A. erythropus. The results revealed the composition and structural characteristics of the gut microbiota and ARGs of A. erythropus, pointing to their high sensitivities to diet habits at both lakes. This study also provides primary data for risk prevention and control of potential harmful pathogens that could endanger public health and therefore are of major significance to epidemiological and public health.}, } @article {pmid36699393, year = {2022}, author = {Lemane, T and Medvedev, P and Chikhi, R and Peterlongo, P}, title = {kmtricks: efficient and flexible construction of Bloom filters for large sequencing data collections.}, journal = {Bioinformatics advances}, volume = {2}, number = {1}, pages = {vbac029}, pmid = {36699393}, issn = {2635-0041}, abstract = {SUMMARY: When indexing large collections of short-read sequencing data, a common operation that has now been implemented in several tools (Sequence Bloom Trees and variants, BIGSI) is to construct a collection of Bloom filters, one per sample. Each Bloom filter is used to represent a set of k-mers which approximates the desired set of all the non-erroneous k-mers present in the sample. However, this approximation is imperfect, especially in the case of metagenomics data. Erroneous but abundant k-mers are wrongly included, and non-erroneous but low-abundant ones are wrongly discarded. We propose kmtricks, a novel approach for generating Bloom filters from terabase-sized collections of sequencing data. Our main contributions are (i) an efficient method for jointly counting k-mers across multiple samples, including a streamlined Bloom filter construction by directly counting, partitioning and sorting hashes instead of k-mers, which is approximately four times faster than state-of-the-art tools; (ii) a novel technique that takes advantage of joint counting to preserve low-abundant k-mers present in several samples, improving the recovery of non-erroneous k-mers. Our experiments highlight that this technique preserves around 8× more k-mers than the usual yet crude filtering of low-abundance k-mers in a large metagenomics dataset.

https://github.com/tlemane/kmtricks.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.}, } @article {pmid36699263, year = {2023}, author = {Bolt Botnen, A and Bjørnsen, MB and Alberdi, A and Gilbert, MTP and Aizpurua, O}, title = {A simplified protocol for DNA extraction from FTA cards for faecal microbiome studies.}, journal = {Heliyon}, volume = {9}, number = {1}, pages = {e12861}, pmid = {36699263}, issn = {2405-8440}, abstract = {As metagenomic studies continue to increase in size and complexity, they are often required to incorporate data from geographically isolated locations or longitudinal time samples. This represents a technical challenge, given that many of the commonly used methods used for sample collection, storage, and DNA extraction are sensitive to differences related to the time, storage and chemistry involved. FTA cards have been previously proposed as a simple, reliable and cost-efficient method for the preservation of animal faecal microbiomes. In this study, we report a simplified extraction methodology for recovering microbiome DNA from faeces stored on FTA cards and compare its performance to a common alternative means of characterising such microbiomes; namely, immediate freezing of the faeces followed by DNA extraction using the Qiagen PowerSoil DNA isolation kit. Our results show that overall the application of our simplified DNA extraction methodology yields microbial community results that have higher diversity and an expanded core microbiome than that found using the PowerSoil methodology. This suggests that the FTA card extraction method presented here is a viable alternative for metagenomic studies using faecal material when traditional freeze-based storage methods are not feasible.}, } @article {pmid36698889, year = {2022}, author = {Zhao, Y and Lian, B and Liu, X and Wang, Q and Zhang, D and Sheng, Q and Cao, L}, title = {Corrigendum: Case report: Cryptogenic giant brain abscess caused by Providencia rettgeri mimicking stroke and tumor in a patient with impaired immunity.}, journal = {Frontiers in neurology}, volume = {13}, number = {}, pages = {1113749}, doi = {10.3389/fneur.2022.1113749}, pmid = {36698889}, issn = {1664-2295}, abstract = {[This corrects the article DOI: 10.3389/fneur.2022.1007435.].}, } @article {pmid36698849, year = {2023}, author = {Peter, VG and Morandi, SC and Herzog, EL and Zinkernagel, MS and Zysset-Burri, DC}, title = {Investigating the Ocular Surface Microbiome: What Can It Tell Us?.}, journal = {Clinical ophthalmology (Auckland, N.Z.)}, volume = {17}, number = {}, pages = {259-271}, pmid = {36698849}, issn = {1177-5467}, abstract = {While pathogens of the eye have been studied for a very long time, the existence of resident microbes on the surface of healthy eyes has gained interest only recently. It appears that commensal microbes are a normal feature of the healthy eye, whose role and properties are currently the subject of extensive research. This review provides an overview of studies that have used 16s rRNA gene sequencing and whole metagenome shotgun sequencing to characterize microbial communities associated with the healthy ocular surface from kingdom to genus level. Bacteria are the primary colonizers of the healthy ocular surface, with three predominant phyla: Proteobacteria, Actinobacteria, and Firmicutes, regardless of the host, environment, and method used. Refining the microbial classification to the genus level reveals a highly variable distribution from one individual and study to another. Factors accounting for this variability are intriguing - it is currently unknown to what extent this is attributable to the individuals and their environment and how much is artifactual. Clearly, it is technically challenging to accurately describe the microorganisms of the ocular surface because their abundance is relatively low, thus, permitting substantial contaminations. More research is needed, including better experimental standards to prevent biases, and the exploration of the ocular surface microbiome's role in a spectrum of healthy to pathological states. Outcomes from such research include the opportunity for therapeutic interventions targeting the microbiome.}, } @article {pmid36698799, year = {2022}, author = {Shumyatsky, G and Burrell, A and Chaney, H and Sami, I and Koumbourlis, AC and Freishtat, RJ and Crandall, KA and Zemanick, ET and Hahn, A}, title = {Using metabolic potential within the airway microbiome as predictors of clinical state in persons with cystic fibrosis.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {1082125}, pmid = {36698799}, issn = {2296-858X}, abstract = {INTRODUCTION: Pulmonary exacerbations (PEx) in persons with cystic fibrosis (CF) are primarily related to acute or chronic inflammation associated with bacterial lung infections, which may be caused by several bacteria that activate similar bacterial genes and produce similar by-products. The goal of our study was to perform a stratified functional analysis of bacterial genes at three distinct time points in the treatment of a PEx in order to determine the role that specific airway microbiome community members may play within each clinical state (i.e., PEx, end of antibiotic treatment, and follow-up). Our secondary goal was to compare the change between clinical states with the metabolic activity of specific airway microbiome community members.

METHODS: This was a prospective observational study of persons with CF treated with intravenous antibiotics for PEx between 2016 and 2020 at Children's National Hospital. Demographic and clinical information as well as respiratory samples were collected at hospital admission for PEx, end of antibiotic treatment, and follow-up. Metagenomic sequencing was performed; MetaPhlAn3 and HUMANn3 were used to assign sequences to bacterial species and bacterial metabolic genes, respectively.

RESULTS: Twenty-two persons with CF, with a mean age of 14.5 (range 7-23) years, experienced 45 PEx during the study period. Two-hundred twenty-one bacterial species were identified in the respiratory samples from the study cohort. Ten bacterial species had differential gene abundance across changes in the clinical state including Staphylococcus aureus, Streptococcus salivarius, and Veillonella atypica (all padj < 0.01 and log2FoldChange > |2|). These corresponded to a differential abundance of bacterial genes, with S. aureus accounting for 81% of the genes more abundant in PEx and S. salivarius accounting for 83% of the genes more abundant in follow-up, all compared to the end of treatment. Lastly, 8,653 metabolic pathways were identified across samples, with again S. aureus and S. salivarius contributing to the differential abundance of pathways (106 in PEx vs. 66 in follow-up, respectively). V. atypica was associated with a single metabolic pathway (UDP-N-acetyl-D-glucosamine biosynthesis) increased in follow-up compared to PEx.

DISCUSSION: Taken together, these data suggest that the metabolic potential of bacterial species can provide more insight into changes across clinical states than the relative abundance of the bacteria alone.}, } @article {pmid36698172, year = {2023}, author = {Kavagutti, VS and Bulzu, PA and Chiriac, CM and Salcher, MM and Mukherjee, I and Shabarova, T and Grujčić, V and Mehrshad, M and Kasalický, V and Andrei, AS and Jezberová, J and Seďa, J and Rychtecký, P and Znachor, P and Šimek, K and Ghai, R}, title = {High-resolution metagenomic reconstruction of the freshwater spring bloom.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {15}, pmid = {36698172}, issn = {2049-2618}, mesh = {*Metagenome ; Fresh Water ; Bacteria ; Plankton ; *Viruses/genetics ; Eukaryota/genetics ; Water ; }, abstract = {BACKGROUND: The phytoplankton spring bloom in freshwater habitats is a complex, recurring, and dynamic ecological spectacle that unfolds at multiple biological scales. Although enormous taxonomic shifts in microbial assemblages during and after the bloom have been reported, genomic information on the microbial community of the spring bloom remains scarce.

RESULTS: We performed a high-resolution spatio-temporal sampling of the spring bloom in a freshwater reservoir and describe a multitude of previously unknown taxa using metagenome-assembled genomes of eukaryotes, prokaryotes, and viruses in combination with a broad array of methodologies. The recovered genomes reveal multiple distributional dynamics for several bacterial groups with progressively increasing stratification. Analyses of abundances of metagenome-assembled genomes in concert with CARD-FISH revealed remarkably similar in situ doubling time estimates for dominant genome-streamlined microbial lineages. Discordance between quantitations of cryptophytes arising from sequence data and microscopic identification suggested the presence of hidden, yet extremely abundant aplastidic cryptophytes that were confirmed by CARD-FISH analyses. Aplastidic cryptophytes are prevalent throughout the water column but have never been considered in prior models of plankton dynamics. We also recovered the first metagenomic-assembled genomes of freshwater protists (a diatom and a haptophyte) along with thousands of giant viral genomic contigs, some of which appeared similar to viruses infecting haptophytes but owing to lack of known representatives, most remained without any indication of their hosts. The contrasting distribution of giant viruses that are present in the entire water column to that of parasitic perkinsids residing largely in deeper waters allows us to propose giant viruses as the biological agents of top-down control and bloom collapse, likely in combination with bottom-up factors like a nutrient limitation.

CONCLUSION: We reconstructed thousands of genomes of microbes and viruses from a freshwater spring bloom and show that such large-scale genome recovery allows tracking of planktonic succession in great detail. However, integration of metagenomic information with other methodologies (e.g., microscopy, CARD-FISH) remains critical to reveal diverse phenomena (e.g., distributional patterns, in situ doubling times) and novel participants (e.g., aplastidic cryptophytes) and to further refine existing ecological models (e.g., factors affecting bloom collapse). This work provides a genomic foundation for future approaches towards a fine-scale characterization of the organisms in relation to the rapidly changing environment during the course of the freshwater spring bloom. Video Abstract.}, } @article {pmid36697964, year = {2023}, author = {Sereika, M and Petriglieri, F and Jensen, TBN and Sannikov, A and Hoppe, M and Nielsen, PH and Marshall, IPG and Schramm, A and Albertsen, M}, title = {Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria.}, journal = {The ISME journal}, volume = {17}, number = {4}, pages = {561-569}, pmid = {36697964}, issn = {1751-7370}, mesh = {RNA, Ribosomal, 16S/genetics/metabolism ; *Geologic Sediments/microbiology ; Electron Transport ; *Bacteria/genetics/metabolism ; Phylogeny ; Fresh Water/microbiology ; }, abstract = {Cable bacteria of the Desulfobulbaceae family are centimeter-long filamentous bacteria, which are capable of conducting long-distance electron transfer. Currently, all cable bacteria are classified into two candidate genera: Candidatus Electronema, typically found in freshwater environments, and Candidatus Electrothrix, typically found in saltwater environments. This taxonomic framework is based on both 16S rRNA gene sequences and metagenome-assembled genome (MAG) phylogenies. However, most of the currently available MAGs are highly fragmented, incomplete, and thus likely miss key genes essential for deciphering the physiology of cable bacteria. Also, a closed, circular genome of cable bacteria has not been published yet. To address this, we performed Nanopore long-read and Illumina short-read shotgun sequencing of selected environmental samples and a single-strain enrichment of Ca. Electronema aureum. We recovered multiple cable bacteria MAGs, including two circular and one single-contig. Phylogenomic analysis, also confirmed by 16S rRNA gene-based phylogeny, classified one circular MAG and the single-contig MAG as novel species of cable bacteria, which we propose to name Ca. Electronema halotolerans and Ca. Electrothrix laxa, respectively. The Ca. Electronema halotolerans, despite belonging to the previously recognized freshwater genus of cable bacteria, was retrieved from brackish-water sediment. Metabolic predictions showed several adaptations to a high salinity environment, similar to the "saltwater" Ca. Electrothrix species, indicating how Ca. Electronema halotolerans may be the evolutionary link between marine and freshwater cable bacteria lineages.}, } @article {pmid36695828, year = {2023}, author = {Hilderbrand, RH and Bambakidis, T and Crump, BC}, title = {The Roles of Microbes in Stream Restorations.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {853-861}, pmid = {36695828}, issn = {1432-184X}, mesh = {Animals ; *Ecosystem ; Rivers ; Fishes ; Biomass ; *Microbiota ; Biofilms ; }, abstract = {The goods and services provided by riverine systems are critical to humanity, and our reliance increases with our growing population and demands. As our activities expand, these systems continue to degrade throughout the world even as we try to restore them, and many efforts have not met expectations. One way to increase restoration effectiveness could be to explicitly design restorations to promote microbial communities, which are responsible for much of the organic matter breakdown, nutrient removal or transformation, pollutant removal, and biomass production in river ecosystems. In this paper, we discuss several design concepts that purposefully create conditions for these various microbial goods and services, and allow microbes to act as ecological restoration engineers. Focusing on microbial diversity and function could improve restoration effectiveness and overall ecosystem resilience to the stressors that caused the need for the restoration. Advances in next-generation sequencing now allow the use of microbial 'omics techniques (e.g., metagenomics, metatranscriptomics) to assess stream ecological conditions in similar fashion to fish and benthic macroinvertebrates. Using representative microbial communities from stream sediments, biofilms, and the water column may greatly advance assessment capabilities. Microbes can assess restorations and ecosystem function where animals may not currently be present, and thus may serve as diagnostics for the suitability of animal reintroductions. Emerging applications such as ecological metatranscriptomics may further advance our understanding of the roles of specific restoration designs towards ecological services as well as assess restoration effectiveness.}, } @article {pmid36695592, year = {2023}, author = {Giacomini, JJ and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Site Specialization of Human Oral Veillonella Species.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0404222}, pmid = {36695592}, issn = {2165-0497}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; *Veillonella/genetics ; Mouth/microbiology ; Tongue/microbiology ; Palatine Tonsil ; *Microbiota ; }, abstract = {Veillonella species are abundant members of the human oral microbiome with multiple interspecies commensal relationships. Examining the distribution patterns of Veillonella species across the oral cavity is fundamental to understanding their oral ecology. In this study, we used a combination of pangenomic analysis and oral metagenomic information to clarify Veillonella taxonomy and to test the site specialist hypothesis for the Veillonella genus, which contends that most oral bacterial species are adapted to live at specific oral sites. Using isolate genome sequences combined with shotgun metagenomic sequence data, we showed that Veillonella species have clear, differential site specificity: Veillonella parvula showed strong preference for supra- and subgingival plaque, while closely related V. dispar, as well as more distantly related V. atypica, preferred the tongue dorsum, tonsils, throat, and hard palate. In addition, the provisionally named Veillonella sp. Human Microbial Taxon 780 showed strong site specificity for keratinized gingiva. Using comparative genomic analysis, we identified genes associated with thiamine biosynthesis and the reductive pentose phosphate cycle that may enable Veillonella species to occupy their respective habitats. IMPORTANCE Understanding the microbial ecology of the mouth is fundamental for understanding human physiology. In this study, metapangenomics demonstrated that different Veillonella species have clear ecological preferences in the oral cavity of healthy humans, validating the site specialist hypothesis. Furthermore, the gene pool of different Veillonella species was found to be reflective of their ecology, illuminating the potential role of vitamins and carbohydrates in determining Veillonella distribution patterns and interspecies interactions.}, } @article {pmid36695006, year = {2023}, author = {Pirillo, V and Orlando, M and Battaglia, C and Pollegioni, L and Molla, G}, title = {Efficient polyethylene terephthalate degradation at moderate temperature: a protein engineering study of LC-cutinase highlights the key role of residue 243.}, journal = {The FEBS journal}, volume = {290}, number = {12}, pages = {3185-3202}, doi = {10.1111/febs.16736}, pmid = {36695006}, issn = {1742-4658}, mesh = {*Polyethylene Terephthalates/metabolism ; Temperature ; *Carboxylic Ester Hydrolases/metabolism ; Protein Engineering ; Hydrolases/chemistry ; }, abstract = {Enzymatic degradation of poly(ethylene terephthalate) (PET) is becoming a reality because of the identification of novel PET-hydrolysing enzymes (PHEs) and the engineering of evolved enzyme variants. Here, improved variants of leaf-branch compost cutinase (LCC), a thermostable enzyme isolated by a metagenomic approach, were generated by a semi-rational protein engineering approach. Starting from a deleted LCC form lacking the secretion signal (ΔLCC), single and double variants possessing a higher activity on PET were isolated. The single-point F243T ΔLCC variant partially (~ 67%) depolymerized amorphous PET film producing ~ 21.9 mm of products after 27 h of reaction at 72 °C. The S101N/F243T ΔLCC double variant reached a further increase in activity on PET. Notably, for both single and double variants the highest conversion yield was obtained at 55 °C. Kinetics studies and molecular dynamics simulations support that a slight decreased affinity for PET is responsible for the superior degradation performance of the S101N/F243T variant and that this stems from a slightly higher flexibility of the active site region close to position 243. Furthermore, our findings question the need for a high reaction temperature for PET degradation, at least for LCC: at ≥ 70 °C, the conversion of amorphous PET into a more crystalline polymer, resistant to enzymatic hydrolysis, is favoured. The evolved S101N/F243T ΔLCC variant is able to depolymerize fully 1.3 g of untreated postconsumer PET waste in ≤ 3 days at 55 °C (using 1.25 mg of enzyme only), this making PET enzymatic degradation by engineering LCC a more ecofriendly and sustainable process.}, } @article {pmid36694900, year = {2022}, author = {Naumova, NB and Kabilov, MR}, title = {About the Biodiversity of the Air Microbiome.}, journal = {Acta naturae}, volume = {14}, number = {4}, pages = {50-56}, pmid = {36694900}, issn = {2075-8251}, abstract = {This brief review focuses on the properties of bioaerosols, presenting some recent results of metagenomic studies of the air microbiome performed using next-generation sequencing. The taxonomic composition and structure of the bioaerosol microbiome may display diurnal and seasonal dynamics and be dependent on meteorological events such as dust storms, showers, fogs, etc., as well as air pollution. The Proteobacteria and Ascomycota members are common dominants in bioaerosols in different troposphere layers. The microbiological composition of the lower troposphere air affects the composition and diversity of the indoor bioaerosol microbiome, and information about the latter is very important, especially during exacerbated epidemiological situations. Few studies focusing on the bioaerosol microbiome of the air above Russia urge intensification of such research.}, } @article {pmid36694818, year = {2023}, author = {Olo Ndela, E and Roux, S and Henke, C and Sczyrba, A and Sime Ngando, T and Varsani, A and Enault, F}, title = {Reekeekee- and roodoodooviruses, two different Microviridae clades constituted by the smallest DNA phages.}, journal = {Virus evolution}, volume = {9}, number = {1}, pages = {veac123}, pmid = {36694818}, issn = {2057-1577}, abstract = {Small circular single-stranded DNA viruses of the Microviridae family are both prevalent and diverse in all ecosystems. They usually harbor a genome between 4.3 and 6.3 kb, with a microvirus recently isolated from a marine Alphaproteobacteria being the smallest known genome of a DNA phage (4.248 kb). A subfamily, Amoyvirinae, has been proposed to classify this virus and other related small Alphaproteobacteria-infecting phages. Here, we report the discovery, in meta-omics data sets from various aquatic ecosystems, of sixteen complete microvirus genomes significantly smaller (2.991-3.692 kb) than known ones. Phylogenetic analysis reveals that these sixteen genomes represent two related, yet distinct and diverse, novel groups of microviruses-amoyviruses being their closest known relatives. We propose that these small microviruses are members of two tentatively named subfamilies Reekeekeevirinae and Roodoodoovirinae. As known microvirus genomes encode many overlapping and overprinted genes that are not identified by gene prediction software, we developed a new methodology to identify all genes based on protein conservation, amino acid composition, and selection pressure estimations. Surprisingly, only four to five genes could be identified per genome, with the number of overprinted genes lower than that in phiX174. These small genomes thus tend to have both a lower number of genes and a shorter length for each gene, leaving no place for variable gene regions that could harbor overprinted genes. Even more surprisingly, these two Microviridae groups had specific and different gene content, and major differences in their conserved protein sequences, highlighting that these two related groups of small genome microviruses use very different strategies to fulfill their lifecycle with such a small number of genes. The discovery of these genomes and the detailed prediction and annotation of their genome content expand our understanding of ssDNA phages in nature and are further evidence that these viruses have explored a wide range of possibilities during their long evolution.}, } @article {pmid36694293, year = {2023}, author = {Wang, G and Jin, Z and George, TS and Feng, G and Zhang, L}, title = {Arbuscular mycorrhizal fungi enhance plant phosphorus uptake through stimulating hyphosphere soil microbiome functional profiles for phosphorus turnover.}, journal = {The New phytologist}, volume = {238}, number = {6}, pages = {2578-2593}, doi = {10.1111/nph.18772}, pmid = {36694293}, issn = {1469-8137}, mesh = {*Mycorrhizae/metabolism ; Phosphorus/metabolism ; Soil ; Phytic Acid/metabolism ; Fungi/metabolism ; *Microbiota ; Bacteria/metabolism ; Plant Roots/metabolism ; Soil Microbiology ; }, abstract = {The extraradical hyphae of arbuscular mycorrhizal (AM) fungi are colonized by different bacteria in natural and agricultural systems, but the mechanisms by which AM fungi interact with the hyphosphere soil microbiome and influence soil organic phosphorus (P) mobilization remain unclear. We grew Medicago in two-compartment microcosms, inoculated with Rhizophagus irregularis, or not, in the root compartment and set up P treatments (without P, with P addition as KH2 PO4 or nonsoluble phytate) in the hyphal compartment. We studied the processes of soil P turnover and characterized the microbiome functional profiles for P turnover in the hyphosphere soil by metagenomic sequencing. Compared with the bulk soil, the hyphosphere soil of R. irregularis was inhabited by a specific bacterial community and their functional profiles for P turnover was stimulated. At the species level, the shift in hyphosphere soil microbiome was characterized by the recruitment of the genome bin2.39 harbouring both gcd and phoD genes and genome bin2.97 harbouring the phoD gene, which synergistically drove nonsoluble phytate mobilization in the hyphosphere soil. Our results suggest that AM fungi recruits a specific hyphosphere soil microbiome and stimulated their functional profiles for P turnover to enhance utilization of phytate.}, } @article {pmid36694290, year = {2023}, author = {Urana, R and Yadav, J and Panchal, S and Sharma, P and Singh, N}, title = {Phytoremediation of PAH compounds by microbial communities in sodic soil.}, journal = {International journal of phytoremediation}, volume = {25}, number = {11}, pages = {1501-1509}, doi = {10.1080/15226514.2023.2170321}, pmid = {36694290}, issn = {1549-7879}, mesh = {Biodegradation, Environmental ; Soil ; *Polycyclic Aromatic Hydrocarbons ; *Microbiota ; Microbial Consortia ; *Soil Pollutants ; Soil Microbiology ; }, abstract = {The PAH degrading microbial consortium was collected from sodic soil of the nursery of Guru Jambheshwar University of Science and Technology, Hisar, Haryana (India). And the soil was artificially amended with phenanthrene and naphthalene to isolate the PAHs degrading microbial consortium. The diversity of microbial consortium was analyzed using the NGS (Next Generation Sequencing) based metagenomic approach. The result of diversity analysis showed species Tepidanaerobacter syntrophicus, Sphingomonas oliophenolica, Arthrobacter psychrochitinipnius, Bifidobacterium bombi, Nocardiodies islandensis, Rhodovibrio sodomensis, Thiorhodococus pfennigii, Aeromicrobium ponti, Steroidobacter dentrificans, Actinomaduria maheshkhaliensis, Dactylosporangium maewongense, Pelotomaculum isophthalicicum, and Nocardioides islandensis were present in the consortium. Moreover, Sphingomonas, Arthrobacter, Sphingobium, Azospirillium, Thirohodococcus, and Pelotomaculum were the prominent pollutant degrader genera in the microbial consortium. Since the bioremediation of these pollutants occurs with a significant reduction in toxicity, the study's perspective is to use this type of consortium for bioremediation of specifically contaminated soil.}, } @article {pmid36693851, year = {2023}, author = {Panda, A and Tuller, T}, title = {Determinants of associations between codon and amino acid usage patterns of microbial communities and the environment inferred based on a cross-biome metagenomic analysis.}, journal = {NPJ biofilms and microbiomes}, volume = {9}, number = {1}, pages = {5}, pmid = {36693851}, issn = {2055-5008}, mesh = {Codon ; *Amino Acids ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {Codon and amino acid usage were associated with almost every aspect of microbial life. However, how the environment may impact the codon and amino acid choice of microbial communities at the habitat level is not clearly understood. Therefore, in this study, we analyzed codon and amino acid usage patterns of a large number of environmental samples collected from diverse ecological niches. Our results suggested that samples derived from similar environmental niches, in general, show overall similar codon and amino acid distribution as compared to samples from other habitats. To substantiate the relative impact of the environment, we considered several factors, such as their similarity in GC content, or in functional or taxonomic abundance. Our analysis demonstrated that none of these factors can fully explain the trends that we observed at the codon or amino acid level implying a direct environmental influence on them. Further, our analysis demonstrated different levels of selection on codon bias in different microbial communities with the highest bias in host-associated environments such as the digestive system or oral samples and the lowest level of selection in soil and water samples. Considering a large number of metagenomic samples here we showed that microorganisms collected from similar environmental backgrounds exhibit similar patterns of codon and amino acid usage irrespective of the location or time from where the samples were collected. Thus our study suggested a direct impact of the environment on codon and amino usage of microorganisms that cannot be explained considering the influence of other factors.}, } @article {pmid36693505, year = {2023}, author = {Kong, Z and Wang, H and Yan, G and Yan, Q and Kim, JR}, title = {Limited dissolved oxygen facilitated nitrogen removal at biocathode during the hydrogenotrophic denitrification process using bioelectrochemical system.}, journal = {Bioresource technology}, volume = {372}, number = {}, pages = {128662}, doi = {10.1016/j.biortech.2023.128662}, pmid = {36693505}, issn = {1873-2976}, mesh = {*Denitrification ; *Nitrates/metabolism ; Nitrogen/metabolism ; Oxygen ; Bioreactors ; Nitrification ; Oxidation-Reduction ; }, abstract = {Effects of limited dissolved oxygen (DO) on hydrogenotrophic denitrification at biocathode was investigated using bioelectrochemical system. It was found that total nitrogen removal increased by 5.9%, as DO reached about 0.24 mg/L with the cathodic chamber unplugged (group R_Exposure). With the presence of limited DO, not only the nitrogen metabolic pathway was influenced, but the composition of microbial communities of ammonia-oxidizing bacteria and nitrite-oxidizing bacteria were enriched accordingly. After metagenomic analysis, enriched genes in R_Exposure were found to be associated with nearly each of nitrogen removal steps as denitrification, nitrification, DNRA, nitrate assimilation and even nitrogen fixation. Moreover, genes encoding both Complexes III and IV constituted the electron transfer chain were significantly enriched, indicating that more electrons would be orientated to the reduction of NO2[-]-N, NO-N and oxygen. Therefore, enhanced nitrogen removal could be attained through the co-respiration of nitrate and oxygen by means of NH4[+]-N oxidation.}, } @article {pmid36692711, year = {2023}, author = {Li, Y and Xiong, L and Yu, H and Xiang, Y and Wei, Y and Zhang, Q and Ji, X}, title = {Biogeochemical sulfur cycling of virus auxiliary metabolic genes involved in Napahai plateau wetland.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {15}, pages = {44430-44438}, pmid = {36692711}, issn = {1614-7499}, support = {32160294//Innovative Research Group Project of the National Natural Science Foundation of China/ ; 31860147//Innovative Research Group Project of the National Natural Science Foundation of China/ ; }, mesh = {*Wetlands ; Phylogeny ; Oxidation-Reduction ; *Microbiota ; Sulfur/metabolism ; }, abstract = {Virus plays important roles in regulating microbial community structure, horizontal gene transfer, and promoting biological evolution, also augmenting host metabolism during infection via the expression of auxiliary metabolic genes (AMGs), and thus affect biogeochemical cycling in the oceans. As the "kidney of the earth," wetlands have rich biodiversity and abundant resources. Based on metagenomic data, 10 AMGs associated with sulfur cycling, i.e., tusA, moaD, dsrE, soxA, soxB, soxC, soxD, soxX, soxY, and soxZ, were analyzed in Napahai plateau wetland. The phylogenetic trees of AMGs involved in sulfur metabolism from different habitats and host origins were constructed. Combined with principal coordinate analysis, it revealed that most AMGs associated with sulfur metabolism clustered separately, indicating the abundance and uniqueness in this region. The sulfur metabolism pathways involved by AMGs were mainly SOX systems, among which sulfur oxidation was associated with moaD and dsrE genes, while sulfur transport was related to tusA genes. It provides an insight into the biogeochemical sulfur cycling in plateau wetlands and lays the foundation for further study on the co-evolution of virus and host.}, } @article {pmid36692297, year = {2023}, author = {Bueno de Mesquita, CP and Wu, D and Tringe, SG}, title = {Methyl-Based Methanogenesis: an Ecological and Genomic Review.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {87}, number = {1}, pages = {e0002422}, pmid = {36692297}, issn = {1098-5557}, mesh = {Humans ; *Archaea/genetics/metabolism ; Methane/metabolism ; *Euryarchaeota/genetics/metabolism ; Metagenomics ; }, abstract = {Methyl-based methanogenesis is one of three broad categories of archaeal anaerobic methanogenesis, including both the methyl dismutation (methylotrophic) pathway and the methyl-reducing (also known as hydrogen-dependent methylotrophic) pathway. Methyl-based methanogenesis is increasingly recognized as an important source of methane in a variety of environments. Here, we provide an overview of methyl-based methanogenesis research, including the conditions under which methyl-based methanogenesis can be a dominant source of methane emissions, experimental methods for distinguishing different pathways of methane production, molecular details of the biochemical pathways involved, and the genes and organisms involved in these processes. We also identify the current gaps in knowledge and present a genomic and metagenomic survey of methyl-based methanogenesis genes, highlighting the diversity of methyl-based methanogens at multiple taxonomic levels and the widespread distribution of known methyl-based methanogenesis genes and families across different environments.}, } @article {pmid36692279, year = {2022}, author = {Olo Ndela, É and Cobigo, LM and Roux, S and Enault, F}, title = {[A better understanding of Earth's viruses thanks to metagenomes].}, journal = {Medecine sciences : M/S}, volume = {38}, number = {12}, pages = {999-1007}, doi = {10.1051/medsci/2022166}, pmid = {36692279}, issn = {1958-5381}, mesh = {Humans ; *Metagenome ; Ecosystem ; Phylogeny ; *Viruses/genetics ; Biological Evolution ; Genome, Viral ; }, abstract = {Despite their large number, viruses present in the environment remain largely unknown. Metagenomic approaches, targeting viruses specifically or not, have allowed us a better understanding of the composition of natural viral communities, with Caudoviricetes, Microviridae, Cressdnaviricota or Phycodnaviridae being the most frequently found viral groups. Metagenomes are gradually revealing the extent of the diversity of these groups and their structure, highlighting the large number of species, genera and even viral families, most of which being seen for the first time. Within these groups, the gene content, infected hosts and inhabited ecosystems are often consistent with the evolutionary history traced with marker genes. Thus, the diversity of viruses and their genes is more a reflection of their ancient origin and long coevolution with their hosts than of their ability to mutate rapidly.}, } @article {pmid36691982, year = {2023}, author = {Boktor, JC and Sharon, G and Verhagen Metman, LA and Hall, DA and Engen, PA and Zreloff, Z and Hakim, DJ and Bostick, JW and Ousey, J and Lange, D and Humphrey, G and Ackermann, G and Carlin, M and Knight, R and Keshavarzian, A and Mazmanian, SK}, title = {Integrated Multi-Cohort Analysis of the Parkinson's Disease Gut Metagenome.}, journal = {Movement disorders : official journal of the Movement Disorder Society}, volume = {38}, number = {3}, pages = {399-409}, doi = {10.1002/mds.29300}, pmid = {36691982}, issn = {1531-8257}, mesh = {Humans ; *Parkinson Disease/diagnosis ; Metagenome/genetics ; Cohort Studies ; *Gastrointestinal Microbiome/genetics ; Feces ; }, abstract = {BACKGROUND: The gut microbiome is altered in several neurologic disorders, including Parkinson's disease (PD).

OBJECTIVES: The aim is to profile the fecal gut metagenome in PD for alterations in microbial composition, taxon abundance, metabolic pathways, and microbial gene products, and their relationship with disease progression.

METHODS: Shotgun metagenomic sequencing was conducted on 244 stool donors from two independent cohorts in the United States, including individuals with PD (n = 48, n = 47, respectively), environmental household controls (HC, n = 29, n = 30), and community population controls (PC, n = 41, n = 49). Microbial features consistently altered in PD compared to HC and PC subjects were identified. Data were cross-referenced to public metagenomic data sets from two previous studies in Germany and China to determine generalizable microbiome features.

RESULTS: We find several significantly altered taxa between PD and controls within the two cohorts sequenced in this study. Analysis across global cohorts returns consistent changes only in Intestinimonas butyriciproducens. Pathway enrichment analysis reveals disruptions in microbial carbohydrate and lipid metabolism and increased amino acid and nucleotide metabolism in PD. Global gene-level signatures indicate an increased response to oxidative stress, decreased cellular growth and microbial motility, and disrupted intercommunity signaling.

CONCLUSIONS: A metagenomic meta-analysis of PD shows consistent and novel alterations in functional metabolic potential and microbial gene abundance across four independent studies from three continents. These data reveal that stereotypic changes in the functional potential of the gut microbiome are a consistent feature of PD, highlighting potential diagnostic and therapeutic avenues for future research. © 2023 The Authors. Movement Disorders published by Wiley Periodicals LLC on behalf of International Parkinson and Movement Disorder Society.}, } @article {pmid36691944, year = {2022}, author = {Hernandez, AI and Dos Santos Azevedo, R and Werhli, AV and Dos Santos Machado, K and Nornberg, BF and F Marins, L}, title = {Phylogenetic analysis, computer modeling and catalytic prediction of an Amazonian soil β-glucosidase against a soybean saponin.}, journal = {Integrative biology : quantitative biosciences from nano to macro}, volume = {14}, number = {8-12}, pages = {204-211}, doi = {10.1093/intbio/zyad001}, pmid = {36691944}, issn = {1757-9708}, mesh = {Animals ; Humans ; *beta-Glucosidase ; *Saponins ; Molecular Docking Simulation ; Phylogeny ; Glycine max ; Computers ; }, abstract = {Saponins are amphipathic glycosides with detergent properties present in vegetables. These compounds, when ingested, can cause difficulties in absorbing nutrients from food and even induce inflammatory processes in the intestine. There is already some evidence that saponins can be degraded by β-glucosidases of the GH3 family. In the present study, we evaluated, through computational tools, the possibility of a β-glucosidase (AMBGL17) obtained from a metagenomic analysis of the Amazonian soil, to catalytically interact with a saponin present in soybean. For this, the amino acid sequence of AMBGL17 was used in a phylogenetic analysis to estimate its origin and to determine its three-dimensional structure. The 3D structure of the enzyme was used in a molecular docking analysis to evaluate its interaction with soy saponin as a ligand. The results of the phylogenetic analysis showed that AMBGL17 comes from a microorganism of the phylum Chloroflexi, probably related to species of the order Aggregatinales. Molecular docking showed that soybean saponin can interact with the catalytic site of AMBGL17, with the amino acid GLY345 being important in this catalytic interaction, especially with a β-1,2 glycosidic bond present in the carbohydrate portion of saponin. In conclusion, AMBGL17 is an enzyme with interesting biotechnological potential in terms of mitigating the anti-nutritional and pro-inflammatory effects of saponins present in vegetables used for human and animal food.}, } @article {pmid36691616, year = {2023}, author = {Boutsika, A and Michailidis, M and Ganopoulou, M and Dalakouras, A and Skodra, C and Xanthopoulou, A and Stamatakis, G and Samiotaki, M and Tanou, G and Moysiadis, T and Angelis, L and Bazakos, C and Molassiotis, A and Nianiou-Obeidat, I and Mellidou, I and Ganopoulos, I}, title = {A wide foodomics approach coupled with metagenomics elucidates the environmental signature of potatoes.}, journal = {iScience}, volume = {26}, number = {1}, pages = {105917}, pmid = {36691616}, issn = {2589-0042}, abstract = {The term "terroir" has been widely employed to link differential geographic phenotypes with sensorial signatures of agricultural food products, influenced by agricultural practices, soil type, and climate. Nowadays, the geographical indications labeling has been developed to safeguard the quality of plant-derived food that is linked to a certain terroir and is generally considered as an indication of superior organoleptic properties. As the dynamics of agroecosystems are highly intricate, consisting of tangled networks of interactions between plants, microorganisms, and the surrounding environment, the recognition of the key molecular components of terroir fingerprinting remains a great challenge to protect both the origin and the safety of food commodities. Furthermore, the contribution of microbiome as a potential driver of the terroir signature has been underestimated. Herein, we present a first comprehensive view of the multi-omic landscape related to transcriptome, proteome, epigenome, and metagenome of the popular Protected Geographical Indication potatoes of Naxos.}, } @article {pmid36691550, year = {2023}, author = {Decsi, K and Kutasy, B and Hegedűs, G and Alföldi, ZP and Kálmán, N and Nagy, Á and Virág, E}, title = {Natural immunity stimulation using ELICE16INDURES® plant conditioner in field culture of soybean.}, journal = {Heliyon}, volume = {9}, number = {1}, pages = {e12907}, pmid = {36691550}, issn = {2405-8440}, abstract = {Recently, climate change has had an increasing impact on the world. Innate defense mechanisms operating in plants - such as PAMP-triggered Immunity (PTI) - help to reduce the adverse effects caused by various abiotic and biotic stressors. In this study, the effects of ELICE16INDURES® plant conditioner for organic farming, developed by the Research Institute for Medicinal Plants and Herbs Ltd. Budakalász Hungary, were studied in a soybean population in Northern Hungary. The active compounds and ingredients of this product were selected in such a way as to facilitate the triggering of general plant immunity without the presence and harmful effects of pathogens, thereby strengthening the healthy plant population and preparing it for possible stress effects. In practice, treatments of this agent were applied at two different time points and two concentrations. The conditioning effect was well demonstrated by using agro-drone and ENDVI determination in the soybean field. The genetic background of healthier plants was investigated by NGS sequencing, and by the expression levels of genes encoding enzymes involved in the catalysis of metabolic pathways regulating PTI. The genome-wide transcriptional profiling resulted in 13 contigs related to PAMP-triggered immunity and activated as a result of the treatments. Further analyses showed 16 additional PTI-related contigs whose gene expression changed positively as a result of the treatments. The gene expression values of genes encoded in these contigs were determined by in silico mRNA quantification and validated by RT-qPCR. Both - relatively low and high treatments - showed an increase in gene expression of key genes involving AOC, IFS, MAPK4, MEKK, and GST. Transcriptomic results indicated that the biosyntheses of jasmonic acid (JA), salicylic acid (SA), phenylpropanoid, flavonoid, phytoalexin, and cellular detoxification processes were triggered in the appropriate molecular steps and suggested that plant immune reactions may be activated also artificially, and innate immunity can be enhanced with proper plant biostimulants.}, } @article {pmid36691230, year = {2023}, author = {Blohs, M and Mahnert, A and Brunnader, K and Flucher, C and Castellani, C and Till, H and Singer, G and Moissl-Eichinger, C}, title = {Acute appendicitis manifests as two microbiome state types with oral pathogens influencing severity.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2145845}, pmid = {36691230}, issn = {1949-0984}, support = {P 32697/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Child ; Adolescent ; Humans ; *Appendicitis/drug therapy/pathology/surgery ; *Gastrointestinal Microbiome ; *Appendix/microbiology/pathology ; *Microbiota ; Bacteria ; Acute Disease ; }, abstract = {Mounting evidence suggests that acute appendicitis (AA) is not one but two diseases: complicated appendicitis, which is associated with necrosis leading to perforation or periappendicular abscess, and uncomplicated appendicitis, which does not necessarily result in perforation. Even though AA is the most frequent cause of surgery from abdominal pain, little is known about the origins and etiopathogenesis of this disease, much less regarding the different disease types. In this study, we investigated the microbiome (inter-domain amplicon and metagenome sequencing) of samples from the appendix, rectum and peritoneum of 60 children and adolescents with AA to assess the composition and potential function of bacteria, archaea and fungi. The analysis of the appendix microbial community revealed a shift depending on the severity of the AA. This shift was reflected by two major community state types that represented the complicated and uncomplicated cases. We could demonstrate that complicated, but not uncomplicated, appendicitis is associated with a significant local expansion of oral, bacterial pathogens in the appendix, most strongly influenced by necrotizing Fusobacterium spp., Porphyromonas and Parvimonas. Uncomplicated appendicitis, however, was characterized by gut-associated microbiomes. Our findings support the hypothesis that two disease types exist in AA, which cannot be distinguished beyond doubt using standard clinical characterization methods or by analysis of the patient's rectal microbiome. An advanced microbiome diagnosis, however, could improve non-surgical treatment of uncomplicated AA.}, } @article {pmid36691096, year = {2023}, author = {King, WL and Richards, SC and Kaminsky, LM and Bradley, BA and Kaye, JP and Bell, TH}, title = {Leveraging microbiome rediversification for the ecological rescue of soil function.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {7}, pmid = {36691096}, issn = {2524-6372}, abstract = {BACKGROUND: Global biodiversity losses threaten ecosystem services and can impact important functional insurance in a changing world. Microbial diversity and function can become depleted in agricultural systems and attempts to rediversify agricultural soils rely on either targeted microbial introductions or retaining natural lands as biodiversity reservoirs. As many soil functions are provided by a combination of microbial taxa, rather than outsized impacts by single taxa, such functions may benefit more from diverse microbiome additions than additions of individual commercial strains. In this study, we measured the impact of soil microbial diversity loss and rediversification (i.e. rescue) on nitrification by quantifying ammonium and nitrate pools. We manipulated microbial assemblages in two distinct soil types, an agricultural and a forest soil, with a dilution-to-extinction approach and performed a microbiome rediversification experiment by re-introducing microorganisms lost from the dilution. A microbiome water control was included to act as a reference point. We assessed disruption and potential restoration of (1) nitrification, (2) bacterial and fungal composition through 16S rRNA gene and fungal ITS amplicon sequencing and (3) functional genes through shotgun metagenomic sequencing on a subset of samples.

RESULTS: Disruption of nitrification corresponded with diversity loss, but nitrification was successfully rescued in the rediversification experiment when high diversity inocula were introduced. Bacterial composition clustered into groups based on high and low diversity inocula. Metagenomic data showed that genes responsible for the conversion of nitrite to nitrate and taxa associated with nitrogen metabolism were absent in the low diversity inocula microcosms but were rescued with high diversity introductions.

CONCLUSIONS: In contrast to some previous work, our data suggest that soil functions can be rescued by diverse microbiome additions, but that the concentration of the microbial inoculum is important. By understanding how microbial rediversification impacts soil microbiome performance, we can further our toolkit for microbial management in human-controlled systems in order to restore depleted microbial functions.}, } @article {pmid36690856, year = {2023}, author = {Pápai, M and Benedek, T and Táncsics, A and Bornemann, TLV and Plewka, J and Probst, AJ and Hussein, D and Maróti, G and Menashe, O and Kriszt, B}, title = {Selective enrichment, identification, and isolation of diclofenac, ibuprofen, and carbamazepine degrading bacteria from a groundwater biofilm.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {15}, pages = {44518-44535}, pmid = {36690856}, issn = {1614-7499}, support = {ÚNKP-22-3-II//Ministry for Innovation and Technology/ ; GeneOil//Lundin Energy Norway/ ; }, mesh = {*Ibuprofen/analysis ; Diclofenac/chemistry ; Ecosystem ; Carbamazepine/analysis ; Bacteria/metabolism ; Biodegradation, Environmental ; *Groundwater ; Biofilms ; Pharmaceutical Preparations ; }, abstract = {Diclofenac, ibuprofen, and carbamazepine are three of the most widely detected and most concerning pharmaceutical residues in aquatic ecosystems. The aim of this study was to identify bacteria that may be involved in their degradation from a bacterial biofilm. Selective enrichment cultures in mineral salt solution containing pharmaceutical compounds as sole source of carbon and energy were set up, and population dynamics were monitored using shotgun metagenome sequencing. Bacterial genomes were reconstructed using genome-resolved metagenomics. Thirty bacterial isolates were obtained, identified at species level, and tested regarding pharmaceutical biodegradation at an initial concentration of 1.5 mg l[-1]. The results indicated that most probably diclofenac biodegrading cultures consisted of members of genera Ferrovibrio, Hydrocarboniphaga, Zavarzinia, and Sphingopyxis, while in ibuprofen biodegradation Nocardioides and Starkeya, and in carbamazepine biodegradation Nocardioides, Pseudonocardia, and Sphingopyxis might be involved. During the enrichments, compared to the initial state the percentage relative abundance of these genera increased up to three orders of magnitude. Except Starkeya, the genomes of these bacteria were reconstructed and annotated. Metabolic analyses of the annotated genomes indicated that these bacteria harbored genes associated with pharmaceutical biodegradation. Stenotrophomonas humi DIC_5 and Rhizobium daejeonense IBU_18 isolates eliminated diclofenac and ibuprofen during the tests in the presence of either glucose (3 g l[-1]) or in R2A broth. Higher than 90% concentration reduction was observed in the case of both compounds.}, } @article {pmid36910129, year = {2022}, author = {Ericsson, AC and Bains, M and McAdams, Z and Daniels, J and Busi, SB and Waschek, JA and Dorsam, GP}, title = {The G Protein-Coupled Receptor, VPAC1, Mediates Vasoactive Intestinal Peptide-Dependent Functional Homeostasis of the Gut Microbiota.}, journal = {Gastro hep advances}, volume = {1}, number = {2}, pages = {253-264}, pmid = {36910129}, issn = {2772-5723}, support = {P20 RR015566/RR/NCRR NIH HHS/United States ; R15 AI101968/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND AND AIMS: Vasoactive intestinal peptide (VIP) is a neuropeptide involved in the regulation of feeding behavior and circadian rhythms, metabolism, and immunity. Previous studies revealed the homeostatic effects of VIP signaling on the gut microbiota. VIP-deficient mice demonstrate a gut microbiota dysbiosis characterized by reduced α-diversity and decreased relative abundance (RA) of Gram-positive Firmicutes. However, the mechanism by which VIP signaling affects changes in the microbiota is unknown.

METHODS: To investigate the role of the 2 cognate G protein-coupled receptors for VIP (VPAC1 and VPAC2) in VIP-mediated homeostasis of the microbiota, fecal samples from VPAC1- and VPAC2-deficient, heterozygous, and wild-type littermate mice were assessed via targeted amplicon sequencing. Their microbiota profiles were additionally compared with microbiota from VIP-deficient, heterozygous, and wild-type littermates, where genotype-dependent changes in the composition and predicted function of each cohort were compared.

RESULTS: While wild-type mice in each line differed in α-diversity and β-diversity, consistent changes in both metrics were observed in VIP-deficient and VPAC1-deficient mice. This includes a dramatic reduction in α-diversity, increased RA of Proteobacteria and Bacteroidetes, and decreased RA of Lachnospiraceae, Ruminococcaceae, Muribaculaceae, and Rikenellaceae. Specific amplicon sequence variants and predicted functions found to differ significantly based on VIP or VPAC1 genotype were concordant in their directions of change. Multiplatform predicted functional profiling suggested a defective VIP-VPAC1 axis was associated with reduced amino acid degradation along with reduced quinol and quinone biosynthesis. Furthermore, alterations in predicted functions include increased sugar degradation, nitrate reduction, and fatty acid biosynthetic pathways, among other changes.

CONCLUSION: We conclude that VIP signaling through VPAC1 is critical for the maintenance of normal function of the gut microbiota.}, } @article {pmid36891249, year = {2022}, author = {Bawaneh, A and Shively, CA and Tooze, JA and Cook, KL}, title = {Impact of gut permeability on the breast microbiome using a non-human primate model.}, journal = {Gut microbiome (Cambridge, England)}, volume = {3}, number = {}, pages = {}, pmid = {36891249}, issn = {2632-2897}, support = {R01 HL087103/HL/NHLBI NIH HHS/United States ; }, abstract = {We previously demonstrated in non-human primates (NHP) that Mediterranean diet consumption shifted the proportional abundance of Lactobacillus in the breast and gut. This data highlights a potential link about gut-breast microbiome interconnectivity. To address this question, we compared bacterial populations identified in matched breast and faecal samples from our NHP study. Dietary pattern concurrently shifted two species in both regions; Streptococcus lutetiensis and Ruminococcus torques. While we observe similar trends in Lactobacillus abundances in the breast and gut, the species identified in each region vary; Mediterranean diet increased Lactobacillus_unspecified species in breast but regulated L. animalis and L. reuteri in the gut.We also investigated the impact of gut permeability on the breast microbiome. Regardless of dietary pattern, subjects that displayed increased physiological measures of gut permeability (elevated plasma lipopolysaccharide, decreased villi length, and decreased goblet cells) displayed a significantly different breast microbiome. Gut barrier dysfunction was associated with increased α-diversity and significant different β-diversity in the breast tissue. Taken together our data supports the presence of a breast microbiome influenced by diet that largely varies from the gut microbiome population but is, however, sensitive to gut permeability.}, } @article {pmid36700086, year = {2021}, author = {Yoshimura, Y and Hamada, A and Augey, Y and Akiyama, M and Sakakibara, Y}, title = {Genomic style: yet another deep-learning approach to characterize bacterial genome sequences.}, journal = {Bioinformatics advances}, volume = {1}, number = {1}, pages = {vbab039}, pmid = {36700086}, issn = {2635-0041}, abstract = {MOTIVATION: Biological sequence classification is the most fundamental task in bioinformatics analysis. For example, in metagenome analysis, binning is a typical type of DNA sequence classification. In order to classify sequences, it is necessary to define sequence features. The k-mer frequency, base composition and alignment-based metrics are commonly used. On the other hand, in the field of image recognition using machine learning, image classification is broadly divided into those based on shape and those based on style. A style matrix was introduced as a method of expressing the style of an image (e.g. color usage and texture).

RESULTS: We propose a novel sequence feature, called genomic style, inspired by image classification approaches, for classifying and clustering DNA sequences. As with the style of images, the DNA sequence is considered to have a genomic style unique to the bacterial species, and the style matrix concept is applied to the DNA sequence. Our main aim is to introduce the genomics style as yet another basic sequence feature for metagenome binning problem in replace of the most commonly used sequence feature k-mer frequency. Performance evaluations showed that our method using a style matrix has the potential for accurate binning when compared with state-of-the-art binning tools based on k-mer frequency.

The source code for the implementation of this genomic style method, along with the dataset for the performance evaluation, is available from https://github.com/friendflower94/binning-style.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.}, } @article {pmid36759732, year = {2021}, author = {Séneca, J and Söllinger, A and Herbold, CW and Pjevac, P and Prommer, J and Verbruggen, E and Sigurdsson, BD and Peñuelas, J and Janssens, IA and Urich, T and Tveit, AT and Richter, A}, title = {Increased microbial expression of organic nitrogen cycling genes in long-term warmed grassland soils.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {69}, pmid = {36759732}, issn = {2730-6151}, support = {W1257-B20//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; ZK74//Austrian Science Fund (Fonds zur Förderung der Wissenschaftlichen Forschung)/ ; 251027/RU//Norges Forskningsråd (Research Council of Norway)/ ; }, abstract = {Global warming increases soil temperatures and promotes faster growth and turnover of soil microbial communities. As microbial cell walls contain a high proportion of organic nitrogen, a higher turnover rate of microbes should also be reflected in an accelerated organic nitrogen cycling in soil. We used a metatranscriptomics and metagenomics approach to demonstrate that the relative transcription level of genes encoding enzymes involved in the extracellular depolymerization of high-molecular-weight organic nitrogen was higher in medium-term (8 years) and long-term (>50 years) warmed soils than in ambient soils. This was mainly driven by increased levels of transcripts coding for enzymes involved in the degradation of microbial cell walls and proteins. Additionally, higher transcription levels for chitin, nucleic acid, and peptidoglycan degrading enzymes were found in long-term warmed soils. We conclude that an acceleration in microbial turnover under warming is coupled to higher investments in N acquisition enzymes, particularly those involved in the breakdown and recycling of microbial residues, in comparison with ambient conditions.}, } @article {pmid36755065, year = {2021}, author = {Armbrecht, L and Eisenhofer, R and Utge, J and Sibert, EC and Rocha, F and Ward, R and Pierella Karlusich, JJ and Tirichine, L and Norris, R and Summers, M and Bowler, C}, title = {Paleo-diatom composition from Santa Barbara Basin deep-sea sediments: a comparison of 18S-V9 and diat-rbcL metabarcoding vs shotgun metagenomics.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {66}, pmid = {36755065}, issn = {2730-6151}, abstract = {Sedimentary ancient DNA (sedaDNA) analyses are increasingly used to reconstruct marine ecosystems. The majority of marine sedaDNA studies use a metabarcoding approach (extraction and analysis of specific DNA fragments of a defined length), targeting short taxonomic marker genes. Promising examples are 18S-V9 rRNA (~121-130 base pairs, bp) and diat-rbcL (76 bp), targeting eukaryotes and diatoms, respectively. However, it remains unknown how 18S-V9 and diat-rbcL derived compositional profiles compare to metagenomic shotgun data, the preferred method for ancient DNA analyses as amplification biases are minimised. We extracted DNA from five Santa Barbara Basin sediment samples (up to ~11 000 years old) and applied both a metabarcoding (18S-V9 rRNA, diat-rbcL) and a metagenomic shotgun approach to (i) compare eukaryote, especially diatom, composition, and (ii) assess sequence length and database related biases. Eukaryote composition differed considerably between shotgun and metabarcoding data, which was related to differences in read lengths (~112 and ~161 bp, respectively), and overamplification of short reads in metabarcoding data. Diatom composition was influenced by reference bias that was exacerbated in metabarcoding data and characterised by increased representation of Chaetoceros, Thalassiosira and Pseudo-nitzschia. Our results are relevant to sedaDNA studies aiming to accurately characterise paleo-ecosystems from either metabarcoding or metagenomic data.}, } @article {pmid36700102, year = {2021}, author = {Blanke, M and Morgenstern, B}, title = {App-SpaM: phylogenetic placement of short reads without sequence alignment.}, journal = {Bioinformatics advances}, volume = {1}, number = {1}, pages = {vbab027}, pmid = {36700102}, issn = {2635-0041}, abstract = {MOTIVATION: Phylogenetic placement is the task of placing a query sequence of unknown taxonomic origin into a given phylogenetic tree of a set of reference sequences. A major field of application of such methods is, for example, the taxonomic identification of reads in metabarcoding or metagenomic studies. Several approaches to phylogenetic placement have been proposed in recent years. The most accurate of them requires a multiple sequence alignment of the references as input. However, calculating multiple alignments is not only time-consuming but also limits the applicability of these approaches.

RESULTS: Herein, we propose Alignment-free phylogenetic placement algorithm based on Spaced-word Matches (App-SpaM), an efficient algorithm for the phylogenetic placement of short sequencing reads on a tree of a set of reference sequences. App-SpaM produces results of high quality that are on a par with the best available approaches to phylogenetic placement, while our software is two orders of magnitude faster than these existing methods. Our approach neither requires a multiple alignment of the reference sequences nor alignments of the queries to the references. This enables App-SpaM to perform phylogenetic placement on a broad variety of datasets.

The source code of App-SpaM is freely available on Github at https://github.com/matthiasblanke/App-SpaM together with detailed instructions for installation and settings. App-SpaM is furthermore available as a Conda-package on the Bioconda channel.

CONTACT: matthias.blanke@biologie.uni-goettingen.de.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics Advances online.}, } @article {pmid36747039, year = {2021}, author = {Alejandre-Colomo, C and Francis, B and Viver, T and Harder, J and Fuchs, BM and Rossello-Mora, R and Amann, R}, title = {Cultivable Winogradskyella species are genomically distinct from the sympatric abundant candidate species.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {51}, pmid = {36747039}, issn = {2730-6151}, support = {AM 73/9-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; AM 73/9-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; AM 73/9-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; AM 73/9-1//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Winogradskyella is a genus within the phylum Bacteroidetes with a clear marine origin. Most members of this genus have been found associated with marine animals and algae, but also with inorganic surfaces such as sand. In this study, we analyzed genomes of eleven species recently isolated from surface seawater samples from the North Sea during a single spring algae bloom. Corresponding metagenomes yielded a single Candidatus species for this genus. All species in culture, with the exception of W. ursingii, affiliated with a Winogradskyella lineage characterized by large genomes (~4.3 ± 0.4 Mb), with high complexity in their carbohydrate and protein degradation genes. Specifically, the polysaccharide utilization loci (PULs) were diverse within each individual strain, indicating large substrate versatility. Although present in the North Sea, the abundances of these strains were at, or below, the detection limit of the metagenomes. In contrast, the single species, classified as Candidatus W. atlantica, to which all North Sea MAGs belonged, affiliated with a lineage in which the cultivated representatives showed small genomes of ~3.0-3.5 Mb, with the MAGs having ~2.3 Mb. In Ca. W. atlantica, genome streamlining has apparently resulted in the loss of biosynthesis pathways for several amino acids including arginine, methionine, leucine and valine, and the PUL loci were reduced to a single one for utilizing laminarin. This as-yet uncultivated species seems to capitalize on sporadically abundant substrates that are released by algae blooms, mainly laminarin. We also suggest that this streamlined genome might be responsible for the lack of growth on plates for this Candidatus species, in contrast to growth of the less abundant but coexisting members of the genus.}, } @article {pmid36747007, year = {2021}, author = {Bowerman, KL and Knowles, SCL and Bradley, JE and Baltrūnaitė, L and Lynch, MDJ and Jones, KM and Hugenholtz, P}, title = {Effects of laboratory domestication on the rodent gut microbiome.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {49}, pmid = {36747007}, issn = {2730-6151}, abstract = {The domestication of the laboratory mouse has influenced the composition of its native gut microbiome, which is now known to differ from that of its wild ancestor. However, limited exploration of the rodent gut microbiome beyond the model species Mus musculus has made it difficult to interpret microbiome variation in a broader phylogenetic context. Here, we analyse 120 de novo and 469 public metagenomically-sequenced faecal and caecal samples from 16 rodent hosts representing wild, laboratory and captive lifestyles. Distinct gut bacterial communities were observed between rodent host genera, with broadly distributed species originating from the as-yet-uncultured bacterial genera UBA9475 and UBA2821 in the families Oscillospiraceae and Lachnospiraceae, respectively. In laboratory mice, Helicobacteraceae were generally depleted relative to wild mice and specific Muribaculaceae populations were enriched in different laboratory facilities, suggesting facility-specific outgrowths of this historically dominant rodent gut family. Several bacterial families of clinical interest, including Akkermansiaceae, Streptococcaceae and Enterobacteriaceae, were inferred to have gained over half of their representative species in mice within the laboratory environment, being undetected in most wild rodents and suggesting an association between laboratory domestication and pathobiont emergence.}, } @article {pmid36739331, year = {2021}, author = {Sun, J and Evans, PN and Gagen, EJ and Woodcroft, BJ and Hedlund, BP and Woyke, T and Hugenholtz, P and Rinke, C}, title = {Recoding of stop codons expands the metabolic potential of two novel Asgardarchaeota lineages.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {30}, pmid = {36739331}, issn = {2730-6151}, support = {FT170100213//Department of Education and Training | Australian Research Council (ARC)/ ; FL150100038//Department of Education and Training | Australian Research Council (ARC)/ ; }, abstract = {Asgardarchaeota have been proposed as the closest living relatives to eukaryotes, and a total of 72 metagenome-assembled genomes (MAGs) representing six primary lineages in this archaeal phylum have thus far been described. These organisms are predicted to be fermentative heterotrophs contributing to carbon cycling in sediment ecosystems. Here, we double the genomic catalogue of Asgardarchaeota by obtaining 71 MAGs from a range of habitats around the globe, including the deep subsurface, brackish shallow lakes, and geothermal spring sediments. Phylogenomic inferences followed by taxonomic rank normalisation confirmed previously established Asgardarchaeota classes and revealed four additional lineages, two of which were consistently recovered as monophyletic classes. We therefore propose the names Candidatus Sifarchaeia class nov. and Ca. Jordarchaeia class nov., derived from the gods Sif and Jord in Norse mythology. Metabolic inference suggests that both classes represent hetero-organotrophic acetogens, which also have the ability to utilise methyl groups such as methylated amines, with acetate as the probable end product in remnants of a methanogen-derived core metabolism. This inferred mode of energy conservation is predicted to be enhanced by genetic code expansions, i.e., stop codon recoding, allowing the incorporation of the rare 21st and 22nd amino acids selenocysteine (Sec) and pyrrolysine (Pyl). We found Sec recoding in Jordarchaeia and all other Asgardarchaeota classes, which likely benefit from increased catalytic activities of Sec-containing enzymes. Pyl recoding, on the other hand, is restricted to Sifarchaeia in the Asgardarchaeota, making it the first reported non-methanogenic archaeal lineage with an inferred complete Pyl machinery, likely providing members of this class with an efficient mechanism for methylamine utilisation. Furthermore, we identified enzymes for the biosynthesis of ester-type lipids, characteristic of bacteria and eukaryotes, in both newly described classes, supporting the hypothesis that mixed ether-ester lipids are a shared feature among Asgardarchaeota.}, } @article {pmid36737514, year = {2021}, author = {Zhao, R and Biddle, JF}, title = {Helarchaeota and co-occurring sulfate-reducing bacteria in subseafloor sediments from the Costa Rica Margin.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {25}, pmid = {36737514}, issn = {2730-6151}, abstract = {Deep sediments host many archaeal lineages, including the Asgard superphylum which contains lineages predicted to require syntrophic partnerships. Our knowledge about sedimentary archaeal diversity and their metabolic pathways and syntrophic partners is still very limited. We present here new genomes of Helarchaeota and the co-occurring sulfate-reducing bacteria (SRB) recovered from organic-rich sediments off Costa Rica Margin. Phylogenetic analyses revealed three new metagenome-assembled genomes (MAGs) affiliating with Helarchaeota, each of which has three variants of the methyl-CoM reductase-like (MCR-like) complex that may enable them to oxidize short-chain alkanes anaerobically. These Helarchaeota have no multi-heme cytochromes but have Group 3b and Group 3c [NiFe] hydrogenases, and formate dehydrogenase, and therefore have the capacity to transfer the reducing equivalents (in the forms of hydrogen and formate) generated from alkane oxidation to external partners. We also recovered five MAGs of SRB affiliated with the class of Desulfobacteria, two of which showed relative abundances (represented by genome coverages) positively correlated with those of the three Helarchaeota. Genome analysis suggested that these SRB bacteria have the capacity of H2 and formate utilization and could facilitate electron transfers from other organisms by means of these reduced substances. Their co-occurrence and metabolic features suggest that Helarchaeota may metabolize synergistically with some SRB, and together exert an important influence on the carbon cycle by mitigating the hydrocarbon emission from sediments to the overlying ocean.}, } @article {pmid36717704, year = {2021}, author = {Busi, SB and de Nies, L and Habier, J and Wampach, L and Fritz, JV and Heintz-Buschart, A and May, P and Halder, R and de Beaufort, C and Wilmes, P}, title = {Persistence of birth mode-dependent effects on gut microbiome composition, immune system stimulation and antimicrobial resistance during the first year of life.}, journal = {ISME communications}, volume = {1}, number = {1}, pages = {8}, pmid = {36717704}, issn = {2730-6151}, support = {ATTRACT/A09/03//Fonds National de la Recherche Luxembourg (National Research Fund)/ ; CORE/C15/SR/10404839//Fonds National de la Recherche Luxembourg (National Research Fund)/ ; PRIDE17/11823097//Fonds National de la Recherche Luxembourg (National Research Fund)/ ; AFR PHD-2013-5824125//Fonds National de la Recherche Luxembourg (National Research Fund)/ ; CORE Junior/14/BM/8066232//Fonds National de la Recherche Luxembourg (National Research Fund)/ ; CRSII5_180241//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (Swiss National Science Foundation)/ ; FZT 118//Deutsche Forschungsgemeinschaft (German Research Foundation)/ ; }, abstract = {Caesarean section delivery (CSD) disrupts mother-to-neonate transmission of specific microbial strains and functional repertoires as well as linked immune system priming. Here we investigate whether differences in microbiome composition and impacts on host physiology persist at 1 year of age. We perform high-resolution, quantitative metagenomic analyses of the gut microbiomes of infants born by vaginal delivery (VD) or by CSD, from immediately after birth through to 1 year of life. Several microbial populations show distinct enrichments in CSD-born infants at 1 year of age including strains of Bacteroides caccae, Bifidobacterium bifidum and Ruminococcus gnavus, whereas others are present at higher levels in the VD group including Faecalibacterium prausnitizii, Bifidobacterium breve and Bifidobacterium kashiwanohense. The stimulation of healthy donor-derived primary human immune cells with LPS isolated from neonatal stool samples results in higher levels of tumour necrosis factor alpha (TNF-α) in the case of CSD extracts over time, compared to extracts from VD infants for which no such changes were observed during the first year of life. Functional analyses of the VD metagenomes at 1 year of age demonstrate a significant increase in the biosynthesis of the natural antibiotics, carbapenem and phenazine. Concurrently, we find antimicrobial resistance (AMR) genes against several classes of antibiotics in both VD and CSD. The abundance of AMR genes against synthetic (including semi-synthetic) agents such as phenicol, pleuromutilin and diaminopyrimidine are increased in CSD children at day 5 after birth. In addition, we find that mobile genetic elements, including phages, encode AMR genes such as glycopeptide, diaminopyrimidine and multidrug resistance genes. Our results demonstrate persistent effects at 1 year of life resulting from birth mode-dependent differences in earliest gut microbiome colonisation.}, } @article {pmid36824343, year = {2021}, author = {Wang, Q and Sun, Q and Li, X and Wang, Z and Zheng, H and Ju, Y and Guo, R and Peng, S and Jia, H}, title = {Linking gut microbiome to bone mineral density: a shotgun metagenomic dataset from 361 elderly women.}, journal = {GigaByte (Hong Kong, China)}, volume = {2021}, number = {}, pages = {gigabyte12}, pmid = {36824343}, issn = {2709-4715}, abstract = {Bone mass loss contributes to the risk of bone fracture in the elderly. Many factors including age, obesity, estrogen and diet, are associated with bone mass loss. Mice studies suggested that the gut microbiome might affect the bone mass by regulating the immune system. However, there has been little evidence from human studies. Bone loss increases after menopause. Therefore, we have recruited 361 Chinese post-menopausal women to collect their fecal samples and metadata to conduct a metagenome-wide association study (MWAS) to investigate the influence of the gut microbiome on bone health. Gut microbiome sequencing data were produced using the BGISEQ-500 sequencer. Bone mineral density (BMD) was calculated using a Hologic dual energy X-ray machine, and body mass index (BMI) and age were also recorded. This collected data allows exploration of the gut microbial diversity and their links to bone mass loss as well as to microbial markers for bone mineral density. In addition, these data are potentially useful in studying the role that the gut microbiota might play in bone mass loss and in exploring the process of bone mass loss.}, } @article {pmid36937228, year = {2017}, author = {Navas-Molina, JA and Hyde, ER and Sanders, J and Knight, R}, title = {The Microbiome and Big Data.}, journal = {Current opinion in systems biology}, volume = {4}, number = {}, pages = {92-96}, pmid = {36937228}, issn = {2452-3100}, support = {P01 DK078669/DK/NIDDK NIH HHS/United States ; R01 HG004872/HG/NHGRI NIH HHS/United States ; U01 HG004866/HG/NHGRI NIH HHS/United States ; U01 HG006537/HG/NHGRI NIH HHS/United States ; }, abstract = {Microbiome datasets have expanded rapidly in recent years. Advances in DNA sequencing, as well as the rise of shotgun metagenomics and metabolomics, are producing datasets that exceed the ability of researchers to analyze them on their personal computers. Here we describe what Big Data is in the context of microbiome research, how this data can be transformed into knowledge about microbes and their functions in their environments, and how the knowledge can be applied to move microbiome research forward. In particular, the development of new high-resolution tools to assess strain-level variability (moving away from OTUs), the advent of cloud computing and centralized analysis resources such as Qiita (for sequences) and GNPS (for mass spectrometry), and better methods for curating and describing "metadata" (contextual information about the sequence or chemical information) are rapidly assisting the use of microbiome data in fields ranging from human health to environmental studies.}, } @article {pmid36690796, year = {2023}, author = {Li, P and Ye, S and Chen, J and Wang, L and Li, Y and Ge, L and Wu, G and Song, L and Wang, C and Sun, Y and Wang, J and Pan, A and Quan, Z and Wu, Y}, title = {Combined metagenomic and metabolomic analyses reveal that Bt rice planting alters soil C-N metabolism.}, journal = {ISME communications}, volume = {3}, number = {1}, pages = {4}, pmid = {36690796}, issn = {2730-6151}, support = {32071657//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {The environmental impacts of genetically modified (GM) plants remain a controversial global issue. To address these issues, comprehensive environmental risk assessments of GM plants is critical for the sustainable development and application of transgenic technology. In this paper, significant differences were not observed between microbial metagenomic and metabolomic profiles in surface waters of the Bt rice (T1C-1, the transgenic line) and non-Bt cultivars (Minghui 63 (the isogenic line) and Zhonghua 11 (the conventional japonica cultivar)). In contrast, differences in these profiles were apparent in the rhizospheres. T1C-1 planting increased soil microbiome diversity and network stability, but did not significantly alter the abundances of potential probiotic or phytopathogenic microorganisms compared with Minghui 63 and Zhonghua 11, which revealed no adverse effects of T1C-1 on soil microbial communities. T1C-1 planting could significantly alter soil C and N, probably via the regulation of the abundances of enzymes related to soil C and N cycling. In addition, integrated multi-omic analysis of root exudate metabolomes and soil microbiomes showed that the abundances of various metabolites released as root exudates were significantly correlated with subsets of microbial populations including the Acidobacteria, Actinobacteria, Chloroflexi, and Gemmatimonadetes that were differentially abundant in T1C-1 and Mnghui 63 soils. Finally, the potential for T1C-1-associated root metabolites to exert growth effects on T1C-1-associated species was experimentally validated by analysis of bacterial cultures, revealing that Bt rice planting could selectively modulate specific root microbiota. Overall, this study indicate that Bt rice can directly modulate rhizosphere microbiome assemblages by altering the metabolic compositions of root exudates that then alters soil metabolite profiles and physiochemical properties. This study unveils the mechanistic associations of Bt plant-microorganism-environment, which provides comprehensive insights into the potential ecological impacts of GM plants.}, } @article {pmid36690779, year = {2023}, author = {Yu, Y and Wang, P and Cao, HY and Teng, ZJ and Zhu, Y and Wang, M and McMinn, A and Chen, Y and Xiang, H and Zhang, YZ and Chen, XL and Zhang, YQ}, title = {Novel D-glutamate catabolic pathway in marine Proteobacteria and halophilic archaea.}, journal = {The ISME journal}, volume = {17}, number = {4}, pages = {537-548}, pmid = {36690779}, issn = {1751-7370}, mesh = {*Glutamic Acid/metabolism ; *Proteobacteria ; Ecosystem ; Bacteria ; Archaea/genetics/metabolism ; }, abstract = {D-glutamate (D-Glu) is an essential component of bacterial peptidoglycans, representing an important, yet overlooked, pool of organic matter in global oceans. However, little is known on D-Glu catabolism by marine microorganisms. Here, a novel catabolic pathway for D-Glu was identified using the marine bacterium Pseudoalteromonas sp. CF6-2 as the model. Two novel enzymes (DgcN, DgcA), together with a transcriptional regulator DgcR, are crucial for D-Glu catabolism in strain CF6-2. Genetic and biochemical data confirm that DgcN is a N-acetyltransferase which catalyzes the formation of N-acetyl-D-Glu from D-Glu. DgcA is a racemase that converts N-acetyl-D-Glu to N-acetyl-L-Glu, which is further hydrolyzed to L-Glu. DgcR positively regulates the transcription of dgcN and dgcA. Structural and biochemical analyses suggested that DgcN and its homologs, which use D-Glu as the acyl receptor, represent a new group of the general control non-repressible 5 (GCN5)-related N-acetyltransferases (GNAT) superfamily. DgcA and DgcN occur widely in marine bacteria (particularly Rhodobacterales) and halophilic archaea (Halobacteria) and are abundant in marine and hypersaline metagenome datasets. Thus, this study reveals a novel D-Glu catabolic pathway in ecologically important marine bacteria and halophilic archaea and helps better understand the catabolism and recycling of D-Glu in these ecosystems.}, } @article {pmid36690342, year = {2023}, author = {Barrón-Sandoval, A and Martiny, JBH and Pérez-Carbajal, T and Bullock, SH and Leija, A and Hernández, G and Escalante, AE}, title = {Functional significance of microbial diversity in arid soils: biological soil crusts and nitrogen fixation as a model system.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {2}, pages = {}, pmid = {36690342}, issn = {1574-6941}, mesh = {Ecosystem ; Nitrogen Fixation ; *Cyanobacteria/genetics ; Desert Climate ; Soil ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; *Microbiota/genetics ; Nitrogen ; }, abstract = {Microbial communities respond to changes in environmental conditions; however, how compositional shifts affect ecosystem processes is still not well-understood and it is often assumed that different microbial communities will function equally under similar environmental conditions. We evaluated this assumption of functional redundancy using biological soil crusts (BSCs) from two arid ecosystems in Mexico with contrasting climate conditions (hot and cold deserts) following an experimental approach both in the field (reciprocal transplants) and in laboratory conditions (common garden), focusing on the community's composition and potential for nitrogen fixation. Potential of nitrogen fixation was assessed through the acetylene reduction assay. Community composition and diversity was determined with T-RFLPs of nifH gene, high throughput sequencing of 16S rRNA gene amplicons and metagenomic libraries. BSCs tended to show higher potential nitrogen fixation rates when experiencing temperatures more similar to their native environment. Moreover, changes in potential nitrogen fixation, taxonomic and functional community composition, and diversity often depended on an interactive effect of origin of the communities and the environment they experienced. We interpret our results as legacy effects that result from ecological specialization of the BSC communities to their native environment. Overall, we present evidence of nonfunctional redundancy of BSCs in terms of nitrogen fixation.}, } @article {pmid36690218, year = {2023}, author = {Dong, K and Qiu, Y and Wang, X and Yu, D and Yu, Z and Feng, J and Wang, J and Gu, R and Zhao, J}, title = {Towards low carbon demand and highly efficient nutrient removal: Establishing denitrifying phosphorus removal in a biofilm-based system.}, journal = {Bioresource technology}, volume = {372}, number = {}, pages = {128658}, doi = {10.1016/j.biortech.2023.128658}, pmid = {36690218}, issn = {1873-2976}, mesh = {*Sewage ; *Phosphorus ; Denitrification ; Nitrates ; Carbon ; Bioreactors ; Nitrogen ; Phosphates ; Organic Chemicals ; Nutrients ; Biofilms ; Waste Disposal, Fluid/methods ; }, abstract = {The combined denitrifying phosphorus removal (DPR) and Anammox process is expected to achieve advanced nutrient removal with low carbon consumption. However, exchanging ammonia/nitrate between them is one limitation. This study investigated the feasibility of conducting DPR in a biofilm reactor to solve that problem. After 46-day anaerobic/aerobic operation, high phosphorus removal efficiency (PRE, 83.15 %) was obtained in the activated sludge (AS) and biofilm co-existed system, in which the AS performed better. Phosphate-accumulating organisms might quickly adapt to the anoxic introduced nitrate, but the following aerobic stage ensured a low effluent orthophosphate (<1.03 mg/L). Because of waste sludge discharging and AS transforming to biofilm, the suspended solids dropped below 60 mg/L on Day 100, resulting in PRE decline (17.17 %) and effluent orthophosphate rise (4.23 mg/L). Metagenomes analysis revealed that Pseudomonas and Thiothrix had genes for denitrification and encoding Pit phosphate transporter, and Candidatus_Competibacter was necessary for biofilm formation.}, } @article {pmid36689947, year = {2023}, author = {Deng, S and Lin, B and Weng, B and Yang, H and Zhou, K and Wu, L and Qin, L and Pan, L}, title = {Clinical Characteristics and Follow-up of Cases of Streptococcus suis Meningitis in Patients of Liuzhou, China.}, journal = {The American journal of tropical medicine and hygiene}, volume = {108}, number = {3}, pages = {477-481}, pmid = {36689947}, issn = {1476-1645}, mesh = {Humans ; *Streptococcus suis ; Follow-Up Studies ; Activities of Daily Living ; *Meningitis, Bacterial ; *Streptococcal Infections/diagnosis ; China ; *Hearing Loss, Sensorineural ; }, abstract = {We analyzed the clinical characteristics and outcomes of patients with Streptococcus suis meningitis in Liuzhou, China, to improve diagnostic accuracy and lower the chances of misdiagnosis. The major clinical manifestations, auxiliary examination results, treatment strategies, treatment efficacy, and follow-up results of 17 consecutively admitted patients with S. suis meningitis were evaluated. The most common clinical manifestations were fever (15/17), sensorineural hearing loss (13/17), headache (11/17), and altered mental status (8/17). In addition, 64.71% of the patients had residual symptoms of sensorineural hearing loss at discharge, and moderate disabilities occurred in 68.75% of the patients in the form of sensorineural deafness (11/17) and hemiparesis (1/17). The cerebrospinal fluid (CSF) of nine patients was used for metagenomic analysis with next-generation sequencing. The metagenomic analysis of CSF of four patients was positive, whereas blood and CSF cultures were negative. The average modified Rankin Scale (mRS) and Activities of Daily Living (ADL) scores improved significantly at the 6-month follow-up compared with those at admission (P < 0.05). There was no correlation between altered mRS and ADL scores and the CSF findings (P > 0.05). Early administration of antibiotics can prevent sensorineural hearing loss. Early CSF metagenomic analysis may be superior to blood and CSF culture.}, } @article {pmid36689879, year = {2023}, author = {Bai, Y and Wang, S and Zhussupbekova, A and Shvets, IV and Lee, PH and Zhan, X}, title = {High-rate iron sulfide and sulfur-coupled autotrophic denitrification system: Nutrients removal performance and microbial characterization.}, journal = {Water research}, volume = {231}, number = {}, pages = {119619}, doi = {10.1016/j.watres.2023.119619}, pmid = {36689879}, issn = {1879-2448}, mesh = {*Nitrates/metabolism ; *Denitrification ; Autotrophic Processes ; Sulfur/metabolism ; Iron ; Phosphates ; Sulfides/metabolism ; Bioreactors/microbiology ; Nitrogen ; }, abstract = {Iron sulfides-based autotrophic denitrification (IAD) is a promising technology for nitrate and phosphate removal from low C:N ratio wastewater due to its cost-effectiveness and low sludge production. However, the slow kinetics of IAD, compared to other sulfur-based autotrophic denitrification (SAD) processes, limits its engineering application. This study constructed a co-electron-donor (FeS and S[0] with a volume ratio of 2:1) iron sulfur autotrophic denitrification (ISAD) biofilter and operated at as short as 1 hr hydraulic retention time (HRT). Long-term operation results showed that the superior total nitrogen and phosphate removals of the ISAD biofilter were 90-100% at 1-12 h HRT, with the highest denitrification rate up to 960 mg/L/d. Considering low sulfate production, HRT of 3 h could be the optimal condition. Such superior performance in the ISAD biofilter was achieved due to the interactions between FeS and S[0], which accelerated the denitrification process and maintained the acidity-alkalinity balance. Metagenomic analysis found that the enriched nitrate-dependent iron-oxidizing (NDFO) bacteria (Acinetobacter and Acidovorax), sulfur-oxidizing bacteria (SOB), and dissimilatory nitrate reduction to ammonia (DNRA) bacteria likely supported stable nitrate reduction. The metabolic pathway analysis showed that completely denitrification and DNRA, coupled with sulfur oxidation, disproportionation, iron oxidation and phosphate precipitation with FeS and S[0] as co-electron donors, were responsible for the high-rate nitrate and phosphate removal. This study provides the potential of ISAD as a highly efficient post-denitrification technology and sheds light on the balanced microbial S-N-Fe transformation.}, } @article {pmid36689828, year = {2023}, author = {Mi, T and Jin, Y and Che, Y and Huang, J and Zhou, R and Wu, C}, title = {Profiling the composition and metabolic functions of microbial community in pellicle-forming radish paocai.}, journal = {International journal of food microbiology}, volume = {388}, number = {}, pages = {110087}, doi = {10.1016/j.ijfoodmicro.2023.110087}, pmid = {36689828}, issn = {1879-3460}, mesh = {*Raphanus ; Fermentation ; Vegetables/microbiology ; Lactobacillus/metabolism ; Bacteria/genetics ; *Yarrowia ; *Microbiota ; }, abstract = {Pellicle formation is an obvious indicator of spoilage and is followed by a loss of flavor in a variety of fermented vegetables. In this study, the pellicle-forming microorganisms were isolated using culture-dependent approaches, then a comparative analysis between the pellicle-forming (PF) radish paocai and normal fermented paocai in the diversity and function of microbial community was conducted by metagenome sequencing. Based on a pairwise t-test and OPLS-DA analysis, diallyl sulfide, (z)-1-allyl-2-(prop-1-en-1-yl) disulfane, and terpineol were considered to be the main components responsible for the unpleasant flavor of PF paocai. Yarrowia spp., Enterobacter spp., and Pichia spp. were the main pellicle-forming microorganisms. All 17 isolated Enterobacter strains showed pectinase-producing and cellulase-producing abilities, and 3 isolated Pichia strains showed gas-producing capacity. According to LEfSe analysis based on metagenomes, unclassified_g__Citrobacter and Yarrowia lipolytica were the uppermost biomarkers that distinguished the PF paocai from normal paocai. Unclassified_g__Lactobacillus and Lactobacillus plantarum were found to be actively engaged in starch and sucrose metabolism, cysteine and methionine metabolism, galactose metabolism, fructose and mannose metabolism, lysine biosynthesis, fatty acid biosynthesis, and arginine biosynthesis, all of which contributed to the flavor formation of paocai. Combining the results of metagenome sequencing with the data obtained based on the culture-dependent method, we could deduce that the growth of Yarrowia lipolytica first promoted the increase of pH and the formation of pellicle, which provided a suitable niche for the growth of some harmful bacteria such as Enterobacter, Citrobacter, and Serratia. These hazardous bacteria then worked in concert to induce the odorous stench and texture softening of paocai, as well as more pellicle formation.}, } @article {pmid36688869, year = {2023}, author = {Fontana, F and Longhi, G and Alessandri, G and Lugli, GA and Mancabelli, L and Tarracchini, C and Viappiani, A and Anzalone, R and Ventura, M and Turroni, F and Milani, C}, title = {Multifactorial Microvariability of the Italian Raw Milk Cheese Microbiota and Implication for Current Regulatory Scheme.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0106822}, pmid = {36688869}, issn = {2379-5077}, mesh = {Animals ; *Cheese/analysis ; Milk/chemistry ; *Microbiota/genetics ; Food Handling/methods ; Whey Proteins/analysis ; Italy ; }, abstract = {Raw milk cheese manufactory is strictly regulated in Europe by the Protected Designation of Origin (PDO) quality scheme, which protects indigenous food products based on geographical and biotechnological features. This study encompassed the collection of 128 raw milk cheese samples across Italy to investigate the resident microbiome correlated to current PDO specifications. Shotgun metagenomic approaches highlighted how the microbial communities are primarily linked to each cheesemaking site and consequently to the use of site-specific Natural Whey Cultures (NWCs), defined by a multifactorial set of local environmental factors rather than solely by cheese type or geographical origin that guide the current PDO specification. Moreover, in-depth functional characterization of Cheese Community State Types (CCSTs) and comparative genomics efforts, including metagenomically assembled genomes (MAGs) of the dominant microbial taxa, revealed NWCs-related unique enzymatic profiles impacting the organoleptic features of the produced cheeses and availability of bioactive compounds to consumers, with putative health implications. Thus, these results highlighted the need for a profound rethinking of the current PDO designation with a focus on the production site-specific microbial metabolism to understand and guarantee the organoleptic features of the final product recognized as PDO. IMPORTANCE The Protected Designation of Origin (PDO) guarantees the traceability of food production processes, and that the production takes place in a well-defined restricted geographical area. Nevertheless, the organoleptic qualities of the same dairy products, i.e., cheeses under the same PDO denomination, differ between manufacturers. The final product's flavor and qualitative aspects can be related to the resident microbial population, not considered by the PDO denomination. Here, we analyzed a complete set of different Italian cheeses produced from raw milk through shotgun sequencing in order to study the variability of the different microbial profiles resident in Italian PDO cheeses. Furthermore, an in-depth functional analysis, along with a comparative genomic analysis, was performed in order to correlate the taxonomic information with the organoleptic properties of the final product. This analysis made it possible to highlight how the PDO denomination should be revisited to understand the effect that Natural Whey Cultures (NWCs), used in the traditional production of raw milk cheese and unique to each manufacturer, impacts on the organoleptic features of the final product.}, } @article {pmid36688698, year = {2023}, author = {Busi, SB and de Nies, L and Pramateftaki, P and Bourquin, M and Kohler, TJ and Ezzat, L and Fodelianakis, S and Michoud, G and Peter, H and Styllas, M and Tolosano, M and De Staercke, V and Schön, M and Galata, V and Wilmes, P and Battin, T}, title = {Glacier-Fed Stream Biofilms Harbor Diverse Resistomes and Biosynthetic Gene Clusters.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0406922}, pmid = {36688698}, issn = {2165-0497}, mesh = {Humans ; *Rivers/microbiology ; Ice Cover ; Bacteria/genetics ; *Microbiota ; Multigene Family ; Biofilms ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antimicrobial resistance (AMR) is a universal phenomenon the origins of which lay in natural ecological interactions such as competition within niches, within and between micro- to higher-order organisms. To study these phenomena, it is crucial to examine the origins of AMR in pristine environments, i.e., limited anthropogenic influences. In this context, epilithic biofilms residing in glacier-fed streams (GFSs) are an excellent model system to study diverse, intra- and inter-domain, ecological crosstalk. We assessed the resistomes of epilithic biofilms from GFSs across the Southern Alps (New Zealand) and the Caucasus (Russia) and observed that both bacteria and eukaryotes encoded twenty-nine distinct AMR categories. Of these, beta-lactam, aminoglycoside, and multidrug resistance were both abundant and taxonomically distributed in most of the bacterial and eukaryotic phyla. AMR-encoding phyla included Bacteroidota and Proteobacteria among the bacteria, alongside Ochrophyta (algae) among the eukaryotes. Additionally, biosynthetic gene clusters (BGCs) involved in the production of antibacterial compounds were identified across all phyla in the epilithic biofilms. Furthermore, we found that several bacterial genera (Flavobacterium, Polaromonas, Superphylum Patescibacteria) encode both atimicrobial resistance genes (ARGs) and BGCs within close proximity of each other, demonstrating their capacity to simultaneously influence and compete within the microbial community. Our findings help unravel how naturally occurring BGCs and AMR contribute to the epilithic biofilms mode of life in GFSs. Additionally, we report that eukaryotes may serve as AMR reservoirs owing to their potential for encoding ARGs. Importantly, these observations may be generalizable and potentially extended to other environments that may be more or less impacted by human activity. IMPORTANCE Antimicrobial resistance is an omnipresent phenomenon in the anthropogenically influenced ecosystems. However, its role in shaping microbial community dynamics in pristine environments is relatively unknown. Using metagenomics, we report the presence of antimicrobial resistance genes and their associated pathways in epilithic biofilms within glacier-fed streams. Importantly, we observe biosynthetic gene clusters associated with antimicrobial resistance in both pro- and eukaryotes in these biofilms. Understanding the role of resistance in the context of this pristine environment and complex biodiversity may shed light on previously uncharacterized mechanisms of cross-domain interactions.}, } @article {pmid36688679, year = {2023}, author = {Chen, Y and Shen, X and Ma, T and Yu, X and Kwok, LY and Li, Y and Sun, Z and Li, D and Zhang, H}, title = {Adjunctive Probio-X Treatment Enhances the Therapeutic Effect of a Conventional Drug in Managing Type 2 Diabetes Mellitus by Promoting Short-Chain Fatty Acid-Producing Bacteria and Bile Acid Pathways.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0130022}, pmid = {36688679}, issn = {2379-5077}, mesh = {Humans ; *Diabetes Mellitus, Type 2/drug therapy ; Bile Acids and Salts/therapeutic use ; *Metformin/therapeutic use ; Fatty Acids, Volatile/therapeutic use ; Bacteria ; }, abstract = {Metformin is a common drug for the management of type 2 diabetes mellitus; however, it causes various adverse gastrointestinal effects, especially after prolonged treatment. It is thus of interest to identify an adjuvant treatment that synergizes with the efficacy of metformin while mitigating its adverse effects. Since previous evidence supports that the gut microbiota is a target of metformin, this study investigated the beneficial effect and mechanism of the coadministration of probiotics with metformin in the management of type 2 diabetes mellitus by conducting a 3-month randomized, double-blind, placebo-controlled clinical trial (n = 27 and 21 in the probiotic and placebo groups, respectively, who completed the trial). Clinical results showed that the coadministration of probiotics with metformin significantly reduced glycated hemoglobin compared with metformin taken alone (P < 0.05). Metagenomic and metabolomic analyses showed that the coadministration of probiotics increased the abundance of gut short-chain fatty acid (SCFA)-producing bacteria and bile acids. Significantly or marginally more bile acids and related metabolites were detected in the probiotic group than in the placebo group postintervention. Taken together, the results of our study showed that the coadministration of probiotics with metformin synergized with the hypoglycemic effect in patients with type 2 diabetes mellitus, which was likely through modulating the gut microbiome and, subsequently, SCFA and bile acid metabolism. Our findings support that cotreatment with probiotics and metformin is beneficial to patients with type 2 diabetes mellitus. IMPORTANCE Metformin causes variable adverse gastrointestinal effects, especially after prolonged treatment. We found that cotreatment with Probio-X and metformin for the management of type 2 diabetes mellitus may promote gut SCFA-producing bacteria and the levels of specific bile acids, thus increasing the secretion of related gastrointestinal hormones and ultimately improving glucose homeostasis.}, } @article {pmid36688647, year = {2023}, author = {DeMers, M and Graham, ED and Heidelberg, JF and Webb, EA}, title = {Metagenome-Assembled Genome of a Novel Cyclobacteriaceae Epibiont of a Heterotrophic Diazotroph.}, journal = {Microbiology resource announcements}, volume = {12}, number = {2}, pages = {e0059422}, pmid = {36688647}, issn = {2576-098X}, abstract = {Here, we describe the metagenome-assembled genome (MAG) HetDA_MAG_SS2, in the family Cyclobacteriaceae. It was found in association with a HetDA cyanobiont isolated from a Station ALOHA Trichodesmium colony. Annotation suggests that HetDA_MAG_SS2 is a chemoorganoheterotroph with the potential for lithoheterotrophy, containing genes for aerobic respiration, mixed acid fermentation, dissimilatory nitrate reduction to ammonium, and sulfide oxidation.}, } @article {pmid36688360, year = {2023}, author = {Koh, C and Frangeul, L and Blanc, H and Ngoagouni, C and Boyer, S and Dussart, P and Grau, N and Girod, R and Duchemin, JB and Saleh, MC}, title = {Ribosomal RNA (rRNA) sequences from 33 globally distributed mosquito species for improved metagenomics and species identification.}, journal = {eLife}, volume = {12}, number = {}, pages = {}, pmid = {36688360}, issn = {2050-084X}, mesh = {Animals ; RNA, Ribosomal, 18S/genetics ; Phylogeny ; *Metagenomics ; Mosquito Vectors/genetics ; RNA, Ribosomal, 28S/genetics ; *Culicidae/genetics ; }, abstract = {Total RNA sequencing (RNA-seq) is an important tool in the study of mosquitoes and the RNA viruses they vector as it allows assessment of both host and viral RNA in specimens. However, there are two main constraints. First, as with many other species, abundant mosquito ribosomal RNA (rRNA) serves as the predominant template from which sequences are generated, meaning that the desired host and viral templates are sequenced far less. Second, mosquito specimens captured in the field must be correctly identified, in some cases to the sub-species level. Here, we generate mosquito rRNA datasets which will substantially mitigate both of these problems. We describe a strategy to assemble novel rRNA sequences from mosquito specimens and produce an unprecedented dataset of 234 full-length 28S and 18S rRNA sequences of 33 medically important species from countries with known histories of mosquito-borne virus circulation (Cambodia, the Central African Republic, Madagascar, and French Guiana). These sequences will allow both physical and computational removal of rRNA from specimens during RNA-seq protocols. We also assess the utility of rRNA sequences for molecular taxonomy and compare phylogenies constructed using rRNA sequences versus those created using the gold standard for molecular species identification of specimens-the mitochondrial cytochrome c oxidase I (COI) gene. We find that rRNA- and COI-derived phylogenetic trees are incongruent and that 28S and concatenated 28S+18S rRNA phylogenies reflect evolutionary relationships that are more aligned with contemporary mosquito systematics. This significant expansion to the current rRNA reference library for mosquitoes will improve mosquito RNA-seq metagenomics by permitting the optimization of species-specific rRNA depletion protocols for a broader range of species and streamlining species identification by rRNA sequence and phylogenetics.}, } @article {pmid36687728, year = {2022}, author = {Moser, B and Moore, D and Khadka, B and Lyons, C and Foxall, T and Andam, CP and Parker, CJ and Ochin, C and Garelnabi, M and Sevigny, J and Thomas, WK and Bigornia, S and Dao, MC}, title = {Association between inflammation, lipopolysaccharide binding protein, and gut microbiota composition in a New Hampshire Bhutanese refugee population with a high burden of type 2 diabetes.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {1059163}, pmid = {36687728}, issn = {2296-861X}, support = {P20 GM113131/GM/NIGMS NIH HHS/United States ; }, abstract = {INTRODUCTION: South Asian refugees experience a high risk of obesity and diabetes yet are often underrepresented in studies on chronic diseases and their risk factors. The gut microbiota and gut permeability, as assessed through circulating lipopolysaccharide binding protein (LBP), may underlie the link between chronic inflammation and type 2 diabetes (T2D). The composition of the gut microbiota varies according to multiple factors including demographics, migration, and dietary patterns, particularly fiber intake. However, there is no evidence on the composition of the gut microbiota and its relationship with metabolic health in refugee populations, including those migrating to the United States from Bhutan. The objective of this study was to examine glycemic status in relation to LBP, systemic inflammation fiber intake, and gut microbiota composition in Bhutanese refugee adults residing in New Hampshire (n = 50).

METHODS: This cross-sectional study included a convenience sample of Bhutanese refugee adults (N = 50) in NH. Established bioinformatics pipelines for metagenomic analysis were used to determine relative genus abundance, species richness, and alpha diversity measures from shallow shotgun sequences. The relationships between inflammatory markers, gut microbiota composition, dietary fiber, and glycemic status were analyzed.

RESULTS: We identified a substantial chronic disease burden in this study population, and observed a correlation between glycemic status, LBP, and inflammation, and a correlation between glycemic status and gut microbiome alpha diversity. Further, we identified a significant correlation between proinflammatory taxa and inflammatory cytokines. SCFA-producing taxa were found to be inversely correlated with age.

CONCLUSION: To date, this is the most comprehensive examination of metabolic health and the gut microbiome in a Bhutanese refugee population in NH. The findings highlight areas for future investigations of inflammation and glycemic impairment, in addition to informing potential interventions targeting this vulnerable population.}, } @article {pmid36687661, year = {2022}, author = {Gattoni, G and de la Haba, RR and Martín, J and Reyes, F and Sánchez-Porro, C and Feola, A and Zuchegna, C and Guerrero-Flores, S and Varcamonti, M and Ricca, E and Selem-Mojica, N and Ventosa, A and Corral, P}, title = {Genomic study and lipidomic bioassay of Leeuwenhoekiella parthenopeia: A novel rare biosphere marine bacterium that inhibits tumor cell viability.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1090197}, pmid = {36687661}, issn = {1664-302X}, abstract = {The fraction of low-abundance microbiota in the marine environment is a promising target for discovering new bioactive molecules with pharmaceutical applications. Phenomena in the ocean such as diel vertical migration (DVM) and seasonal dynamic events influence the pattern of diversity of marine bacteria, conditioning the probability of isolation of uncultured bacteria. In this study, we report a new marine bacterium belonging to the rare biosphere, Leeuwenhoekiella parthenopeia sp. nov. Mr9[T], which was isolated employing seasonal and diel sampling approaches. Its complete characterization, ecology, biosynthetic gene profiling of the whole genus Leeuwenhoekiella, and bioactivity of its extract on human cells are reported. The phylogenomic and microbial diversity studies demonstrated that this bacterium is a new and rare species, barely representing 0.0029% of the bacterial community in Mediterranean Sea metagenomes. The biosynthetic profiling of species of the genus Leeuwenhoekiella showed nine functionally related gene cluster families (GCF), none were associated with pathways responsible to produce known compounds or registered patents, therefore revealing its potential to synthesize novel bioactive compounds. In vitro screenings of L. parthenopeia Mr9[T] showed that the total lipid content (lipidome) of the cell membrane reduces the prostatic and brain tumor cell viability with a lower effect on normal cells. The lipidome consisted of sulfobacin A, WB 3559A, WB 3559B, docosenamide, topostin B-567, and unknown compounds. Therefore, the bioactivity could be attributed to any of these individual compounds or due to their synergistic effect. Beyond the rarity and biosynthetic potential of this bacterium, the importance and novelty of this study is the employment of sampling strategies based on ecological factors to reach the hidden microbiota, as well as the use of bacterial membrane constituents as potential novel therapeutics. Our findings open new perspectives on cultivation and the relationship between bacterial biological membrane components and their bioactivity in eukaryotic cells, encouraging similar studies in other members of the rare biosphere.}, } @article {pmid36687660, year = {2022}, author = {Ariaeenejad, S and Motamedi, E and Kavousi, K and Ghasemitabesh, R and Goudarzi, R and Salekdeh, GH and Zolfaghari, B and Roy, S}, title = {Enhancing the ethanol production by exploiting a novel metagenomic-derived bifunctional xylanase/β-glucosidase enzyme with improved β-glucosidase activity by a nanocellulose carrier.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1056364}, pmid = {36687660}, issn = {1664-302X}, abstract = {Some enzymes can catalyze more than one chemical conversion for which they are physiologically specialized. This secondary function, which is called underground, promiscuous, metabolism, or cross activity, is recognized as a valuable feature and has received much attention for developing new catalytic functions in industrial applications. In this study, a novel bifunctional xylanase/β-glucosidase metagenomic-derived enzyme, PersiBGLXyn1, with underground β-glucosidase activity was mined by in-silico screening. Then, the corresponding gene was cloned, expressed and purified. The PersiBGLXyn1 improved the degradation efficiency of organic solvent pretreated coffee residue waste (CRW), and subsequently the production of bioethanol during a separate enzymatic hydrolysis and fermentation (SHF) process. After characterization, the enzyme was immobilized on a nanocellulose (NC) carrier generated from sugar beet pulp (SBP), which remarkably improved the underground activity of the enzyme up to four-fold at 80°C and up to two-fold at pH 4.0 compared to the free one. The immobilized PersiBGLXyn1 demonstrated 12 to 13-fold rise in half-life at 70 and 80°C for its underground activity. The amount of reducing sugar produced from enzymatic saccharification of the CRW was also enhanced from 12.97 g/l to 19.69 g/l by immobilization of the enzyme. Bioethanol production was 29.31 g/l for free enzyme after 72 h fermentation, while the immobilized PersiBGLXyn1 showed 51.47 g/l production titre. Overall, this study presented a cost-effective in-silico metagenomic approach to identify novel bifunctional xylanase/β-glucosidase enzyme with underground β-glucosidase activity. It also demonstrated the improved efficacy of the underground activities of the bifunctional enzyme as a promising alternative for fermentable sugars production and subsequent value-added products.}, } @article {pmid36687649, year = {2022}, author = {Xi, M and Na, X and Ma, X and Lan, H and Sun, T and Liu, WH and Hung, W and Zhao, A}, title = {Maternal diet associated with infants' intestinal microbiota mediated by predominant long-chain fatty acid in breast milk.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1004175}, pmid = {36687649}, issn = {1664-302X}, abstract = {INTRODUCTION: Long-chain fatty acids in breast milk are affected by the mother's diet and play an important role in the growth, development, and immune construction of infants. This study aims to explore the correlation between maternal diet, breast milk fatty acids (FAs), and the infant intestinal flora.

METHODS: We enrolled 56 paired mothers and their infants; both breast milk samples and infants' fecal samples were collected to determine the long-chain FA content of breast milk by ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS), and metagenomic technology was applied to determine the microbial composition of infant feces. The maternal diet was also investigated using a 24-h dietary recall.

RESULTS: The results indicated that the fat contribution rates of edible oils in the maternal diet are significantly positively correlated with the contents of certain long-chain fatty acids (C16:0, C18:1, C16:1, and C22:4) in breast milk, which mainly regulate the abundance of Lacticaseibacillus rhamnosus, Lacticaseibacillus fermentum, and Lacticaseibacillus paracasei in the infant gut. Through KEGG pathway analysis, our data revealed that the long-chain FAs in different groups of breast milk were significantly correlated with the pathways of biotin metabolism, glycerolipid metabolism, and starch and sucrose metabolism.

DISCUSSION: The results of this study suggest a pathway in which the diets of lactating mothers may affect the composition of the infant intestinal microbiota by influencing breast milk FAs and then further regulating infant health.}, } @article {pmid36687623, year = {2022}, author = {Wang, H and Yan, W and Luo, J and Zeng, X and Zhao, Z and Dou, X and Fu, M}, title = {Fosthiazate inhibits root-knot disease and alters rhizosphere microbiome of Cucumis melo var. saccharinus.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1084010}, pmid = {36687623}, issn = {1664-302X}, abstract = {Root-knot nematodes especially Meloidogyne spp. are considered as most destructive obligate parasites that substantially reduce crop yield and quality. Fosthiazate is an efficient organothiophosphate chemical with nematicidal activity against Meloidogyne spp. The present study aimed to analyze the efficacy of fosthiazate against root-knot disease in Cucumis melo var. saccharinus and its potential effects on rhizosphere microbiome and metabolites. The fosthiazate (40%) was applied two times by spraying on the day of transplanting and during the pollination period (after 31 days). Samples from treatment (fosthiazate 40%: MF) and control groups (untreated plants; MCK) were analysed through metagenomic and metabolomic profiling of rhizospheres. Results revealed that root-knot index of the MF group (9.26 ± 1.28) was significantly (p < 0.05) lower than the MCK group (22.06 ± 0.71) with a control effect of 57.85% after 31 days of the first spray, whereas fosthiazate efficacy reduced to 31.87% after 38 days of second application with significantly (p < 0.05) different root-knot index values (MF: 56 ± 1.43 and; MCK: 82.26 ± 3.87). However, Cucumis melo var. saccharinus fruit yield in both groups (MCK: 21.1 ± 0.9 and MF: 21.53 ± 0.85) showed no differences (p > 0.05). Metagenomic profiling revealed Proteobacteria, Acidobacteriota, and Firmicutes as predominant phyla and Bacillus, Sphingomonas, and Acidibacter as predominant genera in rhizosphere soil samples of both MF and MCK groups. Further, a t-test revealed higher differential enrichment of Firmicutes at phylum level and Bacillus at genus level in MF than MCK. Metabolomic profiling of rhizospheric soil revealed a total of six differential metabolites (p < 0.05), four of them (Sucrose, Hexaonic acid 1, (Z)-9-Octadecenamide 1, and Hexadecanamide) were up-regulated in MF group, whereas two of them (2,3,4-Trihydroxy-3-(Hydroxymethyl) Butanol and Sulfurous acid, 2, ethylhexylundecyl ester) were down-regulated in CK group. Our study concluded that fosthiazate exhibits a better control over the rook-knot disease in the short term and resulted in trackable changes in rhizosphere microbiome and metabolome.}, } @article {pmid36687609, year = {2022}, author = {Malacrinò, A and Abdelfattah, A and Belgacem, I and Schena, L}, title = {Plant genotype influence the structure of cereal seed fungal microbiome.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1075399}, pmid = {36687609}, issn = {1664-302X}, abstract = {Plant genotype is a crucial factor for the assembly of the plant-associated microbial communities. However, we still know little about the variation of diversity and structure of plant microbiomes across host species and genotypes. Here, we used six species of cereals (Avena sativa, Hordeum vulgare, Secale cereale, Triticum aestivum, Triticum polonicum, and Triticum turgidum) to test whether the plant fungal microbiome varies across species, and whether plant species use different mechanisms for microbiome assembly focusing on the plant ears. Using ITS2 amplicon metagenomics, we found that host species influences the diversity and structure of the seed-associated fungal communities. Then, we tested whether plant genotype influences the structure of seed fungal communities across different cultivars of T. aestivum (Aristato, Bologna, Rosia, and Vernia) and T. turgidum (Capeiti, Cappelli, Mazzancoio, Trinakria, and Timilia). We found that cultivar influences the seed fungal microbiome in both species. We found that in T. aestivum the seed fungal microbiota is more influenced by stochastic processes, while in T. turgidum selection plays a major role. Collectively, our results contribute to fill the knowledge gap on the wheat seed microbiome assembly and, together with other studies, might contribute to understand how we can manipulate this process to improve agriculture sustainability.}, } @article {pmid36687589, year = {2022}, author = {Hu, H and Wang, L and Zhao, Q}, title = {Editorial: Molecular insight of chronic infections.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1112456}, pmid = {36687589}, issn = {1664-302X}, } @article {pmid36687577, year = {2022}, author = {Feng, G and Zeng, Y and Wang, HZ and Chen, YT and Tang, YQ}, title = {Proteiniphilum and Methanothrix harundinacea became dominant acetate utilizers in a methanogenic reactor operated under strong ammonia stress.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1098814}, pmid = {36687577}, issn = {1664-302X}, abstract = {Microorganisms in anaerobic digestion (AD) are easily affected by ammonia, especially acetoclastic methanogens. Thus, in ammonia-suppressed AD systems, acetate degradation is reported to be carried out mainly by the cooperation of syntrophic acetate oxidizers and hydrogenotrophic methanogens. Previous studies have revealed ammonia inhibition on microbial flora by AD performance, but the effect mechanism of ammonia on microbial metabolism remains poorly understood. In this study, we constructed a mesophilic chemostat fed with acetate as the sole carbon source, gradually increased the total ammonia nitrogen (TAN) concentration from 1 g L[-1] to 6 g L[-1], and employed the 16S rRNA gene, metagenomics, and metatranscriptomics analysis to characterize the microbial community structure and metabolic behavior. The results showed that even at the TAN of 6 g L[-1] (pH 7.5), the methanogenesis kept normal, the biogas production was approximately 92% of that at TAN of 1 g L[-1] and the acetate degradation ratio reached 99%, suggesting the strong TAN tolerance of the microbial community enriched. 16S rRNA gene analysis suggested that the microbial community structure changed along with the TAN concentration. Methanothrix predominated in methanogens all the time, in which the dominant species was gradually replaced from M. soehngenii to M. harundinacea with the increased TAN. Dominant bacterial species also changed and Proteiniphilum showed a significant positive correlation with increased TAN. Meta-omics analysis showed that the absolute dominant microorganisms at TAN of 6 g L[-1] were M. harundinacea and Proteiniphilum, both of which highly expressed genes for anti-oxidative stress. M. harundinacea and the second dominant methanogen Methanosarcina highly expressed both acetate cleavage and CO2 reduction pathways, suggesting the possibility that these two pathways contributed to methanogenesis together. Proteiniphilum and some other species in Firmicutes and Synergistetes were likely acetate oxidizers in the community as they highly expressed genes for syntrophic acetate oxidization, H2 generation, and electron transfer. These results suggested that Proteiniphilum as well as M. harundinacea have strong ammonia tolerance and played critical roles in acetate degradation under ammonia-suppressed conditions. The achievements of the study would contribute to the regulation and management of the AD process.}, } @article {pmid36687564, year = {2022}, author = {Ahmadi, A and Khezri, A and Nørstebø, H and Ahmad, R}, title = {A culture-, amplification-independent, and rapid method for identification of pathogens and antibiotic resistance profile in bovine mastitis milk.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1104701}, pmid = {36687564}, issn = {1664-302X}, abstract = {INTRODUCTION: Rapid and accurate diagnosis of causative pathogens in mastitis would minimize the imprudent use of antibiotics and, therefore, reduce the spread of antimicrobial resistance. Whole genome sequencing offers a unique opportunity to study the microbial community and antimicrobial resistance (AMR) in mastitis. However, the complexity of milk samples and the presence of a high amount of host DNA in milk from infected udders often make this very challenging.

METHODS: Here, we tested 24 bovine milk samples (18 mastitis and six non-mastitis) using four different commercial kits (Qiagens' DNeasy[®] PowerFood[®] Microbial, Norgens' Milk Bacterial DNA Isolation, and Molzyms' MolYsis™ Plus and Complete5) in combination with filtration, low-speed centrifugation, nuclease, and 10% bile extract of male bovine (Ox bile). Isolated DNA was quantified, checked for the presence/absence of host and pathogen using PCR and sequenced using MinION nanopore sequencing. Bioinformatics analysis was performed for taxonomic classification and antimicrobial resistance gene detection.

RESULTS: The results showed that kits designed explicitly for bacterial DNA isolation from food and dairy matrices could not deplete/minimize host DNA. Following using MolYsis™ Complete 5 + 10% Ox bile + micrococcal nuclease combination, on average, 17% and 66.5% of reads were classified as bovine and Staphylococcus aureus reads, respectively. This combination also effectively enriched other mastitis pathogens, including Escherichia coli and Streptococcus dysgalactiae. Furthermore, using this approach, we identified important AMR genes such as Tet (A), Tet (38), fosB-Saur, and blaZ. We showed that even 40 min of the MinION run was enough for bacterial identification and detecting the first AMR gene.

CONCLUSION: We implemented an effective method (sensitivity of 100% and specificity of 92.3%) for host DNA removal and bacterial DNA enrichment (both gram-negative and positive) directly from bovine mastitis milk. To the best of our knowledge, this is the first culture- and amplification-independent study using nanopore-based metagenomic sequencing for real-time detection of the pathogen (within 5 hours) and the AMR profile (within 5-9 hours), in mastitis milk samples. These results provide a promising and potential future on-farm adaptable approach for better clinical management of mastitis.}, } @article {pmid36686268, year = {2022}, author = {Zuo, S and Wang, H and Zhao, Q and Tang, J and Wang, M and Zhang, Y and Sang, M and Tian, J and Wang, P}, title = {High levels of Bifidobacteriaceae are associated with the pathogenesis of Parkinson's disease.}, journal = {Frontiers in integrative neuroscience}, volume = {16}, number = {}, pages = {1054627}, pmid = {36686268}, issn = {1662-5145}, abstract = {BACKGROUND: The diagnosis of Parkinson's disease (PD) is complex and there are no biomarkers for early identification. Many studies have reported altered gut microbiota in patients with PD compared with healthy individuals. However, results from previous studies vary across countries.

AIMS: The aim of this study was to identify gut microbiota biomarkers that could be used as a marker for the diagnosis of PD.

METHODS: Firstly, the differential gut microbiota was obtained by meta-analysis, and then the results of meta-analysis were validated through metagenomic cohort. Finally, the ROC curve was drawn based on the metagenomic validation results.

RESULTS: The meta-analysis showed a lower relative abundance of Prevotellaceae (p < 0.00001) and Lachnospiraceae (p = 0.002), and a higher of Ruminococcaceae (p < 0.00001), Christensenellaceae (p = 0.03), Bifidobacteriaceae (p < 0.00001), and Verrucomicrobiaceae (p = 0.02) in patients with PD. Only Bifidobacteriaceae was also at high levels in the validation cohort of the metagenome. Meanwhile, three species from the Bifidobacteriaceae, including Scardovia_inopinata (p = 0.022), Bifidobacterium_dentium (p = 0.005), and Scardovia_wiggsiae (p = 0.024) were also high. The ROC curve showed that the three species (71.2%) from Bifidobacteriaceae had good predictive efficiency for PD.

CONCLUSION: Elevated Bifidobacteriaceae may be associated with PD. Elevated three species from the Bifidobacteriaceae, including Scardovia_inopinata, Bifidobacterium_dentium and Scardovia_wiggsiae may provide new potential biomarkers for the diagnosis of PD.}, } @article {pmid36686014, year = {2022}, author = {Brzychcy, K and Dróżdż, I and Skoczylas, S and Płoszaj, T and Sobolewska-Sztychny, D and Skibińska, M and Narbutt, J and Lesiak, A}, title = {Gut microbiota in alopecia areata.}, journal = {Postepy dermatologii i alergologii}, volume = {39}, number = {6}, pages = {1162-1170}, pmid = {36686014}, issn = {1642-395X}, abstract = {INTRODUCTION: In the past few years, the advancement of 16S rRNA metagenomic analysis sequencing has enabled assessing the impact of gut microbiota on the development of skin disease. Alopecia areata (AA) is a nonscarring hair loss disorder with an unknown etiopathogenesis, however, it is hypothesised that a combination of genetic and environmental factors might be involved. Although numerous studies have shown that the microbiome plays a key role at the beginning of skin diseases, the link between AA and gut dysbiosis remains unclear.

AIM: To analyse the intestinal microbiome in patients suffering from AA.

MATERIAL AND METHODS: The study describes the conceivable involvement of gut microbiota in the unclear pathogenesis of AA. We enrolled 25 patients, over 18 years of age with an active state of AA who donated their stool samples. The samples were examined at the human gut microbial community at the species level by metataxonomic analysis of the full-length 16S V3-V4 sequencing.

RESULTS: The four major genera that constitute the microbiome's core are Lachnoclostridium, Bifidobacterium, Streptococcus, and Eubacterium, as well as three major phyla: Firmicutes, Proteobacteria, and Actinobacteria. Firmicutes and Proteobacteria are overrepresented in the microflora, which might suggest a disturbed microflora. Furthermore, the composition of bacterial communities suggests a loss of overall richness and a decrease in taxonomic diversity across all samples.

CONCLUSIONS: This study describes, for the first time, the characteristics of the gut microbiome in AA patients and may provide new insight into the gut microbiome that may play a role in the development of AA.}, } @article {pmid36685570, year = {2022}, author = {Shirane, M and Yawata, N and Motooka, D and Shibata, K and Khor, SS and Omae, Y and Kaburaki, T and Yanai, R and Mashimo, H and Yamana, S and Ito, T and Hayashida, A and Mori, Y and Numata, A and Murakami, Y and Fujiwara, K and Ohguro, N and Hosogai, M and Akiyama, M and Hasegawa, E and Paley, M and Takeda, A and Maenaka, K and Akashi, K and Yokoyama, WM and Tokunaga, K and Yawata, M and Sonoda, KH}, title = {Corrigendum: Intraocular human cytomegaloviruses of ocular diseases are distinct from those of viremia and are capable of escaping from innate and adaptive immunity by exploiting HLA-E-mediated peripheral and central tolerance.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1124440}, doi = {10.3389/fimmu.2022.1124440}, pmid = {36685570}, issn = {1664-3224}, abstract = {[This corrects the article DOI: 10.3389/fimmu.2022.1008220.].}, } @article {pmid36685560, year = {2022}, author = {Liu, X and He, G and Lan, Y and Guo, W and Liu, X and Li, J and Liu, A and He, M and Liu, X and Fan, Z and Zhang, Y}, title = {Virome and metagenomic analysis reveal the distinct distribution of microbiota in human fetal gut during gestation.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1079294}, pmid = {36685560}, issn = {1664-3224}, mesh = {Adult ; Humans ; Pregnancy ; Female ; Virome ; *Microbiota ; Bacteria/genetics ; Metagenome ; *Viruses/genetics ; Fetus ; }, abstract = {Studies have shown that fetal immune cell activation may result from potential exposure to microbes, although the presence of microbes in fetus has been a controversial topic. Here, we combined metagenomic and virome techniques to investigate the presence of bacteria and viruses in fetal tissues (small intestine, cecum, and rectum). We found that the fetal gut is not a sterile environment and has a low abundance but metabolically rich microbiome. Specifically, Proteobacteria and Actinobacteria were the dominant bacteria phyla of fetal gut. In total, 700 species viruses were detected, and Human betaherpesvirus 5 was the most abundant eukaryotic viruses. Especially, we first identified Methanobrevibacter smithii in fetal gut. Through the comparison with adults' gut microbiota we found that Firmicutes and Bacteroidetes gradually became the main force of gut microbiota during the process of growth and development. Interestingly, 6 antibiotic resistance genes were shared by the fetus and adults. Our results indicate the presence of microbes in the fetal gut and demonstrate the diversity of bacteria, archaea and viruses, which provide support for the studies related to early fetal immunity. This study further explores the specific composition of viruses in the fetal gut and the similarities between fetal and adults' gut microbiota, which is valuable for understanding human fetal immunity development during gestation.}, } @article {pmid36685457, year = {2023}, author = {Zhang, D and Wang, Y and Chen, X and He, Y and Zhao, M and Lu, X and Lu, J and Ji, L and Shen, Q and Wang, X and Yang, S and Zhang, W}, title = {Diversity of viral communities in faecal samples of farmed red foxes.}, journal = {Heliyon}, volume = {9}, number = {1}, pages = {e12826}, pmid = {36685457}, issn = {2405-8440}, abstract = {Emerging and existing viruses from various human and animal samples have been studied and analyzed using viral metagenomics, which has proven to be an effective technique. Foxes, as a kind of significant economic animal, are widely raised in China. Viruses carried by foxes may potentially infect humans or other animals. There are currently very few studies of faecal virome in farmed foxes. Using viral metagenomics, we evaluated the faecal virome of twenty-four foxes collected from the same farm in Jilin Province, China. Some sequences more closely related to the families Parvoviridae, Picornaviridae, Smacoviridae, Anelloviridae, and Herpesviridae were detected in the faecal sample. The main animal viruses that infect farmed red foxes were parvovirus and picornavirus. Five smacovirus strains were found and provided evidence for genetic diversity in the genus Smacoviridae. In addition, some viruses infecting avian species or rats were detected in this study. The study helped us better understand faecal virome in farmed red foxes and assisted in the surveillance and prevention of viral diseases in these animals.}, } @article {pmid36685424, year = {2023}, author = {Yang, WJ and Chen, ZH and Zheng, YN}, title = {Valproic acid induced aplastic crisis and Stevens-Johnson syndrome in a single pediatric patient.}, journal = {Heliyon}, volume = {9}, number = {1}, pages = {e12461}, pmid = {36685424}, issn = {2405-8440}, abstract = {Valproic acid (VPA) is a commonly used antiepileptic drug (AED). Aplastic crisis is defined as acute arrest of hematopoiesis. Stevens-Johnson syndrome (SJS) is a fatal cutaneous adverse drug reaction. We herein report a rare case of aplastic crisis and SJS in a single pediatric patient that were probably caused by VPA. A 2-year-old girl was involved in a car accident. She was diagnosed with skull fractures, cerebral contusions, pulmonary contusions, and fractures of the left iliac bone by computed tomography. VPA was administered as prophylaxis for post-traumatic epilepsy. From day 13, she developed repeated high fevers, and multiple antibiotics were ineffective; she was then transferred to our pediatric intensive care unit. After transfer, she developed liver function impairment, decreased peripheral blood cell counts, and skin damage. After withdrawal of the VPA and administration of prednisone, intravenous immunoglobulin, local skin care, and nutritional support, her body temperature normalized and her hematopoietic function and skin lesions successively resolved. She was transferred out of the pediatric intensive care unit on day 56 and discharged on day 70. At the 6-month follow-up, a blood examination was normal, and repeat computed tomography revealed multiple softening foci of the bilateral brain and less subdural effusion than before. To our knowledge, no report to date has described aplastic crisis and SJS in a single patient. The purpose of this paper is to increase clinicians' knowledge in the treatment of adverse drug reactions (ADRs) and emphasize the importance of standardized application and strict monitoring of VPA in patients with post-traumatic brain trauma.}, } @article {pmid36685333, year = {2022}, author = {Player, RA and Aguinaldo, AM and Merritt, BB and Maszkiewicz, LN and Adeyemo, OE and Forsyth, ER and Verratti, KJ and Chee, BW and Grady, SL and Bradburne, CE}, title = {The META tool optimizes metagenomic analyses across sequencing platforms and classifiers.}, journal = {Frontiers in bioinformatics}, volume = {2}, number = {}, pages = {969247}, pmid = {36685333}, issn = {2673-7647}, abstract = {A major challenge in the field of metagenomics is the selection of the correct combination of sequencing platform and downstream metagenomic analysis algorithm, or "classifier". Here, we present the Metagenomic Evaluation Tool Analyzer (META), which produces simulated data and facilitates platform and algorithm selection for any given metagenomic use case. META-generated in silico read data are modular, scalable, and reflect user-defined community profiles, while the downstream analysis is done using a variety of metagenomic classifiers. Reported results include information on resource utilization, time-to-answer, and performance. Real-world data can also be analyzed using selected classifiers and results benchmarked against simulations. To test the utility of the META software, simulated data was compared to real-world viral and bacterial metagenomic samples run on four different sequencers and analyzed using 12 metagenomic classifiers. Lastly, we introduce "META Score": a unified, quantitative value which rates an analytic classifier's ability to both identify and count taxa in a representative sample.}, } @article {pmid36684597, year = {2022}, author = {Zhuang, H and Xiang, K and Gong, S and Zhou, Y and Chen, J}, title = {Cerebral aspergillosis after heart-lung transplantation in a child: Case report with 3-year follow-up and literature review.}, journal = {Frontiers in cardiovascular medicine}, volume = {9}, number = {}, pages = {1042631}, pmid = {36684597}, issn = {2297-055X}, abstract = {There are limited cases of heart-lung transplantation (HLT) in children worldwide owing to lack of donors, demanding surgical teamwork, and arduous post-operative management. Post-transplant management difficulties stem from the possible development of several post-operative complications, with infection being a common complication. Intracranial fungal infections are difficult to diagnose and prone to treatment delays because of their relatively insidious onset and atypical clinical presentation. Here, we present a case of a cerebral infection developed 3 months after HLT in a 10-year-old child, showing no positive results on conventional imaging or cerebrospinal fluid (CSF) examination and culture. On metagenomic next-generation sequencing of the cerebrospinal fluid, the causative organism was finally determined as Aspergillus. After administering 1-year anti-Aspergillus treatment, no recurrence of intracranial fungal infection was noted during the 3-year follow-up. This case illustrates the multifaceted diagnostic techniques for cerebral aspergillosis after HLT and shows the significance of dynamic monitoring of symptoms, such as headache, and of metagenomic sequencing results, trends in intracranial pressure and (1-3)-β-D-glucan levels for guiding diagnosis and treatment.}, } @article {pmid36684137, year = {2022}, author = {Su, X and Chen, L and Zhuang, Z and Zhang, Y and Lin, X and Huang, J and Zhu, Z and Zhang, H and Wu, W}, title = {Large mediastinal mass diagnosed as Nocardia infection by endobronchial ultrasound-guided transbronchial needle aspiration in a ceramic worker: A case report.}, journal = {Frontiers in surgery}, volume = {9}, number = {}, pages = {983074}, pmid = {36684137}, issn = {2296-875X}, abstract = {BACKGROUND: Nocardia is a ubiquitous soil saprophyte transmitted through airborne or direct cutaneous inoculation routes. Although Nocardia is more common in immunocompromised patients, Nocardia may also arise in apparently immunocompetent patients.

CASE PRESENTATION: We report a rare case of Nocardia infection presenting as a large mediastinal mass in an immunocompetent ceramic worker. A 54-year-old man with no previous history of immune dysfunction, a ceramic worker by profession, was referred and admitted to our hospital because of a persistent fever for 19 days. Chest CT showed a large middle mediastinal mass. However, conventional anti-infective treatment was ineffective. Under the guidance of the Virtual bronchoscopic navigation (VBN) system, he underwent Endobronchial ultrasound-guided transbronchial needle aspiration (EBUS-TBNA). The purulent exudate obtained by EBUS-TBNA was further identified as Nocardia by weak acid-fast and metagenomic next-generation sequencing (mNGS). He was subsequently treated with intravenous imipenem/amikacin, switched to intravenous imipenem and oral trimethoprim/sulfamethoxazole, and the clinical symptoms were significantly improved.

CONCLUSIONS: Even in immunocompetent patients, Nocardiosis cannot be excluded. For the public, especially soil contact workers, precautions should be taken to avoid Nocardia infection from occupational exposure. This rare case may provide a diagnosis and treatment reference for clinicians.}, } @article {pmid36683960, year = {2023}, author = {Li, Y and Deng, X and Zhang, N and Shen, Z and Li, R and Shen, Q and Salles, JF}, title = {Rhizosphere suppression hinders antibiotic resistance gene (ARG) spread under bacterial invasion.}, journal = {One health (Amsterdam, Netherlands)}, volume = {16}, number = {}, pages = {100481}, pmid = {36683960}, issn = {2352-7714}, abstract = {The rhizosphere is an extremely important component of the "one health" scenario by linking the soil microbiome and plants, in which the potential enrichment of antibiotic resistance genes (ARGs) might ultimately flow into the human food chain. Despite the increased occurrence of soil-borne diseases, which can lead to increased use of pesticides and antibiotic-producing biocontrol agents, the understanding of the dynamics of ARG spread in the rhizosphere is largely overlooked. Here, tomato seedlings grown in soils conducive and suppressive to the pathogen Ralstonia solanacearum were selected as a model to investigate ARG spread in the rhizosphere with and without pathogen invasion. Metagenomics data revealed that R. solanacearum invasion increased the density of ARGs and mobile genetic elements (MGEs). Although we found ARGs originating from human pathogenic bacteria in both soils, the enrichment was alleviated in the suppressive soil. In summary, the suppressive soil hindered ARG spread through pathogen suppression and had a lower number of taxa carrying antibiotic resistance.}, } @article {pmid36683820, year = {2022}, author = {Liu, L and Zheng, W and Wang, P and Wu, Y and Zhu, G and Yang, R and Gu, L and Huang, W and Kang, Y}, title = {Case Report: Successful treatment of severe pneumocystis carinii pneumonia in a case series of primary nephrotic syndrome after receiving anti-CD20 monoclonal antibody therapy.}, journal = {Frontiers in pediatrics}, volume = {10}, number = {}, pages = {1067634}, pmid = {36683820}, issn = {2296-2360}, abstract = {Rituximab is emerging as a new steroid sparing agent in children with difficult-to-treat nephrotic syndrome due to its ability of depleting CD20-positive B cells. Life-threatening adverse events such as pneumocystis carinii pneumonia may occur even though it seems to be well tolerated. Since rituximab is wildly used in immune-mediated diseases, it is important to manage its severe adverse events. To explore the importance of early diagnosis and treatment of pneumocystis carinii pneumonia in children with primary nephrotic syndrome (PNS) after receiving rituximab therapy, we retrospectively analyzed the clinical data of PNS patients younger than 18 years old with pneumocystis carinii pneumonia who were hospitalized in our center. Clinical features and laboratory test results were retrieved from the electronic medical records. Severe pneumocystis carinii pneumonia occurred in one child with steroid resistant nephrotic syndrome and two with steroid dependent nephrotic syndrome patients after rituximab treatment. These patients were diagnosed in time by metagenomic next-generation sequencing (mNGS) for pathogen detection. Fortunately, all three patients survived after antifungal treatment and achieved complete remission eventually. In conclusion, early diagnosis by using mNGS and timely antifungal treatment is the key to successful management of pneumocystis carinii pneumonia in children with difficult-to-treat PNS.}, } @article {pmid36683707, year = {2022}, author = {Chen, Q and Fan, Y and Zhang, B and Yan, C and Chen, Z and Wang, L and Hu, Y and Huang, Q and Su, J and Ren, J and Xu, H}, title = {Specific fungi associated with response to capsulized fecal microbiota transplantation in patients with active ulcerative colitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1086885}, pmid = {36683707}, issn = {2235-2988}, mesh = {Humans ; *Colitis, Ulcerative/therapy ; *Fecal Microbiota Transplantation/adverse effects ; Feces/microbiology ; Fungi/genetics ; Remission Induction ; Treatment Outcome ; }, abstract = {OBJECTIVE: Fecal microbiota transplantation (FMT) is a novel microbial treatment for patients with ulcerative colitis (UC). In this study, we performed a clinical trial of capsulized FMT in UC patients to determine the association between the gut fungal community and capsulized FMT outcomes.

DESIGN: This study recruited patients with active UC (N = 22) and healthy individuals (donor, N = 9) according to the criteria. The patients received capsulized FMT three times a week. Patient stool samples were collected before (week 0) and after FMT follow-up visits at weeks 1, 4, and 12. Fungal communities were analysed using shotgun metagenomic sequencing.

RESULTS: According to metagenomic analysis, fungal community evenness index was greater in samples collected from patients, and the overall fungal community was clustered among the samples collected from donors. The dominant fungi in fecal samples collected from donors and patients were Ascomycota and Basidiomycota. However, capsulized FMT ameliorated microbial fungal diversity and altered fungal composition, based on metagenomic analysis of fecal samples collected before and during follow-up visits after capsulized FMT. Fungal diversity decreased in samples collected from patients who achieved remission after capsulized FMT, similar to samples collected from donors. Patients achieving remission after capsulized FMT had specific enrichment of Kazachstania naganishii, Pyricularia grisea, Lachancea thermotolerans, and Schizosaccharomyces pombe compared with patients who did not achieve remission. In addition, the relative abundance of P. grisea was higher in remission fecal samples during the follow-up visit. Meanwhile, decreased levels of pathobionts, such as Candida and Debaryomyces hansenii, were associated with remission in patients receiving capsulized FMT.

CONCLUSION: In the metagenomic analysis of fecal samples from donors and patients with UC receiving capsulized FMT, shifts in gut fungal diversity and composition were associated with capsulized FMT and validated in patients with active UC. We also identified the specific fungi associated with the induction of remission. ClinicalTrails.gov (NCT03426683).}, } @article {pmid36683362, year = {2022}, author = {Tandon, K and Ricci, F and Costa, J and Medina, M and Kühl, M and Blackall, LL and Verbruggen, H}, title = {Genomic view of the diversity and functional role of archaea and bacteria in the skeleton of the reef-building corals Porites lutea and Isopora palifera.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {36683362}, issn = {2047-217X}, support = {DP200101613//Australian Research Council/ ; //University of Melbourne/ ; GBMF9206//Gordon and Betty Moore Foundation/ ; }, mesh = {Animals ; *Anthozoa/genetics ; Archaea/genetics ; Coral Reefs ; Bacteria/genetics ; Metagenome ; Genomics ; }, abstract = {At present, our knowledge on the compartmentalization of coral holobiont microbiomes is highly skewed toward the millimeter-thin coral tissue, leaving the diverse coral skeleton microbiome underexplored. Here, we present a genome-centric view of the skeleton of the reef-building corals Porites lutea and Isopora palifera, through a compendium of ∼400 high-quality bacterial and archaeal metagenome-assembled genomes (MAGs), spanning 34 phyla and 57 classes. Skeletal microbiomes harbored a diverse array of stress response genes, including dimethylsulfoniopropionate synthesis (dsyB) and metabolism (DMSP lyase). Furthermore, skeletal MAGs encoded an average of 22 ± 15 genes in P. lutea and 28 ± 23 in I. palifera with eukaryotic-like motifs thought to be involved in maintaining host association. We provide comprehensive insights into the putative functional role of the skeletal microbiome on key metabolic processes such as nitrogen fixation, dissimilatory and assimilatory nitrate, and sulfate reduction. Our study provides critical genomic resources for a better understanding of the coral skeletal microbiome and its role in holobiont functioning.}, } @article {pmid36683075, year = {2023}, author = {Turner, D and Shkoporov, AN and Lood, C and Millard, AD and Dutilh, BE and Alfenas-Zerbini, P and van Zyl, LJ and Aziz, RK and Oksanen, HM and Poranen, MM and Kropinski, AM and Barylski, J and Brister, JR and Chanisvili, N and Edwards, RA and Enault, F and Gillis, A and Knezevic, P and Krupovic, M and Kurtböke, I and Kushkina, A and Lavigne, R and Lehman, S and Lobocka, M and Moraru, C and Moreno Switt, A and Morozova, V and Nakavuma, J and Reyes Muñoz, A and Rūmnieks, J and Sarkar, BL and Sullivan, MB and Uchiyama, J and Wittmann, J and Yigang, T and Adriaenssens, EM}, title = {Abolishment of morphology-based taxa and change to binomial species names: 2022 taxonomy update of the ICTV bacterial viruses subcommittee.}, journal = {Archives of virology}, volume = {168}, number = {2}, pages = {74}, pmid = {36683075}, issn = {1432-8798}, support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; RC2 DK116713/DK/NIDDK NIH HHS/United States ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 220646/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; RC2DK116713/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Bacteriophages ; *Viruses/genetics ; *Caudovirales ; Myoviridae ; *Siphoviridae ; }, abstract = {This article summarises the activities of the Bacterial Viruses Subcommittee of the International Committee on Taxonomy of Viruses for the period of March 2021-March 2022. We provide an overview of the new taxa proposed in 2021, approved by the Executive Committee, and ratified by vote in 2022. Significant changes to the taxonomy of bacterial viruses were introduced: the paraphyletic morphological families Podoviridae, Siphoviridae, and Myoviridae as well as the order Caudovirales were abolished, and a binomial system of nomenclature for species was established. In addition, one order, 22 families, 30 subfamilies, 321 genera, and 862 species were newly created, promoted, or moved.}, } @article {pmid36682619, year = {2023}, author = {Rather, RA and Ara, S and Padder, SA and Sharma, S and Pathak, SP and Baba, TR}, title = {Seasonal fluctuation of water quality and ecogenomic phylogeny of novel potential microbial pollution indicators of Veshaw River Kashmir-Western Himalaya.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {320}, number = {}, pages = {121104}, doi = {10.1016/j.envpol.2023.121104}, pmid = {36682619}, issn = {1873-6424}, mesh = {Humans ; *Water Quality ; Seasons ; Environmental Monitoring ; Escherichia coli ; *Drinking Water ; Phylogeny ; Water Pollution/analysis ; Gram-Negative Bacteria ; Water Microbiology ; }, abstract = {Nearly a billion people, especially in underdeveloped nations, need safe drinking water. Indian studies suggest that most drinking water sources have high coliform levels, and quality assurance is required. This study was conducted in rural parts of South Kashmir in the Western Himalaya from February 2019 to January 2020. Standard river water sampling was done from upstream to downstream of the river. This study examined the detection, molecular identification, and chemical water quality of coliform-contaminated drinking water, which sums up river water pollution. Water quality varied significantly, indicating downstream contamination. Sangam (downstream) had the highest coliform count, showing 72.2600 cfu per litre in summer, while Kongwaton (upstream), near the Veshaw River, had no coliform count in winter. In summer, Sangam (downstream) had the highest water quality metrics (pH 6.847, Electrical conductivity (EC) 71.620 dS/m, Biological oxygen demand (BOD) 1.120 mg/L, and Chemical oxygen demand (COD) 24.637 mg/L) in all seasons. The lowest winter water quality metrics in Kongwaton were pH 8.947, EC 253.680 dS/m, BOD 4.963 mg/L, and COD 51.440 mg/L. Coliforms in water suggest faecal contamination. This study examines the water quality attributes of drinking water and associated factors to determine river pollution. Total DNA was collected and sequenced for 16 S rDNA and metagenomics. Universal primers were used to amplify the bacterial 16 S rRNA. Using BLAST, the amplified 16 S rRNA gene sequence was matched to the NCBI database. A metagenomic study revealed 27 species with different relative abundance. These species include Escherichia coli, E. fergusonii, E. albertii, Klebsiella grimontii, and Shigella dysenteriae. This study is thought to be the first to discriminate against E. fergusonii, E. albertii, K. grimontii, and S. dysenteriae from E. coli and to report on E. fergusonii and E. albertii, K. grimontii, and S. dysenteriae in the river Veshaw water sources in Kulgam, Western Himalaya.}, } @article {pmid36682238, year = {2023}, author = {Zhu, L and Yuan, L and Shuai, XY and Lin, ZJ and Sun, YJ and Zhou, ZC and Meng, LX and Ju, F and Chen, H}, title = {Deciphering basic and key traits of antibiotic resistome in influent and effluent of hospital wastewater treatment systems.}, journal = {Water research}, volume = {231}, number = {}, pages = {119614}, doi = {10.1016/j.watres.2023.119614}, pmid = {36682238}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents/pharmacology ; Wastewater ; Genes, Bacterial ; *Water Purification ; Hospitals ; }, abstract = {Hospital wastewater treatment system (HWTS) is an important source and environmental reservoir of clinically relevant antibiotic resistance genes (ARGs). However, how antibiotic resistome of clinical wastewater changed in HWTS is poorly understood. Herein, the basic quantitative traits (i.e., diversity and abundance) of ARGs in three HWTSs were profiled by metagenomics. In total, 709 ARG subtypes belonging to 20 ARG types were detected with relative abundance ranging from 1.12 × 10[-5] to 7.33 × 10[-1] copies/cell. Notably, most ARGs could not be significantly removed by chlorination treatment in the HWTS. These ARGs were identified to confer resistance to almost all major classes of antibiotics and include ARGs of last-resort antibiotics, such as blaNDM, mcr and tet(X) which were abundantly occurred in HWTS with 19, 5 and 7 variants, respectively. Moreover, qualitative analysis based on metagenome-assembled genome (MAG) analysis revealed that the putative hosts of the identified ARGs were broadly distributed into at least 8 dominant bacterial phyla. Of the 107 ARG-carrying MAGs recovered, 39 encoded multi-antibiotic resistance and 16 belonged to antibiotic resistant pathogens. Further analysis of co-occurrence patterns of ARGs with mobile genetic elements suggested their potential mobility. These key qualitative traits of ARGs provided further information about their phylogeny and genetic context. This study sheds light on the key traits of ARGs associated with resistance dissemination and pathogenicity and health risks of clinical wastewater.}, } @article {pmid36681756, year = {2023}, author = {Hahn, A and Burrell, A and Chaney, H and Sami, I and Koumbourlis, AC and Freishtat, RJ and Crandall, KA and Zemanick, ET}, title = {Therapeutic beta-lactam dosages and broad-spectrum antibiotics are associated with reductions in microbial richness and diversity in persons with cystic fibrosis.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {1217}, pmid = {36681756}, issn = {2045-2322}, mesh = {Child ; Humans ; Adolescent ; *Cystic Fibrosis/complications ; Anti-Bacterial Agents/pharmacology/therapeutic use ; beta-Lactams/therapeutic use ; Lung ; *Anti-Infective Agents/therapeutic use ; }, abstract = {Persons with cystic fibrosis (PwCF) suffer from pulmonary exacerbations (PEx) related in part to lung infection. While higher microbial diversity is associated with higher lung function, the data on the impact of short-term antibiotics on changes in microbial diversity is conflicting. Further, Prevotella secretes beta-lactamases, which may influence recovery of lung function. We hypothesize that sub-therapeutic and broad spectrum antibiotic exposure leads to decreasing microbial diversity. Our secondary aim was to evaluate the concerted association of beta-lactam pharmacokinetics (PK), antibiotic spectrum, microbial diversity, and antibiotic resistance on lung function recovery using a pathway analysis. This was a retrospective observational study of persons with CF treated with IV antibiotics for PEx between 2016 and 2020 at Children's National Hospital; respiratory samples and clinical information were collected at hospital admission for PEx (E), end of antibiotic treatment (T), and follow-up (F). Metagenomic sequencing was performed; PathoScope 2.0 and AmrPlusPlus were used for taxonomic assignment of sequences to bacteria and antibiotic resistance genes (ARGs). M/W Pharm was used for PK modeling. Comparison of categorical and continuous variables and pathway analysis were performed in STATA. Twenty-two PwCF experienced 43 PEx. The study cohort had a mean age of 14.6 years. Only 12/43 beta-lactam courses had therapeutic PK, and 18/43 were broad spectrum. A larger decrease in richness between E and T was seen in the therapeutic PK group (sufficient - 20.1 vs. insufficient - 1.59, p = 0.025) and those receiving broad spectrum antibiotics (broad - 14.5 vs. narrow - 2.8, p = 0.030). We did not detect differences in the increase in percent predicted forced expiratory volume in one second (ppFEV1) at end of treatment compared to PEx based on beta-lactam PK (sufficient 13.6% vs. insufficient 15.1%) or antibiotic spectrum (broad 11.5% vs. narrow 16.6%). While both therapeutic beta-lactam PK and broad-spectrum antibiotics decreased richness between PEx and the end of treatment, we did not detect longstanding changes in alpha diversity or an association with superior recovery of lung function compared with subtherapeutic PK and narrow spectrum antimicrobials.}, } @article {pmid36681701, year = {2023}, author = {Ezzamouri, B and Rosario, D and Bidkhori, G and Lee, S and Uhlen, M and Shoaie, S}, title = {Metabolic modelling of the human gut microbiome in type 2 diabetes patients in response to metformin treatment.}, journal = {NPJ systems biology and applications}, volume = {9}, number = {1}, pages = {2}, pmid = {36681701}, issn = {2056-7189}, support = {EP/S001301/1//RCUK | Engineering and Physical Sciences Research Council (EPSRC)/ ; }, mesh = {Humans ; *Metformin/pharmacology/therapeutic use ; *Diabetes Mellitus, Type 2/drug therapy/metabolism/microbiology ; *Gastrointestinal Microbiome/genetics ; Hypoglycemic Agents/pharmacology/therapeutic use ; Diet ; Bacteria ; }, abstract = {The human gut microbiome has been associated with several metabolic disorders including type 2 diabetes mellitus. Understanding metabolic changes in the gut microbiome is important to elucidate the role of gut bacteria in regulating host metabolism. Here, we used available metagenomics data from a metformin study, together with genome-scale metabolic modelling of the key bacteria in individual and community-level to investigate the mechanistic role of the gut microbiome in response to metformin. Individual modelling predicted that species that are increased after metformin treatment have higher growth rates in comparison to species that are decreased after metformin treatment. Gut microbial enrichment analysis showed prior to metformin treatment pathways related to the hypoglycemic effect were enriched. Our observations highlight how the key bacterial species after metformin treatment have commensal and competing behavior, and how their cellular metabolism changes due to different nutritional environment. Integrating different diets showed there were specific microbial alterations between different diets. These results show the importance of the nutritional environment and how dietary guidelines may improve drug efficiency through the gut microbiota.}, } @article {pmid36681395, year = {2023}, author = {Chen, C and Liu, Y and Tian, H and Ai, L and Yu, H}, title = {Corrigendum to "Metagenomic analysis reveals the impact of JIUYAO microbial diversity on fermentation and the volatile profile of Shaoxing-jiu" [Food Microbiol. 86 (2020) 103326].}, journal = {Food microbiology}, volume = {111}, number = {}, pages = {104205}, doi = {10.1016/j.fm.2022.104205}, pmid = {36681395}, issn = {1095-9998}, } @article {pmid36681377, year = {2023}, author = {Kang, X and Lü, F and Wang, Y and Duan, H and Zhang, H and He, P}, title = {Metagenomic analysis of microbiological risk in bioaerosols during biowaste valorization using Musca domestica.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {320}, number = {}, pages = {121118}, doi = {10.1016/j.envpol.2023.121118}, pmid = {36681377}, issn = {1873-6424}, mesh = {Animals ; *Genes, Bacterial ; *Houseflies/genetics ; Metagenome ; Anti-Bacterial Agents ; Bacteria/genetics ; Metagenomics/methods ; }, abstract = {Bioconversion using insects has gradually become a promising technology for biowaste management and protein production. However, knowledge about microbiological risk of insect related bioaerosols is sparse and conventional methods failed to provide higher resolved information of environmental microbe. In this study, a metagenomic analysis including microorganisms, antibiotic resistance genes (ARGs), virulence factor genes (VFGs), mobile gene elements (MGEs), and endotoxin distribution in bioaerosols during biowaste conversion via Musca domestica revealed that bioaerosols in Fly rearing room possess the highest ARGs abundances and MGEs diversity. Through a metagenome-assembled genomes (MAGs)-based pipeline, compelling evidence of ARGs/VFGs host assignment and ARG-VFG co-occurrence pattern were provided from metagenomic perspective. Bioaerosols in Bioconversion and Maggot separation zone were identified to own high density of MAGs carrying both ARGs and VFGs. Bacteria in Proteobacteria, Actinobacteriota, and Firmicutes phyla were predominate hosts of ARGs and VFGs. Multidrug-Motility, Multidrug-Adherence, and Beta lactam-Motility pairs were the most common ARG-VFG co-occurrence pattern in this study. Results obtained are of great significance for microbiological risk assessment during housefly biowaste conversion process.}, } @article {pmid36680804, year = {2023}, author = {Gao, FZ and He, LY and Bai, H and He, LX and Zhang, M and Chen, ZY and Liu, YS and Ying, GG}, title = {Airborne bacterial community and antibiotic resistome in the swine farming environment: Metagenomic insights into livestock relevance, pathogen hosts and public risks.}, journal = {Environment international}, volume = {172}, number = {}, pages = {107751}, doi = {10.1016/j.envint.2023.107751}, pmid = {36680804}, issn = {1873-6750}, mesh = {Swine ; Humans ; Animals ; *Anti-Bacterial Agents/pharmacology ; Farms ; *Livestock/genetics ; Genes, Bacterial ; Metagenome ; Bacteria/genetics ; Agriculture ; Drug Resistance, Bacterial/genetics ; }, abstract = {Globally extensive use of antibiotics has accelerated antimicrobial resistance (AMR) in the environment. As one of the biggest antibiotic consumers, livestock farms are hotspots in AMR prevalence, especially those in the atmosphere can transmit over long distances and pose inhalation risks to the public. Here, we collected total suspended particulates in swine farms and ambient air of an intensive swine farming area. Bacterial communities and antibiotic resistomes were analyzed using amplicon and metagenomic sequencing approaches. AMR risks and inhalation exposure to potential human-pathogenic antibiotic-resistant bacteria (HPARB) were subsequently estimated with comparison to the reported hospital samples. The results show that swine farms shaped the airborne bacterial community by increasing abundances, reducing diversities and shifting compositions. Swine feces contributed 77% of bacteria to swine farm air, and about 35% to ambient air. Airborne antibiotic resistomes in swine farms mainly conferred resistance to tetracyclines, aminoglycosides and lincosamides, and over 48% were originated from swine feces. Distinct to the hospital air, Firmicutes were dominant bacteria in swine farming environments with conditional pathogens including Clostridium, Streptococcus and Aerococcus being major hosts of antibiotic resistance genes (ARGs). Therein, genomes of S. alactolyticus carrying (transposase/recombinase-associated) ARGs and virulence factor genes were retrieved from the metagenomes of all swine feces and swine farm air samples, but they were not detected in any hospital air samples. This suggests the indication of S. alactolyticus in swine farming environments with potential hazards to human health. Swine farm air faced higher AMR risks than hospital air and swine feces. The inhalation intake of HPARB by a swine farm worker was about three orders of magnitude higher than a person who works in the hospital. Consequently, this study depicted atmospheric transmission of bacteria and antibiotic resistomes from swine feces to the environment.}, } @article {pmid36680718, year = {2023}, author = {Vijayan, J and Nathan, VK and Ammini, P and Ammanamveetil, AMH}, title = {Bacterial diversity in the aquatic system in India based on metagenome analysis-a critical review.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {11}, pages = {28383-28406}, pmid = {36680718}, issn = {1614-7499}, support = {BL/20-21/0310//DSKPDF-UGC/ ; }, mesh = {*Ecosystem ; *Metagenome ; Bacteria/genetics/metabolism ; Metagenomics/methods ; India ; }, abstract = {Microbial analysis has become one of the most critical areas in aquatic ecology and a crucial component for assessing the contribution of microbes in food web dynamics and biogeochemical processes. Initial research was focused on estimating the abundance and distribution of the microbes using microscopy and culture-based analysis, which are undoubtedly complex tasks. Over the past few decades, microbiologists have endeavored to apply and extend molecular techniques to address pertinent questions related to the function and metabolism of microbes in aquatic ecology. Metagenomics analysis has revolutionized aquatic ecology studies involving the investigation of the genome of a mixed community of organisms in an ecosystem to identify microorganisms, their functionality, and the discovery of novel proteins. This review discusses the metagenomics analysis of bacterial diversity in and around different aquatic systems in India.}, } @article {pmid36680277, year = {2023}, author = {Santiago-Rodriguez, TM and Hollister, EB}, title = {Viral Metagenomics as a Tool to Track Sources of Fecal Contamination: A One Health Approach.}, journal = {Viruses}, volume = {15}, number = {1}, pages = {}, pmid = {36680277}, issn = {1999-4915}, mesh = {Animals ; Humans ; *Water Pollution/analysis ; Metagenomics ; *One Health ; Fresh Water ; Soil ; Feces ; }, abstract = {The One Health framework recognizes that human, animal, and environmental health are linked and highly interdependent. Fecal contamination of water, soil, foodstuff, and air may impact many aspects of One Health, and culture, PCR-based, and sequencing methods are utilized in the detection of fecal contamination to determine source, load, and risk to inform targeted mitigation strategies. Viruses, particularly, have been considered as fecal contamination indicators given the narrow host range many exhibit and their association with other biological contaminants. Culture- and molecular-based methods are considered the gold-standards for virus detection and for determining specific sources of fecal contamination via viral indicators. However, viral metagenomics is also being considered as a tool for tracking sources of fecal contamination. In the present review, studies tracking potential sources of fecal contamination in freshwaters, marine waters, foodstuff, soil, and air using viral metagenomics are discussed to highlight the potential of viral metagenomics for optimizing fecal source tracking. Limitations of the use of viral metagenomics to track fecal contamination sources, including sample processing, nucleic acid recovery, sequencing depth, and bioinformatics are also discussed. Finally, the present review discusses the potential of viral metagenomics as part of the toolbox of methods in a One Health approach.}, } @article {pmid36680256, year = {2023}, author = {Pchelin, IM and Tkachev, PV and Azarov, DV and Gorshkov, AN and Drachko, DO and Zlatogursky, VV and Dmitriev, AV and Goncharov, AE}, title = {A Genome of Temperate Enterococcus Bacteriophage Placed in a Space of Pooled Viral Dark Matter Sequences.}, journal = {Viruses}, volume = {15}, number = {1}, pages = {}, pmid = {36680256}, issn = {1999-4915}, mesh = {Humans ; *Bacteriophages ; Enterococcus/genetics ; Genome, Viral ; Sequence Analysis, DNA ; Phylogeny ; Myoviridae/genetics ; }, abstract = {In the human gut, temperate bacteriophages interact with bacteria through predation and horizontal gene transfer. Relying on taxonomic data, metagenomic studies have associated shifts in phage abundance with a number of human diseases. The temperate bacteriophage VEsP-1 with siphovirus morphology was isolated from a sample of river water using Enterococcus faecalis as a host. Starting from the whole genome sequence of VEsP-1, we retrieved related phage genomes in blastp searches of the tail protein and large terminase sequences, and blastn searches of the whole genome sequences, with matches compiled from several different databases, and visualized a part of viral dark matter sequence space. The genome network and phylogenomic analyses resulted in the proposal of a novel genus "Vespunovirus", consisting of temperate, mainly metagenomic phages infecting Enterococcus spp.}, } @article {pmid36680214, year = {2023}, author = {Jansen, D and Matthijnssens, J}, title = {The Emerging Role of the Gut Virome in Health and Inflammatory Bowel Disease: Challenges, Covariates and a Viral Imbalance.}, journal = {Viruses}, volume = {15}, number = {1}, pages = {}, pmid = {36680214}, issn = {1999-4915}, mesh = {Humans ; Virome ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases ; *Bacteriophages ; *Microviridae ; Metagenomics ; }, abstract = {Virome research is a rapidly growing area in the microbiome field that is increasingly associated with human diseases, such as inflammatory bowel disease (IBD). Although substantial progress has been made, major methodological challenges limit our understanding of the virota. In this review, we describe challenges that must be considered to accurately report the virome composition and the current knowledge on the virome in health and IBD. First, the description of the virome shows strong methodological biases related to wetlab (e.g., VLP enrichment) and bioinformatics approaches (viral identification and classification). Second, IBD patients show consistent viral imbalances characterized by a high relative abundance of phages belonging to the Caudovirales and a low relative abundance of phages belonging to the Microviridae. Simultaneously, a sporadic contraction of CrAss-like phages and a potential expansion of the lysogenic potential of the intestinal virome are observed. Finally, despite numerous studies that have conducted diversity analysis, it is difficult to draw firm conclusions due to methodological biases. Overall, we present the many methodological and environmental factors that influence the virome, its current consensus in health and IBD, and a contributing hypothesis called the "positive inflammatory feedback loop" that may play a role in the pathophysiology of IBD.}, } @article {pmid36680116, year = {2022}, author = {Andrianjakarivony, HF and Bettarel, Y and Armougom, F and Desnues, C}, title = {Phage-Host Prediction Using a Computational Tool Coupled with 16S rRNA Gene Amplicon Sequencing.}, journal = {Viruses}, volume = {15}, number = {1}, pages = {}, pmid = {36680116}, issn = {1999-4915}, mesh = {*Bacteria/genetics/virology ; *Bacteriophages/genetics ; Cote d'Ivoire ; Genes, rRNA ; Metagenomics/methods ; Reproducibility of Results ; RNA, Ribosomal, 16S/genetics ; Water ; }, abstract = {Metagenomics studies have revealed tremendous viral diversity in aquatic environments. Yet, while the genomic data they have provided is extensive, it is unannotated. For example, most phage sequences lack accurate information about their bacterial host, which prevents reliable phage identification and the investigation of phage-host interactions. This study aimed to take this knowledge further, using a viral metagenomic framework to decipher the composition and diversity of phage communities and to predict their bacterial hosts. To this end, we used water and sediment samples collected from seven sites with varying contamination levels in the Ebrié Lagoon in Abidjan, Ivory Coast. The bacterial communities were characterized using the 16S rRNA metabarcoding approach, and a framework was developed to investigate the virome datasets that: (1) identified phage contigs with VirSorter and VIBRANT; (2) classified these contigs with MetaPhinder using the phage database (taxonomic annotation); and (3) predicted the phages' bacterial hosts with a machine learning-based tool: the Prokaryotic Virus-Host Predictor. The findings showed that the taxonomic profiles of phages and bacteria were specific to sediment or water samples. Phage sequences assigned to the Microviridae family were widespread in sediment samples, whereas phage sequences assigned to the Siphoviridae, Myoviridae and Podoviridae families were predominant in water samples. In terms of bacterial communities, the phyla Latescibacteria, Zixibacteria, Bacteroidetes, Acidobacteria, Calditrichaeota, Gemmatimonadetes, Cyanobacteria and Patescibacteria were most widespread in sediment samples, while the phyla Epsilonbacteraeota, Tenericutes, Margulisbacteria, Proteobacteria, Actinobacteria, Planctomycetes and Marinimicrobia were most prevalent in water samples. Significantly, the relative abundance of bacterial communities (at major phylum level) estimated by 16S rRNA metabarcoding and phage-host prediction were significantly similar. These results demonstrate the reliability of this novel approach for predicting the bacterial hosts of phages from shotgun metagenomic sequencing data.}, } @article {pmid36680094, year = {2022}, author = {Zhang, F and Gia, A and Chen, G and Gong, L and Behary, J and Hold, GL and Zekry, A and Tang, X and Sun, Y and El-Omar, E and Jiang, XT}, title = {Critical Assessment of Whole Genome and Viral Enrichment Shotgun Metagenome on the Characterization of Stool Total Virome in Hepatocellular Carcinoma Patients.}, journal = {Viruses}, volume = {15}, number = {1}, pages = {}, pmid = {36680094}, issn = {1999-4915}, mesh = {Humans ; Metagenome ; *Carcinoma, Hepatocellular/genetics ; Virome ; Ecosystem ; *Liver Neoplasms/genetics ; *Viruses/genetics ; Metagenomics/methods ; Genome, Viral ; }, abstract = {Viruses are the most abundant form of life on earth and play important roles in a broad range of ecosystems. Currently, two methods, whole genome shotgun metagenome (WGSM) and viral-like particle enriched metagenome (VLPM) sequencing, are widely applied to compare viruses in various environments. However, there is no critical assessment of their performance in recovering viruses and biological interpretation in comparative viral metagenomic studies. To fill this gap, we applied the two methods to investigate the stool virome in hepatocellular carcinoma (HCC) patients and healthy controls. Both WGSM and VLPM methods can capture the major diversity patterns of alpha and beta diversities and identify the altered viral profiles in the HCC stool samples compared with healthy controls. Viral signatures identified by both methods showed reductions of Faecalibacterium virus Taranis in HCC patients' stool. Ultra-deep sequencing recovered more viruses in both methods, however, generally, 3 or 5 Gb were sufficient to capture the non-fragmented long viral contigs. More lytic viruses were detected than lysogenetic viruses in both methods, and the VLPM can detect the RNA viruses. Using both methods would identify shared and specific viral signatures and would capture different parts of the total virome.}, } @article {pmid36680080, year = {2022}, author = {Shen-Gunther, J and Cai, H and Wang, Y}, title = {A Customized Monkeypox Virus Genomic Database (MPXV DB v1.0) for Rapid Sequence Analysis and Phylogenomic Discoveries in CLC Microbial Genomics.}, journal = {Viruses}, volume = {15}, number = {1}, pages = {}, pmid = {36680080}, issn = {1999-4915}, mesh = {Humans ; *Monkeypox virus/genetics ; Phylogeny ; *Mpox (monkeypox) ; High-Throughput Nucleotide Sequencing ; Genomics ; }, abstract = {Monkeypox has been a neglected, zoonotic tropical disease for over 50 years. Since the 2022 global outbreak, hundreds of human clinical samples have been subjected to next-generation sequencing (NGS) worldwide with raw data deposited in public repositories. However, sequence analysis for in-depth investigation of viral evolution remains hindered by the lack of a curated, whole genome Monkeypox virus (MPXV) database (DB) and efficient bioinformatics pipelines. To address this, we developed a customized MPXV DB for integration with "ready-to-use" workflows in the CLC Microbial Genomics Module for whole genomic and metagenomic analysis. After database construction (218 MPXV genomes), whole genome alignment, pairwise comparison, and evolutionary analysis of all genomes were analyzed to autogenerate tabular outputs and visual displays (collective runtime: 16 min). The clinical utility of the MPXV DB was demonstrated by using a Chimpanzee fecal, hybrid-capture NGS dataset (publicly available) for metagenomic, phylogenomic, and viral/host integration analysis. The clinically relevant MPXV DB embedded in CLC workflows proved to be a rapid method of sequence analysis useful for phylogenomic exploration and a wide range of applications in translational science.}, } @article {pmid36680008, year = {2023}, author = {Umair, M and Haider, SA and Rehman, Z and Jamal, Z and Ali, Q and Hakim, R and Bibi, S and Ikram, A and Salman, M}, title = {Genomic Characterization of Dengue Virus Outbreak in 2022 from Pakistan.}, journal = {Vaccines}, volume = {11}, number = {1}, pages = {}, pmid = {36680008}, issn = {2076-393X}, abstract = {Pakistan, a dengue-endemic country, has encountered several outbreaks during the past decade. The current study aimed to explore the serotype and genomic diversity of dengue virus responsible for the 2022 outbreak in Pakistan. From August to October 2022, NS-1 positive blood samples (n = 343) were collected from dengue patients, among which, (85%; n = 293) were positive based on RT-PCR. In terms of gender and age, dengue infection was more prevalent in male patients (63%; n = 184), with more adults (21-30 years; n = 94) being infected. The serotyping results revealed DENV-2 to be the most predominant serotype (62%; n = 183), followed by DENV-1 (37%; n = 109) and DENV-3 (0.32%; n = 1). Moreover, a total of 10 samples (DENV-2; n = 8, DENV-1; n = 2) were subjected to whole-genome sequencing. Among these, four were collected in early 2022, and six were collected between August and October 2022. Phylogenetic analysis of DENV-2 sequenced samples (n = 8) revealed a monophyletic clade of cosmopolitan genotype IVA, which is closely related to sequences from China and Singapore 2018, and DENV-1 samples (n = 2) show genotype III, which is closely related to Pakistan isolates from 2019. We also reported the first whole genome sequence of a coinfection case (DENV1-DENV2) in Pakistan detected through a meta-genome approach. Thus, dengue virus dynamics reported in the current study warrant large-scale genomic surveillance to better respond to future outbreaks.}, } @article {pmid36679121, year = {2023}, author = {Baharin, A and Ting, TY and Goh, HH}, title = {Omics Approaches in Uncovering Molecular Evolution and Physiology of Botanical Carnivory.}, journal = {Plants (Basel, Switzerland)}, volume = {12}, number = {2}, pages = {}, pmid = {36679121}, issn = {2223-7747}, support = {DIP-2020-005//National University of Malaysia/ ; FRGS/1/2019/STG05/UKM/02/10//Ministry of Higher Education/ ; }, abstract = {Systems biology has been increasingly applied with multiple omics for a holistic comprehension of complex biological systems beyond the reductionist approach that focuses on individual molecules. Different high-throughput omics approaches, including genomics, transcriptomics, metagenomics, proteomics, and metabolomics have been implemented to study the molecular mechanisms of botanical carnivory. This covers almost all orders of carnivorous plants, namely Caryophyllales, Ericales, Lamiales, and Oxalidales, except Poales. Studies using single-omics or integrated multi-omics elucidate the compositional changes in nucleic acids, proteins, and metabolites. The omics studies on carnivorous plants have led to insights into the carnivory origin and evolution, such as prey capture and digestion as well as the physiological adaptations of trap organ formation. Our understandings of botanical carnivory are further enhanced by the discoveries of digestive enzymes and transporter proteins that aid in efficient nutrient sequestration alongside dynamic molecular responses to prey. Metagenomics studies revealed the mutualistic relationships between microbes and carnivorous plants. Lastly, in silico analysis accelerated the functional characterization of new molecules from carnivorous plants. These studies have provided invaluable molecular data for systems understanding of carnivorous plants. More studies are needed to cover the diverse species with convergent evolution of botanical carnivory.}, } @article {pmid36678584, year = {2023}, author = {Bilal, H and Xiao, Y and Khan, MN and Chen, J and Wang, Q and Zeng, Y and Lin, X}, title = {Stabilization of Acne Vulgaris-Associated Microbial Dysbiosis with 2% Supramolecular Salicylic Acid.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {16}, number = {1}, pages = {}, pmid = {36678584}, issn = {1424-8247}, abstract = {Facial microbiota dysbiosis is an important factor in causing acne vulgaris. The present study aimed to analyze the effect of 2% Supramolecular Salicylic Acid (SSA) on acne-associated facial bacteria. In the current study, 30 acne vulgaris patients (treated with 2% SSA for eight weeks) and ten volunteers with no facial acne were selected. Samples from acne patients (before and after treatment) and volunteers (not treated) were analyzed via high throughput sequencing, Deblur algorithm, and R microbiome package. After treatment with 2% SSA, the total lesion count and global acne grading system (GAGS) score reduced significantly (p < 0.001). Metagenomic sequencing analysis revealed that the pre-treated acne group had low α and deviated β diversity compared to the control and post-treated acne groups. Due to the treatment with 2% SSA, α diversity index was increased and β diversity was stabilized significantly (p < 0.001). The relative abundance of bacterial genera in the pre-treated acne group was uneven and had a high proportion of Staphylococcus, Ralstonia, and Streptococcus. The proportion of these three genera was significantly decreased in the post-treated group, and overall bacteria genera distribution tends toward the healthy individual. It is concluded that 2% SSA normalizes the microbial communities associated with the skin.}, } @article {pmid36678360, year = {2022}, author = {Cholleti, H and de Jong, J and Blomström, AL and Berg, M}, title = {Investigation of the Virome and Characterization of Issyk-Kul Virus from Swedish Myotis brandtii Bats.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {36678360}, issn = {2076-0817}, support = {50800//Section of Virology, Dept. of Biomedical Sciences and Veterinary Public Health, Swedish University Of Agricultural Sciences, Uppsala, Sweden/ ; }, abstract = {Bats are reservoirs for many different viruses, including some that can be transmitted to and cause disease in humans and/or animals. However, less is known about the bat-borne viruses circulating in Northern European countries such as in Sweden. In this study, saliva from Myotis brandtii bats, collected from south-central Sweden, was analyzed for viruses. The metagenomic analysis identified viral sequences belonging to different viral families, including, e.g., Nairoviridae, Retroviridae, Poxviridae, Herpesviridae and Siphoviridae. Interestingly, through the data analysis, the near-complete genome of Issyk-Kul virus (ISKV), a zoonotic virus within the Nairoviridae family, was obtained, showing 95-99% protein sequence identity to previously described ISKVs. This virus is believed to infect humans via an intermediate tick host or through contact with bat excrete. ISKV has previously been found in bats in Europe, but not previously in the Nordic region. In addition, near full-length genomes of two novel viruses belonging to Picornavirales order and Tymoviridae family were characterized. Taken together, our study has not only identified novel viruses, but also the presence of a zoonotic virus not previously known to circulate in this region. Thus, the results from these types of studies can help us to better understand the diversity of viruses circulating in bat populations, as well as identify viruses with zoonotic potential that could possibly be transmitted to humans.}, } @article {pmid36678350, year = {2022}, author = {Csótó, A and Kovács, C and Pál, K and Nagy, A and Peles, F and Fekete, E and Karaffa, L and Kubicek, CP and Sándor, E}, title = {The Biocontrol Potential of Endophytic Trichoderma Fungi Isolated from Hungarian Grapevines, Part II, Grapevine Stimulation.}, journal = {Pathogens (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {36678350}, issn = {2076-0817}, support = {NN128867//Hungarian National Research, Development and Innovation Fund/ ; K138489//Hungarian National Research, Development and Innovation Fund/ ; PoC022//University of Debrecen Proof of Concept Fund/ ; }, abstract = {In the first part of this two-piece publication, the isolation, identification and in vitro characterization of ten endophytic Trichoderma isolates were reported. Here we report the ability of two different mixes of some of these isolates (Trichoderma simmonsii, Trichoderma orientale and Trichoderma gamsii as well as of Trichoderma afroharzianum and T. simmonsii) to colonize and stimulate the growth of grapevines. Two commercial vineyards about 400 km away from the site of isolation were used as experimental fields, from which the strains of three Trichoderma species were re-isolated up to four years after rootstock soaking treatment with conidiospores, performed before planting. The treatments decreased the overall percentage of lost plants of about 30%, although a low number of lost plants (about 5%) were observed also in the control plot. For all cultivars and clones, the Trichoderma treatments significantly increased both the bud burst ratio and bud burst vigor index. In addition, the grape must parameters such as the Brix degrees, as well as the extract, the D-glucose and the D-fructose concentrations all appeared to be improved, suggesting a potentially higher ethanol content of the produced wine. We conclude that grapevine-endophytic Trichoderma isolates promote plant growth, which could be a useful feature for sustainable agriculture in general and integrated plant production in particular.}, } @article {pmid36678135, year = {2023}, author = {Yang, JC and Jacobs, JP and Hwang, M and Sabui, S and Liang, F and Said, HM and Skupsky, J}, title = {Biotin Deficiency Induces Intestinal Dysbiosis Associated with an Inflammatory Bowel Disease-like Phenotype.}, journal = {Nutrients}, volume = {15}, number = {2}, pages = {}, pmid = {36678135}, issn = {2072-6643}, support = {IK2 CX001717/CX/CSRD VA/United States ; }, mesh = {Animals ; Mice ; *Biotin ; Dysbiosis ; RNA, Ribosomal, 16S/genetics ; *Inflammatory Bowel Diseases/metabolism ; Phenotype ; Inflammation ; }, abstract = {Biotin is an essential vitamin and critical cofactor in several metabolic pathways, and its deficiency has been linked to several disorders including inflammatory bowel disease (IBD). We previously reported that biotin deficiency (BD) in mice, whether modeled through intestine-specific deletion of biotin transporter (SMVT-icKO) or through a biotin-deficient diet, resulted in intestinal inflammation consistent with an IBD-like phenotype. To assess whether the gut microbiome is associated with these BD-induced changes, we collected stool and intestinal samples from both of these mouse models and utilized them for 16S rRNA gene sequencing. We find that both diet-mediated and deletion-mediated BD result in the expansion of opportunistic microbes including Klebsiella, Enterobacter, and Helicobacter, at the expense of mucus-resident microbes including Akkermansia. Additionally, microbiome dysbiosis resulting from diet-mediated BD precedes the onset of the IBD-like phenotypic changes. Lastly, through the use of predictive metagenomics, we report that the resulting BD-linked microbiome perturbations exhibit increased biotin biosynthesis in addition to several other perturbed metabolic pathways. Altogether, these results demonstrate that biotin deficiency results in a specific microbiome composition, which may favor microbes capable of biotin synthesis and which may contribute to intestinal inflammation.}, } @article {pmid36677467, year = {2023}, author = {Abdulkadir, N and Saraiva, JP and Schattenberg, F and Toscan, RB and Borim Correa, F and Harms, H and Müller, S and da Rocha, UN}, title = {Combining Flow Cytometry and Metagenomics Improves Recovery of Metagenome-Assembled Genomes in a Cell Culture from Activated Sludge.}, journal = {Microorganisms}, volume = {11}, number = {1}, pages = {}, pmid = {36677467}, issn = {2076-2607}, support = {VH-NG-1248//Helmholtz Association of German Research Centres/ ; 460129525//Deutsche Forschungsgemeinschaft/ ; 91717355//German Academic Exchange Service/ ; }, abstract = {The recovery of metagenome-assembled genomes is biased towards the most abundant species in a given community. To improve the identification of species, even if only dominant species are recovered, we investigated the integration of flow cytometry cell sorting with bioinformatics tools to recover metagenome-assembled genomes. We used a cell culture of a wastewater microbial community as our model system. Cells were separated based on fluorescence signals via flow cytometry cell sorting into sub-communities: dominant gates, low abundant gates, and outer gates into subsets of the original community. Metagenome sequencing was performed for all groups. The unsorted community was used as control. We recovered a total of 24 metagenome-assembled genomes (MAGs) representing 11 species-level genome operational taxonomic units (gOTUs). In addition, 57 ribosomal operational taxonomic units (rOTUs) affiliated with 29 taxa at species level were reconstructed from metagenomic libraries. Our approach suggests a two-fold increase in the resolution when comparing sorted and unsorted communities. Our results also indicate that species abundance is one determinant of genome recovery from metagenomes as we can recover taxa in the sorted libraries that are not present in the unsorted community. In conclusion, a combination of cell sorting and metagenomics allows the recovery of MAGs undetected without cell sorting.}, } @article {pmid36677461, year = {2023}, author = {Kim, KE and Joo, HM and Lee, TK and Kim, HJ and Kim, YJ and Kim, BK and Ha, SY and Jung, SW}, title = {Covariance of Marine Nucleocytoplasmic Large DNA Viruses with Eukaryotic Plankton Communities in the Sub-Arctic Kongsfjorden Ecosystem: A Metagenomic Analysis of Marine Microbial Ecosystems.}, journal = {Microorganisms}, volume = {11}, number = {1}, pages = {}, pmid = {36677461}, issn = {2076-2607}, support = {NRF-2020R1A2C2005970//National Research Foundation of Korea/ ; Ref. No. 21210466//Ministry of Oceans and Fisheries/ ; PE19170//Korea Polar Research Institute/ ; }, abstract = {Nucleocytoplasmic large DNA viruses (NCLDVs) infect various marine eukaryotes. However, little is known about NCLDV diversity and their relationships with eukaryotic hosts in marine environments, the elucidation of which will advance the current understanding of marine ecosystems. This study characterizes the interplay between NCLDVs and the eukaryotic plankton community (EPC) in the sub-Arctic area using metagenomics and metabarcoding to investigate NCLDVs and EPC, respectively, in the Kongsfjorden ecosystem of Svalbard (Norway) in April and June 2018. Gyrodinium helveticum (Dinophyceae) is the most prevalent eukaryotic taxon in the EPC in April, during which time Mimiviridae (31.8%), Poxviridae (25.1%), Phycodnaviridae (14.7%) and Pandoraviridae (13.1%) predominate. However, in June, the predominant taxon is Aureococcus anophagefferens (Pelagophyceae), and the NCLDVs, Poxviridae (32.9%), Mimiviridae (29.1%), and Phycodnaviridae (18.5%) appear in higher proportions with an increase in Pelagophyceae, Bacillariophyceae, and Chlorophyta groups. Thus, differences in NCLDVs may be caused by changes in EPC composition in response to environmental changes, such as increases in water temperature and light intensity. Taken together, these findings are particularly relevant considering the anticipated impact of NCLDV-induced EPC control mechanisms on polar regions and, therefore, improve the understanding of the Sub-Arctic Kongsfjorden ecosystem.}, } @article {pmid36677415, year = {2023}, author = {Nelli, A and Venardou, B and Skoufos, I and Voidarou, CC and Lagkouvardos, I and Tzora, A}, title = {An Insight into Goat Cheese: The Tales of Artisanal and Industrial Gidotyri Microbiota.}, journal = {Microorganisms}, volume = {11}, number = {1}, pages = {}, pmid = {36677415}, issn = {2076-2607}, support = {Interreg - IPA CBC Greece Albania 2014-2020 Programme, under project CheeseCult//European Union and National Funds of Greece and Albania/ ; }, abstract = {The purpose of this study was to determine for the first time the microbiota in artisanal-type and industrial-type Gidotyri cheeses and investigate the influence of the cheese-making practices on their composition using culture-independent techniques. The microbiota present in artisanal with commercial starters (Artisanal_CS, n = 15), artisanal with in-house starters (Artisanal_IHS, n = 10) and industrial (Ind., n = 9) Gidotyri cheese samples were analyzed using a targeted metagenomic approach (16S rRNA gene). The Ind. Gidotyri cheese microbiota were less complex, dominated by the Streptococcaceae family (91%) that was more abundant compared to the artisanal Gidotyri cheeses (p < 0.05). Artisanal cheeses were more diverse compositionally with specific bacterial species being prevalent to each subtype. Particularly, Loigolactobacillus coryniformis (OTU 175), Secundilactobacillus malefermentans (OTU 48), and Streptococcus parauberis (OTU 50) were more prevalent in Artisanal_IHS cheeses compared to Artisanal_CS (p ≤ 0.001) and Ind. (p < 0.01) Gidotyri cheeses. Carnobacterium maltaromaticum (OTU 23) and Enterobacter hormaechei subsp. hoffmannii (OTU 268) were more prevalent in Artisanal_CS cheeses compared to Artisanal_IHS cheeses (p < 0.05) and Ind. cheeses (p < 0.05). Hafnia alvei (OTU 13) and Acinetobacter colistiniresistens (OTU 111) tended to be more prevalent in Artisanal_CS compared to the other two cheese groups (p < 0.10). In conclusion, higher microbial diversity was observed in the artisanal-type Gidotyri cheeses, with possible bacterial markers specific to each subtype identified with potential application to traceability of the manufacturing processes’ authenticity and cheese quality.}, } @article {pmid36677413, year = {2023}, author = {Herold, M and Hock, L and Penny, C and Walczak, C and Djabi, F and Cauchie, HM and Ragimbeau, C}, title = {Metagenomic Strain-Typing Combined with Isolate Sequencing Provides Increased Resolution of the Genetic Diversity of Campylobacter jejuni Carriage in Wild Birds.}, journal = {Microorganisms}, volume = {11}, number = {1}, pages = {}, pmid = {36677413}, issn = {2076-2607}, support = {C17/BM/11684203//Fonds National de la Recherche/ ; }, abstract = {As the world's leading cause of human gastro-enteritis, the food- and waterborne pathogen Campylobacter needs to be intensively monitored through a One Health approach. Particularly, wild birds have been hypothesized to contribute to the spread of human clinical recurring C. jejuni genotypes across several countries. A major concern in studying epidemiological dynamics is resolving the large genomic diversity of strains circulating in the environment and various reservoirs, challenging to achieve with isolation techniques. Here, we applied a passive-filtration method to obtain isolates and in parallel recovered genotypes from metagenomic sequencing data from associated filter sweeps. For genotyping mixed strains, a reference-based computational workflow to predict allelic profiles of nine extended-MLST loci was utilized. We validated the pipeline by sequencing artificial mixtures of C. jejuni strains and observed the highest prediction accuracy when including obtained isolates as references. By analyzing metagenomic samples, we were able to detect over 20% additional genetic diversity and observed an over 50% increase in the potential to connect genotypes across wild-bird samples. With an optimized filtration method and a computational approach for genotyping strain mixtures, we provide the foundation for future studies assessing C. jejuni diversity in environmental and clinical settings at improved throughput and resolution.}, } @article {pmid36677391, year = {2022}, author = {Buttler, J and Drown, DM}, title = {Accuracy and Completeness of Long Read Metagenomic Assemblies.}, journal = {Microorganisms}, volume = {11}, number = {1}, pages = {}, pmid = {36677391}, issn = {2076-2607}, support = {UL1GM118991/GM/NIGMS NIH HHS/United States ; TL4GM118992/GM/NIGMS NIH HHS/United States ; UL1 GM118991/GM/NIGMS NIH HHS/United States ; RL5 GM118990/GM/NIGMS NIH HHS/United States ; RL5GM118990/GM/NIGMS NIH HHS/United States ; P20 GM103395/GM/NIGMS NIH HHS/United States ; P20GM103395/GM/NIGMS NIH HHS/United States ; }, abstract = {Microbes influence the surrounding environment and contribute to human health. Metagenomics can be used as a tool to explore the interactions between microbes. Metagenomic assemblies built using long read nanopore data depend on the read level accuracy. The read level accuracy of nanopore sequencing has made dramatic improvements over the past several years. However, we do not know if the increased read level accuracy allows for faster assemblers to make as accurate metagenomic assemblies as slower assemblers. Here, we present the results of a benchmarking study comparing three commonly used long read assemblers, Flye, Raven, and Redbean. We used a prepared DNA standard of seven bacteria as our input community. We prepared a sequencing library using a VolTRAX V2 and sequenced using a MinION mk1b. We basecalled with Guppy v5.0.7 using the super-accuracy model. We found that increasing read depth benefited each of the assemblers, and nearly complete community member chromosomes were assembled with as little as 10× read depth. Polishing assemblies using Medaka had a predictable improvement in quality. We found Flye to be the most robust across taxa and was the most effective assembler for recovering plasmids. Based on Flye's consistency for chromosomes and increased effectiveness at assembling plasmids, we would recommend using Flye in future metagenomic studies.}, } @article {pmid36677385, year = {2022}, author = {DuPont, HL and Jiang, ZD and Alexander, AS and DuPont, AW and Brown, EL}, title = {Intestinal IgA-Coated Bacteria in Healthy- and Altered-Microbiomes (Dysbiosis) and Predictive Value in Successful Fecal Microbiota Transplantation.}, journal = {Microorganisms}, volume = {11}, number = {1}, pages = {}, pmid = {36677385}, issn = {2076-2607}, abstract = {IgA-coated bacteria in the gut (IgA-biome) provide a homeostatic function in healthy people through inhibition of microbial invaders and by protecting the epithelial monolayer of the gut. The laboratory methods used to detect this group of bacteria require flow cytometry and DNA sequencing (IgA-Seq). With dysbiosis (reduced diversity of the microbiome), the IgA-biome also is impaired. In the presence of enteric infection, oral vaccines, or an intestinal inflammatory disorder, the IgA-biome focuses on the pathogenic bacteria or foreign antigens, while in other chronic diseases associated with dysbiosis, the IgA-biome is reduced in capacity. Fecal microbiota transplantation (FMT), the use of fecal product from well-screened, healthy donors administered to patients with dysbiosis, has been successful in engrafting the intestine with healthy microbiota and metabolites leading to improve health. Through FMT, IgA-coated bacteria have been transferred to recipients retaining their immune coating. The IgA-biome should be evaluated in FMT studies as these mucosal-associated bacteria are more likely to be associated with successful transplantation than free luminal organisms. Studies of the microbiome pre- and post-FMT should employ metagenomic methods that identify bacteria at least at the species level to better identify organisms of interest while allowing comparisons of microbiota data between studies.}, } @article {pmid36677368, year = {2022}, author = {Morales-Rivera, MF and Valenzuela-Miranda, D and Nuñez-Acuña, G and Benavente, BP and Gallardo-Escárate, C and Valenzuela-Muñoz, V}, title = {Atlantic Salmon (Salmo salar) Transfer to Seawater by Gradual Salinity Changes Exhibited an Increase in The Intestinal Microbial Abundance and Richness.}, journal = {Microorganisms}, volume = {11}, number = {1}, pages = {}, pmid = {36677368}, issn = {2076-2607}, support = {3190320//Agencia Nacional de Investigación y Desarrollo/ ; 15110027//Agencia Nacional de Investigación y Desarrollo/ ; 1210852//Agencia Nacional de Investigación y Desarrollo/ ; 11220307//Agencia Nacional de Investigación y Desarrollo/ ; 3200600//Agencia Nacional de Investigación y Desarrollo/ ; }, abstract = {The host's physiological history and environment determine the microbiome structure. In that sense, the strategy used for the salmon transfer to seawater after parr-smolt transformation may influence the Atlantic salmon's intestinal microbiota. Therefore, this study aimed to explore the diversity and abundance of the Atlantic salmon intestinal microbiota and metagenome functional prediction during seawater transfer under three treatments. One group was exposed to gradual salinity change (GSC), the other to salinity shock (SS), and the third was fed with a functional diet (FD) before the seawater (SW) transfer. The microbial profile was assessed through full-16S rRNA gene sequencing using the Nanopore platform. In addition, metagenome functional prediction was performed using PICRUSt2. The results showed an influence of salinity changes on Atlantic salmon gut microbiota richness, diversity, and taxonomic composition. The findings reveal that GSC and the FD increased the Atlantic salmon smolt microbiota diversity, suggesting a positive association between the intestinal microbial community and fish health during seawater transfer. The reported knowledge can be applied to surveil the microbiome in smolt fish production, improving the performance of Atlantic salmon to seawater transfer.}, } @article {pmid36677344, year = {2022}, author = {Guima, SES and Piubeli, F and Bonfá, MRL and Pereira, RM}, title = {New Insights into the Effect of Fipronil on the Soil Bacterial Community.}, journal = {Microorganisms}, volume = {11}, number = {1}, pages = {}, pmid = {36677344}, issn = {2076-2607}, abstract = {Fipronil is a broad-spectrum insecticide with remarkable efficacy that is widely used to control insect pests around the world. However, its extensive use has led to increasing soil and water contamination. This fact is of concern and makes it necessary to evaluate the risk of undesirable effects on non-target microorganisms, such as the microbial community in water and/or soil. Studies using the metagenomic approach to assess the effects of fipronil on soil microbial communities are scarce. In this context, the present study was conducted to identify microorganisms that can biodegrade fipronil and that could be of great environmental interest. For this purpose, the targeted metabarcoding approach was performed in soil microcosms under two environmental conditions: fipronil exposure and control (without fipronil). After a 35-day soil microcosm period, the 16S ribosomal RNA (rRNA) gene of all samples was sequenced using the ion torrent personal genome machine (PGM) platform. Our study showed the presence of Proteobacteria, Actinobacteria, and Firmicutes in all of the samples; however, the presence of fipronil in the soil samples resulted in a significant increase in the concentration of bacteria from these phyla. The statistical results indicate that some bacterial genera benefited from soil exposure to fipronil, as in the case of bacteria from the genus Thalassobacillus, while others were affected, as in the case of bacteria from the genus Streptomyces. Overall, the results of this study provide a potential contribution of fipronil-degrading bacteria.}, } @article {pmid36677054, year = {2023}, author = {Mukherjee, AG and Wanjari, UR and Kannampuzha, S and Murali, R and Namachivayam, A and Ganesan, R and Dey, A and Babu, A and Renu, K and Vellingiri, B and Ramanathan, G and Priya Doss C, G and Elsherbiny, N and Elsherbini, AM and Alsamman, AM and Zayed, H and Gopalakrishnan, AV}, title = {The Implication of Mechanistic Approaches and the Role of the Microbiome in Polycystic Ovary Syndrome (PCOS): A Review.}, journal = {Metabolites}, volume = {13}, number = {1}, pages = {}, pmid = {36677054}, issn = {2218-1989}, abstract = {As a complex endocrine and metabolic condition, polycystic ovarian syndrome (PCOS) affects women's reproductive health. These common symptoms include hirsutism, hyperandrogenism, ovulatory dysfunction, irregular menstruation, and infertility. No one knows what causes it or how to stop it yet. Alterations in gut microbiota composition and disruptions in secondary bile acid production appear to play a causative role in developing PCOS. PCOS pathophysiology and phenotypes are tightly related to both enteric and vaginal bacteria. Patients with PCOS exhibit changed microbiome compositions and decreased microbial diversity. Intestinal microorganisms also alter PCOS patient phenotypes by upregulating or downregulating hormone release, gut-brain mediators, and metabolite synthesis. The human body's gut microbiota, also known as the "second genome," can interact with the environment to improve metabolic and immunological function. Inflammation is connected to PCOS and may be caused by dysbiosis in the gut microbiome. This review sheds light on the recently discovered connections between gut microbiota and insulin resistance (IR) and the potential mechanisms of PCOS. This study also describes metabolomic studies to obtain a clear view of PCOS and ways to tackle it.}, } @article {pmid36676144, year = {2023}, author = {Kumari, KS and Dixit, S and Gaur, M and Behera, DU and Dey, S and Sahoo, RK and Dash, P and Subudhi, E}, title = {Taxonomic Assignment-Based Genome Reconstruction from Apical Periodontal Metagenomes to Identify Antibiotic Resistance and Virulence Factors.}, journal = {Life (Basel, Switzerland)}, volume = {13}, number = {1}, pages = {}, pmid = {36676144}, issn = {2075-1729}, abstract = {Primary apical periodontitis occurs due to various insults to the dental pulp including microbial infections, physical and iatrogenic trauma, whereas inadequate elimination of intraradicular infection during root canal treatment may lead to secondary apical periodontitis. We explored the complex intra-radicular microbial communities and their functional potential through genome reconstruction. We applied shotgun metagenomic sequencing, binning and functional profiling to identify the significant contributors to infection at the acute and chronic apical periodontal lesions. Our analysis revealed the five classified clusters representing Enterobacter, Enterococcus, Lacticaseibacillus, Pseudomonas, Streptococcus and one unclassified cluster of contigs at the genus level. Of them, the major contributors were Pseudomonas, with 90.61% abundance in acute conditions, whereas Enterobacter followed by Enterococcus with 69.88% and 15.42% abundance, respectively, in chronic conditions. Enterobacter actively participated in antibiotic target alteration following multidrug efflux-mediated resistance mechanisms, predominant in the chronic stage. The prediction of pathways involved in the destruction of the supportive tissues of the tooth in Enterobacter and Pseudomonas support their crucial role in the manifestation of respective disease conditions. This study provides information about the differential composition of the microbiome in chronic and acute apical periodontitis. It takes a step to interpret the role of a single pathogen, solely or predominantly, in establishing endodontic infection types through genome reconstruction following high throughput metagenomic DNA analysis. The resistome prediction sheds a new light on the therapeutic treatment guidelines for endodontists. However, it needs further conclusive research to support this outcome using a larger number of samples with similar etiological conditions, but different demographic origin.}, } @article {pmid36675920, year = {2023}, author = {Otero, A and Barcenas-Peña, A and Lumbsch, HT and Grewe, F}, title = {Reference-Based RADseq Unravels the Evolutionary History of Polar Species in 'the Crux Lichenologorum' Genus Usnea (Parmeliaceae, Ascomycota).}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {9}, number = {1}, pages = {}, pmid = {36675920}, issn = {2309-608X}, support = {CTM2015-64728-C2-1-R//Negaunee Foundation, the Grainger Foundation, the Robert A. Pritzker Center for Meteoritics and Polar Studies and Tawani Foundation, and CRYPTOCOVER/ ; }, abstract = {Nearly 90% of fungal diversity, one of the most speciose branches in the tree of life, remains undescribed. Lichenized fungi as symbiotic associations are still a challenge for species delimitation, and current species diversity is vastly underestimated. The ongoing democratization of Next-Generation Sequencing is turning the tables. Particularly, reference-based RADseq allows for metagenomic filtering of the symbiont sequence and yields robust phylogenomic trees of closely related species. We implemented reference-based RADseq to disentangle the evolution of neuropogonoid lichens, which inhabit harsh environments and belong to Usnea (Parmeliaceae, Ascomycota), one of the most taxonomically intriguing genera within lichenized fungi. Full taxon coverage of neuropogonoid lichens was sampled for the first time, coupled with phenotype characterizations. More than 20,000 loci of 126 specimens were analyzed through concatenated and coalescent-based methods, including time calibrations. Our analysis addressed the major taxonomic discussions over recent decades. Subsequently, two species are newly described, namely U. aymondiana and U. fibriloides, and three species names are resurrected. The late Miocene and Pliocene-Pleistocene boundary is inferred as the timeframe for neuropogonoid lichen diversification. Ultimately, this study helped fill the gap of fungal diversity by setting a solid backbone phylogeny which raises new questions about which factors may trigger complex evolutionary scenarios.}, } @article {pmid36675631, year = {2023}, author = {Cao, Y and Wang, H and Jin, Z and Hang, J and Jiang, H and Wu, H and Zhang, Z}, title = {Characterization of Non-Obstructive Azoospermia in Men Using Gut Microbial Profiling.}, journal = {Journal of clinical medicine}, volume = {12}, number = {2}, pages = {}, pmid = {36675631}, issn = {2077-0383}, support = {7222208//Natural Science Foundation of Beijing Municipality/ ; 81901535//National Natural Science Foundation of China/ ; 82071698//National Natural Science Foundation of China/ ; 82271634//National Natural Science Foundation of China/ ; 2022YFC2702600//National Key Research & Developmental Program of China/ ; }, abstract = {(1) Background: Non-obstructive azoospermia (NOA) is a complex multifactorial disease and the causes of most NOA cases remain unknown. (2) Methods: Here, we performed comprehensive clinical analyses and gut microbial profiling using shotgun metagenomic sequencing in patients with NOA and control individuals. (3) Results: The gut microbial alpha and beta diversity significantly differed between patients with NOA and controls. Several microbial strains, including Bacteroides vulgatus and Streptococcus thermophilus, were significantly more abundant in the NOA group, whereas Bacteroides thetaiotaomicron and Parabacteroides sp. CT06 were enriched in the control group. Moreover, functional pathway analysis suggested that the altered microbiota in NOA suppressed the carbohydrate metabolism pathway, while amino acid metabolism and methane metabolism pathways were enhanced. We observed that the differential microbial species, such as Acinetobacter johnsonii, had a strong correlation with clinical parameters, including age, body mass index, testosterone, and follicle-stimulating hormone. Communication and interplay among microbial genera were significantly increased in NOA than in the control group. (4) Conclusions: Altered microbial composition and functional pathways in the NOA group were revealed, which highlight the utility of gut microbiota in understanding microbiota-related pathogenesis of NOA and might be helpful to the clinical management of NOA.}, } @article {pmid36675151, year = {2023}, author = {Karpe, AV and Hutton, ML and Mileto, SJ and James, ML and Evans, C and Ghodke, AB and Shah, RM and Metcalfe, SS and Liu, JW and Walsh, T and Lyras, D and Palombo, EA and Beale, DJ}, title = {Gut Microbial Perturbation and Host Response Induce Redox Pathway Upregulation along the Gut-Liver Axis during Giardiasis in C57BL/6J Mouse Model.}, journal = {International journal of molecular sciences}, volume = {24}, number = {2}, pages = {}, pmid = {36675151}, issn = {1422-0067}, support = {Probing Biosystems Future Science Platform (FSP)//Commonwealth Scientific and Industrial Research Organisation/ ; }, mesh = {Mice ; Animals ; Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics/metabolism ; *Giardiasis ; Up-Regulation ; Proteome/metabolism ; *Cryptosporidiosis/metabolism ; Mice, Inbred C57BL ; *Cryptosporidium/metabolism ; Metabolomics ; Metabolome ; *Microbiota ; Liver/metabolism ; Oxidation-Reduction ; }, abstract = {Apicomplexan infections, such as giardiasis and cryptosporidiosis, negatively impact a considerable proportion of human and commercial livestock populations. Despite this, the molecular mechanisms of disease, particularly the effect on the body beyond the gastrointestinal tract, are still poorly understood. To highlight host-parasite-microbiome biochemical interactions, we utilised integrated metabolomics-16S rRNA genomics and metabolomics-proteomics approaches in a C57BL/6J mouse model of giardiasis and compared these to Cryptosporidium and uropathogenic Escherichia coli (UPEC) infections. Comprehensive samples (faeces, blood, liver, and luminal contents from duodenum, jejunum, ileum, caecum and colon) were collected 10 days post infection and subjected to proteome and metabolome analysis by liquid and gas chromatography-mass spectrometry, respectively. Microbial populations in faeces and luminal washes were examined using 16S rRNA metagenomics. Proteome-metabolome analyses indicated that 12 and 16 key pathways were significantly altered in the gut and liver, respectively, during giardiasis with respect to other infections. Energy pathways including glycolysis and supporting pathways of glyoxylate and dicarboxylate metabolism, and the redox pathway of glutathione metabolism, were upregulated in small intestinal luminal contents and the liver during giardiasis. Metabolomics-16S rRNA genetics integration indicated that populations of three bacterial families-Autopobiaceae (Up), Desulfovibrionaceae (Up), and Akkermanasiaceae (Down)-were most significantly affected across the gut during giardiasis, causing upregulated glycolysis and short-chained fatty acid (SCFA) metabolism. In particular, the perturbed Akkermanasiaceae population seemed to cause oxidative stress responses along the gut-liver axis. Overall, the systems biology approach applied in this study highlighted that the effects of host-parasite-microbiome biochemical interactions extended beyond the gut ecosystem to the gut-liver axis. These findings form the first steps in a comprehensive comparison to ascertain the major molecular and biochemical contributors of host-parasite interactions and contribute towards the development of biomarker discovery and precision health solutions for apicomplexan infections.}, } @article {pmid36675099, year = {2023}, author = {Evseev, P and Lukianova, A and Tarakanov, R and Tokmakova, A and Popova, A and Kulikov, E and Shneider, M and Ignatov, A and Miroshnikov, K}, title = {Prophage-Derived Regions in Curtobacterium Genomes: Good Things, Small Packages.}, journal = {International journal of molecular sciences}, volume = {24}, number = {2}, pages = {}, pmid = {36675099}, issn = {1422-0067}, support = {21-16-00047//Russian Science Foundation/ ; }, mesh = {Prophages/genetics ; Phylogeny ; *Bacteriophages/genetics ; Genomics ; Bacteria ; *Actinomycetales ; }, abstract = {Curtobacterium is a genus of Gram-positive bacteria within the order Actinomycetales. Some Curtobacterium species (C. flaccumfaciens, C. plantarum) are harmful pathogens of agricultural crops such as soybean, dry beans, peas, sugar beet and beetroot, which occur throughout the world. Bacteriophages (bacterial viruses) are considered to be potential curative agents to control the spread of harmful bacteria. Temperate bacteriophages integrate their genomes into bacterial chromosomes (prophages), sometimes substantially influencing bacterial lifestyle and pathogenicity. About 200 publicly available genomes of Curtobacterium species, including environmental metagenomic sequences, were inspected for the presence of sequences of possible prophage origin using bioinformatic methods. The comparison of the search results with several ubiquitous bacterial groups showed the relatively low level of the presence of prophage traces in Curtobacterium genomes. Genomic and phylogenetic analyses were undertaken for the evaluation of the evolutionary and taxonomic positioning of predicted prophages. The analyses indicated the relatedness of Curtobacterium prophage-derived sequences with temperate actinophages of siphoviral morphology. In most cases, the predicted prophages can represent novel phage taxa not described previously. One of the predicted temperate phages was induced from the Curtobacterium genome. Bioinformatic analysis of the modelled proteins encoded in prophage-derived regions led to the discovery of some 100 putative glycopolymer-degrading enzymes that contained enzymatic domains with predicted cell-wall- and cell-envelope-degrading activity; these included glycosidases and peptidases. These proteins can be considered for the experimental design of new antibacterials against Curtobacterium phytopathogens.}, } @article {pmid36674965, year = {2023}, author = {Sun, Y and Zhang, X and Zhang, A and Landis, JB and Zhang, H and Sun, H and Xiang, QJ and Wang, H}, title = {Population Genomic Analyses Suggest a Hybrid Origin, Cryptic Sexuality, and Decay of Genes Regulating Seed Development for the Putatively Strictly Asexual Kingdonia uniflora (Circaeasteraceae, Ranunculales).}, journal = {International journal of molecular sciences}, volume = {24}, number = {2}, pages = {}, pmid = {36674965}, issn = {1422-0067}, support = {U2003122//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Phylogeny ; *Reproduction, Asexual/genetics ; *Ranunculales ; Metagenomics ; Sexuality ; Genomics ; Alleles ; Seeds ; }, abstract = {Asexual lineages are perceived to be short-lived on evolutionary timescales. Hence, reports for exceptional cases of putative 'ancient asexuals' usually raise questions about the persistence of such species. So far, there have been few studies to solve the mystery in plants. The monotypic Kingdonia dating to the early Eocene, contains only K. uniflora that has no known definitive evidence for sexual reproduction nor records for having congeneric sexual species, raising the possibility that the species has persisted under strict asexuality for a long period of time. Here, we analyze whole genome polymorphism and divergence in K. uniflora. Our results show that K. uniflora is characterized by high allelic heterozygosity and elevated πN/πS ratio, in line with theoretical expectations under asexual evolution. Allele frequency spectrum analysis reveals the origin of asexuality in K. uniflora occurred prior to lineage differentiation of the species. Although divergence within K. uniflora individuals exceeds that between populations, the topologies of the two haplotype trees, however, fail to match each other, indicating long-term asexuality is unlikely to account for the high allele divergence and K. uniflora may have a recent hybrid origin. Phi-test shows a statistical probability of recombination for the conflicting phylogenetic signals revealed by the split network, suggesting K. uniflora engages in undetected sexual reproduction. Detection of elevated genetic differentiation and premature stop codons (in some populations) in genes regulating seed development indicates mutational degradation of sexuality-specific genes in K. uniflora. This study unfolds the origin and persistence mechanism of a plant lineage that has been known to reproduce asexually and presents the genomic consequences of lack of sexuality.}, } @article {pmid36674562, year = {2023}, author = {Ong, SS and Xu, J and Sim, CK and Khng, AJ and Ho, PJ and Kwan, PKW and Ravikrishnan, A and Tan, KB and Tan, QT and Tan, EY and Tan, SM and Putti, TC and Lim, SH and Tang, ELS and Nagarajan, N and Karnani, N and Li, J and Hartman, M}, title = {Profiling Microbial Communities in Idiopathic Granulomatous Mastitis.}, journal = {International journal of molecular sciences}, volume = {24}, number = {2}, pages = {}, pmid = {36674562}, issn = {1422-0067}, support = {NUHSRO/2020/027/T1/Seed-Aug/11//National University Health System/ ; Not applicable//Agency for Science, Technology and Research/ ; }, mesh = {Humans ; Female ; *Granulomatous Mastitis/complications/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Immunoglobulin M ; Suppuration/complications ; }, abstract = {Idiopathic granulomatous mastitis (IGM) is a rare and benign inflammatory breast disease with ambiguous aetiology. Contrastingly, lactational mastitis (LM) is commonly diagnosed in breastfeeding women. To investigate IGM aetiology, we profiled the microbial flora of pus and skin in patients with IGM and LM. A total of 26 patients with IGM and 6 patients with LM were included in the study. The 16S rRNA sequencing libraries were constructed from 16S rRNA gene amplified from total DNA extracted from pus and skin swabs in patients with IGM and LM controls. Constructed libraries were multiplexed and paired-end sequenced on HiSeq4000. Metagenomic analysis was conducted using modified microbiome abundance analysis suite customised R-resource for paired pus and skin samples. Microbiome multivariable association analyses were performed using linear models. A total of 21 IGM and 3 LM paired pus and skin samples underwent metagenomic analysis. Bray−Curtis ecological dissimilarity distance showed dissimilarity across four sample types (IGM pus, IGM skin, LM pus, and LM skin; PERMANOVA, p < 0.001). No characteristic dominant genus was observed across the IGM samples. The IGM pus samples were more diverse than corresponding IGM skin samples (Shannon and Simpson index; Wilcoxon paired signed-rank tests, p = 0.022 and p = 0.07). Corynebacterium kroppenstedtii, reportedly associated with IGM in the literature, was higher in IGM pus samples than paired skin samples (Wilcoxon, p = 0.022). Three other species and nineteen genera were statistically significant in paired IGM pus−skin comparison after antibiotic treatment adjustment and multiple comparisons correction. Microbial profiles are unique between patients with IGM and LM. Inter-patient variability and polymicrobial IGM pus samples cannot implicate specific genus or species as an infectious cause for IGM.}, } @article {pmid36673224, year = {2022}, author = {Munagala, NVTS and Amanchi, PK and Balasubramanian, K and Panicker, A and Nagaraj, N}, title = {Compression-Complexity Measures for Analysis and Classification of Coronaviruses.}, journal = {Entropy (Basel, Switzerland)}, volume = {25}, number = {1}, pages = {}, pmid = {36673224}, issn = {1099-4300}, abstract = {Finding a vaccine or specific antiviral treatment for a global pandemic of virus diseases (such as the ongoing COVID-19) requires rapid analysis, annotation and evaluation of metagenomic libraries to enable a quick and efficient screening of nucleotide sequences. Traditional sequence alignment methods are not suitable and there is a need for fast alignment-free techniques for sequence analysis. Information theory and data compression algorithms provide a rich set of mathematical and computational tools to capture essential patterns in biological sequences. In this study, we investigate the use of compression-complexity (Effort-to-Compress or ETC and Lempel-Ziv or LZ complexity) based distance measures for analyzing genomic sequences. The proposed distance measure is used to successfully reproduce the phylogenetic trees for a mammalian dataset consisting of eight species clusters, a set of coronaviruses belonging to group I, group II, group III, and SARS-CoV-1 coronaviruses, and a set of coronaviruses causing COVID-19 (SARS-CoV-2), and those not causing COVID-19. Having demonstrated the usefulness of these compression complexity measures, we employ them for the automatic classification of COVID-19-causing genome sequences using machine learning techniques. Two flavors of SVM (linear and quadratic) along with linear discriminant and fine K Nearest Neighbors classifer are used for classification. Using a data set comprising 1001 coronavirus sequences (causing COVID-19 and those not causing COVID-19), a classification accuracy of 98% is achieved with a sensitivity of 95% and a specificity of 99.8%. This work could be extended further to enable medical practitioners to automatically identify and characterize coronavirus strains and their rapidly growing mutants in a fast and efficient fashion.}, } @article {pmid36673134, year = {2023}, author = {Zuo, YH and Wu, YX and Hu, WP and Chen, Y and Li, YP and Song, ZJ and Luo, Z and Ju, MJ and Shi, MH and Xu, SY and Zhou, H and Li, X and Jie, ZJ and Liu, XD and Zhang, J}, title = {The Clinical Impact of Metagenomic Next-Generation Sequencing (mNGS) Test in Hospitalized Patients with Suspected Sepsis: A Multicenter Prospective Study.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {13}, number = {2}, pages = {}, pmid = {36673134}, issn = {2075-4418}, support = {81970035//National Natural Science Foundation of China/ ; 19DZ1920104//Science and Technology Commission of Shanghai Municipality/ ; 20DZ2261200//Science and Technology Commission of Shanghai Municipality/ ; }, abstract = {Background: Metagenomic Next Generation Sequencing (mNGS) has the potential to detect pathogens rapidly. We aimed to assess the diagnostic performance of mNGS in hospitalized patients with suspected sepsis and evaluate its role in guiding antimicrobial therapy. Methods: A multicenter, prospective cohort study was performed. We enrolled patients with suspected sepsis, collected clinical characteristics and blood samples, and recorded the 30-day survival. Diagnostic efficacy of mNGS test and blood culture was compared, and the clinical impact of mNGS on antibiotic regimen modification was analyzed. Results: A total of 277 patients were enrolled, and 162 were diagnosed with sepsis. The mortality was 44.8% (121/270). The mNGS test exhibited shorter turn-out time (27.0 (26.0, 29.0) vs. 96.0 (72.0, 140.3) hours, p < 0.001) and higher sensitivity (90.5% vs. 36.0%, p < 0.001) compared with blood culture, especially for fungal infections. The mNGS test showed better performance for patients with mild symptoms, prior antibiotic use, and early stage of infection than blood culture, and was capable of guiding antibiotic regimen modification and improving prognosis. Higher reads of pathogens detected by mNGS were related to 30-day mortality (p = 0.002). Conclusions: Blood mNGS testing might be helpful for early etiological diagnosis of patients with suspected sepsis, guiding the antibiotic regimen modification and improving prognosis.}, } @article {pmid36672969, year = {2023}, author = {Zhang, M and Wang, X and Wang, Z and Mao, S and Zhang, J and Li, M and Pan, H}, title = {Metatranscriptomic Analyses Reveal Important Roles of the Gut Microbiome in Primate Dietary Adaptation.}, journal = {Genes}, volume = {14}, number = {1}, pages = {}, pmid = {36672969}, issn = {2073-4425}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Primates/genetics ; Diet ; Bacteria/metabolism ; Feces/microbiology ; }, abstract = {The gut microbiome plays a vital role in host ecological adaptation, especially dietary adaptations. Primates have evolved a variety of dietary and gut physiological structures that are useful to explore the role of the gut microbiome in host dietary adaptations. Here, we characterize gut microbiome transcriptional activity in ten fecal samples from primates with three different diets and compare the results to their previously reported metagenomic profile. Bacteria related to cellulose degradation, like Bacteroidaceae and Alcaligenaceae, were enriched and actively expressed in the gut microbiome of folivorous primates, and functional analysis revealed that the glycan biosynthesis and metabolic pathways were significantly active. In omnivorous primates, Helicobacteraceae, which promote lipid metabolism, were significantly enriched in expression, and activity and xenobiotic biodegradation and metabolism as well as lipid metabolism pathways were significantly active. In frugivorous primates, the abundance and activity of Elusimicrobiaceae, Neisseriaceae, and Succinivibrionaceae, which are associated with digestion of pectin and fructose, were significantly elevated, and the functional pathways involved in the endocrine system were significantly enriched. In conclusion, the gut microbiome contributes to host dietary adaptation by helping hosts digest the inaccessible nutrients in their specific diets.}, } @article {pmid36672880, year = {2023}, author = {Cervantes-Echeverría, M and Gallardo-Becerra, L and Cornejo-Granados, F and Ochoa-Leyva, A}, title = {The Two-Faced Role of crAssphage Subfamilies in Obesity and Metabolic Syndrome: Between Good and Evil.}, journal = {Genes}, volume = {14}, number = {1}, pages = {}, pmid = {36672880}, issn = {2073-4425}, mesh = {Child ; Humans ; *Metabolic Syndrome/genetics ; Ecosystem ; *Bacteriophages/genetics ; Obesity/genetics ; Metagenomics/methods ; }, abstract = {Viral metagenomic studies of the human gut microbiota have unraveled the differences in phage populations between health and disease, stimulating interest in phages' role on bacterial ecosystem regulation. CrAssphage is a common and abundant family in the gut virome across human populations. Therefore, we explored its role in obesity (O) and obesity with metabolic syndrome (OMS) in a children's cohort. We found a significantly decreased prevalence, diversity, and richness of the crAssphage Alpha subfamily in OMS mainly driven by a decrease in the Alpha_1 and Alpha_4 genera. On the contrary, there was a significant increase in the Beta subfamily in OMS, mainly driven by an increase in Beta_6. Additionally, an overabundance of the Delta_8 genus was observed in OMS. Notably, a decreased abundance of crAssphages was significantly correlated with the overabundance of Bacilli in the same group. The Bacilli class is a robust taxonomical biomarker of O and was also significantly abundant in our OMS cohort. Our results suggest that a loss of stability in the Alpha subfamily of crAssphages is associated with O and OMS. Contrary, an overabundance of the Delta subfamily was found in OMS. Our study advises the importance of considering the dual role (good and evil) of crAssphage subfamilies and their participation in conditions such as O, where we suggest that Alpha loss and Delta gain are associated with obese individuals.}, } @article {pmid36671714, year = {2022}, author = {Kingkaw, A and Raethong, N and Patumcharoenpol, P and Suratannon, N and Nakphaichit, M and Keawsompong, S and Roytrakul, S and Vongsangnak, W}, title = {Analyzing Predominant Bacterial Species and Potential Short-Chain Fatty Acid-Associated Metabolic Routes in Human Gut Microbiome Using Integrative Metagenomics.}, journal = {Biology}, volume = {12}, number = {1}, pages = {}, pmid = {36671714}, issn = {2079-7737}, support = {N42A650235//National Research Council of Thailand/ ; //National Science and Technology Development Agency/ ; //Kasetsart University/ ; }, abstract = {Gut microbiome plays an essential role in host health, and there is interest in utilizing diet to modulate the composition and function of microbial communities. Copra meal hydrolysate (CMH) is commonly used as a natural additive to enhance health. However, the gut microbiome is largely unknown at species level and is associated with metabolic routes involving short-chain fatty acids (SCFAs). In this study, we aimed to analyze, using integrative metagenomics, the predominant species and metabolic routes involved in SCFAs production in the human gut microbiome after treatment with CMH. The effect of CMH treatment on the Thai gut microbiome was demonstrated using 16S rRNA genes with whole-metagenome shotgun (WMGS) sequencing technology. Accordingly, these results revealed that CMH has potentially beneficial effects on the gut microbiome. Twelve predominant bacterial species, as well as their potential metabolic routes, were involved in cooperative microbiome networks under sugar utilization (e.g., glucose, mannose, or xylose) and energy supply (e.g., NADH and ATP) in relation to SCFAs biosynthesis. These findings suggest that CMH may be used as a potential prebiotic diet for modulating and maintaining the gut microbiome. To our knowledge, this is the first study to reveal the predominant bacterial species and metabolic routes in the Thai gut microbiome after treatment with potential prebiotics.}, } @article {pmid36671499, year = {2023}, author = {De Lise, F and Iacono, R and Moracci, M and Strazzulli, A and Cobucci-Ponzano, B}, title = {Archaea as a Model System for Molecular Biology and Biotechnology.}, journal = {Biomolecules}, volume = {13}, number = {1}, pages = {}, pmid = {36671499}, issn = {2218-273X}, support = {2019-3-U.O.//Agenzia Spaziale Italiana/ ; }, mesh = {*Archaea/metabolism ; Bacteria/genetics ; *Euryarchaeota/genetics/metabolism ; Biotechnology ; Molecular Biology ; }, abstract = {Archaea represents the third domain of life, displaying a closer relationship with eukaryotes than bacteria. These microorganisms are valuable model systems for molecular biology and biotechnology. In fact, nowadays, methanogens, halophiles, thermophilic euryarchaeota, and crenarchaeota are the four groups of archaea for which genetic systems have been well established, making them suitable as model systems and allowing for the increasing study of archaeal genes' functions. Furthermore, thermophiles are used to explore several aspects of archaeal biology, such as stress responses, DNA replication and repair, transcription, translation and its regulation mechanisms, CRISPR systems, and carbon and energy metabolism. Extremophilic archaea also represent a valuable source of new biomolecules for biological and biotechnological applications, and there is growing interest in the development of engineered strains. In this review, we report on some of the most important aspects of the use of archaea as a model system for genetic evolution, the development of genetic tools, and their application for the elucidation of the basal molecular mechanisms in this domain of life. Furthermore, an overview on the discovery of new enzymes of biotechnological interest from archaea thriving in extreme environments is reported.}, } @article {pmid36671375, year = {2023}, author = {Galiot, L and Monger, XC and Vincent, AT}, title = {Studying the Association between Antibiotic Resistance Genes and Insertion Sequences in Metagenomes: Challenges and Pitfalls.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {36671375}, issn = {2079-6382}, support = {IA120638//Ministry of Agriculture, Fisheries and Food/ ; RGPIN-2022-03321//Natural Sciences and Engineering Research Council/ ; }, abstract = {Antibiotic resistance is an issue in many areas of human activity. The mobilization of antibiotic resistance genes within the bacterial community makes it difficult to study and control the phenomenon. It is known that certain insertion sequences, which are mobile genetic elements, can participate in the mobilization of antibiotic resistance genes and in the expression of these genes. However, the magnitude of the contribution of insertion sequences to the mobility of antibiotic resistance genes remains understudied. In this study, the relationships between insertion sequences and antibiotic resistance genes present in the microbiome were investigated using two public datasets. The first made it possible to analyze the effects of different antibiotics in a controlled mouse model. The second dataset came from a study of the differences between conventional and organic-raised cattle. Although it was possible to find statistically significant correlations between the insertion sequences and antibiotic resistance genes in both datasets, several challenges remain to better understand the contribution of insertion sequences to the motility of antibiotic resistance genes. Obtaining more complete and less fragmented metagenomes with long-read sequencing technologies could make it possible to understand the mechanisms favoring horizontal transfers within the microbiome with greater precision.}, } @article {pmid36671341, year = {2023}, author = {Vallianou, NG and Skourtis, A and Kounatidis, D and Margellou, E and Panagopoulos, F and Geladari, E and Evangelopoulos, A and Jahaj, E}, title = {The Role of the Respiratory Microbiome in the Pathogenesis of Aspiration Pneumonia: Implications for Diagnosis and Potential Therapeutic Choices.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {36671341}, issn = {2079-6382}, abstract = {Although the lungs were considered to be sterile until recently, the advent of molecular biology techniques, such as polymerase chain reaction, 16 S rRNA sequencing and metagenomics has led to our expanding knowledge of the lung microbiome. These methods may be particularly useful for the identification of the causative agent(s) in cases of aspiration pneumonia, in which there is usually prior administration of antibiotics. The most common empirical treatment of aspiration pneumonia is the administration of broad-spectrum antibiotics; however, this may result in negative cultures from specimens taken from the respiratory tract. Therefore, in such cases, polymerase chain reaction or metagenomic next-generation sequencing may be life-saving. Moreover, these modern molecular methods may assist with antimicrobial stewardship. Based upon factors such as age, altered mental consciousness and recent hospitalization, there is a shift towards the predominance of aerobes, especially Gram-negative bacteria, over anaerobes in aspiration pneumonia. Thus, the therapeutic choices should be expanded to cover multi-drug resistant Gram-negative bacteria in selected cases of aspiration pneumonia.}, } @article {pmid36670455, year = {2023}, author = {Lin, L and Lai, Z and Zhang, J and Zhu, W and Mao, S}, title = {The gastrointestinal microbiome in dairy cattle is constrained by the deterministic driver of the region and the modified effect of diet.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {10}, pmid = {36670455}, issn = {2049-2618}, mesh = {Female ; Humans ; Cattle ; Animals ; *Gastrointestinal Microbiome/genetics ; Lactation ; Rumen/metabolism ; Plant Breeding ; Diet/veterinary ; Fermentation ; Animal Feed/analysis ; }, abstract = {BACKGROUND: Dairy cattle (Bos taurus), especially Holstein cows, which are the highest-producing dairy animals and are widely bred to provide milk products to humans, rely critically on their associated gastrointestinal tract (GIT) microbiota to digest plant feed. However, the region-specific taxonomic composition and function of the GIT microbiome in dairy cattle and the mechanistic basis for the diet-induced effects remain to be elucidated. RESULTS: We collected 120 digesta samples from 10 GIT regions of 12 Holstein cows fed forage- and grain-based diets and characterized their GIT microbiome via functional shotgun metagenomics and the resolution of metagenome-assembled genomes. Our results demonstrated that the GIT microbiome was mainly partitioned into three distinct clusters, four-chambered stomach, small intestine, and large intestine. Moreover, we found that the four-chambered stomach microbiome with the highest diversity had a strong ability to degrade recalcitrant polysaccharide substrates, underpinned by the prevalence of potential cellulosome--producing and plant-derived polysaccharide utilization loci-encoding consortia. In contrast, the post-gastric intestinal microbiome orchestrated alternative fermentation pathways to adapt to nutrient availability and energy acquisition. Diet shifts selectively modified the metabolic cascades of the microbiome in specific GIT regions, evidenced by the loss of fiber-degrading taxa and increased hydrogen sinks in propionate after grain introduction.

CONCLUSIONS: Our findings provide new insights into GIT microbial organization and function in dairy cattle by GIT regions and diet regimes, which offers clues for improving animal production and health in the future. Video Abstract.}, } @article {pmid36670373, year = {2023}, author = {Costa, SS and da Silva Moia, G and Silva, A and Baraúna, RA and de Oliveira Veras, AA}, title = {BADASS: BActeriocin-Diversity ASsessment Software.}, journal = {BMC bioinformatics}, volume = {24}, number = {1}, pages = {24}, pmid = {36670373}, issn = {1471-2105}, mesh = {*Bacteriocins/pharmacology/genetics ; RNA, Ribosomal, 16S/genetics ; Software ; Bacteria/genetics ; Metagenome ; Anti-Bacterial Agents ; }, abstract = {BACKGROUND: Bacteriocins are defined as thermolabile peptides produced by bacteria with biological activity against taxonomically related species. These antimicrobial peptides have a wide application including disease treatment, food conservation, and probiotics. However, even with a large industrial and biotechnological application potential, these peptides are still poorly studied and explored. BADASS is software with a user-friendly graphical interface applied to the search and analysis of bacteriocin diversity in whole-metagenome shotgun sequencing data.

RESULTS: The search for bacteriocin sequences is performed with tools such as BLAST or DIAMOND using the BAGEL4 database as a reference. The putative bacteriocin sequences identified are used to determine the abundance and richness of the three classes of bacteriocins. Abundance is calculated by comparing the reads identified as bacteriocins to the reads identified as 16S rRNA gene using SILVA database as a reference. BADASS has a complete pipeline that starts with the quality assessment of the raw data. At the end of the analysis, BADASS generates several plots of richness and abundance automatically as well as tabular files containing information about the main bacteriocins detected. The user is able to change the main parameters of the analysis in the graphical interface. To demonstrate how the software works, we used four datasets from WMS studies using default parameters. Lantibiotics were the most abundant bacteriocins in the four datasets. This class of bacteriocin is commonly produced by Streptomyces sp.

CONCLUSIONS: With a user-friendly graphical interface and a complete pipeline, BADASS proved to be a powerful tool for prospecting bacteriocin sequences in Whole-Metagenome Shotgun Sequencing (WMS) data. This tool is publicly available at https://sourceforge.net/projects/badass/ .}, } @article {pmid36670134, year = {2023}, author = {Zhao, P and Liu, B and Zhao, H and Lei, Z and Zhou, T}, title = {Significant changes in soil microbial community structure and metabolic function after Mikania micrantha invasion.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {1141}, pmid = {36670134}, issn = {2045-2322}, mesh = {*Mikania ; Soil ; Carbon ; China ; Forests ; Soil Microbiology ; *Microbiota ; Nitrogen ; Phosphorus ; }, abstract = {Currently, Mikania micrantha (M. micrantha) has invaded Guangdong, Guangxi and other provinces in China, causing serious harm to the forests of southeastern China. Soil microorganisms play an important role in the establishment of M. micrantha invasion, affecting plant productivity, community dynamics, and ecosystem function. However, at present, how M. micrantha invasion affects soil carbon, nitrogen, and phosphorus phase functional genes and the environmental factors that cause gene expression changes remain unclear, especially in subtropical forest ecosystems. This study was conducted in Xiangtoushan National Forest Park in Guangdong Province to compare the changes in soil nutrients and microorganisms after M. micrantha invasion of a forest. The microbial community composition and metabolic function were explored by metagenome sequencing. Our results showed that after M. micrantha invasion, the soil was more suitable for the growth of gram-positive bacteria (Gemmatimonadetes). In addition, the soil microbial community structure and enzyme activity increased significantly after M. micrantha invasion. Correlation analysis and Mantel test results suggested that total phosphorus (TP), nitrate nitrogen (NO3[-]-N), and soil dissolved organic matter (DOM; DOC and DON), were the strong correlates of soil microbial nitrogen functional genes, while soil organic matter (SOM), soil organic carbon (SOC), total nitrogen (TN), and available phosphorus (Soil-AP) were strongly correlated with the expression of soil microbial phosphorus functional gene. Mikania micrantha invasion alters soil nutrients, microbial community composition and metabolic function in subtropical forests, creates a more favorable growth environment, and may form a positive feedback process conducive to M. micrantha invasion.}, } @article {pmid36669400, year = {2023}, author = {Sun, S and Wang, Y and Xu, C and Qiao, C and Chen, S and Zhao, C and Liu, Q and Zhang, X}, title = {Reconstruction of microbiome and functionality accelerated crude oil biodegradation of 2,4-DCP-oil-contaminated soil systems using composite microbial agent B-Cl.}, journal = {Journal of hazardous materials}, volume = {447}, number = {}, pages = {130808}, doi = {10.1016/j.jhazmat.2023.130808}, pmid = {36669400}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; Bacteria/genetics/metabolism ; *Petroleum/metabolism ; Soil Microbiology ; Alkanes/metabolism ; *Microbiota ; Soil ; *Soil Pollutants/metabolism ; }, abstract = {Biodegradation is one of the safest and most economical methods for the elimination of toxic chlorophenols and crude oil from the environment. In this study, aerobic degradation of the aforementioned compounds by composite microbial agent B-Cl, which consisted of Bacillus B1 and B2 in a 3:2 ratio, was analyzed. The biodegradation mechanism of B-Cl was assessed based on whole genome sequencing, Fourier transform infrared spectroscopy and gas chromatographic analyses. B-Cl was most effective at reducing Cl[-] concentrations (65.17%) and crude oil biodegradation (59.18%) at 7 d, which was when the content of alkanes ≤ C30 showed the greatest decrease. Furthermore, adding B-Cl solution to soil significantly decreased the 2,4-DCP and oil content to below the detection limit and by 80.68%, respectively, and reconstructed of the soil microbial into a system containing more CPs-degrading (exaA, frmA, L-2-HAD, dehH, ALDH, catABE), aromatic compounds-degrading (pcaGH, catAE, benA-xylX, paaHF) and alkane- and fatty acid-degrading (alkB, atoB, fadANJ) microorganisms. Moreover, the presence of 2,4-DCP was the main hinder of the observed effects. This study demonstrates the importance of adding B-Cl solution to determine the interplay of CPs with microbes and accelerating oil degradation, which can be used for in-situ bioremediation of CPs and oil-contaminated soil.}, } @article {pmid36668684, year = {2023}, author = {Jiang, Z and Huang, M and Jiang, Y and Dong, Y and Shi, L and Li, J and Wang, Y}, title = {Microbial Contributions to Iodide Enrichment in Deep Groundwater in the North China Plain.}, journal = {Environmental science & technology}, volume = {57}, number = {6}, pages = {2625-2635}, doi = {10.1021/acs.est.2c06657}, pmid = {36668684}, issn = {1520-5851}, mesh = {Iodides/analysis ; Iodates/analysis ; *Iodine/analysis ; Iron ; Bacteria/genetics/metabolism ; Oxidation-Reduction ; *Groundwater ; China ; Sulfur/analysis ; *Water Pollutants, Chemical/analysis ; }, abstract = {Microorganisms play crucial roles in the global iodine cycling through iodine oxidation, reduction, volatilization, and deiodination. In contrast to iodate formation in radionuclide-contaminated groundwater by the iodine-oxidizing bacteria, microbial contribution to the formation of high level of iodide in geogenic high iodine groundwater is poorly understood. In this study, our results of comparative metagenomic analyses of deep groundwater with typical high iodide concentrations in the North China Plain revealed the existence of putative dissimilatory iodate-reducing idrABP1P2 gene clusters in groundwater. Heterologous expression and characterization of an identified idrABP1P2 gene cluster confirmed its functional role in iodate reduction. Thus, microbial dissimilatory iodate reduction could contribute to iodide formation in geogenic high iodine groundwater. In addition, the identified iron-reducing, sulfur-reducing, sulfur-oxidizing, and dehalogenating bacteria in the groundwater could contribute to the release and production of iodide through the reductive dissolution of iron minerals, abiotic iodate reduction of derived ferrous iron and sulfide, and dehalogenation of organic iodine, respectively. These microbially mediated iodate reduction and organic iodine dehalogenation processes may also result in the transformation among iodine species and iodide enrichment in other geogenic iodine-rich groundwater systems worldwide.}, } @article {pmid36662619, year = {2023}, author = {Secomandi, S and Gallo, GR and Sozzoni, M and Iannucci, A and Galati, E and Abueg, L and Balacco, J and Caprioli, M and Chow, W and Ciofi, C and Collins, J and Fedrigo, O and Ferretti, L and Fungtammasan, A and Haase, B and Howe, K and Kwak, W and Lombardo, G and Masterson, P and Messina, G and Møller, AP and Mountcastle, J and Mousseau, TA and Ferrer Obiol, J and Olivieri, A and Rhie, A and Rubolini, D and Saclier, M and Stanyon, R and Stucki, D and Thibaud-Nissen, F and Torrance, J and Torroni, A and Weber, K and Ambrosini, R and Bonisoli-Alquati, A and Jarvis, ED and Gianfranceschi, L and Formenti, G}, title = {A chromosome-level reference genome and pangenome for barn swallow population genomics.}, journal = {Cell reports}, volume = {42}, number = {1}, pages = {111992}, pmid = {36662619}, issn = {2211-1247}, support = {/HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; *Swallows/genetics ; Metagenomics ; Genome/genetics ; Genomics ; Chromosomes ; }, abstract = {Insights into the evolution of non-model organisms are limited by the lack of reference genomes of high accuracy, completeness, and contiguity. Here, we present a chromosome-level, karyotype-validated reference genome and pangenome for the barn swallow (Hirundo rustica). We complement these resources with a reference-free multialignment of the reference genome with other bird genomes and with the most comprehensive catalog of genetic markers for the barn swallow. We identify potentially conserved and accelerated genes using the multialignment and estimate genome-wide linkage disequilibrium using the catalog. We use the pangenome to infer core and accessory genes and to detect variants using it as a reference. Overall, these resources will foster population genomics studies in the barn swallow, enable detection of candidate genes in comparative genomics studies, and help reduce bias toward a single reference genome.}, } @article {pmid36662259, year = {2023}, author = {Tomoiagă, RB and Tork, SD and Filip, A and Nagy, LC and Bencze, LC}, title = {Phenylalanine ammonia-lyases: combining protein engineering and natural diversity.}, journal = {Applied microbiology and biotechnology}, volume = {107}, number = {4}, pages = {1243-1256}, pmid = {36662259}, issn = {1432-0614}, support = {PN-III-P1-1.1-TE-2019-2118//Unitatea Executiva pentru Finantarea Invatamantului Superior, a Cercetarii, Dezvoltarii si Inovarii/ ; }, mesh = {*Phenylalanine Ammonia-Lyase/genetics/metabolism ; *Protein Engineering ; Catalytic Domain ; Phenylalanine ; Mutation ; }, abstract = {In this study, rational design and saturation mutagenesis efforts for engineering phenylalanine ammonia-lyase from Petroselinum crispum (PcPAL) provided tailored PALs active towards challenging, highly valuable di-substituted substrates, such as the L-DOPA precursor 3,4-dimethoxy-L-phenylalanine or the 3-bromo-4-methoxy-phenylalanine. The rational design approach and saturation mutagenesis strategy unveiled identical PcPAL variants of improved activity, highlighting the limited mutational variety of the substrate specificity-modulator residues, L134, F137, I460 of PcPAL. Due to the restricted catalytic efficiency of the best performing L134A/I460V and F137V/I460V PcPAL variants, we imprinted these beneficial mutations to PALs of different origins. The variants of PALs from Arabidopsis thaliana (AtPAL) and Anabaena variabilis (AvPAL) showed higher catalytic efficiency than their PcPAL homologues. Further, the engineered PALs were also compared in terms of catalytic efficiency with a novel aromatic ammonia-lyase from Loktanella atrilutea (LaAAL), close relative of the metagenome-derived aromatic ammonia-lyase AL-11, reported recently to possess atypically high activity towards substrates with electron-donor aromatic substituents. Indeed, LaAAL outperformed the engineered Pc/At/AvPALs in the production of 3,4-dimethoxy-L-phenylalanine; however, in case of 3-bromo-4-methoxy derivatives it showed no activity, with computational results supporting the occurrence of steric hindrance. Transferring the unique array of selectivity modulator residues from LaAAL to the well-characterized PALs did not enhance their activity towards the targeted substrates. Moreover, applying the rational design strategy valid for these well-characterized PALs to LaAAL decreased its activity. These results suggest that distinct tailoring rationale is required for LaAAL/AL-11-like aromatic ammonia-lyases, which might represent a distinct PAL subclass, with natural reaction and substrate scope modified through evolutionary processes. KEY POINTS: • PAL-activity for challenging substrates generated by protein engineering • Rational/semi-rational protein engineering reveals constrained mutational variability • Engineered PALs are outperformed by novel ALs of distinct catalytic site signature.}, } @article {pmid36662202, year = {2022}, author = {Dat, TTH and Steinert, G and Cuc, NTK and Cuong, PV and Smidt, H and Sipkema, D}, title = {Diversity of Bacterial Secondary Metabolite Biosynthetic Gene Clusters in Three Vietnamese Sponges.}, journal = {Marine drugs}, volume = {21}, number = {1}, pages = {}, pmid = {36662202}, issn = {1660-3397}, support = {ÐTÐLCN.17/14//Vietnam Ministry of Science and Technology/ ; F07.003.06//BE-Basic Foundation-FES grant from the Dutch Ministry of Economic Affairs/ ; n◦ 607786//MC-ITN-BluePharmTrain funded through the European Union Programme FP7/2007-2013/ under REA grant agreement/ ; }, mesh = {*Actinobacteria/genetics ; Bacteria/genetics ; Biosynthetic Pathways/genetics ; Multigene Family/genetics ; Phylogeny ; *Porifera/microbiology ; Animals ; }, abstract = {Recent reviews have reinforced sponge-associated bacteria as a valuable source of structurally diverse secondary metabolites with potent biological properties, which makes these microbial communities promising sources of new drug candidates. However, the overall diversity of secondary metabolite biosynthetic potential present in bacteria is difficult to access due to the fact that the majority of bacteria are not readily cultured in the laboratory. Thus, use of cultivation-independent approaches may allow accessing "silent" and "cryptic" secondary metabolite biosynthetic gene clusters present in bacteria that cannot yet be cultured. In the present study, we investigated the diversity of secondary metabolite biosynthetic gene clusters (BGCs) in metagenomes of bacterial communities associated with three sponge species: Clathria reinwardti, Rhabdastrella globostellata, and Spheciospongia sp. The results reveal that the three metagenomes contain a high number of predicted BGCs, ranging from 282 to 463 BGCs per metagenome. The types of BGCs were diverse and represented 12 different cluster types. Clusters predicted to encode fatty acid synthases and polyketide synthases (PKS) were the most dominant BGC types, followed by clusters encoding synthesis of terpenes and bacteriocins. Based on BGC sequence similarity analysis, 363 gene cluster families (GCFs) were identified. Interestingly, no GCFs were assigned to pathways responsible for the production of known compounds, implying that the clusters detected might be responsible for production of several novel compounds. The KS gene sequences from PKS clusters were used to predict the taxonomic origin of the clusters involved. The KS sequences were related to 12 bacterial phyla with Actinobacteria, Proteobacteria, and Firmicutes as the most predominant. At the genus level, the KSs were most related to those found in the genera Mycolicibacterium, Mycobacterium, Burkholderia, and Streptomyces. Phylogenetic analysis of KS sequences resulted in detection of two known 'sponge-specific' BGCs, i.e., SupA and SwfA, as well as a new 'sponge-specific' cluster related to fatty acid synthesis in the phylum Candidatus Poribacteria and composed only by KS sequences of the three sponge-associated bacterial communities assessed here.}, } @article {pmid36662175, year = {2022}, author = {Pheiffer, F and Schneider, YK and Hansen, EH and Andersen, JH and Isaksson, J and Busche, T and Rückert, C and Kalinowski, J and Zyl, LV and Trindade, M}, title = {Bioassay-Guided Fractionation Leads to the Detection of Cholic Acid Generated by the Rare Thalassomonas sp.}, journal = {Marine drugs}, volume = {21}, number = {1}, pages = {}, pmid = {36662175}, issn = {1660-3397}, support = {UID87326//National Research Foundation/ ; }, mesh = {Humans ; Cholic Acid ; Phylogeny ; DNA, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Sequence Analysis, DNA ; }, abstract = {Bacterial symbionts of marine invertebrates are rich sources of novel, pharmaceutically relevant natural products that could become leads in combatting multidrug-resistant pathogens and treating disease. In this study, the bioactive potential of the marine invertebrate symbiont Thalassomonas actiniarum was investigated. Bioactivity screening of the strain revealed Gram-positive specific antibacterial activity as well as cytotoxic activity against a human melanoma cell line (A2058). The dereplication of the active fraction using HPLC-MS led to the isolation and structural elucidation of cholic acid and 3-oxo cholic acid. T. actiniarum is one of three type species belonging to the genus Thalassomonas. The ability to generate cholic acid was assessed for all three species using thin-layer chromatography and was confirmed by LC-MS. The re-sequencing of all three Thalassomonas type species using long-read Oxford Nanopore Technology (ONT) and Illumina data produced complete genomes, enabling the bioinformatic assessment of the ability of the strains to produce cholic acid. Although a complete biosynthetic pathway for cholic acid synthesis in this genus could not be determined based on sequence-based homology searches, the identification of putative penicillin or homoserine lactone acylases in all three species suggests a mechanism for the hydrolysis of conjugated bile acids present in the growth medium, resulting in the generation of cholic acid and 3-oxo cholic acid. With little known currently about the bioactivities of this genus, this study serves as the foundation for future investigations into their bioactive potential as well as the potential ecological role of bile acid transformation, sterol modification and quorum quenching by Thalassomonas sp. in the marine environment.}, } @article {pmid36660604, year = {2023}, author = {Fujimoto, K}, title = {Metagenome data-based phage therapy for intestinal bacteria-mediated diseases.}, journal = {Bioscience of microbiota, food and health}, volume = {42}, number = {1}, pages = {8-12}, pmid = {36660604}, issn = {2186-6953}, abstract = {Improvements in genome analysis technology using next-generation sequencing have revealed that abnormalities in the composition of the intestinal microbiota are important in numerous diseases. Furthermore, intestinal commensal pathogens that are directly involved in the onset and exacerbation of disease have been identified. Specific control of them is strongly desired. However, antibiotics are not appropriate for the control of intestinal commensal pathogens because they may kill beneficial bacteria as well. The intestinal tract contains many viruses: most are bacteriophages (phages) that infect intestinal bacteria rather than viruses that infect human cells. Phages have very high specificity for their host bacteria. Therefore, phage therapy is considered potentially useful for controlling intestinal commensal pathogens. However, the intestinal tract is a specialized, anaerobic environment, and it is impossible to isolate phages that infect host intestinal bacteria if the bacteria cannot be cultured. Furthermore, genomic analysis methods for intestinal phages have not been well established, so until recently, a complete picture of the intestinal phage has not been clear. In this review, I summarize the importance of next-generation phage therapy based on metagenomic data and describe a novel therapy against Clostridioides difficile developed using such data.}, } @article {pmid36660475, year = {2023}, author = {Liu, X and Tong, X and Jie, Z and Zhu, J and Tian, L and Sun, Q and Ju, Y and Zou, L and Lu, H and Qiu, X and Li, Q and Liao, Y and Lian, H and Zuo, Y and Chen, X and Rao, W and Ren, Y and Wang, Y and Zi, J and Wang, R and Xu, X and Yang, H and Wang, J and Zong, Y and Liu, W and Hou, Y and Jin, X and Xiao, L and Kristiansen, K and Jia, H and Zhang, T}, title = {Sex differences in the oral microbiome, host traits, and their causal relationships.}, journal = {iScience}, volume = {26}, number = {1}, pages = {105839}, pmid = {36660475}, issn = {2589-0042}, abstract = {The oral microbiome has been implicated in a growing number of diseases; however, determinants of the oral microbiome and their roles remain elusive. Here, we investigated the oral (saliva and tongue dorsum) metagenome, the whole genome, and other omics data in a total of 4,478 individuals and demonstrated that the oral microbiome composition and its major contributing host factors significantly differed between sexes. We thus conducted a sex-stratified metagenome-genome-wide-association study (M-GWAS) and identified 11 differential genetic associations with the oral microbiome (p sex-difference < 5 × 10[-8]). Furthermore, we performed sex-stratified Mendelian randomization (MR) analyses and identified abundant causalities between the oral microbiome and serum metabolites. Notably, sex-specific microbes-hormonal interactions explained the mostly observed sex hormones differences such as the significant causalities enrichments for aldosterone in females and androstenedione in males. These findings illustrate the necessity of sex stratification and deepen our understanding of the interplay between the oral microbiome and serum metabolites.}, } @article {pmid36659812, year = {2023}, author = {Shang, J and Tang, X and Sun, Y}, title = {PhaTYP: predicting the lifestyle for bacteriophages using BERT.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {1}, pages = {}, pmid = {36659812}, issn = {1477-4054}, support = {9678241//City University of Hong Kong/ ; //Hong Kong Innovation and Technology Commission/ ; }, mesh = {Infant, Newborn ; Humans ; *Bacteriophages/genetics ; Metagenomics/methods ; Bacteria ; *Microbiota ; Metagenome ; }, abstract = {Bacteriophages (or phages), which infect bacteria, have two distinct lifestyles: virulent and temperate. Predicting the lifestyle of phages helps decipher their interactions with their bacterial hosts, aiding phages' applications in fields such as phage therapy. Because experimental methods for annotating the lifestyle of phages cannot keep pace with the fast accumulation of sequenced phages, computational method for predicting phages' lifestyles has become an attractive alternative. Despite some promising results, computational lifestyle prediction remains difficult because of the limited known annotations and the sheer amount of sequenced phage contigs assembled from metagenomic data. In particular, most of the existing tools cannot precisely predict phages' lifestyles for short contigs. In this work, we develop PhaTYP (Phage TYPe prediction tool) to improve the accuracy of lifestyle prediction on short contigs. We design two different training tasks, self-supervised and fine-tuning tasks, to overcome lifestyle prediction difficulties. We rigorously tested and compared PhaTYP with four state-of-the-art methods: DeePhage, PHACTS, PhagePred and BACPHLIP. The experimental results show that PhaTYP outperforms all these methods and achieves more stable performance on short contigs. In addition, we demonstrated the utility of PhaTYP for analyzing the phage lifestyle on human neonates' gut data. This application shows that PhaTYP is a useful means for studying phages in metagenomic data and helps extend our understanding of microbial communities.}, } @article {pmid36658397, year = {2023}, author = {Laso-Pérez, R and Wu, F and Crémière, A and Speth, DR and Magyar, JS and Zhao, K and Krupovic, M and Orphan, VJ}, title = {Evolutionary diversification of methanotrophic ANME-1 archaea and their expansive virome.}, journal = {Nature microbiology}, volume = {8}, number = {2}, pages = {231-245}, pmid = {36658397}, issn = {2058-5276}, mesh = {*Archaea ; *Ecosystem ; Phylogeny ; Virome ; Geologic Sediments ; Anaerobiosis ; Methane/metabolism ; Alkanes/metabolism ; }, abstract = {'Candidatus Methanophagales' (ANME-1) is an order-level clade of archaea responsible for anaerobic methane oxidation in deep-sea sediments. The diversity, ecology and evolution of ANME-1 remain poorly understood. In this study, we use metagenomics on deep-sea hydrothermal samples to expand ANME-1 diversity and uncover the effect of virus-host dynamics. Phylogenetic analyses reveal a deep-branching, thermophilic family, 'Candidatus Methanospirareceae', closely related to short-chain alkane oxidizers. Global phylogeny and near-complete genomes show that hydrogen metabolism within ANME-1 is an ancient trait that was vertically inherited but differentially lost during lineage diversification. Metagenomics also uncovered 16 undescribed virus families so far exclusively targeting ANME-1 archaea, showing unique structural and replicative signatures. The expansive ANME-1 virome contains a metabolic gene repertoire that can influence host ecology and evolution through virus-mediated gene displacement. Our results suggest an evolutionary continuum between anaerobic methane and short-chain alkane oxidizers and underscore the effects of viruses on the dynamics and evolution of methane-driven ecosystems.}, } @article {pmid36657602, year = {2023}, author = {Ogunbayo, AE and Sabiu, S and Nyaga, MM}, title = {Evaluation of extraction and enrichment methods for recovery of respiratory RNA viruses in a metagenomics approach.}, journal = {Journal of virological methods}, volume = {314}, number = {}, pages = {114677}, pmid = {36657602}, issn = {1879-0984}, mesh = {Metagenomics/methods ; *Viruses/genetics ; *RNA Viruses/genetics ; RNA, Viral/genetics ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Viral metagenomics is increasingly applied in viral detection and virome characterization. Different extraction and enrichment techniques may be adopted, however, reports on their effective influence on viral recovery is often conflicting. Using a three step enrichment steps, the effect of three extraction kits and the influence of DNase treatment with or without rRNA removal for respiratory RNA virus recovery from nasopharyngeal swab samples was evaluated. The viral cocktail containing six different RNA viruses pooled in equal volume were subjected to the different extraction and enrichment methods, sequenced using the Illumina MiSeq, and analysed using Genome Detective. The PureLink® Viral RNA/DNA Mini Kit (PureLink) was highly efficient with better recovery of all the viral agents in the cocktail. The use of rRNA treatment resulted in increased viral recovery with PureLink and QIAamp® Viral RNA Mini kit, while having comparable recovery rate as DNase only with the QIAamp® MinElute Virus Spin Kit. The observed low reads and genome coverage of some of the viruses could be attributed to their low abundance. Depending on sample matrix, extraction choice and enrichment strategy may influence recovery of respiratory RNA virus in metagenomics studies, therefore individual evaluation and adoption may be necessary for a robust result.}, } @article {pmid36657438, year = {2023}, author = {Zhao, C and Shi, ZJ and Pollard, KS}, title = {Pitfalls of genotyping microbial communities with rapidly growing genome collections.}, journal = {Cell systems}, volume = {14}, number = {2}, pages = {160-176.e3}, pmid = {36657438}, issn = {2405-4720}, support = {R01 HL160862/HL/NHLBI NIH HHS/United States ; }, mesh = {Sequence Analysis, DNA ; Genotype ; *Algorithms ; *Microbiota/genetics ; Metagenome ; }, abstract = {Detecting genetic variants in metagenomic data is a priority for understanding the evolution, ecology, and functional characteristics of microbial communities. Many tools that perform this metagenotyping rely on aligning reads of unknown origin to a database of sequences from many species before calling variants. In this synthesis, we investigate how databases of increasingly diverse and closely related species have pushed the limits of current alignment algorithms, thereby degrading the performance of metagenotyping tools. We identify multi-mapping reads as a prevalent source of errors and illustrate a trade-off between retaining correct alignments versus limiting incorrect alignments, many of which map reads to the wrong species. Then we evaluate several actionable mitigation strategies and review emerging methods showing promise to further improve metagenotyping in response to the rapid growth in genome collections. Our results have implications beyond metagenotyping to the many tools in microbial genomics that depend upon accurate read mapping.}, } @article {pmid36656447, year = {2023}, author = {Zheng, W and Jiang, T and Zhang, Z and Pan, D and Tang, W and Li, Y and Jiang, L and Zhu, H and Yu, X and Chen, G and Wang, J and Zhang, J and Zhang, X}, title = {Otus scops adenovirus: the complete genome sequence of a novel aviadenovirus discovered in a wild owl.}, journal = {Archives of virology}, volume = {168}, number = {2}, pages = {68}, pmid = {36656447}, issn = {1432-8798}, support = {ZR2021QC187//Natural Science Foundation of Shandong Province/ ; 2020XJDN003//Yantai Research Institute for Replacing Old Growth Drivers with New Ones/ ; SDAIT-11-10//Technical system of poultry industry of Shandong Province/ ; }, mesh = {Animals ; Adenoviridae/genetics ; *Aviadenovirus/genetics ; *Strigiformes ; Phylogeny ; Genome, Viral ; *Adenoviridae Infections/veterinary ; }, abstract = {We present the complete genome sequence of an aviadenovirus obtained by metagenomics from cloacal swabs taken from a free-living Eurasian scops owl (Otus scops, a small raptor distributed in Europe and several parts of Asia) in China. Thirty protein coding genes were predicted in this 40,239-bp-long genome, which encodes the largest fiber protein among all reported aviadenoviruses. The viral genome sequence is highly divergent, and the encoded proteins have an average of only 55% amino acid sequence identity to those of other adenoviruses. In phylogenetic analysis, the new owl virus grouped with members of the genus Aviadenovirus and formed a common clade with another owl adenovirus reported previously in Japan. This is the second complete genome sequence of an aviadenovirus discovered in owls, and its proteins have an average of 62% amino acid sequence identity to those of the previously reported owl adenovirus. Combining this result with comparative genomic analysis of all aviadenoviruses, we propose that this owl virus and the previously described Japanese owl adenovirus can be assigned to two new species in the genus Aviadenovirus. This study provides new data on the diversity of aviadenoviruses in wild birds.}, } @article {pmid36656265, year = {2023}, author = {Yu, Y and Yu, X and Zhang, D and Jin, L and Huang, J and Zhu, X and Sun, J and Yu, M and Zhu, L}, title = {Biotransformation of Organophosphate Esters by Rice and Rhizosphere Microbiome: Multiple Metabolic Pathways, Mechanism, and Toxicity Assessment.}, journal = {Environmental science & technology}, volume = {57}, number = {4}, pages = {1776-1787}, doi = {10.1021/acs.est.2c07796}, pmid = {36656265}, issn = {1520-5851}, mesh = {*Oryza ; Rhizosphere ; Esters/metabolism ; *Flame Retardants/analysis ; Organophosphates ; Biotransformation ; Phosphates ; *Microbiota ; Metabolic Networks and Pathways ; Environmental Monitoring ; China ; }, abstract = {The biotransformation behavior and toxicity of organophosphate esters (OPEs) in rice and rhizosphere microbiomes were comprehensively studied by hydroponic experiments. OPEs with lower hydrophobicity were liable to be translocated acropetally, and rhizosphere microbiome could reduce the uptake and translocation of OPEs in rice tissues. New metabolites were successfully identified in rice and rhizosphere microbiome, including hydrolysis, hydroxylated, methylated, and glutathione-, glucuronide-, and sulfate-conjugated products. Rhizobacteria and plants could cooperate to form a complex ecological interaction web for OPE elimination. Furthermore, active members of the rhizosphere microbiome during OPE degradation were revealed and the metagenomic analysis indicated that most of these active populations contained OPE-degrading genes. The results of metabolomics analyses for phytotoxicity assessment implied that several key function metabolic pathways of the rice plant were found perturbed by metabolites, such as diphenyl phosphate and monophenyl phosphate. In addition, the involved metabolism mechanisms, such as the carbohydrate metabolism, amino acid metabolism and synthesis, and nucleotide metabolism in Escherichia coli, were significantly altered after exposure to the products mixture of OPEs generated by rhizosphere microbiome. This work for the first time gives a comprehensive understanding of the entire metabolism of OPEs in plants and associated microbiome, and provides support for the ongoing risk assessment of emerging contaminants and, most critically, their transformation products.}, } @article {pmid36656115, year = {2023}, author = {Yalcin, SS and Kuskonmaz, BB and Perez-Brocal, V and Uckan Cetinkaya, D and Moya, A and Dinleyici, EC}, title = {Human Mastadenovirus A Infection in a Child During the Course of Hematopoietic Stem Cell Transplant.}, journal = {Experimental and clinical transplantation : official journal of the Middle East Society for Organ Transplantation}, volume = {}, number = {}, pages = {}, doi = {10.6002/ect.2022.0049}, pmid = {36656115}, issn = {2146-8427}, abstract = {Following primary infection, human mastadeno- viruses can persist in various tissues. We report a case of a pediatric patient with Fanconi anemia who had a complicated posttransplant course after allogeneic hematopoietic stem cell transplant that was associated with human mastadenovirus infection. Human mastadenovirus reactivation was detected with metagenomic analysis during a 3-month follow- up period; the predominant rate of occurrence of human mastadenoviruses was 1.1% on day 0, 84% on day +15, 90% on day +30, and 42% on day +82. Virus shedding continued up to 3 months after transplant. At 36 months after hematopoietic stem cell transplant, the patient was in good clinical condition with full donor chimerism. Long-term follow-up studies for human mastadenoviruses are needed to determine latency period.}, } @article {pmid36656039, year = {2023}, author = {Liu, Z and Huang, Y and Zhang, T and Meng, D and Jiang, Z and Yang, Z and Yang, Z and Li, L and Gu, Y and Wang, J and Liu, X and Jiang, C and Yin, H}, title = {Viruses Regulate Microbial Community Assembly Together with Environmental Factors in Acid Mine Drainage.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {2}, pages = {e0197322}, pmid = {36656039}, issn = {1098-5336}, mesh = {Humans ; Bacteria/genetics ; Mining ; *Microbiota/genetics ; Microbial Consortia ; *Viruses/genetics ; }, abstract = {Viruses are widespread in various ecosystems, and they play important roles in regulating the microbial community via host-virus interactions. Recently, metagenomic studies showed that there are extremely diverse viruses in different environments from the ocean to the human gut, but the influences of viral communities on microbial communities are poorly understood, especially in extreme environments. Here, we used metagenomics to characterize microbial communities and viral communities in acid mine drainage (AMD) and evaluated how viruses shape microbial community constrained by the harsh environments. Our results showed that AMD viral communities are significantly associated with the microbial communities, and viral diversity has positive correlations with microbial diversity. Viral community explained more variations of microbial community composition than environmental factors in AMD of a polymetallic mine. Moreover, we found that viruses harboring adaptive genes regulate a relative abundance of hosts under the modulation of environmental factors, such as pH. We also observed that viral diversity has significant correlations with the global properties of microbial cooccurrence networks, such as modularity. In addition, the results of null modeling analyses revealed that viruses significantly affect microbial community phylogeny and play important roles in regulating ecological processes of community assembly, such as dispersal limitation and homogenous dispersal. Together, these results revealed that AMD viruses are critical forces driving microbial network and community assembly via host-virus interactions. IMPORTANCE Viruses as mobile genetic elements play critical roles in the adaptive evolution of their hosts in extreme environments. However, how viruses further influence microbial community structure and assembly is still unclear. A recent metagenomic study observed diverse viruses unexplored in acid mine drainage, revealing the associations between the viral community and environmental factors. Here, we showed that viruses together with environmental factors can constrain the relative abundance of host and microbial community assembly in AMD of copper mines and polymetallic mines. Our results highlight the importance of viruses in shaping the microbial community from the individual host level to the community level.}, } @article {pmid36655989, year = {2023}, author = {Portanier, E and Henri, H and Benedetti, P and Sanchis, F and Régis, C and Chevret, P and Zedda, M and El Filali, A and Ruette, S and Devillard, S}, title = {Population genomics of Corsican wildcats: Paving the way toward a new subspecies within the Felis silvestris spp. complex?.}, journal = {Molecular ecology}, volume = {32}, number = {8}, pages = {1908-1924}, doi = {10.1111/mec.16856}, pmid = {36655989}, issn = {1365-294X}, support = {//Direction Régionale de l'Environnement, de l'Aménagement et du Logement Corse/ ; //Laboratoire de Biométrie et Biologie Evolutive/ ; //Office de l'Environnement de la Corse/ ; //Office Français de la Biodiversité/ ; //Université de Lyon/ ; }, mesh = {Cats ; Animals ; *Metagenomics ; Phylogeny ; Genotype ; Genomics ; *Felis/genetics ; }, abstract = {In the context of the current extinction crisis, identifying new conservation units is pivotal to the development of sound conservation measures, especially in highly threatened taxa such as felids. Corsican wildcats are known by Corsican people since a very long time but have been little studied. Meaningful information about their phylogenetic position is lacking. We used ddRADseq to genotype phenotypically homogenous Corsican wildcats at 3671 genome-wide SNPs and reported for the first time their genetic identity. We compared this genomic information to domestic cats Felis silvestris catus from Corsica and mainland France, European wildcats F. s. silvestris and Sardinian wildcats F. s. lybica. Our premise was that if the Corsican wildcat, as a phenotypic entity, also represents a genetic entity, it deserves conservation measures and to be recognized as a conservation unit. Corsican wildcats appeared highly genetically differentiated from European wildcats and genetically closer to Sardinian wildcats than to domestic cats. Domestic cats from Corsica and mainland France were closer to each other and Sardinian wildcats were intermediate between Corsican wildcats and domestic cats. This suggested that Corsican wildcats do not belong to the F. s. silvestris or catus lineages. The inclusion of more high-quality Sardinian samples and Near-Eastern mainland F. s. lybica would constitute the next step toward assessing the status of Corsican wildcat as a subspecies and/or evolutionarily significant unit and tracing back wildcat introduction history of in Corsica.}, } @article {pmid36655544, year = {2023}, author = {Sun, H and Wang, P and Li, Y}, title = {An integrated microbiome project for charactering microbial diversity in classroom based on virtual simulation experiments.}, journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology}, volume = {51}, number = {2}, pages = {171-179}, doi = {10.1002/bmb.21706}, pmid = {36655544}, issn = {1539-3429}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Learning ; Students ; Computational Biology/education ; *Microbiota/genetics ; }, abstract = {Microbiome study requires both molecular techniques and bioinformatics skills, which are challenging for biologists to participate in this growing field. To introduce microbiome concepts and skills to students, a 6-week wet-lab and bioinformatics course for undergraduates was implemented through the project-based learning (PBL) approach. In the saliva microbiome project, students collected their saliva samples, performed DNA extraction and PCR amplification, followed by metagenomic analysis to compare the diversity and abundances of microbes among samples. First, students are required to practice molecular techniques and bioinformatics analysis skills in a virtual simulation lab. To our knowledge, our study is the first one to incorporate a virtual lab into microbiome experience. Then, students applied their recently acquired skills to produce and analyze their own 16S amplicon sequencing data and reported their results via a scientific report. The student learning outcomes show that the Virtual lab can improve students' laboratory techniques and research capabilities. Moreover, a simple pipeline to analyze 16S rRNA gene amplicon sequencing data is introduced in a step-by-step manner that helps students to develop analysis skills. This project can be modified as either a virtual course or a module within another course such as microbiology, molecular biology, and bioinformatics. Our study provides evidence on the positive impact of virtual labs on learning outcomes in undergraduate science education.}, } @article {pmid36655046, year = {2023}, author = {Dutra, J and Gomes, R and Yupanqui García, GJ and Romero-Cale, DX and Santos Cardoso, M and Waldow, V and Groposo, C and Akamine, RN and Sousa, M and Figueiredo, H and Azevedo, V and Góes-Neto, A}, title = {Corrosion-influencing microorganisms in petroliferous regions on a global scale: systematic review, analysis, and scientific synthesis of 16S amplicon metagenomic studies.}, journal = {PeerJ}, volume = {11}, number = {}, pages = {e14642}, pmid = {36655046}, issn = {2167-8359}, mesh = {Humans ; Corrosion ; *Metagenomics/methods ; *Archaea/genetics ; Bacteria/genetics ; Water/metabolism ; }, abstract = {The objective of the current systematic review was to evaluate the taxonomic composition and relative abundance of bacteria and archaea associated with the microbiologically influenced corrosion (MIC), and the prediction of their metabolic functions in different sample types from oil production and transport structures worldwide. To accomplish this goal, a total of 552 published studies on the diversity of microbial communities using 16S amplicon metagenomics in oil and gas industry facilities indexed in Scopus, Web of Science, PubMed and OnePetro databases were analyzed on 10th May 2021. The selection of articles was performed following the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. Only studies that performed amplicon metagenomics to obtain the microbial composition of samples from oil fields were included. Studies that evaluated oil refineries, carried out amplicon metagenomics directly from cultures, and those that used DGGE analysis were removed. Data were thoroughly investigated using multivariate statistics by ordination analysis, bivariate statistics by correlation, and microorganisms' shareability and uniqueness analysis. Additionally, the full deposited databases of 16S rDNA sequences were obtained to perform functional prediction. A total of 69 eligible articles was included for data analysis. The results showed that the sulfidogenic, methanogenic, acid-producing, and nitrate-reducing functional groups were the most expressive, all of which can be directly involved in MIC processes. There were significant positive correlations between microorganisms in the injection water (IW), produced water (PW), and solid deposits (SD) samples, and negative correlations in the PW and SD samples. Only the PW and SD samples displayed genera common to all petroliferous regions, Desulfotomaculum and Thermovirga (PW), and Marinobacter (SD). There was an inferred high microbial activity in the oil fields, with the highest abundances of (i) cofactor, (ii) carrier, and (iii) vitamin biosynthesis, associated with survival metabolism. Additionally, there was the presence of secondary metabolic pathways and defense mechanisms in extreme conditions. Competitive or inhibitory relationships and metabolic patterns were influenced by the physicochemical characteristics of the environments (mainly sulfate concentration) and by human interference (application of biocides and nutrients). Our worldwide baseline study of microbial communities associated with environments of the oil and gas industry will greatly facilitate the establishment of standardized approaches to control MIC.}, } @article {pmid36654677, year = {2023}, author = {Marroquin, TY and Guauque-Olarte, S}, title = {Integrative analysis of gene and protein expression in atherosclerosis-related pathways modulated by periodontal pathogens. Systematic review.}, journal = {The Japanese dental science review}, volume = {59}, number = {}, pages = {8-22}, pmid = {36654677}, issn = {1882-7616}, abstract = {UNLABELLED: The mechanisms modulated by periodontal pathogens in atherosclerosis are not fully understood. Aim: to perform an integrative analysis of gene and protein expression modulated by periodontal pathogens in cells and animal models for atherosclerosis.

METHODS: Cochrane, PRISMA and AMSTAR2 guidelines for systematic reviews were followed. Data search was conducted in Pub-med, LILACS and Science Direct databases. Gene and protein expression data were collected from the included papers to perform an overrepresentation analysis using the Reactome Pathway Analysis tool and the KEGG database.

RESULTS: Thirty-two papers were included in the review, they analyzed the effect of Fusobacterium nucleatum, Porphyromonas gingivalis, Streptococcus anginosus, Streptococcus sanguinis, Tannerella forsythia, and Treponema denticola or/and their virulent factors on gene and protein expression in human cells and animal models of atherosclerosis. Some of the modulated pathways include the immune system, programmed cell death, cellular responses to external stimuli, transport of small molecules, and signal transduction (p < 0.05). Those pathways are known to be involved in different stages of atherosclerosis progression.

CONCLUSION: Based on the performed analysis, it is possible to state that periodontal pathogens have the potential to be a contributing factor for atherosclerosis even in absence of a high-fat diet or high shear stress.}, } @article {pmid36653448, year = {2023}, author = {Valles-Colomer, M and Blanco-Míguez, A and Manghi, P and Asnicar, F and Dubois, L and Golzato, D and Armanini, F and Cumbo, F and Huang, KD and Manara, S and Masetti, G and Pinto, F and Piperni, E and Punčochář, M and Ricci, L and Zolfo, M and Farrant, O and Goncalves, A and Selma-Royo, M and Binetti, AG and Becerra, JE and Han, B and Lusingu, J and Amuasi, J and Amoroso, L and Visconti, A and Steves, CM and Falchi, M and Filosi, M and Tett, A and Last, A and Xu, Q and Qin, N and Qin, H and May, J and Eibach, D and Corrias, MV and Ponzoni, M and Pasolli, E and Spector, TD and Domenici, E and Collado, MC and Segata, N}, title = {The person-to-person transmission landscape of the gut and oral microbiomes.}, journal = {Nature}, volume = {614}, number = {7946}, pages = {125-135}, pmid = {36653448}, issn = {1476-4687}, support = {MR/S005013/1/MRC_/Medical Research Council/United Kingdom ; U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Female ; Humans ; Infant ; *Bacteria/classification/genetics/isolation & purification ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Microbiota/genetics ; Mothers ; *Mouth/microbiology ; Infectious Disease Transmission, Vertical ; Family Characteristics ; Aging ; *Disease Transmission, Infectious ; Time Factors ; Microbial Viability ; *Home Environment ; }, abstract = {The human microbiome is an integral component of the human body and a co-determinant of several health conditions[1,2]. However, the extent to which interpersonal relations shape the individual genetic makeup of the microbiome and its transmission within and across populations remains largely unknown[3,4]. Here, capitalizing on more than 9,700 human metagenomes and computational strain-level profiling, we detected extensive bacterial strain sharing across individuals (more than 10 million instances) with distinct mother-to-infant, intra-household and intra-population transmission patterns. Mother-to-infant gut microbiome transmission was considerable and stable during infancy (around 50% of the same strains among shared species (strain-sharing rate)) and remained detectable at older ages. By contrast, the transmission of the oral microbiome occurred largely horizontally and was enhanced by the duration of cohabitation. There was substantial strain sharing among cohabiting individuals, with 12% and 32% median strain-sharing rates for the gut and oral microbiomes, and time since cohabitation affected strain sharing more than age or genetics did. Bacterial strain sharing additionally recapitulated host population structures better than species-level profiles did. Finally, distinct taxa appeared as efficient spreaders across transmission modes and were associated with different predicted bacterial phenotypes linked with out-of-host survival capabilities. The extent of microorganism transmission that we describe underscores its relevance in human microbiome studies[5], especially those on non-infectious, microbiome-associated diseases.}, } @article {pmid36651919, year = {2023}, author = {Fernandes-Martins, MC and Colman, DR and Boyd, ES}, title = {Relationships between fluid mixing, biodiversity, and chemosynthetic primary productivity in Yellowstone hot springs.}, journal = {Environmental microbiology}, volume = {25}, number = {5}, pages = {1022-1040}, doi = {10.1111/1462-2920.16340}, pmid = {36651919}, issn = {1462-2920}, mesh = {*Bacteria/genetics ; Ecosystem ; *Hot Springs ; Biodiversity ; Metagenome ; }, abstract = {The factors that influence biodiversity and productivity of hydrothermal ecosystems are not well understood. Here we investigate the relationship between fluid mixing, biodiversity, and chemosynthetic primary productivity in three co-localized hot springs (RSW, RSN, and RSE) in Yellowstone National Park that have different geochemistry. All three springs are sourced by reduced hydrothermal fluid, but RSE and RSN receive input of vapour phase gas and oxidized groundwaters, with input of both being substantially higher in RSN. Metagenomic sequencing revealed that communities in RSN were more biodiverse than those of RSE and RSW in all dimensions evaluated. Microcosm activity assays indicate that rates of dissolved inorganic carbon (DIC) uptake were also higher in RSN than in RSE and RSW. Together, these results suggest that increased mixing of reduced volcanic fluid with oxidized fluids generates additional niche space capable of supporting increasingly biodiverse communities that are more productive. These results provide insight into the factors that generate and maintain chemosynthetic biodiversity in hydrothermal systems and that influence the distribution, abundance, and diversity of microbial life in communities supported by chemosynthesis. These factors may also extend to other ecosystems not supported by photosynthesis, including the vast subterranean biosphere and biospheres beneath ice sheets and glaciers.}, } @article {pmid36651762, year = {2023}, author = {Zünd, M and Dunham, SJB and Rothman, JA and Whiteson, KL}, title = {What Lies Beneath? Taking the Plunge into the Murky Waters of Phage Biology.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0080722}, pmid = {36651762}, issn = {2379-5077}, support = {T32 AG00096-38//HHS | NIH | National Institute on Aging (NIA)/ ; }, mesh = {*Bacteriophages/genetics ; *Microbiota ; Biology ; }, abstract = {The sequence revolution revealed that bacteria-infecting viruses, known as phages, are Earth's most abundant biological entities. Phages have far-reaching impacts on the form and function of microbial communities and play a fundamental role in ecological processes. However, even well into the sequencing revolution, we have only just begun to explore the murky waters around the phage biology iceberg. Many viral reads cannot be assigned to a culturable isolate, and reference databases are biased toward more easily collectible samples, which likely distorts our conclusions. This minireview points out alternatives to mapping reads to reference databases and highlights innovative bioinformatic and experimental approaches that can help us overcome some of the challenges in phage research and better decipher the impact of phages on microbial communities. Moving beyond the identification of novel phages, we highlight phage metabolomics as an important influencer of bacterial host cell physiology and hope to inspire the reader to consider the effects of phages on host metabolism and ecosystems at large. We encourage researchers to report unassigned/unknown sequencing reads and contigs and to continue developing alternative methods to investigate phages within sequence data.}, } @article {pmid36651744, year = {2023}, author = {Li, X and Yang, L and Li, D and Yang, X and Wang, Z and Chen, M and Wu, F and Dou, X and Niu, M and Qi, H and Deng, T and Xia, H and Wang, D}, title = {Diagnosis of Neurological Infections in Pediatric Patients from Cell-Free DNA Specimens by Using Metagenomic Next-Generation Sequencing.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0253022}, pmid = {36651744}, issn = {2165-0497}, mesh = {Humans ; Child ; Retrospective Studies ; Cohort Studies ; *Communicable Diseases ; *Viruses ; *Central Nervous System Infections/diagnosis ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; }, abstract = {Central nervous system (CNS) infections can cause significant morbidity and mortality, especially in children. Rapid and accurate pathogenic detection in suspected CNS infections is essential for disease control at the early stage of infection. To evaluate the performance of metagenomic next-generation sequencing (mNGS) of cell-free DNA (cfDNA) in cerebrospinal fluid (CSF) in pediatric patients, we retrospectively analyzed the efficiency of cfDNA mNGS in children with CNS infections (n = 257) or noninfectious neurological disorders (n = 81). The CSF samples of 124 random subjects were used to evaluate the accuracy between mNGS of cfDNA and whole-cell DNA (wcDNA). In total, cfDNA mNGS detected a wide range of microbes with a detection rate of 71.0%, and the sensitivity and total coincidence rate with clinical diagnosis reached 68.9% and 67.5%, respectively. Compared with wcDNA mNGS, cfDNA mNGS had a higher efficacy in detecting viruses (66 versus 13) and Mycobacterium (7 versus 1), with significantly higher reads per million. The dominant causative pathogens were bacteria and viruses in CNS infections, but these presented with different pathogen spectra in different age categories. The best timing for the mNGS test ranged from 1 to 6 days after the start of anti-infection therapy, and the earlier mNGS started, the better was identification of bacterial CNS infections. This study emphasized that cfDNA mNGS had overall superiority to conventional methods on causative pathogen detection in pediatric CNS infections, and it was even better than wcDNA mNGS. Furthermore, research needs to be better validated in large-scale clinical trials to improve the clinical applications of cfDNA mNGS. IMPORTANCE Our study emphasized that cfDNA mNGS had overall superiority to conventional methods on causative pathogen detection in CNS-infected children, and it was even better than wcDNA mNGS. cfDNA mNGS detected a wide range of pathogens with a high total coincidence rate (67.5%) against clinical diagnosis. The best timing for cfDNA mNGS detection ranged from 1 to 6 days, rather than 0 days, after the start of empirical anti-infection therapy. The earlier mNGS started, the better the identifications of bacterial CNS infections. To the best of our knowledge, this research is the first report evaluating the clinical utility of mNGS with different methods (cfDNA versus wcDNA) of extracting DNA from CSF specimens in diagnosing pediatric CNS infections. Meanwhile, this is the largest cohort study that has evaluated the performance of mNGS using cfDNA from CSF specimens in pediatric patients with CNS infections.}, } @article {pmid36651521, year = {2023}, author = {Petrone, ME and Holmes, EC and Harvey, E}, title = {Through an ecological lens: An ecosystem-based approach to zoonotic risk assessment: An ecosystem-based approach to zoonotic risk assessment.}, journal = {EMBO reports}, volume = {24}, number = {2}, pages = {e56578}, pmid = {36651521}, issn = {1469-3178}, mesh = {*Ecosystem ; Biodiversity ; *Viruses ; Public Health ; Risk Assessment ; }, abstract = {Public health strategies to mitigate the emergence of novel pathogenic viruses should implement longitudinal metagenomic surveillance of ecosystems experiencing biodiversity changes to identify generalist viruses.}, } @article {pmid36651466, year = {2023}, author = {Demoliner, M and Filippi, M and Gularte, JS and Silva, MSD and Almeida, PR and Pereira, VMAG and Heldt, FH and Spilki, FR}, title = {Genome of a husavirus from Southern Brazil.}, journal = {Revista do Instituto de Medicina Tropical de Sao Paulo}, volume = {65}, number = {}, pages = {e5}, pmid = {36651466}, issn = {1678-9946}, mesh = {Humans ; Brazil ; *Genome, Viral/genetics ; Phylogeny ; *RNA Viruses/genetics ; }, abstract = {New viruses of the Picornavirales order have been discovered with the increase in the number of sequences obtained by high-throughput sequencing, as well as human stool-associated RNA virus (husavirus [HuV]), found in human stool samples. However, there is much to be clarified about HuV. Its cellular host, evolutionary history, and other biological characteristics are still unknown. Therefore, samples collected from human beings and environmental samples in a watershed in Southern Brazil were processed for the metagenomic library. Upon metagenomic analysis, we identified a HuV (husavirus LMM_67754 OP019707) genome with 8,846 bp, which was reported for the first time in Southern Brazil. The new genome presents only 37% of nucleotide identity with Brazilian strains and more than 90% with genomes from China, Vietnam, Venezuela, and the Netherlands. The HuV phylogeny presents significant differences among genomes, probably because multiple introductions of the virus may have occurred. Many questions still need to be answered about HuV. Therefore, more sequences and studies on this virus are necessary to improve the comprehension of the unknown origin of Picornavirales.}, } @article {pmid36650527, year = {2023}, author = {Zhao, N and Zhang, Q and Guo, Y and Cui, S and Tian, Y and Zhang, Y and Zhou, Y and Wang, X}, title = {Oral microbiome contributes to the failure of orthodontic temporary anchorage devices (TADs).}, journal = {BMC oral health}, volume = {23}, number = {1}, pages = {22}, pmid = {36650527}, issn = {1472-6831}, support = {62076011//National Natural Science Foundation of China,China/ ; PKUSSNMP-202013//National Program for Multidisciplinary Cooperative Treatment on Major Diseases/ ; A2021-021//China Oral Health Foundation/ ; 81671015//National Natural Science Foundation of China/ ; Z171100001017128//Beijing Municipal Science and Technology Commission/ ; }, mesh = {Humans ; *Orthodontic Anchorage Procedures ; Orthodontic Appliance Design ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: The stability of temporary anchorage devices (TADs) is critical in orthodontic clinics. The failure of TADs is multifactorial, and the role of the oral microbiome has not been clearly defined. Herein, we attempted to analyze the contribution of the oral microbiome to the failure of TADs.

METHODS: Next-generation sequencing was adopted for analyzing the microbiome on the TADs from orthodontic patients. 29 TADs (15 failed TADs and 14 successful TADs) were used for 16S rRNA gene sequencing. A total of 135 TADs (62 failed TADs and 73 successful TADs) were collected to conduct metagenomic sequencing. Additionally, 34 verified samples (18 failed TADs and 16 successful TADs) were collected for quantitative real-time polymerase chain reaction analysis (qRT-PCR).

RESULTS: Successful and failed TADs demonstrated discrepancies in microbiome structure, composition, and function. Clear separations were found in β-diversity in 16S rRNA gene sequencing as well as metagenomic sequencing (p < 0.05). Metagenomic sequencing showed that Prevotella intermedia, Eikenella corrodens, Parvimonas spp., Neisseria elongata, and Catonella morbi were enriched in the failed groups. qRT-PCR also demonstrated that the absolute bacteria load of Prevotella intermedia was higher in failed TADs (p < 0.05). Considering functional aspects, the failed group showed enriched genes involved in flagellar assembly, bacterial chemotaxis, and oxidative phosphorylation.

CONCLUSIONS: This study illustrated the compositional and functional differences of microorganisms found on successful and failed TADs, indicating that controlling bacterial adhesion on the surface of TADs is essential for their success rate.}, } @article {pmid36650445, year = {2023}, author = {Aja-Macaya, P and Rumbo-Feal, S and Poza, M and Cañizares, A and Vallejo, JA and Bou, G}, title = {A new and efficient enrichment method for metagenomic sequencing of Monkeypox virus.}, journal = {BMC genomics}, volume = {24}, number = {1}, pages = {29}, pmid = {36650445}, issn = {1471-2164}, support = {Innova Saúde//SERGAS-Galician Healthcare Service/ ; Innova Saúde//SERGAS-Galician Healthcare Service/ ; Innova Saúde//SERGAS-Galician Healthcare Service/ ; Innova Saúde//SERGAS-Galician Healthcare Service/ ; CIBERINFEC//Instituto de Salud Carlos III/ ; PI20/00413//Instituto de Salud Carlos III/ ; CIBERINFEC//Instituto de Salud Carlos III/ ; }, mesh = {Humans ; *Monkeypox virus/genetics ; *Mpox (monkeypox)/diagnosis ; DNA, Viral/genetics ; }, abstract = {BACKGROUND: The methodology described in previous literature for Monkeypox virus (MPXV) sequencing shows low efficiency when using metagenomic approaches. The aim of the present study was to evaluate a new fine-tuned method for extraction and enrichment of genomic MPXV DNA using clinical samples and to compare it to a non-enrichment metagenomic approach.

RESULTS: A new procedure that allows sample enrichment in MPXV DNA, avoiding wasting the sequencing capacity in human DNA, was designed. This procedure consisted of host DNA depletion using a saponin/NaCl combination treatment and DNase, together with high g-force centrifugations. After typical quality control, samples using the enrichment method contained around 96% of reads not classified as human DNA, while the non-enrichment protocol showed around 5-10%. When reads not belonging to Orthopoxvirus were removed, enriched samples kept about 50% of the original read counts, while non-enriched ones kept only 2-7%.

CONCLUSIONS: Results showed a very significant improvement in sequencing efficiency, increasing the number of reads belonging to MPXV, the depth of coverage and the trustworthiness of the consensus sequences. This, in turn, allows for more samples to be included in a single cartridge, reducing costs and time to diagnosis, which can be very important factors when dealing with a contagious disease.}, } @article {pmid36650368, year = {2023}, author = {Raiyani, NM and Singh, SP}, title = {Microbial community and predictive functionalities associated with the marine sediment of Coastal Gujarat.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {15}, pages = {43245-43266}, pmid = {36650368}, issn = {1614-7499}, mesh = {Geologic Sediments/chemistry ; *Microbiota ; *Cyanobacteria ; Bacteroidetes ; Proteobacteria ; RNA, Ribosomal, 16S ; }, abstract = {Marine sediments are complex ecosystems where structures and functions constantly change due to natural and anthropogenic influences. In this investigation, a comprehensive and comparative analysis of the bacterial communities and their functional potential of the pristine and polluted marine sediments were carried out using MiSeq. The phylum Proteobacteria was dominant in all study sites. Other phyla were Actinobacteria, Bacteroidetes, Planctomycetes, Acidobacteria, Chloroflexi, Nitrospirae, Cyanobacteria, Verrucomicrobia, Tenericutes, and Chlorobi. Interestingly, about 50% of genera belong to the unclassified categories. The key genera were identified as Acinetobacter, Bacillus, Pseudomona, Idiomarina, Thalassospira, and Marinobacter, Halomonas, Planctomyces, Psychrobacter, and Vogesella. PICRUSt analysis revealed that major functions are associated with the metabolism category. Additionally, metabolism related to amino acids, carbohydrates, energy generation, xenobiotics degradation, nitrogen, sulfate, and methane were prominent. Similarly, the predicted metabolisms by COG and KEGG were observed in the microbial communities of the marine sediments. To date, a comprehensive description of the microbial life with metabolic potential in these study sites has not been investigated. This study therefore significantly adds to our understanding of the microbiome and its functional attributes of marine sediments.}, } @article {pmid36650285, year = {2023}, author = {Sun, A and Li, CP and Chen, Z and Zhang, S and Li, DY and Yang, Y and Li, LQ and Zhao, Y and Wang, K and Li, Z and Liu, J and Liu, S and Wang, J and Liu, JG}, title = {The compact Casπ (Cas12l) 'bracelet' provides a unique structural platform for DNA manipulation.}, journal = {Cell research}, volume = {33}, number = {3}, pages = {229-244}, pmid = {36650285}, issn = {1748-7838}, mesh = {*Gene Editing ; *DNA/genetics ; Endonucleases/genetics ; CRISPR-Cas Systems ; RNA, Guide, CRISPR-Cas Systems ; }, abstract = {CRISPR-Cas modules serve as the adaptive nucleic acid immune systems for prokaryotes, and provide versatile tools for nucleic acid manipulation in various organisms. Here, we discovered a new miniature type V system, CRISPR-Casπ (Cas12l) (~860 aa), from the environmental metagenome. Complexed with a large guide RNA (~170 nt) comprising the tracrRNA and crRNA, Casπ (Cas12l) recognizes a unique 5' C-rich PAM for DNA cleavage under a broad range of biochemical conditions, and generates gene editing in mammalian cells. Cryo-EM study reveals a 'bracelet' architecture of Casπ effector encircling the DNA target at 3.4 Å resolution, substantially different from the canonical 'two-lobe' architectures of Cas12 and Cas9 nucleases. The large guide RNA serves as a 'two-arm' scaffold for effector assembly. Our study expands the knowledge of DNA targeting mechanisms by CRISPR effectors, and offers an efficient but compact platform for DNA manipulation.}, } @article {pmid36650178, year = {2023}, author = {Rivera-Gutiérrez, X and Morán, P and Taboada, B and Serrano-Vázquez, A and Isa, P and Rojas-Velázquez, L and Pérez-Juárez, H and López, S and Torres, J and Ximénez, C and Arias, CF}, title = {The fecal and oropharyngeal eukaryotic viromes of healthy infants during the first year of life are personal.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {938}, pmid = {36650178}, issn = {2045-2322}, mesh = {Child ; Humans ; Infant ; Eukaryota ; Virome ; *Picornaviridae ; Feces ; *Herpesviridae ; Oropharynx ; Metagenomics/methods ; }, abstract = {Using a metagenomic sequencing approach, we described and compared the diversity and dynamics of the oropharyngeal and fecal eukaryotic virome of nine asymptomatic children in a semi-rural community setting located in the State of Morelos, Mexico. Ninety oropharyngeal swabs and 97 fecal samples were collected starting 2 weeks after birth and monthly thereafter until 12 months of age. In both niches, more than 95% of the total sequence reads were represented by viruses that replicate either in humans or in plants. Regarding human viruses, three families were most abundant and frequent in the oropharynx: Herpesviridae, Picornaviridae, and Reoviridae; in fecal samples, four virus families predominated: Caliciviridae, Picornaviridae, Reoviridae, and Anelloviridae. Both niches showed a high abundance of plant viruses of the family Virgaviridae. Differences in the frequency and abundance of sequence reads and diversity of virus species were observed in both niches and throughout the year of study, with some viruses already present in the first months of life. Our results suggest that the children's virome is dynamic and likely shaped by the environment, feeding, and age. Moreover, composition analysis suggests that the virome composition is mostly individual. Whether this constant exposition to different viruses has a long-term impact on children's health or development remains to be studied.}, } @article {pmid36649845, year = {2023}, author = {Xing, L and Zhang, M and Liu, L and Hu, X and Liu, J and Zhou, X and Chai, Z and Yin, H}, title = {Multiomics provides insights into the succession of microbiota and metabolite during plant leaf fermentation.}, journal = {Environmental research}, volume = {221}, number = {}, pages = {115304}, doi = {10.1016/j.envres.2023.115304}, pmid = {36649845}, issn = {1096-0953}, mesh = {Fermentation ; *Multiomics ; *Microbiota ; Bacteria/genetics/metabolism ; Odorants/analysis ; }, abstract = {The quality of fermented plant products is closely related to microbial metabolism. Here, the associations of bacterial communities, metabolites, and functional genes were explored using multi-omics techniques based on plant leaf fermentation systems. The results showed significant changes in the structure of the microbial community, with a significant decrease in Firmicutes and a significant increase in Proteobacteria. In addition, the concentration of metabolites with antibacterial, antioxidant and aroma properties increased significantly, enhancing the quality of the fermented plant leaves. Integrated macrogenomic and metabolomic analyses indicated that amino acid metabolism could be key metabolic pathway affecting fermentation quality. Actinobacteria, Proteobacteria, Firmicutes were actively involved in tyrosine metabolism (ko00350) and phenylalanine metabolism (ko00360), and are presumed to be the major groups responsible for synthesizing growth and flavor compounds. This study emphasized the important role of microorganisms in the changes of metabolites during the fermentation of plant leaves.}, } @article {pmid36649095, year = {2022}, author = {Peerakietkhajorn, S and Sinso, T}, title = {Bacterial communities in Branchinella thailandensis and Streptocephalus sirindhornae.}, journal = {Polish journal of veterinary sciences}, volume = {25}, number = {4}, pages = {493-500}, doi = {10.24425/pjvs.2022.140857}, pmid = {36649095}, issn = {2300-2557}, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Bacteria ; *Anostraca/genetics/microbiology ; Thailand ; Phylogeny ; DNA, Bacterial/genetics ; }, abstract = {The fairy shrimp is a freshwater crustacean found in both temporary and permanent freshwaters. In Thailand, fairy shrimp are farmed as live food for ornamental fish. This study aimed to investigate the bacterial compositions in two fairy shrimp species, Branchinella thailandensis and Streptocephalus sirindhornae. Both species were cultured, and total DNA was extracted. The V3-V4 region of the 16S rRNA gene was amplified and sequenced using Illumina Miseq. All data were analyzed by Illumina 16S Metagenomics (version 1.0.1) workflow in Base Space- Illumina. Each read was blasted against the Illumina-curated version of the Greengenes database to determine the operational taxonomic units (OTUs) corresponding to the 16S rRNA gene sequence. The results showed that the Shanon-Weiner diversity index of bacterial compositions in B. thailandensis and S. sirindhornae were 2.135 and 3.122, respectively. The evenness and genus-level richness of the bacterial composition in B. thailandensis were 0.364 and 354 genera, respectively. The dominant bacterium found in B. thailandensis was Nevskia. In S. sirindhornae, the evenness and genus-level richness of the bacterial composition were 0.521 and 400 genera, respectively. Azohydromonas was the dominant bacterium. Our results showed that the compositions and proportions of bacterial communities were specific to each species of fairy shrimp. This study will be useful for further experiments in aquaculture and ecological studies related to symbiotic interaction.}, } @article {pmid36648232, year = {2023}, author = {Hawkes, CG and Hinson, AN and Vashishta, A and Read, CB and Carlyon, JA and Lamont, RJ and Uriarte, SM and Miller, DP}, title = {Selenomonas sputigena Interactions with Gingival Epithelial Cells That Promote Inflammation.}, journal = {Infection and immunity}, volume = {91}, number = {2}, pages = {e0031922}, pmid = {36648232}, issn = {1098-5522}, support = {R01 DE011111/DE/NIDCR NIH HHS/United States ; R37 DE011111/DE/NIDCR NIH HHS/United States ; R01 AI139072/AI/NIAID NIH HHS/United States ; R00 DE028346/DE/NIDCR NIH HHS/United States ; P30 CA016059/CA/NCI NIH HHS/United States ; K99 DE028346/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; Inflammation ; *Periodontitis/pathology ; Porphyromonas gingivalis/metabolism ; *Periodontal Diseases ; Cytokines/metabolism ; Epithelial Cells/metabolism ; }, abstract = {Increased prevalence and abundance of Selenomonas sputigena have been associated with periodontitis, a chronic inflammatory disease of tooth-supporting tissues, for more than 50 years. Over the past decade, molecular surveys of periodontal disease using 16S and shotgun metagenomic sequencing approaches have confirmed the disease association of classically recognized periodontal pathogens such as Porphyromonas gingivalis, Treponema denticola, and Tannerella forsythia while highlighting previously underappreciated organisms such as Filifactor alocis and S. sputigena. Despite abundant clinical association between S. sputigena and periodontal disease, we have little to no understanding of its pathogenic potential, and virulence mechanisms have not been studied. In this study, we sought to characterize the response of gingival epithelial cells to infection with S. sputigena. Here, we show that S. sputigena attaches to gingival keratinocytes and induces expression and secretion of cytokines and chemokines associated with inflammation and leukocyte recruitment. We demonstrate that S. sputigena induces signaling through Toll-like receptor 2 (TLR2) and TLR4 but evades activation of TLR5. Cytokines released from S. sputigena-infected keratinocytes induced monocyte and neutrophil chemotaxis. These results show that S. sputigena-host interactions have the potential to contribute to bacterially driven inflammation and tissue destruction, the hallmark of periodontitis. Characterization of previously unstudied pathogens may provide novel approaches to develop therapeutics to treat or prevent periodontal disease.}, } @article {pmid36648111, year = {2023}, author = {Galán-Huerta, KA and Paz-Infanzon, M and Nuzzolo-Shihadeh, L and Ruiz-Higareda, AF and Bocanegra-Ibarias, P and Villareal-Martínez, DZ and Muñoz-Garza, FZ and Guerrero-Putz, MD and Sáenz-Ibarra, B and Barboza-Quintana, O and Ocampo-Candiani, J and Rivas-Estilla, AM and Camacho-Ortiz, A}, title = {Metagenomic Sequencing of Monkeypox Virus, Northern Mexico.}, journal = {Emerging infectious diseases}, volume = {29}, number = {2}, pages = {448-450}, pmid = {36648111}, issn = {1080-6059}, mesh = {Humans ; *Monkeypox virus/genetics ; Phylogeny ; Mexico/epidemiology ; *Mpox (monkeypox)/diagnosis/epidemiology ; Base Sequence ; }, abstract = {Monkeypox virus (MPXV) has gained interest because of a multicountry outbreak of mpox (formerly monkeypox) cases with no epidemiologic link to MPXV-endemic regions. We sequenced the complete genome of MPXV isolated from a patient in northern Mexico. Phylogenetic analysis grouped the virus with isolates from Germany.}, } @article {pmid36647731, year = {2023}, author = {Yang, Y and Jin, H and Li, X and Yan, J}, title = {Biohydrogenation of 1,3-Butadiene to 1-Butene under Acetogenic Conditions by Acetobacterium wieringae.}, journal = {Environmental science & technology}, volume = {57}, number = {4}, pages = {1637-1645}, doi = {10.1021/acs.est.2c05683}, pmid = {36647731}, issn = {1520-5851}, mesh = {*Acetobacterium/genetics ; RNA, Ribosomal, 16S ; }, abstract = {The environmental fate and transformation mechanism(s) of 1,3-butadiene (BD) under anoxic conditions remain largely unexplored. Anaerobic consortia that can biohydrogenate BD to stoichiometric amounts of 1-butene at a maximum rate of 205.7 ± 38.6 μM day[-1] were derived from freshwater river sediment. The formation of 1-butene occurred only in the presence of both H2 and CO2 with concomitant acetate production, suggesting the dependence of BD biohydrogenation on acetogenesis. The 16S rRNA gene-targeted amplicon sequencing revealed the enrichment and dominance of a novel Acetobacterium wieringae population, designated as strain N, in the BD-biohydrogenating community. Multiple genes encoding putative ene-reductases, candidate catalysts for the hydrogenation of the C═C bond in diene compounds, were annotated on the metagenome-assembled genome of strain N, and thus attributed the BD biohydrogenation activity to strain N. Our findings emphasize an essential but overlooked role of certain Acetobacterium members (e.g., strain N) contributing to the natural attenuation of BD in contaminated subsurface environments (e.g., sediment and groundwater). Future efforts to identify and characterize the ene-reductase(s) responsible for BD biohydrogenation in strain N hold promise for the development of industrial biocatalysts capable of stereoselective conversion of BD to 1-butene.}, } @article {pmid36647171, year = {2023}, author = {Pirolo, M and Espinosa-Gongora, C and Alberdi, A and Eisenhofer, R and Soverini, M and Eriksen, EØ and Pedersen, KS and Guardabassi, L}, title = {Bacterial topography of the upper and lower respiratory tract in pigs.}, journal = {Animal microbiome}, volume = {5}, number = {1}, pages = {5}, pmid = {36647171}, issn = {2524-4671}, support = {ESCMID Study Group for Veterinary Microbiology (ESGVM)//European Society of Clinical Microbiology and Infectious Diseases/ ; ESCMID Study Group for Veterinary Microbiology (ESGVM)//European Society of Clinical Microbiology and Infectious Diseases/ ; ESCMID Study Group for Veterinary Microbiology (ESGVM)//European Society of Clinical Microbiology and Infectious Diseases/ ; }, abstract = {BACKGROUND: Understanding the complex structures and interactions of the bacterial communities inhabiting the upper (URT) and lower (LRT) respiratory tract of pigs is at an early stage. The objective of this study was to characterize the bacterial topography of three URT (nostrils, choana, and tonsils) and LRT (proximal trachea, left caudal lobe and secondary bronchi) sites in pigs. Thirty-six post-mortem samples from six pigs were analysed by 16S rRNA gene quantification and sequencing, and the microbiota in nostrils and trachea was additionally profiled by shotgun sequencing.

RESULTS: The bacterial composition obtained by the two methods was congruent, although metagenomics recovered only a fraction of the diversity (32 metagenome-assembled genomes) due to the high proportion (85-98%) of host DNA. The highest abundance of 16S rRNA copies was observed in nostrils, followed by tonsils, trachea, bronchi, choana and lung. Bacterial richness and diversity were lower in the LRT compared to the URT. Overall, Firmicutes and Proteobacteria were identified as predominant taxa in all sample types. Glasserella (15.7%), Streptococcus (14.6%) and Clostridium (10.1%) were the most abundant genera but differences in microbiota composition were observed between the two tracts as well as between sampling sites within the same tract. Clear-cut differences were observed between nasal and tonsillar microbiomes (R-values 0.85-0.93), whereas bacterial communities inhabiting trachea and lung were similar (R-values 0.10-0.17). Moraxella and Streptococcus were more common in bronchial mucosal scraping than in lavage, probably because of mucosal adherence. The bacterial microbiota of the choana was less diverse than that of the nostrils and similar to the tracheal microbiota (R-value 0.24), suggesting that the posterior nasal cavity serves as the primary source of bacteria for the LRT.

CONCLUSION: We provide new knowledge on microbiota composition and species abundance in distinct ecological niches of the pig respiratory tract. Our results shed light on the distribution of opportunistic bacterial pathogens across the respiratory tract and support the hypothesis that bacteria present in the lungs originate from the posterior nasal cavity. Due to the high abundance of host DNA, high-resolution profiling of the pig respiratory microbiota by shotgun sequencing requires methods for host DNA depletion.}, } @article {pmid36647095, year = {2023}, author = {Chen, H and Liang, Y and Wang, R and Wu, Y and Zhang, X and Huang, H and Yu, X and Hong, M and Yang, J and Liao, K and Xu, H and Liu, M and Chen, P and Chen, Y}, title = {Metagenomic next-generation sequencing for the diagnosis of Pneumocystis jirovecii Pneumonia in critically pediatric patients.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {22}, number = {1}, pages = {6}, pmid = {36647095}, issn = {1476-0711}, support = {A2021327//Medical Scientific Research Foundation of Guangdong Province of China/ ; }, mesh = {Child ; Humans ; Bronchoalveolar Lavage Fluid ; High-Throughput Nucleotide Sequencing ; *Pneumocystis carinii/genetics ; *Pneumonia, Pneumocystis/diagnosis ; }, abstract = {OBJECTIVE: The aim of this study was to evaluate the effectiveness of metagenomic next-generation sequencing (mNGS) for the diagnosis of Pneumocystis jirovecii Pneumonia (PCP) in critically pediatric patients.

METHODS: Seventeen critically pediatric patients with PCP and sixty patients diagnosed with non-PCP pneumonia who were admitted in pediatric intensive care unit between June 2018 and July 2021 were enrolled. Conventional methods and mNGS for detecting Pneumocystis jirovecii (P. jirovecii) were compared. The patients' demographics, comorbidities, laboratory test results, antibiotic treatment response and 30 day mortality were analyzed.

RESULT: The mNGS showed a satisfying diagnostic performance with a sensitivity of 100% in detecting P. jirovecii compared with Gomori methenamine silver staining (5.9%), serum (1,3)-β-D-glucan (86.7%) and and LDH (55.6%). The diagnostic specificity of mNGS for PCP was higher than that of serum BDG (56.7%) and LDH (71.4%). In PCP group, over one thirds' cases had mixed infections. Compared with survivors, non-survivors had higher stringently mapped read numbers (SMRNs) in bronchoalveolar lavage fluid (BALF) sample (P < 0.05), suggesting SMRNs were closely associated with the severity of response. The detection for P. jirovecii by mNGS both in BALF and blood samples reached a concordance rate of 100%, and the SMRNs in the BALF were remarkably higher than that in blood samples. Initial antimicrobial treatment was modified in 88.2% of PCP patients based on the mNGS results.

CONCLUSION: The mNGS is a potential and efficient technology in diagnosing PCP and shows a satisfying performance in the detection of co-pathogens. Both blood and BALF samples for mNGS are suggested for the presumptive diagnosis of PCP.}, } @article {pmid36647091, year = {2023}, author = {Ma, J and Zhang, C and Dang, K and Liao, Y and Feng, X and Zhou, P}, title = {Spherical pneumonia caused by Ralstonia mannitolilytica: a case report and literature review.}, journal = {BMC pulmonary medicine}, volume = {23}, number = {1}, pages = {20}, pmid = {36647091}, issn = {1471-2466}, support = {2021YJ0465//Science and Technology Planning Project of Science and Technology Department of Sichuan Province/ ; QNXZ2020007//The 2020 Xinglin Scholars Scientific Research Promotion Plan of Chengdu University of Traditional Chinese Medicine/ ; 20-Q07//the Hundred Talents Plan Project of Hospital of Chengdu University of Traditional Chinese Medicine/ ; }, mesh = {Female ; Humans ; Adult ; *Pneumonia/diagnosis/drug therapy ; Lung/diagnostic imaging ; Ralstonia ; Bronchoalveolar Lavage Fluid ; *Pulmonary Atelectasis ; *Lung Neoplasms ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Spherical pneumonia is an extremely rare condition that is difficult to diagnose. It is a specific type of lung infection that often manifests as a round or round-like mass on chest imaging. Spherical pneumonia is easily misdiagnosed as a pulmonary tumor; therefore, awareness of this disease must be strengthened.

CASE PRESENTATION: The patient was a 29-year-old female who had persistent cough and sputum for approximately 1 month and fever for 5 days. Chest computed tomography (CT) at our hospital revealed a mass in the lower lobe of the right lung near the hilar region, with obstructive pulmonary atelectasis and obstructive pneumonia. Although lung cancer was suspected, Ralstonia mannitolilytica was detected by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid, and no cancer cells or Mycobacterium tuberculosis were detected. Finally, the patient was diagnosed with spherical pneumonia caused by R. mannitolilytica. Anti-infective treatment, symptomatic treatment, and administration of a traditional Chinese medicine decoction were performed based on the syndrome differentiation. After 10 days of treatment, chest CT revealed few lesions in the lower lobe of the right lung, which were significantly reduced compared with those in the past.

CONCLUSIONS: Spherical pneumonia caused by R. mannitolilytica has not yet been reported and differential diagnosis is key in clinical diagnosis. When spherical pneumonia is difficult to diagnose, mNGS may be a better alternative.}, } @article {pmid36646895, year = {2023}, author = {Sibbesen, JA and Eizenga, JM and Novak, AM and Sirén, J and Chang, X and Garrison, E and Paten, B}, title = {Haplotype-aware pantranscriptome analyses using spliced pangenome graphs.}, journal = {Nature methods}, volume = {20}, number = {2}, pages = {239-247}, pmid = {36646895}, issn = {1548-7105}, support = {U01HG010961//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; R01HG010485//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; U41HG010972//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; U24HG011853//U.S. Department of Health & Human Services | NIH | National Human Genome Research Institute (NHGRI)/ ; OT2 OD026682/OD/NIH HHS/United States ; }, mesh = {Haplotypes ; *Computational Biology ; *Gene Expression Profiling ; Metagenomics ; Transcriptome ; }, abstract = {Pangenomics is emerging as a powerful computational paradigm in bioinformatics. This field uses population-level genome reference structures, typically consisting of a sequence graph, to mitigate reference bias and facilitate analyses that were challenging with previous reference-based methods. In this work, we extend these methods into transcriptomics to analyze sequencing data using the pantranscriptome: a population-level transcriptomic reference. Our toolchain, which consists of additions to the VG toolkit and a standalone tool, RPVG, can construct spliced pangenome graphs, map RNA sequencing data to these graphs, and perform haplotype-aware expression quantification of transcripts in a pantranscriptome. We show that this workflow improves accuracy over state-of-the-art RNA sequencing mapping methods, and that it can efficiently quantify haplotype-specific transcript expression without needing to characterize the haplotypes of a sample beforehand.}, } @article {pmid36646520, year = {2023}, author = {Gao, P and Fan, K and Zhang, G and Yin, X and Jia, C and Tian, H}, title = {Coal-mining subsidence changed distribution of the microbiomes and their functional genes in a farmland.}, journal = {Journal of basic microbiology}, volume = {63}, number = {5}, pages = {542-557}, doi = {10.1002/jobm.202200582}, pmid = {36646520}, issn = {1521-4028}, support = {LNY2020-Z06//Foundation of Shandong Provincial Lunan Geology and Exploration Institute/ ; }, mesh = {Farms ; *Coal Mining ; *Microbiota ; Carbon ; Soil/chemistry ; Coal ; China ; }, abstract = {Land subsidence is a serious geological event, and can trigger severe environmental and ecological issues. In this study, the influences of coal-mining subsidence on distribution of farmland microbiomes and their functional genes were investigated by 16 S ribosomal RNA (rRNA) gene and metagenome sequencing. The results showed the existence of a core microbiome, which determined the community compositions across the subsidence farmland. Subsidence decreased the relative abundances of dominant Streptomyces, Nocardioides, and Rhizophagus, but increased the relative abundances of dominant Bradyrhizobium, Rhizobium, and Trichoderma. Subsidence also decreased the relative abundances of genes related to carbon metabolism, Quorum sensing, aminoacyl-transfer RNA (tRNA) biosynthesis, and oxidative phosphorylation, and increased the relative abundances of genes related to two-component system and bacterial chemotaxis. Furthermore, subsidence weakened the biosynthesis of organic carbons by decreasing the relative abundances of genes encoding glycosyl transferases, and strengthened decomposition of degradable organic carbons of the microbiomes and auxiliary activities by increasing the relative abundances of genes encoding glycoside hydrolases and polysaccharide lyases. The concentrations of total phosphorus, Mg[2+] , and Ca[2+] at the lower areas were significantly higher than those at the upper areas, indicating an associated loss of soil nutrients. Canonical correspondence analysis showed that soil moisture, pH, and the concentrations of NH4 [+] and Ca[2+] were the main factors affecting the distribution of the microbiomes and their functional genes. Collectively, this study shows that coal-mining subsidence alters soil physicochemical properties and distribution of farmland microbiomes and their functional genes.}, } @article {pmid36646037, year = {2023}, author = {Bostancıklıoğlu, M and Kaplan, DS and Temiz, E and Yiğit, E}, title = {Local myelin damage in the hippocampus fluctuates gut microbiome profile and memory.}, journal = {Journal of psychiatric research}, volume = {158}, number = {}, pages = {392-402}, doi = {10.1016/j.jpsychires.2023.01.006}, pmid = {36646037}, issn = {1879-1379}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Myelin Sheath ; Dysbiosis/genetics ; RNA, Ribosomal, 16S/genetics ; Hippocampus ; }, abstract = {The concept of the gut-brain axis has focused research on how gut dysbiosis affects myelin biology in the brain. However, this axis has not been tested to determine whether it conveys the effects of myelin damage on the gut microbiome profile. Therefore, we aimed to investigate how myelin biology is correlated with gut microbiome profile. The impact of local myelin damage in the hippocampus on gut microbiome profile was investigated with 16S rRNA metagenomic sequence and molecular analysis of myelin biology-associated proteins, and its reflections on memory performance were tested with behavioral tests. Local myelin damage in the hippocampus triggered severe gut dysbiosis, p < .05, changed memory performance, p < .05, and deviated emotional responses. Moreover, myelin treatment with clemastine improved gut dysbiosis and behavioral deviations. Our study provides animal-based evidence on the direct interaction between glial biology in the hippocampus and gut microbiome profile. This study proposes a framework for generating new hypotheses bridging different systems to the gut-brain axis.}, } @article {pmid36645293, year = {2023}, author = {Huang, X and Erickson, DL and Meng, J}, title = {PhyloPlus: a Universal Tool for Phylogenetic Interrogation of Metagenomic Communities.}, journal = {mBio}, volume = {14}, number = {1}, pages = {e0345522}, pmid = {36645293}, issn = {2150-7511}, support = {U01 FD001418/FD/FDA HHS/United States ; }, mesh = {Humans ; Phylogeny ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Phylogeny is a powerful tool that can be incorporated into quantitative descriptions of community diversity, yet its use has been limited largely due to the difficulty in constructing phylogenies which incorporate the wide genomic diversity of microbial communities. Here, we describe the development of a web portal, PhyloPlus, which enables users to generate customized phylogenies that may be applied to any bacterial or archaeal communities. We demonstrate the power of phylogeny by comparing metrics that employ phylogeny with those that do not when applied to data sets from two metagenomic studies (fermented food, n = 58; human microbiome, n = 60). This example shows how inclusion of all bacterial species identified by taxonomic classifiers (Kraken2 and Kaiju) made the phylogeny perfectly congruent to the corresponding classification outputs. Our phylogeny-based approach also enabled the construction of more constrained null models which (i) shed light into community structure and (ii) minimize potential inflation of type I errors. Construction of such null models allowed for the observation of under-dispersion in 44 (75.86%) food samples, with the metacommunity defined as bacteria that were found in different food matrices. We also observed that closely related species with high abundance and uneven distribution across different sites could potentially exaggerate the dissimilarity between phylogenetically similar communities if they were measured using traditional species-based metrics (Padj. = 0.003), whereas this effect was mitigated by incorporating phylogeny (Padj. = 1). In summary, our tool can provide additional insights into microbial communities of interest and facilitate the use of phylogeny-based approaches in metagenomic analyses. IMPORTANCE There has been an explosion of interest in how microbial diversity affects human health, food safety, and environmental functions among many other processes. Accurately measuring the diversity and structure of those communities is central to understanding their effects. Here, we describe the development of a freely available online tool, PhyloPlus, which allows users to generate custom phylogenies that may be applied to any data set, thereby removing a major obstacle to the application of phylogeny to metagenomic data analysis. We demonstrate that the genetic relatedness of the organisms within those communities is a critical feature of their overall diversity, and that using a phylogeny which captures and quantifies this diversity allows for much more accurate descriptions while preventing misleading conclusions based on estimates that ignore evolutionary relationships.}, } @article {pmid36645288, year = {2023}, author = {Biswas, S}, title = {Synthesis of a Novel Lantibiotic Using Mutacin II Biosynthesis Apparatus.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0303022}, pmid = {36645288}, issn = {2165-0497}, support = {P20 GM113117/GM/NIGMS NIH HHS/United States ; }, mesh = {Amino Acid Sequence ; *Bacteriocins/genetics/pharmacology ; Peptides/chemistry ; Streptococcus mutans/genetics ; }, abstract = {Owing to extensive metagenomic studies, we now have access to numerous sequences of novel bacteriocin-like antimicrobial peptides encoded by various cultivable and noncultivable bacteria. However, relatively rarely, we even have access to these cultivable strains to examine the potency and the targets of the predicted bacteriocins. In this study, we evaluated a heterologous biosynthetic system to produce biologically active nonnative novel lantibiotics, which are modified bacteriocins. We chose Streptococcus mutans, a dental pathogen, as the host organism because it is genetically easy to manipulate and is inherently a prolific producer of various bacteriocins. We chose the S. mutans T8 strain as the host, which produces the lantibiotic mutacin II, to express 10 selected homologs of mutacin II identified from GenBank. These lantibiotic peptides either are novel or have been studied very minimally. The core regions of the selected lantibiotic peptides were fused to the leader sequence of the mutacin II peptide and integrated into the chromosome such that the core region of the native mutacin II was replaced with the new core sequences. By this approach, using the mutacin II biosynthesis machinery, we obtained one bioactive novel lantibiotic peptide with 52% different residues compared to the mutacin II core region. This unknown lantibiotic is encoded by Streptococcus agalactiae and Streptococcus ovuberis strains. Since this peptide displays some homology with nukacin ISK-1, we named it nukacin Spp. 2. This study demonstrated that the mutacin II biosynthesis machinery can be successfully used as an efficient system for the production of biologically active novel lantibiotics. IMPORTANCE In this study, we report for the first time that Streptococcus mutans can be used as a host to produce various nonnative lantibiotics. We showed that in the T8 strain, we could produce bioactive lacticin 481 and nukacin ISK-1, both of which are homologs of mutacin II, using T8's modification and secretion apparatus. Similarly, we also synthesized a novel bioactive lantibiotic, which we named nukacin Spp. 2.}, } @article {pmid36644384, year = {2023}, author = {Wang, D and Guo, M and Li, X and Zhao, D and Wang, M}, title = {Microbiota, co-metabolites, and network pharmacology reveal the alteration of the ginsenoside fraction on inflammatory bowel disease.}, journal = {Journal of ginseng research}, volume = {47}, number = {1}, pages = {54-64}, pmid = {36644384}, issn = {1226-8453}, abstract = {BACKGROUND: Panax ginseng Meyer (P. ginseng) is a traditional natural/herbal medicine. The amelioration on inflammatory bowel disease (IBD) activity rely mainly on its main active ingredients that are referred to as ginsenosides. However, the current literature on gut microbiota, gut microbiota-host co-metabolites, and systems pharmacology has no studies investigating the effects of ginsenoside on IBD.

METHODS: The present study was aimed to investigate the role of ginsenosides and the possible underlying mechanisms in the treatment of IBD in an acetic acid-induced rat model by integrating metagenomics, metabolomics, and complex biological networks analysis. In the study ten ginsenosides in the ginsenoside fraction (GS) were identified using Q-Orbitrap LC-MS.

RESULTS: The results demonstrated the improvement effect of GS on IBD and the regulation effect of ginsenosides on gut microbiota and its co-metabolites. It was revealed that 7 endogenous metabolites, including acetic acid, butyric acid, citric acid, tryptophan, histidine, alanine, and glutathione, could be utilized as significant biomarkers of GS in the treatment of IBD. Furthermore, the biological network studies revealed EGFR, STAT3, and AKT1, which belong mainly to the glycolysis and pentose phosphate pathways, as the potential targets for GS for intervening in IBD.

CONCLUSION: These findings indicated that the combination of genomics, metabolomics, and biological network analysis could assist in elucidating the possible mechanism underlying the role of ginsenosides in alleviating inflammatory bowel disease and thereby reveal the pathological process of ginsenosides in IBD treatment through the regulation of the disordered host-flora co-metabolism pathway.}, } @article {pmid36644130, year = {2023}, author = {Lo Presti, A and Del Chierico, F and Altomare, A and Zorzi, F and Monteleone, G and Putignani, L and Angeletti, S and Cicala, M and Guarino, MPL and Ciccozzi, M}, title = {Phylogenetic analysis of Prevotella copri from fecal and mucosal microbiota of IBS and IBD patients.}, journal = {Therapeutic advances in gastroenterology}, volume = {16}, number = {}, pages = {17562848221136328}, pmid = {36644130}, issn = {1756-283X}, abstract = {BACKGROUND: Prevotella copri is the most abundant member of the genus Prevotella that inhabits the human large intestines. Evidences correlated the increase in Prevotella abundance to inflammatory disorders, suggesting a pathobiont role.

OBJECTIVES: The aim of this study was to investigate the phylogenetic dynamics of P. copri in patients with irritable bowel syndrome (IBS), inflammatory bowel diseases (IBDs) and in healthy volunteers (CTRL).

DESIGN: A phylogenetic approach was used to characterize 64 P. copri 16S rRNA sequences, selected from a metagenomic database of fecal and mucosal samples from 52 patients affected by IBD, 44 by IBS and 59 healthy.

METHODS: Phylogenetic reconstructions were carried out using the maximum likelihood (ML) and Bayesian methods.

RESULTS: Maximum likelihood phylogenetic tree applied onto reference and data sets, assigned all the reads to P. copri clade, in agreement with the taxonomic classification previously obtained. The longer mean genetic distances were observed for both the couples IBD and CTRL and IBD and IBS, respect to the distance between IBS and CTRL, for fecal samples. The intra-group mean genetic distance increased going from IBS to CTRLs to IBD, indicating elevated genetic variability within IBD of P. copri sequences. None clustering based on the tissue inflammation or on the disease status was evidenced, leading to infer that the variability seemed to not be influenced by concomitant diseases, disease phenotypes or tissue inflammation. Moreover, patients with IBS appeared colonized by different strains of P. copri. In IBS, a correlation between isolates and disease grading was observed.

CONCLUSION: The characterization of P. copri phylogeny is relevant to better understand the interactions between microbiota and pathophysiology of IBD and IBS, especially for future development of therapies based on microbes (e.g. probiotics and synbiotics), to restore the microbiota in these bowel diseases.}, } @article {pmid36643409, year = {2022}, author = {Zhang, Y and Zhao, H and Guo, Y and Meng, Y and Yu, S and Pan, B and Zhai, X}, title = {Relationship between thick or greasy tongue-coating microbiota and tongue diagnosis in patients with primary liver cancer.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {903616}, pmid = {36643409}, issn = {1664-302X}, abstract = {Tongue diagnosis is a unique aspect of traditional Chinese medicine for diagnosing diseases before determining proper means of treatment, but it also has the disadvantage of relying on the subjective experience of medical practitioners and lack objective basis. The purpose of this article is to elucidate tongue-coating microbiota and metabolic differences in primary liver cancer (PLC) patients with thick or greasy tongue coatings. Tongue-coating samples were analyzed in 60 PLC patients (30 PLC with thick or greasy tongue-coating patients and 30 PLC with tongue-coating neither thick nor greasy) and 25 healthy controls (HC) using 16S rRNA gene sequencing technology. As compared to healthy individuals, tongue coatings of patients with PLC had elevated levels of Firmicutes and Actinobacteria. The abundance of Fusobacteria, SR1_Absconditabacteria_, and Spirochaete were higher in tongue coatings of healthy controls compared to samples in patients with PLC. In addition to site-specific differences, higher abundances of Fusobacteria and Actinobacteria were observed in thick or greasy tongue-coating patients as compared to non-thick and greasy tongue-coating patients. The inferred metagenomic pathways enriched in the PLC tongue-coating patients were mainly those involved in replication, recombination, and repair of protein. We also identify a tongue-coating microbiome signature to discriminate HC and PLC, including 15 variables on genus level. The prediction performance of the signature showed well in the training and validation cohorts. This research illustrates specific clinical features and bacterial structures in PLC patients with different tongue coatings, which facilitates understanding of the traditional tongue diagnosis.}, } @article {pmid36642550, year = {2023}, author = {Tian, J and Huang, M and Chen, L and Liu, J}, title = {Pathogens of primary cervical intramedullary abscess diagnosed by metagenomic nextgeneration sequencing: A case report.}, journal = {Asian journal of surgery}, volume = {46}, number = {6}, pages = {2633-2634}, doi = {10.1016/j.asjsur.2022.12.145}, pmid = {36642550}, issn = {0219-3108}, mesh = {Humans ; Abscess/diagnosis ; *Spinal Cord Diseases ; Neck ; *Spinal Diseases ; Sensitivity and Specificity ; }, } @article {pmid36642210, year = {2023}, author = {Tang, M and Zeng, W and Qiu, Y and Fang, G and Pan, M and Li, W and Zhang, J}, title = {Clinical features of rare disseminated Mycobacterium colombiense infection in nine patients who are HIV-negative in Guangxi, China.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {128}, number = {}, pages = {321-324}, doi = {10.1016/j.ijid.2023.01.002}, pmid = {36642210}, issn = {1878-3511}, mesh = {Humans ; Retrospective Studies ; China ; *Mycobacterium Infections, Nontuberculous/microbiology ; Mycobacterium avium Complex ; Nontuberculous Mycobacteria ; *HIV Infections ; *Lymphadenopathy ; }, abstract = {OBJECTIVES: Localized or disseminated infection caused by different nontuberculous mycobacteria (NTM) species has been increasingly reported in recent years, but reports of Mycobacterium colombiense infection are extremely rare. Herein, we analyzed the clinical features of patients with disseminated M. colombiense infection.

METHODS: Patients diagnosed with disseminated M. colombiense infection between February 4, 2016 and August 25, 2021 at the First Affiliated Hospital of Guangxi Medical University were retrospectively analyzed.

RESULTS: NTM infection was diagnosed in 248 HIV-negative patients. Of these, nine patients with disseminated M. colombiense infection were enrolled. Five of these patients were positive for anti-interferon-γ autoantibodies. The lung, lymph nodes, bones, and joints were the most commonly involved organs. Anemia, fever, lymphadenopathy, cough and expectoration, and ostealgia were the most common symptoms. The levels of white blood cells and neutrophils were increased in eight patients. M. colombiense was detected by both metagenomic next-generation sequencing (mNGS) and culture in four patients and only by mNGS in the remaining five patients. All patients received combination anti-NTM therapy; five underwent surgery. The condition of eight patients improved, and one died during the treatment.

CONCLUSION: Patients infected with M. colombiense can present as disseminated infections, easily involving multiple organs, such as the lung, lymph nodes, bone, and joints, with fever, lymphadenopathy, and increased white blood cell and neutrophil counts. mNGS plays a crucial role in the early diagnosis of M. colombiense infection. Once diagnosed, timely and effective anti-NTM therapy, combined with local surgery if necessary, can improve the prognosis of patients with this condition.}, } @article {pmid36641874, year = {2023}, author = {Park, H and Uhlemann, AC and Jacobs, SS and Mowbray, C and Jubelirer, T and Kelly, KM and Walters, M and Ladas, EJ}, title = {Title: Obesogenic microbial signatures and the development of obesity in childhood acute lymphoblastic leukemia.}, journal = {Leukemia research}, volume = {126}, number = {}, pages = {107017}, doi = {10.1016/j.leukres.2023.107017}, pmid = {36641874}, issn = {1873-5835}, mesh = {Child ; Humans ; *Pediatric Obesity ; Overweight ; Risk Factors ; Prevalence ; *Precursor Cell Lymphoblastic Leukemia-Lymphoma ; Body Mass Index ; }, abstract = {Childhood acute lymphoblastic leukemia (ALL) is the most common childhood cancer with survival exceeding 90% for standard-risk groups. A debilitating side-effect of treatment is the development of overweight/obesity (OW/OB), which develops in approximately 40% of children by the end of treatment. The microbiome has been associated with the development of OW/OB. We examined fluctuations in the microbiome with the development of OW/OB during the first six months of treatment at diagnosis, and two subsequent timepoints (N = 62). Shotgun metagenomic sequencing was performed on Illumina Nextseq system, and taxa and functional pathways were extracted from sequences using kraken2 and humann2, respectively. An association of increased presence of several species (e.g., Klebsiella pneumoniae, Escherichia coli) was observed in children with OW/OB, while lean-promoting species (Veillonella, Haemophilus, and Akkermansia) were increased in children who maintained a normal weight. Pathway analysis revealed purine nucleotide biosynthesis, sugar nucleotide biosynthesis, and enzyme cofactor biosynthesis were positively correlated with Bacteroides spp. among children with OW/OB. We identified several taxa and functional pathways that may confer increased risk for the development of OW/OB. The associations observed in this pilot are preliminary and warrant further research in the microbiome and the development of OW/OB in childhood ALL.}, } @article {pmid36641850, year = {2023}, author = {Luo, ZH and Li, Q and Chen, N and Tang, LY and Liao, B and Yang, TT and Huang, LN}, title = {Genome-resolved metagenomics reveals depth-related patterns of microbial community structure and functions in a highly stratified, AMD overlaying mine tailings.}, journal = {Journal of hazardous materials}, volume = {447}, number = {}, pages = {130774}, doi = {10.1016/j.jhazmat.2023.130774}, pmid = {36641850}, issn = {1873-3336}, mesh = {*Metagenomics ; *Microbiota ; Acids ; Iron ; Metagenome ; Nitrogen/metabolism ; Sulfur ; }, abstract = {Acid mine drainage (AMD) is a worldwide environmental problem, yet bioremediation is hampered by a limited knowledge of the reductive microbial processes in the AMD ecosystem. Here, we generate extensive metagenome and geochemical datasets to investigate how microbial populations and metabolic capacities driving major element cycles are structured in a highly stratified, AMD overlaying tailings environment. The results demonstrated an explicit depth-dependent differentiation of microbial community composition and function profiles between the surface and deeper tailings layers, paralleling the dramatic shifts in major physical and geochemical properties. Specifically, key genes involved in sulfur and iron oxidation were significantly enriched in the surface tailings, whereas those associated with reductive nitrogen, sulfur, and iron processes were enriched in the deeper layers. Genome-resolved metagenomics retrieved 406 intermediate or high-quality genomes spanning 26 phyla, including major new groups (e.g., Patescibacteria and DPANN). Metabolic models involving nitrogen, sulfur, iron, and carbon cycles were proposed based on the functional potentials of the abundant microbial genomes, emphasizing syntrophy and the importance of lesser-known taxa in the degradation of complex carbon compounds. These results have implications for in situ AMD bioremediation.}, } @article {pmid36641844, year = {2023}, author = {Zhang, N and Lu, D and Sheng, H and Xia, J and Kan, P and Yao, Z and Chen, H and Li, G and Zhu, DZ and Liu, H}, title = {Constructed wetlands as hotspots of antibiotic resistance genes and pathogens: Evidence from metagenomic analysis in Chinese rural areas.}, journal = {Journal of hazardous materials}, volume = {447}, number = {}, pages = {130778}, doi = {10.1016/j.jhazmat.2023.130778}, pmid = {36641844}, issn = {1873-3336}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Waste Disposal, Fluid/methods ; *Wetlands ; China ; }, abstract = {In rural China, many constructed wetlands (CWs) have been developed to treat rural wastewater sustainably. However, due to the scarce information on those rural CWs, it is difficult to analyze the biological contaminants within those systems, such as antibiotic resistance genes (ARGs) and pathogens. Based on the data collected from two pilot-scale, one-year-observed CWs, for the first time, this study explored the accumulation of ARGs and pathogens using the metagenomic sequencing approach and SourceTracker analysis under different hydraulic loading rates. The Shannon index of ARGs in the effluent surpassed the level found in the influent. The DESeq2 analysis showed that up to 21.49% of the total pathogen species had increased relative abundance in the effluent compared with the influent. By combining the contribution of substrate and rhizosphere, the CW became a more influencing factor for ARGs and pathogens contamination than the influent. The network analysis revealed a critical but latent fact that the development of antibiotic-resistant pathogens is highly likely to be triggered by the co-occurrence of ARGs and pathogens. Collectively, from the aspect of biological risk, our study showed that CWs alone might not be an ideal solution for improving wastewater treatment in rural China.}, } @article {pmid36641214, year = {2023}, author = {Chinnam, NB and Syed, A and Hura, GL and Hammel, M and Tainer, JA and Tsutakawa, SE}, title = {Combining small angle X-ray scattering (SAXS) with protein structure predictions to characterize conformations in solution.}, journal = {Methods in enzymology}, volume = {678}, number = {}, pages = {351-376}, pmid = {36641214}, issn = {1557-7988}, support = {P01 CA092584/CA/NCI NIH HHS/United States ; P30 GM124169/GM/NIGMS NIH HHS/United States ; R01 GM137021/GM/NIGMS NIH HHS/United States ; R35 CA220430/CA/NCI NIH HHS/United States ; }, mesh = {Protein Conformation ; X-Ray Diffraction ; Scattering, Small Angle ; X-Rays ; Models, Molecular ; *Proteins/chemistry ; }, abstract = {Accurate protein structure predictions, enabled by recent advances in machine learning algorithms, provide an entry point to probing structural mechanisms and to integrating and querying many types of biochemical and biophysical results. Limitations in such protein structure predictions can be reduced and addressed through comparison to experimental Small Angle X-ray Scattering (SAXS) data that provides protein structural information in solution. SAXS data can not only validate computational predictions, but can improve conformational and assembly prediction to produce atomic models that are consistent with solution data and biologically relevant states. Here, we describe how to obtain protein structure predictions, compare them to experimental SAXS data and improve models to reflect experimental information from SAXS data. Furthermore, we consider the potential for such experimentally-validated protein structure predictions to broadly improve functional annotation in proteins identified in metagenomics and to identify functional clustering on conserved sites despite low sequence homology.}, } @article {pmid36641060, year = {2023}, author = {Papaiakovou, M and Fraija-Fernández, N and James, K and Briscoe, AG and Hall, A and Jenkins, TP and Dunn, J and Levecke, B and Mekonnen, Z and Cools, P and Doyle, SR and Cantacessi, C and Littlewood, DTJ}, title = {Evaluation of genome skimming to detect and characterise human and livestock helminths.}, journal = {International journal for parasitology}, volume = {53}, number = {2}, pages = {69-79}, doi = {10.1016/j.ijpara.2022.12.002}, pmid = {36641060}, issn = {1879-0135}, support = {MR/T020733/1//Medical Research Council/United Kingdom ; 108413/A/15/D//Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Humans ; Livestock ; Phylogeny ; *Helminths/genetics ; DNA ; *Parasites ; }, abstract = {The identification of gastrointestinal helminth infections of humans and livestock almost exclusively relies on the detection of eggs or larvae in faeces, followed by manual counting and morphological characterisation to differentiate species using microscopy-based techniques. However, molecular approaches based on the detection and quantification of parasite DNA are becoming more prevalent, increasing the sensitivity, specificity and throughput of diagnostic assays. High-throughput sequencing, from single PCR targets through to the analysis of whole genomes, offers significant promise towards providing information-rich data that may add value beyond traditional and conventional molecular approaches; however, thus far, its utility has not been fully explored to detect helminths in faecal samples. In this study, low-depth whole genome sequencing, i.e. genome skimming, has been applied to detect and characterise helminth diversity in a set of helminth-infected human and livestock faecal material. The strengths and limitations of this approach are evaluated using three methods to characterise and differentiate metagenomic sequencing data based on (i) mapping to whole mitochondrial genomes, (ii) whole genome assemblies, and (iii) a comprehensive internal transcribed spacer 2 (ITS2) database, together with validation using quantitative PCR (qPCR). Our analyses suggest that genome skimming can successfully identify most single and multi-species infections reported by qPCR and can provide sufficient coverage within some samples to resolve consensus mitochondrial genomes, thus facilitating phylogenetic analyses of selected genera, e.g. Ascaris spp. Key to this approach is both the availability and integrity of helminth reference genomes, some of which are currently contaminated with bacterial and host sequences. The success of genome skimming of faecal DNA is dependent on the availability of vouchered sequences of helminths spanning both taxonomic and geographic diversity, together with methods to detect or amplify minute quantities of parasite nucleic acids in mixed samples.}, } @article {pmid36640820, year = {2023}, author = {Xu, S and Yan, Y and Shuang, C and Zhou, Q and Ji, R and Li, A}, title = {Biological magnetic ion exchange resin on advanced treatment of synthetic wastewater.}, journal = {Bioresource technology}, volume = {372}, number = {}, pages = {128613}, doi = {10.1016/j.biortech.2023.128613}, pmid = {36640820}, issn = {1873-2976}, mesh = {Ion Exchange Resins ; Wastewater ; Charcoal ; Ibuprofen ; *Water Pollutants, Chemical/analysis ; Ion Exchange ; *Water Purification/methods ; }, abstract = {In this work, three biological ion exchange systems and one biological activated carbon (BAC) system were established by employing magnetic ion exchange resin (MIEX), non-magnetic resin (NIEX), polystyrenic resin (DIEX) and granular activated carbon as the biocarrier for advanced treatment of wastewater. Dissolved organic carbon (DOC) removal of four systems all stabilized at about 84% due to biodegradation. The start-up period of bio-MIEX (nearly 40 d) was greatly shorter than that of others (nearly 190 d). Ibuprofen removal was ascribed to adsorption in the initial stage, which subsequently changed to the effect of biodegradation. After the start-up period, ibuprofen removal was nearly 100% (bio-MIEX), 60% (bio-NIEX), 61% (bio-DIEX) and 89% (BAC). According to the surface observation, ATP and protein measurement and metagenomic analysis, the superior performance of bio-MIEX could be attributed to its highest biological activity resulted from the presence of Fe3O4 rather than polymer matrix and surface roughness.}, } @article {pmid36640816, year = {2023}, author = {Liu, D and Zhang, Y and Yang, Q and Li, Y and Li, J and Liao, X}, title = {Fate of ofloxacin in rural wastewater treatment facility: Removal performance, pathways and microbial characteristics.}, journal = {Bioresource technology}, volume = {371}, number = {}, pages = {128611}, doi = {10.1016/j.biortech.2023.128611}, pmid = {36640816}, issn = {1873-2976}, mesh = {*Ofloxacin ; *Sewage/microbiology ; Anti-Bacterial Agents/pharmacology/analysis ; Bacteria/genetics ; Genes, Bacterial ; Wetlands ; }, abstract = {Ofloxacin (OFL) with high biological activity and antimicrobial degradation is a kind of the typical high concentration and environmental risk antibiotics in rural sewage. In this paper, a combined rural sewage treatment facility based on anaerobic baffled reactor and integrated constructed wetlands was built and the removal performance, pathway and mechanism for OFL and conventional pollutants were evaluated. Results showed that the OFL and TN removal efficiency achieved 91.78 ± 3.93 % and 91.44 ± 4.15 %, respectively. Sludge adsorption was the primary removal pathway of OFL. Metagenomics analysis revealed that Proteobacteria was crucial in OFL removal. baca was the dominated antibiotic resistance genes (ARGs). Moreover, carbon metabolism with a high abundance was conductive to detoxify OFL to enhance system stability and performance. Co-occurrence network analysis further elucidated that mutualism was the main survival mode of microorganisms. Denitrifers Microbacterium, Geobacter and Ignavibacterium, were the host of ARGs and participated in OFL biodegradation.}, } @article {pmid36640575, year = {2023}, author = {Zhang, Z and Li, J and Jiang, S and Xu, M and Ma, T and Sun, Z and Zhang, J}, title = {Lactobacillus fermentum HNU312 alleviated oxidative damage and behavioural abnormalities during brain development in early life induced by chronic lead exposure.}, journal = {Ecotoxicology and environmental safety}, volume = {251}, number = {}, pages = {114543}, doi = {10.1016/j.ecoenv.2023.114543}, pmid = {36640575}, issn = {1090-2414}, mesh = {Mice ; Animals ; *Limosilactobacillus fermentum ; Lead/toxicity ; *Microbiota/physiology ; *Probiotics/pharmacology ; Oxidative Stress ; Brain ; }, abstract = {Lead exposure is a global public health safety issue that severely disrupts brain development and causes damage to the nervous system in early life. Probiotics and gut microbes have been highlighted for their critical roles in mitigating lead toxicity. However, the underlying mechanisms by which they work yet to be fully explored. Here, we designed a two-stage experiment using the probiotic Lactobacillus fermentum HNU312 (Lf312) to uncover how probiotics alleviate lead toxicity to the brain during early life. First, we explored the tolerance and adsorption of Lf312 to lead in vitro. Second, the adsorption capacity of the strain was determined and confirmed in vivo. The shotgun metagenome sequencing showed lead exposure-induced imbalance and dysfunction of the gut microbiome. In contrast, Lf312 intake significantly modulated the structure of the microbiome, increased the abundance of beneficial bacteria and short-chain fatty acids (SCFAs)-producing bacteria, and upregulated function-related metabolic pathways such as antioxidants. Notably, Lf312 enhanced the integrity of the blood-brain barrier by increasing the levels of SCFAs in the gut, alleviated inflammation in the brain, and ultimately improved anxiety-like and depression-like behaviours induced by lead exposure in mice. Subsequently, the effective mechanism was confirmed, highlighting that Lf312 worked through integrated strategies, including ionic adsorption and microbiota-gut-brain axis regulation. Collectively, this work elucidated the mechanism by which the gut microbiota mitigates the toxic effects of lead in the brain and provides preventive measures and intervention measures for brain damage due to mass lead poisoning in children.}, } @article {pmid36639807, year = {2023}, author = {Lian, WH and Mohamad, OAA and Dong, L and Zhang, LY and Wang, D and Liu, L and Han, MX and Li, S and Wang, S and Antunes, A and Fang, BZ and Jiao, JY and Li, WJ}, title = {Culturomics- and metagenomics-based insights into the microbial community and function of rhizosphere soils in Sinai desert farming systems.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {4}, pmid = {36639807}, issn = {2524-6372}, support = {2021YFD1500300//National Key Research and Development Program of China/ ; 2021YFD1500300//National Key Research and Development Program of China/ ; 2021YFD1500300//National Key Research and Development Program of China/ ; 2021YFD1500300//National Key Research and Development Program of China/ ; 91951205//National Natural Science Foundation of China/ ; 91951205//National Natural Science Foundation of China/ ; 91951205//National Natural Science Foundation of China/ ; 2021FY100900//National Science and Technology Fundamental Resources Investigation Program of China/ ; 2021FY100900//National Science and Technology Fundamental Resources Investigation Program of China/ ; 2021FY100900//National Science and Technology Fundamental Resources Investigation Program of China/ ; }, abstract = {BACKGROUND: The microbiome of the Sinai Desert farming system plays an important role in the adaptive strategy of growing crops in a harsh, poly-extreme, desert environment. However, the diversity and function of microbial communities under this unfavorable moisture and nutritional conditions have not yet been investigated. Based on culturomic and metagenomic methods, we analyzed the microbial diversity and function of a total of fourteen rhizosphere soil samples (collected from twelve plants in four farms of the Sinai desert), which may provide a valuable and meaningful guidance for the design of microbial inoculants.

RESULTS: The results revealed a wide range of microbial taxa, including a high proportion of novel undescribed lineages. The composition of the rhizosphere microbial communities differed according to the sampling sites, despite similarities or differences in floristics. Whereas, the functional features of rhizosphere microbiomes were significantly similar in different sampling sites, although the microbial communities and the plant hosts themselves were different. Importantly, microorganisms involved in ecosystem functions are different between the sampling sites, for example nitrogen fixation was prevalent in all sample sites while microorganisms responsible for this process were different.

CONCLUSION: Here, we provide the first characterization of microbial communities and functions of rhizosphere soil from the Sinai desert farming systems and highlight its unexpectedly high diversity. This study provides evidence that the key microorganisms involved in ecosystem functions are different between sampling sites with different environment conditions, emphasizing the importance of the functional microbiomes of rhizosphere microbial communities. Furthermore, we suggest that microbial inoculants to be used in future agricultural production should select microorganisms that can be involved in plant-microorganism interactions and are already adapted to a similar environmental setting.}, } @article {pmid36639538, year = {2023}, author = {Zhang, CJ and Liu, YR and Cha, G and Liu, Y and Zhou, XQ and Lu, Z and Pan, J and Cai, M and Li, M}, title = {Potential for mercury methylation by Asgard archaea in mangrove sediments.}, journal = {The ISME journal}, volume = {17}, number = {3}, pages = {478-485}, pmid = {36639538}, issn = {1751-7370}, mesh = {*Mercury/metabolism ; Archaea/genetics/metabolism ; Ecosystem ; Methylation ; Phylogeny ; *Methylmercury Compounds/metabolism ; Geologic Sediments/microbiology ; }, abstract = {Methylmercury (MeHg) is a potent neurotoxin that bioaccumulates along food chains. The conversion of MeHg from mercury (Hg) is mediated by a variety of anaerobic microorganisms carrying hgcAB genes. Mangrove sediments are potential hotspots of microbial Hg methylation; however, the microorganisms responsible for Hg methylation are poorly understood. Here, we conducted metagenomic and metatranscriptomic analyses to investigate the diversity and distribution of putative microbial Hg-methylators in mangrove ecosystems. The highest hgcA abundance and expression occurred in surface sediments in Shenzhen, where the highest MeHg concentration was also observed. We reconstructed 157 metagenome-assembled genomes (MAGs) carrying hgcA and identified several putative novel Hg-methylators, including one Asgard archaea (Lokiarchaeota). Further analysis of MAGs revealed that Deltaproteobacteria, Euryarchaeota, Bacteroidetes, Chloroflexi, and Lokiarchaeota were the most abundant and active Hg-methylating groups, implying their crucial role in MeHg production. By screening publicly available MAGs, 104 additional Asgard MAGs carrying hgcA genes were identified from a wide range of coast, marine, permafrost, and lake sediments. Protein homology modelling predicts that Lokiarchaeota HgcAB proteins contained the highly conserved amino acid sequences and folding structures required for Hg methylation. Phylogenetic tree revealed that hgcA genes from Asgard clustered with fused hgcAB genes, indicating a transitional stage of Asgard hgcA genes. Our findings thus suggest that Asgard archaea are potential novel Hg-methylating microorganisms and play an important role in hgcA evolution.}, } @article {pmid36639537, year = {2023}, author = {Osvatic, JT and Yuen, B and Kunert, M and Wilkins, L and Hausmann, B and Girguis, P and Lundin, K and Taylor, J and Jospin, G and Petersen, JM}, title = {Gene loss and symbiont switching during adaptation to the deep sea in a globally distributed symbiosis.}, journal = {The ISME journal}, volume = {17}, number = {3}, pages = {453-466}, pmid = {36639537}, issn = {1751-7370}, mesh = {Phylogeny ; *Symbiosis/genetics ; Adaptation, Physiological ; Biological Evolution ; Bacteria/genetics ; Water ; *Hydrothermal Vents ; }, abstract = {Chemosynthetic symbioses between bacteria and invertebrates occur worldwide from coastal sediments to the deep sea. Most host groups are restricted to either shallow or deep waters. In contrast, Lucinidae, the most species-rich family of chemosymbiotic invertebrates, has both shallow- and deep-sea representatives. Multiple lucinid species have independently colonized the deep sea, which provides a unique framework for understanding the role microbial symbionts play in evolutionary transitions between shallow and deep waters. Lucinids acquire their symbionts from their surroundings during early development, which may allow them to flexibly acquire symbionts that are adapted to local environments. Via metagenomic analyses of museum and other samples collected over decades, we investigated the biodiversity and metabolic capabilities of the symbionts of 22 mostly deep-water lucinid species. We aimed to test the theory that the symbiont played a role in adaptation to life in deep-sea habitats. We identified 16 symbiont species, mostly within the previously described genus Ca. Thiodiazotropha. Most genomic functions were shared by both shallow-water and deep-sea Ca. Thiodiazotropha, though nitrogen fixation was exclusive to shallow-water species. We discovered multiple cases of symbiont switching near deep-sea hydrothermal vents and cold seeps, where distantly related hosts convergently acquired novel symbionts from a different bacterial order. Finally, analyses of selection revealed consistently stronger purifying selection on symbiont genomes in two extreme habitats - hydrothermal vents and an oxygen-minimum zone. Our findings reveal that shifts in symbiont metabolic capability and, in some cases, acquisition of a novel symbiont accompanied adaptation of lucinids to challenging deep-sea habitats.}, } @article {pmid36639043, year = {2023}, author = {Qian, Y and Hu, L and Wang, Y and Xu, K}, title = {Arsenic methylation behavior and microbial regulation mechanisms in landfill leachate saturated zones.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {320}, number = {}, pages = {121064}, doi = {10.1016/j.envpol.2023.121064}, pmid = {36639043}, issn = {1873-6424}, mesh = {*Arsenic/analysis ; Methylation ; *Water Pollutants, Chemical/analysis ; Bacteria/metabolism ; *Microbiota ; Bacteroidetes/metabolism ; }, abstract = {Arsenic (As) is a potential contaminant in landfill. As methylation has been considered as a detoxification mechanism to address this problem. In this study, microcosm incubation was used to simulate leachate saturation zone (LSZ) and other landfill zones scenarios to explore the As methylation behavior. The As methylation rate of LSZ is 11.75%, which is slightly higher than that of other zone of landfill (10.87%). However, the difference was greatly increased by the addition of moderate content of As(III), with values of 29.25% in LSZ and 4.61% in other zones. The microbial community structure varied greatly between zones and a higher abundance of arsM was observed in the LSZ, which enhanced As methylation. Based on the annotated As functional genes from the KEGG database, the microbial As methylated pathway was summarized. Higher relative abundances of gst and arsC promoted the formation of more trivalent As substrates, stimulating the methylation behavior for As detoxification in the LSZ. According to microbial arsM contribution analysis, unclassified_p__Gemmatimonadetes, unclassified_p__Actinobacteria, unclassified_o_Hydrogenophilales, and Intrasporangium were the primary As methylation bacteria in the LSZ, while unclassified_f__Chitinophagaceae and unclassified_c_Gammaproteobacteria were the primary contributors in other landfill zones. These results highlight the specific As methylation process in the LSZ, and these insights could improve the control of As contamination in landfill sites.}, } @article {pmid36639019, year = {2023}, author = {Lennox-Hvenekilde, D and Bali, AP and Gronenberg, LS and Acevedo-Rocha, C and Sommer, MOA and Genee, HJ}, title = {Metabolic engineering of Escherichia coli for high-level production of free lipoic acid.}, journal = {Metabolic engineering}, volume = {76}, number = {}, pages = {39-49}, doi = {10.1016/j.ymben.2023.01.004}, pmid = {36639019}, issn = {1096-7184}, mesh = {Escherichia coli/metabolism ; Bacterial Proteins/genetics ; *Thioctic Acid ; Metabolic Engineering ; *Escherichia coli Proteins/genetics/metabolism ; }, abstract = {L-Lipoic acid (LA) is an important antioxidant with various industrial applications as a nutraceutical and therapeutic. Currently, LA is produced by chemical synthesis. Cell factory development is complex as LA and its direct precursors only occur naturally in protein-bound forms. Here we report a rationally engineered LA cell factory and demonstrate de novo free LA production from glucose for the first time in E. coli. The pathway represents a significant challenge as the three key enzymes, native Octanoyltransferase (LipB) and Lipoyl Synthase (LipA), and heterologous Lipoamidase (LpA), are all toxic to overexpress in E. coli. To overcome the toxicity of LipB, functional metagenomic selection was used to identify a highly active and non-toxic LipB and LipA from S. liquefaciens. Using high throughput screening, we balanced translation initiation rates and dual, orthogonal induction systems for the toxic genes, LipA and LpA. The optimized strain yielded 2.5 mg free LA per gram of glucose in minimal media, expressing carefully balanced LipB and LipA, Enterococcus faecalis LpA, and a truncated, native, Dihydrolipoyllysine-residue acetyltransferase (AceF) lipoylation domain. When the optimized cell factory strain was cultivated in a fed-batch fermentation, a titer of 87 mg/L free LA in the supernatant was reached after 48 h. This titer is ∼3000-fold higher than previously reported free LA titer and ∼8-fold higher than the previous best total, protein-bound LA titer. The strategies presented here could be helpful in designing, constructing and balancing biosynthetic pathways that harbor toxic enzymes with protein-bound intermediates or products.}, } @article {pmid36638922, year = {2023}, author = {Riller, Q and Fourgeaud, J and Bruneau, J and De Ravin, SS and Smith, G and Fusaro, M and Meriem, S and Magerus, A and Luka, M and Abdessalem, G and Lhermitte, L and Jamet, A and Six, E and Magnani, A and Castelle, M and Lévy, R and Lecuit, MM and Fournier, B and Winter, S and Semeraro, M and Pinto, G and Abid, H and Mahlaoui, N and Cheikh, N and Florkin, B and Frange, P and Jeziorski, E and Suarez, F and Sarrot-Reynauld, F and Nouar, D and Debray, D and Lacaille, F and Picard, C and Pérot, P and Regnault, B and Da Rocha, N and de Cevins, C and Delage, L and Pérot, BP and Vinit, A and Carbone, F and Brunaud, C and Marchais, M and Stolzenberg, MC and Asnafi, V and Molina, T and Rieux-Laucat, F and Notarangelo, LD and Pittaluga, S and Jais, JP and Moshous, D and Blanche, S and Malech, H and Eloit, M and Cavazzana, M and Fischer, A and Ménager, MM and Neven, B}, title = {Late-onset enteric virus infection associated with hepatitis (EVAH) in transplanted SCID patients.}, journal = {The Journal of allergy and clinical immunology}, volume = {151}, number = {6}, pages = {1634-1645}, pmid = {36638922}, issn = {1097-6825}, support = {ZIA AI001222/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Humans ; *Severe Combined Immunodeficiency/therapy/etiology ; CD8-Positive T-Lymphocytes ; *Hematopoietic Stem Cell Transplantation/adverse effects/methods ; *Virus Diseases/etiology ; *Hepatitis/etiology ; *Enterovirus Infections ; }, abstract = {BACKGROUND: Allogenic hematopoietic stem cell transplantation (HSCT) and gene therapy (GT) are potentially curative treatments for severe combined immunodeficiency (SCID). Late-onset posttreatment manifestations (such as persistent hepatitis) are not uncommon.

OBJECTIVE: We sought to characterize the prevalence and pathophysiology of persistent hepatitis in transplanted SCID patients (SCIDH+) and to evaluate risk factors and treatments.

METHODS: We used various techniques (including pathology assessments, metagenomics, single-cell transcriptomics, and cytometry by time of flight) to perform an in-depth study of different tissues from patients in the SCIDH+ group and corresponding asymptomatic similarly transplanted SCID patients without hepatitis (SCIDH-).

RESULTS: Eleven patients developed persistent hepatitis (median of 6 years after HSCT or GT). This condition was associated with the chronic detection of enteric viruses (human Aichi virus, norovirus, and sapovirus) in liver and/or stools, which were not found in stools from the SCIDH- group (n = 12). Multiomics analysis identified an expansion of effector memory CD8[+] T cells with high type I and II interferon signatures. Hepatitis was associated with absence of myeloablation during conditioning, split chimerism, and defective B-cell function, representing 25% of the 44 patients with SCID having these characteristics. Partially myeloablative retransplantation or GT of patients with this condition (which we have named as "enteric virus infection associated with hepatitis") led to the reconstitution of T- and B-cell immunity and remission of hepatitis in 5 patients, concomitantly with viral clearance.

CONCLUSIONS: Enteric virus infection associated with hepatitis is related to chronic enteric viral infection and immune dysregulation and is an important risk for transplanted SCID patients with defective B-cell function.}, } @article {pmid36638095, year = {2023}, author = {Maki, KA and Wolff, B and Varuzza, L and Green, SJ and Barb, JJ}, title = {Multi-amplicon microbiome data analysis pipelines for mixed orientation sequences using QIIME2: Assessing reference database, variable region and pre-processing bias in classification of mock bacterial community samples.}, journal = {PloS one}, volume = {18}, number = {1}, pages = {e0280293}, pmid = {36638095}, issn = {1932-6203}, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Databases, Factual ; High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics ; Data Analysis ; }, abstract = {Microbiome research relies on next-generation sequencing and on downstream data analysis workflows. Several manufacturers have introduced multi-amplicon kits for microbiome characterization, improving speciation, but present unique challenges for analysis. The goal of this methodology study was to develop two analysis pipelines specific to mixed-orientation reads from multi-hypervariable (V) region amplicons. A secondary aim was to assess agreement with expected abundance, considering database and variable region. Mock community sequence data (n = 41) generated using the Ion16S™ Metagenomics Kit and Ion Torrent Sequencing Platform were analyzed using two workflows. Amplicons from V2, V3, V4, V6-7, V8 and V9 were deconvoluted using a specialized plugin based on CutPrimers. A separate workflow using Cutadapt is also presented. Three reference databases (Ribosomal Database Project, Greengenes and Silva) were used for taxonomic assignment. Bray-Curtis, Euclidean and Jensen-Shannon distance measures were used to evaluate overall annotation consistency, and specific taxon agreement was determined by calculating the ratio of observed to expected relative abundance. Reads that mapped to regions V2-V9 varied for both CutPrimers and Cutadapt-based methods. Within the CutPrimers-based pipeline, V3 amplicons had the best agreement with the expected distribution, tested using global distance measures, while V9 amplicons had the worst agreement. Accurate taxonomic annotation varied by genus-level taxon and V region analyzed. For the first time, we present a microbiome analysis pipeline that employs a specialized plugin to allow microbiome researchers to separate multi-amplicon data from the Ion16S Metagenomics Kit into V-specific reads. We also present an additional analysis workflow, modified for Ion Torrent mixed orientation reads. Overall, the global agreement of amplicons with the expected mock community abundances differed across V regions and reference databases. Benchmarking data should be referenced when planning a microbiome study to consider these biases related to sequencing and data analysis for multi-amplicon sequencing kits.}, } @article {pmid36638091, year = {2023}, author = {Kibegwa, FM and Bett, RC and Gachuiri, CK and Machuka, E and Stomeo, F and Mujibi, FD}, title = {Diversity and functional analysis of rumen and fecal microbial communities associated with dietary changes in crossbreed dairy cattle.}, journal = {PloS one}, volume = {18}, number = {1}, pages = {e0274371}, pmid = {36638091}, issn = {1932-6203}, mesh = {Animals ; Cattle ; *Rumen/microbiology ; *Microbiota/genetics ; Metagenome ; Proteobacteria/genetics ; Dietary Fiber/metabolism ; Diet/veterinary ; Animal Feed/analysis ; }, abstract = {The objective of this study was to investigate the effect of varying roughage and concentrate proportions, in diet of crossbreed dairy cattle, on the composition and associated functional genes of rumen and fecal microbiota. We also explored fecal samples as a proxy for rumen liquor samples. Six crossbred dairy cattle were reared on three diets with an increasing concentrate and reducing roughage amount in three consecutive 10-day periods. After each period, individual rumen liquor and fecal samples were collected and analyzed through shotgun metagenomic sequencing. Average relative abundance of identified Operational Taxonomic Units (OTU) and microbial functional roles from all animals were compared between diets and sample types (fecal and rumen liquor). Results indicated that dietary modifications significantly affected several rumen and fecal microbial OTUs. In the rumen, an increase in dietary concentrate resulted in an upsurge in the abundance of Proteobacteria, while reducing the proportions of Bacteroidetes and Firmicutes. Conversely, changes in microbial composition in fecal samples were not consistent with dietary modification patterns. Microbial functional pathway classification identified that carbohydrate metabolism and protein metabolism pathways dominated microbial roles. Assessment of dietary effects on the predicted functional roles of these microbiota revealed that a high amount of dietary concentrate resulted in an increase in central carbohydrate metabolism and a corresponding reduction in protein synthesis. Moreover, we identified several microbial stress-related responses linked to dietary changes. Bacteroides and Clostridium genera were the principal hosts of these microbial functions. Therefore, the roughage to concentrate proportion has more influence on the microbial composition and microbial functional genes in rumen samples than fecal samples. As such, we did not establish a significant relationship between the rumen and fecal metagenome profiles, and the rumen and fecal microbiota from one animal did not correlate more than those from different animals.}, } @article {pmid36637649, year = {2023}, author = {Wani, AK and Akhtar, N and Naqash, N and Rahayu, F and Djajadi, D and Chopra, C and Singh, R and Mulla, SI and Sher, F and Américo-Pinheiro, JHP}, title = {Discovering untapped microbial communities through metagenomics for microplastic remediation: recent advances, challenges, and way forward.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {34}, pages = {81450-81473}, pmid = {36637649}, issn = {1614-7499}, mesh = {Humans ; Microplastics ; Plastics/metabolism ; Metagenomics ; Ecosystem ; *Microbiota ; *Environmental Pollutants/analysis ; *Water Pollutants, Chemical/analysis ; }, abstract = {Microplastics (MPs) are ubiquitous pollutants persisting almost everywhere in the environment. With the increase in anthropogenic activities, MP accumulation is increasing enormously in aquatic, marine, and terrestrial ecosystems. Owing to the slow degradation of plastics, MPs show an increased biomagnification probability of persistent, bioaccumulative, and toxic substances thereby creating a threat to environmental biota. Thus, remediation of MP-pollutants requires efficient strategies to circumvent the mobilization of contaminants leaching into the water, soil, and ultimately to human beings. Over the years, several microorganisms have been characterized by the potential to degrade different plastic polymers through enzymatic actions. Metagenomics (MGs) is an effective way to discover novel microbial communities and access their functional genetics for the exploration and characterization of plastic-degrading microbial consortia and enzymes. MGs in combination with metatranscriptomics and metabolomics approaches are a powerful tool to identify and select remediation-efficient microbes in situ. Advancement in bioinformatics and sequencing tools allows rapid screening, mining, and prediction of genes that are capable of polymer degradation. This review comprehensively summarizes the growing threat of microplastics around the world and highlights the role of MGs and computational biology in building effective response strategies for MP remediation.}, } @article {pmid36636774, year = {2023}, author = {Ferrocino, I and Rantsiou, K and McClure, R and Kostic, T and de Souza, RSC and Lange, L and FitzGerald, J and Kriaa, A and Cotter, P and Maguin, E and Schelkle, B and Schloter, M and Berg, G and Sessitsch, A and Cocolin, L and , }, title = {The need for an integrated multi-OMICs approach in microbiome science in the food system.}, journal = {Comprehensive reviews in food science and food safety}, volume = {22}, number = {2}, pages = {1082-1103}, doi = {10.1111/1541-4337.13103}, pmid = {36636774}, issn = {1541-4337}, mesh = {Humans ; *Artificial Intelligence ; Multiomics ; *Microbiota ; Metabolomics/methods ; Metagenomics/methods ; }, abstract = {Microbiome science as an interdisciplinary research field has evolved rapidly over the past two decades, becoming a popular topic not only in the scientific community and among the general public, but also in the food industry due to the growing demand for microbiome-based technologies that provide added-value solutions. Microbiome research has expanded in the context of food systems, strongly driven by methodological advances in different -omics fields that leverage our understanding of microbial diversity and function. However, managing and integrating different complex -omics layers are still challenging. Within the Coordinated Support Action MicrobiomeSupport (https://www.microbiomesupport.eu/), a project supported by the European Commission, the workshop "Metagenomics, Metaproteomics and Metabolomics: the need for data integration in microbiome research" gathered 70 participants from different microbiome research fields relevant to food systems, to discuss challenges in microbiome research and to promote a switch from microbiome-based descriptive studies to functional studies, elucidating the biology and interactive roles of microbiomes in food systems. A combination of technologies is proposed. This will reduce the biases resulting from each individual technology and result in a more comprehensive view of the biological system as a whole. Although combinations of different datasets are still rare, advanced bioinformatics tools and artificial intelligence approaches can contribute to understanding, prediction, and management of the microbiome, thereby providing the basis for the improvement of food quality and safety.}, } @article {pmid36636577, year = {2023}, author = {Tombuloglu, H and Yaman, C and Boudellioua, I and Cevik, E and Anil, I and Aga, O and Yaman, AB and Qureshi, A and Gunday, ST}, title = {Metagenome analyses of microbial population in geotextile fabrics used in permeable reactor barriers for toluene biodegradation.}, journal = {3 Biotech}, volume = {13}, number = {2}, pages = {40}, pmid = {36636577}, issn = {2190-572X}, abstract = {UNLABELLED: Toluene is one of the hydrocarbons that contaminate soil and groundwater, and has a high cost to remediate, which makes it an environmental pollutant of concern. This study aimed to find bacterial distribution from nonwoven geotextile (GT) fabric specimens in a pilot-scale permeable reactive barrier (PRB). Upon 167 days of incubation with the addition of toluene, the microbial community on the GT surfaces (n = 12) was investigated by the 16S rRNA metagenome sequencing approach. According to taxonomic classification, the Proteobacteria phylum dominated the metagenomes of all the geotextile samples (80-90%). Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database search of the toluene degradation mechanism revealed the susceptible toluene-degrading species. For the toluene-to-benzoate degradation, the Cupriavidus genus, particularly C. gilardii, C. metallidurans, and C. taiwanensis, are likely to be functional. In addition to these species, the Novosphingobium genus was abundantly localized in the GTs, in particular Novosphingobium sp. ABRDHK2. The results suggested the biodegradation potential of these species in toluene remediation. Overall, this work sheds light on the variety of microorganisms found in the geotextile fabrics used in PRBs and the species involved in the biodegradation of toluene from several sources, including soil, sediment, and groundwater.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-023-03460-y.}, } @article {pmid36636374, year = {2023}, author = {Wang, L and Liu, J and Peng, L}, title = {High-Dose Tigecycline for the Treatment of Progressive Pneumonia Caused by Chlamydia psittaci: Case Series and Literature Review.}, journal = {Infection and drug resistance}, volume = {16}, number = {}, pages = {115-124}, pmid = {36636374}, issn = {1178-6973}, abstract = {PURPOSE: To summarize the clinical characteristics of progressive pneumonia caused by Chlamydia psittaci (C. psittaci) and to explore the effect of high-dose tigecycline on severe C psittaci.

PATIENTS AND METHODS: We retrospectively analyzed the clinical characteristics, treatment, and outcomes of three progressive pneumonia patients caused by C. psittaci in our hospital in the past three years.

RESULTS: All three patients showed high fever and progressive dyspnea, and all of them were finally diagnosed by bronchoalveolar lavage fluid (BALF) of metagenomic next-generation sequencing (mNGS). Case 1 rapidly developed into multilobar infiltration after raising a parrot with a normal appearance one week before. Respiratory failure occurred despite the use of moxifloxacin, requiring non-invasive ventilator-assisted ventilation. Case 2 developed discomfort one day after sightseeing in the forest park. Moxifloxacin was ineffective for her and she quickly developed respiratory failure, requiring invasive ventilator-assisted ventilation. Case 3 kept chickens and ducks at home. Respiratory failure and renal failure still occurred rapidly despite the use of doxycycline, requiring invasive ventilator-assisted ventilation and continuous renal replacement therapy (CRRT). After adjusting the antibiotic to high-dose tigecycline (100mg, I.V., q12h), all three patients were treated effectively and no side effects occurred.

CONCLUSION: C. psittaci pneumonia is one of the causes of progressive pneumonia. High-dose tigecycline is safe and effective for the treatment of severe C. psittaci.}, } @article {pmid36636006, year = {2022}, author = {Peng, J and Li, B and He, X and Ding, C}, title = {Lung infection caused by Blastoschizomyces capitatus without immunodeficiency: a case report and review of the literature.}, journal = {Annals of palliative medicine}, volume = {11}, number = {12}, pages = {3826-3832}, doi = {10.21037/apm-22-1289}, pmid = {36636006}, issn = {2224-5839}, mesh = {Male ; Humans ; Aged ; Antifungal Agents/therapeutic use ; Amphotericin B/therapeutic use ; Voriconazole/therapeutic use ; *Mycoses/drug therapy ; *Pneumonia ; Lung ; Dyspnea/drug therapy ; }, abstract = {BACKGROUND: Blastoschizomyces capitatus infection is a rare fungal infection; mainly occurring in immunodeficient patients, which can cause multiple organ involvement. At present, there is no clear designated treatment regimen. This case was a rare example of Blastoschizomyces capitatus lung infection in patient with normal immune function, which was effectively controlled by combined antifungal therapy.

CASE DESCRIPTION: We report a 67-year-old male smoker, who, after cleaning a small bungalow for a long period, without any protective measures, developed cough with expectoration, fever and dyspnea. Pre-admission anti-infective medication (amoxicillin and roxithromycin) had little effect, and the patient's condition worsened. He had a past history of pulmonary tuberculosis with pleurisy 6 years before. Chest computed tomography (CT) showed evidence of old tuberculosis in the right upper lobe and inflammation in both lower lobes. White blood cell count was 14.51×109/L, neutrophils was 13.39×109/L and C-reactive protein (CRP) was 170 mg/L. Broad-spectrum antibiotics piperacillin sodium 4.0 g and tazobactam sodium 0.5 g q8h were administered empirically for 5 days. Blastoschizomyces capitatus infection was confirmed by next generation of macro genome sequencing (NGS) of bronchoalveolar lavage fluid and mass spectrum analysis of sputum. He was then switched to voriconazole antifungal therapy combined with aerosol inhalation of amphotericin B. His temperature normalized, expectoration and dyspnea were relieved. Total white cell count fell to 8.10×109/L, neutrophils to 5.81×109/L, and CRP to 76.8 mg/L.

CONCLUSIONS: This case demonstrates that Blastoschizomyces capitatus infection can occur in patients with normal immune function. Mass spectrometry and metagenomic NGS methods may have an advantage over traditional methods in identifying this fungal infection. In addition, the combination of voriconazole and nebulized amphotericin B can be employed as a novel regimen for treating Blastoschizomyces capitatus infection. For pulmonary infection with a history of environmental exposure, early pathogen identification and culture, and appropriate antibiotic treatment are key to optimizing outcome.}, } @article {pmid36635724, year = {2023}, author = {Berihu, M and Somera, TS and Malik, A and Medina, S and Piombo, E and Tal, O and Cohen, M and Ginatt, A and Ofek-Lalzar, M and Doron-Faigenboim, A and Mazzola, M and Freilich, S}, title = {A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {8}, pmid = {36635724}, issn = {2049-2618}, mesh = {*Soil ; Bacteria/genetics ; *Microbiota/genetics ; Metagenome ; Metagenomics ; Rhizosphere ; Soil Microbiology ; Plant Roots/microbiology ; }, abstract = {BACKGROUND: The design of ecologically sustainable and plant-beneficial soil systems is a key goal in actively manipulating root-associated microbiomes. Community engineering efforts commonly seek to harness the potential of the indigenous microbiome through substrate-mediated recruitment of beneficial members. In most sustainable practices, microbial recruitment mechanisms rely on the application of complex organic mixtures where the resources/metabolites that act as direct stimulants of beneficial groups are not characterized. Outcomes of such indirect amendments are unpredictable regarding engineering the microbiome and achieving a plant-beneficial environment.

RESULTS: This study applied network analysis of metagenomics data to explore amendment-derived transformations in the soil microbiome, which lead to the suppression of pathogens affecting apple root systems. Shotgun metagenomic analysis was conducted with data from 'sick' vs 'healthy/recovered' rhizosphere soil microbiomes. The data was then converted into community-level metabolic networks. Simulations examined the functional contribution of treatment-associated taxonomic groups and linked them with specific amendment-induced metabolites. This analysis enabled the selection of specific metabolites that were predicted to amplify or diminish the abundance of targeted microbes functional in the healthy soil system. Many of these predictions were corroborated by experimental evidence from the literature. The potential of two of these metabolites (dopamine and vitamin B12) to either stimulate or suppress targeted microbial groups was evaluated in a follow-up set of soil microcosm experiments. The results corroborated the stimulant's potential (but not the suppressor) to act as a modulator of plant beneficial bacteria, paving the way for future development of knowledge-based (rather than trial and error) metabolic-defined amendments. Our pipeline for generating predictions for the selective targeting of microbial groups based on processing assembled and annotated metagenomics data is available at https://github.com/ot483/NetCom2 .

CONCLUSIONS: This research demonstrates how genomic-based algorithms can be used to formulate testable hypotheses for strategically engineering the rhizosphere microbiome by identifying specific compounds, which may act as selective modulators of microbial communities. Applying this framework to reduce unpredictable elements in amendment-based solutions promotes the development of ecologically-sound methods for re-establishing a functional microbiome in agro and other ecosystems. Video Abstract.}, } @article {pmid36635670, year = {2023}, author = {Qingyan, Z and Yangyang, X and Miao, Z and Chunming, J}, title = {Peritoneal dialysis related eosinophilic peritonitis: a case report and review of the literature.}, journal = {BMC nephrology}, volume = {24}, number = {1}, pages = {10}, pmid = {36635670}, issn = {1471-2369}, support = {2021-LCYJ-PY-12//Funding for Clinical Trials from the Affiliated Drum Tower Hospital, Medical School of Nanjing University/ ; }, mesh = {Male ; Humans ; Adult ; *Peritoneal Dialysis/adverse effects ; *Peritonitis/diagnosis/drug therapy/etiology ; Anti-Bacterial Agents/therapeutic use ; *Eosinophilia/complications ; Dialysis Solutions/adverse effects ; }, abstract = {BACKGROUND: Overt eosinophilic peritonitis (EP) is a relatively uncommon complication of peritoneal dialysis (PD), although not rare. Here we reported a case of EP relieved after changing dialysate. CASE PRESENTATION: A 28-year old male patient developed cloudy PD effluents within the first month after PD started. Cytological study of PD effluents showed elevated white blood cells and polynuclear cells. Bacteria culture of PD effluents repeated for several times were all negative, and no pathogen was found by metagenomics next generation sequencing (mNGS). Antibiotic therapy for 28-day was ineffective. Based on these and increased eosinophils in peritoneal fluid, he was finally diagnosed as EP. PD dialysate was changed (consists of the same buffer agent and electrolytes, but is packed in bags that do not contain PVC), and the patient's PD effluent became clear. Of note, EP did not relapse 5 months later when the patient started to use the former PD solution again.

CONCLUSION: Although PD effluent turbidity almost always represents infectious peritonitis, there are other differential diagnoses including EP. For patients with cloudy fluid accompanied by mild symptoms who do not response to antibiotic therapy, it is reasonable to consider the possibility of this disease. EP tends to heal spontaneously, however, antihistamines or glucocorticoids are required sometimes to avoid catheter obstruction. For patients with no obvious incentives, replacement of dialysate may be useful.}, } @article {pmid36635574, year = {2023}, author = {McIlroy, SJ and Leu, AO and Zhang, X and Newell, R and Woodcroft, BJ and Yuan, Z and Hu, S and Tyson, GW}, title = {Anaerobic methanotroph 'Candidatus Methanoperedens nitroreducens' has a pleomorphic life cycle.}, journal = {Nature microbiology}, volume = {8}, number = {2}, pages = {321-331}, pmid = {36635574}, issn = {2058-5276}, mesh = {Anaerobiosis ; In Situ Hybridization, Fluorescence ; *Archaea/genetics ; *Bacteria/genetics ; Oxidation-Reduction ; Methanosarcinales/genetics/metabolism ; Methane/metabolism ; }, abstract = {'Candidatus Methanoperedens' are anaerobic methanotrophic (ANME) archaea with global importance to methane cycling. Here meta-omics and fluorescence in situ hybridization (FISH) were applied to characterize a bioreactor dominated by 'Candidatus Methanoperedens nitroreducens' performing anaerobic methane oxidation coupled to nitrate reduction. Unexpectedly, FISH revealed the stable co-existence of two 'Ca. M. nitroreducens' morphotypes: the archetypal coccobacilli microcolonies and previously unreported planktonic rods. Metagenomic analysis showed that the 'Ca. M. nitroreducens' morphotypes were genomically identical but had distinct gene expression profiles for proteins associated with carbon metabolism, motility and cell division. In addition, a third distinct phenotype was observed, with some coccobacilli 'Ca. M. nitroreducens' storing carbon as polyhydroxyalkanoates. The phenotypic variation of 'Ca. M. nitroreducens' probably aids their survival and dispersal in the face of sub-optimal environmental conditions. These findings further demonstrate the remarkable ability of members of the 'Ca. Methanoperedens' to adapt to their environment.}, } @article {pmid36635540, year = {2023}, author = {Albertsen, M}, title = {Long-read metagenomics paves the way toward a complete microbial tree of life.}, journal = {Nature methods}, volume = {20}, number = {1}, pages = {30-31}, pmid = {36635540}, issn = {1548-7105}, mesh = {*Metagenomics ; *Microbiota ; High-Throughput Nucleotide Sequencing ; Metagenome ; Sequence Analysis, DNA ; }, } @article {pmid36634616, year = {2023}, author = {Song, CH and Kim, N and Nam, RH and Choi, SI and Jang, JY and Choi, J and Lee, HN}, title = {Anti-PD-L1 Antibody and/or 17β-Estradiol Treatment Induces Changes in the Gut Microbiome in MC38 Colon Tumor Model.}, journal = {Cancer research and treatment}, volume = {55}, number = {3}, pages = {894-909}, pmid = {36634616}, issn = {2005-9256}, support = {2019R1A2C2085149//National Research Foundation of Korea/ ; }, mesh = {Male ; Female ; Animals ; Mice ; *Gastrointestinal Microbiome ; Cell Line, Tumor ; RNA, Ribosomal, 16S/genetics ; Mice, Inbred C57BL ; *Colonic Neoplasms/drug therapy ; Estradiol/pharmacology ; Estrogens/pharmacology ; }, abstract = {PURPOSE: 17β-Estradiol (E2) supplementation suppresses MC38 tumor growth by downregulating the expression of programmed death-ligand 1 (PD-L1). This study aims to figure out the gut microbiota that respond to anti-PD-L1 and/or estrogen treatment in MC38 colon cancer model.

MATERIALS AND METHODS: A syngeneic colon tumor model was developed by injection of MC38 cells into C57BL/6 background male and female mice. Three days before MC38 cells injection, E2 was supplemented to male mice daily for 1 week. Male and female mice with MC38 tumors (50-100 mm3) were injected with anti-PD-L1 antibody. Fresh feces were collected 26 days after injection of MC38 cells and 16S rRNA metagenomics sequencing of DNA extracted from feces was used to assess gut microbial composition.

RESULTS: At the taxonomic family level, Muribaculaceae was enriched only in the MC38 male control group. In male mice, linear discriminant analysis effect size analysis at the species level revealed that the four microorganisms were commonly regulated in single and combination treatment with anti-PD-L1 and/or E2; a decrease in PAC001068_g_uc and PAC001070_s (family Muribaculaceae) and increase in PAC001716_s and PAC001785_s (family Ruminococcaceae). Interestingly, in the anti-PD-L1 plus E2 group, a decrease in opportunistic pathogens (Enterobacteriaceae group) and an increase in commensal bacteria (Lactobacillus murinus group and Parabacteroides goldsteinii) were observed. Furthermore, the abundance of Parabacteroides goldsteinii was increased in both males and females in the anti-PD-L1 group.

CONCLUSION: Our results suggest that gut microbial changes induced by the pretreatment of estrogen before anti-PD-L1 might contribute to treatment of MC38 colon cancer.}, } @article {pmid36634008, year = {2023}, author = {Llewellyn, T and Nowell, RW and Aptroot, A and Temina, M and Prescott, TAK and Barraclough, TG and Gaya, E}, title = {Metagenomics Shines Light on the Evolution of "Sunscreen" Pigment Metabolism in the Teloschistales (Lichen-Forming Ascomycota).}, journal = {Genome biology and evolution}, volume = {15}, number = {2}, pages = {}, pmid = {36634008}, issn = {1759-6653}, mesh = {Phylogeny ; *Lichens/genetics/microbiology ; Sunscreening Agents/metabolism ; Anthraquinones/metabolism ; *Ascomycota ; Multigene Family ; }, abstract = {Fungi produce a vast number of secondary metabolites that shape their interactions with other organisms and the environment. Characterizing the genes underpinning metabolite synthesis is therefore key to understanding fungal evolution and adaptation. Lichenized fungi represent almost one-third of Ascomycota diversity and boast impressive secondary metabolites repertoires. However, most lichen biosynthetic genes have not been linked to their metabolite products. Here we used metagenomic sequencing to survey gene families associated with production of anthraquinones, UV-protectant secondary metabolites present in various fungi, but especially abundant in a diverse order of lichens, the Teloschistales (class Lecanoromycetes, phylum Ascomycota). We successfully assembled 24 new, high-quality lichenized-fungal genomes de novo and combined them with publicly available Lecanoromycetes genomes from taxa with diverse secondary chemistry to produce a whole-genome tree. Secondary metabolite biosynthetic gene cluster (BGC) analysis showed that whilst lichen BGCs are numerous and highly dissimilar, core enzyme genes are generally conserved across taxa. This suggests metabolite diversification occurs via re-shuffling existing enzyme genes with novel accessory genes rather than BGC gains/losses or de novo gene evolution. We identified putative anthraquinone BGCs in our lichen dataset that appear homologous to anthraquinone clusters from non-lichenized fungi, suggesting these genes were present in the common ancestor of the subphylum Pezizomycotina. Finally, we identified unique transporter genes in Teloschistales anthraquinone BGCs that may explain why these metabolites are so abundant and ubiquitous in these lichens. Our results support the importance of metagenomics for understanding the secondary metabolism of non-model fungi such as lichens.}, } @article {pmid36633196, year = {2023}, author = {Forni, D and Moltrasio, C and Sironi, M and Mozzi, A and Quattri, E and Venegoni, L and Zamprogno, M and Citterio, A and Clerici, M and Marzano, AV and Cagliani, R}, title = {Whole-genome sequencing of hMPXV1 in five Italian cases confirms the occurrence of the predominant epidemic lineage.}, journal = {Journal of medical virology}, volume = {95}, number = {2}, pages = {e28493}, pmid = {36633196}, issn = {1096-9071}, mesh = {Humans ; Phylogeny ; *Genome, Viral ; Mutation ; Whole Genome Sequencing ; *Nucleotides ; }, abstract = {The ongoing outbreak of monkeypox virus (hMPXV1) is the largest recorded in historically nonendemic countries. Genomic surveillance has emerged as a pivotal tool to track the spread and monitor the evolution of viral pathogens. Therefore, to assess the genetic diversity of circulating hMPXV1 in northern Italy in June to July 2022, we sequenced and analyzed five complete genomes of viruses sampled from patients presenting with a typical course of hMPXV1 infection. Phylogenetic analysis confirmed that all five genomes belong to the predominant epidemic lineage (B.1). Inspection of genetic changes and comparison with the reference sequence showed the presence of 12 nucleotide substitutions. Seven are nonsynonymous mutations leading to amino acid changes in six proteins belonging to different functional classes. Moreover, 11 of these 12 nucleotide mutations involve GA>AA or TC>TT replacements, suggesting that host APOBEC3 enzymes are responsible for the generation of substitutions in circulating viruses. Finally, metagenomic analysis evidenced bacterial superinfection (Streptococcus pyogenes) in one patient. Through this study, we contributed to expand the number of complete genomes of viruses circulating in Italy and characterize them as belonging to the predominant outbreak lineage.}, } @article {pmid36632439, year = {2023}, author = {Semenkov, IN and Shelyakin, PV and Nikolaeva, DD and Tutukina, MN and Sharapova, AV and Lednev, SA and Sarana, YV and Gelfand, MS and Krechetov, PP and Koroleva, TV}, title = {Data on the temporal changes in soil properties and microbiome composition after a jet-fuel contamination during the pot and field experiments.}, journal = {Data in brief}, volume = {46}, number = {}, pages = {108860}, pmid = {36632439}, issn = {2352-3409}, abstract = {The soil response to a jet-fuel contamination is uncertain. In this article, original data on the influence of a jet-fuel spillage on the topsoil properties are presented. The data set is obtained during a one-year long pot and field experiments with Dystric Arenosols, Fibric Histosols and Albic Luvisols. Kerosene loads were 1, 5, 10, 25 and 100 g/kg. The data set includes information about temporal changes in kerosene concentration; physicochemical properties, such as рН, moisture, cation exchange capacity, content of soil organic matter, available P and K, exchangeable NH4 [+], and water-soluble NO3 [-]; and biological properties, such as biological consumption of oxygen, and cellulolytic activity. Also, we provide sequencing data on variable regions of 16S ribosomal RNA of microbial communities from the respective soil samples.}, } @article {pmid36631912, year = {2023}, author = {Li, C and Li, X and Guo, R and Ni, W and Liu, K and Liu, Z and Dai, J and Xu, Y and Abduriyim, S and Wu, Z and Zeng, Y and Lei, B and Zhang, Y and Wang, Y and Zeng, W and Zhang, Q and Chen, C and Qiao, J and Liu, C and Hu, S}, title = {Expanded catalogue of metagenome-assembled genomes reveals resistome characteristics and athletic performance-associated microbes in horse.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {7}, pmid = {36631912}, issn = {2049-2618}, mesh = {Horses/genetics ; Humans ; Animals ; Metagenome ; Genome, Bacterial ; *Gastrointestinal Microbiome/genetics ; Drug Resistance, Microbial ; *Athletic Performance ; Metagenomics ; }, abstract = {BACKGROUND: As a domesticated species vital to humans, horses are raised worldwide as a source of mechanical energy for sports, leisure, food production, and transportation. The gut microbiota plays an important role in the health, diseases, athletic performance, and behaviour of horses.

RESULTS: Here, using approximately 2.2 Tb of metagenomic sequencing data from gut samples from 242 horses, including 110 samples from the caecum and 132 samples from the rectum (faeces), we assembled 4142 microbial metagenome-assembled genomes (MAG), 4015 (96.93%) of which appear to correspond to new species. From long-read data, we successfully assembled 13 circular whole-chromosome bacterial genomes representing novel species. The MAG contained over 313,568 predicted carbohydrate-active enzymes (CAZy), over 59.77% of which had low similarity match in CAZy public databases. High abundance and diversity of antibiotic resistance genes (ARG) were identified in the MAG, likely showing the wide use of antibiotics in the management of horse. The abundances of at least 36 MAG (e.g. MAG belonging to Lachnospiraceae, Oscillospiraceae, and Ruminococcus) were higher in racehorses than in nonracehorses. These MAG enriched in racehorses contained every gene in a major pathway for producing acetate and butyrate by fibre fermentation, presenting potential for greater amount of short-chain fatty acids available to fuel athletic performance.

CONCLUSION: Overall, we assembled 4142 MAG from short- and long-read sequence data in the horse gut. Our dataset represents an exhaustive microbial genome catalogue for the horse gut microbiome and provides a valuable resource for discovery of performance-enhancing microbes and studies of horse gut microbiome. Video Abstract.}, } @article {pmid36631881, year = {2023}, author = {Devika, NT and Katneni, VK and Jangam, AK and Suganya, PN and Shekhar, MS and Jithendran, KP}, title = {In silico prediction of potential indigenous microbial biomarkers in Penaeus vannamei identified through meta-analysis and genome-scale metabolic modelling.}, journal = {Environmental microbiome}, volume = {18}, number = {1}, pages = {2}, pmid = {36631881}, issn = {2524-6372}, support = {PDF 2020/000267//Department of Science and Technology, India/ ; Network project on Agricultural Bioinformatics and Computational Biology//Indian Council of Agriculture Research/ ; }, abstract = {BACKGROUND: Understanding the microbiome is crucial as it contributes to the metabolic health of the host and, upon dysbiosis, may influence disease development. With the recent surge in high-throughput sequencing technology, the availability of microbial genomic data has increased dramatically. Amplicon sequence-based analyses majorly profile microbial abundance and determine taxonomic markers. Furthermore, the availability of genome sequences for various microbial organisms has prompted the integration of genome-scale metabolic modelling that provides insights into the metabolic interactions influencing host health. However, the analysis from a single study may not be consistent, necessitating a meta-analysis.

RESULTS: We conducted a meta-analysis and integrated with constraint-based metabolic modelling approach, focusing on the microbiome of pacific white shrimp Penaeus vannamei, an extensively cultured marine candidate species. Meta-analysis revealed that Acinetobacter and Alteromonas are significant indicators of "health" and "disease" specific taxonomic biomarkers, respectively. Further, we enumerated metabolic interactions among the taxonomic biomarkers by applying a constraint-based approach to the community metabolic models (4416 pairs). Under different nutrient environments, a constraint-based flux simulation identified five beneficial species: Acinetobacter spWCHA55, Acinetobacter tandoii SE63, Bifidobacterium pseudolongum 49 D6, Brevundimonas pondensis LVF1, and Lutibacter profundi LP1 mediating parasitic interactions majorly under sucrose environment in the pairwise community. The study also reports the healthy biomarkers that can co-exist and have functionally dependent relationships to maintain a healthy state in the host.

CONCLUSIONS: Toward this, we collected and re-analysed the amplicon sequence data of P. vannamei (encompassing 117 healthy and 142 disease datasets). By capturing the taxonomic biomarkers and modelling the metabolic interaction between them, our study provides a valuable resource, a first-of-its-kind analysis in aquaculture scenario toward a sustainable shrimp farming.}, } @article {pmid36631668, year = {2023}, author = {Fan, K and Chu, H and Eldridge, DJ and Gaitan, JJ and Liu, YR and Sokoya, B and Wang, JT and Hu, HW and He, JZ and Sun, W and Cui, H and Alfaro, FD and Abades, S and Bastida, F and Díaz-López, M and Bamigboye, AR and Berdugo, M and Blanco-Pastor, JL and Grebenc, T and Duran, J and Illán, JG and Makhalanyane, TP and Mukherjee, A and Nahberger, TU and Peñaloza-Bojacá, GF and Plaza, C and Verma, JP and Rey, A and Rodríguez, A and Siebe, C and Teixido, AL and Trivedi, P and Wang, L and Wang, J and Yang, T and Zhou, XQ and Zhou, X and Zaady, E and Tedersoo, L and Delgado-Baquerizo, M}, title = {Soil biodiversity supports the delivery of multiple ecosystem functions in urban greenspaces.}, journal = {Nature ecology & evolution}, volume = {7}, number = {1}, pages = {113-126}, pmid = {36631668}, issn = {2397-334X}, mesh = {Humans ; *Ecosystem ; *Soil ; Parks, Recreational ; Biodiversity ; Plants ; }, abstract = {While the contribution of biodiversity to supporting multiple ecosystem functions is well established in natural ecosystems, the relationship of the above- and below-ground diversity with ecosystem multifunctionality remains virtually unknown in urban greenspaces. Here we conducted a standardized survey of urban greenspaces from 56 municipalities across six continents, aiming to investigate the relationships of plant and soil biodiversity (diversity of bacteria, fungi, protists and invertebrates, and metagenomics-based functional diversity) with 18 surrogates of ecosystem functions from nine ecosystem services. We found that soil biodiversity across biomes was significantly and positively correlated with multiple dimensions of ecosystem functions, and contributed to key ecosystem services such as microbially driven carbon pools, organic matter decomposition, plant productivity, nutrient cycling, water regulation, plant-soil mutualism, plant pathogen control and antibiotic resistance regulation. Plant diversity only indirectly influenced multifunctionality in urban greenspaces via changes in soil conditions that were associated with soil biodiversity. These findings were maintained after controlling for climate, spatial context, soil properties, vegetation and management practices. This study provides solid evidence that conserving soil biodiversity in urban greenspaces is key to supporting multiple dimensions of ecosystem functioning, which is critical for the sustainability of urban ecosystems and human wellbeing.}, } @article {pmid36631002, year = {2023}, author = {Hsu, CL and Lang, S and Demir, M and Fouts, DE and Stärkel, P and Schnabl, B}, title = {Any alcohol use in NAFLD patients is associated with significant changes to the intestinal virome.}, journal = {Hepatology (Baltimore, Md.)}, volume = {77}, number = {6}, pages = {2073-2083}, pmid = {36631002}, issn = {1527-3350}, support = {I01 BX004594/BX/BLRD VA/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; T32 DK007202/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Non-alcoholic Fatty Liver Disease ; Virome ; Alcohol Drinking/adverse effects ; *Alcoholism ; Ethanol ; *Liver Diseases, Alcoholic ; }, abstract = {BACKGROUND AND AIMS: The prevalence of alcohol use disorder (AUD) and metabolic dysfunction-associated fatty liver disease (MAFLD) are increasing worldwide, leading to the increasing likelihood of both etiologies contributing to a patient's liver disease. However, the effects of modest alcohol use in NAFLD are controversial and more studies are needed. We compared the intestinal viromes of patients with AUD and NAFLD in order to evaluate the effect of alcohol consumption on the intestinal viromes of NAFLD patients by extracting virus-like particles and performing metagenomic sequencing.

APPROACH AND RESULTS: Viral nucleic acids were extracted from fecal samples and subjected to metagenomic sequencing. We demonstrate significant differences in the intestinal viromes of NAFLD and AUD patients, and that alcohol use in NAFLD patients reclassified to MAFLD accounted for significant differences in the intestinal viromes. The relative abundance of several Lactococcus phages was more similar between AUD patients and alcohol-consuming MAFLD patients than non-alcohol-consuming MAFLD patients and control subjects, and multivariate modeling using the most discriminating Lactococcus phages could better predict alcohol use in the MAFLD population than the alcohol-associated liver disease/NAFLD Index. Significant differences in the viral composition and diversity were also seen between MAFLD patients with low and moderate alcohol consumption compared with no alcohol consumption.

CONCLUSIONS: The intestinal virome of MAFLD patients who consume low to moderate amounts of alcohol are significantly different from those who do not, and many features of the intestinal virome of alcohol-consuming MAFLD patients resemble that of AUD patients.}, } @article {pmid36630500, year = {2023}, author = {Konno, N and Iwasaki, W}, title = {Machine learning enables prediction of metabolic system evolution in bacteria.}, journal = {Science advances}, volume = {9}, number = {2}, pages = {eadc9130}, pmid = {36630500}, issn = {2375-2548}, mesh = {Phylogeny ; *Bacteria/genetics ; *Evolution, Molecular ; Genomics ; Genome, Bacterial ; }, abstract = {Evolution prediction is a long-standing goal in evolutionary biology, with potential impacts on strategic pathogen control, genome engineering, and synthetic biology. While laboratory evolution studies have shown the predictability of short-term and sequence-level evolution, that of long-term and system-level evolution has not been systematically examined. Here, we show that the gene content evolution of metabolic systems is generally predictable by applying ancestral gene content reconstruction and machine learning techniques to ~3000 bacterial genomes. Our framework, Evodictor, successfully predicted gene gain and loss evolution at the branches of the reference phylogenetic tree, suggesting that evolutionary pressures and constraints on metabolic systems are universally shared. Investigation of pathway architectures and meta-analysis of metagenomic datasets confirmed that these evolutionary patterns have physiological and ecological bases as functional dependencies among metabolic reactions and bacterial habitat changes. Last, pan-genomic analysis of intraspecies gene content variations proved that even "ongoing" evolution in extant bacterial species is predictable in our framework.}, } @article {pmid36630344, year = {2023}, author = {, }, title = {Expression of Concern: Metagenomic analyses of the gut microbiota associated with colorectal adenoma.}, journal = {PloS one}, volume = {18}, number = {1}, pages = {e0280121}, pmid = {36630344}, issn = {1932-6203}, } @article {pmid36629860, year = {2023}, author = {Liang, C and Wagstaff, J and Aharony, N and Schmit, V and Manheim, D}, title = {Managing the Transition to Widespread Metagenomic Monitoring: Policy Considerations for Future Biosurveillance.}, journal = {Health security}, volume = {21}, number = {1}, pages = {34-45}, pmid = {36629860}, issn = {2326-5108}, mesh = {Humans ; *Biosurveillance ; *Communicable Diseases ; Public Health ; Health Policy ; }, abstract = {The technological possibilities and future public health importance of metagenomic sequencing have received extensive attention, but there has been little discussion about the policy and regulatory issues that need to be addressed if metagenomic sequencing is adopted as a key technology for biosurveillance. In this article, we introduce metagenomic monitoring as a possible path to eventually replacing current infectious disease monitoring models. Many key enablers are technological, whereas others are not. We therefore highlight key policy challenges and implementation questions that need to be addressed for "widespread metagenomic monitoring" to be possible. Policymakers must address pitfalls like fragmentation of the technological base, private capture of benefits, privacy concerns, the usefulness of the system during nonpandemic times, and how the future systems will enable better response. If these challenges are addressed, the technological and public health promise of metagenomic sequencing can be realized.}, } @article {pmid36629429, year = {2023}, author = {Dragone, NB and Whittaker, K and Lord, OM and Burke, EA and Dufel, H and Hite, E and Miller, F and Page, G and Slayback, D and Fierer, N}, title = {The Early Microbial Colonizers of a Short-Lived Volcanic Island in the Kingdom of Tonga.}, journal = {mBio}, volume = {14}, number = {1}, pages = {e0331322}, pmid = {36629429}, issn = {2150-7511}, mesh = {Tonga ; *Cyanobacteria/metabolism ; Volcanic Eruptions/analysis ; Sulfur/metabolism ; }, abstract = {The island of Hunga Tonga Hunga Ha'apai (HTHH) in the Kingdom of Tonga was formed by Surtseyan eruptions and persisted for 7 years before being obliterated by a massive volcanic eruption on 15 January 2022. Before it was destroyed, HTHH was an unparalleled natural laboratory to study primary succession on a newly formed landmass. We characterized the microbial communities found on the surface sediments of HTHH using a combination of quantitative PCR, marker gene sequencing, and shotgun metagenomic analyses. Contrary to expectations, photosynthetic cyanobacteria were not detected in these sediments, even though they are typically dominant in the earliest stages of primary succession in other terrestrial environments. Instead, our results suggest that the early sediment communities were composed of a diverse array of bacterial taxa, including trace gas oxidizers, anoxygenic photosynthesizers, and chemolithotrophs capable of metabolizing inorganic sulfur, with these bacteria likely sourced from nearby active geothermal environments. While the destruction of HTHH makes it impossible to revisit the site to conduct in situ metabolic measurements or observe how the microbial communities might have continued to change over time, our results do suggest that the early microbial colonizers have unique origins and metabolic capabilities. IMPORTANCE The volcanic island of Hunga Tonga Hunga Ha'apai in the Kingdom of Tonga represents a very rare example of new island formation and thus a unique opportunity to study how organisms colonize a new landmass. We found that the island was colonized by diverse microbial communities shortly after its formation in 2015, with these microbes likely originating from nearby geothermal environments. Primary succession in this system was distinct from that typically observed in other terrestrial environments, with the early microbial colonizers relying on unique metabolic strategies to survive on the surface of this newly formed island, including the capacity to generate energy via sulfur and trace gas metabolism.}, } @article {pmid36629118, year = {2023}, author = {Chou, PH and Hu, MY and Guh, YJ and Wu, GC and Yang, SH and Tandon, K and Shao, YT and Lin, LY and Chen, C and Tseng, KY and Wang, MC and Zhang, CM and Han, BC and Lin, CC and Tang, SL and Jeng, MS and Chang, CF and Tseng, YC}, title = {Cellular mechanisms underlying extraordinary sulfide tolerance in a crustacean holobiont from hydrothermal vents.}, journal = {Proceedings. Biological sciences}, volume = {290}, number = {1990}, pages = {20221973}, pmid = {36629118}, issn = {1471-2954}, mesh = {Animals ; *Hydrothermal Vents ; Thiosulfates ; Sulfides/toxicity ; *Brachyura/physiology ; Bacteria ; }, abstract = {The shallow-water hydrothermal vent system of Kueishan Island has been described as one of the world's most acidic and sulfide-rich marine habitats. The only recorded metazoan species living in the direct vicinity of the vents is Xenograpsus testudinatus, a brachyuran crab endemic to marine sulfide-rich vent systems. Despite the toxicity of hydrogen sulfide, X. testudinatus occupies an ecological niche in a sulfide-rich habitat, with the underlying detoxification mechanism remaining unknown. Using laboratory and field-based experiments, we characterized the gills of X. testudinatus that are the major site of sulfide detoxification. Here sulfide is oxidized to thiosulfate or bound to hypotaurine to generate the less toxic thiotaurine. Biochemical and molecular analyses demonstrated that the accumulation of thiosulfate and hypotaurine is mediated by the sodium-independent sulfate anion transporter (SLC26A11) and taurine transporter (Taut), which are expressed in gill epithelia. Histological and metagenomic analyses of gill tissues demonstrated a distinct bacterial signature dominated by Epsilonproteobacteria. Our results suggest that thiotaurine synthesized in gills is used by sulfide-oxidizing endo-symbiotic bacteria, creating an effective sulfide-buffering system. This work identified physiological mechanisms involving host-microbe interactions that support life of a metazoan in one of the most extreme environments on our planet.}, } @article {pmid36628836, year = {2023}, author = {Benny, CK and Chakraborty, S}, title = {Dyeing wastewater treatment in horizontal-vertical constructed wetland using organic waste media.}, journal = {Journal of environmental management}, volume = {331}, number = {}, pages = {117213}, doi = {10.1016/j.jenvman.2023.117213}, pmid = {36628836}, issn = {1095-8630}, mesh = {*Wastewater ; Waste Disposal, Fluid/methods ; Wetlands ; Coloring Agents ; *Water Purification/methods ; Nitrogen/analysis ; }, abstract = {A hybrid constructed wetland (CW) system with horizontal and vertical flow combination was evaluated for treating carbon-deficient synthetic dyeing wastewater containing 100 mg/L Reactive Yellow 145 dye. Organic waste products such as cow manure and wood chips were added as media in horizontal CW, and gravel as vertical CW media. Horizontal and vertical CWs were planted with Typha angustifolia. Horizontal CW was operated in continuous mode at hydraulic retention time (HRT) of 3 d and vertical CW in batch mode at 1 d HRT. The results suggested the potential application of a cost-effective horizontal-vertical hybrid CW to remove azo dyes from low-carbon dyeing wastewater. In horizontal CW, organic media was used as the carbon source for microbial dye degradation, resulting in 90% colour removal in the absence of available carbon in dyeing wastewater. Proteobacteria, Firmicutes and Bacteroidetes played a dominant role in dye degradation in horizontal CW. Vertical CW removed dye degradation organics, 69% ammonium-nitrogen and 39% organic-nitrogen. Phytotoxicity assays indicated toxicity reduction along the CW treatment path.}, } @article {pmid36628835, year = {2023}, author = {Liang, Y and Zheng, K and McMinn, A and Wang, M}, title = {Expanding diversity and ecological roles of RNA viruses.}, journal = {Trends in microbiology}, volume = {31}, number = {3}, pages = {229-232}, doi = {10.1016/j.tim.2022.12.004}, pmid = {36628835}, issn = {1878-4380}, mesh = {*Ecosystem ; *RNA Viruses/genetics ; Genome, Viral ; Phylogeny ; }, abstract = {While the diversity of global environmental RNA viruses has remained largely unexplored, recent advances have reported on the discovery of over 10[6] RNA viral contigs from both terrestrial and marine ecosystems that will help us to better understand the diversity, evolution, ecological roles, and transmission of RNA viruses.}, } @article {pmid36628298, year = {2023}, author = {Cui, Z and Meng, L}, title = {Psittacosis Pneumonia: Diagnosis, Treatment and Interhuman Transmission.}, journal = {International journal of general medicine}, volume = {16}, number = {}, pages = {1-6}, pmid = {36628298}, issn = {1178-7074}, abstract = {Psittacosis pneumonia is a zoonosis caused by Chlamydia psittacosis infection, mainly resulting from contact with aerosols of birds or poultry's urine, feces, and excrement. The clinical manifestations range from general symptoms of infection to severe acute respiratory syndrome and systemic diseases, currently diagnosed using metagenomic next-generation sequencing (mNGS) to improve diagnostic accuracy. To date, most reports have only discussed human exposure to poultry disease. However, the latest studies have shown that human-to-human transmission of Chlamydia psittaci occurs not only between infected patients and their close contacts but also between secondary contacts. After looking back on relevant literature at home and abroad in the past ten years, this paper reviews the diagnosis, diagnosis and treatment, and progress in epidemiological research of Psittacosis pneumonia.}, } @article {pmid36627827, year = {2023}, author = {Li, ZM and Kong, CY and Mao, YQ and Huang, JT and Chen, HL and Han, B and Wang, LS}, title = {Ampicillin exacerbates acetaminophen-induced acute liver injury by inducing intestinal microbiota imbalance and butyrate reduction.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {43}, number = {4}, pages = {865-877}, doi = {10.1111/liv.15512}, pmid = {36627827}, issn = {1478-3231}, mesh = {Animals ; Mice ; Acetaminophen/toxicity ; *Gastrointestinal Microbiome ; Butyrates/pharmacology ; Liver ; Ampicillin/adverse effects ; *Chemical and Drug Induced Liver Injury/etiology ; Mice, Inbred C57BL ; }, abstract = {BACKGROUND AND AIMS: Antibiotics (ATBx) and acetaminophen (APAP) are widely used worldwide. APAP is the most common cause of acute liver injury (ALI) and might be used in combination with ATBx in clinics. However, the impact of ATBx on APAP-induced ALI has rarely been studied.

METHODS: First, we compared the effects of seven ATBx on APAP-induced ALI. Then, we analysed faecal, serum and liver samples to investigate the impact of the gut microbiota on this process. Finally, we assessed the role of short-chain fatty acids in this process.

RESULTS: In this work, we found that the ALI was significantly aggravated in the mice treated with ampicillin (Amp) instead of other ATBx. Amp exposure reduced the diversity and altered the composition of gut microbiota. The altered gut microbiota aggravated APAP-induced ALF, which was proven by faecal microbiota transplantation from ATBx-treated mice. Metagenomic analysis showed a significantly decreased Lactobacillus abundance in Amp-treated mice. Gavage with Lactobacillus, especially Lactobacillus rhamnosus, significantly reversed the severer ALF induced by APAP and Amp. Moreover, Lactobacillus supplementation increased butyrate-producing clostridia and lowered butyrate levels in Amp-treated mice. In accordance, butyrate supplementation could also alleviate Amp-aggravated ALI. In addition, inhibition of nuclear factor erythroid 2-related factor 2 counteracted the protective effect of butyrate on aggravated ALI induced by Amp and APAP.

CONCLUSION: Together, this study revealed a potential health impact of Amp that may exacerbate liver damage when co-exposed to excess APAP.}, } @article {pmid36627678, year = {2023}, author = {Fu, J and Shan, J and Cui, Y and Yan, C and Wang, Q and Han, J and Cao, G}, title = {Metabolic disorder and intestinal microflora dysbiosis in chronic inflammatory demyelinating polyradiculoneuropathy.}, journal = {Cell & bioscience}, volume = {13}, number = {1}, pages = {6}, pmid = {36627678}, issn = {2045-3701}, support = {ZR2020MC011//Natural Science Foundation of Shandong Province/ ; }, abstract = {OBJECTIVE: Chronic inflammatory demyelinating polyradiculoneuropathy (CIDP) is a rare acquired immune-mediated neuropathy. Although microbial infection is potentially a contributing factor, a causative link between CIDP and microbial infection remains unclear. There is also no definitive biomarker for CIDP diagnostics and therapies. The present study aimed to characterize the serum metabolic profile and gut microbiome structure in CIDP.

METHODS: Targeted metabolomics profiling of serum, using liquid chromatography-mass spectrometry, and metagenomics sequencing of stool samples from a cohort of CIDP and non-CIDP subjects were performed to evaluate serum metabolic profiles and gut microbiome structure in CIDP subjects relative to healthy controls.

RESULTS: Metabolome data revealed that the bile acids profile was perturbed in CIDP with bile acids and arachidonic acid enriched significantly in CIDP versus non-CIDP controls. Metagenome data revealed that opportunistic pathogens, such as Klebsiella pneumonia and Megamonas funiformis, and genes involved in bacterial infection were notably more abundant in CIDP subjects, while gut microbes related to biotransformation of secondary bile acids were abnormal in CIDP versus non-CIDP subjects. Correlation analysis revealed that changes in secondary bile acids were associated with altered gut microbes, including Bacteroides ovatus, Bacteroides caccae, and Ruminococcus gnavus.

CONCLUSION: Bile acids and arachidonic acid metabolism were disturbed in CIDP subjects and might be affected by the dysbiosis of gut microbial flora. These findings suggest that the combination of bile acids and arachidonic acid could be used as a CIDP biomarker and that modulation of gut microbiota might impact the clinical course of CIDP.}, } @article {pmid36627170, year = {2023}, author = {Nii, T and Maeda, Y and Motooka, D and Naito, M and Matsumoto, Y and Ogawa, T and Oguro-Igashira, E and Kishikawa, T and Yamashita, M and Koizumi, S and Kurakawa, T and Okumura, R and Kayama, H and Murakami, M and Sakaguchi, T and Das, B and Nakamura, S and Okada, Y and Kumanogoh, A and Takeda, K}, title = {Genomic repertoires linked with pathogenic potency of arthritogenic Prevotella copri isolated from the gut of patients with rheumatoid arthritis.}, journal = {Annals of the rheumatic diseases}, volume = {82}, number = {5}, pages = {621-629}, pmid = {36627170}, issn = {1468-2060}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; *Arthritis, Rheumatoid/genetics ; Prevotella/genetics ; Genomics ; Disease Models, Animal ; }, abstract = {OBJECTIVES: Prevotella copri is considered to be a contributing factor in rheumatoid arthritis (RA). However, in some non-Westernised countries, healthy individuals also harbour an abundance of P. copri in the intestine. This study investigated the pathogenicity of RA patient-derived P. copri (P. copri RA) compared with healthy control-derived P. copri (P. copri HC).

METHODS: We obtained 13 P. copri strains from the faeces of patients with RA and healthy controls. Following whole genome sequencing, the sequences of P. copri RA and P. copri HC were compared. To analyse the arthritis-inducing ability of P. copri, we examined two arthritis models (1) a collagen-induced arthritis model harbouring P. copri under specific-pathogen-free conditions and (2) an SKG mouse arthritis model under P. copri-monocolonised conditions. Finally, to evaluate the ability of P. copri to activate innate immune cells, we performed in vitro stimulation of bone marrow-derived dendritic cells (BMDCs) by P. copri RA and P. copri HC.

RESULTS: Comparative genomic analysis revealed no apparent differences in the core gene contents between P. copri RA and P. copri HC, but pangenome analysis revealed the high genome plasticity of P. copri. We identified a P. copri RA-specific genomic region as a conjugative transposon. In both arthritis models, P. copri RA-induced more severe arthritis than P. copri HC. In vitro BMDC stimulation experiments revealed the upregulation of IL-17 and Th17-related cytokines (IL-6, IL-23) by P. copri RA.

CONCLUSION: Our findings reveal the genetic diversity of P. copri, and the genomic signatures associated with strong arthritis-inducing ability of P. copri RA. Our study contributes towards elucidation of the complex pathogenesis of RA.}, } @article {pmid36626997, year = {2023}, author = {Ren, H and Lu, Z and Sun, R and Wang, X and Zhong, J and Su, T and He, Q and Liao, X and Liu, Y and Lian, X and Sun, J}, title = {Functional metagenomics reveals wildlife as natural reservoirs of novel β-lactamases.}, journal = {The Science of the total environment}, volume = {868}, number = {}, pages = {161505}, doi = {10.1016/j.scitotenv.2023.161505}, pmid = {36626997}, issn = {1879-1026}, mesh = {Animals ; *beta-Lactamases/genetics ; *Anti-Bacterial Agents ; Animals, Wild ; Metagenomics/methods ; beta-Lactams ; Bacteria/genetics ; }, abstract = {The antibiotic resistances in bacteria are believed to rapidly evolve over time in the anthropogenic environments which enriched with selection pressures. However, the knowledge regarding the development of antibiotic resistance in wildlife and their habitats is scarce. It is, therefore, of great interest and significance to unveil the yet-unknown antibiotic resistances in wildlife in accordance with One Health concept. To this end, we analyzed the samples taken from wildlife and surrounding environments using a functional metagenomics approach. By functional screening in combination with Illumina sequencing, a total of 32 candidate genes which encoding putative novel β-lactamase were identified. These putative β-lactamase were taxonomically assigned into bacteria of 23 genera from 7 phyla, where Proteobacteria, Actinobacteria and Firmicutes were dominant. The following functional assessment demonstrated that 4 novel β-lactamases, namely blaSSA, blaSSB1, blaSSB2 and blaSSD, were functionally active to confer the phenotypical resistance to bacteria by increasing MICs up to 128-fold. Further analysis indicated that the novel β-lactamases identified in the current study were able to hydrolyze a broad spectrum of β-lactams including cephalosporins, and they were genetically unique comparing with known β-lactamases. The plausible transmission of some novel β-lactamase genes was supported by our results as the same gene was detected in different samples from different sites. This study shed the light on the active role of wildlife and associated environments as natural reservoirs of novel β-lactamases, implying that the antibiotic resistances might evolve in absence of selection pressure and threaten public health once spread into clinically important pathogens.}, } @article {pmid36625891, year = {2023}, author = {Snyder, C and Centlivre, JP and Bhute, S and Shipman, G and Friel, AD and Viver, T and Palmer, M and Konstantinidis, KT and Sun, HJ and Rossello-Mora, R and Nadeau, J and Hedlund, BP}, title = {Microbial Motility at the Bottom of North America: Digital Holographic Microscopy and Genomic Motility Signatures in Badwater Spring, Death Valley National Park.}, journal = {Astrobiology}, volume = {23}, number = {3}, pages = {295-307}, doi = {10.1089/ast.2022.0090}, pmid = {36625891}, issn = {1557-8070}, mesh = {*Microscopy ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Parks, Recreational ; Metagenome ; Metagenomics/methods ; North America ; }, abstract = {Motility is widely distributed across the tree of life and can be recognized by microscopy regardless of phylogenetic affiliation, biochemical composition, or mechanism. Microscopy has thus been proposed as a potential tool for detection of biosignatures for extraterrestrial life; however, traditional light microscopy is poorly suited for this purpose, as it requires sample preparation, involves fragile moving parts, and has a limited volume of view. In this study, we deployed a field-portable digital holographic microscope (DHM) to explore microbial motility in Badwater Spring, a saline spring in Death Valley National Park, and complemented DHM imaging with 16S rRNA gene amplicon sequencing and shotgun metagenomics. The DHM identified diverse morphologies and distinguished run-reverse-flick and run-reverse types of flagellar motility. PICRUSt2- and literature-based predictions based on 16S rRNA gene amplicons were used to predict motility genotypes/phenotypes for 36.0-60.1% of identified taxa, with the predicted motile taxa being dominated by members of Burkholderiaceae and Spirochaetota. A shotgun metagenome confirmed the abundance of genes encoding flagellar motility, and a Ralstonia metagenome-assembled genome encoded a full flagellar gene cluster. This study demonstrates the potential of DHM for planetary life detection, presents the first microbial census of Badwater Spring and brine pool, and confirms the abundance of mobile microbial taxa in an extreme environment.}, } @article {pmid36625651, year = {2023}, author = {Grundy, BS and Parikh, H and Jacob, S and Banura, P and Moore, CC and Liu, J and Houpt, ER}, title = {Pathogen Detection Using Metagenomic Next-Generation Sequencing of Plasma Samples from Patients with Sepsis in Uganda.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0431222}, pmid = {36625651}, issn = {2165-0497}, support = {T32 AI007046/AI/NIAID NIH HHS/United States ; K24 AI102972/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Viremia ; *HIV Infections/complications ; *Epstein-Barr Virus Infections ; Uganda/epidemiology ; Herpesvirus 4, Human ; High-Throughput Nucleotide Sequencing/methods ; *Hepatitis B ; Metagenomics/methods ; }, abstract = {Metagenomic sequencing is a promising new method for pathogen detection. We aimed to detect pathogens from archived plasma using metagenomic sequencing in a previously well-characterized cohort of 254 predominantly HIV-infected patients with sepsis in Uganda. We used Illumina sequencing and the Chan Zuckerberg ID metagenomics platform to sequence and identify pathogens. On average, each plasma sample yielded 3,404,737 ± 2,201,997 reads (mean ± standard deviation), of which 220,032 ± 416,691 (6.3% ± 8.6%) were identified as nonhuman reads. Using a background model filter, 414 genus-specific pathogen identifications were found in the 254 samples. Nineteen pathogens were previously detected positive by quantitative PCR (qPCR), compared to sequencing, which demonstrated 30.2% sensitivity and 99.5% specificity. Sensitivity was higher for viral pathogens than nonviral pathogens (37% versus 5%). For example, HIV viremia was detected in 69% of samples using qPCR, and sequencing revealed 70% sensitivity and 92% specificity. There were 75 genus-specific potential pathogens identified by sequencing in this cohort, including hepatitis B and Epstein-Barr virus (EBV), among several others. qPCR showed a prevalence of hepatitis B and EBV viremia of 17% and 45%, respectively. In-hospital mortality was associated with a lower qPCR threshold cycle value for EBV (adjusted odds ratio, 0.85; P < .001) but not for hepatitis B or HIV. In conclusion, a broad range of potential pathogens were identified by metagenomic sequencing in patients with sepsis in Uganda. Unexpectedly high rates of hepatitis B and EBV viremia were found. Whether these viral infections in HIV patients with sepsis are clinically important requires further study. IMPORTANCE The use of next-generation sequencing (NGS) in blood samples is an emerging technology for clinical microbiology labs. In this work, we performed NGS on plasma samples from a well-characterized cohort, where all samples had been previously tested by PCR for 43 pathogens. Therefore, we could compare sequencing performance against that of PCR and identify clinical correlates. A broad range of potential pathogens were identified by metagenomic sequencing in patients with sepsis in Uganda, particularly viruses, which we confirmed by PCR. In addition to HIV viremia, unexpectedly high rates of hepatitis B and EBV viremia were found, which may have important clinical implications.}, } @article {pmid36625596, year = {2023}, author = {Li, Y and Qian, F and Cheng, X and Wang, D and Wang, Y and Pan, Y and Chen, L and Wang, W and Tian, Y}, title = {Dysbiosis of Oral Microbiota and Metabolite Profiles Associated with Type 2 Diabetes Mellitus.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0379622}, pmid = {36625596}, issn = {2165-0497}, mesh = {Humans ; *Diabetes Mellitus, Type 2 ; Dysbiosis ; Cadaverine ; *Dental Caries ; *Microbiota ; }, abstract = {Several previous studies have shown that oral microbial disorders may be closely related to the occurrence and development of type 2 diabetes mellitus (T2DM). However, whether the function of oral microorganisms and their metabolites have changed in patients with T2DM who have not suffered from any oral diseases has not been reported. We performed metagenomic analyses and nontargeted metabolic analysis of saliva and supragingival plaque samples from patients with T2DM who have not suffered any oral diseases and normal controls. We found that periodontal pathogens such as Porphyromonas gingivalis and Prevotella melaninogenica were significantly enriched, while the abundances of dental caries pathogens such as Streptococcus mutans and Streptococcus sobrinus were not significantly different in patients with T2DM compared to those in normal controls. Metabolomic analyses showed that the salivary levels of cadaverine and L-(+)-leucine of patients with T2DM were significantly higher than those of normal controls, while the supragingival plaque levels of N-acetyldopamine and 3,4-dimethylbenzoic acid in patients with T2DM were significantly higher than those in the normal controls. Additionally, we identified the types of oral microorganisms related to the changes in the levels of circulating metabolites, and the oral microorganisms were involved in the dysregulation of harmful metabolites such as cadaverine and n, n-dimethylarginine. Overall, our study first described the changes in the composition of oral microorganisms and their metabolites in patients with T2DM who have not suffered any oral diseases, which will provide a direct basis for finding oral biomarkers for early warning of oral diseases in T2DM. IMPORTANCE The incidence of oral diseases in type 2 diabetic patients might increase, and the severity might also be more serious. At present, the relationship between oral microorganisms and type 2 diabetes mellitus (T2DM) has become a hot topic in systemic health research. However, whether the function of oral microorganisms and their metabolites have changed in patients with T2DM who have not suffered from any oral diseases has not been reported. We found that even if the oral condition of T2DM is healthy, their oral microbes and metabolites have changed, thus increasing the risk of periodontal disease. Our study first described the changes in the composition of oral microorganisms and their metabolites in T2DM who have not suffered any oral diseases and revealed the correlation between oral microorganisms and their metabolites, which will provide a direct basis for finding oral biomarkers for early warning of oral diseases in patients with T2DM.}, } @article {pmid36625589, year = {2023}, author = {Wu, HX and Wei, FL and Zhang, W and Han, J and Guo, S and Wang, Z and Chen, DX and Hou, W and Hu, ZJ}, title = {Clinical Evaluation of Metagenomic Next-Generation Sequencing Method for the Diagnosis of Suspected Ascitic Infection in Patients with Liver Cirrhosis in a Clinical Laboratory.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0294622}, pmid = {36625589}, issn = {2165-0497}, mesh = {Humans ; Laboratories, Clinical ; *Coinfection ; Metagenomics ; Liver Cirrhosis/complications/diagnosis ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents ; *Peritonitis/diagnosis ; }, abstract = {Metagenomic next-generation sequencing (mNGS), mostly carried out in independent clinical laboratories, has been increasingly applied in clinical pathogen diagnosis. We aimed to explore the feasibility of mNGS in clinical laboratories and analyze its potential in the diagnosis of infectious ascites. Two reference panels composed of 12 strains commonly appearing in peritonitis were constructed to evaluate the performance metrics based on in-house mNGS protocols. The mNGS clinical detection value was analyzed in 211 ascitic samples and compared with culture and composite standards. Finally, eight patients with cirrhosis were prospectively enrolled to verify the clinical value of mNGS in peritoneal infection diagnosis. The mNGS analytical performance showed that the assay had great linearity, specificity, stability, interference, and limits of detection of 33 to 828 CFU/mL. The sensitivity and specificity of mNGS for bacterial or fungal detection using culture standards were 84.2% and 82.0%, respectively. After adjustment using digital PCR and clinical judgment, the sensitivity and specificity increased to 87.2% and 90.1%, respectively. Compared with culture, mNGS detected a broad range of pathogens and more polymicrobial infections (49% versus 9%, P < 0.05). The pathogen results were obtained within 24 h using mNGS in eight prospective cases, which effectively guided antibiotics therapy. mNGS testing in clinical laboratories affiliated with a hospital has certain advantages. It has unique superiority in pathogens detection, particularly in patients with polymicrobial infections. However, considering spectrum characteristics and test cost, pertinent pathogen panels should be developed in clinical practice. IMPORTANCE This study established and evaluated a complete metagenomics next-generation sequencing assay to improve the diagnosis of suspected ascitic infection in a clinical laboratory affiliated with a hospital. The assay is superior to traditional culture testing and will aid in the early and accurate identification of pathogens, particularly in patients with polymicrobial infections. This assay is also essential for precision therapy and can reduce the incidence of drug resistance stemming from irrational use of antibiotics.}, } @article {pmid36625585, year = {2023}, author = {Wicaksono, WA and Egamberdieva, D and Cernava, T and Berg, G}, title = {Viral Community Structure and Potential Functions in the Dried-Out Aral Sea Basin Change along a Desiccation Gradient.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0099422}, pmid = {36625585}, issn = {2379-5077}, mesh = {Humans ; Desiccation ; Bacteria/genetics ; *Viruses ; Metagenome ; *Microbiota/genetics ; }, abstract = {The dried-out Aral Sea basin represents an extreme environment due to a man-made ecological disaster. Studies conducted in this unique environment revealed high levels of pollution and a specifically adapted microbiota; however, viral populations remained entirely unexplored. By employing an in-depth analysis based on the sequencing of metagenomic DNA recovered from rhizosphere samples of Suaeda acuminata (C. A. Mey.) Moq. along a desiccation gradient of 5, 10, and 40 years, we detected a diverse viral community comprising 674 viral populations (viral operational taxonomic units [vOTUs]) dominated by Caudovirales. Targeted analyses highlighted that viral populations in this habitat are subjected to certain dynamics that are driven mainly by the gradient of desiccation, the corresponding salinity, and the rhizosphere bacterial populations. In silico predictions linked the viruses to dominant prokaryotic taxa in the Aral Sea basin, such as Gammaproteobacteria, Actinomycetia, and Bacilli. The lysogenic lifestyle was predicted to be predominant in areas that dried out 5 years ago, representing the early revegetation phase. Metabolic prediction of viral auxiliary metabolic genes (AMGs) suggests that viruses may play a role in the biogeochemical cycles, stress resilience, and competitiveness of their hosts due to the presence of genes that are involved in biofilm formation. Overall, our study provides important insights into viral ecology in an extreme environment and expands our knowledge related to virus occurrence in terrestrial systems. IMPORTANCE Environmental viruses have added a wealth of knowledge to ecological studies with the emergence of metagenomic technology and approaches. They are also becoming recognized as important genetic repositories that underpin the functioning of terrestrial ecosystems but have remain moslty unexplored. Using shotgun metagenome sequencing and bioinformatic tools, we found that the viral community structure was affected during natural revegetation in the dried-up Aral Sea area, a model habitat for investigating natural ecological restoration but still understudied. In this study, we highlight the importance of viruses, elements that are overlooked, for their potential contribution to terrestrial ecosystems, i.e., nutrient cycles, stress resilience, and host competitiveness, during natural revegetation.}, } @article {pmid36625575, year = {2023}, author = {Zhang, XL and Zhou, YR and Xu, SS and Xu, S and Xiong, YJ and Xu, K and Xu, CJ and Che, JJ and Huang, L and Liu, ZG and Wang, BY and Mu, YL and Xiao, SB and Li, K}, title = {Characterization of Gut Microbiota Compositions along the Intestinal Tract in CD163/pAPN Double Knockout Piglets and Their Potential Roles in Iron Absorption.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0190622}, pmid = {36625575}, issn = {2165-0497}, mesh = {Animals ; Swine ; *Gastrointestinal Microbiome/physiology ; RNA, Ribosomal, 16S/genetics ; Antigens, CD ; Colon/microbiology ; }, abstract = {The gut microbiota is known to play a role in regulating host metabolism, yet the mechanisms underlying this regulation are not well elucidated. Our study aimed to characterize the differences in gut microbiota compositions and their roles in iron absorption between wild-type (WT) and CD163/pAPN double-gene-knockout (DKO) weaned piglets. A total of 58 samples along the entire digestive tract were analyzed for microbial community using 16S rRNA gene sequencing. The colonic microbiota and their metabolites were determined by metagenomic sequencing and untargeted liquid chromatography-mass spectrometry (LC-MS), respectively. Our results showed that no alterations in microbial community structure and composition were observed between DKO and WT weaned piglets, with the exception of colonic microbiota. Interestingly, the DKO piglets had selectively increased the relative abundance of the Leeia genus belonging to the Neisseriaceae family and decreased the Ruminococcaceae_UCG_014 genus abundance. Functional capacity analysis showed that organic acid metabolism was enriched in the colon in DKO piglets. In addition, the DKO piglets showed increased iron levels in important tissues compared with WT piglets without any pathological changes. Pearson's correlation coefficient indicated that the specific bacteria such as Leeia and Ruminococcaceae_UCG_014 genus played a key role in host iron absorption. Moreover, the iron levels had significantly (P < 0.05) positive correlation with microbial metabolites, particularly carboxylic acids and their derivatives, which might increase iron absorption by preventing iron precipitation. Overall, this study reveals an interaction between colonic microbiota and host metabolism and has potential significance for alleviating piglet iron deficiency. IMPORTANCE Iron deficiency is a major risk factor for iron deficiency anemia, which is among the most common nutritional disorders in piglets. However, it remains unclear how the gut microbiota interacts with host iron absorption. The current report provides the first insight into iron absorption-microbiome connection in CD163/pAPN double knockout piglets. The present results showed that carboxylic acids and their derivatives contributed to the absorption of nonheme iron by preventing ferric iron precipitation.}, } @article {pmid36624530, year = {2023}, author = {Jacobs, JP and Lagishetty, V and Hauer, MC and Labus, JS and Dong, TS and Toma, R and Vuyisich, M and Naliboff, BD and Lackner, JM and Gupta, A and Tillisch, K and Mayer, EA}, title = {Multi-omics profiles of the intestinal microbiome in irritable bowel syndrome and its bowel habit subtypes.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {5}, pmid = {36624530}, issn = {2049-2618}, support = {U01 DK077738/DK/NIDDK NIH HHS/United States ; P30 DK041301/DK/NIDDK NIH HHS/United States ; R01 DK096606/DK/NIDDK NIH HHS/United States ; IK2 CX001717/CX/CSRD VA/United States ; R03 DK121025/DK/NIDDK NIH HHS/United States ; R01 DK048351/DK/NIDDK NIH HHS/United States ; K23 DK106528/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Irritable Bowel Syndrome ; Multiomics ; RNA, Ribosomal, 16S/genetics ; Feces ; Habits ; }, abstract = {BACKGROUND: Irritable bowel syndrome (IBS) is a common gastrointestinal disorder that is thought to involve alterations in the gut microbiome, but robust microbial signatures have been challenging to identify. As prior studies have primarily focused on composition, we hypothesized that multi-omics assessment of microbial function incorporating both metatranscriptomics and metabolomics would further delineate microbial profiles of IBS and its subtypes.

METHODS: Fecal samples were collected from a racially/ethnically diverse cohort of 495 subjects, including 318 IBS patients and 177 healthy controls, for analysis by 16S rRNA gene sequencing (n = 486), metatranscriptomics (n = 327), and untargeted metabolomics (n = 368). Differentially abundant microbes, predicted genes, transcripts, and metabolites in IBS were identified by multivariate models incorporating age, sex, race/ethnicity, BMI, diet, and HAD-Anxiety. Inter-omic functional relationships were assessed by transcript/gene ratios and microbial metabolic modeling. Differential features were used to construct random forests classifiers.

RESULTS: IBS was associated with global alterations in microbiome composition by 16S rRNA sequencing and metatranscriptomics, and in microbiome function by predicted metagenomics, metatranscriptomics, and metabolomics. After adjusting for age, sex, race/ethnicity, BMI, diet, and anxiety, IBS was associated with differential abundance of bacterial taxa such as Bacteroides dorei; metabolites including increased tyramine and decreased gentisate and hydrocinnamate; and transcripts related to fructooligosaccharide and polyol utilization. IBS further showed transcriptional upregulation of enzymes involved in fructose and glucan metabolism as well as the succinate pathway of carbohydrate fermentation. A multi-omics classifier for IBS had significantly higher accuracy (AUC 0.82) than classifiers using individual datasets. Diarrhea-predominant IBS (IBS-D) demonstrated shifts in the metatranscriptome and metabolome including increased bile acids, polyamines, succinate pathway intermediates (malate, fumarate), and transcripts involved in fructose, mannose, and polyol metabolism compared to constipation-predominant IBS (IBS-C). A classifier incorporating metabolites and gene-normalized transcripts differentiated IBS-D from IBS-C with high accuracy (AUC 0.86).

CONCLUSIONS: IBS is characterized by a multi-omics microbial signature indicating increased capacity to utilize fermentable carbohydrates-consistent with the clinical benefit of diets restricting this energy source-that also includes multiple previously unrecognized metabolites and metabolic pathways. These findings support the need for integrative assessment of microbial function to investigate the microbiome in IBS and identify novel microbiome-related therapeutic targets. Video Abstract.}, } @article {pmid36624507, year = {2023}, author = {Bay, V and Gillespie, A and Ganda, E and Evans, NJ and Carter, SD and Lenzi, L and Lucaci, A and Haldenby, S and Barden, M and Griffiths, BE and Sánchez-Molano, E and Bicalho, R and Banos, G and Darby, A and Oikonomou, G}, title = {The bovine foot skin microbiota is associated with host genotype and the development of infectious digital dermatitis lesions.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {4}, pmid = {36624507}, issn = {2049-2618}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Female ; Cattle ; Animals ; *Digital Dermatitis/microbiology ; RNA, Ribosomal, 16S/genetics ; Genome-Wide Association Study ; *Cattle Diseases/microbiology ; *Communicable Diseases ; *Microbiota/genetics ; Genotype ; }, abstract = {BACKGROUND: Bovine Digital Dermatitis (BDD) is a prevalent infectious disease, causing painful foot skin lesions and lameness in cattle. We describe herein the bovine foot skin microbiota and its associations with BDD using 16S rRNA gene amplicon and shotgun metagenomic sequencing on samples from 259 dairy cows from three UK dairy farms.

RESULTS: We show evidence of dysbiosis, and differences in taxonomy and functional profiles in the bovine foot skin microbiome of clinically healthy animals that subsequently develop BDD lesions, compared to those that do not. Our results suggest that taxonomical and functional differences together with alterations in ecological interactions between bacteria in the normal foot skin microbiome may predispose an animal to develop BDD lesions. Using genome-wide association and regional heritability mapping approaches, we provide first evidence for interactions between host genotype and certain members of the foot skin microbiota. We show the existence of significant genetic variation in the relative abundance of Treponema spp. and Peptoclostridium spp. and identify regions in the bovine genome that explain a significant proportion of this variation.

CONCLUSIONS: Collectively this work shows early changes in taxonomic and functional profiles of the bovine foot-skin microbiota in clinically healthy animals which are associated with subsequent development of BDD and could be relevant to prevention of disease. The description of host genetic control of members of the foot skin microbiota, combined with the association of the latter with BDD development offer new insights into a complex relationship that can be exploited in selective breeding programmes. Video Abstract.}, } @article {pmid36624472, year = {2023}, author = {Wang, H and Ainiwaer, A and Song, Y and Qin, L and Peng, A and Bao, H and Qin, H}, title = {Perturbed gut microbiome and fecal and serum metabolomes are associated with chronic kidney disease severity.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {3}, pmid = {36624472}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome ; Hydroquinones ; Creatinine ; Reactive Oxygen Species ; Metabolome ; Feces/microbiology ; Metabolomics ; *Renal Insufficiency, Chronic/metabolism/microbiology ; }, abstract = {BACKGROUND: Chronic kidney disease (CKD) is a severe public health problem associated with a disordered gut microbiome. However, the functional alterations of microbiota and their cross talk with metabolism pathways based on disease severity remain unclear.

RESULTS: We performed metagenomics and untargeted metabolomics in a cohort of 68 patients with CKD of differing severities and 20 healthy controls to characterize the complex interplay between the gut microbiome and fecal and serum metabolites during CKD progression. We identified 26 microbial species that significantly changed in patients with CKD; 18 species changed as the disease progressed, and eight species changed only in a specific CKD group. These distinct changes in gut microbiota were accompanied by functional alterations in arginine and proline, arachidonic acid, and glutathione metabolism and ubiquinone and other terpenoid-quinone biosynthesis pathways during CKD progression. Further metabolomic analyses revealed that the distributions of toxic and pro-oxidant metabolites from these four essential metabolic pathways varied in the feces and serum as CKD progressed. Furthermore, we observed a complex co-occurrence between CKD severity-related bacteria and the characterized metabolites from the four essential metabolic pathways. Notably, Ruminococcus bromii, fecal hydroquinone, and serum creatinine were identified as the main contributors to the integrated network, indicating their key roles in CKD progression. Moreover, a noninvasive model including R. bromii and fecal hydroquinone, L-cystine, and 12-keto-tetrahydro-LTB4 levels classified the CKD severity (area under the curve [AUC]: > 0.9) and had better performance than the serum creatinine level for mild CKD (AUC: 0.972 vs. 0.896).

CONCLUSIONS: Perturbed CKD severity-related gut microbiota may contribute to unbalanced toxic and pro-oxidant metabolism in the gut and host, accelerating CKD progression, which may be an early diagnostic and therapeutic target for CKD. Video Abstract.}, } @article {pmid36623385, year = {2023}, author = {Wang, Q and Chen, J and Qi, W and Wang, D and Lin, H and Wu, X and Wang, D and Bai, Y and Qu, J}, title = {Dam construction alters planktonic microbial predator‒prey communities in the urban reaches of the Yangtze River.}, journal = {Water research}, volume = {230}, number = {}, pages = {119575}, doi = {10.1016/j.watres.2023.119575}, pmid = {36623385}, issn = {1879-2448}, mesh = {*Plankton ; Ecosystem ; Rivers/microbiology ; Food Chain ; Bacteroidetes ; *Microbiota ; China ; }, abstract = {While dam construction supports social and economic development, changes in hydraulic conditions can also affect natural aquatic ecosystems, especially microbial ecosystems. The compositional and functional traits of multi-trophic microbiota can be altered by dam construction, which may result in changes in aquatic predator-prey interactions. To understand this process, we performed a large-scale sampling campaign in the urban reaches of the dam-impacted Yangtze River (1 995 km) and obtained 211 metagenomic datasets and water quality data. We first compared the compositional traits of planktonic microbial communities upstream, downstream, and in a dam reservoir. Results showed that Bacteroidetes (R-strategy) bacteria were more likely to survive upstream, whilst the reservoir and downstream regions were more conducive to the survival of K-strategy bacteria such as Actinobacteria. Eukaryotic predators tended to be enriched upstream, whilst phototrophs tended to be enriched in the reservoir and downstream regions. Based on bipartite networks, we inferred that the potential microbial predator-prey interactions gradually and significantly decreased from upstream to the downstream and dam regions, affecting 56% of keystone microbial species. Remarkably, functional analysis showed that the abundance of the photosynthetic gene psbO was higher in the reservoir and downstream regions, whilst the abundance of the KEGG carbohydrate metabolic pathway was higher upstream. These results indicate that dam construction in the Yangtze River induced planktonic microbial ecosystem transformation from detritus-based food webs to autotroph-based food webs.}, } @article {pmid36622853, year = {2023}, author = {Hiltemann, S and Rasche, H and Gladman, S and Hotz, HR and Larivière, D and Blankenberg, D and Jagtap, PD and Wollmann, T and Bretaudeau, A and Goué, N and Griffin, TJ and Royaux, C and Le Bras, Y and Mehta, S and Syme, A and Coppens, F and Droesbeke, B and Soranzo, N and Bacon, W and Psomopoulos, F and Gallardo-Alba, C and Davis, J and Föll, MC and Fahrner, M and Doyle, MA and Serrano-Solano, B and Fouilloux, AC and van Heusden, P and Maier, W and Clements, D and Heyl, F and , and Grüning, B and Batut, B}, title = {Galaxy Training: A powerful framework for teaching!.}, journal = {PLoS computational biology}, volume = {19}, number = {1}, pages = {e1010752}, pmid = {36622853}, issn = {1553-7358}, support = {U24 CA199347/CA/NCI NIH HHS/United States ; U24 CA231877/CA/NCI NIH HHS/United States ; U24 HG010263/HG/NHGRI NIH HHS/United States ; U24 HG006620/HG/NHGRI NIH HHS/United States ; R01 AI134384/AI/NIAID NIH HHS/United States ; MR/S035931/1/MRC_/Medical Research Council/United Kingdom ; BB/CCG1720/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *Software ; *Computational Biology/methods ; Data Analysis ; Research Personnel ; }, abstract = {There is an ongoing explosion of scientific datasets being generated, brought on by recent technological advances in many areas of the natural sciences. As a result, the life sciences have become increasingly computational in nature, and bioinformatics has taken on a central role in research studies. However, basic computational skills, data analysis, and stewardship are still rarely taught in life science educational programs, resulting in a skills gap in many of the researchers tasked with analysing these big datasets. In order to address this skills gap and empower researchers to perform their own data analyses, the Galaxy Training Network (GTN) has previously developed the Galaxy Training Platform (https://training.galaxyproject.org), an open access, community-driven framework for the collection of FAIR (Findable, Accessible, Interoperable, Reusable) training materials for data analysis utilizing the user-friendly Galaxy framework as its primary data analysis platform. Since its inception, this training platform has thrived, with the number of tutorials and contributors growing rapidly, and the range of topics extending beyond life sciences to include topics such as climatology, cheminformatics, and machine learning. While initially aimed at supporting researchers directly, the GTN framework has proven to be an invaluable resource for educators as well. We have focused our efforts in recent years on adding increased support for this growing community of instructors. New features have been added to facilitate the use of the materials in a classroom setting, simplifying the contribution flow for new materials, and have added a set of train-the-trainer lessons. Here, we present the latest developments in the GTN project, aimed at facilitating the use of the Galaxy Training materials by educators, and its usage in different learning environments.}, } @article {pmid36622696, year = {2023}, author = {M Salloum, P and D Lavery, S and de Villemereuil, P and W Santure, A}, title = {Local adaptation in shell shape traits of a brooding chiton with strong population genomic differentiation.}, journal = {Evolution; international journal of organic evolution}, volume = {77}, number = {1}, pages = {210-220}, doi = {10.1093/evolut/qpac011}, pmid = {36622696}, issn = {1558-5646}, support = {//Society of Systematic Biologists/ ; }, mesh = {Animals ; *Genetic Variation ; *Polyplacophora ; Metagenomics ; Genetic Drift ; Adaptation, Physiological ; Selection, Genetic ; Phenotype ; Genetics, Population ; }, abstract = {Comparing divergence in quantitative traits and neutral molecular markers, such as QST-FST comparisons, provides a means to distinguish between natural selection and genetic drift as causes of population differentiation in complex polygenic traits. Onithochiton neglectus (Rochebrune, 1881) is a morphologically variable chiton endemic to New Zealand, with populations distributed over a broad latitudinal environmental gradient. In this species, the morphological variants cluster into 2 geographically separated shell shape groups, and the phenotypic variation in shell shape has been hypothesized to be adaptive. Here, we assessed this hypothesis by comparing neutral genomic differentiation between populations (FST) with an index of phenotypic differentiation (PST). We used 7,562 putatively neutral single-nucleotide polymorphisms (SNPs) across 15 populations and 3 clades of O. neglectus throughout New Zealand to infer FST. PST was calculated from 18 shell shape traits and gave highly variable estimates across populations, clades, and shape groups. By systematically comparing PST with FST, we identified evidence of local adaptation in a number of the O. neglectus shell shape traits. This supports the hypothesis that shell shape could be an adaptive trait, potentially correlated with the ability to live and raft in kelp holdfasts.}, } @article {pmid36622170, year = {2023}, author = {Sun, X and Kan, C and Ma, W and Du, Z and Li, M}, title = {Genomic Analysis of the Suspicious SARS-CoV-2 Sequences in the Public Sequencing Database.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0342622}, pmid = {36622170}, issn = {2165-0497}, mesh = {Humans ; *SARS-CoV-2/genetics ; *COVID-19 ; Metagenomics ; Mutation ; Genome, Viral ; }, abstract = {SARS-CoV-2 has infected more than 600 million people. However, the origin of the virus is still unclear; knowing where the virus came from could help us prevent future zoonotic epidemics. Sequencing data, particularly metagenomic data, can profile the genomes of all species in the sample, including those not recognized at the time, thus allowing for the identification of the progenitor of SARS-CoV-2 in samples collected before the pandemic. We analyzed the data from 5,196 SARS-CoV-2-positive sequencing runs in the NCBI's SRA database with collection dates prior to 2020 or unknown. We found that the mutation patterns obtained from these suspicious SARS-CoV-2 reads did not match the genome characteristics of an unknown progenitor of the virus, suggesting that they may derive from circulating SARS-CoV-2 variants or other coronaviruses. Despite a negative result for tracking the progenitor of SARS-CoV-2, the methods developed in the study could assist in pinpointing the origin of various pathogens in the future. IMPORTANCE Sequences that are homologous to the SARS-CoV-2 genome were found in numerous sequencing runs that were not associated with the SARS-CoV-2 studies in the public database. It is unclear whether they are derived from the possible progenitor of SARS-CoV-2 or contamination of more recent SARS-CoV-2 variants circulated in the population due to the lack of information on the collection, library preparation, and sequencing processes. We have developed a computational framework to infer the evolutionary relationship between sequences based on the comparison of mutations, which enabled us to rule out the possibility that these suspicious sequences originate from unknown progenitors of SARS-CoV-2.}, } @article {pmid36622155, year = {2023}, author = {Saak, CC and Pierce, EC and Dinh, CB and Portik, D and Hall, R and Ashby, M and Dutton, RJ}, title = {Longitudinal, Multi-Platform Metagenomics Yields a High-Quality Genomic Catalog and Guides an In Vitro Model for Cheese Communities.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0070122}, pmid = {36622155}, issn = {2379-5077}, support = {DP2 AT010401/AT/NCCIH NIH HHS/United States ; }, mesh = {Humans ; *Cheese/microbiology ; Metagenomics ; Bacteria ; Metagenome/genetics ; *Microbiota/genetics ; }, abstract = {Microbiomes are intricately intertwined with human health, geochemical cycles, and food production. While many microbiomes of interest are highly complex and experimentally intractable, cheese rind microbiomes have proven to be powerful model systems for the study of microbial interactions. To provide a more comprehensive view of the genomic potential and temporal dynamics of cheese rind communities, we combined longitudinal, multi-platform metagenomics of three ripening washed-rind cheeses with whole-genome sequencing of community isolates. Sequencing-based approaches revealed a highly reproducible microbial succession in each cheese and the coexistence of closely related Psychrobacter species and enabled the prediction of plasmid and phage diversity and their host associations. In combination with culture-based approaches, we established a genomic catalog and a paired 16-member in vitro washed-rind cheese system. The combination of multi-platform metagenomic time-series data and an in vitro model provides a rich resource for further investigation of cheese rind microbiomes both computationally and experimentally. IMPORTANCE Metagenome sequencing can provide great insights into microbiome composition and function and help researchers develop testable hypotheses. Model microbiomes, such as those composed of cheese rind bacteria and fungi, allow the testing of these hypotheses in a controlled manner. Here, we first generated an extensive longitudinal metagenomic data set. This data set reveals successional dynamics, yields a phyla-spanning bacterial genomic catalog, associates mobile genetic elements with their hosts, and provides insights into functional enrichment of Psychrobacter in the cheese environment. Next, we show that members of the washed-rind cheese microbiome lend themselves to in vitro community reconstruction. This paired metagenomic data and in vitro system can thus be used as a platform for generating and testing hypotheses related to the dynamics within, and the functions associated with, cheese rind microbiomes.}, } @article {pmid36621696, year = {2023}, author = {Wen, C and Pan, Y and Gao, M and Wang, J and Huang, K and Tu, P}, title = {Altered gut microbiome composition in nontreated plaque psoriasis patients.}, journal = {Microbial pathogenesis}, volume = {175}, number = {}, pages = {105970}, doi = {10.1016/j.micpath.2023.105970}, pmid = {36621696}, issn = {1096-1208}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Psoriasis ; *Microbiota/genetics ; Bacteria/genetics ; Bacteroidetes ; Feces/microbiology ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Recent studies have demonstrated that dysbiosis of the gut microbiota is associated with psoriasis, but these studies showed some conflicting results. Our study examined differences in microbiome composition associated in people with psoriasis and those without. Comparing individuals with their healthy partners was a second strategy. We explored the fecal microbiota among 32 nontreated plaque psoriasis patients, 15 healthy controls and 17 healthy couples by metagenomic gene sequencing. The relative levels of intestinal microbiota of the psoriasis cohort differed from those in healthy controls and these patients' partners. However, there was no microbial diversity among these three cohorts. On the level of the phylum, Firmicutes and Bacteroidetes' relative abundances were reversed. Escherichia coli was significantly enriched in the psoriasis group compared with the healthy people and the healthy spouses. Gene functional analysis indicated that Ribosome (ko03010) was upregulated, Flagellar assembly (ko02040) and Bacterial chemotaxis (ko02030) were downregulated in the psoriasis cohort compared with the healthy individuals and the healthy spouses. The microbiota in severe psoriasis patients differed from those with milder conditions. These findings strongly support the association between intestinal flora and psoriasis. It is necessary to perform more meaningful experiments to identify whether the differences of gut microbiota are the cause or consequences of psoriasis in future.}, } @article {pmid36621219, year = {2023}, author = {Leff, LG and Fasina, K and Engohang-Ndong, J}, title = {Detecting antibiotic resistance genes in anthropogenically impacted streams and rivers.}, journal = {Current opinion in biotechnology}, volume = {79}, number = {}, pages = {102878}, doi = {10.1016/j.copbio.2022.102878}, pmid = {36621219}, issn = {1879-0429}, mesh = {Humans ; *Rivers/microbiology ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Ecosystem ; Drug Resistance, Microbial/genetics ; }, abstract = {Streams and rivers are widely impacted by human activities ranging from hydrological modifications to point and nonpoint pollution. Among the pollutants that enter lotic ecosystems are pharmaceuticals and personal care products, including antibiotics, that may play a role in the occurrence of antibiotic resistance genes (ARGs). Oftentimes, ARGs are detected based on culturing of bacteria or by using quantitative polymerase chain reaction; the limitations of these methods create barriers to our understanding. Use of more exhaustive methods, such as metagenomics, may overcome some of these barriers. The public health and ecological impacts of ARGs may be profound but are largely understudied. Antibiotic resistance is a growing concern for public health.}, } @article {pmid36621001, year = {2023}, author = {Ramos, JGVDS and Richter, CP and Silva, MA and Singolano, GL and Hauagge, G and Lorençon, E and Junior, ILC and Edwiges, T and de Arruda, PV and Vidal, CMS}, title = {Effects of ciprofloxacin on biogas production and microbial community composition in anaerobic digestion of swine wastewater in ASBR type reactor.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-13}, doi = {10.1080/09593330.2022.2164744}, pmid = {36621001}, issn = {1479-487X}, abstract = {In swine farming, antibiotics are often used to reduce disease and promote animal growth. Part of these compounds is not absorbed by the swine body, being excreted and later reaching the treatment systems, soil, and nearby waterbodies. This research sought to investigate the influence of adding ciprofloxacin (CIP) on the anaerobic digestion of swine wastewater. For that, a bench-scale anaerobic sequential batch reactor (ASBR) was used, with 5 L of working volume in six different phases, with volumetric organic loading rate (VOLR) and CIP dosage variation. According to the results, the optimal VOLR for the reactor was 0.60 ± 0.11 gSV L[-1] d[-1], resulting in biogas productivity of 0.51 ± 0.03 Lbiogas L[-1] d[-1]. After initial stability, adding substrate with 0.5 mgCIP L[-1] resulted in an abrupt drop of 82% in the productivity from the 7[th] to 11[th] day of addition, coinciding with volatile acids accumulation. Afterward, the reactor recovered and reached apparent stability, with productivity similar to the previous step without the drug. For 2.5 mgCIP L[-1] in the substrate, the biogas productivity at equilibrium was 11.8% lower than in the phases with the same VOLR and 0.0 and 0.5 mgCIP L[-1]. Organic matter removals near 80% were achieved for both dosages. The 16S rRNA metagenomic analyses showed an increase in the relative abundance of most of the phyla found, indicating that the dosages used allowed the acclimatization of microorganisms and possibly the compound biodegradation.}, } @article {pmid36620205, year = {2022}, author = {Zhang, L and Zhuang, T and Hu, M and Liu, S and Wu, D and Ji, B}, title = {Gut microbiota contributes to lignocellulose deconstruction and nitrogen fixation of the larva of Apriona swainsoni.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {1072893}, pmid = {36620205}, issn = {1664-042X}, abstract = {Apriona swainsoni is a vital forest pest prevalent in China. The larvae of A. swainsoni live solely in the branches of trees and rely entirely on the xylem for nutrition. However, there is still a lack of in-depth research on the gut microbiota's use of almost nitrogen-free wood components to provide bio-organic macromolecular components needed for their growth. Thus, in this study, the metagenome, metaproteome, and metabolome of the A. swainsoni larvae in four gut segments (foregut; midgut; anterior hindgut; posterior hindgut) were analyzed by the multi-omics combined technology, to explore the metabolic utilization mechanism of the corresponding gut microbiota of A. swainsoni. Firstly, we found that the metagenome of different gut segments was not significantly different in general, but there were different combinations of dominant bacteria and genes in different gut segments, and the metaproteome and metabolome of four gut segments were significantly different in general. Secondly, the multi-omics results showed that there were significant gradient differences in the contents of cellulose and hemicellulose in different segments of A. swainsoni, and the expression of corresponding metabolic proteins was the highest in the midgut, suggesting the metabolic characteristics of these lignocellulose components in A. swainsoni gut segments. Finally, we found that the C/N ratio of woody food was significantly lower than that of frass, and metagenomic results showed that nitrogen fixation genes mainly existed in the foregut and two hindgut segments. The expression of the key nitrogen fixing gene nifH occurred in two hindgut parts, indicating the feature of nitrogen fixation of A. swainsoni. In conclusion, our results provide direct evidence that the larvae of A. swainsoni can adapt to the relatively harsh niche conditions through the highly organized gut microbiome in four gut segments, and may play a major role in their growth.}, } @article {pmid36620197, year = {2022}, author = {Marcos, S and Parejo, M and Estonba, A and Alberdi, A}, title = {Recovering High-Quality Host Genomes from Gut Metagenomic Data through Genotype Imputation.}, journal = {Advanced genetics (Hoboken, N.J.)}, volume = {3}, number = {3}, pages = {2100065}, pmid = {36620197}, issn = {2641-6573}, abstract = {Metagenomic datasets of host-associated microbial communities often contain host DNA that is usually discarded because the amount of data is too low for accurate host genetic analyses. However, genotype imputation can be employed to reconstruct host genotypes if a reference panel is available. Here, the performance of a two-step strategy is tested to impute genotypes from four types of reference panels built using different strategies to low-depth host genome data (≈2× coverage) recovered from intestinal samples of two chicken genetic lines. First, imputation accuracy is evaluated in 12 samples for which both low- and high-depth sequencing data are available, obtaining high imputation accuracies for all tested panels (>0.90). Second, the impact of reference panel choice in population genetics statistics on 100 chickens is assessed, all four panels yielding comparable results. In light of the observations, the feasibility and application of the applied imputation strategy are discussed for different species with regard to the host DNA proportion, genomic diversity, and availability of a reference panel. This method enables leveraging insofar discarded host DNA to get insights into the genetic structure of host populations, and in doing so, facilitates the implementation of hologenomic approaches that jointly analyze host and microbial genomic data.}, } @article {pmid36620069, year = {2022}, author = {Robas Mora, M and Fernández Pastrana, VM and Probanza Lobo, A and Jiménez Gómez, PA}, title = {Valorization as a biofertilizer of an agricultural residue leachate: Metagenomic characterization and growth promotion test by PGPB in the forage plant Medicago sativa (alfalfa).}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1048154}, pmid = {36620069}, issn = {1664-302X}, abstract = {The abuse of chemical fertilizers in intensive agriculture has turned out in the contamination of ground and the soil on which they are applied. Likewise, the generation, storage, and destruction of plant residues from the agri-food industry poses a threat to the environment and human health. The current situation of growing demand for food implies the urgent need to find sustainable alternatives to chemical fertilizers and the management of agricultural waste. Valorization of this plant residue to produce natural biofertilizers using microbiological treatments is presented as a sustainable alternative. The microbial activity allows the transformation into simple molecules that are easily absorbed by plants, as well as the stimulation of plant growth. This double direct and indirect action induced significant increases against the variables of germination, viability, and biomass (dry weight). To guarantee biosafety, it is necessary to use new bio-technological tools, such as metagenomics, which allow the taxonomic analysis of microbial communities, detecting the absence of pathogens. In the present paper, a physicochemical and metagenomic characterization of a fertilizer obtained from agricultural plant waste valorization is carried out. Likewise, fertigation treatments were tested to which the Plant Growth Promoting Bacteria (PGPB) Pseudomonas agronomica and Bacillus pretiosus were added, both independently and in consortium. Metagenomic analysis has identified taxa belonging to the kingdoms Bacteria and Archaea; 10 phyla, 25 families, 32 genera and 34 species, none of them previously described as pathogenic. A 1/512 dilution of the fertilizer increased the germination rate of Medicago sativa (alfalfa) by 16% at 144 h, compared to the treatment without fertilizer. Both the fertilizer and the addition of PGPB in a double direct and indirect action induced significant increases against the variables of germination, viability, and biomass (dry weight). Therefore, the use of an agricultural residue is proposed, which after the addition of two new species is transformed into a biofertilizer that significantly induces plant growth in Mendicago sativa plants.}, } @article {pmid36620054, year = {2022}, author = {Rajar, P and Dhariwal, A and Salvadori, G and Junges, R and Åmdal, HA and Berild, D and Fugelseth, D and Saugstad, OD and Lausten-Thomsen, U and Greisen, G and Haaland, K and Petersen, FC}, title = {Microbial DNA extraction of high-host content and low biomass samples: Optimized protocol for nasopharynx metagenomic studies.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1038120}, pmid = {36620054}, issn = {1664-302X}, abstract = {INTRODUCTION: Low microbial biomass and high human DNA content in nasopharyngeal aspirate samples hinder comprehensive characterization of microbiota and resistome. We obtained samples from premature infants, a group with increased risk of developing respiratory disorders and infections, and consequently frequent exposure to antibiotics. Our aim was to devise an optimal protocol for handling nasopharyngeal aspirate samples from premature infants, focusing on host DNA depletion and microbiome and resistome characterization.

METHODS: Three depletion and three DNA extraction protocols were compared, using RT-PCR and whole metagenome sequencing to determine the efficiency of human DNA removal, taxonomic profiling and assignment of antibiotic resistance genes. Protocols were tested using mock communities, as well as pooled and individual patient samples.

RESULTS: The only extraction protocol to retrieve the expected DNA yield from mock community samples was based on a lytic method to improve Gram positive recovery (MasterPure™). Host DNA content in non-depleted aliquots from pooled patient samples was 99%. Only samples depleted with MolYsis™ showed satisfactory, but varied reduction in host DNA content, in both pooled and individual patient samples, allowing for microbiome and resistome characterisation (host DNA content from 15% to 98%). Other depletion protocols either retrieved too low total DNA yields, preventing further analysis, or failed to reduce host DNA content. By using Mol_MasterPure protocol on aliquots from pooled patient samples, we increased the number of bacterial reads by 7.6 to 1,725.8-fold compared to non-depleted reference samples. PCR results were indicative of achieved microbial enrichment. Individual patient samples processed with Mol_MasterPure protocol varied greatly in total DNA yield, host DNA content (from 40% to 98%), species and antibiotic resistance gene richness.

DISCUSSION: Despite high human DNA and low microbial biomass content in nasopharynx aspirates of preterm infants, we were able to reduce host DNA content to levels compatible with downstream shotgun metagenomic analysis, including bacterial species identification and coverage of antibiotic resistance genes. Whole metagenomic sequencing of microbes colonizing the nasopharynx may contribute to explaining the possible role of airway microbiota in respiratory conditions and reveal carriage of antibiotic resistance genes.}, } @article {pmid36620038, year = {2022}, author = {Li, QQ and Zhu, ZR and Liu, QG and An, YT and Wang, YX and Zhang, SB and Li, G}, title = {Characterization of a novel thermostable alkaline lipase derived from a compost metagenomic library and its potential application in the detergent industry.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1088581}, pmid = {36620038}, issn = {1664-302X}, abstract = {Using composted soil samples, a metagenomic library consisting of 36,000 clones was constructed. Then, a novel lipase, Lip54q, which belongs to the VIII family of lipolytic enzymes, was identified from the metagenomic library by functional screening. To explore the enzymatic properties of Lip54q, lip54q was heterologous expressed in Escherichia coli with a high expression level of recombinant protein up to 720 mg/L. The recombinant enzyme showed the highest activity (28,160 U/mg) against a C10 substrate at pH 9.0 and 47°C, and was stable at temperatures ≤50°C and pH 8.0-11.0. Of particular interest, the surfactants, Tween-20, Tween-80 and Tritonx-100, exhibited strong promoting effects on Lip54q activities regardless of whether low concentrations (0.1%) or high concentrations (10%) were used. Application studies of Lip54q using six commercial detergents indicated that the enzyme had strong tolerance and immersion resistance to all six detergents. The results of oil-stain removal experiments suggested that addition of the enzyme to various commercial detergents could significantly improve the abilities of these detergents to remove oil-stains. Furthermore, the results of a molecular docking analysis of Lip54q showed that both the C10 substrate and linoleic acid molecules could form hydrogen bond interactions with the catalytic amino acids, Ser-268, Glu-168, and Asp-192, in the catalytic center of the enzyme, and the hydrogen bond distances were shorter. The electrostatic attraction between the enzyme and the substrate formed by the hydrogen bond with a shorter distance is stronger, which is conducive to the formation of a more stable complex between the enzyme and the substrate, thus increasing the activity of the enzyme to such substrate. These results 1ay a good foundation for application of this enzyme in the detergent industry in the future.}, } @article {pmid36619745, year = {2022}, author = {Zhang, X and Liu, Y and Zhang, M and Wang, Z and Feng, X and Yang, L and Wang, Y and Liu, J and Zhao, D}, title = {Case report: Diagnosis of visceral leishmaniasis using metagenomic next-generation sequencing and bone marrow smear.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1095072}, pmid = {36619745}, issn = {2235-2988}, mesh = {Humans ; *Leishmaniasis, Visceral/diagnosis/drug therapy ; Bone Marrow ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Hospitals ; }, abstract = {Visceral leishmaniasis (VL) is a chronic infectious disease transmitted by sandflies. The primary clinical manifestations are remittent fever, pancytopenia, and splenomegaly. As VL is rare with atypical symptoms, its diagnosis is often incorrect, missed, or delayed. Without appropriate treatment, the case fatality rate of symptomatic disease is more than 95%, but the prognosis is good if diagnosed and treated timeously. We report a case of VL that was diagnosed using metagenomic next-generation sequencing (mNGS) of a peripheral blood sample. By using mNGS and a bone marrow smear, we were able to make a timely diagnosis. The patient was treated with antimony, rapidly recovered, and was discharged from the hospital. This case illustrates the value of mNGS for making a timely diagnosis of VL.}, } @article {pmid36619744, year = {2022}, author = {Wells, RK and Kunihiro, BP and Phankitnirundorn, K and Peres, R and McCracken, TA and Umeda, L and Lee, RH and Kim, DY and Juarez, R and Maunakea, AK}, title = {Gut microbial indicators of metabolic health underlie age-related differences in obesity and diabetes risk among Native Hawaiians and Pacific Islanders.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1035641}, pmid = {36619744}, issn = {2235-2988}, support = {R01 MD016593/MD/NIMHD NIH HHS/United States ; U54 MD007601/MD/NIMHD NIH HHS/United States ; P30 GM131944/GM/NIGMS NIH HHS/United States ; P20 GM103466/GM/NIGMS NIH HHS/United States ; R56 MD014630/MD/NIMHD NIH HHS/United States ; }, mesh = {Humans ; *Diabetes Mellitus, Type 2/epidemiology/microbiology ; *Gastrointestinal Microbiome ; Glycated Hemoglobin ; Hawaii/epidemiology ; Native Hawaiian or Other Pacific Islander ; *Obesity/epidemiology/microbiology ; }, abstract = {Native Hawaiians and Pacific Islanders (NHPIs) suffer from higher prevalence of and mortality to type 2 diabetes mellitus (T2DM) than any other major race/ethnic group in Hawaii. Health inequities in this indigenous population was further exacerbated by the SARS-CoV-2 pandemic. T2DM progression and medical complications exacerbated by COVID-19 are partially regulated by the gut microbiome. However, there is limited understanding of the role of gut bacteria in the context of inflammation-related diseases of health disparities including T2DM and obesity. To address these gaps, we used a community-based research approach from a cohort enriched with NHPI residents on the island of Oahu, Hawaii (N=138). Gut microbiome profiling was achieved via 16s rDNA metagenomic sequencing analysis from stool DNA. Gut bacterial capacity for butyrate-kinase (BUK)-mediated fiber metabolism was assessed using quantitative PCR to measure the abundance of BUK DNA and RNA relative to total bacterial load per stool sample. In our cohort, age positively correlated with hemoglobin A1c (%; R=0.39; P<0.001) and body mass index (BMI; R=0.28; P<0.001). The relative abundance of major gut bacterial phyla significantly varied across age groups, including Bacteroidetes (P<0.001), Actinobacteria (P=0.007), and Proteobacteria (P=0.008). A1c was negatively correlated with the relative levels of BUK DNA copy number (R=-0.17; P=0.071) and gene expression (R=-0.33; P=0.003). Interestingly, we identified specific genera of gut bacteria potentially mediating the effects of diet on metabolic health in this cohort. Additionally, α-diversity among gut bacterial genera significantly varied across T2DM and BMI categories. Together, these results provide insight into age-related differences in gut bacteria that may influence T2DM and obesity in NHPIs. Furthermore, we observed overlapping patterns between gut bacteria and T2DM risk factors, indicating more nuanced, interdependent interactions among these factors as partial determinants of health outcomes. This study adds to the paucity of NHPI-specific data to further elucidate the biological characteristics associated with pre-existing health inequities in this racial/ethnic group that is significantly underrepresented in biomedical research.}, } @article {pmid36619742, year = {2022}, author = {Chen, L and Wang, S and Zhang, Y and Li, Y and Zhang, X and Ma, J and Zou, X and Yao, T and Li, S and Chen, J and Zhou, H and Wu, L and Zhou, Y and Zhang, L}, title = {Multi-omics reveals specific host metabolism-microbiome associations in intracerebral hemorrhage.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {999627}, pmid = {36619742}, issn = {2235-2988}, mesh = {Humans ; Multiomics ; *Microbiota ; Metabolomics ; Metabolome ; Cerebral Hemorrhage ; *Stroke ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Intracerebral hemorrhage (ICH) is the most devastating subtype of stroke, but effective prevention and treatment strategies are lacking. Recently, gut microbiome and its metabolitesis are considered to be an influencing factor of stroke. However, little is known about the effects of the gut microbiome on ICH and host metabolic activity. Therefore, we used 16S sequencing, macrogenomics sequencing and untargeted metabolomics to explore the differences in gut microbial-metabolome interactions between patients with intracerebral hemorrhage and healthy control populations. We found a significant decrease in the phylum of Firmicutes and a significant increase of Bacteroidetes in ICH patients. At the genus level, Streptococcus, Bifidobacterium, Akkermansia, and Lactobacillus were more abundant in ICH patients. Macrogenomic analysis revealed active glycosaminoglycan degradation, heme synthesis, galactose degradation, lipopolysaccharide core region synthesis, and beta-Lactam resistance in ICH patients. Serum untargeted metabolomic analysis combined with ROC curves showed that octanoylcarnitine, decanoylcarnitine, dodecanoylcarnitine, glyceric acid, pyruvic acid, aspartic acid, methylcysteine, pyroglutamic acid, 9E-tetradecenoic acid, N-Acetylneuraminic acid, and aconitic acid were the best markers for the diagnosis of ICH. Correlation analysis showed that microbiome enriched in the gut of ICH patients were significantly correlated with serum metabolites, revealing a close correlation between the gut microbiome of ICH patients and the host metabolome, and significant differences from the healthy population. microbiota-host co-metabolites including pyruvic acid and 9E-tetradecenoic acid is associated with the the National Institutes of Health Stroke Scale (NIHSS) scores. In conclusion, microbiome-related metabolites in ICH patients was associated with the severity of ICH, the microbiota-host co-metabolites may be a potential may be potential therapeutic targets.}, } @article {pmid36619462, year = {2022}, author = {Liang, Y and Xiong, X and Zhang, C and Wang, W and Zhang, G}, title = {Scedosporium apiospermum invasive rhinosinusitis in an elderly patient: diagnosis and treatment.}, journal = {Heliyon}, volume = {8}, number = {12}, pages = {e12476}, pmid = {36619462}, issn = {2405-8440}, abstract = {Scedosporium apiospermum is a ubiquitous organism present in the environment and is rarely identified in rhinosinusitis. We report a case of invasive rhinosinusitis with Scedosporium apiospermum which made a definite diagnosis by metagenomic next-generation sequencing (mNGS) from a biopsy sample. The resection of the Scedosporium apiospermum pathological mass was performed with low-temperature plasma radiofrequency ablation. Six months of continuous oral voriconazole treatment was followed. The patient was asymptomatic with no signs of recurrence during the next 1-year follow-up.}, } @article {pmid36618709, year = {2022}, author = {Lu, XR and Liu, XW and Li, SH and Qin, Z and Bai, LX and Ge, WB and Li, JY and Yang, YJ}, title = {Untargeted lipidomics and metagenomics reveal the mechanism of aspirin eugenol ester relieving hyperlipidemia in ApoE-/- mice.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {1030528}, pmid = {36618709}, issn = {2296-861X}, abstract = {Hyperlipidemia is induced by abnormal lipid metabolism, which can cause the occurrence of cardiovascular diseases and lead to grievous injury to health. Studies showed that AEE had a significant therapeutic effect on hyperlipidemia and is likely to be associated with the up-regulation of cholesterol 7-alpha hydroxylase (CYP7A1), the key enzyme for cholesterol conversion to bile acids, but no research confirmed whether the effect of AEE on hyperlipidemia was related to the gut microbiota and liver lipids. At the same time, more and more studies have shown that gut microbiota and lipids are closely related to hyperlipidemia. Hence, in this study, we investigated the effects of AEE on liver lipids through LC-MS-based untargeted lipidomics and the effects of AEE on gut microbiota based on cecal contents metagenomics by Illumina sequencing in HFD-induced hyperlipidemia ApoE-/- mice at the overall level. The results of lipidomics showed that AEE relieved hyperlipidemia by decreasing the concentration of 10 PEs and 12 SMs in the liver and regulating the pathways of glycerophospholipid metabolic pathway, sphingolipid signaling pathway, and NF-kB signaling pathway. The results of metagenomics concluded that AEE treatment changed the composition of gut microbiota and regulated the functions of lipid transport and metabolism, as well as the metabolism of bile acids and secondary bile acids. The results of the joint analysis between lipidomics and metagenomics showed that the abundance of Verrucomicrobia, Verrucomicrobiales, Candidatus_Gastranaerophilales, and Candidatus_Melainabacteria was significantly positively correlated with the concentration of SM (d18:1/18:0) and PE (16:0/18:1) in the process of AEE alleviating hyperlipidemia in mice. In conclusion, these results suggested that the effect of AEE on hyperlipidemia was closely related to the gut microbiota by the change of bile acids and liver lipids.}, } @article {pmid36618438, year = {2022}, author = {Ramos, RJ and Zhu, C and Joseph, DF and Thaker, S and Lacomb, JF and Markarian, K and Lee, HJ and Petrov, JC and Monzur, F and Buscaglia, JM and Chawla, A and Small-Harary, L and Gathungu, G and Morganstern, JA and Yang, J and Li, J and Pamer, EG and Robertson, CE and Frank, DN and Cross, JR and Li, E}, title = {Metagenomic and bile acid metabolomic analysis of fecal microbiota transplantation for recurrent Clostridiodes difficile and/or inflammatory bowel diseases.}, journal = {Medical research archives}, volume = {10}, number = {10}, pages = {}, pmid = {36618438}, issn = {2375-1916}, support = {R25 AI140472/AI/NIAID NIH HHS/United States ; }, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) is an effective treatment of recurrent Clostridioides difficile infections (rCDI), but has more limited efficacy in treating either ulcerative colitis (UC) or Crohn's disease (CD), two major forms of inflammatory bowel diseases (IBD). We hypothesize that FMT recipients with rCDI and/or IBD have baseline fecal bile acid (BA) compositions that differ significantly from that of their healthy donors and that FMT will normalize the BA compositions.

AIM: To study the effect of single colonoscopic FMT on microbial composition and function in four recipient groups: 1.) rCDI patients without IBD (rCDI-IBD); 2.) rCDI with IBD (rCDI+IBD); 3.) UC patients without rCDI (UC-rCDI); 4.) CD patients without rCDI (CD-rCDI).

METHODS: We performed 16S rRNA gene sequence, shotgun DNA sequence and quantitative bile acid metabolomic analyses on stools collected from 55 pairs of subjects and donors enrolled in two prospective single arm FMT clinical trials (Clinical Trials.gov ID NCT03268213, 479696, UC no rCDI ≥ 2x IND 1564 and NCT03267238, IND 16795). Fitted linear mixed models were used to examine the effects of four recipient groups, FMT status (Donor, pre-FMT, 1-week post-FMT, 3-months post-FMT) and first order Group*FMT interactions on microbial diversity and composition, bile acid metabolites and bile acid metabolizing enzyme gene abundance.

RESULTS: The pre-FMT stools collected from rCDI ± IBD recipients had reduced α-diversity compared to the healthy donor stools and was restored post-FMT. The α-diversity in the pre-FMT stools collected from UC-rCDI or CD-rCDI recipients did not differ significantly from donor stools. FMT normalized some recipient/donor ratios of genus level taxa abundance in the four groups. Fecal secondary BA levels, including some of the secondary BA epimers that exhibit in vitro immunomodulatory activities, were lower in rCDI±IBD and CD-rCDI but not UC-rCDI recipients compared to donors. FMT restored secondary BA levels. Metagenomic baiE gene and some of the eight bile salt hydrolase (BSH) phylotype abundances were significantly correlated with fecal BA levels.

CONCLUSION: Restoration of multiple secondary BA levels, including BA epimers implicated in immunoregulation, are associated with restoration of fecal baiE gene counts, suggesting that the 7-α-dehydroxylation step is rate-limiting.}, } @article {pmid36617769, year = {2023}, author = {Borroni, D and Bonzano, C and Sánchez-González, JM and Rachwani-Anil, R and Zamorano-Martín, F and Pereza-Nieves, J and Traverso, CE and García Lorente, M and Rodríguez-Calvo-de-Mora, M and Esposito, A and Godin, F and Rocha-de-Lossada, C}, title = {Shotgun metagenomic sequencing in culture negative microbial keratitis.}, journal = {European journal of ophthalmology}, volume = {33}, number = {4}, pages = {1589-1595}, doi = {10.1177/11206721221149077}, pmid = {36617769}, issn = {1724-6016}, mesh = {Humans ; Metagenomics/methods ; *Eye Infections ; *Keratitis/diagnosis ; DNA ; Software ; }, abstract = {PURPOSE: To evaluate the microbiota of culture negative Corneal Impression Membrane (CIM) microbial keratitis samples with the use of shotgun metagenomics analysis.

METHODS: DNA of microbial keratitis samples were collected with CIM and extracted using the MasterPure™ Complete DNA and RNA Purification Kit (Epicentre). DNA was fragmented by sonication into fragments of 300 to 400 base pairs (bp) using Bioruptor® (Diagenode, Belgium) and then used as a template for library preparation. DNA libraries were sequenced on Illumina® HiSeq2500. The resulting reads were quality controlled, trimmed and mapped against the human reference genome. The unmapped reads were taxonomically classified using the Kraken software.

RESULTS: 18 microbial keratitis samples were included in the study. Brevundimonas diminuta was found in 5 samples while 6 samples showed the presence of viral infections. Cutibacterium acnes, Staphylococcus aureus, Moraxella lacunata and Pseudomonas alcaligenes were also identified as the presumed putative cause of the infection in 7 samples.

CONCLUSIONS: Shotgun sequencing can be used as a diagnostic tool in microbial keratitis samples. This diagnostic method expands the available tests to diagnose eye infections and could be clinically significant in culture negative samples.}, } @article {pmid36617651, year = {2022}, author = {Chitcharoen, S and Phokaew, C and Mauleekoonphairoj, J and Khongphatthanayothin, A and Sutjaporn, B and Wandee, P and Poovorawan, Y and Nademanee, K and Payungporn, S}, title = {Metagenomic analysis of viral genes integrated in whole genome sequencing data of Thai patients with Brugada syndrome.}, journal = {Genomics & informatics}, volume = {20}, number = {4}, pages = {e44}, pmid = {36617651}, issn = {1598-866X}, abstract = {Brugada syndrome (BS) is an autosomal dominant inheritance cardiac arrhythmia disorder associated with sudden death in young adults. Thailand has the highest prevalence of BS worldwide, and over 60% of patients with BS still have unclear disease etiology. Here, we performeda new viral metagenome analysis pipeline called VIRIN and validated it with whole genome sequencing (WGS) data of HeLa cell lines and hepatocellular carcinoma. Then the VIRIN pipelinewas applied to identify viral integration positions from unmapped WGS data of Thai males, including 100 BS patients (case) and 100 controls. Even though the sample preparation had noviral enrichment step, we can identify several virus genes from our analysis pipeline. The predominance of human endogenous retrovirus K (HERV-K) viruses was found in both cases andcontrols by blastn and blastx analysis. This study is the first report on the full-length HERV-Kassembled genomes in the Thai population. Furthermore, the HERV-K integration breakpointpositions were validated and compared between the case and control datasets. Interestingly,Brugada cases contained HERV-K integration breakpoints at promoters five times more oftenthan controls. Overall, the highlight of this study is the BS-specific HERV-K breakpoint positionsthat were found at the gene coding region "NBPF11" (n = 9), "NBPF12" (n = 8) and longnon-coding RNA (lncRNA) "PCAT14" (n = 4) region. The genes and the lncRNA have been reported to be associated with congenital heart and arterial diseases. These findings provide another aspect of the BS etiology associated with viral genome integrations within the humangenome.}, } @article {pmid36617604, year = {2023}, author = {Kocak, FO and Tanir, SGE and Cetin, AK and Degirmenci, L}, title = {Simulatenous evaluation of composting experiments and metagenome analyses to illuminate the effect of Streptomyces spp. on organic matter degradation.}, journal = {World journal of microbiology & biotechnology}, volume = {39}, number = {3}, pages = {70}, pmid = {36617604}, issn = {1573-0972}, support = {TUBITAK 118O231//the Scientific and Technological Research Council of Turkey (TUBITAK)/ ; TUBITAK 118O231//the Scientific and Technological Research Council of Turkey (TUBITAK)/ ; }, mesh = {*Composting ; Metagenome ; Soil ; *Streptomyces/genetics ; RNA, Ribosomal, 16S/genetics ; Xylans ; Cellulose ; Manure ; }, abstract = {The effect of Streptomyces spp. on organic matter degradation was investigated in the present study. Streptomyces spp. isolated from compost systems were eliminated based on the results of cellulose, starch, xylan degradation tests, morphological inspection, and 16S rRNA analysis. The eliminated strains were re-given to compost systems to determine their effect on organic matter degradation and maturation. Sample analyses indicated that 15 days of composting had been adequate to maintain maturation. The amounts of strains added to the system were high enough to create a detectable change such as inhibition of other microbiota members. Results also indicated a variant change in organic matter degradation due to the added strain. The difference in organic matter degradation between strains depended partially on the segregation of secondary metabolites. On the other hand, strains also inhibited each other in the case of their binary and triple utilization in compost. Another explanation for variant activity was provided based on the enzymatic activity of the strains validated by metagenomic counts evaluation. Metagenome count numbers revealed the tendency of compost microbiota toward degradation products of cellulose. Findings obtained from composting experiments and metagenome analyses indicated the presence of a different degradation route based on xylan activity. Results also implied a decrease in competition between the dominant strain and microbiota members in the case of sequential xylan and cellulose degradation. Meticulous evaluation of results obtained from metagenome analysis also provided some insights on certain conditions regarding the progress of composting along with storage conditions of manure before use.}, } @article {pmid36617187, year = {2023}, author = {Yang, L and Chen, J}, title = {Benchmarking differential abundance analysis methods for correlated microbiome sequencing data.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {1}, pages = {}, pmid = {36617187}, issn = {1477-4054}, support = {R01 GM144351/GM/NIGMS NIH HHS/United States ; R21 HG011662/HG/NHGRI NIH HHS/United States ; R01 GM144351/NH/NIH HHS/United States ; }, mesh = {*Benchmarking ; *Microbiota/genetics ; Linear Models ; Databases, Factual ; Metagenomics/methods ; }, abstract = {Differential abundance analysis (DAA) is one central statistical task in microbiome data analysis. A robust and powerful DAA tool can help identify highly confident microbial candidates for further biological validation. Current microbiome studies frequently generate correlated samples from different microbiome sampling schemes such as spatial and temporal sampling. In the past decade, a number of DAA tools for correlated microbiome data (DAA-c) have been proposed. Disturbingly, different DAA-c tools could sometimes produce quite discordant results. To recommend the best practice to the field, we performed the first comprehensive evaluation of existing DAA-c tools using real data-based simulations. Overall, the linear model-based methods LinDA, MaAsLin2 and LDM are more robust than methods based on generalized linear models. The LinDA method is the only method that maintains reasonable performance in the presence of strong compositional effects.}, } @article {pmid36615876, year = {2023}, author = {Ma, X and Liu, S and Wang, H and Wang, Y and Li, Z and Gu, T and Li, Y and Xin, F and Wen, B}, title = {In Vitro Fermentation of Beechwood Lignin-Carbohydrate Complexes Provides Evidence for Utilization by Gut Bacteria.}, journal = {Nutrients}, volume = {15}, number = {1}, pages = {}, pmid = {36615876}, issn = {2072-6643}, support = {CAAS-ASTIP-G2022-IFST-03//Institute of Food Science and Technology/ ; }, mesh = {*Lignin/chemistry/metabolism ; Fermentation ; *Carbohydrates/chemistry ; Bacteria/metabolism ; Fatty Acids, Volatile/metabolism ; Proteobacteria/metabolism ; }, abstract = {Lignin-carbohydrate complexes (LCCs) are emerging as a new and natural product with pharmacological and nutraceutical potential. It is uncertain, however, whether LCCs have a positive effect on the microbiota of the gut based on the current evidence. Here, the LCC extracted from beechwood (BW-LCC) was used as a substrate for in vitro fermentation. The lignin in BW-LCC consisted of guaiacyl (G) and syringyl (S) units, which are mainly linked by β-O-4 bonds. After 24 h of in vitro fermentation, the pH had evidently declined. The concentrations of acetic acid and propionic acid, the two main short-chain fatty acids (SCFAs), were significantly higher than in the control group (CK). In addition, BW-LCC altered the microbial diversity and composition of gut microbes, including a reduction in the relative abundance of Firmicutes and an increase in the relative abundance of Proteobacteria and Bacteroidetes. The relative abundance of Escherichia coli-Shigella and Bacteroides were the most variable at the genus level. The genes of carbohydrate-active enzymes (CAZymes) also changed significantly with the fermentation and were related to the changes in microbes. Notably, the auxiliary actives (AAs), especially AA1, AA2, and AA3_2, play important roles in lignin degradation and were significantly enriched and concentrated in Proteobacteria. From this study, we are able to provide new perspectives on how gut microbes utilize LCC.}, } @article {pmid36614337, year = {2023}, author = {Ahmad, MF and Abdullah, H and Hassan, MN and Jamaludin, MI and Sivam, A and Komatsu, K and Sapian, IS and Alias, H and Mat Isa, MN and Kuwahara, VS and Yaacob, NS}, title = {Topographically Distinguished Microbiome Taxonomy and Stress-Response Genes of Royal Belum Rainforest and Raja Muda Musa Peat Swamp Revealed through Metagenomic Inquisition.}, journal = {International journal of molecular sciences}, volume = {24}, number = {1}, pages = {}, pmid = {36614337}, issn = {1422-0067}, support = {JPMJSA1509//Ministry of Higher Education/ ; }, mesh = {Animals ; Metagenome ; Wetlands ; Rainforest ; *Musa/genetics ; *Skates, Fish/genetics ; Soil/chemistry ; *Microbiota/genetics ; Bacteria/metabolism ; Archaea/genetics ; Forests ; Eukaryota/genetics ; Soil Microbiology ; }, abstract = {Soil ecosystems are home to a diverse range of microorganisms, but they are only partially understood because no single-cell sequencing or whole-community sequencing provides a complete picture of these complex communities. Using one of such metagenomics approaches, we succeeded in monitoring the microbial diversity and stress-response gene in the soil samples. This study aims to test whether known differences in taxonomic diversity and composition are reflected in functional gene profiles by implementing whole gene sequencing (WGS) metagenomic analysis of geographically dispersed soils from two distinct pristine forests. The study was commenced by sequencing three rainforest soil samples and three peat swamp soil samples. Soil richness effects were assessed by exploring the changes in specific functional gene abundances to elucidate physiological constraints acting on different soil systems and identify variance in functional pathways relevant to soil biogeochemical cycling. Proteobacteria shows abundances of microbial diversity for 52.15% in Royal Belum Reserved Forest and 48.28% in Raja Musa; 177 out of 1,391,841 and 449 out of 3,586,577 protein coding represent acidic stress-response genes for Royal Belum and Raja Musa, respectively. Raja Musa indicates pH 2.5, which is extremely acidic. The analysis of the taxonomic community showed that Royal Belum soils are dominated by bacteria (98% in Sungai Kooi (SK), 98% in Sungai Papan (SP), and 98% in Sungai Ruok (SR), Archaea (0.9% in SK, 0.9% in SP, and 1% in SR), and the remaining were classed under Eukaryota and viruses. Likewise, the soils of Raja Muda Musa are also dominated by bacteria (95% in Raja Musa 1 (RM1), 98% in Raja Musa 2 (RM2), and 96% in Raja Musa 3 (RM3)), followed by Archaea (4% in RM1, 1% in RM2, and 3% in RM3), and the remaining were classed under Eukaryota and viruses. This study revealed that RBFR (Royal Belum Foresr Reserve) and RMFR (Raja Musa Forest Reserve) metagenomes contained abundant stress-related genes assigned to various stress-response pathways, many of which did not show any difference among samples from both sites. Our findings indicate that the structure and functional potential of the microbial community will be altered by future environmental potential as the first glimpse of both the taxonomic and functional composition of soil microbial communities.}, } @article {pmid36614064, year = {2022}, author = {Nuñez-Belmar, J and Morales-Olavarria, M and Vicencio, E and Vernal, R and Cárdenas, JP and Cortez, C}, title = {Contribution of -Omics Technologies in the Study of Porphyromonas gingivalis during Periodontitis Pathogenesis: A Minireview.}, journal = {International journal of molecular sciences}, volume = {24}, number = {1}, pages = {}, pmid = {36614064}, issn = {1422-0067}, support = {11190073//FONDECYT/ ; 11200209//FONDECYT/ ; 1220999//FONDECYT/ ; }, mesh = {Humans ; Porphyromonas gingivalis/genetics ; *Bacteroidaceae Infections/microbiology ; *Periodontitis/pathology ; Virulence ; Metabolomics ; }, abstract = {Periodontitis is a non-communicable chronic inflammatory disease characterized by the progressive and irreversible breakdown of the soft periodontal tissues and resorption of teeth-supporting alveolar bone. The etiology of periodontitis involves dysbiotic shifts in the diversity of microbial communities inhabiting the subgingival crevice, which is dominated by anaerobic Gram-negative bacteria, including Porphyromonas gingivalis. Indeed, P. gingivalis is a keystone pathogen with a repertoire of attributes that allow it to colonize periodontal tissues and influence the metabolism, growth rate, and virulence of other periodontal bacteria. The pathogenic potential of P. gingivalis has been traditionally analyzed using classical biochemical and molecular approaches. However, the arrival of new techniques, such as whole-genome sequencing, metagenomics, metatranscriptomics, proteomics, and metabolomics, allowed the generation of high-throughput data, offering a suitable option for bacterial analysis, allowing a deeper understanding of the pathogenic properties of P. gingivalis and its interaction with the host. In the present review, we revise the use of the different -omics technologies and techniques used to analyze bacteria and discuss their potential in studying the pathogenic potential of P. gingivalis.}, } @article {pmid36613573, year = {2022}, author = {Canuti, M and Rodrigues, B and Lang, AS and Dufour, SC and Verhoeven, JTP}, title = {Novel Divergent Members of the Kitrinoviricota Discovered through Metagenomics in the Intestinal Contents of Red-Backed Voles (Clethrionomys gapperi).}, journal = {International journal of molecular sciences}, volume = {24}, number = {1}, pages = {}, pmid = {36613573}, issn = {1422-0067}, support = {N/A//Ocean Frontier Institute/ ; N/A//Joint Mink Research Committee/ ; }, mesh = {Humans ; Animals ; Gastrointestinal Contents ; Phylogeny ; Arvicolinae/genetics ; Genome, Viral ; *RNA Viruses/genetics ; *Viruses/genetics ; Metagenomics ; }, abstract = {Metagenomic methods are powerful tools to investigate viral diversity in biological or environmental samples and to identify previously unknown viruses. We used RNA metagenomics to identify, in the gut of red-backed voles, the nearly complete genomes of two novel members of the Kitrinoviricota, a phylum including viruses with positive-sense ssRNA genomes encoding an RNA-directed RNA polymerase. The genome of a novel member of the Tombusviridae presented four open reading frames (ORFs); a -1 frameshift is potentially involved in generating the viral replicase. This sequence was part of a phylogenetic clade that did not include any officially classified species. The second genome presented a large ORF coding for a viral polyprotein containing the typical protein domains common to flexiviruses. The sequence clustered with currently known members of the Deltaflexiviridae. Both viruses appear to represent the first members of novel species in yet undefined genera. The identified viruses likely originated from the vole diet as members of the two viral families are known to infect plants and fungi, respectively. Investigating public databases demonstrated that a much higher richness than currently recognized exists for these two viral families, highlighting the need to update taxonomy systems and possibly also include genomes identified through metagenomics.}, } @article {pmid36613265, year = {2022}, author = {Golovkina, DA and Zhurishkina, EV and Ayrapetyan, ON and Komissarov, AE and Krylova, AS and Vinogradova, EN and Toshchakov, SV and Ermilov, FK and Barsegyan, AM and Kulminskaya, AA and Lapina, IM}, title = {Effect of Brown Algae and Lichen Extracts on the SCOBY Microbiome and Kombucha Properties.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {36613265}, issn = {2304-8158}, support = {075-15-2019-1663//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Kombucha tea was made by the fermentation of SCOBY culture of green tea broth with the addition of Fucus vesiculosus algae extract, Cetraria islandica lichen extract and their mixture. Kombucha was also made without the herbal supplements as a control. After 11 days of fermentation, in addition to the yeast Brettanomyces bruxellensis and the bacteria Komagataeibacter rhaeticus and Komagataeibacter hansenii contained in all of the samples, the yeast Zygosaccharomyces bailii and bacteria Komagataeibacter cocois were detected in the samples with the herbal extracts. In all of the kombucha with herbal additives, the total fraction of yeast was decreased as compared to the control. The total content of polyphenols and the antioxidant activity of the beverages with and without the addition of herbal extracts were comparable. The kombucha made with the algae extract showed an increased content of sucrose and organic acids, while the fructose and glucose content in the samples with algae and the mixture of extracts were lower than in the other samples. The samples with the algae extract had the highest organoleptic indicators "aroma", "clarity" and "acidity", while the control samples had slightly higher indicators of "taste" and "aftertaste". The results of this study indicate the potential of algae and lichens as functional supplements for obtaining non-alcoholic fermented beverages with additional nutraceutical value.}, } @article {pmid36613237, year = {2022}, author = {Din, AU and Ahmad, W and Khan, TM and Wang, J and Wu, J}, title = {Metagenomic Analysis of Liquor Starter Culture Revealed Beneficial Microbes' Presence.}, journal = {Foods (Basel, Switzerland)}, volume = {12}, number = {1}, pages = {}, pmid = {36613237}, issn = {2304-8158}, support = {JW; 2019LXXNYKD-02//Luxian People's Government-Southwest Medical University Strategic Cooperation Project/ ; }, abstract = {Wines are complex matrices famous for their pleasant aroma and exceptional flavor. Baijiu (white wine) is a traditional Chinese liquor with a soft mouthfeel, fragrant taste, and long-lasting aftertaste. Baijiu is distilled from sorghum and wheat via solid fermentation. As in wines, the microbial ecosystem of Baijiu is a key decisive factor influencing aroma and consumer preferences. Microbial diversity in Baijiu has been intensively investigated. It is important to note that probiotics are a mixture of bacteria and yeast primarily intended to improve health. Our study aimed to characterize the microbial ecosystem of Zaopei Baijiu Daqu (ZBD) starter cultures for specific microbes with probiotic properties. The DNA samples of ZBD starters were analyzed using a metagenomic 16S rRNA approach to characterize the bacterial and ITS for fungal diversity. Weissella cibaria was the most dominant species in the bacterial community, while Saccharomycopsis fibuligera was the most abundant fungal species. Furthermore, functional prediction analysis identified unique pathways associated with microbial diversity relevant to functional innovation. These associated pathways include fermentation, amino acid metabolism, carbohydrate metabolism, energy metabolism, and membrane transport. This study identified beneficial microbes in the starter culture, opening a path for further in-depth analysis of those microbes by isolating and evaluating them for a valuable role in in vitro and in vivo studies.}, } @article {pmid36612923, year = {2022}, author = {Allsing, N and Kelley, ST and Fox, AN and Sant, KE}, title = {Metagenomic Analysis of Microbial Contamination in the U.S. Portion of the Tijuana River Watershed.}, journal = {International journal of environmental research and public health}, volume = {20}, number = {1}, pages = {}, pmid = {36612923}, issn = {1660-4601}, support = {K01 ES031640/ES/NIEHS NIH HHS/United States ; U54 MD012397/MD/NIMHD NIH HHS/United States ; }, mesh = {*Rivers ; *Environmental Monitoring/methods ; Sewage ; Base Sequence ; Anti-Bacterial Agents ; Water Microbiology ; Feces ; }, abstract = {The Tijuana River watershed is binational, flowing from Tijuana, Mexico into San Diego and Imperial Beach, USA. Aging sewage and stormwater infrastructure in Tijuana has not kept pace with population growth, causing overflows into this watershed during major rainfall or equipment failures. The public health consequences of this impaired watershed on the surrounding communities remain unknown. Here, we performed untargeted metagenomic sequencing to better characterize the sewage contamination in the Tijuana River, identifying potential pathogens and molecular indicators of antibiotic resistance in surface waters. In 2019-2020, water samples were collected within 48 h of major rainfall events at five transborder flow sites and at the mouth of the river in the US portion of the Tijuana River and estuary. After filtration, DNA was extracted and sequenced, and sequences were run through the Kaiju taxonomic classification program. A pathogen profile of the most abundant disease-causing microbes and viruses present in each of the samples was constructed, and specific markers of fecal contamination were identified and linked to each site. Results from diversity analysis between the sites showed clear distinction as well as similarities between sites and dates, and antibiotic-resistant genes were found at each site. This serves as a baseline characterization of microbial exposures to these local communities.}, } @article {pmid36612188, year = {2022}, author = {Rezasoltani, S and Aghdaei, HA and Jasemi, S and Gazouli, M and Dovrolis, N and Sadeghi, A and Schlüter, H and Zali, MR and Sechi, LA and Feizabadi, MM}, title = {Oral Microbiota as Novel Biomarkers for Colorectal Cancer Screening.}, journal = {Cancers}, volume = {15}, number = {1}, pages = {}, pmid = {36612188}, issn = {2072-6694}, abstract = {Alterations of the gut microbiome in cases of colorectal cancer (CRC) hint at the involvement of host-microbe interactions in the onset and progression of CRC and also, possibly, provide novel ways to detect and prevent CRC early. The aim of the present study was to evaluate whether the oral and fecal microbiomes of an individual can be suitable for CRC screening. Oral and fecal samples (n = 80) were gathered in Taleghani hospital, affiliated with Shahid Beheshti University of Medical Sciences, Tehran-Iran, from CRC stage 0 and I patients and healthy controls (HCs), who were screened for the first time. Microbial metagenomics assays were performed for studying microbiota profiles in all oral and fecal samples gathered. An abundance of top bacterial genera from both types of specimens (fecal and saliva samples) revealed a distinction between CRC patients and HCs. In saliva samples, the α diversity index was different between the microbiome of HCs and CRC patients, while β diversity showed a densely clustered microbiome in the HCs but a more dispersed pattern in CRC cases. The α and β diversity of fecal microbiota between HCs and CRC patients showed no statistically significant differences. Bifidobacterium was identified as a potential bacterial biomarker in CRC saliva samples, while Fusobacterium, Dialister, Catonella, Tennerella, Eubacterium-brachy-group, and Fretibacterium were ideal to distinguish HCs from CRC patients. One of the reasons for the heterogeneity of CRC may be the gastrointestinal (GI) tract microbiota, which can also cause systematic resistance to CRC. Moreover, an evaluation of saliva microbiota might offer a suitable screening test for the early detection of this malignancy, providing more accurate results than its fecal counterpart.}, } @article {pmid36611217, year = {2023}, author = {Jiang, JZ and Fang, YF and Wei, HY and Zhu, P and Liu, M and Yuan, WG and Yang, LL and Guo, YX and Jin, T and Shi, M and Yao, T and Lu, J and Ye, LT and Shi, SK and Wang, M and Duan, M and Zhang, DC}, title = {A remarkably diverse and well-organized virus community in a filter-feeding oyster.}, journal = {Microbiome}, volume = {11}, number = {1}, pages = {2}, pmid = {36611217}, issn = {2049-2618}, mesh = {Animals ; *Crassostrea/genetics ; DNA ; *Microbiota ; Seawater ; *Viruses/genetics ; }, abstract = {BACKGROUND: Viruses play critical roles in the marine environment because of their interactions with an extremely broad range of potential hosts. Many studies of viruses in seawater have been published, but viruses that inhabit marine animals have been largely neglected. Oysters are keystone species in coastal ecosystems, yet as filter-feeding bivalves with very large roosting numbers and species co-habitation, it is not clear what role they play in marine virus transmission and coastal microbiome regulation.

RESULTS: Here, we report a Dataset of Oyster Virome (DOV) that contains 728,784 nonredundant viral operational taxonomic unit contigs (≥ 800 bp) and 3473 high-quality viral genomes, enabling the first comprehensive overview of both DNA and RNA viral communities in the oyster Crassostrea hongkongensis. We discovered tremendous diversity among novel viruses that inhabit this oyster using multiple approaches, including reads recruitment, viral operational taxonomic units, and high-quality virus genomes. Our results show that these viruses are very different from viruses in the oceans or other habitats. In particular, the high diversity of novel circoviruses that we found in the oysters indicates that oysters may be potential hotspots for circoviruses. Notably, the viruses that were enriched in oysters are not random but are well-organized communities that can respond to changes in the health state of the host and the external environment at both compositional and functional levels.

CONCLUSIONS: In this study, we generated a first "knowledge landscape" of the oyster virome, which has increased the number of known oyster-related viruses by tens of thousands. Our results suggest that oysters provide a unique habitat that is different from that of seawater, and highlight the importance of filter-feeding bivalves for marine virus exploration as well as their essential but still invisible roles in regulating marine ecosystems. Video Abstract.}, } @article {pmid36611086, year = {2023}, author = {Kheiri, R and Mehrshad, M and Pourbabaee, AA and Ventosa, A and Amoozegar, MA}, title = {Hypersaline Lake Urmia: a potential hotspot for microbial genomic variation.}, journal = {Scientific reports}, volume = {13}, number = {1}, pages = {374}, pmid = {36611086}, issn = {2045-2322}, mesh = {*Lakes/microbiology ; Bacteria/genetics ; Bacteroidetes ; *Euryarchaeota ; Genomics ; Salinity ; }, abstract = {Lake Urmia located in Iran is a hypersaline environment with a salinity of about 27% (w/v). Metagenomic analyses of water samples collected from six locations in the lake exhibited a microbial community dominated by representatives of the family Haloferacaceae (69.8%), mainly those affiliated to only two genera, Haloquadratum (59.3%) and Halonotius (9.1%). Similar to other hypersaline lakes, the bacterial community was dominated by Salinibacter ruber (23.3%). Genomic variation analysis by inspecting single nucleotide variations (SNVs) and insertions/deletions (INDELs) exhibited a high level of SNVs and insertions, most likely through transformation for abundant taxa in the Lake Urmia community. We suggest that the extreme conditions of Lake Urmia and specifically its high ionic concentrations could potentially increase the SNVs and insertions, which can consequently hamper the assembly and genome reconstruction from metagenomic reads of Lake Urmia.}, } @article {pmid36610618, year = {2023}, author = {Meng, LJ and Hu, X and Wen, B and Liu, YH and Luo, GZ and Gao, JZ and Chen, ZZ}, title = {Microplastics inhibit biofloc formation and alter microbial community composition and nitrogen transformation function in aquaculture.}, journal = {The Science of the total environment}, volume = {866}, number = {}, pages = {161362}, doi = {10.1016/j.scitotenv.2022.161362}, pmid = {36610618}, issn = {1879-1026}, mesh = {*Microplastics ; Plastics ; Nitrogen ; Nitrogen Dioxide ; *Microbiota ; Aquaculture/methods ; }, abstract = {Biofloc technology, extensively used in intensive aquaculture systems, can prompt the formation of microbial aggregates. Microplastics (MPs) are detected abundantly in aquaculture waters. This study explored the effects of MPs on biofloc formation, microbial community composition and nitrogen transformation function in simulated biofloc aquaculture production systems. The formation process and settling performance of bioflocs were examined. High-throughput sequencing of 16S and 18S rRNA genes was used to investigate the microbial community compositions of bioflocs. Nitrogen dynamics were monitored and further explained from functional genes and microorganisms related to nitrogen transformation by metagenome sequencing. We found that the aggregates consisting of bioflocs and MPs were formed and the systems with MPs had relatively weak settling performance. No significant differences in bacterial diversity (p > 0.05) but significant differences in eukaryotic diversity (p < 0.05) were found between systems without and with MPs. Significant separations in the microbial communities of prokaryotes (p = 0.01) and eukaryotes (p = 0.01) between systems without and with MPs were observed. The peak concentration of nitrite nitrogen (NO2[-]-N) in systems with MPs was lower than that in systems without MPs (pControl/MPs Low = 0.02 and pControl/MPs High = 0.03), probably due to the low abundance of hao and affiliated Alphaproteobacteria_bacterium_HGW-Alphaproteobacteria-1 and Alphaproteobacteria_bacterium, but the high abundance of nxrA and affiliated Alphaproteobacteria_bacterium_SYSU_XM001 and Hydrogenophaga_pseudoflava that related to nitrification. The low concentration of NO2[-]-N in systems with MPs suggested that the presence of MPs might inhibit ammonia oxidation but promote nitrite oxidation by altering the microbial community structure and function. These results indicated that aggregates consisting of bioflocs and MPs could be formed in aquaculture water, and thus, inhibiting their settlement and altering nitrogen transformation function by affecting the microbial community composition.}, } @article {pmid36610483, year = {2023}, author = {Zhang, X and Jiao, P and Zhang, M and Wu, P and Zhang, Y and Wang, Y and Xu, K and Yu, J and Ma, L}, title = {Impacts of organic loading rate and hydraulic retention time on organics degradation, interspecies interactions and functional traits in thermophilic anaerobic co-digestion of food waste and sewage sludge.}, journal = {Bioresource technology}, volume = {370}, number = {}, pages = {128578}, doi = {10.1016/j.biortech.2023.128578}, pmid = {36610483}, issn = {1873-2976}, mesh = {*Sewage ; Food ; Anaerobiosis ; *Refuse Disposal ; Digestion ; Bioreactors ; Methane/metabolism ; }, abstract = {This study provided novel insights into the effects of organic loading rate (OLR) and hydraulic retention time (HRT) on thermophilic anaerobic co-digestion of food waste and sewage sludge. The obtained maximum methane (CH4) yield of 328 ± 4 mL CH4/g CODfed at HRT of 15 days (OLR = 5.8 g VS/L/d) was partly attributable to the enhanced acidogenesis, acetogenesis, and methanogenesis phases. The increased key enzyme activities, particularly acetate kinase (improved by 5.2-fold), providing substantial methanogenic substrates for efficient CH4 production. The functional syntrophs that were related to syntrophic decarboxylation, novel acetate oxidation & reductive acetyl-CoA, and β-oxidation pathways could drive trophic interactions with methanogens. This markedly stimulated hydrogenotrophic Methanoculleus thermophilus metabolism and concomitantly enriched mixotrophic Methanosarcina thermophila. The distinctive cross-feeding interspecies interactions significantly affected the assembly and dynamics of thermophilic consortia. These findings shed light on the physicochemical and microbial mechanisms of HRT- and OLR-dependent enhancement of methanogenesis.}, } @article {pmid36610305, year = {2023}, author = {Guan, F and Dai, X and Yang, Y and Tabashnik, BE and Wu, Y}, title = {Population Genomics of Nonrecessive Resistance to Bt Toxin Cry1Ac in Helicoverpa armigera From Northern China.}, journal = {Journal of economic entomology}, volume = {116}, number = {2}, pages = {310-320}, doi = {10.1093/jee/toac182}, pmid = {36610305}, issn = {1938-291X}, mesh = {Animals ; *Bacillus thuringiensis/genetics ; Bacillus thuringiensis Toxins/metabolism ; Metagenomics ; Endotoxins ; Insecticide Resistance/genetics ; Bacterial Proteins/genetics ; Hemolysin Proteins/genetics ; *Moths/genetics ; Larva/metabolism ; China ; Gossypium ; }, abstract = {Transgenic crops that produce insecticidal proteins from Bacillus thuringiensis (Bt) have provided control of some key pests since 1996. However, the evolution of resistance by pests reduces the benefits of Bt crops. Resistance to Bt crops that is not recessively inherited is especially challenging to manage. Here we analyzed nonrecessive resistance to Bt toxin Cry1Ac in eight field populations of Helicoverpa armigera sampled in 2018 from northern China, where this global pest has been exposed to Cry1Ac in Bt cotton since 1997. Bioassays revealed 7.5% of field-derived larvae were resistant to Cry1Ac of which 87% had at least one allele conferring nonrecessive resistance. To analyze this nonrecessive resistance, we developed and applied a variant of a genomic mapping approach called quantitative trait locus (QTL)-seq. This analysis identified a region on chromosome 10 associated with nonrecessive resistance to Cry1Ac in all 21 backcross families derived from field-collected moths. Individual sequencing revealed that all 21 field-collected resistant grandparents of the backcross families had a previously identified dominant point mutation in the tetraspanin gene HaTSPAN1 that occurs in the region of chromosome 10 identified by QTL-seq. QTL-seq also revealed a region on chromosome 26 associated with nonrecessive resistance in at most 14% of the backcross families. Overall, the results imply the point mutation in HaTSPAN1 is the primary genetic basis of nonrecessive resistance to Cry1Ac in field populations of H. armigera from northern China. Moreover, because nonrecessive resistance is predominant, tracking the frequency of this point mutation could facilitate resistance monitoring in the region.}, } @article {pmid36610232, year = {2023}, author = {Wu, Z and Han, Y and Wan, Y and Hua, X and Chill, SS and Teshome, K and Zhou, W and Liu, J and Wu, D and Hutchinson, A and Jones, K and Dagnall, CL and Hicks, BD and Liao, L and Hallen-Adams, H and Shi, J and Abnet, CC and Sinha, R and Chaturvedi, A and Vogtmann, E}, title = {Oral microbiome and risk of incident head and neck cancer: A nested case-control study.}, journal = {Oral oncology}, volume = {137}, number = {}, pages = {106305}, pmid = {36610232}, issn = {1879-0593}, support = {ZIA CP010215/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Humans ; Case-Control Studies ; *Head and Neck Neoplasms/epidemiology ; *Microbiota ; Diet ; Porphyromonas gingivalis ; }, abstract = {OBJECTIVES: This nested case-control study in the NIH-AARP Diet and Health Study was carried out to prospectively investigate the relationship of oral microbiome with head and neck cancer (HNC).

MATERIALS AND METHODS: 56 incident HNC cases were identified, and 112 controls were incidence-density matched to cases. DNA extracted from pre-diagnostic oral wash samples was whole-genome shotgun metagenomic sequenced to measure the overall oral microbiome. ITS2 gene qPCR was used to measure the presence of fungi. ITS2 gene sequencing was performed on ITS2 gene qPCR positive samples. We computed taxonomic and functional alpha-diversity and beta-diversity metrics. The presence and relative abundance of groups of red-complex (e.g., Porphyromonas gingivalis) and/or orange-complex (e.g., Fusobacterium nucleatum) periodontal pathogens were compared between cases and controls using conditional logistic regression models and MiRKAT.

RESULTS: Participants with higher taxonomic microbial alpha-diversity had a non-statistically significant decreased risk of HNC. No case-control differences were found for beta diversity by MiRKAT model (all p > 0.05). A greater relative abundance of red-complex periodontal pathogens (OR = 0.51, 95 % CI = 0.26-1.00), orange-complex (OR = 0.38, 95 % CI = 0.18-0.83), and both complexes' pathogens (OR = 0.32, 95 % CI = 0.14-0.75), were associated with reduced risk of HNC. The presence of oral fungi was also strongly associated with reduced risk of HNC compared with controls (OR = 0.39, 95 % CI = 0.17-0.92).

CONCLUSION: Greater taxonomic alpha-diversity, the presence of oral fungi, and the presence or relative abundance of multiple microbial species, including the red- and orange-complex periodontal pathogens, were associated with reduced risk of HNC. Future studies with larger sample sizes are needed to evaluate these associations.}, } @article {pmid36609598, year = {2023}, author = {Yoshida, K and Ueno, T and Koito, K and Hu, D and Yamaguchi, A}, title = {A Comparative Study on Fungal Diversity in Organic and Conventionally Cultivated Lemons During Accelerated Storage.}, journal = {Current microbiology}, volume = {80}, number = {2}, pages = {69}, pmid = {36609598}, issn = {1432-0991}, mesh = {Fruit/microbiology ; *Citrus/microbiology ; *Pesticides ; }, abstract = {There has been a growing interest in organic farming as a countermeasure to the environmental burden caused by chemical pesticides. We analyzed and compared the fungal diversity of lemon fruits from organic and conventional cultivation by automated rRNA intergenic spacer analysis (ARISA), accompanied by isolation of cultured colonies and metagenomic analysis. Lemon peels were cut out and subjected to the analyses at purchase and after accelerated storage at 28 °C. The organic lemons did not decay even after 14 weeks, while most of the conventional lemons did decay. The fungal colony counts were not significantly different, although the number of fungal species together with the Shannon index, considering the abundance of each species, clearly showed more diversity in organic lemons than in conventional lemons (p = 0.011). Fusarium sp. (putative F. solani) accounted for as much as 90% of the relative abundance in the decayed conventional lemons. Metagenomic analysis also supported the lack of fungal diversity in conventional lemons. These results may suggest that organic cultivation maintains the diversity of native fungal flora in lemon fruit and could contribute to preventing decay during ambient storage.}, } @article {pmid36609515, year = {2023}, author = {Wang, Z and Huang, P and You, R and Sun, F and Zhu, S}, title = {MetaBinner: a high-performance and stand-alone ensemble binning method to recover individual genomes from complex microbial communities.}, journal = {Genome biology}, volume = {24}, number = {1}, pages = {1}, pmid = {36609515}, issn = {1474-760X}, mesh = {*Algorithms ; *Microbiota/genetics ; Metagenome ; Genome, Microbial ; Metagenomics/methods ; Sequence Analysis, DNA ; }, abstract = {Binning aims to recover microbial genomes from metagenomic data. For complex metagenomic communities, the available binning methods are far from satisfactory, which usually do not fully use different types of features and important biological knowledge. We developed a novel ensemble binner, MetaBinner, which generates component results with multiple types of features by k-means and uses single-copy gene information for initialization. It then employs a two-stage ensemble strategy based on single-copy genes to integrate the component results efficiently and effectively. Extensive experimental results on three large-scale simulated datasets and one real-world dataset demonstrate that MetaBinner outperforms the state-of-the-art binners significantly.}, } @article {pmid36609227, year = {2023}, author = {Yang, S and Xue, B and Hu, X and Zhou, W and Zhang, M and Zhao, M}, title = {Spinal infection caused by Coxiella burnetii.}, journal = {BMC infectious diseases}, volume = {23}, number = {1}, pages = {6}, pmid = {36609227}, issn = {1471-2334}, support = {Qingdao Outstanding Health Professional Development Fund//Qingdao Outstanding Health Professional Development Fund/ ; }, mesh = {Male ; Humans ; Aged ; *Coxiella burnetii/genetics ; *Q Fever/diagnosis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; Combined Modality Therapy ; Magnetic Resonance Imaging ; }, abstract = {BACKGROUND: Spinal infection caused by Coxiella burnetii is rare and difficult to diagnose. Here we reported a case of spinal infection from Coxiella burnetii detected by the metagenomic next-generation sequencing (mNGS).

CASE PRESENTATION: A 66-year-old male farmer with no medical history reported severe sharp low back pain, numbness and lower limb weakness for three years. Magnetic resonance imaging (MRI) revealed bone destruction and spinal cord compression within L1 and L2. mNGS testing showed that the inspected specimen collected from spinal lesion was detected positively for Coxiella burnetii. After receiving the combined treatment of antibiotic therapy and surgical intervention, the patient recovered well, and the sagittal MRI showed that vertebral edema signals disappeared and the graft of bone fused 16 months after surgery.

CONCLUSION: The mNGS may be benefit for early diagnosis and intervention of non-specific spinal infection, and future studies should validate its effectiveness for clinical use in spinal infections. Additionally, antibiotic therapy combined with surgical intervention plays an important role on the treatment of spinal infection caused by Coxiella burnetii.}, } @article {pmid36608812, year = {2023}, author = {Ye, W and Zheng, Y and Sun, Y and Li, Q and Zhu, H and Xu, G}, title = {Transcriptome analysis of the response of four immune related organs of tilapia (Oreochromis niloticus) to the addition of resveratrol in feed.}, journal = {Fish & shellfish immunology}, volume = {133}, number = {}, pages = {108510}, doi = {10.1016/j.fsi.2022.108510}, pmid = {36608812}, issn = {1095-9947}, mesh = {Animals ; *Tilapia/genetics ; *Cichlids ; Resveratrol ; Peroxisome Proliferator-Activated Receptors/genetics ; Gene Expression Profiling/veterinary ; Transcriptome ; }, abstract = {Resveratrol (RES) has been found to have immunological enhancement effects on Oreochromis niloticus. In O. nilocticus, the liver, spleen and kidney act as immune target tissues, while intestine works for nutrition sensing organ. In the present study, we determined RES administration on these immune tissues transcriptomic response in genetically improved farmed tilapia (GIFT), and further analyzed the relationship between transcriptomic response and intestinal microbiota. As results, hepatic hemosiderin and intestinal goblet cells significantly increased with RES addition. Kyoto encyclopedia of genes and genomes (KEGG) pathways associated with herpes simplex virus 1 infection, calcium signaling pathway, cell adhesion molecules, apoptosis, and mitogen-activated protein kinase (MAPK)/peroxisome proliferators-activated receptors (PPAR) signaling pathways were enriched. In particular, the differentially enriched genes (DEGs) associated pathways were present in different sampling tissues, times, and comparisons, interestingly, the PPAR signaling pathway was enriched with increasing time of RES addition. The assembled DEGs presented verified expression in the kidney, liver, spleen, and intestine tissues, and fabp6 was highly expressed in the intestine. Serial DEGs of fatty acid-binding proteins (fabp7, fabp7a, fabp10a) decreased in the liver and kidney, and fabp6 significantly increased in the spleen. With time, the pathways of energy metabolism, glycan biosynthesis, and metabolism decreased and increased in the intestinal metagenome. Some Candidatus branches significantly increased (C. cerribacteria and C. harrisonbacteria) and while others decreased (C. glodbacteria, etc.), whereas C. verstraetearchaeota fluctuated with RES addition. slc27a6 and dbi were negatively correlated with bacteria involved in the lipid, energy, and carbohydrate metabolism pathways. The present study suggests that RES supplementation affected lipid metabolism in immune-related organs may be related to the PPAR signaling pathway.}, } @article {pmid36608151, year = {2023}, author = {Clasen, SJ and Bell, MEW and Borbón, A and Lee, DH and Henseler, ZM and de la Cuesta-Zuluaga, J and Parys, K and Zou, J and Wang, Y and Altmannova, V and Youngblut, ND and Weir, JR and Gewirtz, AT and Belkhadir, Y and Ley, RE}, title = {Silent recognition of flagellins from human gut commensal bacteria by Toll-like receptor 5.}, journal = {Science immunology}, volume = {8}, number = {79}, pages = {eabq7001}, doi = {10.1126/sciimmunol.abq7001}, pmid = {36608151}, issn = {2470-9468}, mesh = {Animals ; Humans ; Mice ; Bacteria ; *Flagellin/metabolism ; Signal Transduction ; *Toll-Like Receptor 5 ; Intestines ; }, abstract = {Flagellin, the protein subunit of the bacterial flagellum, stimulates the innate immune receptor Toll-like receptor 5 (TLR5) after pattern recognition or evades TLR5 through lack of recognition. This binary response fails to explain the weak agonism of flagellins from commensal bacteria, raising the question of how TLR5 response is tuned. Here, we screened abundant flagellins present in metagenomes from human gut for both TLR5 recognition and activation and uncovered a class of flagellin-TLR5 interaction termed silent recognition. Silent flagellins were weak TLR5 agonists despite pattern recognition. Receptor activity was tuned by a TLR5-flagellin interaction distal to the site of pattern recognition that was present in Salmonella flagellin but absent in silent flagellins. This interaction enabled flagellin binding to preformed TLR5 dimers and increased TLR5 signaling by several orders of magnitude. Silent recognition by TLR5 occurred in human organoids and mice, and silent flagellin proteins were present in human stool. These flagellins were produced primarily by the abundant gut bacteria Lachnospiraceae and were enriched in nonindustrialized populations. Our findings provide a mechanism for the innate immune system to tolerate commensal-derived flagellins while remaining vigilant to the presence of flagellins produced by pathogens.}, } @article {pmid36608056, year = {2023}, author = {Zhai, H and Fukuyama, J}, title = {A convenient correspondence between k-mer-based metagenomic distances and phylogenetically-informed β-diversity measures.}, journal = {PLoS computational biology}, volume = {19}, number = {1}, pages = {e1010821}, pmid = {36608056}, issn = {1553-7358}, mesh = {*Metagenome/genetics ; Phylogeny ; *Algorithms ; Sequence Analysis, DNA/methods ; }, abstract = {k-mer-based distances are often used to describe the differences between communities in metagenome sequencing studies because of their computational convenience and history of effectiveness. Although k-mer-based distances do not use information about taxon abundances, we show that one class of k-mer distances between metagenomes (the Euclidean distance between k-mer spectra, or EKS distances) are very closely related to a class of phylogenetically-informed β-diversity measures that do explicitly use both the taxon abundances and information about the phylogenetic relationships among the taxa. Furthermore, we show that both of these distances can be interpreted as using certain features of the taxon abundances that are related to the phylogenetic tree. Our results allow practitioners to perform phylogenetically-informed analyses when they only have k-mer data available and provide a theoretical basis for using k-mer spectra with relatively small values of k (on the order of 4-5). They are also useful for analysts who wish to know more of the properties of any method based on k-mer spectra and provide insight into one class of phylogenetically-informed β-diversity measures.}, } @article {pmid36607873, year = {2023}, author = {Chen, XB and Zhou, YX and Feng, Y}, title = {Citrobacter freundii induces sepsis with new-onset status seizure in an adult: A case report and literature review.}, journal = {Medicine}, volume = {102}, number = {1}, pages = {e32549}, pmid = {36607873}, issn = {1536-5964}, mesh = {Female ; Humans ; Adult ; Citrobacter freundii ; *Shock, Septic/etiology/drug therapy ; *Sepsis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; Seizures/drug therapy ; *Brain Abscess/drug therapy ; }, abstract = {RATIONALE: Sepsis with brain abscess induced by Citrobacter freundii in adults has rarely been reported and is extremely pathogenic with a high mortality rate. Early diagnosis of the infection still remains challenging.

PATIENT CONCERNS: A 27-year-old woman was transferred to our emergency department for fever, status seizure and refractory hypotension. Administration of midazolam, propofol and sodium valproate could not attenuate the seizure except for the addition of vecuronium. The blood white blood cell count was 42.91 (109/L) with 80% neutrophils, and procalcitonin was 22.46ng/mL.

DIAGNOSES: Both deoxyribonucleic acid and ribonucleic acid of C freundii were detected in blood by metagenomic next-generation sequencing of pathogens,the diagnosis of septic shock and brain abscess caused by C freundii was highly suspected.

INTERVENTIONS: On day 1, antibiotics of cefoperazone sodium and sulbactam sodium 6g/day, immunoglobulin, and hydrocortisone were used with suspected septic shock. Continuous renal replacement therapy was used to eliminate excessive lactate, ammonia, myohemoglobin and creatinine. On day 2, a brain computed tomography scan revealed multiple patchy slightly low densities in the brain, antibiotics were adjusted to meropenem intravenously 3g/day.

OUTCOMES: On day 2, a brain computed tomography scan revealed multiple patchy slightly low densities in the brain, she died on day 3.

LESSONS: Clinicians should consider the possibility of brain abscess when evaluating a patient with new-onset dizziness, fever, seizure, or other neurologic symptoms or signs, especially for patients whose mental status changes. metagenomic next generation sequencing and resistance genes could be considered when cerebrospinal fluid or blood results are negative and clinical manifestations are highly suspected of infection or when the treatment time is limited.}, } @article {pmid36607772, year = {2023}, author = {Tithi, SS and Aylward, FO and Jensen, RV and Zhang, L}, title = {FastViromeExplorer-Novel: Recovering Draft Genomes of Novel Viruses and Phages in Metagenomic Data.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {30}, number = {4}, pages = {391-408}, doi = {10.1089/cmb.2022.0397}, pmid = {36607772}, issn = {1557-8666}, mesh = {*Bacteriophages/genetics ; *Viruses/genetics ; Metagenome/genetics ; Genome, Viral ; Metagenomics ; }, abstract = {Despite the recent surge of viral metagenomic studies, recovering complete virus/phage genomes from metagenomic data is still extremely difficult and most viral contigs generated from de novo assembly programs are highly fragmented, posing serious challenges to downstream analysis and inference. In this study, we develop FastViromeExplorer (FVE)-novel, a computational pipeline for reconstructing complete or near-complete viral draft genomes from metagenomic data. The FVE-novel deploys FVE to efficiently map metagenomic reads to viral reference genomes, performs de novo assembly of the mapped reads to generate contigs, and extends the contigs through iterative assembly to produce final viral scaffolds. We applied FVE-novel to an ocean metagenomic sample and obtained 268 viral scaffolds that potentially come from novel viruses. Through manual examination and validation of the 10 longest scaffolds, we successfully recovered 4 complete viral genomes, 2 are novel as they cannot be found in the existing databases and the other 2 are related to known phages. This hybrid reference-based and de novo assembly approach used by FVE-novel represents a powerful new approach for uncovering near-complete viral genomes in metagenomic data.}, } @article {pmid36606725, year = {2023}, author = {Candel, S and Tyrkalska, SD and Álvarez-Santacruz, C and Mulero, V}, title = {The nasopharyngeal microbiome in COVID-19.}, journal = {Emerging microbes & infections}, volume = {12}, number = {1}, pages = {e2165970}, pmid = {36606725}, issn = {2222-1751}, mesh = {Humans ; *COVID-19 ; Pandemics ; Nasopharynx ; *Microbiota ; Nose ; }, abstract = {The development of novel culture-independent techniques of microbial identification has allowed a rapid progress in the knowledge of the nasopharyngeal microbiota and its role in health and disease. Thus, it has been demonstrated that the nasopharyngeal microbiota defends the host from invading pathogens that enter the body through the upper airways by participating in the modulation of innate and adaptive immune responses. The current COVID-19 pandemic has created an urgent need for fast-track research, especially to identify and characterize biomarkers to predict the disease severity and outcome. Since the nasopharyngeal microbiota diversity and composition could potentially be used as a prognosis biomarker for COVID-19 patients, which would pave the way for strategies aiming to reduce the disease severity by modifying such microbiota, dozens of research articles have already explored the possible associations between changes in the nasopharyngeal microbiota and the severity or outcome of COVID-19 patients. Unfortunately, results are controversial, as many studies with apparently similar experimental designs have reported contradictory data. Herein we put together, compare, and discuss all the relevant results on this issue reported to date. Even more interesting, we discuss in detail which are the limitations of these studies, that probably are the main sources of the high variability observed. Therefore, this work is useful not only for people interested in current knowledge about the relationship between the nasopharyngeal microbiota and COVID-19, but also for researchers who want to go further in this field while avoiding the limitations and variability of previous works.}, } @article {pmid36606497, year = {2023}, author = {Tang, L and Yan, L and Jia, H and Xiong, Y and Ma, X and Chu, H and Sun, Z and Wang, L and Shalitanati, M and Li, K and Hu, D and Zhang, D}, title = {Gut microbial community structure and function of Przewalski's horses varied across reintroduced sites in China.}, journal = {Integrative zoology}, volume = {18}, number = {6}, pages = {1027-1040}, doi = {10.1111/1749-4877.12699}, pmid = {36606497}, issn = {1749-4877}, support = {2019JQ0318//the Beijing Forestry University Outstanding Young Talent Cultivation Project/ ; BX20190042//the Postdoctoral Innovative Talents Support Program/ ; 2020M670177//the China Postdoctoral Science Foundation/ ; }, mesh = {Humans ; Animals ; Horses ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; China ; }, abstract = {Host-associated microbiota can significantly impact host fitness. Therefore, naturally occurring variations in microbiota may influence the health and persistence of their hosts. This finding is particularly important in reintroduced animals, as they typically experience habitat changes during translocations. However, little is known about how microbiomes are altered in response to conservation translocation. Here, we accessed the gut microbiome of Przewalski's horse (Equus przewalskii) populations in China from three nature reserves (i.e. Xinjiang Kalamaili Nature Reserve, KNR; Dunhuang Xihu National Nature Reserve, DXNNR; and Anxi Extreme-arid Desert Nature Reserve, AENR) using 16s rRNA gene and metagenome sequencing. The results showed that the microbial composition and function differed significantly across locations, while a subset of core taxa was consistently present in most of the samples. The abundance of genes encoding microbe-produced enzymes involved in the metabolism of carbohydrates, especially for glycoside hydrolases, was significantly higher in open-spaced KNR populations than in more confined AENR individuals. This study offers detailed and significant differential characters related to the microbial community and metabolic pathways in various reintroduced sites of Przewalski's horse, which might provide a basis for future microecological and conservation research on endangered reintroduced animals.}, } @article {pmid36605757, year = {2022}, author = {Liao, J and Yang, Z and He, Y and Wei, J and Ren, L and Liu, E and Zang, N}, title = {Respiratory tract infection of fatal severe human bocavirus 1 in a 13-month-old child: A case report and literature review.}, journal = {Frontiers in pediatrics}, volume = {10}, number = {}, pages = {949817}, pmid = {36605757}, issn = {2296-2360}, abstract = {Human bocavirus 1 (HBoV1) belongs to the family Parvoviridae and it is acknowledged that HBoV1 is a respiratory pathogen. We report the case of a 13-month-old boy who presented with a cough, shortness of breath, and wheezing, and who eventually died of severe pneumonia and acute respiratory distress syndrome (ARDS). Metagenomics next-generation sequencing (mNGS) showed that HBoV1 was the only detected pathogen. The nasopharyngeal aspirate viral load was 2.08 × 10[10] copies/ml and the serum viral load was 2.37 × 10[5] copies/ml. The child was still oxygen deficient under mechanical ventilation. Chest imaging suggested diffuse lesions in both lungs, an injury caused by ARDS. In this case, the clinical symptoms and signs of the child, the high viral load, viremia, and the detection of mNGS in the tracheal aspirate all supported that HBoV1 could cause severe acute respiratory tract infection in children without other pathogen infections.}, } @article {pmid36605197, year = {2022}, author = {Vos, WAJW and Groenendijk, AL and Blaauw, MJT and van Eekeren, LE and Navas, A and Cleophas, MCP and Vadaq, N and Matzaraki, V and Dos Santos, JC and Meeder, EMG and Fröberg, J and Weijers, G and Zhang, Y and Fu, J and Ter Horst, R and Bock, C and Knoll, R and Aschenbrenner, AC and Schultze, J and Vanderkerckhove, L and Hwandih, T and Wonderlich, ER and Vemula, SV and van der Kolk, M and de Vet, SCP and Blok, WL and Brinkman, K and Rokx, C and Schellekens, AFA and de Mast, Q and Joosten, LAB and Berrevoets, MAH and Stalenhoef, JE and Verbon, A and van Lunzen, J and Netea, MG and van der Ven, AJAM}, title = {The 2000HIV study: Design, multi-omics methods and participant characteristics.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {982746}, pmid = {36605197}, issn = {1664-3224}, mesh = {Male ; Humans ; Female ; *HIV Infections/drug therapy/epidemiology ; Homosexuality, Male ; Prospective Studies ; COVID-19 Vaccines/therapeutic use ; Carotid Intima-Media Thickness ; Longitudinal Studies ; Multiomics ; *COVID-19 ; *Sexual and Gender Minorities ; }, abstract = {BACKGROUND: Even during long-term combination antiretroviral therapy (cART), people living with HIV (PLHIV) have a dysregulated immune system, characterized by persistent immune activation, accelerated immune ageing and increased risk of non-AIDS comorbidities. A multi-omics approach is applied to a large cohort of PLHIV to understand pathways underlying these dysregulations in order to identify new biomarkers and novel genetically validated therapeutic drugs targets.

METHODS: The 2000HIV study is a prospective longitudinal cohort study of PLHIV on cART. In addition, untreated HIV spontaneous controllers were recruited. In-depth multi-omics characterization will be performed, including genomics, epigenomics, transcriptomics, proteomics, metabolomics and metagenomics, functional immunological assays and extensive immunophenotyping. Furthermore, the latent viral reservoir will be assessed through cell associated HIV-1 RNA and DNA, and full-length individual proviral sequencing on a subset. Clinical measurements include an ECG, carotid intima-media thickness and plaque measurement, hepatic steatosis and fibrosis measurement as well as psychological symptoms and recreational drug questionnaires. Additionally, considering the developing pandemic, COVID-19 history and vaccination was recorded. Participants return for a two-year follow-up visit. The 2000HIV study consists of a discovery and validation cohort collected at separate sites to immediately validate any finding in an independent cohort.

RESULTS: Overall, 1895 PLHIV from four sites were included for analysis, 1559 in the discovery and 336 in the validation cohort. The study population was representative of a Western European HIV population, including 288 (15.2%) cis-women, 463 (24.4%) non-whites, and 1360 (71.8%) MSM (Men who have Sex with Men). Extreme phenotypes included 114 spontaneous controllers, 81 rapid progressors and 162 immunological non-responders. According to the Framingham score 321 (16.9%) had a cardiovascular risk of >20% in the next 10 years. COVID-19 infection was documented in 234 (12.3%) participants and 474 (25.0%) individuals had received a COVID-19 vaccine.

CONCLUSION: The 2000HIV study established a cohort of 1895 PLHIV that employs multi-omics to discover new biological pathways and biomarkers to unravel non-AIDS comorbidities, extreme phenotypes and the latent viral reservoir that impact the health of PLHIV. The ultimate goal is to contribute to a more personalized approach to the best standard of care and a potential cure for PLHIV.}, } @article {pmid36605125, year = {2022}, author = {Zhu, L and Hao, Y and Li, W and Shi, B and Dong, H and Gao, P}, title = {Significance of pleural effusion detected by metagenomic next-generation sequencing in the diagnosis of aspiration pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {992352}, pmid = {36605125}, issn = {2235-2988}, mesh = {Female ; Humans ; Male ; Anti-Bacterial Agents/therapeutic use ; Bacteria ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; *Pleural Effusion ; *Pneumonia, Aspiration/diagnosis/drug therapy ; *Pneumonia, Pneumococcal/drug therapy ; Retrospective Studies ; Adult ; Middle Aged ; Aged ; }, abstract = {OBJECTIVE: Using metagenomic next-generation sequencing (mNGS) to profile the bacterial pathogen of pleural infection in aspiration pneumonia for therapeutic decision-making.

METHODS: Collection and analysis of the clinical and laboratory data of aspiration pneumonia patients who underwent mNGS detection of pleural effusion at the Second Hospital of Jilin University from November 2020 and March 2022.

RESULTS: Nine males and one female were included, aged 33 to 69 years. All patients had chest pain, fever, cough, and hypoxemia symptoms; 90% had expectoration. The laboratory tests revealed that all patients had elevated white blood cell, neutrophil, and C-reactive protein (CRP) levels. Furthermore, erythrocyte sedimentation rate (ESR) increased in 8 patients, and procalcitonin increased in only one patient. Chest CT indicated different degrees of lobar pneumonia and pleural effusion in all patients, and biochemical results implied exudative effusion according to Light criteria. Most routine culture results were negative. Among bacteria identified by mNGS, Fusobacterium nucleatum (n=9) was the most common, followed by Parvimonas micra (n=7) and Filifactor alocis (n=6). Three patients underwent surgical treatment after applying targeted antibiotics, thoracic puncture and drainage, and fibrinolytic septum treatment. After the adjusted treatment, the number of white blood cells, neutrophils, and lymphocytes decreased significantly, indicating the eradication of the infection.

CONCLUSIONS: Improving the vigilance of atypical people suffering from aspiration pneumonia is essential. The mNGS detection of pleural effusion clarified the microbial spectrum of aspiration pneumonia, allowing targeted antibiotic administration.}, } @article {pmid36604871, year = {2022}, author = {Ouyang, Y and Zhang, ZF}, title = {[Application status of metagenomics in quality research of traditional Chinese medicinal materials].}, journal = {Zhongguo Zhong yao za zhi = Zhongguo zhongyao zazhi = China journal of Chinese materia medica}, volume = {47}, number = {23}, pages = {6271-6277}, doi = {10.19540/j.cnki.cjcmm.20220809.101}, pmid = {36604871}, issn = {1001-5302}, mesh = {Humans ; *Metagenomics ; Genomics ; *Plants, Medicinal/genetics ; DNA ; Medicine, Chinese Traditional ; Metagenome ; }, abstract = {Metagenomics constructs genomic libraries by directly extracting DNA from all microorganisms from environmental samples, and studies microbial diversity and functional composition by microbiology and genomics. The metagenomic technology and genome sequencing can be used to discover the unculturable environmental microorganisms and study the natural products in the medicinal materials related to them, which overcome the limitations of microbial isolation and culture technology and is of great significance for the discovery of new genes or genomes. The quality and safety of traditional Chinese medicine materials(TCMMs) have always been a hot topic in the research on TCMMs. In addition to the intrinsic characteristics, environmental factors and human intervention also affect the quality and clinical efficacy of TCMMs. Environmental microorganisms, rhizosphere microorganisms, and endophytes play an essential role in the growth, secondary metabolism, processing, and storage of medicinal plants. As an emerging discipline, metagenomics has been used in a variety of fields. It can not only avoid the problems caused by the limited technical conditions or strict experimental requirements but also evaluate the quality of TCMMs from a new perspective. This paper introduced the application status of metagenomics in the research of TCMMs and proposed the theoretical basis and research direction for the application of metagenomics in quality research and identification of TCMMs.}, } @article {pmid36604505, year = {2023}, author = {Jin, H and Quan, K and He, Q and Kwok, LY and Ma, T and Li, Y and Zhao, F and You, L and Zhang, H and Sun, Z}, title = {A high-quality genome compendium of the human gut microbiome of Inner Mongolians.}, journal = {Nature microbiology}, volume = {8}, number = {1}, pages = {150-161}, pmid = {36604505}, issn = {2058-5276}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; RNA, Ribosomal ; }, abstract = {Metagenome-based resources have revealed the diversity and function of the human gut microbiome, but further understanding is limited by insufficient genome quality and a lack of samples from typically understudied populations. Here we used hybrid long-read PromethION and short-read HiSeq sequencing to characterize the faecal microbiota of 60 Inner Mongolian individuals (n = 180 samples over three time points) who were part of a probiotic yogurt intervention trial. We present the Inner Mongolian Gut Genome catalogue, comprising 802 closed and 5,927 high-quality metagenome-assembled genomes. This approach achieved high genome continuity and substantially increased the resolution of genomic elements, including ribosomal RNA operons, metabolic gene clusters, prophages and insertion sequences. Particularly, we report the ribosomal RNA operon copy numbers for uncultured species, over 12,000 previously undescribed gut prophages and the distribution of insertion sequence elements across gut bacteria. Overall, these data provide a high-quality, large-scale resource for studying the human gut microbiota.}, } @article {pmid36604114, year = {2023}, author = {Sun, H and Guo, Y and Wang, H and Yin, A and Hu, J and Yuan, T and Zhou, S and Xu, W and Wei, P and Yin, S and Liu, P and Guo, X and Tang, Y and Yan, Y and Luo, Z and Wang, M and Liang, Q and Wu, P and Zhang, A and Zhou, Z and Chen, Y and Li, Y and Li, J and Shan, J and Zhou, W}, title = {Gut commensal Parabacteroides distasonis alleviates inflammatory arthritis.}, journal = {Gut}, volume = {72}, number = {9}, pages = {1664-1677}, doi = {10.1136/gutjnl-2022-327756}, pmid = {36604114}, issn = {1468-3288}, mesh = {Mice ; Animals ; *Arthritis, Rheumatoid/drug therapy/metabolism ; Bacteroidetes ; Bacteria ; }, abstract = {OBJECTIVE: Gut microbiota dysbiosis is closely linked to the pathogenesis of rheumatoid arthritis (RA). We aimed to identify potential probiotic gut microbes that can ameliorate the development of RA.

DESIGN: Microbiota profiling in patients with RA and healthy individuals was investigated via 16S rDNA bacterial gene sequencing and shotgun metagenomics. Collagen-induced arthritic mice and TNF-α transgenic mice were used to evaluate the roles of the gut commensal Parabacteroides distasonis in RA. The effects of P. distasonis-derived microbial metabolites on the differentiation of CD4[+] T cells and macrophage polarisation were also investigated.

RESULTS: The relative abundance of P. distasonis in new-onset patients with RA and patients with RA with history of the disease was downregulated and this decrease was negatively correlated with Disease Activity Score-28 (DAS28). Oral treatment of arthritic mice with live P. distasonis (LPD) considerably ameliorated RA pathogenesis. LPD-derived lithocholic acid (LCA), deoxycholic acid (DCA), isolithocholic acid (isoLCA) and 3-oxolithocholic acid (3-oxoLCA) had similar and synergistic effects on the treatment of RA. In addition to directly inhibiting the differentiation of Th17 cells, 3-oxoLCA and isoLCA were identified as TGR5 agonists that promoted the M2 polarisation of macrophages. A specific synthetic inhibitor of bile salt hydrolase attenuated the antiarthritic effects of LPD by reducing the production of these four bile acids. The natural product ginsenoside Rg2 exhibited its anti-RA effects by promoting the growth of P. distasonis.

CONCLUSIONS: P. distasonis and ginsenoside Rg2 might represent probiotic and prebiotic agents in the treatment of RA.}, } @article {pmid36603609, year = {2023}, author = {Feng, M and Du, Y and Li, X and Li, F and Qiao, J and Chen, G and Huang, Y}, title = {Insight into universality and characteristics of nitrate reduction coupled with arsenic oxidation in different paddy soils.}, journal = {The Science of the total environment}, volume = {866}, number = {}, pages = {161342}, doi = {10.1016/j.scitotenv.2022.161342}, pmid = {36603609}, issn = {1879-1026}, mesh = {*Arsenic ; Nitrates ; Soil ; RNA, Ribosomal, 16S/genetics ; *Arsenites ; *Oryza/genetics ; Oxidation-Reduction ; }, abstract = {Nitrate reduction coupled with arsenic (As) oxidation strongly influences the bioavailability and toxicity of As in anaerobic environments. In the present study, five representative paddy soils developed from different parent materials were used to investigate the universality and characteristics of nitrate reduction coupled with As oxidation in paddy soils. Experimental results indicated that 99.8 % of highly toxic aqueous As(III) was transformed to dissolved As(V) and Fe-bound As(V) in the presence of nitrate within 2-8 d, suggesting that As was apt to be reserved in its low-toxic and nonlabile form after nitrate treatment. Furthermore, nitrate additions also significantly induced the higher abundance of 16S rRNA and As(III) oxidase (aioA) genes in the five paddy soils, especially in the soils developed from purple sand-earth rock and quaternary red clay, which increased by 10 and 3-5 times, respectively, after nitrate was added. Moreover, a variety of putative novel nitrate-dependent As(III)-oxidizing bacteria were identified based on metagenomic analysis, mainly including Aromatoleum, Paenibacillus, Microvirga, Herbaspirillum, Bradyrhizobium, Azospirillum. Overall, all these findings indicate that nitrate reduction coupled with As(III) oxidation is an important nitrogen-As coupling process prevalent in paddy environments and emphasize the significance of developing and popularizing nitrate-based biotechnology to control As pollution in paddy soils and reduce the risk of As compromising food security.}, } @article {pmid36603585, year = {2023}, author = {Dai, DLY and Petersen, C and Hoskinson, C and Del Bel, KL and Becker, AB and Moraes, TJ and Mandhane, PJ and Finlay, BB and Simons, E and Kozyrskyj, AL and Patrick, DM and Subbarao, P and Bode, L and Azad, MB and Turvey, SE}, title = {Breastfeeding enrichment of B. longum subsp. infantis mitigates the effect of antibiotics on the microbiota and childhood asthma risk.}, journal = {Med (New York, N.Y.)}, volume = {4}, number = {2}, pages = {92-112.e5}, doi = {10.1016/j.medj.2022.12.002}, pmid = {36603585}, issn = {2666-6340}, support = {//CIHR/Canada ; }, mesh = {Child ; Infant ; Female ; Humans ; Breast Feeding ; Anti-Bacterial Agents/adverse effects ; *Sulfalene ; *Microbiota/genetics ; Bifidobacterium longum subspecies infantis ; Oligosaccharides/therapeutic use ; British Columbia ; *Asthma/epidemiology ; }, abstract = {BACKGROUND: Early antibiotic exposure is linked to persistent disruption of the infant gut microbiome and subsequent elevated pediatric asthma risk. Breastfeeding acts as a primary modulator of the gut microbiome during early life, but its effect on asthma development has remained unclear.

METHODS: We harnessed the CHILD cohort to interrogate the influence of breastfeeding on antibiotic-associated asthma risk in a subset of children (n = 2,521). We then profiled the infant microbiomes in a subset of these children (n = 1,338) using shotgun metagenomic sequencing and compared human milk oligosaccharide and fatty acid composition from paired maternal human milk samples for 561 of these infants.

FINDINGS: Children who took antibiotics without breastfeeding had 3-fold higher asthma odds, whereas there was no such association in children who received antibiotics while breastfeeding. This benefit was associated with widespread "re-balancing" of taxonomic and functional components of the infant microbiome. Functional changes associated with asthma protection were linked to enriched Bifidobacterium longum subsp. infantis colonization. Network analysis identified a selection of fucosylated human milk oligosaccharides in paired maternal samples that were positively associated with B. infantis and these broader functional changes.

CONCLUSIONS: Our data suggest that breastfeeding and antibiotics have opposing effects on the infant microbiome and that breastfeeding enrichment of B. infantis is associated with reduced antibiotic-associated asthma risk.

FUNDING: This work was supported in part by the Canadian Institutes of Health Research; the Allergy, Genes and Environment Network of Centres of Excellence; Genome Canada; and Genome British Columbia.}, } @article {pmid36603256, year = {2023}, author = {Niu, X and Han, X and Jin, Y and Yue, J and Zhu, J and Xie, W and Yu, J}, title = {Aerobic granular sludge treating hypersaline wastewater: Impact of pH on granulation and long-term operation at different organic loading rates.}, journal = {Journal of environmental management}, volume = {330}, number = {}, pages = {117164}, doi = {10.1016/j.jenvman.2022.117164}, pmid = {36603256}, issn = {1095-8630}, mesh = {*Wastewater ; *Sewage/chemistry ; Waste Disposal, Fluid/methods ; Aerobiosis ; Bioreactors/microbiology ; Hydrogen-Ion Concentration ; }, abstract = {pH is one of the major parameters that influence the granulation and long-term operation of aerobic granular sludge (AGS). In hypersaline wastewater, the impact of pH on granulation and the extent of organic loading rate (OLR) that AGS can withstand under different pH are still not clear. In this study, AGS was cultivated at 3% salinity in three sequencing batch reactors with influent pH values of 5.0, 7.0, and 9.0, respectively, and the OLR was stepwise increased from 2.4 to 16.8 kg COD/m[3]·d after the granules maturation. The results showed the satisfactory granulation and organic removal under different influent pH conditions, in which the granulation was completed on day 43, 23, and 23, respectively. Neutral influent was the most appropriate for development of salt-tolerant aerobic granular sludge (SAGS), while acidic environment induced the formation of fluffy filamentous granules, and alkaline environment weakened the granule stability. Metagenomic analysis revealed the similar microbial community of neutral and alkaline conditions, with the predominance of genus Paracoccus_f__Rhodobacteraceae. While in acidic environment, fungus Fusarium formed the skeleton of filamentous granules and functioned as the carrier of bacteria including Azoarcus and Pararhodobacter. With the elevation of OLR, SAGSs were found to maintain the compact structure under OLRs of 2.4, 7.2, and 2.4 kg COD/m[3]·d, and obtain high TOC removal (>95.0%) under OLRs of 7.2, 14.4, and 14.4 kg COD/m[3]·d, respectively. For hypersaline high-strength organic wastewater, satisfactory TOC removal could also be obtained at broad pH ranges (5.0-9.0), in which neutral environment was the most suitable and acidic environment was the worst. This study contributed to a better understanding of SAGS granulation and treatment of hypersaline high-strength organic wastewater with different pH values.}, } @article {pmid36603127, year = {2023}, author = {Liu, Z and Zhao, Y and Zhang, B and Wang, J and Zhu, L and Hu, B}, title = {Deterministic Effect of pH on Shaping Soil Resistome Revealed by Metagenomic Analysis.}, journal = {Environmental science & technology}, volume = {57}, number = {2}, pages = {985-996}, doi = {10.1021/acs.est.2c06684}, pmid = {36603127}, issn = {1520-5851}, mesh = {Humans ; *Metagenome ; *Genes, Bacterial ; Soil ; Ecosystem ; Protons ; Anti-Bacterial Agents ; Soil Microbiology ; Hydrogen-Ion Concentration ; }, abstract = {Soil is recognized as the major reservoir of antibiotic resistance genes (ARGs), harboring the most diverse naturally evolved ARGs on the planet. Multidrug resistance genes are a class of ARGs, and their high prevalence in natural soil ecosystems has recently raised concerns. Since most of these genes express proton motive force (PMF) driven efflux pumps, studying whether soil pH is a determinant for the selection of multidrug efflux pump genes and thus shaping the soil resistome are of great interest. In this study, we collected 108 soils with pH values ranging from 4.37 to 9.69 from multiple ecosystems and profiled the composition of ARGs for metagenomes and metagenome-assembled genomes. We observed the multidrug efflux pump genes enriched in the acidic soil resistome, and their abundances have significant soil pH dependence. This reflects the benefits of high soil proton activity on the multidrug efflux pump genes, especially for the PMF-driven inner membrane transferase. In addition, we preliminary indicate the putative microbial participants in pH shaping the soil resistome by applying ecological analyzing tools such as stepwise regression and random forest model fitting. The decisive influence of proton activity on shaping the resistome is more impactful than any other examined factors, and as the consequence, we revisited the influence of edaphic factors on the soil resistome; i.e., the deterministic selection of resistance mechanisms by edaphic factors could lead to the bottom-up shaping of the ARG composition. Such natural developing mechanisms of the resistome are herein suggested to be considered in assessing human-driven ARG transmissions.}, } @article {pmid36602781, year = {2023}, author = {Pichardo, PFA and Hellums, RN and Hao, J and Savatt, JM and Hassen, D and Pellitteri, PK and Alvi, M and Buchanan, AH and Purdy, NC}, title = {Thyroidectomy Outcomes in Patients Identified With RET Pathogenic Variants Through a Population Genomic Screening Program.}, journal = {JAMA otolaryngology-- head & neck surgery}, volume = {149}, number = {3}, pages = {195-202}, pmid = {36602781}, issn = {2168-619X}, mesh = {Male ; Humans ; Female ; Middle Aged ; Thyroidectomy/methods ; *Carcinoma, Medullary/genetics/pathology/surgery ; Retrospective Studies ; Cross-Sectional Studies ; Metagenomics ; Proto-Oncogene Proteins c-ret/genetics ; Proto-Oncogene Mas ; *Thyroid Neoplasms/diagnosis/genetics/surgery ; Genetic Testing ; }, abstract = {IMPORTANCE: Population-based genomic screening can facilitate early detection of medullary thyroid carcinoma (MTC) in patients with pathogenic/likely pathogenic (P/LP) RET variants.

OBJECTIVE: To evaluate the clinical treatment and patient outcomes after identification of P/LP RET proto-oncogene variants associated with the risk of MTC via a population genomic screening program.

DESIGN, SETTING, PARTICIPANTS: This retrospective cross-sectional study was completed between June 1, 2016, and May 31, 2022, for a mean follow-up period of 22.4 months (range, 2-76 months). The study included patients who were identified as having P/LP RET variants through a population genomic screening program at a rural tertiary care center and who underwent thyroidectomy after results disclosure.

MAIN OUTCOMES AND MEASURES: The outcomes of interest were preoperative evaluation and treatment-related outcomes. Measures included imaging and laboratory findings, extent of surgery, pathologic diagnosis, and staging.

RESULTS: Seventy-five patients were identified as having P/LP RET variants exclusively through genomic screening. Twenty of these patients (27%; 11 women [55%] and 9 men [45%]; median age, 48 years [range, 22-73 years]) underwent total thyroidectomy; 13 of these patients (65%) also had a central neck dissection. No patients had clinically apparent disease at the time of surgery. Pathologic findings indicated MTC for 12 patients and papillary thyroid carcinoma in 2. Of patients with MTC, 10 had stage I disease, 1 had stage II disease, 1 had stage III disease, and none had stage IV disease. Based on postoperative surveillance imaging and laboratory results, no patient had evidence of recalcitrant disease.

CONCLUSIONS AND RELEVANCE: In this cross-sectional study, all malignant neoplasms identified on surgical pathology were clinically occult, with surgical intervention based solely on the identification of the P/LP RET variant via population genomic screening. This finding suggests that genomic screening may provide opportunities for early detection and treatment of MTC, with the potential for improved patient outcomes.}, } @article {pmid36602384, year = {2023}, author = {Joo, H and Eom, H and Cho, Y and Rho, M and Song, WJ}, title = {Discovery and Characterization of Polymyxin-Resistance Genes pmrE and pmrF from Sediment and Seawater Microbiome.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0273622}, pmid = {36602384}, issn = {2165-0497}, mesh = {*Polymyxins/pharmacology/metabolism ; Lipid A/chemistry ; Escherichia coli/genetics ; Anti-Bacterial Agents/pharmacology/metabolism ; *Microbiota/genetics ; Drug Resistance, Bacterial/genetics ; }, abstract = {Polymyxins are the last-line antibiotics used to treat Gram-negative pathogens. Thus, the discovery and biochemical characterization of the resistance genes against polymyxins are urgently needed for diagnosis, treatment, and novel antibiotic design. Herein, we report novel polymyxin-resistance genes identified from sediment and seawater microbiome. Despite their low sequence identity against the known pmrE and pmrF, they show in vitro activities in UDP-glucose oxidation and l-Ara4N transfer to undecaprenyl phosphate, respectively, which occur as the part of lipid A modification that leads to polymyxin resistance. The expression of pmrE and pmrF also showed substantially high MICs in the presence of vanadate ions, indicating that they constitute polymyxin resistomes. IMPORTANCE Polymyxins are one of the last-resort antibiotics. Polymyxin resistance is a severe threat to combat multidrug-resistant pathogens. Thus, up-to-date identification and understanding of the related genes are crucial. Herein, we performed structure-guided sequence and activity analysis of five putative polymyxin-resistant metagenomes. Despite relatively low sequence identity to the previously reported polymyxin-resistance genes, at least four out of five discovered genes show reactivity essential for lipid A modification and polymyxin resistance, constituting antibiotic resistomes.}, } @article {pmid36602332, year = {2023}, author = {Distaso, M and Cea-Rama, I and Coscolín, C and Chernikova, TN and Tran, H and Ferrer, M and Sanz-Aparicio, J and Golyshin, PN}, title = {The Mobility of the Cap Domain Is Essential for the Substrate Promiscuity of a Family IV Esterase from Sorghum Rhizosphere Microbiome.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {1}, pages = {e0180722}, pmid = {36602332}, issn = {1098-5336}, mesh = {Esterases/metabolism ; *Sorghum/metabolism ; Rhizosphere ; *Microbiota ; Esters/metabolism ; Substrate Specificity ; Hydrogen-Ion Concentration ; }, abstract = {Metagenomics offers the possibility to screen for versatile biocatalysts. In this study, the microbial community of the Sorghum bicolor rhizosphere was spiked with technical cashew nut shell liquid, and after incubation, the environmental DNA (eDNA) was extracted and subsequently used to build a metagenomic library. We report the biochemical features and crystal structure of a novel esterase from the family IV, EH0, retrieved from an uncultured sphingomonad after a functional screen in tributyrin agar plates. EH0 (optimum temperature [Topt], 50°C; melting temperature [Tm], 55.7°C; optimum pH [pHopt], 9.5) was stable in the presence of 10 to 20% (vol/vol) organic solvents and exhibited hydrolytic activity against p-nitrophenyl esters from acetate to palmitate, preferably butyrate (496 U mg[-1]), and a large battery of 69 structurally different esters (up to 30.2 U mg[-1]), including bis(2-hydroxyethyl)-terephthalate (0.16 ± 0.06 U mg[-1]). This broad substrate specificity contrasts with the fact that EH0 showed a long and narrow catalytic tunnel, whose access appears to be hindered by a tight folding of its cap domain. We propose that this cap domain is a highly flexible structure whose opening is mediated by unique structural elements, one of which is the presence of two contiguous proline residues likely acting as possible hinges, which together allow for the entrance of the substrates. Therefore, this work provides a new role for the cap domain, which until now was thought to be an immobile element that contained hydrophobic patches involved in substrate prerecognition and in turn substrate specificity within family IV esterases. IMPORTANCE A better understanding of structure-function relationships of enzymes allows revelation of key structural motifs or elements. Here, we studied the structural basis of the substrate promiscuity of EH0, a family IV esterase, isolated from a sample of the Sorghum bicolor rhizosphere microbiome exposed to technical cashew nut shell liquid. The analysis of EH0 revealed the potential of the sorghum rhizosphere microbiome as a source of enzymes with interesting properties, such as pH and solvent tolerance and remarkably broad substrate promiscuity. Its structure resembled those of homologous proteins from mesophilic Parvibaculum and Erythrobacter spp. and hyperthermophilic Pyrobaculum and Sulfolobus spp. and had a very narrow, single-entry access tunnel to the active site, with access controlled by a capping domain that includes a number of nonconserved proline residues. These structural markers, distinct from those of other substrate-promiscuous esterases, can help in tuning substrate profiles beyond tunnel and active site engineering.}, } @article {pmid36602206, year = {2022}, author = {John, DV and Aryalakshmi, B and Deora, H and Purushottam, M and Raju, R and Mahadevan, A and Rao, MB and Patil, SA}, title = {Identification of microbial agents in culture-negative brain abscess samples by 16S/18S rRNA gene PCR and sequencing.}, journal = {Tropical biomedicine}, volume = {39}, number = {4}, pages = {489-498}, doi = {10.47665/tb.39.4.002}, pmid = {36602206}, issn = {2521-9855}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; Genes, rRNA ; Bacteria/genetics ; Polymerase Chain Reaction/methods ; Streptococcus/genetics ; *Acanthamoeba ; *Brain Abscess/diagnosis/genetics/microbiology ; DNA, Bacterial/genetics ; }, abstract = {Despite clinical suspicion of an infection, brain abscess samples are often culture-negative in routine microbiological testing. Direct PCR of such samples enables the identification of microbes that may be fastidious, non-viable, or unculturable. Brain abscess samples (n = 217) from neurosurgical patients were subjected to broad range 16S rRNA gene PCR and sequencing for bacteria. All these samples and seven formalin-fixed paraffin-embedded tissue (FFPE) samples were subjected to species-specific 18S rRNA PCR for neurotropic free-living amoeba that harbour pathogenic bacteria. The concordance between smear and/or culture and PCR was 69%. One-third of the samples were smear- and culture-negative for bacterial agents. However, 88% of these culture-negative samples showed the presence of bacterial 16S rRNA by PCR. Sanger sequencing of 27 selected samples showed anaerobic/fastidious gram negative bacteria (GNB, 38%), facultative Streptococci (35%), and aerobic GNB (27%). Targeted metagenomics sequencing of three samples showed multiple bacterial species, including anaerobic and non-culturable bacteria. One FFPE tissue revealed the presence of Acanthamoeba 18S rRNA. None of the frozen brain abscess samples tested was positive for 18S rRNA of Acanthamoeba or Balamuthia mandrillaris. The microbial 16/18S rRNA PCR and sequencing outperformed culture in detecting anaerobes, facultative Streptococci and FLA in brain abscess samples. Genetic analyses of 16S/18S sequences, either through Sanger or metagenomic sequencing, will be an essential diagnostic technology to be included for diagnosing culture-negative brain abscess samples. Characterizing the microbiome of culture-negative brain abscess samples by molecular methods could enable detection and/or treatment of the source of infection.}, } @article {pmid36601307, year = {2022}, author = {Wang, C and Yan, D and Huang, J and Yang, N and Shi, J and Pan, S and Lin, G and Liu, Y and Zhang, Y and Bian, X and Song, Q and Qian, G}, title = {The clinical application of metagenomic next-generation sequencing in infectious diseases at a tertiary hospital in China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {957073}, pmid = {36601307}, issn = {2235-2988}, mesh = {Humans ; Tertiary Care Centers ; China ; *High-Throughput Nucleotide Sequencing ; Bronchoalveolar Lavage Fluid ; *Exudates and Transudates ; Metagenomics ; Nontuberculous Mycobacteria ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Compared with traditional diagnostic methods (TDMs), rapid diagnostic methods for infectious diseases (IDs) are urgently needed. Metagenomic next-generation sequencing (mNGS) has emerged as a promising diagnostic technology for clinical infections.

METHODS: This retrospective observational study was performed at a tertiary hospital in China between May 2019 and August 2022. The chi-square test was used to compare the sensitivity and specificity of mNGS and TDMs. We also performed a subgroup analysis of the different pathogens and samples.

RESULTS: A total of 435 patients with clinical suspicion of infection were enrolled and 372 (85.5%) patients were finally categorized as the ID group. The overall sensitivity of mNGS was significantly higher than that of the TDMs (59.7% vs. 30.1%, P < 0.05). However, there was no significant difference in the overall specificity between the two methods (83.3% vs. 89.6%, P = 0.37). In patients with identified pathogens, the positive rates of mNGS for detecting bacteria (88.7%), fungi (87.9%), viruses (96.9%), and Nontuberculous mycobacteria (NTM; 100%) were significantly higher than those of TDMs (P < 0.05). The positive rate of mNGS for detecting Mycobacterium tuberculosis was not superior to that of TDMs (77.3% vs. 54.5%, P = 0.11). The sensitivity rates of mNGS for pathogen identification in bronchoalveolar lavage fluid, blood, cerebrospinal fluid, pleural fluid, and tissue were 72.6%, 39.3%, 37.5%, 35.0% and 80.0%, respectively.

CONCLUSION: With the potential for screening multiple clinical samples, mNGS has an overall advantage over TDMs. It can effectively identify pathogens, especially those that are difficult to identify using TDMs, such as NTM, chlamydia, and parasites.}, } @article {pmid36600954, year = {2022}, author = {Xu, Y and Wang, Y and Wu, J and Zhao, X and Huang, G and Fang, J}, title = {Coinfection with Hypervirulent Klebsiella pneumoniae and Aspergillus flavus in a Critically Ill Patient with Aspergillus Overlap Syndrome: A Case Report.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {7823-7830}, pmid = {36600954}, issn = {1178-6973}, abstract = {Pulmonary aspergillosis is generally categorized into three groups: allergic bronchopulmonary aspergillosis, chronic pulmonary aspergillosis and invasive pulmonary aspergillosis. Aspergillus overlap syndromes (AOS) defined as the occurrence of more than one form of aspergillus disease in a single individual is not common. We present a 62-year-old-male patient with tachypnea, hypoxemia and shock after 4 weeks of cough, expectoration and intermittent hemoptysis, and 2 days of hyperpyrexia. Cardiac arrest occurring during tracheal intubation was resuscitated successfully. Laboratory examination showed acute kidney failure and severe myelosuppression with leukopenia and thrombocytopenia. Chest computed tomography (CT) scan showed the cavity with aspergilloma in the right upper lung lobe, a mass of consolidation in the right lower lung lobe and hyperdense shadow bronchiectasis in the left lower lobe. Bronchoscopy showed lots of sputum occluding the opening of the right airway bronchus. Laboratory examination showed significantly increased C-reactive protein (CRP) and procalcitonin concentration, serum (1,3)-β-D-glucan (BDG) and aspergillus immunoglobulin G (IgG) levels were also elevated. The metagenomic next-generation sequencing and sputum cultures revealed Klebsiella pneumoniae and Aspergillus flavus infection. Pulmonary aspergillosis, invasive aspergillosis infection and severe pneumonia were diagnosed. Initial caspofungin and meropenem followed by piperacillin-tazobactam sodium and voriconazole were administrated in combination. Continuous renal replacement therapy and mechanical ventilation were also performed. The patient's condition gradually recovered. Oral antifungal therapy was continued for 1 year after discharge and CT images gradually improved. Coinfections with K. pneumoniae and A. flavus in a patient with AOS will complicate clinical conditions. A search of PubMed showed few reports of similar cases. Clinicians should pay enough attention to the polymicrobial interactions and improve clinical management strategies, especially in critically ill patient with AOS.}, } @article {pmid36600937, year = {2022}, author = {Wang, J and Zhu, Y and Mo, Q and Yang, Y}, title = {Case Report: A Chlamydia psittaci pulmonary infection presenting with migratory infiltrates.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {1028989}, pmid = {36600937}, issn = {2296-2565}, mesh = {Humans ; Male ; Middle Aged ; *Chlamydophila psittaci ; High-Throughput Nucleotide Sequencing ; Lung ; *Pneumonia ; *Psittacosis/diagnosis ; }, abstract = {Community-acquired pneumonia is a public health problem in all countries in the world, with a broad range of causative agents and Chlamydia psittaci infection tends to be overlooked. Pulmonary migratory infiltrates are commonly seen in eosinophilic pneumonia, cryptogenic organizing pneumonia, etc. However, the association of Chlamydia psittaci and pulmonary migratory infiltrates has been seldom described in literatures before. We reviewed a 64-year-old man referred to our hospital for treatment against Chlamydia psittaci pneumonia which was diagnosed by metagenomics next generation sequencing (mNGS). During the treatment period, chest imaging showed migratory infiltrates, which has been rarely described before.}, } @article {pmid36599469, year = {2023}, author = {Perry, LM and Cruz, SM and Kleber, KT and Judge, SJ and Darrow, MA and Jones, LB and Basmaci, UN and Joshi, N and Settles, ML and Durbin-Johnson, BP and Gingrich, AA and Monjazeb, AM and Carr-Ascher, J and Thorpe, SW and Murphy, WJ and Eisen, JA and Canter, RJ}, title = {Human soft tissue sarcomas harbor an intratumoral viral microbiome which is linked with natural killer cell infiltrate and prognosis.}, journal = {Journal for immunotherapy of cancer}, volume = {11}, number = {1}, pages = {}, pmid = {36599469}, issn = {2051-1426}, support = {P30 CA093373/CA/NCI NIH HHS/United States ; S10 OD018223/OD/NIH HHS/United States ; S10 RR026825/RR/NCRR NIH HHS/United States ; T32 CA251007/CA/NCI NIH HHS/United States ; S10 OD010786/OD/NIH HHS/United States ; }, mesh = {Adult ; Humans ; Virome ; *Sarcoma/genetics ; Prognosis ; Extremities/pathology ; Killer Cells, Natural ; *Soft Tissue Neoplasms ; Tumor Microenvironment ; }, abstract = {BACKGROUND: Groundbreaking studies have linked the gut microbiome with immune homeostasis and antitumor immune responses. Mounting evidence has also demonstrated an intratumoral microbiome, including in soft tissue sarcomas (STS), although detailed characterization of the STS intratumoral microbiome is limited. We sought to characterize the intratumoral microbiome in patients with STS undergoing preoperative radiotherapy and surgery, hypothesizing the presence of a distinct intratumoral microbiome with potentially clinically significant microbial signatures.

METHODS: We prospectively obtained tumor and stool samples from adult patients with non-metastatic STS using a strict sterile collection protocol to minimize contamination. Metagenomic classification was used to estimate abundance using genus and species taxonomic levels across all classified organisms, and data were analyzed with respect to clinicopathologic factors.

RESULTS: Fifteen patients were enrolled. Most tumors were located at an extremity (67%) and were histologic grade 3 (87%). 40% were well-differentiated/dedifferentiated liposarcoma histology. With a median follow-up of 24 months, 4 (27%) patients developed metastases, and 3 (20%) died. Despite overwhelming human DNA (>99%) intratumorally, we detected a small but consistent proportion of bacterial DNA (0.02-0.03%) in all tumors, including Proteobacteria, Bacteroidetes, and Firmicutes, as well as viral species. In the tumor microenvironment, we observed a strong positive correlation between viral relative abundance and natural killer (NK) infiltration, and higher NK infiltration was associated with superior metastasis-free and overall survival by immunohistochemical, flow cytometry, and multiplex immunofluorescence analyses.

CONCLUSIONS: We prospectively demonstrate the presence of a distinct and measurable intratumoral microbiome in patients with STS at multiple time points. Our data suggest that the STS tumor microbiome has prognostic significance with viral relative abundance associated with NK infiltration and oncologic outcome. Additional studies are warranted to further assess the clinical impact of these findings.}, } @article {pmid36599128, year = {2023}, author = {Wang, H and Yang, Q and Li, D and Wu, J and Yang, S and Deng, Y and Luo, C and Jia, W and Zhong, Y and Peng, P}, title = {Stable Isotopic and Metagenomic Analyses Reveal Microbial-Mediated Effects of Microplastics on Sulfur Cycling in Coastal Sediments.}, journal = {Environmental science & technology}, volume = {57}, number = {2}, pages = {1167-1176}, doi = {10.1021/acs.est.2c06546}, pmid = {36599128}, issn = {1520-5851}, mesh = {Sulfur Isotopes/analysis ; *Microplastics ; *Plastics ; Sulfur ; Isotopes/analysis ; Polyesters ; Sulfates/analysis ; Geologic Sediments/analysis ; }, abstract = {Microplastics are readily accumulated in coastal sediments, where active sulfur (S) cycling takes place. However, the effects of microplastics on S cycling in coastal sediments and their underlying mechanisms remain poorly understood. In this study, the transformation patterns of different S species in mangrove sediments amended with different microplastics and their associated microbial communities were investigated using stable isotopic analysis and metagenomic sequencing. Biodegradable poly(lactic acid) (PLA) microplastics treatment increased sulfate (SO4[2-]) reduction to yield more acid-volatile S and elementary S, which were subsequently transformed to chromium-reducible S (CRS). The S isotope fractionation between SO4[2-] and CRS in PLA treatment increased by 9.1‰ from days 0 to 20, which was greater than 6.8‰ in the control. In contrast, recalcitrant petroleum-based poly(ethylene terephthalate) (PET) and polyvinyl chloride (PVC) microplastics had less impact on the sulfate reduction, resulting in 7.6 and 7.7‰ of S isotope fractionation between SO4[2-] and CRS from days 0 to 20, respectively. The pronounced S isotope fractionation in PLA treatment was associated with increased relative abundance of Desulfovibrio-related sulfate-reducing bacteria, which contributed a large proportion of the microbial genes responsible for dissimilatory sulfate reduction. Overall, these findings provide insights into the potential impacts of microplastics exposure on the biogeochemical S cycle in coastal sediments.}, } @article {pmid36598610, year = {2023}, author = {da Silva, LA and Basso, MF and Ribeiro, BM}, title = {A novel picorna-like virus identified in the cotton boll weevil Anthonomus grandis (Coleoptera: Curculionidae).}, journal = {Archives of virology}, volume = {168}, number = {1}, pages = {29}, pmid = {36598610}, issn = {1432-8798}, support = {193.001532/2016//Fundação de Apoio à Pesquisa do Distrito Federal/ ; 305756/2017-6//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Animals ; *Coleoptera ; *Weevils ; Phylogeny ; *Viruses/genetics ; Nucleotides ; RNA ; Gossypium ; }, abstract = {The cotton boll weevil (CBW; Anthonomus grandis; Coleoptera: Curculionidae) is considered the major insect pest of cotton, causing considerable losses in yield and fiber quality. An increase in the boll weevil population due to increasingly inefficient chemical control measures is of great concernamong cotton producers. The absence of conventional or transgenic cultivars with minimal resistance to CBW has stimulated the search for new molecular and biological tools for efficient control of this insect pest. In this study, we used a metagenomic approach based on RNA deep sequencing to investigate the presence of viruses and coding viral RNA in apparently healthy native adult CBW insects collected from cotton crops in Mato Grosso state, Brazil. Using an Illumina HiSeq 2000 paired-end platform, 138,798 virus-related reads were obtained, and a consensus sequence of a putative new virus, 10,632 nucleotides in length, was assembled. The sequences of the 5' and 3' untranslated regions (UTRs) were determined by rapid amplification of cDNA ends (RACE), followed by Nanopore sequencing. The complete genome sequence included a 5'-UTR (1,158 nucleotides), a 3'-UTR (561 nucleotides), and a single ORF of 8,913 nucleotides encoding a large polyprotein. Sequence analysis of the putative polyprotein showed several regions with high sequence similarity to structural and non-structural proteins of viruses of the family Iflaviridae. Pairwise alignments of polyprotein amino acid sequences showed the highest sequence identity (32.13%) to a partial polyprotein sequence of a putative iflavirus (QKN89051.1) found in samples from wild zoo birds in China. Phylogenetic analysis based on full polyprotein sequences of different iflaviruses indicated that this new picorna-like virus is most closely related to iflaviruses found in lepidopteran insects, and it was therefore tentatively named "Anthonomus grandis iflavirus 1" (AgIV-1). This is, to our knowledge, the first complete viral genome sequence found in CBW, and it could provide a basis for further studies about the infectivity and transmission of this virus and its possible association with symptoms or acute disease. AgIV-1 could potentially be used to develop biological or molecular tools, such as a viral vector to carry interfering RNA molecules for CBW control.}, } @article {pmid36598276, year = {2023}, author = {O'Toole, P and Daly, RA and Keshavarz Afshar, R and Shaffer, M and Wrighton, KC and McGivern, BB}, title = {Draft Metagenome-Assembled Genome Sequence of a Novel Citricoccus Species from Agricultural Soil in Western Colorado.}, journal = {Microbiology resource announcements}, volume = {12}, number = {1}, pages = {e0035922}, pmid = {36598276}, issn = {2576-098X}, support = {1912915//National Science Foundation (NSF)/ ; }, abstract = {Members of the genus Citricoccus are recognized as salt-tolerant soil microorganisms. Here, we report the metagenome-assembled genome sequence of a novel Citricoccus species recovered from untilled, surface agricultural soils in western Colorado.}, } @article {pmid36598253, year = {2023}, author = {Newman, MR and Sanchez, D and Acosta, AM and Connors, BJ}, title = {Taxonomic Profiling of Microbes in Glyphosate-Treated Sediment Microcosms.}, journal = {Microbiology resource announcements}, volume = {12}, number = {1}, pages = {e0118322}, pmid = {36598253}, issn = {2576-098X}, support = {1950018//National Science Foundation (NSF)/ ; }, abstract = {Here, we report the impact of glyphosate on bacterial populations in sediment microcosms, determined using 16S amplicon sequencing and shotgun metagenomics with source material from a suburban creek. The 16S amplicon and metagenomic data reveal that members of the genus Pseudomonas are increased by the treatment.}, } @article {pmid36598237, year = {2023}, author = {Joel, EB and Lenka, JL and Yakubu, B and Kutshik, RJ and Tukur, A and Longdet, IY}, title = {Metagenome-Assembled Genome Sequence of Stenotrophomonas maltophilia Strain UJ_SKK_5.5, Obtained from the Gut Microbiome of a Macrotermes bellicosus Termite Collected from Hot, Arid Nigeria.}, journal = {Microbiology resource announcements}, volume = {12}, number = {1}, pages = {e0106022}, pmid = {36598237}, issn = {2576-098X}, support = {TETFund/DR&D/CE/ NRF/STI/21/VOL1//Tertiary Education Trust Fund (TETFund)/ ; TETFund/DR&D/CE/ NRF/STI/21/VOL1//Tertiary Education Trust Fund (TETFund)/ ; }, abstract = {The metagenome-assembled genome (MAG) sequence of Stenotrophomonas maltophilia strain UJ_SKK_5.5 was obtained from the gut microbiome of Macrotermes bellicosus (termite) from hot, arid Nigeria. The assembled genome (4,313,335 bp) contains 157 contigs, the N50 is 41,072 bp, the GC content is 66.57%, and there are 3,925 protein coding sequences, 3,886 proteins with functional assignments, 39 pseudogenes, and 67 RNA genes.}, } @article {pmid36598235, year = {2023}, author = {Lenka, JL and Yakubu, B and Kutshik, RJ and Joel, EB and Tukur, A and Longdet, IY}, title = {Metagenome-Assembled Genome Sequence of a Strain of Burkholderia cepacia Isolated from the Gut of Macrotermes bellicosus in Nigeria.}, journal = {Microbiology resource announcements}, volume = {12}, number = {1}, pages = {e0077722}, pmid = {36598235}, issn = {2576-098X}, support = {TETFUND/DR&D/CE/NRF/STI/21/VOL1//Tertiary Education Trust Fund (TETFund)/ ; TETFUND/DR&D/CE/NRF/STI/21/VOL1//Tertiary Education Trust Fund (TETFund)/ ; }, abstract = {The efficiency of the termite Macrotermes bellicosus at digesting lignocellulose is due to its gut bacterial symbionts. We report the metagenome-assembled genome sequence of Burkholderia cepacia UJ_SKK_1.2, reconstructed from metagenomes produced from Macrotermes bellicosus gut microbiota. The 7,460,271-bp genome obtained consists of 6,763 protein-coding sequences, with 6,719 functionally assigned genes and 59 RNA genes.}, } @article {pmid36597899, year = {2023}, author = {Umair, M and Rehman, Z and Haider, SA and Usman, M and Rana, MS and Ikram, A and Salman, M}, title = {First report of coinfection and whole-genome sequencing of norovirus and sapovirus in an acute gastroenteritis patient from Pakistan.}, journal = {Journal of medical virology}, volume = {95}, number = {2}, pages = {e28458}, doi = {10.1002/jmv.28458}, pmid = {36597899}, issn = {1096-9071}, mesh = {Infant ; Child ; Humans ; Child, Preschool ; *Sapovirus/genetics ; *Norovirus/genetics ; *Coinfection ; Phylogeny ; Pakistan ; *Caliciviridae Infections/epidemiology ; *Gastroenteritis ; *Viruses ; Genotype ; Feces ; }, abstract = {Acute gastroenteritis is one of the most common diseases in infants and children in developing countries including Pakistan. In Pakistan, rotavirus (RVA) is known to contribute significantly to pediatric diarrheal illness, but the contribution of other viruses is still unclear. In the current study we have identified a case of mixed infection of norovirus (NoV) and sapovirus (SaV) in a 2-year-old child with acute gastroenteritis. The sample was initially processed for the detection of group A RVA through ELISA followed by NoV using RT-PCR assay. The sample tested positive for NoV RNA and was later subjected to whole-genome sequencing using meta-genome approach on Miseq (Illumina) platform. Sequencing results revealed GII.15 genotype of NoV that clustered with viruses from China and USA from 2017 to 2021. We also retrieved the complete genome of SaV (GI.1 genotype) from the same sample and phylogenetic analysis showed clustering with strains reported from Japan, South Korea, US, and Taiwan during 2012-2016. This is the first report from Pakistan that confirms coinfection of NoV and SaV and elucidates their whole genomes. We recommend initiation of NoV and SaV surveillance program to ascertain disease burden and explore genetic diversity, especially as RVA vaccines have been included in national immunization program.}, } @article {pmid36597727, year = {2023}, author = {Böttner, L and Malacrinò, A and Schulze Gronover, C and van Deenen, N and Müller, B and Xu, S and Gershenzon, J and Prüfer, D and Huber, M}, title = {Natural rubber reduces herbivory and alters the microbiome below ground.}, journal = {The New phytologist}, volume = {239}, number = {4}, pages = {1475-1489}, doi = {10.1111/nph.18709}, pmid = {36597727}, issn = {1469-8137}, mesh = {Animals ; Rubber/chemistry/metabolism ; Latex/metabolism ; Herbivory ; *Coleoptera ; Larva ; Plants, Genetically Modified/metabolism ; *Taraxacum/genetics ; }, abstract = {Laticifers are hypothesized to mediate both plant-herbivore and plant-microbe interactions. However, there is little evidence for this dual function. We investigated whether the major constituent of natural rubber, cis-1,4-polyisoprene, a phylogenetically widespread and economically important latex polymer, alters plant resistance and the root microbiome of the Russian dandelion (Taraxacum koksaghyz) under attack of a root herbivore, the larva of the May cockchafer (Melolontha melolontha). Rubber-depleted transgenic plants lost more shoot and root biomass upon herbivory than normal rubber content near-isogenic lines. Melolontha melolontha preferred to feed on artificial diet supplemented with rubber-depleted rather than normal rubber content latex. Likewise, adding purified cis-1,4-polyisoprene in ecologically relevant concentrations to diet deterred larval feeding and reduced larval weight gain. Metagenomics and metabarcoding revealed that abolishing biosynthesis of natural rubber alters the structure but not the diversity of the rhizosphere and root microbiota (ecto- and endophytes) and that these changes depended on M. melolontha damage. However, the assumption that rubber reduces microbial colonization or pathogen load is contradicted by four lines of evidence. Taken together, our data demonstrate that natural rubber biosynthesis reduces herbivory and alters the plant microbiota, which highlights the role of plant-specialized metabolites and secretory structures in shaping multitrophic interactions.}, } @article {pmid36597454, year = {2022}, author = {Li, X and Zhuang, S and He, L and Wang, S and Zhao, M and Lyu, X}, title = {Brain Abscess Caused by Nocardia brevicatena in an Immunocompetent Patient: A Case Report.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {7693-7697}, pmid = {36597454}, issn = {1178-6973}, abstract = {Nocardia brain abscess is relatively rare and generally occurs in immunodeficient patients. Here, we present the first case of brain abscess due to Nocardia brevicatena in an immunocompetent patient, with unknown origin. In this case, a 49-year-old man was admitted to our hospital with limb twitching and complained of a history of intermittent headache. He was diagnosed with brain abscess through brain imaging and cured after craniotomy for abscess excision and targeted antibiotic treatment. Surgical specimens were sent for further detection. The causative organism was identified by weak acid-fast staining, culture and metagenomic next-generation sequencing (mNGS). We hope this case could provide a reference for incoming patients as well as their clinical management.}, } @article {pmid36596569, year = {2023}, author = {Pérot, P and Fourgeaud, J and Rouzaud, C and Regnault, B and Da Rocha, N and Fontaine, H and Le Pavec, J and Dolidon, S and Garzaro, M and Chrétien, D and Morcrette, G and Molina, TJ and Ferroni, A and Leruez-Ville, M and Lortholary, O and Jamet, A and Eloit, M}, title = {Circovirus Hepatitis Infection in Heart-Lung Transplant Patient, France.}, journal = {Emerging infectious diseases}, volume = {29}, number = {2}, pages = {286-293}, pmid = {36596569}, issn = {1080-6059}, mesh = {Female ; Humans ; Middle Aged ; *Circovirus/genetics ; *Heart-Lung Transplantation ; Genome, Viral ; *Hepatitis ; *Hepatitis A ; }, abstract = {In March 2022, a 61-year-old woman in France who had received a heart-lung transplant sought treatment with chronic hepatitis mainly characterized by increased liver enzymes. After ruling out common etiologies, we used metagenomic next-generation sequencing to analyze a liver biopsy sample and identified an unknown species of circovirus, tentatively named human circovirus 1 (HCirV-1). We found no other viral or bacterial sequences. HCirV-1 shared 70% amino acid identity with the closest known viral sequences. The viral genome was undetectable in blood samples from 2017-2019, then became detectable at low levels in September 2020 and peaked at very high titers (10[10] genome copies/mL) in January 2022. In March 2022, we found >10[8] genome copies/g or mL in the liver and blood, concomitant with hepatic cytolysis. We detected HCirV-1 transcripts in 2% of hepatocytes, demonstrating viral replication and supporting the role of HCirV-1 in liver damage.}, } @article {pmid36596171, year = {2023}, author = {Duarte-Coimbra, S and Forcina, G and Pérez-Pardal, L and Beja-Pereira, A}, title = {Characterization of tongue dorsum microbiome in wine tasters.}, journal = {Food research international (Ottawa, Ont.)}, volume = {163}, number = {}, pages = {112259}, doi = {10.1016/j.foodres.2022.112259}, pmid = {36596171}, issn = {1873-7145}, mesh = {*Wine/analysis ; RNA, Ribosomal, 16S/genetics ; Taste ; Tongue ; *Microbiota/genetics ; }, abstract = {Taste plays a paramount role in food and beverage choice, with recent studies pointing to a potential influence of the microorganisms from the tongue dorsum - particularly bacteria - on flavor perception. Thus, the association between tongue dorsum biofilm and taste is a fundamental prerequisite for a better understanding of the role played by these bacteria in wine tasting. To study this impact, we have analyzed the microbiomes from 58 samples of the tongue dorsum surface from professional wine tasters and 30 samples from non professional wine tasters. The microbiome of each sample was characterized through metagenome sequencing of the 16S rRNA gene for taxonomic discrimination of bacteria. A total of 497 taxa were identified in the tongue dorsum, and significant differences in diversity were observed between the wine taster and the control group. The comparison of bacterial diversity between samples collected before and after wine tasting along with the presence of new bacterial taxa indicates a direct effect of wine on the microbiome of frequent wine tasters, particularly in those tasting sparkling wines.}, } @article {pmid36596167, year = {2023}, author = {Zhang, C and Zhang, J and Xin, X and Niu, H and Liao, X and Liu, D}, title = {Reduced formation of biogenic amines in low-salt Zhacai via fermentation under CO2-modified atmosphere.}, journal = {Food research international (Ottawa, Ont.)}, volume = {163}, number = {}, pages = {112256}, doi = {10.1016/j.foodres.2022.112256}, pmid = {36596167}, issn = {1873-7145}, mesh = {Fermentation ; *Carbon Dioxide ; *Amino Acids/metabolism ; Biogenic Amines/analysis ; Vegetables/metabolism ; Atmosphere ; }, abstract = {Reducing sodium salt content in traditional fermented vegetables and developing low-salt fermented products have attracted increasing attention.However, low-salt fermented vegetables are prone to accumulate toxic biogenic amines (BAs) caused by the undesirable metabolism of spoilage microorganisms. This study aimed to investigate the impact of a CO2-modified atmosphere (MA) approach to the fermentation of low-salt Zhacai and the accumulation of BAs. The results show CO2-MA effectively suppressed the production of excessive BAs in low-salt Zhacai, as evidenced by a decrease in the total BA content from 63.66 to 161.41 mg/ kg under natural air conditions to 1.88-24.76 mg/ kg under CO2-MA. Overall, the mechanism of hindering BA formation was closely related to the change in the microbial community and the downregulation of BA-producing enzymes. Lactic acid bacteria, including Lactiplantibacillus plantarum, Weissella spp., and Pediococcus spp., were enriched under CO2-MA, whereas amine-producing microorganisms (e.g., Halomonas spp., Psychrobacter spp., Corynebacterium spp., and Levilactobacillus brevis) were greatly inhibited. Moreover, metagenomic analysis revealed that genes encoding amino acid decarboxylase, amine deiminase, and amine synthase were downregulated, which could be the fundamental reason for BA reduction. This study provides an alternative method for reducing BA production in fermented food.}, } @article {pmid36596124, year = {2023}, author = {Zhu, Q and Chen, L and Peng, Z and Zhang, Q and Huang, W and Yang, F and Du, G and Zhang, J and Wang, L}, title = {The differences in carbohydrate utilization ability between six rounds of Sauce-flavor Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {163}, number = {}, pages = {112184}, doi = {10.1016/j.foodres.2022.112184}, pmid = {36596124}, issn = {1873-7145}, mesh = {*Alcoholic Beverages/analysis ; *Bacteria ; Carbohydrates ; Starch ; }, abstract = {Sauce-flavor Daqu is an important source of fermentation power in baijiu brewing. Revealing carbohydrate metabolism will help to explore the underlying reasons for the difference in fermentation performance of Daqu. In this study, metagenomic and metaproteomic technologies were performed to explore the carbohydrate metabolism network and its active functional microorganisms of Sauce-flavor Daqu. The sugar profile was analyzed using LC-MS to confirm the metabolic network. The results showed that 23 fungi and 5 bacteria were involved in carbohydrate metabolism. Starch metabolism, cellulose metabolism, and glucan metabolism were the main metabolic pathways, in which fungi especially Aspergillus were more involved than bacteria. Among these active microorganisms, Saccharomycopsis fibuligera, Aspergillus oryzae, Monascus purpureus, Byssochlamys spectabilis, Lichtheimia ramosa, Thermomyces lanuginosus, and Thermoascus aurantiacus were significant functional microorganisms with the ability to produce multiple enzymes. Lichtheimia ramosa, Lichtheimia corymbifera and Kroppenstedtia eburnea were biomarkers of Daqu in the first round, granting it a better liquefaction ability. β-amylase derived from wheat also played an important role in starch degradation, and the synergistic effect with α-amylase endowed Daqu with higher liquefaction power in the first two rounds. The results of this study are of great significance for the analysis of the mechanism of Daqu fermentation and provide a reliable theoretical basis for strengthening the fermentation performance of Daqu.}, } @article {pmid36596030, year = {2022}, author = {Zhao, Y and Deng, W and Teng, J and Xu, Y and Pan, P and Jin, D}, title = {Risk factors for 90-day all-cause mortality in post-operative central nervous system infections (PCNSIs): A retrospective study of 99 patients in China.}, journal = {Medicine}, volume = {101}, number = {52}, pages = {e32418}, pmid = {36596030}, issn = {1536-5964}, mesh = {Humans ; Middle Aged ; Retrospective Studies ; *Bacteria ; *Central Nervous System Infections/cerebrospinal fluid ; Risk Factors ; China/epidemiology ; High-Throughput Nucleotide Sequencing ; Sensitivity and Specificity ; }, abstract = {Post-operative central nervous system infections (PCNSIs) are serious complications of craniotomy. Many factors, including patient-related, surgical, and postoperative factors, affect the survival of patients with PCNSIs. Timely and effective implementation of antibiotics targeting pathogenic bacteria is crucial to reduce mortality. Metagenomic next-generation sequencing (mNGS) has been used successfully to detect pathogens associated with infectious diseases. This study was designed to evaluate the factors influencing mortality and to explore the application value of mNGS in patients with PCNSIs. We conducted a retrospective study of patients with PCNSIs in our unit from 1/12/2019 to 28/2/2021. Clinical data, cerebrospinal fluid (CSF) parameters, surgical information, and mNGS results were collected. Follow-up telephone calls were made in June 2021 for 90 days survival after discharge. 99 patients were enrolled, and the overall mortality rate was 36.4% (36/99). Kaplan-Meier survival analysis suggested that the risk factors for poor prognosis included age ≥ 53 years, Glasgow Coma scale (GCS) score ≤ 8, CSF/blood glucose ratio (C/B-Glu) ≤ 0.23, 2 or more operations, mechanical ventilation (MV), and non-mNGS test. MV and poor wound healing were independent risk factors for 90 day mortality according to the multivariate Cox proportional hazards model (OR = 6.136, P = .017, OR = 2.260, P = .035, respectively). Among the enrolled patients, causative pathogens were identified in 37. Gram-negative pathogens were found in 22 (59.5%) patients, and the remaining 15 (40.5%) were Gram-positive pathogens. Univariate analysis showed that white cell count and protein and lactate levels in the CSF of the Gram-negative group were higher than those of the Gram-positive group (P < .05). mNGS and conventional microbiological culture were tested in 34 patients, and the positive detection rate of mNGS was 52.9%, which was significantly higher than that of microbiological culture (52.9% vs 26.5%, χ2 = 4.54, P = .033). The mortality rate of PCNSIs is high, and patients with MV and poor wound healing have a higher mortality risk. Gram-negative pathogens were the predominant pathogens in the patients with PCNSIs. mNGS testing has higher sensitivity and has the potential to reduce the risk of mortality in patients with PCNSIs.}, } @article {pmid36595873, year = {2022}, author = {Yang, Y and Zhu, X and Sun, Y and Qian, K and Liu, Z}, title = {Comparison of next-generation sequencing with traditional methods for pathogen detection in cases of lower respiratory tract infection at a community hospital in Eastern China.}, journal = {Medicine}, volume = {101}, number = {51}, pages = {e32423}, pmid = {36595873}, issn = {1536-5964}, mesh = {Humans ; Staphylococcus aureus ; *Epstein-Barr Virus Infections ; Hospitals, Community ; Herpesvirus 4, Human ; *Respiratory Tract Infections/diagnosis/epidemiology/microbiology ; China/epidemiology ; High-Throughput Nucleotide Sequencing ; }, abstract = {Lower respiratory tract infection (LRTI) is still a threat to human health. Metagenomics next-generation sequencing (NGS) provides an efficient and unbiased way to identify LRTI pathogens, and has been shown to have several advantages over traditional methods. However, its application is currently limited in low-resource settings. Our aim was to collect and analyze data on LRTI cases at a county-level community hospital in Eastern China over one year, in order to compare the efficiency of NGS and traditional methods including culture, nucleic acid amplification and antibody techniques. We performed NGS of bronchoalveolar lavage fluid (BALF) for pathogen identification in 71 patients with LRTI. We compared the detection rates, identified pathogens, and turnaround time of NGS with traditional methods. Pathogens were detected using traditional methods in 19 cases, and the results were compared with those obtained with the NGS technique in 60 cases. The pathogen detection rate of NGS (84.5%) was much higher than that of the traditional methods (26.8%). Moreover, with the traditional methods considered the gold standard, the consistency rate between NGS and traditional methods was 68.4%. For the 19 cases in which the traditional method was used, the main pathogens included invasive Aspergillus (5 cases), Pseudomonas aeruginosa (3 cases), Candida albicans (3 cases), and Staphylococcus aureus (2 cases). Among the 60 cases detected by NGS, the main pathogens included Mycobacterium (12 cases), Streptococcus pneumoniae (5 cases), Klebsiella pneumoniae (3 cases), P. aeruginosa (3 cases), Haemophilus influenzae (3 cases), and S. aureus (3 cases), Aspergillus (9 cases), Pneumocystis jiroveci (5 cases), C. albicans (3 cases), Human Papilloma Virus (9 cases), Epstein-Barr virus (8 cases), and parvovirus (6 cases). In addition, 2 cases of chlamydia and 1 case of mycoplasma infection were detected by NGS. The time taken to perform the NGS tests was significantly shorter than that taken with the traditional method. NGS analysis of bronchoalveolar lavage fluid, in combination with traditional pathogen detection methods, can improve the efficiency of pathogen detection. More attention should be paid to the regional epidemic characteristics of infectious pathogens in LRTI.}, } @article {pmid36595850, year = {2022}, author = {Shui, Y and Wang, H}, title = {Metagenomic next-generation sequencing as an unconventional approach to warn of tumor cells in a patients with non-mucinous pneumonic-type lung adenocarcinoma: Case report.}, journal = {Medicine}, volume = {101}, number = {51}, pages = {e32448}, pmid = {36595850}, issn = {1536-5964}, mesh = {Humans ; Female ; Middle Aged ; Cough ; DNA Copy Number Variations ; Expectorants ; *COVID-19 ; High-Throughput Nucleotide Sequencing ; *Lung Neoplasms/diagnosis/genetics ; *Adenocarcinoma of Lung/genetics ; Anti-Bacterial Agents ; }, abstract = {RATIONALE: Pneumonic-type lung cancer (PTLC) is a special type of lung cancer with cough and expectoration as the main clinical symptoms and inflammatory signals as the main imaging manifestations. PTLC can be easily misdiagnosed as pneumonia, and the diagnosis and treatment are always delayed. Metagenomic next-generation sequencing (mNGS), as an emerging and effective method to identify occult pathogens, has been gradually adopted by clinicians.

PATIENT CONCERNS: A 58-year-old woman with recurrent cough and expectoration was admitted to hospital on January 12th, 2022. She reported that she was diagnosed with pneumonia half a month ago, after treatment with expectorant and antibiotics for 5 days, the symptoms were relieved. However, the symptoms worsened again 10 days after stopping the drugs. On the current presentation, she denied exposure to patients with infection of COVID-19, smoking history, night sweats, weight loss, rash, joint pain, fever, and shortness of breath.

DIAGNOSES: The patient was diagnosed with non-mucinous pneumonic-type lung adenocarcinoma according to the clinical symptoms, changes of CT scans after treatment and cytopathology examinations.

INTERVENTIONS AND OUTCOMES: The patient was initially diagnosed with pulmonary infection according to computerized tomography (CT) scan. Expectorant and antibiotics used. However, the symptoms worsened again 10 days after stopping the drugs. On her return visit, the CT scan did not showed obvious consolidation absorption and was similar to the previous imaging findings. mNGS was performed to detect the occult pathogens. None pathogen was detected, however, 39 copy number variations were found in Human Chromosomal Instability Analysis of mNGS indicating the presence of tumor cells. The cytopathology findings confirmed the presence of lung adenocarcinoma (non-mucinous adenocarcinoma). She was treated with targeted antitumor drugs, and the CT scan after 20 days of targeted antitumor therapy showed obvious absorption of the lesions.

LESSONS: mNGS may have potential value to screen tumor cells in bronchoalveolar lavage fluid of patients with PTLC, especially in the patients whose samples in bronchioli cannot be collected using existing sampling tools.}, } @article {pmid36595694, year = {2023}, author = {Wang, Y and Zhu, D and Ortiz-Velez, LC and Perry, JL and Pennington, MW and Hyser, JM and Britton, RA and Beeton, C}, title = {A bioengineered probiotic for the oral delivery of a peptide Kv1.3 channel blocker to treat rheumatoid arthritis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {2}, pages = {e2211977120}, pmid = {36595694}, issn = {1091-6490}, support = {R21 AI136876/AI/NIAID NIH HHS/United States ; R01 HL132840/HL/NHLBI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; U54 HG006348/HG/NHGRI NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; UM1 HG006348/HG/NHGRI NIH HHS/United States ; }, mesh = {Rats ; Humans ; Animals ; Kv1.3 Potassium Channel/genetics/metabolism ; Peptides/metabolism ; *Arthritis, Rheumatoid/drug therapy ; Inflammation/drug therapy ; *Probiotics/therapeutic use ; Potassium Channel Blockers/pharmacology/therapeutic use ; }, abstract = {Engineered microbes for the delivery of biologics are a promising avenue for the treatment of various conditions such as chronic inflammatory disorders and metabolic disease. In this study, we developed a genetically engineered probiotic delivery system that delivers a peptide to the intestinal tract with high efficacy. We constructed an inducible system in the probiotic Lactobacillus reuteri to secrete the Kv1.3 potassium blocker ShK-235 (LrS235). We show that LrS235 culture supernatants block Kv1.3 currents and preferentially inhibit human T effector memory (TEM) lymphocyte proliferation in vitro. A single oral gavage of healthy rats with LrS235 resulted in sufficient functional ShK-235 in the circulation to reduce inflammation in a delayed-type hypersensitivity model of atopic dermatitis mediated by TEM cells. Furthermore, the daily oral gavage of LrS235 dramatically reduced clinical signs of disease and joint inflammation in rats with a model of rheumatoid arthritis without eliciting immunogenicity against ShK-235. This work demonstrates the efficacy of using the probiotic L. reuteri as a novel oral delivery platform for the peptide ShK-235 and provides an efficacious strategy to deliver other biologics with great translational potential.}, } @article {pmid36595687, year = {2023}, author = {He, X}, title = {Culture-based approaches to studying "microbial dark matter".}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {120}, number = {2}, pages = {e2219691120}, pmid = {36595687}, issn = {1091-6490}, support = {R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 DE030943/DE/NIDCR NIH HHS/United States ; }, mesh = {*Bacteria/genetics ; *Metagenomics ; }, } @article {pmid36595290, year = {2023}, author = {Rovira Rubió, J and Megremis, S and Pasioti, M and Lakoumentas, J and Constantinides, B and Xepapadaki, P and Bachert, C and Finotto, S and Jartti, T and Andreakos, E and Stanic, B and Akdis, CA and Akdis, M and Papadopoulos, NG}, title = {Respiratory virome profiles reflect antiviral immune responses.}, journal = {Allergy}, volume = {78}, number = {5}, pages = {1258-1268}, doi = {10.1111/all.15634}, pmid = {36595290}, issn = {1398-9995}, mesh = {Child, Preschool ; Child ; Humans ; *Antiviral Agents ; Virome ; Leukocytes, Mononuclear ; *Asthma ; Interferons ; Immunity ; }, abstract = {BACKGROUND: From early life, respiratory viruses are implicated in the development, exacerbation and persistence of respiratory conditions such as asthma. Complex dynamics between microbial communities and host immune responses shape immune maturation and homeostasis, influencing health outcomes. We evaluated the hypothesis that the respiratory virome is linked to systemic immune responses, using peripheral blood and nasopharyngeal swab samples from preschool-age children in the PreDicta cohort.

METHODS: Peripheral blood mononuclear cells from 51 children (32 asthmatics and 19 healthy controls) participating in the 2-year multinational PreDicta cohort were cultured with bacterial (Bacterial-DNA, LPS) or viral (R848, Poly:IC, RV) stimuli. Supernatants were analysed by Luminex for the presence of 22 relevant cytokines. Virome composition was obtained using untargeted high throughput sequencing of nasopharyngeal samples. The metagenomic data were used for the characterization of virome profiles and the presence of key viral families (Picornaviridae, Anelloviridae, Siphoviridae). These were correlated to cytokine secretion patterns, identified through hierarchical clustering and principal component analysis.

RESULTS: High spontaneous cytokine release was associated with increased presence of Prokaryotic virome profiles and reduced presence of Eukaryotic and Anellovirus profiles. Antibacterial responses did not correlate with specific viral families or virome profile; however, low antiviral responders had more Prokaryotic and less Eukaryotic virome profiles. Anelloviruses and Anellovirus-dominated profiles were equally distributed among immune response clusters. The presence of Picornaviridae and Siphoviridae was associated with low interferon-λ responses. Asthma or allergy did not modify these correlations.

CONCLUSION: Antiviral cytokine responses at a systemic level reflect the upper airway virome composition. Individuals with low innate interferon responses have higher abundance of Picornaviruses (mostly Rhinoviruses) and bacteriophages. Bacteriophages, particularly Siphoviridae, appear to be sensitive sensors of host antimicrobial capacity, while Anelloviruses are not correlated with TLR-induced immune responses.}, } @article {pmid36593662, year = {2022}, author = {Wu, H and Wang, X and Fang, X and Lian, F and Li, M and Liao, J and Dai, D and Tian, J}, title = {Metformin modulates the gut microbiome in a mice model of high-fat diet-induced glycolipid metabolism disorder.}, journal = {BMJ open diabetes research & care}, volume = {10}, number = {6}, pages = {}, pmid = {36593662}, issn = {2052-4897}, mesh = {Male ; Animals ; Mice ; Diet, High-Fat/adverse effects ; *Metformin/pharmacology ; Glycolipids/pharmacology ; *Gastrointestinal Microbiome ; Mice, Inbred C57BL ; Glucose ; Disease Models, Animal ; }, abstract = {INTRODUCTION: Metformin (MET) can regulate glucose and lipid levels, and the gut microbiota may be involved in the control of metabolism. We hypothesized that MET alleviates glucolipid metabolism disorder by modulating gut microbiota and microbial metabolites.

RESEARCH DESIGN AND METHODS: A total of 24 male C57BL/6 J mice were equally divided into three groups (normal control, model control (MC), and MET-treated groups). Model mice were established by feeding a high-fat diet for 6 weeks. The MET-treated group was administered MET solution (2.5 g/100 mL, 250 mg/kg). Fecal samples were collected to characterize the microbiota system using metagenomic shotgun sequencing and gas chromatography-time of flight-mass spectrometry analysis. Phenotypic and biochemical indices were obtained for further correlation analysis.

RESULTS: Compared with the MC group, MET reduced the levels of weight, glucose, areas under the glucose curve in the glucose tolerance test, triglyceride (TG), and total cholesterol (TC). A decreasing abundance of bacteria, including Parabacteroides distasonis, and an increasing abundance of bacteria, including Bacteroides vulgatus, were observed in the MET-treated group. The 2-deoxytetronic acid declined after MET intervention and was positively correlated with species over-represented in the MC group and negatively correlated with species enriched in the MET-treated group. Additionally, species enriched in the MET-treated group negatively correlated with glucose, areas under the glucose curve in the glucose tolerance test, and TGs. Further, the correlation between the differential metabolites, which decreased after MET intervention, and the phenotypic indices was positive.

CONCLUSIONS: MET-induced restoration of intestinal homeostasis correlates with the amelioration of host glucolipid metabolism.}, } @article {pmid36593361, year = {2023}, author = {Kraberger, S and Serieys, LEK and Riley, SPD and Schmidlin, K and Newkirk, ES and Squires, JR and Buck, CB and Varsani, A}, title = {Novel polyomaviruses identified in fecal samples from four carnivore species.}, journal = {Archives of virology}, volume = {168}, number = {1}, pages = {18}, pmid = {36593361}, issn = {1432-8798}, support = {ZIA BC011090/ImNIH/Intramural NIH HHS/United States ; }, mesh = {Rabbits ; Animals ; Cats ; Humans ; Swine ; *Lynx ; *Polyomavirus/genetics ; *Ursidae ; Phylogeny ; *Deer ; *Puma ; Feces ; }, abstract = {Polyomaviruses are oncogenic viruses that are generally thought to have co-evolved with their hosts. While primate and rodent polyomaviruses are increasingly well-studied, less is known about polyomaviruses that infect other mammals. In an effort to gain insight into polyomaviruses associated with carnivores, we surveyed fecal samples collected in the USA from bobcats (Lynx rufus), pumas (Puma concolor), Canada lynxes (Lynx canadensis), and grizzly bears (Ursus arctos). Using a viral metagenomic approach, we identified six novel polyomavirus genomes. Surprisingly, four of the six genomes showed a phylogenetic relationship to polyomaviruses found in prey animals. These included a putative rabbit polyomavirus from a bobcat fecal sample and two possible deer-trophic polyomaviruses from Canada lynx feces. One polyomavirus found in a grizzly bear sample was found to be phylogenetically distant from previously identified polyomaviruses. Further analysis of the grizzly bear fecal sample showed that it contained anelloviruses that are known to infect pigs, suggesting that the bear might have preyed on a wild or domestic pig. Interestingly, a polyomavirus genome identified in a puma fecal sample was found to be closely related both to raccoon polyomavirus 1 and to Lyon-IARC polyomavirus, the latter of which was originally identified in human saliva and skin swab specimens but has since been found in samples from domestic cats (Felis catus).}, } @article {pmid36593189, year = {2022}, author = {Chen, X and Fang, S and Wan, S and Zhou, W and Sun, C and Li, J}, title = {[Microorganisms capable of degrading neonicotinoids and their metabolic pathways: a review].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {38}, number = {12}, pages = {4462-4497}, doi = {10.13345/j.cjb.220434}, pmid = {36593189}, issn = {1872-2075}, mesh = {Animals ; Neonicotinoids/metabolism ; *Insecticides/analysis/metabolism ; Soil ; Environmental Pollution ; Metabolic Networks and Pathways ; Mammals/metabolism ; }, abstract = {Neonicotinoid compounds are usually considered harmless and eco-friendly in terms of their targeted toxicity compared to that of pyrethroids and phosphorus-containing pesticides. However, overuse of neonicotinoid insecticides resulted in the accumulation of its residuals or intermediates in soil and water, which consequently affected beneficial insects as well as mammals, yielding pollution and secondary risks. This review summarized the recent advances in neonicotinoid degrading microorganisms and their metabolic diversity, with the aim to address the urgent need for degrading these insecticides. These advances may facilitate the development of controllable and reliable technologies for efficiently transforming neonicotinoid insecticides into value-added products by synthetic biology and metagenomics.}, } @article {pmid36592915, year = {2023}, author = {Duan, H and Wang, H and Li, S and Shen, W and Zhuang, Y and Zhang, F and Li, X and Zhai, L and Liu, H and Zhang, L}, title = {Potential to mitigate nitrogen emissions from paddy runoff: A microbiological perspective.}, journal = {The Science of the total environment}, volume = {865}, number = {}, pages = {161306}, doi = {10.1016/j.scitotenv.2022.161306}, pmid = {36592915}, issn = {1879-1026}, mesh = {*Soil ; Nitrogen/analysis ; Ecosystem ; Nitrous Oxide/analysis ; Agriculture/methods ; *Oryza ; China ; Triticum ; Methane/analysis ; Fertilizers/analysis ; }, abstract = {Ditches and ponds are the basic units of agroecosystems that serve irrigation and drainage and also perform the natural ecological function of reducing nitrogen (N) emissions. To better enhance the design and advance management strategies in the paddy field ecosystem to minimize N emission, the N cycling microorganism in the paddy field ecosystem including interconnected fields with rice-wheat rotation, ditches, and ponds in central China was investigated by metagenomic techniques. Our results showed that ditches and ponds may be N removal hotspots by microorganisms in the rice and wheat seasons respectively. Given seasonal variation, the abundance of N-related microorganisms was high during the rice season. However, the Shannon and Simpson indices were lower and the microbial co-occurrence network was destabilized, which could make microbes in the rice season fragile and sensitive. Phytoplankton as key environmental factors affecting the N cycling microbial could promote more stable microbial communities through maintaining a good mutualistic symbiosis. While high algae concentration significantly promotes the abundance of norB than nosZ (P < 0.05), which may result in more N2O production. To trade off N removal and N2O emission, the algae concentration needs to be controlled. Our findings provide a systematic profile of N-related microorganisms in the paddy field ecosystem, and it would benefit in developing effective strategies for limiting N pollution in agriculture.}, } @article {pmid36592686, year = {2023}, author = {Hu, D and Jin, W and Ding, H and Pang, Y and Ma, S and Yang, M and Wu, S and Jiang, M and Pang, L and Luo, S and Ning, Q}, title = {Spirometra mansoni sparganosis identified by metagenomic next-generation sequencing: a case report.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {128}, number = {}, pages = {128-131}, doi = {10.1016/j.ijid.2022.12.038}, pmid = {36592686}, issn = {1878-3511}, mesh = {Male ; Animals ; Humans ; Adult ; *Spirometra/genetics ; *Sparganosis/diagnosis/parasitology/pathology ; Phylogeny ; *Cysticercosis ; High-Throughput Nucleotide Sequencing ; Metagenomics ; }, abstract = {A 30-year-old male patient had a cyst on the left hip and progressive enlargement for more than 2 months. Combined blood tests, magnetic resonance imaging, and pathology findings, cysticercosis infection was suspected. However, the treatment for cysticercosis was ineffective. We conducted a metagenomic next-generation sequencing (mNGS) analysis on the formalin-fixed, paraffin-embedded specimen of the patient's surgically excised tissue, and the results suggested Spirometra mansoni, mNGS was further confirmed by polymerase chain reaction and phylogenetic analysis of cytochrome c oxidase subunit 1 (cox1) gene. Based on these results, we found that mNGS provided a better method of diagnosing parasitic infections.}, } @article {pmid36592375, year = {2023}, author = {White, MFM and Wallace, S}, title = {A New PETase from the Human Saliva Metagenome and Its Functional Modification via Genetic Code Expansion in Bacteria.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {62}, number = {12}, pages = {e202216963}, doi = {10.1002/anie.202216963}, pmid = {36592375}, issn = {1521-3773}, support = {MR/S033882/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Metagenome ; *Saliva/metabolism ; Bacteria/metabolism ; Hydrolases/metabolism ; Plastics ; }, abstract = {The discovery and engineering of new plastic degrading enzymes is an important challenge in chemical biotechnology to enable transition to a more sustainable and circular plastics economy. This field has so far yielded a range of enzymes and microbial pathways for the recycling and valorization of plastic waste. New research from Uttamapinant et al. reports the discovery of a novel polyethylene terephthalate (PET) hydrolase from the human saliva metagenome that displays improved properties and catalytic performance over previously characterized PET hydrolases (PETases). The authors also demonstrate the site-specific incorporation of a photocaged unnatural amino acid, 2,3-diaminopropionic acid (DAP), which upon photodecaging enables covalent binding of DAP to the PET surface. Thus, this work highlights metagenomic datasets as an untapped source of new PET degrading enzymes and the chemical modification of PETases via genetic code expansion, enabling new biotechnologies for the circular plastics economy.}, } @article {pmid36592294, year = {2023}, author = {Fanaei, F and Moussavi, G and Shekoohiyan, S}, title = {Enhanced bioremediation of oil-contaminated soil in a slurry bioreactor by H2O2-stimulation of oil-degrading/biosurfactant-generating bacteria: performance optimization and bacterial metagenomics.}, journal = {Biodegradation}, volume = {34}, number = {1}, pages = {83-101}, pmid = {36592294}, issn = {1572-9729}, mesh = {Biodegradation, Environmental ; Hydrogen Peroxide/analysis ; Metagenomics ; *Soil Pollutants/metabolism ; Soil Microbiology ; *Petroleum ; Soil ; Hydrocarbons/metabolism ; Bioreactors ; Peroxidase ; Peroxidases ; Bacteria/genetics/metabolism ; }, abstract = {Oil-contaminated soil is the main challenge for oil-rich countries, and this study aimed to investigate the performance of the H2O2-stimulated slurry bioreactor for the bioremediation of real oil-contaminated soil. The effect of biomass concentration, soil to water (S/W) ratio, slurry temperature, pH, and H2O2 concentration were optimized for the removal of total petroleum hydrocarbons (TPH) from oil-contaminated soil. TPH removal efficiency, biosurfactants production, and peroxidase and dehydrogenase activities were measured. The optimum conditions for the complete biodegradation of 32 [Formula: see text] in the slurry bioreactor during 6 days were biomass of 2250 mg/L, S/W ratio of 20%, the temperature of 30 °C, pH of 7, and an H2O2 concentration of 120 mg/L. The highest peroxidase, dehydrogenase, surfactin, and rhamnolipid formation were also obtained under optimum conditions. The results pointed out that complete biodegradation of 32 g/kg of TPH in oil-contaminated soil at a short reaction time of 6 days is achievable in the developed process operated under optimum conditions. The GC/FID analysis of solid and liquid phases showed that the bioprocess completely biodegraded the different TPH fractions. H2O2 efficiently stimulated the biosurfactant-generating bacteria to produce peroxidase and thereby accelerating the bioremediation rate. Accordingly, an H2O2-mediated slurry bioreactor inoculated with biosurfactant/peroxidase-generating bacteria is a promising technique for cleaning up oil-contaminated soils.}, } @article {pmid36592056, year = {2023}, author = {Buratin, A and Bortoluzzi, S and Gaffo, E}, title = {Systematic benchmarking of statistical methods to assess differential expression of circular RNAs.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {1}, pages = {}, pmid = {36592056}, issn = {1477-4054}, support = {#20052//Associazione Italiana per la Ricerca sul Cancro/ ; #2017PPS2X4_003//Ministero dell'Istruzione, dell'Università e della Ricerca/ ; }, mesh = {*RNA, Circular ; *Benchmarking/methods ; Sequence Analysis, RNA/methods ; RNA-Seq ; Metagenomics ; RNA/genetics ; }, abstract = {Circular RNAs (circRNAs) are covalently closed transcripts involved in critical regulatory axes, cancer pathways and disease mechanisms. CircRNA expression measured with RNA-seq has particular characteristics that might hamper the performance of standard biostatistical differential expression assessment methods (DEMs). We compared 38 DEM pipelines configured to fit circRNA expression data's statistical properties, including bulk RNA-seq, single-cell RNA-seq (scRNA-seq) and metagenomics DEMs. The DEMs performed poorly on data sets of typical size. Widely used DEMs, such as DESeq2, edgeR and Limma-Voom, gave scarce results, unreliable predictions or even contravened the expected behaviour with some parameter configurations. Limma-Voom achieved the most consistent performance throughout different benchmark data sets and, as well as SAMseq, reasonably balanced false discovery rate (FDR) and recall rate. Interestingly, a few scRNA-seq DEMs obtained results comparable with the best-performing bulk RNA-seq tools. Almost all DEMs' performance improved when increasing the number of replicates. CircRNA expression studies require careful design, choice of DEM and DEM configuration. This analysis can guide scientists in selecting the appropriate tools to investigate circRNA differential expression with RNA-seq experiments.}, } @article {pmid36591907, year = {2023}, author = {Branson, Y and Söltl, S and Buchmann, C and Wei, R and Schaffert, L and Badenhorst, CPS and Reisky, L and Jäger, G and Bornscheuer, UT}, title = {Urethanases for the Enzymatic Hydrolysis of Low Molecular Weight Carbamates and the Recycling of Polyurethanes.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {62}, number = {9}, pages = {e202216220}, doi = {10.1002/anie.202216220}, pmid = {36591907}, issn = {1521-3773}, mesh = {*Polyurethanes/chemistry ; Hydrolysis ; *Carbamates ; Molecular Weight ; Recycling ; Biodegradation, Environmental ; }, abstract = {Enzymatic degradation and recycling can reduce the environmental impact of plastics. Despite decades of research, no enzymes for the efficient hydrolysis of polyurethanes have been reported. Whereas the hydrolysis of the ester bonds in polyester-polyurethanes by cutinases is known, the urethane bonds in polyether-polyurethanes have remained inaccessible to biocatalytic hydrolysis. Here we report the discovery of urethanases from a metagenome library constructed from soil that had been exposed to polyurethane waste for many years. We then demonstrate the use of a urethanase in a chemoenzymatic process for polyurethane foam recycling. The urethanase hydrolyses low molecular weight dicarbamates resulting from chemical glycolysis of polyether-polyurethane foam, making this strategy broadly applicable to diverse polyether-polyurethane wastes.}, } @article {pmid36591383, year = {2023}, author = {Sinha, AK and Parli, BV and Anilkumar, N}, title = {Bacterial distribution in Twilight zone of the Indian sector of Southern Ocean: V3- V4 rDNA hypervariable region data.}, journal = {Data in brief}, volume = {46}, number = {}, pages = {108834}, pmid = {36591383}, issn = {2352-3409}, abstract = {Twilight zones in oceans represent the oceanic waters between 200 m to 1000 m in depth, wherein sunlight is diffused and intensity is <1% of surface value. The activities and diversity of marine micro-organisms in this unique zone are understudied, especially in the Indian Sector of the Southern Ocean. For a better understanding of the microbial environment and diversity in the twilight zone of the Indian sector of Southern Ocean, samples were collected from 200m depth in eddy-influenced waters of Subtropical Front (STF), Sub-Antarctic Front (SAF), Polar Front (PF), waters off Kerguelen (Kw), and Prydz Bay (Pb) waters. In this article, next-generation sequencing (NGS) based amplicon data of 16s rDNA bacterial samples are presented. Hypervariable V3-V4 regions were sequenced using Hiseq platform, and data was processed using Mothur v 1.48.0, and database Silva 138.1nr. Total of nine different phyla is reported from the Southern Ocean at 200m, whereas at order level Synechococcales was found in STF waters only and SAR 11_ Clades were present in all stations.}, } @article {pmid36590589, year = {2022}, author = {Li, S and Qin, J and Zhou, P and Peng, M and Qian, J and Cai, Y and Shi, Q and Tung, TH and Shen, B and Yu, S}, title = {The clinical significance of in-house metagenomic next-generation sequencing for bronchoalveolar lavage fluid diagnostics in patients with lower respiratory tract infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {961746}, pmid = {36590589}, issn = {2235-2988}, mesh = {Humans ; *Clinical Relevance ; Bronchoalveolar Lavage Fluid ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents ; Metagenomics ; *Respiratory Tract Infections/diagnosis ; Sensitivity and Specificity ; }, abstract = {OBJECTIVE: Metagenomic next-generation sequencing (mNGS) technology has the potential to detect a wide range of pathogenic microorganisms. However, reports on the diagnostic value and clinical significance of different platforms of mNGS for patients with lower respiratory tract infections (LRTIs) remain scarce.

METHODS: A total of 306 patients with suspected LRTIs were enrolled from January 2019 to December 2021. The diagnostic performance of conventional methods and mNGS on bronchoalveolar lavage fluid (BALF) were compared. BALF mNGS was performed using a commercial and an in-house laboratory. The diagnostic value and the clinical implications of mNGS for LRTIs were analyzed for the different platforms.

RESULTS: The positive rate of mNGS in the in-house group was higher than that in the commercial group (85.26% vs. 70.67%, p < 0.001). mNGS significantly increased the pathogen detection rate compared with conventional methods [from 70.67% vs. 22.67% (p < 0.001) to 85.26% vs. 30.77% (p < 0.001)]. The pathogens detected using mNGS included bacteria, fungi, viruses, and atypical pathogens. The in-house platform performed well on a wider spectrum of microbial distribution. Furthermore, it showed an advantage in detecting mixed pathogens in immunocompromised patients. Among the mNGS positive cases, 34 (32.0%) cases had their antibiotics adjusted in the commercial group, while 51 (38.3%) cases had a change of treatment in the in-house group. Moreover, the turnaround time of mNGS and the time from mNGS to discharge in the in-house group were significantly shorter than those in the commercial group.

CONCLUSION: In-house mNGS had a higher detection rate and can show a wider spectrum of pathogens, with potential benefits for the clinic by shortening the turnaround time and hospitalization, and it may be more suitable for clinical microbiology laboratories.}, } @article {pmid36590585, year = {2022}, author = {Wang, Y and Chen, J and Wang, X and Guo, C and Peng, X and Liu, Y and Li, T and Du, J}, title = {Novel investigations in retinoic-acid-induced cleft palate about the gut microbiome of pregnant mice.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1042779}, pmid = {36590585}, issn = {2235-2988}, mesh = {Pregnancy ; Female ; Mice ; Animals ; Tretinoin/adverse effects ; *Cleft Palate/chemically induced ; *Gastrointestinal Microbiome ; *Microbiota ; }, abstract = {INTRODUCTION: Cleft palate (CP) is one of the most common congenital birth defects in the craniofacial region, retinoic acid (RA) gavage is the most common method for inducing cleft palate model. Although several mechanisms have been proposed to illuminate RA-induced cleft palate during embryonic development, these findings are far from enough. Many efforts remain to be devoted to studying the etiology and pathogenesis of cleft palate. Recent research is gradually shifting the focus to the effect of retinoic acid on gut microbiota. However, few reports focus on the relationship between the occurrence of CP in embryos and gut microbiota.

METHODS: In our research, we used RA to induce cleft palate model for E10.5 the feces of 5 RA-treated pregnant mice and 5 control pregnant mice were respectively metagenomics analysis.

RESULTS: Compared with the control group, Lactobacillus in the gut microbiome the RA group was significantly increased. GO, KEGG and CAZy analysis of differentially unigenes demonstrated the most abundant metabolic pathway in different groups, lipopolysaccharide biosynthesis, and histidine metabolism.

DISCUSSION: Our findings indicated that changes in the maternal gut microbiome palatal development, which might be related to changes in Lactobacillus and These results provide a new direction in the pathogenesis of CP induced by RA.}, } @article {pmid36590429, year = {2022}, author = {Tiwari, A and Kurittu, P and Al-Mustapha, AI and Heljanko, V and Johansson, V and Thakali, O and Mishra, SK and Lehto, KM and Lipponen, A and Oikarinen, S and Pitkänen, T and , and Heikinheimo, A}, title = {Wastewater surveillance of antibiotic-resistant bacterial pathogens: A systematic review.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {977106}, pmid = {36590429}, issn = {1664-302X}, abstract = {Infectious diseases caused by antibiotic-resistant bacterial (ARB) pathogens are a serious threat to human and animal health. The active surveillance of ARB using an integrated one-health approach can help to reduce the emergence and spread of ARB, reduce the associated economic impact, and guide antimicrobial stewardship programs. Wastewater surveillance (WWS) of ARB provides composite samples for a total population, with easy access to the mixed community microbiome. This concept is emerging rapidly, but the clinical utility, sensitivity, and uniformity of WWS of ARB remain poorly understood especially in relation to clinical evidence in sewershed communities. Here, we systematically searched the literature to identify studies that have compared findings from WWS of ARB and antibiotic resistance genes (ARG) with clinical evidence in parallel, thereby evaluating how likely WWS of ARB and ARG can relate to the clinical cases in communities. Initially, 2,235 articles were obtained using the primary search keywords, and 1,219 articles remained after de-duplication. Among these, 35 articles fulfilled the search criteria, and an additional 13 relevant articles were included by searching references in the primary literature. Among the 48 included papers, 34 studies used a culture-based method, followed by 11 metagenomics, and three PCR-based methods. A total of 28 out of 48 included studies were conducted at the single sewershed level, eight studies involved several countries, seven studies were conducted at national or regional scales, and five at hospital levels. Our review revealed that the performance of WWS of ARB pathogens has been evaluated more frequently for Escherichia coli, Enterococcus spp., and other members of the family Enterobacteriaceae, but has not been uniformly tested for all ARB pathogens. Many wastewater-based ARB studies comparing the findings with clinical evidence were conducted to evaluate the public health risk but not to relate with clinical evidence and to evaluate the performance of WWS of ARB. Indeed, relating WWS of ARB with clinical evidence in a sewershed is not straightforward, as the source of ARB in wastewater cannot be only from symptomatic human individuals but can also be from asymptomatic carriers as well as from animal sources. Further, the varying fates of each bacterial species and ARG within the sewerage make the aim of connecting WWS of ARB with clinical evidence more complicated. Therefore, future studies evaluating the performance of many AMR pathogens and their genes for WWS one by one can make the process simpler and the interpretation of results easier.}, } @article {pmid36590402, year = {2022}, author = {Zhu, Y and Shang, J and Peng, C and Sun, Y}, title = {Phage family classification under Caudoviricetes: A review of current tools using the latest ICTV classification framework.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1032186}, pmid = {36590402}, issn = {1664-302X}, abstract = {Bacteriophages, which are viruses infecting bacteria, are the most ubiquitous and diverse entities in the biosphere. There is accumulating evidence revealing their important roles in shaping the structure of various microbiomes. Thanks to (viral) metagenomic sequencing, a large number of new bacteriophages have been discovered. However, lacking a standard and automatic virus classification pipeline, the taxonomic characterization of new viruses seriously lag behind the sequencing efforts. In particular, according to the latest version of ICTV, several large phage families in the previous classification system are removed. Therefore, a comprehensive review and comparison of taxonomic classification tools under the new standard are needed to establish the state-of-the-art. In this work, we retrained and tested four recently published tools on newly labeled databases. We demonstrated their utilities and tested them on multiple datasets, including the RefSeq, short contigs, simulated metagenomic datasets, and low-similarity datasets. This study provides a comprehensive review of phage family classification in different scenarios and a practical guidance for choosing appropriate taxonomic classification pipelines. To our best knowledge, this is the first review conducted under the new ICTV classification framework. The results show that the new family classification framework overall leads to better conserved groups and thus makes family-level classification more feasible.}, } @article {pmid36590390, year = {2022}, author = {Zhang, X and Huang, Z and Zhong, Z and Li, Q and Bian, F and Yang, C}, title = {Metagenomic insights into the characteristics of soil microbial communities in the decomposing biomass of Moso bamboo forests under different management practices.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1051721}, pmid = {36590390}, issn = {1664-302X}, abstract = {INTRODUCTION: Considering the rapid growth and high biomass productivity, Moso bamboo (Phyllostachys edulis) has high carbon (C) sequestration potential, and different management practices can strongly modify its C pools. Soil microorganisms play an important role in C turnover through dead plant and microbial biomass degradation. To date, little is known about how different management practices affect microbial carbohydrate-active enzymes (CAZymes) and their responses to dead biomass degradation.

METHODS: Based on metagenomics analysis, this study analyzed CAZymes in three comparable stands from each Moso bamboo plantation: undisturbed (M0), extensively managed (M1), and intensively managed (M2).

RESULTS: The results showed that the number of CAZymes encoding plant-derived component degradation was higher than that encoding microbe-derived component degradation. Compared with the M0, the CAZyme families encoding plant-derived cellulose were significantly (p < 0.05) high in M2 and significantly (p < 0.05) low in M1. For microbe-derived components, the abundance of CAZymes involved in the bacterial-derived peptidoglycan was higher than that in fungal-derived components (chitin and glucans). Furthermore, M2 significantly increased the fungal-derived chitin and bacterial-derived peptidoglycan compared to M0, whereas M1 significantly decreased the fungal-derived glucans and significantly increased the bacterial-derived peptidoglycan. Four bacterial phyla (Acidobacteria, Actinobacteria, Proteobacteria, and Chloroflexi) mainly contributed to the degradation of C sources from the plant and microbial biomass. Redundancy analysis (RDA) and mantel test suggested the abundance of CAZyme encoding genes for plant and microbial biomass degradation are significantly correlated with soil pH, total P, and available K. Least Squares Path Modeling (PLS-PM) showed that management practices indirectly affect the CAZyme encoding genes associated with plant and microbial biomass degradation by regulating the soil pH and nutrients (total N and P), respectively.

DISCUSSION: Our study established that M2 and M1 impact dead biomass decomposition and C turnover, contributing to decreased C accumulation and establishing that the bacterial community plays the main role in C turnover in bamboo plantations.}, } @article {pmid36590388, year = {2022}, author = {Lapidus, A and Perez-Rueda, E}, title = {Editorial: Rising stars in Evolutionary and Genomic Microbiology: 2022.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1098065}, doi = {10.3389/fmicb.2022.1098065}, pmid = {36590388}, issn = {1664-302X}, } @article {pmid36588603, year = {2023}, author = {Silva, JR and Henrique-Bana, FC and Villas-Bôas, JK and Colombo Pimentel, T and Spinosa, WA and Prudencio, SH}, title = {Maturation of honey from Uruçú-Amarela (Melipona mondury): Metagenomics, metabolomics by NMR [1]H, physicochemical and antioxidant properties.}, journal = {Food chemistry. Molecular sciences}, volume = {6}, number = {}, pages = {100157}, pmid = {36588603}, issn = {2666-5662}, abstract = {The objective of this study was to characterize the microbiota biodiversity of Uruçú-Amarela honey through metagenomics. Furthermore, the impact of maturation temperatures (20 and 30 °C) and time (0-180 days) on the physicochemical and antioxidant properties was investigated. [1]H NMR was performed to verify metabolites formed during maturation. Uruçú-Amarela honey was mainly composed by lactic acid bacteria and osmophilic yeasts of genus Zygosaccharomyces. Maturation at 30 °C led to a higher fermentation activity, resulting in greater carbohydrate consumption, ethanol formation (0.0-0.6 %) and increased acidity (34.78-45.74 meq/kg) over the 180 days. It also resulted in honey with higher brown color (a* 0.7 to 3.89, b* 17.50-25.29) and antioxidant capacity, corroborating that the maturation is a suitable preservation technique for stingless bee honey, because it does not cause negative changes as it extends the shelf life of the stingless bee honey.}, } @article {pmid36587850, year = {2023}, author = {Liu, Y and Teo, SM and Méric, G and Tang, HHF and Zhu, Q and Sanders, JG and Vázquez-Baeza, Y and Verspoor, K and Vartiainen, VA and Jousilahti, P and Lahti, L and Niiranen, T and Havulinna, AS and Knight, R and Salomaa, V and Inouye, M}, title = {The gut microbiome is a significant risk factor for future chronic lung disease.}, journal = {The Journal of allergy and clinical immunology}, volume = {151}, number = {4}, pages = {943-952}, pmid = {36587850}, issn = {1097-6825}, support = {/WT_/Wellcome Trust/United Kingdom ; RG/13/13/30194/BHF_/British Heart Foundation/United Kingdom ; RG/18/13/33946/BHF_/British Heart Foundation/United Kingdom ; BRC-1215-20014/DH_/Department of Health/United Kingdom ; /MRC_/Medical Research Council/United Kingdom ; /CSO_/Chief Scientist Office/United Kingdom ; }, mesh = {Adult ; Humans ; *Gastrointestinal Microbiome ; Prospective Studies ; *Pulmonary Disease, Chronic Obstructive ; *Asthma ; Risk Factors ; }, abstract = {BACKGROUND: The gut-lung axis is generally recognized, but there are few large studies of the gut microbiome and incident respiratory disease in adults.

OBJECTIVE: We sought to investigate the association and predictive capacity of the gut microbiome for incident asthma and chronic obstructive pulmonary disease (COPD).

METHODS: Shallow metagenomic sequencing was performed for stool samples from a prospective, population-based cohort (FINRISK02; N = 7115 adults) with linked national administrative health register-derived classifications for incident asthma and COPD up to 15 years after baseline. Generalized linear models and Cox regressions were used to assess associations of microbial taxa and diversity with disease occurrence. Predictive models were constructed using machine learning with extreme gradient boosting. Models considered taxa abundances individually and in combination with other risk factors, including sex, age, body mass index, and smoking status.

RESULTS: A total of 695 and 392 statistically significant associations were found between baseline taxonomic groups and incident asthma and COPD, respectively. Gradient boosting decision trees of baseline gut microbiome abundance predicted incident asthma and COPD in the validation data sets with mean area under the curves of 0.608 and 0.780, respectively. Cox analysis showed that the baseline gut microbiome achieved higher predictive performance than individual conventional risk factors, with C-indices of 0.623 for asthma and 0.817 for COPD. The integration of the gut microbiome and conventional risk factors further improved prediction capacities.

CONCLUSIONS: The gut microbiome is a significant risk factor for incident asthma and incident COPD and is largely independent of conventional risk factors.}, } @article {pmid36587690, year = {2023}, author = {Zhou, X and Liu, T and Zhang, S and Kang, B and Duan, X and Yan, Y and Feng, L and Chen, Y}, title = {Metagenomic insight of fluorene-boosted sludge acidogenic fermentation: Metabolic transformation of amino acids and monosaccharides.}, journal = {The Science of the total environment}, volume = {865}, number = {}, pages = {161122}, doi = {10.1016/j.scitotenv.2022.161122}, pmid = {36587690}, issn = {1879-1026}, mesh = {Fermentation ; *Sewage/chemistry ; *Amino Acids ; Monosaccharides ; Fatty Acids, Volatile ; Acids ; Fluorenes ; Hydrogen-Ion Concentration ; Bioreactors ; }, abstract = {Fluorene (Flu) occurs widely in various environments and its toxicity to organisms is well-known. However, the impact of Flu on complicated biochemical processes involving functional microbial community has been reported rarely. In this study, the facilitation of Flu on the volatile fatty acids (VFAs) generation executed by acidogenic microbial population during sludge acidogenic fermentation (37 °C, SRT = 8 d, pH = 10.0) was investigated. The accumulation of VFAs (particularly acetic acid) increased initially and then declined with the increasing of Flu concentration (0-500 mg/kg dry sludge), which reached a maximum (3211.1 mg COD/L) as Flu content was 200 mg/kg dry sludge. The Flu-enhanced VFAs production was primarily attributed to the shift of hydrolysis/acidification, as well as the corresponding functional microbial community and the activity of enzymes. Based on the metagenomics analysis, the conversion of organic substrates, i.e. amino acid and monosaccharide, into VFAs embraced in hydrolysis/acidification shaped by Flu was constructed at the genetic level. The relative abundances of genes included in aminotransfer and deamination process of amino acid and glycolysis of monosaccharide into VFA-precursors (pyruvate, acetyl-CoA and propionyl-CoA), and the further formation of VFAs were improved due to the Flu presence. This study shed light on the Flu-affected microbial processes at the molecular biology level during acidogenic fermentation and was of great significance in resource recovery of sludge containing persistent organic pollutants.}, } @article {pmid36587599, year = {2023}, author = {Zhu, G and Chao, H and Sun, M and Jiang, Y and Ye, M}, title = {Toxicity sharing model of earthworm intestinal microbiome reveals shared functional genes are more powerful than species in resisting pesticide stress.}, journal = {Journal of hazardous materials}, volume = {446}, number = {}, pages = {130646}, doi = {10.1016/j.jhazmat.2022.130646}, pmid = {36587599}, issn = {1873-3336}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Oligochaeta/genetics/microbiology ; *Pesticides/toxicity ; *Microbiota ; Bacteria/genetics ; Soil/chemistry ; *Soil Pollutants/analysis ; }, abstract = {Earthworm intestinal bacteria and indigenous soil bacteria work closely during various biochemical processes and play a crucial role in maintaining the internal stability of the soil environment. However, the response mechanism of these bacterial communities to external pesticide disturbance is unknown. In this study, soil and earthworm gut contents were metagenomically sequenced after exposure to various concentrations of nitrochlorobenzene (0-1026.7 mg kg[-1]). A high degree of similarity was found between the microbial community composition and abundance in the worm gut and soil, both of which decreased significantly (P < 0.05) under elevated pesticide stress. The toxicity sharing model (TSM) showed that the toxicity sharing capacity was 97.4-125.7 % and 100.4-130.2 % for Egenes (genes in the worm gut) and Emet(degradation genes in the worm gut) in the earthworm intestinal microbiome, respectively. This indicated that the earthworm intestinal microbiome assisted in relieving the pesticide toxicity of the indigenous soil microbiome. This study showed that the TSM could quantitatively describe the toxic effect of pesticides on the earthworm intestinal microbiome. It provides a new analytical model for investigating the ecological alliance between earthworm intestinal microbiome and indigenous soil microbiome under pesticide stress while contributing a more profound understanding of the potential to use earthworms to mitigate pesticide pollution in soils and develop earthworm-based soil remediation techniques.}, } @article {pmid36586711, year = {2023}, author = {Dang, Q and Zhao, X and Li, Y and Xi, B}, title = {Revisiting the biological pathway for methanogenesis in landfill from metagenomic perspective-A case study of county-level sanitary landfill of domestic waste in North China plain.}, journal = {Environmental research}, volume = {222}, number = {}, pages = {115185}, doi = {10.1016/j.envres.2022.115185}, pmid = {36586711}, issn = {1096-0953}, mesh = {China ; *Waste Disposal Facilities ; *Methane ; }, abstract = {Landfill is the third highest contributor to anthropogenic methane (CH4) emissions, produced primarily by the anaerobic decomposition of organic matter by microbes. However, how various microbial metabolic processes contribute to CH4 production in domestic waste landfill remains elusive. We addressed this problem by investigating the methanogenic communities, methanogenic functional genes, KEGG modules and KEGG pathways in a county-level MSW sanitary landfill in North China Plain, China. Results showed that Methanomicrobiales, Methanobacteriales, Methanosarcinales, Micrococcales, Corynebacteriales and Bacillales were the dominant methanogens. M00357, M00346, M00567 and M00563 were the four major methane metabolic modules. The most abundant genes were ACSS, ackA and fwd with the relative abundance of 19.26-54.54%, 6.14-25.78% and 6.76-16.51%, respectively. The two essential genes of methanogenesis were detected with the relative abundance of 2.66-9.58% (mtr) and 1.63-9.14% (mcr). These findings indicated that acetotrophic and hydrogenotrophic methanogenesis were the major pathways. Methanomicrobiales, Methanosarcinales and Clostridiales were the key microbes to these pathways identified by co-occurrence network. Analysis of relative contribution of species to function further showed that Micrococcales, Corynebacteriales and Bacillales were special contributors to acetotrophic methanogenesis pathway. Redundancy analysis revealed that above functional genes and microbes were mainly controlled by NH4[+] and pH. Our results can help to provide develop the fine management strategies for methane utilization and emission reduction in landfill.}, } @article {pmid36586708, year = {2023}, author = {Feng, Y and Yang, J and Aminu, D and Han, H and Yan, Y and Wang, Y and Liu, J and Wang, X}, title = {Effects of hydroxyapatite on safe wheat production and soil microbial functional genes in an alkaline soil contaminated with heavy metals.}, journal = {Environmental research}, volume = {220}, number = {}, pages = {115183}, doi = {10.1016/j.envres.2022.115183}, pmid = {36586708}, issn = {1096-0953}, mesh = {Soil ; Triticum/genetics ; Durapatite ; Soil Microbiology ; *Metals, Heavy/toxicity/analysis ; *Soil Pollutants/toxicity/analysis ; }, } @article {pmid36586685, year = {2023}, author = {Liang, C and Ye, Q and Huang, Y and Zhang, Z and Wang, C and Wang, Y and Wang, H}, title = {Distribution of the new functional marker gene (pahE) of aerobic polycyclic aromatic hydrocarbon (PAHs) degrading bacteria in different ecosystems.}, journal = {The Science of the total environment}, volume = {865}, number = {}, pages = {161233}, doi = {10.1016/j.scitotenv.2022.161233}, pmid = {36586685}, issn = {1879-1026}, mesh = {*Polycyclic Aromatic Hydrocarbons/analysis ; Ecosystem ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Bacteria, Aerobic/metabolism ; Soil ; *Soil Pollutants/analysis ; Soil Microbiology ; }, abstract = {Understanding the degradation potentials in PAHs-contaminated sites is significant for formulating effective bioremediation strategies. pahE encoding PAHs hydratase-aldolase has been proven as a better new functional marker gene of aerobic PAHs-degrading bacteria to assess the biodegradation potential of indigenous PAHs-degrading bacterial population. However, the distribution of pahE and its relationship with environmental factors remain unknown. The present study observed spatial variations in the diversity and abundance of pahE across oilfield soils, mangrove sediments, and urban roadside soils. nahE from Pseudomonas, bphE from Hyphomonas oceanitis, nagE from Comamonas testosterone, and novel pahE genes were widely present in these PAHs-polluted ecosystems. The abundance of pahE in PAHs-contaminated sites was in the range of 10[5]-10[6] copies·g[-1] (dry weight). Redundancy analysis and Pearson's correlation analysis implied that the distribution of pahE in the PAHs-contaminated environment was mainly shaped by environmental factors such as PAHs pollution level, nutrient level, salinity, and water content. This work was the first to explore the distribution of the new functional marker gene (pahE) and its links with environmental parameters, which provided new insights into the ecophysiology and distribution of indigenous aerobic PAHs-degrading bacteria in contaminated sites.}, } @article {pmid36586415, year = {2023}, author = {Cheemarla, NR and Hanron, A and Fauver, JR and Bishai, J and Watkins, TA and Brito, AF and Zhao, D and Alpert, T and Vogels, CBF and Ko, AI and Schulz, WL and Landry, ML and Grubaugh, ND and van Dijk, D and Foxman, EF}, title = {Nasal host response-based screening for undiagnosed respiratory viruses: a pathogen surveillance and detection study.}, journal = {The Lancet. Microbe}, volume = {4}, number = {1}, pages = {e38-e46}, pmid = {36586415}, issn = {2666-5247}, support = {R21 AI156208/AI/NIAID NIH HHS/United States ; T32 AI055403/AI/NIAID NIH HHS/United States ; UL1 TR001863/TR/NCATS NIH HHS/United States ; R35 GM143072/GM/NIGMS NIH HHS/United States ; }, mesh = {United States ; Humans ; *COVID-19/diagnosis/epidemiology ; SARS-CoV-2/genetics ; *Viruses/genetics ; Multiplex Polymerase Chain Reaction ; RNA ; }, abstract = {BACKGROUND: Symptomatic patients who test negative for common viruses are an important possible source of unrecognised or emerging pathogens, but metagenomic sequencing of all samples is inefficient because of the low likelihood of finding a pathogen in any given sample. We aimed to determine whether nasopharyngeal CXCL10 screening could be used as a strategy to enrich for samples containing undiagnosed viruses.

METHODS: In this pathogen surveillance and detection study, we measured CXCL10 concentrations from nasopharyngeal swabs from patients in the Yale New Haven health-care system, which had been tested at the Yale New Haven Hospital Clinical Virology Laboratory (New Haven, CT, USA). Patients who tested negative for a panel of respiratory viruses using multiplex PCR during Jan 23-29, 2017, or March 3-14, 2020, were included. We performed host and pathogen RNA sequencing (RNA-Seq) and analysis for viral reads on samples with CXCL10 higher than 1 ng/mL or CXCL10 testing and quantitative RT-PCR (RT-qPCR) for SARS-CoV-2. We used RNA-Seq and cytokine profiling to compare the host response to infection in samples that were virus positive (rhinovirus, seasonal coronavirus CoV-NL63, or SARS-CoV-2) and virus negative (controls).

FINDINGS: During Jan 23-29, 2017, 359 samples were tested for ten viruses on the multiplex PCR respiratory virus panel (RVP). 251 (70%) were RVP negative. 60 (24%) of 251 samples had CXCL10 higher than 150 pg/mL and were identified for further analysis. 28 (47%) of 60 CXCL10-high samples were positive for seasonal coronaviruses. 223 (89%) of 251 samples were PCR negative for 15 viruses and, of these, CXCL10-based screening identified 32 (13%) samples for further analysis. Of these 32 samples, eight (25%) with CXCL10 concentrations higher than 1 ng/mL and sufficient RNA were selected for RNA-Seq. Microbial RNA analysis showed the presence of influenza C virus in one sample and revealed RNA reads from bacterial pathobionts in four (50%) of eight samples. Between March 3 and March 14, 2020, 375 (59%) of 641 samples tested negative for 15 viruses on the RVP. 32 (9%) of 375 samples had CXCL10 concentrations ranging from 100 pg/mL to 1000 pg/mL and four of those were positive for SARS-CoV-2. CXCL10 elevation was statistically significant, and a distinguishing feature was found in 28 (8%) of 375 SARS-CoV-2-negative samples versus all four SARS-CoV-2-positive samples (p=4·4 × 10[-5]). Transcriptomic signatures showed an interferon response in virus-positive samples and an additional neutrophil-high hyperinflammatory signature in samples with high amounts of bacterial pathobionts. The CXCL10 cutoff for detecting a virus was 166·5 pg/mL for optimal sensitivity and 1091·0 pg/mL for specificity using a clinic-ready automated microfluidics-based immunoassay.

INTERPRETATION: These results confirm CXCL10 as a robust nasopharyngeal biomarker of viral respiratory infection and support host response-based screening followed by metagenomic sequencing of CXCL10-high samples as a practical approach to incorporate clinical samples into pathogen discovery and surveillance efforts.

FUNDING: National Institutes of Health, the Hartwell Foundation, the Gruber Foundation, Fast Grants for COVID-19 research from the Mercatus Center, and the Huffman Family Donor Advised Fund.}, } @article {pmid36586330, year = {2023}, author = {Wang, JF and Zhou, HZ and Tang, GH and Huang, JW and Liu, H and Cai, ZX and He, ZW and Zhu, H and Song, XS}, title = {Reducing the inhibitive effect of fluorine and heavy metals on nitrate reduction by hydroxyapatite substrate in constructed wetlands.}, journal = {Journal of hazardous materials}, volume = {446}, number = {}, pages = {130692}, doi = {10.1016/j.jhazmat.2022.130692}, pmid = {36586330}, issn = {1873-3336}, mesh = {Nitrates ; Wetlands ; Fluorine ; *Metals, Heavy ; Bacteria/metabolism ; Nitrogen/metabolism ; *Environmental Pollutants ; Hydroxyapatites ; Waste Disposal, Fluid/methods ; }, abstract = {Bio-toxic inorganic pollutants, e.g., fluorine (F) and heavy metals (HMs), in wastewaters are the potential threats to nitrate (NO3[-]-N) reduction by microorganisms in constructed wetlands (CWs). Selection of suitable substrate with high F and HMs adsorption efficiency and capacity is a potential alternative for simultaneous removal of these pollutants in CWs. Herein, this study investigated the feasibility of applying hydroxyapatite (HA)-gravel media for F and HMs adsorption and its effect on NO3[-]-N reduction in CWs (HA CWs) by comparing the CWs filled with gravel substrate (CK CWs). The results indicated that the removal efficiency of F, Cr, As, and NO3[-]-N in HA CWs increased by 113.6-, 3.3-, 2.7-, and 0.6-folds, respectively, compared to CK CWs. The NO3[-]-N reduction rate decreased by 11-46% in CK CWs after the presence of F and HMs in influent, while for HA CWs, it was only 13-22%. Excellent F and HMs adsorption capacity of HA substrate availed for wetland plants resisting F/HMs toxicity and making catalase activity lower. The HA substrate in CWs resulted in the certain succession of nitrogen-transforming bacteria, e.g., nitrifiers (Nitrospira) and denitrifiers (Thiobacillus and Desulfobacterium). More importantly, key functional genes, including nirK/nirS, korA/korB, ChrA/ChrD, arsA/arsB, catalyzing the processes of nitrogen biotransformation, energy metabolism, NO3[-]-N and metal ions reduction were also enriched in HA CWs. This study highlights HA substrate reduce the inhibitive effect of F and HMs on NO3[-]-N reduction, and provides new insights into how microbiota structurally and functionally respond to different substrates in CWs.}, } @article {pmid36585490, year = {2023}, author = {Zhao, J and Wang, Z and Li, C and Shi, T and Liang, Y and Jiao, N and Zhang, Y}, title = {Significant Differences in Planktonic Virus Communities Between "Cellular Fraction" (0.22 ~ 3.0 µm) and "Viral Fraction" (< 0.22 μm) in the Ocean.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {825-842}, pmid = {36585490}, issn = {1432-184X}, support = {41876174//National Natural Science Foundation of China/ ; }, mesh = {Plankton/genetics ; *Viruses/genetics ; *Bacteriophages ; Seawater ; Genome, Viral ; Oceans and Seas ; Metagenome ; Metagenomics ; }, abstract = {Compared to free-living viruses (< 0.22 m) in the ocean, planktonic viruses in the "cellular fraction" (0.22 ~ 3.0 μm) are now far less well understood, and the differences between them remain largely unexplored. Here, we revealed that even in the same seawater samples, the "cellular fraction" comprised significantly distinct virus communities from the free virioplankton, with only 13.87% overlap in viral contigs at the species level. Compared to the viral genomes deposited in NCBI RefSeq database, 99% of the assembled viral genomes in the "cellular fraction" represented novel genera. Notably, the assembled (near-) complete viral genomes within the "cellular fraction" were significantly larger than that in the "viral fraction," and the "cellular fraction" contained three times more species of giant viruses or jumbo phages with genomes > 200 kb than the "viral fraction." The longest complete genomes of jumbo phage (~ 252 kb) and giant virus (~ 716 kb) were both detected only in the "cellular fraction." Moreover, a relatively higher proportion of proviruses were predicted within the "cellular fraction" than "viral fraction." Besides the substantial divergence in viral community structure, the different fractions also contained their unique viral auxiliary metabolic genes; e.g., those potentially participating in inorganic carbon fixation in deep sea were detected only in the "cellular-fraction" viromes. In addition, there was a considerable divergence in the community structure of both "cellular fraction" and "viral fraction" viromes between the surface and deep-sea habitats, suggesting that they might have similar environmental adaptation properties. The findings deepen our understanding of the complexity of viral community structure and function in the ocean.}, } @article {pmid36585489, year = {2023}, author = {Zhang, Y and Liu, F and Liang, H and Gao, D}, title = {Mediative Mechanism of Freezing/Thawing on Greenhouse Gas Emissions in an Inland Saline-Alkaline Wetland: a Metagenomic Analysis.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {985-996}, pmid = {36585489}, issn = {1432-184X}, support = {31470543//National Natural Science Foundation of China/ ; }, mesh = {*Greenhouse Gases ; Wetlands ; Freezing ; Carbon Dioxide ; Nitrous Oxide ; Carbon ; Methane/analysis ; Soil ; }, abstract = {Inland saline-alkaline wetlands distributed in the mid-high latitude have repeatedly experienced freezing and thawing. However, the response of greenhouse gas (GHG) emission and microbially-mediated carbon and nitrogen cycle to freezing and thawing remains unclear. We monitored the GHG flux in an inland saline-alkaline wetland and found that, compared with the growth period, the average CO2 flux decreased from 171.99 to 76.61-80.71 mg/(m[2]‧h), the average CH4 flux decreased from 10.72 to 1.96-3.94 mg/(m[2]‧h), and the average N2O flux decreased from 56.17 to - 27.14 to - 20.70 μg/(m[2]‧h). Freezing and thawing significantly decreased the relative abundance of functional genes involved in carbon and nitrogen cycles. The aceticlastic methanogenic pathway was the main methanogenic pathway, whereas the Candidatus Methylomirabilis oxyfera was the most abundant methane oxidizer in the wetland. Ammonia-oxidizing archaea and denitrifier belonging to proteobacteria was the major microbial N2O source, while bacteria within clade II nosZ was the major microbial N2O sink. Freezing and thawing reduced the relative abundance of these genes, leading to a decrease in GHG flux.}, } @article {pmid36585105, year = {2023}, author = {Chen, BY and Lin, WZ and Li, YL and Bi, C and Du, LJ and Liu, Y and Zhou, LJ and Liu, T and Xu, S and Shi, CJ and Zhu, H and Wang, YL and Sun, JY and Liu, Y and Zhang, WC and Lu, HX and Wang, YH and Feng, Q and Chen, FX and Wang, CQ and Tonetti, MS and Zhu, YQ and Zhang, H and Duan, SZ}, title = {Roles of oral microbiota and oral-gut microbial transmission in hypertension.}, journal = {Journal of advanced research}, volume = {43}, number = {}, pages = {147-161}, pmid = {36585105}, issn = {2090-1224}, mesh = {Humans ; Animals ; Mice ; *Gastrointestinal Microbiome/physiology ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; Follow-Up Studies ; Mice, Inbred C57BL ; *Microbiota ; *Hypertension ; *Periodontitis ; }, abstract = {INTRODUCTION: Considerable evidence has linked periodontitis (PD) to hypertension (HTN), but the nature behind this connection is unclear. Dysbiosis of oral microbiota leading to PD is known to aggravate different systematic diseases, but the alteration of oral microbiota in HTN and their impacts on blood pressure (BP) remains to be discovered.

OBJECTIVES: To characterize the alterations of oral and gut microbiota and their roles in HTN.

METHODS: We performed a cross-sectional (95 HTN participants and 39 controls) and a 6-month follow-up study (52 HTN participants and 26 controls) to analyze the roles of oral and gut microbiota in HTN. Saliva, subgingival plaques, and feces were collected for 16S rRNA gene sequencing or metagenomic analysis. C57BL/6J mice were pretreated with antibiotics to deplete gut microbiota, and then transplanted with human saliva by gavage to test the impacts of abnormal oral-gut microbial transmission on HTN.

RESULTS: BP in participants with PD was higher than no PD in both cross-sectional and follow-up cohort. Relative abundances of 14 salivary genera, 15 subgingival genera and 10 gut genera significantly altered in HTN and those of 7 salivary genera, 12 subgingival genera and 6 gut genera significantly correlated with BP. Sixteen species under 5 genera were identified as oral-gut transmitters, illustrating the presence of oral-gut microbial transmission in HTN. Veillonella was a frequent oral-gut transmitter stably enriched in HTN participants of both cross-sectional and follow-up cohorts. Saliva from HTN participants increased BP in hypertensive mice. Human saliva-derived Veillonella successfully colonized in mouse gut, more abundantly under HTN condition.

CONCLUSIONS: PD and oral microbiota are strongly associated with HTN, likely through oral-gut transmission of microbes. Ectopic colonization of saliva-derived Veillonella in the gut may aggravate HTN. Therefore, precise manipulations of oral microbiota and/or oral-gut microbial transmission may be useful strategies for better prevention and treatment of HTN.}, } @article {pmid36585101, year = {2023}, author = {Adi Wicaksono, W and Reisenhofer-Graber, T and Erschen, S and Kusstatscher, P and Berg, C and Krause, R and Cernava, T and Berg, G}, title = {Phyllosphere-associated microbiota in built environment: Do they have the potential to antagonize human pathogens?.}, journal = {Journal of advanced research}, volume = {43}, number = {}, pages = {109-121}, pmid = {36585101}, issn = {2090-1224}, mesh = {Humans ; Bacteria ; *Bacillus ; Plants ; *Microbiota ; }, abstract = {INTRODUCTION: The plant microbiota is known to protect its host against invasion by plant pathogens. Recent studies have indicated that the microbiota of indoor plants is transmitted to the local built environment where it might fulfill yet unexplored functions. A better understanding of the interplay of such microbial communities with human pathogens might provide novel cues related to natural inhibition of them.

OBJECTIVE: We studied the plant microbiota of two model indoor plants, Musa acuminata and Chlorophytum comosum, and their effect on human pathogens. The main objective was to identify mechanisms by which the microbiota of indoor plants inhibits human-pathogenic bacteria.

METHODS: Microbial communities and functioning were investigated using a comprehensive set of experiments and methods combining amplicon and shotgun metagenomic analyses with results from interaction assays.

RESULTS: A diverse microbial community was found to be present on Musa and Chlorophytum grown in different indoor environments; the datasets comprised 1066 bacterial, 1261 fungal, and 358 archaeal ASVs. Bacterial communities were specific for each plant species, whereas fungal and archaeal communities were primarily shaped by the built environment. Sphingomonas and Bacillus were found to be prevalent components of a ubiquitous core microbiome in the two model plants; they are well-known for antagonistic activity towards plant pathogens. Interaction assays indicated that they can also antagonize opportunistic human pathogens. Moreover, the native plant microbiomes harbored a broad spectrum of biosynthetic gene clusters, and in parallel, a variety of antimicrobial resistance genes. By conducting comparative metagenomic analyses between plants and abiotic surfaces, we found that the phyllosphere microbiota harbors features that are clearly distinguishable from the surrounding abiotic surfaces.

CONCLUSIONS: Naturally occurring phyllosphere bacteria can potentially act as a protective shield against opportunistic human pathogens. This knowledge and the underlying mechanisms can provide an important basis to establish a healthy microbiome in built environments.}, } @article {pmid36584949, year = {2023}, author = {Fraser, MW and Martin, BC and Wong, HL and Burns, BP and Kendrick, GA}, title = {Sulfide intrusion in a habitat forming seagrass can be predicted from relative abundance of sulfur cycling genes in sediments.}, journal = {The Science of the total environment}, volume = {864}, number = {}, pages = {161144}, doi = {10.1016/j.scitotenv.2022.161144}, pmid = {36584949}, issn = {1879-1026}, mesh = {*Geologic Sediments ; Ecosystem ; Sulfides ; Sulfur ; Australia ; *Microbiota ; }, abstract = {Sulfide intrusion from sediments is an increasingly recognized contributor to seagrass declines globally, yet the relationship between sediment microorganisms and sulfide intrusion has received little attention. Here, we use metagenomic sequencing and stable isotope ([34]S) analysis to examine this relationship in Cockburn Sound, Australia, a seagrass-dominated embayment with a gradient of sulfide stress and seagrass declines. There was a significant positive relationship between sulfide intrusion into seagrasses and sulfate reduction genes in sediment microbial communities, which was greatest at sites with long term seagrass declines. This is the first demonstration of a significant link between sulfur cycling genes present in seagrass sediments and sulfide intrusion in a habitat-forming seagrass that is experiencing long-term shoot density decline. Given that microorganisms respond rapidly to environmental change, the quantitative links established in this study can be used as a potential management tool to enable the prediction of sulfide stress on large habitat forming seagrasses; a global issue expected to worsen with climate change.}, } @article {pmid36584858, year = {2023}, author = {Tang, F and Li, Q and Yue, J and Ge, F and Li, F and Liu, Y and Zhang, D and Tian, J}, title = {Penicillium oxalicum augments soil lead immobilization by affecting indigenous microbial community structure and inorganic phosphate solubilization potential during microbial-induced phosphate precipitation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {319}, number = {}, pages = {120953}, doi = {10.1016/j.envpol.2022.120953}, pmid = {36584858}, issn = {1873-6424}, mesh = {Phosphates/chemistry ; Soil/chemistry ; Lead ; *Penicillium ; Soil Microbiology ; *Soil Pollutants/chemistry ; *Microbiota ; Durapatite ; }, abstract = {Phosphate-solubilizing microorganisms (PSMs) are critically important for increasing soil phosphate (P) and decreasing lead (Pb) bioavailability during microbial-induced phosphate precipitation (MIPP). However, their relative contributions to the indigenous soil microbial communities and P-cycling genes during the MIPP process remain unclear. In this study, inoculation of the PSM P. oxalicum in hydroxyapatite-cultured and Pb-contaminated soil increased soil phosphatase activities, available P (AP) concentrations and reduced available Pb levels. Metagenomics revealed a 3.9-44.0% increase in the abundance of P-cycling genes by P. oxalicum inoculation. No P-cycling genes were assigned to Penicillium. While P. oxalicum increased the complexity of microbial community co-occurrence networks, and improved the directly interrelationships between Penicillium and genera containing P-cycling gene. These results suggesting that P. oxalicum obviously positively affected the regulation of indigenous P-cycling functional communities during the MIPP process. Inorganic P solubilization genes (gcd, ppa, and ppx) have been shown to affect soil AP, suggesting that inorganic P solubilization is the major driver of Pb immobilization improvement following P. oxalicum inoculation. These results enhance our understanding of the significant ecological role of PSMs in governing soil P-cycling and alleviating Pb[2+] biotoxicity during the MIPP process.}, } @article {pmid36584462, year = {2023}, author = {Guan, X and Cheng, Z and Li, Y and Wang, J and Zhao, R and Guo, Z and Zhao, T and Huang, L and Qiu, C and Shi, W and Jin, S}, title = {Mixed organic and inorganic amendments enhance soil microbial interactions and environmental stress resistance of Tibetan barley on plateau farmland.}, journal = {Journal of environmental management}, volume = {330}, number = {}, pages = {117137}, doi = {10.1016/j.jenvman.2022.117137}, pmid = {36584462}, issn = {1095-8630}, mesh = {*Soil ; Tibet ; *Hordeum/genetics ; Farms ; Microbial Interactions ; Soil Microbiology ; }, abstract = {Sufficient crop yield while maintaining soil health and sustainable agricultural development is a global objective, serving a special challenge to certain climate-sensitive plateau areas. Despite conducting trails on a variety of soil amendments in plateau areas, systematic research is lacking regarding the influences of organic and inorganic amendments on soil quality, particularly soil microbiome. To our knowledge, this was the first study that compared the effects of inorganic, organic, and mixed amendments on typical plateau crop hulless barley (Hordeum vulgare L. var. Nudum, also known as "Qingke" in Chinese) over the course of tillering, jointing, and ripening. Microbial communities and their responses to amendments, soil properties and Tibetan hulless barley growth, yield were investigated. Results indicated that mixed organic and inorganic amendments promoted the abundance of rhizosphere microorganisms, enhancing the rhizosphere root-microbes interactions and resistance to pathogenic bacteria and environmental stresses. The rhizosphere abundant and significantly different genera Arthrobacter, Rhodanobacter, Sphingomona, Nocardioides and so on demonstrated their unique adaptation to the plateau environment based on the results of metagenomic binning. The abundance of 23 genes about plant growth and environmental adaptations in the mixed amendment soil were significantly higher than other treatments. Findings from this study suggest that the mixed organic/inorganic amendments can help establish a healthy microbiome and increase soil quality while achieving sufficient hulless barley yields in Tibet and presumably other similar geographic areas of high altitude.}, } @article {pmid36584150, year = {2022}, author = {Nakamura, S and Yumioka, J and Kachi, S and Baba, Y and Kawai, S}, title = {Bacterial and fungal gut microbiota of supralittoral talitrid amphipods feeding on brown macroalgae and paper.}, journal = {PloS one}, volume = {17}, number = {12}, pages = {e0279834}, pmid = {36584150}, issn = {1932-6203}, mesh = {Animals ; *Seaweed/metabolism ; *Gastrointestinal Microbiome ; *Amphipoda/metabolism ; Ecosystem ; Bacteria/genetics/metabolism ; Alginates/metabolism ; }, abstract = {Some macroalgae drift on the ocean and are stranded on coasts, and these stranded brown macroalgae are regarded to be degraded by organisms. Alginate is a major component of brown macroalgae. An uncovering of how carbon is cycled through brown macroalgae is needed to deeply understand coastal ecosystems. In this study, to gain insights into metabolism of brown macroalgae and alginate in the organisms, we initially confirmed that supralittoral talitrid amphipods (beach fleas or sandhoppers collected on the Shibagaki coast in Ishikawa Prefecture, Japan) fed on the brown macroalgae. We then isolated bacteria such as Vibrio sp. with alginate-assimilating capability from the gut of the amphipods. Metagenomic analysis of the gut of amphipods housed in several conditions (e.g. macroalgae or paper as feed, non-sterilized or sterilized environment) showed no condition-dependent compositions of bacteria and fungi, but Vibrio sp. were detected at high frequency, in good agreement with the isolation of Vibrio sp. An intervention study using antibiotics showed that amphipods fed on algae or paper at about the same rate in the presence or absence of antibiotics, and that the antibiotics had no effects on the life span. Moreover, intervention with antibiotics completely killed Vibrio sp. and some other bacteria, and had significant effects on the composition of the flora in the gut, with elimination of the variations observed in the guts of amphipods housed without antibiotics. These data suggest that microbes that were killed by antibiotics, including Vibrio sp., in the gut of talitrid amphipods are not essential for assimilation of brown macroalgae.}, } @article {pmid36583859, year = {2022}, author = {Lau, HCH and Yu, J}, title = {Uncovering novel human gut virome using ultra-deep metagenomic sequencing.}, journal = {Chinese medical journal}, volume = {135}, number = {20}, pages = {2395-2397}, pmid = {36583859}, issn = {2542-5641}, mesh = {Humans ; *Virome ; *Bacteriophages ; Feces ; Metagenome ; Metagenomics ; }, } @article {pmid36583539, year = {2023}, author = {Schnettler, JD and Klein, OJ and Kaminski, TS and Colin, PY and Hollfelder, F}, title = {Ultrahigh-Throughput Directed Evolution of a Metal-Free α/β-Hydrolase with a Cys-His-Asp Triad into an Efficient Phosphotriesterase.}, journal = {Journal of the American Chemical Society}, volume = {145}, number = {2}, pages = {1083-1096}, pmid = {36583539}, issn = {1520-5126}, support = {BB/W000504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Hydrolases ; Acetylcholinesterase ; *Phosphoric Triester Hydrolases/genetics/metabolism ; Biocatalysis ; Catalysis ; }, abstract = {Finding new mechanistic solutions for biocatalytic challenges is key in the evolutionary adaptation of enzymes, as well as in devising new catalysts. The recent release of man-made substances into the environment provides a dynamic testing ground for observing biocatalytic innovation at play. Phosphate triesters, used as pesticides, have only recently been introduced into the environment, where they have no natural counterpart. Enzymes have rapidly evolved to hydrolyze phosphate triesters in response to this challenge, converging onto the same mechanistic solution, which requires bivalent cations as a cofactor for catalysis. In contrast, the previously identified metagenomic promiscuous hydrolase P91, a homologue of acetylcholinesterase, achieves slow phosphotriester hydrolysis mediated by a metal-independent Cys-His-Asp triad. Here, we probe the evolvability of this new catalytic motif by subjecting P91 to directed evolution. By combining a focused library approach with the ultrahigh throughput of droplet microfluidics, we increase P91's activity by a factor of ≈360 (to a kcat/KM of ≈7 × 10[5] M[-1] s[-1]) in only two rounds of evolution, rivaling the catalytic efficiencies of naturally evolved, metal-dependent phosphotriesterases. Unlike its homologue acetylcholinesterase, P91 does not suffer suicide inhibition; instead, fast dephosphorylation rates make the formation of the covalent adduct rather than its hydrolysis rate-limiting. This step is improved by directed evolution, with intermediate formation accelerated by 2 orders of magnitude. Combining focused, combinatorial libraries with the ultrahigh throughput of droplet microfluidics can be leveraged to identify and enhance mechanistic strategies that have not reached high efficiency in nature, resulting in alternative reagents with novel catalytic machineries.}, } @article {pmid36583109, year = {2022}, author = {Szabó, BG and Kiss, R and Makra, N and Pénzes, K and Vad, E and Kamotsay, K and Szabó, D and Ostorházi, E}, title = {Composition and changes of blood microbiota in adult patients with community-acquired sepsis: A pilot study from bench to bedside.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1067476}, pmid = {36583109}, issn = {2235-2988}, mesh = {Humans ; Adult ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Sepsis/microbiology ; Metagenome ; }, abstract = {BACKGROUND: Characteristics of the blood microbiota among adult patients with community-acquired sepsis are poorly understood. Our aim was to analyze the composition of blood microbiota in adult patients with community-acquired sepsis, and correlate changes with non-septic control patients.

METHODS: A prospective observational study was carried out by including adult patients hospitalized for community-acquired sepsis at our center between January and November 2019, by random selection from a pool of eligible patients. Study inclusion was done on the day of sepsis diagnosis. Community acquisition was ascertained by a priori exclusion criteria; sepsis was defined according to the SEPSIS-3 definitions. Each included patient was matched with non-septic control patients by age and gender in a 1:1 fashion enrolled from the general population. Conventional culturing with BacT/ALERT system and 16S rRNA microbiota analysis were performed from blood samples taken in a same time from a patient. Abundance data was analyzed by the CosmosID HUB Microbiome software.

RESULTS: Altogether, 13 hospitalized patients were included, 6/13 (46.2%) with sepsis and 7/13 (53.8%) with septic shock at diagnosis. The most prevalent etiopathogen isolated from blood cultures was Escherichia coli, patients mostly had intraabdominal septic source. At day 28, all-cause mortality was 15.4% (2/13). Compared to non-septic control patients, a relative scarcity of Faecalibacterium, Blautia, Coprococcus and Roseburia genera, with an abundance of Enhydrobacter, Pseudomonas and Micrococcus genera was observed among septic patients. Relative differences between septic vs. non-septic patients were more obvious at the phylum level, mainly driven by Firmicutes (25.7% vs. 63.1%; p<0.01) and Proteobacteria (36.9% vs. 16.6%; p<0.01). The alpha diversity, quantified by the Chao1 index showed statistically significant difference between septic vs. non-septic patients (126 ± 51 vs. 66 ± 26; p<0.01). The Bray-Curtis beta diversity, reported by principal coordinate analysis of total hit frequencies, revealed 2 potentially separate clusters among septic vs. non-septic patients.

CONCLUSION: In adult patients with community-acquired sepsis, specific changes in the composition and abundance of blood microbiota could be detected by 16S rRNA metagenome sequencing, compared to non-septic control patients. Traditional blood culture results only partially correlate with microbiota test results.}, } @article {pmid36583056, year = {2022}, author = {Doster, E and Pinnell, LJ and Noyes, NR and Parker, JK and Anderson, CA and Booker, CW and Hannon, SJ and McAllister, TA and Gow, SP and Belk, KE and Morley, PS}, title = {Evaluating the effects of antimicrobial drug use on the ecology of antimicrobial resistance and microbial community structure in beef feedlot cattle.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {970358}, pmid = {36583056}, issn = {1664-302X}, abstract = {INTRODUCTION: Use of antimicrobial drugs (AMDs) in food producing animals has received increasing scrutiny because of concerns about antimicrobial resistance (AMR) that might affect consumers. Previously, investigations regarding AMR have focused largely on phenotypes of selected pathogens and indicator bacteria, such as Salmonella enterica or Escherichia coli. However, genes conferring AMR are known to be distributed and shared throughout microbial communities. The objectives of this study were to employ target-enriched metagenomic sequencing and 16S rRNA gene amplicon sequencing to investigate the effects of AMD use, in the context of other management and environmental factors, on the resistome and microbiome in beef feedlot cattle.

METHODS: This study leveraged samples collected during a previous longitudinal study of cattle at beef feedlots in Canada. This included fecal samples collected from randomly selected individual cattle, as well as composite-fecal samples from randomly selected pens of cattle. All AMD use was recorded and characterized across different drug classes using animal defined daily dose (ADD) metrics.

RESULTS: Overall, fecal resistome composition was dominated by genes conferring resistance to tetracycline and macrolide-lincosamide-streptogramin (MLS) drug classes. The diversity of bacterial phyla was greater early in the feeding period and decreased over time in the feedlot. This decrease in diversity occurred concurrently as the microbiome represented in different individuals and different pens shifted toward a similar composition dominated by Proteobacteria and Firmicutes. Some antimicrobial drug exposures in individuals and groups were associated with explaining a statistically significant proportion of the variance in the resistome, but the amount of variance explained by these important factors was very small (<0.6% variance each), and smaller than associations with other factors measured in this study such as time and feedlot ID. Time in the feedlot was associated with greater changes in the resistome for both individual animals and composite pen-floor samples, although the proportion of the variance associated with this factor was small (2.4% and 1.2%, respectively).

DISCUSSION: Results of this study are consistent with other investigations showing that, compared to other factors, AMD exposures did not have strong effects on antimicrobial resistance or the fecal microbial ecology of beef cattle.}, } @article {pmid36581858, year = {2022}, author = {Huang, Y and Lu, W and Zeng, M and Hu, X and Su, Z and Liu, Y and Liu, Z and Yuan, J and Li, L and Zhang, X and Huang, L and Hu, W and Wang, X and Li, S and Zhang, H}, title = {Mapping the early life gut microbiome in neonates with critical congenital heart disease: multiomics insights and implications for host metabolic and immunological health.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {245}, pmid = {36581858}, issn = {2049-2618}, mesh = {Infant, Newborn ; Humans ; *Gastrointestinal Microbiome/genetics ; Multiomics ; Inflammation ; Bacteria ; *Heart Defects, Congenital ; Dysbiosis/microbiology ; }, abstract = {BACKGROUND: The early life gut microbiome is crucial in maintaining host metabolic and immune homeostasis. Though neonates with critical congenital heart disease (CCHD) are at substantial risks of malnutrition and immune imbalance, the microbial links to CCHD pathophysiology remain poorly understood. In this study, we aimed to investigate the gut microbiome in neonates with CCHD in association with metabolomic traits. Moreover, we explored the clinical implications of the host-microbe interactions in CCHD.

METHODS: Deep metagenomic sequencing and metabolomic profiling of paired fecal samples from 45 neonates with CCHD and 50 healthy controls were performed. The characteristics of gut microbiome were investigated in three dimensions (microbial abundance, functionality, and genetic variation). An in-depth analysis of gut virome was conducted to elucidate the ecological interaction between gut viral and bacterial communities. Correlations between multilevel microbial features and fecal metabolites were determined using integrated association analysis. Finally, we conducted a subgroup analysis to examine whether the interactions between gut microbiota and metabolites could mediate inflammatory responses and poor surgical prognosis.

RESULTS: Gut microbiota dysbiosis was observed in neonates with CCHD, characterized by the depletion of Bifidobacterium and overgrowth of Enterococcus, which was highly correlated with metabolomic perturbations. Genetic variations of Bifidobacterium and Enterococcus orchestrate the metabolomic perturbations in CCHD. A temperate core virome represented by Siphoviridae was identified to be implicated in shaping the gut bacterial composition by modifying microbial adaptation. The overgrowth of Enterococcus was correlated with systemic inflammation and poor surgical prognosis in subgroup analysis. Mediation analysis indicated that the overgrowth of Enterococcus could mediate gut barrier impairment and inflammatory responses in CCHD.

CONCLUSIONS: We demonstrate for the first time that an aberrant gut microbiome associated with metabolomic perturbations is implicated in immune imbalance and adverse clinical outcomes in neonates with CCHD. Our data support the importance of reconstituting optimal gut microbiome in maintaining host metabolic and immunological homeostasis in CCHD. Video Abstract.}, } @article {pmid36581612, year = {2022}, author = {Li, R and Wang, Y and Hu, H and Tan, Y and Ma, Y}, title = {Metagenomic analysis reveals unexplored diversity of archaeal virome in the human gut.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7978}, pmid = {36581612}, issn = {2041-1723}, mesh = {Humans ; Archaea/genetics ; Metagenome/genetics ; Virome ; *Viruses/genetics ; Metagenomics ; *Archaeal Viruses/genetics ; }, abstract = {The human gut microbiome has been extensively explored, while the archaeal viruses remain largely unknown. Here, we present a comprehensive analysis of the archaeal viruses from the human gut metagenomes and the existing virus collections using the CRISPR spacer and viral signature-based approach. This results in 1279 viral species, of which, 95.2% infect Methanobrevibacteria_A, 56.5% shared high identity (>95%) with the archaeal proviruses, 37.2% have a host range across archaeal species, and 55.7% are highly prevalent in the human population (>1%). A methanogenic archaeal virus-specific gene for pseudomurein endoisopeptidase (PeiW) frequently occurs in the viral sequences (n = 150). Analysis of 33 Caudoviricetes viruses with a complete genome often discovers the genes (integrase, n = 29; mazE, n = 10) regulating the viral lysogenic-lytic cycle, implying the dominance of temperate viruses in the archaeal virome. Together, our work uncovers the unexplored diversity of archaeal viruses, revealing the novel facet of the human gut microbiome.}, } @article {pmid36581267, year = {2023}, author = {Tang, L and Su, C and Wang, Q and Cao, L and Xian, Y and Wen, S and Zhou, Y and Gao, S}, title = {Use of iron-loaded biochar to alleviate anammox performance inhibition under PFOA stress conditions: Integrated analysis of sludge characteristics and metagenomics.}, journal = {The Science of the total environment}, volume = {865}, number = {}, pages = {161178}, doi = {10.1016/j.scitotenv.2022.161178}, pmid = {36581267}, issn = {1879-1026}, mesh = {*Sewage/microbiology ; *Iron ; Metagenomics ; Anaerobic Ammonia Oxidation ; Oxidation-Reduction ; Bioreactors/microbiology ; Nitrogen ; Denitrification ; }, abstract = {The negative effects of perfluorooctanoic acid (PFOA) on biological nitrogen removal performance in wastewater treatment plants, are receiving increasing attention due to the widespread reporting of this issue. In this study, pomelo peel iron-loaded biochar (Fe-PBC) was added to an anammox bioreactor to alleviate the negative effects of PFOA. Results showed that the addition of Fe-PBC increased the ammonia and nitrite removal efficiencies from 77.7 ± 9.6 % and 79.5 ± 5.6 % to 94.45 ± 5.1 % and 95.9 ± 5.0 %, respectively. In addition, Fe-PBC promoted the removal of PFOA from wastewater, increasing the PFOA removal efficiency from 5.2 % to 29.2 ± 4.3 % from 100 to 200 days. The introduction of iron-loaded biochar into the anammox bioreactor increased the CO ratio by 13.64 % by 150 days. In addition, a CO fitting peak was detected in the Fe-PBC, indicating that the Fe-PBC was loaded with microorganisms. Microbial community analysis showed a decrease in the relative abundances of Proteobacteria and Nitrospirae from 31 % and 3.4 % to 16.8 % and 0.9 %, respectively, while the relative abundance of Planctomycetes increased from 26.8 % to 44.1 %. Metagenomic analysis found that the functional genes hzsB and hdh increased from 98,666 ± 11,400 and 3190 ± 460 to 119,333 ± 15,534 and 138,650 ± 11,233 copy numbers/MLSS. The increase in anammox biomass may be attributed to the presence of iron, an essential element for the synthesis of key anammox enzyme. Furthermore, iron was also associated with the enhanced extracellular electron transfer in the anammox system induced by Fe-PBC.}, } @article {pmid36581234, year = {2023}, author = {Zhang, J and Yue, Z and Ding, C and Zhou, Z and Zhang, T and Wang, X}, title = {Metagenomic binning analyses of pig manure composting reveal potential antibiotic-degrading bacteria and their risk of antibiotic resistance genes.}, journal = {Bioresource technology}, volume = {371}, number = {}, pages = {128540}, doi = {10.1016/j.biortech.2022.128540}, pmid = {36581234}, issn = {1873-2976}, mesh = {Swine ; Humans ; Animals ; *Manure/microbiology ; Genes, Bacterial/genetics ; Metagenome ; Anti-Bacterial Agents/pharmacology ; *Composting ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; }, abstract = {Antibiotic-degrading bacteria are commonly used to treat antibiotic contamination, but the antibiotic resistance genes (ARGs) they carry are often overlooked. This study used metagenomic assembly and binning analyses to explore potential antibiotic-degrading bacteria and their ARGs during pig manure composting. The result showed that 35 metagenome-assembled genomes (MAGs) mainly containing alkyl-aryl transferase and decarboxylase genes involved in the removal of antibiotics. Multidrug (124), β-lactam (67), macrolide-lincosamide-streptogramin (MLS) (64), and tetracycline (43) were the central ARG types detected in the 35 MAGs. Furthermore, the risk of ARGs was evaluated using the arg_ranker framework, and 19 MAGs were found to contain intermediate-high-risk ARGs with human-associated-enrichment, gene transferability, and host pathogenicity. Bin 34 of the genus of Geofilum had the highest ARG risk. Bin 6, Bin 11 and Bin 14 of the genus of Limnochorda, Chelatococcus and Niabella, had a lower ARG risk and were considered as potential antibiotic-degrading bacteria.}, } @article {pmid36580984, year = {2023}, author = {Xu, L and Yang, Y and Su, J and He, C and Shi, J and Yan, H and Wei, H}, title = {Simultaneous removal of nitrate, lead, and tetracycline by a fixed-biofilm reactor assembled with kapok fiber and sponge iron: Comparative analysis of operating conditions and biotic community.}, journal = {Environmental research}, volume = {219}, number = {}, pages = {115163}, doi = {10.1016/j.envres.2022.115163}, pmid = {36580984}, issn = {1096-0953}, mesh = {*Nitrates ; *Iron ; Lead ; Tetracycline ; Anti-Bacterial Agents ; Biofilms ; Carbon ; Biota ; Bioreactors ; Nitrogen ; }, abstract = {In recent years, under the condition of lack of carbon source, the presence of composite micro-pollutants make the removal of nitrate seriously damaged, and to find a suitable way to solve this problem is imminent. A fixed-biofilm carrier modified by mixing sponge iron (SI) and kapok fiber (KF) combined with strain Zoogloea sp. FY6 was constructed in this study to get a fixed-biofilm reactor with merit denitrification performance. By adjusting the operation parameters, it can be concluded that when the carbon to nitrogen (C/N) ratio was 1.5, the hydraulic retention time (HRT) was 6.0 h, and the pH was 6.0, the nitrate removal efficiency (NRE) of the fixed-biofilm reactor was up to 95.4% (2.95 mg L[-1] h[-1]). In addition, the fixed-biofilm reactor constructed in this study can remove lead (Pb[2+]) and tetracycline (TC) excellently in the presence of SI and Zoogloea sp. FY6, and the denitrification performance can still maintain a high level under the influence of different concentrations of Pb[2+] and TC. Furthermore, the addition of SI not only removes the compound pollutants, but also protects the toxicity of the pollutant inflow in the bioreactor, and the metabolic process of microorganisms in the bioreactor also removes some of the compound pollutants. The high-throughput data showed the abundance of strain Zoogloea sp. FY6 was still the highest value under the influence of various pollutants, and the metagenomic prediction showed that the fixed-biofilm reactor had perfect denitrification process and iron redox cycle benefits. This study provides a valuable reference for sustainable utilization of natural biological resources and reduction of material costs in wastewater treatment plants (WWTPs).}, } @article {pmid36580779, year = {2023}, author = {Tao, Y and Shen, L and Han, S and Li, Z and Cui, Y and Lin, Y and Qu, J and Zhang, Y}, title = {Metagenomic study of carbon metabolism in black soil microbial communities under lead-lanthanum stress.}, journal = {Journal of hazardous materials}, volume = {446}, number = {}, pages = {130666}, doi = {10.1016/j.jhazmat.2022.130666}, pmid = {36580779}, issn = {1873-3336}, mesh = {Soil/chemistry ; Lanthanum ; Lead/toxicity ; *Metals, Heavy/analysis ; *Microbiota ; *Soil Pollutants/metabolism ; Soil Microbiology ; }, abstract = {Pollution of soil environments with heavy metals (HMs) and rare earth elements (REEs) cannot be ignored. We aimed to determine the effects of lead combined with lanthanum (Pb-La) on microbial community structure, carbon metabolism, and differences in carbon source utilization in black soils using EcoPlates™ and a macrogenomic approach. We found that Pb and La contents and the microbial community structure together influence and shape the response of soil carbon metabolism to Pb-La. Compared with controls, microorganisms under pollution stress preferentially use phenolic and carboxylic acids as growth carbon sources. Under Pb-La stress, the relative abundance of Proteobacteria significantly increased, thereby selectively displacing heavy metal-sensitive phyla, such as Chloroflexi, Acidobacteria, and Thaumarchaeota. Altered functional potential of the microbial carbon cycle manifested as differences in carbon metabolism, methane metabolism, and carbon fixation pathways. Furthermore, an appropriate concentration of La can reduce the environmental toxicity of Pb, whereas a high concentration of La has synergistic toxicity with Pb. These findings have important implications for understanding the impact of HM-REE contamination in microbial communities and the functions associated with carbon metabolism in black soils.}, } @article {pmid36580629, year = {2023}, author = {Richter, JL and Zawadzki, SF and Alves Dos Santos, L and Alnoch, RC and Moure, VR and Mitchell, DA and Krieger, N}, title = {Immobilization of the metagenomic lipase, LipG9, on porous pellets of poly-hydroxybutyrate produced by the double emulsion solvent evaporation technique.}, journal = {Biotechnology and applied biochemistry}, volume = {70}, number = {3}, pages = {1279-1290}, doi = {10.1002/bab.2438}, pmid = {36580629}, issn = {1470-8744}, support = {303287/2019-5//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior/ ; }, mesh = {Emulsions ; *Hydroxybutyrates ; *Lipase ; Polyesters ; Porosity ; Powders ; Solvents ; }, abstract = {This work aimed to produce porous poly-hydroxybutyrate (PHB) pellets in order to evaluate the pellets as a support for immobilization of the metagenomic lipase, LipG9. Four types of pelletized PHB particles with different morphological characteristics were obtained using the double emulsion and solvent evaporation technique (DESE). The micropores of these PHB pellets had similar average diameters (about 3 nm), but the pellets had different specific surface areas: 11.7 m[2] g[-1] for the PHB powder, 8.4 m[2] g[-1] for the control pellets (Ø < 0.5 mm, produced without the pore forming agent), 10.0 m[2] g[-1] for the small pellets (Ø < 0.5 mm), 9.5 m[2] g[-1] for the medium pellets (0.5 < Ø < 0.8 mm) and 8.4 m[2] g[-1] for the large pellets (Ø > 1.4 mm). Purified LipG9 was immobilized by adsorption on these pellets, and the results were compared with those obtained with PHB powder. The highest immobilization yield (83%) was obtained for the medium PHB pellets, followed by large (76%) and small (55%) PHB pellets. The activity of LipG9 immobilized on the pellets, for the synthesis of ethyl oleate in n-hexane, was highest for the medium pellets (22 U g[-1]). The immobilization yield was high for PHB powder (99%) but the esterification activity was slightly lower (20 U g[-1]). These results show that pelletized PHB beads can be used for the immobilization of lipases, with the advantage that pelletized PHB will perform better than PHB powder in large-scale enzyme bioreactors.}, } @article {pmid36579886, year = {2023}, author = {Shen, W and Xiang, H and Huang, T and Tang, H and Peng, M and Cai, D and Hu, P and Ren, H}, title = {KMCP: accurate metagenomic profiling of both prokaryotic and viral populations by pseudo-mapping.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {1}, pages = {}, pmid = {36579886}, issn = {1367-4811}, support = {32000474//National Natural Science Foundation of China/ ; 2021M700640//China Postdoctoral Science Foundation/ ; }, mesh = {*Algorithms ; Sequence Analysis, DNA/methods ; *Software ; Metagenome ; Metagenomics/methods ; }, abstract = {MOTIVATION: The growing number of microbial reference genomes enables the improvement of metagenomic profiling accuracy but also imposes greater requirements on the indexing efficiency, database size and runtime of taxonomic profilers. Additionally, most profilers focus mainly on bacterial, archaeal and fungal populations, while less attention is paid to viral communities.

RESULTS: We present KMCP (K-mer-based Metagenomic Classification and Profiling), a novel k-mer-based metagenomic profiling tool that utilizes genome coverage information by splitting the reference genomes into chunks and stores k-mers in a modified and optimized Compact Bit-Sliced Signature Index for fast alignment-free sequence searching. KMCP combines k-mer similarity and genome coverage information to reduce the false positive rate of k-mer-based taxonomic classification and profiling methods. Benchmarking results based on simulated and real data demonstrate that KMCP, despite a longer running time than all other methods, not only allows the accurate taxonomic profiling of prokaryotic and viral populations but also provides more confident pathogen detection in clinical samples of low depth.

The software is open-source under the MIT license and available at https://github.com/shenwei356/kmcp.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36579850, year = {2023}, author = {Javkar, K and Rand, H and Strain, E and Pop, M}, title = {PRAWNS: compact pan-genomic features for whole-genome population genomics.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {1}, pages = {}, pmid = {36579850}, issn = {1367-4811}, support = {R01 AI100947/AI/NIAID NIH HHS/United States ; //Center for Food Safety and Applied Nutrition/ ; }, mesh = {*Metagenomics ; *Software ; Genomics ; Genome ; Bacteria ; }, abstract = {MOTIVATION: Scientists seeking to understand the genomic basis of bacterial phenotypes, such as antibiotic resistance, today have access to an unprecedented number of complete and nearly complete genomes. Making sense of these data requires computational tools able to perform multiple-genome comparisons efficiently, yet currently available tools cannot scale beyond several tens of genomes.

RESULTS: We describe PRAWNS, an efficient and scalable tool for multiple-genome analysis. PRAWNS defines a concise set of genomic features (metablocks), as well as pairwise relationships between them, which can be used as a basis for large-scale genotype-phenotype association studies. We demonstrate the effectiveness of PRAWNS by identifying genomic regions associated with antibiotic resistance in Acinetobacter baumannii.

PRAWNS is implemented in C++ and Python3, licensed under the GPLv3 license, and freely downloadable from GitHub (https://github.com/KiranJavkar/PRAWNS.git).

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36578080, year = {2022}, author = {Shuwen, H and Yinhang, W and Xingming, Z and Jing, Z and Jinxin, L and Wei, W and Kefeng, D}, title = {Using whole-genome sequencing (WGS) to plot colorectal cancer-related gut microbiota in a population with varied geography.}, journal = {Gut pathogens}, volume = {14}, number = {1}, pages = {50}, pmid = {36578080}, issn = {1757-4749}, support = {No.2022C03026//Key Research and Development Project of Zhejiang Province/ ; No. 82072624//National Natural Science Foundation of China/ ; No. 226-2022-00009//Fundamental Research Funds for the Central Universities/ ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is a multifactorial disease with genetic and environmental factors. Regional differences in risk factors are an important reason for the different incidences of CRC in different regions.

OBJECTIVE: The goal was to clarify the intestinal microbial composition and structure of CRC patients in different regions and construct CRC risk prediction models based on regional differences.

METHODS: A metagenomic dataset of 601 samples from 6 countries in the GMrepo and NCBI databases was collected. All whole-genome sequencing (WGS) data were annotated for species by MetaPhlAn2. We obtained the relative abundance of species composition at the species level and genus level. The MicrobiotaProcess package was used to visualize species composition and PCA. LEfSe analysis was used to analyze the differences in the datasets in each region. Spearman correlation analysis was performed for CRC differential species. Finally, the CRC risk prediction model was constructed and verified in each regional dataset.

RESULTS: The composition of the intestinal bacterial community varied in different regions. Differential intestinal bacteria of CRC in different regions are inconsistent. There was a common diversity of bacteria in all six countries, such as Peptostreptococcus stomatis and Fusobacterium nucleatum at the species level. Peptostreptococcus stomatis (species level) and Peptostreptococcus (genus level) are important CRC-related bacteria that are related to other bacteria in different regions. Region has little influence on the accuracy of the CRC risk prediction model. Peptostreptococcus stomatis is an important variable in CRC risk prediction models in all regions.

CONCLUSION: Peptostreptococcus stomatis is a common high-risk pathogen of CRC worldwide, and it is an important variable in CRC risk prediction models in all regions. However, regional differences in intestinal bacteria had no significant impact on the accuracy of the CRC risk prediction model.}, } @article {pmid36578059, year = {2022}, author = {Kunath, BJ and Hickl, O and Queirós, P and Martin-Gallausiaux, C and Lebrun, LA and Halder, R and Laczny, CC and Schmidt, TSB and Hayward, MR and Becher, D and Heintz-Buschart, A and de Beaufort, C and Bork, P and May, P and Wilmes, P}, title = {Alterations of oral microbiota and impact on the gut microbiome in type 1 diabetes mellitus revealed by integrated multi-omic analyses.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {243}, pmid = {36578059}, issn = {2049-2618}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Diabetes Mellitus, Type 1/microbiology ; Proteomics ; Multiomics ; *Microbiota/genetics ; Mouth/microbiology ; Enterobacteriaceae ; }, abstract = {BACKGROUND: Alterations to the gut microbiome have been linked to multiple chronic diseases. However, the drivers of such changes remain largely unknown. The oral cavity acts as a major route of exposure to exogenous factors including pathogens, and processes therein may affect the communities in the subsequent compartments of the gastrointestinal tract. Here, we perform strain-resolved, integrated meta-genomic, transcriptomic, and proteomic analyses of paired saliva and stool samples collected from 35 individuals from eight families with multiple cases of type 1 diabetes mellitus (T1DM).

RESULTS: We identified distinct oral microbiota mostly reflecting competition between streptococcal species. More specifically, we found a decreased abundance of the commensal Streptococcus salivarius in the oral cavity of T1DM individuals, which is linked to its apparent competition with the pathobiont Streptococcus mutans. The decrease in S. salivarius in the oral cavity was also associated with its decrease in the gut as well as higher abundances in facultative anaerobes including Enterobacteria. In addition, we found evidence of gut inflammation in T1DM as reflected in the expression profiles of the Enterobacteria as well as in the human gut proteome. Finally, we were able to follow transmitted strain-variants from the oral cavity to the gut at the individual omic levels, highlighting not only the transfer, but also the activity of the transmitted taxa along the gastrointestinal tract.

CONCLUSIONS: Alterations of the oral microbiome in the context of T1DM impact the microbial communities in the lower gut, in particular through the reduction of "mouth-to-gut" transfer of Streptococcus salivarius. Our results indicate that the observed oral-cavity-driven gut microbiome changes may contribute towards the inflammatory processes involved in T1DM. Through the integration of multi-omic analyses, we resolve strain-variant "mouth-to-gut" transfer in a disease context. Video Abstract.}, } @article {pmid36577938, year = {2022}, author = {Alshawaqfeh, M and Rababah, S and Hayajneh, A and Gharaibeh, A and Serpedin, E}, title = {MetaAnalyst: a user-friendly tool for metagenomic biomarker detection and phenotype classification.}, journal = {BMC medical research methodology}, volume = {22}, number = {1}, pages = {336}, pmid = {36577938}, issn = {1471-2288}, support = {SEEIT 1/2020//German-Jordanian University/ ; }, mesh = {Humans ; *Software ; *Algorithms ; Metagenomics ; Biomarkers ; Phenotype ; }, abstract = {BACKGROUND: Many metagenomic studies have linked the imbalance in microbial abundance profiles to a wide range of diseases. These studies suggest utilizing the microbial abundance profiles as potential markers for metagenomic-associated conditions. Due to the inevitable importance of biomarkers in understanding the disease progression and the development of possible therapies, various computational tools have been proposed for metagenomic biomarker detection. However, most existing tools require prior scripting knowledge and lack user friendly interfaces, causing considerable time and effort to install, configure, and run these tools. Besides, there is no available all-in-one solution for running and comparing various metagenomic biomarker detection simultaneously. In addition, most of these tools just present the suggested biomarkers without any statistical evaluation for their quality.

RESULTS: To overcome these limitations, this work presents MetaAnalyst, a software package with a simple graphical user interface (GUI) that (i) automates the installation and configuration of 28 state-of-the-art tools, (ii) supports flexible study design to enable studying the dataset under different scenarios smoothly, iii) runs and evaluates several algorithms simultaneously iv) supports different input formats and provides the user with several preprocessing capabilities, v) provides a variety of metrics to evaluate the quality of the suggested markers, and vi) presents the outcomes in the form of publication quality plots with various formatting capabilities as well as Excel sheets.

CONCLUSIONS: The utility of this tool has been verified through studying a metagenomic dataset under four scenarios. The executable file for MetaAnalyst along with its user manual are made available at https://github.com/mshawaqfeh/MetaAnalyst .}, } @article {pmid36577285, year = {2023}, author = {Bambaradeniya, YTB and Magni, PA and Dadour, IR}, title = {Traumatic sheep myiasis: A review of the current understanding.}, journal = {Veterinary parasitology}, volume = {314}, number = {}, pages = {109853}, doi = {10.1016/j.vetpar.2022.109853}, pmid = {36577285}, issn = {1873-2550}, mesh = {Humans ; Animals ; Sheep ; *Sheep Diseases/epidemiology/prevention & control ; *Myiasis/epidemiology/veterinary ; *Diptera ; Weather ; Larva ; }, abstract = {Myiasis, or the infestation of live humans and vertebrate animals by dipterous larvae, is a health issue worldwide. The economic impact and potential threat to animal health and wellbeing of this disease under the animal husbandry sector is considerable. Sheep are a highly vulnerable livestock category exposed to myiasis (sheep strike), due to several unique predisposing factors that attract flies. The successful mitigation of this disease relies on a thorough understanding of fly population dynamics associated with the change in weather patterns and the evaluation of this disease through different branches of science such as chemistry, molecular biology, and microbiology. The present review provides a summary of the existing knowledge of strike in sheep, discussed in relation to the application of volatile organic compounds, metagenomics, and molecular biology, and their use regarding implementing fly control strategies such as traps, and to increase the resilience of sheep to this disease through improving their health and wellbeing.}, } @article {pmid36576625, year = {2023}, author = {Wang, Y and Zhang, X and Lin, Y and Lin, H}, title = {The electron transport mechanism of downflow Leersia hexandra Swartz constructed wetland-microbial fuel cell when used to treat Cr(VI) and p-chlorophenol.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {13}, pages = {37929-37945}, pmid = {36576625}, issn = {1614-7499}, support = {52070051//the National Natural Science Foundation of China/ ; 52170154//the National Natural Science Foundation of China/ ; 2020GXNSFAA297256//Guangxi Science and Technology Program/ ; Guike finance letter [2018]319//Guangxi Colleges and Universities High-level Innovation Team and Outstanding Scholars Program Project/ ; }, mesh = {*Bioelectric Energy Sources/microbiology ; Electron Transport ; Wetlands ; Wastewater ; Electricity ; Poaceae ; Electrodes ; }, abstract = {Constructed wetland-microbial fuel cells are used to treat heavy metal and/or refractory organic wastewater. However, the electron transport mechanism of downflow Leersia hexandra constructed wetland-microbial fuel cells (DLCW-MFCs) is poorly understood when used to treat composite-polluted wastewater containing Cr(VI) and p-chlorophenol (4-CP) (C&P). In this study, metagenomics and in situ electrochemical techniques were used to investigate the electrochemical properties and the electricigens and their dominant gene functions. The DLCW-MFC was used to treat C&P and single-pollutant wastewater containing Cr(VI) (SC) and 4-CP (SP). The results showed that C&P had a higher current response and charge transfer capability and lower solution resistance plus charge transfer resistance. The anode bacteria solution of C&P contained more electron carriers (RF, FMN, FAD, CoQ10, and Cyt c). Metagenomic sequencing indicated that the total relative abundance of the microorganisms associated with electricity production (Desulfovibrio, Pseudomonas, Azospirillum, Nocardia, Microbacterium, Delftia, Geobacter, Acinetobacter, Bacillus, and Clostridium) was the highest in C&P (4.24%). However, Microbacterium was abundant in SP (0.12%), which exerted antagonistic effects on other electricigens. Among the 10 electricigens based on gene annotation, C&P had a higher overall relative abundance of the Unigene gene annotated to the KO pathway and CAZy level B compared with SC and SP, which were 1.31% and 0.582% respectively. Unigene153954 (ccmC), Unigene357497 (coxB), and Unigene1033667 (ubiG) were related to the electron carrier Cyt c, electron transfer, and CoQ biosynthesis, respectively. These were annotated to Desulfovibrio, Delftia, and Pseudomonas, respectively. Unigene161312 (AA1) used phenols and other substrates as electron donors and was annotated to Pseudomonas. Other functional carbohydrate enzyme genes (e.g., GT2, GT4, and GH31) used carbohydrates as donors and were annotated to other electricigens. This study provides a theoretical basis for electron transfer to promote the development of CW-MFCs.}, } @article {pmid36576579, year = {2022}, author = {Bora, SS and Hazarika, DJ and Churaman, A and Naorem, RS and Dasgupta, A and Chakrabarty, R and Kalita, H and Barooah, M}, title = {Common scab disease-induced changes in geocaulosphere microbiome assemblages and functional processes in landrace potato (Solanum tuberosum var. Rongpuria) of Assam, India.}, journal = {Archives of microbiology}, volume = {205}, number = {1}, pages = {44}, pmid = {36576579}, issn = {1432-072X}, mesh = {*Solanum tuberosum ; Plant Diseases ; Soil Microbiology ; *Microbiota ; India ; }, abstract = {Common scab (CS) caused by pathogenic Streptomyces spp. plays a decisive role in the qualitative and quantitative production of potatoes worldwide. Although the CS pathogen is present in Assam's soil, disease signs and symptoms are less obvious in the landrace Rongpuria potatoes that indicate an interesting interaction between the plant and the geocaulosphere microbial population. Toward this, a comparative metagenomics study was performed to elucidate the geocaulosphere microbiome assemblages and functions of low CS-severe (LSG) and moderately severe (MSG) potato plants. Alpha diversity indices showed that CS occurrence modulated microbiome composition and decreased overall microbial abundances. Functional analysis involving cluster of orthologous groups (COG) too confirmed reduced microbial metabolism under disease incidence. The top-three most dominant genera were Pseudomonas (relative abundance: 2.79% in LSG; 12.31% in MSG), Streptomyces (2.55% in LSG; 5.28% in MSG), and Pantoea (2.30% in LSG; 3.51% in MSG). As shown by the high Pielou's J evenness index, the potato geocaulosphere core microbiome was adaptive and resilient to CS infection. The plant growth-promoting traits and potential antagonistic activity of major taxa (Pseudomonads, non-pathogenic Streptomyces spp., and others) against the CS pathogen, i.e., Streptomyces scabiei, point toward selective microbial recruitment and colonization strategy by the plants to its own advantage. KEGG Orthology analysis showed that the CS infection resulted in high abundances of ATP-binding cassette transporters and a two-component system, ubiquitous to the transportation and regulation of metabolites. As compared to the LSG metagenome, the MSG counterpart had a higher representation of important PGPTs related to 1-aminocyclopropane-1-carboxylate deaminase, IAA production, betaine utilization, and siderophore production.}, } @article {pmid36576350, year = {2023}, author = {Wang, G and Lam, WKJ and Ling, L and Ma, ML and Ramakrishnan, S and Chan, DCT and Lee, WS and Cheng, SH and Chan, RWY and Yu, SCY and Tse, IOL and Wong, WT and Jiang, P and Chiu, RWK and Allen Chan, KC and Lo, YMD}, title = {Fragment Ends of Circulating Microbial DNA as Signatures for Pathogen Detection in Sepsis.}, journal = {Clinical chemistry}, volume = {69}, number = {2}, pages = {189-201}, doi = {10.1093/clinchem/hvac197}, pmid = {36576350}, issn = {1530-8561}, mesh = {Humans ; *Cell-Free Nucleic Acids ; DNA/genetics ; *Sepsis/diagnosis ; DNA Fragmentation ; }, abstract = {BACKGROUND: Nuclear-derived cell-free DNA (cfDNA) molecules in blood plasma are nonrandomly fragmented, bearing a wealth of information related to tissues of origin. DNASE1L3 (deoxyribonuclease 1 like 3) is an important player in shaping the fragmentation of nuclear-derived cfDNA molecules, preferentially generating molecules with 5 CC dinucleotide termini (i.e., 5 CC-end motif). However, the fragment end properties of microbial cfDNA and its clinical implication remain to be explored.

METHODS: We performed end motif analysis on microbial cfDNA fragments in plasma samples from patients with sepsis. A sequence context-based normalization method was used to minimize the potential biases for end motif analysis.

RESULTS: The end motif profiles of microbial cfDNA appeared to resemble that of nuclear cfDNA (Spearman correlation coefficient: 0.82, P value 0.001). The CC-end motif was the most preferred end motif in microbial cfDNA, suggesting that DNASE1L3 might also play a role in the fragmentation of microbe-derived cfDNA in plasma. Of note, differential end motifs were present between microbial cfDNA originating from infection-causing pathogens (enriched at the CC-end) and contaminating microbial DNA potentially derived from reagents or the environment (nearly random). The use of fragment end signatures allowed differentiation between confirmed pathogens and contaminating microbes, with an area under the receiver operating characteristic curve of 0.99. The performance appeared to be superior to conventional analysis based on microbial cfDNA abundance alone.

CONCLUSIONS: The use of fragmentomic features could facilitate the differentiation of underlying contaminating microbes from true pathogens in sepsis. This work demonstrates the potential usefulness of microbial cfDNA fragmentomics in metagenomics analysis.}, } @article {pmid36576131, year = {2022}, author = {Mendes, CI and Vila-Cerqueira, P and Motro, Y and Moran-Gilad, J and Carriço, JA and Ramirez, M}, title = {LMAS: evaluating metagenomic short de novo assembly methods through defined communities.}, journal = {GigaScience}, volume = {12}, number = {}, pages = {}, pmid = {36576131}, issn = {2047-217X}, mesh = {*Software ; *Algorithms ; Sequence Analysis, DNA/methods ; Genomics/methods ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {BACKGROUND: The de novo assembly of raw sequence data is key in metagenomic analysis. It allows recovering draft genomes from a pool of mixed raw reads, yielding longer sequences that offer contextual information and provide a more complete picture of the microbial community.

FINDINGS: To better compare de novo assemblers for metagenomic analysis, LMAS (Last Metagenomic Assembler Standing) was developed as a flexible platform allowing users to evaluate assembler performance given known standard communities. Overall, in our test datasets, k-mer De Bruijn graph assemblers outperformed the alternative approaches but came with a greater computational cost. Furthermore, assemblers branded as metagenomic specific did not consistently outperform other genomic assemblers in metagenomic samples. Some assemblers still in use, such as ABySS, MetaHipmer2, minia, and VelvetOptimiser, perform relatively poorly and should be used with caution when assembling complex samples. Meaningful strain resolution at the single-nucleotide polymorphism level was not achieved, even by the best assemblers tested.

CONCLUSIONS: The choice of a de novo assembler depends on the computational resources available, the replicon of interest, and the major goals of the analysis. No single assembler appeared an ideal choice for short-read metagenomic prokaryote replicon assembly, each showing specific strengths. The choice of metagenomic assembler should be guided by user requirements and characteristics of the sample of interest, and LMAS provides an interactive evaluation platform for this purpose. LMAS is open source, and the workflow and its documentation are available at https://github.com/B-UMMI/LMAS and https://lmas.readthedocs.io/, respectively.}, } @article {pmid36576106, year = {2023}, author = {Dhariwal, A and Haugli Bråten, LC and Sturød, K and Salvadori, G and Bargheet, A and Åmdal, H and Junges, R and Berild, D and Zwart, JA and Storheim, K and Petersen, FC}, title = {Differential response to prolonged amoxicillin treatment: long-term resilience of the microbiome versus long-lasting perturbations in the gut resistome.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2157200}, pmid = {36576106}, issn = {1949-0984}, mesh = {Humans ; Amoxicillin/pharmacology/therapeutic use ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Microbiota ; Feces ; }, abstract = {The collateral impact of antibiotics on the microbiome has attained increasing attention. However, the ecological consequences of long-term antibiotic exposure on the gut microbiome, including antibiotic resistance, are still limited. Here, we investigated long-term exposure effects to amoxicillin on the human gut microbiome and resistome. Fecal samples were collected from 20 patients receiving 3-months of amoxicillin or placebo treatment as part of a Norwegian multicenter clinical trial on chronic low back pain (AIM study). Samples were collected at baseline, last day of treatment, and 9 months after antibiotic cessation. The abundance and diversity of microbial and resistome composition were characterized using whole shotgun and functional metagenomic sequencing data. While the microbiome profiles of placebo subjects were stable over time, discernible changes in diversity and overall microbiome composition were observed after amoxicillin treatment. In particular, health-associated short-chain fatty acid producing species significantly decreased in proportion. However, these changes were short-lived as the microbiome showed overall recovery 9 months post-treatment. On the other hand, exposure to long-term amoxicillin was associated with an increase in total antimicrobial resistance gene load and diversity of antimicrobial resistance genes, with persistent changes even at 9 months post-treatment. Additionally, beta-lactam resistance was the most affected antibiotic class, suggesting a targeted response to amoxicillin, although changes at the gene level varied across individuals. Overall, our results suggest that the impact of prolonged amoxicillin exposure was more explicit and long-lasting in the fecal resistome than in microbiome composition. Such information is relevant for designing rational administration guidelines for antibiotic therapies.}, } @article {pmid36575982, year = {2023}, author = {Luo, S and Zhao, Y and Zhu, S and Liu, L and Cheng, K and Ye, B and Han, Y and Fan, J and Xia, M}, title = {Flavonifractor plautii Protects Against Elevated Arterial Stiffness.}, journal = {Circulation research}, volume = {132}, number = {2}, pages = {167-181}, doi = {10.1161/CIRCRESAHA.122.321975}, pmid = {36575982}, issn = {1524-4571}, mesh = {Animals ; Mice ; Humans ; *Matrix Metalloproteinase 2 ; *Vascular Stiffness/physiology ; Pulse Wave Analysis ; Aconitic Acid/pharmacology ; }, abstract = {BACKGROUND: Dysbiosis of gut microbiota plays a pivotal role in vascular dysfunction and microbial diversity was reported to be inversely correlated with arterial stiffness. However, the causal role of gut microbiota in the progression of arterial stiffness and the specific species along with the molecular mechanisms underlying this change remain largely unknown.

METHODS: Participants with elevated arterial stiffness and normal controls free of medication were matched for age and sex. The microbial composition and metabolic capacities between the 2 groups were compared with the integration of metagenomics and metabolomics. Subsequently, Ang II (angiotensin II)-induced and humanized mouse model were employed to evaluate the protective effect of Flavonifractor plautii (F plautii) and its main effector cis-aconitic acid.

RESULTS: Human fecal metagenomic sequencing revealed a significantly high abundance and centrality of F plautii in normal controls, which was absent in the microbial community of subjects with elevated arterial stiffness. Moreover, blood pressure only mediated part of the effect of F plautii on lower arterial stiffness. The microbiome of normal controls exhibited an enhanced capacity for glycolysis and polysaccharide degradation, whereas, those of subjects with increased arterial stiffness were characterized by increased biosynthesis of fatty acids and aromatic amino acids. Integrative analysis with metabolomics profiling further suggested that increased cis-aconitic acid served as the main effector for the protective effect of F plautii against arterial stiffness. Replenishment with F plautii and cis-aconitic acid improved elastic fiber network and reversed increased pulse wave velocity through the suppression of MMP-2 (matrix metalloproteinase-2) and inhibition of MCP-1 (monocyte chemoattractant protein-1) and NF-κB (nuclear factor kappa-B) activation in both Ang II-induced and humanized model of arterial stiffness.

CONCLUSIONS: Our translational study identifies a novel link between F plautii and arterial function and raises the possibility of sustaining vascular health by targeting gut microbiota.}, } @article {pmid36575570, year = {2023}, author = {Zhou, J and Song, W and Tu, Q}, title = {To assemble or not to assemble: metagenomic profiling of microbially mediated biogeochemical pathways in complex communities.}, journal = {Briefings in bioinformatics}, volume = {24}, number = {1}, pages = {}, doi = {10.1093/bib/bbac594}, pmid = {36575570}, issn = {1477-4054}, support = {ZR2020YQ21//National Natural Science Foundation of China/ ; 2019YFA0606700//National Key Research and Development Program of China/ ; }, mesh = {*Metagenome ; *Metagenomics ; High-Throughput Nucleotide Sequencing ; }, abstract = {High-throughput profiling of microbial functional traits involved in various biogeochemical cycling pathways using shotgun metagenomic sequencing has been routinely applied in microbial ecology and environmental science. Multiple bioinformatics data processing approaches are available, including assembly-based (single-sample assembly and multi-sample assembly) and read-based (merged reads and raw data). However, it remains not clear how these different approaches may differ in data analyses and affect result interpretation. In this study, using two typical shotgun metagenome datasets recovered from geographically distant coastal sediments, the performance of different data processing approaches was comparatively investigated from both technical and biological/ecological perspectives. Microbially mediated biogeochemical cycling pathways, including nitrogen cycling, sulfur cycling and B12 biosynthesis, were analyzed. As a result, multi-sample assembly provided the most amount of usable information for targeted functional traits, at a high cost of computational resources and running time. Single-sample assembly and read-based analysis were comparable in obtaining usable information, but the former was much more time- and resource-consuming. Critically, different approaches introduced much stronger variations in microbial profiles than biological differences. However, community-level differences between the two sampling sites could be consistently observed despite the approaches being used. In choosing an appropriate approach, researchers shall balance the trade-offs between multiple factors, including the scientific question, the amount of usable information, computational resources and time cost. This study is expected to provide valuable technical insights and guidelines for the various approaches used for metagenomic data analysis.}, } @article {pmid36575453, year = {2022}, author = {Barone, M and Garelli, S and Rampelli, S and Agostini, A and Matysik, S and D'Amico, F and Krautbauer, S and Mazza, R and Salituro, N and Fanelli, F and Iozzo, P and Sanz, Y and Candela, M and Brigidi, P and Pagotto, U and Turroni, S}, title = {Multi-omics gut microbiome signatures in obese women: role of diet and uncontrolled eating behavior.}, journal = {BMC medicine}, volume = {20}, number = {1}, pages = {500}, pmid = {36575453}, issn = {1741-7015}, support = {613979//Seventh Framework Programme/ ; 245009//Seventh Framework Programme/ ; }, mesh = {Humans ; Female ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Multiomics ; Obesity/genetics ; Diet ; Feeding Behavior/physiology ; Feces/microbiology ; }, abstract = {BACKGROUND: Obesity and related co-morbidities represent a major health challenge nowadays, with a rapidly increasing incidence worldwide. The gut microbiome has recently emerged as a key modifier of human health that can affect the development and progression of obesity, largely due to its involvement in the regulation of food intake and metabolism. However, there are still few studies that have in-depth explored the functionality of the human gut microbiome in obesity and even fewer that have examined its relationship to eating behaviors.

METHODS: In an attempt to advance our knowledge of the gut-microbiome-brain axis in the obese phenotype, we thoroughly characterized the gut microbiome signatures of obesity in a well-phenotyped Italian female cohort from the NeuroFAST and MyNewGut EU FP7 projects. Fecal samples were collected from 63 overweight/obese and 37 normal-weight women and analyzed via a multi-omics approach combining 16S rRNA amplicon sequencing, metagenomics, metatranscriptomics, and lipidomics. Associations with anthropometric, clinical, biochemical, and nutritional data were then sought, with particular attention to cognitive and behavioral domains of eating.

RESULTS: We identified four compositional clusters of the gut microbiome in our cohort that, although not distinctly associated with weight status, correlated differently with eating habits and behaviors. These clusters also differed in functional features, i.e., transcriptional activity and fecal metabolites. In particular, obese women with uncontrolled eating behavior were mostly characterized by low-diversity microbial steady states, with few and poorly interconnected species (e.g., Ruminococcus torques and Bifidobacterium spp.), which exhibited low transcriptional activity, especially of genes involved in secondary bile acid biosynthesis and neuroendocrine signaling (i.e., production of neurotransmitters, indoles and ligands for cannabinoid receptors). Consistently, high amounts of primary bile acids as well as sterols were found in their feces.

CONCLUSIONS: By finding peculiar gut microbiome profiles associated with eating patterns, we laid the foundation for elucidating gut-brain axis communication in the obese phenotype. Subject to confirmation of the hypotheses herein generated, our work could help guide the design of microbiome-based precision interventions, aimed at rewiring microbial networks to support a healthy diet-microbiome-gut-brain axis, thus counteracting obesity and related complications.}, } @article {pmid36575246, year = {2022}, author = {Bornbusch, SL and Clarke, TA and Hobilalaina, S and Reseva, HS and LaFleur, M and Drea, CM}, title = {Microbial rewilding in the gut microbiomes of captive ring-tailed lemurs (Lemur catta) in Madagascar.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {22388}, pmid = {36575246}, issn = {2045-2322}, mesh = {Animals ; Humans ; *Lemur ; *Gastrointestinal Microbiome/genetics ; Madagascar ; Diet ; Ecosystem ; *Strepsirhini ; }, abstract = {Microbial rewilding, whereby exposure to naturalistic environments can modulate or augment gut microbiomes and improve host-microbe symbiosis, is being harnessed as an innovative approach to human health, one that may also have significant value to animal care and conservation. To test for microbial rewilding in animal microbiomes, we used a unique population of wild-born ring-tailed lemurs (Lemur catta) that were initially held as illegal pets in unnatural settings and, subsequently, relocated to a rescue center in Madagascar where they live in naturalistic environments. Using amplicon and shotgun metagenomic sequencing of lemur and environmental microbiomes, we found multiple lines of evidence for microbial rewilding in lemurs that were transitioned from unnatural to naturalistic environments: A lemur's duration of exposure to naturalistic settings significantly correlated with (a) increased compositional similarly to the gut communities of wild lemurs, (b) decreased proportions of antibiotic resistance genes that were likely acquired via human contact during pethood, and (c) greater covariation with soil microbiomes from natural habitats. Beyond the inherent psychosocial value of naturalistic environments, we find that actions, such as providing appropriate diets, minimizing contact with humans, and increasing exposure to natural environmental consortia, may assist in maximizing host-microbe symbiosis in animals under human care.}, } @article {pmid36574894, year = {2023}, author = {El-Liethy, MA and Hemdan, BA and El-Taweel, GE}, title = {New insights for tracking bacterial community structures in industrial wastewater from textile factories to surface water using phenotypic, 16S rRNA isolates identifications and high-throughput sequencing.}, journal = {Acta tropica}, volume = {238}, number = {}, pages = {106806}, doi = {10.1016/j.actatropica.2022.106806}, pmid = {36574894}, issn = {1873-6254}, mesh = {*Wastewater ; RNA, Ribosomal, 16S/genetics ; *Water ; Bacteria ; High-Throughput Nucleotide Sequencing ; Textiles ; }, abstract = {Industrial wastewater can possibly change the microbial ecological environment. There are few studies that focus on the bacterial variety in textile wastewater effluents and after combination with domestic wastewater. Thus, this study aimed to determine dye degrading bacteria from textile wastewater and environmental water samples using cultural method followed by phenotypic using BIOLOG and genotypic identification (16S rRNA) for dye degrading isolates identifications. Moreover, the bacterial communities in three textile and four environmental samples using Illumina MiSeq high-throughput sequencing were investigated. The findings revealed that in textile water samples, the ratio of dye-degrading bacteria (DDB) to total bacterial counts (TBC) was 27%. The identified DDB genera by 16S rRNA based on the cultural approach were Citrobacter spp., Klebsiella spp., Enterobacter spp., Pseudomonas spp., and Aeromonas spp. Regarding to the metagenomics analyses, the environmental samples had 5,598 Operational Toxanomic Units (OTUs) more than textile wastewater samples (1,463 OTUs). Additionally, the most abundant phyla in the textile wastewater were Proteobacteria (24.45-94.83%), Bacteriodetes (0.5-44.84%) and Firmicutes (3.72-67.40%), while, Proteobacteria (30.8-76.3%), bacteroidetes (8.5-50%) and Acentobacteria (0.5-23.12%) were the most abundant phyla in the environmental samples. The maximum abundant bacteria at species level in environmental samples were Aquabacterium parvum (36.71%), Delftia tsuruhatensis (17.61%), Parabacteriodes chartae (15.39%) and Methylorubrum populi (7.51%) in El-Rahawy Drain water (RDW), River Nile water (RNW), wastewater (RWW) from WWTP in Zennin and El-Rahawy Drain sediment (RDS), respectively, whereas the maximum abundant bacteria at species level in textile wastewater were Alkalibacterium pelagium (34.11%), Enterobacter kobei (26.09%) and Chryseobacterium montanum (16.93%) in factory 1 (HBT) sample, SHB sample (before mixing with domestic wastewater) and SHB sample (after mixing with domestic wastewater), respectively. In conclusion, the microbial communities in textile wastewaters are similar to those in environmental samples at the phylum level but distinct at the genus and species levels because they are exposed to a wider range of environmental circumstances.}, } @article {pmid36574886, year = {2023}, author = {Lee, M and Yoo, K and Kim, H and Song, KG and Kim, D and Tiedje, JM and Lee, PH and Park, J}, title = {Metatranscriptional characterization of metabolic dynamics in anaerobic membrane bioreactor producing methane from low-strength wastewater.}, journal = {Bioresource technology}, volume = {370}, number = {}, pages = {128532}, doi = {10.1016/j.biortech.2022.128532}, pmid = {36574886}, issn = {1873-2976}, mesh = {*Wastewater ; Waste Disposal, Fluid/methods ; Anaerobiosis ; Methane/metabolism ; Bioreactors/microbiology ; *Euryarchaeota/metabolism ; Membranes, Artificial ; }, abstract = {An anaerobic membrane bioreactor (AnMBR) with media is an emerging carbon-neutral biotechnology for low-strength wastewater (LSWW) treatment and methane recovery. Understanding metabolic dynamics among methanogens and syntrophic bacteria is important in optimizing the design and operation of AnMBR. However, little is known about it, especially in media-attached microbial communities. This study explored metabolic dynamics to compare media-attached and suspended conditions. Accordingly, metagenomes and metatranscriptomes from AnMBRs with polymeric media and fed with different influent concentrations (350 and 700 mg-COD/L) were analyzed. Metabolic dynamics were profoundly influenced by the different growth habitats and influent conditions, although the applied influent concentrations are within the range of typical LSWW. Metabolic dynamics prediction results suggest that media-attached-growth habitats may have provided a more favorable microenvironment for methanogens to grow and produce methane, especially under low influent conditions. These findings provide significant implications for optimizing floating media design and operation of AnMBR-producing methane from LSWW.}, } @article {pmid36574159, year = {2022}, author = {Onohuean, H and Onohuean, FE and Igbinoba, SI and Ezeonwumelu, JOC and Agu, PC and Ifie, JE and Deusdedit, T and Aja, PM}, title = {Elucidation of chemical profiles and molecular targets of Mondia whitei leave fractions bioactive as novel therapeutics: an in vitro and in silico assay.}, journal = {Journal, genetic engineering & biotechnology}, volume = {20}, number = {1}, pages = {170}, pmid = {36574159}, issn = {2090-5920}, abstract = {BACKGROUND: Mondia whitei root is often used in Africa as a local therapeutic agent for libido enhancement. The fractions of the M. whitei leaves (MWL) lack chemical characterization of their bioactive components and possible molecular targets. We characterized and investigated its molecular target as therapeutic agents in an in vitro and in silico assay. Mineral compositions, antioxidant, and GC-MS characterization were studied. The cytotoxicity effect was measured on HeLa and HT-29 cells by MTT assay. In silico potential inhibitors of Cathepsin B (CathB) as a cancer biomarker were determined.

RESULTS: The flame photometry produced marked Na[+] and K[+]. GC-MS revealed eighteen bioactive components. The fractions (chloroformic 47.00, ethanolic 45.52, and aqueous 40.13) of MWL caused a higher inhibition ratio compared to standards. The MWL showed a significant cytotoxic effect on the treated cell lines at concentrations of 150 and 200 μg/ml and 100, 150, and 200 μg/ml for HT-29 and HeLa cells, respectively. Ten bioactives (MWL 4, 5, 6, 8, 9, 10, 14, 15, 17, and 18) showed potential inhibition of CathB with binding affinities of -4.40 to -8.3 Kcal/Mol. However, MWL 4, 9, 14, and 17 which have higher binding affinities (-6.7, -7.1, -8.2, and -8.3, respectively) than the standard inhibitor (-6.5) were the lead molecules.

CONCLUSION: These chemical profiles and potential molecular targets unraveled in this study propose that MWL has a promising anticancer activity.}, } @article {pmid36572924, year = {2022}, author = {Zhou, Z and St John, E and Anantharaman, K and Reysenbach, AL}, title = {Global patterns of diversity and metabolism of microbial communities in deep-sea hydrothermal vent deposits.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {241}, pmid = {36572924}, issn = {2049-2618}, mesh = {Humans ; *Hydrothermal Vents/microbiology ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Bacteria ; Archaea ; *Microbiota/genetics ; Sulfur/metabolism ; Carbon/metabolism ; Nitrogen/metabolism ; Hydrogen/metabolism ; }, abstract = {BACKGROUND: When deep-sea hydrothermal fluids mix with cold oxygenated fluids, minerals precipitate out of solution and form hydrothermal deposits. These actively venting deep-sea hydrothermal deposits support a rich diversity of thermophilic microorganisms which are involved in a range of carbon, sulfur, nitrogen, and hydrogen metabolisms. Global patterns of thermophilic microbial diversity in deep-sea hydrothermal ecosystems have illustrated the strong connectivity between geological processes and microbial colonization, but little is known about the genomic diversity and physiological potential of these novel taxa. Here we explore this genomic diversity in 42 metagenomes from four deep-sea hydrothermal vent fields and a deep-sea volcano collected from 2004 to 2018 and document their potential implications in biogeochemical cycles.

RESULTS: Our dataset represents 3635 metagenome-assembled genomes encompassing 511 novel and recently identified genera from deep-sea hydrothermal settings. Some of the novel bacterial (107) and archaeal genera (30) that were recently reported from the deep-sea Brothers volcano were also detected at the deep-sea hydrothermal vent fields, while 99 bacterial and 54 archaeal genera were endemic to the deep-sea Brothers volcano deposits. We report some of the first examples of medium- (≥ 50% complete, ≤ 10% contaminated) to high-quality (> 90% complete, < 5% contaminated) MAGs from phyla and families never previously identified, or poorly sampled, from deep-sea hydrothermal environments. We greatly expand the novel diversity of Thermoproteia, Patescibacteria (Candidate Phyla Radiation, CPR), and Chloroflexota found at deep-sea hydrothermal vents and identify a small sampling of two potentially novel phyla, designated JALSQH01 and JALWCF01. Metabolic pathway analysis of metagenomes provides insights into the prevalent carbon, nitrogen, sulfur, and hydrogen metabolic processes across all sites and illustrates sulfur and nitrogen metabolic "handoffs" in community interactions. We confirm that Campylobacteria and Gammaproteobacteria occupy similar ecological guilds but their prevalence in a particular site is driven by shifts in the geochemical environment.

CONCLUSION: Our study of globally distributed hydrothermal vent deposits provides a significant expansion of microbial genomic diversity associated with hydrothermal vent deposits and highlights the metabolic adaptation of taxonomic guilds. Collectively, our results illustrate the importance of comparative biodiversity studies in establishing patterns of shared phylogenetic diversity and physiological ecology, while providing many targets for enrichment and cultivation of novel and endemic taxa. Video Abstract.}, } @article {pmid36572910, year = {2022}, author = {Xu, J and Zheng, Z and Yang, L and Li, R and Ma, X and Zhang, J and Yin, F and Liu, L and Xu, Q and Shen, Q and Shen, X and Wu, C and Liu, J and Qin, N and Sheng, J and Jin, P}, title = {A novel promising diagnosis model for colorectal advanced adenoma and carcinoma based on the progressive gut microbiota gene biomarkers.}, journal = {Cell & bioscience}, volume = {12}, number = {1}, pages = {208}, pmid = {36572910}, issn = {2045-3701}, support = {D171100002617001//Beijing Municipal Science and Technology Commission/ ; 31970111//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Colorectal cancer (CRC), a commonly diagnosed cancer often develops slowly from benign polyps called adenoma to carcinoma. Altered gut microbiota is implicated in colorectal carcinogenesis. It is warranted to find non-invasive progressive microbiota biomarkers that can reflect the dynamic changes of the disease. This study aimed to identify and evaluate potential progressive fecal microbiota gene markers for diagnosing advanced adenoma (AA) and CRC.

RESULTS: Metagenome-wide association was performed on fecal samples from different cohorts of 871 subjects (247 CRC, 234 AA, and 390 controls). We characterized the gut microbiome, identified microbiota markers, and further constructed a colorectal neoplasms classifier in 99 CRC, 94 AA, and 62 controls, and validated the results in 185 CRC, 140 AA, and 291 controls from 3 independent cohorts. 21 species and 277 gene markers were identified whose abundance was significantly increased or decreased from normal to AA and CRC. The progressive gene markers were distributed in metabolic pathways including amino acid and sulfur metabolism. A diagnosis model consisting of four effect indexes was constructed based on the markers, the sensitivities of the Adenoma Effect Index 1 for AA, Adenoma Effect Index 2 for high-grade dysplasia (HGD) adenoma were 71.3% and 76.5%, the specificities were 90.5% and 90.3%, respectively. CRC Effect Index 1 for all stages of CRC and CRC Effect Index 2 for stage III-IV CRC to predict CRC yielded an area under the curve (AUC) of 0.839 (95% CI 0.804-0.873) and 0.857 (95% CI 0.793-0.921), respectively. Combining with fecal immunochemical test (FIT) significantly improved the sensitivity of CRC Effect Index 1 and CRC Effect Index 2 to 96.7% and 100%.

CONCLUSIONS: This study reports the successful diagnosis model establishment and cross-region validation for colorectal advanced adenoma and carcinoma based on the progressive gut microbiota gene markers. The results suggested that the novel diagnosis model can significantly improve the diagnostic performance for advanced adenoma.}, } @article {pmid36571993, year = {2023}, author = {Su, Z and Wen, D and Gu, AZ and Zheng, Y and Tang, Y and Chen, L}, title = {Industrial effluents boosted antibiotic resistome risk in coastal environments.}, journal = {Environment international}, volume = {171}, number = {}, pages = {107714}, doi = {10.1016/j.envint.2022.107714}, pmid = {36571993}, issn = {1873-6750}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Wastewater ; Bacteria/genetics ; Genes, Bacterial ; Sewage ; }, abstract = {Wastewater treatment plants (WWTPs) have been regarded as an important source of antibiotic resistance genes (ARGs) in environment, but out of municipal domestic WWTPs, few evidences show how environment is affected by industrial WWTPs. Here we chose Hangzhou Bay (HZB), China as our study area, where land-based municipal and industrial WWTPs discharged their effluent into the bay for decades. We adopted high-throughput metagenomic sequencing to examine the antibiotic resistome of the WWTP effluent and coastal sediment samples. And we proposed a conceptual framework for the assessment of antibiotic resistome risk, and a new bioinformatic pipeline for the evaluation of the potential horizontal gene transfer (HGT) frequency. Our results revealed that the diversity and abundance of ARGs in the WWTP's effluent were significantly higher than those in the sediment. Furthermore, the antibiotic resistome in the effluent-receiving area (ERA) showed significant difference from that in HZB. For the first time, we identified that industrial WWTP effluent boosted antibiotic resistome risk in coastal sediment. The crucial evidences included: 1) the proportion of ARGs derived from WWTP activated sludge (WA) was higher (14.3 %) and two high-risky polymyxin resistance genes (mcr-4 and mcr-5) were enriched in the industrial effluent receiving area; 2) the HGT potential was higher between resistant microbiome of the industrial effluent and its ERA sediment; and 3) the highest resistome risk was determined in the industrial effluent, and some biocide resistance genes located on high-risky contigs were related to long-term stress of industrial chemicals. These findings highlight the important effects of industrial activities on the development of environmental antimicrobial resistance.}, } @article {pmid36571956, year = {2023}, author = {Zhang, S and Xu, B and Chen, M and Zhang, Q and Huang, J and Cao, Y and Li, B}, title = {Profile and actual transmissibility of Carbapenem resistance genes: Intracellular and extracellular DNA in hospital wastewater.}, journal = {Journal of environmental management}, volume = {329}, number = {}, pages = {117085}, doi = {10.1016/j.jenvman.2022.117085}, pmid = {36571956}, issn = {1095-8630}, mesh = {*Wastewater ; *Anti-Bacterial Agents ; DNA ; beta-Lactamases/genetics ; Plasmids/genetics ; Carbapenems/pharmacology ; Hospitals ; Microbial Sensitivity Tests ; }, abstract = {The current worldwide spread of carbapenem resistance genes (CRGs) has posed a major public health threat, which continues to grow in severity. Hospital wastewaters (HWWs) are major reservoirs for antibiotic resistance genes, while resistomes in HWWs are still poorly characterized when it comes to CRGs. We comprehensively characterized the profile and actual transmissibility of extracellular CRGs (eCRGs) and intracellular CRGs (iCRGs) in HWWs for the first time. In this study, CRGs showed similar relative abundance in treated and untreated HWWs. Meanwhile, HWWs treatments led to the enrichment of blaIMP-8, probably attributed to the promotion of Novosphingobium and Prosthecobacter after treatment. To evaluate the transmission potential of CRGs, extracellular and intracellular carbapenem-resistant plasmids were captured from HWWs by transformation and conjugation, respectively. We found an interesting phenomenon regarding the transmission characteristics of CRGs: blaKPC-carrying plasmids could only be captured by transformation, while blaNDM-carrying plasmids were captured by conjugation. Further experiments showed that HWW treatments increased the conjugation ability of blaNDM. In conclusion, our study demonstrated that HWWs are significant reservoirs of CRGs and various CRGs exhibit different modes of transmission in HWWs. CRGs cannot be removed by membrane bioreactor and chlorine disinfection. An urgent need is to develop more efficient wastewater treatments to limit CRG dissemination.}, } @article {pmid36571495, year = {2023}, author = {Sun, M and Yuan, S and Xia, R and Ye, M and Balcázar, JL}, title = {Underexplored viral auxiliary metabolic genes in soil: Diversity and eco-evolutionary significance.}, journal = {Environmental microbiology}, volume = {25}, number = {4}, pages = {800-810}, doi = {10.1111/1462-2920.16329}, pmid = {36571495}, issn = {1462-2920}, mesh = {Genes, Viral ; *Bacteriophages/genetics ; Biological Evolution ; Bacteria/metabolism ; *Microbiota/genetics ; Soil ; }, abstract = {Bacterial viruses are the most abundant biological entities in soil ecosystems. Owing to the advent of metagenomics and viromics approaches, an ever-increasing diversity of virus-encoded auxiliary metabolic genes (AMGs) have been identified in soils, including those involved in the transformation of carbon, phosphorus, and sulfur, degradation of organic pollutants, and antibiotic resistance, among other processes. These viral AMGs can alter soil biogeochemical processes and metabolic activities by interfering with bacterial host metabolism. It is recognized that viral AMGs compensate for host bacterial metabolism outputs by encoding accessory functional genes and are favourable for the hosts' adaptation to stressed soil environments. The eco-evolutionary mechanisms behind this fascinating diversity of viral AMGs in soil microbiomes have begun to emerge, such as horizontal gene transfer, lytic-lysogenic conversion, and single-nucleotide polymorphisms. In this mini-review, we summarize recent advances in the diversity and function of virus-encoded AMGs in the soil environment, especially focusing on the evolutionary significance of AMGs involved in virus-host interactions. This mini-review also sheds light on the existing gaps and future perspectives that could have major significance for viral AMGs research in soils.}, } @article {pmid36571492, year = {2023}, author = {Parrish, NF and Gaston, DC}, title = {Metagenomics in infectious disease diagnostics: Toward best-use practices to optimize actionable results.}, journal = {Transplant infectious disease : an official journal of the Transplantation Society}, volume = {25}, number = {1}, pages = {e13959}, doi = {10.1111/tid.13959}, pmid = {36571492}, issn = {1399-3062}, mesh = {Humans ; *Metagenomics/methods ; *Communicable Diseases ; High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; }, } @article {pmid36570711, year = {2022}, author = {Zhang, M and Lu, W and Xie, D and Wang, J and Xiao, X and Pu, Y and Meng, J and Lyu, H and Zhao, M}, title = {Metagenomic Next-Generation Sequencing for Diagnostically Challenging Mucormycosis in Patients with Hematological Malignancies.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {7509-7517}, pmid = {36570711}, issn = {1178-6973}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is a fast, sensitive and accurate diagnostic method for pathogens detection. However, reports on the application of mNGS in mucormycosis remain scarce.

METHODS: From January 2019 to December 2021, we recruited 13 patients with hematological malignancies who were suspected of mucormycosis and completed mNGS in D20. Then we retrospectively analyze the clinical data, diagnosis, therapeutic process, and outcomes. In order to evaluate the diagnostic value of mNGS in hematological malignancies patients with suspected mucormycosis.

RESULTS: All patients had high risk factors of Invasive Fungal Disease, including hematopoietic stem cell transplantation, immunosuppression, glucocorticoids, etc. The clinical presentations were pulmonary (n=9), rhino-orbito-cerebral (n=4). But the manifestations were nonspecific. All enrolled patients completed mNGS. And most (8/13, 61.54%) of the samples were from blood. Fungi can be detected in all specimens, including Rhizopus (n=7), Rhizomucor (n=4) and Mucor (n=2). In addition, 7/13 (53.85%) specimens were detected bacteria at the same time and virus were detected in 5/13 (38.46%). Histopathological examination was completed in 5 patients, 3 of which were completely consistent with the results of mNGS. After treatment, 6 patients were cured, while the other 7 patients died.

CONCLUSION: mNGS may be a complementary method for early diagnosis, especially for patients who are not suitable for histopathology examination or unable to obtain culture specimen. mNGS can also help detect bacteria and viruses simultaneously, allowing for appropriate and timely antibiotic administration and thus improving patient outcomes.}, } @article {pmid36569853, year = {2022}, author = {Liu, C and Yang, J and Huang, H and Zhan, S and Xia, X}, title = {Case report: Nocardia gipuzkoensis infection in an immunocompetent patient diagnosed by metagenomic next-generation sequencing and whole genome sequencing.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1053914}, pmid = {36569853}, issn = {1664-3224}, mesh = {Female ; Humans ; Young Adult ; Adult ; *Nocardia Infections/diagnosis/drug therapy ; *Nocardia/genetics ; Sulfamethoxazole/therapeutic use ; High-Throughput Nucleotide Sequencing ; Whole Genome Sequencing ; }, abstract = {The infection of Nocardia gipuzkoensis is a relatively uncommon form of pulmonary nocardiosis seen in clinical patients. In general, nocardiosis tends to occur in patients with immune deficiency. Here, we report a 23-year-old female who was admitted to the hospital due to cough and sputum production over 10 years, diagnosed with bronchiectasis. The N. gipuzkoensis infection was identified by metagenomic next-generation sequencing and whole genome sequencing. Imipenem/cilastatin and compound sulfamethoxazole tablets were used to control the infection and the pulmonary inflammation subsided gradually.}, } @article {pmid36569538, year = {2023}, author = {Kutasy, B and Decsi, K and Hegedűs, G and Virág, E}, title = {Dataset of conditioning effect of herbal extract-based plant biostimulants in pea (Pisum sativum).}, journal = {Data in brief}, volume = {46}, number = {}, pages = {108800}, pmid = {36569538}, issn = {2352-3409}, abstract = {Nowadays, many researchers, farmers and companies focus on the development of an environmentally friendly approach for enhancing field vegetable production and protection. Using next-generation plant biostimulants (PBs) could be effective to enhance tolerance to abiotic and biotic stresses, vegetable crop quality or nutrient efficiency which is particularly important for vegetables with a short growing season, such as Pisum sativum. Two herbal drug-containing plant conditioners Elice16Indures® (supercritical carbon dioxide extract SC-CO2) and Fitokondi® (aqueous extract) developed in the RIMPH Ltd (Hungary) were used in pea field experiments to monitor the potential of enhancing crop quality and defense response against different stress factors. Fresh leaves were collected after treatments for QuantSeq 3' mRNA sequencing at Illumina NextSeq 550 platform and libraries were investigated by genome-wide transcriptional profiling focusing on genes associated with defense response pathways. RNA quantification datasets are presented and 86 bp long sequence reads were pre-processed and assembled that were deposited in the National Center for Biotechnology Information (NCBI), Sequence Read Archive (SRA) and Transcriptome Shotgun Assembly (TSA) databases under the BioProject PRJNA870114. Functional annotation of transcripts and pairwise differential expression with enrichment analyses are presented here to support gene expression analysis experiments.}, } @article {pmid36569206, year = {2022}, author = {Okada, K and Takezawa, K and Tsujimura, G and Imanaka, T and Kuribayashi, S and Ueda, N and Hatano, K and Fukuhara, S and Kiuchi, H and Fujita, K and Motooka, D and Nakamura, S and Koyama, Y and Shimada, S and Nonomura, N}, title = {Localization and potential role of prostate microbiota.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1048319}, pmid = {36569206}, issn = {2235-2988}, mesh = {Humans ; Male ; *Prostate ; In Situ Hybridization, Fluorescence ; Phylogeny ; *Prostatic Hyperplasia/complications ; }, abstract = {INTRODUCTION: We aimed to clarify the presence and localization of the prostate microbiota and examine its association with benign prostate enlargement (BPE).

METHODS: The microbiota of prostate tissues and catheterized urine from 15 patients were analyzed by 16S metagenomic analysis and compared to show that the prostate microbiota was not a contaminant of the urinary microbiota. Fluorescence in situ hybridization (FISH) and in situ hybridization (ISH) using the specific probe for eubacteria was performed on prostate tissue to show the localization of bacteria in the prostate. The BPE group was defined as prostate volume ≥30 mL, and the non-BPE group as prostate volume <30 mL. The microbiota of the two groups were compared to clarify the association between prostate microbiota and BPE.

RESULTS: Faith's phylogenetic diversity index of prostate tissue was significantly higher than that of urine (42.3±3.8 vs 25.5±5.6, P=0.01). Principal coordinate analysis showed a significant difference between the microbiota of prostate tissue and catheterized urine (P<0.01). FISH and ISH showed the presence of bacteria in the prostatic duct. Comparison of prostate microbiota between the BPE and non-BPE groups showed that the Chao1 index of the BPE group was significantly lower than that of the latter [142 (50-316) vs 169 (97-665), P=0.047] and the abundance of Burkholderia was significantly higher in the BPE group than in the latter.

CONCLUSIONS: We demonstrated that the prostate microbiota was located in the prostatic duct and reduced diversity of prostate microbiota was associated with BPE, suggesting that prostate microbiota plays a role in BPE.}, } @article {pmid36569204, year = {2022}, author = {Wang, H and Shi, X and Yang, H and Du, Y and Xue, J}, title = {Metagenomic next-generation sequencing shotgun for the diagnosis of infection in connective tissue diseases: A retrospective study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {865637}, pmid = {36569204}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *Connective Tissue Diseases/diagnosis ; High-Throughput Nucleotide Sequencing ; CD4-Positive T-Lymphocytes ; *Coinfection ; Metagenomics ; Sensitivity and Specificity ; }, abstract = {OBJECTIVE: Patients with connective tissue diseases (CTDs) are at high risk of infection due to various reasons. The purpose of the study was to investigate the infection diagnosis value of metagenomic next-generation sequencing (mNGS) shotgun in CTDs to guide the use of anti-infective therapy more quickly and accurately.

METHODS: In this retrospective study, a total of 103 patients with CTDs admitted with suspected infection between December 2018 and September 2021 were assessed using mNGS as well as conventional microbiological tests (CMT).

RESULTS: Among these 103 patients, 65 were confirmed to have an infection (Group I) and 38 had no infection (Group II). mNGS reached a sensitivity of 92.31% in diagnosing pathogens in Group I. Moreover, mNGS showed good performance in identifying mixed infection. In all infection types, lung infection was the most common. mNGS also played an important role in detecting Pneumocystis jirovecii, which was associated with low CD4+ T-cell counts inextricably.

CONCLUSION: mNGS is a useful tool with outstanding diagnostic potential in identifying pathogens in patients with CTDs and conduce to provide guidance in clinical practice.}, } @article {pmid36569101, year = {2022}, author = {Bartkiene, E and Starkute, V and Zokaityte, E and Klupsaite, D and Mockus, E and Ruzauskas, M and Bartkevics, V and Borisova, A and Rocha, JM and Ozogul, F and Liatukas, Z and Ruzgas, V}, title = {Changes in the physicochemical parameters and microbial community of a new cultivar blue wheat cereal wholemeal during sourdough production.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1031273}, pmid = {36569101}, issn = {1664-302X}, abstract = {Changes in the characteristics of a new cultivar (DS8472-5) of blue wheat during wholemeal fermentation with Pediococcus acidilactici (LUHS29), Liquorilactobacillus uvarum (LUHS245), and Lactiplantibacillus plantarum (LUHS122), including acidity, microbiological and chromaticity parameters, free amino acid (FAA), gamma-aminobutyric acid (GABA), and biogenic amine (BA) contents, macro- and micro-element concentrations and fatty acid (FA) and volatile compounds (VC), were evaluated. In addition, a metagenomic analysis was performed. The lactic acid bacteria (LAB) strains used for fermentation was a significant factor in wholemeal fermentation sample pH, redness (a*) and LAB counts (p ≤ 0.05). In most of the samples, fermentation increased the FAA content in wheat wholemeal, and the highest concentration of GABA was found in DS8472-5 LUHS122 samples. Phenylethylamine (PHE) was found in all wheat wholemeal samples; however, spermidine was only detected in fermented samples and cadaverine only in DS8472-5 LUHS122. Fermented samples showed higher omega-3 and omega-6 contents and a higher number and variety of VC. Analysis of the microbial profile showed that LAB as part of the natural microbiota present in cereal grains also actively participates in fermentation processes induced by industrial bacterial cultures. Finally, all the tested LAB were suitable for DS8472-5 wheat wholemeal fermentation, and the DS8472-5 LUHS122 samples showed the lowest pH and the highest LAB viable counts (3.94, 5.80°N, and 8.92 log10 CFU/g, respectively).}, } @article {pmid36569091, year = {2022}, author = {Li, Y and Yao, XW and Tang, L and Dong, WJ and Lan, TL and Fan, J and Liu, FS and Qin, SB}, title = {Diagnostic efficiency of metagenomic next-generation sequencing for suspected spinal tuberculosis in China: A multicenter prospective study.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1018938}, pmid = {36569091}, issn = {1664-302X}, abstract = {BACKGROUND: The pathogens of suspected spinal tuberculosis (TB) include TB and non-TB bacteria. A rapid and effective diagnostic method that can detect TB and non-TB pathogens simultaneously remains lacking. Here, we used metagenomic next-generation sequencing (mNGS) to detect the pathogens in patients with suspected spinal TB.

METHODS: The enrolled patients with suspected spinal TB were regrouped three times into patients with spinal infection and controls, patients with spinal TB and controls, and patients with non-TB spinal infection and controls. We tested the three groups separately by using mNGS and conventional detection methods.

RESULTS: Ultimately, 100 patients were included in this study. Pathogens were detected in 82 patients. Among the 82 patients, 37 had TB and 45 were infected with other bacteria. In patients with spinal infection, the sensitivity of the mNGS assay was higher than that of culture and pathological examination (p < 0.001, p < 0.001). The specificity of the mNGS assay was not statistically different from that of culture and pathological examination (p = 1.000, p = 1.000). In patients with spinal TB, no statistical difference was found between the sensitivity of the mNGS assay and that of Xpert and T-SPOT.TB (p = 1.000, p = 0.430). The sensitivity of the mNGS assay was higher than that of MGIT 960 culture and pathological examination (p < 0.001, p = 0.006). The specificities of the mNGS assay, Xpert, MGIT 960 culture, and pathological examination were all 100%. The specificity of T-SPOT.TB (78.3%) was lower than that of the mNGS assay (100%; p < 0.001). In patients with non-TB spinal infection, the sensitivity of the mNGS assay was higher than that of bacterial culture and pathological examination (p < 0.001, p < 0.001). The specificity of the mNGS assay was not statistically different from that of bacterial culture and pathological examination (p = 1.000, p = 1.000).

CONCLUSION: Data presented here demonstrated that mNGS can detect TB and non-TB bacteria simultaneously, with high sensitivity, specificity and short detection time. Compared with conventional detection methods, mNGS is a more rapid and effective diagnostic tool for suspected spinal TB.}, } @article {pmid36569089, year = {2022}, author = {Chang, Q and Chen, Z and von Fricken, ME and Liu, Q}, title = {Editorial: New infectious agents in arthropod vectors.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1105082}, pmid = {36569089}, issn = {1664-302X}, } @article {pmid36569084, year = {2022}, author = {Holland, SI and Vázquez-Campos, X and Ertan, H and Edwards, RJ and Manefield, MJ and Lee, M}, title = {Metaproteomics reveals methyltransferases implicated in dichloromethane and glycine betaine fermentation by 'Candidatus Formimonas warabiya' strain DCMF.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1035247}, pmid = {36569084}, issn = {1664-302X}, abstract = {Dichloromethane (DCM; CH2Cl2) is a widespread pollutant with anthropogenic and natural sources. Anaerobic DCM-dechlorinating bacteria use the Wood-Ljungdahl pathway, yet dechlorination reaction mechanisms remain unclear and the enzyme(s) responsible for carbon-chlorine bond cleavage have not been definitively identified. Of the three bacterial taxa known to carry out anaerobic dechlorination of DCM, 'Candidatus Formimonas warabiya' strain DCMF is the only organism that can also ferment non-chlorinated substrates, including quaternary amines (i.e., choline and glycine betaine) and methanol. Strain DCMF is present within enrichment culture DFE, which was derived from an organochlorine-contaminated aquifer. We utilized the metabolic versatility of strain DCMF to carry out comparative metaproteomics of cultures grown with DCM or glycine betaine. This revealed differential abundance of numerous proteins, including a methyltransferase gene cluster (the mec cassette) that was significantly more abundant during DCM degradation, as well as highly conserved amongst anaerobic DCM-degrading bacteria. This lends strong support to its involvement in DCM dechlorination. A putative glycine betaine methyltransferase was also discovered, adding to the limited knowledge about the fate of this widespread osmolyte in anoxic subsurface environments. Furthermore, the metagenome of enrichment culture DFE was assembled, resulting in five high quality and two low quality draft metagenome-assembled genomes. Metaproteogenomic analysis did not reveal any genes or proteins for utilization of DCM or glycine betaine in the cohabiting bacteria, supporting the previously held idea that they persist via necromass utilization.}, } @article {pmid36569080, year = {2022}, author = {Jeilu, O and Simachew, A and Alexandersson, E and Johansson, E and Gessesse, A}, title = {Discovery of novel carbohydrate degrading enzymes from soda lakes through functional metagenomics.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1059061}, pmid = {36569080}, issn = {1664-302X}, abstract = {Extremophiles provide a one-of-a-kind source of enzymes with properties that allow them to endure the rigorous industrial conversion of lignocellulose biomass into fermentable sugars. However, the fact that most of these organisms fail to grow under typical culture conditions limits the accessibility to these enzymes. In this study, we employed a functional metagenomics approach to identify carbohydrate-degrading enzymes from Ethiopian soda lakes, which are extreme environments harboring a high microbial diversity. Out of 21,000 clones screened for the five carbohydrate hydrolyzing enzymes, 408 clones were found positive. Cellulase and amylase, gave high hit ratio of 1:75 and 1:280, respectively. A total of 378 genes involved in the degradation of complex carbohydrates were identified by combining high-throughput sequencing of 22 selected clones and bioinformatics analysis using a customized workflow. Around 41% of the annotated genes belonged to the Glycoside Hydrolases (GH). Multiple GHs were identified, indicating the potential to discover novel CAZymes useful for the enzymatic degradation of lignocellulose biomass from the Ethiopian soda Lakes. More than 73% of the annotated GH genes were linked to bacterial origins, with Halomonas as the most likely source. Biochemical characterization of the three enzymes from the selected clones (amylase, cellulase, and pectinase) showed that they are active in elevated temperatures, high pH, and high salt concentrations. These properties strongly indicate that the evaluated enzymes have the potential to be used for applications in various industrial processes, particularly in biorefinery for lignocellulose biomass conversion.}, } @article {pmid36569062, year = {2022}, author = {Jeilu, O and Gessesse, A and Simachew, A and Johansson, E and Alexandersson, E}, title = {Prokaryotic and eukaryotic microbial diversity from three soda lakes in the East African Rift Valley determined by amplicon sequencing.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {999876}, pmid = {36569062}, issn = {1664-302X}, abstract = {Soda lakes are unique poly-extreme environments with high alkalinity and salinity that support diverse microbial communities despite their extreme nature. In this study, prokaryotic and eukaryotic microbial diversity in samples of the three soda lakes, Lake Abijata, Lake Chitu and Lake Shala in the East African Rift Valley, were determined using amplicon sequencing. Culture-independent analysis showed higher diversity of prokaryotic and eukaryotic microbial communities in all three soda lakes than previously reported. A total of 3,603 prokaryotic and 898 eukaryotic operational taxonomic units (OTUs) were found through culture-independent amplicon sequencing, whereas only 134 bacterial OTUs, which correspond to 3%, were obtained by enrichment cultures. This shows that only a fraction of the microorganisms from these habitats can be cultured under laboratory conditions. Of the three soda lakes, samples from Lake Chitu showed the highest prokaryotic diversity, while samples from Lake Shala showed the lowest diversity. Pseudomonadota (Halomonas), Bacillota (Bacillus, Clostridia), Bacteroidota (Bacteroides), Euryarchaeota (Thermoplasmata, Thermococci, Methanomicrobia, Halobacter), and Nanoarchaeota (Woesearchaeia) were the most common prokaryotic microbes in the three soda lakes. A high diversity of eukaryotic organisms were identified, primarily represented by Ascomycota and Basidiomycota. Compared to the other two lakes, a higher number of eukaryotic OTUs were found in Lake Abijata. The present study showed that these unique habitats harbour diverse microbial genetic resources with possible use in biotechnological applications, which should be further investigated by functional metagenomics.}, } @article {pmid36569054, year = {2022}, author = {Román-Camacho, JJ and García-García, I and Santos-Dueñas, IM and Ehrenreich, A and Liebl, W and García-Martínez, T and Mauricio, JC}, title = {Combining omics tools for the characterization of the microbiota of diverse vinegars obtained by submerged culture: 16S rRNA amplicon sequencing and MALDI-TOF MS.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1055010}, pmid = {36569054}, issn = {1664-302X}, abstract = {Vinegars elaborated in southern Spain are highly valued all over the world because of their exceptional organoleptic properties and high quality. Among the factors which influence the characteristics of the final industrial products, the composition of the microbiota responsible for the process and the raw material used as acetification substrate have a crucial role. The current state of knowledge shows that few microbial groups are usually present throughout acetification, mainly acetic acid bacteria (AAB), although other microorganisms, present in smaller proportions, may also affect the overall activity and behavior of the microbial community. In the present work, the composition of a starter microbiota propagated on and subsequently developing three acetification profiles on different raw materials, an alcohol wine medium and two other natural substrates (a craft beer and fine wine), was characterized and compared. For this purpose, two different "omics" tools were combined for the first time to study submerged vinegar production: 16S rRNA amplicon sequencing, a culture-independent technique, and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS), a culture-dependent method. Analysis of the metagenome revealed numerous taxa from 30 different phyla and highlighted the importance of the AAB genus Komagataeibacter, which was much more frequent than the other taxa, and Acetobacter; interestingly, also archaea from the Nitrososphaeraceae family were detected by 16S rRNA amplicon sequencing. MALDI-TOF MS confirmed the presence of Komagataeibacter by the identification of K. intermedius. These tools allowed for identifying some taxonomic groups such as the bacteria genera Cetobacterium and Rhodobacter, the bacteria species Lysinibacillus fusiformis, and even archaea, never to date found in this medium. Definitely, the effect of the combination of these techniques has allowed first, to confirm the composition of the predominant microbiota obtained in our previous metaproteomics approaches; second, to identify the microbial community and discriminate specific species that can be cultivated under laboratory conditions; and third, to obtain new insights on the characterization of the acetification raw materials used. These first findings may contribute to improving the understanding of the microbial communities' role in the vinegar-making industry.}, } @article {pmid36568998, year = {2022}, author = {Lu, HY and Gao, YB and Qiu, XW and Wang, Q and Liu, CM and Huang, XW and Chen, HY and Zeng, K and Li, CX}, title = {Successful surgical treatment of polybacterial gas gangrene confirmed by metagenomic next-generation sequencing detection: A case report.}, journal = {World journal of clinical cases}, volume = {10}, number = {35}, pages = {13064-13073}, pmid = {36568998}, issn = {2307-8960}, abstract = {BACKGROUND: We report on a case of Vibrio vulnificus (V. vulnificus) detected by metagenomics next-generation sequencing (mNGS) in a 53-year-old male patient with polymicrobial gas gangrene and successful treatment by surgery. This report raises awareness among dermatologists that when a patient is clinically suspected of a special type of pathogenic infection, the mNGS method should be preferred to identify the patient's pathogen infection as soon as possible and then take effective treatment in time to save patients' lives.

CASE SUMMARY: A 53-year-old male who worked in the aquatic market complained of redness and swelling of the lower limbs, blisters and ulcers with fever for 3 d. We used mNGS to test the pathogens in ulcer secretions. The results were returned in 24 h and indicated: V. vulnificus, Fusobacterium necrophorum, Staphylococcus haemolyticus, Staphylococcus aureus, Streptococcus dysgalactiae and Klebsiella aerogenes. This patient was diagnosed with V. vulnificus infection. The emergency operation was performed immediately under combined lumbar and epidural anesthesia: Left leg expansion and exploration (August 10, 2021). After surgery, we continued to use piperacillin sodium tazobactam sodium 4.5 g every 8 h and levofloxacin 0.5 g for anti-infection treatment. The patient underwent further surgery under lumbar anesthesia on August 17, 2021 and August 31, 2021: Left leg deactivation and skin grafting, negative pressure closed drainage and right thigh skin removal. After treatment, the transplanted flap survived.

CONCLUSION: We could confirm the diagnosis of Vibrio vulnificus infection within 24 h through mNGS detection and then immediately performed emergency surgery.}, } @article {pmid36568361, year = {2022}, author = {Nayar, G and Terrizzano, I and Seabolt, E and Agarwal, A and Boucher, C and Ruiz, J and Slizovskiy, IB and Kaufman, JH and Noyes, NR}, title = {ggMOB: Elucidation of genomic conjugative features and associated cargo genes across bacterial genera using genus-genus mobilization networks.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {1024577}, pmid = {36568361}, issn = {1664-8021}, abstract = {Horizontal gene transfer mediated by conjugation is considered an important evolutionary mechanism of bacteria. It allows organisms to quickly evolve new phenotypic properties including antimicrobial resistance (AMR) and virulence. The frequency of conjugation-mediated cargo gene exchange has not yet been comprehensively studied within and between bacterial taxa. We developed a frequency-based network of genus-genus conjugation features and candidate cargo genes from whole-genome sequence data of over 180,000 bacterial genomes, representing 1,345 genera. Using our method, which we refer to as ggMOB, we revealed that over half of the bacterial genomes contained one or more known conjugation features that matched exactly to at least one other genome. Moreover, the proportion of genomes containing these conjugation features varied substantially by genus and conjugation feature. These results and the genus-level network structure can be viewed interactively in the ggMOB interface, which allows for user-defined filtering of conjugation features and candidate cargo genes. Using the network data, we observed that the ratio of AMR gene representation in conjugative versus non-conjugative genomes exceeded 5:1, confirming that conjugation is a critical force for AMR spread across genera. Finally, we demonstrated that clustering genomes by conjugation profile sometimes correlated well with classical phylogenetic structuring; but that in some cases the clustering was highly discordant, suggesting that the importance of the accessory genome in driving bacterial evolution may be highly variable across both time and taxonomy. These results can advance scientific understanding of bacterial evolution, and can be used as a starting point for probing genus-genus gene exchange within complex microbial communities that include unculturable bacteria. ggMOB is publicly available under the GNU licence at https://ruiz-hci-lab.github.io/ggMOB/.}, } @article {pmid36568318, year = {2023}, author = {Yang, A and Wang, C and Chen, P and Zheng, G and Zhao, Z and Liu, J and Zhang, J and Wang, J and Sun, Y and Yang, J and Guo, Y}, title = {Diagnosis by metagenomic next-generation sequencing of invasive pulmonary aspergillosis in an infant with chronic granulomatous disease.}, journal = {Respiratory medicine case reports}, volume = {41}, number = {}, pages = {101792}, pmid = {36568318}, issn = {2213-0071}, abstract = {Invasive pulmonary aspergillosis (IPA) is a serious fungal infection, with a high degree of mortality in immunocompromised individuals. Diagnosis of IPA is challenging in that clinical manifestations are not specific, with sensitivity of traditional detection procedures low. We report a case of IPA in a chronic granulomatous disease (CGD) infant who was initially suspected to have a lung tumor. Aspergillus fumigatus was identified as the pathogen in bronchoalveolar lavage fluid (BALF) by next-generation sequencing (mNGS). The patient recovered rapidly following a change of appropriate antifungal treatment and was discharged. This case highlights the additional value of BALF-mNGS for the diagnosis of pediatric invasive pulmonary fungal infection in immune-deficient children.}, } @article {pmid36567334, year = {2022}, author = {Blostein, F and Bhaumik, D and Davis, E and Salzman, E and Shedden, K and Duhaime, M and Bakulski, KM and McNeil, DW and Marazita, ML and Foxman, B}, title = {Evaluating the ecological hypothesis: early life salivary microbiome assembly predicts dental caries in a longitudinal case-control study.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {240}, pmid = {36567334}, issn = {2049-2618}, support = {F31 DE029992/DE/NIDCR NIH HHS/United States ; P30 ES017885/ES/NIEHS NIH HHS/United States ; R01 DE014899/DE/NIDCR NIH HHS/United States ; T32 HG000040/HG/NHGRI NIH HHS/United States ; }, mesh = {Child ; Child, Preschool ; Humans ; Infant ; Case-Control Studies ; *Dental Caries/epidemiology/microbiology ; Membrane Transport Proteins ; *Microbiota/genetics ; *Saliva/microbiology ; *Streptococcus mutans/genetics/isolation & purification ; }, abstract = {BACKGROUND: Early childhood caries (ECC)-dental caries (cavities) occurring in primary teeth up to age 6 years-is a prevalent childhood oral disease with a microbial etiology. Streptococcus mutans was previously considered a primary cause, but recent research promotes the ecologic hypothesis, in which a dysbiosis in the oral microbial community leads to caries. In this incident, density sampled case-control study of 189 children followed from 2 months to 5 years, we use the salivary bacteriome to (1) prospectively test the ecological hypothesis of ECC in salivary bacteriome communities and (2) identify co-occurring salivary bacterial communities predicting future ECC.

RESULTS: Supervised classification of future ECC case status using salivary samples from age 12 months using bacteriome-wide data (AUC-ROC 0.78 95% CI (0.71-0.85)) predicts future ECC status before S. mutans can be detected. Dirichlet multinomial community state typing and co-occurrence network analysis identified similar robust and replicable groups of co-occurring taxa. Mean relative abundance of a Haemophilus parainfluenzae/Neisseria/Fusobacterium periodonticum group was lower in future ECC cases (0.14) than controls (0.23, P value < 0.001) in pre-incident visits, positively correlated with saliva pH (Pearson rho = 0.33, P value < 0.001) and reduced in individuals who had acquired S. mutans by the next study visit (0.13) versus those who did not (0.20, P value < 0.01). In a subset of whole genome shotgun sequenced samples (n = 30), case plaque had higher abundances of antibiotic production and resistance gene orthologs, including a major facilitator superfamily multidrug resistance transporter (MFS DHA2 family PBH value = 1.9 × 10[-28]), lantibiotic transport system permease protein (PBH value = 6.0 × 10[-6]) and bacitracin synthase I (PBH value = 5.6 × 10[-6]). The oxidative phosphorylation KEGG pathway was enriched in case plaque (PBH value = 1.2 × 10[-8]), while the ABC transporter pathway was depleted (PBH value = 3.6 × 10[-3]).

CONCLUSIONS: Early-life bacterial interactions predisposed children to ECC, supporting a time-dependent interpretation of the ecological hypothesis. Bacterial communities which assemble before 12 months of age can promote or inhibit an ecological succession to S. mutans dominance and cariogenesis. Intragenera competitions and intergenera cooperation between oral taxa may shape the emergence of these communities, providing points for preventive interventions. Video Abstract.}, } @article {pmid36566300, year = {2022}, author = {Abed, JY and Godon, T and Mehdaoui, F and Plante, PL and Boissinot, M and Bergeron, MG and Bélanger, RE and Muckle, G and Poliakova, N and Ayotte, P and Corbeil, J and Rousseau, E}, title = {Gut metagenome profile of the Nunavik Inuit youth is distinct from industrial and non-industrial counterparts.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1415}, pmid = {36566300}, issn = {2399-3642}, mesh = {Humans ; Adolescent ; Young Adult ; Adult ; *Metagenome ; Inuit/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; }, abstract = {Comparative metagenomics studies have highlighted differences in microbiome community structure among human populations over diverse lifestyles and environments. With their unique environmental and historical backgrounds, Nunavik Inuit have a distinctive gut microbiome with undocumented health-related implications. Using shotgun metagenomics, we explored the taxonomic and functional structure of the gut microbiome from 275 Nunavik Inuit ranging from 16 to 30-year-old. Whole-metagenome analyses revealed that Nunavik Inuit youths have a more diverse microbiome than their non-industrialized and industrialized counterparts. A comparison of k-mer content illustrated the uniqueness of the Nunavik gut microbiome. Short-chain fatty acids producing species, and carbohydrates degradation pathways dominated Inuit metagenomes. We identified a taxonomic and functional signature unique to the Nunavik gut microbiome contrasting with other populations using a random forest classifier. Here, we show that the Nunavik Inuit gut microbiome exhibits high diversity and a distinct community structure.}, } @article {pmid36566239, year = {2022}, author = {Cheng, R and Li, X and Jiang, L and Gong, L and Geslin, C and Shao, Z}, title = {Virus diversity and interactions with hosts in deep-sea hydrothermal vents.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {235}, pmid = {36566239}, issn = {2049-2618}, mesh = {Ecosystem ; Phylogeny ; *Hydrothermal Vents/microbiology ; *Viruses/genetics/metabolism ; Sulfur/metabolism ; }, abstract = {BACKGROUND: The deep sea harbors many viruses, yet their diversity and interactions with hosts in hydrothermal ecosystems are largely unknown. Here, we analyzed the viral composition, distribution, host preference, and metabolic potential in different habitats of global hydrothermal vents, including vent plumes, background seawater, diffuse fluids, and sediments.

RESULTS: From 34 samples collected at eight vent sites, a total of 4662 viral populations (vOTUs) were recovered from the metagenome assemblies, encompassing diverse phylogenetic groups and defining many novel lineages. Apart from the abundant unclassified viruses, tailed phages are most predominant across the global hydrothermal vents, while single-stranded DNA viruses, including Microviridae and small eukaryotic viruses, also constitute a significant part of the viromes. As revealed by protein-sharing network analysis, hydrothermal vent viruses formed many novel genus-level viral clusters and are highly endemic to specific vent sites and habitat types. Only 11% of the vOTUs can be linked to hosts, which are the key microbial taxa of hydrothermal habitats, such as Gammaproteobacteria and Campylobacterota. Intriguingly, vent viromes share some common metabolic features in that they encode auxiliary genes that are extensively involved in the metabolism of carbohydrates, amino acids, cofactors, and vitamins. Specifically, in plume viruses, various auxiliary genes related to methane, nitrogen, and sulfur metabolism were observed, indicating their contribution to host energy conservation. Moreover, the prevalence of sulfur-relay pathway genes indicated the significant role of vent viruses in stabilizing the tRNA structure, which promotes host adaptation to steep environmental gradients.

CONCLUSIONS: The deep-sea hydrothermal systems hold untapped viral diversity with novelty. They may affect both vent prokaryotic and eukaryotic communities and modulate host metabolism related to vent adaptability. More explorations are needed to depict global vent virus diversity and its roles in this unique ecosystem. Video Abstract.}, } @article {pmid36566218, year = {2022}, author = {Grevesse, T and Guéguen, C and Onana, VE and Walsh, DA}, title = {Degradation pathways for organic matter of terrestrial origin are widespread and expressed in Arctic Ocean microbiomes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {237}, pmid = {36566218}, issn = {2049-2618}, mesh = {*Humic Substances/analysis ; Oceans and Seas ; Bacteria/genetics ; Carbon ; *Microbiota/genetics ; }, abstract = {BACKGROUND: The Arctic Ocean receives massive freshwater input and a correspondingly large amount of humic-rich organic matter of terrestrial origin. Global warming, permafrost melt, and a changing hydrological cycle will contribute to an intensification of terrestrial organic matter release to the Arctic Ocean. Although considered recalcitrant to degradation due to complex aromatic structures, humic substances can serve as substrate for microbial growth in terrestrial environments. However, the capacity of marine microbiomes to process aromatic-rich humic substances, and how this processing may contribute to carbon and nutrient cycling in a changing Arctic Ocean, is relatively unexplored. Here, we used a combination of metagenomics and metatranscriptomics to assess the prevalence and diversity of metabolic pathways and bacterial taxa involved in aromatic compound degradation in the salinity-stratified summer waters of the Canada Basin in the western Arctic Ocean.

RESULTS: Community-scale meta-omics profiling revealed that 22 complete pathways for processing aromatic compounds were present and expressed in the Canada Basin, including those for aromatic ring fission and upstream funneling pathways to access diverse aromatic compounds of terrestrial origin. A phylogenetically diverse set of functional marker genes and transcripts were associated with fluorescent dissolved organic matter, a component of which is of terrestrial origin. Pathways were common throughout global ocean microbiomes but were more abundant in the Canada Basin. Genome-resolved analyses identified 12 clades of Alphaproteobacteria, including Rhodospirillales, as central contributors to aromatic compound processing. These genomes were mostly restricted in their biogeographical distribution to the Arctic Ocean and were enriched in aromatic compound processing genes compared to their closest relatives from other oceans.

CONCLUSION: Overall, the detection of a phylogenetically diverse set of genes and transcripts implicated in aromatic compound processing supports the view that Arctic Ocean microbiomes have the capacity to metabolize humic substances of terrestrial origin. In addition, the demonstration that bacterial genomes replete with aromatic compound degradation genes exhibit a limited distribution outside of the Arctic Ocean suggests that processing humic substances is an adaptive trait of the Arctic Ocean microbiome. Future increases in terrestrial organic matter input to the Arctic Ocean may increase the prominence of aromatic compound processing bacteria and their contribution to Arctic carbon and nutrient cycles. Video Abstract.}, } @article {pmid36566203, year = {2022}, author = {Dang, T and Kumaishi, K and Usui, E and Kobori, S and Sato, T and Toda, Y and Yamasaki, Y and Tsujimoto, H and Ichihashi, Y and Iwata, H}, title = {Stochastic variational variable selection for high-dimensional microbiome data.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {236}, pmid = {36566203}, issn = {2049-2618}, mesh = {Humans ; Bayes Theorem ; Algorithms ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; }, abstract = {BACKGROUND: The rapid and accurate identification of a minimal-size core set of representative microbial species plays an important role in the clustering of microbial community data and interpretation of clustering results. However, the huge dimensionality of microbial metagenomics datasets is a major challenge for the existing methods such as Dirichlet multinomial mixture (DMM) models. In the approach of the existing methods, the computational burden of identifying a small number of representative species from a large number of observed species remains a challenge.

RESULTS: We propose a novel approach to improve the performance of the widely used DMM approach by combining three ideas: (i) we propose an indicator variable to identify representative operational taxonomic units that substantially contribute to the differentiation among clusters; (ii) to address the computational burden of high-dimensional microbiome data, we propose a stochastic variational inference, which approximates the posterior distribution using a controllable distribution called variational distribution, and stochastic optimization algorithms for fast computation; and (iii) we extend the finite DMM model to an infinite case by considering Dirichlet process mixtures and estimating the number of clusters as a variational parameter. Using the proposed method, stochastic variational variable selection (SVVS), we analyzed the root microbiome data collected in our soybean field experiment, the human gut microbiome data from three published datasets of large-scale case-control studies and the healthy human microbiome data from the Human Microbiome Project.

CONCLUSIONS: SVVS demonstrates a better performance and significantly faster computation than those of the existing methods in all cases of testing datasets. In particular, SVVS is the only method that can analyze massive high-dimensional microbial data with more than 50,000 microbial species and 1000 samples. Furthermore, a core set of representative microbial species is identified using SVVS that can improve the interpretability of Bayesian mixture models for a wide range of microbiome studies. Video Abstract.}, } @article {pmid36566015, year = {2023}, author = {Wang, T and Gao, H and He, C and Gao, L and Wang, B and Hua, R and Du, Y and Liang, C and Xin, S and Shang, H and Wang, Y and Wang, W and Xu, J}, title = {Adult hypertensive rats are more prone to gut microflora perturbation and fibrosis in response to moderate restraint stress.}, journal = {Translational research : the journal of laboratory and clinical medicine}, volume = {254}, number = {}, pages = {92-114}, doi = {10.1016/j.trsl.2022.10.006}, pmid = {36566015}, issn = {1878-1810}, mesh = {Rats ; Animals ; *Gastrointestinal Microbiome ; Blood Pressure ; Rats, Inbred SHR ; *Hypertension ; Fibrosis ; }, abstract = {Hypertension (HTN) is a common endpoint for numerous cardiovascular diseases, the prevalence of which has been quickly increasing due to a wide range of reasons. Previous research has found that following stress, ELISA and 16S rDNA sequencing indicated substantial changes in plasma cytokines or hormones, as well as alterations in gut microbiota in juvenile hypertensive rats. However, it remains still unclear how such interaction modifications affect microbial populations and organismal function. Stress-related hormones show a significant drop. Similar to earlier research, the stress group had dramatically increased release of pro-inflammatory cytokines such as IL-17. Importantly, a unified collection of tools that allows for deep and comprehensive colonic structural investigation has been developed. Stress may limit the transition of macrophages (Mφs) to M1Mφs while increasing the transfer to M2Mφs. Evidence highlighted that tight junction proteins were decreased along with enhancement in intestinal permeability. Morphological analysis revealed that the SHR-S group exhibited considerably higher levels of morphological alterations and fibrosis in colon, heart, and thoracic aorta tissues.Significant improvements in bacteria linked with short-chain fatty acid synthesis, such as Prevotella and Ruminococcus, were discovered by metagenomic analysis. Adult hypertensive rats are more susceptible to gut microbiota disruption and fibrosis as a result of mild restraint stress. This might contribute to some innovative ideas for HTN both treatment and prevention.}, } @article {pmid36565882, year = {2023}, author = {Ariaeenejad, S and Kavousi, K and Han, JL and Ding, XZ and Hosseini Salekdeh, G}, title = {Efficiency of an alkaline, thermostable, detergent compatible, and organic solvent tolerant lipase with hydrolytic potential in biotreatment of wastewater.}, journal = {The Science of the total environment}, volume = {866}, number = {}, pages = {161066}, doi = {10.1016/j.scitotenv.2022.161066}, pmid = {36565882}, issn = {1879-1026}, mesh = {Animals ; Sheep ; *Lipase/chemistry ; Hydrolysis ; *Wastewater ; Detergents ; Solvents/chemistry ; Hydrogen-Ion Concentration ; Temperature ; }, abstract = {Discharging the tannery wastewater into the environment is a serious challenge worldwide due to the release of severe recalcitrant pollutants such as oil compounds and organic materials. The biological treatment through enzymatic hydrolysis is a cheap and eco-friendly method for eliminating fatty substances from wastewater. In this context, lipases can be utilized for bio-treatment of wastewater in multifaceted industrial applications. To overcome the limitations in removing pollutants in the effluent, we aimed to identify a novel robust stable lipase (PersiLipase1) from metagenomic data of tannery wastewater for effective bio-degradation of the oily wastewater pollution. The lipase displayed remarkable thermostability and maintained over 81 % of its activity at 60 °C.After prolonged incubation for 35 days at 60°C, the PersiLipase1 still maintained 53.9 % of its activity. The enzyme also retained over 67 % of its activity in a wide range of pH (4.0 to 9.0). In addition, PersiLipase1 demonstrated considerable tolerance toward metal ions and organic solvents (e.g., retaining >70% activity after the addition of 100 mM of chemicals). Hydrolysis of olive oil and sheep fat by this enzyme showed 100 % efficiency. Furthermore, the PersiLipase1 proved to be efficient for biotreatment of oil and grease from tannery wastewater with the hydrolysis efficiency of 90.76 % ± 0.88. These results demonstrated that the metagenome-derived PersiLipase1 from tannery wastewater has a promising potential for the biodegradation and management of oily wastewater pollution.}, } @article {pmid36565853, year = {2023}, author = {Olorocisimo, JP and Diaz, LA and Co, DE and Carag, HM and Ibana, JA and Velarde, MC}, title = {Lactobacillus delbrueckii reduces anxiety-like behavior in zebrafish through a gut microbiome - brain crosstalk.}, journal = {Neuropharmacology}, volume = {225}, number = {}, pages = {109401}, doi = {10.1016/j.neuropharm.2022.109401}, pmid = {36565853}, issn = {1873-7064}, mesh = {Animals ; *Lactobacillus delbrueckii/genetics/metabolism ; Zebrafish/genetics/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics/metabolism ; Brain/metabolism ; Anxiety ; }, abstract = {Certain bacteria possess the ability to reduce anxiety- and stress-related behaviors through the gut microbiome-brain axis. Such bacteria are called psychobiotics, and can be used to improve mood and cognition. However, only a few bacteria have been characterized as psychobiotics, and their exact mechanism of action remains unclear. Hence, in this study we analyzed three different species under the Lactobacillacea family, namely, Lactobacillus delbrueckii, Lacticaseibacillus casei, and Lacticaseibacillus paracasei for their potential psychobiotic activities. L. delbrueckii treatment reduced anxiety-like behavior and increased brain and gut glutamic acid decarboxylase (gad) gene expression in zebrafish. It also altered zebrafish gut microbial community as determined by PCR-DGGE and 16S rRNA-based metagenomics analysis. Overall, this paper showed that L. delbrueckii but not L. paracasei and L. casei, induced a consistent improvement in anxiety-like behavior in zebrafish, implicating its potential role as a psychobiotic to reduce anxiety. This article is part of the Special Issue on 'Microbiome & the Brain: Mechanisms & Maladies'.}, } @article {pmid36565815, year = {2023}, author = {Miranda, TDS and Schiffler, FB and D'arc, M and Moreira, FRR and Cosentino, MAC and Coimbra, A and Mouta, R and Medeiros, G and Girardi, DL and Wanderkoke, V and Soares, CFA and Francisco, TM and Henry, MD and Afonso, BC and Soffiati, FL and Ferreira, SS and Ruiz-Miranda, CR and Soares, MA and Santos, AFA}, title = {Metagenomic analysis reveals novel dietary-related viruses in the gut virome of marmosets hybrids (Callithrix jacchus x Callithrix penicillata), Brazil.}, journal = {Virus research}, volume = {325}, number = {}, pages = {199017}, pmid = {36565815}, issn = {1872-7492}, mesh = {Animals ; *Callithrix/genetics ; Brazil ; Phylogeny ; Virome ; Metagenomics ; *Viruses/genetics ; Diet ; Genome, Viral ; }, abstract = {Viral metagenomics has contributed enormously to the characterization of a wide range of viruses infecting animals of all phyla in the last decades. Among Neotropical primates, especially those introduced, knowledge about viral diversity remains poorly studied. Therefore, using metagenomics based on virus enrichment, we explored the viral microbiota present in the feces of introduced common marmosets (Callithrix sp.) in three locations from the Silva Jardim region in the State of Rio de Janeiro, Brazil. Fecal samples were collected from nine marmosets, pooled into three sample pools, and sequenced on Illumina MiSeq platform. Sequence reads were analyzed using a viral metagenomic analysis pipeline and two novel insect viruses belonging to the Parvoviridae and Baculoviridae families were identified. The complete genome of a densovirus (Parvoviridae family) of 5,309 nucleotides (nt) was obtained. The NS1 and VP1 proteins share lower than 32% sequence identity with the corresponding proteins of known members of the subfamily Densovirinae. Phylogenetic analysis suggests that this virus represents a new genus, provisionally named Afoambidensovirus due to its discovery in the Brazilian Atlantic Forest. The novel species received the name Afoambidensovirus incertum 1. The complete circular genome of a baculovirus of 107,191 nt was also obtained, showing 60.8% sequence identity with the most closely related member of the Baculoviridae family. Phylogenetic analysis suggests that this virus represents a new species in the Betabaculovirus genus, provisionally named Betabaculovirus incertum 1. In addition, sequences from several families of arthropods in the three pools evaluated were characterized (contigs ranging from 244 to 6,750 nt), corroborating the presence of possible insect hosts with which these new viruses may be associated. Our study expands the knowledge about two viral families known to infect insects, an important component of the marmosets' diet. This identification in hosts' feces samples demonstrates one of the many uses of this type of data and could serve as a basis for future research characterizing viruses in wildlife using noninvasive samples.}, } @article {pmid36565811, year = {2023}, author = {Li, Y and Cao, L and Han, X and Ma, Y and Liu, Y and Gao, S and Zhang, C}, title = {Altered vaginal eukaryotic virome is associated with different cervical disease status.}, journal = {Virologica Sinica}, volume = {38}, number = {2}, pages = {184-197}, pmid = {36565811}, issn = {1995-820X}, mesh = {Female ; Humans ; Virome ; *Papillomavirus Infections/microbiology/pathology ; Eukaryota ; *Uterine Cervical Neoplasms/microbiology/pathology ; *Viruses ; Biomarkers ; Papillomaviridae ; }, abstract = {Viruses are important components of the human body. Growing evidence suggests that they are engaged in the physiology and disease status of the host. Even though the vaginal microbiome is involved in human papillomavirus (HPV) infection and cervical cancer (CC) progression, little is known about the role of the vaginal virome. In this pilot exploratory study, using unbiased viral metagenomics, we aim to investigate the vaginal eukaryotic virome in women with different levels of cervical lesions, and examine their associations with different cervical disease status. An altered eukaryotic virome was observed in women with different levels of lesions and Lactobacillus profiles. Anelloviruses and papillomaviruses are the most commonly detected eukaryotic viruses of the vaginal virome. Higher abundance and richness of anelloviruses and papillomaviruses were associated with low-grade squamous intraepithelial lesion (LSIL) and CC. Besides, higher anellovirus abundance was also associated with lactobacillus-depleted microbiome profiles and bacterial community state (CST) type IV. Furthermore, increased correlations between Anelloviridae and Papillomaviridae occurred in the women with increased cervical disease severity level from LSIL to CC. These data suggest underlying interactions between different microbes as well as the host physiology. Higher abundance and diversity of both anelloviruses and papillomaviruses shared by LSIL and CC suggest that anellovirus may be used as a potential adjunct biomarker to predict the risk of HPV persistent infection and/or CC. Future studies need to focus on the clinical relevance of anellovirus abundance with cervical disease status, and the evaluation of their potential as a new adjunct biomarker for the prediction and prognoses of CC.}, } @article {pmid36565763, year = {2023}, author = {Surti, P and Kailasa, SK and Mungray, AK}, title = {Enhancement of electrode properties using carbon dots functionalized magnetite nanoparticles for azo dye decolorization in microbial fuel cell.}, journal = {Chemosphere}, volume = {313}, number = {}, pages = {137601}, doi = {10.1016/j.chemosphere.2022.137601}, pmid = {36565763}, issn = {1879-1298}, mesh = {*Bioelectric Energy Sources ; Carbon/chemistry ; Azo Compounds/chemistry ; *Magnetite Nanoparticles ; Electrodes ; Electricity ; }, abstract = {Technology integration of nanomaterials with microbial fuel cell (MFC) have led to simultaneous degradation of recalcitrant dyes and energy extraction from textile wastewater. Limited electron transfer capacity and hydrophobicity of electrode are the bottlenecks for enhancing the performance of MFC. Nanomaterials can provide surface functionalities for electron transfers and serve as catalyst for pollutant degradation. In this paper, magnetite nanoparticles functionalized with carbon dots (Fe3O4@CDs) were used to enhance the electron transfer capacity of the electrodes due to numerous surface-active functional groups of CDs and the reversible redox reaction of Fe[2+]/Fe[3+]. Polydopamine (PDA) was used as binder to coat Fe3O4@CDs onto the surface of carbon felt (CF) electrodes in a sono-chemical reaction, favoring to form biocompatible electrodes. Charge transfer resistance of Fe3O4@CDs@PDA-CF was 5.02Ω as compared to 293.34Ω of unmodified CF. Fe3O4@CDs@PDA-CF installed MFC could achieve almost 98% dye degradation efficiency within 48 h and 18.30 mW m[-2] power output as compared to 77% dye degradation and 0.34 mW m[-2] power output by unmodified CF electrode MFC. Moreover, metagenomic analysis of microbial consortia developed in Fe3O4@CDs@PDA-CF MFC showed enrichment of electrogenic and dye degrading microbial communities of Achromobacter. Delftia, Geobacter and Pseudomonas.}, } @article {pmid36565637, year = {2023}, author = {Alvarenga, BO and Paiva, JB and Souza, AIS and Rodrigues, DR and Tizioto, PC and Ferreira, AJP}, title = {Metagenomics analysis of the morphological aspects and bacterial composition of broiler feces.}, journal = {Poultry science}, volume = {102}, number = {2}, pages = {102401}, pmid = {36565637}, issn = {1525-3171}, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Metagenomics ; Chickens/genetics ; *Gastrointestinal Microbiome ; Bacteria/genetics ; Feces/microbiology ; Firmicutes ; }, abstract = {In this descriptive study, we used metagenomics to analyze the relationship between the morphological aspects of chicken feces and its respective bacterial compositions. The microbiota composition was determined by sequencing the V4 region of the 16S rRNA genes collected from fresh broiler feces at 19 d old. In total, 48 samples were collected and divided into 8 groups of 6 samples each. The morphological changes studied were feed passage (FP) and reddish mucus (RM). Each was classified into 3 levels of intensity: 1 (slight), 2 (moderate), or 3 (intense). Thus, the 8 groups studied were feed passage (FP-1; FP-2; FP-3), reddish mucus (RM-1; RM-2; RM-3), normal ileal feces (NIF), and cecal discharge (CD). The alpha diversity (Shannon's index) revealed that the CD group showed greater diversity, and was significantly different from FP-2, FP-3, and RM-1. The beta diversity showed that the CD group samples were more homogeneous than the ileal feces groups. The relative abundance analysis revealed that Firmicutes and Proteobacteria were the most abundant phyla in the ileal feces groups. In CD, Firmicutes and Bacteroidetes were the most abundant. The relative abundance at the genus level revealed 136 different bacterial genera. In the ileal feces groups, the two most abundant genera were Lactobacillus and Escherichia/Shigella, except in the FP-1 and RM-2 groups, which had the opposite order. Unlike the others, the CD group had a higher abundance of Bacteroides and Faecalibacterium. When comparing the NIF group with the others, significant changes were found in the fecal microbiota, with nine genera for the FP groups, 19 for the RM groups, and 61 when compared to CD. The results of the present study suggest that evaluation of fecal morphology is a fundamental task that makes it possible to act quickly and assertively, as the morphological aspects of the feces may be related to the composition and structure of fecal microbiota.}, } @article {pmid36565548, year = {2023}, author = {Wang, R and Cai, Y and Lu, W and Zhang, R and Shao, R and Yau, SY and Stubbs, B and McIntyre, RS and Su, KP and Xu, G and Qi, L and So, KF and Lin, K}, title = {Exercise effect on the gut microbiota in young adolescents with subthreshold depression: A randomized psychoeducation-controlled Trial.}, journal = {Psychiatry research}, volume = {319}, number = {}, pages = {115005}, doi = {10.1016/j.psychres.2022.115005}, pmid = {36565548}, issn = {1872-7123}, mesh = {Humans ; Adolescent ; *Depression/therapy ; *Gastrointestinal Microbiome ; Exercise ; }, abstract = {This 3-month randomized psychoeducation-controlled trial (RCT) of exercise was undertaken in young adolescents with subthreshold depression to examine the impact on gut microbiota. Participants (aged 12-14 years) were randomly assigned to an exercise or a psychoeducation-controlled group. The exercise intervention arm took moderate-intensity exercise, comprised of 30 min of running per day, 4 days a week for 3 months. Psychoeducation intervention consisted of 6 sessions of group activity including gaming, reading, and singing. The gut microbiota was assessed by metagenomic sequencing. After 3-month moderate-intensity exercise, the intervention group increased the relative abundance of Coprococcus, Blautia, Dorea, Tyzzerella at the genus level, as well as Tyzzerella nexilis, Ruminococcus obeum at species level when compared to the psychoeducation-controlled group. Moreover, EggNOG analyses showed that the defense and signal transduction mechanism were highly enriched after the active intervention, and changes were correlated with improvements in depressive symptoms measured by Chinese Patient Depression Questionnaire 9. The KEGG pathway of neurodegenerative diseases was depleted in the microbiome in young adolescents with subthreshold depression after exercise intervention. This 3-month RCT suggests that at both the genus and species levels, aerobic group exercise intervention improved in depressive symptoms and revealed changes in gut microbiota suggesting beneficial effects.}, } @article {pmid36564826, year = {2022}, author = {Chen, H and Jiao, J and Wei, M and Jiang, X and Yang, R and Yu, X and Zhang, G and Zhou, X}, title = {Metagenomic analysis of the interaction between the gut microbiota and colorectal cancer: a paired-sample study based on the GMrepo database.}, journal = {Gut pathogens}, volume = {14}, number = {1}, pages = {48}, pmid = {36564826}, issn = {1757-4749}, support = {82100594//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: Previous evidence has shown that the gut microbiota plays a role in the development and progression of colorectal cancer (CRC). This study aimed to provide quantitative analysis and visualization of the interaction between the gut microbiota and CRC in order to establish a more precise microbiota panel for CRC diagnosis.

METHOD: A paired-sample study was designed by retrieving original metagenomic data from the GMrepo database. The differences in the distribution of the gut microbiota between CRCs and controls were analysed at the species level. A co-occurrence network was established, and the microbial interactions with environmental factors were assessed. Random forest models were used to determine significant biomarkers for differentiating CRC and control samples.

RESULTS: A total of 709 metagenomic samples from 6 projects were identified. After matching, 86 CRC patients and 86 matched healthy controls from six countries were enrolled. A total of 484 microbial species and 166 related genera were analysed. In addition to previously recognized associations between Fusobacterium nucleatum and species belonging to the genera Peptostreptococcus, Porphyromonas, and Prevotella and CRC, we found new associations with the novel species of Parvimonas micra and Collinsella tanakaei. In CRC patients, Bacteroides uniformis and Collinsella tanakaei were positively correlated with age, whereas Dorea longicatena, Adlercreutzia equolifaciens, and Eubacterium hallii had positive associations with body mass index (BMI). Finally, a random forest model was established by integrating different numbers of species with the highest model-building importance and lowest inner subcategory bias. The median value of the area under the receiver operating characteristic curve (AUC) was 0.812 in the training cohort and 0.790 in the validation set.

CONCLUSIONS: Our study provides a novel bioinformatics approach for investigating the interaction between the gut microbiota and CRC using an online free database. The identification of key species and their associated genes should be further emphasized to determine the relative causality of microbial organisms in the development of CRC.}, } @article {pmid36564805, year = {2022}, author = {Li, X and Li, R and Ji, B and Zhao, L and Wang, J and Yan, T}, title = {Integrative metagenomic and metabolomic analyses reveal the role of gut microbiota in antibody-mediated renal allograft rejection.}, journal = {Journal of translational medicine}, volume = {20}, number = {1}, pages = {614}, pmid = {36564805}, issn = {1479-5876}, mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Gastrointestinal Microbiome/genetics ; Dysbiosis ; Antibodies ; Allografts ; Graft Rejection ; }, abstract = {BACKGROUND: Antibody-mediated rejection (AMR) remains one of the major barriers for graft survival after kidney transplantation. Our previous study suggested a gut microbiota dysbiosis in kidney transplantation recipients with AMR. However, alternations in gut microbial function and structure at species level have not been identified. In the present study, we investigated the metagenomic and metabolic patterns of gut microbiota in AMR patients to provide a comprehensive and in-depth understanding of gut microbiota dysbiosis in AMR.

METHODS: We enrolled 60 kidney transplantation recipients, 28 showed AMR and 32 were non-AMR controls with stable post-transplant renal functions. Shotgun sequencing and untargeted LC/MS metabolomic profiling of fecal samples were performed in kidney transplantation recipients with AMR and controls.

RESULTS: Totally, we identified 311 down-regulated and 27 up-regulated gut microbial species associated with AMR after kidney transplantation, resulting in the altered expression levels of 437 genes enriched in 22 pathways, of which 13 were related to metabolism. Moreover, 32 differential fecal metabolites were found in recipients with AMR. Among them, alterations in 3b-hydroxy-5-cholenoic acid, L-pipecolic acid, taurocholate, and 6k-PGF1alpha-d4 directly correlated with changes in gut microbial species and functions. Specific differential fecal species and metabolites were strongly associated with clinical indexes (Cr, BUN, etc.), and could distinguish the recipients with AMR from controls as potential biomarkers.

CONCLUSIONS: Altogether, our findings provided a comprehensive and in-depth understanding of the correlation between AMR and gut microbiota, which is important for the etiological and diagnostic study of AMR after kidney transplantation.}, } @article {pmid36564713, year = {2022}, author = {Liu, Y and Zhu, J and Wang, H and Lu, W and Lee, YK and Zhao, J and Zhang, H}, title = {Machine learning framework for gut microbiome biomarkers discovery and modulation analysis in large-scale obese population.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {850}, pmid = {36564713}, issn = {1471-2164}, mesh = {Humans ; *Gastrointestinal Microbiome ; Obesity ; Feces/microbiology ; Biomarkers ; Machine Learning ; }, abstract = {BACKGROUND: The gut microbiome has proven to be an important factor affecting obesity; however, it remains a challenge to identify consistent biomarkers across geographic locations and perform precisely targeted modulation for obese individuals.

RESULTS: This study proposed a systematic machine learning framework and applied it to 870 human stool metagenomes across five countries to obtain comprehensive regional shared biomarkers and conduct a personalized modulation analysis. In our pipeline, a heterogeneous ensemble feature selection diagram is first developed to determine an optimal subset of biomarkers through the aggregation of multiple techniques. Subsequently, a deep reinforcement learning method was established to alter the targeted composition to the desired healthy target. In this manner, we can realize personalized modulation by counterfactual inference. Consequently, a total of 42 species were identified as regional shared biomarkers, and they showed good performance in distinguishing obese people from the healthy group (area under curve (AUC) =0.85) when demonstrated on validation datasets. In addition, by pooling all counterfactual explanations, we found that Akkermansia muciniphila, Faecalibacterium prausnitzii, Prevotella copri, Bacteroides dorei, Bacteroides eggerthii, Alistipes finegoldii, Alistipes shahii, Eubacterium sp. _CAG_180, and Roseburia hominis may be potential broad-spectrum targets with consistent modulation in the multi-regional obese population.

CONCLUSIONS: This article shows that based on our proposed machine-learning framework, we can obtain more comprehensive and accurate biomarkers and provide modulation analysis for the obese population. Moreover, our machine-learning framework will also be very useful for other researchers to further obtain biomarkers and perform counterfactual modulation analysis in different diseases.}, } @article {pmid36564666, year = {2023}, author = {Minkina, T and Sushkova, S and Delegan, Y and Bren, A and Mazanko, M and Kocharovskaya, Y and Filonov, A and Rajput, VD and Mandzhieva, S and Rudoy, D and Prazdnova, EV and Elena, V and Zelenkova, G and Ranjan, A}, title = {Effect of chicken manure on soil microbial community diversity in poultry keeping areas.}, journal = {Environmental geochemistry and health}, volume = {45}, number = {12}, pages = {9303-9319}, pmid = {36564666}, issn = {1573-2983}, support = {075-15-2019-1880//Government of the Russian Federation/ ; }, mesh = {Animals ; *Soil ; Chickens ; Manure ; Poultry ; Soil Microbiology ; Bacteria/genetics ; *Microbiota ; }, abstract = {The poultry industry is generating a significant amount of waste from chicken droppings that are abundant in microbes as well as macro- and micronutrients suitable for manure. It has the potential to improve the microbial activity and nutrient dynamics in the soil, ultimately improving soil fertility. The present study aimed to investigate the effect of chicken droppings manure (CDM) on the diversity of the soil microbiome in the free walking chicken's area located in Stefanidar, Rostov Region, Russia. The data obtained were compared with 16 s rRNA from control samples located not far from the chicken's free-walking area, but not in direct contact with the droppings. Effect of CDM on the physicochemical characteristics of the soil and changes in its microbial diversity were assessed by employing the metagenomic approaches and 16 s rRNA-based taxonomic assessment. The alpha and beta diversity indices revealed that the application of the CDM significantly improved the soil microbial diversity. The 16S taxonomical analysis confirmed Proteobacteria, Actinobacteria, Bacteroidetes, Firmicutes, and Planctomycetes as abundant bacterial phylum. It also revealed the increase in the total number of the individual operational taxonomic unit (OTU) species, a qualitative indicator of the rich microbial community. The alpha diversity confirmed that the significant species richness of the soil is associated with the CDM treatment. The increased OTUs represent the qualitative indicator of a community that has been studied up to the depth of 5-20 cm of the CDM treatment range. These findings suggested that CDM-mediated microbial richness are believed to confer the cycling of carbon, nitrogen, and sulfur, along with key soil enzymes such as dehydrogenases and catalase carbohydrate-active enzymes. Hence, the application of CDM could improve soil fertility by nutrient cycling caused by changes in soil microbial dynamics, and it could also be a cost-effective sustainable means of improving soil health.}, } @article {pmid36564596, year = {2023}, author = {Wang, W and Wei, X and Wu, L and Shang, X and Cheng, F and Li, B and Zhou, X and Zhang, J}, title = {Correction: The occurrence of antibiotic resistance genes in the microbiota of yak, beef and dairy cattle characterized by a metagenomic approach.}, journal = {The Journal of antibiotics}, volume = {76}, number = {3}, pages = {190}, doi = {10.1038/s41429-022-00590-y}, pmid = {36564596}, issn = {1881-1469}, } @article {pmid36564496, year = {2022}, author = {Allioux, M and Yvenou, S and Merkel, A and Cozannet, M and Aubé, J and Pommellec, J and Le Romancer, M and Lavastre, V and Guillaume, D and Alain, K}, title = {A metagenomic insight into the microbiomes of geothermal springs in the Subantarctic Kerguelen Islands.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {22243}, pmid = {36564496}, issn = {2045-2322}, support = {P30 CA016086/CA/NCI NIH HHS/United States ; }, mesh = {Metagenome ; *Hot Springs/microbiology ; Metagenomics/methods ; Islands ; Archaea ; *Microbiota/genetics ; Phylogeny ; }, abstract = {The Kerguelen Islands, located in the southern part of the Indian Ocean, are very isolated geographically. The microbial diversity and communities present on the island, especially associated to geothermal springs, have never been analyzed with high-throughput sequencing methods. In this article, we performed the first metagenomics analysis of microorganisms present in Kerguelen hot springs. From four hot springs, we assembled metagenomes and recovered 42 metagenome-assembled genomes, mostly associated with new putative taxa based on phylogenomic analyses and overall genome relatedness indices. The 42 MAGs were studied in detail and showed putative affiliations to 13 new genomic species and 6 new genera of Bacteria or Archaea according to GTDB. Functional potential of MAGs suggests the presence of thermophiles and hyperthermophiles, as well as heterotrophs and primary producers possibly involved in the sulfur cycle, notably in the oxidation of sulfur compounds. This paper focused on only four of the dozens of hot springs in the Kerguelen Islands and should be considered as a preliminary study of the microorganisms inhabiting the hot springs of these isolated islands. These results show that more efforts should be made towards characterization of Kerguelen Islands ecosystems, as they represent a reservoir of unknown microbial lineages.}, } @article {pmid36564466, year = {2022}, author = {Fachrul, M and Méric, G and Inouye, M and Pamp, SJ and Salim, A}, title = {Assessing and removing the effect of unwanted technical variations in microbiome data.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {22236}, pmid = {36564466}, issn = {2045-2322}, mesh = {Animals ; Swine ; *Microbiota/genetics ; Metagenome ; Freezing ; Bacteroidetes ; Feces ; }, abstract = {Varying technologies and experimental approaches used in microbiome studies often lead to irreproducible results due to unwanted technical variations. Such variations, often unaccounted for and of unknown source, may interfere with true biological signals, resulting in misleading biological conclusions. In this work, we aim to characterize the major sources of technical variations in microbiome data and demonstrate how in-silico approaches can minimize their impact. We analyzed 184 pig faecal metagenomes encompassing 21 specific combinations of deliberately introduced factors of technical and biological variations. Using the novel Removing Unwanted Variations-III-Negative Binomial (RUV-III-NB), we identified several known experimental factors, specifically storage conditions and freeze-thaw cycles, as likely major sources of unwanted variation in metagenomes. We also observed that these unwanted technical variations do not affect taxa uniformly, with freezing samples affecting taxa of class Bacteroidia the most, for example. Additionally, we benchmarked the performances of different correction methods, including ComBat, ComBat-seq, RUVg, RUVs, and RUV-III-NB. While RUV-III-NB performed consistently robust across our sensitivity and specificity metrics, most other methods did not remove unwanted variations optimally. Our analyses suggest that a careful consideration of possible technical confounders is critical during experimental design of microbiome studies, and that the inclusion of technical replicates is necessary to efficiently remove unwanted variations computationally.}, } @article {pmid36564415, year = {2022}, author = {Wu, L and Xie, X and Li, Y and Liang, T and Zhong, H and Yang, L and Xi, Y and Zhang, J and Ding, Y and Wu, Q}, title = {Gut microbiota as an antioxidant system in centenarians associated with high antioxidant activities of gut-resident Lactobacillus.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {102}, pmid = {36564415}, issn = {2055-5008}, mesh = {Aged, 80 and over ; Young Adult ; Humans ; *Gastrointestinal Microbiome ; Antioxidants ; Lactobacillus ; Centenarians ; Metagenome ; }, abstract = {The gut microbiota plays an important role in human health and longevity, and the gut microbiota of centenarians shows unique characteristics. Nowadays, most microbial research on longevity is usually limited to the bioinformatics level, lacking validating information on culturing functional microorganisms. Here, we combined metagenomic sequencing and large-scale in vitro culture to reveal the unique gut microbial structure of the world's longevity town-Jiaoling, China, centenarians and people of different ages. Functional strains were isolated and screened in vitro, and the possible relationship between gut microbes and longevity was explored and validated in vivo. 247 healthy Cantonese natives of different ages participated in the study, including 18 centenarians. Compared with young adults, the gut microbiota of centenarians exhibits higher microbial diversity, xenobiotics biodegradation and metabolism, oxidoreductases, and multiple species (the potential probiotics Lactobacillus, Akkermansia, the methanogenic Methanobrevibacter, gut butyrate-producing members Roseburia, and SCFA-producing species uncl Clostridiales, uncl Ruminococcaceae) known to be beneficial to host metabolism. These species are constantly changing with age. We also isolated 2055 strains from these samples by large-scale in vitro culture, most of which were detected by metagenomics, with clear complementarity between the two approaches. We also screened an age-related gut-resident Lactobacillus with independent intellectual property rights, and its metabolite (L-ascorbic acid) and itself have good antioxidant effects. Our findings underscore the existence of age-related trajectories in the human gut microbiota, and that distinct gut microbiota and gut-resident as antioxidant systems may contribute to health and longevity.}, } @article {pmid36564391, year = {2022}, author = {Nie, S and Wang, J and Deng, Y and Ye, Z and Ge, Y}, title = {Inflammatory microbes and genes as potential biomarkers of Parkinson's disease.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {101}, pmid = {36564391}, issn = {2055-5008}, mesh = {Humans ; *Parkinson Disease/diagnosis ; *Neurodegenerative Diseases ; RNA, Ribosomal, 16S/genetics ; Inflammation ; Biomarkers ; }, abstract = {As the second-largest neurodegenerative disease in the world, Parkinson's disease (PD) has brought a severe economic and medical burden to our society. Growing evidence in recent years suggests that the gut microbiome may influence PD, but the exact pathogenesis of PD remains unclear. In addition, the current diagnosis of PD could be inaccurate and expensive. In this study, the largest meta-analysis currently of the gut microbiome in PD was analyzed, including 2269 samples by 16S rRNA gene and 236 samples by shotgun metagenomics, aiming to reveal the connection between PD and gut microbiome and establish a model to predict PD. The results showed that the relative abundances of potential pro-inflammatory bacteria, genes and pathways were significantly increased in PD, while potential anti-inflammatory bacteria, genes and pathways were significantly decreased. These changes may lead to a decrease in potential anti-inflammatory substances (short-chain fatty acids) and an increase in potential pro-inflammatory substances (lipopolysaccharides, hydrogen sulfide and glutamate). Notably, the results of 16S rRNA gene and shotgun metagenomic analysis have consistently identified five decreased genera (Roseburia, Faecalibacterium, Blautia, Lachnospira, and Prevotella) and five increased genera (Streptococcus, Bifidobacterium, Lactobacillus, Akkermansia, and Desulfovibrio) in PD. Furthermore, random forest models performed well for PD prediction based on 11 genera (accuracy > 80%) or 6 genes (accuracy > 90%) related to inflammation. Finally, a possible mechanism was presented to explain the pathogenesis of inflammation leading to PD. Our results provided further insights into the prediction and treatment of PD based on inflammation.}, } @article {pmid36563703, year = {2023}, author = {Marais, G and Hardie, D and Brink, A}, title = {A case for investment in clinical metagenomics in low-income and middle-income countries.}, journal = {The Lancet. Microbe}, volume = {4}, number = {3}, pages = {e192-e199}, doi = {10.1016/S2666-5247(22)00328-7}, pmid = {36563703}, issn = {2666-5247}, mesh = {Humans ; *SARS-CoV-2 ; *COVID-19 ; Developing Countries ; Metagenomics ; Investments ; }, abstract = {Clinical metagenomics is the diagnostic approach with the broadest capacity to detect both known and novel pathogens. Clinical metagenomics is costly to run and requires infrastructure, but the use of next-generation sequencing for SARS-CoV-2 molecular epidemiology in low-income and middle-income countries (LMICs) offers an opportunity to direct this infrastructure to the establishment of clinical metagenomics programmes. Local implementation of clinical metagenomics is important to create relevant systems and evaluate cost-effective methodologies for its use, as well as to ensure that reference databases and result interpretation tools are appropriate to local epidemiology. Rational implementation, based on the needs of LMICs and the available resources, could ultimately improve individual patient care in instances in which available diagnostics are inadequate and supplement emerging infectious disease surveillance systems to ensure the next pandemic pathogen is quickly identified.}, } @article {pmid36563511, year = {2023}, author = {Cotto, I and Vilardi, KJ and Huo, L and Fogarty, EC and Khunjar, W and Wilson, C and De Clippeleir, H and Gilmore, K and Bailey, E and Lücker, S and Pinto, AJ}, title = {Low diversity and microdiversity of comammox bacteria in wastewater systems suggest specific adaptations within the Ca. Nitrospira nitrosa cluster.}, journal = {Water research}, volume = {229}, number = {}, pages = {119497}, doi = {10.1016/j.watres.2022.119497}, pmid = {36563511}, issn = {1879-2448}, mesh = {*Wastewater ; *Ammonia/metabolism ; Nitrites/metabolism ; Nitrification ; RNA, Ribosomal, 16S/genetics ; Ecosystem ; Oxidation-Reduction ; Bacteria/metabolism ; Phylogeny ; Archaea/metabolism ; }, abstract = {Studies have found Ca. Nitrospira nitrosa-like bacteria to be the principal or sole comammox bacteria in nitrogen removal systems for wastewater treatment. In contrast, multiple populations of strict ammonia and nitrite oxidizers co-exist in similar systems. This apparent lack of diversity is surprising and could impact the feasibility of leveraging comammox bacteria for nitrogen removal. We used full-length 16S rRNA gene sequencing and genome-resolved metagenomics to compare the species-level diversity of comammox bacteria with that of strict nitrifiers in full-scale wastewater treatment systems and assess whether this comparison is consistent or diverged at the strain-level. Full-length 16S rRNA gene sequencing indicated that Nitrosomonas-like bacteria exhibited higher species-level diversity in comparison with other nitrifying bacteria, while the strain-level diversity (also called microdiversity) of most Nitrospira-like bacteria were higher than Nitrosomonas-like bacteria with few exceptions (one Nitrospira lineage II population). Comammox bacterial metagenome assembled genomes (MAGs) were associated with Ca. Nitrospira nitrosa. The average amino acid identity between principal comammox bacterial MAGs (93% ± 3) across systems was significantly higher than that of the Nitrosomonas-like ammonia oxidizers (73% ± 8), the Nitrospira_A-like nitrite oxidizer (85% ± 4), and the Nitrospira_D-like nitrite oxidizer (83% ± 1). This demonstrated the low species-level diversity of comammox bacteria compared with strict nitrifiers and further suggests that the same comammox population was detected in all systems. Comammox bacteria (Nitrospira lineage II), Nitrosomonas and, Nitrospira_D (Nitrospira lineage II) MAGs were significantly less microdiverse than the Nitrospira_A (lineage I) MAGs. Interestingly, strain-resolved analysis also indicates that different nitrogen removal systems harbor different comammox bacterial strains within the Ca. Nitrospira nitrosa cluster. These results suggest that comammox bacteria associated with Ca. Nitrospira nitrosa have low species- and strain-level diversity in nitrogen removal systems and may thus harbor specific adaptations to the wastewater ecosystem.}, } @article {pmid36563106, year = {2023}, author = {Chai, X and Wang, J and Li, H and Gao, C and Li, S and Wei, C and Huang, J and Tian, Y and Yuan, J and Lu, J and Gao, D and Zheng, Y and Huang, C and Zhou, J and Shi, G and Ke, A and Liu, F and Fan, J and Cai, J}, title = {Intratumor microbiome features reveal antitumor potentials of intrahepatic cholangiocarcinoma.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2156255}, pmid = {36563106}, issn = {1949-0984}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; *Gastrointestinal Microbiome ; *Microbiota/genetics ; Bacteria/genetics ; *Cholangiocarcinoma/genetics/pathology ; Bile Ducts, Intrahepatic/pathology ; *Bile Duct Neoplasms/genetics/pathology ; }, abstract = {Intrahepatic cholangiocarcinoma (ICC) is a rare malignancy with a high prevalence in China. This study aimed to characterize the ICC tissues' bacterial metagenomics signature and explore its antitumor potential for cancer. In this study, 16S rRNA sequencing was carried out on 99 tissues to characterize the features of intratumoral microbiota, followed by single-cell RNA sequencing (scRNA-seq) and multilevel validation. The presence of microbial DNA in tissues was determined using staining, fluorescence in situ hybridization (FISH), and transmission electron microscopy (TEM). A Gram-positive aerobic bacterium, identified as Staphylococcus capitis, was cultured from fresh tissues. Meanwhile, scRNA-seq showed that intratumoral bacteria could be present in multiple cell types. Using 16S rRNA sequencing, we identified a total of 2,320,287 high-quality reads corresponding to 4,594 OTU (operational taxonomic units) sequences. The most abundant bacterial orders include Burkholderiales, Pseudomonadales, Xanthomonadales, Bacillales and Clostridiales. Alpha and Beta diversity analysis revealed specific features in different tissues. In addition, the content of Paraburkholderia fungorum was significantly higher in the paracancerous tissues and negatively correlated with CA199 (Carbohydrate antigen199) levels. The results of in vitro and in vivo experiments suggest that P. fungorum possesses an antitumor activity against tumors. Metabolomics and transcriptomics showed that P. fungorum could inhibit tumor growth through alanine, aspartate and glutamate metabolism. We determined the characteristic profile of the intratumoral microbiota and the antitumor effect of P. fungorum in ICC.}, } @article {pmid36562201, year = {2023}, author = {Dreisbach, C and Alhusen, J and Prescott, S and Dudley, D and Trinchieri, G and Siega-Riz, AM}, title = {Metagenomic characterization of the maternal prenatal gastrointestinal microbiome by pregravid BMI.}, journal = {Obesity (Silver Spring, Md.)}, volume = {31}, number = {2}, pages = {412-422}, pmid = {36562201}, issn = {1930-739X}, support = {F31 NR017821/NR/NINR NIH HHS/United States ; }, mesh = {Pregnancy ; Humans ; Female ; Overweight/complications ; Body Mass Index ; *Gastrointestinal Microbiome ; Obesity/epidemiology ; *Diabetes, Gestational ; }, abstract = {OBJECTIVE: The incidence of women entering into pregnancy with BMI indicating overweight or obesity is rising with concurrent increases in adverse complications such as gestational diabetes. Although several studies have examined the compositional changes to the microbiome across BMI classifications, there has been no investigation regarding changes in microbial function during pregnancy.

METHODS: A total of 105 gastrointestinal microbiome biospecimens were used in this analysis. Biospecimens were sequenced by using the Illumina NovaSeq 6000 shotgun metagenomics platform.

RESULTS: Findings indicate an enrichment in microbiota from the phylum Firmicutes across all pregravid BMI groups with a decrease in α diversity in groups with BMI indicating obesity or overweight compared with a group with BMI indicating normal weight (p = 0.02). More specifically, women with BMI indicating obesity or overweight had enrichment in Bifidobacterium bifidum and B. adolescentis. Women with BMI > 25 kg/m[2] had a higher abundance of microbiota that support biotin synthesis and regulate epithelial cells in the lower gastrointestinal tract. These epithelial cells are responsible for host adaptability to dietary lipid variation and caloric absorption.

CONCLUSIONS: Our analysis suggests that there are differences in microbial composition and function between BMI groups. Future research should consider how these changes contribute to specific clinical outcomes during pregnancy.}, } @article {pmid36561391, year = {2022}, author = {Dastjerdi, A and Floyd, T and Swinson, V and Davies, H and Barber, A and Wight, A}, title = {Parainfluenza and corona viruses in a fallow deer (Dama dama) with fatal respiratory disease.}, journal = {Frontiers in veterinary science}, volume = {9}, number = {}, pages = {1059681}, pmid = {36561391}, issn = {2297-1769}, abstract = {Parainfluenza virus type 3 (PIV-3) and coronaviruses (CoV) are commonly found in respiratory tracts of ruminants and capable of causing clinical disease. Here, we investigated the cause of ill-thrift and sudden death in a five-month-old male fallow deer which occurred in December 2019. The calf was one of the five calves in a herd of 170 deer that, along with three adult hinds, died during a 2-week period. The deer calves were in a shed, sharing airspace with young cattle that had been reported to be coughing. Significant gross pathology was observed in the respiratory and alimentary tracts of the deer calf and histopathology of the lung and trachea was suggestive of likely involvement of PIV-3. Strong and specific cytoplasmic labeling of bronchiolar epithelium and terminal airway, alike those seen with PIV-3 pneumonia in cattle, was observed using a polyclonal bovine PIV-3 antibody. Metagenomic analysis detected a PIV-3 and a CoV in the lung tissue. The PIV-3 L protein gene had the highest sequence identity with those of bovine PIV-3 (83.1 to 98.4%) and phylogenetically clustered with bovine PIV-3 in the genotype C. The CoV spike protein gene shared 96.7% to 97.9% sequence identity with those of bovine CoVs, but only 53.1% identity with SARS-CoV-2 reference virus. We believe this is the first report of PIV-3 and CoV co-infection in fallow deer and their association with fatal pneumonia; major pathology caused by PIV-3.}, } @article {pmid36561390, year = {2022}, author = {Escudeiro, P and Henry, CS and Dias, RPM}, title = {Functional characterization of prokaryotic dark matter: the road so far and what lies ahead.}, journal = {Current research in microbial sciences}, volume = {3}, number = {}, pages = {100159}, pmid = {36561390}, issn = {2666-5174}, abstract = {Eight-hundred thousand to one trillion prokaryotic species may inhabit our planet. Yet, fewer than two-hundred thousand prokaryotic species have been described. This uncharted fraction of microbial diversity, and its undisclosed coding potential, is known as the "microbial dark matter" (MDM). Next-generation sequencing has allowed to collect a massive amount of genome sequence data, leading to unprecedented advances in the field of genomics. Still, harnessing new functional information from the genomes of uncultured prokaryotes is often limited by standard classification methods. These methods often rely on sequence similarity searches against reference genomes from cultured species. This hinders the discovery of unique genetic elements that are missing from the cultivated realm. It also contributes to the accumulation of prokaryotic gene products of unknown function among public sequence data repositories, highlighting the need for new approaches for sequencing data analysis and classification. Increasing evidence indicates that these proteins of unknown function might be a treasure trove of biotechnological potential. Here, we outline the challenges, opportunities, and the potential hidden within the functional dark matter (FDM) of prokaryotes. We also discuss the pitfalls surrounding molecular and computational approaches currently used to probe these uncharted waters, and discuss future opportunities for research and applications.}, } @article {pmid36560955, year = {2022}, author = {Chen, Z and Sun, Y and Chen, L and Zhang, Y and Wang, J and Li, H and Yan, X and Xia, L and Yao, G}, title = {Differences in meat quality between Angus cattle and Xinjiang brown cattle in association with gut microbiota and its lipid metabolism.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {988984}, pmid = {36560955}, issn = {1664-302X}, abstract = {Gut microbiota plays important roles in mediating fat metabolic events in humans and animals. However, the differences of meat quality traits related to the lipid metabolism (MQT-LM) in association with gut microbiota involving in lipid metabolism have not been well explored between Angus cattle (AG) and Xinjiang brown cattle (BC). Ten heads of 18-month-old uncastrated male AG and BC (5 in each group) raised under the identical conditions were selected to test MQT-LM, i.e., the backfat thickness (BFT), the intramuscular fat (IMF) content, the intramuscular adipocyte areas (IAA), the eye muscle area (EMA), the muscle fiber sectional area (MFSA) and the muscle shear force after sacrifice. The gut microbiota composition and structure with its metabolic function were analyzed by means of metagenomics and metabolomics with rectal feces. The correlation of MQT-LM with the gut microbiota and its metabolites was analyzed. In comparison with AG, BC had significant lower EMA, IMF content and IAA but higher BFT and MFSA. Chao1 and ACE indexes of α-diversity were lower. β-diversity between AG and BC were significantly different. The relative abundance of Bacteroidetes, Prevotella and Blautia and Prevotella copri, Blautia wexlerae, and Ruminococcus gnavus was lower. The lipid metabolism related metabolites, i.e., succinate, oxoglutaric acid, L-aspartic acid and L-glutamic acid were lower, while GABA, L-asparagine and fumaric acid were higher. IMF was positively correlated with Prevotella copri, Blautia wexlerae and Ruminococcus gnavus, and the metabolites succinate, oxoglutaric acid, L-aspartic acid and L-glutamic acid, while negatively with GABA, L-asparagine and fumaric acid. BFT was negatively correlated with Blautia wexlerae and the metabolites succinate, L-aspartic acid and L-glutamic acid, while positively with GABA, L-asparagine and fumaric acid. Prevotella Copri, Blautia wexlerae, and Ruminococcus gnavus was all positively correlated with succinate, oxoglutaric acid, while negatively with L-asparagine and fumaric acid. In conclusion, Prevotella copri, Prevotella intermedia, Blautia wexlerae, and Ruminococcus gnavus may serve as the potential differentiated bacterial species in association with MQT-LM via their metabolites of oxoglutaric acid, succinate, fumaric acid, L-aspartic acid, L-asparagine, L-glutamic acid and GABA between BC and AG.}, } @article {pmid36560824, year = {2022}, author = {Kamau, J and Ergunay, K and Webala, PW and Justi, SA and Bourke, BP and Kamau, MW and Hassell, J and Chege, MN and Mwaura, DK and Simiyu, C and Kibiwot, S and Onyuok, S and Caicedo-Quiroga, L and Li, T and Zimmerman, DM and Linton, YM}, title = {A Novel Coronavirus and a Broad Range of Viruses in Kenyan Cave Bats.}, journal = {Viruses}, volume = {14}, number = {12}, pages = {}, pmid = {36560824}, issn = {1999-4915}, mesh = {Animals ; *Alphacoronavirus ; *Astroviridae/genetics ; *Chiroptera ; *COVID-19 ; *Herpesviridae ; Kenya/epidemiology ; Phylogeny ; Retroviridae ; *RNA Viruses/genetics ; SARS-CoV-2 ; }, abstract = {BACKGROUND AND METHODS: To investigate virus diversity in hot zones of probable pathogen spillover, 54 oral-fecal swabs were processed from five bat species collected from three cave systems in Kenya, using metagenome sequencing.

RESULTS: Viruses belonging to the Astroviridae, Circoviridae, Coronaviridae, Dicistroviridae, Herpesviridae and Retroviridae were detected, with unclassified viruses. Retroviral sequences were prevalent; 74.1% of all samples were positive, with distinct correlations between virus, site and host bat species. Detected retroviruses comprised Myotis myotis, Myotis ricketti, Myotis daubentonii and Galidia endogenous retroviruses, murine leukemia virus-related virus and Rhinolophus ferrumequinum retrovirus (RFRV). A near-complete genome of a local RFRV strain with identical genome organization and 2.8% nucleotide divergence from the prototype isolate was characterized. Bat coronavirus sequences were detected with a prevalence of 24.1%, where analyses on the ORF1ab region revealed a novel alphacoronavirus lineage. Astrovirus sequences were detected in 25.9%of all samples, with considerable diversity. In 9.2% of the samples, other viruses including Actinidia yellowing virus 2, bat betaherpesvirus, Bole tick virus 4, Cyclovirus and Rhopalosiphum padi virus were identified.

CONCLUSIONS: Further monitoring of bats across Kenya is essential to facilitate early recognition of possibly emergent zoonotic viruses.}, } @article {pmid36560814, year = {2022}, author = {Xu, Y and Jiang, J and Wang, Z and Tian, J and Shi, W and Cao, C}, title = {Characterization of a Novel Pathogenic Reovirus in Grasshoppers.}, journal = {Viruses}, volume = {14}, number = {12}, pages = {}, pmid = {36560814}, issn = {1999-4915}, mesh = {Animals ; *Grasshoppers ; Phylogeny ; *Reoviridae ; *Orthoreovirus/genetics ; *Reoviridae Infections/veterinary ; }, abstract = {Grasshoppers can swarm in the millions and destroy crops over wide areas, posing a major economic threat to agriculture. A wide range of insect-related viruses has recently been reported in the metagenomics of grasshoppers. Here, we identified and isolated a novel reovirus from grasshoppers, named Acrididae reovirus (ARV). The complete genome of ARV was composed of nine dsRNA segments. Phylogenetic analysis revealed that ARV formed a monophyletic lineage with unclassified insect-associated reoviruses and was sufficiently distinct from known genera of Reoviridae. ARV could replicate in its host Locusta migratoria and result in host death. Lower-dose ARV infection affected ovary development and resulted in a significant reduction in fecundity. The identification and characterization of a novel pathogenic reovirus could potentially promote the development of new biological control agents.}, } @article {pmid36560807, year = {2022}, author = {Nyblade, C and Hensley, C and Parreño, V and Zhou, P and Frazier, M and Frazier, A and Ramesh, A and Lei, S and Degiuseppe, JI and Tan, M and Yuan, L}, title = {A New Gnotobiotic Pig Model of P[6] Human Rotavirus Infection and Disease for Preclinical Evaluation of Rotavirus Vaccines.}, journal = {Viruses}, volume = {14}, number = {12}, pages = {}, pmid = {36560807}, issn = {1999-4915}, support = {R56 AI148426/AI/NIAID NIH HHS/United States ; }, mesh = {Infant ; Child ; Infant, Newborn ; Humans ; Animals ; Swine ; Child, Preschool ; *Rotavirus Infections/prevention & control/veterinary ; *Rotavirus ; *Rotavirus Vaccines ; Feces ; Germ-Free Life ; }, abstract = {Human rotavirus (HRV) is a leading cause of gastroenteritis in children under 5 years of age. Licensed vaccines containing G1P[8] and G1-4P[8] strains are less efficacious against newly emerging P[6] strains, indicating an urgent need for better cross protective vaccines. Here, we report our development of a new gnotobiotic (Gn) pig model of P[6] HRV infection and disease as a tool for evaluating potential vaccine candidates. The Arg HRV (G4P[6]) strain was derived from a diarrheic human infant stool sample and determined to be free of other viruses by metagenomic sequencing. Neonatal Gn pigs were orally inoculated with the stool suspension containing 5.6 × 10[5] fluorescent focus units (FFU) of the virus. Small and large intestinal contents were collected at post inoculation day 2 or 3. The virus was passaged 6 times in neonatal Gn pigs to generate a large inoculum pool. Next, 33-34 day old Gn pigs were orally inoculated with 10[-2], 10[3], 10[4], and 10[5] FFU of Arg HRV to determine the optimal challenge dose. All pigs developed clinical signs of infection, regardless of the inoculum dose. The optimal challenge dose was determined to be 10[5] FFU. This new Gn pig model is ready to be used to assess the protective efficacy of candidate monovalent and multivalent vaccines against P[6] HRV.}, } @article {pmid36560644, year = {2022}, author = {Kuno, G}, title = {Contrasting the Practices of Virus Isolation and Characterization between the Early Period in History and Modern Times: The Case of Japanese Encephalitis Virus.}, journal = {Viruses}, volume = {14}, number = {12}, pages = {}, pmid = {36560644}, issn = {1999-4915}, mesh = {Animals ; Humans ; *Encephalitis Virus, Japanese/genetics ; *Encephalitis, Japanese ; Asia/epidemiology ; *Culicidae ; Vaccination ; }, abstract = {Japanese encephalitis is a serious disease transmitted by mosquitoes. With its recent spread beyond the traditional territory of endemicity in Asia, the magnitude of global threat has increased sharply. While much of the current research are largely focused on changing epidemiology, molecular genetics of virus, and vaccination, little attention has been paid to the early history of virus isolation and phenotypic characterization of this virus. In this review, using this piece of history as an example, I review the transition of the concept and practice of virus isolation and characterization from the early period of history to modern times. The spectacular development of molecular techniques in modern times has brought many changes in practices as well as enormous amount of new knowledge. However, many aspects of virus characterization, in particular, transmission mechanism and host relationship, remain unsolved. As molecular techniques are not perfect in all respects, beneficial accommodation of molecular and biologic data is critically important in many branches of research. Accordingly, I emphasize exercising caution in applying only these modern techniques, point out unrecognized communication problems, and stress that JE research history is a rich source of interesting works still valuable even today and waiting to be discovered.}, } @article {pmid36560627, year = {2022}, author = {Shvets, D and Sandomirsky, K and Porotikova, E and Vinogradova, S}, title = {Metagenomic Analysis of Ampelographic Collections of Dagestan Revealed the Presence of Two Novel Grapevine Viruses.}, journal = {Viruses}, volume = {14}, number = {12}, pages = {}, pmid = {36560627}, issn = {1999-4915}, mesh = {Dagestan ; Phylogeny ; Genome, Viral ; *Plant Viruses/genetics ; *Viroids/genetics ; Plant Diseases ; }, abstract = {In this study, we analyzed the virome of 73 grape samples from two Dagestan ampelographic collections in Russia using high-throughput sequencing of total RNAs. Fourteen viruses and four viroids were identified, with one to eleven of them detected in each plant. For the first time in Russia, we identified grapevine leafroll-associated virus 7 and grapevine Kizil Sapak virus. A total of 206 genomes of viruses and viroids were obtained, and their phylogenetic analysis was carried out. The de novo assembly and tblastx analysis allowed us to obtain contigs of a novel (+) ssRNA genome of a plant virus from the genus Umbravirus, which was tentatively named grapevine umbra-like virus (GULV), as well as contigs of a novel dsDNA pararetrovirus from the genus Caulimovirus, which was tentatively named grapevine pararetrovirus (GPRV). Complete genomes of these viruses were obtained and used for Sequence Demarcation Tool (SDT) analysis and phylogeny studies. GULV and GPRV were detected in 16 and 33 germplasm samples from the Dagestan collections, respectively.}, } @article {pmid36559689, year = {2022}, author = {Andrade, LRS and Felisardo, RJA and Cruz, IA and Bilal, M and Iqbal, HMN and Mulla, SI and Bharagava, RN and Souza, RL and Azevedo, LCB and Ferreira, LFR}, title = {Integrated Biorefinery and Life Cycle Assessment of Cassava Processing Residue-From Production to Sustainable Evaluation.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {24}, pages = {}, pmid = {36559689}, issn = {2223-7747}, abstract = {Commonly known as a subsistence culture, cassava came to be considered a commodity and key to adding value. However, this tuber's processing for starch and flour production is responsible for generating a large amount of waste that causes serious environmental problems. This biomass of varied biochemical composition has excellent potential for producing fuels (biogas, bioethanol, butanol, biohydrogen) and non-energetic products (succinic acid, glucose syrup, lactic acid) via biorefinery. However, there are environmental challenges, leading to uncertainties related to the sustainability of biorefineries. Thus, the provision of information generated in life cycle assessment (LCA) can help reduce bottlenecks found in the productive stages, making production more competitive. Within that, this review concentrates information on the production of value-added products, the environmental impact generated, and the sustainability of biorefineries.}, } @article {pmid36559640, year = {2022}, author = {Postiglione, A and Prigioniero, A and Zuzolo, D and Tartaglia, M and Scarano, P and Maisto, M and Ranauda, MA and Sciarrillo, R and Thijs, S and Vangronsveld, J and Guarino, C}, title = {Quercus ilex Phyllosphere Microbiome Environmental-Driven Structure and Composition Shifts in a Mediterranean Contex.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {24}, pages = {}, pmid = {36559640}, issn = {2223-7747}, abstract = {The intra- and interdomain phyllosphere microbiome features of Quercus ilex L. in a Mediterranean context is reported. We hypothesized that the main driver of the phyllosphere microbiome might be the season and that atmospheric pollutants might have a co-effect. Hence, we investigated the composition of epiphytic bacteria and fungi of leaves sampled in urban and natural areas (in Southern Italy) in summer and winter, using microscopy and metagenomic analysis. To assess possible co-effects on the composition of the phyllosphere microbiome, concentrations of particulate matter and polycyclic aromatic hydrocarbons (PAHs) were determined from sampled leaves. We found that environmental factors had a significative influence on the phyllosphere biodiversity, altering the taxa relative abundances. Ascomycota and Firmicutes were higher in summer and in urban areas, whereas a significant increase in Proteobacteria was observed in the winter season, with higher abundance in natural areas. Network analysis suggested that OTUs belonging to Acidobacteria, Cytophagia, unkn. Firmicutes(p), Actinobacteria are keystone of the Q. ilex phyllosphere microbiome. In addition, 83 genes coding for 5 enzymes involved in PAH degradation pathways were identified. Given that the phyllosphere microbiome can be considered an extension of the ecosystem services offered by trees, our results can be exploited in the framework of Next-Generation Biomonitoring.}, } @article {pmid36558837, year = {2022}, author = {Schulz, A and Sadeghi, B and Stoek, F and King, J and Fischer, K and Pohlmann, A and Eiden, M and Groschup, MH}, title = {Whole-Genome Sequencing of Six Neglected Arboviruses Circulating in Africa Using Sequence-Independent Single Primer Amplification (SISPA) and MinION Nanopore Technologies.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, pmid = {36558837}, issn = {2076-0817}, support = {GR 980/5-1//DFG (German Research Foundation)/ ; AHHFLI001/2019//BMZ (Federal Ministry for Economic Cooperation and Development of Germany)/ ; AA-OR12-370.43//Federal Foreign Office of Germany/ ; EBO-SURSY//WOAH (World Organisation for Animal Health)/ ; }, abstract = {On the African continent, a large number of arthropod-borne viruses (arboviruses) with zoonotic potential have been described, and yet little is known of most of these pathogens, including their actual distribution or genetic diversity. In this study, we evaluated as a proof-of-concept the effectiveness of the nonspecific sequencing technique sequence-independent single primer amplification (SISPA) on third-generation sequencing techniques (MinION sequencing, Oxford Nanopore Technologies, Oxford, UK) by comparing the sequencing results from six different samples of arboviruses known to be circulating in Africa (Crimean-Congo hemorrhagic fever virus (CCHFV), Rift Valley fever virus (RVFV), Dugbe virus (DUGV), Nairobi sheep disease virus (NSDV), Middleburg virus (MIDV) and Wesselsbron virus (WSLV)). All sequenced samples were derived either from previous field studies or animal infection trials. Using this approach, we were able to generate complete genomes for all six viruses without the need for virus-specific whole-genome PCRs. Higher Cq values in diagnostic RT-qPCRs and the origin of the samples (from cell culture or animal origin) along with their quality were found to be factors affecting the success of the sequencing run. The results of this study may stimulate the use of metagenomic sequencing approaches, contributing to a better understanding of the genetic diversity of neglected arboviruses.}, } @article {pmid36558785, year = {2022}, author = {Hu, H and Ling, Y and Wang, X and Wang, H and Zhu, N and Li, Y and Xu, H}, title = {Viral Metagenomics Reveals a Putative Novel HPV Type in Anogenital Wart Tissues.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, pmid = {36558785}, issn = {2076-0817}, abstract = {Viral metagenomics is widely employed to identify novel viruses in biological samples. Recently, although numerous novel human papillomavirus (HPV) types have been identified in clinical samples including anogenital warts (AGWs), many novel HPV sequences remain to be discovered. In this study, a putative novel HPV type designated as HPV-JDFY01 was discovered from library GW05 with 63 sequence reads by the viral metagenomic technique. Its complete genomic sequence was determined by PCR to bridge the gaps between contigs combining Sanger sequencing. The complete genome of HPV-JDFY01 is a 7186 bp encoding 7 open reading frames (ORFs) (E6, E7, E1, E2, E4, L2 and L1) and contains a 487 bp long control region (LCR) between L1 and E6. Sequence and phylogeny analysis indicated that HPV-JDFY01 shared the highest sequence identity of 74.2% with HPV-mSK_244 (MH777383) and well clustered into the genus Gammapapillomavirus. It has the classical genomic organization of Gammapapillomaviruses. Epidemiological investigation showed that one out of the 413 AGW tissue samples was positive for HPV-JDFY01. Further research with large size and different type of samples should be performed to elucidate the epidemiologic status of HPV-JDFY01.}, } @article {pmid36558391, year = {2022}, author = {Feng, C and Zhang, W and Zhang, T and He, Q and Kwok, LY and Tan, Y and Zhang, H}, title = {Heat-Killed Bifidobacterium bifidum B1628 May Alleviate Dextran Sulfate Sodium-Induced Colitis in Mice, and the Anti-Inflammatory Effect Is Associated with Gut Microbiota Modulation.}, journal = {Nutrients}, volume = {14}, number = {24}, pages = {}, pmid = {36558391}, issn = {2072-6643}, support = {32001711, 31972083//National Natural Science Foundation of China/ ; 2021ZD0014//Inner Mongolia Science and Technology Major Projects/ ; MOF and MARA//China Agriculture Research System/ ; }, mesh = {Animals ; Mice ; Anti-Inflammatory Agents/pharmacology ; *Bifidobacterium bifidum/metabolism ; *Colitis/therapy/drug therapy ; Colon/metabolism ; Cytokines/metabolism ; Dextran Sulfate/adverse effects ; Disease Models, Animal ; Dysbiosis/pathology ; *Gastrointestinal Microbiome ; Hot Temperature ; *Inflammatory Bowel Diseases/pathology ; Interleukin-13 ; Mice, Inbred C57BL ; Tumor Necrosis Factor-alpha ; }, abstract = {Inflammatory bowel disease (IBD) is a chronic inflammatory disease associated with gut dysbiosis. This study aimed to investigate the effects of heat-killed Bifidobacterium bifidum B1628 (HB1628) in dextran sulfate sodium (DSS)-induced colitis in mice. The following three mouse groups were included (n = eight per group): NC (normal control), DSS (colitis), and HB1628 (colitis and postbiotic). The mice in the DSS group showed significant weight loss and histological damage, developed bloody diarrhea, scored high in the disease activity index (DAI), and exhibited increases in pro-inflammatory cytokines (interleukin [IL]-1β, IL-6, and tumor necrosis factor [TNF]-α) and decreases in an anti-inflammatory cytokine (IL-13) in the serum. These changes were accompanied by gut microbiota modulation in colitis mice (decreases in Rikenellaceae and Eubacterium; increases in Peptostreptococcaceae, Bacteroides vulgatus, and Parasutterella excrementihominis). The HB1628 group had lower DAIs, histology scores, and serum levels of pro-inflammatory cytokines (IL-1β and TNF-α), but higher levels of an anti-inflammatory cytokine (IL-13), compared with the DSS group, suggesting a less severe inflammatory state after the HB1628 intervention. Additionally, HB1628 improved DSS-induced gut dysbiosis, which is evidenced by increases in intestinal beneficial bacteria, such as Lactobacillus, and decreases in known unfavorable taxa in IBD, e.g., Porphyromonadaceae, Subdoligranulum, Lachnospiraceae bacterium 3_1_46FAA, and Alistipes indistinctus. Functional metagenomics revealed three significantly enriched metabolic pathways in the HB1628 group (namely, the aerobic respiration I [cytochrome c] pathway and the superpathways of L-phenylalanine biosynthesis and L-tryptophan biosynthesis, respectively). In conclusion, our results showed that HB1628 effectively improved the inflammation state and tissue damage in DSS-induced colitis mice, and the symptom relief effect was accompanied by obvious gut microbiota remodulation.}, } @article {pmid36558359, year = {2022}, author = {Bustamante, JM and Dawson, T and Loeffler, C and Marfori, Z and Marchesi, JR and Mullish, BH and Thompson, CC and Crandall, KA and Rahnavard, A and Allegretti, JR and Cummings, BP}, title = {Impact of Fecal Microbiota Transplantation on Gut Bacterial Bile Acid Metabolism in Humans.}, journal = {Nutrients}, volume = {14}, number = {24}, pages = {}, pmid = {36558359}, issn = {2072-6643}, support = {MC_PC_12025/MRC_/Medical Research Council/United Kingdom ; R21 AT010956/AT/NCCIH NIH HHS/United States ; R21AT010956/NH/NIH HHS/United States ; }, mesh = {Humans ; *Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; Feces/microbiology ; Bacteria/genetics ; Bile Acids and Salts/analysis ; }, abstract = {Fecal microbiota transplantation (FMT) is a promising therapeutic modality for the treatment and prevention of metabolic disease. We previously conducted a double-blind, randomized, placebo-controlled pilot trial of FMT in obese metabolically healthy patients in which we found that FMT enhanced gut bacterial bile acid metabolism and delayed the development of impaired glucose tolerance relative to the placebo control group. Therefore, we conducted a secondary analysis of fecal samples collected from these patients to assess the potential gut microbial species contributing to the effect of FMT to improve metabolic health and increase gut bacterial bile acid metabolism. Fecal samples collected at baseline and after 4 weeks of FMT or placebo treatment underwent shotgun metagenomic analysis. Ultra-high-performance liquid chromatography-mass spectrometry was used to profile fecal bile acids. FMT-enriched bacteria that have been implicated in gut bile acid metabolism included Desulfovibrio fairfieldensis and Clostridium hylemonae. To identify candidate bacteria involved in gut microbial bile acid metabolism, we assessed correlations between bacterial species abundance and bile acid profile, with a focus on bile acid products of gut bacterial metabolism. Bacteroides ovatus and Phocaeicola dorei were positively correlated with unconjugated bile acids. Bifidobacterium adolescentis, Collinsella aerofaciens, and Faecalibacterium prausnitzii were positively correlated with secondary bile acids. Together, these data identify several candidate bacteria that may contribute to the metabolic benefits of FMT and gut bacterial bile acid metabolism that requires further functional validation.}, } @article {pmid36557719, year = {2022}, author = {Gazil, V and Bandiaky, ON and Renard, E and Idiri, K and Struillou, X and Soueidan, A}, title = {Current Data on Oral Peri-Implant and Periodontal Microbiota and Its Pathological Changes: A Systematic Review.}, journal = {Microorganisms}, volume = {10}, number = {12}, pages = {}, pmid = {36557719}, issn = {2076-2607}, abstract = {The 5- and 10-year implant success rates in dentistry are nearly 90%. Prevalence of peri-implant diseases is 10% for peri-implantitis and 50% for peri-implant mucositis. To better understand these inflammatory pathologies of infectious origin, it is important to know if the composition of the peri-implant microbiota is comparable with the periodontal microbiota in healthy and pathological conditions. New generation sequencing (NGS) is a recent metagenomic method that analyzes the overall microorganisms present in an ecological niche by exploiting their genome. These methods are of two types: 16S rRNA sequencing and the shotgun technique. For several years, they have been used to explore the oral, periodontal, and, more specifically, peri-implant microbiota. The aim of this systematic review is to analyze the recent results of these new explorations by comparing the periodontal and peri-implant microbiota in patients with healthy and diseased sites and to explore the microbiological characteristics of peri-implantitis. A better knowledge of the composition of the peri-implant microbiota would enable us to optimize our therapeutic strategies. An electronic systematic search was performed using the medical databases PubMed/Medline, Cochrane Library, and ScienceDirect, and Periodontology 2000. The selected articles were published between January 2015 and March 2021. Inclusion criteria included clinical studies comparing healthy and pathological periodontal and peri-implant microbiota exclusively using 16S rRNA sequencing or shotgun sequencing, with enrolled populations free of systemic pathology, and studies without substantial bias. Eight articles were selected and reviewed. All of them used 16S rRNA sequencing exclusively. The assessment of these articles demonstrates the specific character of the peri-implant microbiota in comparison with the periodontal microbiota in healthy and pathological conditions. Indeed, peri-implant diseases are defined by dysbiotic bacterial communities that vary from one individual to another, including known periodontopathogens such as Porphyromonas gingivalis (P.g.) and genera less mentioned in the periodontal disease pattern such as Filifactor alocis. Examination of peri-implant microbiota with 16S rRNA sequencing reveals differences between the periodontal and peri-implant microbiota under healthy and pathological conditions in terms of diversity and composition. The pattern of dysbiotic drift is preserved in periodontal and peri-implant diseases, but when comparing the different types of pathological sites, the peri-implant microbiota has a specificity in the presence of bacteria proper to peri-implantitis and different relative proportions of the microorganisms present.}, } @article {pmid36557703, year = {2022}, author = {Tun, KM and Hsu, M and Batra, K and Lo, CH and Laeeq, T and Vongsavath, T and Mohammed, S and Hong, AS}, title = {Efficacy and Safety of Fecal Microbiota Transplantation in Treatment of Clostridioides difficile Infection among Pediatric Patients: A Systematic Review and Meta-Analysis.}, journal = {Microorganisms}, volume = {10}, number = {12}, pages = {}, pmid = {36557703}, issn = {2076-2607}, abstract = {Background and Aims: Cases of Clostridioides difficile infection have been rising among the pediatric and adolescent population. Fecal microbiota transplantation (FMT) has emerged as an alternative therapy for recurrent C. difficile infection. We aim to perform the first systematic review and meta-analysis investigating the safety and efficacy of fecal microbiota transplantation for C. difficile infection in children and adolescents. Methods: A literature search was performed using variations of the keywords “pediatrics”, “C. difficile infection”, and “fecal microbiota transplantation” in PubMed, EMBASE, CINAHL, Cochrane, and Google Scholar from inception to 30 June 2022. The resulting 575 articles were independently screened by three authors. Fourteen studies that satisfied the eligibility criteria were included in the meta-analysis. Results: The pooled success rate of FMT in the overall cohort was 86% (95% confidence interval: 77−95%; p < 0.001; I2 = 70%). There were 38 serious adverse events in 36 patients with a pooled rate of 2.0% (95% confidence interval: 0.0−3.0%; p = 0.1; I2 = 0.0%) and 47 adverse events in 45 patients with a pooled rate of 15% (95% confidence interval: 5.0−25.0%; p = 0.02; I2 = 54.0%). There was no death associated with FMT. Conclusions: FMT was concluded to be an effective and safe therapy in pediatric and adolescent patients with C. difficile infection. Underlying comorbidities may impede the efficacy. A rigorous screening process of the donors is recommended prior to embarking on FMT. There is no universal and cost-effective way to monitor the long-term outcomes of FMT. While promising, metagenomic sequencing may not be available in settings with limited resources. Robust data from randomized clinical trials is warranted.}, } @article {pmid36557680, year = {2022}, author = {Ahmed, S and Singh, S and Singh, V and Roberts, KD and Zaidi, A and Rodriguez-Palacios, A}, title = {The Weissella Genus: Clinically Treatable Bacteria with Antimicrobial/Probiotic Effects on Inflammation and Cancer.}, journal = {Microorganisms}, volume = {10}, number = {12}, pages = {}, pmid = {36557680}, issn = {2076-2607}, support = {R21 DK118373/DK/NIDDK NIH HHS/United States ; }, abstract = {Weissella is a genus earlier considered a member of the family Leuconostocaceae, which was reclassified into the family Lactobacillaceae in 1993. Recently, there have been studies emphasizing the probiotic and anti-inflammatory potential of various species of Weissella, of which W. confusa and W. cibaria are the most representative. Other species within this genus include: W. paramesenteroides, W. viridescens, W. halotolerans, W. minor, W. kandleri, W. soli, W. ghanensis, W. hellenica, W. thailandensis, W. fabalis, W. cryptocerci, W. koreensis, W. beninensis, W. fabaria, W. oryzae, W. ceti, W. uvarum, W. bombi, W. sagaensis, W. kimchi, W. muntiaci, W. jogaejeotgali, W. coleopterorum, W. hanii, W. salipiscis, and W. diestrammenae. Weissella confusa, W. paramesenteroides, W. koreensis, and W. cibaria are among the few species that have been isolated from human samples, although the identification of these and other species is possible using metagenomics, as we have shown for inflammatory bowel disease (IBD) and healthy controls. We were able to isolate Weissella in gut-associated bacteria (post 24 h food deprivation and laxatives). Other sources of isolation include fermented food, soil, and skin/gut/saliva of insects/animals. With the potential for hospital and industrial applications, there is a concern about possible infections. Herein, we present the current applications of Weissella on its antimicrobial and anti-inflammatory mechanistic effects, the predisposing factors (e.g., vancomycin) for pathogenicity in humans, and the antimicrobials used in patients. To address the medical concerns, we examined 28 case reports focused on W. confusa and found that 78.5% of infections were bacteremia (of which 7 were fatal; 1 for lack of treatment), 8 were associated with underlying malignancies, and 8 with gastrointestinal procedures/diseases of which 2 were Crohn’s disease patients. In cases of a successful resolution, commonly administered antibiotics included: cephalosporin, ampicillin, piperacillin-tazobactam, and daptomycin. Despite reports of Weissella-related infections, the evolving mechanistic findings suggest that Weissella are clinically treatable bacteria with emerging antimicrobial and probiotic benefits ranging from oral health, skin care, obesity, and inflammatory diseases to cancer.}, } @article {pmid36557669, year = {2022}, author = {Chen, Z and Meng, J}, title = {Critical Assessment of Short-Read Assemblers for the Metagenomic Identification of Foodborne and Waterborne Pathogens Using Simulated Bacterial Communities.}, journal = {Microorganisms}, volume = {10}, number = {12}, pages = {}, pmid = {36557669}, issn = {2076-2607}, support = {U01 FD001418/FD/FDA HHS/United States ; }, abstract = {Metagenomics offers the highest level of strain discrimination of bacterial pathogens from complex food and water microbiota. With the rapid evolvement of assembly algorithms, defining an optimal assembler based on the performance in the metagenomic identification of foodborne and waterborne pathogens is warranted. We aimed to benchmark short-read assemblers for the metagenomic identification of foodborne and waterborne pathogens using simulated bacterial communities. Bacterial communities on fresh spinach and in surface water were simulated by generating paired-end short reads of Illumina HiSeq, MiSeq, and NovaSeq at different sequencing depths. Multidrug-resistant Salmonella Indiana SI43 and Pseudomonas aeruginosa PAO1 were included in the simulated communities on fresh spinach and in surface water, respectively. ABySS, IDBA-UD, MaSuRCA, MEGAHIT, metaSPAdes, and Ray Meta were benchmarked in terms of assembly quality, identifications of plasmids, virulence genes, Salmonella pathogenicity island, antimicrobial resistance genes, chromosomal point mutations, serotyping, multilocus sequence typing, and whole-genome phylogeny. Overall, MEGHIT, metaSPAdes, and Ray Meta were more effective for metagenomic identification. We did not obtain an optimal assembler when using the extracted reads classified as Salmonella or P. aeruginosa for downstream genomic analyses, but the extracted reads showed consistent phylogenetic topology with the reference genome when they were aligned with Salmonella or P. aeruginosa strains. In most cases, HiSeq, MiSeq, and NovaSeq were comparable at the same sequencing depth, while higher sequencing depths generally led to more accurate results. As assembly algorithms advance and mature, the evaluation of assemblers should be a continuous process.}, } @article {pmid36557656, year = {2022}, author = {Liaw, RB and Chen, JC and Cheng, MP}, title = {Molecular Cloning and Characterization of a New Family VI Esterase from an Activated Sludge Metagenome.}, journal = {Microorganisms}, volume = {10}, number = {12}, pages = {}, pmid = {36557656}, issn = {2076-2607}, support = {99AS-8.1.3-LI-L1, 111AS-2.1.1-LI-L7//Livestock Research Institute, Council of Agriculture, Executive Yuan/ ; }, abstract = {A new esterase gene, est6, was discovered in an activated sludge metagenomic library. The 729-bp gene encodes a 242-amino acid protein (designated Est6) with a molecular mass of 26.1 kDa. Est6 shared only a moderate identity to a putative hydrolase with the highest BLASTP analysis score. Most of the closely related proteins are uncharacterized and are predicted from genome sequencing data of microorganisms or metagenomic DNA sequences. The phylogenetic analysis of Est6 showed that the protein was assigned to family VI esterases/lipases. The catalytic triad of Est6 was predicted to be Ser135, Asp188, and His219, with Ser135 in a typically conserved pentapeptide (GFSQG) of family VI members, which was further confirmed by site-directed mutagenesis. The est6 gene was overexpressed successfully in its soluble form in Escherichia coli and then purified to its tag-free form and homogeneity by affinity chromatography. The purified Est6 in pH 8.0 buffer was active as a monomer. The optimal conditions for Est6 activity were at a temperature of 45 °C and pH of 8.0 when using p-nitrophenyl acetate as a substrate. The enzyme was stable over wide temperature and pH ranges, and it exhibited activity in the presence of organic solvents, metal cations, or detergents. Furthermore, the enzyme showed significant regioselectivity in the spectrophotometric analysis. In conclusion, Est6 might have the potential for applications in biotechnological processes.}, } @article {pmid36557621, year = {2022}, author = {Gryaznova, M and Lebedeva, O and Kozarenko, O and Smirnova, Y and Burakova, I and Syromyatnikov, M and Maslov, A and Popov, V}, title = {Lower Genital Tract Microbiome in Early Pregnancy in the Eastern European Population.}, journal = {Microorganisms}, volume = {10}, number = {12}, pages = {}, pmid = {36557621}, issn = {2076-2607}, support = {22-24-00802//Russian Science Foundation/ ; }, abstract = {BACKGROUND: It is known that the features of the cervicovaginal microbiome can depend on ethnicity, which might be caused by genetic factors, as well as differences in diet and lifestyle. There is no research on the cervicovaginal microbiome of Eastern European women during early pregnancy.

METHODS: We evaluated the cervical and cervicovaginal microbiome of women with first-trimester pregnancy (n = 22), further delivered at term, using the 16S rRNA sequencing method.

RESULTS: The predominant bacterial species in both groups was Lactobacillus iners, followed by Prevotella copri, Ileibacterium valens, Gardnerella vaginalis and Muribaculum intestinale in the cervical samples, and Gardnerella vaginalis, Prevotella copri, Bifidobacterium longum, Ileibacterium valens and Muribaculum intestinale in the cervicovaginal samples. The cervical microbiome had higher alpha diversity; a higher abundance of Muribaculum intestinale, Aquabacterium parvum and Methyloversatilis universalis; and a lower abundance of Psychrobacillus psychrodurans.

CONCLUSIONS: The Lactobacillus iners-dominated microbiome (CST III) was the predominant type of cervical and cervicovaginal microbiome in early pregnancy in the majority of the women. The presence of soil and animal bacteria in the cervicovaginal microbiome can be explained by the rural origin of patients.}, } @article {pmid36557618, year = {2022}, author = {Mathlouthi, NEH and Kriaa, A and Keskes, LA and Rhimi, M and Gdoura, R}, title = {Virulence Factors in Colorectal Cancer Metagenomes and Association of Microbial Siderophores with Advanced Stages.}, journal = {Microorganisms}, volume = {10}, number = {12}, pages = {}, pmid = {36557618}, issn = {2076-2607}, support = {952583//Twinning European project MICAfrica/ ; }, abstract = {Colorectal cancer (CRC) is a growing public health challenge, featuring a multifactorial etiology and complex host-environment interactions. Recently, increasing evidence has pointed to the role of the gut microbiota in CRC development and progression. To explore the role of gut microbes in CRC, we retrieved metagenomic data from 156 stools from the European Nucleotide Archive database and mapped them against the VFDB database for virulence factors (VFs). GO annotations of VFs and KEGG pathways were then performed to predict the microbial functions and define functional pathways enriched in the tumor-associated microbiota. Interestingly, 306 VFs were detected in the metagenomic data. We revealed the enrichment of adenomas with VFs involved in cell adhesion, whereas in the early stages of CRC they were enriched in both adhesins and isochorismatase. Advanced stages of CRC were enriched with microbial siderophores, especially enterobactin, which was significantly associated with isochorismate synthase. We highlighted higher abundances of porins and transporters involved in antibiotic resistance and the development of biofilm in advanced stages of CRC. Most VFs detected in CRC, particularly in advanced stages, were shown to be included in siderophore biosynthesis pathways. This enrichment of predicted VFs supports the key role of the gut microbiota in the disease.}, } @article {pmid36557612, year = {2022}, author = {Smutin, D and Lebedev, E and Selitskiy, M and Panyushev, N and Adonin, L}, title = {Micro"bee"ota: Honey Bee Normal Microbiota as a Part of Superorganism.}, journal = {Microorganisms}, volume = {10}, number = {12}, pages = {}, pmid = {36557612}, issn = {2076-2607}, abstract = {Honey bees are model organisms for microbiota research. Gut microbiomes are very interesting for surveys due to their simple structure and relationship with hive production. Long-term studies reveal the gut microbiota patterns of various hive members, as well as the functions, sources, and interactions of the majority of its bacteria. But the fungal non-pathogenic part of gut microbiota is almost unexplored, likewise some other related microbiota. Honey bees, as superorganisms, interact with their own microorganisms, the microbial communities of food stores, hive surfaces, and other environments. Understanding microbiota diversity, its transition ways, and hive niche colonization control are necessary for understanding any separate microbiota niche because of their interplay. The long coevolution of bees with the microorganisms populating these niches makes these systems co-dependent, integrated, and stable. Interaction with the environment, hive, and other bees determines caste lifestyle as well as individual microbiota. In this article, we bring together studies on the microbiota of the western honey bee. We show a possible relationship between caste determination and microbiota composition. And what is primary: caste differentiation or microbiota composition?}, } @article {pmid36557590, year = {2022}, author = {Halary, S and Duperron, S and Demay, J and Duval, C and Hamlaoui, S and Piquet, B and Reinhardt, A and Bernard, C and Marie, B}, title = {Metagenome-Based Exploration of Bacterial Communities Associated with Cyanobacteria Strains Isolated from Thermal Muds.}, journal = {Microorganisms}, volume = {10}, number = {12}, pages = {}, pmid = {36557590}, issn = {2076-2607}, support = {2017/0633//ANRT/ ; }, abstract = {Cyanobacteria constitute a pioneer colonizer of specific environments for whom settlement in new biotopes precedes the establishment of composite microbial consortia. Some heterotrophic bacteria constitute cyanobacterial partners that are considered as their cyanosphere, being potentially involved in mutualistic relationships through the exchange and recycling of key nutrients and the sharing of common goods. Several non-axenic cyanobacterial strains have been recently isolated, along with their associated cyanospheres, from the thermal mud of Balaruc-les-Bains (France) and the biofilms of the retention basin where they develop. The community structure and relationships among the members of the isolated cyanobacterial strains were characterized using a metagenomic approach combined with taxonomic and microscopic descriptions of the microbial consortia. The results provided insights into the potential role and metabolic capabilities of the microorganisms of thermal mud-associated cyanobacterial biofilms. Thus, the physical proximity, host-specificity, and genetic potential functions advocate for their complementarity between cyanobacteria and their associated microbiota. Besides these findings, our results also highlighted the great influence of the reference protein database chosen for performing functional annotation of the metagenomes from organisms of the cyanosphere and the difficulty of selecting one unique database that appropriately covers both autotroph and heterotroph metabolic specificities.}, } @article {pmid36557581, year = {2022}, author = {Mandal, S and Mondal, C and Mukherjee, T and Saha, S and Kundu, A and Ghosh, S and Lyndem, LM}, title = {Hymenolepis diminuta Reduce Lactic Acid Bacterial Load and Induce Dysbiosis in the Early Infection of the Probiotic Colonization of Swiss Albino Rat.}, journal = {Microorganisms}, volume = {10}, number = {12}, pages = {}, pmid = {36557581}, issn = {2076-2607}, support = {739/CSIR-UGC NET JUNE 2018//University Grants Commission/ ; }, abstract = {Tapeworm infection continues to be an important cause of morbidity worldwide. Recent metagenomics studies have established a link between gut microbiota and parasite infection. The identification of gut probiotics is of foremost importance to explore its relationship and function with the parasite in the host. In this study, the gut content of hosts infected with tapeworm Hymenolepis diminuta and non-infected host gut were disected out to determine their Lactic acid bacterial (LAB) population in MRS agar and microbial community was analysed by metagenomics. The bacterial count was calculated on a bacterial counting chamber and their morphology was determined microscopically and biochemically. Further, to determine the safety profile antibiotic resistance test, antimicrobial, hemolytic activity, and adhesion capability were calculated. We found six dominant probiotic strains and a decrease in LAB load from 1.7-2.3 × 10[7] CFU/mL in the uninfected group to a range of 8.4 × 10[5] CFU/mL to 3.2 × 10[5] CFU/mL in the infected groups with respect to an increase in the parasite number from 10-18. In addition, we found a depletion in the probiotic relative abundance of Lactobacillus and an enrichment in potentially pathogenic Proteobacteria, Fusobacteria, and Streptococcus. Phylogenetic analysis of the six probiotics revealed a close similarity with different strains of L. brevis, L. johnsonii, L. taiwansis, L. reuteri, L. plantarum, and L. pentosus. Thus, this study suggests that the parasite inhibits probiotic colonization in the gut during its early establishment of infection inside the host.}, } @article {pmid36557580, year = {2022}, author = {Sandybayev, N and Beloussov, V and Strochkov, V and Solomadin, M and Granica, J and Yegorov, S}, title = {Next Generation Sequencing Approaches to Characterize the Respiratory Tract Virome.}, journal = {Microorganisms}, volume = {10}, number = {12}, pages = {}, pmid = {36557580}, issn = {2076-2607}, support = {grant No. AP09259192//The Science Committee of the Ministry of Education and Science of the Republic of Kazakhstan/ ; }, abstract = {The COVID-19 pandemic and heightened perception of the risk of emerging viral infections have boosted the efforts to better understand the virome or complete repertoire of viruses in health and disease, with a focus on infectious respiratory diseases. Next-generation sequencing (NGS) is widely used to study microorganisms, allowing the elucidation of bacteria and viruses inhabiting different body systems and identifying new pathogens. However, NGS studies suffer from a lack of standardization, in particular, due to various methodological approaches and no single format for processing the results. Here, we review the main methodological approaches and key stages for studies of the human virome, with an emphasis on virome changes during acute respiratory viral infection, with applications for clinical diagnostics and epidemiologic analyses.}, } @article {pmid36556458, year = {2022}, author = {Singh, N and Singh, V and Rai, SN and Vamanu, E and Singh, MP}, title = {Metagenomic Analysis of Garden Soil-Derived Microbial Consortia and Unveiling Their Metabolic Potential in Mitigating Toxic Hexavalent Chromium.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {36556458}, issn = {2075-1729}, abstract = {Soil microbial communities connect to the functional environment and play an important role in the biogeochemical cycle and waste degradation. The current study evaluated the distribution of the core microbial population of garden soil in the Varanasi region of Uttar Pradesh, India and their metabolic potential for mitigating toxic hexavalent chromium from wastewater. Metagenomes contain 0.2 million reads and 56.5% GC content. The metagenomic analysis provided insight into the relative abundance of soil microbial communities and revealed the domination of around 200 bacterial species belonging to different phyla and four archaeal phyla. The top 10 abundant genera in garden soil were Gemmata, Planctomyces, Steroidobacter, Pirellula, Pedomicrobium, Rhodoplanes, Nitrospira Mycobacterium, Pseudonocardia, and Acinetobacter. In this study, Gemmata was dominating bacterial genera. Euryarchaeota, Parvarchaeota, and Crenarchaeota archaeal species were present with low abundance in soil samples. X-ray photoelectric spectroscopy (XPS) analysis indicates the presence of carbon, nitrogen-oxygen, calcium, phosphorous, and silica in the soil. Soil-derived bacterial consortia showed high hexavalent chromium [Cr (VI)] removal efficiency (99.37%). The bacterial consortia isolated from garden soil had an important role in the hexavalent chromium bioremediation, and thus, this study could be beneficial for the design of a heavy-metal treatment system.}, } @article {pmid36556446, year = {2022}, author = {Li, P and Chen, T and An, M and Zhang, Y and Li, Y and Li, Y and Wang, J}, title = {Effects of Different Types of Human Disturbance on Total and Nitrogen-Transforming Bacteria in Haihe River.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {36556446}, issn = {2075-1729}, support = {TKS20210214 and TKS20220507//Fundamental Research Funds for the Central Public Welfare Research Institutes/ ; 52070143 and 41506182//National Natural Science Foundation of China/ ; 19JCZDJC40300//Natural Science Foundation of Tianjin City/ ; }, abstract = {Haihe River is the largest water system in North China and is injected into the Bohai Sea in Tianjin City. In this study, different types of human disturbance (urban sewage, industrial pollution, ship disturbance) were selected from the upper reaches of Haihe river Tianjin section down to the estuary that connected with Bohai Sea for evaluation. By metagenomic sequencing, the effects of different types of disturbances on bacteria communities in Haihe sediments were studied, with a special focus on the function of nitrogen-cycling bacteria that were further analyzed through KEGG comparison. By analyzing the physical and chemical characteristics of sediments, results showed that human disturbance caused a large amount of nitrogen input into Haihe River, and different types of human disturbance led to distinct spatial heterogeneity in different sections of Haihe River. The bacteria community was dominated by Proteobacteria, followed by Chloroflexi, Bacteroidetes, Actinobacteria and Acidobacteria. The relative abundance of each phylum varied at different sites as a response to different types of human disturbances. In nitrogen cycling, microorganisms including nitrogen fixation and removal were detected at each site, which indicated the active potential for nitrogen transformation in Haihe River. In addition, a large number of metabolic pathways relating to human diseases were also revealed in urban and pollution sites by function potential, which provided an important basis for the indicative role of urban river ecosystem for public health security. In summary, by evaluating both the ecological role and function potential of bacteria in Haihe River under different types of human disturbance, the knowledge of microorganisms for healthy and disturbed river ecosystems has been broadened, which is also informative for further river management and bioremediation.}, } @article {pmid36556413, year = {2022}, author = {Bassi, C and Guerriero, P and Pierantoni, M and Callegari, E and Sabbioni, S}, title = {Novel Virus Identification through Metagenomics: A Systematic Review.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {36556413}, issn = {2075-1729}, support = {Fondo di Ateneo per la Ricerca (FAR)//University of Ferrara/ ; }, abstract = {Metagenomic Next Generation Sequencing (mNGS) allows the evaluation of complex microbial communities, avoiding isolation and cultivation of each microbial species, and does not require prior knowledge of the microbial sequences present in the sample. Applications of mNGS include virome characterization, new virus discovery and full-length viral genome reconstruction, either from virus preparations enriched in culture or directly from clinical and environmental specimens. Here, we systematically reviewed studies that describe novel virus identification through mNGS from samples of different origin (plant, animal and environment). Without imposing time limits to the search, 379 publications were identified that met the search parameters. Sample types, geographical origin, enrichment and nucleic acid extraction methods, sequencing platforms, bioinformatic analytical steps and identified viral families were described. The review highlights mNGS as a feasible method for novel virus discovery from samples of different origins, describes which kind of heterogeneous experimental and analytical protocols are currently used and provides useful information such as the different commercial kits used for the purification of nucleic acids and bioinformatics analytical pipelines.}, } @article {pmid36556336, year = {2022}, author = {D'aes, J and Fraiture, MA and Bogaerts, B and De Keersmaecker, SCJ and Roosens, NHCJ and Vanneste, K}, title = {Metagenomic Characterization of Multiple Genetically Modified Bacillus Contaminations in Commercial Microbial Fermentation Products.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {36556336}, issn = {2075-1729}, support = {773830//European Union/ ; }, abstract = {Genetically modified microorganisms (GMM) are frequently employed for manufacturing microbial fermentation products such as food enzymes or vitamins. Although the fermentation product is required to be pure, GMM contaminations have repeatedly been reported in numerous commercial microbial fermentation produce types, leading to several rapid alerts at the European level. The aim of this study was to investigate the added value of shotgun metagenomic high-throughput sequencing to confirm and extend the results of classical analysis methods for the genomic characterization of unauthorized GMM. By combining short- and long-read metagenomic sequencing, two transgenic constructs were characterized, with insertions of alpha-amylase genes originating from B. amyloliquefaciens and B. licheniformis, respectively, and a transgenic construct with a protease gene insertion originating from B. velezensis, which were all present in all four investigated samples. Additionally, the samples were contaminated with up to three unculturable Bacillus strains, carrying genetic modifications that may hamper their ability to sporulate. Moreover, several samples contained viable Bacillus strains. Altogether these contaminations constitute a considerable load of antimicrobial resistance genes, that may represent a potential public health risk. In conclusion, our study showcases the added value of metagenomics to investigate the quality and safety of complex commercial microbial fermentation products.}, } @article {pmid36555624, year = {2022}, author = {Levi Mortera, S and Marzano, V and Vernocchi, P and Matteoli, MC and Guarrasi, V and Gardini, S and Del Chierico, F and Rapini, N and Deodati, A and Fierabracci, A and Cianfarani, S and Putignani, L}, title = {Functional and Taxonomic Traits of the Gut Microbiota in Type 1 Diabetes Children at the Onset: A Metaproteomic Study.}, journal = {International journal of molecular sciences}, volume = {23}, number = {24}, pages = {}, pmid = {36555624}, issn = {1422-0067}, mesh = {Adolescent ; Humans ; Child ; Aged ; *Diabetes Mellitus, Type 1 ; *Gastrointestinal Microbiome/physiology ; RNA, Ribosomal, 16S/genetics ; *Insulin-Secreting Cells ; Insulin, Regular, Human ; Insulin ; }, abstract = {Type 1 diabetes (T1D) is a chronic autoimmune metabolic disorder with onset in pediatric/adolescent age, characterized by insufficient insulin production, due to a progressive destruction of pancreatic β-cells. Evidence on the correlation between the human gut microbiota (GM) composition and T1D insurgence has been recently reported. In particular, 16S rRNA-based metagenomics has been intensively employed in the last decade in a number of investigations focused on GM representation in relation to a pre-disease state or to a response to clinical treatments. On the other hand, few works have been published using alternative functional omics, which is more suitable to provide a different interpretation of such a relationship. In this work, we pursued a comprehensive metaproteomic investigation on T1D children compared with a group of siblings (SIBL) and a reference control group (CTRL) composed of aged matched healthy subjects, with the aim of finding features in the T1D patients' GM to be related with the onset of the disease. Modulated metaproteins were found either by comparing T1D with CTRL and SIBL or by stratifying T1D by insulin need (IN), as a proxy of β-cells damage, showing some functional and taxonomic traits of the GM, possibly related to the disease onset at different stages of severity.}, } @article {pmid36555615, year = {2022}, author = {Šerá, J and Huynh, F and Ly, F and Vinter, Š and Kadlečková, M and Krátká, V and Máčalová, D and Koutný, M and Wallis, C}, title = {Biodegradable Polyesters and Low Molecular Weight Polyethylene in Soil: Interrelations of Material Properties, Soil Organic Matter Substances, and Microbial Community.}, journal = {International journal of molecular sciences}, volume = {23}, number = {24}, pages = {}, pmid = {36555615}, issn = {1422-0067}, support = {IGA/FT/2021/009//Tomas Bata University in Zlín/ ; }, mesh = {*Polyesters ; *Soil ; Plastics ; Polyethylene ; Molecular Weight ; Polymers ; Bacteria/genetics ; Microbial Consortia ; Soil Microbiology ; }, abstract = {Conventional and also biodegradable polymer microplastics have started to be broadly present in the environment, if they end up in soil, they may influence both abiotic and biotic soil properties. In this study, the interactions of polyethylene wax together with three biodegradable polyesters PLA, PHB and PBAT with a soil matrix were investigated over a 1-year incubation period. Soil organic matter content was measured using UV-VIS, the microbial biomass amount was measured using qPCR, the mineralisation of polymers was measured using UGA 3000, the surface of polymers was observed with SEM, live/dead microorganisms were determined by fluorescent microscopy and microbial consortia diversity was analyzed using NGS. The amount of humic substances was generally higher in incubations with slowly degrading polyesters, but the effect was temporary. The microbial biomass grew during the incubations; the addition of PHB enhanced fungal biomass whereas PE wax enhanced bacterial biomass. Fungal microbial consortia diversity was altered in incubations with PHB and PBAT. Interestingly, these two polyesters were also covered in biofilm, probably fungal. No such trend was observed in a metagenomic analysis of bacteria, although, bacterial biofilm was probably formed on the PE520 surface. Different methods confirmed the effect of certain polymers on the soil environment.}, } @article {pmid36555488, year = {2022}, author = {Filardo, S and Di Pietro, M and De Angelis, M and Brandolino, G and Porpora, MG and Sessa, R}, title = {In-Silico Functional Metabolic Pathways Associated to Chlamydia trachomatis Genital Infection.}, journal = {International journal of molecular sciences}, volume = {23}, number = {24}, pages = {}, pmid = {36555488}, issn = {1422-0067}, support = {C26A15PC5N//University of Rome "Sapienza"/ ; }, mesh = {Female ; Humans ; Chlamydia trachomatis ; Vagina/metabolism ; *Chlamydia Infections/epidemiology ; *Microbiota ; Metabolic Networks and Pathways ; }, abstract = {The advent of high-throughput technologies, such as 16s rDNA sequencing, has significantly contributed to expanding our knowledge of the microbiota composition of the genital tract during infections such as Chlamydia trachomatis. The growing body of metagenomic data can be further exploited to provide a functional characterization of microbial communities via several powerful computational approaches. Therefore, in this study, we investigated the predicted metabolic pathways of the cervicovaginal microbiota associated with C. trachomatis genital infection in relation to the different Community State Types (CSTs), via PICRUSt2 analysis. Our results showed a more rich and diverse mix of predicted metabolic pathways in women with a CST-IV microbiota as compared to all the other CSTs, independently from infection status. C. trachomatis genital infection further modified the metabolic profiles in women with a CST-IV microbiota and was characterized by increased prevalence of the pathways for the biosynthesis of precursor metabolites and energy, biogenic amino-acids, nucleotides, and tetrahydrofolate. Overall, predicted metabolic pathways might represent the starting point for more precisely designed future metabolomic studies, aiming to investigate the actual metabolic pathways characterizing C. trachomatis genital infection in the cervicovaginal microenvironment.}, } @article {pmid36554758, year = {2022}, author = {Song, D and Huo, T and Zhang, Z and Cheng, L and Wang, L and Ming, K and Liu, H and Li, M and Du, X}, title = {Metagenomic Analysis Reveals the Response of Microbial Communities and Their Functions in Lake Sediment to Environmental Factors.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {24}, pages = {}, pmid = {36554758}, issn = {1660-4601}, mesh = {Humans ; *Lakes/chemistry ; Chlorophyll A ; Bacteria/genetics/metabolism ; *Microbiota ; China ; Geologic Sediments/chemistry ; }, abstract = {Jingpo Lake is the largest mountain barrier lake in China and plays a key role in breeding, power generation, and providing a source of drinking water. Microbes are important participants in the formation of lake resources and energy cycles. However, the ecological protection of Jingpo Lake has faced serious challenges in recent years. In this study, we investigate the responses of the microbial community's composition of sediments at five locations to an environmental gradient representing water quality and water-depth changes using a metagenomic sequence. We found that the diversity and composition of the microbiota sediments were altered spatially and correlated with the physicochemical factors of water samples. In the microbial community, relatively lower Chao1, alternating conditional expectations, and Shannon and Simpson indices were found at the shallowest location with higher total phosphorus and chlorophyll a. Furthermore, the Kyoto Encyclopedia of Genes and Genomes analysis revealed that the metabolism function was the most abundant functional classification in Jingpo Lake. The levels of total phosphorus, chlorophyll a and pH were positively correlated with the abundance of Flavobacterium and the bacterial functions of the carbohydrate metabolism and amino acid metabolism. In conclusion, our results reveal the physical and chemical characteristics, as well as the microbial community characteristics, of Jingpo Lake, which provides new insights for studying the relationship between environmental factors and the bacterial community distribution of freshwater ecosystems, in addition to also providing a theoretical basis for the environmental monitoring and protection of the lake.}, } @article {pmid36554499, year = {2022}, author = {Dania, MI and Faraji, B and Wachira, J}, title = {Micronutrient Biosynthesis Potential of Spontaneous Grain Fermentation Microbiomes.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {24}, pages = {}, pmid = {36554499}, issn = {1660-4601}, support = {U54 MD013376/MD/NIMHD NIH HHS/United States ; UL1 GM118973/GM/NIGMS NIH HHS/United States ; 5UL1GM118973/GM/NIGMS NIH HHS/United States ; 5U54MD013376/NH/NIH HHS/United States ; }, mesh = {Humans ; Fermentation ; Micronutrients/metabolism ; Phylogeny ; Bacteria ; *Microbiota ; Edible Grain ; *Trace Elements/metabolism ; }, abstract = {Fermented foods play an important role in the human diet and particularly so in under-resourced environments where cold preservation is not attainable due to irregular supply of electricity. Fermented foods are reported to support gut health by contributing probiotics. The purpose of this study was to investigate the microbial diversity and metabolic potential of spontaneous millet fermentation. The literature in the field was reviewed and analyses were conducted on publicly available Sequence Read Archive (SRA) datasets. Quality analysis was performed with FastQC, and operational taxonomic units (OTUs) were generated using Quantitative Insights Into Microbial Ecology (QIIME2) and Divisive Amplicon Denoising Algorithm (DADA2) pipelines with Greengenes as the reference database. Metagenomics and pathways analysis were performed with Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt2). Statistical analysis and visualization were accomplished with Statistical Analysis of Metagenomic Profiles (STAMP). At the family taxonomic level, there were differences in the relative abundances of the dominant taxa of bacteria that are involved in the spontaneous fermentation of millet namely Lactobacillaceae, Burkholderiaceae, Streptococcaceae, Leuconostocaceae, and Acetobacteraceae. Clostridiaceae was the dominant family in one dataset. The incidence of Lactobacillaceae and Bifidobacteriaceae suggest the probiotic characteristics of fermented millet. The datasets were collected with fermentations that were mediated by autochthonous microorganisms and the presence of some potential pathogens such as Enterobacteriaceae, Clostridiaceae, Aeromonadaceae, Microbacteiaceae, Pseudomonadaceae, and Neisseriaceae which suggest the need for standardization of fermentation approaches. The genomes show the potential to synthesize metabolites such as essential amino acids and vitamins, suggesting that the respective fermented foods can be further optimized to enhance nutritional benefits.}, } @article {pmid36553749, year = {2022}, author = {Al-Musharaf, S and Aljuraiban, GS and Al-Ajllan, L and Al-Khaldi, N and Aljazairy, EA and Hussain, SD and Alnaami, AM and Sabico, S and Al-Daghri, N}, title = {Vitamin B12 Status and Gut Microbiota among Saudi Females with Obesity.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {24}, pages = {}, pmid = {36553749}, issn = {2304-8158}, support = {IFKSURG-2-009//Research & Innovation, Ministry of Education, in Saudi Arabia/ ; }, abstract = {Previous studies have suggested that dietary habits and dysbiosis of gut microbiota contributed to obesity development. Vitamin B12 is produced by microbes; however, the relationships between vitamin B12, gut microbiome, and obesity are understudied. We aimed to determine the association between vitamin B12 status and gut microbiota relative to obesity in 92 Saudi Arabian females aged 19-25 years who were obese (n = 44) or normal weight (n = 48). Anthropometric, biochemical data, and dietary data were collected. The microbial communities of stool samples were characterized using the shotgun metagenomic sequencing technique. The relationship between vitamin B12 status and gut microbiota composition was identified using Pearson correlation analysis. A statistically significant difference was found in bacterial α- and β-diversity between the groups relative to median serum vitamin B12 level (404.0 pg/mL) and body weight. In the total participants, dietary vitamin B12 intake was inversely correlated with Bifidobacterium kashiwanohense and Blautia wexlerae species. In obese participants, dietary vitamin B12 intake was inversely correlated with Akkermansia muciniphila species and species from the Verrucomicrobia phylum, whereas it was positively correlated with Bacteroides species. Our findings indicate that the abundance (frequency) and diversity (richness) of gut microbiota are associated with vitamin B12 levels and obesity in young females.}, } @article {pmid36553546, year = {2022}, author = {Terrón-Camero, LC and Gordillo-González, F and Salas-Espejo, E and Andrés-León, E}, title = {Comparison of Metagenomics and Metatranscriptomics Tools: A Guide to Making the Right Choice.}, journal = {Genes}, volume = {13}, number = {12}, pages = {}, pmid = {36553546}, issn = {2073-4425}, mesh = {*Bacteria/genetics ; Archaea/genetics ; Software ; *Microbiota/genetics ; Metagenome/genetics ; }, abstract = {The study of microorganisms is a field of great interest due to their environmental (e.g., soil contamination) and biomedical (e.g., parasitic diseases, autism) importance. The advent of revolutionary next-generation sequencing techniques, and their application to the hypervariable regions of the 16S, 18S or 23S ribosomal subunits, have allowed the research of a large variety of organisms more in-depth, including bacteria, archaea, eukaryotes and fungi. Additionally, together with the development of analysis software, the creation of specific databases (e.g., SILVA or RDP) has boosted the enormous growth of these studies. As the cost of sequencing per sample has continuously decreased, new protocols have also emerged, such as shotgun sequencing, which allows the profiling of all taxonomic domains in a sample. The sequencing of hypervariable regions and shotgun sequencing are technologies that enable the taxonomic classification of microorganisms from the DNA present in microbial communities. However, they are not capable of measuring what is actively expressed. Conversely, we advocate that metatranscriptomics is a "new" technology that makes the identification of the mRNAs of a microbial community possible, quantifying gene expression levels and active biological pathways. Furthermore, it can be also used to characterise symbiotic interactions between the host and its microbiome. In this manuscript, we examine the three technologies above, and discuss the implementation of different software and databases, which greatly impact the obtaining of reliable results. Finally, we have developed two easy-to-use pipelines leveraging Nextflow technology. These aim to provide everything required for an average user to perform a metagenomic analysis of marker genes with QIMME2 and a metatranscriptomic study using Kraken2/Bracken.}, } @article {pmid36552939, year = {2022}, author = {Yagupsky, P}, title = {The Past, Present, and Future of Kingella kingae Detection in Pediatric Osteoarthritis.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {12}, number = {12}, pages = {}, pmid = {36552939}, issn = {2075-4418}, abstract = {As a result of the increasing use of improved detection methods, Kingella kingae, a Gram-negative component of the pediatric oropharyngeal microbiota, is increasingly appreciated as the prime etiology of septic arthritis, osteomyelitis, and spondylodiscitis in children aged 6 to 48 months. The medical literature was reviewed to summarize the laboratory methods required for detecting the organism. Kingella kingae is notoriously fastidious, and seeding skeletal system samples onto solid culture media usually fails to isolate it. Inoculation of synovial fluid aspirates and bone exudates into blood culture vials enhances Kingella kingae recovery by diluting detrimental factors in the specimen. The detection of the species has been further improved by nucleic acid amplification tests, especially by using species-specific primers targeting Kingella kingae's rtxA, groEL, and mdh genes in a real-time PCR platform. Although novel metagenomic next-generation technology performed in the patient's plasma sample (liquid biopsy) has not yet reached its full potential, improvements in the sensitivity and specificity of the method will probably make this approach the primary means of diagnosing Kingella kingae infections in the future.}, } @article {pmid36552852, year = {2022}, author = {Zargari Marandi, R and Jørgensen, M and Ilett, EE and Nørgaard, JC and Noguera-Julian, M and Paredes, R and Lundgren, JD and Sengeløv, H and MacPherson, CR}, title = {Pre-Transplant Prediction of Acute Graft-versus-Host Disease Using the Gut Microbiome.}, journal = {Cells}, volume = {11}, number = {24}, pages = {}, pmid = {36552852}, issn = {2073-4409}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; Transplantation, Homologous ; *Graft vs Host Disease ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Bacteria ; }, abstract = {Gut microbiota is thought to influence host responses to allogeneic hematopoietic stem cell transplantation (aHSCT). Recent evidence points to this post-transplant for acute graft-versus-host disease (aGvHD). We asked whether any such association might be found pre-transplant and conducted a metagenome-wide association study (MWAS) to explore. Microbial abundance profiles were estimated using ensembles of Kaiju, Kraken2, and DeepMicrobes calls followed by dimensionality reduction. The area under the curve (AUC) was used to evaluate classification of the samples (aGvHD vs. none) using an elastic net to test the relevance of metagenomic data. Clinical data included the underlying disease (leukemia vs. other hematological malignancies), recipient age, and sex. Among 172 aHSCT patients of whom 42 developed aGVHD post transplantation, a total of 181 pre-transplant tool samples were analyzed. The top performing model predicting risk of aGVHD included a reduced species profile (AUC = 0.672). Beta diversity (37% in Jaccard's Nestedness by mean fold change, p < 0.05) was lower in those developing aGvHD. Ten bacterial species including Prevotella and Eggerthella genera were consistently found to associate with aGvHD in indicator species analysis, as well as relief and impurity-based algorithms. The findings support the hypothesis on potential associations between gut microbiota and aGvHD based on a data-driven approach to MWAS. This highlights the need and relevance of routine stool collection for the discovery of novel biomarkers.}, } @article {pmid36552504, year = {2022}, author = {Hori, K and Taniguchi, T and Elpita, T and Khemgaew, R and Sasaki, S and Gotoh, Y and Yasutomi, I and Misawa, N}, title = {Comprehensive Analyses of the Bacterial Population in Non-Healing Claw Lesions of Dairy Cattle.}, journal = {Animals : an open access journal from MDPI}, volume = {12}, number = {24}, pages = {}, pmid = {36552504}, issn = {2076-2615}, support = {JP21K05923//JSPS KAKENHI/ ; JPMJSA1908//Science and Technology Research Partnership for Sustainable Development/ ; }, abstract = {Non-healing claw lesions (NHCLs) are a newly characterized disorder affecting the deep dermis of the hoof in dairy cattle. Although NHCLs are thought to be associated with bovine digital dermatitis (BDD), their precise etiology is not yet understood. To investigate the bacterial populations present in each type of NHCL (toe necrosis: TN, non-healing white line disease: nhWLD, and a non-healing sole ulcer: nhSU), and the newly added entity non-healing verrucous-like lesions (nhVLL), 16S rRNA-based metagenomic analysis with next-generation sequencing (NGS) was employed. Twelve cases of NHCLs (3 TN, 3 nhWLD, 4 nhSU, and 2 nhVLL) were collected from five dairy farms in two prefectures in Japan. Three samples of healthy hoof dermis collected from two farms and a slaughterhouse were used as controls. Furthermore, culture-dependent and -independent approaches were conducted for detecting Treponema species and Fusobacterium necrophorum. As reported in BDD, Treponema species and F. necrophorum were detected frequently from NHCLs by PCR and immunohistochemistry, but NGS showed that these bacterial genera were not predominant in NHCLs. The predominant bacterial genera in NHCLs differed among the lesions examined, suggesting that Treponema species present predominantly in BDD were not predominant in NHCLs and that the bacterial population in NHCLs may vary among individual cattle and/or farms.}, } @article {pmid36552377, year = {2022}, author = {Esmonde, NPG and Hanna, REB and Patel, JG and Smyth, VJ and Caplat, P and Smyth, W and Jaggers, P and Padget, O and Guilford, T and Perrins, C and Reid, N}, title = {Case Report of Puffinosis in a Manx Shearwater (Puffinus puffinus) Suggesting Environmental Aetiology.}, journal = {Animals : an open access journal from MDPI}, volume = {12}, number = {24}, pages = {}, pmid = {36552377}, issn = {2076-2615}, support = {NE/S007377/1//UK Research and Innovation/ ; 754380//Teagasc - The Irish Agriculture and Food Development Authority/ ; NE/S007474/1//UK Research and Innovation/ ; }, abstract = {Puffinosis is a disease of a range of seabirds characterised by dorsal and ventral blistering of their webbed feet, conjunctivitis, dry necrosis, leg spasticity, head shaking, loss of balance, tremors, and death. It is associated with Manx shearwaters (Puffinus puffinus), frequently affecting chicks within their underground nesting burrows. The aetiology of the disease is unclear but has been attributed to a type-2 coronavirus associated with Neotombicula mites as a potential vector. However, there is some uncertainty given potential laboratory contamination with mouse hepatitis virus and failure to fulfil Koch's postulates, with birds injected with isolates remaining healthy. We describe a detailed case report of puffinosis in a Manx Shearwater covering necropsy, histology, bacteriology, and metagenomics including viral sequencing. We found no evidence of viral infection or parasites. Our results are consistent with an entirely environmental aetiology, with caustic faecal ammonia in damp nesting burrows causing conjunctivitis and foot dermatitis breaking the skin, allowing common soil bacteria (i.e., Flavobacterium, Staphylococcus and Serratia spp., Clostridia perfringens and Enterococcus faecalis) to cause opportunistic infection, debilitating the bird and leading to death. A similar condition (foot pad dermatitis or FPD) has been reported in broiler chickens, attributed to caustic faeces, high humidity, and poor environmental conditions during indoor rearing, preventable by adequate ventilation and husbandry. This is consistent with puffinosis being observed in Shearwater nesting burrows situated in tall, dense, vegetation (e.g., bracken Pteridium aquilinum) but rarely reported in burrows situated in well-ventilated, short coastal grasslands. This proposed environmental aetiology accounts for the disease's non-epizootic prevalence, spatial variation within colonies, and higher frequency in chicks that are restricted to nesting burrows.}, } @article {pmid36551584, year = {2022}, author = {Ganly, I and Hao, Y and Rosenthal, M and Wang, H and Migliacci, J and Huang, B and Katabi, N and Brown, S and Tang, YW and Pei, Z and Yang, L}, title = {Oral Microbiome in Nonsmoker Patients with Oral Cavity Squamous Cell Carcinoma, Defined by Metagenomic Shotgun Sequencing.}, journal = {Cancers}, volume = {14}, number = {24}, pages = {}, pmid = {36551584}, issn = {2072-6694}, support = {P30 CA008748/CA/NCI NIH HHS/United States ; R21 DE025352/DE/NIDCR NIH HHS/United States ; R21DE025352/DE/NIDCR NIH HHS/United States ; P30CA008748/CA/NCI NIH HHS/United States ; }, abstract = {Objectives: Smoking is the commonest cause of oral cavity squamous cell carcinoma (OC-SCC), but the etiology of OC-SCC in nonsmokers is unknown. Our primary goal was to use metagenomic shotgun sequencing (MSS) to define the taxonomic composition and functional potential of oral metagenome in nonsmokers with OC-SCC. Methods: We conducted a case-control study with 42 OC-SCC case and 45 control nonsmokers. MSS was performed on DNA extracted from mouthwash samples. Taxonomic analysis and pathway analysis were done using MetaPhlAn2 and HUMAnN2, respectively. Statistical difference was determined using the Mann-Whitney test controlling false discovery rate. Results: There was no significant difference in age, sex, race, or alcohol consumption between OC-SCC and control patients. There was a significant difference in beta diversity between OC-SCC and controls. At the phylum level, Bacteroidetes and Synergistetes were overly represented in OC-SCC while Actinobacteria and Firmicutes were overly represented in controls. At the genus level, Fusobacterium was overly represented in OC-SCC compared with controls, while Corynebacterium, Streptococcus, Actinomyces, Cryptobacterium, and Selenomonas were overly represented in controls. Bacterial pathway analysis identified overrepresentation in OC-SCC of pathways related to metabolism of flavin, biotin, thiamin, heme, sugars, fatty acids, peptidoglycans, and tRNA and overrepresentation of nucleotides and essential amino acids in controls. Conclusions: The oral microbiome in nonsmoker patients with OC-SCC is significantly different from that of nonsmoker control patients in taxonomic compositions and functional potentials. Our study's MSS findings matched with previous 16S-based methods in taxonomic differentiation but varied greatly in functional differentiation of microbiomes in OC-SCC and controls.}, } @article {pmid36551483, year = {2022}, author = {Yan, S and Zhang, X and Jia, X and Zhang, J and Han, X and Su, C and Zhao, J and Gou, W and Xu, J and Zhang, B}, title = {Characterization of the Composition Variation of Healthy Human Gut Microbiome in Correlation with Antibiotic Usage and Yogurt Consumption.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, pmid = {36551483}, issn = {2079-6382}, support = {P30 AG066615/AG/NIA NIH HHS/United States ; R01 HD038700/HD/NICHD NIH HHS/United States ; R01 HD030880/HD/NICHD NIH HHS/United States ; R01 DK104371/DK/NIDDK NIH HHS/United States ; R01 AG065357/AG/NIA NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; P2C HD050924/HD/NICHD NIH HHS/United States ; }, abstract = {Antibiotic usage and yogurt consumption are the major interventions for gut microbiota, yet their shared characteristics and disparities in healthy human gut microbiome remain unclear. This study aimed to decipher the composition changes among healthy humans, comparing antibiotic usage and yogurt consumption. The relative bacterial abundances of 1113 fecal samples were collected from an ongoing, population-based longitudinal cohort study in China that covered lifestyle, diet, disease status and physical measurements, and biological indicators of participants were obtained by the sequencing of 16S rRNA. The samples were divided into three groups, which were antibiotic users (122), yogurt consumers (497) and controls (494), where data visualization, alpha diversity, beta diversity and LEfSe analysis were conducted. At the family level, the relative abundances of Streptococcaceae, Enterobacteriaceae and Enterococcaceae families in antibiotic users increased almost 50%, 70% and 200%, respectively, while yogurt consumption also increased relative abundances of Streptococcaceae and Enterococcaceae, but not Enterobacteriaceae. Alpha diversity analyses suggested that the microbiome of the antibiotic usage and yogurt consumption groups exhibited an alpha diversity lower than that of the control. LEfSe analysis showed that, at the family level, the number of biomarkers in the yogurt consumption and antibiotic usage group were respectively 5 and 7, lower than that of the control (13). This study demonstrated the importance in considering the potential assistance of yogurt consumption on ARG gene transfer from commensal bacteria to pathogens in the human gut, which may pose a risk for human health. Antibiotic usage and yogurt consumption share more identical changes on healthy human gut flora than disparities. Therefore, in order to understand the potential risks of antibiotic usage and yogurt consumption on antibiotic resistance transmission in human gut microbiota, further research needs to be undertaken.}, } @article {pmid36551455, year = {2022}, author = {Haddad, SF and DeSimone, DC and Chesdachai, S and Gerberi, DJ and Baddour, LM}, title = {Utility of Metagenomic Next-Generation Sequencing in Infective Endocarditis: A Systematic Review.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, pmid = {36551455}, issn = {2079-6382}, abstract = {Blood cultures have been the gold standard for identifying pathogens in infective endocarditis (IE). Blood culture-negative endocarditis (BCNE), however, occurs in 40% or more of IE cases with the bulk of them due to recent antibiotic exposure prior to obtaining blood cultures. Increasingly, molecular techniques are being used for pathogen identification in cases of BCNE and more recently has included metagenomic next-generation sequencing (mNGS). We therefore performed a literature search on August 31, 2022, that assessed the mNGS in IE and 13 publications were identified and included in a systematic review. Eight (61.5%) of them focused only on IE with mNGS performed on cardiac valve tissue in four studies, plasma in three studies and cardiac implantable electronic devices (CIED) in one study. Gram-positive cocci, including Staphylococcus aureus (n = 31, 8.9%), coagulase-negative staphylococci (n = 61, 17.6%), streptococci (n = 130, 37.5%), and Enterococcus faecalis (n = 23, 6.6%) were the predominant organisms identified by mNGS. Subsequent investigations are needed to further define the utility of mNGS in BCNE and its impact on patient outcomes. Despite some pitfalls, mNGS seems to be of value in pathogen identification in IE cases, particularly in those with BCNE. This study was registered and on the Open Science Framework platform.}, } @article {pmid36551425, year = {2022}, author = {Cellier-Goetghebeur, S and Lafontaine, K and Lemay-St-Denis, C and Tsamo, P and Bonneau-Burke, A and Copp, JN and Pelletier, JN}, title = {Discovery of Highly Trimethoprim-Resistant DfrB Dihydrofolate Reductases in Diverse Environmental Settings Suggests an Evolutionary Advantage Unrelated to Antibiotic Resistance.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, pmid = {36551425}, issn = {2079-6382}, support = {RGPIN-N-2018-04686//Natural Sciences and Engineering Research Council/ ; CRC-2020-00171//Canada Research Chairs/ ; }, abstract = {Type B dihydrofolate reductases (DfrB) are intrinsically highly resistant to the widely used antibiotic trimethoprim, posing a threat to global public health. The ten known DfrB family members have been strongly associated with genetic material related to the application of antibiotics. Several dfrB genes were associated with multidrug resistance contexts and mobile genetic elements, integrated both in chromosomes and plasmids. However, little is known regarding their presence in other environments. Here, we investigated the presence of dfrB beyond the traditional areas of enquiry by conducting metagenomic database searches from environmental settings where antibiotics are not prevalent. Thirty putative DfrB homologues that share 62 to 95% identity with characterized DfrB were identified. Expression of ten representative homologues verified trimethoprim resistance in all and dihydrofolate reductase activity in most. Contrary to samples associated with the use of antibiotics, the newly identified dfrB were rarely associated with mobile genetic elements or antibiotic resistance genes. Instead, association with metabolic enzymes was observed, suggesting an evolutionary advantage unrelated to antibiotic resistance. Our results are consistent with the hypothesis that multiple dfrB exist in diverse environments from which dfrB were mobilized into the clinically relevant resistome. Our observations reinforce the need to closely monitor their progression.}, } @article {pmid36551388, year = {2022}, author = {Anju, VT and Busi, S and Imchen, M and Kumavath, R and Mohan, MS and Salim, SA and Subhaswaraj, P and Dyavaiah, M}, title = {Polymicrobial Infections and Biofilms: Clinical Significance and Eradication Strategies.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {12}, pages = {}, pmid = {36551388}, issn = {2079-6382}, abstract = {Biofilms are population of cells growing in a coordinated manner and exhibiting resistance towards hostile environments. The infections associated with biofilms are difficult to control owing to the chronicity of infections and the emergence of antibiotic resistance. Most microbial infections are contributed by polymicrobial or mixed species interactions, such as those observed in chronic wound infections, otitis media, dental caries, and cystic fibrosis. This review focuses on the polymicrobial interactions among bacterial-bacterial, bacterial-fungal, and fungal-fungal aggregations based on in vitro and in vivo models and different therapeutic interventions available for polymicrobial biofilms. Deciphering the mechanisms of polymicrobial interactions and microbial diversity in chronic infections is very helpful in anti-microbial research. Together, we have discussed the role of metagenomic approaches in studying polymicrobial biofilms. The outstanding progress made in polymicrobial research, especially the model systems and application of metagenomics for detecting, preventing, and controlling infections, are reviewed.}, } @article {pmid36550834, year = {2022}, author = {Xu, L and Zhao, Z and Mai, H and Tan, X and Du, Y and Fang, C}, title = {Clinical and chest computed tomography features associated with severe Chlamydia psittaci pneumonia diagnosed by metagenomic next-generation sequencing: A multicenter, retrospective, observational study.}, journal = {Medicine}, volume = {101}, number = {50}, pages = {e32117}, pmid = {36550834}, issn = {1536-5964}, mesh = {Humans ; Middle Aged ; *Psittacosis/diagnosis ; *Chlamydophila psittaci/genetics ; Retrospective Studies ; *COVID-19 ; Interleukin-10 ; SARS-CoV-2 ; Interleukin-6 ; *Pneumonia ; Tomography, X-Ray Computed/methods ; Dyspnea ; High-Throughput Nucleotide Sequencing ; }, abstract = {Chlamydia psittaci pneumonia is a rare disease with varying clinical presentations. Here, we aimed to investigate the clinical and chest computed tomography (CT) features of severe psittacosis pneumonia. Clinical data of 35 patients diagnosed with psittacosis pneumonia were retrospectively analyzed using metagenomic next-generation sequencing. The patients were classified into severe (n = 20) and non-severe (n = 15) groups. The median age of patients was 54 years, and 27 patients (77.1%) had a definite history of bird contact. Severe patients had more underlying comorbidities and were more prone to dyspnea and consciousness disorders than non-severe patients. The neutrophil count and D-dimer, lactate dehydrogenase, interleukin (IL)-2, IL-6, and IL-10 levels were higher, whereas the lymphocyte, CD3 + T cell, and CD4 + T cell counts, CD4+/CD8 + T cell ratio, and albumin level were substantially lower in severe patients than in non-severe patients. Chest CT findings of severe patients revealed large areas of pulmonary consolidation, and ground-glass opacities were observed in some patients, with a higher risk of involving multiple lobes of the lungs and pleural effusion. One patient died of multiple organ failure, whereas the condition of the other 34 patients improved, and they were discharged from the hospital. Patients with severe psittacosis pneumonia often have underlying comorbidities and are prone to developing dyspnea, consciousness disorder, and lesions in both lungs. Serum D-dimer, IL-2, IL-6, and IL-10 levels and lymphocyte, CD3 + T cell, and CD4 + T cell counts are associated with disease severity.}, } @article {pmid36550785, year = {2023}, author = {Ye, D and Huang, J and Wu, J and Xie, K and Gao, X and Yan, K and Zhang, P and Tao, Y and Li, Y and Zang, S and Rong, X and Li, J and Guo, J}, title = {Integrative metagenomic and metabolomic analyses reveal gut microbiota-derived multiple hits connected to development of gestational diabetes mellitus in humans.}, journal = {Gut microbes}, volume = {15}, number = {1}, pages = {2154552}, pmid = {36550785}, issn = {1949-0984}, mesh = {Humans ; Pregnancy ; Female ; *Diabetes, Gestational/microbiology ; *Gastrointestinal Microbiome ; Blood Glucose/metabolism ; Metagenome ; Dopamine/analysis ; Metabolomics ; Bacteria/genetics/metabolism ; }, abstract = {Gestational diabetes mellitus (GDM) is characterized by the development of hyperglycemia and insulin resistance during the second or third trimester of pregnancy, associated with considerable risks to both the mother and developing fetus. Although emerging evidence suggests an association between the altered gut microbiota and GDM, remarkably little is known about the microbial and metabolic mechanisms that link the dysbiosis of the gut microbiota to the development of GDM. In this study, a metagenome-wide association study and serum metabolomics profiling were performed in a cohort of pregnant women with GDM and pregnant women with normal glucose tolerance (NGT). We identified gut microbial alterations associated with GDM and linked to the changes in circulating metabolites. Blood metabolite profiles revealed that GDM patients exhibited a marked increase in 2-hydroxybutyric acid and L-alpha-aminobutyric acid, but a decrease in methionine sulfoxide, allantoin, and dopamine and dopaminergic synapse, when compared with those in NGT controls. Short-chain fatty acid-producing genera, including Faecalibacterium, Prevotella, and Streptococcus, and species Bacteroides coprophilus, Eubacterium siraeum, Faecalibacterium prausnitzii, Prevotella copri, and Prevotella stercorea, were significantly reduced in GDM patients relative to those in NGT controls. Bacterial co-occurrence network analysis revealed that pro-inflammatory bacteria were over-represented as the core species in GDM patients. These microbial and metabolic signatures are closely associated with clinical parameters of glucose metabolism in GDM patients and NGT controls. In conclusion, we identified circulating dopamine insufficiency, imbalanced production of SCFAs, and excessive metabolic inflammation as gut microbiota-driven multiple parallel hits linked to GDM development. This work might explain in part the mechanistic link between altered gut microbiota and GDM pathogenesis, and suggest that gut microbiota may serve as a promising target to intervene in GDM.}, } @article {pmid36550487, year = {2022}, author = {Kinsella, CM and Edridge, AWD and van Zeggeren, IE and Deijs, M and van de Beek, D and Brouwer, MC and van der Hoek, L}, title = {Bacterial ribosomal RNA detection in cerebrospinal fluid using a viromics approach.}, journal = {Fluids and barriers of the CNS}, volume = {19}, number = {1}, pages = {102}, pmid = {36550487}, issn = {2045-8118}, support = {918.19.627//ZonMw,Netherlands/ ; 101001237/ERC_/European Research Council/International ; 917.17.308/ZONMW_/ZonMw/Netherlands ; 721367//Horizon 2020,European Union/ ; }, mesh = {Humans ; RNA, Ribosomal ; RNA, Bacterial ; *Meningitis, Bacterial/cerebrospinal fluid/diagnosis/microbiology ; *Neisseria meningitidis ; Sensitivity and Specificity ; Ribosomes ; Cerebrospinal Fluid/microbiology ; }, abstract = {BACKGROUND: In patients with central nervous system (CNS) infections identification of the causative pathogen is important for treatment. Metagenomic next-generation sequencing techniques are increasingly being applied to identify causes of CNS infections, as they can detect any pathogen nucleic acid sequences present. Viromic techniques that enrich samples for virus particles prior to sequencing may simultaneously enrich ribosomes from bacterial pathogens, which are similar in size to small viruses.

METHODS: We studied the performance of a viromic library preparation technique (VIDISCA) combined with low-depth IonTorrent sequencing (median ~ 25,000 reads per sample) for detection of ribosomal RNA from common pathogens, analyzing 89 cerebrospinal fluid samples from patients with culture proven bacterial meningitis.

RESULTS: Sensitivity and specificity to Streptococcus pneumoniae (n = 24) before and after optimizing threshold parameters were 79% and 52%, then 88% and 90%. Corresponding values for Neisseria meningitidis (n = 22) were 73% and 93%, then 67% and 100%, Listeria monocytogenes (n = 24) 21% and 100%, then 27% and 100%, and Haemophilus influenzae (n = 18) 56% and 100%, then 71% and 100%. A higher total sequencing depth, no antibiotic treatment prior to lumbar puncture, increased disease severity, and higher c-reactive protein levels were associated with pathogen detection.

CONCLUSION: We provide proof of principle that a viromic approach can be used to correctly identify bacterial ribosomal RNA in patients with bacterial meningitis. Further work should focus on increasing assay sensitivity, especially for problematic species (e.g. L. monocytogenes), as well as profiling additional pathogens. The technique is most suited to research settings and examination of idiopathic cases, rather than an acute clinical setting.}, } @article {pmid36550469, year = {2022}, author = {Pan, X and Xu, J and Pan, L and Wang, C and Qiu, J and Huang, X and Yan, C and Mao, M}, title = {Hyperammonemia in a septic patient with Ureaplasma parvum arthritis: a case report.}, journal = {BMC infectious diseases}, volume = {22}, number = {1}, pages = {958}, pmid = {36550469}, issn = {1471-2334}, mesh = {Male ; Humans ; Aged ; Ureaplasma ; Ammonia ; *Hyperammonemia/complications/diagnosis ; *Arthritis, Infectious/complications/diagnosis/drug therapy ; Anti-Bacterial Agents/therapeutic use ; *Ureaplasma Infections/diagnosis ; }, abstract = {BACKGROUND: Septic arthritis requires prompt diagnosis and treatments. Rare pathogens should be considered when patients respond poorly to the initial antibiotic treatments. Ureaplasma parvum is an opportunistic pathogen that commonly resides in the human urogenital tract. Its infection commonly causes hyperammonemia. Hyperammonemia from Ureaplasma parvum septic arthritis has never been reported previously.

CASE PRESENTATION: A 65-year-old male presented with fever and left lower leg pain and swelling for more than ten days. Septic arthritis and sepsis were considered after laboratory tests and arthrocentesis. However, he responded poorly to the antibiotic treatments, including cefoperazone-sulbactam, imipenem-cilastatin, and linezolid. His mental status deteriorated rapidly with elevated blood ammonia levels with unremarkable liver function test and sonogram examination results. Despite the treatments with lactulose, L-ornithine L-aspartate, mannitol, and hemodialysis therapy to lower his ammonia level, his blood ammonia level remained persistently high. Finally, metagenomic sequencing of the left knee synovial fluid reported Ureaplasma parvum, which was considered to contribute to his hyperammonemia.

CONCLUSION: Ureaplasma parvum could cause septic arthritis with hyperammonemia. Genetic tests, such as polymerase chain reaction and next-generation sequencing techniques, could provide a sensitive and fast diagnosis of Ureaplasma parvum.}, } @article {pmid36550399, year = {2022}, author = {Hu, X and Haas, JG and Lathe, R}, title = {The electronic tree of life (eToL): a net of long probes to characterize the microbiome from RNA-seq data.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {317}, pmid = {36550399}, issn = {1471-2180}, support = {MR/P011349/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {RNA-Seq ; *Microbiota/genetics ; Bacteria/genetics ; Archaea ; Metagenome ; *Viruses/genetics ; RNA, Ribosomal/genetics ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Microbiome analysis generally requires PCR-based or metagenomic shotgun sequencing, sophisticated programs, and large volumes of data. Alternative approaches based on widely available RNA-seq data are constrained because of sequence similarities between the transcriptomes of microbes/viruses and those of the host, compounded by the extreme abundance of host sequences in such libraries. Current approaches are also limited to specific microbial groups. There is a need for alternative methods of microbiome analysis that encompass the entire tree of life.

RESULTS: We report a method to specifically retrieve non-human sequences in human tissue RNA-seq data. For cellular microbes we used a bioinformatic 'net', based on filtered 64-mer sequences designed from small subunit ribosomal RNA (rRNA) sequences across the Tree of Life (the 'electronic tree of life', eToL), to comprehensively (98%) entrap all non-human rRNA sequences present in the target tissue. Using brain as a model, retrieval of matching reads, re-exclusion of human-related sequences, followed by contig building and species identification, is followed by confirmation of the abundance and identity of the corresponding species groups. We provide methods to automate this analysis. The method reduces the computation time versus metagenomics by a factor of >1000. A variant approach is necessary for viruses. Again, because of significant matches between viral and human sequences, a 'stripping' approach is essential. Contamination during workup is a potential problem, and we discuss strategies to circumvent this issue. To illustrate the versatility of the method we report the use of the eToL methodology to unambiguously identify exogenous microbial and viral sequences in human tissue RNA-seq data across the entire tree of life including Archaea, Bacteria, Chloroplastida, basal Eukaryota, Fungi, and Holozoa/Metazoa, and discuss the technical and bioinformatic challenges involved.

CONCLUSIONS: This generic methodology is likely to find wide application in microbiome analysis including diagnostics.}, } @article {pmid36550140, year = {2022}, author = {Yeh, YC and Fuhrman, JA}, title = {Effects of phytoplankton, viral communities, and warming on free-living and particle-associated marine prokaryotic community structure.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7905}, pmid = {36550140}, issn = {2041-1723}, mesh = {*Phytoplankton/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Cyanobacteria/genetics ; Eukaryota/genetics ; Water ; Seawater/microbiology ; }, abstract = {Free-living and particle-associated marine prokaryotes have physiological, genomic, and phylogenetic differences, yet factors influencing their temporal dynamics remain poorly constrained. In this study, we quantify the entire microbial community composition monthly over several years, including viruses, prokaryotes, phytoplankton, and total protists, from the San-Pedro Ocean Time-series using ribosomal RNA sequencing and viral metagenomics. Canonical analyses show that in addition to physicochemical factors, the double-stranded DNA viral community is the strongest factor predicting free-living prokaryotes, explaining 28% of variability, whereas the phytoplankton (via chloroplast 16S rRNA) community is strongest with particle-associated prokaryotes, explaining 31% of variability. Unexpectedly, protist community explains little variability. Our findings suggest that biotic interactions are significant determinants of the temporal dynamics of prokaryotes, and the relative importance of specific interactions varies depending on lifestyles. Also, warming influenced the prokaryotic community, which largely remained oligotrophic summer-like throughout 2014-15, with cyanobacterial populations shifting from cold-water ecotypes to warm-water ecotypes.}, } @article {pmid36549484, year = {2023}, author = {Niu, L and Zhao, S and Chen, Y and Li, Y and Zou, G and Tao, Y and Zhang, W and Wang, L and Zhang, H}, title = {Diversity and potential functional characteristics of phage communities colonizing microplastic biofilms.}, journal = {Environmental research}, volume = {219}, number = {}, pages = {115103}, doi = {10.1016/j.envres.2022.115103}, pmid = {36549484}, issn = {1096-0953}, mesh = {Humans ; Microplastics ; Plastics ; *Bacteriophages/genetics ; Bacteria/genetics ; Biofilms ; *Water Pollutants, Chemical/analysis ; }, abstract = {The multiple ecological influences and potential microbial degradation of microplastics are generally attributed to the microbial communities colonized on microplastics. Phages play an important role in the composition and function of their bacterial hosts, yet the occurrence and the potential functional characteristics of phages in the biofilms of microplastics have not been known. This study, for the first time, explored the diversity, composition, and potential function characteristics of phage communities living in the biofilms of PP, PE, and PET microplastics and stones, cultured in the same site, via the metagenome method. The results showed that a total of 240 non-redundant virus OTUs (vOTUs), distributed in at least four orders and seven families, were detected from biofilm metagenomes of microplastics. Compared to stones, some phages were selectively enriched by microplastic biofilms, with 13 vOTUs uniquely colonized on three microplastics, and these vOTUs mainly belong to the family Autographiviridae and Podoviridae. Except for the evenness of PP, the richness index, Chao 1 index, and abundance of phage communities of three microplastics were much higher than that of stone. At least 8 bacterial phyla and 72 genera were possibly infected by phages. Compared to the stones, both composition and abundance of the phages and hosts presented significant and strong correlations for three microplastics. Some of the bacterial hosts on microplastics were likely involved in the microplastic degradation, fermenters, nitrogen transformation processes, and so on. A total of 124 encoding auxiliary metabolic genes (AMGs) were detected from viral contigs. The abundance of AMGs in microplastics was much higher than that of stones, which may provide more direct or indirect support for the bacterial degradation of microplastics. This study provides a new perspective on the occurrence and potential functions of phages on microplastic biofilms, thus expanding our understanding of microbial communities on microplastic biofilms.}, } @article {pmid36549320, year = {2023}, author = {Liou, JM and Jiang, XT and Chen, CC and Luo, JC and Bair, MJ and Chen, PY and Chou, CK and Fang, YJ and Chen, MJ and Chen, CC and Lee, JY and Yang, TH and Yu, CC and Kuo, CC and Chiu, MC and Chen, CY and Shun, CT and Hu, WH and Tsai, MH and Hsu, YC and Tseng, CH and Chang, CY and Lin, JT and El-Omar, EM and Wu, MS and , }, title = {Second-line levofloxacin-based quadruple therapy versus bismuth-based quadruple therapy for Helicobacter pylori eradication and long-term changes to the gut microbiota and antibiotic resistome: a multicentre, open-label, randomised controlled trial.}, journal = {The lancet. Gastroenterology & hepatology}, volume = {8}, number = {3}, pages = {228-241}, doi = {10.1016/S2468-1253(22)00384-3}, pmid = {36549320}, issn = {2468-1253}, mesh = {Adult ; Male ; Humans ; Female ; Middle Aged ; Young Adult ; Anti-Bacterial Agents/adverse effects ; Bismuth/adverse effects ; Levofloxacin/therapeutic use ; *Helicobacter pylori ; Metronidazole/adverse effects ; Clarithromycin/adverse effects ; Esomeprazole/therapeutic use/adverse effects ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; Proton Pump Inhibitors/therapeutic use ; Drug Therapy, Combination ; Australia ; *Helicobacter Infections/drug therapy ; }, abstract = {BACKGROUND: Levofloxacin-based therapy or bismuth-based quadruple therapy are the recommended second-line regimens for Helicobacter pylori eradication after failure of clarithromycin-based therapy. However, resistance to levofloxacin has increased in the past decade. Furthermore, little is known about the long-term effects of H pylori eradication on the antibiotic resistome. In this study, we compared these second-line eradication therapies for efficacy, tolerability, and short-term and long-term effects on the gut microbiota, antibiotic resistome, and metabolic parameters.

METHODS: We did a multicentre, open-label, parallel group, randomised controlled trial at eight hospitals in Taiwan. Adult patients (age ≥20 years) with persistent H pylori infection after first-line clarithromycin-based therapy were randomly assigned (1:1, permuted block sizes of four) to receive levofloxacin-based sequential quadruple therapy for 14 days (EAML14; esomeprazole 40 mg and amoxicillin 1 g for 7 days, followed by esomeprazole 40 mg, metronidazole 500 mg, and levofloxacin 250 mg for 7 days, all twice-daily) or bismuth-based quadruple therapy for 10 days (BQ10; esomeprazole 40 mg twice daily, bismuth tripotassium dicitrate 300 mg four times a day, tetracycline 500 mg four times a day, and metronidazole 500 mg three times a day). All investigators were masked to the randomisation sequence. The primary endpoint was H pylori eradication rate measured by [13]C urea breath test 6 weeks after second-line treatment according to both intention-to-treat (ITT) and per-protocol analysis. The microbiota composition and antibiotic resistome of faecal samples collected at baseline (before treatment) and at 2 weeks, 8 weeks, and 1 year after eradication therapy was profiled by shotgun metagenomic sequencing and 16S rRNA gene sequencing. The frequency of adverse effects and changes in the gut microbiota and antibiotic resistome were assessed in all participants with available data. The trial is complete and registered with ClinicalTrails.gov, NCT03148366.

FINDINGS: Between Feb 25, 2015, and Dec 11, 2020, 560 patients were randomly assigned to receive EAML14 or BQ10 (n=280 per group; 261 [47%] men and 299 [53%] women). Mean age was 55·9 years (SD 12·7) in the EAML14 group and 54·9 years (12·3) in the BQ10 group. Eradication of H pylori was achieved in 246 (88%) of 280 participants in the EAML14 group and 245 (88%) of 280 in the BQ10 group according to ITT analysis (risk difference -0·4%, 95% CI -5·8 to 5·1; p=0·90). In the per-protocol analysis, 246 (90%) of 273 participants in the EAML14 group and 245 (93%) of 264 participants in the BQ10 group achieved H pylori eradication (risk difference 2·7%, 95% CI -0·2 to 7·4; p=0·27). Transient perturbation of faecal microbiota diversity at week 2 was largely restored to basal state 1 year after EAML14 or BQ10. Diversity recovery was slower with BQ10, and recovery in species abundance was partial after both therapies. On shotgun sequencing, we observed significant increases in total resistome after EAML14 (p=0·0002) and BQ10 (p=4·3 × 10[-10]) at week 2, which were restored to pretreatment level by week 8. The resistance rates of Escherichia coli and Klebsiella pneumonia to levofloxacin, ciprofloxacin, ampicillin (ampicillin-sulbactam for K pneumonia), and various cephalosporins were significantly increased in the EAML14 group compared with in the BQ10 group at week 2, which were restored to pretreatment levels and showed no significant differences at week 8 and 1 year. The frequency of any adverse effects was significantly higher after BQ10 therapy (211 [77%] of 273 participants) than after EAML14 therapy (134 [48%] of 277; p<0·0001).

INTERPRETATION: We found no evidence of superiority between levofloxacin-based quadruple therapy and bismuth-based quadruple therapy in the second-line treatment of H pylori infection. The transient increase in the antibiotic resistome and perturbation of faecal microbiota diversity were largely restored to pretreatment state from 2 months to 1 year after eradication therapy.

FUNDING: The Ministry of Science and Technology of Taiwan, the Ministry of Health and Welfare of Taiwan, National Taiwan University Hospital, Taipei Veteran General Hospital, and the Australian Federal Government through the St George and Sutherland Medical Research Foundation.

TRANSLATION: For the Chinese translation of the abstract see Supplementary Materials section.}, } @article {pmid36549300, year = {2023}, author = {Zhu, Y and Dwidar, M and Nemet, I and Buffa, JA and Sangwan, N and Li, XS and Anderson, JT and Romano, KA and Fu, X and Funabashi, M and Wang, Z and Keranahalli, P and Battle, S and Tittle, AN and Hajjar, AM and Gogonea, V and Fischbach, MA and DiDonato, JA and Hazen, SL}, title = {Two distinct gut microbial pathways contribute to meta-organismal production of phenylacetylglutamine with links to cardiovascular disease.}, journal = {Cell host & microbe}, volume = {31}, number = {1}, pages = {18-32.e9}, pmid = {36549300}, issn = {1934-6069}, support = {R21 CA267711/CA/NCI NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; R01 HL103866/HL/NHLBI NIH HHS/United States ; S10 OD016346/OD/NIH HHS/United States ; R01 HL160747/HL/NHLBI NIH HHS/United States ; }, mesh = {Mice ; Animals ; *Cardiovascular Diseases ; *Gastrointestinal Microbiome ; Glutamine ; }, abstract = {Recent studies show gut microbiota-dependent metabolism of dietary phenylalanine into phenylacetic acid (PAA) is critical in phenylacetylglutamine (PAGln) production, a metabolite linked to atherosclerotic cardiovascular disease (ASCVD). Accordingly, microbial enzymes involved in this transformation are of interest. Using genetic manipulation in selected microbes and monocolonization experiments in gnotobiotic mice, we identify two distinct gut microbial pathways for PAA formation; one is catalyzed by phenylpyruvate:ferredoxin oxidoreductase (PPFOR) and the other by phenylpyruvate decarboxylase (PPDC). PPFOR and PPDC play key roles in gut bacterial PAA production via oxidative and non-oxidative phenylpyruvate decarboxylation, respectively. Metagenomic analyses revealed a significantly higher abundance of both pathways in gut microbiomes of ASCVD patients compared with controls. The present studies show a role for these two divergent microbial catalytic strategies in the meta-organismal production of PAGln. Given the numerous links between PAGln and ASCVD, these findings will assist future efforts to therapeutically target PAGln formation in vivo.}, } @article {pmid36548827, year = {2022}, author = {Fu, S and Yuan, Y and Tian, X and Zhou, L and Guo, L and Zhang, D and He, J and Peng, C and Qiu, Y and Ye, C and Liu, Y and Zong, B}, title = {Detection of Colistin Sulfate on Piglet Gastrointestinal Tract Microbiome Alterations.}, journal = {Veterinary sciences}, volume = {9}, number = {12}, pages = {}, pmid = {36548827}, issn = {2306-7381}, support = {D20201607//science and technology research program of Hubei Provincial Department of Education/ ; }, abstract = {The gut microbiome exerts important functions on host health maintenance, whereas excessive antibiotic use may cause gut flora dysfunction resulting in serious disease and dysbiosis. Colistin is a broad-spectrum antibiotic with serious resistance phenomena. However, it is unclear whether colistin alters the gastrointestinal tract microbiome in piglets. In this study, 16s rDNA-based metagenome analyses were used to assess the effects of colistin on the modification of the piglet microbiome in the stomach, duodenum, jejunum, cecum, and feces. Both α- and β-diversity indices showed that colistin modified microbiome composition in these gastrointestinal areas. In addition, colistin influenced microbiome composition at the phylum and genus levels. At the species level, colistin upregulated Mycoplasma hyorhinis, Chlamydia trachomatis, Lactobacillus agilis, Weissella paramesenteroides, and Lactobacillus salivarius abundance, but downregulated Actinobacillus indolicus, Campylobacter fetus, Glaesserella parasuis, Moraxella pluranimalium, Veillonella caviae, Neisseria dentiae, and Prevotella disiens abundance in stomachs. Colistin-fed piglets showed an increased abundance of Lactobacillus mucosae, Megasphaera elsdenii DSM 20460, Fibrobacter intestinalis, and Unidentified rumen bacterium 12-7, but Megamonas funiformis, Uncultured Enterobacteriaceae bacterium, Actinobacillus porcinus, Uncultured Bacteroidales bacterium, and Uncultured Clostridiaceae bacterium abundance was decreased in the cecum. In feces, colistin promoted Mucispirillum schaedleri, Treponema berlinense, Veillonella magna, Veillonella caviae, and Actinobacillus porcinus abundance when compared with controls. Taken together, colistin modified the microbiome composition of gastrointestinal areas in piglets. This study provides new clinical rationalization strategies for colistin on the maintenance of animal gut balance and human public health.}, } @article {pmid36548668, year = {2022}, author = {Zeng, W and Li, Z and Jiang, T and Cheng, D and Yang, L and Hang, T and Duan, L and Zhu, D and Fang, Y and Zhang, Y}, title = {Identification of Bacterial Communities and Tick-Borne Pathogens in Haemaphysalis spp. Collected from Shanghai, China.}, journal = {Tropical medicine and infectious disease}, volume = {7}, number = {12}, pages = {}, pmid = {36548668}, issn = {2414-6366}, support = {GWV-10.1-XK13//Fifth Round of Three-year Action for Public Health System Construction in Shanghai/ ; 2017FY101203//The Special Foundation of Basic Science and Technology Resources Survey of Ministry of Science and Technology of China/ ; 21YF1452200//Shanghai sailing program/ ; }, abstract = {Ticks can carry and transmit a large number of pathogens, including bacteria, viruses and protozoa, posing a huge threat to human health and animal husbandry. Previous investigations have shown that the dominant species of ticks in Shanghai are Haemaphysalis flava and Haemaphysalis longicornis. However, no relevant investigations and research have been carried out in recent decades. Therefore, we investigated the bacterial communities and tick-borne pathogens (TBPs) in Haemaphysalis spp. from Shanghai, China. Ixodid ticks were collected from 18 sites in Shanghai, China, and identified using morphological and molecular methods. The V3-V4 hypervariable regions of the bacterial 16S rRNA gene were amplified from the pooled tick DNA samples and subject to metagenomic analysis. The microbial diversity in the tick samples was estimated using the alpha diversity that includes the observed species index and Shannon index. The Unifrac distance matrix as determined using the QIIME software was used for unweighted Unifrac Principal coordinates analysis (PCoA). Individual tick DNA samples were screened with genus-specific or group-specific nested polymerase chain reaction (PCR) for these TBPs and combined with a sequencing assay to confirm the results of the V3-V4 hypervariable regions of the bacterial 16S rRNA gene. We found H. flava and H. longicornis to be the dominant species of ticks in Shanghai in this study. Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria are the main bacterial communities of Haemaphysalis spp. The total species abundances of Proteobacteria, Firmicutes and Bacteroidetes, are 48.8%, 20.8% and 18.1%, respectively. At the level of genus analysis, H. longicornis and H. flava carried at least 946 genera of bacteria. The bacteria with high abundance include Lactobacillus, Coxiella, Rickettsia and Muribaculaceae. Additionally, Rickettsia rickettsii, Rickettsia japonica, Candidatus Rickettsia jingxinensis, Anaplasma bovis, Ehrlichia ewingii, Ehrlichia chaffeensis, Coxiella spp. and Coxiella-like endosymbiont were detected in Haemaphysalis spp. from Shanghai, China. This study is the first report of bacterial communities and the prevalence of some main pathogens in Haemaphysalis spp. from Shanghai, China, and may provide insights and evidence for bacterial communities and the prevalence of the main pathogen in ticks. This study also indicates that people and other animals in Shanghai, China, are exposed to several TBPs.}, } @article {pmid36548032, year = {2023}, author = {Lenkeit, F and Eckert, I and Sinn, M and Hauth, F and Hartig, JS and Weinberg, Z}, title = {A variant of guanidine-IV riboswitches exhibits evidence of a distinct ligand specificity.}, journal = {RNA biology}, volume = {20}, number = {1}, pages = {10-19}, pmid = {36548032}, issn = {1555-8584}, mesh = {Guanidine/chemistry/metabolism ; *Riboswitch ; Nucleic Acid Conformation ; Ligands ; Guanidines/metabolism ; Acetyltransferases/genetics/metabolism ; }, abstract = {Riboswitches are regulatory RNAs that specifically bind a small molecule or ion. Like metabolite-binding proteins, riboswitches can evolve new ligand specificities, and some examples of this phenomenon have been validated. As part of work based on comparative genomics to discover novel riboswitches, we encountered a candidate riboswitch with striking similarities to the recently identified guanidine-IV riboswitch. This candidate riboswitch, the Gd4v motif, is predicted in four distinct bacterial phyla, thus almost as widespread as the guanidine-IV riboswitch. Bioinformatic and experimental analysis suggest that the Gd4v motif is a riboswitch that binds a ligand other than guanidine. It is found associated with gene classes that differ from genes regulated by confirmed guanidine riboswitches. In inline-probing assays, we showed that free guanidine binds only weakly to one of the tested sequences of the variant. Further tested compounds did not show binding, attenuation of transcription termination, or activation of a genetic reporter construct. We characterized an N-acetyltransferase frequently associated with the Gd4v motif and compared its substrate preference to an N-acetyltransferase that occurs under control of guanidine-IV riboswitches. The substrates of this Gd4v-motif-associated enzyme did not show activity for Gd4v RNA binding or transcription termination. Hence, the ligand of the candidate riboswitch motif remains unidentified. The variant RNA motif is predominantly found in gut metagenome sequences, hinting at a ligand that is highly relevant in this environment. This finding is a first step to determining the identity of this unknown ligand, and understanding how guanidine-IV-riboswitch-like structures can evolve to bind different ligands.}, } @article {pmid36547776, year = {2023}, author = {Wang, DZ and Li, BH and Deng, BL and Guo, FQ and Hu, SS and Yu, NW and Liu, J}, title = {Anti-CASPR2 encephalitis in a liver posttransplant patient receiving immune-suppression and lenvatinib: a case report and literature review.}, journal = {Neurological sciences : official journal of the Italian Neurological Society and of the Italian Society of Clinical Neurophysiology}, volume = {44}, number = {3}, pages = {1069-1072}, pmid = {36547776}, issn = {1590-3478}, mesh = {Female ; Humans ; *Autoantibodies ; *Encephalitis/drug therapy/etiology ; Immunosuppression Therapy/adverse effects ; Liver ; }, abstract = {It has been assumed that patients with strict immunosuppressive treatment after solid organ transplantation have only marginal risk in developing autoimmune encephalitis. We reported a woman in her late 40 s who presented with generalized convulsions and loss of consciousness. After detailed history review, neuropsychological tests, metagenomic next-generation sequencing of serum and cerebrospinal fluid (CSF), magnetic resonance imaging (MRI) brain, and electroencephalogram, she was diagnosed as anti-CASPR2 encephalitis based on the positive anti-CASPR2 auto-antibody in serum and CSF. The patient underwent liver transplantation and has taken lenvatinib for 2 months, in addition to tacrolimus, mycophenotale mofetil, and entecavir administered for half a year. This case was the first report of anti-CASPR2 encephalitis in post-organ transplantation patients. Together with the reports of other encephalitis cases in organ transplantation, it warns the possibility of developing immune-oriented encephalitis in patients undergoing immunosuppression, especially in combination with other treatments of immunomodulatory activity.}, } @article {pmid36547579, year = {2022}, author = {Bhagat, N and Magotra, S and Gupta, R and Sharma, S and Verma, S and Verma, PK and Ali, T and Shree, A and Vakhlu, J}, title = {Invasion and Colonization of Pathogenic Fusarium oxysporum R1 in Crocus sativus L. during Corm Rot Disease Progression.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {12}, pages = {}, pmid = {36547579}, issn = {2309-608X}, abstract = {The corm rot of saffron caused by Fusarium oxysporum (Fox) has been reported to be the most destructive fungal disease of the herb globally. The pathogen, Fusarium oxysporum R1 (Fox R1) isolated by our group from Kashmir, India, was found to be different from Fusarium oxysporum f.sp. gladioli commonly reported corm rot agent of saffron. In the present study, Fox R1 was further characterized using housekeeping genes and pathogenicity tests, as Fusarium oxysporum R1 f.sp. iridacearum race 4. Though Fox R1 invaded the saffron plant through both corm and roots, the corm was found to be the preferred site of infection. In addition, the route of pathogen movement wastracked by monitoring visual symptoms, semi-quantitative PCR, quantitative-PCR (q-PCR), real-time imaging of egfp-tagged Fusarium oxysporum R1, and Fox R1 load quantification. This study is the first study of its kind on the bidirectional pathogenesis from corm to roots and vice-versa, as the literature only reports unidirectional upward movement from roots to other parts of the plant. In addition, the colonization pattern of Fox R1 in saffron corms and roots was studied. The present study involved a systematic elucidation of the mode and mechanism of pathogenesis in the saffron Fusarium oxysporum strain R1 pathosystem.}, } @article {pmid36546857, year = {2023}, author = {Dhakal, D and Kokkaliari, S and Rubin, GM and Paul, VJ and Ding, Y and Luesch, H}, title = {Biosynthesis of Lyngbyastatins 1 and 3, Cytotoxic Depsipeptides from an Okeania sp. Marine Cyanobacterium.}, journal = {Journal of natural products}, volume = {86}, number = {1}, pages = {85-93}, pmid = {36546857}, issn = {1520-6025}, support = {R01 CA172310/CA/NCI NIH HHS/United States ; R35 GM128742/GM/NIGMS NIH HHS/United States ; RM1 GM145426/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Antineoplastic Agents/pharmacology ; *Cyanobacteria/chemistry ; *Depsipeptides/chemistry ; Polyketide Synthases/genetics ; *Neoplasms ; Peptide Synthases/genetics ; Multigene Family ; }, abstract = {Lyngbyastatins (Lbns) 1 (1) and 3 (2) belong to a group of cyclic depsipeptides that inhibit cancer cell proliferation. These compounds have been isolated from different marine cyanobacterial collections, while further development of these compounds relies on their lengthy total synthesis. Biosynthetic studies of these compounds can provide viable strategies to access these compounds and develop new analogs. In this study, we report the identification and characterization of one Lbn biosynthetic gene cluster (BGC) from the marine cyanobacterium Okeania sp. VPG18-21. We initially identified 1 and 2 in the organic extract by mass spectrometry and performed the targeted isolation of these compounds, which feature a (2S,3R)-3-amino-2-methylpentanoic acid (MAP) and a (2S,3R)-3-amino-2-methylhexanoic acid (Amha) moiety, respectively. Parallel metagenomic sequencing of VPG18-21 led to the identification of a putative Lbn BGC that encodes six megaenzymes (LbnA-F), including one polyketide synthase (PKS, LbnE), four nonribosomal peptide synthetases (NRPSs, LbnB-D and -F), and one PKS-NRPS hybrid (LbnA). Bioinformatic analysis of these enzymes suggested that the BGC produces 1 and 2. Furthermore, our biochemical studies of three recombinant adenylation domains uncovered their substrate specificities, supporting the identity of the BGC. Finally, we identified near-complete Lbn-like BGCs in the genomes of two other marine cyanobacteria.}, } @article {pmid36546449, year = {2023}, author = {Fontaine, SS and Kohl, KD}, title = {The microbiome buffers tadpole hosts from heat stress: a hologenomic approach to understand host-microbe interactions under warming.}, journal = {The Journal of experimental biology}, volume = {226}, number = {1}, pages = {}, pmid = {36546449}, issn = {1477-9145}, mesh = {Animals ; Larva ; Host Microbial Interactions ; *Microbiota ; *Thermotolerance ; }, abstract = {Phenotypic plasticity is an important strategy that animals employ to respond and adjust to changes in their environment. Plasticity may occur via changes in host gene expression or through functional changes in their microbiomes, which contribute substantially to host physiology. Specifically, the presence and function of host-associated microbes can impact how animals respond to heat stress. We previously demonstrated that 'depleted' tadpoles, with artificially disrupted microbiomes, are less tolerant to heat than 'colonized' tadpoles, with more natural microbiomes. However, the mechanisms behind these effects are unclear. Here, we compared gene expression profiles of the tadpole gut transcriptome, and tadpole gut microbial metagenome, between colonized and depleted tadpoles under cool or warm conditions. Our goal was to identify differences in host and microbial responses to heat between colonized and depleted tadpoles that might explain their observed differences in heat tolerance. We found that depleted tadpoles exhibited a much stronger degree of host gene expression plasticity in response to heat, while the microbiome of colonized tadpoles was significantly more heat sensitive. These patterns indicate that functional changes in the microbiome in response to heat may allow for a dampened host response, ultimately buffering hosts from the deleterious effects of heat stress. We also identified several specific host and microbial pathways that could be contributing to increased thermal tolerance in colonized tadpoles including amino acid metabolism, vitamin biosynthesis and ROS scavenging pathways. Our results demonstrate that the microbiome influences host plasticity and the response of hosts to environmental stressors.}, } @article {pmid36545212, year = {2022}, author = {Chapman, R and D'Angelo, A and Bagby, S}, title = {Nanopore-based metagenomic sequencing: a diagnostic tool in respiratory tract infection.}, journal = {ERJ open research}, volume = {8}, number = {4}, pages = {}, pmid = {36545212}, issn = {2312-0541}, abstract = {This correspondence highlights the burden of respiratory tract infection and focuses on nanopore sequencing as a promising approach in diagnostics https://bit.ly/3fgs8zg.}, } @article {pmid36545194, year = {2022}, author = {Qiu, D and Xu, N and Zhang, Q and Zhou, W and Wang, Y and Zhang, Z and Yu, Y and Lu, T and Sun, L and Zhou, NY and Peijnenburg, WJGM and Qian, H}, title = {Negative effects of abamectin on soil microbial communities in the short term.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1053153}, pmid = {36545194}, issn = {1664-302X}, abstract = {With the widespread use of abamectin in agriculture, there is increasing urgency to assess the effects of abamectin on soil microorganisms. Here, we treated plant-soil microcosms with abamectin at concentrations of 0.1 and 1.0 mg/kg and quantified the impacts of abamectin on bulk and rhizosphere soil microbial communities by shotgun metagenomics after 7 and 21 days of exposure. Although abamectin was reported to be easily degradable, it altered the composition of the soil microbial communities, disrupted microbial interactions, and decreased community complexity and stability after 7 days of exposure. After treatment with abamectin at a concentration of 1.0 mg/kg, some opportunistic human diseases, and soil-borne pathogens like Ralstonia were enriched in the soil. However, most ecological functions in soil, particularly the metabolic capacities of microorganisms, recovered within 21 days after abamectin treatment. The horizontal and vertical gene transfer under abamectin treatments increased the levels of antibiotic resistance genes dissemination. Overall, our findings demonstrated the negative effects of abamectin on soil ecosystems in the short-term and highlight a possible long-term risk to public and soil ecosystem health associated with antibiotic resistance genes dissemination.}, } @article {pmid36544992, year = {2022}, author = {He, D and Liu, M and Chen, Q and Liu, Y and Tang, Y and Shen, F and Wang, D and Liu, X}, title = {Clinical Characteristics and the Effect of Timing for Metagenomic Next-Generation Sequencing in Critically Ill Patients with Sepsis.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {7377-7387}, pmid = {36544992}, issn = {1178-6973}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has a good performance for the identification of pathogens in infectious diseases, but few studies on the clinical characteristics of mNGS and the effect of timing for mNGS in critically ill patients with sepsis.

METHODS: We retrospectively included all patients diagnosed with sepsis after admission to the intensive care unit (ICU) of a university-affiliated hospital between Aug 1, 2019 and Apr 1, 2021. During the study period, pathogens for all enrolled subjects were obtained by mNGS. We analyzed the composition and positive rate of different samples type for mNGS. And then we used the univariable and multivariable logistic regression to explore the risk factors associated with all-cause mortality at 28 days.

RESULTS: A total of 87 patients were included and 87 samples were analyzed among these patients. The most common sample for mNGS was bronchoalveolar lavage fluid (BALF), about 84% (73/87). The positive rate of pathogens identification by mNGS was higher than conventional culture (92% vs 36%, p < 0.001). In addition to the pathogens detected by conventional culture, mNGS can detect more viruses and fungi. Based on the mNGS report, clinicians made adjustments to the antibiotic regimen for 72% patients. The multivariate binary logistic regression analysis suggested that age (OR, 1.036; 95% CI, 1.005-1.067; p = 0.021) and the sequential organ failure assessment (SOFA) score on the day of mNGS sampling were independent risk factors of death at 28 days (OR, 1.204; 95% CI, 1.038-1.397; p = 0.014).

CONCLUSION: In critically ill patients with sepsis, the most common sample type for mNGS was BALF, and the positive rate of mNGS is higher than conventional cultures, especially in viruses and fungi. Meanwhile, mNGS can guide clinicians in adjusting antibiotic regimens. Age and the SOFA score on the day of mNGS sampling were independent risk factors for death.}, } @article {pmid36544282, year = {2023}, author = {Bai, X and Xu, Q and Zhang, W and Wang, C}, title = {The Gut-Eye Axis: Correlation Between the Gut Microbiota and Autoimmune Dry Eye in Individuals With Sjögren Syndrome.}, journal = {Eye & contact lens}, volume = {49}, number = {1}, pages = {1-7}, doi = {10.1097/ICL.0000000000000953}, pmid = {36544282}, issn = {1542-233X}, mesh = {Humans ; *Sjogren's Syndrome/complications ; *Gastrointestinal Microbiome ; *Autoimmune Diseases/complications/therapy ; Dysbiosis/complications ; *Dry Eye Syndromes/etiology/therapy ; }, abstract = {The impact of gut microbiota on human health, autoimmunity, and disease occurrence has long been recognized since the advancement of metagenomic sequencing technology has enabled a new level of perspective on the human microbiome. Emerging findings also suggest the existence of a gut-eye axis, wherein gut dysbiosis may be a crucial factor affecting the onset and progression of multiple ocular diseases. Sjögren syndrome (SS) is a chronic autoimmune disease mainly affecting the exocrine glands, primarily the lacrimal gland in the eye, resulting in severe dry eye. Although there are currently various treatments for environmental dry eye, the efficacy for SS-related autoimmune dry eye is limited, and new and more effective therapies still need to be explored. The latest studies have demonstrated that the gut microbiota plays a key role in the pathogenesis of autoimmune dry eye. This review describes the effect of gut microbiota on the ocular surface of autoimmune dry eye; introduces the presumable pathways forming the "gut dysbiosis-ocular surface-lacrimal gland axis"; discusses the advantages of restoring intestinal microecology to treat dry eye by fecal microbiota transplantation or probiotics, which are expected to provide perspectives into the correlation between the gut microbiome and dry eye; enhance our understanding of the pathogenesis in autoimmune dry eye; and be useful in the development of future interventions of dry eye by regulating the gut microbiota.}, } @article {pmid36544228, year = {2022}, author = {Sierra, MA and Ryon, KA and Tierney, BT and Foox, J and Bhattacharya, C and Afshin, E and Butler, D and Green, SJ and Thomas, WK and Ramsdell, J and Bivens, NJ and McGrath, K and Mason, CE and Tighe, SW}, title = {Microbiome and metagenomic analysis of Lake Hillier Australia reveals pigment-rich polyextremophiles and wide-ranging metabolic adaptations.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {60}, pmid = {36544228}, issn = {2524-6372}, abstract = {Lake Hillier is a hypersaline lake known for its distinctive bright pink color. The cause of this phenomenon in other hypersaline sites has been attributed to halophiles, Dunaliella, and Salinibacter, however, a systematic analysis of the microbial communities, their functional features, and the prevalence of pigment-producing-metabolisms has not been previously studied. Through metagenomic sequencing and culture-based approaches, our results evidence that Lake Hillier is composed of a diverse set of microorganisms including archaea, bacteria, algae, and viruses. Our data indicate that the microbiome in Lake Hillier is composed of multiple pigment-producer microbes, including Dunaliella, Salinibacter, Halobacillus, Psychroflexus, Halorubrum, many of which are cataloged as polyextremophiles. Additionally, we estimated the diversity of metabolic pathways in the lake and determined that many of these are related to pigment production. We reconstructed complete or partial genomes for 21 discrete bacteria (N = 14) and archaea (N = 7), only 2 of which could be taxonomically annotated to previously observed species. Our findings provide the first metagenomic study to decipher the source of the pink color of Australia's Lake Hillier. The study of this pink hypersaline environment is evidence of a microbial consortium of pigment producers, a repertoire of polyextremophiles, a core microbiome and potentially novel species.}, } @article {pmid36543914, year = {2022}, author = {Chioma, OS and Mallott, EK and Chapman, A and Van Amburg, JC and Wu, H and Shah-Gandhi, B and Dey, N and Kirkland, ME and Blanca Piazuelo, M and Johnson, J and Bernard, GR and Bodduluri, SR and Davison, S and Haribabu, B and Bordenstein, SR and Drake, WP}, title = {Gut microbiota modulates lung fibrosis severity following acute lung injury in mice.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1401}, pmid = {36543914}, issn = {2399-3642}, support = {P20GM125504/GM/NIGMS NIH HHS/United States ; P20 GM125504/GM/NIGMS NIH HHS/United States ; T32AR059039-10/AR/NIAMS NIH HHS/United States ; K24 HL127301/HL/NHLBI NIH HHS/United States ; K12 HL 143956-4/HL/NHLBI NIH HHS/United States ; T32 AR059039/AR/NIAMS NIH HHS/United States ; R56 HL149129/HL/NHLBI NIH HHS/United States ; 1R56HL149129-01A1/HL/NHLBI NIH HHS/United States ; K12 HL143956/HL/NHLBI NIH HHS/United States ; K24 HL127301-01/HL/NHLBI NIH HHS/United States ; }, mesh = {Animals ; Humans ; Mice ; *Acute Lung Injury ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Interleukin-17 ; Mice, Inbred C57BL ; *Pulmonary Fibrosis/metabolism/pathology ; Fibroblasts/metabolism/microbiology ; }, abstract = {Independent studies demonstrate the significance of gut microbiota on the pathogenesis of chronic lung diseases; yet little is known regarding the role of the gut microbiota in lung fibrosis progression. Here we show, using the bleomycin murine model to quantify lung fibrosis in C57BL/6 J mice housed in germ-free, animal biosafety level 1 (ABSL-1), or animal biosafety level 2 (ABSL-2) environments, that germ-free mice are protected from lung fibrosis, while ABSL-1 and ABSL-2 mice develop mild and severe lung fibrosis, respectively. Metagenomic analysis reveals no notable distinctions between ABSL-1 and ABSL-2 lung microbiota, whereas greater microbial diversity, with increased Bifidobacterium and Lactobacilli, is present in ABSL-1 compared to ABSL-2 gut microbiota. Flow cytometric analysis reveals enhanced IL-6/STAT3/IL-17A signaling in pulmonary CD4 + T cells of ABSL-2 mice. Fecal transplantation of ABSL-2 stool into germ-free mice recapitulated more severe fibrosis than transplantation of ABSL-1 stool. Lactobacilli supernatant reduces collagen 1 A production in IL-17A- and TGFβ1-stimulated human lung fibroblasts. These findings support a functional role of the gut microbiota in augmenting lung fibrosis severity.}, } @article {pmid36543896, year = {2022}, author = {Tramice, A and Paris, D and Manca, A and Guevara Agudelo, FA and Petrosino, S and Siracusa, L and Carbone, M and Melck, D and Raymond, F and Piscitelli, F}, title = {Analysis of the oral microbiome during hormonal cycle and its alterations in menopausal women: the "AMICA" project.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {22086}, pmid = {36543896}, issn = {2045-2322}, mesh = {Female ; Humans ; *Luteinizing Hormone ; Follicle Stimulating Hormone ; Menopause ; Menstrual Cycle ; *Microbiota ; }, abstract = {The maintenance of human health is dependent on a symbiotic relationship between humans and associated bacteria. The diversity and abundance of each habitat's signature microbes vary widely among body areas and among them the oral microbiome plays a key role. Significant changes in the oral cavity, predominantly at salivary and periodontal level, have been associated with changes in estrogen levels. However, whether the oral microbiome is affected by hormonal level alterations is understudied. Hence the main objective pursued by AMICA project was to characterize the oral microbiome (saliva) in healthy women through: profiling studies using "omics" technologies (NMR-based metabolomics, targeted lipidomics by LC-MS, metagenomics by NGS); SinglePlex ELISA assays; glycosidase activity analyses and bioinformatic analysis. For this purpose, thirty-nine medically healthy women aged 26-77 years (19 with menstrual cycle and 20 in menopause) were recruited. Participants completed questionnaires assessing detailed medical and medication history and demographic characteristics. Plasmatic and salivary levels of sexual hormones were assessed (FSH, estradiol, LH and progesteron) at day 3 and 14 for women with menstrual cycle and only once for women in menopause. Salivary microbiome composition was assessed through meta-taxonomic 16S sequencing and overall, the salivary microbiome of most women remained relatively stable throughout the menstrual cycle and in menopause. Targeted lipidomics and untargeted metabolomics profiling were assessed through the use of LC-MS and NMR spectroscopy technologies, respectively and significant changes in terms of metabolites were identified in saliva of post-menopausal women in comparison to cycle. Moreover, glycosyl hydrolase activities were screened and showed that the β-D-hexosaminidase activity was the most present among those analyzed. Although this study has not identified significant alterations in the composition of the oral microbiome, multiomics analysis have revealed a strong correlation between 2-AG and α-mannosidase. In conclusion, the use of a multidisciplinary approach to investigate the oral microbiome of healthy women provided some indication about microbiome-derived predictive biomarkers that could be used in the future for developing new strategies to help to re-establish the correct hormonal balance in post-menopausal women.}, } @article {pmid36543238, year = {2023}, author = {Imai, R and Rongduo, W and Kaixin, L and Borjigin, S and Matsumura, H and Masuda, T and Ozawa, T and Oba, M and Makino, S and Nagai, M and Mizutani, T}, title = {Novel recombinant porcine enterovirus G viruses lacking structural proteins are maintained in pig farms in Japan.}, journal = {The Journal of veterinary medical science}, volume = {85}, number = {2}, pages = {252-265}, pmid = {36543238}, issn = {1347-7439}, mesh = {Swine ; Animals ; Female ; *Enteroviruses, Porcine/genetics ; Farms ; *Enterovirus Infections/veterinary ; Japan ; Recombination, Genetic ; Genome, Viral ; Phylogeny ; *Swine Diseases ; }, abstract = {Type 1 recombinant enterovirus G (EV-G), which carries the papain-like cysteine protease (PLCP) gene of torovirus between its 2C/3A regions, and type 2 recombinant EV-G, which carries the torovirus PLCP gene with its flanking regions having non-EV-G sequences in place of the viral structural genes, have been detected in pig farms in several countries. In a previous study, we collected 222 fecal samples from 77 pig farms from 2104 to 2016 and detected one type 2 recombinant EV-G genome by metagenomics sequencing. In this study, we reanalyzed the metagenomic data and detected 11 type 2 recombinant EV-G genomes. In addition, we discovered new type 2 recombinant EV-G genomes of the two strains from two pig farms samples in 2018 and 2019. Thus, we identified the genomes of 13 novel type 2 recombinant EV-Gs isolated from several pig farms in Japan. Type 2 recombinant EV-G has previously been detected only in neonatal piglets. The present findings suggest that type 2 recombinant EV-G replicates in weaning piglets and sows. The detection of type 1 recombinant EV-Gs and type 2 recombinant EV-Gs at 3-year and 2-year intervals, respectively, from the same pig farm suggests that the viruses were persistently infecting or circulating in these farms.}, } @article {pmid36542659, year = {2022}, author = {Liu, Z and Li, L and Xu, W and Yuan, Y and Liang, X and Zhang, L and Wei, Z and Sui, L and Zhao, Y and Cui, Y and Yin, Q and Li, D and Li, Q and Hou, Z and Wei, F and Liu, Q and Wang, Z}, title = {Extensive diversity of RNA viruses in ticks revealed by metagenomics in northeastern China.}, journal = {PLoS neglected tropical diseases}, volume = {16}, number = {12}, pages = {e0011017}, pmid = {36542659}, issn = {1935-2735}, mesh = {Animals ; Humans ; *Ticks ; Metagenomics ; *RNA Viruses/genetics ; *Viruses/genetics ; *Rhabdoviridae ; China ; Phylogeny ; }, abstract = {BACKGROUND: Ticks act as important vectors of infectious agents, and several emerging tick-borne viruses have recently been identified to be associated with human diseases in northeastern China. However, little is known about the tick virome in northeastern China.

METHODS: Ticks collected from April 2020 to July 2021 were pooled for metagenomic analysis to investigate the virome diversity in northeastern China.

RESULTS: In total, 22 RNA viruses were identified, including four each in the Nairoviridae and Phenuiviridae families, three each in the Flaviviridae, Rhabdoviridae, and Solemoviridae families, two in the Chuviridae family, and one each in the Partitiviridae, Tombusviridae families and an unclassified virus. Of these, eight viruses were of novel species, belonging to the Nairoviridae (Ji'an nairovirus and Yichun nairovirus), Phenuiviridae (Mudanjiang phlebovirus), Rhabdoviridae (Tahe rhabdovirus 1-3), Chuviridae (Yichun mivirus), and Tombusviridae (Yichun tombus-like virus) families, and five members were established human pathogens, including Alongshan virus, tick-borne encephalitis virus, Songling virus, Beiji nairovirus, and Nuomin virus. I. persulcatus ticks had significant higher number of viral species than H. japonica, H. concinna, and D. silvarum ticks. Significant differences in tick viromes were observed among Daxing'an, Xiaoxing'an and Changbai mountains.

CONCLUSIONS: These findings showed an extensive diversity of RNA viruses in ticks in northeastern China, revealing potential public health threats from the emerging tick-borne viruses. Further studies are needed to explain the natural circulation and pathogenicity of these viruses.}, } @article {pmid36541755, year = {2023}, author = {Salamzade, R and Swaney, MH and Kalan, LR}, title = {Comparative Genomic and Metagenomic Investigations of the Corynebacterium tuberculostearicum Species Complex Reveals Potential Mechanisms Underlying Associations To Skin Health and Disease.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0357822}, pmid = {36541755}, issn = {2165-0497}, support = {R35 GM137828/GM/NIGMS NIH HHS/United States ; U19 AI142720/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Dermatitis, Atopic ; Corynebacterium/genetics ; Skin ; Genomics ; }, abstract = {Corynebacterium are a diverse genus and dominant member of the human skin microbiome. Recently, we reported that the most prevalent Corynebacterium species found on skin, including Corynebacterium tuberculostearicum and Corynebacterium kefirresidentii, comprise a narrow species complex despite the diversity of the genus. Here, we apply high-resolution phylogenomics and comparative genomics to describe the structure of the C. tuberculostearicum species complex and highlight genetic traits which are enriched or depleted in it relative to other Corynebacterium. Through metagenomic investigations, we also find that individual species within the complex can associate with specific body sites. Finally, we discover that one species from the complex, C. kefirresidentii, increases in relative abundance during atopic dermatitis flares, and show that most genomes of this species encode a colocalized set of putative virulence genes. IMPORTANCE Corynebacterium are commonly found bacteria on the human skin. In this study, we perform comparative genomics to gain insight into genetic traits which differentiate a phylogenetically related group of Corynebacterium, the Corynebacterium tuberculostearicum species complex, that includes the most prevalent species from the genus in skin microbiomes. After resolving the presence of distinct species within the complex, we applied metagenomic analysis to uncover biogeographic associations of individual species within the complex with specific body sites and discovered that one species, commonly found in the nares of individuals, increases in abundance across multiple body sites during atopic dermatitis flares.}, } @article {pmid36541613, year = {2023}, author = {Pan, Y and Fan, Q}, title = {Clostridium Symbiosum Sepsis Diagnosed Using Next-Generation Sequencing in a 2 Year Old Child: A Case Report.}, journal = {Fetal and pediatric pathology}, volume = {42}, number = {3}, pages = {518-521}, doi = {10.1080/15513815.2022.2158696}, pmid = {36541613}, issn = {1551-3823}, mesh = {Male ; Infant, Newborn ; Infant ; Humans ; Child, Preschool ; *Clostridium symbiosum ; Anti-Bacterial Agents/therapeutic use ; *Sepsis/diagnosis/genetics/drug therapy ; Meropenem/therapeutic use ; Sulbactam/therapeutic use ; High-Throughput Nucleotide Sequencing ; }, abstract = {Background: Sepsis is a severe illness that can affect preterm, term, and young infants, and is often associated with negative cultures.Case report: A 2-year-old boy, with a previous partial colectomy after birth, presented with abdominal complaints and clinical sepsis. We empirically treated with meropenem and linezolid. Blood cultures were sterile, and fecal cultures demonstrated no pathogenes. Metagenomic next-generation sequencing identified Clostridium symbiosum from blood sample. The result supported the continued use of the antibiotic regimen. After 1 week, CRP and PCT returned to normal and subsequent de-escalation therapy (cefotaxime sodium sulbactam and metronidazole) was used for anaerobic bacteria. Conclusions: mNGS identified an anaerobic agent responsible for sepsis. From the published sensitivities, the organism was sensitive to the original empiric antibiotic therapy.}, } @article {pmid36541064, year = {2023}, author = {Zhan, W and Liu, Q and Yang, C and Zhao, Z and Yang, L and Wang, Y and Feng, J}, title = {Evaluation of metagenomic next-generation sequencing diagnosis for invasive pulmonary aspergillosis in immunocompromised and immunocompetent patients.}, journal = {Mycoses}, volume = {66}, number = {4}, pages = {331-337}, doi = {10.1111/myc.13557}, pmid = {36541064}, issn = {1439-0507}, support = {//National Major Science and Technology Projects of China/ ; //National Natural Science Foundation of China (82170097 81970083, 81270144, 81570084, and 30800507 to JF)/ ; //the National Key Technology R D Program, China/ ; //Tianjin Key Medical Discipline (Specialty) Construction Project/ ; }, mesh = {Humans ; *Invasive Pulmonary Aspergillosis/diagnosis ; Retrospective Studies ; Aspergillus/genetics ; Bronchoalveolar Lavage Fluid ; High-Throughput Nucleotide Sequencing ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Invasive pulmonary aspergillosis (IPA) can occur in both immunocompromised and non-immunocompromised hosts, and early diagnosis of IPA is difficult. Metagenomic next-generation sequencing (mNGS) is a novel non-migratory pathogen detection method; however, utilising this method for IPA diagnosis is challenging due to the current lack of a unified clinical interpretation standard following Aspergillus detection using mNGS.

OBJECTIVES: To investigate the accuracy of IPA diagnosis by positive bronchoalveolar lavage fluid (BALF) mNGS results in immunocompromised and immunocompetent patients.

METHODS: We retrospectively included patients with confirmed pulmonary infections having a BALF mNGS result of Aspergillus reads ≥1. We compared the accuracy of using mNGS for IPA diagnosis in patients with different immune statuses based on the revised EORTC/MSG criteria.

RESULTS: Overall, 62 mNGS Aspergillus-positive patients were divided into two groups: with (41) and without IPA (21). In univariate logistic regression analysis, immunocompromised function, fever, halo sign on CT image, and multiple masses or nodules were associated with mNGS Aspergillus-positive IPA diagnosis. In multivariate logistic regression analysis, immunocompromised function (OR = 6.68, 95% CI: 1.73-25.87, p = .006) and a halo sign (OR = 7.993, 95% CI: 2.07-30.40, p = .003) were independent risk factors. The concordance rate of IPA diagnosis was significantly higher in immunocompromised patients [82.1% (23/28)] than in non-immunocompromised patients [52.9% (18/34); p = .016].

CONCLUSIONS: For immunocompromised patients, a combination of mNGS testing and lung CT imaging can be used for IPA diagnosis. However, caution is required in IPA diagnosis based on positive mNGS results in non-immunocompromised patients.}, } @article {pmid36539569, year = {2023}, author = {Shi, F and Liu, G and Lin, Y and Guo, CL and Han, J and Chu, ESH and Shi, C and Li, Y and Zhang, H and Hu, C and Liu, R and He, S and Guo, G and Chen, Y and Zhang, X and Coker, OO and Wong, SH and Yu, J and She, J}, title = {Altered gut microbiome composition by appendectomy contributes to colorectal cancer.}, journal = {Oncogene}, volume = {42}, number = {7}, pages = {530-540}, pmid = {36539569}, issn = {1476-5594}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome/genetics ; Dysbiosis/microbiology ; Appendectomy/adverse effects ; Longitudinal Studies ; *Colorectal Neoplasms/genetics/microbiology ; }, abstract = {Appendectomy impacts the homeostasis of gut microbiome in patients. We aimed to study the role of appendectomy in colorectal cancer (CRC) risk through causing gut microbial dysbiosis. Population-based longitudinal study (cohort 1, n = 129,155) showed a 73.0% increase in CRC risk among appendectomy cases throughout 20 years follow-up (Adjusted sub-distribution hazard ratio (SHR) 1.73, 95% CI 1.49-2.01, P < 0.001). Shotgun metagenomic sequencing was performed on fecal samples from cohort 2 (n = 314). Gut microbial dysbiosis in appendectomy subjects was observed with significant enrichment of 7 CRC-promoting bacteria (Bacteroides vulgatus, Bacteroides fragilis, Veillonella dispar, Prevotella ruminicola, Prevotella fucsa, Prevotella dentalis, Prevotella denticola) and depletion of 5 beneficial commensals (Blautia sp YL58, Enterococcus hirae, Lachnospiraceae bacterium Choco86, Collinsella aerofaciens, Blautia sp SC05B48). Microbial network analysis showed increased correlation strengths among enriched bacteria and their enriched oncogenic pathways in appendectomy subjects compared to controls. Of which, B. fragilis was the centrality in the network of the enriched bacteria. We further confirmed that appendectomy promoted colorectal tumorigenesis in mice by causing gut microbial dysbiosis and impaired intestinal barrier function. Collectively, this study revealed appendectomy-induced microbial dysbiosis characterized by enriched CRC-promoting bacteria and depleted beneficial commensals, signifying that the gut microbiome may play a crucial role in CRC development induced by appendectomy.}, } @article {pmid36539432, year = {2022}, author = {Zhou, J and Zhang, Q and Zhao, Y and Zou, Y and Chen, M and Zhou, S and Wang, Z}, title = {The relationship of Megamonas species with nonalcoholic fatty liver disease in children and adolescents revealed by metagenomics of gut microbiota.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {22001}, pmid = {36539432}, issn = {2045-2322}, mesh = {Humans ; Adolescent ; Child ; *Non-alcoholic Fatty Liver Disease/pathology ; *Gastrointestinal Microbiome/genetics ; Firmicutes ; Liver/metabolism ; }, abstract = {Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disease in children and adolescents. The gut microbiota plays an important role in the pathophysiology of NAFLD through the gut-liver axis. Therefore, we aimed to investigate the genus and species of gut microbiota and their functions in children and adolescents with NAFLD. From May 2017 to July 2018, a total of 58 children and adolescents, including 27 abnormal weight (AW) (obese) NAFLD patients, 16 AW non-NAFLD children, and 15 healthy children, were enrolled in this study at Shenzhen Children's Hospital. All of them underwent magnetic resonance spectroscopy (MRS) to quantify the liver fat fraction. Stool samples were collected and analysed with metagenomics. According to body mass index (BMI) and MRS proton density fat fraction (MRS-PDFF), we divided the participants into BMI groups, including the AW group (n = 43) and the Lean group (n = 15); MRS groups, including the NAFLD group (n = 27) and the Control group (n = 31); and BMI-MRS 3 groups, including NAFLD_AW (AW children with NAFLD) (n = 27), Ctrl_AW (n = 16) (AW children without NAFLD) and Ctrl_Lean (n = 15). There was no difference in sex or age among those groups (p > 0.05). In the BMI groups, at the genus level, Dialister, Akkermansia, Odoribacter, and Alistipes exhibited a significant decrease in AW children compared with the Lean group. At the species level, Megamonas hypermegale was increased in the AW group, while Akkermansia muciniphila, Dialister invisus, Alistipes putredinis, Bacteroides massiliensis, Odoribacter splanchnicus, and Bacteroides thetaiotaomicron were decreased in AW children, compared to the Lean group. Compared with the Control group, the genus Megamonas, the species of Megamonas hypermegale and Megamonas rupellensis, increased in the NAFLD group. Furthermore, the genus Megamonas was enriched in the NAFLD_AW group, while Odoribacter, Alistipes, Dialister, and Akkermansia were depleted compared with the Ctrl_Lean or Ctrl_AW group at the genus level. Megamonas hypermegale and Megamonas rupellensis exhibited a significant increase in NAFLD_AW children compared with the Ctrl_Lean or Ctrl_AW group at the species level. Compared with healthy children, the pathways of P461-PWY contributed by the genus Megamonas were significantly increased in NAFLD_AW. We found that compared to healthy children, the genus Megamonas was enriched, while Megamonas hypermegale and Megamonas rupellensis were enriched at the species level in children and adolescents with NAFLD. This indicates that the NAFLD status and/or diet associated with NAFLD patients might lead to the enrichment of the genus Megamonas or Megamonas species.}, } @article {pmid36539168, year = {2023}, author = {Huang, MY and Lo, CY and Lai, CY and Yu, JD and Lee, PT}, title = {Dietary supplementation of synbiotic Leuconostoc mesenteroide B4 and dextran improves immune regulation and disease resistance of Penaeus vannamei against Vibrio parahaemolyticus.}, journal = {Fish & shellfish immunology}, volume = {132}, number = {}, pages = {108498}, doi = {10.1016/j.fsi.2022.108498}, pmid = {36539168}, issn = {1095-9947}, mesh = {Animals ; Disease Resistance ; *Synbiotics ; *Penaeidae ; *Vibrio parahaemolyticus/physiology ; Dextrans/pharmacology ; *Leuconostoc mesenteroides ; Immunity, Innate/genetics ; }, abstract = {White shrimp (Penaeus vannamei) is an important culture species in Taiwan but often encounters disease infection by Vibrio parahaemolyticus that cause acute hepatopancreatic necrosis disease (AHPND). This study investigates the effects of dietary supplementation of Leuconostoc mesenteroide B4 and its fermentate (dextran) on the immune response, intestinal morphology, disease resistance, and immune-related gene expression in white shrimp. In comparison to the control group, the shrimp fed with a diet containing B4+dextran (10[7] CFU B4/g feed and 0.05% dextran) for 14, 28, 42 and 56 days had a significantly higher feed efficiency, weight gain and specific growth rate. A significantly higher villus height in the intestine and higher survival rate after challenging with V. parahaemolyticus was recorded for the B4+dextran group. Flow cytometry analysis demonstrated that the group that had ingested B4+dextran had a higher total hemocyte count and a higher proportion of semi-granulocytes, but a lower percentage of granulocytes compared to the control group. The shotgun metagenomic results in the midgut revealed that Leuco. mesenteroides was barely found in the midgut of the shrimp, suggesting that this microbe and its transient presence in the midgut is not the direct mechanism underlying the improved shrimp growth in the treated sample. Instead, dextran, a key ingredient in the B4 fermentate, on the dynamic of the microbial populations in shrimp, possibly promoting the diversity of gut microbes, especially the beneficial microbes, and thereby rendering protection against AHPND. In terms of comparing the gene expression between the control and synbiotic groups, pre- and post-bacterial challenge, a higher expression level of immune genes was mostly found in the B4+dextran group after challenging it with V. parahaemolyticus (group B4+dextran-VP) in the hepatopancreas and hemocyte. In contrast, the transcript level of immune-related genes was found to be higher in the B4+dextran group than other combinations in the midgut. Taken together, this study found that dietary addition of synbiotic Leuco. mesenteroides B4 and dextran can improve the growth performance, intestinal morphology and microbiome, regulation of immune genes and disease resistance against V. parahaemolyticus infection in white shrimp.}, } @article {pmid36538963, year = {2023}, author = {Luan, YN and Yin, Y and Xu, Y and Zhang, F and Wang, X and Zhao, F and Xiao, Y and Liu, C}, title = {Simultaneous nitrification and denitrification in a novel rotating self-aerated biofilm reactor for decentralized wastewater treatment.}, journal = {Bioresource technology}, volume = {369}, number = {}, pages = {128513}, doi = {10.1016/j.biortech.2022.128513}, pmid = {36538963}, issn = {1873-2976}, mesh = {*Nitrification ; *Denitrification ; Bioreactors/microbiology ; Biofilms ; Nitrogen/metabolism ; Waste Disposal, Fluid ; }, abstract = {Decentralized wastewater pollution in rural areas has become a serious problem for the rural environment. In this study, a novel rotating self-aerated biofilm reactor was developed for decentralized wastewater treatment without any aeration equipment. After the long-term operation of 110 days, the removal efficiency reached to 96.06 % (COD), 98.06 % (NH4[+]-N), and 62.58 % (TN) in the last phase. Under high dissolved oxygen level, the simultaneous nitrification-denitrification (SND) maintained at a stable ratio of 62.53 % and the denitrification rates reached over 28.37 mg/L/h. With the organic loading rate increased, key nitrogen functional bacterial communities such as anoxic denitrifiers (Thiothrix, Flavobacterium, Pseudoxanthomonas, Aquimonas and Azoarcus) and aerobic denitrifiers (Hydrogenophaga, Zoogloea and Terrimonas) increased obviously. Overall, microbial analysis and nitrogen metabolism pathway indicated that an integration of SND process was achieved in this single reactor by the combined action of nitrification, denitrification and comammox without any aeration equipment.}, } @article {pmid36538841, year = {2023}, author = {Dueholm, MKD and Besteman, M and Zeuner, EJ and Riisgaard-Jensen, M and Nielsen, ME and Vestergaard, SZ and Heidelbach, S and Bekker, NS and Nielsen, PH}, title = {Genetic potential for exopolysaccharide synthesis in activated sludge bacteria uncovered by genome-resolved metagenomics.}, journal = {Water research}, volume = {229}, number = {}, pages = {119485}, doi = {10.1016/j.watres.2022.119485}, pmid = {36538841}, issn = {1879-2448}, mesh = {*Sewage/chemistry ; *Metagenomics ; Bacteria/genetics ; Proteins ; Cellulose ; }, abstract = {A good floc formation of activated sludge (AS) is crucial for solid-liquid separation and production of clean effluent during wastewater treatment. Floc formation is partly controlled by self-produced extracellular polymeric substances (EPS) such as exopolysaccharides, proteins, and nucleic acids. Little is known about the composition, structure, and function of EPS in AS and which bacteria produce them. To address this knowledge gap for the exopolysaccharides, we took advantage of 1083 high-quality metagenome-assembled genomes (MAGs) obtained from 23 Danish wastewater treatment plants. We investigated the genomic potential for exopolysaccharide biosynthesis in bacterial species typical in AS systems based on genome mining and gene synteny analyses. Putative gene clusters associated with the biosynthesis of alginate, cellulose, curdlan, diutan, hyaluronic acids, Pel, poly-β-1,6-N-acetyl-d-glucosamine (PNAG), Psl, S88 capsular polysaccharide, salecan, succinoglycan, and xanthan were identified and linked to individual MAGs, providing a comprehensive overview of the genome-resolved potential for these exopolysaccharides in AS bacteria. The approach and results provide a starting point for a more comprehensive understanding of EPS composition in wastewater treatment systems, which may facilitate a more refined regulation of the activated sludge process for improved stability.}, } @article {pmid36538527, year = {2023}, author = {Hill, AA and Kim, M and Zegarra-Ruiz, DF and Chang, LC and Norwood, K and Assié, A and Wu, WH and Renfroe, MC and Song, HW and Major, AM and Samuel, BS and Hyser, JM and Longman, RS and Diehl, GE}, title = {Acute high-fat diet impairs macrophage-supported intestinal damage resolution.}, journal = {JCI insight}, volume = {8}, number = {3}, pages = {}, pmid = {36538527}, issn = {2379-3708}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; S10 RR024574/RR/NCRR NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; T32 AI053831/AI/NIAID NIH HHS/United States ; P30 AI036211/AI/NIAID NIH HHS/United States ; R01 AI125264/AI/NIAID NIH HHS/United States ; K01 DK121934/DK/NIDDK NIH HHS/United States ; }, mesh = {Mice ; Animals ; *Interleukin-10 ; *Diet, High-Fat ; Intestines ; Macrophages/physiology ; Lipids ; }, abstract = {Chronic exposure to high-fat diets (HFD) worsens intestinal disease pathology, but acute effects of HFD in tissue damage remain unclear. Here, we used short-term HFD feeding in a model of intestinal injury and found sustained damage with increased cecal dead neutrophil accumulation, along with dietary lipid accumulation. Neutrophil depletion rescued enhanced pathology. Macrophages from HFD-treated mice showed reduced capacity to engulf dead neutrophils. Macrophage clearance of dead neutrophils activates critical barrier repair and antiinflammatory pathways, including IL-10, which was lost after acute HFD feeding and intestinal injury. IL-10 overexpression restored intestinal repair after HFD feeding and intestinal injury. Macrophage exposure to lipids from the HFD prevented tethering and uptake of apoptotic cells and Il10 induction. Milk fat globule-EGF factor 8 (MFGE8) is a bridging molecule that facilitates macrophage uptake of dead cells. MFGE8 also facilitates lipid uptake, and we demonstrate that dietary lipids interfere with MFGE8-mediated macrophage apoptotic neutrophil uptake and subsequent Il10 production. Our findings demonstrate that HFD promotes intestinal pathology by interfering with macrophage clearance of dead neutrophils, leading to unresolved tissue damage.}, } @article {pmid36538480, year = {2022}, author = {Lundberg, DS and de Pedro Jové, R and Pramoj Na Ayutthaya, P and Karasov, TL and Shalev, O and Poersch, K and Ding, W and Bollmann-Giolai, A and Bezrukov, I and Weigel, D}, title = {Contrasting patterns of microbial dominance in the Arabidopsis thaliana phyllosphere.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {52}, pages = {e2211881119}, pmid = {36538480}, issn = {1091-6490}, mesh = {*Arabidopsis/genetics/microbiology ; Bacteria ; Plants ; Pseudomonas/genetics ; }, abstract = {Sphingomonas is one of the most abundant bacterial genera in the phyllosphere of wild Arabidopsis thaliana, but relative to Pseudomonas, the ecology of Sphingomonas and its interaction with plants is poorly described. We analyzed the genomic features of over 400 Sphingomonas isolates collected from local A. thaliana populations, which revealed much higher intergenomic diversity than for the considerably more uniform Pseudomonas isolates found in the same host populations. Variation in Sphingomonas plasmid complements and additional genomic features suggest high adaptability of this genus, and the widespread presence of protein secretion systems hints at frequent biotic interactions. While some of the isolates showed plant-protective phenotypes in lab tests, this was a rare trait. To begin to understand the extent of strain sharing across alternate hosts, we employed amplicon sequencing and a bulk-culturing metagenomics approach on both A. thaliana and neighboring plants. Our data reveal that both Sphingomonas and Pseudomonas thrive on other diverse plant hosts, but that Sphingomonas is a poor competitor in dying or dead leaves.}, } @article {pmid36538014, year = {2023}, author = {Jia, S and Gao, X and Zhang, Y and Shi, P and Wang, C and Zhou, Q and Ye, L and Zhang, XX}, title = {Tertiary Wastewater Treatment Processes Can Be a Double-Edged Sword for Water Quality Improvement in View of Mitigating Antimicrobial Resistance and Pathogenicity.}, journal = {Environmental science & technology}, volume = {57}, number = {1}, pages = {509-519}, doi = {10.1021/acs.est.2c06168}, pmid = {36538014}, issn = {1520-5851}, mesh = {*Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Virulence ; Quality Improvement ; *Water Purification ; }, abstract = {Despite the high removal efficiency for chemical pollutants by tertiary wastewater treatment processes (TWTPs), there is no definite conclusion in terms of microbial risk mitigation yet. This study utilized metagenomic approaches to reveal the alterations of antibiotic resistance genes (ARGs), virulence factor genes (VFGs), their co-occurrence, and potential hosts during multiple TWTPs. Results showed that the TWTPs reduced chemical pollutants in wastewater, but the denitrifying biofilter (DB) significantly increased the absolute abundances of selected antibiotic-resistant bacteria and ARGs, and simultaneously elevated the relative abundances of ARGs and VFGs through the enrichment of multidrug resistance and offensive genes, respectively. Moreover, the co-occurrence of ARGs and VFGs (e.g., bacA-tapW, mexF-adeG) was only identified after the DB treatment and all carried by Pseudomonas. Then, the ultraviolet and constructed wetland treatment showed good complementarity for microbial risk reduction through mitigating antibiotic resistance and pathogenicity. Network and binning analyses showed that the shift of key operational taxonomic units affiliating to Pseudomonas and Acinetobacter may contribute to the dynamic changes of ARGs and VFGs during the TWTPs. Overall, this study sheds new light on how the TWTPs affect the antibiotic resistome and VFG profiles and what TWTPs should be selected for microbial risk mitigation.}, } @article {pmid36537058, year = {2022}, author = {Ul-Haq, A and Seo, H and Jo, S and Park, H and Kim, S and Lee, Y and Lee, S and Jeong, JH and Song, HY}, title = {Characterization of Fecal Microbiomes of Osteoporotic Patients in Korea.}, journal = {Polish journal of microbiology}, volume = {71}, number = {4}, pages = {601-613}, pmid = {36537058}, issn = {2544-4646}, mesh = {Humans ; Bacteria ; *Microbiota ; *Gastrointestinal Microbiome ; Feces/chemistry ; *Osteoporosis ; RNA, Ribosomal, 16S/genetics ; Biomarkers ; Republic of Korea ; }, abstract = {An imbalanced gut microbiome has been linked to a higher risk of many bone-related diseases. The objective of this study was to discover biomarkers of osteoporosis (OP). So, we collected 76 stool samples (60 human controls and 16 OP patients), extracted DNA, and performed 16S ribosomal ribonucleic acid (rRNA) gene-based amplicon sequencing. Among the taxa with an average taxonomic composition greater than 1%, only the Lachnospira genus showed a significant difference between the two groups. The Linear Discriminant Effect Size analysis and qPCR experiments indicated the Lachnospira genus as a potential biomarker of OP. Moreover, a total of 11 metabolic pathways varied between the two groups. Our study concludes that the genus Lachnospira is potentially crucial for diagnosing and treating osteoporosis. The findings of this study might help researchers better understand OP from a microbiome perspective. This research might develop more effective diagnostic and treatment methods for OP in the future.}, } @article {pmid36536978, year = {2022}, author = {Li, ZY and Xu, KY and Jin, W}, title = {Nanopore techniques as a potent tool in the diagnosis and treatment of endophthalmitis: a literature review.}, journal = {International journal of ophthalmology}, volume = {15}, number = {12}, pages = {2009-2016}, pmid = {36536978}, issn = {2222-3959}, abstract = {Endophthalmitis is a serious ophthalmic disease characterized by changes in the eye's posterior segment, such as hypopyon and intraocular inflammation, vitritis being a hallmark. Infection-caused endophthalmitis can lead to irreversible vision loss, accompanied by eye pain or eye distention, and in the most severe cases the removal of the eyeball. Microorganisms such as bacteria, fungi, viruses, and parasites typically account for the disease and the entry pathways of the microbial can be divided into either endogenous or exogenous approaches, according to the origin of the etiological agents. Exogenous endophthalmitis can be derived from various occasions (such as post-operative complications or trauma) while endogenous endophthalmitis results from the bloodstream which carries pathogens to the eye. This review aims to summarize the application of new technology in pathogen identification of endophthalmitis so as to prevent the disease and better guide clinical diagnosis and treatment.}, } @article {pmid36536626, year = {2022}, author = {Li, M and Hassan, F and Peng, L and Xie, H and Liang, X and Huang, J and Huang, F and Guo, Y and Yang, C}, title = {Mulberry flavonoids modulate rumen bacteria to alter fermentation kinetics in water buffalo.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e14309}, pmid = {36536626}, issn = {2167-8359}, mesh = {Animals ; Female ; Acetates/metabolism ; Bacteria ; *Buffaloes/genetics ; Fermentation ; *Morus/genetics ; Propionates/metabolism ; RNA, Ribosomal, 16S/genetics ; Rumen ; }, abstract = {Mulberry flavonoids can modulate the composition of rumen microbiota in ruminants to improve nutrient digestibility, owing to their strong biological activities. This study aimed to explore the effect of mulberry leaf flavonoids (MLF) on rumen bacteria, fermentation kinetics, and metagenomic functional profile in water buffalo. Forty buffaloes (4 ± 1 lactations) with almost same body weight (av. 600 ± 50 Kg) and days in milk (90 ± 20 d) were randomly allocated to four treatments having different levels of MLF: 0 g/d (control), 15 g/d (MLF15), 30 g/d (MLF30), and 45 g/d (MLF45) supplemented in a basal diet. After 35 days of supplementation, rumen contents were collected to determine rumen fermentation parameters. The 16S rRNA gene sequencing was performed to elucidate rumen bacteria composition. The obtained taxonomic data were analyzed to explore the rumen bacteriome and predict the associated gene functions and metabolic pathways. Results demonstrated a linear increase (p < 0.01) in rumen acetate, propionate, and total VFAs in the MLF45 group as compared to control. No effect of treatment was observed on rumen pH and butyrate contents. Acetate to propionate ratio in the MLF45 group linearly and quadratically decreased (p = 0.001) as compared to MLF15 and control groups. Similarly, MLF45 linearly increased (p < 0.05) the microbial protein (MCP) and NH3-N as compared to other treatments. Treatment adversely affected (p < 0.01) almost all alpha diversity parameters of rumen bacteria except Simpson index. MLF promoted the abundance of Proteobacteria while reducing the relative abundances of Actinobacteria, Acidobacteria, Chloroflexi, and Patescibacteria. The MLF supplementation tended to substantially reduce (0.05 < p < 0.1) the abundance of Actinobacteria, and Patescibacteria while completely eliminating Acidobacteria (p = 0.029), Chloroflexi (p = 0.059), and Gemmatimonadetes (p = 0.03) indicating the negative effect of flavonoids on the growth of these bacteria. However, MLF45 tended to substantially increase (p = 0.07) the abundance (~21.5%) of Acetobacter. The MLF treatment exhibited negative effect on five genera by significantly reducing (Sphingomonas) or eliminating (Arthobactor, unclassified_c__Actinobacteria, norank_c__Subgroup_6, norank_o__Saccharimonadales, and Nocardioides) them from the rumen microbiota. Pearson correlation analysis revealed 3, 5 and 23 positive correlations of rumen bacteria with milk yield, rumen fermentation and serum antioxidant parameters, respectively. A positive correlation of MCP was observed with three bacterial genera (Acetobacter, Enterobacter, and Klebsiella). The relative abundance of Pseudobutyrivibrio and Empedobacter also showed a positive correlation with the ruminal acetate and propionate. The present study indicated 45 g/d as an appropriate dose of MLF which modulated rumen bacteria and its functional profile in water buffalo.}, } @article {pmid36536476, year = {2022}, author = {Deng, J and Leijten, E and Nordkamp, MO and Zheng, G and Pouw, J and Tao, W and Hartgring, S and Balak, D and Rijken, R and Huang, R and Radstake, T and Lu, C and Pandit, A}, title = {Multi-omics integration reveals a core network involved in host defence and hyperkeratinization in psoriasis.}, journal = {Clinical and translational medicine}, volume = {12}, number = {12}, pages = {e976}, pmid = {36536476}, issn = {2001-1326}, mesh = {Humans ; *Multiomics ; *Psoriasis/genetics ; Skin/metabolism ; Gene Expression Profiling ; Transcriptome ; }, abstract = {OBJECTIVES: The precise pathogenesis of psoriasis remains incompletely explored. We aimed to better understand the underlying mechanisms of psoriasis, using a systems biology approach based on transcriptomics and microbiome profiling.

METHODS: We collected the skin tissue biopsies and swabs in both lesional and non-lesional skin of 13 patients with psoriasis, 15 patients with psoriatic arthritis and healthy skin from 12 patients with ankylosing spondylitis. To study the similarities and differences in the molecular profiles between these three conditions, and the associations between the host defence and microbiota composition, we performed high-throughput RNA-sequencing to quantify the gene expression profile in tissues. The metagenomic composition of 16S on local skin sites was quantified by clustering amplicon sequences and counted into operational taxonomic units. We further analysed associations between the transcriptome and microbiome profiling.

RESULTS: We found that lesional and non-lesional samples were remarkably different in terms of their transcriptome profiles. The functional annotation of differentially expressed genes showed a major enrichment in neutrophil activation. By using co-expression gene networks, we identified a gene module that was associated with local psoriasis severity at the site of biopsy. From this module, we found a 'core' set of genes that was functionally involved in neutrophil activation, epidermal cell differentiation and response to bacteria. Skin microbiome analysis revealed that the abundances of Enhydrobacter, Micrococcus and Leptotrichia were significantly correlated with the genes in core network.

CONCLUSIONS: We identified a core gene network that associated with local disease severity and microbiome composition, involved in the inflammation and hyperkeratinization in psoriatic skin.}, } @article {pmid36536283, year = {2022}, author = {Wicaksono, JA and Purwadaria, T and Yulandi, A and Tan, WA}, title = {Bacterial dynamics during the burial of starch-based bioplastic and oxo-low-density-polyethylene in compost soil.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {309}, pmid = {36536283}, issn = {1471-2180}, mesh = {Soil ; Polyethylene ; Starch ; *Composting ; *Biodegradable Plastics ; Bacteria ; }, abstract = {BACKGROUND: Plastic waste accumulation is one of the main ecological concerns in the past decades. A new generation of plastics that are easier to degrade in the environment compared to conventional plastics, such as starch-based bioplastics and oxo-biodegradable plastics, is perceived as a solution to this issue. However, the fate of these materials in the environment are unclear, and less is known about how their presence affect the microorganisms that may play a role in their biodegradation. In this study, we monitored the dynamics of bacterial community in soil upon introduction of commercial carrier bags claimed as biodegradable: cassava starch-based bioplastic and oxo-low-density polyethylene (oxo-LDPE). Each type of plastic bag was buried separately in compost soil and incubated for 30, 60, 90, and 120 days. Following incubation, soil pH and temperature as well as the weight of remaining plastics were measured. Bacterial diversity in soil attached to the surface of remaining plastics was analyzed using Illumina high-throughput sequencing of the V3-V4 region of 16SrRNA gene.

RESULTS: After 120 days, the starch-based bioplastic weight has decreased by 74%, while the oxo-LDPE remained intact with only 3% weight reduction. The bacterial composition in soil fluctuated over time with or without the introduction of either type of plastic. While major bacterial phyla remained similar for all treatment in this study, different types of plastics led to different soil bacterial community structure. None of these bacteria were abundant continuously, but rather they emerged at specific time points. The introduction of plastics into soil increased not only the population of bacteria known for their ability to directly utilize plastic component for their growth, but also the abundance of those that may interact with direct degraders. Bacterial groups that are involved in nitrogen cycling also arose throughout burial.

CONCLUSIONS: The introduction of starch-based bioplastic and oxo-LDPE led to contrasting shift in soil bacterial population overtime, which may determine their fate in the environment.}, } @article {pmid36536265, year = {2022}, author = {Rizk, SM and Magdy, M and De Leo, F and Werner, O and Rashed, MA and Ros, RM and Urzì, C}, title = {aroF and cm2: potential molecular markers for the detection of stone-inhabiting Actinobacteria on cultural heritage sites.}, journal = {Archives of microbiology}, volume = {205}, number = {1}, pages = {32}, pmid = {36536265}, issn = {1432-072X}, mesh = {*Actinobacteria ; Ecosystem ; Bacteria/genetics ; *Actinomycetales ; }, abstract = {Tangible archeological sites and stone monuments are naturally decayed and deteriorated over time, providing substances that can sustain life, although they provide a complicated ecosystem characterized by low nutrition and desiccation. Stone-inhabiting bacteria (SIB) and especially members of the phylum Actinobacteria dominate such environments, particularly the members of the family Geodermatophilaceae. We used the published data of two confirmed SIB species to mine their genomes for specific molecular markers to rapidly survey the presence of SIB in cultural heritage material prior to further analysis. The search focused on the mycosporine-like amino acids (MAAs) synthesis pathway. MAAs are intracellular compounds biosynthesized by the shikimic acid pathway to synthesize aromatic amino acids and were found related to abiotic resistance features in microorganisms. Based on genome mining, the DAHP II (aroF) and a homolog of the Chorismate mutase gene (cm2) were found mostly in Actinobacteria and few other species. After calibration on five stone-inhabiting Actinobacteria (SIAb) species using conventional PCR, newly designed primers were successfully applied to environmental DNA extracted from two Egyptian pyramidal sites using a qPCR approach. This is the first report of aroF and cm2 as qPCR markers to detect SIAb from cultural heritage material prior to proceeding with further analysis (e.g., metagenomics and meta-barcoding analyses).}, } @article {pmid36536072, year = {2023}, author = {Camargo, AP and de Souza, RSC and Jose, J and Gerhardt, IR and Dante, RA and Mukherjee, S and Huntemann, M and Kyrpides, NC and Carazzolle, MF and Arruda, P}, title = {Plant microbiomes harbor potential to promote nutrient turnover in impoverished substrates of a Brazilian biodiversity hotspot.}, journal = {The ISME journal}, volume = {17}, number = {3}, pages = {354-370}, pmid = {36536072}, issn = {1751-7370}, mesh = {*Ecosystem ; Brazil ; Soil Microbiology ; Biodiversity ; *Microbiota ; Bacteria/genetics/metabolism ; Plants/metabolism ; Soil/chemistry ; Phosphorus/metabolism ; Nitrogen/metabolism ; }, abstract = {The substrates of the Brazilian campos rupestres, a grassland ecosystem, have extremely low concentrations of phosphorus and nitrogen, imposing restrictions to plant growth. Despite that, this ecosystem harbors almost 15% of the Brazilian plant diversity, raising the question of how plants acquire nutrients in such a harsh environment. Here, we set out to uncover the taxonomic profile, the compositional and functional differences and similarities, and the nutrient turnover potential of microbial communities associated with two plant species of the campos rupestres-dominant family Velloziaceae that grow over distinct substrates (soil and rock). Using amplicon sequencing data, we show that, despite the pronounced composition differentiation, the plant-associated soil and rock communities share a core of highly efficient colonizers that tend to be highly abundant and is enriched in 21 bacterial families. Functional investigation of metagenomes and 522 metagenome-assembled genomes revealed that the microorganisms found associated to plant roots are enriched in genes involved in organic compound intake, and phosphorus and nitrogen turnover. We show that potential for phosphorus transport, mineralization, and solubilization are mostly found within bacterial families of the shared microbiome, such as Xanthobacteraceae and Bryobacteraceae. We also detected the full repertoire of nitrogen cycle-related genes and discovered a lineage of Isosphaeraceae that acquired nitrogen-fixing potential via horizontal gene transfer and might be also involved in nitrification via a metabolic handoff association with Binataceae. We highlight that plant-associated microbial populations in the campos rupestres harbor a genetic repertoire with potential to increase nutrient availability and that the microbiomes of biodiversity hotspots can reveal novel mechanisms of nutrient turnover.}, } @article {pmid36536008, year = {2022}, author = {Ibragimov, E and Pedersen, AØ and Xiao, L and Cirera, S and Fredholm, M and Karlskov-Mortensen, P}, title = {Analysis of merged transcriptomic and genomic datasets to identify genes and pathways underlying residual feed intake in growing pigs.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {21946}, pmid = {36536008}, issn = {2045-2322}, mesh = {Swine ; Animals ; *Transcriptome ; *Genome-Wide Association Study ; Genotype ; Phenotype ; Eating/genetics ; Quantitative Trait Loci ; Genomics ; Polymorphism, Single Nucleotide ; }, abstract = {Improvement of feed efficiency (FE) in pigs is an important milestone in order to reduce the economic and environmental impact of pig production. The goal of finding biomarkers for FE has persisted for decades. However, due to the complexity of the FE trait, these goals have still not been met. Here, we search for quantitative trait loci (QTL), candidate genes, and biological pathways associated with FE using both genotype and RNA-seq data. We obtained genotype and colon epithelium RNA-seq data for 375 and 96 pigs, respectively. In total, a genome-wide association study (GWAS) and differential expression (DE) analysis led to detection of three QTL on SSC9 and 17 DE-genes associated with FE. Possible intersection points between genes located in QTL and DE-genes were found on levels of transcription factor-target interaction. Moreover, cis-eQTL analysis revealed associations between genotype and expression levels of three DE-genes and three genes located in the GWAS QTLs, which may establish the connection between genotype and phenotype through DE. Finally, single nucleotide polymorphism calling using RNA-seq data for genes located in GWAS QTLs revealed 53 polymorphisms of which eleven were missense variants.}, } @article {pmid36534698, year = {2022}, author = {Griesenauer, B and Xing, Y and Fortney, KR and Gao, X and González-Beiras, C and Nelson, DE and Ren, J and Mitjà, O and Dong, Q and Spinola, SM}, title = {Two Streptococcus pyogenes emm types and several anaerobic bacterial species are associated with idiopathic cutaneous ulcers in children after community-based mass treatment with azithromycin.}, journal = {PLoS neglected tropical diseases}, volume = {16}, number = {12}, pages = {e0011009}, pmid = {36534698}, issn = {1935-2735}, support = {R01 AI027863/AI/NIAID NIH HHS/United States ; R01 AI134727/AI/NIAID NIH HHS/United States ; T32 AI007637/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Child ; Azithromycin/therapeutic use ; Ulcer/drug therapy ; Streptococcus pyogenes/genetics ; *Yaws/diagnosis ; Bacteria, Anaerobic/genetics ; Anaerobiosis ; RNA, Ribosomal, 16S/genetics ; Treponema pallidum/genetics ; *Skin Ulcer/microbiology ; *Haemophilus ducreyi/genetics ; }, abstract = {BACKGROUND: In yaws-endemic areas, two-thirds of exudative cutaneous ulcers (CU) are associated with Treponema pallidum subsp. pertenue (TP) and Haemophilus ducreyi (HD); one-third are classified as idiopathic ulcers (IU). A yaws eradication campaign on Lihir Island in Papua New Guinea utilizing mass drug administration (MDA) of azithromycin initially reduced but failed to eradicate yaws; IU rates remained constant throughout the study. Using 16S rRNA gene sequencing, we previously determined that Streptococcus pyogenes was associated with some cases of IU. Here, we applied shotgun metagenomics to the same samples we analyzed previously by 16S rRNA sequencing to verify this result, identify additional IU-associated microorganisms, and determine why S. pyogenes-associated IU might have persisted after MDA of azithromycin.

We sequenced DNA extracted from 244 CU specimens separated into four groups based upon microorganism-specific PCR results (HD+, TP+, TP+HD+, and TP-HD- or IU). S. pyogenes was enriched in IU (24.71% relative abundance [RA]) specimens compared to other ulcer sub-groups, confirming our prior results. We bioinformatically identified the emm (M protein gene) types found in the S. pyogenes IU specimens and found matches to emm156 and emm166. Only ~39% of IU specimens contained detectable S. pyogenes, suggesting that additional organisms could be associated with IU. In the sub-set of S. pyogenes-negative IU specimens, Criibacterium bergeronii, a member of the Peptostreptococcaceae, and Fusobacterium necrophorum (7.07% versus 0.00% RA and 2.18% versus 0.00% RA, respectively), were enriched compared to the S. pyogenes-positive sub-set. Although a broad range of viruses were detected in the CU specimens, none were specifically associated with IU.

CONCLUSIONS/SIGNIFICANCE: Our observations confirm the association of S. pyogenes with IU in yaws-endemic areas, and suggest that additional anaerobic bacteria, but not other microorganisms, may be associated with this syndrome. Our results should aid in the design of diagnostic tests and selective therapies for CU.}, } @article {pmid36534543, year = {2022}, author = {Öğüt, ND and Hasçelik, G and Atakan, N}, title = {Alterations of the Human Gut Microbiome in Patients With Hidradenitis Suppurativa: A Case-control Study and Review of the Literature.}, journal = {Dermatology practical & conceptual}, volume = {12}, number = {4}, pages = {e2022191}, pmid = {36534543}, issn = {2160-9381}, abstract = {INTRODUCTION: Hidradenitis suppurativa (HS) is a chronic and systemic inflammatory disease that extends beyond the skin. The role of gut microbiome (GM) alterations in the pathogenesis of inflammatory and autoimmune disorders is remarkable.

OBJECTIVES: Based on the hypothesis that dysbiosis in the GM may trigger systemic inflammation in the pathogenesis of HS, this study aimed to investigate whether the GM is altered in HS patients compared with healthy subjects.

METHODS: In the present case-control study, fecal samples from 15 patients with HS and 15 age- and sex-matched healthy individuals were collected and analyzed using 16S rRNA-based metagenomic analysis, New Generation Sequencing (NGS). The V3 and V4-hypervariable regions of the bacterial 16S rDNA gene were amplified from all samples and sequenced by the Illumina MiSeq platform. Bioinformatics analyses were performed in QIIME2.

RESULTS: Shannon alpha diversity index showed significantly reduced diversity in HS patients (P = 0.048). Bray-Curtis Dissimilarity and Jaccard Distance revealed that the gut microbial composition of HS patients was significantly distinctive from that of controls (P = 0.01 and P = 0.007, respectively). The relative abundance of unclassified Clostridiales, unclassified Firmicutes, and Fusicatenibacter in HS was significantly lower than that in controls (P = 0.005, P = 0.029, and P = 0.046, respectively).

CONCLUSIONS: This study indicated that significant alterations in the GM of HS patients could play a critical role in the pathogenesis of HS and might be a trigger for systemic inflammation. Increased understanding of the pathogenesis of HS will shed light on the new potential therapeutic targets and novel treatment options.}, } @article {pmid36534112, year = {2023}, author = {Albers, A and Spille, DC and Suero-Molina, E and Schaumburg, F and Stummer, W and Paulus, W and Thomas, C}, title = {Rapid bacterial identification from formalin-fixed paraffin-embedded neuropathology specimens using 16S rDNA nanopore sequencing.}, journal = {Neuropathology and applied neurobiology}, volume = {49}, number = {1}, pages = {e12871}, doi = {10.1111/nan.12871}, pmid = {36534112}, issn = {1365-2990}, mesh = {Humans ; DNA, Ribosomal ; Paraffin Embedding ; *Nanopore Sequencing ; Sequence Analysis, DNA ; Formaldehyde ; *Nervous System Diseases ; }, } @article {pmid36534026, year = {2022}, author = {Huang, R and Meng, X and Tao, K and Cao, M and Nie, L and Dong, Y and Lyu, Y and Wang, S and Feng, Z}, title = {Discovery and Biosynthesis of the Amodesmycins, Aromatic Polyketide-Siderophore Hybrid Conjugates.}, journal = {Organic letters}, volume = {24}, number = {51}, pages = {9408-9412}, doi = {10.1021/acs.orglett.2c03788}, pmid = {36534026}, issn = {1523-7052}, mesh = {Siderophores ; *Polyketides ; Deferoxamine ; Multigene Family ; *Streptomyces griseus ; }, abstract = {A type II polyketide synthase biosynthetic gene cluster (amd) containing three P450 genes was identified from a soil metagenomic library, and novel benz[h]isoquinoline-desferrioxamine B conjugated compound amodesmycins were isolated from Streptomyces albus J1074 harboring the amd gene cluster. Genetic evidence showed that the benz[h]isoquinoline part and desferrioxamine B part in amodesmycins were derived from the amd gene cluster and S. albus J1074, respectively, while P450 enzymes played critical roles in the conjunction of these two parts.}, } @article {pmid36533929, year = {2023}, author = {Rojas, CA and Holekamp, KE and Viladomat Jasso, M and Souza, V and Eisen, JA and Theis, KR}, title = {Taxonomic, Genomic, and Functional Variation in the Gut Microbiomes of Wild Spotted Hyenas Across 2 Decades of Study.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0096522}, pmid = {36533929}, issn = {2379-5077}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Hyaenidae/genetics ; RNA, Ribosomal, 16S/genetics ; *Carnivora/genetics ; Metagenomics ; }, abstract = {The gut microbiome provides vital functions for mammalian hosts, yet research on its variability and function across adult life spans and multiple generations is limited in large mammalian carnivores. Here, we used 16S rRNA gene and metagenomic high-throughput sequencing to profile the bacterial taxonomic composition, genomic diversity, and metabolic function of fecal samples collected from 12 wild spotted hyenas (Crocuta crocuta) residing in the Masai Mara National Reserve, Kenya, over a 23-year period spanning three generations. The metagenomic data came from four of these hyenas and spanned two 2-year periods. With these data, we determined the extent to which host factors predicted variation in the gut microbiome and identified the core microbes present in the guts of hyenas. We also investigated novel genomic diversity in the mammalian gut by reporting the first metagenome-assembled genomes (MAGs) for hyenas. We found that gut microbiome taxonomic composition varied temporally, but despite this, a core set of 14 bacterial genera were identified. The strongest predictors of the microbiome were host identity and age, suggesting that hyenas possess individualized microbiomes and that these may change with age during adulthood. The gut microbiome functional profiles of the four adult hyenas were also individual specific and were associated with prey abundance, indicating that the functions of the gut microbiome vary with host diet. We recovered 149 high-quality MAGs from the hyenas' guts; some MAGs were classified as taxa previously reported for other carnivores, but many were novel and lacked species-level matches to genomes in existing reference databases. IMPORTANCE There is a gap in knowledge regarding the genomic diversity and variation of the gut microbiome across a host's life span and across multiple generations of hosts in wild mammals. Using two types of sequencing approaches, we found that although gut microbiomes were individualized and temporally variable among hyenas, they correlated similarly to large-scale changes in the ecological conditions experienced by their hosts. We also recovered 149 high-quality MAGs from the hyena gut, greatly expanding the microbial genome repertoire known for hyenas, carnivores, and wild mammals in general. Some MAGs came from genera abundant in the gastrointestinal tracts of canid species and other carnivores, but over 80% of MAGs were novel and from species not previously represented in genome databases. Collectively, our novel body of work illustrates the importance of surveying the gut microbiome of nonmodel wild hosts, using multiple sequencing methods and computational approaches and at distinct scales of analysis.}, } @article {pmid36533926, year = {2023}, author = {Rogério, F and Baroncelli, R and Cuevas-Fernández, FB and Becerra, S and Crouch, J and Bettiol, W and Azcárate-Peril, MA and Malapi-Wight, M and Ortega, V and Betran, J and Tenuta, A and Dambolena, JS and Esker, PD and Revilla, P and Jackson-Ziems, TA and Hiltbrunner, J and Munkvold, G and Buhiniček, I and Vicente-Villardón, JL and Sukno, SA and Thon, MR}, title = {Population Genomics Provide Insights into the Global Genetic Structure of Colletotrichum graminicola, the Causal Agent of Maize Anthracnose.}, journal = {mBio}, volume = {14}, number = {1}, pages = {e0287822}, pmid = {36533926}, issn = {2150-7511}, support = {P30 DK034987/DK/NIDDK NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; }, mesh = {*Zea mays ; Metagenomics ; Ecosystem ; Base Sequence ; *Colletotrichum ; Plant Diseases ; Genetic Variation ; }, abstract = {Understanding the genetic diversity and mechanisms underlying genetic variation in pathogen populations is crucial to the development of effective control strategies. We investigated the genetic diversity and reproductive biology of Colletotrichum graminicola isolates which infect maize by sequencing the genomes of 108 isolates collected from 14 countries using restriction site-associated DNA sequencing (RAD-seq) and whole-genome sequencing (WGS). Clustering analyses based on single-nucleotide polymorphisms revealed three genetic groups delimited by continental origin, compatible with short-dispersal of the pathogen and geographic subdivision. Intra- and intercontinental migration was observed between Europe and South America, likely associated with the movement of contaminated germplasm. Low clonality, evidence of genetic recombination, and high phenotypic diversity were detected. We show evidence that, although it is rare (possibly due to losses of sexual reproduction- and meiosis-associated genes) C. graminicola can undergo sexual recombination. Our results support the hypotheses that intra- and intercontinental pathogen migration and genetic recombination have great impacts on the C. graminicola population structure. IMPORTANCE Plant pathogens cause significant reductions in yield and crop quality and cause enormous economic losses worldwide. Reducing these losses provides an obvious strategy to increase food production without further degrading natural ecosystems; however, this requires knowledge of the biology and evolution of the pathogens in agroecosystems. We employed a population genomics approach to investigate the genetic diversity and reproductive biology of the maize anthracnose pathogen (Colletotrichum graminicola) in 14 countries. We found that the populations are correlated with their geographical origin and that migration between countries is ongoing, possibly caused by the movement of infected plant material. This result has direct implications for disease management because migration can cause the movement of more virulent and/or fungicide-resistant genotypes. We conclude that genetic recombination is frequent (in contrast to the traditional view of C. graminicola being mainly asexual), which strongly impacts control measures and breeding programs aimed at controlling this disease.}, } @article {pmid36533601, year = {2022}, author = {Keeler, EL and Vukmirovic, M and Yan, X and Gulino, K and Ghedin, E and Kaminski, N and Sullivan, KE and Bushman, FD and Collman, RG and Rosenbach, M}, title = {Metagenomic sequencing of the bronchoalveolar lavage extracellular virome and cellular transcriptome of sarcoidosis patients does not detect rubella virus.}, journal = {Sarcoidosis, vasculitis, and diffuse lung diseases : official journal of WASOG}, volume = {39}, number = {4}, pages = {e2022040}, pmid = {36533601}, issn = {2532-179X}, support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; }, abstract = {BACKGROUND: Sarcoidosis is a multisystem granulomatous inflammatory disease of unclear etiology that involves the lung, skin and other organs, with an unknown antigenic trigger. Recently, evidence has been found in both immune deficient and immune competent patients for rubella virus in cutaneous granulomas. These granulomatous lesions share overlapping features with cutaneous sarcoidosis, raising the question of rubella virus in sarcoidosis.

OBJECTIVE: To investigate the presence of rubella virus in sarcoidosis lung samples.

METHODS: We employed metagenomic sequencing to interrogate extracellular virome preparations and cellular transcriptomes from bronchoalveolar lavage (BAL) of 209 sarcoidosis patients for rubella virus sequences.

RESULTS: We found no evidence for rubella virus genomes in acellular fluid or rubella virus gene expression in BAL cells of sarcoidosis patients.

CONCLUSIONS: These findings argue against rubella virus infection or persistence within the lung at time of sampling as a sarcoidosis trigger.}, } @article {pmid36533143, year = {2022}, author = {Charon, J and Buchmann, JP and Sadiq, S and Holmes, EC}, title = {RdRp-scan: A bioinformatic resource to identify and annotate divergent RNA viruses in metagenomic sequence data.}, journal = {Virus evolution}, volume = {8}, number = {2}, pages = {veac082}, pmid = {36533143}, issn = {2057-1577}, abstract = {Despite a rapid expansion in the number of documented viruses following the advent of metagenomic sequencing, the identification and annotation of highly divergent RNA viruses remain challenging, particularly from poorly characterized hosts and environmental samples. Protein structures are more conserved than primary sequence data, such that structure-based comparisons provide an opportunity to reveal the viral 'dusk matter': viral sequences with low, but detectable, levels of sequence identity to known viruses with available protein structures. Here, we present a new open computational resource-RdRp-scan-that contains a standardized bioinformatic toolkit to identify and annotate divergent RNA viruses in metagenomic sequence data based on the detection of RNA-dependent RNA polymerase (RdRp) sequences. By combining RdRp-specific hidden Markov models (HMMs) and structural comparisons, we show that RdRp-scan can efficiently detect RdRp sequences with identity levels as low as 10 per cent to those from known viruses and not identifiable using standard sequence-to-sequence comparisons. In addition, to facilitate the annotation and placement of newly detected and divergent virus-like sequences into the diversity of RNA viruses, RdRp-scan provides new custom and curated databases of viral RdRp sequences and core motifs, as well as pre-built RdRp multiple sequence alignments. In parallel, our analysis of the sequence diversity detected by the RdRp-scan revealed that while most of the taxonomically unassigned RdRps fell into pre-established clusters, some fell into potentially new orders of RNA viruses related to the Wolframvirales and Tolivirales. Finally, a survey of the conserved A, B, and C RdRp motifs within the RdRp-scan sequence database revealed additional variations of both sequence and position that might provide new insights into the structure, function, and evolution of viral polymerases.}, } @article {pmid36532542, year = {2022}, author = {Plaza-Díaz, J and Manzano, M and Ruiz-Ojeda, FJ and Giron, MD and Salto, R and López-Pedrosa, JM and Santos-Fandila, A and Garcia-Corcoles, MT and Rueda, R and Gil, Á}, title = {Intake of slow-digesting carbohydrates is related to changes in the microbiome and its functional pathways in growing rats with obesity induced by diet.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {992682}, pmid = {36532542}, issn = {2296-861X}, abstract = {INTRODUCTION: The main cause of insulin resistance in childhood is obesity, which contributes to future comorbidities as in adults. Although high-calorie diets and lack of exercise contribute to metabolic disease development, food quality rather than the quantity of macronutrients is more important than food density. The purpose of the present study was to examine the effects of changing the quality of carbohydrates from rapidly to slowly digestible carbohydrates on the composition of the gut microbiota and the profiles of the functional pathways in growing rats with obesity due to a high-fat diet (HFD).

METHODS: During the course of 4 weeks, rats growing on an HFD-containing carbohydrates with different digestive rates were fed either HFD-containing carbohydrates with a rapid digestion rate (OBE group) or HFD-containing carbohydrates with a slow digestion rate (OBE-ISR group). A non-obese group (NOB) was included as a reference, and rats were fed on a rodent standard diet (AIN93G). An analysis of gut microbiota was conducted using 16S rRNA-based metagenomics; a linear mixed-effects model (LMM) was used to determine changes in abundance between baseline and 4 weeks of treatment, and functional pathways were identified. Gut microbiota composition at bacterial diversity and relative abundance, at phylum and genus levels, and functional profiles were analyzed by integrating the Integrated Microbial Genomes (IMG) database.

RESULTS: The groups showed comparable gut microbiota at baseline. At the end of the treatment, animals from the ISR group exhibited differences at the phylum levels by decreasing the diversity of Fisher's index and Firmicutes (newly named as Bacillota), and increasing the Pielou's evenness and Bacteroidetes (newly named as Bacteroidota); at the genus level by increasing Alistipes, Bifidobacterium, Bacteroides, Butyricimonas, Lachnoclostridium, Flavonifractor, Ruminiclostridium 5, and Faecalibaculum and decreasing Muribaculum, Blautia, and Ruminiclostridium 9. Remarkably, relative abundances of genera Tyzzerella and Angelakisella were higher in the OBE group compared to NOB and OBE-ISR groups. In addition, some microbiota carbohydrate metabolism pathways such as glycolysis, glucuronic acid degradation, pentose phosphate pathway, methanogenesis, and fatty acid biosynthesis exhibited increased activity in the OBE-ISR group after the treatment. Higher levels of acetate and propionate were found in the feces of the ISR group compared with the NOB and OBE groups.

CONCLUSION: The results of this study demonstrate that replacing rapidly digestible carbohydrates with slowly digestible carbohydrates within an HFD improve the composition of the gut microbiota. Consequently, metabolic disturbances associated with obesity may be prevented.}, } @article {pmid36532514, year = {2022}, author = {Ma, J and Wang, C and Wang, F and Zhang, Y and Liu, Y and Zhang, J and Gao, Z and Zhang, Y and Xie, H and Wang, Y and Fu, L}, title = {Intestinal proline is a potential anti-allergy factor for allergy diagnosis and therapy.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {1036536}, pmid = {36532514}, issn = {2296-861X}, abstract = {Allergy has become a public health problem worldwide, but effective diagnostic and therapeutic approaches are limited currently. Amino acids are essential macronutrients that potentially participated in the allergy process. This work aimed to investigate whether amino acids can be applied as a mediator for allergy diagnosis and therapy. Two cohort studies were performed to investigate the correlation between fecal amino acids and allergy responses, and a spleen cell model was used to validate the role of amino acids in regulating allergy. In a cohort study with 193 volunteers, fecal proline was found to be negatively correlated with serum IgE, and detailed data analysis revealed that people with high-IgE-mediated allergy had decreased odds of high intestinal proline. In another cohort study with distinct allergic and non-allergic individuals, proline concentration was significantly lower in the allergic group. Daily diet and metagenomics analysis showed that the proline intake and microbiota amino acid metabolism were not significantly different, implying that the body's proline metabolism might be different between allergic and non-allergic individuals. Furthermore, the spleen cell model demonstrated that proline specifically targeted Th2 and Treg activity. Overall, this work revealed a tight correlation between gut proline and serum IgE, indicating proline as a promising biomarker and a potential therapeutic method for allergic diseases.}, } @article {pmid36532507, year = {2022}, author = {Wang, S and Abalori, TA and Wang, W and Deng, X and Liu, W and Wang, J and Cao, W}, title = {Response of soil microbial compositional and functional heterogeneity to grazing exclusion in alpine shrub and meadows in the Qinghai-Tibet Plateau.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1038805}, pmid = {36532507}, issn = {1664-302X}, abstract = {Soil microorganisms found in shrub-meadow ecosystems are highly heterogeneous and extremely sensitive to grazing, but changes in microbial compositional and functional heterogeneity during grazing exclusion (GE) have been largely overlooked compared to community diversity. We collected soil samples from heavily grazed plots (6.0 sheep/ha) and GE plots (matrix and patch areas in both), and used a combination of next-generation sequencing, vegetation features, and the associated soil property data to investigate the effect of GE on the composition and function of microbial communities (bacteria fungi, and archaea) in 0-10 cm soils. Regarding community composition, the proportions of species in bacteria, fungi, and archaea were 97.3, 2.3, and 0.4%, respectively. GE significantly affected the species diversity of fungi and archaea but not that of bacteria. GE decreased the heterogeneity of bacteria (2.9% in matrix and 6.2% in patch) and archaea (31.1% in matrix and 19.7% in patch) but increased that of fungi by 1.4% in patch. Regarding community function, enzyme diversity and heterogeneity were increased by 10.4 and 9.4%, respectively, in patch after 6 years of fencing, exemplifying a high level of microbial functional redundancy. The Kyoto Encyclopedia of Genes and Genome pathways-cell growth and death, translation, digestive system, and nucleotide metabolism-were functional biomarkers (linear discriminant analysis effect size method) in matrix-non-grazed plots, whereas lipid metabolism, xenobiotics biodegradation and metabolism, and metabolism of terpenoids and polyketides, cell motility, cancer: overview, endocrine system, and membrane transport were biomarkers in patch-non-grazed plots. Additionally, GE improved the capacity for fatty acid metabolism but decreased the abundance of methane-producing archaea by 42.9%. Redundancy analysis revealed that the factors that affected microbial composition the most were soil aggregates, soil moisture, and the number of plant species, whereas those that affected microbial function the most were soil available phosphorus, soil temperature, and shrub canopy diameter. Our results quantified soil microbial heterogeneity, emphasizing the different responses of the composition and function of bacteria, fungi, and archaea to GE in alpine shrubs and meadows.}, } @article {pmid36532491, year = {2022}, author = {Salgado, O and Guajardo-Leiva, S and Moya-Beltrán, A and Barbosa, C and Ridley, C and Tamayo-Leiva, J and Quatrini, R and Mojica, FJM and Díez, B}, title = {Global phylogenomic novelty of the Cas1 gene from hot spring microbial communities.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1069452}, pmid = {36532491}, issn = {1664-302X}, abstract = {The Cas1 protein is essential for the functioning of CRISPR-Cas adaptive systems. However, despite the high prevalence of CRISPR-Cas systems in thermophilic microorganisms, few studies have investigated the occurrence and diversity of Cas1 across hot spring microbial communities. Phylogenomic analysis of 2,150 Cas1 sequences recovered from 48 metagenomes representing hot springs (42-80°C, pH 6-9) from three continents, revealed similar ecological diversity of Cas1 and 16S rRNA associated with geographic location. Furthermore, phylogenetic analysis of the Cas1 sequences exposed a broad taxonomic distribution in thermophilic bacteria, with new clades of Cas1 homologs branching at the root of the tree or at the root of known clades harboring reference Cas1 types. Additionally, a new family of casposases was identified from hot springs, which further completes the evolutionary landscape of the Cas1 superfamily. This ecological study contributes new Cas1 sequences from known and novel locations worldwide, mainly focusing on under-sampled hot spring microbial mat taxa. Results herein show that circumneutral hot springs are environments harboring high diversity and novelty related to adaptive immunity systems.}, } @article {pmid36532479, year = {2022}, author = {Sampath, V and Song, JH and Jeong, J and Mun, S and Han, K and Kim, IH}, title = {Nourishing neonatal piglets with synthetic milk and Lactobacillus sp. at birth highly modifies the gut microbial communities at the post-weaning stage.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1044256}, pmid = {36532479}, issn = {1664-302X}, abstract = {The importance of probiotics in pig production is widely recognized. However, the precise role of probiotics in regulating the gut microbiota of piglets has not been assessed extensively. Therefore, we intend to examine whether suckling pigs ingesting with synthetic milk (SM) and probiotics along with mother milk has a carryover effect on its growth and gut health at the post-weaning stage. A total of 40 [Duroc× (Yorkshire× Landrace)] neonates with an initial BW of 1.49 ± 0.28 kg were assigned to one of two treatments groups: control (CON) and treatment (TRT). Control group piglets were nourished with synthetic milk, while TRT group piglets were nourished SM with (1 × 10[9] CFU/g) Lactobacillus sp. probiotics. The treatment group piglets showed higher (p < 0.05) body weight and daily gain at week 3 than the CON group piglets. 16S metagenome sequencing showed average demultiplexed reads and denoised reads counts of 157,399 and 74,945, respectively. The total ASV taxonomy number classified with a confidence threshold > 70% (default) on sequence alignment with the SILVA v138 reference database was 4,474. During week 1, Escherichia-Shigella, Clostridium sensu stricto 1, and Bacteroides were confirmed as the major dominant bacterial genera in both the groups at the genus level. However, during week 2, the relative proportion of Escherichia-Shigella, Clostridium sensu stricto 1, and Proteobacteria was decreased, while that of Lactobacillus and Bacteroidota was increased in pigs receiving the probiotic supplement. During weeks 2 and 3, Firmicutes, Proteobacteria, and Bacteroidota phyla were dominant in both groups. During week 6, the relative proportion of Proteobacteria was slightly increased in both groups. Furthermore, Prevotella was confirmed as the major dominant bacterial genus in both groups during weeks 3 and 6. This study suggests that nourishing neonatal piglets with synthetic milk and Lactobacillus sp. probiotics from birth to 21 days would be beneficial to enhance the gut health of piglets and to overcome post-weaning mortality.}, } @article {pmid36532455, year = {2022}, author = {Zhang, Q and Du, G and Chen, J and Li, J and Qiao, Z and Zheng, J and Zhao, D and Zhao, X}, title = {Systematic analysis of Baobaoqu fermentation starter for Wuliangye Baijiu by the combination of metagenomics and metabolomics.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1062547}, pmid = {36532455}, issn = {1664-302X}, abstract = {Baobaoqu (BBQ) is a traditional fermenting power, which is widely applied in Nong-flavor Baijiu brewing. There are two different types of BBQ (premium BBQ and normal BBQ) used in industrial manufacture, but the reasons for the significant differences between two kinds of BBQ have not been clearly illuminated. In this study, the combination of metagenomics and metabolomics was performed to compare the differences in the composition of microbial communities and the components of flavors between premium BBQ and normal BBQ. The results showed that the glycosidase-producing microorganisms are the biomarkers of premium BBQ, contributing a better ability of carbon source utilization than normal BBQ. In addition, several important flavors (ethyl hexanoate, phenylethanol, ethyl acetate) were rich in normal BBQ, which have a significant positive correlation with the biomarkers (Lactobacillus and Pichia kudriavzevii) of normal BBQ. It suggests that the microbial community has an advantage in utilizing raw materials in premium BBQ, while the community was inclined to form flavors in normal BBQ. The differences between two types of BBQ at the microbial and flavor level have theoretical and practical guiding significance in the application of premium and normal BBQ and in the further improvements of taste and quality of Baijiu.}, } @article {pmid36532453, year = {2022}, author = {Díaz-Torres, O and Lugo-Melchor, OY and de Anda, J and Orozco-Nunnelly, DA and Gradilla-Hernández, MS and Senés-Guerrero, C}, title = {Characterizing a subtropical hypereutrophic lake: From physicochemical variables to shotgun metagenomic data.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1037626}, pmid = {36532453}, issn = {1664-302X}, abstract = {Lake Cajititlán is a subtropical and endorheic lake, which is heavily impacted by nutrient pollution. Agricultural runoff and poorly treated wastewater have entered this reservoir at alarming rates during past rainy seasons, causing the cultural eutrophication of this body of water and resulting in several massive fish kill events. In this study, shotgun metagenomic sequencing was used to examine the taxonomic and functional structure of microbial communities in Lake Cajititlán during the rainy season. Several water quality features and their interactions with microbial communities were also assessed to identify the major factors affecting the water quality and biota, specifically fish species. According to current water quality regulations, most of the physicochemical variables analyzed (dissolved oxygen, pH, Secchi disk, NH4 [+], NO3 [-], blue-green algae, total phosphorus, and chlorophyll-a) were outside of the permissible limits. Planktothrix agardhii and Microcystis aeruginosa were the most abundant phytoplankton species, and the dominant bacterial genera were Pseudomonas, Streptomyces, and Flavobacterium, with Pseudomonas fluorescens, Stenotrophomonas maltophilia, and Aeromonas veronii representing the most abundant bacterial species. All of these microorganisms have been reported to be potentially harmful to fish, and the latter three (P. fluorescens, S. maltophilia, A. veronii) also contain genes associated with pathogenicity in fish mortality (fur, luxS, aer, act, aha, exu, lip, ser). Genetic evidence from the microbial communities analyzed herein reveals that anthropogenic sources of nutrients in the lake altered genes involved in nitrogen, phosphorus, sulfur, and carbon metabolism, mainly at the beginning of the rainy season. These findings suggest that abiotic factors influence the structure of the microbial communities, along with the major biogeochemical cycles of Lake Cajititlán, resulting in temporal variations and an excess of microorganisms that can thrive in high-nutrient and low-oxygen environments. After reviewing the literature, this appears to be the first study that focuses on characterizing the water quality of a subtropical hypereutrophic lake through associations between physicochemical variables and shotgun metagenomic data. In addition, there are few studies that have coupled the metabolism of aquatic ecosystems with nutrient cycles.}, } @article {pmid36532441, year = {2022}, author = {Wang, L and Shen, Z and Cheng, X and Hwang, JS and Guo, Y and Sun, M and Cao, J and Liu, R and Fang, J}, title = {Metagenomic insights into the functions of microbial communities in sulfur-rich sediment of a shallow-water hydrothermal vent off Kueishan Island.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {992034}, pmid = {36532441}, issn = {1664-302X}, abstract = {Hydrothermal vent (HTV) systems are important habitats for understanding the biological processes of extremophiles on Earth and their relative contributions to material and energy cycles in the ocean. Current understanding on hydrothermal systems have been primarily focused on deep-sea HTVs, and little is known about the functions and metabolisms of microorganisms in shallow-water HTVs (SW-HTVs), which are distinguished from deep-sea HTVs by a depth limit of 200 m. In this study, we analyzed metagenomes of sulfur-rich sediment samples collected from a SW-HTV of Kueishan Island, located in a marginal sea of the western Pacific Ocean. Comparing with a previously published report of pelagic samples from the nearby sampling site, microbial communities in the SW-HTV sediments enriching with genes of both aerobic and anaerobic respiration inferred variable environments in the tested sediments. Abundant genes of energy metabolism encoding sulfur oxidation, H2 oxidation, and carbon fixation were detected from the sediment samples. Sixty-eight metagenome-assembled-genomes (MAGs) were reconstructed to further understand the metabolism and potential interactions between different microbial taxa in the SW-HTVs sediment. MAGs with the highest abundant were chemolithotrophic sulfur-oxidization bacteria, including Sulfurovum represented Campylobacteria involved sox multienzyme, sulfide oxidation genes and rTCA cycle, and Gammaproteobacteria involved dsr gene and CBB cycle. In addition, Desulfobacterota with the potential to participate in sulfur-disproportionating processes also had higher abundance than the sample's overall mean value. The interaction of these bacterial groups allows the microbial communities to efficiently metabolize a large variety of sulfur compounds. In addition, the potential to use simple organic carbon, such as acetate, was found in chemolithotrophic Campylobacterial MAGs. Collectively, our results revealed the complexity of environmental conditions of the vent sediment and highlight the interactive relationships of the dominant microbial populations in driving sulfur cycles in the SW-HTV sediments off Kueishan Island.}, } @article {pmid36532424, year = {2022}, author = {Pillay, S and Calderón-Franco, D and Urhan, A and Abeel, T}, title = {Metagenomic-based surveillance systems for antibiotic resistance in non-clinical settings.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1066995}, pmid = {36532424}, issn = {1664-302X}, abstract = {The success of antibiotics as a therapeutic agent has led to their ineffectiveness. The continuous use and misuse in clinical and non-clinical areas have led to the emergence and spread of antibiotic-resistant bacteria and its genetic determinants. This is a multi-dimensional problem that has now become a global health crisis. Antibiotic resistance research has primarily focused on the clinical healthcare sectors while overlooking the non-clinical sectors. The increasing antibiotic usage in the environment - including animals, plants, soil, and water - are drivers of antibiotic resistance and function as a transmission route for antibiotic resistant pathogens and is a source for resistance genes. These natural compartments are interconnected with each other and humans, allowing the spread of antibiotic resistance via horizontal gene transfer between commensal and pathogenic bacteria. Identifying and understanding genetic exchange within and between natural compartments can provide insight into the transmission, dissemination, and emergence mechanisms. The development of high-throughput DNA sequencing technologies has made antibiotic resistance research more accessible and feasible. In particular, the combination of metagenomics and powerful bioinformatic tools and platforms have facilitated the identification of microbial communities and has allowed access to genomic data by bypassing the need for isolating and culturing microorganisms. This review aimed to reflect on the different sequencing techniques, metagenomic approaches, and bioinformatics tools and pipelines with their respective advantages and limitations for antibiotic resistance research. These approaches can provide insight into resistance mechanisms, the microbial population, emerging pathogens, resistance genes, and their dissemination. This information can influence policies, develop preventative measures and alleviate the burden caused by antibiotic resistance.}, } @article {pmid36532422, year = {2022}, author = {Liu, X and Zhang, M and Wang, X and Liu, P and Wang, L and Li, Y and Wang, X and Ren, F}, title = {Fecal microbiota transplantation restores normal fecal composition and delays malignant development of mild chronic kidney disease in rats.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1037257}, pmid = {36532422}, issn = {1664-302X}, abstract = {Chronic kidney disease (CKD) is associated with gut microbiome dysbiosis, but the role of intestinal flora in CKD treatment remains to be elucidated. Fecal microbiota transplantation (FMT) can be utilized to re-establish healthy gut microbiota for a variety of diseases, which offers new insight for treating CKD. First, 5/6 nephrectomy rats (Donor CKD) and sham rats (Donor Sham) were used as donors for FMT, and fecal metagenome were analyzed to explore potential therapeutic targets. Then, to assess the effect of FMT on CKD, sterilized 1/2 nephrectomy rats were transplanted with fecal microbiota from Donor sham (CKD/Sham) or Donor CKD (CKD/CKD) rats, and 1/2 nephrectomy rats without FMT (CKD) or no nephrectomy (Sham) were used as model control or normal control. Results showed that Bacteroides uniformis and Anaerotruncus sp. 1XD22-93 were enriched in Donor CKD, while Lactobacillus johnsonii and Lactobacillus intestinalis were reduced. In addition, the increased abundance of microbial functions included tryptophan metabolism and lysine degradation contributing to the accumulation of protein-bound uremic toxins (PBUTs) in Donor CKD. Genome analysis indicated that FMT successfully differentiated groups of gut microbes and altered specific gut microbiota after 1 week of treatment, with Bacteroides uniformis and Anaerotruncus sp. 1XD22-93 increasing in CKD/CKD group as well as Lactobacillus johnsonii and Lactobacillus intestinalis being improved in CKD/Sham group. In comparison to CKD group, substantial PBUT buildup and renal damage were observed in CKD/CKD. Interestingly, compared to CKD or CKD/CKD group, tryptophan metabolism and lysine degradation were efficiently suppressed in CKD/Sham group, while lysine biosynthesis was promoted. Therefore, FMT considerably reduced PBUTs accumulation. After FMT, PBUTs and renal function in CKD/Sham rats remained the same as in Sham group throughout the experimental period. In summary, FMT could delay the malignant development of CKD by modifying microbial amino acid metabolism through altering the microenvironment of intestinal flora, thereby providing a novel potential approach for treating CKD.}, } @article {pmid36532326, year = {2022}, author = {Chhaliyil, P and Fischer, KF and Schoel, B and Chhalliyil, P}, title = {Impact of Refined and Unrefined Sugar and Starch on the Microbiota in Dental Biofilm.}, journal = {Journal of International Society of Preventive & Community Dentistry}, volume = {12}, number = {5}, pages = {554-563}, pmid = {36532326}, issn = {2231-0762}, abstract = {AIMS AND OBJECTIVE: Sugar is not only associated with dental diseases but also, along with carbohydrates, is linked to various health issues including obesity, cancer, diabetes, heart, liver, and kidney-related diseases. At the same time, a polyphenol present in unrefined sugar and starch (UReSS) is shown to inhibit microbial growth and prevent biofilms and dental plaque. The question arises, "is sugar the causative agent for dental diseases, or is its refined form the cause?" The objective of this study is to conduct in-vivo studies of the impact of refined and unrefined sugar and starch on the microbiota of dental biofilm.

MATERIALS AND METHODS: An in-vivo study was performed using saliva and dental biofilm samples collected from 75 healthy subjects. For this study, healthy volunteers (n = 75) were randomly divided into five groups and were given sweet meals either made with refined white sugar and white rice (ReSS) or with unrefined brown sugar and red rice (UReSS). This was followed by using or not using a polyphenolic mouthwash. Before and after 4 h of eating a sweet meal, the saliva and dental plaque were collected and the DNA was analyzed by 16s metagenomic sequencing. The results were expressed in fold change of bacteria from 0 to 4 h. Statistical analyses have been performed by logarithmic linear discriminant analysis (LDA), Student's t-test, and Wilcoxon signed-rank test.

RESULTS: Upon LEfSe and statistical analysis, in-vivo experiments clearly showed that UReSS significantly decreased bacteria associated with dental diseases. In contrast, ReSS showed a significant increase in Actinomyces, Streptococcus, and Selenomonas with a high LDA score (Log 4.2) and statistical significance (P < 0.003). Mouthwash significantly decreased bacterial taxa associated with diseases in both the ReSS and UReSS groups. The in-vivo study showed a significant increase and decrease in Streptococcus levels in refined and unrefined sugar groups, respectively.

CONCLUSION: In conclusion, polyphenols aid in the prevention of dental caries. This study recommends using polyphenol-rich unrefined sugars and carbohydrates for both oral and general health. This study is the first of its kind to bring awareness to the effects of refined and unrefined starch and sugars on the oral microbiota.}, } @article {pmid36532052, year = {2022}, author = {Yan, H and Mo, Y and Liu, S and Luo, X and Liu, L and Zhou, L and Zhang, X and Chen, Y and Cao, K}, title = {Case report: Hemophagocytic lymphohistiocytosis in a child with primary immunodeficiency infected with Talaromyces marneffei.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1038354}, pmid = {36532052}, issn = {1664-3224}, mesh = {Humans ; Child ; *Lymphohistiocytosis, Hemophagocytic/diagnosis/genetics ; *Talaromyces/genetics ; Immunocompromised Host ; Mutation ; }, abstract = {Hemophagocytic lymphohistiocytosis (HLH) is a life-threatening immune-mediated disease that affects patients with known genetic defects and is increasingly found among those with autoimmune diseases and persistent infections. Talaromyces marneffei (TM) is a human opportunistic fungus that commonly infects immunodeficient or immunosuppressed individuals. Few TM-associated secondary HLH cases resulting from autoimmune deficiency have been reported previously. The current case study describes a pediatric patient hospitalized with recurrent fever and lymphadenopathy. The child had abnormal blood cell classification, and microscopy revealed mature granulocytes that phagocytized fungal spores. It was speculated that the patient was infected with TM. The pathogen was detected earlier than the blood culture and confirmed by metagenomic next-generation sequencing. Whole-exome sequencing revealed that the patient had complex mutations associated with immunodeficiency. This included a mutation in exon 3 of the CD40LG gene, c.346G>A, which may be linked to hyper-IgM syndrome, a primary immunodeficiency disease with immunoglobulin conversion recombination defects that could explain the patient's increased susceptibility to serious opportunistic infections. In addition, a heterozygous frameshift variant, c.820dup (p.Asp274GlyfsTer61), was detected in exon 6 of CARD9, a key gene associated with fungal immune surveillance. After 4 days of fungal treatment, the abnormal blood cell clusters disappeared, but other infections occurred in succession for 6 months after rehabilitation. The patient was followed with the aim of providing subsequent immunotherapy. This study found that infection can trigger HLH in HIV-negative individuals, highlighting the importance of early definitive identification of the causative agent and investigation of potential immunodeficiency.}, } @article {pmid36531828, year = {2022}, author = {Tao, H and Hua, F and Chen, Y and Jia, Y}, title = {Metagenomic Next-Generation Sequencing (mNGS) for the Timely Diagnosis of Carbapenem-Resistant Klebsiella pneumoniae in Leukemia Patients.}, journal = {Case reports in infectious diseases}, volume = {2022}, number = {}, pages = {6957028}, pmid = {36531828}, issn = {2090-6625}, abstract = {This report shows the contribution of metagenomic next-generation sequencing (mNGS) as an alternative to challenging diagnostic infection in immunosuppressed individuals. Herein, we report two leukemia patients who developed severe infections due to carbapenem-resistant Klebsiella pneumoniae (CrKP). The mNGS can be strongly recommended as an alternative investigation for patients who are at high risk of infection without positivity on body fluid culture. This can provide the opportunity for adequate therapy.}, } @article {pmid36531423, year = {2022}, author = {Manoussakis, MN and Svolaki, IP and Hazapis, O and Zerva, L and Gorgoulis, VG and Magiorkinis, G}, title = {Postgenomic Bioinformatic Analysis of Nucleic Acid Sequences Expressed in the Salivary Gland Epithelial Cells of Primary Sjögren's Syndrome Patients in Search of Microorganisms and Endogenous Retroviruses.}, journal = {Mediterranean journal of rheumatology}, volume = {33}, number = {3}, pages = {371-374}, pmid = {36531423}, issn = {2529-198X}, abstract = {Several previous studies from our laboratory have indicated that the salivary gland epithelia of primary Sjögren's syndrome (SS) patients are not only the target of autoimmune immune responses, but also key instigators of the chronic salivary gland inflammatory infiltrates of patients. In particular, the comparative analysis of salivary gland tissue specimens and of in-vitro cultured non-neoplastic salivary gland epithelial cell lines (SGEC, of ductal type) from SS-patients and non-SS disease-controls, have unequivocally highlighted the presence of intrinsic activation in the ductal epithelia of SS-patients and of aberrant expression of inflammagenic molecules thereof, that correlate with the severity of local histopathologic changes, as well as of systemic manifestations of the disease. In the same context, we have recently shown that the ductal epithelia of SS-patients manifest cell-autonomous activation of the AIM2 inflammasome owing to the presence of aberrant cytoplasmic accumulations of damaged DNA. These findings not only provide a mechanistic explanation for the intrinsic activation and inflammatory status of SS ductal epithelia, but may also point towards the putative instigating role of an exogenous or endogenous agent (i.e., a micro-organism or an endogenous retrovirus, respectively). On this basis and to further explore the nature of epithelial cell-intrinsic activation in SS, the present proposal aims to investigate the expression of endogenous retroviral and/or non-human nucleic acid sequences of microbial origin in the ductal salivary gland epithelia of SS-patients, using metagenomic analysis of high throughput DNA and RNA genome sequencing data, which will be obtained from SGEC lines derived from SS-patients and disease-controls.}, } @article {pmid36531282, year = {2022}, author = {Gruszecka-Kosowska, A and Ampatzoglou, A and Aguilera-Gómez, M}, title = {Microbiota analysis for risk assessment of xenobiotics: cumulative xenobiotic exposure and impact on human gut microbiota under One Health approach.}, journal = {EFSA journal. European Food Safety Authority}, volume = {20}, number = {Suppl 2}, pages = {e200916}, pmid = {36531282}, issn = {1831-4732}, abstract = {Human gut microbiota is the microbial community that, through the constant bidirectional communication with its host, plays the critical role of maintaining the state of eubiosis and health balance, contributing to food digestion, detoxification, and proper endocrine, neurological, immunological and potentially reproductive health. To this extent, gut microbiota is called the 'second brain' as well as the 'second liver'. Xenobiotics, including environmental pollutants, are widely spread in the environment and easily accessible in food, cosmetics, personal care products, drugs and medicinal products. Thus, the gut microbiota can be exposed to these xenobiotics, which in turn might alter its composition and metabolism that can trigger dysbiosis, and they seem associated with disorders and diseases in the host. A specific group of xenobiotics, called endocrine-disrupting chemicals, is particularly important due to relevant adverse health effects. A considerable challenge in risk assessment is the combined exposure to xenobiotics, for which the integrated approaches, including the One Health concept, are still under development. Nevertheless, recent research advancements focus on molecular data in the search for elucidating crucial microbiome biomarkers, associated with physiopathology and specific dysfunctions triggered by xenobiotic exposure. In this context, the application of meta-omics and integration of genomics, metagenomics, metabolomics, metatranscriptomics, proteomics and multidisciplinary approaches are particularly important.}, } @article {pmid36530948, year = {2023}, author = {Coutinho, MGF and Câmara, GBM and Barbosa, RM and Fernandes, MAC}, title = {SARS-CoV-2 virus classification based on stacked sparse autoencoder.}, journal = {Computational and structural biotechnology journal}, volume = {21}, number = {}, pages = {284-298}, pmid = {36530948}, issn = {2001-0370}, abstract = {Since December 2019, the world has been intensely affected by the COVID-19 pandemic, caused by the SARS-CoV-2. In the case of a novel virus identification, the early elucidation of taxonomic classification and origin of the virus genomic sequence is essential for strategic planning, containment, and treatments. Deep learning techniques have been successfully used in many viral classification problems associated with viral infection diagnosis, metagenomics, phylogenetics, and analysis. Considering that motivation, the authors proposed an efficient viral genome classifier for the SARS-CoV-2 using the deep neural network based on the stacked sparse autoencoder (SSAE). For the best performance of the model, we explored the utilization of image representations of the complete genome sequences as the SSAE input to provide a classification of the SARS-CoV-2. For that, a dataset based on k-mers image representation was applied. We performed four experiments to provide different levels of taxonomic classification of the SARS-CoV-2. The SSAE technique provided great performance results in all experiments, achieving classification accuracy between 92% and 100% for the validation set and between 98.9% and 100% when the SARS-CoV-2 samples were applied for the test set. In this work, samples of the SARS-CoV-2 were not used during the training process, only during subsequent tests, in which the model was able to infer the correct classification of the samples in the vast majority of cases. This indicates that our model can be adapted to classify other emerging viruses. Finally, the results indicated the applicability of this deep learning technique in genome classification problems.}, } @article {pmid36530424, year = {2022}, author = {Zhou, X and Peng, S and Song, T and Tie, D and Tao, X and Jiang, L and Zhang, J}, title = {Neurosyphilis with ocular involvement and normal magnetic resonance imaging results affirmed by metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {985373}, pmid = {36530424}, issn = {2235-2988}, mesh = {Humans ; *Neurosyphilis/diagnostic imaging ; Treponema pallidum/genetics ; Polymerase Chain Reaction/methods ; High-Throughput Nucleotide Sequencing ; Magnetic Resonance Imaging ; }, abstract = {The rapid and accurate identification of pathogenic agents is the key to guide clinicians on diagnosis and medication, especially for intractable diseases, such as neurosyphilis. It is extremely challenging for clinicians to diagnose neurosyphilis with no highly sensitive and specific test available. It is well known that the early transmission and immune evasion ability of Treponema pallidum have earned it the title of "stealth pathogen." Neurosyphilis has complex clinical manifestations, including ocular involvement, which is infrequent and often overlooked, but its neuroimaging results may be normal. Therefore, it is important to find a new test that can detect the presence or absence of Treponema pallidum immediately for the diagnosis of neurosyphilis. We reviewed all the patients admitted to the Sichuan Provincial People's Hospital between 2021 and 2022 who had ocular involvement and whose clinical samples were examined via metagenomic next-generation sequencing (mNGS), and we found 10 candidates for further analysis. The results of magnetic resonance imaging (MRI) were normal for four patients, and three of them met the diagnostic criteria for neurosyphilis confirmed by mNGS. In addition, the results of mNGS from the three patients were further validated using polymerase chain reaction (PCR). Five of the 10 patients had diplopia manifestations; two (20%) experienced abducens nerve palsies, two (20%) had eyelid drooping, and one (10%) had decreased vision. One of the 10 patients (10%) who was HIV positive and five patients had abnormal MRI results. To our knowledge, Treponema pallidum was detected by mNGS in patients with ocular involvement and normal MRI results for the first time. Given this situation, we recommend mNGS as a potential and supplementary tool for the diagnosis and differential diagnosis of neurosyphilis.}, } @article {pmid36529539, year = {2023}, author = {Olmsted, CN and Ort, R and Tran, PQ and McDaniel, EA and Roden, EE and Bond, DR and He, S and McMahon, KD}, title = {Environmental predictors of electroactive bacterioplankton in small boreal lakes.}, journal = {Environmental microbiology}, volume = {25}, number = {3}, pages = {705-720}, doi = {10.1111/1462-2920.16314}, pmid = {36529539}, issn = {1462-2920}, mesh = {*Lakes/microbiology ; Oxidation-Reduction ; Electron Transport ; *Aquatic Organisms ; Soil ; Bacteria ; }, abstract = {Extracellular electron transfer (EET) by electroactive bacteria in anoxic soils and sediments is an intensively researched subject, but EET's function in planktonic ecology has been less considered. Following the discovery of an unexpectedly high prevalence of EET genes in a bog lake's bacterioplankton, we hypothesized that the redox capacities of dissolved organic matter (DOM) enrich for electroactive bacteria by mediating redox chemistry. We developed the bioinformatics pipeline FEET (Find EET) to identify and summarize predicted EET protein-encoding genes from metagenomics data. We then applied FEET to 36 bog and thermokarst lakes and correlated gene occurrence with environmental data to test our predictions. Our results provide indirect evidence that DOM may participate in bacterioplankton EET. We found a similarly high prevalence of genes encoding putative EET proteins in most of these lakes, where oxidative EET strongly correlated with DOM. Numerous novel clusters of multiheme cytochromes that may enable EET were identified. Taxa previously not considered EET-capable were found to carry EET genes. We propose that EET and DOM interactions are of ecologically important to bacterioplankton in small boreal lakes, and that EET, particularly by methylotrophs and anoxygenic phototrophs, should be further studied and incorporated into methane emission models of melting permafrost.}, } @article {pmid36529302, year = {2023}, author = {Xu, A and Xu, S and Tu, Q and Qiao, H and Lin, W and Li, J and He, Y and Xie, T and Pan, L and Pan, Q and Zhao, Y and Su, X and Tong, Y}, title = {A novel virus in the family Marnaviridae as a potential pathogen of Penaeus vannamei glass post-larvae disease.}, journal = {Virus research}, volume = {324}, number = {}, pages = {199026}, pmid = {36529302}, issn = {1872-7492}, mesh = {Animals ; *Penaeidae ; *RNA Viruses ; Genome ; Genomics ; China ; }, abstract = {As an aquatic animal of great commercial relevance, Penaeus vannamei is currently the dominant species of cultured shrimp in China and many other countries worldwide. In recent years, the outbreak of glass post-larvae disease (GPD), which accounts for more than 90% of the mortality of shrimp seedlings in serious cases, in many regions of China has caused significant losses and threatened the sustainability of the aquaculture industry and the economy. It is extremely urgent to determine the infectious agent of GPD in P. vannamei. In this work, we performed metagenomic sequencing of glass post-larvae collected from diseased prawns in Tangshan Hebei, where GPD broke out recently. An evolutionary tree was constructed by MEGA 7 to understand the evolutionary history and relationship of the pathogen genome. A novel virus in the family Marnaviridae was first identified in P. vannamei suffering from GPD, and we tentatively named this virus Baishivirus (GenBank: ON550424). The identified pathogen was validated according to Koch's rule with a pathogenic challenge assay and reverse transcription-polymerase chain reaction. There was only 8% query coverage with 64.96% identity in the Baishivirus genome when compared with its most closely related genome sequence of Wenzhou picorna-like virus 21 reported in 2016. Baishivirus genomic RNA is 9.895 kb in length and encodes three potential open reading frames (ORFs). The identification of Baishivirus in P. vannamei enriches the family Marnaviridae and potentially provides a new candidate to study and prevent GPD in the aquaculture industry.}, } @article {pmid36529164, year = {2023}, author = {Li, S and Jiang, J and Ho, SH and Zhang, S and Zeng, W and Li, F}, title = {Sustainable conversion of antibiotic wastewater using microbial fuel cells: Energy harvesting and resistance mechanism analysis.}, journal = {Chemosphere}, volume = {313}, number = {}, pages = {137584}, doi = {10.1016/j.chemosphere.2022.137584}, pmid = {36529164}, issn = {1879-1298}, mesh = {*Anti-Bacterial Agents/pharmacology ; Wastewater ; *Bioelectric Energy Sources ; Tetracycline ; Genes, Bacterial ; }, abstract = {In this study, tetracycline (TC) can be degraded in microbial fuel cells (MFCs) rapidly and efficiently for the synergistic effect of microbial metabolism and electrical stimulation. Different TC concentrations had different effects on the bioelectric performance of MFCs. Among them, 10 mg/L TC promoted the bioelectric properties of MFCs, the maximum power density reached 1744.4 ± 74.9 mW/cm[2]. In addition, we demonstrated that Geobacter and Chryseobacterium were the dominant species in the anode biofilm, while Azoarcus and Pseudomonas were the prominent species in the effluent, and the initial TC concentration affected the microbial community composition. Furthermore, the addition of TC increased the relative abundance of aadA3, sul1, adeF, cmlA, and tetC in reactors, indicating that a single antibiotic could promote the expression of self-related resistance as well as the expression of other ARGs. Moreover, the presence of TC can increase the relative content of mobile genetic elements (MGEs) and greatly increase the risk of antibiotic resistance genes (ARGs) spreading. Meanwhile, network analysis revealed that some microorganisms (such as Acidovorax caeni, Geobacter soil, and Pseudomonas thermotolerans) and MGEs may be potential hosts for multiple ARGs.}, } @article {pmid36528093, year = {2023}, author = {Milan, M and Bernardini, I and Bertolini, C and Dalla Rovere, G and Manuzzi, A and Pastres, R and Peruzza, L and Smits, M and Fabrello, J and Breggion, C and Sambo, A and Boffo, L and Gallocchio, L and Carrer, C and Sorrentino, F and Bettiol, C and Lodi, GC and Semenzin, E and Varagnolo, M and Matozzo, V and Bargelloni, L and Patarnello, T}, title = {Multidisciplinary long-term survey of Manila clam grown in farming sites subjected to different environmental conditions.}, journal = {The Science of the total environment}, volume = {863}, number = {}, pages = {160796}, doi = {10.1016/j.scitotenv.2022.160796}, pmid = {36528093}, issn = {1879-1026}, mesh = {Animals ; *Bivalvia/metabolism ; Seafood ; Agriculture ; Genomics ; }, abstract = {In recent years recurrent bivalve mass mortalities considerably increased around the world, causing the collapse of natural and farmed populations. Venice Lagoon has historically represented one of the major production areas of the Manila clam Ruditapes philippinarum in Europe. However, in the last 20 years a 75 % decrease in the annual production has been experienced. While climate change and anthropogenic interventions may have played a key role in natural and farmed stocks reductions, no studies investigated at multiple levels the environmental stressors affecting farmed Manila clam to date. In this work we carried out a long-term monitoring campaign on Manila clam reared in four farming sites located at different distances from the southern Venice Lagoon inlet, integrating (meta)genomic approaches (i.e. RNA-seq; microbiota characterization), biometric measurements and chemical-physical parameters. Our study allowed to characterize the molecular mechanisms adopted by this species to cope with the different environmental conditions characterizing farming sites and to propose hypotheses to explain mortality events observed in recent years. Among the most important findings, the disruption of clam's immune response, the spread of Vibrio spp., and the up-regulation of molecular pathways involved in xenobiotic metabolism suggested major environmental stressors affecting clams farmed in sites placed close to Chioggia's inlet, where highest mortality was also observed. Overall, our study provides knowledge-based tools for managing Manila clam farming on-growing areas. In addition, the collected data is a snapshot of the time immediately before the commissioning of MoSE, a system of mobile barriers aimed at protecting Venice from high tides, and will represent a baseline for future studies on the effects of MoSE on clams farming and more in general on the ecology of the Venice Lagoon.}, } @article {pmid36527826, year = {2023}, author = {Lv, Y and Lou, Y and Liu, A and Cheng, Q and Yang, G and Xu, C and Luo, Y and Lou, J and Yu, J and Fang, Y and Zhao, H and Peng, K and Ni, Y and Chen, J}, title = {The impact of exclusive enteral nutrition on the gut microbiome and bile acid metabolism in pediatric Crohn's disease.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {42}, number = {2}, pages = {116-128}, doi = {10.1016/j.clnu.2022.11.018}, pmid = {36527826}, issn = {1532-1983}, mesh = {Child ; Humans ; *Bile Acids and Salts/metabolism ; *Crohn Disease/diet therapy/etiology/metabolism/microbiology ; *Enteral Nutrition ; Firmicutes/isolation & purification ; *Gastrointestinal Microbiome ; Leukocyte L1 Antigen Complex/analysis ; Remission Induction ; Dysbiosis/complications/metabolism/microbiology ; Feces/chemistry/microbiology ; }, abstract = {BACKGROUND: Gut dysbiosis and associated bile acid (BA) metabolism play an important role in the pathogenesis of Crohn's disease (CD). We investigated the impacts of the exclusive enteral nutrition treatment (EEN) on the gut microbiome (GM) and BAs metabolism for patients with CD.

METHODS: Targeted metabolomics analysis and metagenomics analysis were performed in feces to investigate the BA and GM changes of patients before and after 2-months EEN therapy. The Pediatric Crohn's Disease Activity Index (PCDAI) and fecal calprotectin were used to evaluate the severity and mucosal inflammation of CD.

RESULTS: A total of 27 newly diagnosed pediatric patients with CD and 27 healthy controls were recruited in this study. Both GM structure and the secondary BA metabolism were significantly impaired in patients, which could return towards normal levels after EEN treatment. The most abundant taxa Firmicutes and 11 BAs were found closely associated with the PCDAI score and fecal calprotectin. Meanwhile, the close interactions between Firmicute bacteria and BAs might contribute to the remission of CD after EEN treatment. The qPCR data further confirmed that the relative expressions of Firmicutes phylum, and genus Flavonifractor and Clostridium V were improved after EEN treatment.

CONCLUSIONS: Firmicutes bacteria and the balance of primary and secondary BA compositions in the gut were closely associated with the health status of CD disease indicated by the PCDAI score and fecal calprotectin. Understanding the recovery process of gut microbiome and BA metabolism will help us to explore the potential mechanisms of EEN therapy.}, } @article {pmid36527813, year = {2023}, author = {Jan, TR and Lin, CS and Wang, SY and Yang, WY}, title = {Cytokines and cecal microbiome modulations conferred by a dual vaccine in Salmonella-infected layers.}, journal = {Poultry science}, volume = {102}, number = {2}, pages = {102373}, pmid = {36527813}, issn = {1525-3171}, mesh = {Humans ; Animals ; Cytokines ; Salmonella enteritidis ; RNA, Ribosomal, 16S ; Chickens/genetics ; *Salmonella Vaccines ; *Microbiota ; Vaccines, Attenuated ; *Salmonella Infections, Animal/prevention & control ; *Poultry Diseases/prevention & control ; }, abstract = {Zoonotic Salmonella infection is a critical and challenging issue for public health. Since human infections are mainly associated with consuming contaminated chicken products, strategies to reduce Salmonella carriage and shedding are essential. Here we investigate the mechanisms of the live attenuated Salmonella vaccine (AviPro Salmonella Duo) against Salmonella Enteritidis (SE) infection. We focused on inflammatory-related cytokine expressions and cecal microbiota modulations in specific-pathogen-free (SPF) and field layers. Forty-eight 2-day-old SPF layers were randomly allotted into S.SEvc, S.SEc, S.Vc, and S.Ct groups in trial 1. The equal number of filed layers at 25 wk were allocated into SEvc, SEc, Vc, and Ct groups in trial 2. Each group contained 12 layers. Groups were further assigned for vaccination (S.Vc and Vc groups), SE challenge (S.SEc and SEc groups), vaccination and the following SE challenge (S.SEvc and SEvc groups), or the placebo treatment (S.Ct and Ct groups). Cecal tissues and contents of layers on day 14 post-SE-challenges were collected for cytokine mRNA expression and 16S rRNA metagenomic analyses. We found that SE challenges significantly upregulated expressions of IFNγ, IL-1β, IL-12β, and NFκB1A in SPF layers. The vaccine notably counteracted the levels of IFNα, IFNγ, and NFκB1A activated by SE attacks. The vaccination, SE challenge, and their combination did not significantly affect alpha diversities but promoted dissimilarities in microbial communities between groups. Eubacterium_coprostanoligenes and Faecalibacterium_prausnitzii were identified as contributory taxa in the cecal microbiota of SE-challenged and vaccinated SPF layers. A significantly higher abundance of Faecalibacterium_prausnitzii in the ceca further correlated with the vaccination conferred protection against SE infection. In contrast, Oscillibacter_valericigenes and Mediterraneibacter_glycyrrhizinilyticus were featured taxa in Salmonella-infected field layers. Megamonas_hypermegale and Megamonas_rupellensis were identified as featured taxa in vaccinated field layers compared to SE-infected layers. To conclude, applying a dual Salmonella vaccine in this study modulated expressions of inflammatory-related cytokines and the cecal microbiome in layers, contributing to protection against SE infection. The feature microbes are promising for developing predictive indices and as antibiotic alternatives added to feed to reduce the risk of Salmonella shedding and contamination.}, } @article {pmid36527793, year = {2023}, author = {Du, H and Chen, B and Fu, W and Yang, F and Lv, X and Tan, Y and Xi, X and Wang, L and Xu, Y}, title = {Composition and function of viruses in sauce-flavor baijiu fermentation.}, journal = {International journal of food microbiology}, volume = {387}, number = {}, pages = {110055}, doi = {10.1016/j.ijfoodmicro.2022.110055}, pmid = {36527793}, issn = {1879-3460}, mesh = {Fermentation ; Bacteria/genetics/metabolism ; *Microbiota/genetics ; Food ; *Bacteriophages/genetics ; }, abstract = {Viruses are highly abundant in nature, associated with quality and safety of traditional fermented foods. However, the overall viral diversity and function are still poorly understood in food microbiome. Traditional baijiu fermentation is an ideal model system to examine the diversity and function of viruses owing to easy access, stable operation, and domesticated microbial community. Equipped with cutting-edge viral metagenomics, we investigated the viral community in the fermented grain and fermentation environment, as well as their contribution to baijiu fermentation. Viral communities in the fermented grains and fermentation environment are highly similar. The dominant viruses were bacteriophages, mainly including the order Caudovirales and the family Inoviridae. Furtherly, association network analysis showed that viruses and bacteria were significantly negatively correlated (P < 0.01). Viral diversity could significantly influence bacterial and fungal succession (P < 0.05). Moreover, we proved that starter phages could significantly inhibit the growth of Bacillus licheniformis in the logarithmic growth stage (P < 0.05) under culture condition. Based on the functional annotations, viruses and bacteria both showed high distribution of genes related to amino acid and carbohydrate metabolism. In addition, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes were also identified in viruses, indicating that viruses were involved in the decomposition of complex polysaccharides during fermentation. Our results revealed that viruses could crucially affect microbial community and metabolism during traditional fermentation.}, } @article {pmid36527125, year = {2022}, author = {Brusselaers, N and Pereira, M and Alm, J and Engstrand, L and Engstrand Lilja, H}, title = {Effect of proton pump inhibitors in infants with esophageal atresia on the gut microbiome: a pilot cohort.}, journal = {Gut pathogens}, volume = {14}, number = {1}, pages = {47}, pmid = {36527125}, issn = {1757-4749}, abstract = {BACKGROUND: The effects of proton-pump inhibitors (PPIs) on the infant microbiome remain unclear. Swedish pilot cohort study to assess the longitudinal effect of long-term PPI on the infant gut microbiome, including ten newborn infants operated for esophageal atresia exposed to PPIs (mean 57 weeks), compared to healthy one-year-old controls. All children were born vaginally and were otherwise healthy. Within- and between sample diversity of the fecal microbiome was assessed using untargeted whole genome Shotgun metagenomics which sequences all the DNA in the sample and can capture genes rather than a taxonomic fingerprint.

RESULTS: A longer duration of PPI-use was associated with considerable changes in evenness and high variation on diversity within samples compared to a shorter duration of use. The limited difference between baseline samples and controls suggests that this shift was most likely due to the drug exposure and not the underlying alterations on the microbiome. We found no associations with the number of antibiotic treatment episodes among the PPI-users.

CONCLUSION: Prolonged PPI-use may alter the early infant gut microbiome composition, especially those with the most prolonged duration of use.}, } @article {pmid36527083, year = {2022}, author = {Ghale, R and Spottiswoode, N and Anderson, MS and Mitchell, A and Wang, G and Calfee, CS and DeRisi, JL and Langelier, CR}, title = {Prevalence of type-1 interferon autoantibodies in adults with non-COVID-19 acute respiratory failure.}, journal = {Respiratory research}, volume = {23}, number = {1}, pages = {354}, pmid = {36527083}, issn = {1465-993X}, support = {R35 HL140026/HL/NHLBI NIH HHS/United States ; T32 AI007641/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Adult ; Autoantibodies ; *COVID-19 ; Prevalence ; Prospective Studies ; *Interferon Type I ; *Respiratory Distress Syndrome ; *Respiratory Insufficiency/diagnosis/epidemiology ; }, abstract = {Auto-antibodies (Abs) to type I interferons (IFNs) are found in up to 25% of patients with severe COVID-19, and are implicated in disease pathogenesis. It has remained unknown, however, whether type I IFN auto-Abs are unique to COVID-19, or are also found in other types of severe respiratory illnesses. To address this, we studied a prospective cohort of 284 adults with acute respiratory failure due to causes other than COVID-19. We measured type I IFN auto-Abs by radio ligand binding assay and screened for respiratory viruses using clinical PCR and metagenomic sequencing. Three patients (1.1%) tested positive for type I IFN auto-Abs, and each had a different underlying clinical presentation. Of the 35 patients found to have viral infections, only one patient tested positive for type I IFN auto-Abs. Together, our data suggest that type I IFN auto-Abs are uncommon in critically ill patients with acute respiratory failure due to causes other than COVID-19.}, } @article {pmid36526191, year = {2023}, author = {Barbosa, FAS and Brait, LAS and Coutinho, FH and Ferreira, CM and Moreira, EF and de Queiroz Salles, L and Meirelles, PM}, title = {Ecological landscape explains aquifers microbial structure.}, journal = {The Science of the total environment}, volume = {862}, number = {}, pages = {160822}, doi = {10.1016/j.scitotenv.2022.160822}, pmid = {36526191}, issn = {1879-1026}, mesh = {Humans ; *Groundwater/chemistry ; Bacteria/metabolism ; Water Quality ; Gram-Negative Bacteria ; *Microbiota ; }, abstract = {Aquifers have significant social, economic, and ecological importance. They supply 30 % of the freshwater for human consumption worldwide, including agricultural and industrial use. Despite aquifers' importance, the relationships between aquifer categories and their inhabiting microbial communities are still unknown. Characterizing variations within microbial communities' function and taxonomy structure at different aquifers could give a panoramic view of patterns that may enable the detection and prediction of environmental impact caused by multiple sources. Using publicly available shotgun metagenomic datasets, we examined whether soil properties, land use, and climate variables would have a more significant influence on the taxonomy and functional structure of the microbial communities than the ecological landscapes of the aquifer (i.e., Karst, Porous, Saline, Geyser, and Porous Contaminated). We found that these categories are stronger predictors of microbial communities' structure than geographical localization. In addition, our results show that microbial richness and dominance patterns are the opposite of those found in multicellular life, where extreme habitats harbour richer functional and taxonomic microbial communities. We found that low-abundant and recently described candidate taxa, such as the chemolithoautotrophic genus Candidatus Altiarcheum and the Candidate phylum Parcubacteria, are the main contributors to aquifer microbial communities' dissimilarities. Genes related to gram-negative bacteria proteins, cell wall structures, and phage activity were the primary contributors to aquifer microbial communities' dissimilarities among the aquifers' ecological landscapes. The results reported in the present study highlight the utility of using ecological landscapes for investigating aquifer microbial communities. In addition, we suggest that functions played by recently described and low abundant bacterial groups need further investigation once they might affect water quality, geochemical cycles, and the effects of anthropogenic disturbances such as pollution and climatic events on aquifers.}, } @article {pmid36526186, year = {2023}, author = {Nie, S and Mo, S and Gao, T and Yan, B and Shen, P and Kashif, M and Zhang, Z and Li, J and Jiang, C}, title = {Coupling effects of nitrate reduction and sulfur oxidation in a subtropical marine mangrove ecosystem with Spartina alterniflora invasion.}, journal = {The Science of the total environment}, volume = {862}, number = {}, pages = {160930}, doi = {10.1016/j.scitotenv.2022.160930}, pmid = {36526186}, issn = {1879-1026}, mesh = {*Ecosystem ; *Wetlands ; Nitrates/metabolism ; Introduced Species ; Poaceae/metabolism ; Nitrogen/analysis ; Sulfur/metabolism ; China ; }, abstract = {The mangrove ecosystem has a high nitrate reduction capacity, which significantly alleviates severe nitrogen pollution. However, current research on nitrate reduction mechanisms in the mangrove ecosystem is limited. Furthermore, Spartina alterniflora invasion has disrupted the balance of the mangrove ecosystem and the effect of S. alterniflora on nitrate reduction has not yet been fully elucidated. Nitrate reduction was comprehensively investigated in a subtropical mangrove ecosystem in this study, which has been invaded by S. alterniflora for 40 years. Results showed that S. alterniflora significantly increased the relative and absolute abundance of nitrate reduction genes, especially nirS (nitrite reductase), in the mangrove ecosystem. Dissimilatory nitrate reduction to ammonium was the main pathway of nitrate reduction in the mangrove ecosystem. Nitrate reduction was mainly performed by Desulfobacterales and occurred in the shallow layers (0-10 cm) of mangrove sediments. A strong positive correlation was found between nitrate reduction and sulfur oxidation (especially sulfide oxidation), and the sulfide content was significantly positively correlated with the relative abundance of nitrate reduction genes. Moreover, 207 metagenomic assembled genomes (MAGs) were constructed, including 50 MAGs with high numbers (≥ 10) of nitrate reduction genes. This finding indicates that the dominant microbes had strong nitrate reduction potential in mangrove sediments. Our findings highlight the impact of S. alterniflora invasion on nitrate reduction in a subtropical marine mangrove ecosystem. This study provides new insights into our understanding of nitrogen pollution control and contributes to the exploration of new nitrogen-degrading microbes in mangrove ecosystems.}, } @article {pmid36526119, year = {2023}, author = {Zhong, Y and He, J and Zhang, P and Zou, X and Pan, X and Zhang, J}, title = {Novel nitrogen-doped biochar supported magnetite promotes anaerobic digestion: Material characterization and metagenomic analysis.}, journal = {Bioresource technology}, volume = {369}, number = {}, pages = {128492}, doi = {10.1016/j.biortech.2022.128492}, pmid = {36526119}, issn = {1873-2976}, mesh = {*Ferrosoferric Oxide ; *Sewage/microbiology ; Anaerobiosis ; Nitrogen ; Methane ; Bioreactors ; }, abstract = {Although different conductive materials have been applied to anaerobic digestion, there has not been a material that can really combine their merits and make up their shortcoming from each other. In this study, a novel nitrogen-doped biochar supported magnetite (Fe3O4@N-BC) was synthesized. Various material characterizations confirmed that nitrogen atoms were successful doped into the biochar and magnetite precipitated on its surface. 5 g/L Fe3O4@N-BC achieved the highest promotion of cumulative CH4 production by 1.75 times compared with the blank group. Further metagenomic analysis revealed that Fe3O4@N-BC could increase the gene abundances of pilA, MmcA, Fpo, Rnf and HdrEd in bacteria Clotridium, Pseudomonas and Syntrophomonas and archaea Methanosarcina. Redundancy analysis showed that it was electrical conductivity and electron exchange capacity that were the key physicochemical characteristics for Fe3O4@N-BC to facilitating direct interspecies electron transfer. This study provides a reference for future conductive material synthesis and its application for anaerobic digestion.}, } @article {pmid36525577, year = {2023}, author = {Li, Y and Guo, L and Kolton, M and Yang, R and Zhang, M and Qi, F and Soleimani, M and Sun, X and Li, B and Gao, W and Yan, G and Xu, R and Sun, W}, title = {Chemolithotrophic Biological Nitrogen Fixation Fueled by Antimonite Oxidation May Be Widespread in Sb-Contaminated Habitats.}, journal = {Environmental science & technology}, volume = {57}, number = {1}, pages = {231-243}, doi = {10.1021/acs.est.2c06424}, pmid = {36525577}, issn = {1520-5851}, mesh = {*Nitrogen Fixation ; Antimony/analysis/chemistry ; Oxidation-Reduction ; Ecosystem ; *Arsenic ; Nitrogen/analysis ; }, abstract = {Nitrogen (N) deficiency in mining-contaminated habitats usually hinders plant growth and thus hampers tailing revegetation. Biological N fixation (BNF) is an essential biogeochemical process that contributes to the initial accumulation of N in oligotrophic mining-contaminated regions. Previous studies reported that chemolithotrophic rather than heterotrophic diazotrophs frequently dominated in the mining-contaminated regions. Chemolithotrophic diazotrophs may utilize elements abundant in such habitats (e.g., sulfur (S), arsenic (As), and antimony (Sb)) as electron donors to fix N2. BNF fueled by the oxidation of S and As has been detected in previous studies. However, BNF fueled by Sb(III) oxidation (Sb-dependent BNF) has never been reported. The current study observed the presence of Sb-dependent BNF in slurries inoculated from Sb-contaminated habitats across the South China Sb belt, suggesting that Sb-dependent BNF may be widespread in this region. DNA-stable isotope probing identified bacteria associated with Rhodocyclaceae and Rhizobiaceae as putative microorganisms responsible for Sb-dependent BNF. Furthermore, metagenomic-binning demonstrated that Rhodocyclaceae and Rhizobiaceae contained essential genes involved in Sb(III) oxidation, N2 fixation, and carbon fixation, suggesting their genetic potential for Sb-dependent BNF. In addition, meta-analysis indicated that these bacteria are widespread among Sb-contaminated habitats with different niche preferences: Rhodocyclaceae was enriched in river sediments and tailings, while Rhizobiaceae was enriched only in soils. This study may broaden our fundamental understanding of N fixation in Sb-mining regions.}, } @article {pmid36524354, year = {2023}, author = {Premachandra, T and Cauret, CMS and Conradie, W and Measey, J and Evans, BJ}, title = {Population genomics and subgenome evolution of the allotetraploid frog Xenopus laevis in southern Africa.}, journal = {G3 (Bethesda, Md.)}, volume = {13}, number = {2}, pages = {}, pmid = {36524354}, issn = {2160-1836}, mesh = {Animals ; Xenopus laevis/genetics ; *Metagenomics ; *Genome ; Genomics ; Africa, Southern ; Evolution, Molecular ; Phylogeny ; }, abstract = {Allotetraploid genomes have two distinct genomic components called subgenomes that are derived from separate diploid ancestral species. Many genomic characteristics such as gene function, expression, recombination, and transposable element mobility may differ significantly between subgenomes. To explore the possibility that subgenome population structure and gene flow may differ as well, we examined genetic variation in an allotetraploid frog-the African clawed frog (Xenopus laevis)-over the dynamic and varied habitat of its native range in southern Africa. Using reduced representation genome sequences from 91 samples from 12 localities, we found no strong evidence that population structure and gene flow differed substantially by subgenome. We then compared patterns of population structure in the nuclear genome to the mitochondrial genome using Sanger sequences from 455 samples from 183 localities. Our results provide further resolution to the geographic distribution of mitochondrial and nuclear diversity in this species and illustrate that population structure in both genomes corresponds roughly with variation in seasonal rainfall and with the topography of southern Africa.}, } @article {pmid36524338, year = {2023}, author = {Lee, W and Kim, MH and Park, J and Kim, YJ and Kim, E and Heo, EJ and Kim, SH and Kim, G and Shin, H and Kim, SH and Kim, HY}, title = {Seasonal Changes in the Microbial Communities on Lettuce (Lactuca sativa L.) in Chungcheong-do, South Korea.}, journal = {Journal of microbiology and biotechnology}, volume = {33}, number = {2}, pages = {219-227}, pmid = {36524338}, issn = {1738-8872}, mesh = {*Lactuca/microbiology ; Seasons ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenome ; Bacteria ; }, abstract = {Lettuce is one of the most consumed vegetables worldwide. However, it has potential risks associated with pathogenic bacterial contamination because it is usually consumed raw. In this study, we investigated the changes in the bacterial community on lettuce (Lactuca sativa L.) in Chungcheong-do, South Korea, and the prevalence of foodborne pathogens on lettuce in different seasons using 16S rRNA gene-based sequencing. Our data revealed that the Shannon diversity index showed the same tendency in term of the number of OTUs, with the index being greatest for summer samples in comparison to other seasons. Moreover, the microbial communities were significantly different between the four seasons. The relative abundance of Actinobacteriota varied according to the season. Family Micrococcaceae was most dominant in all samples except summer, and Rhizobiaceae was predominant in the microbiome of the summer sample. At the genus level, the relative abundance of Bacillus was greatest in spring samples, whereas Pseudomonas was greatest in winter samples. Potential pathogens, such as Staphylococcus and Clostridium, were detected with low relative abundance in all lettuce samples. We also performed metagenome shotgun sequencing analysis on the selected summer and winter samples, which were expected to be contaminated with foodborne pathogens, to support 16S rRNA gene-based sequencing dataset. Moreover, we could detect seasonal biomarkers and microbial association networks of microbiota on lettuce samples. Our results suggest that seasonal characteristics of lettuce microbial communities, which include diverse potential pathogens, can be used as basic data for food safety management to predict and prevent future outbreaks.}, } @article {pmid36523460, year = {2022}, author = {Baeza, JA}, title = {Mitochondrial genomes assembled from non-invasive eDNA metagenomic scat samples in the endangered Amur tiger Panthera tigris altaica.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e14428}, pmid = {36523460}, issn = {2167-8359}, mesh = {Animals ; *Tigers/genetics ; *Genome, Mitochondrial/genetics ; Endangered Species ; Metagenomics ; Metagenome ; }, abstract = {The Amur or Siberian tiger Panthera tigris altaica (Temminck, 1844) is currently restricted to a small region of its original geographical range in northwestern Asia and is considered 'endangered' by the IUCN Red List of Threatened Species. This solitary, territorial, and large top predator is in major need of genomic resources to inform conservation management strategies. This study formally tested if complete mitochondrial genomes of P. tigris altaica can be assembled from non-enriched metagenomic libraries generated from scat eDNA samples using the Illumina sequencing platform and open-access bioinformatics pipelines. The mitogenome of P. tigris altaica was assembled and circularized using the pipeline GetOrganelle with a coverage ranging from 322.7x to 17.6x in four different scat eDNA samples. A nearly complete mitochondrial genome (101x) was retrieved from a fifth scat eDNA sample. The complete or nearly complete mitochondrial genomes of P. tigris altaica were AT-rich and composed of 13 protein coding genes (PCGs), 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Synteny observed in all assembled mitogenomes was identical to that reported before for P. tigris altaica and other felids. A phylogenomic analysis based on all PCGs demonstrated that the mitochondrial genomes assembled from scat eDNA reliably identify the sequenced samples as belonging to P. tigris and distinguished the same samples from closely and distantly related congeneric species. This study demonstrates that it is viable to retrieve accurate whole and nearly complete mitochondrial genomes of P. tigris altaica (and probably other felids) from scat eDNA samples without library enrichment protocols and using open-access bioinformatics workflows. This new genomic resource represents a new tool to support conservation strategies (bio-prospecting and bio-monitoring) in this iconic cat.}, } @article {pmid36523457, year = {2022}, author = {Chang, W and Feng, W and Yang, Y and Shen, Y and Song, T and Li, Y and Cai, W}, title = {Metagenomics analysis of the effects of Agaricus bisporus mycelia on microbial diversity and CAZymes in compost.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e14426}, pmid = {36523457}, issn = {2167-8359}, mesh = {*Lignin/metabolism ; *Composting ; Laccase/genetics ; Metagenomics ; }, abstract = {Agaricus bisporus growth alters the lignocellulosic composition and structure of compost. However, it is difficult to differentiate the enzyme activities of A. bisporus mycelia from the wider microbial community owing to the complication of completely speareting the mycelia from compost cultures. Macrogenomics analysis was employed in this study to examine the fermentation substrate of A. bisporus before and after mycelial growth, and the molecular mechanism of substrate utilization by A. bisporus mycelia was elucidated from the perspective of microbial communities and CAZymes in the substrate. The results showed that the relative abundance of A. bisporus mycelia increased by 77.57-fold after mycelial colonization, the laccase content was significantly increased and the lignin content was significantly decreased. Analysis of the CAZymes showed that AA10 family was extremely differentiated. Laccase-producing strains associated with AA10 family were mostly bacteria belonging to Thermobifida and Thermostaphylospora, suggesting that these bacteria may play a synergistic role in lignin decomposition along with A. bisporus mycelia. These findings provide preliminary evidence for the molecular mechanism of compost utilization by A. bisporus mycelia and offer a reference for the development and utilization of strains related to lignocellulose degradation.}, } @article {pmid36522829, year = {2023}, author = {Shimomura, Y and Zha, L and Komukai, S and Narii, N and Sobue, T and Kitamura, T and Shiba, S and Mizutani, S and Yamada, T and Sawada, N and Yachida, S}, title = {Mediation effect of intestinal microbiota on the relationship between fiber intake and colorectal cancer.}, journal = {International journal of cancer}, volume = {152}, number = {9}, pages = {1752-1762}, doi = {10.1002/ijc.34398}, pmid = {36522829}, issn = {1097-0215}, mesh = {Male ; Humans ; Middle Aged ; Female ; *Colorectal Neoplasms/diagnosis ; *Gastrointestinal Microbiome ; Cross-Sectional Studies ; *Gemella ; Fusobacterium nucleatum ; }, abstract = {Higher fiber intake has been associated with a lower risk of colorectal cancer (CRC) and has been shown to protect against CRC based on probable evidence. Recent studies revealed a possible mechanism whereby the interaction between intestinal microbiota and fiber intake mediates CRC risk. However, the specific intestinal bacteria and the amount of these bacteria involved in this mechanism are not fully known. Therefore, this single-center study aimed to determine whether specific intestinal bacteria mediated the relationship between fiber intake and CRC risk. We enrolled patients who received colonoscopy at National Cancer Center Hospital. This cross-sectional study included 180 patients with clinically diagnosed CRC and 242 controls. We conducted a causal mediation analysis to assess the natural indirect effect and natural direct effect of specific intestinal bacteria on association between fiber intake and CRC risk. The median age was 64 (interquartile range, 54-70) years, and 58% of the participants were males. We used metagenomics for profiling gut microbiomes. The relative abundance of each species in each sample was calculated. Among the candidate, Fusobacterium nucleatum and Gemella morbillorum had a significant natural indirect effect based on their highest fiber intake compared to the lowest fiber intake, with a risk difference (95% confidence interval, proportion of mediation effect) of -0.06 [-0.09 to -0.03, 23%] and -0.03 [-0.06 to -0.01, 10.5%], respectively. Other bacteria did not display natural indirect effects. In conclusion, Fusobacterium nucleatum and Gemella morbillorum were found to mediate the relationship between fiber intake and CRC risk.}, } @article {pmid36522795, year = {2022}, author = {Xie, F and Jin, W and Si, H and Yuan, Y and Tao, Y and Liu, J and Wang, X and Yang, C and Li, Q and Yan, X and Lin, L and Jiang, Q and Zhang, L and Guo, C and Greening, C and Heller, R and Guan, LL and Pope, PB and Tan, Z and Zhu, W and Wang, M and Qiu, Q and Li, Z and Mao, S}, title = {Correction: An integrated gene catalog and over 10,000 metagenome-assembled genomes from the gastrointestinal microbiome of ruminants.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {228}, pmid = {36522795}, issn = {2049-2618}, } @article {pmid36522762, year = {2022}, author = {Olías-Molero, AI and Botías, P and Cuquerella, M and García-Cantalejo, J and Barcia, E and Torrado, S and Torrado, JJ and Alunda, JM}, title = {Leishmania infantum infection does not affect the main composition of the intestinal microbiome of the Syrian hamster.}, journal = {Parasites & vectors}, volume = {15}, number = {1}, pages = {468}, pmid = {36522762}, issn = {1756-3305}, support = {PR87/19-22646//Proyectos Santander/Complutense/ ; }, mesh = {Cricetinae ; Dogs ; Male ; Animals ; *Leishmania infantum ; Mesocricetus ; *Gastrointestinal Microbiome ; *Leishmaniasis, Visceral/parasitology ; *Leishmaniasis/parasitology ; Immunoglobulin G ; }, abstract = {BACKGROUND: Visceral leishmaniasis (VL) is the most severe form of all leishmanial infections and is caused by infection with protozoa of Leishmania donovani and Leishmania infantum. This parasitic disease occurs in over 80 countries and its geographic distribution is on the rise. Although the interaction between the intestinal microbiome and the immune response has been established in several pathologies, it has not been widely studied in leishmaniasis. The Syrian hamster is the most advanced laboratory model for developing vaccines and new drugs against VL. In the study reported here, we explored the relationship between the intestinal microbiome and infection with L. infantum in this surrogate host.

METHODS: Male Syrian hamsters (120-140 g) were inoculated with 10[8] promastigotes of a canine-derived L. infantum strain or left as uninfected control animals. Infection was maintained for 19 weeks (endpoint) and monitored by an immunoglobulin G (IgG) enyzme-linked immunosorbent assay throughout the experiment. Individual faecal samples, obtained at weeks 16, 18 and 19 post-inoculation, were analysed to determine the 16S metagenomic composition (the operational taxonomic units [OTUs] of the intestinal microbiome and the comparison between groups were FDR (false discovery rate)-adjusted).

RESULTS: Leishmania infantum infection elicited moderate clinical signs and lesions and a steady increase in specific anti-Leishmania serum IgG. The predominant phyla (Firmicutes + Bacteriodetes: > 90%), families (Muribaculaceae + Lachnospiraceae + Ruminococcaceae: 70-80%) and genera found in the uninfected hamsters showed no significant variations throughout the experiment. Leishmania infantum infection provoked a slightly higher-albeit non-significant-value for the Firmicutes/Bacteriodetes ratio but no notable differences were found in the relative abundance or diversity of phyla and families. The microbiome of the infected hamsters was enriched in CAG-352, whereas Lachnospiraceae UCG-004, the [Eubacterium] ventriosum group and Allobaculum were less abundant.

CONCLUSIONS: The lack of extensive significant differences between hamsters infected and uninfected with L. infantum in the higher taxa (phyla, families) and the scarce variation found, which was restricted to genera with a low relative abundance, suggest that there is no clear VL infection-intestinal microbiome axis in hamsters. Further studies are needed (chronic infections, co-abundance analyses, intestinal sampling, functional analysis) to confirm these findings and to determine more precisely the possible relationship between microbiome composition and VL infection.}, } @article {pmid36522631, year = {2022}, author = {Rojas-Jaimes, J and Lindo-Seminario, D and Correa-Núñez, G and Diringer, B}, title = {Characterization of the bacterial microbiome of Amblyomma scalpturatum and Amblyomma ovale collected from Tapirus terrestris and Amblyomma sabanerae collected from Chelonoidis denticulata, Madre de Dios- Peru.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {305}, pmid = {36522631}, issn = {1471-2180}, mesh = {Animals ; Humans ; Male ; Amblyomma ; Peru ; *Ticks/microbiology ; Animals, Wild ; *Turtles ; *Microbiota ; Brazil ; }, abstract = {BACKGROUND: Ticks are arthropods that can host and transmit pathogens to wild animals, domestic animals, and even humans. The microbiome in ticks is an endosymbiotic, pathogenic and is yet to be fully understood.

RESULTS: Adult male Amblyomma scalpturatum (A. scalpturatum) and Amblyomma ovale (A. ovale) ticks were collected from Tapirus terrestris (T. terrestris) captured in the rural area of San Lorenzo Village, and males Amblyomma sabanerae were collected from Chelonoidis denticulate (C. denticulate) of the Gamita Farm in the Amazon region of Madre de Dios, Peru. The Chao1 and Shannon-Weaver analyses indicated a greater bacterial richness and diversity in male A. sabanerae (Amblyomma sabanerae; 613.65-2.03) compared to male A. scalpturatum and A. ovale (A. scalpturatum and A. ovale; 102.17-0.40). Taxonomic analyses identified 478 operational taxonomic units representing 220 bacterial genera in A. sabanerae and 86 operational taxonomic units representing 28 bacterial genera in A. scalpturatum and A. ovale. Of the most prevalent genera was Francisella (73.2%) in A. sabanerae, and Acinetobacter (96.8%) in A. scalpturatum and A. ovale to be considered as the core microbiome of A. sabanerae and A. scalpturatum/A. ovale respectively.

CONCLUSIONS: We found a high bacterial diversity in male of A. sabanerae collected from C. denticulata showed prevalence of Francisella and prevalence of Acinetobacter in male A. scalpturatum and A. ovale collected from T. terrestris. The greatest bacterial diversity and richness was found in males A. sabanerae. This is the first bacterial metagenomic study performed in A. scalpturatum/A. ovale and A. sabanerae collected from T. terrestris and C. denticulata in the Peruvian jungle.}, } @article {pmid36522388, year = {2022}, author = {Villoslada-Blanco, P and Pérez-Matute, P and Íñiguez, M and Recio-Fernández, E and Jansen, D and De Coninck, L and Close, L and Blanco-Navarrete, P and Metola, L and Ibarra, V and Alba, J and Matthijnssens, J and Oteo, JA}, title = {Impact of HIV infection and integrase strand transfer inhibitors-based treatment on the gut virome.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {21658}, pmid = {36522388}, issn = {2045-2322}, mesh = {Humans ; *HIV Infections/drug therapy ; Virome ; *HIV Integrase Inhibitors/pharmacology/therapeutic use ; Dysbiosis/drug therapy ; *Bacteriophages ; *Viruses ; Integrases ; *HIV Integrase ; }, abstract = {Viruses are the most abundant components of the human gut microbiome with a significant impact on health and disease. The effects of human immunodeficiency virus (HIV) infection on gut virome has been scarcely analysed. Several studies suggested that integrase strand transfers inhibitors (INSTIs) are associated with a healthier gut. Thus, the objective of this work was to evaluate the effects of HIV infection and INSTIs on gut virome composition. 26 non-HIV-infected volunteers, 15 naive HIV-infected patients and 15 INSTIs-treated HIV-infected patients were recruited and their gut virome composition was analysed using shotgun sequencing. Bacteriophages were the most abundant and diverse viruses present in gut. HIV infection was accompanied by a decrease in phage richness which was reverted after INSTIs-based treatment. β-diversity of phages revealed that samples from HIV-infected patients clustered separately from those belonging to the control group. Differential abundant analysis showed an increase in phages belonging to Caudoviricetes class in the naive group and a decrease of Malgrandaviricetes class phages in the INSTIs-treated group compared to the control group. Besides, it was observed that INSTIs-based treatment was not able to reverse the increase of lysogenic phages associated with HIV infection or to modify the decrease observed on the relative abundance of Proteobacteria-infecting phages. Our study describes for the first time the impact of HIV and INSTIs on gut virome and demonstrates that INSTIs-based treatments are able to partially restore gut dysbiosis at the viral level, which opens several opportunities for new studies focused on microbiota-based therapies.}, } @article {pmid36522342, year = {2022}, author = {Aliaga Goltsman, DS and Alexander, LM and Lin, JL and Fregoso Ocampo, R and Freeman, B and Lamothe, RC and Perez Rivas, A and Temoche-Diaz, MM and Chadha, S and Nordenfelt, N and Janson, OP and Barr, I and Devoto, AE and Cost, GJ and Butterfield, CN and Thomas, BC and Brown, CT}, title = {Compact Cas9d and HEARO enzymes for genome editing discovered from uncultivated microbes.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7602}, pmid = {36522342}, issn = {2041-1723}, support = {S10 OD018174/OD/NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Gene Editing ; *Escherichia coli/genetics/metabolism ; Endonucleases/genetics/metabolism ; Clustered Regularly Interspaced Short Palindromic Repeats ; Ribonucleases/genetics ; RNA ; CRISPR-Cas Systems/genetics ; Mammals/genetics ; }, abstract = {Programmable, RNA-guided nucleases are diverse enzymes that have been repurposed for biotechnological applications. However, to further expand the therapeutic application of these tools there is a need for targetable systems that are small enough to be delivered efficiently. Here, we mined an extensive genome-resolved metagenomics database and identified families of uncharacterized RNA-guided, compact nucleases (between 450 and 1,050 aa). We report that Cas9d, a new CRISPR type II subtype, contains Zinc-finger motifs and high arginine content, features that we also found in nucleases related to HEARO effectors. These enzymes exhibit diverse biochemical characteristics and are broadly targetable. We show that natural Cas9d enzymes are capable of genome editing in mammalian cells with >90% efficiency, and further engineered nickase variants into the smallest base editors active in E. coli and human cells. Their small size, broad targeting potential, and translatability suggest that Cas9d and HEARO systems will enable a variety of genome editing applications.}, } @article {pmid36522135, year = {2023}, author = {Dorrell, RG and Kuo, A and Füssy, Z and Richardson, EH and Salamov, A and Zarevski, N and Freyria, NJ and Ibarbalz, FM and Jenkins, J and Pierella Karlusich, JJ and Stecca Steindorff, A and Edgar, RE and Handley, L and Lail, K and Lipzen, A and Lombard, V and McFarlane, J and Nef, C and Novák Vanclová, AM and Peng, Y and Plott, C and Potvin, M and Vieira, FRJ and Barry, K and de Vargas, C and Henrissat, B and Pelletier, E and Schmutz, J and Wincker, P and Dacks, JB and Bowler, C and Grigoriev, IV and Lovejoy, C}, title = {Convergent evolution and horizontal gene transfer in Arctic Ocean microalgae.}, journal = {Life science alliance}, volume = {6}, number = {3}, pages = {}, pmid = {36522135}, issn = {2575-1077}, mesh = {*Gene Transfer, Horizontal/genetics ; *Microalgae/genetics ; Arctic Regions ; Oceans and Seas ; Ice Cover ; Bacteria ; }, abstract = {Microbial communities in the world ocean are affected strongly by oceanic circulation, creating characteristic marine biomes. The high connectivity of most of the ocean makes it difficult to disentangle selective retention of colonizing genotypes (with traits suited to biome specific conditions) from evolutionary selection, which would act on founder genotypes over time. The Arctic Ocean is exceptional with limited exchange with other oceans and ice covered since the last ice age. To test whether Arctic microalgal lineages evolved apart from algae in the global ocean, we sequenced four lineages of microalgae isolated from Arctic waters and sea ice. Here we show convergent evolution and highlight geographically limited HGT as an ecological adaptive force in the form of PFAM complements and horizontal acquisition of key adaptive genes. Notably, ice-binding proteins were acquired and horizontally transferred among Arctic strains. A comparison with Tara Oceans metagenomes and metatranscriptomes confirmed mostly Arctic distributions of these IBPs. The phylogeny of Arctic-specific genes indicated that these events were independent of bacterial-sourced HGTs in Antarctic Southern Ocean microalgae.}, } @article {pmid36522100, year = {2023}, author = {Ke, Y and Sun, W and Jing, Z and Zhao, Z and Xie, S}, title = {Seasonal variations of microbial community and antibiotic resistome in a suburb drinking water distribution system in a northern Chinese city.}, journal = {Journal of environmental sciences (China)}, volume = {127}, number = {}, pages = {714-725}, doi = {10.1016/j.jes.2022.07.001}, pmid = {36522100}, issn = {1001-0742}, mesh = {Humans ; Anti-Bacterial Agents ; *Drinking Water ; Genes, Bacterial ; *Microbiota ; Seasons ; China ; }, abstract = {Antibiotic resistance genes (ARGs) are an emerging issue for drinking water safety. However, the seasonal variation of ARGs in drinking water distribution systems (DWDS) is still unclear. This work revealed the tempo-spatial changes of microbial community, ARGs, mobile genetic elements (MGEs) co-occurring with ARGs, ARG hosts in DWDS bulk water by means of metagenome assembly. The microbial community and antibiotic resistome varied with sampling season and site. Temperature, ammonia, chlorite and total plate count (TPC) drove the variations of microbial community structure. Moreover, environmental parameters (total organic carbon (TOC), chlorite, TPC and hardness) shifted antibiotic resistome. ARGs and MGEs co-occurring with ARGs showed higher relative abundance in summer and autumn, which might be attributed to detached pipe biofilm. In particular, ARG-bacitracin and plasmid were the predominant ARG and MGE, respectively. ARG hosts changed with season and site and were more diverse in summer and autumn. In winter and spring, Limnohabitans and Mycobacterium were the major ARG hosts as well as the dominant genera in microbial community. In addition, in summer and autumn, high relative abundance of Achromobacter and Stenotrophomonas were the hosts harboring many kinds of ARGs and MGEs at site in a residential zone (0.4 km from the water treatment plant). Compared with MGEs, microbial community had a greater contribution to the variation of antibiotic resistome. This work gives new insights into the dynamics of ARGs in full-scale DWDS and the underlying factors.}, } @article {pmid36522097, year = {2023}, author = {Ma, Q and Meng, N and Su, J and Li, Y and Gu, J and Wang, Y and Wang, J and Qu, Y and Zhao, Z and Sun, Y}, title = {Unraveling the skatole biodegradation process in an enrichment consortium using integrated omics and culture-dependent strategies.}, journal = {Journal of environmental sciences (China)}, volume = {127}, number = {}, pages = {688-699}, doi = {10.1016/j.jes.2022.06.025}, pmid = {36522097}, issn = {1001-0742}, mesh = {*Skatole/metabolism ; Biodegradation, Environmental ; *Rhodococcus/genetics/metabolism ; Oxygenases/genetics/metabolism ; Pseudomonas/metabolism ; Catechols/metabolism ; }, abstract = {3-Methylindole (skatole) is regarded as one of the most offensive compounds in odor emission. Biodegradation is feasible for skatole removal but the functional species and genes responsible for skatole degradation remain enigmatic. In this study, an efficient aerobic skatole-degrading consortium was obtained. Rhodococcus and Pseudomonas were identified as the two major and active populations by integrated metagenomic and metatranscriptomic analyses. Bioinformatic analyses indicated that the skatole downstream degradation was mainly via the catechol pathway, and upstream degradation was likely catalyzed by the aromatic ring-hydroxylating oxygenase and flavin monooxygenase. Genome binning and gene analyses indicated that Pseudomonas, Pseudoclavibacter, and Raineyella should cooperate with Rhodococcus for the skatole degradation process. Moreover, a pure strain Rhodococcus sp. DMU1 was successfully obtained which could utilize skatole as the sole carbon source. Complete genome sequencing showed that strain DMU1 was the predominant population in the consortium. Further crude enzyme and RT-qPCR assays indicated that strain DMU1 degraded skatole through the catechol ortho-cleavage pathway. Collectively, our results suggested that synergistic degradation of skatole in the consortium should be performed by diverse bacteria with Rhodococcus as the primary degrader, and the degradation mainly proceeded via the catechol pathway.}, } @article {pmid36522074, year = {2023}, author = {Liu, C and Chen, J and Yang, Y and Teng, Y and Chen, H}, title = {Biogeography and diversity patterns of antibiotic resistome in the sediments of global lakes.}, journal = {Journal of environmental sciences (China)}, volume = {127}, number = {}, pages = {421-430}, doi = {10.1016/j.jes.2022.06.024}, pmid = {36522074}, issn = {1001-0742}, mesh = {*Lakes/microbiology ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Ecosystem ; Drug Resistance, Microbial/genetics ; }, abstract = {Lakes act as one of the reservoirs and dispersal routes of antibiotic resistance genes (ARGs) and pathogenic resistant bacteria in aquatic environments. Previous studies reported the occurrence and distribution of ARGs in lakes worldwide; however, few investigated the biogeography and diversity patterns of antibiotic resistome in the environment. To fill this gap, a large-scale data set of sediment metagenomes was collected from globally distributed lakes and characterized comprehensively using metagenomic assembly-based analysis, aiming to shed light on the biogeography and diversity patterns of ARGs in lake ecosystems from a global perspective. Our analyses showed that abundant and diverse ARGs were found in the global lake sediments, including a set of emerging ARGs such as mcr-type and carbapenem-resistant Enterobacteriaceae related genes. Most of the identified ARGs were generally associated with the commonly used antibiotics, suggesting the role of increasing antibiotic consumptions on the resistome prevalence. Spatially, the composition and diversity of ARGs varied across geographical distances and exhibited a scale-dependent distance-decay relationship. Notably, the composition of ARGs was largely shaped by bacterial community structure, and their diversities were co-governed by stochastic process (∼48%) and deterministic process (∼52%). Findings provide a valuable insight to better understand ecological mechanisms of ARGs in lake ecosystems and have important implication for the prevention and control of resistome risk.}, } @article {pmid36522059, year = {2023}, author = {Zhang, X and Liu, S and Sun, H and Huang, K and Ye, L}, title = {Impact of different organic matters on the occurrence of antibiotic resistance genes in activated sludge.}, journal = {Journal of environmental sciences (China)}, volume = {127}, number = {}, pages = {273-283}, doi = {10.1016/j.jes.2022.04.021}, pmid = {36522059}, issn = {1001-0742}, mesh = {*Sewage/microbiology ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; *Environmental Pollutants ; }, abstract = {The occurrence of antibiotic resistance genes (ARGs) in various environments has drawn worldwide attention due to their potential risks. Previous studies have reported that a variety of substances can enhance the occurrence and dissemination of ARGs. However, few studies have compared the response of ARGs under the stress of different organic matters in biological wastewater treatment systems. In this study, seven organic pollutants were added into wastewater treatment bioreactors to investigate their impacts on the ARG occurrence in activated sludge. Based on high-throughput sequencing, it was found that the microbial communities and ARG patterns were significantly changed in the activated sludge exposed to these organic pollutants. Compared with the non-antibiotic refractory organic matters, antibiotics not only increased the abundance of ARGs but also significantly changed the ARG compositions. The increase of Gram-negative bacteria (e.g., Archangium, Prosthecobacter and Dokdonella) carrying ARGs could be the main cause of ARG proliferation. In addition, significant co-occurrence relationships between ARGs and mobile genetic elements were also observed in the sludge samples, which may also affect the ARG diversity and abundance during the organic matter treatment in the bioreactors. Overall, these findings provide new information for better understanding the ARG occurrence and dissemination caused by organic pollutants in wastewater treatment systems.}, } @article {pmid36521740, year = {2023}, author = {Hu, L and Wang, Y and Ci, M and Long, Y}, title = {Unravelling microbial drivers of the sulfate-reduction process inside landfill using metagenomics.}, journal = {Chemosphere}, volume = {313}, number = {}, pages = {137537}, doi = {10.1016/j.chemosphere.2022.137537}, pmid = {36521740}, issn = {1879-1298}, mesh = {*Metagenomics ; *Hydrogen Sulfide/chemistry ; Biotransformation ; Sulfates ; Oxidation-Reduction ; Waste Disposal Facilities ; }, abstract = {Hydrogen sulfide (H2S) is one of the common landfill odor. This research demonstrates that the sulfate transformation behavior is significantly enhanced during the landfill process, accompanied by a shift in microbial structure. The relative abundance of dissimilatory sulfate reduction (DSR) and thiosulfate oxidation by SOX (sulfur-oxidation) complex gradually decreases through the landfill processes while the assimilatory sulfate reduction (ASR) demonstrates the opposite behavior. The major module for landfill sulfate reduction is ASR, accounting for 31.72% ± 2.84% of sulfate metabolism. Based on the functional genes for the sulfate pathway, the drivers for sulfate biotransformation in landfills were determined and further identified their contribution in the sulfate metabolism during landfill processes. Pseudomonas, Methylocaldum, Bacillus, Methylocystis and Hyphomicrobium were the top 5 contributors for ASR pathway, and only one genus Pseudomonas was found for DSR pathway. Among the 26 high-quality metagenome-assembled genomes of sulfate functional species, 24 were considered novel species for sulfuric metabolism. Overall, this study provides unique insight into the sulfate transformation process related to the H2S odor control in landfill management.}, } @article {pmid36521617, year = {2023}, author = {de Menezes, CA and de Souza Almeida, P and Camargo, FP and Delforno, TP and de Oliveira, VM and Sakamoto, IK and Varesche, MBA and Silva, EL}, title = {Two problems in one shot: Vinasse and glycerol co-digestion in a thermophilic high-rate reactor to improve process stability even at high sulfate concentrations.}, journal = {The Science of the total environment}, volume = {862}, number = {}, pages = {160823}, doi = {10.1016/j.scitotenv.2022.160823}, pmid = {36521617}, issn = {1879-1026}, mesh = {*Bioreactors ; *Glycerol ; Anaerobiosis ; Sulfates ; Methane ; Sulfur Oxides ; Biofuels ; Digestion ; }, abstract = {Anaerobic co-digestion (AcoD) of sugarcane vinasse and glycerol can be profitable because of the destination of two biofuel wastes produced in large quantities in Brazil (ethanol and biodiesel, respectively) and the complementary properties of these substrates. Thus, the objective of this study was to assess the effect of increasing the organic loading rate (OLR) from 2 to 20 kg COD m[-3] d[-1] on the AcoD of vinasse and glycerol (50 %:50 % on a COD basis) in a thermophilic (55 °C) anaerobic fluidized bed reactor (AFBR). The highest methane production rate was observed at 20 kg COD m[-3] d[-1] (8.83 L CH4 d[-1] L[-1]), while the methane yield remained stable at around 265 NmL CH4 g[-1] CODrem in all conditions, even when influent vinasse reached 1811 mg SO4[2-] L[-1] (10 kg COD m[-3] d[-1]). Sulfate was not detected in the effluent. Bacterial genera related to sulfate removal, such as Desulfovibrio and Desulfomicrobium, were observed by means of shotgun metagenomic sequencing at 10 kg COD m[-3] d[-1], as well as the acetoclastic archaea Methanosaeta and prevalence of genes encoding enzymes related to acetoclastic methanogenesis. It was concluded that process efficiency and methane production occurred even in higher sulfate concentrations due to glycerol addition.}, } @article {pmid36521611, year = {2023}, author = {Ke, Y and Sun, W and Jing, Z and Zhu, Y and Zhao, Z and Xie, S}, title = {Antibiotic resistome alteration along a full-scale drinking water supply system deciphered by metagenome assembly: Regulated by seasonality, mobile gene elements and antibiotic resistant gene hosts.}, journal = {The Science of the total environment}, volume = {862}, number = {}, pages = {160887}, doi = {10.1016/j.scitotenv.2022.160887}, pmid = {36521611}, issn = {1879-1026}, mesh = {*Genes, Bacterial ; Drug Resistance, Microbial/genetics ; *Drinking Water ; Anti-Bacterial Agents/pharmacology ; Metagenome ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; }, abstract = {Both drinking water treatment processes and distribution can lead to antibiotic resistome variation, yet the variation of antibiotic resistome in the whole drinking water supply system (DWSS) combined with seasonality remains unknown. In this study, microbial community, antibiotic resistome, mobile genetic elements (MGEs) co-existing with antibiotic resistance genes (ARGs) and ARG hosts would be explored along a DWSS for four seasons with metagenome assembly. Multidrug and bacitracin ARGs were dominant ARGs in DWSS. Integrase, plasmids, recombinase and transposase were major MGEs co-existing with ARGs. Filtration and disinfection treatments could alter the ARG relative abundance, mainly via changing the abundance of ARG hosts (Limnohabitans and Polynucleobacter), which was influenced by water total organic carbon (TOC) content. When TOC was relatively high, filtration could proliferate ARGs via promoting antibiotic resistance bacteria (ARB) but chlorine dioxide could decrease ARGs via killing ARB. Filtration played an important role in controlling ARGs by reducing ARB when TOC was relatively low. The stimulation effect of disinfection on ARGs existed in more oligotrophic environment. Distribution could enrich ARGs in higher temperature by increasing MGEs co-occurring with ARGs and diversifying ARG hosts. MGEs co-occurring with ARGs became more abundant and diverse in disinfected water in warmer seasons. Microbial community was the most important factor determining the antibiotic resistome along a DWSS. These findings extend the knowledge about how and why water treatment processes and pipe distribution shape drinking water antibiotic resistome in different seasons.}, } @article {pmid36521240, year = {2023}, author = {Ramalingam, S and Bahuguna, A and Joe, AR and Lim, S and Lee, JS and Kim, SY and Kim, M}, title = {Correlation between the microbiome and pack burst spoilage of Allium sativum supplemented fermented hot pepper paste.}, journal = {International journal of food microbiology}, volume = {387}, number = {}, pages = {110046}, doi = {10.1016/j.ijfoodmicro.2022.110046}, pmid = {36521240}, issn = {1879-3460}, mesh = {*Capsicum ; *Garlic ; Ethanol ; Antioxidants ; Dietary Supplements ; Plant Extracts ; }, abstract = {Gochujang (fermented hot pepper paste) products are well known for their distinct, spicy flavor. However, frequent pack burst spoilage of gochujang products occurs during transportation and storage because of microbial aerogenesis, resulting in considerable economic losses. The present study aimed to prevent pack burst spoilage of gochujang products by supplementing them with garlic ethanol extract. A simulated pack burst experiment revealed that 42.86 % of normal gochujang products were spoiled. Garlic ethanol extract significantly inhibited the growth of Zygosaccharomyces rouxii in gochujang products, with low minimum inhibitory concentration values (12.5-25 mg/mL). Gochujang products supplemented with various concentrations (1 % and 2.5 %) of garlic ethanol extract exhibited marked inhibition of microbial growth, particularly Z. rouxii, and pack burst spoilage. Microbiome analysis revealed that the pack burst samples harbored a high abundance of Z. rouxii. Supplementation of gochujang with 1 % garlic ethanol extract drastically reduced Z. rouxii abundance and prevented pack burst. Moreover, gochujang products supplemented with 1 % garlic ethanol extract exhibited a high hedonic score in the sensory analysis. Based on the results of this study, we concluded that supplementation of gochujang products with 1 % garlic ethanol extract before packaging could be effective in preventing pack burst spoilage of gochujang.}, } @article {pmid36520582, year = {2023}, author = {Zhou, LH and Zhu, RS and Gong, YP and Chen, ZQ and Luo, Y and Cheng, JH and Jiang, YK and Zhao, HZ and Wang, X and Chen, WJ and Zhu, LP}, title = {Diagnostic performance of noncultural methods for central nervous system aspergillosis.}, journal = {Mycoses}, volume = {66}, number = {4}, pages = {308-316}, doi = {10.1111/myc.13555}, pmid = {36520582}, issn = {1439-0507}, support = {2021YFC2300400//National Key Research and Development Program of China/ ; 81971911//National Natural Science Foundation of China/ ; //Shanghai Municipal Science and Technology Major Project/ ; }, mesh = {Humans ; Retrospective Studies ; Abscess ; Granulocyte-Macrophage Colony-Stimulating Factor ; *Aspergillosis/diagnosis ; Sensitivity and Specificity ; Mannans ; *Encephalitis ; Central Nervous System ; }, abstract = {BACKGROUND: Central nervous system (CNS) aspergillosis is an uncommon but fatal disease, the diagnosis of which is still difficult.

OBJECTIVES: We aim to explore the diagnositic performance of noncultural methods for CNS aspergillosis.

METHODS: In this retrospective study, all pathologically confirmed rhinosinusitis patients in whom cerebrospinal fluid (CSF) galactomannan (GM) test and metagenomic next-generation sequencing (mNGS) had been performed were included. We evaluated the diagnostic performances of CSF GM optical density indexes (ODI) at different cut-off values and compared performance with mNGS in patients with and without CNS aspergillosis, as well as in patients with different manifestations of CNS aspergillosis.

RESULTS: Of the 21 proven and probable cases, one had positive culture result, five had positive mNGS results and 10 had a CSF GM ODI of >0.7. Sample concordance between mNGS and GM test was poor, but best diagnostic performance was achieved by combination of GM test (ODI of >0.7) and mNGS, which generated a sensitivity of 61.9% and specificity of 82.6%. Further investigation of combination diagnostic performances in different kind of CNS aspergillosis was also conducted. Lowest sensitivity (42.9%) was identified in abscess group, while increased sensitivity (60.0%) was achieved in abscess with encephalitis groups. Combination test exhibited the best performance for encephalitis patients who had only CSF abnormalities, in whom the sensitivity and specificity were 77.8% and 82.6%, respectively.

CONCLUSIONS: In conclusion, combination of these two tests might be useful for diagnosis of CNS aspergillosis associated with fungal rhinosinusitis, especially in encephalitis patients.}, } @article {pmid36520400, year = {2023}, author = {Desirò, A and Takashima, Y and Bonito, G and Nishizawa, T and Narisawa, K and Bonfante, P}, title = {Investigating Endobacteria that Thrive Within Mucoromycota.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2605}, number = {}, pages = {293-323}, pmid = {36520400}, issn = {1940-6029}, mesh = {Symbiosis ; Phylogeny ; Fungi ; *Mycorrhizae ; *Glomeromycota ; Plants/microbiology ; }, abstract = {Metagenomics approaches have revealed the importance of Mucoromycota in the evolution and functioning of plant microbiomes. Comprised of three subphyla (Glomeromycotina, Mortierellomycotina, and Mucoromycotina), this early diverging lineage of fungi encompasses species of mycorrhizal fungi, root endophytes, plant pathogens, and many decomposers of plant debris. Interestingly, several taxa of Mucoromycota share a common feature, that is, the presence of endobacteria within their mycelia and spores. The study of these endosymbiotic bacteria is still a challenging task. However, given recent improvements in the sensitivity of culture-free approaches, a deeper understanding of such microbial interactions is now possible and fuels an emerging research field. In this chapter, we report how Mucoromycota, in particular Mortierellomycotina, and their endobacteria can be investigated using a combination of diverse cellular biology, microscopy, and molecular techniques.}, } @article {pmid36520397, year = {2023}, author = {Uroz, S and Oger, P}, title = {High-Throughput Screening of Fosmid Libraries for Increased Identification of Novel N-Acyl Homoserine Lactone Degrading Enzymes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2605}, number = {}, pages = {227-240}, pmid = {36520397}, issn = {1940-6029}, mesh = {*Acyl-Butyrolactones ; *Quorum Sensing ; 4-Butyrolactone/metabolism ; High-Throughput Screening Assays/methods ; Ecosystem ; }, abstract = {Functional metagenomics is an essential and effective approach to recover new enzymes from the environment. In this chapter, we describe a procedure to construct metagenomic library to discover new N-acyl homoserine lactone (AHL) degrading enzymes based on a direct method or an indirect enrichment procedure. Applicable to any bacterial ecosystem, it enables rapid identification of functional enzymes effective to degrade AHLs.}, } @article {pmid36520395, year = {2023}, author = {Comtet-Marre, S and Chakoory, O and Peyret, P}, title = {Targeted 16S rRNA Gene Capture by Hybridization and Bioinformatic Analysis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2605}, number = {}, pages = {187-208}, pmid = {36520395}, issn = {1940-6029}, mesh = {RNA, Ribosomal, 16S/genetics ; Phylogeny ; Genes, rRNA ; Sequence Analysis, DNA/methods ; *Metagenomics/methods ; *High-Throughput Nucleotide Sequencing/methods ; Computational Biology ; DNA, Ribosomal/genetics ; }, abstract = {Next-generation sequencing technologies have impressively unlocked capacities to depict the complexity of microbial communities. Microbial community structure is for now routinely monitored by sequencing of 16S rRNA gene, a phylogenetic marker almost conserved among bacteria and archaea. Nevertheless, amplicon sequencing, the most popular used approach, suffers from several biases impacting the picture of microbial communities. Here, we describe an innovative method based on gene capture by hybridization for the targeted enrichment of 16S rDNA biomarker from metagenomic samples. Coupled to near full-length 16S rDNA reconstruction, this approach enables an exhaustive and accurate description of microbial communities by enhancing taxonomic and phylogenetic resolutions. Furthermore, access of captured 16S flanking regions opens link between structure and function in microbial communities.}, } @article {pmid36520393, year = {2023}, author = {Štursová, M and López-Mondéjar, R and Baldrian, P}, title = {Investigating the Bacterial and Fungal Communities Involved in Dead Biomass Degradation in Forest Soils.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2605}, number = {}, pages = {157-168}, pmid = {36520393}, issn = {1940-6029}, mesh = {*Mycobiome ; Soil/chemistry ; Biomass ; Soil Microbiology ; Fungi/metabolism ; Forests ; Bacteria/metabolism ; }, abstract = {Stable isotope probing (SIP) provides the opportunity to label decomposer microorganisms that build their biomass on a specific substrate. In combination with high-throughput sequencing, SIP allows for the identification of microbial community members involved in a particular decomposition process. Further information can be gained (in SIP experiments) through gene-targeted metagenomics and metatranscriptomics, opening the possibility to describe the pool of genes catalyzing specific decomposition reactions in situ and to identify the diversity of genes that are expressed. When combined with gene descriptions of fungal and/or bacterial isolates from the same environment, specific biochemical reactions involved in decomposition can be linked to individual microbial taxa. Here, we describe the use of these methods to explore the decomposer community of fungi and bacteria in forest litter and soil.}, } @article {pmid36520392, year = {2023}, author = {Danneels, B and Carlier, A}, title = {Whole-Genome Sequencing of Bacterial Endophytes From Fresh and Preserved Plant Specimens.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2605}, number = {}, pages = {133-155}, pmid = {36520392}, issn = {1940-6029}, mesh = {*Endophytes/genetics ; *Bacteria/genetics ; Symbiosis/genetics ; Plants/genetics/microbiology ; Plant Leaves/microbiology ; DNA, Bacterial/genetics ; }, abstract = {Many plants harbor symbiotic bacteria in their leaves, sometimes within structures visible with the naked eye. These bacteria play critical roles for host development and defense, but are often not amenable to culture. Gaining insight into the functions of these obligate endophytic bacteria hinges on culture-independent omics approaches, which have seen tremendous development in recent years. We describe in this chapter a set of protocols for the extraction and bioinformatic analysis of bacterial genomic DNA from leaf samples of various origins, including fresh, silica-preserved, or herbarium specimens.}, } @article {pmid36520069, year = {2023}, author = {Howe, KL and Seitz, KW and Campbell, LG and Baker, BJ and Thrash, JC and Rabalais, NN and Rogener, MK and Joye, SB and Mason, OU}, title = {Metagenomics and metatranscriptomics reveal broadly distributed, active, novel methanotrophs in the Gulf of Mexico hypoxic zone and in the marine water column.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {2}, pages = {}, pmid = {36520069}, issn = {1574-6941}, mesh = {*Water ; Gulf of Mexico ; *Plankton/genetics ; Metagenome ; Methane/metabolism ; Phylogeny ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The northern Gulf of Mexico (nGOM) hypoxic zone is a shallow water environment where methane, a potent greenhouse gas, fluxes from sediments to bottom water and remains trapped due to summertime stratification. When the water column is destratified, an active planktonic methanotrophic community could mitigate the efflux of methane, which accumulates to high concentrations, to the atmosphere. To investigate the possibility of such a biofilter in the nGOM hypoxic zone we performed metagenome assembly, and metagenomic and metatranscriptomic read mapping. Methane monooxygenase (pmoA) was an abundant transcript, yet few canonical methanotrophs have been reported in this environment, suggesting a role for non-canonical methanotrophs. To determine the identity of these methanotrophs, we reconstructed six novel metagenome-assembled genomes (MAGs) in the Planctomycetota, Verrucomicrobiota and one putative Latescibacterota, each with at least one pmoA gene copy. Based on ribosomal protein phylogeny, closely related microbes (mostly from Tara Oceans) and isolate genomes were selected and co-analyzed with the nGOM MAGs. Gene annotation and read mapping suggested that there is a large, diverse and unrecognized community of active aerobic methanotrophs in the nGOM hypoxic zone and in the global ocean that could mitigate methane flux to the atmosphere.}, } @article {pmid36519933, year = {2023}, author = {Conti, A and Casagrande Pierantoni, D and Robert, V and Corte, L and Cardinali, G}, title = {MinION Sequencing of Yeast Mock Communities To Assess the Effect of Databases and ITS-LSU Markers on the Reliability of Metabarcoding Analysis.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0105222}, pmid = {36519933}, issn = {2165-0497}, mesh = {Humans ; *Saccharomyces cerevisiae/genetics ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; DNA, Ribosomal/genetics ; *Microbiota ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Microbial communities play key roles both for humans and the environment. They are involved in ecosystem functions, maintaining their stability, and provide important services, such as carbon cycle and nitrogen cycle. Acting both as symbionts and as pathogens, description of the structure and composition of these communities is important. Metabarcoding uses ribosomal DNA (rDNA) (eukaryotic) or rRNA gene (prokaryotic) sequences for identification of species present in a site and measuring their abundance. This procedure requires several technical steps that could be source of bias producing a distorted view of the real community composition. In this work, we took advantage of an innovative "long-read" next-generation sequencing (NGS) technology (MinION) amplifying the DNA spanning from the internal transcribed spacer (ITS) to large subunit (LSU) that can be read simultaneously in this platform, providing more information than "short-read" systems. The experimental system consisted of six fungal mock communities composed of species present at various relative amounts to mimic natural situations characterized by predominant and low-frequency species. The influence of the sequencing platform (MinION and Illumina MiSeq) and the effect of different reference databases and marker sequences on metagenomic identification of species were evaluated. The results showed that the ITS-based database provided more accurate species identification than LSU. Furthermore, a procedure based on a preliminary identification with standard reference databases followed by the production of custom databases, including only the best outputs of the first step, is proposed. This additional step improved the estimate of species proportion of the mock communities and reduced the number of ghost species not really present in the simulated communities. IMPORTANCE Metagenomic analyses are fundamental in many research areas; therefore, improvement of methods and protocols for the description of microbial communities becomes more and more necessary. Long-read sequencing could be used for reducing biases due to the multicopy nature of rDNA sequences and short-read limitations. However, these novel technologies need to be assessed and standardized with controlled experiments, such as mock communities. The interest behind this work was to evaluate how long reads performed identification and quantification of species mixed in precise proportions and how the choice of database affects such analyses. Development of a pipeline that mitigates the effect of the barcoding sequences and the impact of the reference database on metagenomic analyses can help microbiome studies go one step further.}, } @article {pmid36519847, year = {2023}, author = {Enam, SU and Cherry, JL and Leonard, SR and Zheludev, IN and Lipman, DJ and Fire, AZ}, title = {Restriction Endonuclease-Based Modification-Dependent Enrichment (REMoDE) of DNA for Metagenomic Sequencing.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {1}, pages = {e0167022}, pmid = {36519847}, issn = {1098-5336}, support = {R35 GM130366/GM/NIGMS NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; }, mesh = {DNA ; *DNA Restriction Enzymes ; *Escherichia coli/genetics/isolation & purification ; High-Throughput Nucleotide Sequencing ; Metagenome ; *Metagenomics/methods ; *Salmonella enterica/genetics/isolation & purification ; *DNA, Bacterial/genetics ; }, abstract = {Metagenomic sequencing is a swift and powerful tool to ascertain the presence of an organism of interest in a sample. However, sequencing coverage of the organism of interest can be insufficient due to an inundation of reads from irrelevant organisms in the sample. Here, we report a nuclease-based approach to rapidly enrich for DNA from certain organisms, including enterobacteria, based on their differential endogenous modification patterns. We exploit the ability of taxon-specific methylated motifs to resist the action of cognate methylation-sensitive restriction endonucleases that thereby digest unwanted, unmethylated DNA. Subsequently, we use a distributive exonuclease or electrophoretic separation to deplete or exclude the digested fragments, thus enriching for undigested DNA from the organism of interest. As a proof of concept, we apply this method to enrich for the enterobacteria Escherichia coli and Salmonella enterica by 11- to 142-fold from mock metagenomic samples and validate this approach as a versatile means to enrich for genomes of interest in metagenomic samples. IMPORTANCE Pathogens that contaminate the food supply or spread through other means can cause outbreaks that bring devastating repercussions to the health of a populace. Investigations to trace the source of these outbreaks are initiated rapidly but can be drawn out due to the labored methods of pathogen isolation. Metagenomic sequencing can alleviate this hurdle but is often insufficiently sensitive. The approach and implementations detailed here provide a rapid means to enrich for many pathogens involved in foodborne outbreaks, thereby improving the utility of metagenomic sequencing as a tool in outbreak investigations. Additionally, this approach provides a means to broadly enrich for otherwise minute levels of modified DNA, which may escape unnoticed in metagenomic samples.}, } @article {pmid36519836, year = {2023}, author = {Douglas, GM and Kim, S and Langille, MGI and Shapiro, BJ}, title = {Efficient computation of contributional diversity metrics from microbiome data with FuncDiv.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {1}, pages = {}, pmid = {36519836}, issn = {1367-4811}, support = {//National Sciences and Engineering Research Council of Canada/ ; }, mesh = {*Microbiota ; Metagenomics ; Software ; }, abstract = {MOTIVATION: Microbiome datasets with taxa linked to the functions (e.g. genes) they encode are becoming more common as metagenomics sequencing approaches improve. However, these data are challenging to analyze due to their complexity. Summary metrics, such as the alpha and beta diversity of taxa contributing to each function (i.e. contributional diversity), represent one approach to investigate these data, but currently there are no straightforward methods for doing so.

RESULTS: We addressed this gap by developing FuncDiv, which efficiently performs these computations. Contributional diversity metrics can provide novel insights that would be impossible to identify without jointly considering taxa and functions.

FuncDiv is distributed under a GNU Affero General Public License v3.0 and is available at https://github.com/gavinmdouglas/FuncDiv.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36519167, year = {2022}, author = {Liu, Q and Yang, J and Wang, B and Liu, W and Hua, Z and Jiang, H}, title = {Influence of salinity on the diversity and composition of carbohydrate metabolism, nitrogen and sulfur cycling genes in lake surface sediments.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1019010}, pmid = {36519167}, issn = {1664-302X}, abstract = {Exploring functional gene composition is essential for understanding the biogeochemical functions of lakes. However, little is known about the diversity and composition of biogeochemical cycling genes and their influencing factors in saline lakes. In this study, metagenomic analysis was employed to characterize the diversity and composition of microbial functions predicted from genes involved in carbohydrate metabolisms, nitrogen, and sulfur cycles in 17 surface sediments of Qinghai-Tibetan lakes with salinity ranging from 0.7 to 31.5 g L[-1]. The results showed that relative abundances of carbohydrate-active enzyme (CAZy), nitrogen, and sulfur cycling genes were 92.7-116.5, 15.1-18.7, 50.8-63.9 per 1,000 amino acid coding reads, respectively. The Shannon diversity indices of CAZy and sulfur cycling genes decreased with increasing salinity, whereas nitrogen cycling gene diversity showed an opposite trend. Relative abundances of many CAZy (i.e., carbohydrate-binding module and carbohydrate esterase), nitrogen (i.e., anammox and organic degradation and synthesis) and sulfur (i.e., dissimilatory sulfur reduction and oxidation, link between inorganic and organic sulfur transformation, sulfur disproportionation and reduction) cycling gene categories decreased with increasing salinity, whereas some CAZy (i.e., auxiliary activity), nitrogen (i.e., denitrification) and sulfur (i.e., assimilatory sulfate reduction and sulfur oxidation) gene categories showed an increasing trend. The compositions of CAZy, nitrogen, and sulfur cycling genes in the studied lake sediments were significantly (p < 0.05) affected by environmental factors such as salinity, total organic carbon, total nitrogen, and total phosphorus, with salinity having the greatest influence. Together, our results suggest that salinity may regulate the biogeochemical functions of carbohydrate metabolisms, nitrogen, and sulfur cycles in lakes through changing the diversity and composition of microbial functional genes. This finding has great implications for understanding the impact of environmental change on microbial functions in lacustrine ecosystems.}, } @article {pmid36519129, year = {2022}, author = {Li, W and Li, H and Wang, S and Han, K and Liu, Y and An, Z and Wu, H and Li, J and Song, J and Wu, W}, title = {Regional pattern and signatures of gut microbiota in rural residents with coronary heart disease: A metagenomic analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1007161}, pmid = {36519129}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics ; *Microbiota ; *Coronary Disease ; }, abstract = {Coronary heart disease (CHD) is tightly associated with gut microbiota, but microbiota heterogeneity limits the application of microbial biomarkers and personalized interventions demand regional-specific features. The purpose of this study was to comprehensively characterize the regional pattern of gut microbiota in rural residents with CHD and assess the predictive value and clinical correlations of local microbial signatures. We profiled the gut microbiota by shotgun metagenomic sequencing from 19 CHD and 19 healthy residents in rural Xinxiang, China, and tested the physiological parameters. The results indicated that microbial diversity, as well as KEGG orthology (KO) and carbohydrate-active enzymes (CAZymes) functions, deserved no significant disparities between CHD and healthy residents. The relative abundance of Bacteroidetes phylum was significantly lower and unclassified Lachnospiraceae genus, and Eubacterium rectale species were markedly higher in CHD residents compared with the healthy control. Co-occurrence network revealed a more diverse and scattered ecology in CHD residents. LEfSe identified 39 potential biomarkers and butanoate metabolism and glycosyltransferases families were the enhanced KO and CAZymes in CHD residents, respectively. Twenty key signatures were determined by the random forest algorithm and most of them belonged to the Clostridium cluster. These key signatures harbored a superior accuracy of 83.9% to distinguish CHD and healthy residents and, fasting serum insulin, diastolic blood pressure, and body mass index were the top three clinical parameters influencing the gut bacterial community. Furthermore, we also found that low-density lipoprotein and waist circumference had significantly positive correlations with the members of the Clostridium cluster. These findings expand our knowledge in the regional-specific pattern of gut microbiota for rural CHD residents and highlight the non-invasive diagnostic value and clinical correlations of microbial signatures.}, } @article {pmid36518681, year = {2022}, author = {}, title = {Correction to 'AsgeneDB: a curated orthology arsenic metabolism gene database and computational tool for metagenome annotation'.}, journal = {NAR genomics and bioinformatics}, volume = {4}, number = {4}, pages = {lqac094}, doi = {10.1093/nargab/lqac094}, pmid = {36518681}, issn = {2631-9268}, abstract = {[This corrects the article DOI: 10.1093/nargab/lqac080.].}, } @article {pmid36518379, year = {2022}, author = {Usman, S and Razis, AFA and Shaari, K and Azmai, MNA and Saad, MZ and Isa, NM and Nazarudin, MF}, title = {Polystyrene microplastics induce gut microbiome and metabolome changes in Javanese medaka fish (Oryzias javanicus Bleeker, 1854).}, journal = {Toxicology reports}, volume = {9}, number = {}, pages = {1369-1379}, pmid = {36518379}, issn = {2214-7500}, abstract = {Microplastics (MPs) have become emerging pollutants of public health concern, due to their impact on aqua-terrestrial ecosystems and integration into the food web, with evidence of human exposure and unrevealed health implications. There is a paucity of information regarding the effects of MPs exposure on the gut system using metagenomic and metabolomic approaches. In this study, Javanese medaka fish was exposed to 5 µm beads of polystyrene microplastics (PS-MPs) suspensions, at concentrations of 100 μg/L (MP-LOW), 500 μg/L (MP-MED), and 1000 μg/L (MP-HIGH), for a duration of 21 days, and evaluated for gut microbiome and metabolome responses. The results revealed a significant reduction (p < 0.05) in richness and diversity of the gut microbiome in the MP-HIGH group, and identification of 7 bacterial genera as differential features by the Linear discriminant analysis Effect Size (LEfSe). The gut metabolic profile revealed upregulation of 9 metabolites related to energy metabolism, via tricarboxylic acid cycle (TCA), creatine pathway, and urea cycle, as determined by the pathway analysis. Furthermore, positive correlation was found between the genus Aeromonas and glucose, lactate, and creatine metabolites. The study revealed that PS-MPs exposure resulted in altered bacterial microbiome and metabolic disorder related to energy metabolism. It further provided additional data on gut bacterial genera and metabolites associated with MPs toxicity in aquatic organism, which will inevitably enable its future health risks assessment in animals and possibly humans.}, } @article {pmid36518262, year = {2022}, author = {Liu, L and Wu, P and Chen, F and Zhou, J and Guo, A and Shi, K and Zhang, Q}, title = {Multi-omics analyses reveal that the gut microbiome and its metabolites promote milk fat synthesis in Zhongdian yak cows.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e14444}, pmid = {36518262}, issn = {2167-8359}, mesh = {Animals ; Female ; Cattle ; *Milk/chemistry ; *Gastrointestinal Microbiome ; Multiomics ; Metabolomics ; Firmicutes ; Myristic Acids/analysis ; }, abstract = {BACKGROUND: Yak cows produce higher quality milk with higher concentrations of milk fat than dairy cows. Recently, studies have found the yak milk yield and milk fat percentage have decreased significantly over the past decade, highlighting the urgency for yak milk improvement. Therefore, we aimed to analyze how the gut microbiome impacts milk fat synthesis in Zhongdian yak cows.

METHODS: We collected milk samples from Zhongdian yak cows and analyzed the milk fat percentage, selecting five Zhongdian yak cows with a very high milk fat percentage (>7%, 8.70 ± 1.89%, H group) and five Zhongdian yak cows with a very low milk fat percentage (<5%, 4.12 ± 0.43%, L group), and then obtained gut samples of these ten Zhongdian yak cows through rectal palpation. Gut metagenomics, metabolomics, and conjoint metagenomics and metabolomics analyses were performed on these samples, identifying taxonomic changes, functional changes, and changes in gut microbes-metabolite interactions within the milk fat synthesis-associated Zhongdian yak cows gut microbiome, to identify potential regulatory mechanisms of milk fat at the gut microbiome level in Zhongdian yak cows.

RESULTS: The metagenomics analysis revealed Firmicutes and Proteobacteria were significantly more abundant in the gut of the high-milk fat Zhongdian yak cows. These bacteria are involved in the biosynthesis of unsaturated fatty acids and amino acids, leading to greater efficiency in converting energy to milk fat. The metabolomics analysis showed that the elevated gut metabolites in high milk fat percentage Zhongdian yak cows were mainly enriched in lipid and amino acid metabolism. Using a combined metagenomic and metabolomics analysis, positive correlations between Firmicutes (Desulfocucumis, Anaerotignum, Dolosiccus) and myristic acid, and Proteobacteria (Catenovulum, Comamonas, Rubrivivax, Marivita, Succinimouas) and choline were found in the gut of Zhongdian yak cows. These interactions may be the main contributors to methanogen inhibition, producing less methane leading to higher-efficient milk fat production.

CONCLUSIONS: A study of the gut microbe, gut metabolites, and milk fat percentage of Zhongdian yak cows revealed that the variations in milk fat percentage between yak cows may be caused by the gut microbes and their metabolites, especially Firmicutes-myristic acid and Proteobacteria-choline interactions, which are important to milk fat synthesis. Our study provides new insights into the functional roles of the gut microbiome in producing small molecule metabolites and contributing to milk performance traits in yak cows.}, } @article {pmid36517909, year = {2022}, author = {Vasco, K and Guevara, N and Mosquera, J and Zapata, S and Zhang, L}, title = {Characterization of the gut microbiome and resistome of Galapagos marine iguanas (Amblyrhynchus cristatus) from uninhabited islands.}, journal = {Animal microbiome}, volume = {4}, number = {1}, pages = {65}, pmid = {36517909}, issn = {2524-4671}, support = {Faculty discretional fund//Michigan State University/ ; POA 2018//Universidad San Francisco de Quito/ ; POA 2018//Galapagos Science Center/ ; }, abstract = {BACKGROUND: Understanding the natural microbiome and resistome of wildlife from remote places is necessary to monitor the human footprint on the environment including antimicrobial use (AU). Marine iguanas are endemic species from the Galapagos Islands where they are highly affected by anthropogenic factors that can alter their microbiota as well as their abundance and diversity of antimicrobial-resistant genes (ARGs). Thus, this study aims to apply culture-independent approaches to characterize the marine iguana's gut metagenomic composition of samples collected from the uninhabited islands Rabida (n = 8) and Fernandina (Cabo Douglas, n = 30; Punta Espinoza, n = 30). Fresh feces from marine iguanas were analyzed through SmartChip RT-PCR, 16S rRNA, and metagenomic next-generation sequencing (mNGS) to identify their microbiome, microbial-metabolic pathways, resistome, mobilome, and virulome.

RESULTS: The marine iguana's gut microbiome composition was highly conserved despite differences in ecological niches, where 86% of taxa were shared in the three locations. However, site-specific differences were mainly identified in resistome, mobilome, virulorome, and metabolic pathway composition, highlighting the existence of factors that induce microbial adaptations in each location. Functional gut microbiome analyses revealed its role in the biosynthesis and degradation of vitamins, cofactors, proteinogenic amino acids, carbohydrates, nucleosides and nucleotides, fatty acids, lipids, and other compounds necessary for the marine iguanas. The overall bacterial ARG abundance was relatively low (0.006%); nevertheless, the presence of genes encoding resistance to 22 drug classes was identified in the iguana's gut metagenome. ARG-carrying contig and co-occurrence network analyses revealed that commensal bacteria are the main hosts of ARGs. Taxa of public health interest such as Salmonella, Vibrio, and Klebsiella also carried multidrug-resistance genes associated with MGEs which can influence the dissemination of ARGs through horizontal gene transfer.

CONCLUSION: Marine iguanas depend on the gut microbiome for the biosynthesis and degradation of several compounds through a symbiotic relationship. Niche-specific adaptations were evidenced in the pool of microbial accessory genes (i.e., ARGs, MGEs, and virulence) and metabolic pathways, but not in the microbiome composition. Culture-independent approaches outlined the presence of a diverse resistome composition in the Galapagos marine iguanas from remote islands. The presence of AR pathogens in marine iguanas raises concerns about the dispersion of microbial-resistant threats in pristine areas, highlighting wildlife as sentinel species to identify the impact of AU.}, } @article {pmid36517876, year = {2022}, author = {Yin, J and Zhang, Z and Zhu, C and Wang, T and Wang, R and Ruan, L}, title = {Heritability of tomato rhizobacteria resistant to Ralstonia solanacearum.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {227}, pmid = {36517876}, issn = {2049-2618}, mesh = {*Ralstonia solanacearum/genetics ; *Solanum lycopersicum/genetics ; Plant Diseases/prevention & control/microbiology ; Rhizosphere ; Soil ; *Alphaproteobacteria ; Bacteria ; }, abstract = {BACKGROUND: Ralstonia solanacearum (Rs) is a soilborne phytopathogen that causes bacterial wilt and substantial yield losses in many plants, such as tomatoes. A resistant tomato cultivar can recruit a beneficial microbiome from soil to resist Rs. However, whether this recruitment is inheritable from resistant parent to progeny has not been determined.

RESULTS: In the present study, we investigated the rhizosphere microbiomes of tomatoes with clear kinship and different resistance against Rs. Resistant tomatoes grown with the additions of natural soil or its extract showed lower disease indexes than those grown in the sterile soil, demonstrating the importance of soil microbiome in resisting Rs. The results of 16S ribosomal RNA gene amplicon sequencing revealed that the resistant cultivars had more robust rhizosphere microbiomes than the susceptible ones. Besides, the resistant progeny HF12 resembled its resistant parent HG64 in the rhizosphere microbiome. The rhizosphere microbiome had functional consistency between HF12 and HG64 as revealed by metagenomics. Based on multi-omics analysis and experimental validation, two rhizobacteria (Sphingomonas sp. Cra20 and Pseudomonas putida KT2440) were enriched in HF12 and HG64 with the ability to offer susceptible tomatoes considerable protection against Rs. Multiple aspects were involved in the protection, including reducing the virulence-related genes of Rs and reshaping the transcriptomes of the susceptible tomatoes.

CONCLUSIONS: We found promising bacteria to suppress the tomato bacterial wilt in sustainable agriculture. And our research provides insights into the heritability of Rs-resistant tomato rhizobacteria, echoing the inheritance of tomato genetic material. Video Abstract.}, } @article {pmid36517824, year = {2022}, author = {Miao, Q and Liang, T and Pei, N and Liu, C and Pan, J and Li, N and Wang, Q and Chen, Y and Chen, Y and Ma, Y and Jin, W and Zhang, Y and Su, Y and Yao, Y and Huang, Y and Zhou, C and Bao, R and Xu, X and Chen, W and Hu, B and Li, J}, title = {Evaluation of respiratory samples in etiology diagnosis and microbiome characterization by metagenomic sequencing.}, journal = {Respiratory research}, volume = {23}, number = {1}, pages = {345}, pmid = {36517824}, issn = {1465-993X}, support = {SHDC2020CR2031B//Clinical Research Plan of Shanghai Hospital Development Center/ ; }, mesh = {Humans ; Metagenomics/methods ; *Microbiota/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; *Mycobacterium tuberculosis ; *Respiratory Tract Infections/diagnosis ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: The application of clinical mNGS for diagnosing respiratory infections improves etiology diagnosis, however at the same time, it brings new challenges as an unbiased sequencing method informing all identified microbiomes in the specimen.

METHODS: Strategy evaluation and metagenomic analysis were performed for the mNGS data generated between March 2017 and October 2019. Diagnostic strengths of four specimen types were assessed to pinpoint the more appropriate type for mNGS diagnosis of respiratory infections. Microbiome complexity was revealed between patient cohorts and infection types. A bioinformatic pipeline resembling diagnosis results was built based upon multiple bioinformatic parameters.

RESULTS: The positive predictive values (PPVs) for mNGS diagnosing of non-mycobacterium, Nontuberculous Mycobacteria (NTM), and Aspergillus were obviously higher in bronchoalveolar lavage fluid (BALF) demonstrating the potency of BALF in mNGS diagnosis. Lung tissues and sputum were acceptable for diagnosis of the Mycobacterium tuberculosis (MTB) infections. Interestingly, significant taxonomy differences were identified in sufficient BALF specimens, and unique bacteriome and virome compositions were found in the BALF specimens of tumor patients. Our pipeline showed comparative diagnostic strength with the clinical microbiological diagnosis.

CONCLUSIONS: To achieve reliable mNGS diagnosis result, BALF specimens for suspicious common infections, and lung tissues and sputum for doubtful MTB infections are recommended to avoid the false results given by the complexed respiratory microbiomes. Our developed bioinformatic pipeline successful helps mNGS data interpretation and reduces manual corrections for etiology diagnosis.}, } @article {pmid36517256, year = {2023}, author = {Wang, N and Li, J and Zheng, Y and Wang, L}, title = {Schistosoma haematobium infection in a returning Chinese worker.}, journal = {Asian journal of surgery}, volume = {46}, number = {5}, pages = {2254-2255}, doi = {10.1016/j.asjsur.2022.11.131}, pmid = {36517256}, issn = {0219-3108}, mesh = {Animals ; Humans ; East Asian People ; *Schistosoma haematobium ; *Schistosomiasis haematobia/complications/diagnosis ; Urinary Bladder ; Transients and Migrants ; }, } @article {pmid36517072, year = {2023}, author = {Kim, H and Kim, ES and Cho, JH and Song, M and Cho, JH and Kim, S and Keum, GB and Kwak, J and Doo, H and Pandey, S and Park, SH and Lee, JH and Jung, H and Hur, TY and Kim, JK and Oh, KK and Kim, HB and Lee, JH}, title = {Exploring the Microbial Community and Functional Characteristics of the Livestock Feces Using the Whole Metagenome Shotgun Sequencing.}, journal = {Journal of microbiology and biotechnology}, volume = {33}, number = {1}, pages = {51-60}, pmid = {36517072}, issn = {1738-8872}, mesh = {Animals ; Swine ; Livestock ; Metagenome ; Chickens ; *Microbiota ; *Foodborne Diseases/microbiology ; Feces/microbiology ; }, abstract = {The foodborne illness is the important public health concerns, and the livestock feces are known to be one of the major reservoirs of foodborne pathogens. Also, it was reported that 45.5% of foodborne illness outbreaks have been associated with the animal products contaminated with the livestock feces. In addition, it has been known that the persistence of a pathogens depends on many potential virulent factors including the various virulent genes. Therefore, the first step to understanding the public health risk of livestock feces is to identify and describe microbial communities and potential virulent genes that contribute to bacterial pathogenicity. We used the whole metagenome shotgun sequencing to evaluate the prevalence of foodborne pathogens and to characterize the virulence associated genes in pig and chicken feces. Our data showed that the relative abundance of potential foodborne pathogens, such as Bacillus cereus was higher in chickens than pigs at the species level while the relative abundance of foodborne pathogens including Campylobacter coli was only detected in pigs. Also, the microbial functional characteristics of livestock feces revealed that the gene families related to "Biofilm formation and quorum sensing" were highly enriched in pigs than chicken. Moreover, the variety of gene families associated with "Resistance to antibiotics and toxic compounds" were detected in both animals. These results will help us to prepare the scientific action plans to improve awareness and understanding of the public health risks of livestock feces.}, } @article {pmid36516705, year = {2023}, author = {Zhi, R and Deng, J and Xu, Y and Xu, M and Zhang, S and Han, X and Yang, G and Ren, C}, title = {Altered microbial P cycling genes drive P availability in soil after afforestation.}, journal = {Journal of environmental management}, volume = {328}, number = {}, pages = {116998}, doi = {10.1016/j.jenvman.2022.116998}, pmid = {36516705}, issn = {1095-8630}, mesh = {*Ecosystem ; Soil ; Soil Microbiology ; Bacteria/genetics ; *Robinia ; China ; }, abstract = {Soil Phosphorous (P) availability is a limiting factor for plant growth and regulates biological metabolism in plantation ecosystems. The effect of variations in soil microbial P cycling potential on the availability of soil P during succession in plantation ecosystems is unclear. In this study, a metagenomics approach was used to explore variations in the composition and diversity of microbial P genes along a 45-year recovery sequence of Robinia pseudoacacia on the Loess Plateau, as well soil properties were measured. Our results showed that the diversity of P cycling genes (inorganic P solubilization and organic P mineralization genes) increased significantly after afforestation, and the community composition showed clear differences. The gcd and ppx genes were dominant in inorganic P transformation, whereas phnM gene dominated the transformation of organic P. The abundance of genes involved in inorganic P solubilization and organic P mineralization was significantly positively correlated with P availability, particularly for phnM, gcd, ppx, and phnI genes, corresponding to the phyla Gemmatimonadetes, Acidobacteria, Bacteroidetes, and Planctomycetes. The critical drivers of the microbial main genes of soil P cycling were available P (AP) and total N (TN) in soil. Overall, these findings highlight afforestation-induced increases in microbial P cycling genes enhanced soil P availability. and help to better understand how microbial growth metabolism caused by vegetation restoration in ecologically fragile areas affects the soil P cycling.}, } @article {pmid36516158, year = {2022}, author = {Ruaud, A and Pfister, N and Ley, RE and Youngblut, ND}, title = {Interpreting tree ensemble machine learning models with endoR.}, journal = {PLoS computational biology}, volume = {18}, number = {12}, pages = {e1010714}, pmid = {36516158}, issn = {1553-7358}, mesh = {Humans ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Machine Learning ; Metagenome ; *Microbiota ; }, abstract = {Tree ensemble machine learning models are increasingly used in microbiome science as they are compatible with the compositional, high-dimensional, and sparse structure of sequence-based microbiome data. While such models are often good at predicting phenotypes based on microbiome data, they only yield limited insights into how microbial taxa may be associated. We developed endoR, a method to interpret tree ensemble models. First, endoR simplifies the fitted model into a decision ensemble. Then, it extracts information on the importance of individual features and their pairwise interactions, displaying them as an interpretable network. Both the endoR network and importance scores provide insights into how features, and interactions between them, contribute to the predictive performance of the fitted model. Adjustable regularization and bootstrapping help reduce the complexity and ensure that only essential parts of the model are retained. We assessed endoR on both simulated and real metagenomic data. We found endoR to have comparable accuracy to other common approaches while easing and enhancing model interpretation. Using endoR, we also confirmed published results on gut microbiome differences between cirrhotic and healthy individuals. Finally, we utilized endoR to explore associations between human gut methanogens and microbiome components. Indeed, these hydrogen consumers are expected to interact with fermenting bacteria in a complex syntrophic network. Specifically, we analyzed a global metagenome dataset of 2203 individuals and confirmed the previously reported association between Methanobacteriaceae and Christensenellales. Additionally, we observed that Methanobacteriaceae are associated with a network of hydrogen-producing bacteria. Our method accurately captures how tree ensembles use features and interactions between them to predict a response. As demonstrated by our applications, the resultant visualizations and summary outputs facilitate model interpretation and enable the generation of novel hypotheses about complex systems.}, } @article {pmid36515546, year = {2023}, author = {Chen, C and Zhang, Y and Yao, X and Li, S and Wang, G and Huang, Y and Yang, Y and Zhang, A and Liu, C and Zhu, D and Li, H and Yan, Q and Ma, W}, title = {Characterizations of the Gut Bacteriome, Mycobiome, and Virome in Patients with Osteoarthritis.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0171122}, pmid = {36515546}, issn = {2165-0497}, mesh = {Humans ; *Mycobiome ; Virome ; *Microbiota ; *Gastrointestinal Microbiome ; *Viruses/genetics ; Bacteria/genetics ; }, abstract = {The gut microbiota plays an essential role in the regulation of the immune system and the etiology of human autoimmune diseases. However, a holistic understanding of the gut bacteriome, mycobiome, and virome in patients with osteoarthritis (OA) remains lacking. Here, we explored the gut microbiotas of 44 OA patients and 46 healthy volunteers via deep whole-metagenome shotgun sequencing of their fecal samples. The gut bacteriome and mycobiome were analyzed using a reference-based strategy. Gut viruses were identified from the metagenomic assembled contigs, and the gut virome was profiled based on 6,567 nonredundant viral operational taxonomic units (vOTUs). We revealed that the gut microbiome (including bacteriome, mycobiome, and virome) of OA patients is fundamentally altered, characterized by a panel of 279 differentially abundant bacterial species, 10 fungal species, and 627 vOTUs. The representative OA-enriched bacteria included Anaerostipes hadrus (GENOME147149), Prevotella sp900313215 (GENOME08259), Eubacterium_E hallii (GENOME000299), and Blautia A (GENOME001004), while Bacteroides plebeius A (GENOME239725), Roseburia inulinivorans (GENOME 001770), Dialister sp900343095 (GENOME075103), Phascolarctobacterium faecium (GENOME233517), and several members of Faecalibacterium and Prevotella were depleted in OA patients. Fungi such as Debaryomyces fabryi (GenBank accession no. GCA_003708665), Candida parapsilosis (GCA_000182765), and Apophysomyces trapeziformis (GCA_000696975) were enriched in the OA gut microbiota, and Malassezia restricta (GCA_003290485), Aspergillus fumigatus (GCA_003069565), and Mucor circinelloides (GCA_010203745) were depleted. The OA-depleted viruses spanned Siphoviridae (95 vOTUs), Myoviridae (70 vOTUs), and Microviridae (5 vOTUs), while 30 Siphoviridae vOTUs were enriched in OA patients. Functional analysis of the gut bacteriome and virome also uncovered their functional signatures in relation to OA. Moreover, we demonstrated that the OA-associated gut bacterial and viral signatures are tightly interconnected, suggesting that they may impact disease together. Finally, we showed that the multikingdom signatures are effective in discriminating the OA patients from healthy controls, suggesting the potential of gut microbiota for the prediction of OA and related diseases. Our results delineated the fecal bacteriome, mycobiome, and virome landscapes of the OA microbiota and provided biomarkers that will aid in future mechanistic and clinical intervention studies. IMPORTANCE The gut microbiome of OA patients was completely altered compared to that in healthy individuals, including 279 differentially abundant bacterial species, 10 fungal species and 627 viral operational taxonomic units (vOTUs). Functional analysis of the gut bacteriome and virome also revealed their functional signatures in relation to OA. We found that OA-associated gut bacterial and viral signatures were tightly interconnected, indicating that they may affect the disease together. The OA patients can be discriminated effectively from healthy controls using the multikingdom signatures, suggesting the potential of gut microbiota for the prediction of OA and related diseases.}, } @article {pmid36515538, year = {2023}, author = {Mahdavi, KA and Graham, ED and Heidelberg, JF and Webb, EA}, title = {Genome Sequence of the Euphotic Hawaiian Gammaproteobacterium HetDA_MAG_MS8, in the Order Nevskiales, Family Oceanococcaceae, Genus Oceanococcus.}, journal = {Microbiology resource announcements}, volume = {12}, number = {1}, pages = {e0059222}, pmid = {36515538}, issn = {2576-098X}, abstract = {We present a metagenome-assembled genome (MAG), HetDA_MAG_MS8, that was determined to be unique via relative evolutionary divergence (RED) scores and average nucleotide identity (ANI) values. HetDA_MAG_MS8 is in the order Nevskiales, genus Oceanococcus, and was assembled from a heterocytous cyanobiont enrichment from the Hawaii Ocean Time Series. HetDA_MAG_MS8 is predicted to be a facultative, aerobic, anoxygenic photolithoheterotroph that has the potential for sulfide oxidation and dimethylsulfoniopropionate (DMSP) synthesis.}, } @article {pmid36515536, year = {2023}, author = {Rumball, NA and Alm, EW and McLellan, SL}, title = {Genetic Determinants of Escherichia coli Survival in Beach Sand.}, journal = {Applied and environmental microbiology}, volume = {89}, number = {1}, pages = {e0142322}, pmid = {36515536}, issn = {1098-5336}, mesh = {Animals ; Humans ; *Sand ; Escherichia coli ; Lakes ; Michigan ; *Charadriiformes ; Environmental Monitoring/methods ; Feces ; Bathing Beaches ; Water Microbiology ; }, abstract = {Escherichia coli contain a high level of genetic diversity and are generally associated with the guts of warm-blooded animals but have also been isolated from secondary habitats outside hosts. We used E. coli isolates from previous in situ microcosm experiments conducted under actual beach conditions and performed population-level genomic analysis to identify accessory genes associated with survival within the beach sand environment. E. coli strains capable of surviving had been selected for by seeding isolates originating from sand, sewage, and gull waste (n = 528; 176 from each source) into sand, which was sealed in microcosm chambers and buried for 45 days in the backshore beach of Lake Michigan. In the current work, survival-associated genes were identified by comparing the pangenome of viable E. coli populations at the end of the microcosm experiment with the original isolate collection and identifying loci enriched in the out put samples. We found that environmental survival was associated with a wide variety of genetic factors, with the majority corresponding to metabolism enzymes and transport proteins. Of the 414 unique functions identified, most were present across E. coli phylogroups, except B2 which is often associated with human pathogens. Gene modules that were enriched in surviving populations included a betaine biosynthesis pathway, which produces an osmoprotectant, and the GABA (gamma-aminobutyrate) biosynthesis pathway, which aids in pH homeostasis and nutrient use versatility. Overall, these results demonstrate that the genetic flexibility within this species allows for survival in the environment for extended periods. IMPORTANCE Escherichia coli is commonly used as an indicator of recent fecal pollution in recreational water despite its known ability to survive in secondary environments, such as beach sand. These long-term survivors from sand reservoirs can be introduced into the water column through wave action or runoff during precipitation events, thereby impacting the perception of local water quality. Current beach monitoring methods cannot differentiate long-term environmental survivors from E. coli derived from recent fecal input, resulting in inaccurate monitoring results and unnecessary beach closures. This work identified the genetic factors that are associated with long-term survivors, providing insight into the mechanistic basis for E. coli accumulation in beach sand. A greater understanding of the intrinsic ability of E. coli to survive long-term and conditions that promote such survival will provide evidence of the limitations of beach water quality assessments using this indicator.}, } @article {pmid36515525, year = {2023}, author = {Rasmika Dewi, DAP and Shiwa, Y and Ryon, K and Mason, CE and Matsumoto, T and Suzuki, H}, title = {Urban Microbiomes in Narita, Chiba, Japan: Shotgun Metagenome Sequences of a Train Station.}, journal = {Microbiology resource announcements}, volume = {12}, number = {1}, pages = {e0109222}, pmid = {36515525}, issn = {2576-098X}, abstract = {Here, we performed shotgun metagenome sequencing of swab samples collected on floors at a train station in Narita City, Chiba, Japan. The taxonomic analysis revealed that Actinobacteria and Proteobacteria were the dominant phyla. The data will contribute to insight into the microbiome community on the surfaces of urban built environments.}, } @article {pmid36515503, year = {2023}, author = {Roemer, JT and Graham, ED and Heidelberg, JF and Webb, EA}, title = {Metagenome-Assembled Genome of a Cyclobacteriaceae Bacterium, HetDA_MAG_MS6, Isolated from a Trichodesmium Consortium from Station ALOHA.}, journal = {Microbiology resource announcements}, volume = {12}, number = {1}, pages = {e0045422}, pmid = {36515503}, issn = {2576-098X}, abstract = {Here, we describe the metagenome-assembled genome (MAG) HetDA_MAG_MS6. HetDA_MAG_MS6 was obtained from an enrichment of the heterocystous diazotroph HetDA, which was isolated near Station ALOHA. The MAG was placed in the Cyclobacteriaceae family and is predicted to be a chemoorganoheterotroph with the potential for ammonia uptake, phosphonate transport, and sulfolipid biosynthesis.}, } @article {pmid36514196, year = {2023}, author = {Kaur, M and Ferreiro, A and Hung, CY and Dantas, G and Ramasubramanian, AK}, title = {A low-cost, high-throughput microfluidic nano-culture platform for functional metagenomics.}, journal = {Biotechnology progress}, volume = {39}, number = {2}, pages = {e3317}, pmid = {36514196}, issn = {1520-6033}, support = {R15 AI138146/AI/NIAID NIH HHS/United States ; }, mesh = {*Microfluidics ; *Ampicillin ; Metagenomics/methods ; High-Throughput Screening Assays/methods ; }, abstract = {Functional metagenomics is an attractive culture-independent approach for functional screening of diverse microbiomes to identify known and novel genes. Since functional screening can involve sifting through tens of thousands of metagenomic library clones, an easy high-throughput screening approach is desirable. Here, we demonstrate a proof-of-concept application of a low-cost, high-throughput droplet based microfluidic assay to the selection of antibiotic resistance genes from a soil metagenomic library. Metagenomic library members encapsulated in nanoliter volume water-in-oil droplets were printed on glass slides robotically, and cell growth in individual drops in the presence of ampicillin was imaged and quantified to identify ampicillin-resistant clones. From the hits, true positives were confirmed by sequencing and functional validation. The ease of liquid handling, ease of set-up, low cost, and robust workflow makes the droplet-based nano-culture platform a promising candidate for screening and selection assays for functional metagenomic libraries.}, } @article {pmid36513983, year = {2022}, author = {Portik, DM and Brown, CT and Pierce-Ward, NT}, title = {Evaluation of taxonomic classification and profiling methods for long-read shotgun metagenomic sequencing datasets.}, journal = {BMC bioinformatics}, volume = {23}, number = {1}, pages = {541}, pmid = {36513983}, issn = {1471-2105}, mesh = {*Metagenomics/methods ; *Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Benchmarking ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Long-read shotgun metagenomic sequencing is gaining in popularity and offers many advantages over short-read sequencing. The higher information content in long reads is useful for a variety of metagenomics analyses, including taxonomic classification and profiling. The development of long-read specific tools for taxonomic classification is accelerating, yet there is a lack of information regarding their relative performance. Here, we perform a critical benchmarking study using 11 methods, including five methods designed specifically for long reads. We applied these tools to several mock community datasets generated using Pacific Biosciences (PacBio) HiFi or Oxford Nanopore Technology sequencing, and evaluated their performance based on read utilization, detection metrics, and relative abundance estimates.

RESULTS: Our results show that long-read classifiers generally performed best. Several short-read classification and profiling methods produced many false positives (particularly at lower abundances), required heavy filtering to achieve acceptable precision (at the cost of reduced recall), and produced inaccurate abundance estimates. By contrast, two long-read methods (BugSeq, MEGAN-LR & DIAMOND) and one generalized method (sourmash) displayed high precision and recall without any filtering required. Furthermore, in the PacBio HiFi datasets these methods detected all species down to the 0.1% abundance level with high precision. Some long-read methods, such as MetaMaps and MMseqs2, required moderate filtering to reduce false positives to resemble the precision and recall of the top-performing methods. We found read quality affected performance for methods relying on protein prediction or exact k-mer matching, and these methods performed better with PacBio HiFi datasets. We also found that long-read datasets with a large proportion of shorter reads (< 2 kb length) resulted in lower precision and worse abundance estimates, relative to length-filtered datasets. Finally, for classification methods, we found that the long-read datasets produced significantly better results than short-read datasets, demonstrating clear advantages for long-read metagenomic sequencing.

CONCLUSIONS: Our critical assessment of available methods provides best-practice recommendations for current research using long reads and establishes a baseline for future benchmarking studies.}, } @article {pmid36513769, year = {2023}, author = {Taglialegna, A}, title = {A host for redondoviruses.}, journal = {Nature reviews. Microbiology}, volume = {21}, number = {2}, pages = {67}, pmid = {36513769}, issn = {1740-1534}, mesh = {*Host-Parasite Interactions ; Metagenome ; }, abstract = {This study identifies the eukaryotic commensal Entamoeba gingivalis as the main host for human-associated redondoviruses.}, } @article {pmid36513659, year = {2022}, author = {Isaac, S and Flor-Duro, A and Carruana, G and Puchades-Carrasco, L and Quirant, A and Lopez-Nogueroles, M and Pineda-Lucena, A and Garcia-Garcera, M and Ubeda, C}, title = {Microbiome-mediated fructose depletion restricts murine gut colonization by vancomycin-resistant Enterococcus.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7718}, pmid = {36513659}, issn = {2041-1723}, mesh = {Mice ; Animals ; Vancomycin/pharmacology ; Fructose/pharmacology ; *Vancomycin-Resistant Enterococci/genetics ; *Microbiota ; Anti-Bacterial Agents/pharmacology ; Bacteria ; *Gram-Positive Bacterial Infections/microbiology ; }, abstract = {Multidrug-resistant organisms (MDRO) are a major threat to public health. MDRO infections, including those caused by vancomycin-resistant Enterococcus (VRE), frequently begin by colonization of the intestinal tract, a crucial step that is impaired by the intestinal microbiota. However, the specific members of the microbiota that suppress MDRO colonization and the mechanisms of such protection are largely unknown. Here, using metagenomics and mouse models that mimic the patients' exposure to antibiotics, we identified commensal bacteria associated with protection against VRE colonization. We further found a consortium of five strains that was sufficient to restrict VRE gut colonization in antibiotic treated mice. Transcriptomics in combination with targeted metabolomics and in vivo assays indicated that the bacterial consortium inhibits VRE growth through nutrient depletion, specifically by reducing the levels of fructose, a carbohydrate that boosts VRE growth in vivo. Finally, in vivo RNA-seq analysis of each strain of the consortium in combination with ex vivo and in vivo assays demonstrated that a single bacterium (Olsenella sp.) could recapitulate the effect of the consortium. Our results indicate that nutrient depletion by specific commensals can reduce VRE intestinal colonization, which represents a novel non-antibiotic based strategy to prevent infections caused by this multidrug-resistant organism.}, } @article {pmid36513610, year = {2023}, author = {Chiriac, MC and Haber, M and Salcher, MM}, title = {Adaptive genetic traits in pelagic freshwater microbes.}, journal = {Environmental microbiology}, volume = {25}, number = {3}, pages = {606-641}, doi = {10.1111/1462-2920.16313}, pmid = {36513610}, issn = {1462-2920}, mesh = {*Lakes ; *Ecology ; Genomics ; Ecosystem ; Bacteria/genetics ; Phylogeny ; }, abstract = {Pelagic microbes have adopted distinct strategies to inhabit the pelagial of lakes and oceans and can be broadly categorized in two groups: free-living, specialized oligotrophs and patch-associated generalists or copiotrophs. In this review, we aim to identify genomic traits that enable pelagic freshwater microbes to thrive in their habitat. To do so, we discuss the main genetic differences of pelagic marine and freshwater microbes that are both dominated by specialized oligotrophs and the difference to freshwater sediment microbes, where copiotrophs are more prevalent. We phylogenomically analysed a collection of >7700 metagenome-assembled genomes, classified habitat preferences on different taxonomic levels, and compared the metabolic traits of pelagic freshwater, marine, and freshwater sediment microbes. Metabolic differences are mainly associated with transport functions, environmental information processing, components of the electron transport chain, osmoregulation and the isoelectric point of proteins. Several lineages with known habitat transitions (Nitrososphaeria, SAR11, Methylophilaceae, Synechococcales, Flavobacteriaceae, Planctomycetota) and the underlying mechanisms in this process are discussed in this review. Additionally, the distribution, ecology and genomic make-up of the most abundant freshwater prokaryotes are described in details in separate chapters for Actinobacteriota, Bacteroidota, Burkholderiales, Verrucomicrobiota, Chloroflexota, and 'Ca. Patescibacteria'.}, } @article {pmid36513308, year = {2023}, author = {Tang, L and Su, C and Fan, C and Cao, L and Liang, Z and Xu, Y and Chen, Z and Wang, Q and Chen, M}, title = {Metagenomic and extracellular polymeric substances analysis reveals the mechanism of exogenous N-hexanoyl-L-homoserine lactone in alleviating the inhibition of perfluorooctanoic acid on anammox process.}, journal = {Bioresource technology}, volume = {369}, number = {}, pages = {128482}, doi = {10.1016/j.biortech.2022.128482}, pmid = {36513308}, issn = {1873-2976}, mesh = {*Extracellular Polymeric Substance Matrix ; *Anaerobic Ammonia Oxidation ; Quorum Sensing ; Sewage/microbiology ; Bioreactors/microbiology ; Oxidation-Reduction ; Nitrogen ; }, abstract = {To alleviate the negative effects of perfluorooctanoic acid (PFOA) on nitrogen removal via anaerobic ammonia oxidation (anammox), an exogenous signaling factor (N-hexanoyl-L-homoserine lactone, C6-HSL) was introduced into an anammox reactor. Results showed that 2 μmol/L C6-HSL promoted the nitrogen removal efficiency of the anammox reactor under PFOA stress, with the removal efficiencies of ammonia and nitrite increasing from 79.7 ± 4.8 % and 80.8 ± 3.8 %, to 94.4 ± 4.3 % and 97.1 ± 3.8 %. Exogenous C6-HSL enhanced the compactness of the extracellular proteins, and improved the sludge hydrophobicity. Meanwhile, C6-HSL resulted in a microbial shift, with the relative abundance of Planctomycetes increasing from 30.2 % to 49.5 %. Candidatus Kuenenia stuttgartiensis replaced Candidatus Brocadia sp. BL1 as the dominant species, while the available space for other nitrogen-removing bacteria was reduced. Exogenous C6-HSL promoted the expression of anammox-related genes, such as hzsB and hdh, while denitrifying genes were down-regulated. In addition, the relative abundance of HdtS, which synthesizes AHLs, increased by 0.02446%.}, } @article {pmid36513243, year = {2023}, author = {Zhang, Y and Zhou, D and Xia, H and Wang, J and Yang, H and Xu, L and Huang, K and Fang, J}, title = {Metagenomic next-generation sequencing for detection of pathogens in children with hematological diseases complicated with infection.}, journal = {Molecular and cellular probes}, volume = {67}, number = {}, pages = {101889}, doi = {10.1016/j.mcp.2022.101889}, pmid = {36513243}, issn = {1096-1194}, mesh = {Humans ; Child ; *Coinfection ; Retrospective Studies ; *Hematologic Diseases ; High-Throughput Nucleotide Sequencing ; Metagenome ; Sensitivity and Specificity ; }, abstract = {OBJECTIVE: Infection is one of the most common causes of death in children with hematological diseases. Here, we aim to investigate the value of metagenomic next-generation sequencing (mNGS) in the detection of causative pathogens in children with hematological diseases.

METHODS: In this retrospective study, specimens from children with hematological diseases, who were admitted to Sun Yat-Sen University between June 2019 and September 2021, were collected for culture and mNGS.

RESULTS: A total of 67 pediatric patients were enrolled, and 96 specimens were collected. The positive rate of mNGS was significantly higher than that of culture (57.2% vs 12.5%, P < 0.01). The concordance (90.9%, 10/11) between the positive results of the two methods was high. mNGS detected more cases with Pneumocystis jeroveci, Aspergillus flavus, viruses, and some rare pathogens than culture. Mixed infections were detected by mNGS in 16 cases. Clinical anti-infective treatment was adjusted according to the results of mNGS, the conditions of most patients improved.

CONCLUSION: Compared to culture, mNGS shows great advantages in diagnosing bacterial, fungal, viral, and mixed infections in children with hematologic diseases, positively impacting clinical care. mNGS can be used as a complement to culture for pathogen detection.}, } @article {pmid36512579, year = {2022}, author = {, }, title = {Expression of Concern: Host-Associated Metagenomics: A Guide to Generating Infectious RNA Viromes.}, journal = {PloS one}, volume = {17}, number = {12}, pages = {e0279054}, pmid = {36512579}, issn = {1932-6203}, } @article {pmid36512561, year = {2022}, author = {, }, title = {Expression of Concern: Extensive culturomics of 8 healthy samples enhances metagenomics efficiency.}, journal = {PloS one}, volume = {17}, number = {12}, pages = {e0278361}, pmid = {36512561}, issn = {1932-6203}, } @article {pmid36511842, year = {2023}, author = {Lebedeva, OP and Popov, VN and Syromyatnikov, MY and Starkova, NN and Maslov, AY and Kozarenko, ON and Gryaznova, MV}, title = {Female reproductive tract microbiome and early miscarriages.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {131}, number = {2}, pages = {61-76}, pmid = {36511842}, issn = {1600-0463}, support = {22-24-00802//Russian Science Foundation/ ; }, mesh = {Pregnancy ; Female ; Humans ; *Abortion, Spontaneous/etiology ; *Microbiota ; Prognosis ; Bacteria ; Vagina/microbiology ; }, abstract = {Miscarriage is one of the main causes of reproductive loss, which can lead to a number of physical and psychological complications and other long-term consequences. However, the role of vaginal and uterine microbiome in such complications is poorly understood. To review the published data on the function of the female reproductive tract microbiome in the pathogenesis of early miscarriages. The articles published over the past 20 years and deposited in PubMed, Google Academy, Scopus, Elibrary, ResearchGate, and EBSCO databases were analyzed. The review presents new data on the impact of the vaginal and uterine microbiome on the local immunity, including defense against sexually transmitted infections, and its association with other factors of miscarriages. The studies on the microbiome of non-pregnant women with recurrent miscarriages in the anamnesis, patients undergoing IVF, and pregnant women with miscarriages, as well as new directions in the microbiome research are discussed. The majority of studies have demonstrated that the dominant species of the vaginal and uterine microbiome in patients with early miscarriages are non-Lactobacillus bacteria. As many of these bacteria have not previously been detected by cultural studies and their role in obstetric complications is not well defined, further research on the female reproductive tract microbiome, including the microbiome of the cervix uteri, is needed to develop new approaches for the prognosis and prevention of miscarriages.}, } @article {pmid36511688, year = {2023}, author = {Pu, G and Hou, L and Du, T and Zhou, W and Liu, C and Niu, P and Wu, C and Bao, W and Huang, R and Li, P}, title = {Increased Proportion of Fiber-Degrading Microbes and Enhanced Cecum Development Jointly Promote Host To Digest Appropriate High-Fiber Diets.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0093722}, pmid = {36511688}, issn = {2379-5077}, mesh = {Swine ; Animals ; *Digestion ; *Cecum ; Diet/veterinary ; Dietary Fiber/pharmacology ; Intestinal Mucosa ; }, abstract = {Previous study found that appropriate high-fiber diet (containing 19.10% total dietary fiber [TDF], treatment II) did not reduce apparent fiber digestibility of Chinese Suhuai finishing pigs and increased the yield of short-chain fatty acids (SCFAs), but too high-fiber diet (containing 24.11% TDF, treatment IV) significantly reduced apparent fiber digestibility compared with normal diet (containing 16.70% TDF, control group). However, characteristics of microbiota at the species level and histological structure in pigs with the ability to digest appropriate high-fiber diets were still unknown. This study conducted comparative analysis of cecal physiology and microbial populations colonizing cecal mucosa. The results showed intestinal development indexes including cecum length, densities of cecal goblet cells, and renewal of cecal epithelial cells in treatment II and IV had better performance than those in the control. Paludibacter jiangxiensis, Coprobacter fastidiosus, Bacteroides coprocola CAG:162, Bacteroides barnesiae, and Parabacteroides merdae enriched in treatment II expressed large number of glycoside hydrolase (GH)-encoding genes and had the largest number of GH families. In addition, pathogenic bacteria (Shigella sonnei, Mannheimia haemolytica, and Helicobacter felis) were enriched in treatment IV. Correlation analysis revealed that the intestinal development index positively correlated with the relative abundance of cecal mucosal microbiota and the amount of digested fiber. These results indicated that increased proportions of fiber-degrading microbes and enhanced intestinal development jointly promote the host to digest an appropriate high-fiber diet. However, although too-high fiber levels in diet could maintain the adaptive development of cecal epithelium, the proportions of pathogenic bacteria increased, which might lead to a decrease of fiber digestion in pigs. IMPORTANCE Although studies about the effects of dietary fiber on fiber digestion and intestinal microbiota of pigs were widely in progress, few studies have been conducted on the dynamic response of intestinal microbiota to dietary fiber levels, and the characteristics of intestinal microbiota and intestinal epithelial development adapted to high-fiber diet s were still unclear. Appropriate high fiber promoted the thickness of large intestine wall, increased the density of cecal goblet cells, and promoted the renewal of cecal epithelial cells. In addition, appropriate high fiber improves the microbial abundance with fiber-digesting potential. However, excessive dietary fiber caused an increase in the abundance of pathogenic bacteria. These results indicated that an increased proportion of fiber-degrading microbes and enhanced intestinal development jointly promote host to digest appropriate high-fiber diets. However, although too-high fiber levels in diet could maintain the adaptive development of cecal epithelium, the proportions of pathogenic bacteria increased, which might lead to a decrease of fiber digestion in pigs. Our data provided a theoretical basis for rational and efficient utilization of unconventional feed resources in pig production.}, } @article {pmid36511663, year = {2023}, author = {Wang, L and Li, Q and Li, C and Wu, C and Chen, F and Chen, X and Zhang, F}, title = {Nitrate Nitrogen and pH Correlate with Changes in Rhizosphere Microbial Community Assemblages during Invasion of Ambrosia artemisiifolia and Bidens pilosa.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0364922}, pmid = {36511663}, issn = {2165-0497}, mesh = {Nitrates ; Ambrosia ; *Bidens ; Rhizosphere ; Nitrogen ; Introduced Species ; Soil/chemistry ; Plants ; *Microbiota ; Hydrogen-Ion Concentration ; Soil Microbiology ; }, abstract = {The rhizosphere of invasive plants presumably develops different soil microbial assemblages compared with native plants, which may hinder or promote their invasion. However, to date, no studies have clearly explored rhizosphere microbial community assemblages during invasion. The invasive species Ambrosia artemisiifolia L. and Bidens pilosa L. are widely distributed in China and are known to reduce local biodiversity and cause agricultural losses. Monoculture of A. artemisiifolia or B. pilosa, a mixture of each invasive and native species, and monoculture of native species were established to simulate different degrees of invasion. Metagenomic sequencing techniques were used to test microbial community structure and function. The aim was to explore the drivers of the assembly of peculiar functional microbes in the rhizosphere soil of invasive species during the long-term invasive-native species interaction. Compared with the native species, the relative abundance of 34 microbial genera was higher in the rhizosphere soil of the invasive species. The NO3-N concentration in the rhizosphere soil from the A. artemisiifolia and B. pilosa monocultures was lower than that from monocultures of the three native plants, whereas pH followed the opposite trend. The NO3-N concentration was significantly and negatively correlated with Sporichthya, Afipia, Actinokineospora, and Pseudolabrys. pH was positively correlated with Bradyrhizobium, Actinoplanes, Micromonospora, Steroidobacter, Burkholderia, and Labilithrix. The differences in soil microbes, NO3-N concentrations, and pH between native and invasive species suggest that the rhizosphere soil microbial assemblages may vary. The reduced NO3-N concentration and increased pH corelated with changes in rhizosphere microbial community during A. artemisiifolia and B. pilosa invasion. IMPORTANCE Soil microbial communities play a vital role in the growth of invasive plants. Invasive species may shape peculiar functional microbes in the rhizosphere soil of an invasive species to benefit its growth. However, the drivers of the assembly of soil microbial communities in the rhizosphere soil of invasive species remain unclear. Our study established the relationship between soil microbial communities and soil chemical properties during invasion by A. artemisiifolia and B. pilosa. Additionally, it showed that the presence of the invasive plants correlated with changes in NO3-N and pH, as well as in rhizosphere microbial community assemblage. Furthermore, the study provided important insights into the difference in the microbial community assembly between native and invasive plant species.}, } @article {pmid36510838, year = {2023}, author = {Weisse, L and Héchard, Y and Moumen, B and Delafont, V}, title = {Here, there and everywhere: Ecology and biology of the Dependentiae phylum.}, journal = {Environmental microbiology}, volume = {25}, number = {3}, pages = {597-605}, doi = {10.1111/1462-2920.16307}, pmid = {36510838}, issn = {1462-2920}, mesh = {RNA, Ribosomal, 16S/genetics ; *Genome, Bacterial ; *Bacteria/genetics ; Ecology ; Genomics ; Metagenomics ; Phylogeny ; }, abstract = {Our view of bacterial diversity has been dramatically impacted by cultivation-independent approaches such as metagenomics and 16S rRNA gene sequencing. Consequently, most bacterial phyla known to date are only documented by the presence of DNA sequences in databases and lack cultivated representatives. This bacterial majority that is yet-to-be cultivated, is forming the 'Microbial Dark Matter', (MDM) a consortium, whose ecology and biology remain largely unexplored. The Candidatus Dependentiae stands as one of many phyla within this MDM, found worldwide in various environments. Genomic evidence suggests ancestral, unusual adaptations of all Ca. Dependentiae to a host dependent lifestyle. In line with this, protists appear to be important for Ca. Dependentiae biology, as revealed by few recent studies, which enabled their growth in laboratory through host cultivation. However, the Ca. Dependentiae still remain to this day a poorly documented phylum. The present review aims to summarize the current knowledge accumulated on this often found, but rarely highlighted, bacterial phylum.}, } @article {pmid36510283, year = {2022}, author = {Bonczarowska, JH and Susat, J and Mühlemann, B and Jasch-Boley, I and Brather, S and Höke, B and Brather-Walter, S and Schoenenberg, V and Scheschkewitz, J and Graenert, G and Krausse, D and Francken, M and Jones, TC and Wahl, J and Nebel, A and Krause-Kyora, B}, title = {Pathogen genomics study of an early medieval community in Germany reveals extensive co-infections.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {250}, pmid = {36510283}, issn = {1474-760X}, support = {HHSN272201400008C/AI/NIAID NIH HHS/United States ; }, mesh = {Middle Aged ; Humans ; Phylogeny ; *Coinfection ; Mycobacterium leprae/genetics ; *Leprosy/epidemiology/history/microbiology ; DNA, Ancient ; }, abstract = {BACKGROUND: The pathogen landscape in the Early European Middle Ages remains largely unexplored. Here, we perform a systematic pathogen screening of the rural community Lauchheim "Mittelhofen," in present-day Germany, dated to the Merovingian period, between fifth and eighth century CE. Skeletal remains of individuals were subjected to an ancient DNA metagenomic analysis. Genomes of the detected pathogens were reconstructed and analyzed phylogenetically.

RESULTS: Over 30% of the individuals exhibit molecular signs of infection with hepatitis B virus (HBV), parvovirus B19, variola virus (VARV), and Mycobacterium leprae. Seven double and one triple infection were detected. We reconstructed four HBV genomes and one genome each of B19, VARV, and M. leprae. All HBV genomes are of genotype D4 which is rare in Europe today. The VARV strain exhibits a unique pattern of gene loss indicating that viruses with different gene compositions were circulating in the Early Middle Ages. The M. leprae strain clustered in branch 3 together with the oldest to-date genome from the UK.

CONCLUSIONS: The high burden of infectious disease, together with osteological markers of physiological stress, reflect a poor health status of the community. This could have been an indirect result of the climate decline in Europe at the time, caused by the Late Antique Little Ice Age (LALIA). Our findings suggest that LALIA may have created an ecological context in which persistent outbreaks set the stage for major epidemics of severe diseases such as leprosy and smallpox hundreds of years later.}, } @article {pmid36510248, year = {2022}, author = {Jurburg, SD and Buscot, F and Chatzinotas, A and Chaudhari, NM and Clark, AT and Garbowski, M and Grenié, M and Hom, EFY and Karakoç, C and Marr, S and Neumann, S and Tarkka, M and van Dam, NM and Weinhold, A and Heintz-Buschart, A}, title = {The community ecology perspective of omics data.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {225}, pmid = {36510248}, issn = {2049-2618}, mesh = {*Ecology/methods ; *Metagenomics/methods ; Metabolomics/methods ; }, abstract = {The measurement of uncharacterized pools of biological molecules through techniques such as metabarcoding, metagenomics, metatranscriptomics, metabolomics, and metaproteomics produces large, multivariate datasets. Analyses of these datasets have successfully been borrowed from community ecology to characterize the molecular diversity of samples (ɑ-diversity) and to assess how these profiles change in response to experimental treatments or across gradients (β-diversity). However, sample preparation and data collection methods generate biases and noise which confound molecular diversity estimates and require special attention. Here, we examine how technical biases and noise that are introduced into multivariate molecular data affect the estimation of the components of diversity (i.e., total number of different molecular species, or entities; total number of molecules; and the abundance distribution of molecular entities). We then explore under which conditions these biases affect the measurement of ɑ- and β-diversity and highlight how novel methods commonly used in community ecology can be adopted to improve the interpretation and integration of multivariate molecular data. Video Abstract.}, } @article {pmid36509943, year = {2023}, author = {Li, W and Ma, ZS}, title = {The Upper Respiratory Tract Microbiome Network Impacted by SARS-CoV-2.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {1428-1437}, pmid = {36509943}, issn = {1432-184X}, mesh = {Animals ; Humans ; SARS-CoV-2/genetics ; *COVID-19 ; *Chiroptera ; *Microbiota/genetics ; Bacteria/genetics ; Respiratory System ; }, abstract = {The microbiome of upper respiratory tract (URT) acts as a gatekeeper to respiratory health of the host. However, little is still known about the impacts of SARS-CoV-2 infection on the microbial species composition and co-occurrence correlations of the URT microbiome, especially the relationships between SARS-CoV-2 and other microbes. Here, we characterized the URT microbiome based on RNA metagenomic-sequencing datasets from 1737 nasopharyngeal samples collected from COVID-19 patients. The URT-microbiome network consisting of bacteria, archaea, and RNA viruses was built and analyzed from aspects of core/periphery species, cluster composition, and balance between positive and negative interactions. It is discovered that the URT microbiome in the COVID-19 patients is enriched with Enterobacteriaceae, a gut associated family containing many pathogens. These pathogens formed a dense cooperative guild that seemed to suppress beneficial microbes collectively. Besides bacteria and archaea, 72 eukaryotic RNA viruses were identified in the URT microbiome of COVID-19 patients. Only five of these viruses were present in more than 10% of all samples, including SARS-CoV-2 and a bat coronavirus (i.e., BatCoV BM48-31) not detected in humans by routine means. SARS-CoV-2 was inhibited by a cooperative alliance of 89 species, but seems to cooperate with BatCoV BM48-31 given their statistically significant, positive correlations. The presence of cooperative bat-coronavirus partner of SARS-CoV-2 (BatCoV BM48-31), which was previously discovered in bat but not in humans to the best of our knowledge, is puzzling and deserves further investigation given their obvious implications. Possible microbial translocation mechanism from gut to URT also deserves future studies.}, } @article {pmid36509053, year = {2023}, author = {Oldenburg, CE and Hinterwirth, A and Dah, C and Millogo, O and Coulibaly, B and Ouedraogo, M and Sié, A and Chen, C and Zhong, L and Ruder, K and Lebas, E and Nyatigo, F and Arnold, BF and O'Brien, KS and Doan, T}, title = {Gut Microbiome among Children with Uncomplicated Severe Acute Malnutrition in a Randomized Controlled Trial of Azithromycin versus Amoxicillin.}, journal = {The American journal of tropical medicine and hygiene}, volume = {108}, number = {1}, pages = {206-211}, pmid = {36509053}, issn = {1476-1645}, mesh = {Child ; Humans ; Infant ; Azithromycin/therapeutic use ; Amoxicillin/therapeutic use ; *Gastrointestinal Microbiome ; Anti-Bacterial Agents/therapeutic use ; *Severe Acute Malnutrition ; *Malnutrition ; }, abstract = {Antibiotics are routinely used as part of the management of severe acute malnutrition and are known to reduce gut microbial diversity in non-malnourished children. We evaluated gut microbiomes in children participating in a randomized controlled trial (RCT) of azithromycin versus amoxicillin for severe acute malnutrition. Three hundred one children aged 6 to 59 months with uncomplicated severe acute malnutrition (mid-upper arm circumference < 11.5 cm and/or weight-for-height Z-score < -3 without clinical complications) were enrolled in a 1:1 RCT of single-dose azithromycin versus a 7-day course of amoxicillin (standard of care). Of these, 109 children were randomly selected for microbiome evaluation at baseline and 8 weeks. Rectal swabs were processed with metagenomic DNA sequencing. We compared alpha diversity (inverse Simpson's index) at 8 weeks and evaluated relative abundance of microbial taxa using DESeq2. Of 109 children enrolled in the microbiome study, 95 were followed at 8 weeks. We found no evidence of a difference in alpha diversity between the azithromycin and amoxicillin groups at 8 weeks controlling for baseline diversity (mean difference -0.6, 95% CI -1.8 to 0.6, P = 0.30). Gut microbiomes did not diversify during the study. Differentially abundant genera at the P < 0.01 level included Salmonella spp. and Shigella spp., both of which were overabundant in the azithromycin compared with amoxicillin groups. We found no evidence to support an overall difference in gut microbiome diversity between azithromycin and amoxicillin among children with uncomplicated severe acute malnutrition, but potentially pathogenic bacteria that can cause invasive diarrhea were more common in the azithromycin group. Trial Registration: ClinicalTrials.gov NCT03568643.}, } @article {pmid36508860, year = {2023}, author = {Haas, GD and Lee, B}, title = {Paramyxoviruses from bats: changes in receptor specificity and their role in host adaptation.}, journal = {Current opinion in virology}, volume = {58}, number = {}, pages = {101292}, pmid = {36508860}, issn = {1879-6265}, support = {R01 AI123449/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Chiroptera ; Host Adaptation ; Virus Attachment ; Metagenomics ; Host Specificity ; Phylogeny ; }, abstract = {Global metagenomic surveys have revealed that bats host a diverse array of paramyxoviruses, including species from at least five major genera. An essential determinant of successful spillover is the entry of a virus into a new host. We evaluate the role of receptor usage in the zoonotic potential of bat-borne henipaviruses, morbilliviruses, pararubulaviruses, orthorubulaviruses, and jeilongviruses; successful spillover into humans depends upon compatibility of a respective viral attachment protein with its cognate receptor. We also emphasize the importance of postentry restrictions in preventing spillover. Metagenomics and characterization of newly identified paramyxoviruses have greatly improved our understanding of spillover determinants, allowing for better forecasts of which bat-borne viruses may pose the greatest risk for cross-species transmission into humans.}, } @article {pmid36508259, year = {2023}, author = {Cheng, K and Ning, Z and Li, L and Zhang, X and Serrana, JM and Mayne, J and Figeys, D}, title = {MetaLab-MAG: A Metaproteomic Data Analysis Platform for Genome-Level Characterization of Microbiomes from the Metagenome-Assembled Genomes Database.}, journal = {Journal of proteome research}, volume = {22}, number = {2}, pages = {387-398}, pmid = {36508259}, issn = {1535-3907}, mesh = {Humans ; Metagenome ; Proteomics ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Computational Biology ; Metagenomics ; }, abstract = {The studies of microbial communities have drawn increased attention in various research fields such as agriculture, environment, and human health. Recently, metaproteomics has become a powerful tool to interpret the roles of the community members by investigating the expressed proteins of the microbes. However, analyzing the metaproteomic data sets at genome resolution is still challenging because of the lack of efficient bioinformatics tools. Here we develop MetaLab-MAG, a specially designed tool for the characterization of microbiomes from metagenome-assembled genomes databases. MetaLab-MAG was evaluated by analyzing various human gut microbiota data sets and performed comparably or better than searching the gene catalog protein database directly. MetaLab-MAG can quantify the genome-level microbiota compositions and supports both label-free and isobaric labeling-based quantification strategies. MetaLab-MAG removes the obstacles of metaproteomic data analysis and provides the researchers with in-depth and comprehensive information from the microbiomes.}, } @article {pmid36508145, year = {2023}, author = {Xiao, J and Zhu, K and Ma, R and Zhang, C and Lv, K and Ge, D and Liu, R}, title = {Full genome sequence of a novel iflavirus from the aster leafhopper Macrosteles fascifrons.}, journal = {Virus genes}, volume = {59}, number = {2}, pages = {338-342}, pmid = {36508145}, issn = {1572-994X}, support = {2019YFC1200503//National Key Research and Development Program of China/ ; }, mesh = {Animals ; Phylogeny ; *Hemiptera ; Genome, Viral/genetics ; *RNA Viruses/genetics ; Amino Acid Sequence ; Capsid Proteins/genetics ; }, abstract = {The aster leafhopper Macrosteles fascifrons is a common insect pest that feeds on rice and other plants and may serve as a vector to transmit various viruses. Here, we discovered a novel virus from M. fascifrons using metagenomic sequencing. We obtained its complete genome sequence by contig assembly and rapid amplification of cDNA ends, and verified the genome sequence by Sanger sequencing of overlapping segments. Based on homology search and phylogenetic analysis, the new virus belongs to the family Iflaviridae and it is tentatively named "Macrosteles fascifrons iflavirus 1" (MfIV1). Excluding the poly(A) tail, the MfIV1 genome is 10,581 nucleotides in length and it is predicted to encode a polyprotein of 3119 amino acids long, which is likely further processed to several polypeptides with conserved domains, including two rhinovirus like (rhv-like) capsid domains, a cricket paralysis virus (CRPV) capsid domain, a helicase domain, and an RNA-dependent RNA polymerase (RdRp) domain. BLAST searches show that the highest amino acid sequence identity between the capsid proteins of MfIV1 and those of other reported iflaviruses is 60.22%, indicating that MfIV1 is a new member in the family Iflaviridae.}, } @article {pmid36508095, year = {2023}, author = {Behera, BK and Patra, B and Chakraborty, HJ and Rout, AK and Dixit, S and Rai, A and Das, BK and Mohapatra, T}, title = {Bacteriophages diversity in India's major river Ganga: a repository to regulate pathogenic bacteria in the aquatic environment.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {12}, pages = {34101-34114}, pmid = {36508095}, issn = {1614-7499}, mesh = {Humans ; *Environmental Monitoring/methods ; *Bacteriophages ; Rivers ; India ; Bacteria ; Water ; }, abstract = {Bacteriophages are key viruses that can kill thousands of harmful microbes generally present at polluted sites. Such bacteriophages are abundantly present in the river Ganga, where millions of people in India and abroad drink its water and take baths every day for spiritual reasons. Besides bacteriophages, several pathogenic and zoonotic microbes are present in the river Ganga. It is interesting to study the diversity and abundance of bacteria and their respective phages present in polluted or non-polluted sites. Thus, the metagenomics study was carried out at the most polluted sites of river Ganga near Kanpur and non-polluted sites at Farakka, which harbors several harmful bacteria and their phages. The results revealed a significantly higher percentage of Microviridae phage family, ssDNA viruses, and Mimiviridae virus family near Kanpur than Farakka. In addition, compared to Kanpur, Farakka has a more significant percentage of Myoviridae, an unidentified phage family, and Retroviridae viral families. Despite heavy drainage of untreated and contaminated effluents from the leather industry, pesticide industry, paper mills, metropolitan cities, and other sources, the vast number of said phages kills several harmful pathogenic microbes in polluted sites to maintain the Ganga water's healing power or natural sterility. In a polluted aquatic environment, the varieties of bacteriophages were identified in the Ganga and their interaction with the microbial host. The taxonomic diversity of several bacteriophages found in pathogenic host systems was investigated to get exceptional knowledge of these small viruses in the aquatic environment.}, } @article {pmid36507981, year = {2022}, author = {Wang, YL and Zhu, MY and Yuan, ZF and Ren, XY and Guo, XT and Hua, Y and Xu, L and Zhao, CY and Jiang, LH and Zhang, X and Sheng, GX and Jiang, PF and Zhao, ZY and Gao, F}, title = {Proteomic profiling of cerebrospinal fluid in pediatric myelin oligodendrocyte glycoprotein antibody-associated disease.}, journal = {World journal of pediatrics : WJP}, volume = {}, number = {}, pages = {}, pmid = {36507981}, issn = {1867-0687}, support = {LGF19H090020//Natural Science Foundation of Zhejiang Province/ ; 81901679//Young Scientists Fund/ ; }, abstract = {BACKGROUND: Myelin oligodendrocyte glycoprotein (MOG) antibody-associated disease (MOGAD) is an autoimmune demyelinating disorder of the central nervous system.

METHODS: Extracted proteins from 34 cerebrospinal fluid (CSF) samples [patients with MOGAD (MOG group, n = 12); healthy controls (HC group, n = 12); patients with MOG seronegative and metagenomics next-generation sequencing-negative inflammatory neurological diseases (IND group, n = 10)] were processed and subjected to label-free quantitative proteomics. Supervised partial least squares-discriminant analysis (PLS-DA) and orthogonal PLS-DA (O-PLS-DA) models were also performed based on proteomics data. Functional analysis of differentially expressed proteins (DEPs) was performed using Gene Ontology, InterPro, and Kyoto Encyclopedia Genes and Genomes. An enzyme-linked immunosorbent assay was used to determine the complement levels in serum from patients with MOGAD.

RESULTS: Four hundred and twenty-nine DEPs (149 upregulated and 280 downregulated proteins) were identified in the MOG group compared to the HC group according to the P value and fold change (FC). Using the O-PLS-DA model, 872 differentially abundant proteins were identified with variable importance projection (VIP) scores > 1. Five proteins (gamma-glutamyl hydrolase, cathepsin F, interalpha-trypsin inhibitor heavy chain 5, latent transforming growth factor beta-binding protein 4 and leukocyte-associated immunoglobulin-like receptor 1) overlapping between the top 30 DEPs with top-ranked P value and FC and top 30 proteins in PLS-DA VIP lists were acquired. Functional analysis revealed that the dysregulated proteins in the MOG group were primarily involved in complement and coagulation cascades, cell adhesion, axon guidance, and glycosphingolipid biosynthesis compared to the HC group.

CONCLUSION: The proteomic alterations in CSF samples from children with MOGAD identified in the current study might provide opportunities for developing novel biomarker candidates.}, } @article {pmid36507688, year = {2023}, author = {Albright, J and Mick, E and Sanchez-Guerrero, E and Kamm, J and Mitchell, A and Detweiler, AM and Neff, N and Tsitsiklis, A and Hayakawa Serpa, P and Ratnasiri, K and Havlir, D and Kistler, A and DeRisi, JL and Pisco, AO and Langelier, CR}, title = {A 2-Gene Host Signature for Improved Accuracy of COVID-19 Diagnosis Agnostic to Viral Variants.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0067122}, pmid = {36507688}, issn = {2379-5077}, support = {K23 HL138461/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *COVID-19/diagnosis ; SARS-CoV-2/genetics ; COVID-19 Testing ; Pandemics ; Sensitivity and Specificity ; }, abstract = {The continued emergence of SARS-CoV-2 variants is one of several factors that may cause false-negative viral PCR test results. Such tests are also susceptible to false-positive results due to trace contamination from high viral titer samples. Host immune response markers provide an orthogonal indication of infection that can mitigate these concerns when combined with direct viral detection. Here, we leverage nasopharyngeal swab RNA-seq data from patients with COVID-19, other viral acute respiratory illnesses, and nonviral conditions (n = 318) to develop support vector machine classifiers that rely on a parsimonious 2-gene host signature to diagnose COVID-19. We find that optimal classifiers include an interferon-stimulated gene that is strongly induced in COVID-19 compared with nonviral conditions, such as IFI6, and a second immune-response gene that is more strongly induced in other viral infections, such as GBP5. The IFI6+GBP5 classifier achieves an area under the receiver operating characteristic curve (AUC) greater than 0.9 when evaluated on an independent RNA-seq cohort (n = 553). We further provide proof-of-concept demonstration that the classifier can be implemented in a clinically relevant RT-qPCR assay. Finally, we show that its performance is robust across common SARS-CoV-2 variants and is unaffected by cross-contamination, demonstrating its utility for improved accuracy of COVID-19 diagnostics. IMPORTANCE In this work, we study upper respiratory tract gene expression to develop and validate a 2-gene host-based COVID-19 diagnostic classifier and then demonstrate its implementation in a clinically practical qPCR assay. We find that the host classifier has utility for mitigating false-negative results, for example due to SARS-CoV-2 variants harboring mutations at primer target sites, and for mitigating false-positive viral PCR results due to laboratory cross-contamination. Both types of error carry serious consequences of either unrecognized viral transmission or unnecessary isolation and contact tracing. This work is directly relevant to the ongoing COVID-19 pandemic given the continued emergence of viral variants and the continued challenges of false-positive PCR assays. It also suggests the feasibility of pan-respiratory virus host-based diagnostics that would have value in congregate settings, such as hospitals and nursing homes, where unrecognized respiratory viral transmission is of particular concern.}, } @article {pmid36507666, year = {2023}, author = {Diao, Z and Lai, H and Han, D and Yang, B and Zhang, R and Li, J}, title = {Validation of a Metagenomic Next-Generation Sequencing Assay for Lower Respiratory Pathogen Detection.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0381222}, pmid = {36507666}, issn = {2165-0497}, mesh = {Humans ; Metagenome ; *Respiratory Tract Infections/diagnosis ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; }, abstract = {Lower respiratory infection (LRI) is the most fatal communicable disease, with only a few pathogens identified. Metagenomic next-generation sequencing (mNGS), as an unbiased, hypothesis-free, and culture-independent method, theoretically enables the detection of all pathogens in a single test. In this study, we developed and validated a DNA-based mNGS method for the diagnosis of LRIs from bronchoalveolar lavage fluid (BALF). We prepared simulated in silico data sets and published raw data sets from patients to evaluate the performance of our in-house bioinformatics pipeline and compared it with the popular metagenomics pipeline Kraken2-Bracken. In addition, a series of biological microbial communities were used to comprehensively validate the performance of our mNGS assay. Sixty-nine clinical BALF samples were used for clinical validation to determine the accuracy. The in-house bioinformatics pipeline validation showed a recall of 88.03%, precision of 99.14%, and F1 score of 92.26% via single-genome simulated data. Mock in silico microbial community and clinical metagenomic data showed that the in-house pipeline has a stricter cutoff value than Kraken2-Bracken, which could prevent false-positive detection by the bioinformatics pipeline. The validation for the whole mNGS pipeline revealed that overwhelming human DNA, long-term storage at 4°C, and repeated freezing-thawing reduced the analytical sensitivity of the assay. The mNGS assay showed a sensitivity of 95.18% and specificity of 91.30% for pathogen detection from BALF samples. This study comprehensively demonstrated the analytical performance of this laboratory-developed mNGS assay for pathogen detection from BALF, which contributed to the standardization of this technology. IMPORTANCE To our knowledge, this study is the first to comprehensively validate the mNGS assay for the diagnosis of LRIs from BALF. This study exhibited a ready-made example for clinical laboratories to prepare reference materials and develop comprehensive validation schemes for their in-house mNGS assays, which would accelerate the standardization of mNGS testing.}, } @article {pmid36507660, year = {2023}, author = {Zheng, J and Liang, JL and Jia, P and Feng, SW and Lu, JL and Luo, ZH and Ai, HX and Liao, B and Li, JT and Shu, WS}, title = {Diverse Methylmercury (MeHg) Producers and Degraders Inhabit Acid Mine Drainage Sediments, but Few Taxa Correlate with MeHg Accumulation.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0073622}, pmid = {36507660}, issn = {2379-5077}, mesh = {*Methylmercury Compounds/analysis ; Bacteria/genetics ; Phylogeny ; Metagenome ; Firmicutes/genetics ; }, abstract = {Methylmercury (MeHg) is a notorious neurotoxin, and its production and degradation in the environment are mainly driven by microorganisms. A variety of microbial MeHg producers carrying the gene pair hgcAB and degraders carrying the merB gene have been separately reported in recent studies. However, surprisingly little attention has been paid to the simultaneous investigation of the diversities of microbial MeHg producers and degraders in a given habitat, and no studies have been performed to explore to what extent these two contrasting microbial groups correlate with MeHg accumulation in the habitat of interest. Here, we collected 86 acid mine drainage (AMD) sediments from an area spanning approximately 500,000 km[2] in southern China and profiled the sediment-borne putative MeHg producers and degraders using genome-resolved metagenomics. 46 metagenome-assembled genomes (MAGs) containing hgcAB and 93 MAGs containing merB were obtained, including those from various taxa without previously known MeHg-metabolizing microorganisms. These diverse MeHg-metabolizing MAGs were formed largely via multiple independent horizontal gene transfer (HGT) events. The putative MeHg producers from Deltaproteobacteria and Firmicutes as well as MeHg degraders from Acidithiobacillia were closely correlated with MeHg accumulation in the sediments. Furthermore, these three taxa, in combination with two abiotic factors, explained over 60% of the variance in MeHg accumulation. Most of the members of these taxa were characterized by their metabolic potential for nitrogen fixation and copper tolerance. Overall, these findings improve our understanding of the ecology of MeHg-metabolizing microorganisms and likely have implications for the development of management strategies for the reduction of MeHg accumulation in the AMD sediments. IMPORTANCE Microorganisms are the main drivers of MeHg production and degradation in the environment. However, little attention has been paid to the simultaneous investigation of the diversities of microbial MeHg producers and degraders in a given habitat. We used genome-resolved metagenomics to reveal the vast phylogenetic and metabolic diversities of putative MeHg producers and degraders in AMD sediments. Our results show that the diversity of MeHg-metabolizing microorganisms (particularly MeHg degraders) in AMD sediments is much higher than was previously recognized. Via multiple linear regression analysis, we identified both microbial and abiotic factors affecting MeHg accumulation in AMD sediments. Despite their great diversity, only a few taxa of MeHg-metabolizing microorganisms were closely correlated with MeHg accumulation. This work underscores the importance of using genome-resolved metagenomics to survey MeHg-metabolizing microorganisms and provides a framework for the illumination of the microbial basis of MeHg accumulation via the characterization of physicochemical properties, MeHg-metabolizing microorganisms, and the correlations between them.}, } @article {pmid36507520, year = {2022}, author = {Liu, J and Gao, Y}, title = {Tigecycline in the treatment of severe pneumonia caused by Chlamydia psittaci: A case report and literature review.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {1040441}, pmid = {36507520}, issn = {2296-858X}, abstract = {Psittacosis is a zoonotic disease caused by Chlamydia psittaci. Systemic infections are mainly transmitted through the respiratory tract. The most common related disease is human atypical pneumonia, which is a rare pathogen of community-acquired pneumonia. Due to the difficulty of diagnosis, there have been few reports of C. psittaci pneumonia in the past. In recent years, with the widespread application of metagenomic next-generation sequencing (mNGS), the number of reported cases of C. psittaci has increased year by year. However, at present, most hospitals have little understanding of C. psittaci, especially for severe patients, and lack experience in diagnosis and treatment. Herein, we report the case of a 71-year-old woman with severe pneumonia that caused by C. psittaci. This patient was diagnosed through mNGS and was treated with tigecycline successfully. The level of IL-6 in the BALF was significantly increased. We discontinued tigecycline after mNGS of the blood was negative. In this review, we analyzed 53 cases to summarize the etiology, clinical manifestations, diagnosis and treatment strategies of severe C. psittaci pneumonia and hope to raise clinicians' awareness of this disease.}, } @article {pmid36507192, year = {2022}, author = {Li, J and Zhou, CE and Wei, SC and Wang, LN and Shi, MW and Sun, CP and Lin, LJ and Liu, XM}, title = {Diagnostic Value of Metagenomic Next-Generation Sequencing for Pneumonia in Immunocompromised Patients.}, journal = {The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2022}, number = {}, pages = {5884568}, pmid = {36507192}, issn = {1712-9532}, abstract = {INTRODUCTION: The diagnosis of pulmonary infection and the identification of pathogens are still clinical challenges in immunocompromised patients. Metagenomic next-generation sequencing (mNGS) has emerged as a promising infection diagnostic technique. However, its diagnostic value in immunocompromised patients needs further exploration.

PURPOSES: This study was to evaluate the diagnostic value of mNGS compared with comprehensive conventional pathogen tests (CTs) in the etiology of pneumonia in immunocompromised patients and immunocompetent patients.

METHODS: We retrospectively reviewed 53 patients who were diagnosed with pneumonia from May 2019 to June 2021. There were 32 immunocompromised patients and 21 immunocompetent patients with pneumonia who received both mNGS and CTs. The diagnostic performance was compared between mNGS and CTs in immunocompromised patients, using the composite diagnosis as the reference standard. And, the diagnostic value of mNGS for mixed infections was further analyzed.

RESULTS: Compared to immunocompetent patients, the most commonly pathogens, followed by Cytomegalovirus, Pneumocystis jirovecii and Klebsiella pneumoniae in immunocompromised patients. Furthermore, more mixed infections were diagnosed, and bacterial-fungal-virus coinfection was the most frequent combination (43.8%). mNGS can detect more types of pathogenic microorganisms than CTs in both groups (78.1% vs. 62.5%, P = 0.016and 57.1% vs. 42.9%, P = 0.048). The overall diagnostic positive rate of mNGS for pathogens was higher in immunocompromised patients (P = 0.002). In immunocompromised patients, a comparable diagnostic accuracy of mNGS and CTs was found for bacterial, fungal, and viral infections and coinfection. mNGS had a much higher sensitivity for bacterial infections (92.9% vs. 50%, P < 0.001) and coinfections (68.8% vs. 48.3%, P < 0.05), and it had no significant advantage in the detection of fungal infections, mainly due to the high sensitivity for Pneumocystis jirovecii in both groups.

CONCLUSION: mNGS is more valuable in immunocompromised patients and exhibits apparent advantages in detecting bacterial and mixed infections. It may be an alternative or complementary diagnostic method for the diagnosis of complicated infections in immunocompromised patients.}, } @article {pmid36507072, year = {2023}, author = {Di Lorenzo, A and Mangone, I and Colangeli, P and Cioci, D and Curini, V and Vincifori, G and Mercante, MT and Di Pasquale, A and Iannetti, S}, title = {One health system supporting surveillance during COVID-19 epidemic in Abruzzo region, southern Italy.}, journal = {One health (Amsterdam, Netherlands)}, volume = {16}, number = {}, pages = {100471}, pmid = {36507072}, issn = {2352-7714}, abstract = {The Istituti Zooprofilattici Sperimentali (IZSs) are public health institutes dealing with the aetiology and pathogenesis of infectious diseases of domestic and wild animals. During Coronavirus Disease 2019 epidemic, the Italian Ministry of Health appointed the IZSs to carry out diagnostic tests for the detection of SARS-CoV-2 in human samples. In particular, the IZS of Abruzzo and Molise (IZS-Teramo) was involved in the diagnosis of SARS-CoV-2 through testing nasopharyngeal swabs by Real Time RT-PCR. Activities and infrastructures were reorganised to the new priorities, in a "One Health" framework, based on interdisciplinary, laboratory promptness, accreditation of the test for the detection of the RNA of SARS-CoV-2 in human samples, and management of confidentiality of sensitive data. The laboratory information system - SILAB - was implemented with a One Health module for managing data of human origin, with tools for the automatic registration of information improving the quality of the data. Moreover, the "National Reference Centre for Whole Genome Sequencing of microbial pathogens - database and bioinformatics analysis" - GENPAT - formally established at the IZS-Teramo, developed bioinformatics workflows and IT dashboard with ad hoc surveillance tools to support the metagenomics-based SARS-CoV-2 surveillance, providing molecular sequencing analysis to quickly intercept the variants circulating in the area. This manuscript describes the One Health system developed by adapting and integrating both SILAB and GENPAT tools for supporting surveillance during COVID-19 epidemic in the Abruzzo region, southern Italy. The developed dashboard permits the health authorities to observe the SARS-CoV-2 spread in the region, and by combining spatio-temporal information with metagenomics provides early evidence for the identification of emerging space-time clusters of variants at the municipality level. The implementation of the One Health module was designed to be easily modelled and adapted for the management of other diseases and future hypothetical events of pandemic nature.}, } @article {pmid36506522, year = {2022}, author = {Matthews, PC and Campbell, C and Săndulescu, O and Matičič, M and Ruta, SM and Rivero-Juárez, A and van Welzen, BJ and Tan, BK and Garcia, F and Gherlan, GS and Çınar, G and Hasanoğlu, İ and Gmizić, I and Nicolini, LA and Santos, L and Sargsyants, N and Velikov, P and Habibović, S and Fourati, S and Židovec-Lepej, S and Herder, V and Dudman, S and Miron, VD and Irving, W and Şahin, GÖ and , }, title = {Acute severe hepatitis outbreak in children: A perfect storm. What do we know, and what questions remain?.}, journal = {Frontiers in pharmacology}, volume = {13}, number = {}, pages = {1062408}, pmid = {36506522}, issn = {1663-9812}, support = {MC_UU_12014/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {During the first half of 2022, the World Health Organization reported an outbreak of acute severe hepatitis of unknown aetiology (AS-Hep-UA) in children, following initial alerts from the United Kingdom (UK) where a cluster of cases was first observed in previously well children aged <6 years. Sporadic cases were then reported across Europe and worldwide, although in most countries incidence did not increase above the expected baseline. There were no consistent epidemiological links between cases, and microbiological investigations ruled out known infectious causes of hepatitis. In this review, we explore the evidence for the role of viral infection, superimposed on a specific host genetic background, as a trigger for liver pathology. This hypothesis is based on a high prevalence of Human Adenovirus (HAdV) 41F in affected children, together with metagenomic evidence of adeno-associated virus (Adeno-associated viruses)-2, which is a putative trigger for an immune-mediated liver injury. Roles for superantigen-mediated pathology have also been explored, with a focus on the potential contribution of SARS-CoV-2 infection. Affected children also had a high frequency of the MHC allele HLA-DRB1*04:01, supporting an immunological predisposition, and may have been vulnerable to viral coinfections due to disruption in normal patterns of exposure and immunity as a result of population lockdowns during the COVID-19 pandemic. We discuss areas of ongoing uncertainty, and highlight the need for ongoing scrutiny to inform clinical and public health interventions for this outbreak and for others that may evolve in future.}, } @article {pmid36506298, year = {2023}, author = {Huang, Y and Wen, L and Zhang, L and Xu, J and Wang, W and Hu, H and Xu, P and Li, Z and Tang, H}, title = {Community-integrated multi-omics facilitates screening and isolation of the organohalide dehalogenation microorganism.}, journal = {Innovation (Cambridge (Mass.))}, volume = {4}, number = {1}, pages = {100355}, pmid = {36506298}, issn = {2666-6758}, abstract = {A variety of anthropogenic organohalide contaminants generated from industry are released into the environment and thus cause serious pollution that endangers human health. In the present study, we investigated the microbial community composition of industrial saponification wastewater using 16S rRNA sequencing, providing genomic insights of potential organohalide dehalogenation bacteria (OHDBs) by metagenomic sequencing. We also explored yet-to-culture OHDBs involved in the microbial community. Microbial diversity analysis reveals that Proteobacteria and Patescibacteria phyla dominate microbiome abundance of the wastewater. In addition, a total of six bacterial groups (Rhizobiales, Rhodobacteraceae, Rhodospirillales, Flavob a cteriales, Micrococcales, and Saccharimonadales) were found as biomarkers in the key organohalide removal module. Ninety-four metagenome-assembled genomes were reconstructed from the microbial community, and 105 hydrolytic dehalogenase genes within 42 metagenome-assembled genomes were identified, suggesting that the potential for organohalide hydrolytic dehalogenation is present in the microbial community. Subsequently, we characterized the organohalide dehalogenation of an isolated OHDB, Microbacterium sp. J1-1, which shows the dehalogenation activities of chloropropanol, dichloropropanol, and epichlorohydrin. This study provides a community-integrated multi-omics approach to gain functional OHDBs for industrial organohalide dehalogenation.}, } @article {pmid36506031, year = {2022}, author = {Zhang, C and Lin, Y and Huang, C and Huang, Z and Fang, X and Bai, G and Zhang, Z and Li, W and Zhang, W}, title = {Metagenomic next-generation sequencing assists the diagnosis treatment of fungal osteoarticular infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1072539}, pmid = {36506031}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; Metagenomics ; Metagenome ; *Mycoses/diagnosis/drug therapy ; Antifungal Agents/therapeutic use ; *Osteomyelitis/diagnosis/drug therapy ; *Arthritis ; Postoperative Complications ; Anti-Bacterial Agents ; }, abstract = {BACKGROUND: Fungal osteoarticular infection (FOI) is not commonly seen in clinical practice but proposes a great challenge to orthopedic surgeons. In this study, we aimed to investigate the risk factors, the clinical features, and surgical outcomes of FOI in our institution. Specifically, we aimed to explore the role of metagenomic next-generation sequencing (mNGS) in the diagnosis and treatment of FOI.

METHODS: All the patients who were diagnosed and managed with FOI in our institution from January 2007 to December 2020 were retrospectively reviewed, including primary fungal implant-related infection, primary fungal osteomyelitis or arthritis, and fungal infections secondary to bacterial osteomyelitis or implant-related bacterial infections. The potential risk factors and the clinical and surgical features were analyzed. The pathogen data were compared between culture and the mNGS test.

RESULTS: A total of 25 patients were included, namely, 12 primary implant-related infections, 7 primary fungal osteomyelitis or arthritis, and 6 fungal infections secondary to bacterial osteomyelitis or implant-related bacterial infections. Most cases had undergone multiple surgeries or long-term antibiotic treatment. Diagnosis was mainly based on microbial culture and the mNGS test. Optimization of culture methods and the use of mNGS assisted the diagnosis. Specifically, mNGS was performed in 12 patients, 5 of whom were culture-negative. In the remaining seven cases, mNGS demonstrated the same results as culture. Management of FOI was complicated as most patients required multiple surgeries followed by long-term antifungal treatment. In selected cases, antifungal-impregnated cement spacer retention can be an optional choice. The overall success rate was 100% (25/25) for our cohort.

CONCLUSION: We concluded that patients with comorbidities and a history of multiple surgeries or long-term antibiotics are under higher risk for FOI. Use of mNGS assists the diagnosis and treatment of FOI. Surgery combined with long-term antifungal treatment achieved satisfactory outcomes. In selected cases, antifungal-impregnated cement spacer retention can be an optional treatment choice.}, } @article {pmid36506020, year = {2022}, author = {Zhu, L and Lian, Y and Lin, D and Lin, G and Wang, M}, title = {The profile and persistence of clinically critical antibiotic resistance genes and human pathogenic bacteria in manure-amended farmland soils.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1073118}, pmid = {36506020}, issn = {2235-2988}, mesh = {Humans ; *Manure ; *Anti-Bacterial Agents/pharmacology ; Soil ; Drug Resistance, Microbial ; Bacteria/genetics ; Virulence Factors/genetics ; }, abstract = {INTRODUCTION: Microbial contamination in farmlands is usually underestimated and understudied. Different fertilization times and manure origins might introduce and change the microorganism diversity in farmland soils and thus might influence the abundance and persistence of microbial contamination including antibiotic resistance genes (ARGs), human bacterial pathogens (HBPs), and virulence factor genes (VFGs).

METHODS: A 0.5-/1.5-year fertilization experiment was performed, and metagenomic sequencing was conducted to quantify microbial contamination. The resistomes of soil samples revealed that ARGs against antibiotics which were extensively used in veterinary medicine as well as clinically critical ARGs (CCARGs) persisted in manure-amended soils. Here the extended-spectrum beta-lactamase and carbapenemase bla genes, the high-level mobilized colistin resistance gene mcr, the tigecycline resistance gene tet(X), and the vancomycin resistance gene van, all of which can circumvent the defense line of these "last-resort" antibiotics were selected to investigate CCARG pollution in farm environments.

RESULTS: A total of 254 potential HBPs and 2106 VFGs were detected in soil samples. Overall, our results revealed that (1) farmland soils could serve as a reservoir of some important bla, mcr, tet(X), and van gene variants, (2) the diversity and relative abundance of HBPs and VFGs increased significantly with incremental fertilization times and were discrepant among different manureamended soils, and (3) most CCARGs and VFGs coexisted in HBPs.

DISSCUSION: The results of this study suggested a biological risk of manure in spreading antimicrobial resistance and pathogenicity.}, } @article {pmid36504832, year = {2022}, author = {Farzad, R and Ha, AD and Aylward, FO}, title = {Diversity and genomics of giant viruses in the North Pacific Subtropical Gyre.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1021923}, pmid = {36504832}, issn = {1664-302X}, abstract = {Large double-stranded DNA viruses of the phylum Nucleocytoviricota, often referred to as "giant viruses," are ubiquitous members of marine ecosystems that are important agents of mortality for eukaryotic plankton. Although giant viruses are known to be prevalent in marine systems, their activities in oligotrophic ocean waters remain unclear. Oligotrophic gyres constitute the majority of the ocean and assessing viral activities in these regions is therefore critical for understanding overall marine microbial processes. In this study, we generated 11 metagenome-assembled genomes (MAGs) of giant viruses from samples previously collected from Station ALOHA in the North Pacific Subtropical Gyre. Phylogenetic analyses revealed that they belong to the orders Imitervirales (n = 6), Algavirales (n = 4), and Pimascovirales (n = 1). Genome sizes ranged from ~119-574 kbp, and several of the genomes encoded predicted TCA cycle components, cytoskeletal proteins, collagen, rhodopsins, and proteins potentially involved in other cellular processes. Comparison with other marine metagenomes revealed that several have broad distribution across ocean basins and represent abundant viral constituents of pelagic surface waters. Our work sheds light on the diversity of giant viruses present in oligotrophic ocean waters across the globe.}, } @article {pmid36504822, year = {2022}, author = {Kim, J and Kim, E and Kim, B and Kim, J and Lee, HJ and Park, JS and Hwang, S and Rho, M and Pai, H}, title = {Different maturation of gut microbiome in Korean children.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1036533}, pmid = {36504822}, issn = {1664-302X}, abstract = {INTRODUCTION: Gut microbiome plays a crucial role in maintaining human health and is influenced by food intake, age, and other factors.

METHODS: In this study based in Korea, we examined the bacterial taxonomic composition of the gut microbiota in infants (≤ 1 year), toddlers (1-<4 years), and school-aged children (4-13 years) and compared them with those of healthy adults to investigate the microbiota changes in early life and their association with the resistome. We used whole metagenome sequences obtained by Illumina HiSeq sequencing and clinical information of 53 healthy children, and sequence data of 61 adults from our previous study.

RESULTS: Our results indicate that the bacterial proportion of the gut in the population ranging from infants to adults forms three clusters: the Ruminococcus-Eubacterium (G1), Bifidobacterium-Escherichia (G2), and Bacteroides-Faecalibacterium (G3) groups. The gut microbiota of infants and toddlers (100% of infants and 85% of toddlers) constituted mostly of G2 and G3 groups, whereas 90% of adults showed G1-type gut microbiota. School-aged children showed a transitional gut microbiota composition of both infants and adults (31%, 38%, and 31% in G1, G2, and G3, respectively). Notably, the three clusters of microbiota showed significantly different patterns of bacterial diversity (p < 0.001): G2 showed the lowest Shannon index, followed by G3 and G1 (1.41, 2.08, and 2.48, respectively; median Shannon index). When combined with the adult group, alpha diversity showed a positive correlation with age (R[2] = 0.3). Furthermore, clustering the composition of antibiotic resistance genes (ARG) identified two clusters (A1 and A2), and most of G1 (95%) and G3 (80%) belonged to A1. However, G2 showed the least diversity and the highest abundance of ARGs. Nine ARG families showed a significant difference among age groups; three tetracycline resistance genes, tet32, tetO, and tetW, showed a positive correlation, and six other genes, ampC, TEM, ileS, bacA, pmr transferase, and cepA, showed a negative correlation with age.

DISCUSSION: In conclusion, our results highlighted that a delayed persistence of the Bifidobacterium-dominant enterotype with a lower bacterial diversity was observed in Korean children up to 13 years of age, which suggests a different maturation process with a delayed maturation time.}, } @article {pmid36504803, year = {2022}, author = {Lyu, Z and Rotaru, AE and Pimentel, M and Zhang, CJ and Rittmann, SKR}, title = {Editorial: The methane moment - Cross-boundary significance of methanogens: Preface.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1055494}, pmid = {36504803}, issn = {1664-302X}, } @article {pmid36504787, year = {2022}, author = {Wen, Q and Yu, S and Wang, S and Qin, Y and Xia, Q and Wang, S and Chen, G and Shen, C and Song, S}, title = {Impact of intestinal microbiota on metabolic toxicity and potential detoxification of amygdalin.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1030516}, pmid = {36504787}, issn = {1664-302X}, abstract = {Amygdalin (Amy) is metabolized into cyanide in vivo, which may lead to fatal poisoning after oral administration. The defense mechanisms against toxic cyanide have not yet been adequately studied. In this study, comparative toxicokinetics study of Amy was performed in normal and pseudo germ-free rats. The efficiency of cyanide release was significant higher in normal group when given a single oral dose of 440 mg/kg (50% median lethal dose). Thiocyanate, the detoxification metabolite, was firstly detected in feces, caecum, and intestinal microbiota incubation enzymic system. The results suggest intestinal microbiota is involved in bidirectional regulation of toxicity and detoxification of Amy. We further identified the species related to cyanogenesis of Amy with metagenomic sequencing, such as Bifidobacterium pseudolongum, Marvinbryantia formatexigens, and Bacteroides fragilis. Functional analysis of microbiota reveals the detoxification potential of intestinal microbiota for cyanide. Sulfurtransferase superfamily, such as rhodanese, considered as main detoxification enzymes for cyanide, are largely found in Coriobacteriaceae bacterium, Butyricicoccus porcorum, Akkermansia muciniphila, etc. Besides, cyanoamino acid metabolism pathway dominated by Escherichia coli may contribute to the detoxification metabolism of cyanide. In summary, intestinal microbiota may be the first line of defense against the toxicity induced by Amy.}, } @article {pmid36504762, year = {2022}, author = {Gu, L and Wu, H and Zhang, Y and Wu, Y and Jin, Y and Li, T and Ma, L and Zheng, J}, title = {The effects of elemene emulsion injection on rat fecal microbiota and metabolites: Evidence from metagenomic exploration and liquid chromatography-mass spectrometry.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {913461}, pmid = {36504762}, issn = {1664-302X}, abstract = {OBJECTIVE: Elemene emulsion injection (EEI) has been approved for interventional and intracavitary chemotherapy in treating malignant ascites in China, but few studies have focused on the effects of EEI on gut microbiota and metabolites. In this study, we investigated the effects of EEI on the fecal microbiota and metabolites in healthy Sprague-Dawley (SD) rats.

METHODS: We randomly assigned 18 male SD rats to three groups (n = 6 in each group): the sham group (group S), the low-concentration EEI group (L-EEI), and the high-concentration EEI group (H-EEI). The L-EEI and H-EEI rats were administered 14 days of consecutive EEI, 20 mg/kg, and 40 mg/kg intraperitoneally (IP). Group S rats were administered the same volume of normal saline. On day 14, each animal's feces were collected for metagenomic sequencing and metabolomic analysis, and the colonic contents were collected for 16S rRNA sequencing.

RESULTS: EEI could alter the β-diversity but not the α-diversity of the fecal microbiota and induce structural changes in the fecal microbiota. Different concentrations of EEI affect the fecal microbiota differently. The effects of different EEI concentrations on the top 20 bacteria with significant differences at the species level among the three groups were roughly divided into three categories: (1) A positive or negative correlation with the different EEI concentrations. The abundance of Ileibacterium Valens increased as the EEI concentration increased, while the abundance of Firmicutes bacteria and Clostridium sp. CAC: 273 decreased. (2) The microbiota showed a tendency to increase first, then decrease or decrease first, and then increase as EEI concentration increased-the abundance of Prevotella sp. PCHR, Escherichia coli, and Candidatus Amulumruptor caecigallinarius tended to decrease with L-EEI but significantly increased with H-EEI. In contrast, L-EEI significantly increased Ruminococcus bromii and Dorea sp. 5-2 abundance, and Oscillibacter sp. 1-3 abundance tended to increase, while H-EEI significantly decreased them. (3) L-EEI and H-EEI decreased the abundance of bacteria (Ruminococcaceae bacterium, Romboutsia ilealis, and Staphylococcus xylosus). Fecal metabolites, like microbiota, were sensitive to different EEI concentrations and correlated with fecal microbiota and potential biomarkers.

CONCLUSION: This study shows that intraperitoneal EEI modulates the composition of rat fecal microbiota and metabolites, particularly the gut microbiota's sensitivity to different concentrations of EEI. The impact of changes in the microbiota on human health remains unknown, particularly EEI's efficacy in treating tumors.}, } @article {pmid36503863, year = {2023}, author = {Singh, G and Agrawal, H and Bednarek, P}, title = {Specialized metabolites as versatile tools in shaping plant-microbe associations.}, journal = {Molecular plant}, volume = {16}, number = {1}, pages = {122-144}, doi = {10.1016/j.molp.2022.12.006}, pmid = {36503863}, issn = {1752-9867}, mesh = {*Plants/metabolism ; Adaptation, Physiological ; Genomics ; *Microbiota ; }, abstract = {Plants are rich repository of a large number of chemical compounds collectively referred to as specialized metabolites. These compounds are of importance for adaptive processes including responses against changing abiotic conditions and interactions with various co-existing organisms. One of the strikingly affirmed functions of these specialized metabolites is their involvement in plants' life-long interactions with complex multi-kingdom microbiomes including both beneficial and harmful microorganisms. Recent developments in genomic and molecular biology tools not only help to generate well-curated information about regulatory and structural components of biosynthetic pathways of plant specialized metabolites but also to create and screen mutant lines defective in their synthesis. In this review, we have comprehensively surveyed the function of these specialized metabolites and discussed recent research findings demonstrating the responses of various microbes on tested mutant lines having defective biosynthesis of particular metabolites. In addition, we attempt to provide key clues about the impact of these metabolites on the assembly of the plant microbiome by summarizing the major findings of recent comparative metagenomic analyses of available mutant lines under customized and natural microbial niches. Subsequently, we delineate benchmark initiatives that aim to engineer or manipulate the biosynthetic pathways to produce specialized metabolites in heterologous systems but also to diversify their immune function. While denoting the function of these metabolites, we also discuss the critical bottlenecks associated with understanding and exploiting their function in improving plant adaptation to the environment.}, } @article {pmid36503828, year = {2023}, author = {Uenosono, Y and Kawakami, R and Matsumoto, S and Yamaguchi, Y}, title = {Construction of an experimental study and addition of adapter sequences using HiDi DNA polymerase for improving DNA normalization methods relevant to novel gene discovery.}, journal = {Journal of microbiological methods}, volume = {204}, number = {}, pages = {106631}, doi = {10.1016/j.mimet.2022.106631}, pmid = {36503828}, issn = {1872-8359}, mesh = {*DNA/genetics ; *DNA-Directed DNA Polymerase ; Oligonucleotides ; Genetic Association Studies ; }, abstract = {Microorganisms in the environment can be distinguished into dominant and rare microbial species based on their genes. It is difficult to obtain genetic information derived from rare microbial species (rare genes) because of the differences in relative abundance. DNA normalization is an approach that is used to obtain genetic information derived from rare microbial species from an environmental sample. This method involves the addition of adapter sequences for the amplification, denaturation, and reassociation of the DNA fragments and single-stranded DNA (ssDNA)/double-stranded DNA (dsDNA) separation. In this method, the amount of a high-copy-number of DNA fragments and a low-copy-number of DNA fragments can be equalized. Improvements in this technique are expected to provide novel genetic information or genes in rare microbial species. However, few model experimental systems have been reported to validate the DNA normalization techniques. This study is aimed to improve the DNA normalization technique used to obtain genetic information of rare genes from rare microbial species. An experimental study was constructed with two antibiotic resistance genes, whose copy numbers differed up to a million-fold. Both genes were mixed and the mixture of DNA fragments, of high- and low-copy-number, containing these genes was normalized by separating ssDNA/dsDNA fragments using hydroxyapatite. Normalized DNA fragments were introduced into Escherichia coli and DNA normalization was evaluated by counting colonies. Moreover, we improved the method to amplify a low-copy-number of DNA fragments by the addition of adapter sequences to DNA fragments using HiDi DNA polymerase to increase the efficiency of DNA normalization. This normalization method was achieved with a 100,000-fold difference. These methods allowed for quantitative evaluation of the DNA normalization efficiency. The experimental data and methods obtained in this study are expected to improve the DNA normalization efficiency to obtain novel genetic information or genes.}, } @article {pmid36503809, year = {2023}, author = {Chen, J and Yang, Y and Jiang, X and Ke, Y and He, T and Xie, S}, title = {Corrigendum to Metagenomic insights into the profile of antibiotic resistomes in sediments of aquaculture wastewater treatment system <Journal of Environmental Sciences (Volume 113, March 2022), Pages 345-355>.}, journal = {Journal of environmental sciences (China)}, volume = {126}, number = {}, pages = {836}, doi = {10.1016/j.jes.2022.09.022}, pmid = {36503809}, issn = {1001-0742}, } @article {pmid36503599, year = {2022}, author = {Ide, K and Nishikawa, Y and Maruyama, T and Tsukada, Y and Kogawa, M and Takeda, H and Ito, H and Wagatsuma, R and Miyaoka, R and Nakano, Y and Kinjo, K and Ito, M and Hosokawa, M and Yura, K and Suda, S and Takeyama, H}, title = {Targeted single-cell genomics reveals novel host adaptation strategies of the symbiotic bacteria Endozoicomonas in Acropora tenuis coral.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {220}, pmid = {36503599}, issn = {2049-2618}, support = {JPMJCR12A4//Core Research for Evolutional Science and Technology/ ; JPMJCR12A4//Core Research for Evolutional Science and Technology/ ; JP17H06158//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; *Anthozoa/microbiology ; RNA, Ribosomal, 16S/genetics ; Host Adaptation ; *Gammaproteobacteria/genetics ; Symbiosis ; Bacteria ; Genomics ; Coral Reefs ; }, abstract = {BACKGROUND: Endozoicomonas bacteria symbiosis with various marine organisms is hypothesized as a potential indicator of health in corals. Although many amplicon analyses using 16S rRNA gene have suggested the diversity of Endozoicomonas species, genome analysis has been limited due to contamination of host-derived sequences and difficulties in culture and metagenomic analysis. Therefore, the evolutionary and functional potential of individual Endozoicomonas species symbiotic with the same coral species remains unresolved.

RESULTS: In this study, we applied a novel single-cell genomics technique using droplet microfluidics to obtain single-cell amplified genomes (SAGs) for uncultured coral-associated Endozoicomonas spp. We obtained seven novel Endozoicomonas genomes and quantitative bacterial composition from Acropora tenuis corals at four sites in Japan. Our quantitative 16S rRNA gene and comparative genomic analysis revealed that these Endozoicomonas spp. belong to different lineages (Clade A and Clade B), with widely varying abundance among individual corals. Furthermore, each Endozoicomonas species possessed various eukaryotic-like genes in clade-specific genes. It was suggested that these eukaryotic-like genes might have a potential ability of different functions in each clade, such as infection of the host coral or suppression of host immune pathways. These Endozoicomonas species may have adopted different host adaptation strategies despite living symbiotically on the same coral.

CONCLUSIONS: This study suggests that coral-associated Endozoicomonas spp. on the same species of coral have different evolutional strategies and functional potentials in each species and emphasizes the need to analyze the genome of each uncultured strain in future coral-Endozoicomonas relationships studies. Video Abstract.}, } @article {pmid36503581, year = {2022}, author = {Tierney, BT and Singh, NK and Simpson, AC and Hujer, AM and Bonomo, RA and Mason, CE and Venkateswaran, K}, title = {Multidrug-resistant Acinetobacter pittii is adapting to and exhibiting potential succession aboard the International Space Station.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {210}, pmid = {36503581}, issn = {2049-2618}, support = {R01AI151059/NH/NIH HHS/United States ; R01 AI151059/AI/NIAID NIH HHS/United States ; NNH12ZTT001N/NASA/NASA/United States ; }, mesh = {Humans ; *Spacecraft ; Genome-Wide Association Study ; *Acinetobacter/genetics ; Metagenome ; }, abstract = {BACKGROUND: Monitoring the adaptation of microorganisms to the extreme environment of the International Space Station (ISS) is crucial to understanding microbial evolution and infection prevention. Acinetobacter pittii is an opportunistic nosocomial pathogen, primarily impacting immunocompromised patients, that was recently isolated from two missions aboard the ISS.

RESULTS: Here, we report how ISS-associated A. pittii (n = 20 genomes) has formed its own genetically and functionally discrete clade distinct from most Earth-bound isolates (n = 291 genomes). The antimicrobial susceptibility testing of ISS strains and two related clinical isolates demonstrated that ISS strains acquired more resistance, specifically with regard to expanded-spectrum cephalosporins, despite no prediction of increased resistance based on genomic analysis of resistance genes. By investigating 402 longitudinal environmental and host-associated ISS metagenomes, we observed that viable A. pittii is increasing in relative abundance and therefore potentially exhibiting succession, being identified in >2X more metagenomic samples in back-to-back missions. ISS strains additionally contain functions that enable them to survive in harsh environments, including the transcriptional regulator LexA. Via a genome-wide association study, we identified a high level of mutational burden in methionine sulfoxide reductase genes relative to the most closely related Earth strains.

CONCLUSIONS: Overall, these results indicated a step forward in understanding how microorganisms might evolve and alter their antibiotic resistance phenotype in extreme, resource-limited, human-built environments. Video Abstract.}, } @article {pmid36503356, year = {2022}, author = {Sauceda, C and Bayne, C and Sudqi, K and Gonzalez, A and Dulai, PS and Knight, R and Gonzalez, DJ and Gonzalez, CG}, title = {Stool multi-omics for the study of host-microbe interactions in inflammatory bowel disease.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2154092}, pmid = {36503356}, issn = {1949-0984}, support = {U34 DK126626/DK/NIDDK NIH HHS/United States ; R01 DK131005/DK/NIDDK NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; T32 DK007202/DK/NIDDK NIH HHS/United States ; T32 GM007752/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Host Microbial Interactions ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; Multiomics ; *Inflammatory Bowel Diseases/genetics ; }, abstract = {Inflammatory Bowel Disease (IBD) is a chronic immune-mediated inflammatory disease of the gastrointestinal tract that is a growing public burden. Gut microbes and their interactions with hosts play a crucial role in disease pathogenesis and progression. These interactions are complex, spanning multiple physiological systems and data types, making comprehensive disease assessment difficult, and often overwhelming single-omic capabilities. Stool-based multi-omics is a promising approach for characterizing host-gut microbiome interactions using deep integration of technologies such as 16S rRNA sequencing, shotgun metagenomics, meta-transcriptomics, metabolomics, and metaproteomics. The wealth of information generated through multi-omic studies is poised to usher in advancements in IBD research and precision medicine. This review highlights historical and recent findings from stool-based muti-omic studies that have contributed to unraveling IBD's complexity. Finally, we discuss common pitfalls, issues, and limitations, and how future pipelines should address them to standardize multi-omics in IBD research and beyond.}, } @article {pmid36501516, year = {2022}, author = {Holyavka, MG and Goncharova, SS and Sorokin, AV and Lavlinskaya, MS and Redko, YA and Faizullin, DA and Baidamshina, DR and Zuev, YF and Kondratyev, MS and Kayumov, AR and Artyukhov, VG}, title = {Novel Biocatalysts Based on Bromelain Immobilized on Functionalized Chitosans and Research on Their Structural Features.}, journal = {Polymers}, volume = {14}, number = {23}, pages = {}, pmid = {36501516}, issn = {2073-4360}, support = {21-74-20053//Russian Science Foundation/ ; //government assignment for FRC Kazan Scientific Center of RAS/ ; FZGU-2020-0044//Ministry of Science and Higher Education of Russia/ ; }, abstract = {Enzyme immobilization on various carriers represents an effective approach to improve their stability, reusability, and even change their catalytic properties. Here, we show the mechanism of interaction of cysteine protease bromelain with the water-soluble derivatives of chitosan-carboxymethylchitosan, N-(2-hydroxypropyl)-3-trimethylammonium chitosan, chitosan sulfate, and chitosan acetate-during immobilization and characterize the structural features and catalytic properties of obtained complexes. Chitosan sulfate and carboxymethylchitosan form the highest number of hydrogen bonds with bromelain in comparison with chitosan acetate and N-(2-hydroxypropyl)-3-trimethylammonium chitosan, leading to a higher yield of protein immobilization on chitosan sulfate and carboxymethylchitosan (up to 58 and 65%, respectively). In addition, all derivatives of chitosan studied in this work form hydrogen bonds with His158 located in the active site of bromelain (except N-(2-hydroxypropyl)-3-trimethylammonium chitosan), apparently explaining a significant decrease in the activity of biocatalysts. The N-(2-hydroxypropyl)-3-trimethylammonium chitosan displays only physical interactions with His158, thus possibly modulating the structure of the bromelain active site and leading to the hyperactivation of the enzyme, up to 208% of the total activity and 158% of the specific activity. The FTIR analysis revealed that interaction between N-(2-hydroxypropyl)-3-trimethylammonium chitosan and bromelain did not significantly change the enzyme structure. Perhaps this is due to the slowing down of aggregation and the autolysis processes during the complex formation of bromelain with a carrier, with a minimal modification of enzyme structure and its active site orientation.}, } @article {pmid36501007, year = {2022}, author = {Coimbra, VOR and Crovesy, L and Ribeiro-Alves, M and Faller, ALK and Mattos, F and Rosado, EL}, title = {Gut Microbiota Profile in Adults Undergoing Bariatric Surgery: A Systematic Review.}, journal = {Nutrients}, volume = {14}, number = {23}, pages = {}, pmid = {36501007}, issn = {2072-6643}, mesh = {Humans ; RNA, Ribosomal, 16S ; *Bariatric Surgery/methods ; *Gastric Bypass/methods ; *Gastrointestinal Microbiome ; Gastrectomy/methods ; Bacteria/genetics ; *Obesity, Morbid/surgery ; Treatment Outcome ; }, abstract = {Gut microbiota (GM) after bariatric surgery (BS) has been considered as a factor associated with metabolic improvements and weight loss. In this systematic review, we evaluate changes in the GM, characterized by 16S rRNA and metagenomics techniques, in obese adults who received BS. The PubMed, Scopus, Web of Science, and LILACS databases were searched. Two independent reviewers analyzed articles published in the last ten years, using Rayyan QCRI. The initial search resulted in 1275 documents, and 18 clinical trials were included after the exclusion criteria were applied. The predominance of intestinal bacteria phyla varied among studies; however, most of them reported a greater amount of Bacteroidetes (B), Proteobacteria (P), and diversity (D) after BS. Firmicutes (F), B, and the (F/B) ratio was inconsistent, increasing or decreasing after Roux-en-Y gastric bypass (RYGB) and sleeve gastrectomy (SG) were conducted, compared to before surgery. There was a reduction in the relative proportion of F. Moreover, a higher proportion of Actinobacteria (A) was observed after RYGB was conducted. However, the same was not identified when SG procedures were applied. Genera abundance and bacteria predominance varied according to the surgical procedure, with limited data regarding the impact on phyla. The present study was approved by PROSPERO, under registration number CRD42020209509.}, } @article {pmid36499731, year = {2022}, author = {Grellier, N and Suzuki, MT and Brot, L and Rodrigues, AMS and Humbert, L and Escoubeyrou, K and Rainteau, D and Grill, JP and Lami, R and Seksik, P}, title = {Impact of IBD-Associated Dysbiosis on Bacterial Quorum Sensing Mediated by Acyl-Homoserine Lactone in Human Gut Microbiota.}, journal = {International journal of molecular sciences}, volume = {23}, number = {23}, pages = {}, pmid = {36499731}, issn = {1422-0067}, support = {EQU202003010171//Fondation pour la Recherche Médicale/ ; }, mesh = {Humans ; Acyl-Butyrolactones/metabolism ; Ecosystem ; Quorum Sensing/genetics ; Dysbiosis ; *Inflammatory Bowel Diseases/metabolism ; *Crohn Disease ; }, abstract = {Intestinal dysbiosis is a key feature in the pathogenesis of inflammatory bowel disease (IBD). Acyl-homoserine lactones (AHL) are bacterial quorum-sensing metabolites that may play a role in the changes in host cells-gut microbiota interaction observed during IBD. The objective of our study was to investigate the presence and expression of AHL synthases and receptor genes in the human gut ecosystem during IBD. We used an in silico approach, applied to the Inflammatory Bowel Disease Multi'omics Database comprising bacterial metagenomic and metatranscriptomic data from stools of patients with Crohn's disease (CD) (n = 50), ulcerative colitis (UC) (n = 27) and non-IBD controls (n = 26). No known putative AHL synthase gene was identified; however, several putative luxR receptors were observed. Regarding the expression of these receptor genes, the luxR gene from Bacteroides dorei was under-expressed in IBD patients (p = 0.02) compared to non-IBD patients, especially in CD patients (p = 0.02). In the dysbiosis situation, one luxR receptor gene from Bacteroides fragilis appeared to be over-expressed (p = 0.04) compared to that of non-dysbiotic patients. Targeting LuxR receptors of bacterial quorum sensing might represent a new approach to modulate the gut microbiota in IBD.}, } @article {pmid36499517, year = {2022}, author = {Gureev, AP and Khorolskaya, VG and Sadovnikova, IS and Shaforostova, EA and Cherednichenko, VR and Burakova, IY and Plotnikov, EY and Popov, VN}, title = {Age-Related Decline in Nrf2/ARE Signaling Is Associated with the Mitochondrial DNA Damage and Cognitive Impairments.}, journal = {International journal of molecular sciences}, volume = {23}, number = {23}, pages = {}, pmid = {36499517}, issn = {1422-0067}, support = {21-75-30009//Russian Science Support Foundation/ ; }, mesh = {Animals ; Mice ; Antioxidant Response Elements/genetics ; Brain-Derived Neurotrophic Factor/metabolism ; *Cognitive Dysfunction/genetics/metabolism ; *DNA, Mitochondrial/genetics/metabolism ; Hippocampus/metabolism ; Mitochondria/genetics/metabolism ; Signal Transduction ; DNA Damage ; }, abstract = {In this research, we compared the cognitive parameters of 2-, 7-, and 15-month-old mice, changes in mitochondrial DNA (mtDNA) integrity and expression of genes involved in the nuclear erythroid 2-related factor 2/antioxidant response element (Nrf2/ARE) signaling pathway. We showed an age-related decrease in the Nfe2l2 expression in the cerebral cortex, not in the hippocampus. At the same time, we find an increase in the mtDNA copy number in the cerebral cortex, despite the lack of an increase in gene expression, which is involved in the mitochondrial biogenesis regulation. We suppose that increase in mtDNA content is associated with mitophagy downregulation. We supposed that mitophagy downregulation may be associated with an age-related increase in the mtDNA damage. In the hippocampus, we found a decrease in the Bdnf expression, which is involved in the pathways, which play an essential role in regulating long-term memory formation. We showed a deficit of working and reference memory in 15-month-old-mice in the water Morris maze, and a decrease in the exploratory behavior in the open field test. Cognitive impairments in 15-month-old mice correlated with a decrease in Bdnf expression in the hippocampus, Nfe2l2 expression, and an increase in the number of mtDNA damage in the cerebral cortex. Thus, these signaling pathways may be perspective targets for pharmacological intervention to maintain mitochondrial quality control, neuronal plasticity, and prevent the development of age-related cognitive impairment.}, } @article {pmid36499044, year = {2022}, author = {Fang, Z and Chen, Y and Li, Y and Sun, L and Deng, Q and Wang, J and Gooneratne, R}, title = {Oleic Acid Facilitates Cd Excretion by Increasing the Abundance of Burkholderia in Cd-Exposed Mice.}, journal = {International journal of molecular sciences}, volume = {23}, number = {23}, pages = {}, pmid = {36499044}, issn = {1422-0067}, support = {32172215//National Natural Science Foundation of China/ ; 31701706//National Natural Science Foundation of China/ ; }, mesh = {Humans ; Mice ; Animals ; Cadmium/toxicity ; *Burkholderia ; Oleic Acid/pharmacology ; *Gastrointestinal Microbiome ; Feces ; }, abstract = {As a global pollutant, cadmium (Cd) can easily enter the body through food chains, threatening human health. Most Cd is initially absorbed in the gut, with the gut microbiota playing a pivotal role in reducing Cd absorption and accumulation. This study assessed the effects of three fatty acids on Cd accumulation and toxicity in Cd-exposed mice. The results showed that oleic acid (OA) was the most effective in facilitating Cd excretion in mice among these fatty acids. The use of OA led to reduced Cd accumulation in the organs and increased Cd content in the feces. The metagenomic analysis of the gut microbiota showed that the genus Burkholderia was the most significantly restored by OA in Cd-exposed mice. Burkholderia cepacia, as the type species for the genus Burkholderia, also exhibited strong Cd tolerance after treatment with OA. Furthermore, the electron microscopy analysis showed that most of the Cd was adsorbed on the surface of B. cepacia, where the extracellular polymeric substances (EPSs) secreted by B. cepacia play a key role, displaying a strong capacity for Cd adsorption. The peak at 2355 cm[-1] and the total sulfhydryl group content of EPSs showed significant increases following co-treatment with Cd and OA. The results demonstrated the potential roles that gut Burkholderia may play in OA-mediated Cd excretion in mice.}, } @article {pmid36498724, year = {2022}, author = {Wang, W and Chen, O and Liu, W and Gan, L and Li, X and Ma, Q and Hu, X and Jian, X}, title = {Coxiella burnetii and Bartonella Endocarditis Diagnosed by Metagenomic Next-Generation Sequencing.}, journal = {Journal of clinical medicine}, volume = {11}, number = {23}, pages = {}, pmid = {36498724}, issn = {2077-0383}, support = {82002236//National Natural Science Funds of China/ ; }, abstract = {(1) Background: Culture-negative endocarditis is challenging to diagnose. Here, we retrospectively identified 23 cases of Coxiella burnetii and Bartonella endocarditis by metagenomic next-generation sequencing. (2) Methods: Twenty-three patients with culture-negative endocarditis were retrospectively enrolled from Guangdong Provincial People's Hospital (n = 23) between April 2019 and December 2021. Metagenomic next-generation sequencing was performed on blood (n = 22) and excised cardiac valvular tissue samples (n = 22) for etiological identification, and Sanger sequencing was performed for pathogenic diagnostic verification. The demographic and clinical data of the 23 patients were obtained from hospital electronic health records. (3) Results: A total of 23 male patients (median age, 56 years (interquartile range, 16)) with culture-negative endocarditis were diagnosed with Coxiella burnetii (n = 21) or Bartonella (n = 2) species infection by metagenomic next-generation sequencing. All patients underwent cardiac surgery. The resected tissue exhibited both a significantly higher number of unique suspected pathogen read-pairs and more unique pathogen read-pairs than the blood specimens. The results of Sanger sequencing tests on all remaining tissue and blood specimens were positive. Oral doxycycline was added to the antibiotic regimen for at least 1.5 years according to etiology. A total of 21 patients (91%) were discharged, and 20 patients were healthy at the 21-month (interquartile range, 15) follow-up visit. One patient exhibited endocarditis relapse with the same pathogen from inadequate antibiotic administration. The last 2 patients (9%) developed septic shock and multiple organ dysfunction syndrome postoperatively and died shortly after discharge. (4) Conclusions: CNE caused by C. burnetii and Bartonella species is challenging to diagnose and exhibits poor outcome due to delayed treatment. In response, mNGS, characterized by high sensitivity and rapid results, is an effective alternative for the etiological identification of C. burnetii and Bartonella endocarditis.}, } @article {pmid36498382, year = {2022}, author = {Li, XQ and Liu, YQ and Li, YJ and Han, H and Zhang, H and Ji, MF and Chen, ZJ}, title = {Enhancing Mechanisms of the Plant Growth-Promoting Bacterial Strain Brevibacillus sp. SR-9 on Cadmium Enrichment in Sweet Sorghum by Metagenomic and Transcriptomic Analysis.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {23}, pages = {}, pmid = {36498382}, issn = {1660-4601}, support = {Nos. U2004145, 41601332, 51879130//National Natural Science Foundation of China/ ; No. 23A610003//Key Research Project of Colleges and Universities of Henan Province Education Department/ ; No. 23HASTIT018//Program for Science & Tech-nology Innovation Talents in Universities of Henan Province/ ; }, mesh = {Humans ; Cadmium/analysis ; *Sorghum/metabolism/microbiology ; *Soil Pollutants/analysis ; *Brevibacillus/genetics/metabolism ; Soil/chemistry ; Soil Microbiology ; Gene Expression Profiling ; Amino Acids/metabolism ; Plant Roots/metabolism ; Biodegradation, Environmental ; }, abstract = {To explore the mechanism by which the plant growth-promoting bacterium Brevibacillus sp. SR-9 improves sweet sorghum tolerance and enriches soil cadmium (Cd) under pot conditions, the effect of strain SR-9 inoculation on the microbial community of sorghum rhizosphere soil was analyzed by metagenomics. Gene expression in sweet sorghum roots was analyzed using transcriptomics. The results showed that strain SR-9 promoted the growth of sweet sorghum and improved the absorption and enrichment of Cd in the plants. Compared with the uninoculated treatment, the aboveground part and root dry weight in strain SR-9 inoculated with sorghum increased by 21.09% and 17.37%, respectively, and the accumulation of Cd increased by 135% and 53.41%, respectively. High-throughput sequencing showed that strain SR-9 inoculation altered the rhizosphere bacterial community, significantly increasing the relative abundance of Actinobacteria and Firmicutes. Metagenomic analysis showed that after inoculation with strain SR-9, the abundance of genes involved in amino acid transport metabolism, energy generation and conversion, and carbohydrate transport metabolism increased. KEGG functional classification showed that inoculation with strain SR-9 increased the abundance of genes involved in soil microbial metabolic pathways in the rhizosphere soil of sweet sorghum and the activity of soil bacteria. Transcriptome analysis identified 198 upregulated differentially expressed genes in sweet sorghum inoculated with strain SR-9, including those involved in genetic information processing, biological system, metabolism, environmental information processing, cellular process, and human disease. Most of the annotated differentially expressed genes were enriched in the metabolic category and were related to pathways such as signal transduction, carbohydrate metabolism, amino acid metabolism, and biosynthesis of other secondary metabolites. This study showed that plant growth-promoting bacteria can alter the rhizosphere bacterial community composition, increasing the activity of soil bacteria and upregulating gene expression in sweet sorghum roots. The findings enhance our understanding of the microbiological and botanical mechanisms by which plant growth-promoting bacterial inoculation improves the remediation of heavy metals by sorghum.}, } @article {pmid36496925, year = {2022}, author = {Rui, Y and Qiu, G}, title = {Analysis of Gut Microbial Communities and Resistance Genes in Pigs and Chickens in Central China.}, journal = {Animals : an open access journal from MDPI}, volume = {12}, number = {23}, pages = {}, pmid = {36496925}, issn = {2076-2615}, support = {212300410385//The Natural Science Foundation of Henan Province/ ; FCL202013//the Foundation of Central Laboratory of Xinyang Agriculture and Forestry University/ ; 21A230016//the Key Scientific Research Project of Colleges and Universities of Henan Province/ ; 21B230009//the Key Scientific Research Project of Colleges and Universities of Henan Province/ ; XNKJTD-013//Innovative Research Team of Poultry Germplasm Resources Application and Healthy Breeding of Dabie Mountain area in Xinyang Agriculture and Forestry University/ ; }, abstract = {BACKGROUND: Basic data concerning the gut microbiota of the main animal husbandry breeds (pigs and chickens) are scarce in China. The dynamics of gut microbiota (pigs and chickens) in China and antibiotic resistance genes carried by microorganisms in the natural environment are unknown.

METHODS: Free range and factory-farmed Gushi chickens and Huainan pigs were divided into eight groups. Faecal samples were collected from each group, and the metagenomic sequencing method was used to detect each group of samples.

RESULTS: The resistance genes showed the following trend, from high to low relative abundance: tetW was the highest, followed by tetW/N/W, then lnuA; and others from high to low were mdtB, lnuC, ANT6-la, ErmB, mdtC, ErmQ, tetBP, vatE, evgS, acrB, cpxA, mefA, Escherichia coli-ampC, tetL, yojl, AcrF and mdtA. All groups administered enrofloxacin and oregano oil did not develop a drug-resistant phenotype during the 5-day treatment period, as grouped in this trial. In 2022, after Announcement No. 194 of the Ministry of Agriculture and Rural Affairs in China, the antimicrobial resistance (AMR) trend declined, but it did not fundamentally change, presumably due to the impact of environmental pollution caused by the long-term use of antimicrobials.}, } @article {pmid36496380, year = {2022}, author = {Yoon, YM and Hrusch, CL and Fei, N and Barrón, GM and Mills, KAM and Hollinger, MK and Velez, TE and Leone, VA and Chang, EB and Sperling, AI}, title = {Gut microbiota modulates bleomycin-induced acute lung injury response in mice.}, journal = {Respiratory research}, volume = {23}, number = {1}, pages = {337}, pmid = {36496380}, issn = {1465-993X}, support = {5R21AI142360/NH/NIH HHS/United States ; T32AI007090/NH/NIH HHS/United States ; T32 AI007090/AI/NIAID NIH HHS/United States ; 2T32HL007605/NH/NIH HHS/United States ; R21 AI149416/AI/NIAID NIH HHS/United States ; P30 DK042086/DK/NIDDK NIH HHS/United States ; }, mesh = {Mice ; Animals ; *Bleomycin/toxicity ; RNA, Ribosomal, 16S ; Mice, Inbred C57BL ; *Acute Lung Injury/chemically induced/pathology ; Lung/pathology ; Weight Loss ; }, abstract = {BACKGROUND: Airway instillation of bleomycin (BLM) in mice is a widely used, yet challenging, model for acute lung injury (ALI) with high variability in treatment scheme and animal outcomes among investigators. Whether the gut microbiota plays any role in the outcome of BLM-induced lung injury is currently unknown.

METHODS: Intratracheal instillation of BLM into C57BL/6 mice was performed. Fecal microbiomes were analyzed by 16s rRNA amplicon and metagenomic sequencing. Germ-free mice conventionalization and fecal microbiota transfer between SPF mice were performed to determine dominant commensal species that are associated with more severe BLM response. Further, lungs and gut draining lymph nodes of the mice were analyzed by flow cytometry to define immunophenotypes associated with the BLM-sensitive microbiome.

RESULTS: Mice from two SPF barrier facilities at the University of Chicago exhibited significantly different mortality and weight loss during BLM-induced lung injury. Conventionalizing germ-free mice with SPF microbiota from two different housing facilities recapitulated the respective donors' response to BLM. Fecal microbiota transfer from the facility where the mice had worse mortality into the mice in the facility with more survival rendered recipient mice more susceptible to BLM-induced weight loss in a dominant negative manner. BLM-sensitive phenotype was associated with the presence of Helicobacter and Desulfovibrio in the gut, decreased Th17-neutrophil axis during steady state, and augmented lung neutrophil accumulation during the acute phase of the injury response.

CONCLUSION: The composition of gut microbiota has significant impact on BLM-induced wasting and death suggesting a role of the lung-gut axis in lung injury.}, } @article {pmid36496062, year = {2023}, author = {Mazzoli, A and Porzio, AD and Gatto, C and Crescenzo, R and Nazzaro, M and Spagnuolo, MS and Baccigalupi, L and Ricca, E and Amoresano, A and Fontanarosa, C and Bernacchioni, C and Donati, C and Iossa, S and Cigliano, L}, title = {Skeletal muscle insulin resistance and adipose tissue hypertrophy persist beyond the reshaping of gut microbiota in young rats fed a fructose-rich diet.}, journal = {The Journal of nutritional biochemistry}, volume = {113}, number = {}, pages = {109247}, doi = {10.1016/j.jnutbio.2022.109247}, pmid = {36496062}, issn = {1873-4847}, mesh = {Rats ; Animals ; *Insulin Resistance ; *Gastrointestinal Microbiome ; Fructose/adverse effects/metabolism ; Diet ; Adipose Tissue/metabolism ; Insulin/metabolism ; Hypertrophy/metabolism ; Muscle, Skeletal/metabolism ; }, abstract = {To investigate whether short term fructose-rich diet induces changes in the gut microbiota as well as in skeletal muscle and adipose tissue physiology and verify whether they persist even after fructose withdrawal, young rats of 30 d of age were fed for 3 weeks a fructose-rich or control diet. At the end of the 3-weeks period, half of the rats from each group were maintained for further 3 weeks on a control diet. Metagenomic analysis of gut microbiota and short chain fatty acids levels (faeces and plasma) were investigated. Insulin response was evaluated at the whole-body level and both in skeletal muscle and epididymal adipose tissue, together with skeletal muscle mitochondrial function, oxidative stress, and lipid composition. In parallel, morphology and physiological status of epididymal adipose tissue was also evaluated. Reshaping of gut microbiota and increased content of short chain fatty acids was elicited by the fructose diet and abolished by switching back to control diet. On the other hand, most metabolic changes elicited by fructose-rich diet in skeletal muscle and epididymal adipose tissue persisted after switching to control diet. Increased dietary fructose intake even on a short-time basis elicits persistent changes in the physiology of metabolically relevant tissues, such as adipose tissue and skeletal muscle, through mechanisms that go well beyond the reshaping of gut microbiota. This picture delineates a harmful situation, in particular for the young populations, posed at risk of metabolic modifications that may persist in their adulthood.}, } @article {pmid36495431, year = {2023}, author = {Liang, Z and Yao, J and Ma, H and Peng, W and Xia, X and Chen, Y}, title = {A sludge bulking wastewater treatment plant with an oxidation ditch-denitrification filter in a cold region: bacterial community composition and antibiotic resistance genes.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {12}, pages = {33767-33779}, pmid = {36495431}, issn = {1614-7499}, support = {52160005//National Natural Science Foundation of China/ ; 2021D01C047//Natural Science Foundation of Xinjiang Province/ ; }, mesh = {*Sewage/microbiology ; Wastewater ; Anti-Bacterial Agents/pharmacology ; Waste Disposal, Fluid/methods ; Denitrification ; RNA, Ribosomal, 16S ; Bacteria ; Genes, Bacterial ; Bacteroidetes/genetics ; Drug Resistance, Microbial/genetics ; *Water Purification ; }, abstract = {Bacterial community structure of activated sludge directly affects the stable operation of WWTPS, and these bacterial communities may carry a variety of antibiotic resistance genes (ARGs), which is a threat to the public health. This study employed 16S rRNA gene sequencing and metagenomic sequencing to investigate the bacterial community composition and the ARGs in a sludge bulking oxidation ditch-denitrification filter WWTP in a cold region. The results showed that Trichococcus (20.34%), Blautia (7.72%), and Faecalibacterium (3.64%) were the main bacterial genera in the influent. The relative abundances of norank_f_Saprospiraceae and Candidatus_Microthrix reached 10.24% and 8.40%, respectively, in bulking sludge, and those of norank_f_Saprospiraceae and Candidatus_Microthrix decreased to 6.56 and 7.10% after the anaerobic tank, indicating that the anaerobic tank had an inhibitory effect on filamentous bacteria. After 20 mJ/cm[2] UV disinfection, about 540 bacterial genera, such as Romboutsia (7.99%), Rhodoferax (7.98%), and Thermomonas (4.13%), could still be detected in the effluent. The ARGs were 345.11 ppm in the influent and 11.20 ppm in the effluent; 17 subtypes, such as sul1, msrE, aadA5, ErmF, and tet(A), could be detected throughout the entire process. These ARG subtypes were persistent ARGs with a high health risk. Network analysis indicated that the changes in filamentous bacteria norank_f_Saprospiraceae abundance mainly contributed to the abundance shift of MexB, and Acinetobacter mainly increased the abundance of drfA1. These results above will provide theoretical support for the sludge bulking and ARGs controls of WWTPs in cold regions.}, } @article {pmid36495133, year = {2023}, author = {Cerón, S and Clemons, NC and von Bredow, B and Yang, S}, title = {Application of CRISPR-Based Human and Bacterial Ribosomal RNA Depletion for SARS-CoV-2 Shotgun Metagenomic Sequencing.}, journal = {American journal of clinical pathology}, volume = {159}, number = {2}, pages = {111-115}, doi = {10.1093/ajcp/aqac135}, pmid = {36495133}, issn = {1943-7722}, mesh = {Humans ; *SARS-CoV-2/genetics ; *COVID-19 ; RNA, Ribosomal ; Metagenomics/methods ; }, abstract = {OBJECTIVES: The aim of this study is to evaluate the effectiveness of a CRISPR-based human and bacterial ribosomal RNA (rRNA) depletion kit (JUMPCODE Genomics) on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) shotgun metagenomic sequencing in weakly positive respiratory samples.

METHODS: Shotgun metagenomics was performed on 40 respiratory specimens collected from solid organ transplant patients and deceased intensive care unit patients at UCLA Medical Center in late 2020 to early 2021. Human and bacterial rRNA depletion was performed on remnant library pools prior to sequencing by Illumina MiSeq. Data quality was analyzed using Geneious Prime, whereas the identification of SARS-CoV-2 variants and lineages was determined by Pangolin.

RESULTS: The average genome coverage of the rRNA-depleted respiratory specimens increased from 72.55% to 93.71% in overall samples and from 29.3% to 83.3% in 15 samples that failed to achieve sufficient genome coverage using the standard method. Moreover, rRNA depletion enhanced genome coverage to over 85% in 11 (73.3%) of 15 low viral load samples with cycle threshold values up to 35, resulting in the identification of genotypes.

CONCLUSION: The CRISPR-based human and bacterial rRNA depletion enhanced the sensitivity of SARS-CoV-2 shotgun metagenomic sequencing, especially in low viral load samples.}, } @article {pmid36494376, year = {2022}, author = {Agarwal, D and Kuhns, R and Dimitriou, CN and Barlow, E and Wahlin, KJ and Enke, RA}, title = {Bulk RNA sequencing analysis of developing human induced pluripotent cell-derived retinal organoids.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {759}, pmid = {36494376}, issn = {2052-4463}, support = {T32EY026590//U.S. Department of Health & Human Services | NIH | National Eye Institute (NEI)/ ; K99 EY024648/EY/NEI NIH HHS/United States ; P30 EY022589/EY/NEI NIH HHS/United States ; R01 EY031318/EY/NEI NIH HHS/United States ; R01EY031318//U.S. Department of Health & Human Services | NIH | National Eye Institute (NEI)/ ; R00 EY024648/EY/NEI NIH HHS/United States ; EY024648//U.S. Department of Health & Human Services | NIH | Office of Extramural Research, National Institutes of Health (OER)/ ; R15EY028725//U.S. Department of Health & Human Services | NIH | National Eye Institute (NEI)/ ; P30EY022589//U.S. Department of Health & Human Services | NIH | National Eye Institute (NEI)/ ; R21EY031122//U.S. Department of Health & Human Services | NIH | National Eye Institute (NEI)/ ; }, mesh = {Animals ; Humans ; *Organoids ; Retina ; *Pluripotent Stem Cells ; Cell Differentiation/genetics ; Sequence Analysis, RNA ; Mammals ; }, abstract = {Retinogenesis involves the transformation of the anterior developing brain into organized retinal lamellae coordinated by intricate gene signalling networks. This complex process has been investigated in several model organisms such as birds, fish, mammals and amphibians, yet many facets of retinal development are different in humans and remain unexplored. In this regard, human pluripotent stem cell (hPSC)-derived 3D retinal organoids and Next Generation Sequencing (NGS) have emerged as key technologies that have facilitated the discovery of previously unknown details about cell fate specification and gene regulation in the retina. Here we utilized hPSCs integrated with fluorescent reporter genes (SIX6-p2A-eGFP/CRX-p2A-h2b-mRuby3) to generate retinal organoids and carry out bulk RNA sequencing of samples encompassing the majority of retinogenesis (D0-D280). This data set will serve as a valuable reference for the vision research community to characterize differentially expressed genes in the developing human eye.}, } @article {pmid36494363, year = {2022}, author = {Wang, L and Liu, W and Liang, J and Zhao, L and Li, Q and Zhou, C and Cen, H and Weng, Q and Zhang, G}, title = {Mining of novel secondary metabolite biosynthetic gene clusters from acid mine drainage.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {760}, pmid = {36494363}, issn = {2052-4463}, mesh = {*Mining ; *Acids ; Multigene Family ; Biodegradation, Environmental ; Metals ; }, abstract = {Acid mine drainage (AMD) is usually acidic (pH < 4) and contains high concentrations of dissolved metals and metalloids, making AMD a typical representative of extreme environments. Recent studies have shown that microbes play a key role in AMD bioremediation, and secondary metabolite biosynthetic gene clusters (smBGCs) from AMD microbes are important resources for the synthesis of antibacterial and anticancer drugs. Here, 179 samples from 13 mineral types were used to analyze the putative novel microorganisms and secondary metabolites in AMD environments. Among 7,007 qualified metagenome-assembled genomes (MAGs) mined from these datasets, 6,340 MAGs could not be assigned to any GTDB species representative. Overall, 11,856 smBGCs in eight categories were obtained from 7,007 qualified MAGs, and 10,899 smBGCs were identified as putative novel smBGCs. We anticipate that these datasets will accelerate research in the field of AMD bioremediation, aid in the discovery of novel secondary metabolites, and facilitate investigation into gene functions, metabolic pathways, and CNPS cycles in AMD.}, } @article {pmid36494088, year = {2023}, author = {Salvatore, JE and Larsson Lönn, S and Sundquist, J and Kendler, KS and Sundquist, K}, title = {Social genetic effects for drug use disorder among spouses.}, journal = {Addiction (Abingdon, England)}, volume = {118}, number = {5}, pages = {880-889}, doi = {10.1111/add.16108}, pmid = {36494088}, issn = {1360-0443}, support = {R01 DA030005/DA/NIDA NIH HHS/United States ; K01 AA024152/AA/NIAAA NIH HHS/United States ; }, mesh = {Humans ; Male ; Female ; Adult ; *Spouses ; Marriage ; *Substance-Related Disorders/epidemiology/genetics ; Risk Factors ; Educational Status ; }, abstract = {AIMS: Preclinical and human studies suggest that a social partner's genotype may be associated with addiction-related outcomes. This study measured whether spousal genetic makeup is associated with risk of developing drug use disorder (DUD) during marriage and whether the risk associated with a spouse's genotype could be disentangled from potentially confounding rearing environmental effects.

DESIGN: Univariable and multivariable logistic regression analyses.

SETTING: Sweden.

PARTICIPANTS: Men and women born between 1960 and 1990 and in opposite-sex first marriages before age 35 (n = 294 748 couples).

MEASUREMENTS: Outcome was DUD diagnosis (inclusive of opioids, sedatives/hypnotics/anxiolytics, cocaine, cannabis, amphetamine and other psychostimulants, hallucinogens, other drugs of abuse and combinations thereof) obtained from legal, medical and pharmacy registries. The focal predictor was family genetic risk scores for DUD (FGRS-DUD), which were inferred from diagnoses in first- through fifth-degree relatives and weighted by degree of genetic sharing. FGRS-DUD were calculated separately for each partner in a couple.

FINDINGS: Marriage to a spouse with a high FGRS-DUD was associated with increased risk of developing DUD during marriage, ORmales  = 1.68 (95% CI = 1.50, 1.88) and ORfemales  = 1.35 (1.16, 1.56), above and beyond the risk associated with one's own FGRS-DUD. The risk associated with a spouse's FGRS-DUD remained statistically significant after covarying for parental education. As indicated by a series of null interaction effects, there was no evidence that the risk associated with a spouse's FGRS-DUD differed depending on whether the spouse was DUD-affected, probands' probable contact with in-laws and whether the spouse was raised by his/her biological parents or in another home.

CONCLUSIONS: There is relatively robust evidence that a person's risk for developing drug use disorder is associated with the genetic makeup of the person's spouse.}, } @article {pmid36494024, year = {2023}, author = {Yandle, Z and Gonzalez, G and Carr, M and Matthijnssens, J and De Gascun, C}, title = {A viral metagenomic protocol for nanopore sequencing of group A rotavirus.}, journal = {Journal of virological methods}, volume = {312}, number = {}, pages = {114664}, doi = {10.1016/j.jviromet.2022.114664}, pmid = {36494024}, issn = {1879-0984}, mesh = {Humans ; *Rotavirus/genetics ; *Nanopore Sequencing ; Phylogeny ; *Rotavirus Infections ; Polymerase Chain Reaction ; Genome, Viral ; Genotype ; }, abstract = {AIM: Development of an unbiased methodology using Oxford Nanopore Technology (ONT) sequencing to obtain whole-genome sequences (WGS) of Rotavirus A (RVA) from clinical samples.

METHODS: 157 RVA qRT-PCR positive faecal samples were enriched by virus-like particle (VLP) purification and host nuclease digestion to enhance the detection of viral nucleic acids and cDNA generated as per the NetoVIR protocol. ONT sequencing was then performed using the ONT Native Barcoding kit (SQK-LSK-109) on the GridION platform. Data was basecalled, demultiplexed and assembled into near complete RVA genomes. The accuracy and quality of the obtained sequences was assessed by comparing to Sanger sequencing and RVA reference genomes.

RESULTS: The developed protocol generated 146 near-complete RVA WGS out of the 157 RVA-positive clinical samples. The quality of the assembled genomes was assessed by comparison against publicly-available sequences with results showing 98.76 % ± 0.03 % similarity and > 90 % genome coverage. A concordance assessment was performed comparing the identity of partial RVA VP7 and VP4 segments obtained by Sanger sequencing (n = 51) against corresponding nanopore sequences which demonstrated an overall identity of 100.0 % ± 0.02 %.

CONCLUSIONS: The nanopore protocol generated both high quality and accurate RVA WGS extracted from faecal samples. This protocol can be extended to other viral agents in other sample types.}, } @article {pmid36490242, year = {2022}, author = {Lole, K and Ramdasi, A and Patil, S and Thakar, S and Nath, A and Ghuge, O and Gangopadhayya, A and Sudeep, AB and Cherian, S}, title = {Abundance of Phasi-Charoen-like virus in Aedes aegypti mosquito populations in different states of India.}, journal = {PloS one}, volume = {17}, number = {12}, pages = {e0277276}, pmid = {36490242}, issn = {1932-6203}, mesh = {Animals ; Male ; Humans ; *Aedes ; Mosquito Vectors ; India ; *Insect Viruses ; *Chikungunya virus ; }, abstract = {Mosquitoes are known to harbor a large number of insect specific viruses (ISV) in addition to viruses of public health importance. These ISVs are highly species specific and are non-pathogenic to humans or domestic animals. However, there is a potential threat of these ISVs evolving into human pathogens by genome alterations. Some ISVs are known to modulate replication of pathogenic viruses by altering the susceptibility of vector mosquitoes to pathogenic viruses, thereby either inhibiting or enhancing transmission of the latter. In the present study, we report predominance of Phasi Charoen-like virus (PCLV, Family: Phenuviridae) contributing to >60% of the total reads in Aedes aegypti mosquitoes collected from Pune district of Maharashtra state using next generation sequencing based metagenomic analysis of viromes. Similar results were also obtained with mosquitoes from Assam, Tamil Nadu and Karnataka states of India. Comparison of Pune mosquito sequences with PCLV Rio (Brazil) isolate showed 98.90%, 99.027% and 98.88% homologies in the S, M and L segments respectively indicating less genetic heterogeneity of PCLV. The study also demonstrated occurrence of transovarial transmission as seen by detection of PCLV in eggs, larvae, pupae and male mosquitoes. Ae. aegypti mosquitoes collected from Pune also showed a large number of reads for viruses belonging to Baculoviridae, Rhabdoviridae, Genomoviridae and Bunyaviridae families. The role of PCLV in the replication of dengue and chikungunya virus is yet not clear. It warrants further studies to know the significance of PCLV and other ISVs on the replication and transmission of Ae. aegypti borne pathogenic viruses, especially in the absence of prophylactics or therapeutics.}, } @article {pmid36483959, year = {2022}, author = {Zhang, J and Lu, J and Zhu, Y and Huang, Q and Qin, L and Zhu, B}, title = {Rhizosphere microorganisms of Crocus sativus as antagonists against pathogenic Fusarium oxysporum.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1045147}, pmid = {36483959}, issn = {1664-462X}, abstract = {INTRODUCTION: Several microorganisms in the plant root system, especially in the rhizosphere, have their own compositions and functions. Corm rot is the most severe disease of Crocus sativus, leading to more than 50% mortality in field production.

METHODS: In this study, metagenomic sequencing was used to analyze microbial composition and function in the rhizosphere of C. sativus for possible microbial antagonists against pathogenic Fusarium oxysporum.

RESULTS: The microbial diversity and composition were different in the C. sativus rhizosphere from different habitats. The diversity index (Simpson index) was significantly lower in the C. sativus rhizospheric soil from Chongming (Rs_CM) and degenerative C. sativus rhizospheric soil from Chongming (RsD_CM) than in others. Linear discriminant analysis effect size results showed that differences among habitats were mainly at the order (Burkholderiales, Micrococcales, and Hypocreales) and genus (Oidiodendron and Marssonina) levels. Correlation analysis of the relative lesion area of corm rot showed that Asanoa was the most negatively correlated bacterial genus (ρ = -0.7934, p< 0.001), whereas Moniliophthora was the most negatively correlated fungal genus (ρ = -0.7047, p< 0.001). The relative lesion area result showed that C. sativus from Qiaocheng had the highest resistance, followed by Xiuzhou and Jiande. C. sativus groups with high disease resistance had abundant pathogen resistance genes, such as chitinase and β-1,3-glucanase genes, from rhizosphere microorganisms. Further, 13 bacteria and 19 fungi were isolated from C. sativus rhizosphere soils, and antagonistic activity against pathogenic F. oxysporum was observed on potato dextrose agar medium. In vivo corm experiments confirmed that Trichoderma yunnanense SR38, Talaromyces sp. SR55, Burkholderia gladioli SR379, and Enterobacter sp. SR343 displayed biocontrol activity against corm rot disease, with biocontrol efficiency of 20.26%, 31.37%, 39.22%, and 14.38%, respectively.

DISCUSSION: This study uncovers the differences in the microbial community of rhizosphere soil of C. sativus with different corm rot disease resistance and reveals the role of four rhizospheric microorganisms in providing the host C. sativus with resistance against corm rot. The obtained biocontrol microorganisms can also be used for application research and field management.}, } @article {pmid36483821, year = {2022}, author = {Song, P and Li, X}, title = {Diagnostic value of metagenomics next-generation sequencing technology in disseminated strongyloidiasis.}, journal = {World journal of clinical cases}, volume = {10}, number = {33}, pages = {12455-12457}, pmid = {36483821}, issn = {2307-8960}, abstract = {The symptoms of disseminated strongyloidiasis are not typical, and it is difficult for clinicians to identify strongyloidiasis in some non-endemic areas. We report a 70-year-old woman who was diagnosed with Guillain-Barré syndrome due to autonomic disturbance, symmetrical bulbar palsy, and lower-motor-nerve damage in the extremities; her symptoms continued to worsen after hormone and immunoglobulin therapy. Later, parasitic larvae were found in the patient's gastric fluid, and metagenomic next generation sequencing (mNGS) detection of bronchoalveolar-lavage fluid also found a large number of Strongyloides roundworms. The patient was diagnosed with disseminated strongyloidiasis. The patient was given albendazole for anthelmintic treatment, but died two days after being transferred to the intensive care unit due to the excessive strongyloidiasis burden. In recent years, mNGS has been increasingly used in clinical practice, and is becoming the main means of detecting strongyloides stercoralis in non-endemic areas. Especially during the corona virus disease 2019 pandemic, mNGS technology has irreplaceable value in identifying the source of infection.}, } @article {pmid36482486, year = {2022}, author = {Islam, MZ and Tran, M and Xu, T and Tierney, BT and Patel, C and Kostic, AD}, title = {Reproducible and opposing gut microbiome signatures distinguish autoimmune diseases and cancers: a systematic review and meta-analysis.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {218}, pmid = {36482486}, issn = {2049-2618}, support = {P30 DK036836/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Reproducibility of Results ; *Autoimmune Diseases ; *Neoplasms ; }, abstract = {BACKGROUND: The gut microbiome promotes specific immune responses, and in turn, the immune system has a hand in shaping the microbiome. Cancer and autoimmune diseases are two major disease families that result from the contrasting manifestations of immune dysfunction. We hypothesized that the opposing immunological profiles between cancer and autoimmunity yield analogously inverted gut microbiome signatures. To test this, we conducted a systematic review and meta-analysis on gut microbiome signatures and their directionality in cancers and autoimmune conditions.

METHODOLOGY: We searched PubMed, Web of Science, and Embase to identify relevant articles to be included in this study. The study was conducted in accordance with the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) statements and PRISMA 2009 checklist. Study estimates were pooled by a generic inverse variance random-effects meta-analysis model. The relative abundance of microbiome features was converted to log fold change, and the standard error was calculated from the p-values, sample size, and fold change.

RESULTS: We screened 3874 potentially relevant publications. A total of 82 eligible studies comprising 37 autoimmune and 45 cancer studies with 4208 healthy human controls and 5957 disease cases from 27 countries were included in this study. We identified a set of microbiome features that show consistent, opposite directionality between cancers and autoimmune diseases in multiple studies. Fusobacterium and Peptostreptococcus were the most consistently increased genera among the cancer cases which were found to be associated in a remarkable 13 (+0.5 log fold change in 5 studies) and 11 studies (+3.6 log fold change in 5 studies), respectively. Conversely, Bacteroides was the most prominent genus, which was found to be increased in 12 autoimmune studies (+0.2 log fold change in 6 studies) and decreased in six cancer studies (-0.3 log fold change in 4 studies). Sulfur-metabolism pathways were found to be the most frequent pathways among the member of cancer-increased genus and species.

CONCLUSIONS: The surprising reproducibility of these associations across studies and geographies suggests a shared underlying mechanism shaping the microbiome across cancers and autoimmune diseases. Video Abstract.}, } @article {pmid36481500, year = {2023}, author = {Sharma, P and Nadda, AK and Kumar, S}, title = {Microbial community profiling in bio-stimulated municipal solid waste for effective removal of organic pollutants containing endocrine disrupting chemicals.}, journal = {Microbiological research}, volume = {267}, number = {}, pages = {127273}, doi = {10.1016/j.micres.2022.127273}, pmid = {36481500}, issn = {1618-0623}, mesh = {Archaea/genetics ; Bacteria/genetics ; *Endocrine Disruptors/analysis ; *Environmental Pollutants/analysis ; *Microbiota ; Solid Waste/analysis ; }, abstract = {The study was aimed to improve the degradation of organic pollutants in municipal solid waste (MSW) through the bio-stimulation process. The results showed that the physico-chemical properties of MSW (control) had a high value of pH (9.2 ± 0.02); total suspended solids (TSS: 1547 ± 23 mg/kg[-1]), and total dissolved solids (TDS:76 ± 0.67 mg/kg[-1]). After the biostimulation process (biostimulated MSW), the physico-chemical parameters of MSW were reduced as pH (7.1 ± 0.01); TSS (41 ± 0.01 mg/kg[-1]), and TDS (789 ± 03 mg/kg[-1]). Furthermore, the major organic pollutants detected from MSW by gas chromatography-mass spectroscopy (GC-MS) analysis at different retention time (RT) were hexadecane (RT-8.79); pentadecane (RT-9.36); and hexasiloxane (RT-9.43) while these organic pollutants were degraded after the biostimulation process. The whole-genome metagenome sequencing size (%) analyses showed major groups of bacteria (40.82%) followed by fungi (0.05%), virus (0.0032%), and archaea (0.0442%) in MSW. The species richness and evenness of the microbial community were decreased substantially due to the biostimulation treatment. The total number of genes in the biostimulated MSW (PS-3_11267) sample were 465302 whereas the number of genes in the control MSW (PS-4_11268) sample were 256807. Furthermore, the biostimulated MSW (PS-3_11267) aligned the reads to bacteria (19502525), fungi (40030), virus (3339), and archaea (12759) genomes whereas the control sample (PS-4_11268) aligned the reads to bacteria (17057259), fungi (19148), virus (1335), and archaea (18447) genomes. Moreover, the relative abundance at genus level in biostimulated MSW (PS-3_11267) (Ochrobactrum and Phenylobacterium), phylum; (Proteobacteria and Actinobacteria), and species (Chthoniobacter flavus and Vulgatibacter incomptus) level was the most abundant. The results provided valuable information regarding the degradation of organic pollutants in MSW by microbial communities through biostimulation for the prevention of soil pollution and health protection.}, } @article {pmid36481466, year = {2023}, author = {Xu, Y and You, G and Yin, J and Zhang, M and Peng, D and Xu, J and Yang, S and Hou, J}, title = {Salt tolerance evolution facilitates antibiotic resistome in soil microbiota: Evidences from dissemination evaluation, hosts identification and co-occurrence exploration.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {317}, number = {}, pages = {120830}, doi = {10.1016/j.envpol.2022.120830}, pmid = {36481466}, issn = {1873-6424}, mesh = {Humans ; *Genes, Bacterial ; Salt Tolerance ; Anti-Bacterial Agents/pharmacology ; Soil ; *Microbiota ; Soil Microbiology ; }, abstract = {Salinity is considered as one of the vital factors affecting the profiles of antibiotic resistance genes (ARGs) in soils, whereby its roles in shaping the antibiotic resistome were still poorly understood. Here, metagenomic analysis was conducted to track the ARGs distributions and dissemination in soils during salt accumulation and desalinization processes. Neutral-salt accumulation for 45 and 90 days significantly increased the relative abundances of ARGs and mobile genetic elements (MGEs) carrying antibiotic resistance contigs (ARCs). The ARGs within antibiotic efflux and target protection families primarily carried by Streptomyces, Nocardioides, Rhodanobacter and Monashia were largely enriched by salinity. The ARGs subtypes of the resistance-nodulation-division (RND) family, ATP-binding cassette (ABC) family, rRNA methyltransferase and other efflux were closely associated with MGEs, contributing to the enrichment of ARGs. Moreover, the ARGs subtypes and transposons were genetically linked with the salt-tolerance mechanisms of organic osmolyte transporters and K[+] uptake proteins on the same ARC, demonstrating the coselection of ARGs and halotolerant genes. Furthermore, the antibiotic resistome could recover to a normal state after the prolonged incubation by alleviating salt stress. Nevertheless, the acquisition of ARGs by opportunistic pathogens after salt treatment was increased, serving to prioritize further efforts on the health risks correlated with resistance propagation and human exposure in saline soils.}, } @article {pmid36481142, year = {2023}, author = {Song, A and Peng, J and Si, Z and Xu, D and Sun, M and Zhang, J and Wang, S and Wang, E and Bi, J and Chong, F and Fan, F}, title = {Metagenomics reveals the increased antibiotics resistome through prokaryote rather than virome after overuse of rare earth element compounds.}, journal = {The Science of the total environment}, volume = {863}, number = {}, pages = {160704}, doi = {10.1016/j.scitotenv.2022.160704}, pmid = {36481142}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/toxicity ; Virome ; Nitrates ; Ecosystem ; *Metals, Rare Earth ; Metals ; Genes, Bacterial ; Soil ; Metagenomics ; }, abstract = {Rare earth elements (REE) are extensively exploited in the agricultural ecosystems due to their various beneficial roles on plant growth. However, the ecotoxicological effects and environmental risk of REE are poorly assessed. Here, we investigated the effects of lanthanum and cerium nitrate on soil prokaryote and viral metal resistance genes (MRGs) and antibiotics resistance genes (ARGs) using a metagenomic-based approach. We found that relative abundances of prokaryote phyla Bacteroidetes and Chloroflexi decreased with increasing of both REE compounds. In addition, low level REE nitrate (0.05 and 0.1 mmol kg[-1] soil) inhibited the viral family Phycodanaviridae, Rudiviridae, Schitoviridae, whereas high level (0.16 and 0.32 mmol kg[-1] soil) REE nitrate suppressed the viral family Herelleviridae, Iridoviridae, Podoviridae. ARGs were not significantly affected by low level of REE nitrate. However, high level of both REEs nitrate increased the abundances of dominant prokaryote genes resisting to most of the drug classes, such as aminoglycoside, elfamycin, fluoroquinolone, macrolide, rifamycin. Abundance of MRGs in prokaryote did not change consistently with REE nitrate compound type and input rate. MRGs were only partially detected in the virome in some of the treatments, while ARGs was not detected in virome. Together, we demonstrated that overuse of REE nitrate in agriculture would increase the risk of dissemination of ARGs through prokaryotes but not virus, although viral community was substantially shifted.}, } @article {pmid36480496, year = {2022}, author = {Vuong, P and Wise, MJ and Whiteley, AS and Kaur, P}, title = {Ten simple rules for investigating (meta)genomic data from environmental ecosystems.}, journal = {PLoS computational biology}, volume = {18}, number = {12}, pages = {e1010675}, pmid = {36480496}, issn = {1553-7358}, mesh = {*Ecosystem ; *Genomics ; }, } @article {pmid36480164, year = {2023}, author = {Engelberts, JP and Robbins, SJ and Herbold, CW and Moeller, FU and Jehmlich, N and Laffy, PW and Wagner, M and Webster, NS}, title = {Metabolic reconstruction of the near complete microbiome of the model sponge Ianthella basta.}, journal = {Environmental microbiology}, volume = {25}, number = {3}, pages = {646-660}, doi = {10.1111/1462-2920.16302}, pmid = {36480164}, issn = {1462-2920}, support = {294343/ERC_/European Research Council/International ; }, mesh = {Animals ; *Porifera/microbiology ; Phylogeny ; Archaea/metabolism ; *Microbiota ; Symbiosis/physiology ; }, abstract = {Many marine sponges host highly diverse microbiomes that contribute to various aspects of host health. Although the putative function of individual groups of sponge symbionts has been increasingly described, the extreme diversity has generally precluded in-depth characterization of entire microbiomes, including identification of syntrophic partnerships. The Indo-Pacific sponge Ianthella basta is emerging as a model organism for symbiosis research, hosting only three dominant symbionts: a Thaumarchaeotum, a Gammaproteobacterium, and an Alphaproteobacterium and a range of other low abundance or transitory taxa. Here, we retrieved metagenome assembled genomes (MAGs) representing >90% of I. basta's microbial community, facilitating the metabolic reconstruction of the sponge's near complete microbiome. Through this analysis, we identified metabolic complementarity between microbes, including vitamin sharing, described the importance of low abundance symbionts, and characterized a novel microbe-host attachment mechanism in the Alphaproteobacterium. We further identified putative viral sequences, highlighting the role viruses can play in maintaining symbioses in I. basta through the horizontal transfer of eukaryotic-like proteins, and complemented this data with metaproteomics to identify active metabolic pathways in bacteria, archaea, and viruses. This data provide the framework to adopt I. basta as a model organism for studying host-microbe interactions and provide a basis for in-depth physiological experiments.}, } @article {pmid36480163, year = {2023}, author = {Chen, Q and Hou, K and Tang, M and Ying, S and Zhao, X and Li, G and Pan, J and He, X and Xia, H and Li, Y and Lou, Z and Zhang, L}, title = {Screening of potential microbial markers for lung cancer using metagenomic sequencing.}, journal = {Cancer medicine}, volume = {12}, number = {6}, pages = {7127-7139}, pmid = {36480163}, issn = {2045-7634}, mesh = {Humans ; *Early Detection of Cancer ; *Lung Neoplasms/diagnosis/genetics/metabolism ; Bronchoalveolar Lavage Fluid/microbiology ; Lung/pathology ; Biomarkers, Tumor/metabolism ; }, abstract = {INTRODUCTION: Lung cancer is the most prevalent cancer with high mortality in China, and it is associated with the dysbiosis of the lung microbiome. This study attempted to screen for specific microorganisms as potential biomarkers for distinguishing benign lung disease from lung cancer.

METHODS: Bronchoalveolar lavage fluid (BALF) sample was selected in the study instead of saliva to avoid contamination with oral microorganisms, and microbial taxonomic and functional differences in BALF samples from patients with lung cancer and those with those from patients with benign lung diseases were performed based on metagenomic next-generation sequencing, for the first time, so that microorganisms other than bacteria could be included.

RESULTS: The results showed that the intrasample diversity of malignant samples was different from benign samples, and the microbial differences among malignant samples were smaller, with lower microbial diversity, significantly changed microbial abundance and metabolic functions. Metabolic function analysis revealed amino acid-related metabolism was more prevalent in benign samples, whereas carbohydrate-related metabolism was more prevalent in malignant samples. By LEfSe, Metastat and Random Forest analysis, we identified a series of important differential microorganisms. Importantly, the model combining five key genera plus one tumor marker (neuron-specific enolase) as indicators presented the optimal disease typing performance.

CONCLUSION: Thus results suggest the value of these differential microorganisms enriched in tumors in mechanism research and may be potential new targets for lung cancer therapy. More importantly, the biomarkers identified in this study can be conducive to improve the clinical diagnosis of lung cancer and have good application prospects.}, } @article {pmid36479477, year = {2022}, author = {Kiani, AK and Medori, MC and Bonetti, G and Aquilanti, B and Velluti, V and Matera, G and Iaconelli, A and Stuppia, L and Connelly, ST and Herbst, KL and Bertelli, M}, title = {Modern vision of the Mediterranean diet.}, journal = {Journal of preventive medicine and hygiene}, volume = {63}, number = {2 Suppl 3}, pages = {E36-E43}, pmid = {36479477}, issn = {2421-4248}, mesh = {Humans ; *Diet, Mediterranean ; }, abstract = {The Mediterranean diet is the most well-known and researched dietary pattern worldwide. It is characterized by the consumption of a wide variety of foods, such as extra-virgin olive oil (EVOO), legumes, cereals, nuts, fruits, vegetables, dairy products, fish, and wine. Many of these foods provide several phytonutrients, among which polyphenols and vitamins play an important role. Data from several studies have strongly established that nutrition is a key factor in promoting a healthy lifestyle and preventing many chronic diseases. In particular, a large number of studies have established the protective effects of the Mediterranean diet against several chronic diseases, among which are diabetes, cardiovascular diseases, cancer, aging disorders, and against overall mortality. Animal and human translational studies have revealed the biological mechanisms regulating the beneficial effects of the traditional Mediterranean diet. Indeed, several studies demonstrated that this nutritional pattern has lipid-lowering, anticancer, antimicrobial, and anti-oxidative effects. Moreover, the Mediterranean diet is considered environmentally sustainable. In this review, we describe the composition of the Mediterranean diet, assess its beneficial effects, and analyze their epigenomic, genomic, metagenomic, and transcriptomic aspects. In the future it will be important to continue exploring the molecular mechanisms through which the Mediterranean diet exerts its protective effects and to standardize its components and serving sizes to understand more precisely its effects on human health.}, } @article {pmid36479434, year = {2022}, author = {Pandey, D and Kumari, B and Singhal, N and Kumar, M}, title = {BacARscan: an in silico resource to discern diversity in antibiotic resistance genes.}, journal = {Biology methods & protocols}, volume = {7}, number = {1}, pages = {bpac031}, pmid = {36479434}, issn = {2396-8923}, abstract = {Antibiotic resistance has escalated as a significant problem of broad public health significance. Regular surveillance of antibiotic resistance genes (ARGs) in microbes and metagenomes from human, animal and environmental sources is vital to understanding ARGs' epidemiology and foreseeing the emergence of new antibiotic resistance determinants. Whole-genome sequencing (WGS)-based identification of the microbial ARGs using antibiotic resistance databases and in silico prediction tools can significantly expedite the monitoring and characterization of ARGs in various niches. The major hindrance to the annotation of ARGs from WGS data is that most genome databases contain fragmented genes/genomes (due to incomplete assembly). Herein, we describe an insilicoBacterial Antibiotic Resistance scan (BacARscan) (http://proteininformatics.org/mkumar/bacarscan/) that can detect, predict and characterize ARGs in -omics datasets, including short sequencing, reads, and fragmented contigs. Benchmarking on an independent non-redundant dataset revealed that the performance of BacARscan was better than other existing methods, with nearly 92% Precision and 95% F-measure on a combined dataset of ARG and non-ARG proteins. One of the most notable improvements of BacARscan over other ARG annotation methods is its ability to work on genomes and short-reads sequence libraries with equal efficiency and without any requirement for assembly of short reads. Thus, BacARscan can help monitor the prevalence and diversity of ARGs in microbial populations and metagenomic samples from animal, human, and environmental settings. The authors intend to constantly update the current version of BacARscan as and when new ARGs are discovered. Executable versions, source codes, sequences used for development and usage instructions are available at (http://www.proteininformatics.org/mkumar/bacarscan/downloads.html) and GitHub repository (https://github.com/mkubiophysics/BacARscan).}, } @article {pmid36478867, year = {2022}, author = {Hang, L and Wang, E and Feng, Y and Zhou, Y and Meng, Y and Jiang, F and Yuan, J}, title = {Metagenomics and metabolomics analysis to investigate the effect of Shugan decoction on intestinal microbiota in irritable bowel syndrome rats.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1024822}, pmid = {36478867}, issn = {1664-302X}, abstract = {BACKGROUND: The effect of Shugan Decoction (SGD) on intestinal motility and visceral hypersensitivity in Water avoid stress (WAS)-induced diarrhea predominant irritable bowel syndrome (IBS-D) model rats has been confirmed. However, the mechanisms of its action involved in the treatment of IBS-D need to be further studied. Intestinal microbiota plays an important role in maintaining intestinal homeostasis and normal physiological function. Changes in the intestinal microbiota and its metabolites are thought to participate in the pathophysiological process of IBS.

AIM: This study aimed to analyze the influence of SGD on intestinal microbiota and fecal metabolites in IBS-D rats by multiple omics techniques, including metagenomic sequencing and metabolomics.

METHODS: We measured the intestinal motility and visceral sensitivity of three groups of rats by fecal pellets output and colorectal distension (CRD) experiment. In addition, metagenome sequencing analysis was performed to explore the changes in the number and types of intestinal microbiota in IBS-D model rats after SGD treatment. Finally, we also used untargeted metabolomic sequencing to screen the metabolites and metabolic pathways closely related to the therapeutic effect of SGD.

RESULTS: We found that compared with the rats in the control group, the fecal pellets output of the rats in the WAS group increased and the visceral sensitivity threshold was decreased (P < 0.05). Compared with the rats in the WAS group, the fecal pellets output of the SGD group was significantly decreased, and the visceral sensitivity threshold increased (P < 0.05). Besides, compared with the rats in the WAS group, the relative abundance of Bacteroidetes increased in SGD group, while that of Firmicutes decreased at the phylum level, and at the species level, the relative abundance of Bacteroides sp. CAG:714, Lactobacillus reuteri and Bacteroides Barnesiae in SGD group increased, but that of bacterium D42-87 decreased. In addition, compared with the WAS group, several metabolic pathways were significantly changed in SGD group, including Taurine and hypotaurine metabolism, Purine metabolism, Sulfur metabolism, ABC transporters, Arginine and proline metabolism and Bile secretion.

CONCLUSION: SGD can regulate specific intestinal microbiota and some metabolic pathways, which may explain its effect of alleviating visceral hypersensitivity and abnormal intestinal motility in WAS-induced IBS-D rats.}, } @article {pmid36478863, year = {2022}, author = {Malik, PK and Trivedi, S and Kolte, AP and Mohapatra, A and Bhatta, R and Rahman, H}, title = {Effect of an anti-methanogenic supplement on enteric methane emission, fermentation, and whole rumen metagenome in sheep.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1048288}, pmid = {36478863}, issn = {1664-302X}, abstract = {A study was conducted to investigate the impact of an anti-methanogenic product supplementation on enteric methane emissions, whole rumen metagenome and ruminal fermentation in sheep. Twelve adult male sheep were randomly divided into two groups of six animals each. Animals were fed ad libitum on a total mixed ration either without (CON) or with an anti-methanogenic supplement (Harit Dhara-HD). The anti-methanogenic supplement contained 22.1% tannic acid in a 3: 1 ratio of condensed and hydrolysable tannins. The supplementation of product revealed a significant reduction in daily enteric methane emission (21.9 vs. 17.2 g/d) and methane yield (23.2 vs. 18.2) without affecting the nutrient intake and digestibility. However, the propionate concentration in the HD treatment group was significantly higher than in the CON group. On the contrary, the ammonia nitrogen concentration was lower. The anti-methanogenic supplement significantly decreased the ruminal protozoa in the HD treatment group. Whole rumen metagenome analysis revealed that the core bacterial (Bacteroidetes and Firmicutes) and archaeal communities (Methanobrevibacter and Methanosarcina) were comparable between the CON and HD treatment groups. However, the supplementation of anti-methanogenic product led to a considerable reduction in the abundance of Proteobacteria, whereas the abundance of Lentisphaerae was greater. The supplementation significantly decreased the abundance of Methanocaldococcus, Methanococcoides, Methanocella, and Methanoregula methanogens. A total of 36 KO related to methanogenesis were identified in this study. The activities of formate dehydrogenase (EC 1.8.98.6) and tetrahydromethanopterin S-methyltransferase (EC 2.1.1.86) were significantly lowered by the anti-methanogenic product supplementation in sheep. In conclusion, the anti-methanogenic supplement has the potential to decrease enteric methane emission (~22%) at the recommended level (5% of DM) of supplementation. The contribution of minor methanogens vulnerable to supplementation to rumen methanogenesis is not known; hence, the culturing of these archaea should be taken on priority for determining the impact on overall rumen methanogenesis.}, } @article {pmid36478673, year = {2022}, author = {Niu, S and Zhao, L}, title = {Metagenomic next-generation sequencing clinches the diagnosis of Legionella pneumonia in a patient with acute myeloid leukemia: A case report and literature review.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {924597}, pmid = {36478673}, issn = {2235-2988}, mesh = {Humans ; Metagenomics ; *Leukemia, Myeloid, Acute/complications ; *Legionella/genetics ; *Pneumonia/diagnosis ; }, abstract = {Legionella pneumonia caused by Legionella pneumophila is a multi-system disease that is a life-threatening, acute, and severe form of pneumonia. L. pneumophila is widespread and the clinical manifestations of Legionella pneumonia are similar to those of typical and atypical pneumonia. Current diagnostic scores and radiologic evidence have limited diagnostic value. Thus, it is likely that many cases of Legionella pneumonia remain unreported. We describe a woman with a medical history of acute myeloid leukemia who suffered from repeated fever, and no relief following initial empirical antibiotic treatment. Ultimately, she was diagnosed with Legionella pneumonia based on metagenomic next-generation sequencing (mNGS). We also performed a systematic review of the literature and identified 5 other patients who were diagnosed with Legionella pneumonia using mNGS, and reviewed their clinical characteristics, biological characteristics, epidemiological features, laboratory results, clinical findings, and treatments. This literature review showed that accurate etiological diagnosis is becoming increasingly essential for a definitive diagnosis and treatment strategies. The clinical manifestations of Legionella pneumonia are non-specific, and many routine laboratory diagnostic tests cannot identify Legionella. mNGS, an indispensable approach for identifying microorganisms, can provide a promising tool for the rapid and accurate etiological diagnosis methods contributing to early diagnosis, early treatment, and improved prognosis, especially for uncommon species such as L. pneumophila.}, } @article {pmid36478085, year = {2023}, author = {Parada, AE and Mayali, X and Weber, PK and Wollard, J and Santoro, AE and Fuhrman, JA and Pett-Ridge, J and Dekas, AE}, title = {Constraining the composition and quantity of organic matter used by abundant marine Thaumarchaeota.}, journal = {Environmental microbiology}, volume = {25}, number = {3}, pages = {689-704}, doi = {10.1111/1462-2920.16299}, pmid = {36478085}, issn = {1462-2920}, mesh = {*Archaea/metabolism ; *Carbon/metabolism ; Amino Acids/metabolism ; Urea/metabolism ; Nitrogen/metabolism ; }, abstract = {Marine Group I (MGI) Thaumarchaeota were originally described as chemoautotrophic nitrifiers, but molecular and isotopic evidence suggests heterotrophic and/or mixotrophic capabilities. Here, we investigated the quantity and composition of organic matter assimilated by individual, uncultured MGI cells from the Pacific Ocean to constrain their potential for mixotrophy and heterotrophy. We observed that most MGI cells did not assimilate carbon from any organic substrate provided (glucose, pyruvate, oxaloacetate, protein, urea, and amino acids). The minority of MGI cells that did assimilate it did so exclusively from nitrogenous substrates (urea, 15% of MGI and amino acids, 36% of MGI), and only as an auxiliary carbon source (<20% of that subset's total cellular carbon was derived from those substrates). At the population level, MGI assimilation of organic carbon comprised just 0.5%-11% of total biomass carbon. We observed extensive assimilation of inorganic carbon and urea- and amino acid-derived nitrogen (equal to that from ammonium), consistent with metagenomic and metatranscriptomic analyses performed here and previously showing a widespread potential for MGI to perform autotrophy and transport and degrade organic nitrogen. Our results constrain the quantity and composition of organic matter used by MGI and suggest they use it primarily to meet nitrogen demands for anabolism and nitrification.}, } @article {pmid36477500, year = {2023}, author = {Calgaro, M and Romualdi, C and Risso, D and Vitulo, N}, title = {benchdamic: benchmarking of differential abundance methods for microbiome data.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {1}, pages = {}, pmid = {36477500}, issn = {1367-4811}, support = {U24 CA180996/CA/NCI NIH HHS/United States ; //University of Verona/ ; }, mesh = {*Software ; *Benchmarking ; Reproducibility of Results ; Metagenomics ; }, abstract = {SUMMARY: Recently, an increasing number of methodological approaches have been proposed to tackle the complexity of metagenomics and microbiome data. In this scenario, reproducibility and replicability have become two critical issues, and the development of computational frameworks for the comparative evaluations of such methods is of utmost importance. Here, we present benchdamic, a Bioconductor package to benchmark methods for the identification of differentially abundant taxa.

benchdamic is available as an open-source R package through the Bioconductor project at https://bioconductor.org/packages/benchdamic/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36477304, year = {2023}, author = {Richardson, L and Allen, B and Baldi, G and Beracochea, M and Bileschi, ML and Burdett, T and Burgin, J and Caballero-Pérez, J and Cochrane, G and Colwell, LJ and Curtis, T and Escobar-Zepeda, A and Gurbich, TA and Kale, V and Korobeynikov, A and Raj, S and Rogers, AB and Sakharova, E and Sanchez, S and Wilkinson, DJ and Finn, RD}, title = {MGnify: the microbiome sequence data analysis resource in 2023.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D753-D759}, pmid = {36477304}, issn = {1362-4962}, mesh = {Genomics/methods ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Software ; *Sequence Analysis/methods ; }, abstract = {The MGnify platform (https://www.ebi.ac.uk/metagenomics) facilitates the assembly, analysis and archiving of microbiome-derived nucleic acid sequences. The platform provides access to taxonomic assignments and functional annotations for nearly half a million analyses covering metabarcoding, metatranscriptomic, and metagenomic datasets, which are derived from a wide range of different environments. Over the past 3 years, MGnify has not only grown in terms of the number of datasets contained but also increased the breadth of analyses provided, such as the analysis of long-read sequences. The MGnify protein database now exceeds 2.4 billion non-redundant sequences predicted from metagenomic assemblies. This collection is now organised into a relational database making it possible to understand the genomic context of the protein through navigation back to the source assembly and sample metadata, marking a major improvement. To extend beyond the functional annotations already provided in MGnify, we have applied deep learning-based annotation methods. The technology underlying MGnify's Application Programming Interface (API) and website has been upgraded, and we have enabled the ability to perform downstream analysis of the MGnify data through the introduction of a coupled Jupyter Lab environment.}, } @article {pmid36476562, year = {2022}, author = {Liu, Y and Zhang, Z and Ji, M and Hu, A and Wang, J and Jing, H and Liu, K and Xiao, X and Zhao, W}, title = {Comparison of prokaryotes between Mount Everest and the Mariana Trench.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {215}, pmid = {36476562}, issn = {2049-2618}, mesh = {*Metagenomics ; *Bicycling ; }, abstract = {BACKGROUND: Mount Everest and the Mariana Trench represent the highest and deepest places on Earth, respectively. They are geographically separated, with distinct extreme environmental parameters that provide unique habitats for prokaryotes. Comparison of prokaryotes between Mount Everest and the Mariana Trench will provide a unique perspective to understanding the composition and distribution of environmental microbiomes on Earth.

RESULTS: Here, we compared prokaryotic communities between Mount Everest and the Mariana Trench based on shotgun metagenomic analysis. Analyzing 25 metagenomes and 1176 metagenome-assembled genomes showed distinct taxonomic compositions between Mount Everest and the Mariana Trench, with little taxa overlap, and significant differences in genome size, GC content, and predicted optimal growth temperature. However, community metabolic capabilities exhibited striking commonality, with > 90% of metabolic modules overlapping among samples of Mount Everest and the Mariana Trench, with the only exception for CO2 fixations (photoautotrophy in Mount Everest but chemoautotrophy in the Mariana Trench). Most metabolic pathways were common but performed by distinct taxa in the two extreme habitats, even including some specialized metabolic pathways, such as the versatile degradation of various refractory organic matters, heavy metal metabolism (e.g., As and Se), stress resistance, and antioxidation. The metabolic commonality indicated the overall consistent roles of prokaryotes in elemental cycling and common adaptation strategies to overcome the distinct stress conditions despite the intuitively huge differences in Mount Everest and the Mariana Trench.

CONCLUSION: Our results, the first comparison between prokaryotes in the highest and the deepest habitats on Earth, may highlight the principles of prokaryotic diversity: although taxa are habitat-specific, primary metabolic functions could be always conserved. Video abstract.}, } @article {pmid36476263, year = {2022}, author = {Tee, MZ and Er, YX and Easton, AV and Yap, NJ and Lee, IL and Devlin, J and Chen, Z and Ng, KS and Subramanian, P and Angelova, A and Oyesola, O and Sargsian, S and Ngui, R and Beiting, DP and Boey, CCM and Chua, KH and Cadwell, K and Lim, YAL and Loke, P and Lee, SC}, title = {Gut microbiome of helminth-infected indigenous Malaysians is context dependent.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {214}, pmid = {36476263}, issn = {2049-2618}, support = {R01 AI130945/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Metagenomics ; }, abstract = {BACKGROUND: While microbiomes in industrialized societies are well characterized, indigenous populations with traditional lifestyles have microbiomes that are more akin to those of ancient humans. However, metagenomic data in these populations remains scarce, and the association with soil-transmitted helminth infection status is unclear. Here, we sequenced 650 metagenomes of indigenous Malaysians from five villages with different prevalence of helminth infections.

RESULTS: Individuals from villages with higher prevalences of helminth infections have more unmapped reads and greater microbial diversity. Microbial community diversity and composition were most strongly associated with different villages and the effects of helminth infection status on the microbiome varies by village. Longitudinal changes in the microbiome in response to albendazole anthelmintic treatment were observed in both helminth infected and uninfected individuals. Inference of bacterial population replication rates from origin of replication analysis identified specific replicating taxa associated with helminth infection.

CONCLUSIONS: Our results indicate that helminth effects on the microbiota were highly dependent on context, and effects of albendazole on the microbiota can be confounding for the interpretation of deworming studies. Furthermore, a substantial quantity of the microbiome remains unannotated, and this large dataset from an indigenous population associated with helminth infections is a valuable resource for future studies. Video Abstract.}, } @article {pmid36476129, year = {2023}, author = {Zhao, L and Luo, JL and Ali, MK and Spiekerkoetter, E and Nicolls, MR}, title = {The Human Respiratory Microbiome: Current Understandings and Future Directions.}, journal = {American journal of respiratory cell and molecular biology}, volume = {68}, number = {3}, pages = {245-255}, pmid = {36476129}, issn = {1535-4989}, support = {R01 HL095686/HL/NHLBI NIH HHS/United States ; R01 HL158714/HL/NHLBI NIH HHS/United States ; R01 HL138473/HL/NHLBI NIH HHS/United States ; R01 HL141105/HL/NHLBI NIH HHS/United States ; I01 BX005628/BX/BLRD VA/United States ; }, mesh = {Humans ; Lung/microbiology ; *Asthma ; *Pulmonary Disease, Chronic Obstructive/microbiology ; *Microbiota ; *Cystic Fibrosis/microbiology ; }, abstract = {Microorganisms colonize the human body. The lungs and respiratory tract, previously believed to be sterile, harbor diverse microbial communities and the genomes of bacteria (bacteriome), viruses (virome), and fungi (mycobiome). Recent advances in amplicon and shotgun metagenomic sequencing technologies and data-analyzing methods have greatly aided the identification and characterization of microbial populations from airways. The respiratory microbiome has been shown to play roles in human health and disease and is an area of rapidly emerging interest in pulmonary medicine. In this review, we provide updated information in the field by focusing on four lung conditions, including asthma, chronic obstructive pulmonary disease, cystic fibrosis, and idiopathic pulmonary fibrosis. We evaluate gut, oral, and upper airway microbiomes and how they contribute to lower airway flora. The discussion is followed by a systematic review of the lower airway microbiome in health and disease. We conclude with promising research avenues and implications for evolving therapeutics.}, } @article {pmid36475916, year = {2023}, author = {Xu, R and Li, Q and Wang, H and Su, Y and Zhu, W}, title = {Reduction of Redox Potential Exerts a Key Role in Modulating Gut Microbial Taxa and Function by Dietary Supplementation of Pectin in a Pig Model.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0328322}, pmid = {36475916}, issn = {2165-0497}, mesh = {Swine ; Animals ; Pectins ; *Gastrointestinal Microbiome/physiology ; Feces/microbiology ; *Microbiota ; Dietary Supplements ; Oxidation-Reduction ; }, abstract = {Pectin exists in a vast range of plants and has a long history of acting as a functional food additive with potential prebiotic effects on intestinal health. However, knowledge of how pectin regulates gut microbial communities is still insufficient and limited. Here, metatranscriptome sequencing revealed that a pectin-enriched diet (PEC) decreased the abundances of fungal keystone taxa (e.g., amino acid-producing Kazachstania spp.) and their genes involved in oxidative phosphorylation, while it increased the abundance of sulfate-reducing Desulfovibrio spp., and methane-producing Methanobrevibacter spp. in colon microbiomes. Furthermore, we first confirmed that PEC decreased fecal redox potential in a fistula pig model, which could be supported by the enrichment of antioxidants (e.g., inosine) in feces. Fecal metagenome analysis disclosed that certain microbial taxa promoted inosine biosynthesis from pectin degradation, including Prevotella, which plays an essential role in pectin biodegradation. Overall, these results demonstrate that pectin decreases the redox potential in pig hindgut to modulate microbial composition and functions, and specific microorganisms generate reducing agents in the course of pectin degradation to decrease redox potential of microbial ecosystem. IMPORTANCE Collective studies indicate that pectin degradation promotes extensive microorganisms that can be involved in pectin degradation directly or indirectly, or benefit from the altered physiological conditions caused by pectin ingestions. Our study focuses on effects of pectin on gut microbial taxa and functions, as well as its interactions with altered environmental features. Our results demonstrate pectin-induced proreducing shifts on colon microbial taxa and functions, and first confirm that pectin decreases hindgut redox potential, which is an important environmental feature that can modulate microbial communities. These results infer that there is bidirectional regulation between microbiota and redox potential during pectin degradation. In general, this investigation proposes new insights into the pectin-modulating gut microbial ecosystem and also provides new perspectives for targeting modulation of gut microbiota.}, } @article {pmid36475872, year = {2023}, author = {Queiroz, LL and Lacorte, GA and Isidorio, WR and Landgraf, M and de Melo Franco, BDG and Pinto, UM and Hoffmann, C}, title = {High Level of Interaction between Phages and Bacteria in an Artisanal Raw Milk Cheese Microbial Community.}, journal = {mSystems}, volume = {8}, number = {1}, pages = {e0056422}, pmid = {36475872}, issn = {2379-5077}, mesh = {Humans ; Animals ; *Cheese/analysis ; Milk/microbiology ; *Bacteriophages/genetics ; Bacteria/genetics ; *Lactobacillales ; *Microbiota/genetics ; }, abstract = {Microbial starter cultures are used in the production of many cheeses around the world, such as Parmigiano-Reggiano, in Italy, Époisses, in France, and Canastra, in Brazil, providing many of the unique features of these cheeses. Bacteriophages (phages) are ubiquitous and well known to modulate the structure of bacterial communities, and recent data indicate that cheeses contain a high abundance of naturally occurring phages. Here, we analyze the viral and bacterial metagenomes of Canastra cheese: a traditional artisanal Brazilian cheese produced using an endogenous starter culture and raw milk. Over 1,200 viral operational taxonomic units were recovered using both isolated viral-like particles and complete metagenomic DNA. Common viral families identified included Siphoviridae and Myoviridae, with 40% of putative phage genomes unidentified at the family level of classification. We observed very high phage diversity, which varied greatly across different cheese producers, with 28% of phage genomes detected in only one producer. Several metagenome-assembled genomes were recovered for lactic acid-producing bacteria, as well as nonstarter bacterial species, and we identified several phage-bacterium interactions, at the strain level of resolution, varying across distinct cheese producers. We postulate that at least one bacterial strain detected could be endogenous and unique to the Canastra cheese-producing region in Brazil and that its growth seems to be modulated by autochthonous phages present in this artisanal production system. This phage-host relationship is likely to influence the fermentation dynamics and ultimately the sensorial profile of these cheeses, with implications for other similar cheese production systems around the world. IMPORTANCE Our work demonstrated a dynamic yet stable microbial ecosystem during cheese production using an endogenous starter culture. This was observed across several distinct producers and was marked by genomic evidence of continued phage-bacterium interactions, such as the presence of bacterial defense mechanisms. Furthermore, we provide evidence of unique microbial signatures for each individual cheese producer studied in the region, a fact that may have profound consequences on product traceability. This was the first effort to describe and understand the bacteriophage composition and ecological dynamics within the Brazilian Canastra cheese production system. The study of this prototypical backslopping production system provides a solid background for further mechanistic studies of the production of many cheeses around the world.}, } @article {pmid36475839, year = {2023}, author = {Tao, Y and Xun, F and Zhao, C and Mao, Z and Li, B and Xing, P and Wu, QL}, title = {Improved Assembly of Metagenome-Assembled Genomes and Viruses in Tibetan Saline Lake Sediment by HiFi Metagenomic Sequencing.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0332822}, pmid = {36475839}, issn = {2165-0497}, mesh = {*Metagenome ; Lakes ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; Tibet ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Viruses/genetics ; }, abstract = {With the development and reduced costs of high-throughput sequencing technology, environmental dark matter, such as novel metagenome-assembled genomes (MAGs) and viruses, is now being discovered easily. However, due to read length limitations, MAGs and viromes often suffer from genome discontinuity and deficiencies in key functional elements. Here, by applying long-read sequencing technology to sediment samples from a Tibetan saline lake, we comprehensively analyzed the performance of high-fidelity (HiFi) reads and the possibility of integration with short-read next-generation sequencing (NGS) data. In total, 207 full-length nonredundant 16S rRNA gene sequences and 19 full-length nonredundant 18S rRNA genes were directly obtained from HiFi reads, which greatly surpassed the retrieval performance of NGS technology. We carried out a cross-sectional comparison among multiple assembly strategies, referred to as 'NGS', 'Hybrid (NGS+HiFi)', and 'HiFi'. Two MAGs and 29 viruses with circular genomes were reconstructed using HiFi reads alone, indicating the great power of the 'HiFi' approach to assemble high-quality microbial genomes. Among the 3 strategies, the 'Hybrid' approach produced the highest number of medium/high-quality MAGs and viral genomes, while the ratio of MAGs containing 16S rRNA genes was significantly improved in the 'HiFi' assembly results. Overall, our study provides a practical metagenomic resolution for analyzing complex environmental samples by taking advantage of both the short-read and HiFi long-read sequencing methods to extract the maximum amount of information, including data on prokaryotes, eukaryotes, and viruses, via the 'Hybrid' approach. IMPORTANCE To expand the understanding of microbial dark matter in the environment, we did the first comparative evaluation of multiple assembly strategies based on high-throughput short-read and HiFi data from lake sediments metagenomic sequencing. The results demonstrated great improvement of the 'Hybrid' assembly method (short-read next-generation sequencing data plus HiFi data) in the recovery of medium/high-quality MAGs and viral genomes. Further analysis showed that HiFi data is important to retrieve the complete circular prokaryotic and viral genomes. Meanwhile, hundreds of full-length 16S/18S rRNA genes were assembled directly from HiFi data, which facilitated the species composition studies of complex environmental samples, especially for understanding micro-eukaryotes. Therefore, the application of the latest HiFi long-read sequencing could greatly improve the metagenomic assembly integrity and promote environmental microbiome research.}, } @article {pmid36475828, year = {2022}, author = {Hazan, S and Dave, S and Papoutsis, AJ and Deshpande, N and Howell, MC and Martin, LM}, title = {Vitamin C improves gut Bifidobacteria in humans.}, journal = {Future microbiology}, volume = {}, number = {}, pages = {}, doi = {10.2217/fmb-2022-0209}, pmid = {36475828}, issn = {1746-0921}, abstract = {Aims: Numerous beneficial effects of vitamin C (ascorbic acid) supplementation have been reported in the literature. However, data on its effects toward the gut microbiome are limited. We assessed the effect of vitamin C supplementation on the abundance of beneficial bacterial species in the gut microbiome. Materials and methods: Stool samples were analyzed for relative abundance of gut microbiome bacteria using next-generation sequencing-based profiling and metagenomic shotgun analysis. Results: Supplementation with vitamin C increased the abundance of bacteria of the genus Bifidobacterium (p = 0.0001) and affected various species. Conclusion: The beneficial effects of vitamin C supplementation may be attributed to modulation of the gut microbiome and the consequent health benefits thereof.}, } @article {pmid36475774, year = {2023}, author = {Bogomolnaya, L and Talamantes, M and Rocha, J and Nagarajan, A and Zhu, W and Spiga, L and Winter, MG and Konganti, K and Adams, LG and Winter, S and Andrews-Polymenis, H}, title = {Taxonomic and Metagenomic Analyses Define the Development of the Microbiota in the Chick.}, journal = {mBio}, volume = {14}, number = {1}, pages = {e0244422}, pmid = {36475774}, issn = {2150-7511}, support = {R01 AI118807/AI/NIAID NIH HHS/United States ; R21 AI171537/AI/NIAID NIH HHS/United States ; R21 AI166263/AI/NIAID NIH HHS/United States ; R35 GM147470/GM/NIGMS NIH HHS/United States ; R01 DK134692/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Chickens/microbiology ; Isoleucine ; *Microbiota ; Salmonella typhimurium/metabolism ; Cecum/microbiology ; Amino Acids, Branched-Chain/metabolism ; Valine/metabolism ; *Salmonella Infections, Animal/microbiology ; *Poultry Diseases/microbiology ; }, abstract = {Chicks are ideal to follow the development of the intestinal microbiota and to understand how a pathogen perturbs this developing population. Taxonomic/metagenomic analyses captured the development of the chick microbiota in unperturbed chicks and in chicks infected with Salmonella enterica serotype Typhimurium (STm) during development. Taxonomic analysis suggests that colonization by the chicken microbiota takes place in several waves. The cecal microbiota stabilizes at day 12 posthatch with prominent Gammaproteobacteria and Clostridiales. Introduction of S. Typhimurium at day 4 posthatch disrupted the expected waves of intestinal colonization. Taxonomic and metagenomic shotgun sequencing analyses allowed us to identify species present in uninfected chicks. Untargeted metabolomics suggested different metabolic activities in infected chick microbiota. This analysis and gas chromatography-mass spectrometry on ingesta confirmed that lactic acid in cecal content coincides with the stable presence of enterococci in STm-infected chicks. Unique metabolites, including 2-isopropylmalic acid, an intermediate in the biosynthesis of leucine, were present only in the cecal content of STm-infected chicks. The metagenomic data suggested that the microbiota in STm-infected chicks contained a higher abundance of genes, from STm itself, involved in branched-chain amino acid synthesis. We generated an ilvC deletion mutant (STM3909) encoding ketol-acid-reductoisomerase, a gene required for the production of l-isoleucine and l-valine. ΔilvC mutants are disadvantaged for growth during competitive infection with the wild type. Providing the ilvC gene in trans restored the growth of the ΔilvC mutant. Our integrative approach identified biochemical pathways used by STm to establish a colonization niche in the chick intestine during development. IMPORTANCE Chicks are an ideal model to follow the development of the intestinal microbiota and to understand how a pathogen perturbs this developing population. Using taxonomic and metagenomic analyses, we captured the development of chick microbiota to 19 days posthatch in unperturbed chicks and in chicks infected with Salmonella enterica serotype Typhimurium (STm). We show that normal development of the microbiota takes place in waves and is altered in the presence of a pathogen. Metagenomics and metabolomics suggested that branched-chain amino acid biosynthesis is especially important for Salmonella growth in the infected chick intestine. Salmonella mutants unable to make l-isoleucine and l-valine colonize the chick intestine poorly. Restoration of the pathway for biosynthesis of these amino acids restored the colonizing ability of Salmonella. Integration of multiple analyses allowed us to correctly identify biochemical pathways used by Salmonella to establish a niche for colonization in the chick intestine during development.}, } @article {pmid36475767, year = {2023}, author = {Zhao, J and Dellicour, S and Yan, Z and Veit, M and Gill, MS and He, WT and Zhai, X and Ji, X and Suchard, MA and Lemey, P and Su, S}, title = {Early Genomic Surveillance and Phylogeographic Analysis of Getah Virus, a Reemerging Arbovirus, in Livestock in China.}, journal = {Journal of virology}, volume = {97}, number = {1}, pages = {e0109122}, pmid = {36475767}, issn = {1098-5514}, support = {R01 AI153044/AI/NIAID NIH HHS/United States ; U19 AI135995/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Humans ; Mice ; *Arboviruses/genetics ; China/epidemiology ; Genomics ; Livestock/virology ; *Phylogeny ; *Genome, Viral ; }, abstract = {Getah virus (GETV) mainly causes disease in livestock and may pose an epidemic risk due to its expanding host range and the potential of long-distance dispersal through animal trade. Here, we used metagenomic next-generation sequencing (mNGS) to identify GETV as the pathogen responsible for reemerging swine disease in China and subsequently estimated key epidemiological parameters using phylodynamic and spatially-explicit phylogeographic approaches. The GETV isolates were able to replicate in a variety of cell lines, including human cells, and showed high pathogenicity in a mouse model, suggesting the potential for more mammal hosts. We obtained 16 complete genomes and 79 E2 gene sequences from viral strains collected in China from 2016 to 2021 through large-scale surveillance among livestock, pets, and mosquitoes. Our phylogenetic analysis revealed that three major GETV lineages are responsible for the current epidemic in livestock in China. We identified three potential positively selected sites and mutations of interest in E2, which may impact the transmissibility and pathogenicity of the virus. Phylodynamic inference of the GETV demographic dynamics identified an association between livestock meat consumption and the evolution of viral genetic diversity. Finally, phylogeographic reconstruction of GETV dispersal indicated that the sampled lineages have preferentially circulated within areas associated with relatively higher mean annual temperature and pig population density. Our results highlight the importance of continuous surveillance of GETV among livestock in southern Chinese regions associated with relatively high temperatures. IMPORTANCE Although livestock is known to be the primary reservoir of Getah virus (GETV) in Asian countries, where identification is largely based on serology, the evolutionary history and spatial epidemiology of GETV in these regions remain largely unknown. Through our sequencing efforts, we provided robust support for lineage delineation of GETV and identified three major lineages that are responsible for the current epidemic in livestock in China. We further analyzed genomic and epidemiological data to reconstruct the recent demographic and dispersal history of GETV in domestic animals in China and to explore the impact of environmental factors on its genetic diversity and its diffusion. Notably, except for livestock meat consumption, other pig-related factors such as the evolution of live pig transport and pork production do not show a significant association with the evolution of viral genetic diversity, pointing out that further studies should investigate the potential contribution of other host species to the GETV outbreak. Our analysis of GETV demonstrates the need for wider animal species surveillance and provides a baseline for future studies of the molecular epidemiology and early warning of emerging arboviruses in China.}, } @article {pmid36475759, year = {2023}, author = {Chen, BY and Lin, WZ and Li, YL and Bi, C and Du, LJ and Liu, Y and Zhou, LJ and Liu, T and Xu, S and Shi, CJ and Zhu, H and Wang, YL and Sun, JY and Liu, Y and Zhang, WC and Zhang, Z and Zhang, HL and Zhu, YQ and Duan, SZ}, title = {Characteristics and Correlations of the Oral and Gut Fungal Microbiome with Hypertension.}, journal = {Microbiology spectrum}, volume = {11}, number = {1}, pages = {e0195622}, pmid = {36475759}, issn = {2165-0497}, mesh = {Humans ; *Mycobiome ; *Gastrointestinal Microbiome/physiology ; *Microbiota ; *Hypertension ; Mouth ; Feces/microbiology ; Fungi/genetics ; }, abstract = {The mycobiome is an essential constituent of the human microbiome and is associated with various diseases. However, the role of oral and gut fungi in hypertension (HTN) remains largely unexplored. In this study, saliva, subgingival plaques, and feces were collected from 36 participants with HTN and 24 healthy controls for metagenomic sequencing. The obtained sequences were analyzed using the Kraken2 taxonomic annotation pipeline to assess fungal composition and diversity. Correlations between oral and gut fungi and clinic parameters, between fungi within the same sample types, and between different sample types were identified by Spearman's correlation analysis. Overall, the subgingival fungal microbiome had substantially higher alpha diversity than the salivary and fecal fungal microbiomes. The fungal microbiomes of the three sample types displayed distinct beta diversity from each other. Oral fungi but not gut fungi in HTN had beta diversity significantly different from that of controls. Among the fungi shared in the oral cavity and gut, Exophiala was the genus with the most notable changes. Exophiala spinifera was the most abundant salivary species in HTN. Some fungal species directly correlated with blood pressure, including gut Exophiala xenobiotica and Exophiala mesophila. The markedly impaired ecological cocorrelation networks of oral and gut fungi in HTN suggested compromised association among fungal species. Most fungi were shared in the oral cavity and gut, and their correlations suggested the potential interplays between oral and gut fungi. In conclusion, the oral cavity and intestine have unique fungal ecological environments. The fungal enrichment and ecology in HTN, the correlations between oral and gut fungi, and the associations between oral and gut fungi and clinical parameters suggest an important role that the fungal microbiome may play in HTN. IMPORTANCE Our study fills the gap in human studies investigating the oral and gut fungal microbiota in association with blood pressure. It characterizes the diversity and composition of the oral and gut fungal microbiome in human subjects, elucidates the dysbiosis of fungal ecology in a hypertensive population, and establishes oral-gut fungal correlations and fungus-clinical parameter correlations. Targeting fungi in the oral cavity and/or gut may provide novel strategies for the prevention and treatment of hypertension.}, } @article {pmid36474348, year = {2022}, author = {Mukhopadhyay, S and Lee, JJ and Hartman, E and Woodford, E and Dhudasia, MB and Mattei, LM and Daniel, SG and Wade, KC and Underwood, MA and Bittinger, K}, title = {Preterm infants at low risk for early-onset sepsis differ in early fecal microbiome assembly.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2154091}, pmid = {36474348}, issn = {1949-0984}, support = {K23 HD088753/HD/NICHD NIH HHS/United States ; UL1 TR001878/TR/NCATS NIH HHS/United States ; }, mesh = {Infant, Newborn ; Humans ; *Infant, Premature ; Cohort Studies ; *Gastrointestinal Microbiome ; Metagenomics ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Antibiotics are administered near-universally to very low birth weight (VLBW) infants after birth for suspected early-onset sepsis (EOS). We previously identified a phenotypic group of VLBW infants, referred to as low-risk for EOS (LRE), whose risk of EOS is low enough to avoid routine antibiotic initiation. In this cohort study, we compared 18 such infants with 30 infants categorized as non-LRE to determine if the lower risk of pathogen transmission at birth is accompanied by differences in microbiome acquisition and development. We did shotgun metagenomic sequencing of 361 fecal samples obtained serially. LRE infants had a higher human-to-bacterial DNA ratio than non-LRE infants in fecal samples on days 1-3 after birth, confirming lower bacterial acquisition among LRE infants. The microbial diversity and composition in samples from days 4-7 differed between the groups with a predominance of Staphylococcus epidermidis in LRE infants and Enterobacteriaceae sp. in non-LRE infants. Compositional differences were congruent with the distribution of virulence factors and antibiotic resistant genes. After the first week, the overall composition was similar, but changes in relative abundance for several taxa with increasing age differed between groups. Of the nine late-onset bacteremia episodes, eight occurred in non-LRE infants. Species isolated from the blood culture was detected in the pre-antibiotic fecal samples of the infant for all episodes, though these species were also found in infants without bacteremia. In conclusion, LRE infants present a distinct pattern of microbiome development that is aligned with their low risk for EOS. Further investigation to determine the impact of these differences on later outcomes such as late-onset bacteremia is warranted.}, } @article {pmid36474293, year = {2022}, author = {Zhang, H and Guan, W and Li, L and Guo, D and Zhang, X and Guan, J and Luo, R and Zheng, S and Fu, J and Cheng, Y and He, Q}, title = {Dietary carbon loaded with nano-ZnO alters the gut microbiota community to mediate bile acid metabolism and potentiate intestinal immune function in fattening beef cattle.}, journal = {BMC veterinary research}, volume = {18}, number = {1}, pages = {425}, pmid = {36474293}, issn = {1746-6148}, support = {32060773//National Natural Science Foundation of China/ ; 32160804//National Natural Science Foundation of China/ ; GJJ201621//Jiangxi Provincial Department of Education Science and Technology Research Project/ ; GJJ190848//Jiangxi Provincial Department of Science and Technology/ ; 2020YJ0471//Science and Technology Program of Jingdezhen City/ ; 2020YJ0472//Science and Technology Program of Jingdezhen City/ ; 20202BABL20501//Natural Science Foundation of Jiangxi Province/ ; }, mesh = {Cattle ; Animals ; *Carbon ; *Metagenomics ; Diet/veterinary ; Bile Acids and Salts ; Immunity ; }, abstract = {BACKGROUND: To our knowledge, carbon loaded with nano-ZnO (NZnOC) represents a new nutritional additive for the animal husbandry industry. However, the mechanism by which NZnOC mediates beef cattle growth and intestinal health is not fully understood. This study aimed to investigate the effects of carbon loaded with nano-ZnO (NZnOC) supplementation on growth performance, gut microbiota, bile acid (BAs) metabolism and intestinal immunity in fattening cattle. Twenty cattle (16 ± 0.95 months) were randomly assigned to two dietary groups: CON (control, without feed additive) and NZnOC (diet supplemented with 80 mg NZnOC/kg diet dry matter basic) for 60 d. The colon digesta microbiota composition and BAs concentration were determined by microbiota metagenomics and gas chromatography methods, respectively.

RESULTS: The results showed that the NZnOC-supplemented cattle had greater final weight, average daily gain and gain-to-feed ratio than those in the CON group. Cattle fed the NZnOC diet had a higher relative abundance of the secondary BAs synthesizing phyla Firmicutes, Tenericutes and Actinobacteria than those fed the CON diet. Dietary supplementation with NZnOC increased the relative abundance of the secondary BAs synthesis microbiota genera Clostridium, Ruminococcus, Eubacterium, and Brevibacillus in colon digesta. Cattle fed the NZnOC diet had increased activities of 3α-hydroxysteroid dehydrogenase (EC: 1.1.1.52) and bile acid-CoA ligase BaiB (EC: 6.2.1.7) in the colon digesta compared with those fed the CON diet. The primary BAs taurocholic acid, taurochenodeoxycholic acid and taurodeoxycholate acid were significantly decreased by dietary NZnOC supplementation, while the secondary BAs deoxycholic acid, taurolithocholic acid, beta-muricholic acid, 12-ketolithocholic acid and ursodeoxycholic acid were significantly increased. Dietary supplementation with NZnOC increased the mRNA abundance of G protein-coupled bile acid receptor 1, protein kinase cAMP-activated catalytic subunit alpha, cyclic-AMP response element binding protein 1 and interleukin (IL)-10 in the colon mucosa of cattle, while the mRNA abundance of tumor necrosis factor and IL-1β were significantly decreased.

CONCLUSIONS: In summary, dietary supplementation with NZnOC can facilitate the growth performance and intestinal immune function of cattle by improving BAs metabolism. NZnOC can be supplemented in the diet as a safe regulator of gut microbiota and as a feed additive in the ruminants industry.}, } @article {pmid36473906, year = {2022}, author = {Hedžet, S and Rupnik, M and Accetto, T}, title = {Broad host range may be a key to long-term persistence of bacteriophages infecting intestinal Bacteroidaceae species.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {21098}, pmid = {36473906}, issn = {2045-2322}, mesh = {Humans ; *Host Specificity ; Bacteroidaceae ; *Bacteriophages/genetics ; }, abstract = {The longitudinal studies have found that the human gut microbiota is stable over time with some major bacterial lineages or even strains persisting for years. This was recently extended to gut bacteriophages using the metagenomic data. Here, we focused on cultivation of the major Bacteroidetes of human gut, the Bacteroides and Phocaeicola strains, and their bacteriophages from two healthy donors. The persistence of Bacteroides and Phocaeicola species and strains was confirmed. We isolated 28 genetically different phages grouped into seven distinct clusters, two of these were new. Moreover, the bacteriophages from several groups, although being genetically quite homogeneous, had the ability to infect the strains belonging to different species isolated from several sampling time-points and different donors. We propose that the ability to infect several host species, which differ in their nutritional niches, may promote long-term persistence of dominant gut bacteriophage groups.}, } @article {pmid36473884, year = {2022}, author = {Goodarzi, Z and Asad, S and Mehrshad, M}, title = {Genome-resolved insight into the reservoir of antibiotic resistance genes in aquatic microbial community.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {21047}, pmid = {36473884}, issn = {2045-2322}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Microbiota ; }, abstract = {Aquatic microbial communities are an important reservoir of antibiotic resistance genes (ARGs). However, distribution and diversity of different ARG categories in environmental microbes with different ecological strategies is not yet well studied. Despite the potential exposure of the southern part of the Caspian Sea to the release of antibiotics, little is known about its natural resistome profile. We used a combination of Hidden Markov model (HMM), homology alignment and a deep learning approach for comprehensive screening of the diversity and distribution of ARGs in the Caspian Sea metagenomes at genome resolution. Detected ARGs were classified into five antibiotic resistance categories including prevention of access to target (44%), modification/protection of targets (30%), direct modification of antibiotics (22%), stress resistance (3%), and metal resistance (1%). The 102 detected ARG containing metagenome-assembled genomes of the Caspian Sea were dominated by representatives of Acidimicrobiia, Gammaproteobacteria, and Actinobacteria classes. Comparative analysis revealed that the highly abundant, oligotrophic, and genome streamlined representatives of taxa Acidimicrobiia and Actinobacteria modify the antibiotic target via mutation to develop antibiotic resistance rather than carrying extra resistance genes. Our results help with understanding how the encoded resistance categories of each genome are aligned with its ecological strategies.}, } @article {pmid36473838, year = {2022}, author = {Gong, X and Del Río, ÁR and Xu, L and Chen, Z and Langwig, MV and Su, L and Sun, M and Huerta-Cepas, J and De Anda, V and Baker, BJ}, title = {New globally distributed bacterial phyla within the FCB superphylum.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7516}, pmid = {36473838}, issn = {2041-1723}, mesh = {*Genomics ; *Plastic Surgery Procedures ; Bacteria/genetics ; Sulfur ; Nitrogen ; }, abstract = {Microbes in marine sediments play crucial roles in global carbon and nutrient cycling. However, our understanding of microbial diversity and physiology on the ocean floor is limited. Here, we use phylogenomic analyses of thousands of metagenome-assembled genomes (MAGs) from coastal and deep-sea sediments to identify 55 MAGs that are phylogenetically distinct from previously described bacterial phyla. We propose that these MAGs belong to 4 novel bacterial phyla (Blakebacterota, Orphanbacterota, Arandabacterota, and Joyebacterota) and a previously proposed phylum (AABM5-125-24), all of them within the FCB superphylum. Comparison of their rRNA genes with public databases reveals that these phyla are globally distributed in different habitats, including marine, freshwater, and terrestrial environments. Genomic analyses suggest these organisms are capable of mediating key steps in sedimentary biogeochemistry, including anaerobic degradation of polysaccharides and proteins, and respiration of sulfur and nitrogen. Interestingly, these genomes code for an unusually high proportion (~9% on average, up to 20% per genome) of protein families lacking representatives in public databases. Genes encoding hundreds of these protein families colocalize with genes predicted to be involved in sulfur reduction, nitrogen cycling, energy conservation, and degradation of organic compounds. Our findings advance our understanding of bacterial diversity, the ecological roles of these bacteria, and potential links between novel gene families and metabolic processes in the oceans.}, } @article {pmid36473438, year = {2022}, author = {Arnold, AE}, title = {Mycology: Metagenomes illuminate evolutionary relationships and reframe symbiotic interactions.}, journal = {Current biology : CB}, volume = {32}, number = {23}, pages = {R1304-R1306}, doi = {10.1016/j.cub.2022.10.041}, pmid = {36473438}, issn = {1879-0445}, abstract = {An intriguing new study leverages newly generated metagenomes to remap the evolution of the most species-rich clade of fungi, highlighting how some of the most intriguing and visible manifestations of symbioses - lichens - may arise.}, } @article {pmid36472670, year = {2022}, author = {Lupini, L and Bassi, C and Guerriero, P and Raspa, M and Scavizzi, F and Sabbioni, S}, title = {Microbiota and environmental health monitoring of mouse colonies by metagenomic shotgun sequencing.}, journal = {World journal of microbiology & biotechnology}, volume = {39}, number = {1}, pages = {37}, pmid = {36472670}, issn = {1573-0972}, support = {FAR-Sabbioni Silvia//Università degli Studi di Ferrara/ ; }, mesh = {Mice ; Animals ; *Metagenomics ; *Environmental Health ; }, abstract = {Metagenomic next-generation sequencing (mNGS) allows the monitoring of microbiota composition of murine colonies employed for scientific purposes in a single test by assessing the composition of gut microbiome and the detection of pathogens from fecal pellets. In this study, we tested the potential use of mNGS for monitoring both microbiota composition and the presence of pathogens through Environmental Health Monitoring, by using exhaust dust collection filters derived from individually ventilated cages (IVC) systems.mNGS analysis was performed on nucleic acids isolated from filters collecting air from the exhaust of: (1) cages with mice housed in a non-pathogen free facility; (2) animal-free cages with clean chow and bedding from the same facility; (3) cages housing mice from a specific-pathogen free (SPF) facility. mNGS results revealed correspondence between microbiome composition from fecal pellets and filter, including pathogenic bacteria (Helicobacter hepaticus, Helicobacter typhlonius, Chlamydia muridarum, Rodentibacter pneumotropicus, Citrobacter rodentium), intestinal protozoa (Tritrichomonas muris, Spironucleus muris) nematoda (Aspiculuris tetraptera) and eukaryotic parasites (Myocoptes musculinus), present in the colony. Entamoeba muris and Syphacia obvelata were detected in fecal pellets but not in filter. The animal free exhaust dust filter, exposed to clean cages (no mice) placed in the IVC after removal of all mice, exhibited the presence of the same pathogens due to contaminated connecting pipes, confirming the sensitivity of the approach. Conversely, the filter from SPF colony revealed the absence of pathogens.The current use of exhaust dust collection filters in health surveillance requires multiple molecular tests to identify specific pathogens and does not provide information on the colony microbiome. This work provides the proof-of-principle that assaying exhaust dust collection filters by mNGS for microbiota monitoring of laboratory mice is feasible. In its daily application, results suggest the usefulness of the test in SPF facilities, where pathogenic micro-organisms are expected to be absent. mNGS analysis of exhaust dust collection filters allows the analysis of multiple cages, reducing the number of tests required for pathogen detection and corresponding costs, and avoiding the use of sentinel mice.}, } @article {pmid36472532, year = {2022}, author = {Moraitou, M and Forsythe, A and Fellows Yates, JA and Brealey, JC and Warinner, C and Guschanski, K}, title = {Ecology, Not Host Phylogeny, Shapes the Oral Microbiome in Closely Related Species.}, journal = {Molecular biology and evolution}, volume = {39}, number = {12}, pages = {}, pmid = {36472532}, issn = {1537-1719}, mesh = {Animals ; Gorilla gorilla ; Phylogeny ; Dental Calculus ; *Hominidae ; *Microbiota/genetics ; }, abstract = {Host-associated microbiomes are essential for a multitude of biological processes. Placed at the contact zone between external and internal environments, the little-studied oral microbiome has important roles in host physiology and health. Here, we investigate the roles of host evolutionary relationships and ecology in shaping the oral microbiome in three closely related gorilla subspecies (mountain, Grauer's, and western lowland gorillas) using shotgun metagenomics of 46 museum-preserved dental calculus samples. We find that the oral microbiomes of mountain gorillas are functionally and taxonomically distinct from the other two subspecies, despite close evolutionary relationships and geographic proximity with Grauer's gorillas. Grauer's gorillas show intermediate bacterial taxonomic and functional, and dietary profiles. Altitudinal differences in gorilla subspecies ranges appear to explain these patterns, suggesting a close connection between dental calculus microbiomes and the environment, likely mediated through diet. This is further supported by the presence of gorilla subspecies-specific phyllosphere/rhizosphere taxa in the oral microbiome. Mountain gorillas show a high abundance of nitrate-reducing oral taxa, which may promote adaptation to a high-altitude lifestyle by modulating blood pressure. Our results suggest that ecology, rather than evolutionary relationships and geographic distribution, shape the oral microbiome in these closely related species.}, } @article {pmid36472419, year = {2022}, author = {Coker, J and Zhalnina, K and Marotz, C and Thiruppathy, D and Tjuanta, M and D'Elia, G and Hailu, R and Mahosky, T and Rowan, M and Northen, TR and Zengler, K}, title = {A Reproducible and Tunable Synthetic Soil Microbial Community Provides New Insights into Microbial Ecology.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0095122}, pmid = {36472419}, issn = {2379-5077}, support = {T32 GM007198/GM/NIGMS NIH HHS/United States ; }, mesh = {*Soil ; Reproducibility of Results ; Soil Microbiology ; Plant Roots ; *Microbiota ; Plants/microbiology ; }, abstract = {Microbial soil communities form commensal relationships with plants to promote the growth of both parties. The optimization of plant-microbe interactions to advance sustainable agriculture is an important field in agricultural research. However, investigation in this field is hindered by a lack of model microbial community systems and efficient approaches for building these communities. Two key challenges in developing standardized model communities are maintaining community diversity over time and storing/resuscitating these communities after cryopreservation, especially considering the different growth rates of organisms. Here, a model synthetic community (SynCom) of 16 soil microorganisms commonly found in the rhizosphere of diverse plant species, isolated from soil surrounding a single switchgrass plant, has been developed and optimized for in vitro experiments. The model soil community grows reproducibly between replicates and experiments, with a high community α-diversity being achieved through growth in low-nutrient media and through the adjustment of the starting composition ratios for the growth of individual organisms. The community can additionally be cryopreserved with glycerol, allowing for easy replication and dissemination of this in vitro system. Furthermore, the SynCom also grows reproducibly in fabricated ecosystem devices (EcoFABs), demonstrating the application of this community to an existing in vitro plant-microbe system. EcoFABs allow reproducible research in model plant systems, offering the precise control of environmental conditions and the easy measurement of plant microbe metrics. Our results demonstrate the generation of a stable and diverse microbial SynCom for the rhizosphere that can be used with EcoFAB devices and can be shared between research groups for maximum reproducibility. IMPORTANCE Microbes associate with plants in distinct soil communities to the benefit of both the soil microbes and the plants. Interactions between plants and these microbes can improve plant growth and health and are therefore a field of study in sustainable agricultural research. In this study, a model community of 16 soil bacteria has been developed to further the reproducible study of plant-soil microbe interactions. The preservation of the microbial community has been optimized for dissemination to other research settings. Overall, this work will advance soil microbe research through the optimization of a robust, reproducible model community.}, } @article {pmid36471455, year = {2022}, author = {Lee, AH and Jha, AR and Do, S and Scarsella, E and Shmalberg, J and Schauwecker, A and Steelman, AJ and Honaker, RW and Swanson, KS}, title = {Dietary enrichment of resistant starches or fibers differentially alter the feline fecal microbiome and metabolite profile.}, journal = {Animal microbiome}, volume = {4}, number = {1}, pages = {61}, pmid = {36471455}, issn = {2524-4671}, support = {ILLU-538-937//USDA Hatch Grant/ ; }, abstract = {BACKGROUND: Cats are strict carnivores but possess a complex gastrointestinal (GI) microbial community that actively ferments dietary substrates that are not digested and reach the colon. The GI microbiota responses to dietary inclusion of resistant starches versus fibers have not been tested in cats. Thus, our objective was to evaluate the effects of diets enriched in resistant starch or fibers on the fecal characteristics, microbiome, and metabolite profiles of cats. Twelve healthy adult domestic shorthair cats (age = 9.6 ± 4.0 year; body weight = 3.9 ± 1.0 kg) were used in a replicated 3 × 3 Latin square design to test diets that were enriched with: (1) resistant starch (ERS), (2) a fiber-prebiotic-probiotic blend (FPPB), or (3) a fiber-prebiotic-probiotic blend + immune-modulating ingredients (iFPPB). In each 28-day period, 22 days of diet adaptation was followed by fecal and blood sample collection. Fecal samples were used for shotgun metagenomic sequencing. In addition, fecal and blood metabolite measurements and white blood cell stimulation was performed to assess immune function.

RESULTS: A total of 1690 bacterial species were identified, with 259 species differing between fiber-rich and ERS treatments. In comparison with fiber-rich treatments that increased diversity and promoted Firmicutes and Bacteroidetes populations, resistant starch reduced microbial diversity and fecal pH, led to a bloom in Actinobacteria, and modified Kyoto Encyclopedia of Genes and Genomes orthology (KO) terms pertaining to starch and sucrose metabolism, fatty acid biosynthesis and metabolism, epithelial cell signaling, among others. Resistant starch also differentially modified fecal metabolite concentrations with relevance to GI and overall host health (increased butyrate; decreased propionate and protein catabolites - branched-chain fatty acids; phenols and indoles; ammonia) and reduced blood cholesterol, which correlated strongly with microbial taxa and KO terms, and allowed for a high predictive efficiency of diet groups by random forest analysis.

CONCLUSION: Even though domestic cats and other carnivores evolved by eating low-carbohydrate diets rich in protein and fat, our results demonstrate that the feline microbiome and metabolite profiles are highly responsive to dietary change and in directions that are predictable.}, } @article {pmid36470909, year = {2022}, author = {Liu, J and Zhang, Q and Dong, YQ and Yin, J and Qiu, YQ}, title = {Diagnostic accuracy of metagenomic next-generation sequencing in diagnosing infectious diseases: a meta-analysis.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {21032}, pmid = {36470909}, issn = {2045-2322}, mesh = {Humans ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Communicable Diseases/diagnosis/genetics ; Sensitivity and Specificity ; Metagenome ; }, abstract = {Many common pathogens are difficult or impossible to detect using conventional microbiological tests. However, the rapid and untargeted nature of metagenomic next-generation sequencing (mNGS) appears to be a promising alternative. To perform a systematic review and meta-analysis of evidence regarding the diagnostic accuracy of mNGS in patients with infectious diseases. An electronic literature search of Embase, PubMed and Scopus databases was performed. Quality was assessed using the Quality Assessment of Diagnostic Accuracy Studies-2 tool. Summary receiver operating characteristics (sROC) and the area under the curve (AUC) were calculated; A random-effects model was used in cases of heterogeneity. A total of 20 papers were eligible for inclusion and synthesis. The sensitivity and specificity of diagnostic mNGS were 75% and 68%, respectively. The AUC from the SROC was 85%, corresponding to excellent performance. mNGS demonstrated satisfactory diagnostic performance for infections and yielded an overall detection rate superior to conventional methods.}, } @article {pmid36470490, year = {2023}, author = {Xiong, W and Wang, S and Jin, Y and Wu, Z and Liu, D and Su, H}, title = {Insights into nitrogen and phosphorus metabolic mechanisms of algal-bacterial aerobic granular sludge via metagenomics: Performance, microbial community and functional genes.}, journal = {Bioresource technology}, volume = {369}, number = {}, pages = {128442}, doi = {10.1016/j.biortech.2022.128442}, pmid = {36470490}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; Nitrogen ; Phosphorus ; Extracellular Polymeric Substance Matrix ; Metagenomics ; Bioreactors/microbiology ; Bacteria/genetics ; *Microbiota ; Waste Disposal, Fluid ; Denitrification ; Aerobiosis ; }, abstract = {Aiming to propose the potential mechanism for the enhancement of nitrogen (N) and phosphorus (P) removal of algal-bacterial aerobic granular sludge (A-AGS), metagenomic analysis was applied to identify the metabolic pathways. The results showed that chemical oxygen demand, ammonia nitrogen, total N, and total P removal of A-AGS could reach to 94.5%, 97.5%, 78.1%, and 88.5%, respectively. Algae enriched the content of extracellular polymeric substance, which significantly promoted the formation of A-AGS. Further investigations in functional genes suggested that nitrification process (amo, nxr, hao, etc.), denitrification process (nir, nap, nor, etc.), and polyphosphate accumulation (ppk, ppk2, etc.) were enhanced greatly in A-AGS. Notably, genus Thauera was the dominant source of functional genes, which penetrated both in N and P metabolism. The higher N and P removal performance in A-AGS could be attributed to synergistic effect between bacteria and microalgae, which may provide the basic for the application in wastewater treatment.}, } @article {pmid36470452, year = {2023}, author = {Mao, G and Ji, M and Jiao, N and Su, J and Zhang, Z and Liu, K and Chen, Y and Liu, Y}, title = {Monsoon affects the distribution of antibiotic resistome in Tibetan glaciers.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {317}, number = {}, pages = {120809}, doi = {10.1016/j.envpol.2022.120809}, pmid = {36470452}, issn = {1873-6424}, mesh = {*Anti-Bacterial Agents/pharmacology ; Tibet ; *Ice Cover ; Ecosystem ; Genes, Bacterial ; }, abstract = {Antibiotic-resistance gene (ARG) is a biological pollutant and is globally distributed due to increased anthropogenic activities. ARGs in the cryosphere have received increased attention due to global warming, and ARGs in glaciers are predicted to be released into downstream ecosystems during glacier melting. In this study, ARG distribution and influential factors were investigated in 85 samples from 21 Tibetan glaciers, covering snow, ice, and cryoconite habitats. The results revealed ARGs against 29 antibiotics in Tibetan glaciers, dominated by tetracycline, bacitracin, macrolide, and fluoroquinolone resistance. ARGs in snow exhibited biogeographic patterns influenced by atmospheric circulation. Specifically, monsoon-dominated glaciers exhibited a significantly higher abundance of ARGs than the westerly-dominated glaciers, which could be associated with higher antibiotic usage in the Indian subcontinent. Of the 3241 metagenome-assembled genomes obtained, 36.8% of which were identified as ARG hosts and 33.8% were multidrug-resistant. In addition, 90 ARGs were linked to mobile genetic elements (MGEs). 90.9% and 9.1% of MGEs were identified as plasmid and phage in 45 MAGs carrying both ARGs and MGEs. Our study suggests a greater risk of ARGs being released from the monsoon-dominated glaciers, which were the glaciers that melt at high rates and thus need to be carefully monitored.}, } @article {pmid36469554, year = {2022}, author = {Zhao, C and Goldman, M and Smith, BJ and Pollard, KS}, title = {Genotyping Microbial Communities with MIDAS2: From Metagenomic Reads to Allele Tables.}, journal = {Current protocols}, volume = {2}, number = {12}, pages = {e604}, pmid = {36469554}, issn = {2691-1299}, support = {R01 HL160862/HL/NHLBI NIH HHS/United States ; T32 GM067547/GM/NIGMS NIH HHS/United States ; }, mesh = {*Metagenome/genetics ; Genotype ; Alleles ; *Microbiota/genetics ; Nucleotides ; }, abstract = {The Metagenomic Intra-Species Diversity Analysis System 2 (MIDAS2) is a scalable pipeline that identifies single nucleotide variants and gene copy number variants in metagenomes using comprehensive reference databases built from public microbial genome collections (metagenotyping). MIDAS2 is the first metagenotyping tool with functionality to control metagenomic read mapping filters and to customize the reference database to the microbial community, features that improve the precision and recall of detected variants. In this article we present four basic protocols for the most common use cases of MIDAS2, along with supporting protocols for installation and use. In addition, we provide in-depth guidance on adjusting command line parameters, editing the reference database, optimizing hardware utilization, and understanding the metagenotyping results. All the steps of metagenotyping, from raw sequencing reads to population genetic analysis, are demonstrated with example data in two downloadable sequencing libraries of single-end metagenomic reads representing a mixture of multiple bacterial species. This set of protocols empowers users to accurately genotype hundreds of species in thousands of samples, providing rich genetic data for studying the evolution and strain-level ecology of microbial communities. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: Species prescreening Basic Protocol 2: Download MIDAS reference database Basic Protocol 3: Population single nucleotide variant calling Basic Protocol 4: Pan-genome copy number variant calling Support Protocol 1: Installing MIDAS2 Support Protocol 2: Command line inputs Support Protocol 3: Metagenotyping with a custom collection of genomes Support Protocol 4: Metagenotyping with advanced parameters.}, } @article {pmid36468881, year = {2022}, author = {Zhao, R and Farag, IF and Jørgensen, SL and Biddle, JF}, title = {Occurrence, Diversity, and Genomes of "Candidatus Patescibacteria" along the Early Diagenesis of Marine Sediments.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {24}, pages = {e0140922}, pmid = {36468881}, issn = {1098-5336}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; }, mesh = {RNA, Ribosomal, 16S/genetics/metabolism ; *Ecosystem ; Phylogeny ; *Bacteria ; Metagenome ; Geologic Sediments/microbiology ; }, abstract = {The phylum "Candidatus Patescibacteria" (or Candidate Phyla Radiation [CPR]) accounts for roughly one-quarter of microbial diversity on Earth, but the presence and diversity of these bacteria in marine sediments have been rarely charted. Here, we investigate the abundance, diversity, and metabolic capacities of CPR bacteria in three sediment sites (Mohns Ridge, North Pond, and Costa Rica Margin) with samples covering a wide range of redox zones formed during the early diagenesis of organic matter. Through metagenome sequencing, we found that all investigated sediment horizons contain "Ca. Patescibacteria" (0.4 to 28% of the total communities), which are affiliated with the classes "Ca. Paceibacteria," "Ca. Gracilibacteria," "Ca. Microgenomatia," "Ca. Saccharimonadia," "Ca. ABY1," and "Ca. WWE3." However, only a subset of the diversity of marine sediment "Ca. Patescibacteria," especially the classes "Ca. Paceibacteria" and "Ca. Gracilibacteria," can be captured by 16S rRNA gene amplicon sequencing with commonly used universal primers. We recovered 11 metagenome-assembled genomes (MAGs) of CPR from these sediments, most of which are novel at the family or genus level in the "Ca. Paceibacteria" class and are missed by the amplicon sequencing. While individual MAGs are confined to specific anoxic niches, the lack of capacities to utilize the prevailing terminal electron acceptors indicates that they may not be directly selected by the local redox conditions. These CPR bacteria lack essential biosynthesis pathways and may use a truncated glycolysis pathway to conserve energy as fermentative organotrophs. Our findings suggest that marine sediments harbor some novel yet widespread CPR bacteria during the early diagenesis of organic matter, which needs to be considered in population dynamics assessments in this vast environment. IMPORTANCE Ultrasmall-celled "Ca. Patescibacteria" have been estimated to account for one-quarter of the total microbial diversity on Earth, the parasitic lifestyle of which may exert a profound control on the overall microbial population size of the local ecosystems. However, their diversity and metabolic functions in marine sediments, one of the largest yet understudied ecosystems on Earth, remain virtually uncharacterized. By applying cultivation-independent approaches to a range of sediment redox zones, we reveal that "Ca. Patescibacteria" members are rare but widespread regardless of the prevailing geochemical conditions. These bacteria are affiliated with novel branches of "Ca. Patescibacteria" and have been largely missed in marker gene-based surveys. They do not have respiration capacity but may conserve energy by fermenting organic compounds from their episymbiotic hosts. Our findings suggest that these novel "Ca. Patescibacteria" are among the previously overlooked microbes in diverse marine sediments.}, } @article {pmid36468869, year = {2023}, author = {Pratama, A and Ishii, E and Kodama, T and Iida, T and Matsuda, S}, title = {The Xenogeneic Silencer Histone-Like Nucleoid-Structuring Protein Mediates the Temperature and Salinity-Dependent Regulation of the Type III Secretion System 2 in Vibrio parahaemolyticus.}, journal = {Journal of bacteriology}, volume = {205}, number = {1}, pages = {e0026622}, pmid = {36468869}, issn = {1098-5530}, mesh = {Humans ; *Type III Secretion Systems/genetics/metabolism ; Histones/genetics/metabolism ; *Vibrio parahaemolyticus/genetics ; Temperature ; Salinity ; Bacterial Proteins/metabolism ; Virulence Factors/genetics/metabolism ; Gene Expression Regulation, Bacterial ; }, abstract = {The marine bacterium Vibrio parahaemolyticus is a major seafood-borne pathogen that causes acute diarrhea in humans. A crucial virulence determinant of V. parahaemolyticus is the type III secretion system 2 (T3SS2), which is encoded on the Vibrio parahaemolyticus pathogenicity island (Vp-PAI), in which gene expression is dependent on environmental cues, such as temperature and salinity. This characteristic may implicate the adaptation of V. parahaemolyticus from its natural habitat to the human body environment during infection; however, the underlying mechanism remains unknown. Here, we describe the regulatory role of the histone-like nucleoid-structuring protein (H-NS), which is a xenogeneic silencing protein, in T3SS2 gene expression through the conditional silencing of the gene encoding a master regulator of Vp-PAI, VtrB. The hns deletion canceled the temperature- and salinity-dependent differential T3SS2 gene expression. H-NS bound to the vtrB promoter containing AT-rich sequences, and the binding sites partially overlapped the binding sites of two positive regulators of vtrB (i.e., VtrA and ToxR), which may block the transcriptional activation of vtrB. H-NS-family proteins multimerize along the DNA strand, forming stiffened filament and/or bridging DNA duplexes for its target silencing. In V. parahaemolyticus, mutations at conserved residues that are required for the multimerization of H-NS abolished the repressive activity on VtrB expression, supporting the contention that H-NS multimerization is also critical for vtrB silencing in V. parahaemolyticus. Taken together, these findings demonstrate the principal role of H-NS as a thermal and salt switch with sensory and regulatory properties for ensuring T3SS2 gene regulation in V. parahaemolyticus. IMPORTANCE In the major seafood-borne pathogen Vibrio parahaemolyticus, the type III secretion system 2 (T3SS2) is a major virulence factor that is responsible for the enterotoxicity of this bacterium. The expression of T3SS2 varies according to changes in temperature and salinity, but the mechanism via which T3SS2 expression is regulated in response to such physical cues remains unknown. Here, we report that H-NS, a xenogeneic silencer that is widespread in Gram-negative bacteria, modulates the entirety of T3SS2 gene expression through the transcriptional silencing of the gene encoding the T3SS2 master regulator VtrB in a temperature- and salinity-dependent manner. Thus, our findings provide insights into how this pathogen achieves the appropriate control of the expression of virulence genes in the transition between aquatic and human environments.}, } @article {pmid36468852, year = {2022}, author = {Velez-Cortes, F and Wang, H}, title = {Characterization and Spatial Mapping of the Human Gut Metasecretome.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0071722}, pmid = {36468852}, issn = {2379-5077}, support = {R01 AI132403/AI/NIAID NIH HHS/United States ; R01 DK118044/DK/NIDDK NIH HHS/United States ; R21 AI146817/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Bacteria/genetics ; Bacterial Proteins/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Phylogeny ; }, abstract = {Bacterially secreted proteins play an important role in microbial physiology and ecology in many environments, including the mammalian gut. While gut microbes have been extensively studied over the past decades, little is known about the proteins that they secrete into the gastrointestinal tract. In this study, we developed and applied a computational pipeline to a comprehensive catalog of human-associated metagenome-assembled genomes in order to predict and analyze the bacterial metasecretome of the human gut, i.e., the collection of proteins secreted out of the cytoplasm by human gut bacteria. We identified the presence of large and diverse families of secreted carbohydrate-active enzymes and assessed their phylogenetic distributions across different taxonomic groups, which revealed an enrichment in Bacteroidetes and Verrucomicrobia. By mapping secreted proteins to available metagenomic data from endoscopic sampling of the human gastrointestinal tract, we specifically pinpointed regions in the upper and lower intestinal tract along the lumen and mucosa where specific glycosidases are secreted by resident microbes. The metasecretome analyzed in this study constitutes the most comprehensive list of secreted proteins produced by human gut bacteria reported to date and serves as a useful resource for the microbiome research community. IMPORTANCE Bacterially secreted proteins are necessary for the proper functioning of bacterial cells and communities. Secreted proteins provide bacterial cells with the ability to harvest resources from the exterior, import these resources into the cell, and signal to other bacteria. In the human gut microbiome, these actions impact host health and allow the maintenance of a healthy gut bacterial community. We utilized computational tools to identify the major components of human gut bacterially secreted proteins and determined their spatial distribution in the gastrointestinal tract. Our analysis of human gut bacterial secreted proteins will allow a better understanding of the impact of gut bacteria on human health and represents a step toward identifying new protein functions with interesting applications in biomedicine and industry.}, } @article {pmid36468851, year = {2022}, author = {Doré, H and Leconte, J and Guyet, U and Breton, S and Farrant, GK and Demory, D and Ratin, M and Hoebeke, M and Corre, E and Pitt, FD and Ostrowski, M and Scanlan, DJ and Partensky, F and Six, C and Garczarek, L}, title = {Global Phylogeography of Marine Synechococcus in Coastal Areas Reveals Strong Community Shifts.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0065622}, pmid = {36468851}, issn = {2379-5077}, mesh = {*Synechococcus/genetics ; Phylogeography ; Seawater/microbiology ; Phylogeny ; Oceans and Seas ; Phytoplankton ; }, abstract = {Marine Synechococcus comprise a numerically and ecologically prominent phytoplankton group, playing a major role in both carbon cycling and trophic networks in all oceanic regions except in the polar oceans. Despite their high abundance in coastal areas, our knowledge of Synechococcus communities in these environments is based on only a few local studies. Here, we use the global metagenome data set of the Ocean Sampling Day (June 21[st], 2014) to get a snapshot of the taxonomic composition of coastal Synechococcus communities worldwide, by recruitment on a reference database of 141 picocyanobacterial genomes, representative of the whole Prochlorococcus, Synechococcus, and Cyanobium diversity. This allowed us to unravel drastic community shifts over small to medium scale gradients of environmental factors, in particular along European coasts. The combined analysis of the phylogeography of natural populations and the thermophysiological characterization of eight strains, representative of the four major Synechococcus lineages (clades I to IV), also brought novel insights about the differential niche partitioning of clades I and IV, which most often co-dominate the Synechococcus community in cold and temperate coastal areas. Altogether, this study reveals several important characteristics and specificities of the coastal communities of Synechococcus worldwide. IMPORTANCE Synechococcus is the second most abundant phytoplanktonic organism on Earth, and its wide genetic diversity allowed it to colonize all the oceans except for polar waters, with different clades colonizing distinct oceanic niches. In recent years, the use of global metagenomics data sets has greatly improved our knowledge of "who is where" by describing the distribution of Synechococcus clades or ecotypes in the open ocean. However, little is known about the global distribution of Synechococcus ecotypes in coastal areas, where Synechococcus is often the dominant phytoplanktonic organism. Here, we leverage the global Ocean Sampling Day metagenomics data set to describe Synechococcus community composition in coastal areas worldwide, revealing striking community shifts, in particular along the coasts of Europe. As temperature appears as an important driver of the community composition, we also characterize the thermal preferenda of 8 Synechococcus strains, bringing new insights into the adaptation to temperature of the dominant Synechococcus clades.}, } @article {pmid36468273, year = {2023}, author = {Hino, A and Fukushima, K and Kusakabe, S and Ueda, T and Sudo, T and Fujita, J and Motooka, D and Takeda, AK and Shinozaki, NO and Watanabe, S and Yokota, T and Shibayama, H and Nakamura, S and Hosen, N}, title = {Prolonged gut microbial alterations in post-transplant survivors of allogeneic haematopoietic stem cell transplantation.}, journal = {British journal of haematology}, volume = {201}, number = {4}, pages = {725-737}, doi = {10.1111/bjh.18574}, pmid = {36468273}, issn = {1365-2141}, mesh = {Humans ; *Gastrointestinal Microbiome ; Dysbiosis/complications ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Patient Discharge ; *Graft vs Host Disease/microbiology ; *Bronchiolitis Obliterans Syndrome ; }, abstract = {Dysbiosis of the gut microbiota has been reported to increase early complications after allogeneic haematopoietic stem cell transplantation (allo-HSCT). However, it remains unclear whether gut microbial alterations persist during late complications, such as chronic graft-versus-host disease (cGVHD) or secondary cancers. Here, we analysed the gut microbiota of 59 patients who survived for 1-21.7 years (median, 6.4 years) after allo-HSCT. Long-term survivors showed lower gut microbial diversity than the age- and sex-matched healthy controls. This decreased diversity was reflected in the reduced abundance of the butyrate-producing bacteria. Patients with a history of grade 3 acute graft-versus-host disease (aGVHD) exhibited higher Veillonella abundance than patients with a history of grade 1-2 or non-aGVHD cases. The abundance of Faecalibacterium showed no decrease only in limited cGVHD cases. Additionally, the microbial structure in the secondary cancer group was significantly different (p < 0.05) from that in the non-secondary cancer group. This study is the first to show that microbial dysbiosis is present over a 10-year lifetime after discharge following allo-HSCT. Our results suggest that these prolonged gut microbial alterations may be associated with the development and exacerbation of late complications in post-transplant survivors.}, } @article {pmid36468051, year = {2022}, author = {Onohuean, H and Akiyode, AO and Akiyode, O and Igbinoba, SI and Alagbonsi, AI}, title = {Epidemiology of neurodegenerative diseases in the East African region: A meta-analysis.}, journal = {Frontiers in neurology}, volume = {13}, number = {}, pages = {1024004}, pmid = {36468051}, issn = {1664-2295}, abstract = {INTRODUCTION: There is a scarcity of epidemiological data on neurodegenerative diseases (NDs) in East Africa. This meta-analysis provides the regional prevalence of NDs, their contributing factors, and evidence of change over time concerning gender per age or year.

METHODS: Articles were retrieved from electronic databases following the PRISMA standard.

RESULTS: Forty-two studies were reviewed, and 25 were meta-analyzed with a random-effects model. The pool estimate proportion of 15.27%, 95% CI (0.09-0.23) (I[2] = 98.25%), (Q = 1,369.15, p < 0.0001) among a population of 15,813 male/female and 1,257 with NDs. Epidemiological characteristics associated with NDs include Dyskinesias prevalence 55.4%, 95% CI (13.5; 90.9), I[2] (96%) and subsistence farming prevalence 11.3%, 95% CI (5.8; 20.9), I[2] (99%). Publication bias by Egger test was (z = 4.1913, p < 0.0001), while rank correlation test using Kendall's model was (tau = 0.1237, p = 0.3873). Heterogeneity (R[2] design = 5.23%, p design < 0.0001; R[2] size = 52.163%, p size < 0.001; and R[2] period = 48.13, p period < 0.0001. Covariates (R[2] design + size + period = 48.41%, p < 0.001).

CONCLUSION: There is a high prevalence of NDs in the East African region, which could impact life expectancy, morbidity, and quality of life. Thus, early screening and regular surveillance could assist in management strategies.}, } @article {pmid36467746, year = {2022}, author = {Zhao, D and Chong, Y and Hu, J and Zhou, X and Xiao, C and Chen, W}, title = {Proteomics and metagenomics reveal the relationship between microbial metabolism and protein hydrolysis in dried fermented grass carp using a lactic acid bacteria starter culture.}, journal = {Current research in food science}, volume = {5}, number = {}, pages = {2316-2328}, pmid = {36467746}, issn = {2665-9271}, abstract = {A microbial starter culture is expected to improve the quality of traditional fermented fish products. Lactobacillus plantarum was selected for grass carp fermentation due to its high proteolytic activity. To investigate its effects on muscle proteolysis of dried fermented fish, the protein profile and microbial community were analysed by using proteomics and metabolomics. The myofibrillar protein and collagen profiles showed remarkable variation after processing, changes that were related to the development of flavour and texture in fish samples. The starter culture had a marked effect on the microbial composition. Macrococcus and Staphylococcus were the dominant genera, with a relative abundance of 24.79% and 12.53%, respectively. There were significant correlations (P < 0.05) between the dominant genera and the major peptidase genes and quality-related proteins. These findings suggest that microbial activity is involved in proteolysis and affects the flavour and texture of dried fermented fish.}, } @article {pmid36467737, year = {2022}, author = {Jeon, J and Kang, S and Hur, JK and Rho, M}, title = {Metagenomic characterization of sphingomyelinase C in the microbiome of humans and environments.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1015706}, pmid = {36467737}, issn = {2235-2988}, mesh = {Humans ; *Metagenome ; Sphingomyelin Phosphodiesterase/genetics ; Metagenomics ; *Microbiota ; Genomics ; }, abstract = {Bacterial sphingomyelinases (SMases) hydrolyze sphingomyelin and play an important role in membrane dynamics and the host immune system. While the number of sequenced genomes and metagenomes is increasing, a limited number of experimentally validated SMases have been reported, and the genomic diversity of SMases needs to be elucidated extensively. This study investigated the sequence and structural characteristics of SMases in bacterial genomes and metagenomes. Using previously identified SMases, such as the β-toxin of Staphylococcus aureus, we identified 276 putative SMases and 15 metagenomic SMases by a sequence homology search. Among the predicted metagenomic SMases, six non-redundant metagenomic SMases (M-SMase1-6) were selected for further analysis. The predicted SMases were confirmed to contain highly conserved residues in the central metal-binding site; however, the edge metal-binding site showed high diversity according to the taxon. In addition, protein structure modeling of metagenomic SMases confirmed structural conservation of the central metal-binding site and variance of the edge metal-binding site. From the activity assay on M-SMase2 and M-SMase5, we found that they displayed sphingomyelinase activity compared to Bacillus cereus SMase. This study elucidates a comprehensive genomic characterization of SMases and provides insight into the sequence-structure-activity relationship.}, } @article {pmid36467639, year = {2022}, author = {Huang, H}, title = {Captivity and geography influence the antibiotic resistome of non-human primates.}, journal = {Frontiers in veterinary science}, volume = {9}, number = {}, pages = {1020276}, pmid = {36467639}, issn = {2297-1769}, abstract = {INTRODUCTION: Antibiotic resistance poses a serious threat for animals and humans health worldwide. Yet a comprehensive exploration of the influence of captivity and geography on non-human primate (NPH) gut antibiotic resistance remains incomplete.

METHODS: In this study, 131 metagenomic sequencing datasets of five species of NHPs included different regions and lifestyles were selected to perform the antibiotic resistance analysis.

RESULTS: Nineteen related resistance antibiotics and 325 antibiotic resistance genes (ARGs) were obtained. A significantly higher abundance and diversity index of ARGs in the captive NHPs than in the wild was found but not for all of the samples. The biomarker-tracking of ARGs analysis identified key ARGs related to aminoglycoside resistance genes and tetracycline resistance genes.

DISCUSSION: These results suggest that captivity and geography changes associated with human activities can lead to marked changes in the ecology of the NHP gut flora ARGs.}, } @article {pmid36467581, year = {2022}, author = {Zhou, J and Ouyang, J and Gao, Z and Qin, H and Jun, W and Shi, T}, title = {MagMD: Database summarizing the metabolic action of gut microbiota to drugs.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {6427-6430}, pmid = {36467581}, issn = {2001-0370}, abstract = {UNLABELLED: An increasing number of studies have reported that microbiome can affect drug response by altering pharmacokinetics and pharmacodynamics of formation of toxic metabolites. With the development of metagenomic sequencing, gut microbial composition as well as the metabolic function are drawing more and more attention for the patient stratification. The established microbiota databases provide useful information about the gut microbe-drug interactions. However, these databases generally lacked the detailed effects on substance and the metabolites, which are helpful in elucidating the mechanisms underlying drug biotransformation and personalized medicine. To address these issues, in this study, we developed Metabolic action of gut Microbiota to Drugs (MagMD), a database and a web-service covering 32, 678 records of interactions between 2,146 gut microbes, 36 enzymes and 219 substrates (mainly drugs). The detailed annotations for each entry, including the taxonomic level of microbes, the molecular form and PubChem ID of drugs from PubChem Compound Database, types of microbial secreted enzymes and the original reference links can also be accessed from the web service.

MagMD is a publicly available resource, constantly updated. It has an intuitive web interface and can be freely accessed at http://www.unimd.org/magmd.}, } @article {pmid36466712, year = {2022}, author = {Pham, DT and Phan, V}, title = {Representing bacteria with unique genomic signatures.}, journal = {Frontiers in big data}, volume = {5}, number = {}, pages = {1018356}, pmid = {36466712}, issn = {2624-909X}, abstract = {Classifying or identifying bacteria in metagenomic samples is an important problem in the analysis of metagenomic data. This task can be computationally expensive since microbial communities usually consist of hundreds to thousands of environmental microbial species. We proposed a new method for representing bacteria in a microbial community using genomic signatures of those bacteria. With respect to the microbial community, the genomic signatures of each bacterium are unique to that bacterium; they do not exist in other bacteria in the community. Further, since the genomic signatures of a bacterium are much smaller than its genome size, the approach allows for a compressed representation of the microbial community. This approach uses a modified Bloom filter to store short k-mers with hash values that are unique to each bacterium. We show that most bacteria in many microbiomes can be represented uniquely using the proposed genomic signatures. This approach paves the way toward new methods for classifying bacteria in metagenomic samples.}, } @article {pmid36466696, year = {2022}, author = {Yap, M and O'Sullivan, O and O'Toole, PW and Cotter, PD}, title = {Development of sequencing-based methodologies to distinguish viable from non-viable cells in a bovine milk matrix: A pilot study.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1036643}, pmid = {36466696}, issn = {1664-302X}, abstract = {Although high-throughput DNA sequencing-based methods have been of great value for determining the composition of microbial communities in various environments, there is the potential for inaccuracies arising from the sequencing of DNA from dead microorganisms. In this pilot study, we compared different sequencing-based methods to assess their relative accuracy with respect to distinguishing between viable and non-viable cells, using a live and heat-inactivated model community spiked into bovine milk. The methods used were shotgun metagenomics with and without propidium monoazide (PMA) treatment, RNA-based 16S rRNA sequencing and metatranscriptomics. The results showed that methods were generally accurate, though significant differences were found depending on the library types and sequencing technologies. Different molecular targets were the basis for variations in the results generated using different library types, while differences in the derived composition data from Oxford Nanopore Technologies-and Illumina-based sequencing likely reflect a combination of different sequencing depths, error rates and bioinformatics pipelines. Although PMA was successfully applied in this study, further optimisation is required before it can be applied in a more universal context for complex microbiomes. Overall, these methods show promise and represent another important step towards the ultimate establishment of approaches that can be applied to accurately identify live microorganisms in milk and other food niches.}, } @article {pmid36466687, year = {2022}, author = {de Francisco Martínez, P and Morgante, V and González-Pastor, JE}, title = {Isolation of novel cold-tolerance genes from rhizosphere microorganisms of Antarctic plants by functional metagenomics.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1026463}, pmid = {36466687}, issn = {1664-302X}, abstract = {The microorganisms that thrive in Antarctica, one of the coldest environments on the planet, have developed diverse adaptation mechanisms to survive in these extreme conditions. Through functional metagenomics, in this work, 29 new genes related to cold tolerance have been isolated and characterized from metagenomic libraries of microorganisms from the rhizosphere of two Antarctic plants. Both libraries were hosted in two cold-sensitive strains of Escherichia coli: DH10B ΔcsdA and DH10B ΔcsdA Δrnr. The csdA gene encodes a DEAD-box RNA helicase and rnr gene encodes an exoribonuclease, both essential for cold-adaptation. Cold-tolerance tests have been carried out in solid and liquid media at 15°C. Among the cold-tolerance genes identified, 12 encode hypothetical and unknown proteins, and 17 encode a wide variety of different proteins previously related to other well-characterized ones involved in metabolism reactions, transport and membrane processes, or genetic information processes. Most of them have been connected to cold-tolerance mechanisms. Interestingly, 13 genes had no homologs in E. coli, thus potentially providing entirely new adaptation strategies for this bacterium. Moreover, ten genes also conferred resistance to UV-B radiation, another extreme condition in Antarctica.}, } @article {pmid36466681, year = {2022}, author = {Nie, L and Wei, T and Cao, M and Lyu, Y and Wang, S and Feng, Z}, title = {Biosynthesis of coelulatin for the methylation of anthraquinone featuring HemN-like radical S-adenosyl-L-methionine enzyme.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1040900}, pmid = {36466681}, issn = {1664-302X}, abstract = {Bacterial aromatic polyketides are usually biosynthesized by the type II polyketide synthase (PKS-II) system. Advances in deoxyribonucleic acid (DNA) sequencing, informatics, and biotechnologies have broadened opportunities for the discovery of aromatic polyketides. Meanwhile, metagenomics is a biotechnology that has been considered as a promising approach for the discovery of novel natural products from uncultured bacteria. Here, we cloned a type II polyketide biosynthetic gene cluster (BGC) from the soil metagenome, and the heterologous expression of this gene cluster in Streptomyces coelicolor M1146 resulted in the production of three anthraquinones, two of which (coelulatins 2 and 3) had special hydroxymethyl and methyloxymethyl modifications at C2 of the polyketide scaffold. Gene deletion and in vitro biochemical characterization indicated that the HemN-like radical S-adenosyl-L-methionine (SAM) enzyme CoeI exhibits methylation and is involved in C2 modification.}, } @article {pmid36466648, year = {2022}, author = {Tohya, M and Otsuka, T and Yoshimoto, J and Ishizaki, Y and Kirikae, T and Watanabe, S}, title = {Case report: Whole genome sequence of Clostridium perfringens JUM001 causing acute emphysematous cholecystitis.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1066880}, pmid = {36466648}, issn = {1664-302X}, abstract = {A strain of Clostridium perfringens was isolated from the bile sample of a patient with emphysematous cholecystitis who underwent a laparoscopic cholecystectomy, followed by treatment with meropenem and recovery. Metagenomic analysis of the bile sample showed that 99.73% of the bile microbiota consisted of C. perfringens, indicating that C. perfringens JUM001 was the causative pathogen of acute emphysematous cholecystitis in this patient. Complete genome sequencing showed that C. perfringens JUM001 contained a circular chromosome of 3,231,023 bp and two circular plasmids, pJUM001-1 of 49,289 bp and pJUM001-2 of 47,855 bp. JUM001 was found to possess a typing toxin gene, plc, but no other typing toxin genes, indicating that its toxinotype is type A. The plasmids pJUM001-1 and pJUM001-2 belonged to the pCP13-like and pCW3-like families of plasmids, respectively, which are characteristic conjugative and archetypical plasmids of C. perfringens. Phylogenetic analysis showed that JUM001 was closely related to C. perfringens strain JXNC-DD isolated from a dog in China. To our knowledge, this is the first report of whole-genome sequences of a clinical isolate of C. perfringens causing acute emphysematous cholecystitis.}, } @article {pmid36466640, year = {2022}, author = {Dong, Y and Zhang, ZR and Mishra, S and Wong, AC and Huang, JF and Wang, B and Peng, YQ and Gao, J}, title = {Diversity and metabolic potentials of microbial communities associated with pollinator and cheater fig wasps in fig-fig wasp mutualism system.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1009919}, pmid = {36466640}, issn = {1664-302X}, abstract = {Microbial symbionts can influence a myriad of insect behavioral and physiological traits. However, how microbial communities may shape or be shaped by insect interactions with plants and neighboring species remains underexplored. The fig-fig wasp mutualism system offers a unique model to study the roles of microbiome in the interactions between the plants and co-habiting insects because a confined fig environment is shared by two fig wasp species, the pollinator wasp (Eupristina altissima and Eupristina verticillata) and the cheater wasp (Eupristina sp1 and Eupristina sp2). Here, we performed whole genome resequencing (WGS) on 48 individual fig wasps (Eupristina spp.) from Yunnan, China, to reveal the phylogenetic relationship and genetic divergence between pollinator and congeneric cheater wasps associated with the Ficus trees. We then extracted metagenomic sequences to explore the compositions, network structures, and functional capabilities of microbial communities associated with these wasps. We found that the cheaters and pollinators from the same fig species are sister species, which are highly genetically divergent. Fig wasps harbor diverse but stable microbial communities. Fig species dominate over the fig wasp genotype in shaping the bacterial and fungal communities. Variation in microbial communities may be partially explained by the filtering effect from fig and phylogeny of fig wasps. It is worth noting that cheaters have similar microbial communities to their sister pollinators, which may allow cheaters to coexist and gain resources from the same fig species. In terms of metabolic capabilities, some bacteria such as Desulfovibrio and Lachnospiraceae are candidates involved in the nutritional uptake of fig wasps. Our results provide novel insights into how microbiome community and metabolic functions may couple with the fig-wasp mutualistic systems.}, } @article {pmid36466637, year = {2022}, author = {Elokil, AA and Chen, W and Mahrose, K and Elattrouny, MM and Abouelezz, KFM and Ahmad, HI and Liu, HZ and Elolimy, AA and Mandouh, MI and Abdelatty, AM and Li, S}, title = {Early life microbiota transplantation from highly feed-efficient broiler improved weight gain by reshaping the gut microbiota in laying chicken.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1022783}, pmid = {36466637}, issn = {1664-302X}, abstract = {Starting phase of laying chicken life is the building stone for rearing and production stages. Since, fecal microbial transplantation (FMT) regulates the gut microbial diversity and affects the productive performance of the bird. The aim of this study is to evaluate the effect of FMT from feed-efficient broiler chicken could program the diversity of gut microbiota and growth of recipient native slow growing egg-laying chicks. For this, a total of 150 (one-day-old) Jing Hong chicks were randomly assigned into two groups, each group consisted of 5 replicates (n = 15 bird/ replicate). The control group (CON) and FMT recipient birds (FMT) fed on basal diet, the FMT group received an oral daily dose of FMT prepared from Cobb-500 chickens. The FMT performed from the 1d to 28d of age, through the experimental period, feed intake and body weight were recorded weekly. At the end of a 28-day trial, carcass traits were assessed and cecal samples were collected for microbiome assessment via 16S rRNA-based metagenomic analysis to characterize the diversity and functions of microbial communities. The data were statistically analyzed using R software. Body weight and body weight gain increased, and FCR decreased (p = 0.01) in FMT group. The relative abundance of Firmicutes and the Firmicutes/Bacteroidetes (F/B) ratio were increased due to FMT administration (p = 0.01). A higher relative abundance of Lactobacillus, Lactococcus, and Bifidobacterium were presented in the FMT group. Meanwhile, Enterococcus, Helicobacter, and Bacteroides were more abundant in the CON group (p < 0.01). Kyoto encyclopedia of genes and genomes (KEGG) pathways for microbial functions regarding amino acid metabolism, secondary metabolites biosynthesis, carbohydrate metabolism, energy metabolism, and enzyme families, cofactors, and vitamins were significantly annotated in the FMT group. Overall, FMT administration from the donor of highly feed-efficient broilers improved weight gain by reshaping a distinct gut microbiome, which may be related to the metabolism and health in the recipients laying chicks, providing new insight on the application of the FMT technique for early life programming of laying chickens.}, } @article {pmid36466635, year = {2022}, author = {Kim, M and Rhee, C and Wells, M and Shin, J and Lee, J and Shin, SG}, title = {Key players in syntrophic propionate oxidation revealed by metagenome-assembled genomes from anaerobic digesters bioaugmented with propionic acid enriched microbial consortia.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {968416}, pmid = {36466635}, issn = {1664-302X}, abstract = {Propionic acid (HPr) is frequently accumulated in anaerobic digesters due to its thermodynamically unfavorable degradation reaction. Here, we identify key players in HPr oxidation and organic overloading recovery from metagenome-assembled genomes (MAGs) recovered from anaerobic digesters inoculated with HPr-enriched microbial consortia before initiating organic overloading. Two independent HPr-enrichment cultures commonly selected two uncultured microorganisms represented with high relative abundance: Methanoculleus sp002497965 and JABUEY01 sp013314815 (a member of the Syntrophobacteraceae family). The relative abundance of JABUEY01 sp013314815 was 60 times higher in bioaugmented bioreactors compared to their unaugmented counterparts after recovery from organic overloading. Genomic analysis of JABUEY01 sp013314815 revealed its metabolic potential for syntrophic propionate degradation when partnered with hydrogenotrophic methanogens (e.g., Methanoculleus sp002497965) via the methylmalonyl-CoA pathway. Our results identified at least two key species that are responsible for efficient propionate removal and demonstrate their potential applications as microbial cocktails for stable AD operation.}, } @article {pmid36466423, year = {2022}, author = {Grundler, F and Viallon, M and Mesnage, R and Ruscica, M and von Schacky, C and Madeo, F and Hofer, SJ and Mitchell, SJ and Croisille, P and Wilhelmi de Toledo, F}, title = {Long-term fasting: Multi-system adaptations in humans (GENESIS) study-A single-arm interventional trial.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {951000}, pmid = {36466423}, issn = {2296-861X}, abstract = {UNLABELLED: Fasting provokes fundamental changes in the activation of metabolic and signaling pathways leading to longer and healthier lifespans in animal models. Although the involvement of different metabolites in fueling human fasting metabolism is well known, the contribution of tissues and organs to their supply remains partly unclear. Also, changes in organ volume and composition remain relatively unexplored. Thus, processes involved in remodeling tissues during fasting and food reintroduction need to be better understood. Therefore, this study will apply state-of-the-art techniques to investigate the effects of long-term fasting (LF) and food reintroduction in humans by a multi-systemic approach focusing on changes in body composition, organ and tissue volume, lipid transport and storage, sources of protein utilization, blood metabolites, and gut microbiome profiles in a single cohort. This is a prospective, single-arm, monocentric trial. One hundred subjects will be recruited and undergo 9 ± 3 day-long fasting periods (250 kcal/day). We will assess changes in the composition of organs, bones and blood lipid profiles before and after fasting, as well as high-density lipoprotein (HDL) transport and storage, untargeted metabolomics of peripheral blood mononuclear cells (PBMCs), protein persulfidation and shotgun metagenomics of the gut microbiome. The first 32 subjects, fasting for 12 days, will be examined in more detail by magnetic resonance imaging (MRI) and spectroscopy to provide quantitative information on changes in organ volume and function, followed by an additional follow-up examination after 1 and 4 months. The study protocol was approved by the ethics board of the State Medical Chamber of Baden-Württemberg on 26.07.2021 and registered at ClinicalTrials.gov (NCT05031598). The results will be disseminated through peer-reviewed publications, international conferences and social media.

CLINICAL TRIAL REGISTRATION: [ClinicalTrials.gov], identifier [NCT05031598].}, } @article {pmid36466381, year = {2022}, author = {Subramaniam, S and Sabran, MR and Stanslas, J and Kirby, BP}, title = {Effect of aflatoxin B1 exposure on the progression of depressive-like behavior in rats.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {1032810}, pmid = {36466381}, issn = {2296-861X}, abstract = {While it is well documented that aflatoxin B1 (AFB1); one of the most toxic food contaminants is linked to the development of depression. However, the mechanism on how it affects the gut and brain health leading to depressive-like behavior remains unclear. This study was conducted to determine the effect of AFB1 on the progression of depressive-like behavior. Thirty-two (n = 32) male Sprague Dawley rats were randomly allocated into four groups: control, low-dose (5 μg AFB1/kg), high-dose (25 μg AFB1/kg) and positive control group; exposed on chronic unpredictable mild stress (CUMS). After 4 weeks of exposure, sucrose preference test (SPT) and force swim test (FST) were used to measure behavioral despair. Fecal samples were selectively cultured to profile the bacteria. Body weight and relative organs weights were compared among groups. AFB1 and CUMS caused reduction in body weight and food intake as well as increased relative weight of adrenal glands, liver, and brain. Rats in AFB1 and CUMS groups had suppressed sucrose preference and prolonged immobility time in FST, wherein this could indicate anhedonia. Besides, fecal count of Lactobacillus spp. was significantly low following AFB1 exposure, with increasing count of Bifidobacterium spp, in comparison to the control. Indeed, further biochemical analysis and metagenomic approach are warranted to explore the underlying mechanisms on the role of gut microbiota dysbiosis and dysregulation of gut-brain axis due to AFB1 neurotoxicity on the progression of depressive-like behavior.}, } @article {pmid36465813, year = {2022}, author = {Zhang, M and Huang, H and Yang, H and Yang, G and Wang, W and He, J and Wang, G and Yang, X and Zhai, Z}, title = {Recurrent Skin and Soft Tissue Infections Caused by Ureaplasma urealyticum in an Immunocompromised Adult Patient: A Case Report.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {6863-6868}, pmid = {36465813}, issn = {1178-6973}, abstract = {Ureaplasma urealyticum (U. urealyticum) is a normal commensal that colonizes the human genital tract and usually of low virulence; however, it can trigger serious extragenital infections in immunocompromised patient. In this case, a 48-year-old female immunocompromised patient with a four-year history of recurrent ulcer on extremities was presented to our hospital due to aggravation of lesions 10 months before. She was initially diagnosed as Pseudomonas aeruginosa infection secondary to lupus panniculitis and slightly responded to ceftazidime treatment; however, a new rash appeared on her left hip 16 days after admission, which was aggravated even under antibiotic treatment. After multiple negative cultures, U. urealyticum was identified in her left hip tissue using metagenomic next-generation sequencing (mNGS). U. urealyticum was also confirmed in her secretion samples from left hip, left thigh, right calf and uterine neck using mycoplasma culture and quantitative real-time polymerase chain reaction. Her lesions, especially the new rash, were positively responded to sensitive antibiotic treatment. To the best of our knowledge, this is the first case of U. urealyticum induced recurrent skin and soft-tissue infections (SSTIs) in an immunocompromised adult patient. This case suggests that the prevalence of this kind of infections may be underestimated because of the limitation of routine culture. mNGS may be considered to look for atypical pathogens to improve the antimicrobial treatment of complicated infections.}, } @article {pmid36465499, year = {2022}, author = {Zeller, M and Huson, DH}, title = {Comparison of functional classification systems.}, journal = {NAR genomics and bioinformatics}, volume = {4}, number = {4}, pages = {lqac090}, pmid = {36465499}, issn = {2631-9268}, abstract = {In microbiome analysis, functional profiling is based on assigning reads or contigs to terms or nodes in a functional classification system. There are a number of large, general-purpose functional classifications that are in use, such as eggNOG, KEGG, InterPro and SEED. Smaller, special-purpose classifications include CARD, EC, MetaCyc and VFDB. Here, we compare the different classifications in terms of their overlap, redundancy, structure and assignment rates. We also provide mappings between main concepts in different classifications. For the large classifications, we find that eggNOG performs the best with respect to sequence redundancy and structure, SEED has the cleanest hierarchy, whereas KEGG and InterPro:BP might be more informative for medical applications. We illustrate the practical assignment rates for different classifications using a number of metagenomic samples.}, } @article {pmid36464731, year = {2022}, author = {Ruscheweyh, HJ and Milanese, A and Paoli, L and Karcher, N and Clayssen, Q and Keller, MI and Wirbel, J and Bork, P and Mende, DR and Zeller, G and Sunagawa, S}, title = {Cultivation-independent genomes greatly expand taxonomic-profiling capabilities of mOTUs across various environments.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {212}, pmid = {36464731}, issn = {2049-2618}, mesh = {Swine ; Cattle ; Animals ; RNA, Ribosomal, 16S/genetics ; *Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; Soil ; }, abstract = {BACKGROUND: Taxonomic profiling is a fundamental task in microbiome research that aims to detect and quantify the relative abundance of microorganisms in biological samples. Available methods using shotgun metagenomic data generally depend on the deposition of sequenced and taxonomically annotated genomes, usually from cultures of isolated strains, in reference databases (reference genomes). However, the majority of microorganisms have not been cultured yet. Thus, a substantial fraction of microbial community members remains unaccounted for during taxonomic profiling, particularly in samples from underexplored environments. To address this issue, we developed the mOTU profiler, a tool that enables reference genome-independent species-level profiling of metagenomes. As such, it supports the identification and quantification of both "known" and "unknown" species based on a set of select marker genes.

RESULTS: We present mOTUs3, a command line tool that enables the profiling of metagenomes for >33,000 species-level operational taxonomic units. To achieve this, we leveraged the reconstruction of >600,000 draft genomes, most of which are metagenome-assembled genomes (MAGs), from diverse microbiomes, including soil, freshwater systems, and the gastrointestinal tract of ruminants and other animals, which we found to be underrepresented by reference genomes. Overall, two thirds of all species-level taxa lacked a reference genome. The cumulative relative abundance of these newly included taxa was low in well-studied microbiomes, such as the human body sites (6-11%). By contrast, they accounted for substantial proportions (ocean, freshwater, soil: 43-63%) or even the majority (pig, fish, cattle: 60-80%) of the relative abundance across diverse non-human-associated microbiomes. Using community-developed benchmarks and datasets, we found mOTUs3 to be more accurate than other methods and to be more congruent with 16S rRNA gene-based methods for taxonomic profiling. Furthermore, we demonstrate that mOTUs3 increases the resolution of well-known microbial groups into species-level taxa and helps identify new differentially abundant taxa in comparative metagenomic studies.

CONCLUSIONS: We developed mOTUs3 to enable accurate species-level profiling of metagenomes. Compared to other methods, it provides a more comprehensive view of prokaryotic community diversity, in particular for currently underexplored microbiomes. To facilitate comparative analyses by the research community, it is released with >11,000 precomputed profiles for publicly available metagenomes and is freely available at: https://github.com/motu-tool/mOTUs . Video Abstract.}, } @article {pmid36464700, year = {2022}, author = {Cohen, Y and Borenstein, E}, title = {The microbiome's fiber degradation profile and its relationship with the host diet.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {266}, pmid = {36464700}, issn = {1741-7007}, support = {2435/19//Israel Science Foundation/ ; }, mesh = {Humans ; Dietary Fiber ; Diet ; *Gastrointestinal Microbiome ; *Microbiota ; Metagenome ; }, abstract = {BACKGROUND: The relationship between the gut microbiome and diet has been the focus of numerous recent studies. Such studies aim to characterize the impact of diet on the composition of the microbiome, as well as the microbiome's ability to utilize various compounds in the diet and produce metabolites that may be beneficial for the host. Consumption of dietary fibers (DFs)-polysaccharides that cannot be broken down by the host's endogenous enzymes and are degraded primarily by members of the microbiome-is known to have a profound effect on the microbiome. Yet, a comprehensive characterization of microbiome compositional and functional shifts in response to the consumption of specific DFs is still lacking.

RESULTS: Here, we introduce a computational framework, coupling metagenomic sequencing with careful annotation of polysaccharide degrading enzymes and DF structures, for inferring the metabolic ability of a given microbiome sample to utilize a broad catalog of DFs. We demonstrate that the inferred fiber degradation profile (IFDP) generated by our framework accurately reflects the dietary habits of various hosts across four independent datasets. We further demonstrate that IFDPs are more tightly linked to the host diet than commonly used taxonomic and functional microbiome-based profiles. Finally, applying our framework to a set of ~700 metagenomes that represents large human population cohorts from 9 different countries, we highlight intriguing global patterns linking DF consumption habits with microbiome capacities.

CONCLUSIONS: Combined, our findings serve as a proof-of-concept for the use of DF-specific analysis for providing important complementary information for better understanding the relationship between dietary habits and the gut microbiome.}, } @article {pmid36464258, year = {2022}, author = {Pang, CM and Yang, XL and Wang, Y and Zhai, H and Miao, F and Zhang, SM}, title = {[Metagenomic sequencing for diagnosis of sparganosis mansoni: a case report].}, journal = {Zhongguo xue xi chong bing fang zhi za zhi = Chinese journal of schistosomiasis control}, volume = {34}, number = {5}, pages = {556-558}, doi = {10.16250/j.32.1374.2022035}, pmid = {36464258}, issn = {1005-6661}, mesh = {Humans ; *Sparganosis/diagnosis/surgery ; Hospitals ; }, abstract = {The patient was found to develop a migrating mass in the lower abdomen without any known cause in 2000, and the cause had not been identified following multiple diagnoses since then. The mass was found to migrate to the left anterior axillary regions on August 11, 2020. Then, three segments of incomplete white worms were resected through minimally invasive surgery, and metagenomic sequencing revealed sparganosis mansoni. After surgical resection of complete worms was performed on October 21, 2021, the case was cured and discharged from the hospital. Follow-up revealed satisfactory outcomes and no new mass was found throughout the body.}, } @article {pmid36464058, year = {2023}, author = {Xie, T and Zhang, Z and Zhang, D and Tian, Y and Nan, J and Feng, Y}, title = {Hydrothermal pretreatment and compound microbial agents promoting high-quality kitchen waste compost: Superior humification degree and reduction of odour.}, journal = {The Science of the total environment}, volume = {862}, number = {}, pages = {160657}, doi = {10.1016/j.scitotenv.2022.160657}, pmid = {36464058}, issn = {1879-1026}, mesh = {*Soil/chemistry ; *Composting ; Odorants/prevention & control ; Humic Substances/analysis ; Spectrometry, Fluorescence ; }, abstract = {Present study investigated the effects of hydrothermal pretreatment (HTP) and addition of compound microbial agent (CMA) on humification, odour generation and metabolism functions of bacterial communities during composting of kitchen waste (KW). Surprisingly, HTP and CMA addition treatment could promote the humification of compost and the control of odour units in contrast to the control (without HTP and CMA addition). The humic acid to fulvic acid ratio of end compost increase by 187.30 %, while humification index (HIX) increased by 18.87 %. 3D-EEM fluorescence spectroscopy of dissolved organic matter (DOM) demonstrated that it facilitated the synthesis of humified compounds and the decomposition of biodegradable compounds. Moreover, the SUVA254, SUVA280 and E253/E203 increased by 118.6 %, 115.25 % and 42.11 % after HTP and CMA addition indicating an increase in aromatic carbon abundance. VFAs had the higher degradation rate (84.91 %) than other treatments (57.46-77.72 %). Meanwhile, the main contributor to the malodorous odour was isovaleric acid, followed by butyric acid and acetic acid during composting. Mantel test indicated that the humification degree was significantly influenced by environmental parameters (temperature, pH, etc.) and metabolic products (HA, DOC and VFAs). Metagenomic analysis indicated that the biodegradation processes at the thermophilic stage were controlled mainly through genes involved in microbial metabolism. HTP and CMA addition was an eco-friendly and efficient strategy to reduce odour emission and improve the compost quality.}, } @article {pmid36464023, year = {2023}, author = {Tian, S and Sun, X and Xiao, H and Zhou, Y and Huang, X and An, XL and Liu, C and Su, JQ}, title = {Evaluation of rice straw and its transformation products on norfloxacin degradation and antibiotic resistome attenuation during soil incorporation.}, journal = {Chemosphere}, volume = {313}, number = {}, pages = {137451}, doi = {10.1016/j.chemosphere.2022.137451}, pmid = {36464023}, issn = {1879-1298}, mesh = {*Anti-Bacterial Agents/pharmacology ; Soil ; Norfloxacin/pharmacology ; *Oryza/genetics ; Soil Microbiology ; Genes, Bacterial ; }, abstract = {Straw incorporation into reclaimed soils has been demonstrated to increase soil nutrients and has the potential to efficiently increase crop production. However, which incorporation mode is more helpful in the control of antibiotic resistance genes (ARGs) remains unknown. In this study, we systematically compared the occurrence of antibiotic resistome in norfloxacin contaminated soils amended with rice straw (RS) and the transformation products, biochar (RSB) and ash (RSA). RS significantly promoted the degradation of norfloxacin (0.0648 d[-1], 3 times faster than control), whereas RSB had little effect and RSA hindered the degradation. Based on metagenomic analysis, RS and RSB significantly reduced the ARGs relative abundance (0.1421 and 0.1991 compared to 0.2540 in control) at the end of soil incubation. Adonis test indicated that all of amendment treatments significantly affect the microbial communities in soils, whereas only RS and RSB significantly affect the variation of antibiotic resistome. Procrustes analysis confirmed the association of microbial communities and ARGs. Network analysis further revealed that the reduction in Actinobacteria was the main reason for the general decrease of ARGs relative abundance during soil incorporation, whereas Proteobacteria and Bacteroidetes were responsible for temporary promotion of ARGs in RS and RSB at the early stage. Finally, scientifically setting up the usage of rice straw and optimizing the preparation process of biochar are suggested for the synchronous control of the risk of antibiotics and ARGs during soil incorporation.}, } @article {pmid36463869, year = {2022}, author = {Chaunzwa, TL and Del Rey, MQ and Bitterman, DS}, title = {Clinical Informatics Approaches to Understand and Address Cancer Disparities.}, journal = {Yearbook of medical informatics}, volume = {31}, number = {1}, pages = {121-130}, pmid = {36463869}, issn = {2364-0502}, mesh = {Humans ; *Medical Informatics ; *Neoplasms/epidemiology/therapy ; Genomics ; Natural Language Processing ; Proteomics ; }, abstract = {OBJECTIVES: Disparities in cancer incidence and outcomes across race, ethnicity, gender, socioeconomic status, and geography are well-documented, but their etiologies are often poorly understood and multifactorial. Clinical informatics can provide tools to better understand and address these disparities by enabling high-throughput analysis of multiple types of data. Here, we review recent efforts in clinical informatics to study and measure disparities in cancer.

METHODS: We carried out a narrative review of clinical informatics studies related to cancer disparities and bias published from 2018-2021, with a focus on domains such as real-world data (RWD) analysis, natural language processing (NLP), radiomics, genomics, proteomics, metabolomics, and metagenomics.

RESULTS: Clinical informatics studies that investigated cancer disparities across race, ethnicity, gender, and age were identified. Most cancer disparities work within clinical informatics used RWD analysis, NLP, radiomics, and genomics. Emerging applications of clinical informatics to understand cancer disparities, including proteomics, metabolomics, and metagenomics, were less well represented in the literature but are promising future research avenues. Algorithmic bias was identified as an important consideration when developing and implementing cancer clinical informatics techniques, and efforts to address this bias were reviewed.

CONCLUSIONS: In recent years, clinical informatics has been used to probe a range of data sources to understand cancer disparities across different populations. As informatics tools become integrated into clinical decision-making, attention will need to be paid to ensure that algorithmic bias does not amplify existing disparities. In our increasingly interconnected medical systems, clinical informatics is poised to untap the full potential of multi-platform health data to address cancer disparities.}, } @article {pmid36463395, year = {2022}, author = {Zhu, LT and Huang, HN and Avellán-Llaguno, RD and Qin, Y and An, XL and Su, JQ and Huang, Q and Zhu, YG}, title = {Diverse functional genes harboured in extracellular vesicles from environmental and human microbiota.}, journal = {Journal of extracellular vesicles}, volume = {11}, number = {12}, pages = {e12292}, pmid = {36463395}, issn = {2001-3078}, mesh = {Humans ; *Microbiota/genetics ; *Extracellular Vesicles/genetics ; Metagenome/genetics ; Metagenomics ; Feces ; }, abstract = {Exchange of mobile functional genes within microbiota benefits the microbial community. However, the status of the mobile gene pool in environment is still largely unclear, impeding the understanding on the process of gene transfer in natural microbial communities. The release of extracellular vesicles (EVs) by diverse organisms has been proposed to be a vital way in the complex networks of interactions between microbes and their habitats. In this study, we hypothesized that microbial EVs encapsulating functional DNA are widely distributed in the environmental matrix. The prevalence, source and DNA cargoes of EVs in three types of typical microbial habitats were studied. High abundance of EVs comparable to the bacterial concentration was found in human faeces, wastewater and soil. Metagenomic analysis showed the diverse and differential taxonomy of EVs-associated DNA compared to source microbiome. An array of efficient EVs producing species was identified. A wide variety of mobile genes including glycoside hydrolase family 25 were enriched. Antibiotic resistance genes co-localizing with mobile genetic elements were abundant in the EVs. This study provides novel insights into the prevalent EVs as a reservoir for the mobile functional genes in the natural environment.}, } @article {pmid36462818, year = {2023}, author = {Bloomfield, SJ and Zomer, AL and O'Grady, J and Kay, GL and Wain, J and Janecko, N and Palau, R and Mather, AE}, title = {Determination and quantification of microbial communities and antimicrobial resistance on food through host DNA-depleted metagenomics.}, journal = {Food microbiology}, volume = {110}, number = {}, pages = {104162}, doi = {10.1016/j.fm.2022.104162}, pmid = {36462818}, issn = {1095-9998}, mesh = {Animals ; *Anti-Bacterial Agents ; RNA, Ribosomal, 16S/genetics ; Drug Resistance, Bacterial/genetics ; DNA ; *Microbiota ; Seafood ; Salmon ; }, abstract = {Food products carry bacteria unless specifically sterilised. These bacteria can be pathogenic, commensal or associated with food spoilage, and may also be resistant to antimicrobials. Current methods for detecting bacteria on food rely on culturing for specific bacteria, a time-consuming process, or 16S rRNA metabarcoding that can identify different taxa but not their genetic content. Directly sequencing metagenomes of food is inefficient as its own DNA vastly outnumbers the bacterial DNA present. We optimised host DNA depletion enabling efficient sequencing of food microbiota, thereby increasing the proportion of non-host DNA sequenced 13-fold (mean; range: 1.3-40-fold) compared to untreated samples. The method performed best on chicken, pork and leafy green samples which had high mean prokaryotic read proportions post-depletion (0.64, 0.74 and 0.74, respectively), with lower mean prokaryotic read proportions in salmon (0.50) and prawn samples (0.19). We show that bacterial compositions and concentrations of antimicrobial resistance (AMR) genes differed by food type, and that salmon metagenomes were influenced by the production/harvesting method. The approach described in this study is an efficient and effective method of identifying and quantifying the predominant bacteria and AMR genes on food.}, } @article {pmid36462768, year = {2023}, author = {Zhang, B and Zhang, N and He, A and Wang, C and Li, Z and Zhang, G and Xue, R}, title = {Carrier type affects anammox community assembly, species interactions and nitrogen conversion.}, journal = {Bioresource technology}, volume = {369}, number = {}, pages = {128422}, doi = {10.1016/j.biortech.2022.128422}, pmid = {36462768}, issn = {1873-2976}, mesh = {*Nitrogen ; *Anaerobic Ammonia Oxidation ; Bioreactors ; Oxidation-Reduction ; Metagenomics ; Anaerobiosis ; Denitrification ; }, abstract = {The impacts of carrier type on anammox community assembly, species interactions and nitrogen conversion were studied in this work. It was found that in addition to shared species with higher abundance, different carrier types recruited rare species by imposing selection pressure. Results from co-occurrence networks revealed that carrier type strongly influenced interactions between keystone species inhabiting within anammox biofilm through potentially inducing niche differences. Overall, elastic cubic sponges would lead to closer cooperation between different populations, whereas plastic hollow cylinders would trigger fiercer competition. Meanwhile, the results based on metagenomics sequencing showed carrier type significantly affected nitrogen conversion related genes abundances, and higher reads number was detected on the elastic cubic sponges. The information obtained in this work could provide some valuable information for the selection and optimization of carrier type in the anammox process.}, } @article {pmid36462677, year = {2023}, author = {Yang, J and Yu, Q and Su, W and Wang, S and Wang, X and Han, Q and Li, H}, title = {Metagenomics reveals that temperature predicts a small proportion of antibiotic resistomes and mobile genetic elements in polluted water.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {317}, number = {}, pages = {120793}, doi = {10.1016/j.envpol.2022.120793}, pmid = {36462677}, issn = {1873-6424}, mesh = {Animals ; *Genes, Bacterial ; *Bacteria/genetics ; Anti-Bacterial Agents ; Metagenomics ; Temperature ; Water ; Interspersed Repetitive Sequences ; }, abstract = {Climate warming multiplies the threat of antibiotic resistance genes (ARGs) to public health, but whether temperature may predict antibiotic resistomes in water environment remain unknown. Here, by metagenomic sequencing, we investigated the changes of resistome at five different temperature gradients (23, 26, 29, 32, and 35 °C) in polluted water by animal cadaver. Thirty ARG types including 668 subtypes were observed in our samples. Temperature significantly influenced ARG profiles and showed a negative correlation with ARG diversity. The ARG assembly process was dominated by a deterministic process (63.32%-95.08%) but showed a peak pattern with temperature. Notably, temperature may predict approximately 21% of ARGs and 36% of mobile genetic elements (MGEs), while most other ARGs or MGEs were insensitive to temperature. Three types (carbapenem, dicyclomycin, and diaminopyrimidine antibiotic) and 63 subtypes of ARGs that positively correlated with temperature were identified in the polluted water. Notably, we screened 21 subtypes of high-risk ARGs (bacA, mdtA, tetM, etc.) and 22 opportunistic pathogens (Aeromonas, Clostridium, Bacteroides, etc.) and found their positive co-occurrence with temperature, implying these potential biological or genetic pollutants may probably go up under global warming. Our study reveals the predictability of temperature on antibiotic resistance genes, providing a suitable approach to track the fate and spread of ARGs in water environment under climate warming.}, } @article {pmid36462475, year = {2023}, author = {Huang, Y and Wen, X and Li, J and Niu, Q and Tang, A and Li, Q}, title = {Metagenomic insights into role of red mud in regulating fate of compost antibiotic resistance genes mediated by both direct and indirect ways.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {317}, number = {}, pages = {120795}, doi = {10.1016/j.envpol.2022.120795}, pmid = {36462475}, issn = {1873-6424}, mesh = {*Genes, Bacterial ; *Composting ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Manure/microbiology ; }, abstract = {In this study, the amendment of red mud (RM) in dairy manure composting on the fate of antibiotic resistance genes (ARGs) by both direct (bacteria community, mobile genetic elements and quorum sensing) and indirect ways (environmental factors and antibiotics) was analyzed. The results showed that RM reduced the total relative abundances of 10 ARGs and 4 mobile genetic elements (MGEs). And the relative abundances of total ARGs and MGEs decreased by 53.48% and 22.30% in T (with RM added) on day 47 compared with day 0. Meanwhile, the modification of RM significantly increased the abundance of lsrK, pvdQ and ahlD in quorum quenching (QQ) and decreased the abundance of luxS in quorum sensing (QS) (P < 0.05), thereby attenuating the intercellular genes frequency of communication. The microbial community and network analysis showed that 25 potential hosts of ARGs were mainly related to Firmicutes, Proteobacteria and Actinobacteria. Redundancy analysis (RDA) and structural equation model (SEM) further indicated that RM altered microbial community structure by regulating antibiotic content and environmental factors (temperature, pH, moisture content and organic matter content), which then affected horizontal gene transfer (HGT) in ARGs mediated by QS and MGEs. These results provide new insights into the dissemination mechanism and removal of ARGs in composting process.}, } @article {pmid36461738, year = {2023}, author = {Ponlachantra, K and Suginta, W and Robinson, RC and Kitaoku, Y}, title = {AlphaFold2: A versatile tool to predict the appearance of functional adaptations in evolution: Profilin interactions in uncultured Asgard archaea: Profilin interactions in uncultured Asgard archaea.}, journal = {BioEssays : news and reviews in molecular, cellular and developmental biology}, volume = {45}, number = {2}, pages = {e2200119}, doi = {10.1002/bies.202200119}, pmid = {36461738}, issn = {1521-1878}, support = {JPMJCR19S5//JST CREST/ ; //Moore-Simons Project/ ; GBMF9743//Origin of the Eukaryotic Cell/ ; //Vidyasirimedhi Institute of Science and Technology (VISTEC)/ ; }, mesh = {*Archaea/metabolism ; *Profilins/genetics/metabolism ; Actins ; Phylogeny ; Furylfuramide/metabolism ; Eukaryota/metabolism ; }, abstract = {The release of AlphaFold2 (AF2), a deep-learning-aided, open-source protein structure prediction program, from DeepMind, opened a new era of molecular biology. The astonishing improvement in the accuracy of the structure predictions provides the opportunity to characterize protein systems from uncultured Asgard archaea, key organisms in evolutionary biology. Despite the accumulation in metagenomics-derived Asgard archaea eukaryotic-like protein sequences, limited structural and biochemical information have restricted the insight in their potential functions. In this review, we focus on profilin, an actin-dynamics regulating protein, which in eukaryotes, modulates actin polymerization through (1) direct actin interaction, (2) polyproline binding, and (3) phospholipid binding. We assess AF2-predicted profilin structures in their potential abilities to participate in these activities. We demonstrate that AF2 is a powerful new tool for understanding the emergence of biological functional traits in evolution.}, } @article {pmid36461662, year = {2023}, author = {Zbinden, ZD and Douglas, MR and Chafin, TK and Douglas, ME}, title = {Riverscape community genomics: A comparative analytical approach to identify common drivers of spatial structure.}, journal = {Molecular ecology}, volume = {32}, number = {24}, pages = {6743-6765}, doi = {10.1111/mec.16806}, pmid = {36461662}, issn = {1365-294X}, support = {DBI: 2010774//NSF Postdoctoral Research Fellowship/ ; }, mesh = {Humans ; *Ecosystem ; *Genetics, Population ; Genetic Variation/genetics ; Metagenomics ; Environment ; Rivers ; }, abstract = {Genetic differentiation among local groups of individuals, that is, genetic β-diversity, is a key component of population persistence related to connectivity and isolation. However, most genetic investigations of natural populations focus on a single species, overlooking opportunities for multispecies conservation plans to benefit entire communities in an ecosystem. We present an approach to evaluate genetic β-diversity within and among many species and demonstrate how this riverscape community genomics approach can be applied to identify common drivers of genetic structure. Our study evaluated genetic β-diversity in 31 co-distributed native stream fishes sampled from 75 sites across the White River Basin (Ozarks, USA) using SNP genotyping (ddRAD). Despite variance among species in the degree of genetic divergence, general spatial patterns were identified corresponding to river network architecture. Most species (N = 24) were partitioned into discrete subpopulations (K = 2-7). We used partial redundancy analysis to compare species-specific genetic β-diversity across four models of genetic structure: Isolation by distance (IBD), isolation by barrier (IBB), isolation by stream hierarchy (IBH), and isolation by environment (IBE). A significant proportion of intraspecific genetic variation was explained by IBH (x̄ = 62%), with the remaining models generally redundant. We found evidence for consistent spatial modularity in that gene flow is higher within rather than between hierarchical units (i.e., catchments, watersheds, basins), supporting the generalization of the stream hierarchy model. We discuss our conclusions regarding conservation and management and identify the 8-digit hydrologic unit (HUC) as the most relevant spatial scale for managing genetic diversity across riverine networks.}, } @article {pmid36461578, year = {2023}, author = {Rawat, N and Anjali, and Shreyata, and Sabu, B and Jamwal, R and Devi, PP and Yadav, K and Raina, HS and Rajagopal, R}, title = {Understanding the role of insects in the acquisition and transmission of antibiotic resistance.}, journal = {The Science of the total environment}, volume = {858}, number = {Pt 1}, pages = {159805}, doi = {10.1016/j.scitotenv.2022.159805}, pmid = {36461578}, issn = {1879-1026}, mesh = {Animals ; Humans ; *Angiotensin Receptor Antagonists ; *Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Microbial ; Insecta ; Metagenomics ; Anti-Bacterial Agents ; }, abstract = {Antibiotic resistance (AR) is a global healthcare threat that requires a comprehensive assessment. Poorly regulated antibiotic stewardship in clinical and non-clinical settings has led to a horizontal dissemination of AR. A variety of often neglected elements facilitate the circulation of AR from antibiotic sinks like concentrated animal feeding operations and healthcare settings to other environments that include healthy human communities. Insects are one of those elements that have received underwhelming attention as vectors of AR, despite their well-known role in transmitting clinically relevant pathogens. We here make an exhaustive attempt to highlight the role of insects as zoonotic reservoirs of AR by discussing the available literature and deriving realistic inferences. We review the AR associated with insects housing various human-relevant environments, namely, animal farm industry, edible-insects enterprise, healthcare institutes, human settlements, agriculture settings and the wild. We also provide evidence-based accounts of the events of the transmission of AR from insects to humans. We evaluate the clinical threats associated with insect-derived AR and propose the adoption of more sophisticated strategies to understand and mitigate future AR concerns facilitated by insects. Future works include a pan-region assessment of insects for AR in the form of AR bacteria (ARB) and AR determinants (ARDs) and the introduction of modern techniques like whole-genome sequencing, metagenomics, and in-silico modelling.}, } @article {pmid36461576, year = {2023}, author = {Yu, Y and Zhang, Q and Zhang, Z and Zhou, S and Jin, M and Zhu, D and Yang, X and Qian, H and Lu, T}, title = {Plants select antibiotic resistome in rhizosphere in early stage.}, journal = {The Science of the total environment}, volume = {858}, number = {Pt 1}, pages = {159847}, doi = {10.1016/j.scitotenv.2022.159847}, pmid = {36461576}, issn = {1879-1026}, mesh = {Humans ; Rhizosphere ; Anti-Bacterial Agents ; Triticum ; *Hordeum ; Soil ; *Arabidopsis ; }, abstract = {Knowledge of the dissemination and emergence of antibiotic resistance genes (ARGs) in the plant rhizosphere is essential for evaluating the risk of the modern ARGs in soil planetary health. However, little is known about the selection mechanism in the plant rhizosphere. Here, we firstly analyzed the dynamic changes in the rhizosphere antibiotic resistome during the process of three passage enrichment of the rhizosphere microbiome in Arabidopsis thaliana (Col-0) and found evidence that plants directionally enriched levels of beneficial functional bacteria with many ARGs. Using the metagenome, we next evaluated the enrichment potential of the resistome in four common crops (barley, indica rice, japonica rice, and wheat) and found that the wheat rhizosphere harbored more abundant ARGs. Therefore, we finally cultivated the rhizosphere microbiome of wheat for three generations and found that approximately 60 % of ARGs were associated with beneficial bacteria enriched in the wheat rhizosphere, which might enter the soil food web and threaten human health, despite also performing beneficial functions in the plant rhizosphere. Our study provides new insights into the dissemination of ARGs in the plant rhizosphere, and the obtained data may be useful for sustainable and ecologically safe agricultural development.}, } @article {pmid36461401, year = {2022}, author = {Qiu, Y and Wu, Y and Li, L and Chen, S and Zhao, Y and Li, C and Xiang, H and Wang, D and Wei, Y and Wang, Y}, title = {Elucidating the mechanism underlying volatile and non-volatile compound development related to microbial amino acid metabolism during golden pomfret (Trachinotus ovatus) fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {162}, number = {Pt B}, pages = {112095}, doi = {10.1016/j.foodres.2022.112095}, pmid = {36461401}, issn = {1873-7145}, mesh = {Animals ; Fermentation ; *Amino Acids ; *Seafood ; Fishes ; Glutamic Acid ; }, abstract = {Golden pomfret (Trachinotus ovatus) is an important farmed fish in Asia, often consumed following salting and natural microbial fermentation. Flavor development in fermented foods depends on the metabolism of fermenting microbes, especially amino acid metabolism. However, the microbes involved in golden pomfret fermentation and the mechanism by which they regulate flavor development are largely unknown. Accordingly, in this study, we investigated the microbial community and volatile and non-volatile compounds during the traditional fermentation of golden pomfret, focusing on amino acid metabolism. Thirty-five volatile compounds were detected. Glutamate, alanine, and leucine were the main amino acids responsible for the development of the characteristic taste of fermented golden pomfret. Metagenomic analyses were performed, and microbial genes for amino acid metabolism were functionally annotated, revealing the underlying mechanisms of flavor development during fish fermentation. Halobacterium, Clostridium, Natrinema, Alkalibacillus, Natrialba, and Vibrio were the dominant microbial genera with a major contribution to amino acid metabolism during fermentation and were strongly correlated with the majority of volatile compounds. The study provides a theoretical reference for the mechanism of flavor formation and important information on the microbial sources of volatile compounds derived from amino acids.}, } @article {pmid36461382, year = {2022}, author = {Valentino, V and Sequino, G and Cobo-Díaz, JF and Álvarez-Ordóñez, A and De Filippis, F and Ercolini, D}, title = {Evidence of virulence and antibiotic resistance genes from the microbiome mapping in minimally processed vegetables producing facilities.}, journal = {Food research international (Ottawa, Ont.)}, volume = {162}, number = {Pt B}, pages = {112202}, doi = {10.1016/j.foodres.2022.112202}, pmid = {36461382}, issn = {1873-7145}, mesh = {Virulence ; *Vegetables ; Anti-Bacterial Agents ; Drug Resistance, Microbial/genetics ; *Microbiota/genetics ; }, abstract = {Daily consumption of fresh vegetables is highly recommended by international health organizations, because of their high content of nutrients. However, fresh vegetables might harbour several pathogenic microorganisms or contribute to spread antibiotic resistance, thus representing a hazard for consumers. In addition, little is known about the transmission routes of the residential microbiome from the food handling environment to vegetables. Therefore, we collected environmental and food samples from three manufactures producing fresh vegetables to estimate the relevance of the built environment microbiome on that of the finished products. Our results show that food contact surfaces sampled after routine cleaning and disinfection procedures host a highly diverse microbiome, including pathogens such as the enterotoxigenic Bacillus cereus sensu stricto. In addition, we provide evidence of the presence of a wide range of antibiotic resistance and virulence genes on food contact surfaces associated with multiple taxa, thus supporting the hypothesis that selection of resistant and pathogenic taxa might occur on sanitized surfaces. This study also highlights the potential of microbiome mapping routinely applied in food industries monitoring programs to ensure food safety.}, } @article {pmid36461373, year = {2022}, author = {Hou, Y and Zhang, Z and Cui, Y and Peng, C and Fan, Y and Tan, C and Wang, Q and Liu, Z and Gong, J}, title = {Pu-erh tea and theabrownin ameliorate metabolic syndrome in mice via potential microbiota-gut-liver-brain interactions.}, journal = {Food research international (Ottawa, Ont.)}, volume = {162}, number = {Pt B}, pages = {112176}, doi = {10.1016/j.foodres.2022.112176}, pmid = {36461373}, issn = {1873-7145}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Liver ; *Metabolic Syndrome ; Brain ; Obesity ; Tea ; }, abstract = {Metabolic syndrome (MS) is a common metabolic disorder characterized by obesity, insulin resistance, cardiovascular disease and gut microbiota dysbiosis. Pu-erh tea and its ingredient theabrownin have known functions on the reduction of body weight gain and fat accumulation. However, few studies systematicly analyze the different contributions and mechanisms of their anti-metabolic syndrome functions through multi-omics combination analysis. Here, we used metagenomics, transcriptomics and metabolomics technology to investigate the anti-metabolic syndrome mechanism of Pu-erh tea and theabrownin in MS mice. Our results suggested that Pu-erh tea and theabrownin interventions could improve the physiological functions of liver, jejunum and adipose tissues in MS mice. Hepatic transcriptome revealed that both interventions could regulate the circadian rhythm pathway. Glycerophospholipid and linoleic acid metabolism were also modulated by both interventions through serum and brain metabolome analysis. Faecal metagenome demonstrated that both interventions could increase the relative abundance of Clostridiales bacterium 42_27, Blautia coccoides and Firmicutes bacterium ASF500, but decrease the relative abundance of Brevundimonas vesicularis. Otherwise, compared with Pu-erh tea, theabrownin markedly upregulated the levels of hepatic antioxidants (i.e., SOD, GSH), prominently downregulated hepatic inflammatory factors (i.e., IL-1, IL-6, TNF-α) and malondialdehyde oxidant, but modestly reduced obesity-associated short-chain fatty acids in faeces in MS mice. Taken together, our data provided insights into the homogeneous and heterogeneous natural biological functions of theabrownin and Pu-erh tea in the treatment of metabolic syndrome.}, } @article {pmid36461096, year = {2022}, author = {Wang, G and Wang, X and Ma, Y and Cai, S and Yang, L and Fan, Y and Zeng, X and Qiao, S}, title = {Lactobacillus reuteri improves the development and maturation of fecal microbiota in piglets through mother-to-infant microbe and metabolite vertical transmission.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {211}, pmid = {36461096}, issn = {2049-2618}, mesh = {Animals ; Swine ; Female ; Pregnancy ; Humans ; *Limosilactobacillus reuteri ; Mothers ; Feces ; *Microbiota ; *Body Fluids ; Clostridiaceae ; }, abstract = {BACKGROUND: The immature neonatal fecal microbiota substantially impacts the development of gut health and greatly increases the risk of disease. Developing effective strategies to modulate the development of neonatal fecal microbiota has great significance. Herein, we investigated whether the maternal dietary supplementation and oral administration of Lactobacillus reuteri could effectively promote the development and maturation of the fecal microbiome in piglets from birth to weaning.

RESULTS: Metagenomic analysis of colostrum showed that maternal dietary L. reuteri supplementation influenced the overall microbiota composition, decreased the abundance of the phylum Proteobacteria and increased that of the species Bifidobacterium choerinum. KEGG pathway analysis revealed that maternal L. reuteri supplementation enriched the lysine biosynthesis and glycolysis/gluconeogenesis pathways and downregulated the bacterial invasion of epithelial cells in the colostrum. In addition, L. reuteri supplementation significantly altered the metabolite features and modules in umbilical cord blood serum based on metabolomics. Further, a significant covariation was observed between these differential metabolites and the species in colostrum. Maternal dietary L. reuteri supplementation also significantly influenced the microbiota composition and increased the meconium abundance of beneficial bacteria (such as Romboutsia, Lactobacillus, Blautia, Butyricicoccus, and Ruminococcus), some of which were markedly associated with several differential metabolites in umbilical cord blood serum between two groups. Notably, both the maternal dietary supplementation and oral intake of L. reuteri had strong impacts on the overall microbial composition and maturation of fecal microbiota in piglets during early life, and these effects were dependent on the growth stage. Oral administration of L. reuteri promoted diarrhea resistance in neonates, while maternal supplementation of L. reuteri enhanced the abilities of antioxidants and decreased inflammation. Moreover, the administration of L. reuteri via both methods in combination improved the growth performances of piglets.

CONCLUSION: Overall, our data demonstrated that L. reuteri had the ability to modulate the composition of fecal microbiota in newborn piglets by influencing the microbial community and functional composition in the colostrum and by altering several key metabolites in the umbilical cord blood serum. Also, both the maternal dietary supplementation and oral administration of L. reuteri effectively promoted the development and maturation of the fecal microbiome in piglets during early life. Both the maternal dietary supplementation and oral administration of L. reuteri in combination optimized the growth performances of piglets. Video Abstract.}, } @article {pmid36460704, year = {2022}, author = {Kim, HS and Kim, DW and Kim, S and Choe, S}, title = {Biochemical characterization of the two novel mgCas12a proteins from the human gut metagenome.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {20857}, pmid = {36460704}, issn = {2045-2322}, mesh = {Humans ; *Metagenome ; Amino Acid Sequence ; *Endonucleases ; Biological Assay ; Biotechnology ; }, abstract = {CRISPR/Cas9 and Cas12a belonging to the Class II CRISPR system are characterized by a single-component effector protein. Despite unique features of Cas12a like DNA cleavage with 5' staggered ends and a single crRNA, Cas12a has not been adopted in biotechnological applications to the similar extent as Cas9. To better understand the CRISPR/Cas12 systems, we selected two candidates, designated mgCas12a-1 and mgCas12a-2, from an analysis of the human microbiome metagenome (mg) and provided biochemical characterization. These new Cas12a proteins shared about 37% identity in amino acid sequences and shared the same direct repeat sequences in the crRNA with FnCas12a from Francisella novicida. The purification yield of the recombinant proteins was up to 3.6-fold greater than that of FnCas12a. In cell-free DNA cleavage assays, both mgCas12a proteins showed the higher cleavage efficiencies when Mn[2+] was provided with KCl (< 100 mM) than tested other divalent ions. They were able to tolerate ranges of pH points and temperature, and showed the highest cleavage efficiencies at pH 8.0 and 50 °C. In addition, mgCas12a proteins showed 51% less crRNA-independent and 56% less crRNA-dependent non-specific nuclease activity upon prolonged incubation than did FnCas12a. Considering their greater yield in protein preparation and reduced non-specific nuclease activity, our findings may expedite the use of Cas12a especially when genome editing needs to be practiced with the form of ribonucleoproteins.}, } @article {pmid36459997, year = {2023}, author = {Keeler, EL and Merenstein, C and Reddy, S and Taylor, LJ and Cobián-Güemes, AG and Zankharia, U and Collman, RG and Bushman, FD}, title = {Widespread, human-associated redondoviruses infect the commensal protozoan Entamoeba gingivalis.}, journal = {Cell host & microbe}, volume = {31}, number = {1}, pages = {58-68.e5}, pmid = {36459997}, issn = {1934-6069}, support = {P30 AI045008/AI/NIAID NIH HHS/United States ; R61 HL137063/HL/NHLBI NIH HHS/United States ; 75N93021C00015/AI/NIAID NIH HHS/United States ; R35 GM134957/GM/NIGMS NIH HHS/United States ; R33 HL137063/HL/NHLBI NIH HHS/United States ; }, mesh = {Humans ; *Entamoeba/genetics ; *COVID-19 ; *Periodontitis ; *Viruses ; *Bacteriophages ; Bacteria ; }, abstract = {Redondoviruses are circular Rep-encoding single-stranded DNA (CRESS) viruses of high prevalence in healthy humans. Redondovirus abundance is increased in oro-respiratory samples from individuals with periodontitis, acute illness, and severe COVID-19. We investigated potential host cells supporting redondovirus replication in oro-respiratory samples and uncovered the oral amoeba Entamoeba gingivalis as a likely host. Redondoviruses are closely related to viruses of Entamoeba and contain reduced GC nucleotide content, consistent with Entamoeba hosts. Redondovirus and E. gingivalis co-occur in metagenomic data from oral disease and healthy human cohorts. When grown in xenic cultures with feeder bacteria, E. gingivalis was robustly positive for redondovirus RNA and DNA. A DNA proximity-ligation assay (Hi-C) on xenic culture cells showed enriched cross-linking of redondovirus and Entamoeba DNA, supporting E. gingivalis as the redondovirus host. While bacteria are established hosts for bacteriophages within the human virome, this work shows that eukaryotic commensals also contribute an abundant human-associated virus.}, } @article {pmid36459890, year = {2023}, author = {Liu, Q and Li, J and Zhao, Y and Li, X and Zhang, Q and Sui, J and Wang, C and Peng, Y}, title = {Mechanism of suspended sludge impact on anammox enrichment in anoxic biofilm through long term operation and microbial analysis.}, journal = {Water research}, volume = {229}, number = {}, pages = {119412}, doi = {10.1016/j.watres.2022.119412}, pmid = {36459890}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; *Denitrification ; Anaerobic Ammonia Oxidation ; Nitrogen Dioxide ; Reproducibility of Results ; Bioreactors/microbiology ; Oxidation-Reduction ; Anaerobiosis ; Bacteria ; Biofilms ; Nitrogen ; }, abstract = {The basic premise of anammox-technical application reliability in municipal wastewater treatment is substantially enriched anammox bacteria. To enrich the anammox, the special interaction mechanism between the suspended sludge (SS) and anoxic biofilm was investigated over three months in a partial denitrification/anammox biosystem subjected to dynamic changes in SS (absence→ presence→ absence). Results show that the introduction of SS significantly decreased the anammox nitrogen removal efficiency (83.8 ± 6.5%→ 48.7 ± 17.0%). With the presence or absence of SS, the spatial distribution of anammox bacteria within the anoxic biofilm gradually changed between the inner and outer layers, as detected by CLSM-FISH. qPCR and metagenomic sequencing show that changes in the presence and absence status of SS significantly reduced the abundance of the NO reducing functional gene, while the NO supply capacity (NO3[-]→NO) was improved, further favoring the anammox process. Batch tests and typical cycles further demonstrated that the anammox bacteria can stably acquire NO2[-], and anammox bacteria in the anoxic biofilm competed far more NO2[-] than denitrifying bacteria according to the typical pH curve. Accordingly, the abundance of Candidatus Brocadia, as detected by high throughput sequencing, decreased in the anoxic biofilms with the introduction of SS, but greatly increased (0.82%→2.22%) after SS discharge. This study sheds new light on the high in-situ enrichment of anammox in mainstream.}, } @article {pmid36459774, year = {2023}, author = {Li, S and Zhen, Y and Chen, Y and Mi, T and Yu, Z}, title = {Shifts in the spatiotemporal distribution and sources of nitrous oxide in sediment cores from the Bohai Sea and South Yellow Sea.}, journal = {Marine pollution bulletin}, volume = {186}, number = {}, pages = {114390}, doi = {10.1016/j.marpolbul.2022.114390}, pmid = {36459774}, issn = {1879-3363}, mesh = {*Denitrification ; *Nitrous Oxide/analysis ; Nitrification ; Oceans and Seas ; Estuaries ; }, abstract = {N2O is among the most potent greenhouse gases. In this study, we investigated one of the important N2O production hotspots, the continental margins. We looked at N2O spatiotemporal distributions in situ as well as the potential contributions of nitrification and denitrification to N2O production in sediment cores from the Bohai and South Yellow Seas. Real-time PCR and shotgun metagenomics sequencing were used to analyze the microbial communities related to N2O production. The results showed that N2O concentrations roughly decreased with depth-a trend that was consistent throughout the year and showed no significant seasonal variations. When all the research stations along the continental margin were considered, the estuary exhibited the lowest average N2O concentration. Moreover, nitrification was identified as the main process responsible for N2O production in estuary areas. This study demonstrates that spatial, as opposed to temporal, heterogeneity is the primary factor influencing N2O concentration differences in sediments.}, } @article {pmid36459771, year = {2023}, author = {Tada, Y and Marumoto, K and Iwamoto, Y and Takeda, K and Sakugawa, H}, title = {Distribution and phylogeny of mercury methylation, demethylation, and reduction genes in the Seto Inland Sea of Japan.}, journal = {Marine pollution bulletin}, volume = {186}, number = {}, pages = {114381}, doi = {10.1016/j.marpolbul.2022.114381}, pmid = {36459771}, issn = {1879-3363}, mesh = {Humans ; *Mercury/analysis ; *Methylmercury Compounds/analysis ; Phylogeny ; Methylation ; Japan ; Demethylation ; }, abstract = {Mercury (Hg) adversely affects human and environmental health. To evaluate the mercury (Hg) speciation (methylation, demethylation, and reduction) of microorganisms in coastal seawater, we analyzed the microbial functional gene sets involved in Hg methylation (hgcA and hgcB), demethylation (merB), and reduction (merA) using a metagenomic approach in the eastern and western parts (the Kii and Bungo channels, respectively) of the Seto Inland Sea (SIS) of Japan. We determined the concentration of dissolved total mercury (dTHg) and methylated mercury (dMeHg) in seawater. The metagenomic analysis detected hgcAB, merA, and merB in both channels, whereas the phylogenies of these genes differed between them. A correlation between Hg concentration (both dTHg and dMeHg) and the relative abundance of each gene was not observed. Our data suggests that microbial Hg methylation and demethylation could occur in the SIS and there could be a distinct microbial Hg speciation process between the Kii and Bungo channels.}, } @article {pmid36459424, year = {2023}, author = {Yuan, D and Zheng, L and Liu, YX and Cheng, H and Ding, A and Wang, X and Tan, Q and Wang, X and Xing, Y and Xie, E and Wu, H and Wang, S and Zhu, G}, title = {Nitrifiers Cooperate to Produce Nitrous Oxide in Plateau Wetland Sediments.}, journal = {Environmental science & technology}, volume = {57}, number = {1}, pages = {810-821}, doi = {10.1021/acs.est.2c06234}, pmid = {36459424}, issn = {1520-5851}, mesh = {*Nitrous Oxide/analysis ; *Archaea ; Wetlands ; Ammonia ; Oxidation-Reduction ; China ; Bacteria/genetics ; Nitrification ; Soil Microbiology ; }, abstract = {The thawing of dormant plateau permafrost emits nitrous oxide (N2O) through wetlands; however, the N2O production mechanism in plateau wetlands is still unclear. Here, we used the [15]N-[18]O double tracer technique and metagenomic sequencing to analyze the N2O production mechanism in the Yunnan-Kweichow and Qinghai-Tibet plateau wetlands during the summer of 2020. N2O production activity was detected in all 16 sediment samples (elevation 1020-4601 m: 2.55 ± 0.42-26.38 ± 3.25 ng N g[-1] d[-1]) and was promoted by nitrifier denitrification (ND). The key functional genes of ND (amoA, hao, and nirK) belonged to complete ammonia oxidizing (comammox) bacteria, and the key ND species was the comammox bacterium Nitrospira nitrificans. We found that the comammox bacterial species N. nitrificans and the ammonia oxidizing bacterial (AOB) species Nitrosomonas europaea cooperate to produce N2O in the plateau wetland sediments. Furthermore, we inferred that environmental factors (elevation and total organic matter (TOM)) influence the cooperation pattern via N. nitrificans, thus affecting the N2O production activity in the plateau wetland sediments. Our findings advance the mechanistic understanding of nitrifiers in biogeochemical cycles and global climate change.}, } @article {pmid36458224, year = {2022}, author = {Zorina, AS and Maksimov, AY and Maksimova, YG}, title = {Degradation of Nitriles by Mixed Biofilms of Nitrile-Hydrolyzing Bacteria in Submerged Packed-Bed Reactor.}, journal = {Indian journal of microbiology}, volume = {62}, number = {4}, pages = {610-617}, pmid = {36458224}, issn = {0046-8991}, abstract = {UNLABELLED: Degradation of nitriles by mixed biofilms of nitrile-hydrolyzing bacteria Alcaligenes faecalis 2 and Rhodococcus ruber gt 1 grown on basalt and carbon carriers, in a submerged packed-bed reactor was studied. It was shown the formation of a massive mixed biofilm of Al. faecalis 2 and R. ruber gt 1 and the effective removal of nitriles and products of their degradation from the reaction medium. After the accumulation of carboxylic acid and some of the unprocessed substrate, the system adapts to 600-1000 h of biofilter operation, which is expressed in a decrease in the content of substrate and reaction products in the medium. The rate of acetonitrile and acrylonitrile utilization was 0.072-0.086 and 0.039-0.215 g/h, respectively, and acrylonitrile utilization with maximum rate was realized by a mixed biofilm on carbon fibers. Biofilms grown on mixed fibers in a "sandwich"-type reactor had the best characteristics for the transformation of aceto- and acrylonitrile (removal capacity of 99.6-99.9%, nitrile utilization rate of 0.080-0.095 g/h). Biofilms grown on basalt fiber with a diameter of 4-12 μm are also well suited for the degradation of acetonitrile (removal capacity of 100%, nitrile utilization rate of 0.086 g/h). The results of metagenomic analysis showed the resistance of Al. faecalis 2 and R. ruber gt 1 mixed biofilms against leaching from a biofilter and to competitive growth in an open system, indicating the advantages of biofilms over homogeneous biomass for wastewater treatment from nitrile compounds. Biofilms of two species of nitrile hydrolyzing bacteria on basalt and carbon fibers effectively purify water from nitriles in a submerged packed-bed reactor.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-022-01030-z.}, } @article {pmid36458218, year = {2022}, author = {Patel, S and Mandaliya, D and Seshadri, S}, title = {Colonic Microflora Protagonist of Liver Metabolism and Gut Permeability: Study on Mice Model.}, journal = {Indian journal of microbiology}, volume = {62}, number = {4}, pages = {540-549}, pmid = {36458218}, issn = {0046-8991}, abstract = {UNLABELLED: Alteration of gut microflora results in a metabolic imbalance in the liver. In the present study, we investigate the reversal potential of alteration of the colonic microflora via improving metabolism balance and regulating the altered tight junction of the intestinal tract. Animals were fed with high sugar diet to mimic the onset of the pathophysiological conditions of diabetes. Following induction, animals were divided into two reversal groups i.e., crude cefdinir and colon-specific formulated cefdinir, to alter the gut microflora. In the present study, we have tried to quantify the microbial content via metagenome analysis to provide an actual picture of the alteration and subsequent reversal. Expression of mRNA of junctional protein and parameters involved in liver metabolism was determined using qPCR. Results indicated direct effect of altered composition of gut microflora on the gut permeability and metabolic alteration. Metagenomic analysis showed least evenness and richness in the HSD group whereas antibiotic-treated groups showed reversal of microflora towards control group with increased richness, evenness and decreased distance on PCoA plot. This changes in gut microflora composition changes expression of metabolic markers and thus insulin sensitivity. Targeting colonic microflora to have a reversal effect on T2D pathogenesis, found to have a positive impact on liver metabolic state with improved permeability markers of gut with SCFA alteration.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-022-01032-x.}, } @article {pmid36458216, year = {2022}, author = {Kalia, VC and Gong, C and Shanmugam, R and Lee, JK}, title = {Prospecting Microbial Genomes for Biomolecules and Their Applications.}, journal = {Indian journal of microbiology}, volume = {62}, number = {4}, pages = {516-523}, pmid = {36458216}, issn = {0046-8991}, abstract = {Bioactive molecules of microbial origin are finding increasing biotechnological applications. Their sources range from the terrestrial, marine, and endophytic to the human microbiome. These biomolecules have unique chemical structures and related groups, which enable them to improve the efficiency of the bioprocesses. This review focuses on the applications of biomolecules in bioremediation, agriculture, food, pharmaceutical industries, and human health.}, } @article {pmid36458196, year = {2022}, author = {Kuang, Z and Li, F and Duan, Q and Tian, C and Nevo, E and Li, K}, title = {Host diet shapes functionally differentiated gut microbiomes in sympatric speciation of blind mole rats in Upper Galilee, Israel.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1062763}, pmid = {36458196}, issn = {1664-302X}, abstract = {The gut microbiome is important for host nutrient metabolism and ecological adaptation. However, how the gut microbiome is affected by host phylogeny, ecology and diet during sympatric speciation remain unclear. Here, we compare and contrast the gut microbiome of two sympatric blind mole rat species and correlate them with their corresponding host phylogeny, ecology soil metagenomes, and diet to determine how these factors may influence their gut microbiome. Our results indicate that within the host microbiome there is no significant difference in community composition, but the functions between the two sympatric species populations vary significantly. No significant correlations were found between the gut microbiome differentiation and their corresponding ecological soil metagenomes and host phylogeny. Functional enrichment analysis suggests that the host diets may account for the functional divergence of the gut microbiome. Our results will help us understand how the gut microbiome changes with corresponding ecological dietary factors in sympatric speciation of blind subterranean mole rats.}, } @article {pmid36458193, year = {2022}, author = {Zhu, Y and Zhao, W and Yang, X and Zhang, Y and Lin, X and Weng, X and Wang, Y and Cheng, C and Chi, Y and Wei, H and Peng, Z and Hu, Z}, title = {Metagenomic next-generation sequencing for identification of central nervous system pathogens in HIV-infected patients.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1055996}, pmid = {36458193}, issn = {1664-302X}, abstract = {Although considerable interest in metagenomic next-generation sequencing (mNGS) has been attracted in recent years, limited data are available regarding the performance of mNGS in HIV-associated central nervous system (CNS) infection. Here, we conducted a retrospectively analyzing of the cerebrospinal fluid (CSF) mNGS reports and other clinical data from 80 HIV-infected patients admitted to the Second Hospital of Nanjing, China from March, 2018 to March, 2022. In our study, CSF mNGS reported negative result, mono-infection, and mixed infection in 8.8, 36.2, and 55% of the patients, respectively. Epstein-Barr virus (EBV), positive in 52.5% of samples, was the most commonly reported pathogen, followed by cytomegalovirus (CMV), John Cunningham virus (JCV), torque teno virus (TTV), cryptococcus neoformans (CN), toxoplasma Gondii (TE), and mycobacterium tuberculosis (MTB). 76.2% of the EBV identification and 54.2% of the CMV identification were not considered clinically important, and relative less sequence reads were reported in the clinical unimportant identifications. The clinical importance of the presence of TTV in CSF was not clear. Detection of JCV, CN, or TE was 100% suggestive of specific CNS infection, however, 60% of the MTB reports were considered contamination. Moreover, of the 44 (55%) mixed infections reported by mNGS, only 4 (5%) were considered clinical important, and mNGS failed to identify one mixed infection. Additionally, except for MTB, CSF mNGS tended to have high sensitivity to identify the above-mentioned pathogens (almost with 100% sensitivity). Even all the diagnostic strategies were evaluated, the cause of neurological symptoms remained undetermined in 6 (7.5%) patients. Overall, our results suggest that mNGS is a very sensitive tool for detecting common opportunistic CNS pathogen in HIV-infected patients, although its performance in CNS tuberculosis is unsatisfactory. EBV and CMV are commonly detected by CSF mNGS, however, the threshold of a clinical important detection remains to be defined.}, } @article {pmid36458190, year = {2022}, author = {He, Q and Niu, X and Qi, RQ and Liu, M}, title = {Advances in microbial metagenomics and artificial intelligence analysis in forensic identification.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1046733}, pmid = {36458190}, issn = {1664-302X}, abstract = {Microorganisms, which are widely distributed in nature and human body, show unique application value in forensic identification. Recent advances in high-throughput sequencing technology and significant reductions in analysis costs have markedly promoted the development of forensic microbiology and metagenomics. The rapid progression of artificial intelligence (AI) methods and computational approaches has shown their unique application value in forensics and their potential to address relevant forensic questions. Here, we summarize the current status of microbial metagenomics and AI analysis in forensic microbiology, including postmortem interval inference, individual identification, geolocation, and tissue/fluid identification.}, } @article {pmid36458183, year = {2022}, author = {Duan, J and Wang, W and Jiang, T and Bai, X and Liu, C}, title = {Viral metagenomics combined with metabolomics reveals the role of gut viruses in mouse model of depression.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1046894}, pmid = {36458183}, issn = {1664-302X}, abstract = {Depression is a heterogeneous mental disorder that has been linked to disturbances in the gut microbiome. As an essential part of the gut microbiome, gut virome may play critical roles in disease progression and development. However, the relationship between the effect of gut virome on neurotransmitter metabolism and depression is unknown. We evaluated the alterations of gut virome and neurotransmitters in chronic restraint stress (CRS)-induced mouse model of depression based on viral metagenomics and LC-MS/MS metabolomics analyses. The results reveal that the gut virome profile of CRS group differed significantly from CON group. Microviridae was the most abundant differential viral family in both groups, followed by Podoviridae, while Siphoviridae was only enriched in CRS group of the top 100 differential viruses. The differential viruses that predicted to Enterobacteriaceae phage, Gammaproteobacteria phage and Campylobacteraceae phage were enriched in CRS group. Furthermore, 12 differential neurotransmitters primarily involved in the tryptophan metabolism pathway were altered in depressive-like mice. Besides, tryptamine and 5-methoxytryptamine hydrochloride were strongly associated with differential viruses belonging to Podoviridae and Microviridae. Our findings provide new insight into understanding the potential role of the gut virome and metabolites in depression.}, } @article {pmid36458093, year = {2022}, author = {Larsen, PE and Dai, Y}, title = {Modeling interaction networks between host, diet, and bacteria predicts obesogenesis in a mouse model.}, journal = {Frontiers in molecular biosciences}, volume = {9}, number = {}, pages = {1059094}, pmid = {36458093}, issn = {2296-889X}, abstract = {Host-microbiome interactions are known to have substantial effects on human health, but the diversity of the human microbiome makes it difficult to definitively attribute specific microbiome features to a host phenotype. One approach to overcoming this challenge is to use animal models of host-microbiome interaction, but it must be determined that relevant aspects of host-microbiome interactions are reflected in the animal model. One such experimental validation is an experiment by Ridura et al. In that experiment, transplanting a microbiome from a human into a mouse also conferred the human donor's obesity phenotype. We have aggregated a collection of previously published host-microbiome mouse-model experiments and combined it with thousands of sequenced and annotated bacterial genomes and metametabolomic pathways. Three computational models were generated, each model reflecting an aspect of host-microbiome interactions: 1) Predict the change in microbiome community structure in response to host diet using a community interaction network, 2) Predict metagenomic data from microbiome community structure, and 3) Predict host obesogenesis from modeled microbiome metagenomic data. These computationally validated models were combined into an integrated model of host-microbiome-diet interactions and used to replicate the Ridura experiment in silico. The results of the computational models indicate that network-based models are significantly more predictive than similar but non-network-based models. Network-based models also provide additional insight into the molecular mechanisms of host-microbiome interaction by highlighting metabolites and metabolic pathways proposed to be associated with microbiome-based obesogenesis. While the models generated in this study are likely too specific to the animal models and experimental conditions used to train our models to be of general utility in a broader understanding of obesogenesis, the approach detailed here is expected to be a powerful tool of investigating multiple types of host-microbiome interactions.}, } @article {pmid36458015, year = {2022}, author = {Zhaoyang, S and Guowei, S and Jing, P and Yundong, Z and Xinhua, L and Muyun, W and Xiaowei, M and Lixin, L and Xiaoying, C}, title = {Clinical characteristics of the host DNA-removed metagenomic next-generation sequencing technology for detecting SARS-CoV-2, revealing host local immune signaling and assisting genomic epidemiology.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1016440}, pmid = {36458015}, issn = {1664-3224}, mesh = {Humans ; *SARS-CoV-2/genetics ; *COVID-19/diagnosis/epidemiology ; Genomics ; DNA ; High-Throughput Nucleotide Sequencing ; Technology ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) technology has been central in detecting infectious diseases and helping to simultaneously reveal the complex interplay between invaders and their hosts immune response characteristics. However, it needs to be rigorously assessed for clinical utility. The present study is the first to evaluate the clinical characteristics of the host DNA-removed mNGS technology for detecting SARS-CoV-2, revealing host local immune signaling and assisting genomic epidemiology.

METHODS: 46 swab specimens collected from COVID-19 patients were assayed by two approved commercial RT-qPCR kits and mNGS. The evolutionary tree of SARS-CoV-2 was plotted using FigTree directly from one sample. The workflow of removing the host and retaining the host was compared to investigate the influence of host DNA removal on the performances of mNGS. Functional enrichment analysis of DEGs and xCell score were used to explore the characteristics of host local immune signaling.

RESULTS: The detection rate of mNGS achieved 92.9% (26/28) for 28 samples with a Ct value ≤ 35 and 81.1% (30/37) for all 46 samples. The genome coverage of SARS-CoV-2 could reach up to 98.9% when the Ct value is about 20 in swab samples. Removing the host could enhance the sensitivity of mNGS for detecting SARS-CoV-2 from the swab sample but does not affect the species abundance of microbes RNA. Improving the sequencing depth did not show a positive effect on improving the detection sensitivity of SARS-CoV-2. Cell type enrichment scores found multiple immune cell types were differentially expressed between patients with high and low viral load.

CONCLUSIONS: The host DNA-removed mNGS has great potential utility and superior performance on comprehensive identification of SARS-CoV-2 and rapid traceability, revealing the microbiome's transcriptional profiles and host immune responses.}, } @article {pmid36457513, year = {2022}, author = {Liu, B and Li, Y and Suo, L and Zhang, W and Cao, H and Wang, R and Luan, J and Yu, X and Dong, L and Wang, W and Xu, S and Lu, S and Shi, M}, title = {Characterizing microbiota and metabolomics analysis to identify candidate biomarkers in lung cancer.}, journal = {Frontiers in oncology}, volume = {12}, number = {}, pages = {1058436}, pmid = {36457513}, issn = {2234-943X}, abstract = {BACKGROUND: Lung cancer is the leading malignant disease and cause of cancer-related death worldwide. Most patients with lung cancer had insignificant early symptoms so that most of them were diagnosed at an advanced stage. In addition to factors such as smoking, pollution, lung microbiome and its metabolites play vital roles in the development of lung cancer. However, the interaction between lung microbiota and carcinogenesis is lack of systematically characterized and controversial. Therefore, the purpose of this study was to excavate the features of the lung microbiota and metabolites in patients and verify potential biomarkers for lung cancer diagnosis.

METHODS: Lung tissue flushing solutions and bronchoalveolar lavage fluid samples came from patients with lung cancer and non-lung cancer. The composition and variations of the microbiota and metabolites in samples were explored using muti-omics technologies including 16S rRNA amplicon sequencing, metagenomics and metabolomics.

RESULTS: The metabolomics analysis indicated that 40 different metabolites, such as 9,10-DHOME, sphingosine, and cysteinyl-valine, were statistically significant between two groups (VIP > 1 and P < 0.05). These metabolites were significantly enriched into 11 signal pathways including sphingolipid, autophagy and apoptosis signaling pathway (P < 0.05). The analysis of lung microbiota showed that significant changes reflected the decrease of microbial diversity, changes of distribution of microbial taxa, and variability of the correlation networks of lung microbiota in lung cancer patients. In particular, we found that oral commensal microbiota and multiple probiotics might be connected with the occurrence and progression of lung cancer. Moreover, our study found 3 metabolites and 9 species with significantly differences, which might be regarded as the potential clinical diagnostic markers associated with lung cancer.

CONCLUSIONS: Lung microbiota and metabolites might play important roles in the pathogenesis of lung cancer, and the altered metabolites and microbiota might have the potential to be clinical diagnostic markers and therapeutic targets associated with lung cancer.}, } @article {pmid36457116, year = {2022}, author = {Salazar, C and Giménez, M and Riera, N and Parada, A and Puig, J and Galiana, A and Grill, F and Vieytes, M and Mason, CE and Antelo, V and D'Alessandro, B and Risso, J and Iraola, G}, title = {Human microbiota drives hospital-associated antimicrobial resistance dissemination in the urban environment and mirrors patient case rates.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {208}, pmid = {36457116}, issn = {2049-2618}, mesh = {Humans ; Anti-Bacterial Agents/pharmacology ; Sewage ; Drug Resistance, Bacterial/genetics ; *Microbiota/genetics ; Hospitals ; *Cross Infection ; Carbapenems ; }, abstract = {BACKGROUND: The microbial community composition of urban environments is primarily determined by human activity. The use of metagenomics to explore how microbial communities are shaped in a city provides a novel input that can improve decisions on public health measures, architectural design, and urban resilience. Of note, the sewage system in a city acts as a complex reservoir of bacteria, pharmaceuticals, and antimicrobial resistant (AMR) genes that can be an important source of epidemiological information. Hospital effluents are rich in patient-derived bacteria and can thus readily become a birthplace and hotspot reservoir for antibiotic resistant pathogens which are eventually incorporated into the environment. Yet, the scope to which nosocomial outbreaks impact the urban environment is still poorly understood.

RESULTS: In this work, we extensively show that different urban waters from creeks, beaches, sewage spillways and collector pipes enclose discrete microbial communities that are characterized by a differential degree of contamination and admixture with human-derived bacteria. The abundance of human bacteria correlates with the abundance of AMR genes in the environment, with beta-lactamases being the top-contributing class to distinguish low vs. highly-impacted urban environments. Indeed, the abundance of beta-lactamase resistance and carbapenem resistance determinants in the urban environment significantly increased in a 1-year period. This was in line with a pronounced increase of nosocomial carbapenem-resistant infections reported during the same period that was mainly driven by an outbreak-causing, carbapenemase-producing Klebsiella pneumoniae (KPC) ST-11 strain. Genome-resolved metagenomics of urban waters before and after this outbreak, coupled with high-resolution whole-genome sequencing, confirmed the dissemination of the ST-11 strain and a novel KPC megaplasmid from the hospital to the urban environment. City-wide analysis showed that geospatial dissemination of the KPC megaplasmid in the urban environment inversely depended on the sewage system infrastructure.

CONCLUSIONS: We show how urban metagenomics and outbreak genomic surveillance can be coupled to generate relevant information for infection control, antibiotic stewardship, and pathogen epidemiology. Our results highlight the need to better characterize and understand how human-derived bacteria and antimicrobial resistance disseminate in the urban environment to incorporate this information in the development of effluent treatment infrastructure and public health policies. Video Abstract.}, } @article {pmid36457108, year = {2022}, author = {Shen, J and McFarland, AG and Blaustein, RA and Rose, LJ and Perry-Dow, KA and Moghadam, AA and Hayden, MK and Young, VB and Hartmann, EM}, title = {An improved workflow for accurate and robust healthcare environmental surveillance using metagenomics.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {206}, pmid = {36457108}, issn = {2049-2618}, support = {BAA FY2018-OADS-01 Contract 02915/CC/CDC HHS/United States ; }, mesh = {Workflow ; *Metagenomics ; Environmental Monitoring ; *Microbiota/genetics ; Delivery of Health Care ; }, abstract = {BACKGROUND: Effective surveillance of microbial communities in the healthcare environment is increasingly important in infection prevention. Metagenomics-based techniques are promising due to their untargeted nature but are currently challenged by several limitations: (1) they are not powerful enough to extract valid signals out of the background noise for low-biomass samples, (2) they do not distinguish between viable and nonviable organisms, and (3) they do not reveal the microbial load quantitatively. An additional practical challenge towards a robust pipeline is the inability to efficiently allocate sequencing resources a priori. Assessment of sequencing depth is generally practiced post hoc, if at all, for most microbiome studies, regardless of the sample type. This practice is inefficient at best, and at worst, poor sequencing depth jeopardizes the interpretation of study results. To address these challenges, we present a workflow for metagenomics-based environmental surveillance that is appropriate for low-biomass samples, distinguishes viability, is quantitative, and estimates sequencing resources.

RESULTS: The workflow was developed using a representative microbiome sample, which was created by aggregating 120 surface swabs collected from a medical intensive care unit. Upon evaluating and optimizing techniques as well as developing new modules, we recommend best practices and introduce a well-structured workflow. We recommend adopting liquid-liquid extraction to improve DNA yield and only incorporating whole-cell filtration when the nonbacterial proportion is large. We suggest including propidium monoazide treatment coupled with internal standards and absolute abundance profiling for viability assessment and involving cultivation when demanding comprehensive profiling. We further recommend integrating internal standards for quantification and additionally qPCR when we expect poor taxonomic classification. We also introduce a machine learning-based model to predict required sequencing effort from accessible sample features. The model helps make full use of sequencing resources and achieve desired outcomes. Video Abstract CONCLUSIONS: This workflow will contribute to more accurate and robust environmental surveillance and infection prevention. Lessons gained from this study will also benefit the continuing development of methods in relevant fields.}, } @article {pmid36457105, year = {2022}, author = {Panwar, P and Williams, TJ and Allen, MA and Cavicchioli, R}, title = {Population structure of an Antarctic aquatic cyanobacterium.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {207}, pmid = {36457105}, issn = {2049-2618}, mesh = {Antarctic Regions ; *Cyanobacteria/genetics ; Lakes ; *Microbiota ; Nitrogen ; }, abstract = {BACKGROUND: Ace Lake is a marine-derived, stratified lake in the Vestfold Hills of East Antarctica with an upper oxic and lower anoxic zone. Cyanobacteria are known to reside throughout the water column. A Synechococcus-like species becomes the most abundant member in the upper sunlit waters during summer while persisting annually even in the absence of sunlight and at depth in the anoxic zone. Here, we analysed ~ 300 Gb of Ace Lake metagenome data including 59 Synechococcus-like metagenome-assembled genomes (MAGs) to determine depth-related variation in cyanobacterial population structure. Metagenome data were also analysed to investigate viruses associated with this cyanobacterium and the host's capacity to defend against or evade viruses.

RESULTS: A single Synechococcus-like species was found to exist in Ace Lake, Candidatus Regnicoccus frigidus sp. nov., consisting of one phylotype more abundant in the oxic zone and a second phylotype prevalent in the oxic-anoxic interface and surrounding depths. An important aspect of genomic variation pertained to nitrogen utilisation, with the capacity to perform cyanide assimilation and asparagine synthesis reflecting the depth distribution of available sources of nitrogen. Both specialist (host specific) and generalist (broad host range) viruses were identified with a predicted ability to infect Ca. Regnicoccus frigidus. Host-virus interactions were characterised by a depth-dependent distribution of virus type (e.g. highest abundance of specialist viruses in the oxic zone) and host phylotype capacity to defend against (e.g. restriction-modification, retron and BREX systems) and evade viruses (cell surface proteins and cell wall biosynthesis and modification enzymes).

CONCLUSION: In Ace Lake, specific environmental factors such as the seasonal availability of sunlight affects microbial abundances and the associated processes that the microbial community performs. Here, we find that the population structure for Ca. Regnicoccus frigidus has evolved differently to the other dominant phototroph in the lake, Candidatus Chlorobium antarcticum. The geography (i.e. Antarctica), limnology (e.g. stratification) and abiotic (e.g. sunlight) and biotic (e.g. microbial interactions) factors determine the types of niches that develop in the lake. While the lake community has become increasingly well studied, metagenome-based studies are revealing that niche adaptation can take many paths; these paths need to be determined in order to make reasonable predictions about the consequences of future ecosystem perturbations. Video Abstract.}, } @article {pmid36457010, year = {2022}, author = {Liu, L and Yang, Y and Deng, Y and Zhang, T}, title = {Nanopore long-read-only metagenomics enables complete and high-quality genome reconstruction from mock and complex metagenomes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {209}, pmid = {36457010}, issn = {2049-2618}, mesh = {Metagenome/genetics ; Metagenomics ; *Nanopores ; RNA, Ribosomal, 16S/genetics ; Sewage ; *Microbiota/genetics ; Prophages ; }, abstract = {BACKGROUND: The accurate and comprehensive analyses of genome-resolved metagenomics largely depend on the reconstruction of reference-quality (complete and high-quality) genomes from diverse microbiomes. Closing gaps in draft genomes have been approaching with the inclusion of Nanopore long reads; however, genome quality improvement requires extensive and time-consuming high-accuracy short-read polishing.

RESULTS: Here, we introduce NanoPhase, an open-source tool to reconstruct reference-quality genomes from complex metagenomes using only Nanopore long reads. Using Kit 9 and Q20+ chemistries, we first evaluated the feasibility of NanoPhase using a ZymoBIOMICS gut microbiome standard (including 21 strains), then sequenced the complex activated sludge microbiome and reconstructed 275 MAGs with median completeness of ~ 90%. As a result, NanoPhase improved the MAG contiguity (median MAG N50: 735 Kb, 44-86X compared to conventional short-read-based methods) while maintaining high accuracy, allowing for a full and accurate investigation of target microbiomes. Additionally, leveraging these high-contiguity reference-quality genomes, we identified 165 prophages within 111 MAGs, with 5 as active prophages, indicating the prophage was a neglected source of genetic diversity within microbial populations and influencer in shaping microbial composition in the activated sludge microbiome.

CONCLUSIONS: Our results demonstrated that NanoPhase enables reference-quality genome reconstruction from complex metagenomes directly using only Nanopore long reads. Furthermore, besides the 16S rRNA genes and biosynthetic gene clusters, the generated high-accuracy and high-contiguity MAGs improved the host identification of critical mobile genetic elements, e.g., prophage, serving as a genomic blueprint to investigate the microbial potential and ecology in the activated sludge ecosystem. Video Abstract.}, } @article {pmid36456554, year = {2022}, author = {Mäklin, T and Thorpe, HA and Pöntinen, AK and Gladstone, RA and Shao, Y and Pesonen, M and McNally, A and Johnsen, PJ and Samuelsen, Ø and Lawley, TD and Honkela, A and Corander, J}, title = {Strong pathogen competition in neonatal gut colonisation.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7417}, pmid = {36456554}, issn = {2041-1723}, support = {108413/A/15/D/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Female ; Pregnancy ; Infant, Newborn ; Humans ; *Cesarean Section ; *Ecosystem ; Klebsiella ; Metagenomics ; Parturition ; Escherichia coli/genetics ; }, abstract = {Opportunistic bacterial pathogen species and their strains that colonise the human gut are generally understood to compete against both each other and the commensal species colonising this ecosystem. Currently we are lacking a population-wide quantification of strain-level colonisation dynamics and the relationship of colonisation potential to prevalence in disease, and how ecological factors might be modulating these. Here, using a combination of latest high-resolution metagenomics and strain-level genomic epidemiology methods we performed a characterisation of the competition and colonisation dynamics for a longitudinal cohort of neonatal gut microbiomes. We found strong inter- and intra-species competition dynamics in the gut colonisation process, but also a number of synergistic relationships among several species belonging to genus Klebsiella, which includes the prominent human pathogen Klebsiella pneumoniae. No evidence of preferential colonisation by hospital-adapted pathogen lineages in either vaginal or caesarean section birth groups was detected. Our analysis further enabled unbiased assessment of strain-level colonisation potential of extra-intestinal pathogenic Escherichia coli (ExPEC) in comparison with their propensity to cause bloodstream infections. Our study highlights the importance of systematic surveillance of bacterial gut pathogens, not only from disease but also from carriage state, to better inform therapies and preventive medicine in the future.}, } @article {pmid36456547, year = {2022}, author = {Munk, P and Brinch, C and Møller, FD and Petersen, TN and Hendriksen, RS and Seyfarth, AM and Kjeldgaard, JS and Svendsen, CA and van Bunnik, B and Berglund, F and , and Larsson, DGJ and Koopmans, M and Woolhouse, M and Aarestrup, FM}, title = {Genomic analysis of sewage from 101 countries reveals global landscape of antimicrobial resistance.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {7251}, pmid = {36456547}, issn = {2041-1723}, mesh = {*Sewage ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Genomics ; Metagenome ; }, abstract = {Antimicrobial resistance (AMR) is a major threat to global health. Understanding the emergence, evolution, and transmission of individual antibiotic resistance genes (ARGs) is essential to develop sustainable strategies combatting this threat. Here, we use metagenomic sequencing to analyse ARGs in 757 sewage samples from 243 cities in 101 countries, collected from 2016 to 2019. We find regional patterns in resistomes, and these differ between subsets corresponding to drug classes and are partly driven by taxonomic variation. The genetic environments of 49 common ARGs are highly diverse, with most common ARGs carried by multiple distinct genomic contexts globally and sometimes on plasmids. Analysis of flanking sequence revealed ARG-specific patterns of dispersal limitation and global transmission. Our data furthermore suggest certain geographies are more prone to transmission events and should receive additional attention.}, } @article {pmid36455823, year = {2023}, author = {Zhao, L and Pan, J and Ding, Y and Cai, S and Cai, T and Chen, L and Ji, XM}, title = {Coupling continuous poly(3-hydroxybutyrate) synthesis with piperazine-contained wastewater treatment: Fermentation performance and microbial contamination deciphering.}, journal = {International journal of biological macromolecules}, volume = {226}, number = {}, pages = {1523-1532}, doi = {10.1016/j.ijbiomac.2022.11.264}, pmid = {36455823}, issn = {1879-0003}, mesh = {3-Hydroxybutyric Acid ; Fermentation ; *Wastewater ; *Hydroxybutyrates/metabolism ; Polyesters/metabolism ; Nitrogen/metabolism ; Piperazines ; }, abstract = {Open poly(3-hydroxybutyrate) (PHB) fermentation is of great potential, and batch PHB synthesis with piperazine as the nitrogen switch has been realized. However, it is vital to explore the feasibility of continuous PHB fermentation with piperazine-contained wastewater remediation collaboratively. Here, an aerobic membrane bioreactor was constructed for consecutive PHB synthesis. The removal efficiency of piperazine decreased from 100 % to 82.6 % after three cycles, meanwhile, the PHB concentration was 0.39 g·L[-1], 0.18 g·L[-1], and undetected for each cycle. Microbial community analysis showed that Proteobacteria, Actinobacteriota, and Bacteroidota were the main contaminating microbes. Furthermore, three metagenome-assembled genomes related to Flavobacterium collumnare, Herbaspirillum aquaticum, and Microbacterium enclense were identified as the dominant contaminating strains. These microbes obtained nitrogenous substrates transformed by Paracoccus sp. TOH, such as amino acids and dissolved organic matter, as nutrient for accumulation. This study verified the practicability of coupling continuous PHB synthesis with industrial wastewater treatment and revealed the derivation mechanism of contaminating species, which could provide a reference for the targeted nitrogen release gene knockout of functional PHB fermentation chassis.}, } @article {pmid36455775, year = {2023}, author = {Dell'Anno, F and Joaquim van Zyl, L and Trindade, M and Buschi, E and Cannavacciuolo, A and Pepi, M and Sansone, C and Brunet, C and Ianora, A and de Pascale, D and Golyshin, PN and Dell'Anno, A and Rastelli, E}, title = {Microbiome enrichment from contaminated marine sediments unveils novel bacterial strains for petroleum hydrocarbon and heavy metal bioremediation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {317}, number = {}, pages = {120772}, doi = {10.1016/j.envpol.2022.120772}, pmid = {36455775}, issn = {1873-6424}, mesh = {Biodegradation, Environmental ; *Petroleum/analysis ; Bacteria/genetics/metabolism ; *Metals, Heavy/metabolism ; *Polycyclic Aromatic Hydrocarbons/metabolism ; Hydrocarbons/metabolism ; *Microbiota ; Geologic Sediments/microbiology ; }, abstract = {Petroleum hydrocarbons and heavy metals are some of the most widespread contaminants affecting marine ecosystems, urgently needing effective and sustainable remediation solutions. Microbial-based bioremediation is gaining increasing interest as an effective, economically and environmentally sustainable strategy. Here, we hypothesized that the heavily polluted coastal area facing the Sarno River mouth, which discharges >3 tons of polycyclic aromatic hydrocarbons (PAHs) and ∼15 tons of heavy metals (HMs) into the sea annually, hosts unique microbiomes including marine bacteria useful for PAHs and HMs bioremediation. We thus enriched the microbiome of marine sediments, contextually selecting for HM-resistant bacteria. The enriched mixed bacterial culture was subjected to whole-DNA sequencing, metagenome-assembled-genomes (MAGs) annotation, and further sub-culturing to obtain the major bacterial species as pure strains. We obtained two novel isolates corresponding to the two most abundant MAGs (Alcanivorax xenomutans strain-SRM1 and Halomonas alkaliantarctica strain-SRM2), and tested their ability to degrade PAHs and remove HMs. Both strains exhibited high PAHs degradation (60-100%) and HMs removal (21-100%) yield, and we described in detail >60 genes in their MAGs to unveil the possible genetic basis for such abilities. Most promising yields (∼100%) were obtained towards naphthalene, pyrene and lead. We propose these novel bacterial strains and related genetic repertoire to be further exploited for effective bioremediation of marine environments contaminated with both PAHs and HMs.}, } @article {pmid36455385, year = {2022}, author = {Jia, XM and Wu, BX and Chen, BD and Li, KT and Liu, YD and Xu, Y and Wang, J and Zhang, X}, title = {Compositional and functional aberrance of the gut microbiota in treatment naïve patients with primary Sjögren's syndrome.}, journal = {Journal of autoimmunity}, volume = {134}, number = {}, pages = {102958}, doi = {10.1016/j.jaut.2022.102958}, pmid = {36455385}, issn = {1095-9157}, abstract = {OBJECTIVES: To investigate the compositional and functional characteristics of the gut microbiota in primary Sjögren's syndrome (pSS) and compare them with those in systemic lupus erythematosus (SLE).

METHODS: Stool samples from 78 treatment naïve pSS patients and 78 matched healthy controls were detected by shotgun metagenomic sequencing and compared with those from 49 treatment naïve SLE patients. The virulence loads and mimotopes of the gut microbiota were also assessed by sequence alignment.

RESULTS: The gut microbiota of treatment naïve pSS patients had lower richness and evenness and showed a different community distribution than that of healthy controls. The microbial species enriched in the pSS-associated gut microbiota included Lactobacillus salivarius, Bacteroides fragilis, Ruminococcus gnavus, Clostridium bartlettii, Clostridium bolteae, Veillonella parvula, and Streptococcus parasanguinis. Lactobacillus salivarius was the most discriminating species in the pSS patients, especially in those with interstitial lung disease (ILD). Among the differentiating microbial pathways, the superpathway of l-phenylalanine biosynthesis was also further enriched in pSS complicated with ILD. There were more virulence genes carried by the gut microbiota in pSS patients, most of which encoded peritrichous flagella, fimbriae, or curli fimbriae, three types of bacterial surface organelles involved in bacterial colonization and invasion. Five microbial peptides with the potential to mimic pSS-related autoepitopes were also enriched in the pSS gut. SLE and pSS shared significant gut microbial traits, including the community distribution, altered microbial taxonomy and pathways, and enriched virulence genes. However, Ruminococcus torques was depleted in pSS patients but enriched in SLE patients compared to that in healthy controls.

CONCLUSIONS: The gut microbiota in treatment naïve pSS patients was disturbed and shared significant similarity with that in SLE patients.}, } @article {pmid36455350, year = {2022}, author = {Liu, L and Teng, Y and Chen, H and Hu, J}, title = {Characteristics of resistome and bacterial community structure in constructed wetland during dormant period: A fullscale study from Annan wetland.}, journal = {Ecotoxicology and environmental safety}, volume = {248}, number = {}, pages = {114347}, doi = {10.1016/j.ecoenv.2022.114347}, pmid = {36455350}, issn = {1090-2414}, mesh = {*Wetlands ; *Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Ponds ; Proteobacteria ; }, abstract = {As a green technology, constructed wetlands (CWs) can provide a low-cost solution for wastewater treatment. Either as a standalone treatment or integrated with conventional treatment, nutrients, antibiotic resistant bacteria (ARB)/antibiotic resistance genes (ARGs) can be removed by CW efficiently. While, few studies have focused on characteristics of resistome and bacterial community (BC) structure in CW during dormant period. Therefore, in this study, Annan CW (a full-scale hybrid CW) was selected to characterize resistome and BC during dormant period. The profiles of bacteria / ARGs were monitored in combination of shotgun sequencing and metagenomic assembly analysis. And multidrug ARGs are the most abundant in Annan CW, and surface flow wetland had the relatively high ARG diversity and abundance compared with subsurface flow wetland and the front pond. The most dominant phylum in CW is Proteobacteria, while the other dominant phylum in three parts have different order. COD, TP, TN, ARGs, and mobile genetic genes (MGEs) were removed by subsurface flow CW with better performance, but virulent factors (VFs) were removed by surface flow CW with better performance. Based on the spatiotemporal distribution of ARGs, the internal mechanism of ARGs dynamic variation was explored by the redundancy analysis (RDA) and variation partitioning analysis (VPA). BCs, MGEs and environmental factors (EFs) were responsible for 45.6 %, 28.3 % and 15.4 % of the ARGs variations. Among these factors, BCs and MGEs were the major co-drivers impacting the ARG profile, and EFs indirectly influence the ARG profile. This study illustrates the specific functions of ARG risk elimination in different CW components, promotes a better understanding of the efficiency of CWs for the reduction of ARG and ARB, contributing to improve the removal performance of constructed wetlands. And provide management advice to further optimize the operation of CWs during dormant period.}, } @article {pmid36453930, year = {2022}, author = {Wang, Z and Yang, T and Mei, X and Wang, N and Li, X and Yang, Q and Dong, C and Jiang, G and Lin, J and Xu, Y and Shen, Q and Jousset, A and Banerjee, S}, title = {Bio-Organic Fertilizer Promotes Pear Yield by Shaping the Rhizosphere Microbiome Composition and Functions.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0357222}, pmid = {36453930}, issn = {2165-0497}, mesh = {Fertilizers/analysis ; *Pyrus ; Rhizosphere ; Soil/chemistry ; *Microbiota ; Bacteria ; Soil Microbiology ; }, abstract = {Bio-organic fertilizers (BOF) containing both organic amendments and beneficial microorganisms have been consistently shown to improve soils fertility and yield. However, the exact mechanisms which link amendments and yields remain disputed, and the complexity of bio-organic fertilizers may work in parallel in several ways. BOF may directly improve yield by replenishing soil nutrients or introducing beneficial microbial genes or indirectly by altering the soil microbiome to enrich native beneficial microorganisms. In this work, we aim to disentangle the relative contributions of direct and indirect effects on pear yield. We treated pear trees with either chemical fertilizer or organic fertilizer with/without the plant-beneficial bacterium Bacillus velezensis SQR9. We then assessed, in detail, soil physicochemical and biological properties (metagenome sequencing) as well as pear yield. We then evaluated the relative importance of direct and indirect effects of soil amendments on pear yield. Both organic treatments increased plant yield by up to 20%, with the addition of bacteria tripling the increase driven by organic fertilizer alone. This increase could be linked to alterations in soil physicochemical properties, bacterial community function, and metabolism. Supplementation of organic fertilizer SQR9 increased rhizosphere microbiome richness and functional diversity. Fertilizer-sensitive microbes and functions responded as whole guilds. Pear yield was most positively associated with the Mitsuaria- and Actinoplanes-dominated ecological clusters and with gene clusters involved in ion transport and secondary metabolite biosynthesis. Together, these results suggested that bio-organic fertilizers mainly act indirectly on plant yield by creating soil chemical properties which promote a plant-beneficial microbiome. IMPORTANCE Bio-organic fertilization is a widely used, eco-friendly, sustainable approach to increasing plant productivity in the agriculture and fruit industries. However, it remains unclear whether the promotion of fruit productivity is related to specific changes in microbial inoculants, the resident microbiome, and/or the physicochemical properties of rhizosphere soils. We found that bio-organic fertilizers alter soil chemical properties, thus manipulating specific microbial taxa and functions within the rhizosphere microbiome of pear plants to promote yield. Our work unveils the ecological mechanisms which underlie the beneficial impacts of bio-organic fertilizers on yield promotion in fruit orchards, which may help in the design of more efficient biofertilizers to promote sustainable fruit production.}, } @article {pmid36453923, year = {2022}, author = {Li, D and Gai, W and Zhang, J and Cheng, W and Cui, N and Wang, H}, title = {Multisite Metagenomic Next-Generation Sequencing Improved Diagnostic Performance for Sepsis-Associated Lymphopenia Patients.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0353222}, pmid = {36453923}, issn = {2165-0497}, mesh = {Humans ; Reproducibility of Results ; *Lymphopenia/diagnosis ; *Sepsis/complications/diagnosis ; High-Throughput Nucleotide Sequencing ; Metagenome ; Metagenomics ; }, abstract = {A precise and efficient microbiological diagnosis is essential for sepsis. Metagenomic next-generation sequencing (mNGS) is a novel technique for the diagnosis of infectious diseases, but its current application in multisite sampling and interpretation remains controversial. Therefore, this study was undertaken to evaluate the reliability of multisite mNGS tests and the efficiency of plasma mNGS based on lymphocyte subset counts. A prospective observational study was performed on the intubated patients with sepsis-associated lymphopenia from January 2020 to February 2022. During the study period, data on 71 patients with sepsis-induced lymphopenia were collected. Among the 125 mNGS tests, 95 were positive for pathogens, whereas of the 166 conventional microbiological tests (CMTs), 91 were positive. The comparison showed that 38 patients (53.5%) had at least one matched pair of plasma mNGS and CMT results, while for multisite sampling, 47 patients (66.2%) had at least one. Lymphocyte subset analysis showed that T lymphocyte (577 ± 317 versus 395 ± 207, P = 0.005) and CD4[+] T lymphocyte (333 ± 199 versus 230 ± 120, P = 0.009) counts were lower in the matched group. According to receiver operating characteristic (ROC) analysis, a CD4[+] T lymphocyte count lower than 266 cells/mm[3] was predictive of a match result. For sepsis-associated lymphopenia patients, we found that multisite mNGS tests showed a higher positivity rate. With plasma mNGS, a lower CD4[+] T lymphocyte count predicted a better match result with CMT. The lymphocyte subset analysis may promote the clinical interpretation of mNGS results. IMPORTANCE This study was undertaken to evaluate the reliability of pathogenic diagnoses based on multisite mNGS detection at the clinically suspected sites and to analyze the efficiency of plasma mNGS detection based on lymphocyte subset counts in patients with sepsis-associated lymphopenia.}, } @article {pmid36453905, year = {2022}, author = {Han, S and Zhuang, J and Pan, Y and Wu, W and Ding, K}, title = {Different Characteristics in Gut Microbiome between Advanced Adenoma Patients and Colorectal Cancer Patients by Metagenomic Analysis.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0159322}, pmid = {36453905}, issn = {2165-0497}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms ; Intestines ; Bacteria/genetics ; Feces/microbiology ; Firmicutes ; *Adenoma/genetics/microbiology ; }, abstract = {The occurrence and development of colorectal cancer (CRC) and advanced adenoma (AA) are closely related to the gut microbiome, and AA has a high cancerization progression rate to CRC. Current studies have revealed that bacteriological analysis cannot identify CRC from AA. The objective was to explore microbial targets that could identify CRC and AA from a microecological perspective and to figure out the best way to identify CRC based on fecal microbes. The metagenomic sequencing data were used to describe the gut microbiome profile and analyze the differences between microbial abundance and microbial single nucleotide polymorphism (SNP) characteristics in AA and CRC patients. It was found that there were no significant differences in the diversity between the two groups. The abundance of bacteria (e.g., Firmicutes, Clostridia, and Blautia), fungi (Hypocreales), archaea (Methanosarcina, Methanoculleus, and Methanolacinia), and viruses (Alphacoronavirus, Sinsheimervirus, and Gammaretrovirus) differed between AA and CRC patients. Multiple machine-learning algorithms were used to establish prediction models, aiming to identify CRC and AA. The accuracy of the random forest (RF) model based on the gut microbiome was 86.54%. Nevertheless, the accuracy of SNP was 92.31% in identifying CRC from AA. In conclusion, using microbial SNP was the best method to identify CRC, it was superior to using the gut microbiome, and it could provide new targets for CRC screening. IMPORTANCE There are differences in characteristic microorganisms between AA and CRC. However, current studies have indicated that bacteriological analysis cannot identify CC from AA, and thus, we wondered if there were some other targets that could be used to identify CRC from AA in the gut microbiome. The differences of SNPs in the gut microbiota of intraindividuals were significantly smaller than those of interindividuals. In addition, compared with intestinal microbes, SNP was less affected by time with certain stability. It was discovered that microbial SNP was better than the gut microbiome for identifying CRC from AA. Therefore, screening characteristic microbial SNP could provide a new research direction for identifying CRC from AA.}, } @article {pmid36453887, year = {2022}, author = {Zhang, W and Han, N and Zhang, T and Qiang, Y and Peng, X and Li, X and Kan, B}, title = {The Spatial Features and Temporal Changes in the Gut Microbiota of a Healthy Chinese Population.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0131022}, pmid = {36453887}, issn = {2165-0497}, mesh = {Adult ; Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Cohort Studies ; East Asian People ; *Microbiota ; Feces/microbiology ; }, abstract = {In this study, we aimed to understand the characteristics of the gut microbial composition in a healthy Chinese population and to evaluate if they differed across different regions. In addition, we aimed to understand the changes in the gut microbial composition over time. We collected 239 fecal samples from healthy Chinese adults living in four regions and performed a 1-year time cohort study in a small population in Beijing. The Chinese gut microbiota share 34 core bacterial genera and 39 core bacterial species, which exist in all collected samples. Several disease-related microorganisms (DRMs), virulence factors, and antibiotic resistance genes were found in one or more healthy Chinese samples. Differences in gut microbiota were observed in samples from different regions, locations, individuals, and time points. Compared to other factors, time was associated with a lower degree of change in the gut microbiota. Our findings revealed spatial and temporal changes in the gut microbiota of healthy Chinese individuals. Compared to fecal microbiomes of 152 samples in the publicly released the Human Microbiome Project (HMP) project from the United States, samples in this study have higher variability in the fecal microbiome, with higher richness, Shannon diversity indices, and Pielou evenness indexes, at both the genus and species levels. The microbiota data obtained in this study will provide a detailed basis for further understanding the composition of the gut microbiota in the healthy Chinese population. IMPORTANCE China accounts for approximately 1/5th of the world's total population. Differences in environment, ethnicity, and living habits could impart unique features to the structure of the gut microbiota of Chinese individuals. In 2016, we started to investigate healthy Chinese people and their gut microbiomes. Phase I results for 16S rRNA amplicons have been released. However, owing to the limitations of 16S rRNA amplicon sequencing, the gut microbiome of a healthy Chinese population could not be examined thoroughly at the species level, and the detailed changes in the gut microbiota over time need to be investigated. To address these knowledge gaps, we started a phase II study and investigated the basis for variations in the gut microbiome composition in a healthy Chinese population at the species level using shotgun metagenomics technology. In the phase II study, we also conducted a time scale analysis of fecal samples from healthy Chinese subjects, as a pioneered study, which quantitatively clarified the changes in the gut microbiota at both the spatial and temporal levels and elucidated the distribution pattern of DRMs in healthy Chinese individuals.}, } @article {pmid36452947, year = {2022}, author = {Liu, Y and Ma, X and Chen, J and Wang, H and Yu, Z}, title = {Nontuberculous mycobacteria by metagenomic next-generation sequencing: Three cases reports and literature review.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {972280}, pmid = {36452947}, issn = {2296-2565}, mesh = {Humans ; Female ; *Nontuberculous Mycobacteria/genetics ; *High-Throughput Nucleotide Sequencing ; Microbiological Techniques ; Immunocompromised Host ; }, abstract = {BACKGROUND: The increasing worldwide incidence of nontuberculous mycobacterial lung disease (NTM-LD) and the similarity of its manifestations to those of tuberculosis (TB) pose huge challenges in the diagnosis and treatment of NTM-LD, which is commonly misdiagnosed and mistreated as TB. Proper diagnosis and treatment at an early stage can greatly improve patient outcomes.

CASE PRESENTATION: Mycobacterium avium was identified by mNGS in lung tissue of case 1 and bronchioalveolar fluid from case 2 that was not identified using conventional microbiological methods. Multiple NTM species were detected in the blood mNGS samples from case 3 who had disseminated NTM infection. Although NTM was isolated from blood culture, conventional methods failed to identify the organisms to the level of species. All three patients were suffering from and being treated for myelodysplastic syndrome, rheumatoid arthritis, systemic lupus erythematosus, or acute lymphoblastic leukemia, making them immunosuppressed and susceptible to NTM infections. Case 1 and Case 2 significantly improved after anti-NTM treatment, but case 3 succumbed to the infection due to her underlying medical illness despite aggressive treatment.

CONCLUSIONS: The cases in this study demonstrate the effectiveness of mNGS in facilitating and improving the clinical diagnosis of NTM infections. We propose combining mNGS with traditional diagnostic methods to identify pathogens at the early stages of the disease so that targeted treatment can be implemented.}, } @article {pmid36452918, year = {2022}, author = {Singh, A and Kumar, M and Chakdar, H and Pandiyan, K and Kumar, SC and Zeyad, MT and Singh, BN and Ravikiran, KT and Mahto, A and Srivastava, AK and Saxena, AK}, title = {Influence of host genotype in establishing root associated microbiome of indica rice cultivars for plant growth promotion.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1033158}, pmid = {36452918}, issn = {1664-302X}, abstract = {Rice plants display a unique root ecosystem comprising oxic-anoxic zones, harboring a plethora of metabolic interactions mediated by its root microbiome. Since agricultural land is limited, an increase in rice production will rely on novel methods of yield enhancement. The nascent concept of tailoring plant phenotype through the intervention of synthetic microbial communities (SynComs) is inspired by the genetics and ecology of core rhizobiome. In this direction, we have studied structural and functional variations in the root microbiome of 10 indica rice varieties. The studies on α and β-diversity indices of rhizospheric root microbiome with the host genotypes revealed variations in the structuring of root microbiome as well as a strong association with the host genotypes. Biomarker discovery, using machine learning, highlighted members of class Anaerolineae, α-Proteobacteria, and bacterial genera like Desulfobacteria, Ca. Entotheonella, Algoriphagus, etc. as the most important features of indica rice microbiota having a role in improving the plant's fitness. Metabolically, rice rhizobiomes showed an abundance of genes related to sulfur oxidation and reduction, biofilm production, nitrogen fixation, denitrification, and phosphorus metabolism. This comparative study of rhizobiomes has outlined the taxonomic composition and functional diversification of rice rhizobiome, laying the foundation for the development of next-generation microbiome-based technologies for yield enhancement in rice and other crops.}, } @article {pmid36452153, year = {2022}, author = {Tian, Y and Wu, X and Li, Y and He, W and Liu, Z and Myers, FL and Zhou, L}, title = {Case report: Unilateral panuveitis as a manifestation of Alport syndrome in a Chinese pediatric patient.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {934829}, pmid = {36452153}, issn = {1664-8021}, abstract = {Purpose: The study aimed to report a rare case of a patient with Alport syndrome, which was manifested as unilateral non-infectious uveitis after bilateral cataract surgery. Methods: A case report. Results: A 2-year-old boy was diagnosed with unilateral panuveitis based on the clinical and multimodal imaging findings. Intraocular fluid samples for metagenomic next-generation sequencing (mNGS) and microbial culture were negative. However, urine tests found proteinuria and microscopic hematuria. Pathologic findings of the kidney revealed a thickened membrane, and a diagnosis of Alport syndrome was considered. Gene analysis found deletions in exon 1 of COL4A5 and exons 1 and 2 of COL4A6. The uveitis resolved gradually, following the administration of oral steroids. Conclusion: Uveitis may be an ocular manifestation of Alport syndrome.}, } @article {pmid36451314, year = {2023}, author = {Chen, YW and Wu, GH and Lee, BS and Liu, CT and Li, HY and Cheng, SJ and Kuo, WT and Jeng, JH and Chang, PC and Lin, CP and Chou, HE and Hou, HH}, title = {Third-generation sequencing-selected Scardovia wiggsiae promotes periodontitis progression in mice.}, journal = {Journal of periodontal research}, volume = {58}, number = {1}, pages = {155-164}, doi = {10.1111/jre.13077}, pmid = {36451314}, issn = {1600-0765}, support = {109-2314-B-002-027-MY2//Ministry of Science and Technology, Taiwan/ ; 109-2314-B-002-181-MY3//Ministry of Science and Technology, Taiwan/ ; 111-2314-B-002-119//Ministry of Science and Technology, Taiwan/ ; 10912041001//National Taiwan University/ ; 110-S5072//National Taiwan University Hospital/ ; 111-S0255//National Taiwan University Hospital/ ; }, mesh = {Mice ; Animals ; X-Ray Microtomography/adverse effects ; *Alveolar Bone Loss/pathology ; *Periodontitis/metabolism ; *Actinobacteria ; Bacteria ; *Dental Plaque/complications ; }, abstract = {BACKGROUNDS: Periodontitis is an oral-bacteria-directed disease that occurs worldwide. Currently, periodontal pathogens are mostly determined using traditional culture techniques, next-generation sequencing, and microbiological screening system. In addition to the well-known and cultivatable periodontal bacteria, we aimed to discover a novel periodontal pathogen by using DNA sequencing and investigate its role in the progression of periodontitis.

OBJECTIVE: This study identified pathogens from subgingival dental plaque in patients with periodontitis by using the Oxford Nanopore Technology (ONT) third-generation sequencing system and validated the impact of selected pathogen in periodontitis progression by ligature-implanted mice.

METHODS: Twenty-five patients with periodontitis and 25 healthy controls were recruited in this study. Subgingival plaque samples were collected for metagenomic analysis. The ONT third-generation sequencing system was used to confirm the dominant bacteria. A mouse model with ligature implantation and bacterial injection verified the pathogenesis of periodontitis. Neutrophil infiltration and osteoclast activity were evaluated using immunohistochemistry and tartrate-resistant acid phosphatase assays in periodontal tissue. Gingival inflammation was evaluated using pro-inflammatory cytokines in gingival crevicular fluids. Alveolar bone destruction in the mice was evaluated using micro-computed tomography and hematoxylin and eosin staining.

RESULTS: Scardovia wiggsiae (S. wiggsiae) was dominant in the subgingival plaque of the patients with periodontitis. S. wiggsiae significantly deteriorated ligature-induced neutrophil infiltration, osteoclast activation, alveolar bone destruction, and the secretion of interleukin-6, monocyte chemoattractant protein-1, and tumor necrosis factor-α in the mouse model.

CONCLUSION: Our metagenome results suggested that S. wiggsiae is a dominant flora in patients with periodontitis. In mice, the induction of neutrophil infiltration, proinflammatory cytokine secretion, osteoclast activation, and alveolar bone destruction further verified the pathogenic role of S. wiggsiae in the progress of periodontitis. Future studies investigating the metabolic interactions between S. wiggsiae and other periodontopathic bacteria are warranted.}, } @article {pmid36451244, year = {2022}, author = {Palomo, A and Dechesne, A and Pedersen, AG and Smets, BF}, title = {Genomic profiling of Nitrospira species reveals ecological success of comammox Nitrospira.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {204}, pmid = {36451244}, issn = {2049-2618}, mesh = {*Nitrites ; *Ammonia ; Phylogeny ; Bacteria ; Genomics ; }, abstract = {BACKGROUND: The discovery of microorganisms capable of complete ammonia oxidation to nitrate (comammox) has prompted a paradigm shift in our understanding of nitrification, an essential process in N cycling, hitherto considered to require both ammonia oxidizing and nitrite oxidizing microorganisms. This intriguing metabolism is unique to the genus Nitrospira, a diverse taxon previously known to only contain canonical nitrite oxidizers. Comammox Nitrospira have been detected in diverse environments; however, a global view of the distribution, abundance, and diversity of Nitrospira species is still incomplete.

RESULTS: In this study, we retrieved 55 metagenome-assembled Nitrospira genomes (MAGs) from newly obtained and publicly available metagenomes. Combined with publicly available MAGs, this constitutes the largest Nitrospira genome database to date with 205 MAGs, representing 132 putative species, most without cultivated representatives. Mapping of metagenomic sequencing reads from various environments against this database enabled an analysis of the distribution and habitat preferences of Nitrospira species. Comammox Nitrospira's ecological success is evident as they outnumber and present higher species-level richness than canonical Nitrospira in all environments examined, except for marine and wastewaters samples. The type of environment governs Nitrospira species distribution, without large-scale biogeographical signal. We found that closely related Nitrospira species tend to occupy the same habitats, and that this phylogenetic signal in habitat preference is stronger for canonical Nitrospira species. Comammox Nitrospira eco-evolutionary history is more complex, with subclades achieving rapid niche divergence via horizontal transfer of genes, including the gene encoding hydroxylamine oxidoreductase, a key enzyme in nitrification.

CONCLUSIONS: Our study expands the genomic inventory of the Nitrospira genus, exposes the ecological success of complete ammonia oxidizers within a wide range of habitats, identifies the habitat preferences of (sub)lineages of canonical and comammox Nitrospira species, and proposes that horizontal transfer of genes involved in nitrification is linked to niche separation within a sublineage of comammox Nitrospira. Video Abstract.}, } @article {pmid36451103, year = {2022}, author = {Sarkar, S and Kamke, A and Ward, K and Hartung, E and Ran, Q and Feehan, B and Galliart, M and Jumpponen, A and Johnson, L and Lee, STM}, title = {Pseudomonas cultivated from Andropogon gerardii rhizosphere show functional potential for promoting plant host growth and drought resilience.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {784}, pmid = {36451103}, issn = {1471-2164}, support = {OIA-1656006//National Science Foundation/ ; 2020-67019-31803//National Institute of Food and Agriculture/ ; }, mesh = {*Andropogon ; Rhizosphere ; Droughts ; Pseudomonas ; Phylogeny ; *Poa ; Nitrogen ; Nitrate Reductases ; }, abstract = {BACKGROUND: Climate change will result in more frequent droughts that can impact soil-inhabiting microbiomes (rhizobiomes) in the agriculturally vital North American perennial grasslands. Rhizobiomes have contributed to enhancing drought resilience and stress resistance properties in plant hosts. In the predicted events of more future droughts, how the changing rhizobiome under environmental stress can impact the plant host resilience needs to be deciphered. There is also an urgent need to identify and recover candidate microorganisms along with their functions, involved in enhancing plant resilience, enabling the successful development of synthetic communities.

RESULTS: In this study, we used the combination of cultivation and high-resolution genomic sequencing of bacterial communities recovered from the rhizosphere of a tallgrass prairie foundation grass, Andropogon gerardii. We cultivated the plant host-associated microbes under artificial drought-induced conditions and identified the microbe(s) that might play a significant role in the rhizobiome of Andropogon gerardii under drought conditions. Phylogenetic analysis of the non-redundant metagenome-assembled genomes (MAGs) identified a bacterial genome of interest - MAG-Pseudomonas. Further metabolic pathway and pangenome analyses recovered genes and pathways related to stress responses including ACC deaminase; nitrogen transformation including assimilatory nitrate reductase in MAG-Pseudomonas, which might be associated with enhanced drought tolerance and growth for Andropogon gerardii.

CONCLUSIONS: Our data indicated that the metagenome-assembled MAG-Pseudomonas has the functional potential to contribute to the plant host's growth during stressful conditions. Our study also suggested the nitrogen transformation potential of MAG-Pseudomonas that could impact Andropogon gerardii growth in a positive way. The cultivation of MAG-Pseudomonas sets the foundation to construct a successful synthetic community for Andropogon gerardii. To conclude, stress resilience mediated through genes ACC deaminase, nitrogen transformation potential through assimilatory nitrate reductase in MAG-Pseudomonas could place this microorganism as an important candidate of the rhizobiome aiding the plant host resilience under environmental stress. This study, therefore, provided insights into the MAG-Pseudomonas and its potential to optimize plant productivity under ever-changing climatic patterns, especially in frequent drought conditions.}, } @article {pmid36451083, year = {2022}, author = {Sun, J and Qiu, Z and Egan, R and Ho, H and Li, Y and Wang, Z}, title = {Persistent memory as an effective alternative to random access memory in metagenome assembly.}, journal = {BMC bioinformatics}, volume = {23}, number = {1}, pages = {513}, pmid = {36451083}, issn = {1471-2105}, support = {DE-AC02-05CH11231//Biological and Environmental Research/ ; }, mesh = {*Metagenome ; Metagenomics ; *Microbiota ; Software ; Computational Biology ; }, abstract = {BACKGROUND: The assembly of metagenomes decomposes members of complex microbe communities and allows the characterization of these genomes without laborious cultivation or single-cell metagenomics. Metagenome assembly is a process that is memory intensive and time consuming. Multi-terabyte sequences can become too large to be assembled on a single computer node, and there is no reliable method to predict the memory requirement due to data-specific memory consumption pattern. Currently, out-of-memory (OOM) is one of the most prevalent factors that causes metagenome assembly failures.

RESULTS: In this study, we explored the possibility of using Persistent Memory (PMem) as a less expensive substitute for dynamic random access memory (DRAM) to reduce OOM and increase the scalability of metagenome assemblers. We evaluated the execution time and memory usage of three popular metagenome assemblers (MetaSPAdes, MEGAHIT, and MetaHipMer2) in datasets up to one terabase. We found that PMem can enable metagenome assemblers on terabyte-sized datasets by partially or fully substituting DRAM. Depending on the configured DRAM/PMEM ratio, running metagenome assemblies with PMem can achieve a similar speed as DRAM, while in the worst case it showed a roughly two-fold slowdown. In addition, different assemblers displayed distinct memory/speed trade-offs in the same hardware/software environment.

CONCLUSIONS: We demonstrated that PMem is capable of expanding the capacity of DRAM to allow larger metagenome assembly with a potential tradeoff in speed. Because PMem can be used directly without any application-specific code modification, these findings are likely to be generalized to other memory-intensive bioinformatics applications.}, } @article {pmid36451056, year = {2023}, author = {Chivian, D and Jungbluth, SP and Dehal, PS and Wood-Charlson, EM and Canon, RS and Allen, BH and Clark, MM and Gu, T and Land, ML and Price, GA and Riehl, WJ and Sneddon, MW and Sutormin, R and Zhang, Q and Cottingham, RW and Henry, CS and Arkin, AP}, title = {Publisher Correction: Metagenome-assembled genome extraction and analysis from microbiomes using KBase.}, journal = {Nature protocols}, volume = {18}, number = {2}, pages = {658}, doi = {10.1038/s41596-022-00794-4}, pmid = {36451056}, issn = {1750-2799}, } @article {pmid36450914, year = {2022}, author = {Miller, JH and Simpson, C}, title = {When did mammoths go extinct?.}, journal = {Nature}, volume = {612}, number = {7938}, pages = {E1-E3}, pmid = {36450914}, issn = {1476-4687}, mesh = {Animals ; *Metagenomics ; *Mammoths/genetics ; Biota ; }, } @article {pmid36450879, year = {2023}, author = {Deepthi, M and Arvind, K and Saxena, R and Pulikkan, J and Sharma, VK and Grace, T}, title = {Exploring variation in the fecal microbial communities of Kasaragod Dwarf and Holstein crossbred cattle.}, journal = {Antonie van Leeuwenhoek}, volume = {116}, number = {1}, pages = {53-65}, pmid = {36450879}, issn = {1572-9699}, mesh = {Female ; Animals ; Cattle ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; Feces ; *Gastrointestinal Microbiome/genetics ; Alcaligenes/genetics ; }, abstract = {The gut microbiota and its impact on health and nutrition in animals, including cattle has been of intense interest in recent times. Cattle, in particular indigenous varieties like Kasaragod Dwarf cow, have not received the due consideration given to other non-native cattle breeds, and the composition of their fecal microbiome is yet to be established. This study applied 16S rRNA high-throughput sequencing of fecal samples and compared the Kasaragod Dwarf with the highly prevalent Holstein crossbred cattle. Variation in their microbial composition was confirmed by marker gene-based taxonomic analysis. Principle Coordinate Analysis (PCoA) showed the distinct microbial architecture of the two cattle types. While the two cattle types possess unique signature taxa, in Kasaragod Dwarf cattle, many of the identified genera, including Anaerovibrio, Succinivibrio, Roseburia, Coprococcus, Paludibacter, Sutterella, Coprobacillus, and Ruminobacter, have previously been shown to be present in higher abundance in animals with higher feed efficiency. This is the first report of Kasaragod Dwarf cattle fecal microbiome profiling. Our findings highlight the predominance of specific taxa potentially associated with different fermentation products and feed efficiency phenotypes in Kasaragod Dwarf cattle compared to Holstein crossbred cattle.}, } @article {pmid36450245, year = {2022}, author = {Sargsian, S and Chen, Z and Lee, SC and Robertson, A and Thur, RS and Sproch, J and Devlin, JC and Tee, MZ and Er, YX and Copin, R and Heguy, A and Pironti, A and Torres, VJ and Ruggles, KV and Lim, YAL and Bethony, J and Loke, P and Cadwell, K}, title = {Clostridia isolated from helminth-colonized humans promote the life cycle of Trichuris species.}, journal = {Cell reports}, volume = {41}, number = {9}, pages = {111725}, pmid = {36450245}, issn = {2211-1247}, support = {P30 CA016087/CA/NCI NIH HHS/United States ; R01 DK093668/DK/NIDDK NIH HHS/United States ; R01 AI140754/AI/NIAID NIH HHS/United States ; R01 AI130945/AI/NIAID NIH HHS/United States ; R01 DK124336/DK/NIDDK NIH HHS/United States ; R01 AI133977/AI/NIAID NIH HHS/United States ; S10 OD023423/OD/NIH HHS/United States ; R01 HL123340/HL/NHLBI NIH HHS/United States ; T32 AI007180/AI/NIAID NIH HHS/United States ; R01 AI121244/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Animals ; Trichuris ; *Helminths ; Firmicutes ; Life Cycle Stages ; *Trichuriasis ; }, abstract = {Soil-transmitted intestinal worms known as helminths colonize over 1.5 billion people worldwide. Although helminth colonization has been associated with altered composition of the gut microbiota, such as increases in Clostridia, individual species have not been isolated and characterized. Here, we isolate and sequence the genome of 13 Clostridia from the Orang Asli, an indigenous population in Malaysia with a high prevalence of helminth infections. Metagenomic analysis of 650 fecal samples from urban and rural Malaysians confirm the prevalence of species corresponding to these isolates and reveal a specific association between Peptostreptococcaceae family members and helminth colonization. Remarkably, Peptostreptococcaceae isolated from the Orang Asli display superior capacity to promote the life cycle of whipworm species, including hatching of eggs from Trichuris muris and Trichuris trichiura. These findings support a model in which helminths select for gut colonization of microbes that support their life cycle.}, } @article {pmid36449831, year = {2022}, author = {Alsaedi, ZS and Ashy, RA and Shami, AY and Majeed, MA and Alswat, AM and Baz, L and Baeshen, MN and Jalal, RS}, title = {Metagenomic study of the communities of bacterial endophytes in the desert plant Senna Italica and their role in abiotic stress resistance in the plant.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {82}, number = {}, pages = {e267584}, doi = {10.1590/1519-6984.267584}, pmid = {36449831}, issn = {1678-4375}, mesh = {*Endophytes/genetics ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Bacteria/genetics ; Stress, Physiological ; }, abstract = {Plant leaves and roots are home to diverse communities of bacteria, which play a significant role in plant health and growth. Although one of the most unfriendly environments for plant growth is deserts, desert plants can influence their surrounding microbial population and choose favorable bacteria that encourage their growth under these severe circumstances. Senna italica is known for its excellent medicinal values as a traditional medical plant, but little is known about its associated endophytic bacterial community under extreme conditions. In the present study, metagenomic sequencing of 16S rRNA was used to report the diversity of endophytic bacterial communities associated with the leaves and roots of the desert medicinal plant Senna italica that was collected from the Asfan region in northeast Jeddah, Saudi Arabia. Analyses of the 16S rRNA sequences at the taxonomic phylum level revealed that bacterial communities in the roots and leaves samples belonged to five phyla, including Cyanobacteria, Proteobacteria, Actinobacteria, Firmicutes, and unclassified phyla. Results indicated that the most common phyla were Cyanobacteria/Chloroplast and Actinobacteria. Analysis of the 16S rRNA sequences at the taxonomic phylum level revealed that bacterial communities in the roots and leaves samples belonged to twelve genera at the taxonomic genus level. The most abundant ones were highlighted for further analysis, including Okibacterium and Streptomyces found in Actinobacteria, which were the dominant genus in roots samples. However, Streptophyta found in Cyanobacteria/Chloroplast was the dominant genus in leaf samples. Metagenomic analysis of medicinal plants leads to identifying novel organisms or genes that may have a role in abiotic stress resistance in the plant. The study of endophytic microbiome taxonomic, phylogenetic, and functional diversity will better know innovative candidates that may be selected as biological agents to enhance agricultural and industrial processes, especially for crop desert agricultural improvement.}, } @article {pmid36449022, year = {2023}, author = {Hati, S and Ramanuj, K and Basaiawmoit, B and Koringa, P and Desai, M and Ghodasara, DJ and Joshi, KV and Pathan, M and V, S and Bhagora, NJ and Savaliya, FP and Mishra, BK}, title = {Significance of Limosilactobacillus fermentum and Saccharomyces cerevisiae on the Growth Performance, Haematological Traits, Serum Biochemistry, Faecal and Caeca Microbiota of Broiler Chickens.}, journal = {Journal of the American Nutrition Association}, volume = {42}, number = {7}, pages = {706-725}, doi = {10.1080/27697061.2022.2149634}, pmid = {36449022}, issn = {2769-707X}, abstract = {OBJECTIVE: The aim of the study was to supplement Lactobacillus and yeast in broiler feed by replacing immunomodulators to develop antibiotic free meat and egg production by analyzing broiler performance, haematological traits, serum biochemistry, histopathology, fecal bacterial count, and metagenomic analysis of broiler ceca.

METHOD: Two cultures i.e. KGL4 (Limosilactobacillus fermentum MTCC 25515) and WBS2A (Saccharomyces cerevisiae GI: MG101828) were considered for the evaluation of Broiler chicken's health and growth during 42 days study without supplementing immunomodulators and commercial probiotics in poultry feeds. The 96-day-old broiler chickens were grouped into: T1 [Control: basal diet + immunomodulatory factor and commercial probiotic], T2 [Basal diet without immunomodulatory factor and commercial probiotic + KGL4 (10[8] CFU/mL), T3 [Basal diet without immunomodulatory factor and commercial probiotic + WBS2A (10[7] CFU/mL), and T4 [Basal diet without immunomodulatory factor and commercial probiotic + KGL4 + WBS2A in a 1:1 ratio] (Institutional Animal Ethics Committee (IAEC) No. 365/PRS/2022). The following parameters, i.e., body weight gain, feed consumption ratio (FCR), white blood cell count (WBC), red blood cell count (RBC), hemoglobin content, platelet count, cholesterol content, triglycerides, high density lipoprotein (HDL), very low-density lipoprotein (VLDL), fecal counts and metagenomic analysis of broiler ceca samples, were measured.

RESULTS: In the study, amongst various traits, the overall performance of the group treated along with Limosilactobacillus fermentum (KGL4) showed improved results as compared to control group. Limosilactobacillus fermentum (KGL4) treated group had higher body weight gain (2583.04 ± 35.421 g), FCR (1.60 ± 0.019), WBC (235.60 ± 2.562 × 10[3]/µL), hemoglobin content (14.10 ± 0.442 g/dl), and HDL (131.40 ± 11.400 mg/dl). The investigation did not show significant variations in the relative proportions of genus or phylum among various groups during metagenomic analysis of ceca samples. There was also an improvement in haematological traits; no evidence of necrosis in heart, intestine and liver tissues.

CONCLUSIONS: The present study conclude that it is safe to feed Limosilactobacillus fermentum and Saccharomyces cerevisiae to broilers as feed supplements and also supports the current knowledge regarding the use of yeast and lactic acid bacteria as an effective alternative stimulant for maintaining health and growth of broiler chickens.}, } @article {pmid36448813, year = {2022}, author = {Patin, NV and Goodwin, KD}, title = {Long-Read Sequencing Improves Recovery of Picoeukaryotic Genomes and Zooplankton Marker Genes from Marine Metagenomes.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0059522}, pmid = {36448813}, issn = {2379-5077}, mesh = {Animals ; *Metagenome/genetics ; Zooplankton/genetics ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Genome, Microbial ; }, abstract = {Long-read sequencing offers the potential to improve metagenome assemblies and provide more robust assessments of microbial community composition and function than short-read sequencing. We applied Pacific Biosciences (PacBio) CCS (circular consensus sequencing) HiFi shotgun sequencing to 14 marine water column samples and compared the results with those for short-read metagenomes from the corresponding environmental DNA samples. We found that long-read metagenomes varied widely in quality and biological information. The community compositions of the corresponding long- and short-read metagenomes were frequently dissimilar, suggesting higher stochasticity and/or bias associated with PacBio sequencing. Long reads provided few improvements to the assembly qualities, gene annotations, and prokaryotic metagenome-assembled genome (MAG) binning results. However, only long reads produced high-quality eukaryotic MAGs and contigs containing complete zooplankton marker gene sequences. These results suggest that high-quality long-read metagenomes can improve marine community composition analyses and provide important insight into eukaryotic phyto- and zooplankton genetics, but the benefits may be outweighed by the inconsistent data quality. IMPORTANCE Ocean microbes provide critical ecosystem services, but most remain uncultivated. Their communities can be studied through shotgun metagenomic sequencing and bioinformatic analyses, including binning draft microbial genomes. However, most sequencing to date has been done using short-read technology, which rarely yields genome sequences of key microbes like SAR11. Long-read sequencing can improve metagenome assemblies but is hampered by technological shortcomings and high costs. In this study, we compared long- and short-read sequencing of marine metagenomes. We found a wide range of long-read metagenome qualities and minimal improvements to microbiome analyses. However, long reads generated draft genomes of eukaryotic algal species and provided full-length marker gene sequences of zooplankton species, including krill and copepods. These results suggest that long-read sequencing can provide greater genetic insight into the wide diversity of eukaryotic phyto- and zooplankton that interact as part of and with the marine microbiome.}, } @article {pmid36448791, year = {2022}, author = {Ryu, SW and Kim, JS and Oh, BS and Choi, WJ and Yu, SY and Bak, JE and Park, SH and Kang, SW and Lee, J and Jung, WY and Lee, JS and Lee, JH}, title = {Gut Microbiota Eubacterium callanderi Exerts Anti-Colorectal Cancer Activity.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0253122}, pmid = {36448791}, issn = {2165-0497}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Eubacterium ; *Colorectal Neoplasms/therapy ; Bacteria ; }, abstract = {The gut microbiota (GM) is associated with colorectal cancer (CRC) development. However, studies demonstrating the role of GM in CRC are limited to metagenomic analyses. These studies lack direct evidence proving that the candidate strains are involved in CRC, and isolated probiotics for bacteriotherapy. Therefore, to identify novel GM with anti-CRC activity, we previously isolated gut bacteria from the feces of healthy individuals, screened the isolated GM's anti-CRC activity, and discovered that cell-free supernatants of GM isolates demonstrated antiproliferative activity against CRC cells. Here, our study identified one of them as Eubacterium callanderi and chose it for further study because the genus Eubacterium has been suggested to contribute to various aspects of gut health; however, the functions are unknown. First, we confirmed that E. callanderi cell-free supernatant (EcCFS) exerted antiproliferative activity-by inducing apoptosis and cell cycle arrest-that was dose-dependent and specific to cancer cell lines. Next, we discovered that EcCFS active molecules were heat stable and protease insensitive. High-performance liquid chromatography analysis revealed that EcCFS contained high butyrate concentrations possessing anticancer activity. Additionally, gas chromatography-mass spectrometry analysis of the aqueous phase of ethyl acetate-extracted EcCFS and an antiproliferation assay of the aqueous phase and 4-aminobutanoic acid (GABA) suggested that GABA is a possible anti-CRC agent. Finally, in the CT26 allograft mouse model, E. callanderi oral administration and EcCFS peri-tumoral injection inhibited tumor growth in vivo. Therefore, our study reveals that E. callanderi has an anti-CRC effect and suggests that it may be a potential candidate for developing probiotics to control CRC. IMPORTANCE The gut microbiota has been reported to be involved in colorectal cancer, as suggested by metagenomic analysis. However, metagenomic analysis has limitations, such as bias in the analysis and the absence of bacterial resources for follow-up studies. Therefore, we attempted to discover gut microorganisms that are related to colorectal cancer using the culturomics method. In this study, we discovered that Eubacterium callanderi possesses anti-colorectal cancer activity in vitro and in vivo, suggesting that E. callanderi could be used in bacteriotherapy for colorectal cancer treatment.}, } @article {pmid36448778, year = {2022}, author = {Delavy, M and Burdet, C and Sertour, N and Devente, S and Docquier, JD and Grall, N and Volant, S and Ghozlane, A and Duval, X and Mentré, F and d'Enfert, C and Bougnoux, ME and , }, title = {A Clinical Study Provides the First Direct Evidence That Interindividual Variations in Fecal β-Lactamase Activity Affect the Gut Mycobiota Dynamics in Response to β-Lactam Antibiotics.}, journal = {mBio}, volume = {13}, number = {6}, pages = {e0288022}, pmid = {36448778}, issn = {2150-7511}, mesh = {Humans ; *Dysbiosis ; *Candida albicans/physiology ; Monobactams ; Anti-Bacterial Agents ; beta-Lactamases ; }, abstract = {Antibiotics disturb the intestinal bacterial microbiota, leading to gut dysbiosis and an increased risk for the overgrowth of opportunistic pathogens. It is not fully understood to what extent antibiotics affect the fungal fraction of the intestinal microbiota, the mycobiota. There is no report of the direct role of antibiotics in the overgrowth in healthy humans of the opportunistic pathogenic yeast Candida albicans. Here, we have explored the gut mycobiota of 22 healthy subjects before, during, and up to 6 months after a 3-day regimen of third-generation cephalosporins (3GCs). Using ITS1-targeted metagenomics, we highlighted the strong intra- and interindividual diversity of the healthy gut mycobiota. With a specific quantitative approach, we showed that C. albicans prevalence was much higher than previously reported, with all subjects but one being carriers of C. albicans, although with highly variable burdens. 3GCs significantly altered the mycobiota composition and the fungal load was increased both at short and long term. Both C. albicans relative and absolute abundances were increased but 3GCs did not reduce intersubject variability. Variations in C. albicans burden in response to 3GC treatment could be partly explained by changes in the levels of endogenous fecal β-lactamase activity, with subjects characterized by a high increase of β-lactamase activity displaying a lower increase of C. albicans levels. A same antibiotic treatment might thus affect differentially the gut mycobiota and C. albicans carriage, depending on the treated subject, suggesting a need to adjust the current risk factors for C. albicans overgrowth after a β-lactam treatment. IMPORTANCE Fungal infections are redoubtable healthcare-associated complications in immunocompromised patients. Particularly, the commensal intestinal yeast Candida albicans causes invasive infections in intensive care patients and is, therefore, associated with high mortality. These infections are preceded by an intestinal expansion of C. albicans before its translocation into the bloodstream. Antibiotics are a well-known risk factor for C. albicans overgrowth but the impact of antibiotic-induced dysbiosis on the human gut mycobiota-the fungal microbiota-and the understanding of the mechanisms involved in C. albicans overgrowth in humans are very limited. Our study shows that antibiotics increase the fungal proportion in the gut and disturb the fungal composition, especially C. albicans, in a subject-dependent manner. Indeed, variations across subjects in C. albicans burden in response to β-lactam treatment could be partly explained by changes in the levels of endogenous fecal β-lactamase activity. This highlighted a potential new key factor for C. albicans overgrowth. Thus, the significance of our research is in providing a better understanding of the factors behind C. albicans intestinal overgrowth, which might lead to new means to prevent life-threatening secondary infections.}, } @article {pmid36448340, year = {2022}, author = {Wu, Y and Li, A and Cheng, L and Chen, Q and Li, J and Xu, Y and Huo, D}, title = {Deep Shotgun metagenomic and 16S rRNA analysis revealed the microbial diversity of lactic acid bacteria in traditional fermented foods of eastern Hainan, China.}, journal = {Food & function}, volume = {13}, number = {24}, pages = {12938-12952}, doi = {10.1039/d2fo02501a}, pmid = {36448340}, issn = {2042-650X}, mesh = {RNA, Ribosomal, 16S/genetics ; *Lactobacillales/genetics ; Food Microbiology ; *Fermented Foods/microbiology ; Metagenomics ; Fermentation ; China ; }, abstract = {The eastern part of Hainan, China, has a flat terrain and a suitable climate with abundant sunshine and rain. This unique environment makes the tropical microbial resources of natural fermented food unique and rich. Therefore, we combined Shotgun metagenomic sequencing, 16S rRNA sequencing and pure culture technology to analyze the microbial diversity, microbiota composition, species differences and correlation of 30 traditional fermented food samples collected from Wenchang, Qionghai, Wanning and Lingshui in the eastern part of Hainan province, and isolated, identified and preserved the microorganisms in them. The results showed that the microbial community structure differs significantly between samples from different regions and between different substrates. The alpha diversity of microorganisms in traditional fermented foods in the Wanning area was higher than those of the other three areas. The beta diversity indicated that the microbiota structural difference between Wanning and Qionghai was smaller. This is consistent with the fact that the precipitation in the Wanning area is the highest and similar to that of Qionghai. The alpha diversity of microorganisms was the highest in fermented vegetables, followed by fermented grains, and the lowest in fermented seafood. Beta diversity showed that the microbiota composition of fermented grains and fermented vegetables is very similar, but that of fermented seafood is significantly different. The results of microbiota structural analysis showed that firmicutes and proteobacteria are the dominant bacterial phyla, and Lactobacillus plantarum and Lactobacillus fermentum are the dominant species in traditional fermented foods in eastern Hainan. Lactic acid bacteria are the dominant species in traditional fermented foods from the eastern Hainan region of China, regardless of the substrate used in fermentation. According to the microbial functional characteristics, the microbial metabolism and biosynthesis pathways in traditional fermented foods in Hainan tend to be active. In addition, combined with pure culture technology, we isolated, identified and preserved 342 lactic acid bacteria strains from traditional fermented food in eastern Hainan province. This study helped us understand the different characteristics of microbial communities in tropical southern China and supplement the Lactobacillus species resource pool in tropical southern China. Moreover, it provided new insights and directions for the development and utilization of fermented foods.}, } @article {pmid36448268, year = {2023}, author = {Lu, Y and Lv, Y and Zhang, Y and Liu, Q and Xu, X and Xiao, X and Xu, J}, title = {Metatranscriptomes reveal the diverse responses of Thaumarchaeota ecotypes to environmental variations in the northern slope of the South China Sea.}, journal = {Environmental microbiology}, volume = {25}, number = {2}, pages = {410-427}, doi = {10.1111/1462-2920.16289}, pmid = {36448268}, issn = {1462-2920}, mesh = {*Ecotype ; Phylogeny ; *Archaea/metabolism ; Water/metabolism ; Carbon/metabolism ; Nitrogen/metabolism ; Seawater ; }, abstract = {Thaumarchaeota are among the most abundant prokaryotes in the ocean, playing important roles in carbon and nitrogen cycling. Marine Thaumarchaeota ecotypes exhibit depth-related diversification and seasonal changes. However, transcriptomic activities concerning niche partitioning among thaumarchaeal ecotypes remain unclear. Here, we examined the variations in the distribution and transcriptomic activity of marine Thaumarchaeota ecotypes. Three primary ecotypes were identified: a Nitrosopumilus-like clade; a Nitrosopelagicus-like water column A (WCA) clade, thriving in epipelagic water; and a water column B (WCB) clade, dominant in deep water. Depth-related partitioning of the three ecotypes and the seasonal variability of the WCA and WCB ecotypes were observed. Nutrient concentrations, chlorophyll α and salinity were the primary environmental factors. The relative abundance of the WCA ecotype and its transcript abundance of amoA gene were positively correlated with chlorophyll α and salinity, while the WCB ecotype was positively correlated with nitrate and phosphate. Based on high-quality metagenome-assembled genomes, transcriptomic analysis revealed that the three ecotypes exhibited various co-occurring expression patterns of the elemental cycling genes in the nitrogen, carbon, phosphorus, and sulfur cycles. Our results provide transcriptomic evidence of the niche differentiation of marine Thaumarchaeota ecotypes, highlighting the diverse roles of ecotypes and WCA subclades in biogeochemical cycles.}, } @article {pmid36447267, year = {2022}, author = {Li, Y and Qu, T and Li, D and Jing, J and Deng, Q and Wan, X}, title = {Human herpesvirus 7 encephalitis in an immunocompetent adult and a literature review.}, journal = {Virology journal}, volume = {19}, number = {1}, pages = {200}, pmid = {36447267}, issn = {1743-422X}, mesh = {Adult ; Child ; Humans ; *Herpesvirus 7, Human/genetics ; *Encephalitis, Herpes Simplex ; *Roseolovirus Infections/complications/diagnosis ; Electroencephalography ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Human herpesvirus 7 (HHV-7) is a common virus that infects children early and is accompanied by lifelong latency in cells, which is easy to reactivate in immunodeficient adults, but the underlying pathological mechanism is uncertain in immunocompetent adults without peculiar past medical history. Even though the clinical manifestation of the encephalitis caused by HHV-7 is uncommon in immunocompetent adults, the HHV-7 infection should not be neglected for encephalitis for unknown reasons.

CASE PRESENTATION: We reported here a case of HHV-7 encephalitis with epileptic seizures. While the brain computer tomography was standard, electroencephalography displayed slow waves in the temporal and bilateral frontal areas, then HHV-7 DNA was detected in the metagenomic next-generation sequencing of cerebrospinal fluid. Fortunately, the patient recovered after treatment and was discharged 2 months later. We also collected the related cases and explored a better way to illuminate the underlying mechanism.

CONCLUSION: The case indicates clinicians should memorize HHV-7 as an unusual etiology of encephalitis to make an early diagnosis and therapy.}, } @article {pmid36447235, year = {2022}, author = {Sun, X and Zhang, T and Sun, H and Sun, X}, title = {Disseminated nontuberculous mycobacterial infection with cryptic immunodeficiency mimicking malignancy: a case report.}, journal = {BMC pulmonary medicine}, volume = {22}, number = {1}, pages = {452}, pmid = {36447235}, issn = {1471-2466}, support = {2018-I2M-1-003//CAMS Innovation Fund for Medical Sciences/ ; }, mesh = {Humans ; Male ; Middle Aged ; Autoantibodies ; *Mycobacterium Infections, Nontuberculous/diagnosis/drug therapy ; Neoplasm Recurrence, Local ; Nontuberculous Mycobacteria ; *Opportunistic Infections ; Rituximab/therapeutic use ; }, abstract = {BACKGROUND: Nontuberculous mycobacteria (NTM) usually invades vulnerable hosts. Disseminated NTM (dNTM) infection can affect nearly all organs and be easily misdiagnosed as metastatic carcinoma or other systemic diseases, especially in seemingly immunocompetent hosts. Identification of underlying immunodeficiency is critical for the diagnosis and treatment of dNTM. Adult-onset immunodeficiency (AOID) with anti-IFN-γ autoantibodies has recently been recognized as a crucial but frequently neglected risk factor for dNTM infection. Frequent relapses of infection are common in AOID patients despite appropriate anti-infective treatment and B-cell-depleting therapy has shown some promising results. Herein, we report a case of dNTM infection mimicking malignancy in an AOID patient who was successfully treated with rituximab.

CASE PRESENTATION: A middle-aged male presented with fever, productive cough, multifocal skin abscesses and multiple osteolytic lesions with pathological fractures. Chest CT revealed consolidation of the lingula while bronchoscopy showed a mass completely blocking the airway opening of the inferior lingual segment. Metagenomic next-generation sequencing and mycobacterial culture of skin pus and bronchoalveolar lavage fluid reported Mycobacterium Colombiense, confirming the diagnosis of dNTM infection. However, anti-NTM antibiotics alone failed to prevent disease relapse and progression. Further evaluation indicated undetectable serum IFN-γ concentration and high-titer autoantibodies against IFN-γ, suggesting that AOID was the underlying reason for dNTM. Rituximab was added to treatment and successfully controlled the infection without relapse at one-year follow-up.

CONCLUSION: We reported a rare case of disseminated Mycobacterium Colombiense infection manifested with pulmonary mass, pathological fracture and dermapostasis in a host with AOID. Our case demonstrated that AOID should be screened when patients get the episode of disseminated NTM infection particularly when other risk factors are excluded. Besides prolonged anti-NTM therapy, AOID-associated NTM infection should be treated with B-cell-depleting therapy to prevent recurrence.}, } @article {pmid36445691, year = {2022}, author = {Duan, N and Radosevich, M and Zhuang, J and DeBruyn, JM and Staton, M and Schaeffer, SM}, title = {Identification of Novel Viruses and Their Microbial Hosts from Soils with Long-Term Nitrogen Fertilization and Cover Cropping Management.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0057122}, pmid = {36445691}, issn = {2379-5077}, mesh = {*Soil/chemistry ; Nitrogen/analysis ; Soil Microbiology ; Archaea ; *Viruses/genetics ; Carbon ; Fertilization ; }, abstract = {Soils are the largest organic carbon reservoir and are key to global biogeochemical cycling, and microbes are the major drivers of carbon and nitrogen transformations in the soil systems. Thus, virus infection-induced microbial mortality could impact soil microbial structure and functions. In this study, we recovered 260 viral operational taxonomic units (vOTUs) in samples collected from soil taken from four nitrogen fertilization (N-fertilization) and cover-cropping practices at an experimental site under continuous cotton production evaluating conservation agricultural management systems for more than 40 years. Only ~6% of the vOTUs identified were clustered with known viruses in the RefSeq database using a gene-sharing network. We found that 14% of 260 vOTUs could be linked to microbial hosts that cover key carbon and nitrogen cycling taxa, including Acidobacteriota, Proteobacteria, Verrucomicrobiota, Firmicutes, and ammonia-oxidizing archaea, i.e., Nitrososphaeria (phylum Thermoproteota). Viral diversity, community structure, and the positive correlation between abundance of a virus and its host indicate that viruses and microbes are more sensitive to N-fertilization than cover-cropping treatment. Viruses may influence key carbon and nitrogen cycling through control of microbial function and host populations (e.g., Chthoniobacterales and Nitrososphaerales). These findings provide an initial view of soil viral ecology and how it is influenced by long-term conservation agricultural management. IMPORTANCE Bacterial viruses are extremely small and abundant particles that can control the microbial abundance and community composition through infection, which gradually showed their vital roles in the ecological process to influence the nutrient flow. Compared to the substrate control, less is known about the influence of soil viruses on microbial community function, and even less is known about microbial and viral diversity in the soil system. To obtain a more complete knowledge of microbial function dynamics, the interaction between microbes and viruses cannot be ignored. To fully understand this process, it is fundamental to get insight into the correlation between the diversity of viral communities and bacteria which could induce these changes.}, } @article {pmid36445596, year = {2023}, author = {Mahmud, B and Boolchandani, M and Patel, S and Dantas, G}, title = {Functional Metagenomics to Study Antibiotic Resistance.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2601}, number = {}, pages = {379-401}, pmid = {36445596}, issn = {1940-6029}, support = {DP2 DK098089/DK/NIDDK NIH HHS/United States ; R01 GM099538/GM/NIGMS NIH HHS/United States ; }, mesh = {*Metagenomics ; Drug Resistance, Microbial/genetics ; *Metagenome ; Gene Library ; Sequence Analysis, DNA ; }, abstract = {The construction and screening of metagenomic expression libraries have a great potential to identify novel genes with desired functions. Here, we describe metagenomic library preparation from fecal DNA, screening of libraries for antibiotic resistance genes (ARGs), massively parallel DNA sequencing of the enriched DNA fragments, and a computational pipeline for high-throughput assembly and annotation of functionally selected DNA.}, } @article {pmid36445553, year = {2022}, author = {Bora, SS and Naorem, RS and Hazarika, DJ and Dasgupta, A and Churaman, A and Gogoi, M and Barooah, M}, title = {Agricultural Land Use Influences Bacteriophage Community Diversity, Richness, and Heterogeneity.}, journal = {Current microbiology}, volume = {80}, number = {1}, pages = {10}, pmid = {36445553}, issn = {1432-0991}, mesh = {*Bacteriophages/genetics ; Agriculture ; Soil ; Biodiversity ; Tea ; }, abstract = {The last two decades have witnessed a large-scale conversion of crop cultivation areas into small and mid-sized tea plantations in Assam, India. Agricultural land-use pattern positively or negatively influences native hydrology and above- and belowground biodiversity. Very little is known about the effect of agricultural land-use patterns on the soil virus (especially, bacteriophage) community structure and function. This metagenomic-based study evaluated the rhizosphere viral community structure of three interlinked cultivation areas, viz., mixed cropping area (coded as CP1), tea-seed orchard (CP2), and monocropping tea cultivation (CP3). The bacteriophages belonged to four major classes with the dominance of Malgrandaviricetes (CP1: 79.37%; CP2: 64.62%; CP3: 4.85%) followed by Caudoviricetes (CP1: 20.49%; CP2: 35.22%; CP3: 90.29%), Faserviricetes (CP1: 0.03%; CP2: 0.08%; CP3: 3.88%), and Tectiliviricetes (CP1: 0.12%; CP2: 0.07%; CP3: 0.97%). Microviruses dominated the phage population in both CP1 and CP2, representing 79.35% and 64.59% of total bacteriophage abundance. Both CP1 and CP2 had higher bacteriophage richness (species richness, R in CP1: 65; R in CP2: 66) and lower evenness (Pielou's evenness index, J in CP1: 0.531; J in CP2: 0.579) compared to the CP3 (R: 30; J: 0.902). Principal component analysis of edaphic soil factors and bacteriophage community structure showed a reverse-proportional correlation between the levels of Al saturation, and exchangeable Al[3+] ions with that of soil pH, and bacteriophage abundance. Our study indicates that monocropping tea cultivation soil bears less viral richness, abundance, and heterogeneity.}, } @article {pmid36445367, year = {2022}, author = {Abe, R and Akeda, Y and Sakamoto, N and Takeuchi, D and Sugawara, Y and Yamamoto, N and Kerdsin, A and Matsumoto, Y and Motooka, D and Laolerd, W and Santanirand, P and Suzuki, M and Shibayama, K and Tomono, K and Iida, T and Hamada, S}, title = {A Nationwide Plasmidome Surveillance in Thailand Reveals a Limited Variety of New Delhi Metallo-β-Lactamase-Producing Carbapenem-Resistant Enterobacteriaceae Clones and Spreading Plasmids.}, journal = {Journal of clinical microbiology}, volume = {60}, number = {12}, pages = {e0108022}, pmid = {36445367}, issn = {1098-660X}, mesh = {Humans ; *Carbapenem-Resistant Enterobacteriaceae/genetics ; Escherichia coli/genetics ; *Enterobacteriaceae Infections/epidemiology/drug therapy ; Thailand/epidemiology ; Microbial Sensitivity Tests ; beta-Lactamases/genetics ; Enterobacteriaceae/genetics ; Plasmids/genetics ; Klebsiella pneumoniae/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; }, abstract = {Despite frequent identification of plasmids carrying carbapenemase genes, the transfer of plasmids carrying carbapenemase genes is not well recognized in clinical settings because of technical limitations. To investigate the detailed mechanisms of the spread of carbapenem-resistant Enterobacteriaceae (CRE), we performed multifaceted genomic surveillance of CRE isolates in Thailand and analyzed their plasmidome. We analyzed 371 Enterobacteriaceae isolates carrying blaNDM-1 and 114 Enterobacteriaceae isolates carrying blaNDM-5 obtained from clinical samples of 473 patients in 11 representative hospitals located in six provinces in Thailand between 2012 and 2017. The complete structures of plasmids carrying blaNDM and chromosomal phylogeny were determined by combining Southern blotting hybridization analysis and our previously performed whole-genome short-read sequencing data. Dissemination of the blaNDM-5 gene among the Enterobacteriaceae isolates in Thailand was mainly owing to the nationwide clonal spread of Escherichia coli ST410 and regional clonal spreads of Escherichia coli ST361 and ST405. Analysis of blaNDM-1-carrying isolates revealed nationwide dissemination of two specific plasmids and nationwide clonal dissemination of Klebsiella pneumoniae ST16 accompanied with regional disseminations of three distinctive K. pneumoniae clones (ST231, ST14, and ST147) with different plasmids. Dissemination of CRE carrying blaNDM in Thailand is mainly based on nationwide clonal expansions of E. coli ST410 carrying blaNDM-5 and K. pneumoniae ST16 carrying blaNDM-1, nationwide dissemination of two distinctive plasmids carrying blaNDM-1, and accumulation of clonal expansions in regional areas. Although the overuse of antibiotics can promote CRE dissemination, the limited variety of transmitters highlights the importance of preventing horizontal dissemination among patients.}, } @article {pmid36445165, year = {2022}, author = {Jaiswal, S and Aneja, B and Jagannadham, J and Pandey, B and Chhokar, RS and Gill, SC and Ahlawat, OP and Kumar, A and Angadi, UB and Rai, A and Tiwari, R and Iquebal, MA and Kumar, D}, title = {Unveiling the Wheat Microbiome under Varied Agricultural Field Conditions.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0263322}, pmid = {36445165}, issn = {2165-0497}, mesh = {*Triticum/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Soil/chemistry ; Crops, Agricultural/microbiology ; Bacteria/genetics ; Soil Microbiology ; }, abstract = {Wheat being the important staple food crop plays a significant role in nutritional security. A wide variety of microbial communities beneficial to plants and contributing to plant health and production are found in the rhizosphere. The wheat microbiome encompasses an extensive variety of microbial species playing a key role in sustaining the physiology of the crop, nutrient uptake, and biotic/abiotic stress resilience. This report presents wheat microbiome analysis under six different farm practices, namely, organic (Org), timely sown (TS), wheat after pulse crop (WAPC), temperature-controlled phenotyping facility (TCPF), maize-wheat cropping system (MW), and residue burnt field (Bur), using 16S rRNA sequencing methodology. The soil samples collected from either side of the wheat row were mixed to get a final sample set for DNA extraction under each condition. After the data preprocessing, microbial community analysis was performed, followed by functional analysis and annotation. An abundance of the phylum Proteobacteria was observed, followed by Acidobacteria, Actinobacteria, and Gemmatimonadetes in the majority of the samples, while relative abundance was found to vary at the genus level. Analysis against the Carbohydrate-Active Enzymes (CAZy) database showed a high number of glycoside hydrolase genes in the TS, TCPF, and WAPC samples, while the Org, MW, and Bur samples predominantly had glycosyltransferase genes and carbohydrate esterase genes were in the lowest numbers. Also, the Org and TCPF samples showed lower diversity, while rare and abundant species ranged from 12 to 25% and 20 to 32% of the total bacterial species in all the sets, respectively. These variations indicate that the different cropping sequence had a significant impact on soil microbial diversity and community composition, which characterizes its economic and environmental value as a sustainable agricultural approach to maintaining food security and ecosystem health. IMPORTANCE This investigation examined the wheat microbiome under six different agricultural field conditions to understand the role of cropping pattern on soil microbial diversity. This study also elaborated the community composition, which has importance in economic (role of beneficial community leading to higher production) and environmental (role of microbial diversity/community in safeguarding the soil health, etc.) arenas. This could lead to a sustainable farming approach for food security and improved ecosystem health. Also, the majority of the microbes are unculturable; hence, technology-based microcultivation will be a potential approach for harnessing other cultured microorganisms, leading to unique species for commercial production. The outcome of this research-accelerated work can provide an idea to the scientists/breeders/agronomists/pathologists under the mentioned field conditions regarding their influence over their crops.}, } @article {pmid36445161, year = {2022}, author = {Sylvain, FÉ and Leroux, N and Normandeau, É and Holland, A and Bouslama, S and Mercier, PL and Luis Val, A and Derome, N}, title = {Genomic and Environmental Factors Shape the Active Gill Bacterial Community of an Amazonian Teleost Holobiont.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0206422}, pmid = {36445161}, issn = {2165-0497}, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; *Gills/chemistry/microbiology ; Fishes/genetics/microbiology ; *Microbiota/physiology ; Water ; Genomics ; Bacteria/genetics ; }, abstract = {Fish bacterial communities provide functions critical for their host's survival in contrasting environments. These communities are sensitive to environmental-specific factors (i.e., physicochemical parameters, bacterioplankton), and host-specific factors (i.e., host genetic background). The relative contribution of these factors shaping Amazonian fish bacterial communities is largely unknown. Here, we investigated this topic by analyzing the gill bacterial communities of 240 wild flag cichlids (Mesonauta festivus) from 4 different populations (genetic clusters) distributed across 12 sites in 2 contrasting water types (ion-poor/acidic black water and ion-rich/circumneutral white water). Transcriptionally active gill bacterial communities were characterized by a 16S rRNA metabarcoding approach carried on RNA extractions. They were analyzed using comprehensive data sets from the hosts genetic background (Genotyping-By-Sequencing), the bacterioplankton (16S rRNA) and a set of 34 environmental parameters. Results show that the taxonomic structure of 16S rRNA gene transcripts libraries were significantly different between the 4 genetic clusters and also between the 2 water types. However, results suggest that the contribution of the host's genetic background was relatively weak in comparison to the environment-related factors in structuring the relative abundance of different active gill bacteria species. This finding was also confirmed by a mixed-effects modeling analysis, which indicated that the dissimilarity between the taxonomic structure of bacterioplanktonic communities possessed the best explicative power regarding the dissimilarity between gill bacterial communities' structure, while pairwise fixation indexes (FST) from the hosts' genetic data only had a weak explicative power. We discuss these results in terms of bacterial community assembly processes and flag cichlid fish ecology. IMPORTANCE Host-associated microbial communities respond to factors specific to the host physiology, genetic backgrounds, and life history. However, these communities also show different degrees of sensitivity to environment-dependent factors, such as abiotic physico-chemical parameters and ecological interactions. The relative importance of host- versus environment-associated factors in shaping teleost bacterial communities is still understudied and is paramount for their conservation and aquaculture. Here, we studied the relative importance of host- and environment-associated factors structuring teleost bacterial communities using gill samples from a wild Amazonian teleost model (Mesonauta festivus) sampled in contrasting habitats along a 1500 km section of the Amazonian basin, thus ensuring high genetic diversity. Results showed that the contribution of the host's genetic background was weak compared to environment-related bacterioplanktonic communities in shaping gill bacterial assemblages, thereby suggesting that our understanding of teleost microbiome assembly could benefit from further studies focused on the ecological interplay between host-associated and free-living communities.}, } @article {pmid36445112, year = {2022}, author = {Sánchez-Navarro, R and Nuhamunada, M and Mohite, OS and Wasmund, K and Albertsen, M and Gram, L and Nielsen, PH and Weber, T and Singleton, CM}, title = {Long-Read Metagenome-Assembled Genomes Improve Identification of Novel Complete Biosynthetic Gene Clusters in a Complex Microbial Activated Sludge Ecosystem.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0063222}, pmid = {36445112}, issn = {2379-5077}, mesh = {*Metagenome/genetics ; Sewage ; Multigene Family/genetics ; *Microbiota/genetics ; Genome, Bacterial/genetics ; }, abstract = {Microorganisms produce a wide variety of secondary/specialized metabolites (SMs), the majority of which are yet to be discovered. These natural products play multiple roles in microbiomes and are important for microbial competition, communication, and success in the environment. SMs have been our major source of antibiotics and are used in a range of biotechnological applications. In silico mining for biosynthetic gene clusters (BGCs) encoding the production of SMs is commonly used to assess the genetic potential of organisms. However, as BGCs span tens to over 200 kb, identifying complete BGCs requires genome data that has minimal assembly gaps within the BGCs, a prerequisite that was previously only met by individually sequenced genomes. Here, we assess the performance of the currently available genome mining platform antiSMASH on 1,080 high-quality metagenome-assembled bacterial genomes (HQ MAGs) previously produced from wastewater treatment plants (WWTPs) using a combination of long-read (Oxford Nanopore) and short-read (Illumina) sequencing technologies. More than 4,200 different BGCs were identified, with 88% of these being complete. Sequence similarity clustering of the BGCs implies that the majority of this biosynthetic potential likely encodes novel compounds, and few BGCs are shared between genera. We identify BGCs in abundant and functionally relevant genera in WWTPs, suggesting a role of secondary metabolism in this ecosystem. We find that the assembly of HQ MAGs using long-read sequencing is vital to explore the genetic potential for SM production among the uncultured members of microbial communities. IMPORTANCE Cataloguing secondary metabolite (SM) potential using genome mining of metagenomic data has become the method of choice in bioprospecting for novel compounds. However, accurate biosynthetic gene cluster (BGC) detection requires unfragmented genomic assemblies, which have been technically difficult to obtain from metagenomes until very recently with new long-read technologies. Here, we determined the biosynthetic potential of activated sludge (AS), the microbial community used in resource recovery and wastewater treatment, by mining high-quality metagenome-assembled genomes generated from long-read data. We found over 4,000 BGCs, including BGCs in abundant process-critical bacteria, with no similarity to the BGCs of characterized products. We show how long-read MAGs are required to confidently assemble complete BGCs, and we determined that the AS BGCs from different studies have very little overlap, suggesting that AS is a rich source of biosynthetic potential and new bioactive compounds.}, } @article {pmid36445085, year = {2022}, author = {Porras, AM and Zhou, H and Shi, Q and Xiao, X and , and Longman, R and Brito, IL}, title = {Inflammatory Bowel Disease-Associated Gut Commensals Degrade Components of the Extracellular Matrix.}, journal = {mBio}, volume = {13}, number = {6}, pages = {e0220122}, pmid = {36445085}, issn = {2150-7511}, support = {DP2 HL141007/HL/NHLBI NIH HHS/United States ; S10 OD017992/OD/NIH HHS/United States ; }, mesh = {Animals ; Humans ; Mice ; *Colitis/chemically induced/metabolism ; Disease Models, Animal ; *Extracellular Matrix/metabolism ; Inflammation ; *Inflammatory Bowel Diseases/metabolism ; Mice, Inbred C57BL ; Peptide Hydrolases ; Feces/chemistry/microbiology ; }, abstract = {Extracellular matrix (ECM) remodeling has emerged as a key feature of inflammatory bowel disease (IBD), and ECM fragments have been proposed as markers of clinical disease severity. Recent studies report increased protease activity in the gut microbiota of IBD patients. Nonetheless, the relationship between gut microbiota and ECM remodeling has remained unexplored. We hypothesized that members of the human gut microbiome could degrade the host ECM and that bacteria-driven remodeling, in turn, could enhance colonic inflammation. Through a variety of in vitro assays, we first confirmed that multiple bacterial species found in the human gut are capable of degrading specific ECM components. Clinical stool samples obtained from ulcerative colitis patients also exhibited higher levels of proteolytic activity in vitro, compared to those of their healthy counterparts. Furthermore, culture supernatants from bacteria species that are capable of degrading human ECM accelerated inflammation in dextran sodium sulfate (DSS)-induced colitis. Finally, we identified several of the bacterial proteases and carbohydrate degrading enzymes (CAZymes) that are potentially responsible for ECM degradation in vitro. Some of these protease families and CAZymes were also found in increased abundance in a metagenomic cohort of IBD. These results demonstrate that some commensal bacteria in the gut are indeed capable of degrading components of human ECM in vitro and suggest that this proteolytic activity may be involved in the progression of IBD. A better understanding of the relationship between nonpathogenic gut microbes, host ECM, and inflammation could be crucial to elucidating some of the mechanisms underlying host-bacteria interactions in IBD and beyond. IMPORTANCE Healthy gut epithelial cells form a barrier that keeps bacteria and other substances from entering the blood or tissues of the body. Those cells sit on scaffolding that maintains the structure of the gut and informs our immune system about the integrity of this barrier. In patients with inflammatory bowel disease (IBD), breaks are formed in this cellular barrier, and bacteria gain access to the underlying tissue and scaffolding. In our study, we discovered that bacteria that normally reside in the gut can modify and disassemble the underlying scaffolding. Additionally, we discovered that changes to this scaffolding affect the onset of IBD in mouse models of colitis as well as the abilities of these mice to recover. We propose that this new information will reveal how breaks in the gut wall lead to IBD and will open up new avenues by which to treat patients with IBD.}, } @article {pmid36445010, year = {2023}, author = {Zheng, CW and Zhou, C and Luo, YH and Long, M and Long, X and Zhou, D and Bi, Y and Yang, S and Rittmann, BE}, title = {Coremoval of Energetics and Oxyanions via the In Situ Coupling of Catalytic and Enzymatic Destructions: A Solution to Ammunition Wastewater Treatment.}, journal = {Environmental science & technology}, volume = {57}, number = {1}, pages = {666-673}, doi = {10.1021/acs.est.2c05675}, pmid = {36445010}, issn = {1520-5851}, mesh = {*Explosive Agents/analysis/metabolism ; Perchlorates/analysis/metabolism ; Nitrates/analysis/metabolism ; *Metal Nanoparticles ; *Water Pollutants, Chemical/analysis ; Palladium/analysis ; *Water Purification ; Bioreactors/microbiology ; }, abstract = {Ammunition wastewater contains toxic nitrated explosives like RDX and oxyanions like nitrate and perchlorate. Its treatment is challenged by low efficiency due to contaminant recalcitrance and high cost due to multiple processes needed for separately removing different contaminant types. This paper reports a H2-based low-energy strategy featuring the treatment of explosives via catalytic denitration followed by microbial mineralization coupled with oxyanion reduction. After a nitrate- and perchlorate-reducing biofilm incapable of RDX biodegradation was coated with palladium nanoparticles (Pd[0]NPs), RDX was rapidly denitrated with a specific catalytic activity of 8.7 gcat[-1] min[-1], while biological reductions of nitrate and perchlorate remained efficient. In the subsequent 30-day continuous test, >99% of RDX, nitrate, and perchlorate were coremoved, and their effluent concentrations were below their respective regulation levels. Detected intermediates and shallow metagenome analysis suggest that the intermediates after Pd-catalytic denitration of RDX ultimately were enzymatically utilized by the nitrate- and perchlorate-reducing bacteria as additional electron donor sources.}, } @article {pmid36444071, year = {2023}, author = {Liu, Y and Xu, F and Ding, L and Zhang, G and Bai, B and Han, Y and Xiao, L and Song, Y and Li, Y and Wan, S and Li, G}, title = {Microplastics reduce nitrogen uptake in peanut plants by damaging root cells and impairing soil nitrogen cycling.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt B}, pages = {130384}, doi = {10.1016/j.jhazmat.2022.130384}, pmid = {36444071}, issn = {1873-3336}, mesh = {*Nitrogen ; *Soil ; Arachis ; Plastics ; Microplastics ; Rubber ; }, abstract = {Microplastic (MP) pollution severely impairs the sustainable development of modern agriculture. However, the mechanisms underlying the effects of MP contaminants on nutrient cycles in agroecosystems are poorly understood. In this study, we examined the impacts of two types of MPs, polypropylene (PP) and rubber crumb (RC), on nitrogen (N) transformation and N cycling in soil-peanut system. High concentrations of PP (1% w/w) and RC (1% w/w) inhibited vegetative growth and N uptake in peanut plants by damaging root cells and disturbing soil N cycling. These MPs damaged the plasma membranes of root cells and caused oxidative stress, as evidenced by the decreased number of xylem vessels, which in turn inhibited N uptake by roots. Integrated metagenomic and metabolomic analyses revealed that the differential soil metabolite levels in response to MP treatment affected the microbial community structure in the rhizosphere and the expression of key N cycling-related genes, resulting in altered N transformation and the decreased availability of N in rhizosphere soil. These findings provide the first evidence of the effects of MPs on N uptake in peanut plants and shed light on the importance of rational management of MPs for crop growth and yield in agroecosystems.}, } @article {pmid36444055, year = {2023}, author = {Zhang, X and Ding, Z and Usman, S and Zhang, J and Chen, M and Guo, X}, title = {Metagenomics insights into the effects of lactic acid bacteria inoculation on the biological reduction of antibiotic resistance genes in alfalfa silage.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt B}, pages = {130329}, doi = {10.1016/j.jhazmat.2022.130329}, pmid = {36444055}, issn = {1873-3336}, mesh = {*Medicago sativa/genetics ; *Lactobacillales ; Silage ; Anti-Bacterial Agents/pharmacology ; Vancomycin ; Bacitracin ; Drug Resistance, Microbial/genetics ; Aminoglycosides ; }, abstract = {Antibiotic resistance genes (ARGs) are a new type of pollutant and pose major threats to public health. However, the distribution and transmission risk of ARGs in alfalfa silage as the main forage for ruminants have not been studied. This study first deciphered the effects of Lactobacillus plantarum MTD/1 or Lactobacillus buchneri 40788 inoculations on distribution and transmission mechanism of ARGs in alfalfa silage by metagenomics. Results showed that multidrug and bacitracin resistance genes were the dominant ARGs in ensiled alfalfa. The natural ensiling process increased the abundances of bacitracin, beta_lactam, and aminoglycoside in alfalfa silage with 30% DM, and vancomycin in alfalfa silage with 40% DM. Meanwhile, prolonged wilting increased ARG enrichment in fresh alfalfa. Interestingly, alfalfa silage inoculated with L. plantarum MTD/1 or L. buchneri 40788 reduced the abundances of total ARG, and multidrug, MLS, vancomycin, aminoglycoside, tetracycline, and fosmidomycin resistance genes by reductions of the host bacteria and the enrichment of ARGs located in the plasmid. The hosts of ARG in alfalfa silage were mainly derived from harmful bacteria or pathogens, and some of the clinical ARGs were observed in alfalfa silage. Basically, the combined effect of microbes, MGEs, and fermentation quality was the major driver of ARG transfer and dissemination in microecosystem of ensiling, where the microbes appeared to be the crucial factor. In summary, inoculation with the present lactic acid bacteria could reduce ARG abundance in ensiled alfalfa, and a better effect was observed in L. plantarum-treated silage than in L. buchneri treated silage.}, } @article {pmid36443898, year = {2023}, author = {Galardi, MM and Sowa, GM and Crockett, CD and Rudock, R and Smith, AE and Shwe, EE and San, T and Linn, K and Aye, AMM and Ramachandran, PS and Zia, M and Wapniarski, AE and Hawes, IA and Hlaing, CS and Kyu, EH and Thair, C and Mar, YY and Nway, N and Storch, GA and Wylie, KM and Wylie, TN and Dalmau, J and Wilson, MR and Mar, SS}, title = {Pathogen and Antibody Identification in Children with Encephalitis in Myanmar.}, journal = {Annals of neurology}, volume = {93}, number = {3}, pages = {615-628}, doi = {10.1002/ana.26560}, pmid = {36443898}, issn = {1531-8249}, support = {K08 NS096117/NS/NINDS NIH HHS/United States ; }, mesh = {Child ; Humans ; *Meningitis/cerebrospinal fluid/diagnosis ; Prospective Studies ; Myanmar ; *Encephalitis/cerebrospinal fluid ; *Communicable Diseases ; *Infectious Encephalitis ; *Autoimmune Diseases of the Nervous System ; }, abstract = {OBJECTIVE: Prospective studies of encephalitis are rare in regions where encephalitis is prevalent, such as low middle-income Southeast Asian countries. We compared the diagnostic yield of local and advanced tests in cases of pediatric encephalitis in Myanmar.

METHODS: Children with suspected subacute or acute encephalitis at Yangon Children's Hospital, Yangon, Myanmar, were prospectively recruited from 2016-2018. Cohort 1 (n = 65) had locally available diagnostic testing, whereas cohort 2 (n = 38) had advanced tests for autoantibodies (ie, cell-based assays, tissue immunostaining, studies with cultured neurons) and infections (ie, BioFire FilmArray multiplex Meningitis/Encephalitis multiplex PCR panel, metagenomic sequencing, and pan-viral serologic testing [VirScan] of cerebrospinal fluid).

RESULTS: A total of 20 cases (13 in cohort 1 and 7 in cohort 2) were found to have illnesses other than encephalitis. Of the 52 remaining cases in cohort 1, 43 (83%) had presumed infectious encephalitis, of which 2 cases (4%) had a confirmed infectious etiology. Nine cases (17%) had presumed autoimmune encephalitis. Of the 31 cases in cohort 2, 23 (74%) had presumed infectious encephalitis, of which one (3%) had confirmed infectious etiology using local tests only, whereas 8 (26%) had presumed autoimmune encephalitis. Advanced tests confirmed an additional 10 (32%) infections, 4 (13%) possible infections, and 5 (16%) cases of N-methyl-D-aspartate receptor antibody encephalitis.

INTERPRETATION: Pediatric encephalitis is prevalent in Myanmar, and advanced technologies increase identification of treatable infectious and autoimmune causes. Developing affordable advanced tests to use globally represents a high clinical and research priority to improve the diagnosis and prognosis of encephalitis. ANN NEUROL 2023;93:615-628.}, } @article {pmid36443754, year = {2022}, author = {Huh, JW and Kim, MJ and Kim, J and Lee, HG and Ryoo, SB and Ku, JL and Jeong, SY and Park, KJ and Kim, D and Kim, JF and Park, JW}, title = {Enterotypical Prevotella and three novel bacterial biomarkers in preoperative stool predict the clinical outcome of colorectal cancer.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {203}, pmid = {36443754}, issn = {2049-2618}, mesh = {Humans ; *Prevotella/genetics ; Prospective Studies ; Feces ; Bacteria/genetics ; Fusobacterium nucleatum/genetics ; *Colorectal Neoplasms/surgery ; }, abstract = {BACKGROUND: A significant proportion of colorectal cancer (CRC) patients suffer from early recurrence and progression after surgical treatment. Although the gut microbiota is considered as a key player in the initiation and progression of CRC, most prospective studies have been focused on a particular pathobionts such as Fusobacterium nucleatum. Here, we aimed to identify novel prognostic bacteria for CRC by examining the preoperative gut microbiota through 16S ribosomal RNA gene sequencing.

RESULTS: We collected stool samples from 333 patients with primary CRC within 2 weeks before surgery and followed up the patients for a median of 27.6 months for progression and 43.6 months for survival. The sequence and prognosis data were assessed using the log-rank test and multivariate Cox proportional hazard analysis. The gut microbiota was associated with the clinical outcomes of CRC patients (Pprogress = 0.011, Pdecease = 0.007). In particular, the high abundance of Prevotella, a representative genus of human enterotypes, indicated lower risks of CRC progression (P = 0.026) and decease (P = 0.0056), while the occurrence of Alistipes assigned to Bacteroides sp., Pyramidobacter piscolens, Dialister invisus, and Fusobacterium nucleatum indicated a high risk of progression. A microbiota-derived hazard score considering the five prognostic bacteria accurately predicted CRC progression in 1000 random subsamples; it outperformed widely accepted clinical biomarkers such as carcinoembryonic antigen and lymphatic invasion, after adjustment for the clinicopathological stage (adjusted HR 2.07 [95% CI, 1.61-2.64], P = 7.8e-9, C-index = 0.78). PICRUSt2 suggested that microbial pathways pertaining to thiamine salvage and L-histidine degradation underlie the different prognoses.

CONCLUSIONS: The enterotypical genus Prevotella was demonstrated to be useful in improving CRC prognosis, and combined with the four pathobionts, our hazard score based on the gut microbiota should provide an important asset in predicting medical outcomes for CRC patients. Video Abstract.}, } @article {pmid36443683, year = {2022}, author = {Batinovic, S and Stanton, CR and Rice, DTF and Rowe, B and Beer, M and Petrovski, S}, title = {Tyroviruses are a new group of temperate phages that infect Bacillus species in soil environments worldwide.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {777}, pmid = {36443683}, issn = {1471-2164}, support = {VUP17-007//Defence Science Institute/ ; VUP17-007//Defence Science Institute/ ; ID8047//Defence Science and Technology Group/ ; ID8047//Defence Science and Technology Group/ ; }, mesh = {Humans ; *Bacillus/genetics ; Soil ; Phylogeny ; *Bacillus Phages/genetics ; Recombinases ; Tyrosine ; }, abstract = {BACKGROUND: Bacteriophages are widely considered to be highly abundant and genetically diverse, with their role in the evolution and virulence of many pathogens becoming increasingly clear. Less attention has been paid on phages preying on Bacillus, despite the potential for some of its members, such as Bacillus anthracis, to cause serious human disease.

RESULTS: We have isolated five phages infecting the causative agent of anthrax, Bacillus anthracis. Using modern phylogenetic approaches we place these five new Bacillus phages, as well as 21 similar phage genomes retrieved from publicly available databases and metagenomic datasets into the Tyrovirus group, a newly proposed group named so due to the conservation of three distinct tyrosine recombinases. Genomic analysis of these large phages (~ 160-170 kb) reveals their DNA packaging mechanism and genomic features contributing to virion morphogenesis, host cell lysis and phage DNA replication processes. Analysis of the three tyrosine recombinases suggest Tyroviruses undergo a prophage lifecycle that may involve both host integration and plasmid stages. Further we show that Tyroviruses rely on divergent invasion mechanisms, with a subset requiring host S-layer for infection.

CONCLUSIONS: Ultimately, we expand upon our understanding on the classification, phylogeny, and genomic organisation of a new and substantial phage group that prey on critically relevant Bacillus species. In an era characterised by a rapidly evolving landscape of phage genomics the deposition of future Tyroviruses will allow the further unravelling of the global spread and evolutionary history of these Bacillus phages.}, } @article {pmid36443666, year = {2022}, author = {Gupta, A and Malwe, AS and Srivastava, GN and Thoudam, P and Hibare, K and Sharma, VK}, title = {MP4: a machine learning based classification tool for prediction and functional annotation of pathogenic proteins from metagenomic and genomic datasets.}, journal = {BMC bioinformatics}, volume = {23}, number = {1}, pages = {507}, pmid = {36443666}, issn = {1471-2105}, mesh = {*Metagenome ; *Metagenomics ; Genomics ; Machine Learning ; Databases, Protein ; }, abstract = {Bacteria can exceptionally evolve and develop pathogenic features making it crucial to determine novel pathogenic proteins for specific therapeutic interventions. Therefore, we have developed a machine-learning tool that predicts and functionally classifies pathogenic proteins into their respective pathogenic classes. Through construction of pathogenic proteins database and optimization of ML algorithms, Support Vector Machine was selected for the model construction. The developed SVM classifier yielded an accuracy of 81.72% on the blind-dataset and classified the proteins into three classes: Non-pathogenic proteins (Class-1), Antibiotic Resistance Proteins and Toxins (Class-2), and Secretory System Associated and capsular proteins (Class-3). The classifier provided an accuracy of 79% on real dataset-1, and 72% on real dataset-2. Based on the probability of prediction, users can estimate the pathogenicity and annotation of proteins under scrutiny. Tool will provide accurate prediction of pathogenic proteins in genomic and metagenomic datasets providing leads for experimental validations. Tool is available at: http://metagenomics.iiserb.ac.in/mp4 .}, } @article {pmid36443458, year = {2022}, author = {Shaffer, JP and Nothias, LF and Thompson, LR and Sanders, JG and Salido, RA and Couvillion, SP and Brejnrod, AD and Lejzerowicz, F and Haiminen, N and Huang, S and Lutz, HL and Zhu, Q and Martino, C and Morton, JT and Karthikeyan, S and Nothias-Esposito, M and Dührkop, K and Böcker, S and Kim, HW and Aksenov, AA and Bittremieux, W and Minich, JJ and Marotz, C and Bryant, MM and Sanders, K and Schwartz, T and Humphrey, G and Vásquez-Baeza, Y and Tripathi, A and Parida, L and Carrieri, AP and Beck, KL and Das, P and González, A and McDonald, D and Ladau, J and Karst, SM and Albertsen, M and Ackermann, G and DeReus, J and Thomas, T and Petras, D and Shade, A and Stegen, J and Song, SJ and Metz, TO and Swafford, AD and Dorrestein, PC and Jansson, JK and Gilbert, JA and Knight, R and , }, title = {Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity.}, journal = {Nature microbiology}, volume = {7}, number = {12}, pages = {2128-2150}, pmid = {36443458}, issn = {2058-5276}, support = {DP1 AT010885/AT/NCCIH NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Microbiota/genetics ; Metagenome ; Metagenomics ; Earth, Planet ; Soil ; }, abstract = {Despite advances in sequencing, lack of standardization makes comparisons across studies challenging and hampers insights into the structure and function of microbial communities across multiple habitats on a planetary scale. Here we present a multi-omics analysis of a diverse set of 880 microbial community samples collected for the Earth Microbiome Project. We include amplicon (16S, 18S, ITS) and shotgun metagenomic sequence data, and untargeted metabolomics data (liquid chromatography-tandem mass spectrometry and gas chromatography mass spectrometry). We used standardized protocols and analytical methods to characterize microbial communities, focusing on relationships and co-occurrences of microbially related metabolites and microbial taxa across environments, thus allowing us to explore diversity at extraordinary scale. In addition to a reference database for metagenomic and metabolomic data, we provide a framework for incorporating additional studies, enabling the expansion of existing knowledge in the form of an evolving community resource. We demonstrate the utility of this database by testing the hypothesis that every microbe and metabolite is everywhere but the environment selects. Our results show that metabolite diversity exhibits turnover and nestedness related to both microbial communities and the environment, whereas the relative abundances of microbially related metabolites vary and co-occur with specific microbial consortia in a habitat-specific manner. We additionally show the power of certain chemistry, in particular terpenoids, in distinguishing Earth's environments (for example, terrestrial plant surfaces and soils, freshwater and marine animal stool), as well as that of certain microbes including Conexibacter woesei (terrestrial soils), Haloquadratum walsbyi (marine deposits) and Pantoea dispersa (terrestrial plant detritus). This Resource provides insight into the taxa and metabolites within microbial communities from diverse habitats across Earth, informing both microbial and chemical ecology, and provides a foundation and methods for multi-omics microbiome studies of hosts and the environment.}, } @article {pmid36443434, year = {2022}, author = {St Laurent, B and Harding, N and Deason, N and Oy, K and Sok Loeun, C and Sary, M and Sunly, R and Nhep, S and Drury, E and Rockett, K and Sovannaroth, S and Goncalves, S and Kwiatkowski, D and Miles, A}, title = {Population genomics reveal distinct and diverging populations of An. minimus in Cambodia.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1308}, pmid = {36443434}, issn = {2399-3642}, mesh = {Animals ; Humans ; Metagenomics ; Cambodia/epidemiology ; *Anopheles/genetics ; *Malaria/epidemiology ; Mosquito Vectors/genetics ; }, abstract = {Anopheles minimus is an important malaria vector throughout its wide geographic range across Southeast Asia. Genome sequencing could provide important insights into the unique malaria transmission dynamics in this region, where many vector species feed and rest outdoors. We describe results from a study using Illumina deep whole-genome sequencing of 302 wild-caught An. minimus collected from three Cambodian provinces over several years (2010, 2014, 2016) and seasons to examine the level of population structure and genetic diversity within this species. These specimens cluster into four distinct populations of An. minimus s.s., with two populations overlapping geographically. We describe the underlying genetic diversity and divergence of these populations and investigated the genetic variation in genes known to be involved in insecticide resistance. We found strong signals of selection within these An. minimus populations, most of which were present in the two Northeastern Cambodian populations and differ from those previously described in African malaria vectors. Cambodia is the focus of the emergence and spread of drug-resistant malaria parasites, so understanding the underlying genetic diversity and resilience of the vectors of these parasites is key to implementing effective malaria control and elimination strategies. These data are publicly available as part of the MalariaGEN Vector Observatory, an open access resource of genome sequence data.}, } @article {pmid36442629, year = {2023}, author = {Liu, C and Chen, J and Shan, X and Yang, Y and Song, L and Teng, Y and Chen, H}, title = {Meta-analysis addressing the characterization and risk identification of antibiotics and antibiotic resistance genes in global groundwater.}, journal = {The Science of the total environment}, volume = {860}, number = {}, pages = {160513}, doi = {10.1016/j.scitotenv.2022.160513}, pmid = {36442629}, issn = {1879-1026}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; *Groundwater/microbiology ; }, abstract = {Antimicrobial resistance (AMR) is one of the significant global issues to public health. Compared to other aquatic environments, research on AMR in groundwater is scarce. In the study, a meta-analysis was conducted to explore the characteristics and risks of antibiotics and antibiotic resistance genes (ARGs) in global groundwater, using a data set of antibiotic concentrations collected from publications during 2000-2021 and a large-scale metagenomes of groundwater samples (n = 330). The ecotoxicological risks of antibiotics in the global groundwater were evaluated using mixture risk quotient with concentration addition model to consider the synergistic effects of multiple antibiotics. Bioinformatic annotations identified 1413 ARGs belonging to 37 ARG types in the global groundwater, dominated by rifamycin, polyketide, and quinolone resistance genes and including some emerging ARGs such as mcr-family and carbapenem genes. Relatively, the level of ARGs in the groundwater from spring was significantly higher (ANOVA, p < 0.01) than those from the riparian zone, sand and deep aquifer. Similarly, metal resistance genes (MRGs) were prevalent in the global groundwater, and network analysis suggested the MRGs presented non-random co-occurrence with the ARGs in such environments. Taxonomic annotations showed Proteobacteria, Actinobacteria, Eukaryota, Acidobacteria and Thaumarchaeota were the dominant phylum in the groundwater, and the microbial community largely shaped profile of ARGs in the environment. Notably, the ARGs presented co-occurrence with mobile genetic elements, virulence factors and human bacterial pathogens, indicating potential dissemination risk of ARGs in the groundwater. Furthermore, an omics-based approach was used for health risk assessment of antibiotic resistome and screened out 152 risk ARGs in the global groundwater. Comparatively, spring and cold creek presented higher risk index, which deserves more attention to ensure the safety of water supply.}, } @article {pmid36442452, year = {2023}, author = {Ali, K and Zaidi, S and Khan, AA and Khan, AU}, title = {Orally fed EGCG coronate food released TiO2 and enhanced penetrability into body organs via gut.}, journal = {Biomaterials advances}, volume = {144}, number = {}, pages = {213205}, doi = {10.1016/j.bioadv.2022.213205}, pmid = {36442452}, issn = {2772-9508}, mesh = {Animals ; Humans ; *Titanium ; *Tea/chemistry ; Food ; }, abstract = {Owing to unique nano-scale properties, TiO2-NPs (T-NPs) are employed as food-quality enhancers in >900 processed food products. Whereas, epigallocatechin-3-gallate (EGCG), a green tea polyphenol is consumed in traditional brewed tea, globally. Taken together, we aimed to investigate whether human gastric-acid digested T-NPs and complex tea catechins yield ionic species (Ti[4+], Ti[3+] etc.) and active EGCG forms to meet favourable conditions for in vivo bio-genesis of EGCG-coronated TiO2-NPs (ET-NPs) in human gut. Secondly, compared to bare-surface micro and nano-scale TiO2, i.e., T-MPs and T-NPs, respectively, how EGCG coronation on ET-NPs in the gut facilitates the modulation of intrinsic propensity of internalization of TiO2 species into bacteria, body-organs, and gut-microbiota (GM), and immune system. ET-NPs were synthesized in non-toxic aqueous solution at varied pH (3-10) and characterised by state-of-the-arts for crystallinity, surface-charge, EGCG-encapsulation, stability, size, composition and morphology. Besides, flow-cytometry (FCM), TEM, EDS, histopathology, RT-PCR, 16S-rRNA metagenomics and ELISA were also performed to assess the size and surface dependent activities of ET-NPs, T-NPs and T-MPs vis-a-vis planktonic bacteria, biofilm, GM bacterial communities and animal's organs. Electron-microscopic, NMR, FTIR, DLS, XRD and EDS confirmed the EGCG coronation, dispersity, size-stability of ET-NPs, crystallinity and elemental composition of ET-NPs-8 and T-NPs. Besides, FCM, RT-PCR, 16S-rRNA metagenomics, histopathology, SEM and EDS analyses exhibited that EGCG coronation in ET-NPs-8 enhanced the penetration into body organs (i.e., liver and kidney etc.) and metabolically active bacterial communities of GM.}, } @article {pmid36442206, year = {2022}, author = {Zhang, K and Paul, KC and Jacobs, JP and Chou, HL and Duarte Folle, A and Del Rosario, I and Yu, Y and Bronstein, JM and Keener, AM and Ritz, B}, title = {Parkinson's Disease and the Gut Microbiome in Rural California.}, journal = {Journal of Parkinson's disease}, volume = {12}, number = {8}, pages = {2441-2452}, pmid = {36442206}, issn = {1877-718X}, support = {K01 AG072044/AG/NIA NIH HHS/United States ; R01 ES010544/ES/NIEHS NIH HHS/United States ; R01 ES031106/ES/NIEHS NIH HHS/United States ; U54 ES012078/ES/NIEHS NIH HHS/United States ; P01 ES016732/ES/NIEHS NIH HHS/United States ; P50 NS038367/NS/NINDS NIH HHS/United States ; P30 ES007048/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Parkinson Disease ; *Gastrointestinal Microbiome/genetics ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; California ; }, abstract = {BACKGROUND: Increasing evidence connects the gut microbiome to Parkinson's disease (PD) etiology, but little is known about microbial contributions to PD progression and its clinical features.

OBJECTIVE: We aim to explore the association between the gut microbiome with PD, and the microbial association with PD-specific clinical features.

METHODS: In a community-based case-control study of 96 PD patients and 74 controls, microbiome data were obtained from 16S rRNA gene sequencing of fecal samples, and analyzed for microbial diversity, taxa abundance, and predicted functional pathways that differed in PD patients and controls, and their association with PD-specific features (disease duration, motor subtypes, L-DOPA daily dose, and motor function).

RESULTS: PD patients' gut microbiome showed lower species diversity (p = 0.04) and were compositionally different (p = 0.002) compared to controls but had a higher abundance of three phyla (Proteobacteria, Verrucomicrobiota, Actinobacteria) and five genera (Akkermansia, Enterococcus, Hungatella, and two Ruminococcaceae) controlling for sex, race, age, and sequencing platform. Also, 35 Metacyc pathways were predicted to be differentially expressed in PD patients including biosynthesis, compound degradation/utilization/assimilation, generation of metabolites and energy, and glycan pathways. Additionally, the postural instability gait dysfunction subtype was associated with three phyla and the NAD biosynthesis pathway. PD duration was associated with the Synergistota phylum, six genera, and the aromatic compound degradation pathways. Two genera were associated with motor function.

CONCLUSION: PD patients differed from controls in gut microbiome composition and its predicted metagenome. Clinical features were also associated with bacterial taxa and altered metabolic pathways of interest for PD progression.}, } @article {pmid36442156, year = {2022}, author = {van Dongen, KCW and Ioannou, A and Wesseling, S and Beekmann, K and Belzer, C}, title = {Differences in gut microbial fructoselysine degradation activity between breast-fed and formula-fed infants.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {1}, pages = {}, pmid = {36442156}, issn = {1574-6941}, mesh = {Adult ; Female ; Humans ; Infant ; *Gastrointestinal Microbiome ; Breast Feeding ; Infant Formula ; Milk, Human/microbiology ; Feces/microbiology ; }, abstract = {The Amadori product fructoselysine is formed upon heating of food products and is abundantly present in infant formula while being almost absent in breast milk. The human gut microbiota can degrade fructoselysine for which interindividual differences have been described for adults. The aim of this study is to compare functional differences in microbial fructoselysine degradation between breast-fed and formula-fed infants, in view of their different diets and resulting different fructoselysine exposures. First, a publicly available metagenomic dataset with metagenome-assembled genomes (MAGs) from infant fecal samples was analyzed and showed that query genes involved in fructoselysine degradation (frlD/yhfQ) were abundantly present in multiple bacterial taxa in the fecal samples, with a higher prevalence in the formula-fed infants. Next, fecal samples collected from exclusively breast-fed and formula-fed infants were anaerobically incubated with fructoselysine. Both groups degraded fructoselysine, however the fructoselysine degradation activity was significantly higher by fecal samples from formula-fed infants. Overall, this study provides evidence that infant formula feeding, leading to increased dietary fructoselysine exposure, seems to result in an increased fructoselysine degradation activity in the gut microbiota of infants. This indicates that the infant gut microbiota adapts towards dietary fructoselysine exposure.}, } @article {pmid36441816, year = {2022}, author = {Nef, C and Madoui, MA and Pelletier, É and Bowler, C}, title = {Whole-genome scanning reveals environmental selection mechanisms that shape diversity in populations of the epipelagic diatom Chaetoceros.}, journal = {PLoS biology}, volume = {20}, number = {11}, pages = {e3001893}, pmid = {36441816}, issn = {1545-7885}, mesh = {*Diatoms/genetics ; Ecosystem ; Genomics ; Metagenomics ; }, abstract = {Diatoms form a diverse and abundant group of photosynthetic protists that are essential players in marine ecosystems. However, the microevolutionary structure of their populations remains poorly understood, particularly in polar regions. Exploring how closely related diatoms adapt to different environments is essential given their short generation times, which may allow rapid adaptations, and their prevalence in marine regions dramatically impacted by climate change, such as the Arctic and Southern Oceans. Here, we address genetic diversity patterns in Chaetoceros, the most abundant diatom genus and one of the most diverse, using 11 metagenome-assembled genomes (MAGs) reconstructed from Tara Oceans metagenomes. Genome-resolved metagenomics on these MAGs confirmed a prevalent distribution of Chaetoceros in the Arctic Ocean with lower dispersal in the Pacific and Southern Oceans as well as in the Mediterranean Sea. Single-nucleotide variants identified within the different MAG populations allowed us to draw a landscape of Chaetoceros genetic diversity and revealed an elevated genetic structure in some Arctic Ocean populations. Gene flow patterns of closely related Chaetoceros populations seemed to correlate with distinct abiotic factors rather than with geographic distance. We found clear positive selection of genes involved in nutrient availability responses, in particular for iron (e.g., ISIP2a, flavodoxin), silicate, and phosphate (e.g., polyamine synthase), that were further supported by analysis of Chaetoceros transcriptomes. Altogether, these results highlight the importance of environmental selection in shaping diatom diversity patterns and provide new insights into their metapopulation genomics through the integration of metagenomic and environmental data.}, } @article {pmid36441318, year = {2023}, author = {Pan, XR and Chen, L and Zhang, LP and Zuo, JE}, title = {Characteristics of antibiotic resistance gene distribution in rainfall runoff and combined sewer overflow.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {11}, pages = {30766-30778}, doi = {10.1007/s11356-022-24257-1}, pmid = {36441318}, issn = {1614-7499}, support = {2018ZX07105-003//Major Science and Technology Program for Water Pollution Control and Treatment/ ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; }, abstract = {Rainfall runoff and combined sewer overflow (CSO) converge with organic waste, nutrients, and microbes from the ground and wastewater. These pollutants promote the spread and transformation of antibiotic resistance genes (ARGs). In this study, four rainfall runoff and one CSO outfall were chosen, and samples were collected to explore the occurrence and distribution of ARGs. The ARGs were extracted from suspended solids and analyzed using metagenomic sequencing. A total of 888 ARG subtypes, belonging to 17 ARG types, were detected in all samples. Eleven ARG types were shared by all the samples. Multidrug resistance genes had the highest relative abundance. Their total relative abundance reached 1.07 ratio (ARG copy number/16S rRNA gene copy number) and comprised 46.6% of all the ARGs. In all samples, the CSO outfall had the highest total relative abundance (8.25 × 10[-1] ratio) of ARGs, with a ratio ranging ND (not detected)-3.78 × 10[-1] ratio. Furthermore, the relationship between ARG types and environmental factors was determined using redundancy analysis. The results showed that chemical organic demand (COD) and bacterial abundance were positively correlated with most ARG types, including multidrug, bacitracin, aminoglycoside, β-lactam, tetracycline, and sulfonamide. NH3-N, TN, and TP were positively correlated with rifamycin, fosmidomycin, and vancomycin resistance genes. The relationship among the ARG subtypes was investigated using network analyses. The multidrug resistance gene subtypes had the highest frequency of co-occurrence. This study provides insights into the occurrence and distribution of ARGs under non-point source pollution and may contribute to the control of ARGs.}, } @article {pmid36439858, year = {2022}, author = {Liu, B and Zhao, J and Liu, Y and Qiao, W and Jiang, T and Chen, L}, title = {Diversity and temporal dynamics of breast milk microbiome and its influencing factors in Chinese women during the first 6 months postpartum.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1016759}, pmid = {36439858}, issn = {1664-302X}, abstract = {Human breast milk (HBM) plays an important role in providing nutrients, beneficial microorganisms and bioactive components for infants, helping maturation of their immune system and gastrointestinal development. Here, we present a study aiming to investigate the diversity and temporal dynamics of the milk microbiome across the first 6 month postpartum in Chinese healthy breastfeeding women, and to investigate to what extent other variables (e.g., sampling location, infant sex, and mode of delivery) might also be related to variations in the human milk microbiome, and the association with maternal diet and nutrients. Fifty-three healthy pregnant women from four cities were recruited from a China Maternal and Infant Health Cohort Study and breast milk samples were collected and analyzed using 16S rRNA metagenomic sequencing. We illustrated the diversity and temporal dynamics during lactation (Adonis p-value = 3e-04). Firmicutes and Proteobacteria were the most abundant phyla, and Streptococcus, Staphylococcus, Serratia, and Corynebacterium were the core genera. Partitioning around medoids clustering identified two major internal clusters of breast milk microbiota. Cluster 1 was dominated by Acinetobacter and Pseudomonas, while Cluster 2 was dominated by Streptococcus and Staphylococcus. Among other environmental variables, sampling location showed significant influence on breast milk microbiome (Adonis p-value = 4e-04), while infant sex (Adonis p-value = 0.33) and mode of delivery (Adonis p-value = 0.19) were less related to variations in the human milk microbiome. Maternal diet such as tuber was significantly correlated with the relative abundance of Neisseria (rho = 0.34, adjusted p-value = 0.01) and Cutibacterium (rho = -0.35, adjusted p-value = 0.01), and nutrients such as carbohydrates were significantly correlated with the relative abundance of Aquabacterium (rho = -0.39, adjusted p-value = 0.0027), and vitamin B12 was significantly correlated with the relative abundance of Coprococcus (rho = 0.40, adjusted p-value = 0.0018), etc. These results illustrated the dynamic changes of composition and diversity during the lactation phases of the Chinese breast milk microbiome and addressed the importance of geographic location on milk microbiota, and associations with maternal diet consumption, which have potential benefits on the establishment and future health of breastfeeding infants.}, } @article {pmid36439843, year = {2022}, author = {Maus, I and Wibberg, D and Belmann, P and Hahnke, S and Huang, L and Spröer, C and Bunk, B and Blom, J and Sczyrba, A and Pühler, A and Klocke, M and Schlüter, A}, title = {The novel oligopeptide utilizing species Anaeropeptidivorans aminofermentans M3/9[T], its role in anaerobic digestion and occurrence as deduced from large-scale fragment recruitment analyses.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1032515}, pmid = {36439843}, issn = {1664-302X}, abstract = {Research on biogas-producing microbial communities aims at elucidation of correlations and dependencies between the anaerobic digestion (AD) process and the corresponding microbiome composition in order to optimize the performance of the process and the biogas output. Previously, Lachnospiraceae species were frequently detected in mesophilic to moderately thermophilic biogas reactors. To analyze adaptive genome features of a representative Lachnospiraceae strain, Anaeropeptidivorans aminofermentans M3/9[T] was isolated from a mesophilic laboratory-scale biogas plant and its genome was sequenced and analyzed in detail. Strain M3/9[T] possesses a number of genes encoding enzymes for degradation of proteins, oligo- and dipeptides. Moreover, genes encoding enzymes participating in fermentation of amino acids released from peptide hydrolysis were also identified. Based on further findings obtained from metabolic pathway reconstruction, M3/9[T] was predicted to participate in acidogenesis within the AD process. To understand the genomic diversity between the biogas isolate M3/9[T] and closely related Anaerotignum type strains, genome sequence comparisons were performed. M3/9[T] harbors 1,693 strain-specific genes among others encoding different peptidases, a phosphotransferase system (PTS) for sugar uptake, but also proteins involved in extracellular solute binding and import, sporulation and flagellar biosynthesis. In order to determine the occurrence of M3/9[T] in other environments, large-scale fragment recruitments with the M3/9[T] genome as a template and publicly available metagenomes representing different environments was performed. The strain was detected in the intestine of mammals, being most abundant in goat feces, occasionally used as a substrate for biogas production.}, } @article {pmid36439827, year = {2022}, author = {Barretto, C and Combrisson, J and Bokulich, N}, title = {Editorial: Genomics and metagenomics approaches for food value chain quality, safety, and product development.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1056796}, doi = {10.3389/fmicb.2022.1056796}, pmid = {36439827}, issn = {1664-302X}, } @article {pmid36439809, year = {2022}, author = {Swanson, E and Sbissi, I and Ktari, A and Cherif-Silini, H and Ghodhbane-Gtari, F and Tisa, LS and Gtari, M}, title = {Decrypting phytomicrobiome of the neurotoxic actinorhizal species, Coriaria myrtifolia, and dispersal boundary of Frankia cluster 2 in soil outward compatible host rhizosphere.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1027317}, pmid = {36439809}, issn = {1664-302X}, abstract = {The actinorhizal plant, Coriaria myrtifolia, is a neurotoxic plant species endemic to the western Mediterranean area, which forms a nitrogen-fixing symbiosis with members of Frankia cluster 2. Contrarily to other Frankia clusters, the occurrence and mode of dispersal for infective cluster 2 units outside of the host plant rhizosphere remains controversial. The present study was designed to investigate the structure of the microbiomes of C. myrtifolia phytosphere, rhizosphere, and soil samples extending outward linearly up to 1 km. Results showed that the epiphyte and endophyte communities were not significantly different from each other for most of the plant tissues. The communities associated with the below-ground tissues (nodule and root) were significantly different from those found on the above-ground tissues (fruit, leaves, and stems) and had a higher community richness. Coriaria myrtifolia phytomicrobiomes were dominated by Cyanobacteria for leaf, stem, and fruit while Actinobacteria and Proteobacteria were dominant in the root and nodule organelles. The nodule, a special niche for nitrogen fixation, was mainly inhabited by Frankia but contained several non-Frankia bacteria. Beside Frankia cluster 2, the presence of clusters 1, 4, and large numbers of cluster 3 strains have been detected in nodules, roots, and rhizospheres of C. myrtifolia. Despite Frankia being found in all plots using plant trapping bioassays with C. myrtifolia seedlings, Frankia cluster 2 was not detected in soil metagenomes showing the limits of detection by this approach. This result also suggests that in the absence of appropriate host plant species, Frankia cluster 2 has a reduced number of infective units present in the soil outward from the rhizosphere.}, } @article {pmid36439796, year = {2022}, author = {Bandini, F and Vaccari, F and Soldano, M and Piccinini, S and Misci, C and Bellotti, G and Taskin, E and Cocconcelli, PS and Puglisi, E}, title = {Rigid bioplastics shape the microbial communities involved in the treatment of the organic fraction of municipal solid waste.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1035561}, pmid = {36439796}, issn = {1664-302X}, abstract = {While bioplastics are gaining wide interest in replacing conventional plastics, it is necessary to understand whether the treatment of the organic fraction of municipal solid waste (OFMSW) as an end-of-life option is compatible with their biodegradation and their possible role in shaping the microbial communities involved in the processes. In the present work, we assessed the microbiological impact of rigid polylactic acid (PLA) and starch-based bioplastics (SBB) spoons on the thermophilic anaerobic digestion and the aerobic composting of OFMSW under real plant conditions. In order to thoroughly evaluate the effect of PLA and SBB on the bacterial, archaeal, and fungal communities during the process, high-throughput sequencing (HTS) technology was carried out. The results suggest that bioplastics shape the communities' structure, especially in the aerobic phase. Distinctive bacterial and fungal sequences were found for SBB compared to the positive control, which showed a more limited diversity. Mucor racemosus was especially abundant in composts from bioplastics' treatment, whereas Penicillium roqueforti was found only in compost from PLA and Thermomyces lanuginosus in that from SBB. This work shed a light on the microbial communities involved in the OFMSW treatment with and without the presence of bioplastics, using a new approach to evaluate this end-of-life option.}, } @article {pmid36439227, year = {2022}, author = {He, P and Wang, J and Ke, R and Zhang, W and Ning, P and Zhang, D and Yang, X and Shi, H and Fang, P and Ming, Z and Li, W and Zhang, J and Dong, X and Liu, Y and Zhou, J and Xia, H and Yang, S}, title = {Comparison of metagenomic next-generation sequencing using cell-free DNA and whole-cell DNA for the diagnoses of pulmonary infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1042945}, pmid = {36439227}, issn = {2235-2988}, mesh = {Humans ; *Cell-Free Nucleic Acids/genetics ; Sensitivity and Specificity ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Pneumonia ; *Viruses/genetics ; Fungi/genetics ; DNA ; }, abstract = {Although the fast-growing metagenomic next-generation sequencing (mNGS) has been used in diagnosing infectious diseases, low detection rate of mNGS in detecting pathogens with low loads limits its extensive application. In this study, 130 patients with suspected pulmonary infections were enrolled, from whom bronchoalveolar lavage fluid (BALF) samples were collected. The conventional tests and mNGS of cell-free DNA (cfDNA) and whole-cell DNA (wcDNA) using BALF were simultaneously performed. mNGS of cfDNA showed higher detection rate (91.5%) and total coincidence rate (73.8%) than mNGS of wcDNA (83.1% and 63.9%) and conventional methods (26.9% and 30.8%). A total of 70 microbes were detected by mNGS of cfDNA, and most of them (60) were also identified by mNGS of wcDNA. The 31.8% (21/66) of fungi, 38.6% (27/70) of viruses, and 26.7% (8/30) of intracellular microbes can be only detected by mNGS of cfDNA, much higher than those [19.7% (13/66), 14.3% (10/70), and 6.7% (2/30)] only detected by mNGS of wcDNA. After in-depth analysis on these microbes with low loads set by reads per million (RPM), we found that more RPM and fungi/viruses/intracellular microbes were detected by mNGS of cfDNA than by mNGS of wcDNA. Besides, the abilities of mNGS using both cfDNA and wcDNA to detect microbes with high loads were similar. We highlighted the advantage of mNGS using cfDNA in detecting fungi, viruses, and intracellular microbes with low loads, and suggested that mNGS of cfDNA could be considered as the first choice for diagnosing pulmonary infections.}, } @article {pmid36439214, year = {2022}, author = {Qian, B and Zhang, K and Li, Y and Sun, K}, title = {Update on gut microbiota in cardiovascular diseases.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1059349}, pmid = {36439214}, issn = {2235-2988}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Cardiovascular Diseases ; *Hypertension ; Bile Acids and Salts ; *Heart Failure ; }, abstract = {In recent years, due to the development and widespread utilization of metagenomic sequencing and metabolomics, the relationship between gut microbiota and human cardiovascular diseases (CVDs) has received extensive attention. A growing number of studies have shown a strong relationship between gut microbiota and CVDs, such as coronary atherosclerosis, hypertension (HTN) and heart failure (HF). It has also been revealed that intestinal flora-related metabolites, such as trimethylamine-N-oxide (TMAO), short-chain fatty acids (SCFA) and bile acids (BAs), are also related to the development, prevention, treatment and prognosis of CVDs. In this review, we presented and summarized the recent findings on the relationship between gut microbiota and CVDs, and concluded several currently known gut microbiota-related metabolites and the occurrence and development of CVDs.}, } @article {pmid36438623, year = {2022}, author = {Han, N and Yu, J and Wang, M and Ma, Y and Yan, L and Tang, H}, title = {The Value of Metagenomic Next-Generation Sequencing in Leishmaniasis Diagnosis: A Case Series and Literature Review.}, journal = {Open forum infectious diseases}, volume = {9}, number = {11}, pages = {ofac511}, pmid = {36438623}, issn = {2328-8957}, abstract = {BACKGROUND: Leishmaniasis is a zoonotic disease caused by Leishmania spp. and spreads through sandfly bites. Owing to the wide range of nonspecific clinical symptoms, patients with leishmaniasis are frequently misdiagnosed or underdiagnosed.

METHODS: The study participants were 7 metagenomic next-generation sequencing (mNGS)-diagnosed patients with leishmaniasis who could not be diagnosed using conventional methods. Clinical data were retrospectively collected and analyzed. When searching PubMed for mNGS and leishmaniasis, 8 peer-reviewed case reports in English were retrieved.

RESULTS: A total of 7 patients with recurrent fever, pancytopenia, and significant splenomegaly were included in this study. Only 3 individuals tested positive for rK39. Two individuals, 1 of whom was HIV-positive, had Leishmania amastigotes identified in their bone marrow. However, all patients' blood mNGS findings pointed to Leishmania infection, and they were finally diagnosed with leishmaniasis. Sodium stibogluconate therapy with a short course of amphotericin B was administered to all patients. The prognosis for the remaining patients was good, except for 1 who died of multiple organ failure.

CONCLUSIONS: mNGS could be used to identify leishmaniasis, particularly in patients who are difficult to diagnose using conventional approaches.}, } @article {pmid36438054, year = {2022}, author = {Jing, D and Jiang, X and Ren, X and Su, J and Huang, C and Yang, J and Hao, R and Li, X}, title = {Metagenomic nanopore sequencing of ocular microbiome in patients with meibomian gland dysfunction.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {1045990}, pmid = {36438054}, issn = {2296-858X}, abstract = {PURPOSE: To explore the composition of the ocular microbiome in patients with Meibomian gland dysfunction (MGD) using metagenomic nanopore sequencing.

METHODS: A total of 98 participants were recruited from September to December 2021, including 86 patients with MGD and 12 controls. Symptoms and signs of dry eye were assessed, and bacterial samples in the conjunctival sac (CS) and meibomian gland (MG) secretions were then identified by bacterial culture identification and metagenomic nanopore sequencing.

RESULTS: The positive rate of CS bacterial culture in the MGD group was significantly higher than that in the normal group. A more complex composition of bacterial genera was detected in the mild and moderate MGD groups than in the control. However, the severe MGD groups had the simplest composition of bacteria. Metagenomic nanopore sequencing detected more species of bacteria than traditional culture.

CONCLUSION: The CS and MG of MGD patients may have different degrees of bacterial microbiota imbalance. Metagenomic nanopore sequencing technology provides a new way for us to understand the composition of "real-world" ocular surface microorganisms.}, } @article {pmid36438051, year = {2022}, author = {Tong, L and Constancias, F and Hou, A and Chua, SL and Drautz-Moses, DI and Schuster, SC and Yang, L and Williams, RBH and Kjelleberg, S}, title = {Shotgun metagenomic sequencing analysis of ocular surface microbiome in Singapore residents with mild dry eye.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {1034131}, pmid = {36438051}, issn = {2296-858X}, abstract = {The ocular surface microbiome has implications for ocular surface inflammation and immunology. Previous shotgun metagenomics analyses were performed in China, showing results that differed according to environment and age. Patients with Sjogren's syndrome were reported to have altered conjunctival microbiome, but such studies have not been done in milder dry eye. The aim of this study is to describe the conjunctival microbiome in people with mild dry eye in Singapore. Samples were collected from 14 participants with mild dry eye and 10 age-matched comparison participants recruited from Singapore National Eye Centre (SNEC) clinics. Shotgun metagenomic sequencing analysis was employed to evaluate the conjunctival microbiome composition. Proteobacteria formed the predominant phylum in the conjunctiva. As in a study from a coastal city in China, Achromobacter spp. was numerically most abundant. Compared to age-matched controls, the conjunctival microbial composition in mild dry eye was similar. Several microorganisms, including Streptococcus spp. increased in representation with age, and the abundance of Staphylococcus correlated with Schirmer readings. In addition, when cultured corneal epithelial cells were exposed to three strains of Achromobacter xylosoxidans, cytokines such as TNF-α and IL-6 were upregulated in the cell lysates and supernatants. Ourresults suggest that age is an important factor that affects composition of the conjunctival microbiome, and relative abundance of specific microorganism may vary according to the environment of the human host.}, } @article {pmid36437477, year = {2022}, author = {Yang, S and Mao, Q and Wang, Y and He, J and Yang, J and Chen, X and Xiao, Y and He, Y and Zhao, M and Lu, J and Yang, Z and Dai, Z and Liu, Q and Yao, Y and Lu, X and Li, H and Zhou, R and Zeng, J and Li, W and Zhou, C and Wang, X and Shen, Q and Xu, H and Deng, X and Delwart, E and Shan, T and Zhang, W}, title = {Expanding known viral diversity in plants: virome of 161 species alongside an ancient canal.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {58}, pmid = {36437477}, issn = {2524-6372}, support = {2020CPB-C11//Independent Project of Chengdu Research of Giant Panda Breeding/ ; 2107YFC1200201//National Key Research and Development Program of China/ ; BE2017693//Jiangsu Provincial Key Research and Development Program/ ; }, abstract = {BACKGROUND: Since viral metagenomic approach was applied to discover plant viruses for the first time in 2006, many plant viruses had been identified from cultivated and non-cultivated plants. These previous researches exposed that the viral communities (virome) of plants have still largely uncharacterized. Here, we investigated the virome in 161 species belonging to 38 plant orders found in a riverside ecosystem.

RESULTS: We identified 245 distinct plant-associated virus genomes (88 DNA and 157 RNA viruses) belonging to 27 known viral families, orders, or unclassified virus groups. Some viral genomes were sufficiently divergent to comprise new species, genera, families, or even orders. Some groups of viruses were detected that currently are only known to infect organisms other than plants. It indicates a wider host range for members of these clades than previously recognized theoretically. We cannot rule out that some viruses could be from plant contaminating organisms, although some methods were taken to get rid of them as much as possible. The same viral species could be found in different plants and co-infections were common.

CONCLUSIONS: Our data describe a complex viral community within a single plant ecosystem and expand our understanding of plant-associated viral diversity and their possible host ranges.}, } @article {pmid36437193, year = {2023}, author = {Pyke, R and Fortin, N and Wasserscheid, J and Tremblay, J and Schreiber, L and Levesque, MJ and Messina-Pacheco, S and Whyte, L and Wang, F and Lee, K and Cooper, D and Greer, CW}, title = {Biodegradation potential of residue generated during the in-situ burning of oil in the marine environment.}, journal = {Journal of hazardous materials}, volume = {445}, number = {}, pages = {130439}, doi = {10.1016/j.jhazmat.2022.130439}, pmid = {36437193}, issn = {1873-3336}, mesh = {RNA, Ribosomal, 16S/genetics ; Hydrocarbons/metabolism ; Seawater/microbiology ; *Polycyclic Aromatic Hydrocarbons/analysis ; *Petroleum Pollution/analysis ; Biodegradation, Environmental ; *Petroleum/metabolism ; }, abstract = {The biodegradability of residues derived from in-situ burning, an oil spill response strategy which involves burning an oil slick on the sea surface, has not yet been fully studied. With a growing risk of oil spills, the fate of the persistent burn residue containing potentially toxic substances must be better understood. Microcosms were used to study the microbial community response and potential biodegradability of in-situ burn residues generated from Ultra Low Sulphur (ULS) marine diesel. Microcosm studies were conducted using residues originating from the burning of unweathered and weathered diesel, with the addition of a fertilizer and a dispersant. Burn residues were incubated for 6 weeks at 7 °C in natural seawater with continual agitation in the dark. Samples were subsequently sacrificed for chemistry as well as 16S rRNA gene amplicon and shotgun metagenomic sequencing. Chemistry analyses revealed a reduction in hydrocarbon concentrations. Medium chain-length n-alkanes (nC16-nC24) decreased by 8% in unweathered burn residue microcosms and up to 26% in weathered burn residue microcosms. A significant decrease in polycyclic aromatic hydrocarbon (PAH) concentrations was observed only for naphthalene, fluorene and their alkylated homologs, in the microcosms amended with residue produced from burning weathered diesel. Decreases of 2-24%, were identified depending on the compound. Microcosms amended with burn residues had distinct microbial communities marked by an increase in relative abundance of putative hydrocarbon degraders as well as an increase of known hydrocarbon-degradation genes. These novel results suggest that if in-situ burning is performed on ULS marine diesel, some of the indigenous bacteria would respond to the newly available carbon source and some of the residual compounds would be biodegraded. Future studies involving longer incubation periods could give a better understanding of the fate of burn residues by shedding light on the potential biodegradability of the more recalcitrant residual compounds.}, } @article {pmid36437084, year = {2022}, author = {Du, WY and Yao, JQ and Ma, HY and Hu, YX and Zhang, CL and Chen, YG}, title = {[Bacterial Community Structure and Antibiotic Resistance Gene Changes in IFAS+Magnetic Coagulation Process Wastewater Treatment Plant in Cold Regions].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {43}, number = {11}, pages = {5123-5130}, doi = {10.13227/j.hjkx.202112169}, pmid = {36437084}, issn = {0250-3301}, mesh = {*Sewage/microbiology ; Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S ; Wastewater/microbiology ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; *Water Purification ; Bacteria ; Magnetic Phenomena ; }, abstract = {The main objective of this study was to explore the changes in bacterial communities and antibiotic resistance genes (ARGs) in an integrated fixed-film activated sludge (IFAS)+magnetic coagulation process wastewater treatment plant (WWTP) in Xinjiang. The bacterial communities and ARGs in the influent, suspended activated sludge, attached biofilm, and effluent were studied using 16S rRNA gene sequencing and metagenomic sequencing. The results showed that the average relative abundances of Chloroflexi and Nitrospirae in activated sludge were 3.50% and 0.03%, respectively, and their relative abundances in biofilm reached 10.02% and 2.12%, respectively. The average removal rates of NH4[+]-N and TN increased from 91.89% and 66.76% to 97.71% and 91.90% after the reformation of this wastewater treatment plant, respectively, indicating that IFAS enhanced the biological nitrogen removal capacity of wastewater treatment plants in cold regions. The average relative abundances of Ferruginibacter and Rhodoferax related to iron redox in the biological treatment section were 5.24% and 3.72%, respectively, and the relative abundance of Rhodoferax in effluent reached 9.48%, indicating that the magnetic powder had an impact on the bacterial community. The IFAS wastewater treatment plant had an obvious removal effect on ARGs, and the relative abundance of ARGs decreased from 191.08×10[-3]‰ in the influent to 32.58×10[-3]‰ in the effluent. The relative abundance of ARGs in activated sludge was 63.25×10[-3]‰-72.38×10[-3]‰, which was significantly higher than 41.31×10[-3]‰ in biofilm. However, the relative abundances of dominant subtypes of ARGs such as sul2, floR, and rpoB2 in biofilm were 5.77×10[-3]‰, 2.52×10[-3]‰, and 2.03×10[-3]‰, respectively, which were higher than the 3.15×10[-3]‰-3.57×10[-3]‰, 1.73×10[-3]‰-2.24×10[-3]‰, and 1.28×10[-3]‰-1.76×10[-3]‰ in activated sludge. The network analysis indicated that Caldilineaceae_norank and Trichococcus were respectively positively correlated with sul2 and floR. These results can provide theoretical reference for the optimal operation and ARGs control of WWTPs in cold regions.}, } @article {pmid36437083, year = {2022}, author = {Zhang, X and Zhou, JJ and Zhou, M and Luo, XZ and Yan, XJ and Liu, YD and Li, W}, title = {[Metagenomic and Metatranscriptomic Analysis of Nitrogen Removal Functional Microbial Community of Petrochemical Wastewater Biological Treatment Systems].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {43}, number = {11}, pages = {5115-5122}, doi = {10.13227/j.hjkx.202112283}, pmid = {36437083}, issn = {0250-3301}, mesh = {Humans ; *Wastewater ; Nitrogen ; Ammonia ; Denitrification ; China ; *Microbiota/genetics ; Sewage ; }, abstract = {Petrochemicals are one of the pillar industries of China. Despite this, the treatment of petrochemical wastewater has long been seen as a massive challenge in the field of water pollution control, hindering the high-quality and sustainable development of the petrochemical industry. The majority of petrochemical enterprises and zones are located near rivers or seas, so their wastewater discharges can easily cause watershed or regional water ecological risks. Specifically, nitrogen pollution in petrochemical wastewater poses a significant threat to water ecological safety and human health. Sludge samples were collected from a petrochemical wastewater A/O nitrogen removal process line in a chemical industry zone in Shanghai. Metagenomic and metatranscriptomic methods were used to analyze the community structure of microorganisms, the functional characteristics of nitrogen removal bacteria, and the key nitrogen metabolism pathways in different sludges during the period when effluent water quality was stable and fluctuating. During the study, it was found that the nitrite and nitrate removal was relatively stable in this process, but ammonia oxidation fluctuated easily. In the study of microbial communities, it was found to be a nitrification-denitrification pathway that primarily removed nitrogen from the A/O process, and no genes related to ANAMMOX were detected. Approximately 90% of the functional genes responsible for removing nitrogen were responsible for denitrification, whereas only 0.17% of them were involved in the conversion of ammonia nitrogen in the nitrification process. Moreover, the abundance of ammonia-oxidizing bacteria in the process was extremely low, and the main genus was Nitrosomonas. It is likely that this is the main cause of fluctuations in ammonia nitrogen concentration in effluent due to water quality shocks in the process line.}, } @article {pmid36436705, year = {2023}, author = {Lamoureux, C and Rézig, S and Le Bars, H and Le Divenah, F and Tandé, D and Vélo-Suarez, L and Badell, E and Brisse, S and Héry-Arnaud, G and Beauruelle, C}, title = {Corynebacterium ulcerans as filamentous branching rods.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {29}, number = {5}, pages = {600-601}, doi = {10.1016/j.cmi.2022.11.016}, pmid = {36436705}, issn = {1469-0691}, mesh = {Humans ; Corynebacterium ; *Corynebacterium Infections/microbiology ; *Diphtheria/microbiology ; Diphtheria Toxin ; }, } @article {pmid36436665, year = {2023}, author = {Chen, X and Wang, J and Pan, C and Feng, L and Chen, S and Xie, S}, title = {Metagenomic insights into the influence of thallium spill on sediment microbial community.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {317}, number = {}, pages = {120660}, doi = {10.1016/j.envpol.2022.120660}, pmid = {36436665}, issn = {1873-6424}, mesh = {Thallium/toxicity ; Genes, Bacterial ; Bacteria/genetics ; *Metals, Heavy/analysis ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; }, abstract = {Thallium (Tl) is an extremely toxic metal. The release of Tl into the natural environment can pose a potential threat to organisms. So far, information about the impact of Tl on indigenous microorganisms is still very limited. In addition, there has been no report on how sudden Tl spill influences the structure and function of the microbial community. Therefore, this study explored the response of river sediment microbiome to a Tl spill. Residual T1 in the sediment significantly decreased bacterial community diversity. The increase in the abundance of Bacteroidetes in all Tl- impacted sediments suggested the advantage of Bacteroidetes to resist Tl pressure. Under T1 stress, microbial genes related to carbon fixation and gene cysH participating in assimilatory sulfate reduction were down-regulated, while genes related to nitrogen cycling were up-regulated. After T1 spill, increase in both metal resistance genes (MRGs) and antibiotic resistance genes (ARGs) was observed in Tl-impacted sediments. Moreover, the abundance of MRGs and ARGs was significantly correlated with sediment Tl concentration, implying the positive effect of Tl contamination on the proliferation of these resistance genes. Procrustes analysis suggested a significant congruence between profiles of MRGs and bacterial communities. Through LEfSe and co-occurrence network analysis, Trichococcus, Polaromonas, and Arenimonas were identified to be tolerant and resistant to Tl pollution. The colocalization analysis of contigs indicated the co-effects of selection and transfer for MRGs/ARGs were important reasons for the increase in the microbial resistance in Tl-impacted sediments. This study added new insights into the effect of Tl spill on microbial community and highlighted the role of heavy metal spill in the increase of both heavy metal and antibiotic resistance genes.}, } @article {pmid36435493, year = {2023}, author = {Wan, L and Cao, L and Song, C and Cao, X and Zhou, Y}, title = {Metagenomic insights into feasibility of agricultural wastes on optimizing water quality and natural bait by regulating microbial loop.}, journal = {Environmental research}, volume = {217}, number = {}, pages = {114941}, doi = {10.1016/j.envres.2022.114941}, pmid = {36435493}, issn = {1096-0953}, mesh = {Animals ; *Water Quality ; Feasibility Studies ; Powders ; *Agriculture ; Aquaculture/methods ; Nitrogen/analysis ; Fishes/metabolism ; }, abstract = {Effective screening feed substitutes for improving water quality in aquaculture systems has become a trending research topic now. In this study, three typical organic agricultural wastes, including sugar cane bagasse (SC), coconut shell powder (CS), and corn cob powder (CC), were selected to evaluate their potential roles on the optimization of water quality and natural bait compared to aquafeeds. Fish feed resulted in the highest growth rate of fish but the worst water quality. Organic detritus addition markedly improved the water quality, especially soluble reactive phosphorus (SRP, decrease of 56-61%) and ammonium (decrease of 16% in SC, 47% in CC). Specially, SC induced core microbes to mediate nutrients transformation and recycling (N2-fixation, ammonification, nitrification, dissimilatory nitrate reduction to ammonia and organic nutrients decomposition), which facilitated the primary productivity based on their positive relationships. This further reduced the available nutrients (especially SRP) in the water and built a mutually beneficial microbial loop. In addition, SC addition increased the abundance of genes involved in amino acids biosynthesis pathways, photosynthesis, and carbon fixation. These results led to energy transfer to higher trophic levels. The addition of CC had a better effect than SC in terms of lower nitrogen levels and a higher fish growth rate (19% in CC, 5% in SC). However, low temperatures and carbon accumulation jointly drive the anaerobic decomposition, resulting in unhealthy microbial loops and low fish growth rates. In contrast to the direct consumption of fish feed, organic detritus can induce more natural bait to provide food for fish by regulating the microbial loop, as showed by the microbial community composition in the water and fish gut. To comprehensively assess water quality, natural bait, and fish growth and quality, certain organic detritus should be considered as an auxiliary material to partially replace feed for healthy and sustainable aquaculture systems.}, } @article {pmid36434943, year = {2023}, author = {He, X and Li, Z and Li, X and Zhao, H and Hu, Y and Han, W and Wang, C and Yin, C and Chen, Y}, title = {The fecal microbiota of gravidas with fetal growth restriction newborns characterized by metagenomic sequencing.}, journal = {Current research in translational medicine}, volume = {71}, number = {1}, pages = {103354}, doi = {10.1016/j.retram.2022.103354}, pmid = {36434943}, issn = {2452-3186}, mesh = {Pregnancy ; Female ; Infant, Newborn ; Humans ; Fetal Growth Retardation/genetics/pathology ; Placenta ; Case-Control Studies ; *Microbiota ; *Gastrointestinal Microbiome/genetics ; }, abstract = {BACKGROUND: Fetal growth restriction (FGR) is a complex obstetric complication with various causes and of great harm. However, the specific pathogenesis of FGR is unclear, which limits its effective treatment. Gut microbiota dysbiosis was found to be important in pathogenesis of various diseases. However, its role in FGR development remains unclear and needs to be clarified.

METHODS: In our case-control study, we recruited eight FGR and eight control female participants and collected their fecal samples in third trimester before delivery. We performed metagenomic sequencing and bioinformatic analysis to compare the gut microbiota composition and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways between the two groups.

RESULTS: Our results showed that totally 20 gut microbes were significantly different between two groups (p<0•05), and the correlation analysis found that g__Roseomonas and g__unclassified_f__Propionibacteriaceae were significantly positive correlated with both maternal body mass index (BMI) before delivery, placental weight, and neonatal birth weight (BW) percentile (all p<0•05), while g__Marinisporobacter and g__Sphingomonas were significantly negative correlated with both neonatal BMI and neonatal BW percentile (all p<0•05). Through KEGG pathway analysis, we found that the abundance of the Nitrogen metabolism pathway decreased significantly (p<0•05) whereas the abundance of the Amoebiasis pathway increased significantly in the FGR group (p<0•05).

CONCLUSION: In this study, we demonstrated that the occurrence of FGR is associated with the change of gut microbiota of pregnant women.}, } @article {pmid36434737, year = {2022}, author = {Nuccio, EE and Blazewicz, SJ and Lafler, M and Campbell, AN and Kakouridis, A and Kimbrel, JA and Wollard, J and Vyshenska, D and Riley, R and Tomatsu, A and Hestrin, R and Malmstrom, RR and Firestone, M and Pett-Ridge, J}, title = {HT-SIP: a semi-automated stable isotope probing pipeline identifies cross-kingdom interactions in the hyphosphere of arbuscular mycorrhizal fungi.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {199}, pmid = {36434737}, issn = {2049-2618}, mesh = {*Mycorrhizae/physiology ; Phylogeny ; Soil Microbiology ; Ammonia ; Reproducibility of Results ; Soil/chemistry ; Isotopes ; Plants/microbiology ; DNA ; }, abstract = {BACKGROUND: Linking the identity of wild microbes with their ecophysiological traits and environmental functions is a key ambition for microbial ecologists. Of many techniques that strive for this goal, Stable-isotope probing-SIP-remains among the most comprehensive for studying whole microbial communities in situ. In DNA-SIP, actively growing microorganisms that take up an isotopically heavy substrate build heavier DNA, which can be partitioned by density into multiple fractions and sequenced. However, SIP is relatively low throughput and requires significant hands-on labor. We designed and tested a semi-automated, high-throughput SIP (HT-SIP) pipeline to support well-replicated, temporally resolved amplicon and metagenomics experiments. We applied this pipeline to a soil microhabitat with significant ecological importance-the hyphosphere zone surrounding arbuscular mycorrhizal fungal (AMF) hyphae. AMF form symbiotic relationships with most plant species and play key roles in terrestrial nutrient and carbon cycling.

RESULTS: Our HT-SIP pipeline for fractionation, cleanup, and nucleic acid quantification of density gradients requires one-sixth of the hands-on labor compared to manual SIP and allows 16 samples to be processed simultaneously. Automated density fractionation increased the reproducibility of SIP gradients compared to manual fractionation, and we show adding a non-ionic detergent to the gradient buffer improved SIP DNA recovery. We applied HT-SIP to [13]C-AMF hyphosphere DNA from a [13]CO2 plant labeling study and created metagenome-assembled genomes (MAGs) using high-resolution SIP metagenomics (14 metagenomes per gradient). SIP confirmed the AMF Rhizophagus intraradices and associated MAGs were highly enriched (10-33 atom% [13]C), even though the soils' overall enrichment was low (1.8 atom% [13]C). We assembled 212 [13]C-hyphosphere MAGs; the hyphosphere taxa that assimilated the most AMF-derived [13]C were from the phyla Myxococcota, Fibrobacterota, Verrucomicrobiota, and the ammonia-oxidizing archaeon genus Nitrososphaera.

CONCLUSIONS: Our semi-automated HT-SIP approach decreases operator time and improves reproducibility by targeting the most labor-intensive steps of SIP-fraction collection and cleanup. We illustrate this approach in a unique and understudied soil microhabitat-generating MAGs of actively growing microbes living in the AMF hyphosphere (without plant roots). The MAGs' phylogenetic composition and gene content suggest predation, decomposition, and ammonia oxidation may be key processes in hyphosphere nutrient cycling. Video Abstract.}, } @article {pmid36434704, year = {2022}, author = {Qin, Z and Zou, Y and Huang, Z and Yu, N and Deng, Z and Chen, Z and Wang, Y}, title = {Metagenomic next-generation sequencing contributes to the diagnosis of mixed pulmonary infection: a case report.}, journal = {Annals of clinical microbiology and antimicrobials}, volume = {21}, number = {1}, pages = {52}, pmid = {36434704}, issn = {1476-0711}, support = {61627807//National Major Scientific Research Equipment Development Projects/ ; No. 62003107//National Natural Science Foundation of China/ ; No. 2021JJA130136//Natural Science Foundation of Guangxi, China/ ; Z20200599//Health Commission of Guangxi Zhuang Autonomous Region/ ; }, mesh = {Humans ; Female ; Adult ; Sensitivity and Specificity ; Metagenomics/methods ; *Pneumonia/diagnosis/drug therapy ; High-Throughput Nucleotide Sequencing/methods ; Lung/microbiology ; *Coinfection/diagnosis ; *Cryptococcosis/diagnosis/drug therapy ; *Mycobacterium tuberculosis ; *Mycoses ; }, abstract = {BACKGROUND: Pulmonary cryptococcosis (PC) and mixed pulmonary infection are difficult to be diagnosed due to the non-specificity and their overlapping clinical manifestations. In terms of the clinical diagnosis of PC and mixed pulmonary infection, conventional tests have limitations such as a long detection period, a limited range of pathogens, and low sensitivity. Metagenomics next-generation sequencing (mNGS) is a nascent and powerful method that can detect pathogens without culture, to diagnose known and unexplained infections in reduced time.

CASE PRESENTATION: A 43-year-old female was admitted to the hospital after suffering from a cough for one month. At the time of admission, a contrast-enhanced chest CT revealed multiple nodules and plaques in her right lung, as well as the formation of cavities. The blood routine assays showed evidently increased white blood cell count (mainly neutrophils), CRP, and ESR, which suggested she was in the infection phase. The serum CrAg-LFA test showed a positive result. Initially, she was diagnosed with an unexplained pulmonary infection. Bronchoalveolar lavage fluid (BALF) samples were collected for microbial culture, immunological tests and the mNGS. Microbial culture and immunological tests were all negative, while mNGS detected Corynebacterium striatum, Pseudomonas aeruginosa, Streptococcus pneumoniae, and Cryptococcus neoformans. The diagnosis was revised to PC and bacterial pneumonia. Lung infection lesions were healed after she received targeted anti-infection therapy with mezlocillin and fluconazole. In a follow-up after 2 months, the patient's symptoms vanished.

CONCLUSIONS: Here, we demonstrated that mNGS was capable of accurately distinguishing Cryptococcus from M. tuberculosis in pulmonary infection, and notably mNGS was capable of swiftly and precisely detecting pathogens in mixed bacterial and fungal pulmonary infection. Furthermore, the results of mNGS also have the potential to adjust anti-infective therapies.}, } @article {pmid36434671, year = {2022}, author = {Lee, WJ and Ryu, S and Kang, AN and Song, M and Shin, M and Oh, S and Kim, Y}, title = {Molecular characterization of gut microbiome in weaning pigs supplemented with multi-strain probiotics using metagenomic, culturomic, and metabolomic approaches.}, journal = {Animal microbiome}, volume = {4}, number = {1}, pages = {60}, pmid = {36434671}, issn = {2524-4671}, support = {NRF-2021R1A2C3011051//National Research Foundation of Korea/ ; PJ0158652021//Rural Development Administration/ ; }, abstract = {BACKGROUND: Probiotics have been reported to exhibit positive effects on host health, including improved intestinal barrier function, preventing pathogenic infection, and promoting nutrient digestion efficiency. These internal changes are reflected to the fecal microbiota composition and, bacterial metabolites production. In accordance, the application of probiotics has been broadened to industrial animals, including swine, which makes people to pursue better knowledge of the correlation between changes in the fecal microbiota and metabolites. Therefore, this study evaluated the effect of multi-strain probiotics (MSP) supplementation to piglets utilizing multiomics analytical approaches including metagenomics, culturomics, and metabolomics.

RESULTS: Six-week-old piglets were supplemented with MSP composed of Lactobacillus isolated from the feces of healthy piglets. To examine the effect of MSP supplement, piglets of the same age were selected and divided into two groups; one with MSP supplement (MSP group) and the other one without MSP supplement (Control group). MSP feeding altered the composition of the fecal microbiota, as demonstrated by metagenomics analysis. The abundance of commensal Lactobacillus was increased by 2.39%, while Clostridium was decreased, which revealed the similar pattern to the culturomic approach. Next, we investigated the microbial metabolite profiles, specifically SCFAs using HPLC-MS/MS and others using GC-MS, respectively. MSP supplement elevated the abundance of amino acids, including valine, isoleucine and proline as well as the concentration of acetic acid. According to the correlation analyses, these alterations were found out to be crucial in energy synthesizing metabolism, such as branched-chain amino acid (BCAA) metabolism and coenzyme A biosynthesis. Furthermore, we isolated commensal Lactobacillus strains enriched by MSP supplement, and analyzed the metabolites and evaluated the functional improvement, related to tight junction from intestinal porcine enterocyte cell line (IPEC-J2).

CONCLUSIONS: In conclusion, MSP administration to piglets altered their fecal microbiota, by enriching commensal Lactobacillus strains. This change contributed amino acid, acetic acid, and BCAA concentrations to be increased, and energy metabolism pathway was also increased at in vivo and in vitro. These changes produced by MSP supplement suggests the correlation between the various physiological energy metabolism functions induced by health-promoting Lactobacillus and the growth performance of piglets.}, } @article {pmid36434287, year = {2022}, author = {Debnath, T and Deb, S and Das, SK}, title = {Influence of Geochemistry in the Tropical Hot Springs on Microbial Community Structure and Function.}, journal = {Current microbiology}, volume = {80}, number = {1}, pages = {4}, pmid = {36434287}, issn = {1432-0991}, support = {D.O.No. BT/BI/04/058/2002 VOL-II//Department of Biotechnology/ ; }, mesh = {*Hot Springs/microbiology ; Phylogeny ; *Microbiota/genetics ; Archaea/genetics ; Bacteria/genetics ; *Chloroflexi ; }, abstract = {Thermophiles inhabiting high temperatures are considered primitive microorganisms on early Earth. In this regard, several works have demonstrated microbial community composition in geothermal environments. Despite that, studies on hot springs located in the Indian subcontinent viz., Surajkund in the district Hazaribag, Jharkhand; Bakreshwar in the district Birbhum, West Bengal; Tantloi in the district Dumka, and Sidpur in the district Pakur, Jharkhand are scanty. Nonetheless, the metagenomic analysis of these hot springs showed significant differences in the predominant phyla corresponding to geochemical properties. The Chloroflexi, Proteobacteria, Actinobacteria, Deinococcus-Thermus, and Firmicutes were dominant phyla in all the samples. In contrast, Meiothermus was more in comparatively low-temperature hot springs. In addition, archaeal phyla, Euryarchaeota, Candidatus Bathyarchaeota, and Crenarchaeota were predominant in all samples. The canonical correspondence analysis (CCA) showed the abundance of Deinococcus, Thermus, Pyrobaculum, Kocuria, and Geodermatophilus positively correlated with the aqueous concentration of sulfate, fluoride, and argon in relatively high-temperature (≥ 72 °C) hot springs. However, at a lower temperature (≤ 63 °C), Thermodesulfovibrio, Caldilinea, Chloroflexus, Meiothermus, and Tepidimonas are positively correlated with the concentration of zinc, iron, and dissolved oxygen. Further, hierarchical clustering exhibits variations in its functional attributes depending on the temperature gradients. Metagenome analysis predicted carbon, methane, sulfur, and nitrogen metabolism genes, indicating a wide range of bacteria and archaea habitation in these hot springs. In addition, identified several genes encode polyketide biosynthesis pathways. The present study described the microbial community composition and function in the tropical hot springs and their relationship with the environmental variables.}, } @article {pmid36434093, year = {2022}, author = {Feng, Y and Wang, Y and Zhu, B and Gao, GF and Guo, Y and Hu, Y}, title = {Author Correction: Metagenome-assembled genomes and gene catalog from the chicken gut microbiome aid in deciphering antibiotic resistomes.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1289}, doi = {10.1038/s42003-022-04266-z}, pmid = {36434093}, issn = {2399-3642}, } @article {pmid36433735, year = {2022}, author = {Li, JM and Yao, CL and Lin, WH and Surampalli, RY and Zhang, TC and Tseng, TY and Kao, CM}, title = {Toxicity determination, pollution source delineation, and microbial diversity evaluation of PAHs-contaminated sediments for an urban river.}, journal = {Water environment research : a research publication of the Water Environment Federation}, volume = {94}, number = {11}, pages = {e10810}, doi = {10.1002/wer.10810}, pmid = {36433735}, issn = {1554-7531}, support = {107-2221-E-127-001-MY2//Taiwan Ministry of Science and Technology (MOST)/ ; }, abstract = {The Feng-Sang River is a metropolitan river in Kaohsiung City, Taiwan. In this study, Feng-Sang River sediments were analyzed to investigate the distributions and sources of polycyclic aromatic hydrocarbons (PAHs). The Sediment Quality Guidelines (SQGs), potentially carcinogenic PAHs (TEQ[carc]), and toxic equivalence quotient (TEQ) were applied to evaluate influences of PAHs on ecosystems and microbial diversities. Results indicate that PAHs concentrations varied between seasons and locations. The concentrations of ∑16 PAHs ranged from 73.6 to 603.8 ng/kg in dry seasons and from 2.3 to 199.3 ng/kg in wet seasons. This could be because of the flushing effect during wet seasons, which caused the movement and dilution of the PAH-contaminated sediments. Diagnostic ratio analysis infers that high PAHs levels were generated by combustion processes and vehicle traffic, and results from multivariate descriptive statistical analysis also demonstrate that the vehicular traffic pollution could be the major emission source of PAHs contamination. Comparisons of PAHs with SQGs indicate that PAHs concentrations in sediment were below the effects range low (ERL) values, and thus, the immediate threat to organisms might not be significant. The diagnostic ratio analyses are effective methods for PAH source appointment. The metagenomic assay results imply that sediments contained essential microbial species with eminent diversity. The detected PAH-degrading bacteria (Desulfatiglans, Dechloromonas, Sphingomonas, Methylobacterium, Rhodobacter, Clostridium, and Exiguobacterium) played a key role in PAHs biotransformation, and Dechloromonas and Rhodobacter had a higher relative abundance. Results of microbial diversity analyses indicate that the contaminated environment induced the changes of governing microbial groups in sediments. PRACTITIONER POINTS: Diagnostic ratio analyses are effective methods for PAHs source appointment. Microbial composition in sediments are highly affected by anthropogenic pollution. Combustion and vehicle traffic contribute to urban river sediments pollution by PAHs. Dechloromonas and Rhodobacter are dominant PAHs-degrading bacteria in sediments.}, } @article {pmid36432504, year = {2022}, author = {Benítez-Guerrero, T and Vélez-Ixta, JM and Juárez-Castelán, CJ and Corona-Cervantes, K and Piña-Escobedo, A and Martínez-Corona, H and De Sales-Millán, A and Cruz-Narváez, Y and Gómez-Cruz, CY and Ramírez-Lozada, T and Acosta-Altamirano, G and Sierra-Martínez, M and Zárate-Segura, PB and García-Mena, J}, title = {Gut Microbiota Associated with Gestational Health Conditions in a Sample of Mexican Women.}, journal = {Nutrients}, volume = {14}, number = {22}, pages = {}, pmid = {36432504}, issn = {2072-6643}, support = {SECTEI/249/2019-CM-SECTEI/109/2020-CM-SECTEI/124/2021, Convocatoria 2019, Proyectos Científicos, Tecnológicos y/o de Innovación para la atención a problemas específicos de la Ciudad de México relacionados con la investigación y atención de enfermedades cr//Secretaría de Ciencia, Tecnología e Innovación de la CDMX/ ; CONACyT-163235 INFR-2011-01//Consejo Nacional de Ciencia y Tecnología/ ; CONACyT-302670-2019-Apoyos para Adquisición y Mantenimiento de Infraestructura en Insti-tuciones y laboratorios de Investigación Especializada.//Consejo Nacional de Ciencia y Tecnología/ ; }, mesh = {Pregnancy ; Humans ; Female ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/analysis ; *Diabetes, Gestational ; Dysbiosis/microbiology ; Feces/microbiology ; Fatty Acids, Volatile/metabolism ; Bacteria ; *Pre-Eclampsia ; }, abstract = {Gestational diabetes (GD), pre-gestational diabetes (PD), and pre-eclampsia (PE) are morbidities affecting gestational health which have been associated with dysbiosis of the mother's gut microbiota. This study aimed to assess the extent of change in the gut microbiota diversity, short-chain fatty acids (SCFA) production, and fecal metabolites profile in a sample of Mexican women affected by these disorders. Fecal samples were collected from women with GD, PD, or PE in the third trimester of pregnancy, along with clinical and biochemical data. Gut microbiota was characterized by high-throughput DNA sequencing of V3-16S rRNA gene libraries; SCFA and metabolites were measured by High-Pressure Liquid Chromatography (HPLC) and (Fourier Transform Ion Cyclotron Mass Spectrometry (FT-ICR MS), respectively, in extracts prepared from feces. Although the results for fecal microbiota did not show statistically significant differences in alfa diversity for GD, PD, and PE concerning controls, there was a difference in beta diversity for GD versus CO, and a high abundance of Proteobacteria, followed by Firmicutes and Bacteroidota among gestational health conditions. DESeq2 analysis revealed bacterial genera associated with each health condition; the Spearman's correlation analyses showed selected anthropometric, biochemical, dietary, and SCFA metadata associated with specific bacterial abundances, and although the HPLC did not show relevant differences in SCFA content among the studied groups, FT-ICR MS disclosed the presence of interesting metabolites of complex phenolic, valeric, arachidic, and caprylic acid nature. The major conclusion of our work is that GD, PD, and PE are associated with fecal bacterial microbiota profiles, with distinct predictive metagenomes.}, } @article {pmid36431000, year = {2022}, author = {Siddiqui, R and Qaisar, R and Khan, NA and Alharbi, AM and Alfahemi, H and Elmoselhi, A}, title = {Effect of Microgravity on the Gut Microbiota Bacterial Composition in a Hindlimb Unloading Model.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {11}, pages = {}, pmid = {36431000}, issn = {2075-1729}, abstract = {We utilised a ground-based microgravity hindlimb unloading (HU) mouse model to elucidate the gut microbiota bacterial changes in mice under a simulated microgravity environment. Four-month-old, male C57/Bl6 mice were randomly divided into ground-based controls and the HU groups and kept under controlled environmental conditions. For the microgravity environment, the mice were suspended in special cages individually for 20 days. At the end of the suspension, the mice were sacrificed; gut dissections were performed, followed by a metagenomic analysis of bacterial species, which was carried out by extracting DNA and 16S rRNA analysis. The results revealed that the gut bacterial communities of mice under gravity and microgravity were different. Notably, our findings revealed differences in the bacterial community structure. Around 449 bacterial OTUs were specific to mice kept under normal gravity versus 443 bacterial OTUs under microgravity conditions. In contrast, 694 bacterial OTUs were common to both groups. When the relative abundance of taxa was analyzed, Bacteroidetes dominated the gut (64.7%) of normal mice. Conversely, mice in the microgravity environment were dominated by Firmicutes (42.7%), and the relative abundance of Bacteroidetes differed significantly between the two groups (p < 0.05). The distribution of Muribaculaceae between normal mice versus microgravity mice was significantly different, at 62% and 36.4%, respectively (p < 0.05). Furthermore, a significant decrease in 11 bacteria was observed in mice under simulated microgravity, including Akkermansia muciniphila, Eubacterium coprostanoligenes, Bacteroides acidifaciens, Clostridium leptum, Methylorubrum extorquens, Comamonas testosterone, Desulfovibrio fairfieldensis, Bacteroides coprocola, Aerococcus urinaeequi, Helicobacter hepaticus, and Burkholderiales. Further studies are needed to elucidate gut bacterial metabolites of these identified bacterial species in microgravity conditions and normal environment. Notably, the influence of these metabolites on obesity, neuroprotection, musculoskeletal and cardiovascular dysfunction, longevity, inflammation, health, and disease in astronauts ought to be investigated and will be important in developing procedures against adverse effects in astronauts following space travel.}, } @article {pmid36430609, year = {2022}, author = {Tilocca, B and Soggiu, A and Iavarone, F and Greco, V and Putignani, L and Ristori, MV and Macari, G and Spina, AA and Morittu, VM and Ceniti, C and Piras, C and Bonizzi, L and Britti, D and Urbani, A and Figeys, D and Roncada, P}, title = {The Functional Characteristics of Goat Cheese Microbiota from a One-Health Perspective.}, journal = {International journal of molecular sciences}, volume = {23}, number = {22}, pages = {}, pmid = {36430609}, issn = {1422-0067}, support = {AIM1879147 - 2 (Bruno Tilocca)//Attraction International Mobility-AIM, PON-FSE/ ; }, mesh = {Animals ; *Cheese/analysis ; Goats/genetics ; RNA, Ribosomal, 16S/genetics ; *One Health ; Bacteria/genetics ; *Microbiota/genetics ; }, abstract = {Goat cheese is an important element of the Mediterranean diet, appreciated for its health-promoting features and unique taste. A pivotal role in the development of these characteristics is attributed to the microbiota and its continuous remodeling over space and time. Nevertheless, no thorough study of the cheese-associated microbiota using two metaomics approaches has previously been conducted. Here, we employed 16S rRNA gene sequencing and metaproteomics to explore the microbiota of a typical raw goat milk cheese at various ripening timepoints and depths of the cheese wheel. The 16S rRNA gene-sequencing and metaproteomics results described a stable microbiota ecology across the selected ripening timepoints, providing evidence for the microbiologically driven fermentation of goat milk products. The important features of the microbiota harbored on the surface and in the core of the cheese mass were highlighted in both compositional and functional terms. We observed the rind microbiota struggling to maintain the biosafety of the cheese through competition mechanisms and/or by preventing the colonization of the cheese by pathobionts of animal or environmental origin. The core microbiota was focused on other biochemical processes, supporting its role in the development of both the health benefits and the pleasant gustatory nuances of goat cheese.}, } @article {pmid36430244, year = {2022}, author = {Assalin, HB and De Almeida, KCG and Guadagnini, D and Santos, A and Teixeira, CJ and Bordin, S and Rocha, GZ and Saad, MJA}, title = {Proton Pump Inhibitor Pantoprazole Modulates Intestinal Microbiota and Induces TLR4 Signaling and Fibrosis in Mouse Liver.}, journal = {International journal of molecular sciences}, volume = {23}, number = {22}, pages = {}, pmid = {36430244}, issn = {1422-0067}, support = {2014/50907-5; 2019/03196-0; 2020/06397-3//São Paulo Research Foundation/ ; INCT Obesidade e Diabetes CNPq (465693/2014-8)//National Council for Scientific and Technological Development/ ; }, mesh = {Mice ; Humans ; Animals ; Toll-Like Receptor 4/therapeutic use ; *Gastrointestinal Microbiome ; Pantoprazole/pharmacology ; Proton Pump Inhibitors/pharmacology/therapeutic use ; Lipopolysaccharides/pharmacology ; Mice, Inbred C57BL ; *Non-alcoholic Fatty Liver Disease/drug therapy/etiology ; Fibrosis ; }, abstract = {Proton pump inhibitors (PPIs) are one of the most prescribed drugs around the world. PPIs induce microbiota modulation such as obesity both in humans and in animal models. However, since PPIs can induce microbiota modulation despite the absence of a high-fat diet or weight gain, it is an interesting model to correlate microbiota modulation with the establishment of non-alcoholic fatty liver disease (NAFLD). We investigated the effect of pantoprazole treatment on TLR4 signaling and liver histology in C57BL/6J mice for 60 days, trying to correlate microbiota modulation with some aspects of liver injury. We performed glucose (GTT) and insulin (ITT) tolerance tests, serum lipopolysaccharide (LPS) dosage, liver histology, liver and intestine extraction for Western blot and qPCR. Fecal microbiota were investigated via metagenomics. Chronic treatment with pantoprazole induced microbiota modulation and impaired ileum barrier integrity, without an association with insulin resistance. Furthermore, increased circulating LPS and increased Toll-like receptor 4 (TLR4) and TGFβ downstream signaling may have an important role in the development of the observed liver microvesicular steatosis and fibrosis. Finally, this model of PPI-induced changes in microbiota might be useful to investigate liver microvesicular steatosis and fibrosis.}, } @article {pmid36430229, year = {2022}, author = {Mathebela, P and Damane, BP and Mulaudzi, TV and Mkhize-Khwitshana, ZL and Gaudji, GR and Dlamini, Z}, title = {Influence of the Microbiome Metagenomics and Epigenomics on Gastric Cancer.}, journal = {International journal of molecular sciences}, volume = {23}, number = {22}, pages = {}, pmid = {36430229}, issn = {1422-0067}, support = {23108//Department of Surgery, University of Pretoria, the South African Medical Research Council (SAMRC)/ ; 138139//the National Research Foundation (NRF)/ ; }, mesh = {Humans ; Metagenomics ; Dysbiosis/microbiology ; *Stomach Neoplasms/genetics/microbiology ; Epigenomics ; Neoplasm Recurrence, Local ; *Microbiota/genetics ; *Helicobacter pylori/genetics ; Carcinogenesis/pathology ; }, abstract = {Gastric cancer (GC) is one of the major causes of cancer deaths worldwide. The disease is seldomly detected early and this limits treatment options. Because of its heterogeneous and complex nature, the disease remains poorly understood. The literature supports the contribution of the gut microbiome in the carcinogenesis and chemoresistance of GC. Drug resistance is the major challenge in GC therapy, occurring as a result of rewired metabolism. Metabolic rewiring stems from recurring genetic and epigenetic factors affecting cell development. The gut microbiome consists of pathogens such as H. pylori, which can foster both epigenetic alterations and mutagenesis on the host genome. Most of the bacteria implicated in GC development are Gram-negative, which makes it challenging to eradicate the disease. Gram-negative bacterium co-infections with viruses such as EBV are known as risk factors for GC. In this review, we discuss the role of microbiome-induced GC carcinogenesis. The disease risk factors associated with the presence of microorganisms and microbial dysbiosis are also discussed. In doing so, we aim to emphasize the critical role of the microbiome on cancer pathological phenotypes, and how microbiomics could serve as a potential breakthrough in determining effective GC therapeutic targets. Additionally, consideration of microbial dysbiosis in the GC classification system might aid in diagnosis and treatment decision-making, taking the specific pathogen/s involved into account.}, } @article {pmid36430197, year = {2022}, author = {Cuomo, P and Capparelli, R and Alifano, M and Iannelli, A and Iannelli, D}, title = {Gut Microbiota Host-Gene Interaction.}, journal = {International journal of molecular sciences}, volume = {23}, number = {22}, pages = {}, pmid = {36430197}, issn = {1422-0067}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2 ; Host Microbial Interactions ; *Microbiota ; Anti-Bacterial Agents ; }, abstract = {Studies carried out in the last ten years have shown that the metabolites made up from the gut microbiota are essential for multiple functions, such as the correct development of the immune system of newborns, interception of pathogens, and nutritional enrichment of the diet. Therefore, it is not surprising that alteration of the gut microbiota is the starting point of gastrointestinal infection, obesity, type 2 diabetes, inflammatory bowel disease, colorectal cancer, and lung cancer. Diet changes and antibiotics are the major factors damaging the gut microbiota. Early exposure of the newborns to antibiotics may prevent their correct development of the immune system, exposing them to pathogen infections, allergies, and chronic inflammatory diseases. We already know much on how host genes, microbiota, and the environment interact, owing to experiments in several model animals, especially in mice; advances in molecular technology; microbiota transplantation; and comparative metagenomic analysis. However, much more remains to be known. Longitudinal studies on patients undergoing to therapy, along with the identification of bacteria prevalent in responding patients may provide valuable data for improving therapies.}, } @article {pmid36430182, year = {2022}, author = {Santonocito, S and Ferlito, S and Polizzi, A and Ronsivalle, V and Sclafani, R and Valletta, A and Lo Giudice, A and Cavalcanti, R and Spagnuolo, G and Isola, G}, title = {Therapeutic and Metagenomic Potential of the Biomolecular Therapies against Periodontitis and the Oral Microbiome: Current Evidence and Future Perspectives.}, journal = {International journal of molecular sciences}, volume = {23}, number = {22}, pages = {}, pmid = {36430182}, issn = {1422-0067}, mesh = {Humans ; *Periodontitis/microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Periodontium/metabolism ; Dysbiosis/therapy ; }, abstract = {The principles of periodontal therapy are based on the control of microbial pathogens and host factors that contribute to biofilm dysbiosis, with the aim of modulating the progression of periodontitis and periodontal tissue destruction. It is currently known how differently each individual responds to periodontal treatment, depending on both the bacterial subtypes that make up the dysbiotic biofilm and interindividual variations in the host inflammatory response. This has allowed the current variety of approaches for the management of periodontitis to be updated by defining the goals of target strategies, which consist of reducing the periodontopathogenic microbial flora and/or modulating the host-mediated response. Therefore, this review aims to update the current variety of approaches for the management of periodontitis based on recent target therapies. Recently, encouraging results have been obtained from several studies exploring the effects of some targeted therapies in the medium- and long-term. Among the most promising target therapies analyzed and explored in this review include: cell-based periodontal regeneration, mediators against bone resorption, emdogain (EMD), platelet-rich plasma, and growth factors. The reviewed evidence supports the hypothesis that the therapeutic combination of epigenetic modifications of periodontal tissues, interacting with the dysbiotic biofilm, is a key step in significantly reducing the development and progression of disease in periodontal patients and improving the therapeutic response of periodontal patients. However, although studies indicate promising results, these need to be further expanded and studied to truly realize the benefits that targeted therapies could bring in the treatment of periodontitis.}, } @article {pmid36429214, year = {2022}, author = {Zhang, YT and Deng, YK and Zou, YF and Han, BL and Pu, JZ and Rao, JQ and Huang, D and Luo, HB}, title = {Linking Microbial Functional Gene Abundance and Daqu Extracellular Enzyme Activity: Implications for Carbon Metabolism during Fermentation.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {22}, pages = {}, pmid = {36429214}, issn = {2304-8158}, support = {2019YFS0518//Sichuan Science and Technology Project/ ; y2021040//The Innovation Fund of Postgraduate, Sichuan University of Science & Engineering/ ; }, abstract = {Daqu is the starter of Baijiu, it provides the microbes and enzymes necessary for fermentation. Studies have already established carbohydrate metabolism as the primary functional module in Daqu fermentation. The present study investigated the changes in microbial functions and the relationship between carbohydrate metabolism-related functional genes and extracellular enzyme activity during the Daqu fermentation. Amplicon sequencing identified 38 bacterial and 10 fungal phyla in Daqu samples, while shotgun metagenomic sequencing classified and annotated 40.66% of the individual features, of which 40.48% were prokaryotes. KEGG annotation showed that the pathways related to metabolites were less in the early fermentation stage, but higher in the middle and late stages. The functional genes related to pyruvate metabolism, glyoxylate and dicarboxylate metabolism, and propanoate metabolism were relatively high in the early and late stages of fermentation, while that for start and cross metabolism was relatively low. The study also found that amino sugar and nucleoside sugar metabolism were dominant in the middle stage of fermentation. Finally, the correlation network analysis showed that amylase activity positively correlated with many carbon metabolism-related pathways, while liquefaction activity negatively correlated with these pathways. In conclusion, the present study provides a theoretical basis for improving and stabilizing the quality of Daqu.}, } @article {pmid36429047, year = {2022}, author = {Wieland, L and Schwarz, T and Engel, K and Volkmer, I and Krüger, A and Tarabuko, A and Junghans, J and Kornhuber, ME and Hoffmann, F and Staege, MS and Emmer, A}, title = {Epstein-Barr Virus-Induced Genes and Endogenous Retroviruses in Immortalized B Cells from Patients with Multiple Sclerosis.}, journal = {Cells}, volume = {11}, number = {22}, pages = {}, pmid = {36429047}, issn = {2073-4409}, mesh = {Humans ; *Endogenous Retroviruses/genetics ; Herpesvirus 4, Human ; *Epstein-Barr Virus Infections ; *Multiple Sclerosis/genetics ; Leukocytes, Mononuclear/metabolism ; Recurrence ; }, abstract = {The immune pathogenesis of multiple sclerosis (MS) is thought to be triggered by environmental factors in individuals with an unfavorable genetic predisposition. Epstein-Barr virus (EBV) infection is a major risk factor for subsequent development of MS. Human endogenous retroviruses (HERVs) can be activated by EBV, and might be a missing link between an initial EBV infection and the later onset of MS. In this study, we investigated differential gene expression patterns in EBV-immortalized lymphoblastoid B cell lines (LCL) from MS-affected individuals (MSLCL) and controls by using RNAseq and qRT-PCR. RNAseq data from LCL mapped to the human genome and a virtual virus metagenome were used to identify possible biomarkers for MS or disease-relevant risk factors, e.g., the relapse rate. We observed that lytic EBNA-1 transcripts seemed to be negatively correlated with age leading to an increased expression in LCL from younger PBMC donors. Further, HERV-K (HML-2) GAG was increased upon EBV-triggered immortalization. Besides the well-known transactivation of HERV-K18, our results suggest that another six HERV loci are up-regulated upon stimulation with EBV. We identified differentially expressed genes in MSLCL, e.g., several HERV-K loci, ERVMER61-1 and ERV3-1, as well as genes associated with relapses. In summary, EBV induces genes and HERV in LCL that might be suitable as biomarkers for MS or the relapse risk.}, } @article {pmid36428566, year = {2022}, author = {Wu, X and Park, S}, title = {Fecal Bacterial Community and Metagenome Function in Asians with Type 2 Diabetes, According to Enterotypes.}, journal = {Biomedicines}, volume = {10}, number = {11}, pages = {}, pmid = {36428566}, issn = {2227-9059}, support = {2019R1A2C1007203//National Research Foundation of Korea/ ; }, abstract = {The role of gut microbes has been suggested in type 2 diabetes (T2DM) risk. However, their results remain controversial. We hypothesized that Asians with T2DM had different fecal bacterial compositions, co-abundance networks, and metagenome functions compared to healthy individuals, according to enterotypes. This hypothesis was examined using the combined gut microbiota data from human fecal samples from previous studies. The human fecal bacterial FASTA/Q files from 36 different T2DM studies in Asians were combined (healthy, n = 3378; T2DM, n = 551), and operational taxonomic units (OTUs) and their counts were obtained using qiime2 tools. In the machine learning approaches, fecal bacteria rich in T2DM were found. They were separated into two enterotypes, Lachnospiraceae (ET-L) and Prevotellaceae (ET-P). The Shannon and Chao1 indices, representing α-diversity, were significantly lower in the T2DM group compared to the healthy group in ET-L (p < 0.05) but not in ET-P. In the Shapley additive explanations analysis of ET-L, Escherichia fergusonii, Collinsella aerofaciens, Streptococcus vestibularis, and Bifidobacterium longum were higher (p < 0.001), while Phocaeicola vulgatus, Bacteroides uniformis, and Faecalibacterium prausnitzii were lower in the T2DM group than in the healthy group (p < 0.00005). In ET-P, Escherichia fergusonii, Megasphaera elsdenii, and Oscillibacter valericigenes were higher, and Bacteroides koreensis and Faecalibacterium prausnitzii were lower in the T2DM group than in the healthy group. In ET-L and ET-P, bacteria in the healthy and T2DM groups positively interacted with each other within each group (p < 0.0001) but negatively interacted between the T2DM and healthy groups in the network analysis (p < 0.0001). In the metagenome functions of the fecal bacteria, the gluconeogenesis, glycolysis, and amino acid metabolism pathways were higher, whereas insulin signaling and adenosine 5′ monophosphate-activated protein kinase (AMPK) signaling pathways were lower in the T2DM group than in the healthy group for both enterotypes (p < 0.00005). In conclusion, Asians with T2DM exhibited gut dysbiosis, potentially linked to intestinal permeability and the enteric vagus nervous system.}, } @article {pmid36428472, year = {2022}, author = {Wang, Y and Choy, CT and Lin, Y and Wang, L and Hou, J and Tsui, JCC and Zhou, J and Wong, CH and Yim, TK and Tsui, WK and Chan, UK and Siu, PLK and Loo, SKF and Tsui, SKW}, title = {Effect of a Novel E3 Probiotics Formula on the Gut Microbiome in Atopic Dermatitis Patients: A Pilot Study.}, journal = {Biomedicines}, volume = {10}, number = {11}, pages = {}, pmid = {36428472}, issn = {2227-9059}, support = {14119219, 14119420//Research Grants Council of Hong Kong/ ; 06171061//Health and Medical Research Fund from Food and Health Bureau of Hong Kong/ ; }, abstract = {Atopic dermatitis (AD) has been shown to be closely related to gut dysbiosis mediated through the gut−skin axis, and thus the gut microbiome has recently been explored as a potential therapeutic target for the treatment of AD. Contrasting and varying efficacy have been reported since then. In order to investigate the determining factor of probiotics responsiveness in individuals with AD, we initiated the analysis of 41 AD patients with varying disease severity in Hong Kong, whereas the severity was assessed by Eczema Area and Severity Index (EASI) by board certified dermatologist. 16S rRNA sequencing on the fecal samples from AD patients were performed to obtain the metagenomics profile at baseline and after 8 weeks of oral administration of a novel E3 probiotics formula (including prebiotics, probiotics and postbiotics). While EASI of the participants were significantly lower after the probiotics treatment (p < 0.001, paired Wilcoxon signed rank), subjects with mild AD were found to be more likely to respond to the probiotics treatment. Species richness among responders regardless of disease severity were significantly increased (p < 0.001, paired Wilcoxon signed rank). Responders exhibited (1) elevated relative abundance of Clostridium, Fecalibacterium, Lactobacillus, Romboutsia, and Streptococcus, (2) reduced relative abundance of Collinsella, Bifidobacterium, Fusicatenibacter, and Escherichia-Shigella amid orally-intake probiotics identified using the machine learning algorithm and (3) gut microbiome composition and structure resembling healthy subjects after probiotics treatment. Here, we presented the gut microbiome dynamics in AD patients after the administration of the E3 probiotics formula and delineated the unique gut microbiome signatures in individuals with AD who were responding to the probiotics. These findings could guide the future development of probiotics use for AD management.}, } @article {pmid36428451, year = {2022}, author = {Santamarina-García, G and Amores, G and López de Armentia, E and Hernández, I and Virto, M}, title = {Relationship between the Dynamics of Gross Composition, Free Fatty Acids and Biogenic Amines, and Microbial Shifts during the Ripening of Raw Ewe Milk-Derived Idiazabal Cheese.}, journal = {Animals : an open access journal from MDPI}, volume = {12}, number = {22}, pages = {}, pmid = {36428451}, issn = {2076-2615}, support = {IT944-16//Basque Government/ ; }, abstract = {This study reports for the first time the relationship between bacterial succession, characterized by high-throughput sequencing (sequencing of V3-V4 16S rRNA regions), and the evolution of gross composition, free fatty acids (FFAs) and biogenic amines (BAs) during cheese ripening. Specifically, Idiazabal PDO cheese, a raw ewe milk-derived semi-hard o hard cheese, was analysed. Altogether, 8 gross parameters were monitored (pH, dry matter, protein, fat, Ca, Mg, P and NaCl) and 21 FFAs and 8 BAs were detected. The ripening time influenced the concentration of most physico-chemical parameters, whereas the producer mainly affected the gross composition and FFAs. Through an O2PLS approach, the non-starter lactic acid bacteria Lactobacillus, Enterococcus and Streptococcus were reported as positively related to the evolution of gross composition and FFAs release, while only Lactobacillus was positively related to BAs production. Several environmental or non-desirable bacteria showed negative correlations, which could indicate the negative impact of gross composition on their growth, the antimicrobial effect of FFAs and/or the metabolic use of FFAs by these genera, and their ability to degrade BAs. Nonetheless, Obesumbacterium and Chromohalobacter were positively associated with the synthesis of FFAs and BAs, respectively. This research work provides novel information that may contribute to the understanding of possible functional relationships between bacterial communities and the evolution of several cheese quality and safety parameters.}, } @article {pmid36428448, year = {2022}, author = {Su, M and Wang, H and Shi, H and Li, Q and Zhang, Y and Li, T and Ma, Y}, title = {Yeast Products Mediated Ruminal Subenvironmental Microbiota, and Abnormal Metabolites and Digestive Enzymes Regulated Rumen Fermentation Function in Sheep.}, journal = {Animals : an open access journal from MDPI}, volume = {12}, number = {22}, pages = {}, pmid = {36428448}, issn = {2076-2615}, support = {GSSYLXM-02//Education Science and Technology Innovation Project of Gansu Province/ ; 2021YFD1100502//National Key R&D Program of China/ ; GAU-XKTD-2022-20//Discipline Team Project of Gansu Agricultural University/ ; }, abstract = {Yeast products (YP) are commonly used as rumen regulators, but their mechanisms of action are still unclear. Based on our previous studies, we questioned whether yeast products would have an impact on rumen solid-associated (SA) and liquid-associated (LA) microorganisms and alter rumen fermentation patterns. Thirty 3-month-old male sheep weighing 19.27 ± 0.45 kg were selected and randomized into three groups for 60 days: (1) basal diet group (CON group), (2) basal diet add 20 g YP per day (low YP, LYP group) and (3) basal diet add 40 g YP per day (high YP, HYP group). The results demonstrated that the addition of YP increased rumen cellulase activity, butyrate and total volatile fatty acid (TVFA) concentrations (p < 0.05), while it decreased rumen amylase activity and abnormal metabolites, such as lactate, lipopolysaccharides (LPS) and histamine (HIS) (p < 0.05). Metagenomic analysis of rumen microorganisms in three groups revealed that YP mainly influenced the microbial profiles of the SA system. YP increased the relative abundance of R. flavefaciens and decreased methanogens in the SA system (p < 0.05). With the addition of YP, the abundance of only a few lactate-producing bacteria increased in the SA system, including Streptococcus and Lactobacillus (p < 0.05). However, almost all lactate-utilizing bacteria increased in the LA system, including Megasphaera, Selenomonas, Fusobacterium and Veillonella (p < 0.05). In addition, YP increased the abundance of certain GHs family members, including GH43 and GH98 (p < 0.05), but decreased the abundance of some KEGG metabolic pathways involved in starch and sucrose metabolism, biosynthesis of antibiotics and purine metabolism, among others. In conclusion, the addition of YP to high-concentrate diets can change the abundance of major functional microbiota in the rumen, especially in the solid fraction, which in turn affects rumen fermentation patterns and improves rumen digestibility.}, } @article {pmid36427959, year = {2022}, author = {Payami, H}, title = {The many genomes of Parkinson's disease.}, journal = {International review of neurobiology}, volume = {167}, number = {}, pages = {59-80}, doi = {10.1016/bs.irn.2022.07.007}, pmid = {36427959}, issn = {2162-5514}, mesh = {Humans ; *Parkinson Disease/genetics ; *Microbiota ; }, abstract = {Genetic component of Parkinson's disease, once firmly believed non-existent, involves the human genome, mitochondrial genome, and the microbiome. Understanding the genomics of PD requires identification of PD-relevant genes and learning how they interact within the hologenome and with their environment. This chapter is an evidence-based perspective of a geneticist on how far we have come in this endeavor. The contemporary scientific society started with a naive and simplistic view of PD, evolved to accept that Parkinson's disease is probably the most complex disease there is, the progress we have made in discovering the genes and elucidating their functions, and now assembling the parts to create the whole.}, } @article {pmid36427828, year = {2023}, author = {Miao, Z and Miao, Z and Teng, X and Xu, S}, title = {Melatonin alleviates lead-induced fatty liver in the common carps (Cyprinus carpio) via gut-liver axis.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {317}, number = {}, pages = {120730}, doi = {10.1016/j.envpol.2022.120730}, pmid = {36427828}, issn = {1873-6424}, mesh = {Animals ; *Carps ; *Melatonin/pharmacology/metabolism ; Lead/toxicity/metabolism ; Lipopolysaccharides/toxicity ; Liver/metabolism ; *Fatty Liver/metabolism ; }, abstract = {As a widespread aquatic environmental contaminant, Lead (Pb) can provoke hepatic injury in various animals. Melatonin (MT) plays a crucial role in the regulation of inflammatory response. Accumulating evidence elucidates exogenous toxins can elicit hepatic lipid metabolic disorders by influencing the gut microbiome. Nevertheless, the effects of Pb on gut microbiota and hepatic lipid metabolism of the common carps, and whether MT can prevent and cure Pb-induced toxicity via regulating microbiome remains unknown. Here, metagenomic and transcriptomic analysis were subsequently implemented to identify the Pb exposure-triggered prominent alternation of gut-liver signal. In the present study the severe intestinal injury and fatty liver formation caused by Pb in common carp were preliminarily determined. Metagenomic analysis confirmed that the gut microbiome dominant phyla, family and genus of the common carps were Fusobacteria, Fusobacteriaceae and Cetobacterium. Meanwhile, lipopolysaccharide (LPS) biosynthesis pathway was regarded as one of the main responsible for Pb exposure. Subsequently, LPS was demonstrated as the Pb-triggered microbial-derived signal of the common carps by ELISA analysis, and involves in the hepatic metabolic disorders via deteriorating the intestinal barrier. Additionally, it confirmed that hepatocytes ferroptosis associated with Pb-evoked fatty liver of the common carps, and the aggravation of lysosomal dyshomeostasis as well as inhibition of AMPK phosphorylation were referred to lipid metabolic disorders. The results of the present study demonstrated microbial-derived signal induced by aquatic Pb contaminant cause fatty liver formation in the common carps, and the protective effects of MT on Pb toxicity were performed by receding LPS over-synthesis, restraining microbiota-sourced LPS transport, along with attenuation of hepatocytes ferroptosis.}, } @article {pmid36427721, year = {2023}, author = {Ji, Y and Xi, H and Zhao, Z and Jiang, Q and Chen, C and Wang, X and Li, F and Li, N and Sun, C and Feng, X and Lei, L and Han, W and Gu, J}, title = {Metagenomics analysis reveals potential pathways and drivers of piglet gut phage-mediated transfer of ARGs.}, journal = {The Science of the total environment}, volume = {859}, number = {Pt 2}, pages = {160304}, doi = {10.1016/j.scitotenv.2022.160304}, pmid = {36427721}, issn = {1879-1026}, mesh = {Animals ; Swine ; *Bacteriophages/genetics ; Metagenomics ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Bacteria ; Genes, Bacterial ; }, abstract = {The growing prevalence of antibiotic-resistant pathogens has led to a better understanding of the underlying processes that lead to this expansion. Intensive pig farms are considered one of the hotspots for antibiotic resistance gene (ARG) transmission. Phages, as important mobile carriers of ARGs, are widespread in the animal intestine. However, our understanding of phage-associated ARGs in the pig intestine and their underlying drivers is limited. Here, metagenomic sequencing and analysis of viral DNA and total DNA of different intestinal (ileum, cecum and feces) contents in healthy piglets and piglets with diarrhea were separately conducted. We found that phages in piglet ceca are the main repository for ARGs and mobile genetic element (MGE) genes. Phage-associated MGEs are important factors affecting the maintenance and transfer of ARGs. Interestingly, the colocalization of ARGs and MGE genes in piglet gut phages does not appear to be randomly selected but rather related to a specific phage host (Streptococcus). In addition, in the feces of piglets with diarrhea, the abundance of phages carrying ARGs and MGE genes was significantly increased, as was the diversity of polyvalent phages (phages with broad host ranges), which would facilitate the transfection and wider distribution of ARGs in the bacterial community. Moreover, the predicted host spectrum of polyvalent phages in diarrheal feces tended to be potential enteropathogenic genera, which greatly increased the risk of enteropathogens acquiring ARGs. Notably, we also found ARG-homologous genes in the sequences of piglet intestinal mimiviruses, suggesting that the piglet intestinal mimiviruses are a potential repository of ARGs. In conclusion, this study greatly expands our knowledge of the piglet gut microbiome, revealing the underlying mechanisms of maintenance and dissemination of piglet gut ARGs and providing a reference for the prevention and control of ARG pollution in animal husbandry.}, } @article {pmid36427112, year = {2022}, author = {Huang, S and Liu, D and Chen, M and Xi, G and Yang, P and Jia, C and Mao, D}, title = {Effects of Bacillus subtilis subsp. on the microbial community and aroma components of flue-cured tobacco leaves based on metagenome analysis.}, journal = {Archives of microbiology}, volume = {204}, number = {12}, pages = {726}, pmid = {36427112}, issn = {1432-072X}, mesh = {*Metagenome ; Nicotiana ; Odorants ; Bacillus subtilis/genetics ; *Microbiota ; Plant Leaves ; }, abstract = {To improve the sensory quality of aged flue-cured tobacco (FCT), Bacillus subtilis subsp, H11 was inoculated on aged FCT leaves named Pingdingshan DCFB. The metagenome and thecharacteristic aroma substances of aged FCT with different fermentation times (0 h, 12 h, 24 h, and 36 h) were systematically analyzed. The results showed that the content of aroma components and sensory quality of aged FCT were significantly improved when the strain was treated at 35 °C with 25% moisture for 24 h. The inoculation of H11 had a strong influence on the microbial composition and metabolism of the aged FCT leaf surface. Five microorganisms Pantoea (35.04%, 20.12-56.95%), Enterobacter (22.16, 13.60-39.82%), Pseudomonas (12.12, 3.13-26.17%), Terribacillus (8.00%, 4.65-13.01%) and Bacillus (6.54%, 0.67-16.96%) accounted for the largest proportion during the process of fermentation. The content of most neutral flavor components such as ketones and aldehydes in FCT after fermentation was higher than that priorto fermentation. After 24 h fermentation, 3-furfural, 5-methylfurfural, dihydrokiwi lactone and megalotrienone increased by 71.42%, 49.19%, 21.09%, and 10.56%, respectively. Correlation analysis between groups showed that Pseudomonas was significantly correlated with (E, E)-2, 4-heptadienal (P < 0.05), Franconibacter was correlated with damascus ketone (P < 0.05), and Terribacillus was related to the production of β-citral (P < 0.05). GH9 may be involved in the formation of damasone (P < 0.05), and 4-cyclopentene-1, 3-dione was significantly correlated with glycoside hydrolase family 5 (GH5) (P < 0.05). The correlation between 4-oxyisophorone and GH31, GH103, GH73, and GH3 was significant (P < 0.05). Microorganisms and GHs may play important roles in FCT fermentation.}, } @article {pmid36427064, year = {2022}, author = {Silva, JB and Centurion, VB and Duarte, AWF and Galazzi, RM and Arruda, MAZ and Sartoratto, A and Rosa, LH and Oliveira, VM}, title = {Unravelling the genetic potential for hydrocarbon degradation in the sediment microbiome of Antarctic islands.}, journal = {FEMS microbiology ecology}, volume = {99}, number = {1}, pages = {}, doi = {10.1093/femsec/fiac143}, pmid = {36427064}, issn = {1574-6941}, mesh = {RNA, Ribosomal, 16S/genetics ; Antarctic Regions ; Hydrocarbons/metabolism ; *Microbiota/genetics ; Soil Microbiology ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Islands ; *Polycyclic Aromatic Hydrocarbons/metabolism ; }, abstract = {Hydrocarbons may have a natural or anthropogenic origin and serve as a source of carbon and energy for microorganisms in Antarctic soils. Herein, 16S rRNA gene and shotgun sequencing were employed to characterize taxonomic diversity and genetic potential for hydrocarbon degradation of the microbiome from sediments of sites located in two Antarctic islands subjected to different temperatures, geochemical compositions, and levels of presumed anthropogenic impact, named: Crater Lake/Deception Island (pristine area), Whalers Bay and Fumarole Bay/Deception Island (anthropogenic-impacted area), and Hannah Point/Livingston Island (anthropogenic-impacted area). Hydrocarbon concentrations were measured for further correlation analyses with biological data. The majority of the hydrocarbon-degrading genes were affiliated to the most abundant bacterial groups of the microbiome: Proteobacteria and Actinobacteria. KEGG annotation revealed 125 catabolic genes related to aromatic hydrocarbon (styrene, toluene, ethylbenzene, xylene, naphthalene, and polycyclic hydrocarbons) and aliphatic (alkanes and cycloalkanes) pathways. Only aliphatic hydrocarbons, in low concentrations, were detected in all areas, thus not characterizing the areas under study as anthropogenically impacted or nonimpacted. The high richness and abundance of hydrocarbon-degrading genes suggest that the genetic potential of the microbiome from Antarctic sediments for hydrocarbon degradation is driven by natural hydrocarbon occurrence.}, } @article {pmid36426053, year = {2022}, author = {Wakimura, K and Inai, K and Tanida, K and Watanabe, K and Kato, M}, title = {Metabarcoding data of mitochondrial cytochrome c oxidase subunit 1 gene from bulk community of aquatic organisms collected from Nara Prefecture, Japan.}, journal = {Data in brief}, volume = {45}, number = {}, pages = {108599}, pmid = {36426053}, issn = {2352-3409}, abstract = {Riverine metabarcoding data were obtained from the Takamigawa River, a tributary of the Kinokawa River, in Nara Prefecture (Central Honshu, Japan). We extracted DNA from bulk community samples of aquatic organisms, most of which could not be morphologically identified at species level due to their small body size (0.12 - 2 mm length). A partial coding region of the mitochondrial cytochrome c oxidase subunit 1 gene (cox1) was amplified using PCR, and the amplicon was subjected to high-throughput parallel sequencing (Illumina MiSeq). The 313 bp paired-end sequence reads were classified into operational taxonomic units (OTUs), their species boundaries were delineated using the Generalised Mixed Yule Coalescent (GMYC) method, and taxonomic names of the GMYC species were assigned using basic local alignment search tool (BLAST) against International DNA Databases (INSD: GenBank, ENA, and DDBJ).}, } @article {pmid36426021, year = {2022}, author = {Sinha, AK and Parli, BV and Anilkumar, N}, title = {Bacterial distribution in the Equatorial Indian Ocean using Amplicon sequencing of V3-V4 rDNA hypervariable region data.}, journal = {Data in brief}, volume = {45}, number = {}, pages = {108673}, pmid = {36426021}, issn = {2352-3409}, abstract = {The Equatorial Indian Ocean (EIO) is a complex system strongly influenced by Indian Monsoon. During a RAMA (Research Moored Array for African-Asian-Australian Monsoon Analysis and Prediction) mooring maintenance expedition during the Southwest monsoon (August-September 2016) onboard ORV Sagar Kanya, seawater samples from the surface, deep chlorophyll maxima (DCM) and 200m were collected for bacterioplankton community structure. Herein we document our amplicon data of the bacterial community at 4 stations (4.01°S, 1.60°S, 0.36°N and 1.78°N) along the 67°00' E transect. The samples were subjected to next-generation sequencing (NGS), followed by processing with Mothur v 1.48.0, and the taxonomic classification prepared with Silva 138.1nr reference database. Our data indicates Alphaproteobacteria (48 %) and Cyanobacteria (33 %) dominance in the surface and DCM samples.}, } @article {pmid36425980, year = {2022}, author = {Rahmeh, R and Akbar, A and Alomirah, H and Kishk, M and Al-Ateeqi, A and Al-Milhm, S and Shajan, A and Akbar, B and Al-Merri, S and Alotaibi, M and Esposito, A}, title = {Data on microbial diversity of camel milk microbiota determined by 16S rRNA gene sequencing.}, journal = {Data in brief}, volume = {45}, number = {}, pages = {108744}, pmid = {36425980}, issn = {2352-3409}, abstract = {Raw camel milk samples were collected from three geographical locations (south, north and middle Kuwait) during two seasons. Next generation sequencing of the V3-V4 regions of the 16S rRNA gene was used to analyze the bacterial community in camel milk. DNA was extracted from one hundred thirty-three samples, and libraries were prepared using custom fusion primers of the 16S rRNA gene and sequenced on Illumina HiSeq 2500 platform. 16S rRNA gene sequences were aligned against the SILVA database SSU release 138. The high-throughput sequencing data are available at the NCBI database under the Bioproject PRJNA814013. This work describes camel milk's bacterial diversity among different geographical locations and seasons. The distribution of alpha diversity measures among camel milk sample groups collected from different geographical locations and seasons is presented. A significant effect of these parameters on camel milk's bacterial diversity was shown. Linear discriminant analysis (LefSe) showed significant differentially abundant bacteria at the phylum, class, order, family and genus level among the three locations and seasons. LefSe identified a total of 83 and 40 differentially abundant genera in the different geographical locations and seasons, respectively. More details about the bacterial composition of raw camel milk at the phylum and genus level can be found in research article [1]. These data can be used to compare the diversity of milk bacterial community between different milk producing species and camels from different parts of the world. Besides, these findings will contribute to our understanding of the camel microbiome structure and might be useful for designing an appropriate control program in the camel dairy herd. The data described in this article are available in Mendeley Data [2].}, } @article {pmid36424722, year = {2023}, author = {Heo, M and Park, YS and Yoon, H and Kim, NE and Kim, K and Shin, CM and Kim, N and Lee, DH}, title = {Potential of Gut Microbe-Derived Extracellular Vesicles to Differentiate Inflammatory Bowel Disease Patients from Healthy Controls.}, journal = {Gut and liver}, volume = {17}, number = {1}, pages = {108-118}, pmid = {36424722}, issn = {2005-1212}, mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Inflammatory Bowel Diseases/diagnosis/microbiology ; Feces ; *Extracellular Vesicles ; }, abstract = {BACKGROUND/AIMS: This study aimed to evaluate the potential of the stool microbiome and gut microbe-derived extracellular vesicles (EVs) to differentiate between patients with inflammatory bowel disease (IBD) and healthy controls, and to predict relapse in patients with IBD.

METHODS: Metagenomic profiling of the microbiome and bacterial EVs in stool samples of controls (n=110) and patients with IBD (n=110) was performed using 16S rRNA sequencing and then compared. Patients with IBD were divided into two enterotypes based on their microbiome, and the cumulative risk of relapse was evaluated.

RESULTS: There was a significant difference in the composition of the stool microbiome and gut microbe-derived EVs between patients with IBD and controls. The alpha diversity of the microbiome in patients with IBD was significantly lower than that in controls, while the beta diversity also differed significantly between the two groups. These findings were more prominent in gut microbe-derived EVs than in the stool microbiome. The survival curve tended to be different for enterotypes based on the gut microbe-derived EVs; however, this difference was not statistically significant (log-rank test, p=0.166). In the multivariable analysis, elevated fecal calprotectin (>250 mg/kg) was the only significant risk factor associated with relapse (adjusted hazard ratio, 3.147; 95% confidence interval, 1.545 to 6.408; p=0.002).

CONCLUSIONS: Analysis of gut microbe-derived EVs is better at differentiating patients with IBD from healthy controls than stool microbiome analysis.}, } @article {pmid36424489, year = {2023}, author = {Yarnall, MTN and Ioannidi, EI and Schmitt-Ulms, C and Krajeski, RN and Lim, J and Villiger, L and Zhou, W and Jiang, K and Garushyants, SK and Roberts, N and Zhang, L and Vakulskas, CA and Walker, JA and Kadina, AP and Zepeda, AE and Holden, K and Ma, H and Xie, J and Gao, G and Foquet, L and Bial, G and Donnelly, SK and Miyata, Y and Radiloff, DR and Henderson, JM and Ujita, A and Abudayyeh, OO and Gootenberg, JS}, title = {Drag-and-drop genome insertion of large sequences without double-strand DNA cleavage using CRISPR-directed integrases.}, journal = {Nature biotechnology}, volume = {41}, number = {4}, pages = {500-512}, pmid = {36424489}, issn = {1546-1696}, support = {UH3 HL147367/HL/NHLBI NIH HHS/United States ; UG3 HL147367/HL/NHLBI NIH HHS/United States ; R01 EB031957/EB/NIBIB NIH HHS/United States ; R56 HG011857/HG/NHGRI NIH HHS/United States ; R21 AI149694/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *CRISPR-Cas Systems/genetics ; *Integrases ; DNA Cleavage ; Gene Editing ; DNA/genetics ; DNA End-Joining Repair/genetics ; }, abstract = {Programmable genome integration of large, diverse DNA cargo without DNA repair of exposed DNA double-strand breaks remains an unsolved challenge in genome editing. We present programmable addition via site-specific targeting elements (PASTE), which uses a CRISPR-Cas9 nickase fused to both a reverse transcriptase and serine integrase for targeted genomic recruitment and integration of desired payloads. We demonstrate integration of sequences as large as ~36 kilobases at multiple genomic loci across three human cell lines, primary T cells and non-dividing primary human hepatocytes. To augment PASTE, we discovered 25,614 serine integrases and cognate attachment sites from metagenomes and engineered orthologs with higher activity and shorter recognition sequences for efficient programmable integration. PASTE has editing efficiencies similar to or exceeding those of homology-directed repair and non-homologous end joining-based methods, with activity in non-dividing cells and in vivo with fewer detectable off-target events. PASTE expands the capabilities of genome editing by allowing large, multiplexed gene insertion without reliance on DNA repair pathways.}, } @article {pmid36424179, year = {2023}, author = {Simon, MC and Sina, C and Ferrario, PG and Daniel, H and , }, title = {Gut Microbiome Analysis for Personalized Nutrition: The State of Science.}, journal = {Molecular nutrition & food research}, volume = {67}, number = {1}, pages = {e2200476}, doi = {10.1002/mnfr.202200476}, pmid = {36424179}, issn = {1613-4133}, mesh = {Humans ; *Gastrointestinal Microbiome ; Nutritional Status ; Diet ; *Microbiota ; Metagenome ; }, abstract = {Whereas most concepts of personalized nutrition (PN) in the past, included genotyping, recent years have brought new approaches that include microbiome analysis to optimize recommendations for diet and lifestyle changes. The new approach, offered by companies, that microbiome analysis provides a real benefit to either more concise recommendations or for increased compliance to PN, is largely lacking scientific validation. Although the microbiome field shows enormous proliferation, it has some major flaws that make its use in the public health domain currently critical. Starting with the quality and representative character of the stool samples, its processing and analysis as well as assembly of metagenome data and the interpretation. Moreover, there is still no consensus of what constitutes a "normal/healthy" microbiome, nor what features characterize a dysbiotic microbiome. And, based on hundreds of individual parameters and environmental factors, the intestinal microbiome shows a huge variability and consequently changing one factor-such as food intake-is likely to have a limited impact in achieving optimized health. The present review intends to summarize the state of consolidated knowledge on human gut microbiome in the context of diet and disease, its key features, and its influencing factors as well as its "add-on" quality for PN offers.}, } @article {pmid36423788, year = {2023}, author = {Kappel, BA and De Angelis, L and Puetz, A and Ballanti, M and Menghini, R and Marx, N and Federici, M}, title = {Antibiotic-induced gut microbiota depletion exacerbates host hypercholesterolemia.}, journal = {Pharmacological research}, volume = {187}, number = {}, pages = {106570}, doi = {10.1016/j.phrs.2022.106570}, pmid = {36423788}, issn = {1096-1186}, mesh = {Animals ; Humans ; Mice ; *Anti-Bacterial Agents/adverse effects ; Cholesterol/metabolism ; Firmicutes ; *Gastrointestinal Microbiome/drug effects ; *Hypercholesterolemia/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Hypercholesterolemia is a major driver of atherosclerosis, thus contributing to high morbidity and mortality worldwide. Gut microbiota have been identified as modulator of blood lipids including cholesterol levels. Few studies have already linked certain bacteria and microbial mechanisms to host cholesterol. However, in particular mouse models revealed conflicting results depending on genetics and experimental protocol. To gain further insights into the relationship between intestinal bacteria and host cholesterol metabolism, we first performed fecal 16S rRNA targeted metagenomic sequencing in a human cohort (n = 24) naïve for cholesterol lowering drugs. Here, we show alterations in the gut microbiota composition of hypercholesterolemic patients with depletion of Bifidobacteria, expansion of Clostridia and increased Firmicutes/Bacteroidetes ratio. To test whether pharmacological intervention in gut microbiota impacts host serum levels of cholesterol, we treated hypercholesterolemic Apolipoprotein E knockout with oral largely non-absorbable antibiotics. Antibiotics increased serum cholesterol, but only when mice were fed normal chow diet and cholesterol was measured in the random fed state. These elevations in cholesterol already occurred few days after treatment initiation and were reversible after stopping antibiotics with re-acquisition of intestinal bacteria. Gene expression analyses pointed to increased intestinal cholesterol uptake mediated by antibiotics in the fed state. Non-targeted serum metabolomics suggested that diminished plant sterol levels and reduced bile acid cycling were involved microbial mechanisms. In conclusion, our work further enlightens the link between gut microbiota and host cholesterol metabolism. Pharmacological disruption of the gut flora by antibiotics was able to exacerbate serum cholesterol and may impact cardiovascular disease.}, } @article {pmid36423774, year = {2022}, author = {Marimuthu, J and Rangamaran, VR and Subramanian, SHS and Balachandran, KRS and Thenmozhi Kulasekaran, N and Vasudevan, D and Lee, JK and Ramalingam, K and Gopal, D}, title = {Deep-sea sediment metagenome from Bay of Bengal reveals distinct microbial diversity and functional significance.}, journal = {Genomics}, volume = {114}, number = {6}, pages = {110524}, doi = {10.1016/j.ygeno.2022.110524}, pmid = {36423774}, issn = {1089-8646}, mesh = {*Bays ; }, abstract = {Bay of Bengal (BoB) has immense significance with respect to ecological diversity and natural resources. Studies on microbial profiling and their functional significance at sediment level of BoB remain poorly represented. Herein, we describe the microbial diversity and metabolic potentials of BOB deep-sea sediment samples by subjecting the metagenomes to Nanopore sequencing. Taxonomic diversity ascertained at various levels revealed that bacteria belonging to phylum Proteobacteria predominantly represented in sediment samples NIOT_S7 and NIOT_S9. A comparative study with 16S datasets from similar ecological sites revealed depth as a crucial factor in determining taxonomic diversity. KEGG annotation indicated that bacterial communities possess sequence reads corresponding to carbon dioxide fixation, sulfur, nitrogen metabolism, but at varying levels. Additionally, gene sequences related to bioremediation of dyes, plastics, hydrocarbon, antibiotic resistance, secondary metabolite synthesis and metal resistance from both the samples as studied indicate BoB to represent a highly diverse environmental niche for further exploration.}, } @article {pmid36423639, year = {2022}, author = {Díaz-Escandón, D and Tagirdzhanova, G and Vanderpool, D and Allen, CCG and Aptroot, A and Češka, O and Hawksworth, DL and Huereca, A and Knudsen, K and Kocourková, J and Lücking, R and Resl, P and Spribille, T}, title = {Genome-level analyses resolve an ancient lineage of symbiotic ascomycetes.}, journal = {Current biology : CB}, volume = {32}, number = {23}, pages = {5209-5218.e5}, doi = {10.1016/j.cub.2022.11.014}, pmid = {36423639}, issn = {1879-0445}, abstract = {Ascomycota account for about two-thirds of named fungal species.[1] Over 98% of known Ascomycota belong to the Pezizomycotina, including many economically important species as well as diverse pathogens, decomposers, and mutualistic symbionts.[2] Our understanding of Pezizomycotina evolution has until now been based on sampling traditionally well-defined taxonomic classes.[3][,][4][,][5] However, considerable diversity exists in undersampled and uncultured, putatively early-diverging lineages, and the effect of these on evolutionary models has seldom been tested. We obtained genomes from 30 putative early-diverging lineages not included in recent phylogenomic analyses and analyzed these together with 451 genomes covering all available ascomycete genera. We show that 22 of these lineages, collectively representing over 600 species, trace back to a single origin that diverged from the common ancestor of Eurotiomycetes and Lecanoromycetes over 300 million years BP. The new clade, which we recognize as a more broadly defined Lichinomycetes, includes lichen and insect symbionts, endophytes, and putative mycorrhizae and encompasses a range of morphologies so disparate that they have recently been placed in six different taxonomic classes. To test for shared hidden features within this group, we analyzed genome content and compared gene repertoires to related groups in Ascomycota. Regardless of their lifestyle, Lichinomycetes have smaller genomes than most filamentous Ascomycota, with reduced arsenals of carbohydrate-degrading enzymes and secondary metabolite gene clusters. Our expanded genome sample resolves the relationships of numerous "orphan" ascomycetes and establishes the independent evolutionary origins of multiple mutualistic lifestyles within a single, morphologically hyperdiverse clade of fungi.}, } @article {pmid36423580, year = {2022}, author = {Al-Shayeb, B and Skopintsev, P and Soczek, KM and Stahl, EC and Li, Z and Groover, E and Smock, D and Eggers, AR and Pausch, P and Cress, BF and Huang, CJ and Staskawicz, B and Savage, DF and Jacobsen, SE and Banfield, JF and Doudna, JA}, title = {Diverse virus-encoded CRISPR-Cas systems include streamlined genome editors.}, journal = {Cell}, volume = {185}, number = {24}, pages = {4574-4586.e16}, doi = {10.1016/j.cell.2022.10.020}, pmid = {36423580}, issn = {1097-4172}, support = {U01 AI142817/AI/NIAID NIH HHS/United States ; /HHMI/Howard Hughes Medical Institute/United States ; }, mesh = {Animals ; Humans ; *CRISPR-Cas Systems ; Cryoelectron Microscopy ; Gene Editing ; Genome ; *Bacteriophages/genetics ; DNA ; RNA ; Mammals/genetics ; }, abstract = {CRISPR-Cas systems are host-encoded pathways that protect microbes from viral infection using an adaptive RNA-guided mechanism. Using genome-resolved metagenomics, we find that CRISPR systems are also encoded in diverse bacteriophages, where they occur as divergent and hypercompact anti-viral systems. Bacteriophage-encoded CRISPR systems belong to all six known CRISPR-Cas types, though some lack crucial components, suggesting alternate functional roles or host complementation. We describe multiple new Cas9-like proteins and 44 families related to type V CRISPR-Cas systems, including the Casλ RNA-guided nuclease family. Among the most divergent of the new enzymes identified, Casλ recognizes double-stranded DNA using a uniquely structured CRISPR RNA (crRNA). The Casλ-RNA-DNA structure determined by cryoelectron microscopy reveals a compact bilobed architecture capable of inducing genome editing in mammalian, Arabidopsis, and hexaploid wheat cells. These findings reveal a new source of CRISPR-Cas enzymes in phages and highlight their value as genome editors in plant and human cells.}, } @article {pmid36423550, year = {2023}, author = {Luo, T and Dai, X and Chen, Z and Wu, L and Wei, W and Xu, Q and Ni, BJ}, title = {Different microplastics distinctively enriched the antibiotic resistance genes in anaerobic sludge digestion through shifting specific hosts and promoting horizontal gene flow.}, journal = {Water research}, volume = {228}, number = {Pt A}, pages = {119356}, doi = {10.1016/j.watres.2022.119356}, pmid = {36423550}, issn = {1879-2448}, mesh = {Humans ; *Microplastics ; *Sewage ; Gene Flow ; Plastics ; Polyvinyl Chloride ; Anaerobiosis ; Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Drug Resistance, Microbial/genetics ; Polyethylene ; Digestion ; }, abstract = {Both microplastics (MPs) and antibiotic resistance genes (ARGs) are intensively detected in waste activated sludge (WAS). However, the distinctive impacts of different MPs on ARGs emergence, dissemination, and its potential mechanisms remain unclear. In this study, long-term semi-continuous digesters were performed to examine the profiles of ARGs and antibiotic-resistant bacteria (ARB) in response to two different typical MPs (polyethylene (PE) and polyvinyl chloride (PVC)) in anaerobic sludge digestion. Metagenomic results show that PE- and PVC-MPs increase ARGs abundance by 14.8% and 23.6% in digester, respectively. ARB are also enriched by PE- and PVC-MPs, Acinetobacter sp. and Salmonella sp. are the dominant ARB. Further exploration reveals that PVC-MPs stimulates the acquisition of ARGs by human pathogen bacteria (HPB) and functional microorganisms (FMs), but PE-MPs doesn't. Network analysis shows that more ARGs tend to co-occur with HBP and FMs after MPs exposure, and more importantly, new bacteria are observed to acquire ARGs possibly via horizontal gene flow (HGF) in MPs-stressed digester. The genes involved in the HGF process, including reactive oxygen species (ROS) production, cell membrane permeability, extracellular polymeric substances (EPS) secretion, and ATP synthesis, are also enhanced by MPs, thereby attributing to the promoted ARGs dissemination. These findings offer advanced insights into the distinctive contribution of MPs to fate, host, dissemination of ARGs in anaerobic sludge digestion.}, } @article {pmid36423548, year = {2023}, author = {Wu, D and Zhao, J and Su, Y and Yang, M and Dolfing, J and Graham, DW and Yang, K and Xie, B}, title = {Explaining the resistomes in a megacity's water supply catchment: Roles of microbial assembly-dominant taxa, niched environments and pathogenic bacteria.}, journal = {Water research}, volume = {228}, number = {Pt A}, pages = {119359}, doi = {10.1016/j.watres.2022.119359}, pmid = {36423548}, issn = {1879-2448}, support = {MR/P028195/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Humans ; *Drinking Water ; China ; Water Supply ; Bacteria/genetics ; Anti-Bacterial Agents ; }, abstract = {Antibiotic resistance genes (ARGs) in drinking water sources suggest the possible presence of resistant microorganisms that jeopardize human health. However, explanations for the presence of specific ARGs in situ are largely unknown, especially how their prevalence is affected by local microbial ecology, taxa assembly and community-wide gene transfer. Here, we characterized resistomes and bacterial communities in the Taipu River catchment, which feeds a key drinking water reservoir to a global megacity, Shanghai. Overall, ARG abundances decreased significantly as the river flowed downstream towards the reservoir (P < 0.01), whereas the waterborne bacteria assembled deterministically (|βNRI| > 2.0) as a function of temperature and dissolved oxygen conditions with the assembly-dominant taxa (e.g. Ilumatobacteraceae and Cyanobiaceae) defining local resistomes (P < 0.01, Cohen's D = 4.22). Bacterial hosts of intragenomic ARGs stayed at the same level across the catchment (60 ∼ 70 genome copies per million reads). Among them, the putative resistant pathogens (e.g. Burkholderiaceae) carried mixtures of ARGs that exhibited high transmission probability (transfer counts = 126, P < 0.001), especially with the microbial assembly-dominant taxa. These putative resistant pathogens had densities ranging form 3.0 to 4.0 × 10[6] cell/L, which was more pronouncedly affected by resistome and microbial assembly structures than environmental factors (SEM, std-coeff β = 0.62 vs. 0.12). This work shows that microbial assembly and resistant pathogens play predominant roles in prevelance and dissemination of resistomes in receiving water, which deserves greater attention in devisng control strategies for reducing in-situ ARGs and resistant strains in a catchment.}, } @article {pmid36423125, year = {2022}, author = {Ogunbayo, AE and Mogotsi, MT and Sondlane, H and Nkwadipo, KR and Sabiu, S and Nyaga, MM}, title = {Metagenomic Analysis of Respiratory RNA Virome of Children with and without Severe Acute Respiratory Infection from the Free State, South Africa during COVID-19 Pandemic Reveals Higher Diversity and Abundance in Summer Compared with Winter Period.}, journal = {Viruses}, volume = {14}, number = {11}, pages = {}, pmid = {36423125}, issn = {1999-4915}, mesh = {Child ; Animals ; Humans ; Virome ; South Africa/epidemiology ; *COVID-19 ; Seasons ; RNA ; Pandemics ; *Respiratory Tract Infections ; *Pneumonia ; *Viruses/genetics ; Respiratory System ; }, abstract = {Viral respiratory infections contribute to significant morbidity and mortality in children. Currently, there are limited reports on the composition and abundance of the normal commensal respiratory virome in comparison to those in severe acute respiratory infections (SARIs) state. This study characterised the respiratory RNA virome in children ≤ 5 years with (n = 149) and without (n = 139) SARI during the summer and winter of 2020/2021 seasons in South Africa. Nasopharyngeal swabs were, collected, pooled, enriched for viral RNA detection, sequenced using Illumina MiSeq, and analysed using the Genome Detective bioinformatic tool. Overall, Picornaviridae, Paramoxyviridae, Pneumoviridae, Picobirnaviridae, Totiviridae, and Retroviridae families were the most abundant viral population in both groups across both seasons. Human rhinovirus and endogenous retrovirus K113 were detected in most pools, with exclusive detection of Pneumoviridae in SARI pools. Generally, higher viral diversity/abundance was seen in children with SARI and in the summer pools. Several plant/animal viruses, eukaryotic viruses with unclear pathogenicity including a distinct rhinovirus A type, were detected. This study provides remarkable data on the respiratory RNA virome in children with and without SARI with a degree of heterogeneity of known viruses colonizing their respiratory tract. The implication of the detected viruses in the dynamics/progression of SARI requires further investigations.}, } @article {pmid36423093, year = {2022}, author = {Palombieri, A and Fruci, P and Sarchese, V and Robetto, S and Orusa, R and Arbuatti, A and Martella, V and Di Martino, B and Di Profio, F}, title = {Detection and Characterization of a Novel Picornavirus in European Badger (Meles meles).}, journal = {Veterinary sciences}, volume = {9}, number = {11}, pages = {}, pmid = {36423093}, issn = {2306-7381}, support = {IZS PLV 13/20RC//Ministero della Salute/ ; Dipartimenti di Eccellenza 2018 - 2022, CUP_C46C18000530001//Italian Ministry for Education, University and Research/ ; }, abstract = {The recent development of unbiased metagenomic next-generation sequencing has provided a richer view of the wild animal virome making it necessary to expand the knowledge about virus diversity in wildlife, as well as to monitor their potential transmission to domestic animals or humans. In the present study, by screening collections of enteric specimens from wild animals, a novel picornavirus was identified in the intestinal content of a badger (Meles meles). By enrichment with a sequence-independent single-primer amplification (SISPA) approach and deep sequencing with Oxford Nanopore Technologies (ONT) platform, the genome sequence of a novel picornavirus strain, Badger/3A-2019/ITA, was reconstructed. On comparison based on the polyprotein sequences, the virus was distantly related (58.7% and 59.7% sequence identity at the nucleotide and amino acid level, respectively) to the feline picornavirus strain FFUP1, identified in 2012 in Portugal and classified into genus Sakobovirus within the species Sakobuvirus A. Upon phylogenetic, pairwise homology, and distance analyses performed on the P1, 2C[hel], 3C[pro], and 3D[pol] proteins and the complete genomic sequence, the badger picornavirus may be considered a member of a new sakobuvirus species, which we propose as Sakobuvirus B.}, } @article {pmid36423089, year = {2022}, author = {Liu, Y and Sun, L and Tu, Z and Sun, S and Sun, Y and Yi, L and Tu, C and He, B}, title = {Virome Profiling of an Amur leopard cat Reveals Multiple Anelloviruses and a Bocaparvovirus.}, journal = {Veterinary sciences}, volume = {9}, number = {11}, pages = {}, pmid = {36423089}, issn = {2306-7381}, support = {32022083//National Natural Science Foundation of China/ ; }, abstract = {As a small top predator, Amur leopard cat (Prionailurus bengalensis euptilurus) is widely distributed in northeast Asia and plays an important role in the control of small rodent populations and in the maintenance of ecological equilibrium. However, the viruses harbored by this creature have been rarely investigated. Here, we report the DNA and RNA eukaryotic virome profiling of an injured Amur leopard cat followed by PCR validation, which revealed diverse anelloviruses in multiple organs and a bocaparvovirus in the lymph, but no RNA viruses. These anelloviruses have diverse genomic structures and are classified into four phylogroups with viruses of various felines, while the bocaparvovirus is extremely similar to those recovered from diarrheal domestic cats, illustrating the transmission of the virus between domestic animals and wildlife. These data provide the first insight into the genetic diversity of Amur leopard cat viruses, highlighting the need for further investigation of wild animals.}, } @article {pmid36422845, year = {2022}, author = {Ul-Haq, A and Lee, KA and Seo, H and Kim, S and Jo, S and Ko, KM and Moon, SJ and Kim, YS and Choi, JR and Song, HY and Kim, HS}, title = {Characteristic alterations of gut microbiota in uncontrolled gout.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {60}, number = {12}, pages = {1178-1190}, pmid = {36422845}, issn = {1976-3794}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Uric Acid ; Bacteria/genetics ; *Gout/drug therapy ; }, abstract = {Microbiome research has been on the rise recently for a more in-depth understanding of gout. Meanwhile, there is a need to understand the gut microbiome related to uric acid-lowering drug resistance. In this study, 16S rRNA gene-based microbiota analysis was performed for a total of 65 stool samples from 17 healthy controls and 48 febuxostat-treated gout patients (including 28 controlled subjects with decreased uric acid levels and 20 uncontrolled subjects with non-reduced uric acid levels). Alpha diversity of bacterial community decreased in the healthy control, controlled, and uncontrolled groups. In the case of beta diversity, the bacterial community was significantly different among groups (healthy control, controlled, and uncontrolled groups). Taxonomic biomarker analysis revealed the increased population of g-Bifidobacterium in healthy controls and g-Prevotella in uncontrolled patients. PCR further confirmed this result at the species level. Additionally, functional metagenomics predictions led to the exploration of various functional biomarkers, including purine metabolism. The results of this study can serve as a basis for developing potential new strategies for diagnosing and treating gout from microbiome prospects.}, } @article {pmid36422597, year = {2022}, author = {Munjita, SM and Moonga, G and Mukubesa, AN and Ndebe, J and Mubemba, B and Vanaerschot, M and Tato, C and Tembo, J and Kapata, N and Chitanga, S and Changula, K and Kajihara, M and Muleya, W and Takada, A and Fichet-Calvet, E and Zumla, A and Sawa, H and Bates, M and Munsaka, S and Simulundu, E}, title = {Luna Virus and Helminths in Wild Mastomys natalensis in Two Contrasting Habitats in Zambia: Risk Factors and Evidence of Virus Dissemination in Semen.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {11}, pages = {}, pmid = {36422597}, issn = {2076-0817}, support = {EDCTP Reg/Grant RIA2016E-1609//European and Developing Countries Clinical Trials Partnership (EDCTP2) programme under the PANDORA-ID-NET Consortium/ ; Grant number P151847//Africa Centre of Excellence for Infectious Disease of Humans and Animals (ACEIDHA) project/ ; JP22jm0110019//Science and Technology Research Partnership for Sustainable Development (SATREPS)/ ; JP21wm0125008; JP20wm0225003//Japan Program for Infectious Diseases Research and Infrastructure/ ; }, abstract = {Transmission dynamics and the maintenance of mammarenaviruses in nature are poorly understood. Using metagenomic next-generation sequencing (mNGS) and RT-PCR, we investigated the presence of mammarenaviruses and co-infecting helminths in various tissues of 182 Mastomys natalensis rodents and 68 other small mammals in riverine and non-riverine habitats in Zambia. The Luna virus (LUAV) genome was the only mammarenavirus detected (7.7%; 14/182) from M. natalensis. Only one rodent from the non-riverine habitat was positive, while all six foetuses from one pregnant rodent carried LUAV. LUAV-specific mNGS reads were 24-fold higher in semen than in other tissues from males. Phylogenetically, the viruses were closely related to each other within the LUAV clade. Helminth infections were found in 11.5% (21/182) of M. natalensis. LUAV-helminth co-infections were observed in 50% (7/14) of virus-positive rodents. Juvenility (OR = 9.4; p = 0.018; 95% CI: 1.47-59.84), nematodes (OR = 15.5; p = 0.001; 95% CI: 3.11-76.70), cestodes (OR = 10.8; p = 0.025; 95% CI: 1.35-86.77), and being male (OR = 4.6; p = 0.036; 95% CI: 1.10-18.90) were associated with increased odds of LUAV RNA detection. The role of possible sexual and/or congenital transmission in the epidemiology of LUAV infections in rodents requires further study, along with the implications of possible helminth co-infection.}, } @article {pmid36422370, year = {2022}, author = {Begmatov, S and Beletsky, AV and Gruzdev, EV and Mardanov, AV and Glukhova, LB and Karnachuk, OV and Ravin, NV}, title = {Distribution Patterns of Antibiotic Resistance Genes and Their Bacterial Hosts in a Manure Lagoon of a Large-Scale Swine Finishing Facility.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36422370}, issn = {2076-2607}, support = {075-15-2021-1401//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {The spread of antibiotic resistance genes (ARGs) that are present in livestock manures, which are discharged into the environment, is a severe threat to human and animal health. Here, we used 16S rRNA gene profiling and metagenomic analysis to characterize microbial community composition and antibiotic resistance in a manure storage lagoon from a large-scale swine finishing facility. Manure samples were collected at intervals of two years. Both the prokaryotic community and the resistome were dominated by the Firmicutes, Proteobacteria and Bacteroidota. Metagenomic analysis of two samples revealed 726 and 641 ARGs classified into 59 and 46 AMR gene families. Besides multidrug efflux pumps, the predominating ARGs potentially encoded resistance to tetracyclines, macrolide-lincosamide-streptogramin, aminoglycosides, peptide antibiotics, rifamycin, chloramphenicol, and beta-lactams. Genes from all predominant AMR gene families were found in both samples indicating overall long-term stability of the resistome. Antibiotic efflux pumps were the primary type of ARGs in the Proteobacteria, while antibiotic target alteration or protection was the main mechanism of resistance in the Firmicutes, Actinobacteriota and Bacteroidota. Metagenome-assembled genomes (MAG) of four multidrug-resistant strains were assembled. The first MAG, assigned to Escherichia flexneri, contained 46 ARGs, including multidrug efflux pumps, modified porins, beta-lactamases, and genes conferring resistance to peptide antibiotics. The second MAG, assigned to the family Alcaligenaceae, contained 18 ARGs encoding resistance to macrolide-lincosamide-streptogramin, tetracyclines, aminoglycosides and diaminopyrimidins. Two other MAGs representing the genera Atopostipes and Prevotella, contained four and seven ARGs, respectively. All these MAGs represented minor community members and accounted for less than 0.3% of the whole metagenome. Overall, a few lineages originated from the gut but relatively rare in the manure storage lagoon, are the main source of ARGs and some of them carry multiple resistance determinants.}, } @article {pmid36422366, year = {2022}, author = {Aldabaldetrecu, M and Parra, M and Soto-Aguilera, S and Arce, P and Quiroz, APV and Segura, R and Tello, M and Guerrero, J and Modak, B}, title = {Protective Effect of [Cu(NN1)2](ClO4) Complex in Rainbow Trout Challenged against Flavobacterium psychrophilum.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36422366}, issn = {2076-2607}, support = {1180265//FONDECYT/ ; 5392202MC Dicyt//DICYT/ ; 1191902//FONDECYT/ ; }, abstract = {Previously, we reported an in vitro evaluation regarding antibacterial effects against F. psychrophilum by a new Cu (I) complex, [Cu(NN1)2](ClO4). This study presents the results of an in vivo evaluation of [Cu(NN1)2](ClO4) added as a dietary supplement against F. psychrophilum in rainbow trout. The results showed that the administration of [Cu(NN1)2](ClO4) at 29 and 58 µg/g of fish for 15 days does not affect the growth of rainbow trout. On the other hand, the amount of copper present in the liver, intestine, and muscle of rainbow trout was determined. The results showed that the amount of copper in the liver, when compared between treated fish and control fish, does not change. While, in the intestine, an increase in the fish fed at 58 µg/g of fish was observed. In muscle, a slight decrease at 29 µg/g was obtained. Additionally, copper concentrations in the pond water after 15 days of feeding with the [Cu(NN1)2](ClO4) complex showed the highest levels of copper. Finally, the effect of the administration of [Cu(NN1)2](ClO4) for 15 days at 58 µg/g of fish was evaluated against F. psychrophilum, where a 75% survival was obtained during 20 days of challenge.}, } @article {pmid36422301, year = {2022}, author = {Coelho, C and Tiago, I and Veríssimo, A}, title = {Guts Bacterial Communities of Porcellio dilatatus: Symbionts Predominance, Functional Significance and Putative Biotechnological Potential.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36422301}, issn = {2076-2607}, support = {SFRH/BD/148270/2019//Fundação para a Ciência e Tecnologia/ ; PINFRA/22184/2016 POCI-01-0145-FEDER-022184//Fundação para a Ciência e Tecnologia/ ; }, abstract = {Terrestrial isopods are effective herbivorous scavengers with an important ecological role in organic matter cycling. Their guts are considered to be a natural enrichment environment for lignocellulosic biomass (LCB)-degrading bacteria. The main goal of this work was to assess the structural diversity of Porcellio dilatatus gut bacterial communities using NGS technologies, and to predict their functional potential using PICRUSt2 software. Pseudomonadota, Actinomycetota, Bacillota, Cyanobacteria, Mycoplasmatota, Bacteroidota, Candidatus Patescibacteria and Chloroflexota were the most abundant phyla found in P. dilatatus gut bacterial communities. At a family level, we identified the presence of eleven common bacterial families. Functionally, the P. dilatatus gut bacterial communities exhibited enrichment in KEGG pathways related to the functional module of metabolism. With the predicted functional profile of P. dilatatus metagenomes, it was possible to envision putative symbiotic relationships between P. dilatatus gut bacterial communities and their hosts. It was also possible to foresee the presence of a well-adapted bacterial community responsible for nutrient uptake for the host and for maintaining host homeostasis. Genes encoding LCB-degrading enzymes were also predicted in all samples. Therefore, the P. dilatatus digestive tract may be considered a potential source of LCB-degrading enzymes that is not to be neglected.}, } @article {pmid36422019, year = {2022}, author = {Hainsworth, S and Lawrie, AC and Vanniasinkam, T and Grando, D}, title = {Metagenomics of Toenail Onychomycosis in Three Victorian Regions of Australia.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {11}, pages = {}, pmid = {36422019}, issn = {2309-608X}, abstract = {Onychomycosis is a fungal disease of the nail that is found worldwide and is difficult to diagnose accurately. This study used metagenomics to investigate the microbiology of 18 clinically diagnosed mycotic nails and two normal nails for fungi and bacteria using the ITS2 and 16S loci. Four mycotic nails were from Bass Coast, six from Melbourne Metropolitan and eight from Shepparton, Victoria, Australia. The mycotic nails were photographed and metagenomically analysed. The ITS2 sequences for T. rubrum and T. interdigitale/mentagrophytes averaged over 90% of hits in 14/18 nails. The high abundance of sequences of a single dermatophyte, compared to all other fungi in a single nail, made it the most likely infecting agents (MLIA). Trichophyton rubrum and T. interdigitale/mentagrophytes were found in Bass Coast and Shepparton while only T. interdigitale/mentagrophytes was found in Melbourne. Two nails with T. interdigitale/mentagrophytes mixed with high abundance non-dermatophyte moulds (NDMs) (Aspergillus versicolor, Acremonium sclerotigenum) were also observed. The two control nails contained chiefly Fusarium oxysporum and Malassezia slooffiae. For bacteria, Staphylococcus epidermidis was in every nail and was the most abundant, including the control nails, with an overall mean rate of 66.01%. Rothia koreensis, Corynebacterium tuberculostearicum, and Brevibacterium sediminis also featured.}, } @article {pmid36422016, year = {2022}, author = {Gökdemir, FŞ and İşeri, ÖD and Sharma, A and Achar, PN and Eyidoğan, F}, title = {Metagenomics Next Generation Sequencing (mNGS): An Exciting Tool for Early and Accurate Diagnostic of Fungal Pathogens in Plants.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {11}, pages = {}, pmid = {36422016}, issn = {2309-608X}, abstract = {Crop output is directly impacted by infections, with fungi as the major plant pathogens, making accurate diagnosis of these threats crucial. Developing technology and multidisciplinary approaches are turning to genomic analyses in addition to traditional culture methods in diagnostics of fungal plant pathogens. The metagenomic next-generation sequencing (mNGS) method is preferred for genotyping identification of organisms, identification at the species level, illumination of metabolic pathways, and determination of microbiota. Moreover, the data obtained so far show that this new approach is promising as an emerging new trend in fungal disease detection. Another approach covered by mNGS technologies, known as metabarcoding, enables use of specific markers specific to a genetic region and allows for genotypic identification by facilitating the sequencing of certain regions. Although the core concept of mNGS remains constant across applications, the specific sequencing methods and bioinformatics tools used to analyze the data differ. In this review, we focus on how mNGS technology, including metabarcoding, is applied for detecting fungal pathogens and its promising developments for the future.}, } @article {pmid36421817, year = {2022}, author = {Ramos-Lopez, O}, title = {Multi-Omics Nutritional Approaches Targeting Metabolic-Associated Fatty Liver Disease.}, journal = {Genes}, volume = {13}, number = {11}, pages = {}, pmid = {36421817}, issn = {2073-4425}, mesh = {Humans ; *Epigenesis, Genetic ; DNA Methylation/genetics ; Obesity/genetics ; *Insulin Resistance/genetics ; Dysbiosis/complications ; }, abstract = {Currently, metabolic-associated fatty liver disease (MAFLD) is a leading global cause of chronic liver disease, and is expected to become one of the most common indications of liver transplantation. MAFLD is associated with obesity, involving multiple mechanisms such as alterations in lipid metabolism, insulin resistance, hyperinflammation, mitochondrial dysfunction, cell apoptosis, oxidative stress, and extracellular matrix formation. However, the onset and progression of MAFLD is variable among individuals, being influenced by intrinsic (personal) and external environmental factors. In this context, sequence structural variants across the human genome, epigenetic phenomena (i.e., DNA methylation, histone modifications, and long non-coding RNAs) affecting gene expression, gut microbiota dysbiosis, and metabolomics/lipidomic fingerprints may account for differences in MAFLD outcomes through interactions with nutritional features. This knowledge may contribute to gaining a deeper understanding of the molecular and physiological processes underlying MAFLD pathogenesis and phenotype heterogeneity, as well as facilitating the identification of biomarkers of disease progression and therapeutic targets for the implementation of tailored nutritional strategies. This comprehensive literature review highlights the potential of nutrigenetic, nutriepigenetic, nutrimetagenomic, nutritranscriptomics, and nutrimetabolomic approaches for the prevention and management of MAFLD in humans through the lens of precision nutrition.}, } @article {pmid36421395, year = {2022}, author = {Silva, DG and Domingues, CPF and Figueiredo, JF and Dionisio, F and Botelho, A and Nogueira, T}, title = {Estuarine Aquacultures at the Crossroads of Animal Production and Antibacterial Resistance: A Metagenomic Approach to the Resistome.}, journal = {Biology}, volume = {11}, number = {11}, pages = {}, pmid = {36421395}, issn = {2079-7737}, support = {ALG-01-0145-FEDER-028824//Fundação para a Ciência e Tecnologia/ ; UI/BD/153078/2022//Fundação para a Ciência e Tecnologia/ ; }, abstract = {It is recognized that the spread of antibiotic resistance (AR) genes among aquatic environments, including aquaculture and the human environment, can have detrimental effects on human and animal health and the ecosystem. Thus, when transmitted to the human microbiome or pathogens, resistance genes risk human health by compromising the eventual treatment of infections with antibiotic therapy. This study aimed to define the resistance profile of aquaculture farms and their potential risk for spreading. Twenty-four sediments from oyster and gilthead sea bream aquaculture farms located in three Portuguese river estuaries (17 sediments from Sado, 4 from Aveiro, and 3 from Lima) were studied by comparative metagenomic analysis. The computation of the diversity of genes conferring resistance per antibiotic class revealed a significant increase in aminoglycosides, beta-lactams, disinfectants, quinolones, and tetracyclines counts. In all geographic locations under study, the most diverse AR genes confer resistance to the macrolides, tetracyclines and oxazolidinones classes, all of which are medically important for human and animal therapies, as well as resistance to disinfectants. The diversity of mobile genetic elements correlated with the number of AR genes such as tetracyclines, suggesting that AR could be easily mobilized among bacterial genomes and microbiomes.}, } @article {pmid36420990, year = {2022}, author = {Núñez-Sánchez, MA and Herisson, FM and Keane, JM and García-González, N and Rossini, V and Pinhiero, J and Daly, J and Bustamante-Garrido, M and Hueston, CM and Patel, S and Canela, N and Herrero, P and Claesson, MJ and Melgar, S and Nally, K and Caplice, NM and Gahan, CGM}, title = {Microbial bile salt hydrolase activity influences gene expression profiles and gastrointestinal maturation in infant mice.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2149023}, pmid = {36420990}, issn = {1949-0984}, mesh = {Female ; Humans ; Mice ; Animals ; *Transcriptome ; *Gastrointestinal Microbiome ; Amidohydrolases/genetics/metabolism ; Gastrointestinal Tract/microbiology ; Bacteria/genetics ; Basic Helix-Loop-Helix Transcription Factors/metabolism ; }, abstract = {The mechanisms by which early microbial colonizers of the neonate influence gut development are poorly understood. Bacterial bile salt hydrolase (BSH) acts as a putative colonization factor that influences bile acid signatures and microbe-host signaling pathways and we considered whether this activity can influence infant gut development. In silico analysis of the human neonatal gut metagenome confirmed that BSH enzyme sequences are present as early as one day postpartum. Gastrointestinal delivery of cloned BSH to immature gnotobiotic mice accelerated shortening of the colon and regularized gene expression profiles, with monocolonised mice more closely resembling conventionally raised animals. In situ expression of BSH decreased markers of cell proliferation (Ki67, Hes2 and Ascl2) and strongly increased expression of ALPI, a marker of cell differentiation and barrier function. These data suggest an evolutionary paradigm whereby microbial BSH activity potentially influences bacterial colonization and in-turn benefits host gastrointestinal maturation.}, } @article {pmid36419926, year = {2023}, author = {Dlamini, SP and Akanmu, AO and Fadiji, AE and Babalola, OO}, title = {Maize rhizosphere modulates the microbiome diversity and community structure to enhance plant health.}, journal = {Saudi journal of biological sciences}, volume = {30}, number = {1}, pages = {103499}, pmid = {36419926}, issn = {1319-562X}, abstract = {Metagenomic has been explored in investigating microbiome diversity. However, there is limited available information on its application towards securing plant health. Hence, this study adopts the metagenomic approach to unravel the microbiome diversity associated with healthy (LI and MA) and Northern corn leaf blight (NCLB) infected (LID and MAD) maize rhizosphere in the maize growing field at Lichtenburg and Mafikeng, North-West province of South Africa. The extraction of whole DNA from the respective healthy and diseased rhizosphere soils was conducted and sequenced using shotgun metagenomics. A total of 12 bacteria, 4 archaea and 2 fungal phyla were found as predominant across the fields with the use of the SEED subsystem database. The most predominant bacteria phyla included Proteobacteria, Dienococcus-Thermus, Gemmatimonadetes, Chlorobi, Cyanobacteria, Planctomycetes, Verrucomicrobia, Acidobacteria, Firmicutes, Chloroflexi and Bacteroidetes. Archaea consisted of Euryarchaeota, Thaumarchaeota, Crenarchaeota and Korachaeota, while Ascomycota and Basidiomycota were the dominant fungal phyla. Microbial abundance and diversity were higher in the rhizosphere of healthy maize (LI and MA) rhizosphere as compared to the NCLB diseased (LID and MAD), in the order LI > MA > LID > MAD. At phylum and genus level, alpha diversity index showed no significant (p > 0.05) difference in the abundance of the microbial community of healthy and NCLB infected maize rhizosphere, while beta analysis produced a significant (p = 0.01) difference in the microbial diversity in the soil. Taken together, the study revealed that the abundance of microbial diversity in the maize rhizosphere influences the efficacy of the rhizosphere microbiome to modulate microbial functions towards managing and sustaining plant health.}, } @article {pmid36419847, year = {2022}, author = {Fabbrini, M and Candela, M and Turroni, S and Brigidi, P and Rampelli, S}, title = {Exploring clade differentiation of the Faecalibacterium prausnitzii complex.}, journal = {iScience}, volume = {25}, number = {12}, pages = {105533}, pmid = {36419847}, issn = {2589-0042}, abstract = {Faecalibacterium prausnitzii is one of the most prevalent and abundant polyphyletic health-promoting components of the human gut microbiome with a propensity for dysbiotic decreases. To better understand its biology in the human gut, we specifically explored the divergence pressures acting on F. prausnitzii clades on a global scale. Five F. prausnitzii clades were de novo identified from 55 publicly available genomes and 92 high-quality metagenome assembled genomes. Divergence rate indices were constructed and validated to compare the divergence rates among the different clades and between each of the diverging genes. For each clade we identified specific patterns of diverging functionalities, probably reflecting different ecological propensities, in term of inter-host dispersion capacity or exploitation of different substrates in the gut environment. Finally, we speculate that these differences may explain, at least in part, the observed differences in the overall divergence rates of F. prausnitzii clades in human populations.}, } @article {pmid36419426, year = {2022}, author = {Marghoob, MU and Rodriguez-Sanchez, A and Imran, A and Mubeen, F and Hoagland, L}, title = {Diversity and functional traits of indigenous soil microbial flora associated with salinity and heavy metal concentrations in agricultural fields within the Indus Basin region, Pakistan.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1020175}, pmid = {36419426}, issn = {1664-302X}, abstract = {Soil salinization and heavy metal (HM) contamination are major challenges facing agricultural systems worldwide. Determining how soil microbial communities respond to these stress factors and identifying individual phylotypes with potential to tolerate these conditions while promoting plant growth could help prevent negative impacts on crop productivity. This study used amplicon sequencing and several bioinformatic programs to characterize differences in the composition and potential functional capabilities of soil bacterial, fungal, and archaeal communities in five agricultural fields that varied in salinity and HM concentrations within the Indus basin region of Pakistan. The composition of bacteria with the potential to fix atmospheric nitrogen (N) and produce the enzyme 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase were also determined. Microbial communities were dominated by: Euryarchaeota (archaea), Actinobacteria, Proteobacteria, Planctomycetota, Firimicutes, Patescibacteria and Acidobacteria (bacteria), and Ascomycota (fungi), and all soils contained phylotypes capable of N-fixation and ACC-deaminase production. Salinity influenced bacterial, but not archaeal or fungal communities. Both salinity and HM altered the relative abundance of many phylotypes that could potentially promote or harm plant growth. These stress factors also appeared to influence the potential functional capabilities of the microbial communities, especially in their capacity to cycle phosphorous, produce siderophores, and act as symbiotrophs or pathotrophs. Results of this study confirm that farms in this region are at risk due to salinization and excessive levels of some toxic heavy metals, which could negatively impact crop and human health. Changes in soil microbial communities and their potential functional capabilities are also likely to affect several critical agroecosystem services related to nutrient cycling, pathogen suppression, and plant stress tolerance. Many potentially beneficial phylotypes were identified that appear to be salt and HM tolerant and could possibly be exploited to promote these services within this agroecosystem. Future efforts to isolate these phylotypes and determine whether they can indeed promote plant growth and/or carry out other important soil processes are recommended. At the same time, identifying ways to promote the abundance of these unique phylotypes either through modifying soil and crop management practices, or developing and applying them as inoculants, would be helpful for improving crop productivity in this region.}, } @article {pmid36419280, year = {2023}, author = {Liao, J and Dou, Y and Yang, X and An, S}, title = {Soil microbial community and their functional genes during grassland restoration.}, journal = {Journal of environmental management}, volume = {325}, number = {Pt A}, pages = {116488}, doi = {10.1016/j.jenvman.2022.116488}, pmid = {36419280}, issn = {1095-8630}, mesh = {*Soil ; Grassland ; *Microbiota ; Nitrification ; Carbon ; }, abstract = {Soil microbial functional genes are linked with carbon (C) as well as nitrogen (N) cycling processes, and their relative abundances are strongly affected by ecosystem managements. Yet, soil microbial community compositions and their C, N cycling genes' abundance in temperate grasslands remain poorly studied. Here, the Illumina MiSeq sequencing (16 S rRNA gene and internal transcribed spacer [ITS]) and meta-genomic GeoChip sequencing technologies were used to explore the alterations of microbial compositions and functional genes in the topsoil (0-10 cm) following grassland restoration. Grassland restoration increased the relative abundances of the copiotrophs (such as Actinobacteria, Proteobacteria, Bacteroidetes), but reduced the oligotrophs (including Acidobacteria, Chloroflexi, Planctomycetes), suggesting that microorganisms shifted from oligotrophic to copiotrophic groups during grassland restoration. The changes in microbial eco-strategies were also supported by the meta-genomic GeoChip sequencing data. In the early restoration years, the microbial functional genes were dominant with recalcitrant C degradation (pgu, glx, lig, mnp), C fixation (accA, aclB, acsA, rbcL), N fixation (nifH), and nitrification (amoA, hao) related genes. In the later restoration years, the microbial functional genes were dominant with labile C degradation (amyA, amyX, apu, sga, abfA), and denitrification (nosZ, nirS, narG, napA) related genes. The changes in microbial functional genes were mainly related to soil biotic factors (microbial biomass C and N, as well as C- and N-acquiring enzymes). Finally, we made a framework illustrating the changes in microbial eco-strategies and soil C, N cycling processes. This is the first attempt to link microbial functional genes with microbial eco-strategies by incorporating soil microbial meta-genomic information during grassland restoration.}, } @article {pmid36419187, year = {2022}, author = {Zhong, Z and Tang, H and Shen, T and Ma, X and Zhao, F and Kwok, LY and Sun, Z and Bilige, M and Zhang, H}, title = {Bifidobacterium animalis subsp. lactis Probio-M8 undergoes host adaptive evolution by glcU mutation and translocates to the infant's gut via oral-/entero-mammary routes through lactation.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {197}, pmid = {36419187}, issn = {2049-2618}, mesh = {Animals ; Female ; Humans ; Infant ; Bacteria ; *Bifidobacterium animalis ; Breast Feeding ; Lactation ; Milk ; Mutation ; Monosaccharide Transport Proteins/genetics ; Bacterial Proteins/genetics ; }, abstract = {BACKGROUND: Most previous studies attempting to prove the phenomenon of mother-to-infant microbiota transmission were observational, performed only at genus/species-level resolution, and relied entirely on non-culture-based methodologies, impeding interpretation.

RESULTS: This work aimed to use a biomarker strain, Bifidobacterium animalis subsp. lactis Probio-M8 (M8), to directly evaluate the vertical transmission of maternally ingested bacteria by integrated culture-dependent/-independent methods. Our culture and metagenomics results showed that small amounts of maternally ingested bacteria could translocate to the infant gut via oral-/entero-mammary routes through lactation. Interestingly, many mother-infant-pair-recovered M8 homologous isolates exhibited high-frequency nonsynonymous mutations in a sugar transporter gene (glcU) and altered carbohydrate utilization preference/capacity compared with non-mutant isolates, suggesting that M8 underwent adaptive evolution for better survival in simple sugar-deprived lower gut environments.

CONCLUSIONS: This study presented direct and strain-level evidence of mother-to-infant bacterial transmission through lactation and provided insights into the impact of milk microbiota on infant gut colonization. Video Abstract.}, } @article {pmid36419034, year = {2022}, author = {Li, P and Luo, H and Ji, B and Nielsen, J}, title = {Machine learning for data integration in human gut microbiome.}, journal = {Microbial cell factories}, volume = {21}, number = {1}, pages = {241}, pmid = {36419034}, issn = {1475-2859}, support = {NNF15OC0016798//Novo Nordisk Foundation Center for Basic Metabolic Research/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Microbiota ; Metagenomics ; Dysbiosis ; Machine Learning ; }, abstract = {Recent studies have demonstrated that gut microbiota plays critical roles in various human diseases. High-throughput technology has been widely applied to characterize the microbial ecosystems, which led to an explosion of different types of molecular profiling data, such as metagenomics, metatranscriptomics and metabolomics. For analysis of such data, machine learning algorithms have shown to be useful for identifying key molecular signatures, discovering potential patient stratifications, and particularly for generating models that can accurately predict phenotypes. In this review, we first discuss how dysbiosis of the intestinal microbiota is linked to human disease development and how potential modulation strategies of the gut microbial ecosystem can be used for disease treatment. In addition, we introduce categories and workflows of different machine learning approaches, and how they can be used to perform integrative analysis of multi-omics data. Finally, we review advances of machine learning in gut microbiome applications and discuss related challenges. Based on this we conclude that machine learning is very well suited for analysis of gut microbiome and that these approaches can be useful for development of gut microbe-targeted therapies, which ultimately can help in achieving personalized and precision medicine.}, } @article {pmid36418948, year = {2022}, author = {Lappe, RR and Elmore, MG and Lozier, ZR and Jander, G and Miller, WA and Whitham, SA}, title = {Metagenomic identification of novel viruses of maize and teosinte in North America.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {767}, pmid = {36418948}, issn = {1471-2164}, mesh = {Humans ; Zea mays ; Metagenomics ; Metagenome ; *Tombusviridae ; Crops, Agricultural ; *Geminiviridae/genetics ; North America ; }, abstract = {BACKGROUND: Maize-infecting viruses are known to inflict significant agronomic yield loss throughout the world annually. Identification of known or novel causal agents of disease prior to outbreak is imperative to preserve food security via future crop protection efforts. Toward this goal, a large-scale metagenomic approach utilizing high throughput sequencing (HTS) was employed to identify novel viruses with the potential to contribute to yield loss of graminaceous species, particularly maize, in North America.

RESULTS: Here we present four novel viruses discovered by HTS and individually validated by Sanger sequencing. Three of these viruses are RNA viruses belonging to either the Betaflexiviridae or Tombusviridae families. Additionally, a novel DNA virus belonging to the Geminiviridae family was discovered, the first Mastrevirus identified in North American maize.

CONCLUSIONS: Metagenomic studies of crop and crop-related species such as this may be useful for the identification and surveillance of known and novel viral pathogens of crops. Monitoring related species may prove useful in identifying viruses capable of infecting crops due to overlapping insect vectors and viral host-range to protect food security.}, } @article {pmid36418241, year = {2023}, author = {Huang, L and Zhang, X and Pang, L and Sheng, P and Wang, Y and Yang, F and Yu, H and Huang, X and Zhu, Y and Zhang, N and Cai, H and Tang, L and Fang, X}, title = {Viral reactivation in the lungs of patients with severe pneumonia is associated with increased mortality, a multicenter, retrospective study.}, journal = {Journal of medical virology}, volume = {95}, number = {1}, pages = {e28337}, pmid = {36418241}, issn = {1096-9071}, mesh = {Humans ; Retrospective Studies ; Herpesvirus 4, Human/physiology ; *Epstein-Barr Virus Infections ; Cytomegalovirus/physiology ; *Herpesvirus 1, Human ; *Pneumonia ; *Cytomegalovirus Infections ; Lung ; *Pneumonia, Viral ; }, abstract = {Viral reactivation is widespread in patients with severe pneumonia, yet the landscape of viral reactivation in the lungs is not well-known. This study aims to assess the landscape and clinical features of viral reactivation in the early onset of severe pneumonia in ICU patients. The clinical data from 97 patients were collected retrospectively from the intensive care units of five teaching hospitals between June 2018 and July 2021. Metagenomic next-generation sequencing (mNGS) of the bronchoalveolar lavage fluid (BALF) was performed at the onset of severe pneumonia. Cytomegalovirus (CMV), herpes simplex virus-1 (HSV-1), and Epstein-Barr virus (EBV) were the most common reactivated viruses in the lower respiratory tract of patients with severe pneumonia. After adjusting for the risk of confounding and competition of age, sex, sequential organ failure assessment, acute physiology chronic health assessment II and immunosuppression status, viral reactivation resulted in an overall 2.052-fold increase in 28-day all-cause mortality (95% CI: 1.004-4.194). This study showed that CMV, HSV-1, and EBV were the most common reactivated viruses in the lungs of patients with severe pneumonia. The existence of viral reactivations was associated with an increased risk of mortality. The simultaneous reactivation of multiple viruses needs to be considered in the design of clinical trials.}, } @article {pmid36418060, year = {2022}, author = {Fedarko, MW and Kolmogorov, M and Pevzner, PA}, title = {Analyzing rare mutations in metagenomes assembled using long and accurate reads.}, journal = {Genome research}, volume = {32}, number = {11-12}, pages = {2119-2133}, pmid = {36418060}, issn = {1549-5469}, support = {U24 DK131617/DK/NIDDK NIH HHS/United States ; }, mesh = {*Metagenome ; *Bacteria/genetics ; Metagenomics ; Mutation ; }, abstract = {The advent of long and accurate "HiFi" reads has greatly improved our ability to generate complete metagenome-assembled genomes (MAGs), enabling "complete metagenomics" studies that were nearly impossible to conduct with short reads. In particular, HiFi reads simplify the identification and phasing of mutations in MAGs: It is increasingly feasible to distinguish between positions that are prone to mutations and positions that rarely ever mutate, and to identify co-occurring groups of mutations. However, the problems of identifying rare mutations in MAGs, estimating the false-discovery rate (FDR) of these identifications, and phasing identified mutations remain open in the context of HiFi data. We present strainFlye, a pipeline for the FDR-controlled identification and analysis of rare mutations in MAGs assembled using HiFi reads. We show that deep HiFi sequencing has the potential to reveal and phase tens of thousands of rare mutations in a single MAG, identify hotspots and coldspots of these mutations, and detail MAGs' growth dynamics.}, } @article {pmid36418013, year = {2022}, author = {Li, D and Liu, H and Liu, M and Chang, C and Zhao, X and Yu, H and Yan, L and Han, H and Yu, XJ}, title = {Delayed Diagnosis of Acute Q Fever, China.}, journal = {Emerging infectious diseases}, volume = {28}, number = {12}, pages = {2580-2582}, pmid = {36418013}, issn = {1080-6059}, mesh = {Humans ; *Q Fever/diagnosis ; Delayed Diagnosis ; China/epidemiology ; Fever/diagnosis ; }, abstract = {We report a patient in China with fever of unknown origin who visited 3 hospitals in 3 weeks and was finally given a diagnosis of acute Q fever, determined by metagenomics next-generation sequencing. Our results indicate that physicians are unfamiliar with Q fever and the disease is neglected in China.}, } @article {pmid36417437, year = {2022}, author = {Osborn, LJ and Schultz, K and Massey, W and DeLucia, B and Choucair, I and Varadharajan, V and Banerjee, R and Fung, K and Horak, AJ and Orabi, D and Nemet, I and Nagy, LE and Wang, Z and Allende, DS and Willard, BB and Sangwan, N and Hajjar, AM and McDonald, C and Ahern, PP and Hazen, SL and Brown, JM and Claesen, J}, title = {A gut microbial metabolite of dietary polyphenols reverses obesity-driven hepatic steatosis.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {48}, pages = {e2202934119}, pmid = {36417437}, issn = {1091-6490}, support = {R01 DK120679/DK/NIDDK NIH HHS/United States ; P01 HL147823/HL/NHLBI NIH HHS/United States ; R01 DK130227/DK/NIDDK NIH HHS/United States ; U01 AA026938/AA/NIAAA NIH HHS/United States ; S10 OD023436/OD/NIH HHS/United States ; T32 GM088088/GM/NIGMS NIH HHS/United States ; R01 AI153173/AI/NIAID NIH HHS/United States ; P50 AA024333/AA/NIAAA NIH HHS/United States ; }, mesh = {Humans ; Mice ; Animals ; Polyphenols/pharmacology ; *Gastrointestinal Microbiome/physiology ; *Fatty Liver/prevention & control ; Obesity/metabolism ; Diet, High-Fat/adverse effects ; Flavonoids/pharmacology ; }, abstract = {The molecular mechanisms by which dietary fruits and vegetables confer cardiometabolic benefits remain poorly understood. Historically, these beneficial properties have been attributed to the antioxidant activity of flavonoids. Here, we reveal that the host metabolic benefits associated with flavonoid consumption hinge, in part, on gut microbial metabolism. Specifically, we show that a single gut microbial flavonoid catabolite, 4-hydroxyphenylacetic acid (4-HPAA), is sufficient to reduce diet-induced cardiometabolic disease (CMD) burden in mice. The addition of flavonoids to a high fat diet heightened the levels of 4-HPAA within the portal plasma and attenuated obesity, and continuous delivery of 4-HPAA was sufficient to reverse hepatic steatosis. The antisteatotic effect was shown to be associated with the activation of AMP-activated protein kinase α (AMPKα). In a large survey of healthy human gut metagenomes, just over one percent contained homologs of all four characterized bacterial genes required to catabolize flavonols into 4-HPAA. Our results demonstrate the gut microbial contribution to the metabolic benefits associated with flavonoid consumption and underscore the rarity of this process in human gut microbial communities.}, } @article {pmid36417065, year = {2023}, author = {Gu, Q and Ma, J and Zhang, J and Guo, W and Wu, H and Sun, M and Wang, J and Wei, X and Zhang, Y and Chen, M and Xue, L and Ding, Y and Wu, Q}, title = {Nitrogen-metabolising microorganism analysis in rapid sand filters from drinking water treatment plant.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {11}, pages = {29458-29475}, doi = {10.1007/s11356-022-23963-0}, pmid = {36417065}, issn = {1614-7499}, mesh = {*Drinking Water ; Ammonia/metabolism ; Nitrogen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Oxidation-Reduction ; Bacteria/metabolism ; Archaea/genetics/metabolism ; Nitrification ; }, abstract = {Sand filters (SFs) are common treatment processes for nitrogen pollutant removal in drinking water treatment plants (DWTPs). However, the mechanisms on the nitrogen-cycling role of SFs are still unclear. In this study, 16S rRNA gene amplicon sequencing was used to characterise the diversity and composition of the bacterial community in SFs from DWTPs. Additionally, metagenomics approach was used to determine the functional microorganisms involved in nitrogen cycle in SFs. Our results showed that Pseudomonadota, Acidobacteria, Nitrospirae and Chloroflexi dominated in SFs. Subsequently, 85 high-quality metagenome-assembled genomes (MAGs) were retrieved from metagenome datasets of selected SFs involving nitrification, assimilatory nitrogen reduction, denitrification and anaerobic ammonia oxidation (anammox) processes. Read mapping to reference genomes of Nitrospira and the phylogenetic tree of the ammonia monooxygenase subunit A gene, amoA, suggested that Nitrospira is abundantly found in SFs. Furthermore, according to their genetic content, a nitrogen metabolic model in SFs was proposed using representative MAGs and pure culture isolate. Quantitative real-time polymerase chain reaction (qPCR) showed that ammonia-oxidising bacteria (AOB) and archaea (AOA), and complete ammonia oxidisers (comammox) were ubiquitous in the SFs, with the abundance of comammox being higher than that of AOA and AOB. Moreover, we identified a bacterial strain with a high NO3-N removal rate as Pseudomonas sp. DW-5, which could be applied in the bioremediation of micro-polluted drinking water sources. Our study provides insights into functional nitrogen-metabolising microbes in SFs of DWTPs.}, } @article {pmid36416806, year = {2022}, author = {Pavloudi, C and Zafeiropoulos, H}, title = {Deciphering the community structure and the functional potential of a hypersaline marsh microbial mat community.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {12}, pages = {}, doi = {10.1093/femsec/fiac141}, pmid = {36416806}, issn = {1574-6941}, support = {MIS 5017160//RECONNECT/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Bacteria ; Metagenome ; Metagenomics ; Phylogeny ; }, abstract = {Microbial mats are vertically stratified communities of microorganisms characterized by pronounced physiochemical gradients allowing for high species diversity and a wide range of metabolic capabilities. High Throughput Sequencing has the potential to reveal the biodiversity and function of such ecosystems in the cycling of elements. The present study combines 16S rRNA amplicon sequencing and shotgun metagenomics on a hypersaline marsh in Tristomo bay (Karpathos, Greece). Samples were collected in July 2018 and November 2019 from microbial mats, deeper sediment, aggregates observed in the water overlying the sediment, as well as sediment samples with no apparent layering. Metagenomic samples' coassembly and binning revealed 250 bacterial and 39 archaeal metagenome-assembled genomes, with completeness estimates higher than 70% and contamination less than 5%. All MAGs had KEGG Orthology terms related to osmoadaptation, with the 'salt in' strategy ones being prominent. Halobacteria and Bacteroidetes were the most abundant taxa in the mats. Photosynthesis was most likely performed by purple sulphur and nonsulphur bacteria. All samples had the capacity for sulphate reduction, dissimilatory arsenic reduction, and conversion of pyruvate to oxaloacetate. Overall, both sequencing methodologies resulted in similar taxonomic compositions and revealed that the formation of the microbial mat in this marsh exhibits seasonal variation.}, } @article {pmid36416760, year = {2022}, author = {Kircher, B and Woltemate, S and Gutzki, F and Schlüter, D and Geffers, R and Bähre, H and Vital, M}, title = {Predicting butyrate- and propionate-forming bacteria of gut microbiota from sequencing data.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2149019}, pmid = {36416760}, issn = {1949-0984}, mesh = {Humans ; *Gastrointestinal Microbiome ; Butyrates/metabolism ; Propionates/metabolism ; RNA, Ribosomal, 16S/genetics ; Fatty Acids, Volatile/metabolism ; Bacteria ; }, abstract = {The bacteria-derived short-chain fatty acids (SCFAs) butyrate and propionate play important (distinct) roles in health and disease, and understanding the ecology of respective bacteria on a community-wide level is a top priority in microbiome research. Applying sequence data (metagenomics and 16S rRNA gene) to predict SCFAs production in vitro and in vivo, a clear split between butyrate- and propionate-forming bacteria was detected with only very few taxa exhibiting pathways for the production of both SCFAs. After in vitro growth of fecal communities from distinct donors (n = 8) on different substrates (n = 7), abundances of bacteria exhibiting pathways correlated with respective SCFA concentrations, in particular in the case of butyrate. For propionate, correlations were weaker, indicating that its production is less imprinted into the core metabolism compared with butyrate-forming bacteria. Longitudinal measurements in vivo (n = 5 time-points from 20 subjects) also revealed a correlation between abundances of pathway-carrying bacteria and concentrations of the two SCFAs. Additionally, lower bacterial cell concentrations, together with higher stool moisture, promoted overall bacterial activity (measured by flow cytometry and coverage patterns of metagenome-assembled genomes) that led to elevated SCFA concentrations with over-proportional levels of butyrate. Predictions on pathway abundances based on 16S rRNA gene data using our in-house database worked well, yielding similar results as metagenomic-based analyses. Our study indicates that stimulating growth of butyrate- and propionate-producing bacteria directly leads to more production of those compounds, which is governed by two functionally distinct bacterial groups facilitating the development of precision intervention strategies targeting either metabolite.}, } @article {pmid36416092, year = {2023}, author = {Koteska, D and Marter, P and Huang, S and Pradella, S and Petersen, J and Schulz, S}, title = {Volatiles of the Apicomplexan Alga Chromera velia and Associated Bacteria.}, journal = {Chembiochem : a European journal of chemical biology}, volume = {24}, number = {3}, pages = {e202200530}, pmid = {36416092}, issn = {1439-7633}, mesh = {*Alveolata/metabolism ; Gas Chromatography-Mass Spectrometry/methods ; Mass Spectrometry ; Alcohols/metabolism ; Bacteria ; }, abstract = {Volatiles released by the apicomplexan alga Chromera velia CCAP1602/1 and their associated bacteria have been investigated. A metagenome analysis allowed the identification of the most abundant heterotrophic bacteria of the phycosphere, but the isolation of additional strains showed that metagenomics underestimated the complexity of the algal microbiome, However, a culture-independent approach revealed the presence of a planctomycete that likely represents a novel bacterial family. We analysed algal and bacterial volatiles by open-system-stripping analysis (OSSA) on Tenax TA desorption tubes, followed by thermodesorption, cryofocusing and GC-MS-analysis. The analyses of the alga and the abundant bacterial strains Sphingopyxis litoris A01A-101, Algihabitans albus A01A-324, "Coraliitalea coralii" A01A-333 and Litoreibacter sp. A01A-347 revealed sulfur- and nitrogen-containing compounds, ketones, alcohols, aldehydes, aromatic compounds, amides and one lactone, as well as the typical algal products, apocarotenoids. The compounds were identified by gas chromatographic retention indices, comparison of mass spectra and syntheses of reference compounds. A major algal metabolite was 3,4,4-trimethylcyclopent-2-en-1-one, an apocarotenoid indicating the presence of carotenoids related to capsanthin, not reported from algae so far. A low overlap in volatiles bouquets between C. velia and the bacteria was found, and the xenic algal culture almost exclusively released algal components.}, } @article {pmid36414709, year = {2023}, author = {Lee, S and Sieradzki, ET and Nicol, GW and Hazard, C}, title = {Propagation of viral genomes by replicating ammonia-oxidising archaea during soil nitrification.}, journal = {The ISME journal}, volume = {17}, number = {2}, pages = {309-314}, pmid = {36414709}, issn = {1751-7370}, mesh = {*Archaea/metabolism ; *Soil/chemistry ; Nitrification ; Bacteria/genetics ; Ammonia/metabolism ; Soil Microbiology ; Oxidation-Reduction ; Genome, Viral ; Phylogeny ; }, abstract = {Ammonia-oxidising archaea (AOA) are a ubiquitous component of microbial communities and dominate the first stage of nitrification in some soils. While we are beginning to understand soil virus dynamics, we have no knowledge of the composition or activity of those infecting nitrifiers or their potential to influence processes. This study aimed to characterise viruses having infected autotrophic AOA in two nitrifying soils of contrasting pH by following transfer of assimilated CO2-derived [13]C from host to virus via DNA stable-isotope probing and metagenomic analysis. Incorporation of [13]C into low GC mol% AOA and virus genomes increased DNA buoyant density in CsCl gradients but resulted in co-migration with dominant non-enriched high GC mol% genomes, reducing sequencing depth and contig assembly. We therefore developed a hybrid approach where AOA and virus genomes were assembled from low buoyant density DNA with subsequent mapping of [13]C isotopically enriched high buoyant density DNA reads to identify activity of AOA. Metagenome-assembled genomes were different between the two soils and represented a broad diversity of active populations. Sixty-four AOA-infecting viral operational taxonomic units (vOTUs) were identified with no clear relatedness to previously characterised prokaryote viruses. These vOTUs were also distinct between soils, with 42% enriched in [13]C derived from hosts. The majority were predicted as capable of lysogeny and auxiliary metabolic genes included an AOA-specific multicopper oxidase suggesting infection may augment copper uptake essential for central metabolic functioning. These findings indicate virus infection of AOA may be a frequent process during nitrification with potential to influence host physiology and activity.}, } @article {pmid36414646, year = {2022}, author = {Perez-Fernandez, CA and Wilburn, P and Davila, A and DiRuggiero, J}, title = {Adaptations of endolithic communities to abrupt environmental changes in a hyper-arid desert.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {20022}, pmid = {36414646}, issn = {2045-2322}, support = {80NSSC19K0470//National Aeronautics and Space Administration (NASA)/ ; NNX15AP18G//National Aeronautics and Space Administration (NASA)/ ; }, mesh = {*Desert Climate ; Acclimatization ; *Microbiota/genetics ; Metagenome ; Sodium Chloride ; Water ; }, abstract = {The adaptation mechanisms of microbial communities to natural perturbations remain unexplored, particularly in extreme environments. The extremophilic communities of halite (NaCl) nodules from the hyper-arid core of the Atacama Desert are self-sustained and represent a unique opportunity to study functional adaptations and community dynamics with changing environmental conditions. We transplanted halite nodules to different sites in the desert and investigated how their taxonomic, cellular, and biochemical changes correlated with water availability, using environmental data modeling and metagenomic analyses. Salt-in strategists, mainly represented by haloarchaea, significantly increased in relative abundance at sites characterized by extreme dryness, multiple wet/dry cycles, and colder conditions. The functional analysis of metagenome-assembled genomes (MAGs) revealed site-specific enrichments in archaeal MAGs encoding for the uptake of various compatible solutes and for glycerol utilization. These findings suggest that opportunistic salt-in strategists took over the halite communities at the driest sites. They most likely benefited from compounds newly released in the environment by the death of microorganisms least adapted to the new conditions. The observed changes were consistent with the need to maximize cellular bioenergetics when confronted with lower water availability and higher salinity, providing valuable information on microbial community adaptations and resilience to climate change.}, } @article {pmid36414538, year = {2023}, author = {Gebert, JT and Scribano, F and Engevik, KA and Perry, JL and Hyser, JM}, title = {Gastrointestinal organoids in the study of viral infections.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {324}, number = {1}, pages = {G51-G59}, pmid = {36414538}, issn = {1522-1547}, support = {F31 AI169983/AI/NIAID NIH HHS/United States ; F31 DK132942/DK/NIDDK NIH HHS/United States ; F30 DK131828/DK/NIDDK NIH HHS/United States ; R01 DK115507/DK/NIDDK NIH HHS/United States ; R01 AI158683/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Humans ; Cell Differentiation ; *COVID-19 ; SARS-CoV-2 ; Intestines ; Intestinal Mucosa/metabolism ; Organoids/metabolism ; }, abstract = {Viruses are among the most prevalent enteric pathogens. Although virologists historically relied on cell lines and animal models, human intestinal organoids (HIOs) continue to grow in popularity. HIOs are nontransformed, stem cell-derived, ex vivo cell cultures that maintain the cell type diversity of the intestinal epithelium. They offer higher throughput than standard animal models while more accurately mimicking the native tissue of infection than transformed cell lines. Here, we review recent literature that highlights virological advances facilitated by HIOs. We discuss the variations and limitations of HIOs, how HIOs have allowed for the cultivation of previously uncultivatable viruses, and how they have offered insight into tropism, entry, replication kinetics, and host-pathogen interactions. In each case, we discuss exemplary viruses and archetypal studies. We discuss how the speed and flexibility of HIO-based studies contributed to our knowledge of SARS-CoV-2 and antiviral therapeutics. Finally, we discuss the current limitations of HIOs and future directions to overcome these.}, } @article {pmid36414069, year = {2023}, author = {Lü, J and Wang, S and Liu, B and Song, X}, title = {Spatiotemporal heterogeneity of nitrogen transformation potentials in a freshwater estuarine system.}, journal = {The Science of the total environment}, volume = {859}, number = {Pt 2}, pages = {160335}, doi = {10.1016/j.scitotenv.2022.160335}, pmid = {36414069}, issn = {1879-1026}, mesh = {*Nitrogen/analysis ; RNA, Ribosomal, 16S/genetics ; *Geologic Sediments ; Ammonia/analysis ; Nitrates/analysis ; Bacteria/genetics ; Lakes ; Organic Chemicals ; }, abstract = {Under the influence of water diversion, the microbial community composition of estuarine waters and sediments might have complex spatiotemporal variations. Microbial interactions with N are significant for lake water quality. Therefore, the largest lake receiving seasonal water diversion in the North China Plain was selected as the study area. Based on 16S rRNA high-throughput sequencing and metagenomic sequencing techniques, this study analysed temporal (June-December) and spatial (estuary-pelagic zone) changes in the microbial community and functional gene composition of water and sediment. The results showed that the water microbial community composition had temporality, while sediment microbes had spatiality. The main causes of temporality in the aquatic microbial community were temperature and nitrate-N concentration, while those of sediment were flow velocity and N content. Additionally, there were complex interactions between microbial communities and N. In water, temporal variation in the relative abundance of N-related functional genes might have indirectly contributed to inorganic N composition in June (nitrite-N > ammonia-N > nitrate-N) and August (nitrite-N > nitrate-N > ammonia-N). High nitrate-N concentrations in December influenced the microbial community composition. In sediment, the estuary had higher N functional genes than the pelagic estuary, creating a relatively active N cycle and reducing total N levels in the estuary. This study revealed a potentially overlooked N sink and a flow velocity threshold that has great impacts on microbial community composition. This research contributes to a deeper understanding of the estuarine N cycle under the influence of water diversions, with implications for the calculation of global N balances and the management of lake water environments.}, } @article {pmid36413022, year = {2022}, author = {Govorunova, EG and Sineshchekov, OA and Brown, LS and Bondar, AN and Spudich, JL}, title = {Structural Foundations of Potassium Selectivity in Channelrhodopsins.}, journal = {mBio}, volume = {13}, number = {6}, pages = {e0303922}, pmid = {36413022}, issn = {2150-7511}, support = {R35 GM140838/GM/NIGMS NIH HHS/United States ; U01 NS118288/NS/NINDS NIH HHS/United States ; }, mesh = {*Potassium/metabolism ; Channelrhodopsins/genetics ; *Ion Channel Gating/physiology ; Mutation ; Sodium/metabolism ; }, abstract = {Potassium-selective channelrhodopsins (KCRs) are light-gated K[+] channels recently found in the stramenopile protist Hyphochytrium catenoides. When expressed in neurons, KCRs enable high-precision optical inhibition of spiking (optogenetic silencing). KCRs are capable of discriminating K[+] from Na[+] without the conventional K[+] selectivity filter found in classical K[+] channels. The genome of H. catenoides also encodes a third paralog that is more permeable for Na[+] than for K[+]. To identify structural motifs responsible for the unusual K[+] selectivity of KCRs, we systematically analyzed a series of chimeras and mutants of this protein. We found that mutations of three critical residues in the paralog convert its Na[+]-selective channel into a K[+]-selective one. Our characterization of homologous proteins from other protists (Colponema vietnamica, Cafeteria burkhardae, and Chromera velia) and metagenomic samples confirmed the importance of these residues for K[+] selectivity. We also show that Trp102 and Asp116, conserved in all three H. catenoides paralogs, are necessary, although not sufficient, for K[+] selectivity. Our results provide the foundation for further engineering of KCRs for optogenetic needs. IMPORTANCE Recently discovered microbial light-gated ion channels (channelrhodopsins) with a higher permeability for K[+] than for Na[+] (potassium-selective channelrhodopsins [kalium channelrhodopsins, or KCRs]) demonstrate an alternative K[+] selectivity mechanism, unrelated to well-characterized "selectivity filters" of voltage- and ligand-gated K[+] channels. KCRs can be used for optogenetic inhibition of neuronal firing and potentially for the development of gene therapies to treat neurological and cardiovascular disorders. In this study, we identified structural motifs that determine the K[+] selectivity of KCRs that provide the foundation for their further improvement as optogenetic tools.}, } @article {pmid36413016, year = {2022}, author = {France, M and Ma, B and Ravel, J}, title = {Persistence and In Vivo Evolution of Vaginal Bacterial Strains over a Multiyear Time Period.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0089322}, pmid = {36413016}, issn = {2379-5077}, support = {UH2AI083264//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; R01NR015495//HHS | NIH | National Institute of Nursing Research (NINR)/ ; }, mesh = {Female ; Humans ; *Vagina/microbiology ; Bacteria/genetics ; *Microbiota/genetics ; Lactobacillus/genetics ; Metagenome/genetics ; }, abstract = {It is not clear whether the bacterial strains that comprise our microbiota are mostly long-term colonizers or transient residents. Studies have demonstrated decades-long persistence of bacterial strains within the gut, but persistence at other body sites has yet to be determined. The vaginal microbiota (VMB) is often dominated by Lactobacillus, although it is also commonly comprised of a more diverse set of other facultative and obligate anaerobes. Longitudinal studies have demonstrated that these communities can be stable over several menstrual cycles or can fluctuate temporally in species composition. We sought to determine whether the bacterial strains that comprise the VMB were capable of persisting over longer time periods. We performed shotgun metagenomics on paired samples from 10 participants collected 1 and 2 years apart. The resulting sequences were de novo assembled and binned into high-quality metagenome assembled genomes. Persistent strains were identified based on the sequence similarity between the genomes present at the two time points and were found in the VMB of six of the participants, three of which had multiple persistent strains. The VMB of the remaining four participants was similar in species composition at the two time points but was comprised of different strains. For the persistent strains, we were able to identify the mutations that were fixed in the populations over the observed time period, giving insight into the evolution of these bacteria. These results indicate that bacterial strains can persist in the vagina for extended periods of time, providing an opportunity for them to evolve in the host microenvironment. IMPORTANCE The stability of strains within the vaginal microbiota is largely uncharacterized. Should these strains be capable of persisting for extended periods of time, they could evolve within their host in response to selective pressures exerted by the host or by other members of the community. Here, we present preliminary findings demonstrating that bacterial strains can persist in the vagina for at least 1 year. We further characterized in vivo evolution of the persistent strains. Several participants were also found to not have persistent strains, despite having a vaginal microbiota (VMB) with similar species composition at the two time points. Our observations motivate future studies that collect samples from more participants, at more time points, and over even longer periods of time. Understanding which strains persist, what factors drive their persistence, and what selective pressures they face will inform the development and delivery of rationally designed live biotherapeutics for the vagina.}, } @article {pmid36412999, year = {2022}, author = {Hassan, AH and Bebawy, AS and Saad, MT and Mosaad, GS and Saad, BT and Eltayeb, WN and Aboshanab, KM}, title = {Metagenomic nanopore sequencing versus conventional diagnosis for identification of the dieback pathogens of mango trees.}, journal = {BioTechniques}, volume = {73}, number = {6}, pages = {261-272}, doi = {10.2144/btn-2022-0087}, pmid = {36412999}, issn = {1940-9818}, mesh = {*Mangifera/microbiology ; Trees ; Metagenome ; *Nanopore Sequencing ; Plant Diseases/microbiology ; Soil ; }, abstract = {Dieback is one of the most dangerous fungal diseases affecting mango trees. In this study, nanopore metagenome sequencing of the root-soil samples and infected plant tissues was conducted to identify the fungal pathogens present. Soil analysis of the infected mango trees showed the abundance of the Dikarya subkingdom (59%) including Lasiodiplodia theobromae (15%), Alternaria alternata (6%), Ceratocystis huliohia and Colletotrichum gloeosporioides. Analysis of the infected plant tissues revealed the presence of A. alternata (34%). The data were deposited in the National Center of Biotechnology Information (PRJNA767267). In conclusion, nanopore metagenome sequencing analysis was a valuable tool to rapidly identify dieback-associated fungal pathogens.}, } @article {pmid36411909, year = {2022}, author = {Wu, H and Xiong, X and Zhu, M and Zhuo, K and Deng, Y and Cheng, D}, title = {Successful diagnosis and treatment of scrub typhus associated with haemophagocytic lymphohistiocytosis and multiple organ dysfunction syndrome: A case report and literature review.}, journal = {Heliyon}, volume = {8}, number = {11}, pages = {e11356}, pmid = {36411909}, issn = {2405-8440}, abstract = {Scrub typhus is a natural foci disease caused by the bacteria Orientia tsutsugamushi. Symptoms of the disease range from fever to severe multiple organ dysfunction. The diagnosis is based on clinical signs and antibody serological tests, which has poor sensitivity and specificity. Scrub typhus is rarely associated with multiple organ dysfunction syndrome (MODS) and haemophagocytic lymphohistiocytosis (HLH). In this paper, we report a 17-year-old Asian male who was characterized with a persistent fever without eschar. He was diagnosed with scrub typhus using metagenomic next-generation sequencing (mNGS) of the blood after negative of routine examinations. The patient was progressed to HLH and MODS but had a good recovery following anti-rickettsial therapy, dexamethasone, and advanced life support. Besides, we present a brief overview of the literature about scrub typhus and associated complications.}, } @article {pmid36411755, year = {2022}, author = {Fan, C and Gong, L and An, M and Li, Z and Li, X and Fang, J}, title = {Diagnosis and Treatment to a Post-Craniotomy Intracranial Infection Caused by Corynebacterium.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {6681-6687}, pmid = {36411755}, issn = {1178-6973}, abstract = {OBJECTIVE: To explore the perioperative prophylactic medication, identification of Causative pathogen and the treatment strategy of post-craniotomy intracranial infection (PCII) caused by Corynebacterium.

PATIENTS AND METHODS: A 47-year-old overweight male patient with hypertension, diabetes, cerebral hemorrhage and recalcitrant syphilis was clinically diagnosed with PCII based on cerebrospinal fluid (CSF) routine examination (RT), biochemical test (BT), neuroimaging CT and MRI scans, bacterial culture and identification of CSF and clinical manifestations. The risk factors of PCII and perioperative antibiotic prophylaxis were analyzed based on some reviews. The identification of the Corynebacterium Jeikeium (C. Jeikeium) and Corynebacterium simulans (C. simulans) was confirmed by CSF bacterial culture, antibiotics sensitivity in vitro and Metagenomic next-generation sequencing (mNGS) of pathogenic microorganisms, respectively. In addition, individualized therapy schemes were modified according to antimicrobial susceptibility of pathogens and mNGS of pathogenic microorganisms combined with the pathologic and physiological conditions of patients. The efficacy was evaluated depending on the changes in patients' body temperature, clinical manifestation, CSF RT, BT, and other infection-related indicators.

RESULTS: The patient recovered after 5 weeks of individualized comprehensive treatment and was discharged home, no recurrence had been observed for three months.

CONCLUSION: This is likely the first reported case of chronic PCII caused by two species of Corynebacterium simultaneously in high risk patient. The PCII can not be prevented by the perioperative antibiotic prophylaxis recommended by the guidelines, prophylaxis need to be individualized based on the risk of infection and the colonization status of the patient. Causative pathogens can be identified by CSF culture and mNGS of pathogenic microorganisms. A judicious antimicrobial therapy plan should take into account not only the in vitro antimicrobial susceptibility, but also the penetration of the antimicrobial agent into the cerebrospinal fluid. It was an excellent choice to combine intrathecal vancomycin with intravenous linezolid to treat PCII resulted from Corynebacterium.}, } @article {pmid36411639, year = {2022}, author = {Singh, N and Singh, V and Rai, SN and Mishra, V and Vamanu, E and Singh, MP}, title = {Deciphering the gut microbiome in neurodegenerative diseases and metagenomic approaches for characterization of gut microbes.}, journal = {Biomedicine & pharmacotherapy = Biomedecine & pharmacotherapie}, volume = {156}, number = {}, pages = {113958}, doi = {10.1016/j.biopha.2022.113958}, pmid = {36411639}, issn = {1950-6007}, mesh = {Humans ; Metagenomics ; *Gastrointestinal Microbiome/genetics ; *Neurodegenerative Diseases ; Metagenome ; Central Nervous System ; }, abstract = {The central nervous system has essential role in the regulation of the physiological condition of the human body. Gut microbes cause several types of gastrointestinal diseases like ulcer stomach and intestine and irritable bowel syndrome. Microbes present in the human gut can affect brain function by the release of neuroactive metabolites such as neurotransmitters, hormones, and other compounds. Gut microbial-derived metabolites also have an important role in neurological diseases such as Alzheimer's disease, Parkinson's disease, etc. Vital communication between the gut microbes and the central nervous system is known as the microbiota-gut-brain axis. It provides a communication pathway between the gut and brain which is made up of the vagus nerve, immune system components, and neuroendocrine. Disturbance in gut microbiota composition can alter the central nervous system and enteric nervous system functions. Metagenomics has been employed for the identification, and characterization of gut microbes and microbial-derived metabolites. This review is focused on the gut microbes-brain relationship and the role of gut microbes in neurodegenerative diseases. This study is also focused on major metagenomic approaches and their role in gut microbes characterization.}, } @article {pmid36411435, year = {2022}, author = {Miles, AM and McArt, JAA and Lima, SF and Neves, RC and Ganda, E}, title = {The association of hyperketonemia with fecal and rumen microbiota at time of diagnosis in a case-control cohort of early lactation cows.}, journal = {BMC veterinary research}, volume = {18}, number = {1}, pages = {411}, pmid = {36411435}, issn = {1746-6148}, support = {This work is/was supported by the USDA National Institute of Food and Agriculture and Hatch Appropriations under Project #PEN04752 Accession #1023328.//U.S. Department of Agriculture/ ; }, mesh = {Female ; Cattle ; Pregnancy ; Animals ; Rumen/metabolism ; Case-Control Studies ; RNA, Ribosomal, 16S/genetics ; Prospective Studies ; Milk/metabolism ; *Cattle Diseases/diagnosis ; *Ketosis/veterinary ; Lactation ; 3-Hydroxybutyric Acid ; *Microbiota ; }, abstract = {BACKGROUND: Many dairy cows experience a state of energy deficit as they transition from late gestation to early lactation. The aims of this study were to 1) determine if the development of hyperketonemia in early lactation dairy cows is indicated by their gut microbiome, and 2) to identify microbial features which may inform health status. We conducted a prospective nested case-control study in which cows were enrolled 14 to 7 days before calving and followed through their first 14 days in milk (DIM). Hyperketonemic cows (HYK, n = 10) were classified based on a blood β-hydroxybutyrate (BHB) concentration 1.2 mmol/L within their first 14 DIM. For each HYK cow, two non-HYK (CON, n = 20) cows were matched by parity and 3 DIM, with BHB < 1.2 mmol/L. Daily blood BHB measures were used to confirm CON cows maintained their healthy status; some CON cows displayed BHB 1.2 mmol/L after matching and these cows were reclassified as control-HYK (C-HYK, n = 9). Rumen and fecal samples were collected on the day of diagnosis or matching and subjected to 16S rRNA profiling.

RESULTS: No differences in taxa abundance, or alpha and beta diversity, were observed among CON, C-HYK, and HYK health groups for fecal microbiomes. Similar microbiome composition based on beta diversity analysis was detected for all health statuses, however the rumen microbiome of CON and HYK cows were found to be significantly different. Interestingly, highly similar microbiome composition was observed among C-HYK cow rumen and fecal microbiomes, suggesting that these individual animals which initially appear healthy with late onset of hyperketonemia were highly similar to each other. These C-HYK cows had significantly lower abundance of Ruminococcus 2 in their rumen microbiome compared to CON and HYK groups. Multinomial regressions used to compute log-fold changes in microbial abundance relative to health status were not found to have predictive value, therefore were not useful to identify the role of certain microbial features in predicting health status.

CONCLUSIONS: Lower relative abundance of Ruminococcus 2 in C-HYK cow rumens was observed, suggesting these cows may be less efficient at degrading cellulose although the mechanistic role of Ruminococcus spp. in rumen metabolism is not completely understood. Substantial differences in fecal or rumen microbiomes among cows experiencing different levels of energy deficit were not observed, suggesting that hyperketonemia may not be greatly influenced by gut microbial composition, and vice versa. Further studies using higher resolution -omics approaches like meta-transcriptomics or meta-proteomics are needed to decipher the exact mechanisms at play.}, } @article {pmid36411314, year = {2023}, author = {}, title = {Rapid mining of (meta)genomic biodiversity by repurposing CRISPRi for positive selection.}, journal = {Nature biotechnology}, volume = {41}, number = {5}, pages = {620-621}, pmid = {36411314}, issn = {1546-1696}, mesh = {*Biodiversity ; *Genomics ; Mining ; }, } @article {pmid36411313, year = {2023}, author = {Burian, J and Libis, VK and Hernandez, YA and Guerrero-Porras, L and Ternei, MA and Brady, SF}, title = {High-throughput retrieval of target sequences from complex clone libraries using CRISPRi.}, journal = {Nature biotechnology}, volume = {41}, number = {5}, pages = {626-630}, pmid = {36411313}, issn = {1546-1696}, support = {R35 GM122559/GM/NIGMS NIH HHS/United States ; }, mesh = {*Ecosystem ; *Metagenomics ; Clone Cells ; }, abstract = {The capture of metagenomic DNA in large clone libraries provides the opportunity to study microbial diversity that is inaccessible using culture-dependent methods. In this study, we harnessed nuclease-deficient Cas9 to establish a CRISPR counter-selection interruption circuit (CCIC) that can be used to retrieve target clones from complex libraries. Combining modern sequencing methods with CCIC cloning allows for rapid physical access to the genetic diversity present in natural ecosystems.}, } @article {pmid36410491, year = {2023}, author = {Yu, Q and Han, Q and Shi, S and Sun, X and Wang, X and Wang, S and Yang, J and Su, W and Nan, Z and Li, H}, title = {Metagenomics reveals the response of antibiotic resistance genes to elevated temperature in the Yellow River.}, journal = {The Science of the total environment}, volume = {859}, number = {Pt 2}, pages = {160324}, doi = {10.1016/j.scitotenv.2022.160324}, pmid = {36410491}, issn = {1879-1026}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Metagenomics ; Water ; }, abstract = {Climate warming may aggravate the threat of antibiotic resistance genes (ARGs) to environmental and human health. However, whether temperature can predict ARGs and influence their assembly processes remains unknown. Here, we used metagenomic sequencing to explore how gradually elevated water temperature (23 °C, 26 °C, 29 °C, 32 °C, 35 °C) influences ARG and mobile genetic element (MGE) profiles in the Yellow River. In total, 30 ARG types including 679 subtypes were detected in our water samples. Gradually increased temperature remarkably reduced ARG diversity but increased ARG abundance. Approximately 37 % of ARGs and 42 % of MGEs were predicted by temperature, while most others were not sensitive to temperature. For each 1 °C increase in temperature, the ARG abundance rose by 2133 TPM (Transcripts Per kilobase of exon model per Million mapped reads) abundance, and multidrug, tetracycline and peptide resistance genes had the fastest increases. Proteobacteria and Actinobacteria were the primary ARG hosts, with 558 and 226 ARG subtypes, respectively. Although ARG profiles were mainly governed by stochastic process, elevated temperature increased the deterministic process of ARGs in the Yellow River. The abundance of five high-risk ARGs (tetM, mecA, bacA, vatE and tetW) significantly increased with elevated water temperature, and these ARGs co-occurred with several opportunistic pathogens (Delftia, Legionella and Pseudomonas), implying that antibiotic resistance risk may increase under climate warming. Our study explored the possibility of predicting resistomes and their health risks through temperature, providing a novel approach to predict and control ARGs in water environments under climate warming.}, } @article {pmid36409379, year = {2022}, author = {Vishwakarma, A and Srivastava, A and Mishra, S and Verma, D}, title = {Taxonomic and functional profiling of Indian smokeless tobacco bacteriome uncovers several bacterial-derived risks to human health.}, journal = {World journal of microbiology & biotechnology}, volume = {39}, number = {1}, pages = {20}, pmid = {36409379}, issn = {1573-0972}, support = {F 30.442/2018/BSR//University Grants Commission/ ; }, mesh = {Humans ; *Tobacco, Smokeless/microbiology ; Nicotiana ; Phylogeny ; *Lobelia ; Bacteria/genetics ; }, abstract = {Smokeless tobacco (ST) consumption keeps human oral health at high risk which is one of the major reasons for oral tumorigenesis. The chemical constituents of the ST products have been well discussed; however, the inhabitant microbial diversity of the ST products is less explored especially from south Asian regions. Therefore, the present investigation discusses the bacteriome-based analysis of indigenous tobacco products. The study relies on 16S amplicon-based bacteriome analysis of Indian smokeless tobacco (ST) products using a metagenomic approach. A total of 59,15,143 high-quality reads were assigned to 34 phyla, 82 classes, 176 orders, 256 families, 356 genera, and 154 species using the SILVA database. Of the phyla (> 1%), Firmicutes dominate among the Indian smokeless tobacco followed by Proteobacteria, Bacteroidetes, and Actinobacteria (> 1%). Whereas, at the genera level (> 1%), Lysinibacillus, Dickeya, Terribacillus, and Bacillus dominate. The comparative analysis between the loose tobacco (LT) and commercial tobacco (CT) groups showed no significant difference at the phyla level, however, only three genera (Bacillus, Aerococcus, and Halomonas) were identified as significantly different between the groups. It indicates that CT and LT tobacco share similar bacterial diversity and poses equal health risks to human oral health. The phylogenetic investigation of communities by reconstruction of unobserved states (PICRUSt 2.0) based analysis uncovered several genes involved in nitrate/nitrite reduction, biofilm formation, and pro-inflammation that find roles in oral pathogenesis including oral cancer. The strong correlation analysis of these genes with several pathogenic bacteria suggests that tobacco products pose a high bacterial-derived risk to human health. The study paves the way to understand the bacterial diversity of Indian smokeless tobacco products and their putative functions with respect to human oral health. The study grabs attention to the bacterial diversity of the smokeless tobacco products from a country where tobacco consumers are rampantly prevalent however oral health is of least concern.}, } @article {pmid36409152, year = {2022}, author = {Chen, L and Zhao, Y and Wei, J and Huang, W and Ma, Y and Yang, X and Liu, Y and Wang, J and Xia, H and Lou, Z}, title = {Metagenomic Next-Generation Sequencing for the Diagnosis of Neonatal Infectious Diseases.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0119522}, pmid = {36409152}, issn = {2165-0497}, mesh = {Infant, Newborn ; Humans ; *Communicable Diseases/diagnosis ; High-Throughput Nucleotide Sequencing ; *Infant, Newborn, Diseases ; *Cell-Free Nucleic Acids ; Escherichia coli ; Metagenomics ; RNA ; }, abstract = {Infectious diseases pose a fatal risk to neonates. Timely and accurate pathogen detection is crucial for proper clinical diagnosis and therapeutic strategies. Limited sample volumes from neonatal patients seriously hindered the accurate detection of pathogens. Here, we unravel that metagenomic next-generation sequencing (mNGS) of cell-free DNA (cfDNA) and RNA can achieve unbiased detection of trace pathogens from different kinds of body fluid samples and blood samples. We enrolled 168 neonatal patients with suspected infections from whom blood samples (n = 153), cerebrospinal fluid samples (n = 127), and respiratory tract samples (RTSs) (including bronchoalveolar lavage fluids, sputa, and respiratory secretions) (n = 51) were collected and analyzed using mNGS. High rates of positivity (70.2%; 118/168) of mNGS were observed, and the coincidence rate against the final clinical diagnosis in positive mNGS cases reached 68.6% (81/118). The most common causative pathogens were Klebsiella pneumoniae (n = 12), Escherichia coli (n = 12), and Streptococcus pneumoniae (n = 8). mNGS using cfDNA and RNA can identify microbes that cannot be detected by conventional methods in different body fluid and blood samples, and more than 50% of these microbes were identified as causative pathogens. Further local polynomial regression fitting analysis revealed that the best timing for mNGS detection ranged from 1 to 3 days after the start of continuous antimicrobial therapy. Diagnosed and guided by mNGS results, the therapeutic regimens for 86 out of 117 neonatal patients were changed, most of whom (80/86) completely recovered and were discharged, while 44 out of 86 patients completely or partially stopped unnecessary medication. Our findings highlight the importance of mNGS in detecting causative DNA and RNA pathogens in infected neonatal patients. IMPORTANCE To the best of our knowledge, this is the first report on evaluating the performance of mNGS using cfDNA and RNA from body fluid and blood samples for diagnosing neonatal infections. mNGS of RNA and cfDNA can achieve the unbiased detection and identification of trace pathogens from different kinds of neonatal body fluid and blood samples with a high total coincidence rate (226/331; 68.3%) against final clinical diagnoses by sample. The best timing for mNGS detection in neonatal infections ranged from 1 to 3 days, rather than 0 days, after the start of continuous antimicrobial therapy. Our findings highlight the importance of mNGS in detecting causative DNA and RNA pathogens, and the extensive application of mNGS for the diagnosis of neonatal infections can be expected.}, } @article {pmid36409108, year = {2022}, author = {Azad, MA and Wolf, MJ and Strasburg, AP and Daniels, ML and Starkey, JC and Donadio, AD and Abdel, MP and Greenwood-Quaintance, KE and Patel, R}, title = {Comparison of the BioFire Joint Infection Panel to 16S Ribosomal RNA Gene-Based Targeted Metagenomic Sequencing for Testing Synovial Fluid from Patients with Knee Arthroplasty Failure.}, journal = {Journal of clinical microbiology}, volume = {60}, number = {12}, pages = {e0112622}, pmid = {36409108}, issn = {1098-660X}, mesh = {Humans ; *Arthroplasty, Replacement, Knee/adverse effects ; Genes, rRNA ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; Synovial Fluid ; *Arthritis, Infectious/diagnosis ; *Prosthesis-Related Infections/diagnosis/etiology ; *Arthroplasty, Replacement, Hip/adverse effects ; Biomarkers ; }, abstract = {The diagnosis of periprosthetic joint infection (PJI) is challenging, often requiring multiple clinical specimens and diagnostic techniques, some with prolonged result turnaround times. Here, the diagnostic performance of the Investigational Use Only (IUO) BioFire Joint Infection (JI) Panel was compared to 16S rRNA gene-based targeted metagenomic sequencing (tMGS) applied to synovial fluid for PJI diagnosis. Sixty synovial fluid samples from knee arthroplasty failure archived at -80°C were tested. Infectious Diseases Society of America (IDSA) diagnostic criteria were used to classify PJI. For culture-positive PJI with pathogens targeted by the JI panel, JI panel sensitivity was 91% (21/23; 95% confidence interval [CI], 73 to 98%), and tMGS sensitivity was 96% (23/24; 95% CI, 80 to 99%) (P = 0.56). Overall sensitivities of the JI panel and tMGS for PJI diagnosis were 56% (24/43; 95% CI, 41 to 70%) and 93% (41/44; 95% CI, 82 to 98%), respectively (P < 0.001). JI panel and tMGS overall specificities were 100% (16/16; 95% CI, 81 to 100%) and 94% (15/16; 95% CI, 72 to 99%), respectively. While the clinical sensitivity of the JI panel was excellent for on-panel microorganisms, overall sensitivity for PJI diagnosis was low due to the absence of Staphylococcus epidermidis, a common causative pathogen of PJI, on the panel. A PJI diagnostic algorithm for the use of both molecular tests is proposed.}, } @article {pmid36409107, year = {2022}, author = {Noonan, AJC and Qiu, Y and Kieft, B and Formby, S and Liu, T and Dofher, K and Koch, M and Hallam, SJ}, title = {Metagenome-Assembled Genomes for "Candidatus Phormidium sp. Strain AB48" and Co-occurring Microorganisms from an Industrial Photobioreactor Environment.}, journal = {Microbiology resource announcements}, volume = {11}, number = {12}, pages = {e0044722}, pmid = {36409107}, issn = {2576-098X}, abstract = {Here, we report metagenome-assembled genomes for "Candidatus Phormidium sp. strain AB48" and three cooccurring microorganisms from a biofilm-forming industrial photobioreactor environment, using the PacBio sequencing platform. Several mobile genetic elements, including a double-stranded DNA phage and plasmids, were also recovered, with the potential to mediate gene transfer within the biofilm community.}, } @article {pmid36408861, year = {2023}, author = {Shi, LD and Gao, TY and Wei, XW and Shapleigh, JP and Zhao, HP}, title = {pH-Dependent Hydrogenotrophic Denitratation Based on Self-Alkalization.}, journal = {Environmental science & technology}, volume = {57}, number = {1}, pages = {685-696}, doi = {10.1021/acs.est.2c05559}, pmid = {36408861}, issn = {1520-5851}, mesh = {*Nitrites/chemistry ; *Nitrates ; Denitrification ; Oxidation-Reduction ; Hydrogen-Ion Concentration ; Bioreactors ; Nitrogen ; }, abstract = {Producing stable nitrite is a necessity for anaerobic ammonium oxidation (anammox) but remains a huge challenge. Here, we describe the design and operation of a hydrogenotrophic denitratation system that stably reduced >90% nitrate to nitrite under self-alkaline conditions of pH up to 10.80. Manually lowering the pH to a range of 9.00-10.00 dramatically decreased the nitrate-to-nitrite transformation ratio to <20%, showing a significant role of high pH in denitratation. Metagenomics combined with metatranscriptomics indicated that six microorganisms, including a Thauera member, dominated the community and encoded the various genes responsible for hydrogen oxidation and the complete denitrification process. During denitratation at high pH, transcription of periplasmic genes napA, nirS, and nirK, whose products perform nitrate and nitrite reduction, decreased sharply compared to that under neutral conditions, while narG, encoding a membrane-associated nitrate reductase, remained transcriptionally active, as were genes involved in intracellular proton homeostasis. Together with no reduction in only nitrite-amended samples, these results disproved the electron competition between reductions of nitrate and nitrite but highlighted a lack of protons outside cells constraining biological nitrite reduction. Overall, our study presents a stably efficient strategy for nitrite production and provides a major advance in the understanding of denitratation.}, } @article {pmid36408040, year = {2022}, author = {Wang, H and Yan, S and Liu, Y and Li, Y and Cui, G and Ma, X}, title = {Metagenomic next-generation sequencing assists in the diagnosis of Cryptococcus pneumonia: Case series and literature review.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {971511}, pmid = {36408040}, issn = {2296-2565}, mesh = {Humans ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Cryptococcosis/diagnosis ; *Pneumonia ; *Cryptococcus ; }, abstract = {BACKGROUND: Pulmonary cryptococcosis (PC) was once thought to occur only in patients with immune deficiencies, such as tested positive for the Human Immunodeficiency Virus (HIV). However, in recent years, it has been discovered that more than half of the patients with PC in our nation are individuals with normal immune function. As more and more PC cases are recorded, our diagnosis and treatment approaches, as well as our understanding of PC, are gradually improving. In reality, most PC patients still have a high incidence of misdiagnosis on their initial visit. It is primarily linked to the diverse clinical manifestations, atypical imaging findings, and inaccurate diagnostic approaches.

METHODS: The research was conducted from 2019 to 2020. We performed traditional microbiological testing and mNGS on sample from patients with fever of Pulmonary nodules or lung infections. Furthermore, we collected patients' baseline information, clinical features, laboratory and imaging examination results, diagnosis, treatment and outcome. In the end, we confirmed three cases of PC using biopsy and mNGS.

CONCLUSION: Our data demonstrates that mNGS can be utilized as an auxiliary method for PC diagnosis. Early mNGS aids in the identification of pathogens, enabling early diagnosis and treatment, as well as a reduction in the rate of misdiagnosis and illness progression.}, } @article {pmid36407542, year = {2022}, author = {Khan, R and Shah, MD and Shah, L and Lee, PC and Khan, I}, title = {Bacterial polysaccharides-A big source for prebiotics and therapeutics.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {1031935}, pmid = {36407542}, issn = {2296-861X}, abstract = {Bacterial polysaccharides are unique due to their higher purity, hydrophilic nature, and a finer three-dimensional fibrous structure. Primarily, these polymers provide protection, support, and energy to the microorganism, however, more recently several auxiliary properties of these biopolymers have been unmasked. Microbial polysaccharides have shown therapeutic abilities against various illnesses, augmented the healing abilities of the herbal and Western medicines, improved overall health of the host, and have exerted positive impact on the growth of gut dwelling beneficial bacteria. Specifically, the review is discussing the mechanism through which bacterial polysaccharides exert anti-inflammatory, antioxidant, anti-cancer, and anti-microbial properties. In addition, they are holding promising application in the 3D printing. The review is also discussing a perspective about the metagenome-based screening of polysaccharides, their integration with other cutting-edge tools, and synthetic microbiome base intervention of polysaccharides as a strategy for prebiotic intervention. This review has collected interesting information about the bacterial polysaccharides from Google Scholar, PubMed, Scopus, and Web of Science databases. Up to our knowledge, this is the first of its kind review article that is summarizing therapeutic, prebiotics, and commercial application of bacterial polysaccharides.}, } @article {pmid36406447, year = {2022}, author = {Zhang, H and Wu, J and Ji, D and Liu, Y and Lu, S and Lin, Z and Chen, T and Ao, L}, title = {Microbiome analysis reveals universal diagnostic biomarkers for colorectal cancer across populations and technologies.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1005201}, pmid = {36406447}, issn = {1664-302X}, abstract = {The gut microbial dysbiosis is a risk of colorectal cancer (CRC) and some bacteria have been reported as potential markers for CRC diagnosis. However, heterogeneity among studies with different populations and technologies lead to inconsistent results. Here, we investigated six metagenomic profiles of stool samples from healthy controls (HC), colorectal adenoma (CA) and CRC, and six and four genera were consistently altered between CRC and HC or CA across populations, respectively. In FengQ cohort, which composed with 61 HC, 47 CA, and 46 CRC samples, a random forest (RF) model composed of the six genera, denoted as signature-HC, distinguished CRC from HC with an area under the curve (AUC) of 0.84. Similarly, another RF model composed of the four universal genera, denoted as signature-CA, discriminated CRC from CA with an AUC of 0.73. These signatures were further validated in five metagenomic sequencing cohorts and six independent 16S rRNA gene sequencing cohorts. Interestingly, three genera overlapped in the two models (Porphyromonas, Parvimonas and Peptostreptococcus) were with very low abundance in HC and CA, but sharply increased in CRC. A concise RF model on the three genera distinguished CRC from HC or CA with AUC of 0.87 and 0.67, respectively. Functional gene family analysis revealed that Kyoto Encyclopedia of Genes and Genomes Orthogroups categories which were significantly correlated with markers in signature-HC and signature-CA were mapped into pathways related to lipopolysaccharide and sulfur metabolism, which might be vital risk factors of CRC development. Conclusively, our study identified universal bacterial markers across populations and technologies as potential aids in non-invasive diagnosis of CRC.}, } @article {pmid36406432, year = {2022}, author = {Marzano, M and Calasso, M and Caponio, GR and Celano, G and Fosso, B and De Palma, D and Vacca, M and Notario, E and Pesole, G and De Leo, F and De Angelis, M}, title = {Extension of the shelf-life of fresh pasta using modified atmosphere packaging and bioprotective cultures.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1003437}, pmid = {36406432}, issn = {1664-302X}, abstract = {Microbial stability of fresh pasta depends on heat treatment, storage temperature, proper preservatives, and atmosphere packaging. This study aimed at improving the microbial quality, safety, and shelf life of fresh pasta using modified atmosphere composition and packaging with or without the addition of bioprotective cultures (Lactobacillus acidophilus, Lactobacillus casei, Bifidobacterium spp., and Bacillus coagulans) into semolina. Three fresh pasta variants were made using (i) the traditional protocol (control), MAP (20:80 CO2:N2), and barrier packaging, (ii) the experimental MAP (40:60 CO2:N2) and barrier packaging, and (iii) the experimental MAP, barrier packaging, and bioprotective cultures. Their effects on physicochemical properties (i.e., content on macro elements, water activity, headspace O2, CO2 concentrations, and mycotoxins), microbiological patterns, protein, and volatile organic compounds (VOC) were investigated at the beginning and the end of the actual or extended shelf-life through traditional and multi-omics approaches. We showed that the gas composition and properties of the packaging material tested in the experimental MAP system, with or without bioprotective cultures, positively affect features of fresh pasta avoiding changes in their main chemical properties, allowing for a storage longer than 120 days under refrigerated conditions. These results support that, although bioprotective cultures were not all able to grow in tested conditions, they can control the spoilage and the associated food-borne microbiota in fresh pasta during storage by their antimicrobials and/or fermentation products synergically. The VOC profiling, based on gas-chromatography mass-spectrometry (GC-MS), highlighted significant differences affected by the different manufacturing and packaging of samples. Therefore, the use of the proposed MAP system and the addition of bioprotective cultures can be considered an industrial helpful strategy to reduce the quality loss during refrigerated storage and to increase the shelf life of fresh pasta for additional 30 days by allowing the economic and environmental benefits spurring innovation in existing production models.}, } @article {pmid36406426, year = {2022}, author = {Lima, COC and De Castro, GM and Solar, R and Vaz, ABM and Lobo, F and Pereira, G and Rodrigues, C and Vandenberghe, L and Martins Pinto, LR and da Costa, AM and Koblitz, MGB and Benevides, RG and Azevedo, V and Uetanabaro, APT and Soccol, CR and Góes-Neto, A}, title = {Unraveling potential enzymes and their functional role in fine cocoa beans fermentation using temporal shotgun metagenomics.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {994524}, pmid = {36406426}, issn = {1664-302X}, abstract = {Cocoa beans fermentation is a spontaneous process, essential for the generation of quality starting material for fine chocolate production. The understanding of this process has been studied by the application of high-throughput sequencing technologies, which grants a better assessment of the different microbial taxa and their genes involved in this microbial succession. The present study used shotgun metagenomics to determine the enzyme-coding genes of the microbiota found in two different groups of cocoa beans varieties during the fermentation process. The statistical evaluation of the most abundant genes in each group and time studied allowed us to identify the potential metabolic pathways involved in the success of the different microorganisms. The results showed that, albeit the distinction between the initial (0 h) microbiota of each varietal group was clear, throughout fermentation (24-144 h) this difference disappeared, indicating the existence of selection pressures. Changes in the microbiota enzyme-coding genes over time pointed to the distinct ordering of fermentation at 24-48 h (T1), 72-96 h (T2), and 120-144 h (T3). At T1, the significantly more abundant enzyme-coding genes were related to threonine metabolism and those genes related to the glycolytic pathway, explained by the abundance of sugars in the medium. At T2, the genes linked to the metabolism of ceramides and hopanoids lipids were clearly dominant, which are associated with the resistance of microbial species to extreme temperatures and pH values. In T3, genes linked to trehalose metabolism, related to the response to heat stress, dominated. The results obtained in this study provided insights into the potential functionality of microbial community succession correlated to gene function, which could improve cocoa processing practices to ensure the production of more stable quality end products.}, } @article {pmid36406420, year = {2022}, author = {Xu, M and Su, S and Zhang, Z and Jiang, S and Zhang, J and Xu, Y and Hu, X}, title = {Two sides of the same coin: Meta-analysis uncovered the potential benefits and risks of traditional fermented foods at a large geographical scale.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1045096}, pmid = {36406420}, issn = {1664-302X}, abstract = {Traditional fermented foods, which are well-known microbial resources, are also bright national cultural inheritances. Recently, traditional fermented foods have received great attention due to their potential probiotic properties. Based on shotgun metagenomic sequencing data, we analyzed the microbial diversity, taxonomic composition, metabolic pathways, and the potential benefits and risks of fermented foods through a meta-analysis including 179 selected samples, as well as our own sequencing data collected from Hainan Province, China. As expected, raw materials, regions (differentiated by climatic zones), and substrates were the main driving forces for the microbial diversity and taxonomic composition of traditional fermented foods. Interestingly, a higher content of beneficial bacteria but a low biomass of opportunistic pathogens and antibiotic resistance genes were observed in the fermented dairy products, indicating that fermented dairy products are the most beneficial and reliable fermented foods. In contrast, despite the high microbial diversity found in the fermented soy products, their consumption risk was still high due to the enrichment of opportunistic pathogens and transferable antibiotic resistance genes. Overall, we provided the most comprehensive assessment of the microbiome of fermented food to date and generated a new view of its potential benefits and risks related to human health.}, } @article {pmid36406415, year = {2022}, author = {Aoki, W and Kogawa, M and Matsuda, S and Matsubara, K and Hirata, S and Nishikawa, Y and Hosokawa, M and Takeyama, H and Matoh, T and Ueda, M}, title = {Massively parallel single-cell genomics of microbiomes in rice paddies.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1024640}, pmid = {36406415}, issn = {1664-302X}, abstract = {Plant growth-promoting microbes (PGPMs) have attracted increasing attention because they may be useful in increasing crop yield in a low-input and sustainable manner to ensure food security. Previous studies have attempted to understand the principles underlying the rhizosphere ecology and interactions between plants and PGPMs using ribosomal RNA sequencing, metagenomic sequencing, and genome-resolved metagenomics; however, these approaches do not provide comprehensive genomic information for individual species and do not facilitate detailed analyses of plant-microbe interactions. In the present study, we developed a pipeline to analyze the genomic diversity of the rice rhizosphere microbiome at single-cell resolution. We isolated microbial cells from paddy soil and determined their genomic sequences by using massively parallel whole-genome amplification in microfluidic-generated gel capsules. We successfully obtained 3,237 single-amplified genomes in a single experiment, and these genomic sequences provided insights into microbial functions in the paddy ecosystem. Our approach offers a promising platform for gaining novel insights into the roles of microbes in the rice rhizomicrobiome and to develop microbial technologies for improved and sustainable rice production.}, } @article {pmid36406403, year = {2022}, author = {Kato, S and Masuda, S and Shibata, A and Shirasu, K and Ohkuma, M}, title = {Insights into ecological roles of uncultivated bacteria in Katase hot spring sediment from long-read metagenomics.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1045931}, pmid = {36406403}, issn = {1664-302X}, abstract = {Diverse yet-uncultivated bacteria and archaea, i.e., microbial dark matter, are present in terrestrial hot spring environments. Numerous metagenome-assembled genomes (MAGs) of these uncultivated prokaryotes by short-read metagenomics have been reported so far, suggesting their metabolic potential. However, more reliable MAGs, i.e., circularized complete MAGs (cMAGs), have been rarely reported from hot spring environments. Here, we report 61 high-quality (HQ)-MAGs, including 14 cMAGs, of diverse uncultivated bacteria and archaea retrieved from hot spring sediment (52°C, pH 7.2) by highly accurate long-read sequencing using PacBio Sequel II. The HQ MAGs were affiliated with one archaeal and 13 bacterial phyla. Notably, nine of the 14 cMAGs were the first reported cMAGs for the family- to class-level clades that these cMAGs belonged to. The genome information suggests that the bacteria represented by MAGs play a significant role in the biogeochemical cycling of carbon, nitrogen, iron, and sulfur at this site. In particular, the genome analysis of six HQ MAGs including two cMAGs of Armatimonadota, of which members are frequently abundant in hot spring environments, predicts that they are aerobic, moderate thermophilic chemoorganoheterotrophs, and potentially oxidize and/or reduce iron. This prediction is consistent with the environmental conditions where they were detected. Our results expand the knowledge regarding the ecological potential of uncultivated bacteria in moderately-high-temperature environments.}, } @article {pmid36405340, year = {2022}, author = {McLeish, MJ and Zamfir, AD and Babalola, BM and Peláez, A and Fraile, A and García-Arenal, F}, title = {Metagenomics show high spatiotemporal virus diversity and ecological compartmentalisation: Virus infections of melon, Cucumis melo, crops, and adjacent wild communities.}, journal = {Virus evolution}, volume = {8}, number = {2}, pages = {veac095}, pmid = {36405340}, issn = {2057-1577}, abstract = {The emergence of viral diseases results from novel transmission dynamics between wild and crop plant communities. The bias of studies towards pathogenic viruses of crops has distracted from knowledge of non-antagonistic symbioses in wild plants. Here, we implemented a high-throughput approach to compare the viromes of melon (Cucumis melo) and wild plants of crop (Crop) and adjacent boundaries (Edge). Each of the 41-plant species examined was infected by at least one virus. The interactions of 104 virus operational taxonomic units (OTUs) with these hosts occurred largely within ecological compartments of either Crop or Edge, with Edge having traits of a reservoir community. Local scale patterns of infection were characterised by the positive correlation between plant and virus richness at each site, the tendency for increased specialist host use through seasons, and specialist host use by OTUs observed only in Crop, characterised local-scale patterns of infection. In this study of systematically sampled viromes of a crop and adjacent wild communities, most hosts showed no disease symptoms, suggesting non-antagonistic symbioses are common. The coexistence of viruses within species-rich ecological compartments of agro-systems might promote the evolution of a diversity of virus strategies for survival and transmission. These communities, including those suspected as reservoirs, are subject to sporadic changes in assemblages, and so too are the conditions that favour the emergence of disease.}, } @article {pmid36403916, year = {2023}, author = {Chen, S and Zhong, W and Ning, Z and Niu, J and Feng, J and Qin, X and Li, Z}, title = {Effect of homemade compound microbial inoculum on the reduction of terramycin and antibiotic resistance genes in terramycin mycelial dreg aerobic composting and its mechanism.}, journal = {Bioresource technology}, volume = {368}, number = {}, pages = {128302}, doi = {10.1016/j.biortech.2022.128302}, pmid = {36403916}, issn = {1873-2976}, mesh = {*Oxytetracycline ; *Composting ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Mycelium ; }, abstract = {In order to tackle the issue of terramycin mycelial dreg (TMD) diagnosis and removal of terramycin and antibiotic resistance genes (ARGs), this study adopted aerobic composting (AC) technology and added homemade compound microbial inoculum (HCMI) to promote the AC of TMD and enhance the removal of terramycin and ARGs. The findings demonstrated that terramycin residue could be basically harmless after AC. Moreover, HCMI not only reduced QacB and tetH but also increased the degradation rates of VanRA, VanT, and dfrA24 by 40.81%, 5.65%, and 54.18%, respectively. The HCMI improved the removal rate of ARG subtypes to a certain extent. According to redundancy analysis, during AC, the succession of the microbial community had a stronger influence on the variance of ARG subtype than the environmental conditions. Differences in the abundance of various bacteria due to changes in temperature may be an intrinsic mechanism for the variation of ARG subtypes.}, } @article {pmid36403657, year = {2023}, author = {Hamidou Soumana, I and Ryu, MH and Leitao Filho, FS and Yang, J and Orach, J and Nislow, C and Leung, JM and Rider, CF and Carlsten, C}, title = {Exposure to diesel exhaust alters the functional metagenomic composition of the airway microbiome in former smokers.}, journal = {Environmental research}, volume = {216}, number = {Pt 4}, pages = {114826}, doi = {10.1016/j.envres.2022.114826}, pmid = {36403657}, issn = {1096-0953}, mesh = {Humans ; Vehicle Emissions/toxicity/analysis ; Smokers ; *Air Pollution/analysis ; Metagenome ; *Microbiota ; *Air Pollutants/analysis ; }, abstract = {The lung microbiome plays a crucial role in airway homeostasis, yet we know little about the effects of exposures such as air pollution therein. We conducted a controlled human exposure study to assess the impact of diesel exhaust (DE) on the human airway microbiome. Twenty-four participants (former smokers with mild to moderate COPD (N = 9), healthy former smokers (N = 7), and control healthy never smokers (N = 8)) were exposed to DE (300 μg/m[3] PM2.5) and filtered air (FA) for 2 h in a randomized order, separated by a 4-week washout. Endobronchial brushing samples were collected 24 h post-exposure and sequenced for the 16S microbiome, which was analyzed using QIIME2 and PICRUSt2 to examine diversity and metabolic functions, respectively. DE exposure altered airway microbiome metabolic functions in spite of statistically stable microbiome diversity. Affected functions included increases in: superpathway of purine deoxyribonucleosides degradation (pathway differential abundance 743.9, CI 95% 201.2 to 1286.6), thiazole biosynthesis I (668.5, CI 95% 139.9 to 1197.06), and L-lysine biosynthesis II (666.5, CI 95% 73.3 to 1257.7). There was an exposure-by-age effect, such that menaquinone biosynthesis superpathways were the most enriched function in the microbiome of participants aged >60, irrespective of smoking or health status. Moreover, exposure-by-phenotype analysis showed metabolic alterations in former smokers after DE exposure. These observations suggest that DE exposure induced substantial changes in the metabolic functions of the airway microbiome despite the absence of diversity changes.}, } @article {pmid36403441, year = {2023}, author = {Lu, P and Shi, H and Tao, J and Jin, J and Wang, S and Zheng, Q and Liu, P and Xiang, B and Chen, Q and Xu, Y and Li, Z and Tan, J and Cao, P}, title = {Metagenomic insights into the changes in the rhizosphere microbial community caused by the root-knot nematode Meloidogyne incognita in tobacco.}, journal = {Environmental research}, volume = {216}, number = {Pt 4}, pages = {114848}, doi = {10.1016/j.envres.2022.114848}, pmid = {36403441}, issn = {1096-0953}, mesh = {Animals ; *Tylenchoidea/physiology ; Nicotiana ; Rhizosphere ; Ammonia ; Urease/metabolism ; Plant Diseases ; Plant Roots/metabolism ; *Microbiota ; Bacteria/genetics ; Soil ; }, abstract = {Root-knot nematode (RKN) disease is a destructive soil disease that affects crop health and causes huge losses in crop production. To explore the relationships between soil environments, rhizobacterial communities, and plant health, rhizosphere bacterial communities were analyzed using metagenomic sequencing in tobacco samples with different grades of RKN disease. The results showed that the community structure and function of the plant rhizosphere were significantly correlated to the RKN disease. RKN density and urease content were key factors affecting the rhizosphere bacterial community. Urease accelerated the catabolism of urea and led to the production of high concentrations of ammonia, which directly suppressed the development of RKNs or by improving the nutritional and growth status of microorganisms that were antagonistic to RKNs. Further experiments showed that the suppression role of ammonia should be attributed to the direct inhibition of NH3. The bacterial members that were positively correlated with RKN density, contained many plant cell wall degrading enzymes, which might destroy plant cell walls and promote the colonization of RKN in tobacco roots. The analysis of metatranscriptome and metabolism demonstrated the role of these cell wall degrading enzymes. This study offers a comprehensive insight into the relationships between RKNs, bacteria, and soil environmental factors and provides new ideas for the biological control of RKNs.}, } @article {pmid36403054, year = {2022}, author = {Li, W and Wang, B and Tan, M and Song, X and Xie, S and Wang, C}, title = {Analysis of sputum microbial metagenome in COPD based on exacerbation frequency and lung function: a case control study.}, journal = {Respiratory research}, volume = {23}, number = {1}, pages = {321}, pmid = {36403054}, issn = {1465-993X}, support = {18410720900//Shanghai Science and Technology/ ; 18410720900//Shanghai Science and Technology/ ; 18410720900//Shanghai Science and Technology/ ; 18410720900//Shanghai Science and Technology/ ; 18410720900//Shanghai Science and Technology/ ; 18410720900//Shanghai Science and Technology/ ; }, mesh = {Humans ; *Sputum/microbiology ; Metagenome/genetics ; Case-Control Studies ; *Pulmonary Disease, Chronic Obstructive/diagnosis/epidemiology/genetics ; Bacteria/genetics ; Lung/microbiology ; }, abstract = {BACKGROUND: The role of the sputum microbiome in chronic obstructive pulmonary disease (COPD) progression remains elusive. As the advent of the new culture-independent microbial sequencing technique makes it possible to disclose the complex microbiome community of the respiratory tract. The aim of this study was to use metagenomic next-generation sequencing (mNGS) to confirm whether there are differences in sputum microbiome of COPD between different exacerbation frequencies and lung function.

METHODS: Thirty-nine COPD patients were divided into a frequent exacerbators (FE) group (n = 20) and a non-frequent exacerbators (NFE) (n = 19) group according to their exacerbation history, or a mild group (FEV1/pre ≥ 50%, n = 20) and a severe group (FEV1/pre < 50%, n = 19) according to the lung function. Sputum was collected during their stable phase, followed by DNA extraction, untargeted metagenomic next-generation sequencing (mNGS) and bioinformatic analysis.

RESULTS: mNGS identified 3355 bacteria, 71 viruses and 22 fungi at the specie level. It was found that Shannon index and Simpson index in FE group was lower than that in NFE group (p = 0.005, 0.008, respectively) but similar between mild and severe groups. Out of top 10 bacteria taxa, Veillonella, Fusobacterium and Prevotella jejuni had a higher abundance in NFE group, Rothia had a higher abundance in mild group. Linear discriminant analysis revealed that many bacterial taxa were more abundant in NFE group, and they mostly belonged to Actinobacteria, Bacteroidetes and Fusobacteria phyla. Frequency of exacerbations was also found to be negatively correlated with alpha diversity (with Shannon index, r = - 0.423, p = 0.009; with Simpson index, r = - 0.482, p = 0.002). No significant correlation was observed between alpha diversity and FEV1/pre.

CONCLUSIONS: Microbiome diversity in FE group was lower than that in NFE group. There was a significant difference in microbiome taxa abundance between FE and NFE groups, or mild and severe groups. These findings demonstrated that sputum microbiome community dysbiosis was associated with different exacerbation frequencies and lung function in stable COPD.}, } @article {pmid36402995, year = {2022}, author = {Navgire, GS and Goel, N and Sawhney, G and Sharma, M and Kaushik, P and Mohanta, YK and Mohanta, TK and Al-Harrasi, A}, title = {Analysis and Interpretation of metagenomics data: an approach.}, journal = {Biological procedures online}, volume = {24}, number = {1}, pages = {18}, pmid = {36402995}, issn = {1480-9222}, abstract = {Advances in next-generation sequencing technologies have accelerated the momentum of metagenomic studies, which is increasing yearly. The metagenomics field is one of the versatile applications in microbiology, where any interaction in the environment involving microorganisms can be the topic of study. Due to this versatility, the number of applications of this omics technology reached its horizons. Agriculture is a crucial sector involving crop plants and microorganisms interacting together. Hence, studying these interactions through the lenses of metagenomics would completely disclose a new meaning to crop health and development. The rhizosphere is an essential reservoir of the microbial community for agricultural soil. Hence, we focus on the R&D of metagenomic studies on the rhizosphere of crops such as rice, wheat, legumes, chickpea, and sorghum. These recent developments are impossible without the continuous advancement seen in the next-generation sequencing platforms; thus, a brief introduction and analysis of the available sequencing platforms are presented here to have a clear picture of the workflow. Concluding the topic is the discussion about different pipelines applied to analyze data produced by sequencing techniques and have a significant role in interpreting the outcome of a particular experiment. A plethora of different software and tools are incorporated in the automated pipelines or individually available to perform manual metagenomic analysis. Here we describe 8-10 advanced, efficient pipelines used for analysis that explain their respective workflows to simplify the whole analysis process.}, } @article {pmid36402183, year = {2023}, author = {Wei, C and Sun, D and Yuan, W and Li, L and Dai, C and Chen, Z and Zeng, X and Wang, S and Zhang, Y and Jiang, S and Wu, Z and Liu, D and Jiang, L and Peng, S}, title = {Metagenomics revealing molecular profiles of microbial community structure and metabolic capacity in Bamucuo lake, Tibet.}, journal = {Environmental research}, volume = {217}, number = {}, pages = {114847}, doi = {10.1016/j.envres.2022.114847}, pmid = {36402183}, issn = {1096-0953}, mesh = {Tibet ; *Lakes ; Bacteria/genetics/metabolism ; *Microbiota ; Soil Microbiology ; Soil ; Water ; }, abstract = {Microorganisms play critical ecological roles in the global biogeochemical cycles. However, extensive information on the microbial communities in Qinghai-Tibet Plateau (QTP), which is the highest plateau in the world, is still lacking, particularly in high elevation locations above 4500 m. Here, we performed a survey of th e soil and water microbial communities in Bamucuo Lake, Tibet, by using shotgun metagenomic methods. In the soil and water samples, we reconstructed 75 almost complete metagenomic assembly genomes, and 74 of the metagenomic assembly genomes from the water sample represented novel species. Proteobacteria and Actinobacteria were found to be the dominant bacterial phyla, while Euryarchaeota was the dominant archaeal phylum. The largest virus, Pandoravirus salinus, was found in the soil microbial community. We concluded that the microorganisms in Bamucuo Lake are most likely to fix carbon mainly through the 3-hydroxypropionic bi-cycle pathway. This study, for the first time, characterized the microbial community composition and metabolic capacity in QTP high-elevation locations with 4555 m, confirming that QTP is a vast and valuable resource pool, in which many microorganisms can be used to develop new bioactive substances and new antibiotics to which pathogenic microorganisms have not yet developed resistance.}, } @article {pmid36401832, year = {2023}, author = {Zhao, F and Ma, T and Zhang, X and Zhao, Q and Zhu, K and Cao, J and Liu, Z and Shen, X and Li, C}, title = {Holothuria leucospilota Polysaccharides Improve Immunity and the Gut Microbiota in Cyclophosphamide-Treated Immunosuppressed Mice.}, journal = {Molecular nutrition & food research}, volume = {67}, number = {8}, pages = {e2200317}, doi = {10.1002/mnfr.202200317}, pmid = {36401832}, issn = {1613-4133}, mesh = {Mice ; Female ; Animals ; *Holothuria ; *Gastrointestinal Microbiome ; Cyclophosphamide/adverse effects ; Immunosuppressive Agents ; Polysaccharides/chemistry ; Immunologic Factors ; }, abstract = {SCOPE: Immunosuppression is one of the major risk factors for a series of diseases, such as tumor, rheumatoid arthritis, and microbial infection. Various natural products have attracted wide attention due to their immunomodulatory activities. Herein, the study investigates the regulation of Holothuria leucospilota polysaccharides (HLP) in immunosuppressed mice.

METHODS AND RESULTS: Eight-week-old female BALB/c mice are injected intraperitoneally with cyclophosphamide (80 mg kg[-1] body weight day[-1]) to establish the immunosuppressive model. After 12 days of HLP treatment, the immune organ indexes, serum cytokines, and immunoglobulin levels are significantly increased in immunosuppressed mice (p < 0.05). Real-time fluorescent quantitative polymerase chain reaction and western blotting analysis find that HLP improves the immune factors, T-cell markers, and Toll-like receptors (TLR) pathway-related proteins expression. Simultaneously, HLP significantly increases the short-chain fatty acids concentration and regulates the gut microbiota composition (p < 0.05). Furthermore, the metagenomics analysis shows that HLP increases the levels of functional genes involved in amino acid metabolism, carbohydrate metabolism, and growth activity of the gut microbiota.

CONCLUSION: HLP intervention improves the mice's immune function, and the beneficial effects are closely associated with intestinal homeostasis regulation and TLR pathway activation. This study suggests the potential for HLP as prebiotics in novel immunopotentiators development.}, } @article {pmid36401317, year = {2022}, author = {Nata'ala, MK and Avila Santos, AP and Coelho Kasmanas, J and Bartholomäus, A and Saraiva, JP and Godinho Silva, S and Keller-Costa, T and Costa, R and Gomes, NCM and Ponce de Leon Ferreira de Carvalho, AC and Stadler, PF and Sipoli Sanches, D and Nunes da Rocha, U}, title = {MarineMetagenomeDB: a public repository for curated and standardized metadata for marine metagenomes.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {57}, pmid = {36401317}, issn = {2524-6372}, support = {VH-NG-1248 Micro 'Big Data'//Hemlholtz Association/ ; 460129525//Deutsche Forschungsgemeinschaft/ ; 91759074//Petroleum Trust Development Fund, Nigeria/ ; 91759074//Deutscher Akademischer Austauschdienst/ ; }, abstract = {BACKGROUND: Metagenomics is an expanding field within microbial ecology, microbiology, and related disciplines. The number of metagenomes deposited in major public repositories such as Sequence Read Archive (SRA) and Metagenomic Rapid Annotations using Subsystems Technology (MG-RAST) is rising exponentially. However, data mining and interpretation can be challenging due to mis-annotated and misleading metadata entries. In this study, we describe the Marine Metagenome Metadata Database (MarineMetagenomeDB) to help researchers identify marine metagenomes of interest for re-analysis and meta-analysis. To this end, we have manually curated the associated metadata of several thousands of microbial metagenomes currently deposited at SRA and MG-RAST.

RESULTS: In total, 125 terms were curated according to 17 different classes (e.g., biome, material, oceanic zone, geographic feature and oceanographic phenomena). Other standardized features include sample attributes (e.g., salinity, depth), sample location (e.g., latitude, longitude), and sequencing features (e.g., sequencing platform, sequence count). MarineMetagenomeDB version 1.0 contains 11,449 marine metagenomes from SRA and MG-RAST distributed across all oceans and several seas. Most samples were sequenced using Illumina sequencing technology (84.33%). More than 55% of the samples were collected from the Pacific and the Atlantic Oceans. About 40% of the samples had their biomes assigned as 'ocean'. The 'Quick Search' and 'Advanced Search' tabs allow users to use different filters to select samples of interest dynamically in the web app. The interactive map allows the visualization of samples based on their location on the world map. The web app is also equipped with a novel download tool (on both Windows and Linux operating systems), that allows easy download of raw sequence data of selected samples from their respective repositories. As a use case, we demonstrated how to use the MarineMetagenomeDB web app to select estuarine metagenomes for potential large-scale microbial biogeography studies.

CONCLUSION: The MarineMetagenomeDB is a powerful resource for non-bioinformaticians to find marine metagenome samples with curated metadata and stimulate meta-studies involving marine microbiomes. Our user-friendly web app is publicly available at https://webapp.ufz.de/marmdb/ .}, } @article {pmid36401288, year = {2022}, author = {Smith, RH and Glendinning, L and Walker, AW and Watson, M}, title = {Investigating the impact of database choice on the accuracy of metagenomic read classification for the rumen microbiome.}, journal = {Animal microbiome}, volume = {4}, number = {1}, pages = {57}, pmid = {36401288}, issn = {2524-4671}, support = {BB/M010996/1//EASTBIO (East of Scotland Bioscience Doctoral Training Partnership DTP, funded by BBSRC)/ ; BB/S006680/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/S006680/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/D/30002276//UK Research and Innovation/ ; BBS/E/D/30002276//UK Research and Innovation/ ; }, abstract = {Microbiome analysis is quickly moving towards high-throughput methods such as metagenomic sequencing. Accurate taxonomic classification of metagenomic data relies on reference sequence databases, and their associated taxonomy. However, for understudied environments such as the rumen microbiome many sequences will be derived from novel or uncultured microbes that are not present in reference databases. As a result, taxonomic classification of metagenomic data from understudied environments may be inaccurate. To assess the accuracy of taxonomic read classification, this study classified metagenomic data that had been simulated from cultured rumen microbial genomes from the Hungate collection. To assess the impact of reference databases on the accuracy of taxonomic classification, the data was classified with Kraken 2 using several reference databases. We found that the choice and composition of reference database significantly impacted on taxonomic classification results, and accuracy. In particular, NCBI RefSeq proved to be a poor choice of database. Our results indicate that inaccurate read classification is likely to be a significant problem, affecting all studies that use insufficient reference databases. We observed that adding cultured reference genomes from the rumen to the reference database greatly improved classification rate and accuracy. We also demonstrated that metagenome-assembled genomes (MAGs) have the potential to further enhance classification accuracy by representing uncultivated microbes, sequences of which would otherwise be unclassified or incorrectly classified. However, classification accuracy was strongly dependent on the taxonomic labels assigned to these MAGs. We therefore highlight the importance of accurate reference taxonomic information and suggest that, with formal taxonomic lineages, MAGs have the potential to improve classification rate and accuracy, particularly in environments such as the rumen that are understudied or contain many novel genomes.}, } @article {pmid36401059, year = {2023}, author = {Gao, Y and Wang, H and Hu, Y and Li, J and Xu, W and Zhao, L and Su, X and Han, J and Li, T and Fang, X and Liu, L}, title = {Whole-genome metagenomic analysis of the oral microbiota in patients with obstructive sleep apnea.}, journal = {Sleep & breathing = Schlaf & Atmung}, volume = {27}, number = {4}, pages = {1383-1398}, pmid = {36401059}, issn = {1522-1709}, support = {QNC19054//Youth Program for Military Medicine of Chinese PLA General Hospital/ ; 19BJZ34//Military Health Care Project/ ; LB20211A010013//Army Equipment Construction Applied Research Project/ ; }, mesh = {Humans ; Novobiocin ; *Sleep Apnea, Obstructive/diagnosis/therapy ; Cholesterol, LDL ; Lipids ; Continuous Positive Airway Pressure ; *Microbiota/genetics ; }, abstract = {PURPOSE: The oral microbiota is closely associated with systemic health, but few studies have investigated the oral microbiota in patients with obstructive sleep apnea (OSA). This study aimed to identify the variation of oral microbiota among patients with severe OSA, and the change of oral microbiota after treatment with continuous positive airway pressure (CPAP).

METHODS: Participants were enrolled in the study from November 2020 to August 2021. Sleep parameters using full nocturnal polysomnography (PSG) were collected on healthy controls, patients with severe OSA, and patients with severe OSA after CPAP treatment for 3 months. Oral samples were also collected by rubbing disposable medical sterile swabs on the buccal mucosa. Routine blood tests and biochemical indicators were measured using the fully automated biochemical analyzer. Oral microbial composition of oral samples were determined using whole-genome metagenomic analysis in all participants. Correlations were analyzed between the oral microbiota and blood lipids.

RESULTS: Study enrollment included 14 participants, 7 healthy controls and 7 patients with severe OSA. At the species level, the relative abundances of Prevotella, Alloprevotella, Bacteroides, Veillonella_tobetsuensis, Candidatus saccharimonas, and Leptotrichia in the groups with severe OSA were significantly lower than those in the healthy controls (P both < 0.05). The abundances of Capnocytophaga, Veillonella, Bacillus_anthracis, Eikenella, and Kingella were significantly higher whereas the abundances of Gordonia and Streptococcus were significantly lower in the group with severe OSA compared to the severe OSA-CPAP group (P < 0.05 for both). According to the Kyoto Encyclopedia of Genes and Genomes (KEGG), 4 pathways changed in the group with severe OSA compared with healthy controls (P both < 0.05). Pathways related to Novobiocin biosynthesis, 2-Oxocarboxylic acid metabolism, and Histidine metabolism were enriched in the patients with severe OSA. Nine pathways showed significant differences with regard to the relative abundances of phenylalanine metabolism; alanine, aspartate, and glutamate metabolism; one carbon pool by folate; monobactam biosynthesis; 2-oxocarboxylic acid metabolism; arginine biosynthesis and vitamin B6 metabolism; novobiocin biosynthesis; and arginine and proline metabolism, which were significantly higher in the group with severe OSA compared to the severe OSA-CPAP group (P both < 0.05). The Spearman correlation analysis between blood lipid parameters and oral microbiota components showed that negative correlations were observed between total cholesterol and Streptomyces (r =  - 0.893, P = 0.007), and high-density lipoprotein cholesterol (HDL-C) and Gordonia (r = - 0.821, P = 0.023); positive correlations were observed between HDL-C and Candidatus saccharimonas (r = 0.929, P = 0.003), and low-density lipoprotein cholesterol (LDL-C) and Capnocytophaga (r = 0.893, P = 0.007).

CONCLUSION: There was an apparent discrepancy of the oral microbiota and metabolic pathways between the group with severe OSA and controls, and CPAP significantly changed oral microbial abundance and metabolic pathways in patients with severe OSA. Correlation analysis showed that these oral bacteria were strongly correlated with the blood lipids level.}, } @article {pmid36400919, year = {2022}, author = {Scorrano, G and Nielsen, SH and Vetro, DL and Sawafuji, R and Mackie, M and Margaryan, A and Fotakis, AK and Martínez-Labarga, C and Fabbri, PF and Allentoft, ME and Carra, M and Martini, F and Rickards, O and Olsen, JV and Pedersen, MW and Cappellini, E and Sikora, M}, title = {Genomic ancestry, diet and microbiomes of Upper Palaeolithic hunter-gatherers from San Teodoro cave.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1262}, pmid = {36400919}, issn = {2399-3642}, mesh = {Humans ; Animals ; *Proteomics ; Dental Calculus ; Diet ; Genomics ; *Microbiota/genetics ; }, abstract = {Recent improvements in the analysis of ancient biomolecules from human remains and associated dental calculus have provided new insights into the prehistoric diet and genetic diversity of our species. Here we present a multi-omics study, integrating metagenomic and proteomic analyses of dental calculus, and human ancient DNA analysis of the petrous bones of two post-Last Glacial Maximum (LGM) individuals from San Teodoro cave (Italy), to reconstruct their lifestyle and the post-LGM resettlement of Europe. Our analyses show genetic homogeneity in Sicily during the Palaeolithic, representing a hitherto unknown Italian genetic lineage within the previously identified Villabruna cluster. We argue that this lineage took refuge in Italy during the LGM, followed by a subsequent spread to central-western Europe. Analysis of dental calculus showed a diet rich in animal proteins which is also reflected on the oral microbiome composition. Our results demonstrate the power of this approach in the study of prehistoric humans and will enable future research to reach a more holistic understanding of the population dynamics and ecology.}, } @article {pmid36400841, year = {2022}, author = {Lin, Q and Xavier, BB and Alako, BTF and Mitchell, AL and Rajakani, SG and Glupczynski, Y and Finn, RD and Cochrane, G and Malhotra-Kumar, S}, title = {Screening of global microbiomes implies ecological boundaries impacting the distribution and dissemination of clinically relevant antimicrobial resistance genes.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1217}, pmid = {36400841}, issn = {2399-3642}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Bayes Theorem ; *Microbiota/genetics ; Genes, Bacterial ; }, abstract = {Understanding the myriad pathways by which antimicrobial-resistance genes (ARGs) spread across biomes is necessary to counteract the global menace of antimicrobial resistance. We screened 17939 assembled metagenomic samples covering 21 biomes, differing in sequencing quality and depth, unevenly across 46 countries, 6 continents, and 14 years (2005-2019) for clinically crucial ARGs, mobile colistin resistance (mcr), carbapenem resistance (CR), and (extended-spectrum) beta-lactamase (ESBL and BL) genes. These ARGs were most frequent in human gut, oral and skin biomes, followed by anthropogenic (wastewater, bioreactor, compost, food), and natural biomes (freshwater, marine, sediment). Mcr-9 was the most prevalent mcr gene, spatially and temporally; blaOXA-233 and blaTEM-1 were the most prevalent CR and BL/ESBL genes, but blaGES-2 and blaTEM-116 showed the widest distribution. Redundancy analysis and Bayesian analysis showed ARG distribution was non-random and best-explained by potential host genera and biomes, followed by collection year, anthropogenic factors and collection countries. Preferential ARG occurrence, and potential transmission, between characteristically similar biomes indicate strong ecological boundaries. Our results provide a high-resolution global map of ARG distribution and importantly, identify checkpoint biomes wherein interventions aimed at disrupting ARGs dissemination are likely to be most effective in reducing dissemination and in the long term, the ARG global burden.}, } @article {pmid36400799, year = {2022}, author = {Tong, Z and Zhou, X and Chu, Y and Zhang, T and Zhang, J and Zhao, X and Wang, Z and Ding, R and Meng, Q and Yu, J and Wang, J and Kang, Y}, title = {Implications of oral streptococcal bacteriophages in autism spectrum disorder.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {91}, pmid = {36400799}, issn = {2055-5008}, mesh = {Humans ; *Autism Spectrum Disorder/complications/microbiology ; *Streptococcus Phages ; *Gastrointestinal Microbiome ; Mouth/microbiology ; *Bacteriophages/genetics ; }, abstract = {Growing evidence suggests altered oral and gut microbiota in autism spectrum disorder (ASD), but little is known about the alterations and roles of phages, especially within the oral microbiota in ASD subjects. We enrolled ASD (n = 26) and neurotypical subjects (n = 26) with their oral hygiene controlled, and the metagenomes of both oral and fecal samples (n = 104) are shotgun-sequenced and compared. We observe extensive and diverse oral phageome comparable to that of the gut, and clear signals of mouth-to-gut phage strain transfer within individuals. However, the overall phageomes of the two sites are widely different and show even less similarity in the oral communities between ASD and control subjects. The ASD oral phageome exhibits significantly reduced abundance and alpha diversity, but the Streptococcal phages there are atypically enriched, often dominating the community. The over-representation of Streptococcal phages is accompanied by enriched oral Streptococcal virulence factors and Streptococcus bacteria, all exhibiting a positive correlation with the severity of ASD clinical manifestations. These changes are not observed in the parallel sampling of the gut flora, suggesting a previously unknown oral-specific association between the excessive Streptococcal phage enrichment and ASD pathogenesis. The findings provide new evidence for the independent microbiome-mouth-brain connection, deepen our understanding of how the growth dynamics of bacteriophages and oral microbiota contribute to ASD, and point to novel effective therapeutics.}, } @article {pmid36400616, year = {2023}, author = {Secchi, G and Amalfitano, N and Carafa, I and Franciosi, E and Gallo, L and Schiavon, S and Sturaro, E and Tagliapietra, F and Bittante, G}, title = {Milk metagenomics and cheese-making properties as affected by indoor farming and summer highland grazing.}, journal = {Journal of dairy science}, volume = {106}, number = {1}, pages = {96-116}, doi = {10.3168/jds.2022-22449}, pmid = {36400616}, issn = {1525-3198}, mesh = {Female ; Humans ; Cattle ; Animals ; *Cheese/analysis ; Milk ; Farms ; Metagenomics ; Agriculture ; }, abstract = {The study of the complex relationships between milk metagenomics and milk composition and cheese-making efficiency as affected by indoor farming and summer highland grazing was the aim of the present work. The experimental design considered monthly sampling (over 5 mo) of the milk produced by 12 Brown Swiss cows divided into 2 groups: the first remained on a lowland indoor farm from June to October, and the second was moved to highland pastures in July and then returned to the lowland farm in September. The resulting 60 milk samples (2 kg each) were used to analyze milk composition, milk coagulation, curd firming, and syneresis processes, and to make individual model cheeses to measure cheese yields and nutrient recoveries in the cheese. After DNA extraction and Illumina Miseq sequencing, milk microbiota amplicons were also processed by means of an open-source pipeline called Quantitative Insights Into Microbial Ecology (Qiime2, version 2018.2; https://qiime2.org). Out of a total of 44 taxa analyzed, 13 bacterial taxa were considered important for the dairy industry (lactic acid bacteria, LAB, 5 taxa; and spoilage bacteria, 4) and for human (other probiotics, 2) and animal health (pathogenic bacteria, 2). The results revealed the transhumant group of cows transferred to summer highland pastures showed an increase in almost all the LAB taxa, bifidobacteria, and propionibacteria, and a reduction in spoilage taxa. All the metagenomic changes disappeared when the transhumant cows were moved back to the permanent indoor farm. The relationships between 17 microbial traits and 30 compositional and technological milk traits were investigated through analysis of correlation and latent explanatory factor analysis. Eight latent factors were identified, explaining 75.3% of the total variance, 2 of which were mainly based on microbial traits: pro-dairy bacteria (14% of total variance, improving during summer pasturing) and pathogenic bacteria (6.0% of total variance). Some bacterial traits contributed to other compositional-technological latent factors (gelation, udder health, and caseins).}, } @article {pmid36400152, year = {2023}, author = {Xi, C and Li, A and Lai, J and Huang, X and Zhang, P and Yan, S and Jiao, M and Huang, H and Hu, S}, title = {Brain-gut microbiota multimodal predictive model in patients with bipolar depression.}, journal = {Journal of affective disorders}, volume = {323}, number = {}, pages = {140-152}, doi = {10.1016/j.jad.2022.11.026}, pmid = {36400152}, issn = {1573-2517}, mesh = {Humans ; *Bipolar Disorder/diagnostic imaging/drug therapy ; Quetiapine Fumarate/therapeutic use ; *Gastrointestinal Microbiome ; Brain/diagnostic imaging ; Gray Matter ; Magnetic Resonance Imaging/methods ; }, abstract = {BACKGROUND: The "microbiota-gut-brain axis" which bridges the brain and gut microbiota is involved in the pathological mechanisms of bipolar disorder (BD), but rare is known about the exact association patterns and the potential for clinical diagnosis and treatment outcome prediction.

METHODS: At baseline, fecal samples and resting-state MRI data were collected from 103 BD depression patients and 39 healthy controls (HCs) for metagenomic sequencing and network-based functional connectivity (FC), grey matter volume (GMV) analyses. All patients then received 4-weeks quetiapine treatment and were further classified as responders and non-responders. Based on pre-treatment datasets, the correlation networks were established between gut microbiota and neuroimaging measures and the multimodal kernal combination support vector machine (SVM) classifiers were constructed to distinguish BD patients from HCs, and quetiapine responders from non-responders.

RESULTS: The multi-modal pre-treatment characteristics of quetiapine responders, were closer to the HCs compared to non-responders. And the correlation network analyses found the substantial correlations existed in HC between the Anaerotruncus_ unclassified，Porphyromonas_asaccharolytica，Actinomyces_graevenitzii et al. and the functional connectomes involved default mode network (DMN),somatomotor (SM), visual, limbic and basal ganglia networks were disrupted in BD. Moreover, in terms of the multimodal classifier, it reached optimized area under curve (AUC-ROC) at 0.9517 when classified BD from HC, and also acquired 0.8292 discriminating quetiapine responders from non-responders, which consistently better than even using the best unique modality.

LIMITATIONS: Lack post-treatment and external validation datasets; size of HCs is modest.

CONCLUSIONS: Multi-modalities of combining pre-treatment gut microbiota with neuroimaging endophenotypes might be a superior approach for accurate diagnosis and quetiapine efficacy prediction in BD.}, } @article {pmid36399821, year = {2023}, author = {Huang, YH and Yang, YJ and Wu, X and Zhu, CL and Lü, H and Zhao, HM and Xiang, L and Li, H and Mo, CH and Li, YW and Cai, QY and Li, QX}, title = {Adaptation of bacterial community in maize rhizosphere for enhancing dissipation of phthalic acid esters in agricultural soil.}, journal = {Journal of hazardous materials}, volume = {444}, number = {Pt A}, pages = {130292}, doi = {10.1016/j.jhazmat.2022.130292}, pmid = {36399821}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; *Diethylhexyl Phthalate ; Rhizosphere ; Soil ; *Sphingomonadaceae ; Zea mays ; }, abstract = {Rhizospheric degradation is a green and in situ strategy to accelerate dissipation of organic pollutants in soils. However, the mechanism on microbial degradation of phthalic acid esters (PAEs) in rhizosphere is still unclear. Here, the bacterial community and function genes in bulk and rhizospheric soils of maize (Zea mays L.) exposed to gradient concentrations of di-(2-ethylhexyl) phthalate (DEHP) were analyzed with 16 S rRNA, metagenomic sequencing and quantitative PCR (qPCR). Maize rhizosphere significantly increased the dissipation of DEHP by 4.02-11.5% in comparison with bulk soils. Bacterial community in rhizosphere exhibited more intensive response and shaped its beneficial structure and functions to DEHP stress than that in bulk soils. Both rhizospheric and pollution effects enriched more PAE-degrading bacteria (e.g., Bacillus and Rhizobium) and function genes in rhizosphere than in bulk soil, which played important roles in degradation of PAEs in rhizosphere. The PAE-degrading bacteria (including genera Sphingomonas, Sphingopyxis and Lysobacter) identified as keystone species participated in DEHP biodegradation. Identification of PAE intermediates and metagenomic reconstruction of PAE degradation pathways demonstrated that PAE-degrading bacteria degraded PAEs through cooperation with PAE-degrading and non-PAE-degrading bacteria. This study provides a comprehensive knowledge for the microbial mechanism on the superior dissipation of PAEs in rhizosphere.}, } @article {pmid36399503, year = {2023}, author = {Zheng, J and Hu, B and Zhang, X and Ge, Q and Yan, Y and Akresi, J and Piyush, V and Huang, L and Yin, Y}, title = {dbCAN-seq update: CAZyme gene clusters and substrates in microbiomes.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D557-D563}, pmid = {36399503}, issn = {1362-4962}, support = {R01 GM140370/GM/NIGMS NIH HHS/United States ; R21 AI171952/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Humans ; Carbohydrates ; Metagenome/genetics ; *Microbiota/genetics ; Multigene Family ; Polysaccharides/metabolism ; Enzymes/genetics ; Bacteria/enzymology ; Environmental Microbiology ; }, abstract = {Carbohydrate Active EnZymes (CAZymes) are significantly important for microbial communities to thrive in carbohydrate rich environments such as animal guts, agricultural soils, forest floors, and ocean sediments. Since 2017, microbiome sequencing and assembly have produced numerous metagenome assembled genomes (MAGs). We have updated our dbCAN-seq database (https://bcb.unl.edu/dbCAN_seq) to include the following new data and features: (i) ∼498 000 CAZymes and ∼169 000 CAZyme gene clusters (CGCs) from 9421 MAGs of four ecological (human gut, human oral, cow rumen, and marine) environments; (ii) Glycan substrates for 41 447 (24.54%) CGCs inferred by two novel approaches (dbCAN-PUL homology search and eCAMI subfamily majority voting) (the two approaches agreed on 4183 CGCs for substrate assignments); (iii) A redesigned CGC page to include the graphical display of CGC gene compositions, the alignment of query CGC and subject PUL (polysaccharide utilization loci) of dbCAN-PUL, and the eCAMI subfamily table to support the predicted substrates; (iv) A statistics page to organize all the data for easy CGC access according to substrates and taxonomic phyla; and (v) A batch download page. In summary, this updated dbCAN-seq database highlights glycan substrates predicted for CGCs from microbiomes. Future work will implement the substrate prediction function in our dbCAN2 web server.}, } @article {pmid36399502, year = {2023}, author = {Camargo, AP and Nayfach, S and Chen, IA and Palaniappan, K and Ratner, A and Chu, K and Ritter, SJ and Reddy, TBK and Mukherjee, S and Schulz, F and Call, L and Neches, RY and Woyke, T and Ivanova, NN and Eloe-Fadrosh, EA and Kyrpides, NC and Roux, S}, title = {IMG/VR v4: an expanded database of uncultivated virus genomes within a framework of extensive functional, taxonomic, and ecological metadata.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D733-D743}, pmid = {36399502}, issn = {1362-4962}, mesh = {*Databases, Genetic ; *Genome, Viral ; Metadata ; Metagenomics ; Software ; }, abstract = {Viruses are widely recognized as critical members of all microbiomes. Metagenomics enables large-scale exploration of the global virosphere, progressively revealing the extensive genomic diversity of viruses on Earth and highlighting the myriad of ways by which viruses impact biological processes. IMG/VR provides access to the largest collection of viral sequences obtained from (meta)genomes, along with functional annotation and rich metadata. A web interface enables users to efficiently browse and search viruses based on genome features and/or sequence similarity. Here, we present the fourth version of IMG/VR, composed of >15 million virus genomes and genome fragments, a ≈6-fold increase in size compared to the previous version. These clustered into 8.7 million viral operational taxonomic units, including 231 408 with at least one high-quality representative. Viral sequences in IMG/VR are now systematically identified from genomes, metagenomes, and metatranscriptomes using a new detection approach (geNomad), and IMG standard annotation are complemented with genome quality estimation using CheckV, taxonomic classification reflecting the latest taxonomic standards, and microbial host taxonomy prediction. IMG/VR v4 is available at https://img.jgi.doe.gov/vr, and the underlying data are available to download at https://genome.jgi.doe.gov/portal/IMG_VR.}, } @article {pmid36399496, year = {2023}, author = {Terlouw, BR and Blin, K and Navarro-Muñoz, JC and Avalon, NE and Chevrette, MG and Egbert, S and Lee, S and Meijer, D and Recchia, MJJ and Reitz, ZL and van Santen, JA and Selem-Mojica, N and Tørring, T and Zaroubi, L and Alanjary, M and Aleti, G and Aguilar, C and Al-Salihi, SAA and Augustijn, HE and Avelar-Rivas, JA and Avitia-Domínguez, LA and Barona-Gómez, F and Bernaldo-Agüero, J and Bielinski, VA and Biermann, F and Booth, TJ and Carrion Bravo, VJ and Castelo-Branco, R and Chagas, FO and Cruz-Morales, P and Du, C and Duncan, KR and Gavriilidou, A and Gayrard, D and Gutiérrez-García, K and Haslinger, K and Helfrich, EJN and van der Hooft, JJJ and Jati, AP and Kalkreuter, E and Kalyvas, N and Kang, KB and Kautsar, S and Kim, W and Kunjapur, AM and Li, YX and Lin, GM and Loureiro, C and Louwen, JJR and Louwen, NLL and Lund, G and Parra, J and Philmus, B and Pourmohsenin, B and Pronk, LJU and Rego, A and Rex, DAB and Robinson, S and Rosas-Becerra, LR and Roxborough, ET and Schorn, MA and Scobie, DJ and Singh, KS and Sokolova, N and Tang, X and Udwary, D and Vigneshwari, A and Vind, K and Vromans, SPJM and Waschulin, V and Williams, SE and Winter, JM and Witte, TE and Xie, H and Yang, D and Yu, J and Zdouc, M and Zhong, Z and Collemare, J and Linington, RG and Weber, T and Medema, MH}, title = {MIBiG 3.0: a community-driven effort to annotate experimentally validated biosynthetic gene clusters.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D603-D610}, pmid = {36399496}, issn = {1362-4962}, support = {F32 AT011475/AT/NCCIH NIH HHS/United States ; R01 AI155694/AI/NIAID NIH HHS/United States ; U24 AT010811/AT/NCCIH NIH HHS/United States ; }, mesh = {*Genomics ; *Genome ; Multigene Family ; Biosynthetic Pathways/genetics ; }, abstract = {With an ever-increasing amount of (meta)genomic data being deposited in sequence databases, (meta)genome mining for natural product biosynthetic pathways occupies a critical role in the discovery of novel pharmaceutical drugs, crop protection agents and biomaterials. The genes that encode these pathways are often organised into biosynthetic gene clusters (BGCs). In 2015, we defined the Minimum Information about a Biosynthetic Gene cluster (MIBiG): a standardised data format that describes the minimally required information to uniquely characterise a BGC. We simultaneously constructed an accompanying online database of BGCs, which has since been widely used by the community as a reference dataset for BGCs and was expanded to 2021 entries in 2019 (MIBiG 2.0). Here, we describe MIBiG 3.0, a database update comprising large-scale validation and re-annotation of existing entries and 661 new entries. Particular attention was paid to the annotation of compound structures and biological activities, as well as protein domain selectivities. Together, these new features keep the database up-to-date, and will provide new opportunities for the scientific community to use its freely available data, e.g. for the training of new machine learning models to predict sequence-structure-function relationships for diverse natural products. MIBiG 3.0 is accessible online at https://mibig.secondarymetabolites.org/.}, } @article {pmid36399059, year = {2022}, author = {Zhang, Y and Jiang, F and Yang, B and Wang, S and Wang, H and Wang, A and Xu, D and Fan, W}, title = {Improved microbial genomes and gene catalog of the chicken gut from metagenomic sequencing of high-fidelity long reads.}, journal = {GigaScience}, volume = {11}, number = {}, pages = {}, pmid = {36399059}, issn = {2047-217X}, mesh = {Animals ; *Metagenome ; *Chickens/genetics ; RNA, Ribosomal, 16S/genetics ; Metagenomics ; Genome, Microbial ; }, abstract = {BACKGROUND: Due to the importance of chicken production and the remarkable influence of the gut microbiota on host health and growth, tens of thousands of metagenome-assembled genomes (MAGs) have been constructed for the chicken gut microbiome. However, due to the limitations of short-read sequencing and assembly technologies, most of these MAGs are far from complete, are of lower quality, and include contaminant reads.

RESULTS: We generated 332 Gb of high-fidelity (HiFi) long reads from the 5 chicken intestinal compartments and assembled 461 and 337 microbial genomes, of which 53% and 55% are circular, at the species and strain levels, respectively. For the assembled microbial genomes, approximately 95% were regarded as complete according to the "RNA complete" criteria, which requires at least 1 full-length ribosomal RNA (rRNA) operon encoding all 3 types of rRNA (16S, 23S, and 5S) and at least 18 copies of full-length transfer RNA genes. In comparison with the short-read-derived chicken MAGs, 384 (83% of 461) and 89 (26% of 337) strain-level and species-level genomes in this study are novel, with no matches to previously reported sequences. At the gene level, one-third of the 2.5 million genes in the HiFi-derived gene catalog are novel and cannot be matched to the short-read-derived gene catalog. Moreover, the HiFi-derived genomes have much higher continuity and completeness, as well as lower contamination; the HiFi-derived gene catalog has a much higher ratio of complete gene structures. The dominant phylum in our HiFi-assembled genomes was Firmicutes (82.5%), and the foregut was highly enriched in 5 genera: Ligilactobacillus, Limosilactobacillus, Lactobacillus, Weissella, and Enterococcus, all of which belong to the order Lactobacillales. Using GTDB-Tk, all 337 species-level genomes were successfully classified at the order level; however, 2, 35, and 189 genomes could not be classified into any known family, genus, and species, respectively. Among these incompletely classified genomes, 9 and 49 may belong to novel genera and species, respectively, because their 16S rRNA genes have identities lower than 95% and 97% to any known 16S rRNA genes.

CONCLUSIONS: HiFi sequencing not only produced metagenome assemblies and gene structures with markedly improved quality but also recovered a substantial portion of novel genomes and genes that were missed in previous short-read-based metagenome studies. The novel genomes and species obtained in this study will facilitate gut microbiome and host-microbiota interaction studies, thereby contributing to the sustainable development of poultry resources.}, } @article {pmid36398862, year = {2022}, author = {Fouladi, F and Bulik-Sullivan, EC and Glenny, EM and Thornton, LM and Reed, KK and Thomas, S and Kleiman, S and Watters, A and Oakes, J and Huh, EY and Tang, Q and Liu, J and Djukic, Z and Harper, L and Trillo-Ordoñez, Y and Sun, S and Blakely, I and Mehler, PS and Fodor, AA and Tarantino, LM and Bulik, CM and Carroll, IM}, title = {Reproducible changes in the anorexia nervosa gut microbiota following inpatient therapy remain distinct from non-eating disorder controls.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2143217}, pmid = {36398862}, issn = {1949-0984}, support = {P30 DK056350/DK/NIDDK NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; R01 MH118278/MH/NIMH NIH HHS/United States ; R01 MH124871/MH/NIMH NIH HHS/United States ; R01 MH105684/MH/NIMH NIH HHS/United States ; R01 MH119084/MH/NIMH NIH HHS/United States ; T32 DK007737/DK/NIDDK NIH HHS/United States ; R01 MH120170/MH/NIMH NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Anorexia Nervosa/therapy ; Inpatients ; Feces ; *Microbiota ; }, abstract = {The composition of the gut microbiota in patients with anorexia nervosa (AN), and the ability of this microbial community to influence the host, remains uncertain. To achieve a broader understanding of the role of the intestinal microbiota in patients with AN, we collected fecal samples before and following clinical treatment at two geographically distinct eating disorder units (Center of Excellence for Eating Disorders [UNC-CH] and ACUTE Center for Eating Disorders [Denver Health]). Gut microbiotas were characterized in patients with AN, before and after inpatient treatment, and in non-eating disorder (non-ED) controls using shotgun metagenomic sequencing. The impact of inpatient treatment on the AN gut microbiota was remarkably consistent between eating disorder units. Although weight in patients with AN showed improvements, AN microbiotas post-treatment remained distinct from non-ED controls. Additionally, AN gut microbiotas prior to treatment exhibited more fermentation pathways and a lower ability to degrade carbohydrates than non-ED controls. As the intestinal microbiota can influence nutrient metabolism, our data highlight the complex microbial communities in patients with AN as an element needing further attention post inpatient treatment. Additionally, this study defines the effects of renourishment on the AN gut microbiota and serves as a platform to develop precision nutrition approaches to potentially mitigate impediments to recovery.}, } @article {pmid36398548, year = {2022}, author = {Zhang, HY and Tang, MT and Qing, L and Li, DY and Qiao, LN}, title = {[Value of metagenomic next-generation sequencing in children with hemophagocytic syndrome with central nervous system involvement].}, journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics}, volume = {24}, number = {11}, pages = {1226-1230}, pmid = {36398548}, issn = {1008-8830}, mesh = {Child ; Humans ; *Lymphohistiocytosis, Hemophagocytic/diagnosis/genetics ; *Epstein-Barr Virus Infections/complications ; Herpesvirus 4, Human/genetics ; Retrospective Studies ; High-Throughput Nucleotide Sequencing ; Central Nervous System ; }, abstract = {OBJECTIVES: To study the value of metagenomic next-generation sequencing (mNGS) in detecting intracranial Epstein-Barr virus (EBV) infection in children with hemophagocytic syndrome (HPS) with central nervous system involvement.

METHODS: A retrospective analysis was performed for the cerebrospinal fluid mNGS results of 30 HPS children with central nervous system involvement, which were compared with the results of cerebrospinal fluid EBV-DNA detection and serum EBV antibody profile. The change in serum EBV-DNA copy number after treatment was used to evaluate the efficacy of targeted therapy.

RESULTS: The positive rate of EBV in cerebrospinal fluid determined by mNGS was significantly higher than that of EBV-DNA in cerebrospinal fluid (100% vs 10%, P<0.001) and had no significant difference from the positive rate of serum EBV antibody profile (100% vs 93%, P>0.05). The median number of sequences determined by mNGS was 2 400, and serum EBV-DNA copy number before treatment was moderately positively correlated with the number of EBV sequences (rs=0.693, P<0.001). The multiple linear regression analysis showed that the number of sequences determined by mNGS in cerebrospinal fluid increased with the increase in serum EBV-DNA copy number before treatment (P<0.05).

CONCLUSIONS: EBV-associated HPS often results in EBV-infected viral encephalitis, and mNGS can significantly increase the detection rate of EBV in cerebrospinal fluid, which may help with clinical diagnosis.}, } @article {pmid36397417, year = {2022}, author = {Hao, Z and Dang, H and Gao, X and Zhang, C and Deng, A and Tan, Y and Ding, G}, title = {Successful control of scleritis caused by Nocardia farcinica: A case report.}, journal = {Medicine}, volume = {101}, number = {45}, pages = {e31481}, pmid = {36397417}, issn = {1536-5964}, mesh = {Male ; Humans ; Middle Aged ; *Scleritis/diagnosis/drug therapy/etiology ; Amikacin ; *Nocardia ; *Nocardia Infections/diagnosis/drug therapy/complications ; }, abstract = {RATIONALE: Nocardia farcinica is an opportunistic pathogen that rarely causes ocular infections. This study reviewed a case of N. farcinica-mediated scleritis involving the corneal limbus.

PATIENT CONCERNS: A 56-year-old man was admitted to the Department of Keratology of Jinan Second People's Hospital due to "a red and swollen right eye accompanied with severe pain for >1 month." He denied any history of hypertension, diabetes, systemic immune diseases and eye surgery.

DIAGNOSES: Corneal defect and scleral necrosis were observed by slit lamp. Combination of anterior segment optical coherence tomography and ophthalmic ultrasound biomicroscopy was used for diagnosis and evaluation of corneal and scleral conditions. Culture and metagenomic sequencing verified that the pathogen of scleritis was N. farcinica.

INTERVENTIONS: The patient was treated by sulfacetamide sodium eye drops, oral administration of sulfamethoxazole tablets, amikacin anterior chamber flushing, scleral debridement, and allogeneic scleral transplantation.

OUTCOMES: The disease was successfully controlled.

LESSONS: Infectious scleritis caused by N. farcinica is extremely rare. Culture of pathogenic microorganisms remains to be the gold standard for the diagnosis of infectious eye diseases. Metagenomic sequencing shows potential promise in the diagnosis of infectious eye diseases. N. farcinica is sensitive to sulfonamides and amikacin.}, } @article {pmid36396983, year = {2022}, author = {Kong, F and Li, L and Zhang, D and Lian, B and Liu, X and Ren, S and Zhang, Y and Cao, L}, title = {Healthy adults with Streptococcus pneumoniae meningitis and Streptococcus pneumoniae subdural abscess: two case reports and a literature review.}, journal = {The Journal of international medical research}, volume = {50}, number = {11}, pages = {3000605221137470}, pmid = {36396983}, issn = {1473-2300}, mesh = {Male ; Adult ; Humans ; Aged ; *Meningitis, Pneumococcal/diagnosis/diagnostic imaging ; Streptococcus pneumoniae ; Ceftriaxone/therapeutic use ; Abscess ; Vancomycin/therapeutic use ; }, abstract = {We present the cases of two otherwise healthy adults, one with meningitis and another with a subdural abscess, with both conditions attributable to Streptococcus pneumoniae. A 31-year-old man was admitted with a 3-day history of fever, headache, and vomiting. Physical examination revealed intermittent confusion, irritability, and neck stiffness. Cerebrospinal fluid (CSF) culture was positive for S. pneumoniae. Contrast-enhanced magnetic resonance imaging (C-MRI) revealed multiple small lesions on the bilateral frontal lobes. Intravenous ceftriaxone and vancomycin were administered, followed by intravenous moxifloxacin. His symptoms resolved within 3 months. Additionally, a 66-year-old man was admitted for acute fever with confusion, abnormal behavior, and a recent history of acute respiratory infection. Physical examination revealed confusion, neck stiffness, and a positive right Babinski sign. CSF metagenomic analysis detected S. pneumoniae. C-MRI disclosed left occipitotemporal meningoencephalitis with subdural abscesses. Intravenous ceftriaxone was administered for 3 weeks. His condition gradually improved, with resorbed lesions detected on repeat MRI. This study expanded the clinical and imaging spectra of S. pneumoniae meningitis. In healthy adults, S. pneumoniae can invade the brain, but subdural abscess is a rare neuroimaging manifestation. Early diagnosis of S. pneumoniae meningitis by high-throughput sequencing and flexible treatment strategies are necessary for satisfactory outcomes.}, } @article {pmid36396946, year = {2022}, author = {Song, Y and Song, F and Liu, S and Chen, S and Song, Z}, title = {Rapid diagnosis of a complex oral mucosal infection using metagenomic next-generation sequencing: a case report.}, journal = {The Journal of international medical research}, volume = {50}, number = {11}, pages = {3000605221136679}, pmid = {36396946}, issn = {1473-2300}, mesh = {Humans ; Sensitivity and Specificity ; *Metagenomics/methods ; *Communicable Diseases ; High-Throughput Nucleotide Sequencing/methods ; Mucous Membrane ; }, abstract = {The most commonly used methods for pathogen detection and identification in oral mucosal infectious diseases are DNA or RNA quantitative polymerase chain reaction detection, bacterial or fungal cultures, and immunohistochemical analysis. These traditional methods are time-consuming and can only detect one specific targeted pathogen at a time. An efficient and sensitive method with higher species richness is urgently needed. Metagenomic next-generation sequencing (mNGS) is a new method of pathogen detection with high efficiency and sensitivity. In this case report, mNGS was used to identify the pathogens in oral mucosal tissues of a patient with complex oral mucosal infections and oral leukoplakia. Candida albicans, human gamma herpesvirus 4, and many other pathogens were identified using this method. For complex oral mucosal infections, mNGS is a more efficient and sensitive approach that can replace conventional detection methods.}, } @article {pmid36395566, year = {2022}, author = {Elahinik, A and Haarsma, M and Abbas, B and Pabst, M and Xevgenos, D and van Loosdrecht, MCM and Pronk, M}, title = {Glycerol conversion by aerobic granular sludge.}, journal = {Water research}, volume = {227}, number = {}, pages = {119340}, doi = {10.1016/j.watres.2022.119340}, pmid = {36395566}, issn = {1879-2448}, mesh = {*Sewage/chemistry ; *Glycerol ; Wastewater ; Phosphorus/metabolism ; Polyphosphates/metabolism ; Bacteria/metabolism ; }, abstract = {Glycerol is abundantly present in wastewater from industries such as biodiesel production facilities. Glycerol is also a potential carbon source for microbes that are involved in wastewater nutrient removal processes. The conversion of glycerol in biological phosphorus removal of aerobic granular sludge processes has not been explored to date. The current study describes glycerol utilization by aerobic granular sludge and enhanced biological phosphorus removal (EBPR). Robust granules with good phosphorus removal capabilities were formed in an aerobic granular sludge sequencing batch reactor fed with glycerol. The interaction between the fermentative conversion of glycerol and product uptake by polyphosphate accumulating organisms (PAO) was studied using stoichiometric and microbial community analysis. Metagenomic, metaproteomic and microscopic analysis identified a community dominated by Actinobacteria (Tessaracoccus and Micropruina) and a typical PAO known as Ca. Accumulibacter. Glycerol uptake facilitator (glpF) and glycerol kinase (glpK), two proteins involved in the transport of glycerol into the cellular metabolism, were only observed in the genome of the Actinobacteria. The anaerobic conversion appeared to be a combination of a substrate fermentation and product uptake-type reaction. Initially, glycerol fermentation led mainly to the production of 1,3-propanediol (1,3-PDO) which was not taken up under anaerobic conditions. Despite the aerobic conversion of 1,3-PDO stable granulation was observed. Over time, 1,3-PDO production decreased and complete anaerobic COD uptake was observed. The results demonstrate that glycerol-containing wastewater can effectively be treated by the aerobic granular sludge process and that fermentative and polyphosphate accumulating organisms can form a food chain in glycerol-based EBPR processes.}, } @article {pmid36395539, year = {2022}, author = {Warsaba, R and Salcedo-Porras, N and Flibotte, S and Jan, E}, title = {Expansion of viral genomes with viral protein genome linked copies.}, journal = {Virology}, volume = {577}, number = {}, pages = {174-184}, doi = {10.1016/j.virol.2022.10.012}, pmid = {36395539}, issn = {1096-0341}, abstract = {Virus protein-linked genome (VPg) proteins are required for replication. VPgs are duplicated in a subset of RNA viruses however their roles are not fully understood and the extent of viral genomes containing VPg copies has not been investigated in detail. Here, we generated a novel bioinformatics approach to identify VPg sequences in viral genomes using hidden Markov models (HMM) based on alignments of dicistrovirus VPg sequences. From metagenomic datasets of dicistrovirus genomes, we identified 717 dicistrovirus genomes containing VPgs ranging from a single copy to 8 tandem copies. The VPgs are classified into nine distinct types based on their sequence and length. The VPg types but not VPg numbers per viral genome followed specific virus clades, thus suggesting VPgs co-evolved with viral genomes. We also identified VPg duplications in aquamavirus and mosavirus genomes. This study greatly expands the number of viral genomes that contain VPg copies and indicates that duplicated viral sequences are more widespread than anticipated.}, } @article {pmid36395465, year = {2022}, author = {, }, title = {Erratum: A case report of two Kala-azar cases in China diagnosed by metagenomic next-generation sequencing.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {1067340}, doi = {10.3389/fmed.2022.1067340}, pmid = {36395465}, issn = {2296-858X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2022.922894.].}, } @article {pmid36395362, year = {2022}, author = {Moreira, FC and Sarquis, DP and Souza, JES and Avelar, DS and Araújo, TMT and Khayat, AS and Santos, SEBD and de Assumpção, PP}, title = {Treasures from trash in cancer research.}, journal = {Oncotarget}, volume = {13}, number = {}, pages = {1246-1257}, pmid = {36395362}, issn = {1949-2553}, mesh = {Humans ; Software ; High-Throughput Nucleotide Sequencing ; Genomics ; *RNA, Small Untranslated ; *MicroRNAs/genetics ; *Neoplasms/genetics ; }, abstract = {INTRODUCTION: Cancer research has significantly improved in recent years, primarily due to next-generation sequencing (NGS) technology. Consequently, an enormous amount of genomic and transcriptomic data has been generated. In most cases, the data needed for research goals are used, and unwanted reads are discarded. However, these eliminated data contain relevant information. Aiming to test this hypothesis, genomic and transcriptomic data were acquired from public datasets.

MATERIALS AND METHODS: Metagenomic tools were used to explore genomic cancer data; additional annotations were used to explore differentially expressed ncRNAs from miRNA experiments, and variants in adjacent to tumor samples from RNA-seq experiments were also investigated.

RESULTS: In all analyses, new data were obtained: from DNA-seq data, microbiome taxonomies were characterized with a similar performance of dedicated metagenomic research; from miRNA-seq data, additional differentially expressed sncRNAs were found; and in tumor and adjacent to tumor tissue data, somatic variants were found.

CONCLUSIONS: These findings indicate that unexplored data from NGS experiments could help elucidate carcinogenesis and discover putative biomarkers with clinical applications. Further investigations should be considered for experimental design, providing opportunities to optimize data, saving time and resources while granting access to multiple genomic perspectives from the same sample and experimental run.}, } @article {pmid36394716, year = {2023}, author = {Leal, É and Ribeiro, ESD' and Monteiro, FJC and Marques, JP and Dos Santos Mendes, D and Morais, VS and Araújo, ELL and Pandey, RP and Chang, CM and Deng, X and Delwart, E and da Costa, AC and Lima, K}, title = {Aedes aegypti Totivirus identified in mosquitoes in the Brazilian Amazon region.}, journal = {Virus genes}, volume = {59}, number = {1}, pages = {167-172}, pmid = {36394716}, issn = {1572-994X}, support = {CNPq #302677/2019-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Animals ; *Aedes ; *Totivirus/genetics ; Brazil ; *Totiviridae/genetics ; *Viruses ; }, abstract = {The totiviridae family contains viruses with double-stranded RNA genomes of 4.6-7.0 kpb, which encode a capsid protein (CP) and RNA-dependent RNA polymerase (RdRp), and they are approximately 40 nm in diameter with icosahedral symmetry. Totiviruses were first isolated from mosquitoes collected in Shaanxi Province (China). Here, we report a new Aedes aegypti Totivirus (AaTV) identified in mosquitoes from the Amazon rainforest. Mosquitoes (Diptera: Culicidae) were collected from a forest reserve belonging to the Amazon forest in the city of Macapá, Amapá state, Northern Brazil. A viral sequence with a 5748 nucleotide length that was nearly identical to Aedes aegypti Totivirus (AaTV), here named Aedes aegypti Totivirus BR59AP, was detected. A detailed molecular analysis was performed and shows that AaTV-BR59AP is highly related to the AaTV strain from the Caribbean region. We emphasize the importance of the characterization of new viruses in mosquitoes to deepen our understanding of viral diversity in insects and their potential role in disease.}, } @article {pmid36394327, year = {2022}, author = {Mann, E and Shekarriz, S and Surette, MG}, title = {Human Gut Metagenomes Encode Diverse GH156 Sialidases.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {23}, pages = {e0175522}, pmid = {36394327}, issn = {1098-5336}, mesh = {Humans ; Glycoside Hydrolases/genetics ; *Metagenome ; *Neuraminidase/genetics/metabolism ; Polysaccharides ; Sialic Acids/metabolism ; Gastrointestinal Microbiome ; }, abstract = {The intestinal lining is protected by a mucous barrier composed predominantly of complex carbohydrates. Gut microbes employ diverse glycoside hydrolases (GHs) to liberate mucosal sugars as a nutrient source to facilitate host colonization. Intensive catabolism of mucosal glycans, however, may contribute to barrier erosion, pathogen encroachment, and inflammation. Sialic acid is an acidic sugar featured at terminal positions of host glycans. Characterized sialidases from the microbiome belong to the GH33 family, according to CAZy (Carbohydrate-Active enZYmes Database). In 2018 a functional metagenomics screen using thermal spring DNA uncovered the founding member of the GH156 sialidase family, the presence of which has yet to be reported in the context of the human microbiome. A subset of GH156 sequences from the CAZy database containing key sialidase residues was used to build a hidden Markov model. HMMsearch against public databases revealed ~10× more putative GH156 sialidases than currently cataloged by CAZy. Represented phyla include Bacteroidota, Verrucomicrobiota, and Firmicutes_A from human microbiomes, all of which play notable roles in carbohydrate fermentation. Analyses of metagenomic data sets revealed that GH156s are frequently encoded in metagenomes, with a greater variety and abundance of GH156 genes observed in traditional hunter-gatherer or agriculturalist societies than in industrialized societies, particularly relative to individuals with inflammatory bowel disease (IBD). Nineteen GH156s were recombinantly expressed and assayed for sialidase activity. The five GH156 sialidases identified here share limited sequence identity to each other or the founding GH156 family member and are representative of a large subset of the family. IMPORTANCE Sialic acids occupy terminal positions of human glycans where they act as receptors for microbes, toxins, and immune signaling molecules. Microbial enzymes that remove sialic acids, sialidases, are abundant in the human microbiome where they may contribute to shaping the microbiota community structure or contribute to pathology. Furthermore, sialidases have proven to hold therapeutic potential for cancer therapy. Here, we examined the sequence space of a sialidase family of enzymes, GH156, previously unknown in the human gut environment. Our analyses suggest that human populations with disparate dietary practices harbor distinct varieties and abundances of GH156-encoding genes. Furthermore, we demonstrate the sialidase activity of 5 gut-derived GH156s. These results expand the diversity of sialidases that may contribute to host glycan degradation, and these sequences may have biotechnological or clinical utility.}, } @article {pmid36394321, year = {2022}, author = {Shetty, SA and Stege, PB and Hordijk, J and Gijsbers, E and Dierikx, CM and van Duijkeren, E and Franz, E and Willems, RJL and Paganelli, FL and Fuentes, S}, title = {Species-Specific Patterns of Gut Metabolic Modules in Dutch Individuals with Different Dietary Habits.}, journal = {mSphere}, volume = {7}, number = {6}, pages = {e0051222}, pmid = {36394321}, issn = {2379-5042}, mesh = {Adult ; Humans ; *Diet, Vegetarian ; Diet ; Diet, Vegan ; *Microbiota ; Feeding Behavior ; }, abstract = {Diet is an important determinant of the human gut microbiome. Here, we analyzed fecal metagenomes of Dutch adults following omnivorous, pescatarian, vegan, and vegetarian diets. We compared the taxonomic composition of individuals from our study with publicly available gut metagenomes from westernized and non-westernized societies. We observed that, despite long-term transition to diets rich in plant fibers (vegan or vegetarian), the microbiomes of these were typical of westernized populations, and similar in composition to omnivores. Although there were no major differences in metabolic modules, we identified differences in the species that contributed to particular functions, such as carbohydrate degradation and short-chain fatty acid metabolism. Overall, this study shows functional redundancy of the microbiomes among westernized populations, which is independent of long-term individual dietary habits. IMPORTANCE Diet is an important modulator of the human gut microbiome, which is susceptible to increased consumption of plant fibers in vegan or vegetarian lifestyles. To investigate this, we compared the gut microbiome of Dutch adults following omnivorous, pescatarian, vegan and vegetarian diets. We did not observe major differences in the gut microbiome composition and function between individuals with different dietary habits. However, we observed differences in the species that contribute to the core functions of the gut microbiome. Our study thus emphasizes the need to better understand the species-specific functional changes associated with dietary habits in the human gut microbiome.}, } @article {pmid36394280, year = {2022}, author = {Thompson, KN and Oulhote, Y and Weihe, P and Wilkinson, JE and Ma, S and Zhong, H and Li, J and Kristiansen, K and Huttenhower, C and Grandjean, P}, title = {Effects of Lifetime Exposures to Environmental Contaminants on the Adult Gut Microbiome.}, journal = {Environmental science & technology}, volume = {56}, number = {23}, pages = {16985-16995}, doi = {10.1021/acs.est.2c03185}, pmid = {36394280}, issn = {1520-5851}, mesh = {Adult ; Humans ; *Gastrointestinal Microbiome ; *Fluorocarbons ; *Environmental Pollutants/analysis ; *Polychlorinated Biphenyls/analysis ; *Hydrocarbons, Chlorinated ; *Mercury ; Hazardous Substances ; }, abstract = {Emerging experimental evidence indicates that toxicant-induced alterations in gut microbiota composition and activity may affect host homeostasis. However, data from human studies are scarce; to our knowledge, no previous studies have quantified the association of lifetime exposure to environmental chemicals, across multiple time points, with the composition of the adult gut microbiome. Here we studied 124 individuals born in the Faroe Islands in 1986-1987 who were followed approximately every seven years from birth through age 28 years. Organochlorine compounds, including polychlorinated biphenyls (PCBs) and pesticides, perfluoroalkyl substances (PFAS), and mercury (Hg), were measured in cord blood and longitudinally in participants' blood. At age 28, the gut microbiome was assessed using shotgun metagenomic sequencing. Historical contaminant exposures had little direct effect on the adult gut microbiome, while a small number of fastidious anaerobes were weakly linked to recent PFAS/PFOS exposures at age 28. In this cohort, our findings suggest no lasting effects of early life exposures on adult gut microbial composition, but proximal exposures may contribute to gut microbiome alterations. The methods developed and used for this investigation may help in future identification of small but lasting impacts of environmental toxicant exposure on the gut microbiome.}, } @article {pmid36389774, year = {2022}, author = {Fujimoto, K and Uematsu, S}, title = {Phage therapy for Clostridioides difficile infection.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1057892}, pmid = {36389774}, issn = {1664-3224}, mesh = {Humans ; *Clostridioides difficile ; *Phage Therapy ; *Clostridium Infections/therapy/microbiology ; Fecal Microbiota Transplantation ; Diarrhea/therapy ; }, abstract = {Clostridioides difficile is endemic in the intestinal tract of healthy people. However, it is responsible for many healthcare-associated infections, such as nosocomial diarrhea following antibiotic treatment. Importantly, there have been cases of unsuccessful treatment and relapse related to the emergence of highly virulent strains of C. difficile and resistance to antimicrobial agents. Fecal microbiota transplantation (FMT) is considered an effective therapy for recurrent C. difficile infection. However, its safety is of concern because deaths caused by antibiotic-resistant bacterial infections after FMT were reported. Therefore, the development of effective C. difficile-specific treatments is urgently needed. In this review, we summarize the importance of phage therapy against C. difficile, and describe a novel next-generation phage therapy developed using metagenomic data.}, } @article {pmid36389404, year = {2022}, author = {Furstenau, TN and Schneider, T and Shaffer, I and Vazquez, AJ and Sahl, J and Fofanov, V}, title = {MTSv: rapid alignment-based taxonomic classification and high-confidence metagenomic analysis.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e14292}, pmid = {36389404}, issn = {2167-8359}, mesh = {Sequence Analysis, DNA ; *Algorithms ; *Metagenome/genetics ; Databases, Nucleic Acid ; Metagenomics ; }, abstract = {As the size of reference sequence databases and high-throughput sequencing datasets continue to grow, it is becoming computationally infeasible to use traditional alignment to large genome databases for taxonomic classification of metagenomic reads. Exact matching approaches can rapidly assign taxonomy and summarize the composition of microbial communities, but they sacrifice accuracy and can lead to false positives. Full alignment tools provide higher confidence assignments and can assign sequences from genomes that diverge from reference sequences; however, full alignment tools are computationally intensive. To address this, we designed MTSv specifically for alignment-based taxonomic assignment in metagenomic analysis. This tool implements an FM-index assisted q-gram filter and SIMD accelerated Smith-Waterman algorithm to find alignments. However, unlike traditional aligners, MTSv will not attempt to make additional alignments to a TaxID once an alignment of sufficient quality has been found. This improves efficiency when many reference sequences are available per taxon. MTSv was designed to be flexible and can be modified to run on either memory or processor constrained systems. Although MTSv cannot compete with the speeds of exact k-mer matching approaches, it is reasonably fast and has higher precision than popular exact matching approaches. Because MTSv performs a full alignment it can classify reads even when the genomes share low similarity with reference sequences and provides a tool for high confidence pathogen detection with low off-target assignments to near neighbor species.}, } @article {pmid36389228, year = {2022}, author = {Bashir, Y and Khan, AU}, title = {The interplay between the gut-brain axis and the microbiome: A perspective on psychiatric and neurodegenerative disorders.}, journal = {Frontiers in neuroscience}, volume = {16}, number = {}, pages = {1030694}, pmid = {36389228}, issn = {1662-4548}, abstract = {What is the effect of our gut microbial flora on brain? Does the gut microbiome have any role in the causation of psychiatric and neurodegenerative diseases? Does the effect of gut microbiota traverse the gut-brain axis? Questions like these have captured the interest and imagination of the scientific community for quite some time now. Research in the quest for answers to these questions, to unravel the potential role of the microbiota inhabiting the gut in controlling brain functions, has progressed manifold over the last two decades. Although the possibility of microbiome as a key susceptibility factor for neurological disorders viz. Parkinson's disease, Alzheimer's disease, multiple sclerosis, and autism spectrum disorder has bolstered by an increase in the clinical and preclinical evidence, the field is still in its infancy. Given the fact that the diversity of the gut microbiota is affected by various factors including the diet and exercise, the interpretation of such data becomes all the more difficult. Also, such studies have been mostly conducted on animal models, so there is a need for randomized controlled trials in human subjects, corroborated by longitudinal studies, to establish if modulating the gut microbiota can unravel novel therapeutic interventions. Exploring the genomic, metagenomic and metabolomic data from clinical subjects with psychiatric and neurological diseases can prove to be a helpful guide in individual treatment selection.}, } @article {pmid36389176, year = {2022}, author = {Chen, H and Tang, N and Ye, Q and Yu, X and Yang, R and Cheng, H and Zhang, G and Zhou, X}, title = {Alternation of the gut microbiota in metabolically healthy obesity: An integrated multiomics analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1012028}, pmid = {36389176}, issn = {2235-2988}, mesh = {Humans ; Mice ; Animals ; *Gastrointestinal Microbiome ; *Obesity, Metabolically Benign/complications ; Obesity/complications ; Metagenomics ; }, abstract = {BACKGROUND: Although the gut microbiota may be involved in obesity onset and progression, the exact association of the gut microbiota in metabolically healthy obesity (MHO) remains largely unknown.

METHODS: An integrated paired-sample metagenomic analysis was conducted to investigate the gut microbial network and biomarkers of microbial species from the MHO and healthy non-obese subjects in the GMrepo database. Further explorations were performed in the MHO mice model using a multiomics analysis to detect changes in the composition and function of the intestinal microbiome and associated metabolites.

RESULTS: In the human study, 314 matched metagenomic data were qualified for the final analysis. We identified seven significantly changed species possibly involved in MHO pathogenesis (MHO-enriched: Bacteroides vulgatus, Megamonas sp; MHO-depleted: Butyrivibrio crossotus, Faecalibacterium prausnitzii, Bacteroides cellulosilyticus; Eubacterium siraeum; Bacteroides massiliensis). In the murine study, we found 79 significantly-changed species which may have possible associations with the MHO phenotype. The depletion of Bacteroides cellulosilyticus was commonly recognized in the human and murine MHO phenotype. Consistent with the metagenomic data, liquid chromatography-mass spectrometry (LC/MS) revealed significantly changed gut metabolites, which may promote MHO pathogenesis by altering the amino acids and lipid metabolic pathways. In the microbe-metabolites interaction analysis, we identified certain fatty acids (Dodecanedioic acid, Arachidic Acid, Mevalonic acid, etc.) that were significantly correlated with the MHO-enriched or depleted species.

CONCLUSION: This study provides insights into identifying specific microbes and metabolites that may involve in the development of obesity without metabolic disorders. Future modalities for MHO intervention may be further validated by targeting these bacteria and metabolites.}, } @article {pmid36389175, year = {2022}, author = {Deng, W and Xu, H and Wu, Y and Li, J}, title = {Diagnostic value of bronchoalveolar lavage fluid metagenomic next-generation sequencing in pediatric pneumonia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {950531}, pmid = {36389175}, issn = {2235-2988}, mesh = {Pregnancy ; Humans ; Child ; Female ; Bronchoalveolar Lavage Fluid ; *Coinfection ; Sensitivity and Specificity ; High-Throughput Nucleotide Sequencing/methods ; *Pneumonia/diagnosis ; *Viruses/genetics ; *Virus Diseases/diagnosis ; Fungi/genetics ; Bacteria/genetics ; }, abstract = {OBJECTIVES: The aim of this study was to evaluate the diagnostic value of bronchoalveolar lavage fluid (BALF) metagenomic next-generation sequencing (mNGS) versus conventional microbiological tests (CMTs) for pediatric pneumonia.

METHODS: This retrospective observational study enrolled 103 children who were diagnosed with pneumonia and hospitalized at Hubei Maternity and Child Health Care Hospital between 15 October 2020 and 15 February 2022. The pneumonia diagnosis was based on clinical manifestations, lung imaging, and microbiological tests. Pathogens in the lower respiratory tract were detected using CMTs and BALF mNGS (of DNA and RNA). The diagnostic performance of BALF mNGS was compared with that of CMTs.

RESULTS: In 96 patients, pathogens were identified by microbiological tests. The overall pathogen detection rate of mNGS was significantly higher than that of CMTs (91.3% vs. 59.2%, p = 0.000). The diagnostic performance of mNGS varied for different pathogens; however, its sensitivity and accuracy for diagnosing bacterial and viral infections were both higher than those of CMTs (p = 0.000). For the diagnosis of fungi, the sensitivity of mNGS (87.5%) was higher than that of CMTs (25%); however, its specificity and accuracy were lower than those of CMTs (p < 0.01). For the diagnosis of Mycoplasma pneumoniae, the specificity (98.8%) and accuracy (88.3%) of mNGS were high; however, its sensitivity (42.1%) was significantly lower than that of CMTs (100%) (p = 0.001). In 96 patients with definite pathogens, 52 cases (50.5%) were infected with a single pathogen, while 44 cases (42.7%) had polymicrobial infections. Virus-bacteria and virus-virus co-infections were the most common. Staphylococcus aureus, Haemophilus influenzae, rhinovirus, cytomegalovirus, parainfluenza virus, and fungi were more likely to be associated with polymicrobial infections.

CONCLUSIONS: BALF mNGS improved the detection rate of pediatric pneumonia, especially in mixed infections. The diagnostic performance of BALF mNGS varies according to pathogen type. mNGS can be used to supplement CMTs. A combination of mNGS and CMTs may be the best diagnostic strategy.}, } @article {pmid36389165, year = {2022}, author = {Li, Z and Yu, X and Guo, H and Lee, T and Hu, J}, title = {A maximum-type microbial differential abundance test with application to high-dimensional microbiome data analyses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {988717}, pmid = {36389165}, issn = {2235-2988}, support = {U54 MD000538/MD/NIMHD NIH HHS/United States ; R33 AG057382/AG/NIA NIH HHS/United States ; }, mesh = {*Data Analysis ; *Microbiota ; High-Throughput Nucleotide Sequencing ; Computer Simulation ; }, abstract = {BACKGROUND: High-throughput metagenomic sequencing technologies have shown prominent advantages over traditional pathogen detection methods, bringing great potential in clinical pathogen diagnosis and treatment of infectious diseases. Nevertheless, how to accurately detect the difference in microbiome profiles between treatment or disease conditions remains computationally challenging.

RESULTS: In this study, we propose a novel test for identifying the difference between two high-dimensional microbiome abundance data matrices based on the centered log-ratio transformation of the microbiome compositions. The test p-value can be calculated directly with a closed-form solution from the derived asymptotic null distribution. We also investigate the asymptotic statistical power against sparse alternatives that are typically encountered in microbiome studies. The proposed test is maximum-type equal-covariance-assumption-free (MECAF), making it widely applicable to studies that compare microbiome compositions between conditions. Our simulation studies demonstrated that the proposed MECAF test achieves more desirable power than competing methods while having the type I error rate well controlled under various scenarios. The usefulness of the proposed test is further illustrated with two real microbiome data analyses. The source code of the proposed method is freely available at https://github.com/Jiyuan-NYU-Langone/MECAF.

CONCLUSIONS: MECAF is a flexible differential abundance test and achieves statistical efficiency in analyzing high-throughput microbiome data. The proposed new method will allow us to efficiently discover shifts in microbiome abundances between disease and treatment conditions, broadening our understanding of the disease and ultimately improving clinical diagnosis and treatment.}, } @article {pmid36389162, year = {2022}, author = {Zhang, Y and Chen, J and Yi, X and Chen, Z and Yao, T and Tang, Z and Zang, G and Cao, X and Lian, X and Chen, X}, title = {Evaluation of the metagenomic next-generation sequencing performance in pathogenic detection in patients with spinal infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {967584}, pmid = {36389162}, issn = {2235-2988}, mesh = {Humans ; *Metagenomics/methods ; *Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Sensitivity and Specificity ; Suppuration ; }, abstract = {Spinal infection is a rarely occurred pathology, whose diagnosis remains a major challenge due to the low sensitivity of culturing techniques. Metagenomic next-generation sequencing (mNGS) is a novel approach to identify the pathogenic organisms in infectious diseases. In this study, mNGS technology was adopted for pathogenic detection in spinal infection from the tissue and pus samples. Additionally, the diagnostic performance of mNGS for spinal infection was evaluated, by comparing it with that of the conventional microbial culture, with the histopathological results as the gold standard. Overall, 56 samples from 38 patients were enrolled for mNGS testing, and 69 samples were included for microbial culture. 30 patients (78.95%) were identified to be positive by the mNGS method, which was higher than that of microbial culture (17, 44.74%). The sensitivity and specificity of mNGS with pus samples were 84.2% and 100.0%, respectively, which outperformed those of microbial culture (42.1% and 100.0%). The pathogen identification results were applied to medication guidance, and all 38 patients experienced favorable outcomes at three months, followed-up post-treatment, without any adverse effects. These findings proved that mNGS was superior to microbial culture in pathogenic identification of the spinal infection, thereby showing great promise in guiding drug administration and improving clinical outcomes.}, } @article {pmid36389151, year = {2022}, author = {Zhao, M and Yue, R and Wu, X and Gao, Z and He, M and Pan, L}, title = {The diagnostic value of metagenomic next-generation sequencing for identifying Pneumocystis jirovecii infection in non-HIV immunocompromised patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1026739}, pmid = {36389151}, issn = {2235-2988}, mesh = {Humans ; Methenamine/therapeutic use ; *Pneumocystis carinii/genetics ; *Pneumonia, Pneumocystis/diagnosis/drug therapy/microbiology ; High-Throughput Nucleotide Sequencing ; Immunocompromised Host ; }, abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) remains an important cause of morbidity and mortality in non-HIV immunocompromised patients especially in transplant recipients. But its diagnosis remains challenging due to the insuffificient performance of conventional methods for diagnosing Pneumocystis jirovecii(P. jirovecii) infection. Therefore, the auxiliary diagnostic function of metagenomics next-generation sequencing (mNGS) in clinical practice is worth of exploring.

METHOD: 34 non-HIV immunocompromised patients who were diagnosed as PJP by clinical manifestations, imaging findings, immune status of the host, and Methenamine silver staining were tested by mNGS from October 2018 to December 2020 in Sichuan Provincial People's Hospital. The clinical performances of mNGS for P. jirovecii infection diagnosis were also evaluated with genome reads abundance and comparing with other traditional diagnostic methods.

RESULTS: We diagnosed a total of 34 non-HIV PJP patients by the clinical composite diagnosis. Our data shows that, compared with the clinical microbiological test, the detection rate of mNGS for P. jirovecii in non-HIV infected PJP patients is significantly higher than that of Methenamine silver staining and serum 1-3-β-D-glucan. mNGS can be used as an auxiliary diagnostic tool to help diagnosis. The number of reads mapped to the genome of P. jirovecii and the duration of patients from onset to sampling collection were statistically significant between the two groups (Reads>100 and Reads ≤ 100) (8days vs. 23days, p=0.020). In addition, univariate analysis showed that C-reactive protein (15.8mg/L vs.79.56mg/L, p=0.016), lactate dehydrogenase (696U/l vs. 494U/l, p=0.030) and procalcitonin (0.09ng/ml vs. 0.59ng/ml, p=0.028) was also statistically significant between the two groups.

CONCLUSIONS: An effective detection rate was achieved in PJP patients using mNGS testing of bronchoalveolar lavage fluid (BALF) or blood. The study also confirmed that the abundance of reads of P. jirovecii is related to the interval between the onset and sample collection. And the inflammation status during simultaneous mNGS detection might determine the abundance of pathogens. Hence, we conclude that the mNGS strategy could benefit disease diagnosis as well as treatment when complicated clinical infections appeared.}, } @article {pmid36389134, year = {2022}, author = {Ma, W and Zhao, Y and Lu, X and Zhang, L and Ma, X and Gao, J and Hou, J and Liu, Q and Zhao, S and Yao, M and Xing, L}, title = {Negative results of bronchoalveolar lavage fluid metagenomic next-generation sequencing in critically ill patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {962283}, pmid = {36389134}, issn = {2235-2988}, mesh = {Humans ; Bronchoalveolar Lavage Fluid/microbiology ; *Negative Results ; *Critical Illness ; Retrospective Studies ; Sensitivity and Specificity ; High-Throughput Nucleotide Sequencing/methods ; Anti-Bacterial Agents ; }, abstract = {OBJECTIVE: Reports on negative results of metagenomic next-generation sequencing (mNGS) are scarce. We aimed to explore the diagnostic value of negative results in bronchoalveolar lavage fluid (BALF) mNGS and how to deal with the negative results in patients with severe respiratory disease.

METHODS: A retrospective analysis was performed on patients suspected severe community-acquired pneumonia who were admitted to the respiratory intensive care unit of the First Affiliated Hospital of Zhengzhou University from January 2020 to December 2021. According to the final diagnosis as the reference standard, the negative results of mNGS were divided into a true negative group and a false negative group. For enrolled patients, we recorded their demographic data, imaging results, laboratory results, therapeutic processes, and prognoses.

RESULTS: A total of 21 patients were enrolled in this study, including 16 true negative patients and 5 false negative patients. In the true negative group, interstitial lung diseases were the most and neoplastic diseases were following. In addition to mNGS, 9 patients underwent pathological examination, 7 patients were finally diagnosed by medical history, autoantibodies, and point-of-care (POC) ultrasound. 14 patients eventually discontinued antibiotics, 2 patients underwent antibiotic de-escalation, the average interval time of treatment adjustment was 3.56 ± 2.00 days. In the false negative group, the leading missed pathogen was fungi, followed by tuberculosis bacilli. In contrast to 2 patients underwent pathological examination, 3 patients were confirmed by routine microbiological tests.

CONCLUSIONS: Negative results of BALF mNGS can help to rule out infection, but missed diagnoses may also exist. It should be re-evaluated with other clinical informations. Pathological examination or repeated mNGS may be viable options when the diagnosis cannot be confirmed.}, } @article {pmid36389059, year = {2022}, author = {Guo, Y and Wang, S and Chao, X and Li, D and Wang, Y and Guo, Q and Chen, T}, title = {Multi-omics studies reveal ameliorating effects of physical exercise on neurodegenerative diseases.}, journal = {Frontiers in aging neuroscience}, volume = {14}, number = {}, pages = {1026688}, pmid = {36389059}, issn = {1663-4365}, abstract = {INTRODUCTION: Neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease, amyotrophic lateral sclerosis, and Huntington's disease, are heavy burdens to global health and economic development worldwide. Mounting evidence suggests that exercise, a type of non-invasive intervention, has a positive impact on the life quality of elderly with neurodegenerative diseases. X-omics are powerful tools for mapping global biochemical changes in disease and treatment.

METHOD: Three major databases were searched related to current studies in exercise intervention on neurodegenerative diseases using omics tools, including metabolomics, metagenomics, genomics, transcriptomics, and proteomics.

RESULT: We summarized the omics features and potential mechanisms associated with exercise and neurodegenerative diseases in the current studies. Three main mechanisms by which exercise affects neurodegenerative diseases were summed up, including adult neurogenesis, brain-derived neurotrophic factor (BDNF) signaling, and short-chain fatty acids (SCFAs) metabolism.

CONCLUSION: Overall, there is compelling evidence that exercise intervention is a feasible way of preventing the onset and alleviating the severity of neurodegenerative diseases. These studies highlight the importance of exercise as a complementary approach to the treatment and intervention of neurodegenerative diseases in addition to traditional treatments. More mechanisms on exercise interventions for neurodegenerative diseases, the specification of exercise prescriptions, and differentiated exercise programs should be explored so that they can actually be applied to the clinic.}, } @article {pmid36388879, year = {2022}, author = {Feng, Y and Wu, C and Huang, X and Huang, X and Peng, L and Guo, R}, title = {Case report: Successful management of Parvimonas micra pneumonia mimicking hematogenous Staphylococcus aureus pneumonia.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {1017074}, pmid = {36388879}, issn = {2296-858X}, abstract = {Parvimonas micra is an anaerobic Gram-positive coccus frequently found in the oral cavity and gastrointestinal tract, but rarely in the lung. Therefore, pneumonia caused by P. micra is also rare. Although there are some reports of P. micra related pneumonia due to aspiration or blood-borne infection with definite remote infection source, there are no reported cases of hematogenous P. micra pneumonia in healthy adults lacking a remote source of infection. Herein, we described the intact disease of P. micra-related pneumonia mimicking hematogenous Staphylococcus aureus pneumonia in terms of chest imagery and diagnosed via metagenomic next-generation sequencing (mNGS). Interestingly, there was no clear remote pathogenic source identified in the patient. Microbiome analysis revealed dysbiosis of the oral flora possibly related to poor oral hygiene and a long history of smoking. The patient was treated with moxifloxacin for 3 months. Ultimately, computed tomography (CT) of the chest showed total resolution of the lung lesion. Clinicians need to update the etiology of community-acquired pneumonia. When antibiotic therapy is not effective, pathogen examination becomes very important. New methods of pathogen detection such as mNGS should be employed to this end. For the treatment of P. micra pneumonia, no standardized course of treatment was reported. Imaging absorption of lung infections may provide a more objective guidance for the duration of antibiotics in P. micra pneumonia.}, } @article {pmid36388844, year = {2022}, author = {Nurmilah, S and Cahyana, Y and Utama, GL}, title = {Metagenomics analysis of the polymeric and monomeric phenolic dynamic changes related to the indigenous bacteria of black tea spontaneous fermentation.}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {36}, number = {}, pages = {e00774}, pmid = {36388844}, issn = {2215-017X}, abstract = {Spontaneous fermentation during black tea production involves several reactions, including the oxidation of phenolic compounds. This process has usually been studied without considering the potential involvement of indigenous tea microorganisms. This work utilised a metagenomic technique targeting bacterial 16S rRNA genes and evaluated the profile of phenolic compounds generated during the production of black tea. The resulting data were used to develop correlational and predictive functional analyses related to bacterial dynamics and the syntheses of various phenolic compounds. In particular, the genera Methylobacterium and Devosia were correlated with gallic acid and quercetin. Concurrently, the genera Sphingomonas, Chryseobacterium and Aureimonas were correlated with kaempferol, theaflavins, thearubigins and theabrownins. These results, supported by predicted functional analysis based on 16S rRNA genes associated with phenolic compounds, indicated that yfiH (polyphenol oxidase) and katG (catalase-peroxidase) are likely the dominant genes of the bacterial community involved in the black tea production process. This research suggests that bacteria could potentially contribute to the production process of black tea.}, } @article {pmid36388813, year = {2022}, author = {Guang, Y and Shen, X and Tan, Y and Tang, S and Chen, J and Zhang, L and Wang, B and Ye, S and Chen, X and Yang, C and Chen, C and Li, G and Chen, J and Cui, X and Lin, W and Wang, X and Fang, G}, title = {Systematic analysis of microbiota in pregnant Chinese women and its association with miscarriage.}, journal = {Annals of translational medicine}, volume = {10}, number = {20}, pages = {1099}, pmid = {36388813}, issn = {2305-5839}, abstract = {BACKGROUND: Miscarriage is the most common adverse pregnancy outcome and more than 50% of its incidence remains unexplained. Earlier studies have suggested that maternal microbiota might be associated with miscarriage, but the association is insufficiently understood.

METHODS: We used 16S ribosomal RNA (rRNA) amplicon sequencing and metagenomic sequencing technology to characterize the bacterial composition of three sites including the rectum, vagina, and cervix of a case group of 63 pregnant women who had miscarried compared to a control group of 24 pregnant women who underwent voluntary elective abortion.

RESULTS: The alpha-diversity from the rectum and cervix was significantly decreased in the case group relative to the control group. However, we did not find significant differences in microbial diversity of vaginal samples between the two groups. Lactobacillus was the most predominant genus in the cervix and vaginal samples. Gestational age at the time of surgery was positively associated with the rectum microbiota diversity, with an effect size of 10% (P=0.004). Host factors including gestational age and red blood count (RBC) were associated with the rectal microbiota diversity.

CONCLUSIONS: We detected a significantly lower rectal microbiota diversity and a pro-inflammatory tendency in the miscarriage group. This is the first study to investigate the association of microbiota from samples collected from three sites and miscarriage. Further studies are warranted to explore further the role of microbiota in miscarriage.}, } @article {pmid36388691, year = {2022}, author = {Obuya, S and Elkholy, A and Avuthu, N and Behring, M and Bajpai, P and Agarwal, S and Kim, HG and El-Nikhely, N and Akinyi, P and Orwa, J and Afaq, F and Abdalla, M and Michael, A and Farouk, M and Bateman, LB and Fouad, M and Saleh, M and Guda, C and Manne, U and Arafat, W}, title = {A signature of Prevotella copri and Faecalibacterium prausnitzii depletion, and a link with bacterial glutamate degradation in the Kenyan colorectal cancer patients.}, journal = {Journal of gastrointestinal oncology}, volume = {13}, number = {5}, pages = {2282-2292}, pmid = {36388691}, issn = {2078-6891}, support = {P20 GM103427/GM/NIGMS NIH HHS/United States ; P30 CA013148/CA/NCI NIH HHS/United States ; P30 CA036727/CA/NCI NIH HHS/United States ; }, abstract = {BACKGROUND: Colorectal cancer (CRC) is the fifth most diagnosed cancer in Sub-Saharan Africa. In Kenya, CRC incidence rates tripled from 1997 to 2017. In the Moi Teaching and Referral Hospital, Moi University, there has been an increase in CRC cases, notably for younger patients. A suggested pathobiology for this increase is gut microbiome dysbiosis. Since, for the Kenyan CRC patient population, microbiome studies are rare, there is a need for a better understanding of how microbiome dysbiosis influences CRC epidemiology in Kenya. In this single-center study, the focus was on profiling the gut microbiome of Kenyan CRC patients and healthy volunteers and evaluating associations between microbiome profiles and the age of CRC patients.

METHODS: The gut mucosa-associated microbiome of 18 CRC patients and 18 healthy controls were determined by 16S rRNA sequencing and analyzed for alpha and beta diversity, differential abundance, and microbial metabolic profiling.

RESULTS: Alpha diversity metrics showed no significant differences, but beta diversity metrics showed dissimilarities in the microbial communities between CRC patients and healthy controls. The most underrepresented species in the CRC group were Prevotella copri (P. copri) and Faecalibacterium prausnitzii (F. prausnitzii), although Bacteroides fragilis (B. fragilis) and Prevotella nigrescens were overrepresented (linear discriminant analysis, LDA score >2, P<0.05). Also, for CRC patients, significant metagenomic functional alterations were evident in microbial glutamate metabolic pathways (L-glutamate degradation VIII was enriched, and L-glutamate and L-glutamine biosynthesis were diminished) (P<0.05, log2 Fold Change >1). Moreover, the microbiome composition was different for patients under 40 years of age compared to older patients (LDA score >2, P<0.05).

CONCLUSIONS: Microbiome and microbial metabolic profiles of CRC patients are different from those of healthy individuals. CRC microbiome dysbiosis, particularly P. copri and F. prausnitzii depletion and glutamate metabolic alterations, are evident in Kenyan CRC patients.}, } @article {pmid36388153, year = {2022}, author = {Chen, J and Yang, L and Li, L and Goodison, S and Sun, Y}, title = {Alignment-free comparison of metagenomics sequences via approximate string matching.}, journal = {Bioinformatics advances}, volume = {2}, number = {1}, pages = {vbac077}, pmid = {36388153}, issn = {2635-0041}, support = {R01 AI125982/AI/NIAID NIH HHS/United States ; R01 CA241123/CA/NCI NIH HHS/United States ; }, abstract = {SUMMARY: Quantifying pairwise sequence similarities is a key step in metagenomics studies. Alignment-free methods provide a computationally efficient alternative to alignment-based methods for large-scale sequence analysis. Several neural network-based methods have recently been developed for this purpose. However, existing methods do not perform well on sequences of varying lengths and are sensitive to the presence of insertions and deletions. In this article, we describe the development of a new method, referred to as AsMac that addresses the aforementioned issues. We proposed a novel neural network structure for approximate string matching for the extraction of pertinent information from biological sequences and developed an efficient gradient computation algorithm for training the constructed neural network. We performed a large-scale benchmark study using real-world data that demonstrated the effectiveness and potential utility of the proposed method.

The open-source software for the proposed method and trained neural-network models for some commonly used metagenomics marker genes were developed and are freely available at www.acsu.buffalo.edu/~yijunsun/lab/AsMac.html.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36387539, year = {2022}, author = {Chompre, G and Sambolin, L and Cruz, ML and Sanchez, R and Rodriguez, Y and Rodríguez-Santiago, RE and Yamamura, Y and Appleyard, CB}, title = {A one month high fat diet disrupts the gut microbiome and integrity of the colon inducing adiposity and behavioral despair in male Sprague Dawley rats.}, journal = {Heliyon}, volume = {8}, number = {11}, pages = {e11194}, pmid = {36387539}, issn = {2405-8440}, support = {R25 GM082406/GM/NIGMS NIH HHS/United States ; }, abstract = {High-fat diet (HFD) is associated with gut microbiome dysfunction and mental disorders. However, the time-dependence as to when this occurs is unclear. We hypothesized that a short-term HFD causes colonic tissue integrity changes resulting in behavioral changes. Rats were fed HFD or low-fat diet (LFD) for a month and gut microbiome, colon, and behavior were evaluated. Behavioral despair was found in the HFD group. Although obesity was absent, the HFD group showed increased percent weight gain, epididymal fat tissue, and leptin expression. Moreover, the HFD group had increased colonic damage, decreased expression of the tight junction proteins, and higher lipopolysaccharides (LPS) in serum. Metagenomic analysis revealed that the HFD group had more Bacteroides and less S24-7 which correlated with the decreased claudin-5. Finally, HFD group showed an increase of microglia percent area, increased astrocytic projections, and decreased phospho-mTOR. In conclusion, HFD consumption in a short period is still sufficient to disrupt gut integrity resulting in LPS infiltration, alterations in the brain, and behavioral despair even in the absence of obesity.}, } @article {pmid36387171, year = {2022}, author = {Wu, Z and Zhang, S and Li, L and Huang, Z and Huang, D and Hu, Y}, title = {The gut microbiota modulates responses to anti-PD-1 and chemotherapy combination therapy and related adverse events in patients with advanced solid tumors.}, journal = {Frontiers in oncology}, volume = {12}, number = {}, pages = {887383}, pmid = {36387171}, issn = {2234-943X}, abstract = {BACKGROUND: Immune checkpoint inhibitors (ICIs) targeting programmed cell death protein 1 (PD-1) have been widely used in treating different malignancies. Several studies have reported that the gut microbiota modulates the response and adverse events (AEs) to ICIs in melanoma, non-small cell lung cancer (NSCLC), renal cell cancer and hepatocellular carcinoma, but data on other cancer types and ICI combination therapy are limited.

METHODS: Stool samples were collected from patients with cancer who received anti-PD-1 and chemotherapy combination treatment and were analyzed by fecal metagenomic sequencing. The microbiota diversity and composition were compared between the responder (R) and non-responder (NR) groups and the AE vs. the non-AE (NAE) groups. In addition, associated functional genes and metabolic pathways were identified.

RESULTS: At baseline, the microbiota diversity of the groups was similar, but the genera Parabacteroides, Clostridia bacterium UC5.1_2F7, and Bifidobacterium dentium were enriched in the R group, whereas Bacteroides dorei and 11 species of Nocardia were enriched in the NR group. At 6 weeks, the beta diversity was significantly different between the R and NR groups. Further analysis found that 35 genera, such as Alipes, Parabacteroides, Phascolarctobacterium, Collinsella, Ruminiclostridium, Porphyromonas, and Butyricimonas and several genera of the Fibrobacteraceae family, were frequently distributed in the R group, whereas 17 genera, including Enterococcus, Lachnoclostridium, Hungatella, and Bilophila and several genera of the Pseudonocardiaceae and Beijerinckiaceae families, were more abundant in the NR group. A total of 66 and 52 Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs (KOs) were significantly enriched in the R and NR groups, respectively. In addition, pathway analysis revealed functional differences in the gut microbacteria in the R group, including the enrichment of anabolic pathways and DNA damage repair (DDR) pathways. Dynamic comparisons of the bacterial composition at baseline, 6 weeks, and 12 weeks showed that the abundance of Weissella significantly increased in the R group at 6 weeks and the abundance of Fusobacterium and Anaerotruncus significantly increased in the NR group at 12 weeks. Linear discriminant analysis effect size analysis indicated that bacteria of Bacteroidetes, especially Bacteroides, were enriched in the NAE group, whereas flora of Firmcutes, such as Faecalibacterium prausnitzii, Bacteroides fragilis, and Ruminococcus lactaris, were enriched in the AE group.

CONCLUSION: Beta diversity and differences in the gut microbiota modulated AEs and the response to anti-PD-1 blockade combined with chemotherapy, by regulating related anabolic and DDR pathways. Dynamic changes in the intestinal microbiome may predict the efficacy of PD-1 inhibitor-based therapy.}, } @article {pmid36386940, year = {2022}, author = {Young, W and Maclean, P and Dunstan, K and Ryan, L and Peters, J and Armstrong, K and Anderson, R and Dewhurst, H and van Gendt, M and Dilger, RN and Dekker, J and Haggarty, N and Roy, N}, title = {Lacticaseibacillus rhamnosus HN001 alters the microbiota composition in the cecum but not the feces in a piglet model.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {1002369}, pmid = {36386940}, issn = {2296-861X}, abstract = {The probiotic Lacticaseibacillus rhamnosus strain HN001 has been shown to have several beneficial health effects for both pediatric and maternal groups, including reduced risk of eczema in infants and gestational diabetes and postnatal depression in mothers. While L. rhamnosus HN001 appears to modify immune and gut barrier biomarkers, its mode of action remains to be fully elucidated. To gain insights into the role of HN001 on the infant microbiome, the impacts of L. rhamnosus HN001 supplementation was studied in 10-day old male piglets that were fed either infant formula, or infant formula with L. rhamnosus HN001 at a low (1.3 × 10[5] CFU/ml) or high dose (7.9 × 10[6] CFU/ml) daily for 24 days. The cecal and fecal microbial communities were assessed by shotgun metagenome sequencing and host gene expression in the cecum and colon tissue was assessed by RNA-seq. Piglet fecal samples showed only modest differences between controls and those receiving dietary L. rhamnosus HN001. However, striking differences between the three groups were observed for cecal samples. While total lactobacilli were significantly increased only in the high dose L. rhamnosus HN001 group, both high and low dose groups showed an up to twofold reduction across the Firmicutes phylum and up to fourfold increase in Prevotella compared to controls. Methanobrevibacter was also decreased in HN001 fed piglets. Microbial genes involved in carbohydrate and vitamin metabolism were among those that differed in relative abundance between those with and without L. rhamnosus HN001. Changes in the cecal microbiome were accompanied by increased expression of tight junction pathway genes and decreased autophagy pathway genes in the cecal tissue of piglets fed the higher dose of L. rhamnosus HN001. Our findings showed supplementation with L. rhamnosus HN001 caused substantial changes in the cecal microbiome with likely consequences for key microbial metabolic pathways. Host gene expression changes in the cecum support previous research showing L. rhamnosus HN001 beneficially impacts intestinal barrier function. We show that fecal samples may not adequately reflect microbiome composition higher in the gastrointestinal tract, with the implication that effects of probiotic consumption may be missed by examining only the fecal microbiome.}, } @article {pmid36386713, year = {2022}, author = {Song, Y and Wen, S and Li, F and Fischer-Tlustos, A and He, Z and Guan, LL and Steele, M}, title = {Metagenomic analysis provides bases on individualized shift of colon microbiome affected by delaying colostrum feeding in neonatal calves.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1035331}, pmid = {36386713}, issn = {1664-302X}, abstract = {This study investigated the effect of colostrum feeding time on the colon digesta microbiome of 2-day-old dairy calves using whole-genome-based metagenome sequencing, aiming to understand the dynamic changes of the colon microbiome when the colostrum feeding is delayed. In total, 24 male Holstein calves were grouped to different pasteurized colostrum feeding time treatments randomly: TRT0h (45 min after birth, n = 7); TRT6h (6 h after birth, n = 8); and TRT12h (12 h after birth, n = 9). Bacteria, archaea, eukaryotes, and viruses were identified in the colon microbiome, with bacteria (99.20%) being the most predominant domain. Streptococcus, Clostridium, Lactobacillus, Ruminococcus, and Enterococcus were the top five abundant bacteria genera. For colon microbiome functions, 114 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were identified, with nutrients metabolism-related functions "carbohydrate metabolism," "amino acid metabolism," "metabolism of cofactors and vitamins," "metabolism of terpenoids and polyketides," and "metabolism of other amino acids" being the top five secondary level of KEGG hierarchy functions. When colon microbiomes were compared, they were not affected by delaying first colostrum feeding at both taxonomic and functional levels. However, distinct clusters of colon microbiome profiles were shown based on PERMANOVA analysis despite of different colostrum feeding treatment, suggesting the individualized responses. Moreover, the relative abundance of microbial taxa, microbial functions, and differentially expressed genes was compared between the two distinct clusters, and different relationships were observed among host differentially expressed genes, differential levels of microbial taxa, and microbial functions between the two clusters. Our results suggest that the host may play an important role in shaping the colon microbiome of neonatal dairy calves in response to the early life feeding management. Whether the observed colon microbiome shifts affect gut health and function in the long term requires further research.}, } @article {pmid36386712, year = {2022}, author = {Kumar, A and Karthikeyan, OP and Joshi, SJ}, title = {Editorial: Insights in microbiotechnology-2021.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1059702}, pmid = {36386712}, issn = {1664-302X}, } @article {pmid36386692, year = {2022}, author = {Wong Chin, JM and Puchooa, D and Bahorun, T and Neergheen, VS and Aullybux, AA and Beedessee, G and Nazurally, N and Alrefaei, AF and Jeewon, R}, title = {Metabarcoding assessment of fungal diversity in brown algae and sponges of Mauritius.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1003790}, pmid = {36386692}, issn = {1664-302X}, abstract = {Marine fungi are largely associated with second most inhabitants of the marine ecosystem such as sponges and algae. They are important colonizers and play vital ecological roles, such as nutrient cycling, organic matter decomposition, and symbiosis with other organisms. High throughput sequencing methods have been used successfully to reveal unknown fungal communities associated with a number of hosts particularly in the marine environment. However, the diversity of marine fungi associated with sponges and brown algae in Mauritius remains largely unknown. Traditional methods based on culturing do not provide reliable estimate of fungal diversity as only those that are able to grow under laboratory conditions are dominant; in addition, a large proportion of fungi, cultured in vitro remain most of the time unidentifiable, given that there are no sporulating structures to be examined morphologically. To overcome these limitations, we employed Illumina sequencing to unravel fungi species present in the sponges, Iotrochota sp. and Biemna sp. and the brown algae Turbinaria conoides, Sargassum pfeifferae, and Sargassum obovatum, collected from the north of Mauritius. Diversity analyses revealed that Biemna sp. had the highest diversity from the sampled sponges with fungi from 24 orders being recovered while from brown algae; Turbinaria conoides had the highest diversity with recovery of fungal taxa of the orders Botryosphaeriales, Chaetothyriales, Eurotiales, Hypocreales, and Mucorales with the latter four orders being common in both sampled algae and sponges. Beta diversity analyses revealed clustering only in the algae, Turbinaria conoides, and Sargassum pfeifferae and not in the co-occurring sponges, indicating that sampling location did not have much influence on fungal diversity. Our findings provide the first amplicon sequencing based insights of the fungal communities associated with macro-algae and sponges in Mauritius and supplements research on the fungal community existing in the oceans around the world.}, } @article {pmid36386689, year = {2022}, author = {Ma, P and Sun, C and Liu, M and You, H and Shen, Y and Kang, Y and Sun, Y and Yang, Z and Ma, P and Yang, L and Xue, F}, title = {Metagenomic insights into the rumen epithelial integrity responses to the vitamin B1 supplement under high-concentrate diets treatments.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1008373}, pmid = {36386689}, issn = {1664-302X}, abstract = {Subacute ruminal acidosis (SARA) becomes the most common nutritional metabolic disease in high-yielding dairy cows and later fatting beef cattle because of the increasing consumption of high-concentrate diets in modern feeding patterns. Our previous research found a certain piece of evidence that adding 180 mg thiamine/kg DMI could increase the rumen pH and regulate the structure of the rumen microbial community in vivo. However, there is still limited experimental data on the effects of SARA on thiamine status, the damage to the structure of rumen epithelial cells, and the underlying mechanism of the epithelium alterations. For this purpose, a total of 18 Angus bulls (average 22.0-months-old) with an average live weight of 567.6 ± 27.4 kg were randomly allocated into a control treatment (CON), a high-concentrate diet treatment (HC), and a high-concentrate diet with the vitamin B1 supplement treatment (HCB). All bulls were conducted with a 7-day adjustment period followed by a 60-day-long main feeding procedure. Results indicated that ADFI and ADG significantly decreased in the HC treatment compared with CON (P < 0.05), while significantly increased after the VB1 supplement (P < 0.05). Besides, ruminal acetate content was significantly downregulated while propionate was significantly upregulated under the HC treatment compared with CON (P < 0.05); however, these alterations showed a completely inverse regulatory effect on the VB1 supplement compared with HC (P < 0.05). These changes causatively induced a significant decrease in the A/P ratio in the HC treatment compared with CON and HCB treatments (P < 0.05). Bacterial communities in the HC treatment could be separated from those in CON through PCoA axes 1 and 2. Meanwhile, the VB1 supplement significantly altered the bacterial communities compared with the HC treatment, except for HCB-3. Furthermore, the HC treatment significantly upregulated the expression of JNK, Bax, Caspase-8, Caspase-3, Caspase-9, and Cyt-C compared with CON, while significantly downregulated the expression of Bcl-2. The VB1 supplement showed a complete converse gene expression compared with HC. In conclusion, the VB1 supplement could effectively attenuate the alterations that occurred when exposed to high-concentrate diets, and help promote production performance through increased fermentability.}, } @article {pmid36386679, year = {2022}, author = {Kok, NA and Peker, N and Schuele, L and de Beer, JL and Rossen, JWA and Sinha, B and Couto, N}, title = {Host DNA depletion can increase the sensitivity of Mycobacterium spp. detection through shotgun metagenomics in sputum.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {949328}, pmid = {36386679}, issn = {1664-302X}, abstract = {Identification and phenotypic drug-susceptibility testing for mycobacteria are time-consuming and challenging but essential for managing mycobacterial infections. Next-generation sequencing (NGS) technologies can increase diagnostic speed and quality, but standardization is still lacking for many aspects (e.g., unbiased extraction, host depletion, bioinformatic analysis). Targeted PCR approaches directly on sample material are limited by the number of targets that can be included. Unbiased shotgun metagenomics on direct material is hampered by the massive amount of host DNA, which should be removed to improve the microbial detection sensitivity. For this reason, we developed a method for NGS-based diagnosis of mycobacteria directly from patient material. As a model, we used the non-tuberculous mycobacterium (NTM) Mycobacterium abscessus. We first compared the efficiency of three different DNA extraction kits for isolating DNA (quality and concentration). The two most efficient kits were then used in a follow-up study using artificial sputum. Finally, one extraction kit was selected and further evaluated for DNA isolation from a patients' sputum mixture spiked with M. abscessus at three concentrations (final concentrations 10[8], 10[7], 10[6] CFU/ml). The spiked sputum samples were processed with and without saponin treatment (ST) in combination with DNAse treatment prior to bacterial DNA extraction to evaluate the recovery of bacteria and depletion of host DNA by PCR and Illumina sequencing. While Ct values of the qPCR targeting mycobacterial ITS DNA remained rather stable, Ct values in the qPCR targeting the human β-actin gene increased by five Ct values in ST samples. In subsequent Illumina sequencing, a decrease of 89% of reads mapped to the human genome was observed in ST samples. The percentage of reads mapped to M. abscessus (10[8] CFU/ml) increased by 89%, and the sequencing depth increased two times when undergoing ST. In conclusion, the sensitivity of M. abscessus detection in artificial sputum was increased using a saponin pre-treatment step. The saponin followed by the DNase I treatment approach could be efficiently applied to detect and characterize mycobacterial infections, including tuberculosis, directly from sputum.}, } @article {pmid36386659, year = {2022}, author = {Chen, L and Sun, M and Xu, D and Gao, Z and Shi, Y and Wang, S and Zhou, Y}, title = {Gut microbiome of captive wolves is more similar to domestic dogs than wild wolves indicated by metagenomics study.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1027188}, pmid = {36386659}, issn = {1664-302X}, abstract = {Adaptation during the domestication from wolves (Canis lupus) to dogs (Canis lupus familiaris) is a debated ecological topic. Changes in food and environment are major divergences in the domestication of dogs. Gut microbes play an important role in animal adaptation to the food and environmental changes. In this study, shotgun sequencing was performed to compare the species diversity and functional diversity of gut microbes in wild wolves (group CLW, n = 3), captive wolves (group CLC, n = 4), and domestic dogs (group CLF, n = 4). The results found that Bacteroidetes, Firmicutes, Fusobacteria, Proteobacteria and Actinobacteria were the most abundant phyla and Bacteroides, Fusobacterium, Prevotella, Megamonas, Paraprevotella, Faecalibacterium, Clostridium were the most abundant genera in the gut of wolves and dogs. Groups CLW, CLC and CLF have shown significant difference in gut microbial species diversity and functional diversity. Bacteroides, Fusobacterium and Faecalibacterium were most abundant genera in groups CLW, CLC and CLF, respectively. Their abundance varied significantly among groups. Compared to the wild wolves, the intestinal microbiol genes of domestic dogs were significantly enriched in the carbohydrate metabolism pathway of KEGG database. One hundred and seventy-seven enzymes were detected with significantly higher abundance in group CLF than that in group CLW, and 49 enzymes showed extremely significant higher abundance in group CLF than that in group CLW (q < 0.01) base on the function abundance annotated in CAZy database. It is noteworthy that there were also significant differences in the abundance of 140 enzymes between groups CLC and CLW (q < 0.05). Clustering analysis based on both the species and the function abundance of intestinal microbiota all found that groups CLC and CLF clustered into one branch, while samples from group CLW clustered into the other branch. This result suggests that captive wolves are more similar to domestic dogs than wild wolves in both species composition and function composition of intestinal microbiota.}, } @article {pmid36386643, year = {2022}, author = {Chen, J and Li, F and Zhao, X and Wang, Y and Zhang, L and Yan, L and Yu, L}, title = {Change in composition and potential functional genes of microbial communities on carbonatite rinds with different weathering times.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1024672}, pmid = {36386643}, issn = {1664-302X}, abstract = {Organisms and time are important factors for rock weathering to form soils. However, weathering time is usually difficult to quantitatively study, and the potential microorganisms involved in rock weathering are difficult to identify qualitatively. Currently, there is no clear conclusion on how ecological strategies of carbonatite weathering rind microorganisms change with weathering time, and how the microbial composition and functional genes involved in element cycling change over two century-scale weathering time. In this study, we selected abandoned carbonate tombstones as the subject and used the date when the tombstones were erected by humans as the onset of weathering. Using metagenome sequencing methods, we investigated the trends in the composition of fungal, bacterial and archaeal communities of carbonate weathering rind and related elemental cycle functional genes during a weathering time of 19 to 213 years. The results showed that: (1) with the increase in weathering time, at the phylum level, microbial taxa gradually shifted from r-strategists (faster turnover rates, higher mortality rates, higher reproduction, lower competition rate) to K-strategists (slower turnover rates, lower mortality rates, lower reproduction, higher competition rate), which correspondingly increased the abundance of functional genes related to C and N cycles. (2) The properties of the parent rock layer determines the colonization and distribution of weathering rind microorganisms (especially prokaryotic microorganisms) and the corresponding functional gene abundance. Our study provides new insights into the weathering process of carbonate rocks.}, } @article {pmid36386640, year = {2022}, author = {Gao, H and Wang, J and Zhang, S and Li, T}, title = {A Case Report of Two Kala-Azar Cases in China Diagnosed by Metagenomic Next-Generation Sequencing.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {922894}, pmid = {36386640}, issn = {1664-302X}, abstract = {BACKGROUND: Leishmaniasis being a local disease, as kala-azar this particular form is a visceral form. It is transmitted by sandflies, and is a parasitic disease involving the reticuloendothelial system of mononuclear macrophages. Due to its poor prognosis and high fatality rate, the fatality rate of patients without effective treatment can exceed 95%. Thereby, early diagnosis and treatment can significantly improve its prognosis. The metagenomic next-generation sequencing (mNGS) has the advantage of being able to find pathogens that cannot be detected by traditional methods. More importantly, it can conduct nucleic acid detection of pathogens covering a wide range in a short time. For infectious diseases like kala-azar, which is clinically complicated and difficult, mNGS detection provides a basis for accurate etiological diagnosis.

CASE REPORT: We report 2 cases of kala-azar in West China Hospital, Chengdu, China. The first case is a 47-year-old male patient who had recurrent fever for 4 months, accompanied by reduction of red blood cell, white blood cell, and blood platelet. He was detected by mNGS and clinically diagnosed as kala-azar (Leishmania detection), finally died of multiple organ failure. The second patient was a 15-year-old male who had fever for more than 10 days. He was detected by mNGS and clinically diagnosed as kala-azar (Leishmania detection). He recovered and discharged quickly after treatment with sodium stibogluconate.

CONCLUSION: Efforts should be made to improve early etiological diagnosis in order to improve patient prognosis. mNGS detection is beneficial to the diagnosis and treatment of infectious diseases with unknown causes in the early stage of emergency treatment.}, } @article {pmid36386615, year = {2022}, author = {Zhang, X and Wu, K and Han, Z and Chen, Z and Liu, Z and Sun, Z and Shao, L and Zhao, Z and Zhou, L}, title = {Microbial diversity and biogeochemical cycling potential in deep-sea sediments associated with seamount, trench, and cold seep ecosystems.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1029564}, pmid = {36386615}, issn = {1664-302X}, abstract = {Due to their extreme water depths and unique physicochemical conditions, deep-sea ecosystems develop uncommon microbial communities, which play a vital role in biogeochemical cycling. However, the differences in the compositions and functions of the microbial communities among these different geographic structures, such as seamounts (SM), marine trenches (MT), and cold seeps (CS), are still not fully understood. In the present study, sediments were collected from SM, MT, and CS in the Southwest Pacific Ocean, and the compositions and functions of the microbial communities were investigated by using amplicon sequencing combined with in-depth metagenomics. The results revealed that significantly higher richness levels and diversities of the microbial communities were found in SM sediments, followed by CS, and the lowest richness levels and diversities were found in MT sediments. Acinetobacter was dominant in the CS sediments and was replaced by Halomonas and Pseudomonas in the SM and MT sediments. We demonstrated that the microbes in deep-sea sediments were diverse and were functionally different (e.g., carbon, nitrogen, and sulfur cycling) from each other in the seamount, trench, and cold seep ecosystems. These results improved our understanding of the compositions, diversities and functions of microbial communities in the deep-sea environment.}, } @article {pmid36386613, year = {2022}, author = {Shafranskaya, D and Kale, V and Finn, R and Lapidus, AL and Korobeynikov, A and Prjibelski, AD}, title = {MetaGT: A pipeline for de novo assembly of metatranscriptomes with the aid of metagenomic data.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {981458}, pmid = {36386613}, issn = {1664-302X}, abstract = {While metagenome sequencing may provide insights on the genome sequences and composition of microbial communities, metatranscriptome analysis can be useful for studying the functional activity of a microbiome. RNA-Seq data provides the possibility to determine active genes in the community and how their expression levels depend on external conditions. Although the field of metatranscriptomics is relatively young, the number of projects related to metatranscriptome analysis increases every year and the scope of its applications expands. However, there are several problems that complicate metatranscriptome analysis: complexity of microbial communities, wide dynamic range of transcriptome expression and importantly, the lack of high-quality computational methods for assembling meta-RNA sequencing data. These factors deteriorate the contiguity and completeness of metatranscriptome assemblies, therefore affecting further downstream analysis. Here we present MetaGT, a pipeline for de novo assembly of metatranscriptomes, which is based on the idea of combining both metatranscriptomic and metagenomic data sequenced from the same sample. MetaGT assembles metatranscriptomic contigs and fills in missing regions based on their alignments to metagenome assembly. This approach allows to overcome described complexities and obtain complete RNA sequences, and additionally estimate their abundances. Using various publicly available real and simulated datasets, we demonstrate that MetaGT yields significant improvement in coverage and completeness of metatranscriptome assemblies compared to existing methods that do not exploit metagenomic data. The pipeline is implemented in NextFlow and is freely available from https://github.com/ablab/metaGT.}, } @article {pmid36386421, year = {2022}, author = {Gao, S and Li, L and Zhou, X and Dai, X and Lu, L and Chen, Y and Han, J and Huang, X and Xiao, Q and He, H and Liu, Q}, title = {Fatal Rickettsia Japonica Infection Complicating Disseminated Intravascular Coagulation in Yichang, China.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {6613-6623}, pmid = {36386421}, issn = {1178-6973}, abstract = {BACKGROUND: Severe complications may cause a fatal or disabling outcome in patients with Rickettsia japonica infection but are poorly understood.

METHODS: We identified 11 patients with only Rickettsia japonica infection with metagenomics next generation sequencing (mNGS) during April to November 2021 at Yichang Central People's Hospital, China. Clinical data were obtained through review of medical records.

RESULTS: Most patients realized that they had symptoms about one or two days after being bitten. Fever (91%), pulmonary effusion (91%), rash or erythema (100%), abnormal urine (100%), neutropenia (100%), lymphopenia (100%), and thrombocytopenia (100%) were the most common clinical signs. Six severely ill patients were admitted to the intensive care unit and five had mild symptoms. Systemic manifestations such as vomiting (83%), neurological manifestations (100%), and disseminated intravascular coagulation (100%) were more frequently observed in the severe cases, 33.3% of whom developed purpura fulminans requiring amputation or skin graft, and 16.6% died two days after admission. Some patients experienced sequelae.

CONCLUSION: Our study found that patients with critical Rickettsia japonica infection complicating disseminated intravascular coagulation had high risk of poor outcome.}, } @article {pmid36386420, year = {2022}, author = {Shi, Y and Wu, J and Liu, T and Yue, L and Liu, Y and Gu, Y and Qi, Y}, title = {Analysis of Metagenomic Next-Generation Sequencing Results of 25 Pus Samples.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {6515-6524}, pmid = {36386420}, issn = {1178-6973}, abstract = {PURPOSE: To explore the clinical value of detecting pathogens in pus samples by metagenomic next-generation sequencing (mNGS).

METHODS: The 25 pus samples from infected patients were collected in this research. The positive rate and consistency of pathogenic bacteria detected by mNGS and conventional methods were compared. The pathogen types detected by the two methods were analyzed. Furthermore, the modifications of antibiotic treatment therapy were also evaluated based on mNGS results.

RESULTS: The sensitivity of mNGS method in detecting pathogenic bacteria in pus samples was better than that of conventional method (96% vs 40%; P < 0.01). Only 10 samples were detected pathogens by conventional methods, but 24 samples were detected by mNGS method. In specific, the results of conventional methods showed 10 samples had 11 kinds of pathogenic bacteria, of which 9 samples were single pathogen and 1 sample had two kinds of pathogenic bacteria. The results of mNGS method showed 24 samples were detected with 54 kinds of pathogenic bacteria, of which 15 samples were detected with single pathogen, and 9 samples were detected with two or more kinds of pathogenic bacteria. The two methods had 9(36%) consistent results, 14 (56%) completely different results, and 2 (8%) partially consistent results, and the kappa value was 0.19. Notably, mNGS could detect viruses, anaerobic bacteria, and other uncommon pathogens simultaneously.

CONCLUSION: The application of mNGS in the detection of pus specimens from different parts not only have high accuracy rate and also reduce the turnaround time of diagnosis. In addition, the performance of mNGS detection of anaerobic bacteria and caustic bacteria is better than conventional methods. The mNGS diagnosis in pus sample may play an important role in clinical diagnosis and treatment strategy decisions.}, } @article {pmid36386026, year = {2022}, author = {Xiao, YL and Xu, ZG and Wang, JX and Fang, XL and Fu, Y}, title = {Complete mitochondrial genome of a Eurytopic midge, Polypedilum nubifer (Diptera: Chironomidae).}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {7}, number = {11}, pages = {1936-1938}, pmid = {36386026}, issn = {2380-2359}, abstract = {The complete mitochondrial genome of Polypedilum nubifer was sequenced and annotated, and its general features and base composition were analyzed. The mitogenome was 15,896 bp long, comprising 13 protein-coding genes, 22 transport RNA genes, 2 ribosomal RNA genes, and 1 control region. The phylogenetic relationships based on the concatenated nucleotide sequences of 17 metagenomes from families Chironomidae, Ceratopogonidae, and Simuliidae were reconstructed. According to the phylogenetic topologies, P. nubifer was closely related to (P. unifascium + P. vanderplanki) in the maximum likelihood tree.}, } @article {pmid36385454, year = {2023}, author = {Zhou, Y and Zhou, L and Yan, S and Chen, L and Krupovic, M and Wang, Y}, title = {Diverse viruses of marine archaea discovered using metagenomics.}, journal = {Environmental microbiology}, volume = {25}, number = {2}, pages = {367-382}, doi = {10.1111/1462-2920.16287}, pmid = {36385454}, issn = {1462-2920}, mesh = {*Archaea/genetics/virology ; *Archaeal Viruses/genetics ; Genome, Viral ; Metagenomics/methods ; Phylogeny ; Viral Proteins/genetics ; }, abstract = {During the past decade, metagenomics became a method of choice for the discovery of novel viruses. However, host assignment for uncultured viruses remains challenging, especially for archaeal viruses, which are grossly undersampled compared to viruses of bacteria and eukaryotes. Here, we assessed the utility of CRISPR spacer targeting, tRNA gene matching and homology searches for viral signature proteins, such as major capsid proteins, for the assignment of archaeal hosts and validated these approaches on metaviromes from Yangshan Harbor (YSH). We report 35 new genomes of viruses which could be confidently assigned to hosts representing diverse lineages of marine archaea. We show that the archaeal YSH virome is highly diverse, with some viruses enriching the previously described virus groups, such as magroviruses of Marine Group II Archaea (Poseidoniales), and others representing novel groups of marine archaeal viruses. Metagenomic recruitment of Tara Oceans datasets on the YSH viral genomes demonstrated the presence of YSH Poseidoniales and Nitrososphaeria viruses in the global oceans, but also revealed the endemic YSH-specific viral lineages. Furthermore, our results highlight the relationship between the soil and marine thaumarchaeal viruses. We propose three new families within the class Caudoviricetes for the classification of the five complete viral genomes predicted to replicate in marine Poseidoniales and Nitrososphaeria, two ecologically important and widespread archaeal groups. This study illustrates the utility of viral metagenomics in exploring the archaeal virome and provides new insights into the diversity, distribution and evolution of marine archaeal viruses.}, } @article {pmid36384555, year = {2022}, author = {Huang, L and Yi, F and Zhan, C and Lai, K}, title = {Aspergillus tracheobronchitis with Birt-Hogg-Dubè syndrome as a rare cause of chronic cough.}, journal = {BMC pulmonary medicine}, volume = {22}, number = {1}, pages = {420}, pmid = {36384555}, issn = {1471-2466}, mesh = {Humans ; Middle Aged ; *Birt-Hogg-Dube Syndrome/complications/diagnosis/genetics ; Cough/etiology ; Neoplasm Recurrence, Local ; *Bronchitis ; Germ-Line Mutation ; }, abstract = {BACKGROUND: Aspergillus tracheobronchitis (ATB) is confined as a condition of chronic superficial infection of tracheobronchial tree. Its diagnosis is difficult due to atypical manifestations and low detective rate of Aspergillus thus far.

CASE PRESENTATION: Herein, we presented a 45-year-old male patient with a sole chronic productive cough for five years referred to our cough specialist clinic. Chest high-resolution computed tomography showed multiple lung cysts predominantly located in the subpleural lesions and near the mediastinum. Neither bacteria nor fungi were identified by sputum culture. However, metagenomic next-generation sequencing in sputum detected Aspergillus fumigatus DNA. The genetic testing of whole blood suggested the germline mutation of the tumor suppressor gene folliculin, supporting a diagnosis of Birt-Hogg-Dubé (BHD) syndrome. His productive cough symptom significantly improved after receiving itraconazole treatment for 2 months. After discontinuation of antifungal treatment, there was no relapse for four months follow-up. A diagnosis of ATB with BHD syndrome was eventually established in this patient.

CONCLUSION: ATB should be considered in any patient with prolonged unexplained productive cough. Next-generation sequencing technologies may be useful to identify ATB which is uncommon and easily ignored in clinical practice.}, } @article {pmid36383786, year = {2022}, author = {Sánchez-Reyes, A and Fernández-López, MG}, title = {Sketched reference databases for genome-based taxonomy and comparative genomics.}, journal = {Brazilian journal of biology = Revista brasleira de biologia}, volume = {84}, number = {}, pages = {e256673}, doi = {10.1590/1519-6984.256673}, pmid = {36383786}, issn = {1678-4375}, mesh = {Phylogeny ; *Proteomics ; *Proteome ; Genomics ; Computational Biology ; }, abstract = {The analysis of curated genomic, metagenomic and proteomic data is of paramount importance in the fields of biology, medicine, education, and bioinformatics. Although this type of data is usually hosted in raw format on free international repositories, the full access requires lots of computing power and large storage disk space for the domestic user. The purpose of the study is to offer a comprehensive set of microbial genomic and proteomic reference databases in an accessible and easy-to-use form to the scientific community and demonstrate its advantages and usefulness. Also, we present a case study on the applicability of the sketched data, for the determination of overall genomic coherence between two members of the Brucellacea family, which suggests they belong to the same genomospecies that remain as discrete ecotypes. A representative set of genomes, proteomes (from type material), and metagenomes were directly collected from the NCBI Assembly database and Genome Taxonomy Database (GTDB), associated with the major groups of Bacteria, Archaea, Virus, and Fungi. Sketched databases were subsequently created and stored on handy reduced representations by using the MinHash algorithm implemented in Mash software. The obtained dataset contains more than 133 GB of space disk reduced to 883.25 MB and represents 125,110 genomics/proteomic records from eight informative contexts, which have been prefiltered to make them accessible, usable, and user-friendly with limited computational resources. Potential uses of these sketched databases are discussed, including but not limited to microbial species delimitation, estimation of genomic distances and genomic novelties, paired comparisons between proteomes, genomes, and metagenomes; phylogenetic neighbor's exploration and selection, among others.}, } @article {pmid36383678, year = {2022}, author = {Ghaly, TM and Tetu, SG and Penesyan, A and Qi, Q and Rajabal, V and Gillings, MR}, title = {Discovery of integrons in Archaea: Platforms for cross-domain gene transfer.}, journal = {Science advances}, volume = {8}, number = {46}, pages = {eabq6376}, pmid = {36383678}, issn = {2375-2548}, abstract = {Horizontal gene transfer between different domains of life is increasingly being recognized as an important evolutionary driver, with the potential to increase the pace of biochemical innovation and environmental adaptation. However, the mechanisms underlying the recruitment of exogenous genes from foreign domains are mostly unknown. Integrons are a family of genetic elements that facilitate this process within Bacteria. However, they have not been reported outside Bacteria, and thus their potential role in cross-domain gene transfer has not been investigated. Here, we discover that integrons are also present in 75 archaeal metagenome-assembled genomes from nine phyla, and are particularly enriched among Asgard archaea. Furthermore, we provide experimental evidence that integrons can facilitate the recruitment of archaeal genes by bacteria. Our findings establish a previously unknown mechanism of cross-domain gene transfer whereby bacteria can incorporate archaeal genes from their surrounding environment via integron activity. These findings have important implications for prokaryotic ecology and evolution.}, } @article {pmid36383677, year = {2022}, author = {Zheng, D and Yin, G and Liu, M and Hou, L and Yang, Y and Van Boeckel, TP and Zheng, Y and Li, Y}, title = {Global biogeography and projection of soil antibiotic resistance genes.}, journal = {Science advances}, volume = {8}, number = {46}, pages = {eabq8015}, pmid = {36383677}, issn = {2375-2548}, mesh = {Humans ; *Soil ; *Anti-Bacterial Agents/pharmacology ; Soil Microbiology ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; }, abstract = {Although edaphic antibiotic resistance genes (ARGs) pose serious threats to human well-being, their spatially explicit patterns and responses to environmental constraints at the global scale are not well understood. This knowledge gap is hindering the global action plan on antibiotic resistance launched by the World Health Organization. Here, a global analysis of 1088 soil metagenomic samples detected 558 ARGs in soils, where ARG abundance in agricultural habitats was higher than that in nonagricultural habitats. Soil ARGs were mostly carried by clinical pathogens and gut microbes that mediated the control of climatic and anthropogenic factors to ARGs. We generated a global map of soil ARG abundance, where the identified microbial hosts, agricultural activities, and anthropogenic factors explained ARG hot spots in India, East Asia, Western Europe, and the United States. Our results highlight health threats from soil clinical pathogens carrying ARGs and determine regions prioritized to control soil antibiotic resistance worldwide.}, } @article {pmid36383001, year = {2022}, author = {Pimentel, ZT and Thibodeau, PS and Song, B and Zhang, Y}, title = {A Mollicutes Metagenome-Assembled Genome from the Gut of the Pteropod Limacina rangii.}, journal = {Microbiology resource announcements}, volume = {11}, number = {12}, pages = {e0075222}, pmid = {36383001}, issn = {2576-098X}, support = {OCE 1737258//National Science Foundation (NSF)/ ; OIA 165522//National Science Foundation (NSF)/ ; PLR 1440435//National Science Foundation (NSF)/ ; NSF OIA-1929078//National Science Foundation (NSF)/ ; OCE 1321373//National Science Foundation (NSF)/ ; }, abstract = {A nearly complete genome of an uncultured Mollicutes sp. was obtained from the metagenome of the gut of Limacina rangii (open-ocean snail), an important grazer and prey for higher trophic animals along the rapidly warming region of the western Antarctic Peninsula.}, } @article {pmid36382407, year = {2023}, author = {Bonin, N and Doster, E and Worley, H and Pinnell, LJ and Bravo, JE and Ferm, P and Marini, S and Prosperi, M and Noyes, N and Morley, PS and Boucher, C}, title = {MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D744-D752}, pmid = {36382407}, issn = {1362-4962}, support = {R01 AI141810/AI/NIAID NIH HHS/United States ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; *Anti-Infective Agents ; Software ; High-Throughput Nucleotide Sequencing ; }, abstract = {Antimicrobial resistance (AMR) is considered a critical threat to public health, and genomic/metagenomic investigations featuring high-throughput analysis of sequence data are increasingly common and important. We previously introduced MEGARes, a comprehensive AMR database with an acyclic hierarchical annotation structure that facilitates high-throughput computational analysis, as well as AMR++, a customized bioinformatic pipeline specifically designed to use MEGARes in high-throughput analysis for characterizing AMR genes (ARGs) in metagenomic sequence data. Here, we present MEGARes v3.0, a comprehensive database of published ARG sequences for antimicrobial drugs, biocides, and metals, and AMR++ v3.0, an update to our customized bioinformatic pipeline for high-throughput analysis of metagenomic data (available at MEGLab.org). Database annotations have been expanded to include information regarding specific genomic locations for single-nucleotide polymorphisms (SNPs) and insertions and/or deletions (indels) when required by specific ARGs for resistance expression, and the updated AMR++ pipeline uses this information to check for presence of resistance-conferring genetic variants in metagenomic sequenced reads. This new information encompasses 337 ARGs, whose resistance-conferring variants could not previously be confirmed in such a manner. In MEGARes 3.0, the nodes of the acyclic hierarchical ontology include 4 antimicrobial compound types, 59 resistance classes, 233 mechanisms and 1448 gene groups that classify the 8733 accessions.}, } @article {pmid36382399, year = {2023}, author = {Chen, IA and Chu, K and Palaniappan, K and Ratner, A and Huang, J and Huntemann, M and Hajek, P and Ritter, SJ and Webb, C and Wu, D and Varghese, NJ and Reddy, TBK and Mukherjee, S and Ovchinnikova, G and Nolan, M and Seshadri, R and Roux, S and Visel, A and Woyke, T and Eloe-Fadrosh, EA and Kyrpides, NC and Ivanova, NN}, title = {The IMG/M data management and analysis system v.7: content updates and new features.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D723-D732}, pmid = {36382399}, issn = {1362-4962}, mesh = {*Genomics ; *Data Management ; Genome, Bacterial ; Software ; Genome, Archaeal ; Databases, Genetic ; Metagenome ; }, abstract = {The Integrated Microbial Genomes & Microbiomes system (IMG/M: https://img.jgi.doe.gov/m/) at the Department of Energy (DOE) Joint Genome Institute (JGI) continues to provide support for users to perform comparative analysis of isolate and single cell genomes, metagenomes, and metatranscriptomes. In addition to datasets produced by the JGI, IMG v.7 also includes datasets imported from public sources such as NCBI Genbank, SRA, and the DOE National Microbiome Data Collaborative (NMDC), or submitted by external users. In the past couple years, we have continued our effort to help the user community by improving the annotation pipeline, upgrading the contents with new reference database versions, and adding new analysis functionalities such as advanced scaffold search, Average Nucleotide Identity (ANI) for high-quality metagenome bins, new cassette search, improved gene neighborhood display, and improvements to metatranscriptome data display and analysis. We also extended the collaboration and integration efforts with other DOE-funded projects such as NMDC and DOE Biology Knowledgebase (KBase).}, } @article {pmid36380386, year = {2022}, author = {Li, X and Song, J and Shi, X and Huang, M and Liu, L and Yi, G and Yang, N and Xu, G and Zheng, J}, title = {FMO3 deficiency of duck leads to decreased lipid deposition and increased antibacterial activity.}, journal = {Journal of animal science and biotechnology}, volume = {13}, number = {1}, pages = {119}, pmid = {36380386}, issn = {1674-9782}, abstract = {BACKGROUND: Most duck eggs possess a fishy odor, indicating that ducks generally exhibit impaired trimethylamine (TMA) metabolism. TMA accumulation is responsible for this unpleasant odor, and TMA metabolism plays an essential role in trimethylaminuria (TMAU), also known as fish odor syndrome. In this study, we focused on the unusual TMA metabolism mechanism in ducks, and further explored the unclear reasons leading to the debilitating TMA metabolism.

METHODS: To achieve this, transcriptome, proteome, and metagenome analyses were first integrated based on the constructed duck populations with high and low TMA metabolism abilities. Additionally, further experiments were conducted to validate the hypothesis regarding the limited flavin-containing monooxygenase 3 (FMO3) metabolism ability of ducks.

RESULTS: The study demonstrated that liver FMO3 and cecal microbes, including Akkermansia and Mucispirillum, participated in TMA metabolism in ducks. The limited oxidation ability of FMO3 explains the weakening of TMA metabolism in ducks. Nevertheless, it decreases lipid deposition and increases antibacterial activity, contributing to its survival and reproduction during the evolutionary adaptation process.

CONCLUSIONS: This study demonstrated the function of FMO3 and intestinal microbes in regulating TMA metabolism and illustrated the biological significance of FMO3 impairment in ducks.}, } @article {pmid36380056, year = {2022}, author = {Zhang, C and Shi, Y and Burch, M and Olthoff, B and Ericsson, AC and Franklin, CL}, title = {Transfer efficiency and impact on disease phenotype of differing methods of gut microbiota transfer.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {19621}, pmid = {36380056}, issn = {2045-2322}, support = {U42 OD010918/OD/NIH HHS/United States ; }, mesh = {Mice ; Animals ; *Gastrointestinal Microbiome/genetics ; Fecal Microbiota Transplantation/methods ; *Colitis/chemically induced/genetics ; Phenotype ; *Microbiota ; Dextran Sulfate/adverse effects ; Disease Models, Animal ; Mice, Inbred C57BL ; }, abstract = {To test causal relationships between complex gut microbiota (GM) and host outcomes, researchers frequently transfer GM between donor and recipient mice via embryo transfer (ET) rederivation, cross-fostering (CF), and co-housing. In this study, we assess the influence of the transfer method and the differences in baseline donor and recipient microbiota richness, on transfer efficiency. Additionally, recipient mice were subjected to DSS-induced chronic colitis to determine whether disease severity was affected by GM transfer efficiency or features within the GM. We found that the recipient's genetic background, the baseline richness of donor and recipient GM, and the transfer method all influenced the GM transfer efficiency. Recipient genetic background and GM both had significant effects on DSS colitis severity and, unexpectedly, the transfer method was strongly associated with differential disease severity regardless of the other factors.}, } @article {pmid36379985, year = {2022}, author = {Bovo, S and Utzeri, VJ and Ribani, A and Taurisano, V and Schiavo, G and Fontanesi, L}, title = {A genotyping by sequencing approach can disclose Apis mellifera population genomic information contained in honey environmental DNA.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {19541}, pmid = {36379985}, issn = {2045-2322}, support = {2020-2021 RFO program//Università di Bologna/ ; BEE-RER-3 projects - CUP E37G22000030007 - del Regolamento (UE) no. 1308/2013 - (OCM Apicoltura)//Regione Emilia-Romagna/ ; 101017567//EGI-ACE/ ; }, mesh = {Bees/genetics ; Animals ; *DNA, Environmental ; Genotype ; Metagenomics ; *Honey ; DNA ; }, abstract = {Awareness has been raised over the last years on the genetic integrity of autochthonous honey bee subspecies. Genomic tools available in Apis mellifera can make it possible to measure this information by targeting individual honey bee DNA. Honey contains DNA traces from all organisms that contributed or were involved in its production steps, including the honey bees of the colony. In this study, we designed and tested a genotyping by sequencing (GBS) assay to analyse single nucleotide polymorphisms (SNPs) of A. mellifera nuclear genome using environmental DNA extracted from honey. A total of 121 SNPs (97 SNPs informative for honey bee subspecies identification and 24 SNPs associated with relevant traits of the colonies) were used in the assay to genotype honey DNA, which derives from thousands of honey bees. Results were integrated with information derived from previous studies and whole genome resequencing datasets. This GBS method is highly reliable in estimating honey bee SNP allele frequencies of the whole colony from which the honey derived. This assay can be used to identify the honey bee subspecies of the colony that produced the honey and, in turn, to authenticate the entomological origin of the honey.}, } @article {pmid36379940, year = {2022}, author = {Zhang, T and Zhang, W and Feng, C and Kwok, LY and He, Q and Sun, Z}, title = {Stronger gut microbiome modulatory effects by postbiotics than probiotics in a mouse colitis model.}, journal = {NPJ science of food}, volume = {6}, number = {1}, pages = {53}, pmid = {36379940}, issn = {2396-8370}, support = {2020ZD12//Natural Science Foundation of Inner Mongolia (Inner Mongolian Natural Science Foundation)/ ; 31972083//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32001711//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Probiotics are increasingly used as adjunctive therapy to manage gastrointestinal diseases, such as ulcerative colitis. However, probiotic use has posed some safety concerns. Thus, postbiotics are proposed as alternatives to probiotics in clinical applications. However, no study has directly compared the clinical benefits of probiotics and postbiotics. This study compared the beneficial effect of postbiotics and probiotics derived from the strain, Bifidobacterium adolescentis B8598, in a dextran sulfate sodium (DSS)-induced experimental colitis mouse model. Four groups of mice (n = 7 per group) were included in this work: Control (received water plus saline), DSS (received DSS without postbiotic/probiotic), Postbiotic (received DSS plus postbiotic), and Probiotic (received DSS plus probiotic). Our results showed that intragastric administration of both probiotic and postbiotic ameliorated colitis, reflected by decreased histology scores in Postbiotic and Probiotic groups compared with DSS group (P < 0.05). The fecal microbiota alpha diversity was not significantly affected by DSS-, postbiotic, or probiotic treatment. However, the postbiotic treatment showed stronger effects on modulating the fecal microbiota beta diversity, composition, and metagenomic potential than the probiotic treatment. Overall, our findings suggested that probiotics and postbiotics had similar ability to improve disease phenotype but had distinct ability to regulate the gut microbiota and metabolic pathways in the context of ulcerative colitis. In view of the smaller safety concern of postbiotics compared with probiotics and its stronger modulatory effect on the host gut microbiota, we propose that postbiotics are to be considered for use as next-generation biotherapeutics in managing ulcerative colitis or even other diseases.}, } @article {pmid36379846, year = {2023}, author = {Shakir, S and Zaidi, SS and Hashemi, FSG and Nyirakanani, C and Vanderschuren, H}, title = {Harnessing plant viruses in the metagenomics era: from the development of infectious clones to applications.}, journal = {Trends in plant science}, volume = {28}, number = {3}, pages = {297-311}, doi = {10.1016/j.tplants.2022.10.005}, pmid = {36379846}, issn = {1878-4372}, mesh = {*Metagenomics/methods ; *Plant Viruses/genetics ; Plants/genetics ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Recent metagenomic studies which focused on virus characterization in the entire plant environment have revealed a remarkable viral diversity in plants. The exponential discovery of viruses also requires the concomitant implementation of high-throughput methods to perform their functional characterization. Despite several limitations, the development of viral infectious clones remains a method of choice to understand virus biology, their role in the phytobiome, and plant resilience. Here, we review the latest approaches for efficient characterization of plant viruses and technical advances built on high-throughput sequencing and synthetic biology to streamline assembly of viral infectious clones. We then discuss the applications of plant viral vectors in fundamental and applied plant research as well as their technical and regulatory limitations, and we propose strategies for their safer field applications.}, } @article {pmid36379333, year = {2023}, author = {Singh, KS and Paul, D and Gupta, A and Dhotre, D and Klawonn, F and Shouche, Y}, title = {Indian sewage microbiome has unique community characteristics and potential for population-level disease predictions.}, journal = {The Science of the total environment}, volume = {858}, number = {Pt 3}, pages = {160178}, doi = {10.1016/j.scitotenv.2022.160178}, pmid = {36379333}, issn = {1879-1026}, mesh = {Humans ; *Sewage ; Cross-Sectional Studies ; *Metagenomics ; India ; }, abstract = {Sewage wastewater pollutes water and poses a public health issue but it could also prove useful in certain research domains. Sewage is a complex niche relevant for research concerning 'one-health', human health, pollution and antibiotic resistance. Indian gut microbiome is also understudied due to sampling constraints and sewage could be used to explore it. Ostensibly, Indian sewage needs to be studied and here, we performed a cross-sectional pan-India sewage sampling to generate the first comprehensive Indian sewage microbiome. Indian sewage showed predominance of Burkholderiaceae, Rhodocyclaceae, Veillonellaceae, Prevotellaceae, etc. and has high representation of gut microbes. The identified gut microbes have overrepresentation of Veillonellaceae, Rikenellaceae, Streptococcaceae, and Bacillaceae. Imputed metagenomics of sewage microbiome indicated dominance of transport, motility, peptidases, amino acid metabolism, and antibiotic resistance genes. Microbiome-disease associations drawn using simple decision tree and random forest analysis identified specific microbes as potential predictors of diabetes and obesity in a city. Altogether, we generated the first Indian sewage microbiome and our non-invasive, high-throughput workflow could be emulated for future research, wastewater-based epidemiology and designing policies concerning public health.}, } @article {pmid36378489, year = {2022}, author = {Gupta, VK and Bakshi, U and Chang, D and Lee, AR and Davis, JM and Chandrasekaran, S and Jin, YS and Freeman, MF and Sung, J}, title = {TaxiBGC: a Taxonomy-Guided Approach for Profiling Experimentally Characterized Microbial Biosynthetic Gene Clusters and Secondary Metabolite Production Potential in Metagenomes.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0092522}, pmid = {36378489}, issn = {2379-5077}, support = {R35 GM133475/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Metagenome/genetics ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Computational Biology ; Multigene Family/genetics ; }, abstract = {Biosynthetic gene clusters (BGCs) in microbial genomes encode bioactive secondary metabolites (SMs), which can play important roles in microbe-microbe and host-microbe interactions. Given the biological significance of SMs and the current profound interest in the metabolic functions of microbiomes, the unbiased identification of BGCs from high-throughput metagenomic data could offer novel insights into the complex chemical ecology of microbial communities. Currently available tools for predicting BGCs from shotgun metagenomes have several limitations, including the need for computationally demanding read assembly, predicting a narrow breadth of BGC classes, and not providing the SM product. To overcome these limitations, we developed taxonomy-guided identification of biosynthetic gene clusters (TaxiBGC), a command-line tool for predicting experimentally characterized BGCs (and inferring their known SMs) in metagenomes by first pinpointing the microbial species likely to harbor them. We benchmarked TaxiBGC on various simulated metagenomes, showing that our taxonomy-guided approach could predict BGCs with much-improved performance (mean F1 score, 0.56; mean PPV score, 0.80) compared with directly identifying BGCs by mapping sequencing reads onto the BGC genes (mean F1 score, 0.49; mean PPV score, 0.41). Next, by applying TaxiBGC on 2,650 metagenomes from the Human Microbiome Project and various case-control gut microbiome studies, we were able to associate BGCs (and their SMs) with different human body sites and with multiple diseases, including Crohn's disease and liver cirrhosis. In all, TaxiBGC provides an in silico platform to predict experimentally characterized BGCs and their SM production potential in metagenomic data while demonstrating important advantages over existing techniques. IMPORTANCE Currently available bioinformatics tools to identify BGCs from metagenomic sequencing data are limited in their predictive capability or ease of use to even computationally oriented researchers. We present an automated computational pipeline called TaxiBGC, which predicts experimentally characterized BGCs (and infers their known SMs) in shotgun metagenomes by first considering the microbial species source. Through rigorous benchmarking techniques on simulated metagenomes, we show that TaxiBGC provides a significant advantage over existing methods. When demonstrating TaxiBGC on thousands of human microbiome samples, we associate BGCs encoding bacteriocins with different human body sites and diseases, thereby elucidating a possible novel role of this antibiotic class in maintaining the stability of microbial ecosystems throughout the human body. Furthermore, we report for the first time gut microbial BGC associations shared among multiple pathologies. Ultimately, we expect our tool to facilitate future investigations into the chemical ecology of microbial communities across diverse niches and pathologies.}, } @article {pmid36378008, year = {2022}, author = {Fang, C and Xu, L and Lu, J and Tan, H and Lin, J and Zhao, Z}, title = {Clinical Characteristics of Chlamydia psittaci Pneumonia Confirmed by Metagenomic Next-Generation Sequencing.}, journal = {Clinical laboratory}, volume = {68}, number = {11}, pages = {}, doi = {10.7754/Clin.Lab.2022.220139}, pmid = {36378008}, issn = {1433-6510}, mesh = {Humans ; *Chlamydophila psittaci/genetics ; Retrospective Studies ; *Psittacosis/diagnosis ; High-Throughput Nucleotide Sequencing ; *Pneumonia/diagnosis ; }, abstract = {BACKGROUND: Chlamydia psittaci pneumonia has atypical clinical manifestations and the diagnosis may be missed by traditional methods of microbiological diagnosis.

METHODS: Twelve cases of Chlamydia psittaci pneumonia diagnosed by metagenomic next-generation sequencing (mNGS) in Huizhou Central People's Hospital in China between January 2020 and August 2021 were reviewed and analyzed, retrospectively, using hospital records, the clinical characteristics, treatment, and prognosis.

RESULTS: Ten of the 12 cases (83%) were associated with a definite history of bird/poultry contact. Common symptoms included high fever, cough, fatigue, anorexia (12/12, 100%), dyspnea (11/12, 92%), and changes in the level of consciousness and headache (5/12, 42%). There was a marked increase in C-reactive protein and D-dimer levels, but white blood cells and neutrophils were normal or slightly increased. Nine patients (75%) had liver enzyme abnormalities, and six (50%) had cardiac insufficiency and myocardial injury. There was no correlation between the mNGS sequence number of Chlamydia psittaci and the pneumonia severity. The chest imaging manifestations were mainly large areas of consolidation, predominantly in the lower lung lobes. Monotherapies or combinations of doxycycline, moxifloxacin/levofloxacin, and azithromycin were effective for treating Chlamydia psittaci pneumonia.

CONCLUSIONS: The use of mNGS increases the probability of diagnosing Chlamydia psittaci pneumonia, and good prognosis can be achieved with timely use of appropriate antibiotics.}, } @article {pmid36377945, year = {2022}, author = {Aytan-Aktug, D and Grigorjev, V and Szarvas, J and Clausen, PTLC and Munk, P and Nguyen, M and Davis, JJ and Aarestrup, FM and Lund, O}, title = {SourceFinder: a Machine-Learning-Based Tool for Identification of Chromosomal, Plasmid, and Bacteriophage Sequences from Assemblies.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0264122}, pmid = {36377945}, issn = {2165-0497}, support = {75N93019C00076/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Genome, Bacterial ; *Bacteriophages/genetics ; Plasmids/genetics ; Chromosomes, Bacterial/genetics ; Machine Learning ; }, abstract = {High-throughput genome sequencing technologies enable the investigation of complex genetic interactions, including the horizontal gene transfer of plasmids and bacteriophages. However, identifying these elements from assembled reads remains challenging due to genome sequence plasticity and the difficulty in assembling complete sequences. In this study, we developed a classifier, using random forest, to identify whether sequences originated from bacterial chromosomes, plasmids, or bacteriophages. The classifier was trained on a diverse collection of 23,211 chromosomal, plasmid, and bacteriophage sequences from hundreds of bacterial species. In order to adapt the classifier to incomplete sequences, each complete sequence was subsampled into 5,000 nucleotide fragments and further subdivided into k-mers. This three-class classifier succeeded in identifying chromosomes, plasmids, and bacteriophages using k-mer distributions of complete and partial genome sequences, including simulated metagenomic scaffolds with minimum performance of 0.939 area under the receiver operating characteristic curve (AUC). This classifier, implemented as SourceFinder, has been made available as an online web service to help the community with predicting the chromosomal, plasmid, and bacteriophage sources of assembled bacterial sequence data (https://cge.food.dtu.dk/services/SourceFinder/). IMPORTANCE Extra-chromosomal genes encoding antimicrobial resistance, metal resistance, and virulence provide selective advantages for bacterial survival under stress conditions and pose serious threats to human and animal health. These accessory genes can impact the composition of microbiomes by providing selective advantages to their hosts. Accurately identifying extra-chromosomal elements in genome sequence data are critical for understanding gene dissemination trajectories and taking preventative measures. Therefore, in this study, we developed a random forest classifier for identifying the source of bacterial chromosomal, plasmid, and bacteriophage sequences.}, } @article {pmid36377936, year = {2022}, author = {Chen, J and Li, Z and Wang, X and Fan, B and Deng, F and D Yu, H and Ze, X and Zhu, L and Yin, Y and Chen, Y and Zhao, J and Yang, Y and Wang, X}, title = {Isomaltooligosaccharides Sustain the Growth of Prevotella Both In Vitro and in Animal Models.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0262121}, pmid = {36377936}, issn = {2165-0497}, mesh = {Humans ; Animals ; Mice ; Aged ; RNA, Ribosomal, 16S/genetics ; *Gastrointestinal Microbiome ; Feces/microbiology ; Prevotella/genetics ; Carbohydrates ; Models, Animal ; Starch ; }, abstract = {The human digestive tract is colonized by trillions of bacterial cells that play important roles in human health and diseases. It is well known that dietary habits are associated with human microbiota enterotypes. However, the factors that determine the enterotype still remain elusive. In this study, it was first examined, via in vitro batch fermentation, how different carbohydrates affect the Bacteroides and Prevotella enterotypes. Among the 11 substrates (fructo-, galacto-, xylo-, manno-, and isomalto-oligosaccharides [IMO] and lactulose, raffinose, starch, inulin [INU], mannitol, and xylitol) tested, IMO, INU, and starch were found to sustain the growth of Prevotella through batch fermentation. The development of the Prevotella and Bacteroides enterotypes was further simulated in chemostats using fecal samples. IMO coupled with faster dilution rates and lower pH were required to sustain the growth of Prevotella copri in the chemostat based on 16S rRNA gene and metagenomic sequencing. Meanwhile, starch with relatively lower dilution rates and higher pH was required to support the development of the Bacteroides enterotype. Amylo-α-1,6-glucosidase, pectin, and xylan lyases were the carbohydrate-active enzymes associated with the Prevotella enterotype. The Bacteroides enterotype was associated with more diversified carbohydrate-active enzymes. Consistently, since honey contains high isomaltose content, mice fed IMO and honey displayed an increased relative abundance of Prevotella in the colon. In conclusion, both in vitro systems and a mouse model were used to demonstrate that IMO maintains the Prevotella enterotype. This result provides insight into the nutritional requirements underlying gut enterotype formation. IMPORTANCE The Prevotella enterotype type is a human traditional enterotype with high dietary fiber intake, which is related to healthy ageing and Parkinson's disease development. Manipulations of the dwelled gut microbes by dietary isomalto-oligosaccharides efficiently sustained Prevotella type enterotypes, indicating that it can be used in the improvement of elderly health by increasing the gut transit time.}, } @article {pmid36377901, year = {2022}, author = {Wicaksono, WA and Egamberdieva, D and Berg, C and Mora, M and Kusstatscher, P and Cernava, T and Berg, G}, title = {Function-Based Rhizosphere Assembly along a Gradient of Desiccation in the Former Aral Sea.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0073922}, pmid = {36377901}, issn = {2379-5077}, mesh = {Humans ; *Rhizosphere ; Desiccation ; Bacteria/genetics ; Archaea/genetics ; *Microbiota/genetics ; Soil ; Plants ; }, abstract = {The desiccation of the Aral Sea represents one of the largest human-made environmental regional disasters. The salt- and toxin-enriched dried-out basin provides a natural laboratory for studying ecosystem functioning and rhizosphere assembly under extreme anthropogenic conditions. Here, we investigated the prokaryotic rhizosphere communities of the native pioneer plant Suaeda acuminata (C.A.Mey.) Moq. in comparison to bulk soil across a gradient of desiccation (5, 10, and 40 years) by metagenome and amplicon sequencing combined with quantitative PCR (qPCR) analyses. The rhizosphere effect was evident due to significantly higher bacterial abundances but less diversity in the rhizosphere compared to bulk soil. Interestingly, in the highest salinity (5 years of desiccation), rhizosphere functions were mainly provided by archaeal communities. Along the desiccation gradient, we observed a significant change in the rhizosphere microbiota, which was reflected by (i) a decreasing archaeon-bacterium ratio, (ii) replacement of halophilic archaea by specific plant-associated bacteria, i.e., Alphaproteobacteria and Actinobacteria, and (iii) an adaptation of specific, potentially plant-beneficial biosynthetic pathways. In general, both bacteria and archaea were found to be involved in carbon cycling and fixation, as well as methane and nitrogen metabolism. Analysis of metagenome-assembled genomes (MAGs) showed specific signatures for production of osmoprotectants, assimilatory nitrate reduction, and transport system induction. Our results provide evidence that rhizosphere assembly by cofiltering specific taxa with distinct traits is a mechanism which allows plants to thrive under extreme conditions. Overall, our findings highlight a function-based rhizosphere assembly, the importance of plant-microbe interactions in salinated soils, and their exploitation potential for ecosystem restoration approaches. IMPORTANCE The desertification of the Aral Sea basin in Uzbekistan and Kazakhstan represents one of the most serious anthropogenic environmental disasters of the last century. Since the 1960s, the world's fourth-largest inland body of water has been constantly shrinking, which has resulted in an extreme increase of salinity accompanied by accumulation of many hazardous and carcinogenic substances, as well as heavy metals, in the dried-out basin. Here, we investigated bacterial and archaeal communities in the rhizosphere of pioneer plants by combining classic molecular methods with amplicon sequencing as well as metagenomics for functional insights. By implementing a desiccation gradient, we observed (i) remarkable differences in the archaeon-bacterium ratio of plant rhizosphere samples, (ii) replacement of archaeal indicator taxa during succession, and (iii) the presence of specific, potentially plant-beneficial biosynthetic pathways in archaea present during the early stages. In addition, our results provide hitherto-undescribed insights into the functional redundancy between plant-associated archaea and bacteria.}, } @article {pmid36377900, year = {2022}, author = {McGonigle, JM and Bernau, JA and Bowen, BB and Brazelton, WJ}, title = {Metabolic Potential of Microbial Communities in the Hypersaline Sediments of the Bonneville Salt Flats.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0084622}, pmid = {36377900}, issn = {2379-5077}, mesh = {*Calcium Sulfate/metabolism ; Bacteria/genetics ; Archaea/genetics ; Sodium Chloride/metabolism ; *Microbiota/genetics ; Sodium Chloride, Dietary/metabolism ; }, abstract = {The Bonneville Salt Flats (BSF) appear to be entirely desolate when viewed from above, but they host rich microbial communities just below the surface salt crust. In this study, we investigated the metabolic potential of the BSF microbial ecosystem. The predicted and measured metabolic activities provide new insights into the ecosystem functions of evaporite landscapes and are an important analog for potential subsurface microbial ecosystems on ancient and modern Mars. Hypersaline and evaporite systems have been investigated previously as astrobiological analogs for Mars and other salty celestial bodies, but these studies have generally focused on aquatic systems and cultivation-dependent approaches. Here, we present an ecosystem-level examination of metabolic pathways within the shallow subsurface of evaporites. We detected aerobic and anaerobic respiration as well as methanogenesis in BSF sediments. Metagenome-assembled genomes of diverse bacteria and archaea encode a remarkable diversity of metabolic pathways, including those associated with carbon fixation, carbon monoxide oxidation, acetogenesis, methanogenesis, sulfide oxidation, denitrification, and nitrogen fixation. These results demonstrate the potential for multiple energy sources and metabolic pathways in BSF and highlight the possibility for vibrant microbial ecosystems in the shallow subsurface of evaporites. IMPORTANCE The Bonneville Salt Flats is a unique ecosystem created from 10,000 years of desiccation and serves as an important natural laboratory for the investigation of the habitability of salty, halite, and gypsum-rich environments. Here, we show that gypsum-rich mineral deposits host a surprising diversity of organisms and appear to play a key role in stimulating the microbial cycling of sulfur and nitrogen compounds. This work highlights how diverse microbial communities within the shallow subsurface sediments are capable of maintaining an active and sustainable ecosystem, even though the surface salt crust appears to be completely devoid of life.}, } @article {pmid36377682, year = {2023}, author = {Huang, C and Ding, H and Lin, Y and Zhang, Z and Fang, X and Chen, Y and Chen, Y and Zhang, C and Li, W and Zhang, W and Huang, Z}, title = {Diagnosis of Coxiella burnetii Prosthetic Joint Infection Using mNGS and ptNGS: A Case Report and Literature Review.}, journal = {Orthopaedic surgery}, volume = {15}, number = {1}, pages = {371-376}, pmid = {36377682}, issn = {1757-7861}, support = {2019I0011//Foreign Cooperation Project of Science and Technology, Fujian Province/ ; 2019Y9132//Joint Funds for the Innovation of Science and Technology, Fujian Province/ ; 82072458//The National Science Foundation Grant of China/ ; 2021QH1093//The Startup Fund for Scientific Research of Fujian Medical University/ ; 2020Y2002//Fujian Orthopaedic Bone and Joint Disease and Sports Rehabilitation Clinical Medical Research Center/ ; }, mesh = {Male ; Humans ; Aged ; *Coxiella burnetii/genetics ; *Q Fever/diagnosis/drug therapy/microbiology ; Doxycycline ; *Arthritis, Infectious ; High-Throughput Nucleotide Sequencing/methods ; *Joint Prosthesis ; }, abstract = {BACKGROUND: Coxiella burnetii (C. burnetii) is the causative agent of Q fever and is found worldwide; however, prosthetic joint infections caused by C. burnetii are rarely seen. Because of advances in molecular diagnostic techniques, prosthetic joint infection (PJI) caused by C. burnetii can now be diagnosed.

CASE PRESENTATION: A 77-year-old male who had undergone total knee arthroplasty had a displaced prosthesis and periprosthetic osteolysis; he had no obvious signs of infection, and microbiological culture was negative. However, C. burnetii was detected by metagenomic next-generation sequencing (mNGS) and pathogen-targeted next-generation sequencing (ptNGS). Finally, polymerase chain reaction (PCR) confirmed the diagnosis of C. burnetii prosthetic joint infection (PJI). After revision surgery (one-stage revision) and oral antibiotics (doxycycline and moxifloxacin hydrochloride), the patient's symptoms disappeared, and he regained the ability to walk. During the 6-month follow-up, the patient's knee showed no signs of swelling, pain or the recurrence of infection, and he experienced no significant complications. We also present a review of the literature for other cases of C. burnetii PJI.

CONCLUSIONS: The symptoms of C. burnetii PJI may be different from those of Q fever, which may lead to misdiagnosis. mNGS and ptNGS may be helpful for the identification of C. burnetii. Once the diagnosis of C. burnetii PJI is confirmed, doxycycline in combination with a fluoroquinolone can be effectively administered after revision surgery.}, } @article {pmid36377420, year = {2022}, author = {Chaghouri, M and Gennequin, C and Tidahy, LH and Cazier, F and Abi-Aad, E and Veignie, E and Rafin, C}, title = {Low cost and renewable H2S-biofilter inoculated with Trichoderma harzianum.}, journal = {Environmental technology}, volume = {}, number = {}, pages = {1-14}, doi = {10.1080/09593330.2022.2147024}, pmid = {36377420}, issn = {1479-487X}, abstract = {The use of biogas to produce hydrogen is currently gaining more attention. One of the drawbacks for the valorization of biogas is the presence of H2S, a hazardous molecule that can cause damage in the metallic internal structures of industries. In this study, the H2S-removal performance of a fungi-based biofilter was investigated. First, an H2S-resistant fungal species was isolated from an industrial digestate and identified as Trichoderma harzianum. The capacity of this microorganism to metabolize H2S in a mineral medium was confirmed. Then, a bioreactor was constructed and put in place to monitor the elimination of gaseous H2S. A mix of cardboard, perlite, woodchips, and wood pellets was used as filling. Microbial development and the outlet gas composition were monitored during a 60-day experimental process during which H2S was completely removed. 97% of the introduced sulphur was detected in the used filling material (fungal species + packing material) by elemental analysis. 24% of the detected sulphur was identified by ion-exchange chromatography as SO4[2-]. Elemental analysis, gas chromatography, and ion-exchange chromatography were used to determine the bioreactor sulphur balance. Metagenomic analysis underlined that H2S elimination was due to the presence of Trichoderma harzianum with a H2S-specific bacterial consortium.}, } @article {pmid36377253, year = {2023}, author = {Tello, D and Gonzalez-Garcia, LN and Gomez, J and Zuluaga-Monares, JC and Garcia, R and Angel, R and Mahecha, D and Duarte, E and Leon, MDR and Reyes, F and Escobar-Velásquez, C and Linares-Vásquez, M and Cardozo, N and Duitama, J}, title = {NGSEP 4: Efficient and accurate identification of orthogroups and whole-genome alignment.}, journal = {Molecular ecology resources}, volume = {23}, number = {3}, pages = {712-724}, doi = {10.1111/1755-0998.13737}, pmid = {36377253}, issn = {1755-0998}, support = {80740-441-2020//Ministerio de Ciencia Tecnología e Innovación de Colombia/ ; //Universidad de los Andes/ ; }, mesh = {*Software ; *Genome ; Genomics/methods ; Algorithms ; Metagenomics ; }, abstract = {Whole-genome alignment allows researchers to understand the genomic structure and variation among genomes. Approaches based on direct pairwise comparisons of DNA sequences require large computational capacities. As a consequence, pipelines combining tools for orthologous gene identification and synteny have been developed. In this manuscript, we present the latest functionalities implemented in NGSEP 4, to identify orthogroups and perform whole genome alignments. NGSEP implements functionalities for identification of clusters of homologus genes, synteny analysis and whole genome alignment. Our results showed that the NGSEP algorithm for orthogroups identification has competitive accuracy and efficiency in comparison to commonly used tools. The implementation also includes a visualization of the whole genome alignment based on synteny of the orthogroups that were identified, and a reconstruction of the pangenome based on frequencies of the orthogroups among the genomes. NGSEP 4 also includes a new graphical user interface based on the JavaFX technology. We expect that these new developments will be very useful for several studies in evolutionary biology and population genomics.}, } @article {pmid36376937, year = {2022}, author = {Liang, X and Fu, Y and Cao, WT and Wang, Z and Zhang, K and Jiang, Z and Jia, X and Liu, CY and Lin, HR and Zhong, H and Miao, Z and Gou, W and Shuai, M and Huang, Y and Chen, S and Zhang, B and Chen, YM and Zheng, JS}, title = {Gut microbiome, cognitive function and brain structure: a multi-omics integration analysis.}, journal = {Translational neurodegeneration}, volume = {11}, number = {1}, pages = {49}, pmid = {36376937}, issn = {2047-9158}, support = {R24 HD050924/HD/NICHD NIH HHS/United States ; R01 HD030880/HD/NICHD NIH HHS/United States ; R01-HD38700/NH/NIH HHS/United States ; R01-DK104371/DK/NIDDK NIH HHS/United States ; R01-HD30880/NH/NIH HHS/United States ; P30 AG066615/AG/NIA NIH HHS/United States ; R01 AG065357/AG/NIA NIH HHS/United States ; DK056350/NH/NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Cross-Sectional Studies ; Case-Control Studies ; Cognition ; Brain/diagnostic imaging ; }, abstract = {BACKGROUND: Microbiome-gut-brain axis may be involved in the progression of age-related cognitive impairment and relevant brain structure changes, but evidence from large human cohorts is lacking. This study was aimed to investigate the associations of gut microbiome with cognitive impairment and brain structure based on multi-omics from three independent populations.

METHODS: We included 1430 participants from the Guangzhou Nutrition and Health Study (GNHS) with both gut microbiome and cognitive assessment data available as a discovery cohort, of whom 272 individuals provided fecal samples twice before cognitive assessment. We selected 208 individuals with baseline microbiome data for brain magnetic resonance imaging during the follow-up visit. Fecal 16S rRNA and shotgun metagenomic sequencing, targeted serum metabolomics, and cytokine measurements were performed in the GNHS. The validation analyses were conducted in an Alzheimer's disease case-control study (replication study 1, n = 90) and another community-based cohort (replication study 2, n = 1300) with cross-sectional dataset.

RESULTS: We found protective associations of specific gut microbial genera (Odoribacter, Butyricimonas, and Bacteroides) with cognitive impairment in both the discovery cohort and the replication study 1. Result of Bacteroides was further validated in the replication study 2. Odoribacter was positively associated with hippocampal volume (β, 0.16; 95% CI 0.06-0.26, P = 0.002), which might be mediated by acetic acids. Increased intra-individual alterations in gut microbial composition were found in participants with cognitive impairment. We also identified several serum metabolites and inflammation-associated metagenomic species and pathways linked to impaired cognition.

CONCLUSIONS: Our findings reveal that specific gut microbial features are closely associated with cognitive impairment and decreased hippocampal volume, which may play an important role in dementia development.}, } @article {pmid36376928, year = {2022}, author = {Lai, S and Pan, S and Sun, C and Coelho, LP and Chen, WH and Zhao, XM}, title = {metaMIC: reference-free misassembly identification and correction of de novo metagenomic assemblies.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {242}, pmid = {36376928}, issn = {1474-760X}, mesh = {*Metagenome ; Sequence Analysis, DNA/methods ; *Metagenomics/methods ; Machine Learning ; Benchmarking ; Software ; Algorithms ; }, abstract = {Evaluating the quality of metagenomic assemblies is important for constructing reliable metagenome-assembled genomes and downstream analyses. Here, we present metaMIC (https://github.com/ZhaoXM-Lab/metaMIC), a machine learning-based tool for identifying and correcting misassemblies in metagenomic assemblies. Benchmarking results on both simulated and real datasets demonstrate that metaMIC outperforms existing tools when identifying misassembled contigs. Furthermore, metaMIC is able to localize the misassembly breakpoints, and the correction of misassemblies by splitting at misassembly breakpoints can improve downstream scaffolding and binning results.}, } @article {pmid36376589, year = {2023}, author = {Chivian, D and Jungbluth, SP and Dehal, PS and Wood-Charlson, EM and Canon, RS and Allen, BH and Clark, MM and Gu, T and Land, ML and Price, GA and Riehl, WJ and Sneddon, MW and Sutormin, R and Zhang, Q and Cottingham, RW and Henry, CS and Arkin, AP}, title = {Metagenome-assembled genome extraction and analysis from microbiomes using KBase.}, journal = {Nature protocols}, volume = {18}, number = {1}, pages = {208-238}, pmid = {36376589}, issn = {1750-2799}, mesh = {*Metagenome ; Phylogeny ; Genome, Bacterial ; *Microbiota/genetics ; Bacteria/genetics ; Metagenomics ; }, abstract = {Uncultivated Bacteria and Archaea account for the vast majority of species on Earth, but obtaining their genomes directly from the environment, using shotgun sequencing, has only become possible recently. To realize the hope of capturing Earth's microbial genetic complement and to facilitate the investigation of the functional roles of specific lineages in a given ecosystem, technologies that accelerate the recovery of high-quality genomes are necessary. We present a series of analysis steps and data products for the extraction of high-quality metagenome-assembled genomes (MAGs) from microbiomes using the U.S. Department of Energy Systems Biology Knowledgebase (KBase) platform (http://www.kbase.us/). Overall, these steps take about a day to obtain extracted genomes when starting from smaller environmental shotgun read libraries, or up to about a week from larger libraries. In KBase, the process is end-to-end, allowing a user to go from the initial sequencing reads all the way through to MAGs, which can then be analyzed with other KBase capabilities such as phylogenetic placement, functional assignment, metabolic modeling, pangenome functional profiling, RNA-Seq and others. While portions of such capabilities are available individually from other resources, the combination of the intuitive usability, data interoperability and integration of tools in a freely available computational resource makes KBase a powerful platform for obtaining MAGs from microbiomes. While this workflow offers tools for each of the key steps in the genome extraction process, it also provides a scaffold that can be easily extended with additional MAG recovery and analysis tools, via the KBase software development kit (SDK).}, } @article {pmid36376441, year = {2022}, author = {Takahashi, E and Motooka, D and Nakamura, S and Miyoshi, SI and Chowdhury, G and Mukhopadhyay, AK and Dutta, S and Morita, D and Iida, T and Okamoto, K}, title = {Metagenomic analysis of diarrheal stools in Kolkata, India, indicates the possibility of subclinical infection of Vibrio cholerae O1.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {19473}, pmid = {36376441}, issn = {2045-2322}, support = {JP19fm0108002//Japan Agency for Medical Research and Development/ ; }, mesh = {Humans ; *Vibrio cholerae O1/genetics ; Asymptomatic Infections ; Cholera Toxin/genetics ; *Cholera/diagnosis/epidemiology ; Diarrhea/epidemiology ; India/epidemiology ; }, abstract = {We examined the stools of 23 patients in Kolkata, who were diagnosed as cholera patients because Vibrio cholerae O1 was detected from their stools by culturing methods, and further explored by metagenomic sequencing analysis. Subsequently, the presence of the gene encoding A subunit of cholera toxin (ctxA) and the cholera toxin (CT) level in these stool samples were examined. ctxA was examined by both metagenomic sequencing analysis and polymerase chain reaction. In these examinations, two samples did not show positive in any of these tests. The metagenomic analysis showed that the genes for Streptococcus pneumoniae and Salmonella enterica were present in the stools of these two patients, respectively. Therefore, these two patients were not considered to have diarrhea due to V. cholerae infection. From these results, we predicted that some Kolkata residents harbor a small number of V. cholerae in their intestines as a form of subclinical infection with V. cholerae. Next, we analyzed the stool samples of 22 diarrhea patients from which V. cholerae was not isolated. The results showed that 3 of the patients seemed to have subclinical infection of V. cholerae based on the amount of the genes. These results indicated that subclinical infections with V. cholerae O1 occur in Kolkata.}, } @article {pmid36376329, year = {2022}, author = {Shibata, K and Motozono, C and Nagae, M and Shimizu, T and Ishikawa, E and Motooka, D and Okuzaki, D and Izumi, Y and Takahashi, M and Fujimori, N and Wing, JB and Hayano, T and Asai, Y and Bamba, T and Ogawa, Y and Furutani-Seiki, M and Shirai, M and Yamasaki, S}, title = {Symbiotic bacteria-dependent expansion of MR1-reactive T cells causes autoimmunity in the absence of Bcl11b.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6948}, pmid = {36376329}, issn = {2041-1723}, mesh = {Mice ; Animals ; *Receptors, Antigen, T-Cell, alpha-beta/genetics/metabolism ; *Autoimmunity ; Minor Histocompatibility Antigens/genetics ; Receptors, Antigen, T-Cell/metabolism ; Histocompatibility Antigens Class I ; Transcription Factors ; Bacteria/metabolism ; Tumor Suppressor Proteins ; Repressor Proteins ; }, abstract = {MHC class I-related protein 1 (MR1) is a metabolite-presenting molecule that restricts MR1-reactive T cells including mucosal-associated invariant T (MAIT) cells. In contrast to MAIT cells, the function of other MR1-restricted T cell subsets is largely unknown. Here, we report that mice in which a T cell-specific transcription factor, B-cell lymphoma/leukemia 11B (Bcl11b), was ablated in immature thymocytes (Bcl11b[∆iThy] mice) develop chronic inflammation. Bcl11b[∆iThy] mice lack conventional T cells and MAIT cells, whereas CD4[+]IL-18R[+] αβ T cells expressing skewed Traj33 (Jα33)[+] T cell receptors (TCR) accumulate in the periphery, which are necessary and sufficient for the pathogenesis. The disorders observed in Bcl11b[∆iThy] mice are ameliorated by MR1-deficiency, transfer of conventional T cells, or germ-free conditions. We further show the crystal structure of the TCR expressed by Traj33[+] T cells expanded in Bcl11b[∆iThy] mice. Overall, we establish that MR1-reactive T cells have pathogenic potential.}, } @article {pmid36376318, year = {2022}, author = {Wallen, ZD and Demirkan, A and Twa, G and Cohen, G and Dean, MN and Standaert, DG and Sampson, TR and Payami, H}, title = {Metagenomics of Parkinson's disease implicates the gut microbiome in multiple disease mechanisms.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6958}, pmid = {36376318}, issn = {2041-1723}, support = {R01 ES032440/ES/NIEHS NIH HHS/United States ; T32 NS095775/NS/NINDS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Parkinson Disease/genetics ; Dysbiosis/genetics ; Metagenomics/methods ; Metagenome/genetics ; }, abstract = {Parkinson's disease (PD) may start in the gut and spread to the brain. To investigate the role of gut microbiome, we conducted a large-scale study, at high taxonomic resolution, using uniform standardized methods from start to end. We enrolled 490 PD and 234 control individuals, conducted deep shotgun sequencing of fecal DNA, followed by metagenome-wide association studies requiring significance by two methods (ANCOM-BC and MaAsLin2) to declare disease association, network analysis to identify polymicrobial clusters, and functional profiling. Here we show that over 30% of species, genes and pathways tested have altered abundances in PD, depicting a widespread dysbiosis. PD-associated species form polymicrobial clusters that grow or shrink together, and some compete. PD microbiome is disease permissive, evidenced by overabundance of pathogens and immunogenic components, dysregulated neuroactive signaling, preponderance of molecules that induce alpha-synuclein pathology, and over-production of toxicants; with the reduction in anti-inflammatory and neuroprotective factors limiting the capacity to recover. We validate, in human PD, findings that were observed in experimental models; reconcile and resolve human PD microbiome literature; and provide a broad foundation with a wealth of concrete testable hypotheses to discern the role of the gut microbiome in PD.}, } @article {pmid36375784, year = {2022}, author = {Miao, Z and Miao, Z and Liu, M and Xu, S}, title = {Melatonin ameliorates imidacloprid-induced intestinal injury by negatively regulating the PGN/P38MAPK pathway in the common carp (Cyprinuscarpio).}, journal = {Fish & shellfish immunology}, volume = {131}, number = {}, pages = {1063-1074}, doi = {10.1016/j.fsi.2022.11.018}, pmid = {36375784}, issn = {1095-9947}, mesh = {Animals ; *Melatonin/pharmacology ; Peptidoglycan ; p38 Mitogen-Activated Protein Kinases/genetics ; *Water Pollutants, Chemical/toxicity/metabolism ; Neonicotinoids/analysis/toxicity ; *Insecticides/toxicity/metabolism ; *Carps/metabolism ; }, abstract = {Imidacloprid (IMI), one of the most frequently used neonicotinoid insecticides in agriculture, is resided in surface water worldwide and poses a threat to aquatic organisms. Melatonin (MT) provides effective protection against insecticide-induced toxicity, nevertheless, the toxic effects and whether MT attenuates intestinal injury caused by IMI exposure in the common carps remains poorly explored. Previous studies have reported adverse effects of IMI exposure on intestinal health status. Therefore, we first demonstrated that IMI altered the composition and function of the intestinal microbiota, destroying the integrity of intestinal ultrastructure, increasing intestinal permeability. Meanwhile, metagenomic sequencing and ELISA kits results hypothesized that peptidoglycan (PGN) is an IMI-triggered intestinal microbial metabolite. Subsequently, we thus further elucidated that IMI induced an increase in intestinal tight junction permeability by inducing PGN secretion in vitro model. MT addition dramatically attenuated IMI-induced intestinal toxicity by remitting PGN synthesis and thus resecuring tight junction permeability, thereby reducing intestinal injury. SB203580 was supplied as a P38MAPK inhibitor to alleviate the increased permeability of tight junctions induced by IMI/PGN. Therefore, these findings confirmed that MT protects against IMI-induced intestinal injury by negatively regulating PGN/P38MAPK pathway to antagonize the increased tight junction permeability.}, } @article {pmid36375764, year = {2023}, author = {Oliveira, M and Pinto, M and Simões, H and Gomes, JP and Veríssimo, C and Sabino, R}, title = {Molecular detection of Aspergillus in respiratory samples collected from patients at higher risk of chronic pulmonary aspergillosis.}, journal = {Infectious diseases now}, volume = {53}, number = {2}, pages = {104633}, doi = {10.1016/j.idnow.2022.11.002}, pmid = {36375764}, issn = {2666-9919}, mesh = {Humans ; Aspergillus/genetics ; *Pulmonary Aspergillosis/diagnosis/epidemiology ; *Aspergillosis/diagnosis ; Sensitivity and Specificity ; }, abstract = {OBJECTIVE: Aspergillosis diagnosis depends on the detection of Aspergillus in biological samples ─ usually using cultural and immunoenzyme techniques ─ but their sensitivity and specificity varies. We aimed to study the prevalence of Aspergillus in patients at higher risk of chronic pulmonary aspergillosis (i.e., HIV-infected patients and individuals with active or previous tuberculosis), and to determine the potential role of molecular approaches to increase detection of Aspergillus in respiratory samples.

METHODS: The DNA extracted from 43 respiratory samples that had been previously analyzed by immunoenzyme and/or cultural techniques was amplified by real-time multiplex PCR, and the results of these methods were compared. We also sequenced the ITS1 region and the calmodulin gene in 10 respiratory samples to perform a pilot metagenomic study to understand the ability of this methodology to detect potential pathogenic fungi in the lung mycobiome.

RESULTS: Real-time Aspergillus PCR test exhibited a higher positivity rate than the conventional techniques used for aspergillosis diagnosis, particularly in individuals at risk for chronic pulmonary aspergillosis. The metagenomic analysis allowed for the detection of various potentially pathogenic fungi.

CONCLUSIONS: Molecular techniques, including metagenomics, have great ability to detect potentially pathogenic fungi rapidly and efficiently in human biological samples.}, } @article {pmid36375616, year = {2023}, author = {Wu, C and Song, X and Wang, D and Ma, Y and Ren, X and Hu, H and Shan, Y and Ma, X and Cui, J and Ma, Y}, title = {Tracking antibiotic resistance genes in microplastic-contaminated soil.}, journal = {Chemosphere}, volume = {312}, number = {Pt 1}, pages = {137235}, doi = {10.1016/j.chemosphere.2022.137235}, pmid = {36375616}, issn = {1879-1298}, mesh = {*Plastics ; *Anti-Bacterial Agents/pharmacology ; Microplastics ; Genes, Bacterial ; Soil Microbiology ; Drug Resistance, Microbial/genetics ; Soil/chemistry ; }, abstract = {Agricultural soils and microplastics (MPs) are hotspots for antibiotic resistance genes (ARGs). Plastic mulch is the most important source of MPs in agricultural soil. ARGs, mobile genetic elements (MGEs), and their host profiles in long-term mulch MP-exposed soils remain unclear. In the present study, metagenomics was used to investigate the distribution patterns of ARGs and MGEs in eight Chinese provinces with a long history of plastic mulch use. A total of 204 subtypes of ARGs and thousands of MGEs (14 integrons, 28 insertions, and 2993 plasmids) were identified. A similar diversity of ARGs was found among MPs film-contaminated sites. The types of ARGs with a high abundance were more concentrated, and multidrug resistance genes were the dominant ARGs. Soils from regions with a longer history of plastic film use (such as Xinjiang province) had a higher abundance of ARGs and MGEs. The distribution of ARGs and MGEs exhibited a modular network distribution pattern. A total of 27 ARG subtypes and 29 MGEs showed co-occurrence network relationships. More than 10 common hosts of ARGs and MGEs, such as Pseudomonas, were found, and their abundances were highest in three provinces, including Xinjiang. This study may help elucidate the impact mechanism of long-term MP residues on the occurrence and spread of ARGs in soil.}, } @article {pmid36375502, year = {2023}, author = {Guo, X and Lai, CY and Hartmann, EM and Zhao, HP}, title = {Heterotrophic denitrification: An overlooked factor that contributes to nitrogen removal in n-DAMO mixed culture.}, journal = {Environmental research}, volume = {216}, number = {Pt 4}, pages = {114802}, doi = {10.1016/j.envres.2022.114802}, pmid = {36375502}, issn = {1096-0953}, mesh = {*Methane ; *Denitrification ; Nitrogen/metabolism ; Nitrates ; Anaerobiosis ; Bioreactors ; Oxidation-Reduction ; Bacteria/metabolism ; Nitrites ; }, abstract = {Nitrate/nitrite-dependent anaerobic methane oxidation (n-DAMO) has been recognized as a sustainable process for simultaneous removal of nitrogen and methane. The metabolisms of denitrifying anaerobic methanotrophs, including Candidatus Methanoperedens and Candidatus Methylomirabilis, have been well studied. However, potential roles of heterotrophs co-existing with these anaerobic methanotrophs are generally overlooked. In this study, we pulse-fed methane and nitrate into an anaerobic laboratory sequencing batch bioreactor and enriched a mixed culture with stable nitrate removal rate (NRR) of ∼28 mg NO3[-]-N L[-1] d[-1]. Microbial community analysis indicates abundant heterotrophs, e.g., Arenimonas (5.3%-18.9%) and Fimbriimonadales ATM1 (6.4%), were enriched together with denitrifying anaerobic methanotrophs Ca. Methanoperedens (10.8%-13.2%) and Ca. Methylomirabilis (27.4%-34.3%). The results of metagenomics and batch tests suggested that the denitrifying anaerobic methanotrophs were capable of generating methane-derived intermediates (i.e., formate and acetate), which were employed by non-methanotrophic heterotrophs for denitrification and biomass growth. These findings offer new insights into the roles of heterotrophs in n-DAMO mixed culture, which may help to optimize n-DAMO process for nitrogen removal from wastewater.}, } @article {pmid36375448, year = {2023}, author = {Webster, MT and Beaurepaire, A and Neumann, P and Stolle, E}, title = {Population Genomics for Insect Conservation.}, journal = {Annual review of animal biosciences}, volume = {11}, number = {}, pages = {115-140}, doi = {10.1146/annurev-animal-122221-075025}, pmid = {36375448}, issn = {2165-8110}, mesh = {Animals ; Humans ; *Ecosystem ; *Conservation of Natural Resources/methods ; Metagenomics ; Endangered Species ; Biodiversity ; Insecta/genetics ; }, abstract = {Insects constitute vital components of ecosystems. There is alarming evidence for global declines in insect species diversity, abundance, and biomass caused by anthropogenic drivers such as habitat degradation or loss, agricultural practices, climate change, and environmental pollution. This raises important concerns about human food security and ecosystem functionality and calls for more research to assess insect population trends and identify threatened species and the causes of declines to inform conservation strategies. Analysis of genetic diversity is a powerful tool to address these goals, but so far animal conservation genetics research has focused strongly on endangered vertebrates, devoting less attention to invertebrates, such as insects, that constitute most biodiversity. Insects' shorter generation times and larger population sizes likely necessitate different analytical methods and management strategies. The availability of high-quality reference genome assemblies enables population genomics to address several key issues. These include precise inference of past demographic fluctuations and recent declines, measurement of genetic load levels, delineation of evolutionarily significant units and cryptic species, and analysis of genetic adaptation to stressors. This enables identification of populations that are particularly vulnerable to future threats, considering their potential to adapt and evolve. We review the application of population genomics to insect conservation and the outlook for averting insect declines.}, } @article {pmid36375259, year = {2023}, author = {Niles, DT and Lee, RA and Lamb, GS and Dhaheri, FA and Boguniewicz, J}, title = {Plasma cell-free metagenomic next generation sequencing in the clinical setting for the diagnosis of infectious diseases: a systematic review and meta-analysis.}, journal = {Diagnostic microbiology and infectious disease}, volume = {105}, number = {1}, pages = {115838}, doi = {10.1016/j.diagmicrobio.2022.115838}, pmid = {36375259}, issn = {1879-0070}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing ; Retrospective Studies ; Metagenomics ; Plasma ; *Communicable Diseases/diagnosis ; Sensitivity and Specificity ; }, abstract = {Plasma cell-free metagenomic next-generation sequencing (cf-mNGS) is a non-invasive method that may be able to identify thousands of pathogens through a hypothesis-free approach. There is a lack of consensus on how this test compares to conventional microbiologic testing. We conducted a systematic review and meta-analysis of published studies evaluating the accuracy of plasma cf-mNGS in hospitalized patients and present pooled estimates of the positive (PPA) and negative percent agreement (NPA) compared to a composite reference standard that included all conventional microbiological testing and clinical history as assessed by an adjudication panel or clinical treatment team. Five retrospective studies (n = 552) were included. The majority of the patients (56%-88%) were immunocompromised. The pooled PPA was 67% (95% CI, 54%-81%) and the pooled NPA was 70% (95% CI, 63%-77%). The pooled diagnostic performance characteristics suggest that cf-mNGS provides limited evidence for ruling in or out the presence of infection as commonly used.}, } @article {pmid36373138, year = {2022}, author = {Hillary, LS and Adriaenssens, EM and Jones, DL and McDonald, JE}, title = {RNA-viromics reveals diverse communities of soil RNA viruses with the potential to affect grassland ecosystems across multiple trophic levels.}, journal = {ISME communications}, volume = {2}, number = {}, pages = {34}, pmid = {36373138}, issn = {2730-6151}, support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, abstract = {The distribution and diversity of RNA viruses in soil ecosystems are largely unknown, despite their significant impact on public health, ecosystem functions, and food security. Here, we characterise soil RNA viral communities along an altitudinal productivity gradient of peat, managed grassland and coastal soils. We identified 3462 viral contigs in RNA viromes from purified virus-like-particles in five soil-types and assessed their spatial distribution, phylogenetic diversity and potential host ranges. Soil types exhibited minimal similarity in viral community composition, but with >10-fold more viral contigs shared between managed grassland soils when compared with peat or coastal soils. Phylogenetic analyses predicted soil RNA viral communities are formed from viruses of bacteria, plants, fungi, vertebrates and invertebrates, with only 12% of viral contigs belonging to the bacteria-infecting Leviviricetes class. 11% of viral contigs were found to be most closely related to members of the Ourmiavirus genus, suggesting that members of this clade of plant viruses may be far more widely distributed and diverse than previously thought. These results contrast with soil DNA viromes which are typically dominated by bacteriophages. RNA viral communities, therefore, have the potential to exert influence on inter-kingdom interactions across terrestrial biomes.}, } @article {pmid36373106, year = {2022}, author = {Abdulkadir, M}, title = {Global health crisis and antimicrobial resistance: The need for increased metagenomics studies.}, journal = {Annals of medicine and surgery (2012)}, volume = {84}, number = {}, pages = {104817}, pmid = {36373106}, issn = {2049-0801}, } @article {pmid36372753, year = {2022}, author = {Zhuang, SQ and Mao, YX and Deng, FC and Luo, YY and Shi, WY and Li, X and Cao, YQ and Xu, JC and Tang, S}, title = {[Comparative analysis of metagenomic and 16S rDNA sequencing in gut microbiota of healthy elderly].}, journal = {Zhonghua yu fang yi xue za zhi [Chinese journal of preventive medicine]}, volume = {56}, number = {11}, pages = {1618-1624}, doi = {10.3760/cma.j.cn112150-20211222-01177}, pmid = {36372753}, issn = {0253-9624}, support = {DQGG0401//National Research Program for Key Issues in Air Pollution Control, China/ ; 2020YSRF_03//Young Scholar Scientific Research Foundation of National Institute of Environmental Health, China CDC/ ; }, mesh = {Male ; Female ; Humans ; Aged ; *Gastrointestinal Microbiome/genetics ; DNA, Ribosomal/genetics ; Feces ; Sequence Analysis, DNA ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Objective: To explore the differences in subsequent analysis between metagenomic and 16Sr DNA sequencing in compositionally characterizing gut microbiota of healthy elderly. Methods: By using a panel study design, five monthly repeated measurements were performed among 76 healthy older people in Jinan City, Shandong Province. Their fecal samples were collected, and genomic DNA was extracted and analyzed through metagenomic and 16Sr DNA sequencing to compare the composition and diversity of gut microbiota. The correlation between species abundance and α diversity was analyzed by Pearson correlation analysis, and the correlation between species abundance and β diversity was determined by Procrustes analysis. Results: The age of 76 participants was (65.07±2.75), and the body mass index was (25.03±2.40) kg/m[2]. There were 38 males and 38 females. A total of 345 fecal samples were obtained from five monthly repeated measurements. Compared with 16S rDNA sequencing, metagenomic sequencing showed more annotated species at each level. The difference in the number of two sequencing species increased with the decrease of the level. Although there were significant differences in species richness between the two sequencing methods. Their species richness was highly correlated at both phylum (r=0.88, P<0.001) and genus (r=0.77, P<0.001) levels. Bacteroidetes and Firmicutes were the common dominant species. Gut microbiota diversity analysis further showed that there was a significantly positive correlation between α diversity (r=0.70, P<0.001) and β diversities (M[2]=0.84, P<0.05) in the two groups. Conclusion: The annotation efficiency of metagenomic sequencing is much higher than that of 16S rDNA sequencing. The two sequencing methods are consistent in phylum abundance as well as α diversity.}, } @article {pmid36372432, year = {2022}, author = {Kuroda, K and Kubota, K and Kagemasa, S and Nakai, R and Hirakata, Y and Yamamoto, K and Nobu, MK and Narihiro, T}, title = {Novel Cross-domain Symbiosis between Candidatus Patescibacteria and Hydrogenotrophic Methanogenic Archaea Methanospirillum Discovered in a Methanogenic Ecosystem.}, journal = {Microbes and environments}, volume = {37}, number = {4}, pages = {}, pmid = {36372432}, issn = {1347-4405}, mesh = {*Archaea/genetics ; Methanospirillum/genetics ; Symbiosis ; Ecosystem ; In Situ Hybridization, Fluorescence ; Phylogeny ; *Euryarchaeota ; Bacteria/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {To identify novel cross-domain symbiosis between Candidatus Patescibacteria and Archaea, we performed fluorescence in situ hybridization (FISH) on enrichment cultures derived from methanogenic bioreactor sludge with the newly designed 32-520-1066 probe targeting the family-level uncultured clade 32-520/UBA5633 lineage in the class Ca. Paceibacteria. All FISH-detectable 32-520/UBA5633 cells were attached to Methanospirillum, indicating high host specificity. Transmission electron microscopy observations revealed 32-520/UBA5633-like cells that were specifically adherent to the plug structure of Methanospirillum-like rod-shaped cells. The metagenome-assembled genomes of 32-520/UBA5633 encoded unique gene clusters comprising pilin signal peptides and type IV pilins. These results provide novel insights into unseen symbiosis between Ca. Patescibacteria and Archaea.}, } @article {pmid36372382, year = {2023}, author = {Zheng, H and Zhang, Y and Li, S and Feng, X and Wu, Q and Kit Leong, Y and Chang, JS}, title = {Antibiotic sulfadiazine degradation by persulfate oxidation: Intermediates dependence of ecotoxicity and the induction of antibiotic resistance genes.}, journal = {Bioresource technology}, volume = {368}, number = {}, pages = {128306}, doi = {10.1016/j.biortech.2022.128306}, pmid = {36372382}, issn = {1873-2976}, mesh = {*Sulfadiazine/pharmacology/metabolism ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Sulfonamides ; }, abstract = {To preserve the water resources, this study has analyzed the ecotoxicity and antibiotic resistance genes (ARGs) induction capacity of sulfadiazine degradation intermediates resulting from persulfate activation oxidation enhanced by ultraviolet, ultrasound and microwave. The five degradation pathways caused by the contribution discrepancy of electron transfer and singlet oxygen ([1]O2) and variations in the ecotoxicity of different degradation products were analyzed. Microcosm experiment exhibited that the microbial community in actual water changed significantly with SDZ and degradation intermediates, in which the dominant genera were Aeromonas, Cupriavidus, Elizabethkingia and Achromobacter. Except for the selective pressure on bacteria, the degradation intermediates also exert a certain degree or even stronger induction on sulfonamide ARGs (sul4, sul1 and sul2) than SDZ. Furthermore, the potential hosts for sulfonamide ARGs were revealed by network analysis. These results provide a better understanding of antibiotics degradation mechanism and ARGs occurrence, which is useful for controlling the spread of ARGs.}, } @article {pmid36371918, year = {2022}, author = {Dong, X and Yu, K and Jia, X and Zhang, Y and Peng, X}, title = {Perchlorate reduction kinetics and genome-resolved metagenomics identify metabolic interactions in acclimated saline lake perchlorate-reducing consortia.}, journal = {Water research}, volume = {227}, number = {}, pages = {119343}, doi = {10.1016/j.watres.2022.119343}, pmid = {36371918}, issn = {1879-2448}, mesh = {Humans ; Bacteria/genetics/metabolism ; Iodine Radioisotopes/metabolism ; *Lakes/chemistry ; Metagenomics ; Oxidation-Reduction ; *Perchlorates/chemistry/isolation & purification ; *Water Pollutants, Chemical/isolation & purification ; }, abstract = {Perchlorate is a widely detected environmental contaminant in surface and underground water, that seriously impacts human health by inhibiting the uptake of thyroidal radioiodine. Perchlorate reduction due to saline lake microorganisms is not as well understood as that in marine environments. In this study, we enriched a perchlorate-reducing microbial consortium collected from saline lake sediments and found that the perchlorate reduction kinetics of the enriched consortium fit the Michaelis-Menten kinetics well, with a maximum specific substrate reduction rate (qmax) of 0.596 ± 0.001 mg ClO4[-]/mg DW/h and half-saturation constant (Ks) of 16.549 ± 0.488 mg ClO4[-]/L. Furthermore, we used improved metagenome binning to reconstruct high-quality metagenome-assembled genomes from the metagenomes of the microbial consortia, including the perchlorate-reducing bacteria (PRB) Dechloromonas agitata and Wolinella succinogenes, with the genome of W. succinogenes harboring complete functional genes for perchlorate reduction being the first recovered. Given that the electrons were directly transferred to the electronic carrier cytochrome c-553 from the quinone pool, the electron transfer pathway of W. succinogenes was shorter and more efficient than the canonical pattern. This finding provides a theoretical basis for microbial remediation of sites contaminated by high concentrations of perchlorate. Metagenomic binning and metatranscriptomic analyses revealed the gene transcription variation of perchlorate reductase pcr and chlorite dismutase cld by PRB and the synergistic metabolic mechanism.}, } @article {pmid36371463, year = {2022}, author = {Farda, B and Vaccarelli, I and Ercole, C and Djebaili, R and Del Gallo, M and Pellegrini, M}, title = {Exploring structure, microbiota, and metagenome functions of epigean and hypogean black deposits by microscopic, molecular and bioinformatic approaches.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {19405}, pmid = {36371463}, issn = {2045-2322}, mesh = {*Metagenome ; RNA, Ribosomal, 16S/genetics/metabolism ; Computational Biology ; *Microbiota/genetics ; Bacteria ; Phylogeny ; Archaea/genetics ; }, abstract = {This study revealed how Bacteria and Archaea communities and their metabolic functions differed between two groups of black deposits identified in gorge and cave environments. Scanning electron microscopy coupled with energy dispersive spectroscopy was used to analyse the presence of microbial biosignatures and the elemental composition of samples. Metabarcoding of the V3-V4 regions of 16S rRNA was used to investigate Bacteria and Archaea communities. Based on 16S rRNA sequencing results, PICRUSt software was used to predict metagenome functions. Micrographs showed that samples presented microbial biosignatures and microanalyses highlighted Mn concretions and layers on Al-Si surfaces. The 16S rRNA metabarcoding alpha-diversity metrics showed similar Simpson's and Shannon indices and different values of the Chao-1 index. The amplicon sequence variants (ASVs) analysis at the different taxonomic levels showed a diverse genera composition. However, the communities of all samples shared the presence of uncultured ASVs belonging to the Gemmatales family (Phylogenesis: Gemmataceae; Planctomycetes; Planctomycetota; Bacteria). The predicted metagenome functions analysis revealed diverse metabolic profiles of the Cave and Gorge groups. Genes coding for essential Mn metabolism were present in all samples. Overall, the findings on structure, microbiota, and predicted metagenome functions showed a similar microbial contribution to epigean and hypogean black deposits Mn metabolism.}, } @article {pmid36371193, year = {2022}, author = {Liu, Y and Angelov, A and Feiler, W and Baudrexl, M and Zverlov, V and Liebl, W and Vanderhaeghen, S}, title = {Arabinan saccharification by biogas reactor metagenome-derived arabinosyl hydrolases.}, journal = {Biotechnology for biofuels and bioproducts}, volume = {15}, number = {1}, pages = {121}, pmid = {36371193}, issn = {2731-3654}, support = {No. 031B0267B//Bundesministerium für Bildung und Forschung/ ; }, abstract = {BACKGROUND: Plant cell walls represent the most plentiful renewable organic resource on earth, but due to their heterogeneity, complex structure and partial recalcitrance, their use as biotechnological feedstock is still limited.

RESULTS: In order to identify efficient enzymes for polysaccharide breakdown, we have carried out functional screening of metagenomic fosmid libraries from biogas fermenter microbial communities grown on sugar beet pulp, an arabinan-rich agricultural residue, or other sources containing microbes that efficiently depolymerize polysaccharides, using CPH (chromogenic polysaccharide hydrogel) or ICB (insoluble chromogenic biomass) labeled polysaccharide substrates. Seventy-one depolymerase-encoding genes were identified from 55 active fosmid clones by using Illumina and Sanger sequencing and dbCAN CAZyme (carbohydrate-active enzyme) annotation. An around 56 kb assembled DNA fragment putatively originating from Xylanivirga thermophila strain or a close relative was analyzed in detail. It contained 48 ORFs (open reading frames), of which 31 were assigned to sugar metabolism. Interestingly, a large number of genes for enzymes putatively involved in degradation and utilization of arabinose-containing carbohydrates were found. Seven putative arabinosyl hydrolases from this DNA fragment belonging to glycoside hydrolase (GH) families GH51 and GH43 were biochemically characterized, revealing two with endo-arabinanase activity and four with exo-α-L-arabinofuranosidase activity but with complementary cleavage properties. These enzymes were found to act synergistically and can completely hydrolyze SBA (sugar beet arabinan) and DA (debranched arabinan).

CONCLUSIONS: We screened 32,776 fosmid clones from several metagenomic libraries with chromogenic lignocellulosic substrates for functional enzymes to advance the understanding about the saccharification of recalcitrant lignocellulose. Seven putative X. thermophila arabinosyl hydrolases were characterized for pectic substrate degradation. The arabinosyl hydrolases displayed maximum activity and significant long-term stability around 50 °C. The enzyme cocktails composed in this study fully degraded the arabinan substrates and thus could serve for arabinose production in food and biofuel industries.}, } @article {pmid36370947, year = {2023}, author = {Liu, Z and Cui, D and Liu, Y and Wang, H and Yang, L and Chen, H and Qiu, G and Xiong, Z and Shao, P and Luo, X}, title = {Enhanced ammonia nitrogen removal from actual rare earth element tailings (REEs) wastewater by microalgae-bacteria symbiosis system (MBS): Ratio optimization of microalgae to bacteria and mechanism analysis.}, journal = {Bioresource technology}, volume = {367}, number = {}, pages = {128304}, doi = {10.1016/j.biortech.2022.128304}, pmid = {36370947}, issn = {1873-2976}, mesh = {*Microalgae ; Wastewater/microbiology ; Ammonia ; Symbiosis ; Denitrification ; Nitrogen/analysis ; Bacteria/genetics ; Biomass ; }, abstract = {Microalgae-bacteria symbiosis system (MBS) appear to be a promising way for treating the rare earth elements (REEs) wastewater due to the natural symbiotic interactions between microalgae and bacteria. Herein, we investigated the effect of different inoculation ratios of microalgae and bacteria including 3:1 (MB_1), 1:1 (MB_2) and 1:3 (MB_3) on NH4[+]-N removal from REEs wastewater and analyzed the corresponding biological mechanism. The NH4[+]-N removal rate with MB_3 reached 17.69 ± 0.45 mg NH4[+]-N/L d[-1], which was 2.58 times higher than that in single microalgae system. The results were further verified in continuous feeding photobioreactors and kept stable for 100 days. Metagenomic analysis revealed that the abundance of genes related to microalgae assimilation increased by 14 %-50 % in answer to photosynthesis and NH4[+]-N absorption, while that related to nitrification apparently dropped, indicating that MBS was a sustainable method capable of enhancing NH4[+]-N removal from REEs wastewater.}, } @article {pmid36370776, year = {2023}, author = {Dinesh, R and Sreena, CP and Sheeja, TE and Charles, S and Srinivasan, V and Sajith, V and Subila, KP and Haritha, P}, title = {Metagenomics indicates abundance of biofilm related genes and horizontal transfer of multidrug resistant genes among bacterial communities in nano zinc oxide polluted soil.}, journal = {The Science of the total environment}, volume = {859}, number = {Pt 1}, pages = {160032}, doi = {10.1016/j.scitotenv.2022.160032}, pmid = {36370776}, issn = {1879-1026}, mesh = {*Zinc Oxide/toxicity ; Soil ; *Nanoparticles ; Biofilms ; *Metal Nanoparticles/toxicity ; Oxides ; }, abstract = {The unsafe and reckless disposal of metal oxide nanoparticles like ZnO (nZnO) into the soil could seriously impact bacterial behavioural responses and functions. Under such stress, biofilm formation is considered to be a robust mechanism for bacterial survival in soil. We examined the response of bacterial metagenomes in soils exposed to varying levels of Zn (50, 200, 500 and 1000 mg kg[-1]) as nano Zn oxide (nZnO) in terms of biofilm genesis and regulation and their co-occurrences with multidrug resistance genes (MDRGs) and mobile genetic elements (MGEs). The size-specific effects of nZnO were verified using its bulk counterpart (bZnO). Both nZnO and bZnO facilitated profusion of biofilm related genes (BGs) especially at higher Zn levels (500 and 1000 mg kg[-1] Zn), though maximum abundance was registered at a comparatively lower level under nZnO. In general, nZnO favoured an enhancement of genes involved in exopolysaccharide biosynthesis and attachment, while bZnO favoured genes related to capsule formation, chemotaxis and biofilm dispersion. Co-occurrence network analysis revealed significant positive correlations between abundances of BGs, MDRGs and MGEs, indicating an enhanced probability for horizontal gene transfer of MDRGs in nZnO polluted soils.}, } @article {pmid36369999, year = {2022}, author = {Zhang, C and Cheng, H and Zhao, Y and Chen, J and Li, M and Yu, Z and Sun, X and Li, P and Shang, Y and Ma, J and Zheng, J}, title = {Evaluation of Cell-Free DNA-Based Next-Generation Sequencing for Identifying Pathogens in Bacteremia Patients.}, journal = {Polish journal of microbiology}, volume = {71}, number = {4}, pages = {499-507}, pmid = {36369999}, issn = {2544-4646}, mesh = {Humans ; Escherichia coli ; High-Throughput Nucleotide Sequencing ; Genomics ; *Bacteremia ; *Cell-Free Nucleic Acids ; Klebsiella pneumoniae ; Sensitivity and Specificity ; }, abstract = {Rapid detection of bloodstream pathogens would greatly facilitate clinicians to make precise antimicrobial treatment in patients with bacteremia. In this study, 114 plasma samples were collected from patients with identified or suspected bacteremia, and pathogens were detected by the conventional blood culture (BC) and cell-free DNA metagenomics next-generation sequencing (cfDNA mNGS). The present study indicated that 76% (38/50) of positive conventional blood culture (BC[+] group) patients were positively detected by cfDNA mNGS, and only 4% were mismatched between cfDNA mNGS and conventional bacteria culture. Pathogens in 32.8% of suspected bacteremia patients with negative conventional blood culture (BC[-] group) were determined accurately by cfDNA mNGS combined with analyzing the patients' clinical manifestations. Escherichia coli and Klebsiella pneumoniae were the most detected pathogens in identified bacteremia patients by cfDNA mNGS. 76.2% (16/21) of E. coli and 92.3% (12/13) of K. pneumoniae in bacteremia patients were identified by conventional blood cultures that were also detected by cfDNA mNGS. This study demonstrated that genomic coverage of E. coli and K. pneumoniae were more often detected in BC[+] group patients and genomic coverage of Acinetobacter johnsonii and Paucibacter sp. KCTC 42545 was more often detected in BC[-] group patients. In conclusion, cfDNA mNGS could rapidly and precisely provide an alternative detection method for the diagnosis of bacteremia.}, } @article {pmid36369690, year = {2022}, author = {Li, S and Wang, S and Ji, G}, title = {Influences of carbon sources on N2O production during denitrification in freshwaters: Activity, isotopes and functional microbes.}, journal = {Water research}, volume = {226}, number = {}, pages = {119315}, doi = {10.1016/j.watres.2022.119315}, pmid = {36369690}, issn = {1879-2448}, mesh = {*Denitrification ; *Carbon ; Nitrous Oxide ; Nitrogen Isotopes/analysis ; Leucine ; Cellobiose ; Fresh Water ; Glucose ; }, abstract = {Denitrification is one of the major sources of N2O in freshwaters. Diverse forms of organic compounds act as the electron donors for microbial denitrification. However, the influences of carbon sources on N2O production, N2O reduction, isotope fractionation and functional microbes during denitrification were largely unknown. In this study, five forms of carbon sources (i.e. acetate, citrate, glucose, cellobiose and leucine) were used to enrich denitrifiers in freshwater sediments. N2O conversion in the enrichments was investigated by a combination of inhibition technique, natural stable isotope method and metagenomics. Acetylene was effective in inhibiting N2O reduction without influencing the isotopic characteristics during N2O production. Glucose led to the least N2O production and reduction, in accordance with the lowest abundance of both NO and N2O reductases in this enrichment. δ[18]O and site preference value (SP, =δ[15]N[α]-δ[15]N[β]) of N2O were sensitive to discriminate the five carbon sources, except when comparing acetate and leucine. Isotopic values of N2O were not significantly different in these two enrichments due to the similarity of NO reductases - Pseudomonas-type cNorB. Specifically, the enrichment with cellobiose produced N2O with the lowest δ[18]O values (39.4‰±1.1‰), due to Alicycliphilus with both cNorB and qNorB. The enrichment with glucose led to the highest SP values (8.9‰±8.6‰), caused by Thiobacillus-type cNorB. Our results demonstrated the link between carbon sources, N2O production and reduction, isotopic signatures, microbial populations and enzymes during denitrification in freshwaters.}, } @article {pmid36369419, year = {2023}, author = {Baran, B and Krzyżowski, M and Rádai, Z and Francikowski, J and Hohol, M}, title = {Geometry-based navigation in the dark: layout symmetry facilitates spatial learning in the house cricket, Acheta domesticus, in the absence of visual cues.}, journal = {Animal cognition}, volume = {26}, number = {3}, pages = {755-770}, pmid = {36369419}, issn = {1435-9456}, support = {This study was funded by the Polish Ministry of Science//Polish Ministry of Science and Higher Education/ ; Higher Education (the Diamond Grant program//Polish Ministry of Science and Higher Education/ ; id: DI2015025445//Polish Ministry of Science and Higher Education/ ; PI: Bartosz Baran)//Polish Ministry of Science and Higher Education/ ; MH research has been supported by a grant from the Priority Research Area FutureSoc under the Strategic Programme Excellence Initiative at Jagiellonian University.//Excellence Initiative-Jagiellonian University/ ; }, mesh = {Animals ; Cues ; *Gryllidae ; Spatial Learning ; Vision, Ocular ; Insecta ; *Spatial Navigation ; }, abstract = {The capacity to navigate by layout geometry has been widely recognized as a robust strategy of place-finding. It has been reported in various species, although most studies were performed with vision-based paradigms. In the presented study, we aimed to investigate layout symmetry-based navigation in the house cricket, Acheta domesticus, in the absence of visual cues. For this purpose, we used a non-visual paradigm modeled on the Tennessee Williams setup. We ensured that the visual cues were indeed inaccessible to insects. In the main experiment, we tested whether crickets are capable of learning to localize the centrally positioned, inconspicuous cool spot in heated arenas of various shapes (i.e., circular, square, triangular, and asymmetric quadrilateral). We found that the symmetry of the arena significantly facilitates crickets' learning to find the cool spot, indicated by the increased time spent on the cool spot and the decreased latency in locating it in subsequent trials. To investigate mechanisms utilized by crickets, we analyzed their approach paths to the spot. We found that crickets used both heuristic and directed strategies of approaching the target, with the dominance of a semi-directed strategy (i.e., a thigmotactic phase preceding direct navigation to the target). We propose that the poor performance of crickets in the asymmetrical quadrilateral arena may be explained by the difficulty of encoding its layout with cues from a single modality.}, } @article {pmid36369227, year = {2022}, author = {Meslier, V and Quinquis, B and Da Silva, K and Plaza Oñate, F and Pons, N and Roume, H and Podar, M and Almeida, M}, title = {Benchmarking second and third-generation sequencing platforms for microbial metagenomics.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {694}, pmid = {36369227}, issn = {2052-4463}, mesh = {Benchmarking ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; *Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Shotgun metagenomic sequencing is a common approach for studying the taxonomic diversity and metabolic potential of complex microbial communities. Current methods primarily use second generation short read sequencing, yet advances in third generation long read technologies provide opportunities to overcome some of the limitations of short read sequencing. Here, we compared seven platforms, encompassing second generation sequencers (Illumina HiSeq 300, MGI DNBSEQ-G400 and DNBSEQ-T7, ThermoFisher Ion GeneStudio S5 and Ion Proton P1) and third generation sequencers (Oxford Nanopore Technologies MinION R9 and Pacific Biosciences Sequel II). We constructed three uneven synthetic microbial communities composed of up to 87 genomic microbial strains DNAs per mock, spanning 29 bacterial and archaeal phyla, and representing the most complex and diverse synthetic communities used for sequencing technology comparisons. Our results demonstrate that third generation sequencing have advantages over second generation platforms in analyzing complex microbial communities, but require careful sequencing library preparation for optimal quantitative metagenomic analysis. Our sequencing data also provides a valuable resource for testing and benchmarking bioinformatics software for metagenomics.}, } @article {pmid36368924, year = {2022}, author = {Du, C and Zhou, X and Zhang, K and Huang, S and Wang, X and Zhou, S and Chen, Y}, title = {Inactivation of the MSTN gene expression changes the composition and function of the gut microbiome in sheep.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {273}, pmid = {36368924}, issn = {1471-2180}, mesh = {Sheep ; Male ; Female ; Animals ; *Myostatin/genetics ; *Gastrointestinal Microbiome ; Meat ; Gene Expression ; }, abstract = {BACKGROUND: Myostatin (MSTN) negatively regulates the muscle growth in animals and MSTN deficient sheep have been widely reported previously. The goal of this study was to explore how MSTN inactivation influences their gut microbiota composition and potential functions.

RESULTS: We compared the slaughter parameters and meat quality of 3 MSTN-edited male sheep and 3 wild-type male sheep, and analyzed the gut microbiome of the MSTN-edited sheep (8 female and 8 male sheep) and wild-type sheep (8 female and 8 male sheep) through metagenomic sequencing. The results showed that the body weight, carcass weight and eye muscle area of MSTN-edited sheep were significantly higher, but there were no significant differences in the meat quality indexes. At the microbial level, the alpha diversity was significantly higher in the MSTN-edited sheep (P < 0.05), and the microbial composition was significantly different by PCoA analysis in the MSTN-edited and wild-type sheep. The abundance of Firmicutes significantly increased and Bacteroidota significantly decreased in the MSTN-edited sheep. At genus level, the abundance of Flavonifractor, Subdoligranulum, Ruthenibacterium, Agathobaculum, Anaerotignum, Oribacterium and Lactobacillus were significantly increased in the MSTN-edited sheep (P < 0.05). Further analysis of functional differences was found that the carotenoid biosynthesis was significantly increased and the peroxisome, apoptosis, ferroptosis, N-glycan biosynthesis, thermogenesis, and adipocytokines pathways were decreased in the MSTN-edited sheep (P < 0.05). Moreover, carbohydrate-active enzymes (CAZymes) results certified the abundance of the GH13_39, GH4, GH137, GH71 and PL17 were upregulated, and the GT41 and CBM20 were downregulated in the MSTN-edited sheep (P < 0.05).

CONCLUSIONS: Our study suggested that MSTN inactivation remarkably influenced the composition and potential function of hindgut microbial communities of the sheep, and significantly promoted growth performance without affecting meat quality.}, } @article {pmid36368923, year = {2022}, author = {Rosenboom, I and Scheithauer, T and Friedrich, FC and Pörtner, S and Hollstein, L and Pust, MM and Sifakis, K and Wehrbein, T and Rosenhahn, B and Wiehlmann, L and Chhatwal, P and Tümmler, B and Davenport, CF}, title = {Wochenende - modular and flexible alignment-based shotgun metagenome analysis.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {748}, pmid = {36368923}, issn = {1471-2164}, mesh = {Humans ; *Metagenome ; Metagenomics/methods ; Software ; *Microbiota/genetics ; Genome, Human ; Sequence Analysis, DNA/methods ; Algorithms ; }, abstract = {BACKGROUND: Shotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome analysis of fungal, viral, archaeal and bacterial taxonomy, particularly with regard to visualization of read mapping location, normalization options, growth dynamics and functional gene repertoires. Current read classification tools use non-standard output formats, or do not fully show information on mapping location. As reference datasets are not perfect, portrayal of mapping information is critical for judging results effectively.

RESULTS: Our alignment-based pipeline, Wochenende, incorporates flexible quality control, trimming, mapping, various filters and normalization. Results are completely transparent and filters can be adjusted by the user. We observe stringent filtering of mismatches and use of mapping quality sharply reduces the number of false positives. Further modules allow genomic visualization and the calculation of growth rates, as well as integration and subsequent plotting of pipeline results as heatmaps or heat trees. Our novel normalization approach additionally allows calculation of absolute abundance profiles by comparison with reads assigned to the human host genome.

CONCLUSION: Wochenende has the ability to find and filter alignments to all kingdoms of life using both short and long reads, and requires only good quality reference genomes. Wochenende automatically combines multiple available modules ranging from quality control and normalization to taxonomic visualization. Wochenende is available at https://github.com/MHH-RCUG/nf_wochenende .}, } @article {pmid36368782, year = {2022}, author = {Yee, R and Simner, PJ}, title = {Next-Generation Sequencing Approaches to Predicting Antimicrobial Susceptibility Testing Results.}, journal = {Clinics in laboratory medicine}, volume = {42}, number = {4}, pages = {557-572}, doi = {10.1016/j.cll.2022.09.011}, pmid = {36368782}, issn = {1557-9832}, mesh = {*High-Throughput Nucleotide Sequencing/methods ; Anti-Bacterial Agents/pharmacology/therapeutic use ; *Anti-Infective Agents ; Sensitivity and Specificity ; }, } @article {pmid36368555, year = {2023}, author = {Wang, B and Song, L and Li, W and Hou, L and Li, J and Xu, X and Sheng, G}, title = {Distribution and migration of antibiotic resistance genes, as well as their correlation with microbial communities in swine farm and its surrounding environments.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {316}, number = {Pt 2}, pages = {120618}, doi = {10.1016/j.envpol.2022.120618}, pmid = {36368555}, issn = {1873-6424}, mesh = {Swine ; Animals ; Farms ; *Anti-Bacterial Agents/analysis ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; *Microbiota ; Manure/analysis ; Soil/chemistry ; Bacteria/genetics ; Water/analysis ; }, abstract = {The prevalence and correlation of antibiotic resistance genes (ARGs) in pig farm wastewater treatment plants (WWTPs) and surrounding environment were investigated using metagenomics and real time quantitative PCR (q-PCR). The hosts of ARGs were also studied in this study. The abundance of ARGs decreased significantly in the anoxic/oxic (A/O) process and disinfection tank of WWTPs. New ARGs emerged in wastewater that passed though the anaerobic reactor. The abundances of ARGs in the soils and water near pig farm were 10- and 35-fold higher than those in the control, respectively. The abundance of ARGs in wells near pig farm were an order of magnitude higher than that in the control. Similarly, a high abundance of ARGs was detected in swine manure. After composting, most of the ARGs were eliminated, but sul1 increased 10.5-fold. A high-throughput analysis revealed that the pig farm altered the microbial community structure in the surrounding environment, with 52% and 37% of the operational taxonomic units (OTUs) endemic to the soil and water samples near pig farm in comparison with these data in the control, respectively. The phyla Proteobacteria, Choroflexi, and Actinobacteriota dominated the water and soil samples. In addition, three pathogenic genera were found in the surrounding soil and water samples. A metagenomic analysis identified 14 types of ARGs (>1%), with the highest proportion of multidrug ARGs at 47%. A total of 28 subtypes of ARGs were detected (>1%), with macB the most prevalent. The correlation analysis revealed that several key phyla, including Proteobacteria, Actinobacteria and Acidobacteria, were the main potential hosts and posed a positive correlation with the ARGs. Efflux pumps (60-66%) were the primary resistance mechanism, and each resistance mechanism was distributed in similar proportions in the microbial community.}, } @article {pmid36368386, year = {2023}, author = {Zhang, D and Liu, H and Wang, S and Liu, Y and Ji, H}, title = {Wheat bran fermented by Lactobacillus regulated the bacteria-fungi composition and reduced fecal heavy metals concentrations in growing pigs.}, journal = {The Science of the total environment}, volume = {858}, number = {Pt 3}, pages = {159828}, doi = {10.1016/j.scitotenv.2022.159828}, pmid = {36368386}, issn = {1879-1026}, mesh = {Swine ; Animals ; Dietary Fiber ; Lactobacillus ; *Catechin ; *Metals, Heavy ; Caffeic Acids ; Gallic Acid ; }, abstract = {Lactobacillus fermentation can increase the value of wheat bran, but the benefits of fermented wheat bran for pig production are poorly understood. We evaluated the phenolic acid content of wheat bran fermented with Lactobacillus. The bacterial and fungal compositions, short-chain fatty acids, and heavy metals concentrations in the feces of growing pigs were determined, and the correlations between the bacterial and fungal compositions and short-chain fatty acid and heavy metals concentrations were also assessed. The concentrations of phenolic acids (caffeic acid, catechinic acid, and gallic acid) were higher in fermented bran than in control wheat bran. The diversity of feces bacterial species was significantly higher, whereas the diversity of fungi was lower in fermented wheat bran treatment than those in the control group, and pigs consuming fermented and control wheat bran with different bacterial and fungal compositions had different growth rates. The abundance of genera in fungi that were less abundant in the fermented group samples than in the control samples (including Wallemia, Trichosporon, Candida, Aspergillus, and unclassified_f__Microascaceae) was positively correlated with heavy metals concentrations in pig feces, and the abundances of these fungi were negatively correlated with caffeic acid, catechinic acid, and gallic acid concentrations. Metagenomic function predictions indicated that larger amounts of secondary metabolites were synthesized in the fermented group than in the control group. The results provide new insights into the roles of bacterial-fungal interactions in the growth and decreasing environmental pollution of pigs consuming fermented wheat bran.}, } @article {pmid36368254, year = {2022}, author = {Wackett, LP}, title = {Metagenomes of engineered environments: An annotated selection of World Wide Web sites relevant to the topics in environmental microbiology.}, journal = {Environmental microbiology reports}, volume = {14}, number = {6}, pages = {947-948}, doi = {10.1111/1758-2229.13134}, pmid = {36368254}, issn = {1758-2229}, mesh = {*Metagenome ; *Environmental Microbiology ; Internet ; }, } @article {pmid36368113, year = {2022}, author = {Gallego, JLR and Peña-Álvarez, V and Lara, LM and Baragaño, D and Forján, R and Colina, A and Prosenkov, A and Peláez, AI}, title = {Effective bioremediation of soil from the Burgan oil field (Kuwait) using compost: A comprehensive hydrocarbon and DNA fingerprinting study.}, journal = {Ecotoxicology and environmental safety}, volume = {247}, number = {}, pages = {114267}, doi = {10.1016/j.ecoenv.2022.114267}, pmid = {36368113}, issn = {1090-2414}, mesh = {*Composting ; Biodegradation, Environmental ; Oil and Gas Fields ; Soil ; DNA Fingerprinting ; Kuwait ; Hydrocarbons ; }, abstract = {An innovative combination of metagenomic profiling of microbial communities and GC-MS & Pyrolysis-GC-MS fingerprinting methods were used to assess the biodegradation of contaminated soil from the Burgan oil field in Kuwait. The soil was treated with (sludge) compost in microcosms to evaluate the feasibility of this material for bioremediation purposes. The most favourable trial showed a > 80% decrease in TPH, thereby indicating strong potential for full-scale application using a cost-effective technology and thus in line with the principles of the circular economy. The microbial study showed that compost addition enhanced the organic matter and nutrient content of the soil. However, the microorganisms in the compost did not seem to play a relevant role in bioremediation, meaning that compost amendments serve as a biostimulation rather than a bioaugmentation approach. The chemical study of the distinct oil fractions revealed rapidly biodegraded compounds (alkanes, alkyl-aromatics, etc.) and others that were much more refractory (hopanes, benzohopanes, etc.). Of note, although heavy fractions are usually considered recalcitrant to biodegradation, we observed incipient degradation of the asphaltene fraction by means of double-shot thermodesorption and pyrolysis. Finally, chemical fingerprinting also revealed that the treated soil contained some of the compounds found in the compost, such as coprostanol, cholesterol, and plant sterols. This observation would support the use of these compounds as proxies to monitor the effects of compost and to adjust dosages in real-scale bioremediation treatments.}, } @article {pmid36367700, year = {2022}, author = {Mallawaarachchi, V and Lin, Y}, title = {Accurate Binning of Metagenomic Contigs Using Composition, Coverage, and Assembly Graphs.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {29}, number = {12}, pages = {1357-1376}, doi = {10.1089/cmb.2022.0262}, pmid = {36367700}, issn = {1557-8666}, mesh = {*Metagenomics/methods ; Metagenome/genetics ; *Microbiota/genetics ; Algorithms ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenomics enables the recovery of various genetic materials from different species, thus providing valuable insights into microbial communities. Metagenomic binning group sequences belong to different organisms, which is an important step in the early stages of metagenomic analysis pipelines. The classic pipeline followed in metagenomic binning is to assemble short reads into longer contigs and then bin these resulting contigs into groups representing different taxonomic groups in the metagenomic sample. Most of the currently available binning tools are designed to bin metagenomic contigs, but they do not make use of the assembly graphs that produce such assemblies. In this study, we propose MetaCoAG, a metagenomic binning tool that uses assembly graphs with the composition and coverage information of contigs. MetaCoAG estimates the number of initial bins using single-copy marker genes, assigns contigs into bins iteratively, and adjusts the number of bins dynamically throughout the binning process. We show that MetaCoAG significantly outperforms state-of-the-art binning tools by producing similar or more high-quality bins than the second-best binning tool on both simulated and real datasets. To the best of our knowledge, MetaCoAG is the first stand-alone contig-binning tool that directly makes use of the assembly graph information along with other features of the contigs.}, } @article {pmid36619855, year = {2021}, author = {Puetz, LC and Delmont, TO and Aizpurua, O and Guo, C and Zhang, G and Katajamaa, R and Jensen, P and Gilbert, MTP}, title = {Gut Microbiota Linked with Reduced Fear of Humans in Red Junglefowl Has Implications for Early Domestication.}, journal = {Advanced genetics (Hoboken, N.J.)}, volume = {2}, number = {4}, pages = {2100018}, pmid = {36619855}, issn = {2641-6573}, abstract = {Domestication of animals can lead to profound phenotypic modifications within short evolutionary time periods, and for many species behavioral selection is likely at the forefront of this process. Animal studies have strongly implicated that the gut microbiome plays a major role in host behavior and cognition through the microbiome-gut-brain axis. Consequently, herein, it is hypothesized that host gut microbiota may be one of the earliest phenotypes to change as wild animals were domesticated. Here, the gut microbiome community in two selected lines of red junglefowl that are selected for either high or low fear of humans up to eight generations is examined. Microbiota profiles reveal taxonomic differences in gut bacteria known to produce neuroactive compounds between the two selection lines. Gut-brain module analysis by means of genome-resolved metagenomics identifies enrichment in the microbial synthesis and degradation potential of metabolites associated with fear extinction and reduces anxiety-like behaviors in low fear fowls. In contrast, high fear fowls are enriched in gut-brain modules from the butyrate and glutamate pathways, metabolites associated with fear conditioning. Overall, the results identify differences in the composition and functional potential of the gut microbiota across selection lines that may provide insights into the mechanistic explanations of the domestication process.}, } @article {pmid36659332, year = {2017}, author = {Bi, Y and Li, C and Liu, L and Zhou, J and Li, Z and Deng, H and Wu, C and Han, Y and Song, Y and Tan, Y and Wang, X and Du, Z and Cui, Y and Yan, Y and Zhi, F and Liu, G and Qin, N and Zhang, H and Yang, R}, title = {IL-17A-dependent gut microbiota is essential for regulating diet-induced disorders in mice.}, journal = {Science bulletin}, volume = {62}, number = {15}, pages = {1052-1063}, doi = {10.1016/j.scib.2017.07.011}, pmid = {36659332}, issn = {2095-9281}, abstract = {The gut microbiota plays a key role in obesity and related metabolic disorders, and multiple factors including diet, host genotype, and age regulate it. Many studies have examined the contribution of extrinsic factors to the regulation of the gut microbiota, but the importance of the host genetic constitution cannot be ignored. Interleukin 17A (IL-17A), a pro-inflammatory cytokine, is important in the defense against infection and diseases. Here, we investigated the association among IL-17, a high-fat diet (HFD), and the gut microbiota. Mice deficient in IL-17A were resistant to diet-induced obesity and related diseases. Compared with the Il-17a[-/-] mice, wild-type (WT) mice challenged with HFD showed obvious weight fluctuations, such as those seen in type 2 diabetes, and hematological changes similar to those associated with metabolic syndrome. However, housing WT mice and Il-17a[-/-] mice together significantly alleviated these symptoms in the WT mice. A metagenomic analysis of the mouse feces indicated that the microbial community compositions of these two groups differed before HFD feeding. The HFD mediated shifts in the gut microbial compositions, which were associated with the mouse phenotypes. We also identified potentially beneficial and harmful species present during this period, and drew networks of the most abundant species. A functional analysis indicated pathway changes in the WT and Il-17a[-/-] mice when fed the HFD. Collectively, these data underscore the importance of the host factor IL-17A in shaping and regulating the gut microbiota, which conversely, influences the host health.}, } @article {pmid36659481, year = {2017}, author = {Gao, P and Hou, Q and Kwok, LY and Huo, D and Feng, S and Zhang, H}, title = {Effect of feeding Lactobacillus plantarum P-8 on the faecal microbiota of broiler chickens exposed to lincomycin.}, journal = {Science bulletin}, volume = {62}, number = {2}, pages = {105-113}, doi = {10.1016/j.scib.2017.01.001}, pmid = {36659481}, issn = {2095-9281}, abstract = {Poultry and eggs are nutritious and healthy foods that contain high-quality proteins and low levels of fat compared with other meats. Recent studies have shown that poultry performance is closely associated with colonic health. Antibiotics are commonly used in the poultry industry to control diseases and enhance survival rates. However, antibiotic use can also result in host gut dysbiosis and immune dysregulation. Such imbalances compromise poultry health and growth performance. Thus, our study investigated the effect of Lactobacillus (L.) plantarum P-8 on the gut microbiome of chickens co-inoculated with the antibiotic lincomycin. Principal coordinate analysis showed that L. plantarum P-8 treatment shifted the faecal bacterial population structure. At the metagenomic level, the Clusters of Orthologous Groups (COGs) functional categories of P, C, N and A were overrepresented in the probiotic group. Additionally, the relative gene abundances of metabolic pathways involved in flagellar assembly, bacterial chemotaxis, nitrogen metabolism, sulfur metabolism, cofactor and vitamin biosynthesis were also higher in the probiotic group than the control; in contrast genes related to galactose degradation, carbon fixation, multiple sugar transport systems and ribosomes were underrepresented in the probiotic group. Our data suggest that feeding L. plantarum P-8 has the potential to improve metabolic activity and nutrient utilization of poultry. Furthermore, the faecal antibiotic resistomes of the two groups could be separated using principal components analysis, indicating that the probiotic treatment may modulate the intestinal antibiotic resistance gene pool by changing the population structure of the gut microbiota. This study has provided interesting insights into the application of probiotics in the poultry industry.}, } @article {pmid36337362, year = {2021}, author = {Navapurkar, V and Bartholdson Scott, J and Maes, M and Hellyer, TP and Higginson, E and Forrest, S and Pereira-Dias, J and Parmar, S and Heasman-Hunt, E and Polgarova, P and Brown, J and Titti, L and Smith, WP and Scott, J and Rostron, A and Routledge, M and Sapsford, D and Török, ME and McMullan, R and Enoch, DA and Wong, V and , and Curran, MD and Brown, NM and Simpson, AJ and Herre, J and Dougan, G and Conway Morris, A}, title = {Development and implementation of a customised rapid syndromic diagnostic test for severe pneumonia.}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {256}, pmid = {36337362}, issn = {2398-502X}, support = {205214/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MR/N029399/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Background: The diagnosis of pneumonia has been hampered by a reliance on bacterial cultures which take several days to return a result, and are frequently negative. In critically ill patients this leads to the use of empiric, broad-spectrum antimicrobials and compromises good antimicrobial stewardship. The objective of this study was to establish the performance of a syndromic molecular diagnostic approach, using a custom TaqMan array card (TAC) covering 52 respiratory pathogens, and assess its impact on antimicrobial prescribing. Methods: The TAC was validated against a retrospective multi-centre cohort of broncho-alveolar lavage samples. The TAC was assessed prospectively in patients undergoing investigation for suspected pneumonia, with a comparator cohort formed of patients investigated when the TAC laboratory team were unavailable. Co-primary outcomes were sensitivity compared to conventional microbiology and, for the prospective study, time to result. Metagenomic sequencing was performed to validate findings in prospective samples. Antibiotic free days (AFD) were compared between the study cohort and comparator group. Results: 128 stored samples were tested, with sensitivity of 97% (95% confidence interval (CI) 88-100%). Prospectively, 95 patients were tested by TAC, with 71 forming the comparator group. TAC returned results 51 hours (interquartile range 41-69 hours) faster than culture and with sensitivity of 92% (95% CI 83-98%) compared to conventional microbiology. 94% of organisms identified by sequencing were detected by TAC. There was a significant difference in the distribution of AFDs with more AFDs in the TAC group (p=0.02). TAC group were more likely to experience antimicrobial de-escalation (odds ratio 2.9 (95%1.5-5.5)). Conclusions: Implementation of a syndromic molecular diagnostic approach to pneumonia led to faster results, with high sensitivity and impact on antibiotic prescribing.}, } @article {pmid36367339, year = {2023}, author = {Raghwani, J and Faust, CL and François, S and Nguyen, D and Marsh, K and Raulo, A and Hill, SC and Parag, KV and Simmonds, P and Knowles, SCL and Pybus, OG}, title = {Seasonal dynamics of the wild rodent faecal virome.}, journal = {Molecular ecology}, volume = {32}, number = {17}, pages = {4763-4776}, pmid = {36367339}, issn = {1365-294X}, support = {220414/WT_/Wellcome Trust/United Kingdom ; 851550/ERC_/European Research Council/International ; }, mesh = {Animals ; *Virome ; Seasons ; Cross-Sectional Studies ; Animals, Wild ; Arvicolinae ; Murinae ; }, abstract = {Viral discovery studies in wild animals often rely on cross-sectional surveys at a single time point. As a result, our understanding of the temporal stability of wild animal viromes remains poorly resolved. While studies of single host-virus systems indicate that host and environmental factors influence seasonal virus transmission dynamics, comparable insights for whole viral communities in multiple hosts are lacking. Utilizing noninvasive faecal samples from a long-term wild rodent study, we characterized viral communities of three common European rodent species (Apodemus sylvaticus, A. flavicollis and Myodes glareolus) living in temperate woodland over a single year. Our findings indicate that a substantial fraction of the rodent virome is seasonally transient and associated with vertebrate or bacteria hosts. Further analyses of one of the most common virus families, Picornaviridae, show pronounced temporal changes in viral richness and evenness, which were associated with concurrent and up to ~3-month lags in host density, ambient temperature, rainfall and humidity, suggesting complex feedbacks from the host and environmental factors on virus transmission and shedding in seasonal habitats. Overall, this study emphasizes the importance of understanding the seasonal dynamics of wild animal viromes in order to better predict and mitigate zoonotic risks.}, } @article {pmid36366828, year = {2023}, author = {Wang, X and Xu, Q and Hu, K and Wang, G and Shi, K}, title = {A Coculture of Enterobacter and Comamonas Species Reduces Cadmium Accumulation in Rice.}, journal = {Molecular plant-microbe interactions : MPMI}, volume = {36}, number = {2}, pages = {95-108}, doi = {10.1094/MPMI-09-22-0186-R}, pmid = {36366828}, issn = {0894-0282}, mesh = {Cadmium/analysis/metabolism ; *Oryza/metabolism ; Enterobacter/genetics ; *Comamonas/metabolism ; Coculture Techniques ; In Situ Hybridization, Fluorescence ; Soil/chemistry ; *Soil Pollutants/analysis/metabolism ; }, abstract = {The accumulation of cadmium (Cd) in plants is strongly impacted by soil microbes, but its mechanism remains poorly understood. Here, we report the mechanism of reduced Cd accumulation in rice by coculture of Enterobacter and Comamonas species. In pot experiments, inoculation with the coculture decreased Cd content in rice grain and increased the amount of nonbioavailable Cd in Cd-spiked soils. Fluorescence in situ hybridization and scanning electron microscopy detection showed that the coculture colonized in the rhizosphere and rice root vascular tissue and intercellular space. Soil metagenomics data showed that the coculture increased the abundance of sulfate reduction and biofilm formation genes and related bacterial species. Moreover, the coculture increased the content of organic matter, available nitrogen, and potassium and increased the activities of arylsulfatase, β-galactosidase, phenoloxidase, arylamidase, urease, dehydrogenase, and peroxidase in soils. In subsequent rice transcriptomics assays, we found that the inoculation with coculture activated a hypersensitive response, defense-related induction, and mitogen-activated protein kinase signaling pathway in rice. Heterologous protein expression in yeast confirmed the function of four Cd-binding proteins (HIP28-1, HIP28-4, BCP2, and CID8), a Cd efflux protein (BCP1), and three Cd uptake proteins (COPT4, NRAM5, and HKT6) in rice. Succinic acid and phenylalanine were subsequently proved to inhibit rice divalent Cd [Cd(II)] uptake and activate Cd(II) efflux in rice roots. Thus, we propose a model that the coculture protects rice against Cd stress via Cd immobilization in soils and reducing Cd uptake in rice. [Formula: see text] Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.}, } @article {pmid36366580, year = {2022}, author = {Spezia, PG and Baj, A and Drago Ferrante, F and Boutahar, S and Azzi, L and Genoni, A and Dalla Gasperina, D and Novazzi, F and Dentali, F and Focosi, D and Maggi, F}, title = {Detection of Torquetenovirus and Redondovirus DNA in Saliva Samples from SARS-CoV-2-Positive and -Negative Subjects.}, journal = {Viruses}, volume = {14}, number = {11}, pages = {}, pmid = {36366580}, issn = {1999-4915}, mesh = {Humans ; *Torque teno virus/genetics ; SARS-CoV-2/genetics ; Saliva ; *DNA Virus Infections ; *COVID-19/epidemiology ; Viral Load ; DNA, Viral/analysis ; }, abstract = {OBJECTIVES: Torquetenovirus (TTV) and Redondovirus (ReDoV) are the most prevalent viruses found in the human respiratory virome in viral metagenomics studies. A large-scale epidemiological study was performed to investigate their prevalence and loads in saliva samples according to SARS-CoV-2 status.

METHODS: Saliva samples from 448 individuals (73% SARS-CoV-2 negative and 27% SARS-CoV-2 positive) aged 23-88 years were tested. SARS-CoV-2 and TTV were determined in saliva by specific qualitative and quantitative real-time PCRs, respectively. A sub-cohort of 377 subjects was additionally tested for the presence and load of ReDoV in saliva, and a different sub-cohort of 120 subjects for which paired saliva and plasma samples were available was tested for TTV and ReDoV viremia at the same timepoints as saliva.

RESULTS: TTV in saliva was 72% prevalent in the entire cohort, at a mean DNA load of 4.6 log copies/mL, with no difference regardless of SARS-CoV-2 status. ReDoV was found in saliva from 61% of the entire cohort and was more prevalent in the SARS-CoV-2-negative subgroup (65% vs. 52%, respectively). In saliva, the total mean load of ReDoV was very similar to the one of TTV, with a value of 4.4 log copies/mL. The mean viral loads in subjects infected with a single virus, namely, those infected with TTV or ReDoV alone, was lower than in dually infected samples, and Tukey's multiple-comparison test showed that ReDoV single-infected samples resulted in the only true outlier (p = 0.004). Differently from TTV, ReDoV was not detected in any blood samples.

CONCLUSIONS: This study establishes the prevalence and mean value of TTV and ReDoV in saliva samples and demonstrates the existence of differences between these two components of the human virome.}, } @article {pmid36366546, year = {2022}, author = {Slavov, SN}, title = {Viral Metagenomics for Identification of Emerging Viruses in Transfusion Medicine.}, journal = {Viruses}, volume = {14}, number = {11}, pages = {}, pmid = {36366546}, issn = {1999-4915}, mesh = {Humans ; Metagenomics ; *Transfusion Medicine ; *Viruses/genetics ; *Virus Diseases/diagnosis ; Metagenome ; Genome, Viral ; }, abstract = {Viral metagenomics has revolutionized our understanding for identification of unknown or poorly characterized viruses. For that reason, metagenomic studies gave been largely applied for virus discovery in a wide variety of clinical samples, including blood specimens. The emerging blood-transmitted virus infections represent important problem for public health, and the emergence of HIV in the 1980s is an example for the vulnerability of Blood Donation systems to such infections. When viral metagenomics is applied to blood samples, it can give a complete overview of the viral nucleic acid abundance, also named "blood virome". Detailed characterization of the blood virome of healthy donors could identify unknown (emerging) viral genomes that might be assumed as hypothetic transfusion threats. However, it is impossible only by application of viral metagenomics to assign that one viral agent could impact blood transfusion. That said, this is a complex issue and will depend on the ability of the infectious agent to cause clinically important infection in blood recipients, the viral stability in blood derivatives and the presence of infectious viruses in blood, making possible its transmission by transfusion. This brief review summarizes information regarding the blood donor virome and some important challenges for use of viral metagenomics in hemotherapy for identification of transfusion-transmitted viruses.}, } @article {pmid36366489, year = {2022}, author = {Silva, FA and Ferreira, MS and Araújo, PA and Casseb, SMM and Silva, SP and Nunes Neto, JP and Chiang, JO and Rosa Junior, JW and Chagas, LL and Freitas, MNO and Santos, ÉB and Hernández, L and Paz, T and Vasconcelos, PFC and Martins, LC}, title = {Serological and Molecular Evidence of the Circulation of the Venezuelan Equine Encephalitis Virus Subtype IIIA in Humans, Wild Vertebrates and Mosquitos in the Brazilian Amazon.}, journal = {Viruses}, volume = {14}, number = {11}, pages = {}, pmid = {36366489}, issn = {1999-4915}, mesh = {Animals ; Humans ; *Encephalitis Virus, Venezuelan Equine/genetics ; *Culicidae ; Brazil/epidemiology ; Ecosystem ; *Arboviruses ; *Alphavirus ; Vertebrates ; }, abstract = {Understanding the interaction between viruses and ecosystems in areas with or without anthropic interference can contribute to the organization of public health services, as well as prevention and disease control. An arbovirus survey was conducted at Caxiuanã National Forest, Pará, Brazil, where 632 local residents, 338 vertebrates and 15,774 pools of hematophagous arthropods were investigated. Neutralization antibodies of the Venezuelan Equine Encephalitis virus, subtype IIIA, Mucambo virus (MUCV) were detected in 57.3% and 61.5% of humans and wild vertebrates, respectively; in addition, genomic fragments of MUCV were detected in pool of Uranotaenia (Ura.) geometrica. The obtained data suggest an enzootic circulation of MUCV in the area. Understanding the circulation of endemic and neglected arboviruses, such as MUCV, represents an important health problem for the local residents and for the people living in the nearby urban centers.}, } @article {pmid36366436, year = {2022}, author = {Andrade, PS and Valença, IN and Heinisch, MRS and Rocha, EC and Fernandes, LN and Faria, NR and Sabino, EC and Lima-Camara, TN}, title = {First Report of Wenzhou sobemo-like virus 4 in Aedes albopictus (Diptera: Culicidae) in Latin America.}, journal = {Viruses}, volume = {14}, number = {11}, pages = {}, pmid = {36366436}, issn = {1999-4915}, support = {MR/S019510/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Female ; Humans ; *Aedes ; *Zika Virus Infection ; *Zika Virus/genetics ; *Dengue Virus ; Mosquito Vectors ; Latin America ; Brazil ; *Arboviruses ; *RNA Viruses ; }, abstract = {Insect-specific viruses (ISVs) are viruses that replicate exclusively in arthropod cells. Many ISVs have been studied in mosquitoes as many of them act as vectors for human etiological agents, such as arboviruses. Aedes (Stegomyia) albopictus is an important potential vector of several arboviruses in Brazil, such as dengue (DENV), Zika (ZIKV) and chikungunya (CHIKV). The development of next-generation sequencing metagenomics has enabled the discovery and characterization of new ISVs. Ae. albopictus eggs were collected using oviposition traps placed in two urban parks in the city of São Paulo, Brazil. The Aedes albopictus females were divided into pools and the genetic material was extracted and processed for sequencing by metagenomics. Complete genomes of ISV Wenzhou sobemo-like virus 4 (WSLV4) were obtained in three of the four pools tested. This is the first detection of ISV WSLV4 in Ae. albopictus females in Latin America. Further studies on ISVs in Ae. albopictus are needed to better understand the role of this species in the dynamics of arbovirus transmission in the Americas.}, } @article {pmid36365429, year = {2022}, author = {Narsing Rao, MP and Lohmaneeratana, K and Bunyoo, C and Thamchaipenet, A}, title = {Actinobacteria-Plant Interactions in Alleviating Abiotic Stress.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {21}, pages = {}, pmid = {36365429}, issn = {2223-7747}, support = {FF(KU)5.64//Kasetsart University Research and Development Institute (KURDI)/ ; KU Reinventing University 2022//Ministry of Higher Education, Science, Research and Innovation, Thailand/ ; }, abstract = {Abiotic stressors, such as drought, flooding, extreme temperature, soil salinity, and metal toxicity, are the most important factors limiting crop productivity. Plants use their innate biological systems to overcome these abiotic stresses caused by environmental and edaphic conditions. Microorganisms that live in and around plant systems have incredible metabolic abilities in mitigating abiotic stress. Recent advances in multi-omics methods, such as metagenomics, genomics, transcriptomics, and proteomics, have helped to understand how plants interact with microbes and their environment. These methods aid in the construction of various metabolic models of microbes and plants, resulting in a better knowledge of all metabolic exchanges engaged during interactions. Actinobacteria are ubiquitous and are excellent candidates for plant growth promotion because of their prevalence in soil, the rhizosphere, their capacity to colonize plant roots and surfaces, and their ability to produce various secondary metabolites. Mechanisms by which actinobacteria overcome abiotic stress include the production of osmolytes, plant hormones, and enzymes, maintaining osmotic balance, and enhancing nutrient availability. With these characteristics, actinobacteria members are the most promising candidates as microbial inoculants. This review focuses on actinobacterial diversity in various plant regions as well as the impact of abiotic stress on plant-associated actinobacterial diversity and actinobacteria-mediated stress mitigation processes. The study discusses the role of multi-omics techniques in expanding plant-actinobacteria interactions, which aid plants in overcoming abiotic stresses and aims to encourage further investigations into what may be considered a relatively unexplored area of research.}, } @article {pmid36365426, year = {2022}, author = {Hegedűs, G and Kutasy, B and Kiniczky, M and Decsi, K and Juhász, Á and Nagy, Á and Pallos, JP and Virág, E}, title = {Liposomal Formulation of Botanical Extracts may Enhance Yield Triggering PR Genes and Phenylpropanoid Pathway in Barley (Hordeum vulgare).}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {21}, pages = {}, pmid = {36365426}, issn = {2223-7747}, support = {KFI_16-1-2017-0457//Government of Hungary/ ; }, abstract = {This work aimed to study the plant conditioning effect and mode of action of a plant-based biostimulant used in organic farming. This new generation plant biostimulant, named ELICE16INDURES[®], is rich in plant bio-active ingredients containing eleven supercritical botanical extracts encapsulated in nano-scale liposomes. The dose-response (10 to 240 g ha[-1]) relationship was tested in a field population of autumn barley (Hordeum vulgare) test crop, and underlying molecular mechanisms were studied. Applying nanotechnology, cell-identical nanoparticles may help the better uptake and delivery of active ingredients increasing resilience, vitality, and crop yield. The amount of harvested crops showed a significant increase of 27.5% and 39.9% interconnected to higher normalized difference vegetation index (NDVI) of 20% and 25% after the treatment of low and high dosages (20 and 240 g ha[-1]), respectively. Illumina NextSeq 550 sequencing, gene expression profiling, and KEGG-pathway analysis of outstanding dosages indicated the upregulation of pathogenesis-related (PR) and other genes-associated with induced resistance-which showed dose dependency as well.}, } @article {pmid36365369, year = {2022}, author = {Bunyoo, C and Roongsattham, P and Khumwan, S and Phonmakham, J and Wonnapinij, P and Thamchaipenet, A}, title = {Dynamic Alteration of Microbial Communities of Duckweeds from Nature to Nutrient-Deficient Condition.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {21}, pages = {}, pmid = {36365369}, issn = {2223-7747}, support = {2002//Kasetsart University Reinventing University Program/ ; FF(KU)4.64//Kasetsart University Research and Development Institute (KURDI)/ ; 2021-2026//The Science and Technology Research Partnership for Sustainable Development (SATREPS), JICA, Japan/ ; }, abstract = {Duckweeds live with complex assemblages of microbes as holobionts that play an important role in duckweed growth and phytoremediation ability. In this study, the structure and diversity of duckweed-associated bacteria (DAB) among four duckweed subtypes under natural and nutrient-deficient conditions were investigated using V3-V4 16S rRNA amplicon sequencing. High throughput sequencing analysis indicated that phylum Proteobacteria was predominant in across duckweed samples. A total of 24 microbial genera were identified as a core microbiome that presented in high abundance with consistent proportions across all duckweed subtypes. The most abundant microbes belonged to the genus Rhodobacter, followed by other common DAB, including Acinetobacter, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, and Pseudomonas. After nutrient-deficient stress, diversity of microbial communities was significantly deceased. However, the relative abundance of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Pelomonas, Roseateles and Novosphingobium were significantly enhanced in stressed duckweeds. Functional prediction of the metagenome data displayed the relative abundance of essential pathways involved in DAB colonization, such as bacterial motility and biofilm formation, as well as biodegradable ability, such as benzoate degradation and nitrogen metabolism, were significantly enriched under stress condition. The findings improve the understanding of the complexity of duckweed microbiomes and facilitate the establishment of a stable microbiome used for co-cultivation with duckweeds for enhancement of biomass and phytoremediation under environmental stress.}, } @article {pmid36365042, year = {2022}, author = {Barbosa, AD and Long, M and Lee, W and Austen, JM and Cunneen, M and Ratchford, A and Burns, B and Kumarasinghe, P and Ben-Othman, R and Kollmann, TR and Stewart, CR and Beaman, M and Parry, R and Hall, R and Tabor, A and O'Donovan, J and Faddy, HM and Collins, M and Cheng, AC and Stenos, J and Graves, S and Oskam, CL and Ryan, UM and Irwin, PJ}, title = {The Troublesome Ticks Research Protocol: Developing a Comprehensive, Multidiscipline Research Plan for Investigating Human Tick-Associated Disease in Australia.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {11}, pages = {}, pmid = {36365042}, issn = {2076-0817}, support = {APP1169949//National Health and Medical Research Council/ ; }, abstract = {In Australia, there is a paucity of data about the extent and impact of zoonotic tick-related illnesses. Even less is understood about a multifaceted illness referred to as Debilitating Symptom Complexes Attributed to Ticks (DSCATT). Here, we describe a research plan for investigating the aetiology, pathophysiology, and clinical outcomes of human tick-associated disease in Australia. Our approach focuses on the transmission of potential pathogens and the immunological responses of the patient after a tick bite. The protocol is strengthened by prospective data collection, the recruitment of two external matched control groups, and sophisticated integrative data analysis which, collectively, will allow the robust demonstration of associations between a tick bite and the development of clinical and pathological abnormalities. Various laboratory analyses are performed including metagenomics to investigate the potential transmission of bacteria, protozoa and/or viruses during tick bite. In addition, multi-omics technology is applied to investigate links between host immune responses and potential infectious and non-infectious disease causations. Psychometric profiling is also used to investigate whether psychological attributes influence symptom development. This research will fill important knowledge gaps about tick-borne diseases. Ultimately, we hope the results will promote improved diagnostic outcomes, and inform the safe management and treatment of patients bitten by ticks in Australia.}, } @article {pmid36364902, year = {2022}, author = {Liang, T and Li, D and Zunong, J and Li, M and Amaerjiang, N and Xiao, H and Khattab, NM and Vermund, SH and Hu, Y}, title = {Interplay of Lymphocytes with the Intestinal Microbiota in Children with Nonalcoholic Fatty Liver Disease.}, journal = {Nutrients}, volume = {14}, number = {21}, pages = {}, pmid = {36364902}, issn = {2072-6643}, support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; 2022-1G-4262//Capital's Funds for Health Improvement and Research/ ; 7202009//Beijing Natural Science Foundation/ ; 82073574//National Natural Science Foundation of China/ ; }, mesh = {Child ; Humans ; *Non-alcoholic Fatty Liver Disease/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; Verrucomicrobia ; Lymphocytes ; Liver ; }, abstract = {Abnormally high lymphocyte counts are seen in persons with nonalcoholic fatty liver disease (NAFLD). Gut microbiota dysbiosis is a risk factor for NAFLD. We assessed the gut microbiota of 63 healthy children and 63 children with NAFLD using 16S rRNA gene and metagenomic sequencing to explore the relationships. Compared with healthy children (HC group), the Bacteroidetes, Verrucomicrobia, and Akkermansia were less abundant, while the Actinobacteria were more abundant in children with NAFLD (FLD group). To understand the effect of lymphocytes on the gut microbiota of children with NAFLD, we compared the microbiota of 41 children with NAFLD and high numbers of lymphocytes (FLD_HL group) and 22 children with NAFLD and low numbers of lymphocytes (FLD_LL group). The abundances of Bacteroidetes, Verrucobacterium, and Akkermansia increased and Actinobacteria decreased in the FLD_LL group compared to the FLD_HL group. Akkermansia was negatively correlated with lymphocyte count. NAFLD may disturb the gut microbiota in children through reducing the abundance of Akkermansia and increasing the abundance of proinflammatory bacteria, such as Escherichia-Shigella. Conclusions: High lymphocyte counts are associated with disturbances of gut microbiota and emergence of opportunistic pathogens in children with NAFLD.}, } @article {pmid36364873, year = {2022}, author = {Barber, C and Sabater, C and Ávila-Gálvez, MÁ and Vallejo, F and Bendezu, RA and Guérin-Deremaux, L and Guarner, F and Espín, JC and Margolles, A and Azpiroz, F}, title = {Effect of Resistant Dextrin on Intestinal Gas Homeostasis and Microbiota.}, journal = {Nutrients}, volume = {14}, number = {21}, pages = {}, pmid = {36364873}, issn = {2072-6643}, support = {//Roquette Frères (France)/ ; PID2021-122295OB-I00//Ministerio de Ciencia e Innovación, Spain/ ; PID2019-103914RB-I00//Ministerio de Ciencia e Innovación, Spain/ ; AGL2016-78311-R//Ministerio de Ciencia e Innovación, Spain/ ; FJC2019-042125-I//Ministerio de Ciencia e Innovación, Spain/ ; }, mesh = {Humans ; *Dextrins/pharmacology ; *Microbiota ; Intestines ; Prebiotics ; Feces ; Homeostasis ; }, abstract = {Previous studies have shown that a resistant dextrin soluble fibre has prebiotic properties with related health benefits on blood glucose management and satiety. Our aim was to demonstrate the effects of continuous administration of resistant dextrin on intestinal gas production, digestive sensations, and gut microbiota metabolism and composition. Healthy subjects (n = 20) were given resistant dextrin (14 g/d NUTRIOSE[®], Roquette Frères, Lestrem, France) for four weeks. Outcomes were measured before, at the beginning, end, and two weeks after administration: anal evacuations of gas during daytime; digestive perception, girth, and gas production in response to a standard meal; sensory and digestive responses to a comfort meal; volume of colonic biomass by magnetic resonance; taxonomy and metabolic functions of fecal microbiota by shotgun sequencing; metabolomics in urine. Dextrin administration produced an initial increase in intestinal gas production and gas-related sensations, followed by a subsequent decrease, which magnified after discontinuation. Dextrin enlarged the volume of colonic biomass, inducing changes in microbial metabolism and composition with an increase in short chain fatty acids-producing species and modulation of bile acids and biotin metabolism. These data indicate that consumption of a soluble fibre induces an adaptative response of gut microbiota towards fermentative pathways with lower gas production.}, } @article {pmid36364844, year = {2022}, author = {Lin, H and Chen, J and Ma, S and An, R and Li, X and Tan, H}, title = {The Association between Gut Microbiome and Pregnancy-Induced Hypertension: A Nested Case-Control Study.}, journal = {Nutrients}, volume = {14}, number = {21}, pages = {}, pmid = {36364844}, issn = {2072-6643}, support = {81773535//National Natural Science Foundation of China/ ; 2018SK2061//Key Research and Development Program of Hunan Province/ ; }, mesh = {Humans ; Female ; Pregnancy ; *Gastrointestinal Microbiome/physiology ; Dysbiosis/microbiology ; Case-Control Studies ; *Hypertension, Pregnancy-Induced ; Blood Pressure/physiology ; Bacteria/genetics ; }, abstract = {(1) Background: Pregnancy-induced hypertension (PIH) is associated with obvious microbiota dysbiosis in the third trimester of pregnancy. However, the mechanisms behind these changes remain unknown. Therefore, this study aimed to explore the relationship between the gut microbiome in early pregnancy and PIH occurrence. (2) Methods: A nested case-control study design was used based on the follow-up cohort. Thirty-five PIH patients and thirty-five matched healthy pregnant women were selected as controls. The gut microbiome profiles were assessed in the first trimester using metagenomic sequencing. (3) Results: Diversity analyses showed that microbiota diversity was altered in early pregnancy. At the species level, eight bacterial species were enriched in healthy controls: Alistipes putredinis, Bacteroides vulgatus, Ruminococcus torques, Oscillibacter unclassified, Akkermansia muciniphila, Clostridium citroniae, Parasutterella excrementihominis and Burkholderiales bacterium_1_1_47. Conversely, Eubacterium rectale, and Ruminococcus bromii were enriched in PIH patients. The results of functional analysis showed that the changes in these different microorganisms may affect the blood pressure of pregnant women by affecting the metabolism of vitamin K2, sphingolipid, lipid acid and glycine. (4) Conclusion: Microbiota dysbiosis in PIH patients begins in the first trimester of pregnancy, and this may be associated with the occurrence of PIH. Bacterial pathway analyses suggest that the gut microbiome might lead to the development of PIH through the alterations of function modules.}, } @article {pmid36364726, year = {2022}, author = {Xiao, F and Gao, X and Hu, H and Le, J and Chen, Y and Shu, X and Liang, Z and Xu, Y and Wang, Y and Zhang, T}, title = {Exclusive Enteral Nutrition Exerts Anti-Inflammatory Effects through Modulating Microbiota, Bile Acid Metabolism, and Immune Activities.}, journal = {Nutrients}, volume = {14}, number = {21}, pages = {}, pmid = {36364726}, issn = {2072-6643}, support = {81900474//National Natural Science Foundation of China/ ; 81870373//National Natural Science Foundation of China/ ; 19140904300//Shanghai Science and Technology Committee/ ; ZDSYS20200811143757022//Shenzhen Key Laboratory Foundation/ ; 802-012677//Peacock Talent Programs Research Start-up Grant/ ; }, mesh = {Mice ; Animals ; *Enteral Nutrition ; Remission Induction ; Leukocytes, Mononuclear ; *Microbiota ; Bacteria ; Anti-Inflammatory Agents ; Bile Acids and Salts ; }, abstract = {Exclusive enteral nutrition (EEN) can induce remission in patients with pediatric Crohn's disease (CD). This study aims to depict EEN's modification of bile acid (BA) metabolism in pediatric CD and explores the effect of the EEN-enriched BA in inhibiting the inflammatory response. The twelve enrolled pediatric CD patients showed BA dysmetabolism, represented by decreased levels of fecal secondary and unconjugated BAs as determined by UPLC-TQMS, which were accompanied by gut microbiota dysbiosis and reduced BA-metabolizing bacteria including Eubacterium and Ruminococcus genera, assessed by shotgun metagenomic sequencing. EEN treatment induced remission in these patients at eight weeks, and nine patients remained in stable remission for longer than 48 weeks. EEN improved BA dysmetabolism, with some enriched BAs, including hyocholic acid (HCA), α-muricholic acid (αMCA), strongly associated with decreased severity of CD symptoms. These BAs were significantly correlated with the increased abundance of certain bacteria, including Clostridium innocuum and Hungatella hathewayi, which express 3β-hydroxysteroid dehydrogenase and 5β-reductase. HCA could suppress TNF-α production by CD4+ T cells in the peripheral blood mononuclear cells (PBMCs) of CD patients. Moreover, intraperitoneal injection of HCA could attenuate dextran sulfate sodium (DSS)-induced mouse colitis. Our data suggests that BA modification may contribute to the EEN-induced remission of pediatric CD.}, } @article {pmid36364328, year = {2022}, author = {Baćmaga, M and Wyszkowska, J and Borowik, A and Kucharski, J}, title = {Effects of Tebuconazole Application on Soil Microbiota and Enzymes.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {21}, pages = {}, pmid = {36364328}, issn = {1420-3049}, support = {30.610.006-110//University of Warmia and Mazury in Olsztyn, Faculty of Agriculture and Forestry, Department of Soil Science and Microbiology/ ; 010/RID/2018/19//Minister of Education and Science in the range of the program entitled "Regional Initiative of Excellence" for the years 2019-2023/ ; }, mesh = {*Soil/chemistry ; Soil Microbiology ; *Microbiota ; Triazoles/pharmacology ; Bacteria ; RNA, Ribosomal, 16S ; }, abstract = {Identification of pesticide impact on the soil microbiome is of the utmost significance today. Diagnosing the response of bacteria to tebuconazole, used for plant protection, may help isolate the most active bacteria applicable in the bioaugmentation of soils contaminated with this preparation. Bearing in mind the above, a study was undertaken to test the effect of tebuconazole on the diversity of bacteria at all taxonomic levels and on the activity of soil enzymes. It was conducted by means of standard and metagenomic methods. Its results showed that tebuconazole applied in doses falling within the ranges of good agricultural practice did not significantly disturb the biological homeostasis of soil and did not diminish its fertility. Tebuconazole was found to stimulate the proliferation of organotrophic bacteria and fungi, and also the activities of soil enzymes responsible for phosphorus, sulfur, and carbon metabolism. It did not impair the activity of urease responsible for urea hydrolysis, or cause any significant changes in the structure of bacterial communities. All analyzed soil samples were mainly populated by bacteria from the phylum Proteobacteria, Actinobacteria, Firmicutes, Gemmatimonadetes, Acidobacteria, Planctomycetes, and Chloroflexi. Bacteria from the genera Kaistobacter, Arthrobacter, and Streptomyces predominated in the soils contaminated with tebuconazole, whereas these from the Gemmata genus were inactivated by this preparation.}, } @article {pmid36363775, year = {2022}, author = {Lee, CC and Liao, YC and Lee, MC and Cheng, YC and Chiou, SY and Lin, JS and Huang, CC and Watanabe, K}, title = {Different Impacts of Heat-Killed and Viable Lactiplantibacillus plantarum TWK10 on Exercise Performance, Fatigue, Body Composition, and Gut Microbiota in Humans.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36363775}, issn = {2076-2607}, abstract = {Lactiplantibacillus plantarum TWK10, a probiotic strain, has been demonstrated to improve exercise performance, regulate body composition, and ameliorate age-related declines. Here, we performed a comparative analysis of viable and heat-killed TWK10 in the regulation of exercise performance, body composition, and gut microbiota in humans. Healthy adults (n = 53) were randomly divided into three groups: Control, TWK10 (viable TWK10, 3 × 10[11] colony forming units/day), and TWK10-hk (heat-killed TWK10, 3 × 10[11] cells/day) groups. After six-week administration, both the TWK10 and TWK10-hk groups had significantly improved exercise performance and fatigue-associated features and reduced exercise-induced inflammation, compared with controls. Viable TWK10 significantly promoted improved body composition, by increasing muscle mass proportion and reducing fat mass. Gut microbiota analysis demonstrated significantly increasing trends in the relative abundances of Akkermansiaceae and Prevotellaceae in subjects receiving viable TWK10. Predictive metagenomic profiling revealed that heat-killed TWK10 administration significantly enhanced the signaling pathways involved in amino acid metabolisms, while glutathione metabolism, and ubiquinone and other terpenoid-quinone biosynthesis pathways were enriched by viable TWK10. In conclusion, viable and heat-killed TWK10 had similar effects in improving exercise performance and attenuating exercise-induced inflammatory responses as probiotics and postbiotics, respectively. Viable TWK10 was also highly effective in regulating body composition. The differences in efficacy between viable and heat-killed TWK10 may be due to differential impacts in shaping gut microbiota.}, } @article {pmid36363774, year = {2022}, author = {Yang, J and Li, W and Teng, D and Yang, X and Zhang, Y and Li, Y}, title = {Metagenomic Insights into Microbial Community Structure, Function, and Salt Adaptation in Saline Soils of Arid Land, China.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36363774}, issn = {2076-2607}, support = {31960285//National Natural Science Foundation of China/ ; XJEDU2019Y015//the Higher college and university science Foundation of Xinjiang, China/ ; PT2107//the Xinjiang Uygur Autonomous Region innovation environment Construction special project & Science and technology innovation base construction project/ ; }, abstract = {Soil salinization is spread in the dryland of NW China due to the dry or extreme dry climate. Increased salinization damages the health and function of soil systems and influences the microbial community structure and function. Some studies have been conducted to reveal the microbial community structure and isolate the microorganisms of saline soil or salt-lake sediments in this region. However, the functions of microorganisms and their response to salinization, i.e., their adaptation strategy to a wide salinization range in arid environments, are less understood. Here, we applied metagenomics technology to investigate the microbial community structure, function, and their relationship with salinization, and discussed the adaptative strategy of microorganisms to different saline environments. A total of 42 samples were sequenced on the Illumina PE500 platform. The archaea and bacteria constituted the dominant kingdoms; Actinobacteria, Proteobacteria, Bacteroidetes, and Firmicutes were the dominant bacterial phyla; and Euryarchaeota were the dominant archaeal phylum. The microbial communities showed significant structure divergence according to the salt concentration (saline (mean EC 22 mS/cm) and hypersaline (mean EC 70 mS/cm)), wherein the communities were dominated by bacteria in saline soils and archaea in hypersaline soils. Most of the dominant bacterial representation decreased with salinity, while the archaea increased with salinity. KEGG functional annotation showed that at level 2, the cell motility, environmental adaptation, signal transduction, signaling molecules and interaction, glycan biosynthesis and metabolism, and metabolism of other amino acids were reduced from saline to hypersaline, whereas the metabolism of cofactors and vitamins, folding sorting and degradation, replication and repair, transcription and translation, amino acid biosynthesis, glycolysis/gluconeogenesis, and carbon fixation increased with salinity. The increased salt content decreased the carbohydrate activities of microorganisms. The osmolyte regulation substance synthesis and absorption-related genes were more abundant in saline soils than in hypersaline soils, whereas the Na[+]/H[+] antiporter genes (mnhB-E) and H[+]/Na[+]-transporting ATPase genes (atpA-F, I, K) were significantly higher in hypersaline soils. This indicated that in saline soils, microorganisms primarily synthesize and/or uptake compatible solutes to cope with osmotic stress, whereas in the hypersaline habitat, the high-salt-in strategy was predicated to be adopted by the halophilic/extremely halophilic microorganisms, coupled with a high abundance of replication and repair, cofactors and vitamin metabolism, nucleotide metabolism, and carbon fixation to provide energy and ensure cell regeneration. In conclusion, increases in salinity influence the microbial communities' structure and function, as well as the adaptation of microorganisms.}, } @article {pmid36363763, year = {2022}, author = {Kravchenko, I and Rayko, M and Tikhonova, E and Konopkin, A and Abakumov, E and Lapidus, A}, title = {Agricultural Crops Grown in Laboratory Conditions on Chernevaya Taiga Soil Demonstrate Unique Composition of the Rhizosphere Microbiota.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36363763}, issn = {2076-2607}, support = {19-16-00049//Russian Science Foundation/ ; FFEN-2022-0022//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {Chernevaya taiga in West Siberia is a unique environment, with gigantism of grasses and shrubs. Exceptionally high productivity of plants is determined by the synergistic interaction of various factors, with a special role belonging to microorganisms colonizing the plant roots. This research explored whether agricultural plants can recruit specific microorganisms from within virgin Chernevaya Umbrisol and thus increase their productivity. Radish and wheat plants were grown on the Umbrisol (T1) and control Retisol of Scotch pine forest stand (T3) soils in the phytotron, and then a bacterial community analysis of the rhizosphere was performed using high-throughput sequencing of the 16S rRNA genes. In laboratory experiments, the plant physiological parameters were significantly higher when growing on the Umbrisol as compared to the Retisol. Bacterial diversity in T1 soil was considerably higher than in the control sample, and the principal coordinate analysis demonstrated apparent differences in the bacterial communities associated with the plants. Agricultural plants growing in the T1 soil form specific prokaryotic communities, with dominant genera Chthoniobacter, Pseudomonas, Burkholderia, and Massilia. These communities also include less abundant but essential for plant growth nitrifiers Cand. Nitrosocosmius and Nitrospira, and representatives of Proteobacteria, Bacilli, and Actinobacteria, known to be gibberellin-producers.}, } @article {pmid36363749, year = {2022}, author = {Castro-Mejía, JL and Khakimov, B and Aru, V and Lind, MV and Garne, E and Paulová, P and Tavakkoli, E and Hansen, LH and Smilde, AK and Holm, L and Engelsen, SB and Nielsen, DS}, title = {Gut Microbiome and Its Cofactors Are Linked to Lipoprotein Distribution Profiles.}, journal = {Microorganisms}, volume = {10}, number = {11}, pages = {}, pmid = {36363749}, issn = {2076-2607}, support = {4105-00015B//Innovation Fund Denmark/ ; }, abstract = {Increasing evidence indicates that the gut microbiome (GM) plays an important role in dyslipidemia. To date, however, no in-depth characterization of the associations between GM with lipoproteins distributions (LPD) among adult individuals with diverse BMI has been conducted. To determine such associations, we studied blood-plasma LPD, fecal short-chain fatty acids (SCFA) and GM of 262 Danes aged 19-89 years. Stratification of LPD segregated subjects into three clusters displaying recommended levels of lipoproteins and explained by age and body-mass-index. Higher levels of HDL2a and HDL2b were associated with a higher abundance of Ruminococcaceae and Christensenellaceae. Increasing levels of total cholesterol and LDL-1 and LDL-2 were positively associated with Lachnospiraceae and Coriobacteriaceae, and negatively with Bacteroidaceae and Bifidobacteriaceae. Metagenome-sequencing showed a higher abundance of biosynthesis of multiple B-vitamins and SCFA metabolism genes among healthier LPD profiles. Metagenomic-assembled genomes (MAGs) affiliated to Eggerthellaceae and Clostridiales were contributors of these genes and their relative abundance correlated positively with larger HDL subfractions. The study demonstrates that differences in composition and metabolic traits of the GM are associated with variations in LPD among the recruited subjects. These findings provide evidence for GM considerations in future research aiming to shed light on mechanisms of the GM-dyslipidemia axis.}, } @article {pmid36362265, year = {2022}, author = {Nirmalkar, K and Qureshi, F and Kang, DW and Hahn, J and Adams, JB and Krajmalnik-Brown, R}, title = {Shotgun Metagenomics Study Suggests Alteration in Sulfur Metabolism and Oxidative Stress in Children with Autism and Improvement after Microbiota Transfer Therapy.}, journal = {International journal of molecular sciences}, volume = {23}, number = {21}, pages = {}, pmid = {36362265}, issn = {1422-0067}, support = {GR37996//Finch Therapuetics, MA, USA and Arizona Board of regents/ ; }, mesh = {Child ; Humans ; *Autistic Disorder ; RNA, Ribosomal, 16S/genetics/metabolism ; *Autism Spectrum Disorder/genetics/therapy/metabolism ; *Microbiota ; Metagenomics ; Oxidative Stress ; Sulfur ; }, abstract = {Links between gut microbiota and autism spectrum disorder (ASD) have been explored in many studies using 16S rRNA gene amplicon and shotgun sequencing. Based on these links, microbiome therapies have been proposed to improve gastrointestinal (GI) and ASD symptoms in ASD individuals. Previously, our open-label microbiota transfer therapy (MTT) study provided insight into the changes in the gut microbial community of children with ASD after MTT and showed significant and long-term improvement in ASD and GI symptoms. Using samples from the same study, the objective of this work was to perform a deeper taxonomic and functional analysis applying shotgun metagenomic sequencing. Taxonomic analyses revealed that ASD Baseline had many bacteria at lower relative abundances, and their abundance increased after MTT. The relative abundance of fiber consuming and beneficial microbes including Prevotella (P. dentalis, P. enoeca, P. oris, P. meloninogenica), Bifidobacterium bifidum, and a sulfur reducer Desulfovibrio piger increased after MTT-10wks in children with ASD compared to Baseline (consistent at genus level with the previous 16S rRNA gene study). Metabolic pathway analysis at Baseline compared to typically developing (TD) children found an altered abundance of many functional genes but, after MTT, they became similar to TD or donors. Important functional genes that changed included: genes encoding enzymes involved in folate biosynthesis, sulfur metabolism and oxidative stress. These results show that MTT treatment not only changed the relative abundance of important genes involved in metabolic pathways, but also seemed to bring them to a similar level to the TD controls. However, at a two-year follow-up, the microbiota and microbial genes shifted into a new state, distinct from their levels at Baseline and distinct from the TD group. Our current findings suggest that microbes from MTT lead to initial improvement in the metabolic profile of children with ASD, and major additional changes at two years post-treatment. In the future, larger cohort studies, mechanistic in vitro experiments and metatranscriptomics studies are recommended to better understand the role of these specific microbes, functional gene expression, and metabolites relevant to ASD.}, } @article {pmid36362150, year = {2022}, author = {Sterling, KG and Dodd, GK and Alhamdi, S and Asimenios, PG and Dagda, RK and De Meirleir, KL and Hudig, D and Lombardi, VC}, title = {Mucosal Immunity and the Gut-Microbiota-Brain-Axis in Neuroimmune Disease.}, journal = {International journal of molecular sciences}, volume = {23}, number = {21}, pages = {}, pmid = {36362150}, issn = {1422-0067}, support = {N/A//C.E. Hudig UNR Foundation Award for Undergraduate Research/ ; U54 GM104944/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Immunity, Mucosal ; *Gastrointestinal Microbiome/physiology ; *Enteric Nervous System/physiology ; *Parkinson Disease ; Brain/physiology ; }, abstract = {Recent advances in next-generation sequencing (NGS) technologies have opened the door to a wellspring of information regarding the composition of the gut microbiota. Leveraging NGS technology, early metagenomic studies revealed that several diseases, such as Alzheimer's disease, Parkinson's disease, autism, and myalgic encephalomyelitis, are characterized by alterations in the diversity of gut-associated microbes. More recently, interest has shifted toward understanding how these microbes impact their host, with a special emphasis on their interactions with the brain. Such interactions typically occur either systemically, through the production of small molecules in the gut that are released into circulation, or through signaling via the vagus nerves which directly connect the enteric nervous system to the central nervous system. Collectively, this system of communication is now commonly referred to as the gut-microbiota-brain axis. While equally important, little attention has focused on the causes of the alterations in the composition of gut microbiota. Although several factors can contribute, mucosal immunity plays a significant role in shaping the microbiota in both healthy individuals and in association with several diseases. The purpose of this review is to provide a brief overview of the components of mucosal immunity that impact the gut microbiota and then discuss how altered immunological conditions may shape the gut microbiota and consequently affect neuroimmune diseases, using a select group of common neuroimmune diseases as examples.}, } @article {pmid36361709, year = {2022}, author = {Torres-Sánchez, A and Ruiz-Rodríguez, A and Ortiz, P and Moreno, MA and Ampatzoglou, A and Gruszecka-Kosowska, A and Monteoliva-Sánchez, M and Aguilera, M}, title = {Exploring Next Generation Probiotics for Metabolic and Microbiota Dysbiosis Linked to Xenobiotic Exposure: Holistic Approach.}, journal = {International journal of molecular sciences}, volume = {23}, number = {21}, pages = {}, pmid = {36361709}, issn = {1422-0067}, support = {PI20/01278//Instituto de Salud Carlos III/ ; IE_2019-198//FEDER Project Infrastructure/ ; }, mesh = {Animals ; Humans ; Dysbiosis/therapy ; Xenobiotics ; *Probiotics/therapeutic use ; *Microbiota ; *Gastrointestinal Microbiome ; }, abstract = {Variation of gut microbiota in metabolic diseases seems to be related to dysbiosis induced by exposure to multiple substances called Microbiota Disrupting Chemicals (MDCs), which are present as environmental and dietary contaminants. Some recent studies have focused on elucidating the alterations of gut microbiota taxa and their metabolites as a consequence of xenobiotic exposures to find possible key targets involved in the severity of the host disease triggered. Compilation of data supporting the triad of xenobiotic-microbiota-metabolic diseases would subsequently allow such health misbalances to be prevented or treated by identifying beneficial microbe taxa that could be Next Generation Probiotics (NGPs) with metabolic enzymes for MDC neutralisation and mitigation strategies. In this review, we aim to compile the available information and reports focused on variations of the main gut microbiota taxa in metabolic diseases associated with xenobiotic exposure and related microbial metabolite profiles impacting the host health status. We performed an extensive literature search using SCOPUS, Web of Science, and PubMed databases. The data retrieval and thorough analyses highlight the need for more combined metagenomic and metabolomic studies revealing signatures for xenobiotics and triggered metabolic diseases. Moreover, metabolome and microbiome compositional taxa analyses allow further exploration of how to target beneficial NGP candidates according to their alleged variability abundance and potential therapeutic significance. Furthermore, this holistic approach has identified limitations and the need of future directions to expand and integrate key knowledge to design appropriate clinical and interventional studies with NGPs. Apart from human health, the beneficial microbes and metabolites identified could also be proposed for various applications under One Health, such as probiotics for animals, plants and environmental bioremediation.}, } @article {pmid36360204, year = {2022}, author = {Qin, C and Chen, Z and Cao, R and Shi, M and Tian, Y}, title = {Integrated Analysis of the Fecal Metagenome and Metabolome in Bladder Cancer in a Chinese Population.}, journal = {Genes}, volume = {13}, number = {11}, pages = {}, pmid = {36360204}, issn = {2073-4425}, mesh = {Humans ; *Metagenome ; *Urinary Bladder Neoplasms/genetics ; Metabolome ; Metabolomics ; China ; }, abstract = {Bladder cancer (BLCA) is a common malignancy of the urinary system. The gut microbiome produces various metabolites that play functional roles in tumorigenesis and tumor progression. However, the integrative analysis of the gut microbiome and metabolome in BLCA has still been lacking. Thus, the aim of this study was to identify microbial and functional characteristics and metabolites in BLCA in a Chinese population. Metagenomics, targeted metabolomics, bioinformatics, and integrative analysis were used in fecal samples of BLCA patients and healthy individuals. We found gut microbiomes were significantly dysregulated in BLCA patients, including Bifidobacterium, Lactobacillus, Streptococcus, Blautia, and Eubacterium. We also found 11Z-eicosenoic acid, 3-methoxytyrosine, abrine, aniline-2-sulfonate, arachidic acid, conjugated linoleic acids, elaidic acid, glycylleucine, glycylproline, leucyl-glycine, linoelaidic acid, linoleic acid, nicotinamide hypoxanthine dinucleotide, oleic acid, petroselinic acid, and ricinoleic acid to be significantly decreased, while cholesterol sulfate was significantly increased in BLCA patients. Integration of metagenomics and metabolomics revealed interactions between gut microbiota and metabolites and the host. We identified the alterations of gut microbiomes and metabolites in BLCA in a Chinese population. Moreover, we preliminarily revealed the associations between specific gut microbiomes and metabolites. These findings determined potential causative links among gut dysbiosis, dysregulated metabolites, and BLCA.}, } @article {pmid36360179, year = {2022}, author = {Sartaj, K and Patel, A and Matsakas, L and Prasad, R}, title = {Unravelling Metagenomics Approach for Microbial Biofuel Production.}, journal = {Genes}, volume = {13}, number = {11}, pages = {}, pmid = {36360179}, issn = {2073-4425}, mesh = {*Biofuels ; *Metagenomics ; Biomass ; Sugars ; }, abstract = {Renewable biofuels, such as biodiesel, bioethanol, and biobutanol, serve as long-term solutions to fossil fuel depletion. A sustainable approach feedstock for their production is plant biomass, which is degraded to sugars with the aid of microbes-derived enzymes, followed by microbial conversion of those sugars to biofuels. Considering their global demand, additional efforts have been made for their large-scale production, which is ultimately leading breakthrough research in biomass energy. Metagenomics is a powerful tool allowing for functional gene analysis and new enzyme discovery. Thus, the present article summarizes the revolutionary advances of metagenomics in the biofuel industry and enlightens the importance of unexplored habitats for novel gene or enzyme mining. Moreover, it also accentuates metagenomics potentials to explore uncultivable microbiomes as well as enzymes associated with them.}, } @article {pmid36360159, year = {2022}, author = {Xing, P and Zhao, Y and Guan, D and Li, L and Zhao, B and Ma, M and Jiang, X and Tian, C and Cao, F and Li, J}, title = {Effects of Bradyrhizobium Co-Inoculated with Bacillus and Paenibacillus on the Structure and Functional Genes of Soybean Rhizobacteria Community.}, journal = {Genes}, volume = {13}, number = {11}, pages = {}, pmid = {36360159}, issn = {2073-4425}, mesh = {*Bradyrhizobium/genetics ; Glycine max ; Plant Roots/microbiology ; *Bacillus ; Soil/chemistry ; *Paenibacillus/genetics ; Phosphorus ; Nitrogen ; }, abstract = {Plant growth-promoting rhizobacteria (PGPR) are widely used to improve soil nutrients and promote plant growth and health. However, the growth-promoting effect of a single PGPR on plants is limited. Here, we evaluated the effect of applying rhizobium Bradyrhizobium japonicum 5038 (R5038) and two PGPR strains, Bacillus aryabhattai MB35-5 (BA) and Paenibacillus mucilaginosus 3016 (PM), alone or in different combinations on the soil properties and rhizosphere bacterial community composition of soybean (Glycine max). Additionally, metagenomic sequencing was performed to elucidate the profile of functional genes. Inoculation with compound microbial inoculant containing R5038 and BA (RB) significantly improved nodule nitrogenase activity and increased soil nitrogen content, and urease activity increased the abundance of the nitrogen cycle genes and Betaproteobacteria and Chitinophagia in the rhizosphere. In the treatment of inoculant-containing R5038 and PM (RP), significant changes were found for the abundance of Deltaproteobacteria and Gemmatimonadetes and the phosphorus cycle genes, and soil available phosphorus and phosphatase activity were increased. The RBP inoculants composed of three strains (R5038, BA and PM) significantly affected soybean biomass and the N and P contents of the rhizosphere. Compared with RB and RP, RBP consistently increased soybean nitrogen content, and dry weight. Overall, these results showed that several PGPR with different functions could be combined into composite bacterial inoculants, which coordinately modulate the rhizosphere microbial community structure and improve soybean growth.}, } @article {pmid36359992, year = {2022}, author = {Cardin, M and Cardazzo, B and Mounier, J and Novelli, E and Coton, M and Coton, E}, title = {Authenticity and Typicity of Traditional Cheeses: A Review on Geographical Origin Authentication Methods.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {21}, pages = {}, pmid = {36359992}, issn = {2304-8158}, support = {20192413451/ISCR_D1//University of Padua/ ; }, abstract = {Food fraud, corresponding to any intentional action to deceive purchasers and gain an undue economical advantage, is estimated to result in a 10 to 65 billion US dollars/year economical cost worldwide. Dairy products, such as cheese, in particular cheeses with protected land- and tradition-related labels, have been listed as among the most impacted as consumers are ready to pay a premium price for traditional and typical products. In this context, efficient food authentication methods are needed to counteract current and emerging frauds. This review reports the available authentication methods, either chemical, physical, or DNA-based methods, currently used for origin authentication, highlighting their principle, reported application to cheese geographical origin authentication, performance, and respective advantages and limits. Isotope and elemental fingerprinting showed consistent accuracy in origin authentication. Other chemical and physical methods, such as near-infrared spectroscopy and nuclear magnetic resonance, require more studies and larger sampling to assess their discriminative power. Emerging DNA-based methods, such as metabarcoding, showed good potential for origin authentication. However, metagenomics, providing a more in-depth view of the cheese microbiota (up to the strain level), but also the combination of methods relying on different targets, can be of interest for this field.}, } @article {pmid36359961, year = {2022}, author = {Buytaers, FE and Verhaegen, B and Gand, M and D'aes, J and Vanneste, K and Roosens, NHC and Marchal, K and Denayer, S and De Keersmaecker, SCJ}, title = {Metagenomics to Detect and Characterize Viruses in Food Samples at Genome Level? Lessons Learnt from a Norovirus Study.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {21}, pages = {}, pmid = {36359961}, issn = {2304-8158}, support = {RF 17/6316 StEQIDEMIC.be//Belgian Federal Public Service of Health, Food Chain Safety and Environment/ ; }, abstract = {In this proof-of-concept study on food contaminated with norovirus, we investigated the feasibility of metagenomics as a new method to obtain the whole genome sequence of the virus and perform strain level characterization but also relate to human cases in order to resolve foodborne outbreaks. We tested several preparation methods to determine if a more open sequencing approach, i.e., shotgun metagenomics, or a more targeted approach, including hybrid capture, was the most appropriate. The genetic material was sequenced using Oxford Nanopore technologies with or without adaptive sampling, and the data were analyzed with an in-house bioinformatics workflow. We showed that a viral genome sequence could be obtained for phylogenetic analysis with shotgun metagenomics if the contamination load was sufficiently high or after hybrid capture for lower contamination. Relatedness to human cases goes well beyond the results obtained with the current qPCR methods. This workflow was also tested on a publicly available dataset of food spiked with norovirus and hepatitis A virus. This allowed us to prove that we could detect even fewer genome copies and two viruses present in a sample using shotgun metagenomics. We share the lessons learnt on the satisfactory and unsatisfactory results in an attempt to advance the field.}, } @article {pmid36359282, year = {2022}, author = {Drapkina, OM and Ashniev, GA and Zlobovskaya, OA and Yafarova, AA and Dementeva, EV and Kaburova, AN and Meshkov, IO and Sheptulina, AF and Kiselev, AR and Kontsevaya, AV and Zhamalov, LM and Koretskiy, SN and Pokrovskaya, MS and Akinshina, AI and Zagaynova, AV and Lukashina, MV and Kirillov, AV and Abramov, IA and Tolkacheva, LR and Bikaeva, IO and Glazunova, EV and Shipulin, GA and Bobrova, MM and Makarov, VV and Keskinov, AA and Yudin, VS and Yudin, SM}, title = {Diversities in the Gut Microbial Patterns in Patients with Atherosclerotic Cardiovascular Diseases and Certain Heart Failure Phenotypes.}, journal = {Biomedicines}, volume = {10}, number = {11}, pages = {}, pmid = {36359282}, issn = {2227-9059}, support = {388-00154-22-00//Federal Medical Biological Agency/ ; }, abstract = {To continue progress in the treatment of cardiovascular disease, there is a need to improve the overall understanding of the processes that contribute to the pathogenesis of cardiovascular disease (CVD). Exploring the role of gut microbiota in various heart diseases is a topic of great interest since it is not so easy to find such reliable connections despite the fact that microbiota undoubtedly affect all body systems. The present study was conducted to investigate the composition of gut microbiota in patients with atherosclerotic cardiovascular disease (ASCVD) and heart failure syndromes with reduced ejection fraction (HFrEF) and HF with preserved EF (HFpEF), and to compare these results with the microbiota of individuals without those diseases (control group). Fecal microbiota were evaluated by three methods: living organisms were determined using bacterial cultures, total DNA taxonomic composition was estimated by next generation sequencing (NGS) of 16S rRNA gene (V3-V4) and quantitative assessment of several taxa was performed using qPCR (quantitative polymerase chain reaction). Regarding the bacterial culture method, all disease groups demonstrated a decrease in abundance of Enterococcus faecium and Enterococcus faecalis in comparison to the control group. The HFrEF group was characterized by an increased abundance of Streptococcus sanguinus and Streptococcus parasanguinis. NGS analysis was conducted at the family level. No significant differences between patient's groups were observed in alpha-diversity indices (Shannon, Faith, Pielou, Chao1, Simpson, and Strong) with the exception of the Faith index for the HFrEF and control groups. Erysipelotrichaceae were significantly increased in all three groups; Streptococcaceae and Lactobacillaceae were significantly increased in ASCVD and HFrEF groups. These observations were indirectly confirmed with the culture method: two species of Streptococcus were significantly increased in the HFrEF group and Lactobacillus plantarum was significantly increased in the ASCVD group. The latter observation was also confirmed with qPCR of Lactobacillus sp. Acidaminococcaceae and Odoribacteraceae were significantly decreased in the ASCVD and HFrEF groups. Participants from the HFpEF group showed the least difference compared to the control group in all three study methods. The patterns found expand the knowledge base on possible correlations of gut microbiota with cardiovascular diseases. The similarities and differences in conclusions obtained by the three methods of this study demonstrate the need for a comprehensive approach to the analysis of microbiota.}, } @article {pmid36359144, year = {2022}, author = {Hua, D and Hendriks, WH and Xiong, B and Pellikaan, WF}, title = {Starch and Cellulose Degradation in the Rumen and Applications of Metagenomics on Ruminal Microorganisms.}, journal = {Animals : an open access journal from MDPI}, volume = {12}, number = {21}, pages = {}, pmid = {36359144}, issn = {2076-2615}, abstract = {Carbohydrates (e.g., starch and cellulose) are the main energy source in the diets of dairy cows. The ruminal digestion of starch and cellulose is achieved by microorganisms and digestive enzymes. In order to improve their digestibility, the microbes and enzymes involved in starch and cellulose degradation should be identified and their role(s) and activity known. As existing and new analytical techniques are continuously being developed, our knowledge of the amylolytic and cellulolytic microbial community in the rumen of dairy cows has been evolving rapidly. Using traditional culture-based methods, the main amylolytic and cellulolytic bacteria, fungi and protozoa in the rumen of dairy cows have been isolated. These culturable microbes have been found to only account for a small fraction of the total population of microorganisms present in the rumen. A more recent application of the culture-independent approach of metagenomics has acquired a more complete genetic structure and functional composition of the rumen microbial community. Metagenomics can be divided into functional metagenomics and sequencing-based computational metagenomics. Both approaches have been applied in determining the microbial composition and function in the rumen. With these approaches, novel microbial species as well as enzymes, especially glycosyl hydrolases, have been discovered. This review summarizes the current state of knowledge regarding the major amylolytic and cellulolytic microorganisms present in the rumen of dairy cows. The ruminal amylases and cellulases are briefly discussed. The application of metagenomics technology in investigating glycosyl hydrolases is provided and the novel enzymes are compared in terms of glycosyl hydrolase families related to amylolytic and cellulolytic activities.}, } @article {pmid36358819, year = {2022}, author = {Liu, B and Chau, J and Dai, Q and Zhong, C and Zhang, J}, title = {Exploring Gut Microbiome in Predicting the Efficacy of Immunotherapy in Non-Small Cell Lung Cancer.}, journal = {Cancers}, volume = {14}, number = {21}, pages = {}, pmid = {36358819}, issn = {2072-6694}, support = {DBI-1943291//National Science Foundation/ ; //the University of Kansas Start-Up/ ; //the "Play with a Pro" Lung Cancer Research Fund/ ; //the Pilot Grant for Cancer Research of the University of Kansas Cancer Center/ ; }, abstract = {We performed various analyses on the taxonomic and functional features of the gut microbiome from NSCLC patients treated with immunotherapy to establish a model that may predict whether a patient will benefit from immunotherapy. We collected 65 published whole metagenome shotgun sequencing samples along with 14 samples from our previous study. We systematically studied the taxonomical characteristics of the dataset and used both the random forest (RF) and the multilayer perceptron (MLP) neural network models to predict patients with progression-free survival (PFS) above 6 months versus those below 3 months. Our results showed that the RF classifier achieved the highest F-score (85.2%) and the area under the receiver operating characteristic curve (AUC) (95%) using the protein families (Pfam) profile, and the MLP neural network classifier achieved a 99.9% F-score and 100% AUC using the same Pfam profile. When applying the model trained in the Pfam profile directly to predict the treatment response, we found that both trained RF and MLP classifiers significantly outperformed the stochastic predictor in F-score. Our results suggested that such a predictive model based on functional (e.g., Pfam) rather than taxonomic profile might be clinically useful to predict whether an NSCLC patient will benefit from immunotherapy, as both the F-score and AUC of functional profile outperform that of taxonomic profile. In addition, our model suggested that interactive biological processes such as methanogenesis, one-carbon, and amino acid metabolism might be important in regulating the immunotherapy response that warrants further investigation.}, } @article {pmid36358797, year = {2022}, author = {Ito, Z and Koido, S and Kato, K and Odamaki, T and Horiuchi, S and Akasu, T and Saruta, M and Hata, T and Kumagai, Y and Fujioka, S and Misawa, T and Xiao, JZ and Sato, N and Ohkusa, T}, title = {Dysbiosis of the Fecal and Biliary Microbiota in Biliary Tract Cancer.}, journal = {Cancers}, volume = {14}, number = {21}, pages = {}, pmid = {36358797}, issn = {2072-6694}, support = {007//the Jikei University Research Fund, the Fund of Department of Microbiota Research Juntendo Graduate School of Medicine, and Morinaga Milk Co., Ltd./ ; }, abstract = {Characteristic bile duct and gut microbiota have been identified in patients with chronic biliary tract disease. This study aimed to characterize the fecal and bile microbiota in biliary tract cancer (BTC) patients and their relationship. Patients with BTC (n = 30) and benign biliary disease (BBD) without cholangitis (n = 11) were included. Ten healthy, age-matched subjects were also recruited for fecal microbiota comparison. The fecal and bile duct microbiotas were analyzed by sequencing the 16S rRNA gene V3-V4 region. Live bacteria were obtained in the bile from three BTC patients by culture, and metagenomics-based identification was performed. Linear discriminant analysis effect size showed a higher Enterobacteriaceae abundance and a lower Clostridia abundance, including that of Faecalibacterium and Coprococcus, in the BTC patients than in the other subjects. Ten of 17 operational taxonomic units (OTUs) assigned to Enterobacteriaceae in the bile were matched with the OTUs found in the BTC subject fecal samples. Furthermore, a bile-isolated strain possessed the carcinogenic bacterial colipolyketide synthase-encoding gene. Enterobacteriaceae was enriched in the BTC feces, and more than half of Enterobacteriaceae in the bile matched that in the feces at the OTU level. Our data suggests that fecal microbiota dysbiosis may contribute to BTC onset.}, } @article {pmid36358144, year = {2022}, author = {Tóth, AG and Tóth, I and Rózsa, B and Dubecz, A and Patai, ÁV and Németh, T and Kaplan, S and Kovács, EG and Makrai, L and Solymosi, N}, title = {Canine Saliva as a Possible Source of Antimicrobial Resistance Genes.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {11}, pages = {}, pmid = {36358144}, issn = {2079-6382}, support = {Grant Agreement No. 874735 (VEO)//European Union/ ; }, abstract = {While the One Health issues of intensive animal farming are commonly discussed, keeping companion animals is less associated with the interspecies headway of antimicrobial resistance. With the constant advance in veterinary standards, antibiotics are regularly applied in companion animal medicine. Due to the close coexistence of dogs and humans, dog bites and other casual encounters with dog saliva (e.g., licking the owner) are common. According to our metagenome study, based on 26 new generation sequencing canine saliva datasets from 2020 and 2021 reposited in NCBI SRA by The 10,000 Dog Genome Consortium and the Broad Institute within Darwin's Ark project, canine saliva is rich in bacteria with predictably transferable antimicrobial resistance genes (ARGs). In the genome of potentially pathogenic Bacteroides, Capnocytophaga, Corynebacterium, Fusobacterium, Pasteurella, Porphyromonas, Staphylococcus and Streptococcus species, which are some of the most relevant bacteria in dog bite infections, ARGs against aminoglycosides, carbapenems, cephalosporins, glycylcyclines, lincosamides, macrolides, oxazolidinone, penams, phenicols, pleuromutilins, streptogramins, sulfonamides and tetracyclines could be identified. Several ARGs, including ones against amoxicillin-clavulanate, the most commonly applied antimicrobial agent for dog bites, were predicted to be potentially transferable based on their association with mobile genetic elements (e.g., plasmids, prophages and integrated mobile genetic elements). According to our findings, canine saliva may be a source of transfer for ARG-rich bacteria that can either colonize the human body or transport ARGs to the host bacteriota, and thus can be considered as a risk in the spread of antimicrobial resistance.}, } @article {pmid36357781, year = {2023}, author = {Cai, L and Chen, Y and Xiao, S and Liu, R and He, M and Zhang, R and Zeng, Q}, title = {Abundant and cosmopolitan lineage of cyanopodoviruses lacking a DNA polymerase gene.}, journal = {The ISME journal}, volume = {17}, number = {2}, pages = {252-262}, pmid = {36357781}, issn = {1751-7370}, mesh = {*Bacteriophages ; DNA-Directed DNA Polymerase/genetics ; Oceans and Seas ; Phylogeny ; *Synechococcus/virology ; }, abstract = {Cyanopodoviruses affect the mortality and population dynamics of the unicellular picocyanobacteria Prochlorococcus and Synechococcus, the dominant primary producers in the oceans. Known cyanopodoviruses all contain the DNA polymerase gene (DNA pol) that is important for phage DNA replication and widely used in field quantification and diversity studies. However, we isolated 18 cyanopodoviruses without identifiable DNA pol. They form a new MPP-C clade that was separated from the existing MPP-A, MPP-B, and P-RSP2 clades. The MPP-C phages have the smallest genomes (37.3-37.9 kb) among sequenced cyanophages, and show longer latent periods than the MPP-B phages. Metagenomic reads of both clades are highly abundant in surface waters, but the MPP-C phages show higher relative abundance in surface waters than in deeper waters, while MPP-B phages have higher relative abundance in deeper waters. Our study reveals that cyanophages with distinct genomic contents and infection kinetics can exhibit different depth profiles in the oceans.}, } @article {pmid36357577, year = {2023}, author = {Krukowski, H and Valkenburg, S and Madella, AM and Garssen, J and van Bergenhenegouwen, J and Overbeek, SA and Huys, GRB and Raes, J and Glorieux, G}, title = {Gut microbiome studies in CKD: opportunities, pitfalls and therapeutic potential.}, journal = {Nature reviews. Nephrology}, volume = {19}, number = {2}, pages = {87-101}, pmid = {36357577}, issn = {1759-507X}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Renal Insufficiency, Chronic/metabolism ; Dysbiosis/microbiology ; }, abstract = {Interest in gut microbiome dysbiosis and its potential association with the development and progression of chronic kidney disease (CKD) has increased substantially in the past 6 years. In parallel, the microbiome field has matured considerably as the importance of host-related and environmental factors is increasingly recognized. Past research output in the context of CKD insufficiently considered the myriad confounding factors that are characteristic of the disease. Gut microbiota-derived metabolites remain an interesting therapeutic target to decrease uraemic (cardio)toxicity. However, future studies on the effect of dietary and biotic interventions will require harmonization of relevant readouts to enable an in-depth understanding of the underlying beneficial mechanisms. High-quality standards throughout the entire microbiome analysis workflow are also of utmost importance to obtain reliable and reproducible results. Importantly, investigating the relative composition and abundance of gut bacteria, and their potential association with plasma uraemic toxins levels is not sufficient. As in other fields, the time has come to move towards in-depth quantitative and functional exploration of the patient's gut microbiome by relying on confounder-controlled quantitative microbial profiling, shotgun metagenomics and in vitro simulations of microorganism-microorganism and host-microorganism interactions. This step is crucial to enable the rational selection and monitoring of dietary and biotic intervention strategies that can be deployed as a personalized intervention in CKD.}, } @article {pmid36357393, year = {2022}, author = {Su, Q and Liu, Q and Lau, RI and Zhang, J and Xu, Z and Yeoh, YK and Leung, TWH and Tang, W and Zhang, L and Liang, JQY and Yau, YK and Zheng, J and Liu, C and Zhang, M and Cheung, CP and Ching, JYL and Tun, HM and Yu, J and Chan, FKL and Ng, SC}, title = {Faecal microbiome-based machine learning for multi-class disease diagnosis.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6818}, pmid = {36357393}, issn = {2041-1723}, mesh = {Humans ; *COVID-19/diagnosis ; Feces ; Machine Learning ; *Microbiota ; Post-Acute COVID-19 Syndrome ; }, abstract = {Systemic characterisation of the human faecal microbiome provides the opportunity to develop non-invasive approaches in the diagnosis of a major human disease. However, shared microbial signatures across different diseases make accurate diagnosis challenging in single-disease models. Herein, we present a machine-learning multi-class model using faecal metagenomic dataset of 2,320 individuals with nine well-characterised phenotypes, including colorectal cancer, colorectal adenomas, Crohn's disease, ulcerative colitis, irritable bowel syndrome, obesity, cardiovascular disease, post-acute COVID-19 syndrome and healthy individuals. Our processed data covers 325 microbial species derived from 14.3 terabytes of sequence. The trained model achieves an area under the receiver operating characteristic curve (AUROC) of 0.90 to 0.99 (Interquartile range, IQR, 0.91-0.94) in predicting different diseases in the independent test set, with a sensitivity of 0.81 to 0.95 (IQR, 0.87-0.93) at a specificity of 0.76 to 0.98 (IQR 0.83-0.95). Metagenomic analysis from public datasets of 1,597 samples across different populations observes comparable predictions with AUROC of 0.69 to 0.91 (IQR 0.79-0.87). Correlation of the top 50 microbial species with disease phenotypes identifies 363 significant associations (FDR < 0.05). This microbiome-based multi-disease model has potential clinical application in disease diagnostics and treatment response monitoring and warrants further exploration.}, } @article {pmid36357382, year = {2022}, author = {Liu, Y and Elworth, RAL and Jochum, MD and Aagaard, KM and Treangen, TJ}, title = {De novo identification of microbial contaminants in low microbial biomass microbiomes with Squeegee.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6799}, pmid = {36357382}, issn = {2041-1723}, support = {P01 AI152999/AI/NIAID NIH HHS/United States ; R01 DK128187/DK/NIDDK NIH HHS/United States ; R01 HD091731/HD/NICHD NIH HHS/United States ; T15 LM007093/LM/NLM NIH HHS/United States ; T32 HL098069/HL/NHLBI NIH HHS/United States ; R01 NR014792/NR/NINR NIH HHS/United States ; T32 HD098068/HD/NICHD NIH HHS/United States ; }, mesh = {Humans ; Biomass ; *Microbiota/genetics ; Metagenomics/methods ; Metagenome ; Specimen Handling ; }, abstract = {Computational analysis of host-associated microbiomes has opened the door to numerous discoveries relevant to human health and disease. However, contaminant sequences in metagenomic samples can potentially impact the interpretation of findings reported in microbiome studies, especially in low-biomass environments. Contamination from DNA extraction kits or sampling lab environments leaves taxonomic "bread crumbs" across multiple distinct sample types. Here we describe Squeegee, a de novo contamination detection tool that is based upon this principle, allowing the detection of microbial contaminants when negative controls are unavailable. On the low-biomass samples, we compare Squeegee predictions to experimental negative control data and show that Squeegee accurately recovers putative contaminants. We analyze samples of varying biomass from the Human Microbiome Project and identify likely, previously unreported kit contamination. Collectively, our results highlight that Squeegee can identify microbial contaminants with high precision and thus represents a computational approach for contaminant detection when negative controls are unavailable.}, } @article {pmid36357381, year = {2022}, author = {Liu, Q and Su, Q and Zhang, F and Tun, HM and Mak, JWY and Lui, GC and Ng, SSS and Ching, JYL and Li, A and Lu, W and Liu, C and Cheung, CP and Hui, DSC and Chan, PKS and Chan, FKL and Ng, SC}, title = {Multi-kingdom gut microbiota analyses define COVID-19 severity and post-acute COVID-19 syndrome.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6806}, pmid = {36357381}, issn = {2041-1723}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *COVID-19 ; Metagenomics/methods ; Feces/microbiology ; Post-Acute COVID-19 Syndrome ; }, abstract = {Our knowledge of the role of the gut microbiome in acute coronavirus disease 2019 (COVID-19) and post-acute COVID-19 is rapidly increasing, whereas little is known regarding the contribution of multi-kingdom microbiota and host-microbial interactions to COVID-19 severity and consequences. Herein, we perform an integrated analysis using 296 fecal metagenomes, 79 fecal metabolomics, viral load in 1378 respiratory tract samples, and clinical features of 133 COVID-19 patients prospectively followed for up to 6 months. Metagenomic-based clustering identifies two robust ecological clusters (hereafter referred to as Clusters 1 and 2), of which Cluster 1 is significantly associated with severe COVID-19 and the development of post-acute COVID-19 syndrome. Significant differences between clusters could be explained by both multi-kingdom ecological drivers (bacteria, fungi, and viruses) and host factors with a good predictive value and an area under the curve (AUC) of 0.98. A model combining host and microbial factors could predict the duration of respiratory viral shedding with 82.1% accuracy (error ± 3 days). These results highlight the potential utility of host phenotype and multi-kingdom microbiota profiling as a prognostic tool for patients with COVID-19.}, } @article {pmid36356857, year = {2022}, author = {Wang, C and Li, P and Guo, L and Cao, H and Mo, W and Xin, Y and Jv, R and Zhao, Y and Liu, X and Ma, C and Chen, D and Wang, H}, title = {A new potential risk: The impacts of Klebsiella pneumoniae infection on the histopathology, transcriptome and metagenome of Chinese mitten crab (Eriocheir sinensis).}, journal = {Fish & shellfish immunology}, volume = {131}, number = {}, pages = {918-928}, doi = {10.1016/j.fsi.2022.11.010}, pmid = {36356857}, issn = {1095-9947}, mesh = {Animals ; *Brachyura/genetics ; Hepatopancreas/metabolism ; Klebsiella pneumoniae/genetics ; Metagenome ; *Transcriptome ; }, abstract = {Klebsiella pneumoniae is a common conditional pathogen found in natural soil water sources and vegetation and can infect invertebrates, vertebrates, and plants. In this study, we isolated K. pneumoniae from the hepatopancreas of the Chinese mitten crab (Eriocheir sinensis) for the first time and then we analysed its effects of on the histopathological changes, the transcriptome of the hepatopancreas, and the gut microbiota of this crab species. The findings of this study showed that K. pneumoniae infection has led to significant structural changes in the hepatopancreas, such as the production of vacuolated tissue structures, disorganized cell arrangement, and lysis of some hepatopancreatic cells. Also, the infection caused activation of the antioxidant-related enzymes such as SOD and CAT by inducing oxidative stress. The transcriptome of the hepatopancreas identified 10,940 differentially expressed genes (DEGs) in the susceptible (SG) groups and control (CG) groups, and 8495 DEGs in the SG groups and anti-infective (AI) groups. The KEGG pathway revealed upregulated DEGs caused by K. pneumoniae infection that involved in the immune response and apoptotic functional pathways, and also downregulated DEGs involved in the digestive absorption, metabolic, and biosynthetic signaling pathways. Meanwhile, metagenics sequencing revealed that at the phylum, class, order, family, and genus levels, K. pneumoniae infection altered the composition of the gut microbiota of E. sinensis, through increasing the abundance of Prolixibacteraceae, Enterobacterales, and Roseimarinus and decreasing the abundance of Alphaproteobacteria. The flora structure has also been changed between the SG and AI groups, with the abundance of Firmicutes, Erysipelotrichales, and Erysipelotrichaceae that were significantly decreased in the SG groups than in the AI groups. But, the abundance of Acinetobacter was considerably higher than in the AI group. In summary, K. pneumoniae infection induced oxidative stress in E. sinensis, triggered changes in immune-related gene expression, and caused structural changes in the gut microbiota. This study provides data to support the analysis of bacterial infection probes in several crustacean species.}, } @article {pmid36356814, year = {2023}, author = {Peng, Y and Li, L and Dong, Q and Yang, P and Liu, H and Ye, W and Wu, D and Peng, X}, title = {Evaluation of digestate-derived biochar to alleviate ammonia inhibition during long-term anaerobic digestion of food waste.}, journal = {Chemosphere}, volume = {311}, number = {Pt 2}, pages = {137150}, doi = {10.1016/j.chemosphere.2022.137150}, pmid = {36356814}, issn = {1879-1298}, abstract = {The feasibility of using food waste anaerobic digestate-derived biochar (FWDB) to mitigate ammonia toxicity in an anaerobic digester was evaluated. The optimal conditions for preparing and adding the activated FWDB were explored using response surface experiments, and the long-term effects of adding activated FWDB on digester performance under optimum conditions were verified in semi-continuous experiments. The results showed that the optimal preparation and addition conditions for activated FWDB were pyrolysis temperature of 565 °C, particle size of 0-0.30 mm, and dosage of 15.52 g·L[-1]. During the long-term operation of the digesters, when the total ammonia nitrogen (TAN) concentration was higher than 2000 mg·L[-1], the control and experimental digesters showed deteriorated reactor performance. Volatile fatty acids in the control digester accumulated to 20,306 mg·L[-1] after the TAN concentration increased to 3391 mg·L[-1], the methane yield decreased to 31 mL·g VS[-1], and the digester experienced process failure. In contrast, the experimental digester with added activated FWDB only suffered a slight short-term accumulation of acetate and a slight decline in methane yield. This may be attributed to the adsorption of NH4[+]/NH3 by activated FWDB, which reduced the TAN concentration in the anaerobic digestion (AD) system and mitigated ammonia toxicity. Microbial analysis and metagenome predictions demonstrated that the community richness, diversity, and evenness, as well as the abundance of acetogens and related key genes (ACSM1, paaF, and acdA) were higher in the experimental digester than in the control digester. This study provides a closed-loop AD enhancement strategy by pyrolysis of digestate and in-situ supplementation into the digester.}, } @article {pmid36356726, year = {2023}, author = {Zhang, T and Cao, J and Liu, W and Liu, G and Huang, C and Luo, J}, title = {Insights into integrated glycerol-driven partial denitrification-anaerobic ammonium oxidation system using bioinformatic analysis: The dominance of Bacillus spp. and the potential of nitrite producing via assimilatory nitrate reduction.}, journal = {The Science of the total environment}, volume = {858}, number = {Pt 2}, pages = {160048}, doi = {10.1016/j.scitotenv.2022.160048}, pmid = {36356726}, issn = {1879-1026}, mesh = {Denitrification ; Nitrites ; Sewage/microbiology ; Nitrates ; Anaerobiosis ; Glycerol ; Bioreactors/microbiology ; *Bacillus/metabolism ; Computational Biology ; *Ammonium Compounds/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Wastewater/chemistry ; }, abstract = {Partial denitrification-anaerobic ammonium oxidation (PD/A) was considered a novel technology for biological nitrogen removal. In this study, a glycerol-driven PD/A granular sludge reactor was constructed, and its nitrogen removal efficiency and microbial mechanisms were investigated systematically. After optimization, the PD/A reactor achieved 92.3 % of the nitrogen removal (~90 % by anammox) with the influent COD/NO3[-]-N ratio of 2.6, and approximate 1.36 mol NO3[-]-N was required for removing 1 mol NH4[+]-N. Granular sludge with layered structure (anaerobic ammonium oxidizing bacteria (AnAOB) was wrapped by the heterotrophic bacteria) was successfully developed, which resulted in the sludge floating. Bacillus was firstly found to be the dominant genus in PD/A system with an abundance of 46.1 %, whereas the AnAOB only accounted for 0.2-2.8 %. Metatranscriptomic analysis showed that the metabolic characteristics obviously changed during the operation, and the differential expressing genes mainly belonged to ABC transport and quorum sensing pathway. Further analysis about the expressing patterns of nitrogen metabolism related genes indicated that the anammox related genes (mainly from Candidatus Brocadia and Candidatus Jettenia) exhibited a much higher expressing level than other genes. Interestingly, the assimilatory nitrate reduction process in Bacillus showed great NO2[-]-N producing potential, so it was considered to be an essential pathway participating in PD/A process. This study provided a comprehensive insight into the glycerol-driven PD/A system.}, } @article {pmid36356519, year = {2023}, author = {Huang, Y and Hu, W and Dong, M and Yang, Y and Yang, X and Huang, H and Yang, S and Jia, W and Wang, B and Xu, M}, title = {Cable bacteria accelerate the anaerobic removal of pyrene in black odorous river sediments.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt B}, pages = {130305}, doi = {10.1016/j.jhazmat.2022.130305}, pmid = {36356519}, issn = {1873-3336}, mesh = {*Rivers ; *Geologic Sediments/chemistry ; Anaerobiosis ; Bacteria/genetics ; Pyrenes ; }, abstract = {Cable bacteria play an essential role in biogeochemical processes in sediments by long-distance electron transport (LDET). A potential relationship has been found between cable bacteria and organic contaminant removal; however, the mechanisms remain unclear. In this study, the response of cable bacteria to pyrene was investigated in sediments with and without pyrene, and the effect of cable bacteria on pyrene removal was explored by connecting and blocking the paths of cable bacteria to the suboxic zones. The results showed that pyrene significantly influenced the microbial community structure and the composition of cable bacteria. The pyrene removal efficiencies significantly increased with the enrichment of cable bacteria, while sulfur-reducing microorganisms and aromatic compound degraders were also significantly enriched and correlated with cable bacteria abundance. Metagenomic analysis showed that cable bacteria have a potential LDET-bound acetate/formate respiratory pathway to gain energy. The presence of pyrene probably selects and enriches cable bacteria with a high tolerance to organic contaminants and changes the related functional microbial community, leading to the acceleration of pyrene removal. This study provides new insights into the interaction mechanisms between contaminants and cable bacteria, shedding light on the applications of cable bacteria in the bioremediation of contaminants in sediments.}, } @article {pmid36356515, year = {2023}, author = {Jin, X and Liu, S and Zhang, Z and Liu, T and Li, N and Liang, Y and Zheng, J and Peng, N}, title = {Enrofloxacin-induced transfer of multiple-antibiotic resistance genes and emergence of novel resistant bacteria in red swamp crayfish guts and pond sediments.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt B}, pages = {130261}, doi = {10.1016/j.jhazmat.2022.130261}, pmid = {36356515}, issn = {1873-3336}, mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; Astacoidea/genetics ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Ecosystem ; Enrofloxacin/pharmacology ; Genes, Bacterial ; *Ponds/analysis ; Geologic Sediments ; }, abstract = {Antibiotic resistance genes (ARGs) can be transferred from environmental microbes to human pathogens, thus leading to bacterial infection treatment failures. The aquaculture polluted by over-used antibiotics is considered as a notorious reservoir of ARGs. However, the origin, diachronic changes, and mobility of ARGs under antibiotic exposure in aquaculture systems remain elusive. Our findings showed that enrofloxacin application also increased the relative abundance of various ARGs in addition to quinolone-resistance genes and induced ARG dissemination in crayfish gut and sediment bacteria. Further investigation indicated that the transposase-mediated recombination was the major driver of horizontal gene transfer (HGT) of ARGs under antibiotic stress. Notably, enrofloxacin application also induced the generation of some metagenome-assembled genomes (MAGs) carrying multiple ARGs, which were identified as novel species. Additionally, Enterobacteriaceae constituted a mobile ARG pool in aquaculture. Therefore, aquaculture provides potential wide environmental pathways for generation and spread of antibiotic resistance. Our findings of ARG temporal variations and dissemination pattern in aquaculture with artificial use of antibiotics are critical to the management of antibiotic resistance, which is of great ecosystem and health implications.}, } @article {pmid36355999, year = {2022}, author = {Jalili, F and Trigui, H and Maldonado, JFG and Dorner, S and Zamyadi, A and Shapiro, BJ and Terrat, Y and Fortin, N and Sauvé, S and Prévost, M}, title = {Impact of Stagnation on the Diversity of Cyanobacteria in Drinking Water Treatment Plant Sludge.}, journal = {Toxins}, volume = {14}, number = {11}, pages = {}, pmid = {36355999}, issn = {2072-6651}, mesh = {Sewage ; *Drinking Water ; Microcystins ; *Cyanobacteria/genetics ; *Water Purification ; *Microcystis ; }, abstract = {Health-related concerns about cyanobacteria-laden sludge of drinking water treatment plants (DWTPs) have been raised in the past few years. Microscopic taxonomy, shotgun metagenomic sequencing, and microcystin (MC) measurement were applied to study the fate of cyanobacteria and cyanotoxins after controlled sludge storage (stagnation) in the dark in a full-scale drinking water treatment plant within 7 to 38 days. For four out of eight dates, cyanobacterial cell growth was observed by total taxonomic cell counts during sludge stagnation. The highest observed cell growth was 96% after 16 days of stagnation. Cell growth was dominated by potential MC producers such as Microcystis, Aphanocapsa, Chroococcus, and Dolichospermum. Shotgun metagenomic sequencing unveiled that stagnation stress shifts the cyanobacterial communities from the stress-sensitive Nostocales (e.g., Dolichospermum) order towards less compromised orders and potential MC producers such as Chroococcales (e.g., Microcystis) and Synechococcales (e.g., Synechococcus). The relative increase of cyanotoxin producers presents a health challenge when the supernatant of the stored sludge is recycled to the head of the DWTP or discharged into the source. These findings emphasize the importance of a strategy to manage cyanobacteria-laden sludge and suggest practical approaches should be adopted to control health/environmental impacts of cyanobacteria and cyanotoxins in sludge.}, } @article {pmid36355175, year = {2022}, author = {Deledda, A and Palmas, V and Heidrich, V and Fosci, M and Lombardo, M and Cambarau, G and Lai, A and Melis, M and Loi, E and Loviselli, A and Manzin, A and Velluzzi, F}, title = {Dynamics of Gut Microbiota and Clinical Variables after Ketogenic and Mediterranean Diets in Drug-Naïve Patients with Type 2 Diabetes Mellitus and Obesity.}, journal = {Metabolites}, volume = {12}, number = {11}, pages = {}, pmid = {36355175}, issn = {2218-1989}, support = {//AMD (Associazione Medici Diabetologi) onlus "Bando borsa di studio Adolfo Arcangeli 2019"/ ; 13996-0/2018//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; //Laboratoire Therascience, 3 Rue de l'Industrie, 98000 Monaco/ ; }, abstract = {Type 2 diabetes mellitus (T2DM), the most common form of diabetes, is a progressive chronic metabolic disease that has increasingly spread worldwide, enhancing the mortality rate, particularly from cardiovascular diseases (CVD). Lifestyle improvement through diet and physical activity is, together with drug treatment, the cornerstone of T2DM management. The Mediterranean diet (MD), which favors a prevalence of unprocessed vegetable foods and a reduction in red meats and industrial foods, without excluding any food category, is usually recommended. Recently, scientific societies have promoted a very low-calorie ketogenic diet (VLCKD), a multiphasic protocol that limits carbohydrates and then gradually re-introduces them, with a favorable outcome on body weight and metabolic parameters. Indeed, gut microbiota (GM) modifications have been linked to overweight/obesity and metabolic alterations typical of T2DM. Diet is known to affect GM largely, but only a few studies have investigated the effects of VLCKD on GM, especially in T2DM. In this study, we have compared anthropometric, biochemical, lifestyle parameters, the quality of life, and the GM of eleven patients with recently diagnosed T2DM and overweight or obesity, randomly assigned to two groups of six and five patients who followed the VLCKD (KETO) or hypocaloric MD (MEDI) respectively; parameters were recorded at baseline (T0) and after two (T2) and three months (T3). The results showed that VLCKD had more significant beneficial effects than MD on anthropometric parameters, while biochemical improvements did not statistically differ. As for the GM, despite the lack of significant results regarding the alpha and beta diversity, and the Firmicutes/Bacteroidota ratio between the two groups, in the KETO group, a significant increase in beneficial microbial taxa such as Verrucomicrobiota phylum with its members Verrucomicrobiae, Verrucomicrobiales, Akkermansiaceae, and Akkermansia, Christensenellaceae family, Eubacterium spp., and a reduction in microbial taxa previously associated with obesity (Firmicutes and Actinobacteriota) or other diseases (Alistipes) was observed both at T2 and T3. With regards to the MEDI group, variations were limited to a significant increase in Actinobacteroidota phylum at T2 and T3 and Firmicutes phylum at T3. Moreover, a metagenomic alteration linked to some metabolic pathways was found exclusively in the KETO group. In conclusion, both dietary approaches allowed patients to improve their state of health, but VLCKD has shown better results on body composition as well as on GM profile.}, } @article {pmid36354744, year = {2022}, author = {Lean, FZX and Leblond, AL and Byrne, AMP and Mollett, B and James, J and Watson, S and Hurley, S and Brookes, SM and Weber, A and Núñez, A}, title = {Subclinical hepatitis E virus infection in laboratory ferrets in the UK.}, journal = {The Journal of general virology}, volume = {103}, number = {11}, pages = {}, doi = {10.1099/jgv.0.001803}, pmid = {36354744}, issn = {1465-2099}, mesh = {Animals ; Female ; *Hepatitis E virus/genetics ; Ferrets ; RNA, Viral/genetics/analysis ; *Hepatitis E/veterinary ; United Kingdom ; }, abstract = {Ferrets are widely used for experimental modelling of viral infections. However, background disease in ferrets could potentially confound intended experimental interpretation. Here we report the detection of a subclinical infection of ferret hepatitis E virus (FRHEV) within a colony sub-group of female laboratory ferrets that had been enrolled on an experimental viral infection study (non-hepatitis). Lymphoplasmacytic cuffing of periportal spaces was identified on histopathology but was negative for the RNA and antigens of the administered virus. Follow-up viral metagenomic analysis conducted on liver specimens revealed sequences attributed to FRHEV and these were confirmed by reverse-transcriptase polymerase chain reaction. Further genomic analysis revealed contiguous sequences spanning 79-95 % of the FRHEV genome and that the sequences were closely related to those reported previously in Europe. Using in situ hybridization by RNAScope, we confirmed the presence of HEV-specific RNA in hepatocytes. The HEV open reading frame 2 (ORF2) protein was also detected by immunohistochemistry in the hepatocytes and the biliary canaliculi. In conclusion, the results of our study provide evidence of background infection with FRHEV in laboratory ferrets. As this infection can be subclinical, we recommend routine monitoring of ferret populations using virological and liver function tests to avoid incorrect causal attribution of any liver disease detected in in vivo studies.}, } @article {pmid36354350, year = {2022}, author = {Zhong, J and Wu, D and Zeng, Y and Wu, G and Zheng, N and Huang, W and Li, Y and Tao, X and Zhu, W and Sheng, L and Shen, X and Zhang, W and Zhu, R and Li, H}, title = {The Microbial and Metabolic Signatures of Patients with Stable Coronary Artery Disease.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0246722}, pmid = {36354350}, issn = {2165-0497}, mesh = {Humans ; *Coronary Artery Disease ; *Gastrointestinal Microbiome ; Metabolome ; Metagenomics ; Lipid Metabolism ; }, abstract = {Growing evidence indicates an association between gut dysbiosis and coronary artery disease (CAD). However, the underlying mechanisms relevant to stable CAD (SCAD) pathogenesis, based on microbe-host metabolism interactions, are poorly explored. Here, we constructed a quasi-paired cohort based on the metabolic background of metagenomic samples by the propensity score matching (PSM) principle. Compared to healthy controls (HCs), gut microbiome disturbances were observed in SCAD patients, accompanied by differences in serum metabolome, mainly including elevated acylcarnitine and decreased unsaturated fatty acids in SCAD patients, which implicated the reduced cardiac fatty acid oxidation. Moreover, we identified Ralstonia pickettii as the core strain responsible for impaired microbial homeostasis in SCAD patientsm and may be partly responsible for the decrease of host unsaturated fatty acid levels. These findings highlight the importance of unsaturated fatty acids, R. pickettii, and their interaction in the pathogenesis of SCAD. IMPORTANCE Stable coronary artery disease (SCAD) is an early stage of CAD development. It is important to understand the pathogenesis of SCAD and find out the possible prevention and control targets for delaying the progression of CAD. We observed reduced levels of unsaturated fatty acids (USFAs) in SCAD patients. However, the reduced USFAs may be related to Ralstonia Pickettii, which was the core strain responsible for the impaired gut microbial function in SCAD patients, and further affected the host's cardiovascular health by altering amino acids, vitamin B metabolism, and LPS biosynthesis. These findings not only emphasized the importance of USFAs for cardiovascular health, but also R. Pickettii for maintaining microbial function homeostasis. More importantly, our study revealed, for the first time, that enriched R. Pickettii might be responsible for the reduced USFAs in SCAD patients, which adds new evidence on the role of altered gut microbiota for SCAD formation.}, } @article {pmid36354338, year = {2022}, author = {Unno, R and Suzuki, T and Osaki, Y and Matsutani, M and Ishikawa, M}, title = {Causality Verification for the Correlation between the Presence of Nonstarter Bacteria and Flavor Characteristics in Soft-Type Ripened Cheeses.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0289422}, pmid = {36354338}, issn = {2165-0497}, mesh = {*Cheese/analysis/microbiology ; RNA, Ribosomal, 16S ; Bacteria/genetics ; *Lactobacillales ; Ketones/analysis ; Sulfur Compounds/analysis ; }, abstract = {Flavor characteristics of ripened cheese are established by various bacteria, such as lactic acid bacteria, Actinobacteria, and Proteobacteria, which spontaneously develop during the cheese-manufacturing process. We previously revealed the relationship between bacterial microbiota and flavor components in soft-type ripened cheeses by using a multiomics approach that combined metagenomics and metabolomics; however, we could not establish a causal relationship. This study aimed to substantiate the causal nature of the correlations revealed by the multiomics approach by using cheese-ripening tests with single isolate inoculation. The bacterial diversity and composition in surface mold-ripened cheeses from Japan and France varied, depending on the differences between the milks (pasteurized or raw), cheese positions (core or rind), and manufacturers. Although the volatile compounds did not clearly reflect the distinctive characteristics of the cheese samples, nonstarter lactic acid bacteria, Actinobacteria, and Proteobacteria positively correlated with ketones and sulfur compounds, as evidenced by a Spearman's correlation analysis. Cheese-ripening tests conducted after inoculation with single bacterial strains belonging to the above-mentioned taxa confirmed that these bacteria formed volatile compounds, in agreement with the correlations observed. In particular, various flavor compounds, such as acids, esters, ketones, and sulfur compounds, were detected in cheese inoculated with Pseudoalteromonas sp. TS-4-4 strain. These findings provide important insights into the role of nonstarter bacteria in the development of cheese flavor and into the effectiveness of the multiomics approach in screening for bacteria that can improve the quality of cheese products. IMPORTANCE Our previous study revealed that the existence of various bacteria, such as lactic acid bacteria, Actinobacteria, and Proteobacteria, clearly correlated with the abundance of flavor components, such as volatile compounds, in soft-type ripened cheeses via a multiomics approach that used 16S rRNA gene amplicon sequencing and headspace gas chromatography-mass spectrometry. However, this approach only showed correlations derived from statistical analyses rather than causal relationships. Therefore, in the present study, we performed cheese-ripening tests using nonstarter bacteria to substantiate the correlations revealed by the multiomics approach in soft-type ripened cheese. Our results suggest the capability of nonstarter bacteria, such as Proteobacteria, to impart flavor to cheese and the effectiveness of the multiomics approach in screening for microbial isolates that can improve the quality of cheese. Overall, our research provides new insights into the importance of bacteria in cheese production.}, } @article {pmid36354331, year = {2022}, author = {Flurin, L and Hemenway, JJ and Fisher, CR and Vaillant, JJ and Azad, M and Wolf, MJ and Greenwood-Quaintance, KE and Abdel, MP and Patel, R}, title = {Clinical Use of a 16S Ribosomal RNA Gene-Based Sanger and/or Next Generation Sequencing Assay to Test Preoperative Synovial Fluid for Periprosthetic Joint Infection Diagnosis.}, journal = {mBio}, volume = {13}, number = {6}, pages = {e0132222}, pmid = {36354331}, issn = {2150-7511}, mesh = {Humans ; RNA, Ribosomal, 16S ; Genes, rRNA ; Synovial Fluid ; *Prosthesis-Related Infections ; High-Throughput Nucleotide Sequencing ; Retrospective Studies ; *Arthritis, Infectious ; Sensitivity and Specificity ; Biomarkers ; }, abstract = {Preoperative pathogen identification in patients with periprosthetic joint infection (PJI) is typically limited to synovial fluid culture. Whether sequencing-based approaches are of potential use in identification of pathogens in PJI, and if so which approach is ideal, is incompletely defined. The objective of the study was to analyze the accuracy of a 16S rRNA (rRNA) gene-based PCR followed by Sanger sequencing and/or targeted metagenomic sequencing approach (tMGS) performed on synovial fluid for PJI diagnosis. A retrospective study was conducted, analyzing synovial fluids tested between August 2020 and May 2021 at a single center. Subjects with hip, knee, shoulder, and elbow arthroplasties who had synovial fluid aspirated and clinically subjected to sequence-based testing and conventional culture were studied. A total of 154 subjects were included in the study; 118 had noninfectious arthroplasty failure (NIAF), while 36 had PJI. Clinical sensitivity and specificity for diagnosis of PJI were 69% and 100%, respectively, for the sequencing-based approach and 72% and 100%, respectively, for conventional culture (P = 0.74). The combination of both tests was more sensitive (83%) than culture alone (P = 0.04). Results of sequencing-based testing led to changes in treatment in four of 36 (11%) PJI subjects. Microbial identification was achieved using Sanger and next generation sequencing in 19 and 6 subjects, respectively. When combined with culture, the described 16S rRNA gene sequencing-based approach increased sensitivity compared to culture alone, suggesting its potential use in the diagnosis of PJI when synovial fluid culture is negative. IMPORTANCE Periprosthetic joint infection (PJI) is a dreadful complication of joint replacement. Noninvasive identification of infectious pathogens has been traditionnally limited to culture-based testing of synovial fluid which has poor sensitivity. Sanger and Next-generation sequencing (NGS) may be used for synovial fluid testing in PJI, but experience in routine practice is sparse. We used a targeted metagenomic sequencing approach for routine testing of synovial fluid involving NGS when Sanger sequencing had failed or was likely to fail. The objective of this study was to analyze the approach's performance for diagnosis of PJI in comparison to culture for testing synovial fluid. Overall, the sequencing-based approach was not superior to culture for diagnosis of PJI, but yielded positive results in some culture-negative samples.}, } @article {pmid36353067, year = {2022}, author = {Bukavina, L and Prunty, M and Isali, I and Calaway, A and Ginwala, R and Sindhani, M and Ghannoum, M and Mishra, K and Kutikov, A and Uzzo, RG and Ponsky, LE and Abbosh, PH}, title = {Human Gut Mycobiome and Fungal Community Interaction: The Unknown Musketeer in the Chemotherapy Response Status in Bladder Cancer.}, journal = {European urology open science}, volume = {43}, number = {}, pages = {5-13}, pmid = {36353067}, issn = {2666-1683}, abstract = {BACKGROUND: Until recently, the properties of microbiome and mycobiome in humans and its relevance to disease have largely been unexplored. While the interest of microbiome and malignancy over the past few years have burgeoned with advent of new technologies, no research describing the composition of mycobiome in bladder cancer has been done. Deciphering of the metagenome and its aggregate genetic information can be used to understand the functional properties and relationships between the bacteria, fungi, and cancer.

OBJECTIVE: The aim of this project is to characterize the compositional range of the normal versus bladder cancer mycobiome of the gut.

An internal transcribed spacer (ITS) survey of 52 fecal samples was performed to evaluate the gut mycobiome differences between noncancer controls and bladder cancer patients.

Our study evaluated the differences in mycobiome among patients with bladder cancer, versus matched controls. Our secondary analysis evaluated compositional differences in the gut as a function of response status with neoadjuvant chemotherapy. Data demultiplexing and classification were performed using the QIIME v.1.1.1.1 platform. The Ion Torrent-generated fungal ITS sequence data were processed using QIIME (v.1.9.1), and the reads were demultiplexed, quality filtered, and clustered into operation taxonomic units using default parameters. Alpha and beta diversity were computed and plotted in Phyloseq, principal coordinate analysis was performed on Bray-Curtis dissimilarity indices, and a one-way permutational multivariate analysis of variance was used to test for significant differences between cohorts. Phylogenetic Investigation of Communities by Reconstruction of Unobserved States (PICRUSt) was applied to infer functional categories associated with taxonomic composition.

RESULTS AND LIMITATIONS: We found distinctive mycobiome differences between control group (n = 32) and bladder cancer (n = 29) gut flora, and identified an increasing abundance of Tremellales, Hypocreales, and Dothideales. Significant differences in alpha and beta diversity were present between the groups (control vs bladder; p = 0.002), noting distinct compositions within each cohort. A subgroup analysis by sex and neoadjuvant chemotherapy status did not show any further differences in mycobiome composition and diversity. Our results indicate that the gut mycobiome may modulate tumor response to preoperative chemotherapy in bladder cancer patients. We propose that patients with a "favorable" mycobiome composition (eg, high diversity, and low abundance of Agaricomycetes and Saccharomycetes) may have enhanced systemic immune response to chemotherapy through antigen presentation.

CONCLUSIONS: Our study is the first to characterize the enteric mycobiome in patients with bladder cancer and describe complex ecological network alterations, indicating complex bacteria-fungi interactions, particularly highlighted among patients with complete neoadjuvant chemotherapy response.

PATIENT SUMMARY: Our study has demonstrated that the composition of stool mycobiome (fungal inhabitants of the gastrointestinal tract) in patients with bladder cancer is different from that in noncancer individuals. Furthermore, when evaluating how patients respond to chemotherapy given prior to their surgery, our study noted significant differences between patients who responded and those who did not.}, } @article {pmid36352875, year = {2022}, author = {Liu, L and Wang, X and Chen, S and Liu, D and Song, C and Yi, S and Zhu, F and Wang, W and Wang, F and Wang, G and Song, X and Jia, B and Chen, C and Peng, H and Guo, L and Han, B}, title = {Fungal isolates influence the quality of Peucedanum praeruptorum Dunn.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1011001}, pmid = {36352875}, issn = {1664-462X}, abstract = {The symbiotic relationship between beneficial microorganisms and plants plays a vital role in natural and agricultural ecosystems. Although Peucedanum praeruptorum Dunn is widely distributed, its development is greatly limited by early bolting. The reason for early bolting in P. praeruptorum remains poorly characterized. We focus on the plant related microorganisms, including endophytes and rhizosphere microorganisms, by combining the traditional isolation and culture method with metagenomic sequencing technology. We found that the OTUs of endophytes and rhizosphere microorganisms showed a positive correlation in the whole growth stage of P. praeruptorum. Meanwhile, the community diversity of endophytic and rhizosphere fungi showed an opposite change trend, and bacteria showed a similar change trend. Besides, the microbial communities differed during the pre- and post-bolting stages of P. praeruptorum. Beneficial bacterial taxa, such as Pseudomonas and Burkholderia, and fungal taxa, such as Didymella and Fusarium, were abundant in the roots in the pre-bolting stage. Further, a strain belonging to Didymella was obtained by traditional culture and was found to contain praeruptorin A, praeruptorin B, praeruptorin E. In addition, we showed that the fungus could affect its effective components when it was inoculated into P. praeruptorum. This work provided a research reference for the similar biological characteristics of perennial one-time flowering plants, such as Saposhnikovia divaricate, Angelica sinensis and Angelica dahurica.}, } @article {pmid36352504, year = {2022}, author = {Tremblay, J and Schreiber, L and Greer, CW}, title = {High-resolution shotgun metagenomics: the more data, the better?.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {6}, pages = {}, doi = {10.1093/bib/bbac443}, pmid = {36352504}, issn = {1477-4054}, mesh = {Humans ; Sequence Analysis, DNA/methods ; *Metagenomics/methods ; Metagenome ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; }, abstract = {In shotgun metagenomics (SM), the state-of-the-art bioinformatic workflows are referred to as high-resolution shotgun metagenomics (HRSM) and require intensive computing and disk storage resources. While the increase in data output of the latest iteration of high-throughput DNA sequencing systems can allow for unprecedented sequencing depth at a minimal cost, adjustments in HRSM workflows will be needed to properly process these ever-increasing sequence datasets. One potential adaptation is to generate so-called shallow SM datasets that contain fewer sequencing data per sample as compared with the more classic high coverage sequencing. While shallow sequencing is a promising avenue for SM data analysis, detailed benchmarks using real-data are lacking. In this case study, we took four public SM datasets, one massive and the others moderate in size and subsampled each dataset at various levels to mimic shallow sequencing datasets of various sequencing depths. Our results suggest that shallow SM sequencing is a viable avenue to obtain sound results regarding microbial community structures and that high-depth sequencing does not bring additional elements for ecological interpretation. More specifically, results obtained by subsampling as little as 0.5 M sequencing clusters per sample were similar to the results obtained with the largest subsampled dataset for human gut and agricultural soil datasets. For an Antarctic dataset, which contained only a few samples, 4 M sequencing clusters per sample was found to generate comparable results to the full dataset. One area where ultra-deep sequencing and maximizing the usage of all data was undeniably beneficial was in the generation of metagenome-assembled genomes.}, } @article {pmid36352460, year = {2022}, author = {Wei, S and Jespersen, ML and Baunwall, SMD and Myers, PN and Smith, EM and Dahlerup, JF and Rasmussen, S and Nielsen, HB and Licht, TR and Bahl, MI and Hvas, CL}, title = {Cross-generational bacterial strain transfer to an infant after fecal microbiota transplantation to a pregnant patient: a case report.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {193}, pmid = {36352460}, issn = {2049-2618}, mesh = {Adult ; Female ; Humans ; Infant, Newborn ; Pregnancy ; Bacteria ; *Clostridioides difficile ; *Clostridium Infections/therapy/microbiology ; Fecal Microbiota Transplantation/methods ; Feces/microbiology ; Recurrence ; Treatment Outcome ; }, abstract = {BACKGROUND: Fecal microbiota transplantation (FMT) effectively prevents the recurrence of Clostridioides difficile infection (CDI). Long-term engraftment of donor-specific microbial consortia may occur in the recipient, but potential further transfer to other sites, including the vertical transmission of donor-specific strains to future generations, has not been investigated. Here, we report, for the first time, the cross-generational transmission of specific bacterial strains from an FMT donor to a pregnant patient with CDI and further to her child, born at term, 26 weeks after the FMT treatment.

METHODS: A pregnant woman (gestation week 12 + 5) with CDI was treated with FMT via colonoscopy. She gave vaginal birth at term to a healthy baby. Fecal samples were collected from the feces donor, the mother (before FMT, and 1, 8, 15, 22, 26, and 50 weeks after FMT), and the infant (meconium at birth and 3 and 6 months after birth). Fecal samples were profiled by deep metagenomic sequencing for strain-level analysis. The microbial transfer was monitored using single nucleotide variants in metagenomes and further compared to a collection of metagenomic samples from 651 healthy infants and 58 healthy adults.

RESULTS: The single FMT procedure led to an uneventful and sustained clinical resolution in the patient, who experienced no further CDI-related symptoms up to 50 weeks after treatment. The gut microbiota of the patient with CDI differed considerably from the healthy donor and was characterized as low in alpha diversity and enriched for several potential pathogens. The FMT successfully normalized the patient's gut microbiota, likely by donor microbiota transfer and engraftment. Importantly, our analysis revealed that some specific strains were transferred from the donor to the patient and then further to the infant, thus demonstrating cross-generational microbial transfer.

CONCLUSIONS: The evidence for cross-generational strain transfer following FMT provides novel insights into the dynamics and engraftment of bacterial strains from healthy donors. The data suggests FMT treatment of pregnant women as a potential strategy to introduce beneficial strains or even bacterial consortia to infants, i.e., neonatal seeding. Video Abstract.}, } @article {pmid36352436, year = {2022}, author = {Guo, Q and Li, L and Wang, C and Huang, Y and Ma, F and Cong, S and Tan, J and Yao, L and Chen, A and Zheng, L}, title = {Comprehensive virome analysis of the viral spectrum in paediatric patients diagnosed with Mycoplasma pneumoniae pneumonia.}, journal = {Virology journal}, volume = {19}, number = {1}, pages = {181}, pmid = {36352436}, issn = {1743-422X}, mesh = {Child ; Humans ; Infant ; Child, Preschool ; Mycoplasma pneumoniae/genetics ; Virome ; *Coinfection ; *Pneumonia, Mycoplasma/diagnosis/epidemiology ; *Viruses/genetics ; *Respiratory Tract Infections ; *Respiratory Syncytial Virus, Human ; }, abstract = {BACKGROUND: Among hospitalized children suffering from community-acquired pneumonia, Mycoplasma pneumoniae (MP) is one of the most common pathogens. MP often exists as a co-infection with bacteria or viruses, which can exacerbate the clinical symptoms. We investigated the pathogen spectrum in MP-positive and MP-negative samples from hospitalized children with respiratory tract infections in Beijing, China.

METHOD: This study included 1038 samples of nasopharyngeal aspirates obtained between April, 2017 and March, 2018 from hospitalized children under 6 years of age with respiratory tract infections. To explore the impact of MP infection on the composition of the pathogen spectrum, 185 nasopharyngeal aspirates (83 MP-positive/102 MP-negative) were randomly selected for next-generation sequencing and comprehensive metagenomics analysis. Real-time PCR was used to detect and verify common respiratory viruses.

RESULTS: Of the 1038 samples, 454 (43.7%) were infected with MP. In children < 6 years of age, the MP infection rate gradually increased with age, with the highest rate of 74.2% in 5-6-year-olds. The results of metagenomics analysis revealed 11 human, animal and plant virus families, and bacteriophages, including common respiratory viruses, enteroviruses and anelloviruses. The virus family with the highest number of reads in both MP-positive and MP-negative samples was the Pneumoviridae, and the number of reads for human respiratory syncytial virus (HRSV) in MP-positive samples was higher than that in MP-negative samples. Among the 83 MP-positive samples, 47 (56.63%) were co-infected with viruses, the most common of which was influenza virus (IFV). The durations of hospitalization and fever were higher in patients with MP co-infection than MP single infection, but the difference was not statistically significant.

CONCLUSION: The viral family with the highest number of reads in both groups was Pneumoviridae, and the number of reads matched to HRSV in MP-positive samples was much higher than MP-negative samples. Co-infection of MP and IFV infection were the most cases.}, } @article {pmid36352370, year = {2022}, author = {Wu, Z and Wang, Y and Zeng, J and Zhou, Y}, title = {Constructing metagenome-assembled genomes for almost all components in a real bacterial consortium for binning benchmarking.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {746}, pmid = {36352370}, issn = {1471-2164}, mesh = {*Metagenome ; *Benchmarking ; Reproducibility of Results ; Metagenomics/methods ; Bacteria/genetics ; }, abstract = {BACKGROUND: So far, a lot of binning approaches have been intensively developed for untangling metagenome-assembled genomes (MAGs) and evaluated by two main strategies. The strategy by comparison to known genomes prevails over the other strategy by using single-copy genes. However, there is still no dataset with all known genomes for a real (not simulated) bacterial consortium yet.

RESULTS: Here, we continue investigating the real bacterial consortium F1RT enriched and sequenced by us previously, considering the high possibility to unearth all MAGs, due to its low complexity. The improved F1RT metagenome reassembled by metaSPAdes here utilizes about 98.62% of reads, and a series of analyses for the remaining reads suggests that the possibility of containing other low-abundance organisms in F1RT is greatly low, demonstrating that almost all MAGs are successfully assembled. Then, 4 isolates are obtained and individually sequenced. Based on the 4 isolate genomes and the entire metagenome, an elaborate pipeline is then in-house developed to construct all F1RT MAGs. A series of assessments extensively prove the high reliability of the herein reconstruction. Next, our findings further show that this dataset harbors several properties challenging for binning and thus is suitable to compare advanced binning tools available now or benchmark novel binners. Using this dataset, 8 advanced binning algorithms are assessed, giving useful insights for developing novel approaches. In addition, compared with our previous study, two novel MAGs termed FC8 and FC9 are discovered here, and 7 MAGs are solidly unearthed for species without any available genomes.

CONCLUSION: To our knowledge, it is the first time to construct a dataset with almost all known MAGs for a not simulated consortium. We hope that this dataset will be used as a routine toolkit to complement mock datasets for evaluating binning methods to further facilitate binning and metagenomic studies in the future.}, } @article {pmid36351942, year = {2022}, author = {Bianco, K and de Farias, BO and Gonçalves-Brito, AS and Alves do Nascimento, AP and Magaldi, M and Montenegro, K and Flores, C and Oliveira, S and Monteiro, MA and Spisso, BF and Pereira, MU and Ferreira, RG and Albano, RM and Cardoso, AM and Clementino, MM}, title = {Mobile resistome of microbial communities and antimicrobial residues from drinking water supply systems in Rio de Janeiro, Brazil.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {19050}, pmid = {36351942}, issn = {2045-2322}, mesh = {Animals ; Humans ; *Drinking Water/microbiology ; Brazil ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; *Environmental Pollutants ; Genes, Bacterial ; }, abstract = {Antibiotic resistance genes (ARGs) are widespread in the environment due to the overuse of antibiotics and other pollutants, posing a threat to human and animal health. In this study, we evaluated antimicrobial residues, bacterial diversity and ARGs in two important watersheds, Guandu and São João, that supply drinking water to Rio de Janeiro city, Brazil. In addition, tap water samples were collected from three different cities in Rio de Janeiro State, including the metropolitan area of Rio de Janeiro city. Clarithromycin, sulfamethoxazole and azithromycin were found in untreated water and drinking water in all samples. A greater abundance of Proteobacteria was observed in Guandu and São João watersheds, with most of the sequences belonging to the Gammaproteobacteria class. A plasmidome-focused metagenomics approach revealed 4881 (Guandu), 3705 (São João) and 3385 (drinking water) ARGs mainly associated with efflux systems. The genes encoding metallo-β-lactamase enzymes (blaAIM, blaGIM, blaIMP, and blaVIM) were detected in the two watersheds and in drinking water samples. Moreover, we demonstrated the presence of the colistin resistance genes mcr-3 and mcr-4 (both watersheds) and mcr-9 (drinking water and Guandu) for the first time in Brazil. Our data emphasize the importance of introducing measures to reduce the disposal of antibiotics and other pollutants capable of promoting the occurrence and spread of the microbial resistome on aquatic environments and predicting possible negative impacts on human health.}, } @article {pmid36351483, year = {2023}, author = {Corno, G and Ghaly, T and Sabatino, R and Eckert, EM and Galafassi, S and Gillings, MR and Di Cesare, A}, title = {Class 1 integron and related antimicrobial resistance gene dynamics along a complex freshwater system affected by different anthropogenic pressures.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {316}, number = {Pt 2}, pages = {120601}, doi = {10.1016/j.envpol.2022.120601}, pmid = {36351483}, issn = {1873-6424}, mesh = {Humans ; *Integrons/genetics ; *Anti-Bacterial Agents/pharmacology ; Anthropogenic Effects ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Lakes ; }, abstract = {The risk for human health posed by polluted aquatic environments, and especially those carrying antibiotic resistance genes (ARGs) of clinical interest, is still debated. This is because of our limited knowledge of the dynamics of antimicrobial resistance in the environment, the selection mechanisms underlying the spread of ARGs, and the ecological factors potentially favoring their return to humans. The Class 1 integron is one of the most effective platforms for the dissemination of ARGs. In this study we investigated a freshwater system consisting of a lake-river-lake continuum, determining the abundance of class 1 integrons and their associated ARGs by a modulated metagenomic approach. Bacterial abundance and community composition were used to identify the potential carriers of class 1 integrons and their associated ARGs over a period of six months. Class 1 integrons and their ARG cargoes were significantly more abundant in riverine sampling sites receiving treated wastewater. Further, class 1 integrons carried ARGs ranked at the highest risk for human health (e.g., catB genes), in particular, genes encoding resistance to aminoglycosides. Genera of potential pathogens, such as Pseudomonas and Escherichia-Shigella, were correlated with class 1 integrons. The lake-river-lake system demonstrated a clear relationship between the integrase gene of class 1 integrons (intI1) and anthropogenic impact, but also a strong environmental filtering that favored the elimination of intI1 once the human derived stressors were reduced. Overall, the results of this study underline the role class 1 integrons as proxy of anthropogenic pollution and suggest this genetic platform as an important driver of aminoglycoside resistance genes, including high risk ARGs, of potential concern for human health.}, } @article {pmid36349836, year = {2023}, author = {Yuan, ZA and Zhong, LQ and Du, HR and Feng, JN and Liu, XX and Yuan, HY and Guo, JH and Liu, P and Zhang, MH}, title = {Effects of vegetation type differences induced by human disturbance on the nutrition strategy and gut microbiota of Siberian roe deer.}, journal = {Molecular ecology}, volume = {32}, number = {10}, pages = {2534-2550}, doi = {10.1111/mec.16775}, pmid = {36349836}, issn = {1365-294X}, mesh = {Humans ; Animals ; *Deer/physiology ; *Gastrointestinal Microbiome/genetics ; Forests ; Diet/veterinary ; *Microbiota ; }, abstract = {The Siberian roe deer (Capreolus pygargus) is a widely distributed ungulate in northeast China. Due to a series of human disturbance activities such as large-scale forest cutting, deforestation and reclamation, road construction in the past, the appearance and internal structure of forest vegetation in the habitat of Siberian roe have changed significantly. At the same time, Siberian roe population had a series of ecological adaptation responses in the face of such habitat changes. Therefore, two typical vegetation types with differences were selected in the Muling Forest, China. We used nutritional ecology and microbial metagenomic analysis techniques to compare the nutritional selection strategy and the structure and functional characteristics of faecal microbiota of Siberian roe groups in two vegetation types. The results showed that the α diversity of dietary and gut microbes of deer in Natural Forest was higher than that in Plantation Forest. However, the gut microbes of the Plantation Forest group contained more unique enzymes in the functional pathways of carbon metabolism and biosynthesis of amino acids. This study suggests that habitat type is associated with plant community composition, and contributes to changes in the intake proportions of major macronutrients by altering the availability, quality, and composition of certain edible plants. Feeding behaviour may be an important regulatory factor of gut microbiota structure and function of deer. The metabolic function of gut microbiota to different nutrients may affect the microbial community structure. Therefore, our results suggest that the gut microbes of Siberian roe may have coevolved with their diets, and reflect the adaptability of deer populations to environmental changes (e.g., vegetation type). Our study provides new insights into how spatial heterogeneity affects nutrition and microecosystems by describing the interactions among the environment, diet, and symbiotic gut microbes in wild ungulates.}, } @article {pmid36347213, year = {2022}, author = {Brown, TL and Charity, OJ and Adriaenssens, EM}, title = {Ecological and functional roles of bacteriophages in contrasting environments: marine, terrestrial and human gut.}, journal = {Current opinion in microbiology}, volume = {70}, number = {}, pages = {102229}, doi = {10.1016/j.mib.2022.102229}, pmid = {36347213}, issn = {1879-0364}, support = {BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/ E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *Bacteriophages/genetics ; Metagenomics ; Metagenome ; Genome, Viral ; Bacteria/genetics ; }, abstract = {While they are the most abundant biological entities on the planet, the role of bacteriophages (phages) in the microbiome remains enigmatic and understudied. With a rise in the number of metagenomics studies and the publication of highly efficient phage mining programmes, we now have extensive data on the genomic and taxonomic diversity of (mainly) DNA bacteriophages in a wide range of environments. In addition, the higher throughput and quality of sequencing is allowing for strain-level reconstructions of phage genomes from metagenomes. These factors will ultimately help us to understand the role these phages play as part of specific microbial communities, enabling the tracking of individual virus genomes through space and time. Using lessons learned from the latest metagenomic studies, we focus on two explicit aspects of the role bacteriophages play within the microbiome, their ecological role in structuring bacterial populations, and their contribution to microbiome functioning by encoding auxiliary metabolism genes.}, } @article {pmid36346465, year = {2022}, author = {Wang, R and Lai, Y and Fang, Q and Chen, M and Lei, H and Song, C}, title = {Discovery of enzymes to biotransform ginsenoside Rd into ginsenosides F2 and CK using metagenomics and genomic mining.}, journal = {Archives of microbiology}, volume = {204}, number = {12}, pages = {694}, pmid = {36346465}, issn = {1432-072X}, support = {0903-00040031//the Scientific Research Foundation for Talent Introduction of Southwest Medical University/ ; 2020LZXNYDJ28//the Applied Basic Research Cooperation Project of Luzhou Government-Southwest Medical University/ ; }, mesh = {Animals ; *Ginsenosides/metabolism ; *Deer ; *Panax/genetics/microbiology ; beta-Glucosidase/genetics/metabolism ; Biotransformation ; Metagenomics ; }, abstract = {Ginsenosides are the main active components of ginseng, including many types and different contents. Among them, minor ginsenosides have better biological functions and pharmacological activities than those of the major ginsenosides. However, minor ginsenosides cannot be obtained in large quantities, but by means of enzymatic transformation technology, some major ginsenosides can be de-glycosylated at a specific position to generate minor ginsenosides. In this study, we report two glycosidase genes associated with the conversion of ginsenoside Rd to ginsenosides F2 or CK. SWMU-CK-1 was identified among the total genes extracted from the feces of plum deer by local Blast screening for putative ginsenoside conversion function, which could cause the conversion of ginsenoside Rd → F2 → CK. The other gene was found in the Bifidobacterium breve 689b SGAir 0764 chromosome genome, which might have the same function as the β-glucosidase gene testified by the gene matching, named SWMU-F2-2, and can achieve the Rd → F2 transformation. This study reports two genes that enable achieving the biotransformation of rare ginsenosides, while it provides a new insight and a promising approach to explore new genes and develop new functions of existing genes.}, } @article {pmid36346444, year = {2023}, author = {Palmer, B and Lawson, D and Lipson, DA}, title = {Years After a Fire, Biocrust Microbial Communities are Similar to Unburned Communities in a Coastal Grassland.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {1028-1044}, pmid = {36346444}, issn = {1432-184X}, mesh = {Ecosystem ; Grassland ; *Microbiota ; *Fires ; Bacteria/genetics ; Chlorophyll ; Soil ; }, abstract = {Microbial communities are integral for ecosystem processes and their taxonomic composition and function may be altered by a disturbance such as fire. Biocrusts are composed of macroscopic and microscopic organisms and are important for a variety of ecosystem functions, such as nutrient cycling and erosion control. We sought to understand if biocrust community composition and function were altered 1 year after a prescribed fire and 6 years after a wildfire in a coastal California grassland on San Clemente Island. We used shotgun metagenomic sequencing and measurements of chlorophyll content, exopolysaccharide production related to soil stability, and nitrogen fixation. There were no differences in the community composition between unburned samples and the samples burned in the prescribed fire and wildfire. Chlorophyll content differed between the prescribed fire and the controls; however, there were no measured differences in exopolysaccharide production, and nitrogen fixation. However, the wildfire and their respective unburned samples had different functions based on the gene annotations. We compiled one Actinobacteria metagenome-assembled genome from the shotgun sequences which had genes for oxidative and heat stress tolerance. These results suggest that the biocrust community can reach a community composition and function similar to the unburned biocrusts within a year after a prescribed burn and 6 years after a wildfire. However, legacy effects of the wildfire may present themselves in the differences between functional gene sequences. Due to their ability to match the undisturbed community composition and function within years and without intervention, future restoration work should consider the biocrusts in their restoration plans as they may provide valuable ecosystem functions after a disturbance.}, } @article {pmid36346384, year = {2022}, author = {Williams, RBH}, title = {Adapt or perish.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36346384}, issn = {2050-084X}, mesh = {*Metagenomics ; *Microbiota ; }, abstract = {Microbial communities in wastewater treatment plants provide insights into the development and mechanisms of antimicrobial resistance.}, } @article {pmid36346245, year = {2022}, author = {Wright, AA and Harper, SJ}, title = {Draft Genome Sequence of a Washington Isolate of "Candidatus Phytoplasma pruni".}, journal = {Microbiology resource announcements}, volume = {11}, number = {12}, pages = {e0079022}, pmid = {36346245}, issn = {2576-098X}, support = {GR00002025//Washington Tree Fruit Research Commission (WTFRC)/ ; }, abstract = {Illumina sequencing of a Prunus avium tree with X-disease symptoms was performed to obtain a draft genome of "Candidatus Phytoplasma pruni." The genome consists of 14 contigs covering 588,767 bp. This is the first metagenome to be sequenced from the current X-disease epidemic in stone fruit in the Pacific Northwest.}, } @article {pmid36346231, year = {2022}, author = {Dahdouh, E and Fernández-Tomé, L and Cendejas-Bueno, E and Ruiz-Carrascoso, G and Schüffelmann, C and Alós-Díez, M and Lázaro-Perona, F and Castro-Martínez, M and Escosa-García, L and Jiménez-Rodríguez, S and Hierro-Llanillo, L and Mingorance, J}, title = {Intestinal Dominance by Multidrug-Resistant Bacteria in Pediatric Liver Transplant Patients.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0284222}, pmid = {36346231}, issn = {2165-0497}, mesh = {Humans ; Child ; *Drug Resistance, Multiple, Bacterial/genetics ; *Liver Transplantation ; Trimethoprim, Sulfamethoxazole Drug Combination/pharmacology/therapeutic use ; beta-Lactamases/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Carbapenems ; Gram-Negative Bacteria ; Microbial Sensitivity Tests ; }, abstract = {Pediatric liver transplantation (PLTx) is commonly associated with extensive antibiotic treatments that can produce gut microbiome alterations and open the way to dominance by multidrug-resistant organisms (MDROs). In this study, the relationship between intestinal Relative Loads (RLs) of β-lactamase genes, antibiotic consumption, microbiome disruption, and the extraintestinal dissemination of MDROs among PLTx patients is investigated. 28 PLTx patients were included, from whom 169 rectal swabs were collected. Total DNA was extracted and blaCTX-M-1-Family, blaOXA-1, blaOXA-48, and blaVIM were quantified via quantitative polymerase chain reaction (qPCR) and normalized to the total bacterial load (16SrRNA) through LogΔΔCt to determine the RLs. 16SrRNA sequencing was performed for 18 samples, and metagenomic sequencing was performed for 2. Patients' clinical data were retrieved from the hospital's database. At least one of the genes tested were detected in all of the patients. The RLs for blaCTX-M-1-Family, blaOXA-1, blaOXA-48, and blaVIM were higher than 1% of the total bacterial population in 67 (80.73%), 56 (78.87%), 57 (77.03%) and 39 (61.9%) samples, respectively. High RLs for blaCTX-M-1-Family, blaOXA-1, and/or blaOXA-48, were positively associated with the consumption of carbapenems with trimethoprim-sulfamethoxazole and coincided with low diversity in the gut microbiome. Low RLs were associated with the consumption of noncarbapenem β-lactams with aminoglycosides (P < 0.05). Extraintestinal isolates harboring the same gene(s) as those detected intraintestinally were found in 18 samples, and the RLs of the respective swabs were high. We demonstrated a relationship between the consumption of carbapenems with trimethoprim-sulfamethoxazole, intestinal dominance by MDROs and extraintestinal spread of these organisms among PLTx patients. IMPORTANCE In this study, we track the relative intestinal loads of antibiotic resistance genes among pediatric liver transplant patients and determine the relationship between this load, antibiotic consumption, and infections caused by antibiotic-resistant organisms. We demonstrate that the consumption of broad spectrum antibiotics increase this load and decrease the gut microbial diversity among these patients. Moreover, the high loads of resistance genes were related to the extraintestinal spread of multidrug-resistant organisms. Together, our data show that the tracking of the relative intestinal loads of antibiotic resistance genes can be used as a biomarker that has the potential to stop the extraintestinal spread of antibiotic-resistant bacteria via the measurement of the intestinal dominance of these organisms, thereby allowing for the application of preventive measures.}, } @article {pmid36346230, year = {2022}, author = {Goggans, ML and Bilbrey, EA and Quiroz-Moreno, CD and Francis, DM and Jacobi, SK and Kovac, J and Cooperstone, JL}, title = {Short-Term Tomato Consumption Alters the Pig Gut Microbiome toward a More Favorable Profile.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0250622}, pmid = {36346230}, issn = {2165-0497}, mesh = {Humans ; Animals ; Swine ; *Gastrointestinal Microbiome/genetics ; *Solanum lycopersicum ; Feces ; Diet ; Bacteroidetes ; Firmicutes ; Vegetables ; }, abstract = {Diets rich in fruits and vegetables have been shown to exert positive effects on the gut microbiome. However, little is known about the specific effect of individual fruits or vegetables on gut microbe profiles. This study aims to elucidate the effects of tomato consumption on the gut microbiome, as tomatoes account for 22% of vegetable consumption in Western diets, and their consumption has been associated with positive health outcomes. Using piglets as a physiologically relevant model of human metabolism, 20 animals were assigned to either a control or a tomato powder-supplemented diet (both macronutrient matched and isocaloric) for 14 days. The microbiome was sampled rectally at three time points: day 0 (baseline), day 7 (midpoint), and day 14 (end of study). DNA was sequenced using shotgun metagenomics, and reads were annotated using MG-RAST. There were no differences in body weight or feed intake between our two treatment groups. There was a microbial shift which included a higher ratio of Bacteroidota to Bacillota (formerly known as Bacteroidetes and Firmicutes, respectively) and higher alpha-diversity in tomato-fed animals, indicating a shift to a more desirable phenotype. Analyses at both the phylum and genus levels showed global microbiome profile changes (permutational multivariate analysis of variance [PERMANOVA], P ≤ 0.05) over time but not with tomato consumption. These data suggest that short-term tomato consumption can beneficially influence the gut microbial profile, warranting further investigation in humans. IMPORTANCE The composition of the microorganisms in the gut is a contributor to overall health, prompting the development of strategies to alter the microbiome composition. Studies have investigated the role of the diet on the microbiome, as it is a major modifiable risk factor contributing to health; however, little is known about the causal effects of consumption of specific foods on the gut microbiota. A more complete understanding of how individual foods impact the microbiome will enable more evidence-based dietary recommendations for long-term health. Tomatoes are of interest as the most consumed nonstarchy vegetable and a common source of nutrients and phytochemicals across the world. This study aimed to elucidate the effect of short-term tomato consumption on the microbiome, using piglets as a physiologically relevant model to humans. We found that tomato consumption can positively affect the gut microbial profile, which warrants further investigation in humans.}, } @article {pmid36345851, year = {2022}, author = {Walker, H and Shanthikumar, S and Cole, T and Neeland, M and Hanna, D and Haeusler, GM}, title = {Novel approaches to the prediction and diagnosis of pulmonary complications in the paediatric haematopoietic stem cell transplant patient.}, journal = {Current opinion in infectious diseases}, volume = {35}, number = {6}, pages = {493-499}, doi = {10.1097/QCO.0000000000000883}, pmid = {36345851}, issn = {1473-6527}, mesh = {Child ; Humans ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Lung Diseases/diagnosis/etiology/drug therapy ; *Pneumonia/drug therapy ; Bronchoscopy/adverse effects/methods ; Lung ; }, abstract = {PURPOSE OF REVIEW: Haematopoietic stem cell transplant (HSCT) remains the only curative treatment option for many children with relapsed leukaemia, primary immunodeficiencies and haemoglobinopathies. Unfortunately, infectious and noninfectious pulmonary complications following HSCT continue to cause significant morbidity and mortality. This review will focus on recent advances in the field that enhance clinically available diagnostic tools and the role of novel diagnostic techniques.

RECENT FINDINGS: Research continues to highlight the role of standard diagnostic modalities, including imaging using computed topography chest and Fluorodeoxyglucose-positron emission tomography (FDG-PET) in the diagnosis of posttransplant pulmonary infections. Similarly, bronchoalveolar lavage using bronchoscopy to obtain samples for microbiological analysis remains an important tool in the clinical and diagnostic algorithm for these children. The application of more novel diagnostic techniques such as metagenomic next-generation sequencing and the use of specific biomarkers remain potential future tools in children in whom the aetiology of posttransplant lung disease is unknown. The impact of the pulmonary microbiome on infectious and noninfectious pulmonary disease post HSCT is a future research direction.

SUMMARY: Pulmonary infectious complications post HSCT remain a devastating complication for children and their families. Despite improvements in standard and novel diagnostic modalities, the aetiology of pulmonary disease remains unknown for many patients. There is an urgent need for ongoing collaborative research to bridge this critical knowledge gap and lead to better patient outcomes.}, } @article {pmid36345525, year = {2022}, author = {Song, Y and Perlman, K and Gyarmati, P}, title = {Microbial and host factors contribute to bloodstream infection in a pediatric acute lymphocytic leukemia mouse model.}, journal = {Heliyon}, volume = {8}, number = {11}, pages = {e11340}, pmid = {36345525}, issn = {2405-8440}, abstract = {BACKGROUND: Hematological malignancies are the most common cancers in the pediatric population, and T-cell acute lymphocytic leukemia (T-ALL) is the most common hematological malignancy in children. Bloodstream infection (BSI) is a commonly occurring complication in leukemia due to underlying conditions and therapy-induced neutropenia. Several studies identified the gut microbiome as a major source of BSI due to bacterial translocation. This study aimed to investigate changes in the intestinal and fecal microbiome, and their roles in the pathophysiology of BSI in a pediatric T-ALL mouse model using high-throughput shotgun metagenomics sequencing, and metabolomics.

RESULTS: Our results show that BSI in ALL is characterized by an increase of a mucin degrading bacterium (Akkermansia muciniphila) and a decrease of butyrate producer Clostridia spp., along with a decrease in short-chain fatty acid (SCFA) concentrations and differential expression of tight junction proteins in the small intestine. Functional analysis of the small intestinal microbiome indicated a reduced capability of SCFA synthesis, while SCFA supplementation ameliorated the development of BSI in ALL.

CONCLUSIONS: Our data indicates that changes in the microbiome, and the resulting changes in levels of SCFAs contribute significantly to the pathogenesis of bloodstream infection in ALL. Our study provides tailored preventive or therapeutic approaches to reduce BSI-associated mortality in ALL.}, } @article {pmid36344742, year = {2022}, author = {Ouyang, J and Zheng, S and Huang, M and Tang, H and Qiu, X and Chen, S and Wang, Z and Zhou, Z and Gao, Y and Xiong, Y and Zeng, G and Huang, J and He, J and Ren, J and Chen, H and Yan, X}, title = {Chromosome-level genome and population genomics reveal evolutionary characteristics and conservation status of Chinese indigenous geese.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1191}, pmid = {36344742}, issn = {2399-3642}, mesh = {Animals ; *Geese/genetics ; *DNA, Mitochondrial/genetics ; Metagenomics ; Chromosomes ; China ; }, abstract = {Geese are herbivorous birds that play an essential role in the agricultural economy. We construct the chromosome-level genome of a Chinese indigenous goose (the Xingguo gray goose, XGG; Anser cygnoides) and analyze the adaptation of fat storage capacity in the goose liver during the evolution of Anatidae. Genomic resequencing of 994 geese is used to investigate the genetic relationships of geese, which supports the dual origin of geese (Anser cygnoides and Anser anser). Chinese indigenous geese show higher genetic diversity than European geese, and a scientific conservation program can be established to preserve genetic variation for each breed. We also find that a 14-bp insertion in endothelin receptor B subtype 2 (EDNRB2) that determines the white plumage of Chinese domestic geese is a natural mutation, and the linkaged alleles rapidly increase in frequency as a result of genetic hitchhiking, leading to the formation of completely different haplotypes of white geese under strong artificial selection. These genomic resources and our findings will facilitate marker-assisted breeding of geese and provide a foundation for further research on geese genetics and evolution.}, } @article {pmid36344504, year = {2022}, author = {Kato, K and Okazaki, S and Kannan, S and Altae-Tran, H and Esra Demircioglu, F and Isayama, Y and Ishikawa, J and Fukuda, M and Macrae, RK and Nishizawa, T and Makarova, KS and Koonin, EV and Zhang, F and Nishimasu, H}, title = {Structure of the IscB-ωRNA ribonucleoprotein complex, the likely ancestor of CRISPR-Cas9.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6719}, pmid = {36344504}, issn = {2041-1723}, mesh = {Humans ; *CRISPR-Cas Systems ; Cryoelectron Microscopy ; *RNA, Guide, CRISPR-Cas Systems/metabolism ; Endonucleases/metabolism ; RNA/metabolism ; DNA/metabolism ; Ribonucleoproteins/metabolism ; }, abstract = {Transposon-encoded IscB family proteins are RNA-guided nucleases in the OMEGA (obligate mobile element-guided activity) system, and likely ancestors of the RNA-guided nuclease Cas9 in the type II CRISPR-Cas adaptive immune system. IscB associates with its cognate ωRNA to form a ribonucleoprotein complex that cleaves double-stranded DNA targets complementary to an ωRNA guide segment. Although IscB shares the RuvC and HNH endonuclease domains with Cas9, it is much smaller than Cas9, mainly due to the lack of the α-helical nucleic-acid recognition lobe. Here, we report the cryo-electron microscopy structure of an IscB protein from the human gut metagenome (OgeuIscB) in complex with its cognate ωRNA and a target DNA, at 2.6-Å resolution. This high-resolution structure reveals the detailed architecture of the IscB-ωRNA ribonucleoprotein complex, and shows how the small IscB protein assembles with the ωRNA and mediates RNA-guided DNA cleavage. The large ωRNA scaffold structurally and functionally compensates for the recognition lobe of Cas9, and participates in the recognition of the guide RNA-target DNA heteroduplex. These findings provide insights into the mechanism of the programmable DNA cleavage by the IscB-ωRNA complex and the evolution of the type II CRISPR-Cas9 effector complexes.}, } @article {pmid36343820, year = {2023}, author = {Li, H and Xia, W and Liu, X and Wang, X and Liu, G and Chen, H and Zhu, L and Li, D}, title = {Food provisioning results in functional, but not compositional, convergence of the gut microbiomes of two wild Rhinopithecus species: Evidence of functional redundancy in the gut microbiome.}, journal = {The Science of the total environment}, volume = {858}, number = {Pt 2}, pages = {159957}, doi = {10.1016/j.scitotenv.2022.159957}, pmid = {36343820}, issn = {1879-1026}, mesh = {Humans ; Animals ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; *Presbytini ; Bacteria ; Feces ; }, abstract = {The consumption of similar diets has led to the convergence of gut microbial compositions and functions across phylogenetically distinct animals. However, given the functional redundancy in gut microbiomes, it remains unclear whether synchrony occurs in their functions only and not in their composition, even within phylogenetically close animals consuming a similar diet. In this study, we collected fresh fecal samples from a Rhinopithecus roxellana population in April 2021 (before food provisioning) and June and December 2021 (after food provisioning) and used high-throughput sequencing methods (full-length 16S rRNA gene sequencing and metagenomes) to investigate changes in the gut microbiome due to food provisioning. Combining the results from our previous studies on a wild Rhinopithecus bieti population, we found that the artificial food provisions (e.g., apples, carrots, and peanuts) affected the gut microbiome, and synchrony occurred only in its functions and antibiotic resistance gene community in both Rhinopithecus species, reflecting its ecological functional redundancy. Given the current findings (e.g., depletion in probiotic microbes, dysbiosis in the gut microbial community, and changes in the antibiotic resistance gene profile), anthropogenic disturbances (e.g., food provisioning) would have potential negative effects on host health. Therefore, human activity in animal conservation should be rethought from the standpoint of gut microbial diversity.}, } @article {pmid36343807, year = {2023}, author = {Wang, Y and Li, H and Li, Y and Guo, H and Zhou, J and Wang, T}, title = {Metagenomic analysis revealed sources, transmission, and health risk of antibiotic resistance genes in confluence of Fenhe, Weihe, and Yellow Rivers.}, journal = {The Science of the total environment}, volume = {858}, number = {Pt 2}, pages = {159913}, doi = {10.1016/j.scitotenv.2022.159913}, pmid = {36343807}, issn = {1879-1026}, mesh = {Animals ; Humans ; *Rivers/microbiology ; *Metagenomics ; Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; }, abstract = {Rivers are important vectors and reservoirs of antibiotics resistance genes (ARGs). Information regarding transmission and health risk of ARGs in river confluence is still lacking. In this study, metagenomics was used to distinguish contributions of human activities on ARGs and human pathogenic bacteria (HPB) in confluence of Fenhe, Weihe, and Yellow Rivers. Bacitracin resistance gene and bacA were the highest in all rivers, with 1.86 × 10[-2]-7.26 × 10[-2] and 1.79 × 10[-2]-9.12 × 10[-2] copies/16S rRNA copies, respectively. River confluence significantly increased the abundance of ARGs, especially at the confluence of three rivers with the highest 1.53 × 10[-1] copies/16S rRNA copies. Antibiotic efflux and antibiotic target alteration were the dominant resistant mechanisms in three rivers. ARGs profiles were influenced by multiple factors, with the contributions of various factors ranked as microbial communities > physicochemical factors > human activities > mobile genetic elements (MGEs). Notably, human activities and animal feces were important potential contributors of ARGs in the Weihe River and Yellow River. Transposons, as the main MGEs in three rivers, played important roles in ARGs transfer. The confluence of three rivers had the highest abundance of MGEs with the greatest transfer potentials, and therefore exhibiting the largest exposure risk of ARGs with 232.4 copies/cap·d. Furthermore, correlations of ARGs, MGEs, and HPB in different rivers were constructed via co-occurrence modes to systematically illustrate the health risks of ARGs. This study firstly unveiled the transmission and health risk of ARGs in river confluence, providing supports for ARGs control in watershed.}, } @article {pmid36343772, year = {2023}, author = {Perez-Garcia, J and González-Carracedo, M and Espuela-Ortiz, A and Hernández-Pérez, JM and González-Pérez, R and Sardón-Prado, O and Martin-Gonzalez, E and Mederos-Luis, E and Poza-Guedes, P and Corcuera-Elosegui, P and Callero, A and Sánchez-Machín, I and Korta-Murua, J and Pérez-Pérez, JA and Villar, J and Pino-Yanes, M and Lorenzo-Diaz, F}, title = {The upper-airway microbiome as a biomarker of asthma exacerbations despite inhaled corticosteroid treatment.}, journal = {The Journal of allergy and clinical immunology}, volume = {151}, number = {3}, pages = {706-715}, doi = {10.1016/j.jaci.2022.09.041}, pmid = {36343772}, issn = {1097-6825}, mesh = {Humans ; *Anti-Asthmatic Agents/therapeutic use ; RNA, Ribosomal, 16S ; Administration, Inhalation ; *Asthma/drug therapy ; *Microbiota ; Adrenal Cortex Hormones/therapeutic use ; Biomarkers ; }, abstract = {BACKGROUND: The response to inhaled corticosteroids (ICS) in asthma is affected by the interplay of several factors. Among these, the role of the upper-airway microbiome has been scarcely investigated. We aimed to evaluate the association between the salivary, pharyngeal, and nasal microbiome with asthma exacerbations despite receipt of ICS.

METHODS: Samples from 250 asthma patients from the Genomics and Metagenomics of Asthma Severity (GEMAS) study treated with ICS were analyzed. Control/case subjects were defined by the absence/presence of asthma exacerbations in the past 6 months despite being treated with ICS. The bacterial microbiota was profiled by sequencing the V3-V4 region of the 16S rRNA gene. Differences between groups were assessed by PERMANOVA and regression models adjusted for potential confounders. A false discovery rate (FDR) of 5% was used to correct for multiple comparisons. Classification models of asthma exacerbations despite ICS treatment were built with machine learning approaches based on clinical, genetic, and microbiome data.

RESULTS: In nasal and saliva samples, case subjects had lower bacterial diversity (Richness, Shannon, and Faith indices) than control subjects (.007 ≤ P ≤ .037). Asthma exacerbations accounted for 8% to 9% of the interindividual variation of the salivary and nasal microbiomes (.003 ≤ P ≤ .046). Three, 4, and 11 bacterial genera from the salivary, pharyngeal, and nasal microbiomes were differentially abundant between groups (4.09 × 10[-12] ≤ FDR ≤ 0.047). Integrating clinical, genetic, and microbiome data showed good discrimination for the development of asthma exacerbations despite receipt of ICS (AUCtraining: 0.82 and AUCvalidation: 0.77).

CONCLUSION: The diversity and composition of the upper-airway microbiome are associated with asthma exacerbations despite ICS treatment. The salivary microbiome has a potential application as a biomarker of asthma exacerbations despite receipt of ICS.}, } @article {pmid36343662, year = {2022}, author = {Lee, JW and Cowley, ES and Wolf, PG and Doden, HL and Murai, T and Caicedo, KYO and Ly, LK and Sun, F and Takei, H and Nittono, H and Daniel, SL and Cann, I and Gaskins, HR and Anantharaman, K and Alves, JMP and Ridlon, JM}, title = {Formation of secondary allo-bile acids by novel enzymes from gut Firmicutes.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2132903}, pmid = {36343662}, issn = {1949-0984}, support = {R03 AI147127/AI/NIAID NIH HHS/United States ; T15 LM007359/LM/NLM NIH HHS/United States ; T32 GM140935/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Bile Acids and Salts ; Firmicutes/metabolism ; Phylogeny ; *Gastrointestinal Microbiome ; Lithocholic Acid/metabolism ; Deoxycholic Acid/metabolism ; }, abstract = {The gut microbiome of vertebrates is capable of numerous biotransformations of bile acids, which are responsible for intestinal lipid digestion and function as key nutrient-signaling molecules. The human liver produces bile acids from cholesterol predominantly in the A/B-cis orientation in which the sterol rings are "kinked", as well as small quantities of A/B-trans oriented "flat" stereoisomers known as "primary allo-bile acids". While the complex multi-step bile acid 7α-dehydroxylation pathway has been well-studied for conversion of "kinked" primary bile acids such as cholic acid (CA) and chenodeoxycholic acid (CDCA) to deoxycholic acid (DCA) and lithocholic acid (LCA), respectively, the enzymatic basis for the formation of "flat" stereoisomers allo-deoxycholic acid (allo-DCA) and allo-lithocholic acid (allo-LCA) by Firmicutes has remained unsolved for three decades. Here, we present a novel mechanism by which Firmicutes generate the "flat" bile acids allo-DCA and allo-LCA. The BaiA1 was shown to catalyze the final reduction from 3-oxo-allo-DCA to allo-DCA and 3-oxo-allo-LCA to allo-LCA. Phylogenetic and metagenomic analyses of human stool samples indicate that BaiP and BaiJ are encoded only in Firmicutes and differ from membrane-associated bile acid 5α-reductases recently reported in Bacteroidetes that indirectly generate allo-LCA from 3-oxo-Δ[4]-LCA. We further map the distribution of baiP and baiJ among Firmicutes in human metagenomes, demonstrating an increased abundance of the two genes in colorectal cancer (CRC) patients relative to healthy individuals.}, } @article {pmid36343281, year = {2023}, author = {Moutsoglou, DM and Tatah, J and Prisco, SZ and Prins, KW and Staley, C and Lopez, S and Blake, M and Teigen, L and Kazmirczak, F and Weir, EK and Kabage, AJ and Guan, W and Khoruts, A and Thenappan, T}, title = {Pulmonary Arterial Hypertension Patients Have a Proinflammatory Gut Microbiome and Altered Circulating Microbial Metabolites.}, journal = {American journal of respiratory and critical care medicine}, volume = {207}, number = {6}, pages = {740-756}, pmid = {36343281}, issn = {1535-4970}, support = {K08 HL140100/HL/NHLBI NIH HHS/United States ; R01 HL158795/HL/NHLBI NIH HHS/United States ; R01 HL162927/HL/NHLBI NIH HHS/United States ; T32 HL144472/GF/NIH HHS/United States ; F32 HL154533/GF/NIH HHS/United States ; NIH UL1 TR002494//University of Minnesota Clinical Translational Sciences Award/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Pulmonary Arterial Hypertension ; Dysbiosis ; Phylogeny ; Familial Primary Pulmonary Hypertension ; Inflammation ; *Vascular Diseases ; Bile Acids and Salts ; }, abstract = {Rationale: Inflammation drives pulmonary arterial hypertension (PAH). Gut dysbiosis causes immune dysregulation and systemic inflammation by altering circulating microbial metabolites; however, little is known about gut dysbiosis and microbial metabolites in PAH. Objectives: To characterize the gut microbiome and microbial metabolites in patients with PAH. Methods: We performed 16S ribosomal RNA gene and shotgun metagenomics sequencing on stool from patients with PAH, family control subjects, and healthy control subjects. We measured markers of inflammation, gut permeability, and microbial metabolites in plasma from patients with PAH, family control subjects, and healthy control subjects. Measurements and Main Results: The gut microbiome was less diverse in patients with PAH. Shannon diversity index correlated with measures of pulmonary vascular disease but not with right ventricular function. Patients with PAH had a distinct gut microbial signature at the phylogenetic level, with fewer copies of gut microbial genes that produce antiinflammatory short-chain fatty acids (SCFAs) and secondary bile acids and lower relative abundances of species encoding these genes. Consistent with the gut microbial changes, patients with PAH had relatively lower plasma concentrations of SCFAs and secondary bile acids. Patients with PAH also had enrichment of species with the microbial genes that encoded the proinflammatory microbial metabolite trimethylamine. The changes in the gut microbiome and circulating microbial metabolites between patients with PAH and family control subjects were not as substantial as the differences between patients with PAH and healthy control subjects. Conclusions: Patients with PAH have proinflammatory gut dysbiosis, in which lower circulating SCFAs and secondary bile acids may facilitate pulmonary vascular disease. These findings support investigating modulation of the gut microbiome as a potential treatment for PAH.}, } @article {pmid36342154, year = {2022}, author = {Li, J and Dong, C and Lai, Q and Wang, G and Shao, Z}, title = {Frequent Occurrence and Metabolic Versatility of Marinifilaceae Bacteria as Key Players in Organic Matter Mineralization in Global Deep Seas.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0086422}, pmid = {36342154}, issn = {2379-5077}, mesh = {Animals ; *Lignin/metabolism ; *Bacteria/genetics ; Oceans and Seas ; Metagenome ; Bacteroidetes/genetics ; Plants/genetics ; Carbon/metabolism ; }, abstract = {Transfer of animal and plant detritus of both terrestrial and marine origins to the deep sea occurs on a global scale. Microorganisms play an important role in mineralizing them therein, but these are yet to be identified in situ. To observe key bacteria involved, we conducted long-term in situ incubation and found that members of the family Marinifilaceae (MF) occurred as some of the most predominant bacteria thriving on the new inputs of plant and animal biomasses in the deep sea in both marginal and oceanic areas. This taxon is diverse and ubiquitous in marine environments. A total of 11 MAGs belonging to MF were retrieved from metagenomic data and diverged into four subgroups in the phylogenomic tree. Based on metagenomic and metatranscriptomic analyses, we described the metabolic features and in situ metabolizing activities of different subgroups. The MF-2 subgroup, which dominates plant detritus-enriched cultures, specializes in polysaccharide degradation and lignin oxidation and has high transcriptional activities of related genes in situ. Intriguingly, members of this subgroup encode a nitrogen fixation pathway to compensate for the shortage of nitrogen sources inside the plant detritus. In contrast, other subgroups dominating the animal tissue-supported microbiomes are distinguished from MF-2 with regard to carbon and nitrogen metabolism and exhibit high transcriptional activity for proteolysis in situ. Despite these metabolic divergences of MF lineages, they show high in situ transcriptional activities for organic fermentation and anaerobic respiration (reductions of metal and/or dimethyl sulfoxide). These results highlight the role of previously unrecognized Marinifilaceae bacteria in organic matter mineralization in marine environments by coupling carbon and nitrogen cycling with metal and sulfur. IMPORTANCE Microbial mineralization of organic matter has a significant impact on the global biogeochemical cycle. This report confirms the role of Marinifilaceae in organic degradation in the oceans, with a contribution to ocean carbon cycling that has previously been underestimated. It was the dominant taxon thriving on plant and animal biomasses in our in situ incubator, as well as in whale falls and wood falls. At least 9 subgroups were revealed, and they were widely distributed in oceans globally but predominant in organic-matter-rich environments, with an average relative abundance of 8.3%. Different subgroups display a preference for the degradation of different macromolecules (polysaccharides, lignin, and protein) and adapt to their environments via special metabolic mechanisms.}, } @article {pmid36342125, year = {2022}, author = {Alegria Terrazas, R and Robertson-Albertyn, S and Corral, AM and Escudero-Martinez, C and Kapadia, R and Balbirnie-Cumming, K and Morris, J and Hedley, PE and Barret, M and Torres-Cortes, G and Paterson, E and Baggs, EM and Abbott, J and Bulgarelli, D}, title = {Defining Composition and Function of the Rhizosphere Microbiota of Barley Genotypes Exposed to Growth-Limiting Nitrogen Supplies.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0093422}, pmid = {36342125}, issn = {2379-5077}, support = {BB/S002871/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Rhizosphere ; *Hordeum/microbiology ; Nitrogen ; Plant Roots ; *Microbiota/genetics ; Soil ; Genotype ; }, abstract = {The microbiota populating the rhizosphere, the interface between roots and soil, can modulate plant growth, development, and health. These microbial communities are not stochastically assembled from the surrounding soil, but their composition and putative function are controlled, at least partially, by the host plant. Here, we use the staple cereal barley as a model to gain novel insights into the impact of differential applications of nitrogen, a rate-limiting step for global crop production, on the host genetic control of the rhizosphere microbiota. Using a high-throughput amplicon sequencing survey, we determined that nitrogen availability for plant uptake is a factor promoting the selective enrichment of individual taxa in the rhizosphere of wild and domesticated barley genotypes. Shotgun sequencing and metagenome-assembled genomes revealed that this taxonomic diversification is mirrored by a functional specialization, manifested by the differential enrichment of multiple Gene Ontology terms, of the microbiota of plants exposed to nitrogen conditions limiting barley growth. Finally, a plant soil feedback experiment revealed that host control of the barley microbiota underpins the assembly of a phylogenetically diverse group of bacteria putatively required to sustain plant performance under nitrogen-limiting supplies. Taken together, our observations indicate that under nitrogen conditions limiting plant growth, host-microbe and microbe-microbe interactions fine-tune the host genetic selection of the barley microbiota at both taxonomic and functional levels. The disruption of these recruitment cues negatively impacts plant growth. IMPORTANCE The microbiota inhabiting the rhizosphere, the thin layer of soil surrounding plant roots, can promote the growth, development, and health of their host plants. Previous research indicated that differences in the genetic composition of the host plant coincide with variations in the composition of the rhizosphere microbiota. This is particularly evident when looking at the microbiota associated with input-demanding modern cultivated varieties and their wild relatives, which have evolved under marginal conditions. However, the functional significance of these differences remains to be fully elucidated. We investigated the rhizosphere microbiota of wild and cultivated genotypes of the global crop barley and determined that nutrient conditions limiting plant growth amplify the host control on microbes at the root-soil interface. This is reflected in a plant- and genotype-dependent functional specialization of the rhizosphere microbiota, which appears to be required for optimal plant growth. These findings provide novel insights into the significance of the rhizosphere microbiota for plant growth and sustainable agriculture.}, } @article {pmid36342051, year = {2022}, author = {Jiang, H and Cao, HW and Chai, ZX and Chen, XY and Zhang, CF and Zhu, Y and Xin, JW}, title = {Dynamic alterations in yak (Bos grunniens) rumen microbiome in response to seasonal variations in diet.}, journal = {Physiological genomics}, volume = {54}, number = {12}, pages = {514-525}, doi = {10.1152/physiolgenomics.00112.2022}, pmid = {36342051}, issn = {1531-2267}, mesh = {Animals ; Cattle ; RNA, Ribosomal, 16S/genetics ; *Rumen ; *Microbiota/physiology ; Diet ; Bacteroidetes/genetics ; Cellulose ; }, abstract = {Rumen microorganisms play important roles in the healthy growth of yaks. This study investigated changes in yak rumen microbiome during natural grazing at the warm seasons and supplementary feeding at cold seasons. High-throughput sequencing of 16S rRNA and metagenome analysis were conducted to investigate the structures and functions of yak rumen microbial communities. The results indicated that Bacteroidetes and Firmicutes were the most abundant phyla. In addition, Bacteroidetes might play a more important role than Firmicutes during the supplementary feeding stage (spring and winter), but less during natural grazing stage (summer and autumn). KEGG analysis showed that the amino sugar and nucleotide sugar metabolism, glycolysis/gluconeogenesis, pyruvate metabolism, starch and sucrose metabolism, and fructose and mannose metabolism were the main pathways in the microbial community, which were significantly different between seasons. The carbohydrate-active enzymes (CAZyme) annotation revealed that cellulose was an important carbon source for microorganisms in yak rumen. Glycoside hydrolases (GHs) were the most abundant class of CAZymes, followed by glycosyl transferases (GTs), which were important to digestion of oil, cellulose, and hemicellulose in food. These results contribute to the understanding of microbial components and functions in yak rumen.}, } @article {pmid36341458, year = {2022}, author = {Yang, J and Qin, S and Zhang, H}, title = {Precise strategies for selecting probiotic bacteria in treatment of intestinal bacterial dysfunctional diseases.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1034727}, pmid = {36341458}, issn = {1664-3224}, mesh = {Pregnancy ; Female ; Humans ; *Probiotics/therapeutic use ; Bacteria ; *Microbiota ; *Intestinal Diseases ; *Bacterial Infections ; }, abstract = {Abundant microbiota resides in the organs of the body, which utilize the nutrition and form a reciprocal relationship with the host. The composition of these microbiota changes under different pathological conditions, particularly in response to stress and digestive diseases, making the microbial composition and health of the hosts body interdependent. Probiotics are living microorganisms that have demonstrated beneficial effects on physical health and as such are used as supplements to ameliorate symptoms of various digestive diseases by optimizing microbial composition of the gut and restore digestive balance. However, the supplementary effect does not achieve the expected result. Therefore, a targeted screening strategy on probiotic bacteria is crucial, owing to the presence of several bacterial strains. Core bacteria work effectively in maintaining microbiological homeostasis and stabilization in the gastrointestinal tract. Some of the core bacteria can be inherited and acquired from maternal pregnancy and delivery; others can be acquired from contact with the mother, feces, and the environment. Knowing the genera and functions of the core bacteria could be vital in the isolation and selection of probiotic bacteria for supplementation. In addition, other supporting strains of probiotic bacteria are also needed. A comprehensive strategy for mining both core and supporting bacteria before its clinical use is needed. Using metagenomics or other methods of estimation to discern the typically differentiated strains of bacteria is another important strategy to treat dysbiosis. Hence, these two factors are significant to carry out targeted isolation and selection of the functional strains to compose the resulting probiotic preparation for application in both research and clinical use. In conclusion, precise probiotic supplementation, by screening abundant strains of bacteria and isolating specific probiotic strains, could rapidly establish the core microbiota needed to confer resilience, particularly in bacterial dysfunctional diseases. This approach can help identify distinct bacteria which can be used to improve supplementation therapies.}, } @article {pmid36341405, year = {2022}, author = {Wang, X and Xiong, K and Huang, F and Huang, J and Liu, Q and Duan, N and Ruan, H and Jiang, H and Zhu, Y and Lin, L and Song, Y and Zhao, M and Zheng, L and Ye, P and Qian, Y and Hu, Q and Yan, F and Wang, W}, title = {A metagenome-wide association study of the gut microbiota in recurrent aphthous ulcer and regulation by thalidomide.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1018567}, pmid = {36341405}, issn = {1664-3224}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Stomatitis, Aphthous ; Thalidomide/therapeutic use ; Dysbiosis/complications ; Metagenome ; }, abstract = {Recurrent aphthous ulcer (RAU), one of the most common diseases in humans, has an unknown etiology and is difficult to treat. Thalidomide is an important immunomodulatory and antitumor drug and its effects on the gut microbiota still remain unclear. We conducted a metagenomic sequencing study of fecal samples from a cohort of individuals with RAU, performed biochemical assays of cytokines, immunoglobulins and antimicrobial peptides in serum and saliva, and investigated the regulation effects of thalidomide administration and withdrawal. Meanwhile we constructed the corresponding prediction models. Our metagenome-wide association results indicated that gut dysbacteriosis, microbial dysfunction and immune imbalance occurred in RAU patients. Thalidomide regulated gut dysbacteriosis in a species-specific manner and had different sustainable effects on various probiotics and pathogens. A previously unknown association between gut microbiota alterations and RAU was found, and the specific roles of thalidomide in modulating the gut microbiota and immunity were determined, suggesting that RAU may be affected by targeting gut dysbacteriosis and modifying immune imbalance. In-depth insights into sophisticated networks consisting of the gut microbiota and host cells may lead to the development of emerging treatments, including prebiotics, probiotics, synbiotics, and postbiotics.}, } @article {pmid36341392, year = {2022}, author = {Shirane, M and Yawata, N and Motooka, D and Shibata, K and Khor, SS and Omae, Y and Kaburaki, T and Yanai, R and Mashimo, H and Yamana, S and Ito, T and Hayashida, A and Mori, Y and Numata, A and Murakami, Y and Fujiwara, K and Ohguro, N and Hosogai, M and Akiyama, M and Hasegawa, E and Paley, M and Takeda, A and Maenaka, K and Akashi, K and Yokoyama, WM and Tokunaga, K and Yawata, M and Sonoda, KH}, title = {Intraocular human cytomegaloviruses of ocular diseases are distinct from those of viremia and are capable of escaping from innate and adaptive immunity by exploiting HLA-E-mediated peripheral and central tolerance.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1008220}, pmid = {36341392}, issn = {1664-3224}, support = {P30 AR073752/AR/NIAMS NIH HHS/United States ; }, mesh = {Humans ; Cytomegalovirus ; Viremia ; Central Tolerance ; Viral Proteins ; *Cytomegalovirus Infections ; Adaptive Immunity ; Peptides ; Protein Sorting Signals ; *Retinitis ; HLA-E Antigens ; }, abstract = {Human cytomegalovirus (HCMV) infections develop into CMV diseases that result in various forms of manifestations in local organs. CMV-retinitis is a form of CMV disease that develops in immunocompromised hosts with CMV-viremia after viruses in the peripheral circulation have entered the eye. In the HCMV genome, extensive diversification of the UL40 gene has produced peptide sequences that modulate NK cell effector functions when loaded onto HLA-E and are subsequently recognized by the NKG2A and NKG2C receptors. Notably, some HCMV strains carry UL40 genes that encode peptide sequences identical to the signal peptide sequences of specific HLA-A and HLA-C allotypes, which enables these CMV strains to escape HLA-E-restricted CD8[+]T cell responses. Variations in UL40 sequences have been studied mainly in the peripheral blood of CMV-viremia cases. In this study, we sought to investigate how ocular CMV disease develops from CMV infections. CMV gene sequences were compared between the intraocular fluids and peripheral blood of 77 clinical cases. UL40 signal peptide sequences were more diverse, and multiple sequences were typically present in CMV-viremia blood compared to intraocular fluid. Significantly stronger NK cell suppression was induced by UL40-derived peptides from intraocular HCMV compared to those identified only in peripheral blood. HCMV present in intraocular fluids were limited to those carrying a UL40 peptide sequence corresponding to the leader peptide sequence of the host's HLA class I, while UL40-derived peptides from HCMV found only in the peripheral blood were disparate from any HLA class I allotype. Overall, our analyses of CMV-retinitis inferred that specific HCMV strains with UL40 signal sequences matching the host's HLA signal peptide sequences were those that crossed the blood-ocular barrier to enter the intraocular space. UL40 peptide repertoires were the same in the intraocular fluids of all ocular CMV diseases, regardless of host immune status, implying that virus type is likely to be a common determinant in ocular CMV disease development. We thus propose a mechanism for ocular CMV disease development, in which particular HCMV types in the blood exploit peripheral and central HLA-E-mediated tolerance mechanisms and, thus, escape the antivirus responses of both innate and adaptive immunity.}, } @article {pmid36340419, year = {2022}, author = {Pilo, P and Lawless, C and Tiley, AMM and Karki, SJ and Burke, JI and Feechan, A}, title = {Comparison of microscopic and metagenomic approaches to identify cereal pathogens and track fungal spore release in the field.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1039090}, pmid = {36340419}, issn = {1664-462X}, abstract = {Wheat is one of the main staple food crops, and 775 million tonnes of wheat were produced worldwide in 2022. Fungal diseases such as Fusarium head blight, Septoria tritici blotch, spot blotch, tan spot, stripe rust, leaf rust, and powdery mildew cause serious yield losses in wheat and can impact quality. We aimed to investigate the incidence of spores from major fungal pathogens of cereals in the field by comparing microscopic and metagenomic based approaches for spore identification. Spore traps were set up in four geographically distinct UK wheat fields (Carnoustie, Angus; Bishop Burton, Yorkshire; Swindon, Wiltshire; and Lenham, Kent). Six major cereal fungal pathogen genera (Alternaria spp., Blumeria graminis, Cladosporium spp., Fusarium spp., Puccinia spp., and Zymoseptoria spp.) were found using these techniques at all sites. Using metagenomic and BLAST analysis, 150 cereal pathogen species (33 different genera) were recorded on the spore trap tapes. The metagenomic BLAST analysis showed a higher accuracy in terms of species-specific identification than the taxonomic tool software Kraken2 or microscopic analysis. Microscopic data from the spore traps was subsequently correlated with weather data to examine the conditions which promote ascospore release of Fusarium spp. and Zymoseptoria spp. This revealed that Zymoseptoria spp. and Fusarium spp. ascospore release show a positive correlation with relative humidity (%RH). Whereas air temperature (°C) negatively affects Zymoseptoria spp. ascospore release.}, } @article {pmid36339344, year = {2022}, author = {Mao, Y and Shen, H and Yang, C and Jia, Q and Li, J and Chen, Y and Hu, J and Huang, W}, title = {Clinical performance of metagenomic next-generation sequencing for the rapid diagnosis of talaromycosis in HIV-infected patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {962441}, pmid = {36339344}, issn = {2235-2988}, mesh = {Humans ; *Coinfection ; Retrospective Studies ; *Epstein-Barr Virus Infections ; Herpesvirus 4, Human ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *HIV Infections/complications ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Talaromycosis is an invasive endemic mycosis caused by the dimorphic fungus Talaromyces marneffei (T. marneffei, TM). It mainly affects immunodeficient patients, especially HIV-infected individuals, which causes significant morbidity and mortality. Culture-based diagnosis takes a long turnaround time with low sensitivity, leading to treatment delay. In this study, we aimed to evaluate the performance of Metagenomic Next-Generation Sequencing (mNGS) for the rapid diagnosis of talaromycosis in HIV-infected patients.

METHODS: Retrospectively analysis was conducted in HIV-infected cases at Changsha First Hospital (China) from January 2021 to March 2022. Patients who underwent routine microbiological examination and mNGS testing in parallel were enrolled. The clinical final diagnosis was used as a reference standard, and cases were classified into the TM group (60 cases) and the non-TM group (148 cases). The clinical performances of mNGS were compared with culture and serum Galactomannan (GM). The mixed infections detected by mNGS were analyzed. The impact of mNGS detection on treatment was also investigated.

RESULTS: The sensitivity of mNGS test reached 98.3% (95% CI, 89.8-99.9), which was significantly higher than culture (66.7% [95% CI, 53.2-77.9], P < 0.001) and serum GM (83.3% [95% CI, 71.0-91.2], P < 0.05). The specificity of 98.6% (95% CI, 94.7-99.7) was similar to culture (100.0% [95% CI, 96.8-100.0], P = 0.156), and superior to serum GM (91.9% [95% CI, 85.9-95.5], P < 0.05). In bronchoalveolar lavage fluid (BALF) samples, the positive rate of mNGS was 97.6%, which was significantly higher than culture (28.6%, P <0.001). mNGS has excellent performance in the identification of mixed infection in TM group patients. Cytomegalovirus, Epstein-Barr virus and Pneumocystis jirovecii were the most common concurrent pathogens. In summary, 60.0% (36/60) patients were added or adjusted to antimicrobial therapy after mNGS test.

CONCLUSION: mNGS is a powerful technique with high specificity and sensitivity for the rapid diagnosis of talaromycosis. mNGS of BALF samples may be a good option for early identification of T. marneffei in HIV-infected individuals with manifestations of infection. Moreover, mNGS shows excellent performance in mixed infection, which benefits timely treatment and potential mortality reduction.}, } @article {pmid36339336, year = {2022}, author = {Su, Y and Miao, Q and Li, N and Hu, BJ and Pan, J}, title = {Diagnostic accuracy of metagenomic next-generation sequencing for cryptococcosis in immunocompetent and immunocompromised patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {997256}, pmid = {36339336}, issn = {2235-2988}, mesh = {Humans ; *Interleukin-2 ; *Cryptococcosis/diagnosis ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Antigens, Fungal ; Sensitivity and Specificity ; Immunocompromised Host ; }, abstract = {OBJECTIVE: To compare the diagnostic accuracy of metagenomic next-generation sequencing (mNGS) for cryptococcosis in patients with different immune statuses with that of conventional detection.

METHODS: A total of 1442 specimens including 71 specimens from patients with cryptococcosis were analyzed in the study. The chi square test was used to screen the sensitivity and specificity of different detection methods for different specimen types. One-way ANOVA was used to compare the mNGS results with age, CD4, lymphocytes, IFN, IL-6, IL-2 and serum antigen assay.

RESULTS: The sensitivity of mNGS was 44.29% in Cryptococcus infection cases. The positive rate of mNGS results for bronchoalveolar lavage fluid (BALF, 87.50%) from immunocompromised patients was higher than that of BALF from immunocompetent patients (40.00%, p=0.04). The sensitivity of the serum Cryptococcus capsular antigen assay was 80.00% in immunocompetent patients and 96.42% in immunocompromised patients (p = 0.049). A positive rate of detection of Cryptococcus from mNGS was higher when cryptococcal antigen ≥1:160 (p=0.022) in immunocompromised patients. A positive rate of detection of Cryptococcus from mNGS was higher when lymphocyte counts were lower in both immunocompetent patients(p=0.017) and in immunocompromised patients(p=0.029).

CONCLUSIONS: The sensitivity of mNGS is lower than that of serum cryptococcal antigen assay and histopathology in immunocompetent patients. However, BALF detection is recommend for immunocompromised patients compared with tissue and CSF. The positive mNGS result was correlated with lower lymphocyte counts, higher IL-2 and higher serum antigen assay in immunocompromised patients.}, } @article {pmid36339330, year = {2022}, author = {Ye, F and Zhang, W and Dong, J and Peng, M and Fan, C and Deng, W and Zhang, H and Yang, L}, title = {A novel STAT1 loss-of-function mutation associated with Mendelian susceptibility to mycobacterial disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1002140}, pmid = {36339330}, issn = {2235-2988}, mesh = {Humans ; Genetic Predisposition to Disease ; *Mycobacterium Infections/genetics ; Mutation ; *Mycobacterium ; Interferon-gamma/metabolism ; STAT1 Transcription Factor/genetics/metabolism ; }, abstract = {Mendelian susceptibility to mycobacterial diseases (MSMD) is a rare congenital immune deficiency characterized by susceptibility to weakly virulent mycobacteria. Loss-of-function (LOF) mutation of signal transducer and activator of transcription 1 (STAT1) is one of the common genetic causes of MSMD. In this study, we identified a patient who presented with multiple lymph node enlargements and multiple osteolytic disruptions. Mycobacterium gordonae infection was confirmed by metagenomic next-generation sequencing. Whole-exome sequencing identified a novel paternal heterozygous mutation in exon 22 of STAT1 (NM_007315.4, c.1892T>C, p.Val631Ala). This variant was confirmed pathogenic by multiple software predictions. Based on functional assays, STAT1 expression in STAT1[V631A] cells was not different from STAT1[WT] cells. But STAT1[V631A] mutation caused much lower activation of STAT1 when stimulated by interferon-γ (IFN-γ). Fluorescence localization analysis revealed that both STAT1[V631A] and STAT1[WT] proteins were located in the cytoplasm, and only a few STAT1[V631A] proteins were translocated to the nucleus in response to IFN-γ. These results suggest that STAT1[V631A] leads to LOF in IFN-γ-mediated mycobacterial immunity, resulting in MSMD. Treatment with antibiotics has achieved ideal disease control for this patient, and no adverse events occurred during follow-up. The STAT1 LOF deficiency is a genetic cause of MSMD, which should be considered in patients with mycobacterial disease, especially those with bone involvement.}, } @article {pmid36339212, year = {2022}, author = {Liu, J and Tao, J and Chen, W and Wang, T and Chen, X and Shen, M and Ou, Q and Zhang, Y and Ding, Y and Wu, J and Cheng, X and Lu, G and Yan, G}, title = {The application of metagenomic next-generation sequencing for Angiostrongylus eosinophilic meningitis in a pediatric patient: A case report.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {1003013}, pmid = {36339212}, issn = {2296-2565}, mesh = {Animals ; Male ; Humans ; Child ; *Angiostrongylus ; *Angiostrongylus cantonensis/genetics ; *Eosinophilia/diagnosis ; *Meningitis/diagnosis ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Angiostrongylus eosinophilic meningitis (AEM) is a rare yet emerging disease caused by Angiostrongylus cantonensis infection. Its atypical symptoms may delay the diagnosis and cause fatal outcomes, especially in the early stages of infection and among children.

CASE PRESENTATION: Here we reported the use of metagenomic next-generation sequencing (mNGS) to facilitate the diagnosis and treatment of an 8-year-old boy with severe A. cantonensis infection. The mNGS tests consistently identified the infection of A. cantonensis prior to the detection by the immunologic method and confirmed it as AEM. Owing to the multidisciplinary team (MDT)-administrated treatments and close disease monitoring based on regular clinical tests and sequential mNGS tests, the patients eventually fully recovered from severe infectious conditions.

CONCLUSION: This case demonstrated the advantages of mNGS for early diagnosis of AEM in pediatric patients, highlighting its application for pan-pathogen detection, as well as disease monitoring for severe A. cantonensis infection.}, } @article {pmid36339188, year = {2022}, author = {Tian, Y and Xia, H and Zhang, L and Zhou, JX}, title = {Detection of multidrug-resistant Acinetobacter baumannii by metagenomic next-generation sequencing in central nervous system infection after neurosurgery: A case report.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {1028920}, pmid = {36339188}, issn = {2296-2565}, mesh = {Female ; Humans ; Adolescent ; *Acinetobacter baumannii/genetics ; Microbial Sensitivity Tests ; *Neurosurgery ; *Mycobacterium tuberculosis ; High-Throughput Nucleotide Sequencing/methods ; *Central Nervous System Infections ; *Ependymoma ; }, abstract = {BACKGROUND: Central nervous system (CNS) infection is one of the most serious complications after neurosurgery. Traditional clinical methods are difficult to diagnose the pathogen of intracranial infection. Due to recent advances in genomic approaches, especially sequencing technologies, metagenomic next-generation sequencing (mNGS) has been applied in many research and clinical settings.

CASE PRESENTATION: Here, we report a case of CNS infection with Acinetobacter baumannii in a 15-year-old woman, who previously underwent surgery for recurrence of ependymoma in the fourth ventricle. On the eleventh postoperative day, the patient had a high fever and leukocytosis in the cerebrospinal fluid (CSF). mNGS using CSF rapidly and accurately identified the causative pathogen as A. baumannii with carbapenem resistance genes blaOXA-23 and blaOXA-51, which were confirmed by subsequent culture and susceptibility tests within 5 days. During the disease, mNGS, culture, and drug susceptibility testing were continued to monitor changes in pathogenic bacteria and adjust medication. At present, there are no case reports on to the use of mNGS for detecting pathogens in postoperative infection with ependymoma and guide medication.

CONCLUSION: mNGS has great advantages in pathogen identification and even pathogen resistance prediction. Multiple mNGS examinations during the course of the disease play an important role in the dynamic monitoring of pathogens.}, } @article {pmid36338818, year = {2022}, author = {Qiao, N and Wittouck, S and Mattarelli, P and Zheng, J and Lebeer, S and Felis, GE and Gänzle, MG}, title = {After the storm-Perspectives on the taxonomy of Lactobacillaceae.}, journal = {JDS communications}, volume = {3}, number = {3}, pages = {222-227}, pmid = {36338818}, issn = {2666-9102}, abstract = {In 2020, a taxonomic reorganization of the lactic acid bacteria reclassified over 300 species in 7 genera and 2 families into one family, the Lactobacillaceae, with 31 genera including 23 new genera to include organisms formerly classified as Lactobacillus species. This communication aims to provide a debrief on the taxonomic reorganization of lactobacilli to identify shortcomings in the proposed taxonomic framework, and to outline perspectives and opportunities provided by the current taxonomy of the Lactobacillaceae. The current taxonomy of lactobacilli not only necessitates becoming familiar with 23 new genus names but also provides substantial new opportunities in scientific discovery and regulatory approval of these organisms. First, description of new species in the Lactobacillaceae is facilitated and a solid framework for description of novel genera is provided. Second, the current taxonomy greatly enhances the resolution of genus-level sequencing approaches (e.g., 16S rRNA-based metagenomics) when identifying the composition and function of microbial communities. Third, the current taxonomy greatly facilitates the formulation of hypotheses linking phylogeny to metabolism and ecology of lactobacilli.}, } @article {pmid36338208, year = {2022}, author = {Bao, XL and Tang, N and Wang, YZ}, title = {Severe Klebsiella pneumoniae pneumonia complicated by acute intra-abdominal multiple arterial thrombosis and bacterial embolism: A case report.}, journal = {World journal of clinical cases}, volume = {10}, number = {30}, pages = {11101-11110}, pmid = {36338208}, issn = {2307-8960}, abstract = {BACKGROUND: Klebsiella pneumoniae (K. pneumoniae) is a clinically common Gram-negative bacillus that can cause community- and hospital-acquired infections and lead to pneumonia, liver abscesses, bloodstream infections, and other infectious diseases; however, severe pneumonia caused by hypervirulent K. pneumoniae (hvKp) complicated by acute intra-abdominal multiple arterial thrombosis and bacterial embolism is rarely seen in the clinical setting and has not been reported in the literature.

CASE SUMMARY: A 51-year-old man was hospitalized with fever and dyspnea. Persistent mild pain in the middle and upper abdomen began at dawn on the 3[rd] day following admission and developed into persistent severe pain in the left upper abdomen 8 h later. Based on chest computed tomography (CT), bronchoscopy, bronchoalveolar lavage fluid metagenomic next-generation sequencing, abdominal aortic CT angiography (CTA), and culture of the superior mesenteric artery embolus, adult community-acquired severe hvKp pneumonia complicated by acute intra-abdominal multiple arterial thrombosis and bacterial embolism was diagnosed. Notably, he recovered and was discharged from the hospital after receiving effective meropenem anti-infection, endovascular contact thrombolytic, and systemic anticoagulant therapies and undergoing percutaneous thrombus aspiration. Ten days later, the patient returned to the hospital for abdominal CTA examination, which indicated blocked initial common pathway of the celiac trunk and superior mesenteric artery, and local stenosis. Therefore, celiac trunk artery stenting was performed in Chongqing Hospital, and postoperative recovery was good.

CONCLUSION: We report a case of hvKp severe pneumonia complicated by acute intra-abdominal multiple arterial thrombosis and bacterial embolism and suggest that clinicians should consider the possibility of a Gram-negative bacillus infection and conduct effective pathogen detection in a timely fashion when managing patients with severe community-acquired pneumonia before obtaining bacteriologic and drug sensitivity results. At the same time, when patients have severe pulmonary infection complicated by severe abdominal pain, an acute mesenteric artery embolism should be considered to avoid delays in treatment.}, } @article {pmid36338088, year = {2022}, author = {Yang, X and Zhang, T and Lei, CW and Wang, Q and Huang, Z and Chen, X and Wang, HN}, title = {Florfenicol and oxazolidone resistance status in livestock farms revealed by short- and long-read metagenomic sequencing.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1018901}, pmid = {36338088}, issn = {1664-302X}, abstract = {Antibiotic resistance genes (ARGs) as a novel type of environmental pollutant pose a health risk to humans. Oxazolidinones are one of the most important antibiotics for the treatment of Gram-positive bacterial infections in humans. Although oxazolidinones are not utilized in the livestock industry, florfenicol is commonly used on farms to treat bacterial infections, which may contribute to the spread of the cfr, optrA, and poxtA genes on farms. Using metagenomics sequencing, we looked into the antibiotic resistome context of florfenicol and oxazolidinone in 10 large-scale commercial farms in China. We identified 490 different resistance genes and 1,515 bacterial genera in the fecal samples obtained from 10 farms. Florfenicol-resistant Kurthia, Escherichia, and Proteus were widely present in these samples. The situation of florfenicol and oxazolidone resistance in pig farms is even more severe. The total number of genes and the abundance of drug resistance genes were higher in pigs than in chickens, including optrA and poxtA. All the samples we collected had a high abundance of fexA and floR. Through nanopore metagenomic analysis of the genetic environment, we found that plasmids, integrative and conjugative element (ICE), and transposons (Tn7-like and Tn558) may play an important role in the spread of floR, cfr, and optrA. Our findings suggest that florfenicol and oxazolidinone resistance genes have diverse genetic environments and are at risk of co-transmission with, for example, tetracycline and aminoglycoside resistance genes. The spread of florfenicol- and oxazolidinone-resistant bacteria on animal farms should be continuously monitored.}, } @article {pmid36338085, year = {2022}, author = {Ding, P and Ming, Z and Liu, J and Erill, I and Zhang, Z}, title = {Editorial: Microbiome and microbial informatics.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1054811}, doi = {10.3389/fmicb.2022.1054811}, pmid = {36338085}, issn = {1664-302X}, } @article {pmid36338055, year = {2022}, author = {Yang, Z and Fu, H and Su, H and Cai, X and Wang, Y and Hong, Y and Hu, J and Xie, Z and Wang, X}, title = {Multi-omics analyses reveal the specific changes in gut metagenome and serum metabolome of patients with polycystic ovary syndrome.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1017147}, pmid = {36338055}, issn = {1664-302X}, abstract = {OBJECTIVE: The purpose of this study was to investigate the specific alterations in gut microbiome and serum metabolome and their interactions in patients with polycystic ovary syndrome (PCOS).

METHODS: The stool samples from 32 PCOS patients and 18 healthy controls underwent the intestinal microbiome analysis using shotgun metagenomics sequencing approach. Serum metabolome was analyzed by ultrahigh performance liquid chromatography quadrupole time-of-flight mass spectrometry. An integrative network by combining metagenomics and metabolomics datasets was constructed to explore the possible interactions between gut microbiota and circulating metabolites in PCOS, which was further assessed by fecal microbiota transplantation (FMT) in a rat trial.

RESULTS: Fecal metagenomics identified 64 microbial strains significantly differing between PCOS and healthy subjects, half of which were enriched in patients. These changed species showed an ability to perturb host metabolic homeostasis (including insulin resistance and fatty acid metabolism) and inflammatory levels (such as PI3K/Akt/mTOR signaling pathways) by expressing sterol regulatory element-binding transcription factor-1, serine/threonine-protein kinase mTOR, and 3-oxoacyl-[acyl-cattier-protein] synthase III, possibly suggesting the potential mechanisms of gut microbiota underlying PCOS. By integrating multi-omics datasets, the panel comprising seven strains (Achromobacter xylosoxidans, Pseudomonas sp. M1, Aquitalea pelogenes, Porphyrobacter sp. HL-46, Vibrio fortis, Leisingera sp. ANG-Vp, and Sinorhizobium meliloti) and three metabolites [ganglioside GM3 (d18:0/16:0), ceramide (d16:2/22:0), and 3Z,6Z,9Z-pentacosatriene] showed the highest predictivity of PCOS (AUC: 1.0) with sensitivity of 0.97 and specificity of 1.0. Moreover, the intestinal microbiome modifications by FMT were demonstrated to regulate PCOS phenotypes including metabolic variables and reproductive hormones.

CONCLUSION: Our findings revealed key microbial and metabolite features and their interactions underlying PCOS by integrating multi-omics approaches, which may provide novel insights into discovering clinical diagnostic biomarkers and developing efficient therapeutic strategies for PCOS.}, } @article {pmid36338038, year = {2022}, author = {Montso, PK and Mnisi, CM and Ayangbenro, AS}, title = {Caecal microbial communities, functional diversity, and metabolic pathways in Ross 308 broiler chickens fed with diets containing different levels of Marama (Tylosema esculentum) bean meal.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1009945}, pmid = {36338038}, issn = {1664-302X}, abstract = {The caecum of a chicken harbors complex microbial communities that play vital roles in feed digestion, nutrient absorption, and bird health. Understanding the caecal microbial communities could help improve feed utilization efficiency and chicken product quality and, ultimately, deliver sustainable poultry production systems. Thus, this study assessed the caecal microbial communities and their functional diversity and metabolic pathways in broilers reared on diets containing different levels of marama (Tylosema esculentum) bean meal (MBM). A total of 350, day-old male Ross 308 broiler chicks were randomly allocated to five dietary treatments formulated as follows: a soybean-based standard broiler diet (Con_BC); Con_BC in which soybean products were substituted with 7 (M7_BC), 14 (M14_BC), 21 (M21_BC), and 28% (M28_BC) MBM. The dietary treatments were distributed to 35 replicate pens (10 birds each). After 42 days of feeding, the birds were slaughtered and thereafter caecal samples were collected from each replicate pen. Subsequently, the samples were pooled per treatment group for metagenomics sequence analysis. The results revealed that the bacteria domain (99.11%), with Bacteroides, Firmicutes and Proteobacteria being the most prominent phyla (48.28, 47.52, and 4.86%, respectively). Out of 846 genera obtained, the most abundant genera were Bacteroides, Clostridium, Alistipes, Faecalibacterium, Ruminococcus, Eubacterium, and Parabacterioides. At the genus level, the alpha-diversity showed significant (p < 0.05) difference across all treatment groups. Based on the SEED subsystem, 28 functional categories that include carbohydrates (14.65%), clustering-based subsystems (13.01%), protein metabolism (10.12%) were obtained. The KO analysis revealed 183 endogenous pathways, with 100 functional pathways associated with the metabolism category. Moreover, 15 pathways associated with carbohydrates were observed. The glycolysis/gluconeogenesis, galactose metabolism, pyruvate metabolism (15.32, 12.63, and 11.93%) were the most abundant pathways. Moreover, glycoside hydrolases (GH1, GH5, and GH13) were the most prominent carbohydrates-active enzymes. Therefore, results presented in this study suggest that dietary MB meal can improve microbial communities and their functional and metabolic pathways, which may help increase poultry production.}, } @article {pmid36337626, year = {2022}, author = {Dong, S and Wu, C and He, W and Zhong, R and Deng, J and Tao, Y and Zha, F and Liao, Z and Fang, X and Wei, H}, title = {Metagenomic and metabolomic analyses show correlations between intestinal microbiome diversity and microbiome metabolites in ob/ob and ApoE[-/-] mice.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {934294}, pmid = {36337626}, issn = {2296-861X}, abstract = {Obesity and atherosclerosis are the most prevalent metabolic diseases. ApoE[-/-] and ob/ob mice are widely used as models to study the pathogenesis of these diseases. However, how gut microbes, gut bacteriophages, and metabolites change in these two disease models is unclear. Here, we used wild-type C57BL/6J (Wt) mice as normal controls to analyze the intestinal archaea, bacteria, bacteriophages, and microbial metabolites of ob/ob and ApoE[-/-] mice through metagenomics and metabolomics. Analysis of the intestinal archaea showed that the abundances of Methanobrevibacter and Halolamina were significantly increased and decreased, respectively, in the ob/ob group compared with those in the Wt and ApoE[-/-] groups (p < 0.05). Compared with those of the Wt group, the relative abundances of the bacterial genera Enterorhabdus, Alistipes, Bacteroides, Prevotella, Rikenella, Barnesiella, Porphyromonas, Riemerella, and Bifidobacterium were significantly decreased (p < 0.05) in the ob/ob mice, and the relative abundance of Akkermansia was significantly decreased in the ApoE[-/-] group. The relative abundances of A. muciniphila and L. murinus were significantly decreased and increased, respectively, in the ob/ob and ApoE[-/-] groups compared with those of the Wt group (p < 0.05). Lactobacillus_ prophage_ Lj965 and Lactobacillus _ prophage _ Lj771 were significantly more abundant in the ob/ob mice than in the Wt mice. Analysis of the aminoacyl-tRNA biosynthesis metabolic pathway revealed that the enriched compounds of phenylalanine, glutamine, glycine, serine, methionine, valine, alanine, lysine, isoleucine, leucine, threonine, tryptophan, and tyrosine were downregulated in the ApoE[-/-] mice compared with those of the ob/ob mice. Aminoacyl-tRNA synthetases are considered manifestations of metabolic diseases and are closely associated with obesity, atherosclerosis, and type 2 diabetes. These data offer new insight regarding possible causes of these diseases and provide a foundation for studying the regulation of various food nutrients in metabolic disease models.}, } @article {pmid36336469, year = {2022}, author = {Weigert, S and Perez-Garcia, P and Gisdon, FJ and Gagsteiger, A and Schweinshaut, K and Ullmann, GM and Chow, J and Streit, WR and Höcker, B}, title = {Investigation of the halophilic PET hydrolase PET6 from Vibrio gazogenes.}, journal = {Protein science : a publication of the Protein Society}, volume = {31}, number = {12}, pages = {e4500}, pmid = {36336469}, issn = {1469-896X}, mesh = {Humans ; *Hydrolases/chemistry ; Plastics ; Microplastics ; *Vibrio/genetics ; }, abstract = {The handling of plastic waste and the associated ubiquitous occurrence of microplastic poses one of the biggest challenges of our time. Recent investigations of plastic degrading enzymes have opened new prospects for biological microplastic decomposition as well as recycling applications. For polyethylene terephthalate, in particular, several natural and engineered enzymes are known to have such promising properties. From a previous study that identified new PETase candidates by homology search, we chose the candidate PET6 from the globally distributed, halophilic organism Vibrio gazogenes for further investigation. By mapping the occurrence of Vibrios containing PET6 homologs we demonstrated their ubiquitous prevalence in the pangenome of several Vibrio strains. The biochemical characterization of PET6 showed that PET6 has a comparatively lower activity than other enzymes but also revealed a superior turnover at very high salt concentrations. The crystal structure of PET6 provides structural insights into this adaptation to saline environments. By grafting only a few beneficial mutations from other PET degrading enzymes onto PET6, we increased the activity up to three-fold, demonstrating the evolutionary potential of the enzyme. MD simulations of the variant helped rationalize the mutational effects of those mutants and elucidate the interaction of the enzyme with a PET substrate. With tremendous amounts of plastic waste in the Ocean and the prevalence of Vibrio gazogenes in marine biofilms and estuarine marshes, our findings suggest that Vibrio and the PET6 enzyme are worthy subjects to study the PET degradation in marine environments.}, } @article {pmid36336023, year = {2023}, author = {Saran, C and Purchase, D and Saratale, GD and Saratale, RG and Romanholo Ferreira, LF and Bilal, M and Iqbal, HMN and Hussain, CM and Mulla, SI and Bharagava, RN}, title = {Microbial fuel cell: A green eco-friendly agent for tannery wastewater treatment and simultaneous bioelectricity/power generation.}, journal = {Chemosphere}, volume = {312}, number = {Pt 1}, pages = {137072}, doi = {10.1016/j.chemosphere.2022.137072}, pmid = {36336023}, issn = {1879-1298}, mesh = {Humans ; *Bioelectric Energy Sources/microbiology ; Wastewater ; Chromium/metabolism ; Electrodes ; *Water Purification ; Electricity ; }, abstract = {This review paper emphasised on the origin of hexavalent chromium toxicity in tannery wastewater and its remediation using novel Microbial Fuel Cell (MFC) technology, including electroactive bacteria, which are known as exoelectrogens, to simultaneously treat wastewater and its action in the production of bioenergy and the mechanism of Cr[6+] reduction. Also, there are various parameters like electrode, pH, mode of operation, time of operation, and type of exchange membrane used for promising results shown in enhancing MFC production and remediation of Cr[6+]. Destructive anthropological activities, such as leather making and electroplating industries are key sources of hexavalent chromium contamination in aquatic repositories. When Cr[6+] enters the food chain and enters the human body, it has the potential to cause cancer. MFC is a green innovation that generates energy economically through the reduction of toxic Cr[6+] to less toxic Cr[3+]. The organic substrates utilized at the anode of MFC act as electrons (e[-]) donors. This review also highlighted the utilization of cheap substrates to make MFCs more economically suitable and the energy production at minimum cost.}, } @article {pmid36335985, year = {2023}, author = {Cadenas-Castrejón, E and Verleyen, J and Boukadida, C and Díaz-González, L and Taboada, B}, title = {Evaluation of tools for taxonomic classification of viruses.}, journal = {Briefings in functional genomics}, volume = {22}, number = {1}, pages = {31-41}, doi = {10.1093/bfgp/elac036}, pmid = {36335985}, issn = {2041-2657}, mesh = {Humans ; *Ecosystem ; *Viruses/genetics ; Bacteria/genetics ; Metagenome ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; }, abstract = {Viruses are the most abundant infectious agents on earth, and they infect living organisms such as bacteria, plants and animals, among others. They play an important role in the balance of different ecosystems by modulating microbial populations. In humans, they are responsible for some common diseases and may cause severe illnesses. Viral metagenomic studies have become essential and offer the possibility to understand and extend the knowledge of virus diversity and functionality. For these approaches, an essential step is the classification of viral sequences. In this work, 11 taxonomic classification tools were compared by analysing their performances, in terms of sensitivity and precision, to classify reads at the species and family levels using the same (viral and nonviral) datasets and evaluation metrics, as well as their processing times and memory requirements. The results showed that factors such as richness (numbers of viral species in samples), taxonomic level in the classification and read length influence tool performance. High values of viral richness in samples decreased the performances of most tools. Additionally, the classifications were better at higher taxonomic levels, such as families, compared to lower taxonomic levels, such as species, and were more evident in short reads. The results also indicated that BLAST and Kraken2 were the best tools for classifying all types of reads, while FastViromeExplorer and VirusFinder were only good when used for long reads and Centrifuge, DIAMOND, and One Codex when used for short reads. Regarding nonviral datasets (human and bacterial), all tools correctly classified them as nonviral.}, } @article {pmid36335390, year = {2022}, author = {Wang, C and Gao, ZY and Walsh, N and Hadler, S and Lu, QB and Cui, F}, title = {Acute hepatitis of unknown aetiology among children around the world.}, journal = {Infectious diseases of poverty}, volume = {11}, number = {1}, pages = {112}, pmid = {36335390}, issn = {2049-9957}, support = {2021YFC2301604//National Key Research and Development Program of China/ ; BMU20170607//Fundamental Research Funds for the Central Universities and Peking University Health Science Center/ ; BMU2021PY005//Peking University Medicine Fund of Fostering Young Scholars' Scientific & Technological Innovation/ ; L202007//Joint Research Fund for Beijing Natural Science Foundation and Haidian Original Innovation/ ; }, mesh = {Child ; Humans ; *Adenovirus Infections, Human/epidemiology ; *Adenoviruses, Human ; Acute Disease ; Feces ; *Hepatitis ; }, abstract = {By 26 August 2022, the number of cases of acute hepatitis of unknown etiology (AHUA) has drastically increased to 1115 distributed in 35 countries that fulfill the World Health Organization definition. Several hypotheses on the cause of AHUA have been proposed and are being investigated around the world. In the recent United Kingdom (UK) report, human adenovirus (HAdV) with adeno-associated virus (AAV) co-infection is the leading hypothesis. However, there is still limited evidence in establishing the causal relationship between AHUA and any potential aetiology. The leading aetiology continues to be HAdV infection. It is reported that HAdV genomics is not unusual among the population in the UK, especially among AUHA cases. Expanding the surveillance of HAdV and AAV in the population and the environment in the countries with AUHA cases is suggested to be the primary action. Metagenomics should be used in detecting other infectious pathogens on a larger scale, to supplement the detection of viruses in the blood, stool, and liver specimens from AUHA cases. It is useful to develop a consensus-specific case definition of AHUA to better understand the characteristics of these cases globally based on all the collected cases.}, } @article {pmid36334202, year = {2023}, author = {Tian, L and Wang, L and Zhang, X and Huang, X and Wang, F and Zhu, S and Li, X and Guan, Y}, title = {Multi-omics analysis on seasonal variations of the biofilm microbial community in a full-scale pre-denitrification biofilter.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {9}, pages = {24284-24298}, pmid = {36334202}, issn = {1614-7499}, support = {21-1-4-sf-11-nsh//science and technology program for public wellbeing of qingdao/ ; }, mesh = {*Denitrification ; Bioreactors/microbiology ; Seasons ; Multiomics ; Proteomics ; *Microbiota ; Biofilms ; Nitrogen ; }, abstract = {The seasonal variations of biofilm communities in a municipal wastewater treatment plant were investigated using multi-omics techniques. The abundance of the main phyla of microorganisms varied with summer (July 2019) and winter (January 2019) samples considerably, the Bacteroidetes enriched in winter and Chloroflexi in summer. The results of metaproteomic and metagenomic showed that most of the functional microorganisms belonged to the Betaproteobacteria class, and the enrichment of Flavobacteria class in winter guaranteed the stability of denitrification performance to some extent. Seasonal variations affected the proteomic expression profiling, a total of 2835 differentially expressed proteins identified were significantly enriched in quorum sensing, two-component system, ribosome, benzoate degradation, butanoate metabolism, tricarboxylic acid cycle (TCA cycle), and cysteine and methionine metabolism pathways. With the expression of nitrogen metabolic proteins decreases in winter, the overall expression of denitrification-related enzymes in winter was much lower than that in summer, the nitrogen metabolism pathway varied significantly. Seasonal variations also induced the alteration of the biofilm metabolite profile; a total of 66 differential metabolites, 8 potential biomarkers, and 8 perturbed metabolic pathways such as TCA cycle were detected. It was found that most of the perturbed pathways are directly related to nitrogen metabolism, and several amino acids and organic acids associated with the TCA cycle were significantly perturbed, the accumulation of TCA cycle intermediates, ornithine, and L-histidine in winter might be conducive to resisting cold temperatures. Furthermore, the correlation between biofilm microbial communities and metabolites was identified by the combined analysis of metabolomic and metaproteomic. The differences of microbial community structure, function, and metabolism between winter and summer in a full-scale pre-denitrification biofilter were revealed for the first time, strengthening our understanding of the microbial ecology of biofilm communities.}, } @article {pmid36334119, year = {2023}, author = {Zhao, F and Guo, Z and Kwok, LY and Zhao, Z and Wang, K and Li, Y and Sun, Z and Zhao, J and Zhang, H}, title = {Bifidobacterium lactis Probio-M8 improves bone metabolism in patients with postmenopausal osteoporosis, possibly by modulating the gut microbiota.}, journal = {European journal of nutrition}, volume = {62}, number = {2}, pages = {965-976}, pmid = {36334119}, issn = {1436-6215}, support = {2021ZD0014//Inner Mongolia Science and Technology Major Projects/ ; }, mesh = {Female ; Humans ; *Bifidobacterium animalis ; *Gastrointestinal Microbiome ; *Osteoporosis, Postmenopausal/drug therapy ; Calcitriol ; Calcium ; *Probiotics ; }, abstract = {PURPOSE: Postmenopausal osteoporosis (PMO) is usually managed by conventional drug treatment. However, prolonged use of these drugs cause side effects. Gut microbiota may be a potential target for treatment of PMO. This work was a three-month intervention trial aiming to evaluate the added effect of probiotics as adjunctive treatment for PMO.

METHODS: Forty patients with PMO were randomized into probiotic (n = 20; received Bifidobacterium animalis subsp. lactis Probio-M8 [Probio-M8], calcium, calcitriol) and placebo (n = 20; received placebo material, calcium, calcitriol) groups. The bone mineral density of patients was measured at month 0 (0 M; baseline) and month 3 (3 M; after three-month intervention). Blood and fecal samples were collected 0 M and 3 M. Only 15 and 12 patients from Probio-M8 and placebo groups, respectively, provided complete fecal samples for gut microbiota analysis.

RESULTS: No significant change was observed in the bone mineral density of patients at 3 M. Co-administering Probio-M8 improved the bone metabolism, reflected by an increased vitamin D3 level and decreased PTH and procalcitonin levels in serum at 3 M. Fecal metagenomic analysis revealed modest changes in the gut microbiome in both groups at 3 M. Interestingly, Probio-M8 co-administration affected the gut microbial interactive correlation network, particularly the short-chain fatty acid-producing bacteria. Probio-M8 co-administration significantly increased genes encoding some carbohydrate metabolism pathways (including ABC transporters, the phosphotransferase system, and fructose and mannose metabolism) and a choline-phosphate cytidylyltransferase.

CONCLUSIONS: Co-administering Probio-M8 with conventional drugs/supplements was more efficacious than conventional drugs/supplements alone in managing PMO. Our study shed insights into the beneficial mechanism of probiotic adjunctive treatment.

Chinese Clinical Trial Registry (identifier number: ChiCTR1800019268).}, } @article {pmid36333950, year = {2023}, author = {Hammer, TJ and Easton-Calabria, A and Moran, NA}, title = {Microbiome assembly and maintenance across the lifespan of bumble bee workers.}, journal = {Molecular ecology}, volume = {32}, number = {3}, pages = {724-740}, pmid = {36333950}, issn = {1365-294X}, support = {R35 GM131738/GM/NIGMS NIH HHS/United States ; R35GM131738/NH/NIH HHS/United States ; 2018-08156//National Institute of Food and Agriculture/ ; }, mesh = {Humans ; Bees/genetics ; Animals ; Longevity/genetics ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; }, abstract = {How a host's microbiome changes over its lifespan can influence development and ageing. As these temporal patterns have only been described in detail for a handful of hosts, an important next step is to compare microbiome succession more broadly and investigate why it varies. Here we characterize the temporal dynamics and stability of the bumble bee worker gut microbiome. Bumble bees have simple and host-specific gut microbiomes, and their microbial dynamics may influence health and pollination services. We used 16S rRNA gene sequencing, quantitative PCR and metagenomics to characterize gut microbiomes over the lifespan of Bombus impatiens workers. We also sequenced gut transcriptomes to examine host factors that may control the microbiome. At the community level, microbiome assembly is highly predictable and similar to patterns of primary succession observed in the human gut. However, at the strain level, partitioning of bacterial variants among colonies suggests stochastic colonization events similar to those observed in flies and nematodes. We also find strong differences in temporal dynamics among symbiont species, suggesting ecological differences among microbiome members in colonization and persistence. Finally, we show that both the gut microbiome and host transcriptome-including expression of key immunity genes-stabilize, as opposed to senesce, with age. We suggest that in highly social groups such as bumble bees, maintenance of both microbiomes and immunity contribute to inclusive fitness, and thus remain under selection even in old age. Our findings provide a foundation for exploring the mechanisms and functional outcomes of bee microbiome succession.}, } @article {pmid36333799, year = {2022}, author = {Xu, H and Zhang, L and Feng, X and Yang, Q and Zheng, K and Duan, S and Cheng, L}, title = {Metagenomic and proteomic analysis of bacterial retting community and proteome profile in the degumming process of kenaf bast.}, journal = {BMC plant biology}, volume = {22}, number = {1}, pages = {516}, pmid = {36333799}, issn = {1471-2229}, support = {IBFC-YLQN-202102//Yuelu Youth Funds of IBFC/ ; No. 1610242021002//the Central Public-interest Scientific Institution Basal Research Fund/ ; No. 31871675//the National Natural Science Foundation of China/ ; CARS-19-E22//the China Agriculture Research System/ ; ASTIP-IBFC//the Chinese Agricultural Science and Technology Innovation Project/ ; }, mesh = {*Hibiscus/microbiology ; Proteomics ; Proteome ; Chromatography, Liquid ; Tandem Mass Spectrometry ; Bacteria ; }, abstract = {BACKGROUND: Data on the microbial community and functional proteins associated with degumming in kenaf remains scant. Here, we analyzed the microbial communities associated with kenaf (Hibiscus cannabinus) bast fibers during retting to identify potential candidate degumming bacteria. Retting liquids were collected and analyzed at 0 days, 10 days, and 34 days and then evaluated the yield and quality of kenaf fiber at the different retting times. Besides, the microbial communities were characterized using metagenomic and proteomic analysis by LC-MS/MS technology.

RESULTS: The data showed that increase in the retting time significantly improves the softness, dispersion, and fiber whiteness of the kenaf fiber. The relative abundance of Acinetobacter increased from 2.88% at the baseline to 6.64% at the 34th retting. On the other hand, some members of Clostridium were reduced from 3% at the baseline to 2% at the 34th retting. Analysis of carbohydrate active enzymes showed constant changes in the utilization of carbohydrates. Besides, benzoquinone reductase, cellobiose dehydrogenase, glucose 1-oxidase, aryl alcohol oxidase and alcohol oxidase were the top five most abundant enzymes in the retting liquids. This present results demonstrated that the expressions of B7GYR8, Q6RYW5 and Q6FFK2 proteins were suppressed in Acinetobacter with the retting time. On the contrary, P05149 was upregulated with the retting time. In Clostridium, P37698, P52040 and P54937 proteins were upregulated with the retting time.

CONCLUSION: In addition, bacteria Acinetobacter and Clostridium might be playing important roles in the kenaf degumming process. Similarly, up-regulation of P37698, P52040 and P54937 proteins is an important manifestation and mediates important roles in the degumming process.}, } @article {pmid36333777, year = {2022}, author = {Aubé, J and Cambon-Bonavita, MA and Velo-Suárez, L and Cueff-Gauchard, V and Lesongeur, F and Guéganton, M and Durand, L and Reveillaud, J}, title = {A novel and dual digestive symbiosis scales up the nutrition and immune system of the holobiont Rimicaris exoculata.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {189}, pmid = {36333777}, issn = {2049-2618}, support = {P30 CA016086/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Symbiosis ; *Decapoda/genetics ; *Hydrothermal Vents ; Gills ; Immune System ; }, abstract = {BACKGROUND: In deep-sea hydrothermal vent areas, deprived of light, most animals rely on chemosynthetic symbionts for their nutrition. These symbionts may be located on their cuticle, inside modified organs, or in specialized cells. Nonetheless, many of these animals have an open and functional digestive tract. The vent shrimp Rimicaris exoculata is fueled mainly by its gill chamber symbionts, but also has a complete digestive system with symbionts. These are found in the shrimp foregut and midgut, but their roles remain unknown. We used genome-resolved metagenomics on separate foregut and midgut samples, taken from specimens living at three contrasted sites along the Mid-Atlantic Ridge (TAG, Rainbow, and Snake Pit) to reveal their genetic potential.

RESULTS: We reconstructed and studied 20 Metagenome-Assembled Genomes (MAGs), including novel lineages of Hepatoplasmataceae and Deferribacteres, abundant in the shrimp foregut and midgut, respectively. Although the former showed streamlined reduced genomes capable of using mostly broken-down complex molecules, Deferribacteres showed the ability to degrade complex polymers, synthesize vitamins, and encode numerous flagellar and chemotaxis genes for host-symbiont sensing. Both symbionts harbor a diverse set of immune system genes favoring holobiont defense. In addition, Deferribacteres were observed to particularly colonize the bacteria-free ectoperitrophic space, in direct contact with the host, elongating but not dividing despite possessing the complete genetic machinery necessary for this.

CONCLUSION: Overall, these data suggest that these digestive symbionts have key communication and defense roles, which contribute to the overall fitness of the Rimicaris holobiont. Video Abstract.}, } @article {pmid36333738, year = {2022}, author = {Luo, XQ and Wang, P and Li, JL and Ahmad, M and Duan, L and Yin, LZ and Deng, QQ and Fang, BZ and Li, SH and Li, WJ}, title = {Viral community-wide auxiliary metabolic genes differ by lifestyles, habitats, and hosts.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {190}, pmid = {36333738}, issn = {2049-2618}, mesh = {*Bacteriophages/genetics ; Ecosystem ; Genome, Viral ; Genes, Viral ; *Viruses/genetics ; Water ; }, abstract = {BACKGROUND: Viral-encoded auxiliary metabolic genes (AMGs) are important toolkits for modulating their hosts' metabolisms and the microbial-driven biogeochemical cycles. Although the functions of AMGs have been extensively reported in numerous environments, we still know little about the drivers that shape the viral community-wide AMG compositions in natural ecosystems. Exploring the drivers of viral community-wide AMG compositions is critical for a deeper understanding of the complex interplays among viruses, hosts, and the environments.

RESULTS: Here, we investigated the impact of viral lifestyles (i.e., lytic and lysogenic), habitats (i.e., water, particle, and sediment), and prokaryotic hosts on viral AMG profiles by utilizing metagenomic and metatranscriptomic techniques. We found that viral lifestyles were the most important drivers, followed by habitats and host identities. Specifically, irrespective of what habitats viruses came from, lytic viruses exhibited greater AMG diversity and tended to encode AMGs for chaperone biosynthesis, signaling proteins, and lipid metabolism, which could boost progeny reproduction, whereas temperate viruses were apt to encode AMGs for host survivability. Moreover, the lytic and temperate viral communities tended to mediate the microbial-driven biogeochemical cycles, especially nitrogen metabolism, in different manners via AMGs. When focusing on each lifestyle, we further found clear dissimilarity in AMG compositions between water and sediment, as well the divergent AMGs encoded by viruses infecting different host orders.

CONCLUSIONS: Overall, our study provides a first systematic characterization of the drivers of viral community-wide AMG compositions and further expands our knowledge of the distinct interactions of lytic and temperate viruses with their prokaryotic hosts from an AMG perspective, which is critical for understanding virus-host-environment interactions in natural conditions. Video Abstract.}, } @article {pmid36333419, year = {2022}, author = {Sieber, G and Beisser, D and Rothenberger, JL and Shah, M and Schumann, M and Sures, B and Boenigk, J}, title = {Microbial community shifts induced by plastic and zinc as substitutes of tire abrasion.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {18684}, pmid = {36333419}, issn = {2045-2322}, mesh = {*Plastics ; Microplastics ; Zinc/chemistry ; Fresh Water ; *Microbiota ; }, abstract = {Aquatic environments serve as a sink for anthropogenic discharges. A significant part of the discharge is tire wear, which is increasingly being released into the environment, causing environmental disasters due to their longevity and the large number of pollutants they contain. Main components of tires are plastic and zinc, which therefore can be used as substitutes for tire abrasion to study the effect on microbial life. We investigate environmentally realistic concentrations of plastic and zinc on a freshwater microeukaryotic community using high-throughput sequencing of the 18S V9 region over a 14-day exposure period. Apart from a generally unchanged diversity upon exposure to zinc and nanoplastics, a change in community structure due to zinc is evident, but not due to nanoplastics. Evidently, nanoplastic particles hardly affect the community, but zinc exposure results in drastic functional abundance shifts concerning the trophic mode. Phototrophic microorganisms were almost completely diminished initially, but photosynthesis recovered. However, the dominant taxa performing photosynthesis changed from bacillariophytes to chlorophytes. While phototrophic organisms are decreasing in the presence of zinc, the mixotrophic fraction initially benefitted and the heterotrophic fraction were benefitting throughout the exposure period. In contrast to lasting changes in taxon composition, the functional community composition is initially strongly imbalanced after application of zinc but returns to the original state.}, } @article {pmid36332868, year = {2023}, author = {Yang, JH and Huang, DQ and Geng, YC and Ling, YR and Fan, NS and Jin, RC}, title = {Role of quorum sensing-based regulation in development of anaerobic ammonium oxidation process.}, journal = {Bioresource technology}, volume = {367}, number = {}, pages = {128228}, doi = {10.1016/j.biortech.2022.128228}, pmid = {36332868}, issn = {1873-2976}, mesh = {*Sewage/microbiology ; Quorum Sensing ; Anaerobiosis ; Bioreactors/microbiology ; Oxidation-Reduction ; Nitrogen ; Bacteria/genetics ; *Ammonium Compounds ; Denitrification ; }, abstract = {Shortage of anaerobic ammonium oxidation (anammox) sludge greatly limits the extensive full-scale application of anammox-based processes. Although numerous start-up strategies have been proposed, the interaction among microbial consortia and corresponding mechanism during the process development remain unknown. In this study, three reactors were established based on different seed sludges. After 27 days, the anammox process inoculated with anammox granules and activated sludge (1:5) was firstly achieved, and the highest nitrogen removal rate was 1.17 kg N m[-3] d[-1]. Correspondingly, the anammox activity and abundances of related functional genes increased. Notably, the dominant anammox bacteria shifted from Candidatus Kuenenia to Candidatus Brocadia. Metagenomic analysis indicated that quorum sensing-based regulation mainly contributed to the proliferation and accumulation of anammox bacteria. This work provides an insight into the quorum sensing (QS)-regulated microbial interactions in the anammox and activated sludge consortia during the process development.}, } @article {pmid36332295, year = {2022}, author = {Wu, Z and Che, Y and Dang, C and Zhang, M and Zhang, X and Sun, Y and Li, X and Zhang, T and Xia, Y}, title = {Nanopore-based long-read metagenomics uncover the resistome intrusion by antibiotic resistant bacteria from treated wastewater in receiving water body.}, journal = {Water research}, volume = {226}, number = {}, pages = {119282}, doi = {10.1016/j.watres.2022.119282}, pmid = {36332295}, issn = {1879-2448}, mesh = {Animals ; Humans ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Genes, Bacterial ; Metagenomics/methods ; *Nanopores ; *Wastewater/microbiology ; Water ; }, abstract = {Wastewater treatment plant (WWTP) effluent discharge could induce the resistome enrichment in the receiving water environments. However, because of the general lack of a robust antibiotic-resistant bacteria (ARB) identification method, the driving mechanism for resistome accumulation in receiving environment is unclear. Here, we took advantage of the enhanced ARBs recognition by nanopore long reads to distinguish the indigenous ARBs and the accumulation of WWTP-borne ARBs in the receiving water body of a domestic WWTP. A bioinformatic framework (named ARGpore2: https://github.com/sustc-xylab/ARGpore2) was constructed and evaluate to facilitate antibiotic resistance genes (ARGs) and ARBs identification in nanopore reads. ARGs identification by ARGpore2 showed comparable precision and recall to that of the commonly adopt BLASTP-based method, whereas the spectrum of ARBs doubled that of the assembled Illumina dataset. Totally, we identified 33 ARBs genera carrying 65 ARG subtypes in the receiving seawater, whose concentration was in general 10 times higher than clean seawater's. Notably we report a primary resistome intrusion caused by the revival of residual microbes survived from disinfection treatment. These WWTP-borne ARBs, including several animal/human enteric pathogens, contributed up to 85% of the receiving water resistome. Plasmids and class 1 integrons were reckoned as major vehicles facilitating the persistence and dissemination of ARGs. Moreover, our work demonstrated the importance of extensive carrier identification in determining the driving force of multifactor coupled resistome booming in complicated environmental conditions, thereby paving the way for establishing priority for effective ARGs mitigation strategies.}, } @article {pmid36332026, year = {2022}, author = {Adam, PS and Kolyfetis, GE and Bornemann, TLV and Vorgias, CE and Probst, AJ}, title = {Genomic remnants of ancestral methanogenesis and hydrogenotrophy in Archaea drive anaerobic carbon cycling.}, journal = {Science advances}, volume = {8}, number = {44}, pages = {eabm9651}, pmid = {36332026}, issn = {2375-2548}, abstract = {Anaerobic methane metabolism is among the hallmarks of Archaea, originating very early in their evolution. Here, we show that the ancestor of methane metabolizers was an autotrophic CO2-reducing hydrogenotrophic methanogen that possessed the two main complexes, methyl-CoM reductase (Mcr) and tetrahydromethanopterin-CoM methyltransferase (Mtr), the anaplerotic hydrogenases Eha and Ehb, and a set of other genes collectively called "methanogenesis markers" but could not oxidize alkanes. Overturning recent inferences, we demonstrate that methyl-dependent hydrogenotrophic methanogenesis has emerged multiple times independently, either due to a loss of Mtr while Mcr is inherited vertically or from an ancient lateral acquisition of Mcr. Even if Mcr is lost, Mtr, Eha, Ehb, and the markers can persist, resulting in mixotrophic metabolisms centered around the Wood-Ljungdahl pathway. Through their methanogenesis remnants, Thorarchaeia and two newly reconstructed order-level lineages in Archaeoglobi and Bathyarchaeia act as metabolically versatile players in carbon cycling of anoxic environments across the globe.}, } @article {pmid36331819, year = {2022}, author = {Deng, P and Durham, J and Liu, J and Zhang, X and Wang, C and Li, D and Gwag, T and Ma, M and Hennig, B}, title = {Metabolomic, Lipidomic, Transcriptomic, and Metagenomic Analyses in Mice Exposed to PFOS and Fed Soluble and Insoluble Dietary Fibers.}, journal = {Environmental health perspectives}, volume = {130}, number = {11}, pages = {117003}, pmid = {36331819}, issn = {1552-9924}, support = {P30 ES019776/ES/NIEHS NIH HHS/United States ; T32 CA165990/CA/NCI NIH HHS/United States ; P42 ES007380/ES/NIEHS NIH HHS/United States ; P30 CA177558/CA/NCI NIH HHS/United States ; }, mesh = {Mice ; Male ; Animals ; *Inulin/metabolism/pharmacology ; Lipidomics ; Metagenomics ; Transcriptome ; Mice, Inbred C57BL ; Liver ; *Environmental Pollutants/metabolism ; Dietary Fiber/metabolism/pharmacology ; Pectins/metabolism/pharmacology ; Mammals ; }, abstract = {BACKGROUND: Perfluorooctane sulfonate (PFOS) is a persistent environmental pollutant that has become a significant concern around the world. Exposure to PFOS may alter gut microbiota and liver metabolic homeostasis in mammals, thereby increasing the risk of cardiometabolic diseases. Diets high in soluble fibers can ameliorate metabolic disease risks.

OBJECTIVES: We aimed to test the hypothesis that soluble fibers (inulin or pectin) could modulate the adverse metabolic effects of PFOS by affecting microbe-liver metabolism and interactions.

METHODS: Male C57BL/6J mice were fed an isocaloric diet containing different fibers: a) inulin (soluble), b) pectin (soluble), or c) cellulose (control, insoluble). The mice were exposed to PFOS in drinking water (3μg/g per day) for 7 wk. Multi-omics was used to analyze mouse liver and cecum contents.

RESULTS: In PFOS-exposed mice, the number of differentially expressed genes associated with atherogenesis and hepatic hyperlipidemia were lower in those that were fed soluble fiber than those fed insoluble fiber. Shotgun metagenomics showed that inulin and pectin protected against differences in microbiome community in PFOS-exposed vs. control mice. It was found that the plasma PFOS levels were lower in inulin-fed mice, and there was a trend of lower liver accumulation of PFOS in soluble fiber-fed mice compared with the control group. Soluble fiber intake ameliorated the effects of PFOS on host hepatic metabolism gene expression and cecal content microbiome structure.

DISCUSSIONS: Results from metabolomic, lipidomic, and transcriptomic studies suggest that inulin- and pectin-fed mice were less susceptible to PFOS-induced liver metabolic disturbance, hepatic lipid accumulation, and transcriptional changes compared with control diet-fed mice. Our study advances the understanding of interaction between microbes and host under the influences of environmental pollutants and nutrients. The results provide new insights into the microbe-liver metabolic network and the protection against environmental pollutant-induced metabolic diseases by high-fiber diets. https://doi.org/10.1289/EHP11360.}, } @article {pmid36331207, year = {2022}, author = {Yaovi, AB and Sessou, P and Tonouhewa, ABN and Hounmanou, GYM and Thomson, D and Pelle, R and Farougou, S and Mitra, A}, title = {Prevalence of antibiotic-resistant bacteria amongst dogs in Africa: A meta-analysis review.}, journal = {The Onderstepoort journal of veterinary research}, volume = {89}, number = {1}, pages = {e1-e12}, pmid = {36331207}, issn = {2219-0635}, mesh = {Dogs ; Animals ; Humans ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Drug Resistance, Bacterial ; Escherichia coli ; Staphylococcus aureus ; Prevalence ; Bacteria ; }, abstract = {Antimicrobial resistance (AMR) is a global public health threat for both human and veterinary medicine. Increasing evidence suggests that animals are important sources of AMR to humans; however, most of these studies focus on production animals. In order to determine the pattern of AMR in pets, mainly in dogs in Africa, a meta-analysis was performed with AMR studies conducted in African countries and published between January 2000 and January 2021 in four databases: Medline (PubMed), Scopus, Cab abstract and Google Scholar. Seven bacterial strains, namely Staphylococcus aureus, Escherichia coli, Salmonella spp., Pseudomonas aeruginosa, Streptococcus pyogenes, coagulase-negative Staphylococcus (SNC) and Staphylococcus pseudintermedius were included in this study. A total of 18 out of 234 indexed articles met the study criteria. The results revealed that multiple bacteria were resistant to various commonly used antibiotics including enrofloxacin, ciprofloxacin, gentamicin, amoxicillin, clavulanic acid, cotrimoxazole, streptomycin, tetracycline and chloramphenicol. Concerning multidrug resistance, E. coli strains came first with the highest prevalence of 98%, followed by P. aeroginosa (92%) and Salmonella spp. (53%). In contrast, the overall prevalence of multidrug resistance was low for S. aureus (18%) and S. pseudintermedius (25%). It is therefore urgent to find, as soon as possible, alternatives to replace these antibiotics, which have become ineffective in controlling these bacteria in dogs in Africa. Moreover, further metagenomic studies are needed to describe the full resistome and mobilome in dogs regardless of the bacteria.}, } @article {pmid36330877, year = {2023}, author = {Wang, P and Yuan, Q and Wang, X and Hu, B and Wang, C}, title = {Metagenomic insight into the distribution of metal resistance genes within cascade reservoir waters: Synergic impacts of geographic variation and anthropogenic pollution.}, journal = {Environmental research}, volume = {216}, number = {Pt 3}, pages = {114682}, doi = {10.1016/j.envres.2022.114682}, pmid = {36330877}, issn = {1096-0953}, mesh = {*Metagenomics ; Rivers ; Metals ; Water Quality ; *Microbiota ; China ; Environmental Monitoring ; }, abstract = {Metal resistance genes (MRGs) are potential bio-indicators to diagnose contamination stress on riverine ecosystems. Within reservoir systems, river damming weakens hydrodynamic condition and enriches metal contaminants. But, little is known about the synergic impacts of geographic variation and anthropogenic pollution on MRGs. In this study, the abundance, composition and microbes of MRGs in four cascade reservoirs along the Jinsha River, southwestern China were investigated via high-throughput metagenomics. The results showed significant enrichment of chromium, cadmium and lead in Ludila and Xiluodu reservoirs with moderate ecological risks based on the criteria of drinking water quality and aquatic life protection. Nevertheless, at watershed scale, these metals played little role in up-regulating MRGs abundance owing to the limited toxic stress on microbes. Accordingly, geographic variation showed stronger impacts on MRGs composition than metals as revealed by the distance-decay relationship (Pearson correlation, rgeo = 0.24-0.57, rmetal = 0.10-0.41) and co-occurrence network (Node degree to MRGs subtype, ngeo = 180, nmetal = 6). River damming, as an artificial isolation of geographic space, significantly affected MRGs composition. The longer operation history, smaller storage capacity and higher regulation frequency caused the higher dissimilarity of MRGs composition between the reservoir's upstream and downstream areas. In conclusion, the metal pollution level is a prerequisite regulating MRGs; while under the lowly-polluted conditions, geographic variation had stronger impacts on MRGs than metal pollution via altered assembly of microbial communities. This study provides an important guidance for the future environmental management and ecological protection of river-reservoir ecosystems.}, } @article {pmid36330044, year = {2022}, author = {Song, X and Li, Y and Stirling, E and Zhao, K and Wang, B and Zhu, Y and Luo, Y and Xu, J and Ma, B}, title = {AsgeneDB: a curated orthology arsenic metabolism gene database and computational tool for metagenome annotation.}, journal = {NAR genomics and bioinformatics}, volume = {4}, number = {4}, pages = {lqac080}, pmid = {36330044}, issn = {2631-9268}, abstract = {Arsenic (As) is the most ubiquitous toxic metalloid in nature. Microbe-mediated As metabolism plays an important role in global As biogeochemical processes, greatly changing its toxicity and bioavailability. While metagenomic sequencing may advance our understanding of the As metabolism capacity of microbial communities in different environments, accurate metagenomic profiling of As metabolism remains challenging due to low coverage and inaccurate definitions of As metabolism gene families in public orthology databases. Here we developed a manually curated As metabolism gene database (AsgeneDB) comprising 400 242 representative sequences from 59 As metabolism gene families, which are affiliated with 1653 microbial genera from 46 phyla. AsgeneDB achieved 100% annotation sensitivity and 99.96% annotation accuracy for an artificial gene dataset. We then applied AsgeneDB for functional and taxonomic profiling of As metabolism in metagenomes from various habitats (freshwater, hot spring, marine sediment and soil). The results showed that AsgeneDB substantially improved the mapping ratio of short reads in metagenomes from various environments. Compared with other databases, AsgeneDB provides more accurate, more comprehensive and faster analysis of As metabolic genes. In addition, we developed an R package, Asgene, to facilitate the analysis of metagenome sequencing data. Therefore, AsgeneDB and the associated Asgene package will greatly promote the study of As metabolism in microbial communities in various environments.}, } @article {pmid36329642, year = {2023}, author = {Dunay, E and Owens, LA and Dunn, CD and Rukundo, J and Atencia, R and Cole, MF and Cantwell, A and Emery Thompson, M and Rosati, AG and Goldberg, TL}, title = {Viruses in sanctuary chimpanzees across Africa.}, journal = {American journal of primatology}, volume = {85}, number = {1}, pages = {e23452}, pmid = {36329642}, issn = {1098-2345}, support = {R01 AG049395/AG/NIA NIH HHS/United States ; T32 HD007109/HD/NICHD NIH HHS/United States ; R37 AG049395/AG/NIA NIH HHS/United States ; T32 OD010423/OD/NIH HHS/United States ; T32 AI007414/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Africa/epidemiology ; *Pan troglodytes/virology ; *Virus Diseases/epidemiology/veterinary/virology ; Animals, Zoo/virology ; }, abstract = {Infectious disease is a major concern for both wild and captive primate populations. Primate sanctuaries in Africa provide critical protection to thousands of wild-born, orphan primates confiscated from the bushmeat and pet trades. However, uncertainty about the infectious agents these individuals potentially harbor has important implications for their individual care and long-term conservation strategies. We used metagenomic next-generation sequencing to identify viruses in blood samples from chimpanzees (Pan troglodytes) in three sanctuaries in West, Central, and East Africa. Our goal was to evaluate whether viruses of human origin or other "atypical" or unknown viruses might infect these chimpanzees. We identified viruses from eight families: Anelloviridae, Flaviviridae, Genomoviridae, Hepadnaviridae, Parvoviridae, Picobirnaviridae, Picornaviridae, and Rhabdoviridae. The majority (15/26) of viruses identified were members of the family Anelloviridae and represent the genera Alphatorquevirus (torque teno viruses) and Betatorquevirus (torque teno mini viruses), which are common in chimpanzees and apathogenic. Of the remaining 11 viruses, 9 were typical constituents of the chimpanzee virome that have been identified in previous studies and are also thought to be apathogenic. One virus, a novel tibrovirus (Rhabdoviridae: Tibrovirus) is related to Bas-Congo virus, which was originally thought to be a human pathogen but is currently thought to be apathogenic, incidental, and vector-borne. The only virus associated with disease was rhinovirus C (Picornaviridae: Enterovirus) infecting one chimpanzee subsequent to an outbreak of respiratory illness at that sanctuary. Our results suggest that the blood-borne virome of African sanctuary chimpanzees does not differ appreciably from that of their wild counterparts, and that persistent infection with exogenous viruses may be less common than often assumed.}, } @article {pmid36329505, year = {2022}, author = {Li, Y and Yang, R and Häggblom, MM and Li, M and Guo, L and Li, B and Kolton, M and Cao, Z and Soleimani, M and Chen, Z and Xu, Z and Gao, W and Yan, B and Sun, W}, title = {Characterization of diazotrophic root endophytes in Chinese silvergrass (Miscanthus sinensis).}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {186}, pmid = {36329505}, issn = {2049-2618}, mesh = {*Endophytes ; *Poaceae/microbiology ; Nitrogen Fixation ; Bacteria ; Plants/genetics ; Pseudomonas/genetics ; China ; DNA ; Plant Roots/microbiology ; }, abstract = {BACKGROUND: Phytoremediation is a potentially cost-effective way to remediate highly contaminated mine tailing sites. However, nutrient limitations, especially the deficiency of nitrogen (N), can hinder the growth of plants and impair the phytoremediation of mine tailings. Nevertheless, pioneer plants can successfully colonize mine tailings and exhibit potential for tailing phytoremediation. Diazotrophs, especially diazotrophic endophytes, can promote the growth of their host plants. This was tested in a mine-tailing habitat by a combination of field sampling, DNA-stable isotope probing (SIP) analysis, and pot experiments.

RESULTS: Bacteria belonging to the genera Herbaspirillum, Rhizobium, Devosia, Pseudomonas, Microbacterium, and Delftia are crucial endophytes for Chinese silvergrass (Miscanthus sinensis) grown in the tailing, the model pioneer plant selected in this study. Further, DNA-SIP using [15]N2 identified Pseudomonas, Rhizobium, and Exiguobacterium as putative diazotrophic endophytes of M. sinensis. Metagenomic-binning suggested that these bacteria contained essential genes for nitrogen fixation and plant growth promotion. Finally, two diazotrophic endophytes Rhizobium sp. G-14 and Pseudomonas sp. Y-5 were isolated from M. sinensis. Inoculation of another pioneer plant in mine tailings, Bidens pilosa, with diazotrophic endophytes resulted in successful plant colonization, significantly increased nitrogen fixation activity, and promotion of plant growth.

CONCLUSIONS: This study indicated that diazotrophic endophytes have the potential to promote the growth of pioneer plant B. pilosa in mine tailings. Video Abstract.}, } @article {pmid36329273, year = {2022}, author = {Sun, Z and Jiang, X and Wang, B and Tian, F and Zhang, H and Yu, L}, title = {Novel Phocaeicola Strain Ameliorates Dextran Sulfate Sodium-induced Colitis in Mice.}, journal = {Current microbiology}, volume = {79}, number = {12}, pages = {393}, pmid = {36329273}, issn = {1432-0991}, support = {31772090//National Natural Science Foundation of China Key Program/ ; 32001665//National Natural Science Foundation of China Key Program/ ; 31820103010//National Natural Science Foundation of China Key Program/ ; }, mesh = {Humans ; Mice ; Animals ; Dextran Sulfate/toxicity ; *Colitis/chemically induced ; *Colitis, Ulcerative/chemically induced/metabolism/pathology ; Cytokines/metabolism ; Disease Models, Animal ; Body Weight ; Mice, Inbred C57BL ; }, abstract = {Previously, we isolated a novel Phocaeicola strain, Phocaeicola faecalis FXJYN30E22, from the feces of a healthy human from China. Metagenomic analysis revealed that the distribution of FXJYN30E22 differed in the intestinal tract of different hosts. We aimed to determine whether FXJYN30E22 protects against ulcerative colitis by employing a mouse model. In this study, dextran sulfate sodium was used to construct the UC model. The disease activity index, colon length, body weight changes, and histological scores were used as the pathological indicators to assess the anti-inflammatory effect of P. faecalis FXJYN30E22. Further, cytokine levels, tight junction mRNA expression levels, and short-chain fatty acid (SCFA) concentrations were also analyzed. Phocaeicola faecalis FXJYN30E22 could reduce the DSS-induced increase in DAI score, and enhance the colon length and body weight. Phocaeicola faecalis FXJYN30E22 could enhance TJ protein concentration and modulate the level of cytokines to reach levels close to those of the control group. FXJYN30E22 could also upregulate the concentrations of SCFA, which include acetate and butyrate. Based on the correlation analysis, four factors, including interleukin (IL)-6, IL-10, IL-1β levels, and propionate concentration, were related to the protective roles of FXJYN30E22 in UC mice to different degrees. According to an analysis of the genomic information, the potential protective effects of strain FXJYN30E22 may be associated with the secretion of SCFA by specific genes. These findings suggest that oral P. faecalis FXJYN30E22 could help maintain the epithelial barrier by regulating cytokine levels and secreting SCFA.}, } @article {pmid36329216, year = {2023}, author = {Salam, LB and Obayori, OS}, title = {Functional characterization of the ABC transporters and transposable elements of an uncultured Paracoccus sp. recovered from a hydrocarbon-polluted soil metagenome.}, journal = {Folia microbiologica}, volume = {68}, number = {2}, pages = {299-314}, pmid = {36329216}, issn = {1874-9356}, mesh = {DNA Transposable Elements ; ATP-Binding Cassette Transporters/genetics ; Metagenome ; *Paracoccus/genetics ; *Bacterial Toxins ; *Clostridioides difficile/genetics ; Anti-Bacterial Agents/pharmacology ; *Metals, Heavy ; Hydrocarbons ; Soil/chemistry ; }, abstract = {Environmental microorganisms usually exhibit a high level of genomic plasticity and metabolic versatility that allow them to be well-adapted to diverse environmental challenges. This study used shotgun metagenomics to decipher the functional and metabolic attributes of an uncultured Paracoccus recovered from a polluted soil metagenome and determine whether the detected attributes are influenced by the nature of the polluted soil. Functional and metabolic attributes of the uncultured Paracoccus were elucidated via functional annotation of the open reading frames (ORFs) of its contig. Functional tools deployed for the analysis include KEGG, KEGG KofamKOALA, Clusters of Orthologous Groups of proteins (COG), Comprehensive Antibiotic Resistance Database (CARD), and the Antibiotic Resistance Gene-ANNOTation (ARG-ANNOT V6) for antibiotic resistance genes, TnCentral for transposable element, Transporter Classification Database (TCDB) for transporter genes, and FunRich for gene enrichment analysis. Analyses revealed the preponderance of ABC transporter genes responsible for the transport of oligosaccharides (malK, msmX, msmK, lacK, smoK, aglK, togA, thuK, treV, msiK), monosaccharides (glcV, malK, rbsC, rbsA, araG, ytfR, mglA), amino acids (thiQ, ynjD, thiZ, glnQ, gluA, gltL, peb1C, artP, aotP, bgtA, artQ, artR), and several others. Also detected are transporter genes for inorganic/organic nutrients like phosphate/phosphonate, nitrate/nitrite/cyanate, sulfate/sulfonate, bicarbonate, and heavy metals such as nickel/cobalt, molybdate/tungstate, and iron, among others. Antibiotic resistance genes that mediate efflux, inactivation, and target protection were detected, while transposable elements carrying resistance phenotypes for antibiotics and heavy metals were also annotated. The findings from this study have established the resilience, adaptability, and survivability of the uncultured Paracoccus in the hydrocarbon-polluted soil.}, } @article {pmid36329213, year = {2022}, author = {Zaman, S and Gohar, M and Kanwal, H and Chaudhary, A and Imran, M}, title = {Impact of Probiotic Geotrichum candidum QAUGC01 on Health, Productivity, and Gut Microbial Diversity of Dairy Cattle.}, journal = {Current microbiology}, volume = {79}, number = {12}, pages = {376}, pmid = {36329213}, issn = {1432-0991}, mesh = {Female ; Cattle ; Animals ; Rumen/microbiology ; Animal Feed/analysis ; *Gastrointestinal Microbiome ; Dietary Supplements/analysis ; Diet/veterinary ; Milk ; *Probiotics/analysis ; Bacteria/genetics ; Lactation ; }, abstract = {Gut microbial diversity is a determinant of animal productivity and health. Probiotic supplementation in feed has been known to modulate the gut microbial diversity resulting in better feed utilization and resistance against diseases. The current study was designed to determine the probiotic potential of Geotrichum candidum QAUGC01 (VHDP00000000) in Sahiwal-Friesian crossbred dairy cows and its impact on gut microbial diversity, health, and productivity. To evaluate health and productivity, growth performance, determination of blood parameters, serum biochemistry, feed efficiency, milk yield & composition, and nutrients digestibility was determined and compared between control and experimental groups. Moreover, at the end of the experiment, the gut microbial diversity was evaluated through MiSeq (Illumina) sequencing of bacterial and fungal/yeast DNA in dung samples of both control and experimental cows. Inspite of a significant reduction in dry matter intake the increase in feed efficiency and milk yield was observed in experimental cows with normal hematological and serum biochemical profile. The increase in anaerobic bacterial count and decrease in the shredding of pathogenic flora was observed in experimental cows. Metagenomic analysis revealed Proteobacteria, Firmicutes, Actinobacteria and Bacteroidetes to be the four dominating phyla among bacteria and, Ascomycota followed by Basidiomycota and Neocallimastigomycota among the fungal population in both groups. The diversity of the core microbiome revealed high bacterial and Fungal Alpha diversity in the experimental group than in control via the Shannon index. This study provided insights into the safe use of G. candidum as a probiotic, to improve growth performance, health, productivity and gut microbial diversity of dairy cattle.}, } @article {pmid36329015, year = {2022}, author = {Stutz, MR and Dylla, NP and Pearson, SD and Lecompte-Osorio, P and Nayak, R and Khalid, M and Adler, E and Boissiere, J and Lin, H and Leiter, W and Little, J and Rose, A and Moran, D and Mullowney, MW and Wolfe, KS and Lehmann, C and Odenwald, M and De La Cruz, M and Giurcanu, M and Pohlman, AS and Hall, JB and Chaubard, JL and Sundararajan, A and Sidebottom, A and Kress, JP and Pamer, EG and Patel, BK}, title = {Immunomodulatory fecal metabolites are associated with mortality in COVID-19 patients with respiratory failure.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6615}, pmid = {36329015}, issn = {2041-1723}, support = {K23 HL148387/HL/NHLBI NIH HHS/United States ; T32 HL007605/HL/NHLBI NIH HHS/United States ; T32 HL-007605//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; P01 CA023766/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *COVID-19 ; SARS-CoV-2 ; *Pneumonia ; Bile Acids and Salts ; *Respiratory Insufficiency ; Immunity ; }, abstract = {Respiratory failure and mortality from COVID-19 result from virus- and inflammation-induced lung tissue damage. The intestinal microbiome and associated metabolites are implicated in immune responses to respiratory viral infections, however their impact on progression of severe COVID-19 remains unclear. We prospectively enrolled 71 patients with COVID-19 associated critical illness, collected fecal specimens within 3 days of medical intensive care unit admission, defined microbiome compositions by shotgun metagenomic sequencing, and quantified microbiota-derived metabolites (NCT #04552834). Of the 71 patients, 39 survived and 32 died. Mortality was associated with increased representation of Proteobacteria in the fecal microbiota and decreased concentrations of fecal secondary bile acids and desaminotyrosine (DAT). A microbiome metabolic profile (MMP) that accounts for fecal secondary bile acids and desaminotyrosine concentrations was independently associated with progression of respiratory failure leading to mechanical ventilation. Our findings demonstrate that fecal microbiota composition and microbiota-derived metabolite concentrations can predict the trajectory of respiratory function and death in patients with severe SARS-Cov-2 infection and suggest that the gut-lung axis plays an important role in the recovery from COVID-19.}, } @article {pmid36327953, year = {2022}, author = {Ehlers, L and Netz, LAW and Reiner, J and Berlin, P and Bannert, K and Bastian, M and Zechner, D and Lamprecht, G and Jaster, R}, title = {Effects of Bile Duct Ligation and Ghrelin Treatment on the Colonic Barrier and Microbiome of Mice.}, journal = {Pharmacology}, volume = {107}, number = {11-12}, pages = {564-573}, doi = {10.1159/000527142}, pmid = {36327953}, issn = {1423-0313}, mesh = {Mice ; Animals ; Ghrelin/pharmacology/therapeutic use ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics ; Bile Ducts/surgery ; *Cholestasis/microbiology/pathology ; Liver/pathology ; *Microbiota ; Weight Loss ; Solvents ; Disease Models, Animal ; }, abstract = {INTRODUCTION: Cholestatic liver disease (CLD) is associated with intestinal barrier dysfunction. The peptide hormone ghrelin may exert both hepatoprotective and barrier-strengthening effects. Here, we have evaluated these effects under the conditions of experimental cholestasis.

METHODS: C57BL/6J mice with bile duct ligation (BDL) or sham surgery were treated with ghrelin or solvent for 9 days. Liver injury was assessed by histological and laboratory analyses. Paracellular macromolecule permeability and transmural electrical resistance (TMER) of colonic tissues were measured using a Ussing chamber. Expression of tight junction (TJ) genes was quantified by real-time PCR. Amplicon metagenomic sequencing was employed to analyze bacterial 16S rRNA from colonic stool samples.

RESULTS: Mice with BDL exhibited weight loss and signs of severe liver injury. These changes were unaffected by ghrelin treatment. FITC-4-kDa-dextran flux was increased and TMER decreased after BDL. Treatment with ghrelin tended to reduce these effects. Furthermore, application of ghrelin was associated with higher mRNA levels of claudin-4, occludin, and ZO-1 in colonic tissues of mice with BDL. Reduced alpha-diversity of the microbiome was observed in solvent-treated mice with BDL but not in ghrelin-treated animals.

CONCLUSION: Ghrelin treatment did not improve weight loss and liver damage but increased gene expression of colonic TJ proteins and restored the alpha-diversity of the microbiome. Since protective effects of ghrelin might be masked by the severity of the model, we suggest follow-up studies in models of milder CLD.}, } @article {pmid36327844, year = {2023}, author = {Yi, X and Wen, P and Liang, JL and Jia, P and Yang, TT and Feng, SW and Liao, B and Shu, WS and Li, JT}, title = {Phytostabilization mitigates antibiotic resistance gene enrichment in a copper mine tailings pond.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt B}, pages = {130255}, doi = {10.1016/j.jhazmat.2022.130255}, pmid = {36327844}, issn = {1873-3336}, mesh = {*Copper/toxicity ; *Ponds ; Soil Microbiology ; Drug Resistance, Microbial/genetics ; Soil/chemistry ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Mining-impacted environments are distributed globally and have become increasingly recognized as hotspots of antibiotic resistance genes (ARGs). However, there are currently no reports on treatment technologies to deal with such an important environmental problem. To narrow this knowledge gap, we implemented a phytostabilization project in an acidic copper mine tailings pond and employed metagenomics to explore ARG characteristics in the soil samples. Our results showed that phytostabilization decreased the total ARG abundance in 0-10 cm soil layer by 75 %, which was companied by a significant decrease in ARG mobility, and a significant increase in ARG diversity and microbial diversity. Phytostabilization was also found to drastically alter the ARG host composition and to significantly reduce the total abundance of virulence factor genes of ARG hosts. Soil nutrient status, heavy metal toxicity and SO4[2-] concentration were important physicochemical factors to affect the total ARG abundance, while causal mediation analysis showed that their effects were largely mediated by the changes in ARG mobility and microbial diversity. The increase in ARG diversity associated with phytostabilization was mainly mediated by a small subgroup of ARG hosts, most of which could not be classified at the genus level and deserve further research in the future.}, } @article {pmid36327562, year = {2023}, author = {Li, Q and An, Z and Sun, T and Ji, S and Wang, W and Peng, Y and Wang, Z and Salentijn, GIJ and Gao, Z and Han, D}, title = {Sensitive colorimetric detection of antibiotic resistant Staphylococcus aureus on dairy farms using LAMP with pH-responsive polydiacetylene.}, journal = {Biosensors & bioelectronics}, volume = {219}, number = {}, pages = {114824}, doi = {10.1016/j.bios.2022.114824}, pmid = {36327562}, issn = {1873-4235}, abstract = {Rapidly and accurately detecting antibiotic-resistant pathogens in agriculture and husbandry is important since these represent a major threat to public health. While much attention has been dedicated to detecting now-common resistant bacteria, such as methicillin-resistant Staphylococcus aureus, fewer methods have been developed to assess resistance against macrolides in Staphylococcus aureus (SA). Here, we report a visual on-site detection system for macrolide resistant SA in dairy products. First, metagenomic sequencing in raw milk, cow manure, water and aerosol deposit collected from dairy farms around Tianjin was used to identify the most abundant macrolide resistance gene, which was found to be the macB gene. In parallel, SA housekeeping genes were screened to allow selective identification of SA, which resulted in the selection of the SAOUHSC_01275 gene. Next, LAMP assays targeting the above-mentioned genes were developed and interpreted by agarose gel electrophoresis. For on-site application, different pH-sensitive colorimetric LAMP indicators were compared, which resulted in selection of polydiacetylene (PDA) as the most sensitive candidate. Additionally, a semi-quantitative detection could be realized by analyzing the RGB information via smartphone with a LOD of 1.344 × 10[-7] ng/μL of genomic DNA from a milk sample. Finally, the proposed method was successfully carried out at a real farm within 1 h from sample to result by using freeze-dried reagents and portable devices. This is the first instance in which PDA is used to detect LAMP products, and this generic read-out system can be expanded to other antibiotic resistant genes and bacteria.}, } @article {pmid36327224, year = {2022}, author = {Costa, MF and Morales-Marroquín, JA and de Araújo Batista, CE and Alves-Pereira, A and de Almeida Vieira, F and Zucchi, MI}, title = {Population genomics of the neotropical palm Copernicia prunifera (Miller) H. E. Moore: Implications for conservation.}, journal = {PloS one}, volume = {17}, number = {11}, pages = {e0276408}, pmid = {36327224}, issn = {1932-6203}, mesh = {Humans ; *Metagenomics ; *Arecaceae/genetics ; Genetic Drift ; Selection, Genetic ; Inbreeding ; Polymorphism, Single Nucleotide ; Genetic Variation ; }, abstract = {Copernicia prunifera (Miller) H. E. Moore is a palm tree native to Brazil. The products obtained from its leaf extracts are a source of income for local families and the agroindustry. Owing to the reduction of natural habitats and the absence of a sustainable management plan, the maintenance of the natural populations of this palm tree has been compromised. Therefore, this study aimed to evaluate the diversity and genetic structure of 14 C. prunifera populations using single nucleotide polymorphisms (SNPs) identified through genotyping-by-sequencing (GBS) to provide information that contributes to the conservation of this species. A total of 1,013 SNP markers were identified, of which 84 loci showed outlier behavior and may reflect responses to natural selection. Overall, the level of genomic diversity was compatible with the biological aspects of this species. The inbreeding coefficient (f) was negative for all populations, indicating excess heterozygotes. Most genetic variations occurred within populations (77.26%), and a positive correlation existed between genetic and geographic distances. The population structure evaluated through discriminant analysis of principal components (DAPC) revealed low genetic differentiation between populations. The results highlight the need for efforts to conserve C. prunifera as well as its distribution range to preserve its global genetic diversity and evolutionary potential.}, } @article {pmid36327070, year = {2023}, author = {Idowu, GA and Olalemi, AO and Ileke, KD}, title = {COVID-19 face masks attracted Cellulomonas and Acinetobacter bacteria and provided breeding haven for red cotton bug (Dysdercus suturellus) and house cricket (Acheta domesticus).}, journal = {Environmental science and pollution research international}, volume = {30}, number = {9}, pages = {23510-23526}, pmid = {36327070}, issn = {1614-7499}, support = {EA20/1593//British Ecological Society/ ; }, mesh = {Animals ; Humans ; *COVID-19 ; *Gryllidae ; *Cellulomonas ; Pandemics ; Ecosystem ; Masks ; Insecta ; Bacteria ; *Heteroptera ; }, abstract = {This study investigated the possibility of COVID-19 medical face masks to affect bacterial and macrofaunal communities in open soil environment. An estimated 1.24 trillion of face masks have been used and discarded as a result of the COVID-19 pandemic, with a significant part of this ending up in the soil environment, where they degrade gradually over time. Because bacteria and macrofauna are sensitive indicators of changes in soil ecosystem, we investigated possible impacts of face masks on population, distribution, and diversity of these soil species. Effect on soil bacterial community was studied by both culture-based and advanced molecular (metagenomics) approach, while impact on macrofauna was investigated by examining monoliths around heap of masks for soil insects. In both cases, control soil experiments without face masks were also set up and monitored over a period of 48 weeks. The study found that the presence of face masks led to a more diverse bacterial community, although no influence on overall bacterial population was evidenced. More importantly, bacteria belonging to the genera Cellulomonas and Acinetobacter were found prominently around face masks and are believed to be involved in biodegradation of the masks. The bacterial community around the masks was dominated by Proteobacteria (29.7-38.7%), but the diversity of species increased gradually with time. Tiny black ants (Monomorium invidium) were attracted to the face masks to take advantage of water retained by the masks during the period of little rainfall. The heaps of face masks also provided shelter and breeding "haven" for soil insects, notably the red cotton bug (Dysdercus suturellus) and house cricket (Acheta domesticus), thereby impacting positively on the population of insect species in the environment. This study provides insights into the actual impacts of face masks on soil organisms under normal outdoor environmental conditions.}, } @article {pmid36326919, year = {2022}, author = {Amulyasai, B and Anusha, R and Sasikala, C and Ramana, CV}, title = {Phylogenomic analysis of a metagenome-assembled genome indicates a new taxon of an anoxygenic phototroph bacterium in the family Chromatiaceae and the proposal of "Candidatus Thioaporhodococcus" gen. nov.}, journal = {Archives of microbiology}, volume = {204}, number = {12}, pages = {688}, pmid = {36326919}, issn = {1432-072X}, mesh = {Phylogeny ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; DNA, Bacterial/genetics ; Sequence Analysis, DNA ; *Chromatiaceae ; Bacterial Typing Techniques ; Fatty Acids/analysis ; }, abstract = {In this study, three metagenome-assembled genomes of a sediment sample were constructed. A Bin1 (JB001) genome was identified as a photo-litho-auto/heterotroph (purple sulfur bacteria) bacterium with the ability to fix nitrogen, tolerate salt, and to produce bacteriochlorophyll a. It has a genome length of 4.1 Mb and a G + C content of 64.9%. Phylogenetic studies based on concatenated 92 core genes and photosynthetic genes (pufLM and bchY) showed that Bin JB001 is related to Thiococcus pfennigii, "Thioflavicoccus mobilis" and to the Lamprocystis purpurea lineage. Bin JB001 and its closely related members were subjected to the genome-based study of phenotypic and phylogenomic analysis. Genomic similarity indices (dDDH and ANI) showed that Bin JB001 could be defined as a novel species. The average amino acid identity (AAI) and percentage of conserved proteins (POCP) values were below 60 and 50%, respectively. The pan-genome analysis indicated that the pan-genome was an open type wherein Bin JB001 had 855 core genes. This study shows that the binned genome, Bin JB001 could represent a novel species of a new genus under the family Chromatiaceae, for which the name "Candidatus Thioaporhodococcus sediminis" gen. nov. sp. nov. is proposed.}, } @article {pmid36326798, year = {2022}, author = {Li, Z and Shi, J and Lei, Y and Wu, J and Zhang, R and Zhang, X and Jia, L and Wang, Y and Ma, Y and He, P and Ma, Y and Cheng, Q and Zhang, Z and Zhang, K and Lei, Z}, title = {Castration alters the cecal microbiota and inhibits growth in Holstein cattle.}, journal = {Journal of animal science}, volume = {100}, number = {12}, pages = {}, pmid = {36326798}, issn = {1525-3163}, mesh = {Cattle ; Animals ; Male ; *Animal Feed/analysis ; *Ketoglutaric Acids/pharmacology ; Orchiectomy/veterinary ; Methionine/pharmacology ; Testosterone ; Body Composition ; Diet/veterinary ; }, abstract = {To determine the effects of castration on growth performance, serum hormone levels, cecal microbiota composition, and metabolites in cattle. A total of 18 Holstein bulls and steers were divided into bull and steer groups and randomly assigned to 3 pens (3 cattle per pen, and each cattle were separated by a fence) to determine the average daily gain (ADG), daily dry matter intake (DMI), and feed efficiency (G/F). After the finishing trial, six cattle per group were randomly slaughtered. Serum was collected to measure the hormone concentration, and the cecal content was collected to measure the pH, short-chain fatty acids, and digestive enzyme activities. Metagenome sequencing and untargeted metabolomics were used to investigate the microbiota composition, functional profiles, and differential metabolites of the cecal contents. We found that castration significantly decreased ADG, DMI, and G/F in cattle (P < 0.05). The serum testosterone, thyroxine, growth hormone (P < 0.05), and triiodothyronine (P < 0.01) concentrations significantly decreased in the steer group when compared to those of the bull group. The activities of cellulase, xylanase, pectinase, and β-glucosidase (P < 0.05) significantly decreased in the steer group, whereas the activities of lipase and α-amylase significantly increased. Moreover, castration significantly decreased the relative abundance of Ruminococcaceae_bacterium, Treponema_porcinum, Oscillibacter_sp. (P < 0.05), and Alistipes_senegalensis (P < 0.01), whereas the relative abundance of Phocaeicola_plebeius (P < 0.05) was significantly increased. Also, the relative abundance of Phocaeicola_plebeius was negatively correlated with testosterone levels, and the function of the cecal microbiota was enriched in the GH29 and GH97 families in the steer group. Metabolomic analysis indicated that castration increased the levels of L-valine, L-phenylalanine, L-aspartic acid, L-isoleucine, L-lysine, methionine, L-glutamic acid, and L-leucine, while decreasing the levels of α-ketoglutaric acid through the 2-oxocarboxylic acid metabolism pathway. In addition, α-ketoglutaric acid was negatively correlated with Oscillibacter_sp. (P < 0.01). Overall, castration can inhibit cattle growth by altering the composition of the cecal microbiota. Therefore, this study provides a theoretical and practical basis for improving the growth performance of steers.}, } @article {pmid36325561, year = {2022}, author = {Sadak, MS and Sekara, A and Al-Ashkar, I and Habib-Ur-Rahman, M and Skalicky, M and Brestic, M and Kumar, A and Sabagh, AE and Abdelhamid, MT}, title = {Exogenous aspartic acid alleviates salt stress-induced decline in growth by enhancing antioxidants and compatible solutes while reducing reactive oxygen species in wheat.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {987641}, pmid = {36325561}, issn = {1664-462X}, abstract = {Salinity is the primary environmental stress that adversely affects plants' growth and productivity in many areas of the world. Published research validated the role of aspartic acid in improving plant tolerance against salinity stress. Therefore, in the present work, factorial pot trials in a completely randomized design were conducted to examine the potential role of exogenous application of aspartic acid (Asp) in increasing the tolerance of wheat (Triticum aestivum L.) plants against salt stress. Wheat plants were sown with different levels of salinity (0, 30, or 60 mM NaCl) and treated with three levels of exogenous application of foliar spray of aspartic acid (Asp) (0, 0.4, 0.6, or 0.8 mM). Results of the study indicated that salinity stress decreased growth attributes like shoot length, leaf area, and shoot biomass along with photosynthesis pigments and endogenous indole acetic acid. NaCl stress reduced the total content of carbohydrates, flavonoid, beta carotene, lycopene, and free radical scavenging activity (DPPH%). However, Asp application enhanced photosynthetic pigments and endogenous indole acetic acid, consequently improving plant leaf area, leading to higher biomass dry weight either under salt-stressed or non-stressed plants. Exogenous application of Asp, up-regulate the antioxidant system viz. antioxidant enzymes (superoxide dismutase, peroxidase, catalase, and nitrate reductase), and non-enzymatic antioxidants (ascorbate, glutathione, total phenolic content, total flavonoid content, beta carotene, lycopene) contents resulted in declined in reactive oxygen species (ROS). The decreased ROS in Asp-treated plants resulted in reduced hydrogen peroxide, lipid peroxidation (MDA), and aldehyde under salt or non-salt stress conditions. Furthermore, Asp foliar application increased compatible solute accumulation (amino acids, proline, total soluble sugar, and total carbohydrates) and increased radical scavenging activity of DPPH and enzymatic ABTS. Results revealed that the quadratic regression model explained 100% of the shoot dry weight (SDW) yield variation. With an increase in Asp application level by 1.0 mM, the SDW was projected to upsurge through 956 mg/plant. In the quadratic curve model, if Asp is applied at a level of 0.95 mM, the SDW is probably 2.13 g plant[-1]. This study concluded that the exogenous application of aspartic acid mitigated the adverse effect of salt stress damage on wheat plants and provided economic benefits.}, } @article {pmid36325110, year = {2022}, author = {Bright Esegbuyota, I and Hope, O and Oyama, G}, title = {Occurrence of New Delhi Metallo-Beta-Lactamase 1 Producing Enterococcus Species in Oghara Water Nexus: An Emerging Environmental Implications of Resistance Dynamics.}, journal = {Microbiology insights}, volume = {15}, number = {}, pages = {11786361221133731}, pmid = {36325110}, issn = {1178-6361}, abstract = {Various members of the enteric bacteria in recent times are evolving diverse survival mechanisms for antibiotic therapy resulting in failure of treatment in infection and disease cases. The Enterococcus species are potential strains implicated in gastrointestinal tract infection and are recently evolving in the resistance mechanism. The study evaluates the occurrence of New Delhi Metallo-beta-lactamase 1 (NDM-1) amongst Enterococcus species using the phenotypic and genomic characterization of environmental strains in the Oghara water nexus. Presumptive isolates of Enterococcus species were retrieved from various sampled water sources and confirmed using polymerase chain reaction (PCR). Antibiotic susceptibility testing was conducted on confirmed isolates using Kirby-Bauer disk diffusion methods. The result reveals 63 genus isolates confirmed Enterococcus species, of which 42 (67%) were Enterococcus faecium, 15 (23%) were Enterococcus faecalis, and 6 (10%) were other Enterococcus species. Fourteen among the E. faecalis isolates show resistance to Ertapenem-EDTA, while 17 (44.8%) of the E. faecium show resistance to Ertapenem-EDTA to presumptively reveal their NDM-1 phenotype. The PCR detection of the NDM-1 gene further confirmed 23 (36.5%) isolates as positive genotypes amongst the isolates that previously showed presumptive NDM-1 phenotype. It was also observed that 10 (15.9%) of Enterococcus faecium members harbored the NDM-1 genotype, whereas 8 (12.7%) members of the Enterococcus faecalis harbored the NDM-1 genotype. The observation of such resistance determinants necessitates a call for the adroit application of relevant therapeutics in the management of related infections and an environmental health caution to prevent the spread of such resistance potential enteric bacteria pathogens.}, } @article {pmid36325032, year = {2022}, author = {Kinsella, CM and Deijs, M and Becker, C and Broekhuizen, P and van Gool, T and Bart, A and Schaefer, AS and van der Hoek, L}, title = {Host prediction for disease-associated gastrointestinal cressdnaviruses.}, journal = {Virus evolution}, volume = {8}, number = {2}, pages = {veac087}, pmid = {36325032}, issn = {2057-1577}, abstract = {Metagenomic techniques have facilitated the discovery of thousands of viruses, yet because samples are often highly biodiverse, fundamental data on the specific cellular hosts are usually missing. Numerous gastrointestinal viruses linked to human or animal diseases are affected by this, preventing research into their medical or veterinary importance. Here, we developed a computational workflow for the prediction of viral hosts from complex metagenomic datasets. We applied it to seven lineages of gastrointestinal cressdnaviruses using 1,124 metagenomic datasets, predicting hosts of four lineages. The Redondoviridae, strongly associated to human gum disease (periodontitis), were predicted to infect Entamoeba gingivalis, an oral pathogen itself involved in periodontitis. The Kirkoviridae, originally linked to fatal equine disease, were predicted to infect a variety of parabasalid protists, including Dientamoeba fragilis in humans. Two viral lineages observed in human diarrhoeal disease (CRESSV1 and CRESSV19, i.e. pecoviruses and hudisaviruses) were predicted to infect Blastocystis spp. and Endolimax nana respectively, protists responsible for millions of annual human infections. Our prediction approach is adaptable to any virus lineage and requires neither training datasets nor host genome assemblies. Two host predictions (for the Kirkoviridae and CRESSV1 lineages) could be independently confirmed as virus-host relationships using endogenous viral elements identified inside host genomes, while a further prediction (for the Redondoviridae) was strongly supported as a virus-host relationship using a case-control screening experiment of human oral plaques.}, } @article {pmid36324897, year = {2022}, author = {Barquero, A and Marini, S and Boucher, C and Ruiz, J and Prosperi, M}, title = {KARGAMobile: Android app for portable, real-time, easily interpretable analysis of antibiotic resistance genes via nanopore sequencing.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {1016408}, pmid = {36324897}, issn = {2296-4185}, support = {R01 AI141810/AI/NIAID NIH HHS/United States ; }, abstract = {Nanopore technology enables portable, real-time sequencing of microbial populations from clinical and ecological samples. An emerging healthcare application for Nanopore includes point-of-care, timely identification of antibiotic resistance genes (ARGs) to help developing targeted treatments of bacterial infections, and monitoring resistant outbreaks in the environment. While several computational tools exist for classifying ARGs from sequencing data, to date (2022) none have been developed for mobile devices. We present here KARGAMobile, a mobile app for portable, real-time, easily interpretable analysis of ARGs from Nanopore sequencing. KARGAMobile is the porting of an existing ARG identification tool named KARGA; it retains the same algorithmic structure, but it is optimized for mobile devices. Specifically, KARGAMobile employs a compressed ARG reference database and different internal data structures to save RAM usage. The KARGAMobile app features a friendly graphical user interface that guides through file browsing, loading, parameter setup, and process execution. More importantly, the output files are post-processed to create visual, printable and shareable reports, aiding users to interpret the ARG findings. The difference in classification performance between KARGAMobile and KARGA is minimal (96.2% vs. 96.9% f-measure on semi-synthetic datasets of 1 million reads with known resistance ground truth). Using real Nanopore experiments, KARGAMobile processes on average 1 GB data every 23-48 min (targeted sequencing - metagenomics), with peak RAM usage below 500MB, independently from input file sizes, and an average temperature of 49°C after 1 h of continuous data processing. KARGAMobile is written in Java and is available at https://github.com/Ruiz-HCI-Lab/KargaMobile under the MIT license.}, } @article {pmid36324162, year = {2022}, author = {Jiang, C and Chen, H and Grossart, HP and Zhang, Q and Stoks, R and Zhao, Y and Ju, F and Liu, W and Yang, Y}, title = {Frequency of occurrence and habitat selection shape the spatial variation in the antibiotic resistome in riverine ecosystems in eastern China.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {53}, pmid = {36324162}, issn = {2524-6372}, abstract = {BACKGROUND: Riverine ecosystems are one of the most important reservoirs of antibiotic resistance genes (ARGs) in the environment, but the occurrence and controlling factors of ARG distribution in different habitats of riverine ecosystems remain poorly understood. In this study, a metagenomic approach was used to characterize ARG types and their abundance in different habitats (rhizosphere soil, surface bulk soil, bottom bulk soil, and sediment) of riverine ecosystems in eastern China. Sampling sites were located along different rivers of eastern China, which are geographically isolated. Differences in bacterial communities, mobile genetic elements (MGEs), pattern and intensity of human activities, climate, and other environmental factors at the sampling sites and habitats were expected to affect ARG occurrence.

RESULTS: ARGs were observed with high variations in diversity (44-206 subtypes) and abundance (6.85-105.68 ×/Gb). There were significant south-north differences in ARG occurrence in the same habitat, except for surface bulk soil. And the significant difference was found in ARGs among four southern habitats. South-north differences in ARGs of the same habitat were mainly attributed to the combination of different occurrence frequencies and habitat selections of ARGs. Differences in ARG profiles among the four habitats in the south and the north were both mainly attributed to the different occurrence frequencies of ARGs. Bacterial communities and MGEs (Mobile genetic elements) could account for the observed variance in the resistome of riverine ecosystems across eastern China. The co-occurrences of specific ARGs with bacterial communities and MGEs were more frequent at the northern sampling sites than in the south, and co-occurrence patterns (i.e. ARGs and bacterial communities or ARGs and MGEs) varied between the habitats. Moreover, building land in all habitats, except bulk soils, showed significant positive correlations with ARG abundance.

CONCLUSION: This study reveals a high variance in the resistome of riverine ecosystems in eastern China and its controlling factors. We appeal to the importance of assessment of ARGs in the riverine ecosystem and the need for future prevention and intervention of ARG spread.}, } @article {pmid36324140, year = {2022}, author = {Slizovskiy, IB and Oliva, M and Settle, JK and Zyskina, LV and Prosperi, M and Boucher, C and Noyes, NR}, title = {Target-enriched long-read sequencing (TELSeq) contextualizes antimicrobial resistance genes in metagenomes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {185}, pmid = {36324140}, issn = {2049-2618}, support = {R01 AI141810/AI/NIAID NIH HHS/United States ; 1R01AI141810-01/NH/NIH HHS/United States ; }, mesh = {Animals ; Humans ; *Metagenome/genetics ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Metagenomics/methods ; }, abstract = {BACKGROUND: Metagenomic data can be used to profile high-importance genes within microbiomes. However, current metagenomic workflows produce data that suffer from low sensitivity and an inability to accurately reconstruct partial or full genomes, particularly those in low abundance. These limitations preclude colocalization analysis, i.e., characterizing the genomic context of genes and functions within a metagenomic sample. Genomic context is especially crucial for functions associated with horizontal gene transfer (HGT) via mobile genetic elements (MGEs), for example antimicrobial resistance (AMR). To overcome this current limitation of metagenomics, we present a method for comprehensive and accurate reconstruction of antimicrobial resistance genes (ARGs) and MGEs from metagenomic DNA, termed target-enriched long-read sequencing (TELSeq).

RESULTS: Using technical replicates of diverse sample types, we compared TELSeq performance to that of non-enriched PacBio and short-read Illumina sequencing. TELSeq achieved much higher ARG recovery (>1,000-fold) and sensitivity than the other methods across diverse metagenomes, revealing an extensive resistome profile comprising many low-abundance ARGs, including some with public health importance. Using the long reads generated by TELSeq, we identified numerous MGEs and cargo genes flanking the low-abundance ARGs, indicating that these ARGs could be transferred across bacterial taxa via HGT.

CONCLUSIONS: TELSeq can provide a nuanced view of the genomic context of microbial resistomes and thus has wide-ranging applications in public, animal, and human health, as well as environmental surveillance and monitoring of AMR. Thus, this technique represents a fundamental advancement for microbiome research and application. Video abstract.}, } @article {pmid36323319, year = {2022}, author = {Vermeulen, R and Van Staden, ADP and van Zyl, LJ and Dicks, LMT and Trindade, M}, title = {Unusual Class I Lanthipeptides from the Marine Bacteria Thalassomonas viridans.}, journal = {ACS synthetic biology}, volume = {11}, number = {11}, pages = {3608-3616}, pmid = {36323319}, issn = {2161-5063}, mesh = {*Bacteriocins/pharmacology ; Peptides/metabolism ; Escherichia coli/genetics/metabolism ; Protein Processing, Post-Translational ; }, abstract = {A novel class I lanthipeptide produced by the marine bacterium Thalassomonas viridans XOM25[T] was identified using genome mining. The putative lanthipeptides were heterologously coexpressed in Escherichia coli as GFP-prepeptide fusions along with the operon-encoded class I lanthipeptide modification machinery VdsCB. The core peptides, VdsA1 and VdsA2, were liberated from GFP using the NisP protease, purified, and analyzed by collision-induced tandem mass spectrometry. The operon-encoded cyclase and dehydratase, VdsCB, exhibited lanthipeptide synthetase activity via post-translational modification of the VdsA1 and VdsA2 core peptides. Modifications were directed by the conserved double glycine leader containing prepeptides of VdsA1 and VdsA2.}, } @article {pmid36323127, year = {2023}, author = {Yao, JC and Yao, GJ and Wang, ZH and Yan, XJ and Lu, QQ and Li, W and Liu, YD}, title = {Bioaugmentation of intertidal sludge enhancing the development of salt-tolerant aerobic granular sludge.}, journal = {Journal of environmental management}, volume = {325}, number = {Pt B}, pages = {116394}, doi = {10.1016/j.jenvman.2022.116394}, pmid = {36323127}, issn = {1095-8630}, mesh = {*Sewage/chemistry ; Waste Disposal, Fluid/methods ; Bioreactors ; Salinity ; *Water Purification ; Aerobiosis ; }, abstract = {Three parallel bioreactors were operated with different inoculation of activated sludge (R1), intertidal sludge (ItS) (R2), and ItS-added AS (R3), respectively, to explore the effects of ItS bioaugmentation on the formation of salt-tolerant aerobic granular sludge (SAGS) and the enhancement of COD removal performance. The results showed that compared to the control (R1-2), R3 promoted a more rapid development of SAGS with a cultivation time of 25 d. Following 110-day cultivation, R3 exhibited a higher granular diameter of 1.3 mm and a higher hydrophobic aromatic protein content than that in control. Compared to the control, the salt-tolerant performance in R3 was also enhanced with the COD removal efficiency of 96.4% due to the higher sludge specific activity of 14.4 g·gVSS[-1]·d[-1] and the salinity inhibition constant of 49.3 gL[-1]. Read- and genome-resolved metagenomics together indicated that a higher level of tryptophan/tyrosine synthase gene (trpBD, tyrBC) and enrichment of the key gene hosts Rhodobacteraceae, Marinicella in R3, which was about 5.4-fold and 1.4-fold of that in control, could be the driving factors of rapid development of SAGS. Furthermore, the augmented salt-tolerant potential in R3 could result from that R1 was dominated by Rhodospirillaceae, Bacteroidales, which carried more trehalose synthase gene (otsB, treS), while the dominant members Rhodobacteraceae, Marinicella in R3 were main contributors to the glycine betaine synthase gene (ectC, betB, gbsA). This study could provide deeper insights into the rapid development and improved salt-tolerant potential of SAGS via bioaugmentation of intertidal sludge, which could promote the application of hypersaline wastewater treatment.}, } @article {pmid36322790, year = {2023}, author = {Battat, R and Scherl, EJ and Lukin, D and Charilaou, P and Mahtani, P and Gerber, J and Gandara, JA and , and Dündar, F and Zumbo, P and Betel, D and Guo, CJ and Longman, RS}, title = {Increased Primary Bile Acids with Ileocolonic Resection Impact Ileal Inflammation and Gut Microbiota in Inflammatory Bowel Disease.}, journal = {Journal of Crohn's & colitis}, volume = {17}, number = {5}, pages = {795-803}, pmid = {36322790}, issn = {1876-4479}, support = {UL1TR002384/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; *Inflammatory Bowel Diseases/surgery/microbiology ; Inflammation ; *Ileitis/surgery/microbiology ; Colectomy ; Bile Acids and Salts ; }, abstract = {BACKGROUND: Most Crohn's disease [CD] patients require surgery. Ileitis recurs after most ileocolectomies and is a critical determinant for outcomes. The impacts of ileocolectomy-induced bile acid [BA] perturbations on intestinal microbiota and inflammation are unknown. We characterized the relationships between ileocolectomy, stool BAs, microbiota and intestinal inflammation in inflammatory bowel disease [IBD].

METHODS: Validated IBD clinical and endoscopic assessments were prospectively collected. Stool primary and secondary BA concentrations were compared based on ileocolectomy and ileitis status. Primary BA thresholds for ileitis were evaluated. Metagenomic sequencing was use to profile microbial composition and function. Relationships between ileocolectomy, BAs and microbiota were assessed.

RESULTS: In 166 patients, elevated primary and secondary BAs existed with ileocolectomy. With ileitis, only primary BAs [795 vs 398 nmol/g, p = 0.009] were higher compared to without ileitis. The optimal primary BA threshold [≥228 nmol/g] identified ileitis on multivariable analysis [odds ratio = 2.3, p = 0.04]. Microbial diversity, Faecalibacterium prausnitzii and O-acetylhomoserine aminocarboxypropyltransferase [MetY] were decreased with elevated primary BAs. Amongst ileocolectomy patients, only those with elevated primary BAs had diversity, F. prausnitzii and MetY reductions. Those with both ileocolectomy and intermediate [p = 0.002] or high [≥228 nmol/g, p = 9.1e-11]] primary BA concentrations had reduced F. prausnitzii compared to without ileocolectomy. Those with ileocolectomy and low [<29.2 nmol/g] primary BA concentrations had similar F. prausnitzii to those without ileocolectomy [p = 0.13]. MetY was reduced with ileitis [p = 0.02].

CONCLUSIONS: Elevated primary BAs were associated with ileitis, and reduced microbial diversity, F. prausnitzii abundance and enzymatic abundance of MetY [acetate and l-methionine-producing enzyme expressed by F. prausnitzii], and were the only factors associated with these findings after ileocolectomy.}, } @article {pmid36322569, year = {2022}, author = {Litvintseva, AP and Bakhiet, S and Gade, L and Wagner, DD and Bagal, UR and Batra, D and Norris, E and Rishishwar, L and Beer, KD and Siddig, EE and Mhmoud, NA and Chow, NA and Fahal, A}, title = {Genomics and metagenomics of Madurella mycetomatis, a causative agent of black grain mycetoma in Sudan.}, journal = {PLoS neglected tropical diseases}, volume = {16}, number = {11}, pages = {e0010787}, pmid = {36322569}, issn = {1935-2735}, mesh = {Humans ; *Madurella/genetics ; *Mycetoma/microbiology ; Sudan ; Metagenomics ; Genomics ; Neglected Diseases ; }, abstract = {Madurella mycetomatis is one of the main causative agents of mycetoma, a debilitating neglected tropical disease. Improved understanding of the genomic diversity of the fungal and bacterial causes of mycetoma is essential to advances in diagnosis and treatment. Here, we describe a high-quality genome assembly of M. mycetomatis and results of the whole genome sequence analysis of 26 isolates from Sudan. We demonstrate evidence of at least seven genetically diverse lineages and extreme clonality among isolates within these lineages. We also performed shotgun metagenomic analysis of DNA extracted from mycetoma grains and showed that M. mycetomatis reads were detected in all sequenced samples with the average of 11,317 reads (s.d. +/- 21,269) per sample. In addition, 10 (12%) of the 81 tested grain samples contained bacterial reads including Streptococcus sp., Staphylococcus sp. and others.}, } @article {pmid36322421, year = {2022}, author = {Ahlqvist, J and Linares-Pastén, JA and Jasilionis, A and Welin, M and Håkansson, M and Svensson, LA and Wang, L and Watzlawick, H and Ævarsson, A and Friðjónsson, ÓH and Hreggviðsson, GÓ and Ketelsen Striberny, B and Glomsaker, E and Lanes, O and Al-Karadaghi, S and Nordberg Karlsson, E}, title = {Crystal structure of DNA polymerase I from Thermus phage G20c.}, journal = {Acta crystallographica. Section D, Structural biology}, volume = {78}, number = {Pt 11}, pages = {1384-1398}, pmid = {36322421}, issn = {2059-7983}, support = {685778//Horizon 2020 Framework Programme/ ; }, mesh = {*DNA Polymerase I/chemistry/genetics ; Phosphodiesterase I ; Thermus ; Taq Polymerase/chemistry ; *Bacteriophages ; Escherichia coli ; }, abstract = {This study describes the structure of DNA polymerase I from Thermus phage G20c, termed PolI_G20c. This is the first structure of a DNA polymerase originating from a group of related thermophilic bacteriophages infecting Thermus thermophilus, including phages G20c, TSP4, P74-26, P23-45 and phiFA and the novel phage Tth15-6. Sequence and structural analysis of PolI_G20c revealed a 3'-5' exonuclease domain and a DNA polymerase domain, and activity screening confirmed that both domains were functional. No functional 5'-3' exonuclease domain was present. Structural analysis also revealed a novel specific structure motif, here termed SβαR, that was not previously identified in any polymerase belonging to the DNA polymerases I (or the DNA polymerase A family). The SβαR motif did not show any homology to the sequences or structures of known DNA polymerases. The exception was the sequence conservation of the residues in this motif in putative DNA polymerases encoded in the genomes of a group of thermophilic phages related to Thermus phage G20c. The structure of PolI_G20c was determined with the aid of another structure that was determined in parallel and was used as a model for molecular replacement. This other structure was of a 3'-5' exonuclease termed ExnV1. The cloned and expressed gene encoding ExnV1 was isolated from a thermophilic virus metagenome that was collected from several hot springs in Iceland. The structure of ExnV1, which contains the novel SβαR motif, was first determined to 2.19 Å resolution. With these data at hand, the structure of PolI_G20c was determined to 2.97 Å resolution. The structures of PolI_G20c and ExnV1 are most similar to those of the Klenow fragment of DNA polymerase I (PDB entry 2kzz) from Escherichia coli, DNA polymerase I from Geobacillus stearothermophilus (PDB entry 1knc) and Taq polymerase (PDB entry 1bgx) from Thermus aquaticus.}, } @article {pmid36322250, year = {2022}, author = {Salamon, D and Zapała, B and Krawczyk, A and Potasiewicz, A and Nikiforuk, A and Stój, A and Gosiewski, T}, title = {Comparison of iSeq and MiSeq as the two platforms for 16S rRNA sequencing in the study of the gut of rat microbiome.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {22}, pages = {7671-7681}, pmid = {36322250}, issn = {1432-0614}, support = {2021/43/D/NZ5/00469//Narodowe Centrum Nauki/ ; 1/CX/CSRD VA/United States ; 1/CX/CSRD VA/United States ; }, mesh = {Rats ; Animals ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; DNA, Bacterial/genetics ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Amplicon-based next-generation sequencing (NGS) of the 16S ribosomal RNA (16S) regions is a culture-free method used to identify and analyze Procaryota occurring within a given sample. The prokaryotic 16S rRNA gene contains conserved regions and nine variable regions (V1-V9) frequently used for phylogenetic classification of genus or species in diverse microbial populations. This work compares the accuracy and efficacy of two platforms, iSeq and MiSeq from Illumina, used in sequencing 16S rRNA. The most important similarities and differences of 16S microbiome sequencing in 20 fecal rat samples were described. Genetic libraries were prepared according to 16S Metagenomic Sequencing Library Preparation (Illumina) for the V3 and V4 regions of the 16S. The species richness obtained using iSeq technology was lower compared to MiSeq. At the second taxonomy level (L2), the abundance of taxa was comparable for both platforms. At the L7, the taxa abundance was significantly different, and the number of taxa was higher for the MiSeq. The alpha diversity was lower for iSeq than for MiSeq, starting from the order to the species level. The beta diversity estimation revealed statistically significant differences in microbiota diversity starting from the class level to the species level in samples sequenced on two investigated platforms. This work disclosed that the iSeq platform could be used to evaluate the bacterial profile of the samples to characterize the overall profile. The MiSeq System seems to be better for a detailed analysis of the differences in the microbiota composition. KEY POINTS: • iSeq platform allows to shorten the sequencing time three times compared to the MiSeq. • iSeq can only be used for an initial and quick microbiome assessment. • MiSeq is better for a detailed analysis of the differences in the microbiota composition.}, } @article {pmid36321905, year = {2022}, author = {Jia, Z and Lipus, D and Bartholomäus, A and Burckhardt, O and Sondermann, M and Wagner, D and Kallmeyer, J}, title = {Metagenome-Assembled Genome of a Putative Methanogenic Methanosarcina sp. Strain Enriched from Terrestrial High-CO2 Subsurface Sediments.}, journal = {Microbiology resource announcements}, volume = {11}, number = {12}, pages = {e0103922}, pmid = {36321905}, issn = {2576-098X}, support = {419459207//Deutsche Forschungsgemeinschaft (DFG)/ ; 202108080137//China Scholarship Council (CSC)/ ; }, abstract = {A metagenome-assembled genome (MAG), named Methanosarcina sp. strain ERenArc_MAG2, was obtained from a 3-month-old H2/CO2 atmosphere enrichment culture, originally inoculated with 60-m deep drill core sediment collected from the tectonic Eger Rift terrestrial subsurface. Annotation of the recovered draft genome revealed putative archaeal methanogenesis genes in the deep biosphere.}, } @article {pmid36321901, year = {2022}, author = {Zhang, XX and Lv, QB and Yan, QL and Zhang, Y and Guo, RC and Meng, JX and Ma, H and Qin, SY and Zhu, QH and Li, CQ and Liu, R and Liu, G and Li, SH and Sun, DB and Ni, HB}, title = {A Catalog of over 5,000 Metagenome-Assembled Microbial Genomes from the Caprinae Gut Microbiota.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0221122}, pmid = {36321901}, issn = {2165-0497}, mesh = {Sheep ; Animals ; *Metagenome ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics/metabolism ; Genome, Bacterial ; Metagenomics ; Genome, Microbial ; Ruminants ; }, abstract = {Most microbiome studies regarding the ruminant digestive tract have focused on the rumen microbiota, whereas only a few studies were performed on investigating the gut microbiota of ruminants, which limits our understanding of this important component. Herein, the gut microbiota of 30 Caprinae animals (sheep and goats) from six provinces in China was characterized using ultradeep (>100 Gbp per sample) metagenome shotgun sequencing. An inventory of Caprinae gut microbial species containing 5,046 metagenomic assembly genomes (MAGs) was constructed. Particularly, 2,530 of the genomes belonged to uncultured candidate species. These genomes largely expanded the genomic repository of the current microbes in the Caprinae gut. Several enzymes and biosynthetic gene clusters encoded by these Caprinae gut species were identified. In summary, our study extends the gut microbiota characteristics of Caprinae and provides a basis for future studies on animal production and animal health. IMPORTANCE We constructed a microbiota catalog containing 5,046 MAGs from Caprinae gut from six regions of China. Most of the MAGs do not overlap known databases and appear to be potentially new species. We also characterized the functional spectrum of these MAGs and analyzed the differences between different regions. Our study enriches the understanding of taxonomic, functional, and metabolic diversity of Caprinae gut microbiota. We are confident that the manuscript will be of utmost interest to a wide range of readers and be widely applied in future research.}, } @article {pmid36321893, year = {2022}, author = {Wu, Y and Jha, R and Li, A and Liu, H and Zhang, Z and Zhang, C and Zhai, Q and Zhang, J}, title = {Probiotics (Lactobacillus plantarum HNU082) Supplementation Relieves Ulcerative Colitis by Affecting Intestinal Barrier Functions, Immunity-Related Gene Expression, Gut Microbiota, and Metabolic Pathways in Mice.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0165122}, pmid = {36321893}, issn = {2165-0497}, mesh = {Humans ; Animals ; Mice ; *Colitis, Ulcerative/chemically induced/therapy ; *Gastrointestinal Microbiome ; *Lactobacillus plantarum ; *Colitis/chemically induced ; Colon/metabolism ; *Probiotics/therapeutic use ; Metabolic Networks and Pathways ; Gene Expression ; Disease Models, Animal ; }, abstract = {Probiotics can effectively improve ulcerative colitis (UC), but the mechanism is still unclear. Here, shotgun metagenome and transcriptome analyses were performed to explore the therapeutic effect and the mechanism of the probiotic Lactobacillus plantarum HNU082 (Lp082) on UC. The results showed that Lp082 treatment significantly ameliorated dextran sulfate sodium (DSS)-induced UC in mice, which was manifested as increases in body weight, water intake, food intake, and colon length and decreases in disease activity index (DAI), immune organ index, inflammatory factors, and histopathological scores after Lp082 intake. An in-depth study discovered that Lp082 could improve the intestinal mucosal barrier and relieve inflammation by cooptimizing the biological barrier, chemical barrier, mechanical barrier, and immune barrier. Specifically, Lp082 rebuilt the biological barrier by regulating the intestinal microbiome and increasing the production of short-chain fatty acids (SCFAs). Lp082 improved the chemical barrier by reducing intercellular cell adhesion molecule-1 (ICAM-1) and vascular cell adhesion molecule (VCAM) and increasing goblet cells and mucin2. Lp082 ameliorated the mechanical barrier by increasing zonula occludens-1 (ZO-1), zonula occludens-2 (ZO-2), and occludin while decreasing claudin-1 and claudin-2. Lp082 optimized the immune barrier by reducing the content of interleukin-1β (IL-1β), IL-6, tumor necrosis factor-α (TNF-α), myeloperoxidase (MPO), and interferon-γ (IFN-γ) and increasing IL-10, transforming growth factor-β1 (TGF-β1), and TGF-β2, inhibiting the NF-κB signaling pathway. Taken together, probiotic Lp082 can play a protective role in a DSS-induced colitis mouse model by protecting the intestinal mucosal barrier, attenuating the inflammatory response, and regulating microbial imbalance. This study provides support for the development of probiotic-based microbial products as an alternative treatment strategy for UC. IMPORTANCE Many studies have focused on the therapeutic effect of probiotics on ulcerative colitis (UC), but few studies have paid attention to the mechanism of probiotics, especially the therapeutic effect. This study suggests that Lp082 has a therapeutic effect on colitis in mice. Its mechanisms of action include protecting the mucosal barrier and actively modulating the gut microbiome, modulating inflammatory pathways, and reducing neutrophil infiltration. Our study enriches the mechanism and provides a new prospect for probiotics in the treatment of colitis, helps to deepen the understanding of the intestinal mucosal barrier, and provides guidance for the future probiotic treatment of human colitis.}, } @article {pmid36321886, year = {2023}, author = {Zhao, C and Dimitrov, B and Goldman, M and Nayfach, S and Pollard, KS}, title = {MIDAS2: Metagenomic Intra-species Diversity Analysis System.}, journal = {Bioinformatics (Oxford, England)}, volume = {39}, number = {1}, pages = {}, pmid = {36321886}, issn = {1367-4811}, support = {R01 HL160862/HL/NHLBI NIH HHS/United States ; T32 GM067547/GM/NIGMS NIH HHS/United States ; }, mesh = {*Metagenome ; *Software ; Metagenomics ; Genotype ; Databases, Factual ; }, abstract = {SUMMARY: The Metagenomic Intra-Species Diversity Analysis System (MIDAS) is a scalable metagenomic pipeline that identifies single nucleotide variants (SNVs) and gene copy number variants in microbial populations. Here, we present MIDAS2, which addresses the computational challenges presented by increasingly large reference genome databases, while adding functionality for building custom databases and leveraging paired-end reads to improve SNV accuracy. This fast and scalable reengineering of the MIDAS pipeline enables thousands of metagenomic samples to be efficiently genotyped.

The source code is available at https://github.com/czbiohub/MIDAS2.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36319706, year = {2023}, author = {Hill, SC and François, S and Thézé, J and Smith, AL and Simmonds, P and Perrins, CM and van der Hoek, L and Pybus, OG}, title = {Impact of host age on viral and bacterial communities in a waterbird population.}, journal = {The ISME journal}, volume = {17}, number = {2}, pages = {215-226}, pmid = {36319706}, issn = {1751-7370}, support = {220414/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; 102427/Z/13/Z/WT_/Wellcome Trust/United Kingdom ; 090532/Z/09/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; BB/T008806/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; Animals ; *Animals, Wild ; Birds ; *Anseriformes ; Metagenome ; }, abstract = {Wildlife harbour pathogens that can harm human or livestock health and are the source of most emerging infectious diseases. It is rarely considered how changes in wildlife population age-structures or how age-stratified behaviours might alter the level of pathogen detection within a species, or risk of spillover to other species. Micro-organisms that occur in healthy animals can be an important model for understanding and predicting the dynamics of pathogens of greater health concern, which are hard to study in wild populations due to their relative rarity. We therefore used a metagenomic approach to jointly characterise viral and prokaryotic carriage in faeces collected from a healthy wild bird population (Cygnus olor; mute swan) that has been subject to long-term study. Using 223 samples from known individuals allowed us to compare differences in prokaryotic and eukaryotic viral carriage between adults and juveniles at an unprecedented level of detail. We discovered and characterised 77 novel virus species, of which 21% belong putatively to bird-infecting families, and described the core prokaryotic microbiome of C. olor. Whilst no difference in microbiota diversity was observed between juveniles and adult individuals, 50% (4/8) of bird-infecting virus families (picornaviruses, astroviruses, adenoviruses and bornaviruses) and 3.4% (9/267) of prokaryotic families (including Helicobacteraceae, Spirochaetaceae and Flavobacteriaceae families) were differentially abundant and/or prevalent between juveniles and adults. This indicates that perturbations that affect population age-structures of wildlife could alter circulation dynamics and spillover risk of microbes, potentially including pathogens.}, } @article {pmid36319696, year = {2023}, author = {Tierney, BT and Versalovic, J and Fasano, A and Petrosino, JF and Chumpitazi, BP and Mayer, EA and Boetes, J and Smits, G and Parkar, SG and Voreades, N and Kartal, E and Al-Ghalith, GA and Pane, M and Bron, PA and Reid, G and Dhir, R and Mason, CE}, title = {Functional response to a microbial synbiotic in the gastrointestinal system of children: a randomized clinical trial.}, journal = {Pediatric research}, volume = {93}, number = {7}, pages = {2005-2013}, pmid = {36319696}, issn = {1530-0447}, mesh = {Child ; Humans ; Infant ; *Synbiotics ; Gastrointestinal Tract/microbiology ; *Probiotics/therapeutic use ; Constipation/therapy ; Feces/microbiology ; Double-Blind Method ; }, abstract = {BACKGROUND: Oral microbial therapy has been studied as an intervention for a range of gastrointestinal disorders. Though research suggests that microbial exposure may affect the gastrointestinal system, motility, and host immunity in a pediatric population, data have been inconsistent, with most prior studies being in neither a randomized nor placebo-controlled setting. The aim of this randomized, placebo-controlled study was to evaluate the efficacy of a synbiotic on increasing weekly bowel movements (WBMs) in constipated children.

METHODS: Sixty-four children (3-17 years of age) were randomized to receive a synbiotic (n = 33) comprising mixed-chain length oligosaccharides and nine microbial strains, or placebo (n = 31) for 84 days. Stool microbiota was analyzed on samples collected at baseline and completion. The primary outcome was a change from baseline of WBMs in the treatment group compared to placebo.

RESULTS: Treatment increased (p < 0.05) the number of WBMs in children with low baseline WBMs, despite broadly distinctive baseline microbiome signatures. Sequencing revealed that low baseline microbial richness in the treatment group significantly anticipated improvements in constipation (p = 0.00074).

CONCLUSIONS: These findings suggest the potential for (i) multi-species-synbiotic interventions to improve digestive health in a pediatric population and (ii) bioinformatics-based methods to predict response to microbial interventions in children.

IMPACT: Synbiotic microbial treatment improved the number of spontaneous weekly bowel movements in children compared to placebo. Intervention induced an increased abundance of bifidobacteria in children, compared to placebo. All administered probiotic species were enriched in the gut microbiome of the intervention group compared to placebo. Baseline microbial richness demonstrated potential as a predictive biomarker for response to intervention.}, } @article {pmid36319439, year = {2023}, author = {Deng, F and Chen, Y and Sun, QS and Lin, ZB and Min, Y and Zhao, BC and Huang, ZB and Liu, WF and Li, C and Hu, JJ and Liu, KX}, title = {Gut microbiota dysbiosis is associated with sepsis-induced cardiomyopathy in patients: A case-control study.}, journal = {Journal of medical virology}, volume = {95}, number = {1}, pages = {e28267}, doi = {10.1002/jmv.28267}, pmid = {36319439}, issn = {1096-9071}, mesh = {Humans ; *Gastrointestinal Microbiome ; Case-Control Studies ; Dysbiosis/complications ; *Cardiomyopathies/etiology ; *Bacteriophages ; Bacteria/genetics ; *Sepsis/complications ; }, abstract = {BACKGROUND: Myocardial injury is a major complication of sepsis and a key factor affecting prognosis. Therefore, early and accurate diagnosis and timely management of sepsis-induced cardiomyopathy (SICM) are of great significance for the prevention and treatment of sepsis. The gut microbiota has been shown to be closely associated with sepsis or myocardial injury, but the association between the gut microbiota and SICM is not fully understood. This study aimed to explore the link between gut microbiota composition and SICM.

METHODS: A case-control and single-center study of clinical features and gut microbiota profiles by Metagenome and Virome was conducted in SICM patients (n = 15) and sepsis-uninduced cardiomyopathy patients (SNICM, n = 16).

RESULTS: Compared with SNICM patients, SICM patients showed significant myocardial injury and higher 28-day mortality, SOFA scores, lactate levels, and infection levels on admission. Meanwhile, differences in the composition of gut bacteria, archaea, fungi, and viruses were analyzed between the two groups. Differential gut bacteria or viruses were found to have a good predictive effect on SICM. Furthermore, gut bacteria and viruses that differed between the two groups were strongly related. The abundance of Cronobacter and Cronobacter phage was higher in the SICM group than in the SNICM group, and the receiver operating characteristic curve showed that Cronobacter and Cronobacter phage both had a good predictive effect on SICM.

CONCLUSIONS: SICM patients may have specific gut microbiota signatures, and Cronobacter and Cronobacter phages have a good ability to identify and diagnose SICM.}, } @article {pmid36318623, year = {2022}, author = {Karakan, T and Gundogdu, A and Alagözlü, H and Ekmen, N and Ozgul, S and Tunali, V and Hora, M and Beyazgul, D and Nalbantoglu, OU}, title = {Artificial intelligence-based personalized diet: A pilot clinical study for irritable bowel syndrome.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2138672}, pmid = {36318623}, issn = {1949-0984}, mesh = {Humans ; *Irritable Bowel Syndrome/microbiology ; *Gastrointestinal Microbiome ; Artificial Intelligence ; RNA, Ribosomal, 16S ; Diet ; }, abstract = {We enrolled consecutive IBS-M patients (n = 25) according to Rome IV criteria. Fecal samples were obtained from all patients twice (pre-and post-intervention) and high-throughput 16S rRNA sequencing was performed. Six weeks of personalized nutrition diet (n = 14) for group 1 and a standard IBS diet (n = 11) for group 2 were followed. AI-based diet was designed based on optimizing a personalized nutritional strategy by an algorithm regarding individual gut microbiome features. The IBS-SSS evaluation for pre- and post-intervention exhibited significant improvement (p < .02 and p < .001 for the standard IBS diet and personalized nutrition groups, respectively). While the IBS-SSS evaluation changed to moderate from severe in 78% (11 out of 14) of the personalized nutrition group, no such change was observed in the standard IBS diet group. A statistically significant increase in the Faecalibacterium genus was observed in the personalized nutrition group (p = .04). Bacteroides and putatively probiotic genus Propionibacterium were increased in the personalized nutrition group. The change (delta) values in IBS-SSS scores (before-after) in personalized nutrition and standard IBS diet groups are significantly higher in the personalized nutrition group. AI-based personalized microbiome modulation through diet significantly improves IBS-related symptoms in patients with IBS-M. Further large-scale, randomized placebo-controlled trials with long-term follow-up (durability) are needed.}, } @article {pmid36318251, year = {2023}, author = {Stam, M and Lelièvre, P and Hoebeke, M and Corre, E and Barbeyron, T and Michel, G}, title = {SulfAtlas, the sulfatase database: state of the art and new developments.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D647-D653}, pmid = {36318251}, issn = {1362-4962}, mesh = {Humans ; Phylogeny ; *Sulfatases/genetics/chemistry ; Databases, Factual ; }, abstract = {SulfAtlas (https://sulfatlas.sb-roscoff.fr/) is a knowledge-based resource dedicated to a sequence-based classification of sulfatases. Currently four sulfatase families exist (S1-S4) and the largest family (S1, formylglycine-dependent sulfatases) is divided into subfamilies by a phylogenetic approach, each subfamily corresponding to either a single characterized specificity (or few specificities in some cases) or to unknown substrates. Sequences are linked to their biochemical and structural information according to an expert scrutiny of the available literature. Database browsing was initially made possible both through a keyword search engine and a specific sequence similarity (BLAST) server. In this article, we will briefly summarize the experimental progresses in the sulfatase field in the last 6 years. To improve and speed up the (sub)family assignment of sulfatases in (meta)genomic data, we have developed a new, freely-accessible search engine using Hidden Markov model (HMM) for each (sub)family. This new tool (SulfAtlas HMM) is also a key part of the internal pipeline used to regularly update the database. SulfAtlas resource has indeed significantly grown since its creation in 2016, from 4550 sequences to 162 430 sequences in August 2022.}, } @article {pmid36318246, year = {2023}, author = {Lei, B and Xu, Y and Lei, Y and Li, C and Zhou, P and Wang, L and Yang, Q and Li, X and Li, F and Liu, C and Cui, C and Chen, T and Ni, W and Hu, S}, title = {CRAMdb: a comprehensive database for composition and roles of microbiome in animals.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D700-D707}, pmid = {36318246}, issn = {1362-4962}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; Fungi/genetics ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Databases, Factual ; }, abstract = {CRAMdb (a database for composition and roles of animal microbiome) is a comprehensive resource of curated and consistently annotated metagenomes for non-human animals. It focuses on the composition and roles of the microbiome in various animal species. The main goal of the CRAMdb is to facilitate the reuse of animal metagenomic data, and enable cross-host and cross-phenotype comparisons. To this end, we consistently annotated microbiomes (including 16S, 18S, ITS and metagenomics sequencing data) of 516 animals from 475 projects spanning 43 phenotype pairs to construct the database that is equipped with 9430 bacteria, 278 archaea, 2216 fungi and 458 viruses. CRAMdb provides two main contents: microbiome composition data, illustrating the landscape of the microbiota (bacteria, archaea, fungi, and viruses) in various animal species, and microbiome association data, revealing the relationships between the microbiota and various phenotypes across different animal species. More importantly, users can quickly compare the composition of the microbiota of interest cross-host or body site and the associated taxa that differ between phenotype pairs cross-host or cross-phenotype. CRAMdb is freely available at (http://www.ehbio.com/CRAMdb).}, } @article {pmid36318011, year = {2022}, author = {Gil, JC and Hird, SM}, title = {Multiomics Characterization of the Canada Goose Fecal Microbiome Reveals Selective Efficacy of Simulated Metagenomes.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0238422}, pmid = {36318011}, issn = {2165-0497}, mesh = {Animals ; *Metagenome ; RNA, Ribosomal, 16S/genetics ; Geese ; Multiomics ; *Microbiota/genetics ; Metagenomics/methods ; Canada ; }, abstract = {16S rRNA amplicon sequences are predominantly used to identify the taxonomic composition of a microbiome, but they can also be used to generate simulated metagenomes to circumvent costly empirical shotgun sequencing. The effectiveness of using "simulated metagenomes" (shotgun metagenomes simulated from 16S rRNA amplicons using a database of full genomes closely related to the amplicons) in nonmodel systems is poorly known. We sought to determine the accuracy of simulated metagenomes in a nonmodel organism, the Canada goose (Branta canadensis), by comparing metagenomes and metatranscriptomes to simulated metagenomes derived from 16S amplicon sequencing. We found significant differences between the metagenomes, metatranscriptomes, and simulated metagenomes when comparing enzymes, KEGG orthologies (KO), and metabolic pathways. The simulated metagenomes accurately identified the majority (>70%) of the total enzymes, KOs, and pathways. The simulated metagenomes accurately identified the majority of the short-chain fatty acid metabolic pathways crucial to folivores. When narrowed in scope to specific genes of interest, the simulated metagenomes overestimated the number of antimicrobial resistance genes and underestimated the number of genes related to the breakdown of plant matter. Our results suggest that simulated metagenomes should not be used in lieu of empirical sequencing when studying the functional potential of a nonmodel organism's microbiome. Regarding the function of the Canada goose microbiome, we found unexpected amounts of fermentation pathways, and we found that a few taxa are responsible for large portions of the functional potential of the microbiome. IMPORTANCE The taxonomic composition of a microbiome is predominately identified using amplicon sequencing of 16S rRNA genes, but as a single marker, it cannot identify functions (genes). Metagenome and metatranscriptome sequencing can determine microbiome function but can be cost prohibitive. Therefore, computational methods have been developed to generate simulated metagenomes derived from 16S rRNA sequences and databases of full-length genomes. Simulated metagenomes can be an effective alternative to empirical sequencing, but accuracy depends on the genomic database used and whether the database contains organisms closely related to the 16S sequences. These tools are effective in well-studied systems, but the accuracy of these predictions in a nonmodel system is less known. Using a nonmodel bird species, we characterized the function of the microbiome and compared the accuracy of 16S-derived simulated metagenomes to sequenced metagenomes. We found that the simulated metagenomes reflect most but not all functions of empirical metagenome sequencing.}, } @article {pmid36317886, year = {2022}, author = {Zaramela, LS and Tjuanta, M and Moyne, O and Neal, M and Zengler, K}, title = {synDNA-a Synthetic DNA Spike-in Method for Absolute Quantification of Shotgun Metagenomic Sequencing.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0044722}, pmid = {36317886}, issn = {2379-5077}, mesh = {*Metagenome/genetics ; *Microbiota/genetics ; Bacteria/genetics ; Plasmids ; DNA ; }, abstract = {Microbiome studies have the common goal of determining which microbial taxa are present, respond to specific conditions, or promote phenotypic changes in the host. Most of these studies rely on relative abundance measurements to drive conclusions. Inherent limitations of relative values are the inability to determine whether an individual taxon is more or less abundant and the magnitude of this change between the two samples. These limitations can be overcome by using absolute abundance quantifications, which can allow for a more complete understanding of community dynamics by measuring variations in total microbial loads. Obtaining absolute abundance measurements is still technically challenging. Here, we developed synthetic DNA (synDNA) spike-ins that enable precise and cost-effective absolute quantification of microbiome data by adding defined amounts of synDNAs to the samples. We designed 10 synDNAs with the following features: 2,000-bp length, variable GC content (26, 36, 46, 56, or 66% GC), and negligible identity to sequences found in the NCBI database. Dilution pools were generated by mixing the 10 synDNAs at different concentrations. Shotgun metagenomic sequencing showed that the pools of synDNAs with different percentages of GC efficiently reproduced the serial dilution, showing high correlation (r = 0.96; R[2] ≥ 0.94) and significance (P < 0.01). Furthermore, we demonstrated that the synDNAs can be used as DNA spike-ins to generate linear models and predict with high accuracy the absolute number of bacterial cells in complex microbial communities. IMPORTANCE The synDNAs designed in this study enable accurate and reproducible measurements of absolute amount and fold changes of bacterial species in complex microbial communities. The method proposed here is versatile and promising as it can be applied to bacterial communities or genomic features like genes and operons, in addition to being easily adaptable by other research groups at a low cost. We also made the synDNAs' sequences and the plasmids available to encourage future application of the proposed method in the study of microbial communities.}, } @article {pmid36316777, year = {2022}, author = {de Frémont, GM and Salmona, M and Maillet, F and Garzaro, M and Bertinchamp, R and Simonnet, A and Feghoul, L and Maki, G and Roelens, M and Chotard, E and Picard, C and Oksenhendler, E and LeGoff, J and Boutboul, D}, title = {Human adenoviral (HAdV) chronic arthritis expands the infectious spectrum of primary agammaglobulinemia.}, journal = {Virology journal}, volume = {19}, number = {1}, pages = {172}, pmid = {36316777}, issn = {1743-422X}, mesh = {Adult ; Humans ; *Adenoviruses, Human ; *Agammaglobulinemia/complications/diagnosis ; Adenoviridae/genetics ; *Arthritis/diagnosis/complications ; Immunoglobulins, Intravenous/therapeutic use ; }, abstract = {Inborn errors of immunity (IEI) are a heterogeneous entity with an increasing number of late diagnoses. Besides infections, inflammatory manifestations are a growing part of the clinical landscape of IEI. These complications are of unknown causes and often lead to the prescription of immunosuppressive agents that worsen the underlying immune defect. We here report the case of an adult patient diagnosed with chronic Human Adenovirus C-1 arthritis in the setting of primary agammaglobulinemia. Metagenomic next-generation sequencing led to the correct diagnosis and high-dose intravenous immunoglobulins resulted in complete recovery. This observation gives new insights into adenoviral immunity and underlines the importance of metagenomics in the diagnosis of inflammatory manifestations in immunocompromised patients.}, } @article {pmid36316749, year = {2022}, author = {Fujimoto, K and Miyaoka, D and Uematsu, S}, title = {Characterization of the human gut virome in metabolic and autoimmune diseases.}, journal = {Inflammation and regeneration}, volume = {42}, number = {1}, pages = {32}, pmid = {36316749}, issn = {1880-9693}, support = {21ae0121048h0001//Japan Agency for Medical Research and Development/ ; 21fk0108619h0001//Japan Agency for Medical Research and Development/ ; }, abstract = {The intestinal microbiome is dominated by bacteria and plays a pivotal role in the occurrence and development of disease, including several metabolic and autoimmune disorders. While intestinal viral communities, primarily made up of bacteriophages, are also thought to play a role in disease pathogenesis in the gastrointestinal tract, they have received much less attention than intestinal bacteria. Thus, there is limited information about the relationship between bacteriophages and disease. This review explores a potential role for the intestinal viral microbiome in various metabolic and autoimmune diseases.}, } @article {pmid36316719, year = {2022}, author = {Monroig, V and Tarquinio, KM}, title = {Diabetic ketoacidosis and coronavirus disease 2019-associated mucormycosis: a case report.}, journal = {Journal of medical case reports}, volume = {16}, number = {1}, pages = {400}, pmid = {36316719}, issn = {1752-1947}, mesh = {Female ; Humans ; Adolescent ; *Mucormycosis/complications/diagnosis/therapy ; *Diabetic Ketoacidosis/complications/diagnosis/therapy ; *COVID-19/complications ; Antifungal Agents/therapeutic use ; *Brain Abscess/microbiology ; *Encephalitis/drug therapy ; *Diabetes Mellitus/drug therapy ; }, abstract = {BACKGROUND: Mucormycosis is a rare, life-threatening fungal infection that affects immunocompromised hosts. Diabetes mellitus is a common predisposing condition and most often presents with rhino-orbital-cerebral infection. Association with coronavirus disease 2019 infection was revealed following a resurgence in cases of mucormycosis during the second wave of the pandemic wherein poorly controlled diabetes mellitus was the most significant risk factor in the affected population. Rhino-orbital-cerebral mucormycosis has a high mortality rate, and cerebral involvement is a poor prognostic factor. Herein, we report a case of newly diagnosed diabetes mellitus with concurrent coronavirus disease 2019 infection complicated by diabetic ketoacidosis and rhinocerebral mucormycosis at presentation, describe the diagnostic and therapeutic challenges, and discuss the interventions that ultimately resulted in a favorable clinical response.

CASE PRESENTATION: We describe the case of a previously healthy 13-year-old African American female patient with newly diagnosed diabetes mellitus and concurrent severe acute respiratory syndrome coronavirus 2 infection whose disease course was complicated by rhinocerebral mucormycosis. She presented with fever, altered mental status, and Kussmaul respirations and was diagnosed with diabetic ketoacidosis with concern for cerebral edema. Concern for infectious cerebritis arose due to recurring fevers and persistently altered mental status despite correction of her metabolic derangements. This raised concern for infectious cerebritis and prompted evaluation with serial head imaging, lumbar puncture, and initiation of broad empiric antimicrobial regimen. Head imaging revealed an evolving cerebral abscess, and fungal deoxyribonucleic acid was identified on blood metagenomics testing, which ultimately confirmed the diagnosis of rhinocerebral mucormycosis. Treatment was challenging as she required surgical debridement of the frontal lobe and aggressive antifungal therapy complicated by electrolyte derangements and electrocardiogram changes that necessitated modification of the antimicrobial regimen. Despite these challenges and high mortality rate, the patient was discharged from the hospital in stable condition to inpatient rehabilitation service for reconditioning after prolonged hospitalization.

CONCLUSION: Rhinocerebral mucormycosis mortality is associated with delays in therapeutic interventions, thus a high index of suspicion and early recognition were essential for timely initiation of antifungal therapy and surgical debridement.}, } @article {pmid36316646, year = {2022}, author = {Das, A and Schatz, MC}, title = {Sketching and sampling approaches for fast and accurate long read classification.}, journal = {BMC bioinformatics}, volume = {23}, number = {1}, pages = {452}, pmid = {36316646}, issn = {1471-2105}, support = {U01 CA253481/CA/NCI NIH HHS/United States ; }, mesh = {Sequence Analysis, DNA/methods ; *High-Throughput Nucleotide Sequencing/methods ; *Software ; Metagenomics/methods ; Metagenome ; Algorithms ; }, abstract = {BACKGROUND: In modern sequencing experiments, quickly and accurately identifying the sources of the reads is a crucial need. In metagenomics, where each read comes from one of potentially many members of a community, it can be important to identify the exact species the read is from. In other settings, it is important to distinguish which reads are from the targeted sample and which are from potential contaminants. In both cases, identification of the correct source of a read enables further investigation of relevant reads, while minimizing wasted work. This task is particularly challenging for long reads, which can have a substantial error rate that obscures the origins of each read.

RESULTS: Existing tools for the read classification problem are often alignment or index-based, but such methods can have large time and/or space overheads. In this work, we investigate the effectiveness of several sampling and sketching-based approaches for read classification. In these approaches, a chosen sampling or sketching algorithm is used to generate a reduced representation (a "screen") of potential source genomes for a query readset before reads are streamed in and compared against this screen. Using a query read's similarity to the elements of the screen, the methods predict the source of the read. Such an approach requires limited pre-processing, stores and works with only a subset of the input data, and is able to perform classification with a high degree of accuracy.

CONCLUSIONS: The sampling and sketching approaches investigated include uniform sampling, methods based on MinHash and its weighted and order variants, a minimizer-based technique, and a novel clustering-based sketching approach. We demonstrate the effectiveness of these techniques both in identifying the source microbial genomes for reads from a metagenomic long read sequencing experiment, and in distinguishing between long reads from organisms of interest and potential contaminant reads. We then compare these approaches to existing alignment, index and sketching-based tools for read classification, and demonstrate how such a method is a viable alternative for determining the source of query reads. Finally, we present a reference implementation of these approaches at https://github.com/arun96/sketching .}, } @article {pmid36316342, year = {2022}, author = {Alessandri, G and Fontana, F and Mancabelli, L and Lugli, GA and Tarracchini, C and Argentini, C and Longhi, G and Viappiani, A and Milani, C and Turroni, F and van Sinderen, D and Ventura, M}, title = {Exploring species-level infant gut bacterial biodiversity by meta-analysis and formulation of an optimized cultivation medium.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {88}, pmid = {36316342}, issn = {2055-5008}, mesh = {Humans ; Infant ; Child ; *Gastrointestinal Microbiome ; Ecosystem ; Bacteria/genetics ; Biodiversity ; Metagenomics ; }, abstract = {In vitro gut cultivation models provide host-uncoupled, fast, and cost-efficient solutions to investigate the effects of intrinsic and extrinsic factors impacting on both composition and functionality of the intestinal microbial ecosystem. However, to ensure the maintenance and survival of gut microbial players and preserve their functions, these systems require close monitoring of several variables, including oxygen concentration, pH, and temperature, as well as the use of a culture medium satisfying the microbial nutritional requirements. In this context, in order to identify the macro- and micro-nutrients necessary for in vitro cultivation of the infant gut microbiota, a meta-analysis based on 1669 publicly available shotgun metagenomic samples corresponding to fecal samples of healthy, full-term infants aged from a few days to three years was performed to define the predominant species characterizing the "infant-like" gut microbial ecosystem. A subsequent comparison of growth performances was made using infant fecal samples that contained the most abundant bacterial taxa of the infant gut microbiota, when cultivated on 18 different culture media. This growth analysis was performed by means of flow cytometry-based bacterial cell enumeration and shallow shotgun sequencing, which allowed the formulation of an optimized growth medium, i.e., Infant Gut Super Medium (IGSM), which maintains and sustains the infant gut microbial biodiversity under in vitro growth conditions. Furthermore, this formulation was used to evaluate the in vitro effect of two drugs commonly used in pediatrics, i.e., acetaminophen and simethicone, on the taxonomic composition of the infant gut microbiota.}, } @article {pmid36315188, year = {2022}, author = {Kamani, J and González-Miguel, J and Msheliza, EG and Goldberg, TL}, title = {Straw-Colored Fruit Bats (Eidolon helvum) and Their Bat Flies (Cyclopodia greefi) in Nigeria Host Viruses with Multifarious Modes of Transmission.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {22}, number = {11}, pages = {545-552}, doi = {10.1089/vbz.2022.0025}, pmid = {36315188}, issn = {1557-7759}, mesh = {Animals ; *Chiroptera/virology ; *Diptera/virology ; Nigeria/epidemiology ; Phylogeny ; *Rhabdoviridae/genetics ; Rhabdoviridae Infections/transmission/virology ; }, abstract = {Background: Bat flies (Diptera: Hippoboscoidea: Nycteribiidae and Streblidae) are increasingly appreciated as hosts of "bat-associated" viruses. We studied straw-colored fruit bats (Eidolon helvum) and their nycteribiid bat flies (Cyclopodia greefi) in Nigeria to investigate the role of bat flies in vectoring or maintaining viruses. Methods: We captured bats and bat flies across northern Nigeria. We used metagenomics to identify viruses in 40 paired samples (20 flies from 20 bats). We characterized viruses using genomic and phylogenetic methods, and we compared infection frequencies in bats and their bat flies. Results: In 20 bats, we detected two individuals (10%) infected with eidolon helvum parvovirus 1 (BtPAR4) (Parvoviridae; Tetraparvovirus), previously described in Ghana, and 10 bats (50%) with a novel parvovirus in the genus Amdoparvovirus (Parvoviridae). The amdoparvoviruses include Aleutian disease virus of mink and viruses of other carnivores but have not previously been identified in bats or in Africa. In 20 paired bat flies (each fly from 1 bat) all (100%) were infected with a novel virus in the genus Sigmavirus (Rhabdoviridae). The sigmaviruses include vertically transmitted viruses of dipterans. We did not detect BtPAR4 in any bat flies, and we did not detect the novel sigmavirus in any bats. However, we did detect the novel amdoparvovirus in 3 out of 20 bat flies sampled (15%), including in 2 bat flies from bats in which we did not detect this virus. Discussion: Our results show that bats and their bat flies harbor some viruses that are specific to mammals and insects, respectively, and other viruses that may transmit between bats and arthropods. Our results also greatly expand the geographic and host range of the amdoparvoviruses and suggest that some could be transmitted by arthropods. Bat flies may serve as biological vectors, mechanical vectors, or maintenance hosts for "bat-associated" viruses.}, } @article {pmid36314838, year = {2022}, author = {Schmidt, EW and Lin, Z}, title = {Translating Marine Symbioses toward Drug Development.}, journal = {mBio}, volume = {13}, number = {6}, pages = {e0249922}, pmid = {36314838}, issn = {2150-7511}, mesh = {Animals ; *Porifera/microbiology ; Bacteria/metabolism ; Drug Development ; Drug Discovery ; *Biological Products/metabolism ; }, abstract = {Chemists have studied marine animals for the better part of a century because they contain a diverse array of bioactive compounds. Tens of thousands of compounds have been reported, many with elaborate structural motifs and biological mechanisms of action found nowhere else. The challenge holding back the field has long been that of supply. Compounds are sometimes obtained by cultivating marine animals or by wild harvest, but this often presents logistical and environmental challenges. Some of the most medically important marine animal compounds are supplied by synthesis, often through multistep procedures that delay drug development. A relatively small number of such agents have been approved by the U.S. Food and Drug Administration, often after a heroic effort. In a recent mBio paper, Uppal and coworkers (https://doi.org/10.1128/mBio.01524-22) address key hurdles underlying the supply issue, discovering an uncultivated new bacterial genus from a marine sponge and reconstituting the biosynthetic pathway for expression.}, } @article {pmid36314799, year = {2022}, author = {Bauer, MJ and Peri, AM and Lüftinger, L and Beisken, S and Bergh, H and Forde, BM and Buckley, C and Cuddihy, T and Tan, P and Paterson, DL and Whiley, DM and Harris, PNA}, title = {Optimized Method for Bacterial Nucleic Acid Extraction from Positive Blood Culture Broth for Whole-Genome Sequencing, Resistance Phenotype Prediction, and Downstream Molecular Applications.}, journal = {Journal of clinical microbiology}, volume = {60}, number = {11}, pages = {e0101222}, pmid = {36314799}, issn = {1098-660X}, support = {SERC 5891_HarrisP//Pathology Queensland, Study Education and Research Committee/ ; //Royal Brisbane and Women's Hospital Foundation (RBWH Foundation)/ ; }, mesh = {*Blood Culture/methods ; Microbial Sensitivity Tests ; Anti-Bacterial Agents/pharmacology ; Phenotype ; *Nucleic Acids ; }, abstract = {The application of direct metagenomic sequencing from positive blood culture broth may solve the challenges of sequencing from low-bacterial-load blood samples in patients with sepsis. Forty prospectively collected blood culture broth samples growing Gram-negative bacteria were extracted using commercially available kits to achieve high-quality DNA. Species identification via metagenomic sequencing and susceptibility prediction via a machine-learning algorithm (AREScloud) were compared to conventional methods and other rapid diagnostic platforms (Accelerate Pheno and blood culture identification [BCID] panel). A two-kit method (using MolYsis Basic and Qiagen DNeasy UltraClean kits) resulted in optimal extractions. Taxonomic profiling by direct metagenomic sequencing matched conventional identification in 38/40 (95%) samples. In two polymicrobial samples, a second organism was missed by sequencing. Prediction models were able to accurately infer susceptibility profiles for 6 common pathogens against 17 antibiotics, with an overall categorical agreement (CA) of 95% (increasing to >95% for 5/6 of the most common pathogens, if Klebsiella oxytoca was excluded). The performance of whole-genome sequencing (WGS)-antimicrobial susceptibility testing (AST) was suboptimal for uncommon pathogens (e.g., Elizabethkingia) and some β-lactamase inhibitor antibiotics (e.g., ticarcillin-clavulanate). The time to pathogen identification was the fastest with BCID (1 h from blood culture positivity). Accelerate Pheno provided a susceptibility result in approximately 8 h. Illumina-based direct sequencing methods provided results in time frames similar to those of conventional culture-based methods. Direct metagenomic sequencing from blood cultures for pathogen detection and susceptibility prediction is feasible. Additional work is required to optimize algorithms for uncommon species and complex resistance genotypes as well as to streamline methods to provide more rapid results.}, } @article {pmid36314793, year = {2022}, author = {Bradbury, RS and Sapp, SGH and Potters, I and Mathison, BA and Frean, J and Mewara, A and Sheorey, H and Tamarozzi, F and Couturier, MR and Chiodini, P and Pritt, B}, title = {Where Have All the Diagnostic Morphological Parasitologists Gone?.}, journal = {Journal of clinical microbiology}, volume = {60}, number = {11}, pages = {e0098622}, pmid = {36314793}, issn = {1098-660X}, mesh = {Animals ; Humans ; *Parasitic Diseases/diagnosis/parasitology ; *Parasites/genetics ; Microscopy/methods ; Feces/parasitology ; Bacteria ; }, abstract = {Advances in laboratory techniques have revolutionized parasitology diagnostics over the past several decades. Widespread implementation of rapid antigen detection tests has greatly expanded access to tests for global parasitic threats such as malaria, while next-generation amplification and sequencing methods allow for sensitive and specific detection of human and animal parasites in complex specimen matrices. Recently, the introduction of multiplex panels for human gastrointestinal infections has enhanced the identification of common intestinal protozoa in feces along with bacterial and viral pathogens. Despite the benefits provided by novel diagnostics, increased reliance on nonmicroscopy-based methods has contributed to the progressive, widespread loss of morphology expertise for parasite identification. Loss of microscopy and morphology skills has the potential to negatively impact patient care, public health, and epidemiology. Molecular- and antigen-based diagnostics are not available for all parasites and may not be suitable for all specimen types and clinical settings. Furthermore, inadequate morphology experience may lead to missed and inaccurate diagnoses and erroneous descriptions of new human parasitic diseases. This commentary highlights the need to maintain expert microscopy and morphological parasitology diagnostic skills within the medical and scientific community. We proposed that light microscopy remains an important part of training and practice in the diagnosis of parasitic diseases and that efforts should be made to train the next generation of morphological parasitologists before the requisite knowledge, skills, and capacity for this complex and important mode of diagnosis are lost. In summary, the widespread, progressive loss of morphology expertise for parasite identification negatively impacts patient care, public health, and epidemiology.}, } @article {pmid36314760, year = {2022}, author = {Florent, P and Cauchie, HM and Herold, M and Ogorzaly, L}, title = {Bacteriophages pass through candle-shaped porous ceramic filters: Application for the collection of viruses in soil water.}, journal = {MicrobiologyOpen}, volume = {11}, number = {5}, pages = {e1314}, pmid = {36314760}, issn = {2045-8827}, mesh = {*Bacteriophages/genetics ; Soil ; Porosity ; Water ; *Viruses ; Ceramics ; }, abstract = {Despite the ubiquity of viruses in soils, their diversity in soil water has not been explored, mainly due to the difficulty of collecting them. In hydrology, soil water is usually collected using porous candles. This study proposes using these porous candles as a new tool for sampling viruses in soil water to analyze their passage through the ceramic part of the candles. The recovery of the viruses was determined after filtration under laboratory conditions using three model bacteriophages (MS2, ΦX174, and Φ6) and Escherichia coli, at neutral and acidic pH. Then, a field experiment was carried out where soil water filtration and viral identification by metagenomic shotgun were performed. At neutral pH, all bacteriophages tested successfully passed through the porous candles during the filtration process, with reductions of 0.02 log, 0.16 log, and 0.55 log for MS2 ΦX174 and Φ6, respectively. At pH 4.4, the passage of MS2 was not affected while ΦX174 underwent a slight reduction in recovery, probably caused by adsorption onto the filter material. Regarding the application of the porous candles in the field, the results obtained allowed the successful recovery of viruses, exposing porous candles as a new method suitable for the collection of viruses from soil water in the context of the study of viral communities.}, } @article {pmid36314746, year = {2022}, author = {Gobert, A and Evers, MS and Morge, C and Sparrow, C and Delafont, V}, title = {Comparison of DNA purification methods for high-throughput sequencing of fungal communities from wine fermentation.}, journal = {MicrobiologyOpen}, volume = {11}, number = {5}, pages = {e1321}, pmid = {36314746}, issn = {2045-8827}, mesh = {*Wine/analysis/microbiology ; Fermentation ; *Mycobiome ; High-Throughput Nucleotide Sequencing ; DNA ; DNA, Fungal/genetics ; }, abstract = {High-throughput sequencing approaches, which target a taxonomically discriminant locus, allow for in-depth insight into microbial communities' compositions. Although microorganisms are historically investigated by cultivation on artificial culture media, this method presents strong limitations, since only a limited proportion of microorganisms can be grown in vitro. This pitfall appears even more limiting in enological and winemaking processes, during which a wide range of molds, yeasts, and bacteria are observed at the different stages of the fermentation course. Such an understanding of those dynamic communities and how they impact wine quality therefore stands as a major challenge for the future of enology. As of now, although high-throughput sequencing has already allowed for the investigation of fungal communities, there is no available comparative study focusing on the performance of microbial deoxyribonucleic acid (DNA) extraction in enological matrixes. This study aims to provide a comparison of five selected extraction methods, assayed on both must and fermenting must, as well as on finished wine. These procedures were evaluated according to their extraction yields, the purity of their extracted DNA, and the robustness of downstream molecular analyses, including polymerase chain reaction and high-throughput sequencing of fungal communities. Altogether, two out of the five assessed microbial DNA extraction methods (DNeasy PowerSoil Pro Kit and E.Z.N.A.® Food DNA Kit) appeared suitable for robust evaluations of the microbial communities in wine samples. Consequently, this study provides robust tools for facilitated upcoming studies to further investigate microbial communities during winemaking using high-throughput sequencing.}, } @article {pmid36314265, year = {2023}, author = {Colman, RJ and Mizuno, T and Fukushima, K and Haslam, DB and Hyams, JS and Boyle, B and Noe, JD and D'Haens, GR and Van Limbergen, J and Chun, K and Yang, J and Denson, LA and Ollberding, NJ and Vinks, AA and Minar, P}, title = {Real world population pharmacokinetic study in children and young adults with inflammatory bowel disease discovers novel blood and stool microbial predictors of vedolizumab clearance.}, journal = {Alimentary pharmacology & therapeutics}, volume = {57}, number = {5}, pages = {524-539}, pmid = {36314265}, issn = {1365-2036}, support = {T32 DK007727/DK/NIDDK NIH HHS/United States ; K23 DK105229/DK/NIDDK NIH HHS/United States ; R03 DK118314/DK/NIDDK NIH HHS/United States ; R01 DK132408/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Child ; Young Adult ; Adolescent ; Treatment Outcome ; Gastrointestinal Agents ; *Inflammatory Bowel Diseases ; Antibodies, Monoclonal, Humanized/adverse effects ; *Colitis, Ulcerative/drug therapy/chemically induced ; }, abstract = {BACKGROUND: Vedolizumab for inflammatory bowel disease (IBD) is often intensified based on distinct pharmacokinetics in children. Prior adult-specific population pharmacokinetic models have identified limited covariates of drug clearance.

AIMS: To establish a population pharmacokinetic model for children and young adults to identify novel covariates of drug clearance to better account for paediatric-specific inter-patient variability in vedolizumab pharmacokinetics; a key secondary exploratory aim was to identify microbial signatures of pharmacokinetic outcomes in a subset of patients.

METHODS: The study included data from 463 observed vedolizumab concentrations (59 peaks and 404 troughs) from 74 patients with IBD (52 with Crohn's disease and 22 with ulcerative colitis or unclassified IBD, median age 16 years). Pharmacokinetic analysis was conducted with non-linear mixed effects modelling. For the evaluation of the exposure-response relationship, clinical outcomes were evaluated by trough levels, clearance and vedolizumab exposure. Whole-genome metagenomic sequencing was conducted at baseline and week 2.

RESULTS: A two-compartment population pharmacokinetic model was identified with a clear correlation between CL and weight, erythrocyte sedimentation rate, and hypoalbuminemia. Trough concentrations before infusion 3 (37 μg/ml) and before infusion 4 (20 μg/ml) best predicted steroid-free clinical remission at infusion 4. Using faecal metagenomics, we identified an early (baseline and week 2) abundance of butyrate-producing species and pathways that were associated with an infusion 4 trough concentration >20 μg/ml.

CONCLUSIONS: This novel paediatric vedolizumab pharmacokinetic model could inform precision dosing. While additional studies are needed, an abundance of faecal butyrate producers is associated with early response to vedolizumab, suggesting that microbial analysis may be beneficial to biological selection.}, } @article {pmid36313418, year = {2022}, author = {Xu, T and Sun, H and Yi, L and Yang, M and Zhu, J and Huang, Y and Pan, H and Li, H and Li, W and Zhao, H and Wei, H and Zhao, S}, title = {Comparing the taxonomic and functional profiles of gut microbiota from three pig breeds by metagenomic sequencing.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {999535}, pmid = {36313418}, issn = {1664-8021}, abstract = {To investigate the difference of microbial communities among Diannan small-ear (DNSE), Dahe black (DHB) and Yorkshire (YS) pigs, we compared the microbial taxonomic and functional composition using a metagenomic approach. A total of 1,002,362 non-redundant microbial genes were identified, DHB and YS pigs had more similar genetic makeup compared with DNSE pigs. Bacteroidetes, Firmicutes and Spirochetes were the three most abundant phyla for all pig breeds, and DNSE pigs had a higher abundance of Prevotella genus than DHB and YS pigs. The functional profiles varied among the three pig breeds, DNSE pigs had more active carbohydrate metabolism and more abundant antibiotic resistance genes than the other two pig breeds. Moreover, we found that peptide and macrolide resistances genes in DNSE pigs were more abundant than that in DHB pigs (p < 0.05). This study will help to provide a theoretical basis for the development of native pig breeds in Yunnan Province, China.}, } @article {pmid36312977, year = {2022}, author = {Han, Z and Xiao, J and Song, Y and Zhao, X and Sun, Q and Lu, H and Zhang, K and Li, J and Li, J and Si, F and Zhang, G and Zhao, H and Jia, S and Zhou, J and Wang, D and Zhu, S and Yan, D and Xu, W and Fu, X and Zhang, Y}, title = {Highly diverse ribonucleic acid viruses in the viromes of eukaryotic host species in Yunnan province, China.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1019444}, pmid = {36312977}, issn = {1664-302X}, abstract = {BACKGROUND: The diversity in currently documented viruses and their morphological characteristics indicates the need for understanding the evolutionary characteristics of viruses. Notably, further studies are needed to obtain a comprehensive landscape of virome, the virome of host species in Yunnan province, China.

MATERIALS AND METHODS: We implemented the metagenomic next-generation sequencing strategy to investigate the viral diversity, which involved in 465 specimens collected from bats, pangolins, monkeys, and other species. The diverse RNA viruses were analyzed, especially focusing on the genome organization, genetic divergence and phylogenetic relationships.

RESULTS: In this study, we investigated the viral composition of eight libraries from bats, pangolins, monkeys, and other species, and found several diverse RNA viruses, including the Alphacoronavirus from bat specimens. By characterizing the genome organization, genetic divergence, and phylogenetic relationships, we identified five Alphacoronavirus strains, which shared phylogenetic association with Bat-CoV-HKU8-related strains. The pestivirus-like virus related to recently identified Dongyang pangolin virus (DYPV) strains from dead pangolin specimens, suggesting that these viruses are evolving. Some genomes showed higher divergence from known species (e.g., calicivirus CS9-Cali-YN-CHN-2020), and many showed evidence of recombination events with unknown or known strains (e.g., mamastroviruses BF2-astro-YN-CHN-2020 and EV-A122 AKM5-YN-CHN-2020). The newly identified viruses showed extensive changes and could be assigned as new species, or even genus (e.g., calicivirus CS9-Cali-YN-CHN-2020 and iflavirus Ifla-YN-CHN-2020). Moreover, we identified several highly divergent RNA viruses and estimated their evolutionary characteristics among different hosts, providing data for further examination of their evolutionary dynamics.

CONCLUSION: Overall, our study emphasizes the close association between emerging viruses and infectious diseases, and the need for more comprehensive surveys.}, } @article {pmid36312974, year = {2022}, author = {Lv, J and Ye, Y and Zhong, Y and Liu, W and Chen, M and Guo, A and Lv, J and Ma, H}, title = {Microbial diversity and functional genes of red vinasse acid based on metagenome analysis.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1025886}, pmid = {36312974}, issn = {1664-302X}, abstract = {Red vinasse acid has a distinct flavor and a vivid red color that are directly tied to the intricate metabolic activities of microorganisms that produce it. In this study, metagenomic technology was used to mine its functional genes and examine the microbial diversity of red vinasse acid. The findings revealed the identification of 2,609 species, 782 genera, and 63 phyla of microorganisms, and the dominant genus was Lactobacillus. Amino acid metabolism and carbohydrate metabolism were significant activities among the 16,093 and 49,652 genes that were annotated in the evolutionary genealogy of genes: Non-supervised Orthologous Groups (eggNOG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. In gluconeogenesis, red vinasse acid encodes 194 genes controlling the transporter protein systems of different sugars and has key enzyme genes that catalyze the conversion of intracellular sugars into glycolytic intermediates. In amino acid flavor formation, red vinasse acid contains 32 control genes for branched-chain aminotransferase (BCAT), 27 control genes for aromatic-amino-acid transaminase (ArAT), 60 control genes for keto acid invertase, 123 control genes for alcohol/aldehyde dehydrogenase, and 27 control genes for acetyl esterase, which have the basis for the formation of strong flavor substances from amino acids.}, } @article {pmid36312950, year = {2022}, author = {Ravichandar, JD and Rutherford, E and Chow, CT and Han, A and Yamamoto, ML and Narayan, N and Kaplan, GG and Beck, PL and Claesson, MJ and Dabbagh, K and Iwai, S and DeSantis, TZ}, title = {Strain level and comprehensive microbiome analysis in inflammatory bowel disease via multi-technology meta-analysis identifies key bacterial influencers of disease.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {961020}, pmid = {36312950}, issn = {1664-302X}, abstract = {OBJECTIVE: Inflammatory bowel disease (IBD) is a heterogenous disease in which the microbiome has been shown to play an important role. However, the precise homeostatic or pathological functions played by bacteria remain unclear. Most published studies report taxa-disease associations based on single-technology analysis of a single cohort, potentially biasing results to one clinical protocol, cohort, and molecular analysis technology. To begin to address this key question, precise identification of the bacteria implicated in IBD across cohorts is necessary.

METHODS: We sought to take advantage of the numerous and diverse studies characterizing the microbiome in IBD to develop a multi-technology meta-analysis (MTMA) as a platform for aggregation of independently generated datasets, irrespective of DNA-profiling technique, in order to uncover the consistent microbial modulators of disease. We report the largest strain-level survey of IBD, integrating microbiome profiles from 3,407 samples from 21 datasets spanning 15 cohorts, three of which are presented for the first time in the current study, characterized using three DNA-profiling technologies, mapping all nucleotide data against known, culturable strain reference data.

RESULTS: We identify several novel IBD associations with culturable strains that have so far remained elusive, including two genome-sequenced but uncharacterized Lachnospiraceae strains consistently decreased in both the gut luminal and mucosal contents of patients with IBD, and demonstrate that these strains are correlated with inflammation-related pathways that are known mechanisms targeted for treatment. Furthermore, comparative MTMA at the species versus strain level reveals that not all significant strain associations resulted in a corresponding species-level significance and conversely significant species associations are not always re-captured at the strain level.

CONCLUSION: We propose MTMA for uncovering experimentally testable strain-disease associations that, as demonstrated here, are beneficial in discovering mechanisms underpinning microbiome impact on disease or novel targets for therapeutic interventions.}, } @article {pmid36312940, year = {2022}, author = {Jing, C and Wang, J and Xie, Y and Zhang, J and Guo, Y and Tian, T and Tang, J and Ju, F and Wang, C and Liu, Y and Zhang, Z and Yang, X and Zhang, H}, title = {Investigation of the growth performance, blood status, gut microbiome and metabolites of rabbit fed with low-nicotine tobacco.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1026680}, pmid = {36312940}, issn = {1664-302X}, abstract = {Tobacco contains a large amount of bioactive ingredients which can be used as source of feed. The objective of this study was to evaluate the effects of dietary addition of low-nicotine tobacco (LNT) on the growth performance, blood status, cecum microbiota and metabolite composition of meat rabbits. A total of 80 Kangda meat rabbits of similar weight were assigned randomly as four groups, and three of them were supplemented with 5%, 10%, and 20% LNT, respectively, with the other one fed with basal diet as control group. Each experiment group with 20 rabbits was raised in a single cage. The experiments lasted for 40 days with a predictive period of 7 days. The results revealed that LNT supplementation had no significant effect on the growth performance, but increased the half carcass weight compared with control group. Dietary supplemention of LNT decreased the triglycerides and cholesterol content in rabbit serum, and significantly increased the plasma concentration of lymphocytes (LYM), monocytes, eosinophils, hemoglobin HGB and red blood cells. In addition, LNT supplementation significantly changed the microbial diversity and richness, and metagenomic analysis showed that LNT supplementation significantly increased Eubacterium_siraeum_group, Alistipes, Monoglobus and Marvinbryantia at genus level. Moreover, LC-MS data analysis identified a total of 308 metabolites that markedly differed after LNT addition, with 190 significantly upregulated metabolites and 118 significantly downregulated metabolites. Furthermore, the correlation analysis showed that there was a significant correlation between the microbial difference and the rabbit growth performance. Overall, these findings provide theoretical basis and data support for the application of LNT in rabbits.}, } @article {pmid36312510, year = {2022}, author = {Wu, GX and Zhou, JY and Hong, WJ and Huang, J and Yan, SQ}, title = {Treatment failure in a patient infected with Listeria sepsis combined with latent meningitis: A case report.}, journal = {World journal of clinical cases}, volume = {10}, number = {29}, pages = {10565-10574}, pmid = {36312510}, issn = {2307-8960}, abstract = {BACKGROUND: Listeria is a food-borne disease, which is rarely prevalent in the normal population; it mostly occurs in pregnant women, newborns, immunodeficiency patients, and the elderly. The main manifestations of this disease in patients include sepsis, meningitis, etc, and the mortality rate remains high, although the onset of meningitis is relatively insidious.

CASE SUMMARY: A 75-year-old man presented with a fever for 1 wk and was admitted to the hospital for diagnosis and management of a lung infection. His condition improved after receiving anti-infective treatment for 2 wk. However, soon after he was discharged from the hospital, he developed fever again, and gradually developed various neurological symptoms, impaired consciousness, and stiff neck. Thereafter, through the cerebrospinal fluid metagenomic testing and blood culture, the patient was diagnosed with Listeria monocytogenes meningitis and sepsis. The patient died after being given active treatment, which included penicillin application and invasive respiratory support.

CONCLUSION: This case highlights the ultimate importance of early identification and timely application of the various sensitive antibiotics, such as penicillin, vancomycin, meropenem, etc. Therefore, for high-risk populations with unknown causes of fever, multiple blood cultures, timely cerebrospinal fluid examination, and metagenomic detection technology can assist in confirming the diagnosis quickly, thereby guiding the proper application of antibiotics and improving the prognosis.}, } @article {pmid36312470, year = {2022}, author = {Kaplina, A and Zaikova, E and Ivanov, A and Volkova, Y and Alkhova, T and Nikiforov, V and Latypov, A and Khavkina, M and Fedoseeva, T and Pervunina, T and Skorobogatova, Y and Volkova, S and Ulyantsev, V and Kalinina, O and Sitkin, S and Petrova, N}, title = {Intestinal microbiome changes in an infant with right atrial isomerism and recurrent necrotizing enterocolitis: A case report and review of literature.}, journal = {World journal of clinical cases}, volume = {10}, number = {29}, pages = {10583-10599}, pmid = {36312470}, issn = {2307-8960}, abstract = {BACKGROUND: Necrotizing enterocolitis (NEC) is a multifactorial disease that predominantly affects premature neonates. Intestinal dysbiosis plays a critical role in NEC pathogenesis in premature neonates. The main risk factor for NEC in term infants is mesenteric hypoperfusion associated with ductal-dependent congenital heart disease (CHD) that eventually leads to intestinal ischemia. The incidence of NEC in neonates with critical CHD is 6.8%-13%. However, the role of the intestinal microbiome in NEC pathogenesis in infants with ductal-dependent CHD remains unclear.

CASE SUMMARY: A male term neonate with right atrial isomerism underwent modified Blalock-Taussig shunt placement on the 14[th] day of life and had persistent mesenteric hypoperfusion after surgery. The patient had episodes of NEC stage IIA on the 1[st] and 28[th] days after cardiac surgery. Fecal microbial composition was analyzed before and after cardiac surgery by sequencing region V4 of the 16S rRNA gene. Before surgery, species belonging to genera Veillonella and Clostridia and class Gammaproteobacteria were detected, Bifidobacteriaceae showed a low abundance. The first NEC episode was associated with postoperative hemodynamic instability, intestinal ischemia-reperfusion injury during cardiopulmonary bypass, and a high abundance of Clostridium paraputrificum (Clostridium sensu stricto I) (56.1%). Antibacterial therapy after the first NEC episode resulted in increased abundance of Gammaproteobacteria, decreased abundance of Firmicutes, and low alpha diversity. These changes in the microbial composition promoted the growth of Clostridium sensu stricto I (72.0%) before the second NEC episode.

CONCLUSION: A high abundance of Clostridium sensu stricto I and mesenteric hypoperfusion may have contributed to NEC in the present case.}, } @article {pmid36311836, year = {2022}, author = {Ford, GJ and Swanson, CR and Bradshaw Allen, RT and Marshall, JR and Mattey, AP and Turner, NJ and Clapés, P and Flitsch, SL}, title = {Three-Component Stereoselective Enzymatic Synthesis of Amino-Diols and Amino-Polyols.}, journal = {JACS Au}, volume = {2}, number = {10}, pages = {2251-2258}, pmid = {36311836}, issn = {2691-3704}, abstract = {Amino-polyols represent attractive chemical building blocks but can be challenging to synthesize because of the high density of asymmetric functionalities and the need for extensive protecting-group strategies. Here we present a three-component strategy for the stereoselective enzymatic synthesis of amino-diols and amino-polyols using a diverse set of prochiral aldehydes, hydroxy ketones, and amines as starting materials. We were able to combine biocatalytic aldol reactions, using variants of d-fructose-6-phosphate aldolase (FSA), with reductive aminations catalyzed by IRED-259, identified from a metagenomic library. A two-step process, without the need for intermediate isolation, was developed to avoid cross-reactivity of the carbonyl components. Stereoselective formation of the 2R,3R,4R enantiomers of amino-polyols was observed and confirmed by X-ray crystallography.}, } @article {pmid36311720, year = {2022}, author = {Mayer-Blackwell, K and Johnson, AM and Potchen, N and Minot, SS and Heptinstall, J and Seaton, K and Sawant, S and Shen, X and Tomaras, GD and Fiore-Gartland, A and Kublin, JG}, title = {Multi-trial analysis of HIV-1 envelope gp41-reactive antibodies among global recipients of candidate HIV-1 vaccines.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {983313}, pmid = {36311720}, issn = {1664-3224}, support = {UM1 AI068618/AI/NIAID NIH HHS/United States ; UM1 AI068635/AI/NIAID NIH HHS/United States ; UM1 AI068614/AI/NIAID NIH HHS/United States ; P30 AI064518/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *HIV-1 ; HIV Antibodies ; *AIDS Vaccines ; *HIV Infections/prevention & control ; *HIV Seropositivity ; Immunoglobulin G ; }, abstract = {Many participants in HIV-1 vaccine trials, who have not previously been exposed to or vaccinated against HIV-1, display serum immunoglobulin antibodies that bind the gp41 region of HIV-1 envelope prior to vaccination. Previous studies have hypothesized that these pre-existing antibodies may be cross-reactive and may skew future vaccine responses. In 12 large studies conducted by the HIV Vaccine Trial Network (HVTN) (n=1470 individuals), we find wide variation among participants in the pre-vaccine levels of gp41-reactive antibodies as measured by the binding antibody multiplex assay (BAMA). In the absence of exposure to the gp41 immunogen, anti-gp41 IgG levels were temporally stable over 26-52 weeks in repeated measures of placebo recipients. The analysis revealed that the geometric mean of pre-vaccine anti-gp41 IgG response was greater among participants in South Africa compared with participants in the United States. With gene-level metagenomic sequencing of pre-vaccination fecal samples collected from participants in one trial (HVTN 106), we detected positive associations between pre-vaccine anti-gp41 IgG and abundance of genes from multiple taxa in the Eubacteriales order. The genes most strongly associated with higher baseline anti-gp41 IgG mapped to a clade containing Blautia wexlerae and closely related strains. In trials with vaccine products containing the full or partial portion of gp41 immunogen alongside a gp120 immunogen, we did not find evidence that individuals with higher baseline anti-gp41 IgG had different levels of anti-gp120 IgG after vaccination compared to individuals with lower pre-vaccine anti-gp41 levels (pooled estimate of standardized mean difference -0.01 with a 95% CI [-0.37; 0.34]).}, } @article {pmid36311106, year = {2022}, author = {Lin, S and Liu, Z and Wang, Y and Li, J and Wang, G and Ye, J and Wang, H and He, H}, title = {Soil metagenomic analysis on changes of functional genes and microorganisms involved in nitrogen-cycle processes of acidified tea soils.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {998178}, pmid = {36311106}, issn = {1664-462X}, abstract = {Nitrogen (N) is the first essential nutrient for tea growth. However, the effect of soil acidification on soil N cycle and N forms in tea plantation are unclear. In this study, the nitrogen contents, soil enzyme activity and N mineralization rate in acidified soil of tea plantation were measured. Moreover, the effects of soil acidification on N cycling functional genes and functional microorganisms were explored by soil metagenomics. The results showed that the NH4 [+]-N, available N and net N mineralization rate in the acidified tea soil decreased significantly, while the NO3 [-]-N content increased significantly. The activities of sucrase, protease, catalase and polyphenol oxidase in the acidified tea soil decreased significantly. The abundance of genes related to ammonification, dissimilatory N reduction, nitrification and denitrification pathway in the acidified tea soil increased significantly, but the abundance of functional genes related to glutamate synthesis and assimilatory N reduction pathway were opposite. In addition, the abundance of Proteobacteria, Actinobacteria, Chloroflexi, Nitrospirae, Actinomadura, Nitrospira etc. microorganisms related to nitrification, denitrification and pathogenic effect increased significantly in the acidified tea soil. The correlation results showed that soil pH and N forms were correlated with soil enzyme activity, N cycling function genes and microbial changes. In conclusion, soil acidification results in significant changes in enzyme activity, gene abundance and microorganism involved in various N cycle processes in acidified tea soil, which leads to imbalance of soil N form ratio and is not conducive to N transformation and absorption of tea trees.}, } @article {pmid36310873, year = {2022}, author = {Liang, Y and Dong, T and Li, M and Zhang, P and Wei, X and Chen, H and Wang, Y and Gao, X}, title = {Clinical diagnosis and etiology of patients with Chlamydia psittaci pneumonia based on metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1006117}, pmid = {36310873}, issn = {2235-2988}, mesh = {Humans ; *Chlamydophila psittaci/genetics ; Retrospective Studies ; Sensitivity and Specificity ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Pneumonia/diagnosis/microbiology ; *Coinfection/microbiology ; }, abstract = {The incidence of severe Chlamydia psittaci (C. psittaci) pneumonia and coinfections is increasing. Early detection of this condition is needed to prevent negative outcomes, along with detailed descriptions of its associated clinical characteristics. Our study contributes by undertaking etiological analysis of patients with C. psittaci pneumonia based on metagenomic next-generation sequencing (mNGS). A retrospective analysis of 30 patients with C. psittaci pneumonia was undertaken and confirmed by mNGS or polymerase chain reaction (PCR). Clinical manifestations of the severe and non-severe C. psittaci pneumonia groups were compared for clinical reference. Etiological analyses were also performed to comprehensively understand pathogeny and coinfection with other respiratory pathogens in C. psittaci patients. The absolute value of lymphocytes (LYM) in the severe group was lower than in the non-severe group. At the same time, neutrophil-to-lymphocyte ratio (NLR), procalcitonin (PCT), alanine aminotransferase (ALT), D-II polymer, brain natriuretic peptide (BNP), myoglobin (MYO), and cardiac troponin I (cTnI) were significantly higher (P < 0.05) in the severe group. mNGS has a broader pathogen spectrum and can more sensitively detect C. psittaci and other low-abundance pathogens with a higher positive detection rate (100%, 13/13 vs. 46%, 6/13, P <0.05) than conventional culture methods. mNGS detected the following dominant species associated with C. psittaci in patients: bacteria (53.2%, 39% gram-positive, 61% gram-negative), fungi (12.9%), and viruses (33.9%). A total of 73.3% (11/15) of patients had suspected coinfections, with a coinfection rate of 91.7% (11/12) in the severe group. No coinfection or death occurred in the non-severe group. Prognosis in the severe group was poor, with a mortality rate of 27.3% (3/11) for patients with coinfection. Eight of 11 patients with coinfections (72.7%) recovered. In conclusion, the clinical symptoms of severe C. psittaci pneumonia manifested as abnormal inflammatory indicators, impaired liver function, myocardial injury, coagulation, and relatively low immune responses. The higher proportion of patients with coinfections in our study supports the use of mNGS for comprehensive early detection of respiratory infections in patients with C. psittaci pneumonia. Simultaneous early identification of coinfections would further improve the clinical treatment of these patients.}, } @article {pmid36310860, year = {2022}, author = {Zhang, Y and Niazi, SA and Yang, Y and Wang, Y and Cao, X and Liu, Y and Li, Y and Zhou, Q}, title = {Smoking by altering the peri-implant microbial community structure compromises the responsiveness to treatment.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1040765}, pmid = {36310860}, issn = {2235-2988}, mesh = {Humans ; Smoking/adverse effects ; *Peri-Implantitis ; Smokers ; *Microbiota ; Prostheses and Implants ; }, abstract = {Smoking is an essential risk factor for peri-implant diseases. It also hampers the clinical outcomes of peri-implant therapies. Nonetheless, the effect of smoking can go undetected until the emergence of clinical signs. Bacterial-induced inflammation is responsible for the initiation and progression of peri-implant diseases. We hypothesize that smoking impacts the peri-implant microbiome even in status of clinical health, putting it into a sub-healthy condition that responds poorly to peri-implant treatments. To validate this, peri-implant plaque samples from 18 participants including 10 smokers (S) and 8 non-smokers (NS), who had received implant prostheses were analyzed using metagenomic shotgun sequencing. The results showed that in addition to taxonomical and functional differences, the local stability in the S group was also shown to be much higher than that in the NS group, indicating greater stubbornness of the peri-implant microbiome associated with smoking. Besides, the topological structures were also distinct between the two groups. The highly connected species interacted more preferentially with each other in the S group (eigenvector centralization, 0.0273 in S and 0.0183 in NS), resulting in a greater tendency of forming small-world modules (modularity, 0.714 in S and 0.582 in NS). While in the NS group, inter-species correlations were more evenly distributed (clustering coefficient, 0.532 in S and 0.666 in NS). These alterations overall explained the greater stubbornness of the peri-implant microbiome associated with smoking, which may cause poor responsiveness to peri-implant therapies. From a microbial perspective, this may be a potential reason why smoking impacts negatively on the outcome of peri-implant treatments.}, } @article {pmid36309502, year = {2022}, author = {Ciciani, M and Demozzi, M and Pedrazzoli, E and Visentin, E and Pezzè, L and Signorini, LF and Blanco-Miguez, A and Zolfo, M and Asnicar, F and Casini, A and Cereseto, A and Segata, N}, title = {Automated identification of sequence-tailored Cas9 proteins using massive metagenomic data.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6474}, pmid = {36309502}, issn = {2041-1723}, support = {U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {*CRISPR-Associated Protein 9/genetics/metabolism ; *CRISPR-Cas Systems/genetics ; RNA, Guide, Kinetoplastida/genetics ; Metagenome ; Gene Editing/methods ; Endonucleases/metabolism ; }, abstract = {The identification of the protospacer adjacent motif (PAM) sequences of Cas9 nucleases is crucial for their exploitation in genome editing. Here we develop a computational pipeline that was used to interrogate a massively expanded dataset of metagenome and virome assemblies for accurate and comprehensive PAM predictions. This procedure allows the identification and isolation of sequence-tailored Cas9 nucleases by using the target sequence as bait. As proof of concept, starting from the disease-causing mutation P23H in the RHO gene, we find, isolate and experimentally validate a Cas9 which uses the mutated sequence as PAM. Our PAM prediction pipeline will be instrumental to generate a Cas9 nuclease repertoire responding to any PAM requirement.}, } @article {pmid36309500, year = {2022}, author = {Perez-Coronel, E and Michael Beman, J}, title = {Multiple sources of aerobic methane production in aquatic ecosystems include bacterial photosynthesis.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6454}, pmid = {36309500}, issn = {2041-1723}, mesh = {*Ecosystem ; *Lakes/microbiology ; Methane/metabolism ; Bacteria/genetics/metabolism ; Photosynthesis ; }, abstract = {Aquatic ecosystems are globally significant sources of the greenhouse gas methane to the atmosphere. Until recently, methane production was thought to be a strictly anaerobic process confined primarily to anoxic sediments. However, supersaturation of methane in oxygenated waters has been consistently observed in lakes and the ocean (termed the 'methane paradox'), indicating that methane can be produced under oxic conditions through unclear mechanisms. Here we show aerobic methane production from multiple sources in freshwater incubation experiments under different treatments and based on biogeochemical, metagenomic, and metatranscriptomic data. We find that aerobic methane production appears to be associated with (bacterio)chlorophyll metabolism and photosynthesis, as well as with Proteobacterial degradation of methylphosphonate. Genes encoding pathways for putative photosynthetic- and methylphosphonate-based methane production also co-occur in Proteobacterial metagenome-assembled genomes. Our findings provide insight into known mechanisms of aerobic methane production, and suggest a potential co-occurring mechanism associated with bacterial photosynthesis in aquatic ecosystems.}, } @article {pmid36309273, year = {2023}, author = {Pinnell, LJ and Kuiper, G and Huebner, KL and Doster, E and Parker, JK and Alekozai, N and Powers, JG and Wallen, RL and Belk, KE and Morley, PS}, title = {More than an anthropogenic phenomenon: Antimicrobial resistance in ungulates from natural and agricultural environments.}, journal = {The Science of the total environment}, volume = {858}, number = {Pt 1}, pages = {159789}, doi = {10.1016/j.scitotenv.2022.159789}, pmid = {36309273}, issn = {1879-1026}, mesh = {Cattle ; Animals ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Macrolides ; Tetracyclines ; Agriculture ; }, abstract = {Widely considered an anthropogenic phenomenon, antimicrobial resistance (AMR) is a naturally occurring mechanism that microorganisms use to gain competitive advantage. AMR represents a significant threat to public health and has generated criticism towards the overuse of antimicrobial drugs. Livestock have been proposed as important reservoirs for AMR accumulation. Here, we show that assemblages of AMR genes in cattle and ungulates from natural environments (Yellowstone and Rocky Mountain National Parks) are all dominated by genes conferring resistance to tetracyclines. However, cattle feces contained higher proportions of erm(A-X) genes conferring resistance to macrolide antibiotics. Medically important AMR genes differed between cattle and natural ungulates, but cumulatively were more predominant in natural soils. Our findings suggest that the commonly described predominance of tetracycline resistance in cattle feces is a natural phenomenon among multiple ungulate species and not solely a result of antimicrobial drug exposure. Yet, the virtual absence of macrolide resistance genes in natural ungulates suggests that macrolide usage in agriculture may enrich these genes in cattle. Our results show that antimicrobial use in agriculture may be promoting a potential reservoir for specific types of AMR (i.e., macrolide resistance) but that a significant proportion of the ungulate resistome appears to have natural origins.}, } @article {pmid36309130, year = {2023}, author = {Li, B and Hong, C and Fan, Z and Cai, S and He, Q and Lan, X and Lai, Q and Ji, Y and Luo, W and Li, J and Cheng, X and Liu, M and Gu, Y and Lu, G and Li, S and Wang, Y and Weng, X and Niu, X and Liu, Q and Jalan, R and Chen, J}, title = {Prognostic and therapeutic significance of microbial cell-free DNA in plasma of people with acute decompensation of cirrhosis.}, journal = {Journal of hepatology}, volume = {78}, number = {2}, pages = {322-332}, doi = {10.1016/j.jhep.2022.10.008}, pmid = {36309130}, issn = {1600-0641}, mesh = {Humans ; *Cytomegalovirus Infections/complications/diagnosis/drug therapy ; Prognosis ; *Acute-On-Chronic Liver Failure/etiology/complications ; Cytomegalovirus/genetics ; Liver Cirrhosis/diagnosis/complications ; *Sepsis/diagnosis/drug therapy/complications ; *Hematologic Neoplasms/complications ; }, abstract = {BACKGROUND & AIMS: Although the effect of bacterial infection on cirrhosis has been well-described, the effect of non-hepatotropic virus (NHV) infection is unknown. This study evaluated the genome fragments of circulating microorganisms using metagenomic next-generation sequencing (mNGS) in individuals with acute decompensation (AD) of cirrhosis, focusing on NHVs, and related the findings to clinical outcomes.

METHODS: Plasma mNGS was performed in 129 individuals with AD of cirrhosis in the study cohort. Ten healthy volunteers and 20, 39, and 81 individuals with stable cirrhosis, severe sepsis and hematological malignancies, respectively, were enrolled as controls. Validation assays for human cytomegalovirus (CMV) reactivation were performed in a validation cohort (n = 58) and exploratory treatment was instituted.

RESULTS: In the study cohort, 188 microorganisms were detected in 74.4% (96/129) of patients, including viruses (58.0%), bacteria (34.1%), fungi (7.4%) and chlamydia (0.5%). A NHV signature was identified in individuals with AD, and CMV was the most frequent NHV, which correlated with the clinical effect of empirical antibiotic treatment, progression to acute-on-chronic liver failure, and 90-day mortality. The NHV signature in individuals with acute-on-chronic liver failure was similar to that in those with sepsis and hematological malignancies. CMV was detected in 24.1% (14/58) of patients in the validation cohort. Of the 14 cases with detectable CMV by mNGS, nine were further validated by real-time PCR or pp65 antigenemia testing. Three patients with CMV reactivation received ganciclovir therapy in an exploratory manner and experienced clinical resolutions.

CONCLUSIONS: The results of this study suggest that NHVs may play a pathogenic role in complicating the course of AD. Further validation is needed to define whether this should be incorporated into the routine management of individuals with AD of cirrhosis.

IMPACT AND IMPLICATIONS: A non-hepatotropic virus (NHV) signature, which was similar to that in individuals with sepsis and hematological malignancies, was identified in individuals with acute decompensation of cirrhosis. The detected viral signature had clinical correlates, including clinical efficacy of empirical antibiotic treatment, progression to acute-on-chronic liver failure and short-term mortality. Cytomegalovirus reactivation, which is treatable, may adversely affect clinical outcomes in some individuals with decompensated cirrhosis. Routine screening for NHVs, especially cytomegalovirus, may be useful for the management of individuals with acute decompensation of cirrhosis.}, } @article {pmid36308935, year = {2023}, author = {Cao, X and Zhang, C and Zhang, S and Sakamaki, T and Wang, H and Li, XN}, title = {Simultaneous removal of sediment and water contaminants in a microbial electrochemical system with embedded active electrode by in-situ utilization of electrons.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt A}, pages = {130172}, doi = {10.1016/j.jhazmat.2022.130172}, pmid = {36308935}, issn = {1873-3336}, mesh = {*Geologic Sediments/chemistry ; *Electrons ; Water/chemistry ; Sulfamethoxazole/metabolism ; Biodegradation, Environmental ; Electrodes ; Pyrenes ; }, abstract = {In the water environment such as lakes, there is a phenomenon that the sediment and overlying water are polluted at the same time. In this study, A microbial electrochemical system with an embedded active electrode was developed for simultaneous removal of polycyclic aromatic hydrocarbons in sediment and antibiotics in overlying water by in-situ utilization of electrons. In the closed-circuit group, the pyrene concentration in sediment decreased from 9.94 to 2.08 mg/L in 96 d, and the sulfamethoxazole concentration in water decreased from 5.12 to 1.12 mg/L in 168 h. These values were 18.71 % and 31.21 % higher, respectively, than those of the open-circuit group. The pyrene degradation pathway may be from polycyclic aromatic substances to low-cyclic aromatic hydrocarbons via successive breakdown of benzene rings. Multiple metabolites produced by reduction verified that SMX or its intermediates were reductively degraded in water. On the active electrode, the relative abundances of Acetobacterium and Piscinibacter, which were genera related to SMX degradation, was promoted, while the electricity-producing genus Pseudomonas was inhibited. ccdA, pksS, torC, and acsE genes related to extracellular electron transport may accelerate electron transport. Electrons could be transferred to SMX under the influence of proteins involved in extracellular electron transport, and SMX could be degraded reductively as an electron acceptor by microbes. Generation of electrons and in-situ utilization for simultaneous removal of solid-liquid two-phase pollutants will provide mechanistic insight into pollutant biodegradation by microbial electrochemistry and promote the development of sustainable bioremediation strategies for surface water.}, } @article {pmid36308931, year = {2023}, author = {Li, Y and Guo, L and Yang, R and Yang, Z and Zhang, H and Li, Q and Cao, Z and Zhang, X and Gao, P and Gao, W and Yan, G and Huang, D and Sun, W}, title = {Thiobacillus spp. and Anaeromyxobacter spp. mediate arsenite oxidation-dependent biological nitrogen fixation in two contrasting types of arsenic-contaminated soils.}, journal = {Journal of hazardous materials}, volume = {443}, number = {Pt A}, pages = {130220}, doi = {10.1016/j.jhazmat.2022.130220}, pmid = {36308931}, issn = {1873-3336}, mesh = {Nitrogen Fixation ; *Arsenic ; Nitrogen ; *Arsenites ; *Thiobacillus/genetics ; Soil Microbiology ; Soil/chemistry ; Bacteria ; }, abstract = {As(III) oxidation-dependent biological nitrogen fixing (As-dependent BNF) bacteria use a novel biogeochemical process observed in tailings recently. However, our understanding of microorganisms responsible for As-dependent BNF is limited and whether such a process occurs in As-contaminated soils is still unknown. In this study, two contrasting types of soils (surface soils versus river sediments) heavily contaminated by As were selected to study the occurrence of As-dependent BNF. BNF was observed in sediments and soils amended with As(III), whereas no apparent BNF was found in the cultures without As(III). The increased abundances of the nitrogenase gene (nifH) and As(III) oxidation gene (aioA) suggest that an As-dependent BNF process was catalyzed by microorganisms harboring nifH and aioA. In addition, DNA-SIP demonstrated that Thiobacillus spp. and Anaeromyxobacter spp. were putative As-dependent BNF bacteria in As-contaminated soils and sediments, respectively. Metagenomic analysis further suggested that these taxa contained genes responsible for BNF, As(III) oxidation, and CO2 fixation, demonstrating their capability for serving as As-dependent BNF. These results indicated the occurrence of As-dependent BNF in various As-contaminated habitats. The contrasting geochemical conditions in different types of soil suggested that these conditions may enrich different As-dependent BNF bacteria (Thiobacillus spp. for soils and Anaeromyxobacter spp. for sediments).}, } @article {pmid36308713, year = {2023}, author = {Wang, W and Huang, S and Nong, L and Li, X and Li, D and Zhang, B and Li, T}, title = {Clinicopathologic Analysis of Kikuchi-Fujimoto Disease and Etiologic Exploration Using Metagenomic Next-Generation Sequencing.}, journal = {Archives of pathology & laboratory medicine}, volume = {147}, number = {7}, pages = {767-773}, doi = {10.5858/arpa.2021-0529-OA}, pmid = {36308713}, issn = {1543-2165}, mesh = {Humans ; Female ; Male ; *Histiocytic Necrotizing Lymphadenitis/diagnosis/pathology ; *Epstein-Barr Virus Infections ; Retrospective Studies ; Herpesvirus 4, Human ; *Autoimmune Diseases ; High-Throughput Nucleotide Sequencing ; }, abstract = {CONTEXT.—: Kikuchi-Fujimoto lymphadenitis, also known as Kikuchi-Fujimoto disease (KFD), is a self-limited lymphoproliferative disease, with no definitive causative agent confirmed by traditional methods.

OBJECTIVES.—: To further explore the clinicopathologic features of KFD and clarify related pathogenic factors.

DESIGN.—: A retrospective analysis was performed in a collection of KFD cases to review the clinical and histopathologic features, and metagenomic next-generation sequencing (mNGS) was used in 64 formalin-fixed, paraffin-embedded (FFPE) tissues from patients with KFD.

RESULTS.—: One hundred five of the 170 patients with KFD (61.8%) were female; 10 patients had autoimmune diseases. Four pathologic subtypes were classified: necrotic (45.9%, 78 of 170), phagocytic (32.4%, 55 of 170), proliferative (17.1%, 29 of 170), and xanthomatous (4.7%, 8 of 170). Patients younger than 40 years with unilateral cervical lymphadenopathy and small vessel fibrinous degeneration accounted for significant differences among the 4 pathologic subtypes (P < .05). Among 64 patients with KFD, 9 had detectable bacterial or viral DNA-of 6 bacterial cases, 1 involved Chlamydia psittaci; while of 3 viral cases, 1 involved human beta herpesvirus 6B and 2 involved Epstein-Barr virus. No significant relationships were found between the pathologic subtypes and specific pathogens.

CONCLUSIONS.—: Only a small proportion of patients with KFD had autoimmune diseases or infections from specific pathogens, suggesting that KFD is likely a reactive lesion of lymph nodes to various circumstances. To our knowledge, this is the first and the largest study to detect pathogens with the use of mNGS on FFPE samples in KFD. Our study also further confirms that mNGS can be used on FFPE samples to detect potentially infectious agents in clinical settings.}, } @article {pmid36307519, year = {2022}, author = {Martínez-Puchol, S and Cardona, L and Drago, M and Gazo, M and Bofill-Mas, S}, title = {Viral metagenomics reveals persistent as well as dietary acquired viruses in Antarctic fur seals.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {18207}, pmid = {36307519}, issn = {2045-2322}, support = {CTM2017-83319-P//Ministerio de Ciencia, Innovación y Universidades/ ; }, mesh = {Animals ; Humans ; *Fur Seals ; *Viruses/genetics ; Metagenomics ; Climate Change ; Diet ; Antarctic Regions ; }, abstract = {Viruses linked to animals inhabiting Antarctic latitudes remain poorly studied. Remote environments hosting large pinniped populations may be prone to exposure of immunologically naïve animals to new infectious agents due to increasing human presence or introduction of new animal species. Antarctic fur seals (Arctocephalus gazella) inhabiting the Western Antarctic Peninsula and the South Shetland Islands are challenged because of climate change and increased anthropogenic activity. In the present study, the fecal and serum virome of A. gazella was characterized by applying target enrichment next generation sequencing. The resulting viromes were dominated by CRESS-DNA sequences. Viruses known to infect vertebrate and invertebrate hosts were also observed in fecal samples. Fur seal picornavirus was present in all the fecal pools studied suggesting it is a prevalent virus in these species. Six different viruses presenting similarities with previously described A. gazella viruses or other otariids and mammal viruses were identified as potential new A. gazella viruses. Also, diet-derived viruses such as crustacean viruses were present in fecal content. Penguin viruses, but not fish viruses, were also detected. Obtained results contribute to a better understanding of the viral community present in these species, which is relevant for its conservation.}, } @article {pmid36307482, year = {2022}, author = {Gunter, HM and Youlten, SE and Madala, BS and Reis, ALM and Stevanovski, I and Wong, T and Kummerfield, SK and Deveson, IW and Santini, NS and Marcellin, E and Mercer, TR}, title = {Library adaptors with integrated reference controls improve the accuracy and reliability of nanopore sequencing.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6437}, pmid = {36307482}, issn = {2041-1723}, mesh = {*Nanopore Sequencing ; Reproducibility of Results ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; RNA ; }, abstract = {Library adaptors are short oligonucleotides that are attached to RNA and DNA samples in preparation for next-generation sequencing (NGS). Adaptors can also include additional functional elements, such as sample indexes and unique molecular identifiers, to improve library analysis. Here, we describe Control Library Adaptors, termed CAPTORs, that measure the accuracy and reliability of NGS. CAPTORs can be integrated within the library preparation of RNA and DNA samples, and their encoded information is retrieved during sequencing. We show how CAPTORs can measure the accuracy of nanopore sequencing, evaluate the quantitative performance of metagenomic and RNA sequencing, and improve normalisation between samples. CAPTORs can also be customised for clinical diagnoses, correcting systematic sequencing errors and improving the diagnosis of pathogenic BRCA1/2 variants in breast cancer. CAPTORs are a simple and effective method to increase the accuracy and reliability of NGS, enabling comparisons between samples, reagents and laboratories, and supporting the use of nanopore sequencing for clinical diagnosis.}, } @article {pmid36307411, year = {2022}, author = {Zhu, K and Schäffer, AA and Robinson, W and Xu, J and Ruppin, E and Ergun, AF and Ye, Y and Sahinalp, SC}, title = {Strain level microbial detection and quantification with applications to single cell metagenomics.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6430}, pmid = {36307411}, issn = {2041-1723}, support = {R01 AI143254/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Metagenomics/methods ; *Metagenome/genetics ; High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics ; Algorithms ; Sequence Analysis, DNA/methods ; }, abstract = {Computational identification and quantification of distinct microbes from high throughput sequencing data is crucial for our understanding of human health. Existing methods either use accurate but computationally expensive alignment-based approaches or less accurate but computationally fast alignment-free approaches, which often fail to correctly assign reads to genomes. Here we introduce CAMMiQ, a combinatorial optimization framework to identify and quantify distinct genomes (specified by a database) in a metagenomic dataset. As a key methodological innovation, CAMMiQ uses substrings of variable length and those that appear in two genomes in the database, as opposed to the commonly used fixed-length, unique substrings. These substrings allow to accurately decouple mixtures of highly similar genomes resulting in higher accuracy than the leading alternatives, without requiring additional computational resources, as demonstrated on commonly used benchmarking datasets. Importantly, we show that CAMMiQ can distinguish closely related bacterial strains in simulated metagenomic and real single-cell metatranscriptomic data.}, } @article {pmid36306620, year = {2022}, author = {Ai, J and Li, Y and Lv, Y and Zhong, X and Li, J and Yang, A}, title = {Study on microbes and antibiotic resistance genes in karst primitive mountain marshes - A case study of Niangniang Mountain in Guizhou, China.}, journal = {Ecotoxicology and environmental safety}, volume = {247}, number = {}, pages = {114210}, doi = {10.1016/j.ecoenv.2022.114210}, pmid = {36306620}, issn = {1090-2414}, mesh = {Humans ; *Wetlands ; *Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Ecosystem ; Plant Breeding ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; China ; }, abstract = {Previous research on antibiotic resistance genes and microorganisms centered on those in urban sewage treatment plants, breeding farms, hospitals and others with serious antibiotic pollution. However, at present, there are evident proofs that antibiotic resistance genes (ARGs) indeed exist in a primitive environment hardly without any human's footprints. Accordingly, an original karst mountain swamp ecosystem in Niangniang Mountain, Guizhou, China, including herbaceous swamp, shrub swamp, sphagnum bog and forest swamp, was selected to analyze the physical and chemical parameters of sediments. Moreover, microbial compositions, functions, as well as their connections with ARGs were assayed and analyzed using metagenomic technology. The results showed that there was no significant difference in the dominant microorganisms and ARGs in the four marshes, in which the dominant bacteria phyla were Proteobacteria (37.82 %), Acidobacteriota (22.17 %) and Actinobacteriota (20.64 %); the dominant archaea Euryarchaeota. (1.00 %); and the dominant eukaryotes Ascomycota (0.07 %), with metabolism as their major functions. Based on the ARDB database, the number of ARGs annotated reached 209 including 30 subtypes, and the dominant ARGs were all Bacitracin resistance genes (bacA, 84.77 %). In terms of the diversity of microorganisms and ARGs, the herbaceous swamp ranked the top, and the shrub swamp were at the bottom. Correlation analysis between microorganisms and resistance genes showed that, apart from aac2ic, macB, smeE, tetQ, and tetL, other ARGs were positively correlated with microorganisms. Among them, baca coexisted with microorganisms. Pearson correlation analysis results showed that contrary to ARGs, microorganisms were more affected by environmental factors.}, } @article {pmid36306091, year = {2023}, author = {Jameson, E and Taubert, M and Angel, R and Coyotzi, S and Chen, Y and Eyice, Ö and Schäfer, H and Murrell, JC and Neufeld, JD and Dumont, MG}, title = {DNA-, RNA-, and Protein-Based Stable-Isotope Probing for High-Throughput Biomarker Analysis of Active Microorganisms.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {261-282}, pmid = {36306091}, issn = {1940-6029}, mesh = {RNA, Ribosomal, 16S/genetics/chemistry ; Carbon Isotopes/chemistry ; Isotope Labeling/methods ; *DNA/chemistry ; *Proteins/chemistry ; Biomarkers ; RNA, Messenger ; }, abstract = {Stable-isotope probing (SIP) enables researchers to target active populations within complex microbial communities, which is achieved by providing growth substrates enriched in heavy isotopes, usually in the form of [13]C, [18]O, or [15]N. After growth on the substrate and subsequent extraction of microbial biomarkers, typically nucleic acids or proteins, the SIP technique is used for the recovery and analysis of isotope-labelled biomarkers from active microbial populations. In the years following the initial development of DNA- and RNA-based SIP, it was common practice to characterize labelled populations by targeted gene analysis. Such approaches usually involved fingerprint-based analyses or sequencing clone libraries containing 16S rRNA genes or functional marker gene amplicons. Although molecular fingerprinting remains a valuable approach for rapid confirmation of isotope labelling, recent advances in sequencing technology mean that it is possible to obtain affordable and comprehensive amplicon profiles, or even metagenomes and metatranscriptomes from SIP experiments. Not only can the abundance of microbial groups be inferred from metagenomes, but researchers can bin, assemble, and explore individual genomes to build hypotheses about the metabolic capabilities of labelled microorganisms. Analysis of labelled mRNA is a more recent advance that can provide independent metatranscriptome-based analysis of active microorganisms. The power of metatranscriptomics is that mRNA abundance often correlates closely with the corresponding activity of encoded enzymes, thus providing insight into microbial metabolism at the time of sampling. Together, these advances have improved the sensitivity of SIP methods and allowed using labelled substrates at environmentally relevant concentrations. Particularly as methods improve and costs continue to drop, we expect that the integration of SIP with multiple omics-based methods will become prevalent components of microbial ecology studies, leading to further breakthroughs in our understanding of novel microbial populations and elucidation of the metabolic function of complex microbial communities. In this chapter, we provide protocols for obtaining labelled DNA, RNA, and proteins that can be used for downstream omics-based analyses.}, } @article {pmid36306090, year = {2023}, author = {Rebets, Y and Kormanec, J and Lutzhetskyy, A and Bernaerts, K and Anné, J}, title = {Cloning and Expression of Metagenomic DNA in Streptomyces lividans and Its Subsequent Fermentation for Optimized Production.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {213-260}, pmid = {36306090}, issn = {1940-6029}, mesh = {Streptomyces lividans/genetics/metabolism ; Cloning, Molecular ; Fermentation ; Escherichia coli/genetics/metabolism ; Plasmids/genetics ; *Streptomyces/genetics/metabolism ; *Actinomycetales/metabolism ; *Actinobacteria/genetics ; DNA/metabolism ; Genetic Vectors/genetics ; }, abstract = {The choice of an expression system for the metagenomic DNA of interest is of vital importance for the detection of any particular gene or gene cluster. Most of the screens to date have used the Gram-negative bacterium Escherichia coli as a host for metagenomic gene libraries. However, the use of E. coli introduces a potential host bias since only 40% of the enzymatic activities may be readily recovered by random cloning in E. coli. To recover some of the remaining 60%, alternative cloning hosts such as Streptomyces spp. have been used. Streptomycetes are high-GC Gram-positive bacteria belonging to the Actinomycetales and they have been studied extensively for more than 25 years as an alternative expression system. They are extremely well suited for the expression of DNA from other actinomycetes and genomes of high GC content. Furthermore, due to its high innate, extracellular secretion capacity, Streptomyces can be a better system than E. coli for the production of many extracellular proteins. In this article, an overview is given about the materials and methods for growth and successful expression and secretion of heterologous proteins from diverse origin using Streptomyces lividans as a host. More in detail, an overview is given about the protocols of transformation, type of plasmids used and of vectors useful for integration of DNA into the host chromosome, and accompanying cloning strategies. In addition, various control elements for gene expression including synthetic promoters are discussed, and methods to compare their strength are described. Stable and efficient marker-less integration of the gene of interest under the control of the promoter of choice into S. lividans chromosome via homologous recombination using pAMR23A-based system will be explained. Finally, a basic protocol for bench-top bioreactor experiments which can form the start in the production process optimization and up-scaling will be provided.}, } @article {pmid36306089, year = {2023}, author = {Kohm, K and Lutz, VT and Friedrich, I and Hertel, R}, title = {CRISPR-Cas9 Shaped Viral Metagenomes Associated with Bacillus subtilis.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {205-212}, pmid = {36306089}, issn = {1940-6029}, mesh = {*Bacillus subtilis/genetics ; CRISPR-Cas Systems/genetics ; Metagenome ; *Bacteriophages ; }, abstract = {Phages are viruses of bacteria and have been known for over a century. They do not have a metabolism or protein synthesis machinery and rely on host cells for replication. The model organism Bacillus subtilis has served as a host strain for decades and enabled the isolation of many unique viral strains. However, many viral species representatives remained orphans as no, or only a few, related phages were ever re-isolated.The presented protocol describes how a CRISPR-Cas9 system with an artificial CRISPR-array can be set up and used to discriminate abundant and well-known B. subtilis phage from a host-based metagenome enrichment. The obtained viral suspension can be used for metagenome sequencing and isolating new viral strains.}, } @article {pmid36306088, year = {2023}, author = {Friedrich, I and Hertel, R}, title = {Isolation of a Host-Confined Phage Metagenome Allows the Detection of Phages Both Capable and Incapable of Plaque Formation.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {195-203}, pmid = {36306088}, issn = {1940-6029}, mesh = {*Metagenome ; *Bacteriophages/genetics ; Metagenomics/methods ; Bacteria/genetics ; Genomics ; Genome, Viral ; }, abstract = {Bacteriophages, also called phages, are viruses of bacteria. They are the most common and diverse biological entities on this planet. For metagenomic investigation, their diversity is also their biggest obstacle. The direct metagenomic sequence of environmental phage communities often leads to short genomic fragments limiting the investigation to a few individual aspects of phage biology and diversity.The presented protocol for generating a host-associated metagenome reduces the phage diversity to a concise and accessible size. Metagenome sequencing often leads to complete genomes, and the availability of a suitable host system ensures further experimental investigation.}, } @article {pmid36306087, year = {2023}, author = {Molina-Espeja, P and Fernandez-Lopez, L and Golyshin, PN and Ferrer, M}, title = {Assigning Functions of Unknown Enzymes by High-Throughput Enzyme Characterization.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {181-194}, pmid = {36306087}, issn = {1940-6029}, mesh = {*Esterases/metabolism ; *Lipase/metabolism ; Phospholipases ; High-Throughput Screening Assays/methods ; }, abstract = {The discovery of new enzymes is strongly enabled by the implementation of high-throughput screening methods to detect enzymatic activity in single organisms or clone expression libraries, or to benchmark their performances against known prototypes. In this chapter, a number of methods, applicable at high-throughput scale, are described that allow the screening and characterization of enzymes relevant to biotechnology, particularly, ester-hydrolases (esterases, lipases, phospholipases, and polyester hydrolases).}, } @article {pmid36306086, year = {2023}, author = {Han, Y and Dierkes, RF and Streit, WR}, title = {Metagenomic Screening of a Novel PET Esterase via In Vitro Expression System.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {167-179}, pmid = {36306086}, issn = {1940-6029}, mesh = {*Esterases/genetics/metabolism ; *Metagenome ; Metagenomics ; Polyethylene Terephthalates/metabolism ; High-Throughput Nucleotide Sequencing ; }, abstract = {Metagenomic screening is a widely applied biotechnological approach for screening of novel industrial enzymes. The traditional method of metagenomic screening is based on the functional analyses of heterologously expressed environmental genes in a suitable host, which is the bottleneck of this method. To avoid limitation from the clone-dependent system, an in vitro expression technology has been developed in combination with next-generation sequencing and bioinformatics. First, the sequence profile of a target enzyme, e.g., poly(ethylene terephthalate) esterase in this protocol, is constructed according to the sequences of well-characterized enzymes. Then, the sequence screening is performed with this computationally generated profile among all available metagenomic databases. Afterwards, the candidate genes are synthesized and expressed in vitro with RNA polymerase and translation machinery from special cell extract. Finally, such in vitro produced enzymes are directly applied for the functional analyses. Comparing to the traditional screening methods, this in vitro screening technology can not only save time and materials, but also be easily developed for high-throughput screening with an automatic pipetting robot.}, } @article {pmid36306084, year = {2023}, author = {Chow, J and Pérez-García, P and Dierkes, RF and Zhang, H and Streit, WR}, title = {The PET-Degrading Potential of Global Metagenomes: From In Silico Mining to Active Enzymes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {139-151}, pmid = {36306084}, issn = {1940-6029}, mesh = {*Polyethylene Terephthalates/chemistry/metabolism ; *Metagenome ; Esterases/genetics/chemistry ; Metagenomics ; Plastics ; Hydrolases/genetics/metabolism ; }, abstract = {Against the background of the steadily increasing amount of plastic waste in the sea and on land, it is more important than ever to find ways out of this situation. In recent years, microorganisms have been discovered that are capable of degrading artificial polymers such as polyethylene terephthalate (PET). Even if the turnover rates of the enzymes responsible for this reaction may be too low to solve the global plastic pollution problem, it is still of great societal interest to find microorganisms that are able to degrade the polymer. The corresponding enzymes, PET esterases (PETases) can be used in biotechnological processes and could contribute to a resource-saving circular economy. In this chapter, we present a sequence-based in silico screening method to find new PETases in metagenomic datasets. This method can easily be adapted to find other enzyme classes. We also list a number of assays that can be used to test the enzymes for activity on PET as well as other substrates.}, } @article {pmid36306083, year = {2023}, author = {Macdonald, JFH and Krohn, I and Streit, WR}, title = {Screening Metagenomes for Algae Cell Wall Carbohydrates Degrading Hydrolases in Enrichment Cultures.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {125-137}, pmid = {36306083}, issn = {1940-6029}, mesh = {*Metagenome ; Hydrolases/metabolism ; *Rhodophyta/metabolism ; Carbohydrates ; Cell Wall ; }, abstract = {Sustainable use of natural products is one of the key challenges for the future. An increasing focus is on marine organic matter, mostly algae. New biotechnological tools for processing high amounts of micro- and macroalgae are necessary for efficient industrial degradation of marine matter. Secreted glycosyl hydrolases can be enriched and tested on the specific algae cell wall polymers of all algae groups (Rhodophyta; Phaeophyceae; Chlorophyta/Charophyta). Metagenomic analyses established new possibilities to screen algae-associated microbiomes for novel degrading enzymes in combination with sequence-based function prediction.}, } @article {pmid36306082, year = {2023}, author = {Thakor, A and Cheng, J and Charles, TC}, title = {Isolation of Genes Encoding Carbon Metabolism Pathways from Complex Microbial Communities.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {115-123}, pmid = {36306082}, issn = {1940-6029}, mesh = {*Carbon/metabolism ; Escherichia coli/genetics/metabolism ; *Microbiota ; Metagenome ; Metagenomics ; Fermentation ; }, abstract = {The ability to produce high-value products using bacteria will increasingly rely on continued research to make large-scale bacterial fermentation cost-efficient. Engineering bacteria to use alternate carbon sources as feedstock provides an opportunity to reduce production costs. Using inexpensive carbon sources from various forms of waste provides an opportunity to substantially reduce feedstock costs. Functional carbon metabolism pathways can be identified by the introduction of metagenomic libraries into the organism of interest followed by screening for the desired phenotype. We present here a method to transfer metagenomic libraries from E. coli to Pseudomonas alloputida, followed by screening for use of galactose as a sole carbon source.}, } @article {pmid36306081, year = {2023}, author = {Castillo Villamizar, GA and Nacke, H and Daniel, R}, title = {Functional Metagenomics Approach for the Discovery of Novel Genes Encoding Phosphatase Activity.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {103-114}, pmid = {36306081}, issn = {1940-6029}, mesh = {*Metagenomics ; Metagenome ; Phosphoric Monoester Hydrolases/genetics/metabolism ; *6-Phytase/genetics ; Phosphates ; }, abstract = {Phosphate release from inorganic and organic phosphorus compounds can be enzymatically mediated. Phosphate-releasing enzymes, comprising acid and alkaline phosphatases, are recognized as useful biocatalysts in applications such as plant and animal nutrition, bioremediation, and diagnostic analysis. Here, we describe a functional metagenomics approach enabling rapid identification of genes encoding these enzymes. The target genes are detected based on small- and large-insert metagenomic libraries derived from diverse environments. This approach has the potential to unveil entirely new phosphatase families or subfamilies and members of known enzyme classes that hydrolyze phosphomonoester bonds such as phytases. Additionally, we provide a strategy for efficient heterologous expression of phosphatase genes.}, } @article {pmid36306080, year = {2023}, author = {Adam-Beyer, N and Perner, M}, title = {Activity-Based Screening of Metagenomic Fosmid Libraries for Hydrogen-Uptake Enzymes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {91-101}, pmid = {36306080}, issn = {1940-6029}, mesh = {*Hydrogenase/genetics ; Hydrogen ; Escherichia coli/genetics ; Metagenomics ; Metagenome ; Gene Library ; }, abstract = {Here, we outline how to identify hydrogenase enzymes from metagenomic fosmid libraries through an activity-based screening approach. A metagenomic fosmid library is constructed in E. coli and the fosmids are transferred into a hydrogenase deletion mutant of Shewanella oneidensis MR-1 (ΔhyaB) via triparental mating. If a fosmid clone exhibits hydrogen-uptake activity, S. oneidensis' phenotype is restored and hydrogenase activity is indicated by a color change of the medium from yellow to colorless. The screen enables screening of 48 metagenomic fosmid clones in parallel.}, } @article {pmid36306079, year = {2023}, author = {Santana-Pereira, ALR}, title = {Identification of PKS Gene Clusters from Metagenomic Libraries Using a Next-Generation Sequencing Approach.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {73-90}, pmid = {36306079}, issn = {1940-6029}, mesh = {*Polyketide Synthases/genetics ; Metagenome ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing ; Multigene Family ; *Biological Products ; }, abstract = {Microbial secondary metabolites have been an important source of bioactive compounds with diverse applications from medicine to agriculture, noticeably those encoded by polyketide synthase (PKS) clusters due to their astounding chemical diversity. While most discovered compounds originate from culturable microorganisms, yet-to-be cultured microbes represent a reservoir of previously inaccessible compounds. The advent and development of metagenomics have allowed not only the characterization of these microorganisms but also their metabolic potential, making viable the prospection of environmental PKS for natural product discovery.Study of environmental PKSs often relies on the construction of metagenomic libraries and their mining, with clones containing PKS clusters identified via amplification of conserved domains and then screened for an activity of interest. Compounds produced by clones exhibiting the desired bioactivity can be isolated and characterized. However, these approaches can be less sensitive and biased against more divergent clusters, in addition to precluding the use of bioinformatics for cluster characterization prior to expression. While direct shotgun sequencing of metagenomes has identified and profiled a great number of PKSs from different environments and yet-to-be cultured microorganisms, it does not lend itself well to heterologous expression, the cruxes of natural product discovery.Here, we describe a strategy for sequencing entire metagenomic libraries while maintaining correspondence between sequence and clone, allowing the full characterization and annotation of all clusters present in a library using bioinformatic tools and then seamlessly passing clones of interest for activity screening through heterologous expression. Once a library is sequenced, the methods herein can be adapted for the mining of any biosynthetic gene cluster of interest within a metagenomic library.}, } @article {pmid36306078, year = {2023}, author = {Tansirichaiya, S and Hutton, W and Roberts, AP}, title = {Functional and Sequence-Specific Screening Protocols for the Detection of Novel Antimicrobial Resistance Genes in Metagenomic DNA.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {51-72}, pmid = {36306078}, issn = {1940-6029}, support = {MRF_MRF-145-0004-TPG-AVISO/MRF/MRF/United Kingdom ; MR/S004793/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Metagenomics ; *Anti-Infective Agents/pharmacology ; DNA ; }, abstract = {Antimicrobial resistance (AMR) is an increasingly important global challenge for healthcare systems as well as agricultural food production systems. Our ability to prepare for, and respond to, emerging AMR threats is dependent on our knowledge of genes able to confer AMR that are circulating within various environmental, animal, and human microbiomes. Targeted, sequence-specific, detection of AMR genes and functional resistance assays, described here, carried out on metagenomic DNA gives us unique insights into the presence of AMR genes and how these are associated with mobile genetic elements that may be responsible for their dissemination and can also provide important information about the mechanisms of resistance underpinning the phenotype.}, } @article {pmid36306077, year = {2023}, author = {Weiland-Bräuer, N and Saleh, L and Schmitz, RA}, title = {Functional Metagenomics as a Tool to Tap into Natural Diversity of Valuable Biotechnological Compounds.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {23-49}, pmid = {36306077}, issn = {1940-6029}, mesh = {*Ecosystem ; *Metagenomics ; Metagenome ; Biotechnology ; Biodiversity ; }, abstract = {The marine ecosystem covers more than 70% of the world's surface, and oceans represent a source of varied types of organisms due to the diversified environment. Consequently, the marine environment is an exceptional depot of novel bioactive natural products, with structural and chemical features generally not found in terrestrial habitats. Here, in particular, microbes represent a vast source of unknown and probably new physiological characteristics. They have evolved during extended evolutionary processes of physiological adaptations under various environmental conditions and selection pressures. However, to date, the biodiversity of marine microbes and the versatility of their bioactive compounds and metabolites have not been fully explored. Thus, metagenomic tools are required to exploit the untapped marine microbial diversity and their bioactive compounds. This chapter focuses on function-based marine metagenomics to screen for bioactive molecules of value for biotechnology. Functional metagenomic strategies are described, including sampling in the marine environment, constructing marine metagenomic large-insert libraries, and examples on function-based screens for quorum quenching and anti-biofilm activities.}, } @article {pmid36306076, year = {2023}, author = {Hollensteiner, J and Wemheuer, F and Schneider, D and Pfeiffer, B and Wemheuer, B}, title = {Extraction of Total DNA and RNA from Marine Filter Samples and Generation of a Universal cDNA as Universal Template for Marker Gene Studies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {13-21}, pmid = {36306076}, issn = {1940-6029}, mesh = {DNA, Complementary/genetics ; RNA, Ribosomal, 16S/genetics ; *DNA/genetics ; *Microbiota ; Sequence Analysis, DNA ; Metagenomics/methods ; Phylogeny ; }, abstract = {Microbial communities play an important role in marine ecosystem processes. Although the number of studies targeting marker genes such as the 16S rRNA gene has increased during the last years, the vast majority of marine diversity are rather unexplored. Moreover, most studies focused on the entire microbial community and thus do not assess the active fraction of the microbial community. Here, we describe a detailed protocol for the simultaneous extraction of DNA and RNA from marine water samples and the generation of cDNA from the isolated RNA that can be used as a universal template in various marker gene studies.}, } @article {pmid36306075, year = {2023}, author = {Simon, C and Daniel, R}, title = {Construction of Small-Insert and Large-Insert Metagenomic Libraries.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2555}, number = {}, pages = {1-12}, pmid = {36306075}, issn = {1940-6029}, mesh = {Gene Library ; *Metagenomics/methods ; *Metagenome ; Biodiversity ; Plasmids/genetics ; }, abstract = {The vast majority of the Earth's biological diversity are hidden in uncultured and yet uncharacterized microbial genomes. The construction of metagenomic libraries is one cultivation-independent molecular approach to assess this unexplored genetic reservoir. High numbers of novel biocatalysts have been identified by function-based or sequence-based screening of metagenomic libraries derived from various environments. Here, we describe detailed protocols for the construction of metagenomic small-insert and large-insert libraries in plasmids and fosmids, respectively, from environmental DNA.}, } @article {pmid36305829, year = {2023}, author = {Wishart, DS and Girod, S and Peters, H and Oler, E and Jovel, J and Budinski, Z and Milford, R and Lui, VW and Sayeeda, Z and Mah, R and Wei, W and Badran, H and Lo, E and Yamamoto, M and Djoumbou-Feunang, Y and Karu, N and Gautam, V}, title = {ChemFOnt: the chemical functional ontology resource.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D1220-D1229}, pmid = {36305829}, issn = {1362-4962}, mesh = {Databases, Factual ; Gene Ontology ; Genomics ; Proteomics ; *Software ; *Databases, Chemical ; }, abstract = {The Chemical Functional Ontology (ChemFOnt), located at https://www.chemfont.ca, is a hierarchical, OWL-compatible ontology describing the functions and actions of >341 000 biologically important chemicals. These include primary metabolites, secondary metabolites, natural products, food chemicals, synthetic food additives, drugs, herbicides, pesticides and environmental chemicals. ChemFOnt is a FAIR-compliant resource intended to bring the same rigor, standardization and formal structure to the terms and terminology used in biochemistry, food chemistry and environmental chemistry as the gene ontology (GO) has brought to molecular biology. ChemFOnt is available as both a freely accessible, web-enabled database and a downloadable Web Ontology Language (OWL) file. Users may download and deploy ChemFOnt within their own chemical databases or integrate ChemFOnt into their own analytical software to generate machine readable relationships that can be used to make new inferences, enrich their omics data sets or make new, non-obvious connections between chemicals and their direct or indirect effects. The web version of the ChemFOnt database has been designed to be easy to search, browse and navigate. Currently ChemFOnt contains data on 341 627 chemicals, including 515 332 terms or definitions. The functional hierarchy for ChemFOnt consists of four functional 'aspects', 12 functional super-categories and a total of 173 705 functional terms. In addition, each of the chemicals are classified into 4825 structure-based chemical classes. ChemFOnt currently contains 3.9 million protein-chemical relationships and ∼10.3 million chemical-functional relationships. The long-term goal for ChemFOnt is for it to be adopted by databases and software tools used by the general chemistry community as well as the metabolomics, exposomics, metagenomics, genomics and proteomics communities.}, } @article {pmid36305482, year = {2023}, author = {Semmouri, I and Asselman, J}, title = {Allometric scaling improves the characterization of complex community transcriptomes.}, journal = {Molecular ecology resources}, volume = {23}, number = {1}, pages = {10-12}, doi = {10.1111/1755-0998.13727}, pmid = {36305482}, issn = {1755-0998}, mesh = {Humans ; *Transcriptome ; Body Size ; *Ecology ; RNA ; }, abstract = {Allometric scaling, that is scaling patterns in physiological processes relative to body size, can be used to overcome the current limitations in metatranscriptomics. Metatranscriptomics refers to the use of RNA transcripts to characterize a complex community. In contrast to metagenomics, metatranscriptomics allows one to simultaneously address community composition and functionality through the characterization of the community transcriptome. Hence, insights into metabolic processes and molecular pathways can also be obtained. Despite its increasing use in community ecology, a major limitation and source of error is the variation in RNA transcript abundance across organisms varying in body size. Hence, this may lead to incorrect estimations of the community structure and functioning as larger RNA quantities from larger individuals may overestimate their community contribution.}, } @article {pmid36305395, year = {2022}, author = {Ju, Y and Wang, X and Wang, Y and Li, C and Yue, L and Chen, F}, title = {[Application of metagenomic and culturomic technologies in fecal microbiota transplantation: a review].}, journal = {Sheng wu gong cheng xue bao = Chinese journal of biotechnology}, volume = {38}, number = {10}, pages = {3594-3605}, doi = {10.13345/j.cjb.220573}, pmid = {36305395}, issn = {1872-2075}, mesh = {Humans ; *Fecal Microbiota Transplantation ; Metagenomics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Bacteria ; }, abstract = {Fecal microbiota transplantation (FMT) refers to using the intestinal microorganisms present in the feces or processed feces from healthy people for treating various types of diseases, such as digestive and metabolic diseases. The rapid development of metagenomic and culturomic technologies in gut microbiome analysis provides powerful tools for the FMT research and its clinical applications. Metagenomics technologies comprehensively revealed the diversity and functions of gut microbiota under health and disease conditions, while culturomics technologies helped isolation and identification of "unculturable" bacteria in the human gut under conventional culture conditions. The combination of these two technologies not only enabled us better understand the FMT regularities of cause and effect in clinical practices, but also effectively promoted its applications. Considering the above advantages, this article summarized the applications of metagenomics and culturomics technologies in FMT and prospected its future development trend.}, } @article {pmid36304333, year = {2022}, author = {Cremers, G and Jetten, MSM and Op den Camp, HJM and Lücker, S}, title = {Metascan: METabolic Analysis, SCreening and ANnotation of Metagenomes.}, journal = {Frontiers in bioinformatics}, volume = {2}, number = {}, pages = {861505}, pmid = {36304333}, issn = {2673-7647}, abstract = {Large scale next generation metagenomic sequencing of complex environmental samples paves the way for detailed analysis of nutrient cycles in ecosystems. For such an analysis, large scale unequivocal annotation is a prerequisite, which however is increasingly hampered by growing databases and analysis time. Hereto, we created a hidden Markov model (HMM) database by clustering proteins according to their KEGG indexing. HMM profiles for key genes of specific metabolic pathways and nutrient cycles were organized in subsets to be able to analyze each important elemental cycle separately. An important motivation behind the clustered database was to enable a high degree of resolution for annotation, while decreasing database size and analysis time. Here, we present Metascan, a new tool that can fully annotate and analyze deeply sequenced samples with an average analysis time of 11 min per genome for a publicly available dataset containing 2,537 genomes, and 1.1 min per genome for nutrient cycle analysis of the same sample. Metascan easily detected general proteins like cytochromes and ferredoxins, and additional pmoCAB operons were identified that were overlooked in previous analyses. For a mock community, the BEACON (F1) score was 0.72-0.93 compared to the information in NCBI GenBank. In combination with the accompanying database, Metascan provides a fast and useful annotation and analysis tool, as demonstrated by our proof-of-principle analysis of a complex mock community metagenome.}, } @article {pmid36304302, year = {2022}, author = {Czech, L and Stamatakis, A and Dunthorn, M and Barbera, P}, title = {Metagenomic Analysis Using Phylogenetic Placement-A Review of the First Decade.}, journal = {Frontiers in bioinformatics}, volume = {2}, number = {}, pages = {871393}, pmid = {36304302}, issn = {2673-7647}, abstract = {Phylogenetic placement refers to a family of tools and methods to analyze, visualize, and interpret the tsunami of metagenomic sequencing data generated by high-throughput sequencing. Compared to alternative (e. g., similarity-based) methods, it puts metabarcoding sequences into a phylogenetic context using a set of known reference sequences and taking evolutionary history into account. Thereby, one can increase the accuracy of metagenomic surveys and eliminate the requirement for having exact or close matches with existing sequence databases. Phylogenetic placement constitutes a valuable analysis tool per se, but also entails a plethora of downstream tools to interpret its results. A common use case is to analyze species communities obtained from metagenomic sequencing, for example via taxonomic assignment, diversity quantification, sample comparison, and identification of correlations with environmental variables. In this review, we provide an overview over the methods developed during the first 10 years. In particular, the goals of this review are 1) to motivate the usage of phylogenetic placement and illustrate some of its use cases, 2) to outline the full workflow, from raw sequences to publishable figures, including best practices, 3) to introduce the most common tools and methods and their capabilities, 4) to point out common placement pitfalls and misconceptions, 5) to showcase typical placement-based analyses, and how they can help to analyze, visualize, and interpret phylogenetic placement data.}, } @article {pmid36304298, year = {2022}, author = {Karp, PD and Paley, S and Krummenacker, M and Kothari, A and Wannemuehler, MJ and Phillips, GJ}, title = {Pathway Tools Management of Pathway/Genome Data for Microbial Communities.}, journal = {Frontiers in bioinformatics}, volume = {2}, number = {}, pages = {869150}, pmid = {36304298}, issn = {2673-7647}, support = {R01 AI160719/AI/NIAID NIH HHS/United States ; R01 GM080746/GM/NIGMS NIH HHS/United States ; }, abstract = {The Pathway Tools (PTools) software provides a suite of capabilities for storing and analyzing integrated collections of genomic and metabolic information in the form of organism-specific Pathway/Genome Databases (PGDBs). A microbial community is represented in PTools by generating a PGDB from each metagenome-assembled genome (MAG). PTools computes a metabolic reconstruction for each organism, and predicts its operons. The properties of individual MAGs can be investigated using the many search and visualization operations within PTools. PTools also enables the user to investigate the properties of the microbial community by issuing searches across the full community, and by performing comparative operations across genome and pathway information. The software can generate a metabolic network diagram for the community, and it can overlay community omics datasets on that network diagram. PTools also provides a tool for searching for metabolic transformation routes across an organism community.}, } @article {pmid36304297, year = {2022}, author = {Mageeney, CM and Trubl, G and Williams, KP}, title = {Improved Mobilome Delineation in Fragmented Genomes.}, journal = {Frontiers in bioinformatics}, volume = {2}, number = {}, pages = {866850}, pmid = {36304297}, issn = {2673-7647}, abstract = {The mobilome of a microbe, i.e., its set of mobile elements, has major effects on its ecology, and is important to delineate properly in each genome. This becomes more challenging for incomplete genomes, and even more so for metagenome-assembled genomes (MAGs), where misbinning of scaffolds and other losses can occur. Genomic islands (GIs), which integrate into the host chromosome, are a major component of the mobilome. Our GI-detection software TIGER, unique in its precise mapping of GI termini, was applied to 74,561 genomes from 2,473 microbial species, each species containing at least one MAG and one isolate genome. A species-normalized deficit of ∼1.6 GIs/genome was measured for MAGs relative to isolates. To test whether this undercount was due to the higher fragmentation of MAG genomes, TIGER was updated to enable detection of split GIs whose termini are on separate scaffolds or that wrap around the origin of a circular replicon. This doubled GI yields, and the new split GIs matched the quality of single-scaffold GIs, except that highly fragmented GIs may lack central portions. Cross-scaffold search is an important upgrade to GI detection as fragmented genomes increasingly dominate public databases. TIGER2 better captures MAG microdiversity, recovering niche-defining GIs and supporting microbiome research aims such as virus-host linking and ecological assessment.}, } @article {pmid36304283, year = {2022}, author = {Smith, BJ and Li, X and Shi, ZJ and Abate, A and Pollard, KS}, title = {Scalable Microbial Strain Inference in Metagenomic Data Using StrainFacts.}, journal = {Frontiers in bioinformatics}, volume = {2}, number = {}, pages = {867386}, pmid = {36304283}, issn = {2673-7647}, abstract = {While genome databases are nearing a complete catalog of species commonly inhabiting the human gut, their representation of intraspecific diversity is lacking for all but the most abundant and frequently studied taxa. Statistical deconvolution of allele frequencies from shotgun metagenomic data into strain genotypes and relative abundances is a promising approach, but existing methods are limited by computational scalability. Here we introduce StrainFacts, a method for strain deconvolution that enables inference across tens of thousands of metagenomes. We harness a "fuzzy" genotype approximation that makes the underlying graphical model fully differentiable, unlike existing methods. This allows parameter estimates to be optimized with gradient-based methods, speeding up model fitting by two orders of magnitude. A GPU implementation provides additional scalability. Extensive simulations show that StrainFacts can perform strain inference on thousands of metagenomes and has comparable accuracy to more computationally intensive tools. We further validate our strain inferences using single-cell genomic sequencing from a human stool sample. Applying StrainFacts to a collection of more than 10,000 publicly available human stool metagenomes, we quantify patterns of strain diversity, biogeography, and linkage-disequilibrium that agree with and expand on what is known based on existing reference genomes. StrainFacts paves the way for large-scale biogeography and population genetic studies of microbiomes using metagenomic data.}, } @article {pmid36304282, year = {2022}, author = {Saenz, C and Nigro, E and Gunalan, V and Arumugam, M}, title = {MIntO: A Modular and Scalable Pipeline For Microbiome Metagenomic and Metatranscriptomic Data Integration.}, journal = {Frontiers in bioinformatics}, volume = {2}, number = {}, pages = {846922}, pmid = {36304282}, issn = {2673-7647}, abstract = {Omics technologies have revolutionized microbiome research allowing the characterization of complex microbial communities in different biomes without requiring their cultivation. As a consequence, there has been a great increase in the generation of omics data from metagenomes and metatranscriptomes. However, pre-processing and analysis of these data have been limited by the availability of computational resources, bioinformatics expertise and standardized computational workflows to obtain consistent results that are comparable across different studies. Here, we introduce MIntO (Microbiome Integrated meta-Omics), a highly versatile pipeline that integrates metagenomic and metatranscriptomic data in a scalable way. The distinctive feature of this pipeline is the computation of gene expression profile through integrating metagenomic and metatranscriptomic data taking into account the community turnover and gene expression variations to disentangle the mechanisms that shape the metatranscriptome across time and between conditions. The modular design of MIntO enables users to run the pipeline using three available modes based on the input data and the experimental design, including de novo assembly leading to metagenome-assembled genomes. The integrated pipeline will be relevant to provide unique biochemical insights into microbial ecology by linking functions to retrieved genomes and to examine gene expression variation. Functional characterization of community members will be crucial to increase our knowledge of the microbiome's contribution to human health and environment. MIntO v1.0.1 is available at https://github.com/arumugamlab/MIntO.}, } @article {pmid36304272, year = {2022}, author = {Karaoz, U and Brodie, EL}, title = {microTrait: A Toolset for a Trait-Based Representation of Microbial Genomes.}, journal = {Frontiers in bioinformatics}, volume = {2}, number = {}, pages = {918853}, pmid = {36304272}, issn = {2673-7647}, abstract = {Remote sensing approaches have revolutionized the study of macroorganisms, allowing theories of population and community ecology to be tested across increasingly larger scales without much compromise in resolution of biological complexity. In microbial ecology, our remote window into the ecology of microorganisms is through the lens of genome sequencing. For microbial organisms, recent evidence from genomes recovered from metagenomic samples corroborate a highly complex view of their metabolic diversity and other associated traits which map into high physiological complexity. Regardless, during the first decades of this omics era, microbial ecological research has primarily focused on taxa and functional genes as ecological units, favoring breadth of coverage over resolution of biological complexity manifested as physiological diversity. Recently, the rate at which provisional draft genomes are generated has increased substantially, giving new insights into ecological processes and interactions. From a genotype perspective, the wide availability of genome-centric data requires new data synthesis approaches that place organismal genomes center stage in the study of environmental roles and functional performance. Extraction of ecologically relevant traits from microbial genomes will be essential to the future of microbial ecological research. Here, we present microTrait, a computational pipeline that infers and distills ecologically relevant traits from microbial genome sequences. microTrait maps a genome sequence into a trait space, including discrete and continuous traits, as well as simple and composite. Traits are inferred from genes and pathways representing energetic, resource acquisition, and stress tolerance mechanisms, while genome-wide signatures are used to infer composite, or life history, traits of microorganisms. This approach is extensible to any microbial habitat, although we provide initial examples of this approach with reference to soil microbiomes.}, } @article {pmid36304264, year = {2022}, author = {Hsieh, YP and Hung, YM and Tsai, MH and Lai, LC and Chuang, EY}, title = {16S-ITGDB: An Integrated Database for Improving Species Classification of Prokaryotic 16S Ribosomal RNA Sequences.}, journal = {Frontiers in bioinformatics}, volume = {2}, number = {}, pages = {905489}, pmid = {36304264}, issn = {2673-7647}, abstract = {Analyzing 16S ribosomal RNA (rRNA) sequences allows researchers to elucidate the prokaryotic composition of an environment. In recent years, third-generation sequencing technology has provided opportunities for researchers to perform full-length sequence analysis of bacterial 16S rRNA. RDP, SILVA, and Greengenes are the most widely used 16S rRNA databases. Many 16S rRNA classifiers have used these databases as a reference for taxonomic assignment tasks. However, some of the prokaryotic taxonomies only exist in one of the three databases. Furthermore, Greengenes and SILVA include a considerable number of taxonomies that do not have the resolution to the species level, which has limited the classifiers' performance. In order to improve the accuracy of taxonomic assignment at the species level for full-length 16S rRNA sequences, we manually curated the three databases and removed the sequences that did not have a species name. We then established a taxonomy-based integrated database by considering both taxonomies and sequences from all three 16S rRNA databases and validated it by a mock community. Results showed that our taxonomy-based integrated database had improved taxonomic resolution to the species level. The integrated database and the related datasets are available at https://github.com/yphsieh/ItgDB.}, } @article {pmid36303791, year = {2021}, author = {Gerhardt, K and Ruiz-Perez, CA and Rodriguez-R, LM and Conrad, RE and Konstantinidis, KT}, title = {RecruitPlotEasy: An Advanced Read Recruitment Plot Tool for Assessing Metagenomic Population Abundance and Genetic Diversity.}, journal = {Frontiers in bioinformatics}, volume = {1}, number = {}, pages = {826701}, pmid = {36303791}, issn = {2673-7647}, abstract = {Mapping of short metagenomic (or metatranscriptomic) read data to reference isolate or single-cell genomes or metagenome-assembled genomes (MAGs) to assess microbial population relative abundance and/or structure represents an essential task of many studies across environmental and clinical settings. The filtering for the quality of the read match and assessment of read mapping results are frequently performed without visual aids or with the assistance of visualizations produced through ad-hoc, in-house approaches. Here, we introduce RecruitPlotEasy, a fully automated, user-friendly pipeline for these purposes that integrates statistical approaches to quantify intra-population sequence and gene-content diversity and identify co-occurring relative populations in the sample. Hence, RecruitPlotEasy should also greatly facilitate population genetics studies. RecruitPlotEasy is implemented in Python and R languages and is freely available open source software under the Artistic License 2.0 from https://github.com/KGerhardt/RecruitPlotEasy.}, } @article {pmid36303775, year = {2021}, author = {Hu, B and Canon, S and Eloe-Fadrosh, EA and Anubhav, and Babinski, M and Corilo, Y and Davenport, K and Duncan, WD and Fagnan, K and Flynn, M and Foster, B and Hays, D and Huntemann, M and Jackson, EKP and Kelliher, J and Li, PE and Lo, CC and Mans, D and McCue, LA and Mouncey, N and Mungall, CJ and Piehowski, PD and Purvine, SO and Smith, M and Varghese, NJ and Winston, D and Xu, Y and Chain, PSG}, title = {Challenges in Bioinformatics Workflows for Processing Microbiome Omics Data at Scale.}, journal = {Frontiers in bioinformatics}, volume = {1}, number = {}, pages = {826370}, pmid = {36303775}, issn = {2673-7647}, abstract = {The nascent field of microbiome science is transitioning from a descriptive approach of cataloging taxa and functions present in an environment to applying multi-omics methods to investigate microbiome dynamics and function. A large number of new tools and algorithms have been designed and used for very specific purposes on samples collected by individual investigators or groups. While these developments have been quite instructive, the ability to compare microbiome data generated by many groups of researchers is impeded by the lack of standardized application of bioinformatics methods. Additionally, there are few examples of broad bioinformatics workflows that can process metagenome, metatranscriptome, metaproteome and metabolomic data at scale, and no central hub that allows processing, or provides varied omics data that are findable, accessible, interoperable and reusable (FAIR). Here, we review some of the challenges that exist in analyzing omics data within the microbiome research sphere, and provide context on how the National Microbiome Data Collaborative has adopted a standardized and open access approach to address such challenges.}, } @article {pmid36303747, year = {2021}, author = {Salzberg, SL and Wood, DE}, title = {Releasing the Kraken.}, journal = {Frontiers in bioinformatics}, volume = {1}, number = {}, pages = {808003}, pmid = {36303747}, issn = {2673-7647}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; }, abstract = {Ten years ago, the dramatic rise in the number of microbial genomes led to an inflection point, when the approach of finding short, exact matches in a comprehensive database became just as accurate as older, slower approaches. The new idea led to a method that was hundreds of times times faster than those that came before. Today, exact k-mer matching is a standard technique at the heart of many microbiome analysis tools.}, } @article {pmid36303603, year = {2022}, author = {Dong, Y and Wang, P and Yang, X and Chen, M and Li, J}, title = {Potential of gut microbiota for lipopolysaccharide biosynthesis in European women with type 2 diabetes based on metagenome.}, journal = {Frontiers in cell and developmental biology}, volume = {10}, number = {}, pages = {1027413}, pmid = {36303603}, issn = {2296-634X}, abstract = {The abnormal accumulation of lipopolysaccharide (LPS) plays a crucial role in promoting type 2 diabetes (T2D). However, the capability of the gut microbiota to produce LPS in patients with T2D is still unclear, and evidence characterizing the patterns of gut microbiota with LPS productivity remains rare. This study aimed to uncover the profiles of LPS-biosynthesis-related enzymes and pathways, and explore the potential of LPS-producing gut microbiota in T2D. The gut metagenomic sequencing data from a European female cohort with normal glucose tolerance or untreated T2D were analyzed in this study. The sequence search revealed that the relative abundance of the critical enzymes responsible for LPS biosynthesis was significantly high in patients with T2D, especially for N-acetylglucosamine deacetylase, 3-deoxy-D-manno-octulosonic-acid transferase, and lauroyl-Kdo2-lipid IVA myristoyltransferase. The functional analysis indicated that a majority of pathways involved in LPS biosynthesis were augmented in patients with T2D. A total of 1,173 species from 335 genera containing the gene sequences of LPS enzymes, including LpxA/B/C/D/H/K/L/M and/or WaaA, coexisted in controls and patients with T2D. Critical taxonomies with discriminative fecal abundance between groups were revealed, which exhibited different associations with enzymes. Moreover, the identified gut microbial markers had correlations with LPS enzymes and were subsequently associated with microbial pathways. The present findings delineated the potential capability of gut microbiota toward LPS biosynthesis in European women and highlighted a gut microbiota-based mechanistic link between the disturbance in LPS biosynthesis and T2D. The restoration of LPS levels through gut microbiota manipulation might offer potential approaches for preventing and treating T2D.}, } @article {pmid36302955, year = {2023}, author = {Uzun, M and Koziaeva, V and Dziuba, M and Alekseeva, L and Krutkina, M and Sukhacheva, M and Baslerov, R and Grouzdev, D}, title = {Recovery and genome reconstruction of novel magnetotactic Elusimicrobiota from bog soil.}, journal = {The ISME journal}, volume = {17}, number = {2}, pages = {204-214}, pmid = {36302955}, issn = {1751-7370}, support = {20-34-90116//Russian Foundation for Basic Research (RFBR)/ ; }, mesh = {*Wetlands ; Bacteria/genetics/metabolism ; *Magnetosomes ; Genome, Bacterial ; Gram-Negative Bacteria/genetics ; }, abstract = {Studying the minor part of the uncultivated microbial majority ("rare biosphere") is difficult even with modern culture-independent techniques. The enormity of microbial diversity creates particular challenges for investigating low-abundance microbial populations in soils. Strategies for selective sample enrichment to reduce community complexity can aid in studying the rare biosphere. Magnetotactic bacteria, apart from being a minor part of the microbial community, are also found in poorly studied bacterial phyla and certainly belong to a rare biosphere. The presence of intracellular magnetic crystals within magnetotactic bacteria allows for their significant enrichment using magnetic separation techniques for studies using a metagenomic approach. This work investigated the microbial diversity of a black bog soil and its magnetically enriched fraction. The poorly studied phylum representatives in the magnetic fraction were enriched compared to the original soil community. Two new magnetotactic species, Candidatus Liberimonas magnetica DUR002 and Candidatus Obscuribacterium magneticum DUR003, belonging to different classes of the relatively little-studied phylum Elusimicrobiota, were proposed. Their genomes contain clusters of magnetosome genes that differ from the previously described ones by the absence of genes encoding magnetochrome-containing proteins and the presence of unique Elusimicrobiota-specific genes, termed mae. The predicted obligately fermentative metabolism in DUR002 and lack of flagellar motility in the magnetotactic Elusimicrobiota broadens our understanding of the lifestyles of magnetotactic bacteria and raises new questions about the evolutionary advantages of magnetotaxis. The findings presented here increase our understanding of magnetotactic bacteria, soil microbial communities, and the rare biosphere.}, } @article {pmid36302811, year = {2022}, author = {Aalam, SMM and Crasta, DN and Roy, P and Miller, AL and Gamb, SI and Johnson, S and Till, LM and Chen, J and Kashyap, P and Kannan, N}, title = {Genesis of fecal floatation is causally linked to gut microbial colonization in mice.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {18109}, pmid = {36302811}, issn = {2045-2322}, support = {P30 DK084567/DK/NIDDK NIH HHS/United States ; R01 DK114007/DK/NIDDK NIH HHS/United States ; }, mesh = {Mice ; Humans ; Animals ; *Gastrointestinal Microbiome ; Feces/microbiology ; Fecal Microbiota Transplantation ; Metagenomics ; Bacteria/genetics ; }, abstract = {The origin of fecal floatation phenomenon remains poorly understood. Following our serendipitous discovery of differences in buoyancy of feces from germ-free and conventional mice, we characterized microbial and physical properties of feces from germ-free and gut-colonized (conventional and conventionalized) mice. The gut-colonization associated differences were assessed in feces using DNA, bacterial-PCR, scanning electron microscopy, FACS, thermogravimetry and pycnometry. Based on the differences in buoyancy of feces, we developed levô in fimo test (LIFT) to distinguish sinking feces (sinkers) of germ-free mice from floating feces (floaters) of gut-colonized mice. By simultaneous tracking of microbiota densities and gut colonization kinetics in fecal transplanted mice, we provide first direct evidence of causal relationship between gut microbial colonization and fecal floatation. Rare discordance in LIFT and microbiota density indicated that enrichment of gasogenic gut colonizers may be necessary for fecal floatation. Finally, fecal metagenomics analysis of 'floaters' from conventional and syngeneic fecal transplanted mice identified colonization of > 10 gasogenic bacterial species including highly prevalent B. ovatus, an anaerobic commensal bacteria linked with flatulence and intestinal bowel diseases. The findings reported here will improve our understanding of food microbial biotransformation and gut microbial regulators of fecal floatation in human health and disease.}, } @article {pmid36302709, year = {2023}, author = {Valyraki, N and Maillart, E and Pourcher, V and Shor, N and Tran, S and Boudot de la Motte, M and Houillier, C and Domont, F and Morvan, E and Touat, M and Del Mar Amador, M and Aboab, J and Mathon, B and Hesters, A and Vignal-Clermont, C and Dehais, C and Bonnin, S and Lafitte, F and Villain, N and Varnous, S and Gout, O and Eloit, M and Rodriguez, C and Deschamps, R}, title = {Human pegivirus identified in severe myelitis and optic neuritis in immunocompromised patients: A pathogenic role for a forgotten virus?.}, journal = {Revue neurologique}, volume = {179}, number = {4}, pages = {361-367}, doi = {10.1016/j.neurol.2022.06.011}, pmid = {36302709}, issn = {0035-3787}, mesh = {Humans ; Pegivirus ; *Myelitis/diagnosis/etiology ; *Optic Neuritis ; *Encephalitis ; Immunocompromised Host ; }, abstract = {The role of Human pegivirus (HPgV) in patients with encephalitis has been recently questioned. We present cases of 4 patients with similar clinical, biological, and radiological characteristics, including a past history of transplantation with long-term immunosuppression and a progressive course of severe and predominantly myelitis, associated in 3 cases with optic neuropathy causing blindness. Extensive workup was negative but analysis of the CSF by use of pan-microorganism DNA- and RNA-based shotgun metagenomics was positive for HPgV. This case series further supports the hypothesis of HPgV CNS infection and highlights the utility of metagenomic next-generation sequencing of CSF in immunocompromised patients.}, } @article {pmid36302646, year = {2022}, author = {Kim, YT and Jeong, J and Mun, S and Yun, K and Han, K and Jeong, SN}, title = {Comparison of the oral microbial composition between healthy individuals and periodontitis patients in different oral sampling sites using 16S metagenome profiling.}, journal = {Journal of periodontal & implant science}, volume = {52}, number = {5}, pages = {394-410}, pmid = {36302646}, issn = {2093-2278}, support = {//Wonkwang University/Korea ; }, abstract = {PURPOSE: The purpose of this study was to compare the microbial composition of 3 types of oral samples through 16S metagenomic sequencing to determine how to resolve some sampling issues that occur during the collection of sub-gingival plaque samples.

METHODS: In total, 20 subjects were recruited. In both the healthy and periodontitis groups, samples of saliva and supra-gingival plaque were collected. Additionally, in the periodontitis group, sub-gingival plaque samples were collected from the deepest periodontal pocket. After DNA extraction from each sample, polymerase chain reaction amplification was performed on the V3-V4 hypervariable region on the 16S rRNA gene, followed by metagenomic sequencing and a bioinformatics analysis.

RESULTS: When comparing the healthy and periodontitis groups in terms of alpha-diversity, the saliva samples demonstrated much more substantial differences in bacterial diversity than the supra-gingival plaque samples. Moreover, in a comparison between the samples in the case group, the diversity score of the saliva samples was higher than that of the supra-gingival plaque samples, and it was similar to that of the sub-gingival plaque samples. In the beta-diversity analysis, the sub-gingival plaque samples exhibited a clustering pattern similar to that of the periodontitis group. Bacterial relative abundance analysis at the species level indicated lower relative frequencies of bacteria in the healthy group than in the periodontitis group. A statistically significant difference in frequency was observed in the saliva samples for specific pathogenic species (Porphyromonas gingivalis, Treponema denticola, and Prevotella intermedia). The saliva samples exhibited a similar relative richness of bacterial communities to that of sub-gingival plaque samples.

CONCLUSIONS: In this 16S oral microbiome study, we confirmed that saliva samples had a microbial composition that was more similar to that of sub-gingival plaque samples than to that of supra-gingival plaque samples within the periodontitis group.}, } @article {pmid36302093, year = {2022}, author = {Joublin-Delavat, A and Touahri, K and Crétin, P and Morot, A and Rodrigues, S and Jesus, B and Trigodet, F and Delavat, F}, title = {Genetic and physiological insights into the diazotrophic activity of a non-cyanobacterial marine diazotroph.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {6510-6523}, pmid = {36302093}, issn = {1462-2920}, mesh = {Humans ; Nitrogen Fixation/genetics ; *Noncommunicable Diseases ; *Cyanobacteria/genetics ; Oceans and Seas ; Nitrogen ; }, abstract = {Nitrogen (N2) fixation, or diazotrophy, supports a large part of primary production in oceans. Culture-independent approaches highlighted the presence in abundance of marine non-cyanobacterial diazotrophs (NCD), but their ecophysiology remains elusive, mostly because of the low number of isolated NCD and because of the lack of available genetic tools for these isolates. Here, a dual genetic and functional approach allowed unveiling the ecophysiology of a marine NCD affiliated to the species Vibrio diazotrophicus. Physiological characterization of the first marine NCD mutant obtained so far was performed using a soft-gellan assay, demonstrating that a ΔnifH mutant is not able to grow in nitrogen-free media. Furthermore, we demonstrated that V. diazotrophicus produces a thick biofilm under diazotrophic conditions, suggesting biofilm production as an adaptive response of this NCD to cope with the inhibition of nitrogen fixation by molecular oxygen. Finally, the genomic signature of V. diazotrophicus is essentially absent from metagenomic data of Tara Ocean expeditions, despite having been isolated from various marine environments. We think that the genetically tractable V. diazotrophicus strain used in this study may serve as an ideal model to study the ecophysiology of these overlooked procaryotic group.}, } @article {pmid36302091, year = {2022}, author = {Le Gac, M and Mary, L and Metegnier, G and Quéré, J and Siano, R and Rodríguez, F and Destombe, C and Sourisseau, M}, title = {Strong population genomic structure of the toxic dinoflagellate Alexandrium minutum inferred from meta-transcriptome samples.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {5966-5983}, doi = {10.1111/1462-2920.16257}, pmid = {36302091}, issn = {1462-2920}, mesh = {*Dinoflagellida/genetics ; Transcriptome ; Metagenomics ; Gene Flow ; Population Density ; }, abstract = {Despite theoretical expectations, marine microeukaryote population are often highly structured and the mechanisms behind such patterns remain to be elucidated. These organisms display huge census population sizes, yet genotyping usually requires clonal strains originating from single cells, hindering proper population sampling. Estimating allelic frequency directly from population wide samples, without any isolation step, offers an interesting alternative. Here, we validate the use of meta-transcriptome environmental samples to determine the population genetic structure of the dinoflagellate Alexandrium minutum. Strain and meta-transcriptome based results both indicated a strong genetic structure for A. minutum in Western Europe, to the level expected between cryptic species. The presence of numerous private alleles, and even fixed polymorphism, would indicate ancient divergence and absence of gene flow between populations. Single nucleotide polymorphisms (SNPs) displaying strong allele frequency differences were distributed throughout the genome, which might indicate pervasive selection from standing genetic variation (soft selective sweeps). However, a few genomic regions displayed extremely low diversity that could result from the fixation of adaptive de novo mutations (hard selective sweeps) within the populations.}, } @article {pmid36301254, year = {2023}, author = {Safari-Alighiarloo, N and Emami, Z and Rezaei-Tavirani, M and Alaei-Shahmiri, F and Razavi, S}, title = {Gut Microbiota and Their Associated Metabolites in Diabetes: A Cross Talk Between Host and Microbes-A Review.}, journal = {Metabolic syndrome and related disorders}, volume = {21}, number = {1}, pages = {3-15}, doi = {10.1089/met.2022.0049}, pmid = {36301254}, issn = {1557-8518}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Diabetes Mellitus, Type 2 ; Dysbiosis ; Metabolomics/methods ; Metabolome ; }, abstract = {Dysbiosis of the gut microbiota's composition and function is important in developing insulin resistance and diabetes. Diabetes has also been linked to changes in the circulating and fecal metabolites. Evidence suggests the associations between the gut microbiota and the aberrant diabetes-related metabolome. Metabolites play a crucial role in the host-microbiota interactions. Researchers have used a combination of metagenomic and metabolomic approaches to investigate the relationships between gut microbial dysbiosis and metabolic abnormalities in diabetes. We summarized current discoveries on the associations between the gut microbiota and metabolites in type 1 diabetes, type 2 diabetes, and gestational diabetes mellitus in the scoping review. According to research, the gut microbiota changes might involve in the development of diabetes through modulating the host's metabolic pathways such as immunity, energy metabolism, lipid metabolism, and amino acid metabolism. These results add to our understanding of the interplay between the host and gut microbiota metabolism.}, } @article {pmid36301116, year = {2022}, author = {Nishioka, T and Tamaki, H}, title = {Improved Cultivation and Isolation of Diverse Endophytic Bacteria Inhabiting Dendrobium Roots by Using Simply Modified Agar Media.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0223822}, pmid = {36301116}, issn = {2165-0497}, mesh = {*Dendrobium/genetics/microbiology ; Agar ; RNA, Ribosomal, 16S/genetics ; Endophytes/genetics ; Culture Media ; Bacteria ; Phylogeny ; }, abstract = {Dendrobium plants are members of the family Orchidaceae, many of which are endangered orchids with ornamental and medicinal values. Dendrobium endophytic microbes have attracted attention for the development of strategies for plant protection and utilization of medicinal principles. However, the role of endophytic bacteria is poorly elucidated due to the lack of their successful cultivation. This study obtained a total of 749 endophytic isolates from Dendrobium roots using solid media prepared by simply modified methods (separate sterilization of phosphate and agar [PS] and use of gellan gum as a gelling reagent [GG]) and by a conventional method of autoclaving the phosphate and agar together (PT method). Notably, based on a comparison of 16S rRNA gene sequences between the isolates and the Dendrobium root endophyte community, we successfully retrieved more than 50% (17 out of 30) of the predominant endophytic bacterial operational taxonomic units (OTUs) using PS and GG media, which is a much higher recovery rate than that of PT medium (16.7%). We further found that a number of recalcitrant bacteria, including phylogenetically novel isolates and members of even the rarely cultivated phyla Acidobacteriota and Verrucomicrobiota, were obtained only when using PS and/or GG medium. Intriguingly, the majority of these recalcitrant bacteria formed colonies faster on PS or GG medium than on PT medium, which may have contributed to their successful isolation. Taken together, this study succeeded in isolating a wide variety of Dendrobium endophytic bacteria, including predominant ones using PS and GG media, and enables performance of future studies to clarify their unknown roles associated with the growth of Dendrobium plants. IMPORTANCE Dendrobium endophytic bacteria are of great interest since their functions may contribute to the protection of endangered orchids with ornamental and medicinal values. To understand and reveal the "true roles" of the endophytes, obtaining those axenic cultures is necessary even in the metagenomic era. However, no effective methods for isolating a variety of endophytic bacteria have been established. This study first demonstrated that the use of simply modified medium is quite effective and indeed allows the isolation of more than half of the predominant endophytic bacteria inhabiting Dendrobium roots. Besides, even phylogenetically novel and/or recalcitrant endophytic bacteria were successfully obtained by the same strategy. The obtained endophytic bacteria could serve as "living material" for elucidating their unprecedented functions related to the conservation of endangered orchid plants. Furthermore, the culture method used in this study may enable the isolation of various endophytic bacteria dominating not only in orchid plants but also in other useful plants.}, } @article {pmid36301097, year = {2022}, author = {Mandro, JA and Nakamura, FM and Gontijo, JB and Tsai, SM and Venturini, AM}, title = {Metagenome-Assembled Genomes from Amazonian Soil Microbial Consortia.}, journal = {Microbiology resource announcements}, volume = {11}, number = {11}, pages = {e0080422}, pmid = {36301097}, issn = {2576-098X}, support = {130292/2019-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 140032/2015-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; 311008/2016-0//Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; 2014/50320-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2015/12282-6//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2015/23758-1//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2018/14974-0//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; 2019/25931-3//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; Fung Global Fellows Program//Princeton University | Princeton Institute for International and Regional Studies (PIIRS)/ ; }, abstract = {Here, we report 17 metagenome-assembled genomes (MAGs) recovered from microbial consortia of forest and pasture soils in the Brazilian Eastern Amazon. The bacterial MAGs have the potential to act in important ecological processes, including carbohydrate degradation and sulfur and nitrogen cycling.}, } @article {pmid36301086, year = {2022}, author = {Biggel, M and Horlbog, J and Nüesch-Inderbinen, M and Chattaway, MA and Stephan, R}, title = {Epidemiological links and antimicrobial resistance of clinical Salmonella enterica ST198 isolates: a nationwide microbial population genomic study in Switzerland.}, journal = {Microbial genomics}, volume = {8}, number = {10}, pages = {}, pmid = {36301086}, issn = {2057-5858}, mesh = {Humans ; *Salmonella enterica ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; Microbial Sensitivity Tests ; Switzerland/epidemiology ; Metagenomics ; Drug Resistance, Bacterial/genetics ; Ciprofloxacin/pharmacology ; Genomics ; *Anti-Infective Agents/pharmacology ; }, abstract = {Salmonella is a leading cause of foodborne outbreaks and systemic infections worldwide. Emerging multi-drug resistant Salmonella lineages such as a ciprofloxacin-resistant subclade (CIP[R]) within Salmonella enterica serovar Kentucky ST198 threaten the effective prevention and treatment of infections. To understand the genomic diversity and antimicrobial resistance gene content associated with S. Kentucky in Switzerland, we whole-genome sequenced 70 human clinical isolates obtained between 2010 and 2020. Most isolates belonged to ST198-CIP[R]. High- and low-level ciprofloxacin resistance among CIP[R] isolates was associated with variable mutations in ramR and acrB in combination with stable mutations in quinolone-resistance determining regions (QRDRs). Analysis of isolates from patients with prolonged ST198 colonization indicated subclonal adaptions with the ramR locus as a mutational hotspot. SNP analyses identified multiple clusters of near-identical isolates, which were often associated with travel but included spatiotemporally linked isolates from Switzerland. The largest SNP cluster was associated with travellers returning from Indonesia, and investigation of global data linked >60 additional ST198 salmonellosis isolates to this cluster. Our results emphasize the urgent need for implementing whole-genome sequencing as a routine tool for Salmonella surveillance and outbreak detection.}, } @article {pmid36300946, year = {2022}, author = {Greenlon, A and Sieradzki, E and Zablocki, O and Koch, BJ and Foley, MM and Kimbrel, JA and Hungate, BA and Blazewicz, SJ and Nuccio, EE and Sun, CL and Chew, A and Mancilla, CJ and Sullivan, MB and Firestone, M and Pett-Ridge, J and Banfield, JF}, title = {Quantitative Stable-Isotope Probing (qSIP) with Metagenomics Links Microbial Physiology and Activity to Soil Moisture in Mediterranean-Climate Grassland Ecosystems.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0041722}, pmid = {36300946}, issn = {2379-5077}, mesh = {*Ecosystem ; *Soil Microbiology ; Grassland ; Soil/chemistry ; Carbon/metabolism ; Bacteria/genetics ; Isotopes/metabolism ; DNA/metabolism ; }, abstract = {The growth and physiology of soil microorganisms, which play vital roles in biogeochemical cycling, are shaped by both current and historical soil environmental conditions. Here, we developed and applied a genome-resolved metagenomic implementation of quantitative stable isotope probing (qSIP) with an H2[18]O labeling experiment to identify actively growing soil microorganisms and their genomic capacities. qSIP enabled measurement of taxon-specific growth because isotopic incorporation into microbial DNA requires production of new genome copies. We studied three Mediterranean grassland soils across a rainfall gradient to evaluate the hypothesis that historic precipitation levels are an important factor controlling trait selection. We used qSIP-informed genome-resolved metagenomics to resolve the active subset of soil community members and identify their characteristic ecophysiological traits. Higher year-round precipitation levels correlated with higher activity and growth rates of flagellar motile microorganisms. In addition to heavily isotopically labeled bacteria, we identified abundant isotope-labeled phages, suggesting phage-induced cell lysis likely contributed to necromass production at all three sites. Further, there was a positive correlation between phage activity and the activity of putative phage hosts. Contrary to our expectations, the capacity to decompose the diverse complex carbohydrates common in soil organic matter or oxidize methanol and carbon monoxide were broadly distributed across active and inactive bacteria in all three soils, implying that these traits are not highly selected for by historical precipitation. IMPORTANCE Soil moisture is a critical factor that strongly shapes the lifestyle of soil organisms by changing access to nutrients, controlling oxygen diffusion, and regulating the potential for mobility. We identified active microorganisms in three grassland soils with similar mineral contexts, yet different historic rainfall inputs, by adding water labeled with a stable isotope and tracking that isotope in DNA of growing microbes. By examining the genomes of active and inactive microorganisms, we identified functions that are enriched in growing organisms, and showed that different functions were selected for in different soils. Wetter soil had higher activity of motile organisms, but activity of pathways for degradation of soil organic carbon compounds, including simple carbon substrates, were comparable for all three soils. We identified many labeled, and thus active bacteriophages (viruses that infect bacteria), implying that the cells they killed contributed to soil organic matter. The activity of these bacteriophages was significantly correlated with activity of their hosts.}, } @article {pmid36300928, year = {2022}, author = {Chen, J and Zeng, P and Gong, L and Zhang, X and Ling, Z and Bi, K and Shi, F and Wang, K and Zhang, Q and Jiang, J and Zhang, Y and Uede, T and El-Omar, EM and Diao, H}, title = {Osteopontin Exacerbates High-Fat Diet-Induced Metabolic Disorders in a Microbiome-Dependent Manner.}, journal = {mBio}, volume = {13}, number = {6}, pages = {e0253122}, pmid = {36300928}, issn = {2150-7511}, mesh = {Animals ; Humans ; Mice ; Diet, High-Fat ; *Gastrointestinal Microbiome ; *Metabolic Diseases ; Mice, Inbred C57BL ; Obesity ; Osteopontin/pharmacology/therapeutic use ; Microbiota ; }, abstract = {The gut microbiome is involved in metabolic disorders. Osteopontin (OPN), as a key cytokine, contributes to various inflammation-related diseases. The underlying role of OPN in the microbiome remains poorly understood. Here, we investigated whether OPN could modulate metabolic disorders by affecting gut microbiota. In our present study, we found that the expression of OPN was elevated in individuals with obesity compared to that observed in healthy controls. There was a positive correlation between plasma OPN levels and body mass index (BMI) in humans. Moreover, OPN significantly exacerbated lipid accumulation and metabolic disorders in high-fat diet (HFD)-fed mice. Importantly, OPN significantly aggravated HFD-induced gut dysbiosis with a key signature profile. Fecal microbiota transplantation also supported the role of OPN in HFD-induced metabolic disorders in a microbiota-dependent manner. Moreover, the microbiome shift of OPN-deficient mice would be compensated to resemble those of wild-type mice by feeding with either OPN-containing milk or recombinant OPN protein in vivo. Furthermore, metagenomic analysis showed that OPN induced a higher abundance of Dorea and a lower abundance of Lactobacillus, which were positively and negatively correlated with body weight, respectively. Indeed, the abundance of Dorea was significantly decreased after Lactobacillus administration, suggesting that OPN may regulate the intestinal abundance of Dorea by reducing the colonization of Lactobacillus. We further confirmed that OPN decreased the adhesion of Lactobacillus to intestinal epithelial cells through the Notch signaling pathway. This study suggested that OPN could exacerbate HFD-induced metabolic dysfunctions through the OPN-induced alteration of the gut microbiome. Therefore, OPN could be a potential therapeutic target for metabolic syndrome. IMPORTANCE Gut microbiota are involved in metabolic disorders. However, microbiome-based therapeutic interventions are not always effective, which might be due to interference of the host factors. Here, we identified a strong positive correlation between OPN levels and BMI in humans. Next, we confirmed that OPN could aggravate high-fat diet-induced metabolic disorders in mice. Importantly, we found that fecal microbiota transplantation from OPN-deficient mice significantly alleviated metabolic disorders in WT mice. OPN directly induces the remodeling of the gut microbiota both in vitro and in vivo. These findings indicate that OPN could contribute to metabolic disorders by inducing an alteration of gut microbiota. OPN regulated the relative abundance of Lactobacillus by decreasing the adhesion of Lactobacillus to intestinal epithelial cells through the Notch signaling pathway. These data identify OPN as a potential pharmaceutical target for weight control and for the treatment of metabolic disorders.}, } @article {pmid36299999, year = {2022}, author = {Ryon, KA and Tierney, BT and Frolova, A and Kahles, A and Desnues, C and Ouzounis, C and Gibas, C and Bezdan, D and Deng, Y and He, D and Dias-Neto, E and Elhaik, E and Afshin, E and Grills, G and Iraola, G and Suzuki, H and Werner, J and Udekwu, K and Schriml, L and Bhattacharyya, M and Oliveira, M and Zambrano, MM and Hazrin-Chong, NH and Osuolale, O and Łabaj, PP and Tiasse, P and Rapuri, S and Borras, S and Pozdniakova, S and Shi, T and Sezerman, U and Rodo, X and Sezer, ZH and Mason, CE}, title = {A history of the MetaSUB consortium: Tracking urban microbes around the globe.}, journal = {iScience}, volume = {25}, number = {11}, pages = {104993}, pmid = {36299999}, issn = {2589-0042}, support = {P20 GM103466/GM/NIGMS NIH HHS/United States ; }, abstract = {The MetaSUB Consortium, founded in 2015, is a global consortium with an interdisciplinary team of clinicians, scientists, bioinformaticians, engineers, and designers, with members from more than 100 countries across the globe. This network has continually collected samples from urban and rural sites including subways and transit systems, sewage systems, hospitals, and other environmental sampling. These collections have been ongoing since 2015 and have continued when possible, even throughout the COVID-19 pandemic. The consortium has optimized their workflow for the collection, isolation, and sequencing of DNA and RNA collected from these various sites and processing them for metagenomics analysis, including the identification of SARS-CoV-2 and its variants. Here, the Consortium describes its foundations, and its ongoing work to expand on this network and to focus its scope on the mapping, annotation, and prediction of emerging pathogens, mapping microbial evolution and antibiotic resistance, and the discovery of novel organisms and biosynthetic gene clusters.}, } @article {pmid36299728, year = {2022}, author = {Colmant, AMG and Charrel, RN and Coutard, B}, title = {Jingmenviruses: Ubiquitous, understudied, segmented flavi-like viruses.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {997058}, pmid = {36299728}, issn = {1664-302X}, abstract = {Jingmenviruses are a group of viruses identified recently, in 2014, and currently classified by the International Committee on Taxonomy of Viruses as unclassified Flaviviridae. These viruses closely related to flaviviruses are unique due to the segmented nature of their genome. The prototype jingmenvirus, Jingmen tick virus (JMTV), was discovered in Rhipicephalus microplus ticks collected from China in 2010. Jingmenviruses genomes are composed of four to five segments, encoding for up to seven structural proteins and two non-structural proteins, both of which display strong similarities with flaviviral non-structural proteins (NS2B/NS3 and NS5). Jingmenviruses are currently separated into two phylogenetic clades. One clade includes tick- and vertebrate-associated jingmenviruses, which have been detected in ticks and mosquitoes, as well as in humans, cattle, monkeys, bats, rodents, sheep, and tortoises. In addition to these molecular and serological detections, over a hundred human patients tested positive for jingmenviruses after developing febrile illness and flu-like symptoms in China and Serbia. The second phylogenetic clade includes insect-associated jingmenvirus sequences, which have been detected in a wide range of insect species, as well as in crustaceans, plants, and fungi. In addition to being found in various types of hosts, jingmenviruses are endemic, as they have been detected in a wide range of environments, all over the world. Taken together, all of these elements show that jingmenviruses correspond exactly to the definition of emerging viruses at risk of causing a pandemic, since they are already endemic, have a close association with arthropods, are found in animals in close contact with humans, and have caused sporadic cases of febrile illness in multiple patients. Despite these arguments, the vast majority of published data is from metagenomics studies and many aspects of jingmenvirus replication remain to be elucidated, such as their tropism, cycle of transmission, structure, and mechanisms of replication and restriction or epidemiology. It is therefore crucial to prioritize jingmenvirus research in the years to come, to be prepared for their emergence as human or veterinary pathogens.}, } @article {pmid36299622, year = {2022}, author = {Gao, Y and Sohn, MB and Wang, J}, title = {Editorial: Gut virome and human health.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1043256}, pmid = {36299622}, issn = {2235-2988}, mesh = {Humans ; *Virome ; Metagenomics ; *Viruses/genetics ; }, } @article {pmid36299531, year = {2022}, author = {Horiba, K and Torii, Y and Aizawa, Y and Yamaguchi, M and Haruta, K and Okumura, T and Suzuki, T and Kawano, Y and Kawada, JI and Hara, S and Saitoh, A and Giske, CG and Ogi, T and Ito, Y}, title = {Performance of Nanopore and Illumina Metagenomic Sequencing for Pathogen Detection and Transcriptome Analysis in Infantile Central Nervous System Infections.}, journal = {Open forum infectious diseases}, volume = {9}, number = {10}, pages = {ofac504}, pmid = {36299531}, issn = {2328-8957}, abstract = {BACKGROUND: Infantile central nervous system infections (CNSIs) can be life-threatening and cause severe sequelae. However, the causative microorganism remains unknown in >40% of patients with aseptic infections. This study aimed to analyze the metagenome for detection of pathogens and the transcriptome for host immune responses during infection in a single cerebrospinal fluid (CSF) sample using 2 different next-generation sequencing (NGS) platforms, Nanopore and Illumina.

METHODS: Twenty-eight CNSIs patients (<12 months) were enrolled, and 49 clinical samples (28 CSF and 21 blood) were collected. The DNA extracted from all 49 samples was sequenced using the Illumina sequencer for the detection of pathogens. Extracted RNA was obtained in sufficient quantities from 23 CSF samples and subjected to sequencing on both Nanopore and Illumina platforms. Human-derived reads subtracted during pathogen detection were used for host transcriptomic analysis from both Nanopore and Illumina sequencing.

RESULTS: RNA metagenomic sequencing using both sequencing platforms revealed putative viral pathogens in 10 cases. DNA sequencing using the Illumina sequencer detected 2 pathogens. The results of Nanopore and Illumina RNA sequencing were consistent; however, the mapping coverage and depth to the detected pathogen genome of Nanopore RNA sequencing were greater than those of Illumina. Host transcriptomic analysis of Nanopore sequencing revealed highly expressed genes related to the antiviral roles of innate immunity from pathogen-identified cases.

CONCLUSIONS: The use of Nanopore RNA sequencing for metagenomic diagnostics of CSF samples should help to elucidate both pathogens and host immune responses of CNSI and could shed light on the pathogenesis of these infections.}, } @article {pmid36299420, year = {2023}, author = {Chen, NFG and Chaguza, C and Gagne, L and Doucette, M and Smole, S and Buzby, E and Hall, J and Ash, S and Harrington, R and Cofsky, S and Clancy, S and Kapsak, CJ and Sevinsky, J and Libuit, K and Park, DJ and Hemarajata, P and Garrigues, JM and Green, NM and Sierra-Patev, S and Carpenter-Azevedo, K and Huard, RC and Pearson, C and Incekara, K and Nishimura, C and Huang, JP and Gagnon, E and Reever, E and Razeq, J and Muyombwe, A and Borges, V and Ferreira, R and Sobral, D and Duarte, S and Santos, D and Vieira, L and Gomes, JP and Aquino, C and Savino, IM and Felton, K and Bajwa, M and Hayward, N and Miller, H and Naumann, A and Allman, R and Greer, N and Fall, A and Mostafa, HH and McHugh, MP and Maloney, DM and Dewar, R and Kenicer, J and Parker, A and Mathers, K and Wild, J and Cotton, S and Templeton, KE and Churchwell, G and Lee, PA and Pedrosa, M and McGruder, B and Schmedes, S and Plumb, MR and Wang, X and Barcellos, RB and Godinho, FMS and Salvato, RS and Ceniseros, A and Breban, MI and Grubaugh, ND and Gallagher, GR and Vogels, CBF}, title = {Development of an amplicon-based sequencing approach in response to the global emergence of human monkeypox virus.}, journal = {medRxiv : the preprint server for health sciences}, volume = {}, number = {}, pages = {}, pmid = {36299420}, support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; }, abstract = {The 2022 multi-country monkeypox (mpox) outbreak concurrent with the ongoing COVID-19 pandemic has further highlighted the need for genomic surveillance and rapid pathogen whole genome sequencing. While metagenomic sequencing approaches have been used to sequence many of the early mpox infections, these methods are resource intensive and require samples with high viral DNA concentrations. Given the atypical clinical presentation of cases associated with the outbreak and uncertainty regarding viral load across both the course of infection and anatomical body sites, there was an urgent need for a more sensitive and broadly applicable sequencing approach. Highly multiplexed amplicon-based sequencing (PrimalSeq) was initially developed for sequencing of Zika virus, and later adapted as the main sequencing approach for SARS-CoV-2. Here, we used PrimalScheme to develop a primer scheme for human monkeypox virus that can be used with many sequencing and bioinformatics pipelines implemented in public health laboratories during the COVID-19 pandemic. We sequenced clinical samples that tested presumptive positive for human monkeypox virus with amplicon-based and metagenomic sequencing approaches. We found notably higher genome coverage across the virus genome, with minimal amplicon drop-outs, in using the amplicon-based sequencing approach, particularly in higher PCR cycle threshold (lower DNA titer) samples. Further testing demonstrated that Ct value correlated with the number of sequencing reads and influenced the percent genome coverage. To maximize genome coverage when resources are limited, we recommend selecting samples with a PCR cycle threshold below 31 Ct and generating 1 million sequencing reads per sample. To support national and international public health genomic surveillance efforts, we sent out primer pool aliquots to 10 laboratories across the United States, United Kingdom, Brazil, and Portugal. These public health laboratories successfully implemented the human monkeypox virus primer scheme in various amplicon sequencing workflows and with different sample types across a range of Ct values. Thus, we show that amplicon based sequencing can provide a rapidly deployable, cost-effective, and flexible approach to pathogen whole genome sequencing in response to newly emerging pathogens. Importantly, through the implementation of our primer scheme into existing SARS-CoV-2 workflows and across a range of sample types and sequencing platforms, we further demonstrate the potential of this approach for rapid outbreak response.}, } @article {pmid36298863, year = {2022}, author = {Van Doorslaer, K}, title = {Revisiting Papillomavirus Taxonomy: A Proposal for Updating the Current Classification in Line with Evolutionary Evidence.}, journal = {Viruses}, volume = {14}, number = {10}, pages = {}, pmid = {36298863}, issn = {1999-4915}, support = {1R03DE030211-01/DE/NIDCR NIH HHS/United States ; 1R01AI165638-01A1/AI/NIAID NIH HHS/United States ; P30CA023074/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; Humans ; Phylogeny ; Papillomaviridae/genetics ; Viral Proteins/genetics ; *Viruses/genetics ; DNA, Circular ; Nucleotides ; *Papillomavirus Infections/genetics ; Genome, Viral ; }, abstract = {Papillomaviruses infect a wide array of animal hosts and are responsible for roughly 5% of all human cancers. Comparative genomics between different virus types belonging to specific taxonomic groupings (e.g., species, and genera) has the potential to illuminate physiological differences between viruses with different biological outcomes. Likewise, extrapolation of features between related viruses can be very powerful but requires a solid foundation supporting the evolutionary relationships between viruses. The current papillomavirus classification system is based on pairwise sequence identity. However, with the advent of metagenomics as facilitated by high-throughput sequencing and molecular tools of enriching circular DNA molecules using rolling circle amplification, there has been a dramatic increase in the described diversity of this viral family. Not surprisingly, this resulted in a dramatic increase in absolute number of viral types (i.e., sequences sharing <90% L1 gene pairwise identity). Many of these novel viruses are the sole member of a novel species within a novel genus (i.e., singletons), highlighting that we have only scratched the surface of papillomavirus diversity. I will discuss how this increase in observed sequence diversity complicates papillomavirus classification. I will propose a potential solution to these issues by explicitly basing the species and genera classification on the evolutionary history of these viruses based on the core viral proteins (E1, E2, and L1) of papillomaviruses. This strategy means that it is possible that a virus identified as the closest neighbor based on the E1, E2, L1 phylogenetic tree, is not the closest neighbor based on L1 nucleotide identity. In this case, I propose that a virus would be considered a novel type if it shares less than 90% identity with its closest neighbors in the E1, E2, L1 phylogenetic tree.}, } @article {pmid36298860, year = {2022}, author = {Gulyaeva, A and Garmaeva, S and Kurilshikov, A and Vich Vila, A and Riksen, NP and Netea, MG and Weersma, RK and Fu, J and Zhernakova, A}, title = {Diversity and Ecology of Caudoviricetes Phages with Genome Terminal Repeats in Fecal Metagenomes from Four Dutch Cohorts.}, journal = {Viruses}, volume = {14}, number = {10}, pages = {}, pmid = {36298860}, issn = {1999-4915}, support = {Starting Grant 715772/ERC_/European Research Council/International ; Consolidator grant 101001678/ERC_/European Research Council/International ; }, mesh = {Humans ; Metagenome ; *Bacteriophages/genetics ; Metagenomics ; *Viruses/genetics ; Genome, Viral ; Terminal Repeat Sequences ; }, abstract = {The human gut harbors numerous viruses infecting the human host, microbes, and other inhabitants of the gastrointestinal tract. Most of these viruses remain undiscovered, and their influence on human health is unknown. Here, we characterize viral genomes in gut metagenomic data from 1950 individuals from four population and patient cohorts. We focus on a subset of viruses that is highly abundant in the gut, remains largely uncharacterized, and allows confident complete genome identification—phages that belong to the class Caudoviricetes and possess genome terminal repeats. We detect 1899 species-level units belonging to this subset, 19% of which do not have complete representative genomes in major public gut virome databases. These units display diverse genomic features, are predicted to infect a wide range of microbial hosts, and on average account for <1% of metagenomic reads. Analysis of longitudinal data from 338 individuals shows that the composition of this fraction of the virome remained relatively stable over a period of 4 years. We also demonstrate that 54 species-level units are highly prevalent (detected in >5% of individuals in a cohort). Finally, we find 34 associations between highly prevalent phages and human phenotypes, 24 of which can be explained by the relative abundance of potential hosts.}, } @article {pmid36298741, year = {2022}, author = {Costa, VA and Geoghegan, JL and Holmes, EC and Harvey, E}, title = {Genetic Reassortment between Endemic and Introduced Macrobrachium rosenbergii Nodaviruses in the Murray-Darling Basin, Australia.}, journal = {Viruses}, volume = {14}, number = {10}, pages = {}, pmid = {36298741}, issn = {1999-4915}, mesh = {Animals ; *Palaemonidae ; Capsid Proteins/genetics ; Phylogeny ; *Carps ; Australia ; *Nodaviridae/genetics ; *Viruses ; RNA-Dependent RNA Polymerase ; }, abstract = {Macrobrachium rosenbergii nodavirus (MrNV)-the aetiological agent of white tail disease-is a major limiting factor of crustacean aquaculture as it causes up to 100% mortality in M. rosenbergii larvae and juveniles. Despite the importance of MrNV, there have been few studies on the phylogenetic diversity and geographic range of this virus in Australian waterways. Here, we detected MrNV genomes in common carp (Cyprinus carpio) metatranscriptomes sampled at five freshwater sites across the Murray-Darling Basin (MDB), Australia. We identified genetic divergence of the RNA-dependent RNA polymerase gene between MrNV sequences identified in the northern and southern rivers of the MDB. Northern viruses exhibited strong phylogenetic clustering with MrNV from China, whereas the southern viruses were more closely related to MrNV from Australia. However, all five viruses were closely related in the capsid protein, indicative of genetic reassortment of the RNA1 and RNA2 segments between Australian and introduced MrNV. In addition, we identified Macrobrachium australiense in two of the five MrNV-positive libraries, suggesting that these species may be important reservoir hosts in the MDB. Overall, this study reports the first occurrence of MrNV outside of the Queensland region in Australia and provides evidence for genetic reassortment between endemic and introduced MrNV.}, } @article {pmid36298723, year = {2022}, author = {Hernández, LHA and da Paz, TYB and Silva, SPD and Silva, FSD and Barros, BCV and Nunes, BTD and Casseb, LMN and Medeiros, DBA and Vasconcelos, PFDC and Cruz, ACR}, title = {First Genomic Evidence of a Henipa-like Virus in Brazil.}, journal = {Viruses}, volume = {14}, number = {10}, pages = {}, pmid = {36298723}, issn = {1999-4915}, mesh = {Animals ; *Henipavirus Infections/epidemiology ; Brazil/epidemiology ; *Hendra Virus ; *Nipah Virus ; Genomics ; *Chiroptera ; }, abstract = {The viral genus Henipavirus includes two highly virulent zoonotic viruses of serious public health concern. Hendra henipavirus and Nipah henipavirus outbreaks are restricted to Australia and Southeast Asia, respectively. The Henipavirus genus comprises mostly bat-borne viruses, but exceptions have already been described as novel viruses with rodents and shrews as reservoir animals. In the Americas, scarce evidence supports the circulation of these viruses. In this communication, we report a novel henipa-like virus from opossums (Marmosa demerarae) from a forest fragment area in the Peixe-Boi municipality, Brazil, after which the virus was named the Peixe-Boi virus (PBV). The application of next-generation sequencing and metagenomic approach led us to discover the original evidence of a henipa-like virus genome in Brazil and South America and the original description of a henipa-like virus in marsupial species. These findings emphasize the importance of further studies to characterize PBV and clarify its ecology, impact on public health, and its relationship with didelphid marsupials and henipaviruses.}, } @article {pmid36297740, year = {2022}, author = {Mackie, J and Kinoti, WM and Chahal, SI and Lovelock, DA and Campbell, PR and Tran-Nguyen, LTT and Rodoni, BC and Constable, FE}, title = {Targeted Whole Genome Sequencing (TWG-Seq) of Cucumber Green Mottle Mosaic Virus Using Tiled Amplicon Multiplex PCR and Nanopore Sequencing.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {20}, pages = {}, pmid = {36297740}, issn = {2223-7747}, support = {VG16086//Horticulture Innovation Australia/ ; }, abstract = {Rapid and reliable detection tools are essential for disease surveillance and outbreak management, and genomic data is essential to determining pathogen origin and monitoring of transmission pathways. Low virus copy number and poor RNA quality can present challenges for genomic sequencing of plant viruses, but this can be overcome by enrichment of target nucleic acid. A targeted whole genome sequencing (TWG-Seq) approach for the detection of cucumber green mottle mosaic virus (CGMMV) has been developed where overlapping amplicons generated using two multiplex RT-PCR assays are then sequenced using the Oxford Nanopore MinION. Near complete coding region sequences were assembled with ≥100× coverage for infected leaf tissue dilution samples with RT-qPCR cycle quantification (Cq) values from 11.8 to 38 and in seed dilution samples with Cq values 13.8 to 27. Consensus sequences assembled using this approach showed greater than 99% nucleotide similarity when compared to genomes produced using metagenomic sequencing. CGMMV could be confidently detected in historical seed isolates with degraded RNA. Whilst limited access to, and costs associated with second-generation sequencing platforms can influence diagnostic outputs, the portable Nanopore technology offers an affordable high throughput sequencing alternative when combined with TWG-Seq for low copy or degraded samples.}, } @article {pmid36297000, year = {2022}, author = {Rey-Mariño, A and Francino, MP}, title = {Nutrition, Gut Microbiota, and Allergy Development in Infants.}, journal = {Nutrients}, volume = {14}, number = {20}, pages = {}, pmid = {36297000}, issn = {2072-6643}, support = {PID2019-105969GB-I00//Ministry of Science and Innovation, Spain/ ; 816303//European Commission/ ; }, mesh = {Infant ; Humans ; *Gastrointestinal Microbiome ; *Hypersensitivity/etiology ; *Microbiota ; Metagenomics ; Diet ; }, abstract = {The process of gut microbiota development in infants is currently being challenged by numerous factors associated with the contemporary lifestyle, including diet. A thorough understanding of all aspects of microbiota development will be necessary for engineering strategies that can modulate it in a beneficial direction. The long-term consequences for human development and health of alterations in the succession pattern that forms the gut microbiota are just beginning to be explored and require much further investigation. Nevertheless, it is clear that gut microbiota development in infancy bears strong associations with the risk for allergic disease. A useful understanding of microbial succession in the gut of infants needs to reveal not only changes in taxonomic composition but also the development of functional capacities through time and how these are related to diet and various environmental factors. Metagenomic and metatranscriptomic studies have started to produce insights into the trends of functional repertoire and gene expression change within the first year after birth. This understanding is critical as during this period the most substantial development of the gut microbiota takes place and the relations between gut microbes and host immunity are established. However, further research needs to focus on the impact of diet on these changes and on how diet can be used to counteract the challenges posed by modern lifestyles to microbiota development and reduce the risk of allergic disease.}, } @article {pmid36296361, year = {2022}, author = {Goodman, AZ and Papudeshi, B and Doane, MP and Mora, M and Kerr, E and Torres, M and Nero Moffatt, J and Lima, L and Nosal, AP and Dinsdale, E}, title = {Epidermal Microbiomes of Leopard Sharks (Triakis semifasciata) Are Consistent across Captive and Wild Environments.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296361}, issn = {2076-2607}, abstract = {Characterizations of shark-microbe systems in wild environments have outlined patterns of species-specific microbiomes; however, whether captivity affects these trends has yet to be determined. We used high-throughput shotgun sequencing to assess the epidermal microbiome belonging to leopard sharks (Triakis semifasciata) in captive (Birch Aquarium, La Jolla California born and held permanently in captivity), semi-captive (held in captivity for <1 year in duration and scheduled for release; Scripps Institute of Oceanography, San Diego, CA, USA) and wild environments (Moss Landing and La Jolla, CA, USA). Here, we report captive environments do not drive epidermal microbiome compositions of T. semifasciata to significantly diverge from wild counterparts as life-long captive sharks maintain a species-specific epidermal microbiome resembling those associated with semi-captive and wild populations. Major taxonomic composition shifts observed were inverse changes of top taxonomic contributors across captive duration, specifically an increase of Pseudoalteromonadaceae and consequent decrease of Pseudomonadaceae relative abundance as T. semifasciata increased duration in captive conditions. Moreover, we show captivity did not lead to significant losses in microbial α-diversity of shark epidermal communities. Finally, we present a novel association between T. semifasciata and the Muricauda genus as Metagenomes associated genomes revealed a consistent relationship across captive, semi-captive, and wild populations. Since changes in microbial communities is often associated with poor health outcomes, our report illustrates that epidermally associated microbes belonging to T. semifasciata are not suffering detrimental impacts from long or short-term captivity. Therefore, conservation programs which house sharks in aquariums are providing a healthy environment for the organisms on display. Our findings also expand on current understanding of shark epidermal microbiomes, explore the effects of ecologically different scenarios on benthic shark microbe associations, and highlight novel associations that are consistent across captive gradients.}, } @article {pmid36296332, year = {2022}, author = {Alsaadi, A and Ganesen, SSK and Amelia, TSM and Moanis, R and Peeters, E and Vigneswari, S and Bhubalan, K}, title = {Polyhydroxyalkanoate (PHA) Biopolymer Synthesis by Marine Bacteria of the Malaysian Coral Triangle Region and Mining for PHA Synthase Genes.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296332}, issn = {2076-2607}, support = {RAGS/2012/UMT/SG06/2//Universiti Malaysia Terengganu/ ; }, abstract = {Polyhydroxyalkanoate (PHA), a biodegradable and plastic-like biopolymer, has been receiving research and industrial attention due to severe plastic pollution, resource depletion, and global waste issues. This has spurred the isolation and characterisation of novel PHA-producing strains through cultivation and non-cultivation approaches, with a particular interest in genes encoding PHA synthesis pathways. Since sea sponges and sediment are marine benthic habitats known to be rich in microbial diversity, sponge tissues (Xestospongia muta and Aaptos aaptos) and sediment samples were collected in this study from Redang and Bidong islands located in the Malaysian Coral Triangle region. PHA synthase (phaC) genes were identified from sediment-associated bacterial strains using a cultivation approach and from sponge-associated bacterial metagenomes using a non-cultivation approach. In addition, phylogenetic diversity profiling was performed for the sponge-associated bacterial community using 16S ribosomal ribonucleic acid (16S rRNA) amplicon sequencing to screen for the potential presence of PHA-producer taxa. A total of three phaC genes from the bacterial metagenome of Aaptos and three phaC genes from sediment isolates (Sphingobacterium mizutaii UMTKB-6, Alcaligenes faecalis UMTKB-7, Acinetobacter calcoaceticus UMTKB-8) were identified. Produced PHA polymers were shown to be composed of 5C to nC monomers, with previously unreported PHA-producing ability of the S. mizutaii strain, as well as a 3-hydroxyvalerate-synthesising ability without precursor addition by the A. calcoaceticus strain.}, } @article {pmid36296241, year = {2022}, author = {Rodrigues, CJC and de Carvalho, CCCR}, title = {Marine Bioprospecting, Biocatalysis and Process Development.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296241}, issn = {2076-2607}, support = {101000327 (Project FuturEnzyme)//European Union/ ; PD/BD/135140/2017 and COVID/BD/151843/2021//Fundação para a Ciência e Tecnologia/ ; UIDB/04565/2020, UIDP/04565/2020 and LA/P/0140/2020//Fundação para a Ciência e Tecnologia/ ; }, abstract = {Oceans possess tremendous diversity in microbial life. The enzymatic machinery that marine bacteria present is the result of extensive evolution to assist cell survival under the harsh and continuously changing conditions found in the marine environment. Several bacterial cells and enzymes are already used at an industrial scale, but novel biocatalysts are still needed for sustainable industrial applications, with benefits for both public health and the environment. Metagenomic techniques have enabled the discovery of novel biocatalysts, biosynthetic pathways, and microbial identification without their cultivation. However, a key stage for application of novel biocatalysts is the need for rapid evaluation of the feasibility of the bioprocess. Cultivation of not-yet-cultured bacteria is challenging and requires new methodologies to enable growth of the bacteria present in collected environmental samples, but, once a bacterium is isolated, its enzyme activities are easily measured. High-throughput screening techniques have also been used successfully, and innovative in vitro screening platforms to rapidly identify relevant enzymatic activities continue to improve. Small-scale approaches and process integration could improve the study and development of new bioprocesses to produce commercially interesting products. In this work, the latest studies related to (i) the growth of marine bacteria under laboratorial conditions, (ii) screening techniques for bioprospecting, and (iii) bioprocess development using microreactors and miniaturized systems are reviewed and discussed.}, } @article {pmid36296186, year = {2022}, author = {Guzzo, GL and Mittinty, MN and Llamas, B and Andrews, JM and Weyrich, LS}, title = {Individuals with Inflammatory Bowel Disease Have an Altered Gut Microbiome Composition of Fungi and Protozoa.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296186}, issn = {2076-2607}, abstract = {It is known that the bacterial gut microbiome is altered in inflammatory bowel disease (IBD), but far less is known about the role of eukaryotic microorganisms in IBD. While eukaryotes are rarer than bacteria within the gastrointestinal environment, the current literature suggests that they may also be implicated in IBD. In our study, we characterized these often-neglected eukaryotic microbial communities by identifying fungi and protozoa in published shotgun stool metagenomes from 355 people with IBD (206 with Crohn's disease, 126 with ulcerative colitis, and 23 with IBD-unclassified) and 471 unaffected healthy individuals. The individuals with IBD had a higher prevalence of fungi, particularly Saccharomyces cerevisiae, and a lower prevalence of protozoa, particularly Blastocystis species (subtypes 1, 2, 3, and 4). Regression analysis showed that disease state, age, and BMI were associated with the prevalence and abundance of these two genera. We also characterized the eukaryotic gut microbiome in a shotgun stool metagenomic dataset from people with IBD who received fecal transplants, with samples pre- and post-transplantation, and from their donors. We found that in some FMT recipients, a single eukaryotic species remained stable over time, while in other recipients, the eukaryotic composition varied. We conclude that the eukaryotic gut microbiome is altered and varies over time in IBD, and future studies should aim to include these microbes when characterizing the gut microbiome in IBD.}, } @article {pmid36296177, year = {2022}, author = {Leite, MFA and van den Broek, SWEB and Kuramae, EE}, title = {Current Challenges and Pitfalls in Soil Metagenomics.}, journal = {Microorganisms}, volume = {10}, number = {10}, pages = {}, pmid = {36296177}, issn = {2076-2607}, abstract = {Soil microbial communities are essential components of agroecological ecosystems that influence soil fertility, nutrient turnover, and plant productivity. Metagenomics data are increasingly easy to obtain, but studies of soil metagenomics face three key challenges: (1) accounting for soil physicochemical properties; (2) incorporating untreated controls; and (3) sharing data. Accounting for soil physicochemical properties is crucial for better understanding the changes in soil microbial community composition, mechanisms, and abundance. Untreated controls provide a good baseline to measure changes in soil microbial communities and separate treatment effects from random effects. Sharing data increases reproducibility and enables meta-analyses, which are important for investigating overall effects. To overcome these challenges, we suggest establishing standard guidelines for the design of experiments for studying soil metagenomics. Addressing these challenges will promote a better understanding of soil microbial community composition and function, which we can exploit to enhance soil quality, health, and fertility.}, } @article {pmid36295797, year = {2022}, author = {Tian, Y and Rimal, B and Gui, W and Koo, I and Smith, PB and Yokoyama, S and Patterson, AD}, title = {Early Life Polychlorinated Biphenyl 126 Exposure Disrupts Gut Microbiota and Metabolic Homeostasis in Mice Fed with High-Fat Diet in Adulthood.}, journal = {Metabolites}, volume = {12}, number = {10}, pages = {}, pmid = {36295797}, issn = {2218-1989}, support = {Project PEN047702 and Accession number 1009993//the USDA National Institute of Food and Federal Appropriations/ ; S10 OD021750 (ADP)/NH/NIH HHS/United States ; R01 ES028288/ES/NIEHS NIH HHS/United States ; S10 OD021750/OD/NIH HHS/United States ; R01 ES028288 (ADP)/NH/NIH HHS/United States ; }, abstract = {Evidence supports the potential influence of persistent organic pollutants (POPs) on the pathogenesis and progression of obesity and diabetes. Diet-toxicant interactions appear to be important in diet-induced obesity/diabetes; however, the factors influencing this interaction, especially the early life environmental exposure, are unclear. Herein, we investigated the metabolic effects following early life five-day exposure (24 μg/kg body weight per day) to 3,3',4,4',5-pentacholorobiphenyl (PCB 126) at four months after exposure in mice fed with control (CTRL) or high-fat diet (HFD). Activation of aryl hydrocarbon receptor (AHR) signaling as well as higher levels of liver nucleotides were observed at 4 months after PCB 126 exposure in mice, independent of diet status. Inflammatory responses including higher levels of serum cytokines and adipose inflammatory gene expression caused by early life PCB 126 were observed only in HFD-fed mice in adulthood. Notably, early life PCB 126 exposure worsened HFD-induced impaired glucose homeostasis characterized by glucose intolerance and elevated gluconeogenesis and tricarboxylic acid (TCA) cycle flux without worsening the effects of HFD related to adiposity in adulthood. Furthermore, early life PCB 126 exposure resulted in diet-dependent changes in bacterial community structure and function later in life, as indicated by metagenomic and metabolomic analyses. These data contribute to a more comprehensive understanding of the interactions between diet and early life environmental chemical exposure.}, } @article {pmid36295794, year = {2022}, author = {Zhang, N and Peng, Y and Zhao, L and He, P and Zhu, J and Liu, Y and Liu, X and Liu, X and Deng, G and Zhang, Z and Feng, M}, title = {Integrated Analysis of Gut Microbiome and Lipid Metabolism in Mice Infected with Carbapenem-Resistant Enterobacteriaceae.}, journal = {Metabolites}, volume = {12}, number = {10}, pages = {}, pmid = {36295794}, issn = {2218-1989}, support = {31701032//The National Natural Science Foundation of China/ ; 20DZ2255900//The Science and Technology Commission of Shanghai/ ; SHDC12021612//The Shenkang Hospital Development Center of Shanghai/ ; }, abstract = {The disturbance in gut microbiota composition and metabolism has been implicated in the process of pathogenic bacteria infection. However, the characteristics of the microbiota and the metabolic interaction of commensals−host during pathogen invasion remain more than vague. In this study, the potential associations of gut microbes with disturbed lipid metabolism in mice upon carbapenem-resistant Escherichia coli (CRE) infection were explored by the biochemical and multi-omics approaches including metagenomics, metabolomics and lipidomics, and then the key metabolites−reaction−enzyme−gene interaction network was constructed. Results showed that intestinal Erysipelotrichaceae family was strongly associated with the hepatic total cholesterol and HDL-cholesterol, as well as a few sera and fecal metabolites involved in lipid metabolism such as 24, 25-dihydrolanosterol. A high-coverage lipidomic analysis further demonstrated that a total of 529 lipid molecules was significantly enriched and 520 were depleted in the liver of mice infected with CRE. Among them, 35 lipid species showed high correlations (|r| > 0.8 and p < 0.05) with the Erysipelotrichaceae family, including phosphatidylglycerol (42:2), phosphatidylglycerol (42:3), phosphatidylglycerol (38:5), phosphatidylcholine (42:4), ceramide (d17:1/16:0), ceramide (d18:1/16:0) and diacylglycerol (20:2), with correlation coefficients higher than 0.9. In conclusion, the systematic multi-omics study improved the understanding of the complicated connection between the microbiota and the host during pathogen invasion, which thereby is expected to lead to the future discovery and establishment of novel control strategies for CRE infection.}, } @article {pmid36294560, year = {2022}, author = {Iossi, MR and Palú, IA and Soares, DM and Vieira, WG and Alves, LS and Stevani, CV and Caitano, CEC and Atum, SVF and Freire, RS and Dias, ES and Zied, DC}, title = {Metaprofiling of the Bacterial Community in Colonized Compost Extracts by Agaricus subrufescens.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {10}, pages = {}, pmid = {36294560}, issn = {2309-608X}, support = {Process number 2018/21492-2//São Paulo Research Foundation/ ; }, abstract = {It is well-known that bacteria and fungi play important roles in the relationships between mycelium growth and the formation of fruiting bodies. The sun mushroom, Agaricus subrufescens, was discovered in Brazil ca. 1960 and it has become known worldwide due to its medicinal and nutritional properties. This work evaluated the bacterial community present in mushroom-colonized compost extract (MCCE) prepared from cultivation of A. subrufescens, its dynamics with two different soaking times and the influence of the application of those extracts on the casing layer of a new compost block for A. subrufescens cultivation. MCCEs were prepared through initial submersion of the colonized compost for 1 h or 24 h in water followed by application on casing under semi-controlled conditions. Full-length 16S rRNA genes of 1 h and 24 h soaked MCCE were amplified and sequenced using nanopore technology. Proteobacteria, followed by Firmicutes and Planctomycetes, were found to be the most abundant phyla in both the 1 h and 24 h soaked MCCE. A total of 275 different bacterial species were classified from 1 h soaked MCCE samples and 166 species from 24 h soaked MCCE, indicating a decrease in the bacterial diversity with longer soaking time during the preparation of MCCE. The application of 24 h soaked MCCE provided increases of 25% in biological efficiency, 16% in precociousness, 53% in the number of mushrooms and 40% in mushroom weight compared to control. Further investigation is required to determine strategies to enhance the yield and quality of the agronomic traits in commercial mushroom cultivation.}, } @article {pmid36293448, year = {2022}, author = {Malicka, M and Magurno, F and Piotrowska-Seget, Z}, title = {Phenol and Polyaromatic Hydrocarbons Are Stronger Drivers Than Host Plant Species in Shaping the Arbuscular Mycorrhizal Fungal Component of the Mycorrhizosphere.}, journal = {International journal of molecular sciences}, volume = {23}, number = {20}, pages = {}, pmid = {36293448}, issn = {1422-0067}, support = {2017/25/N/NZ8/01676//National Science Centre, Poland/ ; }, mesh = {*Mycorrhizae/physiology ; Soil Microbiology ; Phenol ; *Glomeromycota ; Soil/chemistry ; Plants/genetics ; Hydrocarbons ; *Polycyclic Aromatic Hydrocarbons ; DNA, Ribosomal/genetics ; *Microbiota ; Plant Roots/microbiology ; }, abstract = {Changes in soil microbial communities in response to hydrocarbon pollution are critical indicators of disturbed ecosystem conditions. A core component of these communities that is functionally adjusted to the life-history traits of the host and environmental factors consists of arbuscular mycorrhizal fungi (AMF). AMF communities associated with Poa trivialis and Phragmites australis growing at a phenol and polynuclear aromatic hydrocarbon (PAH)-contaminated site and at an uncontaminated site were compared based on LSU rDNA sequencing. Dissimilarities in species composition and community structures indicated soil pollution as the main factor negatively affecting the AMF diversity. The AMF communities at the contaminated site were dominated by fungal generalists (Rhizophagus, Funneliformis, Claroideoglomus, Paraglomus) with wide ecological tolerance. At the control site, the AMF communities were characterized by higher taxonomic and functional diversity than those exposed to the contamination. The host plant identity was the main driver distinguishing the two AMF metacommunities. The AMF communities at the uncontaminated site were represented by Polonospora, Paraglomus, Oehlia, Nanoglomus, Rhizoglomus, Dominikia, and Microdominikia. Polonosporaceae and Paraglomeraceae were particularly dominant in the Ph. australis mycorrhizosphere. The high abundance of early diverging AMF could be due to the use of primers able to detect lineages such as Paraglomeracae that have not been recognized by previously used 18S rDNA primers.}, } @article {pmid36293097, year = {2022}, author = {Escuder-Rodríguez, JJ and DeCastro, ME and Saavedra-Bouza, A and Becerra, M and González-Siso, MI}, title = {Insights on Microbial Communities Inhabiting Non-Volcanic Hot Springs.}, journal = {International journal of molecular sciences}, volume = {23}, number = {20}, pages = {}, pmid = {36293097}, issn = {1422-0067}, support = {ED431C 2020/08//Xunta de Galicia/ ; RTI2018-099249-B-I00//MINISTERIO DE CIENCIA, INNOVACIÓN Y UNIVERSIDADES/ ; }, mesh = {Bacteria/metabolism ; Biodiversity ; *Hot Springs/microbiology ; *Microbiota ; Peptide Hydrolases/metabolism ; Phylogeny ; Sulfur/metabolism ; }, abstract = {The northwest of Spain has an abundance of non-volcanic hot springs that, until recently, had only been used for thermalism activities. One of such hot springs, Muiño da Veiga, has now been explored using metagenomics to study the microbial community that inhabits these high-temperature circumneutral continental waters. Sequencing of the metagenome allowed the characterization of its composition, diversity, metabolic connections and potential as a source for thermozymes, as well as its ability to assemble MAGs. A diverse microbial community dominated by Bacteria domain members was revealed, particularly from the early-branching Aquificales group. The most abundant genus was Sulfurihydrogenibium, known for its implication in sulfur cycling and for forming mats that enable novel niches. The variety of primary producers with autotrophic pathways (and specifically the sulfur oxidizing pathway) expands the range of available nutrients, and the increase in biomass forms thicker mats, resulting in more available niches and broader microbial diversity. Nonetheless, certain metabolic pathways were attributed to less abundant members of the microbial community, reinforcing the idea that the rare biosphere plays important roles in the network of interactions present in an ecosystem and acts as genetic reservoirs. In addition, three of the assembled MAGs represent novel microbial diversity found in this hot spring. Moreover, the presence of enzymes and microorganisms with possible biotechnological applications was confirmed, including proteases, lipases and cell-wall degrading enzymes, pointing to the potential for the hot spring as a source for thermozymes.}, } @article {pmid36293066, year = {2022}, author = {Vanstokstraeten, R and Mackens, S and Callewaert, E and Blotwijk, S and Emmerechts, K and Crombé, F and Soetens, O and Wybo, I and Vandoorslaer, K and Mostert, L and De Geyter, D and Muyldermans, A and Blockeel, C and Piérard, D and Demuyser, T}, title = {Culturomics to Investigate the Endometrial Microbiome: Proof-of-Concept.}, journal = {International journal of molecular sciences}, volume = {23}, number = {20}, pages = {}, pmid = {36293066}, issn = {1422-0067}, mesh = {Pregnancy ; Humans ; Female ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenomics/methods ; Bacteria ; Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization ; }, abstract = {The microbiome of the reproductive tract has been associated with (sub)fertility and it has been suggested that dysbiosis reduces success rates and pregnancy outcomes. The endometrial microbiome is of particular interest given the potential impact on the embryo implantation. To date, all endometrial microbiome studies have applied a metagenomics approach. A sequencing-based technique, however, has its limitations, more specifically in adequately exploring low-biomass settings, such as intra-uterine/endometrial samples. In this proof-of-concept study, we demonstrate the applicability of culturomics, a high-throughput culturing approach, to investigate the endometrial microbiome. Ten subfertile women undergoing diagnostic hysteroscopy and endometrial biopsy, as part of their routine work-up at Brussels IVF, were included after their informed consent. Biopsies were used to culture microbiota for up to 30 days in multiple aerobic and anaerobic conditions. Subsequent WASPLab[®]-assisted culturomics enabled a standardized methodology. Matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) or 16S rRNA sequencing was applied to identify all of bacterial and fungal isolates. Eighty-three bacterial and two fungal species were identified. The detected species were in concordance with previously published metagenomics-based endometrial microbiota analyses as 77 (91%) of them belonged to previously described genera. Nevertheless, highlighting the added value of culturomics to identify most isolates at the species level, 53 (62.4%) of the identified species were described in the endometrial microbiota for the first time. This study shows the applicability and added value of WASPLab[®]-assisted culturomics to investigate the low biomass endometrial microbiome at a species level.}, } @article {pmid36293010, year = {2022}, author = {Ferrandi, EE and Bassanini, I and Bertuletti, S and Riva, S and Tognoli, C and Vanoni, M and Monti, D}, title = {Functional Characterization and Synthetic Application of Is2-SDR, a Novel Thermostable and Promiscuous Ketoreductase from a Hot Spring Metagenome.}, journal = {International journal of molecular sciences}, volume = {23}, number = {20}, pages = {}, pmid = {36293010}, issn = {1422-0067}, support = {CN00000033, PNRR MUR -M4C2 -D. D. n.1034, 17.06.2022//National Biodiversity Future Center/ ; }, mesh = {*Hot Springs ; Metagenome ; *Short Chain Dehydrogenase-Reductases ; Hydroxysteroid Dehydrogenases/genetics ; Ketones ; Steroids ; Water ; Cholic Acid ; Pharmaceutical Preparations ; Solvents ; Substrate Specificity ; }, abstract = {In a metagenome mining-based search of novel thermostable hydroxysteroid dehydrogenases (HSDHs), enzymes that are able to selectively oxidize/reduce steroidal compounds, a novel short-chain dehydrogenase/reductase (SDR), named Is2-SDR, was recently discovered. This enzyme, found in an Icelandic hot spring metagenome, shared a high sequence similarity with HSDHs, but, unexpectedly, showed no activity in the oxidation of the tested steroid substrates, e.g., cholic acid. Despite that, Is2-SDR proved to be a very active and versatile ketoreductase, being able to regio- and stereoselectively reduce a diversified panel of carbonylic substrates, including bulky ketones, α- and β-ketoesters, and α-diketones of pharmaceutical relevance. Further investigations showed that Is2-SDR was indeed active in the regio- and stereoselective reduction of oxidized steroid derivatives, and this outcome was rationalized by docking analysis in the active site model. Moreover, Is2-SDR showed remarkable thermostability, with an apparent melting temperature (TM) around 75 °C, as determined by circular dichroism analysis, and no significant decrease in catalytic activity, even after 5 h at 80 °C. A broad tolerance to both water-miscible and water-immiscible organic solvents was demonstrated as well, thus, confirming the potential of this new biocatalyst for its synthetic application.}, } @article {pmid36292810, year = {2022}, author = {Ghosh, S and Namin, SM and Jung, C}, title = {Differential Bacterial Community of Bee Bread and Bee Pollen Revealed by 16s rRNA High-Throughput Sequencing.}, journal = {Insects}, volume = {13}, number = {10}, pages = {}, pmid = {36292810}, issn = {2075-4450}, support = {NRF- 2018R1A6A1A03024862//National Research Foundation of Korea/ ; 20211362A00-2123-BD01//Korean forest service/ ; }, abstract = {We investigated the bacterial community of bee bread and bee pollen samples using an approach through 16 s rRNA high-throughput sequencing. The results revealed a higher bacterial diversity in bee bread than in bee pollen as depicted in taxonomic profiling, as well as diversity indices such as the Shannon diversity index (3.7 to 4.8 for bee bread and 1.1 to 1.7 for bee pollen samples) and Simpson’s index (>0.9 for bee bread and 0.4−0.5 for bee pollen). Principal component analysis showed a distinct difference in bacterial communities. The higher bacterial diversity in the bee bread than bee pollen could presumably be due to factors such as storage period, processing of food, fermentation, and high sugar environment. However, no effect of the feed (rapeseed or oak pollen patties or even natural inflow) was indicated on the bacterial composition of bee bread, presumably because of the lack of restriction of foraged pollen inflow in the hive. The diverse bacterial profile of the bee bread could contribute to the nutritional provisioning as well as enhance the detoxification process; however, a thorough investigation of the functional role of individual bacteria genera remains a task for future studies.}, } @article {pmid36292799, year = {2022}, author = {Bhattacharya, C and Tierney, BT and Ryon, KA and Bhattacharyya, M and Hastings, JJA and Basu, S and Bhattacharya, B and Bagchi, D and Mukherjee, S and Wang, L and Henaff, EM and Mason, CE}, title = {Supervised Machine Learning Enables Geospatial Microbial Provenance.}, journal = {Genes}, volume = {13}, number = {10}, pages = {}, pmid = {36292799}, issn = {2073-4425}, support = {U01 DA053941/DA/NIDA NIH HHS/United States ; R01 AI151059/AI/NIAID NIH HHS/United States ; R01 AI125416/AI/NIAID NIH HHS/United States ; R21 AI129851/AI/NIAID NIH HHS/United States ; R21 EB031466/EB/NIBIB NIH HHS/United States ; }, mesh = {*Metagenomics/methods ; Metagenome ; *Microbiota/genetics ; Supervised Machine Learning ; Cities ; }, abstract = {The recent increase in publicly available metagenomic datasets with geospatial metadata has made it possible to determine location-specific, microbial fingerprints from around the world. Such fingerprints can be useful for comparing microbial niches for environmental research, as well as for applications within forensic science and public health. To determine the regional specificity for environmental metagenomes, we examined 4305 shotgun-sequenced samples from the MetaSUB Consortium dataset-the most extensive public collection of urban microbiomes, spanning 60 different cities, 30 countries, and 6 continents. We were able to identify city-specific microbial fingerprints using supervised machine learning (SML) on the taxonomic classifications, and we also compared the performance of ten SML classifiers. We then further evaluated the five algorithms with the highest accuracy, with the city and continental accuracy ranging from 85-89% to 90-94%, respectively. Thereafter, we used these results to develop Cassandra, a random-forest-based classifier that identifies bioindicator species to aid in fingerprinting and can infer higher-order microbial interactions at each site. We further tested the Cassandra algorithm on the Tara Oceans dataset, the largest collection of marine-based microbial genomes, where it classified the oceanic sample locations with 83% accuracy. These results and code show the utility of SML methods and Cassandra to identify bioindicator species across both oceanic and urban environments, which can help guide ongoing efforts in biotracing, environmental monitoring, and microbial forensics (MF).}, } @article {pmid36292745, year = {2022}, author = {Sánchez-Pellicer, P and Navarro-Moratalla, L and Núñez-Delegido, E and Agüera-Santos, J and Navarro-López, V}, title = {How Our Microbiome Influences the Pathogenesis of Alopecia Areata.}, journal = {Genes}, volume = {13}, number = {10}, pages = {}, pmid = {36292745}, issn = {2073-4425}, mesh = {Humans ; *Alopecia Areata/genetics ; RNA, Ribosomal, 16S/genetics ; *Autoimmune Diseases/genetics ; *Microbiota ; }, abstract = {Alopecia areata is a multifactorial autoimmune-based disease with a complex pathogenesis. As in all autoimmune diseases, genetic predisposition is key. The collapse of the immune privilege of the hair follicle leading to scalp loss is a major pathogenic event in alopecia areata. The microbiota considered a bacterial ecosystem located in a specific area of the human body could somehow influence the pathogenesis of alopecia areata, as it occurs in other autoimmune diseases. Moreover, the Next Generation Sequencing of the 16S rRNA bacterial gene and the metagenomic methodology have provided an excellent characterization of the microbiota. The aim of this narrative review is to examine the published literature on the cutaneous and intestinal microbiota in alopecia areata to be able to establish a pathogenic link. In this review, we summarize the influence of the microbiota on the development of alopecia areata. We first introduce the general pathogenic mechanisms that cause alopecia areata to understand the influence that the microbiota may exert and then we summarize the studies that have been carried out on what type of gut and skin microbiota is found in patients with this disease.}, } @article {pmid36292643, year = {2022}, author = {Li, M and Tyx, RE and Rivera, AJ and Zhao, N and Satten, GA}, title = {What Can We Learn about the Bias of Microbiome Studies from Analyzing Data from Mock Communities?.}, journal = {Genes}, volume = {13}, number = {10}, pages = {}, pmid = {36292643}, issn = {2073-4425}, support = {R21AI154236//National Institute of Health/ ; R01GM116065//National Institute of Health/ ; R01GM141074//National Institute of Health/ ; U24OD023382//National Institute of Health/ ; }, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenomics/methods ; Bacteria/genetics ; Bias ; }, abstract = {It is known that data from both 16S and shotgun metagenomics studies are subject to biases that cause the observed relative abundances of taxa to differ from their true values. Model community analyses, in which the relative abundances of all taxa in the sample are known by construction, seem to offer the hope that these biases can be measured. However, it is unclear whether the bias we measure in a mock community analysis is the same as we measure in a sample in which taxa are spiked in at known relative abundance, or if the biases we measure in spike-in samples is the same as the bias we would measure in a real (e.g., biological) sample. Here, we consider these questions in the context of 16S rRNA measurements on three sets of samples: the commercially available Zymo cells model community; the Zymo model community mixed with Swedish Snus, a smokeless tobacco product that is virtually bacteria-free; and a set of commercially available smokeless tobacco products. Each set of samples was subject to four different extraction protocols. The goal of our analysis is to determine whether the patterns of bias observed in each set of samples are the same, i.e., can we learn about the bias in the commercially available smokeless tobacco products by studying the Zymo cells model community?}, } @article {pmid36291869, year = {2022}, author = {Marongiu, L and Venturelli, S and Allgayer, H}, title = {Involvement of HHV-4 (Epstein-Barr Virus) and HHV-5 (Cytomegalovirus) in Inflammatory Bowel Disease and Colorectal Cancer: A Meta-Analysis.}, journal = {Cancers}, volume = {14}, number = {20}, pages = {}, pmid = {36291869}, issn = {2072-6694}, support = {no grant number provided by funder//PASCOE pharmazeutische Praeparate GmbH/ ; no grant number provided by funder//Alfried Krupp von Bohlen und Halbach Foundation, Essen/ ; }, abstract = {Gastrointestinal diseases (GDs) include colorectal cancer (CRC), gastric cancer (GC), and inflammatory bowel disease (IBD). CRC and GC are typically diagnosed at later stages of development, reducing patients' chances of survival. IBD is characterized by chronic intestinal inflammation and is a significant risk factor for the development of CRC. Chronic bacterial infections have been shown to promote some GDs, but the role of viruses in the etiology of these diseases is less clear. The present meta-analysis retrieved literature on the viral prevalence in GD patients, measuring the GD risk in odd ratios. By quantifying the study heterogeneity, the literature bias was fundamentally included in the analysis. The analysis also included 11 metagenomic studies. Our meta-analysis retrieved 11,413 studies, with 196 suitable for analysis. HHV-4 (Epstein-Barr virus) was identified as a significant risk factor for the development of IBD, and HHV-5 (cytomegalovirus) as a risk factor for both CRC and IBD. Polyomaviruses and the Hepatitis B virus were also, less strongly, involved in the risk of CRC and IBD. No relations withstanding the literature bias were identified for GC. The study discusses these findings, as well as the role of other viruses in the etiology of CRC and IBD.}, } @article {pmid36291712, year = {2022}, author = {Sato, H and Sasaki, K and Hara, T and Tsuji, Y and Arao, Y and Otsuka, C and Hamano, Y and Ogita, M and Kobayashi, S and di Luccio, E and Hirotsu, T and Doki, Y and Eguchi, H and Satoh, T and Uchida, S and Ishii, H}, title = {Pancreatic Cancer Research beyond DNA Mutations.}, journal = {Biomolecules}, volume = {12}, number = {10}, pages = {}, pmid = {36291712}, issn = {2218-273X}, mesh = {Humans ; Tumor Suppressor Protein p53/metabolism ; *Volatile Organic Compounds ; Proto-Oncogene Proteins p21(ras)/genetics/metabolism ; *Pancreatic Neoplasms/metabolism ; *Carcinoma, Pancreatic Ductal/metabolism ; Mutation ; DNA/therapeutic use ; Cyclin-Dependent Kinases/metabolism ; }, abstract = {Pancreatic ductal adenocarcinoma (PDAC) is caused by genetic mutations in four genes: KRAS proto-oncogene and GTPase (KRAS), tumor protein P53 (TP53), cyclin-dependent kinase inhibitor 2A (CDKN2A), and mothers against decapentaplegic homolog 4 (SMAD4), also called the big 4. The changes in tumors are very complex, making their characterization in the early stages challenging. Therefore, the development of innovative therapeutic approaches is desirable. The key to overcoming PDAC is diagnosing it in the early stages. Therefore, recent studies have investigated the multifaced characteristics of PDAC, which includes cancer cell metabolism, mesenchymal cells including cancer-associated fibroblasts and immune cells, and metagenomics, which extend to characterize various biomolecules including RNAs and volatile organic compounds. Various alterations in the KRAS-dependent as well as KRAS-independent pathways are involved in the refractoriness of PDAC. The optimal combination of these new technologies is expected to help treat intractable pancreatic cancer.}, } @article {pmid36291654, year = {2022}, author = {Fang, C and Zuo, K and Fu, Y and Zhu, X and Li, J and Zhong, J and Xu, L and Yang, X}, title = {Aggravated Gut Microbiota and Metabolomic Imbalances Are Associated with Hypertension Patients Comorbid with Atrial Fibrillation.}, journal = {Biomolecules}, volume = {12}, number = {10}, pages = {}, pmid = {36291654}, issn = {2218-273X}, mesh = {Humans ; *Atrial Fibrillation ; *Gastrointestinal Microbiome ; *Hypertension ; Stearic Acids ; Arachidonic Acids ; Linoleic Acids ; Palmitic Acids ; Oleic Acids ; }, abstract = {Disordered gut microbiota (GM) as the co-contributor of atrial fibrillation (AF) and hypertension (HTN) might be associated with AF risk in HTN. This study aimed to explore the altered GM community and metabolic patterns between 27 HTN patients with AF (HTN-AF) and 27 non-AF HTN patients through fecal metagenomic and serum metabolomic analysis. Compared to non-AF HTN patients, significant microbial alterations (p = 0.004), including increased microbial diversity (p < 0.05), shifted enterotype dominated by Prevotella to Bacteroides, and abundant disease-linked genera Ruminococcus, Streptococcus, Veillonella, Dorea, and Enterococcus, were observed in HTN-AF patients. A species-based random forest prediction model was associated with the risk of AF occurrence in HTN patients. Furthermore, GM metabolic profiles dramatically differed between HTN and HTN-AF patients, especially the imbalance of saturated and unsaturated fatty acids. In HTN-AF patients, circulating palmitic acid and arachidonic acid levels were significantly elevated, while the levels of tetracosahexaenoic acid, oleic acid, linoleic acid, and stearic acid were decreased (p < 0.001, VIP > 1), mediating 85.99% of gut microbial indirect effects on AF (p < 0.001). Thus, our findings preliminarily indicated that exacerbated dysbiosis of GM and relevant metabolites was associated with high AF susceptibility and might be a potential target for AF prediction and prevention in HTN.}, } @article {pmid36291597, year = {2022}, author = {Miao, Q and Zhang, X and Wang, Y and Li, X and Wang, Z and Tian, L and Qu, L and Wei, Y}, title = {Characterization of Novel Pectinolytic Enzymes Derived from the Efficient Lignocellulose Degradation Microbiota.}, journal = {Biomolecules}, volume = {12}, number = {10}, pages = {}, pmid = {36291597}, issn = {2218-273X}, mesh = {*Polygalacturonase/metabolism ; Lignin/metabolism ; *Microbiota/genetics ; Metagenomics ; }, abstract = {Diverse pectinolytic enzymes are widely applied in the food, papermaking, and other industries, and they account for more than 25% of the global industrial enzyme demands. Efficient lignocellulose degradation microbiota are reservoirs of pectinolytic enzymes and other lignocellulose-degrading genes. Metagenomics has been widely used to discover new pectinolytic enzymes. Here, we used a metagenomic strategy to characterize pectinolytic genes from one efficient lignocellulose-degrading microbiota derived from pulp and paper wastewater treatment microbiota. A total of 23 predicted full-length GH28 and PL1 family pectinolytic genes were selectively cloned and expressed in Escherichia coli, and 5 of the expressed proteins had pectinolytic activities. Among them, the characterization of one pectinolytic enzyme, PW-pGH28-3, which has a 58.4% identity with an exo-polygalacturonase gene of Aquipluma nitroreducens, was further investigated. The optimal pH and optimal temperature of PW-pGH28-3 were 8.0 and 40 °C, respectively, and its pectinolytic activity at the optimal condition was 13.5 ± 1.1 U/mg protein. Bioinformatics analyses and structural modeling suggest that PW-pGH28-3 is a novel secretory exo-polygalacturonase, which is confirmed by its hydrolysates of polygalacturonic acid. The detection of PW-pGH28-3 and other pectinolytic genes showed that efficient lignocellulose degradation microbiota could provide potential efficient pectinolytic enzymes for industrial application. In the future, improving metagenomic screening efficiency would discover efficient lignocellulose-degrading enzymes and lead to the sustainable and green utilization of lignocellulose.}, } @article {pmid36291121, year = {2022}, author = {Mishra, AK and Sudalaimuthuasari, N and Hazzouri, KM and Saeed, EE and Shah, I and Amiri, KMA}, title = {Tapping into Plant-Microbiome Interactions through the Lens of Multi-Omics Techniques.}, journal = {Cells}, volume = {11}, number = {20}, pages = {}, pmid = {36291121}, issn = {2073-4409}, mesh = {*Plant Roots/metabolism ; Genome-Wide Association Study ; *Microbiota ; Soil/chemistry ; Plants/metabolism ; Pheromones/metabolism ; }, abstract = {This review highlights the pivotal role of root exudates in the rhizosphere, especially the interactions between plants and microbes and between plants and plants. Root exudates determine soil nutrient mobilization, plant nutritional status, and the communication of plant roots with microbes. Root exudates contain diverse specialized signaling metabolites (primary and secondary). The spatial behavior of these metabolites around the root zone strongly influences rhizosphere microorganisms through an intimate compatible interaction, thereby regulating complex biological and ecological mechanisms. In this context, we reviewed the current understanding of the biological phenomenon of allelopathy, which is mediated by phytotoxic compounds (called allelochemicals) released by plants into the soil that affect the growth, survival, development, ecological infestation, and intensification of other plant species and microbes in natural communities or agricultural systems. Advances in next-generation sequencing (NGS), such as metagenomics and metatranscriptomics, have opened the possibility of better understanding the effects of secreted metabolites on the composition and activity of root-associated microbial communities. Nevertheless, understanding the role of secretory metabolites in microbiome manipulation can assist in designing next-generation microbial inoculants for targeted disease mitigation and improved plant growth using the synthetic microbial communities (SynComs) tool. Besides a discussion on different approaches, we highlighted the advantages of conjugation of metabolomic approaches with genetic design (metabolite-based genome-wide association studies) in dissecting metabolome diversity and understanding the genetic components of metabolite accumulation. Recent advances in the field of metabolomics have expedited comprehensive and rapid profiling and discovery of novel bioactive compounds in root exudates. In this context, we discussed the expanding array of metabolomics platforms for metabolome profiling and their integration with multivariate data analysis, which is crucial to explore the biosynthesis pathway, as well as the regulation of associated pathways at the gene, transcript, and protein levels, and finally their role in determining and shaping the rhizomicrobiome.}, } @article {pmid36290431, year = {2022}, author = {Lai, KP and Boncan, DAT and Yang, L and Leung, CCT and Ho, JCH and Lin, X and Chan, TF and Kong, RYC and Tse, WKF}, title = {Osmotic Gradient Is a Factor That Influences the Gill Microbiota Communities in Oryzias melastigma.}, journal = {Biology}, volume = {11}, number = {10}, pages = {}, pmid = {36290431}, issn = {2079-7737}, support = {17-314; 18-319//National Institute for Basic Biology/ ; 82160282; 41977371//National Natural Science Foundation of China/ ; 123-2018; 127-2019//University of Tokyo/ ; }, abstract = {The fish gill is the first tissue that is exposed to the external media and undergoes continuous osmotic challenges. Recently, our group published an article entitled "Integrated Omics Approaches Revealed the Osmotic Stress-Responsive Genes and Microbiota in Gill of Marine Medaka" in the journal mSystems (e0004722, 2022), and suggested the possible host-bacterium interaction in the fish gill during osmotic stress. The previous study was performed by the progressive fresh water transfer (i.e., seawater to fresh water transfer via 50% seawater (FW)). Our group hypothesized that osmotic gradient could be a factor that determines the microbiota communities in the gill. The current 16S rRNA metagenomic sequencing study found that the direct transfer (i.e., seawater to fresh water (FWd)) could result in different gill microbiota communities in the same fresh water endpoints. Pseduomonas was the dominant bacteria (more than 55%) in the FWd gill. The Kyoto Encyclopedia of Genes and Genomes and MetaCyc analysis further suggested that the FWd group had enhanced osmosensing pathways, such as the ATP-binding cassette transporters, taurine degradation, and energy-related tricarboxylic acid metabolism compared to the FW group.}, } @article {pmid36290099, year = {2022}, author = {Libisch, B and Abdulkadir, S and Keresztény, T and Papp, PP and Olasz, F and Fébel, H and Sándor, ZJ and Rasschaert, G and Lambrecht, E and Heyndrickx, M and Szabó, A and Kovács, M and Posta, K}, title = {Detection of Acquired Antibiotic Resistance Genes in Domestic Pig (Sus scrofa) and Common Carp (Cyprinus carpio) Intestinal Samples by Metagenomics Analyses in Hungary.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {10}, pages = {}, pmid = {36290099}, issn = {2079-6382}, support = {GINOP-2.3.2-15-2016-00046//Hungarian Ministry of Innovation and Technology/ ; TKP2020-NKA-24//Hungarian National Research, Development and Innovation Office/ ; Grant Agreement ID 101036768//European Commission/ ; RRF-2.3.1-21-2022-00007//Hungarian National Laboratory Project/ ; NKFI K 132687//Hungarian National Research, Development and Innovation Office/ ; 2019-2.1.11-TÉT-2020-00141//Hungarian National Research, Development and Innovation Office/ ; One Health 2020-4.1.1-TKP2020//Hungarian National Research, Development and Innovation Office/ ; }, abstract = {The aim of this study was metagenomics analyses of acquired antibiotic-resistance genes (ARGs) in the intestinal microbiome of two important food-animal species in Hungary from a One Health perspective. Intestinal content samples were collected from 12 domestic pigs (Sus scrofa) and from a common carp (Cyprinus carpio). Shotgun metagenomic sequencing of DNA purified from the intestinal samples was performed on the Illumina platform. The ResFinder database was applied for detecting acquired ARGs in the assembled metagenomic contigs. Altogether, 59 acquired ARG types were identified, 51 genes from domestic pig and 12 genes from the carp intestinal microbiome. ARG types belonged to the antibiotic classes aminoglycosides (27.1%), tetracyclines (25.4%), β-lactams (16.9%), and others. Of the identified ARGs, tet(E), a blaOXA-48-like β-lactamase gene, as well as cphA4, ampS, aadA2, qnrS2, and sul1, were identified only in carp but not in swine samples. Several of the detected acquired ARGs have not yet been described from food animals in Hungary. The tet(Q), tet(W), tet(O), and mef(A) genes detected in the intestinal microbiome of domestic pigs had also been identified from free-living wild boars in Hungary, suggesting a possible relationship between the occurrence of acquired ARGs in domestic and wild animal populations.}, } @article {pmid36289674, year = {2022}, author = {Wehedy, E and Murugesan, S and George, CR and Shatat, IF and Al Khodor, S}, title = {Characterization of the Urinary Metagenome and Virome in Healthy Children.}, journal = {Biomedicines}, volume = {10}, number = {10}, pages = {}, pmid = {36289674}, issn = {2227-9059}, support = {SDR200055//Sidra Medical and Research Center/ ; }, abstract = {Recent advances in next-generation sequencing and metagenomic studies have provided insights into the microbial profile of different body sites. However, research on the microbial composition of urine is limited, particularly in children. The goal of this study was to optimize and develop reproducible metagenome and virome protocols using a small volume of urine samples collected from healthy children. We collected midstream urine specimens from 40 healthy children. Using the metagenomics shotgun approach, we tested various protocols. Different microbial roots such as Archaea, Bacteria, Eukaryota, and Viruses were successfully identified using our optimized urine protocol. Our data reflected much variation in the microbial fingerprints of children. Girls had significantly higher levels of Firmicutes, whereas boys had significantly higher levels of Actinobacteria. The genus Anaerococcus dominated the urinary bacteriome of healthy girls, with a significant increase in Anaerococcus prevotii, Anaerococcus vaginalis, and Veillonella parvula (p-value < 0.001) when compared with that of boys. An increased relative abundance of Xylanimonas and Arthrobacter, with a significantly high abundance of Arthrobacter sp. FB24 (p-value 0.0028) and Arthrobacter aurescences (p-value 0.015), was observed in boys. The urinary mycobiome showed a significant rise in the genus Malassezia and Malassezia globose fungus (p-value 0.009) in girls, whereas genus Saccharomyces (p-value 0.009) was significantly high in boys. The beta diversity of the urinary mycobiome was found to differ between different age groups. Boys had significantly more Mastadenovirus and Human mastadenovirus-A in their urinary virome than girls. With increasing age, we noticed an increase in the relative abundance of the order Caudovirales. Our optimized protocols allowed us to identify the unique microbes for each sex by using an adequate volume of urine (3−10 mL) to screen for the bacteriome, mycobiome, and virome profiles in the urine of healthy children. To the best of our knowledge, this is the first study to characterize the metagenomics profiles of urine in a healthy pediatric population.}, } @article {pmid36289401, year = {2022}, author = {Gant, V and Singer, M}, title = {Combining pathogen and host metagenomics for a better sepsis diagnostic.}, journal = {Nature microbiology}, volume = {7}, number = {11}, pages = {1713-1714}, pmid = {36289401}, issn = {2058-5276}, mesh = {Humans ; *Metagenomics ; *Sepsis/diagnosis ; Host-Pathogen Interactions ; }, } @article {pmid36289228, year = {2022}, author = {Al-Ashhab, A and Marmen, S and Schweitzer-Natan, O and Bolotin, E and Patil, H and Viner-Mozzini, D and Aharonovich, D and Hershberg, R and Minz, D and Carmeli, S and Cytryn, E and Sukenik, A and Sher, D}, title = {Freshwater microbial metagenomes sampled across different water body characteristics, space and time in Israel.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {652}, pmid = {36289228}, issn = {2052-4463}, mesh = {*Cyanobacteria ; Ecosystem ; Israel ; Lakes ; *Metagenome ; }, abstract = {Freshwater bodies are critical components of terrestrial ecosystems. The microbial communities of freshwater ecosystems are intimately linked water quality. These microbes interact with, utilize and recycle inorganic elements and organic matter. Here, we present three metagenomic sequence datasets (total of 182.9 Gbp) from different freshwater environments in Israel. The first dataset is from diverse freshwater bodies intended for different usages - a nature reserve, irrigation and aquaculture facilities, a tertiary wastewater treatment plant and a desert rainfall reservoir. The second represents a two-year time-series, collected during 2013-2014 at roughly monthly intervals, from a water reservoir connected to an aquaculture facility. The third is from several time-points during the winter and spring of 2015 in Lake Kinneret, including a bloom of the cyanobacterium Microcystis sp. These datasets are accompanied by physical, chemical, and biological measurements at each sampling point. We expect that these metagenomes will facilitate a wide range of comparative studies that seek to illuminate new aspects of freshwater microbial ecosystems and inform future water quality management approaches.}, } @article {pmid36289209, year = {2022}, author = {Kim, CY and Ma, J and Lee, I}, title = {HiFi metagenomic sequencing enables assembly of accurate and complete genomes from human gut microbiota.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6367}, pmid = {36289209}, issn = {2041-1723}, mesh = {Humans ; *Metagenome/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Sequence Analysis, DNA ; High-Throughput Nucleotide Sequencing ; Nucleotides ; }, abstract = {Advances in metagenomic assembly have led to the discovery of genomes belonging to uncultured microorganisms. Metagenome-assembled genomes (MAGs) often suffer from fragmentation and chimerism. Recently, 20 complete MAGs (cMAGs) have been assembled from Oxford Nanopore long-read sequencing of 13 human fecal samples, but with low nucleotide accuracy. Here, we report 102 cMAGs obtained by Pacific Biosciences (PacBio) high-accuracy long-read (HiFi) metagenomic sequencing of five human fecal samples, whose initial circular contigs were selected for complete prokaryotic genomes using our bioinformatics workflow. Nucleotide accuracy of the final cMAGs was as high as that of Illumina sequencing. The cMAGs could exceed 6 Mbp and included complete genomes of diverse taxa, including entirely uncultured RF39 and TANB77 orders. Moreover, cMAGs revealed that regions hard to assemble by short-read sequencing comprised mostly genomic islands and rRNAs. HiFi metagenomic sequencing will facilitate cataloging accurate and complete genomes from complex microbial communities, including uncultured species.}, } @article {pmid36289064, year = {2022}, author = {Nzabarushimana, E and Tang, H}, title = {Functional profile of host microbiome indicates Clostridioides difficile infection.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2135963}, pmid = {36289064}, issn = {1949-0984}, support = {R01 AI143254/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Clostridioides difficile/genetics ; *Gastrointestinal Microbiome ; *Clostridium Infections/therapy ; Fecal Microbiota Transplantation/methods ; *Microbiota ; Anti-Bacterial Agents/therapeutic use ; Treatment Outcome ; }, abstract = {Clostridioides difficile infection (CDI) is a gastro-intestinal (GI) infection that illustrates how perturbations in symbiotic host-microbiome interactions render the GI tract vulnerable to the opportunistic pathogens. CDI also serves as an example of how such perturbations could be reversed via gut microbiota modulation mechanisms, especially fecal microbiota transplantation (FMT). However, microbiome-mediated diagnosis of CDI remains understudied. Here, we evaluated the diagnostic capabilities of the fecal microbiome on the prediction of CDI. We used the metagenomic sequencing data from ten previous studies, encompassing those acquired from CDI patients treated by FMT, CDI-negative patients presenting other intestinal health conditions, and healthy volunteers taking antibiotics. We designed a hybrid species/function profiling approach that determines the abundances of microbial species in the community contributing to its functional profile. These functionally informed taxonomic profiles were then used for classification of the microbial samples. We used logistic regression (LR) models using these features, which showed high prediction accuracy (with an average AUC≥0.91), substantiating that the species/function composition of the gut microbiome has a robust diagnostic prediction of CDI. We further assessed the confounding impact of antibiotic therapy on CDI prediction and found that it is distinguishable from the CDI impact. Finally, we devised a log-odds score computed from the output of the LR models to quantify the likelihood of CDI in a gut microbiome sample and applied it to evaluating the effectiveness of FMT based on post-FMT microbiome samples. The results showed that the gut microbiome of patients exhibited a gradual but steady improvement after receiving successful FMT, indicating the restoration of the normal microbiome functions.}, } @article {pmid36288838, year = {2022}, author = {Fransson, E and Gudnadottir, U and Hugerth, LW and Itzel, EW and Hamsten, M and Boulund, F and Pennhag, A and Du, J and Schuppe-Koistinen, I and Brusselaers, N and Engstrand, L}, title = {Cohort profile: the Swedish Maternal Microbiome project (SweMaMi) - assessing the dynamic associations between the microbiome and maternal and neonatal adverse events.}, journal = {BMJ open}, volume = {12}, number = {10}, pages = {e065825}, pmid = {36288838}, issn = {2044-6055}, mesh = {Infant ; Pregnancy ; Infant, Newborn ; Female ; Humans ; Child ; Sweden/epidemiology ; *Premature Birth ; Pregnancy Trimester, Third ; Cohort Studies ; *Microbiota ; }, abstract = {PURPOSE: The Swedish Maternal Microbiome (SweMaMi) project was initiated to better understand the dynamics of the microbiome in pregnancy, with longitudinal microbiome sampling, shotgun metagenomics, extensive questionnaires and health registry linkage.

PARTICIPANTS: Pregnant women were recruited before the 20th gestational week during 2017-2021 in Sweden. In total, 5439 pregnancies (5193 unique women) were included. For 3973 pregnancies (73%), samples were provided at baseline, and for 3141 (58%) at all three timepoints (second and third trimester and postpartum). In total, 38 591 maternal microbiome samples (vaginal, faecal and saliva) and 3109 infant faecal samples were collected. Questionnaires were used to collect information on general, reproductive and mental health, diet and lifestyle, complemented by linkage to the nationwide health registries, also used to follow up the health of the offspring (up to age 10).

FINDINGS TO DATE: The cohort is fairly representative for the total Swedish pregnant population (data from 2019), with 41% first-time mothers. Women with university level education, born in Sweden, with normal body mass index, not using tobacco-products and aged 30-34 years were slightly over-represented.

FUTURE PLANS: The sample and data collection were finalised in November 2021. The next steps are the characterisation of the microbial DNA and linkage to the health and demographic information from the questionnaires and registries. The role of the microbiome on maternal and neonatal outcomes and early-childhood diseases will be explored (including preterm birth, miscarriage) and the role and interaction of other risk factors and confounders (including endometriosis, polycystic ovarian syndrome, diet, drug use). This is currently among the largest pregnancy cohorts in the world with longitudinal design and detailed and standardised microbiome sampling enabling follow-up of both mothers and children. The findings are expected to contribute greatly to the field of reproductive health focusing on pregnancy and neonatal outcomes.}, } @article {pmid36288395, year = {2022}, author = {Gorman, M and Xu, R and Prakoso, D and Salvador, LCM and Rajeev, S}, title = {Leptospira enrichment culture followed by ONT metagenomic sequencing allows better detection of Leptospira presence and diversity in water and soil samples.}, journal = {PLoS neglected tropical diseases}, volume = {16}, number = {10}, pages = {e0010589}, pmid = {36288395}, issn = {1935-2735}, mesh = {Animals ; Humans ; *Leptospira/genetics ; Water ; *Leptospirosis/diagnosis/epidemiology ; Zoonoses ; Soil ; }, abstract = {BACKGROUND: Leptospirosis, a life-threatening disease in humans and animals, is one of the most widespread global zoonosis. Contaminated soil and water are the major transmission sources in humans and animals. Clusters of disease outbreaks are common during rainy seasons.

In this study, to detect the presence of Leptospira, we applied PCR, direct metagenomic sequencing, and enrichment culture followed by PCR and metagenomic sequencing on water and soil samples. Direct sequencing and enrichment cultures followed by PCR or sequencing effectively detected pathogenic and nonpathogenic Leptospira compared to direct PCR and 16S amplification-based metagenomic sequencing in soil or water samples. Among multiple culture media evaluated, Ellinghausen-McCullough-Johnson-Harris (EMJH) media containing antimicrobial agents was superior in recovering and detecting Leptospira from the environmental samples. Our results show that enrichment culture followed by PCR can be used to confirm the presence of pathogenic Leptospira in environmental samples. Additionally, metagenomic sequencing on enrichment cultures effectively detects the abundance and diversity of Leptospira spp. from environmental samples.

CONCLUSIONS/SIGNIFICANCE: The selection of methodology is critical when testing environmental samples for the presence of Leptospira. Selective enrichment culture improves Leptospira detection efficacy by PCR or metagenomic sequencing and can be used successfully to understand the presence and diversity of pathogenic Leptospira during environmental surveillance.}, } @article {pmid36288294, year = {2023}, author = {Narayana, JK and Aliberti, S and Mac Aogáin, M and Jaggi, TK and Ali, NABM and Ivan, FX and Cheng, HS and Yip, YS and Vos, MIG and Low, ZS and Lee, JXT and Amati, F and Gramegna, A and Wong, SH and Sung, JJY and Tan, NS and Tsaneva-Atanasova, K and Blasi, F and Chotirmall, SH}, title = {Microbial Dysregulation of the Gut-Lung Axis in Bronchiectasis.}, journal = {American journal of respiratory and critical care medicine}, volume = {207}, number = {7}, pages = {908-920}, pmid = {36288294}, issn = {1535-4970}, mesh = {Animals ; Mice ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Lung/microbiology ; *Bronchiectasis/drug therapy ; *Microbiota ; }, abstract = {Rationale: Emerging data support the existence of a microbial "gut-lung" axis that remains unexplored in bronchiectasis. Methods: Prospective and concurrent sampling of gut (stool) and lung (sputum) was performed in a cohort of n = 57 individuals with bronchiectasis and subjected to bacteriome (16S rRNA) and mycobiome (18S Internal Transcribed Spacer) sequencing (total, 228 microbiomes). Shotgun metagenomics was performed in a subset (n = 15; 30 microbiomes). Data from gut and lung compartments were integrated by weighted similarity network fusion, clustered, and subjected to co-occurrence analysis to evaluate gut-lung networks. Murine experiments were undertaken to validate specific Pseudomonas-driven gut-lung interactions. Results: Microbial communities in stable bronchiectasis demonstrate a significant gut-lung interaction. Multibiome integration followed by unsupervised clustering reveals two patient clusters, differing by gut-lung interactions and with contrasting clinical phenotypes. A high gut-lung interaction cluster, characterized by lung Pseudomonas, gut Bacteroides, and gut Saccharomyces, is associated with increased exacerbations and greater radiological and overall bronchiectasis severity, whereas the low gut-lung interaction cluster demonstrates an overrepresentation of lung commensals, including Prevotella, Fusobacterium, and Porphyromonas with gut Candida. The lung Pseudomonas-gut Bacteroides relationship, observed in the high gut-lung interaction bronchiectasis cluster, was validated in a murine model of lung Pseudomonas aeruginosa infection. This interaction was abrogated after antibiotic (imipenem) pretreatment in mice confirming the relevance and therapeutic potential of targeting the gut microbiome to influence the gut-lung axis. Metagenomics in a subset of individuals with bronchiectasis corroborated our findings from targeted analyses. Conclusions: A dysregulated gut-lung axis, driven by lung Pseudomonas, associates with poorer clinical outcomes in bronchiectasis.}, } @article {pmid36288274, year = {2022}, author = {France, MT and Brown, SE and Rompalo, AM and Brotman, RM and Ravel, J}, title = {Identification of shared bacterial strains in the vaginal microbiota of related and unrelated reproductive-age mothers and daughters using genome-resolved metagenomics.}, journal = {PloS one}, volume = {17}, number = {10}, pages = {e0275908}, pmid = {36288274}, issn = {1932-6203}, support = {R01 AI116799/AI/NIAID NIH HHS/United States ; R01 NR015495/NR/NINR NIH HHS/United States ; R01 AI060892/AI/NIAID NIH HHS/United States ; }, mesh = {Child ; Humans ; Female ; Adolescent ; *Microbiota/genetics ; Vagina/microbiology ; Reproduction ; Bacteria/genetics ; Metagenomics ; }, abstract = {It has been suggested that the human microbiome might be vertically transmitted from mother to offspring and that early colonizers may play a critical role in development of the immune system. Studies have shown limited support for the vertical transmission of the intestinal microbiota but the derivation of the vaginal microbiota remains largely unknown. Although the vaginal microbiota of children and reproductive age women differ in composition, the vaginal microbiota could be vertically transmitted. To determine whether there was any support for this hypothesis, we examined the vaginal microbiota of daughter-mother pairs from the Baltimore metropolitan area (ages 14-27, 32-51; n = 39). We assessed whether the daughter's microbiota was similar in composition to their mother's using metataxonomics. Permutation tests revealed that while some pairs did have similar vaginal microbiota, the degree of similarity did not exceed that expected by chance. Genome-resolved metagenomics was used to identify shared bacterial strains in a subset of the families (n = 22). We found a small number of bacterial strains that were shared between mother-daughter pairs but identified more shared strains between individuals from different families, indicating that vaginal bacteria may display biogeographic patterns. Earlier-in-life studies are needed to demonstrate vertical transmission of the vaginal microbiota.}, } @article {pmid36288125, year = {2022}, author = {Kardos, G and Sárközi, R and Laczkó, L and Marton, S and Makrai, L and Bányai, K and Fodor, L}, title = {Genetic Diversity of Actinobacillus pleuropneumoniae Serovars in Hungary.}, journal = {Veterinary sciences}, volume = {9}, number = {10}, pages = {}, pmid = {36288125}, issn = {2306-7381}, support = {OTKA 132833//Hungarian Scientific Research Fund/ ; SA-27/2021//Eötvös Loránd Research Network/ ; }, abstract = {A total of 114 Actinobacillus pleuropneumoniae isolates from porcine hemorrhagic necrotic pleuropneumonia were characterized by the examination of biotype, serovar, antibiotic resistance genes, and genes of toxin production. Pulsed-field gel electrophoresis was used to analyze their genetic relationship, which identified 16 clusters. Serovar 2 (50 isolates), serovar 13 (25 isolates), serovar 9 (11 isolates), and serovar 16 (7 isolates) were the most frequent serovars. Serovar 2 formed nine distinguishable clusters; serovar 13 and serovar 16 were less diverse, exhibiting two potentially related subclusters; serovar 9 was represented by a single cluster. Remarkably small differences were seen in the core genome when nine representative isolates of serovar 13 were subjected to whole-genome sequencing. Tetracycline resistance was relatively frequent in the two clusters of serovar 13; one of them was also frequently resistant against beta-lactams. Resistance in other serovars was sporadic. All isolates carried the apxIV gene. The toxin profiles of serovar 2 were characterized by the production of ApxII and ApxIII toxins, except for a small cluster of three isolates: serovar 9 and serovar 16 isolates produced ApxI and ApxII toxins. Serovar 13 carried apxII and apxIBD genes, indicating the production of the ApxII toxin, but not of ApxI or ApxIII. The unusually high frequency and low diversity of serovar 13 are not explained by its virulence properties, but the high frequency of resistance to beta-lactams and tetracyclines may have played a role in its spread. The emergence of serovar 16 may be facilitated by its high virulence, also explaining its high clonality.}, } @article {pmid36287957, year = {2022}, author = {Le, KTN and Maldonado, JFG and Goitom, E and Trigui, H and Terrat, Y and Nguyen, TL and Husk, B and Shapiro, BJ and Sauvé, S and Prévost, M and Dorner, S}, title = {Shotgun Metagenomic Sequencing to Assess Cyanobacterial Community Composition following Coagulation of Cyanobacterial Blooms.}, journal = {Toxins}, volume = {14}, number = {10}, pages = {}, pmid = {36287957}, issn = {2072-6651}, mesh = {Microcystins/analysis ; *Drinking Water/analysis ; *Cyanobacteria/genetics ; *Microcystis/genetics ; Lakes/microbiology ; Nitrogen/analysis ; Phosphorus/analysis ; }, abstract = {The excessive proliferation of cyanobacteria in surface waters is a widespread problem worldwide, leading to the contamination of drinking water sources. Short- and long-term solutions for managing cyanobacterial blooms are needed for drinking water supplies. The goal of this research was to investigate the cyanobacteria community composition using shotgun metagenomics in a short term, in situ mesocosm experiment of two lakes following their coagulation with ferric sulfate (Fe2(SO4)3) as an option for source water treatment. Among the nutrient paramenters, dissolved nitrogen was related to Microcystis in both Missisquoi Bay and Petit Lac St. François, while the presence of Synechococcus was related to total nitrogen, dissolved nitrogen, dissolved organic carbon, and dissolved phosphorus. Results from the shotgun metagenomic sequencing showed that Dolichospermum and Microcystis were the dominant genera in all of the mesocosms in the beginning of the sampling period in Missisquoi Bay and Petit Lac St. François, respectively. Potentially toxigenic genera such as Microcystis were correlated with intracellular microcystin concentrations. A principal component analysis showed that there was a change of the cyanobacterial composition at the genus level in the mesocosms after two days, which varied across the studied sites and sampling time. The cyanobacterial community richness and diversity did not change significantly after its coagulation by Fe2(SO4)3 in all of the mesocosms at either site. The use of Fe2(SO4)3 for an onsite source water treatment should consider its impact on cyanobacterial community structure and the reduction of toxin concentrations.}, } @article {pmid36287893, year = {2022}, author = {Duarte, B and Figueiredo, A and Ramalhosa, P and Canning-Clode, J and Caçador, I and Fonseca, VF}, title = {Unravelling the Portuguese Coastal and Transitional Waters' Microbial Resistome as a Biomarker of Differential Anthropogenic Impact.}, journal = {Toxics}, volume = {10}, number = {10}, pages = {}, pmid = {36287893}, issn = {2305-6304}, support = {UIDB/04292/2020//Fundação para a Ciência e Tecnologia/ ; UIDB/04292/2020//Fundação para a Ciência e Tecnologia/ ; UIDP/04046/2020//Fundação para a Ciência e Tecnologia/ ; LA/P/0069/2020//Fundação para a Ciência e Tecnologia/ ; UE-contract-287589//European Union/ ; CEECIND/00511/2017//Fundação para a Ciência e Tecnologia/ ; 2021.00244.CEECIND//Fundação para a Ciência e Tecnologia/ ; M1420-01-0145-FEDER-000001//European Regional Development Fund/ ; CEECINST/00098/2018//Fundação para a Ciência e Tecnologia/ ; }, abstract = {Portugal mainland and Atlantic archipelagos (Madeira and Azores) provide a wide array of coastal ecosystems with varying typology and degrees of human pressure, which shape the microbial communities thriving in these habitats, leading to the development of microbial resistance traits. The samples collected on the Portuguese northeast Atlantic coast waters show an unequivocal prevalence of Bacteria over Archaea with a high prevalence of Proteobacteria, Cyanobacteria, Bacteroidetes and Actinobacteria. Several taxa, such as the Vibrio genus, showed significant correlations with anthropogenic pollution. These anthropogenic pressures, along with the differences in species diversity among the surveyed sites, lead to observed differences in the presence and resistance-related sequences' abundance (set of all metal and antibiotic resistant genes and their precursors in pathogenic and non-pathogenic bacteria). Gene ontology terms such as antibiotic resistance, redox regulation and oxidative stress response were prevalent. A higher number of significant correlations were found between the abundance of resistance-related sequences and pollution, inorganic pressures and density of nearby population centres when compared to the number of significant correlations between taxa abundance at different phylogenetic levels and the same environmental traits. This points towards predominance of the environmental conditions over the sequence abundance rather than the taxa abundance. Our data suggest that the whole resistome profile can provide more relevant or integrative answers in terms of anthropogenic disturbance of the environment, either as a whole or grouped in gene ontology groups, appearing as a promising tool for impact assessment studies which, due to the ubiquity of the sequences across microbes, can be surveyed independently of the taxa present in the samples.}, } @article {pmid36287790, year = {2022}, author = {Cho, HW and Choi, S and Seo, K and Kim, KH and Jeon, JH and Kim, CH and Lim, S and Jeong, S and Chun, JL}, title = {Gut microbiota profiling in aged dogs after feeding pet food contained Hericium erinaceus.}, journal = {Journal of animal science and technology}, volume = {64}, number = {5}, pages = {937-949}, pmid = {36287790}, issn = {2055-0391}, abstract = {Health concern of dogs is the most important issue for pet owners. People who have companied the dogs long-term provide the utmost cares for their well-being and healthy life. Recently, it was revealed that the population and types of gut microbiota affect the metabolism and immunity of the host. However, there is little information on the gut microbiome of dogs. Hericium erinaceus (H. erinaceus; HE) is one of the well-known medicinal mushrooms and has multiple bioactive components including polyphenol, β-glucan, polysaccharides, ergothioneine, hericerin, erinacines, etc. Here we tested a pet food that contained H. erinaceus for improvement in the gut microbiota environment of aged dogs. A total of 18 dogs, each 11 years old, were utilized. For sixteen weeks, the dogs were fed with 0.4 g of H. erinaceus (HE-L), or 0.8 g (HE-H), or without H. erinaceus (CON) per body weight (kg) with daily diets (n = 6 per group). Taxonomic analysis was performed using metagenomics to investigate the difference in the gut microbiome. Resulting from principal coordinates analysis (PCoA) to confirm the distance difference between the groups, there was a significant difference between HE-H and CON due to weighted Unique fraction metric (Unifrac) distance (p = 0.047), but HE-L did not have a statistical difference compared to that of CON. Additionally, the result of Linear discriminate analysis of effect size (LEfSe) showed that phylum Bacteroidetes in HE-H and its order Bacteroidales increased, compared to that of CON, Additionally, phylum Firmicutes in HE-H, and its genera (Streptococcus, Tyzzerella) were reduced. Furthermore, at the family level, Campylobacteraceae and its genus Campylobacter in HE-H was decreased compared to that of CON. Summarily, our data demonstrated that the intake of H. erinaceus can regulate the gut microbial community in aged dogs, and an adequate supply of HE on pet diets would possibly improve immunity and anti-obesity on gut-microbiota in dogs.}, } @article {pmid36287644, year = {2023}, author = {Walsh, LH and Coakley, M and Walsh, AM and O'Toole, PW and Cotter, PD}, title = {Bioinformatic approaches for studying the microbiome of fermented food.}, journal = {Critical reviews in microbiology}, volume = {49}, number = {6}, pages = {693-725}, doi = {10.1080/1040841X.2022.2132850}, pmid = {36287644}, issn = {1549-7828}, mesh = {*Microbiota/genetics ; Metagenome ; Computational Biology/methods ; *Fermented Foods ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {High-throughput DNA sequencing-based approaches continue to revolutionise our understanding of microbial ecosystems, including those associated with fermented foods. Metagenomic and metatranscriptomic approaches are state-of-the-art biological profiling methods and are employed to investigate a wide variety of characteristics of microbial communities, such as taxonomic membership, gene content and the range and level at which these genes are expressed. Individual groups and consortia of researchers are utilising these approaches to produce increasingly large and complex datasets, representing vast populations of microorganisms. There is a corresponding requirement for the development and application of appropriate bioinformatic tools and pipelines to interpret this data. This review critically analyses the tools and pipelines that have been used or that could be applied to the analysis of metagenomic and metatranscriptomic data from fermented foods. In addition, we critically analyse a number of studies of fermented foods in which these tools have previously been applied, to highlight the insights that these approaches can provide.}, } @article {pmid36287140, year = {2022}, author = {Huang, W and Han, D and Cai, Q and Yi, X and Tang, J and Fang, Y and Lu, Y}, title = {First identification of human infection with Erysipelothrix Piscisicarius by metagenomic next-generation sequencing.}, journal = {Emerging microbes & infections}, volume = {11}, number = {1}, pages = {2781-2784}, pmid = {36287140}, issn = {2222-1751}, mesh = {Humans ; *Erysipelothrix/genetics ; Metagenomics ; Metagenome ; High-Throughput Nucleotide Sequencing ; }, } @article {pmid36287108, year = {2023}, author = {Ponziani, FR and Nesci, A and Caputo, C and Salvatore, L and Picca, A and Del Chierico, F and Paroni Sterbini, F and Marzetti, E and Di Giorgio, A and Santoro, L and Putignani, L and Gasbarrini, A and Santoliquido, A and Pompili, M}, title = {High prevalence of lower limb atherosclerosis is linked with the gut-liver axis in patients with primary biliary cholangitis.}, journal = {Liver international : official journal of the International Association for the Study of the Liver}, volume = {43}, number = {2}, pages = {370-380}, pmid = {36287108}, issn = {1478-3231}, mesh = {Humans ; Female ; *Liver Cirrhosis, Biliary/complications ; *Non-alcoholic Fatty Liver Disease/epidemiology/complications ; Tumor Necrosis Factor-alpha ; *Hypercholesterolemia/complications ; Prevalence ; Vascular Cell Adhesion Molecule-1 ; *Atherosclerosis/epidemiology/complications ; Lower Extremity ; }, abstract = {BACKGROUND AND AIMS: Hypercholesterolemia is frequent in people with primary biliary cholangitis (PBC); however, it does not seem to confer an increased risk of cardiovascular disease. We aimed to evaluate the prevalence of peripheral arterial disease in PBC women and its association with the gut-liver axis and systemic inflammation.

METHODS: Thirty patients affected by PBC and hypercholesterolemia were enrolled, with equal-sized groups of women with non-alcoholic fatty liver disease (NAFLD) and healthy controls (CTRL). All patients underwent Doppler ultrasound examination of peripheral arteries, assessment of flow-mediated dilation, quantification of circulating cytokines and vasoactive mediators and characterization of the gut microbiota.

RESULTS: PBC patients had a higher prevalence of lower extremity arterial disease (LEAD) defined as atherosclerotic plaques in any of femoral, popliteal and/or tibial arteries compared with both NAFLD and CTRL women (83.3% vs. 53.3% and 50%, respectively; p = .01). Factors associated with LEAD at univariate analysis were VCAM-1 (p = .002), ICAM-1 (p = .003), and TNF-alpha (p = .04) serum levels, but only VCAM-1 (OR 1.1, 95% CI 1.0-1.1; p = .04) and TNF-alpha (OR 1.12, 95% CI 0.99-1.26; p = .04) were confirmed as independent predictors in the multivariate model. Gut microbiota analysis revealed that Acidaminococcus (FDR = 0.0008), Bifidobacterium (FDR = 0.001) and Oscillospira (FDR = 0.03) were differentially expressed among groups. Acidaminococcus, which was increased in PBC, was positively correlated with TNF-alpha serum levels. Down-regulation of metabolic pathways linked to fatty acid and butyrate metabolism, glyoxylate metabolism and branched-chain amino acids degradation was found in the functional gut metagenome of PBC women.

CONCLUSIONS: LEAD is common in patients affected by PBC and is associated with inflammatory markers and alterations in the gut-liver axis.}, } @article {pmid36287061, year = {2022}, author = {Li, Y and Shi, X and Zuo, Y and Li, T and Liu, L and Shen, Z and Shen, J and Zhang, R and Wang, S}, title = {Multiplexed Target Enrichment Enables Efficient and In-Depth Analysis of Antimicrobial Resistome in Metagenomes.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0229722}, pmid = {36287061}, issn = {2165-0497}, mesh = {Humans ; *Metagenome ; *Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Sewage ; Metagenomics/methods ; }, abstract = {Antibiotic resistance genes (ARGs) pose a serious threat to public health and ecological security in the 21st century. However, the resistome only accounts for a tiny fraction of metagenomic content, which makes it difficult to investigate low-abundance ARGs in various environmental settings. Thus, a highly sensitive, accurate, and comprehensive method is needed to describe ARG profiles in complex metagenomic samples. In this study, we established a high-throughput sequencing method based on targeted amplification, which could simultaneously detect ARGs (n = 251), mobile genetic element genes (n = 8), and metal resistance genes (n = 19) in metagenomes. The performance of amplicon sequencing was compared with traditional metagenomic shotgun sequencing (MetaSeq). A total of 1421 primer pairs were designed, achieving extremely high coverage of target genes. The amplicon sequencing significantly improved the recovery of target ARGs (~9 × 10[4]-fold), with higher sensitivity and diversity, less cost, and computation burden. Furthermore, targeted enrichment allows deep scanning of single nucleotide polymorphisms (SNPs), and elevated SNPs detection was shown in this study. We further performed this approach for 48 environmental samples (37 feces, 20 soils, and 7 sewage) and 16 clinical samples. All samples tested in this study showed high diversity and recovery of targeted genes. Our results demonstrated that the approach could be applied to various metagenomic samples and served as an efficient tool in the surveillance and evolution assessment of ARGs. Access to the resistome using the enrichment method validated in this study enabled the capture of low-abundance resistomes while being less costly and time-consuming, which can greatly advance our understanding of local and global resistome dynamics. IMPORTANCE ARGs, an increasing global threat to human health, can be transferred into health-related microorganisms in the environment by horizontal gene transfer, posing a serious threat to public health. Advancing profiling methods are needed for monitoring and predicting the potential risks of ARGs in metagenomes. Our study described a customized amplicon sequencing assay that could enable a high-throughput, targeted, in-depth analysis of ARGs and detect a low-abundance portion of resistomes. This method could serve as an efficient tool to assess the variation and evolution of specific ARGs in the clinical and natural environment.}, } @article {pmid36287009, year = {2022}, author = {Fisher, S and De Villers, D and Du Plessis, M and Hattingh, K and Saulse, C and Basson, G and Barker, A and Innalegwu Daniel, A and Al-Hashimi, A and Hitzeroth, A and Makhalanyane, T and Mavumengwana, V and Gokul, A and Keyster, M and Klein, A}, title = {Draft Whole-Genome Sequence of Penicillium simplicissimum A4, a Putative Endophyte from Echium plantagineum.}, journal = {Microbiology resource announcements}, volume = {11}, number = {11}, pages = {e0085422}, pmid = {36287009}, issn = {2576-098X}, support = {120411//National Research Foundation (NRF)/ ; }, abstract = {We report the draft whole-genome sequence of the putative endophytic fungus Penicillium simplicissimum A4, isolated from the roots of Echium plantagineum plants. The genome was sequenced using PacBio technology with an estimated genome size of 39 Mb.}, } @article {pmid36286994, year = {2022}, author = {Zhong, YW and Zhou, P and Cheng, H and Zhou, YD and Pan, J and Xu, L and Li, M and Tao, CH and Wu, YH and Xu, XW}, title = {Metagenomic Features Characterized with Microbial Iron Oxidoreduction and Mineral Interaction in Southwest Indian Ridge.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0061422}, pmid = {36286994}, issn = {2165-0497}, mesh = {*Metagenome ; *Iron ; Phylogeny ; Minerals ; Sulfur/metabolism ; Oxidation-Reduction ; Carbon/metabolism ; RNA, Ribosomal, 16S ; }, abstract = {The Southwest Indian Ridge (SWIR) is one of the typical representatives of deep-sea ultraslow-spreading ridges, and has increasingly become a hot spot of studying subsurface geological activities and deep-sea mining management. However, the understanding of microbial activities is still limited on active hydrothermal vent chimneys in SWIR. In this study, samples from an active black smoker and a diffuse vent located in the Longqi hydrothermal region were collected for deep metagenomic sequencing, which yielded approximately 290 GB clean data and 295 mid-to-high-quality metagenome-assembled genomes (MAGs). Sulfur oxidation conducted by a variety of Gammaproteobacteria, Alphaproteobacteria, and Campylobacterota was presumed to be the major energy source for chemosynthesis in Longqi hydrothermal vents. Diverse iron-related microorganisms were recovered, including iron-oxidizing Zetaproteobacteria, iron-reducing Deferrisoma, and magnetotactic bacterium. Twenty-two bacterial MAGs from 12 uncultured phyla harbored iron oxidase Cyc2 homologs and enzymes for organic carbon degradation, indicated novel chemolithoheterotrophic iron-oxidizing bacteria that affected iron biogeochemistry in hydrothermal vents. Meanwhile, potential interactions between microbial communities and chimney minerals were emphasized as enriched metabolic potential of siderophore transportation, and extracellular electron transfer functioned by multi-heme proteins was discovered. Composition of chimney minerals probably affected microbial iron metabolic potential, as pyrrhotite might provide more available iron for microbial communities. Collectively, this study provides novel insights into microbial activities and potential mineral-microorganism interactions in hydrothermal vents. IMPORTANCE Microbial activities and interactions with minerals and venting fluid in active hydrothermal vents remain unclear in the ultraslow-spreading SWIR (Southwest Indian Ridge). Understanding about how minerals influence microbial metabolism is currently limited given the obstacles in cultivating microorganisms with sulfur or iron oxidoreduction functions. Here, comprehensive descriptions on microbial composition and metabolic profile on 2 hydrothermal vents in SWIR were obtained based on cultivation-free metagenome sequencing. In particular, autotrophic sulfur oxidation supported by minerals was presumed, emphasizing the role of chimney minerals in supporting chemosynthesis. Presence of novel heterotrophic iron-oxidizing bacteria was also indicated, suggesting overlooked biogeochemical pathways directed by microorganisms that connected sulfide mineral dissolution and organic carbon degradation in hydrothermal vents. Our findings offer novel insights into microbial function and biotic interactions on minerals in ultraslow-spreading ridges.}, } @article {pmid36286976, year = {2022}, author = {Starikova, EV and Galeeva, JS and Andreev, DN and Sokolov, PS and Fedorov, DE and Manolov, AI and Pavlenko, AV and Klimina, KM and Veselovsky, VA and Zaborovsky, AV and Evdokimov, VV and Andreev, NG and Devkota, MK and Fomenko, AK and Khar'kovskii, VA and Asadulin, PO and Kucher, SA and Cheremushkina, AS and Yanushevich, OO and Maev, IV and Krikheli, NI and Levchenko, OV and Ilina, EN and Govorun, VM}, title = {[Composition of oropharyngeal microbiota in patients with COVID-19 of different pneumonia severity].}, journal = {Terapevticheskii arkhiv}, volume = {94}, number = {8}, pages = {963-972}, doi = {10.26442/00403660.2022.08.201780}, pmid = {36286976}, issn = {0040-3660}, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *COVID-19 ; *Microbiota ; Oropharynx/microbiology ; Lung ; }, abstract = {AIM: To identify features of the taxonomic composition of the oropharyngeal microbiota of COVID-19 patients with different disease severity.

MATERIALS AND METHODS: The study group included 156 patients hospitalized with confirmed diagnosis of COVID-19 in the clinical medical center of Yevdokimov Moscow State University of Medicine and Dentistry between April and June 2021. There were 77 patients with mild pneumonia according to CT (CT1) and 79 patients with moderate to severe pneumonia (CT2 and CT3). Oropharyngeal swabs were taken when the patient was admitted to the hospital. Total DNA was isolated from the samples, then V3V4 regions of the 16s rRNA gene were amplified, followed by sequencing using Illumina HiSeq 2500 platform. DADA2 algorithm was used to obtain amplicon sequence variants (ASV).

RESULTS: When comparing the microbial composition of the oropharynx of the patients with different forms of pneumonia, we have identified ASVs associated with the development of both mild and severe pneumonia outside hospital treatment. Based on the results obtained, ASVs associated with a lower degree of lung damage belong predominantly to the class of Gram-negative Firmicutes (Negativicutes), to various classes of Proteobacteria, as well as to the order Fusobacteria. In turn, ASVs associated with a greater degree of lung damage belong predominantly to Gram-positive classes of Firmicutes Bacilli and Clostridia. While being hospitalized, patients with severe pneumonia demonstrated negative disease dynamics during treatment significantly more often.

CONCLUSION: We have observed differences in the taxonomic composition of the oropharyngeal microbiota in patients with different forms of pneumonia developed outside hospital treatment against COVID-19. Such differences might be due to the presumed barrier function of the oropharyngeal microbiota, which reduces the risk of virus titer increase.}, } @article {pmid36285994, year = {2022}, author = {Zhang, JS and Chu, CH and Yu, OY}, title = {Oral Microbiome and Dental Caries Development.}, journal = {Dentistry journal}, volume = {10}, number = {10}, pages = {}, pmid = {36285994}, issn = {2304-6767}, abstract = {Dental caries remains the most prevalent oral disease worldwide. The development of dental caries is highly associated with the microbiota in the oral cavity. Microbiological research of dental caries has been conducted for over a century, with conventional culture-based methods and targeted molecular methods being used in order to identify the microorganisms related to dental caries. These methods' major limitation is that they can identify only part of the culturable microorganisms in the oral cavity. Introducing sequencing-based technology and bioinformatics analysis has boosted oral microbiome research and greatly expanded the understanding of complex oral microbiology. With the continuing revolution of molecular technologies and the accumulated sequence data of the oral microbiome, researchers have realized that microbial composition alone may be insufficient to uncover the relationship between caries and the microbiome. Most updated evidence has coupled metagenomics with transcriptomics and metabolomics techniques in order to comprehensively understand the microbial contribution to dental caries. Therefore, the objective of this article is to give an overview of the research of the oral microbiome and the development of dental caries. This article reviews the classical concepts of the microbiological aspect of dental caries and updates the knowledge of caries microbiology with the results of current studies on the oral microbiome. This paper also provides an update on the caries etiological theory, the microorganisms related to caries development, and the shifts in the microbiome in dental caries development.}, } @article {pmid36284711, year = {2022}, author = {Keren, R and Méheust, R and Santini, JM and Thomas, A and West-Roberts, J and Banfield, JF and Alvarez-Cohen, L}, title = {Global genomic analysis of microbial biotransformation of arsenic highlights the importance of arsenic methylation in environmental and human microbiomes.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {559-572}, pmid = {36284711}, issn = {2001-0370}, abstract = {Arsenic is a ubiquitous toxic element, the global cycle of which is highly affected by microbial redox reactions and assimilation into organoarsenic compounds through sequential methylation reactions. While microbial biotransformation of arsenic has been studied for decades, the past years have seen the discovery of multiple new genes related to arsenic metabolism. Still, most studies focus on a small set of key genes or a small set of cultured microorganisms. Here, we leveraged the recently greatly expanded availability of microbial genomes of diverse organisms from lineages lacking cultivated representatives, including those reconstructed from metagenomes, to investigate genetic repertoires of taxonomic and environmental controls on arsenic metabolic capacities. Based on the collection of arsenic-related genes, we identified thirteen distinct metabolic guilds, four of which combine the aio and ars operons. We found that the best studied phyla have very different combinations of capacities than less well-studied phyla, including phyla lacking isolated representatives. We identified a distinct arsenic gene signature in the microbiomes of humans exposed or likely exposed to drinking water contaminated by arsenic and that arsenic methylation is important in soil and in human microbiomes. Thus, the microbiomes of humans exposed to arsenic have the potential to exacerbate arsenic toxicity. Finally, we show that machine learning can predict bacterial arsenic metabolism capacities based on their taxonomy and the environment from which they were sampled.}, } @article {pmid36284144, year = {2022}, author = {Han, Y and Kinfu, BM and Blombach, F and Cackett, G and Zhang, H and Pérez-García, P and Krohn, I and Salomon, J and Besirlioglu, V and Mirzaeigarakani, T and Schwaneberg, U and Chow, J and Werner, F and Streit, WR}, title = {A novel metagenome-derived viral RNA polymerase and its application in a cell-free expression system for metagenome screening.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {17882}, pmid = {36284144}, issn = {2045-2322}, mesh = {*Metagenome ; *Viral Replicase Complex Proteins ; Cell-Free System/metabolism ; RNA, Viral/metabolism ; DNA-Directed RNA Polymerases/genetics/metabolism ; Metagenomics/methods ; Escherichia coli/genetics/metabolism ; }, abstract = {The mining of genomes from non-cultivated microorganisms using metagenomics is a powerful tool to discover novel proteins and other valuable biomolecules. However, function-based metagenome searches are often limited by the time-consuming expression of the active proteins in various heterologous host systems. We here report the initial characterization of novel single-subunit bacteriophage RNA polymerase, EM1 RNAP, identified from a metagenome data set obtained from an elephant dung microbiome. EM1 RNAP and its promoter sequence are distantly related to T7 RNA polymerase. Using EM1 RNAP and a translation-competent Escherichia coli extract, we have developed an efficient medium-throughput pipeline and protocol allowing the expression of metagenome-derived genes and the production of proteins in cell-free system is sufficient for the initial testing of the predicted activities. Here, we have successfully identified and verified 12 enzymes acting on bis(2-hydroxyethyl) terephthalate (BHET) in a completely clone-free approach and proposed an in vitro high-throughput metagenomic screening method.}, } @article {pmid36283493, year = {2022}, author = {Zhang, P and Zhang, ZH and Liang, J and Shen, DY and Li, J and Wang, D and Jin, FF and Song, H and Zhang, JY and Xu, WQ and Tang, YM and Xu, XJ}, title = {Metagenomic next-generation sequencing for the diagnosis of fever of unknown origin in pediatric patients with hematological malignancy.}, journal = {Clinica chimica acta; international journal of clinical chemistry}, volume = {537}, number = {}, pages = {133-139}, doi = {10.1016/j.cca.2022.10.008}, pmid = {36283493}, issn = {1873-3492}, mesh = {Humans ; Child ; *Fever of Unknown Origin/diagnosis/genetics ; Interleukin-6 ; Sensitivity and Specificity ; High-Throughput Nucleotide Sequencing/methods ; *Bacterial Infections ; *Hematologic Neoplasms/complications/genetics ; }, abstract = {BACKGROUND AND AIMS: The aim of this study was to evaluate the performance of metagenomic next-generation sequencing (mNGS) in identifying microbiological etiologies in pediatric patients with hematological malignancies undergoing fever of unknown origin (FUO).

METHODS: A total of 147 children with hematological malignancy suffering febrile diseases without definite microbiological etiologies under conventional tests were enrolled. The clinical record, serum inflammatory biomarkers and mNGS results were analyzed.

RESULTS: At least one microorganism was identified by mNGS in 112 of 147 patients (76.2 %). Two or more types of organisms were detected simultaneously in 35.7 % (40/112) of samples. Of the 112 cases with positive mNGS results, the reported microorganisms were considered as etiologies of fever in 50 (44.6 %) cases. The initial antimicrobial regimens were adjusted according to the mNGS results in 48 cases, with 41 patients' febrile diseases resolved. Totally, 27.9 % (41/147) of patients benefit from mNGS. High IL-6 (>390 pg/mL) level was associated with bacterial infection and could help to interpret the results of mNGS.

CONCLUSION: mNGS is a novel approach to determine the microbiological etiology of FUO in hematological malignancy patients, which benefits about a quarter of all patients tested. Integration of IL-6 can improve the diagnostic precision of bacterial infection.}, } @article {pmid36283165, year = {2022}, author = {Papakonstantinou, A and Nuciforo, P and Borrell, M and Zamora, E and Pimentel, I and Saura, C and Oliveira, M}, title = {The conundrum of breast cancer and microbiome - A comprehensive review of the current evidence.}, journal = {Cancer treatment reviews}, volume = {111}, number = {}, pages = {102470}, doi = {10.1016/j.ctrv.2022.102470}, pmid = {36283165}, issn = {1532-1967}, mesh = {Humans ; Female ; *Breast Neoplasms ; *Microbiota ; Bacteria ; *Gastrointestinal Microbiome ; }, abstract = {Disturbance of the microbial balance of a habitat can have detrimental effects on the health of the individual and, in addition, polymorphic microbiomes were recently suggested as emerging cancer hallmarks. Modern sequencing and metagenomics techniques have allowed characterization of intratumoral microbiome composition even in tissues such as the breast. We conducted a comprehensive literature review on different aspects related to the microbial landscape of the breast tissue and breast tumors, as well as its relation to systemic therapy. Emerging data suggest varying microbiome composition intratumorally compared to the normal breast tissue and other tumor types. Differences in the microbes present in normal breast and cancerous lesions of the breast have also been described, as well as potential correlation between microbiome composition and breast cancer subtype and stage. The interplay between gut and breast microbiome is not well understood although bacterial allocation through mesenteric lymph nodes has been suggested as a possible pathway. Moreover, gut bacteria with estrogen metabolizing properties are of special interest in the context of breast cancer and available knowledge and reported studies are hereby described. The relationship of gut microbiome and cancer therapy is another aspect of interest and available data are presented. Notwithstanding, the field of microbiome in the context of breast cancer is starting to evolve and a number of questions arise, with the gut-breast-cancer therapy axis in the center.}, } @article {pmid36283158, year = {2022}, author = {Liao, H and Li, H and Duan, CS and Zhou, XY and An, XL and Zhu, YG and Su, JQ}, title = {Metagenomic and viromic analysis reveal the anthropogenic impacts on the plasmid and phage borne transferable resistome in soil.}, journal = {Environment international}, volume = {170}, number = {}, pages = {107595}, doi = {10.1016/j.envint.2022.107595}, pmid = {36283158}, issn = {1873-6750}, mesh = {Humans ; *Bacteriophages ; Soil ; Anthropogenic Effects ; Metagenomics ; }, abstract = {Anthropogenic land use changes have been recognized with significant effects on the abundance and diversity of antibiotic resistance genes (ARGs) in soil, but their impacts on ARGs with potential health risk remained poorly understood. In this study, paired metagenomes and viromes were obtained from soils (Anthrosols and Nitisols) with different land uses including urban parks, road verge, forests, vegetable and paddy in a subtropical city, Xiamen, and soils (Anthrosols) with various long-term fertilization treatments in Dezhou located in temperate region, respectively, to explore the influence of anthropogenic activity on soil resistome. The diversity and abundance of antibiotic resistance genes (ARGs) were profiled, and the risk associated factors of ARGs, i.e., genetic location, host, and co-existence with virulence factors (VFs), were systematically investigated at reads and contigs level. We observed that agricultural areas significantly enriched human-related ARGs and viruses, and positively related with clinical ARGs. Most of the ARG-carrying contigs were chromosomes (∼85 %), while, human-related ARGs presented a higher odds ratio to locate on plasmids. Soil VFs exhibited land use pattern and distinct distribution between chromosome and plasmids, but less mobile than ARGs. Analysis of 131,014 soil viral genomes indicated that they barely encoded ARGs, nevertheless, transduction of VLPs was implicated in the spread of ARGs. The results can be mutually verified in Xiamen and Dezhou datasets. Overall, the agricultural soils with dry-farming are hotspots for the clinical ARGs, and the transmission of clinical ARGs between human dominated environments and soil is primarily mediated by plasmids, rather than bacterial chromosomes, and the transduction of human-gut related viruses could participate the process. These results highlight the importance of tracking the fate of clinical ARGs for better evaluating the impacts of human activities on soil resistome.}, } @article {pmid36283075, year = {2022}, author = {Liu, H and Xu, R and Häggblom, MM and Zhang, J and Sun, X and Gao, P and Li, J and Yan, W and Gao, W and Gao, P and Liu, G and Zhang, H and Sun, W}, title = {Immobile Iron-Rich Particles Promote Arsenic Retention and Regulate Arsenic Biotransformation in Treatment Wetlands.}, journal = {Environmental science & technology}, volume = {56}, number = {22}, pages = {15627-15637}, doi = {10.1021/acs.est.2c04421}, pmid = {36283075}, issn = {1520-5851}, mesh = {*Arsenic/analysis ; Wetlands ; Iron ; Adsorption ; Oxidation-Reduction ; Biotransformation ; Bacteria ; *Water Pollutants, Chemical ; }, abstract = {Remediation of arsenic (As)-contaminated wastewater by treatment wetlands (TWs) remains a technological challenge due to the low As adsorption capacity of wetland substrates and the release of adsorbed As to pore water. This study investigated the feasibility of using immobile iron-rich particles (IIRP) to promote As retention and to regulate As biotransformation in TWs. Iron-rich particles prepared were immobilized in the interspace of a gravel substrate. TWs with IIRP amendment (IIRP-TWs) achieved a stable As removal efficiency of 63 ± 4% over 300 days, while no As removal or release was observed in TWs without IIRP after 180 days of continuous operation. IIRP amendment provided additional adsorption sites and increased the stability of adsorbed As due to the strong binding affinity between As and Fe oxides. Microbially mediated As(III) oxidation was intensified by iron-rich particles in the anaerobic bottom layer of IIRP-TWs. Myxococcus and Fimbriimonadaceae were identified as As(III) oxidizers. Further, metagenomic binning suggested that these two bacterial taxa may have the capability for anaerobic As(III) oxidation. Overall, this study demonstrated that abiotic and biotic effects of IIRP contribute to As retention in TWs and provided insights into the role of IIRP for the remediation of As contamination.}, } @article {pmid36282942, year = {2022}, author = {Deng, Y and Chen, H and Huang, Y and Zhang, Y and Ren, H and Fang, M and Wang, Q and Chen, W and Hale, RC and Galloway, TS and Chen, D}, title = {Long-Term Exposure to Environmentally Relevant Doses of Large Polystyrene Microplastics Disturbs Lipid Homeostasis via Bowel Function Interference.}, journal = {Environmental science & technology}, volume = {56}, number = {22}, pages = {15805-15817}, doi = {10.1021/acs.est.1c07933}, pmid = {36282942}, issn = {1520-5851}, mesh = {Humans ; Mice ; Animals ; *Microplastics/toxicity ; Polystyrenes/toxicity ; Plastics/toxicity ; Dysbiosis/chemically induced ; Homeostasis ; Inflammation/chemically induced ; Lipids ; *Water Pollutants, Chemical/toxicity ; Mammals/metabolism ; }, abstract = {The question of whether long-term chronic exposure to microplastics (MPs) could induce dose- and size-dependent adverse effects in mammals remains controversial and poorly understood. Our study explored potential health risks from dietary exposure to environmentally relevant doses of polystyrene (PS) MPs, through a mouse model and integrated analyses of the interruptions of fecal microbial metagenomes and plasma lipidomes. After 21 weeks of exposure to the MPs (40-100 μm), mice mainly exhibited gut microbiota dysbiosis, tissue inflammation, and plasma lipid metabolism disorder, although no notable accumulation of MPs was observed in the gut or liver. The change of the relative abundance of microbiota was strongly associated with the exposure dose and size of MPs while less significant effects were observed in gut damage and abnormal lipid metabolism. Moreover, multiomics data suggested that the host abnormal lipid metabolism was closely related to bowel function disruptions, including gut microbiota dysbiosis, increased gut permeability, and inflammation induced by MPs. We revealed for the first time that even without notable accumulation in mouse tissues, long-term exposure to MPs at environmentally relevant doses could still induce widespread health risks. This raises concern on the health risks from the exposure of humans and other mammals to environmentally relevant dose MPs.}, } @article {pmid36282811, year = {2022}, author = {Garrido-Sanz, L and Àngel Senar, M and Piñol, J}, title = {Drastic reduction of false positive species in samples of insects by intersecting the default output of two popular metagenomic classifiers.}, journal = {PloS one}, volume = {17}, number = {10}, pages = {e0275790}, pmid = {36282811}, issn = {1932-6203}, mesh = {Animals ; *Metagenomics/methods ; *Metagenome ; High-Throughput Nucleotide Sequencing/methods ; DNA ; Insecta/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {The use of high-throughput sequencing to recover short DNA reads of many species has been widely applied on biodiversity studies, either as amplicon metabarcoding or shotgun metagenomics. These reads are assigned to taxa using classifiers. However, for different reasons, the results often contain many false positives. Here we focus on the reduction of false positive species attributable to the classifiers. We benchmarked two popular classifiers, BLASTn followed by MEGAN6 (BM) and Kraken2 (K2), to analyse shotgun sequenced artificial single-species samples of insects. To reduce the number of misclassified reads, we combined the output of the two classifiers in two different ways: (1) by keeping only the reads that were attributed to the same species by both classifiers (intersection approach); and (2) by keeping the reads assigned to some species by any classifier (union approach). In addition, we applied an analytical detection limit to further reduce the number of false positives species. As expected, both metagenomic classifiers used with default parameters generated an unacceptably high number of misidentified species (tens with BM, hundreds with K2). The false positive species were not necessarily phylogenetically close, as some of them belonged to different orders of insects. The union approach failed to reduce the number of false positives, but the intersection approach got rid of most of them. The addition of an analytic detection limit of 0.001 further reduced the number to ca. 0.5 false positive species per sample. The misidentification of species by most classifiers hampers the confidence of the DNA-based methods for assessing the biodiversity of biological samples. Our approach to alleviate the problem is straightforward and significantly reduced the number of reported false positive species.}, } @article {pmid36281177, year = {2022}, author = {Feng, W and Jiang, X and Zhang, R and Guo, Z and Gao, D}, title = {Diagnosis of an Acinetobacter pittii from a patient in China with a multiplex PCR-based targeted gene sequencing platform of the cerebrospinal fluid: A case report with literature review.}, journal = {Medicine}, volume = {101}, number = {42}, pages = {e31130}, pmid = {36281177}, issn = {1536-5964}, mesh = {Humans ; Male ; Middle Aged ; *Multiplex Polymerase Chain Reaction ; *Ceftazidime ; Vancomycin ; Xylose ; Valproic Acid ; High-Throughput Nucleotide Sequencing/methods ; Staphylococcus epidermidis ; Mannitol ; }, abstract = {BACKGROUND: The traditional diagnosis model has great challenges for the etiological diagnosis of the central nervous system (CNS) diseases with similar clinical manifestations, especially for the diagnosis of rare pathogens. It is very important to make rapid and accurate identification of pathogens for guiding clinical choices in administering countermeasures.

CASE SUMMARY: On August 22, 2020, a 49 years old Chinese male patient had a headache for two days, and then the computed tomography (CT) scan of the brain showed subarachnoid hemorrhage. Subsequently, he underwent twice craniotomy and about 3 weeks of hospitalization. Since September 20, the patient was in the local rehabilitation hospital for hyperbaric oxygen therapy for about three weeks. Then the patient developed acute purulent meningoencephalitis. In the absence of diagnosis of specific pathogenic bacteria, vancomycin (1 g every 12 hours), ceftazidime (2 g every 8 hours), mannitol dehydration (125 mL, every 8 hours), and sodium valproate (0.4 g tid) was used timely according to cerebrospinal fluid (CSF) examination and clinical manifestations. CSF smear and routine culture test were negative during hospitalization. We used the metagenomic next-generation sequencing (mNGS) analysis of CSF for quick and accurate diagnosis, which identified human herpesvirus type 4 (EBV), Corynebacterium corynebacterium, Achromobacter xylose oxidation, and Acinetobacter baumannii, But the mapping degree was not high. Then, we used the modified method-multiplex PCR-based targeted gene sequencing platform (ptNGS) to detect CSF samples and found that the sequences detected were Acinetobacter pittii (A. pittii) and Staphylococcus epidermidis. S. epidermidis might come from skin colonization during lumbar puncture, so it was excluded from the etiological diagnosis. Therefore, we highly suspected that A. pittii was the pathogen in this case. After about three weeks of hospitalization treatment, the patient's symptoms were relieved.

CONCLUSION: In conclusion, empirical medication before the identification of pathogens is very important. The ptNGS may be an effective method for the diagnosis of pathogens.}, } @article {pmid36280854, year = {2022}, author = {Zhang, J and Li, X and Klümper, U and Lei, H and Berendonk, TU and Guo, F and Yu, K and Yang, C and Li, B}, title = {Deciphering chloramphenicol biotransformation mechanisms and microbial interactions via integrated multi-omics and cultivation-dependent approaches.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {180}, pmid = {36280854}, issn = {2049-2618}, mesh = {Anti-Bacterial Agents/metabolism ; Biodegradation, Environmental ; Biotransformation ; Chloramphenicol ; Choline/metabolism ; Ecosystem ; *Environmental Pollutants ; Glucose/metabolism ; Methanol/metabolism ; Microbial Interactions ; Oxidoreductases ; Sewage ; *Sphingomonas/metabolism ; Wastewater ; }, abstract = {BACKGROUND: As a widely used broad-spectrum antibiotic, chloramphenicol is prone to be released into environments, thus resulting in the disturbance of ecosystem stability as well as the emergence of antibiotic resistance genes. Microbes play a vital role in the decomposition of chloramphenicol in the environment, and the biotransformation processes are especially dependent on synergistic interactions and metabolite exchanges among microbes. Herein, the comprehensive chloramphenicol biotransformation pathway, key metabolic enzymes, and interspecies interactions in an activated sludge-enriched consortium were elucidated using integrated multi-omics and cultivation-based approaches.

RESULTS: The initial biotransformation steps were the oxidization at the C1-OH and C3-OH groups, the isomerization at C2, and the acetylation at C3-OH of chloramphenicol. Among them, the isomerization is an entirely new biotransformation pathway of chloramphenicol discovered for the first time. Furthermore, we identified a novel glucose-methanol-choline oxidoreductase responsible for the oxidization of the C3-OH group in Sphingomonas sp. and Caballeronia sp. Moreover, the subsequent biotransformation steps, corresponding catalyzing enzymes, and the microbial players responsible for each step were deciphered. Synergistic interactions between Sphingomonas sp. and Caballeronia sp. or Cupriavidus sp. significantly promoted chloramphenicol mineralization, and the substrate exchange interaction network occurred actively among key microbes.

CONCLUSION: This study provides desirable strain and enzyme resources for enhanced bioremediation of chloramphenicol-contaminated hotspot sites such as pharmaceutical wastewater and livestock and poultry wastewater. The in-depth understanding of the chloramphenicol biotransformation mechanisms and microbial interactions will not only guide the bioremediation of organic pollutants but also provide valuable knowledge for environmental microbiology and biotechnological exploitation. Video Abstract.}, } @article {pmid36280853, year = {2022}, author = {Muscatt, G and Hilton, S and Raguideau, S and Teakle, G and Lidbury, IDEA and Wellington, EMH and Quince, C and Millard, A and Bending, GD and Jameson, E}, title = {Crop management shapes the diversity and activity of DNA and RNA viruses in the rhizosphere.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {181}, pmid = {36280853}, issn = {2049-2618}, support = {MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; EP/L016494/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; BB/T009152/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/L025892/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/M017982/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/T/000PR9817/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Rhizosphere ; Soil Microbiology ; Plant Roots/microbiology ; *Microbiota/genetics ; Soil/chemistry ; Bacteria/genetics ; *RNA Viruses/genetics ; *Bacteriophages/genetics ; *Brassica napus ; DNA ; }, abstract = {BACKGROUND: The rhizosphere is a hotspot for microbial activity and contributes to ecosystem services including plant health and biogeochemical cycling. The activity of microbial viruses, and their influence on plant-microbe interactions in the rhizosphere, remains undetermined. Given the impact of viruses on the ecology and evolution of their host communities, determining how soil viruses influence microbiome dynamics is crucial to build a holistic understanding of rhizosphere functions.

RESULTS: Here, we aimed to investigate the influence of crop management on the composition and activity of bulk soil, rhizosphere soil, and root viral communities. We combined viromics, metagenomics, and metatranscriptomics on soil samples collected from a 3-year crop rotation field trial of oilseed rape (Brassica napus L.). By recovering 1059 dsDNA viral populations and 16,541 ssRNA bacteriophage populations, we expanded the number of underexplored Leviviricetes genomes by > 5 times. Through detection of viral activity in metatranscriptomes, we uncovered evidence of "Kill-the-Winner" dynamics, implicating soil bacteriophages in driving bacterial community succession. Moreover, we found the activity of viruses increased with proximity to crop roots, and identified that soil viruses may influence plant-microbe interactions through the reprogramming of bacterial host metabolism. We have provided the first evidence of crop rotation-driven impacts on soil microbial communities extending to viruses. To this aim, we present the novel principal of "viral priming," which describes how the consecutive growth of the same crop species primes viral activity in the rhizosphere through local adaptation.

CONCLUSIONS: Overall, we reveal unprecedented spatial and temporal diversity in viral community composition and activity across root, rhizosphere soil, and bulk soil compartments. Our work demonstrates that the roles of soil viruses need greater consideration to exploit the rhizosphere microbiome for food security, food safety, and environmental sustainability. Video Abstract.}, } @article {pmid36279912, year = {2023}, author = {Krishnaswamy, VG and Mani, K and Senthil Kumar, P and Rangasamy, G and Sridharan, R and Rethnaraj, C and Amirtha Ganesh, SS and Kalidas, S and Palanisamy, V and Chellama, NJ and Chowdula, S and Parthasarathy, V and Rajendran, S}, title = {Prevalence of differential microbiome in healthy, diseased and nipped colonies of corals, Porites lutea in the Gulf of Kachchh, north-west coast of India.}, journal = {Environmental research}, volume = {216}, number = {Pt 2}, pages = {114622}, doi = {10.1016/j.envres.2022.114622}, pmid = {36279912}, issn = {1096-0953}, mesh = {Animals ; *Anthozoa/microbiology ; Prevalence ; Coral Reefs ; *Microbiota ; Bacteria/genetics ; }, abstract = {Coral reefs are constantly subjected to multiple stresses like diseases and fish predation, which can profoundly influence the coral microbiome. This study investigated the differences in bacterial community structure of healthy, white syndrome affected and blenny nipped coral colonies of Porites lutea, collected from the coral reefs of Gulf of Kachchh, north-west coast of India. Present study observed that the stressed coral colonies harbored more OTUs and contained higher diversity values compared to healthy corals colonies. Similarly, beta diversity analysis indicated the dissimilarities among the three coral samples analyzed. Though the taxonomy analysis indicated bacterial phyla like Proteobacteria, Firmicutes, Bacteroidetes, and Actinobacteria among the entire coral samples studied, there was a variation in their relative abundances. Huge variations were observed in the relative dominance at the bacterial genera level. About 13phyla and 11 genera was identified in healthy coral. The PBN sample was found to contain Proteobacteria, Cyanobacteria, Verrucomicrobia, and Lentisphaerae as dominant phyla and Endozoicomonas, Dyella, Woeseia, and Winogradskyella as dominant genera. The PWS sample contained Proteobacteria, Lentisphaerae, Spirochaetes, and Tenericutes as dominant phyla and Endozoicomonas, Arcobacter, Sunxiuqinia, and Carboxylicivirgia as dominant genera. Among the healthy samples, sequences belonging to Uncultured Rhodospirillaceae were dominant, while Woeseia and sequences belonging to Uncultured Rhodovibrionaceae were dominant among the blenny nipped white syndrome infected corals. Although any previously established pathogen was not identified, present study revealed the presence of a potentially pathogenic bacterium, Arcobacter, among the diseased corals. It also demonstrated a dynamic microbiome among the Porites lutea colonies on subjecting to various stresses.}, } @article {pmid36279751, year = {2022}, author = {Bellerba, F and Serrano, D and Johansson, H and Pozzi, C and Segata, N and NabiNejad, A and Piperni, E and Gnagnarella, P and Macis, D and Aristarco, V and Accornero, CA and Manghi, P and Guerrieri-Gonzaga, A and Biffi, R and Bottiglieri, L and Trovato, C and Zampino, MG and Corso, F and Bellocco, R and Raimondi, S and Rescigno, M and Gandini, S}, title = {Colorectal cancer, Vitamin D and microbiota: A double-blind Phase II randomized trial (ColoViD) in colorectal cancer patients.}, journal = {Neoplasia (New York, N.Y.)}, volume = {34}, number = {}, pages = {100842}, pmid = {36279751}, issn = {1476-5586}, mesh = {Humans ; Female ; Male ; Vitamin D ; Vitamins/therapeutic use ; Dietary Supplements ; *Colorectal Neoplasms/drug therapy ; *Microbiota ; }, abstract = {BACKGROUND: Several studies suggest a role of gut microbiota in colorectal cancer (CRC) initiation and progression. Vitamin D (vitD) blood levels are also inversely correlated with CRC risk and prognosis. However, these factors' interplay remains unknown.

METHODS: 74 CRC patients after standard treatment were randomized to 1-year 2000 IU/day vitD or placebo.  Baseline and post-treatment fecal microbiota for shotgun metagenomics sequencing was collected. Coda-lasso and Principal Component Analysis were used to select and summarize treatment-associated taxa and pathways. Associations between vitD and taxa/pathways were investigated with logistic regression. Mediation analysis was performed to study if treatment-associated taxa mediated the effect of supplementation on 25(OH)D levels. Cox proportional-hazards model was used for disease-free survival (DFS).

RESULTS: 60 patients were analyzed. Change in alpha diversity (Shannon: p = 0.77; Simpson: p = 0.63) and post-treatment beta diversity (p = 0.70) were comparable between arms. Post-treatment abundances of 63 taxa and 32 pathways differed between arms. The 63 taxa also mediated the effect of supplementation on 25(OH)D (p = 0.02). There were sex differences in vitD levels, microbiota and pathways. Pathways of essential amino acids' biosynthesis were more abundant in supplemented women. Fusobacterium nucleatum presence at baseline was associated with worse DFS (p = 0.02). Those achieving vitD sufficiency (25(OH)D≥30 ng/ml) had lower post-treatment abundances (p = 0.05). Women were more likely to have F. nucleatum post-treatment (p = 0.02).

CONCLUSIONS: VitD supplementation may contribute shaping the gut microbiota and the microbiota may partially mediate the effect of supplementation on 25(OH)D. The observed sex-specific differences highlight the necessity of including sex/gender as a variable in microbiome studies.}, } @article {pmid36279689, year = {2022}, author = {Liu, Y and Chen, J and Lang, H and Zheng, H}, title = {Bartonella choladocola sp. nov. and Bartonella apihabitans sp. nov., two novel species isolated from honey bee gut.}, journal = {Systematic and applied microbiology}, volume = {45}, number = {6}, pages = {126372}, doi = {10.1016/j.syapm.2022.126372}, pmid = {36279689}, issn = {1618-0984}, mesh = {Bees ; Animals ; Sheep ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; Base Composition ; DNA, Bacterial/genetics ; Bacterial Typing Techniques ; Sequence Analysis, DNA ; *Bartonella/genetics ; Fatty Acids/analysis ; }, abstract = {Bartonella is one of the noncore bacterial genera in the honey bee (Apis mellifera) gut. So far, only one species, Bartonella apis, has been described from the honey bee gut. Previous analyses based on the genomic information of isolates and metagenome-assembled genomes suggested the existence of multiple Bartonella species in the bee guts. Here, 10 strains were isolated and characterized from the gut of A. mellifera from Jilin Province, China. New isolates shared ＞95% 16S rRNA gene sequence similarity with other species of the genus Bartonella. Phylogenetic analysis revealed that new isolates clustered with other type strains of Bartonella, and the bee gut Bartonella could be classified into three clades. The in silico DDH and average nucleotide identity values between strains of different clusters from the honey bee gut are 29.1-32.5% and 87.6-89.3%, all below the recommended 70.0% and 95% cutoff points. Cells are Gram-staining-negative rods and can grow on the surface of Brain Heart Infusion agar plates supplemented with defibrinated sheep blood in an aerobic environment with 5% CO2 at 35-37 °C. Strains from different species varied in both phenotypic and chemotaxonomic characterizations. Comparative genomic analysis indicated that B. choladocola had unique sets of genes encoding invasin, representing the potential for this species to both live as a gut symbiont and also as an erythrocytic pathogen. Thus, we propose two novel species Bartonella choladocola sp. nov. whose type strain is W8125[T](=JCM 35030[T] = ACCC 62057[T]), and Bartonella apihabitans sp. nov. whose type strain is W8097[T](=JCM 35029[T] = ACCC 62056[T]).}, } @article {pmid36278460, year = {2022}, author = {Suryaletha, K and Savithri, AV and Nayar, SA and Asokan, S and Rajeswary, D and Thomas, S}, title = {Demystifying Bacteriocins of Human Microbiota by Genome Guided Prospects: An Impetus to Rekindle the Antimicrobial Research.}, journal = {Current protein & peptide science}, volume = {23}, number = {12}, pages = {811-822}, pmid = {36278460}, issn = {1875-5550}, mesh = {Humans ; *Bacteriocins/genetics/pharmacology ; Anti-Bacterial Agents/pharmacology ; *Microbiota ; Bacteria/genetics ; }, abstract = {The human microbiome is a reservoir of potential bacteriocins that can counteract multidrug resistant bacterial pathogens. Unlike antibiotics, bacteriocins selectively inhibit a spectrum of competent bacteria and are said to safeguard gut commensals, reducing the chance of dysbiosis. Bacteriocinogenic probiotics or bacteriocins of human origin will be more pertinent in human physiological conditions for therapeutic applications to act against invading pathogens. Recent advancement in the omics approach enables the mining of diverse and novel bacteriocins by identifying biosynthetic gene clusters from the human microbial genome, pangenome or shotgun metagenome, which is a breakthrough in the discovery line of novel bacteriocins. This review summarizes the most recent trends and therapeutic potential of bacteriocins of human microbial origin, the advancement in the in silico algorithms and databases in the discovery of novel bacteriocin, and how to bridge the gap between the discovery of bacteriocin genes from big datasets and their in vitro production. Besides, the later part of the review discussed the various impediments in their clinical applications and possible solution to bring them into the frontline therapeutics to control infections, thereby meeting the challenges of global antimicrobial resistance.}, } @article {pmid36277249, year = {2022}, author = {Lu, H and Ma, L and Zhang, H and Feng, L and Yu, Y and Zhao, Y and Li, L and Zhou, Y and Song, L and Li, W and Zhao, J and Liu, L}, title = {The Comparison of Metagenomic Next-Generation Sequencing with Conventional Microbiological Tests for Identification of Pathogens and Antibiotic Resistance Genes in Infectious Diseases.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {6115-6128}, pmid = {36277249}, issn = {1178-6973}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has been widely studied, due to its ability of detecting all the microbial genetic information unbiasedly in a sample at one time and not relying on traditional culture. However, the application of mNGS in the diagnosis of clinical pathogens remains challenging.

METHODS: From December 2019 to March 2021, 134 specimens including Broncho alveolar lavage fluid (BAFL), blood, sputum, cerebrospinal fluid (CSF), bile, pleural fluid, pus, were continuously collected in The First Hospital of Qinhuangdao, and their retrospective diagnoses were classified into infectious disease (128, 95.5%) and noninfectious disease (6, 4.5%). The pathogen-detection performance of mNGS was compared with conventional microbiological tests (CMT) and culture method. In addition, the antibiotic resistance genes (ARGs) and evolutionary relationship of common drug-resistant A. baumannii were also analyzed.

RESULTS: Compared with CMT and culture methods, mNGS showed higher sensitivity in pathogen detection (74.2% vs 57.8%; P < 0.001 and 66.3% vs 31.7%; P < 0.001, respectively). Importantly, for cases that mNGS-positive only, 18 (35%) cases result in diagnosis modification, and 7 (23%) cases confirmed the clinical diagnosis. In 17 cases that A. baumannii were both detected in mNGS and culture, ade genes were the most frequently detected ARGs (from 13 cases), followed by sul2 and APH(3")-Ib (both from 12 cases). High consistency was observed among these ARGs and the related phenotype (100% for ade genes, 91.6% for sul2 and APH(3")-Ib). A. baumannii strains were classified into three groups, and most were well-clustered. It suggested those strains may be the epidemic strains.

CONCLUSION: In our study, mNGS had a higher sensitivity than CMT and culture method. And the result of ARGs frequency and cluster analysis of A. baumannii was of great significance to the anti-infective therapy.}, } @article {pmid36277011, year = {2022}, author = {Wang, L and Zha, P and Wang, Y and Kong, Y and Su, Y and Dai, L and Wang, Y}, title = {The Value of Macrogene Second-Generation Sequencing in the Diagnosis, Guidance of Drug Use, and Efficacy Monitoring of Infectious Pneumonia in Premature Infants.}, journal = {Computational and mathematical methods in medicine}, volume = {2022}, number = {}, pages = {4398614}, pmid = {36277011}, issn = {1748-6718}, mesh = {Infant ; Humans ; Infant, Newborn ; Procalcitonin ; C-Reactive Protein/metabolism ; Infant, Premature ; Interleukin-6 ; Retrospective Studies ; *Pneumonia/diagnosis/drug therapy ; *Bacterial Infections ; High-Throughput Nucleotide Sequencing ; Anti-Bacterial Agents/therapeutic use ; }, abstract = {OBJECTIVE: A group-controlled trial was conducted to explore the value of macrogene second-generation sequencing in the diagnosis, drug use, and efficacy monitoring of infectious pneumonia in premature infants.

METHODS: One hundred and thirty-eight premature infants with suspected infectious pneumonia treated in our hospital from March 2019 to June 2022 were selected as subjects. All patients underwent deep phlegm extraction and were randomly divided into two groups. 69 cases of control group were treated with general bacterial and fungal culture. The lavage fluid of the remaining 69 cases of observation group were detected by metagenomic next-generation sequencing (mNGS). The number of diagnosed preterm infants with infectious pneumonia was compared between the two groups, and the diagnostic value of the two methods was analyzed by the receiver operator characteristic (ROC) curve. Then, the differences in clinical efficacy, antimicrobial neonatal intensive care unit (NICU) use time, antimicrobial adjustment frequency, NICU stay time, hospital stay, and serum inflammatory factors were compared between the two groups.

RESULTS: The positive rate of mNGS pathogen detection in the lavage fluid of the observation group was 92.75% (64/69). The positive rate of the culture of the lavage fluid of the control group was 52.17% (36/69). The ROC curve analysis showed that the ROC AUC of traditional culture was 0.752 (95%CI = 0.610-0.894), and that of mNCS was 0.934 (95%CI = 0.854-0.999). In the observation group, there were 35 cases of bacterial infection, 20 cases of fungi, 4 cases of virus, and 5 cases of Chlamydia psittaci. In the control group, 26 cases of bacterial infection and 9 cases of fungi were detected; but viruses and other mycoplasmas could not be detected. After 2 weeks of treatment, the effective rate of the observation group was 95.31%, while that of the control group was 69.44%. The NICU use time, adjustment frequency, NICU stay time, and hospitalization time of antibiotics in the observation group were significantly less than those in the control group, and the difference was statistically significant (P < 0.05). After treatment, the levels of serum interleukin-6 (IL-6), procalcitonin (PCT), and hypersensitivity-C-reactive protein (hs-CRP) in observation group were significantly higher than those in control group, and the difference was statistically significant (P < 0.05).

CONCLUSION: mNGS can improve the efficiency of clinical diagnosis of infectious pneumonia in premature infants, effectively improve the detection rate of pathogens and the clinical efficacy of premature infants. At the same time, it can also assist the clinical efficacy monitoring and adjust the treatment plan at any time.}, } @article {pmid36276816, year = {2022}, author = {Rehman, AU and Siddiqui, NZ and Farooqui, NA and Alam, G and Gul, A and Ahmad, B and Asim, M and Khan, AI and Xin, Y and Zexu, W and Song Ju, H and Xin, W and Lei, S and Wang, L}, title = {Morchella esculenta mushroom polysaccharide attenuates diabetes and modulates intestinal permeability and gut microbiota in a type 2 diabetic mice model.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {984695}, pmid = {36276816}, issn = {2296-861X}, abstract = {Type 2 diabetes mellitus (T2DM) is a health issue that causes serious worldwide economic problems. It has previously been reported that natural polysaccharides have been studied with regard to regulating the gut microbiota, which plays an important role in T2DM. Here, we investigate the effects of Morchella esculenta polysaccharide (MEP) on a high-fat diet (HFD) and streptozotocin (STZ)-induced T2DM in BALB/c mice. The administration of MEP effectively regulated hyperglycemia and hyperlipidemia and improved insulin sensitivity. We also determined an improvement in gut microbiota composition by 16sRNA pyrosequencing. Treatment with MEP showed an increase in beneficial bacteria, i.e., Lactobacillus and Firmicutes, while the proportion of the opportunistic bacteria Actinobacteria, Corynebacterium, and Facklamia decreased. Furthermore, the treatment of T2DM mice with MEP resulted in reduced endotoxemia and insulin resistance-related pro-inflammatory cytokines interleukin 1β (IL-1β), tumor necrosis factor-alpha (TNF-α), and interleukin 6 (IL-6). Moreover, MEP treatment improved intestinal permeability by modulating the expression of the colon tight-junction proteins zonula occludens-1 (ZO-1), occludin, claudin-1, and mucin-2 protein (MUC2). Additionally, MEP administration affects the metagenome of microbial communities in T2DM mice by altering the functional metabolic pathways. All these findings suggested that MEP is a beneficial prebiotic associated with ameliorating the gut microbiota and its metabolites in T2DM.}, } @article {pmid36275068, year = {2022}, author = {Zhou, YJ and Gu, HY and Tang, QQ and Li, F and Zhu, J and Ai, T and Zhu, K and Xu, BY and Wang, Q and Huang, AL and Chen, J and Zhang, ZZ}, title = {Case report: A case of severe acute hepatitis of unknown origin.}, journal = {Frontiers in pediatrics}, volume = {10}, number = {}, pages = {975628}, pmid = {36275068}, issn = {2296-2360}, abstract = {According to analyses of etiology, clinical features, diagnostic methods, and treatment strategies by summarizing a case of unexplained acute hepatitis recently experienced, we are aiming to provide some information to enrich the clinical experience in diagnosis and treatment of severe acute hepatitis of unknown etiology in young children. A boy, aged 10 years and 6 months old, was admitted to the hospital due to acute abdominal pain, jaundice, and exceptionally high levels of ALT and AST. A range of measures, including patient history, physical examination, and routine laboratory testing, were performed. Furthermore, strategies such as trio-based next-generation sequencing (Trio-NGS) and liver biopsy, as well as metagenomic NGS (mNGS) of blood and liver samples were also performed. In summary, this case was an acute severe non-A-E hepatitis that is a probable case with hepatitis of unknown origin. Immunohistochemical analysis showed an immune injury in liver tissues. Torque teno virus (TTV) sequences were detected by mNGS assay. As for treatment strategies, in addition to general treatment, this patient also underwent plasmapheresis and methylprednisolone treatment due to disease deterioration. The patient's liver function was improved afterward and discharged after one month of treatment. Taken together, this work reported the clinical feature and treatment of severe acute hepatitis with non-A-E hepatitis in detail. The potential mechanism of liver damage might be due to an immune attack in which TTV might play a role as a co-factor.}, } @article {pmid36275026, year = {2022}, author = {Abdelbary, MMH and Hatting, M and Bott, A and Dahlhausen, A and Keller, D and Trautwein, C and Conrads, G}, title = {The oral-gut axis: Salivary and fecal microbiome dysbiosis in patients with inflammatory bowel disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1010853}, pmid = {36275026}, issn = {2235-2988}, mesh = {Mice ; Animals ; Dysbiosis/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Gastrointestinal Microbiome/genetics ; Feces/microbiology ; *Inflammatory Bowel Diseases/microbiology ; *Microbiota ; Bacteria ; Escherichia ; Inflammation/complications ; Cytokines/genetics ; }, abstract = {Inflammatory bowel disease (IBD) is a group of chronic inflammatory disorders that fall into two main categories: Crohn's disease (CD) and ulcerative colitis (UC). The gastrointestinal tract extends from the mouth to the anus and harbors diverse bacterial communities. Several sequencing-based studies have identified an intestinal enrichment of oral-associated bacteria and demonstrated their ability to induce intestinal inflammation in mice, suggesting that intestinal pathobionts originate from the oral cavity, particularly members of the genus Streptococcus. This study aimed to investigate the composition of the salivary and fecal microbiome of IBD patients (n = 14) compared to healthy controls (n = 12) and to determine the abundance of common bacterial taxa in both niches. Metagenomic DNA was extracted from saliva and fecal samples, and the 16S rRNA gene was targeted for sequencing. Our results revealed that the overall microbial composition of saliva was significantly altered in the IBD patients compared to the control subjects (p = 0.038). At the genus level, Veillonella and Prevotella were highly abundant in IBD (median: 25.4% and 22.2%, respectively) compared to the control group (17.9% and 13.4%, respectively). In contrast, Neisseria, Streptococcus, Haemophilus, and Fusobacterium were associated with a healthy gut state. Regarding the fecal microbiome, the IBD group had a significantly higher abundance of Clostridium sensu stricto 1 and Escherichia-Shigella (both comprising pathogenic bacteria) compared with the control group. Members of both bacterial groups have previously been shown to positively correlate with intestinal inflammation and high expression of pro-inflammatory cytokines that disrupt intestinal barrier integrity. In addition, we demonstrate that the increased abundance of Clostridium sensu stricto 1 and Escherichia-Shigella has also been associated with significant upregulation of certain metabolic pathways in the feces of the IBD group, including bacterial invasion of epithelial cells. Streptococcus was the only common genus detected in both the salivary and fecal microbiome and represented the oral-gut axis in our study. Using culture-based methods, we isolated 57 and 91 Streptococcus strains from saliva as well as 40 and 31 strains from fecal samples of the controls and IBD patients, respectively. The phylogenetic tree of streptococci based on sodA sequences revealed several patient-specific clusters comprising salivary and fecal streptococcal isolates from the same patient and belonging to the same species, suggesting that the oral cavity is an endogenous reservoir for intestinal strains.}, } @article {pmid36275025, year = {2022}, author = {Xu, L and Zhou, Z and Wang, Y and Song, C and Tan, H}, title = {Improved accuracy of etiological diagnosis of spinal infection by metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {929701}, pmid = {36275025}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *C-Reactive Protein ; *Metagenomics ; High-Throughput Nucleotide Sequencing ; Sensitivity and Specificity ; }, abstract = {Currently, the use of metagenomic next-generation sequencing (mNGS), a new approach to identify organisms in infectious diseases, is rarely reported in the diagnosis of spinal infection. This study aimed to evaluate the potential value of mNGS in etiological diagnosis of spinal infection. In this retrospective study, the clinical data of patients with suspected spinal infection were collected by electronic medical records. Specimens obtained from each patient were tested via mNGS assay and other conventional microbiological tests (CMTs). The sensitivity and specificity of mNGS and CMTs were calculated using the final clinical diagnosis as the golden standard. In total, 108 patients were eligible for the study, with the mean length of stay of 42.8 days. Regarding the overall identification of pathogens, mNGS exhibited a better performance than CMTs, and several nontuberculous mycobacteria, fungi, and bacteria were newly discovered. In the diagnosis of spinal infection, the sensitivity, specificity, and area under the curve of mNGS were 90.72%, 81.82%, and 0.89, respectively, which were all higher than 52.17%, 56.25%, and 0.72 of the CMTs. At hospital discharge, the C-reactive protein, erythrocyte sedimentation rate, and white blood cell count of patients significantly decreased compared with hospitalization (all p < 0.05), and 88.89% showed good outcomes. These findings may suggest that mNGS has a better diagnostic accuracy in pathogenic identification of patients with suspected spinal infection, and patients treated with NGS-guided antimicrobial therapy mostly seem to have good outcomes.}, } @article {pmid36275015, year = {2022}, author = {Wu, D and Wang, W and Xun, Q and Wang, H and Liu, J and Zhong, Z and Ouyang, C and Yang, Q}, title = {Metagenomic next-generation sequencing indicates more precise pathogens in patients with pulmonary infection: A retrospective study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {977591}, pmid = {36275015}, issn = {2235-2988}, mesh = {Humans ; Retrospective Studies ; *Coinfection/microbiology ; Sensitivity and Specificity ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Pneumonia/diagnosis/microbiology ; *Nucleic Acids ; }, abstract = {BACKGROUND: Timely identification of causative pathogens is important for the diagnosis and treatment of pulmonary infections. Metagenomic next-generation sequencing (mNGS), a novel approach to pathogen detection, can directly sequence nucleic acids of specimens, providing a wide range of microbial profile. The purpose of this study was to evaluate the diagnostic performance of mNGS in the bronchoalveolar lavage fluid (BALF) of patients with suspected pulmonary infection.

METHODS: From April 2019 to September 2021, 502 patients with suspected pneumonia, who underwent both mNGS of BALF and conventional microbiological tests (CMTs), were classified into different groups based on comorbidities. The diagnostic performances of mNGS and CMTs were compared. Comprehensive clinical analysis was used as the reference standard.

RESULTS: The diagnostic accuracy and sensitivity of mNGS were 74.9% (95% confidence interval [CI], 71.7-78.7%) and 72.5% (95% CI, 68.2-76.8%) respectively, outperformed those of CMTs (36.9% diagnostic accuracy, 25.4% sensitivity). For most pathogens, the detection rate of mNGS was higher than that of CMTs. Polymicrobial infections most often occurred in immunocompromised patients (22.1%). Only 2.3% patients without underlying diseases developed polymicrobial infections. Additionally, the spectrums of pathogens also varied among the different groups. We found the positive predictive values (PPV) to be dependent upon both the pathogen of interest as well as the immunologic status of the patient (e.g., the PPV of Mycobacterium tuberculosis was 94.9% while the PPV of Pneumocystis jirovecii in immunocompetent individuals was 12.8%). This information can help physicians interpret mNGS results.

CONCLUSION: mNGS of BALF can greatly enhance the accuracy and detection rate of pathogens in patients with pulmonary infections. Moreover, the comorbidities and types of pathogens should be taken consideration when interpreting the results of mNGS.}, } @article {pmid36274742, year = {2022}, author = {Frey, B and Rast, BM and Qi, W and Stierli, B and Brunner, I}, title = {Long-term mercury contamination does not affect the microbial gene potential for C and N cycling in soils but enhances detoxification gene abundance.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1034138}, pmid = {36274742}, issn = {1664-302X}, abstract = {Soil microorganisms are key transformers of mercury (Hg), a toxic and widespread pollutant. It remains uncertain, however, how long-term exposure to Hg affects crucial microbial functions, such as litter decomposition and nitrogen cycling. Here, we used a metagenomic approach to investigate the state of soil functions in an agricultural floodplain contaminated with Hg for more than 80 years. We sampled soils along a gradient of Hg contamination (high, moderate, low). Hg concentrations at the highly contaminated site (36 mg kg[-1] dry soil on average) were approximately 10 times higher than at the moderately contaminated site (3 mg kg[-1] dry soil) and more than 100 times higher than at the site with low contamination (0.25 mg kg[-1] dry soil; corresponding to the natural background concentration in Switzerland). The analysis of the CAZy and NCyc databases showed that carbon and nitrogen cycling was not strongly affected with high Hg concentrations, although a significant change in the beta-diversity of the predicted genes was observed. The only functional classes from the CAZy database that were significantly positively overrepresented under higher Hg concentrations were genes involved in pectin degradation, and from the NCyc database dissimilatory nitrate reduction and N-fixation. When comparing between low and high Hg concentrations the genes of the EggNOG functional category of inorganic ion transport and metabolism, two genes encoding Hg transport proteins and one gene involved in heavy metal transport detoxification were among those that were highly significantly overrepresented. A look at genes specifically involved in detoxification of Hg species, such as the mer and hgc genes, showed a significant overrepresentation when Hg contamination was increased. Normalized counts of these genes revealed a dominant role for the phylum Proteobacteria. In particular, most counts for almost all mer genes were found in Betaproteobacteria. In contrast, hgc genes were most abundant in Desulfuromonadales. Overall, we conclude from this metagenomic analysis that long-term exposure to high Hg triggers shifts in the functional beta-diversity of the predicted microbial genes, but we do not see a dramatic change or breakdown in functional capabilities, but rather functional redundancy.}, } @article {pmid36274733, year = {2022}, author = {Pascoal, F and Areosa, I and Torgo, L and Branco, P and Baptista, MS and Lee, CK and Cary, SC and Magalhães, C}, title = {The spatial distribution and biogeochemical drivers of nitrogen cycle genes in an Antarctic desert.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {927129}, pmid = {36274733}, issn = {1664-302X}, abstract = {Antarctic deserts, such as the McMurdo Dry Valleys (MDV), represent extremely cold and dry environments. Consequently, MDV are suitable for studying the environment limits on the cycling of key elements that are necessary for life, like nitrogen. The spatial distribution and biogeochemical drivers of nitrogen-cycling pathways remain elusive in the Antarctic deserts because most studies focus on specific nitrogen-cycling genes and/or organisms. In this study, we analyzed metagenome and relevant environmental data of 32 MDV soils to generate a complete picture of the nitrogen-cycling potential in MDV microbial communities and advance our knowledge of the complexity and distribution of nitrogen biogeochemistry in these harsh environments. We found evidence of nitrogen-cycling genes potentially capable of fully oxidizing and reducing molecular nitrogen, despite the inhospitable conditions of MDV. Strong positive correlations were identified between genes involved in nitrogen cycling. Clear relationships between nitrogen-cycling pathways and environmental parameters also indicate abiotic and biotic variables, like pH, water availability, and biological complexity that collectively impose limits on the distribution of nitrogen-cycling genes. Accordingly, the spatial distribution of nitrogen-cycling genes was more concentrated near the lakes and glaciers. Association rules revealed non-linear correlations between complex combinations of environmental variables and nitrogen-cycling genes. Association rules for the presence of denitrification genes presented a distinct combination of environmental variables from the remaining nitrogen-cycling genes. This study contributes to an integrative picture of the nitrogen-cycling potential in MDV.}, } @article {pmid36274732, year = {2022}, author = {Matharu, D and Ponsero, AJ and Dikareva, E and Korpela, K and Kolho, KL and de Vos, WM and Salonen, A}, title = {Bacteroides abundance drives birth mode dependent infant gut microbiota developmental trajectories.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {953475}, pmid = {36274732}, issn = {1664-302X}, abstract = {BACKGROUND AND AIMS: Birth mode and other early life factors affect a newborn's microbial colonization with potential long-term health effects. Individual variations in early life gut microbiota development, especially their effects on the functional repertoire of microbiota, are still poorly characterized. This study aims to provide new insights into the gut microbiome developmental trajectories during the first year of life.

METHODS: Our study comprised 78 term infants sampled at 3 weeks, 3 months, 6 months, and 12 months (n = 280 total samples), and their mothers were sampled in late pregnancy (n = 50). Fecal DNA was subjected to shotgun metagenomic sequencing. Infant samples were studied for taxonomic and functional maturation, and maternal microbiota was used as a reference. Hierarchical clustering on taxonomic profiles was used to identify the main microbiota developmental trajectories in the infants, and their associations with perinatal and postnatal factors were assessed.

RESULTS: In line with previous studies, infant microbiota composition showed increased alpha diversity and decreased beta diversity by age, converging toward an adult-like profile. However, we did not observe an increase in functional alpha diversity, which was stable and comparable with the mother samples throughout all the sampling points. Using a de novo clustering approach, two main infant microbiota clusters driven by Bacteroidaceae and Clostridiaceae emerged at each time point. The clusters were associated with birth mode and their functions differed mainly in terms of biosynthetic and carbohydrate degradation pathways, some of which consistently differed between the clusters for all the time points. The longitudinal analysis indicated three main microbiota developmental trajectories, with the majority of the infants retaining their characteristic cluster until 1 year. As many as 40% of vaginally delivered infants were grouped with infants delivered by C-section due to their clear and persistent depletion in Bacteroides. Intrapartum antibiotics, any perinatal or postnatal factors, maternal microbiota composition, or other maternal factors did not explain the depletion in Bacteroides in the subset of vaginally born infants.

CONCLUSION: Our study provides an enhanced understanding of the compositional and functional early life gut microbiota trajectories, opening avenues for investigating elusive causes that influence non-typical microbiota development.}, } @article {pmid36274720, year = {2022}, author = {Zou, B and Long, F and Xue, F and Qu, M and Chen, C and Zhang, X and Xu, L}, title = {Alleviation effects of niacin supplementation on beef cattle subjected to heat stress: A metagenomic insight.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {975346}, pmid = {36274720}, issn = {1664-302X}, abstract = {The objective of this study was to investigate the alleviation effects of niacin supplementation on beef cattle subjected to heat stress and to provide a theoretical basis for exploring the alleviation methods of heat stress environmental factors on the rumen of beef cattle. In the experiment, 36 Jinjiang bull cattle with a body weight of about 400 ± 20.0 kg were randomly divided into three treatments, each treatment contains four replicates, with three cattle in each replicate. Treatments included thermoneutral treatment (TN; temperature: 24-25°C, humidity: 45-55%), heat stress treatment, exposure to environmental temperature (HS; average THI: 82.74), and heat stress supplemented with niacin treatment (HN; high temperature + 800 mg/kg NA). Measured indicators were body temperature, respiratory rate, production performances, rumen fermentations, and microbial diversity. Results showed that adding niacin reduced the body temperature and respiratory rate (P < 0.05) but had no significant effect on the production performances compared with heat-stressed beef cattle. HS treatment significantly increased body temperature and respiratory rate (P < 0.01), while decreasing the content of acetic acid, butyric acid, and total volatile fatty acids (P < 0.05) compared with the TN treatment. Supplement of niacin did not affect ruminal fermentation parameters (P > 0.05) but had a decreased tendency on A/P (P < 0.1). Microbial diversity results showed that, at the phylum level, the relative abundance of Desulfobacterota in the HS treatment was increased compared with TN and HN treatment (P < 0.05). At the genus level, the relative abundance of Succiniclasticum and Family_XIII_AD3011 group in the HN treatment significantly proliferated compared with the HS treatment (P < 0.05). In conclusion, niacin supplementation may alleviate heat stress by proliferating those bacteria belonging to the phylum Succiniclasticum, which may further contribute to the digestion of cellulose and the improvement of the metabolic function of Jinjiang cattle under heat-stress conditions.}, } @article {pmid36274714, year = {2022}, author = {Zheng, Y and Shi, J and Chen, Q and Deng, C and Yang, F and Wang, Y}, title = {Identifying individual-specific microbial DNA fingerprints from skin microbiomes.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {960043}, pmid = {36274714}, issn = {1664-302X}, abstract = {Skin is an important ecosystem that links the human body and the external environment. Previous studies have shown that the skin microbial community could remain stable, even after long-term exposure to the external environment. In this study, we explore two questions: Do there exist strains or genetic variants in skin microorganisms that are individual-specific, temporally stable, and body site-independent? And if so, whether such microorganismal genetic variants could be used as markers, called "fingerprints" in our study, to identify donors? We proposed a framework to capture individual-specific DNA microbial fingerprints from skin metagenomic sequencing data. The fingerprints are identified on the frequency of 31-mers free from reference genomes and sequence alignments. The 616 metagenomic samples from 17 skin sites at 3-time points from 12 healthy individuals from Integrative Human Microbiome Project were adopted. Ultimately, one contig for each individual is assembled as a fingerprint. And results showed that 89.78% of the skin samples despite body sites could identify their donors correctly. It is observed that 10 out of 12 individual-specific fingerprints could be aligned to Cutibacterium acnes. Our study proves that the identified fingerprints are temporally stable, body site-independent, and individual-specific, and can identify their donors with enough accuracy. The source code of the genetic identification framework is freely available at https://github.com/Ying-Lab/skin_fingerprint.}, } @article {pmid36274695, year = {2022}, author = {Khanna, K and Kohli, SK and Sharma, N and Kour, J and Devi, K and Bhardwaj, T and Dhiman, S and Singh, AD and Sharma, N and Sharma, A and Ohri, P and Bhardwaj, R and Ahmad, P and Alam, P and Albalawi, TH}, title = {Phytomicrobiome communications: Novel implications for stress resistance in plants.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {912701}, pmid = {36274695}, issn = {1664-302X}, abstract = {The agricultural sector is a foremost contributing factor in supplying food at the global scale. There are plethora of biotic as well as abiotic stressors that act as major constraints for the agricultural sector in terms of global food demand, quality, and security. Stresses affect rhizosphere and their communities, root growth, plant health, and productivity. They also alter numerous plant physiological and metabolic processes. Moreover, they impact transcriptomic and metabolomic changes, causing alteration in root exudates and affecting microbial communities. Since the evolution of hazardous pesticides and fertilizers, productivity has experienced elevation but at the cost of impeding soil fertility thereby causing environmental pollution. Therefore, it is crucial to develop sustainable and safe means for crop production. The emergence of various pieces of evidence depicting the alterations and abundance of microbes under stressed conditions proved to be beneficial and outstanding for maintaining plant legacy and stimulating their survival. Beneficial microbes offer a great potential for plant growth during stresses in an economical manner. Moreover, they promote plant growth with regulating phytohormones, nutrient acquisition, siderophore synthesis, and induce antioxidant system. Besides, acquired or induced systemic resistance also counteracts biotic stresses. The phytomicrobiome exploration is crucial to determine the growth-promoting traits, colonization, and protection of plants from adversities caused by stresses. Further, the intercommunications among rhizosphere through a direct/indirect manner facilitate growth and form complex network. The phytomicrobiome communications are essential for promoting sustainable agriculture where microbes act as ecological engineers for environment. In this review, we have reviewed our building knowledge about the role of microbes in plant defense and stress-mediated alterations within the phytomicrobiomes. We have depicted the defense biome concept that infers the design of phytomicrobiome communities and their fundamental knowledge about plant-microbe interactions for developing plant probiotics.}, } @article {pmid36274682, year = {2022}, author = {Tao, L and Zhang, C and Ying, Z and Xiong, Z and Vaisman, HS and Wang, C and Shi, Z and Shi, R}, title = {Long-term continuous mono-cropping of Macadamia integrifolia greatly affects soil physicochemical properties, rhizospheric bacterial diversity, and metabolite contents.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {952092}, pmid = {36274682}, issn = {1664-302X}, abstract = {Macadamia integrifolia is the most economically important Proteaceae crop known for its edible nuts. The present study was conducted to examine the effect of continuous cultivation (for 1, 5, and 20 years) of M. integrifolia on soil quality, bacterial diversity, and metabolites. Soil rhizospheres from three different Macadamia rhizosphere orchards, 1-year monoculture orchard (CK), 5-year monoculture orchard (Y5), and 20-year monoculture orchard (Y20), were analyzed through metagenomic and metabolomic profiling. The soil physicochemical properties, including organic matter, and available nutrients (P, N, and K) were first increased significantly (p < 0.05) from the CK to the Y5 group and then decreased (p < 0.05) from the Y5 to the Y20 group. The soil pH continuously decreased (p < 0.05) over time from CK to Y20. Metagenomic profiling revealed that Actinobacteria, Acidobacteria, and Proteobacteria were the top three abundant phyla with their inconsistent relative abundance patterns from CK to Y20 (CK: 23.76%, Y5: 34. 06%, and Y20: 31.55%), (CK: 13.59%, Y5: 18.59%, and Y20: 21.35%), and (CK: 27.59%, Y5: 15.98%, and Y20: 17.08%), respectively. Furthermore, the Y5 rhizospheres had a higher number of beneficial bacterial genera belonging to Proteobacteria and Actinobacteria than the Y20 rhizospheres. The KEGG annotation analysis revealed that cellular processes, organism systems, metabolism, and genetic information were the most enriched functional categories. CAZy database screening indicated the highest enrichment of glycoside hydrolases following the glycoside transferases and carbohydrate-binding modules. Differential metabolite analysis revealed the highest number of metabolites (11) in the Y5 group than in the Y20 group (6). It is concluded that continuous monoculture of M. integrifolia improves the soil physicochemical properties, bacterial diversity, and metabolite contents in short-term planted orchards which, however, are deteriorated in long-term planted orchards.}, } @article {pmid36274442, year = {2022}, author = {Tims, S and Marsaux, C and Pinto, A and Daly, A and Karall, D and Kuhn, M and Santra, S and Roeselers, G and Knol, J and MacDonald, A and Scholl-Bürgi, S}, title = {Altered gut microbiome diversity and function in patients with propionic acidemia.}, journal = {Molecular genetics and metabolism}, volume = {137}, number = {3}, pages = {308-322}, doi = {10.1016/j.ymgme.2022.09.012}, pmid = {36274442}, issn = {1096-7206}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Propionic Acidemia ; Propionates ; Feces/microbiology ; Butyrates ; }, abstract = {Propionic acidemia (PA) is an inherited metabolic disorder of propionate metabolism, where the gut microbiota may play a role in pathophysiology and therefore, represent a relevant therapeutic target. Little is known about the gut microbiota composition and activity in patients with PA. Although clinical practice varies between metabolic treatment centers, management of PA requires combined dietary and pharmaceutical treatments, both known to affect the gut microbiota. This study aimed to characterize the gut microbiota and its metabolites in fecal samples of patients with PA compared with healthy controls from the same household. Eight patients (aged 3-14y) and 8 controls (4-31y) were recruited from Center 1 (UK) and 7 patients (11-33y) and 6 controls (15-54y) from Center 2 (Austria). Stool samples were collected 4 times over 3 months, alongside data on dietary intakes and medication usage. Several microbial taxa differed between patients with PA and controls, particularly for Center 1, e.g., Proteobacteria levels were increased, whereas butyrate-producing genera, such as Roseburia and Faecalibacterium, were decreased. Most measured microbial metabolites were lower in patients with PA, and butyrate was particularly depleted in patients from Center 1. Furthermore, microbiota profile of these patients showed the lowest compositional and functional diversity, and lowest stability over 3 months. As the first study to map the gut microbiota of patients with PA, this work represents an important step forward for developing new therapeutic strategies to further improve PA clinical status. New dietary strategies should consider microbial propionate production as well as butyrate production and microbiota stability.}, } @article {pmid36274162, year = {2022}, author = {Focardi, A and Moore, LR and Raina, JB and Seymour, JR and Paulsen, IT and Tetu, SG}, title = {Plastic leachates impair picophytoplankton and dramatically reshape the marine microbiome.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {179}, pmid = {36274162}, issn = {2049-2618}, mesh = {Plastics/chemistry ; Polyvinyl Chloride ; *Water Pollutants, Chemical/chemistry ; *Microbiota/genetics ; Zinc ; Water ; }, abstract = {BACKGROUND: Each year, approximately 9.5 million metric tons of plastic waste enter the ocean with the potential to adversely impact all trophic levels. Until now, our understanding of the impact of plastic pollution on marine microorganisms has been largely restricted to the microbial assemblages that colonize plastic particles. However, plastic debris also leaches considerable amounts of chemical additives into the water, and this has the potential to impact key groups of planktonic marine microbes, not just those organisms attached to plastic surfaces.

RESULTS: To investigate this, we explored the population and genetic level responses of a marine microbial community following exposure to leachate from a common plastic (polyvinyl chloride) or zinc, a specific plastic additive. Both the full mix of substances leached from polyvinyl chloride (PVC) and zinc alone had profound impacts on the taxonomic and functional diversity of our natural planktonic community. Microbial primary producers, both prokaryotic and eukaryotic, which comprise the base of the marine food web, were strongly impaired by exposure to plastic leachates, showing significant declines in photosynthetic efficiency, diversity, and abundance. Key heterotrophic taxa, such as SAR11, which are the most abundant planktonic organisms in the ocean, also exhibited significant declines in relative abundance when exposed to higher levels of PVC leachate. In contrast, many copiotrophic bacteria, including members of the Alteromonadales, dramatically increased in relative abundance under both exposure treatments. Moreover, functional gene and genome analyses, derived from metagenomes, revealed that PVC leachate exposure selects for fast-adapting, motile organisms, along with enrichment in genes usually associated with pathogenicity and an increased capacity to metabolize organic compounds leached from PVC.

CONCLUSIONS: This study shows that substances leached from plastics can restructure marine microbial communities with the potential for significant impacts on trophodynamics and biogeochemical cycling. These findings substantially expand our understanding of the ways by which plastic pollution impact life in our oceans, knowledge which is particularly important given that the burden of plastic pollution in the marine environment is predicted to continue to rise. Video Abstract.}, } @article {pmid36273894, year = {2022}, author = {Sato, Y and Takebe, H and Oishi, K and Yasuda, J and Kumagai, H and Hirooka, H and Yoshida, T}, title = {Identification of 146 Metagenome-assembled Genomes from the Rumen Microbiome of Cattle in Japan.}, journal = {Microbes and environments}, volume = {37}, number = {4}, pages = {}, pmid = {36273894}, issn = {1347-4405}, mesh = {Cattle ; Animals ; *Metagenome ; Rumen ; Japan ; Bacteria/metabolism ; Phylogeny ; *Microbiota ; Cellulose/metabolism ; Metagenomics ; }, abstract = {The rumen contains a complex microbial ecosystem that degrades plant materials, such as cellulose and hemicellulose. We herein reconstructed 146 nonredundant, rumen-specific metagenome-assembled genomes (MAGs), with ≥50% completeness and <10% contamination, from cattle in Japan. The majority of MAGs were potentially novel strains, encoding various enzymes related to plant biomass degradation and volatile fatty acid production. The MAGs identified in the present study may be valuable resources to enhance the resolution of future taxonomical and functional studies based on metagenomes and metatranscriptomes.}, } @article {pmid36273597, year = {2023}, author = {Lin, Y and Zhang, L and Wu, J and Yang, K}, title = {Wild birds-the sentinel of antibiotic resistance for urban river: Study on egrets and Jinjiang river in Chengdu, China.}, journal = {Environmental research}, volume = {216}, number = {Pt 3}, pages = {114566}, doi = {10.1016/j.envres.2022.114566}, pmid = {36273597}, issn = {1096-0953}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Birds/microbiology ; China ; *Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Metagenomics ; *Rivers ; Environmental Monitoring ; }, abstract = {Antibiotic resistance has become a comprehensive and complicated environmental problem. It is of great importance to effectively determine the abundance of various antibiotic resistance genes (ARGs) in the environment. Here, we attempted to find a practical method for monitoring environmental antibiotic resistance. The results of culture-based analysis of antibiotic resistance and metagenomic sequencing indicate that egrets inhabiting along the urban river (Jinjiang River) can be used as the sentinel of environmental antibiotic resistance. The antibiotic resistance in the environment fluctuated with time, while that in the wild bird was relatively stable. The network analysis based on metagenomic sequencing data gave the co-occurrence pattern of ARGs. The overall situation of the antibiotic resistance in the river was determined by quantifying several module hub genes of the co-occurrence network in river sediments. The temporal and spatial distribution of ARGs in Jinjiang River is highly correlated with that of human gut-specific bacteriophage (crAssphage), which indicates that one main source of the antibiotic resistance in the river is likely to be municipal sewage. The mobility potential of ARGs varying among different niches suggests the transmission direction of antibiotic resistance in the environment.}, } @article {pmid36273241, year = {2023}, author = {Larkin, AA and Hagstrom, GI and Brock, ML and Garcia, NS and Martiny, AC}, title = {Basin-scale biogeography of Prochlorococcus and SAR11 ecotype replication.}, journal = {The ISME journal}, volume = {17}, number = {2}, pages = {185-194}, pmid = {36273241}, issn = {1751-7370}, support = {T32AI141346//U.S. Department of Health & Human Services | National Institutes of Health (NIH)/ ; 395890//Simons Foundation/ ; OCE-1559002//National Science Foundation (NSF)/ ; OCE-1848576//National Science Foundation (NSF)/ ; NA18OAR4320123//United States Department of Commerce | National Oceanic and Atmospheric Administration (NOAA)/ ; }, mesh = {*Ecotype ; *Prochlorococcus ; Seawater/microbiology ; Indian Ocean ; Metagenome ; }, abstract = {Establishing links between microbial diversity and environmental processes requires resolving the high degree of functional variation among closely related lineages or ecotypes. Here, we implement and validate an improved metagenomic approach that estimates the spatial biogeography and environmental regulation of ecotype-specific replication patterns (RObs) across ocean regions. A total of 719 metagenomes were analyzed from meridional Bio-GO-SHIP sections in the Atlantic and Indian Ocean. Accounting for sequencing bias and anchoring replication estimates in genome structure were critical for identifying physiologically relevant biological signals. For example, ecotypes within the dominant marine cyanobacteria Prochlorococcus exhibited distinct diel cycles in RObs that peaked between 19:00-22:00. Additionally, both Prochlorococcus ecotypes and ecotypes within the highly abundant heterotroph Pelagibacter (SAR11) demonstrated systematic biogeographies in RObs that differed from spatial patterns in relative abundance. Finally, RObs was significantly regulated by nutrient stress and temperature, and explained by differences in the genomic potential for nutrient transport, energy production, cell wall structure, and replication. Our results suggest that our new approach to estimating replication is reflective of gross population growth. Moreover, this work reveals that the interaction between adaptation and environmental change drives systematic variability in replication patterns across ocean basins that is ecotype-specific, adding an activity-based dimension to our understanding of microbial niche space.}, } @article {pmid36273146, year = {2022}, author = {Sato, Y and Wippler, J and Wentrup, C and Ansorge, R and Sadowski, M and Gruber-Vodicka, H and Dubilier, N and Kleiner, M}, title = {Fidelity varies in the symbiosis between a gutless marine worm and its microbial consortium.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {178}, pmid = {36273146}, issn = {2049-2618}, mesh = {Animals ; Bacteria/genetics ; *Microbial Consortia ; Phylogeny ; Sulfates ; Sulfur ; *Symbiosis ; *Annelida/microbiology ; }, abstract = {BACKGROUND: Many animals live in intimate associations with a species-rich microbiome. A key factor in maintaining these beneficial associations is fidelity, defined as the stability of associations between hosts and their microbiota over multiple host generations. Fidelity has been well studied in terrestrial hosts, particularly insects, over longer macroevolutionary time. In contrast, little is known about fidelity in marine animals with species-rich microbiomes at short microevolutionary time scales, that is at the level of a single host population. Given that natural selection acts most directly on local populations, studies of microevolutionary partner fidelity are important for revealing the ecological and evolutionary processes that drive intimate beneficial associations within animal species.

RESULTS: In this study on the obligate symbiosis between the gutless marine annelid Olavius algarvensis and its consortium of seven co-occurring bacterial symbionts, we show that partner fidelity varies across symbiont species from strict to absent over short microevolutionary time. Using a low-coverage sequencing approach that has not yet been applied to microbial community analyses, we analysed the metagenomes of 80 O. algarvensis individuals from the Mediterranean and compared host mitochondrial and symbiont phylogenies based on single-nucleotide polymorphisms across genomes. Fidelity was highest for the two chemoautotrophic, sulphur-oxidizing symbionts that dominated the microbial consortium of all O. algarvensis individuals. In contrast, fidelity was only intermediate to absent in the sulphate-reducing and spirochaetal symbionts with lower abundance. These differences in fidelity are likely driven by both selective and stochastic forces acting on the consistency with which symbionts are vertically transmitted.

CONCLUSIONS: We hypothesize that variable degrees of fidelity are advantageous for O. algarvensis by allowing the faithful transmission of their nutritionally most important symbionts and flexibility in the acquisition of other symbionts that promote ecological plasticity in the acquisition of environmental resources. Video Abstract.}, } @article {pmid36272971, year = {2022}, author = {Feng, L and Zhang, Y and Liu, W and Du, D and Jiang, W and Wang, Z and Wang, Z and Hu, Z}, title = {Effects of heat stress on 16S rDNA, metagenome and metabolome in Holstein cows at different growth stages.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {644}, pmid = {36272971}, issn = {2052-4463}, support = {CARS-36//Earmarked Fund for Modern Agro-industry Technology Research System/ ; 31772624//National Natural Science Foundation of China (National Science Foundation of China)/ ; 32172760//National Natural Science Foundation of China (National Science Foundation of China)/ ; 2020LZGC014//Department of Science and Technology of Shandong Province/ ; }, mesh = {Animals ; Cattle ; Female ; Diet/veterinary ; DNA, Ribosomal/analysis/metabolism ; *Heat-Shock Response ; *Lactation/physiology ; Metabolome ; *Metagenome ; Milk/metabolism ; }, abstract = {Heat stress is an important issue in dairy cattle feeding management affecting summer health and economic efficiency. This experiment combined 16S rDNA sequencing(3,864,982 tags, 30 sequencing data), metagenomic sequencing(1,269,441,128 reads, 18 sequencing data), metabolomics analysis(72 sequencing data) and blood index analysis. Ten cows in each animal type (growing heifers, heifers, and lactating cows) were selected for sample collection in April and August. Here, we characterized both the changes in metabolites, rumen microbial communities and their functional potential and the effects of heat stress on serum biochemical, immune, oxidative stress, and hormonal indices derived from rumen fluid and serum samples from cows during different growth stages and in different climates. The generated data expand the resources for the rumen microbiome related to heat stress and age and provide useful datasets for research on developing therapeutic strategies to achieve high summer milk production in cows. These datasets will help researchers study the effects of heat stress on the physiological metabolism of Holstein cows and the time-dependent changes associated with growth stages.}, } @article {pmid36272588, year = {2023}, author = {Volk, A and Lee, J}, title = {Cyanobacterial blooms: A player in the freshwater environmental resistome with public health relevance?.}, journal = {Environmental research}, volume = {216}, number = {Pt 2}, pages = {114612}, doi = {10.1016/j.envres.2022.114612}, pmid = {36272588}, issn = {1096-0953}, mesh = {*Ecosystem ; Public Health ; *Cyanobacteria/genetics ; Fresh Water/microbiology ; Harmful Algal Bloom ; Anti-Bacterial Agents/pharmacology ; Lakes/microbiology ; }, abstract = {Cyanobacterial harmful algal blooms (cyanoHABs) are an ecological concern because of large ecosystem-disrupting blooms and a global public health concern because of the cyanotoxins produced by certain bloom-forming species. Another threat to global public health is the dissemination of antibiotic resistance (AR) in freshwater environmental reservoirs from anthropogenic sources, such as wastewater discharge and urban and agricultural runoff. In this study, cyanobacteria are now hypothesized to play a role in the environmental resistome. A non-systematic literature review of studies using molecular techniques (such as PCR and metagenomic sequencing) was conducted to explore indirect and direct ways cyanobacteria might contribute to environmental AR. Results show cyanobacteria can host antibiotic resistance genes (ARGs) and might promote the spread of ARGs in bacteria due to the significant contribution of mobile genetic elements (MGEs) located in genera such as Microcystis. However, cyanobacteria may promote or inhibit the spread of ARGs in environmental freshwater bacteria due to other factors as well. The purpose of this review is to 1) consider the role of cyanobacteria as AR hosts, since cyanoHABs are historically considered to be a separate problem from AR, and 2) to identify the knowledge gap in understanding cyanobacteria as ARG reservoirs. Cyanobacterial blooms, as well as other biotic (e.g. interactions with protists or cyanophages) and abiotic factors, should be studied further using advanced methods such as shotgun metagenomic and long read sequencing to clarify the extent of their functional ARGs/MGEs and influences on environmental AR.}, } @article {pmid36272542, year = {2023}, author = {Cancela, F and Marandino, A and Panzera, Y and Betancour, G and Mirazo, S and Arbiza, J and Ramos, N}, title = {A combined approach of rolling-circle amplification-single site restriction endonuclease digestion followed by next generation sequencing to characterize the whole genome and intra-host variants of human Torque teno virus.}, journal = {Virus research}, volume = {323}, number = {}, pages = {198974}, pmid = {36272542}, issn = {1872-7492}, abstract = {Torque Teno Virus (TTV) was initially associated with post-transfusion hepatitis, but growing evidence of its ubiquity in humans is compatible to no apparent clinical significance. TTV is a small non-enveloped virus with a circular single-negative-stranded DNA genome, belonging to the Anelloviridae family. Currently, TTVs are divided in seven phylogenetic groups and are further classified into 21 species. Studies about diversity of TTV in different conditions are receiving increasing interest and in this sense, sequencing of whole genomes for better genetic characterization becomes even more important. Since its discovery in 1997, few TTV complete genomes have been reported worldwide. This is probably due, among other reasons, to the great genetic heterogeneity among TTV strains that prevents its amplification and sequencing by conventional PCR and cloning methods. In addition, although metagenomics approach is useful in these cases, it remains a challenging tool for viromic analysis. With the aim of contributing to the expansion of the TTV whole genomes dataset and to study intra-host variants, we employed a methodology that combined a rolling-circle amplification approach followed by EcoRI digestion, generating a DNA fragment of ∼4Kb consistent with TTV genome length which was sequenced by Illumina next generation sequencing. A genogroup 3 full-length consensus TTV genome was obtained and co-infection with other species (at least those with a single EcoRI cleavage site) was not identified. Additionally, bioinformatics analysis allowed to identify the spectrum of TTV intra-host variants which provides evidence of a complex evolution dynamics of these DNA circular viruses, similarly to what occurs with RNA viruses.}, } @article {pmid36272486, year = {2023}, author = {Yangyao, J and Chen, H and Wang, Y and Kan, P and Yao, J and Zhang, D and Sun, W and Yao, Z}, title = {Metagenomic insights into the functional genes across transects in a typical estuarine marsh.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 2}, pages = {159593}, doi = {10.1016/j.scitotenv.2022.159593}, pmid = {36272486}, issn = {1879-1026}, mesh = {*Wetlands ; *Ecosystem ; Soil/chemistry ; Metagenomics ; Carbon ; }, abstract = {Salt marshes are potentially one of the most efficient carbon (C) sinks worldwide and perform important ecosystem functions, but sea level rise alters marsh sediments properties and thus threatens microbial roles in ecosystem functioning. Yet, the mechanisms of interactions of biochemical processes with microorganisms and their functions are still not fully understood. Here, this study investigated metagenomic taxonomic and functional profiling from the water-land conjugation up to about 300 m, 1000 m, and 2500 m in three parallel transects, respectively, in Hangzhou Bay, China. The results showed that soil physicochemical factors drove metagenomic taxonomic and functional genes in the 2500-m transect significantly different from other sites. The 2500-m transect had a greater abundance of Chloroflexi and Acidobacteria but lower in Proteobacteria. The metagenomic functional genes related to Phosphorus Metabolism (PHO) and Potassium Metabolism (POT) increased in the 2500 m. Additionally, nutrient-cycling functions and the genera of Anaeromyxobacter, Roseiflexus, and Geobacter related to PHO, POT at 2500 m were significantly greater than those of other transects. Carbon cycling functions within Carbohydrates (CHO) also differed significantly across transects. These research results demonstrated that the relative abundance of metagenomic microorganisms and their functional genes were significantly separated across the three transects. The vegetation type, salinity, and soil properties might be among the influencing factors.}, } @article {pmid36272393, year = {2022}, author = {Pin, L and Lutao, X and Linjie, L and Qunjie, P and Weijun, F and Wang, D}, title = {A new choice for human rabies diagnosis: A case report of metagenomics next-generation sequencing in diagnosis of human rabies.}, journal = {Journal of infection and public health}, volume = {15}, number = {11}, pages = {1276-1278}, doi = {10.1016/j.jiph.2022.10.003}, pmid = {36272393}, issn = {1876-035X}, mesh = {Male ; Humans ; Animals ; Dogs ; Middle Aged ; *Rabies/diagnosis ; *Pulmonary Edema/drug therapy ; Amantadine/therapeutic use ; Ribavirin/therapeutic use ; High-Throughput Nucleotide Sequencing ; Sensitivity and Specificity ; }, abstract = {PURPOSE: We report a case of human rabies diagnosed by the metagenomics next-generation sequencing (mNGS). A 59-year-old man developed clinical rabies 20 days after he was bitten by dogs. Treatment included induction of coma initially; rabies vaccine was not administered. The patient was treated with propofol, midazolam, recombinant human interferon α2b, ribavirin, and amantadine. Penehyclidine was administrated to relieved the rabies induced pulmonary edema and the salivation.

RESULTS: The patient's situation got worse on the 26th day after admition, and died on the 29th day finally.

CONCLUSION: The mNGS might be a new choice for human rabies diagnosis，penehyclidine was effective in decreasing the rabies induced pulmonary edema and the salivation.}, } @article {pmid36272199, year = {2022}, author = {Liu, S and Cai, H and Zhao, X and Wu, Z and Chen, Q and Xu, X and Zhong, S and Sun, W and Ni, J}, title = {Comammox biogeography subject to anthropogenic interferences along a high-altitude river.}, journal = {Water research}, volume = {226}, number = {}, pages = {119225}, doi = {10.1016/j.watres.2022.119225}, pmid = {36272199}, issn = {1879-2448}, mesh = {Humans ; *Ammonia ; *Archaea/genetics ; Rivers ; Nitrates ; Altitude ; Oxidation-Reduction ; Nitrification ; Bacteria/genetics ; Macrolides ; Phylogeny ; }, abstract = {The recent discovery of comammox Nitrospira performing complete ammonia oxidation to nitrate has overturned the long-held dogma of two-step nitrification on Earth, yet little is known about the effect of urbanization interference on their distribution. Using gene-centric metagenomics, we provided the first blueprints about comammox community, biogeography, and environmental drivers along a high-elevation (> 2000 m) river flowing through the largest city on the vulnerable Qinghai-Tibetan Plateau. Our study confirmed a wide presence and diversity of yet-uncultured comammox clade B across wet and dry seasons, with average 3.0 and 2.0 times as abundant as clade-A amoA genes in water and sediments, respectively. Species identified from freshwater and drinking water treatment plants dominated the comammox guilds (58∼100%), suggesting this plateau river shared a similar comammox assemblage with the above habitat types. Compared with the urban area harboring more abundant canonical Nitrospira identified in wastewater (average 24%), the upstream suburban reach had a smaller human population but larger proportions of comammox in ammonia-oxidizing prokaryotes (24∼72% of abundances) and Nitrospira sublineages I/II. Higher contents of nitrate and nitrite in water, and antibiotics in water and sediments, may restrain comammox niches in nitrifiers over the urban area. Further random forest analysis revealed that lincosamides and quinolones were the most important antibiotic predictors for the niche differentiations between comammox and canonical nitrifiers in water, while macrolides for those in sediments. Finally, by incubation experiments, we demonstrated higher activity contributions of benthic comammox in the suburban area (36.2∼92.8% of potential ammonia-oxidation rates) than in the urban reach, and that the contribution variation had significant negative relations with macrolides and their major components. Overall, this study highlighted that anthropogenic activities hampered the advantage of riverine complete nitrifiers over the canonical two-step ones.}, } @article {pmid36271396, year = {2022}, author = {Wen, T and Xie, P and Penton, CR and Hale, L and Thomashow, LS and Yang, S and Ding, Z and Su, Y and Yuan, J and Shen, Q}, title = {Specific metabolites drive the deterministic assembly of diseased rhizosphere microbiome through weakening microbial degradation of autotoxin.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {177}, pmid = {36271396}, issn = {2049-2618}, mesh = {Rhizosphere ; Soil Microbiology ; Citrulline ; alpha-Tocopherol ; *Microbiota ; *Fusarium ; Bacteria/genetics ; Soil ; Sugars ; Galactitol ; }, abstract = {BACKGROUND: Process and function that underlie the assembly of a rhizosphere microbial community may be strongly linked to the maintenance of plant health. However, their assembly processes and functional changes in the deterioration of soilborne disease remain unclear. Here, we investigated features of rhizosphere microbiomes related to Fusarium wilt disease and assessed their assembly by comparison pair of diseased/healthy sequencing data. The untargeted metabolomics was employed to explore potential community assembly drivers, and shotgun metagenome sequencing was used to reveal the mechanisms of metabolite-mediated process after soil conditioning.

RESULTS: Results showed the deterministic assembly process associated with diseased rhizosphere microbiomes, and this process was significantly correlated to five metabolites (tocopherol acetate, citrulline, galactitol, octadecylglycerol, and behenic acid). Application of the metabolites resulted in a deterministic assembly of microbiome with the high morbidity of watermelon. Furthermore, metabolite conditioning was found to weaken the function of autotoxin degradation undertaken by specific bacterial group (Bradyrhizobium, Streptomyces, Variovorax, Pseudomonas, and Sphingomonas) while promoting the metabolism of small-molecule sugars and acids initiated from another bacterial group (Anaeromyxobacter, Bdellovibrio, Conexibacter, Flavobacterium, and Gemmatimonas). Video Abstract CONCLUSION: These findings strongly suggest that shifts in a metabolite-mediated microbial community assembly process underpin the deterministic establishment of soilborne Fusarium wilt disease and reveal avenues for future research focusing on ameliorating crop loss due to this pathogen.}, } @article {pmid36271077, year = {2022}, author = {Guo, Y and Betzen, B and Salcedo, A and He, F and Bowden, RL and Fellers, JP and Jordan, KW and Akhunova, A and Rouse, MN and Szabo, LJ and Akhunov, E}, title = {Population genomics of Puccinia graminis f.sp. tritici highlights the role of admixture in the origin of virulent wheat rust races.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6287}, pmid = {36271077}, issn = {2041-1723}, mesh = {*Triticum/genetics ; Plant Diseases/genetics ; Metagenomics ; *Basidiomycota/genetics ; }, abstract = {Puccinia graminis f.sp. tritici (Pgt) causes stem rust disease in wheat that can result in severe yield losses. The factors driving the evolution of its virulence and adaptation remain poorly characterized. We utilize long-read sequencing to develop a haplotype-resolved genome assembly of a U.S. isolate of Pgt. Using Pgt haplotypes as a reference, we characterize the structural variants (SVs) and single nucleotide polymorphisms in a diverse panel of isolates. SVs impact the repertoire of predicted effectors, secreted proteins involved in host-pathogen interaction, and show evidence of purifying selection. By analyzing global and local genomic ancestry we demonstrate that the origin of 8 out of 12 Pgt clades is linked with either somatic hybridization or sexual recombination between the diverged donor populations. Our study shows that SVs and admixture events appear to play an important role in broadening Pgt virulence and the origin of highly virulent races, creating a resource for studying the evolution of Pgt virulence and preventing future epidemic outbreaks.}, } @article {pmid36270766, year = {2022}, author = {Ali, MJ}, title = {Fungal microbiome (mycobiome) and virome of the lacrimal sac in patients with PANDO: the lacriome paper 5.}, journal = {The British journal of ophthalmology}, volume = {}, number = {}, pages = {}, doi = {10.1136/bjo-2022-322433}, pmid = {36270766}, issn = {1468-2079}, abstract = {PURPOSE: To study the fungal microbiome (mycobiome) and the virome of the lacrimal sacs in patients with primary acquired nasolacrimal duct obstruction (PANDO).

METHODS: A prospective study was performed on 10 consecutive samples of the lacrimal sac contents obtained from patients with PANDO. The samples were obtained from the lacrimal sacs under endoscopy guidance and immediately transported on ice to the laboratory. Following DNA extraction and library preparation, a whole shotgun metagenome sequencing was performed on the Illumina platform (NOVASEQ 6000). The fungal internal transcript spacer analysis was performed using the PIPITS v2.7 . The viral taxonomy profiling was performed using Kraken2 against the virus database.

RESULTS: The taxonomic hit distribution across the lacrimal sac samples showed rich fungal diversity (4 phyla, 12 classed, 21 families and 26 genera). The major phyla were Ascomycota and Basidiomycota, and the key genera identified were Alternaria, Hyphopichia, Malassezia, Aspergillus and Epicoccum. The virome analysis identified 13 phyla, 15 classes and 27 families. The viruses were commonly from the families Poxviridae, Retroviridae, Siphoviridae and Myoviridae, Poxviridae being the most prevalent family. The BeAn 58058 virus, a member of the Poxviridae family, was the most abundant in all the samples.

CONCLUSION: The present study is the first whole metagenome sequencing exclusively of the fungal microbiome and virome from the lacrimal sacs of patients with PANDO. The lacrimal sacs harbour diverse fungal and viral communities with distinct ecosystem dynamics. Further studies of their functions and interactions with the hosts would provide valuable insights.}, } @article {pmid36270683, year = {2022}, author = {Mahapatra, S and Mohanty, S and Mishra, R and Prasad, P}, title = {An overview of cancer and the human microbiome.}, journal = {Progress in molecular biology and translational science}, volume = {191}, number = {1}, pages = {83-139}, doi = {10.1016/bs.pmbts.2022.07.007}, pmid = {36270683}, issn = {1878-0814}, mesh = {Humans ; *Microbiota ; Symbiosis ; *Neoplasms ; }, abstract = {Mutual beneficial associations with the microbial consortia are an essential requisite of human life. Microbial communities have both a symbiotic and a pathogenic standpoint, which portrays a context-dependent scenario of the human microbiome. The symbiotic assemblage works to develop indispensable functions of the human body such as immune system, digestive system, defense against colonization by pathobionts and their toxins, etc. Furthermore, any deviation in the resource utilization by the symbionts due to host factors comprising lifestyle changes, diet, drugs, immunocompromised states, and co-morbidities could perturb beneficial microbes communities and promote the invasion by opportunistic pathogens thus, disrupting the homeostatic state. Microbial infestations have proved to be carcinogenic but this does not spontaneously establish a cancer hallmark, rather they initiate a cascade of events that disturbs the normal cellular activities finally these defective machineries invade distant sites of the body, submitting to a devastative transformed internal milieu. Significant technological and system biology advances have been made in elucidating a lucid but complex basis of such microbe-associated malignancies. This chapter discusses the recent advances, without compromising the concepts of the inception studies, including a brief version of the microbial status in cancer generation, mechanistic approaches adapted, therapeutic interventions, system biology approaches with special mention on the study design gaps, challenges in addressing the drawbacks and finally with a perspective of the future targeted studies, has been a focus of this piece of work.}, } @article {pmid36270682, year = {2022}, author = {Ahrodia, T and Das, S and Bakshi, S and Das, B}, title = {Structure, functions, and diversity of the healthy human microbiome.}, journal = {Progress in molecular biology and translational science}, volume = {191}, number = {1}, pages = {53-82}, doi = {10.1016/bs.pmbts.2022.07.003}, pmid = {36270682}, issn = {1878-0814}, mesh = {Humans ; *Microbiota ; Bacteria/genetics ; Metagenome ; *Gastrointestinal Microbiome ; Archaea ; }, abstract = {Taxonomic composition and functional potency of microbes associated with different parts of the human body have largely been explored by culture-independent metagenome sequencing. The diverse microbiota living throughout the human body is made up of thousands of microbial taxa from all three domains of life: Archaea, Bacteria, and Eukarya. Microbial load and functional potency in different body sites are well distinct and have minimal resemblance at higher taxonomic levels between the two habitats. The highest microbial load, diversity, and functional potency including biosynthesis of essential nutrients, chemical modifications of dietary components, and sources of immunomodulatory molecules, are found in the gut microbiome. However, the inter-individual diversity and dynamics of the human microbiome in a given body habitat vary greatly over time. Both environmental factors and host genetics contribute significantly to shaping microbial community structure and its stability. A basic understanding of native microbial compositions and their functional potency and stability in different parts of healthy humans living across geography will help us to identify disease-specific microbiota and develop potential microbiome-based therapeutics. Here, we updated our current understanding of the diversity, dynamics, and functional potency of microbiomes associated with different parts of the human body.}, } @article {pmid36270681, year = {2022}, author = {Ghosh, TS and Das, M}, title = {Emerging tools for understanding the human microbiome.}, journal = {Progress in molecular biology and translational science}, volume = {191}, number = {1}, pages = {29-51}, doi = {10.1016/bs.pmbts.2022.06.027}, pmid = {36270681}, issn = {1878-0814}, mesh = {Humans ; *High-Throughput Nucleotide Sequencing/methods ; *Microbiota ; Metagenome ; Metagenomics/methods ; Computational Biology/methods ; }, abstract = {Recent advances in sequencing technologies, experimental protocols and approaches in data generation and analysis have enabled us to investigate the human microbiome at an unprecedented level of resolution. The current chapter aims to provide an understanding of the different computational and bioinformatic strategies adopted to answer the different questions of a typical microbiome investigation and how the upstream DNA sequencing methodologies can affect this. The chapter enlist the state-of-the-art in metagenomic data analysis along with the available strategies to perform an integrated investigation of the human microbiome along with other data layers.}, } @article {pmid36270389, year = {2022}, author = {Zhu, X and Huang, H and He, Y and Wang, X and Jia, J and Feng, X and Li, D and Li, H}, title = {A preliminary study on the feasibility of industrialization for n-caproic acid recovery from food wastewater: From lab to pilot.}, journal = {Bioresource technology}, volume = {366}, number = {}, pages = {128154}, doi = {10.1016/j.biortech.2022.128154}, pmid = {36270389}, issn = {1873-2976}, mesh = {*Caproates ; Wastewater ; Food ; Bioreactors/microbiology ; Fermentation ; Industrial Development ; Feasibility Studies ; *Refuse Disposal ; Lactic Acid ; }, abstract = {Food wastewater is associated with greenhouse gas emission and has a significant water footprint. Here, the platform chemical n-caproate was recovered from liquor brewing wastewater at maximum and mean concentrations of 26.4 g/L and 17.0 ± 4.3 g/L, respectively, after 377 d operation. Laboratory-scale lactate-driven chain elongation (CE) process was implemented first. Taxonomic composition and metagenomic data analyses revealed that Caproiciproducens (e.g., Ruminococcaceae bacterium CPB6) and bacteria affiliated with Lachnospiraceae transformed lactate to n-caproate by reverse β-oxidation and/or fatty acid biosynthesis. The lactate-driven CE process was then scaled up from 2.5 L to 500 L and achieved a n-caproate production of 14.5 ± 0.6 g/L within 96 h. n-Caproic acid was extracted at a concentration and purity of 815.9 ± 8.3 g/L and 88.6 ± 8.9 %, respectively. The present study demonstrated a commercially viable strategy for resource recovery and carbon fixation from food waste streams.}, } @article {pmid36270377, year = {2023}, author = {Evariste, L and Mouchet, F and Pinelli, E and Flahaut, E and Gauthier, L and Barret, M}, title = {Gut microbiota impairment following graphene oxide exposure is associated to physiological alterations in Xenopus laevis tadpoles.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 2}, pages = {159515}, doi = {10.1016/j.scitotenv.2022.159515}, pmid = {36270377}, issn = {1879-1026}, mesh = {Animals ; *Gastrointestinal Microbiome ; Larva ; *Graphite/toxicity ; Xenopus laevis ; *Microbiota ; Bacteria/genetics ; }, abstract = {Graphene-based nanomaterials such as graphene oxide (GO) possess unique properties triggering high expectations for the development of technological applications. Thus, GO is likely to be released in aquatic ecosystems. It is essential to evaluate its ecotoxicological potential to ensure a safe use of these nanomaterials. In amphibians, previous studies highlighted X. laevis tadpole growth inhibitions together with metabolic disturbances and genotoxic effects following GO exposure. As GO is known to exert bactericidal effects whereas the gut microbiota constitutes a compartment involved in host homeostasis regulation, it is important to determine if this microbial compartment constitutes a toxicological pathway involved in known GO-induced host physiological impairments. This study investigates the potential link between gut microbial communities and host physiological alterations. For this purpose, X. laevis tadpoles were exposed during 12 days to GO. Growth rate was monitored every 2 days and genotoxicity was assessed through enumeration of micronucleated erythrocytes. Genomic DNA was also extracted from the whole intestine to quantify gut bacteria and to analyze the community composition. GO exposure led to a dose dependent growth inhibition and genotoxic effects were detected following exposure to low doses. A transient decrease of the total bacteria was noticed with a persistent shift in the gut microbiota structure in exposed animals. Genotoxic effects were associated to gut microbiota remodeling characterized by an increase of the relative abundance of Bacteroides fragilis. The growth inhibitory effects would be associated to a shift in the Firmicutes/Bacteroidetes ratio while metagenome inference suggested changes in metabolic pathways and upregulation of detoxification processes. This work indicates that the gut microbiota compartment is a biological compartment of interest as it is integrative of host physiological alterations and should be considered for ecotoxicological studies as structural or functional impairments could lead to later life host fitness loss.}, } @article {pmid36270147, year = {2022}, author = {Lu, JJ and Zhang, H and Li, W and Yi, JB and Sun, FY and Zhao, YW and Feng, L and Li, Z and Dong, WY}, title = {Biofilm stratification in counter-diffused membrane biofilm bioreactors (MBfRs) for aerobic methane oxidation coupled to aerobic/anoxic denitrification: Effect of oxygen pressure.}, journal = {Water research}, volume = {226}, number = {}, pages = {119243}, doi = {10.1016/j.watres.2022.119243}, pmid = {36270147}, issn = {1879-2448}, mesh = {Biofilms ; Bioreactors ; *Denitrification ; In Situ Hybridization, Fluorescence ; *Methane ; Oxidation-Reduction ; Oxygen ; }, abstract = {Aerobic methane oxidation coupled with denitrification (AME-D) executed in membrane biofilm bioreactors (MBfRs) provides a high promise for simultaneously mitigating methane (CH4) emissions and removing nitrate in wastewater. However, systematically experimental investigation on how oxygen partial pressure affects the development and characteristics of counter-diffusional biofilm, as well as its spatial stratification profiles, and the cooperative interaction of the biofilm microbes, is still absent. In this study, we combined Optical Coherence Tomography (OCT) with Confocal Laser Scanning Microscopy (CLSM) to in-situ characterize the development of counter-diffusion biofilm in the MBfR for the first time. It was revealed that oxygen partial pressure onto the MBfR was capable of manipulating biofilm thickness and spatial stratification, and then managing the distribution of functional microbes. With the optimized oxygen partial pressure of 5.5 psig (25% oxygen content), the manipulated counter-diffusional biofilm in the AME-D process obtained the highest denitrification efficiency, due mainly to that this biofilm had the proper dynamic balance between the aerobic-layer and anoxic-layer where suitable O2 gradient and sufficient aerobic methanotrophs were achieved in aerobic-layer to favor methane oxidation, and complete O2 depletion and accessible organic sources were kept to avoid constraining denitrification activity in anoxic-layer. By using metagenome analysis and Fluorescence in situ hybridization (FISH) staining, the spatial distribution of the functional microbes within counter-diffused biofilm was successfully evidenced, and Rhodocyclaceae, one typical aerobic denitrifier, was found to survive and gradually enriched in the aerobic layer and played a key role in denitrification aerobically. This in-situ biofilm visualization and characterization evidenced directly for the first time the cooperative path of denitrification for AME-D in the counter-diffused biofilm, which involved aerobic methanotrophs, heterotrophic aerobic denitrifiers, and heterotrophic anoxic denitrifiers.}, } @article {pmid36270146, year = {2022}, author = {Yan, G and Sun, X and Dong, Y and Gao, W and Gao, P and Li, B and Yan, W and Zhang, H and Soleimani, M and Yan, B and Häggblom, MM and Sun, W}, title = {Vanadate reducing bacteria and archaea may use different mechanisms to reduce vanadate in vanadium contaminated riverine ecosystems as revealed by the combination of DNA-SIP and metagenomic-binning.}, journal = {Water research}, volume = {226}, number = {}, pages = {119247}, doi = {10.1016/j.watres.2022.119247}, pmid = {36270146}, issn = {1879-2448}, mesh = {Humans ; *Archaea/genetics/metabolism ; *Metagenome ; Vanadates/metabolism ; Vanadium/metabolism ; Ecosystem ; Anaerobiosis ; Bacteria/genetics/metabolism ; Methane/metabolism ; Methanosarcina/genetics ; Oxidation-Reduction ; Isotopes ; DNA/metabolism ; }, abstract = {Vanadium (V) is a transitional metal that poses health risks to exposed humans. Microorganisms play an important role in remediating V contamination by reducing more toxic and mobile vanadate (V(V)) to less toxic and mobile V(IV). In this study, DNA-stable isotope probing (SIP) coupled with metagenomic-binning was used to identify microorganisms responsible for V(V) reduction and determine potential metabolic mechanisms in cultures inoculated with a V-contaminated river sediment. Anaeromyxobacter and Geobacter spp. were identified as putative V(V)-reducing bacteria, while Methanosarcina spp. were identified as putative V(V)-reducing archaea. The bacteria may use the two nitrate reductases NarG and NapA for respiratory V(V) reduction, as has been demonstrated previously for other species. It is proposed that Methanosarcina spp. may reduce V(V) via anaerobic methane oxidation pathways (AOM-V) rather than via respiratory V(V) reduction performed by their bacterial counterparts, as indicated by the presence of genes associated with anaerobic methane oxidation coupled with metal reduction in the metagenome assembled genome (MAG) of Methanosarcina. Briefly, methane may be oxidized through the "reverse methanogenesis" pathway to produce electrons, which may be further captured by V(V) to promote V(V) reduction. More specially, V(V) reduction by members of Methanosarcina may be driven by electron transport (CoMS-SCoB heterodisulfide reductase (HdrDE), F420H2 dehydrogenases (Fpo), and multi-heme c-type cytochrome (MHC)). The identification of putative V(V)-reducing bacteria and archaea and the prediction of their different pathways for V(V) reduction expand current knowledge regarding the potential fate of V(V) in contaminated sites.}, } @article {pmid36269761, year = {2022}, author = {Feng, S and Ji, HL and Wang, H and Zhang, B and Sterzenbach, R and Pan, C and Guo, X}, title = {MetaLP: An integrative linear programming method for protein inference in metaproteomics.}, journal = {PLoS computational biology}, volume = {18}, number = {10}, pages = {e1010603}, pmid = {36269761}, issn = {1553-7358}, support = {R01 AT011618/AT/NCCIH NIH HHS/United States ; R01 HL134828/HL/NHLBI NIH HHS/United States ; R15 LM013460/LM/NLM NIH HHS/United States ; }, mesh = {Humans ; *Programming, Linear ; *Tandem Mass Spectrometry ; RNA, Ribosomal, 16S/genetics ; Proteins/chemistry ; Peptides/chemistry ; }, abstract = {Metaproteomics based on high-throughput tandem mass spectrometry (MS/MS) plays a crucial role in characterizing microbiome functions. The acquired MS/MS data is searched against a protein sequence database to identify peptides, which are then used to infer a list of proteins present in a metaproteome sample. While the problem of protein inference has been well-studied for proteomics of single organisms, it remains a major challenge for metaproteomics of complex microbial communities because of the large number of degenerate peptides shared among homologous proteins in different organisms. This challenge calls for improved discrimination of true protein identifications from false protein identifications given a set of unique and degenerate peptides identified in metaproteomics. MetaLP was developed here for protein inference in metaproteomics using an integrative linear programming method. Taxonomic abundance information extracted from metagenomics shotgun sequencing or 16s rRNA gene amplicon sequencing, was incorporated as prior information in MetaLP. Benchmarking with mock, human gut, soil, and marine microbial communities demonstrated significantly higher numbers of protein identifications by MetaLP than ProteinLP, PeptideProphet, DeepPep, PIPQ, and Sipros Ensemble. In conclusion, MetaLP could substantially improve protein inference for complex metaproteomes by incorporating taxonomic abundance information in a linear programming model.}, } @article {pmid36269715, year = {2022}, author = {, }, title = {Retraction: Metagenomic analysis exploring taxonomic and functional diversity of bacterial communities of a Himalayan urban fresh water lake.}, journal = {PloS one}, volume = {17}, number = {10}, pages = {e0275944}, pmid = {36269715}, issn = {1932-6203}, } @article {pmid36269375, year = {2022}, author = {Yu, P and Li, M and Sun, R and Zhan, J and Pan, Y}, title = {Primary exploring the value of metagenomic next-generation sequencing in detecting pathogenic bacteria of cholangitis with biliary atresia after Kasai operation.}, journal = {Pediatric surgery international}, volume = {38}, number = {12}, pages = {1931-1937}, pmid = {36269375}, issn = {1437-9813}, support = {2022qn08//Xi'an Institutes of Health grants/ ; 2021G04//Xi'an Children's Hospital fund/ ; }, mesh = {Child ; Humans ; *Biliary Atresia/surgery ; Portoenterostomy, Hepatic ; Retrospective Studies ; *Cholangitis/diagnosis ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing ; }, abstract = {PURPOSE: To evaluate the value of metagenomic next-generation sequencing (mNGS) in detecting pathogenic bacteria of cholangitis for patients with biliary atresia after Kasai operation.

METHODS: This study retrospectively analyzed patients of biliary atresia with cholangitis after Kasai operation who were admitted to Xi'an Children's Hospital from July 2019 to December 2021. Both blood culture and mNGS were carried out in all of these patients. We compared the detection rate of pathogenic bacteria, pathogenic bacteria spectrum, test time, inflammatory indicators and liver function. All the patients were followed up for 0.5-3 years to evaluate the onset of cholangitis and the survival status of autologous liver.

RESULTS: This study included total of 30 cholangitis occurred in 25 patients. There were significant differences in the detection rate of pathogenic bacteria [23.3 vs.73.3%, P < 0.05] and the test time [120 (114.5-120) vs.16 (16-21) h, P < 0.001] between the blood culture and mNGS. These two methods showed significant statistical differences in comparing inflammatory indicators (CRP, PCT) and liver function (TB, DB, GGT) before and after anti-infection. Four kinds of bacteria were detected by blood cultures and ten kinds of bacteria were detected by mNGS. Cholangitis occurred 3 times in one case (4%) and twice in three cases (12%). Autologous liver survived in 17 cases (68%).

CONCLUSION: Comparing with traditional blood culture, mNGS is more efficient, convenient and accurate in the detection of pathogens. It provides a new method for accurately detecting pathogenic bacteria of cholangitis after Kasai operation.}, } @article {pmid36269282, year = {2022}, author = {Govender, KN and Eyre, DW}, title = {Benchmarking taxonomic classifiers with Illumina and Nanopore sequence data for clinical metagenomic diagnostic applications.}, journal = {Microbial genomics}, volume = {8}, number = {10}, pages = {}, pmid = {36269282}, issn = {2057-5858}, mesh = {Humans ; *Nanopores ; Benchmarking/methods ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Nucleotides ; }, abstract = {Culture-independent metagenomic detection of microbial species has the potential to provide rapid and precise real-time diagnostic results. However, it is potentially limited by sequencing and taxonomic classification errors. We use simulated and real-world data to benchmark rates of species misclassification using 100 reference genomes for each of the ten common bloodstream pathogens and six frequent blood-culture contaminants (n=1568, only 68 genomes were available for Micrococcus luteus). Simulating both with and without sequencing error for both the Illumina and Oxford Nanopore platforms, we evaluated commonly used classification tools including Kraken2, Bracken and Centrifuge, utilizing mini (8 GB) and standard (30-50 GB) databases. Bracken with the standard database performed best, the median percentage of reads across both sequencing platforms identified correctly to the species level was 97.8% (IQR 92.7:99.0) [range 5:100]. For Kraken2 with a mini database, a commonly used combination, median species-level identification was 86.4% (IQR 50.5:93.7) [range 4.3:100]. Classification performance varied by species, with Escherichia coli being more challenging to classify correctly (probability of reads being assigned to the correct species: 56.1-96.0%, varying by tool used). Human read misclassification was negligible. By filtering out shorter Nanopore reads we found performance similar or superior to Illumina sequencing, despite higher sequencing error rates. Misclassification was more common when the misclassified species had a higher average nucleotide identity to the true species. Our findings highlight taxonomic misclassification of sequencing data occurs and varies by sequencing and analysis workflow. To account for 'bioinformatic contamination' we present a contamination catalogue that can be used in metagenomic pipelines to ensure accurate results that can support clinical decision making.}, } @article {pmid36269227, year = {2022}, author = {White, RT and Anstey, SI and Kasimov, V and Jenkins, C and Devlin, J and El-Hage, C and Pannekoek, Y and Legione, AR and Jelocnik, M}, title = {One clone to rule them all: Culture-independent genomics of Chlamydia psittaci from equine and avian hosts in Australia.}, journal = {Microbial genomics}, volume = {8}, number = {10}, pages = {}, pmid = {36269227}, issn = {2057-5858}, mesh = {Horses ; Animals ; *Chlamydophila psittaci/genetics ; *Psittacosis/veterinary ; Birds ; Australia ; Genomics ; Clone Cells ; }, abstract = {Chlamydia psittaci is an avian pathogen with zoonotic potential. In Australia, C. psittaci has been well reported as a cause of reproductive loss in mares which subsequently have been the source of infection and illness in some in-contact humans. To date, molecular typing studies describe the predominant and clonal C. psittaci sequence type (ST)24 strains in horse, psittacine, and human infections. We sought to assess the clonality between ST24 strains and the emergence of equine ST24 with a comprehensive genomics approach. We used culture-independent probe-based and metagenomic whole-genome sequencing to investigate 13 C . psittaci genomes from horses, psittacines, and a pigeon from Australia. Published genomes of 36 C . psittaci strains were also used to contextualise our Australian dataset and investigate lineage diversity. We utilised a single-nucleotide polymorphism (SNP) based clustering and multi-locus sequence typing (MLST) approach. C. psittaci has four major phylogenetic groups (PG1-4) based on core-genome SNP-based phylogeny. PG1 contained clonal global and Australian equine, psittacine, and human ST24 genomes, with a median pairwise SNP distance of 68 SNPs. PG2, PG3, and PG4 had greater genomic diversity, including diverse STs collected from birds, livestock, human, and horse hosts from Europe and North America and a racing pigeon from Australia. We show that the clustering of C. psittaci by MLST was congruent with SNP-based phylogeny. The monophyletic ST24 clade has four major sub-lineages. The genomes of 17 Australian human, equine, and psittacine strains collected between 2008 and 2021 formed the predominant ST24 sub-lineage 1 (emerged circa 1979). Despite a temporal distribution of 13 years, the genomes within sub-lineage 1 had a median pairwise SNP distance of 32 SNPs, suggesting a recent population expansion or potential cross-host transmission. However, two C. psittaci genomes collected in 2015 from Victorian parrots clustered into distinct ST24 sub-lineage 4 (emerged circa 1965) with ovine strain C19/98 from Germany. This work describes a comprehensive phylogenomic characterisation of ST24 and identifies a timeline of potential bird-to-equine spillover events.}, } @article {pmid36268985, year = {2022}, author = {Peng, L and Shi, YB and Zheng, L and Hu, LQ and Weng, XB}, title = {Clinical features of patients with talaromycosis marneffei and microbiological characteristics of the causative strains.}, journal = {Journal of clinical laboratory analysis}, volume = {36}, number = {11}, pages = {e24737}, pmid = {36268985}, issn = {1098-2825}, support = {2019A610381//Natural Science Foundation of Ningbo/ ; 2019C50087//Ningbo Public Welfare Foundation/ ; }, mesh = {Humans ; *HIV Infections/complications ; Retrospective Studies ; *Mycoses/diagnosis/microbiology ; China ; Antifungal Agents/therapeutic use ; }, abstract = {BACKGROUND: Talaromyces marneffei (T. marneffei) is a temperature-dependent dimorphic fungus that is mainly prevalent in Southeast Asia and South China and often causes disseminated life-threatening infections. This study aimed to investigate the clinical features and improve the early diagnosis of talaromycosis marneffei in nonendemic areas.

METHODS: We retrospectively analyzed the medical records of six cases of T. marneffei infection. We describe the clinical manifestations, laboratory tests, and imaging manifestations of the six patients.

RESULTS: Talaromyces marneffei infection was confirmed by sputum culture, blood culture, tissue biopsy, and metagenomic next-generation sequencing (mNGS). In this study, there were five disseminated-type patients and two HIV patients. One patient died within 24 h, and the others demonstrated considerable improvement after definitive diagnosis.

CONCLUSIONS: Due to the lack of significant clinical presentations of talaromycosis marneffei, many cases may be easily misdiagnosed in nonendemic areas. It is particularly important to analyze the imaging manifestations and laboratory findings of infected patients. With the rapid development of molecular biology, mNGS may be a rapid and effective diagnostic method.}, } @article {pmid36268708, year = {2023}, author = {Kandathil, AJ and Benner, SE and Bloch, EM and Shrestha, R and Ajayi, O and Zhu, X and Caturegli, PP and Shoham, S and Sullivan, D and Gebo, K and Quinn, TC and Casadevall, A and Hanley, D and Pekosz, A and Redd, AD and Balagopal, A and Tobian, AAR}, title = {Absence of pathogenic viruses in COVID-19 convalescent plasma.}, journal = {Transfusion}, volume = {63}, number = {1}, pages = {23-29}, pmid = {36268708}, issn = {1537-2995}, support = {R01 AI152078/AI/NIAID NIH HHS/United States ; R01 AI120938/AI/NIAID NIH HHS/United States ; R01 HL059842/HL/NHLBI NIH HHS/United States ; R01 AI052733/AI/NIAID NIH HHS/United States ; K23 HL151826/HL/NHLBI NIH HHS/United States ; R01 DK131926/DK/NIDDK NIH HHS/United States ; R01 AI138810/AI/NIAID NIH HHS/United States ; R21 DA053145/DA/NIDA NIH HHS/United States ; R01 AI128779/AI/NIAID NIH HHS/United States ; R01 DA013806/DA/NIDA NIH HHS/United States ; }, mesh = {Humans ; *Epstein-Barr Virus Infections ; Seroepidemiologic Studies ; Herpesvirus 4, Human/genetics ; *COVID-19/therapy ; COVID-19 Serotherapy ; SARS-CoV-2/genetics ; *Anelloviridae/genetics ; *Torque teno virus/genetics ; Cytomegalovirus/genetics ; *Cytomegalovirus Infections ; DNA ; DNA, Viral/genetics ; *DNA Virus Infections ; }, abstract = {BACKGROUND: It is important to maintain the safety of blood products by avoiding the transfusion of units with known and novel viral pathogens. It is unknown whether COVID-19 convalescent plasma (CCP) may contain pathogenic viruses (either newly acquired or reactivated) that are not routinely screened for by blood centers.

METHODS: The DNA virome was characterized in potential CCP donors (n = 30) using viral genome specific PCR primers to identify DNA plasma virome members of the Herpesviridae [Epstein Barr Virus (EBV), cytomegalovirus (CMV), human herpesvirus 6A/B, human herpesvirus 7] and Anelloviridae [Torque teno viruses (TTV), Torque teno mini viruses (TTMV), and Torque teno midi viruses (TTMDV)] families. In addition, the RNA plasma virome was characterized using unbiased metagenomic sequencing. Sequencing was done on a HiSeq2500 using high output mode with a read length of 2X100 bp. The sequencing reads were taxonomically classified using Kraken2. CMV and EBV seroprevalence were evaluated using a chemiluminescent immunoassay.

RESULTS: TTV and TTMDV were detected in 12 (40%) and 4 (13%) of the 30 study participants, respectively; TTMDV was always associated with infection with TTV. We did not observe TTMV DNAemia. Despite CMV and EBV seroprevalences of 33.3% and 93.3%, respectively, we did not detect Herpesviridae DNA among the study participants. Metagenomic sequencing did not reveal any human RNA viruses in CCP, including no evidence of circulating SARS-CoV-2.

DISCUSSION: There was no evidence of pathogenic viruses, whether newly acquired or reactivated, in CCP despite the presence of non-pathogenic Anelloviridae. These results confirm the growing safety data supporting CCP.}, } @article {pmid36268227, year = {2022}, author = {Shi, J and Wu, W and Wu, K and Ni, C and He, G and Zheng, S and Cheng, F and Yi, Y and Ren, R and Jiang, X}, title = {The diagnosis of leptospirosis complicated by pulmonary tuberculosis complemented by metagenomic next-generation sequencing: A case report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {922996}, pmid = {36268227}, issn = {2235-2988}, mesh = {Humans ; Male ; Aged ; *Mycobacterium tuberculosis/genetics ; *Tuberculosis, Pulmonary/complications/diagnosis/microbiology ; Sputum/microbiology ; *Tuberculosis ; *Leptospirosis/complications/diagnosis ; High-Throughput Nucleotide Sequencing ; *Leptospira/genetics ; Sensitivity and Specificity ; }, abstract = {Leptospirosis is a zoonotic infection caused by the pathogenic Leptospira. Leptospirosis is transmitted mainly through contact with contaminated rivers, lakes, or animals carrying Leptospira. Human leptospirosis has a wide range of non-specific clinical manifestations ranging from fever, hypotension, and myalgia to multi-organ dysfunction, which severely hampers the timely clinical diagnosis and treatment of leptospirosis. Therefore, there is an urgent clinical need for an efficient strategy/method that can be used for the accurate diagnosis of leptospirosis, especially in critically ill patients. Here, we report a case of a 75-year-old male patient with clinical presentation of fever, cough, and diarrhea. Initial laboratory tests and a computed tomography (CT) scan of the chest suggested only tuberculosis. The patient was finally diagnosed with pulmonary tuberculosis (PTB) combined with leptospirosis by sputum Xpert MTB RIF, epidemiological investigations, and delayed serological testing. Furthermore, through metagenomic next-generation sequencing (mNGS) of clinical samples of cerebrospinal fluid (CSF), urine, plasma and sputum, the causative pathogens were identified as Mycobacterium tuberculosis complex and Leptospira spp. With specific treatment for both leptospirosis and tuberculosis, and associated supportive care (e.g., hemodialysis), the patient showed a good prognosis. This case report suggests that mNGS can generate a useful complement to conventional pathogenic diagnostic methods through more detailed etiological screening (i.e., at the level of species or species complex).}, } @article {pmid36268225, year = {2022}, author = {Khorsand, B and Asadzadeh Aghdaei, H and Nazemalhosseini-Mojarad, E and Nadalian, B and Nadalian, B and Houri, H}, title = {Overrepresentation of Enterobacteriaceae and Escherichia coli is the major gut microbiome signature in Crohn's disease and ulcerative colitis; a comprehensive metagenomic analysis of IBDMDB datasets.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1015890}, pmid = {36268225}, issn = {2235-2988}, mesh = {Humans ; *Colitis, Ulcerative ; *Crohn Disease/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Escherichia coli ; Siderophores ; Lipopolysaccharides ; *Inflammatory Bowel Diseases/microbiology ; Feces/microbiology ; *Escherichia coli Infections ; Sulfur ; Nitrogen ; }, abstract = {OBJECTIVES: A number of converging strands of research suggest that the intestinal Enterobacteriaceae plays a crucial role in the development and progression of inflammatory bowel disease (IBD), however, the changes in the abundance of Enterobacteriaceae species and their related metabolic pathways in Crohn's disease (CD) and ulcerative colitis (UC) compared to healthy people are not fully explained by comprehensive comparative metagenomics analysis. In the current study, we investigated the alternations of the Enterobacterales population in the gut microbiome of patients with CD and UC compared to healthy subjects.

METHODS: Metagenomic datasets were selected from the Integrative Human Microbiome Project (HMP2) through the Inflammatory Bowel Disease Multi'omics Database (IBDMDB). We performed metagenome-wide association studies on fecal samples from 191 CD patients, 132 UC patients, and 125 healthy controls (HCs). We used the metagenomics dataset to study bacterial community structure, relative abundance, differentially abundant bacteria, functional analysis, and Enterobacteriaceae-related biosynthetic pathways.

RESULTS: Compared to the gut microbiome of HCs, six Enterobacteriaceae species were significantly elevated in both CD and UC patients, including Escherichia coli, Klebsiella variicola, Klebsiella quasipneumoniae, Klebsiella pneumoniae, Proteus mirabilis, Citrobacter freundii, and Citrobacter youngae, while Klebsiella oxytoca, Morganella morganii, and Citrobacter amalonaticus were uniquely differentially abundant and enriched in the CD cohort. Four species were uniquely differentially abundant and enriched in the UC cohort, including Citrobacter portucalensis, Citrobacter pasteurii, Citrobacter werkmanii, and Proteus hauseri. Our analysis also showed a dramatically increased abundance of E. coli in their intestinal bacterial community. Biosynthetic pathways of aerobactin siderophore, LPS, enterobacterial common antigen, nitrogen metabolism, and sulfur relay systems encoded by E. coli were significantly elevated in the CD samples compared to the HCs. Menaquinol biosynthetic pathways were associated with UC that belonged to K. pneumoniae strains.

CONCLUSIONS: In conclusion, compared with healthy people, the taxonomic and functional composition of intestinal bacteria in CD and UC patients was significantly shifted to Enterobacteriaceae species, mainly E. coli and Klebsiella species.}, } @article {pmid36267886, year = {2022}, author = {Wang, T and Cao, D and Han, J}, title = {Acute invasive mucormycosis rhinosinusitis causing multigroup cranial nerve injury and meningitis-A case report.}, journal = {Frontiers in neurology}, volume = {13}, number = {}, pages = {873694}, pmid = {36267886}, issn = {1664-2295}, abstract = {This study reported a case of a Rhino-Orbital-Cerebral Mycosis (ROCM) patient with multiple groups of cranial nerve damage as the primary clinical manifestation, confirmed by histopathology and cerebrospinal fluid metagenomic next-generation sequencing (mNGS) technology. Relying on the MRI3D-SPACE technology, we observed the location and extent of the cranial nerve damage in the patient. The results suggested that fungal meningoencephalitis caused by mucor may enter the skull retrograde along the cranial nerve perineurium. The patient was admitted to the hospital with a preliminary diagnosis of mucormycosis infection after 1.5 days of mouth deviation. We treated the patient immediately with intravenous amphotericin B liposomes. After 21 days of hospitalization, the clinical symptoms of the patient did not improve significantly. The patient was discharged due to financial difficulties and antifungal treatment at home, and his disease had stabilized at the 6-month follow-up.}, } @article {pmid36266337, year = {2022}, author = {Kalantar, KL and Neyton, L and Abdelghany, M and Mick, E and Jauregui, A and Caldera, S and Serpa, PH and Ghale, R and Albright, J and Sarma, A and Tsitsiklis, A and Leligdowicz, A and Christenson, SA and Liu, K and Kangelaris, KN and Hendrickson, C and Sinha, P and Gomez, A and Neff, N and Pisco, A and Doernberg, SB and Derisi, JL and Matthay, MA and Calfee, CS and Langelier, CR}, title = {Integrated host-microbe plasma metagenomics for sepsis diagnosis in a prospective cohort of critically ill adults.}, journal = {Nature microbiology}, volume = {7}, number = {11}, pages = {1805-1816}, pmid = {36266337}, issn = {2058-5276}, support = {K23 HL138461/HL/NHLBI NIH HHS/United States ; R01 HL155418/HL/NHLBI NIH HHS/United States ; R35 HL140026/HL/NHLBI NIH HHS/United States ; F32 HL151117/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Humans ; *Critical Illness ; Prospective Studies ; *Sepsis/diagnosis ; Cohort Studies ; RNA ; }, abstract = {We carried out integrated host and pathogen metagenomic RNA and DNA next generation sequencing (mNGS) of whole blood (n = 221) and plasma (n = 138) from critically ill patients following hospital admission. We assigned patients into sepsis groups on the basis of clinical and microbiological criteria. From whole-blood gene expression data, we distinguished patients with sepsis from patients with non-infectious systemic inflammatory conditions using a trained bagged support vector machine (bSVM) classifier (area under the receiver operating characteristic curve (AUC) = 0.81 in the training set; AUC = 0.82 in a held-out validation set). Plasma RNA also yielded a transcriptional signature of sepsis with several genes previously reported as sepsis biomarkers, and a bSVM sepsis diagnostic classifier (AUC = 0.97 training set; AUC = 0.77 validation set). Pathogen detection performance of plasma mNGS varied on the basis of pathogen and site of infection. To improve detection of virus, we developed a secondary transcriptomic classifier (AUC = 0.94 training set; AUC = 0.96 validation set). We combined host and microbial features to develop an integrated sepsis diagnostic model that identified 99% of microbiologically confirmed sepsis cases, and predicted sepsis in 74% of suspected and 89% of indeterminate sepsis cases. In summary, we suggest that integrating host transcriptional profiling and broad-range metagenomic pathogen detection from nucleic acid is a promising tool for sepsis diagnosis.}, } @article {pmid36265810, year = {2022}, author = {Carson, TL and Buro, AW and Miller, D and Peña, A and Ard, JD and Lampe, JW and Yi, N and Lefkowitz, E and William, VP and Morrow, C and Wilson, L and Barnes, S and Demark-Wahnefried, W}, title = {Rationale and study protocol for a randomized controlled feeding study to determine the structural- and functional-level effects of diet-specific interventions on the gut microbiota of non-Hispanic black and white adults.}, journal = {Contemporary clinical trials}, volume = {123}, number = {}, pages = {106968}, pmid = {36265810}, issn = {1559-2030}, support = {R01 CA253219/CA/NCI NIH HHS/United States ; T32 CA090314/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Male ; Humans ; Female ; *Gastrointestinal Microbiome ; White People ; Feces/microbiology ; Diet ; Bacteria/genetics ; Randomized Controlled Trials as Topic ; }, abstract = {BACKGROUND: Colorectal cancer (CRC), the third leading cause of cancer-related deaths in the US, has been associated with an overrepresentation or paucity of several microbial taxa in the gut microbiota, but causality has not been established. Black men and women have among the highest CRC incidence and mortality rates of any racial/ethnic group. This study will examine the impact of the Dietary Approaches to Stop Hypertension (DASH) diet on gut microbiota and fecal metabolites associated with CRC risk.

METHODS: A generally healthy sample of non-Hispanic Black and white adults (n = 112) is being recruited to participate in a parallel-arm randomized controlled feeding study. Participants are randomized to receive the DASH diet or a standard American diet for a 28-day period. Fecal samples are collected weekly throughout the study to analyze changes in the gut microbiota using 16 s rRNA and selected metagenomics. Differences in bacterial alpha and beta diversity and taxa that have been associated with CRC (Bacteroides, Fusobacterium, Clostridium, Lactobacillus, Bifidobacterium, Ruminococcus, Porphyromonas, Succinivibrio) are being evaluated. Covariate measures include body mass index, comorbidities, medication history, physical activity, stress, and demographic characteristics.

CONCLUSION: Our findings will provide preliminary evidence for the DASH diet as an approach for cultivating a healthier gut microbiota across non-Hispanic Black and non-Hispanic White adults. These results can impact clinical, translational, and population-level approaches for modification of the gut microbiota to reduce risk of chronic diseases including CRC.

TRIAL REGISTRATION: This study was registered on ClinicalTrials.gov, identifier NCT04538482, on September 4, 2020 (https://clinicaltrials.gov/ct2/show/NCT04538482).}, } @article {pmid36265688, year = {2023}, author = {Estanyol-Torres, N and Domenech-Coca, C and González-Domínguez, R and Miñarro, A and Reverter, F and Moreno-Muñoz, JA and Jiménez, J and Martín-Palomas, M and Castellano-Escuder, P and Mostafa, H and García-Vallvé, S and Abasolo, N and Rodríguez, MA and Torrell, H and Del Bas, JM and Sanchez-Pla, A and Caimari, A and Mas-Capdevila, A and Andres-Lacueva, C and Crescenti, A}, title = {A mixture of four dietary fibres ameliorates adiposity and improves metabolic profile and intestinal health in cafeteria-fed obese rats: an integrative multi-omics approach.}, journal = {The Journal of nutritional biochemistry}, volume = {111}, number = {}, pages = {109184}, doi = {10.1016/j.jnutbio.2022.109184}, pmid = {36265688}, issn = {1873-4847}, mesh = {Rats ; Male ; Animals ; *Adiposity ; Rats, Wistar ; Obesity/metabolism ; Dietary Fiber/pharmacology ; Metabolome ; Cholesterol ; *Sexually Transmitted Diseases ; }, abstract = {The aim of this study was to assess the effects of a mixture of four dietary fibers on obese rats. Four groups of male Wistar rats were fed with either standard chow (STD) or cafeteria diet (CAF) and were orally supplemented with either fibre mixture (2 g kg[-1] of body weight) (STD+F or CAF+F groups) or vehicle (STD+VH or CAF+VH groups). We studied a wide number of biometric, biochemical, transcriptomic, metagenomic and metabolomic variables and applied an integrative multivariate approach based on multiple factor analysis and Pearson's correlation analysis. A significant reduction in body weight, adiposity, HbA1c and HDL-cholesterol serum levels, and colon MPO activity was observed, whereas cecal weight and small intestine length:weight ratio were significantly increased in F-treated groups compared to control animals. CAF+F rats displayed a significant enhancement in energy expenditure, fat oxidation and fresh stool weight, and a significant reduction in adiponectin and LPS serum levels, compared to control group. Animals in STD+F group showed reduced serum LDL-cholesterol levels and a significant reduction in total cholesterol levels in the liver compared to STF+VH group. The intervention effect was reflected at the metabolomic (i.e., production of short-chain fatty acids, phenolic acids, and amino acids), metagenomic (i.e., modulation of Ruminococcus and Lactobacillus genus) and transcriptomic (i.e., expression of tight junctions and proteolysis) levels. Altogether, our integrative multi-omics approach highlights the potential of supplementation with a mixture of fibers to ameliorate the impairments triggered by obesity in terms of adiposity, metabolic profile, and intestinal health.}, } @article {pmid36265247, year = {2023}, author = {Liu, YD and Yuan, G and An, YT and Zhu, ZR and Li, G}, title = {Molecular cloning and characterization of a novel bifunctional cellobiohydrolase/β-xylosidase from a metagenomic library of mangrove soil.}, journal = {Enzyme and microbial technology}, volume = {162}, number = {}, pages = {110141}, doi = {10.1016/j.enzmictec.2022.110141}, pmid = {36265247}, issn = {1879-0909}, mesh = {*Cellulose 1,4-beta-Cellobiosidase/genetics/metabolism ; Soil ; Phylogeny ; Molecular Docking Simulation ; Enzyme Stability ; Substrate Specificity ; Hydrogen-Ion Concentration ; *Xylosidases/metabolism ; Cloning, Molecular ; Glycoside Hydrolases/metabolism ; }, abstract = {A metagenomic library of mangrove soil samples consisting of approximately 11,000 clones was constructed, and a rare bifunctional cellobiohydrolase/β-xylosidase Cbh2124 was identified by functional screening. Cbh2124 displayed the highest homology (56.43%) with a protein of the glycoside hydrolase 10 (GH10) family from Proteobacteria. Phylogenetic analysis confirmed that Cbh2124 belongs to the GH10 family. The recombinant enzyme showed a strong cellobiohydrolase activity and a relatively high β-xylosidase activity, and its catalytic efficiency to the cellobiose substrate was as high as 1.27 × 10[5] s[-1]·mM[-1], the highest efficiency among reported cellobiohydrolases. Of particular interest, some enzymatic properties of the β-xylosidase activity of Cbh2124 were significantly different from those of the cellobiohydrolase activity. The optimal pH and temperature of the cellobiohydrolase activity of Cbh2124 was 6.4 and 36 °C, and the activity was essentially lost after treatment at 45 °C for 1 h. The optimal pH and temperature of the β-xylosidase activity of Cbh2124 was 8.0 and 60 °C, and the residual activity was still over 90% after treatment at 80 °C for 6 h. The molecular docking results of the β-xylosidase activity of Cbh2124 revealed the additional presence of catalytic amino acids Ser175 and Lys420, thus increasing the number of hydrogen bonds involved in the catalytic process, which possibly let to the improved thermostability compared with that of the cellobiohydrolase activity.}, } @article {pmid36265239, year = {2022}, author = {González-Castillo, A and Carballo, JL and Bautista-Guerrero, E}, title = {Bacterial diversity associated with the excavating sponge Thoosa mismalolli from East Pacific Coral reefs.}, journal = {Marine genomics}, volume = {66}, number = {}, pages = {100994}, doi = {10.1016/j.margen.2022.100994}, pmid = {36265239}, issn = {1876-7478}, mesh = {Animals ; *Coral Reefs ; Phylogeny ; Bacteria/genetics ; Archaea/genetics ; Metagenome ; *Porifera/genetics ; }, abstract = {Thoosa mismalolli is one of the most abundant and common excavating sponges along Mexican and Central America shallow reefs. This sponge harbors a microbiome unknown so far. In the present study, the metagenome of T. mismalolli was sequenced, and total reads obtained were classified, and contigs were assembled to analyze the microbiota. The results showed that the highest number of contigs was assigned to the phylum 'Candidatus Poribacteria' (8848), followed by the phylum Proteobacteria (6415), and Chloroflexi (3972). 22 MAGs with <8.5% redundancy using MaxBin 2 were detected: 'Candidatus Poribacteria' (5), Proteobacteria (5), Chloroflexi (6), Gemmatimonadetes (2), Actinobacteria (2), and Thaumarchaeota (2). The phylogenetic tree based on the 139 single-copy gene (SCG) suggested a subdivision into two clades of the phylum Proteobacteria. The presence Thaumarchaeota is also interesting to highlight because contains ammonia-oxidizing archaea considered key members of the global nitrogen and carbon biogeochemical cycles. In addition, shotgun metagenomic analysis revealed that protein sequences associated for amino acids (13.0%) and carbohydrate metabolism (12.4%) predominated. In this study, the first microbiome and functional potential of T. mismalolli is reported, which also represents the first investigation of a microbiota sponge in the Mexican Pacific reefs.}, } @article {pmid36264997, year = {2022}, author = {Li, Y and Shi, M and Zhang, B and Wu, J and Wang, Y and Li, M and Wu, Y and Hu, X and Hu, D and Huang, Z and Wronski, T}, title = {Effects of different weaning times on the stress response and the intestinal microbiota composition of female forest musk deer (Moschus berezovskii) and their fawns.}, journal = {PloS one}, volume = {17}, number = {10}, pages = {e0276542}, pmid = {36264997}, issn = {1932-6203}, mesh = {Humans ; Animals ; Female ; *Gastrointestinal Microbiome/genetics ; *Deer/physiology ; Weaning ; Hydrocortisone ; Forests ; Receptors, Cholinergic ; Receptor Protein-Tyrosine Kinases ; }, abstract = {The effects of mother-infant separation (i.e., weaning) on the physiology, psychology and nutrition of mammalian infants have attracted much attention. Forest musk deer (FMD) is a first-class protected species in China and listed endangered in the IUCN Red List. The captive breeding population is not only an important source for restocking of wild resources, but also a necessary way to supply the market with legal musk. So far, there is no scientific basis for the appropriate separation time of FMD females and their infants. Therefore, we used metagenome sequencing and enzyme-linked immunosorbent assays to study changes in the fecal cortisol concentration, as well as the intestinal microbiome composition and function of females and fawns at three different separation times, i.e., after 80 days, 90 days and 100 days. The results showed that the increment of the cortisol concentration in female FMD increased with increasing lactation time. The increment of cortisol concentration in infant FMD was highest in the 80 days weaning group, but there was no significant difference between the 90 days and the 100 days separation time. Based on the annotation results of COG, KEGG and CAZy databases, the abundance of different functions annotated by the intestinal microbiome of mothers and fawns of the 90 days weaning group changed slightly after separation. Based on the above results, the separation of mother and infant FMD is recommended after 90 days, i.e., the separation time that triggered the lowest rate of weaning stress and that supported a relatively stable gastro-intestinal physiology.}, } @article {pmid36264306, year = {2022}, author = {Amin, AB and Zhang, L and Zhang, J and Mao, S}, title = {Fermented soybean meal modified the rumen microbiome to enhance the yield of milk components in Holstein cows.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {22}, pages = {7627-7642}, pmid = {36264306}, issn = {1432-0614}, support = {2021YFF1000703-01//National Key research and Development Program of China/ ; }, mesh = {Animals ; Cattle ; Female ; Pregnancy ; Acetates/metabolism ; Animal Feed ; Diet/veterinary ; Dietary Supplements ; Fermentation ; *Fermented Foods ; Lactation ; Methionine/metabolism ; *Microbiota ; Milk Proteins/metabolism/pharmacology ; Propionates/metabolism ; RNA, Ribosomal, 16S/metabolism ; Rumen/microbiology ; Glycine max/metabolism ; }, abstract = {The study was conducted to evaluate the rumen microbiota as well as the milk composition and milk component yields of Holstein cows supplemented with fermented soybean meal (FSBM). Eighteen Holstein cows in their 2nd parity with 54.38 ± 11.12 SD days in milking (DIM) were divided into two dietary groups (CON and TRT) of nine cows per group. The cows in the TRT group received 300 g of FSBM per cow per day in addition to the conventional diet, while each cow in the CON group was supplemented with 350 g of soybean meal (SBM) in their diet daily throughout the 28-day feeding trial. Rumen bacterial composition was detected via 16S rRNA sequencing, and the functional profiles of bacterial communities were predicted. Milk composition, milk yield, as well as rumen fermentation parameters, and serum biochemistry were also recorded. The inclusion of FSBM into the diets of Holstein cows increased the milk urea nitrogen (MUN), milk protein yield, fat corrected milk (FCM), and milk fat yield while the milk somatic cell count (SCC) was decreased. In the rumen, the relative abundances of Fibrobacterota, and Spirochaetota phyla were increased in the TRT group, while the percentage of Proteobacteria was lower. In addition, the supplementation of FSBM to Holstein cows increased the acetate percentage, rumen pH, and acetate to propionate ratio, while the proportion of propionate and propionate % was observed to decrease in the TRT group. The KEGG pathway and functional prediction revealed an upregulation in the functional genes associated with the biosynthesis of amino acids in the TRT group. This enrichment in functional genes resulted in an improved synthesis of several essential amino acids including lysine, methionine, and branch chain amino acids (BCAA) which might be responsible for the increased milk protein yield. Future studies should employ shotgun metagenomics, transcriptomics, and metabolomics technology to investigate the effects of FSBM on other rumen microbiomes and milk protein synthesis in the mammary gland in Holstein cows. KEY POINTS: • The supplementation of fermented soybean meal (FSBM) to Holstein cows modified the proportion of rumen bacteria. • Predicted metabolic pathways and functional genes of rumen bacteria revealed an enrichment in pathway and genes associated with biosynthesis of amino acids in the group fed FSBM. • The cows supplemented with FSBM record an improved rumen fermentation. • Cows supplemented with FSBM recorded an increased yield of milk protein and milk fat.}, } @article {pmid36264256, year = {2022}, author = {Gadson, O and Bevilacqua, JG and Fishman, CB and Hahn, AS and McAdam, AC and Bleacher, J and Johnson, SS}, title = {Metagenome-Assembled Genome of a Putative Chemoheterotroph from Volcanic Terrain in Hawaii.}, journal = {Microbiology resource announcements}, volume = {11}, number = {11}, pages = {e0055622}, pmid = {36264256}, issn = {2576-098X}, support = {//NASA | Goddard Space Flight Center (GSFC)/ ; }, abstract = {Here, we present the draft genome for a new putative species, Gaiellasilicea maunaloa, most closely related to Gaiella occulta, within the phylum Actinobacteria. This group contains Gram-negative, aerobic mesophilic species. This metagenome-assembled genome (MAG) contributes to knowledge of life in volcanic environments and may inform investigations of life beyond Earth.}, } @article {pmid36264141, year = {2022}, author = {Rühlemann, MC and Wacker, EM and Ellinghaus, D and Franke, A}, title = {MAGScoT: a fast, lightweight and accurate bin-refinement tool.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {24}, pages = {5430-5433}, pmid = {36264141}, issn = {1367-4811}, support = {//German Research Foundation/ ; SFB 1182//Collaborative Research Center 1182: Origin and Function of Metaorganisms/ ; //DFG Research Unit 5042/ ; }, mesh = {*Algorithms ; Metagenomics ; Metagenome ; *Microbiota ; }, abstract = {MOTIVATION: Recovery of metagenome-assembled genomes (MAGs) from shotgun metagenomic data is an important task for the comprehensive analysis of microbial communities from variable sources. Single binning tools differ in their ability to leverage specific aspects in MAG reconstruction, the use of ensemble binning refinement tools is often time consuming and computational demand increases with community complexity. We introduce MAGScoT, a fast, lightweight and accurate implementation for the reconstruction of highest-quality MAGs from the output of multiple genome-binning tools.

RESULTS: MAGScoT outperforms popular bin-refinement solutions in terms of quality and quantity of MAGs as well as computation time and resource consumption.

MAGScoT is available via GitHub (https://github.com/ikmb/MAGScoT) and as an easy-to-use Docker container (https://hub.docker.com/repository/docker/ikmb/magscot).

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36263822, year = {2023}, author = {Alcock, BP and Huynh, W and Chalil, R and Smith, KW and Raphenya, AR and Wlodarski, MA and Edalatmand, A and Petkau, A and Syed, SA and Tsang, KK and Baker, SJC and Dave, M and McCarthy, MC and Mukiri, KM and Nasir, JA and Golbon, B and Imtiaz, H and Jiang, X and Kaur, K and Kwong, M and Liang, ZC and Niu, KC and Shan, P and Yang, JYJ and Gray, KL and Hoad, GR and Jia, B and Bhando, T and Carfrae, LA and Farha, MA and French, S and Gordzevich, R and Rachwalski, K and Tu, MM and Bordeleau, E and Dooley, D and Griffiths, E and Zubyk, HL and Brown, ED and Maguire, F and Beiko, RG and Hsiao, WWL and Brinkman, FSL and Van Domselaar, G and McArthur, AG}, title = {CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database.}, journal = {Nucleic acids research}, volume = {51}, number = {D1}, pages = {D690-D699}, pmid = {36263822}, issn = {1362-4962}, mesh = {Anti-Bacterial Agents/pharmacology ; *Databases, Factual ; *Drug Resistance, Microbial ; Genes, Bacterial ; Likelihood Functions ; *Machine Learning ; Software ; Molecular Sequence Annotation ; *Data Curation ; }, abstract = {The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation and interpretation of resistomes. As of version 3.2.4, CARD encompasses 6627 ontology terms, 5010 reference sequences, 1933 mutations, 3004 publications, and 5057 AMR detection models that can be used by the accompanying Resistance Gene Identifier (RGI) software to annotate genomic or metagenomic sequences. Focused curation enhancements since 2020 include expanded β-lactamase curation, incorporation of likelihood-based AMR mutations for Mycobacterium tuberculosis, addition of disinfectants and antiseptics plus their associated ARGs, and systematic curation of resistance-modifying agents. This expanded curation includes 180 new AMR gene families, 15 new drug classes, 1 new resistance mechanism, and two new ontological relationships: evolutionary_variant_of and is_small_molecule_inhibitor. In silico prediction of resistomes and prevalence statistics of ARGs has been expanded to 377 pathogens, 21,079 chromosomes, 2,662 genomic islands, 41,828 plasmids and 155,606 whole-genome shotgun assemblies, resulting in collation of 322,710 unique ARG allele sequences. New features include the CARD:Live collection of community submitted isolate resistome data and the introduction of standardized 15 character CARD Short Names for ARGs to support machine learning efforts.}, } @article {pmid36263411, year = {2022}, author = {Zhao, C and Wang, L and Ke, S and Chen, X and Kenéz, Á and Xu, W and Wang, D and Zhang, F and Li, Y and Cui, Z and Qiao, Y and Wang, J and Sun, W and Zhao, J and Yao, J and Yu, Z and Cao, Y}, title = {Yak rumen microbiome elevates fiber degradation ability and alters rumen fermentation pattern to increase feed efficiency.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {11}, number = {}, pages = {201-214}, pmid = {36263411}, issn = {2405-6383}, abstract = {Rumen microbes play an important role in ruminant energy supply and animal performance. Previous studies showed that yak (Bos grunniens) rumen microbiome and fermentation differ from other ruminants. However, little is understood about the features of the rumen microbiome that make yak adapted to their unique environmental and dietary conditions. This study was to investigate the rumen microbiome and metabolome to understand how yak adapt to the coarse forage and harsh environment in the Qinghai-Tibetan plateau. Nine female Qaidam yellow cattle (Bos taurus), 9 dzomo (hybrids of cattle and yak) and 9 female plateau yak (B. grunniens), about 5 to 6 years old, were used in this study. Rumen fermentation parameters, fibrolytic enzyme activities, and rumen metataxonomic were determined. Then 18 (6 samples per group) were selected for rumen metagenomic and metabolome analysis. Metataxonomic analysis revealed that the rumen microbiota was significantly different among plateau yak, Qaidam yellow cattle, and dzomo (P < 0.05). Metagenomic analysis displayed a larger gene pool encoding a richer repertoire of carbohydrate-active enzymes in the rumen microbiome of plateau yak and dzomo than Qaidam yellow cattle (P < 0.05). Some of the genes encoding glycoside hydrolases that mediate the digestion of cellulose and hemicellulose were significantly enriched in the rumen of plateau yak than Qaidam yellow cattle, but glycoside hydrolase 57 that primarily includes amylases was abundant in Qaidam yellow cattle (P < 0.05). The rumen fermentation profile differed also, Qaidam yellow cattle having a higher molar proportion of acetate but a lower molar proportion of propionate than dzomo and plateau yak (P < 0.05). Based on metabolomic analysis, rumen microbial metabolic pathways and metabolites were different. Differential metabolites are mainly amino acids, carboxylic acids, sugars, and bile acids. Changes in rumen microbial composition could explain the above results. The present study showed that the rumen microbiome of plateau yak helps its host to adapt to the Qinghai-Tibetan plateau. In particular, the plateau yak rumen microbiome has more enzymes genes involved in cellulase and hemicellulase than that of cattle, resulting higher fibrolytic enzyme activities in yak, further providing stronger fiber degradation function.}, } @article {pmid36262997, year = {2022}, author = {Yin, K and Liu, L and Fan, G}, title = {Classification and Drug Resistance Analysis of Pathogenic Bacteria in Patients with Bacterial Pneumonia in Emergency Intensive Care Unit.}, journal = {Contrast media & molecular imaging}, volume = {2022}, number = {}, pages = {6980091}, pmid = {36262997}, issn = {1555-4317}, mesh = {Humans ; *Cefoperazone ; Microbial Sensitivity Tests ; Drug Resistance, Bacterial ; Sulbactam ; Ceftazidime ; Levofloxacin ; Tigecycline ; Amikacin ; Azithromycin ; Gram-Negative Bacteria ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Imipenem ; Intensive Care Units ; Piperacillin, Tazobactam Drug Combination ; *Pneumonia, Bacterial/drug therapy ; Amoxicillin ; Gentamicins ; Ciprofloxacin ; }, abstract = {OBJECTIVE: This study aimed to compare the identification efficiency of metagenome next generation sequencing (mNGS) and traditional methods in detecting pathogens in patients with severe bacterial pneumonia (BP) and further analyze the drug resistance of common pathogens.

METHODS: A total of 180 patients with severe BP who were admitted to our hospital from June 2017 to July 2020 were selected as the research objects. Alveolar lavage fluid from the patients were collected, and pathogens were detected by the mNGS technology and traditional etiological detection technology. Common pathogens detected by mNGS were tested for the drug sensitivity test. The difference between mNGS and traditional detection method in the identification of pathogenic bacteria in severe BP patients was compared, and the distribution characteristics and drug resistance of pathogenic bacteria were analyzed.

RESULTS: The positive rate of mNGS detection was 92.22%, which was significantly higher than that of the traditional culture method (58.33%, P < 0.05). 347 strains of pathogenic bacteria were detected by mNGS, including 256 strains of Gram-negative bacteria (G[-]), 89 strains of Gram-positive bacteria (G[+]), and 2 strains of fungi. Among G[-] bacteria, Acinetobacter baumannii had higher resistance to piperacillin/tazobactam, ceftazidime, imipenem, levofloxacin, amikacin, ciprofloxacin, gentamicin, and the lowest resistance to tigecycline. The resistance of Klebsiella pneumoniae to piperacillin/tazobactam and ceftazidime was higher. Pseudomonas aeruginosa had low resistance to all the drugs. Escherichia coli had high drug resistance to most drugs, and the drug resistant rates to cefoperazone/sulbactam, piperacillin/tazobactam, ceftazidime, imipenem, and gentamicin were all more than 50.00%. G[+] bacteria had high resistance to penicillin, azithromycin, amoxicillin and levofloxacin, and amoxicillin and levofloxacin had high resistance, up to 100.00%.

CONCLUSION: mNGS has high sensitivity for the identification of pathogenic bacteria in patients with BP. G[-] bacteria were the main pathogens of BP, but both G[-] and G[+] bacteria had high resistance to a variety of antibacterial drugs.}, } @article {pmid36262169, year = {2022}, author = {Xie, J and Wang, J and Zhao, F and Qiu, X and Chen, J and Jia, Y and Qin, P and Zhu, Y and Zhang, J and Wang, B}, title = {Metagenomic Analysis of Gut Microbiome in Gout Patients with Different Chinese Traditional Medicine Treatments.}, journal = {Evidence-based complementary and alternative medicine : eCAM}, volume = {2022}, number = {}, pages = {6466149}, pmid = {36262169}, issn = {1741-427X}, abstract = {INTRODUCTION: Changes in eating habits have made gout a metabolic disease of increasing concern. Previous studies have indicated that there are significant differences in species composition and abundance of gut microbiome in gout patients compared with average. Considering that traditional Chinese medicine has a momentous effect in treating gout, the research study aimed to explore the differences of genomic and metabolomics of gut microbiome before and after traditional Chinese medicine treatment in patients with gout.

METHOD: 30 patients with gout and 29 matched controls were recruited of which 16 patients took H treatment and 14 patients took T treatment. Stools were collected twice for patients before and after treatment and only once for controls. A total of 89 samples were annotated with metagenomic species and functions, and the enrichment analysis of differential genes and KO pathway was carried out.

RESULT: The results showed a decrease in the diversity of gut microbiome in gout patients and the gene abundance and metabolomics had great differences among study groups. The number of bacterial genera also had significant differences among treatment groups. Moreover, among different groups, the regulation of different species was variously correlated. The correlation between species and clinical laboratory indicators in the rising group was stronger than that in the decreasing group and the upregulation of some strain was related to the content of urea nitrogen.

CONCLUSION: After the traditional Chinese medicine treatment, the glutathione pathway was significantly enriched and some pathogenic bacteria were significantly inhibited. The study suggests that traditional Chinese medicine treatment may exert its therapeutic effect by inhibiting relevant pathways.}, } @article {pmid36261965, year = {2022}, author = {Yuan, B and Ma, Y and Ren, J and Ding, G and Zhou, N and Liang, J and Sun, Y}, title = {Risk assessment of three sheep stocking modes via identification of bacterial genomes carrying antibiotic resistance genes and virulence factor genes.}, journal = {Journal of environmental management}, volume = {323}, number = {}, pages = {116270}, doi = {10.1016/j.jenvman.2022.116270}, pmid = {36261965}, issn = {1095-8630}, mesh = {Sheep/genetics ; Animals ; *Anti-Bacterial Agents/pharmacology ; *Virulence Factors ; Genes, Bacterial ; Escherichia coli ; Drug Resistance, Microbial/genetics ; Genome, Bacterial ; Feces/microbiology ; Risk Assessment ; Tetracyclines ; }, abstract = {In order to protect the prairie ecological environment, intensive farming has become a prevalent method of sheep stocking. However, the link between captivity stocking mode and ecological risk of sheep feces is still poorly understood. In this study, metagenomics was used to identify the environmental risk of sheep feces among three stocking modes. Our results showed that captivity mode (C) elevated antibiotic resistance in feces, with the abundance of antibiotic resistance genes (ARGs) (5.381 copies/cell) higher than that of half-pen stocking (Fh) (1.093 copies/cell) and grazing mode (Fr) (0.315 copies/cell) (Duncan's test, P < 0.05). Virulence factor genes (VFGs) analysis showed offensive virulence factors had the highest abundance in captivity feces (C: 3.826 copies/cell, Fh: 0.342 copies/cell, Fr: 0.163 copies/cell) (Duncan's test, P < 0.05). 15 metagenome-assembled genomes (MAGs) were identified as potential pathogenic antibiotic resistant bacteria (PARB) and revealed that Escherichia, Klebsiella may be the main host of ARGs and VFGs in sheep feces. Furthermore, the minimal inhibition concentrations (MIC) of tetracycline of E. coli in the captivity feces was 8.6 times and 4.7 times than that of grazing and half-pen stocking samples, respectively. The Non-metric multidimensional scaling (NMDS) revealed that high stocking density leads to feces causing increased harm to the environment. Although feces from sheep raised in captivity and half-pen stocking modes are easier to collect, they are more harmful to the environment and aerobic composting should be done before their application to farmland. This work provides a guideline for better control of the environmental risk of sheep feces from different stocking modes.}, } @article {pmid36261869, year = {2022}, author = {Lourenço, TGB and de Oliveira, AM and Tsute Chen, G and Colombo, APV}, title = {Oral-gut bacterial profiles discriminate between periodontal health and diseases.}, journal = {Journal of periodontal research}, volume = {57}, number = {6}, pages = {1227-1237}, doi = {10.1111/jre.13059}, pmid = {36261869}, issn = {1600-0765}, support = {00239/2016-7//National Council for Scientific and Technological Development (CNPq)/ ; 001//Coordination of Improvement of Higher Education Personnel (CAPES)/ ; E-26/202.256/2019; E-26/201.162/2014//Foundation for Research Financial Support in the State of Rio de Janeiro (FAPERJ)/ ; E-26/201.162/2014//Foundation for Research Financial Support in the State of Rio de Janeiro (FAPERJ)/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; *Periodontitis/diagnosis/microbiology ; Aggregatibacter actinomycetemcomitans/genetics ; *Periodontal Diseases/microbiology ; }, abstract = {OBJECTIVE: This investigation explored oral-gut microbial signatures with potential to distinguish among periodontal conditions.

BACKGROUND DATA: The interplay between the oral and gut microbiomes may be a critical pathway linking periodontal diseases and systemic inflammatory disorders. The mechanisms by which oral microorganisms translocate to the gut and cause microbial dysbiosis, favoring an inflammatory state, are still unknown. As a first approach, characterization of oral-gut microbial profiles associated with periodontal health and diseases can provide insights on such mechanisms of etiology and pathogenesis.

METHODS: Fecal and saliva samples from individuals with periodontal health (PH, 8), gingivitis (GG, 17), and periodontitis (PD, 24) were analyzed for their microbial composition by 16S rRNA gene sequencing. Microbial taxa were compared and correlated to periodontal parameters. Multivariate discriminant analysis (MDA) was carried out to identify profiles related to health and disease.

RESULTS: Few significant differences in oral-gut taxa were detected among clinical groups, although increase in fecal Fusobacterium nucleatum ss vincentii and salivary Aggregatibacter actinomycetemcomitans, Parvimonas micra, and Fretibacterium sp. HMT358 were strongly correlated with deep pockets and inflammation (p < .01). Over 50% of the fecal microbiota comprised microorganisms shared between oral and gut sites, whereas oral taxa were detected in approximately 9%, particularly enriched in GG fecal samples (p = .04). Trends for lower fecal richness and higher salivary diversity in PD compared to PH were observed. MDA was able to classify correctly 82% of the patients into the clinical groups. Main classifiers of periodontitis were high BMI, older age, and enrichment of oral-fecal Leptotrichia sp. HMT4, Peptostreptococcus stomatis, Dialister invisus, and a novel Lautropia sp. HMTC89-like organism.

CONCLUSION: Within the limitations of an exploratory investigation, specific profiles of oral-gut taxa, including known and potential novel organisms, combined with social-demographic features were able to discriminate individuals with periodontal diseases in this study population.}, } @article {pmid36261866, year = {2023}, author = {Luna, LW and Naka, LN and Thom, G and Knowles, LL and Sawakuchi, AO and Aleixo, A and Ribas, CC}, title = {Late Pleistocene landscape changes and habitat specialization as promoters of population genomic divergence in Amazonian floodplain birds.}, journal = {Molecular ecology}, volume = {32}, number = {1}, pages = {214-228}, doi = {10.1111/mec.16741}, pmid = {36261866}, issn = {1365-294X}, mesh = {Animals ; *Genetic Variation ; *Metagenomics ; Ecosystem ; Phylogeography ; Birds/genetics ; Phylogeny ; DNA, Mitochondrial/genetics ; }, abstract = {Although vicariant processes are expected to leave similar genomic signatures among codistributed taxa, ecological traits such as habitat and stratum can influence genetic divergence within species. Here, we combined landscape history and habitat specialization to understand the historical and ecological factors responsible for current levels of genetic divergence in three species of birds specialized in seasonally flooded habitats in muddy rivers and which are widespread in the Amazon basin but have isolated populations in the Rio Branco. Populations of the white-bellied spinetail (Mazaria propinqua), lesser wagtail-tyrant (Stigmatura napensis) and bicolored conebill (Conirostrum bicolor) are currently isolated in the Rio Branco by the black-waters of the lower Rio Negro, offering a unique opportunity to test the effect of river colour as a barrier to gene flow. We used ultraconserved elements (UCEs) to test alternative hypotheses of population history in a comparative phylogeographical approach by modelling genetic structure, demographic history and testing for shared divergence time among codistributed taxa. Our analyses revealed that (i) all three populations from the Rio Branco floodplains are genetically distinct from other populations along the Amazon River floodplains; (ii) these divergences are the result of at least two distinct events, consistent with species habitat specialization; and (iii) the most likely model of population evolution includes lower population connectivity during the Late Pleistocene transition (~250,000 years ago), with gene flow being completely disrupted after the Last Glacial Maximum (~21,000 years ago). Our findings highlight how landscape evolution modulates population connectivity in habitat specialist species and how organisms can have different responses to the same historical processes of environmental change, depending on their habitat affinity.}, } @article {pmid36261802, year = {2022}, author = {Iša, P and Taboada, B and García-López, R and Boukadida, C and Ramírez-González, JE and Vázquez-Pérez, JA and Hernández-Terán, A and Romero-Espinoza, JÁ and Muñoz-Medina, JE and Grajales-Muñiz, C and Rincón-Rubio, A and Matías-Florentino, M and Sanchez-Flores, A and Mendieta-Condado, E and Barrera-Badillo, G and López, S and Hernández-Rivas, L and López-Martínez, I and Ávila-Ríos, S and Arias, CF}, title = {Metagenomic analysis reveals differences in the co-occurrence and abundance of viral species in SARS-CoV-2 patients with different severity of disease.}, journal = {BMC infectious diseases}, volume = {22}, number = {1}, pages = {792}, pmid = {36261802}, issn = {1471-2334}, mesh = {Humans ; SARS-CoV-2/genetics ; *COVID-19 ; *Coinfection/epidemiology ; *Viruses/genetics ; DNA, Circular ; Severity of Illness Index ; }, abstract = {BACKGROUND: SARS-CoV-2 infections have a wide spectrum of clinical manifestations whose causes are not completely understood. Some human conditions predispose to severe outcome, like old age or the presence of comorbidities, but many other facets, including coinfections with other viruses, remain poorly characterized.

METHODS: In this study, the eukaryotic fraction of the respiratory virome of 120 COVID-19 patients was characterized through whole metagenomic sequencing.

RESULTS: Genetic material from respiratory viruses was detected in 25% of all samples, whereas human viruses other than SARS-CoV-2 were found in 80% of them. Samples from hospitalized and deceased patients presented a higher prevalence of different viruses when compared to ambulatory individuals. Small circular DNA viruses from the Anneloviridae (Torque teno midi virus 8, TTV-like mini virus 19 and 26) and Cycloviridae families (Human associated cyclovirus 10), Human betaherpesvirus 6, were found to be significantly more abundant in samples from deceased and hospitalized patients compared to samples from ambulatory individuals. Similarly, Rotavirus A, Measles morbillivirus and Alphapapilomavirus 10 were significantly more prevalent in deceased patients compared to hospitalized and ambulatory individuals.

CONCLUSIONS: Results show the suitability of using metagenomics to characterize a broader peripheric virological landscape of the eukaryotic virome in SARS-CoV-2 infected patients with distinct disease outcomes. Identified prevalent viruses in hospitalized and deceased patients may prove important for the targeted exploration of coinfections that may impact prognosis.}, } @article {pmid36261779, year = {2022}, author = {Aldas-Vargas, A and Poursat, BAJ and Sutton, NB}, title = {Potential and limitations for monitoring of pesticide biodegradation at trace concentrations in water and soil.}, journal = {World journal of microbiology & biotechnology}, volume = {38}, number = {12}, pages = {240}, pmid = {36261779}, issn = {1573-0972}, mesh = {*Pesticides/metabolism ; Soil ; Water ; Biodegradation, Environmental ; *Groundwater/chemistry ; }, abstract = {Pesticides application on agricultural fields results in pesticides being released into the environment, reaching soil, surface water and groundwater. Pesticides fate and transformation in the environment depend on environmental conditions as well as physical, chemical and biological degradation processes. Monitoring pesticides biodegradation in the environment is challenging, considering that traditional indicators, such as changes in pesticides concentration or identification of pesticide metabolites, are not suitable for many pesticides in anaerobic environments. Furthermore, those indicators cannot distinguish between biotic and abiotic pesticide degradation processes. For that reason, the use of molecular tools is important to monitor pesticide biodegradation-related genes or microorganisms in the environment. The development of targeted molecular (e.g., qPCR) tools, although laborious, allowed biodegradation monitoring by targeting the presence and expression of known catabolic genes of popular pesticides. Explorative molecular tools (i.e., metagenomics & metatranscriptomics), while requiring extensive data analysis, proved to have potential for screening the biodegradation potential and activity of more than one compound at the time. The application of molecular tools developed in laboratory and validated under controlled environments, face challenges when applied in the field due to the heterogeneity in pesticides distribution as well as natural environmental differences. However, for monitoring pesticides biodegradation in the field, the use of molecular tools combined with metadata is an important tool for understanding fate and transformation of the different pesticides present in the environment.}, } @article {pmid36261508, year = {2023}, author = {Lin, L and Lai, Z and Yang, H and Zhang, J and Qi, W and Xie, F and Mao, S}, title = {Genome-centric investigation of bile acid metabolizing microbiota of dairy cows and associated diet-induced functional implications.}, journal = {The ISME journal}, volume = {17}, number = {1}, pages = {172-184}, pmid = {36261508}, issn = {1751-7370}, mesh = {Animals ; Female ; Cattle ; *Bile Acids and Salts ; *Microbiota ; Metagenome ; Intestines/microbiology ; Diet ; }, abstract = {Although the importance of bile acid (BA)-related microbial strains and enzymes is increasingly recognized for monogastric animals, a lack of knowledge about BA metabolism in dairy cows limits functional applications aimed at the targeted modulation of microbe-host interactions for animal production and health. In the present study, 108 content samples from six intestinal regions of dairy cows were used for shotgun metagenomic sequencing. Overall, 372 high-quality metagenome-assembled genomes (MAGs) were involved in BA deconjugation, oxidation, and dehydroxylation pathways. Furthermore, the BA-metabolizing microbiome predominately occurred in the large intestine, resulting in the accumulation of secondary unconjugated BAs. Comparative genomic analysis revealed that the bile salt hydrolase (BSH)-carrying microbial populations managed with the selective environment of the dairy cow intestine by adopting numerous host mucin glycan-degrading abilities. A sequence similarity network analysis classified 439 BSH homologs into 12 clusters and identified different clusters with diverse evolution, taxonomy, signal peptides, and ecological niches. Our omics data further revealed that the strains of Firmicutes bacterium CAG-110 processed the increased abundance of BSHs from Cluster 1, coinciding with the changes in the colon cholic acid concentration after grain introduction, and were intricately related to intestinal inflammation. This study is the first to use a genome-centric approach and whole intestine-targeted metabolomics to reveal microbial BA metabolism and its diet-induced functional implications in dairy cows. These findings provide insight into the manipulation of intestinal microorganisms for improving host health.}, } @article {pmid36261472, year = {2022}, author = {Lam, TJ and Ye, Y}, title = {Meta-analysis of microbiome association networks reveal patterns of dysbiosis in diseased microbiomes.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {17482}, pmid = {36261472}, issn = {2045-2322}, support = {R01 AI143254/AI/NIAID NIH HHS/United States ; R21 CA143254/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Dysbiosis/microbiology ; *Microbiota/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Microbial Interactions ; }, abstract = {The human gut microbiome is composed of a diverse and dynamic population of microbial species which play key roles in modulating host health and physiology. While individual microbial species have been found to be associated with certain disease states, increasing evidence suggests that higher-order microbial interactions may have an equal or greater contribution to host fitness. To better understand microbial community dynamics, we utilize networks to study interactions through a meta-analysis of microbial association networks between healthy and disease gut microbiomes. Taking advantage of the large number of metagenomes derived from healthy individuals and patients with various diseases, together with recent advances in network inference that can deal with sparse compositional data, we inferred microbial association networks based on co-occurrence of gut microbial species and made the networks publicly available as a resource (GitHub repository named GutNet). Through our meta-analysis of inferred networks, we were able to identify network-associated features that help stratify between healthy and disease states such as the differentiation of various bacterial phyla and enrichment of Proteobacteria interactions in diseased networks. Additionally, our findings show that the contributions of taxa in microbial associations are disproportionate to their abundances and that rarer taxa of microbial species play an integral part in shaping dynamics of microbial community interactions. Network-based meta-analysis revealed valuable insights into microbial community dynamics between healthy and disease phenotypes. We anticipate that the healthy and diseased microbiome association networks we inferred will become an important resource for human-related microbiome research.}, } @article {pmid36259934, year = {2022}, author = {Jarrige, D and Haridas, S and Bleykasten-Grosshans, C and Joly, M and Nadalig, T and Sancelme, M and Vuilleumier, S and Grigoriev, IV and Amato, P and Bringel, F}, title = {High-quality genome of the basidiomycete yeast Dioszegia hungarica PDD-24b-2 isolated from cloud water.}, journal = {G3 (Bethesda, Md.)}, volume = {12}, number = {12}, pages = {}, pmid = {36259934}, issn = {2160-1836}, mesh = {*Saccharomyces cerevisiae/genetics ; Water ; *Basidiomycota/genetics ; Sequence Analysis, DNA ; }, abstract = {The genome of the basidiomycete yeast Dioszegia hungarica strain PDD-24b-2 isolated from cloud water at the summit of puy de Dôme (France) was sequenced using a hybrid PacBio and Illumina sequencing strategy. The obtained assembled genome of 20.98 Mb and a GC content of 57% is structured in 16 large-scale contigs ranging from 90 kb to 5.56 Mb, and another 27.2 kb contig representing the complete circular mitochondrial genome. In total, 8,234 proteins were predicted from the genome sequence. The mitochondrial genome shows 16.2% cgu codon usage for arginine but has no canonical cognate tRNA to translate this codon. Detected transposable element (TE)-related sequences account for about 0.63% of the assembled genome. A dataset of 2,068 hand-picked public environmental metagenomes, representing over 20 Tbp of raw reads, was probed for D. hungarica related ITS sequences, and revealed worldwide distribution of this species, particularly in aerial habitats. Growth experiments suggested a psychrophilic phenotype and the ability to disperse by producing ballistospores. The high-quality assembled genome obtained for this D. hungarica strain will help investigate the behavior and ecological functions of this species in the environment.}, } @article {pmid36259734, year = {2022}, author = {Zhao, D and Zhang, S and Kumar, S and Zhou, H and Xue, Q and Sun, W and Zhou, J and Xiang, H}, title = {Comparative Genomic Insights into the Evolution of Halobacteria-Associated "Candidatus Nanohaloarchaeota".}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0066922}, pmid = {36259734}, issn = {2379-5077}, mesh = {*Euryarchaeota ; Phylogeny ; Halobacterium ; Archaea ; Genomics ; *Microbiota ; }, abstract = {Members of the phylum "Candidatus Nanohaloarchaeota," a representative lineage within the DPANN superphylum, are characterized by their nanosized cells and symbiotic lifestyle with Halobacteria. However, the development of the symbiosis remains unclear. Here, we propose two novel families, "Candidatus Nanoanaerosalinaceae" and "Candidatus Nanohalalkaliarchaeaceae" in "Ca. Nanohaloarchaeota," represented by five dereplicated metagenome-assembled genomes obtained from hypersaline sediments or related enrichment cultures of soda-saline lakes. Phylogenetic analyses reveal that the two novel families are placed at the root of the family "Candidatus Nanosalinaceae," including the cultivated taxa. The two novel families prefer hypersaline sediments, and the acid shift of predicted proteomes indicates a "salt-in" strategy for hypersaline adaptation. They contain a lower proportion of putative horizontal gene transfers from Halobacteria than "Ca. Nanosalinaceae," suggesting a weaker association with Halobacteria. Functional prediction and historical events reconstruction disclose that they exhibit divergent potentials in carbohydrate and organic acid metabolism and environmental responses. Globally, comparative genomic analyses based on the new families enrich the taxonomic and functional diversity of "Ca. Nanohaloarchaeota" and provide insights into the evolutionary process of "Ca. Nanohaloarchaeota" and their symbiotic relationship with Halobacteria. IMPORTANCE The DPANN superphylum is a group of archaea widely distributed in various habitats. They generally have small cells and have a symbiotic lifestyle with other archaea. The archaeal symbiotic interaction is vital to understanding microbial communities. However, the formation and evolution of the symbiosis between the DPANN lineages and other diverse archaea remain unclear. Based on phylogeny, habitat distribution, hypersaline adaptation, host prediction, functional potentials, and historical events of "Ca. Nanohaloarchaeota," a representative phylum within the DPANN superphylum, we report two novel families representing intermediate stages, and we infer the evolutionary process of "Ca. Nanohaloarchaeota" and their Halobacteria-associated symbiosis. Altogether, this research helps in understanding the evolution of symbiosis in "Ca. Nanohaloarchaeota" and provides a model for the evolution of other DPANN lineages.}, } @article {pmid36259361, year = {2022}, author = {Cheng, H and Sun, Y and Yang, Q and Deng, M and Yu, Z and Zhu, G and Qu, J and Liu, L and Yang, L and Xia, Y}, title = {A rapid bacterial pathogen and antimicrobial resistance diagnosis workflow using Oxford nanopore adaptive sequencing method.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {6}, pages = {}, doi = {10.1093/bib/bbac453}, pmid = {36259361}, issn = {1477-4054}, support = {2021YFA1202500//National Key Research and Development Program of China/ ; JCYJ20180302144721183//Science, Technology and Innovation Commission of Shenzhen Municipality of Basic Research Funds/ ; 2020B1515020003//Guangdong Natural Science Foundation for Distinguished Young Scholar/ ; ZDSYS20200811//Shenzhen Key Laboratory of Gene Regulation and Systems Biology, Southern University of Science and Technology/ ; KQTD20 200909113758004//Shenzhen Science and Technology Program/ ; 42007216//National Natural Science Foundation of China/ ; }, mesh = {Humans ; *Anti-Bacterial Agents ; *Nanopores ; Workflow ; Drug Resistance, Bacterial/genetics ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; Bacteria/genetics ; DNA ; }, abstract = {Metagenomic sequencing analysis (mNGS) has been implemented as an alternative approach for pathogen diagnosis in recent years, which is independent of cultivation and is able to identify all potential antibiotic resistance genes (ARGs). However, current mNGS methods have to deal with low amounts of prokaryotic deoxyribonucleic acid (DNA) and high amounts of host DNA in clinical samples, which significantly decrease the overall microbial detection resolution. The recently released nanopore adaptive sampling (NAS) technology facilitates immediate mapping of individual nucleotides to a given reference as each molecule is sequenced. User-defined thresholds allow for the retention or rejection of specific molecules, informed by the real-time reference mapping results, as they are physically passing through a given sequencing nanopore. We developed a metagenomics workflow for ultra-sensitive diagnosis of bacterial pathogens and ARGs from clinical samples, which is based on the efficient selective 'human host depletion' NAS sequencing, real-time species identification and species-specific resistance gene prediction. Our method increased the microbial sequence yield at least 8-fold in all 21 sequenced clinical Bronchoalveolar Lavage Fluid (BALF) samples (4.5 h from sample to result) and accurately detected the ARGs at species level. The species-level positive percent agreement between metagenomic sequencing and laboratory culturing was 100% (16/16) and negative percent agreement was 100% (5/5) in our approach. Further work is required for a more robust validation of our approach with large sample size to allow its application to other infection types.}, } @article {pmid36259208, year = {2022}, author = {Lemieux, A and Colby, GA and Poulain, AJ and Aris-Brosou, S}, title = {Viral spillover risk increases with climate change in High Arctic lake sediments.}, journal = {Proceedings. Biological sciences}, volume = {289}, number = {1985}, pages = {20221073}, pmid = {36259208}, issn = {1471-2954}, mesh = {*Lakes ; Climate Change ; Phylogeny ; Arctic Regions ; *Viruses/genetics ; Soil ; }, abstract = {The host spectrum of viruses is quite diverse, as they can sustainedly infect a few species to several phyla. When confronted with a new host, a virus may even infect it and transmit sustainably in this new host, a process called 'viral spillover'. However, the risk of such events is difficult to quantify. As climate change is rapidly transforming environments, it is becoming critical to quantify the potential for spillovers. To address this issue, we resorted to a metagenomics approach and focused on two environments, soil and lake sediments from Lake Hazen, the largest High Arctic freshwater lake in the world. We used DNA and RNA sequencing to reconstruct the lake's virosphere in both its sediments and soils, as well as its range of eukaryotic hosts. We then estimated the spillover risk by measuring the congruence between the viral and the eukaryotic host phylogenetic trees, and show that spillover risk increases with runoff from glacier melt, a proxy for climate change. Should climate change also shift species range of potential viral vectors and reservoirs northwards, the High Arctic could become fertile ground for emerging pandemics.}, } @article {pmid36258280, year = {2023}, author = {Al-Emran, HM and Rahman, S and Hasan, MS and Ul Alam, R and Islam, OK and Anwar, A and Jahid, MIK and Hossain, A}, title = {Microbiome analysis revealing microbial interactions and secondary bacterial infections in COVID-19 patients comorbidly affected by Type 2 diabetes.}, journal = {Journal of medical virology}, volume = {95}, number = {1}, pages = {e28234}, pmid = {36258280}, issn = {1096-9071}, mesh = {Humans ; Aged ; *COVID-19/complications/epidemiology/microbiology ; SARS-CoV-2 ; *Diabetes Mellitus, Type 2/complications ; *Coinfection/complications ; *Microbiota ; Bacteria/genetics ; *Bacterial Infections/epidemiology/complications ; Microbial Interactions ; }, abstract = {The mortality of coronavirus disease 2019 (COVID-19) disease is very high among the elderly or individuals having comorbidities such as obesity, cardiovascular diseases, lung infections, hypertension, and/or diabetes. Our study characterizes the metagenomic features in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2)-infected patients with or without type 2 diabetes, to identify the microbial interactions associated with its fatal consequences.This study compared the baseline nasopharyngeal microbiome of SARS-CoV-2-infected diabetic and nondiabetic patients with controls adjusted for age and gender. The metagenomics based on next-generation sequencing was performed using Ion GeneStudio S5 Series and the data were analyzed by the Vegan-package in R. All three groups possessed significant bacterial diversity and dissimilarity indexes (p < 0.05). Spearman's correlation coefficient network analysis illustrated 183 significant positive correlations and 13 negative correlations of pathogenic bacteria (r = 0.6-1.0, p < 0.05), and 109 positive correlations between normal flora and probiotic bacteria (r > 0.6, p < 0.05). The SARS-CoV-2 diabetic group exhibited a significant increase in pathogens and secondary infection-causing bacteria (p < 0.05) with a simultaneous decrease of normal flora (p < 0.05). The dysbiosis of the bacterial community might be linked with severe consequences of COVID-19-infected diabetic patients, although a few probiotic strains inhibited numerous pathogens in the same pathological niches. This study suggested that the promotion of normal flora and probiotics through dietary supplementation and excessive inflammation reduction by preventing secondary infections might lead to a better outcome for those comorbid patients.}, } @article {pmid36257972, year = {2023}, author = {Rogers, TJ and Buongiorno, J and Jessen, GL and Schrenk, MO and Fordyce, JA and de Moor, JM and Ramírez, CJ and Barry, PH and Yücel, M and Selci, M and Cordone, A and Giovannelli, D and Lloyd, KG}, title = {Chemolithoautotroph distributions across the subsurface of a convergent margin.}, journal = {The ISME journal}, volume = {17}, number = {1}, pages = {140-150}, pmid = {36257972}, issn = {1751-7370}, mesh = {*Geologic Sediments/chemistry ; Phylogeny ; Metagenomics/methods ; Bacteria/genetics/metabolism ; *Microbiota ; Carbon/metabolism ; Sulfur/metabolism ; }, abstract = {Subducting oceanic crusts release fluids rich in biologically relevant compounds into the overriding plate, fueling subsurface chemolithoautotrophic ecosystems. To understand the impact of subsurface geochemistry on microbial communities, we collected fluid and sediments from 14 natural springs across a ~200 km transect across the Costa Rican convergent margin and performed shotgun metagenomics. The resulting 404 metagenome-assembled genomes (MAGs) cluster into geologically distinct regions based on MAG abundance patterns: outer forearc-only (25% of total relative abundance), forearc/arc-only (38% of total relative abundance), and delocalized (37% of total relative abundance) clusters. In the outer forearc, Thermodesulfovibrionia, Candidatus Bipolaricaulia, and Firmicutes have hydrogenotrophic sulfate reduction and Wood-Ljungdahl (WL) carbon fixation pathways. In the forearc/arc, Anaerolineae, Ca. Bipolaricaulia, and Thermodesulfovibrionia have sulfur oxidation, nitrogen cycling, microaerophilic respiration, and WL, while Aquificae have aerobic sulfur oxidation and reverse tricarboxylic acid carbon fixation pathway. Transformation-based canonical correspondence analysis shows that MAG distribution corresponds to concentrations of aluminum, iron, nickel, dissolved inorganic carbon, and phosphate. While delocalized MAGs appear surface-derived, the subsurface chemolithoautotrophic, metabolic, and taxonomic landscape varies by the availability of minerals/metals and volcanically derived inorganic carbon. However, the WL pathway persists across all samples, suggesting that this versatile, energy-efficient carbon fixation pathway helps shape convergent margin subsurface ecosystems.}, } @article {pmid36257428, year = {2023}, author = {Semedo, M and Song, B}, title = {Sediment metagenomics reveals the impacts of poultry industry wastewater on antibiotic resistance and nitrogen cycling genes in tidal creek ecosystems.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 2}, pages = {159496}, doi = {10.1016/j.scitotenv.2022.159496}, pmid = {36257428}, issn = {1879-1026}, mesh = {Animals ; *Wastewater/analysis ; Metagenomics ; Poultry ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; *Microbiota ; Anti-Bacterial Agents/pharmacology/analysis ; Nitrogen/analysis ; }, abstract = {The intensification of the poultry industry may lead to the increased spread of antibiotic resistance genes (ARGs) in the environment. However, the impacts of wastewater discharge from poultry processing plants on the sediment resistome are relatively unexplored. Furthermore, its relationships with important biogeochemical pathways, such as the N cycle, are virtually unknown. The overall objective of this study was to examine the abundance and diversity of antibiotic resistance and N cycling genes in sediment microbial communities impacted by poultry industry wastewater. We performed a metagenomic investigation of sediments in an impacted and a reference tidal creek. We also quantified the abundance of the clinical class 1 integron-integrase gene (intI1) through qPCR as a secondary marker of anthropogenic contamination. Abundance and diversity of ARGs were substantially higher in the impacted tidal creek, especially near the wastewater discharge. Abundances of ARGs conferring resistance to macrolides, tetracyclines, and streptogramins were also higher in the impacted creek than the reference creek. From the N cycling genes detected in the metagenomes, nrfA, the genetic marker for dissimilatory nitrate reduction to ammonia (DNRA), had the strongest positive relationship with the total abundance of ARGs, which may indicate an increased potential of eutrophication in ARG-impacted ecosystems due to nitrogen retention. This study demonstrates that wastewater discharge from a poultry processing plant can increase the spread of ARGs, which may result in negative impacts on ecosystem health.}, } @article {pmid36257123, year = {2022}, author = {Guevarra, RB and Hwang, J and Lee, H and Kim, HJ and Lee, Y and Danko, D and Ryon, KA and Young, BG and Mason, CE and Jang, S}, title = {Metagenomic characterization of bacterial community and antibiotic resistance genes found in the mass transit system in Seoul, South Korea.}, journal = {Ecotoxicology and environmental safety}, volume = {246}, number = {}, pages = {114176}, doi = {10.1016/j.ecoenv.2022.114176}, pmid = {36257123}, issn = {1090-2414}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Seoul ; *Metagenomics ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Genes, Bacterial ; }, abstract = {Mass transit systems, including subways and buses, are useful environments for studying the urban microbiome, as the vast majority of populations in urban areas use public transportation. Microbial communities in urban environments include both human- and environment-associated bacteria that play roles in health and pathogen transmission. In this study, we used shotgun metagenomic sequencing to profile microbial communities sampled from various surfaces found in subway stations and bus stops within the Seoul mass transit system. The metagenomic approach and network analysis were used to investigate broad-spectrum antibiotic resistance genes (ARGs) and their co-occurrence patterns. We uncovered 598 bacterial species in 76 samples collected from various surfaces within the Seoul mass transit system. All samples were dominated by the potential human pathogen Salmonella enterica (40 %) and the human skin bacterium Cutibacterium acnes (19 %). Significantly abundant biomarkers detected in subway station samples were associated with bacteria typically found in the human oral cavity and respiratory tract, whereas biomarkers detected in bus stop samples were associated with bacteria commonly found in soil, water, and plants. Temperature and location had significant effects on microbial community structure and diversity. In total, 41 unique ARG subtypes were identified, associated with single-drug or multidrug resistance to clinically important and extensively used antibiotics, including aminoglycosides, carbapenem, glycopeptide, and sulfonamides. We revealed that Seoul subway stations and bus stops possess unique microbiomes containing potential human pathogens and ARGs. These findings provide insights for refining location-specific responses to reduce exposure to potentially causative agents of infectious diseases, improving public health.}, } @article {pmid36256818, year = {2022}, author = {Dexter, GN and Navas, LE and Grigg, JC and Bajwa, H and Levy-Booth, DJ and Liu, J and Louie, NA and Nasseri, SA and Jang, SK and Renneckar, S and Eltis, LD and Mohn, WW}, title = {Bacterial catabolism of acetovanillone, a lignin-derived compound.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {43}, pages = {e2213450119}, pmid = {36256818}, issn = {1091-6490}, mesh = {*Lignin/metabolism ; *Biotin ; Acetophenones ; Adenosine Triphosphate ; }, abstract = {Bacterial catabolic pathways have considerable potential as industrial biocatalysts for the valorization of lignin, a major component of plant-derived biomass. Here, we describe a pathway responsible for the catabolism of acetovanillone, a major component of several industrial lignin streams. Rhodococcus rhodochrous GD02 was previously isolated for growth on acetovanillone. A high-quality genome sequence of GD02 was generated. Transcriptomic analyses revealed a cluster of eight genes up-regulated during growth on acetovanillone and 4-hydroxyacetophenone, as well as a two-gene cluster up-regulated during growth on acetophenone. Bioinformatic analyses predicted that the hydroxyphenylethanone (Hpe) pathway proceeds via phosphorylation and carboxylation, before β-elimination yields vanillate from acetovanillone or 4-hydroxybenzoate from 4-hydroxyacetophenone. Consistent with this prediction, the kinase, HpeHI, phosphorylated acetovanillone and 4-hydroxyacetophenone. Furthermore, HpeCBA, a biotin-dependent enzyme, catalyzed the ATP-dependent carboxylation of 4-phospho-acetovanillone but not acetovanillone. The carboxylase's specificity for 4-phospho-acetophenone (kcat/KM = 34 ± 2 mM[-1] s[-1]) was approximately an order of magnitude higher than for 4-phospho-acetovanillone. HpeD catalyzed the efficient dephosphorylation of the carboxylated products. GD02 grew on a preparation of pine lignin produced by oxidative catalytic fractionation, depleting all of the acetovanillone, vanillin, and vanillate. Genomic and metagenomic searches indicated that the Hpe pathway occurs in a relatively small number of bacteria. This study facilitates the design of bacterial strains for biocatalytic applications by identifying a pathway for the degradation of acetovanillone.}, } @article {pmid36255324, year = {2022}, author = {Miranda-Carrazco, A and Navarro-Noya, YE and Govaerts, B and Verhulst, N and Dendooven, L}, title = {Nitrogen Fertilizer Application Alters the Root Endophyte Bacterial Microbiome in Maize Plants, but Not in the Stem or Rhizosphere Soil.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0178522}, pmid = {36255324}, issn = {2165-0497}, mesh = {*Soil/chemistry ; Endophytes ; Nitrogen ; Zea mays/microbiology ; Fertilizers ; Rhizosphere ; Bacteria/genetics ; *Microbiota ; Crops, Agricultural ; Soil Microbiology ; }, abstract = {Plant-associated microorganisms that affect plant development, their composition, and their functionality are determined by the host, soil conditions, and agricultural practices. How agricultural practices affect the rhizosphere microbiome has been well studied, but less is known about how they might affect plant endophytes. In this study, the metagenomic DNA from the rhizosphere and endophyte communities of root and stem of maize plants was extracted and sequenced with the "diversity arrays technology sequencing," while the bacterial community and functionality (organized by subsystems from general to specific functions) were investigated in crops cultivated with or without tillage and with or without N fertilizer application. Tillage had a small significant effect on the bacterial community in the rhizosphere, but N fertilizer had a highly significant effect on the roots, but not on the rhizosphere or stem. The relative abundance of many bacterial species was significantly different in the roots and stem of fertilized maize plants, but not in the unfertilized ones. The abundance of N cycle genes was affected by N fertilization application, most accentuated in the roots. How these changes in bacterial composition and N genes composition might affect plant development or crop yields has still to be unraveled. IMPORTANCE We investigated the bacterial community structure in the rhizosphere, root, and stem of maize plants cultivated under different agricultural techniques, i.e., with or without N fertilization, and with or without tillage. We found that the bacterial community was defined mostly by the plant compartment and less by agricultural techniques. In the roots, N fertilizer application affected the bacterial community structure, the microbiome functionality, and the abundance of genes involved in the N cycle, but the effect in the rhizosphere and stem was much smaller. Contrary, tillage did not affect the maize microbiome. This study enriches our knowledge about the plant-microbiome system and how N fertilization application affected it.}, } @article {pmid36254868, year = {2022}, author = {Karnachuk, OV and Lukina, AP and Kadnikov, VV and Sherbakova, VA and Beletsky, AV and Mardanov, AV and Ravin, NV}, title = {Targeted isolation based on metagenome-assembled genomes reveals a phylogenetically distinct group of thermophilic spirochetes from deep biosphere.}, journal = {Environmental microbiology}, volume = {24}, number = {10}, pages = {4964}, doi = {10.1111/1462-2920.16214}, pmid = {36254868}, issn = {1462-2920}, } @article {pmid36254507, year = {2022}, author = {Chang, SY and Santos, CAQ}, title = {Could cell-free DNA and host biomarkers assist in antimicrobial stewardship with organ transplant recipients?.}, journal = {Transplant infectious disease : an official journal of the Transplantation Society}, volume = {24}, number = {5}, pages = {e13971}, doi = {10.1111/tid.13971}, pmid = {36254507}, issn = {1399-3062}, mesh = {Anti-Bacterial Agents/therapeutic use ; *Anti-Infective Agents/therapeutic use ; *Antimicrobial Stewardship/methods ; Biomarkers ; *Cell-Free Nucleic Acids ; Humans ; *Organ Transplantation/adverse effects/methods ; Transplant Recipients ; }, abstract = {BACKGROUND: Antimicrobial stewardship in solid organ transplant (SOT) recipients is important to prevent antimicrobial-associated complications, but traditional stewardship principles are challenging to implement for SOT patients. Newer methodologies to optimize stewardship efforts are needed.

METHODS: PubMed was searched using the keywords "cell free DNA," "metagenomic sequencing," "host biomarker," "antimicrobial stewardship," and "SOT."

RESULTS: Metagenomic sequencing of cell free DNA has the potential to be a stewardship tool for SOT recipients. Various studies have shown its use for antimicrobial de-escalation and duration shortening. Host gene expression profiles can differentiate between infectious and noninfectious syndromes and may assist in stewardship efforts. However, information in immunocompromised hosts is conflicting.

CONCLUSION: Microbial cell free DNA sequencing and host gene expression profiling show promise as stewardship tools in SOT recipients. Future studies on antimicrobial stewardship in SOT recipients should focus on their clinical use and feasibility.}, } @article {pmid36253620, year = {2022}, author = {Qiao, S and Liu, C and Sun, L and Wang, T and Dai, H and Wang, K and Bao, L and Li, H and Wang, W and Liu, SJ and Liu, H}, title = {Gut Parabacteroides merdae protects against cardiovascular damage by enhancing branched-chain amino acid catabolism.}, journal = {Nature metabolism}, volume = {4}, number = {10}, pages = {1271-1286}, pmid = {36253620}, issn = {2522-5812}, mesh = {Humans ; Mice ; Animals ; Male ; *Cardiovascular Diseases ; Amino Acids, Branched-Chain/metabolism ; Bacteroides/metabolism ; Obesity/complications/metabolism ; Mice, Obese ; Mechanistic Target of Rapamycin Complex 1/metabolism ; *Atherosclerosis/prevention & control ; Apolipoproteins E ; }, abstract = {Obesity, dyslipidemia and gut dysbiosis are all linked to cardiovascular diseases. A Ganoderma meroterpene derivative (GMD) has been shown to alleviate obesity and hyperlipidemia through modulating the gut microbiota in obese mice. Here we show that GMD protects against obesity-associated atherosclerosis by increasing the abundance of Parabacteroides merdae in the gut and enhancing branched-chain amino acid (BCAA) catabolism. Administration of live P. merdae to high-fat-diet-fed ApoE-null male mice reduces atherosclerotic lesions and enhances intestinal BCAA degradation. The degradation of BCAAs is mediated by the porA gene expressed in P. merdae. Deletion of porA from P. merdae blunts its capacity to degrade BCAAs and leads to inefficacy in fighting against atherosclerosis. We further show that P. merdae inhibits the mTORC1 pathway in atherosclerotic plaques. In support of our preclinical findings, an in silico analysis of human gut metagenomic studies indicates that P. merdae and porA genes are depleted in the gut microbiomes of individuals with atherosclerosis. Our results provide mechanistic insights into the therapeutic potential of GMD through P. merdae in treating obesity-associated cardiovascular diseases.}, } @article {pmid36253480, year = {2022}, author = {Wu, M and Li, J and Leu, AO and Erler, DV and Stark, T and Tyson, GW and Yuan, Z and McIlroy, SJ and Guo, J}, title = {Anaerobic oxidation of propane coupled to nitrate reduction by a lineage within the class Symbiobacteriia.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6115}, pmid = {36253480}, issn = {2041-1723}, mesh = {Alkanes/metabolism ; *Ammonium Compounds ; Anaerobiosis ; Butanes ; Carbon ; Carbon Dioxide ; Ecosystem ; Ethane/metabolism ; Fumarates ; Methane/metabolism ; *Nitrates/metabolism ; Oxidation-Reduction ; Propane/metabolism ; Sulfates/metabolism ; }, abstract = {Anaerobic microorganisms are thought to play a critical role in regulating the flux of short-chain gaseous alkanes (SCGAs; including ethane, propane and butane) from terrestrial and aquatic ecosystems to the atmosphere. Sulfate has been confirmed to act as electron acceptor supporting microbial anaerobic oxidation of SCGAs, yet several other energetically more favourable acceptors co-exist with these gases in anaerobic environments. Here, we show that a bioreactor seeded with biomass from a wastewater treatment facility can perform anaerobic propane oxidation coupled to nitrate reduction to dinitrogen gas and ammonium. The bioreactor was operated for more than 1000 days, and we used [13]C- and [15]N-labelling experiments, metagenomic, metatranscriptomic, metaproteomic and metabolite analyses to characterize the microbial community and the metabolic processes. The data collectively suggest that a species representing a novel order within the bacterial class Symbiobacteriia is responsible for the observed nitrate-dependent propane oxidation. The closed genome of this organism, which we designate as 'Candidatus Alkanivorans nitratireducens', encodes pathways for oxidation of propane to CO2 via fumarate addition, and for nitrate reduction, with all the key genes expressed during nitrate-dependent propane oxidation. Our results suggest that nitrate is a relevant electron sink for SCGA oxidation in anaerobic environments, constituting a new microbially-mediated link between the carbon and nitrogen cycles.}, } @article {pmid36252903, year = {2023}, author = {Sun, Y and Guo, J and Wei, F and Chen, X and Li, M and Li, C and Xia, S and Zhang, G and You, W and Cong, X and Yu, T and Wang, S}, title = {Microbial functional communities and the antibiotic resistome profile in a high-selenium ecosystem.}, journal = {Chemosphere}, volume = {311}, number = {Pt 1}, pages = {136858}, doi = {10.1016/j.chemosphere.2022.136858}, pmid = {36252903}, issn = {1879-1298}, mesh = {*Selenium/pharmacology/analysis ; Anti-Bacterial Agents/pharmacology ; Ecosystem ; *Microbiota ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Soil ; Soil Microbiology ; Genes, Bacterial ; }, abstract = {Enshi City, in the Hubei Province of China, is known as the world capital of selenium with the most abundant selenium resource. An important selenium hyperaccumulator plant, Cardamine violifolia, was found to naturally grow in this high-selenium ecosystem. However, relatively little is known about the impact of the selenium levels on microbial community and functional shifts in C. violifolia rhizosphere. Here, we tested the hypothesis that underground microbial diversity and function vary along a selenium gradient, including antibiotic resistance genes (ARGs). Comprehensive metagenomic analyses, such as taxonomic investigation, functional detection, and ARG annotation, showed that selenium, mercury, cadmium, lead, arsenic, and available phosphorus and potassium were correlated with microbial diversity and function. Thaumarchaeota was exclusively dominant in the highest selenium concentration of mine outcrop, and Rhodanobacter and Nitrospira were predominant in the high-selenium ecosystem. The plant C. violifolia enriched a high concentration of selenium in the rhizosphere compared to those in the bulk soil, and it recruited Variovorax and Polaromonas in its rhizosphere. Microbial abundance showed a trend of increasing first and then decreasing from low to high selenium concentrations. Annotation of ARGs showed that the multidrug resistance genes adeF, mtrA, and poxtA, the aminoglycoside resistance gene rpsL, and the sulfonamide resistant gene sul2 were enriched in the high-selenium system. It was discovered that putative antibiotic resistant bacteria displayed obvious differences in the farmland and the soils with various selenium concentrations, indicating that a high-selenium ecosystem harbors the specific microbes with a higher capacity to enrich or resist selenium, toxic metals, or antibiotics. Taken together, these results reveal the effects of selenium concentration and the selenium hyperaccumulator plant C. violifolia on shaping the microbial functional community and ARGs. Metalloid selenium-inducible antibiotic resistance is worth paying attention to in future.}, } @article {pmid36252326, year = {2022}, author = {de Diego, GA and Penas-Steinhardt, A and Ferro, JP and Palacio, MJ and Ossana, NA and Eissa, BL and Belforte, F}, title = {Impact of exposure to arsenic on the bacterial microbiota associated with river biofilms in the Pampas region.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {252}, number = {}, pages = {106319}, doi = {10.1016/j.aquatox.2022.106319}, pmid = {36252326}, issn = {1879-1514}, mesh = {Humans ; *Arsenic/toxicity ; RNA, Ribosomal, 16S/genetics ; *Water Pollutants, Chemical/toxicity ; *Microbiota ; Bacteria/genetics ; Biofilms ; Water ; }, abstract = {Freshwater contamination by arsenic (As) is a worldwide problem. It may be found in Pampean streams of Argentina at concentrations higher than those recommended by international organizations and stipulated by national regulations. Exposure to high As concentrations causes serious consequences to both human health and the environment. The general objective of this work was to evaluate the effect of As on the biofilm microbiota structure from Naveira stream, Luján, Province of Buenos Aires (Coordinates: 34º34'02″ S 59º03'51″ W). The biofilm collected was cultivated in glass aquaria at different As III concentrations (0, 0.2 and 20 mg / L), inside incubation chambers under controlled conditions (16 h light: 8 h dark and 24 ± 1 °C) and constant aeration for 31 d, with partial water renewal every 9 d. We amplified the hypervariable regions V3 and V4 of the bacterial 16S rRNA gene from biofilm bacterial community samples to determine the diversity and abundance of the different taxa. The taxonomic composition of each sample, the alpha diversity of each treatment and the main metabolic pathways were analyzed. Principal Component Analysis of the present phyla and a Linear Discriminant Analysis of the metabolic pathways was also performed. Significant changes were observed in relation to the taxonomic composition of the bacterial community after exposure to the metalloid. However, this effect was not observed at the low concentration used (0.2 mg / L), which is the one that corresponds to ecologically relevant levels. The significantly affected phyla were Verrucomicrobiota, Acidobacteriota, Patescibacteria, Hydrogenedentes and WPS-2. The relative abundances of the Verrucomicrobiota, WPS-2 and Patescibacteria groups were notably decreased in the treatment with high As, while the Acidobacteria group was increased in both treatments with As. The stream samples showed greater bacterial diversity than those grown in the laboratory without As. Finally, it was possible to characterize the metabolic profile of the biofilm developed under natural conditions in the leaves of the aquatic plant Elodea canadensis in the Naveira stream. In addition, results showed that biosynthesis-related pathways were more abundant at the high As concentration treatment (20 mg / L).}, } @article {pmid36251729, year = {2022}, author = {Garcia Bardales, PF and Schiaffino, F and Huynh, S and Paredes Olortegui, M and Peñataro Yori, P and Pinedo Vasquez, T and Manzanares Villanueva, K and Curico Huansi, GE and Shapiama Lopez, WV and Cooper, KK and Parker, CT and Kosek, MN}, title = {"Candidatus Campylobacter infans" detection is not associated with diarrhea in children under the age of 2 in Peru.}, journal = {PLoS neglected tropical diseases}, volume = {16}, number = {10}, pages = {e0010869}, pmid = {36251729}, issn = {1935-2735}, support = {D43 TW010913/TW/FIC NIH HHS/United States ; R01 AI158576/AI/NIAID NIH HHS/United States ; R21 AI163801/AI/NIAID NIH HHS/United States ; }, mesh = {Child ; Humans ; *Campylobacter Infections/diagnosis/epidemiology ; RNA, Ribosomal, 16S/genetics ; Peru/epidemiology ; *Campylobacter/genetics ; Diarrhea/epidemiology/diagnosis ; Feces ; }, abstract = {A working hypothesis is that less common species of Campylobacter (other than C. jejuni and C. coli) play a role in enteric disease among children in low resource settings and explain the gap between the detection of Campylobacter using culture and culture independent methods. "Candidatus Campylobacter infans" (C. infans), was recently detected in stool samples from children and hypothesized to play a role in Campylobacter epidemiology in low- and middle-income countries (LMIC). This study determined the prevalence of C. infans in symptomatic and asymptomatic stool samples from children living in Iquitos, Peru. Stool samples from 215 children with diarrhea and 50 stool samples from children without diarrhea under the age of two were evaluated using a multiplex qPCR assay to detect Campylobacter spp. (16S rRNA), Campylobacter jejuni / Campylobacter coli (cadF gene), C. infans (lpxA), and Shigella spp. (ipaH). C. infans was detected in 7.9% (17/215) symptomatic samples and 4.0% (2/50) asymptomatic samples. The association between diarrhea and the presence of these targets was evaluated using univariate logistic regressions. C. infans was not associated with diarrhea. Fifty-one percent (75/146) of Campylobacter positive fecal samples were negative for C. jejuni, C. coli, and C. infans via qPCR. Shotgun metagenomics confirmed the presence of C. infans among 13 out of 14 positive C. infans positive stool samples. C infans explained only 20.7% of the diagnostic gap in stools from children with diarrhea and 16.7% of the gap in children without diarrhea. We posit that poor cadF primer performance better explains the observed gap than the prevalence of atypical non-C. jejuni/coli species.}, } @article {pmid36251393, year = {2022}, author = {Giri, S and Uehara, O and Takada, A and Paudel, D and Morikawa, T and Arakawa, T and Nagasawa, T and Abiko, Y and Furuichi, Y}, title = {The effect of Porphyromonas gingivalis on the gut microbiome of mice in relation to aging.}, journal = {Journal of periodontal research}, volume = {57}, number = {6}, pages = {1256-1266}, doi = {10.1111/jre.13062}, pmid = {36251393}, issn = {1600-0765}, mesh = {Mice ; Animals ; *Porphyromonas gingivalis ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S ; Tumor Necrosis Factor-alpha ; Mice, Inbred C57BL ; Aging ; RNA, Messenger ; }, abstract = {BACKGROUND AND OBJECTIVE: The translocation of oral bacteria, including Porphyromonas gingivalis, to the gut has been shown to alter gut microbiome. However, the effect of P. gingivalis on gut microbiome in relation to aging has not been demonstrated. We hypothesize that P. gingivalis has more detrimental effect on gut environment with increased age. The objective of this study is to investigate the effect of P. gingivalis on gut environment using aged mice.

MATERIALS AND METHODS: C57BL/6J mice aged 4 weeks (young) or 76 weeks (old) were divided into four groups: control-young, control-old, P. gingivalis-administered young, and P. gingivalis-administered old. P. gingivalis was orally administered thrice weekly for 5 weeks. At 30 days after the last P. gingivalis administration, 16S rRNA sequencing was performed to study the gut microbiome. The mRNA and protein expression of intestinal junctional barrier molecules and the levels of the inflammatory cytokines IL-1β and TNF-α in the serum were evaluated.

RESULTS: Significant differences in the gut microbiomes between the groups, in terms of taxonomic abundance, bacterial diversity, and predicted metagenome function, were observed. A significant reduction in the alpha diversity and in the abundance of beneficial bacteria, such as Akkermansia and Clostridiaceae, in the P. gingivalis-administered old mice was observed. The mRNA and protein levels of Claudin-1 and Claudin-2 in the intestine were significantly elevated, while E-cadherin was significantly downregulated in the P. gingivalis-administered old mice, as were the serum levels of IL-1β and TNF-α.

CONCLUSION: The effect of P. gingivalis on the gut environment is more pronounced in old mice than in young mice.}, } @article {pmid36251278, year = {2022}, author = {Ross, DE and Lipus, D and Gulliver, D}, title = {Predominance of Methanomicrobiales and diverse hydrocarbon-degrading taxa in the Appalachian coalbed biosphere revealed through metagenomics and genome-resolved metabolisms.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {5984-5997}, doi = {10.1111/1462-2920.16251}, pmid = {36251278}, issn = {1462-2920}, mesh = {*Methanomicrobiales/metabolism ; *Metagenomics ; Metagenome ; Hydrocarbons/metabolism ; Methane/metabolism ; Bacteria ; }, abstract = {Coalbed deposits are a unique subsurface environment and represent an underutilized resource for methane generation. Microbial communities extant in coalbed deposits are responsible for key subsurface biogeochemical cycling and could be utilized to enhance methane production in areas where existing gas wells have depleted methane stores, or in coalbeds that are unmined, or conversely be utilized for mitigation of methane release. Here we utilize metagenomics and metagenome-assembled genomes (MAGs) to identify extant microbial lineages and genome-resolved microbial metabolisms of coalbed produced water, which has not yet been explored in the Appalachian Basin (AppB). Our analyses resulted in the recovery of over 40 MAGs from 8 coalbed methane wells. The most commonly identified taxa among samples were hydrogenotrophic methanogens from the order Methanomicrobiales and these dominant MAGs were highly similar to one another. Conversely, low-abundance coalbed bacterial populations were taxonomically and functionally diverse, mostly belonging to a variety of Proteobacteria classes, and encoding various hydrocarbon solubilization and degradation pathways. The data presented herein provides novel insights into AppB coalbed microbial ecology, and our findings provide new perspectives on underrepresented Methanocalculus species and low-relative abundance bacterial assemblages in coalbed environments, and their potential roles in stimulation or mitigation of methane release.}, } @article {pmid36250063, year = {2022}, author = {Wan, J and Duan, L and Chen, Q and Wang, L and Bai, J and Hu, J and Lu, X and Zhang, T and Song, W and Yang, D and Shan, Y and Yan, Z}, title = {Corrigendum: Potential clinical impact of metagenomic next-generation sequencing of plasma for cervical spine injury with sepsis in ICU: A retrospective study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1022341}, doi = {10.3389/fcimb.2022.1022341}, pmid = {36250063}, issn = {2235-2988}, abstract = {[This corrects the article DOI: 10.3389/fcimb.2022.948602.].}, } @article {pmid36250060, year = {2022}, author = {Monshizadeh, M and Zomorodi, S and Mortensen, K and Ye, Y}, title = {Revealing bacteria-phage interactions in human microbiome through the CRISPR-Cas immune systems.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {933516}, pmid = {36250060}, issn = {2235-2988}, support = {R01 AI143254/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; CRISPR-Cas Systems ; Humans ; Immune System ; *Microbiota/genetics ; }, abstract = {The human gut microbiome is composed of a diverse consortium of microorganisms. Relatively little is known about the diversity of the bacteriophage population and their interactions with microbial organisms in the human microbiome. Due to the persistent rivalry between microbial organisms (hosts) and phages (invaders), genetic traces of phages are found in the hosts' CRISPR-Cas adaptive immune system. Mobile genetic elements (MGEs) found in bacteria include genetic material from phage and plasmids, often resultant from invasion events. We developed a computational pipeline (BacMGEnet), which can be used for inference and exploratory analysis of putative interactions between microbial organisms and MGEs (phages and plasmids) and their interaction network. Given a collection of genomes as the input, BacMGEnet utilizes computational tools we have previously developed to characterize CRISPR-Cas systems in the genomes, which are then used to identify putative invaders from publicly available collections of phage/prophage sequences. In addition, BacMGEnet uses a greedy algorithm to summarize identified putative interactions to produce a bacteria-MGE network in a standard network format. Inferred networks can be utilized to assist further examination of the putative interactions and for discovery of interaction patterns. Here we apply the BacMGEnet pipeline to a few collections of genomic/metagenomic datasets to demonstrate its utilities. BacMGEnet revealed a complex interaction network of the Phocaeicola vulgatus pangenome with its phage invaders, and the modularity analysis of the resulted network suggested differential activities of the different P. vulgatus' CRISPR-Cas systems (Type I-C and Type II-C) against some phages. Analysis of the phage-bacteria interaction network of human gut microbiome revealed a mixture of phages with a broad host range (resulting in large modules with many bacteria and phages), and phages with narrow host range. We also showed that BacMGEnet can be used to infer phages that invade bacteria and their interactions in wound microbiome. We anticipate that BacMGEnet will become an important tool for studying the interactions between bacteria and their invaders for microbiome research.}, } @article {pmid36250052, year = {2022}, author = {Chen, M and Lai, Z and Cheng, M and Liang, T and Lin, Z}, title = {Rare brain and pulmonary abscesses caused by oral pathogens started with acute gastroenteritis diagnosed by metagenome next-generation sequencing: A case report and literature review.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {949840}, pmid = {36250052}, issn = {2235-2988}, mesh = {Adult ; Anti-Bacterial Agents ; Brain/diagnostic imaging ; *Gastroenteritis ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Lung Abscess ; Male ; Metagenome ; Young Adult ; }, abstract = {Odontogenic brain and pulmonary abscesses are extremely rare infectious diseases. It is mainly caused by the upward or downward transmission of local infection or blood-borne spread. In recent years, with the wide application of some novel testing methods in clinical practice, the diagnosis of unexplained infections such as odontogenic abscesses in different organs has gradually become clear. We report a case of a 21-year-old male who was healthy and had not received any oral treatment before onset. He started with acute gastroenteritis-related symptoms, then developed meningitis-related symptoms seven days later with septic shock. No obvious abscess lesions were found on head computed tomography (CT) at admission, and the etiology was not clear by routine examination, which was very easy to misdiagnose as a serious infection caused by intestinal pathogens. But odontogenic pathogens were found both in his blood and cerebrospinal fluid through metagenomic next-generation sequencing (mNGS) analysis. Subsequently, rechecked imaging examination displayed multiple brain and pulmonary abscesses. Finally, it was diagnosed as an odontogenic brain and pulmonary abscess. After an extremely lengthy anti-infection course (13 weeks of intravenous antibiotics plus 2 weeks of oral antibiotics) and surgery, the patient was improved and discharged from the hospital. From this case, we could see that the development of new diagnostic technologies such as mNGS plays an important role in the early and confirmed diagnosis of diseases previously difficult to diagnose such as odontogenic polymicrobial infections and ultimately helps to improve the prognosis of these patients.}, } @article {pmid36250045, year = {2022}, author = {Lv, L and Ruan, G and Ping, Y and Cheng, Y and Tian, Y and Xiao, Z and Zhao, X and Chen, D and Wei, Y}, title = {Clinical study on sequential treatment of severe diarrhea irritable bowel syndrome with precision probiotic strains transplantation capsules, fecal microbiota transplantation capsules and live combined bacillus subtilis and enterococcus faecium capsules.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1025889}, pmid = {36250045}, issn = {2235-2988}, mesh = {Abdominal Pain ; Bacillus subtilis ; Diarrhea/therapy ; *Enterococcus faecium ; Fecal Microbiota Transplantation ; Feces ; Humans ; *Irritable Bowel Syndrome/therapy ; *Probiotics/therapeutic use ; Quality of Life ; Treatment Outcome ; }, abstract = {OBJECTIVE: To study the effect of precision probiotic strains transplantation capsules on diarrhea irritable bowel syndrome compared with fecal microbiota transplantation capsules and live combined bacillus subtilis and enterococcus faecium capsules.

METHODS: Two patients with severe irritable bowel syndrome were treated with precision probiotic strains transplantation capsules, fecal microbiota transplantation capsules and live combined bacillus subtilis and enterococcus faecium capsules in sequence. IBS-SSS, IBS-QoL, GSRS, stool frequency, stool character, degree of abdominal pain, GAD-7, and PHQ9 scores of patients at 0, 2, 4, 6, 8, 10, and 12 weeks of treatment were monitored and recorded, and stool samples were collected for metagenomics and metabolomics.

RESULTS: It was found that the IBS-SSS score of patient case 1 decreased by 175 points and that of patient case 2 decreased by 100 points after treatment of precision probiotic strains transplantation capsules. There was no significant decrease after fecal microbiota transplantation capsules and live combined bacillus subtilis and enterococcus faecium capsules were used. At the same time, compared with fecal microbiota transplantation and live combined bacillus subtilis and enterococcus faecium capsules, the IBS QoL, stool frequency, stool character, degree of abdominal pain and GAD-7 score of patient case 1 improved more significantly by the precision probiotic strains transplantation capsules. And the stool frequency and stool character score of patient case 2 decreased more significantly. Intestinal microbiota also improved more significantly after the precise capsule transplantation treatment. And we found Eubacterium_ Eligens showed the same change trend in the treatment of two patients, which may play a role in the treatment.

CONCLUSION: precision probiotic strains transplantation capsules is more beneficial to improve the intestinal microbiota of patients than microbiota transplantation capsule and live combined bacillus subtilis and enterococcus faecium capsules, so as to better alleviate clinical symptoms. This study provides a more perfect and convenient therapeutic drugs for the treatment of IBS.}, } @article {pmid36248884, year = {2022}, author = {Gill, T and Stauffer, P and Asquith, M and Laderas, T and Martin, TM and Davin, S and Schleisman, M and Ramirez, C and Ogle, K and Lindquist, I and Nguyen, J and Planck, SR and Shaut, C and Diamond, S and Rosenbaum, JT and Karstens, L}, title = {Axial spondyloarthritis patients have altered mucosal IgA response to oral and fecal microbiota.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {965634}, pmid = {36248884}, issn = {1664-3224}, support = {R01 EY029266/EY/NEI NIH HHS/United States ; P30 EY010572/EY/NEI NIH HHS/United States ; K01 DK116706/DK/NIDDK NIH HHS/United States ; T32 HL083808/HL/NHLBI NIH HHS/United States ; T15 LM007088/LM/NLM NIH HHS/United States ; }, mesh = {Amino Acids ; *Axial Spondyloarthritis ; Clostridiales/genetics ; Feces/chemistry ; *Gastrointestinal Microbiome/genetics ; Humans ; Immunoglobulin A/analysis ; Propionates ; RNA, Ribosomal, 16S/analysis/genetics ; }, abstract = {Axial spondyloarthritis (axSpA) is an inflammatory arthritis involving the spine and the sacroiliac joint with extra-articular manifestations in the eye, gut, and skin. The intestinal microbiota has been implicated as a central environmental component in the pathogenesis of various types of spondyloarthritis including axSpA. Additionally, alterations in the oral microbiota have been shown in various rheumatological conditions, such as rheumatoid arthritis (RA). Therefore, the aim of this study was to investigate whether axSpA patients have an altered immunoglobulin A (IgA) response in the gut and oral microbial communities. We performed 16S rRNA gene (16S) sequencing on IgA positive (IgA[+]) and IgA negative (IgA[-]) fractions (IgA-SEQ) from feces (n=17 axSpA; n=14 healthy) and saliva (n=14 axSpA; n=12 healthy), as well as on IgA-unsorted fecal and salivary samples. PICRUSt2 was used to predict microbial metabolic potential in axSpA patients and healthy controls (HCs). IgA-SEQ analyses revealed enrichment of several microbes in the fecal (Akkermansia, Ruminococcaceae, Lachnospira) and salivary (Prevotellaceae, Actinobacillus) microbiome in axSpA patients as compared with HCs. Fecal microbiome from axSpA patients showed a tendency towards increased alpha diversity in IgA[+] fraction and decreased diversity in IgA[-] fraction in comparison with HCs, while the salivary microbiome exhibits a significant decrease in alpha diversity in both IgA[+] and IgA[-] fractions. Increased IgA coating of Clostridiales Family XIII in feces correlated with disease severity. Inferred metagenomic analysis suggests perturbation of metabolites and metabolic pathways for inflammation (oxidative stress, amino acid degradation) and metabolism (propanoate and butanoate) in axSpA patients. Analyses of fecal and salivary microbes from axSpA patients reveal distinct populations of immunoreactive microbes compared to HCs using the IgA-SEQ approach. These bacteria were not identified by comparing their relative abundance alone. Predictive metagenomic analysis revealed perturbation of metabolites/metabolic pathways in axSpA patients. Future studies on these immunoreactive microbes may lead to better understanding of the functional role of IgA in maintaining microbial structure and human health.}, } @article {pmid36248358, year = {2022}, author = {Song, T and Peng, S and Zhou, X and Jiang, L and Zhang, J}, title = {Case Report: Diagnosis of vertebral alveolar echinococcosis upon next-generation sequencing in a suspected tuberculosis.}, journal = {Frontiers in surgery}, volume = {9}, number = {}, pages = {984640}, pmid = {36248358}, issn = {2296-875X}, abstract = {INTRODUCTION: Alveolar echinococcosis (AE), caused by larval stages of Echinococcus multilocularis, is a rare zoonotic disease that mainly involves the liver. The diagnosis of extrahepatic AE is usually difficult. Here, we describe a rare case of vertebral alveolar echinococcosis with a suspected history of spinal tuberculosis, diagnosed by metagenomic next-generation sequencing (mNGS).

CASE PRESENTATION: A 44-year-old woman presented with repetitive neck and back pain, with a surgical history of suspected spinal tuberculosis. Magnetic resonance imaging (MRI) showed cystic masses in the craniocervical junction region and effusion around lumbar vertebrae. Multiple culture tests were performed to detect tuberculosis and other pathogens through puncture of the effusion and of cerebrospinal fluid, but the results were all negative. Finally, mNGS of the effusion fluid was performed and Echinococcus multilocularis were detected. The results were further confirmed by Sanger sequencing.

CONCLUSION: This case emphasizes a role of mNGS in the diagnosis of infectious diseases with unknown pathogen. As a newly emerged sensitive and accurate diagnostic strategy, mNGS provides clinicians an opportunity to clarify pathogens in complicated infectious cases, especially in patients with a history of multiple infections.}, } @article {pmid36247976, year = {2022}, author = {Yek, C and Pacheco, AR and Vanaerschot, M and Bohl, JA and Fahsbender, E and Aranda-Díaz, A and Lay, S and Chea, S and Oum, MH and Lon, C and Tato, CM and Manning, JE}, title = {Metagenomic Pathogen Sequencing in Resource-Scarce Settings: Lessons Learned and the Road Ahead.}, journal = {Frontiers in epidemiology}, volume = {2}, number = {}, pages = {}, pmid = {36247976}, issn = {2674-1199}, support = {ZIA AI001066/ImNIH/Intramural NIH HHS/United States ; }, abstract = {Metagenomic next-generation sequencing (mNGS) is the process of sequencing all genetic material in a biological sample. The technique is growing in popularity with myriad applications including outbreak investigation, biosurveillance, and pathogen detection in clinical samples. However, mNGS programs are costly to build and maintain, and additional obstacles faced by low- and middle-income countries (LMICs) may further widen global inequities in mNGS capacity. Over the past two decades, several important infectious disease outbreaks have highlighted the importance of establishing widespread sequencing capacity to support rapid disease detection and containment at the source. Using lessons learned from the COVID-19 pandemic, LMICs can leverage current momentum to design and build sustainable mNGS programs, which would form part of a global surveillance network crucial to the elimination of infectious diseases.}, } @article {pmid36247830, year = {2022}, author = {Sarkar, O and Rova, U and Christakopoulos, P and Matsakas, L}, title = {Effect of metals on the regulation of acidogenic metabolism enhancing biohydrogen and carboxylic acids production from brewery spent grains: Microbial dynamics and biochemical analysis.}, journal = {Engineering in life sciences}, volume = {22}, number = {10}, pages = {650-661}, pmid = {36247830}, issn = {1618-0240}, abstract = {The present study reports the mixed culture acidogenic production of biohydrogen and carboxylic acids (CA) from brewery spent grains (BSG) in the presence of high concentrations of cobalt, iron, nickel, and zinc. The metals enhanced biohydrogen output by 2.39 times along with CA biosynthesis by 1.73 times. Cobalt and iron promoted the acetate and butyrate pathways, leading to the accumulation of 5.14 gCOD/L of acetic and 11.36 gCOD/L of butyric acid. The production of solvents (ethanol + butanol) was higher with zinc (4.68 gCOD/L) and cobalt (4.45 gCOD/L). A combination of all four metals further enhanced CA accumulation to 42.98 gCOD/L, thus surpassing the benefits accrued from supplementation with individual metals. Additionally, 0.36 and 0.31 mol green ammonium were obtained from protein-rich brewery spent grain upon supplementation with iron and cobalt, respectively. Metagenomic analysis revealed the high relative abundance of Firmicutes (>90%), of which 85.02% were Clostridium, in mixed metal-containing reactors. Finally, a significant correlation of dehydrogenase activity with CA and biohydrogen evolution was observed upon metal addition.}, } @article {pmid36247599, year = {2022}, author = {Lu, Y and Cong, P and Kuang, S and Tang, L and Li, Y and Dong, J and Song, W}, title = {Long-term excessive application of K2SO4 fertilizer alters bacterial community and functional pathway of tobacco-planting soil.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {1005303}, pmid = {36247599}, issn = {1664-462X}, abstract = {To improve tobacco leaf quality, excessive K2SO4 fertilizers were applied to soils in major tobacco-planting areas in China. However, the effects of K2SO4 application on soil microbial community and functions are still unclear. An eight-year field experiment with three kinds of K2SO4 amounts (low amount, K2O 82.57 kg hm[-2], LK; moderate amount, K2O 165.07 kg hm[-2], MK; high amount, K2O 247.58 kg hm[-2], HK) was established to assess the effects of K2SO4 application on the chemical and bacterial characteristics of tobacco-planting soil using 16S rRNA gene and metagenomic sequencing approaches. Results showed that HK led to lower pH and higher nitrogen (N), potassium (K), sulfur(S) and organic matter contents of the soil than LK. The bacterial community composition of HK was significantly different from those of MK and LK, while these of MK and LK were similar. Compared to LK, HK increased the relative abundance of predicted copiotrophic groups (e.g. Burkholderiaceae, Rhodospirillaceae families and Ellin6067 genus) and potentially beneficial bacteria (e.g. Gemmatimonadetes phylum and Bacillus genus) associated with pathogens and heavy metal resistance, N fixation, dissolution of phosphorus and K. While some oligotrophic taxa (e.g. Acidobacteria phylum) related to carbon, N metabolism exhibited adverse responses to HK. Metagenomic analysis suggested that the improvement of pathways related to carbohydrate metabolism and genetic information processing by HK might be the self-protection mechanism of microorganisms against environmental stress. Besides, the redundancy analysis and variation partitioning analysis showed that soil pH, available K and S were the primary soil factors in shifting the bacterial community and KEGG pathways. This study provides a clear understanding of the responses of soil microbial communities and potential functions to excessive application of K2SO4 in tobacco-planting soil.}, } @article {pmid36247458, year = {2022}, author = {Shanmuganathan, R and Tangavel, C and K S, SVA and Muthurajan, R and Nayagam, SM and Matchado, MS and Rajendran, S and Kanna, RM and Shetty, AP}, title = {Comparative metagenomic analysis of human intervertebral disc nucleus pulposus and cartilaginous end plates.}, journal = {Frontiers in cardiovascular medicine}, volume = {9}, number = {}, pages = {927652}, pmid = {36247458}, issn = {2297-055X}, abstract = {STUDY DESIGN: The diversity of microflora inhabiting endplate (EP) and nucleus pulposus (NP) tissues of human intervertebral disc (IVD) was profiled through NGS-supported 16S rRNA amplicon sequencing. Sixteen EP and their corresponding NP were excised from the brain-dead voluntary organ donors with no clinical history of low back pain, and 12 herniated and 8 degenerated NP tissues isolated from the patients undergoing spinal surgery were subjected to study the alteration in the microbial diversity.

OBJECTIVES: To understand in normal IVD, whether the colonization of bacteria to the NP is through the EP in discs with intact annulus fibrosus. To identify significantly differing microbial population(s) between normal and diseased IVD (NP).

BACKGROUND OF THE STUDY: There is increasing evidence for subclinical infection by fastidious low, growing bacteria to be a cause of disc degeneration. Although the presence of bacteria in NP has been reported well in literature, the source of bacteria is not clearly proved as the disc is avascular in healthy condition. Documentation of similar bacterial populations in the EP and NP may add proof that bacterial inoculation of NP occurs via the EP.

MATERIALS AND METHODS: Sixteen EP and their corresponding NP excised from brain-dead voluntary organ donors with no history of back pain and 20 diseased discs collected from patients undergoing microdiscectomy/fusion surgery were used for profiling microbiome through 16S rRNA amplicon sequencing using primers specific for V1-V9 hypervariable regions. Changes in bacterial diversity and abundance were analysed to identify the key microbial populations in normal IVD NP and EP tissues and those significantly altered in diseased IVD (NP).

RESULTS: NP and EP shared a similar spectrum of microbiome but with varying abundance. The five dominant phyla identified were Proteobacteria, Firmicutes, Actinobacteria, OD1, and Bacteroidetes. Proteobacteria was found to be the most abundant phyla in both NP (62%) and EP (53%) of the normal IVD. This was followed by Firmicutes (16%), Actinobacteriota (11%), OD1 (Parcubacteria) (7.6%), and Bacteroidetes (2%) in NP and Firmicutes (23.4%), OD1 (Parcubacteria) (17.6%), Actinobacteriota (2.8%), and Bacteroidetes (2.6%) in EP, respectively. Under diseased conditions, Proteobacteria (68%) was dominant when compared with other phyla. However, there was no significant difference in the abundance of Proteobacteria between the normal and diseased discs. Interestingly, the other dominant phyla such as Firmicutes (Normal-NP: 16.2%; Diseased-NP: 4.02%) and Actinobacteria (Normal-NP: 11%; Diseased-NP: 0.99%) showed a significant reduction in degenerated discs. To understand the key microbial populations that are significantly altered during disease, correlation analysis was performed among the three phyla, which revealed a negative correlation in the ratio of Actinobacteria + Firmicutes vs. Proteobacteria (p = 0.001) in DD.

CONCLUSION: Results of our study clearly demonstrated a similar bacterial diversity but with varying abundance between the EP and NP, suggesting the existence of the endplate-nucleus pulposus axis in the normal IVD microbiome. Further, our results have indicated that the changes in the abundance of Actinobacteria + Firmicutes vs. Proteobacteria during DDD need further investigation.}, } @article {pmid36247251, year = {2022}, author = {Wei, P and Wu, L and Li, Y and Shi, J and Luo, Y and Wu, W and Feng, J}, title = {Metagenomic next-generation sequencing for the detection of pathogenic microorganisms in patients with pulmonary infection.}, journal = {American journal of translational research}, volume = {14}, number = {9}, pages = {6382-6388}, pmid = {36247251}, issn = {1943-8141}, abstract = {OBJECTIVE: To explore the clinical value of metagenomic next-generation sequencing (mNGS) in diagnosing pulmonary infectious diseases.

METHODS: A retrospective analysis was performed on 82 patients with pulmonary infection who were admitted to the Eighth Affiliated Hospital of Guangxi Medical University & Guigang City People's Hospital from January 2020 to December 2021. The pathogens were detected by mNGS and conventional methods (culture and PCR). Then, the type and number of detected pathogens, as well as the specificity and sensitivity, were compared between the two methods. In addition, the positive rates of bacteria, fungi, tubercle bacillus, and mixed infection in bronchoalveolar lavage fluid, sputum, pleural effusion, and blood detected by mNGS, and the advantage in required test time were evaluated.

RESULTS: More types and numbers of pathogens were detected by mNGS with a higher sensitivity but a lower specificity, as compared to the conventional detection methods (all P<0.05). The positive rates and integrity rates of bacteria, fungi, and tubercle bacillus detected by mNGS were higher than those by conventional methods (all P<0.05). Moreover, there was no difference in the overall sensitivity of mNGS among different sample types, but the sensitivities of mNGS in bronchoalveolar lavage fluid and sputum samples were significantly higher than those of conventional methods (both P<0.05). The average test time for mNGS was shorter than that of conventional methods.

CONCLUSION: mNGS can detect more types and numbers of pathogenic microorganisms, improve the detection sensitivity, and reduce the detection time in patients with pulmonary infection.}, } @article {pmid36246801, year = {2022}, author = {Li, T and Chen, YX and Lin, JJ and Lin, WX and Zhang, WZ and Dong, HM and Cai, SX and Meng, Y}, title = {Successful treatment of disseminated nocardiosis diagnosed by metagenomic next-generation sequencing: A case report and review of literature.}, journal = {World journal of clinical cases}, volume = {10}, number = {28}, pages = {10120-10129}, pmid = {36246801}, issn = {2307-8960}, abstract = {BACKGROUND: Nocardia paucivorans is an infrequently found bacterium with the potential to cause severe infection, with a predilection for the central nervous system, both in immunocompromised and immunocompetent individuals. Rapid etiological diagnosis of nocardiosis can facilitate timely and rational antimicrobial treatment. Metagenomic next-generation sequencing (mNGS) can improve the rate and reduce the turnaround time for the detection of Nocardia.

CASE SUMMARY: A 49-year-old man was admitted to hospital with cough and hemoptysis. Imaging revealed pulmonary consolidation as well as multiple brain lesions. Nocardia asiatica and Nocardia beijingensis were rapidly detected by mNGS of bronchoalveolar lavage fluid (BALF) while bacterial culture of BALF and pathological biopsy of lung tissue were negative. In early stages, he was treated with trimethoprim-sulfamethoxazole (TMP-SMZ) and linezolid by individual dose adjustment based on serum concentrations and the adverse effects of thrombocytopenia and leukopenia. The treatment was then replaced by TMP-SMZ and ceftriaxone or minocycline. He was treated with 8 mo of parenteral and/or oral antibiotics, and obvious clinical improvement was achieved with resolution of pulmonary and brain lesions on repeat imaging.

CONCLUSION: mNGS provided fast and precise pathogen detection of Nocardia. In disseminated nocardiosis, linezolid is an important alternative that can give a better outcome with the monitoring of linezolid serum concentrations and platelet count.}, } @article {pmid36246283, year = {2022}, author = {Zhang, H and Zhou, F and Huang, J and Liu, X and Xu, H and Liang, J and Wang, J and Chen, J and Liu, L and Li, Y and Hu, X and Chen, X and Liu, C and Zhang, K}, title = {Severe skin and subcutaneous pythiosis in China: Metagenomic identification and characterization of Pythium insidiosum.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1002460}, pmid = {36246283}, issn = {1664-302X}, abstract = {Pythium insidiosum is a rare fungus-like pathogen that is known to cause pythiosis in mammals with high morbidity and mortality. Identification of the pathogen is essential for timely treatment and rational use of antibiotics. However, Pythium insidiosum is difficult to detect via conventional microbiological tests. The current gold standard is polymerase chain reaction, which is lacking in most hospitals since human pythiosis is rare in China. In this study, we used metagenomic Next-Generation Sequencing and identified Pythium insidiosum in a 56-year-old Chinese male who was hospitalized due to severe edema in the right lower limb with scattered darkening indurations. The patient had a history of cirrhosis and occupational exposure to swamp water. Serological level of immune biomarkers indicated immunodeficiency, and Proteinase 3-Anti-Neutrophil Cytoplasmic Antibody was positive. Surgical incision of the lesions revealed radiating and reticular cutaneous ulcers. Microbial infections were suspected but conventional tests failed to discover the etiology. Empirical use of penicillin, vancomycin, and ceftriaxone had no effect. As a result, the peripheral blood and tissue biopsies were sent for metagenomic Next-Generation Sequencing, which reported Pythium insidiosum. This finding was corroborated by pathological staining, whole-genome sequencing, and internal transcribed spacer sequencing. Notably, antifungal treatment was ineffective, but the patient responded well to oral trimethoprim-sulfamethoxazole, which may be due to the folp gene found in Pythium insidiosum genome. Our study prompts future studies to determine the optimal treatment of skin pythiosis.}, } @article {pmid36246281, year = {2022}, author = {Yang, C and Bai, X and Hu, T and Xue, X and Su, X and Zhang, X and Wu, T and Zhang, M and Shen, X and Dong, X}, title = {Integrated metagenomics and targeted-metabolomics analysis of the effects of phenylalanine on loperamide-induced constipation in rats.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1018008}, pmid = {36246281}, issn = {1664-302X}, abstract = {Functional constipation is a common functional gastrointestinal disease. In our previous study, we found that the gut microbiota structure was disordered and the level of phenylalanine (Phe) in serum was decreased in constipated women. We conducted the present study to elucidate the role of Phe in remodeling the composition of gut microbiota and the relationship between gut microbiota and serum metabolites. Here, we demonstrated that Phe treatment significantly enhanced intestinal motility, suppressed inflammatory responses, and prevented intestinal barrier damage in rats with loperamide (Lop)-induced constipation. By metagenomic sequencing, the disbalanced gut microbial profile was analyzed in constipated rats. Phe treatment reversed changes in the abundance of several gut bacteria at the phylum, genus, and species levels. Further, we observed distinct metabolic patterns in constipated rats through targeted metabolomics and identified constipation-related gut microbial species linked to changes in circulating neurotransmitter metabolites. The abundances of species s_Lactobacillus murinus, s_Enterococcus italicus, s_Lactobacillus animalis, s_Lactobacillus apodemi, s_Enterococcus faecalis, and s_Lactobacillus backii were positively correlated with L-asparagine, L-Glutamic acid, Putrescine, and Spermidine levels. The abundances of s_Lactobacillus johnsonii and s_Butyricimonas virosa were negatively correlated with L-asparagine, L-Glutamic acid, Putrescine, and Spermidine levels. Taken together, our findings suggest that Phe can ameliorate the development of Lop-induced constipation in rats by remodeling the gut microbial community structure and changing metabolite levels.}, } @article {pmid36246273, year = {2022}, author = {Bradley, ES and Zeamer, AL and Bucci, V and Cincotta, L and Salive, MC and Dutta, P and Mutaawe, S and Anya, O and Tocci, C and Moormann, A and Ward, DV and McCormick, BA and Haran, JP}, title = {Oropharyngeal microbiome profiled at admission is predictive of the need for respiratory support among COVID-19 patients.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1009440}, pmid = {36246273}, issn = {1664-302X}, support = {U01 CA261276/CA/NCI NIH HHS/United States ; }, abstract = {The oropharyngeal microbiome, the collective genomes of the community of microorganisms that colonizes the upper respiratory tract, is thought to influence the clinical course of infection by respiratory viruses, including Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), the causative agent of Coronavirus Infectious Disease 2019 (COVID-19). In this study, we examined the oropharyngeal microbiome of suspected COVID-19 patients presenting to the Emergency Department and an inpatient COVID-19 unit with symptoms of acute COVID-19. Of 115 initially enrolled patients, 50 had positive molecular testing for COVID-19+ and had symptom duration of 14 days or less. These patients were analyzed further as progression of disease could most likely be attributed to acute COVID-19 and less likely a secondary process. Of these, 38 (76%) went on to require some form of supplemental oxygen support. To identify functional patterns associated with respiratory illness requiring respiratory support, we applied an interpretable random forest classification machine learning pipeline to shotgun metagenomic sequencing data and select clinical covariates. When combined with clinical factors, both species and metabolic pathways abundance-based models were found to be highly predictive of the need for respiratory support (F1-score 0.857 for microbes and 0.821 for functional pathways). To determine biologically meaningful and highly predictive signals in the microbiome, we applied the Stable and Interpretable RUle Set to the output of the models. This analysis revealed that low abundance of two commensal organisms, Prevotella salivae or Veillonella infantium (< 4.2 and 1.7% respectively), and a low abundance of a pathway associated with LPS biosynthesis (< 0.1%) were highly predictive of developing the need for acute respiratory support (82 and 91.4% respectively). These findings suggest that the composition of the oropharyngeal microbiome in COVID-19 patients may play a role in determining who will suffer from severe disease manifestations.}, } @article {pmid36246257, year = {2022}, author = {Alam, K and Mazumder, A and Sikdar, S and Zhao, YM and Hao, J and Song, C and Wang, Y and Sarkar, R and Islam, S and Zhang, Y and Li, A}, title = {Streptomyces: The biofactory of secondary metabolites.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {968053}, pmid = {36246257}, issn = {1664-302X}, abstract = {Natural products derived from microorganisms serve as a vital resource of valuable pharmaceuticals and therapeutic agents. Streptomyces is the most ubiquitous bacterial genus in the environments with prolific capability to produce diverse and valuable natural products with significant biological activities in medicine, environments, food industries, and agronomy sectors. However, many natural products remain unexplored among Streptomyces. It is exigent to develop novel antibiotics, agrochemicals, anticancer medicines, etc., due to the fast growth in resistance to antibiotics, cancer chemotherapeutics, and pesticides. This review article focused the natural products secreted by Streptomyces and their function and importance in curing diseases and agriculture. Moreover, it discussed genomic-driven drug discovery strategies and also gave a future perspective for drug development from the Streptomyces.}, } @article {pmid36246256, year = {2022}, author = {Kang, L and Luo, W and Dai, Q and Zhou, H and Wei, W and Tang, J and Han, H and Yuan, Y and Long, J and Zhang, Z and Hong, M}, title = {Giant pandas' staple food bamboo phyllosphere fungal community and its influencing factors.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1009588}, pmid = {36246256}, issn = {1664-302X}, abstract = {Giant pandas have developed a series of foraging strategies to adapt to their special bamboo diets. Although bamboo is an important food resource for giant pandas in Liziping National Nature Reserve (Liziping NR), China, there are relatively few studies on their phyllosphere fungal community and its influencing factors. Herein, we used ITS1 amplification and metagenomic sequencing to analyze the phyllosphere fungi diversity and functions (KEGG, CAZyme, and antibiotic resistance gene) and explore the influencing factors for the three giant pandas foraging bamboo species (Arundinaria spanostachya, AS; Yushania lineolate, YL; and Fargesia ferax, FF) over different seasons (spring vs. autumn) in Liziping NR, China. We found that Ascomycota and Basidiomycota were the most dominant phyla in the bamboo phyllosphere. The alpha diversity (e.g., the Sobs index and Shannon index) was relatively higher in autumn samples than in spring samples, and the community structure differed significantly between the three bamboo species in spring and autumn. Some biotic and abiotic variables (e.g., the elevation and mean base diameter of bamboo) significantly influenced the abundance, diversity, and community structure of the bamboo phyllosphere fungal community. Moreover, the functional analysis showed the differences in the glycoside hydrolase community and antibiotic resistance gene (ARG) profile between spring and autumn samples. Co-occurrence network modeling suggested that AS phyllosphere fungal communities in autumn employed a much more complex network than that in spring, and the abundance of multidrug, tetracycline, and glycopeptide resistance genes was high and closely correlated with other ARGs. These results indicate that fungal community's abundance, diversity, and community structure are mainly affected by the season, host species, and elevation. The season and host species are major factors affecting the biological functions (KEGG and CAZyme), ARGs, and interactions between sympatric bacterial and fungal communities in bamboo phyllosphere. This integrated study can provide a reference basis for the seasonal management of bamboo resources foraged by wild giant pandas, and predict the risk of antibiotic resistance in bamboo phyllosphere fungal flora in Liziping NR (Xiaoxiangling mountains), China.}, } @article {pmid36246251, year = {2022}, author = {Kang, J and Liu, Y and Chen, X and Xu, F and Wang, H and Xiong, W and Li, X}, title = {Metagenomic insights into the antibiotic resistomes of typical Chinese dairy farm environments.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {990272}, pmid = {36246251}, issn = {1664-302X}, abstract = {Antibiotic resistance genes (ARGs) in the environment pose a threat to human and animal health. Dairy cows are important livestock in China; however, a comprehensive understanding of antibiotic resistance in their production environment has not been well clarified. In this study, we used metagenomic methods to analyze the resistomes, microbiomes, and potential ARG bacterial hosts in typical dairy farm environments (including feces, wastewater, and soil). The ARGs resistant to tetracyclines, MLS, β-lactams, aminoglycoside, and multidrug was dominant in the dairy farm ecosystem. The abundance and diversity of total ARGs in dairy feces and wastewater were significantly higher than in soil (P < 0.05). The same environmental samples from different dairy have similar resistomes and microbiomes. A high detection rate of tet(X) in wastewater and feces (100% and 71.4%, respectively), high abundance (range from 5.74 to 68.99 copies/Gb), and the finding of tet(X5) challenged the clinical application of the last antibiotics resort of tigecycline. Network analysis identified Bacteroides as the dominant genus in feces and wastewater, which harbored the greatest abundance of their respective total ARG coverage and shared ARGs. These results improved our understanding of ARG profiles and their bacterial hosts in dairy farm environments and provided a basis for further surveillance.}, } @article {pmid36246216, year = {2022}, author = {Kröber, E and Mankowski, A and Schäfer, H}, title = {Microorganisms associated with Sporobolus anglicus, an invasive dimethylsulfoniopropionate producing salt marsh plant, are an unrecognized sink for dimethylsulfide.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {950460}, pmid = {36246216}, issn = {1664-302X}, abstract = {BACKGROUND: Saltmarshes are hotspots of organosulfur compound cycling due to production of dimethylsulfoniopropionate (DMSP) by benthic microorganisms, macroalgae, and saltmarsh vegetation. Degradation of DMSP is a source of dimethylsulfide (DMS), an important precursor for formation of secondary organic aerosol. Microorganisms degrading DMS play a role in controlling the amount of DMS available for emission into the atmosphere. Previous work has implicated sediment microbial populations as a major sink for DMS. Here, we show that Sporobolus anglicus (previously known as Spartina anglica), a widely distributed saltmarsh plant, is colonized by DMS-degrading microorganisms.

METHODS: Dimethylsulfide degradation potential was assessed by gas chromatography and [13]C-DMS stable isotope probing, microbial community diversity and functional genetic potential in phyllosphere and rhizosphere samples was assessed by high-throughput sequencing of 16S rRNA gene amplicons, cloning and sequencing of methanethiol oxidase genes, and by metagenomic analysis of phyllosphere microbial communities.

RESULTS: The DMS degradation potential of microbial communities recovered from phyllosphere and rhizosphere samples was similar. Active DMS-degraders were identified by [13]C-DMS stable isotope probing and included populations related to Methylophaga and other Piscirickettsiaceae in rhizosphere samples. DMS-degraders in the phyllosphere included Xanthomonadaceae and Halothiobacillaceae. The diversity in sediment samples of the methanethiol oxidase (mtoX) gene, a marker for metabolism of methanethiol during DMS and DMSP degradation, was similar to previously detected saltmarsh mtoX, including those of Methylophaga and Methylococcaeae. Phyllosphere mtoX genes were distinct from sediment mtoX and did not include close relatives of cultivated bacteria. Microbial diversity in the phyllosphere of S. anglicus was distinct compared to those of model plants such as rice, soybean, clover and Arabidopsis and showed a dominance of Gammaproteobacteria rather than Alphaproteobacteria.

CONCLUSION: The potential for microbial DMS degradation in the phyllosphere and rhizosphere of Sporobolus anglicus suggest that DMS cycling in saltmarshes is more complex than previously recognised and calls for a more detailed assessment of how aboveground activities affect fluxes of DMS.}, } @article {pmid36246212, year = {2022}, author = {Elbehery, AHA and Deng, L}, title = {Insights into the global freshwater virome.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {953500}, pmid = {36246212}, issn = {1664-302X}, abstract = {Viruses are by far the most abundant life forms on this planet. Yet, the full viral diversity remains mostly unknown, especially in environments like freshwater. Therefore, we aimed to study freshwater viruses in a global context. To this end, we downloaded 380 publicly available viral metagenomes (>1 TB). More than 60% of these metagenomes were discarded based on their levels of cellular contamination assessed by ribosomal DNA content. For the remaining metagenomes, assembled contigs were decontaminated using two consecutive steps, eventually yielding 273,365 viral contigs longer than 1,000 bp. Long enough contigs (≥ 10 kb) were clustered to identify novel genomes/genome fragments. We could recover 549 complete circular and high-quality draft genomes, out of which 10 were recognized as being novel. Functional annotation of these genomes showed that most of the annotated coding sequences are DNA metabolic genes or phage structural genes. On the other hand, taxonomic analysis of viral contigs showed that most of the assigned contigs belonged to the order Caudovirales, particularly the families of Siphoviridae, Myoviridae, and Podoviridae. The recovered viral contigs contained several auxiliary metabolic genes belonging to several metabolic pathways, especially carbohydrate and amino acid metabolism in addition to photosynthesis as well as hydrocarbon degradation and antibiotic resistance. Overall, we present here a set of prudently chosen viral contigs, which should not only help better understanding of freshwater viruses but also be a valuable resource for future virome studies.}, } @article {pmid36245062, year = {2022}, author = {Geisler, C and Schlicht, K and Knappe, C and Rohmann, N and Hartmann, K and Türk, K and Settgast, U and Schulte, DM and Demetrowitsch, T and Jensen-Kroll, J and Pisarevskaja, A and Brix, F and Gruber, B and Rimbach, G and Döring, F and Rosenstiel, P and Franke, A and Schreiber, S and Henning, CHCA and Lieb, W and Nöthlings, U and Schwarz, K and Laudes, M}, title = {Cohort profile: the Food Chain Plus (FoCus) cohort.}, journal = {European journal of epidemiology}, volume = {37}, number = {10}, pages = {1087-1105}, pmid = {36245062}, issn = {1573-7284}, support = {FoCus//Bundesministerium für Bildung und Forschung/ ; 0315540A//Bundesministerium für Bildung und Forschung/ ; }, mesh = {Female ; Humans ; Male ; Cohort Studies ; *Diabetes Mellitus, Type 2/epidemiology ; Food Chain ; Inflammation ; Obesity/epidemiology ; Adolescent ; Young Adult ; Adult ; Middle Aged ; Aged ; Aged, 80 and over ; }, abstract = {The Food Chain Plus (FoCus) cohort was launched in 2011 for population-based research related to metabolic inflammation. To characterize this novel pathology in a comprehensive manner, data collection included multiple omics layers such as phenomics, microbiomics, metabolomics, genomics, and metagenomics as well as nutrition profiling, taste perception phenotyping and social network analysis. The cohort was set-up to represent a Northern German population of the Kiel region. Two-step recruitment included the randomised enrolment of participants via residents' registration offices and via the Obesity Outpatient Centre of the University Medical Center Schleswig-Holstein (UKSH). Hence, both a population- and metabolic inflammation- based cohort was created. In total, 1795 individuals were analysed at baseline. Baseline data collection took place between 2011 and 2014, including 63% females and 37% males with an age range of 18-83 years. The median age of all participants was 52.0 years [IQR: 42.5; 63.0 years] and the median baseline BMI in the study population was 27.7 kg/m[2] [IQR: 23.7; 35.9 kg/m[2]]. In the baseline cohort, 14.1% of participants had type 2 diabetes mellitus, which was more prevalent in the subjects of the metabolic inflammation group (MIG; 31.8%). Follow-up for the assessment of disease progression, as well as the onset of new diseases with changes in subject's phenotype, diet or lifestyle factors is planned every 5 years. The first follow-up period was finished in 2020 and included 820 subjects.}, } @article {pmid36244970, year = {2022}, author = {Thomann, AK and Wüstenberg, T and Wirbel, J and Knoedler, LL and Thomann, PA and Zeller, G and Ebert, MP and Lis, S and Reindl, W}, title = {Depression and fatigue in active IBD from a microbiome perspective-a Bayesian approach to faecal metagenomics.}, journal = {BMC medicine}, volume = {20}, number = {1}, pages = {366}, pmid = {36244970}, issn = {1741-7015}, mesh = {Amino Acids ; Bayes Theorem ; Depression ; Fatigue ; Feces/microbiology ; Glycosaminoglycans ; Humans ; *Inflammatory Bowel Diseases ; Metagenomics ; *Microbiota ; Pectins ; }, abstract = {BACKGROUND: Extraintestinal symptoms are common in inflammatory bowel diseases (IBD) and include depression and fatigue. These are highly prevalent especially in active disease, potentially due to inflammation-mediated changes in the microbiota-gut-brain axis. The aim of this study was to investigate the associations between structural and functional microbiota characteristics and severity of fatigue and depressive symptoms in patients with active IBD.

METHODS: We included clinical data of 62 prospectively enrolled patients with IBD in an active disease state. Patients supplied stool samples and completed the questionnaires regarding depression and fatigue symptoms. Based on taxonomic and functional metagenomic profiles of faecal gut microbiota, we used Bayesian statistics to investigate the associative networks and triangle motifs between bacterial genera, functional modules and symptom severity of self-reported fatigue and depression.

RESULTS: Associations with moderate to strong evidence were found for 3 genera (Odoribacter, Anaerotruncus and Alistipes) and 3 functional modules (pectin, glycosaminoglycan and central carbohydrate metabolism) with regard to depression and for 4 genera (Intestinimonas, Anaerotruncus, Eubacterium and Clostridiales g.i.s) and 2 functional modules implicating amino acid and central carbohydrate metabolism with regard to fatigue.

CONCLUSIONS: This study provides the first evidence of association triplets between microbiota composition, function and extraintestinal symptoms in active IBD. Depression and fatigue were associated with lower abundances of short-chain fatty acid producers and distinct pathways implicating glycan, carbohydrate and amino acid metabolism. Our results suggest that microbiota-directed therapeutic approaches may reduce fatigue and depression in IBD and should be investigated in future research.}, } @article {pmid36244921, year = {2023}, author = {Brennan, GL and Logares, R}, title = {Tracking contemporary microbial evolution in a changing ocean.}, journal = {Trends in microbiology}, volume = {31}, number = {4}, pages = {336-345}, doi = {10.1016/j.tim.2022.09.001}, pmid = {36244921}, issn = {1878-4380}, mesh = {*Adaptation, Physiological ; Oceans and Seas ; }, abstract = {Ocean microbes are fundamental for the functioning of the Earth system. Yet, our understanding of how they are reacting to global change in terms of evolution is limited. Microbes typically grow in large populations and reproduce quickly, which may allow them to rapidly adapt to environmental stressors compared to larger organisms. However, genetic evidence of contemporary evolution in wild microbes is scarce. We must begin coordinated efforts to establish new microbial time-series and explore novel tools, experiments, and data to fill this knowledge gap. The development of coordinated microbial 'genomic' observatories will provide the unprecedented opportunity to track contemporary microbial evolution in the ocean and explore the role of evolution in enabling wild microbes to respond to global change.}, } @article {pmid36244438, year = {2023}, author = {Pacholak, A and Zgoła-Grześkowiak, A and Kaczorek, E}, title = {Dynamics of microbial communities during biotransformation of nitrofurantoin.}, journal = {Environmental research}, volume = {216}, number = {Pt 2}, pages = {114531}, doi = {10.1016/j.envres.2022.114531}, pmid = {36244438}, issn = {1096-0953}, mesh = {Humans ; *Nitrofurantoin/chemistry/metabolism/pharmacology ; Biotransformation ; Biodegradation, Environmental ; Biodiversity ; *Microbiota ; Microbial Consortia ; }, abstract = {The purpose of this research was to investigate the biodegradation of nitrofurantoin (NFT), a typical nitrofuran antibiotic of potential carcinogenic properties, by two microbial communities derived from distinct environmental niches - mountain stream (NW) and seaport water (SS). The collected environmental samples represent the reserve of the protected area with no human intervention and the contaminated area that concentrates intense human activities. The structure, composition, and diversity of the communities were analyzed at three timepoints during NFT biodegradation. Comamonadaceae (43.2%) and Pseudomonadaceae (19.6%) were the most abundant families in the initial NW sample. The top families in the initial SS sample included Aeromonadaceae (31.4%) and Vibrionaceae (25.3%). The proportion of the most abundant families in both consortia was remarkably reduced in all samples treated with NFT. The biodiversity significantly increased in both consortia treated with NFT suggesting that NFT significantly alters community structure in the aquatic systems. In this study, NFT removal efficiency and transformation products were also studied. The biodegradation rate decreased with the increasing initial NFT concentration. Biodegradation followed similar pathways for both consortia and led to the formation of transformation products: 1-aminohydantoin, semicarbazide (SEM), and hydrazine (HYD). SEM and HYD were detected for the first time as NFT biotransformation products. This study demonstrates that the structure of the microbial community may be directly correlated with the presence of NFT. Enchanced biodiversity of the microbial community does not have to be correlated with increase in functional capacity, such as the ability to biodegradation because higher biodiversity corresponded to lower biodegradation. Our findings provide new insights into the effect of NFT contamination on aquatic microbiomes. The study also increases our understanding of the environmental impact of nitrofuran residues and their biodegradation.}, } @article {pmid36244140, year = {2022}, author = {Liu, J and Bao, Z and Wang, C and Wei, J and Wei, Y and Chen, M}, title = {Understanding of mercury and methylmercury transformation in sludge composting by metagenomic analysis.}, journal = {Water research}, volume = {226}, number = {}, pages = {119204}, doi = {10.1016/j.watres.2022.119204}, pmid = {36244140}, issn = {1879-2448}, mesh = {*Methylmercury Compounds ; *Mercury ; Sewage ; *Composting ; Metagenome ; Bacteria/genetics/metabolism ; Bacteroidetes ; }, abstract = {Municipal sewage especially the produced sewage sludge is a significant source releasing mercury (Hg) to the environment. However, the Hg speciation especially methylmercury (MeHg) transformation in sewage sludge treatment process remains poorly understood. This study investigated the transformation of Hg speciation especially MeHg in sludge composting. The distribution of Hg transformation related gene pairs hgcAB and merAB, and their putative microbial hosts were comprehensively analyzed. Both Hg (from 3.16±0.22 mg/kg to 3.20±0.19 mg/kg) and MeHg content (from 4.77±0.64 ng/g to 4.36±0.37 ng/g) were not obviously changed before and after composting, but about 19.69% of Hg and 27.36% of MeHg were lost according to mass balance calculation. The metagenomic analysis further revealed that anaerobes (Desulfobacterota and Euryarchaeota) were the mainly putative Hg methylators especially carrying high abundance of hgcA gene in the initial periods of composting. Among the 151 reconstructed metagenome-assembled genomes (MAGs), only 4 hgcA gene carriers (Myxococcota, Firmicutes, Cyclobacteriaceae, and Methanothermobacter) and 16 merB gene carriers were identified. But almost all of the MAGs carried hgcB gene and merA gene. The merA gene was widely distributed in genomes, which indicated the widespread functionality of microbes for reducing Hg(II) to Hg(0). The hgcA carrying microbes tends to present the similar metabolic pathways including methanogenesis and sulfur metabolism. Besides, both the irregular distribution of hgcA in various species (including Actinobacteria, Archaea, Bacteroidetes, Desulfobacterota, Euryarchaeota, and Nitrospirae, etc.) and opposite evolution trends between hgcA gene abundance and its host genome abundance can be an indication of horizontal gene transfer or gene deletions of hgcA during composting. Our findings thus revealed that sludge composting is not only a hotspot for Hg speciation transformation, but also a potential hotspot for MeHg transformation.}, } @article {pmid36243881, year = {2022}, author = {Sola, L and Quadu, E and Bortolazzo, E and Bertoldi, L and Randazzo, CL and Pizzamiglio, V and Solieri, L}, title = {Insights on the bacterial composition of Parmigiano Reggiano Natural Whey Starter by a culture-dependent and 16S rRNA metabarcoding portrait.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {17322}, pmid = {36243881}, issn = {2045-2322}, mesh = {Amino Acids, Branched-Chain ; Bacteria/genetics ; *Food Microbiology ; Galactose ; *Lactobacillus/genetics ; Purines ; RNA, Ribosomal, 16S/genetics ; Whey ; Whey Proteins ; }, abstract = {Natural whey starters (NWS) are undefined bacterial communities produced daily from whey of the previous cheese-making round, by application of high temperature. As a result, in any dairy plant, NWS are continuously evolving, undefined mixtures of several strains and/or species of lactic acid bacteria, whose composition and performance strongly depend on the selective pressure acting during incubation. While NWS is critical to assure consistency to cheese-making process, little is known about the composition, functional features, and plant-to-plant fluctuations. Here, we integrated 16S rRNA metabarcoding and culture-dependent methods to profile bacterial communities of 10 NWS sampled in the production area of Parmigiano Reggiano cheese. 16S rRNA metabarcoding analysis revealed two main NWS community types, namely NWS type-H and NWS type-D. Lactobacillus helveticus was more abundant in NWS type-H, whilst Lactobacillus delbrueckii/St. thermophilus in NWS type-D, respectively. Based on the prediction of metagenome functions, NWS type-H samples were enriched in functional pathways related to galactose catabolism and purine metabolism, while NWS type-D in pathways related to aromatic and branched chain amino acid biosynthesis, which are flavor compound precursors. Culture-dependent approaches revealed low cultivability of individual colonies as axenic cultures and high genetic diversity in the pool of cultivable survivors. Co-culturing experiments showed that fermentative performance decreases by reducing the bacterial complexity of inoculum, suggesting that biotic interactions and cross-feeding relationships could take place in NWS communities, assuring phenotypic robustness. Even though our data cannot directly predict these ecological interactions, this study provides the basis for experiments targeted at understanding how selective regime affects composition, bacterial interaction, and fermentative performance in NWS.}, } @article {pmid36243638, year = {2023}, author = {Zhou, X and Zheng, J and Zhang, J}, title = {Allergic Bronchopulmonary Mycosis Caused by Schizophyllum commune Diagnosed by Metagenomic Next-Generation Sequencing.}, journal = {Archivos de bronconeumologia}, volume = {59}, number = {2}, pages = {111-112}, doi = {10.1016/j.arbres.2022.09.013}, pmid = {36243638}, issn = {1579-2129}, mesh = {Humans ; *Invasive Pulmonary Aspergillosis/diagnosis ; *Schizophyllum/genetics ; High-Throughput Nucleotide Sequencing ; }, } @article {pmid36243451, year = {2022}, author = {Thompson, TP and Megaw, J and Kelly, SA and Hopps, J and Gilmore, BF}, title = {Microbial communities of halite deposits and other hypersaline environments.}, journal = {Advances in applied microbiology}, volume = {120}, number = {}, pages = {1-32}, doi = {10.1016/bs.aambs.2022.06.001}, pmid = {36243451}, issn = {0065-2164}, mesh = {Archaea/genetics ; Glycerol ; Metagenomics ; *Microbiota ; Phylogeny ; *Sodium Chloride ; }, abstract = {Large regions of Earth's surface are underlain by salt deposits that evaporated from ancient oceans and are populated by extreme halophilic microbes. While the microbiology of ancient evaporites has been well studied, the ecology of halite deposits and more recently formed NaCl "salticle" stalactite structures (speleothems) in a Triassic halite mine are less well characterized. The microbiome of Kilroot Salt Mine was profiled using conventional and enhanced culturing techniques. From this, 89 halophilic archaeal isolates from six known genera, and 55 halophilic or halotolerant bacterial isolates from 18 genera were obtained. Culture-independent metagenomic approaches also revealed that culturing techniques were inadvertently biased toward specific taxa, and the need for optimized isolation procedures are required to enhance cultivation diversity. Speleothems formed from saturated brines are unique structures that have the potential to entomb haloarchaea cells for thousands of years within fluid inclusions. The presence of such fluid inclusions, alongside the high abundance of genes related to glycerol metabolism, biofilm formation, and persister cell formation is highly suggestive of an environmental niche that could promote longevity and survivability. Finally, previous studies reporting the discovery of novel biocatalysts from the Kilroot mine microbiome, suggests that this environment may be an untapped source of chemical diversity with high biodiscovery potential.}, } @article {pmid36243187, year = {2022}, author = {Yun, Y and Su, T and Gui, Z and Tian, X and Chen, Y and Cao, Y and Yang, S and Xie, J and Anwar, N and Li, M and Li, G and Ma, T}, title = {Stress-responses of microbes in oil reservoir under high tetracycline exposure and their environmental risks.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {315}, number = {}, pages = {120355}, doi = {10.1016/j.envpol.2022.120355}, pmid = {36243187}, issn = {1873-6424}, mesh = {*Oil and Gas Fields ; Genes, Bacterial ; RNA, Ribosomal, 16S ; Tetracycline ; Anti-Bacterial Agents/analysis ; *Microbiota ; }, abstract = {As the groundwater ecosystem is connected with surface, antibiotics and antibiotic resistance genes (ARGs) in aquatic environments will gradually infiltrate into the deep environment, posing a potential threat to groundwater ecosystem. However, knowledge on the environmental risk of antibiotics and ARGs in groundwater ecosystem and their ecological process still remains unexplored. In this study, lab-scale oil reservoirs under high tetracycline stress were performed to evaluate the dynamics of microbial communities, ARGs and potential functions by using 16S rRNA gene sequencing and metagenomics analysis. Although the presence of antibiotics remarkably reduced the microbial abundance and diversity in a short term, but remain stable or even increased after a long-term incubation. Antibiotic stress caused a greater diversity and abundance of ARGs, and higher numbers of ARGs-related species with the capacity to transfer ARGs to other microbes through horizontal gene transfer. Thus, a much more frequent associations of microbial community at both node- and network-level and a selective pressure on enrichment of antibiotic resistant bacteria related to "anaerobic n-alkane degradation" and "methylotrophic methanogenesis" were observed. It is important to emphasize that high antibiotic stress could also prevent some microbes related to "Sulfate reduction", "Fe(II) oxidation", "Nitrate reduction", and "Xylene and Toluene degradation". This study provides an insight into the long-term stress-responses of microbial communities and functions in oil reservoir under tetracycline exposure, which may help to elucidate the effect of antibiotic stress on biogeochemical cycling with microbial involvement in groundwater ecosystem.}, } @article {pmid36242841, year = {2022}, author = {Lalitha, P and Prajna, NV and Gunasekaran, R and Teja, GV and Sharma, SS and Hinterwirth, A and Ruder, K and Zhong, L and Chen, C and Deiner, M and Huang, C and Pinsky, BA and Lietman, TM and Doan, T and Seitzman, GD and , }, title = {Deep sequencing analysis of clinical samples from patients with acute infectious conjunctivitis during the COVID-19 delta surge in Madurai, India.}, journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology}, volume = {157}, number = {}, pages = {105318}, pmid = {36242841}, issn = {1873-5967}, support = {R01 EY032041/EY/NEI NIH HHS/United States ; }, mesh = {Humans ; *COVID-19 ; SARS-CoV-2 ; Prospective Studies ; India/epidemiology ; *Conjunctivitis/epidemiology ; *Adenoviruses, Human/genetics ; Acute Disease ; High-Throughput Nucleotide Sequencing ; }, abstract = {BACKGROUND: Seasonal outbreaks of infectious conjunctivitis remain a public health issue. Determination of outbreak etiologies in the context of a worldwide pandemic may provide useful information to guide public health strategies. The aim of this study was to identify pathogens associated with outpatient infectious conjunctivitis during the COVID-19 Delta surge.

METHODS: This prospective study was conducted from April 2021 to September 2021. All outpatients presenting to the Aravind Eye Center (Madurai, India) with signs and symptoms consistent with acute infectious conjunctivitis were eligible. Three swabs were obtained from each participant: one from each conjunctiva and one from the anterior nares. Samples were processed for metagenomic RNA deep sequencing (RNA-seq).

RESULTS: Samples from 106 study participants were sequenced. The most common presenting symptoms were tearing (86%) and itching (71%). Preauricular lymphadenopathy was present in 38% of participants. 20% of participants had close contacts with similar symptoms. Systemic symptoms such as coughing, runny nose, vomiting or diarrhea were uncommonly reported. 60% of all participants used some medicated eye drops upon enrollment. 75% of study participants demonstrated infection with human adenovirus D (HAdV-D). 11% of conjunctivitis was associated with SARS-CoV-2. 15% had no definitive pathogen detected. 8% of all participants had codetection of more than one pathogen on RNA-seq.

CONCLUSIONS: During the COVID-19 Delta surge in India, HAdV-D was the most common pathogen associated with infectious conjunctivitis. SARS-CoV-2 was the second most common associated pathogen. Seasonal surveillance may be necessary for the determination of emerging and reemerging pathogens responsible for infectious conjunctivitis.}, } @article {pmid36242065, year = {2022}, author = {Chen, X and Tang, K and Zhang, M and Liu, S and Chen, M and Zhan, P and Fan, W and Chen, CA and Zhang, Y}, title = {Genome-centric insight into metabolically active microbial population in shallow-sea hydrothermal vents.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {170}, pmid = {36242065}, issn = {2049-2618}, mesh = {Cytochromes/genetics/metabolism ; *Epsilonproteobacteria/genetics ; Formates/metabolism ; *Gammaproteobacteria/genetics/metabolism ; Humans ; Hydrogen/metabolism ; *Hydrothermal Vents/microbiology ; *Microbiota ; Oxidoreductases ; Oxygen/metabolism ; Phylogeny ; Sulfur/metabolism ; }, abstract = {BACKGROUND: Geothermal systems have contributed greatly to both our understanding of the functions of extreme life and the evolutionary history of life itself. Shallow-sea hydrothermal systems are ecological intermediates of deep-sea systems and terrestrial springs, harboring unique and complexed ecosystems, which are well-lit and present physicochemical gradients. The microbial communities of deep-sea and terrestrial geothermal systems have been well-studied at the population genome level, yet little is known about the communities inhabiting the shallow-sea hydrothermal systems and how they compare to those inhabiting other geothermal systems.

RESULTS: Here, we used genome-resolved metagenomic and metaproteomic approaches to probe into the genetic potential and protein expression of microorganisms from the shallow-sea vent fluids off Kueishantao Island. The families Nautiliaceae and Campylobacteraceae within the Epsilonbacteraeota and the Thiomicrospiraceae within the Gammaproteobacteria were prevalent in vent fluids over a 3-year sampling period. We successfully reconstructed the in situ metabolic modules of the predominant populations within the Epsilonbacteraeota and Gammaproteobacteria by mapping the metaproteomic data back to metagenome-assembled genomes. Those active bacteria could use the reductive tricarboxylic acid cycle or Calvin-Benson-Bassham cycle for autotrophic carbon fixation, with the ability to use reduced sulfur species, hydrogen or formate as electron donors, and oxygen as a terminal electron acceptor via cytochrome bd oxidase or cytochrome bb3 oxidase. Comparative metagenomic and genomic analyses revealed dramatic differences between submarine and terrestrial geothermal systems, including microbial functional potentials for carbon fixation and energy conversion. Furthermore, shallow-sea hydrothermal systems shared many of the major microbial genera that were first isolated from deep-sea and terrestrial geothermal systems, while deep-sea and terrestrial geothermal systems shared few genera.

CONCLUSIONS: The metabolic machinery of the active populations within Epsilonbacteraeota and Gammaproteobacteria at shallow-sea vents can mirror those living at deep-sea vents. With respect to specific taxa and metabolic potentials, the microbial realm in the shallow-sea hydrothermal system presented ecological linkage to both deep-sea and terrestrial geothermal systems. Video Abstract.}, } @article {pmid36242054, year = {2022}, author = {Xie, YG and Luo, ZH and Fang, BZ and Jiao, JY and Xie, QJ and Cao, XR and Qu, YN and Qi, YL and Rao, YZ and Li, YX and Liu, YH and Li, A and Seymour, C and Palmer, M and Hedlund, BP and Li, WJ and Hua, ZS}, title = {Functional differentiation determines the molecular basis of the symbiotic lifestyle of Ca. Nanohaloarchaeota.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {172}, pmid = {36242054}, issn = {2049-2618}, mesh = {Amino Acids, Acidic/genetics/metabolism ; Amino Acids, Basic/genetics/metabolism ; *Archaea ; *Euryarchaeota/genetics ; Metagenome ; Nucleotides/metabolism ; Phylogeny ; Polysaccharides/metabolism ; }, abstract = {BACKGROUND: Candidatus Nanohaloarchaeota, an archaeal phylum within the DPANN superphylum, is characterized by limited metabolic capabilities and limited phylogenetic diversity and until recently has been considered to exclusively inhabit hypersaline environments due to an obligate association with Halobacteria. Aside from hypersaline environments, Ca. Nanohaloarchaeota can also have been discovered from deep-subsurface marine sediments.

RESULTS: Three metagenome-assembled genomes (MAGs) representing a new order within the Ca. Nanohaloarchaeota were reconstructed from a stratified salt crust and proposed to represent a novel order, Nucleotidisoterales. Genomic features reveal them to be anaerobes capable of catabolizing nucleotides by coupling nucleotide salvage pathways with lower glycolysis to yield free energy. Comparative genomics demonstrated that these and other Ca. Nanohaloarchaeota inhabiting saline habitats use a "salt-in" strategy to maintain osmotic pressure based on the high proportion of acidic amino acids. In contrast, previously described Ca. Nanohaloarchaeota MAGs from geothermal environments were enriched with basic amino acids to counter heat stress. Evolutionary history reconstruction revealed that functional differentiation of energy conservation strategies drove diversification within Ca. Nanohaloarchaeota, further leading to shifts in the catabolic strategy from nucleotide degradation within deeper lineages to polysaccharide degradation within shallow lineages.

CONCLUSIONS: This study provides deeper insight into the ecological functions and evolution of the expanded phylum Ca. Nanohaloarchaeota and further advances our understanding on the functional and genetic associations between potential symbionts and hosts. Video Abstract.}, } @article {pmid36241909, year = {2022}, author = {He, X and Wang, X and Fan, G and Li, F and Wu, W and Wang, Z and Fu, M and Wei, X and Ma, S and Ma, X}, title = {Metagenomic analysis of viromes in tissues of wild Qinghai vole from the eastern Tibetan Plateau.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {17239}, pmid = {36241909}, issn = {2045-2322}, mesh = {Animals ; Arvicolinae/genetics ; Feces ; Metagenomics ; Phylogeny ; Rodentia/genetics ; Tibet ; *Virome ; *Viruses/genetics ; }, abstract = {Rodents are natural reservoirs of diverse zoonotic viruses and widely distributed on the Tibetan Plateau. A comprehensive understanding of the virome in local rodent species could provide baseline of viral content and assist in efforts to reduce the risk for future emergence of rodent related zoonotic diseases. A total of 205 tissue and fecal samples from 41 wild Qinghai voles were collected. Metagenomic analyses were performed to outline the characteristics of the viromes, and phylogenetic analyses were used to identify the novel viral genomes. The virome distribution among five tissues (liver, lung, spleen, small intestine with content and feces) was also compared. We identified sequences related to 46 viral families. Novel viral genomes from distinct evolutionary lineages with known viruses were characterized for their genomic and evolutionary characteristics, including Hepatovirus, Hepacivirus, Rotavirus, and Picobirnavirus. Further analyses revealed that the core virome harbored by rodent internal tissues were quite different from the virome found in intestine and fecal samples. These findings provide an overview of the viromes in wild Qinghai voles, which are unique and the most common rodent species in the eastern Tibetan Plateau. A high diversity of viruses is likely present in rodent species in this area.}, } @article {pmid36240919, year = {2023}, author = {Lozada, M and Diéguez, MC and García, PE and Dionisi, HM}, title = {Microbial communities associated with kelp detritus in temperate and subantarctic intertidal sediments.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 1}, pages = {159392}, doi = {10.1016/j.scitotenv.2022.159392}, pmid = {36240919}, issn = {1879-1026}, mesh = {*Kelp ; Ecosystem ; RNA, Ribosomal, 16S ; *Macrocystis ; *Microbiota/physiology ; Alginates ; }, abstract = {Kelp forests, among the most productive ecosystems on Earth, cover large areas of the South Atlantic coast. Sediment heterotrophic bacteria have a pivotal role in the degradation of kelp biomass, however, the response of sediment microbial communities to periodic kelp biomass inputs is mostly unknown. Here, we show that kelp biomass induced rapid changes in overlying water chemistry and shifts in sediment microbial communities, which differed in the experimental systems containing Macrocystis pyrifera (M) and Undaria pinnatifida (U) with sediments of the respective regions. We observed results compatible with the degradation of labile, high molecular weight compounds into smaller and more refractory compounds towards the end of the incubations. The capability of microbial communities to degrade alginate, the major component of kelp cell walls, significantly increased with respect to controls after kelp biomass addition (Absorbance at 235 nm 1.2 ± 0.3 and 1.0 ± 0.2 for M and U, respectively, controls <0.2, t = 4 days). Shifts in microbial community structure (based on 16S rRNA gene amplicon sequencing) were tightly related to the kelp treatment and, to a lesser extent, to the sediment provenance (Principal Coordinates Analysis, 80 % of variation explained in the first two axes). Dissolved oxygen, pH, salinity, alginolytic potential, Absorbance at 235 and 600 nm, total N, total C, and SUVA index correlated significantly with community structure. Differentially abundant populations between kelp-amended treatments and controls included members of the Flavobacteriia class (Algibacter and Polaribacter), and Gammaproteobacteria (Psychromonas and Marinomonas), among others. Metagenomes of M and U-amended sediments contained sequences from 18 of the 19 enzyme families related to alginate or fucoidan degradation. Specific taxonomic groups were associated with enzyme classes targeting different substrates, suggesting niche differentiation. This work expands our knowledge on the patterns of microbial assemblages from intertidal sediments in response to kelp biomass inputs.}, } @article {pmid36240916, year = {2023}, author = {Ma, T and Cheng, C and Xing, L and Sun, Y and Wu, G}, title = {Quorum sensing responses of r-/K-strategists Nitrospira in continuous flow and sequencing batch nitrifying biofilm reactors.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 1}, pages = {159328}, doi = {10.1016/j.scitotenv.2022.159328}, pmid = {36240916}, issn = {1879-1026}, mesh = {*Quorum Sensing ; *Nitrites/metabolism ; Biofilms ; Nitrification ; Acyl-Butyrolactones/metabolism ; Bacteria/metabolism ; }, abstract = {A better understanding of r-/K-strategists nitrifiers will help to balance the design and operation of bioprocesses for efficient pollution removal from wastewater. The objectives of study were to investigate the nitrite oxidation biokinetics, biofilm property, microbial community and quorum sensing (QS) of nitrifying biofilm in a continuously flow reactor (CFR) and a sequencing batch reactor (SBR). Results showed that nitrite-oxidizing bacteria were estimated to have a nitrite half saturation constant of 76.23 and 224.73 μM in CFR and SBR, respectively. High-throughput and metagenomic sequencing results showed that Nitrospira and Candidatus Nitrospira defluvii were the dominated nitrite-oxidizing taxa performing nitrite oxidation in both reactors. Nitrifying biofilm developed in CFR and SBR showed obviously different properties. Biofilm in SBR had an obviously higher ratio of polysaccharide and protein in extracellular polymeric substances, and higher thickness than in CFR. Metagenomics and chemical analysis revealed various types of acyl-homoserine lactone (AHL) circuit genes (e.g., luxI, lasI, hdtS) and four types of AHL signaling substances (e.g., C6-HSL, C8-HSL, C10-HSL and 3-oxo-C10-HSL) in nitrifying biofilm. The concentrations of these AHLs in biomass and water phases were obviously higher in SBR than that in CFR. Together, AHLs-based QS might affect the formation of nitrifying biofilm and thus contribute to the different biokinetics of Nitrospira in CFR and SBR. Our insights may reveal the molecular mechanism of Nitrospira for different biokinetics, and indicate the AHL association with Nitrospira adaptation to various conditions.}, } @article {pmid36240665, year = {2023}, author = {Okoye, CO and Wang, Y and Gao, L and Wu, Y and Li, X and Sun, J and Jiang, J}, title = {The performance of lactic acid bacteria in silage production: A review of modern biotechnology for silage improvement.}, journal = {Microbiological research}, volume = {266}, number = {}, pages = {127212}, doi = {10.1016/j.micres.2022.127212}, pmid = {36240665}, issn = {1618-0623}, mesh = {Animals ; Silage/analysis/microbiology ; *Lactobacillales ; Lactobacillus/genetics/metabolism ; Fermentation ; Biotechnology ; *Agricultural Inoculants ; }, abstract = {Ensiling is a microbial-driven process used to preserve fresh forage in bio-refinery and animal production. The biochemical changes that ensue during ensiling have aided the search for new silage additives, emphasizing the potential of certain microbial strains that are more efficient in biopreservation. Lactic acid bacteria (LAB) species are widely recognized for their varied application as additives in the fermentation of crops or forage biomasses during ensiling. However, inconsistency in silage quality in recent times could be interpreted by the lack of information on gene expression and molecular mechanisms of microbiota involved in silage production. Modern research has focused on unraveling nutrient-rich animal feed with improved LAB inoculants. Therefore, this review elucidates the role of LAB inoculants in silage production as well as the modern biotechnology approaches, including metabolomics, proteomics, metagenomics, genomics, transcriptomics, and genetic manipulation, which are powerful tools for identifying, improving, and developing high-performance LAB strains. In addition, the review highlighted the trends and future perspectives of LAB development for silage improvement, pertinent for animal feed breakthroughs in sustainable agriculture.}, } @article {pmid36240278, year = {2022}, author = {Oki, H and Kawahara, K and Iimori, M and Imoto, Y and Nishiumi, H and Maruno, T and Uchiyama, S and Muroga, Y and Yoshida, A and Yoshida, T and Ohkubo, T and Matsuda, S and Iida, T and Nakamura, S}, title = {Structural basis for the toxin-coregulated pilus-dependent secretion of Vibrio cholerae colonization factor.}, journal = {Science advances}, volume = {8}, number = {41}, pages = {eabo3013}, pmid = {36240278}, issn = {2375-2548}, mesh = {Bacterial Proteins/metabolism ; *Cholera/metabolism ; Fimbriae Proteins/genetics/metabolism ; Fimbriae, Bacterial ; Humans ; *Vibrio cholerae/metabolism ; }, abstract = {Colonization of the host intestine is the most important step in Vibrio cholerae infection. The toxin-coregulated pilus (TCP), an operon-encoded type IVb pilus (T4bP), plays a crucial role in this process, which requires an additional secreted protein, TcpF, encoded on the same TCP operon; however, its mechanisms of secretion and function remain elusive. Here, we demonstrated that TcpF interacts with the minor pilin, TcpB, of TCP and elucidated the crystal structures of TcpB alone and in complex with TcpF. The structural analyses reveal how TCP recognizes TcpF and its secretory mechanism via TcpB-dependent pilus elongation and retraction. Upon binding to TCP, TcpF forms a flower-shaped homotrimer with its flexible N terminus hooked onto the trimeric interface of TcpB. Thus, the interaction between the minor pilin and the N terminus of the secreted protein, namely, the T4bP secretion signal, is key for V. cholerae colonization and is a new potential therapeutic target.}, } @article {pmid36239871, year = {2023}, author = {Haji Zamani, N and Hosseini, H and Ziafati Kafi, Z and Sadri, N and Hojabr Rajeoni, A and Esmaeelzadeh Dizaji, R and Molouki, A and FallahMehrabadi, MH and Abdoshah, M and Ghalyanchilangeroudi, A}, title = {Whole-genome characterization of avian picornaviruses from diarrheic broiler chickens co-infected with multiple picornaviruses in Iran.}, journal = {Virus genes}, volume = {59}, number = {1}, pages = {79-90}, pmid = {36239871}, issn = {1572-994X}, mesh = {Animals ; *Picornaviridae ; Chickens ; Phylogeny ; Iran ; Genome, Viral ; Diarrhea/veterinary/genetics ; *Poultry Diseases ; }, abstract = {Gastrointestinal symptoms in poultry are caused by several factors, such as infecting viruses. Several avian picornaviruses can cause diarrhea in these valuable animals. Poultry flocks in Iran suffer from gastrointestinal diseases, and information on picornaviruses is limited. In this study, two genera of avian picornaviruses were isolated from poultry and identified by the viral metagenomics. Fecal samples were collected from broiler chicken flocks affected with diarrhea from Gilan province Iran. The results showed that Eastern chicken flocks carried two genera of picornaviridae belonging to Sicinivirus A (SiV A) and Megrivirus C (MeV C). The Western chicken flocks carried SiV A based on whole-genome sequencing data. SiV A had type II [IRES] and MeV C contained a type IVB [IRES] 5'UTR. Phylogenetic results showed that all these three picornaviruses were similar to the Hungarian isolates. Interestingly, two different picornavirus genera were simultaneously co-infected with Eastern flocks. This phenomenon could increase and facilitate the recombination and evolution rate of picornaviruses and consequently cause this diversity of gastrointestinal diseases in poultry. This is the first report and complete genome sequencing of Sicinivirus and Megrivirus in Iran. Further studies are needed to evaluate the pathogenic potential of these picornaviruses.}, } @article {pmid36239777, year = {2023}, author = {Tian, C and Lv, Y and Yang, Z and Zhang, R and Zhu, Z and Ma, H and Li, J and Zhang, Y}, title = {Microbial Community Structure and Metabolic Potential at the Initial Stage of Soil Development of the Glacial Forefields in Svalbard.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {933-946}, pmid = {36239777}, issn = {1432-184X}, support = {41676177//National Natural Science Foundation of China/ ; 41921006//National Natural Science Foundation of China/ ; 41676175//National Natural Science Foundation of China/ ; 41676188//National Natural Science Foundation of China/ ; SL2020MS022//Oceanic Interdisciplinary Program of Shanghai Jiao Tong University/ ; 21TQ1400201//Shanghai Pilot Program for Basic Research of Shanghai Jiao Tong University/ ; }, mesh = {*Soil/chemistry ; Svalbard ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Microbiota/genetics ; Ice Cover/microbiology ; Soil Microbiology ; }, abstract = {Microbial communities have been identified as the primary inhabitants of Arctic forefields. However, the metabolic potential of microbial communities in these newly exposed soils remains underexplored due to limited access. Here, we sampled the very edge of the glacial forefield in Svalbard and performed the 16S rRNA genes and metagenomic analysis to illustrate the ecosystem characteristics. Burkholderiales and Micrococcales were the dominant bacterial groups at the initial stage of soil development of glacial forefields. 214 metagenome-assembled genomes were recovered from glacier forefield microbiome datasets, including only 2 belonging to archaea. Analysis of these metagenome-assembled genomes revealed that 41% of assembled genomes had the genetic potential to use nitrate and nitrite as electron acceptors. Metabolic pathway reconstruction for these microbes suggested versatility for sulfide and thiosulfate oxidation, H2 and CO utilization, and CO2 fixation. Our results indicate the importance of anaerobic processes in elemental cycling in the glacial forefields. Besides, a range of genes related to adaption to low temperature and other stresses were detected, which revealed the presence of diverse mechanisms of adaption to the extreme environment of Svalbard. This research provides ecological insight into the initial stage of the soil developed during the retreating of glaciers.}, } @article {pmid36239472, year = {2023}, author = {Hemstrom, W and Jones, M}, title = {snpR: User friendly population genomics for SNP data sets with categorical metadata.}, journal = {Molecular ecology resources}, volume = {23}, number = {4}, pages = {962-973}, doi = {10.1111/1755-0998.13721}, pmid = {36239472}, issn = {1755-0998}, mesh = {Ecosystem ; Genomics ; Metadata ; *Metagenomics ; *Software ; *Polymorphism, Single Nucleotide ; }, abstract = {The analysis of genomic data can be an intimidating process, particularly for researchers who are not experienced programmers. Commonly used analyses are spread across many programs, each requiring their own specific input formats, and so data must often be repeatedly reorganized and transformed into new formats. Analyses often require splitting data according to metadata variables such as population or family, which can be challenging to manage in large data sets. Here, we introduce snpR, a user-friendly data analysis package in R for processing SNP genomic data. snpR is designed to automate data subsetting and analyses across categorical metadata while also streamlining repeated analyses by integrating approaches contained in many different packages in a single ecosystem. snpR facilitates iterative and efficient analyses centred on a single R object for an entire analysis pipeline.}, } @article {pmid36239393, year = {2022}, author = {Hickl, O and Queirós, P and Wilmes, P and May, P and Heintz-Buschart, A}, title = {binny: an automated binning algorithm to recover high-quality genomes from complex metagenomic datasets.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {6}, pages = {}, pmid = {36239393}, issn = {1477-4054}, support = {PRIDE/11823097//National Research Fund/ ; ERC-CoG 863664/ERC_/European Research Council/International ; }, mesh = {*Metagenome ; Metagenomics/methods ; Algorithms ; Cluster Analysis ; *Microbiota/genetics ; }, abstract = {The reconstruction of genomes is a critical step in genome-resolved metagenomics and for multi-omic data integration from microbial communities. Here, we present binny, a binning tool that produces high-quality metagenome-assembled genomes (MAG) from both contiguous and highly fragmented genomes. Based on established metrics, binny outperforms or is highly competitive with commonly used and state-of-the-art binning methods and finds unique genomes that could not be detected by other methods. binny uses k-mer-composition and coverage by metagenomic reads for iterative, nonlinear dimension reduction of genomic signatures as well as subsequent automated contig clustering with cluster assessment using lineage-specific marker gene sets. When compared with seven widely used binning algorithms, binny provides substantial amounts of uniquely identified MAGs and almost always recovers the most near-complete ($\gt 95\%$ pure, $\gt 90\%$ complete) and high-quality ($\gt 90\%$ pure, $\gt 70\%$ complete) genomes from simulated datasets from the Critical Assessment of Metagenome Interpretation initiative, as well as substantially more high-quality draft genomes, as defined by the Minimum Information about a Metagenome-Assembled Genome standard, from a real-world benchmark comprised of metagenomes from various environments than any other tested method.}, } @article {pmid36239235, year = {2022}, author = {Ciuoderis, KA and Berg, MG and Perez, LJ and Hadji, A and Perez-Restrepo, LS and Aristizabal, LC and Forberg, K and Yamaguchi, J and Cardona, A and Weiss, S and Qiu, X and Hernandez-Ortiz, JP and Averhoff, F and Cloherty, GA and Osorio, JE}, title = {Oropouche virus as an emerging cause of acute febrile illness in Colombia.}, journal = {Emerging microbes & infections}, volume = {11}, number = {1}, pages = {2645-2657}, pmid = {36239235}, issn = {2222-1751}, mesh = {Humans ; Colombia/epidemiology ; Phylogeny ; *Bunyaviridae Infections/complications/epidemiology ; }, abstract = {Arbovirus infections are frequent causes of acute febrile illness (AFI) in tropical countries. We conducted health facility-based AFI surveillance at four sites in Colombia (Cucuta, Cali, Villavicencio, Leticia) during 2019-2022. Demographic, clinical and risk factor data were collected from persons with AFI that consented to participate in the study (n = 2,967). Serologic specimens were obtained and tested for multiple pathogens by RT-PCR and rapid test (Antigen/IgM), with 20.7% identified as dengue positive from combined testing. Oropouche virus (OROV) was initially detected in serum by metagenomic next-generation sequencing (mNGS) and virus target capture in a patient from Cúcuta. Three additional infections from Leticia were confirmed by conventional PCR, sequenced, and isolated in tissue culture. Phylogenetic analysis determined there have been at least two independent OROV introductions into Colombia. To assess OROV spread, a RT-qPCR dual-target assay was developed which identified 87/791 (10.9%) viremic cases in AFI specimens from Cali (3/53), Cucuta (3/19), Villavicencio (38/566), and Leticia (43/153). In parallel, an automated anti-nucleocapsid antibody assay detected IgM in 27/503 (5.4%) and IgG in 92/568 (16.2%) patients screened, for which 24/68 (35.3%) of PCR positives had antibodies. Dengue was found primarily in people aged <18 years and linked to several clinical manifestations (weakness, skin rash and petechiae), whereas Oropouche cases were associated with the location, climate phase, and odynophagia symptom. Our results confirm OROV as an emerging pathogen and recommend increased surveillance to determine its burden as a cause of AFI in Colombia.}, } @article {pmid36239189, year = {2023}, author = {Ghorbani, Y and Schwenger, KJP and Sharma, D and Jung, H and Yadav, J and Xu, W and Lou, W and Poutanen, S and Hota, SS and Comelli, EM and Philpott, D and Jackson, TD and Okrainec, A and Gaisano, HY and Allard, JP}, title = {Effect of faecal microbial transplant via colonoscopy in patients with severe obesity and insulin resistance: A randomized double-blind, placebo-controlled Phase 2 trial.}, journal = {Diabetes, obesity & metabolism}, volume = {25}, number = {2}, pages = {479-490}, doi = {10.1111/dom.14891}, pmid = {36239189}, issn = {1463-1326}, support = {TB2-138775//CIHR/Canada ; }, mesh = {Humans ; *Insulin Resistance ; *Obesity, Morbid ; Quality of Life ; Obesity/complications/therapy ; Colonoscopy ; Double-Blind Method ; }, abstract = {AIM: To assess the effects of faecal microbial transplant (FMT) from lean people to subjects with obesity via colonoscopy.

MATERIAL AND METHODS: In a double-blind, randomized controlled trial, subjects with a body mass index ≥ 35 kg/m[2] and insulin resistance were randomized, in a 1:1 ratio in blocks of four, to either allogenic (from healthy lean donor; n = 15) or autologous FMT (their own stool; n = 13) delivered in the caecum and were followed for 3 months. The main outcome was homeostatic model assessment of insulin resistance (HOMA-IR) and secondary outcomes were glycated haemoglobin levels, lipid profile, weight, gut hormones, endotoxin, appetite measures, intestinal microbiome (IM), metagenome, serum/faecal metabolites, quality of life, anxiety and depression scores.

RESULTS: In the allogenic versus autologous groups, HOMA-IR and clinical variables did not change significantly, but IM and metabolites changed favourably (P < 0.05): at 1 month, Coprococcus, Bifidobacterium, Bacteroides and Roseburia increased, and Streptococcus decreased; at 3 months, Bacteroides and Blautia increased. Several species also changed significantly. For metabolites, at 1 month, serum kynurenine decreased and faecal indole acetic acid and butenylcarnitine increased, while at 3 months, serum isoleucine, leucine, decenoylcarnitine and faecal phenylacetic acid decreased. Metagenomic pathway representations and network analyses assessing relationships with clinical variables, metabolites and IM were significantly enhanced in the allogenic versus autologous groups. LDL and appetite measures improved in the allogenic (P < 0.05) but not in the autologous group.

CONCLUSIONS: Overall, in those with obeisty, allogenic FMT via colonoscopy induced favourable changes in IM, metabolites, pathway representations and networks even though other metabolic variables did not change. LDL and appetite variables may also benefit.}, } @article {pmid36238714, year = {2022}, author = {Merrill, BD and Carter, MM and Olm, MR and Dahan, D and Tripathi, S and Spencer, SP and Yu, B and Jain, S and Neff, N and Jha, AR and Sonnenburg, ED and Sonnenburg, JL}, title = {Ultra-deep Sequencing of Hadza Hunter-Gatherers Recovers Vanishing Gut Microbes.}, journal = {bioRxiv : the preprint server for biology}, volume = {}, number = {}, pages = {}, pmid = {36238714}, support = {DP1 AT009892/AT/NCCIH NIH HHS/United States ; F32 DK128865/DK/NIDDK NIH HHS/United States ; R01 DK085025/DK/NIDDK NIH HHS/United States ; T32 AI007328/AI/NIAID NIH HHS/United States ; }, abstract = {The gut microbiome is a key modulator of immune and metabolic health. Human microbiome data is biased towards industrialized populations, providing limited understanding of the distinct and diverse non-industrialized microbiomes. Here, we performed ultra-deep metagenomic sequencing and strain cultivation on 351 fecal samples from the Hadza, hunter-gatherers in Tanzania, and comparative populations in Nepal and California. We recover 94,971 total genomes of bacteria, archaea, bacteriophages, and eukaryotes, 43% of which are absent from existing unified datasets. Analysis of in situ growth rates, genetic pN/pS signatures, high-resolution strain tracking, and 124 gut-resident species vanishing in industrialized populations reveals differentiating dynamics of the Hadza gut microbiome. Industrialized gut microbes are enriched in genes associated with oxidative stress, possibly a result of microbiome adaptation to inflammatory processes. This unparalleled view of the Hadza gut microbiome provides a valuable resource that expands our understanding of microbes capable of colonizing the human gut and clarifies the extensive perturbation brought on by the industrialized lifestyle.}, } @article {pmid36238454, year = {2022}, author = {Xue, F and Mo, Q and Ma, P and Zhang, J and Wang, S and Zheng, C and Sun, Y and Liu, M and Yang, Z and Bai, H}, title = {Metagenomic insights into the modulatory effects of kelp powder (Thallus laminariae)-Treated dairy milk on growth performances and physiological lipometabolic processes of kunming mice.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {949809}, pmid = {36238454}, issn = {2296-861X}, abstract = {Kelp powder, supplemented with a dairy cow diet, effectively improved the milk polyunsaturated fatty acids (PUFAs) content. However, little information exists on the downstream effects of the kelp-treated milk on body health, gut microbiota, and nutrient metabolism. For this purpose, 48 3-week old Kunming (KM) male mice with an average body weight of 16.1 g ± 0.2 g were randomly divided into the control treatment (CON, fed with standard chow), the common milk supplement treatment (Milk), and the kelp powder-treated milk supplement treatment (KPM). The experiment lasted for 35 days, with a 7-day long adaptive period and a 28-day long main trial. Phenotypic parameters including growth performances and serum lipids-related parameters were first measured, and results indicated that Milk and KPM supplement significantly promoted the total body weight gain (P < 0.05), while significantly decreasing the feed conversion ratio compared with CON (P < 0.05). No significant differences were observed in the blood lipids content among all three treatments, however, the triglyceride content showed a decreasing trend after KPM supplement treatment. Further, activities of liver lipometabolic-related enzymes were investigated to determine the underlying factors that impacted physiological lipid metabolism. KPM treatment showed a significant reductive effect on the activity of lipogenesis-related enzymes, such as FAS and ACC, while a significant stimulative effect on the activity of lipolysis-related enzymes included the ATGL and CPT1 compared with CON (P < 0.05). Finally, gastrointestinal tract development and cecal microbiota community that correlated with body lipid degradation and absorption were measured to determine the underlying mechanism of KPM supplementation on physiological lipid metabolism. Results indicated that supplementation with KPM significantly enhanced cecal bacteria diversity which was reflected in the significant increase of Chao1 and ACE indexes. Besides, starch-degraded bacteria such as Faecalibacterium, Ruminococcaceae, and Streptococcus are significant decreased (P < 0.05), while cellulose-degraded bacteria including Parabacteroides, Prevotella, Lactobacillus, Clostridium, and Bifidobacterium are significantly increased (P < 0.05) after KPM supplement, which may further restrict the energy generation and therefore reduce the lipid deposition. In summary, kelp supplement helped increase the milk PUFAs content, enhance the bacterial diversity and relative abundances of probiotics, which finally modulated physiological lipid metabolism, and promote growth performances.}, } @article {pmid36237437, year = {2022}, author = {Wang, C and You, Z and Fu, J and Chen, S and Bai, D and Zhao, H and Song, P and Jia, X and Yuan, X and Xu, W and Zhao, Q and Pang, F}, title = {Application of metagenomic next-generation sequencing in the diagnosis of pulmonary invasive fungal disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {949505}, pmid = {36237437}, issn = {2235-2988}, mesh = {C-Reactive Protein ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Invasive Fungal Infections/diagnosis ; *Lung Diseases, Fungal/diagnosis/microbiology ; Metagenomics/methods ; *Mycoses ; *Pneumonia/microbiology ; Procalcitonin ; Retrospective Studies ; Sensitivity and Specificity ; Serum Albumin ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is increasingly being used to detect pathogens directly from clinical specimens. However, the optimal application of mNGS and subsequent result interpretation can be challenging. In addition, studies reporting the use of mNGS for the diagnosis of invasive fungal infections (IFIs) are rare.

OBJECTIVE: We critically evaluated the performance of mNGS in the diagnosis of pulmonary IFIs, by conducting a multicenter retrospective analysis. The methodological strengths of mNGS were recognized, and diagnostic cutoffs were determined.

METHODS: A total of 310 patients with suspected pulmonary IFIs were included in this study. Conventional microbiological tests (CMTs) and mNGS were performed in parallel on the same set of samples. Receiver operating characteristic (ROC) curves were used to evaluate the performance of the logarithm of reads per kilobase per million mapped reads [lg(RPKM)], and read counts were used to predict true-positive pathogens.

RESULT: The majority of the selected patients (86.5%) were immunocompromised. Twenty species of fungi were detected by mNGS, which was more than was achieved with standard culture methods. Peripheral blood lymphocyte and monocyte counts, as well as serum albumin levels, were significantly negatively correlated with fungal infection. In contrast, C-reactive protein and procalcitonin levels showed a significant positive correlation with fungal infection. ROC curves showed that mNGS [and especially lg(RPKM)] was superior to CMTs in its diagnostic performance. The area under the ROC curve value obtained for lg(RPKM) in the bronchoalveolar lavage fluid of patients with suspected pulmonary IFIs, used to predict true-positive pathogens, was 0.967, and the cutoff value calculated from the Youden index was -5.44.

CONCLUSIONS: In this study, we have evaluated the performance of mNGS-specific indicators that can identify pathogens in patients with IFIs more accurately and rapidly than CMTs, which will have important clinical implications.}, } @article {pmid36237436, year = {2022}, author = {Zhang, J and Gao, L and Zhu, C and Jin, J and Song, C and Dong, H and Li, Z and Wang, Z and Chen, Y and Yang, Z and Tan, Y and Wang, L}, title = {Clinical value of metagenomic next-generation sequencing by Illumina and Nanopore for the detection of pathogens in bronchoalveolar lavage fluid in suspected community-acquired pneumonia patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1021320}, pmid = {36237436}, issn = {2235-2988}, mesh = {Bacteria/genetics ; Bronchoalveolar Lavage Fluid/microbiology ; *Community-Acquired Infections/diagnosis ; Fungi/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; *Nanopores ; *Pneumonia/diagnosis ; Sensitivity and Specificity ; }, abstract = {At present, metagenomic next-generation sequencing (mNGS) based on Illumina platform has been widely reported for pathogen detection. There are few studies on the diagnosis of major pathogens and treatment regulation using mNGS based on Illumina versus Nanopore. We aim to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) by Illumina and Nanopore for the detection of pathogens in bronchoalveolar lavage fluid (BALF) in suspected community-acquired pneumonia (CAP) patients. BALF samples collected from 66 suspected CAP patients within 48 hours of hospitalization were divided into two parts, one for conventional culture and the other for mNGS by two platforms (Illumina and Nanopore). The clinical value based on infection diagnosis, diagnostic performance for main pathogens and treatment guidance were assessed. More types of species were detected by Nanopore than Illumina, especially in viruses, fungus and mycobacterium. Illumina and Nanopore showed similar detectability in bacterium except for mycobacterium tuberculosis complex/nontuberculosis mycobacteria. Pathogenic infection was established or excluded in 53 of 66 patients. There was little difference in the coincidence rate between Illumina and Nanopore with the clinical diagnosis, but both were superior to the culture (57.81%, 59.38%, 25%, respectively). Compared with Illumina, the diagnostic area under the curve of Nanopore was higher in fungi, but lower in bacteria and Chlamydia psittaci. There was no statistically significant difference between Illumina and Nanopore in guiding drug treatment (56.1% vs. 50%, p=0.43), but both were superior to the culture (56.1% vs. 28.8%, p=0.01; 50% vs. 28.8%, p=0.01). Single inflammatory indicators could not be used to determine whether the patients with culture-negative BALF were established or excluded from infection. The species detected at 1 h and 4 h by Nanopore were consistent to some extent, and its turn-around time (TAT) was significantly shorter than Illumina (p<0.01). Illumina and Nanopore both have its own advantages in pathogenic diagnosis and play similar roles in infection diagnosis and guiding clinical treatment. Nanopore has a relatively short TAT, which may be promising in rapid etiological diagnosis of acute and critically ill patients.}, } @article {pmid36237422, year = {2022}, author = {Yu, L and Zhang, Y and Zhou, J and Zhang, Y and Qi, X and Bai, K and Lou, Z and Li, Y and Xia, H and Bu, H}, title = {Metagenomic next-generation sequencing of cell-free and whole-cell DNA in diagnosing central nervous system infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {951703}, pmid = {36237422}, issn = {2235-2988}, mesh = {*Cell-Free Nucleic Acids ; *Central Nervous System Infections/diagnosis ; DNA ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Central nervous system (CNS) infections pose a fatal risk to patients. However, the limited sample volumes of cerebrospinal fluid (CSF) and low detection efficiency seriously hinder the accurate detection of pathogens using conventional methods.

METHODS: We evaluated the performance of metagenomics next-generation sequencing (mNGS) in diagnosing CNS infections. CSF samples from 390 patients clinically diagnosed with CNS infections were used for the mNGS of cell-free DNA (cfDNA) (n =394) and whole-cell DNA (wcDNA) (n =150).

RESULTS: The sensitivity of mNGS using cfDNA was 60.2% (237/394, 95% confidence interval [CI] 55.1%-65.0%), higher than that of mNGS using wcDNA (32.0%, 95% [CI] 24.8%-40.2%, 48/150) and conventional methods (20.9%, 95% [CI] 16.2%-26.5%, 54/258) (P < 0.01, respectively). The accuracy of mNGS using cfDNA in positive samples was 82.6%. Most of viral (72.6%) and mycobacterial (68.8%) pathogens were only detected by the mNGS of cfDNA. Meningitis and encephalitis with Streptococcus pneumoniae infection might be more likely to result in critically ill diseases, while Human alphaherpesvirus 3 was prone to cause non-critically ill diseases.

CONCLUSIONS: This is the first report on evaluating and emphasizing the importance of mNGS using CSF cfDNA in diagnosing CNS infections, and its extensive application in diagnosing CNS infections could be expected, especially for viral and mycobacterial CNS infections.}, } @article {pmid36235725, year = {2022}, author = {Ramos-Lopez, O and Martinez, JA and Milagro, FI}, title = {Holistic Integration of Omics Tools for Precision Nutrition in Health and Disease.}, journal = {Nutrients}, volume = {14}, number = {19}, pages = {}, pmid = {36235725}, issn = {2072-6643}, support = {CB12/03/30002//Centro de Investigación Biomédica en Red/ ; Obekit (PT024)//Gobierno de Navarra/ ; Microbiota (PI035)//Gobierno de Navarra/ ; Nutribiota (0011-1411-2018-000040)//Gobierno de Navarra/ ; (UABC-PTC-796)//PRODEP-Mexico/ ; }, mesh = {Epigenomics/methods ; Genomics/methods ; Humans ; Metabolomics/methods ; Proteomics/methods ; *RNA, Long Noncoding ; }, abstract = {The combination of multiple omics approaches has emerged as an innovative holistic scope to provide a more comprehensive view of the molecular and physiological events underlying human diseases (including obesity, dyslipidemias, fatty liver, insulin resistance, and inflammation), as well as for elucidating unique and specific metabolic phenotypes. These omics technologies include genomics (polymorphisms and other structural genetic variants), epigenomics (DNA methylation, histone modifications, long non-coding RNA, telomere length), metagenomics (gut microbiota composition, enterotypes), transcriptomics (RNA expression patterns), proteomics (protein quantities), and metabolomics (metabolite profiles), as well as interactions with dietary/nutritional factors. Although more evidence is still necessary, it is expected that the incorporation of integrative omics could be useful not only for risk prediction and early diagnosis but also for guiding tailored dietary treatments and prognosis schemes. Some challenges include ethical and regulatory issues, the lack of robust and reproducible results due to methodological aspects, the high cost of omics methodologies, and high-dimensional data analyses and interpretation. In this review, we provide examples of system biology studies using multi-omics methodologies to unravel novel insights into the mechanisms and pathways connecting the genotype to clinically relevant traits and therapy outcomes for precision nutrition applications in health and disease.}, } @article {pmid36233330, year = {2022}, author = {Zhang, Y and Ma, C and Han, Y and Jin, H and Luo, H and Hao, X and Li, M}, title = {Integrative Analysis of the Nasal Microbiota and Serum Metabolites in Bovines with Respiratory Disease by 16S rRNA Sequencing and Gas Chromatography/Mass Selective Detector-Based Metabolomics.}, journal = {International journal of molecular sciences}, volume = {23}, number = {19}, pages = {}, pmid = {36233330}, issn = {1422-0067}, support = {31960036//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Cattle ; *Cattle Diseases ; Chromatography, Gas ; Lactic Acid ; Metabolomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Respiration Disorders ; *Respiratory Tract Diseases/veterinary ; Sarcosine ; }, abstract = {Bovine respiratory disease (BRD) continues to pose a serious threat to the cattle industry, resulting in substantial economic losses. As a multifactorial disease, pathogen infection and respiratory microbial imbalance are important causative factors in the occurrence and development of BRD. Integrative analyses of 16S rRNA sequencing and metabolomics allow comprehensive identification of the changes in microbiota and metabolism associated with BRD, making it possible to determine which pathogens are responsible for the disease and to develop new therapeutic strategies. In our study, 16S rRNA sequencing and metagenomic analysis were used to describe and compare the composition and diversity of nasal microbes in healthy cattle and cattle with BRD from different farms in Yinchuan, Ningxia, China. We found a significant difference in nasal microbial diversity between diseased and healthy bovines; notably, the relative abundance of Mycoplasma bovis and Pasteurella increased. This indicated that the composition of the microbial community had changed in diseased bovines compared with healthy ones. The data also strongly suggested that the reduced relative abundance of probiotics, including Pasteurellales and Lactobacillales, in diseased samples contributes to the susceptibility to bovine respiratory disease. Furthermore, serum metabolomic analysis showed altered concentrations of metabolites in BRD and that a significant decrease in lactic acid and sarcosine may impair the ability of bovines to generate energy and an immune response to pathogenic bacteria. Based on the correlation analysis between microbial diversity and the metabolome, lactic acid (2TMS) was positively correlated with Gammaproteobacteria and Bacilli and negatively correlated with Mollicutes. In summary, microbial communities and serum metabolites in BRD were characterized by integrative analysis. This study provides a reference for monitoring biomarkers of BRD, which will be critical for the prevention and treatment of BRD in the future.}, } @article {pmid36233028, year = {2022}, author = {Kato, T and Kagawa, M and Suda, W and Tsuboi, Y and Inoue-Suzuki, S and Kikuchi, J and Hattori, M and Ohta, T and Ohno, H}, title = {Integrated Multi-Omics Analysis Reveals Differential Effects of Fructo-Oligosaccharides (FOS) Supplementation on the Human Gut Ecosystem.}, journal = {International journal of molecular sciences}, volume = {23}, number = {19}, pages = {}, pmid = {36233028}, issn = {1422-0067}, support = {not applicable//Japan Aerospace Exploration Agency/ ; }, mesh = {Fructose/pharmacology ; Humans ; Immunoglobulin A/metabolism ; *Microbiota ; *Oligosaccharides/metabolism/pharmacology ; Prebiotics ; }, abstract = {Changes in the gut ecosystem, including the microbiome and the metabolome, and the host immune system after fructo-oligosaccharide (FOS) supplementation were evaluated. The supplementation of FOS showed large inter-individual variability in the absolute numbers of fecal bacteria and an increase in Bifidobacterium. The fecal metabolome analysis revealed individual variability in fructose utilization in response to FOS supplementation. In addition, immunoglobulin A(IgA) tended to increase upon FOS intake, and peripheral blood monocytes significantly decreased upon FOS intake and kept decreasing in the post-FOS phase. Further analysis using a metagenomic approach showed that the differences could be at least in part due to the differences in gene expressions of enzymes that are involved in the fructose metabolism pathway. While the study showed individual differences in the expected health benefits of FOS supplementation, the accumulation of "personalized" knowledge of the gut ecosystem with its genetic expression may enable effective instructions on prebiotic consumption to optimize health benefits for individuals in the future.}, } @article {pmid36232990, year = {2022}, author = {Kobayashi, T and Iwaki, M and Nakajima, A and Nogami, A and Yoneda, M}, title = {Current Research on the Pathogenesis of NAFLD/NASH and the Gut-Liver Axis: Gut Microbiota, Dysbiosis, and Leaky-Gut Syndrome.}, journal = {International journal of molecular sciences}, volume = {23}, number = {19}, pages = {}, pmid = {36232990}, issn = {1422-0067}, mesh = {Dysbiosis/complications ; Endotoxins/metabolism ; Fructose/metabolism ; *Gastrointestinal Microbiome ; Humans ; Liver/metabolism ; *Non-alcoholic Fatty Liver Disease/metabolism ; }, abstract = {Global lifestyle changes have led to an increased incidence of non-alcoholic fatty liver disease (NAFLD) and non-alcoholic steatohepatitis (NASH), requiring further in-depth research to understand the mechanisms and develop new therapeutic strategies. In particular, high-fat and high-fructose diets have been shown to increase intestinal permeability, which can expose the liver to endotoxins. Indeed, accumulating evidence points to a link between these liver diseases and the intestinal axis, including dysbiosis of the gut microbiome and leaky-gut syndrome. Here, we review the mechanisms contributing to these links between the liver and small intestine in the pathogenesis of NAFLD/NASH, focusing on the roles of intestinal microbiota and their metabolites to influence enzymes essential for proper liver metabolism and function. Advances in next-generation sequencing technology have facilitated analyses of the metagenome, providing new insights into the roles of the intestinal microbiota and their functions in physiological and pathological mechanisms. This review summarizes recent research linking the gut microbiome to liver diseases, offering new research directions to elucidate the detailed mechanisms and novel targets for treatment and prevention.}, } @article {pmid36232865, year = {2022}, author = {Sun, P and Zhu, H and Li, X and Shi, W and Guo, Y and Du, X and Zhang, L and Su, L and Qin, C}, title = {Comparative Metagenomics and Metabolomes Reveals Abnormal Metabolism Activity Is Associated with Gut Microbiota in Alzheimer's Disease Mice.}, journal = {International journal of molecular sciences}, volume = {23}, number = {19}, pages = {}, pmid = {36232865}, issn = {1422-0067}, mesh = {*Alzheimer Disease/pathology ; Amino Acids, Aromatic ; Animals ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Metabolome ; Mice ; Neurotransmitter Agents ; Vitamins ; }, abstract = {A common symptom in Alzheimer's disease (AD) is cognitive decline, of which the potential pathogenesis remains unclear. In order to understand the mechanism of gut microbiota in AD, it is necessary to clarify the relationship between gut microbiota and metabolites. Behavioral tests, pathological examination, metagenomics, and metabolomics were applied to analyze the difference of gut microbiota and metabolome between APP[swe]/PS1[ΔE9] (PAP) mice with cognitive decline and age-matched controls, and their possible correlations. Our results showed that PAP mice and health mice had different structures of the bacterial communities in the gut. The abundances and diversities of the bacterial communities in health mice were higher than in PAP mice by metagenomics analysis. The abundances of Libanicoccus massiliensis, Paraprevotella clara, and Lactobacillus amylovorus were significantly increased in PAP mice, while the abundances of Turicibacter sanguinis, Dubosiella newyorkensis, and Prevotella oris were greatly reduced. Furthermore, PAP mice possessed peculiar metabolic phenotypes in stool, serum, and hippocampus relative to WT mice, as is demonstrated by alterations in neurotransmitters metabolism, lipid metabolism, aromatic amino acids metabolism, energy metabolism, vitamin digestion and absorption, and bile metabolism. Microbiota-host metabolic correlation analysis suggests that abnormal metabolism in stool, serum, and hippocampus of PAP mice may be modulated by the gut microbiota, especially T. sanguinis, D. newyorkensis, and P. oris. Therefore, abnormal metabolism activity is associated with gut microbiota in Alzheimer's disease mice. Our results imply that modifying host metabolism through targeting gut microbiota may be a novel and viable strategy for the prevention and treatment of AD in the future.}, } @article {pmid36232449, year = {2022}, author = {Frickmann, H and Weinreich, F and Loderstädt, U and Poppert, S and Tannich, E and Bull, J and Kreikemeyer, B and Barrantes, I}, title = {Metagenomic Sequencing for the Diagnosis of Plasmodium spp. with Different Levels of Parasitemia in EDTA Blood of Malaria Patients-A Proof-of-Principle Assessment.}, journal = {International journal of molecular sciences}, volume = {23}, number = {19}, pages = {}, pmid = {36232449}, issn = {1422-0067}, support = {36K2-S-45 1922//Federal Ministry of Defence/ ; }, mesh = {Edetic Acid ; Humans ; *Malaria/diagnosis ; *Nucleic Acids ; Parasitemia/diagnosis ; *Plasmodium/genetics ; Plasmodium falciparum/genetics ; Plasmodium vivax/genetics ; Real-Time Polymerase Chain Reaction ; }, abstract = {Molecular diagnostic approaches are increasingly included in the diagnostic workup and even in the primary diagnosis of malaria in non-endemic settings, where it is difficult to maintain skillful microscopic malaria detection due to the rarity of the disease. Pathogen-specific nucleic acid amplification, however, bears the risk of overlooking other pathogens associated with febrile illness in returnees from the tropics. Here, we assessed the discriminatory potential of metagenomic sequencing for the identification of different Plasmodium species with various parasitemia in EDTA blood of malaria patients. Overall, the proportion of Plasmodium spp.-specific sequence reads in the assessed samples showed a robust positive correlation with parasitemia (Spearman r = 0.7307, p = 0.0001) and a robust negative correlation with cycle threshold (Ct) values of genus-specific real-time PCR (Spearman r = -0.8626, p ≤ 0.0001). Depending on the applied bioinformatic algorithm, discrimination on species level was successful in 50% (11/22) to 63.6% (14/22) instances. Limiting factors for the discrimination on species level were very low parasitemia, species-depending lacking availability of reliable reference genomes, and mixed infections with high variance of the proportion of the infecting species. In summary, metagenomic sequencing as performed in this study is suitable for the detection of malaria in human blood samples, but the diagnostic detection limit for a reliable discrimination on species level remains higher than for competing diagnostic approaches like microscopy and PCR.}, } @article {pmid36231339, year = {2022}, author = {Xu, P and Chen, X and Li, K and Meng, R and Pu, Y}, title = {Metagenomic Analysis of Microbial Alliances for Efficient Degradation of PHE: Microbial Community Structure and Reconstruction of Metabolic Network.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {19}, pages = {}, pmid = {36231339}, issn = {1660-4601}, mesh = {Bacteria ; Biodegradation, Environmental ; Metabolic Networks and Pathways/genetics ; *Microbiota ; *Phenanthrenes/metabolism ; *Polycyclic Aromatic Hydrocarbons/analysis ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Polycyclic aromatic hydrocarbons are a widespread organic pollutant worldwide. In this study, a highly efficient phenanthrene (PHE)-degrading microbial community was enriched from oil extraction soil, which could degrade 500 mg/L PHE within 4 days. Using 16S rRNA sequencing, the dominant bacteria in this community at the phylum level were found to be Proteobacteria, Actinobacteria, and Firmicutes. Metagenomic annotation of genes revealed the metabolic pathways and the contribution of different bacteria to the degradation process. Pseudomonadaceae contributed multiple functional genes in the degradation process. This study revealed the functional genes, metabolic pathways, and microbial interactions of the microbial community, which are expected to provide guidance for practical management.}, } @article {pmid36231135, year = {2022}, author = {Chan, LC and Zhang, Y and Kuang, X and Koohi-Moghadam, M and Wu, H and Lam, TYC and Chiou, J and Wen, C}, title = {Captopril Alleviates Chondrocyte Senescence in DOCA-Salt Hypertensive Rats Associated with Gut Microbiome Alteration.}, journal = {Cells}, volume = {11}, number = {19}, pages = {}, pmid = {36231135}, issn = {2073-4409}, mesh = {Acetates ; Animals ; Antihypertensive Agents ; Captopril/adverse effects ; Chondrocytes ; *Desoxycorticosterone Acetate/adverse effects ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome ; *Hypertension ; RNA, Ribosomal, 16S ; Rats ; }, abstract = {Gut microbiota is the key controller of healthy aging. Hypertension and osteoarthritis (OA) are two frequently co-existing age-related pathologies in older adults. Both are associated with gut microbiota dysbiosis. Hereby, we explore gut microbiome alteration in the Deoxycorticosterone acetate (DOCA)-induced hypertensive rat model. Captopril, an anti-hypertensive medicine, was chosen to attenuate joint damage. Knee joints were harvested for radiological and histological examination; meanwhile, fecal samples were collected for 16S rRNA and shotgun sequencing. The 16S rRNA data was annotated using Qiime 2 v2019.10, while metagenomic data was functionally profiled with HUMAnN 2.0 database. Differential abundance analyses were adopted to identify the significant bacterial genera and pathways from the gut microbiota. DOCA-induced hypertension induced p16INK4a+ senescent cells (SnCs) accumulation not only in the aorta and kidney (p < 0.05) but also knee joint, which contributed to articular cartilage degradation and subchondral bone disturbance. Captopril removed the p16INK4a + SnCs from different organs, partially lowered blood pressure, and mitigated cartilage damage. Meanwhile, these alterations were found to associate with the reduction of Escherichia-Shigella levels in the gut microbiome. As such, gut microbiota dysbiosis might emerge as a metabolic link in chondrocyte senescence induced by DOCA-triggered hypertension. The underlying molecular mechanism warrants further investigation.}, } @article {pmid36231116, year = {2022}, author = {Zeng, Y and Liang, JQ}, title = {Nasal Microbiome and Its Interaction with the Host in Childhood Asthma.}, journal = {Cells}, volume = {11}, number = {19}, pages = {}, pmid = {36231116}, issn = {2073-4409}, mesh = {*Asthma ; Child ; Dysbiosis ; Humans ; Infant ; *Microbiota ; Respiratory System ; *Respiratory Tract Infections ; }, abstract = {Childhood asthma is a major chronic non-communicable disease in infants and children, often triggered by respiratory tract infections. The nasal cavity is a reservoir for a broad variety of commensal microbes and potential pathogens associated with respiratory illnesses including asthma. A healthy nasal microenvironment has protective effects against respiratory tract infections. The first microbial colonisation in the nasal region is initiated immediately after birth. Subsequently, colonisation by nasal microbiota during infancy plays important roles in rapidly establishing immune homeostasis and the development and maturation of the immune system. Dysbiosis of microbiota residing in the mucosal surfaces, such as the nasopharynx and guts, triggers immune modulation, severe infection, and exacerbation events. Nasal microbiome dysbiosis is related to the onset of symptomatic infections. Dynamic interactions between viral infections and the nasal microbiota in early life affect the later development of respiratory infections. In this review, we summarise the existing findings related to nasal microbiota colonisation, dynamic variations, and host-microbiome interactions in childhood health and respiratory illness with a particular examination of asthma. We also discuss our current understanding of biases produced by environmental factors and technical concerns, the importance of standardised research methods, and microbiome modification for the prevention or treatment of childhood asthma. This review lays the groundwork for paying attention to an essential but less emphasized topic and improves the understanding of the overall composition, dynamic changes, and influence of the nasal microbiome associated with childhood asthma.}, } @article {pmid36230772, year = {2022}, author = {Bawaneh, A and Wilson, AS and Levi, N and Howard-McNatt, MM and Chiba, A and Soto-Pantoja, DR and Cook, KL}, title = {Intestinal Microbiota Influence Doxorubicin Responsiveness in Triple-Negative Breast Cancer.}, journal = {Cancers}, volume = {14}, number = {19}, pages = {}, pmid = {36230772}, issn = {2072-6694}, support = {CCR18547795//Susan G. Komen Breast Cancer Foundation/ ; P30CA012197/NH/NIH HHS/United States ; }, abstract = {Triple-negative breast cancer (TNBC) is highly aggressive with a poor 5-year survival rate. Targeted therapy options are limited and most TNBC patients are treated with chemotherapy. This study aimed to determine whether doxorubicin (Dox) shifts the gut microbiome and whether gut microbiome populations influence chemotherapeutic responsiveness. Female BALB/c mice (n = 115) were injected with 4T1-luciferase cells (a murine syngeneic TNBC model) and treated with Dox and/or antibiotics, high-fat diet-derived fecal microbiota transplant (HFD-FMT), or exogenous lipopolysaccharide (LPS). Metagenomic sequencing was performed on fecal DNA samples. Mice that received Dox were stratified into Dox responders or Dox nonresponders. Mice from the Dox responders and antibiotics + Dox groups displayed reduced tumor weight and metastatic burden. Metagenomic analysis showed that Dox was associated with increased Akkermansia muciniphila proportional abundance. Moreover, Dox responders showed an elevated proportional abundance of Akkermansia muciniphila prior to Dox treatment. HFD-FMT potentiated tumor growth and decreased Dox responsiveness. Indeed, lipopolysaccharide, a structural component of Gram-negative bacteria, was increased in the plasma of Dox nonresponders and FMT + Dox mice. Treatment with exogenous LPS increases intestinal inflammation, reduces Dox responsiveness, and increases lung metastasis. Taken together, we show that modulating the gut microbiota through antibiotics, HFD-FMT, or by administering LPS influenced TNBC chemotherapy responsiveness, lung metastasis, and intestinal inflammation.}, } @article {pmid36230584, year = {2022}, author = {Zhang, J and He, Y and Xia, L and Yi, J and Wang, Z and Zhao, Y and Song, X and Li, J and Liu, H and Liang, X and Nie, S and Liu, L}, title = {Expansion of Colorectal Cancer Biomarkers Based on Gut Bacteria and Viruses.}, journal = {Cancers}, volume = {14}, number = {19}, pages = {}, pmid = {36230584}, issn = {2072-6694}, support = {82173602//National Natural Science Foundation of China/ ; 81974491//National Natural Science Foundation of China/ ; BJ GYQZHX2021006//Beijing Bethune Public Welfare Foundation/ ; CXPJJH122006-1003//Chen Xiao-Ping foundation for the development of science and technology of Hubei province/ ; WJ2021Z001//Health Commission of Hubei Province scientific research project/ ; 2020020601012250//Applied Basic Research Program of Wuhan Science and Technology Bureau/ ; }, abstract = {The alterations in gut bacteria are closely related to colorectal cancer. However, studies on adenoma are still scarce. Besides, the associations of gut viruses with colorectal tumor, and the interactions of bacteria with viruses in colorectal tumors are still under exploration. Therefore, a metagenomic sequencing of stool samples from patients with colorectal adenoma (CRA), colorectal cancer (CRC), and healthy controls was performed to identify changes in gut microbiome in patients with colorectal tumors. Five CRC-enriched bacteria (Peptostreptococcus stomatis, Clostridium symbiosum, Hungatella hathewayi, Parvimonas micra, and Gemella morbillorum) were identified as a diagnostic model to identify CRC patients, and the efficacy of the diagnostic model was verifiable in 1523 metagenomic samples from ten cohorts of eight different countries. We identified the positive association of Bacteroides fragilis with PD-L1 expression and PD-1 checkpoint pathway, providing a possible direction for studying bacterial carcinogenesis mechanisms. Furthermore, the increased interactions within the microbiome in patients may play roles in the development of CRC. In conclusion, this study identified novel microbiota combinations with discrimination for colorectal tumor, and revealed the potential interactions of gut bacteria with viruses in the adenoma-carcinoma sequence, which implies that the microbiome, but not only bacteria, should be paid more attention in further studies.}, } @article {pmid36230372, year = {2022}, author = {Yamamoto, FY and Ellis, M and Bowles, PR and Suehs, BA and Carvalho, PLPF and Older, CE and Hume, ME and Gatlin, DM}, title = {Dietary Supplementation of a Commercial Prebiotic, Probiotic and Their Combination Affected Growth Performance and Transient Intestinal Microbiota of Red Drum (Sciaenops ocellatus L.).}, journal = {Animals : an open access journal from MDPI}, volume = {12}, number = {19}, pages = {}, pmid = {36230372}, issn = {2076-2615}, support = {CNPq 207141/2014-2//Brazilian National Council for Scientific and Technological Development/ ; N/A//Texas A&M AgriLife Research/ ; }, abstract = {In the present study, the potential synergism between beneficial lactic acid bacteria (Pediococcus acidilactici) contained in a probiotic and a mixture of fermentable complex carbohydrates and autolyzed brewer's yeast (or prebiotic) were explored in red drum. Four experimental diets were formulated from practical ingredients, and the basal diet was supplemented with either probiotic, prebiotic, or both supplements. Red drum juveniles (~5.5 g) were offered the four experimental diets for 56 days, and at the end of the feeding trial fish fed diets supplemented with probiotic had significantly better weight gain than those fed the non-supplemented diets, and higher protein content in their whole-body composition. Transient intestinal microbiome alpha and beta diversity were significantly affected by the dietary treatments. Interestingly, a higher relative abundance of the lactic acid genus Pediococcus was observed for fish fed diets supplemented with the prebiotic. A higher relative abundance was also observed for the predicted functions of the microbial metagenome, and many of these pathways involved the biosynthesis of essential amino acids, vitamins, and nucleotides. Even though no potential synergistic effect was observed, the individual inclusion of these prebiotic and probiotic supplements positively affected the intestinal health and growth performance of red drum, respectively.}, } @article {pmid36229832, year = {2022}, author = {Buhler, KJ and Fernando, C and Hill, JE and Galloway, T and Carriere, S and Fenton, H and Fauteux, D and Jenkins, EJ}, title = {Combining deep sequencing and conventional molecular approaches reveals broad diversity and distribution of fleas and Bartonella in rodents and shrews from Arctic and Subarctic ecosystems.}, journal = {Parasites & vectors}, volume = {15}, number = {1}, pages = {366}, pmid = {36229832}, issn = {1756-3305}, support = {RGPIN-2018-04900//Natural Sciences and Engineering Research Council of Canada/ ; NST-1718-0012//Polar Knowledge Canada/ ; }, mesh = {Animals ; Arvicolinae ; *Bartonella/genetics ; *Bartonella Infections/epidemiology/veterinary ; Citrate (si)-Synthase/genetics ; DNA, Bacterial/genetics ; DNA, Intergenic ; Ecosystem ; *Flea Infestations/veterinary ; High-Throughput Nucleotide Sequencing ; Rodentia/microbiology ; Shrews ; *Siphonaptera/microbiology ; }, abstract = {BACKGROUND: Bartonella are intracellular bacteria that are transmitted via animal scratches, bites and hematophagous arthropods. Rodents and their associated fleas play a key role in the maintenance of Bartonella worldwide, with > 22 species identified in rodent hosts. No studies have addressed the occurrence and diversity of Bartonella species and vectors for small mammals in Arctic and Subarctic ecosystems, which are increasingly impacted by invasive species and climate change.

METHODS: In this study, we characterized the diversity of rodent fleas using conventional PCR targeting the mitochondrial cytochrome c oxidase II gene (COII) and Bartonella species in rodents and shrews (n = 505) from northern Canada using conventional PCR targeting the ITS (intergenic transcribed spacer) region and gltA (citrate synthase) gene. Metagenomic sequencing of a portion of the gltA gene was completed on a subset of 42 rodents and four rodent flea pools.

RESULTS: Year, total summer precipitation the year prior to sampling, average minimum spring temperature and small mammal species were significant factors in predicting Bartonella positivity. Occurrence based on the ITS region was more than double that of the gltA gene and was 34% (n = 349) in northern red-backed voles, 35% (n = 20) in meadow voles, 37% (n = 68) in deer mice and 31% (n = 59) in shrews. Six species of Bartonella were identified with the ITS region, including B. grahamii, B. elizabethae, B. washoensis, Candidatus B. rudakovii, B. doshiae, B. vinsonii subsp. berkhoffii and subsp. arupensis. In addition, 47% (n = 49/105) of ITS amplicons had < 97% identity to sequences in GenBank, possibly due to a limited reference library or previously unreported species. An additional Bartonella species (B. heixiaziensis) was detected during metagenomic sequencing of the gltA gene in 6/11 rodents that had ITS sequences with < 97% identity in GenBank, highlighting that a limited reference library for the ITS marker likely accounted for low sequence similarity in our specimens. In addition, one flea pool from a northern red-backed vole contained multiple species (B. grahamii and B. heixiaziensis).

CONCLUSION: Our study calls attention to the usefulness of a combined approach to determine the occurrence and diversity of Bartonella communities in hosts and vectors.}, } @article {pmid36229545, year = {2022}, author = {Gounot, JS and Chia, M and Bertrand, D and Saw, WY and Ravikrishnan, A and Low, A and Ding, Y and Ng, AHQ and Tan, LWL and Teo, YY and Seedorf, H and Nagarajan, N}, title = {Genome-centric analysis of short and long read metagenomes reveals uncharacterized microbiome diversity in Southeast Asians.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {6044}, pmid = {36229545}, issn = {2041-1723}, mesh = {Asian People/genetics ; *Bacteriocins/genetics ; Cross-Sectional Studies ; Genome, Human ; Humans ; Metagenome/genetics ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Despite extensive efforts to address it, the vastness of uncharacterized 'dark matter' microbial genetic diversity can impact short-read sequencing based metagenomic studies. Population-specific biases in genomic reference databases can further compound this problem. Leveraging advances in hybrid assembly (using short and long reads) and Hi-C technologies in a cross-sectional survey, we deeply characterized 109 gut microbiomes from three ethnicities in Singapore to comprehensively reconstruct 4497 medium and high-quality metagenome assembled genomes, 1708 of which were missing in short-read only analysis and with >28× N50 improvement. Species-level clustering identified 70 (>10% of total) novel gut species out of 685, improved reference genomes for 363 species (53% of total), and discovered 3413 strains unique to these populations. Among the top 10 most abundant gut bacteria in our study, one of the species and >80% of strains were unrepresented in existing databases. Annotation of biosynthetic gene clusters (BGCs) uncovered more than 27,000 BGCs with a large fraction (36-88%) unrepresented in current databases, and with several unique clusters predicted to produce bacteriocins that could significantly alter microbiome community structure. These results reveal significant uncharacterized gut microbial diversity in Southeast Asian populations and highlight the utility of hybrid metagenomic references for bioprospecting and disease-focused studies.}, } @article {pmid36229418, year = {2022}, author = {Wei, G and Zhang, G and Li, M and Liu, C and Wei, F and Wang, Y and Huang, Z and Chen, Z and Zheng, Y and Chen, S and Dong, L}, title = {Core rhizosphere microbiome of Panax notoginseng and its associations with belowground biomass and saponin contents.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {6238-6251}, doi = {10.1111/1462-2920.16245}, pmid = {36229418}, issn = {1462-2920}, mesh = {Rhizosphere ; *Panax notoginseng/microbiology ; Soil Microbiology ; Biomass ; *Saponins ; Plant Roots/microbiology ; *Microbiota/genetics ; }, abstract = {The core rhizosphere microbiome is critical for plant fitness. However, its contribution to the belowground biomass and saponin contents of Panax notoginseng remains unclear. High-throughput sequencing of amplicon and metagenome was performed to obtain the microbiome profiles and functional traits in P. notoginseng rhizosphere across a large spatial scale. We obtained 639 bacterial and 310 fungal core OTUs, which were mainly affected by soil pH and organic matter (OM). The core taxa were grouped into four ecological clusters (i.e. high pH, low pH, high OM and low OM) for sharing similar habitat preferences. Furthermore, structural equation modelling (SEM) and correlation analyses revealed that the diversity and composition of core microbiomes, as well as the metagenome-derived microbial functions, were related to belowground biomass and saponin contents. Key microbial genera related to the two plant indicators were also identified. In short, this study explored the main driving environmental factors of core microbiomes in the P. notoginseng rhizosphere and revealed that the core microbiomes and microbial functions potentially contributed to the belowground biomass and saponin contents of the plant. This work may enhance our understanding of interactions between microbes and perennial plants and improve our ability to manage root microbiota for the sustainable production of herbal medicine.}, } @article {pmid36228621, year = {2022}, author = {Tang, B and Tang, L and He, W and Jiang, X and Hu, C and Li, Y and Zhang, Y and Pang, K and Lei, Y and Li, S and Liu, S and Wang, S and Yang, M and Li, Z and Zhao, F and Yang, S}, title = {Correlation of gut microbiota and metabolic functions with the antibody response to the BBIBP-CorV vaccine.}, journal = {Cell reports. Medicine}, volume = {3}, number = {10}, pages = {100752}, pmid = {36228621}, issn = {2666-3791}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; COVID-19 Vaccines ; Antibody Formation ; *COVID-19 ; Fatty Acids, Volatile/metabolism ; }, abstract = {Increasing evidence indicates that gut microbiota may play a key role in vaccination immunity. Here, we investigate whether the human gut microbiota and metabolic function correlate with the BBIBP-CorV vaccine response. A total of 207 participants who received the BBIBP-CorV vaccine are enrolled. The gut microbiome and metabolic functions are investigated using metagenomic sequencing and metabolomic assays. We find that BBIBP-CorV vaccination is accompanied by altered microbiome composition and functional pathways, and the gut microbiome and its functional profiles correlate with the vaccine response. The levels of short-chain fatty acids (SCFAs) are much higher in the high antibody response group compared to the low response group, and several SCFAs display a positive correlation with the antibody response. Our study highlights that the gut microbiome and its function is associated with the BBIBP-CorV vaccine response, providing evidence for further exploration of microbiome modulation to improve COVID-19 vaccine efficacy.}, } @article {pmid36228567, year = {2022}, author = {Le Sayec, M and Xu, Y and Laiola, M and Gallego, FA and Katsikioti, D and Durbidge, C and Kivisild, U and Armes, S and Lecomte, M and Fança-Berthon, P and Fromentin, E and Plaza Oñate, F and Cruickshank, JK and Rodriguez-Mateos, A}, title = {The effects of Aronia berry (poly)phenol supplementation on arterial function and the gut microbiome in middle aged men and women: Results from a randomized controlled trial.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {41}, number = {11}, pages = {2549-2561}, doi = {10.1016/j.clnu.2022.08.024}, pmid = {36228567}, issn = {1532-1983}, mesh = {Male ; Middle Aged ; Humans ; Female ; *Photinia/chemistry ; Pulse Wave Analysis ; *Gastrointestinal Microbiome ; Phenol/pharmacology ; Blood Pressure ; Phenols/pharmacology ; Double-Blind Method ; Dietary Supplements ; Plant Extracts/pharmacology ; Butyrates ; }, abstract = {BACKGROUND AND AIMS: Berry (poly)phenol consumption has been associated with cardioprotective benefits, however little is known on the role the gut microbiome may play on such health benefits. Our objective was to investigate the effects of aronia berry (poly)phenol consumption on cardiometabolic health and gut microbiome richness and composition in prehypertensive middle-aged men and women.

METHODS: A total of 102 prehypertensive participants were included in a parallel 12-week randomized double-blind placebo-controlled trial. Volunteers were randomly allocated to daily consume an encapsulated (poly)phenol-rich aronia berry extract (Aronia, n = 51) or a matched maltodextrin placebo (Control, n = 51). Blood pressure (BP) and arterial function (office and 24 h), endothelial function (measured as flow-mediated dilation), serum biochemistry (including blood lipids), plasma and urine (poly)phenol metabolites as well as gut microbiome composition through shotgun metagenomic sequencing were monitored over the study period. Relationships between vascular outcomes, (poly)phenol metabolites and gut microbiome were investigated using an integrated multi-levels approach.

RESULTS: A significant improvement in arterial indices measured as augmentation index (AIx) and pulse wave velocity (PWV) was found in the Aronia compared to Control group (awake Δ PWV = -0.24 m/s; 95% CI: -0.79, -0.01 m/s, P < 0.05; 24 h peripheral Δ AIx = -6.8; -11.2, -2.3, %, P = 0.003; 24 h central Δ AIx = -3.3; -5.5, -1.0, %, P = 0.006). No changes in BP, endothelial function or blood lipids were found following the intervention. Consumption of aronia (poly)phenols led to a significant increase in gut microbiome gene richness and in the abundance of butyrate-producing species such as Lawsonibacter asaccharolyticus and Intestinimonas butyriciproducens species, compared to Control group. Results from an approach including metabolomic, metagenomic and clinical outcomes highlighted associations between aronia-derived phenolic metabolites, arterial stiffness, and gut microbiome.

CONCLUSIONS: Aronia berry (poly)phenol consumption improved arterial function in prehypertensive middle-aged individuals, possibly via modulation of gut microbiome richness and composition based on the associations observed between these parameters.

CLINICAL TRIAL REGISTRY: The National Institutes of Health (NIH)-randomized trial records held on the NIH ClinicalTrials.gov website (NCT03434574). Aronia Berry Consumption on Blood Pressure.}, } @article {pmid36228150, year = {2022}, author = {Lu, E and Jiang, H and Yang, L and Wu, N and Lu, M}, title = {Metagenomic next-generation sequencing for the diagnosis of Pneumocystis jirovecii pneumonia in solid organ transplant recipients.}, journal = {Chinese medical journal}, volume = {135}, number = {22}, pages = {2756-2758}, pmid = {36228150}, issn = {2542-5641}, mesh = {Humans ; *Pneumonia, Pneumocystis/diagnosis ; *Pneumocystis carinii/genetics ; *Organ Transplantation/adverse effects ; High-Throughput Nucleotide Sequencing ; Transplant Recipients ; }, } @article {pmid36227987, year = {2022}, author = {Schulz, L and Guo, Z and Zarzycki, J and Steinchen, W and Schuller, JM and Heimerl, T and Prinz, S and Mueller-Cajar, O and Erb, TJ and Hochberg, GKA}, title = {Evolution of increased complexity and specificity at the dawn of form I Rubiscos.}, journal = {Science (New York, N.Y.)}, volume = {378}, number = {6616}, pages = {155-160}, doi = {10.1126/science.abq1416}, pmid = {36227987}, issn = {1095-9203}, mesh = {*Carbon Dioxide/chemistry ; Oxygen/chemistry ; Photosynthesis ; *Ribulose-Bisphosphate Carboxylase/chemistry/genetics ; *Evolution, Molecular ; Substrate Specificity ; *Catalytic Domain/genetics ; Metagenome ; Firmicutes/enzymology ; }, abstract = {The evolution of ribulose-1,5-bisphosphate carboxylase/oxygenases (Rubiscos) that discriminate strongly between their substrate carbon dioxide and the undesired side substrate dioxygen was an important event for photosynthetic organisms adapting to an oxygenated environment. We use ancestral sequence reconstruction to recapitulate this event. We show that Rubisco increased its specificity and carboxylation efficiency through the gain of an accessory subunit before atmospheric oxygen was present. Using structural and biochemical approaches, we retrace how this subunit was gained and became essential. Our work illuminates the emergence of an adaptation to rising ambient oxygen levels, provides a template for investigating the function of interactions that have remained elusive because of their essentiality, and sheds light on the determinants of specificity in Rubisco.}, } @article {pmid36227700, year = {2022}, author = {Yin, Z and Ye, L and Jing, C}, title = {Genome-Resolved Metagenomics and Metatranscriptomics Reveal that Aquificae Dominates Arsenate Reduction in Tengchong Geothermal Springs.}, journal = {Environmental science & technology}, volume = {56}, number = {22}, pages = {16473-16482}, doi = {10.1021/acs.est.2c05764}, pmid = {36227700}, issn = {1520-5851}, mesh = {*Hot Springs ; Metagenomics ; Arsenates ; Carbon Dioxide/metabolism ; Bacteria/genetics/metabolism ; *Arsenic/metabolism ; Phylogeny ; }, abstract = {Elevated arsenic (As) is common in geothermal springs, shaping the evolution of As metabolism genes and As transforming microbes. Herein, genome-level microbial metabolisms and As cycling strategies in Tengchong geothermal springs were demonstrated for the first time based on metagenomic and metatranscriptomic analyses. Sulfur cycling was dominated by Aquificae oxidizing thiosulfate via the sox system, fueling the respiration and carbon dioxide fixation processes. Arsenate reduction via arsC [488.63 ± 271.60 transcripts per million (TPM)] and arsenite efflux via arsB (442.98 ± 284.81 TPM) were the primary detoxification pathway, with most genes and transcripts contributed by the members in phylum Aquificae. A complete arsenotrophic cycle was also transcriptionally active as evidenced by the detection of aioA transcripts and arrA transcript reads mapped onto metagenome-assembled genomes (MAGs) affiliated with Crenarchaeota. MAGs affiliated with Aquificae had great potential of reducing arsenate via arsC and fixing nitrogen and carbon dioxide via nifDHK and reductive tricarboxylic acid (rTCA) cycle, respectively. Aquificae's arsenate reduction potential via arsC was observed for the first time at the transcriptional level. This study expands the diversity of the arsC-based arsenate-reducing community and highlights the importance of Aquificae to As biogeochemistry.}, } @article {pmid36226871, year = {2022}, author = {Tian, P and Wu, L and Kudo, M and Hayashi, M and Qin, L and Gao, M and Xu, A and Liu, T}, title = {TangNaiKang, herbal formulation, alleviates obesity in diabetic SHR/cp rats through modulation of gut microbiota and related metabolic functions.}, journal = {Pharmaceutical biology}, volume = {60}, number = {1}, pages = {2002-2010}, pmid = {36226871}, issn = {1744-5116}, mesh = {Animals ; Body Weight ; Cholesterol/pharmacology ; DNA, Ribosomal/pharmacology ; *Diabetes Mellitus/drug therapy ; *Drugs, Chinese Herbal/pharmacology/therapeutic use ; Fatty Acids, Volatile ; *Gastrointestinal Microbiome ; Obesity/drug therapy/metabolism ; Rats ; Rats, Inbred SHR ; Rats, Inbred WKY ; Triglycerides ; }, abstract = {CONTEXT: Tangnaikang (TNK) is a Chinese herbal formulation that has lipid-lowering effects, but its effect on reducing obesity has not been studied.

OBJECTIVE: To observe the effect of TNK on obesity and explore its effect on gut microbiota of obese rats.

MATERIALS AND METHODS: The SHR/NDmcr-cp rats were divided into three groups: (1) 3.24 g/kg TNK (High TNK), (2) 1.62 g/kg TNK (Low TNK), and (3) an untreated control (CON). Wistar-Kyoto rats were used as normal controls (WKY). After 8 weeks of TNK oral administration, body weight, abdominal circumference, triglycerides (TC) and total cholesterol (CHO) were measured. Gut microbiota diversity was studied by 16S rDNA sequencing, and metagenomes analysis was conducted to determine alteration in functional gene expression.

RESULTS: The body weight (496.60 ± 6.0 g vs. 523.40 ± 5.6 g), abdomen circumference (24.00 ± 0.11 cm vs. 24.87 ± 0.25 cm), TC (3.04 ± 0.16 mmol/L vs. 4.97 ± 0.21 mmol/L), CHO (2.42 ± 0.15 mmol/L vs. 2.84 ± 0.09 mmol/L) of rats in the High TNK group were decreased significantly (all p < 0.05). TNK administration regulates intestinal flora, up-regulates Eisenbergiella and down-regulates Clostridium_sensu_stricto_1, which is beneficial to the production of short-chain fatty acids (SCFAs). Metagenomes analysis shows that TNK is closely related to the fatty acid synthesis pathway.

DISCUSSION AND CONCLUSIONS: TNK can regulate gut microbiota to reduce obesity, which may be related to fatty acid metabolism. Our research supports the clinical application of TNK preparation and provides a new perspective for the treatment of obesity.}, } @article {pmid36226140, year = {2022}, author = {Li, S and Jiang, W and Wang, CY and Weng, L and Du, B and Peng, JM}, title = {A case of disseminated Legionnaires' disease: The value of metagenome next-generation sequencing in the diagnosis of Legionnaires.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {955955}, pmid = {36226140}, issn = {2296-858X}, abstract = {BACKGROUND: Legionella rarely causes hospital-acquired pneumonia (HAP), although it is one of the most common pathogens of community-acquired pneumonia. Hospital-acquired Legionnaires' disease, mainly occurring in immunocompromised patients, is often delayed in diagnosis with high mortality. The use of the metagenome Next-Generation Sequencing (mNGS) method, which is fast and unbiased, allows for the early detection and identification of microorganisms using a culture-independent strategy.

CASE REPORT: A 52-year-old male, with a past medical history of Goods syndrome, was admitted due to nephrotic syndrome. The patient developed severe pneumonia, rhabdomyolysis, and soft tissue infection after receiving immunosuppressive therapy. He did not respond well to empiric antibiotics and was eventually transferred to the medical intensive care unit because of an acute respiratory failure and septic shock. The patient then underwent a comprehensive conventional microbiological screening in bronchoalveolar lavage fluid (BALF) and blood, and the results were all negative. As a last resort, mNGS of blood was performed. Extracellular cell-free and intracellular DNA fragments of Legionella were detected in plasma and blood cell layer by mNGS, respectively. Subsequent positive results of polymerase chain reaction for Legionella in BALF and soft tissue specimens confirmed the diagnosis of disseminated Legionnaires' disease involving the lungs, soft tissue, and blood stream. The patient's condition improved promptly after a combination therapy of azithromycin and moxifloxacin. He was soon extubated and discharged from ICU with good recovery.

CONCLUSION: Early recognition and diagnosis of disseminated Legionnaires' disease is challenging. The emergence and innovation of mNGS of blood has the potential to address this difficult clinical issue.}, } @article {pmid36225905, year = {2022}, author = {Han, Y and Xu, J and Yan, Y and Zhao, X}, title = {Dynamics of the gut microbiota in rats after hypobaric hypoxia exposure.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e14090}, pmid = {36225905}, issn = {2167-8359}, mesh = {Rats ; Animals ; *Gastrointestinal Microbiome/genetics ; Hypoxia/microbiology ; Feces/microbiology ; Bacteria, Anaerobic ; Fatty Acids, Volatile ; }, abstract = {BACKGROUND: Gut microbiota plays an important role in host health and is influenced by multiple factors. Hypobaric hypoxia usually existing at high altitude conditions can adversely affect normal physiological functions. However, the dynamic changes of gut microbiota influenced by hypobaric hypoxia have not been elucidated.

METHODS: In this study, we collected fecal samples from seven rats at 14 time points from entering the hypobaric chamber (eight time points) to leaving the chamber (six time points) and five rats served as normoxic controls. Metagenome sequencing was performed on all samples and the dynamics of taxa and functions were analyzed.

RESULTS: We found that the α-diversity was changed in the first 5 days after entering or leaving the hypobaric chamber. The β-diversity analysis revealed that gut microbiota structure was significantly separated among 14 time points. After entering the chamber, the relative abundance of Bacteroides decreased and the most abundant genus turned into Prevotella. The abundance of Firmicutes and Bacteroidetes showed an opposite trend and both have a significant change within 5 days after entering or leaving the hypobaric hypoxia chamber. Some obligate anaerobic bacteria belonging to Desulfovibrio and Alistipes were significantly enriched after entering the chamber for 5 weeks, whereas Probiotics like Bifidobacterium and Lactococcus, and short-chain fatty acids producers like Butyrivibrio and Pseudobutyrivibrio were significantly enriched after leaving the chamber for 3 weeks. Microbial functions like 'Two-component regulatory system', 'beta-carotene biosynthesis' and 'Fatty acid biosynthesis' were significantly enriched after entering the chamber for 5 weeks. Hypobaric hypoxia conditions could deeply affect the diversity and structure of gut microbiota. The alterations of abundance of dominant taxa (Firmicutes and Bacteroidetes), increased anaerobes and decreased probiotics induced by hypobaric hypoxia conditions might affect the host health.}, } @article {pmid36225772, year = {2022}, author = {Huang, J and Wang, L and Xu, Y and Hu, X and Yu, R and Chen, S and Wang, B}, title = {Empyema caused by Eikenella halliae diagnosed by metagenomic next-generation sequencing (mNGS) after pulmonary surgery: A case report.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {897602}, pmid = {36225772}, issn = {2296-2565}, mesh = {*Eikenella ; *Empyema/diagnosis ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Metagenomics/methods ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Empyema is one of the complications of pulmonary surgery for lung cancer, the incidence of which is not very high, but in severe cases, it can even lead to death, and it is always difficult to diagnose the cause by conventional methods.

CASE PRESENTATION: In this study, we report a clinical case of empyema caused by Eikenella halliae after pulmonary surgery in a 55-year-old man. He had a fever, cough, and expectoration for 3 days and was diagnosed with right hydropneumothorax and empyema, pneumonia, postoperative malignant tumor of the right lower lobe (adenocarcinoma), and hypertension. The microbiology laboratory reported Gram-negative bacteria in pleural effusion, which was preliminarily considered as Eikenella based on culture and 16S rRNA sequencing. Furthermore, metagenomic next-generation sequencing (mNGS) of sputum samples was performed two times and reported negative results and the presence of E. halliae, respectively. The pathogen was finally confirmed as E. halliae by whole genome sequencing, suggesting the high-resolution ability of mNGS in the clinical diagnosis of this case.

CONCLUSION: To our knowledge, this is the first case report of E. halliae infection in China, indicating increased pathogenicity of Eikenella sp. in immunocompromised patients, especially after invasive operations. Our findings emphasize that mNGS allows bacterial diagnosis of empyema and can significantly improve the accuracy of the diagnosis.}, } @article {pmid36225748, year = {2022}, author = {Liao, Y and Li, WR and Zhu, Y and Luo, SH and Liao, Q and Wan, CM}, title = {Invasive Bordetella pertussis Infection in Infants: A Case Report.}, journal = {Open forum infectious diseases}, volume = {9}, number = {10}, pages = {ofac478}, pmid = {36225748}, issn = {2328-8957}, abstract = {Infants are more likely to develop severe pertussis. We report a malignant pertussis case in a 2-month-old boy with respiratory failure, severe pneumonia, septic shock, and encephalopathy. Bordetella pertussis was detected from nasopharyngeal secretions by polymerase chain reaction, as well as both blood and cerebrospinal fluid samples via metagenomics next-generation sequencing.}, } @article {pmid36225723, year = {2022}, author = {Shimizu, K and Hirata, H and Tokuhira, N and Ueda, A and Motooka, D and Nakamura, S and Ogura, H}, title = {A case of massive refractory diarrhea in a patient with COVID-19.}, journal = {Acute medicine & surgery}, volume = {9}, number = {1}, pages = {e793}, pmid = {36225723}, issn = {2052-8817}, abstract = {BACKGROUND: The new coronavirus disease (COVID-19) causes gastrointestinal symptoms as well as respiratory symptoms.

CASE PRESENTATION: A 60-year-old man was transferred with respiratory difficulty. He was diagnosed as having COVID-19 and was intubated and placed on mechanical ventilation. He suffered from diarrhea from day 12 and produced a maximum of approximately 6,384 mL/day of watery diarrhea on day 21. He required massive transfusion. Adsorbents and pectin-containing oligomeric formulas were administered, which decreased the amount of diarrhea. Fecal metagenomic analysis showed the proportions of the genera Enterococcus and Staphylococcus were the most dominate at the genus level. The proportion of Bacteroidetes was <1%. Thereafter, his diarrhea decreased to several times, and he was transferred to another ward on day 104.

CONCLUSION: Therapy for intestinal complications as well as that for pneumonia might be important in treating COVID-19.}, } @article {pmid36225370, year = {2022}, author = {Fang, L and Liu, Z and Lu, Z and Huang, R and Xiang, R}, title = {Identification and characterization of a novel metallo β-lactamase, SZM-1, in Shenzhen Bay, South China.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {996834}, pmid = {36225370}, issn = {1664-302X}, abstract = {Metallo β-Lactamases (MBLs) degrade most clinical β-lactam antibiotics, especially Carbapenem, posing a huge threat to global health. Studies on environmental MBLs are important for risk assessment of the MBLs transmission among connected habitats, and between environment and human. Here, we described a novel metallo β-Lactamases, named SZM-1 (Shenzhen metallo-β-lactamase), from an Arenimonas metagenome-assembled genome recovered from the river sediment in the Shenzhen Bay area, south China. Phylogenetic analysis, primary sequence comparison, structural modeling suggested that the SZM-1 belongs to B1 MBL family, likely harboring a typical di-zinc catalytic center. Furthermore, the gene encoding the MBLs was cloned into Escherichia coli TOP10 for Carba NP test and antimicrobial susceptibility test. The results indicated that the SZM-1 had carbapenemase activity, and conferred the carrier to increased resistance toward carbapenems. Taken together, our results raise alarms about the emergence and spread of the SZM-1, and suggest further surveillance, especially in hospital settings and clinical isolates, to determine whether bla SZM-1 is a mobilizable antibiotic resistance.}, } @article {pmid36225369, year = {2022}, author = {Zeng, F and Zhu, Y and Zhang, D and Zhao, Z and Li, Q and Ma, P and Zhang, G and Wang, Y and Wu, S and Guo, S and Sun, G}, title = {Metagenomic analysis of the soil microbial composition and salt tolerance mechanism in Yuncheng Salt Lake, Shanxi Province.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1004556}, pmid = {36225369}, issn = {1664-302X}, abstract = {The soil in Yuncheng Salt Lake has serious salinization and the biogeographic environment affects the composition and distribution of special halophilic and salt-tolerant microbial communities in this area. Therefore, this study collected soils at distances of 15, 30, and 45 m from the Salt Lake and used non-saline soil (60 m) as a control to explore the microbial composition and salt tolerance mechanisms using metagenomics technology. The results showed that the dominant species and abundance of salt-tolerant microorganisms changed gradually with distance from Salt Lake. The salt-tolerant microorganisms can increase the expression of the Na[+]/H[+] antiporter by upregulating the Na[+]/H[+] antiporter subunit mnhA-G to respond to salt stress, simultaneously upregulating the genes in the betaine/proline transport system to promote the conversion of choline into betaine, while also upregulating the trehalose/maltose transport system encode genes to promote the synthesis of trehalose to resist a high salt environment.}, } @article {pmid36225357, year = {2022}, author = {Guo, R and Zhang, S and Chen, J and Shen, W and Zhang, G and Wang, J and Zhang, F and Pan, Q and Xie, T and Ai, D and Dong, J and Suo, J and Sun, Y and Liu, S}, title = {Comparison of gut microflora of donkeys in high and low altitude areas.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {964799}, pmid = {36225357}, issn = {1664-302X}, abstract = {Donkeys' gut microbe is critical for their health and adaptation to the environment. Little research has been conducted on the donkey gut microbiome compared with other domestic animals. The Tibetan Plateau is an extreme environment. In this study, 6 Qinghai donkeys (QH) from the Tibetan Plateau and 6 Dezhou donkeys (DZ) were investigated, and the contents of 4 parts-stomach, small intestine, cecum, and rectum-were collected. 16S rRNA sequencing and metagenomic sequencing were used to analyze the composition and diversity of gut microbial communities in donkeys. The results showed that the flora diversity and richness of the hindgut were significantly higher than those of the foregut (p < 0.01), with no sex differences, and the community structure and composition of the same or adjacent regions (stomach, small intestine, cecum, and rectum) were similar. Besides, the flora diversity and richness of QH on the Tibetan Plateau were significantly higher than those of DZ (p < 0.05). The major pathways associated with QH were signal transduction mechanisms and carbohydrate transport and metabolism, and Bacteroidales were the major contributors to these functions. Our study provides novel insights into the contribution of microbiomes to the adaptive evolution of donkeys.}, } @article {pmid36225235, year = {2022}, author = {Zhang, S and Wu, G and Shi, Y and Liu, T and Xu, L and Dai, Y and Chang, W and Ma, X}, title = {Understanding etiology of community-acquired central nervous system infections using metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {979086}, pmid = {36225235}, issn = {2235-2988}, mesh = {Animals ; *Central Nervous System Infections/cerebrospinal fluid/diagnosis/epidemiology ; *Epstein-Barr Virus Infections ; Herpesvirus 4, Human ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; Retrospective Studies ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Community-acquired central nervous system infections (CA-CNS infections) have the characteristics of acute onset and rapid progression, and are associated with high levels of morbidity and mortality worldwide. However, there have been only limited studies on the etiology of this infections. Here, metagenomic next-generation sequencing (mNGS), a comprehensive diagnosis method, facilitated us to better understand the etiology of CA-CNS infections.

METHODS: We conducted a single-center retrospective study between September 2018 and July 2021 in which 606 cerebrospinal fluid (CSF) samples were collected from suspected CNS infectious patients for mNGS testing, and all positive samples were included in this analysis.

RESULTS: After the exclusion criteria, a total of 131 mNGS-positive samples were finally enrolled. Bacterial, viral, fungal, parasitic, specific pathogen and mixed infections were accounted for 32.82% (43/131), 13.74% (18/131), 0.76% (1/131), 2.29% (3/131) and 6.87% (9/131), respectively. A total of 41 different pathogens were identified, including 16 bacteria, 12 viruses, 10 fungi, and 1 parasite and 3 specific pathogens. The most frequent infecting pathogens are Epstein-Barr virus (n = 14), Herpes simplex virus 1 (n = 14), Mycobacterium tuberculosis (n = 13), Streptococcus pneumoniae (n = 13), and Cryptococcus neoformans (n = 8). Some difficult-to-diagnose pathogen infections were also detected by mNGS, such as Streptococcus suis, Pseudorabies virus, Bunyavirus, Orientia tsutsugamushi and Toxoplasma gondii.

CONCLUSION: In this study, mNGS identified a wide variety of pathogens of CA-CNS infections and many of which could not be detected by conventional methods. Our data provide a better understanding of the etiology of CA-CNS infections and show that mNGS represents a comparative screening of CSF in an unbiased manner for a broad range of human pathogens.}, } @article {pmid36225234, year = {2022}, author = {Herman, MA and Irazoqui, JE and Samuel, BS and Vega, N}, title = {Editorial: C. elegans host-microbiome interactions: From medical to ecological and evolutionary model.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1035545}, pmid = {36225234}, issn = {2235-2988}, support = {DP2 DK116645/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Biological Evolution ; *Caenorhabditis elegans ; Dysbiosis ; Humans ; *Microbiota ; }, } @article {pmid36225233, year = {2022}, author = {Hou, JN and Liu, HD and Tan, QY and Cao, FA and Wang, SL and Yao, MY and Zhao, YC}, title = {Risk factors of in-hospital mortality in patients with pneumocystis pneumonia diagnosed by metagenomics next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {994175}, pmid = {36225233}, issn = {2235-2988}, mesh = {Adult ; Albumins ; C-Reactive Protein ; High-Throughput Nucleotide Sequencing ; Hospital Mortality ; Humans ; L-Lactate Dehydrogenase ; Metagenomics ; Middle Aged ; *Pneumonia, Pneumocystis/complications/diagnosis ; Retrospective Studies ; Risk Factors ; }, abstract = {OBJECTIVES: The metagenomic next-generation sequencing (mNGS) test is useful for rapid and accurate detection and identification of pathogenic microorganisms. The aim of the present study was to investigate the factors associated with in-hospital mortality in pneumocystis pneumonia (PCP) patients with mNGS-assisted diagnosis.

METHODS: Our study enrolled 154 patients with mNGS-positive PCP from August 2018 to February 2022 at the First Affiliated Hospital of Zhengzhou University respectively. Patients were divided into the survivor group (n=98) and the death group (n=56) according to whether in-hospital death occurred. Baseline characteristics, patients' pre-hospital symptoms and patients' CT imaging performance during hospitalization were carefully compared between the two groups. Risk factors for the occurrence of in-hospital death were sought by selecting indicators that were significantly different between the two groups for modelling and performing multiple logistic regression analysis.

RESULTS: Compared with the in-hospital death patients, the survivors were younger and had higher levels of albumin (ALB) (age: 50.29 ± 14.63 years vs 59.39 ± 12.27 years, p<0.001; ALB: 32.24 ± 5.62 g/L vs 29.34 ± 5.42g/L, p=0.002; respectively), while the levels of lactate dehydrogenase (LDH) and C-reactive protein CRP were lower (LDH: 574.67 ± 421.24 U/L vs 960.80 ± 714.94 U/L, p=0.001; CRP: 54.97 ± 55.92 mg/L vs80.45 ± 73.26 mg/L, p=0.018; respectively). Multiple logistic regression analysis revealed that age, the baseline LDH and CRP levels were all positively associated with high in-hospital mortality [age: OR(95%CI): 1.115 (1.062-1.172), p<0.001; LDH: OR(95%CI): 1.002 (1.001-1.003), p<0.001; CRP: OR(95%CI): 1.008 (1.000-1.017), p=0.045; respectively] while the platelet counts was negatively associated with it [OR(95%CI): 0.986 (0.979-0.992), p<0.001].

CONCLUSIONS: Old age, high baseline levels of LDH and CRP and low platelet counts were risk factors of the in-hospital mortality in mNGS positive PCP patients.}, } @article {pmid36224660, year = {2022}, author = {Sanders, JG and Yan, W and Mjungu, D and Lonsdorf, EV and Hart, JA and Sanz, CM and Morgan, DB and Peeters, M and Hahn, BH and Moeller, AH}, title = {A low-cost genomics workflow enables isolate screening and strain-level analyses within microbiomes.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {212}, pmid = {36224660}, issn = {1474-760X}, support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; T32 AI145821/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; *Genome, Bacterial ; Genomics ; Metagenome ; *Microbiota/genetics ; Pan troglodytes/genetics ; Phylogeny ; Workflow ; }, abstract = {Earth's environments harbor complex consortia of microbes that affect processes ranging from host health to biogeochemical cycles. Understanding their evolution and function is limited by an inability to isolate genomes in a high-throughput manner. Here, we present a workflow for bacterial whole-genome sequencing using open-source labware and the OpenTrons robotics platform, reducing costs to approximately $10 per genome. We assess genomic diversity within 45 gut bacterial species from wild-living chimpanzees and bonobos. We quantify intraspecific genomic diversity and reveal divergence of homologous plasmids between hosts. This enables population genetic analyses of bacterial strains not currently possible with metagenomic data alone.}, } @article {pmid36224580, year = {2022}, author = {Lu, Y and Li, W and Li, Y and Zhai, W and Zhou, X and Wu, Z and Jiang, S and Liu, T and Wang, H and Hu, R and Zhou, Y and Zou, J and Hu, P and Guan, G and Xu, Q and Canário, AVM and Chen, L}, title = {Population genomics of an icefish reveals mechanisms of glacier-driven adaptive radiation in Antarctic notothenioids.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {231}, pmid = {36224580}, issn = {1741-7007}, mesh = {Animals ; Antarctic Regions ; Fishes/genetics ; Genome ; *Ice Cover ; Metagenomics ; Oxygen ; *Perciformes ; Phylogeny ; }, abstract = {BACKGROUND: Antarctica harbors the bulk of the species diversity of the dominant teleost fish suborder-Notothenioidei. However, the forces that shape their evolution are still under debate.

RESULTS: We sequenced the genome of an icefish, Chionodraco hamatus, and used population genomics and demographic modelling of sequenced genomes of 52 C. hamatus individuals collected mainly from two East Antarctic regions to investigate the factors driving speciation. Results revealed four icefish populations with clear reproduction separation were established 15 to 50 kya (kilo years ago) during the last glacial maxima (LGM). Selection sweeps in genes involving immune responses, cardiovascular development, and photoperception occurred differentially among the populations and were correlated with population-specific microbial communities and acquisition of distinct morphological features in the icefish taxa. Population and species-specific antifreeze glycoprotein gene expansion and glacial cycle-paced duplication/degeneration of the zona pellucida protein gene families indicated fluctuating thermal environments and periodic influence of glacial cycles on notothenioid divergence.

CONCLUSIONS: We revealed a series of genomic evidence indicating differential adaptation of C. hamatus populations and notothenioid species divergence in the extreme and unique marine environment. We conclude that geographic separation and adaptation to heterogeneous pathogen, oxygen, and light conditions of local habitats, periodically shaped by the glacial cycles, were the key drivers propelling species diversity in Antarctica.}, } @article {pmid36224545, year = {2022}, author = {Espinoza, JL and Dupont, CL}, title = {VEBA: a modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes.}, journal = {BMC bioinformatics}, volume = {23}, number = {1}, pages = {419}, pmid = {36224545}, issn = {1471-2105}, support = {P01 AI118687/AI/NIAID NIH HHS/United States ; R01 AI170111/AI/NIAID NIH HHS/United States ; 1R01AI170111-01/NH/NIH HHS/United States ; }, mesh = {*Archaea/genetics ; Bacteria/genetics ; Cluster Analysis ; Ecosystem ; Eukaryota/genetics ; Genome, Viral ; Humans ; *Metagenome ; Metagenomics/methods ; }, abstract = {BACKGROUND: With the advent of metagenomics, the importance of microorganisms and how their interactions are relevant to ecosystem resilience, sustainability, and human health has become evident. Cataloging and preserving biodiversity is paramount not only for the Earth's natural systems but also for discovering solutions to challenges that we face as a growing civilization. Metagenomics pertains to the in silico study of all microorganisms within an ecological community in situ, however, many software suites recover only prokaryotes and have limited to no support for viruses and eukaryotes.

RESULTS: In this study, we introduce the Viral Eukaryotic Bacterial Archaeal (VEBA) open-source software suite developed to recover genomes from all domains. To our knowledge, VEBA is the first end-to-end metagenomics suite that can directly recover, quality assess, and classify prokaryotic, eukaryotic, and viral genomes from metagenomes. VEBA implements a novel iterative binning procedure and hybrid sample-specific/multi-sample framework that yields more genomes than any existing methodology alone. VEBA includes a consensus microeukaryotic database containing proteins from existing databases to optimize microeukaryotic gene modeling and taxonomic classification. VEBA also provides a unique clustering-based dereplication strategy allowing for sample-specific genomes and genes to be directly compared across non-overlapping biological samples. Finally, VEBA is the only pipeline that automates the detection of candidate phyla radiation bacteria and implements the appropriate genome quality assessments. VEBA's capabilities are demonstrated by reanalyzing 3 existing public datasets which recovered a total of 948 MAGs (458 prokaryotic, 8 eukaryotic, and 482 viral) including several uncharacterized organisms and organisms with no public genome representatives.

CONCLUSIONS: The VEBA software suite allows for the in silico recovery of microorganisms from all domains of life by integrating cutting edge algorithms in novel ways. VEBA fully integrates both end-to-end and task-specific metagenomic analysis in a modular architecture that minimizes dependencies and maximizes productivity. The contributions of VEBA to the metagenomics community includes seamless end-to-end metagenomics analysis but also provides users with the flexibility to perform specific analytical tasks. VEBA allows for the automation of several metagenomics steps and shows that new information can be recovered from existing datasets.}, } @article {pmid36223744, year = {2022}, author = {Di Gesù, CM and Matz, LM and Bolding, IJ and Fultz, R and Hoffman, KL and Gammazza, AM and Petrosino, JF and Buffington, SA}, title = {Maternal gut microbiota mediate intergenerational effects of high-fat diet on descendant social behavior.}, journal = {Cell reports}, volume = {41}, number = {2}, pages = {111461}, pmid = {36223744}, issn = {2211-1247}, support = {P30 DK056338/DK/NIDDK NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; R01 HD109095/HD/NICHD NIH HHS/United States ; T32 AG067952/AG/NIA NIH HHS/United States ; }, mesh = {Animals ; *Diet, High-Fat/adverse effects ; Dysbiosis ; Female ; *Gastrointestinal Microbiome ; Male ; Mice ; Pregnancy ; Social Behavior ; }, abstract = {Dysbiosis of the maternal gut microbiome during pregnancy is associated with adverse neurodevelopmental outcomes. We previously showed that maternal high-fat diet (MHFD) in mice induces gut dysbiosis, social dysfunction, and underlying synaptic plasticity deficits in male offspring (F1). Here, we reason that, if HFD-mediated changes in maternal gut microbiota drive offspring social deficits, then MHFD-induced dysbiosis in F1 female MHFD offspring would likewise impair F2 social behavior. Metataxonomic sequencing reveals reduced microbial richness among female F1 MHFD offspring. Despite recovery of microbial richness among MHFD-descendant F2 mice, they display social dysfunction. Post-weaning Limosilactobacillus reuteri treatment increases the abundance of short-chain fatty acid-producing taxa and rescues MHFD-descendant F2 social deficits. L. reuteri exerts a sexually dimorphic impact on gut microbiota configuration, increasing discriminant taxa between female cohorts. Collectively, these results show multigenerational impacts of HFD-induced dysbiosis in the maternal lineage and highlight the potential of maternal microbiome-targeted interventions for neurodevelopmental disorders.}, } @article {pmid36223712, year = {2022}, author = {Fan, L and Zhu, X and Sun, S and Yu, C and Huang, X and Ness, R and Dugan, LL and Shu, L and Seidner, DL and Murff, HJ and Fodor, AA and Azcarate-Peril, MA and Shrubsole, MJ and Dai, Q}, title = {Ca:Mg ratio, medium-chain fatty acids, and the gut microbiome.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {41}, number = {11}, pages = {2490-2499}, pmid = {36223712}, issn = {1532-1983}, support = {UL1 TR000445/TR/NCATS NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; R01 DK110166/DK/NIDDK NIH HHS/United States ; P30 CA068485/CA/NCI NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; UL1 RR024975/RR/NCRR NIH HHS/United States ; R01 CA202936/CA/NCI NIH HHS/United States ; R01 CA149633/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Coconut Oil ; Calcium ; Maltose ; Magnesium ; Fatty Acids/metabolism ; Ketone Bodies ; Sucrose ; Fructose ; Glucose ; }, abstract = {BACKGROUND & AIMS: Ketogenic medium-chain fatty acids (MCFAs) with profound health benefits are commonly found in dairy products, palm kernel oil and coconut oil. We hypothesize that magnesium (Mg) supplementation leads to enhanced gut microbial production of MCFAs and, in turn, increased circulating MCFAs levels.

METHODS: We tested this hypothesis in the Personalized Prevention of Colorectal Cancer Trial (PPCCT) (NCT01105169), a double-blind 2 × 2 factorial randomized controlled trial enrolling 240 participants. Six 24-h dietary recalls were performed for all participants at the baseline and during the intervention period. Based on the baseline 24-h dietary recalls, the Mg treatment used a personalized dose of Mg supplementation that would reduce the calcium (Ca): Mg intake ratio to around 2.3. We measured plasma MCFAs, sugars, ketone bodies and tricarboxylic acid cycle (TCA cycle) metabolites using the Metabolon's global Precision Metabolomics™ LC-MS platform. Whole-genome shotgun metagenomics (WGS) sequencing was performed to assess microbiota in stool samples, rectal swabs, and rectal biopsies.

RESULTS: Personalized Mg treatment (mean dose 205.58 mg/day with a range from 77.25 to 389.55 mg/day) significantly increased the plasma levels of C7:0, C8:0, and combined C7:0 and C8:0 by 18.45%, 25.28%, and 24.20%, respectively, compared to 14.15%, 10.12%, and 12.62% decreases in the placebo arm. The effects remain significant after adjusting for age, sex, race and baseline level (P = 0.0126, P = 0.0162, and P = 0.0031, respectively) and FDR correction at 0.05 (q = 0.0324 for both C7:0 and C8:0). Mg treatment significantly reduced the plasma level of sucrose compared to the placebo arm (P = 0.0036 for multivariable-adjusted and P = 0.0216 for additional FDR correction model) whereas alterations in daily intakes of sucrose, fructose, glucose, maltose and C8:0 from baseline to the end of trial did not differ between two arms. Mediation analysis showed that combined C7:0 and C8:0 partially mediated the effects of Mg treatment on total and individual ketone bodies (P for indirect effect = 0.0045, 0.0043, and 0.03, respectively). The changes in plasma levels of C7:0 and C8:0 were significantly and positively correlated with the alterations in stool microbiome α diversity (r = 0.51, p = 0.0023 and r = 0.34, p = 0.0497, respectively) as well as in stool abundance for the signatures of MCFAs-related microbiota with acyl-ACP thioesterase gene producing C7:0 (r = 0.46, p = 0.0067) and C8:0 (r = 0.49, p = 0.003), respectively, following Mg treatment.

CONCLUSIONS: Optimizing Ca:Mg intake ratios to around 2.3 through 12-week personalized Mg supplementation leads to increased circulating levels of MCFAs (i.e. C7:0 and C8:0), which is attributed to enhanced production from gut microbial fermentation and, maybe, sucrose consumption.}, } @article {pmid36223010, year = {2022}, author = {Lüth, T and Graspeuntner, S and Neumann, K and Kirchhoff, L and Masuch, A and Schaake, S and Lupatsii, M and Tse, R and Griesinger, G and Trinh, J and Rupp, J}, title = {Improving analysis of the vaginal microbiota of women undergoing assisted reproduction using nanopore sequencing.}, journal = {Journal of assisted reproduction and genetics}, volume = {39}, number = {11}, pages = {2659-2667}, pmid = {36223010}, issn = {1573-7330}, support = {J10_2020//Universität zu Lübeck/ ; }, mesh = {Female ; Humans ; RNA, Ribosomal, 16S/genetics ; *Nanopore Sequencing ; Prospective Studies ; *Microbiota/genetics ; High-Throughput Nucleotide Sequencing/methods ; Reproduction ; }, abstract = {PURPOSE: Subclinical alterations of the vaginal microbiome have been described to be associated with female infertility and may serve as predictors for failure of in vitro fertilization treatment. While large prospective studies to delineate the role of microbial composition are warranted, integrating microbiome information into clinical management depends on economical and practical feasibility, specifically on a short duration from sampling to final results. The currently most used method for microbiota analysis is either metagenomics sequencing or amplicon-based microbiota analysis using second-generation methods such as sequencing-by-synthesis approaches (Illumina), which is both expensive and time-consuming. Thus, additional approaches are warranted to accelerate the usability of the microbiome as a marker in clinical praxis.

METHODS: Herein, we used a set of ten selected vaginal swabs from women undergoing assisted reproduction, comparing and performing critical optimization of nanopore-based microbiota analysis with the results from MiSeq-based data as a quality reference.

RESULTS: The analyzed samples carried varying community compositions, as shown by amplicon-based analysis of the V3V4 region of the bacterial 16S rRNA gene by MiSeq sequencing. Using a stepwise procedure to optimize adaptation, we show that a close approximation of the microbial composition can be achieved within a reduced time frame and at a minimum of costs using nanopore sequencing.

CONCLUSIONS: Our work highlights the potential of a nanopore-based methodical setup to support the feasibility of interventional studies and contribute to the development of microbiome-based clinical decision-making in assisted reproduction.}, } @article {pmid36222702, year = {2022}, author = {Xu, S and Liu, Y and Zhang, Z and Xu, Y and Qi, Z}, title = {Distributional Pattern of Bacteria, Protists, and Diatoms in Ocean according to Water Depth in the Northern South China Sea.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0275921}, pmid = {36222702}, issn = {2165-0497}, mesh = {*Diatoms/genetics ; Water ; Biodiversity ; Eukaryota ; Bacteria/genetics ; *Microbiota/genetics ; China ; Oceans and Seas ; }, abstract = {Ocean microbiomes provide insightful details about the condition of water and the global impact of marine ecosystems. A fine-scale analysis of ocean microbes may shed light on the dynamics and function of the ocean microbiome community. In this study, we evaluated the changes in the community and function of marine bacteria, protists, and diatoms corresponding to different ocean depths using next-generation sequencing methods. We found that diatoms displayed a potential water-depth pattern in species richness (alpha diversity) and community composition (beta diversity). However, for bacteria and protists, there was no significant relationship between water depth and species richness. This may be related to the biological characteristics of diatoms. The photosynthesis of diatoms and their distribution may be associated with the fluctuating light regime in the underwater climate. Moreover, salinity displayed negative effects on the abundance of some diatom and bacterial groups, which indicates that salinity may be one of the factors restricting ocean microorganism diversity. In addition, compared to the global ocean microbiome composition, function, and antibiotic resistance genes, a water depth pattern due to the fine-scale region was not observed in this study. IMPORTANCE Fine-scale analysis of ocean microbes provides insights into the dynamics and functions of the ocean microbiome community. Here, using amplicon and metagenome sequencing methods, we found that diatoms in the northern South China Sea displayed a potential water-depth pattern in species richness and community composition, which may be related to their biological characteristics. The potential effects of the differences in geographic sites mainly occurred in the diatom and bacterial communities. Moreover, given the correlation between the environmental factors and relative abundance of antibiotic resistance genes (ARGs), the study of ocean ARG distribution patterns should integrate the potential effects of environmental factors.}, } @article {pmid36221927, year = {2023}, author = {Holmes, IA and Grundler, MC}, title = {Phylogenetically under-dispersed gut microbiomes are not correlated with host genomic heterozygosity in a genetically diverse reptile community.}, journal = {Molecular ecology}, volume = {32}, number = {1}, pages = {258-274}, pmid = {36221927}, issn = {1365-294X}, support = {T32 AI145821/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; Phylogeny ; *Microbiota ; Genomics ; Reptiles/genetics ; }, abstract = {While key elements of fitness in vertebrate animals are impacted by their microbiomes, the host genetic characteristics that factor into microbiome composition are not fully understood. Here, we correlate host genomic heterozygosity and gut microbiome phylogenetic diversity across a community of reptiles in southwestern New Mexico to test hypotheses about the behaviour of host genes that drive microbiome assembly. We find that microbiome communities are phylogenetically under-dispersed relative to random expectations, and that host heterozygosity is not correlated with microbiome diversity. Our analyses reinforce results from functional genomic work that identify conserved host immune and nonimmune genes as key players in microbiome assembly, rather than gene families that rely on heterozygosity for their function.}, } @article {pmid36221922, year = {2022}, author = {Lee, HJ and Cho, IS and Jeong, RD}, title = {Nanopore Metagenomics Sequencing for Rapid Diagnosis and Characterization of Lily Viruses.}, journal = {The plant pathology journal}, volume = {38}, number = {5}, pages = {503-512}, pmid = {36221922}, issn = {1598-2254}, support = {PJ014947032022//Rural Development Administration/ ; }, abstract = {Lilies (Lilium spp.) are one of the most important ornamental flower crops grown in Korea. Most viral diseases in lilies are transmitted by infected bulbs, which cause serious economic losses due to reduced yields. Various diagnostic techniques and high-throughput sequencing methods have been used to detect lily viruses. According to Oxford Nanopore Technologies (ONT), MinION is a compact and portable sequencing device. In this study, three plant viruses, lily mottle, lily symptomless, and plantago asiatica mosaic virus, were detected in lily samples using the ONT platform. As a result of genome assembly of reads obtained through ONT, 100% coverage and 90.3-93.4% identity were obtained. Thus, we show that the ONT platform is a promising tool for the diagnosis and characterization of viruses that infect crops.}, } @article {pmid36221916, year = {2022}, author = {Mansour, A and Mannaa, M and Hewedy, O and Ali, MG and Jung, H and Seo, YS}, title = {Versatile Roles of Microbes and Small RNAs in Rice and Planthopper Interactions.}, journal = {The plant pathology journal}, volume = {38}, number = {5}, pages = {432-448}, pmid = {36221916}, issn = {1598-2254}, support = {PJ01574901//Rural Development Administration/ ; }, abstract = {Planthopper infestation in rice causes direct and indirect damage through feeding and viral transmission. Host microbes and small RNAs (sRNAs) play essential roles in regulating biological processes, such as metabolism, development, immunity, and stress responses in eukaryotic organisms, including plants and insects. Recently, advanced metagenomic approaches have facilitated investigations on microbial diversity and its function in insects and plants, highlighting the significance of microbiota in sustaining host life and regulating their interactions with the environment. Recent research has also suggested significant roles for sRNA-regulated genes during rice-planthopper interactions. The response and behavior of the rice plant to planthopper feeding are determined by changes in the host transcriptome, which might be regulated by sRNAs. In addition, the roles of microbial symbionts and sRNAs in the host response to viral infection are complex and involve defense-related changes in the host transcriptomic profile. This review reviews the structure and potential functions of microbes and sRNAs in rice and the associated planthopper species. In addition, the involvement of the microbiota and sRNAs in the rice-planthopper-virus interactions during planthopper infestation and viral infection are discussed.}, } @article {pmid36221387, year = {2022}, author = {Cai, DH and Wang, J and Fang, XL}, title = {Successful treatment of Talaromyces marneffei pneumonia in a HIV-negative renal transplantation recipient: A case report.}, journal = {Medicine}, volume = {101}, number = {40}, pages = {e30958}, pmid = {36221387}, issn = {1536-5964}, mesh = {Antifungal Agents/therapeutic use ; *HIV Infections/drug therapy ; Humans ; *Kidney Transplantation/adverse effects ; Moxifloxacin ; Mycoses ; *Pneumonia/drug therapy ; Tacrolimus/therapeutic use ; Talaromyces ; Voriconazole/therapeutic use ; }, abstract = {RATIONALE: Talaromyces marneffei causes life-threatening opportunistic fungal infections in immunocompromised patients. It often has a poorer prognosis in non-human immunodeficiency virus (HIV)-infected than in HIV-infected individuals because of delayed diagnosis and improper treatment.

PATIENT CONCERNS: A 51-year-old man presented with complaints of pyrexia, cough, and expectoration that had lasted for 15 day. This patient has been taking anti-rejection medication since kidney transplant in 2011.

DIAGNOSIS: T marneffei pneumonia; post renal transplantation; renal insufficiency; hypertension.

INTERVENTIONS: Intravenous moxifloxacin was administered on admission. After the etiology was established, moxifloxacin was discontinued and replaced with voriconazole. The tacrolimus dose was adjusted based on the blood concentration of tacrolimus and voriconazole.

OUTCOMES: The patient was successfully treated and followed-up without recurrence for 1 year.

LESSONS: A high degree of caution should be maintained for the possibility of T marneffei infection in immunodeficient non-HIV patients who live in or have traveled to T marneffei endemic areas. Early diagnosis and appropriate treatment can prevent progression of T marneffei infection and achieve a cure. Metagenomic next-generation sequencing (mNGS) can aid the physician in reaching an early pathogenic diagnosis. Close monitoring of tacrolimus and voriconazole blood levels during treatment remains a practical approach at this time.}, } @article {pmid36220843, year = {2022}, author = {West, KA and Yin, X and Rutherford, EM and Wee, B and Choi, J and Chrisman, BS and Dunlap, KL and Hannibal, RL and Hartono, W and Lin, M and Raack, E and Sabino, K and Wu, Y and Wall, DP and David, MM and Dabbagh, K and DeSantis, TZ and Iwai, S}, title = {Multi-angle meta-analysis of the gut microbiome in Autism Spectrum Disorder: a step toward understanding patient subgroups.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {17034}, pmid = {36220843}, issn = {2045-2322}, support = {R44 DA043954/DA/NIDA NIH HHS/United States ; }, mesh = {*Autism Spectrum Disorder/genetics ; Bacteria/genetics ; Child ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; *Microbiota ; }, abstract = {Observational studies have shown that the composition of the human gut microbiome in children diagnosed with Autism Spectrum Disorder (ASD) differs significantly from that of their neurotypical (NT) counterparts. Thus far, reported ASD-specific microbiome signatures have been inconsistent. To uncover reproducible signatures, we compiled 10 publicly available raw amplicon and metagenomic sequencing datasets alongside new data generated from an internal cohort (the largest ASD cohort to date), unified them with standardized pre-processing methods, and conducted a comprehensive meta-analysis of all taxa and variables detected across multiple studies. By screening metadata to test associations between the microbiome and 52 variables in multiple patient subsets and across multiple datasets, we determined that differentially abundant taxa in ASD versus NT children were dependent upon age, sex, and bowel function, thus marking these variables as potential confounders in case-control ASD studies. Several taxa, including the strains Bacteroides stercoris t__190463 and Clostridium M bolteae t__180407, and the species Granulicatella elegans and Massilioclostridium coli, exhibited differential abundance in ASD compared to NT children only after subjects with bowel dysfunction were removed. Adjusting for age, sex and bowel function resulted in adding or removing significantly differentially abundant taxa in ASD-diagnosed individuals, emphasizing the importance of collecting and controlling for these metadata. We have performed the largest (n = 690) and most comprehensive systematic analysis of ASD gut microbiome data to date. Our study demonstrated the importance of accounting for confounding variables when designing statistical comparative analyses of ASD- and NT-associated gut bacterial profiles. Mitigating these confounders identified robust microbial signatures across cohorts, signifying the importance of accounting for these factors in comparative analyses of ASD and NT-associated gut profiles. Such studies will advance the understanding of different patient groups to deliver appropriate therapeutics by identifying microbiome traits germane to the specific ASD phenotype.}, } @article {pmid36220832, year = {2022}, author = {Hu, Y and Chen, Y and Xu, J and Wang, X and Luo, S and Mao, B and Zhou, Q and Li, W}, title = {Metagenomic discovery of novel CRISPR-Cas13 systems.}, journal = {Cell discovery}, volume = {8}, number = {1}, pages = {107}, pmid = {36220832}, issn = {2056-5968}, support = {31621004//National Natural Science Foundation of China (National Science Foundation of China)/ ; 31621004//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, } @article {pmid36219973, year = {2022}, author = {Muñoz-García, A and Arbeli, Z and Boyacá-Vásquez, V and Vanegas, J}, title = {Metagenomic and genomic characterization of heavy metal tolerance and resistance genes in the rhizosphere microbiome of Avicennia germinans in a semi-arid mangrove forest in the tropics.}, journal = {Marine pollution bulletin}, volume = {184}, number = {}, pages = {114204}, doi = {10.1016/j.marpolbul.2022.114204}, pmid = {36219973}, issn = {1879-3363}, mesh = {*Avicennia/genetics ; Wetlands ; Rhizosphere ; Metagenomics ; Cadmium ; *Metals, Heavy/toxicity ; *Microbiota ; }, abstract = {Mangroves are often exposed to heavy metals that accumulate in the food chain, generate toxicity to mangrove plants and affect microbial diversity. This study determined the abundance of genes associated with resistance and tolerance to heavy metals in the rhizosphere microbiome of Avicennia germinans from a semi-arid mangrove of La Guajira-Colombia by metagenomics and genomics approach. Twenty-eight genes associated with tolerance and 49 genes related to resistance to heavy metals were detected. Genes associated with tolerance and resistance to Cu, especially cusA and copA, were the most abundant. The highest number of genes for tolerance and resistance were for Zn and Co, respectively. The isolate Vibrio fluvialis showed the ability to tolerate Cu, Ni, Zn, and Cd. This work used a complementary approach of metagenomics and genomics to characterize the potential of mangrove microorganisms to tolerate and resist heavy metals and the influence of salinity on their abundance.}, } @article {pmid36219101, year = {2022}, author = {Pi, Y and Zhang, X and Wu, Y and Wang, Z and Bai, Y and Liu, X and Han, D and Zhao, J and Tobin, I and Zhao, J and Zhang, G and Wang, J}, title = {Alginate Alleviates Dextran Sulfate Sodium-Induced Colitis by Promoting Bifidobacterium animalis and Intestinal Hyodeoxycholic Acid Synthesis in Mice.}, journal = {Microbiology spectrum}, volume = {10}, number = {6}, pages = {e0297922}, pmid = {36219101}, issn = {2165-0497}, mesh = {Mice ; Animals ; *Bifidobacterium animalis ; Dextran Sulfate/toxicity ; Alginates/adverse effects/metabolism ; RNA, Ribosomal, 16S/genetics ; *Colitis/chemically induced/therapy ; Colon/microbiology ; *Inflammatory Bowel Diseases ; Anti-Inflammatory Agents/adverse effects ; Inflammation/metabolism ; Disease Models, Animal ; }, abstract = {Alginate (ALG) is known to alleviate intestinal inflammation in inflammatory bowel disease, but its mechanism of action remains elusive. In the present study, we studied the involvement of the intestinal microbiota and bile acid (BA) metabolism in ALG-mediated anti-inflammatory effects in mice. A combination of 16S rRNA gene amplicon sequencing, shotgun metagenomic sequencing, and targeted BA metabolomic profiling was employed to investigate structural and functional differences in the colonic microbiota and BA metabolism in dextran sulfate sodium (DSS)-treated mice with or without dietary supplementation of ALG. We further explored the role of the intestinal microbiota as well as a selected ALG-enriched bacterium and BA in DSS-induced colitis. Dietary ALG alleviated DSS-mediated intestinal inflammation and enriched a small set of bacteria including Bifidobacterium animalis in the colon (P < 0.05). Additionally, ALG restored several bacteria carrying secondary BA-synthesizing enzymes such as 7α-hydroxysteroid dehydrogenase and BA hydrolase to healthy levels in DSS-treated mice. Although a majority of BAs were suppressed by DSS, a few secondary BAs such as hyodeoxycholic acid (HDCA) were markedly enriched by ALG. Furthermore, ALG significantly upregulated the expression of a major BA receptor, the farnesoid X receptor, while suppressing NF-κB and c-Jun N-terminal kinase (JNK) activation. Depletion of the intestinal microbiota completely abrogated the protective effect of ALG in DSS-treated mice. Similar to ALG, B. animalis and HDCA exerted a strong anti-inflammatory effect in DSS-induced colitis by downregulating inflammatory cytokines (interleukin-1β [IL-1β], IL-6, and tumor necrosis factor alpha [TNF-α]). Taken together, these results indicated that ALG achieves its alleviating effect on intestinal inflammation through regulation of the microbiota by enriching B. animalis to promote the biosynthesis of specific secondary BAs such as HDCA. These findings have revealed intricate interactions among the intestinal microbiota, BA metabolism, and intestinal health and further provided a novel strategy to improve intestinal health through targeted manipulation of the intestinal microbiota and BA metabolism. IMPORTANCE ALG has been shown to ameliorate inflammatory bowel disease (IBD), but little is known about the mechanism of its anti-inflammatory action. This study was the first to demonstrate that ALG provided a preventive effect against colitis in an intestinal microbiota-dependent manner. Furthermore, we confirmed that by selectively enriching intestinal B. animalis and secondary BA (HDCA), ALG contributed to the attenuation of DSS-induced colitis. These findings contribute to a better understanding of the mechanism of action of ALG on the attenuation of colitis and provide new approaches to IBD therapy by regulating gut microbial BA metabolism.}, } @article {pmid36218363, year = {2022}, author = {Cao, H and Bougouffa, S and Park, TJ and Lau, A and Tong, MK and Chow, KH and Ho, PL}, title = {Sharing of Antimicrobial Resistance Genes between Humans and Food Animals.}, journal = {mSystems}, volume = {7}, number = {6}, pages = {e0077522}, pmid = {36218363}, issn = {2379-5077}, mesh = {Humans ; Animals ; Swine/genetics ; *Anti-Bacterial Agents/pharmacology ; *Drug Resistance, Bacterial/genetics ; Bacteria/genetics ; Genes, Bacterial ; Metagenome ; }, abstract = {The prevalence and propagation of antimicrobial resistance (AMR) are serious global public health concerns. The large and the ever-increasing use of antibiotics in livestock is also considered a great concern. The extent of the similarity of acquired antibiotic resistance genes (ARGs) between humans and food animals and the driving factors underlying AMR transfer between them are not clear, although a link between ARGs in both hosts was proposed. To address this question, with swine and chicken as examples of food animals, we analyzed over 1,000 gut metagenomes of humans and food animals from over the world. A relatively high abundance and diversity of ARGs were observed in swine compared with those in humans as a whole. Commensal bacteria, particularly species from Clostridiales, contribute the most ARGs associated with mobile genetic elements (MGEs) and were found in both humans and food animals. Further studies demonstrate that overrepresented MGEs, namely, Tn4451/Tn4453 and TnAs3, are attributed mainly to the sharing between humans and food animals. A member of large resolvase family site-specific recombinases, TnpX, is found in Tn4451/Tn4453 which facilitates the insertions of the transient circular molecule. Although the variance in the transferability of ARGs in humans is higher than that in swine, a higher average transferability was observed in swine than that in humans. In conclusion, the potential antibiotic resistance hot spots with higher transferability in food animals observed in the present study emphasize the importance of surveillance for emerging resistance threats before they spread. IMPORTANCE Antimicrobial resistance (AMR) has proven to be a global public health concern. To conquer this increasingly worrying trend, an overarching, One Health approach has been used that brings together different sectors, but the fundamental knowledge of the relationship between humans, food animals, and their environments is not mature yet or is lacking in some aspect. With swine and chicken as examples of food animals, a large global data set of over 1,000 human and food animal gut metagenomes was analyzed with a focus on acquired antibiotic resistance genes (ARGs) associated with mobile genetic elements (MGEs) to answer this question. Outputs from this work open a new avenue to further our understanding of ARG transferability in food animals. It is a necessary milestone to better equip governmental agencies to monitor and pre-empt antibiotic resistance hot spots. This work will assist and give guidance on how to decipher other links within any One Health initiatives with expected positive feedback to human health.}, } @article {pmid36217535, year = {2022}, author = {Penney, NC and Yeung, DKT and Garcia-Perez, I and Posma, JM and Kopytek, A and Garratt, B and Ashrafian, H and Frost, G and Marchesi, JR and Purkayastha, S and Hoyles, L and Darzi, A and Holmes, E}, title = {Multi-omic phenotyping reveals host-microbe responses to bariatric surgery, glycaemic control and obesity.}, journal = {Communications medicine}, volume = {2}, number = {}, pages = {127}, pmid = {36217535}, issn = {2730-664X}, support = {MR/S004033/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {BACKGROUND: Resolution of type 2 diabetes (T2D) is common following bariatric surgery, particularly Roux-en-Y gastric bypass. However, the underlying mechanisms have not been fully elucidated.

METHODS: To address this we compare the integrated serum, urine and faecal metabolic profiles of participants with obesity ± T2D (n = 80, T2D = 42) with participants who underwent Roux-en-Y gastric bypass or sleeve gastrectomy (pre and 3-months post-surgery; n = 27), taking diet into account. We co-model these data with shotgun metagenomic profiles of the gut microbiota to provide a comprehensive atlas of host-gut microbe responses to bariatric surgery, weight-loss and glycaemic control at the systems level.

RESULTS: Here we show that bariatric surgery reverses several disrupted pathways characteristic of T2D. The differential metabolite set representative of bariatric surgery overlaps with both diabetes (19.3% commonality) and body mass index (18.6% commonality). However, the percentage overlap between diabetes and body mass index is minimal (4.0% commonality), consistent with weight-independent mechanisms of T2D resolution. The gut microbiota is more strongly correlated to body mass index than T2D, although we identify some pathways such as amino acid metabolism that correlate with changes to the gut microbiota and which influence glycaemic control.

CONCLUSION: We identify multi-omic signatures associated with responses to surgery, body mass index, and glycaemic control. Improved understanding of gut microbiota - host co-metabolism may lead to novel therapies for weight-loss or diabetes. However, further experiments are required to provide mechanistic insight into the role of the gut microbiota in host metabolism and establish proof of causality.}, } @article {pmid36217343, year = {2022}, author = {Fang, C and Xu, L and Tan, J and Tan, H and Lin, J and Zhao, Z}, title = {Omadacycline for the Treatment of Severe Chlamydia psittaci Pneumonia Complicated with Multiple Organ Failure: A Case Report.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {5831-5838}, pmid = {36217343}, issn = {1178-6973}, abstract = {Psittacosis is a rare zoonotic disease caused by Chlamydia psittaci infection, and tetracyclines are the preferred treatment. Omadacycline is a novel tetracycline that has a strong in vitro antibacterial activity against atypical pathogens, including C. psittaci; however, clinical data for its usage are lacking. We report a patient with severe C. psittaci-induced pneumonia presenting with a high fever, muscle aches, severe hepatic and renal insufficiency, and acute respiratory failure requiring tracheal intubation and mechanical ventilation. The condition was diagnosed using metagenomic next-generation sequencing. The patient was discharged after treatment with omadacycline. The findings of this study suggest that metagenomic next-generation sequencing is valuable for the rapid and accurate diagnosis of psittacosis. With its good safety profile and no requirement for dose adjustment in special populations, omadacycline is a new option for the treatment of severe C. psittaci pneumonia. However, additional case reports are needed to support this conclusion.}, } @article {pmid36216964, year = {2022}, author = {Chang, A and Mzava, O and Djomnang, LK and Lenz, JS and Burnham, P and Kaplinsky, P and Andama, A and Connelly, J and Bachman, CM and Cattamanchi, A and Steadman, A and De Vlaminck, I}, title = {Metagenomic DNA sequencing to quantify Mycobacterium tuberculosis DNA and diagnose tuberculosis.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {16972}, pmid = {36216964}, issn = {2045-2322}, support = {DP2 AI138242/AI/NIAID NIH HHS/United States ; R01 AI146165/AI/NIAID NIH HHS/United States ; R01 AI151059/AI/NIAID NIH HHS/United States ; T32 GM008267/GM/NIGMS NIH HHS/United States ; }, mesh = {Biomarkers ; DNA ; Humans ; *Mycobacterium tuberculosis/genetics ; Nontuberculous Mycobacteria/genetics ; Sensitivity and Specificity ; Sequence Analysis, DNA ; Sputum/microbiology ; *Tuberculosis/diagnosis/microbiology ; }, abstract = {Tuberculosis (TB) remains a significant cause of mortality worldwide. Metagenomic next-generation sequencing has the potential to reveal biomarkers of active disease, identify coinfection, and improve detection for sputum-scarce or culture-negative cases. We conducted a large-scale comparative study of 428 plasma, urine, and oral swab samples from 334 individuals from TB endemic and non-endemic regions to evaluate the utility of a shotgun metagenomic DNA sequencing assay for tuberculosis diagnosis. We found that the composition of the control population had a strong impact on the measured performance of the diagnostic test: the use of a control population composed of individuals from a TB non-endemic region led to a test with nearly 100% specificity and sensitivity, whereas a control group composed of individuals from TB endemic regions exhibited a high background of nontuberculous mycobacterial DNA, limiting the diagnostic performance of the test. Using mathematical modeling and quantitative comparisons to matched qPCR data, we found that the burden of Mycobacterium tuberculosis DNA constitutes a very small fraction (0.04 or less) of the total abundance of DNA originating from mycobacteria in samples from TB endemic regions. Our findings suggest that the utility of a minimally invasive metagenomic sequencing assay for pulmonary tuberculosis diagnostics is limited by the low burden of M. tuberculosis and an overwhelming biological background of nontuberculous mycobacterial DNA.}, } @article {pmid36216115, year = {2022}, author = {Yin, X and Zheng, J and Liu, Y and Li, Y and Yu, X and Li, Y and Wang, X}, title = {Metagenomic evidence for increasing antibiotic resistance in progeny upon parental antibiotic exposure as the cost of hormesis.}, journal = {Chemosphere}, volume = {309}, number = {Pt 2}, pages = {136738}, doi = {10.1016/j.chemosphere.2022.136738}, pmid = {36216115}, issn = {1879-1298}, mesh = {*Anti-Bacterial Agents/toxicity ; *Tumor Necrosis Factor-alpha/genetics ; Hormesis ; Sulfamethazine ; Toll-Like Receptor 3/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; }, abstract = {Antibiotics are widely consumed in the intensive mariculture industry. A better understanding of the effect of antibiotics on intergenerational antibiotic resistance in organisms is urgent since intergenerational transmission is crucial for the spread of antibiotic resistance genes (ARGs) in the environment. Herein, marine medaka (Oryzias melastigma) chronically exposed to low doses of sulfamethazine (SMZ) hormetically affected the progeny, characterized by increased richness and diversity of fecal microbiota and intestinal barrier-related gene up-regulation. Progeny immunity was modulated and caused by genetic factors due to the absence of significant SMZ accumulation in F1 embryos. In addition, some of the top genera in the progeny were positively correlated with immune diseases, while the expression of some immune-related genes, such as TNFα, IL1R2, and TLR3 changed significantly. This further indicated that the host selection caused by changes in progeny immunity was probably the primary determinant of progeny intestinal microbial colonization. Metagenomic analysis revealed that Proteobacteria represented the primary carriers of ARGs, while parental SMZ exposure facilitated the distribution and enrichment of multiple ARGs involved in the antibiotic inactivation in the progeny by promoting the diversity of Gammaproteobacteria and Bacteroidetes, further illustrating that antibiotic selection pressure persisted even if the offspring were not exposed. Therefore, SMZ induced hormesis in the progeny at the expense of increasing antibiotic resistance. Collectively, these findings provide a comprehensive overview of the intergenerational effect of antibiotics and serve as a reminder that the ARG transmission induced by the intergenerational impact of antibiotics on organisms should not be ignored.}, } @article {pmid36216056, year = {2023}, author = {Yi, W and Ji, Y and Gao, H and Luo, S and Pan, R and Song, J and He, Y and Li, Y and Wu, Y and Yan, S and Liang, Y and Sun, X and Jin, X and Mei, L and Cheng, J and Su, H}, title = {Effects of urban particulate matter on gut microbiome and partial schizophrenia-like symptoms in mice: Evidence from shotgun metagenomic and metabolomic profiling.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 1}, pages = {159305}, doi = {10.1016/j.scitotenv.2022.159305}, pmid = {36216056}, issn = {1879-1026}, mesh = {Animals ; Mice ; *Gastrointestinal Microbiome ; Particulate Matter/toxicity ; *Schizophrenia ; Dizocilpine Maleate/pharmacology ; Phosphorylcholine/pharmacology ; Feces ; Estriol ; Estrogens ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Epidemiological evidence reported that particulate matter (PM) was associated with increased schizophrenia (SCZ) risk. Disturbance of gut microbiome was involved in SCZ. However, it remains unclear whether PM induces SCZ-like symptoms and how gut microbiome regulates them. Therefore, a multi-omics animal experiment was conducted to verify how urban PM induces SCZ-like behavior and altered gut microbiota and metabolic pathways.

METHODS: Using a completely random design, mice were divided into three groups: PM group, control group and MK801 group, which received daily tracheal instillation of PM solution, sterile PBS solution and intraperitoneal injection of MK801 (establish SCZ model), respectively. After a 14-day intervention, feces were collected for multi-omics testing (shotgun metagenomic sequencing and untargeted metabolomic profiling), followed by open field test, tail suspension test, and passive avoidance test. Besides, fecal microbiome of PM group and control group were transplanted into "pseudo-sterile" mice, then behavioral tests were conducted.

RESULTS: Similar to MK801 group, mice in PM group showed SCZ-like symptoms, including increased spontaneous activity, excitability, anxiety and decreased learning and spatial memory. PM exposure significantly increased the relative abundance of Verrucomicrobia and decreased that of Fibrobacteres et al. The metabolism pathways of estrogen signaling (estriol, 16-glucuronide-estriol and 21-desoxycortisol) and choline metabolism (phosphocholine) were significantly altered by PM exposure. Verrucomicrobia was negatively correlated with the level of estriol, which was correlated with decreased learning and spatial memory. Fibrobacteres and Deinococcus-Thermus were positively correlated with the level of phosphocholine, which was correlated with increased spontaneous activity, excitability and anxiety. Fecal microbiome transplantation from PM group mice reproduced excitability and anxiety symptoms.

CONCLUSIONS: Exposure to PM may affect composition of gut microbiome and alterations of estrogen signaling pathway and choline metabolism pathway, which were associated with partial SCZ-like behaviors. But whether gut microbiome regulates these metabolic pathways and behaviors remains to be determined.}, } @article {pmid36216053, year = {2023}, author = {Yang, X and Ni, K and Shi, Y and Yi, X and Ji, L and Wei, S and Jiang, Y and Zhang, Y and Cai, Y and Ma, Q and Tang, S and Ma, L and Ruan, J}, title = {Metagenomics reveals N-induced changes in carbon-degrading genes and microbial communities of tea (Camellia sinensis L.) plantation soil under long-term fertilization.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 2}, pages = {159231}, doi = {10.1016/j.scitotenv.2022.159231}, pmid = {36216053}, issn = {1879-1026}, mesh = {Soil/chemistry ; Carbon/analysis ; *Camellia sinensis/metabolism ; Soil Microbiology ; Metagenomics ; *Microbiota ; Nitrogen/analysis ; Tea ; *Chitinases ; *Cellulases ; Fertilization ; }, abstract = {Soil organic carbon (SOC) is an important C pool of the global ecosystem and is affected by various agricultural practices including fertilization. Excessive nitrogen (N) application is an important field management measure in tea plantation systems. However, the mechanism underlying the impact of N fertilization on SOC, especially the microscopic mechanism remain unclear. The present study explored the effects of N fertilization on C-cycling genes, SOC-degrading enzymes and microbes expressing these enzymes by using a metagenomic approach in a tea plantation under long-term fertilization with different N rates. Results showed that N application significantly changed the abundance of C-cycling genes, SOC-degrading enzymes, especially those associated with labile and recalcitrant C degradation. In addition, the beta-glucosidase and chitinase-expressing microbial communities showed a significant difference under different N rates. At the phylum level, microbial taxa involved in C degradation were highly similar and abundant, while at the genus level, only specific taxa performed labile and recalcitrant C degradation; these SOC-degrading microbes were significantly enriched under N application. Redundancy analysis (RDA) revealed that the soil and pruned litter properties greatly influenced the SOC-degrading communities; pH and DOC of the soil and biomass and total polyphenol (TP) of the pruned litter exerted significant effects. Additionally, the random forest (RF) algorithm revealed that soil pH and dominant taxa efficiently predicted the beta-glucosidase abundance, while soil pH and DOC, pruned litter TP, and the highly abundant microbial taxa efficiently predicted chitinase abundance. Our study indicated that long-term N fertilization exerted a significant positive effect on SOC-degrading enzymes and microbes expressing these enzymes, resulting in potential impact on soil C storage in a perennial tea plantation ecosystem.}, } @article {pmid36215840, year = {2022}, author = {Hu, J and Chen, Q and Zhong, S and Liu, Y and Gao, Q and Graham, EB and Chen, H and Sun, W}, title = {Insight into co-hosts of nitrate reduction genes and antibiotic resistance genes in an urban river of the qinghai-tibet plateau.}, journal = {Water research}, volume = {225}, number = {}, pages = {119189}, doi = {10.1016/j.watres.2022.119189}, pmid = {36215840}, issn = {1879-2448}, mesh = {Humans ; *Rivers/microbiology ; *Anti-Bacterial Agents/pharmacology ; Nitrates ; Genes, Bacterial ; Tibet ; Drug Resistance, Microbial/genetics ; Bacteria ; Water ; Sulfonamides ; }, abstract = {Microbial co-hosts of nitrate reduction genes (NRGs) and antibiotic resistance genes (ARGs) have been recently reported, but their ecology and biochemical role in urban waterways remain largely unknown. Here, we collected 29 surface water and 29 sediment samples in the Huangshui River on the Qinghai-Tibet Plateau during the wet and dry season, and 11 water samples from wastewater treatment plants and wetlands along the river. Using metagenomic sequencing, we retrieved 278 medium-to-high-quality metagenome-assembled genomes (MAGs) of NRG-ARG co-hosts, mainly belonging to the phyla Proteobacteria, Actinobacteriota, and Bacteroidota. Of microorganisms carrying ARGs, a high proportion (75.3%‒94.9%) also encoded NRGs, supporting nitrate reducing bacteria as dominant hosts of ARGs. Seasonal changes in antibiotic levels corresponded to significant variation in the relative abundance of NRG-ARG co-host in both water and sediments, resulting in a concomitant change in antibiotic resistance pathways. In contrast, the contribution of NRG-ARG co-hosts to nitrate reduction was stable between seasons. We identify specific antibiotics (e.g., sulphonamides) and microbial taxa (e.g., Acinetobacter and Hafnia) that may disproportionately impact these relationships to serve as a basis for laboratory investigations into bioremediation strategies. Our study suggests that highly abundant nitrate reducing microorganisms in contaminated environments may also directly impact human health as carriers of antibiotic resistance.}, } @article {pmid36215489, year = {2022}, author = {Colman, DR and Kraus, EA and Thieringer, PH and Rempfert, K and Templeton, AS and Spear, JR and Boyd, ES}, title = {Deep-branching acetogens in serpentinized subsurface fluids of Oman.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {42}, pages = {e2206845119}, pmid = {36215489}, issn = {1091-6490}, mesh = {Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; *Carbon Monoxide/metabolism ; *Ferredoxins/metabolism ; Hydrogen/metabolism ; Magnesium Silicates ; Oman ; Water/metabolism ; }, abstract = {Little is known of acetogens in contemporary serpentinizing systems, despite widely supported theories that serpentinite-hosted environments supported the first life on Earth via acetogenesis. To address this knowledge gap, genome-resolved metagenomics was applied to subsurface fracture water communities from an area of active serpentinization in the Samail Ophiolite, Sultanate of Oman. Two deeply branching putative bacterial acetogen types were identified in the communities belonging to the Acetothermia (hereafter, types I and II) that exhibited distinct distributions among waters with lower and higher water-rock reaction (i.e., serpentinization influence), respectively. Metabolic reconstructions revealed contrasting core metabolic pathways of type I and II Acetothermia, including in acetogenic pathway components (e.g., bacterial- vs. archaeal-like carbon monoxide dehydrogenases [CODH], respectively), hydrogen use to drive acetogenesis, and chemiosmotic potential generation via respiratory (type I) or canonical acetogen ferredoxin-based complexes (type II). Notably, type II Acetothermia metabolic pathways allow for use of serpentinization-derived substrates and implicate them as key primary producers in contemporary hyperalkaline serpentinite environments. Phylogenomic analyses indicate that 1) archaeal-like CODH of the type II genomes and those of other serpentinite-associated Bacteria derive from a deeply rooted horizontal transfer or origin among archaeal methanogens and 2) Acetothermia are among the earliest evolving bacterial lineages. The discovery of dominant and early-branching acetogens in subsurface waters of the largest near-surface serpentinite formation provides insight into the physiological traits that likely facilitated rock-supported life to flourish on a primitive Earth and possibly on other rocky planets undergoing serpentinization.}, } @article {pmid36215419, year = {2022}, author = {Zhang, L and Hao, S and Dou, Q and Dong, T and Qi, WK and Huang, X and Peng, Y and Yang, J}, title = {Multi-Omics Analysis Reveals the Nitrogen Removal Mechanism Induced by Electron Flow during the Start-up of the Anammox-Centered Process.}, journal = {Environmental science & technology}, volume = {56}, number = {22}, pages = {16115-16124}, doi = {10.1021/acs.est.2c02181}, pmid = {36215419}, issn = {1520-5851}, mesh = {*Nitrogen/metabolism ; *Denitrification ; Bioreactors ; Electrons ; Anaerobic Ammonia Oxidation ; Oxidation-Reduction ; Wastewater ; Sewage ; }, abstract = {Significant progress in understanding the key enzymes or species of anammox has been made; however, the nitrogen removal mechanism in complex coupling systems centered on anammox remains limited. In this study, by the combination of metagenomics-metatranscriptomics analyses, the nitrogen removal in the anammox-centered coupling system that entails partial denitrification (PD) and hydrolytic acidification (HA, A-PDHA) was elucidated to be the nitrogen transformation driven by the electron generation-transport-consumption process. The results showed that a total nitrogen (TN) removal efficiency of >98%, with a TN effluence of <1 mg/L and a TN removal contribution via anammox of >98%, was achieved after 59 days under famine operation and alkaline conditions during the start-up process. Further investigation confirmed that famine operation promoted the activity of genes responsible for electron generation in anammox, and increased the abundance or expression of genes related to electron consumption. Alkaline conditions enhanced the electron generation for PD by upregulating the activity of glyceraldehyde 3-phosphate dehydrogenase and strengthened electron transfer by increasing the gene encoding quinone pool. Altogether, these variations in the electron flow led to efficient nitrogen removal. These results improve our understanding of the nitrogen removal mechanism and application of the anammox-centered coupling systems in treating nitrogen wastewater.}, } @article {pmid36214570, year = {2022}, author = {Utter, DR and Cavanaugh, CM and Borisy, GG}, title = {Genome-Centric Dynamics Shape the Diversity of Oral Bacterial Populations.}, journal = {mBio}, volume = {13}, number = {6}, pages = {e0241422}, pmid = {36214570}, issn = {2150-7511}, support = {R01 DE030136/DE/NIDCR NIH HHS/United States ; UL1 TR001102/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; *Microbiota/genetics ; Bacteria/genetics ; Metagenome ; Genome, Bacterial ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; }, abstract = {Two major viewpoints have been put forward for how microbial populations change, differing in whether adaptation is driven principally by gene-centric or genome-centric processes. Longitudinal sampling at microbially relevant timescales, i.e., days to weeks, is critical for distinguishing these mechanisms. Because of its significance for both microbial ecology and human health and its accessibility and high level of curation, we used the oral microbiota to study bacterial intrapopulation genome dynamics. Metagenomes were generated by shotgun sequencing of total community DNA from the healthy tongues of 17 volunteers at four to seven time points obtained over intervals of days to weeks. We obtained 390 high-quality metagenome-assembled genomes (MAGs) defining population genomes from 55 genera. The vast majority of genes in each MAG were tightly linked over the 2-week sampling window, indicating that the majority of the population's genomes were temporally stable at the MAG level. MAG-defined populations were composed of up to 5 strains, as determined by single-nucleotide-variant frequencies. Although most were stable over time, individual strains carrying over 100 distinct genes that rose from low abundance to dominance in a population over a period of days were detected. These results indicate a genome-wide as opposed to a gene-level process of population change. We infer that genome-wide selection of ecotypes is the dominant mode of adaptation in the oral populations over short timescales. IMPORTANCE The oral microbiome represents a microbial community of critical relevance to human health. Recent studies have documented the diversity and dynamics of different bacteria to reveal a rich, stable ecosystem characterized by strain-level dynamics. However, bacterial populations and their genomes are neither monolithic nor static; their genomes are constantly evolving to lose, gain, or alter their functional potential. To better understand how microbial genomes change in complex communities, we used culture-independent approaches to reconstruct the genomes (MAGs) for bacterial populations that approximated different species, in 17 healthy donors' mouths over a 2-week window. Our results underscored the importance of strain-level dynamics, which agrees with and expands on the conclusions of previous research. Altogether, these observations reveal patterns of genomic dynamics among strains of oral bacteria occurring over a matter of days.}, } @article {pmid36213767, year = {2022}, author = {Zhu, M and Wang, Q and Wang, M and Wang, S and Gong, Q and Zhang, X and Chen, L}, title = {Rare Hepatic Cryptococcosis Mimicked Metastatic Liver Cancer and Confirmed by Metagenomic Next-Generation Sequencing in an Immunocompetent Patient: A Case Report.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {5753-5758}, pmid = {36213767}, issn = {1178-6973}, abstract = {BACKGROUND: Cryptococcus neoformans (C. neoformans) is commonly presented in immunocompromised individuals and causes cryptococcosis mostly in the respiratory and/or central nervous system. Liver cryptococcosis is exceedingly rare and sometimes difficult to diagnose through conventional assays.

CASE PRESENTATION: The present study reports a rare case of liver cryptococcosis characterized by increased serum carbohydrate antigen 19-9 (CA19-9) level and intrahepatic multiple nodules without other symptoms in an immunocompetent woman. Her cancer family history and imaging examinations initially suspected metastatic liver malignancy. But no sign of the malignant tumor was found after endoscopy, 18-fluorine fluorodeoxyglucose positron emission tomography-computed tomography, and liver biopsy. The histopathology of the liver biopsy specimen indicated chronic inflammatory granuloma and then infectious diseases were suspected. However, traditional microbiologic testing failed to identify any potential pathogen. Eventually, metagenomic next-generation sequencing (mNGS) was applied to identify the definite diagnosis of liver cryptococcosis by acquiring the genome sequence of C. neoformans. Fortunately, after 6-month diagnostic anti-fungal therapy of fluconazole, the liver nodules effectively faded away and the serum CA19-9 level gradually regressed to the normal range.

CONCLUSION: We identified a rare case of hepatic cryptococcosis by mNGS in an immunocompetent patient. When conventional methods have difficulties in the diagnosis of a specific pathogen, mNGS has the advantage of early and accurate identification of potential pathogens from the specimen.}, } @article {pmid36212884, year = {2022}, author = {Jackson, SA and Duan, M and Zhang, P and Ihua, MW and Stengel, DB and Duan, D and Dobson, ADW}, title = {Isolation, identification, and biochemical characterization of a novel bifunctional phosphomannomutase/phosphoglucomutase from the metagenome of the brown alga Laminaria digitata.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1000634}, pmid = {36212884}, issn = {1664-302X}, abstract = {Macroalgae host diverse epiphytic bacterial communities with potential symbiotic roles including important roles influencing morphogenesis and growth of the host, nutrient exchange, and protection of the host from pathogens. Macroalgal cell wall structures, exudates, and intra-cellular environments possess numerous complex and valuable carbohydrates such as cellulose, hemi-cellulose, mannans, alginates, fucoidans, and laminarin. Bacterial colonizers of macroalgae are important carbon cyclers, acquiring nutrition from living macroalgae and also from decaying macroalgae. Seaweed epiphytic communities are a rich source of diverse carbohydrate-active enzymes which may have useful applications in industrial bioprocessing. With this in mind, we constructed a large insert fosmid clone library from the metagenome of Laminaria digitata (Ochrophyta) in which decay was induced. Subsequent sequencing of a fosmid clone insert revealed the presence of a gene encoding a bifunctional phosphomannomutase/phosphoglucomutase (PMM/PGM) enzyme 10L6AlgC, closely related to a protein from the halophilic marine bacterium, Cobetia sp. 10L6AlgC was subsequently heterologously expressed in Escherichia coli and biochemically characterized. The enzyme was found to possess both PMM and PGM activity, which had temperature and pH optima of 45°C and 8.0, respectively; for both activities. The PMM activity had a K m of 2.229 mM and V max of 29.35 mM min[-1] mg[-1], while the PGM activity had a K m of 0.5314 mM and a V max of 644.7 mM min[-1] mg[-1]. Overall characterization of the enzyme including the above parameters as well as the influence of various divalent cations on these activities revealed that 10L6AlgC has a unique biochemical profile when compared to previously characterized PMM/PGM bifunctional enzymes. Thus 10L6AlgC may find utility in enzyme-based production of biochemicals with different potential industrial applications, in which other bacterial PMM/PGMs have previously been used such as in the production of low-calorie sweeteners in the food industry.}, } @article {pmid36212869, year = {2022}, author = {Jiang, H and Bao, J and Xing, Y and Cao, G and Li, X and Chen, Q}, title = {Metabolomic and metagenomic analyses of the Chinese mitten crab Eriocheir sinensis after challenge with Metschnikowia bicuspidata.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {990737}, pmid = {36212869}, issn = {1664-302X}, abstract = {Milky disease caused by Metschnikowia bicuspidata fungus has significantly harmed the Chinese mitten crab Eriocheir sinensis aquaculture industry. However, the effect of M. bicuspidata infection on the metabolism and intestinal flora of the crab remains unclear. In this study, we aimed to explore the changes in the metabolism and intestinal flora E. sinensis after 48 h of infection with M. bicuspidata, using metabolomic and metagenomic analyses. Metabolomic analysis results revealed 420 significantly different metabolites between the infected and control groups, and these metabolites were enriched in 58 metabolic pathways. M. bicuspidata infection decreased the levels of metabolites related to amino acid biosynthesis, the tricarboxylic acid cycle, as well as lysine, histidine, linolenic, arachidonic, and linoleic acid metabolism. These results indicated that M. bicuspidata infection significantly affected the energy metabolism, growth, and immunity of E. sinensis. The results of metagenomic analysis showed that the anaerobes and ascomycetes populations significantly increased and decreased, respectively, after M. bicuspidata infection. These changes in intestinal flora significantly upregulated metabolic and synthetic pathways while downregulating immunity-related pathways. The results of integrated metabolomic and metagenomic analyses showed that 55 differentially expressed genes and 28 operational taxonomic units were correlated with 420 differential metabolites. Thus, the intestinal flora changes caused by M. bicuspidata infection also affected the metabolites. This study provides novel insights into the metabolic-and intestinal microflora-based effects of M. bicuspidata infection in E. sinensis, as well as a theoretical basis for the interaction between fungi and crustaceans.}, } @article {pmid36212858, year = {2022}, author = {Zhu, F and Fang, Y and Wang, Z and Wang, P and Yang, K and Xiao, L and Wang, R}, title = {Salicylic acid remodeling of the rhizosphere microbiome induces watermelon root resistance against Fusarium oxysporum f. sp. niveum infection.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1015038}, pmid = {36212858}, issn = {1664-302X}, abstract = {Fusarium wilt disease poses a severe threat to watermelon cultivation by affecting the yield and quality of the fruit. We had previously found that the rhizosphere microbiome has a significant impact on the ability of watermelon plants to resist Fusarium wilt development and that salicylic acid (SA) is closely related to this phenomenon. Therefore, in this study, the role of SA as a mediator between plants and microbes in activating resistance against Fusarium oxysporum f. sp. niveum (FON) infection was explored through physiological, biochemical, and metagenomic sequencing experiments. We demonstrated that exogenous SA treatment could specifically increase some beneficial rhizosphere species that can confer resistance against FON inoculation, such as Rhodanobacter, Sphingomonas, and Micromonospora. Functional annotation analysis indicated that SA application significantly increased the relative abundance of glycoside hydrolase and polysaccharide lyase genes in the microbiome, which may play an essential role in increasing plant lipids. Moreover, network interaction analysis suggested that the highly expressed AAC6_IIC gene may be manipulated through SA signal transduction pathways. In conclusion, these results provide a novel strategy for controlling Fusarium wilt in watermelons from the perspective of environmental ecology, that is, by manipulating the rhizosphere microbiome through SA to control Fusarium wilt.}, } @article {pmid36212853, year = {2022}, author = {Yang, X and Fan, X and Jiang, H and Zhang, Q and Basangwangdui, and Zhang, Q and Dang, S and Long, R and Huang, X}, title = {Simulated seasonal diets alter yak rumen microbiota structure and metabolic function.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1006285}, pmid = {36212853}, issn = {1664-302X}, abstract = {Yak is the only ruminant on the Qinghai-Tibetan Plateau that grazes year-round. Although previous research has shown that yak rumen microbiota fluctuates in robust patterns with seasonal foraging, it remains unclear whether these dynamic shifts are driven by changes in environment or nutrient availability. The study examines the response of yak rumen microbiota (bacteria, fungi, and archaea) to simulated seasonal diets, excluding the contribution of environmental factors. A total of 18 adult male yaks were randomly divided into three groups, including a nutrition stress group (NSG, simulating winter pasture), a grazing simulation group (GSG, simulating warm season pasture), and a supplementation group (SG, simulating winter pasture supplemented with feed concentrates). Volatile fatty acids (VFAs) profiling showed that ruminal acetate, propionate and total VFA contents were significantly higher (p < 0.05) in GSG rumen. Metagenomic analysis showed that Bacteroidetes (53.9%) and Firmicutes (37.1%) were the dominant bacterial phyla in yak rumen across dietary treatments. In GSG samples, Actinobacteriota, Succinivibrionaceae_UCG-002, and Ruminococcus albus were the most abundant, while Bacteroides was significantly more abundant in NSG samples (p < 0.05) than that in GSG. The known fiber-degrading fungus, Neocallimastix, was significantly more abundant in NSG and SG samples, while Cyllamyces were more prevalent in NSG rumen than in the SG rumen. These findings imply that a diverse consortium of microbes may cooperate in response to fluctuating nutrient availability, with depletion of known rumen taxa under nutrient deficiency. Archaeal community composition showed less variation between treatments than bacterial and fungal communities. Additionally, Orpinomyces was significantly positively correlated with acetate levels, both of which are prevalent in GSG compared with other groups. Correlation analysis between microbial taxa and VFA production or between specific rumen microbes further illustrated a collective response to nutrient availability by gut microbiota and rumen VFA metabolism. PICRUSt and FUNGuild functional prediction analysis indicated fluctuation response of the function of microbial communities among groups. These results provide a framework for understanding how microbiota participate in seasonal adaptations to forage availability in high-altitude ruminants, and form a basis for future development of probiotic supplements to enhance nutrient utilization in livestock.}, } @article {pmid36212851, year = {2022}, author = {Duan, Y and Xing, Y and Zeng, S and Dan, X and Mo, Z and Zhang, J and Li, Y}, title = {Integration of metagenomic and metabolomic insights into the effects of microcystin-LR on intestinal microbiota of Litopenaeus vannamei.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {994188}, pmid = {36212851}, issn = {1664-302X}, abstract = {Microcystin-LR (MC-LR) is a hazardous substance that threaten the health of aquatic animals. Intestinal microbes and their metabolites can interact with hosts to influence physiological homeostasis. In this study, the shrimp Litopenaeus vannamei were exposed to 1.0 μg/l MC-LR for 72 h, and the toxic effects of MC-LR on the intestinal microbial metagenomic and metabolomic responses of the shrimp were investigated. The results showed that MC-LR stress altered the gene functions of intestinal microbial, including ABC transporter, sulfur metabolism and riboflavin (VB2) metabolism, and induced a significant increase of eight carbohydrate metabolism enzymes. Alternatively, intestinal metabolic phenotypes were also altered, especially ABC transporters, protein digestion and absorption, and the biosynthesis and metabolism of amino acid. Furthermore, based on the integration of intestinal microbial metagenomic and metabolome, four bacteria species (Demequina globuliformis, Demequina sp. NBRC 110055, Sphingomonas taxi and Sphingomonas sp. RIT328) and three metabolites (yangonin, α-hederin and soyasaponin ii) biomarkers were identified. Overall, our study provides new insights into the effects of MC-LR on the intestinal microbial functions of L. vannamei.}, } @article {pmid36212847, year = {2022}, author = {Sun, Q and Li, L and Zhou, H and Wu, Y and Gao, Y and Wu, B and Qiu, Y and Zhou, Z and Song, Q and Zhao, J and Wu, P}, title = {The detection of urinary viruses is associated with aggravated symptoms and altered bacteriome in female with overactive bladder.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {984234}, pmid = {36212847}, issn = {1664-302X}, abstract = {Although it is known that changes in bacterial components of the urinary microbiome are associated with overactive bladder (OAB), the specific role of viruses is still insufficiently investigated. The aim of the present study is to evaluate the role of urinary viruses in woman with OAB, and analyze the potential relationship between viruses, bacteria and disease. Catheterized urine samples were collected from 55 women with OAB and 18 control individuals. OAB patients fulfilling the following criteria were considered eligible for this study: female, 18 years of age or older; presented with classic OAB symptoms defined by the International Continence Society; and OAB Symptom Score (OABSS) total score ≥ 3 points and question 3 (urgency) score ≥ 2 points. Based on results of metagenomic next-generation sequencing (mNGS), all participants were divided into virus-infected and virus-uninfected groups for analysis. The results of mNGS showed that the diversity of the OAB group was lower than that of the control group when focused on bacterial sequences, which was consistent with our previous study. According to the questionnaire filled out by the patients, OABSS and 8-item OAB questionnaire, female OAB patients who had viruses detected in their urine had more severe symptoms. In parallel, John Cunningham virus (mainly subtype 7 and subtype 2) was the most frequently detected virus in urine. Correlation analysis indicated that risk factors for virus infection in OAB patients include age, habit of holding urine and pelvic surgery history. Given our preliminary data, viral infection can aggravate OAB severity and affect the composition of bacterial. Further research is required to explain how viral infections can aggravate OAB patient symptoms and cause bacterial changes.}, } @article {pmid36212846, year = {2022}, author = {Camacho, A and Rochera, C and Picazo, A}, title = {Effect of experimentally increased nutrient availability on the structure, metabolic activities, and potential microbial functions of a maritime Antarctic microbial mat.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {900158}, pmid = {36212846}, issn = {1664-302X}, abstract = {The role of competitive interactions based on resource utilisation was explored in a phototrophic microbial mat from Byers Peninsula (Maritime Antarctica). Shotgun metagenomic profiling of the mat showed a taxonomic and functionally diverse microbial community. The heterotrophic bacterial community was dominated by Proteobacteria, where genera typically found in polar habitats, such as Janthinobacterium, Pseudomonas, and Polaromonas, were highly prevalent. Cyanobacteria played the main role as primary producers, accompanied by diatoms and chlorophytes. To test the potential effects of the inorganic nutrient (N and P) availability on this community, a fully factorial nitrate and phosphorus addition experiment was conducted in situ. The mat exhibited a functional and structural response to the nutrient amendments. Compared to the undisturbed mat, phosphorus fertilisation favoured the growth of (non-heterocystous) cyanobacteria relative to that of diatoms, as indicated by changes in the carotenoid pigment biomarkers. Although no mat accretion was visible, fertilisation improved the phototrophic activity, and, mainly, when P was amended, the production of exopolymeric substances was favoured, whereas further changes in the vertical distribution of primary production activity were observed as well. Illumina amplicon sequencing of the 16S rRNA gene also demonstrated changes in the relative abundance of heterotrophic prokaryotes, which were detectable from the phylum to the genus level and mainly related to the amendment of nitrogen. Predictions made on the functional skills of these shifted prokaryotic communities indicated changes in abundance selecting taxa with a metabolic adaptation to the new nutrient scenarios. They mainly consisted of the enhancement of ecological strategies and metabolic regulatory mechanisms related to the uptake and metabolising of either nitrogen or phosphorus, regulated by its availability whether in a balanced way or not. This study is a pioneer in demonstrating how shifts in the regional dynamic of nutrients might alter the metabolic equilibrium of these initially considered homeostatic benthic communities. They can be accordingly considered as taxonomically diverse microbiomes with a functional repertoire still inclined to respond to the biogeochemical alteration of nutrient cycles, although occurring in a cold extreme environment where biological activity is partially restricted by environmental harshness.}, } @article {pmid36212658, year = {2022}, author = {Zhao, Y and Lian, B and Liu, X and Wang, Q and Zhang, D and Sheng, Q and Cao, L}, title = {Case report: Cryptogenic giant brain abscess caused by Providencia rettgeri mimicking stroke and tumor in a patient with impaired immunity.}, journal = {Frontiers in neurology}, volume = {13}, number = {}, pages = {1007435}, pmid = {36212658}, issn = {1664-2295}, abstract = {The highly lethal cryptogenic brain abscess can be easily misdiagnosed. However, cryptogenic brain abscess caused by Providencia rettgeri is rarely reported. We present the case of a cryptogenic Providencia rettgeri brain abscess and analyze the clinical manifestations, imaging findings, treatment, and outcome to improve the level of awareness, aid in accurate diagnosis, and highlight effective clinical management. A 39-year-old man was admitted to the hospital after experiencing acute speech and consciousness disorder for 1 day. The patient had a medical history of nephrotic syndrome and membranous nephropathy requiring immunosuppressant therapy. Magnetic resonance imaging revealed giant, space-occupying lesions involving the brain stem, basal ganglia, and temporal-parietal lobes without typical ring enhancement, mimicking a tumor. Initial antibiotic treatment was ineffective. Afterward, pathogen detection in cerebrospinal fluid using metagenomic next-generation sequencing revealed Providencia rettgeri. Intravenous maximum-dose ampicillin was administered for 5 weeks, and the patient's symptoms resolved. Cryptogenic Providencia rettgeri brain abscess typically occurs in patients with impaired immunity. Our patient exhibited a sudden onset with non-typical neuroimaging findings, requiring differentiation of the lesion from stroke and brain tumor. Metagenomic next-generation sequencing was important in identifying the pathogen. Rapid diagnosis and appropriate use of antibiotics were key to obtaining a favorable outcome.}, } @article {pmid36212529, year = {2022}, author = {Suminda, GGD and Bhandari, S and Won, Y and Goutam, U and Kanth Pulicherla, K and Son, YO and Ghosh, M}, title = {High-throughput sequencing technologies in the detection of livestock pathogens, diagnosis, and zoonotic surveillance.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {5378-5392}, pmid = {36212529}, issn = {2001-0370}, abstract = {Increasing globalization, agricultural intensification, urbanization, and climatic changes have resulted in a significant recent increase in emerging infectious zoonotic diseases. Zoonotic diseases are becoming more common, so innovative, effective, and integrative research is required to better understand their transmission, ecological implications, and dynamics at wildlife-human interfaces. High-throughput sequencing (HTS) methodologies have enormous potential for unraveling these contingencies and improving our understanding, but they are only now beginning to be realized in livestock research. This study investigates the current state of use of sequencing technologies in the detection of livestock pathogens such as bovine, dogs (Canis lupus familiaris), sheep (Ovis aries), pigs (Sus scrofa), horses (Equus caballus), chicken (Gallus gallus domesticus), and ducks (Anatidae) as well as how it can improve the monitoring and detection of zoonotic infections. We also described several high-throughput sequencing approaches for improved detection of known, unknown, and emerging infectious agents, resulting in better infectious disease diagnosis, as well as surveillance of zoonotic infectious diseases. In the coming years, the continued advancement of sequencing technologies will improve livestock research and hasten the development of various new genomic and technological studies on farm animals.}, } @article {pmid36212359, year = {2022}, author = {Liu, S and Storti, M and Finazzi, G and Bowler, C and Dorrell, RG}, title = {A metabolic, phylogenomic and environmental atlas of diatom plastid transporters from the model species Phaeodactylum.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {950467}, pmid = {36212359}, issn = {1664-462X}, abstract = {Diatoms are an important group of algae, contributing nearly 40% of total marine photosynthetic activity. However, the specific molecular agents and transporters underpinning the metabolic efficiency of the diatom plastid remain to be revealed. We performed in silico analyses of 70 predicted plastid transporters identified by genome-wide searches of Phaeodactylum tricornutum. We considered similarity with Arabidopsis thaliana plastid transporters, transcriptional co-regulation with genes encoding core plastid metabolic pathways and with genes encoded in the mitochondrial genomes, inferred evolutionary histories using single-gene phylogeny, and environmental expression trends using Tara Oceans meta-transcriptomics and meta-genomes data. Our data reveal diatoms conserve some of the ion, nucleotide and sugar plastid transporters associated with plants, such as non-specific triose phosphate transporters implicated in the transport of phosphorylated sugars, NTP/NDP and cation exchange transporters. However, our data also highlight the presence of diatom-specific transporter functions, such as carbon and amino acid transporters implicated in intricate plastid-mitochondria crosstalk events. These confirm previous observations that substrate non-specific triose phosphate transporters (TPT) may exist as principal transporters of phosphorylated sugars into and out of the diatom plastid, alongside suggesting probable agents of NTP exchange. Carbon and amino acid transport may be related to intricate metabolic plastid-mitochondria crosstalk. We additionally provide evidence from environmental meta-transcriptomic/meta- genomic data that plastid transporters may underpin diatom sensitivity to ocean warming, and identify a diatom plastid transporter (J43171) whose expression may be positively correlated with temperature.}, } @article {pmid36211959, year = {2022}, author = {Zhang, B and Gui, R and Wang, Q and Jiao, X and Li, Z and Wang, J and Han, L and Zhou, L and Wang, H and Wang, X and Fan, X and Lyu, X and Song, Y and Zhou, J}, title = {Comparing the application of mNGS after combined pneumonia in hematologic patients receiving hematopoietic stem cell transplantation and chemotherapy: A retrospective analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {969126}, pmid = {36211959}, issn = {2235-2988}, mesh = {*Coinfection/microbiology ; *Hematopoietic Stem Cell Transplantation/adverse effects ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; *Pneumonia/microbiology ; Retrospective Studies ; Sensitivity and Specificity ; *Virus Diseases ; }, abstract = {Rapid and accurate pathogen identification is essential for timely and effective treatment of pneumonia. Here, we describe the use of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage (BALF) fluid to identify pathogens in patients with hematologic comorbid respiratory symptoms in a retrospective study with 84 patients. In the transplantation group, 8 cases (19.5%) and 47 cases (97.9%) were positive for BALF by conventional method detection and mNGS detection, respectively, and 6 cases (14.0%) and 41 cases (91.1%) in chemotherapy group, respectively. The detection rate of mNGS in both groups was significantly higher than that of conventional detection methods (all P<0.05). Pseudomonas aeruginosa and Streptococcus pneumoniae were the most common bacterial infections in the transplantation and chemotherapy groups, respectively. Aspergillus was the most common fungal infection in both groups. Human betaherpesvirus 5 (HHV-5), torque teno virus and human betaherpesvirus 7 (HHV-7) were the most common pathogen species in both groups. The most common type of infection in patients in the transplantation and chemotherapy groups was the mixed infection of bacteria-virus. Most patients in the transplantation group had mixed infections based on multiple viruses, with 42 cases of viral infections in the transplantation group and 30 cases of viral infections in the chemotherapy group, which were significantly higher in the transplantation group than in the chemotherapy group (χ2 = 5.766, P=0.016). and the mixed infection of virus-virus in the transplantation group was significantly higher than that in the chemotherapy group (27.1% vs 4.4%, P=0.003). The proportion of death due to pulmonary infection was significantly higher in the transplantation group than in the chemotherapy group (76.9% vs 16.7%, χ2 = 9.077, P=0.003). This study demonstrated the value of mNGS of BALF in improving the diagnosis and prognosis of hematologic comorbid pneumonia, helping patients to obtain timely and effective treatment, and giving guidance on the overall treatment plan for patients, with particular benefit for patients with hematologic chemotherapy comorbid pneumonia.}, } @article {pmid36211955, year = {2022}, author = {Kong, M and Li, W and Kong, Q and Dong, H and Han, A and Jiang, L}, title = {Application of metagenomic next-generation sequencing in cutaneous tuberculosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {942073}, pmid = {36211955}, issn = {2235-2988}, mesh = {Antitubercular Agents/therapeutic use ; Child ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Metagenome ; *Metagenomics ; *Tuberculosis/diagnosis/microbiology ; }, abstract = {Tuberculous infection in a skin wound is a rare but well-known condition. This study describes a child infected with tuberculosis after being wounded. Because of swelling and pain in his wrist tissue, he was admitted to the Affiliated Hospital of Jining Medical University of Shandong Province on 16 October 2021. His medical history only included a wound. He was discharged after debridement. The laboratory data were normal. Two months after surgery, his wound was still swollen and painful. Secretions from the wound were sent for metagenomic next-generation sequencing (mNGS), which revealed three reads related to the Mycobacterium tuberculosis complex group (MTBC). A diagnosis of cutaneous tuberculosis (TB) was made. The wound disappeared after anti-TB drugs were administered. This case demonstrates that, while TB presenting as a severe cutaneous wound is rare, it should be considered in the clinical diagnosis. Clinicians should also pay attention to extrapulmonary infection with MTBC in patients, particularly in some long-suffering patients, and identify the specific pathogen as soon as possible. mNGS could help to identify pathogens and facilitate early treatment, thereby improving the prognosis.}, } @article {pmid36211486, year = {2022}, author = {Wallingford, JC and Neve Myers, P and Barber, CM}, title = {Effects of addition of 2-fucosyllactose to infant formula on growth and specific pathways of utilization by Bifidobacterium in healthy term infants.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {961526}, pmid = {36211486}, issn = {2296-861X}, abstract = {Oligosaccharides in human milk support health via intestinal microbiome. We studied effects of addition of 2-fucosyllactose (2'FL) to the infant formula on infant growth, occurrence of adverse events (AE), and infant microbiome, including expression of microbial genes that metabolize 2'FL. Our hypothesis was that while 2'FL would not affect growth, it would cause changes in microbiome metabolism. In a double-blinded randomized controlled study fashion, the infant formula ± 2'FL or human milk was fed to healthy term infants for 16 weeks. Fecal samples obtained at baseline and week 16 were analyzed for microbial populations, metagenomic species concept (MGS), and genetics of gut metabolic modules (GMMs). There were no effects of addition of 2'FL on growth or AEs. There were no significant differences by feeding group in MGS richness or Shannon diversity at baseline, but formula groups each had significantly greater richness (p < 0.05) and diversity (p < 0.05) after 16 weeks of feeding than the breastfed group. While two glycosyl hydrolase (GH) families (GH42 and GH112) were significantly increased, two other GH families (GH20 and GH2) were significantly decreased in the test formula group compared to the control formula group; although modest, addition of 2'FL resulted in changes in microbiome in the direction of breastfed infants, consistent with internal metabolism of HMOs by Bifidobacterium.}, } @article {pmid36210425, year = {2022}, author = {Klimenko, ES and Belkova, NL and Romanitsa, AI and Pogodina, AV and Rychkova, LV and Darenskaya, MA}, title = {Differences in Gut Microbiota Composition and Predicted Metabolic Functions: a Pilot Study of Adolescents with Normal Weight and Obesity.}, journal = {Bulletin of experimental biology and medicine}, volume = {173}, number = {5}, pages = {628-632}, pmid = {36210425}, issn = {1573-8221}, mesh = {Adolescent ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Obesity/genetics ; Phylogeny ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Understanding the principles underlying the stability and sustainability of the gut microbiome of adolescents with normal weight and obesity will make it possible to implement a personalized approach to the correction of metabolic disorders. The article presents the results of a pilot study of the diversity and metabolic potential of the gut microbiome in adolescents with normal body weight and obesity. Biological material was studied using metagenomic sequencing of the V3-V4 variable regions of the 16S rRNA gene. In all adolescents with normal weight, similar degree of the phylogenetic relationship between the bacterial taxa of the community was demonstrated. In contrast, obese adolescents were characterized by the presence of phylogenetically distinct taxa in the gut microbiota. However, even with differences in taxonomic composition, the gut microbial community can compensate for the absence of certain taxonomic groups by implementing the necessary metabolic functions using other phylogenetically close taxa.}, } @article {pmid36210003, year = {2022}, author = {Wasana, WP and Senevirathne, A and Nikapitiya, C and Lee, JS and Kang, DH and Kwon, KK and Oh, C and De Zoysa, M}, title = {Probiotic effects of Pseudoalteromonas ruthenica: Antibacterial, immune stimulation and modulation of gut microbiota composition.}, journal = {Fish & shellfish immunology}, volume = {131}, number = {}, pages = {229-243}, doi = {10.1016/j.fsi.2022.09.070}, pmid = {36210003}, issn = {1095-9947}, mesh = {Animals ; *Gastrointestinal Microbiome ; Zebrafish ; *Probiotics/pharmacology ; Anti-Bacterial Agents/pharmacology ; }, abstract = {This study aimed to characterise and evaluate the probiotic properties of a newly isolated marine bacterium, strain S6031. The isolated strain was identified as Pseudoalteromonas ruthenica. In vivo experiments were conducted with P. ruthenica-immersed larvae and P. ruthenica-enriched Artemia fed to adult zebrafish. Disease tolerance of larval zebrafish against Edwardsiella piscicida was demonstrated by 66.34% cumulative per cent survival (CPS) in the P. ruthenica-exposed group, which was higher than the CPS of the control (46.67%) at 72 h post challenge (hpc). Heat-stressed larvae had 55% CPS in the P. ruthenica-immersed group, while the control had 30% CPS at 60 hpc. Immune-stress response gene transcripts (muc5.1, muc5.2, muc5.3, alpi2, alpi3, hsp70, and hsp90a) were induced, while pro-inflammatory genes (tnfα, il1b, and il6) were downregulated in P. ruthenica-immersed larvae compared to the control. This trend was confirmed by low pro-inflammatory and high stress-responsive protein expression levels in P. ruthenica-exposed larvae. Adult zebrafish had higher CPS (27.2%) in the P. ruthenica-fed group than the control (9.52%) upon E. piscicida challenge, suggesting increased disease tolerance. Histological analysis demonstrated modulation of goblet cell density and average villus height in the P. ruthenica-supplemented group. Metagenomics analysis clearly indicated modulation of alpha diversity indices and the relative abundance of Proteobacteria in the P. ruthenica-supplemented zebrafish gut. Furthermore, increased Firmicutes colonisation and reduced Bacteroidetes abundance in the gut were observed upon P. ruthenica supplementation. Additionally, this study confirmed the concentration-dependent increase of colony dispersion and macrophage uptake upon mucin treatment. In summary, P. ruthenica possesses remarkable functional properties as a probiotic that enhances host defence against diseases and thermal stress.}, } @article {pmid36209976, year = {2022}, author = {Cao, L and He, L and Wang, S and Xu, L and Zhuang, S}, title = {Severe community-acquired pneumonia caused by Chlamydia pecorum.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {124}, number = {}, pages = {171-173}, doi = {10.1016/j.ijid.2022.09.037}, pmid = {36209976}, issn = {1878-3511}, mesh = {Male ; Sheep ; Humans ; Animals ; *Chlamydia Infections/diagnosis/drug therapy ; *Chlamydia/genetics ; *Community-Acquired Infections/diagnosis/drug therapy ; *Pneumonia/diagnosis/drug therapy ; }, abstract = {Chlamydia pecorum is a zoonotic pathogen. Here, we report the first case of human infection with C. pecorum. A man aged 51 years with high fever and dry cough was diagnosed with severe community-acquired pneumonia and respiratory failure. C. pecorum was found responsible for the infection, which was detected from bronchoalveolar lavage fluid through metagenomic next-generation sequencing. C. pecorum infection was further identified by quantitative polymerase chain reaction and complement fixation test. The patient's condition improved rapidly after targeted treatment. He was a farmer with diabetes mellitus and had a history of close contact with sheep, which might result in C. pecorum infection. Our report could provide a direction for the diagnosis and treatment of human C. pecorum pneumonia.}, } @article {pmid36209779, year = {2023}, author = {Ritchie, G and Strodl, E and Parham, S and Bambling, M and Cramb, S and Vitetta, L}, title = {An exploratory study of the gut microbiota in major depression with anxious distress.}, journal = {Journal of affective disorders}, volume = {320}, number = {}, pages = {595-604}, doi = {10.1016/j.jad.2022.10.001}, pmid = {36209779}, issn = {1573-2517}, mesh = {Humans ; Male ; Female ; Young Adult ; Adult ; Middle Aged ; *Depressive Disorder, Major/psychology ; *Gastrointestinal Microbiome/genetics ; Depression/diagnosis ; RNA, Ribosomal, 16S/genetics ; Anxiety/diagnosis ; }, abstract = {OBJECTIVES: To explore differences in the diversity and composition of the gut microbiome between major depressive disorder (MDD) with and without anxious distress.

METHODS: The study comprised 117 participants (79 female, 36 male, 2 other, mean age 38.2 ± 13.4 years) with a current major depressive episode (MDE) with (n = 63) and without (n = 54) the anxious distress specifier. A clinical psychologist administered the structured clinical interview for the DSM-5-RV to confirm a diagnosis of depression. Participants provided stool samples which were immediately frozen and stored at -80 °C. These samples were analysed using the Illumina 16S Metagenomics sequencing protocol in which the sequencing primers target the V3 and V4 regions of the 16S rRNA gene. Participants also completed mental health questionnaires to assess severity of depression (BDI-II), generalized anxiety (GAD-7), and stress (PSS).

RESULTS: There were no significant group differences in α-diversity (Shannon's diversity Index; Simpson Index), richness (ACE; Chao1), (Pielou's) evenness, or beta diversity (Bray-Curtis dissimilarity index and weighted UniFrac distance) of gut bacteria. Significant group differences in the relative abundance of gut microbiota however were observed at each taxonomical level, including across 15 genera and 18 species.

LIMITATIONS: This was an exploratory study that needs to be replicated across larger samples and compared with a healthy control group.

CONCLUSIONS: The research contributes to knowledge of the depressive gut microbial profile unique to the anxious distress subtype of MDD.}, } @article {pmid36209621, year = {2022}, author = {Prajna, NV and Lalitha, P and Teja, GV and Gunasekaran, R and Sharma, SS and Hinterwirth, A and Ruder, K and Zhong, L and Chen, C and Deiner, M and Huang, C and Pinsky, BA and Lietman, TM and Seitzman, GD and Doan, T and , }, title = {Outpatient human coronavirus associated conjunctivitis in India.}, journal = {Journal of clinical virology : the official publication of the Pan American Society for Clinical Virology}, volume = {157}, number = {}, pages = {105300}, pmid = {36209621}, issn = {1873-5967}, support = {R01 EY032041/EY/NEI NIH HHS/United States ; }, mesh = {Humans ; SARS-CoV-2 ; *COVID-19 ; *Coinfection/epidemiology ; Outpatients ; Prospective Studies ; India/epidemiology ; *Conjunctivitis ; RNA ; }, abstract = {BACKGROUND: Viral conjunctivitis (pink eye) can be highly contagious and is of public health importance. There remains significant debate whether SARS-CoV-2 can present as a primary conjunctivitis. The aim of this study was to identify pathogens associated with outpatient infectious conjunctivitis during the COVID-19 Delta surge.

METHODS: This prospective study was conducted in the spring and summer months of 2021. 106 patients with acute conjunctivitis who presented to the Aravind Eye Center in Madurai, India were included. One anterior nasal swab and one conjunctival swab of each eye were obtained for each enrolled patient. Samples were subsequently processed for unbiased metagenomic RNA deep sequencing (RNA-seq). Outcomes included clinical findings and codetection of other pathogens with SARS-CoV-2 in patients with conjunctivitis.

RESULTS: Among the 13 patients identified with human coronavirus RNA fragments in their swabs, 6 patients had SARS-CoV-2 infection, 5 patients had coinfections of SARS-CoV-2 and human adenovirus (HAdV), 1 patient had a coinfection with human coronavirus OC43 and HAdV, and 1 patient had a coinfection of Vittaforma corneae and SARS-CoV-2. 30% had bilateral disease and symptoms on presentation. Petechial hemorrhage was noted in 33% of patients with SARS-CoV-2 infection. No patients with SARS-CoV-2 or SARS-CoV-2 and HAdV infections had subepithelial infiltrates on presentation. All patients denied systemic symptoms.

CONCLUSIONS: Among the patients presented with conjunctivitis associated with human coronavirus infection, over 50% of the patients had co-infections with other circulating pathogens, suggesting the public-health importance of broad pathogen testing and surveillance in the outpatient conjunctivitis population.}, } @article {pmid36209606, year = {2023}, author = {Chen, J and Chen, H and Liu, C and Huan, H and Teng, Y}, title = {Evaluation of FEAST for metagenomics-based source tracking of antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {442}, number = {}, pages = {130116}, doi = {10.1016/j.jhazmat.2022.130116}, pmid = {36209606}, issn = {1873-3336}, mesh = {*Metagenomics/methods ; *Anti-Bacterial Agents/pharmacology ; Sewage ; Drug Resistance, Microbial/genetics ; Rivers ; Genes, Bacterial ; }, abstract = {A metagenomics-based technological framework has been proposed for evaluating the potential and utility of FEAST as an ARG profile-based source apportionment tool. To this end, a large panel of metagenomic data sets was analyzed, associating with eight source types of ARGs in environments. Totally, 1089 different ARGs were found in the 604 source metagenomes, and 396 ARG indicators were identified as the source-specific fingerprints to characterize each of the source types. With the source fingerprints, predictive performance of FEAST was checked using "leave-one-out" cross-validation strategy. Furthermore, artificial sink communities were simulated to evaluate the FEAST for source apportionment of ARGs. The prediction of FEAST showed high accuracy values (0.933 ± 0.046) and specificity values (0.959 ± 0.041), confirming its suitability to discriminate samples from different source types. The apportionment results reflected well the expected output of artificial communities which were generated with different ratios of source types to simulate various contamination levels. Finally, the validated FEAST was applied to track the sources of ARGs in river sediments. Results showed STP effluents were the main contributor of ARGs, with an average contribution of 76 %, followed by sludge (10 %) and aquaculture effluent (2.7 %), which were basically consistent with the actual environment in the area.}, } @article {pmid36209605, year = {2023}, author = {Bi, L and Han, LL and Du, S and Yu, DT and He, JZ and Zhang, LM and Hu, HW}, title = {Cross-biome soil viruses as an important reservoir of virulence genes.}, journal = {Journal of hazardous materials}, volume = {442}, number = {}, pages = {130111}, doi = {10.1016/j.jhazmat.2022.130111}, pmid = {36209605}, issn = {1873-3336}, mesh = {*Soil ; Ecosystem ; Virulence/genetics ; Soil Microbiology ; *Viruses/genetics ; }, abstract = {Viruses can significantly influence the composition and functions of their host communities and enhance host pathogenicity via the transport of virus-encoded virulence genes. However, the contribution of viral communities to the dissemination of virulence genes across various biomes across a large scale is largely unknown. Here, we constructed 29,283 soil viral contigs (SVCs) from viral size fraction metagenomes and public databases. A total of 1310 virulence genes were identified from 1164 SVCs in a wide variety of soil biomes, including grassland, agricultural and forest soils. The virulence gene gmd was the most abundant one, followed by csrA, evpJ, and pblA. A great proportion of viruses encoding virulence genes were uncharacterized. Virus-host linkage analysis revealed that most viruses were linked to only one bacterial genus, whereas several SVCs were associated with more than one bacterial genus and even two bacterial phyla, suggesting the potential risk of spreading virulence genes across different bacterial communities via viruses. Altogether, we provided new evidence for the prevalence of virulence genes in soil viruses across biomes, which advanced our understanding of the potential role of soil viruses in driving the pathogenesis of their hosts in terrestrial ecosystems.}, } @article {pmid36209213, year = {2022}, author = {Wang, C and Zhang, L and Jiang, X and Ma, W and Geng, H and Wang, X and Li, M}, title = {Toward efficient and high-fidelity metagenomic data from sub-nanogram DNA: evaluation of library preparation and decontamination methods.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {225}, pmid = {36209213}, issn = {1741-7007}, mesh = {DNA/genetics ; *Decontamination ; Endonucleases/genetics ; Gene Library ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenomics/methods ; Reproducibility of Results ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Shotgun metagenomic sequencing has greatly expanded the understanding of microbial communities in various biological niches. However, it is still challenging to efficiently convert sub-nanogram DNA to high-quality metagenomic libraries and obtain high-fidelity data, hindering the exploration of niches with low microbial biomass.

RESULTS: To cope with this challenge comprehensively, we evaluated the performance of various library preparation methods on 0.5 pg-5 ng synthetic microbial community DNA, characterized contaminants, and further applied different in silico decontamination methods. First, we discovered that whole genome amplification prior to library construction led to worse outcomes than preparing libraries directly. Among different non-WGA-based library preparation methods, we found the endonuclease-based method being generally good for different amounts of template and the tagmentation-based method showing specific advantages with 0.5 pg template, based on evaluation metrics including fidelity, proportion of designated reads, and reproducibility. The load of contaminating DNA introduced by library preparation varied from 0.01 to 15.59 pg for different kits and accounted for 0.05 to 45.97% of total reads. A considerable fraction of the contaminating reads were mapped to human commensal and pathogenic microbes, thus potentially leading to erroneous conclusions in human microbiome studies. Furthermore, the best performing in silico decontamination method in our evaluation, Decontam-either, was capable of recovering the real microbial community from libraries where contaminants accounted for less than 10% of total reads, but not from libraries with heavy and highly varied contaminants.

CONCLUSIONS: This study demonstrates that high-quality metagenomic data can be obtained from samples with sub-nanogram microbial DNA by combining appropriate library preparation and in silico decontamination methods and provides a general reference for method selection for samples with varying microbial biomass.}, } @article {pmid36209178, year = {2022}, author = {Kwak, S and Crook, N and Yoneda, A and Ahn, N and Ning, J and Cheng, J and Dantas, G}, title = {Functional mining of novel terpene synthases from metagenomes.}, journal = {Biotechnology for biofuels and bioproducts}, volume = {15}, number = {1}, pages = {104}, pmid = {36209178}, issn = {2731-3654}, support = {T32-DK-077653/DK/NIDDK NIH HHS/United States ; DP2-DK-098089/NH/NIH HHS/United States ; }, abstract = {BACKGROUND: Terpenes are one of the most diverse and abundant classes of natural biomolecules, collectively enabling a variety of therapeutic, energy, and cosmetic applications. Recent genomics investigations have predicted a large untapped reservoir of bacterial terpene synthases residing in the genomes of uncultivated organisms living in the soil, indicating a vast array of putative terpenoids waiting to be discovered.

RESULTS: We aimed to develop a high-throughput functional metagenomic screening system for identifying novel terpene synthases from bacterial metagenomes by relieving the toxicity of terpene biosynthesis precursors to the Escherichia coli host. The precursor toxicity was achieved using an inducible operon encoding the prenyl pyrophosphate synthetic pathway and supplementation of the mevalonate precursor. Host strain and screening procedures were finely optimized to minimize false positives arising from spontaneous mutations, which avoid the precursor toxicity. Our functional metagenomic screening of human fecal metagenomes yielded a novel β-farnesene synthase, which does not show amino acid sequence similarity to known β-farnesene synthases. Engineered S. cerevisiae expressing the screened β-farnesene synthase produced 120 mg/L β-farnesene from glucose (2.86 mg/g glucose) with a productivity of 0.721 g/L∙h.

CONCLUSIONS: A unique functional metagenomic screening procedure was established for screening terpene synthases from metagenomic libraries. This research proves the potential of functional metagenomics as a sequence-independent avenue for isolating targeted enzymes from uncultivated organisms in various environmental habitats.}, } @article {pmid36209079, year = {2022}, author = {Zhao, L and Wang, C and Peng, S and Zhu, X and Zhang, Z and Zhao, Y and Zhang, J and Zhao, G and Zhang, T and Heng, X and Zhang, L}, title = {Pivotal interplays between fecal metabolome and gut microbiome reveal functional signatures in cerebral ischemic stroke.}, journal = {Journal of translational medicine}, volume = {20}, number = {1}, pages = {459}, pmid = {36209079}, issn = {1479-5876}, mesh = {Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Ischemic Stroke ; Metabolome ; Metabolomics ; RNA, Ribosomal, 16S ; }, abstract = {BACKGROUND: Integrative analysis approaches of metagenomics and metabolomics have been widely developed to understand the association between disease and the gut microbiome. However, the different profiling patterns of different metabolic samples in the association analysis make it a matter of concern which type of sample is the most closely associated with gut microbes and disease. To address this lack of knowledge, we investigated the association between the gut microbiome and metabolomic profiles of stool, urine, and plasma samples from ischemic stroke patients and healthy subjects.

METHODS: We performed metagenomic sequencing (feces) and untargeted metabolomics analysis (feces, plasma, and urine) from ischemic stroke patients and healthy volunteers. Differential analyses were conducted to find key differential microbiota and metabolites for ischemic stroke. Meanwhile, Spearman's rank correlation and linear regression analyses were used to study the association between microbiota and metabolites of different metabolic mixtures.

RESULTS: Untargeted metabolomics analysis shows that feces had the most abundant features and identified metabolites, followed by urine and plasma. Feces had the highest number of differential metabolites between ischemic stroke patients and the healthy group. Based on the association analysis between metagenomics and metabolomics of fecal, urine, and plasma, fecal metabolome showed the strongest association with the gut microbiome. There are 1073, 191, and 81 statistically significant pairs (P < 0.05) in the correlation analysis for fecal, urine, and plasma metabolome. Fecal metabolites explained the variance of alpha-diversity of the gut microbiome up to 31.1%, while urine and plasma metabolites only explained the variance of alpha-diversity up to 13.5% and 10.6%. Meanwhile, there were more significant differential metabolites in feces than urine and plasma associated with the stroke marker bacteria.

CONCLUSIONS: The systematic association analysis between gut microbiome and metabolomics reveals that fecal metabolites show the strongest association with the gut microbiome, followed by urine and plasma. The findings would promote the association study between the gut microbiome and fecal metabolome to explore key factors that are associated with diseases. We also provide a user-friendly web server and a R package to facilitate researchers to conduct the association analysis of gut microbiome and metabolomics.}, } @article {pmid36208825, year = {2022}, author = {Dong, ZX and Tang, QH and Li, WL and Wang, ZW and Li, XJ and Fu, CM and Li, D and Qian, K and Tian, WL and Guo, J}, title = {Honeybee (Apis mellifera) resistance to deltamethrin exposure by Modulating the gut microbiota and improving immunity.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {314}, number = {}, pages = {120340}, doi = {10.1016/j.envpol.2022.120340}, pmid = {36208825}, issn = {1873-6424}, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome ; Bacteria ; *Pesticides ; *Environmental Pollutants ; Defensins ; }, abstract = {Honeybees (Apis mellifera) are important economic insects and play important roles in pollination and maintenance of ecological balance. However, the use of pesticides has posed a substantial threat to bees in recent years, with the more widely used deltamethrin being the most harmful. In this study, we found that deltamethrin exposure significantly reduced bee survival in a dose-dependent manner (p = 0.025). In addition, metagenomic sequencing further revealed that DM exposure significantly reduced the diversity of the bee gut microbiota (Chao1, p < 0.0001; Shannon, p < 0.0001; Simpson, p < 0.0001) and decreased the relative abundance of core species of the gut microbiota. Importantly, in studies of GF-bees, we found that the colonization of important gut bacteria such as Gilliamella apicola and Lactobacillus kunkeei significantly increased bee resistance to DM (survival rate increased from 16.7 to 66.7%). Interestingly, we found that the immunity-genes Defensin-2 and Toll were significantly upregulated in bees after the colonization of gut bacteria. These results suggest that gut bacteria may protect against DM stress by improving host immunity. Our findings provide an important rationale for protecting honeybees from pollutants from the perspective of gut microbes.}, } @article {pmid36208685, year = {2022}, author = {Wang, G and Jiang, Z and Xiao, Q and Jiang, C and Shi, X}, title = {Visible spectrophotometric assay for characterization of ω-transaminases.}, journal = {Analytical biochemistry}, volume = {658}, number = {}, pages = {114933}, doi = {10.1016/j.ab.2022.114933}, pmid = {36208685}, issn = {1096-0309}, mesh = {*Transaminases ; *Dimethyl Sulfoxide ; Amines ; Solvents ; }, abstract = {Omega-transaminases (ω-TAs) have attracted considerable interest for their use in asymmetric synthesis of chiral amines with a high degree of optical purity and yield. The rapid evaluation of the characteristics of newly identified or engineered ω-TAs is important for industrial applications. In this study, a visible spectrophotometric assay was developed for rapid quantitative determination of ω-TA activities based on the transamination of 2-(4-nitrophenyl)ethan-1-amine to generate a red product (E)-N-(4-nitrophenethyl)-2-(4-nitrophenyl)ethen-1-amine. After various co-solvents were evaluated, dimethyl sulfoxide (DMSO) was considered optimal because the red product exhibits good solubility and retains its original color. The red product dissolved in DMSO has its highest absorbance at 465 nm, and its concentration has a good linear relationship with the absorbance. A spectrophotometric assay was established and validated using conventional HPLC analysis (<10% divergence). This method was then used to characterize an ω-TA from thermophilic Geobacillus thermoleovorans and an ω-TA obtained from the metagenome of a soda lake. The results demonstrated that ω-transaminase enzymatic properties could be characterized simply, rapidly, and at low cost, using this newly established visible spectrophotometric assay method.}, } @article {pmid36208631, year = {2022}, author = {Afrizal, A and Jennings, SAV and Hitch, TCA and Riedel, T and Basic, M and Panyot, A and Treichel, N and Hager, FT and Wong, EO and Wolter, B and Viehof, A and von Strempel, A and Eberl, C and Buhl, EM and Abt, B and Bleich, A and Tolba, R and Blank, LM and Navarre, WW and Kiessling, F and Horz, HP and Torow, N and Cerovic, V and Stecher, B and Strowig, T and Overmann, J and Clavel, T}, title = {Enhanced cultured diversity of the mouse gut microbiota enables custom-made synthetic communities.}, journal = {Cell host & microbe}, volume = {30}, number = {11}, pages = {1630-1645.e25}, doi = {10.1016/j.chom.2022.09.011}, pmid = {36208631}, issn = {1934-6069}, mesh = {Mice ; Animals ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Bacteria ; Metagenome ; Intestines ; Disease Models, Animal ; Mammals/genetics ; }, abstract = {Microbiome research needs comprehensive repositories of cultured bacteria from the intestine of mammalian hosts. We expanded the mouse intestinal bacterial collection (www.dsmz.de/miBC) to 212 strains, all publicly available and taxonomically described. This includes strain-level diversity, small-sized bacteria, and previously undescribed taxa (one family, 10 genera, and 39 species). This collection enabled metagenome-educated prediction of synthetic communities (SYNs) that capture key functional differences between microbiomes, notably identifying communities associated with either resistance or susceptibility to DSS-induced colitis. Additionally, nine species were used to amend the Oligo-Mouse Microbiota (OMM)12 model, yielding the OMM19.1 model. The added strains compensated for phenotype differences between OMM12 and specific pathogen-free mice, including body composition and immune cells in the intestine and associated lymphoid tissues. Ready-to-use OMM stocks are available for future studies. In conclusion, this work improves our knowledge of gut microbiota diversity in mice and enables functional studies via the modular use of isolates.}, } @article {pmid36207958, year = {2022}, author = {Zhao, ZL and Tang, X and He, CW and Liu, YL and Li, XY and Wang, R and Li, Y and Cao, SY and Sun, B and Tong, ZH}, title = {[Clinical characteristics and outcomes of acute respiratory distress syndrome caused by severe Chlamydia psittaci pneumonia].}, journal = {Zhonghua jie he he hu xi za zhi = Zhonghua jiehe he huxi zazhi = Chinese journal of tuberculosis and respiratory diseases}, volume = {45}, number = {10}, pages = {1015-1021}, doi = {10.3760/cma.j.cn112147-20220221-00139}, pmid = {36207958}, issn = {1001-0939}, support = {82070005//National Natural Science Foundation of China/ ; Z151100004015049//Program of Science and Technology of the Beijing Municipal/ ; }, mesh = {Aged ; Alanine Transaminase ; Aspartate Aminotransferases ; Azithromycin ; *Chlamydophila psittaci ; Creatinine ; Humans ; Middle Aged ; Moxifloxacin ; Natriuretic Peptide, Brain ; *Pneumonia ; *Respiratory Distress Syndrome/therapy ; *Respiratory Insufficiency ; }, abstract = {Objective: To investigate the clinical characteristics and outcomes of acute respiratory distress syndrome (ARDS) caused by Chlamydia psittaci pneumonia. Methods: From June 2016 to January 2021, 10 cases were diagnosed as severe Chlamydia psittaci pneumonia induced ARDS in Intensive Care Unit of Respiratory and Critical Care Medicine Department (RICU) of Beijing Chao-Yang Hospital Affiliated to Capital Medical University. We collected the clinical data including clinical features, laboratory tests, imaging and outcomes of the patients. Results: The pathogenic diagnosis was confirmed by metagenomic Next-generation Sequencing (mNGS) in these 10 patients, with a median age of 59 (46, 67) years. In addition to high fever, cough and dyspnea, the patients also had multiple organ involvement. Six patients had elevated peripheral leukocyte count, 10 cases had increased type B natriuretic peptide, 7 cases had increased aspartate aminotransferase/alanine aminotransferase, 9 cases had hyponatremia and 3 cases had elevated creatinine. The imaging findings were bilateral consolidation with air bronchogram and infiltrates, and pleural effusion were found in 5 cases. All cases were combined with respiratory failure. Six patients received invasive mechanical ventilation. Nine patients received moxifloxacin and one patient was administrated with Azithromycin. All the patients were improved and discharged after the treatment, and the mean duration of RICU stay was 13.5 (11, 16.7) days. One month follow-up of nine patients showed significant improvement in lung lesions. Conclusions: Severe Chlamydia psittiaci pneumonia may be complicated with respiratory failure and/or multiple organ involvement. For severe pneumonia with an exposure history of sick birds, the possibility of Chlamydia psittaci infection should be considered. mNGS may help etiological diagnosis. All patients in this study had a good prognosis after targeted treatment.}, } @article {pmid36207852, year = {2022}, author = {Wang, CY and Xu, HM and Tian, J and Hong, SQ and Liu, G and Wang, SX and Gao, F and Liu, J and Liu, FR and Yu, H and Wu, X and Chen, BQ and Shen, FF and Zheng, G and Yu, J and Shu, M and Liu, L and Du, LJ and Li, P and Xu, ZW and Zhu, MQ and Huang, LS and Huang, HY and Li, HB and Huang, YY and Wang, D and Wu, F and Bai, ST and Tang, JJ and Shan, QW and Lan, LC and Zhu, CH and Xiong, Y and Tian, JM and Wu, JH and Hao, JH and Zhao, HY and Lin, AW and Song, SS and Lin, DJ and Zhou, QH and Guo, YP and Wu, JZ and Yang, XQ and Zhang, XH and Guo, Y and Cao, Q and Luo, LJ and Tao, ZB and Yang, WK and Zhou, YK and Chen, Y and Feng, LJ and Zhu, GL and Zhang, YH and Xue, P and Li, XQ and Tang, ZZ and Zhang, DH and Su, XW and Qu, ZH and Zhang, Y and Zhao, SY and Qi, ZZ and Pang, L and Wang, CY and Deng, HL and Liu, XL and Chen, YH and Shu, S}, title = {[A multicenter epidemiological study of acute bacterial meningitis in children].}, journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics}, volume = {60}, number = {10}, pages = {1045-1053}, doi = {10.3760/cma.j.cn112140-20220608-00522}, pmid = {36207852}, issn = {0578-1310}, support = {82071812//National Natural Science Foundation of China/ ; S20A0003//Special Fund of the Central guiding local Scientific and Technological Development/ ; }, mesh = {Adolescent ; *Brain Abscess ; Child ; Child, Preschool ; Escherichia coli ; Female ; Humans ; *Hydrocephalus ; Infant ; Infant, Newborn ; Male ; *Meningitis, Bacterial/diagnosis/epidemiology ; Retrospective Studies ; Streptococcus agalactiae ; Streptococcus pneumoniae ; *Subdural Effusion ; beta-Lactamases ; }, abstract = {Objective: To analyze the clinical epidemiological characteristics including composition of pathogens , clinical characteristics, and disease prognosis acute bacterial meningitis (ABM) in Chinese children. Methods: A retrospective analysis was performed on the clinical and laboratory data of 1 610 children <15 years of age with ABM in 33 tertiary hospitals in China from January 2019 to December 2020. Patients were divided into different groups according to age,<28 days group, 28 days to <3 months group, 3 months to <1 year group, 1-<5 years of age group, 5-<15 years of age group; etiology confirmed group and clinically diagnosed group according to etiology diagnosis. Non-numeric variables were analyzed with the Chi-square test or Fisher's exact test, while non-normal distrituction numeric variables were compared with nonparametric test. Results: Among 1 610 children with ABM, 955 were male and 650 were female (5 cases were not provided with gender information), and the age of onset was 1.5 (0.5, 5.5) months. There were 588 cases age from <28 days, 462 cases age from 28 days to <3 months, 302 cases age from 3 months to <1 year of age group, 156 cases in the 1-<5 years of age and 101 cases in the 5-<15 years of age. The detection rates were 38.8% (95/245) and 31.5% (70/222) of Escherichia coli and 27.8% (68/245) and 35.1% (78/222) of Streptococcus agalactiae in infants younger than 28 days of age and 28 days to 3 months of age; the detection rates of Streptococcus pneumonia, Escherichia coli, and Streptococcus agalactiae were 34.3% (61/178), 14.0% (25/178) and 13.5% (24/178) in the 3 months of age to <1 year of age group; the dominant pathogens were Streptococcus pneumoniae and the detection rate were 67.9% (74/109) and 44.4% (16/36) in the 1-<5 years of age and 5-<15 years of age . There were 9.7% (19/195) strains of Escherichia coli producing ultra-broad-spectrum β-lactamases. The positive rates of cerebrospinal fluid (CSF) culture and blood culture were 32.2% (515/1 598) and 25.0% (400/1 598), while 38.2% (126/330)and 25.3% (21/83) in CSF metagenomics next generation sequencing and Streptococcus pneumoniae antigen detection. There were 4.3% (32/790) cases of which CSF white blood cell counts were normal in etiology confirmed group. Among 1 610 children with ABM, main intracranial imaging complications were subdural effusion and (or) empyema in 349 cases (21.7%), hydrocephalus in 233 cases (14.5%), brain abscess in 178 cases (11.1%), and other cerebrovascular diseases, including encephalomalacia, cerebral infarction, and encephalatrophy, in 174 cases (10.8%). Among the 166 cases (10.3%) with unfavorable outcome, 32 cases (2.0%) died among whom 24 cases died before 1 year of age, and 37 cases (2.3%) had recurrence among whom 25 cases had recurrence within 3 weeks. The incidences of subdural effusion and (or) empyema, brain abscess and ependymitis in the etiology confirmed group were significantly higher than those in the clinically diagnosed group (26.2% (207/790) vs. 17.3% (142/820), 13.0% (103/790) vs. 9.1% (75/820), 4.6% (36/790) vs. 2.7% (22/820), χ[2]=18.71, 6.20, 4.07, all P<0.05), but there was no significant difference in the unfavorable outcomes, mortility, and recurrence between these 2 groups (all P>0.05). Conclusions: The onset age of ABM in children is usually within 1 year of age, especially <3 months. The common pathogens in infants <3 months of age are Escherichia coli and Streptococcus agalactiae, and the dominant pathogen in infant ≥3 months is Streptococcus pneumoniae. Subdural effusion and (or) empyema and hydrocephalus are common complications. ABM should not be excluded even if CSF white blood cell counts is within normal range. Standardized bacteriological examination should be paid more attention to increase the pathogenic detection rate. Non-culture CSF detection methods may facilitate the pathogenic diagnosis.}, } @article {pmid36207493, year = {2023}, author = {Nobu, MK and Nakai, R and Tamazawa, S and Mori, H and Toyoda, A and Ijiri, A and Suzuki, S and Kurokawa, K and Kamagata, Y and Tamaki, H}, title = {Unique H2-utilizing lithotrophy in serpentinite-hosted systems.}, journal = {The ISME journal}, volume = {17}, number = {1}, pages = {95-104}, pmid = {36207493}, issn = {1751-7370}, mesh = {Autotrophic Processes ; *Hydrogen ; *Microbiota ; Glycine ; Oxidoreductases ; }, abstract = {Serpentinization of ultramafic rocks provides molecular hydrogen (H2) that can support lithotrophic metabolism of microorganisms, but also poses extremely challenging conditions, including hyperalkalinity and limited electron acceptor availability. Investigation of two serpentinization-active systems reveals that conventional H2-/CO2-dependent homoacetogenesis is thermodynamically unfavorable in situ due to picomolar CO2 levels. Through metagenomics and thermodynamics, we discover unique taxa capable of metabolism adapted to the habitat. This included a novel deep-branching phylum, "Ca. Lithacetigenota", that exclusively inhabits serpentinite-hosted systems and harbors genes encoding alternative modes of H2-utilizing lithotrophy. Rather than CO2, these putative metabolisms utilize reduced carbon compounds detected in situ presumably serpentinization-derived: formate and glycine. The former employs a partial homoacetogenesis pathway and the latter a distinct pathway mediated by a rare selenoprotein-the glycine reductase. A survey of microbiomes shows that glycine reductases are diverse and nearly ubiquitous in serpentinite-hosted environments. "Ca. Lithacetigenota" glycine reductases represent a basal lineage, suggesting that catabolic glycine reduction is an ancient bacterial innovation by Terrabacteria for gaining energy from geogenic H2 even under hyperalkaline, CO2-poor conditions. Unique non-CO2-reducing metabolisms presented here shed light on potential strategies that extremophiles may employ for overcoming a crucial obstacle in serpentinization-associated environments, features potentially relevant to primordial lithotrophy in early Earth.}, } @article {pmid36207492, year = {2023}, author = {Šimek, K and Mukherjee, I and Szöke-Nagy, T and Haber, M and Salcher, MM and Ghai, R}, title = {Cryptic and ubiquitous aplastidic cryptophytes are key freshwater flagellated bacterivores.}, journal = {The ISME journal}, volume = {17}, number = {1}, pages = {84-94}, pmid = {36207492}, issn = {1751-7370}, mesh = {In Situ Hybridization, Fluorescence ; *Ecosystem ; *Cryptophyta/genetics/microbiology ; Heterotrophic Processes ; Bacteria/genetics ; Lakes ; Phylogeny ; }, abstract = {Morphology-based microscopic approaches are insufficient for a taxonomic classification of bacterivorous heterotrophic nanoflagellates (HNF) in aquatic environments since their cells do not display reliably distinguishable morphological features. This leads to a considerable lack of ecological insights into this large and taxonomically diverse functional guild. Here, we present a combination of fluorescence in situ hybridization followed by catalyzed reporter deposition (CARD-FISH) and environmental sequence analyses which revealed that morphologically indistinguishable, so far largely cryptic and uncultured aplastidic cryptophytes are ubiquitous and prominent protistan bacterivores in diverse freshwater ecosystems. Using a general probe for Cryptophyceae and its heterotrophic CRY1 lineage, we analyzed different water layers in 24 freshwater lakes spanning a broad range of trophic states, sizes and geographical locations. We show that bacterivorous aplastidic cryptophytes and the CRY1 lineage accounted for ca. 2/3 and ¼ of total HNF, respectively, in both epilimnetic and hypolimnetic samples. These heterotrophic cryptophytes were generally smaller and more abundant than their chloroplast-bearing counterparts. They had high uptake rates of bacteria, hinting at their important roles in channeling carbon flow from prokaryotes to higher trophic levels. The worldwide ubiquity of Cryptophyceae and its CRY1 lineage was supported by 18S rRNA gene sequence analyses across a diverse set of 297 freshwater metagenomes. While cryptophytes have been considered to be mainly plastidic "algae", we show that it is the aplastidic counterparts that contribute considerably to bacterial mortality rates. Additionally, our results suggest an undiscovered diversity hidden amongst these abundant and morphologically diverse aplastidic cryptophytes.}, } @article {pmid36207343, year = {2022}, author = {Rigou, S and Santini, S and Abergel, C and Claverie, JM and Legendre, M}, title = {Past and present giant viruses diversity explored through permafrost metagenomics.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5853}, pmid = {36207343}, issn = {2041-1723}, mesh = {Genome, Viral/genetics ; *Giant Viruses/genetics ; Humans ; Metagenomics ; *Permafrost ; Phylogeny ; Soil ; *Viruses/genetics ; }, abstract = {Giant viruses are abundant in aquatic environments and ecologically important through the metabolic reprogramming of their hosts. Less is known about giant viruses from soil even though two of them, belonging to two different viral families, were reactivated from 30,000-y-old permafrost samples. This suggests an untapped diversity of Nucleocytoviricota in this environment. Through permafrost metagenomics we reveal a unique diversity pattern and a high heterogeneity in the abundance of giant viruses, representing up to 12% of the sum of sequence coverage in one sample. Pithoviridae and Orpheoviridae-like viruses were the most important contributors. A complete 1.6 Mb Pithoviridae-like circular genome was also assembled from a 42,000-y-old sample. The annotation of the permafrost viral sequences revealed a patchwork of predicted functions amidst a larger reservoir of genes of unknown functions. Finally, the phylogenetic reconstructions not only revealed gene transfers between cells and viruses, but also between viruses from different families.}, } @article {pmid36207335, year = {2022}, author = {Tao, J and Wang, W and Weissman, JL and Zhang, Y and Chen, S and Zhu, Y and Zhang, C and Hou, S}, title = {Size-fractionated microbiome observed during an eight-month long sampling in Jiaozhou Bay and the Yellow Sea.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {605}, pmid = {36207335}, issn = {2052-4463}, support = {Nos. 42141003//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {*Bays/microbiology ; China ; Genome, Microbial ; Metagenome ; *Microbiota ; Oceans and Seas ; }, abstract = {Jiaozhou Bay is a typical semi-enclosed bay with a temperate climate imposed by strong anthropogenic influence. To investigate microbial biodiversity and ecosystem services in this highly dynamic coastal environment, we conducted a monthly microbial survey spanning eight months at two stations in the bay and the open Yellow Sea starting in April 2015. This report provides a comprehensive inventory of amplicon sequences and environmental microbial genomes from this survey. In total, 2,543 amplicon sequence variants were obtained with monthly relative abundance profiles in three size fractions (>2.7 μm, 2.7-0.7 μm, and 0.7-0.22 μm). Shotgun metagenomes yielded 915 high-quality metagenome-assembled genomes with ≥50% completeness and ≤5% contamination. These environmental genomes comprise 27 bacterial and 5 archaeal phyla. We expect this comprehensive dataset will facilitate a better understanding of coastal microbial ecology.}, } @article {pmid36206910, year = {2023}, author = {Saravanakumar, C and Neethu, CS and Purvaja, R and Sunantha, G and Robin, RS and Ramesh, R}, title = {Networking and co-occurrence of virulent and multidrug resistant environmental bacteria in different aquatic systems: A gap in MDR-virulence transfer?.}, journal = {The Science of the total environment}, volume = {857}, number = {Pt 1}, pages = {159221}, doi = {10.1016/j.scitotenv.2022.159221}, pmid = {36206910}, issn = {1879-1026}, mesh = {Virulence/genetics ; *Vibrio parahaemolyticus ; Drug Resistance, Multiple, Bacterial ; Anti-Bacterial Agents/pharmacology ; Virulence Factors/genetics ; Phospholipases ; }, abstract = {Co-occurrence of resistance and virulence is often overlooked in aquatic bacteria as environmental reservoirs, while transmission of these characteristics to clinically significant strains present unforeseen problems in future. In this investigation, environmental bacteria identified concurrently from multiple aquatic habitats viz., groundwater, canal, river and coastal waters were profiled for antibiotic resistance, metal tolerance, virulence factors and genes coding for these determinants. Strains from polluted river and canal exhibited higher resistance and virulence, especially Pseudomonas gessardii and P. fluorescens displayed high antibiotic resistance index (ARI > 0.6-0.8) with Alkaline Protease and Phospholipase production. Opportunistic pathogens including Vibrio parahaemolyticus, V. alginolyticus, V. vulnificus, Corynebacterium and Comamonas testosteroni expressed all three virulence factors with relatively low resistance. However, V. vulnificus and V. alginolyticus exhibited multiclass antibiotic resistance (5/6 classes). Metagenomic analysis revealed that genes corresponding to beta-lactam resistance were significantly higher (p < 0.05) in freshwater than seawater, while multidrug resistance gene were higher (p < 0.05) in seawater. In all aquatic bodies, abundant virulence genes belonged to secretion system proteins followed by motility related genes. Culturable bacteria revealed differential distribution of positive and negative correlation between 31 targeted genes with expressed resistance and virulence. Among Acinetobacter, significant positive correlation was found between Phospholipase production, other virulence genes (OVGs) and resistance to DNA Synthesis Inhibitors (DSI). In Pseudomonas, positive correlation was detected between toxin genes (toxA, eta, hlyA and stx) and resistance to cell wall synthesis inhibitors (CSI) as well as with OVGs and adhesion genes (eae, afa, papC and papA). Network analysis displayed unique clustering of genes ncc, arsB, strA, merA and intI dominated by non-pathogens and distinct clustering of genes pho, erm, nfsA, trh, lasB, tdh and invA by Vibrio. This investigation extends insight on co-occurring resistance and virulence in aquatic reservoir bacteria that could pose serious threats to public health in future.}, } @article {pmid36206682, year = {2022}, author = {Ya, T and Liu, J and Zhang, M and Wang, Y and Huang, Y and Hai, R and Zhang, T and Wang, X}, title = {Metagenomic insights into the symbiotic relationship in anammox consortia at reduced temperature.}, journal = {Water research}, volume = {225}, number = {}, pages = {119184}, doi = {10.1016/j.watres.2022.119184}, pmid = {36206682}, issn = {1879-2448}, mesh = {*Sewage/microbiology ; Bioreactors/microbiology ; Temperature ; Glyceraldehyde/metabolism ; Anaerobic Ammonia Oxidation ; Oxidation-Reduction ; Nitrogen/metabolism ; Bacteria/genetics/metabolism ; Amino Acids ; Lactates/metabolism ; Glycosyltransferases/metabolism ; Folic Acid/metabolism ; Anaerobiosis ; *Ammonium Compounds/metabolism ; }, abstract = {Anammox as a promising biological nitrogen removal technology has attracted much attention. However, cold temperature would limit its wide application and little is known about the microbial interactions between anammox bacteria (AnAOB) and heterotrophic bacteria at cold temperature. Here, we observed reduced temperature (25-15 °C) promoted the secretion of EPS and thus stimulated bigger size of granular sludge in a laboratory-scale anammox reactor. We further combined co-occurrence network analysis and genome-centered metagenomics to explore the potential interactions between AnAOB and heterotrophic bacteria. Network analysis suggested 22 out of 25 positively related species were reported as definite heterotrophic bacteria in subnetwork of AnAOB. Genome-centered metagenomics analysis yielded 23 metagenomic assembly genomes (MAGs), and we found that Acidobacteriota-affiliated bacteria could biosynthesize most polysaccharides (PS) precursors and contain the most glycosyltransferases and transporters to facilitate exopolysaccharides biosynthesis, together with partial PS precursors produced by AnAOB. AMX1 as the only anammox genome could synthesize most amino acids and cross feed with some heterotrophs to affect the extracellular protein function. Additionally, Bacteroidota, Planctomycetota, Chloroflexota, and Proteobacteria could contribute folate and molybdopterin cofactor for AMX1 to benefit their activity and growth. Superphylum Patescibacteria could survive by cross-feeding with AnAOB and heterotrophic organisms about organic compounds (Glyceraldehyde-3P and lactate). These cross-feedings maintained the stability of anammox reactor performance and emphasize the importance of heterotrophs in anammox system at reduced temperature.}, } @article {pmid36206680, year = {2022}, author = {Xu, C and Lu, J and Shen, C and Wang, J and Li, F}, title = {Deciphering the mechanisms shaping the plastisphere antibiotic resistome on riverine microplastics.}, journal = {Water research}, volume = {225}, number = {}, pages = {119192}, doi = {10.1016/j.watres.2022.119192}, pmid = {36206680}, issn = {1879-2448}, mesh = {*Microplastics ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Plastics ; Vancomycin ; Polyethylene Terephthalates ; Bacteria/genetics ; *Rifamycins ; Water ; }, abstract = {Microplastics in urban rivers provide bacterial niches and serve as dispersal vectors for antibiotic resistant genes (ARGs) dissemination, which may exacerbate risks in the aquatic systems. However, whether MPs in the river would also selectively enrich ARGs and the underlying mechanisms shaping the resistome on MPs remains largely unknown. In this study, we explored the occurrence of ARGs, bacterial communities, and mobile genetic elements (MGEs) on MPs and in waters from the Huangpu River in China. Microplastics were widely distributed in the river (1.78 ± 0.84 items/L), with overwhelming percentages of polyethylene terephthalate fibers. Although reduced ARG abundances were observed on MPs than in waters, MPs selectively enriched the ARGs resistant to Rifamycin and Vancomycin. A clear variation for ARG profiles was elucidated between water and MPs samples. Network analysis suggested that MPs created a unique niche for the genus Afipia to colonize, potentially contributing to the vertical dissemination of ARGs. Additionally, the co-occurrence between ARGs and MGEs revealed that the MPs favor the propagation of some plasmid-associated ARGs mediated by horizontal gene transfer. The null model-based stochasticity ratio and the neutral community model suggested that the ARG assembly on MPs was dominantly driven by stochastic process. The results further indicated that microbial communities and MGEs played significant roles in shaping ARG profiles and dynamics on MPs. Our findings provided new insights into the ecological processes of antibiotic resistome of the aquatic plastisphere.}, } @article {pmid36206369, year = {2022}, author = {Braga, LPP and Orland, C and Emilson, EJS and Fitch, AA and Osterholz, H and Dittmar, T and Basiliko, N and Mykytczuk, NCS and Tanentzap, AJ}, title = {Viruses direct carbon cycling in lake sediments under global change.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {41}, pages = {e2202261119}, pmid = {36206369}, issn = {1091-6490}, mesh = {Amino Sugars/metabolism ; Bacteria/genetics/metabolism ; Carbon/metabolism ; Carbon Cycle ; *Greenhouse Gases/metabolism ; Lakes/microbiology ; *Viruses/genetics/metabolism ; Water/metabolism ; }, abstract = {Global change is altering the vast amount of carbon cycled by microbes between land and freshwater, but how viruses mediate this process is poorly understood. Here, we show that viruses direct carbon cycling in lake sediments, and these impacts intensify with future changes in water clarity and terrestrial organic matter (tOM) inputs. Using experimental tOM gradients within sediments of a clear and a dark boreal lake, we identified 156 viral operational taxonomic units (vOTUs), of which 21% strongly increased with abundances of key bacteria and archaea, identified via metagenome-assembled genomes (MAGs). MAGs included the most abundant prokaryotes, which were themselves associated with dissolved organic matter (DOM) composition and greenhouse gas (GHG) concentrations. Increased abundances of virus-like particles were separately associated with reduced bacterial metabolism and with shifts in DOM toward amino sugars, likely released by cell lysis rather than higher molecular mass compounds accumulating from reduced tOM degradation. An additional 9.6% of vOTUs harbored auxiliary metabolic genes associated with DOM and GHGs. Taken together, these different effects on host dynamics and metabolism can explain why abundances of vOTUs rather than MAGs were better overall predictors of carbon cycling. Future increases in tOM quantity, but not quality, will change viral composition and function with consequences for DOM pools. Given their importance, viruses must now be explicitly considered in efforts to understand and predict the freshwater carbon cycle and its future under global environmental change.}, } @article {pmid36206017, year = {2022}, author = {Cui, N and Faure, G and Singh, A and Macrae, R and Zhang, F}, title = {Microfluidic Enrichment and Computational Analysis of Rare Sequences from Mixed Genomic Samples for Metagenomic Mining.}, journal = {The CRISPR journal}, volume = {5}, number = {5}, pages = {677-684}, pmid = {36206017}, issn = {2573-1602}, support = {DP1 HL141201/HL/NHLBI NIH HHS/United States ; R01 HG009761/HG/NHGRI NIH HHS/United States ; }, mesh = {*CRISPR-Cas Systems/genetics ; *Gene Editing/methods ; Microfluidics ; Metagenome/genetics ; Genomics ; }, abstract = {Many powerful molecular biology tools have their origins in natural systems, including restriction modification enzymes and the CRISPR effectors, Cas9, Cas12, and Cas13. Heightened interest in these systems has led to mining of genomic and metagenomic data to identify new orthologs of these proteins, new types of CRISPR systems, and uncharacterized natural systems with novel mechanisms. To accelerate metagenomic mining, we developed a high-throughput, low-cost droplet microfluidic-based method for enrichment of rare sequences in a mixed starting population. Using a computational pipeline, we then searched in the enriched data for the presence of CRISPR-Cas systems, identifying a previously unknown CRISPR-Cas system. Our approach enables researchers to efficiently mine metagenomic samples for sequences of interest, greatly accelerating the search for nature's treasures.}, } @article {pmid36204644, year = {2022}, author = {Nienhold, R and Mensah, N and Frank, A and Graber, A and Koike, J and Schwab, N and Hernach, C and Zsikla, V and Willi, N and Cathomas, G and Hamelin, B and Graf, S and Junt, T and Mertz, KD}, title = {Unbiased screen for pathogens in human paraffin-embedded tissue samples by whole genome sequencing and metagenomics.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {968135}, pmid = {36204644}, issn = {2235-2988}, mesh = {*Bacteria/genetics ; Formaldehyde ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenomics/methods ; Paraffin Embedding ; Whole Genome Sequencing ; }, abstract = {Identification of bacterial pathogens in formalin fixed, paraffin embedded (FFPE) tissue samples is limited to targeted and resource-intensive methods such as sequential PCR analyses. To enable unbiased screening for pathogens in FFPE tissue samples, we established a whole genome sequencing (WGS) method that combines shotgun sequencing and metagenomics for taxonomic identification of bacterial pathogens after subtraction of human genomic reads. To validate the assay, we analyzed more than 100 samples of known composition as well as FFPE lung autopsy tissues with and without histological signs of infections. Metagenomics analysis confirmed the pathogenic species that were previously identified by species-specific PCR in 62% of samples, showing that metagenomics is less sensitive than species-specific PCR. On the other hand, metagenomics analysis identified pathogens in samples, which had been tested negative for multiple common microorganisms and showed histological signs of infection. This highlights the ability of this assay to screen for unknown pathogens and detect multi-microbial infections which is not possible by histomorphology and species-specific PCR alone.}, } @article {pmid36204638, year = {2022}, author = {Deng, Q and Cao, Y and Wan, X and Wang, B and Sun, A and Wang, H and Wang, Y and Wang, H and Gu, H}, title = {Nanopore-based metagenomic sequencing for the rapid and precise detection of pathogens among immunocompromised cancer patients with suspected infections.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {943859}, pmid = {36204638}, issn = {2235-2988}, mesh = {High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; *Nanopore Sequencing ; *Nanopores ; *Neoplasms/complications ; Prospective Studies ; }, abstract = {Cancer patients are at high risk of infections and infection-related mortality; thereby, prompt diagnosis and precise anti-infectives treatment are critical. This study aimed to evaluate the performance of nanopore amplicon sequencing in identifying microbial agents among immunocompromised cancer patients with suspected infections. This prospective study enlisted 56 immunocompromised cancer patients with suspected infections. Their body fluid samples such as sputum and blood were collected, and potential microbial agents were detected in parallel by nanopore amplicon sequencing and the conventional culture method. Among the 56 body fluid samples, 47 (83.9%) samples were identified to have at least one pathogen by nanopore amplicon sequencing, but only 25 (44.6%) samples exhibited a positive finding by culture. Among 31 culture-negative samples, nanopore amplicon sequencing successfully detected pathogens in 22 samples (71.0%). Nanopore amplicon sequencing showed a higher sensitivity in pathogen detection than that of the conventional culture method (83.9% vs. 44.6%, P<0.001), and this advantage both existed in blood samples (38.5% vs. 0%, P=0.039) and non-blood samples (97.7% vs. 58.1%, P<0.001). Compared with the culture method, nanopore amplicon sequencing illustrated more samples with bacterial infections (P<0.001), infections from fastidious pathogens (P=0.006), and co-infections (P<0.001). The mean turnaround time for nanopore amplicon sequencing was about 17.5 hours, which was shorter than that of the conventional culture assay. This study suggested nanopore amplicon sequencing as a rapid and precise method for detecting pathogens among immunocompromised cancer patients with suspected infections. The novel and high-sensitive method will improve the outcomes of immunocompromised cancer patients by facilitating the prompt diagnosis of infections and precise anti-infectives treatment.}, } @article {pmid36204622, year = {2022}, author = {Banerjee, S and Bedics, A and Tóth, E and Kriszt, B and Soares, AR and Bóka, K and Táncsics, A}, title = {Isolation of Pseudomonas aromaticivorans sp. nov from a hydrocarbon-contaminated groundwater capable of degrading benzene-, toluene-, m- and p-xylene under microaerobic conditions.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {929128}, pmid = {36204622}, issn = {1664-302X}, abstract = {Members of the genus Pseudomonas are known to be widespread in hydrocarbon contaminated environments because of their remarkable ability to degrade a variety of petroleum hydrocarbons, including BTEX (benzene, toluene, ethylbenzene and xylene) compounds. During an enrichment investigation which aimed to study microaerobic xylene degradation in a legacy petroleum hydrocarbon-contaminated groundwater, a novel Gram-stain-negative, aerobic, motile and rod-shaped bacterial strain, designated as MAP12[T] was isolated. It was capable of degrading benzene, toluene, meta- and para- xylene effectively under both aerobic and microaerobic conditions. The 16S rRNA gene sequence analysis revealed that strain MAP12[T] belongs to the genus Pseudomonas, with the highest 16S rRNA gene similarity to Pseudomonas linyingensis LYBRD3-7 [T] (98.42%), followed by Pseudomonas sagittaria JCM 18195 [T] (98.29%) and Pseudomonas alcaliphila JCM 10630 [T] (98.08%). Phylogenomic tree constructed using a concatenated alignment of 92 core genes indicated that strain MAP12[T] is distinct from any known Pseudomonas species. The draft genome sequence of strain MAP12[T] is 4.36 Mb long, and the G+C content of MAP12[T] genome is 65.8%. Orthologous average nucleotide identity (OrthoANI) and digital DNA-DNA hybridization (dDDH) analyses confirmed that strain MAP12[T] is distinctly separated from its closest neighbors (OrthoANI < 89 %; dDDH < 36%). Though several members of the genus Pseudomonas are well known for their aerobic BTEX degradation capability, this is the first report of a novel Pseudomonas species capable of degrading xylene under microaerobic conditions. By applying genome-resolved metagenomics, we were able to partially reconstruct the genome of strain MAP12 [T] from metagenomics sequence data and showed that strain MAP12 [T] was an abundant member of the xylene-degrading bacterial community under microaerobic conditions. Strain MAP12[T] contains ubiquinone 9 (Q9) as the major respiratory quinone and diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine as major polar lipids. The major cellular fatty acids of strain MAP12[T] are summed feature 3 (C16:1ω6c and/or C16:1ω7c), C16:0 and summed feature 8 (C18:1ω6c and/or C18:1ω7c). The results of this polyphasic study support that strain MAP12[T] represents a novel species of the genus Pseudomonas, hence the name of Pseudomonas aromaticivorans sp. nov. is proposed for this strain considering its aromatic hydrocarbon degradation capability. The type strain is MAP12[T] (=LMG 32466, =NCAIM B.02668).}, } @article {pmid36204618, year = {2022}, author = {Wang, N and Zhu, X and Zuo, Y and Liu, J and Yuan, F and Guo, Z and Zhang, L and Sun, Y and Gong, C and Song, C and Xu, X}, title = {Metagenomic evidence of suppressed methanogenic pathways along soil profile after wetland conversion to cropland.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {930694}, pmid = {36204618}, issn = {1664-302X}, abstract = {Wetland conversion to cropland substantially suppresses methane (CH4) emissions due to the strong suppression of methanogenesis, which consists of various pathways. In this study, we evaluated the cultivation impacts on four predominant CH4 production pathways, including acetate, carbon dioxide (CO2), methylamines, and methanol, in a wetland and cultivated cropland in northeastern China. The results showed significant suppression of CH4 production potential and the abundance of genes for all four methanogenic pathways in cropland. The consistency between CH4 production and methanogenesis genes indicates the robustness of genomic genes in analyzing methanogenesis. The suppression effects varied across seasons and along soil profiles, most evident in spring and 0 to 30 cm layers. The acetate pathway accounted for 55% in wetland vs. 70% in the cropland of all functional genes for CH4 production; while the other three pathways were stronger in response to cultivation, which presented as stronger suppressions in both abundance of functional genes (declines are 52% of CO2 pathway, 68% of methanol pathway, and 62% of methylamines pathway, vs. 19% of acetate pathway) and their percentages in four pathways (from 20 to 15% for CO2, 15 to 9% for methylamines, and 10 to 6% for methanol pathway vs. 55 to 70% for acetate pathway). The structural equation models showed that substrate availability was most correlated with CH4 production potential in the wetland, while the positive correlations of acetate, CO2, and methylamine pathways with CH4 production potential were significant in the cropland. The quantitative responses of four CH4 production pathways to land conversion reported in this study provide benchmark information for validating the CH4 model in simulating CH4 cycling under land use and land cover change.}, } @article {pmid36204330, year = {2022}, author = {Griffin, LE and Radhakrishnan, S and Pellizzon, MA}, title = {Addition of Soluble Fiber in Low-Fat Purified Diets Maintains Cecal and Colonic Morphology, Modulates Bacterial Populations and Predicted Functions, and Improves Glucose Tolerance Compared with Traditional AIN Diets in Male Mice.}, journal = {Current developments in nutrition}, volume = {6}, number = {10}, pages = {nzac105}, pmid = {36204330}, issn = {2475-2991}, abstract = {BACKGROUND: Purified diets (PDs) contain refined ingredients with one main nutrient, allowing for greater control relative to grain-based diets (GBDs), which contain unrefined grains and animal byproducts. Traditional PDs like the American Institute of Nutrition (AIN)-76A (76A) and AIN-93G (93G) can negatively impact metabolic and gut health when fed long term, in part due to lower total fiber, no soluble fiber, and higher sucrose content.

OBJECTIVE: Two studies were conducted to determine how PDs with reduced sucrose and increased fiber (soluble and insoluble) influence metabolic and gut health in mice compared with traditional AIN PDs or GBDs.

METHODS: In study 1, C57Bl/6N mice (n = 75) consumed a GBD [LabDiet 5002 (5002)], 76A, 93G, or 2 PDs with reduced sucrose and higher fiber for 88 d. Body composition and metabolic parameters were assessed. In study 2, C57Bl/6N mice (n = 54) consumed either 2 GBDs (LabDiet 5001 or 5002) or PDs with different types/levels of fiber for 14 d. Microbiome alterations and predicted functional metagenomic changes were measured.

RESULTS: The PD with 75 g cellulose and 25 g inulin per 4084 kcals marginally influenced body weight and adiposity, but improved glucose tolerance relative to 93G (P = 0.0131) and 76A (P = 0.0014). Cecal and colonic weights were lower in mice fed cellulose-based PDs compared with those fed GBDs and soluble-fiber PDs. Soluble-fiber PDs reduced alpha diversity and showed similar beta diversity, which differed from cellulose-based PDs and GBDs. Certain genera associated with improved gut health such as Bifidobacteria and Akkermansia were significantly elevated by soluble-fiber PDs (P ≤ 0.01). Metabolic pathways related to carbohydrate and fatty acid metabolism were affected by PDs.

CONCLUSIONS: PDs formulated with lower sucrose and increased fiber content, particularly soluble fiber, blunted elevations in metabolic parameters and favorably impacted the microbiota and metagenome in C57BL/6N mice.}, } @article {pmid36204265, year = {2022}, author = {Li, Y and Wang, J and He, L and Xu, X and Wang, J and Ren, C and Guo, Y and Zhao, F}, title = {Different mechanisms driving increasing abundance of microbial phosphorus cycling gene groups along an elevational gradient.}, journal = {iScience}, volume = {25}, number = {10}, pages = {105170}, pmid = {36204265}, issn = {2589-0042}, abstract = {Microbes play an integral role in forest soil phosphorus (P) cycling. However, the variation of microbial P-cycling functional genes and their controlling factors in forest soils is unclearly. We used metagenomics to investigate changes in the abundance of genes involved in P-starvation response regulation, P-uptake and transport, and P-solubilization and mineralization along the five elevational gradients. Our results showed the abundance of three P cycling gene groups increasing along the elevational gradient. Acidobacteria and Proteobacteria were the dominant microbial phyla determining the turnover of soil P-solubilization and immobilization. Along the elevational gradient, soil substrates are the major factor explaining variation in P-starvation response regulation genes. Soil environment is the main driver of P-uptake and transport and P-solubilization and mineralization genes. This study provided insights into the regulation of P-cycling from a microbial functional profile perspective, highlighting the importance of substrate and environmental factors for P-cycling genes in forest soils.}, } @article {pmid36204250, year = {2022}, author = {Shen, Z and Thomashow, LS and Ou, Y and Tao, C and Wang, J and Xiong, W and Liu, H and Li, R and Shen, Q and Kowalchuk, GA}, title = {Shared Core Microbiome and Functionality of Key Taxa Suppressive to Banana Fusarium Wilt.}, journal = {Research (Washington, D.C.)}, volume = {2022}, number = {}, pages = {9818073}, pmid = {36204250}, issn = {2639-5274}, abstract = {Microbial contributions to natural soil suppressiveness have been reported for a range of plant pathogens and cropping systems. To disentangle the mechanisms underlying suppression of banana Panama disease caused by Fusarium oxysporum f. sp. cubense tropical race 4 (Foc4), we used amplicon sequencing to analyze the composition of the soil microbiome from six separate locations, each comprised of paired orchards, one potentially suppressive and one conducive to the disease. Functional potentials of the microbiomes from one site were further examined by shotgun metagenomic sequencing after soil suppressiveness was confirmed by greenhouse experiments. Potential key antagonists involved in disease suppression were also isolated, and their activities were validated by a combination of microcosm and pot experiments. We found that potentially suppressive soils shared a common core community with relatively low levels of F. oxysporum and relatively high proportions of Myxococcales, Pseudomonadales, and Xanthomonadales, with five genera, Anaeromyxobacter, Kofleria, Plesiocystis, Pseudomonas, and Rhodanobacter being significantly enriched. Further, Pseudomonas was identified as a potential key taxon linked to pathogen suppression. Metagenomic analysis showed that, compared to the conducive soil, the microbiome in the disease suppressive soil displayed a significantly greater incidence of genes related to quorum sensing, biofilm formation, and synthesis of antimicrobial compounds potentially active against Foc4. We also recovered a higher frequency of antagonistic Pseudomonas isolates from disease suppressive experimental field sites, and their protective effects against banana Fusarium wilt disease were demonstrated under greenhouse conditions. Despite differences in location and soil conditions, separately located suppressive soils shared common characteristics, including enrichment of Myxococcales, Pseudomonadales, and Xanthomonadales, and enrichment of specific Pseudomonas populations with antagonistic activity against the pathogen. Moreover, changes in functional capacity toward an increase in quorum sensing, biofilm formation, and antimicrobial compound synthesizing involve in disease suppression.}, } @article {pmid36203993, year = {2022}, author = {Qu, C and Chen, Y and Ouyang, Y and Huang, W and Liu, F and Yan, L and Lu, R and Zeng, Y and Liu, Z}, title = {Metagenomics next-generation sequencing for the diagnosis of central nervous system infection: A systematic review and meta-analysis.}, journal = {Frontiers in neurology}, volume = {13}, number = {}, pages = {989280}, pmid = {36203993}, issn = {1664-2295}, abstract = {OBJECTIVE: It is widely acknowledged that central nervous system (CNS) infection is a serious infectious disease accompanied by various complications. However, the accuracy of current detection methods is limited, leading to delayed diagnosis and treatment. In recent years, metagenomic next-generation sequencing (mNGS) has been increasingly adopted to improve the diagnostic yield. The present study sought to evaluate the value of mNGS in CNS infection diagnosis.

METHODS: Following the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) 2022 guidelines, we searched relevant articles published in seven databases, including PubMed, Web of Science, and Cochrane Library, published from January 2014 to January 2022. High-quality articles related to mNGS applications in the CNS infection diagnosis were included. The comparison between mNGS and the gold standard of CNS infection, such as culture, PCR or serology, and microscopy, was conducted to obtain true positive (TP), true negative (TN), false positive (FP), and false negative (FN) values, which were extracted for sensitivity and specificity calculation.

RESULTS: A total of 272 related studies were retrieved and strictly selected according to the inclusion and exclusion criteria. Finally, 12 studies were included for meta-analysis and the pooled sensitivity was 77% (95% CI: 70-82%, I [2] = 39.69%) and specificity was 96% (95% CI: 93-98%, I [2] = 72.07%). Although no significant heterogeneity in sensitivity was observed, a sub-group analysis was conducted based on the pathogen, region, age, and sample pretreatment method to ascertain potential confounders. The area under the curve (AUC) of the summary receiver operating characteristic curve (SROC) of mNGS for CNS infection was 0.91 (95% CI: 0.88-0.93). Besides, Deek's Funnel Plot Asymmetry Test indicated no publication bias in the included studies (Figure 3, p > 0.05).

CONCLUSION: Overall, mNGS exhibits good sensitivity and specificity for diagnosing CNS infection and diagnostic performance during clinical application by assisting in identifying the pathogen. However, the efficacy remains inconsistent, warranting subsequent studies for further performance improvement during its clinical application.

STUDY REGISTRATION NUMBER: INPLASY202120002.}, } @article {pmid36203793, year = {2022}, author = {Clinton, NA and Hameed, SA and Agyei, EK and Jacob, JC and Oyebanji, VO and Jabea, CE}, title = {Crosstalk between the Intestinal Virome and Other Components of the Microbiota, and Its Effect on Intestinal Mucosal Response and Diseases.}, journal = {Journal of immunology research}, volume = {2022}, number = {}, pages = {7883945}, pmid = {36203793}, issn = {2314-7156}, mesh = {*Bacteriophages ; *Gastrointestinal Microbiome ; Intestinal Mucosa ; *Microbiota ; Virome ; *Viruses ; }, abstract = {In recent years, there has been ample evidence illustrating the effect of microbiota on gut immunity, homeostasis, and disease. Most of these studies have engaged more efforts in understanding the role of the bacteriome in gut mucosal immunity and disease. However, studies on the virome and its influence on gut mucosal immunity and pathology are still at infancy owing to limited metagenomic tools. Nonetheless, the existing studies on the virome have largely been focused on the bacteriophages as these represent the main component of the virome with little information on endogenous retroviruses (ERVs) and eukaryotic viruses. In this review, we describe the gut virome, and its role in gut mucosal response and disease progression. We also explore the crosstalk between the virome and other microorganisms in the gut mucosa and elaborate on how these interactions shape the gut mucosal immunity going from bacteriophages through ERVs to eukaryotic viruses. Finally, we elucidate the potential contribution of this crosstalk in the pathogenesis of inflammatory bowel diseases and colon cancer.}, } @article {pmid36202926, year = {2023}, author = {Barnum, TP and Coates, JD}, title = {Chlorine redox chemistry is widespread in microbiology.}, journal = {The ISME journal}, volume = {17}, number = {1}, pages = {70-83}, pmid = {36202926}, issn = {1751-7370}, mesh = {*Chlorates ; *Chlorine/metabolism ; Chlorides/metabolism ; Oxidation-Reduction ; Bacteria/metabolism ; }, abstract = {Chlorine is abundant in cells and biomolecules, yet the biology of chlorine oxidation and reduction is poorly understood. Some bacteria encode the enzyme chlorite dismutase (Cld), which detoxifies chlorite (ClO2[-]) by converting it to chloride (Cl[-]) and molecular oxygen (O2). Cld is highly specific for chlorite and aside from low hydrogen peroxide activity has no known alternative substrate. Here, we reasoned that because chlorite is an intermediate oxidation state of chlorine, Cld can be used as a biomarker for oxidized chlorine species. Cld was abundant in metagenomes from various terrestrial habitats. About 5% of bacterial and archaeal genera contain a microorganism encoding Cld in its genome, and within some genera Cld is highly conserved. Cld has been subjected to extensive horizontal gene transfer. Genes found to have a genetic association with Cld include known genes for responding to reactive chlorine species and uncharacterized genes for transporters, regulatory elements, and putative oxidoreductases that present targets for future research. Cld was repeatedly co-located in genomes with genes for enzymes that can inadvertently reduce perchlorate (ClO4[-]) or chlorate (ClO3[-]), indicating that in situ (per)chlorate reduction does not only occur through specialized anaerobic respiratory metabolisms. The presence of Cld in genomes of obligate aerobes without such enzymes suggested that chlorite, like hypochlorous acid (HOCl), might be formed by oxidative processes within natural habitats. In summary, the comparative genomics of Cld has provided an atlas for a deeper understanding of chlorine oxidation and reduction reactions that are an underrecognized feature of biology.}, } @article {pmid36202810, year = {2022}, author = {Jiang, WX and Li, PY and Chen, XL and Zhang, YS and Wang, JP and Wang, YJ and Sheng, Q and Sun, ZZ and Qin, QL and Ren, XB and Wang, P and Song, XY and Chen, Y and Zhang, YZ}, title = {A pathway for chitin oxidation in marine bacteria.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5899}, pmid = {36202810}, issn = {2041-1723}, mesh = {Amino Acids ; Bacteria/metabolism ; *Chitin/metabolism ; *Mixed Function Oxygenases/metabolism ; Monosaccharides ; Phosphates ; Polysaccharides/metabolism ; }, abstract = {Oxidative degradation of chitin, initiated by lytic polysaccharide monooxygenases (LPMOs), contributes to microbial bioconversion of crystalline chitin, the second most abundant biopolymer in nature. However, our knowledge of oxidative chitin utilization pathways, beyond LPMOs, is very limited. Here, we describe a complete pathway for oxidative chitin degradation and its regulation in a marine bacterium, Pseudoalteromonas prydzensis. The pathway starts with LPMO-mediated extracellular breakdown of chitin into C1-oxidized chitooligosaccharides, which carry a terminal 2-(acetylamino)-2-deoxy-D-gluconic acid (GlcNAc1A). Transmembrane transport of oxidized chitooligosaccharides is followed by their hydrolysis in the periplasm, releasing GlcNAc1A, which is catabolized in the cytoplasm. This pathway differs from the known hydrolytic chitin utilization pathway in enzymes, transporters and regulators. In particular, GlcNAc1A is converted to 2-keto-3-deoxygluconate 6-phosphate, acetate and NH3 via a series of reactions resembling the degradation of D-amino acids rather than other monosaccharides. Furthermore, genomic and metagenomic analyses suggest that the chitin oxidative utilization pathway may be prevalent in marine Gammaproteobacteria.}, } @article {pmid36202367, year = {2023}, author = {Parthipan, P and Cheng, L and Dhandapani, P and Rajasekar, A}, title = {Metagenomics diversity analysis of sulfate-reducing bacteria and their impact on biocorrosion and mitigation approach using an organometallic inhibitor.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 2}, pages = {159203}, doi = {10.1016/j.scitotenv.2022.159203}, pmid = {36202367}, issn = {1879-1026}, mesh = {*Biofilms ; Corrosion ; *Desulfovibrio ; Steel ; Sulfates ; }, abstract = {Sulfate-reducing bacteria (SRB) have impacted the biocorrosion process for various industrial sectors, especially in the oil and gas industry. The higher stability over extreme conditions is the key parameter for their survival in such environments. So far, many materials have been tried to minimize or control the growth of SRB. In the present study, an organo-metallic compound of the zinc sorbate (ZS) was successfully synthesized by the simple co-precipitation method and its improved antibacterial activity against SRB. The SRB consortia are enriched from the sub-surface soil sample and identified by 16s rDNA sequencing by targeting the V3-V4 region. The most dominating genera identified with sulfate-reducing capability are Sulfurospirillum (42 %), Shewanella (19 %) Bacteroides (14 %), and Desulfovibrio (8 %). Further biocorrosion experiments are conducted by weight loss methods. Higher corrosion current density (Icorr) and less charge transfer resistance (Rct) are observed for the SRB consortia. Concurrently, higher Rct is kept for the inhibitor-included systems. The slowest release of the sorbate into the medium suppressed the growth of the SRB bacterial cells with 86 ± 3 % corrosion inhibition efficiency and prevented further corrosion reactions by forming a protective layer over the surface of the carbon steel API 5LX. The surface analysis strongly confirmed that SRB caused pitting corrosion, which has been suppressed in the inhibitor-included systems.}, } @article {pmid36202244, year = {2023}, author = {Zou, C and Wang, M and Chen, Y and Qin, Y and Zhao, Y and Qiao, L and Zhu, S and Chen, T and Yuan, Y}, title = {Effects of different cathodic potentials on performance, microbial community structure and function for bioelectrochemical-stimulated dechlorination of 2,4,6-trichlorophenol in sediments.}, journal = {Environmental research}, volume = {216}, number = {Pt 1}, pages = {114477}, doi = {10.1016/j.envres.2022.114477}, pmid = {36202244}, issn = {1096-0953}, mesh = {*Chlorophenols/chemistry ; *Microbiota ; Electrodes ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; }, abstract = {Bioelectrochemical systems with biocathodes constitute a promising means to enhance the biological dechlorination of 2,4,6-trichlorophenol (2,4,6-TCP) in constructed wetland (CW) sediments. However, the effect of different cathodic potentials on the structure and function of 2,4,6-TCP-reducing biocathode communities in CW sediments is largely unknown. Here, we evaluated the performance and microbial community structure of 2,4,6-TCP-reducing biocathode systems at different cathodic potentials (- 0.5, - 0.7, - 0.9, and - 1.1 V vs. saturated calomel electrode). The dechlorination efficiency of 2,4,6-TCP with the biocathode relatively increased by 16.02%-33.17% compared to that in the open circuit. The highest 2,4,6-TCP dechlorination efficiency (92.34 ± 0.86%) was observed at - 0.7 V in sediment, which may be due to the highest abundance of functional genera (e.g., Pseudomonas, Spirochaeta) at - 0.7 V. Metagenomic analysis provided new insights into the metabolic potential of microorganisms in CW sediments and suggested possible 2,4,6-TCP conversion pathways in sediments. 2,4,6-TCP was gradually dechlorinated to form 4-chlorophenol, followed by a ring-opening step via the activities of chlorophenol reductive dehalogenase and oxygenase (e.g., cprA, tfdB). Interestingly, micro-electrical stimulation enhanced the expression of chlorophenol reductive dehalogenase (cprA). Therefore, our findings at the molecular and gene expression levels provide insights into the effects of different cathodic potentials on the performance and community structure of 2,4,6-TCP-reducing biocathode systems in CW sediments.}, } @article {pmid36202201, year = {2022}, author = {Cifuentes, SG and Graham, J and Loayza, F and Saraiva, C and Salinas, L and Trueba, G and Cárdenas, PA}, title = {Evaluation of changes in the faecal resistome associated with children's exposure to domestic animals and food animal production.}, journal = {Journal of global antimicrobial resistance}, volume = {31}, number = {}, pages = {212-215}, pmid = {36202201}, issn = {2213-7173}, support = {D43 TW010540/TW/FIC NIH HHS/United States ; R01 AI135118/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Drug Resistance, Bacterial/genetics ; Metagenomics ; Animals, Domestic ; Feces ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents ; }, abstract = {OBJECTIVES: The paediatric gut microbiota is a reservoir of antimicrobial resistance genes. Environmental factors such as a child's exposure to faecal contamination and antimicrobial resistance genes of animal origin likely shape the resistome of infants and children. This study measured how different levels of exposure to domestic or food animals affect the structure of the intestinal resistome in children between 1 and 7 years of age.

METHODS: One hundred nineteen faecal samples from 39 children were analysed according to the level of exposure to domestic or food animals and categorized into three risk groups. Using high-throughput sequencing with an Illumina NovaSeq 6000 SP platform, we performed faecal resistome analyses using the ResFinder database. Additionally, ResistoXplorer was used to characterize the resistomes of children differentially exposed to domestic animals.

RESULTS: Our data indicated that specific antimicrobial resistance genes such as those that confer resistance to MATFPR (macrolide, aminoglycoside, tetracycline, fluoroquinolone, phenicol, and rifamycin) and tetracyclines were statistically less abundant in the group of children without exposure to animals (group 2), compared with the groups exposed to domestic and food animals (groups 1 and 3). However, the overall resistome structure among the children was not affected by the different levels of exposure to animals.

CONCLUSIONS: This study suggests that animal exposure is a risk factor for young children acquiring specific antimicrobial resistance genes from domestic animals or animal production areas. However, the overall resistome structure was not affected.}, } @article {pmid36201636, year = {2022}, author = {Su, Q and Liu, Q and Zhang, L and Xu, Z and Liu, C and Lu, W and Ching, JY and Li, A and Mak, JWY and Lui, GCY and Ng, SSS and Chow, KM and Hui, DS and Chan, PK and Chan, FKL and Ng, SC}, title = {Antibiotics and probiotics impact gut antimicrobial resistance gene reservoir in COVID-19 patients.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2128603}, pmid = {36201636}, issn = {1949-0984}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *COVID-19/complications ; Drug Resistance, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; *Probiotics/therapeutic use ; SARS-CoV-2/genetics ; Tetracyclines ; Vancomycin ; Post-Acute COVID-19 Syndrome ; *COVID-19 Drug Treatment ; }, abstract = {Dysbiosis of gut microbiota is well-described in patients with coronavirus 2019 (COVID-19), but the dynamics of antimicrobial resistance genes (ARGs) reservoir, known as resistome, is less known. Here, we performed longitudinal fecal metagenomic profiling of 142 patients with COVID-19, characterized the dynamics of resistome from diagnosis to 6 months after viral clearance, and reported the impact of antibiotics or probiotics on the ARGs reservoir. Antibiotic-naive patients with COVID-19 showed increased abundance and types, and higher prevalence of ARGs compared with non-COVID-19 controls at baseline. Expansion in resistome was mainly driven by tetracycline, vancomycin, and multidrug-resistant genes and persisted for at least 6 months after clearance of SARS-CoV-2. Patients with expanded resistome exhibited increased prevalence of Klebsiella sp. and post-acute COVID-19 syndrome. Antibiotic treatment resulted in further increased abundance of ARGs whilst oral probiotics (synbiotic formula, SIM01) significantly reduced the ARGs reservoir in the gut microbiota of COVID-19 patients during the acute infection and recovery phase. Collectively, these findings shed new insights on the dynamic of ARGs reservoir in COVID-19 patients and the potential role of microbiota-directed therapies in reducing the burden of accumulated ARGs.}, } @article {pmid36201117, year = {2022}, author = {Nie, L and Cao, M and Ji, Q and Gao, Y and Wang, S and Lyu, Y and Feng, Z}, title = {Regulated Expression of an Environmental DNA-Derived Type II Polyketide Gene Cluster in Streptomyces Hosts Identified a New Tetracenomycin Derivative TCM Y.}, journal = {Current microbiology}, volume = {79}, number = {11}, pages = {336}, pmid = {36201117}, issn = {1432-0991}, support = {31770049//National Natural Science Foundation of China/ ; }, mesh = {*Biological Products/metabolism ; *DNA, Environmental ; Multigene Family ; Naphthacenes ; *Polyketides/metabolism ; Soil ; *Streptomyces/genetics/metabolism ; }, abstract = {As bacterial natural products have been proved to be the most important source of many therapeutic medicines, the need to discover novel natural products becomes extremely urgent. Despite the fact that the majority of bacterial species are yet to be cultured in a laboratory setting, and that most of the bacterial natural product biosynthetic genes are silent, "metagenomics technology" offers a solution to help clone natural product biosynthetic genes from environmental samples, and genetic engineering enables the silent biosynthetic genes to be activated. In this work, a type II polyketide biosynthetic gene cluster was identified from a soil metagenomic library and was activated by over-expression of a SARP regulator gene in the gene cluster in Streptomyces hosts. A new tetracenomycin type compound tetracenomycin Y was identified from the fermentation broth. This study shows that metagenomics and genetic engineering could be combined to provide access to new natural metabolites.}, } @article {pmid36200987, year = {2023}, author = {Wang, B and Du, P and Huang, S and He, D and Chen, J and Wen, X and Yang, J and Xian, S and Cheng, Z}, title = {Comparison of the caecal microbial community structure and physiological indicators of healthy and infection Eimeria tenella chickens during peak of oocyst shedding.}, journal = {Avian pathology : journal of the W.V.P.A}, volume = {52}, number = {1}, pages = {51-61}, doi = {10.1080/03079457.2022.2133681}, pmid = {36200987}, issn = {1465-3338}, mesh = {Animals ; *Eimeria tenella/genetics ; Chickens/microbiology ; *Poultry Diseases/microbiology ; Oocysts/physiology ; *Coccidiosis/parasitology/veterinary ; *Microbiota ; }, abstract = {Eimeria tenella (E. tenella), an important intestinal parasite of chicken caeca, causes coccidiosis and brings large economic losses to the poultry industry annually. Gut microorganismal alterations directly affect the health of the body. To understand how E. tenella affects its host, we analysed the changes in caecal microbial diversity and the physiological and morphological changes during the peak of oocyst shedding. Infected and healthy chickens differed significantly in caecal pathology and blood indicators. At the genus level, the abundances of Faecalibacterium, Clostridium, Lachnoclostridium, Gemmiger, Flavonifractor, Pseudoflavonifractor and Oscillibacter were significantly decreased in the infected samples, whereas Escherichia, Nocardia and Chlamydia were significantly increased. Functional gene pathways related to replication, recombination and repair, and transcription were significantly decreased, and functional genes related to metabolism were highly significantly reduced in the infected samples. Furthermore, in the infected samples, E. tenella reduced the haemoglobin levels and red blood cell counts, greatly reduced the beneficial bacteria and increased the potentially pathogenic bacteria. This study provides a research basis for further understanding the pathogenic mechanisms of E. tenella and provides insight for potential new drug development.RESEARCH HIGHLIGHTS First simultaneous description of caecal microbiota and physiological indicators during E. tenella infection.Metagenomics used to explore functional properties of chicken caecal microbiota during E. tenella infection.Caecal microbial compositions and functional genes altered significantly after infection.Blood indicators and caecal morphology were significantly altered in the infected group.}, } @article {pmid36200912, year = {2022}, author = {Kutshik, RJ and Yakubu, B and Joel, EB and Lenka, JL and Tukur, A and Longdet, IY}, title = {Assembly of Olivibacter sp. Strain UJ_SKK_5.1 Genome Sequence, Isolated from Metagenomes of Macrotermes bellicosus Guts Collected from Hot, Arid Nigeria.}, journal = {Microbiology resource announcements}, volume = {11}, number = {11}, pages = {e0089522}, pmid = {36200912}, issn = {2576-098X}, support = {TETFund/DR&D/CE/NRF/STI/21/VOL1//Tertiary Education Trust Fund (TETFund)/ ; }, abstract = {The metagenome-assembled genome sequence of Olivibacter sp. strain UJ_SKK_5.1 was generated from the metagenome of a Macrotermes bellicosus (termites) gut collected from Nigeria's hot, arid environment. The assembled genome (6,135,249 bp) contains 432 contigs, with an N50 value of 22,779 bp, GC content of 41.1%, 5,043 protein-coding sequences, 5,034 proteins with functional assignments, and 9 pseudogenes and 48 RNA genes.}, } @article {pmid36199818, year = {2022}, author = {Mustafa, SS and Batool, R and Kamran, M and Javed, H and Jamil, N}, title = {Evaluating the Role of Wastewaters as Reservoirs of Antibiotic-Resistant ESKAPEE Bacteria Using Phenotypic and Molecular Methods.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {5715-5728}, pmid = {36199818}, issn = {1178-6973}, abstract = {INTRODUCTION: Wastewaters carrying thousands of human specimens from the community and representing the diversity of antibiotic-resistant bacteria (ARB) and antibiotic-resistance genes (ARGs) directly from the community mirror the extent of AR spread in the community and environment. This study aimed to investigate the occurrence and distribution of antibiotic-resistant ESKAPEE bacteria in the community versus clinical settings through monitoring nonclinical and clinical wastewaters.

METHODOLOGY: Seven wastewater samples were collected from different environmental sources. Isolates were obtained on general and selective media, biochemically characterized and antimicrobial-susceptibility tests performed by disk diffusion against 13 antibiotics according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines using MastDisc disk cartridges, and 16S rRNA metagenomic analysis was performed for two water samples.

RESULTS: Of 43 isolates, all representatives of the ESKAPEE group were recovered from clinical wastewaters, but Gram-positive cocci were not obtained from nonclinical wastewaters. The most predominant isolate was Pseudomonas aeruginosa (n=15; 33%), followed by Escherichia coli (n=9; 20%). Complete (100%) resistance to eleven of the tested antibiotics was observed, with only a few isolates being susceptible to clarithromycin, amikacin, and gentamicin. The lowest (79%) resistance rate was observed for linezolid. The multiple antibiotic resistance (MAR) index was calculated, and the resistance phenotype was independent of the wastewater source, indicated by x [2] (P=0.766). Metagenomic analysis replicated the results, as Pseudomonas spp., Acinetobacter spp., and Escherichia spp. were found to be predominant. The integrase gene (IntI1) was also amplified in Escherichia coli, Klebsiella pneumoniae, and Pseudomonas aeruginosa.

CONCLUSION: Wastewaters are significant carriers of drug-resistant ESKAPEE bacteria and play an important role in their dissemination. This study endorses the periodic surveillance of water systems to evaluate the presence and burden of antibiotic-resistant pathogens.}, } @article {pmid36198385, year = {2022}, author = {Bamola, VD and Dubey, D and Samanta, P and Kedia, S and Ahuja, V and Madempudi, RS and Neelamraju, J and Chaudhry, R}, title = {Role of a probiotic strain in the modulation of gut microbiota and cytokines in inflammatory bowel disease.}, journal = {Anaerobe}, volume = {78}, number = {}, pages = {102652}, doi = {10.1016/j.anaerobe.2022.102652}, pmid = {36198385}, issn = {1095-8274}, mesh = {Humans ; *Gastrointestinal Microbiome ; Cytokines ; *Probiotics/therapeutic use ; Bifidobacterium ; *Inflammatory Bowel Diseases/therapy ; Tumor Necrosis Factor-alpha ; }, abstract = {OBJECTIVE: To assess the effect of a probiotic strain Bacillus clausii UBBC-07 on gut microbiota and cytokines in IBD patients.

METHOD: Patients were randomly allocated to either placebo or probiotic Bacillus clausii UBBC-07 for four weeks along with the standard medical treatment (SMT). Enrolled patients were evaluated before and after intervention for presence of the given probiotic, change in gut microbiota, change in serum cytokines, serotonin and dopamine, symptoms of disease, physical, behavioral and psychological parameters.

RESULTS: Probiotic strain Bacillus clausii UBBC-07 showed good survival in IBD patients in the treatment group (p < 0.01) without any reported adverse event. Metagenomic analysis showed that the given probiotic strain was able to modulate the gut microbiota in treated group. Phylum Firmicutes was increased and phylum Bacteroidetes was decreased in the probiotic treated group. A significant increase was observed in the abundance of anaerobic bacterial genera Lactobacillus, Bifidobacterium and Faecalibacterium in the probiotic treated group (p < 0.01) as compared to placebo group. Significant increase was observed in IL-10 (p < 0.05) and variable decrease in the secretion of IL-1β, TNF- α, IL-6, IL -17 and IL -23 in probiotic treated group. In the treatment group a significant decrease in the symptoms of IBD and improvement in the psychological parameter to various degrees was noted.

CONCLUSION: These results indicated that probiotic strain B clausii UBBC-07 affected the gut microbiota and cytokine secretion and shown efficacy in IBD patients.}, } @article {pmid36198381, year = {2023}, author = {Chen, F and Li, S and Guo, R and Song, F and Zhang, Y and Wang, X and Huo, X and Lv, Q and Ullah, H and Wang, G and Ma, Y and Yan, Q and Ma, X}, title = {Meta-analysis of fecal viromes demonstrates high diagnostic potential of the gut viral signatures for colorectal cancer and adenoma risk assessment.}, journal = {Journal of advanced research}, volume = {49}, number = {}, pages = {103-114}, pmid = {36198381}, issn = {2090-1224}, mesh = {Humans ; Virome ; *Gastrointestinal Microbiome ; *Viruses ; *Adenoma/diagnosis ; Risk Assessment ; Biomarkers ; *Colorectal Neoplasms/diagnosis/microbiology ; }, abstract = {INTRODUCTION: Viruses have been reported as inducers of tumorigenesis. Little studies have explored the impact of the gut virome on the progression of colorectal cancer. However, there is still a problem with the repeatability of viral signatures across multiple cohorts.

OBJECTIVES: The present study aimed to reveal the repeatable gut vial signatures of colorectal cancer and adenoma patients and decipher the potential of viral markers in disease risk assessment for diagnosis.

METHODS: 1,282 available fecal metagenomes from 9 published studies for colorectal cancer and adenoma were collected. A gut viral catalog was constructed via a reference-independent approach. Viral signatures were identified by cross-cohort meta-analysis and used to build predictive models based on machine learning algorithms. New fecal samples were collected to validate the generalization of predictive models.

RESULTS: The gut viral composition of colorectal cancer patients was drastically altered compared with healthy, as evidenced by changes in some Siphoviridae and Myoviridae viruses and enrichment of Microviridae, whereas the virome variation in adenoma patients was relatively low. Cross-cohort meta-analysis identified 405 differential viruses for colorectal cancer, including several phages of Porphyromonas, Fusobacterium, and Hungatella that were enriched in patients and some control-enriched Ruminococcaceae phages. In 9 discovery cohorts, the optimal risk assessment model obtained an average cross-cohort area under the curve of 0.830 for discriminating colorectal cancer patients from controls. This model also showed consistently high accuracy in 2 independent validation cohorts (optimal area under the curve, 0.906). Gut virome analysis of adenoma patients identified 88 differential viruses and achieved an optimal area under the curve of 0.772 for discriminating patients from controls.

CONCLUSION: Our findings demonstrate the gut virome characteristics in colorectal cancer and adenoma and highlight gut virus-bacterial synergy in the progression of colorectal cancer. The gut viral signatures may be new targets for colorectal cancer treatment. In addition, high repeatability and predictive power of the prediction models suggest the potential of gut viral biomarkers in non-invasive diagnostic tests of colorectal cancer and adenoma.}, } @article {pmid36198208, year = {2022}, author = {Wang, D and Wang, Y and Liu, L and Chen, Y and Wang, C and Xu, X and Yang, Y and Wang, Y and Zhang, T}, title = {Niche differentiation and symbiotic association among ammonia/nitrite oxidizers in a full-scale rotating biological contactor.}, journal = {Water research}, volume = {225}, number = {}, pages = {119137}, doi = {10.1016/j.watres.2022.119137}, pmid = {36198208}, issn = {1879-2448}, mesh = {Ammonia ; Nitrites ; Nitrification ; Archaea/genetics ; Nitrogen ; *Betaproteobacteria/genetics ; Oxidation-Reduction ; *Ammonium Compounds ; Phylogeny ; Soil Microbiology ; }, abstract = {Although the distribution of ammonia/nitrite oxidizers had been profiled in different habitats, current understanding is still limited regarding their niche differentiation in the integrated biofilm reactors, the symbiotic associations of ammonia/nitrite oxidizers, as well as the parasitic interaction between viruses and those functional organisms involved in the nitrogen cycle. Here, the integrated metagenomics and metatranscriptomics are applied to profile the ammonia/nitrite oxidizers communities and transcriptional activities changes along the flowpath of a concatenated full-scale rotating biological contactor (RBC) (frontend Stage-A and backend Stage-B). 19 metagenome-assembled genomes (MAGs) of ammonia/nitrite oxidizers were recovered by using a hybrid assembly approach, including four ammonia-oxidizing bacteria (AOB), two ammonia-oxidizing archaea (AOA), two complete ammonia oxidation bacteria (comammox), eight nitrite-oxidizing bacteria (NOB), and three anaerobic ammonium oxidation bacteria (anammox). Diverse AOB and anammox dominated Stage-A and collectively contributed to nitrogen conversion. With the decline of ammonia concentration along the flowpath, comammox and AOA appeared and increased in relative abundance in Stage-B, accounting for 8.8% of the entire community at the end of this reactor, and their dominating role in nitrogen turnover was indicated by the high transcription activity of their corresponding function genes. Moreover, the variation in the abundance of viruses infecting ammonia and nitrite oxidizers suggests that viruses likely act as a biotic factor mediating ammonia/nitrite oxidizer populations. This study demonstrates that complex factors shaped niche differentiation and symbiotic associations of ammonia/nitrite oxidizers in the RBC and highlights the importance of RBCs as model systems for the investigation of biotic and abiotic factors affecting the composition of microbiomes.}, } @article {pmid36197791, year = {2023}, author = {Brennan, GL}, title = {Sequencing our way to more accurate community abundance.}, journal = {Molecular ecology resources}, volume = {23}, number = {1}, pages = {13-15}, pmid = {36197791}, issn = {1755-0998}, support = {//Georgina L. Brennan Marie Skłodowska-Curie Individual Fellowship/ ; }, mesh = {*Biodiversity ; *Metagenomics/methods ; Metagenome ; Ecology ; Oceans and Seas ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {Over the last two decades, there has been a huge increase in our understanding of microbial diversity, structure and composition enabled by high-throughput sequencing technologies. Yet, it is unclear how the number of sequences translates to the number of cells or species within the community. In some cases, additional observational data may be required to ensure relative abundance patterns from sequence reads are biologically meaningful. The goal of DNA-based methods for biodiversity assessments is to obtain robust community abundance data, simultaneously, from environmental samples. In this issue of Molecular Ecology Resources, Pierella Karlusich et al. (2022) describe a new method for quantifying phytoplankton cell abundance. Using Tara Oceans data sets, the authors propose the photosynthetic gene psbO for reporting accurate relative abundance of the entire phytoplankton community from metagenomic data. The authors demonstrate higher correlations with traditional optical methods (including microscopy and flow cytometry), using their new method, improving upon molecular abundance assessments using multicopy marker genes. Furthermore, to facilitate application of their approach, the authors curated a psbO gene database for accessible taxonomic queries. This is an important step towards improving species abundance estimates from molecular data and eventually reporting of absolute species abundance, enhancing our understanding of community dynamics.}, } @article {pmid36197077, year = {2022}, author = {Hu, S and Xu, H and Meng, X and Bai, X and Xu, J and Ji, J and Ying, C and Chen, Y and Shen, P and Zhou, Y and Zheng, B and Xiao, Y}, title = {Population genomics of emerging Elizabethkingia anophelis pathogens reveals potential outbreak and rapid global dissemination.}, journal = {Emerging microbes & infections}, volume = {11}, number = {1}, pages = {2590-2599}, pmid = {36197077}, issn = {2222-1751}, mesh = {Humans ; Phylogeny ; *Metagenomics ; Genome, Bacterial ; *Flavobacteriaceae Infections/epidemiology/microbiology ; Disease Outbreaks ; }, abstract = {Elizabethkingia anophelis is an emerging species and has increasingly been reported to cause life-threatening infections and even outbreaks in humans. Nevertheless, there is little data regarding the E. anophelis geographical distribution, phylogenetic structure, and transmission across the globe, especially in Asia. We utilize whole-genome sequencing (WGS) data to define a global population framework, phylogenetic structure, geographical distribution, and transmission evaluation of E. anophelis pathogens. The geographical distribution diagram revealed the emerging pathogenic bacteria already distributed in various countries worldwide, especially in the USA and China. Strikingly, phylogenetic analysis showed a part of our China original E. anophelis shared the same ancestor with the USA outbreak strain, which implies the possibility of localized outbreaks and global spread. These closer related strains also contained ICEEaI, which might insert into a disrupted DNA repair mutY gene and made the strain more liable to mutation and outbreak infection. BEAST analysis showed that the most recent common ancestor for ICEEaI E. anophelis was dated twelve years ago, and China might be the most likely recent source of this bacteria. Our study sheds light on the potential possibility of E. anophelis causing the large-scale outbreak and rapid global dissemination. Continued genomic surveillance of the dynamics of E. anophelis populations will generate further knowledge for optimizing future prevent global outbreak infections.}, } @article {pmid36197061, year = {2022}, author = {Vega, MAP and Scholes, RC and Brady, AR and Daly, RA and Narrowe, AB and Bosworth, LB and Wrighton, KC and Sedlak, DL and Sharp, JO}, title = {Pharmaceutical Biotransformation is Influenced by Photosynthesis and Microbial Nitrogen Cycling in a Benthic Wetland Biomat.}, journal = {Environmental science & technology}, volume = {56}, number = {20}, pages = {14462-14477}, doi = {10.1021/acs.est.2c03566}, pmid = {36197061}, issn = {1520-5851}, mesh = {*Ammonium Compounds ; Atenolol ; Biotransformation ; Denitrification ; Emtricitabine/metabolism ; Metoprolol ; Nitrate Reductases/metabolism ; Nitrification ; Nitrogen/metabolism ; Nitrous Oxide ; Oxygen ; Pharmaceutical Preparations ; Photosynthesis ; Trimethoprim ; Water ; *Wetlands ; }, abstract = {In shallow, open-water engineered wetlands, design parameters select for a photosynthetic microbial biomat capable of robust pharmaceutical biotransformation, yet the contributions of specific microbial processes remain unclear. Here, we combined genome-resolved metatranscriptomics and oxygen profiling of a field-scale biomat to inform laboratory inhibition microcosms amended with a suite of pharmaceuticals. Our analyses revealed a dynamic surficial layer harboring oxic-anoxic cycling and simultaneous photosynthetic, nitrifying, and denitrifying microbial transcription spanning nine bacterial phyla, with unbinned eukaryotic scaffolds suggesting a dominance of diatoms. In the laboratory, photosynthesis, nitrification, and denitrification were broadly decoupled by incubating oxic and anoxic microcosms in the presence and absence of light and nitrogen cycling enzyme inhibitors. Through combining microcosm inhibition data with field-scale metagenomics, we inferred microbial clades responsible for biotransformation associated with membrane-bound nitrate reductase activity (emtricitabine, trimethoprim, and atenolol), nitrous oxide reduction (trimethoprim), ammonium oxidation (trimethoprim and emtricitabine), and photosynthesis (metoprolol). Monitoring of transformation products of atenolol and emtricitabine confirmed that inhibition was specific to biotransformation and highlighted the value of oscillating redox environments for the further transformation of atenolol acid. Our findings shed light on microbial processes contributing to pharmaceutical biotransformation in open-water wetlands with implications for similar nature-based treatment systems.}, } @article {pmid36195901, year = {2022}, author = {Kelly, JB and Carlson, DE and Low, JS and Thacker, RW}, title = {Novel trends of genome evolution in highly complex tropical sponge microbiomes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {164}, pmid = {36195901}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Evolution, Molecular ; *Lipopolysaccharides ; Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; Phylogeny ; Steroids ; Sterols ; }, abstract = {BACKGROUND: Tropical members of the sponge genus Ircinia possess highly complex microbiomes that perform a broad spectrum of chemical processes that influence host fitness. Despite the pervasive role of microbiomes in Ircinia biology, it is still unknown how they remain in stable association across tropical species. To address this question, we performed a comparative analysis of the microbiomes of 11 Ircinia species using whole-metagenomic shotgun sequencing data to investigate three aspects of bacterial symbiont genomes-the redundancy in metabolic pathways across taxa, the evolution of genes involved in pathogenesis, and the nature of selection acting on genes relevant to secondary metabolism.

RESULTS: A total of 424 new, high-quality bacterial metagenome-assembled genomes (MAGs) were produced for 10 Caribbean Ircinia species, which were evaluated alongside 113 publicly available MAGs sourced from the Pacific species Ircinia ramosa. Evidence of redundancy was discovered in that the core genes of several primary metabolic pathways could be found in the genomes of multiple bacterial taxa. Across hosts, the metagenomes were depleted in genes relevant to pathogenicity and enriched in eukaryotic-like proteins (ELPs) that likely mimic the hosts' molecular patterning. Finally, clusters of steroid biosynthesis genes (CSGs), which appear to be under purifying selection and undergo horizontal gene transfer, were found to be a defining feature of Ircinia metagenomes.

CONCLUSIONS: These results illustrate patterns of genome evolution within highly complex microbiomes that illuminate how associations with hosts are maintained. The metabolic redundancy within the microbiomes could help buffer the hosts from changes in the ambient chemical and physical regimes and from fluctuations in the population sizes of the individual microbial strains that make up the microbiome. Additionally, the enrichment of ELPs and depletion of LPS and cellular motility genes provide a model for how alternative strategies to virulence can evolve in microbiomes undergoing mixed-mode transmission that do not ultimately result in higher levels of damage (i.e., pathogenicity) to the host. Our last set of results provides evidence that sterol biosynthesis in Ircinia-associated bacteria is widespread and that these molecules are important for the survival of bacteria in highly complex Ircinia microbiomes. Video Abstract.}, } @article {pmid36195416, year = {2022}, author = {Dreher, TW and Davis, EW and Wilhelm, FM and Burnet, SH and Mueller, RS}, title = {Genome sequence of freshwater nontoxigenic Limnoraphis associated with microcystin-producing blooms.}, journal = {Harmful algae}, volume = {118}, number = {}, pages = {102309}, doi = {10.1016/j.hal.2022.102309}, pmid = {36195416}, issn = {1878-1470}, mesh = {*Cyanobacteria/genetics ; Lakes/microbiology ; Microcystins ; *Microcystis/genetics ; Phycobilisomes ; Phycocyanin ; Phycoerythrin ; }, abstract = {A sample from a 2019 cyanobacterial bloom in a freshwater reservoir in eastern Oregon, USA, was used to produce a metagenome from which the complete, circular 7.3 Mbp genome of Limnoraphis sp. WC205 was assembled. The Limnoraphis sp. WC205 genome contains gas vesicle genes, genes for N2-fixation and genes for both phycocyanin- and phycoerythrin-containing phycobilisomes. Limnoraphis was present in Willow Creek Reservoir throughout the summer and fall, coexisting with various other cyanobacteria in blooms that were associated with microcystin. The absence of cyanotoxin genes from the Limnoraphis sp. WC205 genome showed this cyanobacterium to be non-toxigenic, although it is predicted to produce cyanobactins closely related to Microcystis aeruginosa microcyclamides. DNA sequence corresponding to the Microcystis mcyG gene identified Microcystis as the microcystin producer in this lake.}, } @article {pmid36195216, year = {2022}, author = {Liczbiński, P and Borowski, S and Cieciura-Włoch, W}, title = {Anaerobic co-digestion of kitchen waste with hyperthermophilically pretreated grass for biohydrogen and biomethane production.}, journal = {Bioresource technology}, volume = {364}, number = {}, pages = {128053}, doi = {10.1016/j.biortech.2022.128053}, pmid = {36195216}, issn = {1873-2976}, abstract = {Anaerobic digestion of kitchen waste with grass after hyperthermophilic pretreatment was performed in semi-continuously operated reactors. The greatest methane yield of 293 NmlCH4/gVS (volatile solids) was reported for the mixture of both substrates at 55 °C with a solids retention time of 30 d and the corresponding organic lading rate of 1.72 kgVS/m[3]/d. In contrast, pretreated grass subjected to thermophilic digestion produced only 131 NmlCH4/gVS. However, when mesophilic conditions were applied, the digestion process turned into dark fermentation, especially visible for the mixture. Metagenomic analysis revealed the dominance Ruminococcaceae, Atopobiaceae and Lactobacillaceae at a family level in mesophilic processes, whereas Petrotogaceae, Synergistaceae, Hungateiclostridiaceae, Planococcaceae and two methanogens Methanosarcinaceae and Methanothermobacteriaceae were the most frequent microbes of thermophilic digestion. Kitchen waste can successfully be co-digested with hyperthermophilically pretreated grass at high loading rates, however the digesters must be operated at thermophilic temperatures.}, } @article {pmid36194989, year = {2022}, author = {Imchen, M and Anju, VT and Busi, S and Mohan, MS and Subhaswaraj, P and Dyavaiah, M and Kumavath, R}, title = {Metagenomic insights into taxonomic, functional diversity and inhibitors of microbial biofilms.}, journal = {Microbiological research}, volume = {265}, number = {}, pages = {127207}, doi = {10.1016/j.micres.2022.127207}, pmid = {36194989}, issn = {1618-0623}, mesh = {Biofilms ; *Metagenome ; *Metagenomics ; Microplastics ; Pharmaceutical Preparations ; Plastics ; Quorum Sensing ; }, abstract = {Microbial cells attached to inert or living surfaces adopt biofilm mode with self-produced exopolysaccharide matrix containing polysaccharides, proteins, and extracellular DNA, for protection from adverse external stimuli. Biofilms in hospitals and industries serve as a breeding ground for drug-resistant pathogens and ARG enrichment that are linked to pathogenicity and also impede industrial production process. Biofilm formation, including virulence and pathogenicity, is regulated through quorum sensing (QS), a means of bacterial cell to cell communication for cooperative physiological processes. Hence, QS inhibition through quorum quenching (QQ) is a feasible approach to inhibit biofilm formation. In contrast, biofilms have beneficial roles in promoting plant growth, biocontrol, and wastewater treatment. Furthermore, polymicrobial biofilms can harbour novel compounds and species of industrial and pharmaceutical interest. Hence, surveillance of biofilm microbiome structure and functional attributes is crucial to determine the extent of the risk it poses and to harness its bioactive potential. One of the most preferred approaches to delineate the microbiome is culture-independent metagenomics. In this context, this review article explores the biofilm microbiome in built and natural settings such as agriculture, household appliances, wastewater treatment plants, hospitals, microplastics, and dental biofilm. We have also discussed the recent reports on discoveries of novel QS and biofilm inhibitors through conventional, metagenomics, and machine learning approaches. Finally, we present biofilm-derived novel metagenome-assembled genomes (MAGs), genomes, and taxa of medical and industrial interest.}, } @article {pmid36194603, year = {2022}, author = {Parker, CT and Schiaffino, F and Huynh, S and Paredes Olortegui, M and Peñataro Yori, P and Garcia Bardales, PF and Pinedo Vasquez, T and Curico Huansi, GE and Manzanares Villanueva, K and Shapiama Lopez, WV and Cooper, KK and Kosek, MN}, title = {Shotgun metagenomics of fecal samples from children in Peru reveals frequent complex co-infections with multiple Campylobacter species.}, journal = {PLoS neglected tropical diseases}, volume = {16}, number = {10}, pages = {e0010815}, pmid = {36194603}, issn = {1935-2735}, support = {D43 TW010913/TW/FIC NIH HHS/United States ; R01 AI158576/AI/NIAID NIH HHS/United States ; R21 AI163801/AI/NIAID NIH HHS/United States ; }, mesh = {*Campylobacter/genetics ; *Campylobacter Infections/epidemiology/microbiology ; Child ; *Coinfection/epidemiology ; Diarrhea/epidemiology/microbiology ; Feces/microbiology ; Humans ; Infant ; Metagenomics ; Peru/epidemiology ; Reinfection ; }, abstract = {Campylobacter spp. are a major cause of bacterial diarrhea worldwide and are associated with high rates of mortality and linear growth faltering in children living in low- to middle-income countries (LMICs). Campylobacter jejuni and Campylobacter coli are most often the causative agents of enteric disease among children in LMICs. However, previous work on a collection of stool samples from children under 2 years of age, living in a low resource community in Peru with either acute diarrheal disease or asymptomatic, were found to be qPCR positive for Campylobacter species but qPCR negative for C. jejuni and C. coli. The goal of this study was to determine if whole-genome shotgun metagenomic sequencing (WSMS) could identify the Campylobacter species within these samples. The Campylobacter species identified in these stool samples included C. jejuni, C. coli, C. upsaliensis, C. concisus, and the potential new species of Campylobacter, "Candidatus Campylobacter infans". Moreover, WSMS results demonstrate that over 65% of the samples represented co-infections with multiple Campylobacter species present in a single stool sample, a novel finding in human populations.}, } @article {pmid36194536, year = {2022}, author = {Malayil, L and Ramachandran, P and Chattopadhyay, S and Allard, SM and Bui, A and Butron, J and Callahan, MT and Craddock, HA and Murray, R and East, C and Sharma, M and Kniel, K and Micallef, S and Hashem, F and Gerba, CP and Ravishankar, S and Parveen, S and May, E and Handy, E and Kulkarni, P and Anderson-Coughlin, B and Craighead, S and Gartley, S and Vanore, A and Duncan, R and Foust, D and Haymaker, J and Betancourt, W and Zhu, L and Mongodin, EF and Sapkota, A and Pop, M and Sapkota, AR}, title = {Variations in Bacterial Communities and Antibiotic Resistance Genes Across Diverse Recycled and Surface Water Irrigation Sources in the Mid-Atlantic and Southwest United States: A CONSERVE Two-Year Field Study.}, journal = {Environmental science & technology}, volume = {56}, number = {21}, pages = {15019-15033}, pmid = {36194536}, issn = {1520-5851}, mesh = {United States ; RNA, Ribosomal, 16S/genetics ; *Anti-Bacterial Agents/pharmacology ; Longitudinal Studies ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Water ; *Disinfectants ; Agricultural Irrigation ; Wastewater ; Genes, Bacterial ; }, abstract = {Reduced availability of agricultural water has spurred increased interest in using recycled irrigation water for U.S. food crop production. However, there are significant knowledge gaps concerning the microbiological quality of these water sources. To address these gaps, we used 16S rRNA gene and metagenomic sequencing to characterize taxonomic and functional variations (e.g., antimicrobial resistance) in bacterial communities across diverse recycled and surface water irrigation sources. We collected 1 L water samples (n = 410) between 2016 and 2018 from the Mid-Atlantic (12 sites) and Southwest (10 sites) U.S. Samples were filtered, and DNA was extracted. The V3-V4 regions of the 16S rRNA gene were then PCR amplified and sequenced. Metagenomic sequencing was also performed to characterize antibiotic, metal, and biocide resistance genes. Bacterial alpha and beta diversities were significantly different (p < 0.001) across water types and seasons. Pathogenic bacteria, such as Salmonella enterica, Staphylococcus aureus, and Aeromonas hydrophilia were observed across sample types. The most common antibiotic resistance genes identified coded against macrolides/lincosamides/streptogramins, aminoglycosides, rifampin and elfamycins, and their read counts fluctuated across seasons. We also observed multi-metal and multi-biocide resistance across all water types. To our knowledge, this is the most comprehensive longitudinal study to date of U.S. recycled water and surface water used for irrigation. Our findings improve understanding of the potential differences in the risk of exposure to bacterial pathogens and antibiotic resistance genes originating from diverse irrigation water sources across seasons and U.S. regions.}, } @article {pmid36194530, year = {2022}, author = {Kang, AN and Mun, D and Ryu, S and Jae Lee, J and Oh, S and Kyu Kim, M and Song, M and Oh, S and Kim, Y}, title = {Culturomic-, metagenomic-, and transcriptomic-based characterization of commensal lactic acid bacteria isolated from domestic dogs using Caenorhabditis elegans as a model for aging.}, journal = {Journal of animal science}, volume = {100}, number = {12}, pages = {}, pmid = {36194530}, issn = {1525-3163}, support = {//National Research Foundation of Korea/ ; //Cooperative Research Program for Agriculture Science and Technology Development/ ; NRF-2021R1A2C3011051//Rural Development Administration, Republic of Korea/ ; }, mesh = {Dogs ; Animals ; *Lactobacillales ; Caenorhabditis elegans/genetics/microbiology ; *Probiotics/pharmacology ; Metagenome ; Longevity ; }, abstract = {In tandem with the fast expansion of the pet-economy industry, the present aging research has been noticing the function of probiotics in extending the healthy lifetime of domestic animals. In this study, we aimed to understand the bacterial compositions of canine feces and isolating lactic acid bacteria (LAB) as commensal LAB as novel potential probiotics for the use of antiaging using Caenorhabditis elegans surrogate animal model. Under an anaerobic, culturomic, and metagenomic analysis, a total of 305 commensal LAB were isolated from diverse domestic dogs, and four strains, Lactobacillus amylolyticus, L. salivarius, Enterococcus hirae, and E. faecium, made prominence as commensal LAB by enhancing C. elegans life span and restored neuronal degeneration induced by aging by upregulating skn-1, ser-7, and odr-3, 7, 10. Importantly, whole transcriptome results and integrative network analysis revealed extensive mRNA encoding protein domains and functional pathways of naturally aging C. elegans were examined and we built the gene informatics basis. Taken together, our findings proposed that a specific gene network corresponding to the pathways differentially expressed during the aging and selected commensal LAB as potential probiotic strains could be provided beneficial effects in the aging of domestic animals by modulating the dynamics of gut microbiota.}, } @article {pmid36193874, year = {2022}, author = {Yang, Z and Chen, Z and Lin, X and Yao, S and Xian, M and Ning, X and Fu, W and Jiang, M and Li, N and Xiao, X and Feng, M and Lian, Z and Yang, W and Ren, X and Zheng, Z and Zhao, J and Wei, N and Lu, W and Roponen, M and Schaub, B and Wong, GWK and Su, Z and Wang, C and Li, J}, title = {Rural environment reduces allergic inflammation by modulating the gut microbiota.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2125733}, pmid = {36193874}, issn = {1949-0984}, mesh = {Animals ; Bacteria/genetics ; Dust ; Endotoxins ; *Gastrointestinal Microbiome ; *Hypersensitivity/microbiology/prevention & control ; Immunoglobulin E ; Inflammation ; Mice ; Ovalbumin ; }, abstract = {Rural environments and microbiota are linked to a reduction in the prevalence of allergies. However, the mechanism underlying the reduced allergies modulated by rural residency is unclear. Here, we assessed gut bacterial composition and metagenomics in urban and rural children in the EuroPrevall-INCO cohort. Airborne dusts, including mattress and rural henhouse dusts, were profiled for bacterial and fungal composition by amplicon sequencing. Mice were repeatedly exposed to intranasal dust extracts and evaluated for their effects on ovalbumin (OVA)-induced allergic airway inflammation, and gut microbiota restoration was validated by fecal microbiota transplant (FMT) from dust-exposed donor mice. We found that rural children had fewer allergies and unique gut microbiota with fewer Bacteroides and more Prevotella. Indoor dusts in rural environments harbored higher endotoxin level and diversity of bacteria and fungi, whereas indoor urban dusts were enriched with Aspergillus and contained elevated pathogenic bacteria. Intranasal administration of rural dusts before OVA sensitization reduced respiratory eosinophils and blood IgE level in mice and also led to a recovery of gut bacterial diversity and Ruminiclostridium in the mouse model. FMT restored the protective effect by reducing OVA-induced lung eosinophils in recipient mice. Together, these results support a cause-effect relationship between exposure to dust microbiota and allergy susceptibility in children and mice. Specifically, rural environmental exposure modulated the gut microbiota, which was essential in reducing allergy in children from Southern China. Our findings support the notion that the modulation of gut microbiota by exposure to rural indoor dust may improve allergy prevention.}, } @article {pmid36193440, year = {2022}, author = {Wang, S and Li, G and Liao, Z and Liu, T and Ma, T}, title = {A novel alkane monooxygenase (alkB) clade revealed by massive genomic survey and its dissemination association with IS elements.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e14147}, pmid = {36193440}, issn = {2167-8359}, mesh = {*Alkanes/metabolism ; Cytochrome P-450 CYP4A/genetics ; *DNA Transposable Elements ; Genomics ; Receptor Protein-Tyrosine Kinases/genetics ; Gammaproteobacteria/enzymology/genetics ; Alphaproteobacteria/enzymology/genetics ; }, abstract = {BACKGROUND: Alkanes are important components of fossil energy, such as crude oil. The alkane monooxygenase encoded by alkB gene performs the initial step of alkane degradation under aerobic conditions. The alkB gene is well studied due to its ubiquity as well as the availability of experimentally functional evidence. The alkBFGHJKL and alkST clusters are special kind of alkB-type alkane hydroxylase system, which encode all proteins necessary for converting alkanes into corresponding fatty acids.

METHODS: To explore whether the alkBFGHJKL and alkST clusters were widely distributed, we performed a large-scale analysis of isolate and metagenome assembled genome data (>390,000 genomes) to identify these clusters, together with distributions of corresponding taxonomy and niches. The set of alk-genes (including but not limited to alkBGHJ) located near each other on a DNA sequence was defined as an alk-gene cluster in this study. The alkB genes with alkGHJ located nearby on a DNA sequence were picked up for the investigation of putative alk-clusters.

RESULTS: A total of 120 alk-gene clusters were found in 117 genomes. All the 117 genomes are from strains located only in α- and γ-proteobacteria. The alkB genes located in alk-gene sets were clustered into a deeply branched mono-clade. Further analysis showed similarity organization types of alk-genes were observed within closely related species. Although a large number of IS elements were observed nearby, they did not lead to the wide spread of the alk-gene cluster. The uneven distribution of these elements indicated that there might be other factors affecting the transmission of alk-gene clusters.

CONCLUSIONS: We conducted systematic bioinformatics research on alk-genes located near each other on a DNA sequence. This benchmark dataset of alk-genes can provide base line for exploring its evolutional and ecological importance in future studies.}, } @article {pmid36193360, year = {2022}, author = {Kavitake, D and Suryavanshi, MV and Kandasamy, S and Devi, PB and Shouche, Y and Shetty, PH}, title = {Bacterial diversity of traditional fermented food, Idli by high thorough-put sequencing.}, journal = {Journal of food science and technology}, volume = {59}, number = {10}, pages = {3918-3927}, pmid = {36193360}, issn = {0022-1155}, abstract = {UNLABELLED: The bacterial composition of naturally fermented Indian food, Idli was studied by high-throughput Illumina amplicon sequencing at different taxonomic levels. Metagenomic investigation revealed fold change with respect to some of the phylotypes in 06[th] to 12[th] h of fermentation, suggesting the synergistic mode of nutrition. After 12[th] h fermentation, bacterial populations were stabilized towards 15[th] h fermentation. The bacterial phyla found as Firmicutes, Fusobacteria, Proteobacteria, Actinobacteria, Bacteroidetes and others in various proportions with respective to fermentation time. Among these Firmicutes and Proteobacteria were the predominant bacterial associates in this product. Initially at 0[th] h time interval Firmicutes (7%) and Proteobacteria (93%) were present adequately in the product which has been changed to Firmicutes (68%), Proteobacteria (31%) at the end of the fermentation (15[th] h). Phylum Firmicutes represented various major genus such as Lactococcus, Weissella, Lactobacillus, Enterococcus, Bacillus and Macrococcus whereas Proteobacteria revealed the presence of Enterobacter, Erwinia, Serratia, Pseudoalteromonas, Vibrio and Klebsiella genus. Co-occurrence and Co-exclusion network were developed to ensure the positive and negative association in the eubacterial genus detected in entire batter fermentation event. Some genera like Weissella, Lactococcus and Enterococcus are showing increase in abundances in auxiliary succession events can be established for starter culture development.

SUPPLEMENTARY MATERIAL: The online version contains supplementary material available at 10.1007/s13197-022-05421-4.}, } @article {pmid36193103, year = {2022}, author = {Gao, Y and Zhang, X and Liu, J and Gong, L and Chen, G and Zhou, X}, title = {Chlamydia psittaci pneumonia complicated with organizing pneumonia: A case report and literature review.}, journal = {IDCases}, volume = {30}, number = {}, pages = {e01584}, pmid = {36193103}, issn = {2214-2509}, abstract = {A patient with pneumonia had a fever for 2 weeks. After the initial anti-infection treatment failed, he was diagnosed with C. psittaci pneumonia complicated with organizing pneumonia, through next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) and lung biopsy. He was treated with antibiotics and corticosteroids for 2 months.}, } @article {pmid36192998, year = {2022}, author = {Ruiz-Rico, M and Renwick, S and Vancuren, SJ and Robinson, AV and Gianetto-Hill, C and Allen-Vercoe, E and Barat, JM}, title = {Influence of free and immobilized chitosan on a defined human gut microbial ecosystem.}, journal = {Food research international (Ottawa, Ont.)}, volume = {161}, number = {}, pages = {111890}, doi = {10.1016/j.foodres.2022.111890}, pmid = {36192998}, issn = {1873-7145}, mesh = {Bacteroidetes/metabolism ; *Chitosan/metabolism ; Clostridium ; Ecosystem ; *Gastrointestinal Microbiome ; Gastrointestinal Tract ; Humans ; }, abstract = {In this work, the influence of different forms of presentation of chitosan in the human gut microbiota with a defined bacterial community was evaluated. First, the susceptibility of individual gut bacterial isolates against chitosan was studied within a concentration range between 0.125 and 1 mg/mL. Then, the impact of chitosan (0.25 and 1 mg/mL) on a defined human gut microbial ecosystem was studied by metagenomic and metabonomic analyses. The results showed that chitosan in its free form had a high impact on individual isolates with a minimum inhibitory concentration below 1 mg/mL for most of the strains studied. In comparison, chitosan immobilized in the different carriers displayed a diverse effect on gut microbiota. The most susceptible strains were Agathobacter rectalis strain 16-6-I 1 FAA, Clostridium spiroforme strain 16-6-I 21 FAA and Mediterraneibacter faecis strain 16-6-I 30 FAA. The impact of the different modes of presentation of chitosan was strain-specific and species-specific when compared to results obtained from analysis of other strains within the genera Agathobacter, Clostridium and Mediterraneibacter, and therefore a study using a defined ecosystem was needed to extrapolate the results. Significant decreases in defined community richness and diversity and changes in metabolic profile were observed after exposure to free chitosan. Free chitosan produced significant reductions in the abundance of the genera Lachnoclostridium, Anaerotignum, Blautia, Enterococcus, Eubacterium and Ruthenibacterium together with a slight decrease of the production of SCFAs, among other fermentation by-products. The immobilized chitosan significantly alleviated the impact caused by the antimicrobial polymer and significantly increased the relative abundance of the Bacteroidetes phylum compared to free chitosan. These results suggest the significance of assessing the impact of new ingredients and materials included in food on the human gut microbiota with models that simulate the gastrointestinal environment, such as in vitro bioreactor systems.}, } @article {pmid36192803, year = {2022}, author = {Ma, S and Shungin, D and Mallick, H and Schirmer, M and Nguyen, LH and Kolde, R and Franzosa, E and Vlamakis, H and Xavier, R and Huttenhower, C}, title = {Population structure discovery in meta-analyzed microbial communities and inflammatory bowel disease using MMUPHin.}, journal = {Genome biology}, volume = {23}, number = {1}, pages = {208}, pmid = {36192803}, issn = {1474-760X}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R24DK110499/DK/NIDDK NIH HHS/United States ; P30DK043351/DK/NIDDK NIH HHS/United States ; }, mesh = {Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases ; *Microbiota ; }, abstract = {Microbiome studies of inflammatory bowel diseases (IBD) have achieved a scale for meta-analysis of dysbioses among populations. To enable microbial community meta-analyses generally, we develop MMUPHin for normalization, statistical meta-analysis, and population structure discovery using microbial taxonomic and functional profiles. Applying it to ten IBD cohorts, we identify consistent associations, including novel taxa such as Acinetobacter and Turicibacter, and additional exposure and interaction effects. A single gradient of dysbiosis severity is favored over discrete types to summarize IBD microbiome population structure. These results provide a benchmark for characterization of IBD and a framework for meta-analysis of any microbial communities.}, } @article {pmid36192528, year = {2022}, author = {Austin, RM and Zuckerman, M and Honap, TP and Lee, H and Ward, GK and Warinner, C and Sankaranarayanan, K and Hofman, CA}, title = {Remembering St. Louis individual-structural violence and acute bacterial infections in a historical anatomical collection.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1050}, pmid = {36192528}, issn = {2399-3642}, mesh = {Adult ; Black or African American ; Anti-Bacterial Agents ; *Bacterial Infections ; *Dental Calculus ; Humans ; Male ; United States ; Violence ; Young Adult ; }, abstract = {Incomplete documentary evidence, variable biomolecular preservation, and limited skeletal responses have hindered assessment of acute infections in the past. This study was initially developed to explore the diagnostic potential of dental calculus to identify infectious diseases, however, the breadth and depth of information gained from a particular individual, St. Louis Individual (St.LI), enabled an individualized assessment and demanded broader disciplinary introspection of ethical research conduct. Here, we document the embodiment of structural violence in a 23-year-old Black and/or African American male, who died of lobar pneumonia in 1930s St. Louis, Missouri. St.LI exhibits evidence of systemic poor health, including chronic oral infections and a probable tuberculosis infection. Metagenomic sequencing of dental calculus recovered three pre-antibiotic era pathogen genomes, which likely contributed to the lobar pneumonia cause of death (CoD): Klebsiella pneumoniae (13.8X); Acinetobacter nosocomialis (28.4X); and Acinetobacter junii (30.1X). Ante- and perimortem evidence of St.LI's lived experiences chronicle the poverty, systemic racism, and race-based structural violence experienced by marginalized communities in St. Louis, which contributed to St.LI's poor health, CoD, anatomization, and inclusion in the Robert J. Terry Anatomical Collection. These same embodied inequalities continue to manifest as health disparities affecting many contemporary communities in the United States.}, } @article {pmid36192523, year = {2022}, author = {Mach, N and Midoux, C and Leclercq, S and Pennarun, S and Le Moyec, L and Rué, O and Robert, C and Sallé, G and Barrey, E}, title = {Mining the equine gut metagenome: poorly-characterized taxa associated with cardiovascular fitness in endurance athletes.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {1032}, pmid = {36192523}, issn = {2399-3642}, mesh = {Animals ; *Athletes ; Fatty Acids ; Glucose ; Glycogen ; Horses ; Humans ; *Metagenome ; }, abstract = {Emerging evidence indicates that the gut microbiome contributes to endurance exercise performance. Still, the extent of its functional and metabolic potential remains unknown. Using elite endurance horses as a model system for exercise responsiveness, we built an integrated horse gut gene catalog comprising ~25 million unique genes and 372 metagenome-assembled genomes. This catalog represents 4179 genera spanning 95 phyla and functional capacities primed to exploit energy from dietary, microbial, and host resources. The holo-omics approach shows that gut microbiomes enriched in Lachnospiraceae taxa are negatively associated with cardiovascular capacity. Conversely, more complex and functionally diverse microbiomes are associated with higher glucose concentrations and reduced accumulation of long-chain acylcarnitines and non-esterified fatty acids in plasma, suggesting increased ß-oxidation capacity in the mitochondria. In line with this hypothesis, more fit athletes show upregulation of mitochondrial-related genes involved in energy metabolism, biogenesis, and Ca[2+] cytosolic transport, all of which are necessary to improve aerobic work power, spare glycogen usage, and enhance cardiovascular capacity. The results identify an associative link between endurance performance and gut microbiome composition and gene function, laying the basis for nutritional interventions that could benefit horse athletes.}, } @article {pmid36191158, year = {2022}, author = {Qi, Q and Zhao, J and Tian, R and Zeng, Y and Xie, C and Gao, Q and Dai, T and Wang, H and He, JS and Konstantinidis, KT and Yang, Y and Zhou, J and Guo, X}, title = {Microbially enhanced methane uptake under warming enlarges ecosystem carbon sink in a Tibetan alpine grassland.}, journal = {Global change biology}, volume = {28}, number = {23}, pages = {6906-6920}, doi = {10.1111/gcb.16444}, pmid = {36191158}, issn = {1365-2486}, mesh = {*Ecosystem ; *Methane/analysis ; Grassland ; Carbon Sequestration ; Soil/chemistry ; Carbon ; Carbon Dioxide/analysis ; Tibet ; }, abstract = {The alpine grasslands of the Tibetan Plateau store 23.2 Pg soil organic carbon, which becomes susceptible to microbial degradation with climate warming. However, accurate prediction of how the soil carbon stock changes under future climate warming is hampered by our limited understanding of belowground complex microbial communities. Here, we show that 4 years of warming strongly stimulated methane (CH4) uptake by 93.8% and aerobic respiration (CO2) by 11.3% in the soils of alpine grassland ecosystem. Due to no significant effects of warming on net ecosystem CO2 exchange (NEE), the warming-stimulated CH4 uptake enlarged the carbon sink capacity of whole ecosystem. Furthermore, precipitation alternation did not alter such warming effects, despite the significant effects of precipitation on NEE and soil CH4 fluxes were observed. Metagenomic sequencing revealed that warming led to significant shifts in the overall microbial community structure and the abundances of functional genes, which contrasted to no detectable changes after 2 years of warming. Carbohydrate utilization genes were significantly increased by warming, corresponding with significant increases in soil aerobic respiration. Increased methanotrophic genes and decreased methanogenic genes were observed under warming, which significantly (R[2] = .59, p < .001) correlated with warming-enhanced CH4 uptakes. Furthermore, 212 metagenome-assembled genomes were recovered, including many populations involved in the degradation of various organic matter and a highly abundant methylotrophic population of the Methyloceanibacter genus. Collectively, our results provide compelling evidence that specific microbial functional traits for CH4 and CO2 cycling processes respond to climate warming with differential effects on soil greenhouse gas emissions. Alpine grasslands may play huge roles in mitigating climate warming through such microbially enhanced CH4 uptake.}, } @article {pmid36190831, year = {2022}, author = {Brown, DC and Aggarwal, N and Turner, RJ}, title = {Exploration of the presence and abundance of multidrug resistance efflux genes in oil and gas environments.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {10}, pages = {}, doi = {10.1099/mic.0.001248}, pmid = {36190831}, issn = {1465-2080}, mesh = {Anti-Bacterial Agents ; *Disinfectants ; Drug Resistance, Multiple ; Geologic Sediments ; Hydrocarbons/metabolism ; *Hydrocarbons, Aromatic ; Wastewater ; }, abstract = {As sequencing technology improves and the cost of metagenome sequencing decreases, the number of sequenced environments increases. These metagenomes provide a wealth of data in the form of annotated and unannotated genes. The role of multidrug resistance efflux pumps (MDREPs) is the removal of antibiotics, biocides and toxic metabolites created during aromatic hydrocarbon metabolism. Due to their naturally occurring role in hydrocarbon metabolism and their role in biocide tolerance, MDREP genes are of particular importance for the protection of pipeline assets. However, the heterogeneity of MDREP genes creates a challenge during annotation and detection. Here we use a selection of primers designed to target MDREPs in six pure species and apply them to publicly available metagenomes associated with oil and gas environments. Using in silico PCR with relaxed primer binding conditions we probed the metagenomes of a shale reservoir, a heavy oil tailings pond, a civil wastewater treatment, two marine sediments exposed to hydrocarbons following the Deepwater Horizon oil spill and a non-exposed marine sediment to assess the presence and abundance of MDREP genes. Through relaxed primer binding conditions during in silico PCR, the prevalence of MDREPs was determined. The percentage of nucleotide sequences identified by the MDREP primers was partially augmented by exposure to hydrocarbons in marine sediment and in shale reservoir compared to hydrocarbon-free marine sediments while tailings ponds and wastewater had the highest percentages. We believe this approach lays the groundwork for a supervised method of identifying poorly conserved genes within metagenomes.}, } @article {pmid36190520, year = {2022}, author = {Chen, M and Zhang, M and Shi, M and Hu, X}, title = {Diagnosis and Analysis of Clinical Characteristics of Chlamydia psittaci Pneumonia.}, journal = {Vector borne and zoonotic diseases (Larchmont, N.Y.)}, volume = {22}, number = {10}, pages = {499-504}, doi = {10.1089/vbz.2022.0013}, pmid = {36190520}, issn = {1557-7759}, mesh = {Animals ; *Chlamydophila psittaci ; Retrospective Studies ; Moxifloxacin ; *Psittacosis/diagnosis/drug therapy/veterinary ; *Pneumonia/complications/drug therapy/veterinary ; Fever/veterinary ; Anti-Bacterial Agents/therapeutic use ; Amides ; *Nucleic Acids ; }, abstract = {Objective: We assessed the clinical characteristics of three patients with Chlamydia psittaci-associated pneumonia. Methods: Clinical data for three patients with C. psittaci-associated pneumonia admitted to our hospital from June 2020 to December 2020 were retrospectively analyzed, and the diagnosis, clinical features, and treatment of the disease are summarized. Results: Fever, headache, and fatigue were the main symptoms in all three patients, whereas local respiratory symptoms such as cough and expectoration were not obvious. Not all patients had a definite contact history with poultry and birds. Chest computed tomography (CT) showed inflammatory exudation, consolidation, and bronchial inflation signs on one side of the lungs, which progressed rapidly. Treatment with beta-amides did not result in positive clinical responses. Combined with clinical manifestations, the disease was confirmed by detection of C. psittaci nucleic acid sequences in alveolar lavage fluid and blood by metagenomic second-generation sequencing technology. Fever and malaise were rapidly relieved after the administration of moxifloxacin-based regimens and levels of infectious blood markers decreased; and the consolidation shadow on chest CT was gradually absorbed. Conclusion: Early application of metagenomic second-generation sequencing in patients with community-acquired pneumonia due to rare and complex pathogens that cannot be diagnosed by conventional tests and for whom empirical anti-infective therapy is ineffective is important for definitive diagnosis and selection of appropriate antibacterial drugs.}, } @article {pmid36190425, year = {2022}, author = {Wang, L and Wu, Y and Xu, J and Huang, Q and Zhao, Y and Dong, S and Wang, X and Cao, X and Wang, C and Wu, A and Zhou, D and Chen, C and Yang, H and Li, J and Konstantinos, P and Tu, Q and Zhang, G and Yin, J}, title = {Colicins of Escherichia coli Lead to Resistance against the Diarrhea-Causing Pathogen Enterotoxigenic E. coli in Pigs.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0139622}, pmid = {36190425}, issn = {2165-0497}, mesh = {Animals ; Swine ; Male ; *Colicins/genetics/metabolism ; *Enterotoxigenic Escherichia coli/genetics/metabolism ; *Escherichia coli Infections/veterinary ; Diarrhea/veterinary ; *Bacteriocins/genetics ; Exotoxins ; *Anti-Infective Agents ; }, abstract = {Gut microbes can affect host adaptation to various environment conditions. Escherichia coli is a common gut species, including pathogenic strains and nonpathogenic strains. This study was conducted to investigate the effects of different E. coli strains in the gut on the health of pigs. In this study, the complete genomes of two E. coli strains isolated from pigs were sequenced. The whole genomes of Y18J and the enterotoxigenic E. coli strain W25K were compared to determine their roles in pig adaptation to disease. Y18J was isolated from feces of healthy piglets and showed strong antimicrobial activity against W25K in vitro. Gene knockout experiments and complementation analysis followed by modeling the microbe-microbe interactions demonstrated that the antagonistic mechanism of Y18J against W25K relied on the bacteriocins colicin B and colicin M. Compared to W25K, Y18J is devoid of exotoxin-coding genes and has more secondary-metabolite-biosynthetic gene clusters. W25K carries more genes involved in genome replication, in accordance with a shorter cell cycle observed during a growth experiment. The analysis of gut metagenomes in different pig breeds showed that colicins B and M were enriched in Laiwu pigs, a Chinese local breed, but were scarce in boars and Duroc pigs. IMPORTANCE This study revealed the heterogeneity of E. coli strains from pigs, including two strains studied by both in silico and wet experiments in detail and 14 strains studied by bioinformatics analysis. E. coli Y18J may improve the adaptability of pigs toward disease resistance through the production of colicins B and M. Our findings could shed light on the pathogenic and harmless roles of E. coli in modern animal husbandry, leading to a better understanding of intestinal-microbe-pathogen interactions in the course of evolution.}, } @article {pmid36190421, year = {2022}, author = {Wang, Q and Cai, L and Zhang, R and Wei, S and Li, F and Liu, Y and Xu, Y}, title = {A Unique Set of Auxiliary Metabolic Genes Found in an Isolated Cyanophage Sheds New Light on Marine Phage-Host Interactions.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0236722}, pmid = {36190421}, issn = {2165-0497}, mesh = {*Bacteriophages/genetics ; Phylogeny ; Ecosystem ; Genome, Viral ; Ketoglutaric Acids ; Proteomics ; Mannose-6-Phosphate Isomerase/genetics ; Oxygenases/genetics ; Ferrous Compounds ; }, abstract = {Cyanophages, viruses that infect cyanobacteria, are abundant and widely distributed in aquatic ecosystems, playing important roles in regulating the abundance, activity, diversity, and evolution of cyanobacteria. A T4-like cyanophage, S-SCSM1, infecting Synechococcus and Prochlorococcus strains of different ecotypes, was isolated from the South China Sea in this study. For the first time, a mannose-6-phosphate isomerase (MPI) gene was identified in the cultured cyanophage. At least 11 phylogenetic clusters of cyanophage MPIs were retrieved and identified from the marine metagenomic data sets, indicating that cyanophage MPIs in the marine environment are extremely diverse. The existence of 24 genes encoding 2-oxoglutarate (2OG)-Fe(II) oxygenase superfamily proteins in the S-SCSM1 genome emphasizes their potential importance and diverse functions in reprogramming host metabolism during phage infection. Novel cell wall synthesis and modification genes found in the S-SCSM1 genome indicate that diverse phenotypic modifications imposed by phages on cyanobacterial hosts remain to be discovered. Two noncoding RNAs of cis-regulatory elements in the S-SCSM1 genome were predicted to be associated with host exopolysaccharide metabolism and photosynthesis. The isolation and genomic characterization of cyanophage S-SCSM1 provide more information on the genetic diversity of cyanophages and phage-host interactions in the marine environment. IMPORTANCE Cyanophages play important ecological roles in aquatic ecosystems. Genomic and proteomic characterizations of the T4-like cyanophage S-SCSM1 indicate that novel and diverse viral genes and phage-host interactions in the marine environment remain unexplored. The first identified mannose-6-phosphate isomerase (MPI) gene from a cultured cyanophage was found in the S-SCSM1 genome, although MPIs were previously found in viral metagenomes at high frequencies similar to those of the cyanophage photosynthetic gene psbA. The presence of 24 genes encoding 2-oxoglutarate (2OG)-Fe(II) oxygenase superfamily proteins, novel cell wall synthesis and modification genes, a nonbleaching protein A gene, and 2 noncoding RNAs of cis-regulatory elements in the S-SCSM1 genome as well as the presence of a virion-associated regulatory protein indicate the diverse functions that cyanophages have in reprogramming the metabolism and modifying the phenotypes of hosts during infection.}, } @article {pmid36190327, year = {2022}, author = {Vulcano, F and Hahn, CJ and Roerdink, D and Dahle, H and Reeves, EP and Wegener, G and Steen, IH and Stokke, R}, title = {Phylogenetic and functional diverse ANME-1 thrive in Arctic hydrothermal vents.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {11}, pages = {}, pmid = {36190327}, issn = {1574-6941}, mesh = {Arctic Regions ; Geologic Sediments ; *Hydrothermal Vents ; Methane/metabolism ; Phylogeny ; Sulfates ; }, abstract = {The methane-rich areas, the Loki's Castle vent field and the Jan Mayen vent field at the Arctic Mid Ocean Ridge (AMOR), host abundant niches for anaerobic methane-oxidizers, which are predominantly filled by members of the ANME-1. In this study, we used a metagenomic-based approach that revealed the presence of phylogenetic and functional different ANME-1 subgroups at AMOR, with heterogeneous distribution. Based on a common analysis of ANME-1 genomes from AMOR and other geographic locations, we observed that AMOR subgroups clustered with a vent-specific ANME-1 group that occurs solely at vents, and with a generalist ANME-1 group, with a mixed environmental origin. Generalist ANME-1 are enriched in genes coding for stress response and defense strategies, suggesting functional diversity among AMOR subgroups. ANME-1 encode a conserved energy metabolism, indicating strong adaptation to sulfate-methane-rich sediments in marine systems, which does not however prevent global dispersion. A deep branching family named Ca. Veteromethanophagaceae was identified. The basal position of vent-related ANME-1 in phylogenomic trees suggests that ANME-1 originated at hydrothermal vents. The heterogeneous and variable physicochemical conditions present in diffuse venting areas of hydrothermal fields could have favored the diversification of ANME-1 into lineages that can tolerate geochemical and environmental variations.}, } @article {pmid36190242, year = {2022}, author = {Charon, J and Kahlke, T and Larsson, ME and Abbriano, R and Commault, A and Burke, J and Ralph, P and Holmes, EC}, title = {Diverse RNA Viruses Associated with Diatom, Eustigmatophyte, Dinoflagellate, and Rhodophyte Microalgae Cultures.}, journal = {Journal of virology}, volume = {96}, number = {20}, pages = {e0078322}, pmid = {36190242}, issn = {1098-5514}, mesh = {*Diatoms/genetics ; *Dinoflagellida/genetics ; *Microalgae/genetics ; Phylogeny ; *RNA Viruses/genetics ; Plants ; RNA ; Genome, Viral ; }, abstract = {Unicellular microalgae are of immense ecological importance with growing commercial potential in industries such as renewable energy, food, and pharmacology. Viral infections can have a profound impact on the growth and evolution of their hosts. However, very little is known of the diversity within, and the effect of, unicellular microalgal RNA viruses. In addition, identifying RNA viruses in these organisms that could have originated more than a billion years ago constitutes a robust data set to dissect molecular events and address fundamental questions in virus evolution. We assessed the diversity of RNA viruses in eight microalgal cultures, including representatives from the diatom, eustigmatophyte, dinoflagellate, red algae, and euglenid groups. Using metatranscriptomic sequencing combined with bioinformatic approaches optimized to detect highly divergent RNA viruses, we identified 10 RNA virus sequences, with nine constituting new viral species. Most of the newly identified RNA viruses belonged to the double-stranded Totiviridae, Endornaviridae, and Partitiviridae, greatly expanding the reported host range for these families. Two new species belonging to the single-stranded RNA viral clade Marnaviridae, commonly associated with microalgal hosts, were also identified. This study highlights that a substantial diversity of RNA viruses likely exists undetected within the unicellular microalgae. It also highlights the necessity for RNA viral characterization and for investigation of the effects of viral infections on microalgal physiology, biology, and growth, considering their environmental and industrial roles. IMPORTANCE Our knowledge of the diversity of RNA viruses infecting microbial algae-the microalgae-is minimal. However, describing the RNA viruses infecting these organisms is of primary importance at both the ecological and economic scales because of the fundamental roles these organisms play in aquatic environments and their growing value across a range of industrial fields. Using metatranscriptomic sequencing, we aimed to reveal the RNA viruses present in cultures of eight microalgae species belonging to the diatom, dinoflagellate, eustigmatophyte, rhodophyte, and euglena major clades of algae. Accordingly, we identified 10 new divergent RNA virus species belonging to RNA virus families as diverse as the double-stranded Totiviridae, Endornaviridae, and Partitiviridae and the single-stranded Marnaviridae. By expanding the known diversity of RNA viruses infecting unicellular eukaryotes, this study contributes to a better understanding of the early evolution of the virosphere and will inform the use of microalgae in industrial applications.}, } @article {pmid36190231, year = {2022}, author = {Bolivar-Torres, HH and Marín-Paredes, R and Ramos-Madrigal, C and Servín-Garcidueñas, LE}, title = {Metagenome-Assembled Genome of Acidibrevibacterium fodinaquatile FLA01 from Fumarole Sediments from the Los Azufres Geothermal Field.}, journal = {Microbiology resource announcements}, volume = {11}, number = {10}, pages = {e0082322}, pmid = {36190231}, issn = {2576-098X}, support = {PAPIIT IA210617//UNAM | Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México (DGAPA)/ ; PAPIIT IA208019//UNAM | Dirección General de Asuntos del Personal Académico, Universidad Nacional Autónoma de México (DGAPA)/ ; }, abstract = {The Los Azufres geothermal field contains diverse microbial communities inhabiting thermal springs whose bacterial genomic diversity is being analyzed. Here, we describe a metagenome-assembled genome of Acidibrevibacterium fodinaquatile FLA01 obtained from fumarole sediment sequencing data. The genome contained genes for carbon fixation, osmotic shock, and heavy metal resistance.}, } @article {pmid36190138, year = {2022}, author = {Weissman, JL and Peras, M and Barnum, TP and Fuhrman, JA}, title = {Benchmarking Community-Wide Estimates of Growth Potential from Metagenomes Using Codon Usage Statistics.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0074522}, pmid = {36190138}, issn = {2379-5077}, mesh = {Humans ; *Metagenome/genetics ; Benchmarking ; Codon Usage ; *Microbiota/genetics ; }, abstract = {Trait inference from mixed-species assemblages is a central problem in microbial ecology. Frequently, sequencing information from an environment is available, but phenotypic measurements from individual community members are not. With the increasing availability of molecular data for microbial communities, bioinformatic approaches that map metagenome to (meta)phenotype are needed. Recently, we developed a tool, gRodon, that enables the prediction of the maximum growth rate of an organism from genomic data on the basis of codon usage patterns. Our work and that of other groups suggest that such predictors can be applied to mixed-species communities in order to derive estimates of the average community-wide maximum growth rate. Here, we present an improved maximum growth rate predictor designed for metagenomes that corrects a persistent GC bias in the original gRodon model for metagenomic prediction. We benchmark this predictor with simulated metagenomic data sets to show that it has superior performance on mixed-species communities relative to earlier models. We go on to provide guidance on data preprocessing and show that calling genes from assembled contigs rather than directly from reads dramatically improves performance. Finally, we apply our predictor to large-scale metagenomic data sets from marine and human microbiomes to illustrate how community-wide growth prediction can be a powerful approach for hypothesis generation. Altogether, we provide an updated tool with clear guidelines for users about the uses and pitfalls of metagenomic prediction of the average community-wide maximal growth rate. IMPORTANCE Microbes dominate nearly every known habitat, and therefore tools to survey the structure and function of natural microbial communities are much needed. Metagenomics, in which the DNA content of an entire community of organisms is sequenced all at once, allows us to probe the genetic diversity contained in a habitat. Yet, mapping metagenomic information to the actual traits of community members is a difficult and largely unsolved problem. Here, we present and validate a tool that allows users to predict the average maximum growth rate of a microbial community directly from metagenomic data. Maximum growth rate is a fundamental characteristic of microbial species that can give us a great deal of insight into their ecological role, and by applying our community-level predictor to large-scale metagenomic data sets from marine and human-associated microbiomes, we show how community-wide growth prediction can be a powerful approach for hypothesis generation.}, } @article {pmid36189372, year = {2022}, author = {Zhang, Q and Liu, X and Liu, Y and Wang, H and Zhao, R and Lv, X and Wei, X and Zhou, K}, title = {Nasal and cutaneous mucormycosis in two patients with lymphoma after chemotherapy and target therapy: Early detection by metagenomic next-generation sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {960766}, pmid = {36189372}, issn = {2235-2988}, mesh = {Amphotericin B/therapeutic use ; Anti-Bacterial Agents ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Lymphoma ; Metagenomics/methods ; *Mucormycosis/diagnosis/drug therapy/microbiology ; }, abstract = {Mucormycosis is a conditionally pathogenic fungal disease with high morbidity that mainly affects patients with decreased immunity. Diagnosis relies on the histopathological examination of microorganisms with the typical structure of mucormycetes in tissues and subsequent confirmation via culture. Early detection of causative microorganisms is critical to rapidly administer appropriately targeted antibiotics. Metagenomic next-generation sequencing (mNGS) is an innovative and sensitive technique used to identify pathogenic strains. Here we used mNGS to timely diagnose an infection with Lichtheimia ramosa and Mucor irregularis in two patients with hematologic malignancies; the infections manifested as nasal and cutaneous infections and developed after chemotherapy and small molecule targeted therapy. Following treatment with amphotericin B cholesteryl sulfate complex, the symptoms were reduced significantly, and both patients obtained successful outcomes. Additionally, we searched and summarized the current medical literature on the successful diagnosis of mucormycosis using mNGS. These cases indicated that mNGS, a novel culture-independent method, is capable of rapid, sensitive, and accurate identification of pathogens. mNGS may be a complementary method for the early identification of mucormycosis, allowing for appropriate and timely antibiotic administration and thus improving patient outcomes.}, } @article {pmid36189365, year = {2022}, author = {Li, M and Yan, K and Jia, P and Wei, E and Wang, H}, title = {Metagenomic next-generation sequencing may assist diagnosis of cat-scratch disease.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {946849}, pmid = {36189365}, issn = {2235-2988}, mesh = {Anti-Bacterial Agents/therapeutic use ; *Bartonella henselae/genetics ; *Cat-Scratch Disease/diagnosis/drug therapy ; Diagnosis, Differential ; High-Throughput Nucleotide Sequencing ; Humans ; }, abstract = {Bartonella henselae, the pathogen that causes cat-scratch disease (CSD), is relatively rare in the clinic. CSD usually causes mild clinical manifestations, which self-heal in a matter of weeks. However, in immunocompromised patients, CSD may cause systemic disorders that can lead to critical illness. Due to the diversity of symptom signs and the lack of a golden standard for diagnosis, identifying atypical CSD in a timely manner presents a challenge. Metagenomic next-generation sequencing (mNGS), is a promising technology that has been widely used in the detection of pathogens in clinical infectious diseases in recent years. mNGS can detect multiple pathogens quickly and accurately from any given source. Here, we present a case of atypical CSD, which was diagnosed using mNGS. The patient manifested a fever of unknown infectious origin, and routine antibiotic treatment was ineffective. mNGS was employed to test the patient's peripheral blood, which led to the detection of B. henselae. This was rarely seen in previous CSD reports. We surmised that the patient presented with atypical CSD and thus a targeted therapy was recommended. Crucially, the patient recovered rapidly. Based on this case study findings, we recommend that CSD should be included in the differential diagnosis for fever of unknown origin and that mNGS may be helpful in the diagnosis of CSD.}, } @article {pmid36189364, year = {2022}, author = {Lv, Z and Chen, Y and Zhou, H and Chen, Z and Yao, Q and Ren, J and Liu, X and Liu, S and Deng, X and Pang, Y and Chen, W and Yang, H and Xu, P}, title = {Genomic characterization of two metagenome-assembled genomes of Tropheryma whipplei from China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {947486}, pmid = {36189364}, issn = {2235-2988}, mesh = {Fluoroquinolones ; Genomics ; *Metagenome ; Phylogeny ; *Tropheryma/genetics ; Virulence Factors ; }, abstract = {Whipple's disease is a rare chronic systemic disease that affects almost any organ system of the body caused by the intracellular bacterium Tropheryma whipplei, which is found ubiquitously in the environment. Sequencing of the T. whipplei genome has revealed that it has a reduced genome (0.93 Mbp), a characteristic shared with other intracellular bacteria. Until our research started, 19 T. whipplei strains had been sequenced from cultures originated in France, Canada, and Germany. The genome of T. whipplei bacterium has not been studied in Asia yet. Here, two metagenome-assembled genomes (MAGs) of T. whipplei from China were reconstructed through metagenomic next-generation sequencing (mNGS) and genome binning. We also provided genomic insights into the geographical role and genomic features by analyzing the whole genome. The whole-genome phylogenetic tree was constructed based on single-nucleotide polymorphism (SNP) distance calculations and then grouped by distance similarity. The phylogenetic tree shows inconsistencies with geographic origins, thus suggesting that the variations in geographical origins cannot explain the phylogenetic relationships among the 21 T. whipplei strains. The two Chinese strains were closely related to each other, and also found to be related to strains from Germany (T. whipplei TW08/27) and France (T. whipplei Bcu26 and T. whipplei Neuro1). Furthermore, the Average Nucleotide Identity (ANI) matrix also showed no association between geographic origins and genomic similarities. The pan-genome analysis revealed that T. whipplei has a closed pan-genome composed of big core-genomes and small accessory genomes, like other intracellular bacteria. By examining the genotypes of the sequenced strains, all 21 T. whipplei strains were found to be resistant to fluoroquinolones, due to the genetic mutations in genes gyrA, gyrB, parC, and parE. The 21 T. Whipplei strains shared the same virulence factors, except for the alpC gene, which existed in 7 out of the 21 T. whipplei strains. When comparing 21 entire T. whipplei pan-genomes from various nations, it was discovered that the bacterium also possessed a closed genome, which was a trait shared by intracellular pathogens.}, } @article {pmid36189350, year = {2022}, author = {Sakai, SA and Aoshima, M and Sawada, K and Horasawa, S and Yoshikawa, A and Fujisawa, T and Kadowaki, S and Denda, T and Matsuhashi, N and Yasui, H and Goto, M and Yamazaki, K and Komatsu, Y and Nakanishi, R and Nakamura, Y and Bando, H and Hamaya, Y and Kageyama, SI and Yoshino, T and Tsuchihara, K and Yamashita, R}, title = {Fecal microbiota in patients with a stoma decreases anaerobic bacteria and alters taxonomic and functional diversities.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {925444}, pmid = {36189350}, issn = {2235-2988}, mesh = {Bacteria, Anaerobic/genetics/metabolism ; *Colorectal Neoplasms/microbiology/surgery ; Fatty Acids, Volatile/metabolism ; Feces/microbiology ; Humans ; Methane ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Colorectal cancer (CRC) is one of the most common malignant diseases. Generally, stoma construction is performed following surgery for the resection of the primary tumor in patients with CRC. The association of CRC with the gut microbiota has been widely reported, and the gut microbiota is known to play an important role in the carcinogenesis, progression, and treatment of CRC. In this study, we compared the microbiota of patients with CRC between with and without a stoma using fecal metagenomic sequencing data from SCRUM-Japan MONSTAR-SCREEN, a joint industry-academia cancer research project in Japan. We found that the composition of anaerobes was reduced in patients with a stoma. In particular, the abundance of Alistipes, Akkermansia, Intestinimonas, and methane-producing archaea decreased. We also compared gene function (e.g., KEGG Orthology and KEGG pathway) and found that gene function for methane and short-chain fatty acids (SCFAs) production was underrepresented in patients with a stoma. Furthermore, a stoma decreased Shannon diversity based on taxonomic composition but increased that of the KEGG pathway. These results suggest that the feces of patients with a stoma have a reduced abundance of favorable microbes for cancer immunotherapy. In conclusion, we showed that a stoma alters the taxonomic and functional profiles in feces and may be a confounding factor in fecal microbiota analysis.}, } @article {pmid36189343, year = {2022}, author = {Lv, LJ and Li, SH and Wen, JY and Wang, GY and Li, H and He, TW and Lv, QB and Xiao, MC and Duan, HL and Chen, MC and Yi, ZT and Yan, QL and Yin, AH}, title = {Deep metagenomic characterization of gut microbial community and function in preeclampsia.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {933523}, pmid = {36189343}, issn = {2235-2988}, mesh = {Bacitracin ; *Bacteriocins ; Biomarkers ; Chlorophyll ; Dysbiosis ; Feces/microbiology ; Female ; Folic Acid ; Humans ; Metagenome ; *Microbiota ; *Porphyrins ; *Pre-Eclampsia ; Pregnancy ; Pyridoxal Phosphate ; RNA, Ribosomal, 16S/genetics ; Rhamnose ; Riboflavin ; }, abstract = {Preeclampsia (PE) is a pregnancy complication characterized by severe hypertension and multiple organ damage. Gut microbiota has been linked to PE by previous amplicon sequencing studies. To resolve the PE gut microbiota in a higher taxonomy resolution, we performed shotgun metagenomic sequencing on the fecal samples from 40 early-onset PE and 37 healthy pregnant women. We recovered 1,750 metagenome-assembled genomes (representing 406 species) from the metagenomic dataset and profiled their abundances. We found that PE gut microbiota had enriched in some species belonging to Blautia, Pauljensenia, Ruminococcus, and Collinsella and microbial functions such as the bacitracin/lantibiotics transport system, maltooligosaccharide transport system, multidrug efflux pump, and rhamnose transport system. Conversely, the gut microbiome of healthy pregnant women was enriched in species of Bacteroides and Phocaeicola and microbial functions including the porphyrin and chlorophyll metabolism, pyridoxal-P biosynthesis, riboflavin metabolism, and folate biosynthesis pathway. PE diagnostic potential of gut microbial biomarkers was developed using both species and function profile data. These results will help to explore the relationships between gut bacteria and PE and provide new insights into PE early warning.}, } @article {pmid36189246, year = {2022}, author = {Santiago-Rodriguez, TM and Hollister, EB}, title = {Unraveling the viral dark matter through viral metagenomics.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {1005107}, pmid = {36189246}, issn = {1664-3224}, mesh = {Computational Biology ; Genome, Viral ; Metagenomics ; *Microbiota ; *Viruses/genetics ; }, abstract = {Viruses are part of the microbiome and have essential roles in immunology, evolution, biogeochemical cycles, health, and disease progression. Viruses influence a wide variety of systems and processes, and the continued discovery of novel viruses is anticipated to reveal new mechanisms influencing the biology of diverse environments. While the identity and roles of viruses continue to be discovered and understood through viral metagenomics, most of the sequences in virome datasets cannot be attributed to known viruses or may be only distantly related to species already described in public sequence databases, at best. Such viruses are known as the viral dark matter. Ongoing discoveries from the viral dark matter have provided insights into novel viruses from a variety of environments, as well as their potential in immunological processes, virus evolution, health, disease, therapeutics, and surveillance. Increased understanding of the viral dark matter will continue with a combination of cultivation, microscopy, sequencing, and bioinformatic efforts, which are discussed in the present review.}, } @article {pmid36188134, year = {2022}, author = {Tran, DM and Huynh, TU and Nguyen, TH and Do, TO and Nguyen, QV and Nguyen, AD}, title = {Metagenomic next-generation sequencing of the microbiome dataset from the surface water sample collected from Serepok River in Yok Don National Park, Vietnam.}, journal = {Data in brief}, volume = {45}, number = {}, pages = {108614}, pmid = {36188134}, issn = {2352-3409}, abstract = {The Central Highlands region is considered as the center with the highest biodiversity in Vietnam because it has the majority of national parks such as Yok Don, Chu Yang Sin, Bidoup-Nui Ba, Ta Dung, Chu Mon Ray, and Kon Ka Kinh and nature reserves such as Ngoc Linh, Kon Chu Rang, Ea So, Nam Ka, and Nam Nung with different ecosystems [1]. Of the national parks and nature reserves, Yok Don has the most different ecosystem. Yok Don is the second biggest national park, and it is the only national park that conserves dry deciduous dipterocarp forests in Vietnam [2]. Presently, the decrease in forest area and global warming have led to the continuous reduction in microbial resources in this region. Thus, a dataset of the soil microbiome in this region has been established to explore microbial resources for conservation and further application in sustainable agricultural production in this region [3]; however, to the best of our knowledge, a dataset of water microbiome remains unknown. This work presented a microbiome dataset from surface water samples collected from Serepok River in Yok Don National Park, Vietnam. Metagenomic next-generation sequencing was used to characterize microbial communities in the sample. The raw sequence in this work was uploaded in Fastq format on NCBI, which can be accessed at https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA853090. This metagenome dataset can provide valuable information on surface water microbial communities and their functionality. It can also be used for further studies on the conservation and application of indigenous microbial resources for sustainable crop production in this region.}, } @article {pmid36188001, year = {2022}, author = {Szydlowski, L and Ehlich, J and Szczerbiak, P and Shibata, N and Goryanin, I}, title = {Novel species identification and deep functional annotation of electrogenic biofilms, selectively enriched in a microbial fuel cell array.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {951044}, pmid = {36188001}, issn = {1664-302X}, abstract = {In this study, electrogenic microbial communities originating from a single source were multiplied using our custom-made, 96-well-plate-based microbial fuel cell (MFC) array. Developed communities operated under different pH conditions and produced currents up to 19.4 A/m3 (0.6 A/m2) within 2 days of inoculation. Microscopic observations [combined scanning electron microscopy (SEM) and energy dispersive spectroscopy (EDS)] revealed that some species present in the anodic biofilm adsorbed copper on their surface because of the bioleaching of the printed circuit board (PCB), yielding Cu2 + ions up to 600 mg/L. Beta- diversity indicates taxonomic divergence among all communities, but functional clustering is based on reactor pH. Annotated metagenomes showed the high presence of multicopper oxidases and Cu-resistance genes, as well as genes encoding aliphatic and aromatic hydrocarbon-degrading enzymes, corresponding to PCB bioleaching. Metagenome analysis revealed a high abundance of Dietzia spp., previously characterized in MFCs, which did not grow at pH 4. Binning metagenomes allowed us to identify novel species, one belonging to Actinotalea, not yet associated with electrogenicity and enriched only in the pH 7 anode. Furthermore, we identified 854 unique protein-coding genes in Actinotalea that lacked sequence homology with other metagenomes. The function of some genes was predicted with high accuracy through deep functional residue identification (DeepFRI), with several of these genes potentially related to electrogenic capacity. Our results demonstrate the feasibility of using MFC arrays for the enrichment of functional electrogenic microbial consortia and data mining for the comparative analysis of either consortia or their members.}, } @article {pmid36188000, year = {2022}, author = {Hu, X and Chen, X and Tang, Y and Xu, Z and Zeng, Y and Wang, Y and Zhao, Y and Wu, Y and Wang, G}, title = {Effects of g-C3N4 on bacterial community and tetracycline resistance genes in two typical sediments in tetracycline pollution remediation.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {964401}, pmid = {36188000}, issn = {1664-302X}, abstract = {Photocatalysis, as a novel technique, has been widely used for antibiotic pollution remediation in wastewater. In the processes of degradation and removal of antibiotics, the impact of photocatalysts on microenvironment is very important but remains poorly understood. In the present study, the effect of typical photocatalyst g-C3N4 (Graphitic carbon nitride) on microbial community was investigated in two sediment types (riverbed sediment and pig-farm sediment) polluted by tetracycline (TC) in central southern China. The riverbed sediment and pig farm sediment samples were respectively exposed to g-C3N4 (25, 75, 125 mg⋅kg[-1]) and TC (60, 120, 180 mg⋅L[-1]) treatments alone or combination for 30 days, respectively. The bacterial community and antibiotic resistance genes (ARGs) of the treated sediments were analyzed by Illumina sequencing and metagenomic sequencing. Studies had shown that: TC, g-C3N4, and TC/g-C3N4 have significant effects on the changes of microbial communities and components in riverbed sediment, but they do not exist in pig farm sediment. The most alterations of microbial taxa were Acidobacteriota, Actinobacteriota, and Desulfobacterota in riverbed sediment, and Elusimicrobiota in the pig farm sediment under various treatments. Through network analysis, it was found that the distribution of microorganisms in the pig farm sediment is more complex and more stable. The addition of g-C3N4 reduced the absolute abundance of ARGs in the two examined sediments, but not significantly changed their relative abundance of ARGs. The g-C3N4 application was beneficial to the removal of TC residues and to the prevention of the generation and transmission of ARGs in sediments. Our results suggested that g-C3N4 was a suitable photocatalyst with excellent application prospect for the removal of TC residues and the control of ARGs in environment.}, } @article {pmid36187998, year = {2022}, author = {Stromecki, A and Murray, L and Fullerton, H and Moyer, CL}, title = {Unexpected diversity found within benthic microbial mats at hydrothermal springs in Crater Lake, Oregon.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {876044}, pmid = {36187998}, issn = {1664-302X}, abstract = {Crater Lake, Oregon is an oligotrophic freshwater caldera lake fed by thermally and chemically enriched hydrothermal springs. These vents distinguish Crater Lake from other freshwater systems and provide a unique ecosystem for study. This study examines the community structure of benthic microbial mats occurring with Crater Lake hydrothermal springs. Small subunit rRNA gene amplicon sequencing from eight bacterial mats was used to assess community structure. These revealed a relatively homogeneous, yet diverse bacterial community. High alpha diversity and low beta diversity indicate that these communities are likely fueled by homogeneous hydrothermal fluids. An examination of autotrophic taxa abundance indicates the potential importance of iron and sulfur inputs to the primary productivity of these mats. Chemoautotrophic potential within the mats was dominated by iron oxidation from Gallionella and Mariprofundus and by sulfur oxidation from Sulfuricurvum and Thiobacillus with an additional contribution of nitrite oxidation from Nitrospira. Metagenomic analysis showed that cbbM genes were identified as Gallionella and that aclB genes were identified as Nitrospira, further supporting these taxa as autotrophic drivers of the community. The detection of several taxa containing arsC and nirK genes suggests that arsenic detoxification and denitrification processes are likely co-occurring in addition to at least two modes of carbon fixation. These data link the importance of the detected autotrophic metabolisms driven by fluids derived from benthic hydrothermal springs to Crater Lake's entire lentic ecosystem.}, } @article {pmid36187977, year = {2022}, author = {Shami, AY and Abulfaraj, AA and Refai, MY and Barqawi, AA and Binothman, N and Tashkandi, MA and Baeissa, HM and Baz, L and Abuauf, HW and Ashy, RA and Jalal, RS}, title = {Abundant antibiotic resistance genes in rhizobiome of the human edible Moringa oleifera medicinal plant.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {990169}, pmid = {36187977}, issn = {1664-302X}, abstract = {Moringa oleifera (or the miracle tree) is a wild plant species widely grown for its seed pods and leaves, and is used in traditional herbal medicine. The metagenomic whole genome shotgun sequencing (mWGS) approach was used to characterize antibiotic resistance genes (ARGs) of the rhizobiomes of this wild plant and surrounding bulk soil microbiomes and to figure out the chance and consequences for highly abundant ARGs, e.g., mtrA, golS, soxR, oleC, novA, kdpE, vanRO, parY, and rbpA, to horizontally transfer to human gut pathogens via mobile genetic elements (MGEs). The results indicated that abundance of these ARGs, except for golS, was higher in rhizosphere of M. oleifera than that in bulk soil microbiome with no signs of emerging new soil ARGs in either soil type. The most highly abundant metabolic processes of the most abundant ARGs were previously detected in members of phyla Actinobacteria, Proteobacteria, Acidobacteria, Chloroflexi, and Firmicutes. These processes refer to three resistance mechanisms namely antibiotic efflux pump, antibiotic target alteration and antibiotic target protection. Antibiotic efflux mechanism included resistance-nodulation-cell division (RND), ATP-binding cassette (ABC), and major facilitator superfamily (MFS) antibiotics pumps as well as the two-component regulatory kdpDE system. Antibiotic target alteration included glycopeptide resistance gene cluster (vanRO), aminocoumarin resistance parY, and aminocoumarin self-resistance parY. While, antibiotic target protection mechanism included RbpA bacterial RNA polymerase (rpoB)-binding protein. The study supports the claim of the possible horizontal transfer of these ARGs to human gut and emergence of new multidrug resistant clinical isolates. Thus, careful agricultural practices are required especially for plants used in circles of human nutrition industry or in traditional medicine.}, } @article {pmid36187731, year = {2022}, author = {Liu, L and Yuan, M and Sun, S and Wang, J and Shi, Y and Yu, Y and Su, X}, title = {The Performance of Metagenomic Next-Generation Sequence in the Diagnosis of Suspected Opportunistic Infections in Patients with Acquired Immunodeficiency Syndrome.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {5645-5653}, pmid = {36187731}, issn = {1178-6973}, abstract = {BACKGROUND: For acquired immunodeficiency syndrome (AIDS) patients with suspected opportunistic infections, the rapid and accurate identification of pathogens remains a challenge. Metagenomic next-generation sequencing (mNGS) has emerged as a pan-pathogen assay for infectious diseases diagnosis, but its guiding significance for diagnosis and antimicrobials treatment in AIDS patients with suspected opportunistic infections is still not well established. In this study, we compared the microbiological diagnostic value of mNGS with that of conventional microbiological tests (CMTs) in AIDS patients with suspected opportunistic infections.

METHODS: From January 2018 to February 2021, a retrospective study was performed at four tertiary teaching hospitals in China and data of 86 AIDS patients with suspected opportunistic infections were collected. The pathogen detection performance of mNGS and CMTs were compared.

RESULTS: Positive agreement between mNGS and clinical diagnosis was significantly higher than that of CMTs (65/86 (75.6%) vs 37/86 (43.0%)). In addition, mNGS identified more bacterial (25 vs 2), fungal (5 vs 3), viral (9 vs 2) organisms compared with CMTs. Mixed infection were detected in 34 patients by mNGS combined with CMTs. Viruses (94.1%, 32/34) and fungi (94.1%, 32/34) were commonly seen in the mixed infection cases. mNGS helped identify the pathogen or guide appropriate treatment in 49/86 (57%) patients. Meanwhile, CMTs also contributed in the decision of appropriate treatment in 28 patients. The successful de-escalation or discontinuation of treatment was supported in 37 patients with the help of mNGS. We observed a significant reduction in the number of patients being prescribed foscarnet (52.3% vs 23.26%, p < 0.001), moxifloxacin (34.9% vs 10.5%, p = 0.005), and levofloxacin (32.6% vs 14%, p = 0.001) before and after mNGS.

CONCLUSION: For AIDS patients with suspected opportunistic infections, mNGS can provide early, noninvasive, and rapid microbiological diagnosis. mNGS may lead to a more precise antimicrobial treatment and reduced the unreasonable use of antimicrobials.}, } @article {pmid36187510, year = {2022}, author = {Vadaq, N and Zhang, Y and Meeder, E and Van de Wijer, L and Gasem, MH and Joosten, LA and Netea, MG and de Mast, Q and Matzaraki, V and Schellekens, A and Fu, J and van der Ven, AJ}, title = {Microbiome-Related Indole and Serotonin Metabolites are Linked to Inflammation and Psychiatric Symptoms in People Living with HIV.}, journal = {International journal of tryptophan research : IJTR}, volume = {15}, number = {}, pages = {11786469221126888}, pmid = {36187510}, issn = {1178-6469}, abstract = {BACKGROUND: People living with HIV (PLHIV) exhibit dysregulation of tryptophan metabolism. Altered gut microbiome composition in PLHIV might be involved. Mechanistic consequences within the 3 major tryptophan metabolism pathways (serotonin, kynurenine, and indoles), and functional consequences for platelet, immune and behavioral functions are unknown. We investigated plasma tryptophan metabolites, gut microbiome composition, and their association with platelet function, inflammation, and psychiatric symptoms.

METHODS: This study included 211 PLHIV on long-term antiretroviral treatment (ART). Plasma tryptophan pathway metabolites were measured using time-of-flight mass spectrometry. Bacterial composition was profiled using metagenomic sequencing. Platelet reactivity and serotonin levels were quantified by flowcytometry and ELISA, respectively. Circulating inflammatory markers were determined using ELISA. Symptoms of depression and impulsivity were measured by DASS-42 and BIS-11 self-report questionnaires, respectively.

RESULTS: Plasma serotonin and indole metabolites were associated with gut bacterial composition. Notably, species enriched in PLHIV were associated with 3-methyldioxyindole. Platelet serotonin concentrations were elevated in PLHIV, without effects on platelet reactivity. Plasma serotonin and indole metabolites were positively associated with plasma IL-10 and TNF-α concentrations. Finally, higher tryptophan, serotonin, and indole metabolites were associated with lower depression and anxiety, whereas higher kynurenine metabolites were associated with increased impulsivity.

CONCLUSION: Our results suggest that gut bacterial composition and dysbiosis in PLHIV on ART contribute to tryptophan metabolism, which may have clinical consequences for immune function and behavior.}, } @article {pmid36185528, year = {2022}, author = {Widiyani, P and Sudarwanto, MB and Latif, H and Lukman, DW and Thong, D and Rahayu, P}, title = {A preliminary metagenomics study of bacteria present in the dirt of Swiftlet farmhouses based on nitrite levels in edible bird's nest on Sumatera Island, Indonesia.}, journal = {Veterinary world}, volume = {15}, number = {7}, pages = {1798-1803}, pmid = {36185528}, issn = {0972-8988}, abstract = {BACKGROUND AND AIM: Since the past decade, metagenomics has been used to evaluate sequenced deoxyribonucleic acid of all microorganisms in several types of research. Nitrite contamination originates from the natural environment in Swiftlet farmhouses (SFHs) and can influence nitrite levels in edible bird's nest (EBN). It is strongly speculated that the conversion process into nitrite is influenced by the bacteria present in SFHs. Nitrite can cause adverse effects on human health. The previous research has focused on the characteristics of bacteria that may influence the nitrite conversion process in SFHs. This study aimed to a metagenomics analysis of bacteria present in the dirt of SFHs and evaluated nitrite levels in EBN on Sumatera Island.

MATERIALS AND METHODS: In total, 18 SFHs on Sumatera Island were selected, and EBN and dirt samples were collected from each SFH, resulting in 18 EBN and 18 dirt SFH samples. Raw uncleaned white EBN and dirt from three areas of SFH were collected. The samples were analyzed for nitrite levels using a spectrophotometer, and the metagenomics sequencing of SFH dirt samples was performed using the MinIon nanopore method. The sequenced data were analyzed using the EPI2ME software.

RESULTS: Of the 18 raw uncleaned white EBN samples, 9 (50%) had <30 ppm nitrite levels. The top five bacterial genera in SFH dirt samples in Group A (nitrite levels >30 ppm) were Aeromonas, Escherichia, Acinetobacter, Arcobacter, and Acetoanaerobium. Those in Group B (nitrite levels <30 ppm) were Aeromonas, Pseudomonas, Shewanella, Escherichia, and Acinetobacter. There were 12 genera of nitrifying bacteria in Group A and 8 in Group B. The total cumulative read of nitrifying bacteria in Groups A and B were 87 and 38 reads, respectively.

CONCLUSION: This is the first study to show that characteristic bacteria present in the dirt of SFHs might significantly influence the conversion from nitrogen to nitrite. Approximately 50% of raw uncleaned EBN samples had <30 ppm nitrite levels. Aeromonas was the most dominant bacterial genus found in Groups A and B. The variations in genus and cumulative reads nitrifying bacteria in group A were greater than those in Group B. This study provides information on the characteristics of bacteria that may influence the nitrite conversion process in SFHs. Metagenomics data were obtained from the reading using the software EPI2ME. Further research is needed on the bacterial target species that can convert nitrite in SFHs.}, } @article {pmid36185401, year = {2022}, author = {Li, X and Li, J and Shi, Y and Wu, G and Wang, M and Zhang, Y and Xia, H}, title = {Application of metagenomic next-generation sequencing technique for diagnosing a specific case of necrotizing meningoencephalitis caused by human herpesvirus 2.}, journal = {Open life sciences}, volume = {17}, number = {1}, pages = {1217-1222}, pmid = {36185401}, issn = {2391-5412}, abstract = {Reactivation of latent human herpesvirus 2 (HHV-2) can cause spontaneous recovering aseptic meningitis and recurrent meningitis in adults, but it rarely affects the brain parenchyma to cause encephalitis. Here, we report the case of a 37-year-old male patient admitted to our hospital due to fever with a progressive headache for 3 days and paroxysmal episodes of unconsciousness for 1 day. Brain magnetic resonance imaging (MRI) revealed viral meningoencephalitis. Then, metagenomics next-generation sequencing (mNGS) was applied, which detected 12,024 unique sequences of HHV-2 in cerebrospinal fluid (2022), indicating HHV-2 encephalitis. After antiviral treatment, the patient's symptoms improved, and he was discharged. During the 1-month follow-up, the patient recovered without any new symptoms, but a brain MRI revealed significant atrophy of the original foci. The patient was finally diagnosed with HHV-2 necrotizing meningoencephalitis, which is extremely rare. mNGS helped with the clinical diagnosis and strengthened our understanding of HHV-2 infections in the central nervous system.}, } @article {pmid36184671, year = {2022}, author = {Armbrecht, L and Weber, ME and Raymo, ME and Peck, VL and Williams, T and Warnock, J and Kato, Y and Hernández-Almeida, I and Hoem, F and Reilly, B and Hemming, S and Bailey, I and Martos, YM and Gutjahr, M and Percuoco, V and Allen, C and Brachfeld, S and Cardillo, FG and Du, Z and Fauth, G and Fogwill, C and Garcia, M and Glüder, A and Guitard, M and Hwang, JH and Iizuka, M and Kenlee, B and O'Connell, S and Pérez, LF and Ronge, TA and Seki, O and Tauxe, L and Tripathi, S and Zheng, X}, title = {Ancient marine sediment DNA reveals diatom transition in Antarctica.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5787}, pmid = {36184671}, issn = {2041-1723}, mesh = {Antarctic Regions ; DNA, Ancient ; *Diatoms/genetics ; Ecosystem ; Eukaryota ; Geologic Sediments ; }, abstract = {Antarctica is one of the most vulnerable regions to climate change on Earth and studying the past and present responses of this polar marine ecosystem to environmental change is a matter of urgency. Sedimentary ancient DNA (sedaDNA) analysis can provide such insights into past ecosystem-wide changes. Here we present authenticated (through extensive contamination control and sedaDNA damage analysis) metagenomic marine eukaryote sedaDNA from the Scotia Sea region acquired during IODP Expedition 382. We also provide a marine eukaryote sedaDNA record of ~1 Mio. years and diatom and chlorophyte sedaDNA dating back to ~540 ka (using taxonomic marker genes SSU, LSU, psbO). We find evidence of warm phases being associated with high relative diatom abundance, and a marked transition from diatoms comprising <10% of all eukaryotes prior to ~14.5 ka, to ~50% after this time, i.e., following Meltwater Pulse 1A, alongside a composition change from sea-ice to open-ocean species. Our study demonstrates that sedaDNA tools can be expanded to hundreds of thousands of years, opening the pathway to the study of ecosystem-wide marine shifts and paleo-productivity phases throughout multiple glacial-interglacial cycles.}, } @article {pmid36184305, year = {2023}, author = {Lockwood, MB and Chlipala, GE and Maeinschein-Cline, M and DeVon, HA and Lichvar, AB and Samra, MK and Park, CG and Campara, M and Doorenbos, AZ and Tussing-Humphreys, LM and Spaggiari, M and Bronas, UG and Steel, JL and Green, SS}, title = {Pain Interference in End Stage Kidney Disease is Associated with Changes in Gut Microbiome Features Before and After Kidney Transplantation.}, journal = {Pain management nursing : official journal of the American Society of Pain Management Nurses}, volume = {24}, number = {1}, pages = {68-77}, pmid = {36184305}, issn = {1532-8635}, support = {K23 NR018482/NR/NINR NIH HHS/United States ; K24 AT011995/AT/NCCIH NIH HHS/United States ; L30 NR020114/NR/NINR NIH HHS/United States ; U01 DK123787/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; *Kidney Transplantation/adverse effects ; *Gastrointestinal Microbiome/genetics ; *Kidney Failure, Chronic ; Feces ; Pain ; Inflammation ; }, abstract = {BACKGROUND: Pain, a common debilitating symptom among kidney transplant recipients (KTRs), is among the most common and undertreated symptoms after kidney transplantation.

AIMS: Characterize associations between gut microbiome features and pain interference before and after kidney transplantation.

DESIGN: Longitudinal, repeated measures study, collecting fecal specimens and pain interference data pretransplant and 3 months posttransplant.

SETTING: Participants were recruited at the kidney transplant clinic at the University of Illinois Hospital & Health Sciences System.

PARTICIPANTS/SUBJECTS: 19 living donor kidney transplant recipients.

METHODS: We assessed fecal microbial community structure with shotgun metagenomic sequencing; we used pain interference scores derived from the Patient-Reported Outcomes Measurement Information System-57.

RESULTS: We measured a reduction in the Shannon diversity index in both groups after transplantation but observed no significant differences between groups at either time point. We did observe significant differences in fecal microbial Bray-Curtis similarity index among those reporting pain interference pre- transplant versus no pain interference at 3-months posttransplant (R = .306, p = .022), and between pain interference groups at posttransplant (R = .249, p = .041). Pairwise models showed significant differences between groups posttransplant in relative abundances of several taxa, including a 5-fold reduction.ßin Akkermansia among those with pain interference and a higher relative abundance of taxa associated with chronic inflammation in those with pain interference posttransplant. Functional gene analysis identified two features that were significantly enriched in those with pain interference, including a peptide transport system gene.

CONCLUSIONS: Gut microbiota community structure differs between groups with and without pain interference at 3 months after kidney transplantation. Several taxa involved in intestinal barrier integrity and chronic inflammation were associated with posttransplant pain.}, } @article {pmid36183892, year = {2022}, author = {Dong, X and Huang, Z and Peng, X and Jia, X}, title = {Advanced simultaneous nitrogen and phosphorus removal for non-sterile wastewater through a novel coupled yeast-sludge system: Performance, microbial interaction, and mechanism.}, journal = {Chemosphere}, volume = {309}, number = {Pt 1}, pages = {136645}, doi = {10.1016/j.chemosphere.2022.136645}, pmid = {36183892}, issn = {1879-1298}, mesh = {*Sewage ; *Wastewater ; Phosphorus/metabolism ; Nitrogen ; Saccharomyces cerevisiae/metabolism ; Denitrification ; In Situ Hybridization, Fluorescence ; Bioreactors ; Carbon ; Microbial Interactions ; Waste Disposal, Fluid/methods ; }, abstract = {A novel coupled yeast-sludge system (CYSS) was constructed by the yeast Candida sp. PNY integrated with activated sludge to treat non-sterile mainstream wastewater. After 240-day cultivation, compared with single activated sludge, simultaneous removal efficiency of total organic carbon (TOC), nitrogen and phosphorus increased by 19.5% (176.34 mg TOC g[-1] d[-1]), 21.3% (11.25 mg TN g[-1] d[-1]) and 15.0% (6.95 mg TP g[-1] d[-1]), respectively, while the amount of sludge reduced by 50%. Amplicon sequencing analysis showed that the abundance of Nitrosomonas, Nitrospira, Zoogloea, Dechloromonas, and Candidatus Accumulibacter significantly decreased to 0% on Day 200. Abundance of nirS and nirK for denitrification significantly decreased in CYSS by quantitative PCR (qPCR), and the copies of nirS and nirK were 3.37-fold and 1.71-fold decrease from Day 0 to Day 240, respectively. The results of Fluorescence in situ hybridization and co-occurrence network showed that Candida sp. PNY predominated its distribution in CYSS, and strongly connected with environmental variables based on network analysis. Furthermore, this study reconstructed the carbon, nitrogen and phosphorus metabolic pathways of the CYSS based on metagenomics.}, } @article {pmid36183890, year = {2022}, author = {Huang, JN and Wen, B and Miao, L and Liu, X and Li, ZJ and Ma, TF and Xu, L and Gao, JZ and Chen, ZZ}, title = {Microplastics drive nitrification by enriching functional microorganisms in aquaculture pond waters.}, journal = {Chemosphere}, volume = {309}, number = {Pt 1}, pages = {136646}, doi = {10.1016/j.chemosphere.2022.136646}, pmid = {36183890}, issn = {1879-1298}, mesh = {*Nitrification ; RNA, Ribosomal, 16S/genetics ; *Plastics ; Ammonia ; Microplastics ; Nitrites ; Ponds ; Phylogeny ; Aquaculture ; Nitrogen ; Water ; Oxidation-Reduction ; }, abstract = {The plastisphere refers to biofilm formation on the microplastic (MP) surface, but its subsequent functions, especially driving the nitrogen biogeochemical cycle, are rarely studied. Here, MPs were incubated in the pelagic water and benthic water-sediment interface of an aquaculture pond, and the two corresponding microcosms amended with incubated plastisphere were simulated. The results showed decreased ammonia concentrations and increased nitrification rates in microcosms with either pelagic or benthic plastispheres. To uncover the possible mechanisms, the community structure and function of the plastisphere were investigated. As clarified by 16S rRNA, the community diversity of the pelagic plastisphere was significantly higher than that of the corresponding hydrosphere. Plastisphere communities, especially those incubated in pelagic water, were separated from the hydrosphere. Moreover, the abundance of Proteobacteria increased while the abundance of Cyanobacteria decreased in both plastispheres. Metagenome further revealed that the abundance of amoA and annotated Nitrososphaeraceae_archaeon and hao and affiliated Nitrosomonas_europaea, which contributed to ammonia oxidation to nitrite, was higher in the benthic plastisphere. Comparing the pelagic plastisphere with the corresponding hydrosphere, however, the abundance of nxrA and annotated Nitrobacter hamburgensis and nxrB and the affiliated Nitrospira moscoviensis, which are involved in nitrite oxidation, was more abundant in the plastisphere. These findings suggest that the plastisphere might selectively enrich functional microorganisms and genes in a habitat-dependent manner to promote nitrification in aquaculture ponds.}, } @article {pmid36182984, year = {2022}, author = {Öztürk, Hİ and Demirci, T and Akın, N and Oğul, A}, title = {Elucidation of the initial bacterial community of Ezine PDO cheese using next-generation sequencing.}, journal = {Archives of microbiology}, volume = {204}, number = {10}, pages = {656}, pmid = {36182984}, issn = {1432-072X}, mesh = {Animals ; *Cheese/microbiology ; Food Microbiology ; High-Throughput Nucleotide Sequencing ; *Microbiota/genetics ; Milk/microbiology ; Streptococcus thermophilus/genetics ; }, abstract = {This study aims to reveal initial bacterial consortia of Ezine PDO cheeses comprehensively by following a metagenomic approach. A total of 8 artisanal Ezine cheese samples were collected from the Bayramiç and Ezine districts of Çanakkale province of Turkey. Ezine cheese was found to contain Firmicutes, Bacteroidetes, and Proteobacteria phyla dominantly. Streptococcus, Lactococcus, and Lactobacillus genera dominated the microbiota with relative abundances of 4.47-56.07%, 7.33-20.34%, and 1.21-25.12%, respectively, followed by Bacteroides and Prevotella genera. Excluding two cheese samples obtained from the Ezine district, the most dominant species was Streptococcus thermophilus (8.24-54.34%). It was also found in greater proportions in the cheeses of the Bayramiç district. Unexpectedly, Lactobacillus graminis (11.50-23.63%) was the most abundant species in two samples collected from the Ezine district. However, lower bacterial diversity was determined in the samples collected from the Bayramiç district. The lowest species richness was 129 OTU-species in the cheeses from the Bayramiç district while the highest species richness was 267 OTU-species in cheeses from the Ezine district. In addition, the Simpson index was the highest in cheeses from the Ezine district, where different species were evenly distributed. Permutational multivariate analysis of variance tests also confirmed that the differences in the structure of bacterial consortia in cheeses from two different districts were statistically significant. This study will provide pioneer data for further investigations on the role of complex bacterial composition in maintaining and improving the quality and safety of Ezine cheese.}, } @article {pmid36182913, year = {2022}, author = {Tian, J and Hou, X and Ge, M and Xu, H and Yu, B and Liu, J and Shao, R and Holmes, EC and Lei, C and Shi, M}, title = {The diversity and evolutionary relationships of ticks and tick-borne bacteria collected in China.}, journal = {Parasites & vectors}, volume = {15}, number = {1}, pages = {352}, pmid = {36182913}, issn = {1756-3305}, support = {20142BBG70097//"Medical youth top talent project of Hubei" Fellowship and Science and Technology Project of Jiangxi/ ; FL170100022//Australian Research Council Australia Laureate Fellowship/ ; KQTD20200820145822023//Shenzhen Science and Technology Program/ ; 2019ZT08Y464//Guangdong Province "Pearl River Talent Plan" Innovation and Entrepreneurship Team Project/ ; }, mesh = {Animals ; *Borrelia/genetics ; Coxiella/genetics ; DNA, Mitochondrial/genetics ; Humans ; *Ixodes/microbiology ; *Rickettsia/genetics ; *Tick-Borne Diseases/epidemiology/microbiology ; }, abstract = {BACKGROUND: Ticks (order Ixodida) are ectoparasites, vectors and reservoirs of many infectious agents affecting humans and domestic animals. However, the lack of information on tick genomic diversity leaves significant gaps in the understanding of the evolution of ticks and associated bacteria.

RESULTS: We collected > 20,000 contemporary and historical (up to 60 years of preservation) tick samples representing a wide range of tick biodiversity across diverse geographic regions in China. Metagenomic sequencing was performed on individual ticks to obtain the complete or near-complete mitochondrial (mt) genome sequences from 46 tick species, among which mitochondrial genomes of 23 species were recovered for the first time. These new mt genomes data greatly expanded the diversity of many tick groups and revealed five cryptic species. Utilizing the same metagenomic sequence data we identified divergent and abundant bacteria in Haemaphysalis, Ixodes, Dermacentor and Carios ticks, including nine species of pathogenetic bacteria and potentially new species within the genus Borrelia. We also used these data to explore the evolutionary relationship between ticks and their associated bacteria, revealing a pattern of long-term co-divergence relationship between ticks and Rickettsia and Coxiella bacteria.

CONCLUSIONS: In sum, our study provides important new information on the genetic diversity of ticks based on an analysis of mitochondrial DNA as well as on the prevalence of tick-borne pathogens in China. It also sheds new light on the long-term evolutionary and ecological relationships between ticks and their associated bacteria.}, } @article {pmid36182700, year = {2022}, author = {Gopalakrishnan, S and Ebenesersdóttir, SS and Lundstrøm, IKC and Turner-Walker, G and Moore, KHS and Luisi, P and Margaryan, A and Martin, MD and Ellegaard, MR and Magnússon, ÓÞ and Sigurðsson, Á and Snorradóttir, S and Magnúsdóttir, DN and Laffoon, JE and van Dorp, L and Liu, X and Moltke, I and Ávila-Arcos, MC and Schraiber, JG and Rasmussen, S and Juan, D and Gelabert, P and de-Dios, T and Fotakis, AK and Iraeta-Orbegozo, M and Vågene, ÅJ and Denham, SD and Christophersen, A and Stenøien, HK and Vieira, FG and Liu, S and Günther, T and Kivisild, T and Moseng, OG and Skar, B and Cheung, C and Sandoval-Velasco, M and Wales, N and Schroeder, H and Campos, PF and Guðmundsdóttir, VB and Sicheritz-Ponten, T and Petersen, B and Halgunset, J and Gilbert, E and Cavalleri, GL and Hovig, E and Kockum, I and Olsson, T and Alfredsson, L and Hansen, TF and Werge, T and Willerslev, E and Balloux, F and Marques-Bonet, T and Lalueza-Fox, C and Nielsen, R and Stefánsson, K and Helgason, A and Gilbert, MTP}, title = {The population genomic legacy of the second plague pandemic.}, journal = {Current biology : CB}, volume = {32}, number = {21}, pages = {4743-4751.e6}, pmid = {36182700}, issn = {1879-0445}, mesh = {Humans ; *Plague/epidemiology/genetics ; Pandemics/history ; Metagenomics ; Genome, Bacterial ; Phylogeny ; }, abstract = {Human populations have been shaped by catastrophes that may have left long-lasting signatures in their genomes. One notable example is the second plague pandemic that entered Europe in ca. 1,347 CE and repeatedly returned for over 300 years, with typical village and town mortality estimated at 10%-40%.[1] It is assumed that this high mortality affected the gene pools of these populations. First, local population crashes reduced genetic diversity. Second, a change in frequency is expected for sequence variants that may have affected survival or susceptibility to the etiologic agent (Yersinia pestis).[2] Third, mass mortality might alter the local gene pools through its impact on subsequent migration patterns. We explored these factors using the Norwegian city of Trondheim as a model, by sequencing 54 genomes spanning three time periods: (1) prior to the plague striking Trondheim in 1,349 CE, (2) the 17[th]-19[th] century, and (3) the present. We find that the pandemic period shaped the gene pool by reducing long distance immigration, in particular from the British Isles, and inducing a bottleneck that reduced genetic diversity. Although we also observe an excess of large FST values at multiple loci in the genome, these are shaped by reference biases introduced by mapping our relatively low genome coverage degraded DNA to the reference genome. This implies that attempts to detect selection using ancient DNA (aDNA) datasets that vary by read length and depth of sequencing coverage may be particularly challenging until methods have been developed to account for the impact of differential reference bias on test statistics.}, } @article {pmid36182683, year = {2022}, author = {Neugent, ML and Kumar, A and Hulyalkar, NV and Lutz, KC and Nguyen, VH and Fuentes, JL and Zhang, C and Nguyen, A and Sharon, BM and Kuprasertkul, A and Arute, AP and Ebrahimzadeh, T and Natesan, N and Xing, C and Shulaev, V and Li, Q and Zimmern, PE and Palmer, KL and De Nisco, NJ}, title = {Recurrent urinary tract infection and estrogen shape the taxonomic ecology and function of the postmenopausal urogenital microbiome.}, journal = {Cell reports. Medicine}, volume = {3}, number = {10}, pages = {100753}, pmid = {36182683}, issn = {2666-3791}, support = {R01 DK131267/DK/NIDDK NIH HHS/United States ; }, mesh = {Female ; Humans ; Postmenopause ; *Urinary Tract Infections/drug therapy ; Estrogens ; *Microbiota/genetics ; Lactobacillus ; *Anti-Infective Agents ; }, abstract = {Postmenopausal women are severely affected by recurrent urinary tract infection (rUTI). The urogenital microbiome is a key component of the urinary environment. However, changes in the urogenital microbiome underlying rUTI susceptibility are unknown. Here, we perform shotgun metagenomics and advanced culture on urine from a controlled cohort of postmenopausal women to identify urogenital microbiome compositional and function changes linked to rUTI susceptibility. We identify candidate taxonomic biomarkers of rUTI susceptibility in postmenopausal women and an enrichment of lactobacilli in postmenopausal women taking estrogen hormone therapy. We find robust correlations between Bifidobacterium and Lactobacillus and urinary estrogens in women without urinary tract infection (UTI) history. Functional analyses reveal distinct metabolic and antimicrobial resistance gene (ARG) signatures associated with rUTI. Importantly, we find that ARGs are enriched in the urogenital microbiomes of women with rUTI history independent of current UTI status. Our data suggest that rUTI and estrogen shape the urogenital microbiome in postmenopausal women.}, } @article {pmid36182642, year = {2023}, author = {Lin, CH and Lai, HC and Wu, MS}, title = {Gut-oriented disease modifying therapy for Parkinson's disease.}, journal = {Journal of the Formosan Medical Association = Taiwan yi zhi}, volume = {122}, number = {1}, pages = {9-18}, doi = {10.1016/j.jfma.2022.09.010}, pmid = {36182642}, issn = {0929-6646}, mesh = {Humans ; *Parkinson Disease/therapy ; *Gastrointestinal Microbiome/physiology ; *Enteric Nervous System/metabolism ; }, abstract = {Neuropathology studies have shown that the pathognomonic feature of Parkinson's disease (PD), one of the most common neurodegenerative disorders, may start from the gut enteric nervous system and then spread to the central dopaminergic neurons through the gut-brain axis. With the advent of metagenomic sequencing and metabolomic analysis, a plethora of evidence has revealed different gut microbiomes and gut metabolites in patients with PD compared with unaffected controls. Currently, although dopaminergic treatments and deep brain stimulation can provide some symptomatic benefits for motor symptoms of the disease, their long-term use is problematic. A mechanism-targeted therapy to halt the neurodegeneration is lacking. The recently observed gut microenvironmental changes in the early stages of the disease play a vital role in the PD pathogenesis. Patients whose disease begins in the gut may benefit most from interventions that target the gut microenvironments. In this review, we will summarize the current studies demonstrating multifunctional roles of gut microbiota in the gut-brain axis of PD and the currently available evidence for targeting the gut microbiota as a novel approach to potential disease-modifying therapy in PD.}, } @article {pmid36182197, year = {2023}, author = {Zhang, L and Lan, S and Dou, Q and Hao, S and Wang, Y and Wang, X and Zhang, R and Peng, Y and Yang, J}, title = {Metagenomic insights into responses of microbial population and key functional genes to fulvic acid during partial nitritation.}, journal = {Journal of environmental sciences (China)}, volume = {124}, number = {}, pages = {952-962}, doi = {10.1016/j.jes.2022.03.003}, pmid = {36182197}, issn = {1001-0742}, mesh = {*Ammonium Compounds/metabolism ; Bacteria/genetics/metabolism ; Benzopyrans ; Bioreactors/microbiology ; Metagenomics ; NAD/metabolism ; Nitrites/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Oxygen/metabolism ; *Sewage/microbiology ; }, abstract = {The long-term impact of fulvic acid (FA) on partial nitritation (PN) system was initially examined in this study. The obtained results revealed that the FA lower than 50 mg/L had negligible effect on the nitrite accumulation rate (NAR nearly 100%) and ammonium removal rate (ARR 56.85%), while FA over 50 mg/L decreased ARR from 56.85% to 0.7%. Sludge characteristics analysis found that appropriate FA (<50 mg/L) exposure promoted the settling performance and granulation of PN sludge by removing Bacteroidetes and accumulating Chloroflexi. The analysis of metagenomics suggested that the presence of limited FA (0-50 mg/L) stimulated the generation of NADH, which favors the denitrification and nitrite reduction. The negative impact of FA on the PN system could be divided into two stages. Initially, limited FA (50-120 mg/L) was decomposed by Anaerolineae to stimulate the growth and propagation of heterotrophic bacteria (Thauera). Increasing heterotrophs competed with AOB (Nitrosomonas) for dissolved oxygen, causing AOB to be eliminated and ARR to declined. Subsequently, when FA dosage was over 120 mg/L, Anaerolineae were inhibited and heterotrophic bacteria reduced, resulting in the abundance of AOB recovered. Nevertheless, the ammonium transformation pathway was suppressed because genes amoABC and hao were obviously reduced, leading to the deterioration of reactor performance. Overall, these results provide theoretical guidance for the practical application of PN for the treatment of FA-containing sewage.}, } @article {pmid36181827, year = {2023}, author = {Chen, JS and Hussain, B and Tsai, HC and Nagarajan, V and Koner, S and Hsu, BM}, title = {Analysis and interpretation of hot springs water, biofilms, and sediment bacterial community profiling and their metabolic potential in the area of Taiwan geothermal ecosystem.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 1}, pages = {159115}, doi = {10.1016/j.scitotenv.2022.159115}, pmid = {36181827}, issn = {1879-1026}, mesh = {*Hot Springs/microbiology ; Ecosystem ; RNA, Ribosomal, 16S/genetics ; Water/chemistry ; Taiwan ; Bacteria/genetics ; Biofilms ; *Metals, Heavy ; Sulfates ; }, abstract = {Microorganisms developed a mechanism that copes with heat, acidity, and high dissolved metal concentrations that likely first evolved. The geothermal fluids emerging in the geothermal springs of Taiwan, located at a subduction zone, are still under signs of progress in the characterization of the various microbial taxonomic changes over time. However, no systematic studies have been performed to compare water, biofilms, and sediment bacterial communities and the primary driving force of dissolved and mineral substrates capable of supporting microbial metabolism. In this study, 16S rRNA gene sequencing was employed for bacterial community exploration, and their potential metabolic pathways involved from water, biofilms, and sediment samples, collected from the geothermal valley (Ti-re-ku). Metagenomic data revealed that the water samples had higher bacterial diversity and richness than biofilms and sediment samples. At the genus level, Alicyclobacillus, Thiomonas, Acidocella, Metallibacterium, Picrophilus, and Legionella were significantly abundant in the water samples. The biofilms were rich in Aciditerrimonas, Bacillus, Acidithiobacillus, and Lysinibacillus, whereas the sediment samples were abundant in Sulfobacillus. The PICRUSt2-predicted functional results revealed that heavy metal-related functions such as heavy-metal exporter system, cobalt‑zinc‑cadmium resistance, arsenical pump, high-affinity nickel-transport, and copper resistance metabolisms were significant in the water samples. Moreover, sulfur-related pathways such as thiosulfate oxidation, dissimilatory sulfate reduction, and assimilatory sulfate reduction were important in water samples, followed by biofilms and sediment. Therefore, our findings highlighted the comparative taxonomic diversity and functional composition contributions to geothermal fluid, with implications for understanding the evolution and ecological niche dimension of microbes which are the key to geothermal ecosystem function.}, } @article {pmid36181699, year = {2023}, author = {Hu, M and Le, Y and Sardans, J and Yan, R and Zhong, Y and Sun, D and Tong, C and Peñuelas, J}, title = {Moderate salinity improves the availability of soil P by regulating P-cycling microbial communities in coastal wetlands.}, journal = {Global change biology}, volume = {29}, number = {1}, pages = {276-288}, doi = {10.1111/gcb.16465}, pmid = {36181699}, issn = {1365-2486}, support = {SGR2017-1005//Catalan Government/ ; CIVP20A6621//Fundación Ramón Areces/ ; 42171102//National Natural Science Foundation of China/ ; 2021J01177//Natural Science Foundation of Fujian Province/ ; PID2020-115770RB-I00//Spanish Government/ ; }, mesh = {*Wetlands ; Soil ; Salinity ; *Microbiota ; Fresh Water ; }, abstract = {Accelerated sea-level rise is expected to cause the salinization of freshwater wetlands, but the responses to salinity of the availability of soil phosphorus (P) and of microbial genes involved in the cycling of P remain unexplored. We conducted a field experiment to investigate the effects of salinity on P cycling by soil microbial communities and their regulatory roles on P availability in coastal freshwater and brackish wetlands. Salinity was positively correlated with P availability, with higher concentrations of labile P but lower concentrations of moderately labile P in the brackish wetland. The diversity and richness of microbial communities involved in P cycling were higher in the brackish wetland than the freshwater wetland. Salinity substantially altered the composition of the P-cycling microbial community, in which those of the brackish wetland were separated from those of the freshwater wetland. Metagenomic sequence analysis indicated that functional genes involved in the solubilization of inorganic P and the subsequent transport and regulation of P were more abundant in coastal soils. The relative abundances of most of the target genes differed between the wetlands, with higher abundances of P-solubilization (gcd and ppa) and -mineralization (phoD, phy, and ugpQ) genes and lower abundances of P-transport genes (pstB, ugpA, ugpB, ugpE, and pit) in the brackish wetland. A significant positive correlation between the concentration of labile P and the abundances of the target genes suggested that salinity may, at least in part, improve P availability by regulating the P-cycling microbial community. Our results suggest that the P-cycling microbial community abundance and P availability respond positively to moderate increases in salinity by promoting the microbial solubilization and mineralization of soil P. Changes in microbial communities and microbially mediated P cycling may represent microbial strategies to adapt to moderate salinity levels, which in turn control soil function and nutrient balance.}, } @article {pmid36181435, year = {2022}, author = {Zhang, X and Huang, Y and Liu, Y and Xu, W and Pan, J and Zheng, X and Du, H and Zhang, C and Lu, Z and Zou, D and Liu, Z and Cai, M and Xiong, J and Zhu, Y and Dong, Z and Jiang, H and Dong, H and Jiang, J and Luo, Z and Huang, L and Li, M}, title = {An Ancient Respiratory System in the Widespread Sedimentary Archaea Thermoprofundales.}, journal = {Molecular biology and evolution}, volume = {39}, number = {10}, pages = {}, pmid = {36181435}, issn = {1537-1719}, mesh = {*Archaea/genetics/metabolism ; *Hydrogenase/chemistry/genetics/metabolism ; Sodium Chloride/metabolism ; Phylogeny ; Respiratory System/metabolism ; Amino Acids/genetics ; Antiporters/genetics/metabolism ; }, abstract = {Thermoprofundales, formerly Marine Benthic Group D (MBG-D), is a ubiquitous archaeal lineage found in sedimentary environments worldwide. However, its taxonomic classification, metabolic pathways, and evolutionary history are largely unexplored because of its uncultivability and limited number of sequenced genomes. In this study, phylogenomic analysis and average amino acid identity values of a collection of 146 Thermoprofundales genomes revealed five Thermoprofundales subgroups (A-E) with distinct habitat preferences. Most of the microorganisms from Subgroups B and D were thermophiles inhabiting hydrothermal vents and hot spring sediments, whereas those from Subgroup E were adapted to surface environments where sunlight is available. H2 production may be featured in Thermoprofundales as evidenced by a gene cluster encoding the ancient membrane-bound hydrogenase (MBH) complex. Interestingly, a unique structure separating the MBH gene cluster into two modular units was observed exclusively in the genomes of Subgroup E, which included a peripheral arm encoding the [NiFe] hydrogenase domain and a membrane arm encoding the Na+/H+ antiporter domain. These two modular structures were confirmed to function independently by detecting the H2-evolving activity in vitro and salt tolerance to 0.2 M NaCl in vivo, respectively. The peripheral arm of Subgroup E resembles the proposed common ancestral respiratory complex of modern respiratory systems, which plays a key role in the early evolution of life. In addition, molecular dating analysis revealed that Thermoprofundales is an early emerging archaeal lineage among the extant MBH-containing microorganisms, indicating new insights into the evolution of this ubiquitous archaea lineage.}, } @article {pmid36181424, year = {2023}, author = {Soldatos, A and Nutman, TB and Johnson, T and Dowell, SF and Sejvar, JJ and Wilson, MR and DeRisi, JL and Inati, SK and Groden, C and Evans, C and O'Connell, EM and Toliva, BO and Aceng, JR and Aryek-Kwe, J and Toro, C and Stratakis, CA and Buckler, AG and Cantilena, C and Palmore, TN and Thurm, A and Baker, EH and Chang, R and Fauni, H and Adams, D and Macnamara, EF and Lau, CC and Malicdan, MCV and Pusey-Swerdzewski, B and Downing, R and Bunga, S and Thomas, JD and Gahl, WA and Nath, A}, title = {Genomic analysis, immunomodulation and deep phenotyping of patients with nodding syndrome.}, journal = {Brain : a journal of neurology}, volume = {146}, number = {3}, pages = {968-976}, pmid = {36181424}, issn = {1460-2156}, support = {K08NS096117//Mentored Clinical Scientist Development/ ; }, mesh = {United States ; Humans ; *Nodding Syndrome ; Cohort Studies ; *Onchocerciasis ; Immunomodulation ; Genomics ; }, abstract = {The aetiology of nodding syndrome remains unclear, and comprehensive genotyping and phenotyping data from patients remain sparse. Our objectives were to characterize the phenotype of patients with nodding syndrome, investigate potential contributors to disease aetiology, and evaluate response to immunotherapy. This cohort study investigated members of a single-family unit from Lamwo District, Uganda. The participants for this study were selected by the Ugandan Ministry of Health as representative for nodding syndrome and with a conducive family structure for genomic analyses. Of the eight family members who participated in the study at the National Institutes of Health (NIH) Clinical Center, three had nodding syndrome. The three affected patients were extensively evaluated with metagenomic sequencing for infectious pathogens, exome sequencing, spinal fluid immune analyses, neurometabolic and toxicology testing, continuous electroencephalography and neuroimaging. Five unaffected family members underwent a subset of testing for comparison. A distinctive interictal pattern of sleep-activated bursts of generalized and multifocal epileptiform discharges and slowing was observed in two patients. Brain imaging showed two patients had mild generalized cerebral atrophy, and both patients and unaffected family members had excessive metal deposition in the basal ganglia. Trace metal biochemical evaluation was normal. CSF was non-inflammatory and one patient had CSF-restricted oligoclonal bands. Onchocerca volvulus-specific antibodies were present in all patients and skin snips were negative for active onchocerciasis. Metagenomic sequencing of serum and CSF revealed hepatitis B virus in the serum of one patient. Vitamin B6 metabolites were borderline low in all family members and CSF pyridoxine metabolites were normal. Mitochondrial DNA testing was normal. Exome sequencing did not identify potentially causal candidate gene variants. Nodding syndrome is characterized by a distinctive pattern of sleep-activated epileptiform activity. The associated growth stunting may be due to hypothalamic dysfunction. Extensive testing years after disease onset did not clarify a causal aetiology. A trial of immunomodulation (plasmapheresis in two patients and intravenous immunoglobulin in one patient) was given without short-term effect, but longer-term follow-up was not possible to fully assess any benefit of this intervention.}, } @article {pmid36181381, year = {2022}, author = {Ma, X and Brinker, E and Cao, W and Graff, EC and Wang, X}, title = {Effect of mineral oil as a lubricant to collect feces from cats for microbiome studies.}, journal = {Journal of veterinary internal medicine}, volume = {36}, number = {6}, pages = {1974-1980}, pmid = {36181381}, issn = {1939-1676}, support = {//Alabama Agriculture Experiment Station/ ; //Auburn University College of Veterinary Medicine Animal Health and Disease Research/ ; 180254//Auburn University Intramural Grant Program/ ; EC22-023//EveryCat Health Foundation/ ; 1928770//National Science Foundation/ ; 1018100//USDA National Institute of Food and Agriculture/ ; }, mesh = {Male ; Cats ; Animals ; *Mineral Oil ; Lubricants ; Cohort Studies ; Feces ; *Microbiota ; DNA ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Fecal specimens are critical for disease screening, diagnosis, and gut microbiome research. For domestic cats, lubricants are often necessary to obtain a sufficient quantity of sample. However, the effect of lubrication on feline microbiome analysis has not been assessed.

OBJECTIVES: To evaluate if lubrication using mineral oil during cat feces sample collection affects the DNA extraction, metagenomic sequencing yield, and the microbial composition and diversity in subsequent gut microbiome analyses.

ANIMALS: Eight 6-year-old male, neutered, domestic short-haired cats housed in a research facility.

METHODS: Cohort study. The gut microbiomes were investigated for fecal sample collection with and without lubrication using whole-genome shotgun metagenomic sequencing.

RESULTS: Fecal specimens were collected using a fecal loop under sedation without lubrication and with mineral oil lubrication. There were no significant differences between the 2 groups in the microbial DNA yield in ng/mg fecal sample (75.75 [25.8-125.7] vs 60.72 [33.49-87.95], P = .95), metagenomic sequencing yield in Gbp (10.31 [6.29-14.32] vs 13.53 [12.04-15.02], P = .2), proportion of host contamination (0.1 [0.02-0.18] vs 0.15 [0-0.3], P = .84), relative taxonomy abundance (P > .8), or the number of microbial genes covered (408 132 [341 556-474 708] vs 425 697 [358 505-492 889], P = .31).

Fecal sampling with mineral oil lubrication did not change the microbial DNA extraction yield, metagenomic sequencing yield, level of host contamination, the microbial composition and diversity in subsequent gut microbiome analyses. Here we reported a proven cat-friendly protocol for fecal sample collection in clinical and research setting for gut microbiome analyses.}, } @article {pmid36180859, year = {2022}, author = {Wang, J and Ye, J and Yang, L and Chen, X and Fang, H and Liu, Z and Xia, G and Zhang, Y and Zhang, Z}, title = {Inconsistency analysis between metagenomic next-generation sequencing results of cerebrospinal fluid and clinical diagnosis with suspected central nervous system infection.}, journal = {BMC infectious diseases}, volume = {22}, number = {1}, pages = {764}, pmid = {36180859}, issn = {1471-2334}, support = {2108085MH298//Anhui Provincial Natural Science Foundation/ ; 2019GMFY02, 2021lcxk027//the Scientific research project of the Second Hospital of Anhui Medical University/ ; }, mesh = {*Central Nervous System Infections/diagnosis ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenomics/methods ; Retrospective Studies ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Recently, with the rapid progress of metagenomic next-generation sequencing (mNGS), inconsistency between mNGS results and clinical diagnoses has become more common. There is currently no reasonable explanation for this, and the interpretation of mNGS reports still needs to be standardised.

METHODS: A retrospective analysis was conducted on 47 inpatients with suspected central nervous system (CNS) infections, and clinical data were recorded. The final diagnosis was determined by an expert group based on the patient's clinical manifestation, laboratory examination, and response to treatment. mNGS results were compared with the final diagnosis, and any inconsistencies that occurred were investigated. Finally, the credibility of mNGS results was evaluated using the integral approach, which consists of three parts: typical clinical features, positive results with the traditional method, and cerebrospinal fluid cells ≥ 100 (× 10[6]/L) or protein ≥ 500 mg/L, with one point for each item.

RESULTS: Forty-one patients with suspected CNS infection were assigned to infected (ID, 31/41, 75.61%) and non-infected groups (NID, 10/41, 24.39%) after assessment by a panel of experts according to the composite diagnostic criteria. For mNGS-positive results, 20 of the 24 pathogens were regarded as contaminants when the final score was ≤ 1. The remaining 11 pathogens detected by mNGS were all true positives, which was consistent with the clinical diagnosis when the score was ≥ 2. For mNGS negative results, when the score was ≥ 2, the likelihood of infection may be greater than when the score is ≤ 1.

CONCLUSION: The integral method is effective for evaluating mNGS results. Regardless of whether the mNGS result was positive or negative, the possibility of infection was greater when the score was ≥ 2. A negative mNGS result does not necessarily indicate that the patient was not clinically infected, and, therefore, clinical features are more important.}, } @article {pmid36180850, year = {2022}, author = {Flint, A and Laidlaw, A and Li, L and Raitt, C and Rao, M and Cooper, A and Weedmark, K and Carrillo, C and Tamber, S}, title = {Choice of DNA extraction method affects detection of bacterial taxa from retail chicken breast.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {230}, pmid = {36180850}, issn = {1471-2180}, mesh = {Animals ; *Bacteria ; *Chickens ; DNA, Bacterial/analysis ; High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; Real-Time Polymerase Chain Reaction ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Sequence-based methods for the detection of bacteria such as 16S rRNA amplicon sequencing and metagenomics can provide a comprehensive view of the bacterial microbiome of food. These methods rely on the detection of gene sequences to indicate the presence of viable bacteria. This indirect form of detection can be prone to experimental artefacts. Sample handling and processing are key sources of variation that require standard approaches. Extracting sufficient quantities of high quality DNA from food matrices is challenging because target bacterial species are usually minor components of the microbiota and foods contain an array of compounds that are inhibitory to downstream DNA applications. Here, three DNA extraction methods are compared for their ability to extract high quality bacterial DNA from retail chicken breast rinses, with or without enrichment. Method performance was assessed by comparing ease of use, DNA yield, DNA quality, PCR amplicon yield, and the detection of bacterial taxa by 16S rRNA amplicon sequencing.

RESULTS: All three DNA extraction methods yielded DNA of sufficient quantity and quality to perform quantitative PCR and 16S rRNA amplicon sequencing. The extraction methods differed in ease of use, with the two commercial kits (PowerFood, PowerSoil) offering considerable time and cost savings over a hybrid method that used laboratory reagents for lysis and commercial column based kits for further purification. Bacterial richness as determined by 16S rRNA amplicon sequencing was similar across the three DNA extraction methods. However, differences were noted in the relative abundance of bacterial taxa, with significantly higher abundance of Gram-positive genera detected in the DNA samples prepared using the PowerFood DNA extraction kit.

CONCLUSION: The choice of DNA extraction method can affect the detection of bacterial taxa by 16S rRNA amplicon sequencing in chicken meat rinses. Investigators should be aware of this procedural bias and select methods that are fit for the purposes of their investigation.}, } @article {pmid36180580, year = {2022}, author = {McDowell, A and Kang, J and Yang, J and Jung, J and Oh, YM and Kym, SM and Shin, TS and Kim, TB and Jee, YK and Kim, YK}, title = {Machine-learning algorithms for asthma, COPD, and lung cancer risk assessment using circulating microbial extracellular vesicle data and their application to assess dietary effects.}, journal = {Experimental & molecular medicine}, volume = {54}, number = {9}, pages = {1586-1595}, pmid = {36180580}, issn = {2092-6413}, mesh = {Algorithms ; Animals ; *Asthma/diagnosis/etiology ; *Extracellular Vesicles ; *Lung Neoplasms/etiology ; Machine Learning ; Mice ; *Pulmonary Disease, Chronic Obstructive ; Risk Assessment ; }, abstract = {Although mounting evidence suggests that the microbiome has a tremendous influence on intractable disease, the relationship between circulating microbial extracellular vesicles (EVs) and respiratory disease remains unexplored. Here, we developed predictive diagnostic models for COPD, asthma, and lung cancer by applying machine learning to microbial EV metagenomes isolated from patient serum and coded by their accumulated taxonomic hierarchy. All models demonstrated high predictive strength with mean AUC values ranging from 0.93 to 0.99 with various important features at the genus and phylum levels. Application of the clinical models in mice showed that various foods reduced high-fat diet-associated asthma and lung cancer risk, while COPD was minimally affected. In conclusion, this study offers a novel methodology for respiratory disease prediction and highlights the utility of serum microbial EVs as data-rich features for noninvasive diagnosis.}, } @article {pmid36180320, year = {2023}, author = {Huss, P and Chen, J and Raman, S}, title = {High-throughput approaches to understand and engineer bacteriophages.}, journal = {Trends in biochemical sciences}, volume = {48}, number = {2}, pages = {187-197}, pmid = {36180320}, issn = {0968-0004}, support = {R21 AI156785/AI/NIAID NIH HHS/United States ; T32 GM135066/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteriophages/genetics ; Genome, Viral ; }, abstract = {Bacteriophage research has been vital to fundamental aspects of modern biology. Advances in metagenomics have revealed treasure troves of new and uncharacterized bacteriophages ('phages') that are not yet understood. However, our ability to find new phages has outpaced our understanding of how sequence encodes function in phages. Traditional approaches for characterizing phages are limited in scale and face hurdles in determining how changes in sequence drive function. We describe powerful emerging technologies that can be used to clarify sequence-function relationships in phages through high-throughput genome engineering. Using these approaches, up to 10[5] variants can be characterized through pooled selection experiments and deep sequencing. We describe caveats when using these tools and provide examples of basic science and engineering goals that are pursuable using these approaches.}, } @article {pmid36179843, year = {2023}, author = {Yu, X and Chen, H and Liu, Y and Yu, L and Wang, K and Xue, G}, title = {Iron scraps packing rapidly enhances nitrogen removal in an aerobic sludge system and the mechanism.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 1}, pages = {159081}, doi = {10.1016/j.scitotenv.2022.159081}, pmid = {36179843}, issn = {1879-1026}, mesh = {*Sewage ; *Nitrogen ; Denitrification ; Iron ; Bioreactors ; Nitrification ; Wastewater ; }, abstract = {Simultaneous nitrification and denitrification (SND) has the advantage of energy saving and carbon demand reduction. Here, readily available low-cost iron scraps packing was added to an aerobic sludge system. This successfully enhanced the efficiency of total nitrogen removal from 37.7 ± 13.2 % to 62.7 ± 7.9 % over 2 days. While electrons from iron biocorrosion did not contribute to nitrate reduction, iron promoted heterotrophic denitrification. The iron scraps changed the spatial distribution of the microbial community, where more denitrification bacteria accumulated around the packing and higher denitrification capacity was noted. Metagenomic analysis of the sludge cultured in the presence of iron scraps for 2 days revealed that, with the exception of the enriched amoA/B/C gene expression, the abundance of other key nitrogen removal genes showed little variation. Furthermore, the structure of the microbial community was unchanged probably due to the relatively short culturing period. However, metatranscriptomic analysis indicated that iron increased the abundance of nitrifying bacteria (i.e. unclassified Nitrosomonas, Nitrosomonas sp. Is79A3 and Nitrospira defluvii) and promoted higher expression of nitrification genes. Notably, iron scraps packing decreased the abundance of the key denitrification bacteria Thauera sp. MZ1T from 52.92 to 7.58 %. The expression of napA/B also decreased, while expression of narG/H/I increased by 9 to 23 fold and a 2 to 3 fold over expression was noted for nirS, norB/C and nosZ in the presence of iron scraps. This suggested that aerobic denitrification was inhibited and anaerobic denitrification was promoted. This study has provided in-depth understanding of the influence of iron on SND to improve the application of iron-supported biological processes.}, } @article {pmid36179670, year = {2022}, author = {Narunsky-Haziza, L and Sepich-Poore, GD and Livyatan, I and Asraf, O and Martino, C and Nejman, D and Gavert, N and Stajich, JE and Amit, G and González, A and Wandro, S and Perry, G and Ariel, R and Meltser, A and Shaffer, JP and Zhu, Q and Balint-Lahat, N and Barshack, I and Dadiani, M and Gal-Yam, EN and Patel, SP and Bashan, A and Swafford, AD and Pilpel, Y and Knight, R and Straussman, R}, title = {Pan-cancer analyses reveal cancer-type-specific fungal ecologies and bacteriome interactions.}, journal = {Cell}, volume = {185}, number = {20}, pages = {3789-3806.e17}, pmid = {36179670}, issn = {1097-4172}, support = {DP1 AT010885/AT/NCCIH NIH HHS/United States ; U24 CA248454/CA/NCI NIH HHS/United States ; P50 DA026306/DA/NIDA NIH HHS/United States ; U24 DK131617/DK/NIDDK NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; F30 CA243480/CA/NCI NIH HHS/United States ; P01 DA012065/DA/NIDA NIH HHS/United States ; R00 AA020235/AA/NIAAA NIH HHS/United States ; P30 MH062512/MH/NIMH NIH HHS/United States ; HHSN261201500003I/CA/NCI NIH HHS/United States ; HHSN261201400008C/CA/NCI NIH HHS/United States ; }, mesh = {DNA, Fungal/analysis ; Fungi/genetics ; Humans ; *Mycobiome ; *Neoplasms ; }, abstract = {Cancer-microbe associations have been explored for centuries, but cancer-associated fungi have rarely been examined. Here, we comprehensively characterize the cancer mycobiome within 17,401 patient tissue, blood, and plasma samples across 35 cancer types in four independent cohorts. We report fungal DNA and cells at low abundances across many major human cancers, with differences in community compositions that differ among cancer types, even when accounting for technical background. Fungal histological staining of tissue microarrays supported intratumoral presence and frequent spatial association with cancer cells and macrophages. Comparing intratumoral fungal communities with matched bacteriomes and immunomes revealed co-occurring bi-domain ecologies, often with permissive, rather than competitive, microenvironments and distinct immune responses. Clinically focused assessments suggested prognostic and diagnostic capacities of the tissue and plasma mycobiomes, even in stage I cancers, and synergistic predictive performance with bacteriomes.}, } @article {pmid36179649, year = {2022}, author = {Liu, J and Wang, J and Zhou, Y and Han, H and Liu, W and Li, D and Li, F and Cao, D and Lei, Q}, title = {Integrated omics analysis reveals differences in gut microbiota and gut-host metabolite profiles between obese and lean chickens.}, journal = {Poultry science}, volume = {101}, number = {11}, pages = {102165}, pmid = {36179649}, issn = {1525-3171}, mesh = {Animals ; *Chickens ; *Gastrointestinal Microbiome ; Obesity/genetics/veterinary ; Abdominal Fat/metabolism ; Adipose Tissue/metabolism ; }, abstract = {Abdominal fat is the major adipose tissue in chickens. In chicken, the deposition of abdominal fat affects meat yield and quality. Previous reports suggest that gut microbiota composition and function are associated with lipid metabolism. In this study, we used comparative metagenomics and metabolomics analysis to determine the gut microbiota and gut-host metabolite profiles in Shouguang (SG; a Chinese chicken breed with low-fat deposition) and Luqin (LQ; a fatty-type chicken breed with a fast growth rate) chickens. The results showed that LQ chickens had higher body weight, eviscerated yield, abdominal fat yield, abdominal fat ratio, and triglyceride (TG) content in the breast muscle than SG chickens. Untargeted metabolomics analyses showed a total of 11 liver metabolites, 19 plasma metabolites, and 30 cecal metabolites differentially enriched in LQ and SG chickens based on variable importance in the projection (VIP) ≥ 1 and P ≤ 0.05. These metabolites are involved in lipid and amino acid metabolism. The relative abundance of bacteria in the microbiota differed significantly between the 2 chicken breeds. The functional prediction of microbiota abundant in LQ chickens was starch and lactose degradation. Erysipelatoclostridium was abundant in LQ chickens and significantly positively correlated to palmitoyl ethanolamide (PEA), a key regulator of lipid metabolism. Our findings revealed differences in liver and plasma metabolites between chicken breeds with different adipose deposition capacities. Long-chain acylcarnitines might be important markers of adipose deposition differences in chickens. The cecum's microbial communities and metabolome profiles significantly differed between LQ and SG chickens. However, the relationship between cecal microbiota and their metabolites and liver and plasma metabolites is not thoroughly understood. Future research will focus on relating tissue metabolite changes to intestinal microbiota and their effects on body fat deposition.}, } @article {pmid36179077, year = {2022}, author = {Douglas, GM and Hayes, MG and Langille, MGI and Borenstein, E}, title = {Integrating phylogenetic and functional data in microbiome studies.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {22}, pages = {5055-5063}, pmid = {36179077}, issn = {1367-4811}, mesh = {Phylogeny ; *Microbiota/genetics ; Metagenomics ; Software ; }, abstract = {MOTIVATION: Microbiome functional data are frequently analyzed to identify associations between microbial functions (e.g. genes) and sample groups of interest. However, it is challenging to distinguish between different possible explanations for variation in community-wide functional profiles by considering functions alone. To help address this problem, we have developed POMS, a package that implements multiple phylogeny-aware frameworks to more robustly identify enriched functions.

RESULTS: The key contribution is an extended balance-tree workflow that incorporates functional and taxonomic information to identify functions that are consistently enriched in sample groups across independent taxonomic lineages. Our package also includes a workflow for running phylogenetic regression. Based on simulated data we demonstrate that these approaches more accurately identify gene families that confer a selective advantage compared with commonly used tools. We also show that POMS in particular can identify enriched functions in real-world metagenomics datasets that are potential targets of strong selection on multiple members of the microbiome.

These workflows are freely available in the POMS R package at https://github.com/gavinmdouglas/POMS.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36179022, year = {2022}, author = {Nair, S and Zhang, Z and Li, H and Zhao, H and Shen, H and Kao, SJ and Jiao, N and Zhang, Y}, title = {Inherent tendency of Synechococcus and heterotrophic bacteria for mutualism on long-term coexistence despite environmental interference.}, journal = {Science advances}, volume = {8}, number = {39}, pages = {eabf4792}, pmid = {36179022}, issn = {2375-2548}, abstract = {Mutualism between Synechococcus and heterotrophic bacteria has been found to support their prolonged survival in nutrient-depleted conditions. However, environmental interference on the fate of their mutualism is not understood. Here, we show that exogenous nutrients disrupt their established mutualism. Once the exogenous nutrients were exhausted, Synechococcus and heterotrophic bacteria gradually reestablished their metabolic mutualism during 450 days of culture, which revived unhealthy Synechococcus cells. Using metagenomics, metatranscriptomics, and the [15]N tracer method, we reveal that the associated bacterial nitrogen fixation triggered the reestablishment of the mutualism and revival of Synechococcus health. During this process, bacterial community structure and functions underwent tremendous adjustments to achieve the driving effect, and a cogeneration of nitrogen, phosphorus, iron, and vitamin by the heterotrophic bacteria sustained Synechococcus's prolonged healthy growth. Our findings suggest that Synechococcus and heterotrophic bacteria may have an inherent tendency toward mutualism despite environmental interference. This may exhibit their coevolutionary adaptations in nutrient-deficient environments.}, } @article {pmid36178961, year = {2022}, author = {Jung, TH and Hwang, HJ and Han, KS}, title = {Correlation of attention deficit hyperactivity disorder with gut microbiota according to the dietary intake of Korean elementary school students.}, journal = {PloS one}, volume = {17}, number = {9}, pages = {e0275520}, pmid = {36178961}, issn = {1932-6203}, mesh = {Animals ; *Attention Deficit Disorder with Hyperactivity/epidemiology ; Butyrates ; Eating ; Fatty Acids, Volatile ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Republic of Korea/epidemiology ; Students ; }, abstract = {We investigated the impact of dietary patterns on the gut microbiota and concentration of short-chain fatty acids in the feces of Korean elementary school students. The dietary intake and ADHD assessment of 40 Korean elementary school students were analyzed using a dish-based semi-quantitative food frequency questionnaire. Analysis of gut microbiota and short-chain fatty acids composition were performed using the real-time polymerase chain reaction, metagenomics, and gas chromatography methods. The dietary patterns of participants were divided into four groups: healthy, processed food, fish and shellfish, and meat. The participants were also divided into two groups according to their ADHD scores: 0-30, control group; over 30, ADHD group. The ADHD score of the processed food group was significantly higher than that of the healthy group. The processed food and ADHD groups showed significantly higher abundance of harmful bacteria, such as the Enterobacter, Escherichia coli, and Clostridium strains, and markedly lower abundance of beneficial bacteria, such as the Bifidobacterium and Ruminococcus strains, than the control group. The heat maps of metagenomics indicated that each group was separated into distinct clusters, and the processed food and ADHD groups showed significantly lower α-diversity of gut microbiota than the control group. In these groups, the concentration of acetate or butyrate in the feces was significantly lower than that in the control group. These results may indicate that imbalanced diets can disturb the colonic microbial balance and are likely to become a potential risk factor for the prevalence of ADHD.}, } @article {pmid36178955, year = {2022}, author = {Dimopoulos, EA and Carmagnini, A and Velsko, IM and Warinner, C and Larson, G and Frantz, LAF and Irving-Pease, EK}, title = {HAYSTAC: A Bayesian framework for robust and rapid species identification in high-throughput sequencing data.}, journal = {PLoS computational biology}, volume = {18}, number = {9}, pages = {e1010493}, pmid = {36178955}, issn = {1553-7358}, support = {210119/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Algorithms ; Bayes Theorem ; *DNA, Ancient ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {Identification of specific species in metagenomic samples is critical for several key applications, yet many tools available require large computational power and are often prone to false positive identifications. Here we describe High-AccuracY and Scalable Taxonomic Assignment of MetagenomiC data (HAYSTAC), which can estimate the probability that a specific taxon is present in a metagenome. HAYSTAC provides a user-friendly tool to construct databases, based on publicly available genomes, that are used for competitive read mapping. It then uses a novel Bayesian framework to infer the abundance and statistical support for each species identification and provide per-read species classification. Unlike other methods, HAYSTAC is specifically designed to efficiently handle both ancient and modern DNA data, as well as incomplete reference databases, making it possible to run highly accurate hypothesis-driven analyses (i.e., assessing the presence of a specific species) on variably sized reference databases while dramatically improving processing speeds. We tested the performance and accuracy of HAYSTAC using simulated Illumina libraries, both with and without ancient DNA damage, and compared the results to other currently available methods (i.e., Kraken2/Bracken, KrakenUniq, MALT/HOPS, and Sigma). HAYSTAC identified fewer false positives than both Kraken2/Bracken, KrakenUniq and MALT in all simulations, and fewer than Sigma in simulations of ancient data. It uses less memory than Kraken2/Bracken, KrakenUniq as well as MALT both during database construction and sample analysis. Lastly, we used HAYSTAC to search for specific pathogens in two published ancient metagenomic datasets, demonstrating how it can be applied to empirical datasets. HAYSTAC is available from https://github.com/antonisdim/HAYSTAC.}, } @article {pmid36177468, year = {2022}, author = {Van Cauwenberghe, J and Santamaría, RI and Bustos, P and González, V}, title = {Novel lineages of single-stranded DNA phages that coevolved with the symbiotic bacteria Rhizobium.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {990394}, pmid = {36177468}, issn = {1664-302X}, abstract = {This study describes novel single-stranded DNA phages isolated from common bean agriculture soils by infection of the nitrogen-fixing symbiotic bacteria Rhizobium etli and R. phaseoli. A total of 29 phages analyzed have 4.3-6 kb genomes in size and GC 59-60%. They belong to different clades unrelated to other Microviridae subfamilies. Three-dimensional models of the major capsid protein (MCP) showed a conserved β-barrel structural "jelly-roll" fold. A variable-length loop in the MCPs distinguished three Rhizobium microvirus groups. Microviridae subfamilies were consistent with viral clusters determined by the protein-sharing network. All viral clusters, except for Bullavirinae, included mostly microviruses identified in metagenomes from distinct ecosystems. Two Rhizobium microvirus clusters, chaparroviruses, and chicoviruses, were included within large viral unknown clusters with microvirus genomes identified in diverse metagenomes. A third Rhizobium microvirus cluster belonged to the subfamily Amoyvirinae. Phylogenetic analysis of the MCP confirms the divergence of the Rhizobium microviruses into separate clades. The phylogeny of the bacterial hosts matches the microvirus MCP phylogeny, suggesting a coevolutionary history between the phages and their bacterial host. This study provided essential biological information on cultivated microvirus for understanding the evolution and ecological diversification of the Microviridae family in diverse microbial ecosystems.}, } @article {pmid36177457, year = {2022}, author = {Tarracchini, C and Fontana, F and Mancabelli, L and Lugli, GA and Alessandri, G and Turroni, F and Ventura, M and Milani, C}, title = {Gut microbe metabolism of small molecules supports human development across the early stages of life.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1006721}, pmid = {36177457}, issn = {1664-302X}, abstract = {From birth to adulthood, the human gut-associated microbial communities experience profound changes in their structure. However, while the taxonomical composition has been extensively explored, temporal shifts in the microbial metabolic functionalities related to the metabolism of bioactive small molecules are still largely unexplored. Here, we collected a total of 6,617 publicly available human fecal shotgun metagenomes and 42 metatranscriptomes from infants and adults to explore the dynamic changes of the microbial-derived small molecule metabolisms according to the age-related development of the human gut microbiome. Moreover, by selecting metagenomic data from 250 breastfed and 217 formula-fed infants, we also investigated how feeding types can shape the metabolic functionality of the incipient gut microbiome. From the small molecule metabolism perspective, our findings suggested that the human gut microbial communities are genetically equipped and prepared to metabolically evolve toward the adult state as early as 1 month after birth, although at the age of 4 years, it still appeared functionally underdeveloped compared to adults. Furthermore, in respect of formula-fed newborns, breastfed infants showed enrichment in microbial metabolic functions related to specific amino acids present at low concentrations in human milk, highlighting that the infant gut microbiome has specifically evolved to synthesize bioactive molecules that can complement the human breast milk composition contributing to complete nutritional supply of infant.}, } @article {pmid36177060, year = {2022}, author = {Akond, Z and Rahman, H and Ahsan, MA and Mosharaf, MP and Alam, M and Mollah, MNH}, title = {Comprehensive In Silico Analysis of RNA Silencing-Related Genes and Their Regulatory Elements in Wheat (Triticum aestivum L.).}, journal = {BioMed research international}, volume = {2022}, number = {}, pages = {4955209}, pmid = {36177060}, issn = {2314-6141}, mesh = {Case-Control Studies ; Gene Expression Regulation, Plant/genetics ; Genes, Plant/genetics ; Hormones ; *MicroRNAs ; Phylogeny ; Plant Proteins/genetics/metabolism ; RNA Interference ; RNA, Small Interfering ; RNA-Dependent RNA Polymerase/genetics ; Stress, Physiological ; *Triticum/genetics/metabolism ; }, abstract = {Dicer-like (DCL), Argonaute (AGO), and RNA-dependent RNA polymerase (RDR) are known as the three major gene families that act as the critical components of RNA interference or silencing mechanisms through the noncoding small RNA molecules (miRNA and siRNA) to regulate the expressions of protein-coding genes in eukaryotic organisms. However, most of their characteristics including structures, chromosomal location, subcellular locations, regulatory elements, and gene networking were not rigorously studied. Our analysis identified 7 TaDCL, 39 TaAGO, and 16 TaRDR genes as RNA interference (RNAi) genes from the wheat genome. Phylogenetic analysis of predicted RNAi proteins with the RNAi proteins of Arabidopsis and rice showed that the predicted proteins of TaDCL, TaAGO, and TaRDR groups are clustered into four, eight, and four subgroups, respectively. Domain, 3D protein structure, motif, and exon-intron structure analyses showed that these proteins conserve identical characteristics within groups and maintain differences between groups. The nonsynonymous/synonymous mutation ratio (Ka/Ks) < 1 suggested that these protein sequences conserve some purifying functions. RNAi genes networking with TFs revealed that ERF, MIKC-MADS, C2H2, BBR-BPC, MYB, and Dof are the key transcriptional regulators of the predicted RNAi-related genes. The cis-regulatory element (CREs) analysis detected some important CREs of RNAi genes that are significantly associated with light, stress, and hormone responses. Expression analysis based on an online database exhibited that almost all of the predicted RNAi genes are expressed in different tissues and organs. A case-control study from the gene expression level showed that some RNAi genes significantly responded to the drought and heat stresses. Overall results would therefore provide an excellent basis for in-depth molecular investigation of these genes and their regulatory elements for wheat crop improvement against different stressors.}, } @article {pmid36176899, year = {2022}, author = {Ennis, NJ and Dharumadurai, D and Sevigny, JL and Wilmot, R and Alnaimat, SM and Bryce, JG and Thomas, WK and Tisa, LS}, title = {Draft Genomes Sequences of 11 Geodermatophilaceae Strains Isolated from Building Stones from New England and Indian Stone Ruins found at historic sites in Tamil Nadu, India.}, journal = {Journal of genomics}, volume = {10}, number = {}, pages = {69-77}, pmid = {36176899}, issn = {1839-9940}, abstract = {Metagenomic analysis of stone microbiome from samples collected in New England, USA and Tamil Nadu, India identified numerous Actinobacteria including Geodermatphilaceae. A culture-dependent approach was performed as a companion study with this culture-independent metagenomic analysis of these stone samples and resulted in the isolation of eleven Geodermatphilaceae strains (2 Geodermatophilus and 9 Blastococcus strains). The genomes of the 11 Geodermatphilaceae strains were sequenced and analyzed. The genomes for the two Geodermatophilus isolates, DF1-2 and TF2-6, were 4.45 and 4.75 Mb, respectively, while the Blastococcus genomes ranged in size from 3.98 to 5.48 Mb. Phylogenetic analysis, digital DNA:DNA hybridization (dDDH), and comparisons of the average nucleotide identities (ANI) suggest the isolates represent novel Geodermatophilus and Blastococcus species. Functional analysis of the Geodermatphilaceae genomes provides insight on the stone microbiome niche.}, } @article {pmid36176456, year = {2022}, author = {Zhang, C and Zhang, Y and Zhao, T and Mou, T and Jing, W and Chen, J and Hao, W and Gu, S and Cui, M and Sun, Y and Wei, B}, title = {Schisandrin alleviates the cognitive impairment in rats with Alzheimer's disease by altering the gut microbiota composition to modulate the levels of endogenous metabolites in the plasma, brain, and feces.}, journal = {Frontiers in pharmacology}, volume = {13}, number = {}, pages = {888726}, pmid = {36176456}, issn = {1663-9812}, abstract = {Schisandrin is one of the main active compounds isolated from the fruit of Schisandrae chinensis Fructus, which is scientifically proven to have beneficial effects on Alzheimer's disease (AD) treatment at the cellular and whole organism level. However, the oral availability of schisandrin is very low, thus implying that the underlying mechanism of therapeutic effect on AD treatment is yet to be clarified fully. Therefore, we speculated that the therapeutic effect of schisandrin on AD is mainly by regulating the imbalance of the gut microbiota (GM). In this study, behavioral experiments and H&E staining were used to confirm the pharmacological effects of schisandrin on rats with AD. 16S rDNA gene sequencing and feces, plasma, and brain metabolomics techniques were utilized to investigate the therapeutic effects and the underlying mechanisms of schisandrin on cognitive impairment in rats with AD. The results indicated that schisandrin improved cognitive impairment and hippocampal cell loss in rats. The UPLC-QTOF/MS-based metabolomics studies of the feces, plasma, and brain revealed that 44, 96, and 40 potential biomarkers, respectively, were involved in the treatment mechanism of schisandrin. Schisandrin improved the metabolic imbalance in rats with AD, and the metabolic changes mainly affected the primary bile acid biosynthesis, sphingolipid metabolism, glycerophospholipid metabolism, and unsaturated fatty acid biosynthesis. Schisandrin can improve the GM structure disorder and increase the abundance of beneficial bacteria in the gut of rats with AD. The predictive metagenomics analysis indicated that the altered GM was mainly involved in lipid metabolism, steroid hormone biosynthesis, arachidonic acid metabolism, biosynthesis of unsaturated fatty acids, and bacterial invasion of epithelial cells. Spearman's correlation analysis showed a significant correlation between affected bacteria and metabolites in various metabolic pathways. Overall, the data underline that schisandrin improves the cognitive impairment in rats with AD by affecting the composition of the GM community, thus suggesting the potential therapeutic effect of schisandrin on the brain-gut axis in rats with AD at the metabolic level.}, } @article {pmid36175536, year = {2022}, author = {Kwok, KTT and de Rooij, MMT and Messink, AB and Wouters, IM and Smit, LAM and Cotten, M and Heederik, DJJ and Koopmans, MPG and Phan, MVT}, title = {Establishing farm dust as a useful viral metagenomic surveillance matrix.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {16308}, pmid = {36175536}, issn = {2045-2322}, support = {/WT_/Wellcome Trust/United Kingdom ; MC_UU_12014/12/MRC_/Medical Research Council/United Kingdom ; 799417/MCCC_/Marie Curie/United Kingdom ; 220977/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Chickens ; *Dust ; Farms ; Humans ; Metagenome ; Metagenomics ; }, abstract = {Farm animals may harbor viral pathogens, some with zoonotic potential which can possibly cause severe clinical outcomes in animals and humans. Documenting the viral content of dust may provide information on the potential sources and movement of viruses. Here, we describe a dust sequencing strategy that provides detailed viral sequence characterization from farm dust samples and use this method to document the virus communities from chicken farm dust samples and paired feces collected from the same broiler farms in the Netherlands. From the sequencing data, Parvoviridae and Picornaviridae were the most frequently found virus families, detected in 85-100% of all fecal and dust samples with a large genomic diversity identified from the Picornaviridae. Sequences from the Caliciviridae and Astroviridae familes were also obtained. This study provides a unique characterization of virus communities in farmed chickens and paired farm dust samples and our sequencing methodology enabled the recovery of viral genome sequences from farm dust, providing important tracking details for virus movement between livestock animals and their farm environment. This study serves as a proof of concept supporting dust sampling to be used in viral metagenomic surveillance.}, } @article {pmid36175462, year = {2022}, author = {Morozova, MV and Borisova, MA and Snytnikova, OA and Achasova, KM and Litvinova, EA and Tsentalovich, YP and Kozhevnikova, EN}, title = {Colitis-associated intestinal microbiota regulates brain glycine and host behavior in mice.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {16345}, pmid = {36175462}, issn = {2045-2322}, mesh = {Animals ; Brain ; Choline ; *Colitis ; *Fabaceae ; Female ; *Gastrointestinal Microbiome ; Glycine ; Inflammation ; *Inflammatory Bowel Diseases ; Male ; Mice ; Receptors, N-Methyl-D-Aspartate ; }, abstract = {Inflammatory bowel diseases (IBD) are chronic and relapsing inflammatory disorders of the gastrointestinal tract with complex etiology and no strategies for complete cure. IBD are often complicated by mental disorders like anxiety and depression, indicating substantial shifts in the microbiota gut-brain axis. However, the mechanisms connecting IBD to mental diseases are still under debate. Here we use Muc2 knockout mouse model of chronic colitis to uncouple the effects of the intestinal microbiota on host behavior from chronic inflammation in the gut. Muc2 knockout male mice exhibit high exploratory activity, reduced anxiety-related behaviors, impaired sensorimotor gating, and altered social preference towards males and females. Microbial transfer to wild-type mice via littermate co-housing shows that colitis-associated microbiota rather than inflammation per se defines behavioral features in Muc2 colitis model. Metagenomic profiling and combination of antibiotic treatments revealed that bacterial species Akkermansia muciniphila is associated with the behavioral phenotype in mutants, and that its intestinal abundance correlates with social preference towards males. Metabolomic analysis together with pharmacological inhibition of Gly and NMDA receptors helped us to determine that brain glycine is responsible for the behavioral phenotype in Muc2 mice. Blood and brain metabolic profiles suggest that microbiota-dependent changes in choline metabolism might be involved in regulation of central glycine neurotransmission. Taken together, our data demonstrates that colitis-associated microbiota controls anxiety, sensorimotor gating and social behavior via metabolic regulation of the brain glycinergic system, providing new venues to combat neurological complications of IBD.}, } @article {pmid36175428, year = {2022}, author = {Peters, SL and Borges, AL and Giannone, RJ and Morowitz, MJ and Banfield, JF and Hettich, RL}, title = {Experimental validation that human microbiome phages use alternative genetic coding.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5710}, pmid = {36175428}, issn = {2041-1723}, support = {R01 GM103600/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteriophages/genetics ; Chromatography, Liquid ; Codon, Terminator ; Glutamine ; Humans ; *Microbiota/genetics ; Proteomics ; Tandem Mass Spectrometry ; }, abstract = {Previous bioinformatic analyses of metagenomic data have indicated that bacteriophages can use genetic codes different from those of their host bacteria. In particular, reassignment of stop codon TAG to glutamine (a variation known as 'genetic code 15') has been predicted. Here, we use LC-MS/MS-based metaproteomics of human fecal samples to provide experimental evidence of the use of genetic code 15 in two crAss-like phages. Furthermore, the proteomic data from several phage structural proteins supports the reassignment of the TAG stop codon to glutamine late in the phage infection cycle. Thus, our work experimentally validates the expression of genetic code 15 in human microbiome phages.}, } @article {pmid36174929, year = {2022}, author = {Cheng, WY and Liu, WX and Ding, Y and Wang, G and Shi, Y and Chu, ESH and Wong, S and Sung, JJY and Yu, J}, title = {High Sensitivity of Shotgun Metagenomic Sequencing in Colon Tissue Biopsy by Host DNA Depletion.}, journal = {Genomics, proteomics & bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.gpb.2022.09.003}, pmid = {36174929}, issn = {2210-3244}, abstract = {The high host genetic background of tissue biopsies hinders the application of shotgun metagenomic sequencing in characterizing the tissue microbiota. We proposed an optimized method that removed host DNA from colon biopsies and examined the effect on metagenomic analysis. Human or mouse colon biopsies were divided into two groups, with one group undergoing host DNA depletion and the other serving as the control. Host DNAs were removed through differential lysis of mammalian and bacterial cells before sequencing. The impact of host DNA depletion on microbiota was compared based on phylogenetic diversity analyses and regression analyses. Removing host DNA enhanced bacterial sequencing depth and improved species discovery, increasing bacterial reads by 2.46 ± 0.20 fold while reducing host reads by 6.80% ± 1.06%. Moreover, 3.40 times more of bacterial species were detected after host DNA depletion. This was confirmed from mouse colon tissues, increasing bacterial reads by 5.46 ± 0.42 fold while decreasing host reads by 10.2% ± 0.83%. Similarly, significantly more species were detected in the mouse colon tissue upon host DNA depletion (P < 0.001). Furthermore, an increased microbial richness was evident in the host DNA-depleted samples compared with non-depleted controls in human colon biopsies and mouse colon tissues (P < 0.001). Our optimized method of host DNA depletion improved the sensitivity of shotgun metagenomic sequencing in bacterial detection in the biopsy, which may yield a more accurate taxonomic profile of the tissue microbiota and identify bacteria that are important for disease initiation or progression.}, } @article {pmid36174730, year = {2022}, author = {Zhang, Y and Zhang, Q and Peng, H and Zhang, W and Li, M and Feng, J and He, J and Su, J}, title = {The changing C/N of aggressive aniline: Metagenomic analysis of pollutant removal, metabolic pathways and functional genes.}, journal = {Chemosphere}, volume = {309}, number = {Pt 1}, pages = {136598}, doi = {10.1016/j.chemosphere.2022.136598}, pmid = {36174730}, issn = {1879-1298}, mesh = {*Wastewater ; Denitrification ; Sewage ; Bioreactors ; *Environmental Pollutants ; Nitrification ; Nitrogen/metabolism ; Aniline Compounds/metabolism ; Metabolic Networks and Pathways/genetics ; }, abstract = {In order to optimize the degradation of high-concentration aniline wastewater, the operation of sequencing batch bioaugmentation reactors with different aniline concentrations (200 mg/L, 600 mg/L, 1000 mg/L) was studied. The results showed that the removal rates of aniline and COD in the three reactors could reach 100%. When the aniline increased to 600 mg/L, the nitrogen removal efficiency reached the peak (51.85%). The increase of aniline inhibited the nitrification, while denitrification was enhanced due to the increase of C/N ratio. But this change was reversed by the toxicity of high concentrations of aniline. The metagenomic analysis showed that when the aniline concentration was 600 mg/L, the abundance distribution of microbial samples was more uniform. The improved of aniline concentration had led to the increase of aromatic compounds degradation metabolic pathways. In addition, the abundance of aniline degradation and nitrogen metabolism genes (dmpB, xylE, norB) was also promoted.}, } @article {pmid36174682, year = {2023}, author = {Gu, Z and Bao, M and He, C and Chen, W}, title = {Transformation of dissolved organic matter in landfill leachate during a membrane bioreactor treatment.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 2}, pages = {159066}, doi = {10.1016/j.scitotenv.2022.159066}, pmid = {36174682}, issn = {1879-1026}, mesh = {*Water Pollutants, Chemical/analysis ; Dissolved Organic Matter ; RNA, Ribosomal, 16S ; Benzene/analysis ; Bioreactors ; }, abstract = {In this study, a cutting-edge mass spectrometry (MS) technique, Orbitrap fusion MS with ultrahigh resolution, was used to analyze the molecular composition, chemical properties, formation mechanism, and environmental impact of refractory dissolved organic matter (rDOM) in leachate. The results showed that the bioavailable DOM (bDOM) and rDOM constituents varied substantially during the biological treatment of landfill leachate. Compared with bDOM, the rDOM in leachate had a higher degree of unsaturation, aromaticity, and oxidation, and a larger molecular weight, and contained more organic matter with benzene ring and biphenyl structures. Using high-throughput 16S rRNA sequencing, metagenomics, the Kendrick mass defect (KMD), and a mass difference network (MDiN), it was found that rDOM in leachate is generated through carboxylation (+COO), dehydro-oligomerization (-H2), and chain scission (-CH2) pathways due to the activity of microbes such as Patescibacteria, Chloroflexi, and Proteobacteria. Compared with Suwannee River fulvic acid (SRFA), the rDOM in leachate contained more organics with nitrogen, sulfur, benzene rings, and biphenyls. If the rDOM in leachate enters the environment it will affect the composition of the original organic matter, and its biogeochemical transformation and environmental fate will then need to be monitored and may require special attention.}, } @article {pmid36174681, year = {2023}, author = {Yang, F and Wang, X and Tian, X and Zhang, Z and Zhang, K and Zhang, K}, title = {Cow manure simultaneously reshaped antibiotic and metal resistome in the earthworm gut tract by metagenomic analysis.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 1}, pages = {159010}, doi = {10.1016/j.scitotenv.2022.159010}, pmid = {36174681}, issn = {1879-1026}, mesh = {Animals ; Female ; Cattle ; *Manure ; *Oligochaeta ; Anti-Bacterial Agents/pharmacology ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Livestock ; Metals ; }, abstract = {Earthworm conversion is an eco-friendly biological process that converts livestock waste into a benign nutrient-rich organic fertilizer. However, little is known about the impacts of earthworm-converted livestock manure on the antibiotic resistome in the earthworm gut microbiota. Herein, lab-scale vermicomposting was performed to comprehensively evaluate the shift of antibiotic resistance genes (ARGs) in the earthworm gut-feeding on cow manure (CM)-by metagenomic analysis. The effects of copper (Cu) as a food addictive were also evaluated. CM substantially enriched the antibiotic resistome in the foregut and midgut, while it decreased in the hindgut. A similar trend was observed for metal resistance genes (MRGs). Notably, Cu in the CM had little effect on composition of ARGs and MRGs in earthworm gut. The earthworm gut microbiome altered by CM was responsible for the shift of ARGs and MRGs. In wormcast, Cu (100 and 300 mg/kg) significantly increased the abundance of ARGs and MRGs. Our study provides valuable insight into the response of ARGs and MRGs to CM in earthworm gut, and underscores the need for the judicious use of heavy metals as feed additives in livestock and poultry farming.}, } @article {pmid36174465, year = {2022}, author = {García-Santibañez, T and Rosenblueth, M and Bolaños, LM and Martínez-Romero, J and Martínez-Romero, E}, title = {The divergent genome of Scorpion Group 1 (SG1) intracellular bacterium from the venom glands of Vaejovis smithi (Scorpiones: Vaejovidae).}, journal = {Systematic and applied microbiology}, volume = {45}, number = {6}, pages = {126358}, doi = {10.1016/j.syapm.2022.126358}, pmid = {36174465}, issn = {1618-0984}, mesh = {Animals ; *Scorpions/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Bacteria/genetics ; Metagenomics ; }, abstract = {Scorpions were among the first animals on land around 430 million years ago. Like many arachnids, scorpions have evolved complex venoms used to paralyze their prey and for self-defense. Here we sequenced and analyzed the metagenomic DNA from venom glands from Vaejovis smithi scorpions. A metagenome-assembled genome (MAG) of 624,025 bp was obtained corresponding to the previously reported Scorpion Group 1 (SG1). The SG1 genome from venom glands had a low GC content (25.8%) characteristic of reduced genomes, many hypothetical genes and genes from the reported minimal set of bacterial genes. Phylogenomic reconstructions placed the uncultured SG1 distant from other reported bacteria constituting a taxonomic novelty. By PCR we detected SG1 in all tested venom glands from 30 independent individuals. Microscopically, we observed SG1 inside epithelial cells from the venom glands using FISH and its presence in scorpion embryos suggested that SG1 is transferred from mother to offspring.}, } @article {pmid36174355, year = {2022}, author = {Centurion, VB and Campanaro, S and Basile, A and Treu, L and Oliveira, VM}, title = {Microbiome structure in biofilms from a volcanic island in Maritime Antarctica investigated by genome-centric metagenomics and metatranscriptomics.}, journal = {Microbiological research}, volume = {265}, number = {}, pages = {127197}, doi = {10.1016/j.micres.2022.127197}, pmid = {36174355}, issn = {1618-0623}, mesh = {Antarctic Regions ; Biofilms ; Metagenome ; *Metagenomics/methods ; *Microbiota/genetics ; Reactive Oxygen Species ; }, abstract = {Antarctica is the coldest and driest continent on Earth, characterized by polyextreme environmental conditions, where species adapted form complex networks of interactions. Microbial communities growing in these harsh environments can form biofilms that help the associated species to survive and thrive. A rich body of knowledge describes environmental biofilm communities; however, most studies have focused on dominant community members rather than functional complexity and metabolic potential. To overcome these limitations, the present study used genome-centric metagenomics to describe two biofilm samples subjected to different temperature collected in Deception Island, Maritime Antarctica. The results unraveled a complex biofilm microbiome represented by 180 metagenome-assembled genomes. The potential metabolic interactions were investigated using metabolic flux balance analysis and revealed that purple bacteria are the community members with the highest correlations with other bacteria. Due to their predicted mixotrophic behavior, they may play a crucial role in the microbiome, likely supporting the heterotrophic species in biofilms. Metatranscriptomics results revealed that the chaperone system and proteins counteracting ROS and toxic compounds have a major role in maintaining bacterial cell homeostasis in sediments of volcanic origin.}, } @article {pmid36173700, year = {2022}, author = {Wirth, J and Young, M}, title = {Viruses in Subsurface Environments.}, journal = {Annual review of virology}, volume = {9}, number = {1}, pages = {99-119}, doi = {10.1146/annurev-virology-093020-015957}, pmid = {36173700}, issn = {2327-0578}, mesh = {Ecology ; Metagenome ; Metagenomics ; *Viruses/genetics ; }, abstract = {Over the past 20 years, our knowledge of virus diversity and abundance in subsurface environments has expanded dramatically through application of quantitative metagenomic approaches. In most subsurface environments, viral diversity and abundance rival viral diversity and abundance observed in surface environments. Most of these viruses are uncharacterized in terms of their hosts and replication cycles. Analysis of accessory metabolic genes encoded by subsurface viruses indicates that they evolved to replicate within the unique features of their environments. The key question remains: What role do these viruses play in the ecology and evolution of the environments in which they replicate? Undoubtedly, as more virologists examine the role of viruses in subsurface environments, new insights will emerge.}, } @article {pmid36172625, year = {2022}, author = {Song, P and Li, H and Liu, T and Liu, Y and Ma, X and Su, L}, title = {Disseminated Strongyloidiasis Misdiagnosed as Guillain-Barré Syndrome: The Value of High-Throughput Genetic Sequencing of Pathogenic Microorganisms in Parasitic Infections.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {5601-5607}, pmid = {36172625}, issn = {1178-6973}, abstract = {BACKGROUND: With the widespread use of steroids and immunosuppressants in mainland China, disseminated strongyloidiasis is becoming a severely underestimated tropical disease due to the lack of disease-specific manifestations and well-established diagnostic methods.

CASE PRESENTATION: Here, we report a 70-year-old woman who was diagnosed with Guillain-Barré syndrome due to autonomic disturbance, symmetrical bulbar palsy, and lower-motor-nerve damage in the extremities; her symptoms continued to worsen after hormone and immunoglobulin therapy. Later, parasitic larvae were found in the patient's gastric fluid, and metagenomic Next Generation Sequencing (mNGS) detection of bronchoalveolar-lavage fluid also found a large number of Strongyloides roundworms. The patient was diagnosed with disseminated strongyloidiasis. The patient was given albendazole for anthelmintic treatment, but died two days after being transferred to the ICU due to the excessive strongyloidiasis burden.

CONCLUSION: This case highlights the combined application of mNGS and traditional testing in the clinical diagnosis of difficult and critical parasitic infections in immunocompromised patients. mNGS is a new, adjunct diagnostic method to rapidly screen for possible parasitic etiologies.}, } @article {pmid36172503, year = {2022}, author = {Zhang, K and Lin, R and Chang, Y and Zhou, Q and Zhang, Z}, title = {16S-FASAS: an integrated pipeline for synthetic full-length 16S rRNA gene sequencing data analysis.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e14043}, pmid = {36172503}, issn = {2167-8359}, mesh = {RNA, Ribosomal, 16S/genetics ; Genes, rRNA ; Phylogeny ; Sequence Analysis, DNA/methods ; *Bacteria/genetics ; *Data Analysis ; }, abstract = {BACKGROUND: The full-length 16S rRNA sequencing can better improve the taxonomic and phylogenetic resolution compared to the partial 16S rRNA gene sequencing. The 16S-FAS-NGS (16S rRNA full-length amplicon sequencing based on a next-generation sequencing platform) technology can generate high-quality, full-length 16S rRNA gene sequences using short-read sequencers, together with assembly procedures. However there is a lack of a data analysis suite that can help process and analyze the synthetic long read data.

RESULTS: Herein, we developed software named 16S-FASAS (16S full-length amplicon sequencing data analysis software) for 16S-FAS-NGS data analysis, which provided high-fidelity species-level microbiome data. 16S-FASAS consists of data quality control, de novo assembly, annotation, and visualization modules. We verified the performance of 16S-FASAS on both mock and fecal samples. In mock communities, we proved that taxonomy assignment by MegaBLAST had fewer misclassifications and tended to find more low abundance species than the USEARCH-UNOISE3-based classifier, resulting in species-level classification of 85.71% (6/7), 85.71% (6/7), 72.72% (8/11), and 70% (7/10) of the target bacteria. When applied to fecal samples, we found that the 16S-FAS-NGS datasets generated contigs grouped into 60 and 56 species, from which 71.62% (43/60) and 76.79% (43/56) were shared with the Pacbio datasets.

CONCLUSIONS: 16S-FASAS is a valuable tool that helps researchers process and interpret the results of full-length 16S rRNA gene sequencing. Depending on the full-length amplicon sequencing technology, the 16S-FASAS pipeline enables a more accurate report on the bacterial complexity of microbiome samples. 16S-FASAS is freely available for use at https://github.com/capitalbio-bioinfo/FASAS.}, } @article {pmid36172496, year = {2022}, author = {Abduweli Uyghurturk, D and Lu, Y and Urata, J and C Dvorak, C and Den Besten, P}, title = {Dental caries as a risk factor for bacterial blood stream infection (BSI) in children undergoing hematopoietic cell transplantation (HCT).}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e14040}, pmid = {36172496}, issn = {2167-8359}, support = {T32 DE007306/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; Child ; *Dental Caries/epidemiology ; Bacteria ; Streptococcus ; *Bacterial Infections ; *Sepsis ; Risk Factors ; *Hematopoietic Stem Cell Transplantation/adverse effects ; }, abstract = {BACKGROUND: Hematopoietic cell transplantation (HCT) is a potentially curative therapy for a wide range of pediatric malignant and nonmalignant diseases. However, complications, including blood stream infection (BSI) remain a major cause of morbidity and mortality. While certain bacteria that are abundant in the oral microbiome, such as S. mitis, can cause BSI, the role of the oral microbial community in the etiology of BSI is not well understood. The finding that the use of xylitol wipes, which specifically targets the cariogenic bacteria S. mutans is associated with reduced BSI in pediatric patients, lead us to investigate dental caries as a risk factor for BSI.

METHODS: A total of 41 pediatric patients admitted for allogenic or autologous HCT, age 8 months to 25 years, were enrolled. Subjects with high dental caries risk were identified as those who had dental restorations completed within 2 months of admission for transplant, or who had untreated decay. Fisher's exact test was used to determine if there was a significant association between caries risk and BSI. Dental plaque and saliva were collected on a cotton swab from a subset of four high caries risk (HCR) and four low caries risk (LCR) children following pretransplant conditioning. 16SrRNA sequencing was used to compare the microbiome of HCR and LCR subjects and to identify microbes that were significantly different between the two groups.

RESULTS: There was a statistically significant association between caries risk and BSI (p < 0.035) (Fisher's exact test). Multivariate logistic regression analysis showed children in the high dental caries risk group were 21 times more likely to have BSI, with no significant effect of age or mucositis severity. HCR subjects showed significantly reduced microbial alpha diversity as compared to LCR subjects. LEfse metagenomic analyses, showed the oral microbiome in HCR children enriched in order Lactobacillales. This order includes Streptococcus and Lactobacillus, both which contain bacteria primarily associated with dental caries.

DISCUSSION: These findings support the possibility that the cariogenic microbiome can enhance the risk of BSI in pediatric populations. Future metagenomic analyses to measure microbial differences at, before, and after conditioning related to caries risk, may further unravel the complex relationship between the oral microbiome, and whether it affects health outcomes such as BSI.}, } @article {pmid36172112, year = {2022}, author = {Wang, J and Xu, D and Qu, B and Geng, C}, title = {Adult intracranial infection caused by an extended-spectrum-beta-lactamase-producing strain of hypervirulent Klebsiella pneumoniae: a case report.}, journal = {Annals of translational medicine}, volume = {10}, number = {17}, pages = {941}, pmid = {36172112}, issn = {2305-5839}, abstract = {BACKGROUND: Klebsiella pneumoniae is a conditional pathogen related to several infectious diseases. Few studies reported Klebsiella pneumoniae meningitis in the Chinese population, guidelines on diagnosis and treatment of Klebsiella pneumoniae meningitis should be considered due to its high lethality. Here, we report a case of adult intracranial infection caused by extended-spectrum-beta-lactamase (ESBL)-producing hypervirulent Klebsiella pneumoniae (hvKP) in a 65-year-old female, providing new insight for clinical awareness and epidemiological surveillance for ESBL-producing hvKP infection.

CASE DESCRIPTION: A 65-year-old female who had a recurrent fever for more than 1 month, and vomiting for 1 week was admitted to our hospital. The computed tomography (CT) results and laboratory results indicated systematic infection, and the blood culture confirmed the infection of Klebsiella pneumoniae. A combination of antibiotics including vancomycin, caspofungin, dexamethasone, and posaconazole oral suspension was given to the patient. Further, she exhibited a convulsion with unconsciousness, the CT revealed lacunar infarction and encephalomalacia. The following physical examination showed slight neck resistance, a weak light response of the eye, low muscle tension, suspicious left Babinski sign (+), and right Babinski sign (-). The CT and cerebrospinal fluid (CSF) analyses confirmed the diagnosis of intracranial infection caused by Klebsiella pneumoniae. We employed CSF microbial metagenomic next-generation sequencing (mNGS) was employed and the results suggested the high sequence of Klebsiella pneumoniae with drug-resistant gene SHV-type beta-lactamases (blaSHV). Subsequently, 2 g meropenem every 8 hours (q8h) prolonged for 3 hours was applied to treat intracranial infection, and her body temperature and infectious manifestations were gradually relieved. The CT results represented that pulmonary edema and pleural effusion were gradually dissipated and absorbed. Based on the improvement of clinical manifestations, the patient was discharged from the hospital and a close follow-up was conducted.

CONCLUSIONS: An ESBL-producing strain of hvKP could lead to invasive infection such as severe intracranial infection, with a relatively favorable prognosis. The outcome of the disease caused by Klebsiella pneumoniae infection is firmly related to the phenotypic features, for instance, virulence factors and antibiotic susceptibility. Due to its high lethality, timely empiric anti-infection therapy and close surveillance are necessary for patients with Klebsiella pneumoniae infection in the clinic.}, } @article {pmid36171758, year = {2022}, author = {Chai, J and Liu, X and Usdrowski, H and Deng, F and Li, Y and Zhao, J}, title = {Geography, niches, and transportation influence bovine respiratory microbiome and health.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {961644}, pmid = {36171758}, issn = {2235-2988}, mesh = {Animals ; Bacteria/genetics ; Cattle ; *Cattle Diseases/microbiology ; Geography ; Lung ; *Microbiota ; RNA, Ribosomal, 16S ; }, abstract = {Bovine respiratory disease (BRD), one of the most common and infectious diseases in the beef industry, is associated with the respiratory microbiome and stressors of transportation. The impacts of the bovine respiratory microbiota on health and disease across different geographic locations and sampling niches are poorly understood, resulting in difficult identification of BRD causes. In this study, we explored the effects of geography and niches on the bovine respiratory microbiome and its function by re-analyzing published metagenomic datasets and estimated the main opportunistic pathogens that changed after transportation. The results showed that diversity, composition, structure, and function of the bovine nasopharyngeal microbiota were different across three worldwide geographic locations. The lung microbiota also showed distinct microbial composition and function compared with nasopharyngeal communities from different locations. Although different signature microbiota for each geographic location were identified, a module with co-occurrence of Mycoplasma species was observed in all bovine respiratory communities regardless of geography. Moreover, transportation, especially long-distance shipping, could increase the relative abundance of BRD-associated pathogens. Lung microbiota from BRD calves shaped clusters dominated with different pathogens. In summary, geography, sampling niches, and transportation are important factors impacting the bovine respiratory microbiome and disease, and clusters of lung microbiota by different bacterial species may explain BRD pathogenesis, suggesting the importance of a deeper understanding of bovine respiratory microbiota in health.}, } @article {pmid36171634, year = {2022}, author = {Carda-Diéguez, M and Moazzez, R and Mira, A}, title = {Functional changes in the oral microbiome after use of fluoride and arginine containing dentifrices: a metagenomic and metatranscriptomic study.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {159}, pmid = {36171634}, issn = {2049-2618}, mesh = {Adult ; Ammonia ; Arginine/therapeutic use ; Bacteria/genetics ; Cariostatic Agents/therapeutic use ; *Dental Caries/prevention & control ; *Dental Plaque ; *Dentifrices/therapeutic use ; Double-Blind Method ; Fluorides/therapeutic use ; Humans ; Metagenome/genetics ; *Microbiota/genetics ; *Periodontitis ; Phosphates/therapeutic use ; Tooth Remineralization ; Toothpastes ; }, abstract = {BACKGROUND: Tooth decay is one of the most prevalent diseases worldwide, and efficient tooth brushing with a fluoride-containing dentifrice is considered fundamental to caries prevention. Fluoride-containing dentifrices have been extensively studied in relation to enamel resistance to demineralization. Arginine (Arg) has also been proposed as a promising prebiotic to promote pH buffering through ammonia production. Here, we present the first metagenomic (DNA sequencing of the whole microbial community) and metatranscriptomic (RNAseq of the same community) analyses of human dental plaque to evaluate the effect of brushing with fluoride (Fl) and a Fl+Arg containing dentifrices on oral microbial composition and activity. Fifty-three patients were enrolled in a longitudinal clinical intervention study with two arms, including 26 caries-active and 27 caries-free adults. After a minimum 1-week washout period, dental plaque samples were collected at this post-washout baseline, 3 months after the use of a 1450-ppm fluoride dentifrice, and after 6 months of using a 1450-ppm fluoride with 1.5% arginine dentifrice.

RESULTS: There was a shift in both the composition and activity of the plaque microbiome after 3 months of brushing with the fluoride-containing toothpaste compared to the samples collected at the 1-week post-washout period, both for caries-active and caries-free sites. Although several caries-associated bacteria were reduced, there was also an increase in several health- and periodontitis-associated bacteria. Over 400 genes changed proportion in the metagenome, and between 180 and 300 genes changed their expression level depending on whether caries-free or caries-active sites were analyzed. The metagenome and metatranscriptome also changed after the subjects brushed with the Fl+Arg dentifrice. There was a further decrease of both caries- and periodontitis-associated organisms. In both caries-free and caries-active sites, a decrease of genes from the arginine biosynthesis pathway was also observed, in addition to an increase in the expression of genes associated with the arginine deiminase pathway, which catabolizes arginine into ammonia, thereby buffering acidic pH. Bacterial richness and diversity were not affected by either of the two treatments in the two arms of the study.

CONCLUSIONS: Our data demonstrate that long-term use of both assayed dentifrices changes the bacterial composition and functional profiles of human dental plaque towards a healthier microbial community, both in caries-free and caries-active sites. This observation was especially apparent for the Fl+Arg dentifrice. Thus, we conclude that the preventive benefits of tooth brushing go beyond the physical removal of dental plaque and that the active ingredients formulated within dentifrices have a positive effect not only on enamel chemistry but also on the metabolism of oral microbial populations. Video Abstract.}, } @article {pmid36171387, year = {2022}, author = {Lu, J and Rincon, N and Wood, DE and Breitwieser, FP and Pockrandt, C and Langmead, B and Salzberg, SL and Steinegger, M}, title = {Metagenome analysis using the Kraken software suite.}, journal = {Nature protocols}, volume = {17}, number = {12}, pages = {2815-2839}, pmid = {36171387}, issn = {1750-2799}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; U24 CA180922/CA/NCI NIH HHS/United States ; R35 GM139602/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Metagenome ; Software ; Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenomic experiments expose the wide range of microscopic organisms in any microbial environment through high-throughput DNA sequencing. The computational analysis of the sequencing data is critical for the accurate and complete characterization of the microbial community. To facilitate efficient and reproducible metagenomic analysis, we introduce a step-by-step protocol for the Kraken suite, an end-to-end pipeline for the classification, quantification and visualization of metagenomic datasets. Our protocol describes the execution of the Kraken programs, via a sequence of easy-to-use scripts, in two scenarios: (1) quantification of the species in a given metagenomics sample; and (2) detection of a pathogenic agent from a clinical sample taken from a human patient. The protocol, which is executed within 1-2 h, is targeted to biologists and clinicians working in microbiome or metagenomics analysis who are familiar with the Unix command-line environment.}, } @article {pmid36170781, year = {2022}, author = {Jiang, H and Wen, Y and Qian, R and Liu, S and Tang, X and Huang, W and Chen, H}, title = {Novel insights into aerobic duration control-based partial nitritation in source-separated blackwater treatment: Growth type, inoculation source, and comammox threat.}, journal = {Journal of environmental management}, volume = {324}, number = {}, pages = {116319}, doi = {10.1016/j.jenvman.2022.116319}, pmid = {36170781}, issn = {1095-8630}, mesh = {*Sewage/microbiology ; *Nitrites ; Bioreactors/microbiology ; Ammonia ; Nitrification ; Bacteria ; Oxidation-Reduction ; Nitrogen ; }, abstract = {Aerobic duration control (ADC), whereby aeration is terminated before nitrite is extremely oxidized during the nitrification process, is an effective strategy to achieve partial nitritation (PN) for blackwater. This study evaluated the effects of microbial growth type, influent ammonia-oxidizing organisms (AOO), and comammox bacteria from seeding sludge to ADC-based PN. The long-term operation of lab-scale reactors and model simulations were implemented to select the best growth type. The biofilm formed on the inner wall of the activated sludge reactor decreased the nitrite accumulation ratio (NAR) from 99.2% to 77.2%. Meanwhile, the NAR of the pure-biofilm reactor decreased from 95.9% to 47.8%. The deteriorated PN of the biofilm-related reactors was due to the extended solid retention time and increased substrate saturation constants of AOOs compared with those of nitrite-oxidizing organisms (NOO). Periodic biofilm carrier regeneration and biofilm thickness control can recover PN performance but are difficult to implement. In contrast, the optimized activated sludge reactor exhibited high (NAR >94%) and stable (>3 months) PN performance when treating real blackwater. Nitrifiers were found in blackwater, and chemically enhanced high-rate activated sludge pretreatment removed more NOOs than AOOs (41.8% vs. 24.3%) and increased the influent AOO/NOO ratio. Interestingly, the influent AOOs supported fast PN start-up in the moving-bed biofilm reactor without the initial inoculation of activated sludge. Moreover, model simulations verified that high and stable PN could also be realized in an activated sludge reactor by the continuous inoculation of influent AOOs, which is a novel PN start-up strategy. Metagenomic analyses showed that the comammox bacteria from the seeding sludge eventually disappeared owing to their intrinsic specific growth rates and free ammonia inhibition. The findings of this study will provide insightful guidelines for PN application in decentralized and semi-centralized wastewater treatment systems.}, } @article {pmid36170451, year = {2022}, author = {Rozman, V and Mohar Lorbeg, P and Treven, P and Accetto, T and Golob, M and Zdovc, I and Bogovič Matijašić, B}, title = {Lactic acid bacteria and bifidobacteria deliberately introduced into the agro-food chain do not significantly increase the antimicrobial resistance gene pool.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2127438}, pmid = {36170451}, issn = {1949-0984}, mesh = {Anti-Bacterial Agents/pharmacology ; Bifidobacterium/genetics ; Drug Resistance, Bacterial/genetics ; Food Chain ; *Gastrointestinal Microbiome ; Gene Pool ; Humans ; *Lactobacillales/genetics ; Tetracyclines ; }, abstract = {Lactic acid bacteria (LAB) and bifidobacteria may serve as reservoirs of antimicrobial resistance, but the risk posed by strains intentionally introduced into the agro-food chain has not yet been thoroughly investigated. The aim of our study was to evaluate whether probiotics, starter and protective cultures, and feed additives represent a risk to human health. In addition to commercial strains of LAB and bifidobacteria, isolates from human milk or colostrum, intestinal mucosa or feces, and fermented products were analyzed. Phenotypic susceptibility data of 474 strains showed that antimicrobial resistance was more common in intestinal isolates than in commercial strains. Antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs) were characterized in the whole genome sequences of 1114 strains using comparative genomics. Intrinsic ARGs were abundant in enterococci, bifidobacteria, and lactococci but were considered non-risky due to the absence of MGEs. The results revealed that 13.8% of commercial strains contained acquired ARGs, most frequently for tetracycline. We associated 75.5% of the acquired ARGs with known or novel MGEs, and their potential for transmission was assessed by examining metagenomic sequences. We confirmed that ARGs and MGEs were not as abundant or diverse in commercial strains as in human intestinal isolates or isolates from human milk, suggesting that strains intentionally introduced into the agro-food chain do not pose a significant threat. However, attention should be paid especially to individual probiotic strains containing elements that have been shown to have high potential for transferability in the gut microbiota.Abbreviations: ARG, antimicrobial resistance gene; ICE, integrative and conjugative element; IME, integrative and mobilizable element; LAB, lactic acid bacteria; MDR, multidrug resistance; MIC, minimum inhibitory concentration; MGE, mobile genetic element; TRRPP, tetracycline-resistant ribosomal protection protein; WGS, whole genome sequences.}, } @article {pmid36169892, year = {2022}, author = {Wani, AK and Akhtar, N and Singh, R and Chopra, C and Kakade, P and Borde, M and Al-Khayri, JM and Suprasanna, P and Zimare, SB}, title = {Prospects of advanced metagenomics and meta-omics in the investigation of phytomicrobiome to forecast beneficial and pathogenic response.}, journal = {Molecular biology reports}, volume = {49}, number = {12}, pages = {12165-12179}, pmid = {36169892}, issn = {1573-4978}, mesh = {*Metagenomics/methods ; *Microbiota/genetics ; Rhizosphere ; Metabolomics/methods ; Plants/genetics ; }, abstract = {Microorganisms dwell in diverse plant niches as non-axenic biotic components that are beneficial as well pathogenic for the host. They improve nutrients-uptake, stress tolerance, phytohormone synthesis, and strengthening the defense system through phyllosphere, rhizosphere, and endosphere. The negative consequences of the microbial communities are largely in the form of diseases characterized by certain symptoms such as gall, cankers, rots etc. Uncultivable and unspecified nature of different phytomicrobiomes communities is a challenge in the management of plant disease, a leading cause for the loss of the plant products. Metagenomics has opened a new gateway for the exploration of microorganisms that are hitherto unknown, enables investigation of the functional aspect of microbial gene products through metatranscriptomics and metabolomics. Metagenomics offers advantages of characterizing previously unknown microorganisms from extreme environments like hot springs, glaciers, deep seas, animal gut etc. besides bioprospecting gene products such as Taq polymerase, bor encoded indolotryptoline, hydrolases, and polyketides. This review provides a detailed account of the phytomicrobiome networks and highlights the importance and limitations of metagenomics and other meta-omics approaches for the understanding of plant microbial diversity with special focus on the disease control and its management.}, } @article {pmid36169826, year = {2023}, author = {Huo, Q and Li, R and Chen, C and Wang, C and Long, T and Liu, X}, title = {Study on potential microbial community to the waste water treatment from bauxite desilication process.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {6}, pages = {15438-15453}, pmid = {36169826}, issn = {1614-7499}, mesh = {Aluminum Oxide ; Wastewater ; Bacteria/genetics ; *Microbiota/genetics ; *Water Purification ; }, abstract = {Discharging waste water from the bauxite desilication process will bring potential environmental risk from the residual ions and organic compounds, especially hydrolyzed polyacrylamide. Characterization of the microbial community diversity in waste water plays an important role in the biological treatment of waste water. In this study, eight waste water samples from five flotation plants in China were investigated. The microbial community and functional profiles within the waste water were analyzed by a metagenomic sequencing method and associated with geochemical properties. The results revealed that Proteobacteria and Firmicutes were the dominant bacterial phyla. Both phylogenetical and clusters of orthologous groups' analyses indicated that Tepidicella, Paracoccus, Pseudomonas, and Exiguobacterium could be the dominant bacterial genera in the waste water from bauxite desilication process for their abilities to biodegrade complex organic compounds. The results of the microbial community diversity and functional gene compositions analyses provided a beneficial orientation for the biotreatment of waste water, as well as regenerative using of water resources. Besides, this study revealed that waste water from bauxite desilication process was an ideal ecosystem to find novel microorganisms, such as efficient strains for bio-desilication and bio-desulfurization of bauxite.}, } @article {pmid36169685, year = {2022}, author = {Lin, S and Li, Q and Xu, Z and Chen, Z and Tao, Y and Tong, Y and Wang, T and Chen, S and Wang, P}, title = {Detection of the role of intestinal flora and tryptophan metabolism involved in antidepressant-like actions of crocetin based on a multi-omics approach.}, journal = {Psychopharmacology}, volume = {239}, number = {11}, pages = {3657-3677}, pmid = {36169685}, issn = {1432-2072}, support = {81703688//the National Natural Science Foundation of China/ ; 2022C03050//the key research and development project of Zhejiang Provinc/ ; 2017YFE0130100//key projects of international scientific and technological innovation cooperation between governments/ ; LQ22H280014//Zhejiang Provincial Natural Science Foundation of China under Grant/ ; 21ywb80//Taizhou Social development science and technology program/ ; }, mesh = {Animals ; Mice ; *Tryptophan/metabolism ; Receptors, Aryl Hydrocarbon/metabolism ; Serotonin/metabolism ; Depression/metabolism ; Indoleamine-Pyrrole 2,3,-Dioxygenase/metabolism ; *Gastrointestinal Microbiome ; Kynurenic Acid/metabolism ; Serotonin Plasma Membrane Transport Proteins/metabolism ; Occludin/metabolism/pharmacology ; Arachidonic Acid/metabolism/pharmacology ; Antidepressive Agents/pharmacology/therapeutic use/metabolism ; Hippocampus ; Inflammation/metabolism ; Cytokines/metabolism ; Mitogen-Activated Protein Kinases/metabolism ; Arginine/pharmacology ; Stress, Psychological/drug therapy ; }, abstract = {RATIONALE: Depression is a serious mood disorder, and crocetin has a variety of pharmacological activities, including antidepressant effect. The alterations of intestinal flora have a significant correlation with depression, and crocetin can alter the composition of intestinal flora in mice with depression-like behaviors.

OBJECTIVE: This study investigated the underlying antidepressant mechanisms of crocetin through multi-omics coupled with biochemical technique validation.

METHODS: Chronic unpredictable stress (CUMS) was used to induce mice model of depression to evaluate the antidepressant effect of crocetin through behavioral tests, and the metagenomic and metabolomic were used to explore the potential mechanisms involved. In order to verify its underlying mechanism, western blot (WB), Elisa, immune histological and HPLC techniques were used to detect the level of inflammatory cytokines and the level of metabolites/proteins related to tryptophan metabolism in crocetin-treated mice.

RESULTS: Crocetin ameliorated depression-like behaviors and increased mobility in depressive mice induced by CUMS. Metagenomic results showed that crocetin regulated the structure of intestinal flora, as well as significantly regulated the function gene related to derangements in energy metabolism and amino acid metabolism in mice with depression-like behaviors. Metabolomic results showed that the tryptophan metabolism, arginine metabolism and arachidonic acid metabolism played an essential role in exerting antidepressant-like effect of crocetin. According to multi-omics approaches and validation results, tryptophan metabolism and inflammation were identified and validated as valuable biological processes involved in the antidepressant effects of crocetin. Crocetin regulated the tryptophan metabolism in mice with depression-like behaviors, including increased aryl hydrocarbon receptor (AhR) expression, reduced indoleamine 2,3-dioxygenase 1 (IDO1) and serotonin transporter (SERT) expression in the hippocampus, elevated the content of 5-HT, kynurenic acid in serum and 5-HT, tryptophan in hippocampus. In addition, crocetin also attenuated inflammation in mice with depression-like behaviors, which presented with reducing the production of inflammatory cytokines in serum and colon. Meanwhile, crocetin up-regulated the expression of zonula occludens 1 (ZO-1) and occludin in ileum and colon to repair the intestinal barrier for preventing inflammation transfer.

CONCLUSION: Our findings clarify that crocetin exerted antidepressant effects through its anti-inflammation, repairment of intestinal barrier, modulatory on the intestinal flora and metabolic disorders, which further regulated tryptophan metabolism and impacted mitogen-activated protein kinase (MAPK) signaling pathway to enhance neural plasticity, thereby protect neural.}, } @article {pmid36169415, year = {2022}, author = {Yang, A and Chen, C and Hu, Y and Zheng, G and Chen, P and Xie, Z and Fan, H and Sun, Y and Wu, P and Jiang, W and Wang, C and Zhang, J and Zhang, D and Wang, J and Hu, X and Xia, H and Yin, G and Guo, Y}, title = {Application of Metagenomic Next-Generation Sequencing (mNGS) Using Bronchoalveolar Lavage Fluid (BALF) in Diagnosing Pneumonia of Children.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0148822}, pmid = {36169415}, issn = {2165-0497}, mesh = {Child ; Humans ; Bronchoalveolar Lavage Fluid ; Sensitivity and Specificity ; *Metagenomics/methods ; High-Throughput Nucleotide Sequencing/methods ; *Pneumonia/diagnosis/microbiology ; Bacteria/genetics ; Anti-Bacterial Agents ; }, abstract = {Pneumonia is the leading cause of death in children; the pathogens are often difficult to diagnose. In this study, the performance of metagenomic next-generation sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) samples from 112 children with confirmed pneumonia has been evaluated. mNGS performed a significantly higher positive detection rate (91.07%, 95% confidence interval [CI] 83.80% to 95.40%) and coincidence rate against the final diagnosis (72.32%, 95% CI 62.93% to 80.15%) than that of conventional methods (70.54%, 95% CI 61.06% to 78.58% and 56.25%, 95% CI 46.57% to 65.50%, respectively) (P < 0.01 and P < 0.05, respectively). Bacteria, viruses, and their mixed infections were common in children with pneumonia. Streptococcus pneumoniae was the most common bacterial pathogen in children with pneumonia, while Haemophilus parainfluenzae and Haemophilus influenzae seemed more likely to cause nonsevere pneumonia in children. In contrast, human cytomegalovirus (CMV) infection and the simultaneous bacterial infections could cause severe pneumonia, especially in children with underlying diseases. After adjustments of antibiotics based on mNGS and conventional methods, the conditions improved in 109 (97.32%) children. mNGS of BALF samples has shown great advantages in diagnosing the pathogenic etiology of pneumonia in children, especially when considering the limited volumes of BALF and the previous use of empirical antibiotics, contributing to the timely adjustment of antibiotic treatments, which can potentially improve the prognosis and decrease the mortality. IMPORTANCE Our study indicates high efficiency of mNGS using BALF for the detection of causative pathogens that cause pneumonia in children. mNGS can be a potential diagnostic tool to supplement conventional methods for children's pneumonia.}, } @article {pmid36169314, year = {2022}, author = {Mauch, E and Serra Moncadas, L and Andrei, AS}, title = {Complete Genome Sequence of an Uncultivated Freshwater Bacteroidota Lineage.}, journal = {Microbiology resource announcements}, volume = {11}, number = {10}, pages = {e0076622}, pmid = {36169314}, issn = {2576-098X}, support = {193240//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 193240//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; }, abstract = {We report here a complete metagenome-assembled genome belonging to the AKYH767 order within the Bacteroidota phylum. The recovered genome stems from a nonaxenic Amoebozoa culture from Lake Zürich and was assembled as a circular element at a length of 4.1 Mbp and a coverage of 115×.}, } @article {pmid36169030, year = {2022}, author = {Simpson, JB and Redinbo, MR}, title = {Multi-omic analysis of host-microbial interactions central to the gut-brain axis.}, journal = {Molecular omics}, volume = {18}, number = {10}, pages = {896-907}, doi = {10.1039/d2mo00205a}, pmid = {36169030}, issn = {2515-4184}, support = {P30 CA016086/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Host Microbial Interactions ; Brain ; *Gastrointestinal Microbiome/physiology ; Neurotransmitter Agents ; Brain-Gut Axis ; }, abstract = {The gut microbiota impact numerous aspects of human physiology, including the central nervous system (CNS). Emerging work is now focusing on the microbial factors underlying the bi-directional communication network linking host and microbial systems within the gastrointestinal tract to the CNS, the "gut-brain axis". Neurotransmitters are key coordinators of this network, and their dysregulation has been linked to numerous neurological disease states. As the bioavailability of neurotransmitters is modified by gut microbes, it is critical to unravel the influence of the microbiota on neurotransmitters in the context of the gut-brain axis. Here we review foundational studies that defined molecular relationships between the microbiota, neurotransmitters, and the gut-brain axis. We examine links between the gut microbiome, behavior, and neurological diseases, as well as microbial influences on neurotransmitter bioavailability and physiology. Finally, we review multi-omics technologies uniquely applicable to this area, including high-throughput genetics, modern metabolomics, structure-guided metagenomics, targeted proteomics, and chemogenetics. Interdisciplinary studies will continue to drive the discovery of molecular mechanisms linking the gut microbiota to clinical manifestations of neurobiology.}, } @article {pmid36168550, year = {2022}, author = {Inam, Z and Felton, E and Burrell, A and Chaney, H and Sami, I and Koumbourlis, AC and Freishtat, RJ and Zemanick, ET and Crandall, KA and Hahn, A}, title = {Impact of Antibiotics on the Lung Microbiome and Lung Function in Children With Cystic Fibrosis 1 Year After Hospitalization for an Initial Pulmonary Exacerbation.}, journal = {Open forum infectious diseases}, volume = {9}, number = {9}, pages = {ofac466}, pmid = {36168550}, issn = {2328-8957}, abstract = {BACKGROUND: Cystic fibrosis (CF) is characterized by recurrent pulmonary exacerbations (PEx) and lung function decline. PEx are frequently treated with antibiotics. However, little is known about the effects of antibiotics on the airway microbiome of persons with CF over time. The purpose of this study was to evaluate changes in the microbiome and lung function in persons with CF over 1 year following an initial study pulmonary exacerbation (iPEx).

METHODS: Twenty children aged ≤18 years with CF were enrolled in the study, which occurred prior to the routine administration of highly effective modulator therapy. Respiratory samples and spirometry were obtained at a minimum of quarterly visits and up to 1 year after an iPEx. Metagenomic sequencing was performed, and bacterial taxa were assigned using MetaPhlAn 2.0. Paired t test, analysis of variance, and generalized least squares regression were used to compare outcome variables.

RESULTS: The mean age of study participants at the time of the iPEx was 10.6 years. There were 3 ± 1.6 PEx treated with antibiotics per person during the study period. Bacterial richness was similar at 1 year compared to iPEx (40.3 vs 39.3, P = .852), whereas the mean Shannon diversity index was significantly higher at 1 year (2.84 vs 1.62, P < .001). The number of PEx treated with antibiotics was not associated with changes in microbial diversity but was associated with changes in lung function.

CONCLUSIONS: In our 1-year prospective study, we found that microbial diversity increased despite decreases in lung function associated with repeated PEx events requiring antibiotic therapy.}, } @article {pmid36168472, year = {2021}, author = {Elliott, TM and Harris, PN and Roberts, LW and Doidge, M and Hurst, T and Hajkowicz, K and Forde, B and Paterson, DL and Gordon, LG}, title = {Cost-effectiveness analysis of whole-genome sequencing during an outbreak of carbapenem-resistant Acinetobacter baumannii.}, journal = {Antimicrobial stewardship & healthcare epidemiology : ASHE}, volume = {1}, number = {1}, pages = {e62}, pmid = {36168472}, issn = {2732-494X}, abstract = {BACKGROUND: Whole-genome sequencing (WGS) shotgun metagenomics (metagenomics) attempts to sequence the entire genetic content straight from the sample. Diagnostic advantages lie in the ability to detect unsuspected, uncultivatable, or very slow-growing organisms.

OBJECTIVE: To evaluate the clinical and economic effects of using WGS and metagenomics for outbreak management in a large metropolitan hospital.

DESIGN: Cost-effectiveness study.

SETTING: Intensive care unit and burn unit of large metropolitan hospital.

PATIENTS: Simulated intensive care unit and burn unit patients.

METHODS: We built a complex simulation model to estimate pathogen transmission, associated hospital costs, and quality-adjusted life years (QALYs) during a 32-month outbreak of carbapenem-resistant Acinetobacter baumannii (CRAB). Model parameters were determined using microbiology surveillance data, genome sequencing results, hospital admission databases, and local clinical knowledge. The model was calibrated to the actual pathogen spread within the intensive care unit and burn unit (scenario 1) and compared with early use of WGS (scenario 2) and early use of WGS and metagenomics (scenario 3) to determine their respective cost-effectiveness. Sensitivity analyses were performed to address model uncertainty.

RESULTS: On average compared with scenario 1, scenario 2 resulted in 14 fewer patients with CRAB, 59 additional QALYs, and $75,099 cost savings. Scenario 3, compared with scenario 1, resulted in 18 fewer patients with CRAB, 74 additional QALYs, and $93,822 in hospital cost savings. The likelihoods that scenario 2 and scenario 3 were cost-effective were 57% and 60%, respectively.

CONCLUSIONS: The use of WGS and metagenomics in infection control processes were predicted to produce favorable economic and clinical outcomes.}, } @article {pmid36167925, year = {2022}, author = {Kim, DW and Ahn, JH and Cha, CJ}, title = {Biodegradation of plastics: mining of plastic-degrading microorganisms and enzymes using metagenomics approaches.}, journal = {Journal of microbiology (Seoul, Korea)}, volume = {60}, number = {10}, pages = {969-976}, pmid = {36167925}, issn = {1976-3794}, mesh = {Biodegradation, Environmental ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Plastics/metabolism ; }, abstract = {Plastic pollution exacerbated by the excessive use of synthetic plastics and its recalcitrance has been recognized among the most pressing global threats. Microbial degradation of plastics has gained attention as a possible eco-friendly countermeasure, as several studies have shown microbial metabolic capabilities as potential degraders of various synthetic plastics. However, still defined biochemical mechanisms of biodegradation for the most plastics remain elusive, because the widely used culture-dependent approach can access only a very limited amount of the metabolic potential in each microbiome. A culture-independent approach, including metagenomics, is becoming increasingly important in the mining of novel plastic-degrading enzymes, considering its more expanded coverage on the microbial metabolism in microbiomes. Here, we described the advantages and drawbacks associated with four different metagenomics approaches (microbial community analysis, functional metagenomics, targeted gene sequencing, and whole metagenome sequencing) for the mining of plastic-degrading microorganisms and enzymes from the plastisphere. Among these approaches, whole metagenome sequencing has been recognized among the most powerful tools that allow researchers access to the entire metabolic potential of a microbiome. Accordingly, we suggest strategies that will help to identify plastisphere-enriched sequences as de novo plastic-degrading enzymes using the whole metagenome sequencing approach. We anticipate that new strategies for metagenomics approaches will continue to be developed and facilitate to identify novel plastic-degrading microorganisms and enzymes from microbiomes.}, } @article {pmid36167833, year = {2022}, author = {Xiao, R and Luo, G and Liao, W and Chen, S and Han, S and Liang, S and Lin, Y}, title = {Association of human gut microbiota composition and metabolic functions with Ficus hirta Vahl dietary supplementation.}, journal = {NPJ science of food}, volume = {6}, number = {1}, pages = {45}, pmid = {36167833}, issn = {2396-8370}, abstract = {Ficus hirta Vahl (FHV), a traditional herbal ingredient of the tonic diet, receives increasing popularity in southern China. However, it is largely unknown that how a FHV diet (FHVD) affects the human gut microbiome. In this exploratory study, a total of 43 healthy individuals were randomized into the FHVD (n = 25) and Control (n = 18) groups to receive diet intervention for 8 weeks. 16S rRNA gene sequencing, metagenomic sequencing and metabolic profile of participants were measured to assess the association between FHV diet and gut microbiome. A preservation effect of Faecalibacterium and enrichment of Dialister, Veillonella, Clostridium, and Lachnospiraceae were found during the FHVD. Accordingly, the pathway of amino acid synthesis, citrate cycle, coenzyme synthesis, and partial B vitamin synthesis were found to be more abundant in the FHVD. In addition, serine, glutamine, gamma-aminobutyric acid, tryptamine, and short-chain fatty acids (SCFAs) were higher after the FHVD. The conjoint analysis of FHV components and in-vitro fermentation confirmed that the improved SCFAs concentration was collectively contributed by the increasing abundance of key enzyme genes and available substrates. In conclusion, the muti-omics analysis showed that the FHVD optimized the structure of the gut microbial community and its metabolic profile, leading to a healthy tendency, with a small cluster of bacteria driving the variation rather than a single taxon.}, } @article {pmid36167684, year = {2022}, author = {Seong, HJ and Roux, S and Hwang, CY and Sul, WJ}, title = {Marine DNA methylation patterns are associated with microbial community composition and inform virus-host dynamics.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {157}, pmid = {36167684}, issn = {2049-2618}, mesh = {*Bacteriophages/genetics ; DNA ; DNA Methylation/genetics ; Metagenome/genetics ; Metagenomics ; Methyltransferases/genetics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: DNA methylation in prokaryotes is involved in many different cellular processes including cell cycle regulation and defense against viruses. To date, most prokaryotic methylation systems have been studied in culturable microorganisms, resulting in a limited understanding of DNA methylation from a microbial ecology perspective. Here, we analyze the distribution patterns of several microbial epigenetics marks in the ocean microbiome through genome-centric metagenomics across all domains of life.

RESULTS: We reconstructed 15,056 viral, 252 prokaryotic, 56 giant viral, and 6 eukaryotic metagenome-assembled genomes from northwest Pacific Ocean seawater samples using short- and long-read sequencing approaches. These metagenome-derived genomes mostly represented novel taxa, and recruited a majority of reads. Thanks to single-molecule real-time (SMRT) sequencing technology, base modification could also be detected for these genomes. This showed that DNA methylation can readily be detected across dominant oceanic bacterial, archaeal, and viral populations, and microbial epigenetic changes correlate with population differentiation. Furthermore, our genome-wide epigenetic analysis of Pelagibacter suggests that GANTC, a DNA methyltransferase target motif, is related to the cell cycle and is affected by environmental conditions. Yet, the presence of this motif also partitions the phylogeny of the Pelagibacter phages, possibly hinting at a competitive co-evolutionary history and multiple effects of a single methylation mark.

CONCLUSIONS: Overall, this study elucidates that DNA methylation patterns are associated with ecological changes and virus-host dynamics in the ocean microbiome. Video Abstract.}, } @article {pmid36167169, year = {2022}, author = {Deng, Y and Yang, S and Zhao, H and Luo, J and Yang, W and Hou, C}, title = {Antibiotics-induced changes in intestinal bacteria result in the sensitivity of honey bee to virus.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {314}, number = {}, pages = {120278}, doi = {10.1016/j.envpol.2022.120278}, pmid = {36167169}, issn = {1873-6424}, mesh = {Bees ; Animals ; *Anti-Bacterial Agents/toxicity ; *Virus Diseases ; Antiviral Agents ; Tetracyclines ; Bacteria ; }, abstract = {Antibiotics are omnipresent in the environment due to their widespread use, and they have wide-ranging negative impacts on organisms. Virus resistance differs substantially between domesticated Apis mellifera and wild Apis cerana, although both are commonly raised in China. Here, we investigated whether antibiotics can increase the sensitivity of honey bees to viral infection using the Israeli acute paralysis virus (IAPV) and tetracycline as representative virus and antibiotic. Although IAPV multiplied to lower levels in A. cerana than A. mellifera, resulting in decreased mortality (P < 0.01), there was no significant difference in immune responses to viral infection between the two species. Adult worker bees (A. cerana and A. mellifera) were treated with or without tetracycline to demonstrate the prominent role of gut microbiota against viral infection, and found Lactobacillus played a vital antiviral role in A. cerana. In A. cerana but not A. mellifera, tetracycline treatment reduced clearly bee survival and increased susceptibility to IAPV infection (P < 0.01). Our findings revealed that long-term antibiotic treatment in A. mellifera had altered the native gut microbiome and promoted the sensitivity to viral infection. We highlight the effects of antibiotics exposure on resistance to microbial and viral infection.}, } @article {pmid36166999, year = {2022}, author = {Sun, Z and Li, J and Fan, Y and Meng, J}, title = {A quantified nitrogen metabolic network by reaction kinetics and mathematical model in a single-stage microaerobic system treating low COD/TN wastewater.}, journal = {Water research}, volume = {225}, number = {}, pages = {119112}, doi = {10.1016/j.watres.2022.119112}, pmid = {36166999}, issn = {1879-2448}, mesh = {*Wastewater ; *Nitrogen ; Denitrification ; Biological Oxygen Demand Analysis ; Bioreactors/microbiology ; Ammonia ; Sewage ; Kinetics ; Nitrites ; Nitrates ; Nitrogen Dioxide ; Oxidation-Reduction ; Models, Theoretical ; Metabolic Networks and Pathways ; Oxygen ; }, abstract = {A single-stage intermittent aeration microaerobic reactor (IAMR) has been developed for the cost-effective nitrogen removal from piggery wastewater with a low ratio of chemical oxygen demand (COD) to total nitrogen (TN). In this study, a quantified nitrogen metabolic network was constructed based on the metagenomics, reaction kinetics and mathematical model to provide a revealing insight into the nitrogen removal mechanism in the IAMR. Metagenomics revealed that a complex nitrogen metabolic network, including aerobic ammonia and nitrite oxidation, anammox, denitrification via nitrate and nitrite, and nitrate respiration, existed in the IAMR. A novel method for solving kinetic parameters with high stability was developed based on a genetic algorithm. Use this method to calculate the kinetics of various reactions involved in nitrogen metabolism. Kinetics revealed that simultaneous partial nitritation-anammox (PN/A) and partial denitrification-anammox (PDN/A) were the dominant approaches to nitrogen removal in the IAMR. Finally, a kinetics-based model was proposed for quantitatively describing the nitrogen metabolic network under the limitation of COD. 58% ∼ 67% of nitrogen was removed via the anammox-based processes (PN/A and PDN/A), but only 7% ∼ 12% and 1% ∼ 2% of nitrogen were removed via heterotrophic denitrification of nitrite and nitrate, respectively. The half-inhibition constant of dissolved oxygen (DO) on anammox was simulated as 0.37 ∼ 0.60 mg L[-1], filling the gap in quantifying DO inhibition on anammox. High-frequency intermittent aeration was identified as the crucial measure to suppress nitrite-oxidizing bacteria, although it has a high affinity for DO and NO2[-]-N. In continuous aeration mode, the simulated NO3[-]-N in the IAMR would rise by 39.6%. The research provides a novel insight into the nitrogen removal mechanism in single-stage microaerobic systems and provides a reliable approach to practicing PN/A and PDN/A for cost-effective nitrogen removal.}, } @article {pmid36166626, year = {2022}, author = {Eusébio, N and Castelo-Branco, R and Sousa, D and Preto, M and D'Agostino, P and Gulder, TAM and Leão, PN}, title = {Discovery and Heterologous Expression of Microginins from Microcystis aeruginosa LEGE 91341.}, journal = {ACS synthetic biology}, volume = {11}, number = {10}, pages = {3493-3503}, pmid = {36166626}, issn = {2161-5063}, mesh = {*Microcystis/genetics/chemistry/metabolism ; Polyketide Synthases/genetics/metabolism ; *Cyanobacteria/metabolism ; Protease Inhibitors/metabolism ; Lipopeptides/metabolism ; Amino Acids/metabolism ; }, abstract = {Microginins are a large family of cyanobacterial lipopeptide protease inhibitors. A hybrid polyketide synthase/non-ribosomal peptide synthetase biosynthetic gene cluster (BGC) found in several microginin-producing strains─mic─was proposed to encode the production of microginins, based on bioinformatic analysis. Here, we explored a cyanobacterium, Microcystis aeruginosa LEGE 91341, which contains a mic BGC, to discover 12 new microginin variants. The new compounds contain uncommon amino acids, namely, homophenylalanine (Hphe), homotyrosine (Htyr), or methylproline, as well as a 3-aminodecanoic acid (Ada) residue, which in some variants was chlorinated at its terminal methyl group. We have used direct pathway cloning (DiPaC) to heterologously express the mic BGC from M. aeruginosa LEGE 91341 in Escherichia coli, which led to the production of several microginins. This proved that the mic BGC is, in fact, responsible for the biosynthesis of microginins and paves the way to accessing new variants from (meta)genome data or through pathway engineering.}, } @article {pmid36166104, year = {2023}, author = {Liu, H and Wu, W and Luo, Y}, title = {Oral and intravenous iron treatment alter the gut microbiome differentially in dialysis patients.}, journal = {International urology and nephrology}, volume = {55}, number = {3}, pages = {759-767}, pmid = {36166104}, issn = {1573-2584}, support = {Sz2019016//Provincial special matching funds of Shanxi Provincial People's Hospital/ ; }, mesh = {Humans ; Iron ; *Gastrointestinal Microbiome ; Renal Dialysis ; Ferric Oxide, Saccharated ; *Renal Insufficiency, Chronic ; *Anemia ; }, abstract = {OBJECTIVE: Chronic kidney disease (CKD) is often complicated by anemia, which seriously affects the quality-of-life and prognosis of patients. These patients usually need iron replacement therapy. Oral iron affects the composition and abundance of intestinal flora by increasing intestinal iron concentration.

METHODS: We undertook an interventional study to investigate the effects of oral versus intravenous iron therapy on the gut microbiota. Oral ferrous succinate tablets (n = 14) or intravenous iron sucrose (n = 14) was administered to anemic maintenance hemodialysis (MHD) patients for 2 months.

RESULTS: Oral and intravenous iron treatments had different effects on gut microbial composition and diversity. After oral iron treatment, the α-diversity was decreased, while at the phylum level, the abundance of Firmicutes was reduced and the abundance of Bacteroides was increased. At the genus level, the abundance of Blautia and Coprococcus was decreased, and the abundance of Bacteroidetes was increased. Oral iron therapy was associated with a higher abundance of Lactobacillus compared with that measured in intravenous iron-treated patients. According to metagenome function prediction analysis, oral iron increased the metabolic processes of phenylalanine, valine, leucine, and isoleucine. These changes may increase uremic toxin levels, thereby increasing the progression of renal disease.

CONCLUSION: Iron therapy affects the diversity and composition of gut flora in MHD patients. Oral iron affects the number of bacteria and increases amino acid metabolism compared with intravenous iron. These results indicate that intravenous iron may be more appropriate for MHD patients.}, } @article {pmid36165858, year = {2022}, author = {Kukkar, D and Sharma, PK and Kim, KH}, title = {Recent advances in metagenomic analysis of different ecological niches for enhanced biodegradation of recalcitrant lignocellulosic biomass.}, journal = {Environmental research}, volume = {215}, number = {Pt 2}, pages = {114369}, doi = {10.1016/j.envres.2022.114369}, pmid = {36165858}, issn = {1096-0953}, mesh = {Biofuels ; Biomass ; *Ecosystem ; Fossil Fuels ; Lignin ; *Metagenomics/methods ; Soil/chemistry ; Sulfur ; }, abstract = {Lignocellulose wastes stemming from agricultural residues can offer an excellent opportunity as alternative energy solutions in addition to fossil fuels. Besides, the unrestrained burning of agricultural residues can lead to the destruction of the soil microflora and associated soil sterilization. However, the difficulties associated with the biodegradation of lignocellulose biomasses remain as a formidable challenge for their sustainable management. In this respect, metagenomics can be used as an effective option to resolve such dilemma because of its potential as the next generation sequencing technology and bioinformatics tools to harness novel microbial consortia from diverse environments (e.g., soil, alpine forests, and hypersaline/acidic/hot sulfur springs). In light of the challenges associated with the bulk-scale biodegradation of lignocellulose-rich agricultural residues, this review is organized to help delineate the fundamental aspects of metagenomics towards the assessment of the microbial consortia and novel molecules (such as biocatalysts) which are otherwise unidentifiable by conventional laboratory culturing techniques. The discussion is extended further to highlight the recent advancements (e.g., from 2011 to 2022) in metagenomic approaches for the isolation and purification of lignocellulolytic microbes from different ecosystems along with the technical challenges and prospects associated with their wide implementation and scale-up. This review should thus be one of the first comprehensive reports on the metagenomics-based analysis of different environmental samples for the isolation and purification of lignocellulose degrading enzymes.}, } @article {pmid36165830, year = {2022}, author = {Afzal, S and Singh, NK}, title = {Effect of zinc and iron oxide nanoparticles on plant physiology, seed quality and microbial community structure in a rice-soil-microbial ecosystem.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {314}, number = {}, pages = {120224}, doi = {10.1016/j.envpol.2022.120224}, pmid = {36165830}, issn = {1873-6424}, mesh = {Soil/chemistry ; *Oryza/metabolism ; *Zinc Oxide/chemistry ; Zinc ; Soil Microbiology ; Nitrites ; Lignin ; Ammonia ; Rhizosphere ; *Soil Pollutants/analysis ; *Microbiota ; Nitrogen ; Plant Physiological Phenomena ; Seeds/chemistry ; Carbon ; Micronutrients ; Streptomycin ; Magnetic Iron Oxide Nanoparticles ; Sulfates ; Chitin ; }, abstract = {In this study, we assessed the impact of zinc oxide (ZnO) and iron oxide (FeO) (<36 nm) nanoparticles (NPs) as well as their sulphate salt (bulk) counterpart (0, 25, 100 mg/kg) on rice growth and seed quality as well as the microbial community in the rhizosphere environment of rice. During the rice growing season 2021-22, all experiments were conducted in a greenhouse (temperature: day 30 °C; night 20 °C; relative humidity: 70%; light period: 16 h/8 h, day/night) in rice field soil. Results showed that low concentrations of FeO and ZnO NPs (25 mg/kg) promoted rice growth (height (29%, 16%), pigment content (2%, 3%)) and grain quality parameters such as grains per spike (8%, 9%), dry weight of grains (12%, 14%) respectively. As compared to the control group, the Zn (2%) and Fe (5%) accumulations at their respective low concentrations of NP treatments showed stimulation. Interestingly, our results showed that at low concentration of both the NPs the soil microbes had more diversity and richness than those in the bulk treated and control soil group. Although a number of phyla were affected by the presence of NPs, the strongest effects were observed for change in the abundance of the three phyla for Proteobacteria, Actinobacteria, and Planctomycetes. The rhizosphere environment was notably enriched with potential streptomycin producers, carbon and nitrogen fixers, and lignin degraders with regard to functional groups of microorganisms. However, microbial communities mainly responsible for chitin degradation, ammonia oxidation, and nitrite reduction were found to be decreased. The results from this study highlight significant changes in several plant-based endpoints, as well as the rhizosphere soil microorganisms. It further adds information to our understanding of the nanoscale-specific impacts of important micronutrient oxides on both rice and its associated soil microbiome.}, } @article {pmid36165828, year = {2022}, author = {Bertucci, A and Hoede, C and Dassié, E and Gourves, PY and Suin, A and Le Menach, K and Budzinski, H and Daverat, F}, title = {Impact of environmental micropollutants and diet composition on the gut microbiota of wild european eels (Anguilla anguilla).}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {314}, number = {}, pages = {120207}, doi = {10.1016/j.envpol.2022.120207}, pmid = {36165828}, issn = {1873-6424}, mesh = {Animals ; *Anguilla ; *Gastrointestinal Microbiome ; Environmental Biomarkers ; *Arsenic ; Hexachlorocyclohexane ; Persistent Organic Pollutants ; *Metals, Heavy ; Diet ; *Water Pollutants, Chemical/toxicity ; }, abstract = {In fish, the gut microbiome plays a crucial role in homeostasis and health and is affected by several organic and inorganic environmental contaminants. Amphidromous fish are sentinel species, particularly exposed to these stressors. We used whole metagenome sequencing to characterize the gut microbiome of wild European eels (Anguilla anguilla) at a juvenile stage captured from three sites with contrasted pollution levels in term of heavy metals and persistent organic pollutants. The objectives were to identify what parameters could alter the gut microbiome of this catadromous fish and to explore the potential use of microbiota as bioindicators of environment quality. We identified a total of 1079 microbial genera. Overall, gut microbiome was dominated by Proteobacteria, Firmicutes and Actinobacteria. Alpha and beta diversity were different amongst sites and could be explained by a reduced number of environmental and biological factors, specifically the relative abundance of fish preys in eels' diet, PCB101, γHCH (lindane), transnonachlor and arsenic. Furthermore, we identified a series of indicator taxa with differential abundance between the three sites. Changes in the microbial communities in the gut caused by environmental pollutants were previously undocumented in European eels. Our results indicate that microbiota might represent another route by which pollutants affect the health of these aquatic sentinel organisms.}, } @article {pmid36165648, year = {2022}, author = {Ajvazi, X and Serra Moncadas, L and Andrei, AS}, title = {Study of Complete Genome Sequence of Uncultivated Hyphomonadaceae sp.}, journal = {Microbiology resource announcements}, volume = {11}, number = {10}, pages = {e0076522}, pmid = {36165648}, issn = {2576-098X}, support = {193240//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 193240//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; }, abstract = {We report here a complete metagenome-assembled genome sequence belonging to the Proteobacteria phylum within the Hyphomonadaceae family. The circular chromosome was obtained from a metagenomic long-read sequencing run and displays a length of 4.1 Mbp along with a GC content of 62.5% at a coverage of 81×.}, } @article {pmid36165647, year = {2022}, author = {Bernet, J and Serra Moncadas, L and Andrei, AS}, title = {Complete Genome Sequence of an Uncultivated Freshwater Flavobacterium sp. Strain.}, journal = {Microbiology resource announcements}, volume = {11}, number = {10}, pages = {e0065922}, pmid = {36165647}, issn = {2576-098X}, support = {193240//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 193240//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; }, abstract = {Here, we report the complete metagenome-assembled genome of an uncultivated freshwater Flavobacterium sp. recovered from a nonaxenic Amoebozoa sp. culture. The chromosome was obtained from a metagenomic long-read sequencing run and was assembled as a circular element at a 51× coverage, length of 3.8 Mbp and a G+C content of 37.37%.}, } @article {pmid36165644, year = {2022}, author = {Rubin, IMC and Mollerup, S and Broholm, C and Baker, A and Holm, MKA and Pedersen, MS and Pinholt, M and Westh, H and Petersen, AM}, title = {Synbiotic Intervention with Lactobacilli, Bifidobacteria, and Inulin in Healthy Volunteers Increases the Abundance of Bifidobacteria but Does Not Alter Microbial Diversity.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {19}, pages = {e0108722}, pmid = {36165644}, issn = {1098-5336}, mesh = {Humans ; Bifidobacterium ; *Bifidobacterium animalis ; Feces/microbiology ; Healthy Volunteers ; Inulin ; Lactobacillus ; Lactobacillus acidophilus ; Prebiotics ; *Probiotics/pharmacology ; *Synbiotics ; }, abstract = {Synbiotics combine probiotics and prebiotics and are being investigated for potential health benefits. In this single-group-design trial, we analyzed changes in the gut microbiome, stool quality, and gastrointestinal well-being in 15 healthy volunteers after a synbiotic intervention comprising Lacticaseibacillus rhamnosus (LGG), Lactobacillus acidophilus (LA-5), Lacticaseibacillus paracasei subsp. paracasei (L. CASEI 431), and Bifidobacterium animalis subsp. lactis BB-12 and 20 g of chicory-derived inulin powder consumed daily for 4 weeks. Fecal samples were collected at baseline and at completion of the intervention, and all participants completed a fecal diary based on the Bristol Stool Scale and recorded their gastrointestinal well-being. No adverse effects were observed after consumption of the synbiotic product, and stool consistency and frequency remained almost unchanged during the trial. Microbiome analysis of the fecal samples was achieved using shotgun sequencing followed by taxonomic profiling. No changes in alpha and beta diversity were seen after the intervention. Greater relative abundances of Bifidobacteriaceae were observed in 12 subjects, with indigenous bifidobacteria species constituting the main increase. All four probiotic organisms increased in abundance, and L. rhamnosus, B. animalis, and L. acidophilus were differentially abundant, compared to baseline. Comparison of the fecal strains to the B. animalis subsp. lactis BB-12 reference genome and the sequenced symbiotic product revealed only a few single-nucleotide polymorphisms differentiating the probiotic B. animalis subsp. lactis BB-12 from the fecal strains identified, indicating that this probiotic strain was detectable after the intervention. IMPORTANCE The effects of probiotics/synbiotics are seldom investigated in healthy volunteers; therefore, this study is important, especially considering the safety aspects of multiple probiotics together with prebiotic fiber in consumption by humans. The study explores at the potential of a synbiotic intervention with lactobacilli, bifidobacteria, and inulin in healthy volunteers and tracks the ingested probiotic strain B. animalis subsp. lactis.}, } @article {pmid36165045, year = {2022}, author = {Shareefdeen, H and Hill, C}, title = {The gut virome in health and disease: new insights and associations.}, journal = {Current opinion in gastroenterology}, volume = {38}, number = {6}, pages = {549-554}, pmid = {36165045}, issn = {1531-7056}, mesh = {Bacteria ; *Bacteriophages ; *COVID-19 ; Humans ; Infant, Newborn ; Metagenomics ; *Microbiota ; Virome ; *Viruses ; }, abstract = {PURPOSE OF REVIEW: Recent years have seen great strides made in the field of viral metagenomics. Many studies have reported alterations in the virome in different disease states. The vast majority of the human intestinal virome consists of bacteriophages, viruses that infect bacteria. The dynamic relationship between gut bacterial populations and bacteriophages is influenced by environmental factors that also impact host health and disease. In this review, we focus on studies highlighting the dynamics of the gut virome and fluctuations associated with disease states.

RECENT FINDINGS: Novel correlations have been identified between the human gut virome and diseases such as obesity, necrotizing enterocolitis and severe acute respiratory syndrome coronavirus 2 infection. Further associations between the virome and cognition, diet and geography highlight the complexity of factors that can influence the dynamic relationship between gut bacteria, bacteriophages and health.

SUMMARY: Here, we highlight some novel associations between the virome and health that will be the foundation for future studies in this field. The future development of microbiome-based interventions, identification of biomarkers, and novel therapeutics will require a thorough understanding of the gut virome and its dynamics.}, } @article {pmid36164761, year = {2022}, author = {Hooi, SL and Dwiyanto, J and Rasiti, H and Toh, KY and Wong, RKM and Lee, JWJ}, title = {A case report of improvement on ADHD symptoms after fecal microbiota transplantation with gut microbiome profiling pre- and post-procedure.}, journal = {Current medical research and opinion}, volume = {38}, number = {11}, pages = {1977-1982}, doi = {10.1080/03007995.2022.2129232}, pmid = {36164761}, issn = {1473-4877}, mesh = {Female ; Humans ; Young Adult ; Adult ; Fecal Microbiota Transplantation/methods ; *Gastrointestinal Microbiome ; *Clostridioides difficile ; *Attention Deficit Disorder with Hyperactivity/therapy ; *Clostridium Infections ; Feces ; }, abstract = {BACKGROUND: Recent studies demonstrate the association of the gut microbiome in regulating interactions between the central nervous system and intestinal function. Individuals with attention-deficit hyperactivity disorder (ADHD) have been shown to have unique gut microbial signature, with depletion of beneficial commensal microbes. Fecal microbiota transplant (FMT) restores the imbalanced gut microbiome and may replete missing microbes to increase production of hormones and neurotransmitters regulating human behavior and cognition.

RESEARCH DESIGN & METHODS: Here, we present an interesting case of a 22-year-old woman treated with FMT primarily to treat recurrent Clostridioides difficile infection, which coincidentally alleviated her ADHD symptoms. We also present the pre- and post-FMT gut microbiota profiles conducted using shotgun metagenomic sequencing on the patient's fecal samples to thereby highlight potential microbial-associated mechanisms associated with the relief of ADHD symptoms.

RESULTS & CONCLUSIONS: Our case report provides preliminary evidence regarding the use of FMT in a patient with C. difficile and ADHD. We speculate that gut microbiome modulation, in particular the gain or loss of specific microbial species and pathways involving the metabolism of SCFAs, tryptophan and GABA, may merit further exploration as a potential therapeutic strategy for ADHD.}, } @article {pmid36164404, year = {2022}, author = {Yunes, RA and Poluektova, EU and Belkina, TV and Danilenko, VN}, title = {Lactobacilli: Legal Regulation and Prospects for New Generation Drugs.}, journal = {Applied biochemistry and microbiology}, volume = {58}, number = {5}, pages = {652-664}, pmid = {36164404}, issn = {0003-6838}, abstract = {The global probiotics industry has been undergoing major changes in recent years. Approaches to finding and creating new probiotics, as well as a paradigm of their use in food, medicine, and pharmacology are changing. The catalyst proved to be the increasing popularity and availability of omics technologies, in particular, metagenomic studies of human and animal microbiomes. However, the efficiency and safety of drugs based on probiotic strains, as well as their marketing rates, largely depend on the levels of legal and technical regulation in the field. The present review discusses the aspects of legal regulation in Russia, the European Union and the United States, along with the advantages and disadvantages of probiotics and postbiotics. A consensus is emerging that postbiotics have a number of advantages over classical live probiotic cultures. The review also focuses on the lactobacilli family, which includes the largest number of probiotic strains studied so far and still holds a leading position among probiotics. On the legislative front, Russia is often ahead of its time with adopting such laws as the Federal Law No. 492-FZ on biosecurity, which defined the concept of human and animal microbiota and set forth legislative guidelines for its preservation. The new field of research referred to as microbiome nutrigenomics aims to achieve this goal.}, } @article {pmid36164267, year = {2022}, author = {Sharpton, SR and Oh, TG and Madamba, E and Wang, C and Yu, RT and Atkins, AR and Huan, T and Downes, M and Evans, RM and Loomba, R}, title = {Gut metagenome-derived signature predicts hepatic decompensation and mortality in NAFLD-related cirrhosis.}, journal = {Alimentary pharmacology & therapeutics}, volume = {56}, number = {10}, pages = {1475-1485}, pmid = {36164267}, issn = {1365-2036}, support = {UL1 TR001442/TR/NCATS NIH HHS/United States ; P42 ES010337/ES/NIEHS NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; U01 AA029019/AA/NIAAA NIH HHS/United States ; R01 DK124318/DK/NIDDK NIH HHS/United States ; U01 DK061734/DK/NIDDK NIH HHS/United States ; P01 HL147835/HL/NHLBI NIH HHS/United States ; R01 DK121378/DK/NIDDK NIH HHS/United States ; R01 DK106419/DK/NIDDK NIH HHS/United States ; R01 DK057978/DK/NIDDK NIH HHS/United States ; P30 CA014195/CA/NCI NIH HHS/United States ; }, mesh = {Adult ; Humans ; *Non-alcoholic Fatty Liver Disease/complications/diagnosis/genetics ; *Hepatic Encephalopathy/etiology/genetics ; *Esophageal and Gastric Varices/complications ; Ascites/complications ; Prospective Studies ; *End Stage Liver Disease/complications ; Metagenome/genetics ; Rifaximin ; Lactulose ; Gastrointestinal Hemorrhage/etiology ; Severity of Illness Index ; Liver Cirrhosis/diagnosis/genetics/complications ; }, abstract = {BACKGROUND: There are limited data on the diagnostic accuracy of gut microbial signatures for predicting hepatic decompensation in patients with cirrhosis.

AIMS: To determine whether a stool metagenome-derived signature accurately detects hepatic decompensation and mortality risk in cirrhosis secondary to non-alcoholic fatty liver disease (NAFLD) METHODS: Shotgun metagenomic sequencing was performed on faecal samples collected at study entry from a prospective cohort of adults with NAFLD-related cirrhosis. A Random Forest machine learning algorithm was utilised to identify a metagenomic signature of decompensated cirrhosis (defined by ascites, hepatic encephalopathy or variceal haemorrhage) and subsequently validated in an external cohort. A Cox proportional hazards regression model was used to examine predictors of all-cause mortality.

RESULTS: In all, 25 adults with NAFLD-related cirrhosis (training cohort) were included. Among the 16 participants with decompensated cirrhosis, 33% had ascites, 56% had hepatic encephalopathy and 22% had experienced a variceal haemorrhage (not mutually exclusive). We identified a stool metagenomic signature comprising 13 discriminatory species that reliably distinguished decompensated NAFLD-related cirrhosis (diagnostic accuracy, 0.97, 95% confidence interval [CI] 0.96-0.99). Diagnostic accuracy of the 13-species signature remained high after adjustment for lactulose (area under the curve [AUC] 0.99) and rifaximin use (AUC 0.93). The discriminative ability of 13-species metagenomic signature was robust in an independent test cohort (AUC 0.95, 95% CI 0.81-1.00). The 13-species metagenomic signature (hazard ratio [HR] 1.54, 95% CI 1.10-2.15, p = 0.01) was a stronger predictor of mortality than the Model for End-Stage Liver Disease score (HR 1.25, 95% CI 1.03-1.53, p = 0.03).

CONCLUSIONS: This study provides evidence for a gut metagenome-derived signature with high diagnostic accuracy for hepatic decompensation that predicts risk of mortality in NAFLD-related cirrhosis.}, } @article {pmid36163498, year = {2022}, author = {Beck, LC and Masi, AC and Young, GR and Vatanen, T and Lamb, CA and Smith, R and Coxhead, J and Butler, A and Marsland, BJ and Embleton, ND and Berrington, JE and Stewart, CJ}, title = {Strain-specific impacts of probiotics are a significant driver of gut microbiome development in very preterm infants.}, journal = {Nature microbiology}, volume = {7}, number = {10}, pages = {1525-1535}, pmid = {36163498}, issn = {2058-5276}, support = {221745/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents ; Bifidobacterium/genetics ; *Bifidobacterium bifidum ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; *Probiotics ; }, abstract = {The development of the gut microbiome from birth plays important roles in short- and long-term health, but factors influencing preterm gut microbiome development are poorly understood. In the present study, we use metagenomic sequencing to analyse 1,431 longitudinal stool samples from 123 very preterm infants (<32 weeks' gestation) who did not develop intestinal disease or sepsis over a study period of 10 years. During the study period, one cohort had no probiotic exposure whereas two cohorts were given different probiotic products: Infloran (Bifidobacterium bifidum and Lactobacillus acidophilus) or Labinic (B. bifidum, B. longum subsp. infantis and L. acidophilus). Mothers' own milk, breast milk fortifier, antibiotics and probiotics were significantly associated with the gut microbiome, with probiotics being the most significant factor. Probiotics drove microbiome transition into different preterm gut community types (PGCTs), each enriched in a different Bifidobacterium sp. and significantly associated with increased postnatal age. Functional analyses identified stool metabolites associated with PGCTs and, in preterm-derived organoids, sterile faecal supernatants impacted intestinal, organoid monolayer, gene expression in a PGCT-specific manner. The present study identifies specific influencers of gut microbiome development in very preterm infants, some of which overlap with those impacting term infants. The results highlight the importance of strain-specific differences in probiotic products and their impact on host interactions in the preterm gut.}, } @article {pmid36163472, year = {2022}, author = {Pinto, G and Shetty, SA and Zoetendal, EG and Gonçalves, RFS and Pinheiro, AC and Almeida, C and Azeredo, J and Smidt, H}, title = {An in vitro fermentation model to study the impact of bacteriophages targeting Shiga toxin-encoding Escherichia coli on the colonic microbiota.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {74}, pmid = {36163472}, issn = {2055-5008}, mesh = {*Bacteriophages/genetics ; Coliphages/genetics ; Colon ; *Escherichia coli Infections/microbiology/prevention & control ; Fermentation ; Humans ; *Microbiota ; Shiga Toxin ; *Shiga-Toxigenic Escherichia coli ; }, abstract = {Lytic bacteriophages are considered safe for human consumption as biocontrol agents against foodborne pathogens, in particular in ready-to-eat foodstuffs. Phages could, however, evolve to infect different hosts when passing through the gastrointestinal tract (GIT). This underlines the importance of understanding the impact of phages towards colonic microbiota, particularly towards bacterial families usually found in the colon such as the Enterobacteriaceae. Here we propose in vitro batch fermentation as model for initial safety screening of lytic phages targeting Shiga toxin-producing Escherichia coli (STEC). As inoculum we used faecal material of three healthy donors. To assess phage safety, we monitored fermentation parameters, including short chain fatty acid production and gas production/intake by colonic microbiota. We performed shotgun metagenomic analysis to evaluate the outcome of phage interference with colonic microbiota composition and functional potential. During the 24 h incubation, concentrations of phage and its host were also evaluated. We found the phage used in this study, named E. coli phage vB_EcoS_Ace (Ace), to be safe towards human colonic microbiota, independently of the donors' faecal content used. This suggests that individuality of donor faecal microbiota did not interfere with phage effect on the fermentations. However, the model revealed that the attenuated STEC strain used as phage host perturbed the faecal microbiota as based on metagenomic analysis, with potential differences in metabolic output. We conclude that the in vitro batch fermentation model used in this study is a reliable safety screening for lytic phages intended to be used as biocontrol agents.}, } @article {pmid36163270, year = {2023}, author = {Bonnet, S and Benavides, M and Le Moigne, FAC and Camps, M and Torremocha, A and Grosso, O and Dimier, C and Spungin, D and Berman-Frank, I and Garczarek, L and Cornejo-Castillo, FM}, title = {Diazotrophs are overlooked contributors to carbon and nitrogen export to the deep ocean.}, journal = {The ISME journal}, volume = {17}, number = {1}, pages = {47-58}, pmid = {36163270}, issn = {1751-7370}, mesh = {*Nitrogen Fixation ; Nitrogen ; Carbon ; Seawater/microbiology ; *Cyanobacteria/genetics ; Pacific Ocean ; }, abstract = {Diazotrophs are widespread microorganisms that alleviate nitrogen limitation in 60% of our oceans, thereby regulating marine productivity. Yet, the group-specific contribution of diazotrophs to organic matter export has not been quantified, which so far has impeded an accurate assessment of their impact on the biological carbon pump. Here, we examine the fate of five groups of globally-distributed diazotrophs by using an original combination of mesopelagic particle sampling devices across the subtropical South Pacific Ocean. We demonstrate that cyanobacterial and non-cyanobacterial diazotrophs are exported down to 1000 m depth. Surprisingly, group-specific export turnover rates point to a more efficient export of small unicellular cyanobacterial diazotrophs (UCYN) relative to the larger and filamentous Trichodesmium. Phycoerythrin-containing UCYN-B and UCYN-C-like cells were recurrently found embedded in large (>50 µm) organic aggregates or organized into clusters of tens to hundreds of cells linked by an extracellular matrix, presumably facilitating their export. Beyond the South Pacific, our data are supported by analysis of the Tara Oceans metagenomes collected in other ocean basins, extending the scope of our results globally. We show that, when diazotrophs are found in the euphotic zone, they are also systematically present in mesopelagic waters, suggesting their transport to the deep ocean. We thus conclude that diazotrophs are a significant part of the carbon sequestered in the deep ocean and, therefore, they need to be accounted in regional and global estimates of export.}, } @article {pmid36162579, year = {2023}, author = {Sun, R and Cao, Z and Wen, X and Ma, L and Zhou, Y and Li, J and Fu, M and Zhu, P and Li, K and Li, Q}, title = {Quinone redox cycling drives lignocellulose depolymerization and degradation in composting environments based on metagenomics analysis.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 1}, pages = {159009}, doi = {10.1016/j.scitotenv.2022.159009}, pmid = {36162579}, issn = {1879-1026}, mesh = {*Composting ; Lignin/metabolism ; Metagenomics ; Soil ; Quinones ; Oxidation-Reduction ; Manure/microbiology ; }, abstract = {In this study, the effect of Fe[3+] on the quinone redox cycling driving lignocellulosic degradation in composting systems was investigated. The results showed that the degradation rates of cellulose, hemicellulose, and lignin were higher in the experimental group (CT) with Fe2(SO4)3 addition than in the blank group (CK) (CT, 52.55 %, 45.14 %, 56.98 %; CK, 49.63 %, 37.34 %, 52.3 %). Changes in the abundance of key enzymes for quinone reduction (AA3_1, AA3_2, AA6) and the structural succession of microbial communities were analyzed by metagenomic analysis. Among them, Fe2(SO4)3 had the most significant effect on AA3_2, with an approximately 8-fold increase in abundance compared to the beginning of composting. The dominant phylum in the composting process was Actinobacteria. In conclusion, the addition of Fe2(SO4)3 contributed to the quinone redox cycling and effectively improved the degradation rate of lignocellulose in composting.}, } @article {pmid36162065, year = {2022}, author = {Liu, K and Schiff, SL and Wu, L and Molot, LA and Venkiteswaran, JJ and Paterson, MJ and Elgood, RJ and Tsuji, JM and Neufeld, JD}, title = {Large Fractionation in Iron Isotopes Implicates Metabolic Pathways for Iron Cycling in Boreal Shield Lakes.}, journal = {Environmental science & technology}, volume = {56}, number = {20}, pages = {14840-14851}, doi = {10.1021/acs.est.2c04247}, pmid = {36162065}, issn = {1520-5851}, mesh = {*Cyanobacteria ; Ferrous Compounds ; Geologic Sediments/microbiology ; Iron ; Iron Isotopes ; *Lakes/microbiology ; Metabolic Networks and Pathways ; Minerals ; Water ; }, abstract = {Stable Fe isotopes have only recently been measured in freshwater systems, mainly in meromictic lakes. Here we report the δ[56]Fe of dissolved, particulate, and sediment Fe in two small dimictic boreal shield headwater lakes: manipulated eutrophic Lake 227, with annual cyanobacterial blooms, and unmanipulated oligotrophic Lake 442. Within the lakes, the range in δ[56]Fe is large (ca. -0.9 to +1.8‰), spanning more than half the entire range of natural Earth surface samples. Two layers in the water column with distinctive δ[56]Fe of dissolved (dis) and particulate (spm) Fe were observed, despite differences in trophic states. In the epilimnia of both lakes, a large Δ[56]Fedis-spm fractionation of 0.4-1‰ between dissolved and particulate Fe was only observed during cyanobacterial blooms in Lake 227, possibly regulated by selective biological uptake of isotopically light Fe by cyanobacteria. In the anoxic layers in both lakes, upward flux from sediments dominates the dissolved Fe pool with an apparent Δ[56]Fedis-spm fractionation of -2.2 to -0.6‰. Large Δ[56]Fedis-spm and previously published metagenome sequence data suggest active Fe cycling processes in anoxic layers, such as microaerophilic Fe(II) oxidation or photoferrotrophy, could regulate biogeochemical cycling. Large fractionation of stable Fe isotopes in these lakes provides a potential tool to probe Fe cycling and the acquisition of Fe by cyanobacteria, with relevance for understanding biogeochemical cycling of Earth's early ferruginous oceans.}, } @article {pmid36161930, year = {2022}, author = {Hogg, CJ and Belov, K}, title = {Reply to DeWoody et al.: Inequitable access to affordable sequencing limits the benefits from population genomic insights.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {40}, pages = {e2211129119}, pmid = {36161930}, issn = {1091-6490}, mesh = {Costs and Cost Analysis ; *Metagenomics ; *Problem Solving ; Sequence Analysis, DNA ; }, } @article {pmid36161902, year = {2022}, author = {Li, ML and Wang, S and Xu, P and Tian, HY and Bai, M and Zhang, YP and Shao, Y and Xiong, ZJ and Qi, XG and Cooper, DN and Zhang, G and Zhu, HH and Wu, DD}, title = {Functional genomics analysis reveals the evolutionary adaptation and demographic history of pygmy lorises.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {40}, pages = {e2123030119}, pmid = {36161902}, issn = {1091-6490}, mesh = {*Adaptation, Biological/genetics ; Animals ; *Biological Evolution ; Demography ; Hibernation ; *Lorisidae/genetics ; Metagenomics ; Metalloendopeptidases/genetics ; }, abstract = {Lorises are a group of globally threatened strepsirrhine primates that exhibit many unusual physiological and behavioral features, including a low metabolic rate, slow movement, and hibernation. Here, we assembled a chromosome-level genome sequence of the pygmy loris (Xanthonycticebus pygmaeus) and resequenced whole genomes from 50 pygmy lorises and 6 Bengal slow lorises (Nycticebus bengalensis). We found that many gene families involved in detoxification have been specifically expanded in the pygmy loris, including the GSTA gene family, with many newly derived copies functioning specifically in the liver. We detected many genes displaying evolutionary convergence between pygmy loris and koala, including PITRM1. Significant decreases in PITRM1 enzymatic activity in these two species may have contributed to their characteristic low rate of metabolism. We also detected many evolutionarily convergent genes and positively selected genes in the pygmy loris that are involved in muscle development. Functional assays demonstrated the decreased ability of one positively selected gene, MYOF, to up-regulate the fast-type muscle fiber, consistent with the lower proportion of fast-twitch muscle fibers in the pygmy loris. The protein product of another positively selected gene in the pygmy loris, PER2, exhibited weaker binding to the key circadian core protein CRY, a finding that may be related to this species' unusual circadian rhythm. Finally, population genomics analysis revealed that these two extant loris species, which coexist in the same habitat, have exhibited an inverse relationship in terms of their demography over the past 1 million years, implying strong interspecies competition after speciation.}, } @article {pmid36161886, year = {2022}, author = {Li, HZ and Yang, K and Liao, H and Lassen, SB and Su, JQ and Zhang, X and Cui, L and Zhu, YG}, title = {Active antibiotic resistome in soils unraveled by single-cell isotope probing and targeted metagenomics.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {40}, pages = {e2201473119}, pmid = {36161886}, issn = {1091-6490}, mesh = {*Anti-Bacterial Agents/pharmacology ; *Bacteria/drug effects/genetics/pathogenicity ; DNA Transposable Elements ; *Drug Resistance, Bacterial ; Genes, Bacterial ; Humans ; *Metagenomics ; Single-Cell Analysis ; Soil ; *Soil Microbiology ; Virulence Factors/genetics ; }, abstract = {Antimicrobial resistance (AMR) in soils represents a serious risk to human health through the food chain and human-nature contact. However, the active antibiotic-resistant bacteria (ARB) residing in soils that primarily drive AMR dissemination are poorly explored. Here, single-cell Raman-D2O coupled with targeted metagenomics is developed as a culture-independent approach to phenotypically and genotypically profiling active ARB against clinical antibiotics in a wide range of soils. This method quantifies the prevalence (contamination degree) and activity (spread potential) of soil ARB and reveals a clear elevation with increasing anthropogenic activities such as farming and the creation of pollution, thereby constituting a factor that is critical for the assessment of AMR risks. Further targeted sorting and metagenomic sequencing of the most active soil ARB uncover several uncultured genera and a pathogenic strain. Furthermore, the underlying resistance genes, virulence factor genes, and associated mobile genetic elements (including plasmids, insertion sequences, and prophages) are fully deciphered at the single-cell level. This study advances our understanding of the soil active AMR repertoire by linking the resistant phenome to the genome. It will aid in the risk assessment of environmental AMR and guide the combat under the One Health framework.}, } @article {pmid36161861, year = {2022}, author = {Omi, M and Matsuo, Y and Araki-Sasaki, K and Oba, S and Yamada, H and Hirota, K and Takahashi, K}, title = {16S rRNA nanopore sequencing for the diagnosis of ocular infection: a feasibility study.}, journal = {BMJ open ophthalmology}, volume = {7}, number = {1}, pages = {}, pmid = {36161861}, issn = {2397-3269}, mesh = {Abscess ; DNA, Bacterial/genetics ; *Eye Infections, Bacterial/diagnosis ; Feasibility Studies ; Humans ; *Nanopore Sequencing ; *Nanopores ; RNA, Ribosomal, 16S/genetics ; }, abstract = {OBJECTIVE: We conducted a feasibility study to verify the effectiveness of 16S ribosomal RNA (rRNA) gene analysis using the nanopore sequencer MinION for identifying causative bacteria in several types of ocular infections.

METHODS AND ANALYSIS: Four cases of corneal ulcers, one case of endophthalmitis and one case of a conjunctival abscess were included in this study. DNA was extracted from corneal scraping, vitreous samples and secretions from the conjunctival abscess. We conducted 16S rRNA gene amplicon sequencing using MinION and metagenomic DNA analysis. The efficacy of bacterial identification was verified by comparing the conventional culture method with smear observations.

RESULTS: 16S rRNA gene sequencing analysis with MinION identified the causative organisms promptly with high accuracy in approximately 4 hours, from ophthalmic specimens. The results of the conventional culture method and 16S rRNA gene sequencing were consistent in all cases. In four of the six cases, a greater variety of organisms was found in the 16S rRNA gene analysis than in bacterial culture.

CONCLUSION: Using our workflow, 16S rRNA gene analysis using MinION enabled rapid and accurate identification possible in various kinds of bacterial ocular infections.}, } @article {pmid36161499, year = {2023}, author = {Alonso-Reyes, DG and Galván, FS and Irazoqui, JM and Amadio, A and Tschoeke, D and Thompson, F and Albarracín, VH and Farias, ME}, title = {Dissecting Light Sensing and Metabolic Pathways on the Millimeter Scale in High-Altitude Modern Stromatolites.}, journal = {Microbial ecology}, volume = {86}, number = {2}, pages = {914-932}, pmid = {36161499}, issn = {1432-184X}, support = {2019-03216//PICT RAICES/ ; G603//PIUNT/ ; }, mesh = {*Altitude ; *Cyanobacteria/genetics/metabolism ; Photosynthesis ; Light ; Lakes/microbiology ; }, abstract = {Modern non-lithifying stromatolites on the shore of the volcanic lake Socompa (SST) in the Puna are affected by several extreme conditions. The present study assesses for the first time light utilization and functional metabolic stratification of SST on a millimeter scale through shotgun metagenomics. In addition, a scanning-electron-microscopy approach was used to explore the community. The analysis on SST unveiled the profile of a photosynthetic mat, with cyanobacteria not directly exposed to light, but placed just below a high-UV-resistant community. Calvin-Benson and 3-hydroxypropinate cycles for carbon fixation were abundant in upper, oxic layers, while the Wood-Ljungdahl pathway was dominant in the deeper anoxic strata. The high abundance of genes for UV-screening and oxidant-quenching pigments and CPF (photoreactivation) in the UV-stressed layers could indicate that the zone itself works as a UV shield. There is a remarkable density of sequences associated with photoreceptors in the first two layers. Also, genetic evidence of photosynthesis split in eukaryotic (layer 1) and prokaryotic (layer 2). Photoheterotrophic bacteria, aerobic photoautotrophic bacteria, and anaerobic photoautotrophic bacteria coexist by selectively absorbing different parts of the light spectrum (blue, red, and IR respectively) at different positions of the mat. Genes for oxygen, nitrogen, and sulfur metabolism account for the microelectrode chemical data and pigment measurements performed in previous publications. We also provide here an explanation for the vertical microbial mobility within the SST described previously. Finally, our study points to SST as ideal modern analogues of ancient ST.}, } @article {pmid36161453, year = {2022}, author = {Lugli, GA and Fontana, F and Tarracchini, C and Mancabelli, L and Milani, C and Turroni, F and Ventura, M}, title = {Exploring the biodiversity of Bifidobacterium asteroides among honey bee microbiomes.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {5666-5679}, pmid = {36161453}, issn = {1462-2920}, mesh = {Bees ; Animals ; Phylogeny ; *Bifidobacterium/genetics ; *Microbiota/genetics ; Metagenome ; }, abstract = {Bifidobacterium asteroides is considered the ancestor of the genus Bifidobacterium, which has evolved in close touch with the hindgut of social insects. However, recent studies revealed high intraspecies biodiversity within this taxon, uncovering the putative existence of multiple bifidobacterial species, thus, suggesting its reclassification. Here, a genomic investigation of 98 B. asteroides-related genomes retrieved from public repositories and reconstructed from metagenomes of the hindgut of Apis mellifera and Apis cerana was performed to shed light on the genetic variability of this taxon. Phylogenetic and genomic analyses revealed the existence of eight clusters, of which five have been recently characterized with a representative type strain of the genus and three were represented by putative novel bifidobacterial species inhabiting the honeybee gut. Then, the dissection of 366 shotgun metagenomes of honeybee guts revealed a pattern of seven B. asteroides-related taxa within A. mellifera that co-exist with the host, while A. cerana microbiome was characterized by the predominance of one of the novel species erroneously classified as B. asteroides. A further glycobiome analysis unveiled a conserved repertoire of glycosyl hydrolases (GHs) reflecting degradative abilities towards a broad range of simple carbohydrates together with genes encoding specific GHs of each B. asteroides-related taxa.}, } @article {pmid36161195, year = {2022}, author = {Verma, NK and Tan, SJ and Chen, J and Chen, H and Ismail, MH and Rice, SA and Bifani, P and Hariharan, S and Paul, VD and Sriram, B and Dam, LC and Chan, CC and Ho, P and Goh, BC and Chung, SJ and Goh, KCM and Thong, SH and Kwa, AL and Ostrowski, A and Aung, TT and Razali, H and Low, SWY and Bhattacharyya, MS and Gautam, HK and Lakshminarayanan, R and Sicheritz-Pontén, T and Clokie, MRJ and Moreira, W and van Steensel, MAM}, title = {inPhocus: Current State and Challenges of Phage Research in Singapore.}, journal = {PHAGE (New Rochelle, N.Y.)}, volume = {3}, number = {1}, pages = {6-11}, pmid = {36161195}, issn = {2641-6549}, abstract = {Bacteriophages and phage-derived proteins are a promising class of antibacterial agents that experience a growing worldwide interest. To map ongoing phage research in Singapore and neighboring countries, Lee Kong Chian School of Medicine, Nanyang Technological University Singapore (NTU) and Yong Loo Lin School of Medicine, National University of Singapore (NUS) recently co-organized a virtual symposium on Bacteriophage and Bacteriophage-Derived Technologies, which was attended by more than 80 participants. Topics were discussed relating to phage life cycles, diversity, the roles of phages in biofilms and the human gut microbiome, engineered phage lysins to combat polymicrobial infections in wounds, and the challenges and prospects of clinical phage therapy. This perspective summarizes major points discussed during the symposium and new perceptions that emerged after the panel discussion.}, } @article {pmid36160848, year = {2022}, author = {Ghori, I and Tubassam, M and Ahmad, T and Zuberi, A and Imran, M}, title = {Gut microbiome modulation mediated by probiotics: Positive impact on growth and health status of Labeo rohita.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {949559}, pmid = {36160848}, issn = {1664-042X}, abstract = {The current study was targeted to determine the effect of probiotics on the growth, physiology, and gut microbiology of Labeo rohita fingerlings. One hundred and twenty fishes were divided into four dietary groups, each in triplicate for a feeding trial of 90 days. These treatments included T0 (control, basal diet) used as the reference, and three probiotic-supplemented diets represented as Tbc (Bacillus cereus), Tgc (Geotrichum candidum), and Tmc (B. cereus and G. candidum). The probiotics were supplemented at a level of 1 × 10[9] CFU/g feed. Fishes nurtured on probiotic-added diet showed significantly high physiological improvement (p < 0.05) in terms of growth, feed utilization capacity, hematological profile, and digestive enzymes as compared to control. The fish were subjected to a challenge test after a 90-day feeding trial. The Tmc exhibited maximum fish growth when challenged by Staphylococcus aureus and showed fish survival when compared to control, in which fish mortality was examined. Fish gut microbial composition was modulated by probiotic treatments, especially in Tgc and Tmc as compared to control. The absence of opportunistic pathogens such as Staphylococcus saprophyticus and Sporobolomyces lactosus and detection of lower levels of Trichosporon and Cryptococcus in treated groups indicate the gut modulation driven by applied probiotics. The G. candidum QAUGC01 was retrieved in yeast metagenomics data, which might be due to the production of polyamines by them that facilitated adherence and consequent persistence. In conclusion, it can be suggested that the probiotic-supplemented diet could enhance fish growth and feed efficiency through community modulation and digestive enzymes, which could be a milestone in local aquaculture.}, } @article {pmid36160793, year = {2022}, author = {Huang, M and Li, S and Wu, X and Xu, D and Tang, L and Chen, Z}, title = {An isolated pulmonary nodule secondary to Streptococcus intermedius infection in an otherwise healthy 10-year-old boy: A case report and literature review.}, journal = {Frontiers in pediatrics}, volume = {10}, number = {}, pages = {921258}, pmid = {36160793}, issn = {2296-2360}, abstract = {Streptococcus intermedius, as a Gram-positive commensal bacterium, tends to cause various infections, such as brain and liver abscesses, endocarditis, and empyema, especially in immunocompromised patients. However, an isolated pulmonary nodule caused by S. intermedius in previously healthy individuals without traditional risk factors is rarely reported. Herein, we present a case of a 10-year-old immunocompetent boy referred to our department with a 5-day history of intermittent, left-sided chest pain. Chest X-ray and computed tomography revealed a left lung nodule. Although his blood, sputum, and bronchoalveolar lavage fluid cultures were negative, metagenomic next-generation sequencing (mNGS) showed only the presence of S. intermedius in ultrasonography-guided lung biopsy tissue and pleural fluid (416 and 110 reads, respectively). He was then successfully treated with appropriate intravenous antibiotics and avoided surgical intervention. To the best of our knowledge, this is the first report of S. intermedius-related pulmonary nodule confirmed by mNGS analysis in healthy children. For achieving proper diagnosis and treatment, infection with S. intermedius should be included in the differential diagnosis when coming across such a similar pulmonary nodule. mNGS, as a valuable supplement to conventional culture methods, is an essential diagnostic tool for identifying pathogens without typical characteristics.}, } @article {pmid36160259, year = {2022}, author = {Cardenas Alegria, O and Pires Quaresma, M and Dias Dantas, CW and Silva Guedes Lobato, EM and de Oliveira Aragão, A and Patroca da Silva, S and Costa Barros da Silva, A and Ribeiro Cruz, AC and Ramos, RTJ and Carneiro, AR}, title = {Impacts of soybean agriculture on the resistome of the Amazonian soil.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {948188}, pmid = {36160259}, issn = {1664-302X}, abstract = {The soils of the Amazon are complex environments with different organisms cohabiting in continuous adaptation processes; this changes significantly when these environments are modified for the development of agricultural activities that alter the chemical, macro, and microbiological compositions. The metagenomic variations and the levels of the environmental impact of four different soil samples from the Amazon region were evaluated, emphasizing the resistome. Soil samples from the organic phase from the different forest, pasture, and transgenic soybean monocultures of 2-14 years old were collected in triplicate at each site. The samples were divided into two groups, and one group was pre-treated to obtain genetic material to perform sequencing for metagenomic analysis; another group carried out the chemical characterization of the soil, determining the pH, the content of cations, and heavy metals; these were carried out in addition to identifying with different databases the components of the microbiological communities, functional genes, antibiotic and biocide resistance genes. A greater diversity of antibiotic resistance genes was observed in the forest soil. In contrast, in monoculture soils, a large number of biocide resistance genes were evidenced, highlighting the diversity and abundance of crop soils, which showed better resistance to heavy metals than other compounds, with a possible dominance of resistance to iron due to the presence of the acn gene. For up to 600 different genes for resistance to antibiotics and 256 genes for biocides were identified, most of which were for heavy metals. The most prevalent was resistance to tetracycline, cephalosporin, penam, fluoroquinolone, chloramphenicol, carbapenem, macrolide, and aminoglycoside, providing evidence for the co-selection of these resistance genes in different soils. Furthermore, the influence of vegetation cover on the forest floor was notable as a protective factor against the impact of human contamination. Regarding chemical characterization, the presence of heavy metals, different stress response mechanisms in monoculture soils, and the abundance of mobile genetic elements in crop and pasture soils stand out. The elimination of the forest increases the diversity of genes for resistance to biocides, favoring the selection of genes for resistance to antibiotics in soils.}, } @article {pmid36160245, year = {2022}, author = {Xu, Y and Huang, Y and Guo, L and Zhang, S and Wu, R and Fang, X and Xu, H and Nie, Q}, title = {Metagenomic analysis reveals the microbiome and antibiotic resistance genes in indigenous Chinese yellow-feathered chickens.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {930289}, pmid = {36160245}, issn = {1664-302X}, abstract = {Yellow-feathered chickens have great nutritional value and are widely and traditionally used in China, on an industrial scale as broilers. The presence of intestinal microbes has been shown to correlate with poultry performance and serves as an essential reservoir of antibiotic resistance genes (ARGs). Antibiotic resistance is a major public health concern. Here, we investigated functional characteristics of the gut microbiome of indigenous Chinese yellow-feathered chickens (the Huiyang Bearded, Xinghua, Huaixiang, Zhongshan Shanlan, Qingyuan Partridge, and Yangshan chickens) through metagenomic sequencing and reconstructed 409 draft genomes, including 60 novel species and 6 novel genera. Furthermore, we assessed the functions of the intestinal microbial communities and examined the ARGs within them. The results showed that the microbial populations of yellow-feathered broilers were primarily dominated by Bacteroidetes and Firmicutes at the phylum level and Bacteroides at the genus level. Furthermore, the Qingyuan Partridge chicken showed a significantly higher abundance of Prevotella than the other five breeds of chicken. Principal coordinates analysis indicated significant differences in the structures of microbial communities and ARGs, based on the binary Jaccard distance, among the six chicken breeds. Moreover, 989 ARGs conferring tetracycline, multidrug, and aminoglycoside resistance were identified, which represented more than 80% of the faecal resistomes; the most abundant gene in the yellow-feathered chickens was tet(Q). In addition, we found the greatest abundance of resistance genes in Xinghua chickens, indicating that Xinghua chickens are highly resistant to antibiotics. Overall, our findings revealed differences in the gut microbial community structure of indigenous Chinese yellow-feathered broiler breeds and the composition and characteristics of ARGs and antibiotic resistance that enabled us to reconstruct the yellow-feathered chicken gut microbial community genomes. The current data significantly improves our knowledge of the gut microbiome and antibiotic resistance of popular broiler breeds in China.}, } @article {pmid36160207, year = {2022}, author = {Zhang, T and Li, M and Shi, T and Yan, Y and Niyazbekova, Z and Wang, X and Li, Z and Jiang, Y}, title = {Transmission of the gut microbiome in cohousing goats and pigs.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {948617}, pmid = {36160207}, issn = {1664-302X}, abstract = {Social interaction facilitates the horizontal transmission of the microbiota between different individuals. However, little is known about the level of microbiota transmission in different livestock animals and different digestive tracts. The Hainan black goat and Wuzhishan pig are typical tropical local breeds on Hainan Island in China. Thus, we sampled and analyzed the gut microbiome in Hainan black goats (cecum and rumen) and Wuzhishan pigs (cecum) to study horizontal transmission by rearing them in the same pen (six goats and six pigs) or separate pens (nine goats and nine pigs). De novo assembly and binning recovered 3,262 strain-level and 2,488 species-level metagenome-assembled genomes (MAGs) using ∼1.3 Tb sequencing data. Of these MAGs, 1,856 MAGs were identified as novel strain. Compared with goats living in separate pens, social interaction in the same pen promotes community homogeneity in the rumen microbiome (P < 0.05) and the cecum microbiome (P < 0.05), respectively. Notably, approximately 7.08% (231/3262) of the gut microbial population could transmit during cohousing, 12 strains only in inter-species transmission, versus 190 strains only in intra-species transmission, and 10 strains only in foregut and hindgut transmission. In addition, the social contact group has high transmitted strain abundance, which is correlated with community composition. This study provided a new insight into the influence of social interaction on the animal gut microbiota.}, } @article {pmid36160204, year = {2022}, author = {Pollio, AR and Jiang, J and Lee, SS and Gandhi, JS and Knott, BD and Chunashvili, T and Conte, MA and Walls, SD and Hulseberg, CE and Farris, CM and Reinbold-Wasson, DD and Hang, J}, title = {Discovery of Rickettsia spp. in mosquitoes collected in Georgia by metagenomics analysis and molecular characterization.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {961090}, pmid = {36160204}, issn = {1664-302X}, abstract = {Arthropods have a broad and expanding worldwide presence and can transmit a variety of viral, bacterial, and parasite pathogens. A number of Rickettsia and Orientia species associated with ticks, fleas, lice, and mites have been detected in, or isolated from, patients with febrile illness and/or animal reservoirs throughout the world. Mosquitoes are not currently considered vectors for Rickettsia spp. pathogens to humans or to animals. In this study, we conducted a random metagenome next-generation sequencing (NGS) of 475 pools of Aedes, Culex, and Culiseta species of mosquitoes collected in Georgia from 2018 to 2019, identifying rickettsial gene sequences in 33 pools of mosquitoes. We further confirmed the findings of the Rickettsia by genus-specific quantitative PCR (qPCR) and multi-locus sequence typing (MLST). The NGS and MLST results indicate that Rickettsia spp. are closely related to Rickettsia bellii, which is not known to be pathogenic in humans. The results, together with other reports of Rickettsia spp. in mosquitoes and the susceptibility and transmissibility experiments, suggest that mosquitoes may play a role in the transmission cycle of Rickettsia spp.}, } @article {pmid36160188, year = {2022}, author = {Cosentino, MAC and D'arc, M and Moreira, FRR and Cavalcante, LTF and Mouta, R and Coimbra, A and Schiffler, FB and Miranda, TDS and Medeiros, G and Dias, CA and Souza, AR and Tavares, MCH and Tanuri, A and Soares, MA and Dos Santos, AFA}, title = {Discovery of two novel Torque Teno viruses in Callithrix penicillata provides insights on Anelloviridae diversification dynamics.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1002963}, pmid = {36160188}, issn = {1664-302X}, abstract = {The development of high-throughput sequencing (HTS) technologies and metagenomics protocols deeply impacted the discovery of viral diversity. Moreover, the characterization of novel viruses in the Neotropical primates (NP) is central for the comprehension of viral evolution dynamics in those hosts, due to their evolutionary proximity to Old World primates, including humans. In the present work, novel anelloviruses were detected and characterized through HTS protocols in the NP Callithrix penicillata, the common black-tufted marmoset. De novo assembly of generated sequences was carried out, and a total of 15 contigs were identified with complete Anelloviridae ORF1 gene, two of them including a flanking GC-rich region, confirming the presence of two whole novel genomes of ~3 kb. The identified viruses were monophyletic within the Epsilontorquevirus genus, a lineage harboring previously reported anelloviruses infecting hosts from the Cebidae family. The genetic divergence found in the new viruses characterized two novel species, named Epsilontorquevirus callithrichensis I and II. The phylogenetic pattern inferred for the Epsilontorquevirus genus was consistent with the topology of their host species tree, echoing a virus-host diversification model observed in other viral groups. This study expands the host span of Anelloviridae and provides insights into their diversification dynamics, highlighting the importance of sampling animal viral genomes to obtain a clearer depiction of their long-term evolutionary processes.}, } @article {pmid36159864, year = {2022}, author = {Qiu, Q and Deng, J and Deng, H and Yao, D and Yan, Y and Ye, S and Shang, X and Deng, Y and Han, L and Zheng, G and Roy, B and Chen, Y and Han, L and Huang, R and Fang, X and Lu, C}, title = {Association of the characteristics of the blood metabolome and gut microbiome with the outcome of methotrexate therapy in psoriasis.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {937539}, pmid = {36159864}, issn = {1664-3224}, mesh = {Fatty Acids ; *Gastrointestinal Microbiome/physiology ; Humans ; Lipids ; Metabolome ; Methotrexate/therapeutic use ; Prospective Studies ; *Psoriasis/drug therapy ; RNA, Ribosomal, 16S ; }, abstract = {Metabolic status and gut microecology are implicated in psoriasis. Methotrexate (MTX) is usually the first-line treatment for this disease. However, the relationship between MTX and host metabolic status and the gut microbiota is unclear. This study aimed to characterize the features of blood metabolome and gut microbiome in patients with psoriasis after treatment with MTX. Serum and stool samples were collected from 15 patients with psoriasis. Untargeted liquid chromatography-mass spectrometry and metagenomics sequencing were applied to profile the blood metabolome and gut microbiome, respectively. We found that the response to MTX varied according to metabolomic and metagenomic features at baseline; for example, patients who had high levels of serum nutrient molecular and more enriched gut microbiota had a poor response. After 16 weeks of MTX, we observed a reduction in microbial activity pathways, and patients with a good response showed more microbial activity and less biosynthesis of serum fatty acid. We also found an association between the serum metabolome and the gut microbiome before intervention with MTX. Carbohydrate metabolism, transporter systems, and protein synthesis within microbes were associated with host metabolic clusters of lipids, benzenoids, and organic acids. These findings suggest that the metabolic status of the blood and the gut microbiome is involved in the effectiveness of MTX in psoriasis, and that inhibition of symbiotic intestinal microbiota may be one of the mechanisms of action of MTX. Prospective studies in larger sample sizes are needed to confirm these findings.}, } @article {pmid36159676, year = {2022}, author = {Spiess, S and Sasiain Conde, A and Kucera, J and Novak, D and Thallner, S and Kieberger, N and Guebitz, GM and Haberbauer, M}, title = {Bioelectrochemical methanation by utilization of steel mill off-gas in a two-chamber microbial electrolysis cell.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {972653}, pmid = {36159676}, issn = {2296-4185}, abstract = {Carbon capture and utilization has been proposed as one strategy to combat global warming. Microbial electrolysis cells (MECs) combine the biological conversion of carbon dioxide (CO2) with the formation of valuable products such as methane. This study was motivated by the surprising gap in current knowledge about the utilization of real exhaust gas as a CO2 source for methane production in a fully biocatalyzed MEC. Therefore, two steel mill off-gases differing in composition were tested in a two-chamber MEC, consisting of an organic substrate-oxidizing bioanode and a methane-producing biocathode, by applying a constant anode potential. The methane production rate in the MEC decreased immediately when steel mill off-gas was tested, which likely inhibited anaerobic methanogens in the presence of oxygen. However, methanogenesis was still ongoing even though at lower methane production rates than with pure CO2. Subsequently, pure CO2 was studied for methanation, and the cathodic biofilm successfully recovered from inhibition reaching a methane production rate of 10.8 L m[-2]d[-1]. Metagenomic analysis revealed Geobacter as the dominant genus forming the anodic organic substrate-oxidizing biofilms, whereas Methanobacterium was most abundant at the cathodic methane-producing biofilms.}, } @article {pmid36159645, year = {2022}, author = {Liu, L and Sun, B and Ying, W and Liu, D and Wang, Y and Sun, J and Wang, W and Yang, M and Hui, X and Zhou, Q and Hou, J and Wang, X}, title = {Rapid diagnosis of Talaromyces marneffei infection by metagenomic next-generation sequencing technology in a Chinese cohort of inborn errors of immunity.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {987692}, pmid = {36159645}, issn = {2235-2988}, mesh = {*Antifungal Agents/therapeutic use ; China ; *High-Throughput Nucleotide Sequencing ; Humans ; Mycoses ; Talaromyces ; Technology ; }, abstract = {Talaromyces marneffei (T. marneffei) is an opportunistic pathogen. Patients with inborn errors of immunity (IEI) have been increasingly diagnosed with T. marneffei in recent years. The disseminated infection of T. marneffei can be life-threatening without timely and effective antifungal therapy. Rapid and accurate pathogenic microbiological diagnosis is particularly critical for these patients. A total of 505 patients with IEI were admitted to our hospital between January 2019 and June 2022, among whom T. marneffei was detected in 6 patients by metagenomic next-generation sequencing (mNGS), and their clinical and immunological characteristics were summarized. We performed a systematic literature review on T. marneffei infections with published immunodeficiency-related gene mutations. All patients in our cohort were confirmed to have genetic mutations in IL12RB1, IFNGR1, STAT1, STAT3, and CD40LG. T. marneffei was detected in both the blood and lymph nodes of P1 with IL12RB1 mutations, and the clinical manifestations were serious and included recurrent fever, weight loss, severe anemia, splenomegaly and lymphadenopathy, all requiring long-term antifungal therapy. These six patients received antifungal treatment, which relieved symptoms and improved imaging findings. Five patients survived, while one patient died of sepsis after hematopoietic stem cell transplantation. The application of mNGS methods for pathogen detection in IEI patients and comparison with traditional diagnosis methods were investigated. Traditional diagnostic methods and mNGS tests were performed simultaneously in 232 patients with IEI. Compared to the traditional methods, the sensitivity and specificity of mNGS in diagnosing T. marneffei infection were 100% and 98.7%, respectively. The reporting time for T. marneffei detection was approximately 26 hours by mNGS, 3-14 days by culture, and 6-11 days by histopathology. T. marneffei infection was first reported in IEI patients with IL12RB1 gene mutation, which expanded the IEI lineage susceptible to T. marneffei. For IEI patients with T. marneffei infection, we highlight the application of mNGS in pathogenic detection. mNGS is recommended as a front-line diagnostic test for rapidly identifying pathogens in complex and severe infections.}, } @article {pmid36159175, year = {2022}, author = {Chakoory, O and Comtet-Marre, S and Peyret, P}, title = {RiboTaxa: combined approaches for rRNA genes taxonomic resolution down to the species level from metagenomics data revealing novelties.}, journal = {NAR genomics and bioinformatics}, volume = {4}, number = {3}, pages = {lqac070}, pmid = {36159175}, issn = {2631-9268}, abstract = {Metagenomic classifiers are widely used for the taxonomic profiling of metagenomics data and estimation of taxa relative abundance. Small subunit rRNA genes are a gold standard for phylogenetic resolution of microbiota, although the power of this marker comes down to its use as full-length. We aimed at identifying the tools that can efficiently lead to taxonomic resolution down to the species level. To reach this goal, we benchmarked the performance and accuracy of rRNA-specialized versus general-purpose read mappers, reference-targeted assemblers and taxonomic classifiers. We then compiled the best tools (BBTools, FastQC, SortMeRNA, MetaRib, EMIRGE, VSEARCH, BBMap and QIIME 2's Sklearn classifier) to build a pipeline called RiboTaxa. Using metagenomics datasets, RiboTaxa gave the best results compared to other tools (i.e. Kraken2, Centrifuge, METAXA2, phyloFlash, SPINGO, BLCA, MEGAN) with precise taxonomic identification and relative abundance description without false positive detection (F-measure of 100% and 83.7% at genus level and species level, respectively). Using real datasets from various environments (i.e. ocean, soil, human gut) and from different approaches (e.g. metagenomics and gene capture by hybridization), RiboTaxa revealed microbial novelties not discerned by current bioinformatics analysis opening new biological perspectives in human and environmental health.}, } @article {pmid36158512, year = {2022}, author = {Chen, YY and Guo, Y and Xue, XH and Pang, F}, title = {Application of metagenomic next-generation sequencing in the diagnosis of infectious diseases of the central nervous system after empirical treatment.}, journal = {World journal of clinical cases}, volume = {10}, number = {22}, pages = {7760-7771}, pmid = {36158512}, issn = {2307-8960}, abstract = {BACKGROUND: The diagnostic value of metagenomic next-generation sequencing (mNGS) in central nervous system (CNS) infectious diseases after empirical treatment has not been reported.

AIM: To investigate the diagnostic value of mNGS of cerebrospinal fluid (CSF) in the empirically treated CNS infectious diseases.

METHODS: A total of 262 CSF samples from patients with suspected CNS infections were collected between August 2020 and December 2021. Both mNGS and conventional methods were used for testing. The conventional methods included microbial culture, smear, polymerase chain reaction, etc.

RESULTS: Among 262 suspected cases, 183 cases (69.84%) were diagnosed as CNS infection, including 86 cases of virus infection (47.00%), 70 cases of bacterial infection (38.25%) and 27 cases of fungal infection (14.76%). The sensitivity and specificity of mNGS were 65.6% (95%CI: 58.2%-72.3%) and 89.6% (95%CI: 79.1%-95.3%), respectively. The PPV of mNGS was 94.5% (95%CI: 88.6%-97.6%), and the NPV was 48.8% (95%CI: 39.7%-57.9%). The pathogen detective sensitivity and accuracy of mNGS were higher than those of conventional methods (Sensitivity: 65.6% vs 37.2%; P < 0.001; Accuracy: 72.0% vs 50%, P < 0.001). The results showed that compared with conventional methods, mNGS technology was a more sensitive method for the diagnosis of CNS infection after empirical treatment.

CONCLUSION: mNGS can be a better method applied in the diagnosis of CNS infection after empirical treatment.}, } @article {pmid36158025, year = {2022}, author = {Qu, H and Zhao, YH and Zhu, WM and Liu, L and Zhu, M}, title = {Maternal peripartum bacteremia caused by intrauterine infection with Comamonas kerstersii: A case report.}, journal = {World journal of clinical cases}, volume = {10}, number = {21}, pages = {7585-7591}, pmid = {36158025}, issn = {2307-8960}, abstract = {BACKGROUND: Comamonas kerstersii (C. kerstersii) infections have considered as non-pathogenic to humans, however due to new techniques such as matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF-MS), more cases have been identified.

CASE SUMMARY: This is the first report of a maternal patient with a C. kerstersii bacteremia following caesarean section. Due to the severity of the patient's condition; high fever and rapidly progressing organ damage, the patient was transferred to the intensive care unit. C. kerstersii was detected by metagenomic next-generation sequencing testing. Based on the drug sensitivity test, appropriate antibiotic treatment was given and the patient recovered fully.

CONCLUSION: This case report confirms that the detection via MALDI-TOF-MS and metagenomic next-generation sequencing testing provides a reliable basis for the diagnosis of this rare bacterial infection.}, } @article {pmid36157187, year = {2022}, author = {Vientós-Plotts, AI and Ericsson, AC and McAdams, ZL and Rindt, H and Reinero, CR}, title = {Respiratory dysbiosis in cats with spontaneous allergic asthma.}, journal = {Frontiers in veterinary science}, volume = {9}, number = {}, pages = {930385}, pmid = {36157187}, issn = {2297-1769}, support = {T32 GM008396/GM/NIGMS NIH HHS/United States ; }, abstract = {Deviations from a core airway microbiota have been associated with the development and progression of asthma as well as disease severity. Pet cats represent a large animal model for allergic asthma, as they spontaneously develop a disease similar to atopic childhood asthma. This study aimed to describe the lower airway microbiota of asthmatic pet cats and compare it to healthy cats to document respiratory dysbiosis occurring with airway inflammation. We hypothesized that asthmatic cats would have lower airway dysbiosis characterized by a decrease in richness, diversity, and alterations in microbial community composition including identification of possible pathobionts. In the current study, a significant difference in airway microbiota composition was documented between spontaneously asthmatic pet cats and healthy research cats mirroring the finding of dysbiosis in asthmatic humans. Filobacterium and Acinetobacter spp. were identified as predominant taxa in asthmatic cats without documented infection based on standard culture and could represent pathobionts in the lower airways of cats. Mycoplasma felis, a known lower airway pathogen of cats, was identified in 35% of asthmatic but not healthy cats. This article has been published alongside "Temporal changes of the respiratory microbiota as cats transition from health to experimental acute and chronic allergic asthma" (1).}, } @article {pmid36155629, year = {2022}, author = {Teseo, S and Otani, S and Brinch, C and Leroy, S and Ruiz, P and Desvaux, M and Forano, E and Aarestrup, FM and Sapountzis, P}, title = {A global phylogenomic and metabolic reconstruction of the large intestine bacterial community of domesticated cattle.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {155}, pmid = {36155629}, issn = {2049-2618}, mesh = {Amino Acids ; Animals ; *Bacteria/genetics ; Carbohydrates ; Cattle ; Intestine, Large ; Mammals/microbiology ; *Metagenomics ; Phylogeny ; }, abstract = {BACKGROUND: The large intestine is a colonization site of beneficial microbes complementing the nutrition of cattle but also of zoonotic and animal pathogens. Here, we present the first global gene catalog of cattle fecal microbiomes, a proxy of the large intestine microbiomes, from 436 metagenomes from six countries.

RESULTS: Phylogenomics suggested that the reconstructed genomes and their close relatives form distinct branches and produced clustering patterns that were reminiscent of the metagenomics sample origin. Bacterial taxa had distinct metabolic profiles, and complete metabolic pathways were mainly linked to carbohydrates and amino acids metabolism. Dietary changes affected the community composition, diversity, and potential virulence. However, predicted enzymes, which were part of complete metabolic pathways, remained present, albeit encoded by different microbes.

CONCLUSIONS: Our findings provide a global insight into the phylogenetic relationships and the metabolic potential of a rich yet understudied bacterial community and suggest that it provides valuable services to the host. However, we tentatively infer that members of that community are not irreplaceable, because similar to previous findings, symbionts of complex bacterial communities of mammals are expendable if there are substitutes that can perform the same task. Video Abstract.}, } @article {pmid36155528, year = {2022}, author = {Liang, F and Chen, CY and Li, YP and Ke, YC and Ho, EP and Jeng, CF and Lin, CH and Chen, SK}, title = {Early Dysbiosis and Dampened Gut Microbe Oscillation Precede Motor Dysfunction and Neuropathology in Animal Models of Parkinson's Disease.}, journal = {Journal of Parkinson's disease}, volume = {12}, number = {8}, pages = {2423-2440}, doi = {10.3233/JPD-223431}, pmid = {36155528}, issn = {1877-718X}, mesh = {Humans ; Mice ; Animals ; Infant ; *Parkinson Disease ; alpha-Synuclein/metabolism ; *Gastrointestinal Microbiome/physiology ; Dysbiosis ; Disease Models, Animal ; }, abstract = {BACKGROUND: Studies have shown different gut microbiomes in patients with Parkinson's disease (PD) compared to unaffected controls. However, when the gut microbiota shift toward dysbiosis in the PD process remains unclear.

OBJECTIVE: We aim to investigate the changes in gut microbiota, locomotor function, and neuropathology longitudinally in PD rodent models.

METHODS: Fecal microbiota were longitudinally assessed by sequencing the V4-V5 region of the 16S ribosomal RNA gene in a human mutant α-synuclein over-expressing mouse model of PD, SNCA p.A53T mice, and the non-transgenic littermate controls. The locomotor function, neuronal integrity, and α-synuclein expression in the different brain regions were compared between groups. Human fecal microbiota communities from 58 patients with PD and 46 unaffected controls were also analyzed using metagenomic sequencing for comparison.

RESULTS: Compared to non-transgenic littermate controls, the altered gut microbiota of the SNCA p.A53T mice can be detected as early as 2 months old, and the diurnal oscillation of the gut microbiome was dampened throughout PD progression starting from 4 months old. However, neuropathology changes and motor deficits were observed starting at 6 months old. Similar changes in altered gut microbiota were also observed in another PD genetic mouse model carrying the LRRK2 p.G2019S mutation at 2 months old. Among the commonly enriched gut microbiota in both PD genetic mouse models, the abundance of Parabateroides Merdae and Ruminococcus torques were also increased in human PD patients compared to controls.

CONCLUSION: These findings revealed the altered gut microbiota communities and oscillations preceding the occurrence of neuropathy and motor dysfunction in the PD process.}, } @article {pmid36155191, year = {2023}, author = {Nagata, N and Takeuchi, T and Masuoka, H and Aoki, R and Ishikane, M and Iwamoto, N and Sugiyama, M and Suda, W and Nakanishi, Y and Terada-Hirashima, J and Kimura, M and Nishijima, T and Inooka, H and Miyoshi-Akiyama, T and Kojima, Y and Shimokawa, C and Hisaeda, H and Zhang, F and Yeoh, YK and Ng, SC and Uemura, N and Itoi, T and Mizokami, M and Kawai, T and Sugiyama, H and Ohmagari, N and Ohno, H}, title = {Human Gut Microbiota and Its Metabolites Impact Immune Responses in COVID-19 and Its Complications.}, journal = {Gastroenterology}, volume = {164}, number = {2}, pages = {272-288}, pmid = {36155191}, issn = {1528-0012}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *COVID-19 ; Cross-Sectional Studies ; SARS-CoV-2 ; Feces/chemistry ; Immunity ; Cytokines ; Vitamin B 6/analysis ; }, abstract = {BACKGROUND & AIMS: We investigate interrelationships between gut microbes, metabolites, and cytokines that characterize COVID-19 and its complications, and we validate the results with follow-up, the Japanese 4D (Disease, Drug, Diet, Daily Life) microbiome cohort, and non-Japanese data sets.

METHODS: We performed shotgun metagenomic sequencing and metabolomics on stools and cytokine measurements on plasma from 112 hospitalized patients with SARS-CoV-2 infection and 112 non-COVID-19 control individuals matched by important confounders.

RESULTS: Multiple correlations were found between COVID-19-related microbes (eg, oral microbes and short-chain fatty acid producers) and gut metabolites (eg, branched-chain and aromatic amino acids, short-chain fatty acids, carbohydrates, neurotransmitters, and vitamin B6). Both were also linked to inflammatory cytokine dynamics (eg, interferon γ, interferon λ3, interleukin 6, CXCL-9, and CXCL-10). Such interrelationships were detected highly in severe disease and pneumonia; moderately in the high D-dimer level, kidney dysfunction, and liver dysfunction groups; but rarely in the diarrhea group. We confirmed concordances of altered metabolites (eg, branched-chain amino acids, spermidine, putrescine, and vitamin B6) in COVID-19 with their corresponding microbial functional genes. Results in microbial and metabolomic alterations with severe disease from the cross-sectional data set were partly concordant with those from the follow-up data set. Microbial signatures for COVID-19 were distinct from diabetes, inflammatory bowel disease, and proton-pump inhibitors but overlapping for rheumatoid arthritis. Random forest classifier models using microbiomes can highly predict COVID-19 and severe disease. The microbial signatures for COVID-19 showed moderate concordance between Hong Kong and Japan.

CONCLUSIONS: Multiomics analysis revealed multiple gut microbe-metabolite-cytokine interrelationships in COVID-19 and COVID-19related complications but few in gastrointestinal complications, suggesting microbiota-mediated immune responses distinct between the organ sites. Our results underscore the existence of a gut-lung axis in COVID-19.}, } @article {pmid36155009, year = {2022}, author = {Hong, Y and Tu, Q and Cheng, H and Huangfu, X and Chen, Z and He, Q}, title = {Chronic high-dose silver nanoparticle exposure stimulates N2O emissions by constructing anaerobic micro-environment.}, journal = {Water research}, volume = {225}, number = {}, pages = {119104}, doi = {10.1016/j.watres.2022.119104}, pmid = {36155009}, issn = {1879-2448}, mesh = {*Silver/pharmacology ; Denitrification ; Nitrous Oxide/metabolism ; *Metal Nanoparticles ; Nitrites ; Anaerobiosis ; }, abstract = {Silver nanoparticles (Ag-NPs) were found to be responsible for nitrous oxide (N2O) generation; however, the mechanism of Ag-NP induced N2O production remains controversial and needs to be elucidated. In this study, chronic Ag-NP exposure experiments were conducted in five independent sequencing batch biofilm reactors to systematically assess the effects of Ag-NPs on N2O emission. The results indicated that a low dose of Ag-NPs (< 1 mg/L) slightly suppressed N2O generation by less than 22.99% compared with the no-Ag-NP control method. In contrast, a high dose (5 mg/L) of Ag-NPs stimulated N2O emission by 67.54%. ICP-MS and SEM-EDS together revealed that high Ag-NP content accumulated on the biofilm surface when exposed to 5 mg/L Ag-NPs. N2O and DO microelectrodes, as well as N2O isotopic composition analyses, further demonstrated that the accumulated Ag-NPs construct the anaerobic zone in the biofilm, which is the primary factor for the stimulation of the nitrite reduction pathway to release N2O. A metagenomic analysis further attributed the higher N2O emissions under exposure to a high dose of Ag-NPs to the higher relative abundance of narB and nirK genes (i.e. 1.52- and 1.29-fold higher, respectively). These findings collectively suggest that chronic exposure to high doses of Ag-NPs could enhance N2O emissions by forming anaerobic micro-environments in biofilms.}, } @article {pmid36155007, year = {2022}, author = {Zhang, J and Yang, C and Hu, J and Zhang, Y and Lai, Y and Gong, H and Guo, F and Li, X and Ye, L and Li, B}, title = {Deciphering a novel chloramphenicols resistance mechanism: Oxidative inactivation of the propanediol pharmacophore.}, journal = {Water research}, volume = {225}, number = {}, pages = {119127}, doi = {10.1016/j.watres.2022.119127}, pmid = {36155007}, issn = {1879-2448}, mesh = {*Sewage ; Wastewater ; *Thiamphenicol ; Metagenomics ; Anti-Bacterial Agents ; Chloramphenicol/pharmacology ; Oxidoreductases ; Oxidative Stress ; Genes, Bacterial ; }, abstract = {Expanding knowledge about new types of antibiotic resistance genes is of great significance in dealing with the global antibiotic resistance crisis. Herein, a novel oxidoreductase capO was discovered to be responsible for oxidative inactivation of chloramphenicol and thiamphenicol. The antibiotic resistance mechanism was comprehensively deciphered using multi-omics and multiscale computational approaches. A 66,383 bp DNA fragment carrying capO was shared among four chloramphenicol-resistant strains, and the co-occurrence of capO with a mobile genetic element cluster revealed its potential mobility among different taxa. Metagenomic analysis of 772 datasets indicated that chloramphenicol was the crucial driving factor for the development and accumulation of capO in activated sludge bioreactors treating antibiotic production wastewater. Therefore, we should pay sufficient attention to its possible prevalence and transfer to pathogens, especially in some hotspot environments contaminated with high concentrations of chloramphenicols. This finding significantly expands our knowledge boundary about chloramphenicols resistance mechanisms.}, } @article {pmid36154593, year = {2023}, author = {Kumar, R and Harilal, S and Al-Sehemi, AG and Pannipara, M and Mathew, GE and Mathew, B}, title = {Advancements in COVID-19 Testing: An In-depth Overview.}, journal = {Current pharmaceutical biotechnology}, volume = {24}, number = {9}, pages = {1122-1148}, doi = {10.2174/1389201023666220921144150}, pmid = {36154593}, issn = {1873-4316}, mesh = {Humans ; *COVID-19/diagnosis ; SARS-CoV-2 ; COVID-19 Testing ; Artificial Intelligence ; Clinical Laboratory Techniques/methods ; Sensitivity and Specificity ; }, abstract = {COVID-19 rapidly evolved as a pandemic, killing and hospitalising millions of people, and creating unprecedented hurdles for communities and health care systems worldwide. The rapidly evolving pandemic prompted the head of the World Health Organisation to deliver a critical message: "test, test, test." The response from the diagnostic industry and researchers worldwide was overwhelming, resulting in more than a thousand commercial tests being available worldwide. Several sampling approaches and diagnostic techniques have been employed from the early stages of the pandemic, such as SARS-CoV-2 detection by targeting the viral RNA or protein indirectly via antibody testing, biochemical estimation, and various imaging techniques, and many are still in the various stages of development and yet to be marketed. Accurate testing techniques and appropriate sampling are the need of the hour to manage, diagnose and treat the pandemic, especially in the current crisis where SARS-CoV-2 undergoes constant mutation, evolving into various strains, which are pretty challenging. The article discusses various testing techniques as well as screening methods for detection, treatment, and management of COVID-19 transmissions, such as NAAT, PCR, isothermal detection including RT-LAMP, RPA, NASBA, RCA, SDA, NEAR, and TMA, CRISPR strategy, nanotechnology approach, metagenomic profiling, point of care tests, virus neutralization test, ELISA, biomarker estimation, utilization of imaging techniques such as CT, ultrasonography, brain MRI in COVID-19 complications, and other novel strategies including microarray methods, microfluidic methods and artificial intelligence with an emphasis on advancements in the testing strategies for the diagnosis, management, and prevention of COVID-19.}, } @article {pmid36154550, year = {2022}, author = {}, title = {Statement of Retraction: Metagenomics for taxonomy profiling: tools and approaches.}, journal = {Bioengineered}, volume = {13}, number = {6}, pages = {14750}, doi = {10.1080/21655979.2022.2126093}, pmid = {36154550}, issn = {2165-5987}, } @article {pmid36154277, year = {2022}, author = {Herrera, G and Arboleda, JC and Pérez-Jaramillo, JE and Patarroyo, MA and Ramírez, JD and Muñoz, M}, title = {Microbial Interdomain Interactions Delineate the Disruptive Intestinal Homeostasis in Clostridioides difficile Infection.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0050222}, pmid = {36154277}, issn = {2165-0497}, mesh = {Humans ; *Clostridioides difficile/genetics ; *Clostridium Infections/microbiology ; *Microbiota ; Bacteria ; Anti-Bacterial Agents ; Homeostasis ; Virulence Factors/genetics ; *Anti-Infective Agents ; Butyrates ; }, abstract = {Clostridioides difficile infection (CDI) creates an imbalance in the intestinal microbiota due to the interaction of the components making up this ecosystem, but little is known about the impact of this disease on other microbial members. This work has thus been aimed at evaluating the taxonomic composition, potential gene-associated functions, virulence factors, and antimicrobial resistance profiles of gut microbiomes. A total of 48 DNA samples obtained from patients with health care facility-acquired (HCFO) and community-onset (CO) diarrhea were distributed in the following four groups according to CDI status: HCFO/+ (n = 13), HCFO/- (n = 8), CO/+ (n = 13), and CO/- (n = 14). These samples were subjected to shotgun metagenomics sequencing. Although the CDI groups' microbiota had microbiome alterations, the greatest imbalance was observed in the in the HCFO+/- groups, with an increase in common pathogens and phage populations, as well as a decrease in beneficial microorganisms that leads to a negative impact on some intestinal homeostasis-related metabolic processes. A reduction in the relative abundance of butyrate metabolism-associated genes was also detected in the HCFO groups (P < 0.01), with an increase in some virulence factors and antibiotic-resistance markers. A set of 51 differentially abundant species in the groups with potential association to CDI enabled its characterization, leading to their spatial separation by onset. Strong correlations between phages and some archaeal and bacterial phyla were identified. This highlighted the need to study the microbiota's various components since their imbalance is multifactorial, with some pathogens contributing to a greater or lesser extent because of their interaction with the ecosystem they inhabit. IMPORTANCE Clostridioides difficile infection represents a serious public health problem in different countries due to its high morbi-mortality and the high costs it represents for health care systems. Studies have shown the impact of this infection on intestinal microbiome homeostasis, mainly on bacterial populations. Our research provides evidence of the impact of CDI at both the compositional (bacteria, archaea, and viruses), and functional levels, allowing us to understand that the alterations of the microbiota occur systemically and are caused by multiple perturbations generated by different members of the microbiota as well as by some pathogens that take advantage of the imbalance to proliferate. Likewise, the 51 differentially abundant species in the study groups with potential association to CDI found in this study could help us envisage future treatments against this and other inflammatory diseases, improving future therapeutic options for patients.}, } @article {pmid36154187, year = {2022}, author = {Khongchatee, A and Wongsurawat, T and Suriye, K and Jenjaroenpun, P and Leekitcharoenphon, P and Kruasuwan, W and Foongladda, S}, title = {Full-Length 16S rRNA Gene Amplicon and Metagenome Taxonomic Profiling of Beneficial Microbes in Poultry and Swine Probiotic Product.}, journal = {Microbiology resource announcements}, volume = {11}, number = {10}, pages = {e0069022}, pmid = {36154187}, issn = {2576-098X}, support = {CRP6305032080//Agricultural Research Development Agency (ARDA)/ ; }, abstract = {Analysis of feed supplements can highlight microbial diversity and the prevalence of antimicrobial resistance (AMR), allowing users to monitor the safety of their animals. The 16S amplicon and metagenomic data generated by nanopore sequencing revealed that Bacillus was the dominant prokaryote, and AMR genes were detected in the animal probiotic products.}, } @article {pmid36154176, year = {2022}, author = {Pallenberg, ST and Pust, MM and Rosenboom, I and Hansen, G and Wiehlmann, L and Dittrich, AM and Tümmler, B}, title = {Impact of Elexacaftor/Tezacaftor/Ivacaftor Therapy on the Cystic Fibrosis Airway Microbial Metagenome.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0145422}, pmid = {36154176}, issn = {2165-0497}, mesh = {Humans ; Chloride Channel Agonists/therapeutic use/pharmacology ; *Cystic Fibrosis/drug therapy/genetics ; *Cystic Fibrosis Transmembrane Conductance Regulator/genetics/pharmacology ; Metagenome ; Mutation ; Quality of Life ; Child ; Adolescent ; }, abstract = {The introduction of mutation-specific combination therapy with the cystic fibrosis transmembrane conductance regulator (CFTR) modulators elexacaftor/tezacaftor/ivacaftor (ELX/TEZ/IVA) has substantially improved lung function and quality of life of people with cystic fibrosis (CF). Collecting deep cough swabs and induced sputum, this postapproval study examined the effect of 14- and 50-week treatment with ELX/TEZ/IVA on the airway microbial metagenome of pancreatic- insufficient CF patients aged 12 years and older. Compared to pretreatment, the total bacterial load decreased, the individual species were more evenly distributed in the community, and the individual microbial metagenomes became more similar in their composition. However, the microbial network remained vulnerable to fragmentation. The initial shift of the CF metagenome was attributable to the ELX/TEZ/IVA-mediated gain of CFTR activity followed by a diversification driven by a group of commensals at the 1-year time point that are typical for healthy airways. IMPORTANCE Shotgun metagenome sequencing of respiratory secretions with spike-in controls for normalization demonstrated that 1 year of high-efficient CFTR modulation with elexacaftor/tezacaftor/ivacaftor extensively reduced the bacterial load. Longer observation periods will be necessary to resolve whether the partial reversion of the basic defect that is achieved with ELX/TEZ/IVA is sufficient in the long run to render the CF lungs robust against the recolonization with common opportunistic pathogens.}, } @article {pmid36153618, year = {2022}, author = {Lakshmanan, AP and Murugesan, S and Al Khodor, S and Terranegra, A}, title = {The potential impact of a probiotic: Akkermansia muciniphila in the regulation of blood pressure-the current facts and evidence.}, journal = {Journal of translational medicine}, volume = {20}, number = {1}, pages = {430}, pmid = {36153618}, issn = {1479-5876}, mesh = {Adult ; Akkermansia ; Blood Pressure ; Humans ; *Hypertension/therapy ; *Probiotics/pharmacology/therapeutic use ; Verrucomicrobia ; }, abstract = {Akkermansia muciniphila (A. muciniphila) is present in the human gut microbiota from infancy and gradually increases in adulthood. The potential impact of the abundance of A. muciniphila has been studied in major cardiovascular diseases including elevated blood pressure or hypertension (HTN). HTN is a major factor in premature death worldwide, and approximately 1.28 billion adults aged 30-79 years have hypertension. A. muciniphila is being considered a next-generation probiotic and though numerous studies had highlighted the positive role of A. muciniphila in lowering/controlling the HTN, however, few studies had highlighted the negative impact of increased abundance of A. muciniphila in the management of HTN. Thus, in the review, we aimed to discuss the current facts, evidence, and controversy about the role of A. muciniphila in the pathophysiology of HTN and its potential effect on HTN management/regulation, which could be beneficial in identifying the drug target for the management of HTN.}, } @article {pmid36152674, year = {2022}, author = {Corander, J and Hanage, WP and Pensar, J}, title = {Causal discovery for the microbiome.}, journal = {The Lancet. Microbe}, volume = {3}, number = {11}, pages = {e881-e887}, pmid = {36152674}, issn = {2666-5247}, support = {U54 GM088558/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Microbiota ; Metagenomics/methods ; Causality ; Metagenome ; }, abstract = {Measurement and manipulation of the microbiome is generally considered to have great potential for understanding the causes of complex diseases in humans, developing new therapies, and finding preventive measures. Many studies have found significant associations between the microbiome and various diseases; however, Koch's classical postulates remind us about the importance of causative reasoning when considering the relationship between microbes and a disease manifestation. Although causal discovery in observational microbiome data faces many challenges, methodological advances in causal structure learning have improved the potential of data-driven prediction of causal effects in large-scale biological systems. In this Personal View, we show the capability of existing methods for inferring causal effects from metagenomic data, and we highlight ways in which the introduction of causal structures that are more flexible than existing structures offers new opportunities for causal reasoning. Our observations suggest that microbiome research can further benefit from tools developed in the past 5 years in causal discovery and learn from their applications elsewhere.}, } @article {pmid36152543, year = {2023}, author = {Yang, G and Xu, H and Luo, Y and Hei, S and Song, G and Huang, X}, title = {Novel electro-assisted micro-aerobic cathode biological technology induces oxidative demethylation of N, N-dimethylformamide for efficient ammonification of refractory membrane-making wastewater.}, journal = {Journal of hazardous materials}, volume = {442}, number = {}, pages = {130001}, doi = {10.1016/j.jhazmat.2022.130001}, pmid = {36152543}, issn = {1873-3336}, mesh = {*Wastewater ; *Dimethylformamide ; Ammonia/metabolism ; Bioreactors ; Nitrification ; Nitrogen/metabolism ; Electrodes ; Oxygen ; Demethylation ; Denitrification ; }, abstract = {Recalcitrant and toxicological membrane-making wastewater displays negative impacts on environment, and this is difficult to treat efficiently using conventional hydrolytic acidification. In this study, a novel electro-assisted biological reactor with micro-aerobic cathode (EABR-MAC) was developed to improve the biodegradation and ammonification of N, N-dimethylformamide (DMF) in membrane-making wastewater, and the metabolic mechanism using metagenomic sequencing as comprehensively illustrated. The results showed that EABR-MAC significantly improved the ammonification of refractory organonitrogen and promoted DMF oxidative degradation by driving the electron transferred to the cathode. Additionally, the inhibition rates of oxygen uptake rate and nitrification in EABR-MAC were both lower under different cathode aeration frequency conditions. Microbial community analysis indicated that the functional fermentation bacteria and exoelectrogens, which were correlated with COD removal, ammonification, and detoxification, were significantly enriched upon electrostimulation, and the positive biological connections increased to form highly connected communities instead of competition. The functional genes revealed that EABR-MAC forcefully intervened with the metabolic pathway, so that DMF converted to formamide and ammonia by oxidative demethylation and formamide hydrolysis. The results of this study provide a promising strategy for efficient conversion of organonitrogen into ammonia nitrogen, and offer a new insight into the effects of electrostimulation on microbial metabolism.}, } @article {pmid36152521, year = {2022}, author = {Grose, C}, title = {Metagenomic sequencing of cerebrospinal fluid from children with meningitis.}, journal = {EBioMedicine}, volume = {84}, number = {}, pages = {104287}, pmid = {36152521}, issn = {2352-3964}, mesh = {Child ; High-Throughput Nucleotide Sequencing ; Humans ; *Meningitis/cerebrospinal fluid/diagnosis ; Metagenome ; *Metagenomics ; }, } @article {pmid36151459, year = {2023}, author = {Yamamoto, M and Takaki, Y and Kashima, H and Tsuda, M and Tanizaki, A and Nakamura, R and Takai, K}, title = {In situ electrosynthetic bacterial growth using electricity generated by a deep-sea hydrothermal vent.}, journal = {The ISME journal}, volume = {17}, number = {1}, pages = {12-20}, pmid = {36151459}, issn = {1751-7370}, mesh = {*Hydrothermal Vents/microbiology ; Phylogeny ; Metagenomics ; *Microbiota/genetics ; Bacteria ; Electricity ; }, abstract = {Electroautotrophic microorganisms have attracted great attention since they exhibit a new type of primary production. Here, in situ electrochemical cultivation was conducted using the naturally occurring electromotive forces at a deep-sea hydrothermal vent. The voltage and current generation originating from the resulting microbial activity was observed for 12 days of deployment, with fluctuation in response to tidal cycles. A novel bacterium belonging to the genus Thiomicrorhabdus dominated the microbial community specifically enriched on the cathode. Metagenomic analysis provided the draft genome of the bacterium and the gene repertoire indicated that the bacterium has the potential for thio-autotrophic growth, which is a typical physiological feature of the members of the genus, while the bacterium had a unique gene cluster encoding multi-heme cytochrome c proteins responsible for extracellular electron transfer. Herein, we propose this bacterium as a new species, specifically enriched during electricity generation, as 'Candidatus Thiomicrorhabdus electrophagus'. This finding suggests the natural occurrence of electrosynthetic microbial populations using the geoelectricity in deep-sea hydrothermal environments.}, } @article {pmid36151458, year = {2023}, author = {Maciel-Guerra, A and Baker, M and Hu, Y and Wang, W and Zhang, X and Rong, J and Zhang, Y and Zhang, J and Kaler, J and Renney, D and Loose, M and Emes, RD and Liu, L and Chen, J and Peng, Z and Li, F and Dottorini, T}, title = {Dissecting microbial communities and resistomes for interconnected humans, soil, and livestock.}, journal = {The ISME journal}, volume = {17}, number = {1}, pages = {21-35}, pmid = {36151458}, issn = {1751-7370}, mesh = {Animals ; Humans ; Anti-Bacterial Agents ; *Anti-Infective Agents ; Chickens/microbiology ; Escherichia coli/genetics ; Genes, Bacterial ; Livestock/microbiology ; *Microbiota ; *Soil Microbiology ; Drug Resistance, Bacterial ; }, abstract = {A debate is currently ongoing as to whether intensive livestock farms may constitute reservoirs of clinically relevant antimicrobial resistance (AMR), thus posing a threat to surrounding communities. Here, combining shotgun metagenome sequencing, machine learning (ML), and culture-based methods, we focused on a poultry farm and connected slaughterhouse in China, investigating the gut microbiome of livestock, workers and their households, and microbial communities in carcasses and soil. For both the microbiome and resistomes in this study, differences are observed across environments and hosts. However, at a finer scale, several similar clinically relevant antimicrobial resistance genes (ARGs) and similar associated mobile genetic elements were found in both human and broiler chicken samples. Next, we focused on Escherichia coli, an important indicator for the surveillance of AMR on the farm. Strains of E. coli were found intermixed between humans and chickens. We observed that several ARGs present in the chicken faecal resistome showed correlation to resistance/susceptibility profiles of E. coli isolates cultured from the same samples. Finally, by using environmental sensing these ARGs were found to be correlated to variations in environmental temperature and humidity. Our results show the importance of adopting a multi-domain and multi-scale approach when studying microbial communities and AMR in complex, interconnected environments.}, } @article {pmid36151114, year = {2022}, author = {Dekkers, KF and Sayols-Baixeras, S and Baldanzi, G and Nowak, C and Hammar, U and Nguyen, D and Varotsis, G and Brunkwall, L and Nielsen, N and Eklund, AC and Bak Holm, J and Nielsen, HB and Ottosson, F and Lin, YT and Ahmad, S and Lind, L and Sundström, J and Engström, G and Smith, JG and Ärnlöv, J and Orho-Melander, M and Fall, T}, title = {An online atlas of human plasma metabolite signatures of gut microbiome composition.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5370}, pmid = {36151114}, issn = {2041-1723}, mesh = {Biomarkers ; Cross-Sectional Studies ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolome ; Metabolomics/methods ; Middle Aged ; Uremic Toxins ; }, abstract = {Human gut microbiota produce a variety of molecules, some of which enter the bloodstream and impact health. Conversely, dietary or pharmacological compounds may affect the microbiota before entering the circulation. Characterization of these interactions is an important step towards understanding the effects of the gut microbiota on health. In this cross-sectional study, we used deep metagenomic sequencing and ultra-high-performance liquid chromatography linked to mass spectrometry for a detailed characterization of the gut microbiota and plasma metabolome, respectively, of 8583 participants invited at age 50 to 64 from the population-based Swedish CArdioPulmonary bioImage Study. Here, we find that the gut microbiota explain up to 58% of the variance of individual plasma metabolites and we present 997 associations between alpha diversity and plasma metabolites and 546,819 associations between specific gut metagenomic species and plasma metabolites in an online atlas (https://gutsyatlas.serve.scilifelab.se/). We exemplify the potential of this resource by presenting novel associations between dietary factors and oral medication with the gut microbiome, and microbial species strongly associated with the uremic toxin p-cresol sulfate. This resource can be used as the basis for targeted studies of perturbation of specific metabolites and for identification of candidate plasma biomarkers of gut microbiota composition.}, } @article {pmid36149894, year = {2022}, author = {Zhang, L and Chen, L and Yu, XA and Duvallet, C and Isazadeh, S and Dai, C and Park, S and Frois-Moniz, K and Duarte, F and Ratti, C and Alm, EJ and Ling, F}, title = {MicrobiomeCensus estimates human population sizes from wastewater samples based on inter-individual variability in gut microbiomes.}, journal = {PLoS computational biology}, volume = {18}, number = {9}, pages = {e1010472}, pmid = {36149894}, issn = {1553-7358}, mesh = {*COVID-19 ; *Gastrointestinal Microbiome/genetics ; Humans ; Pandemics ; Population Density ; Sewage ; Wastewater ; }, abstract = {The metagenome embedded in urban sewage is an attractive new data source to understand urban ecology and assess human health status at scales beyond a single host. Analyzing the viral fraction of wastewater in the ongoing COVID-19 pandemic has shown the potential of wastewater as aggregated samples for early detection, prevalence monitoring, and variant identification of human diseases in large populations. However, using census-based population size instead of real-time population estimates can mislead the interpretation of data acquired from sewage, hindering assessment of representativeness, inference of prevalence, or comparisons of taxa across sites. Here, we show that taxon abundance and sub-species diversisty in gut-associated microbiomes are new feature space to utilize for human population estimation. Using a population-scale human gut microbiome sample of over 1,100 people, we found that taxon-abundance distributions of gut-associated multi-person microbiomes exhibited generalizable relationships with respect to human population size. Here and throughout this paper, the human population size is essentially the sample size from the wastewater sample. We present a new algorithm, MicrobiomeCensus, for estimating human population size from sewage samples. MicrobiomeCensus harnesses the inter-individual variability in human gut microbiomes and performs maximum likelihood estimation based on simultaneous deviation of multiple taxa's relative abundances from their population means. MicrobiomeCensus outperformed generic algorithms in data-driven simulation benchmarks and detected population size differences in field data. New theorems are provided to justify our approach. This research provides a mathematical framework for inferring population sizes in real time from sewage samples, paving the way for more accurate ecological and public health studies utilizing the sewage metagenome.}, } @article {pmid36148930, year = {2022}, author = {Pettke, A and Filén, F and Widgren, K and Jacks, A and Glans, H and Andreasson, S and Muradrasoli, S and Helgesson, S and Hauzenberger, E and Karlberg, ML and Walai, N and Bjerkner, A and Gourlé, H and Gredmark-Russ, S and Lindsjö, OK and Sondén, K and Asgeirsson, H}, title = {Ten-Week Follow-Up of Monkeypox Case-Patient, Sweden, 2022.}, journal = {Emerging infectious diseases}, volume = {28}, number = {10}, pages = {2074-2077}, pmid = {36148930}, issn = {1080-6059}, mesh = {DNA, Viral ; Disease Outbreaks ; Follow-Up Studies ; Humans ; Male ; *Mpox (monkeypox)/diagnosis/epidemiology ; Monkeypox virus/genetics ; Sweden/epidemiology ; }, abstract = {A previously healthy male patient had detectable monkeypox virus DNA in saliva 76 days after laboratory confirmation of infection. A comprehensive characterization of viral kinetics and a detailed follow-up indicated a declining risk for transmission during the weeks after monkeypox symptoms appeared.}, } @article {pmid36148364, year = {2022}, author = {Yan, H and Li, Z and Xia, H and Li, Q and Bai, H}, title = {A case report on mixed pulmonary infection of Nocardia nova, Mycobacterium tuberculosis, and Aspergillus fumigatus based on metagenomic next-generation sequencing.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {927338}, pmid = {36148364}, issn = {2296-2565}, mesh = {Aspergillus fumigatus/genetics ; *Coinfection/diagnosis ; Glucocorticoids ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Lung ; *Mycobacterium tuberculosis/genetics ; Nocardia ; *Pneumonia ; }, abstract = {BACKGROUND: Pulmonary infection is one of the common complications of long-term use of glucocorticoids. Severe infections not only increase the length of hospital stay and treatment costs but also cause progression or recurrence of the primary disease.

CASE DESCRIPTION: Herein, we reported a case of mixed pulmonary infection secondary to glucocorticoid use. Rare pathogens such as Nocardia nova, Mycobacterium tuberculosis, Aspergillus fumigatus, and cytomegalovirus were detected by metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid and lung puncture tissue. Combining the results of conventional pathogen detection and clinical symptoms, the patient was diagnosed with mixed pulmonary infection by multiple pathogens. After timely targeted medication, the patient was finally discharged with a good prognosis.

CONCLUSION: To our knowledge, this is the first case report on mixed pulmonary infection with pathogens including Nocardia nova, Mycobacterium tuberculosis, Aspergillus fumigatus, and human cytomegalovirus. As a new clinical diagnostic method, mNGS has great advantages in diagnosis of diseases such as mixed infections.}, } @article {pmid36148301, year = {2022}, author = {Tous, N and Marcos, S and Goodarzi Boroojeni, F and Pérez de Rozas, A and Zentek, J and Estonba, A and Sandvang, D and Gilbert, MTP and Esteve-Garcia, E and Finn, R and Alberdi, A and Tarradas, J}, title = {Novel strategies to improve chicken performance and welfare by unveiling host-microbiota interactions through hologenomics.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {884925}, pmid = {36148301}, issn = {1664-042X}, abstract = {Fast optimisation of farming practices is essential to meet environmental sustainability challenges. Hologenomics, the joint study of the genomic features of animals and the microbial communities associated with them, opens new avenues to obtain in-depth knowledge on how host-microbiota interactions affect animal performance and welfare, and in doing so, improve the quality and sustainability of animal production. Here, we introduce the animal trials conducted with broiler chickens in the H2020 project HoloFood, and our strategy to implement hologenomic analyses in light of the initial results, which despite yielding negligible effects of tested feed additives, provide relevant information to understand how host genomic features, microbiota development dynamics and host-microbiota interactions shape animal welfare and performance. We report the most relevant results, propose hypotheses to explain the observed patterns, and outline how these questions will be addressed through the generation and analysis of animal-microbiota multi-omic data during the HoloFood project.}, } @article {pmid36147838, year = {2022}, author = {Liu, YH and Ma, YM and Tian, HO and Yang, B and Han, WX and Zhao, WH and Chai, HL and Zhang, ZS and Wang, LF and Chen, L and Xing, Y and Ding, YL and Zhao, L}, title = {First determination of DNA virus and some additional bacteria from Melophagus ovinus (sheep ked) in Tibet, China.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {988136}, pmid = {36147838}, issn = {1664-302X}, abstract = {Melophagus ovinus (sheep ked) is one of the common ectoparasites in sheep. In addition to causing direct damage to the host through biting and sucking blood, sheep ked is a potential vector of helminths, protozoa, bacteria, and viruses. Sheep M. ovinus samples from three regions in Tibet were selected for DNA extraction. The 16S rDNA V3-V4 hypervariable region was amplified, after genomic DNA fragmentation, Illumina Hiseq libraries were constructed. The 16S rRNA sequencing and viral metagenomics sequencing were separately conducted on the Illumina Novaseq 6000 platform and molecular biology software and platforms were employed to analyze the sequencing data. Illumina PE250 sequencing results demonstrated that the dominant bacteria phylum in M. ovinus from Tibet, China was Proteobacteria, where 29 bacteria genera were annotated. The dominant bacterial genera were Bartonella, Wolbachia, and Arsenophonus; Bartonella chomelii, Wolbachia spp., and Arsenophonus spp. were the dominant bacterial species in M. ovinus from Tibet, China. We also detected Kluyvera intermedia, Corynebacterium maris DSM 45190, Planomicrobium okeanokoites, and Rhodococcus erythropolis, of which the relative abundance of Kluyvera intermedia was high. Illumina Hiseq sequencing results demonstrated that 4 virus orders were detected in M. ovinus from Tibet, China, and 3 samples were annotated into 29 families, 30 families, and 28 families of viruses, respectively. Virus families related to vertebrates and insects mainly included Mimiviridae, Marseilleviridae, Poxviridae, Ascoviridae, Iridoviridae, Baculoviridae, Hytrosaviridae, Nudiviridae, Polydnaviridae, Adomaviridae, Asfarviridae, Hepeviridae, Herpesviridae, and Retroviridae; at the species level, the relative abundance of Tupanvirus_soda_lake, Klosneuvirus_KNV1, and Indivirus_ILV1 was higher. African swine fever virus and many poxviruses from the family Poxviridae were detected, albeit their relative abundance was low. The dominant bacterial phylum of M. ovinus from Tibet, China was Proteobacteria, and the dominant bacterial genera were Bartonella, Wolbachia, and Arsenophonus, where 23 out of 29 annotated bacteria genera were first reported in M. ovinus. Kluyvera intermedia, Corynebacterium maris DSM 45190, Planomicrobium okeanokoites, and Rhodococcus erythropolis were detected for the first time. All DNA viruses detected in this study have been reported in M. ovinus for the first time.}, } @article {pmid36147601, year = {2022}, author = {Zhou, Z and Lv, H and Lv, J and Shi, Y and Huang, H and Chen, L and Shi, D}, title = {Alterations of gut microbiota in cirrhotic patients with spontaneous bacterial peritonitis: A distinctive diagnostic feature.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {999418}, pmid = {36147601}, issn = {2235-2988}, mesh = {Bacteria/genetics ; Dysbiosis/diagnosis/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; *Limosilactobacillus reuteri ; Liver Cirrhosis/complications/diagnosis ; *Peritonitis/diagnosis ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Spontaneous bacterial peritonitis (SBP) is a severe infection in cirrhotic patients that requires early diagnosis to improve the long-term outcome. Alterations in the gut microbiota have been shown to correlate with the development and progression of liver cirrhosis. However, the relationship between SBP and gut microbiota remains unknown.

METHODS: In this study, we applied 16S rRNA pyrosequencing of feces to ascertain possible links between the gut microbiota and SBP. We recruited 30 SBP patients, 30 decompensated cirrhotic patients without SBP (NSBP) and 30 healthy controls. Metagenomic functional prediction of bacterial taxa was achieved using PICRUSt.

RESULTS: The composition of the gut microbiota in the SBP patients differed remarkably from that in the NSBP patients and healthy individuals. The microbial richness was significantly decreased, while the diversity was increased in the SBP patients. Thirty-four bacterial taxa containing 15 species, mainly pathogens such as Klebsiella pneumoniae, Serratia marcescens and Prevotella oris, were dominant in the SBP group, while 42 bacterial taxa containing 16 species, especially beneficial species such as Faecalibacterium prausnitzii, Methanobrevibacter smithii and Lactobacillus reuteri, were enriched in the NSBP group. Notably, we found that 18 gene functions of gut microbiota were different between SBP patients and NSBP patients, which were associated with energy metabolism and functional substance metabolism. Five optimal microbial markers were determined using a random forest model, and the combination of Lactobacillus reuteri, Rothia mucilaginosa, Serratia marcescens, Ruminococcus callidus and Neisseria mucosa achieved an area under the curve (AUC) value of 0.8383 to distinguish SBP from decompensated cirrhosis.

CONCLUSIONS: We described the obvious dysbiosis of gut microbiota in SBP patients and demonstrated the potential of microbial markers as noninvasive diagnostic tools for SBP at an early stage.}, } @article {pmid36146871, year = {2022}, author = {Sasivimolrattana, T and Chantratita, W and Sensorn, I and Chaiwongkot, A and Oranratanaphan, S and Bhattarakosol, P}, title = {Human Virome in Cervix Controlled by the Domination of Human Papillomavirus.}, journal = {Viruses}, volume = {14}, number = {9}, pages = {}, pmid = {36146871}, issn = {1999-4915}, mesh = {*Alphapapillomavirus ; *Cervix Uteri/virology ; *Coinfection ; DNA, Viral/genetics ; Female ; Humans ; Papillomaviridae/genetics ; *Papillomavirus Infections ; Uterine Cervical Neoplasms ; *Virome/genetics ; Viruses ; }, abstract = {Although other co-viral infections could also be considered influencing factors, cervical human papillomavirus (HPV) infection is the main cause of cervical cancer. Metagenomics have been employed in the NGS era to study the microbial community in each habitat. Thus, in this investigation, virome capture sequencing was used to examine the virome composition in the HPV-infected cervix. Based on the amount of HPV present in each sample, the results revealed that the cervical virome of HPV-infected individuals could be split into two categories: HPV-dominated (HD; ≥60%) and non-HPV-dominated (NHD; <60%). Cervical samples contained traces of several human viral species, including the molluscum contagiosum virus (MCV), human herpesvirus 4 (HHV4), torque teno virus (TTV), and influenza A virus. When compared to the HD group, the NHD group had a higher abundance of several viruses. Human viral diversity appears to be influenced by HPV dominance. This is the first proof that the diversity of human viruses in the cervix is impacted by HPV abundance. However, more research is required to determine whether human viral variety and the emergence of cancer are related.}, } @article {pmid36146854, year = {2022}, author = {Yang, S and Zhang, D and Ji, Z and Zhang, Y and Wang, Y and Chen, X and He, Y and Lu, X and Li, R and Guo, Y and Shen, Q and Ji, L and Wang, X and Li, Y and Zhang, W}, title = {Viral Metagenomics Reveals Diverse Viruses in Tissue Samples of Diseased Pigs.}, journal = {Viruses}, volume = {14}, number = {9}, pages = {}, pmid = {36146854}, issn = {1999-4915}, mesh = {*Anelloviridae/genetics ; Animals ; Metagenome ; Metagenomics ; Phylogeny ; Swine ; *Virus Diseases/veterinary ; *Viruses/genetics ; }, abstract = {The swine industry plays an essential role in agricultural production in China. Diseases, especially viral diseases, affect the development of the pig industry and threaten human health. However, at present, the tissue virome of diseased pigs has rarely been studied. Using the unbiased viral metagenomic approach, we investigated the tissue virome in sick pigs (respiratory symptoms, reproductive disorders, high fever, diarrhea, weight loss, acute death and neurological symptoms) collected from farms of Anhui, Jiangsu and Sichuan Province, China. The eukaryotic viruses identified belonged to the families Anelloviridae, Arteriviridae, Astroviridae, Flaviviridae, Circoviridae and Parvoviridae; prokaryotic virus families including Siphoviridae, Myoviridae and Podoviridae occupied a large proportion in some samples. This study provides valuable information for understanding the tissue virome in sick pigs and for the monitoring, preventing, and treating of viral diseases in pigs.}, } @article {pmid36146797, year = {2022}, author = {Pérot, P and Bigot, T and Temmam, S and Regnault, B and Eloit, M}, title = {Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery.}, journal = {Viruses}, volume = {14}, number = {9}, pages = {}, pmid = {36146797}, issn = {1999-4915}, mesh = {High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; *Metagenomics/methods ; Viral Proteins/genetics ; *Viruses/genetics ; }, abstract = {We present Microseek, a pipeline for virus identification and discovery based on RVDB-prot, a comprehensive, curated and regularly updated database of viral proteins. Microseek analyzes metagenomic Next Generation Sequencing (mNGS) raw data by performing quality steps, de novo assembly, and by scoring the Lowest Common Ancestor (LCA) from translated reads and contigs. Microseek runs on a local computer. The outcome of the pipeline is displayed through a user-friendly and dynamic graphical interface. Based on two representative mNGS datasets derived from human tissue and plasma specimens, we illustrate how Microseek works, and we report its performances. In silico spikes of known viral sequences, but also spikes of fake Neopneumovirus viral sequences generated with variable evolutionary distances from known members of the Pneumoviridae family, were used. Results were compared to Chan Zuckerberg ID (CZ ID), a reference cloud-based mNGS pipeline. We show that Microseek reliably identifies known viral sequences and performs well for the detection of distant pseudoviral sequences, especially in complex samples such as in human plasma, while minimizing non-relevant hits.}, } @article {pmid36146789, year = {2022}, author = {Busse, L and Tisza, M and DiRuggiero, J}, title = {Viruses Ubiquity and Diversity in Atacama Desert Endolithic Communities.}, journal = {Viruses}, volume = {14}, number = {9}, pages = {}, pmid = {36146789}, issn = {1999-4915}, support = {80NSSC19K0470/NASA/NASA/United States ; NNX15AP18G/NASA/NASA/United States ; }, mesh = {Calcium Carbonate ; Calcium Sulfate ; Desert Climate ; *Microbiota ; *Viruses/genetics ; }, abstract = {Viruses are key players in the environment, and recent metagenomic studies have revealed their diversity and genetic complexity. Despite progress in understanding the ecology of viruses in extreme environments, viruses' dynamics and functional roles in dryland ecosystems, which cover about 45% of the Earth's land surfaces, remain largely unexplored. This study characterizes virus sequences in the metagenomes of endolithic (within rock) microbial communities ubiquitously found in hyper-arid deserts. Taxonomic classification and network construction revealed the presence of novel and diverse viruses in communities inhabiting calcite, gypsum, and ignimbrite rocks. Viral genome maps show a high level of protein diversity within and across endolithic communities and the presence of virus-encoded auxiliary metabolic genes. Phage-host relationships were predicted by matching tRNA, CRISPR spacer, and protein sequences in the viral and microbial metagenomes. Primary producers and heterotrophic bacteria were found to be putative hosts to some viruses. Intriguingly, viral diversity was not correlated with microbial diversity across rock substrates.}, } @article {pmid36146775, year = {2022}, author = {Hesse, RD and Roach, M and Kerr, EN and Papudeshi, B and Lima, LFO and Goodman, AZ and Hoopes, L and Scott, M and Meyer, L and Huveneers, C and Dinsdale, EA}, title = {Phage Diving: An Exploration of the Carcharhinid Shark Epidermal Virome.}, journal = {Viruses}, volume = {14}, number = {9}, pages = {}, pmid = {36146775}, issn = {1999-4915}, support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; *Bacteriophages/genetics ; *Diving ; Ecosystem ; Epidermis ; Metagenomics ; *Sharks ; *Virome ; }, abstract = {The epidermal microbiome is a critical element of marine organismal immunity, but the epidermal virome of marine organisms remains largely unexplored. The epidermis of sharks represents a unique viromic ecosystem. Sharks secrete a thin layer of mucus which harbors a diverse microbiome, while their hydrodynamic dermal denticles simultaneously repel environmental microbes. Here, we sampled the virome from the epidermis of three shark species in the family Carcharhinidae: the genetically and morphologically similar Carcharhinus obscurus (n = 6) and Carcharhinus galapagensis (n = 10) and the outgroup Galeocerdo cuvier (n = 15). Virome taxonomy was characterized using shotgun metagenomics and compared with a suite of multivariate analyses. All three sharks retain species-specific but highly similar epidermal viromes dominated by uncharacterized bacteriophages which vary slightly in proportional abundance within and among shark species. Intraspecific variation was lower among C. galapagensis than among C. obscurus and G. cuvier. Using both the annotated and unannotated reads, we were able to determine that the Carcharhinus galapagensis viromes were more similar to that of G. cuvier than they were to that of C. obscurus, suggesting that behavioral niche may be a more prominent driver of virome than host phylogeny.}, } @article {pmid36146740, year = {2022}, author = {Souza, JVC and Santos, HO and Leite, AB and Giovanetti, M and Bezerra, RDS and Carvalho, E and Bernardino, JST and Viala, VL and Haddad, R and Ciccozzi, M and Alcantara, LCJ and Sampaio, SC and Covas, DT and Kashima, S and Elias, MC and Slavov, SN}, title = {Viral Metagenomics for the Identification of Emerging Infections in Clinical Samples with Inconclusive Dengue, Zika, and Chikungunya Viral Amplification.}, journal = {Viruses}, volume = {14}, number = {9}, pages = {}, pmid = {36146740}, issn = {1999-4915}, mesh = {Arboviruses/genetics ; *Chikungunya Fever/diagnosis/epidemiology ; *Chikungunya virus/genetics ; Communicable Diseases, Emerging ; *Dengue/diagnosis/epidemiology ; *Dengue Virus/genetics ; Humans ; Metagenomics ; Phylogeny ; Real-Time Polymerase Chain Reaction ; *Zika Virus/genetics ; *Zika Virus Infection ; }, abstract = {Viral metagenomics is increasingly being used for the identification of emerging and re-emerging viral pathogens in clinical samples with unknown etiology. The objective of this study was to shield light on the metavirome composition in clinical samples obtained from patients with clinical history compatible with an arboviral infection, but that presented inconclusive results when tested using RT-qPCR. The inconclusive amplification results might be an indication of the presence of an emerging arboviral agent that is inefficiently amplified by conventional PCR techniques. A total of eight serum samples with inconclusive amplification results for the routinely tested arboviruses-dengue (DENV), Zika (ZIKV), and Chikungunya (CHIKV) obtained during DENV and CHIKV outbreaks registered in the state of Alagoas, Northeast Brazil between July and August 2021-were submitted to metagenomic next-generation sequencing assay using NextSeq 2000 and bioinformatic pipeline for viral discovery. The performed bioinformatic analysis revealed the presence of two arboviruses: DENV type 2 (DENV-2) and CHIKV with a high genome coverage. Further, the metavirome of those samples revealed the presence of multiple commensal viruses apparently without clinical significance. The phylogenetic analysis demonstrated that the DENV-2 genome belonged to the Asian/American genotype and clustered with other Brazilian strains. The identified CHIKV genome was taxonomically assigned as ECSA genotype, which is circulating in Brazil. Together, our results reinforce the utility of metagenomics as a valuable tool for viral identification in samples with inconclusive arboviral amplification. Viral metagenomics is one of the most potent methods for the identification of emerging arboviruses.}, } @article {pmid36146717, year = {2022}, author = {Wiederkehr, MA and Qi, W and Schoenbaechler, K and Fraefel, C and Kubacki, J}, title = {Virus Diversity, Abundance, and Evolution in Three Different Bat Colonies in Switzerland.}, journal = {Viruses}, volume = {14}, number = {9}, pages = {}, pmid = {36146717}, issn = {1999-4915}, mesh = {Animals ; *Chiroptera ; Genome, Viral ; *Middle East Respiratory Syndrome Coronavirus ; Nucleotides ; Phylogeny ; Switzerland/epidemiology ; }, abstract = {Bats are increasingly recognized as reservoirs for many different viruses that threaten public health, such as Hendravirus, Ebolavirus, Nipahvirus, and SARS- and MERS-coronavirus. To assess spillover risk, viromes of bats from different parts of the world have been investigated in the past. As opposed to most of these prior studies, which determined the bat virome at a single time point, the current work was performed to monitor changes over time. Specifically, fecal samples of three endemic Swiss bat colonies consisting of three different bat species were collected over three years and analyzed using next-generation sequencing. Furthermore, single nucleotide variants of selected DNA and RNA viruses were analyzed to investigate virus genome evolution. In total, sequences of 22 different virus families were found, of which 13 are known to infect vertebrates. Most interestingly, in a Vespertilio murinus colony, sequences from a MERS-related beta-coronavirus were consistently detected over three consecutive years, which allowed us to investigate viral genome evolution in a natural reservoir host.}, } @article {pmid36146668, year = {2022}, author = {Esnault, G and Earley, B and Cormican, P and Waters, SM and Lemon, K and Cosby, SL and Lagan, P and Barry, T and Reddington, K and McCabe, MS}, title = {Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1.}, journal = {Viruses}, volume = {14}, number = {9}, pages = {}, pmid = {36146668}, issn = {1999-4915}, mesh = {Animals ; Anti-Bacterial Agents ; Cattle ; *Cattle Diseases ; Genomics ; *Herpesvirus 1, Bovine/genetics ; Metagenomics/methods ; *Nanopores ; *Viruses/genetics ; }, abstract = {Bovine respiratory disease (BRD), which is the leading cause of morbidity and mortality in cattle, is caused by numerous known and unknown viruses and is responsible for the widespread use of broad-spectrum antibiotics despite the use of polymicrobial BRD vaccines. Viral metagenomics sequencing on the portable, inexpensive Oxford Nanopore Technologies MinION sequencer and sequence analysis with its associated user-friendly point-and-click Epi2ME cloud-based pathogen identification software has the potential for point-of-care/same-day/sample-to-result metagenomic sequence diagnostics of known and unknown BRD pathogens to inform a rapid response and vaccine design. We assessed this potential using in vitro viral cell cultures and nasal swabs taken from calves that were experimentally challenged with a single known BRD-associated DNA virus, namely, bovine herpes virus 1. Extensive optimisation of the standard Oxford Nanopore library preparation protocols, particularly a reduction in the PCR bias of library amplification, was required before BoHV-1 could be identified as the main virus in the in vitro cell cultures and nasal swab samples within approximately 7 h from sample to result. In addition, we observed incorrect assignment of the bovine sequence to bacterial and viral taxa due to the presence of poor-quality bacterial and viral genome assemblies in the RefSeq database used by the EpiME Fastq WIMP pathogen identification software.}, } @article {pmid36146660, year = {2022}, author = {Howard-Jones, AR and Pham, D and Jeoffreys, N and Eden, JS and Hueston, L and Kesson, AM and Nagendra, V and Samarasekara, H and Newton, P and Chen, SC and O'Sullivan, MV and Maddocks, S and Dwyer, DE and Kok, J}, title = {Emerging Genotype IV Japanese Encephalitis Virus Outbreak in New South Wales, Australia.}, journal = {Viruses}, volume = {14}, number = {9}, pages = {}, pmid = {36146660}, issn = {1999-4915}, mesh = {Animals ; Australia ; Disease Outbreaks ; *Encephalitis Virus, Japanese/genetics ; *Encephalitis, Japanese/diagnosis/epidemiology ; Genotype ; Humans ; New South Wales/epidemiology ; Prospective Studies ; }, abstract = {The detection of a new and unexpected Japanese encephalitis virus (JEV) outbreak in March 2022 in Australia, where JEV is not endemic, demanded the rapid development of a robust diagnostic framework to facilitate the testing of suspected patients across the state of New South Wales (NSW). This nascent but comprehensive JEV diagnostic service encompassed serological, molecular and metagenomics testing within a centralised reference laboratory. Over the first three months of the outbreak (4 March 2022 to 31 May 2022), 1,061 prospective samples were received from 878 NSW residents for JEV testing. Twelve confirmed cases of Japanese encephalitis (JE) were identified, including ten cases diagnosed by serology alone, one case by metagenomic next generation sequencing and real-time polymerase chain reaction (RT-PCR) of brain tissue and serology, and one case by RT-PCR of cerebrospinal fluid, providing an incidence of JE over this period of 0.15/100,000 persons in NSW. As encephalitis manifests in <1% of cases of JEV infection, the population-wide prevalence of JEV infection is likely to be substantially higher. Close collaboration with referring laboratories and clinicians was pivotal to establishing successful JEV case ascertainment for this new outbreak. Sustained and coordinated animal, human and environmental surveillance within a OneHealth framework is critical to monitor the evolution of the current outbreak, understand its origins and optimise preparedness for future JEV and arbovirus outbreaks.}, } @article {pmid36146653, year = {2022}, author = {Yutin, N and Rayko, M and Antipov, D and Mutz, P and Wolf, YI and Krupovic, M and Koonin, EV}, title = {Varidnaviruses in the Human Gut: A Major Expansion of the Order Vinavirales.}, journal = {Viruses}, volume = {14}, number = {9}, pages = {}, pmid = {36146653}, issn = {1999-4915}, support = {Intramural funds/NH/NIH HHS/United States ; }, mesh = {Adenosine Triphosphatases/genetics ; *Bacteriophages/genetics ; Capsid Proteins/genetics ; Humans ; Intestines ; Phylogeny ; Prophages/genetics ; *Viruses ; }, abstract = {Bacteriophages play key roles in the dynamics of the human microbiome. By far the most abundant components of the human gut virome are tailed bacteriophages of the realm Duplodnaviria, in particular, crAss-like phages. However, apart from duplodnaviruses, the gut virome has not been dissected in detail. Here we report a comprehensive census of a minor component of the gut virome, the tailless bacteriophages of the realm Varidnaviria. Tailless phages are primarily represented in the gut by prophages, that are mostly integrated in genomes of Alphaproteobacteria and Verrucomicrobia and belong to the order Vinavirales, which currently consists of the families Corticoviridae and Autolykiviridae. Phylogenetic analysis of the major capsid proteins (MCP) suggests that at least three new families should be established within Vinavirales to accommodate the diversity of prophages from the human gut virome. Previously, only the MCP and packaging ATPase genes were reported as conserved core genes of Vinavirales. Here we report an extended core set of 12 proteins, including MCP, packaging ATPase, and previously undetected lysis enzymes, that are shared by most of these viruses. We further demonstrate that replication system components are frequently replaced in the genomes of Vinavirales, suggestive of selective pressure for escape from yet unknown host defenses or avoidance of incompatibility with coinfecting related viruses. The results of this analysis show that, in a sharp contrast to marine viromes, varidnaviruses are a minor component of the human gut virome. Moreover, they are primarily represented by prophages, as indicated by the analysis of the flanking genes, suggesting that there are few, if any, lytic varidnavirus infections in the gut at any given time. These findings complement the existing knowledge of the human gut virome by exploring a group of viruses that has been virtually overlooked in previous work.}, } @article {pmid36145435, year = {2022}, author = {Balázs, B and Tóth, Z and Nagy, JB and Majoros, L and Tóth, Á and Kardos, G}, title = {Faecal Carriage of Carbapenem-Resistant Acinetobacter baumannii: Comparison to Clinical Isolates from the Same Period (2017-2019).}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {9}, pages = {}, pmid = {36145435}, issn = {2076-0817}, abstract = {Increasing prevalence of A. baumannii was found in the faecal samples of inpatients without infection caused by A. baumannii (0.15%; 55/7806). The aim of the study was to determine whether there is a relationship between the clinical strains and the increased faecal occurrence. Characteristics of faecal and clinical isolates were compared between 2017 and 2019, and the direction of causality was assessed by Granger causality tests. In the case of the antibiotic resistance, faecal carriage of carbapenem-resistant Acinetobacter baumannii (CRAb) was Granger-caused by prevalence of CRAb in inpatients (F = 15.84, p < 0.001), but inpatient prevalence was not Granger-caused by CRAb faecal carriage (F = 0.03, p = 0.855). Whole genomes of 16 faecal isolates were sequenced by Illumina MiSeq; cgMLST types were determined. In faecal isolates, the occurrence of carbapenem resistance was lower than among the clinical isolates from the same period; only blaOXA-72 harbouring ST636 and ST492 were detected, and the blaOXA-23 harbouring ST2 and ST49 strains previously dominant in clinical isolates were absent. Carriage of blaOXA-72 was linked to pMAL-1-like and pA105-2-like plasmids in ST636 and ST492 isolates, respectively, both in clinical and faecal isolates. The new ST636 and ST492 strains may colonise the gut microbiota of the patients, which thus may play a role as a reservoir.}, } @article {pmid36145357, year = {2022}, author = {Mokrousov, I and Slavchev, I and Solovieva, N and Dogonadze, M and Vyazovaya, A and Valcheva, V and Masharsky, A and Belopolskaya, O and Dimitrov, S and Zhuravlev, V and Portugal, I and Perdigão, J and Dobrikov, GM}, title = {Molecular Insight into Mycobacterium tuberculosis Resistance to Nitrofuranyl Amides Gained through Metagenomics-like Analysis of Spontaneous Mutants.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {15}, number = {9}, pages = {}, pmid = {36145357}, issn = {1424-8247}, support = {19-15-00028//Russian Science Foundation/ ; АААА-А21-121021600206-5//Federal Service for Surveillance on Consumer Rights Protection and Human Wellbeing/ ; KP-06-N39/7//Bulgarian Science Fund/ ; KP-06-N41/3//Bulgarian Science Fund/ ; UID/DTP/04138/2019//Fundação para a Ciência e Tecnologia/ ; CEECIND/00394/2017//Fundação para a Ciência e Tecnologia/ ; }, abstract = {We performed synthesis of new nitrofuranyl amides and investigated their anti-TB activity and primary genetic response of mycobacteria through whole-genome sequencing (WGS) of spontaneous resistant mutants. The in vitro activity was assessed on reference strain Mycobacterium tuberculosis H37Rv. The most active compound 11 was used for in vitro selection of spontaneous resistant mutants. The same mutations in six genes were detected in bacterial cultures grown under increased concentrations of 11 (2×, 4×, 8× MIC). The mutant positions were presented as mixed wild type and mutant alleles while increasing the concentration of the compound led to the semi-proportional and significant increase in mutant alleles. The identified genes belong to different categories and pathways. Some of them were previously reported as mediating drug resistance or drug tolerance, and counteracting oxidative and nitrosative stress, in particular: Rv0224c, fbiC, iniA, and Rv1592c. Gene-set interaction analysis revealed a certain weak interaction for gene pairs Rv1592-Rv1639c and Rv1592-Rv0224c. To conclude, this study experimentally demonstrated a multifaceted primary genetic response of M. tuberculosis to the action of nitrofurans. All three 11-treated subcultures independently presented the same six SNPs, which suggests their non-random occurrence and likely causative relationship between compound action and possible resistance mechanism.}, } @article {pmid36145068, year = {2022}, author = {Pang, L and Zhi, Q and Jian, W and Liu, Z and Lin, H}, title = {The Oral Microbiome Impacts the Link between Sugar Consumption and Caries: A Preliminary Study.}, journal = {Nutrients}, volume = {14}, number = {18}, pages = {}, pmid = {36145068}, issn = {2072-6643}, support = {81903345//National Natural Science Foundation of China/ ; }, mesh = {Adolescent ; Candida albicans ; *Dental Caries/etiology ; Dietary Sugars/adverse effects ; Humans ; Lactobacillus ; *Microbiota ; Phosphotransferases ; Streptococcus mutans ; Sugars ; }, abstract = {BACKGROUND: The excessive and frequent intake of refined sugar leads to caries. However, the relationship between the amount of sugar intake and the risk of caries is not always consistent. Oral microbial profile and function may impact the link between them. This study aims to identify the plaque microbiota characteristics of caries subjects with low (CL) and high (CH) sugar consumption, and of caries-free subjects with low (FL) and high sugar (FH) consumption.

METHODS: A total of 40 adolescents were enrolled in the study, and supragingival plaque samples were collected and subjected to metagenomic analyses. The caries status, sugar consumption, and oral-health behaviors of the subjects were recorded.

RESULTS: The results indicate that the CL group showed a higher abundance of several cariogenic microorganisms Lactobacillus, A. gerencseriae, A. dentails, S. mutans, C. albicans, S. wiggsiae and P. acidifaciens. C. gingivalis, and P. gingivalis, which were enriched in the FH group. In terms of gene function, the phosphotransferase sugar uptake system, phosphotransferase system, and several two-component responses-regulator pairs were enriched in the CL group.

CONCLUSION: Overall, our data suggest the existence of an increased cariogenic microbial community and sugar catabolism potential in the CL group, and a healthy microbial community in the FH group, which had self-stabilizing functional potential.}, } @article {pmid36144468, year = {2022}, author = {Syromyatnikov, M and Nesterova, E and Gladkikh, M and Smirnova, Y and Gryaznova, M and Popov, V}, title = {Characteristics of the Gut Bacterial Composition in People of Different Nationalities and Religions.}, journal = {Microorganisms}, volume = {10}, number = {9}, pages = {}, pmid = {36144468}, issn = {2076-2607}, support = {project FZGW-2020-0001, unique number of the register of State tasks 075001X39782002//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {High-throughput sequencing has made it possible to extensively study the human gut microbiota. The links between the human gut microbiome and ethnicity, religion, and race remain rather poorly understood. In this review, data on the relationship between gut microbiota composition and the nationality of people and their religion were generalized. The unique gut microbiome of a healthy European (including Slavic nationality) is characterized by the dominance of the phyla Firmicutes, Bacteroidota, Actinobacteria, Proteobacteria, Fusobacteria, and Verrucomicrobia. Among the African population, the typical members of the microbiota are Bacteroides and Prevotella. The gut microbiome of Asians is very diverse and rich in members of the genera Prevotella, Bacteroides Lactobacillus, Faecalibacterium, Ruminococcus, Subdoligranulum, Coprococcus, Collinsella, Megasphaera, Bifidobacterium, and Phascolarctobacterium. Among Buddhists and Muslims, the Prevotella enterotype is characteristic of the gut microbiome, while other representatives of religions, including Christians, have the Bacteroides enterotype. Most likely, the gut microbiota of people of different nationalities and religions are influenced by food preferences. The review also considers the influences of pathologies such as obesity, Crohn's disease, cancer, diabetes, etc., on the bacterial composition of the guts of people of different nationalities.}, } @article {pmid36144417, year = {2022}, author = {Esposito, AM and Esposito, MM and Ptashnik, A}, title = {Phylogenetic Diversity of Animal Oral and Gastrointestinal Viromes Useful in Surveillance of Zoonoses.}, journal = {Microorganisms}, volume = {10}, number = {9}, pages = {}, pmid = {36144417}, issn = {2076-2607}, abstract = {Great emphasis has been placed on bacterial microbiomes in human and animal systems. In recent years, advances in metagenomics have allowed for the detection and characterization of more and more native viral particles also residing in these organisms. The digestive tracts of animals and humans-from the oral cavity, to the gut, to fecal excretions-have become one such area of interest. Next-generation sequencing and bioinformatic analyses have uncovered vast phylogenetic virome diversity in companion animals, such as dogs and cats, as well as farm animals and wildlife such as bats. Zoonotic and arthropod-borne illnesses remain major causes of worldwide outbreaks, as demonstrated by the devastating COVID-19 pandemic. This highlights the increasing need to identify and study animal viromes to prevent such disastrous cross-species transmission outbreaks in the coming years. Novel viruses have been uncovered in the viromes of multiple organisms, including birds, bats, cats, and dogs. Although the exact consequences for public health have not yet become clear, many analyses have revealed viromes dominated by RNA viruses, which can be the most problematic to human health, as these genomes are known for their high mutation rates and immune system evasion capabilities. Furthermore, in the wake of worldwide disruption from the COVID-19 pandemic, it is evident that proper surveillance of viral biodiversity is crucial. For instance, gut viral metagenomic analysis in dogs has shown close relationships between the highly abundant canine coronavirus and human coronavirus strains 229E and NL63. Future studies and vigilance could potentially save many lives.}, } @article {pmid36144397, year = {2022}, author = {Goel, A and Ncho, CM and Jeong, CM and Gupta, V and Jung, JY and Ha, SY and Yang, JK and Choi, YH}, title = {Effects of Dietary Supplementation of Solubles from Shredded, Steam-Exploded Pine Particles on the Performance and Cecum Microbiota of Acute Heat-Stressed Broilers.}, journal = {Microorganisms}, volume = {10}, number = {9}, pages = {}, pmid = {36144397}, issn = {2076-2607}, support = {2020193C10-2022-BA01//Korea Forest Service/ ; 2019H1D3A1A01071142//National Research Foundation of Korea/ ; }, abstract = {Heat stress (HS) negatively influences livestock productivity, but it can be, at least in part, mitigated by nutritional interventions. One such intervention is to use byproducts from various sources that are likely to be included in the consumer chain. Thus, the present study investigated the effects of dietary supplementation of solubles from shredded, steam-exploded pine particles (SSPPs) on the performance and cecum microbiota in broilers subjected to acute HS. One-week-old Ross 308 broilers (n = 108) were fed 0%, 0.1%, or 0.4% SSPP in their diets. On the 37th day, forty birds were allocated to one of four groups; namely, a group fed a control diet without SSPPs at thermoneutral temperature (NT) (0% NT) and acute heat-stressed birds with 0% (0% HS), 0.1% (0.1% HS), and 0.4% (0.4% HS) SSPP-supplemented diets. The NT was maintained at 21.0 °C, while the HS room was increased to 31 °C. The final BW, percent difference in body weight (PDBW), and feed intake (FI) were lower in HS birds, but PDBW was reversely associated with dietary SSPP. Similarly, HS birds had a higher rectal temperature (RT) and ΔT in comparison to birds kept at NT. The FI of SSPP-supplemented birds was not significant, indicating lower HS effects. Plasma triglyceride was decreased in HS birds but not affected in 0.1% HS birds in comparison to 0% NT birds. OTUs and Chao1 were increased by 0.1% HS compared to 0% NT. Unweighted Unifrac distances for 0.1% HS were different from 0% NT and 0.4% HS. The favorable bacterial phylum (Tenericutes) and genera (Faecalibacterium and Anaerofustis) were increased, while the pathogenic genus (Enterococcus) was decreased, in SSPP-supplemented birds. In sum, production performances are negatively affected under acute HS. Dietary supplementation of SSPPs is beneficial for improving community richness indices and unweighted Unifrac distances, and it enhanced the advantageous bacterial phyla and reduced virulent genera and triglyceride hydrolysis in acute HS broilers. Our results indicate that dietary SSPPs modulates the microbial profile of the cecum while resulting in relatively less weight loss and lower rectal temperature compared to control.}, } @article {pmid36144349, year = {2022}, author = {Gontijo, JB and Paula, FS and Venturini, AM and Mandro, JA and Bodelier, PLE and Tsai, SM}, title = {Insights into the Genomic Potential of a Methylocystis sp. from Amazonian Floodplain Sediments.}, journal = {Microorganisms}, volume = {10}, number = {9}, pages = {}, pmid = {36144349}, issn = {2076-2607}, support = {2014/50320-4, 2017/26138-0, 2018/14974-0, 2019/25924-7, and 2019/25931-3//São Paulo Research Foundation/ ; }, abstract = {Although floodplains are recognized as important sources of methane (CH4) in the Amazon basin, little is known about the role of methanotrophs in mitigating CH4 emissions in these ecosystems. Our previous data reported the genus Methylocystis as one of the most abundant methanotrophs in these floodplain sediments. However, information on the functional potential and life strategies of these organisms living under seasonal flooding is still missing. Here, we described the first metagenome-assembled genome (MAG) of a Methylocystis sp. recovered from Amazonian floodplains sediments, and we explored its functional potential and ecological traits through phylogenomic, functional annotation, and pan-genomic approaches. Both phylogenomics and pan-genomics identified the closest placement of the bin.170_fp as Methylocystis parvus. As expected for Type II methanotrophs, the Core cluster from the pan-genome comprised genes for CH4 oxidation and formaldehyde assimilation through the serine pathway. Furthermore, the complete set of genes related to nitrogen fixation is also present in the Core. Interestingly, the MAG singleton cluster revealed the presence of unique genes related to nitrogen metabolism and cell motility. The study sheds light on the genomic characteristics of a dominant, but as yet unexplored methanotroph from the Amazonian floodplains. By exploring the genomic potential related to resource utilization and motility capability, we expanded our knowledge on the niche breadth of these dominant methanotrophs in the Amazonian floodplains.}, } @article {pmid36144342, year = {2022}, author = {Yang, Z and Yao, Y and Sun, M and Li, G and Zhu, J}, title = {Metagenomics Reveal Microbial Effects of Lotus Root-Fish Co-Culture on Nitrogen Cycling in Aquaculture Pond Sediments.}, journal = {Microorganisms}, volume = {10}, number = {9}, pages = {}, pmid = {36144342}, issn = {2076-2607}, support = {U20A2010//National Natural Science Foundation of China/ ; 2019YFD0900302//National Key Research and Development Program of China/ ; }, abstract = {Feed input leads to a large amount of nitrogen-containing sediment accumulating in the substrate in the pond culture process, threatening the safety of aquaculture production. Planting lotus roots (Nelumbo nucifera Gaertn.) in ponds can accelerate the removal of bottom nitrogen, while the role of nitrogen cycle-related microorganisms in the removal is still unclear. In this study, eight yellow catfish (Pelteobagrus fulvidraco) culture ponds with the same basic situation were divided into fishponds with planted lotus roots and ponds with only fish farming. Sediment samples were taken from the fishponds with planted lotus roots and the ponds with only fish farming before and after fish farming, marked as FPB, FPA, FOB, and FOA, respectively, and subjected to physicochemical and metagenomic sequencing analyses. The results show that the contents of NH4+, NO2−, TN, TP, and OM were significantly lower (p < 0.05) in FPA than in FOA. The abundance of metabolic pathways for inorganic nitrogen transformation and ammonia assimilation increased considerably after culture compared to the sediments before culture. A total of eight ammonia production pathways and two ammonia utilization pathways were annotated in the sediments of the experimental ponds, with a very high abundance of ammonia assimilation. Acinetobacter and Pseudomonas (34.67%, 18.02%) were the dominant bacteria in the pond sediments before culture, which changed to Thiobacillus (12.16%) after culture. The FPA had significantly higher relative abundances of Thiobacillus denitrificans and Sulfuricella denitrificans, and the FOA had significantly a higher abundance of Microcystis aeruginosa compared to other samples. The massive growth of Microcystis aeruginosa provided two new inorganic nitrogen metabolic pathways and one organic nitrogen metabolic pathway for FOA. The relative abundances of these three microorganisms were negatively correlated with NH4+ content (p < 0.01) and significantly positively correlated with AP, OM content, and pH value. Compared with ponds with only fish farming, lotus root−fish co-culture can significantly reduce the nitrogen content in sediment, increase the abundance of denitrifying bacteria, and inhibit algae growth. Still, it has little effect on the abundance of nitrogen cycle-related enzymes and genes. In summary, it is shown that, although lotus roots promote the growth of denitrifying microorganisms in the sediment, nitrogen removal relies mainly on nutrient uptake by lotus roots.}, } @article {pmid36144222, year = {2022}, author = {Miglani, R and Parveen, N and Kumar, A and Ansari, MA and Khanna, S and Rawat, G and Panda, AK and Bisht, SS and Upadhyay, J and Ansari, MN}, title = {Degradation of Xenobiotic Pollutants: An Environmentally Sustainable Approach.}, journal = {Metabolites}, volume = {12}, number = {9}, pages = {}, pmid = {36144222}, issn = {2218-1989}, abstract = {The ability of microorganisms to detoxify xenobiotic compounds allows them to thrive in a toxic environment using carbon, phosphorus, sulfur, and nitrogen from the available sources. Biotransformation is the most effective and useful metabolic process to degrade xenobiotic compounds. Microorganisms have an exceptional ability due to particular genes, enzymes, and degradative mechanisms. Microorganisms such as bacteria and fungi have unique properties that enable them to partially or completely metabolize the xenobiotic substances in various ecosystems.There are many cutting-edge approaches available to understand the molecular mechanism of degradative processes and pathways to decontaminate or change the core structure of xenobiotics in nature. These methods examine microorganisms, their metabolic machinery, novel proteins, and catabolic genes. This article addresses recent advances and current trends to characterize the catabolic genes, enzymes and the techniques involved in combating the threat of xenobiotic compounds using an eco-friendly approach.}, } @article {pmid36144194, year = {2022}, author = {Li-Gao, R and Grubbs, K and Bertoni, AG and Hoffman, KL and Petrosino, JF and Ramesh, G and Wu, M and Rotter, JI and Chen, YI and Evans, AM and Robinson, RJ and Sommerville, L and Mook-Kanamori, D and Goodarzi, MO and Michelotti, GA and Sheridan, PA}, title = {The Roles of Gut Microbiome and Plasma Metabolites in the Associations between ABO Blood Groups and Insulin Homeostasis: The Microbiome and Insulin Longitudinal Evaluation Study (MILES).}, journal = {Metabolites}, volume = {12}, number = {9}, pages = {}, pmid = {36144194}, issn = {2218-1989}, support = {UL1TR001881/TR/NCATS NIH HHS/United States ; R01DK109588/NH/NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; R01 HL105756/HL/NHLBI NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; UL1 TR001881/TR/NCATS NIH HHS/United States ; P30 DK063491/DK/NIDDK NIH HHS/United States ; R01 DK109588/DK/NIDDK NIH HHS/United States ; }, abstract = {Non-O blood groups are associated with decreased insulin sensitivity and risk of type 2 diabetes. A recent study pinpointed the associations between ABO blood groups and gut microbiome, which may serve as potential mediators for the observed increased disease risks. We aimed to characterize associations between ABO haplotypes and insulin-related traits as well as potential mediating pathways. We assessed insulin homeostasis in African Americans (AAs; n = 109) and non-Hispanic whites (n = 210) from the Microbiome and Insulin Longitudinal Evaluation Study. The ABO haplotype was determined by six SNPs located in the ABO gene. Based on prior knowledge, we included 21 gut bacteria and 13 plasma metabolites for mediation analysis. In the white study cohort (60 ± 9 years, 42% male), compared to the O1 haplotype, A1 was associated with a higher Matsuda insulin sensitivity index, while a lower relative abundance of Bacteroides massiliensis and lactate levels. Lactate was a likely mediator of this association but not Bacteroides massiliensis. In the AAs group (57 ± 8 years, 33% male), we found no association between any haplotype and insulin-related traits. In conclusion, the A1 haplotype may promote healthy insulin sensitivity in non-Hispanic whites and lactate likely play a role in this process but not selected gut bacteria.}, } @article {pmid36144180, year = {2022}, author = {Wu, C and Fei, J and Xu, Q and Tao, Y and Zhou, Z and Wang, Y and Wu, J and Gu, HF}, title = {Interaction between Plasma Metabolomics and Intestinal Microbiome in db/db Mouse, an Animal Model for Study of Type 2 Diabetes and Diabetic Kidney Disease.}, journal = {Metabolites}, volume = {12}, number = {9}, pages = {}, pmid = {36144180}, issn = {2218-1989}, support = {CPU20190228HFG//Cooperation Research Grant/ ; CPU20180815HFG//China Pharmaceutical University/ ; }, abstract = {Evidence has demonstrated that either metabolites or intestinal microbiota are involved in the pathogenesis of type 2 diabetes (T2D) and diabetic kidney disease (DKD). To explore the interaction between plasma metabolomics and intestinal microbiome in the progress of T2D-DKD, in the current study, we analyzed metabolomics in the plasma of db/db mice with liquid chromatography-mass spectrometry and also examined intestinal prokaryotes and entire gut microbiome dysbiosis at the genus level with both 16S rDNA and metagenomic sequencing techniques. We found that Negativibacillus and Rikenella were upregulated, while Akkermansia, Candidatus, Erysipelatoclostridium and Ileibacterium were downregulated in the colon of db/db mice compared with non-diabetic controls. In parallel, a total of 91 metabolites were upregulated, while 23 were downregulated in the plasma of db/db mice. The top five upregulated metabolites included D-arabinose 5-phosphate, estrone 3-sulfate, L-theanine, 3'-aenylic acid and adenosine 5'-monophosphate, and the five most significantly downregulated metabolites were aurohyocholic acid sodium salt, calcium phosphorylcholine chloride, tauro-alpha-muricholic acid sodium salt, galactinol and phosphocholine. These plasma metabolites were interacted with intestinal microbiomes, which are mainly involved in the pathways related to the biosynthesis of unsaturated fatty acids, fatty acid elongation, steroid biosynthesis, and D-arginine and D-ornithine metabolism. In the differential metabolites, N-acetyl-L-ornithine, ornithine and L-kyn could be metabolized by the correspondingly differential ontology genes in the intestinal metagenome. The current study thereby provides evidence for a gut-metabolism-kidney axis in the metabolism of db/db mice, in which the gut microbiome and circulating metabolomics interact, and suggests that information from this axis may contribute to our understanding of T2D and DKD pathogenesis.}, } @article {pmid36143456, year = {2022}, author = {Olunoiki, E and Rehner, J and Bischoff, M and Koshel, E and Vogt, T and Reichrath, J and Becker, SL}, title = {Characteristics of the Skin Microbiome in Selected Dermatological Conditions: A Narrative Review.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {9}, pages = {}, pmid = {36143456}, issn = {2075-1729}, abstract = {The skin is the largest and outermost organ of the human body. The microbial diversity of the skin can be influenced by several variable factors such as physiological state, lifestyle, and geographical locations. Recent years have seen increased interest in research aiming at an improved understanding of the relationship between the human microbiota and several diseases. Albeit understudied, interesting correlations between the skin microbiota and several dermatological conditions have been observed. Studies have shown that a decrease or increase in the abundance of certain microbial communities can be implicated in several dermatological pathologies. This narrative review (i) examines the role of the skin microbiota in the maintenance of skin homeostasis and health, (ii) provides examples on how some common skin diseases (acne inversa, candidiasis, psoriasis) are associated with the dysbiosis of microbial communities, and (iii) describes how recent research approaches used in skin microbiome studies may lead to improved, more sensitive diagnostics and individual therapeutics in the foreseeable future.}, } @article {pmid36143382, year = {2022}, author = {Tausch, SH and Loka, TP and Schulze, JM and Andrusch, A and Klenner, J and Dabrowski, PW and Lindner, MS and Nitsche, A and Renard, BY}, title = {PathoLive-Real-Time Pathogen Identification from Metagenomic Illumina Datasets.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {9}, pages = {}, pmid = {36143382}, issn = {2075-1729}, support = {2515NIK043//Federal Ministry of Health/ ; Live-DREAM//Federal Ministry of Education and Research/ ; }, abstract = {Over the past years, NGS has become a crucial workhorse for open-view pathogen diagnostics. Yet, long turnaround times result from using massively parallel high-throughput technologies as the analysis can only be performed after sequencing has finished. The interpretation of results can further be challenged by contaminations, clinically irrelevant sequences, and the sheer amount and complexity of the data. We implemented PathoLive, a real-time diagnostics pipeline for the detection of pathogens from clinical samples hours before sequencing has finished. Based on real-time alignment with HiLive2, mappings are scored with respect to common contaminations, low-entropy areas, and sequences of widespread, non-pathogenic organisms. The results are visualized using an interactive taxonomic tree that provides an easily interpretable overview of the relevance of hits. For a human plasma sample that was spiked in vitro with six pathogenic viruses, all agents were clearly detected after only 40 of 200 sequencing cycles. For a real-world sample from Sudan, the results correctly indicated the presence of Crimean-Congo hemorrhagic fever virus. In a second real-world dataset from the 2019 SARS-CoV-2 outbreak in Wuhan, we found the presence of a SARS coronavirus as the most relevant hit without the novel virus reference genome being included in the database. For all samples, clinically irrelevant hits were correctly de-emphasized. Our approach is valuable to obtain fast and accurate NGS-based pathogen identifications and correctly prioritize and visualize them based on their clinical significance: PathoLive is open source and available on GitLab and BioConda.}, } @article {pmid36143265, year = {2022}, author = {Reider, S and Watschinger, C and Längle, J and Pachmann, U and Przysiecki, N and Pfister, A and Zollner, A and Tilg, H and Plattner, S and Moschen, AR}, title = {Short- and Long-Term Effects of a Prebiotic Intervention with Polyphenols Extracted from European Black Elderberry-Sustained Expansion of Akkermansia spp.}, journal = {Journal of personalized medicine}, volume = {12}, number = {9}, pages = {}, pmid = {36143265}, issn = {2075-4426}, support = {not applicable//Christian Doppler Research Association/ ; not applicable//IPRONA AG/SPA/ ; }, abstract = {(1) Background: The intestinal microbiome has emerged as a central factor in human physiology and its alteration has been associated with disease. Therefore, great hopes are placed in microbiota-modulating strategies. Among various approaches, prebiotics, substrates with selective metabolization conferring a health benefit to the host, are promising candidates. Herein, we studied the prebiotic properties of a purified extract from European black elderberries, with a high and standardized content of polyphenols and anthocyanins. (2) Methods: The ELDERGUT trial represents a 9-week longitudinal intervention study divided into 3 distinct phases, namely a baseline, an intervention and a washout period, three weeks each. The intervention consisted of capsules containing 300 mg elderberry extract taken twice a day. Patient-reported outcomes and biosamples were collected weekly. Microbiome composition was assessed using 16S amplicon metagenomics. (3) Results: The supplementation was well tolerated. Microbiome trajectories were highly individualized with a profound shift in diversity indices immediately upon initiation and after termination of the compound. This was accompanied by corresponding changes in species abundance over time. Of particular interest, the relative abundance of Akkermansia spp. continued to increase in a subset of participants even beyond the supplementation period. Associations with participant metadata were detected.}, } @article {pmid36142786, year = {2022}, author = {Mayorga, L and Serrano-Gómez, G and Xie, Z and Borruel, N and Manichanh, C}, title = {Intercontinental Gut Microbiome Variances in IBD.}, journal = {International journal of molecular sciences}, volume = {23}, number = {18}, pages = {}, pmid = {36142786}, issn = {1422-0067}, support = {PI20/00130//Instituto de Salud Carlos III/ ; 812969/MCCC_/Marie Curie/United Kingdom ; PI17/00614//Instituto de Salud Carlos III/ ; }, mesh = {Biomarkers ; *Colitis, Ulcerative/diagnosis ; *Crohn Disease/diagnosis ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; *Inflammatory Bowel Diseases ; }, abstract = {The development of biomarkers for inflammatory bowel disease (IBD) diagnosis would be relevant in a generalized context. However, intercontinental investigation on these microbial biomarkers remains scarce. We examined taxonomic microbiome variations in IBD using published DNA shotgun metagenomic data. For this purpose, we used sequenced data from our previous Spanish Crohn's disease (CD) and ulcerative colitis (UC) cohort, downloaded sequence data from a Chinese CD cohort, and downloaded taxonomic and functional profiling tables from a USA CD and UC cohort. At the global level, geographical location and disease phenotype were the main explanatory covariates of microbiome variations. In healthy controls (HC) and UC, geography turned out to be the most important factor, while disease intestinal location was the most important one in CD. Disease severity correlated with lower alpha-diversity in UC but not in CD. Across geography, alpha-diversity was significantly different independently of health status, except for CD. Despite recruitment from different countries and with different disease severity scores, CD patients may harbor a very similar microbial taxonomic profile. Our study pointed out that geographic location, disease activity status, and other environmental factors are important contributing factors in microbiota changes in IBD. We therefore strongly recommend taking these factors into consideration for future IBD studies to obtain globally valid and reproducible biomarkers.}, } @article {pmid36142744, year = {2022}, author = {Zhang, T and Huang, S and Qiu, J and Wu, X and Yuan, H and Park, S}, title = {Beneficial Effect of Gastrodia elata Blume and Poria cocos Wolf Administration on Acute UVB Irradiation by Alleviating Inflammation through Promoting the Gut-Skin Axis.}, journal = {International journal of molecular sciences}, volume = {23}, number = {18}, pages = {}, pmid = {36142744}, issn = {1422-0067}, support = {2019R1A2C1007203//National Research Foundation of Korea/ ; }, mesh = {Agaricales ; Animals ; Butylene Glycols ; Cellulose ; *Gastrodia ; Inflammation/drug therapy ; Interleukin-13 ; Interleukin-4 ; Intestines ; Lipopolysaccharides ; Malondialdehyde ; Mice ; Mice, Inbred ICR ; Plant Extracts/pharmacology/therapeutic use ; Propionates ; RNA, Messenger ; Skin ; Tretinoin ; Tumor Necrosis Factor-alpha/genetics ; Ultraviolet Rays ; Water ; *Wolfiporia ; }, abstract = {Bioactive compounds in some herbs can, directly and indirectly, protect against photoaging. We evaluated the effects of Gastrodia elata Blume (GE) and Poria cocos Wolf (PC) water extracts on ultraviolet (UV) B-induced skin lesions by acute UVB exposure in ICR mice and explored their mechanism of action. After removing the hair on the back of the mice, UVB (280-310 nm) was exposed to the back for 30 min to induce skin damage. Four UVB exposure groups were divided into the following according to the local application (1,3-butanediol extract) on the dorsal skin and oral intake (0.3 g water extract/kg body weight/day): 1,3-butanediol and cellulose(control; UV-Con), retinoic acid (positive-control; UV-Positive), PC extracts (UV-PC), and GE extracts (UV-GE). The fifth group had no UVB exposure with the same treatment as the UV-Con (Normal-control). The erythema, burns, erosion, and wounds of the UV-PC and UV-PC groups were alleviated, and the most significant improvements occurred in the UV-PC group. PC and GE reduced the thickness of the dorsal skin tissue, the penetration of mast cells, and malondialdehyde contents. The mRNA expression of TNF-α, IL-13, and IL-4, inflammatory factors, were also reduced significantly in the dorsal skin of the UV-PC and UV-GE groups. UV-PC, UV-GE, and UV-Positive showed improvements in UV-induced intestinal tissue inflammation. UV-Con deteriorated the intestinal morphology, and PC and GE alleviated it. The α-diversity of the fecal microbiota decreased in the UV-control, and UV-PC and UV-GE prevented the decrease. Fecal metagenome analysis revealed increased propionate biosynthesis in the UV-PC group but decreased lipopolysaccharide biosynthesis in the UV-PC and UV-GE groups compared to UV-Con. In conclusion, the local application and intake of PC and GE had significant therapeutic effects on acute UV-induced skin damage by reducing oxidative stress and proinflammatory cytokines, potentially promoting the gut-microbiota-gut-skin axis.}, } @article {pmid36142684, year = {2022}, author = {Gladkov, GV and Kimeklis, AK and Afonin, AM and Lisina, TO and Orlova, OV and Aksenova, TS and Kichko, AA and Pinaev, AG and Andronov, EE}, title = {The Structure of Stable Cellulolytic Consortia Isolated from Natural Lignocellulosic Substrates.}, journal = {International journal of molecular sciences}, volume = {23}, number = {18}, pages = {}, pmid = {36142684}, issn = {1422-0067}, support = {18-16-00073//Russian Science Foundation/ ; }, mesh = {Bacteria/metabolism ; Cellulose/metabolism ; *Lignin/metabolism ; *Microbial Consortia ; }, abstract = {Recycling plant matter is one of the challenges facing humanity today and depends on efficient lignocellulose degradation. Although many bacterial strains from natural substrates demonstrate cellulolytic activities, the CAZymes (Carbohydrate-Active enZYmes) responsible for these activities are very diverse and usually distributed among different bacteria in one habitat. Thus, using microbial consortia can be a solution to rapid and effective decomposition of plant biomass. Four cellulolytic consortia were isolated from enrichment cultures from composting natural lignocellulosic substrates-oat straw, pine sawdust, and birch leaf litter. Enrichment cultures facilitated growth of similar, but not identical cellulose-decomposing bacteria from different substrates. Major components in all consortia were from Proteobacteria, Actinobacteriota and Bacteroidota, but some were specific for different substrates-Verrucomicrobiota and Myxococcota from straw, Planctomycetota from sawdust and Firmicutes from leaf litter. While most members of the consortia were involved in the lignocellulose degradation, some demonstrated additional metabolic activities. Consortia did not differ in the composition of CAZymes genes, but rather in axillary functions, such as ABC-transporters and two-component systems, usually taxon-specific and associated with CAZymes. Our findings show that enrichment cultures can provide reproducible cellulolytic consortia from various lignocellulosic substrates, the stability of which is ensured by tight microbial relations between its components.}, } @article {pmid36142415, year = {2022}, author = {Iacono, R and Strazzulli, A and Giglio, R and Bitetti, F and Cobucci-Ponzano, B and Moracci, M}, title = {Valorization of Biomasses from Energy Crops for the Discovery of Novel Thermophilic Glycoside Hydrolases through Metagenomic Analysis.}, journal = {International journal of molecular sciences}, volume = {23}, number = {18}, pages = {}, pmid = {36142415}, issn = {1422-0067}, support = {PON01 01966, funded in the frame of Operative National Programme Research and Competi-tiveness 2007-2013 D. D. Prot. n. 01/Ric. 18.1.2010//Ministero dell'Università e della Ricerca Scentifica/ ; }, mesh = {Archaea/chemistry ; Biomass ; Crops, Agricultural ; *Glycoside Hydrolases/chemistry/genetics ; Metagenomics ; Starch ; *alpha-Glucosidases ; }, abstract = {The increasing interest for environmentally friendly technologies is driving the transition from fossil-based economy to bioeconomy. A key enabler for circular bioeconomy is to valorize renewable biomasses as feedstock to extract high value-added chemicals. Within this transition the discovery and the use of robust biocatalysts to replace toxic chemical catalysts play a significant role as technology drivers. To meet both the demands, we performed microbial enrichments on two energy crops, used as low-cost feed for extremophilic consortia. A culture-dependent approach coupled to metagenomic analysis led to the discovery of more than 300 glycoside hydrolases and to characterize a new α-glucosidase from an unknown hyperthermophilic archaeon. Aglu1 demonstrated to be the most active archaeal GH31 on 4Np-α-Glc and it showed unexpected specificity vs. kojibiose, revealing to be a promising candidate for biotechnological applications such as the liquefaction/saccharification of starch.}, } @article {pmid36142289, year = {2022}, author = {Graziano, S and Caldara, M and Gullì, M and Bevivino, A and Maestri, E and Marmiroli, N}, title = {A Metagenomic and Gene Expression Analysis in Wheat (T. durum) and Maize (Z. mays) Biofertilized with PGPM and Biochar.}, journal = {International journal of molecular sciences}, volume = {23}, number = {18}, pages = {}, pmid = {36142289}, issn = {1422-0067}, support = {818431//European Union/ ; }, mesh = {Charcoal/chemistry ; Fertilizers/analysis ; Gene Expression ; Plant Roots ; Soil/chemistry ; Soil Microbiology ; *Triticum/genetics ; Water/metabolism ; *Zea mays/metabolism ; }, abstract = {Commodity crops, such as wheat and maize, are extremely dependent on chemical fertilizers, a practice contributing greatly to the increase in the contaminants in soil and water. Promising solutions are biofertilizers, i.e., microbial biostimulants that when supplemented with soil stimulate plant growth and production. Moreover, the biofertilizers can be fortified when (i) provided as multifunctional consortia and (ii) combined with biochar with a high cargo capacity. The aim of this work was to determine the molecular effects on the soil microbiome of different biofertilizers and delivery systems, highlight their physiological effects and merge the data with statistical analyses. The measurements of the physiological parameters (i.e., shoot and root biomass), transcriptomic response of genes involved in essential pathways, and characterization of the rhizosphere population were analyzed. The results demonstrated that wheat and maize supplemented with different combinations of selected microbial consortia and biochar have a positive effect on plant growth in terms of shoot and root biomass; the treatments also had a beneficial influence on the biodiversity of the indigenous rhizo-microbial community, reinforcing the connection between microbes and plants without further spreading contaminants. There was also evidence at the transcriptional level of crosstalk between microbiota and plants.}, } @article {pmid36142138, year = {2022}, author = {Borroni, D and Paytuví-Gallart, A and Sanseverino, W and Gómez-Huertas, C and Bonci, P and Romano, V and Giannaccare, G and Rechichi, M and Meduri, A and Oliverio, GW and Rocha-de-Lossada, C and On Behalf Of Lucy Consortium, }, title = {Exploring the Healthy Eye Microbiota Niche in a Multicenter Study.}, journal = {International journal of molecular sciences}, volume = {23}, number = {18}, pages = {}, pmid = {36142138}, issn = {1422-0067}, mesh = {Cross-Sectional Studies ; DNA ; *Health Promotion ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {PURPOSE: This study aims to explore and characterize healthy eye microbiota.

METHODS: Healthy subjects older than 18 years were selected for this descriptive cross-sectional study. Samples were collected with an eSwab with 1 mL of Liquid Amies Medium (Copan Brescia, Italy). Following DNA extraction, libraries preparation, and amplification, PCR products were purified and end-repaired for barcode ligation. Libraries were pooled to a final concentration of 26 pM. Template preparation was performed with Ion Chef according to Ion 510, Ion 520, and Ion 530 Kit-Chef protocol. Sequencing of the amplicon libraries was carried out on a 520 or 530 chip using the Ion Torrent S5 system (Thermo Fisher; Waltham, MA, USA). Raw reads were analyzed with GAIA (v 2.02).

RESULTS: Healthy eye microbiota is a low-diversity microbiome. The vast majority of the 137 analyzed samples were highly enriched with Staphylococcus, whereas only in a few of them, other genera such as Bacillus, Pseudomonas, and Corynebacterium predominate. We found an average of 88 genera with an average Shannon index of 0.65.

CONCLUSION: We identified nine different ECSTs. A better understanding of healthy eye microbiota has the potential to improve disease diagnosis and personalized regimens to promote health.}, } @article {pmid36141538, year = {2022}, author = {Li, N and Li, H and Zhu, C and Liu, C and Su, G and Chen, J}, title = {Controlling AMR in the Pig Industry: Is It Enough to Restrict Heavy Metals?.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {18}, pages = {}, pmid = {36141538}, issn = {1660-4601}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Disinfectants/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Manure ; *Metals, Heavy/analysis ; Soil ; Swine ; }, abstract = {Heavy metals have the potential to influence the transmission of antimicrobial resistance (AMR). However, the effect on AMR caused by heavy metals has not been clearly revealed. In this study, we used a microcosm experiment and metagenomics to examine whether common levels of Cu and Zn in pig manure influence AMR transmission in manured soil. We found that the abundance of 204 ARGs significantly increased after manure application, even though the manure did not contain antibiotic residuals. However, the combined addition of low Cu and Zn (500 and 1000 mg/kg, respectively) only caused 14 ARGs to significantly increase, and high Cu and Zn (1000 and 3000 mg/kg, respectively) caused 27 ARGs to significantly increase. The disparity of these numbers suggested that factors within the manure were the primary driving reasons for AMR transmission, rather than metal amendments. A similar trend was found for biocide and metal resistance genes (BMRGs) and mobile genetic elements (MGEs). This study offers deeper insights into AMR transmission in relation to the effects of manure application and heavy metals at commonly reported levels. Our findings recommend that more comprehensive measures in controlling AMR in the pig industry are needed apart from restricting heavy metal additions.}, } @article {pmid36140733, year = {2022}, author = {Hilt, EE and Ferrieri, P}, title = {Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases.}, journal = {Genes}, volume = {13}, number = {9}, pages = {}, pmid = {36140733}, issn = {2073-4425}, mesh = {*Anti-Infective Agents ; *Communicable Diseases/diagnosis/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics ; Whole Genome Sequencing ; }, abstract = {Next-generation sequencing (NGS) technologies have become increasingly available for use in the clinical microbiology diagnostic environment. There are three main applications of these technologies in the clinical microbiology laboratory: whole genome sequencing (WGS), targeted metagenomics sequencing and shotgun metagenomics sequencing. These applications are being utilized for initial identification of pathogenic organisms, the detection of antimicrobial resistance mechanisms and for epidemiologic tracking of organisms within and outside hospital systems. In this review, we analyze these three applications and provide a comprehensive summary of how these applications are currently being used in public health, basic research, and clinical microbiology laboratory environments. In the public health arena, WGS is being used to identify and epidemiologically track food borne outbreaks and disease surveillance. In clinical hospital systems, WGS is used to identify multi-drug-resistant nosocomial infections and track the transmission of these organisms. In addition, we examine how metagenomics sequencing approaches (targeted and shotgun) are being used to circumvent the traditional and biased microbiology culture methods to identify potential pathogens directly from specimens. We also expand on the important factors to consider when implementing these technologies, and what is possible for these technologies in infectious disease diagnosis in the next 5 years.}, } @article {pmid36140732, year = {2022}, author = {D'Argenio, V and Veneruso, I and Gong, C and Cecarini, V and Bonfili, L and Eleuteri, AM}, title = {Gut Microbiome and Mycobiome Alterations in an In Vivo Model of Alzheimer's Disease.}, journal = {Genes}, volume = {13}, number = {9}, pages = {}, pmid = {36140732}, issn = {2073-4425}, mesh = {*Alzheimer Disease/metabolism ; Animals ; Biomarkers ; Dysbiosis ; Ecosystem ; *Gastrointestinal Microbiome ; Mice ; *Mycobiome ; }, abstract = {Gut microbiota has emerged as an important key regulator of health and disease status. Indeed, gut microbial dysbiosis has been identified in an increasing number of diseases, including neurodegenerative disorders. Accordingly, microbial alterations have been reported also in Alzheimer's disease (AD), suggesting possible pathogenetic mechanisms contributing to the development of specific AD hallmarks and exacerbating metabolic alterations and neuroinflammation. The identification of these mechanisms is crucial to develop novel, targeted therapies and identify potential biomarkers for diagnostic purposes. Thus, the possibility to have AD in vivo models to study this microbial ecosystem represents a great opportunity for translational applications. Here, we characterized both gut microbiome and mycobiome of 3xTg-AD mice, one of the most widely used AD models, to identify specific microbial alterations with respect to the wild-type counterpart. Interestingly, we found a significant reduction of the Coprococcus and an increased abundance of Escherichia_Shigella and Barnesiella genera in the AD mice compatible with a pro-inflammatory status and the development of AD-related pathogenetic features. Moreover, the fungal Dipodascaceae family was significantly increased, thus suggesting a possible contribution to the metabolic alterations found in AD. Our data point out the strict connection between bacterial dysbiosis and AD and, even if further studies are required to clarify the underlining mechanisms, it clearly indicates the need for extensive metagenomic studies over the bacterial counterpart.}, } @article {pmid36140548, year = {2022}, author = {Bronkhorst, AJ and Ungerer, V and Oberhofer, A and Gabriel, S and Polatoglou, E and Randeu, H and Uhlig, C and Pfister, H and Mayer, Z and Holdenrieder, S}, title = {New Perspectives on the Importance of Cell-Free DNA Biology.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {12}, number = {9}, pages = {}, pmid = {36140548}, issn = {2075-4418}, abstract = {Body fluids are constantly replenished with a population of genetically diverse cell-free DNA (cfDNA) fragments, representing a vast reservoir of information reflecting real-time changes in the host and metagenome. As many body fluids can be collected non-invasively in a one-off and serial fashion, this reservoir can be tapped to develop assays for the diagnosis, prognosis, and monitoring of wide-ranging pathologies, such as solid tumors, fetal genetic abnormalities, rejected organ transplants, infections, and potentially many others. The translation of cfDNA research into useful clinical tests is gaining momentum, with recent progress being driven by rapidly evolving preanalytical and analytical procedures, integrated bioinformatics, and machine learning algorithms. Yet, despite these spectacular advances, cfDNA remains a very challenging analyte due to its immense heterogeneity and fluctuation in vivo. It is increasingly recognized that high-fidelity reconstruction of the information stored in cfDNA, and in turn the development of tests that are fit for clinical roll-out, requires a much deeper understanding of both the physico-chemical features of cfDNA and the biological, physiological, lifestyle, and environmental factors that modulate it. This is a daunting task, but with significant upsides. In this review we showed how expanded knowledge on cfDNA biology and faithful reverse-engineering of cfDNA samples promises to (i) augment the sensitivity and specificity of existing cfDNA assays; (ii) expand the repertoire of disease-specific cfDNA markers, thereby leading to the development of increasingly powerful assays; (iii) reshape personal molecular medicine; and (iv) have an unprecedented impact on genetics research.}, } @article {pmid36140263, year = {2022}, author = {Kovtun, AS and Averina, OV and Angelova, IY and Yunes, RA and Zorkina, YA and Morozova, AY and Pavlichenko, AV and Syunyakov, TS and Karpenko, OA and Kostyuk, GP and Danilenko, VN}, title = {Alterations of the Composition and Neurometabolic Profile of Human Gut Microbiota in Major Depressive Disorder.}, journal = {Biomedicines}, volume = {10}, number = {9}, pages = {}, pmid = {36140263}, issn = {2227-9059}, support = {20-14-00132//Russian Science Foundation/ ; }, abstract = {Major depressive disorder (MDD) is among the most prevalent mental disorders worldwide. Factors causing the pathogenesis of MDD include gut microbiota (GM), which interacts with the host through the gut-brain axis. In previous studies of GM in MDD patients, 16S rRNA sequencing was used, which provided information about composition but not about function. In our study, we analyzed whole metagenome sequencing data to assess changes in both the composition and functional profile of GM. We looked at the GM of 36 MDD patients, compared with that of 38 healthy volunteers. Comparative taxonomic analysis showed decreased abundances of Faecalibacterium prausnitzii, Roseburia hominis, and Roseburia intestinalis, and elevated abundances of Escherichia coli and Ruthenibacterium lactatiformans in the GM of MDD patients. We observed decreased levels of bacterial genes encoding key enzymes involved in the production of arginine, asparagine, glutamate, glutamine, melatonin, acetic, butyric and conjugated linoleic acids, and spermidine in MDD patients. These genes produced signature pairs with Faecalibacterium prausntizii and correlated with decreased levels of this species in the GM of MDD patients. These results show the potential impact of the identified biomarker bacteria and their metabolites on the pathogenesis of MDD, and should be confirmed in future metabolomic studies.}, } @article {pmid36139998, year = {2022}, author = {Alvarado, AC and Chekabab, SM and Predicala, BZ and Korber, DR}, title = {Impact of Raised without Antibiotics Measures on Antimicrobial Resistance and Prevalence of Pathogens in Sow Barns.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {9}, pages = {}, pmid = {36139998}, issn = {2079-6382}, support = {20170069//Saskatchewan Ministry of Agriculture/ ; }, abstract = {The growing concern over the emergence of antimicrobial resistance (AMR) in animal production as a result of extensive and inappropriate antibiotic use has prompted many swine farmers to raise their animals without antibiotics (RWA). In this study, the impact of implementing an RWA production approach in sow barns on actual on-farm antibiotic use, the emergence of AMR, and the abundance of pathogens was investigated. Over a 13-month period, fecal and nasopharynx samples were collected at 3-month intervals from sows raised in RWA barns and sows in conventional barns using antibiotics in accordance with the new regulations (non-RWA). Whole genome sequencing (WGS) was used to determine the prevalence of AMR and the presence of pathogens in those samples. Records of all drug use from the 13-month longitudinal study indicated a significant reduction in antimicrobial usage in sows from RWA barns compared to conventional non-RWA barns. Antifolates were commonly administered to non-RWA sows, whereas β-lactams were widely used to treat sows in RWA barns. Metagenomic analyses demonstrated an increased abundance of pathogenic Actinobacteria, Firmicutes, and Proteobacteria in the nasopharynx microbiome of RWA sows relative to non-RWA sows. However, WGS analyses revealed that the nasal microbiome of sows raised under RWA production exhibited a significant increase in the frequency of resistance genes coding for β-lactams, MDR, and tetracycline.}, } @article {pmid36138831, year = {2022}, author = {Garralda, MD and Weiner, S and Arensburg, B and Maureille, B and Vandermeersch, B}, title = {Dental Paleobiology in a Juvenile Neanderthal (Combe-Grenal, Southwestern France).}, journal = {Biology}, volume = {11}, number = {9}, pages = {}, pmid = {36138831}, issn = {2079-7737}, support = {00//Ministerio de Educación y Ciencia, Spain/ ; }, abstract = {Combe-Grenal site (Southwest France) was excavated by F. Bordes between 1953 and 1965. He found several human remains in Mousterian levels 60, 39, 35 and especially 25, corresponding to MIS 4 (~75-70/60 ky BP) and with Quina Mousterian lithics. One of the fossils found in level 25 is Combe-Grenal IV, consisting of a fragment of the left corpus of a juvenile mandible. This fragment displays initial juvenile periodontitis, and the two preserved teeth (LLP4 and LLM1) show moderate attrition and dental calculus. The SEM tartar analysis demonstrates the presence of cocci and filamentous types of bacteria, the former being more prevalent. This result is quite different from those obtained for the two adult Neanderthals Kebara 2 and Subalyuk 1, where more filamentous bacteria appear, especially in the Subalyuk 1 sample from Central Europe. These findings agree with the available biomedical data on periodontitis and tartar development in extant individuals, despite the different environmental conditions and diets documented by numerous archeological, taphonomical and geological data available on Neanderthals and present-day populations. New metagenomic analyses are extending this information, and despite the inherent difficulties, they will open important perspectives in studying this ancient human pathology.}, } @article {pmid36138466, year = {2022}, author = {Keller-Costa, T and Kozma, L and Silva, SG and Toscan, R and Gonçalves, J and Lago-Lestón, A and Kyrpides, NC and Nunes da Rocha, U and Costa, R}, title = {Metagenomics-resolved genomics provides novel insights into chitin turnover, metabolic specialization, and niche partitioning in the octocoral microbiome.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {151}, pmid = {36138466}, issn = {2049-2618}, mesh = {Animals ; Ankyrins ; *Anthozoa/microbiology ; Chitin ; *Chitinases ; *Gammaproteobacteria ; Metagenomics/methods ; *Microbiota/genetics ; Oxygen ; Phylogeny ; Protein Serine-Threonine Kinases ; *Rhodobacteraceae ; Symbiosis ; }, abstract = {BACKGROUND: The role of bacterial symbionts that populate octocorals (Cnidaria, Octocorallia) is still poorly understood. To shed light on their metabolic capacities, we examined 66 high-quality metagenome-assembled genomes (MAGs) spanning 30 prokaryotic species, retrieved from microbial metagenomes of three octocoral species and seawater.

RESULTS: Symbionts of healthy octocorals were affiliated with the taxa Endozoicomonadaceae, Candidatus Thioglobaceae, Metamycoplasmataceae, unclassified Pseudomonadales, Rhodobacteraceae, unclassified Alphaproteobacteria and Ca. Rhabdochlamydiaceae. Phylogenomics inference revealed that the Endozoicomonadaceae symbionts uncovered here represent two species of a novel genus unique to temperate octocorals, here denoted Ca. Gorgonimonas eunicellae and Ca. Gorgonimonas leptogorgiae. Their genomes revealed metabolic capacities to thrive under suboxic conditions and high gene copy numbers of serine-threonine protein kinases, type 3-secretion system, type-4 pili, and ankyrin-repeat proteins, suggesting excellent capabilities to colonize, aggregate, and persist inside their host. Contrarily, MAGs obtained from seawater frequently lacked symbiosis-related genes. All Endozoicomonadaceae symbionts harbored endo-chitinase and chitin-binging protein-encoding genes, indicating that they can hydrolyze the most abundant polysaccharide in the oceans. Other symbionts, including Metamycoplasmataceae and Ca. Thioglobaceae, may assimilate the smaller chitin oligosaccharides resulting from chitin breakdown and engage in chitin deacetylation, respectively, suggesting possibilities for substrate cross-feeding and a role for the coral microbiome in overall chitin turnover. We also observed sharp differences in secondary metabolite production potential between symbiotic lineages. Specific Proteobacteria taxa may specialize in chemical defense and guard other symbionts, including Endozoicomonadaceae, which lack such capacity.

CONCLUSION: This is the first study to recover MAGs from dominant symbionts of octocorals, including those of so-far unculturable Endozoicomonadaceae, Ca. Thioglobaceae and Metamycoplasmataceae symbionts. We identify a thus-far unanticipated, global role for Endozoicomonadaceae symbionts of corals in the processing of chitin, the most abundant natural polysaccharide in the oceans and major component of the natural zoo- and phytoplankton feed of octocorals. We conclude that niche partitioning, metabolic specialization, and adaptation to low oxygen conditions among prokaryotic symbionts likely contribute to the plasticity and adaptability of the octocoral holobiont in changing marine environments. These findings bear implications not only for our understanding of symbiotic relationships in the marine realm but also for the functioning of benthic ecosystems at large. Video Abstract.}, } @article {pmid36138352, year = {2022}, author = {Liu, G and Zhang, BF and Chang, J and Hu, XL and Li, C and Xu, TT and Liu, SQ and Hu, DF}, title = {Population genomics reveals moderate genetic differentiation between populations of endangered Forest Musk Deer located in Shaanxi and Sichuan.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {668}, pmid = {36138352}, issn = {1471-2164}, support = {31872962//National Natural Science Foundation of China/ ; 2019HB2096001006//The Biodiversity Survey, Monitoring and Assessment Project (2019-2023) of the Ministry of Ecology and Environment/ ; }, mesh = {Animals ; China ; *Deer/genetics ; *Endangered Species ; Forests ; *Genetics, Population ; Metagenomics ; Nucleotides ; Phylogeny ; }, abstract = {BACKGROUND: Many endangered species exist in small, genetically depauperate, or inbred populations, hence promoting genetic differentiation and reducing long-term population viability. Forest Musk Deer (Moschus berezovskii) has been subject to illegal hunting for hundreds of years due to the medical and commercial values of musk, resulting in a significant decline in population size. However, it is still unclear to what extent the genetic exchange and inbreeding levels are between geographically isolated populations. By using whole-genome data, we reconstructed the demographic history, evaluated genetic diversity, and characterized the population genetic structure of Forest Musk Deer from one wild population in Sichuan Province and two captive populations from two ex-situ centers in Shaanxi Province.

RESULTS: SNP calling by GATK resulted in a total of 44,008,662 SNPs. Principal component analysis (PCA), phylogenetic tree (NJ tree), ancestral component analysis (ADMIXTURE) and the ABBA-BABA test separated Sichuan and Shaanxi Forest Musk Deer as two genetic clusters, but no obvious genetic differentiation was observed between the two captive populations. The average pairwise FST value between the populations in Sichuan and Shaanxi ranged from 0.05-0.07, suggesting a low to moderate genetic differentiation. The mean heterozygous SNPs rate was 0.14% (0.11%-0.15%) for Forest Musk Deer at the genomic scale, and varied significantly among three populations (Chi-square = 1.22, p < 0.05, Kruskal-Wallis Test), with the Sichuan population having the lowest (0.11%). The nucleotide diversity of three populations varied significantly (p < 0.05, Kruskal-Wallis Test), with the Sichuan population having the lowest genetic θπ (1.69 × 10[-3]).

CONCLUSIONS: Genetic diversity of Forest Musk Deer was moderate at the genomic scale compared with other endangered species. Genetic differentiation between populations in Sichuan and Shaanxi may not only result from historical biogeographical factors but also be associated with contemporary human disturbances. Our findings provide scientific aid for the conservation and management of Forest Musk Deer. They can extend the proposed measures at the genomic level to apply to other musk deer species worldwide.}, } @article {pmid36137486, year = {2022}, author = {Afridi, MS and Fakhar, A and Kumar, A and Ali, S and Medeiros, FHV and Muneer, MA and Ali, H and Saleem, M}, title = {Harnessing microbial multitrophic interactions for rhizosphere microbiome engineering.}, journal = {Microbiological research}, volume = {265}, number = {}, pages = {127199}, doi = {10.1016/j.micres.2022.127199}, pmid = {36137486}, issn = {1618-0623}, mesh = {Crops, Agricultural ; *Microbiota ; Plant Roots ; *Rhizosphere ; Soil ; Soil Microbiology ; }, abstract = {The rhizosphere is a narrow and dynamic region of plant root-soil interfaces, and it's considered one of the most intricate and functionally active ecosystems on the Earth, which boosts plant health and alleviates the impact of biotic and abiotic stresses. Improving the key functions of the microbiome via engineering the rhizosphere microbiome is an emerging tool for improving plant growth, resilience, and soil-borne diseases. Recently, the advent of omics tools, gene-editing techniques, and sequencing technology has allowed us to unravel the entangled webs of plant-microbes interactions, enhancing plant fitness and tolerance to biotic and abiotic challenges. Plants secrete signaling compounds with low molecular weight into the rhizosphere, that engage various species to generate a massive deep complex array. The underlying principle governing the multitrophic interactions of the rhizosphere microbiome is yet unknown, however, some efforts have been made for disease management and agricultural sustainability. This review discussed the intra- and inter- microbe-microbe and microbe-animal interactions and their multifunctional roles in rhizosphere microbiome engineering for plant health and soil-borne disease management. Simultaneously, it investigates the significant impact of immunity utilizing PGPR and cover crop strategy in increasing rhizosphere microbiome functions for plant development and protection using omics techniques. The ecological engineering of rhizosphere plant interactions could be used as a potential alternative technology for plant growth improvement, sustainable disease control management, and increased production of economically significant crops.}, } @article {pmid36136668, year = {2022}, author = {Bennato, F and Martino, C and Di Domenico, M and Ianni, A and Chai, B and Di Marcantonio, L and Cammà, C and Martino, G}, title = {Metagenomic Characterization and Volatile Compounds Determination in Rumen from Saanen Goat Kids Fed Olive Leaves.}, journal = {Veterinary sciences}, volume = {9}, number = {9}, pages = {}, pmid = {36136668}, issn = {2306-7381}, support = {F/170011/01-05/X42//Ministry of Economic Development/ ; }, abstract = {The accumulation and disposal of by-products deriving from the agro-food industry represents a problem both from an economic and environmental point of view. The use of these matrices in zootechnical nutrition could represent a feasible solution. The aim of the study was to examine the effect of a diet containing olive leaves (OL), a by-product of the olive industry, on the ruminal microbial community of Saanen goat kids and on volatile organic compounds (VOCs) produced during the digestion. Twenty goat kids were randomly divided into two groups of ten goat kids each. The control group (CTR) was fed with a standard diet, while the experimental group (OL+) received a custom-formulated diet containing 10 % OL on a dry matter (DM) basis. After 30 days of trial, genomic DNA was extracted from the rumen liquor and prepared for 16S rRNA-gene sequencing to characterize the rumen microbiota; furthermore, rumen VOCs were also characterized by solid-phase microextraction coupled with gas chromatography-mass spectrometry. The Shannon’s alpha index was not significantly different between the two groups, on the contrary, Bray-Curtis (p < 0.01) and Jaccard (p < 0.01) distances evidenced that feed affected microbial community. Eleven genera were influenced by OL supplementation, with a significant increase (p < 0.05) in Paludibacter, Fibrobacter, Sphaerochaeta Christensenella, Rikenella, Oligosphaera, Candidatus Endomicrobium, Anaerovorax, and Atopobium was observed, while the percentages of Bacteroides and Selenomonas were reduced (p < 0.05). Differences were also observed between the two groups at the family level (p < 0.004). Fibrobacteriaceae, Christensenellaceae, Coriobacteriaceae, Oligosphaeraceae, Candidatus Endomicrobium, and Planctomycetaceae were significantly higher (p < 0.05) in goat kids fed OL diet compared to CTR, while the levels of other identified families, Succinivibrionaceae and Bifidobacteriaceae, were opposite (p < 0.05). Finally, results showed that the main phyla in both groups were Bacteroidetes and Firmicutes; however, no significant differences in the relative abundance of any phyla were observed between the two groups. In addition to what has been reported, the analysis of VOCs at the rumen level showed the ability of the OL integration to induce an increase in hexanoic acid and a parallel decrease in decanal. Furthermore, only in OL+ samples there was the accumulation of α-terpineol to which a wide range of interesting biological properties is attributed. The presence of VOCs associated with health status suggests a favorable role of OL in preserving and improving animal welfare.}, } @article {pmid36136471, year = {2022}, author = {Ma, C and Ma, P and He, Z and Mi, X}, title = {A Combined Catalytic Ozonation-MBR Approach to Remove Contaminants from the Mature Landfill Leachate in the Yellow River Basin.}, journal = {Toxics}, volume = {10}, number = {9}, pages = {}, pmid = {36136471}, issn = {2305-6304}, abstract = {The mature landfill leachate (MLL) is characterized by a large number of fulvic acids and humic acids, which is refractory organic matter and can be cleaned by ozone oxidation. However, the poor property of mass transfer prohibits the widespread use of ozone oxidation in actual leachate treatment. Meanwhile, some combined processes are adopted to treat the mature landfill leachate, which places catalytic ozonation before the membrane bioreactor (MBR) process to enhance the biodegradability of MLL. Thus, this research is conducted to investigate the practicability of applying nano-Fe3O4 loaded cow-dung ash (Fe3O4@CDA) and biological post-treatment with MBR for the effective removal of pollutants from MLL and puts forward the variation of organics in leachate between catalytic ozonation and MBR. The addition of catalytic ozonation not only improved the removal of hazardous organics but also enhanced the biodegradability of the leachate and favored the subsequent MBR process. Chemical oxygen demand (COD) removal in the catalytic ozonation step was optimized, and 53% removal was obtained at pH = 7, catalyst dosage = 1.0 g/L, and O3 dosage = 3.0 g/L. After the MBR process, COD in effluent stabilized in the range of 57.85-65.38 mg/L, and the variation range of the ammonia nitrogen (NH3-N) concentration was 5.98-10.24 mg/L. The catalytic ozonation-MBR integrated process showed strong feasibility in dealing with the biologically pre-treated leachate.}, } @article {pmid36135885, year = {2022}, author = {Li, C and Maqbool, T and Kang, H and Zhang, Z}, title = {In-Situ Sludge Reduction Performance and Mechanism in Sulfidogenic Anoxic-Oxic-Anoxic Membrane Bioreactors.}, journal = {Membranes}, volume = {12}, number = {9}, pages = {}, pmid = {36135885}, issn = {2077-0375}, support = {52170041//National Natural Science Foundation of China/ ; }, abstract = {The excess sludge generated from the activated sludge process remains a big issue. Sustainable approaches that achieve in situ sludge reduction with satisfactory effluent quality deserve attention. This study explored the sludge reduction performance of sulfidogenic anoxic-oxic-anoxic (AOA) membrane bioreactors. The dynamics of the microbial community and metabolic pathways were further analyzed to elucidate the internal mechanism of sludge reduction. Compared with the conventional anoxic-oxic-oxic membrane bioreactor (MBRcontrol), AOAS150 (150 mg/L SO4[2-] in the membrane tank) and AOAS300 (300 mg/L SO4[2-] in the membrane tank) reduced biomass production by 40.39% and 47.45%, respectively. The sulfide reduced from sulfate could enhance the sludge decay rate and decrease sludge production. Extracellular polymeric substances (EPSs) destruction and aerobic lysis contributed to sludge reduction in AOA bioreactors. The relative abundance of Bacteroidetes (phylum), sulfate-reducing bacteria (SRB, genus), and Ignavibacterium (genus) increased in AOA bioreactors compared with MBRcontrol. Our metagenomic analysis indicated that the total enzyme-encoding genes involved in glycolysis, denitrification, and sulfate-reduction processes decreased over time in AOAS300 and were lower in AOAS300 than AOAS150 at the final stage of operation. The excess accumulation of sulfide in AOAS300 may inactive the functional bacteria, and sulfide inhibition induced sludge reduction.}, } @article {pmid36135710, year = {2022}, author = {Tan, Y and Du, H and Zhang, H and Fang, C and Jin, G and Chen, S and Wu, Q and Zhang, Y and Zhang, M and Xu, Y}, title = {Geographically Associated Fungus-Bacterium Interactions Contribute to the Formation of Geography-Dependent Flavor during High-Complexity Spontaneous Fermentation.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0184422}, pmid = {36135710}, issn = {2165-0497}, mesh = {Humans ; Fermentation ; *Bacteria/metabolism ; *Microbiota/physiology ; Fungi/physiology ; Geography ; }, abstract = {Fermented foods often have attractive flavor characteristics to meet various human demands. An ever-challenging target is the production of fermented foods with equal flavor profiles outside the product's origin. However, the formation of geography-dependent flavor in high-complexity fermentations remains poorly understood. Here, taking Chinese liquor (baijiu) fermentation as an example, we collected 403 samples from 9 different locations in China across a latitude range of 27°N to 37°N. We revealed and validated the geography-dependent flavor formation patterns by using culture-independent (metabolomics, metagenomics, and metatranscriptomics) and culture-dependent tools. We found that the baijiu microbiomes along with their metabolites were flavor related and geography dependent. The geographical characteristics were determined mainly by 20 to 40 differentiated chemical markers in metabolites and the latitude-dependent fungal structure of the microbiome. About 48 to 156 core microbiota members out of 735 bacterial genera and 290 fungal genera contributed to the chemical markers. The contributions of both fungi and bacteria were greater than those from either bacteria or fungi alone. Representatively, we revealed that dynamic interdependent interactions between yeasts and Lactobacillus facilitated the metabolism of heterocyclic flavor chemicals such as 2-acetylpyrrole, 2,3,5-trimethylpyrazine, and 2-acetylfuran. Moreover, we found that the intraspecific genomic diversity and microbial structure were two biotic factors that contributed to dynamic microbiome assembly. Based on the assembly pattern, adjusting the composition and distribution of initial species was one option to regulate the formation of diverse flavor characteristics. Our study provided a rationale for developing a microbiome design to achieve a defined flavor goal. IMPORTANCE People consume many spontaneously fermented foods and beverages with different flavors on a daily basis. One crucial and hotly discussed question is how to reproduce fermented food flavor without geographical limitations to meet diverse human demands. The constantly enriched knowledge of the microbial contribution to fermented flavor offers valuable insights into flavor biotechnological development. However, we still have a poor understanding of what factors limit the reproduction of fermented flavor outside the product's origin in high-complexity spontaneous fermentations. Here, taking baijiu fermentation as an example, we revealed that geography-dependent flavor was contributed mainly by fungus-bacterium cooperative metabolism. The distinct initial microbial composition, distribution, and intraspecific genomic diversity limited reproducible microbial interactions and metabolism in different geographical areas. The abundant microbial resources and predicted fungus-bacterium interactions found in baijiu fermentation enable us to design a synthetic microbial community to reproduce desired flavor profiles in the future.}, } @article {pmid36135388, year = {2022}, author = {Peroumal, D and Sahu, SR and Kumari, P and Utkalaja, BG and Acharya, N}, title = {Commensal Fungus Candida albicans Maintains a Long-Term Mutualistic Relationship with the Host To Modulate Gut Microbiota and Metabolism.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0246222}, pmid = {36135388}, issn = {2165-0497}, mesh = {Mice ; Animals ; *Candida albicans/genetics ; *Gastrointestinal Microbiome/physiology ; Symbiosis ; Obesity ; Hormones ; Body Weight ; DNA, Ribosomal ; }, abstract = {Candida albicans survives as a commensal fungus in the gastrointestinal tract, and that its excessive growth causes infections in immunosuppressed individuals is widely accepted. However, any mutualistic relationship that may exist between C. albicans and the host remains undetermined. Here, we showed that a long-term feeding of C. albicans does not cause any noticeable infections in the mouse model. Our 16S and 18S ribosomal DNA (rDNA) sequence analyses suggested that C. albicans colonizes in the gut and modulates microbiome dynamics, which in turn mitigates high-fat-diet-induced uncontrolled body weight gain and metabolic hormonal imbalances. Interestingly, adding C. albicans to a nonobesogenic diet stimulated the appetite-regulated hormones and helped the mice maintain a healthy body weight. In concert, our results suggest a mutualism between C. albicans and the host, contrary to the notion that C. albicans is always an adversary and indicating it can instead be a bona fide admirable companion of the host. Finally, we discuss its potential translational implication as a probiotic, especially in obese people or people dependent on high-fat calorie intakes to manage obesity associated complications. IMPORTANCE Candida albicans is mostly considered an opportunistic pathogen that causes fetal systemic infections. However, this study demonstrates that in its commensal state, it maintains a long-term mutualistic relationship with the host and regulates microbial dynamics in the gut and host physiology. Thus, we concluded that C. albicans is not always an adversary but rather can be a bona fide admirable companion of the host. More importantly, as several genomic knockout strains of C. albicans were shown to be avirulent, such candidate strains may be explored further as preferable probiotic isolates to control obesity.}, } @article {pmid36135379, year = {2022}, author = {Du, J and Zhang, J and Zhang, D and Zhou, Y and Wu, P and Ding, W and Wang, J and Ouyang, C and Yang, Q}, title = {Background Filtering of Clinical Metagenomic Sequencing with a Library Concentration-Normalized Model.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0177922}, pmid = {36135379}, issn = {2165-0497}, mesh = {Sensitivity and Specificity ; *Metagenomics/methods ; *Metagenome ; High-Throughput Nucleotide Sequencing/methods ; Gene Library ; }, abstract = {Metagenomic next-generation sequencing (mNGS) can accurately detect pathogens in clinical samples. However, wet-lab contamination constrains mNGS analysis and may result in erroneous interpretation of results. Many existing methods rely on large-scale observational microbiome studies and may not be applicable to clinical mNGS tests. By generation of a pretrained profile of common laboratory contaminants, we developed an mNGS noise-filtering model based on the inverse linear relationship between microbial sequencing reads and sample library concentration, named the background elimination and correction by library concentration-normalized (BECLEAN) model. Its efficacy was evaluated with bacteria- and yeast-spiked samples and 28 cerebrospinal fluid (CSF) specimens. The diagnostic accuracy, precision, sensitivity, and specificity of BECLEAN with reference to conventional methods and diagnosis were 92.9%, 86.7%, 100%, and 86.7%, respectively. BECLEAN led to a dramatic reduction of background noise without affecting the true-positive rate and thus can provide a time-saving and convenient tool in various clinical settings. IMPORTANCE Most of the existing methods to remove wet-lab contamination rely on large-scale observational microbiome studies and may not be applicable to clinical mNGS testing in individual cases. In clinical settings, only a handful of samples might be sequenced in a run. The lab-specific microbiome can complicate existing statistical approaches for removing contamination from small-scale clinical metagenomic sequencing data sets; thus, use of a preliminary lab-specific training set is necessary. Our study provides a rapid and accurate background-filtering tool for clinical metagenomic sequencing by generation of a pretrained profile of common laboratory contaminants. Notably, our work demonstrates that the inverse linear relationship between microbial sequencing reads and library concentration can serve to identify true contaminants and evaluate the relative abundance of a taxon in samples by comparing the observed microbial reads to the model-predicted value. Our findings extend the previously published research and demonstrate confirmatory results in clinical settings.}, } @article {pmid36131174, year = {2023}, author = {Su, C and Zhou, X and Lu, P and Dai, X and Chen, Z and Liang, B and Tian, Y and Chen, M}, title = {Role of coke media strategy in an adsorption-biological coupling technology for wastewater treatment performance, microbial community, and metabolic pathways features.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {5}, pages = {13469-13482}, pmid = {36131174}, issn = {1614-7499}, mesh = {Wastewater ; Waste Disposal, Fluid/methods ; *Coke ; Adsorption ; Bioreactors ; Nitrification ; *Microbiota ; Nitrogen/metabolism ; *Water Purification ; Carbon ; Phosphorus ; Metabolic Networks and Pathways ; Phosphates ; Denitrification ; Sewage/microbiology ; }, abstract = {With the increase of wastewater discharge, the requirement of wastewater treatment technology is gradually increased. How to treat wastewater economically, while making the treatment process short, easy to manage and low running cost, is the focus of attention. Adsorption-biological coupling technology could make adsorption and biodegradation complement each other, which has coupled accumulation effect. In this study, with coke as the adsorbent, the efficiency of the adsorption-biological coupling reactor on the treatment of total phosphorus (TP), chemical oxygen demand (COD), and ammonia nitrogen (NH3-N) in domestic wastewater under different influent modes was investigated. Meanwhile, microbial community and metabolic pathways analysis of the reactor were carried out. Results showed that when the influent modes of the coupling reactor was once a day and the daily sewage treatment capacity was 2 L, the treatment efficiency of TP, COD, and NH3-N was the best. The removal rate of TP and NH3-N was 87.96% and 96.14%, respectively. The dominant phylum was Proteobacteria (39.84-44.49%), and the dominant genus was Sphingomonas (4.27-7.16%), and Gemmatimonas (1.27-3.58%). According to the metagenomic analysis, carbon metabolism process was evenly distributed in U (upper), M (middle), and L (lower) layers of the coupling reactor. Phosphate metabolism was mainly in the U layer at first, then in the M and L layers gradually. Carbon metabolism and phosphate metabolism provided sufficient energy for microbial degradation of pollutants. Nitrogen removal in the reactor mainly happened in the S and Z layers by nitrification (M00528) and denitrification (M00529), respectively.}, } @article {pmid36130883, year = {2023}, author = {Kato-Kogoe, N and Kamiya, K and Sakaguchi, S and Omori, M and Komori, E and Kudo, A and Nakamura, S and Nakano, T and Ueno, T and Tamaki, J and Hoshiga, M}, title = {Salivary Microbiota Associated with Peripheral Microvascular Endothelial Dysfunction.}, journal = {Journal of atherosclerosis and thrombosis}, volume = {30}, number = {7}, pages = {820-833}, pmid = {36130883}, issn = {1880-3873}, mesh = {Humans ; Aged ; Saliva/microbiology ; RNA, Ribosomal, 16S/genetics ; *Microbiota ; *Hyperemia ; *Atherosclerosis ; }, abstract = {AIMS: Oral health is associated with atherosclerotic cardiovascular disease (ACVD). We previously identified the salivary microbiota characteristics of patients with ACVD. However, whether salivary microbiota is characteristic under impaired vascular endothelial function before ACVD onset remains unclear. Therefore, we aimed to evaluate the characteristics of salivary microbiota associated with peripheral microvascular endothelial dysfunction.

METHODS: We collected saliva samples from 172 community-dwelling elderly individuals without a history of ACVD and performed 16S rRNA metagenomic analysis. We assessed the peripheral microvascular endothelial function using reactive hyperemia index (RHI) and compared the salivary microbiota in the groups with normal (RHI ≥ 2.10), borderline, and abnormal (RHI ＜1.67) peripheral endothelial function. Furthermore, we applied machine learning techniques to evaluate whether salivary microbiota could discriminate between individuals with normal and abnormal endothelial function.

RESULTS: The number of operational taxonomic units (OTUs) was higher in the abnormal group than in the normal group (p=0.037), and differences were found in the overall salivary microbiota structure (unweighted UniFrac distances, p=0.038). The linear discriminant analysis (LDA) effect size (LEfSe) algorithm revealed several significantly differentially abundant bacterial genera between the two groups. An Extra Trees classifier model was built to discriminate between groups with normal and abnormal vascular endothelial function based on the microbial composition at the genus level (AUC=0.810).

CONCLUSIONS: The salivary microbiota in individuals with endothelial dysfunction was distinct from that in individuals with normal endothelial function, indicating that the salivary microbiota may be related to endothelial function.}, } @article {pmid36130784, year = {2022}, author = {Brown, MA and Jabeen, M and Bharj, G and Hinks, TSC}, title = {Non-typeable Haemophilus influenzae airways infection: the next treatable trait in asthma?.}, journal = {European respiratory review : an official journal of the European Respiratory Society}, volume = {31}, number = {165}, pages = {}, pmid = {36130784}, issn = {1600-0617}, mesh = {*Asthma/complications/diagnosis/drug therapy ; Cell Adhesion Molecule-1 ; Cytokines ; Haemophilus influenzae ; Humans ; Inflammasomes ; Interleukin-12 ; Interleukin-17/metabolism ; Interleukin-6 ; Interleukin-8 ; Macrolides ; NLR Family, Pyrin Domain-Containing 3 Protein ; *Pulmonary Disease, Chronic Obstructive/metabolism ; Respiratory System ; Tumor Necrosis Factors ; }, abstract = {Asthma is a complex, heterogeneous condition that affects over 350 million people globally. It is characterised by bronchial hyperreactivity and airways inflammation. A subset display marked airway neutrophilia, associated with worse lung function, higher morbidity and poor response to treatment. In these individuals, recent metagenomic studies have identified persistent bacterial infection, particularly with non-encapsulated strains of the Gram-negative bacterium Haemophilus influenzae. Here we review knowledge of non-typeable H. influenzae (NTHi) in the microbiology of asthma, the immune consequences of mucosal NTHi infection, various immune evasion mechanisms, and the clinical implications of NTHi infection for phenotyping and targeted therapies in neutrophilic asthma. Airway neutrophilia is associated with production of neutrophil chemokines and proinflammatory cytokines in the airways, including interleukin (IL)-1β, IL-6, IL-8, IL-12, IL-17A and tumour necrosis factor. NTHi adheres to and invades the lower respiratory tract epithelium, inducing the NLR family pyrin domain containing 3 (NLRP3) and absent in melanoma 2 (AIM2) inflammasomes. NTHi reduces expression of tight-junction proteins, impairing epithelial integrity, and can persist intracellularly. NTHi interacts with rhinoviruses synergistically via upregulation of intracellular cell adhesion molecule 1 and promotion of a neutrophilic environment, to which NTHi is adapted. We highlight the clinical relevance of this emerging pathogen and its relevance for the efficacy of long-term macrolide therapy in airways diseases, we identify important unanswered questions and we propose future directions for research.}, } @article {pmid36130198, year = {2022}, author = {Bai, Y and Zhao, T and Gao, M and Zou, Y and Lei, X}, title = {A Novel Gene Alignment in Dorea sp. AM58-8 Produces 7-Dehydroxy-3β Bile Acids from Primary Bile Acids.}, journal = {Biochemistry}, volume = {61}, number = {24}, pages = {2870-2878}, doi = {10.1021/acs.biochem.2c00264}, pmid = {36130198}, issn = {1520-4995}, mesh = {Animals ; *Bile Acids and Salts ; *Bacteria ; Operon ; Mammals ; }, abstract = {Bile acids are essential metabolites and signaling molecules in mammals. Primary bile acids are synthesized from cholesterol in the liver. At the same time, the microbiota in the mammalian gut has many interactions with bile acid, including various biotransformation processes such as 7-dehydroxylation and 3-epimerization. 7-Dehydroxylation is mediated by a bile acid-inducible (bai) operon, while 7-dehydroxylation and 3-epimerization are independently observed in only a few strains. Herein, we describe a novel microbe, Dorea sp. AM58-8, that can accomplish a two-step transformation and turn primary bile acids into both 3α secondary bile acids like deoxycholic acid and lithocholic acid, and 3β secondary bile acids like isodeoxycholic acid and isolithocholic acid. We subsequently characterized BaiA, BaiB, BaiE, and their substrate profiles biochemically. The potential bai gene clusters in the metagenomes were further mined. Their evolution, potential functions, and possible regulatory pathways were predicted using bioinformatics based on our understanding of the 7-dehydroxylation pathway in Dorea sp. AM58-8. This study of Dorea sp. AM58-8 also helps us distinguish the inactive bacteria that seem to have the 7-dehydroxylation pathway proteins and discover the 7-dehydroxylation pathway in other mammalian gut microbes.}, } @article {pmid36130161, year = {2022}, author = {Wang, L and Soto, A and Remue, L and Rosales Rosas, AL and De Coninck, L and Verwimp, S and Bouckaert, J and Vanwinkel, M and Matthijnssens, J and Delang, L}, title = {First Report of Mutations Associated With Pyrethroid (L1014F) and Organophosphate (G119S) Resistance in Belgian Culex (Diptera: Culicidae) Mosquitoes.}, journal = {Journal of medical entomology}, volume = {59}, number = {6}, pages = {2072-2079}, doi = {10.1093/jme/tjac138}, pmid = {36130161}, issn = {1938-2928}, mesh = {Animals ; *Culex ; *Pyrethrins/pharmacology ; Belgium ; *Culicidae ; Organophosphates/pharmacology ; Acetylcholinesterase/genetics ; Insecticide Resistance/genetics ; *Insecticides/pharmacology ; Mosquito Vectors/genetics ; Mutation ; }, abstract = {The emergence of West Nile virus and Usutu virus in Europe poses a significant risk to public health. In the absence of efficient antiviral therapy or vaccine candidates, the only strategy to control these arboviruses is to target the Culex (Diptera: Culicidae) mosquito vector. However, the selection pressure caused by exposure to insecticides for vector control or agricultural pest control can lead to insecticide resistance, thereby reducing the efficacy of insecticide-based vector control interventions. In Culex mosquitoes, two of the most common amino acid substitutions associated with insecticide resistance are the kdr L1014F in voltage gated sodium channels and G119S in acetylcholinesterase. In this study, Culex pipiens biotype pipiens, Culex torrentium, and Culex modestus were sampled from 2019 to 2021 in three distinct environmental habitats (urban, peri-urban, and agricultural) in and around the city of Leuven, Belgium. Individual mosquitoes were screened for two mutations resulting in L1014F and G119S amino acid substitutions. Both mutations were observed in Cx. pipiens and Cx. modestus but not in Cx. torrentium mosquitoes across the four collection sites. Furthermore, multi-resistance or cross-resistance in Cx. pipiens could be a threat in these areas, as both mutations were observed at low frequencies. These results provide the first report of kdr L1014F and ace-1 G119S resistance mutations in Cx. pipiens and Cx. modestus mosquitoes from Belgium, highlighting the importance of mosquito surveillance to design effective arbovirus outbreak control strategies.}, } @article {pmid36130056, year = {2022}, author = {Ziemski, M and Adamov, A and Kim, L and Flörl, L and Bokulich, NA}, title = {Reproducible acquisition, management and meta-analysis of nucleotide sequence (meta)data using q2-fondue.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {22}, pages = {5081-5091}, pmid = {36130056}, issn = {1367-4811}, support = {#2021-362//Strategic Focus Area 'Personalized Health and Related Technologies/ ; //Swiss Federal Institutes of Technology/ ; 310030_204275/SNSF_/Swiss National Science Foundation/Switzerland ; //Swiss Government Excellence/ ; }, mesh = {*Software ; Base Sequence ; *Ecosystem ; Metadata ; Metagenome ; }, abstract = {MOTIVATION: The volume of public nucleotide sequence data has blossomed over the past two decades and is ripe for re- and meta-analyses to enable novel discoveries. However, reproducible re-use and management of sequence datasets and associated metadata remain critical challenges. We created the open source Python package q2-fondue to enable user-friendly acquisition, re-use and management of public sequence (meta)data while adhering to open data principles.

RESULTS: q2-fondue allows fully provenance-tracked programmatic access to and management of data from the NCBI Sequence Read Archive (SRA). Unlike other packages allowing download of sequence data from the SRA, q2-fondue enables full data provenance tracking from data download to final visualization, integrates with the QIIME 2 ecosystem, prevents data loss upon space exhaustion and allows download of (meta)data given a publication library. To highlight its manifold capabilities, we present executable demonstrations using publicly available amplicon, whole genome and metagenome datasets.

q2-fondue is available as an open-source BSD-3-licensed Python package at https://github.com/bokulich-lab/q2-fondue. Usage tutorials are available in the same repository. All Jupyter notebooks used in this article are available under https://github.com/bokulich-lab/q2-fondue-examples.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36129562, year = {2022}, author = {Boros, Á and Albert, M and Urbán, P and Herczeg, R and Gáspár, G and Balázs, B and Cságola, A and Pankovics, P and Gyenesei, A and Reuter, G}, title = {Unusual "Asian-origin" 2c to 2b point mutant canine parvovirus (Parvoviridae) and canine astrovirus (Astroviridae) co-infection detected in vaccinated dogs with an outbreak of severe haemorrhagic gastroenteritis with high mortality rate in Hungary.}, journal = {Veterinary research communications}, volume = {46}, number = {4}, pages = {1355-1361}, pmid = {36129562}, issn = {1573-7446}, support = {FK134311//Hungarian Scientific Research Fund/ ; }, mesh = {Dogs ; Animals ; *Parvovirus, Canine/genetics ; *Astroviridae/genetics ; *Parvoviridae ; Phylogeny ; *Coinfection/veterinary/epidemiology ; Hungary/epidemiology ; *Parvoviridae Infections/epidemiology/veterinary ; *Dog Diseases/epidemiology/prevention & control ; *Gastroenteritis/epidemiology/prevention & control/veterinary ; Disease Outbreaks ; }, abstract = {In this study, the aetiological background of an outbreak of severe haemorrhagic gastroenteritis (HGE) in a colony of purebred Jack Russell Terriers vaccinated against CPV-2 in Hungary was investigated. Canine parvovirus 2 (CPV-2, Parvoviridae) and canine astrovirus (CaAstV, Astroviridae) co-infection was identified by viral metagenomics and next-generation sequencing (VM-NGS) methods from a rectal swab of an affected 7-week-old puppy. The complete coding sequence of CPV-2 strain FR1/CPV2-2021-HUN (ON733252) and the complete genome of CaAstV strain FR1/CaAstV-2021-HUN (ON733251) were determined by VM-NGS and PCR methods. Results of sequence and phylogenetic analyses showed that CPV-2 strain FR1/CPV2-2021-HUN was different from the applied vaccine strains and previously identified strains from Hungary but showed high sequence identity (> 99.8%) and close phylogenetic relationship to recently described "Asian-origin" CPV-2c strains from Italy. But, based on the single amino acid difference on position 426 of VP2 (Glu/Asp) between the study strain and the closest relatives, FR1/CPV2-2021-HUN belonged to the 2b antigenic type rather than 2c. The CaAstV strain FR1/CaAstV-2021-HUN showed close relationship with a CaAstV strain identified previously from a diarrhoeic dog in Hungary. Both viruses were continuously detectable by PCR in additional enteric samples, and the CPV-2 could also be detected in several (n = 32) tissue samples from 9 affected deceased puppies. Further comparative studies are necessary to confirm the role of the point mutation causing the change in the antigenic type of this "Asian-origin" CPV-2 and/or the role of CaAstV co-infection in the development and/or severity of (haemorrhagic) gastroenteritis among dogs vaccinated against CPV-2.}, } @article {pmid36128620, year = {2022}, author = {Li, Y and Sun, H and Huang, Y and Yin, A and Zhang, L and Han, J and Lyu, Y and Xu, X and Zhai, Y and Sun, H and Wang, P and Zhao, J and Sun, S and Dong, H and Zhu, F and Wang, Q and Augusto Rohde, L and Xie, X and Sun, X and Xiong, L}, title = {Gut metagenomic characteristics of ADHD reveal low Bacteroides ovatus-associated host cognitive impairment.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2125747}, pmid = {36128620}, issn = {1949-0984}, mesh = {Animals ; *Attention Deficit Disorder with Hyperactivity/microbiology ; Bacteroides ; Cognition ; *Cognitive Dysfunction ; *Gastrointestinal Microbiome/physiology ; Humans ; Rats ; }, abstract = {Attention-deficit/hyperactivity disorder (ADHD) is a highly heterogeneous psychiatric disorder that can have three phenotypical presentations: inattentive (I-ADHD), hyperactive-impulsive (HI-ADHD), and combined (C-ADHD). Environmental factors correlated with the gut microbiota community have been implicated in the development of ADHD. However, whether different ADHD symptomatic presentations are associated with distinct microbiota compositions and whether patients could benefit from the correction of aberrant bacterial colonization are still largely unclear. We carried out metagenomic shotgun analysis with 207 human fecal samples to characterize the gut microbial profiles of patients with ADHD grouped according to their phenotypical presentation. Then, we transplanted the candidate low-abundance bacteria identified in patient subgroups into ADHD rats and evaluated ADHD-associated behaviors and neuronal activation in these rats. Patients with C-ADHD had a different gut microbial composition from that of healthy controls (HCs) (p = .02), but not from that of I-ADHD patients. Eight species became progressively attenuated or enriched when comparing the compositions of HCs to those of I-ADHD and C-ADHD; in particular, the abundance of Bacteroides ovatus was depleted in patients with C-ADHD. In turn, Bacteroides ovatus supplementation ameliorated spatial working memory deficits and reversed θ electroencephalogram rhythm alterations in ADHD rats. In addition, Bacteroides ovatus induced enhanced neuronal activation in the hippocampal CA1 subregion. These findings indicate that gut microbial characteristics that are unique to patients with C-ADHD may be masked when considering a more heterogeneous group of patients. We link the gut microbiota to brain function in an ADHD animal model, suggesting the relevance of testing a potential bacteria-based intervention for some aspects of ADHD.}, } @article {pmid36126709, year = {2023}, author = {Loiola, M and Silva, AET and Krull, M and Barbosa, FA and Galvão, EH and Patire, VF and Cruz, ICS and Barros, F and Hatje, V and Meirelles, PM}, title = {Mangrove microbial community recovery and their role in early stages of forest recolonization within shrimp ponds.}, journal = {The Science of the total environment}, volume = {855}, number = {}, pages = {158863}, doi = {10.1016/j.scitotenv.2022.158863}, pmid = {36126709}, issn = {1879-1026}, mesh = {Animals ; *Ecosystem ; Ponds ; Forests ; Wetlands ; Soil/chemistry ; Crustacea ; *Microbiota ; }, abstract = {Shrimp farming is blooming worldwide, posing a severe threat to mangroves and its multiple goods and ecosystem services. Several studies reported the impacts of aquaculture on mangrove biotic communities, including microbiomes. However, little is known about how mangrove soil microbiomes would change in response to mangrove forest recolonization. Using genome-resolved metagenomics, we compared the soil microbiome of mangrove forests (both with and without the direct influence of shrimp farming effluents) with active shrimp farms and mangroves under a recolonization process. We found that the structure and composition of active shrimp farms microbial communities differ from the control mangrove forests, mangroves under the impact of the shrimp farming effluents, and mangroves under recolonization. Shrimp farming ponds microbiomes have lower microbial diversity and are dominated by halophilic microorganisms, presenting high abundance of multiple antibiotic resistance genes. On the other hand, control mangrove forests, impacted mangroves (exposed to the shrimp farming effluents), and recolonization ponds were more diverse, with a higher abundance of genes related to carbon mobilization. Our data also indicated that the microbiome is recovering in the mangrove recolonization ponds, performing vital metabolic functions and functionally resembling microbiomes found in those soils of neighboring control mangrove forests. Despite highlighting the damage caused by the habitat changes in mangrove soil microbiome community and functioning, our study sheds light on these systems incredible recovery capacity. Our study shows the importance of natural mangrove forest recovery, enhancing ecosystem services by the soil microbial communities even in a very early development stage of mangrove forest, thus encouraging mangrove conservation and restoration efforts worldwide.}, } @article {pmid36126430, year = {2022}, author = {Mendes Dos Santos, MA and Dias, LS and Ramirez Pavon, JA and Viniski, AE and Campos Souza, CL and Pepato, MA and Correa de Azevedo, V and Teixeira Nunes, MR and Slhessarenko, RD}, title = {Regional mutations in CHIKV-ECSA genomes and detection of other viruses in the serum of acute febrile patients by a metagenomic approach in Mato Grosso, Central-Western Brazil, 2018.}, journal = {Virology}, volume = {576}, number = {}, pages = {18-29}, doi = {10.1016/j.virol.2022.08.013}, pmid = {36126430}, issn = {1096-0341}, mesh = {Humans ; Amino Acids/genetics ; Brazil/epidemiology ; *Chikungunya Fever/epidemiology ; *Chikungunya virus/genetics ; Fever ; Genotype ; Mutation ; Phylogeny ; *Viruses ; Genome, Viral ; }, abstract = {Mato Grosso (MT) State is part of central western Brazil and has a tropical permissive environment that favors arbovirus outbreaks. A metagenomic approach was used to identify viral genomes in seven pools of serum from patients (n=65) with acute febrile disease. Seven chikungunya virus (CHIKV) genomes were determined, showing four amino acid changes found only in CHIKV genomes obtained in MT since 2018: nsP2:T31I, nsP3: A388V, E3:T201I and E3:H57R, in addition to other mutations in E1, nsP2 and nsP4. Six parvovirus B19 (B19V) genotype I genomes (4771-5131 nt) showed four aa alterations (NS1:N473D, R579Q; VP1:I716T; and 11 kDa:V44A) compared to most similar B19V from the USA. Coinfection between CHIKV and B19V was evidenced in 22/65 (33.8%) patients by RT‒PCR and PCR, respectively. Other viruses found in these pools include human pegivirus C, torque teno virus 3, an unclassified TTV and torque teno mini virus. Metagenomics represents a useful approach to detect viruses in the serum of acute febrile patients suspected of arbovirus disease.}, } @article {pmid36126379, year = {2022}, author = {Roessler, J and Leistner, DM and Landmesser, U and Haghikia, A}, title = {Modulatory role of gut microbiota in cholesterol and glucose metabolism: Potential implications for atherosclerotic cardiovascular disease.}, journal = {Atherosclerosis}, volume = {359}, number = {}, pages = {1-12}, doi = {10.1016/j.atherosclerosis.2022.08.018}, pmid = {36126379}, issn = {1879-1484}, mesh = {*Atherosclerosis ; *Cardiovascular Diseases/metabolism ; Cholesterol/metabolism ; *Gastrointestinal Microbiome ; Glucose/metabolism ; Humans ; }, abstract = {Accumulating evidence suggests an important role of gut microbiota in physiological processes of host metabolism as well as cardiometabolic disease. Recent advances in metagenomic and metabolomic research have led to discoveries of novel pathways in which intestinal microbial metabolism of dietary nutrients is linked to metabolic profiles and cardiovascular disease risk. A number of metaorganismal circuits have been identified by microbiota transplantation studies and experimental models using germ-free rodents. Many of these pathways involve gut microbiota-related bioactive metabolites that impact host metabolism, in particular lipid and glucose homeostasis, partly via specific host receptors. In this review, we summarize the current knowledge of how the gut microbiome can impact cardiometabolic phenotypes and provide an overview of recent advances of gut microbiome research. Finally, the potential of modulating intestinal microbiota composition and/or targeting microbiota-related pathways for novel preventive and therapeutic strategies in cardiometabolic and cardiovascular diseases will be discussed.}, } @article {pmid36125864, year = {2022}, author = {Pallen, MJ and Rodriguez-R, LM and Alikhan, NF}, title = {Naming the unnamed: over 65,000 Candidatus names for unnamed Archaea and Bacteria in the Genome Taxonomy Database.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {9}, pages = {}, doi = {10.1099/ijsem.0.005482}, pmid = {36125864}, issn = {1466-5034}, support = {MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Archaea/genetics ; Bacteria/genetics ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; *Fatty Acids/chemistry ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Thousands of new bacterial and archaeal species and higher-level taxa are discovered each year through the analysis of genomes and metagenomes. The Genome Taxonomy Database (GTDB) provides hierarchical sequence-based descriptions and classifications for new and as-yet-unnamed taxa. However, bacterial nomenclature, as currently configured, cannot keep up with the need for new well-formed names. Instead, microbiologists have been forced to use hard-to-remember alphanumeric placeholder labels. Here, we exploit an approach to the generation of well-formed arbitrary Latinate names at a scale sufficient to name tens of thousands of unnamed taxa within GTDB. These newly created names represent an important resource for the microbiology community, facilitating communication between bioinformaticians, microbiologists and taxonomists, while populating the emerging landscape of microbial taxonomic and functional discovery with accessible and memorable linguistic labels.}, } @article {pmid36125772, year = {2022}, author = {Bornemann, TLV and Adam, PS and Probst, AJ}, title = {Reconstruction of Archaeal Genomes from Short-Read Metagenomes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2522}, number = {}, pages = {487-527}, pmid = {36125772}, issn = {1940-6029}, mesh = {Genome, Archaeal ; Lipids ; *Metagenome ; *Nucleic Acids ; RNA ; }, abstract = {As the majority of biological diversity remains unexplored and uncultured, investigating it requires culture-independent approaches. Archaea in particular suffer from a multitude of issues that make their culturing problematic, from them being frequently members of the rare biosphere, to low growth rates, to them thriving under very specific and often extreme environmental and community conditions that are difficult to replicate. OMICs techniques are state of the art approaches that allow direct high-throughput investigations of environmental samples at all levels from nucleic acids to proteins, lipids, and secondary metabolites. Metagenomics, as the foundation for other OMICs techniques, facilitates the identification and functional characterization of the microbial community members and can be combined with other methods to provide insights into the microbial activities, both on the RNA and protein levels. In this chapter, we provide a step-by-step workflow for the recovery of archaeal genomes from metagenomes, starting from raw short-read sequences. This workflow can be applied to recover bacterial genomes as well.}, } @article {pmid36125771, year = {2022}, author = {Adam, PS and Bornemann, TLV and Probst, AJ}, title = {Progress and Challenges in Studying the Ecophysiology of Archaea.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2522}, number = {}, pages = {469-486}, pmid = {36125771}, issn = {1940-6029}, mesh = {Alkanes ; *Archaea/genetics ; *Genome, Archaeal ; Methane ; Phylogeny ; }, abstract = {It has been less than two decades since the study of archaeal ecophysiology has become unshackled from the limitations of cultivation and amplicon sequencing through the advent of metagenomics. As a primer to the guide on producing archaeal genomes from metagenomes, we briefly summarize here how different meta'omics, imaging, and wet lab methods have contributed to progress in understanding the ecophysiology of Archaea. We then peer into the history of how our knowledge on two particularly important lineages was assembled: the anaerobic methane and alkane oxidizers, encountered primarily among Euryarchaeota, and the nanosized, mainly parasitic, members of the DPANN superphylum.}, } @article {pmid36125585, year = {2022}, author = {Aydin, S and Erözden, AA and Tavşanlı, N and Müdüroğlu, A and Çalışkan, M and Kara, İ}, title = {Anthocyanin Addition to Kefir: Metagenomic Analysis of Microbial Community Structure.}, journal = {Current microbiology}, volume = {79}, number = {11}, pages = {327}, pmid = {36125585}, issn = {1432-0991}, support = {38774//Istanbul Üniversitesi/ ; }, mesh = {Anthocyanins ; Fermentation ; *Kefir/microbiology ; *Microbiota ; Streptococcus thermophilus ; }, abstract = {The addition of anthocyanin to kefir for the production of more functional and bio-diversified kefir beverages has the potential to increase kefir's healthful activities. In the present study, anthocyanin extracts, obtained from black carrots, were added into kefir mixture during the fermentation process in different concentrations (1% and 5%, w/v). These kefir samples were then analyzed in terms of their microbiological qualities by metagenomic analysis. The results of the analyses show that the addition of anthocyanin has significant impacts on the community structure of kefir microbiome which in turn directly affects the expected health impacts of the beverage. Kefir with no anthocyanin included predominantly probiotic bacteria such as Lactococcus lactis (34%) and Lactobacillus kefiri (34%). On the other hand, kefir with 1% anthocyanin demonstrated a more balanced distribution of probiotic species like Lb. kefiri (17%), Leuconostoc mesenteroides (9%), and Lc. lactis (5%) at similar abundance rates. 5% anthocyanin kefir demonstrated the highest polarity in the community with a strong dominance of probiotic Lb. kefiri (72%), and distinctly less abundant bacteria such as Streptococcus salivarius subsp. thermophilus (3%). These findings provide that fortification with anthocyanins can be utilized to enhance the quality, composition, and beneficial functions of kefir.}, } @article {pmid36125556, year = {2022}, author = {Yang, S and Zhang, D and Zhang, Y and Fan, Z and Jiang, L and Wang, Y and Zhang, W}, title = {Multiple novel smaco-like viruses identified in chicken cloaca swabs.}, journal = {Archives of virology}, volume = {167}, number = {12}, pages = {2703-2708}, pmid = {36125556}, issn = {1432-8798}, support = {2017YFC1200201//Key Technologies Research and Development Program/ ; BE2017693//Jiangsu Provincial Key Research and Development Program/ ; 2020CPB-C11//Chengdu Giant Panda Breeding Research Foundation/ ; ZR2019MC036//Natural Science Foundation of Shandong Province/ ; }, mesh = {Animals ; Phylogeny ; *Genome, Viral ; *Chickens ; DNA, Viral/genetics ; DNA Viruses/genetics ; Metagenomics/methods ; }, abstract = {Viral metagenomics has been used in numerous animal virus discoveries. Recently, an unprecedented diversity of CRESS DNA viruses was identified using this method, and this has expanded our understanding of the environmental distribution and host range of CRESS DNA viruses. In this study, using an unbiased viral metagenomics approach, we investigated the fecal virome of chickens collected from two farms of Anhui Province, China. Five novel CRESS DNA viruses were obtained and characterized. The genome of the five viruses is 2,401-2,742 bp in length, containing two ORFs in the same orientation. Phylogenetic analysis indicated that all five viruses have a closer genetic relationship to smacoviruses than to other viruses in the order Cremevirales. Pairwise comparison of Rep amino acid sequences showed that these five viruses had only low amino acid sequence identity (8.9%-30.6%) to members of the family Smacoviridae, and the sequence identity among the five smaco-like viruses and other unclassified smacovirus strains was 70.3-95.8%. These findings broaden our knowledge of the genetic diversity of CRESS DNA viruses and provide a basis for classification of unclassified smacoviruses.}, } @article {pmid36125316, year = {2022}, author = {Schuettenberg, A and Piña, A and Metrailer, M and Peláez-Sánchez, RG and Agudelo-Flórez, P and Lopez, JÁ and Ryle, L and Monroy, FP and Altin, JA and Ladner, JT}, title = {Highly Multiplexed Serology for Nonhuman Mammals.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0287322}, pmid = {36125316}, issn = {2165-0497}, mesh = {Animals ; *Antibodies, Viral ; Antibody Formation ; Enzyme-Linked Immunosorbent Assay/methods ; *Immunosorbents ; Mammals ; }, abstract = {Emerging infectious diseases represent a serious and ongoing threat to humans. Most emerging viruses are maintained in stable relationships with other species of animals, and their emergence within the human population results from cross-species transmission. Therefore, if we want to be prepared for the next emerging virus, we need to broadly characterize the diversity and ecology of viruses currently infecting other animals (i.e., the animal virosphere). High-throughput metagenomic sequencing has accelerated the pace of virus discovery. However, molecular assays can detect only active infections and only if virus is present within the sampled fluid or tissue at the time of collection. In contrast, serological assays measure long-lived antibody responses to infections, which can be detected within the blood, regardless of the infected tissues. Therefore, serological assays can provide a complementary approach for understanding the circulation of viruses, and while serological assays have historically been limited in scope, recent advancements allow thousands to hundreds of thousands of antigens to be assessed simultaneously using <1 μL of blood (i.e., highly multiplexed serology). The application of highly multiplexed serology for the characterization of the animal virosphere is dependent on the availability of reagents that can be used to capture or label antibodies of interest. Here, we evaluate the utility of commercial immunoglobulin-binding proteins (protein A and protein G) to enable highly multiplexed serology in 25 species of nonhuman mammals, and we describe a competitive fluorescence-linked immunosorbent assay (FLISA) that can be used as an initial screen for choosing the most appropriate capture protein for a given host species. IMPORTANCE Antibodies are generated in response to infections with viruses and other pathogens, and they help protect against future exposures. Mature antibodies are long lived, are highly specific, and can bind to their protein targets with high affinity. Thus, antibodies can also provide information about an individual's history of viral exposures, which has important applications for understanding the epidemiology and etiology of disease. In recent years, there have been large advances in the available methods for broadly characterizing antibody-binding profiles, but thus far, these have been utilized primarily with human samples only. Here, we demonstrate that commercial antibody-binding reagents can facilitate modern antibody assays for a wide variety of mammalian species, and we describe an inexpensive and fast approach for choosing the best reagent for each animal species. By studying antibody-binding profiles in captive and wild animals, we can better understand the distribution and prevalence of viruses that could spill over into humans.}, } @article {pmid36125273, year = {2022}, author = {Uppal, S and Metz, JL and Xavier, RKM and Nepal, KK and Xu, D and Wang, G and Kwan, JC}, title = {Uncovering Lasonolide A Biosynthesis Using Genome-Resolved Metagenomics.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0152422}, pmid = {36125273}, issn = {2150-7511}, support = {R21 CA209189/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; RNA, Ribosomal, 16S/genetics ; Polyketide Synthases/genetics ; Phylogeny ; Symbiosis/genetics ; Acyl Carrier Protein/genetics ; Metagenomics ; *Porifera/microbiology ; Bacteria/genetics ; *Biological Products/pharmacology ; *Antineoplastic Agents ; Acyltransferases/genetics ; }, abstract = {Invertebrates, particularly sponges, have been a dominant source of new marine natural products. For example, lasonolide A (LSA) is a potential anticancer molecule isolated from the marine sponge Forcepia sp., with nanomolar growth inhibitory activity and a unique cytotoxicity profile against the National Cancer Institute 60-cell-line screen. Here, we identified the putative biosynthetic pathway for LSA. Genomic binning of the Forcepia sponge metagenome revealed a Gram-negative bacterium belonging to the phylum Verrucomicrobia as the candidate producer of LSA. Phylogenetic analysis showed that this bacterium, here named "Candidatus Thermopylae lasonolidus," only has 88.78% 16S rRNA identity with the closest relative, Pedosphaera parvula Ellin514, indicating that it represents a new genus. The lasonolide A (las) biosynthetic gene cluster (BGC) was identified as a trans-acyltransferase (AT) polyketide synthase (PKS) pathway. Compared with its host genome, the las BGC exhibits a significantly different GC content and pentanucleotide frequency, suggesting a potential horizontal acquisition of the gene cluster. Furthermore, three copies of the putative las pathway were identified in the candidate producer genome. Differences between the three las repeats were observed, including the presence of three insertions, two single-nucleotide polymorphisms, and the absence of a stand-alone acyl carrier protein in one of the repeats. Even though the verrucomicrobial producer shows signs of genome reduction, its genome size is still fairly large (about 5 Mbp), and, compared to its closest free-living relative, it contains most of the primary metabolic pathways, suggesting that it is in the early stages of reduction. IMPORTANCE While sponges are valuable sources of bioactive natural products, a majority of these compounds are produced in small quantities by uncultured symbionts, hampering the study and clinical development of these unique compounds. Lasonolide A (LSA), isolated from marine sponge Forcepia sp., is a cytotoxic molecule active at nanomolar concentrations, which causes premature chromosome condensation, blebbing, cell contraction, and loss of cell adhesion, indicating a novel mechanism of action and making it a potential anticancer drug lead. However, its limited supply hampers progression to clinical trials. We investigated the microbiome of Forcepia sp. using culture-independent DNA sequencing, identified genes likely responsible for LSA synthesis in an uncultured bacterium, and assembled the symbiont's genome. These insights provide future opportunities for heterologous expression and cultivation efforts that may minimize LSA's supply problem.}, } @article {pmid36124804, year = {2022}, author = {Pu, L and Shamir, R}, title = {3CAC: improving the classification of phages and plasmids in metagenomic assemblies using assembly graphs.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {Suppl_2}, pages = {ii56-ii61}, doi = {10.1093/bioinformatics/btac468}, pmid = {36124804}, issn = {1367-4811}, support = {ECCB2022//United State-Israel Binational Science Foundation/ ; //United States National Science Foundation/ ; //Edmond J. Safra Center for Bioinformatics at Tel-Aviv University/ ; //Planning and Budgeting Committee/ ; //Council for Higher Education/ ; }, mesh = {*Bacteriophages/genetics ; Humans ; *Metagenome ; Metagenomics ; Plasmids/genetics ; Software ; }, abstract = {MOTIVATION: Bacteriophages and plasmids usually coexist with their host bacteria in microbial communities and play important roles in microbial evolution. Accurately identifying sequence contigs as phages, plasmids and bacterial chromosomes in mixed metagenomic assemblies is critical for further unraveling their functions. Many classification tools have been developed for identifying either phages or plasmids in metagenomic assemblies. However, only two classifiers, PPR-Meta and viralVerify, were proposed to simultaneously identify phages and plasmids in mixed metagenomic assemblies. Due to the very high fraction of chromosome contigs in the assemblies, both tools achieve high precision in the classification of chromosomes but perform poorly in classifying phages and plasmids. Short contigs in these assemblies are often wrongly classified or classified as uncertain.

RESULTS: Here we present 3CAC, a new three-class classifier that improves the precision of phage and plasmid classification. 3CAC starts with an initial three-class classification generated by existing classifiers and improves the classification of short contigs and contigs with low confidence classification by using proximity in the assembly graph. Evaluation on simulated metagenomes and on real human gut microbiome samples showed that 3CAC outperformed PPR-Meta and viralVerify in both precision and recall, and increased F1-score by 10-60 percentage points.

The 3CAC software is available on https://github.com/Shamir-Lab/3CAC.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36124775, year = {2022}, author = {Li, T and Yin, Y}, title = {Critical assessment of pan-genomic analysis of metagenome-assembled genomes.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {6}, pages = {}, pmid = {36124775}, issn = {1477-4054}, support = {58-8042-7-089//United States Department of Agriculture/ ; R21 AI171952/AI/NIAID NIH HHS/United States ; DBI-1933521//National Science Foundation/ ; R01 GM140370/GM/NIGMS NIH HHS/United States ; 2019-YIN//Nebraska Tobacco Settlement Biomedical Research Enhancement Funds/ ; }, mesh = {*Metagenome ; Phylogeny ; *Genome, Bacterial ; Genomics ; Sequence Analysis, DNA/methods ; Metagenomics/methods ; }, abstract = {Pan-genome analyses of metagenome-assembled genomes (MAGs) may suffer from the known issues with MAGs: fragmentation, incompleteness and contamination. Here, we conducted a critical assessment of pan-genomics of MAGs, by comparing pan-genome analysis results of complete bacterial genomes and simulated MAGs. We found that incompleteness led to significant core gene (CG) loss. The CG loss remained when using different pan-genome analysis tools (Roary, BPGA, Anvi'o) and when using a mixture of MAGs and complete genomes. Contamination had little effect on core genome size (except for Roary due to in its gene clustering issue) but had major influence on accessory genomes. Importantly, the CG loss was partially alleviated by lowering the CG threshold and using gene prediction algorithms that consider fragmented genes, but to a less degree when incompleteness was higher than 5%. The CG loss also led to incorrect pan-genome functional predictions and inaccurate phylogenetic trees. Our main findings were supported by a study of real MAG-isolate genome data. We conclude that lowering CG threshold and predicting genes in metagenome mode (as Anvi'o does with Prodigal) are necessary in pan-genome analysis of MAGs. Development of new pan-genome analysis tools specifically for MAGs are needed in future studies.}, } @article {pmid36124109, year = {2022}, author = {Fu, Y and Zhu, X and Cao, P and Shen, C and Qian, X and Miao, H and Yu, Y and Wang, H and Zhai, X}, title = {Metagenomic Next-Generation Sequencing in the Diagnosis of Infectious Fever During Myelosuppression Among Pediatric Patients with Hematological and Neoplastic Diseases.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {5425-5434}, pmid = {36124109}, issn = {1178-6973}, abstract = {PURPOSE: To analyze the contribution of metagenomic next-generation sequencing (mNGS) in the guidance of clinical treatment and outcomes of infection during myelosuppression among children with hematological and neoplastic diseases.

PATIENTS AND METHODS: The clinical data and results of mNGS assay of febrile patients suspected of infection were retrospectively collected. The characteristics of pathogenic microorganisms and clinical course of myelosuppressed children with hematological diseases were summarized.

RESULTS: Our study included 70 patients (45 males) with a median age of 5 years (range: 0.5 to 13 y). During the study period, there were 96 events of suspected infection. According to comprehensive clinical diagnosis, 73 blood infections, 43 pneumonia and 2 urinary tract infections occurred. The positive rate of mNGS was significantly higher than that of traditional microbial detection (83.3% vs 17.7%). The main pathogens detected by mNGS were Pseudomonas aeruginosa, Acinetobacter, human herpesvirus, Candida and Aspergillus. The average duration of fever was 4.9 days and 11.6 days (P < 0.05), and the average cost of anti-infection treatment was RMB ¥28,077 and 39,898 (P < 0.05) among children received mNGS within 48 hours and more than 48 hours after the onset of infection symptoms.

CONCLUSION: mNGS contributes to clinical management of children with infection during myelosuppression, especially among patients with negative traditional microbial detection. Early implementation of mNGS in children with symptoms has a tendency to reduce the time of infection, fever and the cost of treatment.}, } @article {pmid36123651, year = {2022}, author = {Li, Q and Vehik, K and Li, C and Triplett, E and Roesch, L and Hu, YJ and Krischer, J}, title = {A robust and transformation-free joint model with matching and regularization for metagenomic trajectory and disease onset.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {661}, pmid = {36123651}, issn = {1471-2164}, support = {U24DK097771/DK/NIDDK NIH HHS/United States ; CA21765/CA/NCI NIH HHS/United States ; CA21765/CA/NCI NIH HHS/United States ; }, mesh = {Cohort Studies ; Feces ; Humans ; *Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {BACKGROUND: To identify operational taxonomy units (OTUs) signaling disease onset in an observational study, a powerful strategy was selecting participants by matched sets and profiling temporal metagenomes, followed by trajectory analysis. Existing trajectory analyses modeled individual OTU or microbial community without adjusting for the within-community correlation and matched-set-specific latent factors.

RESULTS: We proposed a joint model with matching and regularization (JMR) to detect OTU-specific trajectory predictive of host disease status. The between- and within-matched-sets heterogeneity in OTU relative abundance and disease risk were modeled by nested random effects. The inherent negative correlation in microbiota composition was adjusted by incorporating and regularizing the top-correlated taxa as longitudinal covariate, pre-selected by Bray-Curtis distance and elastic net regression. We designed a simulation pipeline to generate true biomarkers for disease onset and the pseudo biomarkers caused by compositionality. We demonstrated that JMR effectively controlled the false discovery and pseudo biomarkers in a simulation study generating temporal high-dimensional metagenomic counts with random intercept or slope. Application of the competing methods in the simulated data and the TEDDY cohort showed that JMR outperformed the other methods and identified important taxa in infants' fecal samples with dynamics preceding host disease status.

CONCLUSION: Our method JMR is a robust framework that models taxon-specific trajectory and host disease status for matched participants without transformation of relative abundance, improving the power of detecting disease-associated microbial features in certain scenarios. JMR is available in R package mtradeR at https://github.com/qianli10000/mtradeR.}, } @article {pmid36123522, year = {2022}, author = {Ayala-Muñoz, D and Macalady, JL and Sánchez-España, J and Falagán, C and Couradeau, E and Burgos, WD}, title = {Microbial carbon, sulfur, iron, and nitrogen cycling linked to the potential remediation of a meromictic acidic pit lake.}, journal = {The ISME journal}, volume = {16}, number = {12}, pages = {2666-2679}, pmid = {36123522}, issn = {1751-7370}, mesh = {*Lakes/microbiology ; *Iron ; Carbon ; Sulfur ; Bacteria/genetics ; Sulfates ; Acids ; Sulfides ; Oxidation-Reduction ; Nitrogen ; }, abstract = {Cueva de la Mora is a permanently stratified acidic pit lake and a model system for extreme acid mine drainage (AMD) studies. Using a combination of amplicon sequencing, metagenomics and metatranscriptomics we performed a taxonomically resolved analysis of microbial contributions to carbon, sulfur, iron, and nitrogen cycling. We found that active green alga Coccomyxa onubensis dominated the upper layer and chemocline. The chemocline had activity for iron(II) oxidation carried out by populations of Ca. Acidulodesulfobacterium, Ferrovum, Leptospirillium, and Armatimonadetes. Predicted activity for iron(III) reduction was only detected in the deep layer affiliated with Proteobacteria. Activity for dissimilatory nitrogen cycling including nitrogen fixation and nitrate reduction was primarily predicted in the chemocline. Heterotrophic archaeal populations with predicted activity for sulfide oxidation related to uncultured Thermoplasmatales dominated in the deep layer. Abundant sulfate-reducing Desulfomonile and Ca. Acidulodesulfobacterium populations were active in the chemocline. In the deep layer, uncultured populations from the bacterial phyla Actinobacteria, Chloroflexi, and Nitrospirae contributed to both sulfate reduction and sulfide oxidation. Based on this information we evaluated the potential for sulfide mineral precipitation in the deep layer as a tool for remediation. We argue that sulfide precipitation is not limited by microbial genetic potential but rather by the quantity and quality of organic carbon reaching the deep layer as well as by oxygen additions to the groundwater enabling sulfur oxidation. Addition of organic carbon and elemental sulfur should stimulate sulfate reduction and limit reoxidation of sulfide minerals.}, } @article {pmid36123442, year = {2022}, author = {Hedlund, BP and Chuvochina, M and Hugenholtz, P and Konstantinidis, KT and Murray, AE and Palmer, M and Parks, DH and Probst, AJ and Reysenbach, AL and Rodriguez-R, LM and Rossello-Mora, R and Sutcliffe, IC and Venter, SN and Whitman, WB}, title = {SeqCode: a nomenclatural code for prokaryotes described from sequence data.}, journal = {Nature microbiology}, volume = {7}, number = {10}, pages = {1702-1708}, pmid = {36123442}, issn = {2058-5276}, mesh = {*Metagenome ; *Prokaryotic Cells ; }, abstract = {Most prokaryotes are not available as pure cultures and therefore ineligible for naming under the rules and recommendations of the International Code of Nomenclature of Prokaryotes (ICNP). Here we summarize the development of the SeqCode, a code of nomenclature under which genome sequences serve as nomenclatural types. This code enables valid publication of names of prokaryotes based upon isolate genome, metagenome-assembled genome or single-amplified genome sequences. Otherwise, it is similar to the ICNP with regard to the formation of names and rules of priority. It operates through the SeqCode Registry (https://seqco.de/), a registration portal through which names and nomenclatural types are registered, validated and linked to metadata. We describe the two paths currently available within SeqCode to register and validate names, including Candidatus names, and provide examples for both. Recommendations on minimal standards for DNA sequences are provided. Thus, the SeqCode provides a reproducible and objective framework for the nomenclature of all prokaryotes regardless of cultivability and facilitates communication across microbiological disciplines.}, } @article {pmid36123347, year = {2022}, author = {Wu, R and Smith, CA and Buchko, GW and Blaby, IK and Paez-Espino, D and Kyrpides, NC and Yoshikuni, Y and McDermott, JE and Hofmockel, KS and Cort, JR and Jansson, JK}, title = {Structural characterization of a soil viral auxiliary metabolic gene product - a functional chitosanase.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5485}, pmid = {36123347}, issn = {2041-1723}, support = {P41 RR001209/RR/NCRR NIH HHS/United States ; P30 GM133894/GM/NIGMS NIH HHS/United States ; }, mesh = {Carbon ; Chitin ; Glycoside Hydrolases/metabolism ; *Soil ; Viral Proteins/genetics ; *Viruses/genetics ; }, abstract = {Metagenomics is unearthing the previously hidden world of soil viruses. Many soil viral sequences in metagenomes contain putative auxiliary metabolic genes (AMGs) that are not associated with viral replication. Here, we establish that AMGs on soil viruses actually produce functional, active proteins. We focus on AMGs that potentially encode chitosanase enzymes that metabolize chitin - a common carbon polymer. We express and functionally screen several chitosanase genes identified from environmental metagenomes. One expressed protein showing endo-chitosanase activity (V-Csn) is crystalized and structurally characterized at ultra-high resolution, thus representing the structure of a soil viral AMG product. This structure provides details about the active site, and together with structure models determined using AlphaFold, facilitates understanding of substrate specificity and enzyme mechanism. Our findings support the hypothesis that soil viruses contribute auxiliary functions to their hosts.}, } @article {pmid36123315, year = {2022}, author = {Fontana, F and Alessandri, G and Tarracchini, C and Bianchi, MG and Rizzo, SM and Mancabelli, L and Lugli, GA and Argentini, C and Vergna, LM and Anzalone, R and Longhi, G and Viappiani, A and Taurino, G and Chiu, M and Turroni, F and Bussolati, O and van Sinderen, D and Milani, C and Ventura, M}, title = {Designation of optimal reference strains representing the infant gut bifidobacterial species through a comprehensive multi-omics approach.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {5825-5839}, pmid = {36123315}, issn = {1462-2920}, mesh = {Humans ; Infant ; *Bifidobacterium/genetics ; *Multiomics ; Reproducibility of Results ; Feces/microbiology ; Metagenomics ; Bacteria ; }, abstract = {The genomic era has resulted in the generation of a massive amount of genetic data concerning the genomic diversity of bacterial taxa. As a result, the microbiological community is increasingly looking for ways to define reference bacterial strains to perform experiments that are representative of the entire bacterial species. Despite this, there is currently no established approach allowing a reliable identification of reference strains based on a comprehensive genomic, ecological, and functional context. In the current study, we developed a comprehensive multi-omics approach that will allow the identification of the optimal reference strains using the Bifidobacterium genus as test case. Strain tracking analysis based on 1664 shotgun metagenomics datasets of healthy infant faecal samples were employed to identify bifidobacterial strains suitable for in silico and in vitro analyses. Subsequently, an ad hoc bioinformatic tool was developed to screen local strain collections for the most suitable species-representative strain alternative. The here presented approach was validated using in vitro trials followed by metagenomics and metatranscriptomics analyses. Altogether, these results demonstrated the validity of the proposed model for reference strain selection, thus allowing improved in silico and in vitro investigations both in terms of cross-laboratory reproducibility and relevance of research findings.}, } @article {pmid36123312, year = {2022}, author = {Perez-Molphe-Montoya, E and Küsel, K and Overholt, WA}, title = {Redefining the phylogenetic and metabolic diversity of phylum Omnitrophota.}, journal = {Environmental microbiology}, volume = {24}, number = {11}, pages = {5437-5449}, doi = {10.1111/1462-2920.16170}, pmid = {36123312}, issn = {1462-2920}, mesh = {RNA, Ribosomal, 16S/genetics/metabolism ; Phylogeny ; *Ecosystem ; *Metagenome ; Bacteria ; }, abstract = {The candidate phylum Omnitrophica-recently termed Omnitrophota, and originally known as OP3-is an understudied bacterial clade that has primarily been found in aquatic ecosystems. To characterize the diversity and ecology of this phylum, we reconstructed 55 Omnitrophota metagenome-assembled genomes (MAGs) from a well-characterized groundwater system within central Germany and placed them within the context of publicly available genomes. Seven clades were identified, four of which contained novel genomes obtained from our groundwater system. All clades exhibited the capacity for type IV pili, type II secretion systems, glycogen storage, and carbohydrate degradation. Only the characterized Cand. Omnitrophus magneticus genome exhibited functions associated with magnetosome construction. Clades were characterized by sets of traits rather than unique pathways, which were then used to infer ecological strategies. These lifestyles consisted of mixotrophs, obligate fermenters, and versatile respiratory heterotrophs. Patterns in 16S rRNA gene amplicons from a 6 years, monthly sampled groundwater time-series dataset reflected the persistent and widespread occurrence of Clade 7 Wood-Ljungdahl utilizing mixotrophs and highlight this group as a core member of the groundwater community. Overall, this study uncovered, characterized, and contextualized the metabolic and phylogenetic diversity within phylum Omnitrophota, and predicts that environmental populations may mediate both nitrogen and sulfur cycling, along with organic matter production and degradation within aquatic ecosystems.}, } @article {pmid36122838, year = {2023}, author = {Thompson, DS and Fu, C and Gandhi, T and Fowler, JC and Frueh, BC and Weinstein, BL and Petrosino, J and Hadden, JK and Carlson, M and Coarfa, C and Madan, A}, title = {Differential co-expression networks of the gut microbiota are associated with depression and anxiety treatment resistance among psychiatric inpatients.}, journal = {Progress in neuro-psychopharmacology & biological psychiatry}, volume = {120}, number = {}, pages = {110638}, pmid = {36122838}, issn = {1878-4216}, support = {U54 HG004973/HG/NHGRI NIH HHS/United States ; P42 ES027725/ES/NIEHS NIH HHS/United States ; R25 GM056929/GM/NIGMS NIH HHS/United States ; R25 GM069234/GM/NIGMS NIH HHS/United States ; P50 MD015496/MD/NIMHD NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; P30 CA125123/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Depression ; Inpatients ; Anxiety ; Biomarkers ; }, abstract = {BACKGROUND: Comorbid anxiety and depression are common and are associated with greater disease burden than either alone. Our recent efforts have identified an association between gut microbiota dysfunction and severity of anxiety and depression. In this follow-up, we applied Differential Co-Expression Analysis (DiffCoEx) to identify potential gut microbiota biomarker(s) candidates of treatment resistance among psychiatric inpatients.

METHODS: In a sample of convenience, 100 psychiatric inpatients provided clinical data at admission and discharge; fecal samples were collected early during the hospitalization. Whole genome shotgun sequencing methods were used to process samples. DiffCoEx was used to identify clusters of microbial features significantly different based on treatment resistance status. Once overlapping features were identified, a knowledge-mining tool was used to review the literature using a list of microbial species/pathways and a select number of medical subject headlines (MeSH) terms relevant for depression, anxiety, and brain-gut-axis dysregulation. Network analysis used overlapping features to identify microbial interactions that could impact treatment resistance.

RESULTS: DiffCoEx analyzed 10,403 bacterial features: 43/44 microbial features associated with depression treatment resistance overlapped with 43/114 microbial features associated with anxiety treatment resistance. Network analysis resulted in 8 biological interactions between 16 bacterial species. Clostridium perfringens evidenced the highest connection strength (0.95). Erysipelotrichaceae bacterium 6_1_45 has been most widely examined, is associated with inflammation and dysbiosis, but has not been associated with depression or anxiety.

CONCLUSION: DiffCoEx potentially identified gut bacteria biomarker candidates of depression and anxiety treatment-resistance. Future efforts in psychiatric microbiology should examine the mechanistic relationship of identified pro-inflammatory species, potentially contributing to a biomarker-based algorithm for treatment resistance.}, } @article {pmid36121926, year = {2022}, author = {Carratto, TMT and Moraes, VMS and Recalde, TSF and Oliveira, MLG and Teixeira Mendes-Junior, C}, title = {Applications of massively parallel sequencing in forensic genetics.}, journal = {Genetics and molecular biology}, volume = {45}, number = {3 Suppl 1}, pages = {e20220077}, pmid = {36121926}, issn = {1415-4757}, abstract = {Massively parallel sequencing, also referred to as next-generation sequencing, has positively changed DNA analysis, allowing further advances in genetics. Its capability of dealing with low quantity/damaged samples makes it an interesting instrument for forensics. The main advantage of MPS is the possibility of analyzing simultaneously thousands of genetic markers, generating high-resolution data. Its detailed sequence information allowed the discovery of variations in core forensic short tandem repeat loci, as well as the identification of previous unknown polymorphisms. Furthermore, different types of markers can be sequenced in a single run, enabling the emergence of DIP-STRs, SNP-STR haplotypes, and microhaplotypes, which can be very useful in mixture deconvolution cases. In addition, the multiplex analysis of different single nucleotide polymorphisms can provide valuable information about identity, biogeographic ancestry, paternity, or phenotype. DNA methylation patterns, mitochondrial DNA, mRNA, and microRNA profiling can also be analyzed for different purposes, such as age inference, maternal lineage analysis, body-fluid identification, and monozygotic twin discrimination. MPS technology also empowers the study of metagenomics, which analyzes genetic material from a microbial community to obtain information about individual identification, post-mortem interval estimation, geolocation inference, and substrate analysis. This review aims to discuss the main applications of MPS in forensic genetics.}, } @article {pmid36121483, year = {2022}, author = {Gill, SP and Hunter, WR and Coulson, LE and Banat, IM and Schelker, J}, title = {Synthetic and biological surfactant effects on freshwater biofilm community composition and metabolic activity.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {19-20}, pages = {6847-6859}, pmid = {36121483}, issn = {1432-0614}, mesh = {Biofilms ; Ecosystem ; Fresh Water/chemistry ; Glucosidases/pharmacology ; *Leucyl Aminopeptidase/metabolism/pharmacology ; Sodium Dodecyl Sulfate ; *Surface-Active Agents/pharmacology ; Water/pharmacology ; }, abstract = {Surfactants are used to control microbial biofilms in industrial and medical settings. Their known toxicity on aquatic biota, and their longevity in the environment, has encouraged research on biodegradable alternatives such as rhamnolipids. While previous research has investigated the effects of biological surfactants on single species biofilms, there remains a lack of information regarding the effects of synthetic and biological surfactants in freshwater ecosystems. We conducted a mesocosm experiment to test how the surfactant sodium dodecyl sulfate (SDS) and the biological surfactant rhamnolipid altered community composition and metabolic activity of freshwater biofilms. Biofilms were cultured in the flumes using lake water from Lake Lunz in Austria, under high (300 ppm) and low (150 ppm) concentrations of either surfactant over a four-week period. Our results show that both surfactants significantly affected microbial diversity. Up to 36% of microbial operational taxonomic units were lost after surfactant exposure. Rhamnolipid exposure also increased the production of the extracellular enzymes, leucine aminopeptidase, and glucosidase, while SDS exposure reduced leucine aminopeptidase and glucosidase. This study demonstrates that exposure of freshwater biofilms to chemical and biological surfactants caused a reduction of microbial diversity and changes in biofilm metabolism, exemplified by shifts in extracellular enzyme activities. KEY POINTS: • Microbial biofilm diversity decreased significantly after surfactant exposure. • Exposure to either surfactant altered extracellular enzyme activity. • Overall metabolic activity was not altered, suggesting functional redundancy.}, } @article {pmid36121227, year = {2022}, author = {Ramos-Tapia, I and Nuñez, R and Salinas, C and Salinas, P and Soto, J and Paneque, M}, title = {Study of Wetland Soils of the Salar de Atacama with Different Azonal Vegetative Formations Reveals Changes in the Microbiota Associated with Hygrophile Plant Type on the Soil Surface.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0053322}, pmid = {36121227}, issn = {2165-0497}, mesh = {Bacteria/genetics ; *Microbiota/genetics ; Phylogeny ; Plants ; RNA, Ribosomal, 16S/genetics ; *Soil Microbiology ; *Wetlands ; }, abstract = {Salar de Atacama is located approximately 55 km south of San Pedro de Atacama in the Antofagasta region, Chile. The high UV irradiation and salt concentration and extreme drought make Salar de Atacama an ideal site to search for novel soil microorganisms with unique properties. Here, we used a metataxonomic approach (16S rRNA V3-V4) to identify and characterize the soil microbiota associated with different surface azonal vegetation formations, including strict hygrophiles (Baccharis juncea, Juncus balticus, and Schoenoplectus americanus), transitional hygrophiles (Distichlis spicata, Lycium humile, and Tessaria absinthioides), and their various combinations. We detected compositional differences among the soil surface microbiota associated with each plant formation in the sampling area. There were changes in soil microbial phylogenetic diversity from the strict to the transitional hygrophiles. Moreover, we found alterations in the abundance of bacterial phyla and genera. Halobacteriota and Actinobacteriota might have facilitated water uptake by the transitional hygrophiles. Our findings helped to elucidate the microbiota of Salar de Atacama and associate them with the strict and transitional hygrophiles indigenous to the region. These findings could be highly relevant to future research on the symbiotic relationships between microbiota and salt-tolerant plants in the face of climate change-induced desertification. IMPORTANCE The study of the composition and diversity of the wetland soil microbiota associated with hygrophilous plants in a desert ecosystem of the high Puna in northern Chile makes it an ideal approach to search for novel extremophilic microorganisms with unique properties. These microorganisms are adapted to survive in ecological niches, such as those with high UV irradiation, extreme drought, and high salt concentration; they can be applied in various fields, such as biotechnology and astrobiology, and industries, including the pharmaceutical, food, agricultural, biofuel, cosmetic, and textile industries. These microorganisms can also be used for ecological conservation and restoration. Extreme ecosystems are a unique biological resource and biodiversity hot spots that play a crucial role in maintaining environmental sustainability. The findings could be highly relevant to future research on the symbiotic relationships between microbiota and extreme-environment-tolerant plants in the face of climate change-induced desertification.}, } @article {pmid36121163, year = {2022}, author = {Fierer, N and Holland-Moritz, H and Alexiev, A and Batther, H and Dragone, NB and Friar, L and Gebert, MJ and Gering, S and Henley, JB and Jech, S and Kibby, EM and Melie, T and Patterson, WB and Peterson, E and Schutz, K and Stallard-Olivera, E and Sterrett, J and Walsh, C and Mansfeldt, C}, title = {A Metagenomic Investigation of Spatial and Temporal Changes in Sewage Microbiomes across a University Campus.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0065122}, pmid = {36121163}, issn = {2379-5077}, support = {T32 GM008759/GM/NIGMS NIH HHS/United States ; T32 GM142607/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Sewage/microbiology ; Wastewater ; Universities ; *Microbiota/genetics ; Metagenome/genetics ; Bacteria/genetics ; }, abstract = {Wastewater microbial communities are not static and can vary significantly across time and space, but this variation and the factors driving the observed spatiotemporal variation often remain undetermined. We used a shotgun metagenomic approach to investigate changes in wastewater microbial communities across 17 locations in a sewer network, with samples collected from each location over a 3-week period. Fecal material-derived bacteria constituted a relatively small fraction of the taxa found in the collected samples, highlighting the importance of environmental sources to the sewage microbiome. The prokaryotic communities were highly variable in composition depending on the location within the sampling network, and this spatial variation was most strongly associated with location-specific differences in sewage pH. However, we also observed substantial temporal variation in the composition of the prokaryotic communities at individual locations. This temporal variation was asynchronous across sampling locations, emphasizing the importance of independently considering both spatial and temporal variation when assessing the wastewater microbiome. The spatiotemporal patterns in viral community composition closely tracked those of the prokaryotic communities, allowing us to putatively identify the bacterial hosts of some of the dominant viruses in these systems. Finally, we found that antibiotic resistance gene profiles also exhibit a high degree of spatiotemporal variability, with most of these genes unlikely to be derived from fecal bacteria. Together, these results emphasize the dynamic nature of the wastewater microbiome, the challenges associated with studying these systems, and the utility of metagenomic approaches for building a multifaceted understanding of these microbial communities and their functional attributes. IMPORTANCE Sewage systems harbor extensive microbial diversity, including microbes derived from both human and environmental sources. Studies of the sewage microbiome are useful for monitoring public health and the health of our infrastructure, but the sewage microbiome can be highly variable in ways that are often unresolved. We sequenced DNA recovered from wastewater samples collected over a 3-week period at 17 locations in a single sewer system to determine how these communities vary across time and space. Most of the wastewater bacteria, and the antibiotic resistance genes they harbor, were not derived from human feces, but human usage patterns did impact how the amounts and types of bacteria and bacterial genes we found in these systems varied over time. Likewise, the wastewater communities, including both bacteria and their viruses, varied depending on location within the sewage network, highlighting the challenges and opportunities in efforts to monitor and understand the sewage microbiome.}, } @article {pmid36121162, year = {2022}, author = {Bulzu, PA and Kavagutti, VS and Andrei, AS and Ghai, R}, title = {The Evolutionary Kaleidoscope of Rhodopsins.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0040522}, pmid = {36121162}, issn = {2379-5077}, mesh = {*Rhodopsins, Microbial/genetics ; *Rhodopsin/genetics ; Phylogeny ; }, abstract = {Rhodopsins are widely distributed across all domains of life where they perform a plethora of functions through the conversion of electromagnetic radiation into physicochemical signals. As a result of an extensive survey of available genomic and metagenomic sequencing data, we reported the existence of novel clades and exotic sequence motifs scattered throughout the evolutionary radiations of both Type-1 and Type-3 rhodopsins that will likely enlarge the optogenetics toolbox. We expanded the typical rhodopsin blueprint by showing that a highly conserved and functionally important arginine residue (i.e., Arg82) was substituted multiple times during evolution by an extensive amino acid spectrum. We proposed the umbrella term Alt-rhodopsins (AltRs) for all such proteins that departed Arg82 orthodoxy. Some AltRs formed novel clades in the rhodopsin phylogeny and were found in giant viruses. Some newly uncovered AltRs were phylogenetically close to heliorhodopsins, which allowed a closer examination of the phylogenetic border between Type-1 rhodopsins and heliorhodopsins. Comprehensive phylogenetic trees and ancestral sequence reconstructions allowed us to advance the hypothesis that proto-heliorhodopsins were a eukaryotic innovation before their subsequent diversification into the extant Type-3 rhodopsins. IMPORTANCE The rhodopsin scaffold is remarkably versatile and widespread, coupling light availability to energy production and other light-dependent cellular responses with minor alterations to critical residues. We described an unprecedented spectrum of substitutions at one of the most conserved amino acids in the rhodopsin fold, Arg82. We denoted such phylogenetically diverse rhodopsins with the umbrella name Alt-rhodopsins (AltR) and described a distinct branch of AltRs in giant viruses. Intriguingly, some AltRs were the closest phylogenetic neighbors to Heliorhodopsins (HeRs) whose origins have remained enigmatic. Our analyses of HeR origins in the light of AltRs led us to posit a most unusual evolutionary trajectory that suggested a eukaryotic origin for HeRs before their diversification in prokaryotes.}, } @article {pmid36121066, year = {2022}, author = {Shi, T and Zhang, T and Wang, X and Wang, X and Shen, W and Guo, X and Liu, Y and Li, Z and Jiang, Y}, title = {Metagenomic Analysis of in Vitro Ruminal Fermentation Reveals the Role of the Copresent Microbiome in Plant Biomass Degradation.}, journal = {Journal of agricultural and food chemistry}, volume = {70}, number = {38}, pages = {12095-12106}, doi = {10.1021/acs.jafc.2c03522}, pmid = {36121066}, issn = {1520-5118}, mesh = {Animals ; Biomass ; Fatty Acids, Volatile/metabolism ; Fermentation ; *Metagenome ; *Microbiota ; Pectins/metabolism ; Rumen/metabolism ; Xylans/metabolism ; }, abstract = {In vitro ruminal fermentation is considered an efficient way to degrade crop residue. To better understand the microbial communities and their functions during in vitro ruminal fermentation, the microbiome and short chain fatty acid (SCFA) production were investigated using the metagenomic sequencing and rumen simulation technique (RUSITEC) system. A total of 1677 metagenome-assembled genomes (MAGs) were reconstructed, and 298 MAGs were found copresenting in metagenomic data of the current work and 58 previously ruminal representative samples. Additionally, the domains related to pectin and xylan degradation were overrepresented in the copresent MAGs compared with total MAGs. Among the copresent MAGs, we obtained 14 MAGs with SCFA-synthesis-related genes positively correlated with SCFA concentrations. The MAGs obtained from this study enable a better understanding of dominant microbial communities across in vivo and in vitro ruminal fermentation and show promise for pointing out directions for further research on in vitro ruminal fermentation.}, } @article {pmid36120548, year = {2022}, author = {Lee, J and Um, S and Kim, SH}, title = {Metabolomic analysis of halotolerant endophytic bacterium Salinivibrio costicola isolated from Suaeda maritima (L.) dumort.}, journal = {Frontiers in molecular biosciences}, volume = {9}, number = {}, pages = {967945}, pmid = {36120548}, issn = {2296-889X}, abstract = {In this study, the Salinivibrio costicola strain was isolated from Suaeda maritima (L.) Dumort. collected in Sinan, Republic of Korea. The endophytic characteristics of the Gram-negative bacterium S. costicola were verified with metagenomics sequencing of S. maritima. S. costicola was cultivated for 3 days in a liquid medium with 3.3% sea salt and analyzed the metabolites produced by the strain cultured in five different bacterial cultivation media. From the bacterial cultures, polyhydroxybutyrate derivatives were detected using high-resolution mass spectrometry, and three major compounds were isolated by high-performance liquid chromatography. The chemical structures of the compounds were elucidated using nuclear magnetic resonance and MS analyses. The relationship between the compounds was confirmed with Global Natural Product Social Molecular Networking, which showed clustering of the compounds. From the S. maritima extract, polyhydroxybutyrate derivatives produced by S. costicola were detected as being accumulated in the host plant.}, } @article {pmid36120127, year = {2022}, author = {Cao, P and Wei, X and Wang, G and Chen, X and Han, J and Li, Y}, title = {Microbial inoculants and garbage fermentation liquid reduced root-knot nematode disease and As uptake in Panax quinquefolium cultivation by modulating rhizosphere microbiota community.}, journal = {Chinese herbal medicines}, volume = {14}, number = {1}, pages = {58-69}, pmid = {36120127}, issn = {2589-3610}, abstract = {OBJECTIVE: To find a suitable ecological cultivation measure to solve the problem of root-knot nematode disease of Panax quinquefolium (Panacis Quinquefolii Radix) and the heavy metals accumulating in its roots.

METHODS: Three-year-old P. quinquefolium was treated with four different combinations of microbial inoculant (MI) and garbage fermentation liquid (GFL) [the joint application of 'TuXiu' MI and Fifty potassium MI (TF), the combination use of 'No. 1' MI and Fifty potassium MI (NF), 'Gulefeng' poly-γ-glutamic acid MI (PGA), GFL], and the untreated control (CK). Here, high-throughput sequencing, ICP-MS and UPLC were employed to systematically characterize changes of microbial diversity and structure composition, heavy metals (As, Cd and Pb) content and ginsenoside content among different treatments.

RESULTS: The results revealed that different MIs and GFL could increase the root dry weight of P. quinquefolium, PGA enhanced it by 83.24%, followed by GFL (49.93%), meanwhile, PGA and GFL were able to lessen root-knot nematode disease incidence by 57.25% and 64.35%. The treatment of PGA and GFL can also effectively reduce heavy metals in roots. The As content in GFL and PGA was decreased by 52.17% and 43.48% respectively, while the Cd and Pb contents of GFL and PGA was decreased somewhat. Additionally, the content of total ginsenosides was increased by 42.14% and 42.07%, in response to TF and NF, respectively. Our metagenomic analysis showed that the relative abundance of particular soil microbial community members related to the biocontrol of root-knot nematode disease and plant pathogen (i.e., Chaetomium in NF, Xylari in GFL, and Microascus in PGA), heavy metal bioremediation (Hyphomacrobium in PGA and Xylaria in GFL), and nitrogen fixation (Nordella and Nitrospira in TF) was significantly increased; notably, potential harmful microflora, such as Plectosaphaerella and Rhizobacter, were more abundant in the control group.

CONCLUSION: MI and GFL could improve the quality of P. quinquefolium by modifying its rhizosphere microbial community structure and composition, both of them are beneficial to the development of ecological cultivation of P. quinquefolium.}, } @article {pmid36119925, year = {2022}, author = {Prasetiyono, BWHE and Widiyanto, W and Pandupuspitasari, NS}, title = {Gut Microbiota Profiles in Dairy Cattle from Highland and Coastal Regions Using Shotgun Metagenomic Approach.}, journal = {BioMed research international}, volume = {2022}, number = {}, pages = {3659052}, pmid = {36119925}, issn = {2314-6141}, mesh = {Animals ; Cattle ; Firmicutes ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {There is significant difference in milk production of highland and coastal regions in Indonesia of which the latter is critically low. The recent studies indicate a possibility of improving the milk yield and quality by manipulating the gut microbiota, for which profiling and abundance of gut microbiota in these divergent regions need to be addressed. The present study was the first of its kind to explore the dairy cattle gut microbiota diversity, abundance, and functional annotation of the two divergent Indonesian regions, the highland and coastal regions, by shotgun metagenomic approach. Unfavorable environmental conditions such as type of forage grass in coastal regions and high temperature remain a limiting factor; however, the improvement through manipulating the gut microbiota was not considered until recently to improve the quality and quantity of coastal region dairy cattle. The application of recent advance technologies can help achieve this goal on sustainable basis. The results show Bacteroidetes in higher abundance in coastal region (FPP) than in highland (Salatiga) while Firmicutes were higher in Salatiga. Furthermore, a collective physiology of the community was found by annotating the sequences against KEGG, eggNOG, and CAZy databases. To identify the role in pathways, an mPATH analysis was performed to have insight into the microbiota community in different metabolic pathways. The identified targets can be used as prebiotic and/or probiotic to improve the average milk yield of coastal region dairy cattle by manipulating the dairy feed with desired microbes.}, } @article {pmid36119702, year = {2022}, author = {Wang, L and Wang, F and Yang, C and Luo, F}, title = {Central nervous system infection caused by Mycobacterium houstonense: A case report.}, journal = {Frontiers in neurology}, volume = {13}, number = {}, pages = {908086}, pmid = {36119702}, issn = {1664-2295}, abstract = {BACKGROUND: Mycobacterium houstonense is a rapidly growing mycobacterium (RGM) that belongs to the unnamed third biovariant complex of the Mycobacterium fortuitum group, which is rarely responsible for human infection. Approximately 76% of infections caused by the M. fortuitum group occur after open fractures or skin, soft tissue, bone, or puncture wounds. To date, only a few cases of human infectious disease caused by M. houstonense have been reported worldwide.

CASE PRESENTATION: We present a case of a 26-year-old man with a central nervous system (CNS) infection caused by M. houstonense. The patient was transferred to our hospital because of headaches and muscle strength changes. One month prior to presentation at our hospital, the patient was diagnosed with tuberculous meningitis at the other two hospitals, but his condition did not improve after anti-tuberculous treatment, antibiotics, and anti-viral treatment before admission to our hospital. Lumbar puncture was performed at both previous hospitals, as well as at our hospital; the results consistently indicated high cerebrospinal fluid (CSF) opening pressure. M. houstonense was detected in the CSF of the second hospital's lumbar puncture by metagenomic next-generation sequencing (mNGS) but was not identified at our hospital. The patient was discharged from our hospital after receiving non-tuberculous mycobacterium (NTM) treatment for 1 month according to the Chinese NTM guidelines. However, the patient died 20 days after discharge.

CONCLUSION: Since it is difficult to identify M. houstonense, this is the first case of human CNS infection caused by M. houstonense in China. This case may be considered by neurologists and infectious physicians when CNS infection does not respond to conventional treatment, especially in the uncommon type of NTM.}, } @article {pmid36118848, year = {2022}, author = {Rabapane, KJ and Ijoma, GN and Matambo, TS}, title = {Insufficiency in functional genomics studies, data, and applications: A case study of bio-prospecting research in ruminant microbiome.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {946449}, pmid = {36118848}, issn = {1664-8021}, abstract = {Over the last two decades, biotechnology has advanced at a rapid pace, propelled by the incorporation of bio-products into various aspects of pharmaceuticals, industry, and the environment. These developments have sparked interest in the bioprospecting of microorganisms and their products in a variety of niche environments. Furthermore, the use of omics technologies has greatly aided our analyses of environmental samples by elucidating the microbial ecological framework, biochemical pathways, and bio-products. However, the more often overemphasis on taxonomic identification in most research publications, as well as the data associated with such studies, is detrimental to immediate industrial and commercial applications. This review identifies several factors that contribute to the complexity of sequence data analysis as potential barriers to the pragmatic application of functional genomics, utilizing recent research on ruminants to demonstrate these limitations in the hopes of broadening our horizons and drawing attention to this gap in bioprospecting studies for other niche environments as well. The review also aims to emphasize the importance of routinely incorporating functional genomics into environmental metagenomics analyses in order to improve solutions that drive rapid industrial biocatalysis developments from derived outputs with the aim of achieving potential benefits in energy-use reduction and environmental considerations for current and future applications.}, } @article {pmid36118360, year = {2022}, author = {Liu, Z and Ding, X and Haider, MS and Ali, F and Yu, H and Chen, X and Tan, S and Zu, Y and Liu, W and Ding, B and Zheng, A and Zheng, J and Qian, Z and Ashfaq, H and Yu, D and Li, K}, title = {A metagenomic insight into the Yangtze finless porpoise virome.}, journal = {Frontiers in veterinary science}, volume = {9}, number = {}, pages = {922623}, pmid = {36118360}, issn = {2297-1769}, abstract = {The Yangtze finless porpoise (Neophocaena phocaenoides asiaeorientalis) inhabiting the Yantze River, China is critically endangered because of the influences of infectious disease, human activity, and water contamination. Viral diseases are one of the crucial factors that threatening the health of Yangtze finless porpoise. However, there are few studies which elaborate the viral diversity of Yangtze finless. Therefore, this study was performed to investigate the viral diversity of Yangtze finless by metagenomics. Results indicated that a total of 12,686,252 high-quality valid sequences were acquired and 2,172 virus reads were recognized. Additionally, we also obtained a total of 10,600 contigs. Phages was the most abundant virus in the samples and the ratio of DNA and RNA viruses were 69.75 and 30.25%, respectively. Arenaviridae, Ackermannviridae and Siphoviridae were the three most predominant families in all the samples. Moreover, the majority of viral genus were Mammarenavirus, Limestonevirus and Lambdavirus. The results of gene prediction indicated that these viruses play vital roles in biological process, cellular component, molecular function, and disease. To the best of our knowledge, this is the first report on the viral diversity of Yangtze finless porpoise, which filled the gaps in its viral information. Meanwhile, this study can also provide a theoretical basis for the establishment of the prevention and protection system for virus disease of Yangtze finless porpoise.}, } @article {pmid36118221, year = {2022}, author = {Gu, X and Zhao, L and Tan, J and Zhang, Q and Fu, L and Li, J}, title = {Characterization of a novel β-agarase from Antarctic macroalgae-associated bacteria metagenomic library and anti-inflammatory activity of the enzymatic hydrolysates.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {972272}, pmid = {36118221}, issn = {1664-302X}, abstract = {An agarase gene (aga1904) that codes a protein with 640 amino acids was obtained from the metagenomic library of macroalgae-associated bacteria collected from King George Island, Antarctica. Gene aga1904 was expressed in Escherichia coli BL21 (DE3) and recombinant Aga1904 was purified by His Bind Purification kit. The optimal temperature and pH for the activity of Aga1904 were 50°C and 6.0, respectively. Fe[3+] and Cu[2+] significantly inhibited the activity of Aga1904. The V max and K m values of recombinant Aga1904 were 108.70 mg/ml min and 6.51 mg/ml, respectively. The degradation products of Aga1904 against agarose substrate were mainly neoagarobiose, neoagarotetraose, and neoagarohexaose analyzed by thin layer chromatography. The cellular immunoassay of enzymatic hydrolysates was subsequently carried out, and the results showed that agaro-oligosaccharides dominated by neoagarobiose significantly inhibited key pro-inflammatory markers including, nitric oxide (NO), interleukins 6 (IL-6), and tumor necrosis factor α (TNF-α). This work provides a promising candidate for development recombinant industrial enzyme to prepare agaro-oligosaccharides, and paved up a new path for the exploitation of natural anti-inflammatory agent in the future.}, } @article {pmid36118217, year = {2022}, author = {Achee, NL and , }, title = {The Remote Emerging Disease Intelligence-NETwork.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {961065}, pmid = {36118217}, issn = {1664-302X}, abstract = {Accurate prediction of zoonotic spillover events requires a detailed understanding of baseline pathogens circulating in differing global environments. By characterizing the diversity and determining the natural baseline of pathogens in a given biological system, any perturbations to this balance can be detected, leading to estimates of risk for emerging diseases. As epidemics and probability for pandemics increase, there is a fundamental need for building global collaborations to fill gaps in the surveillance effort, especially to build remote in-county capacity and standardize timely sample processing and data analysis. To this point, a new consortium, the Remote Emerging Disease Intelligence-NETwork (REDI-NET) has been established to enhance surveillance approaches and characterize natural pathogens in temperate, tropical forest, and tropical grassland biomes. The REDI-NET is envisioned to be a long-term, phased initiative. All phases will integrate accompanying training resources such as videos reflecting SOPs and Quick Reference Guides. Routine bio- and xenosurveillance will facilitate the characterization of ecological parameters, enhance the accuracy of vector species identification using artificial intelligence technology, and guide the establishment of epidemiological risk thresholds critical for mitigating disease outbreaks in a timely manner. A key deliverable of the REDI-NET is a custom-designed electronically merged (e-MERGE) data pipeline and alert dashboard that integrates remotely captured data with state-of-the-art metagenomic next-generation sequencing technology. This pipeline incorporates data generated from field and laboratory best practices, to furnish health decision-makers with a centralized, timely, and rigorous database to efficiently search interdisciplinary and heterogeneous data sources necessary to alert, prepare and mitigate health threats. The e-MERGE pipeline, once fully established, will be a flexible, scalable, and expandable tool for varied health applications. Program success will result in an operational framework that addresses resource gaps in pathogen surveillance and enhances health protection with broad global applicability. The objective of this manuscript is to introduce the REDI-NET framework to anticipated stakeholders engaged in metagenomics, epidemiological surveillance, and One Health with a focus on Phase 1.}, } @article {pmid36118036, year = {2022}, author = {Jiang, J and Yang, W and Wu, Y and Peng, W and Zhang, W and Pan, P and Hu, C and Li, Y and Li, Y}, title = {Metagenomic next-generation sequencing for identifying pathogens in patients with rheumatic diseases and diffuse pulmonary lesions: A retrospective diagnostic study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {963611}, pmid = {36118036}, issn = {2235-2988}, mesh = {Anti-Bacterial Agents ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Lung/diagnostic imaging ; Middle Aged ; *Pneumonia ; Retrospective Studies ; *Rheumatic Diseases/diagnosis ; Sensitivity and Specificity ; }, abstract = {OBJECTIVE: Lung involvement is a major cause of morbidity and mortality in patients with rheumatic diseases. This study aimed to assess the application value of metagenomic next-generation sequencing (mNGS) for identifying pathogens in patients with rheumatic diseases and diffuse pulmonary lesions.

METHODS: This retrospective study included patients who were diagnosed with rheumatic diseases and presenting diffuse pulmonary lesions on chest radiography in Xiangya Hospital from July 2018 to May 2022. Clinical characteristics were summarized, including demographics, symptoms, comorbidities, radiological and laboratory findings, and clinical outcomes. Pulmonary infection features of these patients were analyzed. Furthermore, diagnostic performance of mNGS and conventional methods (including smear microscopy, culture, polymerase chain reaction assay, and serum immunological test) in identifying pulmonary infections and causative pathogens were compared.

RESULTS: A total of 98 patients were included, with a median age of 58.0 years old and a female proportion of 59.2%. Of these patients, 71.4% showed the evidence of pulmonary infections. Combining the results of mNGS and conventional methods, 129 infection events were detected, including 45 bacterial, 40 fungal and 44 viral infection events. Pulmonary mixed infections were observed in 38.8% of patients. The detection rates of mNGS for any pathogen (71.4% vs 40.8%, P < 0.001) and mixed pathogens (40.8% vs 12.2%, P < 0.001) were higher than that of conventional methods. Moreover, mNGS had a significantly higher sensitivity (97.1% vs. 57.1%, P < 0.001) than conventional methods in identifying pulmonary infections, while its specificity (92.9% vs. 96.4%, P = 0.553) were comparable to conventional methods. Antimicrobial and antirheumatic treatments were markedly modified based on mNGS results in patients with rheumatic diseases and diffuse pulmonary lesions.

CONCLUSIONS: For patients diagnosed with rheumatic diseases and presenting diffuse pulmonary lesions, mNGS is a powerful complement to conventional methods in pathogen identification due to its high efficiency and broad spectrum. Early application of mNGS can provide guidance for precision treatment, and may reduce mortality and avoid antibiotic abuse.}, } @article {pmid36118026, year = {2022}, author = {Jiao, M and Ma, X and Li, Y and Wang, H and Liu, Y and Guo, W and Lv, J}, title = {Metagenomic next-generation sequencing provides prognostic warning by identifying mixed infections in nocardiosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {894678}, pmid = {36118026}, issn = {2235-2988}, mesh = {*Coinfection ; *Communicable Diseases ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Nocardia Infections/diagnosis ; Prognosis ; Retrospective Studies ; }, abstract = {Nocardia is an opportunistic pathogen that mainly involves immunosuppressed patients and causes a high mortality rate. As an emerging approach to detect infectious pathogens, metagenomic next-generation sequencing (mNGS) was reported in the detection of Nocardia. However, there is no evidence demonstrating the effect of mNGS on the prognosis of Nocardia infection. In this retrospective study, we included 18 nocardiosis patients. Nocardia species were detected by mNGS from their clinical samples. All the patients were diagnosed with nocardiosis by clinical experts through a comprehensive evaluation. Of these 18 patients, fever is the most frequent initial symptom. Compared to traditional culture methods, mNGS provides a faster turnaround time (TAT) and higher sensitivity. Pulmonary nocardiosis was the most common clinical presentation in the study. mNGS detected 13 types of Nocardia species, of which Nocardia abscessus and Nocardia cyriacigeorgica were the most common species. The study's most noteworthy discovery is that mNGS outperforms culture at detecting mixed infections (more than one pathogen detected in one clinical specimen, including bacteria, fungi, and excluding virus), and number of infectious species was an independent risk factor for nocardiosis patients' prognostics after adjusting age, ICU days, gender and underlying diseases (adjusted HR = 1.47, 95% CI: 1.09-1.98, p = 0.011). As a result, we believe that by detecting mixed infections (more than one pathogenic species), mNGS can provide a clinical risk warning for the prognosis of nocardiosis.}, } @article {pmid36116646, year = {2023}, author = {Kozjek, M and Vengust, D and Radošević, T and Žitko, G and Koren, S and Toplak, N and Jerman, I and Butala, M and Podlogar, M and Viršek, MK}, title = {Dissecting giant hailstones: A glimpse into the troposphere with its diverse bacterial communities and fibrous microplastics.}, journal = {The Science of the total environment}, volume = {856}, number = {Pt 1}, pages = {158786}, doi = {10.1016/j.scitotenv.2022.158786}, pmid = {36116646}, issn = {1879-1026}, mesh = {Microplastics ; Plastics/chemistry ; RNA, Ribosomal, 16S ; Bacteria ; *Environmental Pollutants ; *Water Pollutants, Chemical/analysis ; Environmental Monitoring ; }, abstract = {The formation of giant hailstones is a rare weather event that has devastating consequences in inhabited areas. This hazard has been occurring more frequently and with greater size of hailstones in recent years, and thus needs to be better understood. While the generally accepted mechanism is thought to be a process similar to the formation of smaller hailstones but with exceptional duration and stronger updrafts, recent evidence suggests that biotic and abiotic factors also influence the growth of these unusually large ice chunks. In this study, we improved these findings by determining the distribution of a wide variety of these factors throughout the hail volume and expanding the search to include new particles that are common in the environment and are of anthropogenic origin. We melted the concentric layers of several giant hailstones that fell to the ground over a small region in Slovenia in 2019. The samples, up to 13 cm in diameter, were analyzed for biotic and abiotic constituents that could have influenced their formation. Using 16S rRNA-based metagenomics approaches, we identified a highly diverse bacterial community, and by using scanning electron microscopy and Raman spectroscopy, we found natural and synthetic fibers concentrated in the cores of the giant hailstones. For the first time, we were able to detect the existence of microplastic fibers in giant hailstones and determine the changes in the distribution of sand within the volume of the samples. Our results suggest that changes in the composition of hail layers and their great diversity are important factors that should be considered in research. It also appears that anthropogenic microfiber pollutants were a significant factor in the formation of the giant hailstones analyzed in this study.}, } @article {pmid36116499, year = {2022}, author = {Singh, A and Varma, A and Prasad, R and Porwal, S}, title = {Bioprospecting uncultivable microbial diversity in tannery effluent contaminated soil using shotgun sequencing and bio-reduction of chromium by indigenous chromate reductase genes.}, journal = {Environmental research}, volume = {215}, number = {Pt 2}, pages = {114338}, doi = {10.1016/j.envres.2022.114338}, pmid = {36116499}, issn = {1096-0953}, mesh = {Bacteria/genetics ; Biodegradation, Environmental ; Bioprospecting ; Chromium/analysis ; Cytosine ; DNA ; Guanine ; *Nucleic Acids ; Oxidoreductases ; Phylogeny ; Soil/chemistry ; *Soil Pollutants/analysis/toxicity ; }, abstract = {The tannery industry generates a consequential threat to the environment by producing a large amount of potentially toxic metal-containing waste. Bioremediation has been a promising approach for treating potentially toxic metals, but the efficiency of remediation in microbes is one of the factors limiting their application in tanneries waste treatment. The motivation behind the present work was to explore the microbial diversity and chromate reductase genes present in the tannery effluent-contaminated soil using metagenomics approach. The use of shotgun sequencing enabled the identification of operational parameters that influence microbiome composition and their ability to reduce Chromium (Cr) concentration. The Cr concentration in Kanpur tannery effluent contaminated soil sample was 700 ppm which is many folds than the approved permissible limit by World Health Organisation (WHO) for Cr is 100 ppm. Metagenomic Deoxyribo Nucleic Acid (DNA) was extracted to explore taxonomic community structure, phylogenetic linkages, and functional profile. With a Guanine-Cytosine (GC) abundance of 54%, total of 45,163,604 high-quality filtered reads were obtained. Bacteria (83%), Archaebacteria (14%), and Viruses (3%) were discovered in the structural biodiversity. Bacteria were classified to phylum level, with Proteobacteria (52%) being the dominant population, followed by Bacteriodetes (15%), Chloroflexi (15%), Spirochaetes (7%), Thermotogae (5%), Actinobacteria (4%), and Firmicutes (1%). The OXR genes were cloned and checked for their efficiency to reduce Cr concentration. Insitu validation of OXR8 gene showed a reduction of Cr concentration from 700 ppm to 24 ppm in 72 h (96.51% reduction). The results of this study suggests that there is a huge reservoir of microbes and chromate reductase genes which are unexplored yet.}, } @article {pmid36116269, year = {2022}, author = {Gül, F and Karadayı, S and Yurdabakan, Z and Özbek, T and Karadayı, B}, title = {Investigating changes in salivary microbiota due to dental treatment: A metagenomic analysis study for forensic purposes.}, journal = {Forensic science international}, volume = {340}, number = {}, pages = {111447}, doi = {10.1016/j.forsciint.2022.111447}, pmid = {36116269}, issn = {1872-6283}, mesh = {Adolescent ; Adult ; Bacteria/genetics ; *Dental Caries ; Humans ; Metagenomics/methods ; *Microbiota/genetics ; Middle Aged ; RNA, Ribosomal, 16S/genetics ; Saliva/microbiology ; Young Adult ; }, abstract = {The advent of next generation sequencing techniques as well as the existing traditional culture methods has enabled metagenomic studies on the usability of microbiomes for the forensic identification of individuals to gain momentum. However, before the utilization of microbiomes as a potential technique for real forensic case resolutions, it is necessary to understand the stability of the microbiota compositions in an individual's biological samples and the factors responsible for their variations. In the present study, we compared the microbiota compositions present in the saliva of individuals with active dental caries before and after treatment from a forensic and clinical perspective using an approach based on the sequencing of all the variable regions (V1-V9) of the bacterial 16 S rRNA gene. For this purpose, 10 individuals were included in the study comprising of 8 individuals between the ages of 18-50 years with at least 3 deep dentin caries as patients and 2 healthy individuals without any dental or gingival diseases as controls. Saliva samples were collected from the patients at two timepoints, before and after treatment, as well as from the healthy individuals (before and after control) at an interval of 1 month. The collected 20 saliva samples were subjected to metagenomic analysis using the MinION device, which was developed by Oxford Nanopore Technologies (ONT Oxford, UK). Bioinformatic analyses were performed on the obtained data and the results were evaluated using statistical comparison methods and alpha/beta diversity analyses within the scope of the study objective. On evaluation using the distance metrics, it was observed that the microbial compositions in the saliva of individuals with active caries remained relatively stable after treatment. However, the relative abundance levels of bacteria of 28 genera and species showed statistically significant differences before and after treatment (p < 0.05). As a result, although the composition of salivary microbiome remained relatively stable after caries treatment, there were significant changes in many types of bacteria, especially at the species level, between the BT and AT samples. Our results provide a framework for further forensic and clinical investigations regarding the factors that affect human salivary microbiome diversity.}, } @article {pmid36116192, year = {2022}, author = {Wang, D and Meng, Y and Meng, F}, title = {Genome-centric metagenomics insights into functional divergence and horizontal gene transfer of denitrifying bacteria in anammox consortia.}, journal = {Water research}, volume = {224}, number = {}, pages = {119062}, doi = {10.1016/j.watres.2022.119062}, pmid = {36116192}, issn = {1879-2448}, mesh = {Amino Acids ; Anaerobic Ammonia Oxidation ; Animals ; Bacteria/metabolism ; *Bioreactors/microbiology ; Biotin/genetics/metabolism ; Carbohydrates ; Denitrification ; *Gene Transfer, Horizontal ; Metagenomics ; Methionine/genetics/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Swine ; Thiamine/metabolism ; Vitamins/metabolism ; }, abstract = {Denitrifying bacteria with high abundances in anammox communities play crucial roles in achieving stable anammox-based systems. Despite the relative constant composition of denitrifying bacteria, their functional diversity remains to be explored in anammox communities. Herein, a total of 77 high-quality metagenome-assembled genomes (MAGs) of denitrifying bacteria were recovered from the anammox community in a full-scale swine wastewater treatment plant. Among these microbes, a total of 26 MAGs were affiliated with the seven dominant denitrifying genera that have total abundances higher than 1%. A meta-analysis of these species suggested that external organics reduced the abundances of genus Ignavibacterium and species MAG.305 of UTPRO2 in anammox communities. Comparative genome analysis revealed functional divergence across different denitrifying bacteria, largely owing to their distinct capabilities for carbohydrate (including endogenous and exogenous) utilization and vitamin (e.g., pantothenate and thiamine) biosynthesis. Serval microbes in this system contained fewer genes encoding biotin, pantothenate and methionine biosynthesis compared with their related species from other habitats. In addition, the genes encoding energy production and conversion (73 genes) and inorganic ion transport (53 genes) putatively transferred from other species to denitrifying bacteria, while these denitrifying bacteria (especially genera UTPRO2 and SCN-69-89) likely donated the genes encoding nutrients (e.g., inorganic ion and amino acid) transporter (64 genes) for other members to utilize new metabolites. Collectively, these findings highlighted the functional divergence of these denitrifying bacteria and speculated that the genetic interactions within anammox communities through horizontal gene transfer may be one of the reasons for their functional divergence.}, } @article {pmid36115643, year = {2022}, author = {Hijazi, G and Dakroub, F and Khoueiry, P and El-Kurdi, A and Ezzeddine, A and Alkalamouni, H and Alansari, K and Althani, AA and Mathew, S and AlKhatib, HA and Yassine, HM and Zaraket, H}, title = {Viral metagenomics analysis of stool specimens from children with unresolved gastroenteritis in Qatar.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {105}, number = {}, pages = {105367}, doi = {10.1016/j.meegid.2022.105367}, pmid = {36115643}, issn = {1567-7257}, mesh = {Humans ; Child ; Infant ; Child, Preschool ; Qatar/epidemiology ; Feces ; *Gastroenteritis/diagnosis/epidemiology ; *Rotavirus/genetics ; *Viruses/genetics ; }, abstract = {Acute gastroenteritis (AGE) is associated with significant global morbidity and mortality, especially among children under five years of age. Viruses are well established as etiologic agents of gastroenteritis since they are the most common pathogens that contribute to the disease burden in developing countries. Despite the advances in molecular diagnosis, a substantial proportion of AGE etiology remain unresolved. We implemented a viral metagenomics pipeline to determine the potential viral etiology associated with AGE among children under the age of five years in Qatar with undiagnosed etiology. Following enriching for the viral genome, ∼1.3 billion sequences were generated from 89 stool specimens using the Illumina HiSeq platform, of which 7% were mapped to viral genomes. Human viruses were detected in 34 specimens (38.2%); 14 were adenovirus, nine coxsackievirus A16, five rotavirus (G9P[8] and G4P[8]), four norovirus (GII), one influenza A virus (H3), and one respiratory syncytial virus A (RSVA). In conclusion, the viral metagenomics approach is useful for determining AGE's etiology when routine molecular diagnostic assays fail.}, } @article {pmid36115596, year = {2022}, author = {Guman, MSS and Hoozemans, JB and Haal, S and de Jonge, PA and Aydin, Ö and Lappa, D and Meijnikman, AS and Westerink, F and Acherman, Y and Bäckhed, F and de Brauw, M and Nielsen, J and Nieuwdorp, M and Groen, AK and Gerdes, VEA}, title = {Adipose Tissue, Bile Acids, and Gut Microbiome Species Associated With Gallstones After Bariatric Surgery.}, journal = {Journal of lipid research}, volume = {63}, number = {11}, pages = {100280}, pmid = {36115596}, issn = {1539-7262}, mesh = {Humans ; *Gallstones/etiology/surgery ; *Gastrointestinal Microbiome/genetics ; Bile Acids and Salts ; Longitudinal Studies ; *Bariatric Surgery/adverse effects ; Adipose Tissue ; Bacteria ; }, abstract = {Several risk factors are associated with gallstone disease after bariatric surgery, but the underlying pathophysiological mechanisms of gallstone formation are unclear. We hypothesize that gallstone formation after bariatric surgery is induced by different pathways compared with gallstone formation in the general population, since postoperative formation occurs rapidly in patients who did not develop gallstones in preceding years. To identify both pathophysiological and potentially protective mechanisms against postoperative gallstone formation, we compared the preoperative fasting metabolome, fecal microbiome, and liver and adipose tissue transcriptome obtained before or during bariatric surgery of obese patients with and without postoperative gallstones. In total, 88 patients were selected from the BARIA longitudinal cohort study. Within this group, 32 patients had postoperative gallstones within 2 years. Gut microbiota metagenomic analyses showed group differences in abundance of 41 bacterial species, particularly abundance of Lactobacillaceae and Enterobacteriaceae in patients without gallstones. Subcutaneous adipose tissue transcriptomic analyses revealed four genes that were suppressed in gallstone patients compared with patients without gallstones. These baseline gene expression and gut microbiota composition differences might relate to protective mechanisms against gallstone formation after bariatric surgery. Moreover, baseline fasting blood samples of patients with postoperative gallstones showed increased levels of several bile acids. Overall, we revealed different genes and bacteria associated with gallstones than those previously reported in the general population, supporting the hypothesis that gallstone formation after bariatric surgery follows a different trajectory. Further research is necessary to confirm the involvement of the bile acids, adipose tissue activity, and microbial species observed here.}, } @article {pmid36115554, year = {2022}, author = {Perez-Marron, J and Sanders, C and Gomez, E and Escopete, S and Owerkowicz, T and Orwin, PM}, title = {Community and shotgun metagenomic analysis of Alligator mississippiensis oral cavity and GI tracts reveal complex ecosystems and potential reservoirs of antibiotic resistance.}, journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology}, volume = {274}, number = {}, pages = {111319}, doi = {10.1016/j.cbpa.2022.111319}, pmid = {36115554}, issn = {1531-4332}, mesh = {*Alligators and Crocodiles/genetics ; Animals ; *Colorectal Neoplasms ; Drug Resistance, Microbial ; Humans ; Metagenomics/methods ; *Microbiota/genetics ; Mouth/microbiology ; }, abstract = {We report here the community structure and functional analysis of the microbiome of the Alligator mississippiensis GI tract from the oral cavity through the entirety of the digestive tract. Although many vertebrate microbiomes have been studied in recent years, the archosaur microbiome has only been given cursory attention. In the oral cavity we used amplicon-based community analysis to examine the structure of the oral microbiome during alligator development. We found a community that diversified over time and showed many of the hallmarks we would expect of a stable oral community. This is a bit surprising given the rapid turnover of alligator teeth but suggests that the stable gumline microbes are able to rapidly colonize the emerging teeth. As we move down the digestive tract, we were able to use both long and short read sequencing approaches to evaluate the community using a shotgun metagenomics approach. Long read sequencing was applied to samples from the stomach/duodenum, and the colorectal region, revealing a fairly uniform and low complexity community made up primarily of proteobacteria at the top of the gut and much more diversity in the colon. We used deep short read sequencing to further interrogate this colorectal community. The two sequencing approaches were concordant with respect to community structure but substantially more detail was available in the short read data, in spite of high levels of host DNA contamination. Using both approaches we were able to show that the colorectal community is a potential reservoir for antibiotic resistance, human pathogens such as Clostridiodes difficile and a possible source of novel antimicrobials or other useful secondary metabolites.}, } @article {pmid36115504, year = {2022}, author = {Cheng, Q and Fan, C and Liu, F and Li, Y and Hou, H and Ma, Y and Tan, Y and Li, Y and Hai, Y and Wu, T and Zhang, L and Zhang, Y}, title = {Structural and functional dysbiosis of gut microbiota in Tibetan subjects with coronary heart disease.}, journal = {Genomics}, volume = {114}, number = {6}, pages = {110483}, doi = {10.1016/j.ygeno.2022.110483}, pmid = {36115504}, issn = {1089-8646}, mesh = {Humans ; *Coronary Disease ; *Lysine ; }, abstract = {The gut microbiota plays a crucial role in coronary heart disease (CHD). However, only a few studies focusing on the relationship between gut microbiota and CHD in ethnic populations are available. Here, we employed shotgun sequencing of the gut metagenome to analyze the taxonomic composition and functional annotation of the gut microbiota of 14 CHD patients, 13 patients with non-stenosis coronary heart disease (NCHD), and 18 healthy controls (HT) in Tibetan subjects. We found that the α-diversity of the gut microbiota was not significantly different among the three groups., whereas β-diversity was significantly altered in the CHD group compared with HT. Based on the receiver operating characteristic curve (ROC) analysis, the relative abundance of Proteobacteria species effectively distinguished patients with CHD from the control group. Most of the enriched species belonged to Proteobacteria. The pathways that contributed the most to the differences between groups were amino acid metabolism-related pathways, especially lysine biosynthesis. The enzymes of the lysine biosynthesis pathway, including K01714 and K00821, were significantly decreased in the CHD group. Our findings increase the understanding of the association between CHD pathogenesis and gut microbiota in the Tibetan population, thus paving the way for the development of improved diagnostic methods and treatments for Tibetan patients with CHD.}, } @article {pmid36115338, year = {2022}, author = {Pedersen, TK and Brown, EM and Plichta, DR and Johansen, J and Twardus, SW and Delorey, TM and Lau, H and Vlamakis, H and Moon, JJ and Xavier, RJ and Graham, DB}, title = {The CD4[+] T cell response to a commensal-derived epitope transitions from a tolerant to an inflammatory state in Crohn's disease.}, journal = {Immunity}, volume = {55}, number = {10}, pages = {1909-1923.e6}, pmid = {36115338}, issn = {1097-4180}, support = {R01 DK126910/DK/NIDDK NIH HHS/United States ; U19 AI110495/AI/NIAID NIH HHS/United States ; P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 DK127171/DK/NIDDK NIH HHS/United States ; R01 HL157717/HL/NHLBI NIH HHS/United States ; R01 DK097485/DK/NIDDK NIH HHS/United States ; }, mesh = {CD4-Positive T-Lymphocytes ; *Crohn Disease ; Epitopes, T-Lymphocyte ; Humans ; *Immunodominant Epitopes ; Interleukin-10 ; Interleukin-17 ; }, abstract = {Reciprocal interactions between host T helper cells and gut microbiota enforce local immunological tolerance and modulate extra-intestinal immunity. However, our understanding of antigen-specific tolerance to the microbiome is limited. Here, we developed a systematic approach to predict HLA class-II-specific epitopes using the humanized bacteria-originated T cell antigen (hBOTA) algorithm. We identified a diverse set of microbiome epitopes spanning all major taxa that are compatible with presentation by multiple HLA-II alleles. In particular, we uncovered an immunodominant epitope from the TonB-dependent receptor SusC that was universally recognized and ubiquitous among Bacteroidales. In healthy human subjects, SusC-reactive T cell responses were characterized by IL-10-dominant cytokine profiles, whereas in patients with active Crohn's disease, responses were associated with elevated IL-17A. Our results highlight the potential of targeted antigen discovery within the microbiome to reveal principles of tolerance and functional transitions during inflammation.}, } @article {pmid36114063, year = {2023}, author = {Li, J and Lin, Z and Liang, B and Zhan, W and Han, X and Guan, R and Jian, X}, title = {Identification of Enterocytozoon bieneusi in an HIV-negative bronchiectasis patient with respiratory infection based on metagenomic next-generation sequencing: A case report.}, journal = {Indian journal of medical microbiology}, volume = {42}, number = {}, pages = {97-99}, doi = {10.1016/j.ijmmb.2022.07.017}, pmid = {36114063}, issn = {1998-3646}, mesh = {Humans ; *Enterocytozoon/genetics ; Albendazole ; High-Throughput Nucleotide Sequencing ; *HIV Seropositivity ; *Microsporidiosis/diagnosis ; Genotype ; Feces ; Phylogeny ; China ; Prevalence ; }, abstract = {Bronchiectasis is often caused by serious infections. Infections caused by Enterocytozoon bieneusi (E. bieneusi) is most common in the immunocompromised host, such as HIV-positive patients. Herein, we reported an HIV-negative patient with bronchiectasis infected with E. bieneusi, which diagnosed by mNGS and validated by Sanger sequencing. During the treatment of albendazole, the patient gradually recovered. This is the first report of a case of respiratory E. bieneusi infection in a bronchiectasis patient. This finding highlights the efficacy of mNGS for pathogen diagnosis in bronchiectasis patients and the potential treatment option of albendazole for bronchiectasis patients with E. bieneusi infection.}, } @article {pmid36113855, year = {2022}, author = {Isaac, AL and Tritto, M and Colwell, RR and Armstrong, DG}, title = {Metagenomics of diabetic foot ulcer undergoing treatment with total contact casting: a case study.}, journal = {Journal of wound care}, volume = {31}, number = {Sup9}, pages = {S45-S49}, doi = {10.12968/jowc.2022.31.Sup9.S45}, pmid = {36113855}, issn = {0969-0700}, mesh = {Anti-Bacterial Agents/therapeutic use ; *Diabetes Mellitus/drug therapy ; *Diabetic Foot/microbiology ; Humans ; *Microbiota/genetics ; Tetracyclines ; Wound Healing ; }, abstract = {OBJECTIVE: Diabetic foot ulcers (DFUs) are characterised by the presence of many microbes, some of which may not be identified by traditional culture techniques. Total contact casting (TCC) remains the gold-standard for offloading, yet little is known about the microbiome of wounds that progress from hard-to-heal to closed within a TCC.

METHOD: A patient with a DFU underwent weekly treatment with TCC to closure. Samples for next-generation sequencing (NGS) and bioinformatics analysis of tissue samples were collected during each visit. Detection, identification, characterisation of the microbial community and abundance of microbes in each sample were compared.

RESULTS: Abundance of microbes, identified by species and strain, changed with each treatment visit. By the final week of treatment, species diversity of the wound microbiome had decreased significantly, highlighted by an observed decrease in the number of total microorganisms present. Resistance genes for tetracyclines were detected in the first sample, but not in subsequent samples.

CONCLUSION: The results of this study suggest dynamic microbiological changes associated with DFUs as they progress to healing within a TCC. As NGS becomes more readily available, further studies will be helpful to gain an improved understanding of the significance of the wound microbiome in patients with DFUs.}, } @article {pmid36113426, year = {2022}, author = {, and , }, title = {Gut microbiome of multiple sclerosis patients and paired household healthy controls reveal associations with disease risk and course.}, journal = {Cell}, volume = {185}, number = {19}, pages = {3467-3486.e16}, pmid = {36113426}, issn = {1097-4172}, support = {R01 NS087226/NS/NINDS NIH HHS/United States ; R01 NS098023/NS/NINDS NIH HHS/United States ; R01 NS124882/NS/NINDS NIH HHS/United States ; R35 NS111644/NS/NINDS NIH HHS/United States ; }, mesh = {Fatty Acids, Volatile ; *Gastrointestinal Microbiome ; Humans ; Interferon-beta ; *Multiple Sclerosis ; Phytic Acid ; Pyruvates ; }, abstract = {Changes in gut microbiota have been associated with several diseases. Here, the International Multiple Sclerosis Microbiome Study (iMSMS) studied the gut microbiome of 576 MS patients (36% untreated) and genetically unrelated household healthy controls (1,152 total subjects). We observed a significantly increased proportion of Akkermansia muciniphila, Ruthenibacterium lactatiformans, Hungatella hathewayi, and Eisenbergiella tayi and decreased Faecalibacterium prausnitzii and Blautia species. The phytate degradation pathway was over-represented in untreated MS, while pyruvate-producing carbohydrate metabolism pathways were significantly reduced. Microbiome composition, function, and derived metabolites also differed in response to disease-modifying treatments. The therapeutic activity of interferon-β may in part be associated with upregulation of short-chain fatty acid transporters. Distinct microbial networks were observed in untreated MS and healthy controls. These results strongly support specific gut microbiome associations with MS risk, course and progression, and functional changes in response to treatment.}, } @article {pmid36113358, year = {2022}, author = {Wojciechowski, S and Majchrzak-Górecka, M and Biernat, P and Odrzywołek, K and Pruss, Ł and Zych, K and Jan Majta, and Milanowska-Zabel, K}, title = {Machine learning on the road to unlocking microbiota's potential for boosting immune checkpoint therapy.}, journal = {International journal of medical microbiology : IJMM}, volume = {312}, number = {7}, pages = {151560}, doi = {10.1016/j.ijmm.2022.151560}, pmid = {36113358}, issn = {1618-0607}, mesh = {Humans ; *Microbiota ; *Gastrointestinal Microbiome ; Treatment Outcome ; Machine Learning ; Dysbiosis ; }, abstract = {The intestinal microbiota is a complex and diverse ecological community that fulfills multiple functions and substantially impacts human health. Despite its plasticity, unfavorable conditions can cause perturbations leading to so-called dysbiosis, which have been connected to multiple diseases. Unfortunately, understanding the mechanisms underlying the crosstalk between those microorganisms and their host is proving to be difficult. Traditionally used bioinformatic tools have difficulties to fully exploit big data generated for this purpose by modern high throughput screens. Machine Learning (ML) may be a potential means of solving such problems, but it requires diligent application to allow for drawing valid conclusions. This is especially crucial as gaining insight into the mechanistic basis of microbial impact on human health is highly anticipated in numerous fields of study. This includes oncology, where growing amounts of studies implicate the gut ecosystems in both cancerogenesis and antineoplastic treatment outcomes. Based on these reports and first signs of clinical benefits related to microbiota modulation in human trials, hopes are rising for the development of microbiome-derived diagnostics and therapeutics. In this mini-review, we're inspecting analytical approaches used to uncover the role of gut microbiome in immune checkpoint therapy (ICT) with the use of shotgun metagenomic sequencing (SMS) data.}, } @article {pmid36112576, year = {2022}, author = {Váradi, A and Kaszab, E and Kardos, G and Prépost, E and Szarka, K and Laczkó, L}, title = {Rapid genotyping of targeted viral samples using Illumina short-read sequencing data.}, journal = {PloS one}, volume = {17}, number = {9}, pages = {e0274414}, pmid = {36112576}, issn = {1932-6203}, mesh = {Genome ; Genotype ; *High-Throughput Nucleotide Sequencing/methods ; *Software ; }, abstract = {The most important information about microorganisms might be their accurate genome sequence. Using current Next Generation Sequencing methods, sequencing data can be generated at an unprecedented pace. However, we still lack tools for the automated and accurate reference-based genotyping of viral sequencing reads. This paper presents our pipeline designed to reconstruct the dominant consensus genome of viral samples and analyze their within-host variability. We benchmarked our approach on numerous datasets and showed that the consensus genome of samples could be obtained reliably without further manual data curation. Our pipeline can be a valuable tool for fast identifying viral samples. The pipeline is publicly available on the project's GitHub page (https://github.com/laczkol/QVG).}, } @article {pmid36112078, year = {2023}, author = {Stothart, MR and McLoughlin, PD and Poissant, J}, title = {Shallow shotgun sequencing of the microbiome recapitulates 16S amplicon results and provides functional insights.}, journal = {Molecular ecology resources}, volume = {23}, number = {3}, pages = {549-564}, doi = {10.1111/1755-0998.13713}, pmid = {36112078}, issn = {1755-0998}, support = {D20EQ-051//Morris Animal Foundation/ ; 2016-06459//Natural Sciences and Engineering Research Council of Canada/ ; 2019-04388//Natural Sciences and Engineering Research Council of Canada/ ; }, mesh = {Animals ; Horses/genetics ; RNA, Ribosomal, 16S/genetics ; *High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; Metagenome ; Bacteria ; Metagenomics/methods ; }, abstract = {Prevailing 16S rRNA gene-amplicon methods for characterizing the bacterial microbiome of wildlife are economical, but result in coarse taxonomic classifications, are subject to primer and 16S copy number biases, and do not allow for direct estimation of microbiome functional potential. While deep shotgun metagenomic sequencing can overcome many of these limitations, it is prohibitively expensive for large sample sets. Here we evaluated the ability of shallow shotgun metagenomic sequencing to characterize taxonomic and functional patterns in the faecal microbiome of a model population of feral horses (Sable Island, Canada). Since 2007, this unmanaged population has been the subject of an individual-based, long-term ecological study. Using deep shotgun metagenomic sequencing, we determined the sequencing depth required to accurately characterize the horse microbiome. In comparing conventional vs. high-throughput shotgun metagenomic library preparation techniques, we validate the use of more cost-effective laboratory methods. Finally, we characterize similarities between 16S amplicon and shallow shotgun characterization of the microbiome, and demonstrate that the latter recapitulates biological patterns first described in a published amplicon data set. Unlike for amplicon data, we further demonstrate how shallow shotgun metagenomic data provide useful insights regarding microbiome functional potential which support previously hypothesized diet effects in this study system.}, } @article {pmid36111782, year = {2022}, author = {de Nies, L and Busi, SB and Kunath, BJ and May, P and Wilmes, P}, title = {Mobilome-driven segregation of the resistome in biological wastewater treatment.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {36111782}, issn = {2050-084X}, mesh = {Humans ; Drug Resistance, Microbial/genetics ; Wastewater ; *Fosfomycin ; Bacitracin ; Metagenomics ; *Water Purification ; Anti-Bacterial Agents/pharmacology ; *Bacteriophages/genetics ; Aminoglycosides ; Sulfonamides ; Genes, Bacterial ; }, abstract = {Biological wastewater treatment plants (BWWTP) are considered to be hotspots for the evolution and subsequent spread of antimicrobial resistance (AMR). Mobile genetic elements (MGEs) promote the mobilization and dissemination of antimicrobial resistance genes (ARGs) and are thereby critical mediators of AMR within the BWWTP microbial community. At present, it is unclear whether specific AMR categories are differentially disseminated via bacteriophages (phages) or plasmids. To understand the segregation of AMR in relation to MGEs, we analyzed meta-omic (metagenomic, metatranscriptomic and metaproteomic) data systematically collected over 1.5 years from a BWWTP. Our results showed a core group of 15 AMR categories which were found across all timepoints. Some of these AMR categories were disseminated exclusively (bacitracin) or primarily (aminoglycoside, MLS and sulfonamide) via plasmids or phages (fosfomycin and peptide), whereas others were disseminated equally by both. Combined and timepoint-specific analyses of gene, transcript and protein abundances further demonstrated that aminoglycoside, bacitracin and sulfonamide resistance genes were expressed more by plasmids, in contrast to fosfomycin and peptide AMR expression by phages, thereby validating our genomic findings. In the analyzed communities, the dominant taxon Candidatus Microthrix parvicella was a major contributor to several AMR categories whereby its plasmids primarily mediated aminoglycoside resistance. Importantly, we also found AMR associated with ESKAPEE pathogens within the BWWTP, and here MGEs also contributed differentially to the dissemination of the corresponding ARGs. Collectively our findings pave the way toward understanding the segmentation of AMR within MGEs, thereby shedding new light on resistome populations and their mediators, essential elements that are of immediate relevance to human health.}, } @article {pmid36111438, year = {2022}, author = {Wu, Y and Li, A and Liu, H and Zhang, Z and Zhang, C and Ma, C and Zhang, L and Zhang, J}, title = {Lactobacillus plantarum HNU082 alleviates dextran sulfate sodium-induced ulcerative colitis in mice through regulating gut microbiome.}, journal = {Food & function}, volume = {13}, number = {19}, pages = {10171-10185}, doi = {10.1039/d2fo02303b}, pmid = {36111438}, issn = {2042-650X}, mesh = {Animals ; Claudin-1/metabolism ; Claudin-2/metabolism ; *Colitis/metabolism ; *Colitis, Ulcerative/pathology ; Colon/metabolism ; Dextran Sulfate/adverse effects ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Humans ; Intercellular Adhesion Molecule-1/metabolism ; Interleukin-10/metabolism ; Interleukin-6/metabolism ; *Lactobacillus plantarum/metabolism ; Mice ; Mice, Inbred C57BL ; NF-kappa B/metabolism ; Peroxidase/metabolism ; RNA, Messenger/metabolism ; Transforming Growth Factor beta1/metabolism ; Transforming Growth Factor beta2/adverse effects/metabolism ; Tumor Necrosis Factor-alpha/metabolism ; }, abstract = {Probiotics have shown good efficacy in the prevention of ulcerative colitis (UC), but the specific mechanism remains unclear. Therefore, shotgun metagenomic and transcriptome analyses were performed to explore the preventive effect of a potential probiotic Lactobacillus plantarum HNU082 (Lp082) on UC and its specific mechanism. The results showed that Lp082 intervention ameliorated dextran sulfate sodium (DSS)-induced UC in mice, which was manifested in the increase in body weight, water intake, food intake, and colon length and the decrease in the DAI index, immune organ index, inflammatory factors and histopathological scores after Lp082 intake. The mechanism is deeply studied and it is discovered that Lp082 improves the intestinal mucosal barrier by co-optimizing biological barriers, chemical barriers, mechanical barriers, and immune barriers. Specifically, Lp082 improved the biological barrier by increasing the diversity, optimizing the species composition and the structure of the gut microbiota, increasing bacteria producing short chain fatty acids (SCFAs), and activating microbial metabolic pathways producing SCFAs so as to enhance the content of SCFAs. Lp082 optimized the chemical barrier by decreasing the mRNA expression of ICAM-1 and VCAM and by increasing the content of goblet cells and the mRNA expression and immunofluorescent protein content of mucin2. Lp082 ameliorated the mechanical barrier by decreasing the mRNA expression of claudin-1 and claudin-2, and by increasing the mRNA expression of ZO-1 and ZO-2 and the immunofluorescent protein content of ZO-1. Lp082 also optimized the immune barrier by increasing the mRNA expression of IL-10, TGF-β1, and TGF-β2 and by decreasing the mRNA expression and protein contents of IL-6, tumour necrosis factor-alpha (TNF-α) and myeloperoxidase (MPO). In addition, Lp082 can also regulate the metabolic pathways of inflammation and disease in mice, and notably, Lp082 inhibits the NF-κB signaling pathway by inhibiting NF-κB signaling molecules to alleviate UC. In conclusion, improving gut microbiota dysbiosis, protecting the intestinal mucosal barrier, regulating inflammatory and disease pathways, and affecting neutrophil infiltration are the potential mechanisms of probiotic Lp082 in alleviating UC. Our study enriches the mechanism and provides a new prospect for Lactobacillus plantarum HNU082 in the prevention of colitis, provides support for the development of probiotic-based microbial products as an alternative prevention strategy for UC, and provides guidance for the future probiotic prevention of human colitis.}, } @article {pmid36111147, year = {2022}, author = {Di Carlo, P and Serra, N and Alduina, R and Guarino, R and Craxì, A and Giammanco, A and Fasciana, T and Cascio, A and Sergi, CM}, title = {A systematic review on omics data (metagenomics, metatranscriptomics, and metabolomics) in the role of microbiome in gallbladder disease.}, journal = {Frontiers in physiology}, volume = {13}, number = {}, pages = {888233}, pmid = {36111147}, issn = {1664-042X}, abstract = {Microbiotas are the range of microorganisms (mainly bacteria and fungi) colonizing multicellular, macroscopic organisms. They are crucial for several metabolic functions affecting the health of the host. However, difficulties hamper the investigation of microbiota composition in cultivating microorganisms in standard growth media. For this reason, our knowledge of microbiota can benefit from the analysis of microbial macromolecules (DNA, transcripts, proteins, or by-products) present in various samples collected from the host. Various omics technologies are used to obtain different data. Metagenomics provides a taxonomical profile of the sample. It can also be used to obtain potential functional information. At the same time, metatranscriptomics can characterize members of a microbiome responsible for specific functions and elucidate genes that drive the microbiotas relationship with its host. Thus, while microbiota refers to microorganisms living in a determined environment (taxonomy of microorganisms identified), microbiome refers to the microorganisms and their genes living in a determined environment and, of course, metagenomics focuses on the genes and collective functions of identified microorganisms. Metabolomics completes this framework by determining the metabolite fluxes and the products released into the environment. The gallbladder is a sac localized under the liver in the human body and is difficult to access for bile and tissue sampling. It concentrates the bile produced in the hepatocytes, which drains into bile canaliculi. Bile promotes fat digestion and is released from the gallbladder into the upper small intestine in response to food. Considered sterile originally, recent data indicate that bile microbiota is associated with the biliary tract's inflammation and carcinogenesis. The sample size is relevant for omic studies of rare diseases, such as gallbladder carcinoma. Although in its infancy, the study of the biliary microbiota has begun taking advantage of several omics strategies, mainly based on metagenomics, metabolomics, and mouse models. Here, we show that omics analyses from the literature may provide a more comprehensive image of the biliary microbiota. We review studies performed in this environmental niche and focus on network-based approaches for integrative studies.}, } @article {pmid36111106, year = {2022}, author = {Gao, H and Wang, J and Zhang, S and Li, T}, title = {A Case Report of Two Kala-azar Cases in China Diagnosed by Metagenomic Next-Generation Sequencing.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {922894}, pmid = {36111106}, issn = {2296-858X}, abstract = {BACKGROUND: Leishmaniasis being a local disease, as kala-azar this particular form is a visceral form. It is transmitted by sandflies, and is a parasitic disease involving the reticuloendothelial system of mononuclear macrophages. Due to its poor prognosis and high fatality rate, the fatality rate of patients without effective treatment can exceed 95%. Thereby, early diagnosis and treatment can significantly improve its prognosis. The metagenomic next-generation sequencing (mNGS) has the advantage of being able to find pathogens that cannot be detected by traditional methods. More importantly, it can conduct nucleic acid detection of pathogens covering a wide range in a short time. For infectious diseases like kala-azar, which is clinically complicated and difficult, mNGS detection provides a basis for accurate etiological diagnosis.

CASE REPORT: We report 2 cases of kala-azar in West China Hospital, Chengdu, China. The first case is a 47-year-old male patient who had recurrent fever for 4 months, accompanied by reduction of red blood cell, white blood cell, and blood platelet. He was detected by mNGS and clinically diagnosed as kala-azar (Leishmania detection), finally died of multiple organ failure. The second patient was a 15-year-old male who had fever for more than 10 days. He was detected by mNGS and clinically diagnosed as kala-azar (Leishmania detection). He recovered and discharged quickly after treatment with sodium stibogluconate.

CONCLUSION: Efforts should be made to improve early etiological diagnosis in order to improve patient prognosis. mNGS detection is beneficial to the diagnosis and treatment of infectious diseases with unknown causes in the early stage of emergency treatment.}, } @article {pmid36110128, year = {2022}, author = {Meng, J and Ji, H and Chen, L and Liu, A}, title = {Comparison of Droplet Digital PCR and Metagenomic Next-Generation Sequencing Methods for the Detection of Human Herpesvirus 6B Infection Using Cell-Free DNA from Patients Receiving CAR-T and Hematopoietic Stem Cell Transplantation.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {5353-5364}, pmid = {36110128}, issn = {1178-6973}, abstract = {PURPOSE: The aim of this study was to examine and compare the differences between droplet digital PCR (ddPCR) and metagenomic next-generation sequencing (mNGS) in the detection of human herpesvirus 6B (HHV-6B). Long-term monitoring of HHV-6B viral load in patients receiving chimeric antigen receptor-modified T-cell (CAR-T) therapy and hematopoietic stem cell transplantation (HSCT) can be used to identify immune effector cell-associated neurotoxicity syndrome (ICANS) and guide drug therapy.

METHODS: Twenty-seven patients with suspected HHV-6B infection who had both mNGS and ddPCR test results were analyzed retrospectively, including 19 patients who received CAR T-cell therapy and 8 who received HSCT. The HHV-6B probe and primers were designed, and the performance of the ddPCR assay was evaluated. Subsequently, ddPCR was performed utilizing blood and urine. Data on clinical information and mNGS investigations were collected.

RESULTS: The ddPCR test results correlated significantly with the mNGS test results (P < 0.001, R[2] = 0.672). Of the 27 time-paired samples, ddPCR showed positive HHV-6B detection in 20 samples, while mNGS alone showed positive HHV-6B detection in 12 samples. ddPCR detected additional HHV-6B infections in 8 samples that would have been missed if only mNGS were used. In addition, the first HHV-6B infection event was detected at a median of 14 days after CAR T-cell infusion (range, 8 to 19 days). Longitudinal monitoring of HHV-6B by ddPCR was performed to assess the effectiveness of antiviral therapy. The data showed that with antiviral treatment HHV-6B viral load gradually decreased.

CONCLUSION: Our results indicated that ddPCR improved the HHV-6B positive detection ratio and was an effective adjunct to mNGS methods. Furthermore, the longitudinal detection and quantification of HHV-6B viral load in patients undergoing CAR T-cell therapy and HSCT may serve as a guide for drug treatment.}, } @article {pmid36109646, year = {2022}, author = {Kang, JTL and Teo, JJY and Bertrand, D and Ng, A and Ravikrishnan, A and Yong, M and Ng, OT and Marimuthu, K and Chen, SL and Chng, KR and Gan, YH and Nagarajan, N}, title = {Long-term ecological and evolutionary dynamics in the gut microbiomes of carbapenemase-producing Enterobacteriaceae colonized subjects.}, journal = {Nature microbiology}, volume = {7}, number = {10}, pages = {1516-1524}, pmid = {36109646}, issn = {2058-5276}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacterial Proteins/genetics/metabolism ; *Carbapenem-Resistant Enterobacteriaceae/genetics ; Escherichia coli/genetics ; *Gastrointestinal Microbiome ; Humans ; Klebsiella pneumoniae/genetics ; beta-Lactamases/genetics/metabolism ; }, abstract = {Long-term colonization of the gut microbiome by carbapenemase-producing Enterobacteriaceae (CPE) is a growing area of public health concern as it can lead to community transmission and rapid increase in cases of life-threatening CPE infections. Here, leveraging the observation that many subjects are decolonized without interventions within a year, we used longitudinal shotgun metagenomics (up to 12 timepoints) for detailed characterization of ecological and evolutionary dynamics in the gut microbiome of a cohort of CPE-colonized subjects and family members (n = 46; 361 samples). Subjects who underwent decolonization exhibited a distinct ecological shift marked by recovery of microbial diversity, key commensals and anti-inflammatory pathways. In addition, colonization was marked by elevated but unstable Enterobacteriaceae abundances, which exhibited distinct strain-level dynamics for different species (Escherichia coli and Klebsiella pneumoniae). Finally, comparative analysis with whole-genome sequencing data from CPE isolates (n = 159) helped identify substrain variation in key functional genes and the presence of highly similar E. coli and K. pneumoniae strains with variable resistance profiles and plasmid sharing. These results provide an enhanced view into how colonization by multi-drug-resistant bacteria associates with altered gut ecology and can enable transfer of resistance genes, even in the absence of overt infection and antibiotic usage.}, } @article {pmid36109637, year = {2022}, author = {Ianiro, G and Punčochář, M and Karcher, N and Porcari, S and Armanini, F and Asnicar, F and Beghini, F and Blanco-Míguez, A and Cumbo, F and Manghi, P and Pinto, F and Masucci, L and Quaranta, G and De Giorgi, S and Sciumè, GD and Bibbò, S and Del Chierico, F and Putignani, L and Sanguinetti, M and Gasbarrini, A and Valles-Colomer, M and Cammarota, G and Segata, N}, title = {Variability of strain engraftment and predictability of microbiome composition after fecal microbiota transplantation across different diseases.}, journal = {Nature medicine}, volume = {28}, number = {9}, pages = {1913-1923}, pmid = {36109637}, issn = {1546-170X}, support = {U01 CA230551/CA/NCI NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents ; *Clostridium Infections/microbiology/therapy ; Fecal Microbiota Transplantation/methods ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; Treatment Outcome ; }, abstract = {Fecal microbiota transplantation (FMT) is highly effective against recurrent Clostridioides difficile infection and is considered a promising treatment for other microbiome-related disorders, but a comprehensive understanding of microbial engraftment dynamics is lacking, which prevents informed applications of this therapeutic approach. Here, we performed an integrated shotgun metagenomic systematic meta-analysis of new and publicly available stool microbiomes collected from 226 triads of donors, pre-FMT recipients and post-FMT recipients across eight different disease types. By leveraging improved metagenomic strain-profiling to infer strain sharing, we found that recipients with higher donor strain engraftment were more likely to experience clinical success after FMT (P = 0.017) when evaluated across studies. Considering all cohorts, increased engraftment was noted in individuals receiving FMT from multiple routes (for example, both via capsules and colonoscopy during the same treatment) as well as in antibiotic-treated recipients with infectious diseases compared with antibiotic-naïve patients with noncommunicable diseases. Bacteroidetes and Actinobacteria species (including Bifidobacteria) displayed higher engraftment than Firmicutes except for six under-characterized Firmicutes species. Cross-dataset machine learning predicted the presence or absence of species in the post-FMT recipient at 0.77 average AUROC in leave-one-dataset-out evaluation, and highlighted the relevance of microbial abundance, prevalence and taxonomy to infer post-FMT species presence. By exploring the dynamics of microbiome engraftment after FMT and their association with clinical variables, our study uncovered species-specific engraftment patterns and presented machine learning models able to predict donors that might optimize post-FMT specific microbiome characteristics for disease-targeted FMT protocols.}, } @article {pmid36109636, year = {2022}, author = {Schmidt, TSB and Li, SS and Maistrenko, OM and Akanni, W and Coelho, LP and Dolai, S and Fullam, A and Glazek, AM and Hercog, R and Herrema, H and Jung, F and Kandels, S and Orakov, A and Thielemann, R and von Stetten, M and Van Rossum, T and Benes, V and Borody, TJ and de Vos, WM and Ponsioen, CY and Nieuwdorp, M and Bork, P}, title = {Drivers and determinants of strain dynamics following fecal microbiota transplantation.}, journal = {Nature medicine}, volume = {28}, number = {9}, pages = {1902-1912}, pmid = {36109636}, issn = {1546-170X}, mesh = {*Clostridium Infections/therapy ; Fecal Microbiota Transplantation ; Feces ; *Gastrointestinal Microbiome/genetics ; Gastrointestinal Tract ; Humans ; *Microbiota ; }, abstract = {Fecal microbiota transplantation (FMT) is a therapeutic intervention for inflammatory diseases of the gastrointestinal tract, but its clinical mode of action and subsequent microbiome dynamics remain poorly understood. Here we analyzed metagenomes from 316 FMTs, sampled pre and post intervention, for the treatment of ten different disease indications. We quantified strain-level dynamics of 1,089 microbial species, complemented by 47,548 newly constructed metagenome-assembled genomes. Donor strain colonization and recipient strain resilience were mostly independent of clinical outcomes, but accurately predictable using LASSO-regularized regression models that accounted for host, microbiome and procedural variables. Recipient factors and donor-recipient complementarity, encompassing entire microbial communities to individual strains, were the main determinants of strain population dynamics, providing insights into the underlying processes that shape the post-FMT gut microbiome. Applying an ecology-based framework to our findings indicated parameters that may inform the development of more effective, targeted microbiome therapies in the future, and suggested how patient stratification can be used to enhance donor microbiota colonization or the displacement of recipient microbes in clinical practice.}, } @article {pmid36109557, year = {2022}, author = {Jung, J and Bugenyi, AW and Lee, MR and Choi, YJ and Song, KD and Lee, HK and Son, YO and Lee, DS and Lee, SC and Son, YJ and Heo, J}, title = {High-quality metagenome-assembled genomes from proximal colonic microbiomes of synbiotic-treated korean native black pigs reveal changes in functional capacity.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {14595}, pmid = {36109557}, issn = {2045-2322}, mesh = {Animals ; Female ; Health Promotion ; Metagenome ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Republic of Korea ; Sus scrofa/genetics ; Swine ; *Synbiotics ; }, abstract = {Synbiotics are feed supplements with the potential to promote health and productivity in pigs partly, through modulation of the intestinal microbiome. Our study used shotgun sequencing and 16S rRNA gene sequencing techniques to characterize the effect of a synbiotic containing three Lactobacillus species and a fructo-oligosaccharide on the proximal colonic microbiome of 4- to 7-month-old Korean native black gilts. With shotgun sequencing we constructed unique metagenome-assembled genomes of gut microbiota in Native Black Pig for the first time, which we then used for downstream analysis. Results showed that synbiotic treatment did not alter microbial diversity and evenness within the proximal colons, but altered composition of some members of the Lactobacillaceae, Enterococcaceae and Streptococcaceae families. Functional analysis of the shotgun sequence data revealed 8 clusters of orthologous groups (COGs) that were differentially represented in the proximal colonic microbiomes of synbiotic-treated Jeju black pigs relative to controls. In conclusion, our results show that administering this synbiotic causes changes in the functional capacity of the proximal colonic microbiome of the Korean native black pig. This study improves our understanding of the potential impact of synbiotics on the colonic microbiome of Korean native black pigs.}, } @article {pmid36109427, year = {2023}, author = {Nidhi, S and Tripathi, P and Tripathi, V}, title = {Phylogenetic Analysis of Anti-CRISPR and Member Addition in the Families.}, journal = {Molecular biotechnology}, volume = {65}, number = {2}, pages = {273-281}, pmid = {36109427}, issn = {1559-0305}, mesh = {Humans ; Phylogeny ; *Bacteria/genetics ; *Bacteriophages/genetics ; Metagenome ; CRISPR-Cas Systems ; }, abstract = {CRISPR-Cas is a widespread anti-viral adaptive immune system in the microorganisms. Viruses living in bacteria or some phages carry anti-CRISPR proteins to evade immunity by CRISPR-Cas. The anti-CRISPR proteins are prevalent in phages capable of lying dormant in a CRISPR-carrying host, while their orthologs frequently found in virulent phages. Here, we propose a probabilistic strategy of ancestral sequence reconstruction (ASR) and Hidden Markov Model (HMM) profile search to fish out sequences of anti-CRISPR proteins from environmental metagenomic, human microbiome metagenomic, human microbiome reference genome, and NCBI's non-redundant databases. Our results revealed that the metagenome database dark matter might contain anti-CRISPR encoding genes.}, } @article {pmid36108841, year = {2023}, author = {Sharma, U and Rawat, D and Mukherjee, P and Farooqi, F and Mishra, V and Sharma, RS}, title = {Ecological life strategies of microbes in response to antibiotics as a driving factor in soils.}, journal = {The Science of the total environment}, volume = {854}, number = {}, pages = {158791}, doi = {10.1016/j.scitotenv.2022.158791}, pmid = {36108841}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents ; Soil/chemistry ; Soil Microbiology ; Bacteria ; *Microbiota ; }, abstract = {Antibiotics as a selection pressure driving the evolution of soil microbial communities is not well understood. Since microbial functions govern ecosystem services, an ecological framework is required to understand and predict antibiotic-induced functional and structural changes in microbial communities. Therefore, metagenomic studies explaining the impacts of antibiotics on soil microbial communities were mined, and alterations in microbial taxa were analyzed through an ecological lens using Grimes's Competitor-Stress tolerator-Ruderal (CSR) model. We propose considering antibiotics as the primary abiotic factor mentioned in the CSR model and classifying non-susceptible microbial taxa as degraders, resistant, and resilient groups analogous to competitors, stress tolerators, and ruderal strategists, respectively. Firmicutes, Bacteroidetes, Actinobacteria, and Proteobacteria were among the phyla harboring most members with antibiotic-resistant groups. However, some antibiotic-resistant microbes in these phyla could not only tolerate but also subsist solely on antibiotics, while others degraded antibiotics as a part of secondary metabolism. Irrespective of their taxonomic affiliation, microbes with each life strategy displayed similar phenotypic characteristics. Therefore, it is recommended to consider microbial functional traits associated with each life strategy while analyzing the ecological impacts of antibiotics. Also, potential ecological crises posed by antibiotics through changes in microbial community and ecosystem functions were visualized. Applying ecological theory to understand and predict antibiotics-induced changes in microbial communities will also provide better insight into microbial behavior in the background of emerging contaminants and help develop a robust ecological classification system of microbes.}, } @article {pmid36108825, year = {2023}, author = {Tarek, MH and Garner, E}, title = {A proposed framework for the identification of indicator genes for monitoring antibiotic resistance in wastewater: Insights from metagenomic sequencing.}, journal = {The Science of the total environment}, volume = {854}, number = {}, pages = {158698}, doi = {10.1016/j.scitotenv.2022.158698}, pmid = {36108825}, issn = {1879-1026}, mesh = {Animals ; Humans ; *Wastewater ; *Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Anti-Bacterial Agents/pharmacology ; Water ; }, abstract = {Antibiotic resistance is one of the greatest threats to global human and animal health of our time. Municipal wastewater has been identified as a hotspot of antibiotic resistance contamination to water bodies. However, there are numerous potential antibiotic resistant pathogens and their associated antibiotic resistance genes (ARGs), making it difficult to implement routine monitoring that addresses the breadth of the problem. The objective of this study was to identify candidate indicator ARGs for monitoring antibiotic resistance in wastewater and receiving water bodies. We developed a framework to identify indicator ARGs that incorporated clinical relevance, abundance in wastewater, geographic ubiquity, environmental relevance, ARG mobility, associations with mobile genetic elements, and the availability of quantitative analytical methods. To identify indicator ARGs, published metagenomic sequencing data from 191 wastewater samples originating from 64 countries across the world were obtained from online public repositories. Through ARG annotation and network analysis, this framework revealed 56 candidate indicator ARGs distributed across four modules of strongly correlated ARGs, with one ARG from each module (oqxA, ermB, sul1, and mexE) proposed as a minimally redundant monitoring target. The results of this study provide the basis for antibiotic resistance surveillance and monitoring framework in wastewater and contaminated waterways.}, } @article {pmid36108783, year = {2022}, author = {Atim, SA and Ashraf, S and Belij-Rammerstorfer, S and Ademun, AR and Vudriko, P and Nakayiki, T and Niebel, M and Shepherd, J and Balinandi, S and Nakanjako, G and Abaasa, A and Johnson, PCD and Odongo, S and Esau, M and Bahati, M and Kaleebu, P and Lutwama, JJ and Masembe, C and Lambe, T and Thomson, EC and Tweyongyere, R}, title = {Risk factors for Crimean-Congo Haemorrhagic Fever (CCHF) virus exposure in farming communities in Uganda.}, journal = {The Journal of infection}, volume = {85}, number = {6}, pages = {693-701}, pmid = {36108783}, issn = {1532-2742}, support = {MC_UU_12014/8/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 107743/WT_/Wellcome Trust/United Kingdom ; MC_UU_00027/1/MRC_/Medical Research Council/United Kingdom ; 102789/Z/13/A/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Female ; Animals ; Humans ; Cattle ; Dogs ; *Hemorrhagic Fever Virus, Crimean-Congo ; *Hemorrhagic Fever, Crimean/epidemiology ; Uganda/epidemiology ; Cross-Sectional Studies ; *Ticks ; Goats ; Risk Factors ; Agriculture ; }, abstract = {BACKGROUND: Crimean-Congo Haemorrhagic Fever (CCHF) is an emerging human-health threat causing sporadic outbreaks in livestock farming communities. However, the full extent and the risks associated with exposure of such communities has not previously been well-described.

METHODS: We collected blood samples from 800 humans, 666 cattle, 549 goats and 32 dogs in districts within and outside Ugandan cattle corridor in a cross-sectional survey, and tested for CCHFV-specific IgG antibodies using Enzyme-Linked Immunosorbent Assays. Sociodemographic and epidemiological data were recorded using structured questionnaire. Ticks were collected to identify circulating nairoviruses by metagenomic sequencing.

RESULTS: CCHFV seropositivity was in 221/800 (27·6%) in humans, 612/666 (91·8%) in cattle, 413/549 (75·2%) in goats and 18/32 (56·2%) in dogs. Human seropositivity was associated with livestock farming (AOR=5·68, p<0·0001), age (AOR=2·99, p=0·002) and collecting/eating engorged ticks (AOR=2·13, p=0·004). In animals, seropositivity was higher in cattle versus goats (AOR=2·58, p<0·0001), female sex (AOR=2·13, p=0·002) and heavy tick infestation (>50 ticks: AOR=3·52, p=0·004). CCHFV was identified in multiple tick pools of Rhipicephalus appendiculatus.

INTERPRETATION: The very high CCHF seropositivity especially among livestock farmers and multiple regional risk factors associated exposures, including collecting/eating engorged ticks previously unrecognised, highlights need for further surveillance and sensitisation and control policies against the disease.}, } @article {pmid36108739, year = {2022}, author = {Klau, LJ and Podell, S and Creamer, KE and Demko, AM and Singh, HW and Allen, EE and Moore, BS and Ziemert, N and Letzel, AC and Jensen, PR}, title = {The Natural Product Domain Seeker version 2 (NaPDoS2) webtool relates ketosynthase phylogeny to biosynthetic function.}, journal = {The Journal of biological chemistry}, volume = {298}, number = {10}, pages = {102480}, pmid = {36108739}, issn = {1083-351X}, support = {R01 GM085770/GM/NIGMS NIH HHS/United States ; }, mesh = {*Biological Products ; Genome ; Metagenomics/methods ; Peptide Synthases/genetics/chemistry ; Phylogeny ; *Polyketide Synthases/genetics/chemistry ; *Software ; Web Browser ; }, abstract = {The Natural Product Domain Seeker (NaPDoS) webtool detects and classifies ketosynthase (KS) and condensation domains from genomic, metagenomic, and amplicon sequence data. Unlike other tools, a phylogeny-based classification scheme is used to make broader predictions about the polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) genes in which these domains are found. NaPDoS is particularly useful for the analysis of incomplete biosynthetic genes or gene clusters, as are often observed in poorly assembled genomes and metagenomes, or when loci are not clustered, as in eukaryotic genomes. To help support the growing interest in sequence-based analyses of natural product biosynthetic diversity, here we introduce version 2 of the webtool, NaPDoS2, available at http://napdos.ucsd.edu/napdos2. This update includes the addition of 1417 KS sequences, representing a major expansion of the taxonomic and functional diversity represented in the webtool database. The phylogeny-based KS classification scheme now recognizes 41 class and subclass assignments, including new type II PKS subclasses. Workflow modifications accelerate run times, allowing larger datasets to be analyzed. In addition, default parameters were established using statistical validation tests to maximize KS detection and classification accuracy while minimizing false positives. We further demonstrate the applications of NaPDoS2 to assess PKS biosynthetic potential using genomic, metagenomic, and PCR amplicon datasets. These examples illustrate how NaPDoS2 can be used to predict biosynthetic potential and detect genes involved in the biosynthesis of specific structure classes or new biosynthetic mechanisms.}, } @article {pmid36108705, year = {2022}, author = {Yi, SW and Lee, HG and So, KM and Kim, E and Jung, YH and Kim, M and Jeong, JY and Kim, KH and Oem, JK and Hur, TY and Oh, SI}, title = {Effect of feeding raw potato starch on the composition dynamics of the piglet intestinal microbiome.}, journal = {Animal bioscience}, volume = {35}, number = {11}, pages = {1698-1710}, pmid = {36108705}, issn = {2765-0189}, support = {PJ01564401//Rural Development Administration/ ; }, abstract = {OBJECTIVE: Raw potato starch (RPS) is resistant to digestion, escapes absorption, and is metabolized by intestinal microflora in the large intestine and acts as their energy source. In this study, we compared the effect of different concentrations of RPS on the intestinal bacterial community of weaned piglets.

METHODS: Male weaned piglets (25-days-old, 7.03±0.49 kg) were either fed a corn/soybean-based control diet (CON, n = 6) or two treatment diets supplemented with 5% RPS (RPS5, n = 4) or 10% RPS (RPS10, n = 4) for 20 days and their fecal samples were collected. The day 0 and 20 samples were analyzed using a 16S rRNA gene sequencing technology, followed by total genomic DNA extraction, library construction, and high-throughput sequencing. After statistical analysis, five phyla and 45 genera accounting for over 0.5% of the reads in any of the three groups were further analyzed. Furthermore, short-chain fatty acids (SCFAs) in the day 20 fecal samples were analyzed using gas chromatography.

RESULTS: Significant changes were not observed in the bacterial composition at the phylum level even after 20 d post feeding (dpf); however, the abundance of Intestinimonas and Barnesiella decreased in both RPS treatment groups compared to the CON group. Consumption of 5% RPS increased the abundance of Roseburia (p<0.05) and decreased the abundance of Clostridium (p<0.01) and Mediterraneibacter (p< 0.05). In contrast, consumption of 10% RPS increased the abundance of Olsenella (p<0.05) and decreased the abundance of Campylobacter (p<0.05), Kineothrix (p<0.05), Paraprevotella (p<0.05), and Vallitalea (p<0.05). Additionally, acetate (p<0.01), butyrate (p<0.05), valerate (p = 0.01), and total SCFAs (p = 0.01) were upregulated in the RPS5 treatment group.

CONCLUSION: Feeding 5% RPS altered bacterial community composition and promoted gut health in weaned piglets. Thus, resistant starch as a feed additive may prevent diarrhea in piglets during weaning.}, } @article {pmid36108700, year = {2022}, author = {Choi, S and Cha, J and Song, M and Son, J and Park, MR and Lim, YJ and Kim, TH and Lee, KT and Park, W}, title = {Analysis of 16S rRNA gene sequencing data for the taxonomic characterization of the vaginal and the fecal microbial communities in Hanwoo.}, journal = {Animal bioscience}, volume = {35}, number = {11}, pages = {1808-1816}, pmid = {36108700}, issn = {2765-0189}, support = {PJ0148262020//Rural Development Administration/ ; }, abstract = {OBJECTIVE: The study of Hanwoo (Korean native cattle) has mainly been focused on meat quality and productivity. Recently the field of microbiome research has increased dramatically. However, the information on the microbiome in Hanwoo is still insufficient, especially relationship between vagina and feces. Therefore, the purpose of this study is to examine the microbial community characteristics by analyzing the 16S rRNA sequencing data of Hanwoo vagina and feces, as well as to confirm the difference and correlation between vaginal and fecal microorganisms. As a result, the goal is to investigate if fecal microbiome can be used to predict vaginal microbiome.

METHODS: A total of 31 clinically healthy Hanwoo that delivered healthy calves more than once in Cheongju, South Korea were enrolled in this study. During the breeding season, we collected vaginal and fecal samples and sequenced the microbial 16S rRNA genes V3-V4 hypervariable regions from microbial DNA of samples.

RESULTS: The results revealed that the phylum-level microorganisms with the largest relative distribution were Firmicutes, Actinobacteria, Bacteroidetes, and Proteobacteria in the vagina, and Firmicutes, Bacteroidetes, and Spirochaetes in the feces, respectively. In the analysis of alpha, beta diversity, and effect size measurements (LefSe), the results showed significant differences between the vaginal and fecal samples. We also identified the function of these differentially abundant microorganisms by functional annotation analyses. But there is no significant correlation between vaginal and fecal microbiome.

CONCLUSION: There is a significant difference between vaginal and fecal microbiome, but no significant correlation. Therefore, it is difficult to interrelate vaginal microbiome as fecal microbiome in Hanwoo. In a further study, it will be necessary to identify the genetic relationship of the entire microorganism between vagina and feces through the whole metagenome sequencing analysis and meta-transcriptome analysis to figure out their relationship.}, } @article {pmid36108613, year = {2022}, author = {Li, L and Mac Aogáin, M and Xu, T and Jaggi, TK and Chan, LLY and Qu, J and Wei, L and Liao, S and Cheng, HS and Keir, HR and Dicker, AJ and Tan, KS and De Yun, W and Koh, MS and Ong, TH and Lim, AYH and Abisheganaden, JA and Low, TB and Hassan, TM and Long, X and Wark, PAB and Oliver, B and Drautz-Moses, DI and Schuster, SC and Tan, NS and Fang, M and Chalmers, JD and Chotirmall, SH}, title = {Neisseria species as pathobionts in bronchiectasis.}, journal = {Cell host & microbe}, volume = {30}, number = {9}, pages = {1311-1327.e8}, doi = {10.1016/j.chom.2022.08.005}, pmid = {36108613}, issn = {1934-6069}, support = {SCAF/17/03/CSO_/Chief Scientist Office/United Kingdom ; }, mesh = {Animals ; *Bronchiectasis/epidemiology ; Humans ; Metagenome ; Mice ; *Microbiota ; Neisseria/genetics ; }, abstract = {Neisseria species are frequently identified in the bronchiectasis microbiome, but they are regarded as respiratory commensals. Using a combination of human cohorts, next-generation sequencing, systems biology, and animal models, we show that bronchiectasis bacteriomes defined by the presence of Neisseria spp. associate with poor clinical outcomes, including exacerbations. Neisseria subflava cultivated from bronchiectasis patients promotes the loss of epithelial integrity and inflammation in primary epithelial cells. In vivo animal models of Neisseria subflava infection and metabolipidome analysis highlight immunoinflammatory functional gene clusters and provide evidence for pulmonary inflammation. The murine metabolipidomic data were validated with human Neisseria-dominant bronchiectasis samples and compared with disease in which Pseudomonas-, an established bronchiectasis pathogen, is dominant. Metagenomic surveillance of Neisseria across various respiratory disorders reveals broader importance, and the assessment of the home environment in bronchiectasis implies potential environmental sources of exposure. Thus, we identify Neisseria species as pathobionts in bronchiectasis, allowing for improved risk stratification in this high-risk group.}, } @article {pmid36108576, year = {2022}, author = {Ma, L and Sun, R and Yang, H and Li, J and Wen, X and Cao, Z and Zhou, Y and Fu, M and Li, Q}, title = {Metagenomics analysis revealed the coupling of lignin degradation with humus formation mediated via shell powder during composting.}, journal = {Bioresource technology}, volume = {363}, number = {}, pages = {127949}, doi = {10.1016/j.biortech.2022.127949}, pmid = {36108576}, issn = {1873-2976}, mesh = {*Actinobacteria/metabolism ; Amino Acids ; Bacteria/metabolism ; *Composting ; Dietary Sugars ; Lignin/metabolism ; Manure ; Powders ; Soil ; Sugars ; }, abstract = {This study was the first to explore the effect of shell powder (SP) on lignin degradation and humus (HS) formation during composting. The results showed that the treatment group (T) with SP consumed more polyphenols, reducing sugar and amino acids than the control group (CK), especially the rate of reducing sugar consumption in T (50.61 %) was significantly higher than CK (28.40 %). SP greatly enhanced the efficiency of lignin degradation (T:45.47 %; CK:24.63 %) and HS formation (T:34.93 %; CK:20.16 %). The content of HA in T was 12.94 mg/g while CK was 12.06 mg/g. SP maintained a continuous increase in the relative abundance of AA1, AA3 after cooling phase. Meanwhile, T (48.98 %) significantly increased the abundance of Actinobacteria compared with CK (37.19 %). Actinobacteria, AA1 and AA3 were identified as the main factors promoting lignin degradation and HS formation by correlation analysis. Therefore, adding SP could be a novel strategy to improve compost quality.}, } @article {pmid36108513, year = {2022}, author = {Liu, J and Chu, G and Wang, Q and Zhang, Z and Lu, S and She, Z and Zhao, Y and Jin, C and Guo, L and Ji, J and Gao, M}, title = {Metagenomic analysis and nitrogen removal performance evaluation of activated sludge from a sequencing batch reactor under different salinities.}, journal = {Journal of environmental management}, volume = {323}, number = {}, pages = {116213}, doi = {10.1016/j.jenvman.2022.116213}, pmid = {36108513}, issn = {1095-8630}, mesh = {ATP-Binding Cassette Transporters/metabolism ; Amines ; Bioreactors ; Denitrification ; Metagenomics ; Nitrification ; Nitrites ; *Nitrogen/analysis ; Peroxidases/metabolism ; Reactive Oxygen Species ; Salinity ; *Sewage ; Superoxide Dismutase/metabolism ; Waste Disposal, Fluid/methods ; }, abstract = {The effect of salinity on the nitrogen removal performance and microbial community of activated sludge was investigated in a sequencing batch reactor. The NH4[+]-N removal efficiency was over 95% at 0-4% salinity, indicating that the nitrification performance of activated sludge was slightly affected by lower salinity. The obvious nitrite accumulation was observed with the increment of the salinity to 5%, followed by a notable decline in the nitrogen removal performance at 6% salinity. The salinity inhibited the microbial activity, and the specific rate of nitrification and denitrification was decreased by the increasing salinity obviously. Additionally, the lower activity of superoxide dismutase and peroxidase and higher reactive oxygen species content in activated sludge might account for the deteriorative nitrogen removal performance at 6% salinity. Metagenomics analysis revealed that the genes encoding the ABC-type quaternary amine transporter in the ABC transporter pathway were abundant in the activated sludge at 2% and 4% salinity, and the higher salinity of 6% led to the loss of the genes encoding the p-type Na[+] transporter in the ABC transporter pathway. These results indicated that the salinity could weaken the ABC transporter pathway for the balance of osmotic pressure in activated sludge. The microbial activity and nitrogen removal performance of activated sludge were decreased due to the unbalanced osmotic pressure at higher salinity.}, } @article {pmid36108399, year = {2022}, author = {Sun, H and Xia, J and Wu, B and Ren, H and Zhang, X and Ye, L}, title = {Aerobic starvation treatment of activated sludge enhances the degradation efficiency of refractory organic compounds.}, journal = {Water research}, volume = {224}, number = {}, pages = {119069}, doi = {10.1016/j.watres.2022.119069}, pmid = {36108399}, issn = {1879-2448}, mesh = {Benzhydryl Compounds ; Bioreactors/microbiology ; Fluorocarbons ; Gabapentin ; Humans ; Phenols ; RNA, Ribosomal, 16S/genetics ; *Sewage/chemistry ; *Wastewater ; }, abstract = {Many refractory organic compounds (ROCs) in wastewater are toxic to human and aquatic organisms. Here, we reported an aerobic starvation approach to improve the degradation efficiencies of ROCs in activated sludge systems. The highest degradation rates of bisphenol AF (BPAF) (11.4 mg/g VSS · h) and gabapentin (GBP) (8.9 mg/g VSS · h) were achieved on the second day of the starvation process. While, the degradation rate of bisphenol A (BPA) on the 43rd day reached the maximum value of 0.8 mg/g VSS ·h, which was significantly higher than that of the seeding sludge (0.01 mg/g VSS · h). To investigate the mechanisms of this finding, we applied magnetic-nanoparticle mediated isolation, 16S rRNA gene sequencing, metagenomic sequencing and metatranscriptomic sequencing to analyze the microbial community structures and functions during the starvation process. The results showed that the increase of the BPA degradation ability was caused by the increase of the relative abundance of BPA degrading bacteria (Sphingomonas, Achromobacter, etc.), while, the enhancement of BPAF and GBP degradation was attributed to the increase of the expression of ROC degrading genes. Overall, these results improve our understanding of the microbial ecology of starved activated sludge and provide useful information for the future development of ROC removal technologies.}, } @article {pmid36108398, year = {2022}, author = {Wang, C and Yang, Y and Wang, Y and Wang, D and Xu, X and Wang, Y and Li, L and Yang, C and Zhang, T}, title = {Absolute quantification and genome-centric analyses elucidate the dynamics of microbial populations in anaerobic digesters.}, journal = {Water research}, volume = {224}, number = {}, pages = {119049}, doi = {10.1016/j.watres.2022.119049}, pmid = {36108398}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Bioreactors ; *Euryarchaeota/metabolism ; Fatty Acids, Volatile ; Methane/metabolism ; Sewage ; }, abstract = {Anaerobic digestion (AD) relies on myriads of functions performed by complex microbial communities in customized settings, thus, a comprehensive investigation on the AD microbiome is central to the fine-tuned control. Most current AD microbiome studies are based on relative abundance, which hinders the interpretation of microbes' dynamics and inter-sample comparisons. Here, we developed an absolute quantification (AQ) approach that integrated cellular spike-ins with metagenomic sequencing to elucidate microbial community variations and population dynamics in four anaerobic digesters. Using this method, 253 microbes were defined as decaying populations with decay rates ranging from -0.05 to -5.85 d[-1], wherein, a population from Flavobacteriaceae family decayed at the highest rates of -3.87 to -5.85 d[-1] in four digesters. Meanwhile, 25 microbes demonstrated the growing trend in the AD processes with growth rates ranging from 0.11 to 1.77 d[-1], and genome-centric analysis assigned some of the populations to the functional niches of hydrolysis, short-chain fatty acids metabolism, and methane generation. Additionally, we observed that the specific activity of methanogens was lower in the prolonged digestion stage, and redundancy analysis revealed that the feedstock composition and the digestion duration were the two key parameters in governing the AD microbial compositions.}, } @article {pmid36108099, year = {2022}, author = {Paul, LJ and Ericsson, AC and Andrews, FM and McAdams, Z and Keowen, ML and St Blanc, MP and Banse, HE}, title = {Dietary and management factors influence the equine gastric microbiome.}, journal = {Journal of the American Veterinary Medical Association}, volume = {260}, number = {S3}, pages = {S111-S120}, doi = {10.2460/javma.22.07.0277}, pmid = {36108099}, issn = {1943-569X}, mesh = {Horses ; Animals ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Stomach Ulcer/veterinary ; Gastric Mucosa/pathology ; *Horse Diseases/pathology ; Diet/veterinary ; }, abstract = {OBJECTIVE: The purpose of this study was to characterize the relationship of diet and management factors with the glandular gastric mucosal microbiome. We hypothesize that the gastric mucosal microbial community is influenced by diet and management factors. Our specific objective is to characterize the gastric mucosal microbiome in relation to these factors.

ANIMALS: 57 client-owned horses in the southern Louisiana region with and without equine glandular gastric disease.

PROCEDURES: Diet and management data were collected via a questionnaire. Gastroscopy was used for evaluation of equine gastric ulcer syndrome and collection of glandular mucosal pinch biopsies. 16S rRNA amplicon sequencing was used for microbiome analysis. Similarity and diversity indices and sequence read counts of individual taxa were compared between diet and management factors.

RESULTS: Differences were detected in association with offering hay, type of hay, sweet feed, turnout, and stalling. Offering hay and stalling showed differences in similarity indices, whereas hay type, sweet feed, and turnout showed differences in similarity and diversity indices. Offering hay, hay type, and sweet feed were also associated with differences in individual sequence read counts.

CLINICAL RELEVANCE: This study provides preliminary characterization of the complex relationship between the glandular gastric microbiome and diet/management factors. The ideal microbiome to promote a healthy glandular gastric environment remains unknown.}, } @article {pmid36108023, year = {2022}, author = {Suzuki, TA and Fitzstevens, JL and Schmidt, VT and Enav, H and Huus, KE and Mbong Ngwese, M and Grießhammer, A and Pfleiderer, A and Adegbite, BR and Zinsou, JF and Esen, M and Velavan, TP and Adegnika, AA and Song, LH and Spector, TD and Muehlbauer, AL and Marchi, N and Kang, H and Maier, L and Blekhman, R and Ségurel, L and Ko, G and Youngblut, ND and Kremsner, P and Ley, RE}, title = {Codiversification of gut microbiota with humans.}, journal = {Science (New York, N.Y.)}, volume = {377}, number = {6612}, pages = {1328-1332}, pmid = {36108023}, issn = {1095-9203}, support = {/WT_/Wellcome Trust/United Kingdom ; R35 GM128716/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteria/classification/genetics ; Child ; *Gastrointestinal Microbiome/genetics ; *Host Microbial Interactions ; Humans ; Metagenome ; Oxygen/metabolism ; }, abstract = {The gut microbiomes of human populations worldwide have many core microbial species in common. However, within a species, some strains can show remarkable population specificity. The question is whether such specificity arises from a shared evolutionary history (codiversification) between humans and their microbes. To test for codiversification of host and microbiota, we analyzed paired gut metagenomes and human genomes for 1225 individuals in Europe, Asia, and Africa, including mothers and their children. Between and within countries, a parallel evolutionary history was evident for humans and their gut microbes. Moreover, species displaying the strongest codiversification independently evolved traits characteristic of host dependency, including reduced genomes and oxygen and temperature sensitivity. These findings all point to the importance of understanding the potential role of population-specific microbial strains in microbiome-mediated disease phenotypes.}, } @article {pmid36107983, year = {2022}, author = {Koo, H and Morrow, CD}, title = {Time series strain tracking analysis post fecal transplantation identifies individual specific patterns of fecal dominant donor, recipient, and unrelated microbial strains.}, journal = {PloS one}, volume = {17}, number = {9}, pages = {e0274633}, pmid = {36107983}, issn = {1932-6203}, mesh = {*Anti-Bacterial Agents ; *Fecal Microbiota Transplantation ; Feces ; Nucleotides ; Time Factors ; }, abstract = {BACKGROUND: Fecal microbial transplantation (FMT) has been used with the therapeutic intent to change the functions of the gut microbial community in metabolism and host immunity. For most of these therapies, the recipients are not given antibiotics to eliminate the microbial community prior to transplant with donor fecal microbes resulting in the initial gut microbial community following FMT consisting of a consortium of donor and recipient microbes. The detailed analysis of the fecal samples from these FMT over time provides a unique opportunity to study the changes in the gut microbial strain community that occurs following the introduction of new microbial strains (donor) into an established community (recipient).

METHODS: In this study, we have metagenomic data set consisting of 5 FMT that contained donor, recipient and recipient post FMT taken multiple times for periods up to 535 days after the FMT. We used two established strain tracking methods, Window-based Single Nucleotide Variant (SNV) Similarity (WSS) and StrainPhlAn, to determine the presence of donor and recipient microbial strains following FMT. To assess recombination between donor and recipient strains of Bacteroides vulgatus post FMT, we used BLAST+ to analyze the data sets for Bacteroidales-specific antimicrobial proteins (BSAP-3) that have known functions to restrict species specific replication.

RESULTS: We found that Alistipes onderdonkii, Alistipes shahii, Alistipes putredinis, and Parabacteroides merdae, all had patterns post FMT consisting of either dominant donor or recipient microbial strains in the feces. In contrast, the analysis of Bacteroides spp. in five FMT pairs revealed inter-individual oscillation over time with the appearance of either donor or recipient fecal strain dominance. In some instances, B. vulgatus and B. uniformis were also identified after FMT that were not related to either the donor or recipient. Finally, in one of the FMT, we identified a distinct B. vulgatus strain post-FMT that matched the pre-FMT strain but was BSAP-3 positive, suggesting a possible recombination event between the donor and recipient strains.

CONCLUSION: The complex oscillating patterns of the appearance of fecal dominant donor, recipient or unrelated strains following extended times post FMT provide new insights into the dynamics of the microbial community interactions with the recipients following FMT. The result from our analysis has implications for the use of FMT to predictably change the biological functions of the gut community in metabolism and host immunity.}, } @article {pmid36107603, year = {2022}, author = {Wang, Z and Zhang, J and Hao, Z and Meng, L and Han, Z and Hong, Z}, title = {Tuberculosis infection related hemophagocytic lymphohistiocytosis diagnosed in patient with GZMB mutation: A case report and literature review.}, journal = {Medicine}, volume = {101}, number = {35}, pages = {e30283}, pmid = {36107603}, issn = {1536-5964}, mesh = {Adult ; Granzymes ; Humans ; *Latent Tuberculosis/complications ; *Lymphohistiocytosis, Hemophagocytic/complications/diagnosis/genetics ; Male ; Mutation ; *Neoplasms/complications ; *Tuberculosis/complications/diagnosis ; }, abstract = {BACKGROUND: Secondary hemophagocytic lymphohistiocytosis (HLH) is a life-threatening syndrome associated with infections, tumors and connective tissue disease. However rapid identification of the underlying infectious cause of HLH is challenging because traditional etiological diagnostics are time-consuming and sometimes fail to identify the pathogens. Metagenomic next-generation sequencing (mNGS) may be a potential optimal solution, which may help improve the clinical diagnosis of underlying infections in hematological diseases.

CASE PRESENTATION: A 28-year-old man presented with a 2-month history of intermittent fever and cytopenia. The HLH was diagnosed based on the manifestations of fever, splenomegaly, anemia, thrombocytopenia, hyperferritinemia, hyperglyceridemia, and elevated IL-2R levels. High-through-put sequencing analysis detected a GZMB mutation. While the initial detection of cultures and smears of tuberculosis was negative, TB infection was eventually identified by mNGS of blood sample. The symptoms rapidly abated during the initial administration of TB.

CONCLUSION: The present case proposed that mNGS might be an effective diagnostic tool for diagnosing rare infectious cause of secondary HLH. GZMB mutation was first discovered to be present in secondary HLH.}, } @article {pmid36107142, year = {2022}, author = {Luu, LDW and Singh, H and Castaño-Rodríguez, N and Leach, ST and Riordan, SM and Tedla, N and Krishnan, U and Kaakoush, NO}, title = {Changes to the upper gastrointestinal microbiotas of children with reflux oesophagitis and oesophageal metaplasia.}, journal = {Microbial genomics}, volume = {8}, number = {9}, pages = {}, pmid = {36107142}, issn = {2057-5858}, mesh = {Bacteria/genetics ; Child ; Cytokines ; *Esophagitis, Peptic/drug therapy ; *Gastrointestinal Microbiome ; Humans ; Metaplasia/drug therapy ; *Microbiota/genetics ; Prospective Studies ; Proton Pump Inhibitors/therapeutic use ; RNA, Ribosomal, 16S/genetics ; Retrospective Studies ; *Upper Gastrointestinal Tract ; }, abstract = {Little is known of the relationships among paediatric upper gastrointestinal microbiotas, and the impact of medication use and disease on their diversity. Here, we investigated the diversity of three microbiotas in the upper gastrointestinal tract of paediatric patients in relation to each other and to host factors. Oral, oesophageal and gastric microbiotas from a prospective paediatric cohort (n=54) were profiled using the 16S rRNA gene and ITS2 amplicon sequencing. 16S rRNA gene amplicon sequencing of oesophageal biopsies from a retrospective paediatric cohort (n=96) and shotgun metagenomics data from oesophageal brushings (n=88) were employed for genomic signature validation. Bacterial diversity and composition showed substantial differences across oral, oesophageal and gastric fluid samples that were not replicated for fungi, and the presence of reflux led to increased homogeneity in the bacterial component of these three microbiotas. The oral and oesophageal microbiotas were associated with age, sex, history of oesophageal atresia and presence of oesophageal metaplasia, with the latter characterized by Prevotella enrichment. Proton pump inhibitor use was associated with increased oral bacterial richness in the gastric fluid, and this correlated with increased levels of gastric pro-inflammatory cytokines. Profiling of oesophageal biopsies from a retrospective paediatric cohort confirmed an increased Prevotella prevalence in samples with metaplasia. Analysis of metagenome-derived oesophageal Prevotella melaninogenica genomes identified strain-specific features that were significantly increased in prevalence in samples with metaplasia. Prevotella enrichment is a signature associated with paediatric oesophageal metaplasia, and proton pump inhibitor use substantially alters the paediatric gastric microenvironment.}, } @article {pmid36106847, year = {2023}, author = {Verburgt, CM and Dunn, KA and Ghiboub, M and Lewis, JD and Wine, E and Sigall Boneh, R and Gerasimidis, K and Shamir, R and Penny, S and Pinto, DM and Cohen, A and Bjorndahl, P and Svolos, V and Bielawski, JP and Benninga, MA and de Jonge, WJ and Van Limbergen, JE}, title = {Successful Dietary Therapy in Paediatric Crohn's Disease is Associated with Shifts in Bacterial Dysbiosis and Inflammatory Metabotype Towards Healthy Controls.}, journal = {Journal of Crohn's & colitis}, volume = {17}, number = {1}, pages = {61-72}, pmid = {36106847}, issn = {1876-4479}, support = {/CAPMC/CIHR/Canada ; 2015-2019//Canadian Association of Gastroenterology-Crohn's Colitis Canada New Investigator/ ; 35235//Canadian Foundation of Innovation John R. Evans Leadership fund/ ; //Nova Scotia Health Research Foundation/ ; //IWK Health Centre Research Associateship/ ; //CIHR-SPOR-Chronic Diseases/ ; //Wetenschappelijke Adviesraad of Stichting Steun Emma kinderziekenhuis/ ; 585718//Crohn's and Colitis Foundation/ ; /CAPMC/CIHR/Canada ; }, mesh = {Child ; Humans ; Bacteria/genetics ; *Crohn Disease/drug therapy ; Dysbiosis/therapy ; Escherichia coli ; Firmicutes ; Proteobacteria ; Remission Induction ; Case-Control Studies ; }, abstract = {BACKGROUND AND AIMS: Nutritional therapy with the Crohn's Disease Exclusion Diet + Partial Enteral Nutrition [CDED+PEN] or Exclusive Enteral Nutrition [EEN] induces remission and reduces inflammation in mild-to-moderate paediatric Crohn's disease [CD]. We aimed to assess if reaching remission with nutritional therapy is mediated by correcting compositional or functional dysbiosis.

METHODS: We assessed metagenome sequences, short chain fatty acids [SCFA] and bile acids [BA] in 54 paediatric CD patients reaching remission after nutritional therapy [with CDED + PEN or EEN] [NCT01728870], compared to 26 paediatric healthy controls.

RESULTS: Successful dietary therapy decreased the relative abundance of Proteobacteria and increased Firmicutes towards healthy controls. CD patients possessed a mixture of two metabotypes [M1 and M2], whereas all healthy controls had metabotype M1. M1 was characterised by high Bacteroidetes and Firmicutes, low Proteobacteria, and higher SCFA synthesis pathways, and M2 was associated with high Proteobacteria and genes involved in SCFA degradation. M1 contribution increased during diet: 48%, 63%, up to 74% [Weeks 0, 6, 12, respectively.]. By Week 12, genera from Proteobacteria reached relative abundance levels of healthy controls with the exception of E. coli. Despite an increase in SCFA synthesis pathways, remission was not associated with increased SCFAs. Primary BA decreased with EEN but not with CDED+PEN, and secondary BA did not change during diet.

CONCLUSION: Successful dietary therapy induced correction of both compositional and functional dysbiosis. However, 12 weeks of diet was not enough to achieve complete correction of dysbiosis. Our data suggests that composition and metabotype are important and change quickly during the early clinical response to dietary intervention. Correction of dysbiosis may therefore be an important future treatment goal for CD.}, } @article {pmid36106575, year = {2023}, author = {Huang, YW and Wang, WH and Lan, MY}, title = {Analysing sinonasal microbiota of fungal rhinosinusitis by next-generation sequencing.}, journal = {Clinical otolaryngology : official journal of ENT-UK ; official journal of Netherlands Society for Oto-Rhino-Laryngology & Cervico-Facial Surgery}, volume = {48}, number = {2}, pages = {313-320}, doi = {10.1111/coa.13980}, pmid = {36106575}, issn = {1749-4486}, support = {MOST1102628B075020//Ministry of Science and Technology, Taiwan/ ; V109 C080//Taipei Veterans General Hospital/ ; V111C007//Taipei Veterans General Hospital/ ; }, mesh = {Humans ; Prospective Studies ; *Microbiota/genetics ; Bacteria/genetics ; Streptococcus ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {OBJECTIVES: Fungal rhinosinusitis is an inflammatory disease of the nose that may lead to life-threatening complications. This study compared the bacterial and fungal microbiomes between patients with invasive fungal rhinosinusitis (IFRS) and non-IFRS (NIFRS).

DESIGN: This was a prospective study including 18 IFRS and NIFRS patients. Fungal and bacterial microbiomes from surgical specimens were sequenced from amplicons of the internal transcribed spacer 1 (ITS1) region and the V3-V4 region of the 16S locus, respectively. Microbiomes were generated using the Illumina MiSeq System 2 x 301 base pair chemistry with a paired-end protocol.

SETTING: Tertiary medical centre.

RESULTS: Targeted metagenomics identified Aspergillus spp. as the predominant fungus in both IFRS and NIFRS patients. Based on phylum and genera level diversity, and abundance differences, significant differences of operational taxonomic units (OTUs) (Fusobacterium, Prevotella, Pseudomonas, Neisseria and Streptococcus) were more abundant in NIFRS compared with IFRS patients.

CONCLUSIONS: This is the first study to analyse bacterial and fungal microbiomes in patients with IFRS and NIFRS via ITS1 and 16S genomics sequencing. Bacterial microbiomes from patients with IFRS demonstrated dysbiosis (alterations in diversity and abundance) compared to those from patients with NIFRS.}, } @article {pmid36106339, year = {2022}, author = {Van Wyk, JC and Sewell, BT and Danson, MJ and Tsekoa, TL and Sayed, MF and Cowan, DA}, title = {Engineering enhanced thermostability into the Geobacillus pallidus nitrile hydratase.}, journal = {Current research in structural biology}, volume = {4}, number = {}, pages = {256-270}, pmid = {36106339}, issn = {2665-928X}, abstract = {Nitrile hydratases (NHases) are important biocatalysts for the enzymatic conversion of nitriles to industrially-important amides such as acrylamide and nicotinamide. Although thermostability in this enzyme class is generally low, there is not sufficient understanding of its basis for rational enzyme design. The gene expressing the Co-type NHase from the moderate thermophile, Geobacillus pallidus RAPc8 (NRRL B-59396), was subjected to random mutagenesis. Four mutants were selected that were 3 to 15-fold more thermostable than the wild-type NHase, resulting in a 3.4-7.6 kJ/mol increase in the activation energy of thermal inactivation at 63 °C. High resolution X-ray crystal structures (1.15-1.80 Å) were obtained of the wild-type and four mutant enzymes. Mutant 9E, with a resolution of 1.15 Å, is the highest resolution crystal structure obtained for a nitrile hydratase to date. Structural comparisons between the wild-type and mutant enzymes illustrated the importance of salt bridges and hydrogen bonds in enhancing NHase thermostability. These additional interactions variously improved thermostability by increased intra- and inter-subunit interactions, preventing cooperative unfolding of α-helices and stabilising loop regions. Some hydrogen bonds were mediated via a water molecule, specifically highlighting the significance of structured water molecules in protein thermostability. Although knowledge of the mutant structures makes it possible to rationalize their behaviour, it would have been challenging to predict in advance that these mutants would be stabilising.}, } @article {pmid36106052, year = {2022}, author = {Boucherabine, S and Nassar, R and Mohamed, L and Olsen, M and Alqutami, F and Zaher, S and Hachim, M and Alkhajeh, A and McKirdy, S and Alghafri, R and Tajouri, L and Senok, A}, title = {Healthcare Derived Smart Watches and Mobile Phones are Contaminated Niches to Multidrug Resistant and Highly Virulent Microbes.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {5289-5299}, pmid = {36106052}, issn = {1178-6973}, abstract = {BACKGROUND: As high touch wearable devices, the potential for microbial contamination of smart watches is high. In this study, microbial contamination of smart watches of healthcare workers (HCWs) was assessed and compared to the individual's mobile phone and hands.

METHODS: This study was part of a larger point prevalence survey of microbial contamination of mobile phones of HCWs at the emergency unit of a tertiary care facility. Swabs from smart watches, mobile phones and hands were obtained from four HCWs with dual ownership of these digital devices. Bacterial culture was carried out for all samples and those from smart watches and mobile phones were further assessed using shotgun metagenomic sequencing.

RESULTS: Majority of the participants were females (n/N = 3/4; 75%). Although they all use their digital devices at work and believe that these devices could harbour microbes, cleaning in the preceding 24 hours was reported by one individual. Predominant organisms identified on bacterial culture were multidrug resistant Staphylococcus hominis and Staphylococcus epidermidis. At least one organism identified from the hands was also detected on all mobile phones and two smart watches. Shotgun metagenomics analysis demonstrated greater microbial number and diversity on mobile phones compared to smart watches. All devices had high signatures of Pseudomonas aeruginosa and associated bacteriophages and antibiotic resistance genes. Almost half of the antibiotic resistance genes (n/N = 35/75;46.6%) were present on all devices and majority were related to efflux pumps. Of the 201 virulence factor genes (VFG) identified, majority (n/N = 148/201;73%) were associated with P. aeruginosa with 96% (n/N = 142/148) present on smart watches and mobile phones.

CONCLUSION: This first report on microbial contamination of smart watches using metagenomics next generation sequencing showed similar pattern of contamination with microbes, VFG and antibiotic resistance genes across digital devices. Further studies on microbial contamination of wearable digital devices are urgently needed.}, } @article {pmid36105576, year = {2022}, author = {Chehade, SB and Green, GBH and Graham, CD and Chakraborti, A and Vashai, B and Moon, A and Williams, MB and Vickers, B and Berryhill, T and Van Der Pol, W and Wilson, L and Powell, ML and Smith, DL and Barnes, S and Morrow, C and Mukhtar, MS and Kennedy, GD and Bibb, JA and Watts, SA}, title = {A modified standard American diet induces physiological parameters associated with metabolic syndrome in C57BL/6J mice.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {929446}, pmid = {36105576}, issn = {2296-861X}, support = {R01 MH126948/MH/NIMH NIH HHS/United States ; }, abstract = {Investigations into the causative role that western dietary patterns have on obesity and disease pathogenesis have speculated that quality and quantity of dietary fats and/or carbohydrates have a predictive role in the development of these disorders. Standard reference diets such as the AIN-93 rodent diet have historically been used to promote animal health and reduce variation of results across experiments, rather than model modern human dietary habits or nutrition-related pathologies. In rodents high-fat diets (HFDs) became a classic tool to investigate diet-induced obesity (DIO). These murine diets often relied on a single fat source with the most DIO consistent HFDs containing levels of fat up to 45-60% (kcal), higher than the reported human intake of 33-35% (kcal). More recently, researchers are formulating experimental animal (pre-clinical) diets that reflect mean human macro- and micronutrient consumption levels described by the National Health and Nutrition Examination Survey (NHANES). These diets attempt to integrate relevant ingredient sources and levels of nutrients; however, they most often fail to include high-fructose corn syrup (HFCS) as a source of dietary carbohydrate. We have formulated a modified Standard American Diet (mSAD) that incorporates relevant levels and sources of nutrient classes, including dietary HFCS, to assess the basal physiologies associated with mSAD consumption. Mice proffered the mSAD for 15 weeks displayed a phenotype consistent with metabolic syndrome, exhibiting increased adiposity, fasting hyperglycemia with impaired glucose and insulin tolerance. Metabolic alterations were evidenced at the tissue level as crown-like structures (CLS) in adipose tissue and fatty acid deposition in the liver, and targeted 16S rRNA metagenomics revealed microbial compositional shifts between dietary groups. This study suggests diet quality significantly affects metabolic homeostasis, emphasizing the importance of developing relevant pre-clinical diets to investigate chronic diseases highly impacted by western dietary consumption patterns.}, } @article {pmid36105149, year = {2022}, author = {Chen, S and Niu, C and Lv, W}, title = {Multi-omics insights reveal the remodeling of gut mycobiome with P. gingivalis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {937725}, pmid = {36105149}, issn = {2235-2988}, mesh = {Animals ; Feces/microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; Mice ; *Mycobiome ; Porphyromonas gingivalis ; }, abstract = {As a keystone periodontal pathogen, Porphyromonas gingivalis (P. gingivalis) was suggested to be involved in the progression of systemic diseases by altering the intestinal microecology. However, studies concerning gut microbiome have focused entirely on the bacterial component, while the fungal community (gut mycobiome) has been overlooked. In this study, we aimed to characterize the alteration of gut mycobiome profile with P. gingivalis administration using mice fecal samples. Metagenomic analysis showed a distinct composition pattern of mycobiome and significant difference of beta diversity between control and the P. gingivalis group. Some fungal species were differentially characterized with P. gingivalis administration, among which Pyricularia pennisetigena and Alternaria alternata showed positive correlation with P. gingivalis. KEGG functional analyses revealed that three pathways, namely, "pentose and glucuronate interconversions", "metabolic pathways", and "two-component system", were statistically enriched with P. gingivalis administration. Moreover, the alteration of gut mycobiome was also closely related with serum metabolites, especially lipid and tryptophan metabolic pathways. Taken together, this study demonstrated the alteration of fungal composition and function with P. gingivalis administration for the first time, and investigated the fungi-bacterial interaction and fungi-metabolite interaction preliminarily, providing a whole insight into gut mycobiome remodeling with oral pathobiont through multi-omics analyses.}, } @article {pmid36104920, year = {2022}, author = {Li, T and Li, R and Cao, Y and Tao, C and Deng, X and Ou, Y and Liu, H and Shen, Z and Li, R and Shen, Q}, title = {Soil antibiotic abatement associates with the manipulation of soil microbiome via long-term fertilizer application.}, journal = {Journal of hazardous materials}, volume = {439}, number = {}, pages = {129704}, doi = {10.1016/j.jhazmat.2022.129704}, pmid = {36104920}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents/pharmacology ; *Fertilizers/analysis ; Genes, Bacterial ; Manure/microbiology ; *Microbiota ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The effects of different fertilization on microbial communities and resistome in agricultural soils with a history of fresh manure application remains largely unclear. Here, soil antibiotic resistance genes (ARGs), mobile genetic elements (MGEs) and microbial communities were deciphered using metagenomics approach from a long-term field experiment with different fertilizer inputs. A total of 541 ARG subtypes were identified, with Multidrug, Macrolides-Lincosamides-Streptogramins (MLS), and Bacitracin resistance genes as the most universal ARG types. The abundance of ARGs detected in manure (2.52 ARGs/16 S rRNA) treated soils was higher than chemical fertilizer (2.42 ARGs/16 S rRNA) or compost (2.37 ARGs/16 S rRNA) amended soils. The higher abundance of MGEs and the enrichment of Proteobacteria were observed in manure treated soils than in chemical fertilizer or compost amended soils. Proteobacter and Actinobacter were recognized as the main potential hosts of ARGs revealed by network analysis. Further soil pH was identified as the key driver in determining the composition of both microbial community and resistome. The present study investigated the mechanisms driving the microbial community, MGEs and ARG profiles of long-term fertilized soils with ARGs contamination, and our findings could support strategies to manage the dissemination of soil ARGs.}, } @article {pmid36104726, year = {2022}, author = {Calabrese, FM and Ameur, H and Nikoloudaki, O and Celano, G and Vacca, M and Junior, WJ and Manzari, C and Vertè, F and Di Cagno, R and Pesole, G and De Angelis, M and Gobbetti, M}, title = {Metabolic framework of spontaneous and synthetic sourdough metacommunities to reveal microbial players responsible for resilience and performance.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {148}, pmid = {36104726}, issn = {2049-2618}, mesh = {*Bread/analysis ; Edible Grain ; Fermentation ; Food Microbiology ; *Microbiota/genetics ; }, abstract = {BACKGROUND: In nature, microbial communities undergo changes in composition that threaten their resiliency. Here, we interrogated sourdough, a natural cereal-fermenting metacommunity, as a dynamic ecosystem in which players are subjected to continuous environmental and spatiotemporal stimuli.

RESULTS: The inspection of spontaneous sourdough metagenomes and transcriptomes revealed dominant, subdominant and satellite players that are engaged in different functional pathways. The highest microbial richness was associated with the highest number of gene copies per pathway. Based on meta-omics data collected from 8 spontaneous sourdoughs and their identified microbiota, we de novo reconstructed a synthetic microbial community SDG. We also reconstructed SMC-SD43 from scratch using the microbial composition of its spontaneous sourdough equivalent for comparison. The KEGG number of dominant players in the SDG was not affected by depletion of a single player, whereas the subdominant and satellite species fluctuated, revealing unique contributions. Compared to SMC-SD43, SDG exhibited broader transcriptome redundancy. The invariant volatilome profile of SDG after in situ long-term back slopping revealed its stability. In contrast, SMC-SD43 lost many taxon members. Dominant, subdominant and satellite players together ensured gene and transcript redundancy.

CONCLUSIONS: Our study demonstrates how, by starting from spontaneous sourdoughs and reconstructing these communities synthetically, it was possible to unravel the metabolic contributions of individual players. For resilience and good performance, the sourdough metacommunity must include dominant, subdominant and satellite players, which together ensure gene and transcript redundancy. Overall, our study changes the paradigm and introduces theoretical foundations for directing food fermentations. Video Abstract.}, } @article {pmid36104720, year = {2022}, author = {Ren, X and Cao, S and Akami, M and Mansour, A and Yang, Y and Jiang, N and Wang, H and Zhang, G and Qi, X and Xu, P and Guo, T and Niu, C}, title = {Gut symbiotic bacteria are involved in nitrogen recycling in the tephritid fruit fly Bactrocera dorsalis.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {201}, pmid = {36104720}, issn = {1741-7007}, mesh = {Animals ; Bacteria/genetics/metabolism ; Drosophila/metabolism ; Larva/metabolism ; *Nitrogen/metabolism ; Symbiosis ; *Tephritidae/metabolism/microbiology ; }, abstract = {BACKGROUND: Nitrogen is considered the most limiting nutrient element for herbivorous insects. To alleviate nitrogen limitation, insects have evolved various symbiotically mediated strategies that enable them to colonize nitrogen-poor habitats or exploit nitrogen-poor diets. In frugivorous tephritid larvae developing in fruit pulp under nitrogen stress, it remains largely unknown how nitrogen is obtained and larval development is completed.

RESULTS: In this study, we used metagenomics and metatranscriptomics sequencing technologies as well as in vitro verification tests to uncover the mechanism underlying the nitrogen exploitation in the larvae of Bactrocera dorsalis. Our results showed that nitrogenous waste recycling (NWR) could be successfully driven by symbiotic bacteria, including Enterobacterales, Lactobacillales, Orbales, Pseudomonadales, Flavobacteriales, and Bacteroidales. In this process, urea hydrolysis in the larval gut was mainly mediated by Morganella morganii and Klebsiella oxytoca. In addition, core bacteria mediated essential amino acid (arginine excluded) biosynthesis by ammonium assimilation and transamination.

CONCLUSIONS: Symbiotic bacteria contribute to nitrogen transformation in the larvae of B. dorsalis in fruit pulp. Our findings suggest that the pattern of NWR is more likely to be applied by B. dorsalis, and M. morganii, K. oxytoca, and other urease-positive strains play vital roles in hydrolysing nitrogenous waste and providing metabolizable nitrogen for B. dorsalis.}, } @article {pmid36103095, year = {2022}, author = {Varada, VV and Kumar, S and Chhotaray, S and Tyagi, AK}, title = {Host-specific probiotics feeding influence growth, gut microbiota, and fecal biomarkers in buffalo calves.}, journal = {AMB Express}, volume = {12}, number = {1}, pages = {118}, pmid = {36103095}, issn = {2191-0855}, support = {NCVTC/Budget/2019-20/860//ICAR-NCVTC/ ; }, abstract = {The current study is aimed to evaluate the effect of host-specific probiotics on the gut microbiome, performance, and select fecal biomarkers of gut health in preruminant buffalo calves. Eight Murrah buffalo calves (3-5 days old; 32.52 ± 0.43 kg average body weight (BW)) were randomly allocated into two groups as follows; 1) Group I (n = 4) fed basal diet alone (CON); 2) Group II (n = 4) supplemented with a lyophilized probiotic formulation at a dose rate of 1 g/day/head (1 × 10[9] CFU/g) having Limosilactobacillus reuteri BF-E7 and Ligilactobacillus salivarius BF-17 along with basal diet (PF) for 30 days. Results revealed that final BW (kg), average daily gain (g/day), average dry matter intake (g/day), and structural growth measurements were significantly (P < 0.05) increased in the probiotics supplemented group (PF) compared to the control (CON). Fecal pH, fecal moisture, and fecal score were reduced (P < 0.05) in PF than in CON. Moreover, levels of fecal propionate, lactate, and ammonia altered positively in PF compared with CON. The relative abundance of Firmicutes tended to be higher (P = 0.10) in the probiotics fed group than CON. However, the relative abundance of Proteobacteria was significantly lower (P = 0.03) for calves fed probiotics on day 15. A trend was observed in Bacteroides (P = 0.07) and Lactobacillus (P = 0.08) abundances in the feces of the PF than in CON. Overall, it can be concluded that the administration of probiotic formulations significantly improved the performance and gut health of buffalo calves via modulating the gut microbiota composition.}, } @article {pmid36102858, year = {2023}, author = {Fourgeaud, J and Regnault, B and Faury, H and Da Rocha, N and Jamet, A and Stirnemann, J and Eloit, M and Perot, P and Leruez-Ville, M and Driessen, M and , }, title = {Fetal Zika virus infection diagnosed by metagenomic next-generation sequencing of amniotic fluid.}, journal = {Ultrasound in obstetrics & gynecology : the official journal of the International Society of Ultrasound in Obstetrics and Gynecology}, volume = {61}, number = {1}, pages = {116-117}, doi = {10.1002/uog.26074}, pmid = {36102858}, issn = {1469-0705}, mesh = {Pregnancy ; Female ; Humans ; *Zika Virus Infection/diagnosis ; Amniotic Fluid ; *Zika Virus/genetics ; Prenatal Care ; High-Throughput Nucleotide Sequencing ; }, } @article {pmid36102785, year = {2022}, author = {Thornber, K and Bashar, A and Ahmed, MS and Bell, A and Trew, J and Hasan, M and Hasan, NA and Alam, MM and Chaput, DL and Haque, MM and Tyler, CR}, title = {Antimicrobial Resistance in Aquaculture Environments: Unravelling the Complexity and Connectivity of the Underlying Societal Drivers.}, journal = {Environmental science & technology}, volume = {56}, number = {21}, pages = {14891-14903}, pmid = {36102785}, issn = {1520-5851}, mesh = {Humans ; *Drug Resistance, Bacterial ; *Anti-Bacterial Agents/pharmacology ; Aquaculture ; Rural Population ; Global Health ; }, abstract = {Food production environments in low- and middle-income countries (LMICs) are recognized as posing significant and increasing risks to antimicrobial resistance (AMR), one of the greatest threats to global public health and food security systems. In order to maximize and expedite action in mitigating AMR, the World Bank and AMR Global Leaders Group have recommended that AMR is integrated into wider sustainable development strategies. Thus, there is an urgent need for tools to support decision makers in unravelling the complex social and environmental factors driving AMR in LMIC food-producing environments and in demonstrating meaningful connectivity with other sustainable development issues. Here, we applied the Driver-Pressure-State-Impact-Response (DPSIR) conceptual framework to an aquaculture case study site in rural Bangladesh, through the analysis of distinct social, microbiological, and metagenomic data sets. We show how the DPSIR framework supports the integration of these diverse data sets, first to systematically characterize the complex network of societal drivers of AMR in these environments and second to delineate the connectivity between AMR and wider sustainable development issues. Our study illustrates the complexity and challenges of addressing AMR in rural aquaculture environments and supports efforts to implement global policy aimed at mitigating AMR in aquaculture and other rural LMIC food-producing environments.}, } @article {pmid36102704, year = {2022}, author = {Boguniewicz, J and Demmler-Harrison, GJ and Lotze, TE and Jarjour, IT and Whitehead, WE and Frontiero, J and Dutta, A and Fogarty, T and Hunter, JV and Ogunbona, OB and Pareek, AV and Cameron, LH}, title = {Management of Extensive Central Nervous System Cladophialophora bantiana Infection in a 9-Year-Old Child.}, journal = {The Pediatric infectious disease journal}, volume = {41}, number = {11}, pages = {e481-e486}, doi = {10.1097/INF.0000000000003680}, pmid = {36102704}, issn = {1532-0987}, mesh = {Amphotericin B ; Antifungal Agents/therapeutic use ; Ascomycota ; Central Nervous System ; *Central Nervous System Infections/drug therapy ; *Cerebral Ventriculitis/drug therapy ; Child ; Female ; Humans ; *Phaeohyphomycosis/diagnosis/drug therapy/microbiology ; }, abstract = {BACKGROUND: Pediatric central nervous system (CNS) phaeohyphomycosis is a rare invasive fungal infection associated with high mortality.

METHODS: We describe a child with progressive neurologic symptoms whose ultimate diagnosis was Cladophialophora bantiana -associated CNS phaeohyphomycosis. We discuss her clinical presentation, medical and surgical management and review the current literature.

RESULTS: A 9-year-old female presented with acute onset of headaches, ophthalmoplegia and ataxia. Initial infectious work-up was negative, including serial fungal cerebrospinal fluid cultures. Over 2 months, she experienced progressive cognitive and motor declines, and imaging revealed worsening meningitis, ventriculitis and cerebritis. Ultimately, Cladophialophora was detected by plasma metagenomic next-generation sequencing (mNGS). Fourth ventricle fluid sampling confirmed the diagnosis of C. bantiana infection. Given the extent of her disease, complete surgical resection was not feasible. She required multiple surgical debridement procedures and prolonged antifungal therapy, including the instillation of intraventricular amphotericin B. With aggressive surgical and medical management, despite her continued neurologic deficits, she remains alive 3 years after her initial diagnosis. To our knowledge, this is one of a few published pediatric cases of CNS phaeohyphomycosis and the first with the causative pathogen identified by plasma mNGS.

CONCLUSION: CNS phaeohyphomycosis is a serious, life-threatening infection. The preferred management includes a combination of surgical resection and antifungal therapy. In cases complicated by refractory ventriculitis, intraventricular antifungal therapy can be considered as adjuvant therapy. Direct sampling of the CNS for pathogen identification and susceptibility testing is the gold standard for diagnosis; however, the use of plasma mNGS may expedite the diagnosis.}, } @article {pmid36100999, year = {2022}, author = {Bell, E and Rattray, JE and Sloan, K and Sherry, A and Pilloni, G and Hubert, CRJ}, title = {Hyperthermophilic endospores germinate and metabolize organic carbon in sediments heated to 80°C.}, journal = {Environmental microbiology}, volume = {24}, number = {11}, pages = {5534-5545}, pmid = {36100999}, issn = {1462-2920}, mesh = {RNA, Ribosomal, 16S/genetics ; *Geologic Sediments/microbiology ; *Carbon ; Archaea/genetics ; Spores, Bacterial/genetics ; Bacteria, Anaerobic/genetics ; Firmicutes/genetics ; }, abstract = {Cold surface sediments host a seedbank of functionally diverse thermophilic bacteria. These thermophiles are present as endospores, which are widely dispersed in aquatic environments. Here, we investigated the functional potential of endospore populations in cold surface sediments heated to 80°C. Microbial production of acetate was observed at 80°C and could be enhanced by supplying additional organic carbon substrates. Comparison of 16S rRNA gene amplicon libraries from 80°C enrichments to sediments heated to lower temperatures (50-70°C) showed that temperature selects for distinct populations of endospore-forming bacteria. Whereas sulfate-reducing thermophiles were enriched in 50-70°C incubations, 80°C exceeds their thermal tolerance and selects for hyperthermophilic organotrophic bacteria that are similarly detected in amplicon libraries from sediments heated to 90°C. Genome-resolved metagenomics revealed novel carbon cycling members of Symbiobacteriales, Thermosediminibacteraceae, Thermanaeromonas and Calditerricola with the genomic potential for the degradation of carbohydrates, sugars, amino acids and nucleotides. Endospores of thermophilic bacteria are deposited on seabed sediments worldwide where they remain dormant as they are buried in the accumulating sediments. Our results suggest that endospore populations could be activated by temperature increases encountered during burial and show the potential for organotrophic metabolic activity contributing to acetate generation in deep hot sediments.}, } @article {pmid36100971, year = {2022}, author = {Xiao, C and Wang, JT and Su, C and Miao, Z and Tang, J and Ouyang, Y and Yan, Y and Jiang, Z and Fu, Y and Shuai, M and Gou, W and Xu, F and Yu, EY and Liang, Y and Liang, X and Tian, Y and Wang, J and Huang, F and Zhang, B and Wang, H and Chen, YM and Zheng, JS}, title = {Associations of dietary diversity with the gut microbiome, fecal metabolites, and host metabolism: results from 2 prospective Chinese cohorts.}, journal = {The American journal of clinical nutrition}, volume = {116}, number = {4}, pages = {1049-1058}, pmid = {36100971}, issn = {1938-3207}, support = {R01 HD038700/HD/NICHD NIH HHS/United States ; R01 HD030880/HD/NICHD NIH HHS/United States ; R01-HD30880/GF/NIH HHS/United States ; R24 HD050924/HD/NICHD NIH HHS/United States ; R01 DK104371/DK/NIDDK NIH HHS/United States ; }, mesh = {Bile Acids and Salts ; China ; Ecosystem ; Feces/chemistry ; *Gastrointestinal Microbiome ; Humans ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Dietary diversity is essential for human health. The gut ecosystem provides a potential link between dietary diversity, host metabolism, and health, yet this mechanism is poorly understood.

OBJECTIVES: Here, we aimed to investigate the relation between dietary diversity and the gut environment as well as host metabolism from a multiomics perspective.

METHODS: Two independent longitudinal Chinese cohorts (a discovery and a validation cohort) were included in the present study. Dietary diversity was evaluated with FFQs. In the discovery cohort (n = 1916), we performed shotgun metagenomic and 16S ribosomal ribonucleic acid (rRNA) sequencing to profile the gut microbiome. We used targeted metabolomics to quantify fecal and serum metabolites. The associations between dietary diversity and the microbial composition were replicated in the validation cohort (n = 1320).

RESULTS: Dietary diversity was positively associated with α diversity of the gut microbiota. We identified dietary diversity-related gut environment features, including the microbial structure (β diversity), 68 microbial genera, 18 microbial species, 8 functional pathways, and 13 fecal metabolites. We further found 332 associations of dietary diversity and related gut environment features with circulating metabolites. Both the dietary diversity and diversity-related features were inversely correlated with 4 circulating secondary bile acids. Moreover, 16 mediation associations were observed among dietary diversity, diversity-related features, and the 4 secondary bile acids.

CONCLUSIONS: These results suggest that high dietary diversity is associated with the gut microbial environment. The identified key microbes and metabolites may serve as hypotheses to test for preventing metabolic diseases.}, } @article {pmid36100957, year = {2022}, author = {Jia, L and Weng, S and Wu, J and Tian, X and Zhang, Y and Wang, X and Wang, J and Yan, D and Wang, W and Fang, F and Zhu, Z and Qiu, C and Zhang, W and Xu, Y and Wan, Y}, title = {Preexisting antibodies targeting SARS-CoV-2 S2 cross-react with commensal gut bacteria and impact COVID-19 vaccine induced immunity.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2117503}, pmid = {36100957}, issn = {1949-0984}, mesh = {Animals ; Antibodies, Monoclonal ; Antibodies, Viral ; *COVID-19/prevention & control ; COVID-19 Vaccines ; Escherichia coli ; *Gastrointestinal Microbiome ; Humans ; Mice ; SARS-CoV-2 ; *Viral Vaccines ; }, abstract = {The origins of preexisting SARS-CoV-2 cross-reactive antibodies and their potential impacts on vaccine efficacy have not been fully clarified. In this study, we demonstrated that S2 was the prevailing target of the preexisting S protein cross-reactive antibodies in both healthy human and SPF mice. A dominant antibody epitope was identified on the connector domain of S2 (1147-SFKEELDKYFKNHT-1160, P144), which could be recognized by preexisting antibodies in both human and mouse. Through metagenomic sequencing and fecal bacteria transplant, we demonstrated that the generation of S2 cross-reactive antibodies was associated with commensal gut bacteria. Furthermore, six P144 reactive monoclonal antibodies were isolated from naïve SPF mice and were proven to cross-react with commensal gut bacteria collected from both human and mouse. A variety of cross-reactive microbial proteins were identified using LC-MS, of which E. coli derived HSP60 and HSP70 proteins were confirmed to be able to bind to one of the isolated monoclonal antibodies. Mice with high levels of preexisting S2 cross-reactive antibodies mounted higher S protein specific binding antibodies, especially against S2, after being immunized with a SARS-CoV-2 S DNA vaccine. Similarly, we found that levels of preexisting S2 and P144-specific antibodies correlated positively with RBD binding antibody titers after two doses of inactivated SARS-CoV-2 vaccination in human. Collectively, our study revealed an alternative origin of preexisting S2-targeted antibodies and disclosed a previously neglected aspect of the impact of gut microbiota on host anti-SARS-CoV-2 immunity.}, } @article {pmid36100953, year = {2022}, author = {Bai, X and Sun, Y and Li, Y and Li, M and Cao, Z and Huang, Z and Zhang, F and Yan, P and Wang, L and Luo, J and Wu, J and Fan, D and Chen, H and Zhi, M and Lan, P and Zeng, Z and Wu, X and Miao, Y and Zuo, T}, title = {Landscape of the gut archaeome in association with geography, ethnicity, urbanization, and diet in the Chinese population.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {147}, pmid = {36100953}, issn = {2049-2618}, mesh = {Adult ; Archaea ; Bacteria/genetics ; Diet ; Ethnicity ; *Gastrointestinal Microbiome/genetics ; Geography ; Humans ; *Urbanization ; }, abstract = {BACKGROUND AND AIMS: The human gut is home to a largely underexplored microbiome component, the archaeome. Little is known of the impact of geography, urbanization, ethnicity, and diet on the gut archaeome in association with host health. We aim to delineate the variation of the human gut archaeome in healthy individuals and its association with environmental factors and host homeostasis.

METHODS: Using metagenomic sequencing, we characterized the fecal archaeomes of 792 healthy adult subjects from 5 regions in China, spanning 6 ethnicities (Han, Zang, Miao, Bai, Dai, and Hani), consisting of both urban and rural residents for each ethnicity. In addition, we sampled 119 host variables (including lifestyle, diet, and blood parameters) and interrogated the influences of those factors, individually and combined, on gut archaeome variations.

RESULTS: Population geography had the strongest impact on the gut archaeome composition, followed by urbanization, dietary habit, and ethnicity. Overall, the metadata had a cumulative effect size of 11.0% on gut archaeome variation. Urbanization decreased both the α-diversity (intrinsic microbial diversity) and the β-diversity (inter-individual dissimilarities) of the gut archaeome, and the archaea-to-bacteria ratios in feces, whereas rural residents were enriched for Methanobrevibacter smithii in feces. Consumption of buttered milk tea (a characteristic diet of the rural Zang population) was associated with increased abundance of M. smithii. M. smithii was at the central hub of archaeal-bacterial interactions in the gut microecology, where it was positively correlated with the abundances of a multitude of short chain fatty acid (SCFA)-producing bacteria (including Roseburia faecis, Collinsella aerofaciens, and Prevotella copri). Moreover, a decreased abundance of M. smithii was associated with increased human blood levels of cholinesterase in the urban population, coinciding with the increasing prevalence of noncommunicable diseases (such as dementia) during urbanization.

CONCLUSIONS: Our data highlight marked contributions of environmental and host factors (geography, urbanization, ethnicity, and habitual diets) to gut archaeome variations across healthy individuals, and underscore the impact of urbanization on the gut archaeome in association with host health in modern society. Video Abstract.}, } @article {pmid36100950, year = {2022}, author = {Pitta, DW and Indugu, N and Melgar, A and Hristov, A and Challa, K and Vecchiarelli, B and Hennessy, M and Narayan, K and Duval, S and Kindermann, M and Walker, N}, title = {The effect of 3-nitrooxypropanol, a potent methane inhibitor, on ruminal microbial gene expression profiles in dairy cows.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {146}, pmid = {36100950}, issn = {2049-2618}, mesh = {Animals ; Cattle ; *Euryarchaeota/metabolism ; Female ; *Methane/metabolism ; Methanobacteriaceae/metabolism ; Methanol/metabolism ; Propanols ; Rumen/microbiology ; Transcriptome ; }, abstract = {BACKGROUND: Enteric methane emissions from dairy cows are an environmental problem as well as a gross feed energy loss to the animal. Methane is generated in the rumen by methanogenic archaea from hydrogen (H2) + carbon dioxide and from H2 + methanol or methylamines. The methanogenic substrates are provided by non-methanogens during feed fermentation. Methane mitigation approaches have yielded variable results, partially due to an incomplete understanding of the contribution of hydrogenotrophic and methylotrophic archaea to methanogenesis. Research indicates that 3-nitrooxypropanol (3-NOP) reduces enteric methane formation in dairy cows by inhibiting methyl-coenzyme M reductase (MCR), the enzyme responsible for methane formation. The purpose of this study was to utilize metagenomic and metatranscriptomic approaches to investigate the effect of 3-NOP on the rumen microbiome and to determine the fate of H2 that accumulates less than expected under inhibited methanogenesis.

RESULTS: The inhibitor 3-NOP was more inhibitory on Methanobrevibacter species than methanol-utilizing Methanosphaera and tended to reduce the gene expression of MCR. Under inhibited methanogenesis by 3-NOP, fluctuations in H2 concentrations were accompanied by changes in the expression of [FeFe] hydrogenases in H2-producing bacteria to regulate the amount of H2 production. No previously reported alternative H2 sinks increased under inhibited methanogenesis except for a significant increase in gene expression of enzymes involved in the butyrate pathway.

CONCLUSION: By taking a metatranscriptomic approach, this study provides novel insights on the contribution of methylotrophic methanogens to total methanogenesis and regulation of H2 metabolism under normal and inhibited methanogenesis by 3-NOP in the rumen. Video Abstract.}, } @article {pmid36100874, year = {2022}, author = {Elmore, MG and Groves, CL and Hajimorad, MR and Stewart, TP and Gaskill, MA and Wise, KA and Sikora, E and Kleczewski, NM and Smith, DL and Mueller, DS and Whitham, SA}, title = {Detection and discovery of plant viruses in soybean by metagenomic sequencing.}, journal = {Virology journal}, volume = {19}, number = {1}, pages = {149}, pmid = {36100874}, issn = {1743-422X}, mesh = {Metagenomics ; *Plant Viruses/genetics ; *Potyvirus/genetics ; Glycine max/genetics ; }, abstract = {BACKGROUND: Viruses negatively impact soybean production by causing diseases that affect yield and seed quality. Newly emerging or re-emerging viruses can also threaten soybean production because current control measures may not be effective against them. Furthermore, detection and characterization of new plant viruses requires major efforts when no sequence or antibody-based resources are available.

METHODS: In this study, soybean fields were scouted for virus-like disease symptoms during the 2016-2019 growing seasons. Total RNA was extracted from symptomatic soybean parts, cDNA libraries were prepared, and RNA sequencing was performed using high-throughput sequencing (HTS). A custom bioinformatic workflow was used to identify and assemble known and unknown virus genomes.

RESULTS: Several viruses were identified in single or mixed infections. Full- or nearly full-length genomes were generated for tobacco streak virus (TSV), alfalfa mosaic virus (AMV), tobacco ringspot virus (TRSV), soybean dwarf virus (SbDV), bean pod mottle virus (BPMV), soybean vein necrosis virus (SVNV), clover yellow vein virus (ClYVV), and a novel virus named soybean ilarvirus 1 (SIlV1). Two distinct ClYVV isolates were recovered, and their biological properties were investigated in Nicotiana benthamiana, broad bean, and soybean. In addition to infections by individual viruses, we also found that mixed viral infections in various combinations were quite common.

CONCLUSIONS: Taken together, the results of this study showed that HTS-based technology is a valuable diagnostic tool for the identification of several viruses in field-grown soybean and can provide rapid information about expected viruses as well as viruses that were previously not detected in soybean.}, } @article {pmid36100442, year = {2022}, author = {Shoskes, A and Hassett, C and Dani, D and Majeed, A}, title = {Pearls & Oy-sters: Seronegative Eastern Equine Encephalitis in an Immunocompromised Stem Cell Transplant Recipient.}, journal = {Neurology}, volume = {99}, number = {22}, pages = {1004-1007}, doi = {10.1212/WNL.0000000000201334}, pmid = {36100442}, issn = {1526-632X}, mesh = {Male ; Humans ; *Encephalomyelitis, Eastern Equine ; Immunocompromised Host ; Brain ; Magnetic Resonance Imaging ; Stem Cell Transplantation/adverse effects ; }, abstract = {Altered mental status in immunosuppressed patients has a wide differential diagnosis. In this case, a 27-year-old man presented with encephalopathy, nausea, vomiting, and fevers. His medical history was significant for acute myeloid leukemia in remission after allogenic hematopoietic stem cell transplantation 17 months prior complicated by graft vs host disease affecting his skin treated with sirolimus. A lumbar puncture was performed with a lymphocytic pleocytosis, mildly elevated protein, and negative Gram-stain and bacterial and fungal cultures. His examination deteriorated, and he became comatose with loss of pupillary and corneal reflexes. An MRI of his brain demonstrated T2/fluid-attenuated inversion recovery signal abnormality involving the bilateral basal ganglia, mesial temporal lobes, and entire brainstem along with bilateral temporal parenchymal and leptomeningeal enhancement. Ultimately, diagnosis was made through metagenomic PCR sequencing from his CSF. This case highlights diagnostic challenges in immunosuppressed patients because antibodies against the causative antigen were negative (potentially related to decreased antibody production in the setting of immunosuppression).}, } @article {pmid36099860, year = {2022}, author = {Jurick Ii, WM}, title = {Biotechnology approaches to reduce antimicrobial resistant postharvest pathogens, mycotoxin contamination, and resulting product losses.}, journal = {Current opinion in biotechnology}, volume = {78}, number = {}, pages = {102791}, doi = {10.1016/j.copbio.2022.102791}, pmid = {36099860}, issn = {1879-0429}, mesh = {Humans ; *Mycotoxins/analysis ; Food Contamination/prevention & control/analysis ; Food Microbiology ; Food ; *Anti-Infective Agents/pharmacology ; Fungi ; }, abstract = {Postharvest fungal pathogens of stored fruits, nuts, and vegetables cause food spoilage and some produce mycotoxins that harm human health. These fungi can develop resistance to the chemicals used for their control despite judicious use, rotating different chemistries, and routine resistance monitoring. Once antimicrobial resistance develops, these fungi are difficult to control and persist in the field, packing, and storage environments. Therefore, new tools and approaches for control with reduced emphasis on chemicals and movement toward durable, innovative approaches (e.g. double-stranded RNA, translational metagenomics, and host-induced gene silencing) are warranted. The focus of this review is on formative breakthroughs to combat postharvest pathogens and the mycotoxins they produce via translation of fundamental science using biotechnology tools.}, } @article {pmid36099099, year = {2022}, author = {Ninomiya, K and Paudel, D and Uehara, O and Morikawa, T and Islam, ST and Khurelchuluun, A and Ariwansa, D and Yoshida, K and Matsuoka, H and Hajime, H and Kayoko, F and Nakamura, K and Abiko, Y}, title = {Effect of Systemic Administration of Amitriptyline on Oral Microbes in Rats.}, journal = {In vivo (Athens, Greece)}, volume = {36}, number = {5}, pages = {2134-2142}, pmid = {36099099}, issn = {1791-7549}, mesh = {*Amitriptyline/pharmacology ; Animals ; Antidepressive Agents ; *Gastrointestinal Microbiome ; Rats ; Rats, Sprague-Dawley ; }, abstract = {BACKGROUND/AIM: Amitriptyline is a major tricyclic antidepressant that is also used to relieve chronic orofacial pain. Recently, alterations in gut flora due to various antidepressants have been demonstrated. However, it remains unknown how antidepressants affect the oral environment, including microbiota and innate immunity. The aim of this study was to investigate the effects of amitriptyline on oral microflora and antimicrobial peptides.

MATERIALS AND METHODS: Sprague-Dawley rats were intraperitoneally injected with amitriptyline for 2 weeks. The DNA extracted from the oral swabs were used to perform 16SrRNA sequencing to evaluate the oral microbiome. Quantitative RT-PCR was performed to evaluate the mRNA levels of antimicrobial peptides in the buccal tissues.

RESULTS: No significant differences in salivary flow rates were observed between the amitriptyline and control groups. Taxonomic analysis showed significant alterations in bacteria such as Corynebacterium, Rothia, and Porphyromonas due to amitriptyline administration. The beta diversity showed significant differences between the amitriptyline and control groups. Additionally, the predicted metagenome functions were significantly different between the two groups. The mRNA expression levels of antimicrobial peptides in the amitriptyline group were significantly higher as compared to controls.

CONCLUSION: Systemic administration of amitriptyline may affect the oral environment, including oral microbes and innate immunity in the oral mucosa.}, } @article {pmid36098925, year = {2022}, author = {Sharma, R and Patil, C and Majeed, J and Kumar, S and Aggarwal, G}, title = {Next-generation sequencing in the biodiversity conservation of endangered medicinal plants.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {49}, pages = {73795-73808}, pmid = {36098925}, issn = {1614-7499}, mesh = {Biodiversity ; Computational Biology ; Genomics ; High-Throughput Nucleotide Sequencing ; *Plants, Medicinal/genetics ; }, abstract = {Medicinal plants have been used as traditional herbal medicines in the treatment of various types of diseases. However, the increased demand for these plants highlights the importance of conservation specifically for endangered species. Significant advancements in next-generation sequencing (NGS) technologies have accelerated medicinal plant research while reducing costs and time demands. NGS systems enable high-throughput whole genome sequencing as well as direct RNA sequencing and transcriptome analysis. The sequence data sets created can be used in a variety of areas of study, including biodiversity conservation, comparative genomics, transcriptomic analysis, single cell mining, metagenomics, epigenetics, molecular marker discovery, multi genome sequencing, and so on. Commercial sequencing service providers are constantly working to improve technologies to address bioinformatics problems in NGS data analysis. Several genome sequencing projects on medicinal plants have been completed recently and a few more are in the works. In some medicinal plants, massive NGS-based data has been developed. In the present review, we have attempted to briefly discuss advancements in NGS technology on medicinally essential plants in India. The review will also provide ideas for applying NGS technologies for exploring genomes of various endangered medicinal plants whose genome sequences are not normally available and thus provides valuable insights for the conservation of these vulnerable species.}, } @article {pmid36098649, year = {2022}, author = {Chou, JY and Hsu, PC and Leu, JY}, title = {Enforcement of Postzygotic Species Boundaries in the Fungal Kingdom.}, journal = {Microbiology and molecular biology reviews : MMBR}, volume = {86}, number = {4}, pages = {e0009822}, pmid = {36098649}, issn = {1098-5557}, mesh = {*Metagenomics ; *Genetic Speciation ; Hybridization, Genetic ; }, abstract = {Understanding the molecular basis of speciation is a primary goal in evolutionary biology. The formation of the postzygotic reproductive isolation that causes hybrid dysfunction, thereby reducing gene flow between diverging populations, is crucial for speciation. Using various advanced approaches, including chromosome replacement, hybrid introgression and transcriptomics, population genomics, and experimental evolution, scientists have revealed multiple mechanisms involved in postzygotic barriers in the fungal kingdom. These results illuminate both unique and general features of fungal speciation. Our review summarizes experiments on fungi exploring how Dobzhansky-Muller incompatibility, killer meiotic drive, chromosome rearrangements, and antirecombination contribute to postzygotic reproductive isolation. We also discuss possible evolutionary forces underlying different reproductive isolation mechanisms and the potential roles of the evolutionary arms race under the Red Queen hypothesis and epigenetic divergence in speciation.}, } @article {pmid36098560, year = {2022}, author = {Hu, R and Liu, S and Huang, W and Nan, Q and Strong, PJ and Saleem, M and Zhou, Z and Luo, Z and Shu, F and Yan, Q and He, Z and Wang, C}, title = {Evidence for Assimilatory Nitrate Reduction as a Previously Overlooked Pathway of Reactive Nitrogen Transformation in Estuarine Suspended Particulate Matter.}, journal = {Environmental science & technology}, volume = {56}, number = {20}, pages = {14852-14866}, doi = {10.1021/acs.est.2c04390}, pmid = {36098560}, issn = {1520-5851}, mesh = {*Ammonium Compounds/metabolism ; Bacteria/genetics/metabolism ; Denitrification ; Ecosystem ; Nitrate Reductases/metabolism ; Nitrates/metabolism ; Nitrite Reductases/metabolism ; *Nitrogen/analysis ; Nitrogen Oxides ; Organic Chemicals/metabolism ; Oxidation-Reduction ; Particulate Matter ; }, abstract = {Suspended particulate matter (SPM) contributes to the loss of reactive nitrogen (Nr) in estuarine ecosystems. Although denitrification and anaerobic ammonium oxidation in SPM compensate for the current imbalance of global nitrogen (N) inputs and sinks, it is largely unclear whether other pathways for Nr transformation exist in SPM. Here, we combined stable isotope measurements with metagenomics and metatranscriptomics to verify the occurrence of dissimilatory nitrate reduction to ammonium (DNRA) in the SPM of the Pearl River Estuary (PRE). Surprisingly, the conventional functional genes of DNRA (nirBD) were abundant and highly expressed in SPM, which was inconsistent with a low potential rate. Through taxonomic and comparative genomic analyses, we demonstrated that nitrite reductase (NirBD) in conjunction with assimilatory nitrate reductase (NasA) performed assimilatory nitrate reduction (ANR) in SPM, and diverse alpha- and gamma-proteobacterial lineages were identified as key active heterotrophic ANR bacteria. Moreover, ANR was predicted to have a relative higher occurrence than denitrification and DNRA in a survey of Nr transformation pathways in SPM across the PRE spanning 65 km. Collectively, this study characterizes a previously overlooked pathway of Nr transformation mediated by heterotrophic ANR bacteria in SPM and has important implications for our understanding of N cycling in estuaries.}, } @article {pmid36097654, year = {2022}, author = {Yoshimura, M and Shimizu, K and Nakura, Y and Kawahara, K and Katano, H and Motooka, D and Takeuchi, M and Nagamune, K and Imamura, Y and Nakamura, S and Yasukawa, K and Hasegawa, H and Yoshida, Y and Yanagihara, I}, title = {A fatal case of hemophagocytic lymphohistiocytosis associated with gestational psittacosis without symptoms of pneumonia.}, journal = {The journal of obstetrics and gynaecology research}, volume = {48}, number = {12}, pages = {3325-3330}, doi = {10.1111/jog.15429}, pmid = {36097654}, issn = {1447-0756}, support = {JP17fk0108210//Japan Agency for Medical Research and Development/ ; JP19fk0108104//Japan Agency for Medical Research and Development/ ; JP21fk0108143//Japan Agency for Medical Research and Development/ ; JP18K08431//JSPS KAKENHI/ ; JP20H03654//JSPS KAKENHI/ ; JP21K16329//JSPS KAKENHI/ ; 14533524//SENTAN, Japan Science and TechnologyAgency/ ; }, mesh = {Humans ; Female ; Pregnancy ; *Psittacosis/complications/diagnosis ; *Lymphohistiocytosis, Hemophagocytic ; *Chlamydophila psittaci ; *Pneumonia/complications/diagnosis ; Lung ; }, abstract = {Psittacosis is a zoonotic infection caused by Chlamydia psittaci. Most patients present with acute respiratory symptoms and systemic illness. When C. psittaci infects pregnant women, it causes severe clinical manifestations called gestational psittacosis. Here we report a case of gestational psittacosis. Our patient lacked respiratory symptoms, and pathological postmortem examinations revealed severe placentitis. Both DNA and immunohistochemical analyses were positive for C. psittaci from formalin-fixed paraffin-embedded tissues. The chlamydial DNA in the placenta was about 100 times more abundant than that in the lungs; therefore, the placenta rather than the lungs was the probable target of the C. psittaci infection during this pregnancy. We could not identify the source of infection. Gestational psittacosis should be considered in the differential diagnosis for fever of unknown origin during pregnancy, even in cases lacking respiratory symptoms.}, } @article {pmid36097471, year = {2022}, author = {Zhu, M and Zhang, S and Shi, Q and Sun, X and Zhang, X and Wang, H and Liu, Y and Sun, M}, title = {Swollen inguinal lymph nodes with low fever and night sweat: diagnosis and treatment of case of cat-scratch disease lymphadenitis with sinus formation.}, journal = {Heliyon}, volume = {8}, number = {9}, pages = {e10448}, pmid = {36097471}, issn = {2405-8440}, abstract = {A 52-year-old woman complained of inguinal lymph node enlargement, low fever and night sweats for 20 days. After pathological biopsy and metagenomic sequencing, she was diagnosed as having Bartonella henselae infection. Her lymph nodes were accompanied by multiple ulcers in the affected area and sinus formation. Azithromycin was administered according to the Sanford Guide to Antimicrobial Therapy 2020, combined with wound repair and partial resection of inguinal lymph nodes. The patient showed good recovery after the operation. In all, lymphadenitis associated with B. henselae infection is difficult to diagnose. Lymphadenitis with suppuration and sinus formation needs multidisciplinary consultation. When the causal pathogen is unknown, metagenomic sequencing is recommended for a definite diagnosis.}, } @article {pmid36097175, year = {2022}, author = {Zaidi, AH and Pratama, MY and Omstead, AN and Gorbonova, A and Mansoor, R and Melton-Kreft, R and Jobe, BA and Wagner, PL and Kelly, RJ and Goel, A}, title = {A blood-based circulating microbial metagenomic panel for early diagnosis and prognosis of oesophageal adenocarcinoma.}, journal = {British journal of cancer}, volume = {127}, number = {11}, pages = {2016-2024}, pmid = {36097175}, issn = {1532-1827}, support = {R01 CA202797/CA/NCI NIH HHS/United States ; R01 CA184792/CA/NCI NIH HHS/United States ; R01 CA181572/CA/NCI NIH HHS/United States ; R01 CA072851/CA/NCI NIH HHS/United States ; R01 CA227602/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Metagenome ; Early Detection of Cancer ; *Esophageal Neoplasms/diagnosis/genetics ; *Adenocarcinoma/diagnosis/genetics/pathology ; Prognosis ; *Gastroesophageal Reflux/genetics ; Carcinogenesis ; Escherichia coli ; Biomarkers ; }, abstract = {BACKGROUND: Emerging evidence indicates the potential clinical significance of specific microbial signatures as diagnostic and prognostic biomarkers, in multiple cancers. However, to date, no studies have systematically interrogated circulating metagenome profiling in oesophageal adenocarcinoma (EAC) patients, particularly as novel non-invasive, early detection, surveillance and prognostic classifiers.

METHODS: Metagenome sequencing was performed on 81 serum specimens collected across EAC spectrum, with sequencing reads classified using Bracken and MetaPhlAn3. Followed by the Linear Discriminant Analysis effect size (LEfSe) method to identify microbial profiles between groups. Logistic regression and Kaplan-Meier analyses were used to build classifiers.

RESULTS: A significant loss of alpha and beta diversity was identified in serum specimens from EAC patients. We observed a shift in microbial taxa between each group-at the phylum, genus, and species level-with Lactobacillus sakei as the most prominent species in gastroesophageal reflux (GERD) vs other patient groups. Interestingly, LEfSe analysis identified a complete loss of Lactobacillus (L. Sakei and L. Curvatus), Collinsella stercoris and Bacteroides stercoris but conversely a significant increase in Escherichia coli in patients with EAC. Finally, we developed a metagenome panel that discriminated EAC from GERD patients with an AUC value of 0.89 (95% CI: 0.78-0.95; P < 0.001) and this panel in conjunction with the TNM stage was a robust predictor of overall survival (≥24 months; AUC = 0.84 (95% CI: 0.66-0.92; P = 0.006)).

CONCLUSION: This study firstly describes unique blood-based microbial profiles in patients across EAC carcinogenesis, that are further utilised to establish a novel circulating diagnostic and prognostic metagenomic signature for EAC.

TRANSLATIONAL RELEVANCE: Accumulating data indicates the clinical relevance of specific microbial signatures as diagnostic and prognostic biomarkers, in multiple cancers. However, to date, no studies have systematically interrogated circulating metagenome profiling in patients with oesophageal adenocarcinoma (EAC). Herein, we performed metagenome sequencing in serum specimens from EAC patients 81 collected across EAC spectrum and observed a significant loss of alpha and beta diversity, with a shift in microbial taxa between each group-at the phylum, genus, and species level-with Lactobacillus sakei as the most prominent species in gastroesophageal reflux (GERD) vs other patient groups. Interestingly, LEfSe analysis identified a complete loss of Lactobacillus (L. Sakei and L. Curvatus), Collinsella stercoris and Bacteroides stercoris but conversely a significant increase in Escherichia coli in patients with EAC. Finally, we developed a metagenome panel that discriminated EAC from GERD patients with an AUC value of 0.89 and this panel, in conjunction with the TNM stage, was a robust predictor of overall survival. This study for the first time describes unique blood-based microbial profiles in patients across EAC carcinogenesis, that are further utilised to establish a novel circulating diagnostic and prognostic metagenomic signature for EAC.}, } @article {pmid36097140, year = {2023}, author = {Koonin, EV and Krupovic, M and Dolja, VV}, title = {The global virome: How much diversity and how many independent origins?.}, journal = {Environmental microbiology}, volume = {25}, number = {1}, pages = {40-44}, doi = {10.1111/1462-2920.16207}, pmid = {36097140}, issn = {1462-2920}, mesh = {*Virome ; Phylogeny ; *Viruses/genetics ; Metagenomics ; Virion ; Genome, Viral ; }, abstract = {Viruses are considered to be the most abundant biological entities on earth. They also display striking genetic diversity as emphatically demonstrated by the recent advances of metagenomics and metatranscriptomics. But what are the limits of this diversity, that is, how many virus species in the earth virome? By combining the available estimates of the number of prokaryote species with those of the virome size, we obtain back-of-the-envelope estimates of the total number of distinct virus species, which come out astronomically large, from about 10[7] to about 10[9] . The route of virus origins apparently involved non-viral replicators capturing and exapting various cellular proteins to become virus capsid subunits. How many times in the history of life has this happened? In other words, how many realms of viruses, the highest rank taxa that are supposed to be monophyletic, comprise the global virome? We argue that viruses emerged on a number (even if far from astronomical) independent occasions, so the number of realms will considerably increase from the current 6, by splitting some of the current realms, giving the realm status to some of the currently unclassified groups of viruses and discovery of new distinct groups.}, } @article {pmid36096891, year = {2022}, author = {Li, T and Zhang, Z and Ma, Y and Song, Y and Yang, G and Han, X and Zhang, X}, title = {Nitrogen deposition experiment mimicked with NH4NO3 overestimates the effect on soil microbial community composition and functional potential in the Eurasian steppe.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {49}, pmid = {36096891}, issn = {2524-6372}, support = {32071547//National Natural Science Foundation of China/ ; 32071547//National Natural Science Foundation of China/ ; 32071547//National Natural Science Foundation of China/ ; 32071547//National Natural Science Foundation of China/ ; 32071547//National Natural Science Foundation of China/ ; 32071547//National Natural Science Foundation of China/ ; 32071547//National Natural Science Foundation of China/ ; }, abstract = {BACKGROUND: The nitrogenous compound deposited from the atmosphere to the soil is complex, but most field experiments mimic nitrogen deposition with the acid NH4NO3 alone. Thus, whether the acid and non-acid nitrogenous compounds have similar effects on biodiversity and ecosystem functions remains understudied. We mimicked nitrogen deposition with acidic NH4NO3 and (NH4)2SO4, and non-acidic urea, slow-released urea and NH4HCO3 in a temperate steppe, and quantified soil microbial taxonomic and functional gene composition with amplicon sequencing and shotgun metagenomics, respectively.

RESULTS: While NH4NO3 and (NH4)2SO4 significantly altered the soil microbial taxonomic and functional composition as well as their carbon decomposition potential, the other three compounds had smaller effects.

CONCLUSION: Our results suggested that previous nitrogen deposition experiments mimicked with NH4NO3 or (NH4)2SO4 alone may have overestimated the effect on biodiversity and ecosystem functions in the Eurasian steppe and similar ecosystems affected by mainly nonacidic nitrogen deposition.}, } @article {pmid36096231, year = {2022}, author = {Chi, S and Xu, W and Han, Y}, title = {ARGs distribution and high-risk ARGs identification based on continuous application of manure in purple soil.}, journal = {The Science of the total environment}, volume = {853}, number = {}, pages = {158667}, doi = {10.1016/j.scitotenv.2022.158667}, pmid = {36096231}, issn = {1879-1026}, mesh = {Swine ; Animals ; *Manure/analysis ; *Soil/chemistry ; Anti-Bacterial Agents/analysis ; Fertilizers/analysis ; Genes, Bacterial ; Soil Microbiology ; Drug Resistance, Microbial/genetics ; Livestock ; Tetracyclines ; Poultry ; Bacteria/genetics ; Chickens/genetics ; Carbon ; }, abstract = {Tetracyclines (TCs) are one of the most widely used antibiotics in livestock and poultry industry. Sichuan province and Chongqing city are the provinces and cities with the most concentrated purple soil distribution in China, as well as the largest livestock and poultry breeding scale. Purple soils with low organic carbon content and poor structure, and manure fertilizers were heavily applied to improve soil quality. However, the research on antibiotic resistance genes (ARGs) dispersal in purple soils is limited. Overall, 234 ARGs subtypes belonging to 15 types were detected in all soils. Long-term application of livestock manures significantly changed the characteristics of ARGs, mobile genetic elements (MGEs), pathogen species and bacterial communities in the soil, and increased by 103.2 %, 13.1 %, 188.6 % and 43.7 % in chicken manure treatments compared with the control, respectively. Partial equation PLS-PM analysis further reveals that the main driving factor of ARGs is bacterial abundance, while bacterial diversity has a negative effect on ARGs abundance. Through ANOVA and network analysis, it was found that 30 ARGs were significantly affected by manure, its relative abundance is 0.8-1.4 times that of the control treatment. The qPCR results also proved that the relative abundance of ARGs including sul2, etc. increased with the increase of manure application and these resistance genes in chicken manure treatments were higher than in pig manure treatments. These resistance genes pose a high risk to public health, and chicken manure application posed a higher risk than pig manure. The TC content in the 40-60 cm soil layer was higher in medium- and high-volume pig manure, which was at risk of being transported to groundwater. Our research results deepen the understanding of ARGs transmission in purple soil under agricultural activities and emphasize the species and distribution of antibiotic resistance genes may differ across soil and manure types.}, } @article {pmid36096222, year = {2022}, author = {Wang, Y and Zhang, R and Lei, Y and Song, L}, title = {Antibiotic resistance genes in landfill leachates from seven municipal solid waste landfills: Seasonal variations, hosts, and risk assessment.}, journal = {The Science of the total environment}, volume = {853}, number = {}, pages = {158677}, doi = {10.1016/j.scitotenv.2022.158677}, pmid = {36096222}, issn = {1879-1026}, mesh = {Anti-Bacterial Agents/analysis ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Risk Assessment ; Seasons ; *Solid Waste/analysis ; Waste Disposal Facilities ; *Water Pollutants, Chemical/analysis ; }, abstract = {Landfills are reservoir of antibiotics and antibiotic resistance. Antibiotic resistance would transport to the environment through landfill leachate, posing threaten to the environment. However, long term monitoring on antibiotic resistance genes in landfill leachate transportation is limited. Furthermore, antibiotic resistance gene hosts and their risk assessment are lacking. In this study, we investigated the seasonal variation of ARGs sulI, tetO and tetW in seven Chinese municipal solid waste landfill leachates over two years (2017-2018) by quantitative polymerase chain reaction. We also evaluated the associated bacterial hosts and their risk levels based on metagenomics and omics-based framework for assessing the health risk of antimicrobial resistance genes, respectively. Because sulI, tetO and tetW are abundant and the most frequently detected ARGs in global landfill system, they are selected as target ARGs. Results showed that the relative content of target ARGs in 2017 was 100 times higher than that in 2018, suggesting ARGs attenuation. The hosts of sulI were phyla of Lentisphaerae and Proteobacteria, whereas the hosts of tetO and tetW were Bacteroidetes and Firmicutes. Remarkably, the host species include pathogenic bacterium (Salmonella enterica, Labilibaculum filiforme, Bacteroidales bacterium, Anaeromassilibacillus senegalensis, and Pseudochrobactrum sp. B5). ARGs tetO and tetW belong to the Rank II level with characters of enrichment in the human-associated environment and gene mobility, and sulI ranked as Rank VI. In addition, among 1210 known ARGs in the landfill leachate, 78 ARGs belonged to risk Rank I (enrichment in human-associated environment, gene mobility and pathogenicity), demonstrating high health risk of landfill system. These results demonstrate that antibiotic resistance in landfill and landfill leachate have high health risk and the kind of ARGs with high abundance in human-associated environment, gene mobility and pathogenicity should be paid more attention.}, } @article {pmid36096031, year = {2022}, author = {Zhang, Y and Liu, C and Chen, H and Chen, J and Li, J and Teng, Y}, title = {Metagenomic insights into resistome coalescence in an urban sewage treatment plant-river system.}, journal = {Water research}, volume = {224}, number = {}, pages = {119061}, doi = {10.1016/j.watres.2022.119061}, pmid = {36096031}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; *Genes, Bacterial ; Humans ; Rivers/microbiology ; *Sewage/microbiology ; Virulence Factors ; }, abstract = {The effluents of sewage treatment plants (eSTP) are one of the critical contributors of antibiotic resistiome in rivers. Recently, community coalescence has been focused as the entire microbiome interchanges with one another. While works have reported the prevalence of antibiotic resistance genes (ARGs) in eSTP and their effects on river resistome, little research has investigated the extent of resistome coalescence in the environment. In the study, we have addressed the issue and focused on the resistome coalescence of eSTP in an urban river with a typical effluent/river coalescence model, by utilizing high-throughput sequencing (HTS)-based metagenomic assembly analysis. In all, a total of 609 ARGs were found in the eSTP-river system, conferring resistance to 30 antibiotic classes and including some emerging ARGs such as mcr-type, tetX and carbapenemase genes. Statistical analyses including linear discriminant analysis effect size (LEfSe) showed the coalescence of STP effluents increased the diversity and abundance of river resistome, indicating its low resistance to disturb the invasion of resistome community in eSTP. After coalescence in the river, the imprints of STP-derived ARGs presented a temporary increase and gradually decreased trend along the flow path. Further, an innovative fast expectation-maximization microbial source tracking (FEAST) method was used to quantitatively apportion the coalescence event, and demonstrated the contribution of eSTP on river resistome and its attenuation dynamics in the downstream. Notably, correlation-based network analysis and contig-based co-occurrence analysis showed the coalesced resistome in the downstream river co-occurred with human bacterial pathogens, mobile genetic elements and virulence factor genes, indicating potential resistome dissemination risk in the environment. This study provides more profound understanding of resistome coalescence between engineered and natural contexts, which is helpful for optimizing strategies to prevent and control resistome risk in aquatic environment.}, } @article {pmid36095141, year = {2022}, author = {Wu, YY and Gou, W and Yan, Y and Liu, CY and Yang, Y and Chen, D and Xie, K and Jiang, Z and Fu, Y and Zhu, HL and Zheng, JS and Chen, YM}, title = {Gut microbiota and acylcarnitine metabolites connect the beneficial association between equol and adiposity in adults: a prospective cohort study.}, journal = {The American journal of clinical nutrition}, volume = {116}, number = {6}, pages = {1831-1841}, doi = {10.1093/ajcn/nqac252}, pmid = {36095141}, issn = {1938-3207}, mesh = {Adult ; Female ; Humans ; Male ; Adiposity ; Carnitine ; Equol/urine ; *Gastrointestinal Microbiome ; *Isoflavones/pharmacology ; Obesity ; Prospective Studies ; Middle Aged ; }, abstract = {BACKGROUND: Many studies have investigated the effects of soy isoflavones on weight control, but few have focused on the role of equol, a gut-derived metabolite of daidzein with greater bioavailability than other soy isoflavones.

OBJECTIVES: This study examined the association of equol production with obesity and explored the mediating roles of equol-related gut microbiota and microbial carnitine metabolites.

METHODS: This 6.6-y prospective study included 2958 Chinese adults (2011 females and 947 males) aged 60.6 ± 6.0 y (mean ± SD) at baseline. Urinary equol and isoflavones were measured using HPLC-tandem MS. BMI, percentage fat mass (%FM), and serum triglycerides (TGs) were assessed every 3 y. Metagenomics sequencing and assessment of carnitine metabolites in feces were performed in a subsample of 897 participants.

RESULTS: Urinary equol, but not daidzein and genistein, was independently and inversely associated with the obesity-related indicators of BMI, %FM, and a biomarker (TGs). Equol producers (EPs) had lower odds of adiposity conditions and a reduced risk of 6.6-y obesity progression than non-EPs among total participants. Gut microbial analyses indicated that EPs had higher microbiome species richness (P = 3.42 × 10-5) and significantly different β-diversity of gut microbiota compared with the non-EP group (P = 0.001), with 20 of 162 species differing significantly. EPs (compared with non-EPs) had higher abundances of Alistipes senegalensis and Coprococcus catus but lower abundances of Ruminococcus gnavus (false discovery rate <0.05). Among the 7 determined fecal acylcarnitine metabolites, palmitoylcarnitine, oleylcarnitine 18:1, and stearylcarnitine were inversely associated with EPs but positively correlated with obesity conditions and progression. Path analyses indicated that the beneficial association between equol and obesity might be mediated by gut microbiota and decreased production of 3 acylcarnitines in feces.

CONCLUSIONS: This study suggests a beneficial association between equol and obesity, mediated by the gut microbiome and acylcarnitines, in adults.This trial was registered at clinicaltrials.gov as NCT03179657.}, } @article {pmid36094201, year = {2022}, author = {Yu, SJ and Bajagai, YS and Petranyi, F and Stanley, D}, title = {Phytogen Improves Performance during Spotty Liver Disease by Impeding Bacterial Metabolism and Pathogenicity.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {18}, pages = {e0075822}, pmid = {36094201}, issn = {1098-5336}, mesh = {Amino Acids ; Animal Feed/analysis ; Animals ; Bacteria ; *Chickens/microbiology ; Lipopolysaccharides ; *Liver Diseases/microbiology ; Poultry ; Virulence ; Vitamins ; }, abstract = {A range of antibiotic alternative products is increasingly studied and manufactured in the current animal agriculture, particularly in the poultry industry. Phytogenic feed additives are known for their remarkable ability to suppress pathogens such as Clostridium spp., Escherichia coli, and Salmonella. Other than enhancing biosecurity, improvements in productivity and performance were also observed. However, clear mechanisms for these improvements were not established. In this study, 20,000 Lohman-Brown layers were provided with phytogenic supplement from 16 to 40 weeks of age, and performance parameters were assessed against the same number of unsupplemented control birds. The performance results showed that the birds with phytogenic supplementation presented consistently reduced mortality, increased rate of lay, and increased average egg weight. Functional analysis through shotgun sequencing of cecal metagenomes confirmed a substantial functional shift in the microbial community, showing that phytogen significantly reduced the range of microbial functions, including the production of essential vitamins, cofactors, energy, and amino acids. Functional data showed that phytogen supplementation induced a phenotypic shift in intestinal bacteria LPS phenotype toward the less pathogenic form. The study corroborates the use of phytogenic products in antibiotic-free poultry production systems. The productivity improvements in the number and weight of eggs produced during Spotty Liver Disease justify further optimizing phytogenic alternatives for use in high-risk open and free-range poultry systems. IMPORTANCE The present study establishes the beneficial effects of the continuous phytogenic supplementation reflected in reduced diarrhea and mortality and higher egg productivity under normal conditions and during a natural outbreak of Spotty Liver Disease. Our data points to the importance of phytogen-driven alteration of microbial pathogenicity and fitness-related functional capabilities revealed on the commercial layer farm. Phytogenic product showed an ability to improve the bird's welfare and sustainability in free-range poultry production systems.}, } @article {pmid36093695, year = {2023}, author = {Raghavan, K and Dedeepiya, VD and Yamamoto, N and Ikewaki, N and Sonoda, T and Iwasaki, M and Kandaswamy, RS and Senthilkumar, R and Preethy, S and Abraham, SJK}, title = {Benefits of Gut Microbiota Reconstitution by Beta 1,3-1,6 Glucans in Subjects with Autism Spectrum Disorder and Other Neurodegenerative Diseases.}, journal = {Journal of Alzheimer's disease : JAD}, volume = {94}, number = {s1}, pages = {S241-S252}, pmid = {36093695}, issn = {1875-8908}, mesh = {Humans ; *Gastrointestinal Microbiome ; alpha-Synuclein ; Glucans ; *Autism Spectrum Disorder/therapy/microbiology ; *Neurodegenerative Diseases/therapy ; }, abstract = {BACKGROUND: Aureobasidium pullulans (black yeast) AFO-202 strain-produced beta glucan, Nichi Glucan, has been shown to improve the behavior and sleep pattern along with an increase in α-synuclein and melatonin in children with autism spectrum disorder (ASD).

OBJECTIVE: In this randomized pilot clinical study, we have evaluated the gut microbiota of subjects with ASD after consumption of Nichi Glucan.

METHODS: Eighteen subjects with ASD were randomly allocated: six subjects in the control group (Group 1): conventional treatment comprising remedial behavioral therapies and L-carnosine 500 mg per day, and 12 subjects (Group 2) underwent supplementation with Nichi Glucan 0.5 g twice daily along with the conventional treatment for 90 days.

RESULTS: Whole genome metagenome (WGM) sequencing of the stool samples at baseline and after intervention showed that among genera of relevance, the abundance of Enterobacteriaceae was decreased almost to zero in Group 2 after intervention, whereas it increased from 0.36% to 0.85% in Group 1. The abundance of Bacteroides increased in Group 1, whereas it decreased in Group 2. The abundance of Prevotella increased while the abundance of Lactobacillus decreased in both Group 1 and Group 2. Among species, a decrease was seen in Escherichia coli, Akkermansia muciniphila CAG:154, Blautia spp., Coprobacillus sp., and Clostridium bolteae CAG:59, with an increase of Faecalibacterium prausnitzii and Prevotella copri, which are both beneficial.

CONCLUSION: AFO-202 beta 1,3-1,6 glucan, in addition to balancing the gut microbiome in children with ASD and its role in effective control of curli-producing Enterobacteriaceae that leads to α-synuclein misfolding and accumulation, may have a prophylactic role in Parkinson's and Alzheimer's diseases as well.}, } @article {pmid36093274, year = {2022}, author = {Sanyal, A and Agarwal, S and Ramakrishnan, U and Garg, KM and Chattopadhyay, B}, title = {Using Environmental Sampling to Enable Zoonotic Pandemic Preparedness.}, journal = {Journal of the Indian Institute of Science}, volume = {102}, number = {2}, pages = {711-730}, pmid = {36093274}, issn = {0970-4140}, abstract = {The current pandemic caused by the SARS CoV-2, tracing back its origin possibly to a coronavirus associated with bats, has ignited renewed interest in understanding zoonotic spillovers across the globe. While research is more directed towards solving the problem at hand by finding therapeutic strategies and novel vaccine techniques, it is important to address the environmental drivers of pathogen spillover and the complex biotic and abiotic drivers of zoonoses. The availability of cutting-edge genomic technologies has contributed enormously to preempt viral emergence from wildlife. However, there is still a dearth of studies from species-rich South Asian countries, especially from India. In this review, we outline the importance of studying disease dynamics through environmental sampling from wildlife in India and how ecological parameters of both the virus and the host community may play a role in mediating cross-species spillovers. Non-invasive sampling using feces, urine, shed hair, saliva, shed skin, and feathers has been instrumental in providing genetic information for both the host and their associated pathogens. Here, we discuss the advances made in environmental sampling protocols and strategies to generate genetic data from such samples towards the surveillance and characterization of potentially zoonotic pathogens. We primarily focus on bat-borne or small mammal-borne zoonoses and propose a conceptual framework for non-invasive strategies to tackle the threat of emerging zoonotic infections.}, } @article {pmid36093194, year = {2022}, author = {Shi, X and Gao, B and Srivastava, A and Izzi, Z and Abdalla, Y and Shen, W and Raj, D}, title = {Alterations of gut microbial pathways and virulence factors in hemodialysis patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {904284}, pmid = {36093194}, issn = {2235-2988}, support = {U01 DK099914/DK/NIDDK NIH HHS/United States ; R01 DK125256/DK/NIDDK NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Metagenome ; Metagenomics ; Renal Dialysis ; Virulence Factors/genetics ; }, abstract = {Alterations in gut microbiota might contribute to uremic toxicity and immune dysregulation in patients with end-stage renal disease. Hemodialysis patients are prone to infection and higher mortality following sepsis. The virulence factors in the gut metagenome have not been well studied in hemodialysis patients, which could be employed by microorganisms to successfully thrive and flourish in their hosts. In this study, we performed shotgun metagenomics sequencing on fecal DNA collected from 16 control subjects and 24 hemodialysis patients. Our analysis shows that a number of microbial species, metabolic pathways, antibiotic resistance, and virulence factors were significantly altered in hemodialysis patients compared with controls. In particular, erythromycin resistance methylase, pyridoxamine 5-phosphate oxidase, and streptothricin-acetyl-transferase were significantly increased in hemodialysis patients. The findings in our study laid a valuable foundation to further elucidate the causative role of virulence factors in predisposing HD patients to infection and to develop treatment strategies to reduce the genetic capacities of antibiotic resistance and virulence factors in HD patients.}, } @article {pmid36093186, year = {2022}, author = {Zhou, K and Deng, N and Yi, X and Cai, Y and Peng, M and Xiao, N}, title = {Baohe pill decoction for diarrhea induced by high-fat and high-protein diet is associated with the structure of lactase-producing bacterial community.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {1004845}, pmid = {36093186}, issn = {2235-2988}, mesh = {Animals ; Bifidobacterium ; Diarrhea/drug therapy/microbiology ; *Diet, High-Protein ; *Drugs, Chinese Herbal/chemistry/pharmacology ; Lactase/genetics ; Mice ; }, abstract = {BACKGROUND: This study investigated the effects of Baohe pill decoction on the diversity and community composition of lactase-producing bacteria in the intestinal contents of mice with diarrhea induced by high-fat and high-protein diet, which provided an experimental basis for the study on the therapeutic mechanism of Baohe pill decoction.

MATERIALS AND METHODS: The Traditional Chinese Medicine Systems Pharmacology (TCMSP), DisGeNET, UniProt, National Center for Biotechnology Information (NCBI), and GeneCards databases were used to collect the potential targets with active ingredients of Baohe pill decoction, diarrhea, and lactase, and then construct correlation networks. Fifteen Kunming mice were randomly divided into the control group (CN), natural recovery group (NR), and Baohe pill decoction treatment group (BHP), with five mice in each group. After constructing a mouse diarrhea model by HFHPD induction, BHP was gavaged with Baohe pill decoction, and the other groups were gavaged with distilled water of equal. The intestinal contents were collected from ileal to jejunal and analyzed using metagenomic sequencing to characterize the intestinal content of lactase-producing bacteria in mice.

RESULTS: The core active ingredients related to diarrhea in Baohe pill decoction were quercetin, luteolin, kaempferol, forsythin, and wogonin. And there was no intersection between the potential targets with the active ingredient of Baohe pill, lactase, and diarrhea. After the intervention of Baohe pill decoction, the Observed species, Chao1 index, and Operational Taxonomic Units (OTU) number increased in BHP (P > 0.05), while the Pielous evenness and Shannon index decreased (P > 0.05). In Beta diversity, the community structure of the NR was significantly different from CN and BHP (P < 0.05), and the community structure of the CN was not significant difference from BHP (P > 0.05). Compared to NR, the relative abundance of Bifidobacterium and Amycolatopsis increased, while the relative abundance of Lachnoclostridium, Sinorhizobium, Cedecea, and Escherichia decreased in BHP, but none of the significant differences (P > 0.05).

CONCLUSION: The therapeutic effect of Baohe pill decoction on diarrhea induced by HFHPD does not appear to involve the body's lactase gene targets directly, but is associated with the change of the construction of lactase-producing bacterial communities.}, } @article {pmid36091563, year = {2022}, author = {Qu, J and Xu, H and Lv, X}, title = {Disseminated alveolar echinococcosis in a patient diagnosed by metagenomic next-generation sequencing: A case report.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {972619}, pmid = {36091563}, issn = {2296-2565}, mesh = {Animals ; *Echinococcosis/diagnosis/parasitology/pathology ; *Echinococcus multilocularis/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Middle Aged ; Tomography, X-Ray Computed ; }, abstract = {BACKGROUND: Alveolar echinococcosis (AE) is a parasitic zoonosis with high mortality and disability rates. Diverse clinical manifestations and mimicking of differential diagnoses such as tuberculosis and malignancy pose a diagnostic dilemma. With the rapid development of molecular diagnostic techniques in recent years, metagenomic next-generation sequencing (mNGS) has become an attractive approach for the etiological diagnosis of infectious diseases.

CASE PRESENTATION: we report a case of 51-year-old Chinese Tibetan male presented with 3-year low-back pain and 4-month discomfort in the right upper quadrant of the abdomen. He had been in good health. He was diagnosed with tuberculosis and was given anti-tuberculosis treatment a month prior to the visit, but the symptoms were not relieved. Abdominal computerized tomography (CT) revealed a hypodense lesion with uneven enhancement in the liver, and two ring-enhancing cystic lesions in the right abdominal wall. Lumbar spine enhanced MRI showed lesions of mixed density with uneven enhancement in the L1 vertebra and paraspinal tissue. The pathological results of the liver biopsy revealed parasitic infection and possibly echinococcosis. The metagenomic next-generation sequencing (mNGS) of the puncture fluid of abdominal cysts using Illumina X10 sequencer revealed 585 sequence reads matching Echinococcus multilocularis. Disseminated AE was diagnosed. Albendazole (400 mg, twice daily) was used, and the patient was in stable condition during follow-up.

CONCLUSIONS: mNGS may be a useful tool for the diagnosis of AE. The case would help clinicians to improve their diagnostic skills.}, } @article {pmid36090605, year = {2022}, author = {Yang, X and Wu, W and Wang, Y and Wu, W and Huang, X and Xu, L}, title = {A Case of Secondary Pulmonary Syphilis - The Utility of mNGS in Bronchoalveolar Lavage Fluid: A Case Report.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {5215-5219}, pmid = {36090605}, issn = {1178-6973}, abstract = {Syphilis is a sexually transmitted infectious disease caused by Treponema pallidum. Here, we report a rare case of secondary pulmonary syphilis, which was diagnosed by metagenomic next-generation sequencing (mNGS) in bronchoalveolar lavage fluid (BALF). Direct pulmonary involvement by T. pallidum was suggested by a positive mNGS result in BALF. One month after treatment with benzathine penicillin G (2.4 million units, three doses), a repeated CT scan showed the radiological resolution. To our knowledge, this is the first reported case of secondary pulmonary syphilis diagnosed by mNGS in BALF.}, } @article {pmid36090168, year = {2022}, author = {Vientós-Plotts, AI and Ericsson, AC and McAdams, ZL and Rindt, H and Reinero, CR}, title = {Temporal changes of the respiratory microbiota as cats transition from health to experimental acute and chronic allergic asthma.}, journal = {Frontiers in veterinary science}, volume = {9}, number = {}, pages = {983375}, pmid = {36090168}, issn = {2297-1769}, support = {T32 GM008396/GM/NIGMS NIH HHS/United States ; }, abstract = {In humans, deviation from a core airway microbiota may predispose to development, exacerbation, or progression of asthma. We proposed to describe microbiota changes using 16 rRNA sequencing in samples from the upper and lower airways, and rectal swabs of 8 cats after experimental induction of asthma using Bermuda grass allergen, in acute (6 weeks) and chronic (36 weeks) stages. We hypothesized that asthma induction would decrease richness and diversity and alter microbiota composition and structure in the lower airways, without significantly impacting other sites. After asthma induction, richness decreased in rectal (p = 0.014) and lower airway (p = 0.016) samples. B diversity was significantly different between health and chronic asthma in all sites, and between all time points for lower airways. In healthy lower airways Pseudomonadaceae comprised 80.4 ± 1.3% whereas Sphingobacteriaceae and Xanthobacteraceae predominated (52.4 ± 2.2% and 33.5 ± 2.1%, respectively), and Pseudomonadaceae was absent, in 6/8 cats with chronic asthma. This study provides evidence that experimental induction of asthma leads to dysbiosis in the airways and distant sites in both the acute and chronic stages of disease. This article has been published alongside "Respiratory dysbiosis in cats with spontaneous allergic asthma" (1).}, } @article {pmid36090094, year = {2022}, author = {Mi, W and Hu, Z and Xu, L and Bian, X and Lian, W and Yin, S and Zhao, S and Gao, W and Guo, C and Shi, T}, title = {Quercetin positively affects gene expression profiles and metabolic pathway of antibiotic-treated mouse gut microbiota.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {983358}, pmid = {36090094}, issn = {1664-302X}, abstract = {Quercetin has a wide range of biological properties that can be used to prevent or decrease particular inflammatory diseases. In this study, we aimed to investigate the gene expression profile and metabolic pathway of the gut microbiota of an antibiotic-treated mouse model administered quercetin. Blood, feces, and intestinal tissue samples were collected and metagenomic sequencing, enzyme-linked immunosorbent assay, and western blot analysis were used to detect variations. The results showed that the quercetin-treated group exhibited increased levels of health beneficial bacterial species, including Faecalibaculum rodentium (103.13%), Enterorhabdus caecimuris (4.13%), Eggerthella lenta (4%), Roseburia hominis (1.33%), and Enterorhabdus mucosicola (1.79%), compared with the model group. These bacterial species were positively related to butyrate, propionate, and intestinal tight junction proteins (zonula occludens-1 and occludin) expression, but negatively related to serum lipopolysaccharide and tumor necrosis factor-α level. In addition, the metabolic pathway analysis showed that dietary quercetin significantly enhanced spliceosomes (111.11%), tight junctions (62.96%), the citrate cycle (10.41%), pyruvate metabolism (6.95%), and lysine biosynthesis (5.06%), but decreasing fatty acid biosynthesis (23.91%) and N-glycan (7.37%) biosynthesis. Furthermore, these metabolic pathway changes were related to relative changes in the abundance of 10 Kyoto Encyclopedia of Genes and Genomes genes (K00244, K00341, K02946, K03737, K01885, k10352, k11717, k10532, K02078, K01191). In conclusion, dietary quercetin increased butyrate-producing bacterial species, and the acetyl-CoA-mediated increased butyrate accelerated carbohydrate, energy metabolism, reduced cell motility and endotoxemia, and increased the gut barrier function, thereby leading to healthy colonic conditions for the host.}, } @article {pmid36090067, year = {2022}, author = {Nonthakaew, N and Panbangred, W and Songnuan, W and Intra, B}, title = {Plant growth-promoting properties of Streptomyces spp. isolates and their impact on mung bean plantlets' rhizosphere microbiome.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {967415}, pmid = {36090067}, issn = {1664-302X}, abstract = {Phytophthora is an important, highly destructive pathogen of many plants, which causes considerable crop loss, especially durians in Thailand. In this study, we selectively isolated Streptomyces from the rhizosphere soil with a potent anti-oomycete activity against Phytophthora palmivora CbP03. Two strains (SNN087 and SNN289) demonstrated exceptional plant growth-promoting properties in pot experiment. Both strains promoted mung bean (Vigna radiate) growth effectively in both sterile and non-sterile soils. Metagenomic analysis revealed that Streptomyces sp. SNN289 may modify the rhizosphere microbial communities, especially promoting microbes beneficial for plant growth. The relative abundance of bacterial genera Bacillus, Sphingomonas, Arthrobacter, and Pseudarthrobacter, and fungal genera Coprinellus and Chaetomium were noticeably increased, whereas a genus Fusarium was slightly reduced. Interestingly, Streptomyces sp. SNN289 exhibited an exploratory growth, which allows it to survive in a highly competitive environment. Based on whole genome sequence analysis combined with an ANI and dDDH values, this strain should be classifiable as a new species. Functional annotation was also used to characterize plant-beneficial genes in SNN087 and SNN289 genomes for production of siderophores, 3-indole acetic acid (IAA), ammonia, and solubilized phosphate. AntiSMASH genome analysis and preliminary annotation revealed biosynthetic gene clusters with possible secondary metabolites. These findings emphasize the potential for application of strain SNN289 as a bioinoculant for sustainable agricultural practice.}, } @article {pmid36090029, year = {2022}, author = {Liang, X and Zhang, S and Zhang, D and Hu, L and Zhang, L and Peng, Y and Xu, Y and Hou, H and Zou, C and Liu, X and Chen, Y and Lu, F}, title = {Metagenomics-based systematic analysis reveals that gut microbiota Gd-IgA1-associated enzymes may play a key role in IgA nephropathy.}, journal = {Frontiers in molecular biosciences}, volume = {9}, number = {}, pages = {970723}, pmid = {36090029}, issn = {2296-889X}, abstract = {Background: IgA nephropathy (IgAN) is the most common type of glomerulonephritis in Asia. Its pathogenesis involves higher expression of galactose-deficient IgA1 (Gd-IgA1) and dysregulated intestinal mucosal immunity. The objective of this study was to explore whether specific gut microbiota and associated enzymes affect Gd-IgA1 in IgAN. Methods: This study carried out shotgun metagenomic sequencing with Illumina on fecal samples collected from 20 IgAN patients (IgAN group) and 20 healthy controls (HCs group) who were recruited from January 2016 to December 2018 at the Second Clinical College of Guangzhou University of Chinese Medicine. Differences analysis in gut microbiota was performed to determine the overall microbiota composition, the representative enterotypes, and the microbiota abundance. Correlations between gut microbiota and clinical indicators were assessed by Spearman's analysis. Moreover, the functional prediction of microbial communities and the quantitative calculation of enzymes encoded by microbiome were performed using the MetaCyc pathway and the bioBakery three platform, respectively. Results: Bacteroides plebeius and Bacteroides vulgatus levels were higher, while Prevotella copri and Alistipes putredinis levels were lower in the IgAN group compared to HCs group. Enterotype I characterized by Bacteroides was closely related to the IgAN patients. Moreover, Bacteroides fragilis, Flavonifractor plautii and Ruminococcus gnavus were characteristic bacteria enriched in IgAN patients. Spearman's correlation analysis found that Eggerthella lenta and Ruminococcus bromii were positively correlated with urine protein-creatinine ratio, while Ruminococcus gnavus showed a direct association with red blood cells in urine, and Bacteroides vulgatus and Ruminococcus gnavus were positively correlated with eGFR. These results indicated that intestinal dysbacteriosis occurred in IgAN patients and was associated with clinical and biochemical features. In addition, MetaCyc pathway analysis predicted microbiota-related metabolic pathways, including the biosynthesis of amino acids and glycans, were associated with the IgAN group. Microbial enzymes analysis highlighted that Gd-IgA1-associated α-galactosidase and α-N-acetyl-galactosaminidase secreted by Flavonifractor plautii were enriched in IgAN patients. Conclusion: These findings suggested that α-galactosidase and α-N-acetyl-galactosaminidase secreted by Flavonifractor plautii might be related to the production of Gd-IgA1, indicating that enzymes originated from abnormal intestinal microbiota may contribute to the production of Gd-IgA1 and play an important role in the pathogenesis of IgAN.}, } @article {pmid36089219, year = {2022}, author = {Li, W and Wang, L and Li, X and Zheng, X and Cohen, MF and Liu, YX}, title = {Sequence-based Functional Metagenomics Reveals Novel Natural Diversity of Functioning CopA in Environmental Microbiomes.}, journal = {Genomics, proteomics & bioinformatics}, volume = {}, number = {}, pages = {}, doi = {10.1016/j.gpb.2022.08.006}, pmid = {36089219}, issn = {2210-3244}, abstract = {Exploring the natural diversity of functional genes/proteins from environmental DNA in high-throughput remains challenging. In this study, we developed a sequence-based functional metagenomics procedure for mining the diversity of copper resistance gene copA in global microbiomes, by combining the metagenomic assembly technology, local BLAST, evolutionary trace analysis (ETA), chemical synthesis, and conventional functional genomics. In total, 87 metagenomes were collected from a public database and subjected to copA detection, resulting in 93,899 hits. Manual curation of 1214 hits of high-confidence led to the retrieval of 517 unique CopA candidates, which were further subjected to ETA. Eventually, 175 novel copA sequences of high-quality were discovered. Phylogenetic analysis showed that almost all these putative CopA proteins are distantly related to known CopA proteins, with 55 sequences from totally unknown species. Ten novel and three known copA genes were chemically synthesized for further functional genomic tests using the Cu-sensitive Escherichia coli (ΔcopA). The growth test and Cu uptake determination showed that five novel clones had positive effects on host Cu resistance and uptake. One recombinant harboring copA-like 15 (copAL15) successfully restored Cu resistance of the host with a substantially enhanced Cu uptake. Two novel copA genes were fused with the gfp gene and expressed in E. coli for microscopic observation. Imaging results showed that they were successfully expressed and their proteins were localized to the membrane. The results here greatly expand the diversity of known CopA proteins, and the sequence-based procedure developed overcomes biases in length, screening methods, and abundance of conventional functional metagenomics.}, } @article {pmid36089141, year = {2022}, author = {Zheng, M and Shao, S and Chen, Y and Chen, B and Wang, M}, title = {Metagenomics analysis of microbial community distribution in large-scale and step-by-step purification system of swine wastewater.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {313}, number = {}, pages = {120137}, doi = {10.1016/j.envpol.2022.120137}, pmid = {36089141}, issn = {1873-6424}, mesh = {Ammonia/analysis ; Animals ; Bacteria/genetics ; *Chlorella ; *Environmental Pollutants/analysis ; Metagenomics ; *Microbiota ; Nitrogen/analysis ; Sewage/chemistry ; Swine ; Wastewater/chemistry ; *Water Purification/methods ; }, abstract = {Biological treatment is one of the most widely used methods to treat swine wastewater in wastewater treatment plants. The microbial community plays an important role in the swine slurry treatment system. However, limited information is available regarding the correlation between pollutant concentration and dominant microbial community in swine wastewater. This work aimed to study the profiling of microbial communities and their abundance in the 40 M[3]/day large-scale and step-by-step treatment pools of swine wastewater. Metagenome sequencing was applied to study the changes of microbial community structure in biochemical reaction pools. The results showed that in the heavily polluted pools, it was mainly Proteobacteria, Cyanobacteria, Chlorella and other strains that could tolerate high concentration of ammonia nitrogen to remove nitrogen and absorb chemical oxygen demand (COD). In the moderately polluted pools, Nitrospirae, Actinobacteria and other strains further cooperated to purify swine wastewater. In the later stage, the emergence of Brachionus indicated the reduction of water pollution. The dominant microbes and their abundance changed with the purification of swine wastewater in different stages. Moreover, the dominant microflora of swine wastewater treatment pools at all levels reflected little difference in phylum classification level, while in genus classification level, the dominant microflora manifested great difference. Findings demonstrated that the microorganisms maintained ecological balance and absorbed the nutrients in the swine wastewater treatment pools, so as to play the role of purifying sewage. Therefore, the stepwise purification of swine wastewater can be realized by adding bacteria and microalgae of different genera.}, } @article {pmid36089127, year = {2022}, author = {Wang, Z and Zhang, W and Xing, X and Li, X and Zheng, D and Bao, H and Xing, L}, title = {Effects of ferroferric oxide on propionate methanogenesis in sequencing batch reactors: Microbial community structure and metagenomic analysis.}, journal = {Bioresource technology}, volume = {363}, number = {}, pages = {127909}, doi = {10.1016/j.biortech.2022.127909}, pmid = {36089127}, issn = {1873-2976}, mesh = {Acetates ; Adenosine Triphosphatases ; Anaerobiosis ; Bacteria/genetics ; Bioreactors/microbiology ; Humic Substances ; Metagenomics ; Methane ; *Microbiota ; NAD ; Oxides ; *Propionates ; Riboflavin ; Wastewater/microbiology ; }, abstract = {This study investigated the effects of ferroferric oxide (Fe3O4) on propionate methanogenesis in anaerobic sequencing batch reactor (ASBR). Compared to ASBRC (without Fe3O4 addition), the addition of 10 g/L Fe3O4 (ASBRFe) decreased the maximum methane production rate by 69.6 % when propionate was used as the sole substrate. The addition of Fe3O4 reduced the contents of humic substances, riboflavin and nicotinamide adenine dinucleotide in extracellular polymeric substances. Therefore, Fe3O4 inhibited interspecies electron transfer of microorganisms through electronic mediators. Microbial community analysis revealed that Fe3O4 addition increased the relative abundance of acetate oxidizing bacterium (Mesotoga), but decreased the abundance of hydrogenotrophic methanogen (Methanobacterium). Further metagenomics analysis indicated that Fe3O4 increased the abundance of acetate oxidation genes and decreased that of hydrogenotrophic methanogenesis, quorum sensing and V/A-type ATPase genes. Thus, Fe3O4 reduced propionate methanogenesis during anaerobic digestion. The overall results indicate that Fe3O4 addition inhibits methanogenesis for treatment of propionate-contaminated wastewater in ASBR.}, } @article {pmid36089033, year = {2022}, author = {Isa, KNM and Jalaludin, J and Hashim, Z and Than, LTL and Hashim, JH and Norbäck, D}, title = {Fungi composition in settled dust associated with fractional exhaled nitric oxide in school children with asthma.}, journal = {The Science of the total environment}, volume = {853}, number = {}, pages = {158639}, doi = {10.1016/j.scitotenv.2022.158639}, pmid = {36089033}, issn = {1879-1026}, mesh = {Child ; Humans ; Adolescent ; *Dust ; Breath Tests ; Cross-Sectional Studies ; Fractional Exhaled Nitric Oxide Testing ; Nitric Oxide/analysis ; *Asthma/epidemiology ; Fungi ; }, abstract = {Fungi exposure has been significantly linked to respiratory illness. However, numerous fungi taxa that are potentially allergenic still undocumented and leave a barrier to establishing a clear connection between exposure and health risks. This study aimed to evaluate the association of fungi composition in settled dust with fractional exhaled nitric oxide (FeNO) levels among school children with doctor-diagnosed asthma. A cross-sectional study was undertaken among secondary school students in eight schools in the urban area of Hulu Langat, Selangor, Malaysia. A total of 470 school children (aged 14 years old) were randomly selected and their FeNO levels were measured and allergic skin prick tests were conducted. The settled dust samples were collected and analysed by using metagenomic technique to determine the fungi composition. The general linear regression with complex sampling was employed to determine the interrelationship. In total, 2645 fungal operational taxonomic units (OTUs) were characterised from the sequencing process which belongs to Ascomycota (60.7 %), Basidiomycota (36.4 %), Glomeromycota (2.9 %) and Chytridiomycota (0.04 %). The top five mostly abundance in all dust samples were Aspergillus clavatus (27.2 %), followed by Hyphoderma multicystidium (12.2 %), Verrucoconiothyrium prosopidis (9.4 %), Ganoderma tuberculosum (9.2 %), and Heterochaete shearii (7.2 %). The regression results indicated that A. clavatus, Brycekendrickomyces acaciae, Candida parapsilosis, Hazslinszkyomyces aloes, H. multicystidium, H. shearii, Starmerella meliponinorum, V. prosopidis were associated in increased of FeNO levels among the asthmatic group at 0.992 ppb (95 % CI = 0.34-1.68), 2.887 ppb (95 % CI = 2.09-3.76), 0.809 ppb (95 % CI = 0.14-1.49), 0.647 ppb (95 % CI = 0.36-0.94), 1.442 ppb (95 % CI = 0.29-2.61), 1.757 ppb (95 % CI = 0.59-2.87), 1.092 ppb (95 % CI = 0.43-1.75) and 1.088 ppb (95 % CI = 0.51-1.62), respectively. To our knowledge, this is a new finding. The findings pointed out that metagenomics profiling of fungi could enhance our understanding of a complex interrelation between rare and unculturable fungi with airway inflammation.}, } @article {pmid36088366, year = {2022}, author = {Liu, MC and Zhang, JT and Chen, JJ and Zhu, Y and Fu, BK and Hu, ZY and Fang, LQ and Zhang, XA and Liu, W}, title = {A global dataset of microbial community in ticks from metagenome study.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {560}, pmid = {36088366}, issn = {2052-4463}, support = {81825019//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Animals ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Microbiota/genetics ; Systematic Reviews as Topic ; *Ticks/microbiology ; }, abstract = {Ticks are important vectors of various zoonotic pathogens that can infect animals and humans, and most documented tick-borne pathogens have a strong bias towards microorganisms with strong disease phenotypes. The recent development of next-generation sequencing (NGS) has enabled the study of microbial communities, referred to as microbiome. Herein, we undertake a systematic review of published literature to build a comprehensive global dataset of microbiome determined by NGS in field-collected ticks. The dataset comprised 4418 records from 76 literature involving geo-referenced occurrences for 46 species of ticks and 219 microorganism families, revealing a total of 83 emerging viruses identified from 24 tick species belonging to 6 tick genera since 1980. The viral, bacterial and eukaryotic composition was compared regarding the tick species, their live stage and types of the specimens, or the geographic location. The data can assist the further investigation of ecological, biogeographical and epidemiological features of the tick-borne disease.}, } @article {pmid36088112, year = {2022}, author = {Liu, MK and Liu, CY and Tian, XH and Feng, J and Guo, XJ and Liu, Y and Zhang, XY and Tang, YM}, title = {Bioremediation of degraded pit mud by indigenous microbes for Baijiu production.}, journal = {Food microbiology}, volume = {108}, number = {}, pages = {104096}, doi = {10.1016/j.fm.2022.104096}, pmid = {36088112}, issn = {1095-9998}, mesh = {*Alcoholic Beverages/microbiology ; *Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Fermentation ; }, abstract = {Microbes in pit mud play key roles in fermentation cellars for Chinese strong-flavor Baijiu (SFB) production. Pit mud, however, is frequently degraded during production, compromising the quality of the end product. In this study, a bioremediation method was used to restore degraded pit mud (DPM) using indigenous microbes derived from SFB production. Metabolomics and metagenomics were used to determine the dynamics of prokaryotes during DPM restoration and their link to SFB production. The composition of flavor compounds in SFB changed (P = 0.0001) before and after restoration of DPM. Consistent with the improved sensory quality, the ethyl caproate/ethyl lactate ratio, an SFB quality measure, increased after restoration (P < 0.001). The concentrations of humus, NH4[+], available phosphorus, and available potassium in DPM increased during the restoration process (P < 0.05), which is consistent with high-quality pit mud. The relative abundance of microbes that are beneficial to SFB fermentation, such as Caproiciproducens, a bacterium that produces caproic acid, increased during the restoration process. Furthermore, a total of 18 metabolic pathways were enriched (P < 0.05) from DPM before and after restoration. This includes butanoate metabolism and pyruvate metabolism, which are related to the synthesis of key flavor esters in SFB.}, } @article {pmid36087524, year = {2022}, author = {Morsli, M and Boudet, A and Kerharo, Q and Stephan, R and Salipante, F and Dunyach-Remy, C and Houhamdi, L and Fournier, PE and Lavigne, JP and Drancourt, M}, title = {Real-time metagenomics-based diagnosis of community-acquired meningitis: A prospective series, southern France.}, journal = {EBioMedicine}, volume = {84}, number = {}, pages = {104247}, pmid = {36087524}, issn = {2352-3964}, mesh = {Anti-Bacterial Agents ; Bacteria/genetics ; Escherichia coli/genetics ; Haemophilus influenzae/genetics ; Humans ; *Meningitis, Bacterial/diagnosis ; Multilocus Sequence Typing ; Multiplex Polymerase Chain Reaction/methods ; *Neisseria meningitidis/genetics ; Streptococcus pneumoniae/genetics ; }, abstract = {BACKGROUND: Point-Of-Care (POC) diagnosis of life-threatening community-acquired meningitis currently relies on multiplexed RT-PCR assays, that lack genotyping and antibiotic susceptibility profiling. We assessed the usefulness of real-time metagenomics (RTM) directly applied to the cerebrospinal fluid (CSF) for the identification, typing and susceptibility profiling of pathogens responsible for community-acquired meningitis.

METHODS: A series of 52 CSF samples from patients suspected of having community-acquired meningitis, were investigated at POC by direct RTM in parallel to routine real-time multiplex PCR (RT-PCR) and bacterial culture, for the detection of pathogens. RTM-generated sequences were blasted in real-time against an in-house database incorporating the panel of 12 most prevalent pathogens and against NCBI using EPI2ME online software, for pathogen identification. In-silico antibiogram and genotype prediction were determined using the ResFinder bio-tool and MLST online software.

FINDINGS: Over eight months, routine multiplex RT-PCR yielded 49/52 positive CSFs, including 21 Streptococcus pneumoniae, nine Neisseria meningitidis, eight Haemophilus influenzae, three Streptococcus agalactiae, three Herpesvirus-1, two Listeria monocytogenes, and one each of Escherichia coli, Staphylococcus aureus and Varicella-Zoster Virus. Parallel RTM agreed with the results of 47/52 CSFs and revealed two discordant multiplex RT-PCR false positives, one H. influenzae and one S. pneumoniae. Both multiplex RT-PCR and RTM agreed on the negativity of three CSFs. While multiplex RT-PCR routinely took 90 min, RTM took 120 min, although the pipeline analysis detected the pathogen genome after 20 min of sequencing in 33 CSF samples; and after two hours in 14 additional CSFs; yielding > 50% genome coverage in 19 CSFs. RTM identified 14 pathogen genotypes, including a majority of H. influenzae b, N. meningitidis B and S. pneumoniae 11A and 3A. In all 16 susceptible cultured bacteria, the in-silico antibiogram agreed with the in-vitro antibiogram in 10 cases, available within 48 h in routine bacteriology.

INTERPRETATION: In addition to pathogen detection, RTM applied to CSF samples offered supplementary information on bacterial profiling and genotyping. These data provide the proof-of-concept that RTM could be implemented in a POC laboratory for one-shot diagnostic and genomic surveillance of pathogens responsible for life-threatening meningitis.

FUNDING: This work was supported by the French Government under the Investments in the Future programme managed by the National Agency for Research reference: Méditerranée Infection 10-IAHU-03.}, } @article {pmid36087469, year = {2022}, author = {Jiao, H and Huang, Z and Chen, Z and Wang, H and Liu, H and Wei, Z}, title = {Lead removal in flue gas from sludge incineration by denitrification: Insights from metagenomics and metaproteomics.}, journal = {Ecotoxicology and environmental safety}, volume = {244}, number = {}, pages = {114059}, doi = {10.1016/j.ecoenv.2022.114059}, pmid = {36087469}, issn = {1090-2414}, mesh = {Carrier Proteins ; Denitrification ; Humans ; Humic Substances ; *Incineration ; Lead ; Metagenomics ; Minerals ; Phosphates ; *Sewage/chemistry ; }, abstract = {Flue gas lead emission during sludge incineration damages to human health and ecological environment seriously. Therefore, a denitrifying bio-trickling filter (DNBTF) for lead removal in flue gas from sludge incineration was investigated. Lead removal efficiency was up to 90.7% in 60 days' operation. Lead speciation in biofilms of DNBTF consists of 84.27% residue lead, 15.18% organic bound lead, and less than 1% exchangeable and reducible lead. Lead resistant bacteria and lead resistant-denitrifying bacteria accounted for 85.04% and 58.25%, respectively. Lead resistant microorganisms(Pseudomonas, Azoarcus, Stappia, Pararhodobacter, Paracoccus, Azospirillum, Hyphomonas, Rhodobacter, Polymorphum, Brevunimonas, Stenotrophomonas) could resist the toxicity of Pb[2+] in flue gas by transport protein and binding protein, and detoxify Pb[2+] in flue gas by extracellular polymeric substances (EPS) adsorption, protein binding and precipitation under the action of resistance genes, such as pbrAB, golT, troABCD, znuABC, czcABCD, pcoB, copA, as shown by integrated metagenomic and metaproteomic analyses. The biofilm was characterized by FTIR, XRD, 3D-EEM, and SEM-EDS. XRD and SEM-EDS spectra indicated the formation of pyromorphite from bioconversion of lead in flue gas. Lead-containing flue gas was bio-stabilized in the form of pyromorphite and HA-Pb via complexation of humic acids in extracellular polymeric substances (EPS), biosorption and biodeposition. This provides a new way of sludge incineration flue gas lead removal using a denitrifying biotricking filter.}, } @article {pmid36086955, year = {2022}, author = {Mancabelli, L and Milani, C and Fontana, F and Lugli, GA and Tarracchini, C and Viappiani, A and Ciociola, T and Ticinesi, A and Nouvenne, A and Meschi, T and Turroni, F and Ventura, M}, title = {Untangling the link between the human gut microbiota composition and the severity of the symptoms of the COVID-19 infection.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {6453-6462}, pmid = {36086955}, issn = {1462-2920}, mesh = {Humans ; *Gastrointestinal Microbiome ; *COVID-19 ; SARS-CoV-2 ; Dysbiosis/microbiology ; Pandemics ; Bacteria/genetics ; }, abstract = {Recent pandemic infection caused by SARS-CoV-2 (COVID-19) led the scientific community to investigate the possible causes contributing to the physiopathology of this disease. In this context, analyses of the intestinal microbiota highlighted possible correlation between host-associated bacterial communities and development of the COVID-19. Nevertheless, a detailed investigation of the role of the human microbiota in the severity of the symptoms of this disease is still lacking. This study performed a comprehensive meta-analysis of 323 faecal samples from public and novel Italian data sets based on the shotgun metagenomic approach. In detail, the comparative analyses revealed possible differences in the microbial biodiversity related to the individual health status, highlighting a species richness decrease in COVID-19 patients with a severe prognosis. Moreover, healthy subjects resulted characterized by a higher abundance of protective and health-supporting bacterial species, while patients affected by COVID-19 disease displayed a significant increase of opportunistic pathogen bacteria involved in developing putrefactive dysbiosis. Furthermore, prediction of the microbiome functional capabilities suggested that individuals affected by COVID-19 subsist in an unbalanced metabolism characterized by an overrepresentation of enzymes involved in the protein metabolism at the expense of carbohydrates oriented pathways, which can impact on disease severity and in excessive systemic inflammation.}, } @article {pmid36086900, year = {2023}, author = {Bell, KL and Turo, KJ and Lowe, A and Nota, K and Keller, A and Encinas-Viso, F and Parducci, L and Richardson, RT and Leggett, RM and Brosi, BJ and Burgess, KS and Suyama, Y and de Vere, N}, title = {Plants, pollinators and their interactions under global ecological change: The role of pollen DNA metabarcoding.}, journal = {Molecular ecology}, volume = {32}, number = {23}, pages = {6345-6362}, doi = {10.1111/mec.16689}, pmid = {36086900}, issn = {1365-294X}, support = {2021-67012-35153//USDA-NIFA/ ; BB/CSP1720/1//Biotechnology and Biological Sciences Research Council (BBSRC)/ ; }, mesh = {*Ecosystem ; *DNA Barcoding, Taxonomic/methods ; Pollen/genetics ; Plants/genetics ; DNA ; Pollination/genetics ; }, abstract = {Anthropogenic activities are triggering global changes in the environment, causing entire communities of plants, pollinators and their interactions to restructure, and ultimately leading to species declines. To understand the mechanisms behind community shifts and declines, as well as monitoring and managing impacts, a global effort must be made to characterize plant-pollinator communities in detail, across different habitat types, latitudes, elevations, and levels and types of disturbances. Generating data of this scale will only be feasible with rapid, high-throughput methods. Pollen DNA metabarcoding provides advantages in throughput, efficiency and taxonomic resolution over traditional methods, such as microscopic pollen identification and visual observation of plant-pollinator interactions. This makes it ideal for understanding complex ecological networks and their responses to change. Pollen DNA metabarcoding is currently being applied to assess plant-pollinator interactions, survey ecosystem change and model the spatiotemporal distribution of allergenic pollen. Where samples are available from past collections, pollen DNA metabarcoding has been used to compare contemporary and past ecosystems. New avenues of research are possible with the expansion of pollen DNA metabarcoding to intraspecific identification, analysis of DNA in ancient pollen samples, and increased use of museum and herbarium specimens. Ongoing developments in sequencing technologies can accelerate progress towards these goals. Global ecological change is happening rapidly, and we anticipate that high-throughput methods such as pollen DNA metabarcoding are critical for understanding the evolutionary and ecological processes that support biodiversity, and predicting and responding to the impacts of change.}, } @article {pmid36085530, year = {2022}, author = {Tian, L and Li, Q and Cai, X and Wang, Y and Wang, Y and Mao, Y}, title = {Dynamic distribution and potential transmission of antibiotic resistance genes in activated sludge.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {19-20}, pages = {6785-6797}, pmid = {36085530}, issn = {1432-0614}, support = {41907214//National Natural Science Foundation of China/ ; 2022A1515011961//Natural Science Foundation of Guangdong Province/ ; 20200813153536001//The Stable Support Program of Colleges and Universities in Shenzhen/ ; 860-000002110245//Natural Science Foundation of Shenzhen University/ ; }, mesh = {Aminoglycosides ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Nitrogen ; *Sewage/microbiology ; Sulfonamides ; Wastewater/microbiology ; beta-Lactams ; }, abstract = {Public concerns are increasing regarding the prevalence and transmission of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs), especially ARG persistence and dissemination in activated sludge (AS). However, the temporal dynamics of ARGs in the AS of WWTPs over a long period of time and their transfer potential after the treatment process upgrade (e.g., total nitrogen reduction from 20 to 15 mg/L in effluent) remain poorly explored. Here, metagenomic sequencing was performed to quantify the ARGs in AS samples from two WWTPs with different treatment processes over a 2-year period. A total of 368 and 426 ARG subtypes affiliated with 20 ARG types were identified separately in the two WWTPs and the similar core ARGs were shared by all 54 samples. There were significant differences in ARG composition in different treatment processes, yet the abundance and diversity of ARGs in the AS samples demonstrated no distinct seasonal patterns. Notably, after the treatment process upgrade, the relative abundance of sulfonamide, beta-lactam, and aminoglycoside resistance genes was reduced by more than 10%, and the transfer potential of ARGs in bacterial pathogens decreased greatly, which suggested that an upgrade could limit the prevalence and transmission of ARGs. Variation partitioning analysis showed that metal resistance genes rather than bacterial community represented the significantly influential factor in shaping ARGs, and some key genera correlated with ARGs were identified through network analysis. These results will deepen our understanding of the dynamic changes in ARG profiles in AS systems and guide wastewater treatment plant upgrades. KEY POINTS: • The potential transfer of ARGs decreased after the treatment process upgrade • Metal resistance genes were the most influential factor in shaping ARG composition • Co-occurrence networks displayed potential hosts of beta-lactam resistance genes.}, } @article {pmid36085351, year = {2022}, author = {Dai, D and Dai, F and Chen, J and Jin, M and Li, M and Hu, D and Liu, Z and Zhang, Z and Xu, F and Chen, WH}, title = {Integrated multi-omics reveal important roles of gut contents in intestinal ischemia-reperfusion induced injuries in rats.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {938}, pmid = {36085351}, issn = {2399-3642}, mesh = {Animals ; *Gastrointestinal Microbiome ; Ischemia ; Metabolomics ; Rats ; Reperfusion ; *Reperfusion Injury ; }, abstract = {Intestinal ischemia-reperfusion (IIR) is a life-threatening clinical event with damaging signals whose origin and contents are unclear. Here we observe that IIR significantly affect the metabolic profiles of most organs by unbiased organ-wide metabolic analysis of gut contents, blood, and fifteen organs in rats (n = 29). Remarkably, correlations between gut content metabolic profiles and those of other organs are the most significant. Gut contents are also the only ones to show dynamic correlations during IIR. Additionally, according to targeted metabolomics analysis, several neurotransmitters are considerably altered in the gut during IIR, and displayed noteworthy correlations with remote organs. Likewise, metagenomics analysis (n = 35) confirm the effects of IIR on gut microbiota, and identify key species fundamental to the changes in gut metabolites, particularly neurotransmitters. Our multi-omics results establish key roles of gut contents in IIR induced remote injury and provide clues for future exploration.}, } @article {pmid36084501, year = {2022}, author = {Zhang, W and Lu, X and Chen, S and Liu, Y and Peng, D and Wang, Z and Li, R}, title = {Molecular epidemiology and population genomics of tet(X4), blaNDM or mcr-1 positive Escherichia coli from migratory birds in southeast coast of China.}, journal = {Ecotoxicology and environmental safety}, volume = {244}, number = {}, pages = {114032}, doi = {10.1016/j.ecoenv.2022.114032}, pmid = {36084501}, issn = {1090-2414}, mesh = {Animals ; Anti-Bacterial Agents ; Birds ; China ; Colistin ; Escherichia coli/genetics ; *Escherichia coli Infections/epidemiology/microbiology/veterinary ; *Escherichia coli Proteins/genetics ; Metagenomics ; Microbial Sensitivity Tests ; Molecular Epidemiology ; Plasmids/genetics ; beta-Lactamases/genetics ; }, abstract = {The emergence of multidrug-resistant (MDR) bacteria harboring tet(X4), blaNDM or mcr-1 posed a serious threat to public health. Wild birds, especially migratory birds, were considered as one of important transmission vectors for antibiotic resistance genes (ARGs) globally, however, few studies were performed on the genomic epidemiology of critical resistance genes among them. Isolates harboring tet(X4), mcr-1 or blaNDM from migratory birds were identified and characterized by PCR, antimicrobial susceptibility testing, conjugation assays, whole genome sequencing and bioinformatics analysis. A total of 14 tet(X4)-bearing E. coli, 4 blaNDM-bearing E. coli and 23 mcr-1-bearing E. coli isolates were recovered from 1060 fecal samples of migratory birds. All isolates were MDR bacteria and most plasmids carrying tet(X4), blaNDM or mcr-1 were conjugative. We first identified an E. coli of migratory bird origin carrying blaNDM-4, which was located on a conjugative IncHI2 plasmid and embedded on a novel MDR region flanked by IS26 that could generate the circular intermediate. The emergency of E. coli isolates co-harboring mcr-1 and blaNDM-5 in migratory birds indicated the coexistence of ARGs in migratory birds was a novel threat. This study revealed the prevalence and molecular characteristics of three important ARGs in migratory birds, provided evidence that migratory birds were potential vectors of novel resistance genes and highlighted the monitoring of ARGs in migratory birds should be strengthened to prevent the spread of ARGs in a One Health strategy.}, } @article {pmid36084062, year = {2022}, author = {Brown, KT and Southgate, PC and Hewavitharane, CA and Lal, MM}, title = {Saving the sea cucumbers: Using population genomic tools to inform fishery and conservation management of the Fijian sandfish Holothuria (Metriatyla) scabra.}, journal = {PloS one}, volume = {17}, number = {9}, pages = {e0274245}, pmid = {36084062}, issn = {1932-6203}, mesh = {Animals ; Echinodermata ; Fisheries ; *Holothuria/genetics ; Humans ; Metagenomics ; *Sea Cucumbers/genetics ; }, abstract = {The sea cucumber Holothuria (Metriatyla) scabra, known as sandfish, is a high-value tropical echinoderm central to the global bêche-de-mer (BDM) trade. This species has been heavily exploited across its natural range, with overharvesting and ineffective fishery management leaving stocks in the Pacific region heavily depleted. In Fiji, sandfish stocks have not recovered since a 1988 harvest ban, with surveys reporting declining populations and recruitment failure. Therefore, to inform fishery management policy for the wild sandfish resource and to guide hatchery-based restocking efforts, a high-resolution genomic audit of Fijian populations was carried out. A total of 6,896 selectively-neutral and 186 putatively-adaptive genome-wide SNPs (DArTseq) together with an independent oceanographic particle dispersal model were used to investigate genetic structure, diversity, signatures of selection, relatedness and connectivity in six wild populations. Three genetically distinct populations were identified with shallow but significant differentiation (average Fst = 0.034, p≤0.05), comprising (1) Lakeba island (Lau archipelago), (2) Macuata (Vanua Levu), and (3) individuals from Yasawa, Ra, Serua island and Kadavu comprising the final unit. Small reductions in allelic diversity were observed in marginal populations in eastern Fiji (overall mean A = 1.956 vs. Lau, A = 1.912 and Macuata, A = 1.939). Signatures of putative local adaptation were also discovered in individuals from Lakeba island, suggesting that they be managed as a discrete unit. An isolation-by-distance model of genetic structure for Fijian sandfish is apparent, with population fragmentation occurring towards the east. Hatchery-based production of juveniles is promising for stock replenishment, however great care is required during broodstock source population selection and juvenile releases into source areas only. The successful use of genomic data here has the potential to be applied to other sea cucumber species in Fiji, and other regions involved in the global BDM trade. While preliminary insights into the genetic structure and connectivity of sandfish in Fiji have been obtained, further local, regional and distribution-wide investigations are required to better inform conservation efforts, wild stock management and hatchery-based restocking interventions for this valuable invertebrate.}, } @article {pmid36083885, year = {2022}, author = {Papp, M and Békési, L and Farkas, R and Makrai, L and Judge, MF and Maróti, G and Tőzsér, D and Solymosi, N}, title = {Natural diversity of the honey bee (Apis mellifera) gut bacteriome in various climatic and seasonal states.}, journal = {PloS one}, volume = {17}, number = {9}, pages = {e0273844}, pmid = {36083885}, issn = {1932-6203}, mesh = {Animals ; Bees ; Humans ; *Metagenomics ; Seasons ; }, abstract = {As pollinators and producers of numerous human-consumed products, honey bees have great ecological, economic and health importance. The composition of their bacteriota, for which the available knowledge is limited, is essential for their body's functioning. Based on our survey, we performed a metagenomic analysis of samples collected by repeated sampling. We used geolocations that represent the climatic types of the study area over two nutritionally extreme periods (March and May) of the collection season. Regarding bacteriome composition, a significant difference was found between the samples from March and May. The samples' bacteriome from March showed a significant composition difference between cooler and warmer regions. However, there were no significant bacteriome composition differences among the climatic classes of samples taken in May. Based on our results, one may conclude that the composition of healthy core bacteriomes in honey bees varies depending on the climatic and seasonal conditions. This is likely due to climatic factors and vegetation states determining the availability and nutrient content of flowering plants. The results of our study prove that in order to gain a thorough understanding of a microbiome's natural diversity, we need to obtain the necessary information from extreme ranges within the host's healthy state.}, } @article {pmid36083447, year = {2022}, author = {Zhu, Q and Mirarab, S}, title = {Assembling a Reference Phylogenomic Tree of Bacteria and Archaea by Summarizing Many Gene Phylogenies.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2569}, number = {}, pages = {137-165}, pmid = {36083447}, issn = {1940-6029}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Evolution, Molecular ; Gene Transfer, Horizontal ; Phylogeny ; Software ; }, abstract = {Phylogenomics is the inference of phylogenetic trees based on multiple marker genes sampled in the genomes of interest. An important challenge in phylogenomics is the potential incongruence among the evolutionary histories of individual genes, which can be widespread in microorganisms due to the prevalence of horizontal gene transfer. This protocol introduces the procedures for building a phylogenetic tree of a large number of microbial genomes using a broad sampling of marker genes that are representative of whole-genome evolution. The protocol highlights the use of a gene tree summary method, which can effectively reconstruct the species tree while accounting for the topological conflicts among individual gene trees. The pipeline described in this protocol is scalable to tens of thousands of genomes while retaining high accuracy. We discussed multiple software tools, libraries, and scripts to enable convenient adoption of the protocol. The protocol is suitable for microbiology and microbiome studies based on public genomes and metagenomic data.}, } @article {pmid36083388, year = {2022}, author = {Aurelle, D and Pratlong, M and Oury, N and Haguenauer, A and Gélin, P and Magalon, H and Adjeroud, M and Romans, P and Vidal-Dupiol, J and Claereboudt, M and Noûs, C and Reynes, L and Toulza, E and Bonhomme, F and Mitta, G and Pontarotti, P}, title = {Species and population genomic differentiation in Pocillopora corals (Cnidaria, Hexacorallia).}, journal = {Genetica}, volume = {150}, number = {5}, pages = {247-262}, pmid = {36083388}, issn = {1573-6857}, support = {ANR-11-LABX-0061//Agence Nationale de la Recherche/ ; ANR-12-ADAP-0016//Agence Nationale de la Recherche/ ; }, mesh = {Animals ; *Anthozoa/genetics ; Genetic Structures ; Metagenomics ; Sequence Analysis, DNA ; Species Specificity ; }, abstract = {Correctly delimiting species and populations is a prerequisite for studies of connectivity, adaptation and conservation. Genomic data are particularly useful to test species differentiation for organisms with few informative morphological characters or low discrimination of cytoplasmic markers, as in Scleractinians. Here we applied Restriction site Associated DNA sequencing (RAD-sequencing) to the study of species differentiation and genetic structure in populations of Pocillopora spp. from Oman and French Polynesia, with the objectives to test species hypotheses, and to study the genetic structure among sampling sites within species. We focused here on coral colonies morphologically similar to P. acuta (damicornis type β). We tested the impact of different filtering strategies on the stability of the results. The main genetic differentiation was observed between samples from Oman and French Polynesia. These samples corresponded to different previously defined primary species hypotheses (PSH), i.e., PSHs 12 and 13 in Oman, and PSH 5 in French Polynesia. In Oman, we did not observe any clear differentiation between the two putative species PSH 12 and 13, nor between sampling sites. In French Polynesia, where a single species hypothesis was studied, there was no differentiation between sites. Our analyses allowed the identification of clonal lineages in Oman and French Polynesia. The impact of clonality on genetic diversity is discussed in light of individual-based simulations.}, } @article {pmid36083005, year = {2022}, author = {Chen, J and Zhang, X}, title = {dICC: distance-based intraclass correlation coefficient for metagenomic reproducibility studies.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {21}, pages = {4969-4971}, pmid = {36083005}, issn = {1367-4811}, support = {R01 GM144351/GM/NIGMS NIH HHS/United States ; R21 HG011662/HG/NHGRI NIH HHS/United States ; }, mesh = {Reproducibility of Results ; *Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {SUMMARY: Due to the sparsity and high dimensionality, microbiome data are routinely summarized into pairwise distances capturing the compositional differences. Many biological insights can be gained by analyzing the distance matrix in relation to some covariates. A microbiome sampling method that characterizes the inter-sample relationship more reproducibly is expected to yield higher statistical power. Traditionally, the intraclass correlation coefficient (ICC) has been used to quantify the degree of reproducibility for a univariate measurement using technical replicates. In this work, we extend the traditional ICC to distance measures and propose a distance-based ICC (dICC). We derive the asymptotic distribution of the sample-based dICC to facilitate statistical inference. We illustrate dICC using a real dataset from a metagenomic reproducibility study.

dICC is implemented in the R CRAN package GUniFrac.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36082890, year = {2022}, author = {Banik, S and Bardhan, M and Basak, S}, title = {Genetic, Epigenetic, and Molecular Biology of Obesity: From Pathology to Therapeutics the Way Forward.}, journal = {The Journal of the Association of Physicians of India}, volume = {70}, number = {9}, pages = {11-12}, doi = {10.5005/japi-11001-0080}, pmid = {36082890}, issn = {0004-5772}, mesh = {Child ; Child, Preschool ; Epigenesis, Genetic ; Humans ; Molecular Biology ; *Pediatric Obesity/genetics ; Polymorphism, Single Nucleotide ; Risk Factors ; }, abstract = {Obesity is a globally expanding silent epidemic having multiple risk factors and consequences associated with it. Genetic factors have been found to be playing undeniable roles in obesity. Intermingled relationship between epigenetics, metagenomics, and the environment influences obesity traits. High precision diagnostic tools have outlined many single nucleotide polymorphisms (SNPs), as well as many novel genes, that have been identified that create an obesogenic environment. Rare single-gene diseases can lead to early childhood obesity and less satiety. With almost 30% of the global population being under the grip of obesity, the coming days are alarming. This review summarizes the existing knowledge on the genetic causes of obesity including the epidemiology as well as the issues of concern and new additions to the list. Furthermore, we discuss the ways to enhance the healthcare outcome for patients of obesity through interdepartmental collaborations apart from pharmacological therapy that is still limited to a few drugs. The teamwork of geneticists, genetic counselors, physicians, bariatric surgeons, nurses, endocrinologists, and pharmacists may provide promising results in intervention.}, } @article {pmid36082501, year = {2023}, author = {Özdemir, A and Yozgat, A and Işgın-Atıcı, K and Avcı, E and Yıldız, BD and Gündoğdu, A and Nalbantoğlu, U and Turhan, T and Doğruman-Al, F and Büyüktuncer, Z}, title = {Potential associations between alterations in gut microbiome and obesity-related traits after the bariatric surgery.}, journal = {Journal of human nutrition and dietetics : the official journal of the British Dietetic Association}, volume = {36}, number = {3}, pages = {981-996}, doi = {10.1111/jhn.13087}, pmid = {36082501}, issn = {1365-277X}, mesh = {Humans ; *Obesity, Morbid/surgery ; *Gastrointestinal Microbiome ; *Bariatric Surgery ; Diet ; Cholesterol ; }, abstract = {BACKGROUND: This study aimed to examine the effects of both obesity and bariatric surgery on gut microbiome, dietary intake, as well as metabolic and inflammatory parameters.

METHODS: All participants (15 with morbid obesity who had bariatric surgery, 8 with morbid obesity and 11 non-obese) were followed up for a 6-month period with interviews at baseline (M0), at the end of 3 (M3) and 6 months (M6). Dietary assessment was done, and blood and faecal samples were collected.

RESULTS: Dietary energy and nutrient intakes as well as serum glucose levels, total cholesterol, low-density lipoprotein (LDL)-cholesterol and high sensitivity C-reactive protein (hs-CRP) levels decreased after surgery (p < 0.05, for each). Participants with morbid obesity had higher levels of Firmicutes and lower levels of Bacteroidetes at M0 compared to non-obese participants. The abundances of Bacteroidetes increased (p = 0.02), whereas that of Firmicutes decreased (p > 0.05) after the surgery, leading to a significant decrease in Firmicutes/Bacteroidetes ratio (p = 0.01). At sub-phylum level, the abundances of Lactobacillus and Bifidobacterium decreased, whereas those of Akkermansia increased after the surgery (p < 0.01, for each). Although participants who were morbidly obese had a distinct profile according to ß-diversity indices at M0, it became similar with the profile of non-obese participants (p > 0.05) at M3 and M6. Similarly, α-diversity indices were lower in subjects with morbid obesity at M0, but became similar to levels in non-obese controls at M6.

CONCLUSION: This study confirmed that bariatric surgery has substantial impacts on gut microbiome's composition and diversity, as well as anthropometrical measurements and biochemical parameters, which were associated with the alterations in dietary intake patterns.}, } @article {pmid36081945, year = {2022}, author = {Zheng, J and Wu, Q and Zhang, L and Zou, Y and Wang, M and He, L and Guo, S}, title = {Anti-inflammatory activities of Qingfei oral liquid and its influence on respiratory microbiota in mice with ovalbumin-induced asthma.}, journal = {Frontiers in pharmacology}, volume = {13}, number = {}, pages = {911667}, pmid = {36081945}, issn = {1663-9812}, abstract = {Dysbiosis of respiratory microbiota is closely related to the pathophysiological processes of asthma, including airway inflammation. Previous studies have shown that Qingfei oral liquid (QF) can alleviate airway inflammation and airway hyper-responsiveness in respiratory syncytial virus-infected asthmatic mice, but its effect on the respiratory microbiota is unknown. We therefore aimed to observe the effects of QF on airway inflammation and respiratory microbiota in ovalbumin (OVA)-induced asthmatic mice. We also explored the potential mechanism of QF in reducing airway inflammation by regulating respiratory microbiota. Hematoxylin and eosin as well as periodic acid-Schiff staining were performed to observe the effects of QF on lung pathology in asthmatic mice. Cytokine levels in bronchoalveolar lavage fluid (BALF) specimens were also measured. Changes in respiratory microbiota were analyzed using 16S rRNA gene sequencing, followed by taxonomical analysis. In order to verify the metagenomic function prediction results, the expression of key proteins related to the MAPK and NOD-like receptor signaling pathways in the lung tissues were detected by immunohistochemistry. The current study found that QF had a significant anti-inflammatory effect in the airways of asthmatic mice. This is mainly attributed to a reduction in lung pathology changes and regulating cytokine levels in BALF. Analysis of the respiratory microbiota in asthmatic mice showed that the abundance of Proteobacteria at the phylum level and Pseudomonas at the genus level increased significantly and QF could significantly regulate the dysbiosis of respiratory microbiota in asthmatic mice. Metagenomic functional prediction showed that QF can downregulate the MAPK and Nod-like receptor signaling pathways. Immunohistochemical results showed that QF could downregulate the expression of p-JNK, p-P38, NLRP3, Caspase-1, and IL-1β, which are all key proteins in the signaling pathway of lung tissue. Our study therefore concluded that QF may reduce airway inflammation in asthmatic mice by regulating respiratory microbiota, and to the possibly downregulate MAPK and Nod-like receptor signaling pathways as its underlying mechanism.}, } @article {pmid36081802, year = {2022}, author = {Zhai, Y and Wei, C}, title = {Open pangenome of Lactococcus lactis generated by a combination of metagenome-assembled genomes and isolate genomes.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {948138}, pmid = {36081802}, issn = {1664-302X}, abstract = {Lactococcus lactis (L. lactis) is a well isolated and cultured lactic acid bacterium, but if utilizing the isolate genomes alone, the genome-based analysis of this taxon would be incomplete, because there are still uncultured strains in some ecological niches. In this study, we recovered 93 high-quality metagenome-assembled genomes (MAGs) of L. lactis from food and human gut metagenomes with a culture-independent method. We then constructed a unified genome catalog of L. lactis by integrating these MAGs with 70 publicly available isolated genomes. Having this comprehensive resource, we assessed the genomic diversity and phylogenetic relationships to further explore the genetic and functional properties of L. lactis. An open pangenome of L. lactis was generated using our genome catalog, consisting of 13,066 genes in total, from which 5,448 genes were not identified in the isolate genomes. The core genome-based phylogenetic analysis showed that L. lactis strains we collected were separated into two main subclades corresponding to two subspecies, with some uncultured phylogenetic lineages discovered. The species disparity was also indicated in PCA analysis based on accessory genes of our pangenome. These various analyzes shed further light on unexpectedly high diversity within the taxon at both genome and gene levels and gave clues about its population structure and evolution. Lactococcus lactis has a long history of safe use in food fermentations and is considered as one of the important probiotic microorganisms. Obtaining the complete genetic information of L. lactis is important to the food and health industry. However, it can naturally inhabit many environments other than dairy products, including drain water and human gut samples. Here we presented an open pan-genome of L. lactis constructed from 163 high-quality genomes obtained from various environments, including MAGs recovered from environmental metagenomes and isolate genomes. This study expanded the genetic information of L. lactis about one third, including more than 5,000 novel genes found in uncultured strains. This more complete gene repertoire of L. lactis is crucial to further understanding the genetic and functional properties. These properties may be harnessed to impart additional value to dairy fermentation or other industries.}, } @article {pmid36081793, year = {2022}, author = {Khan, MN and Khan, SI and Rana, MI and Ayyaz, A and Khan, MY and Imran, M}, title = {Intermittent fasting positively modulates human gut microbial diversity and ameliorates blood lipid profile.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {922727}, pmid = {36081793}, issn = {1664-302X}, abstract = {AIM: The aim was to evaluate the impact of intermittent fasting (IF) on human body mass index (BMI) and serum lipid profile thorough constructive rectification of gut microbiota.

METHODS AND RESULTS: Fourteen healthy women and thirty-one men were included in the study. Their blood and fecal samples were collected before and at the end of the study. Blood parameters, anthropometric values, and gut microbiology were noted to investigate the impact of intermittent fasting (IF) on human gut microbiota and physiology. Our data revealed that IF reduces the body weight and improves blood lipid profile, such as increasing high-density lipoprotein (HDL) and decreasing total cholesterol, triglycerides, and low- and very low-density lipoprotein levels. IF also decreases culturable aerobic bacterial count and increased fungal count. It was also found that the gut metagenome is altered considerably after IF. The human fecal bacterial diversity exhibited significant changes in decreased overall bacterial population, increased bacterial diversity (alpha diversity), and promoted evenness within the bacterial population at the species level. Anti-inflammatory bacteria Lactobacillus and Bifidobacterium were favorably increased, while pathogenic bacteria were decreased.

CONCLUSION: Collectively, these results indicated that IF could improve lipid profile and body weight in humans, and the potential mechanisms might be via regulating gut microbiota.

We demonstrated for the first time that IF improved body weight and blood lipid profile, indicating that IF could mitigate gut microbiota in humans.}, } @article {pmid36081629, year = {2022}, author = {Casaburi, G and Wei, J and Kazi, S and Liu, J and Wang, K and Tao, GZ and Lin, PY and Dunn, JCY and Henrick, BM and Frese, SA and Sylvester, KG}, title = {Metabolic model of necrotizing enterocolitis in the premature newborn gut resulting from enteric dysbiosis.}, journal = {Frontiers in pediatrics}, volume = {10}, number = {}, pages = {893059}, pmid = {36081629}, issn = {2296-2360}, abstract = {Necrotizing enterocolitis (NEC) is a leading cause of premature newborn morbidity and mortality. The clinical features of NEC consistently include prematurity, gut dysbiosis and enteral inflammation, yet the pathogenesis remains obscure. Herein we combine metagenomics and targeted metabolomics, with functional in vivo and in vitro assessment, to define a novel molecular mechanism of NEC. One thousand six hundred and forty seven publicly available metagenomics datasets were analyzed (NEC = 245; healthy = 1,402) using artificial intelligence methodologies. Targeted metabolomic profiling was used to quantify the concentration of specified fecal metabolites at NEC onset (n = 8), during recovery (n = 6), and in age matched controls (n = 10). Toxicity assays of discovered metabolites were performed in vivo in mice and in vitro using human intestinal epithelial cells. Metagenomic and targeted metabolomic analyses revealed significant differences in pyruvate fermentation pathways and associated intermediates. Notably, the short chain fatty acid formate was elevated in the stool of NEC patients at disease onset (P = 0.005) dissipated during recovery (P = 0.02) and positively correlated with degree of intestinal injury (r [2] = 0.86). In vitro, formate caused enterocyte cytotoxicity in human cells through necroptosis (P < 0.01). In vivo, luminal formate caused significant dose and development dependent NEC-like injury in newborn mice. Enterobacter cloacae and Klebsiella pneumoniae were the most discriminatory taxa related to NEC dysbiosis and increased formate production. Together, these data suggest a novel biochemical mechanism of NEC through the microbial production of formate. Clinical efforts to prevent NEC should focus on reducing the functional consequences of newborn gut dysbiosis associated metabolic pathways.}, } @article {pmid36081364, year = {2022}, author = {Molina Ortiz, JP and Read, MN and McClure, DD and Holmes, A and Dehghani, F and Shanahan, ER}, title = {High throughput genome scale modeling predicts microbial vitamin requirements contribute to gut microbiome community structure.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2118831}, pmid = {36081364}, issn = {1949-0984}, mesh = {Animals ; Bacteroides/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics/methods ; Mice ; Phylogeny ; Vitamins ; }, abstract = {Human gut microbiome structure and emergent metabolic outputs impact health outcomes. However, what drives such community characteristics remains underexplored. Here, we rely on high throughput genomic reconstruction modeling, to infer the metabolic attributes and nutritional requirements of 816 gut strains, via a framework termed GEMNAST. This has been performed in terms of a group of human vitamins to examine the role vitamin exchanges have at different levels of community organization. We find that only 91 strains can satisfy their vitamin requirements (prototrophs) while the rest show various degrees of auxotrophy/specialization, highlighting their dependence on external sources, such as other members of the microbial community. Further, 79% of the strains in our sample were mapped to 11 distinct vitamin requirement profiles with low phylogenetic consistency. Yet, we find that human gut microbial community enterotype indicators display marked metabolic differences. Prevotella strains display a metabolic profile that can be complemented by strains from other genera often associated with the Prevotella enterotype and agrarian diets, while Bacteroides strains occupy a prototrophic profile. Finally, we identify pre-defined interaction modules (IMs) of gut species from human and mice predicted to be driven by, or highly independent of vitamin exchanges. Our analysis provides mechanistic grounding to gut microbiome stability and to co-abundance-based observations, a fundamental step toward understanding emergent processes that influence health outcomes. Further, our work opens a path to future explorations in the field through applications of GEMNAST to additional nutritional dimensions.}, } @article {pmid36079806, year = {2022}, author = {Liu, L and Chen, X and Liu, L and Qin, H}, title = {Clostridium butyricum Potentially Improves Immunity and Nutrition through Alteration of the Microbiota and Metabolism of Elderly People with Malnutrition in Long-Term Care.}, journal = {Nutrients}, volume = {14}, number = {17}, pages = {}, pmid = {36079806}, issn = {2072-6643}, support = {81972221, 81730102 and 31970111//National Natural Science Foundation of China/ ; }, mesh = {Aged ; *Clostridium butyricum ; Fatty Acids, Volatile/metabolism ; Humans ; Long-Term Care ; *Malnutrition ; *Microbiota ; Single-Blind Method ; Vitamins ; }, abstract = {Recent research advances examining the gut microbiome and its association with human health have indicated that microbiota-targeted intervention is a promising means for health modulation. In this study, elderly people in long-term care (aged 83.2 ± 5.3 year) with malnutrition (MNA-SF score ≤ 7) were recruited in a community hospital for a 12-week randomized, single-blind clinical trial with Clostridium butyricum. Compared with the basal fluctuations of the control group, an altered gut microbiome was observed in the intervention group, with increased (p < 0.05) Coprobacillus species, Carnobacterium divergens, and Corynebacterium_massiliense, and the promoted growth of the beneficial organisms Akketmanse muciniphila and Alistipes putredinis. A concentrated profile of 14 increased Kyoto Encyclopedia of Genes and Genomes (KEGG) orthologs (KOs) that were enriched in cofactor/vitamin production and carbohydrate metabolism pathways were discovered; the genes were found to be correlated (p < 0.05) with an elevated abundance of plasma metabolites and short-chain fatty acids (SCFAs), unsaturated medium- to long-chain fatty acids (MFA, LFA), carnitines, and amino acids, thus suggesting a coordinated ameliorated metabolism. Proinflammatory factor interferon-gamma (IFN-γ) levels decreased (p < 0.05) throughout the intervention, while the gut barrier tight junction protein, occludin, rose in abundance (p = 0.059), and the sensitive nutrition biomarker prealbumin improved, in contrast to the opposite changes in control. Based on our results obtained during a relatively short intervention time, C. butyricum might have great potential for improving nutrition and immunity in elderly people in long-term care with malnutrition through the alteration of gut microbiota, increasing the abundance of beneficial bacteria and activating the metabolism in SCFA and cofactor/vitamin production, bile acid metabolism, along with efficient energy generation.}, } @article {pmid36079632, year = {2022}, author = {Franchi, E and Cardaci, A and Pietrini, I and Fusini, D and Conte, A and De Folly D'Auris, A and Grifoni, M and Pedron, F and Barbafieri, M and Petruzzelli, G and Vocciante, M}, title = {Nature-Based Solutions for Restoring an Agricultural Area Contaminated by an Oil Spill.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {17}, pages = {}, pmid = {36079632}, issn = {2223-7747}, support = {3500047416//Eni Rewind S.p.A/ ; }, abstract = {A feasibility study is presented for a bioremediation intervention to restore agricultural activity in a field hit by a diesel oil spill from an oil pipeline. The analysis of the real contaminated soil was conducted following two approaches. The first concerned the assessment of the biodegradative capacity of the indigenous microbial community through laboratory-scale experimentation with different treatments (natural attenuation, landfarming, landfarming + bioaugmentation). The second consisted of testing the effectiveness of phytoremediation with three plant species: Zea mays (corn), Lupinus albus (lupine) and Medicago sativa (alfalfa). With the first approach, after 180 days, the different treatments led to biodegradation percentages between 83 and 96% for linear hydrocarbons and between 76 and 83% for branched ones. In case of contamination by petroleum products, the main action of plants is to favor the degradation of hydrocarbons in the soil by stimulating microbial activity thanks to root exudates. The results obtained in this experiment confirm that the presence of plants favors a decrease in the hydrocarbon content, resulting in an improved degradation of up to 18% compared with non-vegetated soils. The addition of plant growth-promoting bacteria (PGPB) isolated from the contaminated soil also promoted the growth of the tested plants. In particular, an increase in biomass of over 50% was found for lupine. Finally, the metagenomic analysis of the contaminated soil allowed for evaluating the evolution of the composition of the microbial communities during the experimentation, with a focus on hydrocarbon- oxidizing bacteria.}, } @article {pmid36079205, year = {2022}, author = {Uskoković, V and Wu, VM}, title = {Altering Microbiomes with Hydroxyapatite Nanoparticles: A Metagenomic Analysis.}, journal = {Materials (Basel, Switzerland)}, volume = {15}, number = {17}, pages = {}, pmid = {36079205}, issn = {1996-1944}, abstract = {Hydroxyapatite (HAp), the most abundant biological material among mammals, has been recently demonstrated to possess moderate antibacterial properties. Metagenomics provides a series of tools for analyzing the simultaneous interaction of materials with larger communities of microbes, which may aid in optimizing the antibacterial activity of a material such as HAp. Here, a microbiome intrinsic to the sample of sandy soil collected from the base of an African Natal plum (Carissa macrocarpa) shrub surrounding the children's sandbox at the Arrowhead Park in Irvine, California was challenged with HAp nanoparticles and analyzed with next-generation sequencing for hypervariable 16S ribosomal DNA base pair homologies. HAp nanoparticles overwhelmingly reduced the presence of Gram-negative phyla, classes, orders, families, genera and species, and consequently elevated the relative presence of their Gram-positive counterparts. Thermodynamic, electrostatic and chemical bonding arguments were combined in a model proposed to explain this selective affinity. The ability of amphiphilic surface protrusions of lipoteichoic acid in Gram-positive bacteria and mycolic acid in mycobacteria to increase the dispersibility of the bacterial cells and assist in their resistance to capture by the solid phase is highlighted. Within the Gram-negative group, the variability of the distal, O-antigen portion of the membrane lipopolysaccharide was shown to be excessive and the variability of its proximal, lipid A portion insufficient to explain the selectivity based on chemical sequence arguments. Instead, flagella-driven motility proves to be a factor favoring the evasion of binding to HAp. HAp displayed a preference toward binding to less pathogenic bacteria than those causative of disease in humans, while taxa having a positive agricultural effect were largely captured by HAp, indicating an evolutionary advantage this may have given it as a biological material. The capacity to selectively sequester Gram-negative microorganisms and correspondingly alter the composition of the microbiome may open up a new avenue in environmental and biomedical applications of HAp.}, } @article {pmid36078440, year = {2022}, author = {Zhang, K and Li, K and Tong, M and Xia, Y and Cui, Y and Liu, Z and Chen, Q and Li, Q and Hu, F and Yang, F}, title = {Distribution Pattern and Influencing Factors of Heavy Metal Resistance Genes in the Yellow River Sediments of Henan Section.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {17}, pages = {}, pmid = {36078440}, issn = {1660-4601}, mesh = {China ; Environmental Monitoring/methods ; Geologic Sediments/microbiology ; Humans ; *Metals, Heavy/analysis ; Risk Assessment ; Rivers/microbiology ; *Water Pollutants, Chemical/analysis ; }, abstract = {The transformation of heavy metal resistance genes (MRGs) in the environment has attracted increasing attention in recent years. However, few studies have reported the MRG content in the Yellow River, one of the main irrigation water sources in the North China Plain. In this study, we quantified MRG abundance by a metagenomic approach, and assessed the influence on MRGs of both bioavailable and total heavy metal (HM) content. The results indicate that Cu-resistant genes are the most common genes, and the prevalence of arsM needs more attention. Comamonadaceae is the dominant family in the Yellow River, and the presence of organic pollutants may contribute to the prevalence of Vicinamibacteraceae, Nocardioidaceae, and Flavobacteriacea. The results of the Mantel test and Spearman analysis indicate that both the bioavailable fractions and total content of HMs could have little influence on MRGs. Network analysis results indicate that some dominant bacteria could be the potential hosts of some prevalent MRGs, which may exert an adverse impact on human health.}, } @article {pmid36077990, year = {2022}, author = {Wei, L and Zhou, W and Zhu, Z}, title = {Comparison of Changes in Gut Microbiota in Wild Boars and Domestic Pigs Using 16S rRNA Gene and Metagenomics Sequencing Technologies.}, journal = {Animals : an open access journal from MDPI}, volume = {12}, number = {17}, pages = {}, pmid = {36077990}, issn = {2076-2615}, support = {NO ygz2022101//Chongqing Medical and Pharmaceutical College/ ; NO KJQN202202821//Chongqing Education Commission of China/ ; }, abstract = {Gut microbiota diversity is a result of co-evolution between microorganisms and their hosts. However, there are few studies on the evolution of the gut microbiota of wild boars and domestic pigs. Therefore, this study aimed to analyze the composition and function of the gut microbiota of wild boars and domestic pigs using 16S rRNA gene V3-V4 region sequencing, 16S rRNA gene full-length sequencing, and metagenomic sequencing. This study showed that after a long evolution, as compared to wild boars, the domestic pigs exhibited significantly increased relative abundances of Lactobacillus, Lactobacillus reuteri, Lactobacillus johnsonii, Lactobacillus sp.DJF_WC5, and Lactobacillus; s_uncultured bacterium, while the relative abundances of Bifidobacterium and Methanococcaceae decreased significantly. In addition, the relative abundances of "carbohydrate metabolism", "starch and sucrose metabolism", "valine, leucine, and isoleucine biosynthesis", "lysine biosynthesis", and starch-degrading CAZymes were significantly increased in the domestic pigs, while the relative abundances of "environmental adaptation", "immune system", "fatty acid degradation and synthesis", and cellulose-hemicellulose-degrading CAZymes were significantly increased in the wild boars. Finally, the diversity of ARGs and the "antimicrobial resistance genes" in domestic pigs also increased significantly. This study illustrates that the gut microbiota composition and function of wild boars and domestic pigs changed during the long evolution process. These findings provide a basic research theory for the evolution of gut microbiota and the treatment of health and disease.}, } @article {pmid36077748, year = {2022}, author = {Obón-Santacana, M and Mas-Lloret, J and Bars-Cortina, D and Criado-Mesas, L and Carreras-Torres, R and Díez-Villanueva, A and Moratalla-Navarro, F and Guinó, E and Ibáñez-Sanz, G and Rodríguez-Alonso, L and Mulet-Margalef, N and Mata, A and García-Rodríguez, A and Duell, EJ and Pimenoff, VN and Moreno, V}, title = {Meta-Analysis and Validation of a Colorectal Cancer Risk Prediction Model Using Deep Sequenced Fecal Metagenomes.}, journal = {Cancers}, volume = {14}, number = {17}, pages = {}, pmid = {36077748}, issn = {2072-6694}, support = {FIS PI17/00092//Instituto de Salud Carlos III/ ; GCTRA18022MORE//Asociación Española Contra el Cáncer/ ; }, abstract = {The gut microbiome is a potential modifiable risk factor for colorectal cancer (CRC). We re-analyzed all eight previously published stool sequencing data and conducted an MWAS meta-analysis. We used cross-validated LASSO predictive models to identify a microbiome signature for predicting the risk of CRC and precancerous lesions. These models were validated in a new study, Colorectal Cancer Screening (COLSCREEN), including 156 participants that were recruited in a CRC screening context. The MWAS meta-analysis identified 95 bacterial species that were statistically significantly associated with CRC (FDR < 0.05). The LASSO CRC predictive model obtained an area under the receiver operating characteristic curve (aROC) of 0.81 (95%CI: 0.78−0.83) and the validation in the COLSCREEN dataset was 0.75 (95%CI: 0.66−0.84). This model selected a total of 32 species. The aROC of this CRC-trained model to predict precancerous lesions was 0.52 (95%CI: 0.41−0.63). We have identified a signature of 32 bacterial species that have a good predictive accuracy to identify CRC but not precancerous lesions, suggesting that the identified microbes that were enriched or depleted in CRC are merely a consequence of the tumor. Further studies should focus on CRC as well as precancerous lesions with the intent to implement a microbiome signature in CRC screening programs.}, } @article {pmid36077231, year = {2022}, author = {Purushothaman, S and Meola, M and Egli, A}, title = {Combination of Whole Genome Sequencing and Metagenomics for Microbiological Diagnostics.}, journal = {International journal of molecular sciences}, volume = {23}, number = {17}, pages = {}, pmid = {36077231}, issn = {1422-0067}, support = {Nr. 310030_192515/SNSF_/Swiss National Science Foundation/Switzerland ; }, mesh = {Computational Biology ; Humans ; *Metagenome ; *Metagenomics ; Whole Genome Sequencing ; Workflow ; }, abstract = {Whole genome sequencing (WGS) provides the highest resolution for genome-based species identification and can provide insight into the antimicrobial resistance and virulence potential of a single microbiological isolate during the diagnostic process. In contrast, metagenomic sequencing allows the analysis of DNA segments from multiple microorganisms within a community, either using an amplicon- or shotgun-based approach. However, WGS and shotgun metagenomic data are rarely combined, although such an approach may generate additive or synergistic information, critical for, e.g., patient management, infection control, and pathogen surveillance. To produce a combined workflow with actionable outputs, we need to understand the pre-to-post analytical process of both technologies. This will require specific databases storing interlinked sequencing and metadata, and also involves customized bioinformatic analytical pipelines. This review article will provide an overview of the critical steps and potential clinical application of combining WGS and metagenomics together for microbiological diagnosis.}, } @article {pmid36076928, year = {2022}, author = {Ravin, NV and Rudenko, TS and Smolyakov, DD and Beletsky, AV and Gureeva, MV and Samylina, OS and Grabovich, MY}, title = {History of the Study of the Genus Thiothrix: From the First Enrichment Cultures to Pangenomic Analysis.}, journal = {International journal of molecular sciences}, volume = {23}, number = {17}, pages = {}, pmid = {36076928}, issn = {1422-0067}, support = {20-14-00137//Russian Science Foundation/ ; }, mesh = {DNA, Bacterial/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Sulfur/metabolism ; *Thiothrix/genetics/metabolism ; }, abstract = {Representatives of the genus Thiothrix are filamentous, sulfur-oxidizing bacteria found in flowing waters with counter-oriented sulfide and oxygen gradients. They were first described at the end of the 19th century, but the first pure cultures of this species only became available 100 years later. An increase in the number of described Thiothrix species at the beginning of the 21st century shows that the classical phylogenetic marker, 16S rRNA gene, is not informative for species differentiation, which is possible based on genome analysis. Pangenome analysis of the genus Thiothrix showed that the core genome includes genes for dissimilatory sulfur metabolism and central metabolic pathways, namely the Krebs cycle, Embden-Meyerhof-Parnas pathway, glyoxylate cycle, Calvin-Benson-Bassham cycle, and genes for phosphorus metabolism and amination. The shell part of the pangenome includes genes for dissimilatory nitrogen metabolism and nitrogen fixation, for respiration with thiosulfate. The dispensable genome comprises genes predicted to encode mainly hypothetical proteins, transporters, transcription regulators, methyltransferases, transposases, and toxin-antitoxin systems.}, } @article {pmid36076388, year = {2022}, author = {Marzoli, F and Antonelli, P and Saviane, A and Tassoni, L and Cappellozza, S and Belluco, S}, title = {Bombyx mori from a food safety perspective: A systematic review.}, journal = {Food research international (Ottawa, Ont.)}, volume = {160}, number = {}, pages = {111679}, doi = {10.1016/j.foodres.2022.111679}, pmid = {36076388}, issn = {1873-7145}, mesh = {Allergens ; Animals ; *Bombyx ; *Edible Insects ; Food Safety ; *Hypersensitivity ; Insecta ; }, abstract = {Bombyx mori (BM) is an economically important insect for silk production, and it is also farmed and used as food in different countries around the world. The present systematic review aims to assess the suitability of BM as an edible insect, retrieving data from scientific papers reporting microbiological, chemical, and allergenic hazards of silkworm consumed as either whole insects or insect derivatives. We considered all studies published in peer-reviewed journals in English, French, and Spanish languages. No time limits were imposed. We searched PUBMED, WEB of Science Core Collection, and EMBASE databases. The last literature search was carried out on May 5th, 2021. Data were collected in pre-defined tabular forms for the aforementioned hazards. In total, 65 records investigating the safety aspects were included after screening: 32 on microbiological hazards; 27 on chemical hazards; 16 on allergenic hazards. Concerning microbiological aspects, a high presence of Enterococcus in raw insects (5.00 % to 70.10 %) was reported through metagenomic analysis. Through non-metagenomic methods (classical and biomolecular microbiology techniques), Bacillus cereus and Pseudomonas fluorescens were the most commonly investigated and detected bacteria in the unprocessed insects, while B. cereus and Enterobacteriaceae were studied and reported in insect-based food. The foodborne pathogens Listeria monocytogenes and Salmonella spp. were never detected. Concerning toxicological aspects, three studies assessed the toxicity of BM powder in laboratory animals, but no negative effects were observed. Regarding heavy metal bioaccumulation in BM, evidence was reported for As, Cu, and, Zn. Allergic reactions following the ingestion of BM or derivative products are due to proteins that are widespread in arthropods. Furthermore, BM proteins can undergo possible cross-reactions with proteins of other insect species or crustaceans. However, heat treatments do not seem to reduce the allergenic potential of the silkworm proteins. The major limitation of the present review is that we could include only scientific literature published in Western languages, while the majority of relevant studies were conducted in Asian countries and part of them are published in Asian languages. In conclusion, scientific evidence regarding microbiological and chemical hazards of BM relevant for food safety is very limited. In the present work microbiological and chemical hazards relevant for food safety were identified in BM, however their presence do not impair the use as food but suggest the need for a risk assessment under specific conditions of production and use. Allergic reactions are possible in sensitive individuals following the ingestion of edible BM.}, } @article {pmid36076344, year = {2023}, author = {Xu, H and Qian, Y and Jia, S and Shi, Z and Zhong, Q}, title = {Comparative analysis of subgingival microbiota in patients with mild, moderate, and severe chronic periodontitis.}, journal = {Oral diseases}, volume = {29}, number = {7}, pages = {2865-2877}, doi = {10.1111/odi.14373}, pmid = {36076344}, issn = {1601-0825}, support = {20184Y0244//Shanghai Municipal Health and Family Planning Commission/ ; }, mesh = {Humans ; *Chronic Periodontitis/therapy ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; Gingival Crevicular Fluid ; *Microbiota/genetics ; }, abstract = {In this study, we explored the suspected pathogens of chronic periodontitis at different stages of occurrence and development. We collected 100 gingival crevicular fluid samples, 27, 27, and 26 from patients with mild, moderate, and severe chronic periodontitis, respectively, and 20 from healthy individuals. Pathogens were detected using a 16S rRNA metagenomic approach. Quantitative Insights in Microbial Ecology, Mothur, and other software were used to analyze the original data, draw relative abundance histograms and heat maps, and calculate flora abundance and diversity indexes. We identified 429 operational taxonomic units, covering 13 phyla, 20 classes, 32 orders, 66 families, and 123 genera from the four groups of samples. Each group showed microbial diversity, and the number of new species of bacterial flora in the gingival crevicular fluid samples gradually increased from the healthy to the severe chronic periodontitis group. There was a significant difference in the relative abundance of the core flora at the phylum, class, order, family, and genus classification levels. Our data indicated a certain correlation between the changes in the subgingival microbial structure and the occurrence and development of chronic periodontitis, which might be able to provide a reference for the diagnosis, treatment and prevention of chronic periodontitis.}, } @article {pmid36076296, year = {2022}, author = {Yang, HH and He, XJ and Nie, JM and Guan, SS and Chen, YK and Liu, M}, title = {Central nervous system aspergillosis misdiagnosed as Toxoplasma gondii encephalitis in a patient with AIDS: a case report.}, journal = {AIDS research and therapy}, volume = {19}, number = {1}, pages = {40}, pmid = {36076296}, issn = {1742-6405}, mesh = {*Acquired Immunodeficiency Syndrome/complications ; *Aspergillosis/complications/diagnosis/drug therapy ; Brain ; Diagnostic Errors ; *Encephalitis/diagnosis/drug therapy/etiology ; *HIV Infections/complications ; Humans ; Male ; Middle Aged ; *Toxoplasmosis, Cerebral/cerebrospinal fluid/diagnosis/drug therapy ; }, abstract = {BACKGROUND: Patients with acquired immunodeficiency syndrome (AIDS) tend to suffer from several central nervous system (CNS) infections due to hypoimmunity. However, CNS aspergillosis (CNSAG) is extremely rare and difficult to diagnose. Thus, it is easily misdiagnosed.

CASE PRESENTATION: We reported a 47-year-old male AIDS patient with ghosting vision and anhidrosis on the left head and face. He was accordingly diagnosed with Toxoplasma gondii encephalitis (TE) at other hospitals, for which he received regular anti-Toxoplasma gondii and anti-human immunodeficiency virus (anti-HIV) treatment. Then, the patient was transferred to our hospital due to a lack of any improvement with the prescribed treatment. The patient's neurological examination revealed no abnormalities at admission, only a slight change in the cerebrospinal fluid. His cranial magnetic resonance imaging (MRI) revealed multiple abnormal signals in the brain parenchyma, and his blood was positive for Toxoplasma gondii IgG antibody. The initial diagnosis at our hospital was also TE. Considering the poor efficacy of anti-TE treatment, cerebrospinal fluid metagenomics next-generation sequencing (mNGS) was performed, but no pathogenic bacteria were detected. However, Aspergillus fumigatus was detected in the cerebrospinal fluid via targeted next-generation sequencing (tNGS) and bronchoalveolar alveolar lavage fluid via mNGS. The diagnosis was accordingly revised to CNSAG combined with his other clinical manifestations. After administering voriconazole antifungal therapy, the patient's symptoms were relieved, with improved absorption of the intracranial lesions.

CONCLUSIONS: The present case experience indicates the need for clinicians to strengthen their understanding of CNSAG. Moreover, for patients with diagnostic difficulties, early mNGS and tNGS (using biological samples with only a few pathogens) are helpful for early diagnosis and treatment, potentially allowing patients to achieve favorable outcomes.}, } @article {pmid36076153, year = {2022}, author = {Guo, Y and Song, B and Li, A and Wu, Q and Huang, H and Li, N and Yang, Y and Adams, JM and Yang, L}, title = {Higher pH is associated with enhanced co-occurrence network complexity, stability and nutrient cycling functions in the rice rhizosphere microbiome.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {6200-6219}, doi = {10.1111/1462-2920.16185}, pmid = {36076153}, issn = {1462-2920}, mesh = {Rhizosphere ; *Oryza ; Soil Microbiology ; *Microbiota/genetics ; Soil ; Nutrients ; Hydrogen-Ion Concentration ; }, abstract = {The rice rhizosphere microbiota is crucial for crop yields and nutrient use efficiency. However, little is known about how co-occurrence patterns, keystone taxa and functional gene assemblages relate to soil pH in the rice rhizosphere soils. Using shotgun metagenome analysis, the rice rhizosphere microbiome was investigated across 28 rice fields in east-central China. At higher pH sites, the taxonomic co-occurrence network of rhizosphere soils was more complex and compact, as defined by higher average degree, graph density and complexity. Network stability was greatest at medium pH (6.5 < pH < 7.5), followed by high pH (7.5 < pH). Keystone taxa were more abundant at higher pH and correlated significantly with key ecosystem functions. Overall functional genes involved in C, N, P and S cycling were at a higher relative abundance in higher pH rhizosphere soils, excepting C degradation genes (e.g. key genes involved in starch, cellulose, chitin and lignin degradation). Our results suggest that the rice rhizosphere soil microbial network is more complex and stable at higher pH, possibly indicating increased efficiency of nutrient cycling. These observations may indicate routes towards more efficient soil management and understanding of the potential effects of soil acidification on the rice rhizosphere system.}, } @article {pmid36076058, year = {2022}, author = {Ravi, A and Troncoso-Rey, P and Ahn-Jarvis, J and Corbin, KR and Harris, S and Harris, H and Aydin, A and Kay, GL and Le Viet, T and Gilroy, R and Pallen, MJ and Page, AJ and O'Grady, J and Warren, FJ}, title = {Hybrid metagenome assemblies link carbohydrate structure with function in the human gut microbiome.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {932}, pmid = {36076058}, issn = {2399-3642}, support = {BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012512/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10343/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BS/E/F/000PR10346/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10348/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10349/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10352/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics ; *Microbiota ; Starch/metabolism ; }, abstract = {Complex carbohydrates that escape small intestinal digestion, are broken down in the large intestine by enzymes encoded by the gut microbiome. This is a symbiotic relationship between microbes and host, resulting in metabolic products that influence host health and are exploited by other microbes. However, the role of carbohydrate structure in directing microbiota community composition and the succession of carbohydrate-degrading microbes, is not fully understood. In this study we evaluate species-level compositional variation within a single microbiome in response to six structurally distinct carbohydrates in a controlled model gut using hybrid metagenome assemblies. We identified 509 high-quality metagenome-assembled genomes (MAGs) belonging to ten bacterial classes and 28 bacterial families. Bacterial species identified as carrying genes encoding starch binding modules increased in abundance in response to starches. The use of hybrid metagenomics has allowed identification of several uncultured species with the functional potential to degrade starch substrates for future study.}, } @article {pmid36075991, year = {2022}, author = {Ngetich, DK and Bett, RC and Gachuiri, CK and Kibegwa, FM}, title = {Diversity of gut methanogens and functional enzymes associated with methane metabolism in smallholder dairy cattle.}, journal = {Archives of microbiology}, volume = {204}, number = {10}, pages = {608}, pmid = {36075991}, issn = {1432-072X}, mesh = {Animals ; Cattle ; *Euryarchaeota/metabolism ; Female ; Kenya ; Methane/metabolism ; Rumen ; Ruminants ; }, abstract = {Methane is a greenhouse gas with disastrous consequences when released to intolerable levels. Ruminants produce methane during gut fermentation releasing it through belching and/or flatulence. To better understand the diversity of methanogens and functional enzymes associated with methane metabolism in dairy cows, 48 samples; 6 rumen fluid and 42 dung samples were collected from Kenyan and Tanzanian farms and were analyzed using shotgun metagenomic approach. Statistical analysis for species frequency, relative abundance, percentages, and P values were undertaken using MS Excel and IBM SPSS statistics 20. The results showed archaea from 5 phyla, 9 classes, 16 orders, 25 families, 59 genera, and 87 species. Gut sites significantly contributed to the presence and distribution of various methanogens (P < 0.01). The class Methanomicrobia was abundant in the rumen samples (~ 39%) and dung (~ 44%). The most abundant (~ 17%) methanogen species identified was Methanocorpusculum labreanum. However, some taxonomic class data were unclassified (~ 6% in the rumen and ~ 4% in the dung). Five functional enzymes: Glycine/Serine hydroxymethyltransferase, Formylmethanofuran-tetrahydromethanopterin N-formyltransferase, Formate dehydrogenase, anaerobic carbon monoxide dehydrogenase, and catalase-peroxidase associated with methane metabolism were identified. KEGG functional metabolic analysis for the enzymes identified during this study was significant (P < 0.05) for five metabolism processes. The methanogen species abundances from this study in numbers/kind can be utilized exclusively or jointly as indirect selection criteria for methane mitigation. When targeting functional genes of the microbes/animal for better performance, the concern not to affect the host animal's functionality should be undertaken. Future studies should consider taxonomically categorizing unclassified species.}, } @article {pmid36075807, year = {2023}, author = {Zysset-Burri, DC and Morandi, S and Herzog, EL and Berger, LE and Zinkernagel, MS}, title = {The role of the gut microbiome in eye diseases.}, journal = {Progress in retinal and eye research}, volume = {92}, number = {}, pages = {101117}, doi = {10.1016/j.preteyeres.2022.101117}, pmid = {36075807}, issn = {1873-1635}, mesh = {Humans ; *Gastrointestinal Microbiome/physiology ; *Central Serous Chorioretinopathy ; *Microbiota ; *Uveitis ; *Macular Degeneration ; *Retinal Artery Occlusion ; }, abstract = {The gut microbiome is a complex ecosystem of microorganisms and their genetic entities colonizing the gastrointestinal tract. When in balanced composition, the gut microbiome is in symbiotic interaction with its host and maintains intestinal homeostasis. It is involved in essential functions such as nutrient metabolism, inhibition of pathogens and regulation of immune function. Through translocation of microbes and their metabolites along the epithelial barrier, microbial dysbiosis induces systemic inflammation that may lead to tissue destruction and promote the onset of various diseases. Using whole-metagenome shotgun sequencing, several studies have shown that the composition and associated functional capacities of the gut microbiome are associated with age-related macular degeneration, retinal artery occlusion, central serous chorioretinopathy and uveitis. In this review, we provide an overview of the current knowledge about the gut microbiome in eye diseases, with a focus on interactions between the microbiome, specific microbial-derived metabolites and the immune system. We explain how these interactions may be involved in the pathogenesis of age-related macular degeneration, retinal artery occlusion, central serous chorioretinopathy and uveitis and guide the development of new therapeutic approaches by microbiome-altering interventions for these diseases.}, } @article {pmid36075417, year = {2023}, author = {Zhang, M and Wang, Y and Bai, M and Jiang, H and Cui, R and Lin, K and Tan, C and Gao, C and Zhang, C}, title = {Metagenomics analysis of antibiotic resistance genes, the bacterial community and virulence factor genes of fouled filters and effluents from household water purifiers in drinking water.}, journal = {The Science of the total environment}, volume = {854}, number = {}, pages = {158572}, doi = {10.1016/j.scitotenv.2022.158572}, pmid = {36075417}, issn = {1879-1026}, mesh = {*Drinking Water/analysis ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; *Water Purification/methods ; Bacteria ; Drug Resistance, Microbial/genetics ; Metagenomics ; }, abstract = {The aim of this study was to explore the influence and removal of household water purifiers (HWPs) on emerging contaminants in drinking water, and their distribution characteristics. The antibiotic resistance genes (ARGs), mobile genetic elements (MGEs), virulence factor genes (VFGs) and bacterial communities were profiled in the fouled filters, influents, and effluents from HWPs with five steps of filtration after 150 days operation, using metagenomics. The results showed that the diversity of dominant species in Poly Propylene 1 μm (PP1) and nanofiltration membrane (NM) was significantly higher than that in other filters. Post-activated carbon (AC) was used to detect low species richness or diversity, and the highest proportion of dominant species, which contributes to the greater microbial risk of HWPs effluents in drinking water. The number of dominant bacterial genera in the filters disinfected with chloramine was higher than that in the same group disinfected with chlorine. The bacterial species richness or diversity in water was reduced by the purification of HWPs because the filter elements effectively trapped a variety of microorganisms. The relative abundance of Antibiotic efflux in the effluents of chlorinated and chloraminated HWPs was 5.58 × 10[-3] and 4.60 × 10[-3], respectively, which was the main resistance mechanism. High abundance of VFGs was found in HWPs effluents and the relative abundance of aggressive VFGs was significantly higher than those of defensive VFGs. Based on the co-occurrence results, 243 subtypes of ARGs co-occurred with VFGs, and a variety of bacteria were thought to be possible ARGs hosts, which indicated that the host bacteria of VFGs in HWP effluents had a stronger attack ability. The effluent of HWPs with only filtration processes is exposed to the risk of ARGs and VFGs. This study helps to understand the actual purification effect of HWPs and provides a theoretical reference for the management and control of ARGs pollution in domestic drinking water.}, } @article {pmid36075413, year = {2022}, author = {Prado, T and Brandão, ML and Fumian, TM and Freitas, L and Chame, M and Leomil, L and Magalhães, MGP and Degrave, WMS and Leite, JPG and Miagostovich, MP}, title = {Virome analysis in lakes of the South Shetland Islands, Antarctica - 2020.}, journal = {The Science of the total environment}, volume = {852}, number = {}, pages = {158537}, doi = {10.1016/j.scitotenv.2022.158537}, pmid = {36075413}, issn = {1879-1026}, mesh = {Humans ; Lakes ; Antarctic Regions ; Virome ; Prospective Studies ; *Viruses/genetics ; *RNA Viruses ; *Microbiota ; Islands ; }, abstract = {Polar freshwater ecosystems are characterized by a distinct microbiota. However, little is known about viral diversity and abundance, especially regarding the ecology of RNA viruses. We used shotgun metagenomic analysis on samples from Antarctic ecosystems, and report here the characterization of the virome fraction, from different lakes located in the South Shetland Islands (Penguin, Ardley, Deception and King George Island) in the Peninsula Antarctica, in the summer season 2020. DNA viruses (99.4 %) prevailed over RNA viruses (0.6 %) in the lake samples. Six viral orders were identified in the metagenomic libraries: Caudovirales (dsDNA), which was prevalent in most lakes; Picornavirales (ssRNA+); Sobelivirales (ssRNA+); Tolivirales (ssRNA+); Petitvirales (ssDNA) and Baphyvirales (ssDNA), including eight viral families (Herelleviridae, Siphoviridae, Myoviridae, Microviridae, Marnaviridae, Bacilladnaviridae, Barnaviridae and Tombusviridae) and several other, mainly non-classified ssRNA[(+)] viruses in the lakes of Ardley Island. Bacteriophages (dsDNA) (Herelleviridae family) infecting the phylum Firmicutes and Siphoviridae were predominant in most lakes evaluated. Functional analysis demonstrated a prevalence of unknown proteins (68 %) in the virome. Our prospective study provides virome analysis data from different lakes in the South Shetland Islands, Antarctica, opening exploratory lines for future research related to the biodiversity and viral ecology in this extreme ecosystem.}, } @article {pmid36075400, year = {2022}, author = {Fan, X and Deng, H and Qiu, J and Ji, H and Shen, X}, title = {Antibiotics-induced depression in mice via the microbiota-gut-brain axis.}, journal = {Journal of affective disorders}, volume = {318}, number = {}, pages = {152-158}, doi = {10.1016/j.jad.2022.08.059}, pmid = {36075400}, issn = {1573-2517}, mesh = {Adrenocorticotropic Hormone ; Animals ; Anti-Bacterial Agents/adverse effects ; Brain-Derived Neurotrophic Factor ; Brain-Gut Axis ; Corticosterone ; *Depression/etiology ; Disease Models, Animal ; Dysbiosis ; *Gastrointestinal Microbiome ; Mice ; Mice, Inbred C57BL ; NF-kappa B/metabolism ; Norepinephrine ; Serotonin ; Stress, Psychological/complications ; }, abstract = {BACKGROUND: Intestinal dysbacteriosis is associated with depression. This study aimed to establish an antibiotics-induced depression mouse model and explore the mechanism of antibiotic-induced depression.

METHODS: C57BL/6 J mice were treated with antibiotics to prepare the antibiotic-induced depression mouse model. Behavioral tests and depression-related bio-markers were examined. To understand the abundance of different bacteria in intestinal flora and screen out the predominant bacterial species, metagenomic analysis of feces was carried out. Finally, we detected the expression of NF-κB-p65 and p-NF-κB-p65 in PFC and the hippocampus using Western blot.

RESULTS: Mixtures A and B caused depression-like behavior in mice. Norepinephrine, 5-hydroxytryptamine, and brain-derived neurotrophic factor in hippocampus and PFC of antibiotic-induced depression mice significantly decreased. The serum adrenocorticotropic hormone and corticosterone concentrations increased. The abundance values of Bacteroides thetaiotaomicron, Klebsiella oxytoca, and Klebsiella aerogenes in antibiotic-induced depression mice significantly increased, and the characteristic KO genes and metabolic pathways in antibiotic-induced depression mice were significantly different with in CUMS depression mice (the positive control) and normal mice. The relative levels of p-NF-κB-p65 in antibiotics-induced depression mice were significantly higher than in normal mice.

LIMITATIONS: How dysbacteriosis induces inflammation in the central nervous system is unclear.

CONCLUSIONS: Specific antibiotic mixture can cause depression-like behavior and changes of depression-related bio-markers in mice. The antibiotic-induced depression mice display changes in the species and metabolism of intestinal bacterial flora. The activation of NF-κB inflammatory signaling pathway in the central nervous system may act as one of the mechanisms in the development of antibiotic-induced depression.}, } @article {pmid36075331, year = {2022}, author = {Ren, Z and Luo, W}, title = {Metagenomic analysis reveals the diversity and distribution of antibiotic resistance genes in thermokarst lakes of the Yellow River Source Area.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {313}, number = {}, pages = {120102}, doi = {10.1016/j.envpol.2022.120102}, pmid = {36075331}, issn = {1873-6424}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Ice ; Lakes ; *Rifamycins ; *Rivers ; }, abstract = {Thermokarst lakes form as the results of ice-rich permafrost thawing and act as important water resources in cold regions. However, the distributions of antibiotic resistance genes (ARGs) in thermokarst lakes are far less studied. Using metagenomic sequencing approach, we provided the first study to document ARGs in thermokarst lakes of the Yellow River Source Area on the Qinghai-Tibet Plateau (QTP). The results revealed that both sediment and water of the thermokarst lakes harbor diverse ARGs. Multidrug resistance genes were the most diverse, while rifamycin resistance genes were the most abundant with rpoB2 and rpoB genes having the highest proportion. Sediment samples contained more ARGs than water samples, but their composition differed between the two types of samples. However, the composition variations of sediment and water ARGs were closely correlated. The Sorensen dissimilarities of ARGs were controlled by strong turnover processes in sediment samples, and by turnover and nestedness in water samples. High contributions of nestedness were found between sediment and water samples. Moreover, ARGs in water had more significant relationships with environmental variables than that in sediment. Given the role of thermokarst lakes as important water resources in permafrost landscape, as well as intensifying influences of climate change and anthropogenetic activities, thermokarst lakes could bring potential ARG risks, warranting further investigation and evaluation.}, } @article {pmid36075329, year = {2022}, author = {Khatoon, M and Jakhesara, SJ and Rank, DN and Joshi, CG and Kunjadiya, AP}, title = {Exploration of rumen microbial and carbohydrate-active enzyme profiles in cattle fed coir a lignin-rich diet using a metagenomic approach.}, journal = {Gene}, volume = {846}, number = {}, pages = {146868}, doi = {10.1016/j.gene.2022.146868}, pmid = {36075329}, issn = {1879-0038}, mesh = {Animal Feed ; Animals ; Bacteria ; Carbohydrates ; Cattle ; Diet ; Glycoside Hydrolases ; Glycosyltransferases ; *Lignin/analogs & derivatives ; Plant Breeding ; RNA, Ribosomal, 16S/genetics ; *Rumen ; }, abstract = {Lignocellulosic biomass is a rich source of feed for cattle. Amongst them, coconut coir may be the potential source of feed supplements. To assess, the effect of various concentrations of coconut coir (0 %, 21 % and 40 %) as a feed supplement on the rumen microbiome of cattle (Kankrej breed), a metagenomic (16S rRNA gene amplicon and shotgun sequencing) study was performed. The Alpha diversity estimation from the amplicon study suggested that the group of cattle fed food without the coconut coir has a higher number of genera than the cattle fed with mixed ration. Within the liquid fraction, bacterial phyla Bacteroidetes were abundant followed by Firmicutes and Fibrobacteres, whereas the proportion of Tenericutes, TM7, SRI, Verrucomicrobia, Lentisphaerae, and Elusimicrobia had decreased with the rise in the coir concentration. While within the solid fractions, the proportion of Elusimicrobia increased, but the count of Bacteriodetes, Firmicutes, Fibrobacteres Tenericutes, TM7, SRI, Verrucomicrobia, and Lentisphaerae decreased with an increase in coir percentages. The results obtained from shotgun sequencing show similar results for bacterial diversity. The functions associated with carbohydrate metabolism were abundant in both the treatments as compared to the control. Functions related to glycoside hydrolases, glycosyltransferases and carbohydrate-binding modules were abundant in both the treatments as compared to control. Thus, the study indicates that the microbiome does alter after feeding coir as a supplement and may be used as feed for cattle.}, } @article {pmid36074890, year = {2023}, author = {Kullar, R and Chisari, E and Snyder, J and Cooper, C and Parvizi, J and Sniffen, J}, title = {Next-Generation Sequencing Supports Targeted Antibiotic Treatment for Culture Negative Orthopedic Infections.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {76}, number = {2}, pages = {359-364}, pmid = {36074890}, issn = {1537-6591}, mesh = {Humans ; *Prosthesis-Related Infections/diagnosis/drug therapy/microbiology ; *Arthritis, Infectious/diagnosis ; High-Throughput Nucleotide Sequencing/methods ; Anti-Bacterial Agents/therapeutic use ; Prostheses and Implants ; }, abstract = {The isolation of an infective pathogen can be challenging in some patients with active, clinically apparent infectious diseases. Despite efforts in the microbiology lab to improve the sensitivity of culture in orthopedic implant-associated infections, the clinically relevant information often falls short of expectations. The management of peri-prosthetic joint infections (PJI) provides an excellent example of the use and benefits of newer diagnostic technologies to supplement the often-inadequate yield of traditional culture methods as a substantial percentage of orthopedic infections are culture-negative. Next-generation sequencing (NGS) has the potential to improve upon this yield. Bringing molecular diagnostics into practice can provide critical information about the nature of the infective organisms and allow targeted therapy in these otherwise challenging situations. This review article describes the current state of knowledge related to the use and potential of NGS to diagnose infections, particularly in the setting of PJIs.}, } @article {pmid36073806, year = {2022}, author = {Hakim, D and Wandro, S and Zengler, K and Zaramela, LS and Nowinski, B and Swafford, A and Zhu, Q and Song, SJ and Gonzalez, A and McDonald, D and Knight, R}, title = {Zebra: Static and Dynamic Genome Cover Thresholds with Overlapping References.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0075822}, pmid = {36073806}, issn = {2379-5077}, support = {DP1 AT010885/AT/NCCIH NIH HHS/United States ; U24 CA248454/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; *Algorithms ; Staphylococcus aureus/genetics ; Metagenome ; Metagenomics/methods ; *Microbiota ; }, abstract = {Assigning taxonomy remains a challenging topic in microbiome studies, due largely to ambiguity of reads which overlap multiple reference genomes. With the Web of Life (WoL) reference database hosting 10,575 reference genomes and growing, the percentage of ambiguous reads will only increase. The resulting artifacts create both the illusion of co-occurrence and a long tail end of extraneous reference hits that confound interpretation. We introduce genome cover, the fraction of reference genome overlapped by reads, to distinguish these artifacts. We show how to dynamically predict genome cover by read count and examine our model in Staphylococcus aureus monoculture. Our modeling cleanly separates both S. aureus and true contaminants from the false artifacts of reference overlap. We next introduce saturated genome cover, the true fraction of a reference genome overlapped by sample contents. Genome cover may not saturate for low abundance or low prevalence bacteria. We assuage this worry with examination of a large human fecal data set. By compositing the metric across like samples, genome cover saturates even for rare species. We note that it is a threshold on saturated genome cover, not genome cover itself, which indicates a spurious reference hit or distant relative. We present Zebra, a method to compute and threshold the genome cover metric across like samples, a recurrence to estimate genome cover and confirm saturation, and provide guidance for choosing cover thresholds in real world scenarios. Standalone genome cover and integration into Woltka are available: https://github.com/biocore/zebra_filter, https://github.com/qiyunzhu/woltka. IMPORTANCE Taxonomic assignment, assigning sequences to specific taxonomic units, is a crucial processing step in microbiome analyses. Issues in taxonomic assignment affect interpretation of what microbes are present in each sample and may be associated with specific environmental or clinical conditions. Assigning importance to a particular taxon relies strongly on independence of assigned counts. The false inclusion of thousands of correlated taxa makes interpretation ambiguous, leading to underconstrained results which cannot be reproduced. The importance sometimes attached to implausible artifacts such as anthrax or bubonic plague is especially problematic. We show that the Zebra filter retrieves only the nearest relatives of sample contents enabling more reproducible and biologically plausible interpretation of metagenomic data.}, } @article {pmid36073802, year = {2022}, author = {Li, C and Hao, L and Lü, F and Duan, H and Zhang, H and He, P}, title = {Syntrophic Acetate-Oxidizing Microbial Consortia Enriched from Full-Scale Mesophilic Food Waste Anaerobic Digesters Showing High Biodiversity and Functional Redundancy.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0033922}, pmid = {36073802}, issn = {2379-5077}, mesh = {Humans ; Microbial Consortia/genetics ; Ammonia/metabolism ; Anaerobiosis ; Food ; RNA, Ribosomal, 16S/genetics ; *Refuse Disposal ; Bacteria/genetics ; Oxidation-Reduction ; *Euryarchaeota/genetics ; Acetates/metabolism ; }, abstract = {Syntrophic acetate oxidation (SAO) coupled with hydrogenotrophic methanogenesis (HM) plays a vital role in the anaerobic digestion of protein-rich feedstocks such as food wastes. However, current knowledge of the biodiversity and genetic potential of the involved microbial participants, especially syntrophic acetate-oxidizing bacteria (SAOB), is limited due to the low abundance of these microorganisms and challenges in their isolation. The intent of this study was to enrich and identify potential SAOB. Therefore, we conducted continuous acetate feeding under high ammonia concentrations using two separate inoculum consortia of microorganisms that originated from full-scale mesophilic food waste digesters, which lasted for more than 200 days. Using 16S rRNA gene amplicon and metagenomic analyses, we observed a convergence of the experimental microbial communities during the enrichment regarding taxonomic composition and metabolic functional composition. Stable carbon isotope analyses of biogas indicated that SAO-HM was the dominant methanogenic pathway during the enrichment process. The hydrogenotrophic methanogen Methanoculleus dominated the archaeal community. The enriched SAO community featured high biodiversity and metabolic functional redundancy. By analyzing the metagenome-assembled genomes, the known SAOB Syntrophaceticus schinkii and six uncultured populations were identified to have the genetic potential to perform SAO through the conventional reversed Wood-Ljungdahl pathway, while another six bacteria were found to encode the reversed Wood-Ljungdahl pathway combined with a glycine cleavage system as novel SAOB candidates. These results showed that the food waste anaerobic digesters harbor diverse SAOB and highlighted the importance of the glycine cleavage system for acetate oxidation. IMPORTANCE Syntrophic acetate oxidation to CO2 and H2, together with hydrogenotrophic methanogenesis, contributes to much of the carbon flux in the anaerobic digestion of organic wastes, especially at high ammonia concentrations. A deep understanding of the biodiversity, metabolic genetic potential, and ecology of the SAO community can help to improve biomethane production from wastes for clean energy production. Here, we enriched the SAO-HM functional guild obtained from full-scale food waste anaerobic digesters and recorded dynamic changes in community taxonomic composition and functional profiles. By reconstructing the metabolic pathways, diverse known and novel bacterial members were found to have SAO potential via the reversed Wood-Ljungdahl (WL) pathway alone, or via the reversed WL pathway with a glycine cleavage system (WLP-GCS), and those catalyzing WLP-GCS showed higher microbial abundance. This study revealed the biodiversity and metabolic functional redundancy of SAOB in full-scale anaerobic digester systems and provided inspiration for further genome-centric studies.}, } @article {pmid36073480, year = {2022}, author = {Silva, JM and Almeida, JR}, title = {Characterizing Genomics Repositories Using Feature-Based Classification.}, journal = {Studies in health technology and informatics}, volume = {298}, number = {}, pages = {167-168}, doi = {10.3233/SHTI220932}, pmid = {36073480}, issn = {1879-8365}, mesh = {*Genome ; *Genomics ; }, abstract = {In the last decades, the field of metagenomics aided by NGS technologies has grown exponentially and is now a cornerstone tool in medicine. However, even with the current technologies, obtaining a conclusive identification of an organism can be challenging due to using reference-based methods. Consequently, when releasing a new repository of genomic data that contains de-novo sequences, it is problematic to characterize its content. In this paper, we propose a novel method for organism identification and the creation and characterization of genomic databases. For identification, we propose a three-step pipeline for reference-free reconstruction, reference-based classification and features-based classification. On the other hand, for content exposition and extraction, the sequences and their identification are aggregated into a web database catalogue.}, } @article {pmid36073352, year = {2022}, author = {Grouzdev, D and Gaisin, V and Lunina, O and Krutkina, M and Krasnova, E and Voronov, D and Baslerov, R and Sigalevich, P and Savvichev, A and Gorlenko, V}, title = {Microbial communities of stratified aquatic ecosystems of Kandalaksha Bay (White Sea) shed light on the evolutionary history of green and brown morphotypes of Chlorobiota.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {10}, pages = {}, doi = {10.1093/femsec/fiac103}, pmid = {36073352}, issn = {1574-6941}, mesh = {Bays ; *Chlorobi/genetics ; *Microbiota/genetics ; Photosynthesis ; Phylogeny ; Water ; }, abstract = {Anoxygenic photoautotrophic metabolism of green sulfur bacteria of the family Chlorobiaceae played a significant role in establishing the Earth's biosphere. Two known major ecological forms of these phototrophs differ in their pigment composition and, therefore, in color: the green and brown forms. The latter form often occurs in low-light environments and is specialized to harvest blue light, which can penetrate to the greatest depth in the water column. In the present work, metagenomic sequencing was used to investigate the natural population of brown Chl. phaeovibrioides ZM in a marine stratified Zeleny Mys lagoon in the Kandalaksha Bay (the White Sea) to supplement the previously obtained genomes of brown Chlorobiaceae. The genomes of brown and green Chlorobiaceae were investigated using comparative genome analysis and phylogenetic and reconciliation analysis to reconstruct the evolution of these ecological forms. Our results support the suggestion that the last common ancestor of Chlorobiaceae belonged to the brown form, i.e. it was adapted to the conditions of low illumination. However, despite the vertical inheritance of these characteristics, among modern Chlorobiaceae populations, the genes responsible for synthesizing the pigments of the brown form are subject to active horizontal transfer.}, } @article {pmid36073311, year = {2022}, author = {McLean, AR and Torres-Morales, J and Dewhirst, FE and Borisy, GG and Mark Welch, JL}, title = {Site-tropism of streptococci in the oral microbiome.}, journal = {Molecular oral microbiology}, volume = {37}, number = {6}, pages = {229-243}, pmid = {36073311}, issn = {2041-1014}, support = {R01 DE016937/DE/NIDCR NIH HHS/United States ; R01 DE022586/DE/NIDCR NIH HHS/United States ; R01 DE027958/DE/NIDCR NIH HHS/United States ; R01 DE030136/DE/NIDCR NIH HHS/United States ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Streptococcus/genetics ; *Microbiota/genetics ; Metagenome ; Bacteria/genetics ; Mouth/microbiology ; Tropism ; Phylogeny ; }, abstract = {A detailed understanding of where bacteria localize is necessary to advance microbial ecology and microbiome-based therapeutics. The site-specialist hypothesis predicts that most microbes in the human oral cavity have a primary habitat type within the mouth where they are most abundant. We asked whether this hypothesis accurately describes the distribution of the members of the genus Streptococcus, a clinically relevant taxon that dominates most oral sites. Prior analysis of 16S rRNA gene sequencing data indicated that some oral Streptococcus clades are site-specialists while others may be generalists. However, within complex microbial populations composed of numerous closely related species and strains, such as the oral streptococci, genome-scale analysis is necessary to provide the resolution to discriminate closely related taxa with distinct functional roles. Here, we assess whether individual species within this genus are specialists using publicly available genomic sequence data that provide species-level resolution. We chose a set of high-quality representative genomes for human oral Streptococcus species. Onto these genomes, we mapped shotgun metagenomic sequencing reads from supragingival plaque, tongue dorsum, and other sites in the oral cavity. We found that every abundant Streptococcus species in the healthy human oral cavity showed strong site-tropism and that even closely related species such as S. mitis, S. oralis, and S. infantis specialized in different sites. These findings indicate that closely related bacteria can have distinct habitat distributions in the absence of dispersal limitation and under similar environmental conditions and immune regimes. Substantial overlap between the core genes of these three species suggests that site-specialization is determined by subtle differences in genomic content.}, } @article {pmid36072369, year = {2022}, author = {Duan, W and Yang, Y and Zhao, J and Yan, T and Tian, X}, title = {Application of metagenomic next-generation sequencing in the diagnosis and treatment of recurrent urinary tract infection in kidney transplant recipients.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {901549}, pmid = {36072369}, issn = {2296-2565}, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; *Kidney Transplantation ; Metagenomics ; Sensitivity and Specificity ; *Urinary Tract Infections/diagnosis ; }, abstract = {BACKGROUND: Rapid and accurate pathogen diagnosis is an urgent unmet clinical need for recurrent urinary tract infection (RUTI) in kidney transplant recipients (KTRs). Metagenomic next-generation sequencing (mNGS) may offer another strategy for diagnosing uropathogens but remains to be studied.

METHODS: Nineteen KTRs with RUTI were collected in this study. The uropathogens were detected and compared by mNGS and urine culture, respectively. Modifications of the anti-infection strategy were also assessed.

RESULTS: Rich and diverse pathogens were revealed by mNGS. mNGS was significantly higher than culture in total positive rate (100.0% vs. 31.6%; p < 0.01) and in identification rates for bacteria (89.5% vs. 31.6%; p < 0.01), for viruses (57.9% vs. 0; p < 0.01), and for fungi (42.1% vs. 0; p < 0.01), respectively. mNGS identified a significantly higher proportion of mixed infections than culture (89.5% vs. 10.5%; p < 0.01). The anti-infection therapies were adjusted in two (33.3%) and 12 (76.9%) cases guided by culture and mNGS, respectively.

CONCLUSION: mNGS has more remarkable etiological diagnostic performance compared with urine culture for KTRs with RUTI to guide anti-infection strategies and, in turn, protect the graft.}, } @article {pmid36070704, year = {2022}, author = {Wanapaisan, P and Chuansangeam, M and Nopnipa, S and Mathuranyanon, R and Nonthabenjawan, N and Ngamsombat, C and Thientunyakit, T and Muangpaisan, W}, title = {Association between Gut Microbiota with Mild Cognitive Impairment and Alzheimer's Disease in a Thai Population.}, journal = {Neuro-degenerative diseases}, volume = {22}, number = {2}, pages = {43-54}, doi = {10.1159/000526947}, pmid = {36070704}, issn = {1660-2862}, mesh = {Humans ; Aged ; *Alzheimer Disease/diagnosis ; *Gastrointestinal Microbiome ; Southeast Asian People ; *Cognitive Dysfunction/complications ; Neuroimaging ; }, abstract = {BACKGROUND: Mild cognitive impairment (MCI) and Alzheimer's disease (AD) are common in older adults. Much recent work has implicated the connection between the gut and the brain via bidirectional communication of the gastrointestinal tract and the central nervous system through biochemical signaling. Altered gut microbiota composition has shown controversial results based on geographic location, age, diet, physical activity, psychological status, underlying diseases, medication, and drug use.

OBJECTIVES: This study aimed to investigate the relationships of gut microbiota with MCI and AD.

METHODS: 16S metagenome profiles from stool collection of participant groups (normal; n = 20, MCI; n = 12, AD; n = 20) were analyzed. The diagnosis of cognitive conditions was made by standard criteria consisting of clinical interviews, physical examinations, cognitive assessments, laboratory examinations, and neuroimaging by both structural neuroimaging and amyloid positron emission tomography scans. Correlations between medical factors with food frequency and the fecal microbiome were elucidated.

RESULTS: A significant difference at the operational taxonomic unit level was observed. The significantly higher abundance of bacteria in nondementia patients belonged to the Clostridiales order, including Clostridium sensu stricto 1 (p < 0.0001), Fusicatenibacter (p = 0.0007), Lachnospiraceae (p = 0.001), Agathobacter (p = 0.021), and Fecalibacterium (p < 0.0001). In contrast, Escherichia-Shigella (p = 0.0002), Bacteroides (p = 0.0014), Holdemanella (p < 0.0001), Romboutsia (p = 0.001), and Megamonas (p = 0.047) were the dominant genera in the AD group. Left and right hippocampus and right amygdala volumes were significantly decreased in the AD group (p < 0.001) and significantly correlated with the groups of bacteria that were significantly different between groups.

CONCLUSION: There was a relationship between the composition of the gut microbiome and neurodegenerative disorders, including MCI and AD. Reduction of Clostridiaceae and increases in Enterobacteriaceae and Bacteroides were associated with persons with MCI and AD, consistent with previous studies. The altered gut microbiome could be potentially targeted for the early diagnosis of dementia and the reduction of AD risk.}, } @article {pmid36069707, year = {2022}, author = {Capo, E and Feng, C and Bravo, AG and Bertilsson, S and Soerensen, AL and Pinhassi, J and Buck, M and Karlsson, C and Hawkes, J and Björn, E}, title = {Expression Levels of hgcAB Genes and Mercury Availability Jointly Explain Methylmercury Formation in Stratified Brackish Waters.}, journal = {Environmental science & technology}, volume = {56}, number = {18}, pages = {13119-13130}, pmid = {36069707}, issn = {1520-5851}, mesh = {Humans ; *Mercury/analysis ; *Methylmercury Compounds/metabolism ; Oxygen ; Saline Waters ; Sulfides ; Water ; *Water Pollutants, Chemical/analysis ; }, abstract = {Neurotoxic methylmercury (MeHg) is formed by microbial methylation of inorganic divalent Hg (Hg[II]) and constitutes severe environmental and human health risks. The methylation is enabled by hgcA and hgcB genes, but it is not known if the associated molecular-level processes are rate-limiting or enable accurate prediction of MeHg formation in nature. In this study, we investigated the relationships between hgc genes and MeHg across redox-stratified water columns in the brackish Baltic Sea. We showed, for the first time, that hgc transcript abundance and the concentration of dissolved Hg[II]-sulfide species were strong predictors of both the Hg[II] methylation rate and MeHg concentration, implying their roles as principal joint drivers of MeHg formation in these systems. Additionally, we characterized the metabolic capacities of hgc[+] microorganisms by reconstructing their genomes from metagenomes (i.e., hgc[+] MAGs), which highlighted the versatility of putative Hg[II] methylators in the water column of the Baltic Sea. In establishing relationships between hgc transcripts and the Hg[II] methylation rate, we advance the fundamental understanding of mechanistic principles governing MeHg formation in nature and enable refined predictions of MeHg levels in coastal seas in response to the accelerating spread of oxygen-deficient zones.}, } @article {pmid36069586, year = {2022}, author = {, }, title = {Expression of Concern for Amrane et al., "Clostridium scindens Is Present in the Gut Microbiota during Clostridium difficile Infection: a Metagenomic and Culturomic Analysis".}, journal = {Journal of clinical microbiology}, volume = {60}, number = {10}, pages = {e0107622}, doi = {10.1128/jcm.01076-22}, pmid = {36069586}, issn = {1098-660X}, } @article {pmid36069579, year = {2022}, author = {Koyama, K and Mikawa, Y and Nakagawa, S and Kurashiki, R and Ohshiro, T and Suzuki, H}, title = {New Platform for Screening Genetic Libraries at Elevated Temperatures: Biological and Genomic Information and Genetic Tools of Geobacillus thermodenitrificans K1041.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {18}, pages = {e0105122}, pmid = {36069579}, issn = {1098-5336}, mesh = {DNA Restriction Enzymes/genetics ; DNA Restriction-Modification Enzymes/genetics ; Escherichia coli/genetics ; *Escherichia coli Proteins/genetics ; Genetic Vectors ; Genomics ; *Geobacillus/genetics ; Plasmids/genetics ; Temperature ; }, abstract = {Geobacillus thermodenitrificans K1041 is an unusual thermophile that is highly transformable via electroporation, making it a promising host for screening genetic libraries at elevated temperatures. In this study, we determined its biological properties, draft genome sequence, and effective vectors and also optimized the electroporation procedures in an effort to enhance its utilization. The organism exhibited swarming motility but not detectable endospore formation, and growth was rapid at 60°C under neutral and relatively low-salt conditions. Although the cells showed negligible acceptance of shuttle plasmids from general strains of Escherichia coli, methylation-controlled plasmids from dam mutant strains were efficiently accepted, suggesting circumvention of a restriction-modification system in G. thermodenitrificans K1041. We optimized the electroporation procedure to achieve efficiencies of 10[3] to 10[5] CFU/μg for five types of plasmids, which exhibited the different copy numbers and segregational stabilities in G. thermodenitrificans K1041. Some sets of plasmids were compatible. Moreover, we observed substantial plasmid-directed production of heterologous proteins in the intracellular or extracellular environments. Our successful construction of a library of promoter mutants using K1041 cells as hosts and subsequent screening at elevated temperatures to identify improved promoters revealed that G. thermodenitrificans K1041 was practical as a library host. The draft genomic sequence of the organism contained 3,384 coding genes, including resA and mcrB genes, which are involved in restriction-modification systems. Further examination revealed that in-frame deletions of resA increased transformation efficiencies, but mcrB deletion had no effect. The ΔresA mutant exhibited transformation efficiencies of >10[5] CFU/μg for some plasmids. IMPORTANCE Geobacillus thermodenitrificans K1041 has yet to be fully characterized. Although it is transformable via electroporation, it rarely accepts Escherichia coli-derived plasmids. This study clarified the biological and genomic properties of G. thermodenitrificans K1041. Additionally, we developed an electroporation procedure resulting in efficient acceptance of E. coli-derived plasmids. This procedure produced transformants using small amounts of plasmids immediately after the ligation reaction. Thus, G. thermodenitrificans K1041 was identified as a host for screening promoter mutants at elevated temperatures. Furthermore, because this strain efficiently produced heterologous proteins, it could serve as a host for screening thermostable proteins encoded in random mutant libraries or metagenomes. We also generated a ΔresA mutant that exhibited transformation efficiencies of >10[5] CFU/μg, which were highest in cases of electroporation-based transformation of Geobacillus spp. with E. coli-derived plasmids. Our findings provide a new platform for screening diverse genetic libraries at elevated temperatures.}, } @article {pmid36069554, year = {2022}, author = {Piatkowski, BT and Carper, DL and Carrell, AA and Chen, IA and Clum, A and Daum, C and Eloe-Fadrosh, EA and Gilbert, D and Granath, G and Huntemann, M and Jawdy, SS and Klarenberg, IJ and Kostka, JE and Kyrpides, NC and Lawrence, TJ and Mukherjee, S and Nilsson, MB and Palaniappan, K and Pelletier, DA and Pennacchio, C and Reddy, TBK and Roux, S and Shaw, AJ and Warshan, D and Živković, T and Weston, DJ}, title = {Draft Metagenome Sequences of the Sphagnum (Peat Moss) Microbiome from Ambient and Warmed Environments across Europe.}, journal = {Microbiology resource announcements}, volume = {11}, number = {10}, pages = {e0040022}, pmid = {36069554}, issn = {2576-098X}, support = {504399//Joint Genome Institute (JGI)/ ; DEB-1754756//National Science Foundation (NSF)/ ; //U.S. Department of Energy (DOE)/ ; DESC0020362//U.S. Department of Energy (DOE)/ ; }, abstract = {We present 49 metagenome assemblies of the microbiome associated with Sphagnum (peat moss) collected from ambient, artificially warmed, and geothermally warmed conditions across Europe. These data will enable further research regarding the impact of climate change on plant-microbe symbiosis, ecology, and ecosystem functioning of northern peatland ecosystems.}, } @article {pmid36069455, year = {2022}, author = {Maringanti, VS and Bucci, V and Gerber, GK}, title = {MDITRE: Scalable and Interpretable Machine Learning for Predicting Host Status from Temporal Microbiome Dynamics.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0013222}, pmid = {36069455}, issn = {2379-5077}, support = {1R01GM130777//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; }, mesh = {Humans ; RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Machine Learning ; Software ; Metagenomics/methods ; }, abstract = {Longitudinal microbiome data sets are being generated with increasing regularity, and there is broad recognition that these studies are critical for unlocking the mechanisms through which the microbiome impacts human health and disease. However, there is a dearth of computational tools for analyzing microbiome time-series data. To address this gap, we developed an open-source software package, Microbiome Differentiable Interpretable Temporal Rule Engine (MDITRE), which implements a new highly efficient method leveraging deep-learning technologies to derive human-interpretable rules that predict host status from longitudinal microbiome data. Using semi-synthetic and a large compendium of publicly available 16S rRNA amplicon and metagenomics sequencing data sets, we demonstrate that in almost all cases, MDITRE performs on par with or better than popular uninterpretable machine learning methods, and orders-of-magnitude faster than the prior interpretable technique. MDITRE also provides a graphical user interface, which we show through case studies can be used to derive biologically meaningful interpretations linking patterns of microbiome changes over time with host phenotypes. IMPORTANCE The human microbiome, or collection of microbes living on and within us, changes over time. Linking these changes to the status of the human host is crucial to understanding how the microbiome influences a variety of human diseases. Due to the large scale and complexity of microbiome data, computational methods are essential. Existing computational methods for linking changes in the microbiome to the status of the human host are either unable to scale to large and complex microbiome data sets or cannot produce human-interpretable outputs. We present a new computational method and software package that overcomes the limitations of previous methods, allowing researchers to analyze larger and more complex data sets while producing easily interpretable outputs. Our method has the potential to enable new insights into how changes in the microbiome over time maintain health or lead to disease in humans and facilitate the development of diagnostic tests based on the microbiome.}, } @article {pmid36069454, year = {2022}, author = {Pandolfo, M and Telatin, A and Lazzari, G and Adriaenssens, EM and Vitulo, N}, title = {MetaPhage: an Automated Pipeline for Analyzing, Annotating, and Classifying Bacteriophages in Metagenomics Sequencing Data.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0074122}, pmid = {36069454}, issn = {2379-5077}, support = {BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R506552/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Humans ; *Bacteriophages/genetics ; Reproducibility of Results ; Metagenomics/methods ; *Microbiota/genetics ; *Viruses ; }, abstract = {Phages are the most abundant biological entities on the planet, and they play an important role in controlling density, diversity, and network interactions among bacterial communities through predation and gene transfer. To date, a variety of bacteriophage identification tools have been developed that differ in the phage mining strategies used, input files requested, and results produced. However, new users attempting bacteriophage analysis can struggle to select the best methods and interpret the variety of results produced. Here, we present MetaPhage, a comprehensive reads-to-report pipeline that streamlines the use of multiple phage miners and generates an exhaustive report. The report both summarizes and visualizes the key findings and enables further exploration of key results via interactive filterable tables. The pipeline is implemented in Nextflow, a widely adopted workflow manager that enables an optimized parallelization of tasks in different locations, from local server to the cloud; this ensures reproducible results from containerized packages. MetaPhage is designed to enable scalability and reproducibility; also, it can be easily expanded to include new miners and methods as they are developed in this continuously growing field. MetaPhage is freely available under a GPL-3.0 license at https://github.com/MattiaPandolfoVR/MetaPhage. IMPORTANCE Bacteriophages (viruses that infect bacteria) are the most abundant biological entities on earth and are increasingly studied as members of the resident microbiota community in many environments, from oceans to soils and the human gut. Their identification is of great importance to better understand complex bacterial dynamics and microbial ecosystem function. A variety of metagenome bacteriophage identification tools have been developed that differ in the phage mining strategies used, input files requested, and results produced. To facilitate the management and the execution of such a complex workflow, we developed MetaPhage (MP), a comprehensive reads-to-report pipeline that streamlines the use of multiple phage miners and generates an exhaustive report. The pipeline is implemented in Nextflow, a widely adopted workflow manager that enables an optimized parallelization of tasks. MetaPhage is designed to enable scalability and reproducibility and offers an installation-free, dependency-free, and conflict-free workflow execution.}, } @article {pmid36069451, year = {2022}, author = {Teudt, F and Otani, S and Aarestrup, FM}, title = {Global Distribution and Diversity of Prevalent Sewage Water Plasmidomes.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0019122}, pmid = {36069451}, issn = {2379-5077}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; *Sewage/microbiology ; Drug Resistance, Bacterial ; Macrolides ; Plasmids/genetics ; Bacteria ; }, abstract = {Sewage water from around the world contains an abundance of short plasmids, several of which harbor antimicrobial resistance genes (ARGs). The global dynamics of plasmid-derived antimicrobial resistance and functions are only starting to be unveiled. Here, we utilized a previously created data set of 159,332 assumed small plasmids from 24 different global sewage samples. The detailed phylogeny, as well as the interplay between their protein domains, ARGs, and predicted bacterial host genera, were investigated to understand sewage plasmidome dynamics globally. A total of 58,429 circular elements carried genes encoding plasmid-related features, and MASH distance analyses showed a high degree of diversity. A single (yet diverse) cluster of 520 predicted Acinetobacter plasmids was predominant among the European sewage water. Our results suggested a prevalence of plasmid-backbone gene combinations over others. This could be related to selected bacterial genera that act as bacterial hosts. These combinations also mirrored the geographical locations of the sewage samples. Our functional domain network analysis identified three groups of plasmids. However, these backbone domains were not exclusive to any given group, and Acinetobacter was the dominant host genus among the theta-replicating plasmids, which contained a reservoir of the macrolide resistance gene pair msr(E) and mph(E). Macrolide resistance genes were the most common in the sewage plasmidomes and were found in the largest number of unique plasmids. While msr(E) and mph(E) were limited to Acinetobacter, erm(B) was disseminated among a range of Firmicutes plasmids, including Staphylococcus and Streptococcus, highlighting a potential reservoir of antibiotic resistance for these pathogens from around the globe. IMPORTANCE Antimicrobial resistance is a global threat to human health, as it inhibits our ability to treat infectious diseases. This study utilizes sewage water plasmidomes to identify plasmid-derived features and highlights antimicrobial resistance genes, particularly macrolide resistance genes, as abundant in sewage water plasmidomes in Firmicutes and Acinetobacter hosts. The emergence of macrolide resistance in these bacteria suggests that macrolide selective pressure exists in sewage water and that the resident bacteria can readily acquire macrolide resistance via small plasmids.}, } @article {pmid36069449, year = {2022}, author = {Shi, C and Beller, L and Wang, L and Rosales Rosas, A and De Coninck, L and Héry, L and Mousson, L and Pagès, N and Raes, J and Delang, L and Vega-Rúa, A and Failloux, AB and Matthijnssens, J}, title = {Bidirectional Interactions between Arboviruses and the Bacterial and Viral Microbiota in Aedes aegypti and Culex quinquefasciatus.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0102122}, pmid = {36069449}, issn = {2150-7511}, mesh = {Humans ; Animals ; Female ; *Culex ; *Aedes ; *Arboviruses ; *Zika Virus ; *Zika Virus Infection ; Mosquito Vectors ; *West Nile virus ; *Viruses ; *Microbiota ; Bacteria ; Sucrose ; Water ; }, abstract = {Mosquitoes are important vectors for many arboviruses. It is becoming increasingly clear that various symbiotic microorganisms (including bacteria and insect-specific viruses; ISVs) in mosquitoes have the potential to modulate the ability of mosquitoes to transmit arboviruses. In this study, we compared the bacteriome and virome (both eukaryotic viruses and bacteriophages) of female adult Aedes aegypti and Culex quinquefasciatus mosquitoes fed with sucrose/water, blood, or blood spiked with Zika virus (ZIKV) or West Nile virus (WNV), respectively. Furthermore, we investigated associations between the microbiota and vector competence. We show that the influence of arboviruses on the mosquito microbiome-and vice versa-is distinct for each combination of arbovirus/mosquito species. The presence of ZIKV resulted in a temporarily increased Aedes ISV diversity. However, this effect was distinct for different ISVs: some ISVs decreased following the blood meal (Aedes aegypti totivirus), whereas other ISVs increased only when the blood contained ZIKV (Guadeloupe mosquito virus). Also, the diversity of the Aedes bacteriome depended on the diet and the presence of ZIKV, with a lower diversity observed for mosquitoes receiving blood without ZIKV. In Cx. quinquefasciatus, some ISVs increased in WNV-infected mosquitoes (Guadeloupe Culex tymo-like virus). Particularly, the presence of Wenzhou sobemo-like virus 3 (WSLV3) was associated with the absence of infectious WNV in mosquito heads, suggesting that WSLV3 might affect vector competence for WNV. Distinct profiles of bacteriophages were identified in Culex mosquitoes depending on diet, despite the lack of clear changes in the bacteriome. Overall, our data demonstrate a complex three-way interaction among arboviruses, resident microbiota, and the host, which is distinct for different arbovirus-mosquito combinations. A better understanding of these interactions may lead to the identification of microbiota able to suppress the ability of arbovirus transmission to humans, and hence improved arbovirus control measures. IMPORTANCE In this study, we first utilized the single mosquito microbiome analysis, demonstrating a complex three-way interaction among arboviruses, resident microbiota, and the host, which is distinct for different arbovirus-mosquito combinations. Some of the previously described "core virus" increased in the mosquitos receiving viral blood meal, like Guadeloupe mosquito virus and Guadeloupe Culex tymo-like virus, suggesting their potential roles in ZIKV and WNV infection. Notably, Wenzhou sobemo-like virus 3 was associated with the absence of infectious WNV in heads of Culex mosquitoes, which might affect vector competence for WNV. A better understanding of these interactions will lead to the identification of microbiota able to suppress the ability of arbovirus transmission to humans, and hence improved arbovirus control measures.}, } @article {pmid36069437, year = {2022}, author = {Eddie, BJ and Bird, LJ and Pelikan, C and Mussmann, M and Martínez-Pérez, C and Pinamang, P and Malanoski, AP and Glaven, SM}, title = {Conservation of Energetic Pathways for Electroautotrophy in the Uncultivated Candidate Order Tenderiales.}, journal = {mSphere}, volume = {7}, number = {5}, pages = {e0022322}, pmid = {36069437}, issn = {2379-5042}, support = {P 31010/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {*Carbon Dioxide/metabolism ; *Chromatiaceae ; Sulfur ; Iron/metabolism ; Cytochromes ; Oxidoreductases ; Heme ; }, abstract = {Electromicrobiology can be used to understand extracellular electron uptake in previously undescribed chemolithotrophs. Enrichment and characterization of the uncultivated electroautotroph "Candidatus Tenderia electrophaga" using electromicrobiology led to the designation of the order Tenderiales. Representative Tenderiales metagenome-assembled genomes (MAGs) have been identified in a number of environmental surveys, yet a comprehensive characterization of conserved genes for extracellular electron uptake has thus far not been conducted. Using comparative genomics, we identified conserved orthologous genes within the Tenderiales and nearest-neighbor orders important for extracellular electron uptake based on a previously proposed pathway from "Ca. Tenderia electrophaga." The Tenderiales contained a conserved cluster we designated uetABCDEFGHIJ, which encodes proteins containing features that would enable transport of extracellular electrons to cytoplasmic membrane-bound energy-transducing complexes such as two conserved cytochrome cbb3 oxidases. For example, UetJ is predicted to be an extracellular undecaheme c-type cytochrome that forms a heme wire. We also identified clusters of genes predicted to facilitate assembly and maturation of electron transport proteins, as well as cellular attachment to surfaces. Autotrophy among the Tenderiales is supported by the presence of carbon fixation and stress response pathways that could allow cellular growth by extracellular electron uptake. Key differences between the Tenderiales and other known neutrophilic iron oxidizers were revealed, including very few Cyc2 genes in the Tenderiales. Our results reveal a possible conserved pathway for extracellular electron uptake and suggest that the Tenderiales have an ecological role in coupling metal or mineral redox chemistry and the carbon cycle in marine and brackish sediments. IMPORTANCE Chemolithotrophic bacteria capable of extracellular electron uptake to drive energy metabolism and CO2 fixation are known as electroautotrophs. The recently described order Tenderiales contains the uncultivated electroautotroph "Ca. Tenderia electrophaga." The "Ca. Tenderia electrophaga" genome contains genes proposed to make up a previously undescribed extracellular electron uptake pathway. Here, we use comparative genomics to show that this pathway is well conserved among Tenderiales spp. recovered by metagenome-assembled genomes. This conservation extends to near neighbors of the Tenderiales but not to other well-studied chemolithotrophs, including iron and sulfur oxidizers, indicating that these genes may be useful markers of growth using insoluble extracellular electron donors. Our findings suggest that extracellular electron uptake and electroautotrophy may be pervasive among the Tenderiales, and the geographic locations from which metagenome-assembled genomes were recovered offer clues to their natural ecological niche.}, } @article {pmid36068766, year = {2022}, author = {Zhou, L and Zhao, Z and Shao, L and Fang, S and Li, T and Gan, L and Guo, C}, title = {Predicting the abundance of metal resistance genes in subtropical estuaries using amplicon sequencing and machine learning.}, journal = {Ecotoxicology and environmental safety}, volume = {241}, number = {}, pages = {113844}, doi = {10.1016/j.ecoenv.2022.113844}, pmid = {36068766}, issn = {1090-2414}, mesh = {Bacteria/genetics ; Ecosystem ; *Estuaries ; Genes, Bacterial ; Machine Learning ; *Metals, Heavy/analysis/toxicity ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Heavy metals are a group of anthropogenic contaminants in estuary ecosystems. Bacteria in estuaries counteract the highly concentrated metal toxicity through metal resistance genes (MRGs). Presently, metagenomic technology is popularly used to study MRGs. However, an easier and less expensive method of acquiring MRG information is needed to deepen our understanding of the fate of MRGs. Thus, this study explores the feasibility of using a machine learning approach-namely, random forests (RF)-to predict MRG abundance based on the 16S rRNA amplicon sequenced datasets from subtropical estuaries in China. Our results showed that the total MRG abundance could be predicted by RF models using bacterial composition at different taxonomic levels. Among them, the relative abundance of bacterial phyla had the highest predicted accuracy (71.7 %). In addition, the RF models constructed by bacterial phyla predicted the abundance of six MRG types and nine MRG subtypes with substantial accuracy (R[2] > 0.600). Five bacterial phyla (Firmicutes, Bacteroidetes, Patescibacteria, Armatimonadetes, and Nitrospirae) substantially determined the variations in MRG abundance. Our findings prove that RF models can predict MRG abundance in South China estuaries during the wet season by using the bacterial composition obtained by 16S rRNA amplicon sequencing.}, } @article {pmid36068680, year = {2022}, author = {Chen, Y and Fan, LC and Chai, YH and Xu, JF}, title = {Advantages and challenges of metagenomic sequencing for the diagnosis of pulmonary infectious diseases.}, journal = {The clinical respiratory journal}, volume = {16}, number = {10}, pages = {646-656}, pmid = {36068680}, issn = {1752-699X}, support = {81925001//National Natural Science Foundation of China/ ; 81800063//National Natural Science Foundation of China/ ; 2016036//Shanghai Leading Talent Program/ ; }, mesh = {*Communicable Diseases/diagnosis ; Fungi/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Lung/microbiology ; Metagenomics/methods ; Sensitivity and Specificity ; }, abstract = {OBJECTIVE: We aim to familiarize the application status of metagenomic sequencing in diagnosing pulmonary infections, to compare metagenomic sequencing with traditional diagnostic methods, to conclude the advantages and limitations of metagenomic sequencing, and to provide some advice for clinical practice and some inspiration for associated researches.

DATA SOURCES: The data were obtained from peer-reviewed literature, white papers, and meeting reports.

RESULTS: This review focused on the applications of untargeted metagenomic sequencing in lungs infected by bacteria, viruses, fungi, chlamydia pneumoniae, Mycoplasma pneumoniae, parasites, and other pathogens. Compared with conventional diagnostic methods, metagenomic sequencing is better in detecting novel, rare, and unexpected pathogens and being applied in co-infections. Meanwhile, it can also provide more comprehensive information about pathogens. However, metagenomic sequencing still has limitations. Also, the situations that should be applied in and how the results should be interpreted are discussed in this review.

CONCLUSION: Metagenomic sequencing improves efficiency to identify pathogens compared with traditional diagnostic methods and can be applied in clinical diagnosis. However, the technology of metagenomic sequencing still needs to be improved. Also, clinicians should learn more about when to use metagenomic sequencing and how to interpret its results.}, } @article {pmid36068270, year = {2022}, author = {Ke, S and Weiss, ST and Liu, YY}, title = {Dissecting the role of the human microbiome in COVID-19 via metagenome-assembled genomes.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5235}, pmid = {36068270}, issn = {2041-1723}, support = {RF1 AG067744/AG/NIA NIH HHS/United States ; R01 HD093761/HD/NICHD NIH HHS/United States ; U01 HL089856/HL/NHLBI NIH HHS/United States ; R01 AI141529/AI/NIAID NIH HHS/United States ; UH3 OD023268/OD/NIH HHS/United States ; U19 AI095219/AI/NIAID NIH HHS/United States ; }, mesh = {*COVID-19 ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome/genetics ; *Microbiota ; SARS-CoV-2/genetics ; }, abstract = {Coronavirus disease 2019 (COVID-19), primarily a respiratory disease caused by infection with Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is often accompanied by gastrointestinal symptoms. However, little is known about the relation between the human microbiome and COVID-19, largely due to the fact that most previous studies fail to provide high taxonomic resolution to identify microbes that likely interact with SARS-CoV-2 infection. Here we used whole-metagenome shotgun sequencing data together with assembly and binning strategies to reconstruct metagenome-assembled genomes (MAGs) from 514 COVID-19 related nasopharyngeal and fecal samples in six independent cohorts. We reconstructed a total of 11,584 medium-and high-quality microbial MAGs and obtained 5403 non-redundant MAGs (nrMAGs) with strain-level resolution. We found that there is a significant reduction of strain richness for many species in the gut microbiome of COVID-19 patients. The gut microbiome signatures can accurately distinguish COVID-19 cases from healthy controls and predict the progression of COVID-19. Moreover, we identified a set of nrMAGs with a putative causal role in the clinical manifestations of COVID-19 and revealed their functional pathways that potentially interact with SARS-CoV-2 infection. Finally, we demonstrated that the main findings of our study can be largely validated in three independent cohorts. The presented results highlight the importance of incorporating the human gut microbiome in our understanding of SARS-CoV-2 infection and disease progression.}, } @article {pmid36068230, year = {2022}, author = {Li, JT and Jia, P and Wang, XJ and Ou, SN and Yang, TT and Feng, SW and Lu, JL and Fang, Z and Liu, J and Liao, B and Shu, WS and Liang, JL}, title = {Metagenomic and metatranscriptomic insights into sulfate-reducing bacteria in a revegetated acidic mine wasteland.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {71}, pmid = {36068230}, issn = {2055-5008}, mesh = {Bacteria ; *Metagenome ; *Metagenomics ; Phylogeny ; Sulfates/metabolism ; }, abstract = {The widespread occurrence of sulfate-reducing microorganisms (SRMs) in temporarily oxic/hypoxic aquatic environments indicates an intriguing possibility that SRMs can prevail in constantly oxic/hypoxic terrestrial sulfate-rich environments. However, little attention has been given to this possibility, leading to an incomplete understanding of microorganisms driving the terrestrial part of the global sulfur (S) cycle. In this study, genome-centric metagenomics and metatranscriptomics were employed to explore the diversity, metabolic potential, and gene expression profile of SRMs in a revegetated acidic mine wasteland under constantly oxic/hypoxic conditions. We recovered 16 medium- to high-quality metagenome-assembled genomes (MAGs) containing reductive dsrAB. Among them, 12 and four MAGs belonged to Acidobacteria and Deltaproteobacteria, respectively, harboring three new SRM genera. Comparative genomic analysis based on seven high-quality MAGs (completeness >90% and contamination <10%; including six acidobacterial and one deltaproteobacterial) and genomes of three additional cultured model species showed that Acidobacteria-related SRMs had more genes encoding glycoside hydrolases, oxygen-tolerant hydrogenases, and cytochrome c oxidases than Deltaproteobacteria-related SRMs. The opposite pattern was observed for genes encoding superoxide reductases and thioredoxin peroxidases. Using VirSorter, viral genome sequences were found in five of the 16 MAGs and in all three cultured model species. These prophages encoded enzymes involved in glycoside hydrolysis and antioxidation in their hosts. Moreover, metatranscriptomic analysis revealed that 15 of the 16 SRMs reported here were active in situ. An acidobacterial MAG containing a prophage dominated the SRM transcripts, expressing a large number of genes involved in its response to oxidative stress and competition for organic matter.}, } @article {pmid36068216, year = {2022}, author = {Nishijima, S and Nagata, N and Kiguchi, Y and Kojima, Y and Miyoshi-Akiyama, T and Kimura, M and Ohsugi, M and Ueki, K and Oka, S and Mizokami, M and Itoi, T and Kawai, T and Uemura, N and Hattori, M}, title = {Extensive gut virome variation and its associations with host and environmental factors in a population-level cohort.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5252}, pmid = {36068216}, issn = {2041-1723}, mesh = {Bacteria ; *Bacteriophages/genetics ; Humans ; Metagenome ; Metagenomics ; *Virome/genetics ; }, abstract = {Indigenous bacteriophage communities (virome) in the human gut have a huge impact on the structure and function of gut bacterial communities (bacteriome), but virome variation at a population scale is not fully investigated yet. Here, we analyse the gut dsDNA virome in the Japanese 4D cohort of 4198 deeply phenotyped individuals. By assembling metagenomic reads, we discover thousands of high-quality phage genomes including previously uncharacterised phage clades with different bacterial hosts than known major ones. The distribution of host bacteria is a strong determinant for the distribution of phages in the gut, and virome diversity is highly correlated with anti-viral defence mechanisms of the bacteriome, such as CRISPR-Cas and restriction-modification systems. We identify 97 various intrinsic/extrinsic factors that significantly affect the virome structure, including age, sex, lifestyle, and diet, most of which showed consistent associations with both phages and their predicted bacterial hosts. Among the metadata categories, disease and medication have the strongest effects on the virome structure. Overall, these results present a basis to understand the symbiotic communities of bacteria and their viruses in the human gut, which will facilitate the medical and industrial applications of indigenous viruses.}, } @article {pmid36068003, year = {2022}, author = {Ahn, HK and Kim, K and Park, J and Kim, KH}, title = {Urinary microbiome profile in men with genitourinary malignancies.}, journal = {Investigative and clinical urology}, volume = {63}, number = {5}, pages = {569-576}, pmid = {36068003}, issn = {2466-054X}, support = {NRF-2018R1C1B6007564//National Research Foundation of Korea/ ; }, mesh = {Bacteria ; Humans ; Male ; *Microbiota/genetics ; *Prostatic Neoplasms/pathology ; RNA, Ribosomal, 16S/genetics ; *Urinary Bladder Neoplasms/pathology ; *Urinary Tract ; }, abstract = {PURPOSE: Recent advances in molecular biology technology have allowed identification of microbial communities in the urinary tract, and urinary microbiome is associated with various urological diseases. In this study, we aimed to characterize the urinary microbiome of genitourinary malignancies.

MATERIALS AND METHODS: Metagenomic analysis of urinary DNA was performed in 85 patients including 30 with bladder cancer (BC), 27 with prostate cancer (PC), 12 with renal cancer (RC), and 16 with non-cancer (NC). 16S rRNA gene sequencing was conducted after amplification of the V3-V4 region.

RESULTS: PC and RC had significantly lower Shannon index than BC, and beta diversity showed significantly different microbiome composition between four groups. We identified six genera of Cutibacterium, Peptoniphilus, Sphingomonas, Staphylococcus, Micrococcus, and Moraxella, which showed significantly different abundance between the four groups. When each of the malignancies were compared to NC at the species level, Micrococcus sp. was significantly increased in BC. We also identified 12 and five species with increased populations in PC and RC, respectively. Of these, Cutibacterium acnes, Cutibacterium granulosum, Peptoniphilus lacydonensis, and Tessaracoccus were significantly increased in both PC and RC.

CONCLUSIONS: Urinary microbiome composition was different depending on the type of genitourinary malignancies, and we identified bacteria that are significantly associated with each type of malignancy. Specifically, several bacterial species were associated both PC and RC, suggesting that PC and RC share a similar pathogenesis-related urinary microbiome.}, } @article {pmid36067158, year = {2022}, author = {Martiny, HM and Munk, P and Brinch, C and Aarestrup, FM and Petersen, TN}, title = {A curated data resource of 214K metagenomes for characterization of the global antimicrobial resistome.}, journal = {PLoS biology}, volume = {20}, number = {9}, pages = {e3001792}, pmid = {36067158}, issn = {1545-7885}, mesh = {Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents ; Genes, Bacterial ; *Metagenome/genetics ; Metagenomics/methods ; }, abstract = {The growing threat of antimicrobial resistance (AMR) calls for new epidemiological surveillance methods, as well as a deeper understanding of how antimicrobial resistance genes (ARGs) have been transmitted around the world. The large pool of sequencing data available in public repositories provides an excellent resource for monitoring the temporal and spatial dissemination of AMR in different ecological settings. However, only a limited number of research groups globally have the computational resources to analyze such data. We retrieved 442 Tbp of sequencing reads from 214,095 metagenomic samples from the European Nucleotide Archive (ENA) and aligned them using a uniform approach against ARGs and 16S/18S rRNA genes. Here, we present the results of this extensive computational analysis and share the counts of reads aligned. Over 6.76∙108 read fragments were assigned to ARGs and 3.21∙109 to rRNA genes, where we observed distinct differences in both the abundance of ARGs and the link between microbiome and resistome compositions across various sampling types. This collection is another step towards establishing global surveillance of AMR and can serve as a resource for further research into the environmental spread and dynamic changes of ARGs.}, } @article {pmid36066261, year = {2022}, author = {Lipus, D and Jia, Z and Bartholomäus, A and Burckhardt, O and Sondermann, M and Wagner, D and Kallmeyer, J}, title = {Circular Metagenome-Assembled Genome of Methanobacterium sp. Strain ERen5, a Putative Methanogenic, H2-Utilizing Terrestrial Subsurface Archaeon.}, journal = {Microbiology resource announcements}, volume = {11}, number = {10}, pages = {e0067622}, pmid = {36066261}, issn = {2576-098X}, support = {419459207//Deutsche Forschungsgemeinschaft (DFG)/ ; }, abstract = {A circular, single-contig Methanobacterium sp. metagenome-assembled genome (MAG) was recovered from high-CO2 enrichments inoculated with drill core material from the tectonic Eger Rift terrestrial subsurface. Annotation of the recovered MAG highlighted putative methanogenesis genes, providing valuable information on archaeal activity in the deep biosphere.}, } @article {pmid36066249, year = {2022}, author = {Babalola, OO and Dlamini, SP and Akanmu, AO}, title = {Shotgun Metagenomic Survey of the Diseased and Healthy Maize (Zea mays L.) Rhizobiomes.}, journal = {Microbiology resource announcements}, volume = {11}, number = {10}, pages = {e0049822}, pmid = {36066249}, issn = {2576-098X}, support = {UID: 123634//National Research Foundation (NRF)/ ; }, abstract = {The effective functioning of the rhizosphere microbiome significantly contributes to plant development, disease resistance, and agricultural sustainability. Hence, it is a major predictor of plant health. This study evaluated the microbial diversities and functions associated with healthy and diseased maize rhizosphere at selected farms in North West Province, South Africa.}, } @article {pmid36065055, year = {2022}, author = {Ong, CT and Ross, EM and Boe-Hansen, G and Turni, C and Hayes, BJ and Fordyce, G and Tabor, AE}, title = {Adaptive sampling during sequencing reveals the origins of the bovine reproductive tract microbiome across reproductive stages and sexes.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {15075}, pmid = {36065055}, issn = {2045-2322}, mesh = {Animals ; Australia ; Cattle ; Female ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Pregnancy ; }, abstract = {Cattle enterprises are one of the major livestock production systems globally and are forecasted to have stable growth in the next decade. To facilitate sustainable live weight production, optimal reproductive performance is essential. Microbial colonisation in the reproductive tract has been demonstrated as one of the factors contributing to bovine reproductive performance. Studies also implied that reproductive metagenomes are different at each stage of the estrous cycle. This study applied Oxford Nanopore Technologies' adaptive long-read sequencing to profile the bovine reproductive microbiome collected from tropical cattle in northern Queensland, Australia. The microbiome samples were collected from cattle of different sexes, reproductive status and locations to provide a comprehensive view of the bovine reproductive microbiome in northern Australian cattle. Ascomycota, Firmicutes and Proteobacteria were abundant phyla identified in the bovine reproductive metagenomes of Australian cattle regardless of sexes, reproductive status and location. The species level taxonomical investigation suggested that gastrointestinal metagenome and the surrounding environment were potentially the origins of the bovine reproductive metagenome. Functional profiles further affirmed this implication, revealing that the reproductive metagenomes of the prepubertal and postpartum animals were dominated by microorganisms that catabolise dietary polysaccharides as an energy substrate while that of the pregnant animals had the function of harvesting energy from aromatic compounds. Bovine reproductive metagenome investigations can be employed to trace the origins of abnormal metagenomes, which is beneficial for disease prevention and control. Additionally, our results demonstrated different reproductive metagenome diversities between cattle from two different locations. The variation in diversity within one location can serve as the indicator of abnormal reproductive metagenome, but between locations inferences cannot be made. We suggest establishing localised metagenomic indices that can be used to infer abnormal reproductive metagenomes which contribute to abortion or sub-fertility.}, } @article {pmid36063723, year = {2022}, author = {Li, Y and Yu, Y and Wu, X and Liu, B and Ma, H and Zhao, X and Cao, S and Ding, S and Li, T and Wang, X and Wang, P and Xu, X and Zhao, J and Liu, Y and Lan, C and Wang, J and Chen, L and Zeng, Q}, title = {Specially designed yogurt supplemented with combination of pro- and prebiotics relieved constipation in mice and humans.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {103-104}, number = {}, pages = {111802}, doi = {10.1016/j.nut.2022.111802}, pmid = {36063723}, issn = {1873-1244}, mesh = {Humans ; Mice ; Animals ; *Prebiotics ; Yogurt ; Quality of Life ; Constipation/therapy ; *Gastrointestinal Microbiome ; }, abstract = {OBJECTIVE: Functional constipation is a gastrointestinal disorder that affects millions of people and is correlated with gut microbiome dysbiosis. The currently available treatments are ineffective; therefore, novel treatment schemes targeting the gut microbiome are desired. The aim of this study was to assess the effects of yogurt supplemented with seven probiotic strains and six types of dietary fibers on functional constipation.

METHODS: In the mouse study, mice with induced constipation were administered the yogurt once a day for 1 wk, with fecal parameters and intestinal transit rate measured. In the clinical study, participants with constipation (N = 86) were given the yogurt once daily (200 g) for 4 wk. Fecal and blood samples along with Patient Assessment of Constipation-symptoms and Patient Assessment of Constipation-Quality of Life Scale questionnaires were collected to evaluate the safety and efficacy of the yogurt. Shotgun metagenomic sequencing was performed to analyze fecal samples of both mice and humans.

RESULTS: We found that constipated mice had different gut microbiomes compared with those in healthy controls; yogurt treatment significantly relieved constipation-related symptoms and resulted in shifts in the microbiome. Yogurt also relieved symptoms of antibiotic-induced constipation in mice and restored the gut microbiome to a certain extent. In the clinical trial with 86 patients, yogurt administration significantly improved constipation symptoms and showed no serious adverse effects (was generally considered safe). However, subsequent metagenomic profiling of the gut microbiome did not reveal significant changes in the microbial composition, in contrast to the results in mice. We hypothesize that the differences in dosage between mice and humans may attribute to such discrepancies, and microbiome changes may not be necessary for improvements of constipation symptoms in humans.

CONCLUSION: Results from this study showed that yogurt can potentially be used for the treatment of constipation.}, } @article {pmid36063685, year = {2022}, author = {Bhosle, A and Wang, Y and Franzosa, EA and Huttenhower, C}, title = {Progress and opportunities in microbial community metabolomics.}, journal = {Current opinion in microbiology}, volume = {70}, number = {}, pages = {102195}, doi = {10.1016/j.mib.2022.102195}, pmid = {36063685}, issn = {1879-0364}, support = {R24 DK110499/DK/NIDDK NIH HHS/United States ; U19 AI110820/AI/NIAID NIH HHS/United States ; }, mesh = {*Metabolomics ; *Microbiota ; Metabolome/physiology ; Metagenomics ; }, abstract = {The metabolome lies at the interface of host-microbiome crosstalk. Previous work has established links between chemically diverse microbial metabolites and a myriad of host physiological processes and diseases. Coupled with scalable and cost-effective technologies, metabolomics is thus gaining popularity as a tool for characterization of microbial communities, particularly when combined with metagenomics as a window into microbiome function. A systematic interrogation of microbial community metabolomes can uncover key microbial compounds, metabolic capabilities of the microbiome, and also provide critical mechanistic insights into microbiome-linked host phenotypes. In this review, we discuss methods and accompanying resources that have been developed for these purposes. The accomplishments of these methods demonstrate that metabolomes can be used to functionally characterize microbial communities, and that microbial properties can be used to identify and investigate chemical compounds.}, } @article {pmid36063068, year = {2022}, author = {Debnath, S and Seth, D and Pramanik, S and Adhikari, S and Mondal, P and Sherpa, D and Sen, D and Mukherjee, D and Mukerjee, N}, title = {A comprehensive review and meta-analysis of recent advances in biotechnology for plant virus research and significant accomplishments in human health and the pharmaceutical industry.}, journal = {Biotechnology & genetic engineering reviews}, volume = {}, number = {}, pages = {1-33}, doi = {10.1080/02648725.2022.2116309}, pmid = {36063068}, issn = {2046-5556}, abstract = {Secondary metabolites made by plants and used through their metabolic routes are today's most reliable and cost-effective way to make pharmaceuticals and improve health. The concept of genetic engineering is used for molecular pharming. As more people use plants as sources of nanotechnology systems, they are adding to this. These systems are made up of viruses-like particles (VLPs) and virus nanoparticles (VNPs). Due to their superior ability to be used as plant virus expression vectors, plant viruses are becoming more popular in pharmaceuticals. This has opened the door for them to be used in research, such as the production of medicinal peptides, antibodies, and other heterologous protein complexes. This is because biotechnological approaches have been linked with new bioinformatics tools. Because of the rise of high-throughput sequencing (HTS) and next-generation sequencing (NGS) techniques, it has become easier to use metagenomic studies to look for plant virus genomes that could be used in pharmaceutical research. A look at how bioinformatics can be used in pharmaceutical research is also covered in this article. It also talks about plant viruses and how new biotechnological tools and procedures have made progress in the field.}, } @article {pmid36061864, year = {2022}, author = {Lin, M and Wang, K and Qiu, L and Liang, Y and Tu, C and Chen, M and Wang, Z and Wu, J and Huang, Y and Tan, C and Chen, Q and Zheng, X and Liu, J}, title = {Tropheryma whipplei detection by metagenomic next-generation sequencing in bronchoalveolar lavage fluid: A cross-sectional study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {961297}, pmid = {36061864}, issn = {2235-2988}, mesh = {Bronchoalveolar Lavage Fluid/microbiology ; Cross-Sectional Studies ; Female ; *High-Throughput Nucleotide Sequencing ; Humans ; Male ; Middle Aged ; Retrospective Studies ; *Tropheryma/genetics ; }, abstract = {Tropheryma whipplei is the bacterium associated with Whipple's disease (WD), a chronic systemic infectious disease primarily involving the gastrointestinal tract. T. whipplei can also be detected in different body site of healthy individuals, including saliva and feces. Traditionally, Tropheryma whipplei has a higher prevalence in bronchoalveolar lavage fluid (BALF) of immunocompromised individuals. Few studies have explored the significance of the detection of T. whipplei in BALF. Herein, we retrospectively reviewed 1725 BALF samples which detected for metagenomic next-generation sequencing (mNGS) from March 2019 to April 2022 in Zhuhai, China. Seventy BALs (70/1725, 4.0%) from 70 patients were positive for T. whipplei. Forty-four patients were male with an average age of 50 years. The main symptoms included cough (23/70), expectoration (13/70), weight loss (9/70), and/or dyspnea (8/70), but gastrointestinal symptoms were rare. Chronic liver diseases were the most common comorbidity (n=15, 21.4%), followed by diabetes mellitus (n=13, 18.6%). Only nine patients (12.9%) were immunocompromised. Twenty-four patients (34.3%) were finally diagnosed with reactivation tuberculosis and 15 patients (21.4%) were diagnosed with lung tumors, including 13 primary lung adenocarcinoma and two lung metastases. Fifteen patients (21.4%) had pneumonia. Among the 20 samples, T. whipplei was the sole agent, and Mycobacterium tuberculosis complex was the most common detected other pathogens. Among the non-tuberculosis patients, 31 (31/46, 67.4%) had ground glass nodules or solid nodules on chest CT. Our study indicates that T. whipplei should be considered as a potential contributing factor in some lung diseases. For non-immunocompromised patients, the detection of T. whipplei also needs attention. The mNGS technology improves the detection and attention of rare pathogens. In the future, the infection, colonization, and prognosis of T. whipplei in lung still need to be studied.}, } @article {pmid36061756, year = {2022}, author = {Korvigo, I and Igolkina, AA and Kichko, AA and Aksenova, T and Andronov, EE}, title = {Be aware of the allele-specific bias and compositional effects in multi-template PCR.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13888}, pmid = {36061756}, issn = {2167-8359}, mesh = {Humans ; Alleles ; *Bacteria ; RNA, Ribosomal, 16S/genetics ; Polymerase Chain Reaction/methods ; *Nucleic Acid Amplification Techniques ; }, abstract = {High-throughput sequencing of amplicon libraries is the most widespread and one of the most effective ways to study the taxonomic structure of microbial communities, even despite growing accessibility of whole metagenome sequencing. Due to the targeted amplification, the method provides unparalleled resolution of communities, but at the same time perturbs initial community structure thereby reducing data robustness and compromising downstream analyses. Experimental research of the perturbations is largely limited to comparative studies on different PCR protocols without considering other sources of experimental variation related to characteristics of the initial microbial composition itself. Here we analyse these sources and demonstrate how dramatically they effect the relative abundances of taxa during the PCR cycles. We developed the mathematical model of the PCR amplification assuming the heterogeneity of amplification efficiencies and considering the compositional nature of data. We designed the experiment-five consecutive amplicon cycles (22-26) with 12 replicates for one real human stool microbial sample-and estimated the dynamics of the microbial community in line with the model. We found the high heterogeneity in amplicon efficiencies of taxa that leads to the non-linear and substantial (up to fivefold) changes in relative abundances during PCR. The analysis of possible sources of heterogeneity revealed the significant association between amplicon efficiencies and the energy of secondary structures of the DNA templates. The result of our work highlights non-trivial changes in the dynamics of real-life microbial communities due to their compositional nature. Obtained effects are specific not only for amplicon libraries, but also for any studies of metagenome dynamics.}, } @article {pmid36061424, year = {2022}, author = {Rodrigues, CJC and de Carvalho, CCCR}, title = {Cultivating marine bacteria under laboratory conditions: Overcoming the "unculturable" dogma.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {964589}, pmid = {36061424}, issn = {2296-4185}, abstract = {Underexplored seawater environments may contain biological resources with potential for new biotechnological applications. Metagenomic techniques revolutionized the study of bacterial communities but culture dependent methods will still be important to help the biodiscovery of new products and enzymes from marine bacteria. In this context, we promoted the growth of bacteria from a marine rock pond by culture dependent techniques and compared the results with culture independent methods. The total number of bacteria and diversity were studied in different agar plate media during 6 weeks. Agar plate counting was of the same order of magnitude of direct microscopy counts. The highest efficiency of cultivation was 45% attained in marine agar medium. Molecular analysis revealed 10 different phyla of which only four were isolated by the culture dependent method. On the other hand, four taxonomic orders were detected by cultivation but not by the molecular technique. These include bacteria from the phyla Bacillota and Actinomycetota. Our study shows that it is possible to grow more than the traditionally considered 1% of bacteria from a seawater sample using standard agar plate techniques and laboratorial conditions. The results also demonstrate the importance of culture methods to grow bacteria not detected by molecular approaches for future biotechnological applications.}, } @article {pmid36061192, year = {2022}, author = {Aasmets, O and Krigul, KL and Org, E}, title = {Evaluating the clinical relevance of the enterotypes in the Estonian microbiome cohort.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {917926}, pmid = {36061192}, issn = {1664-8021}, abstract = {Human gut microbiome is subject to high inter-individual and temporal variability, which complicates building microbiome-based applications, including applications that can be used to improve public health. Categorizing the microbiome profiles into a small number of distinct clusters, such as enterotyping, has been proposed as a solution that can ameliorate these shortcomings. However, the clinical relevance of the enterotypes is poorly characterized despite a few studies marking the potential for using the enterotypes for disease diagnostics and personalized nutrition. To gain a further understanding of the clinical relevance of the enterotypes, we used the Estonian microbiome cohort dataset (n = 2,506) supplemented with diagnoses and drug usage information from electronic health records to assess the possibility of using enterotypes for disease diagnostics, detecting disease subtypes, and evaluating the susceptibility for developing a condition. In addition to the previously established 3-cluster enterotype model, we propose a 5-cluster community type model based on our data, which further separates the samples with extremely high Bacteroides and Prevotella abundances. Collectively, our systematic analysis including 231 phenotypic factors, 62 prevalent diseases, and 33 incident diseases greatly expands the knowledge about the enterotype-specific characteristics; however, the evidence suggesting the practical use of enterotypes in clinical practice remains scarce.}, } @article {pmid36060782, year = {2022}, author = {Sindi, AS and Stinson, LF and Lean, SS and Chooi, YH and Leghi, GE and Netting, MJ and Wlodek, ME and Muhlhausler, BS and Geddes, DT and Payne, MS}, title = {Effect of a reduced fat and sugar maternal dietary intervention during lactation on the infant gut microbiome.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {900702}, pmid = {36060782}, issn = {1664-302X}, abstract = {OBJECTIVE: A growing body of literature has shown that maternal diet during pregnancy is associated with infant gut bacterial composition. However, whether maternal diet during lactation affects the exclusively breastfed infant gut microbiome remains understudied. This study sets out to determine whether a two-week of a reduced fat and sugar maternal dietary intervention during lactation is associated with changes in the infant gut microbiome composition and function.

DESIGN: Stool samples were collected from four female and six male (n = 10) infants immediately before and after the intervention. Maternal baseline diet from healthy mothers aged 22-37 was assessed using 24-h dietary recall. During the 2-week dietary intervention, mothers were provided with meals and their dietary intake was calculated using FoodWorks 10 Software. Shotgun metagenomic sequencing was used to characterize the infant gut microbiome composition and function.

RESULTS: In all but one participant, maternal fat and sugar intake during the intervention were significantly lower than at baseline. The functional capacity of the infant gut microbiome was significantly altered by the intervention, with increased levels of genes associated with 28 bacterial metabolic pathways involved in biosynthesis of vitamins (p = 0.003), amino acids (p = 0.005), carbohydrates (p = 0.01), and fatty acids and lipids (p = 0.01). Although the dietary intervention did not affect the bacterial composition of the infant gut microbiome, relative difference in maternal fiber intake was positively associated with increased abundance of genes involved in biosynthesis of storage compounds (p = 0.016), such as cyanophycin. Relative difference in maternal protein intake was negatively associated with Veillonella parvula (p = 0.006), while positively associated with Klebsiella michiganensis (p = 0.047). Relative difference in maternal sugar intake was positively associated with Lactobacillus paracasei (p = 0.022). Relative difference in maternal fat intake was positively associated with genes involved in the biosynthesis of storage compounds (p = 0.015), fatty acid and lipid (p = 0.039), and metabolic regulator (p = 0.038) metabolic pathways.

CONCLUSION: This pilot study demonstrates that a short-term maternal dietary intervention during lactation can significantly alter the functional potential, but not bacterial taxonomy, of the breastfed infant gut microbiome. While the overall diet itself was not able to change the composition of the infant gut microbiome, changes in intakes of maternal protein and sugar during lactation were correlated with changes in the relative abundances of certain bacterial species.Clinical trial registration: Australian New Zealand Clinical Trials Registry (ACTRN12619000606189).}, } @article {pmid36060752, year = {2022}, author = {Lv, Q and Li, Z and Sui, A and Yang, X and Han, Y and Yao, R}, title = {The role and mechanisms of gut microbiota in diabetic nephropathy, diabetic retinopathy and cardiovascular diseases.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {977187}, pmid = {36060752}, issn = {1664-302X}, abstract = {Type 2 diabetes mellitus (T2DM) and T2DM-related complications [such as retinopathy, nephropathy, and cardiovascular diseases (CVDs)] are the most prevalent metabolic diseases. Intriguingly, overwhelming findings have shown a strong association of the gut microbiome with the etiology of these diseases, including the role of aberrant gut bacterial metabolites, increased intestinal permeability, and pathogenic immune function affecting host metabolism. Thus, deciphering the specific microbiota, metabolites, and the related mechanisms to T2DM-related complications by combined analyses of metagenomics and metabolomics data can lead to an innovative strategy for the treatment of these diseases. Accordingly, this review highlights the advanced knowledge about the characteristics of the gut microbiota in T2DM-related complications and how it can be associated with the pathogenesis of these diseases. Also, recent studies providing a new perspective on microbiota-targeted therapies are included.}, } @article {pmid36060746, year = {2022}, author = {Kumar, R and Chaudhry, V and Prakash, O}, title = {Editorial: Multi-omics profiling of unique niches to reveal the microbial and metabolite composition.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {997191}, pmid = {36060746}, issn = {1664-302X}, } @article {pmid36060745, year = {2022}, author = {Budeli, P and Ekwanzala, MD and Momba, MNB}, title = {Hormetic effect of 17α-ethynylestradiol on activated sludge microbial community response.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {961736}, pmid = {36060745}, issn = {1664-302X}, abstract = {Synthetic estrogen analogues are among the most potent estrogenic contaminants in effluents from wastewater treatment plants. Although its effects have been well elucidated in the feminization of male fish and interference with the endocrine systems in humans, it has not been fully explored in the activated sludge (AS) microbiome, particularly EE2 (17α-ethynylestradiol). Therefore, in this study, the bacterial community shift in a 6-day laboratory-scale reactor in environmental (0, 5, 10, and 100 ng/L) and predictive elevated concentrations (5, 10, and 100 mg/L) of EE2 was investigated using culture-based and metagenomics approaches. Results showed significant changes (t-test, all p < 0.05) between initial and final physicochemical parameters (pH, DO, and EC). Although environmental concentrations showed a slight decrease in microbial counts (5.6 × 10[6] to 4.6 × 10[6] CFU/ml) after a 24-h incubation for the culturable approach, the predictive elevated concentrations (5 to 100 mg/L) revealed a drastic microbial counts reduction (5.6 × 10[6] to 8 × 10[2] CFU/ml). The metagenomic data analysis uncovered that bacterial communities in the control sample were dominated by Proteobacteria, followed by Bacteroidetes and Firmicutes. The taxonomic classification after exposure of microbial communities in various concentrations revealed significant differences in community composition between environmental concentration (Shannon indices between 2.58 to 3.68) and predictive elevated concentrations (Shannon indices between 2.24 and 2.84; t-test, all p < 0.05). The EE2 enriched seven OTUs were Novosphingobium, Cloacibacterium, Stenotrophomonas, Enterobacteriaceae_unclassified, Stenotrophomonas, Enterobacteriaceae_unclassified and Rhodobacteraceae_unclassified. These results were supported by a dehydrogenase activity (DHA) test, which demonstrated less (about 40%) DHA in predictive elevated concentrations than in environmental concentrations. Notwithstanding, these findings suggest that EE2 may possess potent hormetic effect as evidenced by promotion of microbiome richness and dehydrogenase activity of AS in lower EE2 doses.}, } @article {pmid36060741, year = {2022}, author = {Liu, Q and Kong, W and Cui, X and Hu, S and Shi, Z and Wu, J and Zhang, Y and Qiu, L}, title = {Dynamic succession of microbial compost communities and functions during Pleurotus ostreatus mushroom cropping on a short composting substrate.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {946777}, pmid = {36060741}, issn = {1664-302X}, abstract = {Cultivating oyster mushrooms (Pleurotus ostreatus), a typical primary decomposer of lignocellulose, on a short composting substrate is a novel procedure which possesses energy conserves, reduced the chance of infection by competitive species, shorter production duration and achieved high production efficiency. However, the microbiome and microbial metabolic functions in the composting substrate during the mushroom cropping is unknown. In the present study, the contents of hemicellulose, cellulose and lignin and the activities of protease, laccase and cellulase were evaluated in the corncob short composting substrate from before oyster mushroom spawning to first flush fructification; meanwhile the changes in the microbiome and microbial metabolic functions were surveyed by using metagenomic sequencing. Results showed that the hemicellulose, cellulose and lignin in the short composting substrate were decomposed of 42.76, 34.01, and 30.18%, respectively, during the oyster mushroom cropping process. In addition, the contents of hemicellulose, cellulose and lignin in the composting substrate were reduced rapidly and negatively correlated with the abundance of the Actinobacteria phylum. The activities of protease, laccase and cellulase fastly increased in the period of before oyster mushroom spawning to full colonization and were positively correlated to the abundance of Actinobacteria phylum. The total abundance of bacteria domain gradually decreased by only approximately 15%, while the abundance of Actinobacteria phylum increased by 68% and was positively correlated with that of oyster mushroom. The abundance of oyster mushroom increased by 50 times from spawning to first flush fructification. The dominant genera, all in the order of Actinomycetales, were Cellulosimicrobium, Mycobacterium, Streptomyces and Saccharomonospora. The total abundance of genes with functions annotated in the Clusters of Orthologous Groups of proteins (COG) for Bacteria and Archaea and Kyoto Encyclopedia of Genes and Genomes (KEGG) database for all three life domains was positively correlated. The three metabolic pathways for carbohydrates, amino acids and energy were the primary enrichment pathways in KEGG pathway, accounting for more than 30% of all pathways, during the mushroom cropping in which the glycine metabolic pathway, carbon fixation pathways in prokaryotes and methane metabolism were all dominated by bacteria. The genes of cellulolytic enzymes, hemicellulolytic enzymes, laccase, chitinolytic enzymes, peptidoglycanlytic enzymes and ammonia assimilation enzymes with abundances from 0.28 to 0.24%, 0.05 to 0.02%, 0.02 to 0.01%, 0.14 to 0.08%, 0.39 to 0.16%, and 0.13 to 0.12% during the mushroom cropping identified in the Evolutionary Genealogy of Genes: Non-supervised Orthologous Groups (eggNOG) database for all three life domains were all aligned to COG database. These results indicated that bacteria, especially Actinomycetales, were the main metabolism participants in the short composting substrate during the oyster mushroom cropping. The relationship between oyster mushrooms and bacteria was cooperative, Actinomycetales were oyster mushroom growth promoting bacteria (OMGPB).}, } @article {pmid36060643, year = {2022}, author = {Zhang, Y and Zeng, Z and Li, F and Peng, Z and Xia, H and Zeng, Y and Chen, H and Wang, Y and Xie, W and Zhang, Y and Tang, Z}, title = {Metagenomic next-generation sequencing in diagnosing Pneumocystis jirovecii pneumonia: A case report.}, journal = {Open life sciences}, volume = {17}, number = {1}, pages = {938-943}, pmid = {36060643}, issn = {2391-5412}, abstract = {It remains a huge challenge for clinicians to diagnose Pneumocystis jirovecii pneumonia (PJP) by a conventional method, which leads to delay in diagnosing PJP, accounting for higher mortality in patients with rheumatoid arthritis (RA). A 69-year-old woman, who suffered from RA for years, developed acute respiratory failure. The computed tomography scan showed diffused effusion and ground glass opacity in both lungs, which could not be differentiated from interstitial pneumonia. Metagenomic next-generation sequencing (mNGS) revealed P. jirovecii in both serum and bronchoalveolar lavage fluid with reads per million (RPM) of 17 and 437, while other diagnostic tests did not detect any pathogenic microorganism. The results were verified by quantitative polymerase chain reaction (mtSSU region) against the same samples. The DNA RPM of P. jirovecii declined notably after treatment with trimethoprim/sulfamethoxazole. The patient was discharged without treatment and finally passed away. This case fully highlights the sensitivity of mNGS in early diagnosis of PJP, which is of great significance for prognosis and treatment. Nonetheless, the clinical application of mNGS is worth further standardization and normalization.}, } @article {pmid36060233, year = {2022}, author = {Zheng, MM and Shang, LM and Du, CK and Zhang, L and Sun, W and Wang, ZP and Zhu, YC and Tian, Y}, title = {Corynebacterium striatum Endocarditis After Renal Transplantation Confirmed by Metagenomic Next-Generation Sequencing: Case Report and Literature Review.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {4899-4906}, pmid = {36060233}, issn = {1178-6973}, abstract = {BACKGROUND: Potent immune-suppressive therapy has been demonstrated to increase the risk of infective endocarditis (IE) in renal recipients. Reports of Corynebacterium striatum (C. striatum) endocarditis in renal recipients are scarce, thus limiting understanding of the disease.

CASE PRESENTATION: We describe a case of native valve endocarditis caused by C. striatum in a 35-year-old male patient. The young man with end-stage renal failure underwent kidney transplantation because of autosomal dominant polycystic kidney disease. Ceftazidime was administered after the surgery according to routine procedures, and the patient was discharged on the 14th day after the surgery without any evidence of infection. The patient experienced fever on the 56th day, and Corynebacterium was cultured from the patient's blood, in agreement with the results of testing of the donor kidney preservation solution. On the 64th day, multiple thromboses were found in the right external iliac artery, particularly around the anastomotic orifice of the transplanted renal artery. Vegetation was found in the posterior mitral valve tip on the 65th day. The patient had symptoms of persistent angina pectoris and chest tightness and underwent mitral valve replacement and vegetative resection. The patient eventually died. C. striatum was detected in the mitral valve and vegetation tissue with metagenomic next-generation sequencing.

CONCLUSION: C. striatum may cause endocarditis and endanger patients' lives and thus warrants greater attention. Genotypic assays such as metagenomic next-generation sequencing are demonstrated to be effective in confirming species identity. Adequate anti-infection therapy and early surgery are required after IE is discovered.}, } @article {pmid36059644, year = {2022}, author = {Xu, L and Ma, Y and Fang, C and Peng, Z and Gao, F and Moll, JM and Qin, S and Yu, Q and Hou, Y and Kristiansen, K and Fang, W and Brix, S and Zhang, L}, title = {Genomic and microbial factors affect the prognosis of anti-pd-1 immunotherapy in nasopharyngeal carcinoma.}, journal = {Frontiers in oncology}, volume = {12}, number = {}, pages = {953884}, pmid = {36059644}, issn = {2234-943X}, abstract = {Antibodies targeting the programmed cell death protein-1 (PD-1) molecule have been reported to hold promising antitumor activities in patients with nasopharyngeal carcinoma (NPC). However, only a small subset of NPC patients benefits from the anti-PD-1 monotherapy and factors that affect the treatment response need further investigation. This study aimed to examine the impact of multiple genetic and environmental factors on outcome of anti-PD-1 immunotherapy by identifying tumor size, tumor mutation burden (TMB) based on whole exon sequencing, human leukocyte antigen class I (HLA-I) homo-/heterozygosity and supertypes, blood Epstein-Barr virus (EBV) DNA load, T cell proportions, and interferon-γ(IFN-γ) levels in a cohort of 57 NPC patients that received Nivolumab or Camrelizumab treatment. Moreover, we profiled the longitudinal changes in gut microbiota composition using shotgun metagenomics sequencing. We observed that high TMB combined with HLA-I heterozygosity was associated with improved clinical outcomes. In agreement with previous studies, we found that patients with higher plasma EBV DNA load showed worse progression-free survival. We found no evidence for an effect of gut bacterial diversity on the treatment response, but identified a higher abundance of seven specific gut bacteria at baseline of non-responders, including Blautia wexlera and Blautia obeum, as well as four other bacteria belonging to the Clostridiales order, and one Erysipelatoclostridium. Combined, this study provides insight into the influence of several genetic and environmental factors on anti-PD-1 immunotherapy responses in NPC patients.}, } @article {pmid36059453, year = {2022}, author = {Li, L and Yang, K and Li, C and Zhang, H and Yu, H and Chen, K and Yang, X and Liu, L}, title = {Metagenomic shotgun sequencing and metabolomic profiling identify specific human gut microbiota associated with diabetic retinopathy in patients with type 2 diabetes.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {943325}, pmid = {36059453}, issn = {1664-3224}, mesh = {Case-Control Studies ; *Diabetes Mellitus, Type 2/metabolism ; *Diabetic Retinopathy/genetics/metabolism ; *Gastrointestinal Microbiome/genetics ; Humans ; Lysine ; }, abstract = {BACKGROUND: Diabetic retinopathy (DR) is a common microvascular complication of diabetes mellitus (DM) and is one of the leading causes of blindness among DM patients. However, the molecular mechanism involving DR remains unclear.

METHODS: A case-control study with age-, sex-, and duration-matched diabetic patients and controls was conducted, which included 15 type 2 DM (T2DM) patients with DR and 15 T2DM patients without DR. Shotgun sequencing and non-targeted metabolomic profiling analyses of fecal samples were performed, and comprehensive bioinformatics analyses were conducted.

RESULTS: Using metagenomic analyses, we identified 293,460 unique genes in the non-DR group, while that in the DR group was 283,235, and the number of overlapping genes was 1,237,914. Regarding phylum levels, Actinobacteria decreased but Bacteroidetes increased in the DR group when compared with those in the control group. Regarding genus levels, Bifidobacterium and Lactobacillus decreased. Cellular processes, environmental information processes, and metabolism-related pathways were found at higher levels in the gut microbiome of DR patients. Using metabolomic analyses, we found 116 differentially expressed metabolites with a positive ion model and 168 differentially expressed metabolites with a negative ion model between the two groups. Kyoto Encyclopedia of Genes and Genomes annotation revealed six pathways with different levels between DR and diabetic controls, namely, cellular processes, environmental information processing, genetic information processing, human diseases, organismal systems and metabolism. Moreover, lysine biosynthesis and lysine degradation were enriched using a positive model, but histidine metabolism and β-alanine metabolism were enriched using a negative model.

CONCLUSIONS: Together, the metagenomic profiles of DR patients indicated different gut microbiota compositions and characteristic fecal metabolic phenotypes in DR patients. Our findings of microbial pathways therefore provided potential etiological and therapeutic targets for DR patients.}, } @article {pmid36058285, year = {2022}, author = {Mao, Q and Sun, G and Qian, Y and Qian, Y and Li, W and Wang, X and Shen, Q and Yang, S and Zhou, C and Wang, H and Zhang, W}, title = {Viral metagenomics of pharyngeal secretions from children with acute respiratory diseases with unknown etiology revealed diverse viruses.}, journal = {Virus research}, volume = {321}, number = {}, pages = {198912}, doi = {10.1016/j.virusres.2022.198912}, pmid = {36058285}, issn = {1872-7492}, mesh = {Child ; Child, Preschool ; Humans ; Infant ; Metagenomics ; *Nucleic Acids ; Phylogeny ; *Picornaviridae ; *Respiratory Tract Infections ; *Viruses/genetics ; }, abstract = {Acute respiratory tract infections are a major public health problem and the leading cause of morbidity in children younger than 5 years old. This study investigated the potential reasons of unexplained acute respiratory infections in children in Xuzhou and its environs during 2018-2019.We collected pharyngeal swab samples from 411 children under the age of five who presented with symptoms of unexplained acute respiratory infection and were negative for bacteria, mycoplasma, and influenza viruses. Using viral metagenomic techniques, viral nucleic acids were extracted, enriched, and sequenced from the samples. Results indicated that Picornaviridae, Parvoviridae, Paramyxoviridae, Coronaviridae, and Anelloviridae were the five virus families with the highest relative content of sequence reads. And we detected 35 HBoV-positive and 12 HEV-positive samples out of 411 samples by the polymerase chain reaction (PCR). Partial or nearly complete genome sequences of viruses belonging to the families Picornaviridae, Parvoviridae, and Anelloviridae were characterized, and phylogenetic trees were constructed based on the nucleic acid or amino acid sequences of the predicted viral open reading frames (ORFs), as well as genotyping of the viruses. In addition, we observed recombination events in the Saffold virus and Coxsackievirus A9 by analyzing the genetic characteristics of the viruses revealed in this study. This study provides vital information for the prevention and treatment of acute respiratory infections in children younger than five years old.}, } @article {pmid36058281, year = {2022}, author = {Singh, AK and Nakhate, SP and Gupta, RK and Chavan, AR and Poddar, BJ and Prakash, O and Shouche, YS and Purohit, HJ and Khardenavis, AA}, title = {Mining the landfill soil metagenome for denitrifying methanotrophic taxa and validation of methane oxidation in microcosm.}, journal = {Environmental research}, volume = {215}, number = {Pt 1}, pages = {114199}, doi = {10.1016/j.envres.2022.114199}, pmid = {36058281}, issn = {1096-0953}, mesh = {Bacteria/genetics/metabolism ; Metagenome ; *Methane ; Nitrogen ; Oxidation-Reduction ; *Soil/chemistry ; Soil Microbiology ; Waste Disposal Facilities ; }, abstract = {In the present study, the microbial community residing at different depths of the landfill was characterized to assess their roles in serving as a methane sink. Physico-chemical characterization revealed the characteristic signatures of anaerobic degradation of organic matter in the bottom soil (50-60 cm) and, active process of aerobic denitrification in the top soil (0-10 cm). This was also reflected from the higher abundance of bacterial domain in the top soil metagenome represented by dominant phyla Proteobacteria and Actinobacteria which are prime decomposers of organic matter in landfill soils. The multiple fold higher relative abundances of the two most abundant genera; Streptomyces and Intrasporangium in the top soil depicted greater denitrifying taxa in top soil than the bottom soil. Amongst the aerobic methanotrophs, the genera Methylomonas, Methylococcus, Methylocella, and Methylacidiphilum were abundantly found in the top soil metagenome that were essential for oxidizing methane generated in the landfill. On the other hand, the dominance of archaeal domain represented by Methanosarcina and Methanoculleus in the bottom soil highlighted the complete anaerobic digestion of organic components via acetoclasty, carboxydotrophy, hydrogenotrophy, methylotrophy. Functional characterization revealed a higher abundance of methane monooxygenase gene in the top soil and methyl coenzyme M reductase gene in the bottom soil that correlated with the higher relative abundance of aerobic methanotrophs in the top soil while methane generation being the active process in the highly anaerobic bottom soil in the landfill. The activity dependent abundance of endogenous microbial communities in the different zones of the landfill was further validated by microcosm studies in serum bottles which established the ability of the methanotrophic community for methane metabolism in the top soil and their potential to serve as sink for methane. The study provides a better understanding about the methanotrophs in correlation with their endogenous environment, so that these bacteria can be used in resolving the environmental issues related to methane and nitrogen management at landfill site.}, } @article {pmid36058098, year = {2022}, author = {Xia, Y and Jiang, X and Wang, Y and Huang, Q and Chen, D and Hou, C and Mu, Y and Shen, J}, title = {Enhanced anaerobic reduction of nitrobenzene at high salinity by betaine acting as osmoprotectant and regulator of metabolism.}, journal = {Water research}, volume = {223}, number = {}, pages = {118982}, doi = {10.1016/j.watres.2022.118982}, pmid = {36058098}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Betaine ; Nitrobenzenes ; *Salinity ; Wastewater ; }, abstract = {Anaerobic technology is extensively applied in the treatment of industrial organic wastewater, but high salinity always triggers microbial cell dehydration, causing the failure of the anaerobic process. In this work, betaine, one kind of compatible solutes which could balance the osmotic pressure of anaerobic biomass, was exogenously added for enhancing the anaerobic reduction of nitrobenzene (NB) at high salinity. Only 100 mg L[-1] betaine dosing could significantly promote the removal efficiency of NB within 35 h at 9% salinity (36.92 ± 4.02% without betaine and 72.94 ± 6.57% with betaine). The relieving effects on salt stress could be observed in the promotion of more extracellular polymeric substances (EPS) secretion with betaine addition. Additionally, the oxidation-reduction potential (ORP), as well as the electron transfer system (ETS) value, was increased with betaine addition, which was reflected in the improvement of system removal efficiency and enzyme activity. Microbial community analysis demonstrated that Bacillus and Clostridiisalibacter which were positively correlated with the stability of the anaerobic process were enriched with betaine addition at high salinity. Metagenomic analysis speculated that the encoding genes for salt tolerance (kdpB/oadA/betA/opuD/epsP/epsH) and NB degradation (nfsA/wrbA/ccdA/menC) obtained higher relative abundance with betaine addition under high salt environment, which might be the key to improving salt tolerance of anaerobic biomass. The long-term assessment demonstrated that exogenous addition betaine played an important role in maintaining the stability of the anaerobic system, which would be a potential strategy to achieve a high-efficiency anaerobic process under high salinity conditions.}, } @article {pmid36057234, year = {2022}, author = {Li, R and Zhu, L and Wang, Y and Zhu, YG}, title = {Metagenomic insights into environmental risk of field microplastics in an urban river.}, journal = {Water research}, volume = {223}, number = {}, pages = {119018}, doi = {10.1016/j.watres.2022.119018}, pmid = {36057234}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; Genes, Bacterial ; *Microbiota ; *Microplastics ; Plastics ; Virulence Factors ; Water ; }, abstract = {Microplastics (MPs) are emerging as anthropogenic vectors for the colonization and transportation of microbial communities in aquatic ecosystems. However, the composition of the microbiome and its environmental risk on field MPs at watershed scale has rarely been explored. Here, geographical distributions of microbiome, antibiotic resistance genes (ARGs) and virulence factors (VFs) on field MPs at watershed scale were characterized and their potential environmental risks were evaluated based on the data from metagenomic analyzes. The succession of microbial communities on MPs was observed along the watershed, and some ARGs and VFs were significantly enriched on MPs in urban region in comparison with rural region. Potential environmental risk of MPs conducted by Projection Pursuit Regression model in midstream (peri-urban region) and downstream (urban region) were significantly higher than that in upstream (rural region), and exhibit close relationships with MPs concentration and water velocity. Furthermore, our source tracking results demonstrated that the microbiome, ARGs and VFs in urban region MPs were largely derived from rural region MPs. Our results caution us that special attention should be paid to the risks posed by MPs in urban water bodies, and highlight the threat of MPs from rural upstream areas.}, } @article {pmid36056907, year = {2022}, author = {von Takach, B and Ranjard, L and Burridge, CP and Cameron, SF and Cremona, T and Eldridge, MDB and Fisher, DO and Frankenberg, S and Hill, BM and Hohnen, R and Jolly, CJ and Kelly, E and MacDonald, AJ and Moussalli, A and Ottewell, K and Phillips, BL and Radford, IJ and Spencer, PBS and Trewella, GJ and Umbrello, LS and Banks, SC}, title = {Population genomics of a predatory mammal reveals patterns of decline and impacts of exposure to toxic toads.}, journal = {Molecular ecology}, volume = {31}, number = {21}, pages = {5468-5486}, pmid = {36056907}, issn = {1365-294X}, mesh = {Animals ; *Metagenomics ; Bufo marinus/genetics ; Predatory Behavior ; *Marsupialia/genetics ; Australia/epidemiology ; }, abstract = {Mammal declines across northern Australia are one of the major biodiversity loss events occurring globally. There has been no regional assessment of the implications of these species declines for genomic diversity. To address this, we conducted a species-wide assessment of genomic diversity in the northern quoll (Dasyurus hallucatus), an Endangered marsupial carnivore. We used next generation sequencing methods to genotype 10,191 single nucleotide polymorphisms (SNPs) in 352 individuals from across a 3220-km length of the continent, investigating patterns of population genomic structure and diversity, and identifying loci showing signals of putative selection. We found strong heterogeneity in the distribution of genomic diversity across the continent, characterized by (i) biogeographical barriers driving hierarchical population structure through long-term isolation, and (ii) severe reductions in diversity resulting from population declines, exacerbated by the spread of introduced toxic cane toads (Rhinella marina). These results warn of a large ongoing loss of genomic diversity and associated adaptive capacity as mammals decline across northern Australia. Encouragingly, populations of the northern quoll established on toad-free islands by translocations appear to have maintained most of the initial genomic diversity after 16 years. By mapping patterns of genomic diversity within and among populations, and investigating these patterns in the context of population declines, we can provide conservation managers with data critical to informed decision-making. This includes the identification of populations that are candidates for genetic management, the importance of remnant island and insurance/translocated populations for the conservation of genetic diversity, and the characterization of putative evolutionarily significant units.}, } @article {pmid36056757, year = {2023}, author = {Kharofa, J and Apewokin, S and Alenghat, T and Ollberding, NJ}, title = {Metagenomic analysis of the fecal microbiome in colorectal cancer patients compared to healthy controls as a function of age.}, journal = {Cancer medicine}, volume = {12}, number = {3}, pages = {2945-2957}, pmid = {36056757}, issn = {2045-7634}, mesh = {Humans ; *Colorectal Neoplasms/genetics ; Metagenome ; Metagenomics ; Fusobacterium nucleatum ; Carcinogenesis/genetics ; *Microbiota ; }, abstract = {BACKGROUND AND AIMS: Colorectal cancer (CRC) incidence is increasing in young patients without a clear etiology. Emerging data have implicated the fecal microbiome in CRC carcinogenesis. However, its impact on young onset CRC is poorly defined.

METHODS: We performed a meta-analysis of fecal metagenomics sequencing data from n = 692 patients with CRC and n = 602 healthy controls from eleven studies to evaluate features of the fecal metagenome associated with CRC. We hypothesized that known carcinogenic virulence factors (colibactin, fadA) and species abundance may be differentially enriched in young CRC patients relative to older CRC patients and controls.

RESULTS: Summary odds ratios (OR) for CRC were increased with the presence of colibactin (OR 1.92 95% CI 1.08-3.38), fadA (OR 4.57 95% CI 1.63-12.85), and F. nucleatum (OR 6.93 95% CI 3.01-15.96) in meta-analysis models adjusted for age, gender, and body mass index. The OR for CRC for the presence of E.coli was 2.02 (0.92-4.45). An increase in the prevalence of Fusobacterium nucleatum (OR = 1.40 [1.18; 1.65]) and Escherichia coli (OR = 1.14 [1.02; 1.28]) per 10-year increase in age was observed in models including samples from both CRC and healthy controls. Species relative abundance was differentially enriched in young CRC patients for five species-Intestinimonas butyriciproducens, Holdemania filiformis, Firimicutues bacterium CAG 83, Bilophilia wadsworthia, and Alistipes putredinis.

CONCLUSION: In this study, we observed strong associations with CRC status for colibactin, fadA, and Fusobacterium nucleatum with CRC relative to controls. In addition, we identified several microbial species differentially enriched in young colorectal cancer patients. Studies targeting the young CRC patients are warranted to elucidate underlying preclinical mechanisms.}, } @article {pmid36056619, year = {2022}, author = {Gill, SP and Learman, DR and Annis, ML and Woolnough, DA}, title = {Freshwater mussels and host fish gut microbe community composition shifts after agricultural contaminant exposure.}, journal = {Journal of applied microbiology}, volume = {133}, number = {6}, pages = {3645-3658}, pmid = {36056619}, issn = {1365-2672}, support = {F16AP00639//U.S. Fish and Wildlife Service/ ; }, mesh = {Animals ; Female ; *Gastrointestinal Microbiome ; *Bivalvia ; Fresh Water ; Seafood ; *Bass ; *Water Pollutants, Chemical ; }, abstract = {AIMS: We examined the effects of a mixture of contaminants found in agricultural watersheds on the gut microbiota and physiology of both the freshwater mussel Lampsilis cardium, and L. cardium host fish Micropterus salmoides.

METHODS AND RESULTS: Lampsilis cardium and M. salmoides were exposed to three concentrations of agricultural contaminants for 60 days (observing behaviour daily) before being sampled for gut microbiota analyses. DNA was extracted from the gut samples, amplified via PCR, and sequenced using the Illumina Mi-Seq platform. Only L. cardium guts had differing microbiota across treatments, with an increase in potentially pathogenic Aeromonas. We also provide novel evidence of a core microbiota within L. cardium and M. salmoides. In terms of physiology, female L. cardium exhibited a decrease in movement and marsupial gill display in contaminant exposures.

CONCLUSIONS: Exposure to contaminants from agricultural watersheds may affect population recruitment within freshwater mussel communities over time. Specifically, increased pathogenic micro-organisms and altered behaviour can reduce the likelihood of glochidia dispersal.

This study supports emerging research that contaminants found in agricultural watersheds may be a factor in freshwater mussel population declines. It also provides novel evidence that unionids have a core gut microbiota.}, } @article {pmid36056292, year = {2023}, author = {Guo, W and Cui, S and Tang, X and Zhang, Q and Zhao, J and Mao, B and Zhang, H}, title = {Intestinal Microbiomics and Metabolomics Insights into the Hepatoprotective Effects of Lactobacillus paracasei CCFM1222 Against the Acute Liver Injury in Mice.}, journal = {Probiotics and antimicrobial proteins}, volume = {15}, number = {5}, pages = {1063-1077}, pmid = {36056292}, issn = {1867-1314}, mesh = {Mice ; Animals ; *Lacticaseibacillus paracasei ; Lipopolysaccharides/pharmacology ; Liver/metabolism ; Antioxidants/pharmacology ; Metabolomics ; }, abstract = {In recent years, acute liver injury (ALI) has received wide-range attention in the world due to its relatively high morbidity and mortality. This study aimed to explore the hepatoprotective effect of Lactobacillus paracasei CCFM1222 against lipopolysaccharide (LPS)-induced ALI mice and further elaborate its mechanism of action from the perspective of intestinal microbiomics and metabolomics. The results displayed that L. paracasei CCFM1222 pretreatment significantly decreased the serum ALT, and AST levels, inhibited the releases of hepatic TNF-α, IL-1β, and IL-6 levels, and activated the SOD, CAT, and GSH-Px activities in LPS-treated mice. The cecal short-chain fatty acid (SCFAs) levels were increased in LPS-treated mice with L. paracasei CCFM1222 pretreatment. In addition, L. paracasei CCFM1222 pretreatment remarkably shifted the intestinal microbiota composition, including the higher abundance of Faecalibaculum, Bifidobacterium, and lower abundance of the Prevotellaceae NK3B31 group, which is positively associated with the cecal propionic, butyric, valeric, isobutyric, and isovaleric acids. The metabolomics based on UPLC-QTOF/MS revealed that L. paracasei CCFM1222 pretreatment significantly regulated the composition of feces metabolites in LPS-treated mice, especially the potential biomarker-related butanoate metabolism, vitamin B6 metabolism, D-glutamine and D-glutamate metabolism, tryptophan metabolism, caffeine metabolism, arginine biosynthesis, arginine, and proline metabolism. Moreover, L. paracasei CCFM1222 pretreatment remarkably regulated the expression of gene-associated ALI (including Tlr4, Myd88, Nf-kβ, iNOS, Cox2, Iκ-Bα, Nrf2, and Sirt-1). In conclusion, these results suggest the possibility that L. paracasei CCFM1222 supplementation has beneficial effects on preventing the occurrence and development of ALI by inhibiting the inflammatory responses and altering intestinal microbiota composition and their metabolites.}, } @article {pmid36055570, year = {2022}, author = {Ullah, N and Kakakhel, MA and Khan, I and Gul Hilal, M and Lajia, Z and Bai, Y and Sajjad, W and Yuxi, L and Ullah, H and Almohaimeed, HM and Al-Sarraj, F and Assiri, R and Aggad, WS and Alharbi, NA and Alshehri, AM and Liu, G and Sun, H and Zhang, C}, title = {Structural and compositional segregation of the gut microbiota in HCV and liver cirrhotic patients: A clinical pilot study.}, journal = {Microbial pathogenesis}, volume = {171}, number = {}, pages = {105739}, doi = {10.1016/j.micpath.2022.105739}, pmid = {36055570}, issn = {1096-1208}, mesh = {Bacteria/genetics ; Dysbiosis/microbiology ; Enterobacteriaceae/genetics ; *Gastrointestinal Microbiome ; Hepacivirus/genetics ; *Hepatitis C/complications ; Humans ; Liver Cirrhosis ; *Liver Diseases ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Gut microbial dysbiosis during the development of Hepatitis C virus and liver-related diseases is not well studied. Nowadays, HCV and liver cirrhosis are the major concerns that cause gut bacterial alteration, which leads to dysbiosis. For this purpose, the present study was aimed at correlating the gut bacterial community of the control group in comparison to HCV and liver cirrhotic patients. A total of 23 stool samples were collected, including control (9), liver cirrhotic (8), and HCV (6). The collected samples were subjected to 16 S rRNA Illumina gene sequencing. In comparison with control, a significant gut bacterial alteration was observed in the progression of HCV and liver cirrhosis. Overall, Firmicutes were significantly abundant in the whole study. No significant difference was observed in the alpha diversity of the control and patient studies. Additionally, the beta diversity based on non-metric multidimensional scaling (NMDS) has a significant difference (p = 0.005) (ANOSIM R[2] = 0.14) in all groups. The discriminative results based on the LEfSe tool revealed that the HCV-infected patients had higher Enterobacteriaceae and Enterobacterial, as well as Lactobacillus and Bacilli in comparison than the liver-cirrhotic patients. These taxa were significantly different from the control group (p < 0.05). Regarding prospects, a detailed analysis of the function through metagenomics and transcriptomics is needed.}, } @article {pmid36055541, year = {2022}, author = {Wang, X and Yang, H and Liu, X and Wang, J}, title = {Formation mechanisms and assembly patterns of anammox biofilm induced by carrier type: Novel insights based on low-strength wastewater treatment.}, journal = {Bioresource technology}, volume = {362}, number = {}, pages = {127863}, doi = {10.1016/j.biortech.2022.127863}, pmid = {36055541}, issn = {1873-2976}, mesh = {Anaerobic Ammonia Oxidation ; Anaerobiosis ; Bacteria/genetics/metabolism ; Biofilms ; *Bioreactors/microbiology ; Nitrogen/metabolism ; Oxidation-Reduction ; Sewage ; *Water Purification ; }, abstract = {The morphological structure, properties, microbial community and function of anammox biofilms induced by large-pore carriers (Bls), small-pore carriers, filament carriers and non-carriers (Bn) in low-strength wastewater were comprehensively studied. The carriers promoted biomass accumulation and agglomeration, with Bls demonstrating the highest biomass proportion of 0.76, the highest specific anammox activity (0.41 kgN/(kgVSS·d)[-1]) and the largest aggregates. Hydraulic shearing stimulated Bn to secrete most extracellular polymeric substances and capture more inorganic ions for enhanced strength. Metagenomic sequencing showed that the four biofilms shared a common core flora, but differed in cross-metabolism. The proportion of the functional bacterium Candidatus Brocadia was highest in Bls, while the increase in heterotrophic bacteria in Bn supported stronger metabolic capacity. Finally, the proposed anisotropic or isotropic carrier structure was identified as the key to generating "uniform development" and "central development" models. This study is helpful for understanding the anammox aggregation mechanism and carrier optimization.}, } @article {pmid36055510, year = {2022}, author = {Wang, Z and Liu, X and Zhou, W and Sinclair, F and Shi, L and Xu, J and Gui, H}, title = {Land use intensification in a dry-hot valley reduced the constraints of water content on soil microbial diversity and multifunctionality but increased CO2 production.}, journal = {The Science of the total environment}, volume = {852}, number = {}, pages = {158397}, doi = {10.1016/j.scitotenv.2022.158397}, pmid = {36055510}, issn = {1879-1026}, mesh = {*Soil/chemistry ; *Ecosystem ; Soil Microbiology ; Carbon Dioxide/analysis ; Water ; Carbon/analysis ; Bacteria ; China ; Grassland ; }, abstract = {Conversion of abandoned land (mainly savanna) into cropland generally occurs in fragile ecosystems such as dry-hot valleys (DHVs) in southwest China, with the intent of increasing land productivity and conducting ecological restoration. However, the effects of conversion on soil microbial communities and carbon turnover of savanna ecosystems remain unclear, since savannas could be a vital but overlooked carbon sink. To illustrate the ecological consequences of land-use change (LUC) for savanna ecosystems, a 1-year field experiment was conducted in DHVs of southwest China. The soil properties, microbial respiration, and metagenomics from two different land-use types (grassland and mango plantation) were examined to reveal the effects of regional LUC on soil C turnover and microbial traits. Conversion from degraded grassland into cropland increased the contribution of soil microclimate to the microbial community composition, reduced the constraints of soil water content (SWC), and further decreased nutrient availability. LUC reshaped the composition and structure of soil bacterial communities. Specifically, soil dominant microbes that belonged to Actinobacteria and Proteobacteria were significantly enriched by conversion, while rare microbes that belonged to a wider range of phyla were generally depleted, leading to an overall decrease in community diversity. In addition, LUC-induced changes in soil characteristics and microbial communities further decreased soil multifunctionality as well as the carbon use efficiency of microbes. Intensified microbial respiration and a significant increase in the soil CO2 efflux were observed following LUC, which could drive changes in soil microbial community composition and functions (such as growth and regeneration). In summary, through simultaneously reducing constraints on SWC and decreasing nutrient availability, conversion from degraded grassland to cropland in a DHV decreased soil microbial diversity and multifunctionality, and increased microbial respiration and soil CO2 efflux. Our study provides new insights for understanding the role and mechanisms of LUC in soil carbon turnover in ecologically fragile areas such as DHVs.}, } @article {pmid36055486, year = {2022}, author = {Gong, X and Chen, Z and Deng, Y and Zhao, D and Gao, P and Zhang, L and Tu, Q and Qu, L and Zheng, L and Zhang, Y and Song, C and Liu, J}, title = {Contrasting archaeal and bacterial community assembly processes and the importance of rare taxa along a depth gradient in shallow coastal sediments.}, journal = {The Science of the total environment}, volume = {852}, number = {}, pages = {158411}, doi = {10.1016/j.scitotenv.2022.158411}, pmid = {36055486}, issn = {1879-1026}, mesh = {*Archaea ; RNA, Ribosomal, 16S/genetics ; *Geologic Sediments/chemistry ; Phylogeny ; Bacteria/genetics ; }, abstract = {Marine microbial communities assemble along a sediment depth gradient and are responsible for processing organic matter. Composition of the microbial community along the depth is affected by various biotic and abiotic factors, e.g., the change of redox gradient, the availability of organic matter, and the interactions of different taxa. The community structure is also subjected to some random changes caused by stochastic processes of birth, death, immigration and emigration. However, the high-resolution shifts of microbial community and mechanisms of the vertical assembly processes in marine sediments remain poorly described. Archaeal and bacterial communities were analyzed based on 16S rRNA gene amplicon sequencing and metagenomes in the Bohai Sea sediment samples. The archaeal community was dominated by Thaumarchaeota with increased alpha diversity along depth. Proteobacteria was the dominant bacterial group with decreased alpha diversity as depth increased. Sampling sites and depths collectively affected the beta-diversity for both archaeal and bacterial communities. The dominant mechanism determining archaeal community assembly was determinism, which was mostly contributed by homogeneous selection, i.e., consistent selection pressures in different locations or depths. In contrast, bacterial community assembly was dominated by stochasticity. Co-occurrence networks among different taxa and key functional genes revealed a tight community with low modularity in the bottom sediment, and disproportionately more interactions among low abundant ASVs. This suggests a significant contribution to community stabilization by rare taxa, and suggests that the bottom layer, rather than surface sediments may represent a hotspot for benthic microbial interactions.}, } @article {pmid36055451, year = {2022}, author = {Zhou, M and Liu, Z and Zhang, B and Yang, J and Hu, B}, title = {Interaction between arsenic metabolism genes and arsenic leads to a lose-lose situation.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {312}, number = {}, pages = {119971}, doi = {10.1016/j.envpol.2022.119971}, pmid = {36055451}, issn = {1873-6424}, mesh = {*Arsenic/analysis ; Metagenomics ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Microorganisms are essential for modifying arsenic morphology, mobility, and toxicity. Still, knowledge of the microorganisms responsible for arsenic metabolism in specific arsenic-contaminated fields, such as metallurgical plants is limited. We sampled on-field soils from three depths at 70 day intervals to explore the distribution and transformation of arsenic in the soil. Arsenic-metabolizing microorganisms were identified from the mapped gene sequences. Arsenic metabolism pathways were constructed with metagenomics and AsChip analysis (a high-throughput qPCR chip for arsenic metabolism genes). It has been shown in the result that 350 genera of arsenic-metabolizing microorganisms carrying 17 arsenic metabolism genes in field soils were identified, as relevant to arsenic reduction, arsenic methylation, arsenic respiration, and arsenic oxidation, respectively. Arsenic reduction genes were the only genes shared by the 10 high-ranking arsenic-metabolizing microorganisms. Arsenic reduction genes (arsABCDRT and acr3) accounted for 73.47%-78.11% of all arsenic metabolism genes. Such genes dominated arsenic metabolism, mediating the reduction of 14.11%-19.86% of As(V) to As(III) in 0-100 cm soils. Arsenic reduction disrupts microbial energy metabolism, DNA replication and repair and membrane transport. Arsenic reduction led to a significant decrease in the abundance of 17 arsenic metabolism genes (p < 0.0001). The critical role of arsenic-reducing microorganisms in the migration and transformation of arsenic in metallurgical field soils, was emphasized with such results. These results were of pronounced significance for understanding the transformation behavior of arsenic and the precise regulation of arsenic in field soil.}, } @article {pmid36055158, year = {2022}, author = {Beura, S and Kundu, P and Das, AK and Ghosh, A}, title = {Metagenome-scale community metabolic modelling for understanding the role of gut microbiota in human health.}, journal = {Computers in biology and medicine}, volume = {149}, number = {}, pages = {105997}, doi = {10.1016/j.compbiomed.2022.105997}, pmid = {36055158}, issn = {1879-0534}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Inflammatory Bowel Diseases/metabolism ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Metabolic activities of the microbial population are important to maintain the balance of almost all the ecosystems on earth. In the human gut environment, these microbial communities play essential roles in digestion and help to maintain biochemical homeostasis by synthesizing several vital metabolic compounds. Imbalance in the microbial abundance and community structure in the human gut microbiota leads to different diseases and metabolic disorders. Studying the metabolic interplay between the microbial consortia within the host environment is the key to exploring the cause behind the development of various diseases condition. However, mapping the entire biochemical characteristic of human gut microbiota may not be feasible only through experimental approaches. Therefore, the advanced systems biology approach, i.e., metagenome-scale community metabolic modelling, is introduced for understanding the metabolic role and interaction pattern of the entire microbiome. This in silico method directly uses the metagenomic information to model the microbial communities, which mimic the metabolic behavior of the human gut microbiome. This review discusses the recent development of metagenome-scale community metabolic model reconstruction tools and their application in studying the inter-link between the human gut microbiome and health. The application of the community metabolic models to study the metabolic profile of the human gut microbiome has also been investigated. Alteration of the metabolic fluxes associated with different biochemical activities in type 1 diabetics, type 2 diabetics, inflammatory bowel diseases (IBD), gouty arthritis, colorectal cancer (CRC), etc., has also been assessed with the metagenome-scale models. Thus, modelling the microbial communities combined with advanced experimental design may lead to novel therapeutic approaches like personalized microbiome modelling for treating human disease.}, } @article {pmid36055123, year = {2022}, author = {Nandi, SK and Basu, S and Bhattacharjya, A and Dey Ghosh, R and Bose, CK and Mukhopadhyay, S and Bhattacharya, R}, title = {Interplay of gut microbiome, fatty acids, and the endocannabinoid system in regulating development, progression, immunomodulation, and chemoresistance of cancer.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {103-104}, number = {}, pages = {111787}, doi = {10.1016/j.nut.2022.111787}, pmid = {36055123}, issn = {1873-1244}, mesh = {Humans ; *Gastrointestinal Microbiome ; Endocannabinoids/pharmacology ; Fatty Acids/pharmacology ; Drug Resistance, Neoplasm ; Fatty Acids, Volatile/metabolism ; Immunomodulation ; Immunity ; *Fatty Acids, Omega-3/pharmacology ; *Neoplasms/drug therapy ; Tumor Microenvironment ; }, abstract = {The roles of gut microorganisms in cancer are diverse. Studies on metagenomics and bioinformatics have documented diverse microbial etiology in different tumors. Evidence supports that a commensal microbiome could provide a promising strategy to treat and prevent cancer through interference in several biologic processes, such as host cell survival and death, host immune function, inflammation, oncogenic signaling, and several hormone receptor signaling and detoxification pathways. The cumulative evidence recommends that metabolites of commensal gut microorganisms (e.g., short-chain fatty acids, omega-3 and -6 fatty acids) play an important role in cancer prevention, with a robust antiproliferative effect of omega-3 fatty acids. Intriguingly, the endocannabinoid system (omega-3 and -6 fatty acid-derived neurotransmitter of the body) shows diverse effects on cancer prevention and oncogenesis depending on the context of the tumor microenvironment. Thus, an interplay of gut microorganisms with their fatty acid metabolites and the endocannabinoid system play an important role in the development, progression, immunomodulation, and chemoresistance of cancer. In this review, we highlight aspects of the current knowledge of and interactions between the microbiome with fatty acids and the host endocannabinoid system. We also document their effect on host immunomodulation and chemoresistance, and discuss how these insights might translate into future development of microbiome-targeted therapeutic interventions.}, } @article {pmid36054683, year = {2023}, author = {Fan, L and Chen, J and Pan, L and Xin, X and Geng, B and Yang, L and Wang, Q and Ma, W and Lou, Y and Bian, J and Cui, X and Li, J and Wang, L and Chen, Z and Wang, W and Cui, C and Li, S and Gao, Q and Song, Q and Deng, Y and Fan, J and Yu, J and Zhang, H and Li, Y and Cai, J}, title = {Alterations of Gut Microbiome, Metabolome, and Lipidome in Takayasu Arteritis.}, journal = {Arthritis & rheumatology (Hoboken, N.J.)}, volume = {75}, number = {2}, pages = {266-278}, doi = {10.1002/art.42331}, pmid = {36054683}, issn = {2326-5205}, mesh = {Humans ; *Takayasu Arteritis/drug therapy ; *Gastrointestinal Microbiome/genetics ; Lipidomics ; Inflammation ; Metabolome ; *Behcet Syndrome ; *Cardiovascular Diseases ; }, abstract = {OBJECTIVE: Mounting evidence has linked microbiome and metabolome to systemic autoimmunity and cardiovascular diseases (CVDs). Takayasu arteritis (TAK) is a rare disease that shares features of immune-related inflammatory diseases and CVDs, about which there is relatively limited information. This study was undertaken to characterize gut microbial dysbiosis and its crosstalk with phenotypes in TAK.

METHODS: To address the discriminatory signatures, we performed shotgun sequencing of fecal metagenome across a discovery cohort (n = 97) and an independent validation cohort (n = 75) including TAK patients, healthy controls, and controls with Behçet's disease (BD). Interrogation of untargeted metabolomics and lipidomics profiling of plasma and fecal samples were also used to refine features mediating associations between microorganisms and TAK phenotypes.

RESULTS: A combined model of bacterial species, including unclassified Escherichia, Veillonella parvula, Streptococcus parasanguinis, Dorea formicigenerans, Bifidobacterium adolescentis, Lachnospiraceae bacterium 7 1 58FAA, Escherichia coli, Streptococcus salivarius, Klebsiella pneumoniae, Bifidobacterium longum, and Lachnospiraceae Bacterium 5 1 63FAA, distinguished TAK patients from controls with areas under the curve (AUCs) of 87.8%, 85.9%, 81.1%, and 71.1% in training, test, and validation sets including healthy or BD controls, respectively. Diagnostic species were directly or indirectly (via metabolites or lipids) correlated with TAK phenotypes of vascular involvement, inflammation, discharge medication, and prognosis. External validation against publicly metagenomic studies (n = 184) on hypertension, atrial fibrillation, and healthy controls, confirmed the diagnostic accuracy of the model for TAK.

CONCLUSION: This study first identifies the discriminatory gut microbes in TAK. Dysbiotic microbes are also linked to TAK phenotypes directly or indirectly via metabolic and lipid modules. Further explorations of the microbiome-metagenome interface in TAK subtype prediction and pathogenesis are suggested.}, } @article {pmid36054088, year = {2022}, author = {Chong, YM and Chan, YF and Jamaluddin, MFH and Hasan, MS and Pang, YK and Ponnampalavanar, S and Syed Omar, SF and Sam, IC}, title = {Rhinovirus/enterovirus was the most common respiratory virus detected in adults with severe acute respiratory infections pre-COVID-19 in Kuala Lumpur, Malaysia.}, journal = {PloS one}, volume = {17}, number = {9}, pages = {e0273697}, pmid = {36054088}, issn = {1932-6203}, support = {R01 NR009547/NR/NINR NIH HHS/United States ; }, mesh = {Adult ; *COVID-19/epidemiology ; *Enterovirus/genetics ; Female ; Humans ; Malaysia/epidemiology ; Male ; Pandemics ; Real-Time Polymerase Chain Reaction ; *Respiratory Tract Infections ; Rhinovirus/genetics ; *Viruses/genetics ; }, abstract = {BACKGROUND: Severe acute respiratory infections (SARI) pose a great global burden. The contribution of respiratory viruses to adult SARI is relatively understudied in Asia. We aimed to determine viral aetiology of adult SARI patients in Kuala Lumpur, Malaysia.

METHODS: The prevalence of 20 common (mainly viral) respiratory pathogens, and MERS-CoV, SARS-CoV and 5 bacterial select agents was investigated from May 2017 to October 2019 in 489 SARI adult patients in Kuala Lumpur, Malaysia, using molecular assays (Luminex NxTAG-RPP kit and qPCR assays). Viral metagenomics analysis was performed on 105 negative samples.

RESULTS: Viral respiratory pathogens were detected by PCR in 279 cases (57.1%), including 10 (2.0%) additional detections by metagenomics analysis. The most detected viruses were rhinovirus/enterovirus (RV/EV) (49.1%) and influenza virus (7.4%). Three melioidosis cases were detected but no SARS-CoV, MERS-CoV or other bacterial select agents. Bacterial/viral co-detections and viral co-detections were found in 44 (9.0%) and 27 (5.5%) cases respectively, mostly involving RV/EV. Independent predictors of critical disease were male gender, chronic lung disease, lack of runny nose and positive blood culture with a significant bacterial pathogen. Asthma and sore throat were associated with increased risk of RV/EV detection, while among RV/EV cases, males and those with neurological disease were at increased risk of critical disease.

CONCLUSIONS: Prior to the COVID-19 pandemic, the high prevalence of respiratory viruses in adults with SARI was mainly attributed to RV/EV. Continued surveillance of respiratory virus trends contributes to effective diagnostic, prevention, and treatment strategies.}, } @article {pmid36053854, year = {2023}, author = {Xia, Y and Zhou, W and Du, Y and Wang, Y and Zhu, M and Zhao, Y and Wu, Z and Zhang, W}, title = {Difference of microbial community and gene composition with saccharification function between Chinese nongxiangxing daqu and jiangxiangxing daqu.}, journal = {Journal of the science of food and agriculture}, volume = {103}, number = {2}, pages = {637-647}, doi = {10.1002/jsfa.12175}, pmid = {36053854}, issn = {1097-0010}, support = {No.2018YFE0127400//the National Key R&D Program of China/ ; }, mesh = {Fermentation ; Bacteria/genetics ; *Microbiota ; *Bacillus/genetics ; China ; Alcoholic Beverages/analysis ; }, abstract = {BACKGROUND: The saccharification function of daqu is usually characterized by two indicators: saccharification power and liquefaction power. Daqu provides diverse microbial saccharifying enzymes for hydrolyzing carbohydrate in Baijiu fermenting grain. Obviously, the composition of microbial communities and enzymatic genes in different types of daqu cultured at varied temperatures is different. However, these differences in saccharification function are not fully understood.

RESULTS: The findings suggested that the saccharification power and liquefaction power of jiangxiangxing daqu were lower than those of nongxiangxing daqu throughout the production process. We employed metagenomics to find evidence that a mode of multiple saccharifying enzymes involving amylase, cellulase and hemicellulase originating from various microbes exists in daqu. Moreover, a totality of 541 related differential genes were obtained, some of which, annotated to genera of Aspergillus, Lactobacillus and Weissella, were significantly enriched (P < 0.05) in nongxiangxing daqu, while others, annotated to thermophilic genera of Virgibacillus, Bacillus, Kroppenstedtia and Saccharopolyspora, showed a higher relative abundance in jiangxiangxing daqu (P < 0.05).

CONCLUSION: Various microbial communities of daqu showed diverse saccharification capacity during cultivation of different parameters. These findings are helpful in comprehending the saccharification functional genes of daqu. © 2022 Society of Chemical Industry.}, } @article {pmid36053818, year = {2022}, author = {Da Silva, O and Ayata, SD and Ser-Giacomi, E and Leconte, J and Pelletier, E and Fauvelot, C and Madoui, MA and Guidi, L and Lombard, F and Bittner, L}, title = {Genomic differentiation of three pico-phytoplankton species in the Mediterranean Sea.}, journal = {Environmental microbiology}, volume = {24}, number = {12}, pages = {6086-6099}, pmid = {36053818}, issn = {1462-2920}, mesh = {Mediterranean Sea ; *Phytoplankton/genetics ; Ecosystem ; Genomics ; *Stramenopiles ; }, abstract = {For more than a decade, high-throughput sequencing has transformed the study of marine planktonic communities and has highlighted the extent of protist diversity in these ecosystems. Nevertheless, little is known relative to their genomic diversity at the species-scale as well as their major speciation mechanisms. An increasing number of data obtained from global scale sampling campaigns is becoming publicly available, and we postulate that metagenomic data could contribute to deciphering the processes shaping protist genomic differentiation in the marine realm. As a proof of concept, we developed a findable, accessible, interoperable and reusable (FAIR) pipeline and focused on the Mediterranean Sea to study three a priori abundant protist species: Bathycoccus prasinos, Pelagomonas calceolata and Phaeocystis cordata. We compared the genomic differentiation of each species in light of geographic, environmental and oceanographic distances. We highlighted that isolation-by-environment shapes the genomic differentiation of B. prasinos, whereas P. cordata is impacted by geographic distance (i.e. isolation-by-distance). At present time, the use of metagenomics to accurately estimate the genomic differentiation of protists remains challenging since coverages are lower compared to traditional population surveys. However, our approach sheds light on ecological and evolutionary processes occurring within natural marine populations and paves the way for future protist population metagenomic studies.}, } @article {pmid36212901, year = {2021}, author = {Shifera, AS and Pockrandt, C and Rincon, N and Ge, Y and Lu, J and Varabyou, A and Jedlicka, AE and Sun, K and Scott, AL and Eberhart, C and Thorne, JE and Salzberg, SL}, title = {Identification of microbial agents in tissue specimens of ocular and periocular sarcoidosis using a metagenomics approach.}, journal = {F1000Research}, volume = {10}, number = {}, pages = {820}, pmid = {36212901}, issn = {2046-1402}, support = {R01 HG006677/HG/NHGRI NIH HHS/United States ; R35 GM130151/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; *Sarcoidosis/diagnosis/genetics ; }, abstract = {Background: Metagenomic sequencing has the potential to identify a wide range of pathogens in human tissue samples. Sarcoidosis is a complex disorder whose etiology remains unknown and for which a variety of infectious causes have been hypothesized. We sought to conduct metagenomic sequencing on cases of ocular and periocular sarcoidosis, none of them with previously identified infectious causes. Methods: Archival tissue specimens of 16 subjects with biopsies of ocular and periocular tissues that were positive for non-caseating granulomas were used as cases. Four archival tissue specimens that did not demonstrate non-caseating granulomas were also included as controls. Genomic DNA was extracted from tissue sections. DNA libraries were generated from the extracted genomic DNA and the libraries underwent next-generation sequencing. Results: We generated between 4.8 and 20.7 million reads for each of the 16 cases plus four control samples. For eight of the cases, we identified microbial pathogens that were present well above the background, with one potential pathogen identified for seven of the cases and two possible pathogens for one of the cases. Five of the eight cases were associated with bacteria (Campylobacter concisus, Neisseria elongata, Streptococcus salivarius, Pseudopropionibacterium propionicum, and Paracoccus yeei), two cases with fungi (Exophiala oligosperma, Lomentospora prolificans and Aspergillus versicolor) and one case with a virus (Mupapillomavirus 1). Interestingly, four of the five bacterial species are also part of the human oral microbiome. Conclusions: Using a metagenomic sequencing we identified possible infectious causes in half of the ocular and periocular sarcoidosis cases analyzed. Our findings support the proposition that sarcoidosis could be an etiologically heterogenous disease. Because these are previously banked samples, direct follow-up in the respective patients is impossible, but these results suggest that sequencing may be a valuable tool in better understanding the etiopathogenesis of sarcoidosis and in diagnosing and treating this disease.}, } @article {pmid36300174, year = {2021}, author = {Huong, NHT and Toan, ND and Quy, DT and Khanh, TH and Thinh, LQ and Nhan, LNT and Minh, NNQ and Turner, H and Thwaites, L and Irani, S and Hung, NT and Tan, LV}, title = {Study protocol: The clinical features, epidemiology, and causes of paediatric encephalitis in southern Vietnam.}, journal = {Wellcome open research}, volume = {6}, number = {}, pages = {133}, pmid = {36300174}, issn = {2398-502X}, support = {204904/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Encephalitis is a major cause of morbidity and mortality worldwide. The clinical syndrome of encephalitis consists of altered mental status, seizures, neurologic signs, and is often accompanied by fever, headache, nausea, and vomiting. The encephalitis in children has been known that more common than in adult, with the incidence rate of infants was 3.9 times higher than that of people 20-44 years of age. The reported incidence of hospitalization attributed to paediatric encephalitis ranged from 3 to 13 admissions per 100,000 children per year with the overall mortality ranging from 0 to 7%. There are however more than 100 pathogens that can cause encephalitis and accurate diagnosis is challenging. Over 50% of patients with encephalitis are left undiagnosed despite extensive laboratory investigations. Furthermore, recent studies in high-income settings have suggested autoimmune encephalitis has now surpassed infectious aetiologies, mainly due to increased awareness and diagnostic capacity, which further challenges routine diagnosis and clinical management, especially in developing countries. There are limited contemporary data on the causes of encephalitis in children in Vietnam. Improving our knowledge of the causative agents of encephalitis in this resource-constrained setting remains critical to informing case management, resource distribution and vaccination strategy. Therefore, we conduct a prospective observational study to characterise the clinical, microbiological, and epidemiological features of encephalitis in a major children's hospital in southern Vietnam. Admission clinical samples will be collected alongside meta clinical data and from each study participants. A combination of classical assays (serology and PCR) and metagenomic next-generation sequencing will used to identify the causative agents. Undiagnosed patients with clinical presentations compatible with autoimmune encephalitis will then be tested for common forms of the disease. Finally, using direct- and indirect costs, we will estimate the economic burden of hospitalization and seven days post hospital discharge of paediatric encephalitis in our setting.}, } @article {pmid36160698, year = {2021}, author = {Li, X and Cheng, Z and Dang, C and Zhang, M and Zheng, Y and Yu Xia, }, title = {Metagenomic and viromic data mining reveals viral threats in biologically treated domestic wastewater.}, journal = {Environmental science and ecotechnology}, volume = {7}, number = {}, pages = {100105}, pmid = {36160698}, issn = {2666-4984}, abstract = {Activated sludge (AS), a common biological secondary treatment process in wastewater treatment plants (WWTPs), is known to remove a large spectrum of microorganisms. Yet little is known about its effect on the entire viral community. After compiling 3 Tbp of next-generation sequencing (NGS) metagenomic/viromic datasets consisted of 119 sub-datasets of influent, effluent, and AS samples from 27 WWTPs, viral removal efficacy is evaluated through data mining. The normalized abundance of viruses suggests effluents exhibit the highest viral prevalence (3.21 ± 3.26%, n = 13) followed by the AS (0.48 ± 0.25%, n = 57) and influents (0.23 ± 0.17%, n = 17). In contrast, plasmids, representing genetic element of bacteria, show higher average prevalence (0.73 ± 0.82%, n = 17) in influents than those of the AS (0.63 ± 0.26%, n = 57) and effluents (0.35 ± 0.42%, n = 13). Furthermore, the abundance-occupancy analysis identifies 142 core phage viruses and 17 non-phages core viruses, including several pathogenic viruses in the AS virome. The persistent occurrence of pathogenic viruses, coupled with non-favorable virus removal by the AS treatment, reveals the hidden virus threats in biologically treated domestic wastewater. The mechanisms for why viruses persist and the possibility that WWTPs are potential hotspots for viral survival deserve attention.}, } @article {pmid36119002, year = {2020}, author = {Xu, LL and Ling, XF and Zhao, SJ and Wang, RF and Wang, ZT}, title = {Distribution and diversity of endophytic fungi in Gentiana rigescens and cytotoxic activities.}, journal = {Chinese herbal medicines}, volume = {12}, number = {3}, pages = {297-302}, pmid = {36119002}, issn = {2589-3610}, abstract = {OBJECTIVE: In the present study, Gentiana rigescens was screened for fungi communities to clarify their diversity and community assemblage in hosts. Meanwhile, the identification and activity assays of the strains were also conducted.

METHODS: By culture-dependent (endophytic fungi isolations from plant sections) and culture-independent (metagenomic library and cloning from plant sections) techniques, fungi communities were studied. The metagenomic library was generated using direct DNA isolation of whole plants, plant radixes, plant stems, plant leaves, plant flowers and soils around the plant. Meanwhile, endophytes were isolated from all parts of G. rigescens plants. After fermentation of the fungi isolations, all the isolates were evaluated for their cytotoxicity against four kinds of human cancer cell lines (HCT116, BEL7404, A549, MDA-MB-231).

RESULTS: Eventually, 200 strains were isolated and 103 strains were further identified through the internal transcribed spacer (ITS, ITS1 and ITS2 regions) sequence by using the universal primers ITS5 and ITS4. A total of 59,106 fungal sequences corresponding to 374 putative operational taxonomic units (OTU) were identified by 454 pyrosequencing. Through 454 pyrosequencing, the main fungal genera were Sebacina, Botrytis, Mycosphaerella, Boletus and Gibberella, and the major fungal genera which were directly isolated were Aspergillus, Fusarium, Penicillium and Alternaria. Activity assays showed strains 5-26 (Aspergillus sp.) and 6-2 (Fusarium avenaceum) had the outstanding cytotoxicity to all the tested cell lines with IC50 values <5 μg/mL.

CONCLUSION: This study revealed the abundance of endogenetic fungal resources and a variety of genetic information in G. rigescens by high-throughput 454 sequencing technology and fungi isolation methods. Activity assays indicated that endophytes were a promising natural source of potential anticancer agents.}, } @article {pmid36052951, year = {2023}, author = {Nielsen, TK and Forero-Junco, LM and Kot, W and Moineau, S and Hansen, LH and Riber, L}, title = {Detection of nucleotide modifications in bacteria and bacteriophages: Strengths and limitations of current technologies and software.}, journal = {Molecular ecology}, volume = {32}, number = {6}, pages = {1236-1247}, doi = {10.1111/mec.16679}, pmid = {36052951}, issn = {1365-294X}, support = {801199//European Union's Horizon 2020 Research and Innovation Program/ ; HFSP-RGP0024/2018//Human Frontier Science Program/ ; R324-2019-2001//Lundbeck Foundation/ ; NNF19SA0059348//Novo Nordisk Foundation Center for Basic Metabolic Research/ ; }, mesh = {*Nucleotides/metabolism ; *Bacteriophages/genetics ; Software ; Metagenome ; Bacteria/genetics/metabolism ; DNA/genetics ; }, abstract = {RNA and DNA modifications occur in eukaryotes and prokaryotes, as well as in their viruses, and serve a wide range of functions, from gene regulation to nucleic acid protection. Although the first nucleotide modification was discovered almost 100 years ago, new and unusual modifications are still being described. Nucleotide modifications have also received more attention lately because of their increased significance, but also because new sequencing approaches have eased their detection. Chiefly, third generation sequencing platforms PacBio and Nanopore offer direct detection of modified bases by measuring deviations of the signals. These unusual modifications are especially prevalent in bacteriophage genomes, the viruses of bacteria, where they mostly appear to protect DNA against degradation from host nucleases. In this Opinion article, we highlight and discuss current approaches to detect nucleotide modifications, including hardwares and softwares, and look onward to future applications, especially for studying unusual, rare, or complex genome modifications in bacteriophages. The ability to distinguish between several types of nucleotide modifications may even shed new light on metagenomic studies.}, } @article {pmid36051770, year = {2022}, author = {Xue, Y and Zheng, M and Wu, S and Liu, Y and Huang, X}, title = {Corrigendum: Changes in the species and functional composition of activated sludge communities revealed mechanisms of partial nitrification established by ultrasonication.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {1006638}, doi = {10.3389/fmicb.2022.1006638}, pmid = {36051770}, issn = {1664-302X}, abstract = {[This corrects the article DOI: 10.3389/fmicb.2022.960608.].}, } @article {pmid36051762, year = {2022}, author = {Tian, B and Yao, JH and Lin, X and Lv, WQ and Jiang, LD and Wang, ZQ and Shen, J and Xiao, HM and Xu, H and Xu, LL and Cheng, X and Shen, H and Qiu, C and Luo, Z and Zhao, LJ and Yan, Q and Deng, HW and Zhang, LS}, title = {Metagenomic study of the gut microbiota associated with cow milk consumption in Chinese peri-/postmenopausal women.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {957885}, pmid = {36051762}, issn = {1664-302X}, support = {P20 GM109036/GM/NIGMS NIH HHS/United States ; R01 AG061917/AG/NIA NIH HHS/United States ; R01 AR069055/AR/NIAMS NIH HHS/United States ; U19 AG055373/AG/NIA NIH HHS/United States ; }, abstract = {Cow milk consumption (CMC) and alterations of gut bacterial composition are proposed to be closely related to human health and disease. Our research aims to investigate the changes in human gut microbial composition in Chinese peri-/postmenopausal women with different CMC habits. A total of 517 subjects were recruited and questionnaires about their CMC status were collected; 394 subjects were included in the final analyses. Fecal samples were used for studying gut bacterial composition. All the subjects were divided into a control group (n = 248) and a CMC group (n = 146) according to their CMC status. Non-parametric tests and LEfSe at different taxonomic levels were used to reveal differentially abundant taxa and functional categories across different CMC groups. Relative abundance (RA) of one phylum (p_Actinobacteria), three genera (g_Bifidobacterium, g_Anaerostipes, and g_Bacteroides), and 28 species diversified significantly across groups. Specifically, taxa g_Anaerostipes (p < 0.01), g_Bacteroides (p < 0.05), s_Anaerostipes_hadrus (p < 0.01), and s_Bifidobacterium_pseudocatenulatum (p < 0.01) were positively correlated with CMC levels, but p_Actinobacteria (p < 0.01) and g_Bifidobacterium (p < 0.01) were negatively associated with CMC levels. KEGG module analysis revealed 48 gut microbiome functional modules significantly (p < 0.05) associated with CMC, including Vibrio cholerae pathogenicity signature, cholera toxins (p = 9.52e-04), and cephamycin C biosynthesis module (p = 0.0057), among others. In conclusion, CMC was associated with changes in gut microbiome patterns including beta diversity and richness of some gut microbiota. The alterations of certain bacteria including g_Anaerostipes and s_Bifidobacterium_pseudocatenulatum in the CMC group should be important for human health. This study further supports the biological value of habitual cow milk consumption.}, } @article {pmid36051758, year = {2022}, author = {Huang, L and Wu, X and Guo, S and Lv, Y and Zhou, P and Huang, G and Duan, Z and Sun, W}, title = {Metagenomic-based characterization of the gut virome in patients with polycystic ovary syndrome.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {951782}, pmid = {36051758}, issn = {1664-302X}, abstract = {BACKGROUND: Polycystic ovary syndrome (PCOS) is a complex disease that afflicts women of reproductive age, and its pathological mechanism has not been well explained. The gut microbiota is believed to be closely related to the development of PCOS. Although an important component of the gut microbiome, the role of the gut virome in the development of PCOS is still unclear.

METHODS: In this study, we profiled and compared the gut viral community of 50 patients with PCOS and 43 healthy women based on the analysis of their fecal whole-metagenome dataset.

RESULTS: The gut virome of PCOS patients exhibited a significant decrease in within-sample viral diversity and a remarkable alteration of the overall virome composition compared with that of healthy controls. At the family level, Siphoviridae was significantly depleted in the gut virome of patients, while Quimbyviridae was enriched. We identified 1,089 viral operational taxonomic units (vOTUs) that differed in relative abundance between the two groups, of which 455 vOTUs were enriched in PCOS patients (including numerous Bacteroidaceae phages) and 634 were enriched in controls (including numerous viruses predicted to infect Oscillospiraceae, Prevotellaceae, and Ruminococcaceae). Functional comparison of the PCOS-enriched and control-enriched vOTUs uncovered the viral functional signatures associated with PCOS. Furthermore, we demonstrated gut viral signatures for disease discrimination and achieved an area under the receiver operator characteristic curve (AUC) of 0.938, demonstrating the potential of the gut virome in the prediction of PCOS.

CONCLUSION: Our findings reveal specific alterations in viral diversity and taxonomic and functional compositions of the gut virome of PCOS patients. Further studies on the etiology of PCOS and the gut viral community will offer new prospects for treating and preventing PCOS and its related diseases.}, } @article {pmid36050760, year = {2022}, author = {Zhan, Y and Cao, J and Ji, L and Zhang, M and Shen, Q and Xu, P and Zhuang, X and Qin, S and Hua, F and Sun, L and Li, F and Chen, H and Cheng, Y}, title = {Impaired mitochondria of Tregs decreases OXPHOS-derived ATP in primary immune thrombocytopenia with positive plasma pathogens detected by metagenomic sequencing.}, journal = {Experimental hematology & oncology}, volume = {11}, number = {1}, pages = {48}, pmid = {36050760}, issn = {2162-3619}, support = {81500090//National Natural Science Foundation of China/ ; 81878898//National Natural Science Foundation of China/ ; 21ZR1459000//Science and Technology Commission of Shanghai Municipality/ ; 20XD1401000//Program of the Shanghai Academic/Technology Researcher leader/ ; 20DZ2254300//Shanghai Engineering Research Center of Tumor Multi-Target Gene Diagnosis/ ; ZK2019B30//Key Subject Construction Program of Shanghai Health Administrative Authority/ ; }, abstract = {BACKGROUND: Primary immune thrombocytopenia (ITP) is an autoimmune disease. Some ITP patients are associated with pathogen infection undetected with conventional technologies. Investigating the changes of T cells and potential metabolic mechanism are important for better understanding of ITP.

METHODS: The study enrolled 75 newly diagnosed ITP patients. The pathogens of patients were detected by metagenomic next-generation sequencing (mNGS). Plasma lipids were measured by liquid chromatography-mass spectrometry (LC-MS). CD4 T cell and CD8 T cell were analyzed using flow cytometry. Mitochondrial reactive oxygen species (ROS) and mitochondrial membrane potential were measured by flow cytometry. Seahorse XF real-time ATP rate assay was used to investigate the change of cellular metabolism.

RESULTS: Positive plasma pathogens were detected in seven ITP patients. Of them, 5 (71.4%) positive pathogen-ITP patients were no response (NR) after first-line treatment with corticosteroids. Regulatory T cells (Tregs) increased significantly in positive pathogen-ITP patients compared to negative pathogen-ITP patients and healthy controls (HC). Mitochondrial membrane potential of Th17 and Tregs were decreased in positive pathogen-ITP and negative pathogen-ITP patients, compared to HC (all p < 0.05). The overall metabolism flux of positive pathogen-ITP patients was decreased, as compared to HC (p = 0.004), of them a higher proportion of glycolysis-derived ATP and a smaller proportion of oxidative phosphorylation (OXPHOS)-derived ATP were found in Tregs. The ATP rate index of Tregs was decreased significantly in positive pathogen-ITP patients compared to negative pathogen-ITP patients and HC (p < 0.05).

CONCLUSIONS: Impaired mitochondria function of Tregs in positive pathogen-ITP patients caused a decrease of OXPHOS-derived ATP and overall metabolism flux that might be the cause of steroid resistance in ITP patients.}, } @article {pmid36050758, year = {2022}, author = {Breyer, E and Zhao, Z and Herndl, GJ and Baltar, F}, title = {Global contribution of pelagic fungi to protein degradation in the ocean.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {143}, pmid = {36050758}, issn = {2049-2618}, mesh = {Carbohydrates ; *Fungi/genetics ; *Nitrogen ; Oceans and Seas ; Peptide Hydrolases/genetics ; Proteolysis ; Water ; }, abstract = {BACKGROUND: Fungi are important degraders of organic matter responsible for reintegration of nutrients into global food chains in freshwater and soil environments. Recent evidence suggests that they are ubiquitously present in the oceanic water column where they play an active role in the degradation of carbohydrates. However, their role in processing other abundant biomolecules in the ocean in comparison with that of prokaryotes remains enigmatic. Here, we performed a global-ocean multi-omics analysis of all fungal-affiliated peptidases (main enzymes responsible for cleaving proteins), which constitute the major fraction (> 50%) of marine living and detrital biomass. We determined the abundance, expression, diversity, taxonomic affiliation, and functional classification of the genes encoding all pelagic fungal peptidases from the epi- and mesopelagic layers.

RESULTS: We found that pelagic fungi are active contributors to protein degradation and nitrogen cycling in the global ocean. Dothideomycetes are the main fungi responsible for protease activity in the surface layers, whereas Leotiomycetes dominate in the mesopelagic realm. Gene abundance, diversity, and expression increased with increasing depth, similar to fungal CAZymes. This contrasts with the total occurrence of prokaryotic peptidases and CAZymes which are more uniformly distributed in the oceanic water column, suggesting potentially different ecological niches of fungi and prokaryotes. In-depth analysis of the most widely expressed fungal protease revealed the potentially dominating role of saprotrophic nutrition in the oceans.

CONCLUSIONS: Our findings expand the current knowledge on the role of oceanic fungi in the carbon cycle (carbohydrates) to the so far unknown global participation in nitrogen (proteins) degradation, highlighting potentially different ecological niches occupied by fungi and prokaryotes in the global ocean. Video Abstract.}, } @article {pmid36050658, year = {2022}, author = {Karpinets, TV and Wu, X and Solley, T and El Alam, MB and Sims, TT and Yoshida-Court, K and Lynn, E and Ahmed-Kaddar, M and Biegert, G and Yue, J and Song, X and Sun, H and Petrosino, JF and Mezzari, MP and Okhuysen, P and Eifel, PJ and Jhingran, A and Lin, LL and Schmeler, KM and Ramondetta, L and Ajami, N and Jenq, RR and Futreal, A and Zhang, J and Klopp, AH and Colbert, LE}, title = {Metagenomes of rectal swabs in larger, advanced stage cervical cancers have enhanced mucus degrading functionalities and distinct taxonomic structure.}, journal = {BMC cancer}, volume = {22}, number = {1}, pages = {945}, pmid = {36050658}, issn = {1471-2407}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; T32 CA101642/CA/NCI NIH HHS/United States ; P30CA016672/NH/NIH HHS/United States ; CA101642-14/NH/NIH HHS/United States ; }, mesh = {Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolic Networks and Pathways ; Metagenome ; Mucus ; *Uterine Cervical Neoplasms ; }, abstract = {BACKGROUND: Gut microbiome community composition differs between cervical cancer (CC) patients and healthy controls, and increased gut diversity is associated with improved outcomes after treatment. We proposed that functions of specific microbial species adjoining the mucus layer may directly impact the biology of CC.

METHOD: Metagenomes of rectal swabs in 41 CC patients were examined by whole-genome shotgun sequencing to link taxonomic structures, molecular functions, and metabolic pathway to patient's clinical characteristics.

RESULTS: Significant association of molecular functions encoded by the metagenomes was found with initial tumor size and stage. Profiling of the molecular function abundances and their distributions identified 2 microbial communities co-existing in each metagenome but having distinct metabolism and taxonomic structures. Community A (Clostridia and Proteobacteria predominant) was characterized by high activity of pathways involved in stress response, mucus glycan degradation and utilization of degradation byproducts. This community was prevalent in patients with larger, advanced stage tumors. Conversely, community B (Bacteroidia predominant) was characterized by fast growth, active oxidative phosphorylation, and production of vitamins. This community was prevalent in patients with smaller, early-stage tumors.

CONCLUSIONS: In this study, enrichment of mucus degrading microbial communities in rectal metagenomes of CC patients was associated with larger, more advanced stage tumors.}, } @article {pmid36050292, year = {2022}, author = {Zeng, S and Patangia, D and Almeida, A and Zhou, Z and Mu, D and Paul Ross, R and Stanton, C and Wang, S}, title = {A compendium of 32,277 metagenome-assembled genomes and over 80 million genes from the early-life human gut microbiome.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5139}, pmid = {36050292}, issn = {2041-1723}, support = {MR/W016184/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Adult ; Child ; Child, Preschool ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome/genetics ; Metagenomics ; *Microbiota/genetics ; Phylogeny ; }, abstract = {Age-specific reference genomes of the human gut microbiome can provide higher resolution for metagenomic analyses including taxonomic classification, strain-level genomic investigation and functional characterization. We present the Early-Life Gut Genomes (ELGG) catalog with 32,277 genomes representing 2172 species from 6122 fecal metagenomes collected from children under 3 years old spanning delivery mode, gestational age, feeding pattern, and geography. The ELGG substantially expanded the phylogenetic diversity by 38% over the isolate microbial genomes, and the genomic landscape of the early-life microbiome by increasing recruitment of metagenomic reads to 82.8%. More than 60% of the ELGG species lack an isolate representative. The conspecific genomes of the most abundant species from children differed in gene diversity and functions compared to adults. The ELGG genomes encode over 80 million protein sequences, forming the Early-Life Gut Proteins (ELGP) catalog with over four million protein clusters, 29.5% of which lacked functional annotations. The ELGG and ELGP references provided new insights into the early-life human gut microbiome and will facilitate studies to understand the development and mechanisms of disturbances of the human gut microbiome in early life.}, } @article {pmid36049713, year = {2022}, author = {Zhang, S and Su, J and Ali, A and Huang, T and Sun, Y and Ren, Y}, title = {Hydrophilic spongy biochar crosslinked with starch and polyvinyl alcohol biocarrier for nitrate, phosphorus, and cadmium removal in low carbon wastewater: Enhanced performance mechanism and detoxification.}, journal = {Bioresource technology}, volume = {362}, number = {}, pages = {127875}, doi = {10.1016/j.biortech.2022.127875}, pmid = {36049713}, issn = {1873-2976}, mesh = {Bioreactors ; Cadmium ; Carbon ; Charcoal ; Denitrification ; Nitrates ; Nitrogen ; Nitrogen Oxides ; *Phosphorus ; Polyvinyl Alcohol ; Starch ; *Wastewater ; }, abstract = {This study aims to develop a functional biocarrier with hydrophilic spongy biochar crosslinked with starch and polyvinyl alcohol (WSB/starch-PVA) for simultaneous removal of NO3[-]-N, total phosphorus (TP) and Cd[2+] in low carbon wastewater. Results showed that the WSB/starch-PVA bioreactor achieved the maximum NO3[-]-N removal efficiency in subphase 1.2 with 98.07 % (3.64 mg L[-1]h[-1]) versus control (75.30 %, 2.81 mg L[-1]h[-1]), and removed 54.84 % and 73.97 % of TP and Cd[2+]. Material characterization suggested that functional groups (related to C, N and O) on biocarrier and biofilm, and biogenic co-precipitation facilitated TP and Cd[2+] removal. The WSB made the biocarrier pores larger and regular, and decreased fluorescent soluble microbial products. The predicted metagenome further suggested that central citrate cycle, oxidative phosphorylation of bio-community, and NO3[-]-N removal were enhanced. Functions for microbial induced co-precipitation, Cd[2+] transport/efflux, antioxidants, and enhanced biofilm formation favored the NO3[-]-N/TP removal and Cd[2+] detoxification.}, } @article {pmid36049506, year = {2022}, author = {Das, N and Bhuyan, B and Pandey, P}, title = {Correlation of soil microbiome with crude oil contamination drives detection of hydrocarbon degrading genes which are independent to quantity and type of contaminants.}, journal = {Environmental research}, volume = {215}, number = {Pt 1}, pages = {114185}, doi = {10.1016/j.envres.2022.114185}, pmid = {36049506}, issn = {1096-0953}, mesh = {Anthracenes/analysis/metabolism ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Hydrocarbons ; *Microbiota ; Naphthalenes/analysis/metabolism ; *Petroleum/analysis ; *Phenanthrenes/analysis ; Pyrenes/metabolism ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {The impacts of crude oil contamination on soil microbial populations were explored in seven different polluted areas near oil and gas drilling sites and refineries of Assam, India. Using high-throughput sequencing techniques, the functional genes and metabolic pathways involved in the bioconversion of crude oil contaminants by the indigenous microbial community were explored. Total petroleum hydrocarbon (TPH) concentrations in soil samples ranged from 1109.47 to 75,725.33 mg/kg, while total polyaromatic hydrocarbon (PAH) concentrations ranged from 0.780 to 560.05 mg/kg. Pyrene, benzo[a]anthracene, naphthalene, phenanthrene, and anthracene had greater quantities than the maximum permitted limits, suggesting a greater ecological risk, in comparison to other polyaromatic hydrocarbons. According to the metagenomic data analysis, the bacterial phyla Proteobacteria, Actinobacteria, Acidobacteria, and Bacteroides were the most prevalent among all polluted areas. The most prominent hydrocarbon degraders in the contaminated sites included Burkholderia, Mycobacterium, Polaromonas, and Pseudomonas. However, the kinds of pollutants and their concentrations did not correlate with the abundances of respective degrading genes for all polluted locations, as some of the sites with little to low PAH contamination had significant abundances of corresponding functional genes for degradation. Thus, the findings of this study imply that the microbiome of hydrocarbon-contaminated areas, which are biologically involved in the degradation process, has various genes, operons and catabolic pathways that are independent of the presence of a specific kind of contaminant.}, } @article {pmid36049483, year = {2022}, author = {Gao, J and Zhao, X and Hu, S and Huang, Z and Hu, M and Jin, S and Lu, B and Sun, K and Wang, Z and Fu, J and Weersma, RK and He, X and Zhou, H}, title = {Gut microbial DL-endopeptidase alleviates Crohn's disease via the NOD2 pathway.}, journal = {Cell host & microbe}, volume = {30}, number = {10}, pages = {1435-1449.e9}, doi = {10.1016/j.chom.2022.08.002}, pmid = {36049483}, issn = {1934-6069}, mesh = {Acetylmuramyl-Alanyl-Isoglutamine/chemistry/metabolism ; Animals ; *Colitis ; *Crohn Disease/metabolism ; Endopeptidases ; *Gastrointestinal Microbiome ; Ligands ; Mice ; Nod2 Signaling Adaptor Protein/genetics ; Peptidoglycan/metabolism ; }, abstract = {The pattern-recognition receptor NOD2 senses bacterial muropeptides to regulate host immunity and maintain homeostasis. Loss-of-function mutations in NOD2 are associated with Crohn's disease (CD), but how the variations in microbial factors influence NOD2 signaling and host pathology is elusive. We demonstrate that the Firmicutes peptidoglycan remodeling enzyme, DL-endopeptidase, increased the NOD2 ligand level in the gut and impacted colitis outcomes. Metagenomic analyses of global cohorts (n = 857) revealed that DL-endopeptidase gene abundance decreased globally in CD patients and negatively correlated with colitis. Fecal microbiota from CD patients with low DL-endopeptidase activity predisposed mice to colitis. Administering DL-endopeptidase, but not an active site mutant, alleviated colitis via the NOD2 pathway. Therapeutically restoring NOD2 ligands with a DL-endopeptidase-producing Lactobacillus salivarius strain or mifamurtide, a clinical analog of muramyl dipeptide, exerted potent anti-colitis effects. Our study suggests that the depletion of DL-endopeptidase contributes to CD pathogenesis through NOD2 signaling, providing a therapeutically modifiable target.}, } @article {pmid36049303, year = {2022}, author = {Yang, F and Shen, S and Gao, W and Ma, Y and Han, B and Ding, Y and Wang, X and Zhang, K}, title = {Deciphering discriminative antibiotic resistance genes and pathogens in agricultural soil following chemical and organic fertilizer.}, journal = {Journal of environmental management}, volume = {322}, number = {}, pages = {116110}, doi = {10.1016/j.jenvman.2022.116110}, pmid = {36049303}, issn = {1095-8630}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Fertilizers/analysis ; Genes, Bacterial ; Manure ; *Soil ; Soil Microbiology ; }, abstract = {Fertilizers containing rich nutrients can change the profiles of antibiotic resistant pathogens (ARPs) and antibiotic resistance genes (ARGs) in receiving soils; however, the discriminative ARGs and ARPs in agricultural soil following different fertilizer applications remain unknown. Using metagenomic sequencing combined with binning approach, the present study investigated the discriminative ARGs and ARPs under various fertilizer applications (chemical and organic fertilizer) in a 8-year field experiment. VanR, multidrug ARG transporter, vanS, ermA, and arnA were the discriminative ARGs in the chemical fertilizer group, whereas rosB, multidrug transporter, mexW, and aac(3)-I were enhanced in the organic fertilizer group. The metagenomic binning approach revealed that both fertilizer applications caused pathogen proliferation. Chemical fertilizer caused the increase in the pathogenic genus Luteimonas, and organic fertilizer facilitated the proliferation of the pathogenic genera Dokdonella and Pseudomonas. The pathogenic species Pseudomonas_H sp014836765, carrying mexW and multidrug transporter, was enriched only in the organic fertilizer group, indicating that it was a discriminative ARP in the organic fertilizer group. Our results demonstrated that fertilizer application, particularly organic fertilizer application, can facilitate the proliferation of ARGs and ARPs in the receiving soil, posing the risk of the development and spread of soil-borne ARPs.}, } @article {pmid36049255, year = {2022}, author = {Whitman, WB and Chuvochina, M and Hedlund, BP and Hugenholtz, P and Konstantinidis, KT and Murray, AE and Palmer, M and Parks, DH and Probst, AJ and Reysenbach, AL and Rodriguez-R, LM and Rossello-Mora, R and Sutcliffe, I and Venter, SN}, title = {Development of the SeqCode: A proposed nomenclatural code for uncultivated prokaryotes with DNA sequences as type.}, journal = {Systematic and applied microbiology}, volume = {45}, number = {5}, pages = {126305}, pmid = {36049255}, issn = {1618-0984}, support = {P20 GM103440/GM/NIGMS NIH HHS/United States ; }, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Base Sequence ; Phylogeny ; RNA, Ribosomal, 16S ; }, abstract = {Over the last fifteen years, genomics has become fully integrated into prokaryotic systematics. The genomes of most type strains have been sequenced, genome sequence similarity is widely used for delineation of species, and phylogenomic methods are commonly used for classification of higher taxonomic ranks. Additionally, environmental genomics has revealed a vast diversity of as-yet-uncultivated taxa. In response to these developments, a new code of nomenclature, the Code of Nomenclature of Prokaryotes Described from Sequence Data (SeqCode), has been developed over the last two years to allow naming of Archaea and Bacteria using DNA sequences as the nomenclatural types. The SeqCode also allows naming of cultured organisms, including fastidious prokaryotes that cannot be deposited into culture collections. Several simplifications relative to the International Code of Nomenclature of Prokaryotes (ICNP) are implemented to make nomenclature more accessible, easier to apply and more readily communicated. By simplifying nomenclature with the goal of a unified classification, inclusive of both cultured and uncultured taxa, the SeqCode will facilitate the naming of taxa in every biome on Earth, encourage the isolation and characterization of as-yet-uncultivated taxa, and promote synergies between the ecological, environmental, physiological, biochemical, and molecular biological disciplines to more fully describe prokaryotes.}, } @article {pmid36049234, year = {2022}, author = {Ma, Z and Lu, YY and Wang, Y and Lin, R and Yang, Z and Zhang, F and Wang, Y}, title = {Metric learning for comparing genomic data with triplet network.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {5}, pages = {}, doi = {10.1093/bib/bbac345}, pmid = {36049234}, issn = {1477-4054}, mesh = {*Algorithms ; Learning ; Metagenome ; *Metagenomics/methods ; }, abstract = {Many biological applications are essentially pairwise comparison problems, such as evolutionary relationships on genomic sequences, contigs binning on metagenomic data, cell type identification on gene expression profiles of single-cells, etc. To make pair-wise comparison, it is necessary to adopt suitable dissimilarity metric. However, not all the metrics can be fully adapted to all possible biological applications. It is necessary to employ metric learning based on data adaptive to the application of interest. Therefore, in this study, we proposed MEtric Learning with Triplet network (MELT), which learns a nonlinear mapping from original space to the embedding space in order to keep similar data closer and dissimilar data far apart. MELT is a weakly supervised and data-driven comparison framework that offers more adaptive and accurate dissimilarity learned in the absence of the label information when the supervised methods are not applicable. We applied MELT in three typical applications of genomic data comparison, including hierarchical genomic sequences, longitudinal microbiome samples and longitudinal single-cell gene expression profiles, which have no distinctive grouping information. In the experiments, MELT demonstrated its empirical utility in comparison to many widely used dissimilarity metrics. And MELT is expected to accommodate a more extensive set of applications in large-scale genomic comparisons. MELT is available at https://github.com/Ying-Lab/MELT.}, } @article {pmid36048399, year = {2022}, author = {Zhu, M and Wang, C and Yang, S and Du, X and Zhu, Y and Zhang, T and Lv, Y and Zhao, W}, title = {Alterations in Gut Microbiota Profiles of Mice Infected with Echinococcus granulosus sensu lato Microbiota Profiles of Mice Infected with E. granulosus s.l.}, journal = {Acta parasitologica}, volume = {67}, number = {4}, pages = {1594-1602}, pmid = {36048399}, issn = {1896-1851}, support = {No.81860366//the National Natural Science Foundation of China/ ; No.32060805//the National Natural Science Foundation of China/ ; No. 2021BEG03088//Key Technology Research and Development Program of Shandong/ ; 2019AAC03264//he Natural Science Foundation of Ningxia/ ; 2020AAC02039//the Natural Science Foundation of Ningxia Hui Autonomous Region/ ; }, mesh = {Animals ; Humans ; Mice ; *Echinococcus granulosus/genetics ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Echinococcosis/parasitology ; *Microbiota ; Genotype ; }, abstract = {OBJECTIVE: Cystic echinococcosis is a kind of parasitic disease that seriously endangers human and animal health. At present, its prevention and treatment still do not achieve the desired results. The aims of this study were to explore the effect of CE on intestinal microflora in mice.

METHODS: In this study, 16S rRNA metagenome sequencing and bioinformatics were used to analyze the intestinal flora of mice infected with E. granulosus s.l. Changes in intestinal microbial community abundance were investigated and the differences in microbial populations of mice infected with E. granulosus s.l. were screened.

RESULTS: Our results show that at the phylum level, nine abundant taxa were identified, the relative abundance of Firmicutes and Proteobacteria were enriched in infected mice, whereas Bacteroidetes and Patescibacteria were enriched in control mice (P < 0.01). At the class level, 13 abundant taxa were identified, the relative abundance of Bacilli was enriched in control mice, but decreased in infected mice (P < 0.01). At the order level, 15 abundant taxa were identified, the relative abundance of Lactobacillales was enriched in control mice, but decreased in infected mice (P < 0.01). At the family level, 28 abundant taxa were identified, enriched bacteria in the infected mice was Streptococcaceae, while the enriched bacteria in the control group was Lactobacillaceae (P < 0.01). At the genus level, 79 abundant taxa were identified, enriched bacteria in the infected mice was Streptococcus, while the enriched bacteria in the control group was uncultured_bacterium_f_Eggerthellaceae (P < 0.01). At the species level, 80 abundant taxa were identified, enriched bacteria in the infected mice was uncultured_bacterium_g_Streptococcus, while the enriched bacteria in the control group was uncultured_bacterium_f_Eggerthellaceae (P < 0.01). 39 KEGG pathways were identified that were differentially enriched between the infected and control mice.

CONCLUSION: This study comprehensively demonstrates the differential intestinal microbiota of infected mice and analyzes the metabolic pathways related to the specific microbiota. This could provide new targets and research direction for the treatment and prevention of diseases caused by E. granulosus s.l.}, } @article {pmid36047990, year = {2022}, author = {Zhao, J and Zheng, M and Su, Z and Liu, T and Li, J and Guo, J and Yuan, Z and Hu, S}, title = {Selective Enrichment of Comammox Nitrospira in a Moving Bed Biofilm Reactor with Sufficient Oxygen Supply.}, journal = {Environmental science & technology}, volume = {56}, number = {18}, pages = {13338-13346}, doi = {10.1021/acs.est.2c03299}, pmid = {36047990}, issn = {1520-5851}, mesh = {*Ammonia ; *Ammonium Compounds ; Bacteria/genetics ; Biofilms ; Bioreactors ; In Situ Hybridization, Fluorescence ; Nitrification ; Oxidation-Reduction ; Oxygen ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Wastewater/microbiology ; }, abstract = {The recent discovery of comammox (complete ammonia oxidation) Nitrospira has upended the long-held nitrification paradigm. Although comammox Nitrospira have been identified in wastewater treatment systems, the conditions for their dominance over canonical ammonia oxidizers remain unclear. Here, we report the dominance of comammox Nitrospira in a moving bed biofilm reactor (MBBR) fed with synthetic mainstream wastewater. Integrated 16S rRNA gene amplicon sequencing, fluorescence in situ hybridization (FISH), and metagenomic sequencing methods demonstrated the selective enrichment of comammox bacteria when the MBBR was operated at a dissolved oxygen (DO) concentration above 6 mg O2/L. The dominance of comammox Nitrospira over canonical ammonia oxidizers (i.e., Nitrosomonas) was attributed to the low residual ammonium concentration (0.02-0.52 mg N/L) formed in the high-DO MBBR. Two clade A comammox Nitrospira were identified, which are phylogenetically close to Candidatus Nitrospira nitrosa. Interestingly, cryosectioning-FISH showed these two comammox species spatially distributed on the surface of the biofilm. Moreover, the ammonia-oxidizing activity of comammox Nitrospira-dominated biofilms was susceptible to the oxygen supply, which dropped by half with the DO concentration decrease from 6 to 2 mg O2/L. These features collectively suggest a low apparent oxygen affinity for the comammox Nitrospira-dominated biofilms in the high-DO nitrifying MBBR.}, } @article {pmid36047582, year = {2022}, author = {Lu, X and Liu, T and Zhou, J and Liu, J and Yuan, Z and Guo, L}, title = {Subgingival microbiome in periodontitis and type 2 diabetes mellitus: an exploratory study using metagenomic sequencing.}, journal = {Journal of periodontal & implant science}, volume = {52}, number = {4}, pages = {282-297}, pmid = {36047582}, issn = {2093-2278}, support = {81670982//National Natural Science Foundation of China/China ; }, abstract = {PURPOSE: To explore differences in the subgingival microbiome according to the presence of periodontitis and/or type 2 diabetes mellitus (T2D), a metagenomic sequencing analysis of the subgingival microbiome was performed.

METHODS: Twelve participants were divided into 4 groups based on their health conditions (periodontitis, T2D, T2D complicated with periodontitis, and generally healthy). Subgingival plaque was collected for metagenomic sequencing, and gingival crevicular fluids were collected to analyze the concentrations of short-chain fatty acids.

RESULTS: The shifts in the subgingival flora from the healthy to periodontitis states were less prominent in T2D subjects than in subjects without T2D. The pentose and glucuronate interconversion, fructose and mannose metabolism, and galactose metabolism pathways were enriched in the periodontitis state, while the phosphotransferase system, lipopolysaccharide (LPS) and peptidoglycan biosynthesis, bacterial secretion system, sulfur metabolism, and glycolysis pathways were enriched in the T2D state. Multiple genes whose expression was upregulated from the red and orange complex bacterial genomes were associated with bacterial biofilm formation and pathogenicity. The concentrations of propionic acid and butyric acid were significantly higher in subjects with periodontitis, with or without T2D, than in healthy subjects.

CONCLUSIONS: T2D patients are more susceptible to the presence of periodontal pathogens and have a higher risk of developing periodontitis. The pentose and glucuronate interconversion, fructose and mannose metabolism, galactose metabolism, and glycolysis pathways may represent the potential microbial functional association between periodontitis and T2D, and butyric acid may play an important role in the interaction between these 2 diseases. The enrichment of the LPS and peptidoglycan biosynthesis, bacterial secretion system, and sulfur metabolism pathways may cause T2D patients to be more susceptible to periodontitis.}, } @article {pmid36047475, year = {2022}, author = {Umar, S and Anderson, BD and Chen, K and Wang, GL and Ma, MJ and Gray, GC}, title = {Metagenomic analysis of endemic viruses in oral secretions from Chinese pigs.}, journal = {Veterinary medicine and science}, volume = {8}, number = {5}, pages = {1982-1992}, pmid = {36047475}, issn = {2053-1095}, support = {R01AI108993-01A1/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Circovirus ; *Influenza A virus ; *Porcine Reproductive and Respiratory Syndrome/epidemiology ; *Porcine respiratory and reproductive syndrome virus ; Swine ; *Swine Diseases ; }, abstract = {BACKGROUND: Pigs are unique reservoirs for virus ecology. Despite the increased use of improved biosecurity measures, pig viruses readily circulate in Chinese swine farms.

OBJECTIVES: The main objective of this study was to examine archived swine oral secretion samples with a panel of pan-species viral assays such that we might better describe the viral ecology of swine endemic viruses in Chinese farms.

METHODOLOGY: Two hundred (n = 200) swine oral secretion samples, collected during 2015 and 2016 from healthy pigs on six swine farms in two provinces in China, were screened with molecular pan-species assays for coronaviruses (CoVs), adenoviruses (AdVs), enteroviruses (EVs), and paramyxoviruses (PMV). Samples were also screened for porcine circovirus (PCV) 3, porcine reproductive and respiratory syndrome virus (PRRSV) and influenza A virus (IAV).

RESULTS: Among 200 swine oral secretion samples, 152 (76.0%) were found to have at least one viral detection. Thirty-four samples (17%) were positive for more than one virus, including 24 (70.5%) with dual detection and 10 (29.5%) with triple detection. Seventy-eight (39.0%) samples were positive for porcine AdVs, 22 (11.0%) were positive for porcine CoVs, 21 (10.5%) were positive for IAVs, 13 (6.5%) were positive for PCV, 7 (3.5%) were positive for PMV, six (3.0%) were positive for PRRSV and five (2.5%) were positive for porcine EV.

CONCLUSION: Our findings underscore the high prevalence of numerous viruses among production pigs in China and highlight the need for routine, periodic surveillance for novel virus emergence with the goal of protecting pigs.}, } @article {pmid36047200, year = {2022}, author = {Miyanaga, K and Asada, A and Komoto, M and Ohshima, Y and Morimoto, H and Yasukawa, T and Matsuura, R and Morito, K and Takayama, K and Uozumi, Y and Nagasawa, K}, title = {Prophylactic Administration of Magnesium Oxide Prevents Dextran Sulfate Sodium-Induced Colonic Injury in Mice.}, journal = {Biological & pharmaceutical bulletin}, volume = {45}, number = {9}, pages = {1312-1320}, doi = {10.1248/bpb.b22-00278}, pmid = {36047200}, issn = {1347-5215}, mesh = {Animals ; *Colitis/chemically induced/drug therapy/prevention & control ; Dextran Sulfate ; Disease Models, Animal ; Magnesium ; *Magnesium Oxide/adverse effects ; Male ; Mice ; Mice, Inbred C57BL ; }, abstract = {We previously demonstrated that per os administration and ad libitum ingestion of a magnesium chloride (MgCl2) solution had a prophylactic effect on dextran sulfate sodium (DSS)-induced colitis in mice, magnesium being considered to play a role in this preferable action. Magnesium oxide (MgO) is a commercially available magnesium formulation, but whether or not it prevents development of colitis is unknown. In this study, we investigated the effect of MgO administration on development of colitis in DSS-treated male C57BL/6J mice. Experimental colitis was induced by ad libitum ingestion of 1% (w/v) DSS, and the colitis severity was evaluated by disease activity index (DAI) scores, histological assessment and colonic expression of inflammatory cytokines. A 1 mg/mL MgO solution was administered to mice through ad libitum ingestion from a day before DSS treatment to the end of the experimental period of 12 d. In addition, the effects of DSS, MgO and their combination on the gut microbiota were investigated by 16S ribosomal RNA metagenome analysis. DSS-induced elevation of DAI scores was partially but significantly decreased by MgO administration, while MgO administration had no apparent effect on the shortened colonic length, elevated mRNA expression of colonic interleukin-1β and tumor necrosis factor-α, increased accumulation of colonic mast cells, or altered features of the gut microbiota in DSS-treated mice. Overall, we demonstrated that MgO had a prophylactic effect on the development of colitis in DSS-treated mice by preventing histological colonic damage, but not colonic inflammation or alteration of the gut microbiota.}, } @article {pmid36046746, year = {2022}, author = {Zhou, JJ and Ding, WC and Liu, YC and Gao, YL and Xu, L and Geng, RL and Ye, Y and Chai, YF}, title = {Diagnostic Value of Metagenomic Next-Generation Sequencing for Pulmonary Infection in Intensive Care Unit and Non-Intensive Care Unit Patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {929856}, pmid = {36046746}, issn = {2235-2988}, mesh = {High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; *Metagenomics/methods ; *Pneumonia/microbiology ; Prospective Studies ; Sensitivity and Specificity ; }, abstract = {OBJECTIVE: To evaluate the diagnostic performance of metagenomic next-generation sequencing (mNGS) and culture in pathogen detection among intensive care unit (ICU) and non-ICU patients with suspected pulmonary infection.

METHODS: In this prospective study, sputum samples were collected from patients with suspected pulmonary infection for 2 consecutive days and then subjected to DNA or RNA sequencing by mNGS or culture; 62 ICU patients and 60 non-ICU patients were admitted. In the end, comparisons were made on the pathogen species identified by mNGS and culture, the overall performance of these two methods in pathogen detection, and the most common pathogens detected by mNGS between the ICU and non-ICU groups.

RESULTS: In DNA and RNA sequencing, the positive rate of pathogen detection reached 96.69% (117/121) and 96.43% (108/112), respectively. In culture tests, the positive rate of the pathogen was 39.34% (48/122), much lower than that of DNA and RNA sequencing. In general, the positive rate of pathogen detection by sputum mNGS was significantly higher than that of sputum culture in the total and non-ICU groups (p < 0.001) but did not show a significant difference when compared to the result of sputum culture in the ICU group (p = 0.08). Haemophilus spp., Candida albicans, Enterococcus spp., and viruses from the mNGS results were excluded before comparing the overall performance of these two methods in pathogen detection. Specifically, among the 10 most common bacteria implied from the mNGS results, significant differences were observed in the number of cases of Haemophilus parainfluenzae, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, Stenotrophomonas maltophilia, Staphylococcus aureus, and Enterococcus faecalis between the ICU and non-ICU groups (p < 0.05).

CONCLUSIONS: This study demonstrated the superiority of mNGS over culture in detecting all kinds of pathogen species in sputum samples. These results indicate that mNGS may serve as a valuable tool to identify pathogens, especially for ICU patients who are more susceptible to mixed infections.}, } @article {pmid36046481, year = {2022}, author = {Yang, A and Hu, Y and Chen, P and Zheng, G and Hu, X and Zhang, J and Wang, J and Wang, C and Huang, Z and Zhang, Y and Guo, Y}, title = {Diagnosis by metagenomic next-generation sequencing of a Talaromyces marneffei bloodstream infection in an HIV-negative child: A case report.}, journal = {Frontiers in pediatrics}, volume = {10}, number = {}, pages = {903617}, pmid = {36046481}, issn = {2296-2360}, abstract = {BACKGROUND: Talaromyces marneffei (TM) bloodstream infections are life- threatening in immunocompromised individuals. The lack of specific clinical features for these infections and poor sensitivity associated with routine examination procedures make diagnosis challenging. Untimely diagnosis and delayed antifungal treatment threatens the life of such patients.

CASE DESCRIPTION: We report a case of a TM bloodstream infection, confirmed by the results of blood culture, of a child who was HIV negative and possessed a CD40LG gene mutation. A diagnosis of TM was established by blood metagenomic next-generation sequencing (mNGS) of the patient's blood, which was confirmed by microbiological culture of blood. On admission, this previously healthy male patient was 8-months of age, who presented with recurrent fever and a cough of 6-days in duration. His condition did not improve after antibacterial treatment for 5-days, with significant and recurrent fever and worsening spirit. He was referred to the Department of Pediatrics in our tertiary medical institution with a white blood cell count of 21.5[*]10∧9/L, C-reactive protein of 47.98 mg/L, and procalcitonin of 0.28 ng/mL. A bloodstream infection was not excluded and blood was collected for microbial culture. The patient received a 1-day treatment of cefoperazone sulbactam and 6-days of imipenem cilastatin. Symptoms did not improve and fever persisted. Blood was submitted for mNGS analysis and within 14-h, 14,352 TM reads were detected with a relative abundance of 98.09%. Antibiotic treatment was immediately changed to intravenous amphotericin B combined with oral itraconazole. The condition of the child gradually improved. Blood culture showed TM on the 7th day after hospitalization, confirming bloodstream infection. After the 13th day of hospital admission, the patient's body temperature dropped close to 38°C and was discharged on the 30th day of hospitalization. Oral itraconazole was prescribed with follow up at the outpatient clinic.

CONCLUSIONS: HIV-negative patients with CD40LG mutations may be potential hosts for TM. TM infections are rare in children and their detection by conventional microbial culture methods are inadequate for an early diagnosis. mNGS is a rapid detection method that permits early diagnosis of uncommon infectious agents, such as TM, allowing for improved patient outcomes.}, } @article {pmid36046038, year = {2022}, author = {He, GQ and Xiao, L and Pan, Z and Wu, JR and Liang, DN and Guo, X and Jiang, MY and Gao, J}, title = {Case report: A rare case of pulmonary mucormycosis caused by Lichtheimia ramosa in pediatric acute lymphoblastic leukemia and review of Lichtheimia infections in leukemia.}, journal = {Frontiers in oncology}, volume = {12}, number = {}, pages = {949910}, pmid = {36046038}, issn = {2234-943X}, abstract = {Mucormycosis caused by Lichtheimia ramosa is an emerging and uncommon opportunistic infection in patients with hematological malignancies, with high mortality rates. Herein, we first report a case of pulmonary mucormycosis with Lichtheimia ramosa in a 3-year-old girl recently diagnosed with B-cell acute lymphoblastic leukemia. The diagnosis was made using computerized tomography of the lung, metagenomic next-generation sequencing (mNGS) of blood and sputum specimens, and microscopic examination to detect the development of Lichtheimia ramosa on the surgical specimen. She was effectively treated after receiving prompt treatment with amphotericin B and posaconazole, followed by aggressive surgical debridement. In our case, the fungal isolates were identified as Lichtheimia ramosa using mNGS, which assisted clinicians in quickly and accurately diagnosing and initiating early intensive treatment. This case also indicated the importance of strong clinical suspicion, as well as aggressive antifungal therapy combined with surgical debridement of affected tissues.}, } @article {pmid36045603, year = {2022}, author = {Lindstedt, K and Buczek, D and Pedersen, T and Hjerde, E and Raffelsberger, N and Suzuki, Y and Brisse, S and Holt, K and Samuelsen, Ø and Sundsfjord, A}, title = {Detection of Klebsiella pneumoniae human gut carriage: a comparison of culture, qPCR, and whole metagenomic sequencing methods.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2118500}, pmid = {36045603}, issn = {1949-0984}, mesh = {Adult ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Multiple, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; *Klebsiella Infections/diagnosis ; Klebsiella pneumoniae/genetics ; }, abstract = {Klebsiella pneumoniae is an important opportunistic healthcare-associated pathogen and major contributor to the global spread of antimicrobial resistance. Gastrointestinal colonization with K. pneumoniae is a major predisposing risk factor for infection and forms an important hub for the dispersal of resistance. Current culture-based detection methods are time consuming, give limited intra-sample abundance and strain diversity information, and have uncertain sensitivity. Here we investigated the presence and abundance of K. pneumoniae at the species and strain level within fecal samples from 103 community-based adults by qPCR and whole metagenomic sequencing (WMS) compared to culture-based detection. qPCR demonstrated the highest sensitivity, detecting K. pneumoniae in 61.2% and 75.8% of direct-fecal and culture-enriched sweep samples, respectively, including 52/52 culture-positive samples. WMS displayed lower sensitivity, detecting K. pneumoniae in 71.2% of culture-positive fecal samples at a 0.01% abundance cutoff, and was inclined to false positives in proportion to the relative abundance of other Enterobacterales present. qPCR accurately quantified K. pneumoniae to 16 genome copies/reaction while WMS could estimate relative abundance to at least 0.01%. Quantification by both methods correlated strongly with each other (Spearman's rho = 0.91). WMS also supported accurate intra-sample K. pneumoniae sequence type (ST)-level diversity detection from fecal microbiomes to 0.1% relative abundance, agreeing with the culture-based detected ST in 16/19 samples. Our results show that qPCR and WMS are sensitive and reliable tools for detection, quantification, and strain analysis of K. pneumoniae from fecal samples with potential to support infection control and enhance insights in K. pneumoniae gastrointestinal ecology.}, } @article {pmid36045433, year = {2022}, author = {Lee, SA and Kim, M and Kim, HS and Ahn, CY}, title = {Extra benefit of microalgae in raw piggery wastewater treatment: pathogen reduction.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {142}, pmid = {36045433}, issn = {2049-2618}, mesh = {Biomass ; *Microalgae ; Nitrogen ; Wastewater ; *Water Purification ; }, abstract = {BACKGROUND: Monitoring microbial communities especially focused on pathogens in newly developed wastewater treatment systems is recommended for public health. Thus, we investigated the microbial community shift in a pilot-scale microalgal treatment system for piggery wastewater.

RESULTS: Microalgae showed reasonable removal efficiencies for COD and ammonia, resulting in higher transparency of the final effluent. Metagenome and microbial diversity analyses showed that heterotrophic microalgal cultivation barely changed the bacterial community; however, the mixotrophic microalgal cultivation induced a sudden change. In addition, an evaluation of risk groups (RGs) of bacteria showed that raw piggery wastewater included abundant pathogens, and the microalgal treatment of the raw piggery wastewater decreased the RG2 pathogens by 63%. However, co-cultivation of microalgae and the most dominant RG2 pathogen, Oligella, showed no direct effects between them.

CONCLUSIONS: Thus, a microbial interaction network was constructed to elucidate algae-bacteria interrelationships, and the decrease in Oligella was indirectly connected with microalgal growth via Brevundimonas, Sphingopyxis, and Stenotrophomonas. In a validation test, 3 among 4 connecting bacterial strains exhibited inhibition zones against Oligella. Therefore, we showed that microalgal wastewater treatment causes a decrease in RG2 bacteria, which is an indirect impact of microalgae associated with bacteria. Video abstract.}, } @article {pmid36045431, year = {2022}, author = {Meng, Y and Li, S and Zhang, C and Zheng, H}, title = {Strain-level profiling with picodroplet microfluidic cultivation reveals host-specific adaption of honeybee gut symbionts.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {140}, pmid = {36045431}, issn = {2049-2618}, mesh = {Animals ; Bacteria/genetics ; Bees ; Bifidobacterium/genetics ; Metagenome ; *Microbiota ; *Microfluidics ; Symbiosis ; }, abstract = {BACKGROUND: Symbiotic gut microbes have a rich genomic and metabolic pool and are closely related to hosts' health. Traditional sequencing profiling masks the genomic and phenotypic diversity among strains from the same species. Innovative droplet-based microfluidic cultivation may help to elucidate the inter-strain interactions. A limited number of bacterial phylotypes colonize the honeybee gut, while individual strains possess unique genomic potential and critical capabilities, which provides a particularly good model for strain-level analyses.

RESULTS: Here, we construct a droplet-based microfluidic platform and generated ~ 6 × 10[8] droplets encapsulated with individual bacterial cells from the honeybee gut and cultivate in different media. Shotgun metagenomic analysis reveals significant changes in community structure after droplet-based cultivation, with certain species showing higher strain-level diversity than in gut samples. We obtain metagenome-assembled genomes, and comparative analysis reveal a potential novel cluster from Bifidobacterium in the honeybee. Interestingly, Lactobacillus panisapium strains obtained via droplet cultivation from Apis mellifera contain a unique set of genes encoding L-arabinofuranosidase, which is likely important for the survival of bacteria in competitive environments.

CONCLUSIONS: By encapsulating single bacteria cells inside microfluidic droplets, we exclude potential interspecific competition for the enrichment of rare strains by shotgun sequencing at high resolution. The comparative genomic analysis reveals underlying mechanisms for host-specific adaptations, providing intriguing insights into microbe-microbe interactions. The current approach may facilitate the hunting for elusive bacteria and paves the way for large-scale studies of more complex animal microbial communities. Video Abstract.}, } @article {pmid36045380, year = {2022}, author = {Yin, HC and Wan, DC and Chen, HY}, title = {Metagenomic analysis of viral diversity and a novel astroviruse of forest rodent.}, journal = {Virology journal}, volume = {19}, number = {1}, pages = {138}, pmid = {36045380}, issn = {1743-422X}, mesh = {Animals ; Feces ; Forests ; Genome, Viral ; Humans ; Metagenome ; Metagenomics ; Phylogeny ; *Plant Viruses/genetics ; *RNA Viruses/genetics ; Rodentia/genetics ; }, abstract = {BACKGROUND: Rodents are important virus reservoirs and natural hosts for multiple viruses. They are one of the wild animals that are extremely threatening to the spread of human viruses. Therefore, research on rodents carrying viruses and identifying new viruses that rodents carry is of great significance for preventing and controlling viral diseases.

METHODS: In this study, fecal samples from six species of forest rodents in Northeast China were sequenced using metagenomics, and an abundance of virome information was acquired. Selection of important zoonotic in individual rodents for further sequence and evolutionary analysis.

RESULTS: Among the top 10 most abundant viral families, RNA virus include Orthomyxoviridae, Picornaviridae, Bunyaviridae and Arenaviridae, DNA virus include Herpesviridae, Insect virus include Nodaviridae and Baculoviridae, Plant virus Tombusviridae and Phage (Myoriviridae). Except for Myoviridae, there was no significant difference in the abundance of virus families in the feces of each rodent species. In addition, a new strain of astrovirus was discovered, with an ORF and genome arrangement comparable to other rodent astroviruses.The newly identified astrovirus had the highest similarity with the rodent astrovirus isolate, CHN/100.

CONCLUSIONS: The data obtained in this study provided an overview of the viral community present in these rodent fecal samples, revealing some rodent-associated viruses closely related to known human or animal pathogens. Strengthening our understanding of unclassified viruses harbored by rodents present in the natural environment could provide scientific guidance for preventing and controlling new viral outbreaks that can spread via rodents.}, } @article {pmid36044594, year = {2022}, author = {Swarte, JC and Li, Y and Hu, S and Björk, JR and Gacesa, R and Vich Vila, A and Douwes, RM and Collij, V and Kurilshikov, A and Post, A and Klaassen, MAY and Eisenga, MF and Gomes-Neto, AW and Kremer, D and Jansen, BH and Knobbe, TJ and Berger, SP and Sanders, JF and Heiner-Fokkema, MR and Porte, RJ and Cuperus, FJC and de Meijer, VE and Wijmenga, C and Festen, EAM and Zhernakova, A and Fu, J and Harmsen, HJM and Blokzijl, H and Bakker, SJL and Weersma, RK}, title = {Gut microbiome dysbiosis is associated with increased mortality after solid organ transplantation.}, journal = {Science translational medicine}, volume = {14}, number = {660}, pages = {eabn7566}, doi = {10.1126/scitranslmed.abn7566}, pmid = {36044594}, issn = {1946-6242}, mesh = {Dysbiosis ; *Gastrointestinal Microbiome/genetics ; *Hematopoietic Stem Cell Transplantation ; Humans ; *Organ Transplantation ; Virulence Factors ; }, abstract = {Organ transplantation is a life-saving treatment for patients with end-stage disease, but survival rates after transplantation vary considerably. There is now increasing evidence that the gut microbiome is linked to the survival of patients undergoing hematopoietic cell transplant, yet little is known about the role of the gut microbiome in solid organ transplantation. We analyzed 1370 fecal samples from 415 liver and 672 renal transplant recipients using shotgun metagenomic sequencing to assess microbial taxonomy, metabolic pathways, antibiotic resistance genes, and virulence factors. To quantify taxonomic and metabolic dysbiosis, we also analyzed 1183 age-, sex-, and body mass index-matched controls from the same population. In addition, a subset of 78 renal transplant recipients was followed longitudinally from pretransplantation to 24 months after transplantation. Our data showed that both liver and kidney transplant recipients suffered from gut dysbiosis, including lower microbial diversity, increased abundance of unhealthy microbial species, decreased abundance of important metabolic pathways, and increased prevalence and diversity of antibiotic resistance genes and virulence factors. These changes were found to persist up to 20 years after transplantation. Last, we demonstrated that the use of immunosuppressive drugs was associated with the observed dysbiosis and that the extent of dysbiosis was associated with increased mortality after transplantation. This study represents a step toward potential microbiome-targeted interventions that might influence the outcomes of recipients of solid organ transplantation.}, } @article {pmid36044481, year = {2022}, author = {Mtshali, K and Khumalo, ZTH and Kwenda, S and Arshad, I and Thekisoe, OMM}, title = {Exploration and comparison of bacterial communities present in bovine faeces, milk and blood using 16S rRNA metagenomic sequencing.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0273799}, pmid = {36044481}, issn = {1932-6203}, mesh = {Animals ; Bacteria/genetics ; Bacteroidetes/genetics ; Cattle ; Feces/microbiology ; Female ; *Microbiota/genetics ; *Milk/microbiology ; RNA, Ribosomal, 16S/genetics ; South Africa ; }, abstract = {Cattle by-products like faeces, milk and blood have many uses among rural communities; aiding to facilitate everyday household activities and occasional rituals. Ecologically, the body sites from which they are derived consist of distinct microbial communities forming a complex ecosystem of niches. We aimed to explore and compare the faecal, milk and blood microbiota of cows through 16S rRNA sequencing. All downstream analyses were performed using applications in R Studio (v3.6.1). Alpha-diversity metrics showed significant differences between faeces and blood; faeces and milk; but non-significant between blood and milk using Kruskal-Wallis test, P < 0,05. The beta-diversity metrics on Principal Coordinate Analysis and Non-Metric Dimensional Scaling significantly clustered samples by type (PERMANOVA test, P < 0,05). The overall analysis revealed a total of 30 phyla, 74 classes, 156 orders, 243 families and 408 genera. Firmicutes, Bacteroidota and Proteobacteria were the most abundant phyla overall. A total of 58 genus-level taxa occurred concurrently between the body sites. The important taxa could be categorized into four potentially pathogenic clusters i.e. arthropod-borne; food-borne and zoonotic; mastitogenic; and metritic and abortigenic. A number of taxa were significantly differentially abundant (DA) between sites based on the Wald test implemented in DESeq2 package. Majority of the DA taxa (i.e. Romboutsia, Paeniclostridium, Monoglobus, Akkermansia, Turicibacter, Bacteroides, Candidatus_Saccharimonas, UCG-005 and Prevotellaceae_UCG-004) were significantly enriched in faeces in comparison to milk and blood, except for Anaplasma which was greatly enriched in blood and was in turn the largest microbial genus in the entire analysis. This study provides insights into the microbial community composition of the sampled body sites and its extent of overlapping. It further highlights the potential risk of disease occurrence and transmission between the animals and the community of Waaihoek in KwaZulu-Natal, Republic of South Africa pertaining to their unsanitary practices associated with the use of cattle by-products.}, } @article {pmid36043790, year = {2022}, author = {Kuroda, K and Yamamoto, K and Nakai, R and Hirakata, Y and Kubota, K and Nobu, MK and Narihiro, T}, title = {Symbiosis between Candidatus Patescibacteria and Archaea Discovered in Wastewater-Treating Bioreactors.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0171122}, pmid = {36043790}, issn = {2150-7511}, mesh = {*Archaea/metabolism ; Symbiosis/genetics ; Wastewater ; Phylogeny ; In Situ Hybridization, Fluorescence ; Sewage ; Bacteria/genetics ; *Euryarchaeota ; Bioreactors ; Protein Sorting Signals/genetics ; }, abstract = {Each prokaryotic domain, Bacteria and Archaea, contains a large and diverse group of organisms characterized by their ultrasmall cell size and symbiotic lifestyles (potentially commensal, mutualistic, and parasitic relationships), namely, Candidatus Patescibacteria (also known as the Candidate Phyla Radiation/CPR superphylum) and DPANN archaea, respectively. Cultivation-based approaches have revealed that Ca. Patescibacteria and DPANN symbiotically interact with bacterial and archaeal partners and hosts, respectively, but that cross-domain symbiosis and parasitism have never been observed. By amending wastewater treatment sludge samples with methanogenic archaea, we observed increased abundances of Ca. Patescibacteria (Ca. Yanofskybacteria/UBA5738) and, using fluorescence in situ hybridization (FISH), discovered that nearly all of the Ca. Yanofskybacteria/UBA5738 cells were attached to Methanothrix (95.7 ± 2.1%) and that none of the cells were attached to other lineages, implying high host dependency and specificity. Methanothrix filaments (multicellular) with Ca. Yanofskybacteria/UBA5738 attached had significantly more cells with no or low detectable ribosomal activity (based on FISH fluorescence) and often showed deformations at the sites of attachment (based on transmission electron microscopy), suggesting that the interaction is parasitic. Metagenome-assisted metabolic reconstruction showed that Ca. Yanofskybacteria/UBA5738 lacks most of the biosynthetic pathways necessary for cell growth and universally conserves three unique gene arrays that contain multiple genes with signal peptides in the metagenome-assembled genomes of the Ca. Yanofskybacteria/UBA5738 lineage. The results shed light on a novel cross-domain symbiosis and inspire potential strategies for culturing CPR and DPANN. IMPORTANCE One highly diverse phylogenetic group of Bacteria, Ca. Patescibacteria, remains poorly understood, but, from the few cultured representatives and metagenomic investigations, they are thought to live symbiotically or parasitically with other bacteria or even with eukarya. We explored the possibility of symbiotic interactions with Archaea by amending wastewater treatment sludge samples that were rich in Ca. Patescibacteria and Archaea with an isolate archaeon that is closely related to a methanogen population abundant in situ (Methanothrix). This strategic cultivation successfully established enrichment cultures that were mainly comprised of Ca. Patescibacteria (family level lineage Ca. Yanofskybacteria/UBA5738) and Methanothrix, in which we found highly specific physical interactions between the two organisms. Microscopic observations based on transmission electron microscopy, target-specific fluorescence in situ hybridization, and metagenomic analyses showed evidence that the interaction is likely parasitic. The results show a novel cross-domain parasitism between Bacteria and Archaea and suggest that the amendment of host Archaea may be an effective approach in culturing novel Ca. Patescibacteria.}, } @article {pmid36043739, year = {2022}, author = {Li, JC and Nie, G and Dai, HF}, title = {A Case of Spontaneous Mediastinal and Subcutaneous Emphysema in a Patient with HIV-Infected Pneumonia.}, journal = {Current HIV research}, volume = {20}, number = {6}, pages = {479-484}, pmid = {36043739}, issn = {1873-4251}, mesh = {Male ; Humans ; Young Adult ; Adult ; *Mediastinal Emphysema/diagnostic imaging/etiology ; Mediastinum/diagnostic imaging ; HIV ; *HIV Infections/complications ; *Subcutaneous Emphysema/etiology/complications ; }, abstract = {BACKGROUND: Acquired immunodeficiency syndrome is a chronic infectious disease with high mortality and is caused by the Human Immunodeficiency Virus (HIV). Pneumonia caused by HIV is common, but it rarely causes spontaneous mediastinal and subcutaneous emphysema.

CASE PRESENTATION: A 21-year-old man with severe pneumonia was hospitalized owing to dyspnea that had been persisting for 1 day; blood test results confirmed HIV infection. Initial chest Computed Tomography (CT) did not reveal mediastinal or subcutaneous emphysema. However, after 21 days of treatment, the patient experienced discomfort in the neck region and experienced the feeling of snowflakes on applying pressure. Chest CT showed mediastinal and subcutaneous emphysema, located in the bilateral cervical roots, anterior upper chest wall, left axillary chest wall, mediastinum, and other parts. Metagenomic Next Generation Sequencing (mNGS) of the sputum and blood samples suggested multiple pathogenic infections. Antiinfection treatment was initiated, and changes in the patient's condition were monitored. The patient's subcutaneous emphysema improved during the follow-up.

CONCLUSION: In HIV-infected patients with sudden mediastinal and subcutaneous emphysema, mNGS can be used to determine the etiological agent during symptomatic treatment. Targeted antipathogen therapy is helpful in improving the condition of patients with subcutaneous emphysema.}, } @article {pmid36042984, year = {2022}, author = {Rios-Miguel, AB and Smith, GJ and Cremers, G and van Alen, T and Jetten, MSM and Op den Camp, HJM and Welte, CU}, title = {Microbial paracetamol degradation involves a high diversity of novel amidase enzyme candidates.}, journal = {Water research X}, volume = {16}, number = {}, pages = {100152}, pmid = {36042984}, issn = {2589-9147}, abstract = {Pharmaceuticals are relatively new to nature and often not completely removed in wastewater treatment plants (WWTPs). Consequently, these micropollutants end up in water bodies all around the world posing a great environmental risk. One exception to this recalcitrant conversion is paracetamol, whose full degradation has been linked to several microorganisms. However, the genes and corresponding proteins involved in microbial paracetamol degradation are still elusive. In order to improve our knowledge of the microbial paracetamol degradation pathway, we inoculated a bioreactor with sludge of a hospital WWTP (Pharmafilter, Delft, NL) and fed it with paracetamol as the sole carbon source. Paracetamol was fully degraded without any lag phase and the enriched microbial community was investigated by metagenomic and metatranscriptomic analyses, which demonstrated that the microbial community was very diverse. Dilution and plating on paracetamol-amended agar plates yielded two Pseudomonas sp. isolates: a fast-growing Pseudomonas sp. that degraded 200 mg/L of paracetamol in approximately 10 h while excreting 4-aminophenol, and a slow-growing Pseudomonas sp. that degraded paracetamol without obvious intermediates in more than 90 days. Each Pseudomonas sp. contained a different highly-expressed amidase (31% identity to each other). These amidase genes were not detected in the bioreactor metagenome suggesting that other as-yet uncharacterized amidases may be responsible for the first biodegradation step of paracetamol. Uncharacterized deaminase genes and genes encoding dioxygenase enzymes involved in the catabolism of aromatic compounds and amino acids were the most likely candidates responsible for the degradation of paracetamol intermediates based on their high expression levels in the bioreactor metagenome and the Pseudomonas spp. genomes. Furthermore, cross-feeding between different community members might have occurred to efficiently degrade paracetamol and its intermediates in the bioreactor. This study increases our knowledge about the ongoing microbial evolution towards biodegradation of pharmaceuticals and points to a large diversity of (amidase) enzymes that are likely involved in paracetamol metabolism in WWTPs.}, } @article {pmid36042721, year = {2022}, author = {Maini, ZA and Lopez, CM}, title = {Transitions in bacterial communities across two fermentation-based virgin coconut oil (VCO) production processes.}, journal = {Heliyon}, volume = {8}, number = {8}, pages = {e10154}, pmid = {36042721}, issn = {2405-8440}, abstract = {Despite being one of the most used methods of virgin coconut oil (VCO) production, there is no metagenomic study that details the bacterial community shifts during fermentation-based VCO production. The identification and quantification of bacteria associated with coconut milk fermentation is useful for detecting the dominant microbial genera actively involved in VCO production which remains largely undescribed. Describing the constitutive microbial genera involved in this traditional fermentation practice can be used as a preliminary basis for improving industrial practices and developing better fermentation procedures. In this study, we utilized 16S rRNA metagenomic sequencing to trace the transitions in microbial community profiles as coconut milk is fermented to release VCO in two VCO production lines. The results show that difference in the microbiome composition between the different processing steps examined in this work was mainly due to the abundance of the Leuconostoc genus in the raw materials and its decline and transition into the lactic acid bacteria groups Weissella, Enterococcus, Lactobacillus, Lactococcus, and Streptococcus during the latter stages of fermentation. A total of 17 genera with relative abundances greater than 0.01% constitute the core microbiome of the two processing lines and account for 74%-97% of the microbial abundance in all coconut-derived samples. Significant correlations were shown through an analysis of the Spearman's rank between and within the microbial composition and pH at the genus level. The results of the present study show that the dynamics of VCO fermentation rely on the shifts in abundances of various members of the Lactobacillales order.}, } @article {pmid36042605, year = {2022}, author = {Pi, Y and Wang, J and Wang, Z}, title = {Massive pericardial effusion due to chronic active Epstein-Barr virus infection successfully treated with PD-1 blockade: A case report.}, journal = {Medicine}, volume = {101}, number = {34}, pages = {e30298}, pmid = {36042605}, issn = {1536-5964}, mesh = {Adult ; Chronic Disease ; *Epstein-Barr Virus Infections/drug therapy/therapy ; Female ; Herpesvirus 4, Human/genetics ; Humans ; *Lymphoproliferative Disorders/complications/drug therapy ; *Pericardial Effusion/etiology/therapy ; Persistent Infection ; Programmed Cell Death 1 Receptor/therapeutic use ; }, abstract = {RATIONALE: Chronic active Epstein-Barr virus (EBV) infection (CAEBV) is a rare but life-threatening EBV-positive lymphoproliferative disorder. Currently, treatment options for CAEBV are limited. Allogeneic hematopoietic stem cell transplantation (allo-HSCT) is the only way to cure CAEBV. Here, we report a rare case of CAEBV manifesting as massive pericardial effusion that was successfully treated with programmed cell death protein-1 (PD-1) blockade immunotherapy.

PATIENT CONCERNS: A 36-year-old woman with intermittent chest distress and dyspnea for 8 months was admitted to our center on October 25, 2021. Laboratory tests showed leukocytopenia and elevated liver enzyme levels. Initial echocardiography revealed massive pericardial effusion.

DIAGNOSIS: High levels of EBV-DNA were detected in the pericardial fluid by metagenomic next-generation sequencing. The pathological diagnosis of her left inguinal lymph node and skin lesions revealed systemic CAEBV.

INTERVENTIONS: The patient received sintilimab injection at a dose of 200 mg every 2 weeks in combined with lenalidomide 10 mg once daily.

OUTCOMES: The patient achieved complete resolution of pericardial effusion 5 months after PD-1 blockade immunotherapy without apparent adverse effects.

LESSONS: CAEBV is a rare but life-threatening EBV-positive lymphoproliferative disease. We present a rare case of massive pericardial effusion caused by systemic CAEBV, which was successfully treated with sintilimab. This case highlights the promising curative effect of PD-1 blockade immunotherapy in systemic CAEBV, especially for patients not suitable for allo-HSCT.}, } @article {pmid36042406, year = {2022}, author = {Poussin, C and Khachatryan, L and Sierro, N and Narsapuram, VK and Meyer, F and Kaikala, V and Chawla, V and Muppirala, U and Kumar, S and Belcastro, V and Battey, JND and Scotti, E and Boué, S and McHardy, AC and Peitsch, MC and Ivanov, NV and Hoeng, J}, title = {Crowdsourced benchmarking of taxonomic metagenome profilers: lessons learned from the sbv IMPROVER Microbiomics challenge.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {624}, pmid = {36042406}, issn = {1471-2164}, mesh = {Benchmarking ; *Crowdsourcing ; *Metagenome ; Metagenomics/methods ; Software ; }, abstract = {BACKGROUND: Selection of optimal computational strategies for analyzing metagenomics data is a decisive step in determining the microbial composition of a sample, and this procedure is complex because of the numerous tools currently available. The aim of this research was to summarize the results of crowdsourced sbv IMPROVER Microbiomics Challenge designed to evaluate the performance of off-the-shelf metagenomics software as well as to investigate the robustness of these results by the extended post-challenge analysis. In total 21 off-the-shelf taxonomic metagenome profiling pipelines were benchmarked for their capacity to identify the microbiome composition at various taxon levels across 104 shotgun metagenomics datasets of bacterial genomes (representative of various microbiome samples) from public databases. Performance was determined by comparing predicted taxonomy profiles with the gold standard.

RESULTS: Most taxonomic profilers performed homogeneously well at the phylum level but generated intermediate and heterogeneous scores at the genus and species levels, respectively. kmer-based pipelines using Kraken with and without Bracken or using CLARK-S performed best overall, but they exhibited lower precision than the two marker-gene-based methods MetaPhlAn and mOTU. Filtering out the 1% least abundance species-which were not reliably predicted-helped increase the performance of most profilers by increasing precision but at the cost of recall. However, the use of adaptive filtering thresholds determined from the sample's Shannon index increased the performance of most kmer-based profilers while mitigating the tradeoff between precision and recall.

CONCLUSIONS: kmer-based metagenomic pipelines using Kraken/Bracken or CLARK-S performed most robustly across a large variety of microbiome datasets. Removing non-reliably predicted low-abundance species by using diversity-dependent adaptive filtering thresholds further enhanced the performance of these tools. This work demonstrates the applicability of computational pipelines for accurately determining taxonomic profiles in clinical and environmental contexts and exemplifies the power of crowdsourcing for unbiased evaluation.}, } @article {pmid36042402, year = {2022}, author = {Twort, VG and Blande, D and Duplouy, A}, title = {One's trash is someone else's treasure: sequence read archives from Lepidoptera genomes provide material for genome reconstruction of their endosymbionts.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {209}, pmid = {36042402}, issn = {1471-2180}, mesh = {Animals ; *Lepidoptera ; Phylogeny ; *Spiroplasma/genetics ; Symbiosis/genetics ; *Wolbachia/genetics ; }, abstract = {BACKGROUND: Maternally inherited bacterial symbionts are extremely widespread in insects. They owe their success to their ability to promote their own transmission through various manipulations of their hosts' life-histories. Many symbionts however very often go undetected. Consequently, we have only a restricted idea of the true symbiont diversity in insects, which may hinder our understanding of even bigger questions in the field such as the evolution or establishment of symbiosis.

RESULTS: In this study, we screened publicly available Lepidoptera genomic material for two of the most common insect endosymbionts, namely Wolbachia and Spiroplasma, in 1904 entries, encompassing 106 distinct species. We compared the performance of two screening software, Kraken2 and MetaPhlAn2, to identify the bacterial infections and using a baiting approach we reconstruct endosymbiont genome assemblies. Of the 106 species screened, 20 (19%) and nine (8.5%) were found to be infected with either Wolbachia or Spiroplasma, respectively. Construction of partial symbiotic genomes and phylogenetic analyses suggested the Wolbachia strains from the supergroup B were the most prevalent type of symbionts, while Spiroplasma infections were scarce in the Lepidoptera species screened here.

CONCLUSIONS: Our results indicate that many of the host-symbiont associations remain largely unexplored, with the majority of associations we identify never being recorded before. This highlights the usefulness of public databases to explore the hidden diversity of symbiotic entities, allowing the development of hypotheses regarding host-symbiont associations. The ever-expanding genomic databases provide a diverse databank from which one can characterize and explore the true diversity of symbiotic entities.}, } @article {pmid36042324, year = {2022}, author = {Dharamshi, JE and Gaarslev, N and Steffen, K and Martin, T and Sipkema, D and Ettema, TJG}, title = {Genomic diversity and biosynthetic capabilities of sponge-associated chlamydiae.}, journal = {The ISME journal}, volume = {16}, number = {12}, pages = {2725-2740}, pmid = {36042324}, issn = {1751-7370}, mesh = {Animals ; Ecosystem ; Phylogeny ; *Chlamydia/genetics ; Bacteria ; Genomics ; *Porifera ; }, abstract = {Sponge microbiomes contribute to host health, nutrition, and defense through the production of secondary metabolites. Chlamydiae, a phylum of obligate intracellular bacteria ranging from animal pathogens to endosymbionts of microbial eukaryotes, are frequently found associated with sponges. However, sponge-associated chlamydial diversity has not yet been investigated at the genomic level and host interactions thus far remain unexplored. Here, we sequenced the microbiomes of three sponge species and found high, though variable, Chlamydiae relative abundances of up to 18.7% of bacteria. Using genome-resolved metagenomics 18 high-quality sponge-associated chlamydial genomes were reconstructed, covering four chlamydial families. Among these, Candidatus Sororchlamydiaceae shares a common ancestor with Chlamydiaceae animal pathogens, suggesting long-term co-evolution with animals. Based on gene content, sponge-associated chlamydiae resemble members from the same family more than sponge-associated chlamydiae of other families, and have greater metabolic versatility than known chlamydial animal pathogens. Sponge-associated chlamydiae are also enriched in genes for degrading diverse compounds found in sponges. Unexpectedly, we identified widespread genetic potential for secondary metabolite biosynthesis across Chlamydiae, which may represent an unexplored source of novel natural products. This finding suggests that Chlamydiae members may partake in defensive symbioses and that secondary metabolites play a wider role in mediating intracellular interactions. Furthermore, sponge-associated chlamydiae relatives were found in other marine invertebrates, pointing towards wider impacts of the Chlamydiae phylum on marine ecosystems.}, } @article {pmid36042219, year = {2022}, author = {Parikh, VN and Ioannidis, AG and Jimenez-Morales, D and Gorzynski, JE and De Jong, HN and Liu, X and Roque, J and Cepeda-Espinoza, VP and Osoegawa, K and Hughes, C and Sutton, SC and Youlton, N and Joshi, R and Amar, D and Tanigawa, Y and Russo, D and Wong, J and Lauzon, JT and Edelson, J and Mas Montserrat, D and Kwon, Y and Rubinacci, S and Delaneau, O and Cappello, L and Kim, J and Shoura, MJ and Raja, AN and Watson, N and Hammond, N and Spiteri, E and Mallempati, KC and Montero-Martín, G and Christle, J and Kim, J and Kirillova, A and Seo, K and Huang, Y and Zhao, C and Moreno-Grau, S and Hershman, SG and Dalton, KP and Zhen, J and Kamm, J and Bhatt, KD and Isakova, A and Morri, M and Ranganath, T and Blish, CA and Rogers, AJ and Nadeau, K and Yang, S and Blomkalns, A and O'Hara, R and Neff, NF and DeBoever, C and Szalma, S and Wheeler, MT and Gates, CM and Farh, K and Schroth, GP and Febbo, P and deSouza, F and Cornejo, OE and Fernandez-Vina, M and Kistler, A and Palacios, JA and Pinsky, BA and Bustamante, CD and Rivas, MA and Ashley, EA}, title = {Deconvoluting complex correlates of COVID-19 severity with a multi-omic pandemic tracking strategy.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {5107}, pmid = {36042219}, issn = {2041-1723}, support = {R01 GM121404/GM/NIGMS NIH HHS/United States ; U01 HG009080/HG/NHGRI NIH HHS/United States ; K08 HL143185/HL/NHLBI NIH HHS/United States ; U24 OD026629/OD/NIH HHS/United States ; R01 HL144843/HL/NHLBI NIH HHS/United States ; }, mesh = {*COVID-19/epidemiology ; Genome, Viral ; Genome-Wide Association Study ; Humans ; *Pandemics ; SARS-CoV-2/genetics ; }, abstract = {The SARS-CoV-2 pandemic has differentially impacted populations across race and ethnicity. A multi-omic approach represents a powerful tool to examine risk across multi-ancestry genomes. We leverage a pandemic tracking strategy in which we sequence viral and host genomes and transcriptomes from nasopharyngeal swabs of 1049 individuals (736 SARS-CoV-2 positive and 313 SARS-CoV-2 negative) and integrate them with digital phenotypes from electronic health records from a diverse catchment area in Northern California. Genome-wide association disaggregated by admixture mapping reveals novel COVID-19-severity-associated regions containing previously reported markers of neurologic, pulmonary and viral disease susceptibility. Phylodynamic tracking of consensus viral genomes reveals no association with disease severity or inferred ancestry. Summary data from multiomic investigation reveals metagenomic and HLA associations with severe COVID-19. The wealth of data available from residual nasopharyngeal swabs in combination with clinical data abstracted automatically at scale highlights a powerful strategy for pandemic tracking, and reveals distinct epidemiologic, genetic, and biological associations for those at the highest risk.}, } @article {pmid36041618, year = {2022}, author = {Yang, Y and Li, L and Huang, F and Hu, X and Cao, X and Mi, J and Liao, X and Xing, S}, title = {The fate of antibiotic resistance genes and their association with bacterial and archaeal communities during advanced treatment of pig farm wastewater.}, journal = {The Science of the total environment}, volume = {851}, number = {Pt 2}, pages = {158364}, doi = {10.1016/j.scitotenv.2022.158364}, pmid = {36041618}, issn = {1879-1026}, mesh = {Swine ; Animals ; *Wastewater/microbiology ; *Anti-Bacterial Agents/pharmacology ; Farms ; Archaea/genetics ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; }, abstract = {Advanced wastewater treatment plants are widely used in most large-scale pig farms in southern China. However, the fate of antibiotic resistance genes (ARGs) and their association with bacterial and archaeal communities during advanced wastewater treatment remain unclear. In this study, the profiles of ARGs in typical advanced wastewater treatment plants were surveyed using metagenomic analysis. The results showed that 279- 326 different subtypes of ARGs were detected in raw wastewater, with a total abundance of 5.98 ± 0.48 copies per bacterial cell. During the advanced wastewater treatment, the abundance and number of ARGs were significantly reduced. Microbial communities (bacteria and archaea) contributed the most to the variation in ARG abundance and composition (PCA axis_1), accounting for 10.8 % and 15.7 %, respectively, followed by mobile genetic elements (MGEs) and physicochemical factors. Special attention should be given to potential pathogenic bacteria such as Escherichia, Streptococcus, Enterococcus and Staphylococcus and archaea such as Methanocorpusculum, Candidatus Methanoplasma and Candidatus Methanomethylophilus, which were important potential ARG hosts. Bacterial communities may indirectly affect ARG variation by affecting archaeal communities. These findings indicated that ARG levels in pig farm wastewater can be effectively reduced during advanced treatment and highlighted the important role played by archaea, which should not be ignored.}, } @article {pmid36041613, year = {2022}, author = {Li, Q and Tian, L and Cai, X and Wang, Y and Mao, Y}, title = {Plastisphere showing unique microbiome and resistome different from activated sludge.}, journal = {The Science of the total environment}, volume = {851}, number = {Pt 2}, pages = {158330}, doi = {10.1016/j.scitotenv.2022.158330}, pmid = {36041613}, issn = {1879-1026}, mesh = {*Sewage/microbiology ; Polyvinyl Chloride ; Genes, Bacterial ; Microplastics ; Plastics ; *Microbiota ; Anti-Bacterial Agents/pharmacology ; Tetracycline ; Wastewater/microbiology ; }, abstract = {Plastisphere (the biofilm on microplastics) in wastewater treatment plants (WWTPs) may enrich pathogens and antibiotic resistance genes (ARGs) which can cause risks to the ecological environment by discharging into receiving waters. However, the microbiome and resistome of plastisphere in activated sludge (AS) systems remain inconclusive. Here, metagenome was applied to investigate the microbial composition, functions and ARGs of the Polyvinyl chloride (PVC) plastisphere in lab-scale reactors, and revealed the effects of tetracycline (TC) and/or Cu(II) pressures on them. The results indicated that the plastisphere provided a new niche for microbiota showing unique functions distinct from the AS. Particularly, various potentially pathogenic bacteria tended to enrich in PVC plastisphere. Moreover, various ARGs were detected in plastisphere and AS, but the plastisphere had more potential ARGs hosts and a stronger correlation with ARGs. The ARGs abundances increased after exposure to TC and/or Cu(II) pressures, especially tetracycline resistance genes (TRGs), and the results further showed that TRGs with different resistance mechanisms were separately enriched in plastisphere and AS. Furthermore, the exogenous pressures from Cu(II) or/and TC also enhanced the association of potential pathogens with TRGs in PVC plastisphere. The findings contribute to assessing the potential risks of spreading pathogens and ARGs through microplastics in WWTPs.}, } @article {pmid36041603, year = {2022}, author = {Shao, Y and Zhou, Z and Zuo, Y and Jiang, J and Wang, L and Sun, Y and He, J and Qiu, J and An, Y and Jiang, LM}, title = {Sludge decay kinetics and metagenomic analysis uncover discrepant metabolic mechanisms in two different sludge in situ reduction systems.}, journal = {The Science of the total environment}, volume = {851}, number = {Pt 2}, pages = {158346}, doi = {10.1016/j.scitotenv.2022.158346}, pmid = {36041603}, issn = {1879-1026}, mesh = {*Sewage/microbiology ; Waste Disposal, Fluid ; Bioreactors ; Anaerobiosis ; Kinetics ; L-Lactate Dehydrogenase ; Hydrolases ; *Environmental Pollutants ; Citrates ; Adenosine Triphosphate ; }, abstract = {A comparative study was conducted between an anaerobic side-stream reactor (ASSR) process and a sludge process reduction (SPR) activated sludge (SPRAS) process for uncovering crucial metabolic mechanisms governing sludge reduction. Both of two processes were efficient in removing pollutants, while the SPRAS (62.3 %) obtained much higher sludge reduction than the ASSR (27.9 %). The highest rate coefficients of sludge decay, heterotroph lysis and particles hydrolysis were 0.106, 0.219 and 0.054 d[-1] in the SPR module, followed by ASSR with coefficients of 0.060, 0.135 and 0.047 d[-1]. The SPR module achieved an 81.9 % higher sludge decay mass with a 32.8 % smaller volume than the ASSR module. The SPR module preferentially enriched hydrolytic/fermentative and slow-growing bacteria. Metagenomic analysis revealed that SPR strengthened the key hydrolases and L-lactate dehydrogenase in the glycolysis pathways and weakened the citrate cycle, inducing metabolic uncoupling due to the reduced biosynthesis of ATP. Inserting ASSR only altered the ATP biosynthesis pathway, but maintenance metabolism was dominant for sludge reduction, with a long sludge retention time prolonging the food chain for predation.}, } @article {pmid36041519, year = {2022}, author = {Shi, F and Almerick T Boncan, D and Wan, HT and Chan, TF and Zhang, EL and Lai, KP and Wong, CK}, title = {Hepatic metabolism gene expression and gut microbes in offspring, subjected to in-utero PFOS exposure and postnatal diet challenges.}, journal = {Chemosphere}, volume = {308}, number = {Pt 1}, pages = {136196}, doi = {10.1016/j.chemosphere.2022.136196}, pmid = {36041519}, issn = {1879-1298}, mesh = {Body Weight ; Carbohydrates ; Diet, High-Fat ; Fatty Acids, Volatile/metabolism ; Female ; *Gastrointestinal Microbiome ; Gene Expression ; Humans ; Lipid Metabolism ; Lipids ; Liver/metabolism ; Polysaccharides/metabolism ; *Prenatal Exposure Delayed Effects/metabolism ; Sucrose/metabolism ; Vitamins/metabolism/pharmacology ; }, abstract = {We examined the changes in hepatic metabolic gene expression and gut microbiota of offspring exposed to PFOS in-utero. At GD17.5, our data showed that PFOS exposure decreased fetal bodyweights and hepatic metabolic gene expressions but increased relative liver mass and lipid accumulation. At PND21, in-utero high-dose PFOS-exposed offspring exhibited significantly greater bodyweight (catch-up-growth), associated with significant induction of hepatic metabolic gene expression. In addition, 16SrRNA-sequencing of the cecal samples revealed an increase in carbohydrate catabolism but a reduction in microbial polysaccharide synthesis and short-chain fatty acid (SCFA) metabolism. From PND21-80, a postnatal diet-challenge for the offspring was conducted. At PND80 under a normal diet, in-utero high-dose PFOS-exposed offspring maintained the growth "catch-up" effect. In contrast, in a high-fat-diet, the bodyweight of in-utero high-dose PFOS-exposed adult offspring were significantly lesser than the corresponding low-dose and control groups. Even though in the high-fat-diet, the in-utero PFOS-exposed adult offspring showed significant upregulation of hepatic metabolic genes, the lower bodyweight suggests that they had difficulty utilizing high-fat nutrients. Noteworthy, the metagenomic data showed a significant reduction in the biosynthesis of microbial polysaccharides, vitamin B, and SCFAs in the PFOS-exposed adult offspring. Furthermore, the observed effects were significantly reduced in the PFOS-exposed adult offspring with the high-fat diet but supplemented with sucrose. Our study demonstrated that in-utero PFOS exposure caused inefficient fat metabolism and increased the risk of hepatic steatosis in offspring.}, } @article {pmid36041490, year = {2022}, author = {Bahk, YY and Ahn, SK and Jeon, HJ and Na, BK and Lee, SK and Shin, HJ}, title = {An Evaluation of a New Quantitative Point-of Care Diagnostic to Measure Glucose-6-phosphate Dehydrogenase Activity.}, journal = {The Korean journal of parasitology}, volume = {60}, number = {4}, pages = {281-288}, pmid = {36041490}, issn = {1738-0006}, support = {2020R1F1A1070882//National Research Foundation of Korea/ ; 2022R1F1A1066481, 2018M3A9H5055614//National Research Foundation of Korea/ ; //Ministry of Science and ICT/ ; }, mesh = {*Antimalarials/therapeutic use ; Glucosephosphate Dehydrogenase/therapeutic use ; *Glucosephosphate Dehydrogenase Deficiency/diagnosis/epidemiology ; Humans ; *Malaria/epidemiology ; *Malaria, Vivax/epidemiology ; Point-of-Care Systems ; Primaquine ; Reagent Kits, Diagnostic ; }, abstract = {Malaria continues to be one of the most crucial infectious burdens in endemic areas worldwide, as well as for travelers visiting malaria transmission regions. It has been reported that 8-aminoquinolines are effective against the Plasmodium species, particularly primaquine, for anti-hypnozoite therapy in P. vivax malaria. However, primaquine causes acute hemolytic anemia in individuals with glucose-6-phosphate dehydrogenase (G6PD) deficiency. Therefore, G6PD deficiency testing should precede hypnozoite elimination with 8-aminoquinoline. Several point-of-care devices have been developed to detect G6PD deficiency. The aim of the present study was to evaluate the performance of a novel, quantitative G6PD diagnostics based on a metagenomic blue fluorescent protein (mBFP). We comparatively evaluated the sensitivity and specificity of the G6PD diagnostic modality with standard methods using 120 human whole blood samples. The G6PD deficiency was spectrophotometrically confirmed. The performance of the G6PD quantitative test kit was compared with that of a licensed control medical device, the G6PD strip. The G6PD quantitative test kit had a sensitivity of 95% (95% confidence interval (CI): 89.3-100%) and a specificity of 100% (95% CI: 94.3-100%). This study shows that the novel diagnostic G6PD quantitative test kit could be a cost-effective and time-efficient, and universally mandated screening tool for G6PD deficiency.}, } @article {pmid36040926, year = {2022}, author = {Santona, A and Mhmoud, NA and Siddig, EE and Deligios, M and Fiamma, M and Paglietti, B and Bakhiet, SM and Rubino, S and Fahal, AH}, title = {Metagenomic detection of eumycetoma causative agents from households of patients residing in two Sudanese endemic villages in White Nile State.}, journal = {PLoS neglected tropical diseases}, volume = {16}, number = {8}, pages = {e0010385}, pmid = {36040926}, issn = {1935-2735}, mesh = {Animals ; *Madurella ; Metagenomics ; *Mycetoma/microbiology ; Neglected Diseases/diagnosis ; Soil ; }, abstract = {Eumycetoma is a chronic debilitating fungal disease endemic to tropical and subtropical regions, with Sudan featuring the highest eumycetoma incidence. Among the 50 species of fungi most commonly associated with eumycetoma Madurella mycetomatis (M. mycetomatis) is often referenced as the most common pathogen. However, there is an enormous knowledge gap related to this neglected disease and its pathogenesis, epidemiological features, and host-specific factors that could contribute to either the host susceptibility and resistance. In this study, we were able to utilize a metagenomic approach and samples collected from clinical black grains (BG) and familiar household environments aimed to assay both the habitat of eumycetoma-associated fungi and its possible connection with eumycetoma patients living in two different eumycetoma endemic villages within the White Nile State of Sudan. DNA sequencing targeting the fungal ITS2 domain was performed on soil, animal dung, housing walls and roofs, and Acacia-species thorn samples and compared with culture-dependent methods of fungal isolation. Additionally, we compared the soil samples obtained in the endemic zone with that from non-endemic zones, including Wagga village in Kassala State and Port Sudan suburb in Port Sudan State. Overall, a total of 392 Amplicon Sequence Variants (ASVs) were detected by ITS2 metagenomics Eumycetoma causative organisms accounted for 10% of total ASVs which included 11 genera: Exserohilum (2%), Aspergillus (1.7%), Curvularia (1%), Alternaria (0.9%), Madurella (0.5%), Fusarium (0.4%), Cladosporium (0.2%) Exophiala (0.15%), and, in a lesser extent, Microascus (0.05%) Bipolaris and Acremonium (0.01%) for each. Only five genera were identified by culture method, which included Fusarium (29%), Aspergillus (28%), Alternaria (2.5%), Bipolaris (1.6%), and Chaetomium (0.8%). M. mycetomatis was detected within all the studied patients' houses, accounting for 0.7% of total sequences. It was the first common eumycetoma-associated agent detected in soil samples and the third common in the dung and wall samples. In contrast, it was not detected in the roof or thorn samples nor in the soils from non-endemic regions. Exserohilum rostratum, Aspergillus spp and Cladosporium spp were detected in all samples. M. mycetomatis and other eumycetoma-associated fungal identified in the patients' black grains (BG) samples by metagenomics were identified in the environmental samples. Only Acremonium alternatum and Falciformispora senegalensis, responsible for eumycetoma in two patients were not detected, suggesting the infections in these patients happened outside these endemic areas. The soil, animal dung, and houses built from the same soil and dung are the main risk factors for M. mycetomatis infection in these endemic villages. Furthermore, the poor hygienic and environmental conditions, walking barefooted, and the presence of animals within the houses increase the risk of M. mycetomatis and other fungi causing eumycetoma.}, } @article {pmid36040253, year = {2022}, author = {Koutrouli, M and Morris, JH and Jensen, LJ}, title = {U-CIE [/juː 'siː/]: Color encoding of high-dimensional data.}, journal = {Protein science : a publication of the Protein Society}, volume = {31}, number = {9}, pages = {e4388}, pmid = {36040253}, issn = {1469-896X}, mesh = {*Color ; }, abstract = {Data visualization is essential to discover patterns and anomalies in large high-dimensional datasets. New dimensionality reduction techniques have thus been developed for visualizing omics data, in particular from single-cell studies. However, jointly showing several types of data, for example, single-cell expression and gene networks, remains a challenge. Here, we present 'U-CIE, a visualization method that encodes arbitrary high-dimensional data as colors using a combination of dimensionality reduction and the CIELAB color space to retain the original structure to the extent possible. U-CIE first uses UMAP to reduce high-dimensional data to three dimensions, partially preserving distances between entities. Next, it embeds the resulting three-dimensional representation within the CIELAB color space. This color model was designed to be perceptually uniform, meaning that the Euclidean distance between any two points should correspond to their relative perceptual difference. Therefore, the combination of UMAP and CIELAB thus results in a color encoding that captures much of the structure of the original high-dimensional data. We illustrate its broad applicability by visualizing single-cell data on a protein network and metagenomic data on a world map and on scatter plots.}, } @article {pmid36040200, year = {2022}, author = {Flurin, L and Wolf, MJ and Fisher, CR and Cano Cevallos, EJ and Vaillant, JJ and Pritt, BS and DeSimone, DC and Patel, R}, title = {Pathogen Detection in Infective Endocarditis Using Targeted Metagenomics on Whole Blood and Plasma: a Prospective Pilot Study.}, journal = {Journal of clinical microbiology}, volume = {60}, number = {9}, pages = {e0062122}, pmid = {36040200}, issn = {1098-660X}, support = {R01 AR056647/AR/NIAMS NIH HHS/United States ; R01AR056647//HHS | NIH | National Institute of Arthritis and Musculoskeletal and Skin Diseases (NIAMS)/ ; //Mayo Clinic (The Mayo Clinic)/ ; }, mesh = {*Endocarditis/diagnosis/microbiology ; *Endocarditis, Bacterial/diagnosis/microbiology ; Humans ; Metagenomics ; Pilot Projects ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Initial microbiologic diagnosis of infective endocarditis (IE) relies on blood cultures and Bartonella and Coxiella burnetii serology. Small case series and one prospective study have preliminarily reported application of metagenomic sequencing on blood or plasma for IE diagnosis. Here, results of a prospective pilot study evaluating targeted metagenomic sequencing (tMGS) for blood-based early pathogen detection and identification in IE are reported. Subjects diagnosed with possible or definite IE at a single institution were prospectively enrolled with informed consent from October 2020 to July 2021. Blood was drawn and separated into whole blood and plasma. Both specimen types were subjected to nucleic acid extraction and PCR targeting the V1-V3 region of the 16S ribosomal RNA gene, followed by next-generation sequencing on an Illumina MiSeqTM platform. 35 subjects, 28 (80%) with definite and 7 (20%) with possible IE were enrolled, including 6 (17%) with blood culture-negative endocarditis (BCNE). Overall, 20 whole blood (59%) and 16 plasma (47%) samples tested positive (P = 0.47). When results of whole blood and plasma testing were combined, a positive tMGS result was found in 23 subjects (66%). tMGS identified a potential pathogen in 5 of 6 culture-negative IE cases. Although further study is needed, the results of this pilot study suggest that blood-based tMGS may provide pathogen identification in subjects with IE, including in culture-negative cases.}, } @article {pmid36040144, year = {2022}, author = {Huang, Y and Yu, Z and Liu, L and Che, Y and Zhang, T}, title = {Acesulfame Anoxic Biodegradation Coupled to Nitrate Reduction by Enriched Consortia and Isolated Shinella spp.}, journal = {Environmental science & technology}, volume = {56}, number = {18}, pages = {13096-13106}, doi = {10.1021/acs.est.2c03656}, pmid = {36040144}, issn = {1520-5851}, mesh = {Biodegradation, Environmental ; Carbon ; *Environmental Pollutants ; *Nitrates ; Sweetening Agents ; Thiazines ; }, abstract = {Acesulfame (ACE) is considered to be an emerging pollutant associated with growing concerns. Although aerobic biodegradation of ACE has been observed in wastewater treatment plants worldwide and verified in pure cultures, limited information is available on ACE biodegradation under anoxic conditions, which are ubiquitous in natural environments. Here, we found that ACE could be mineralized completely via a process coupled with nitrate reduction by enriched consortia, with the highest degradation rate of 9.95 mg ACE/g VSS·h[-1]. Meanwhile, three novel ACE-degrading strains affiliated with Shinella were isolated, examined, and sequenced, revealing that the isolates could utilize ACE as the sole carbon source under both aerobic and anoxic conditions, with maximum degradation rates of 30.3 mg ACE/g VSS·h[-1] and 8.92 mg ACE/g VSS·h[-1], respectively. Additionally, the biodegradation of ACE was suspected to be a plasmid-mediated process based on comparative genomic analysis. In ACE-degrading consortia, 83 near-complete metagenome-assembled genomes (MAGs) were obtained via Illumina and Nanopore sequencing, showing that Proteobacteria and Bacteroidetes were the dominant phyla. Moreover, nine MAGs affiliated with Hyphomicrobiales were proposed to be the major ACE degraders in the enrichments. This study demonstrated that ACE could be degraded under anoxic conditions, providing novel insights into ACE biodegradation in the environment.}, } @article {pmid36039907, year = {2023}, author = {Wang, R and Sun, R and Zhang, Z and Vannini, C and Di Giuseppe, G and Liang, A}, title = {"Candidatus Euplotechlamydia quinta," a novel chlamydia-like bacterium hosted by the ciliate Euplotes octocarinatus (Ciliophora, Spirotrichea).}, journal = {The Journal of eukaryotic microbiology}, volume = {70}, number = {2}, pages = {e12945}, doi = {10.1111/jeu.12945}, pmid = {36039907}, issn = {1550-7408}, mesh = {Phylogeny ; *Euplotes/genetics ; RNA, Ribosomal, 16S/genetics ; Bacteria/genetics ; *Chlamydia/genetics ; *Ciliophora/genetics ; Symbiosis ; Sequence Analysis, DNA ; }, abstract = {Our knowledge of ciliate endosymbiont diversity greatly expanded over the past decades due to the development of characterization methods for uncultivable bacteria. Chlamydia-like bacteria have been described as symbionts of free-living amoebae and other phylogenetically diverse eukaryotic hosts. In the present work, a systematic survey of the bacterial diversity associated with the ciliate Euplotes octocarinatus strain Zam5b-1 was performed, using metagenomic screening as well as classical full-cycle rRNA approach, and a novel chlamydial symbiont was characterized. The metagenomic screening revealed 16S rRNA gene sequences from Polynucleobacter necessarius, three previously reported accessory symbionts, and a novel chlamydia-like bacterium. Following the full-cycle rRNA approach, we obtained the full-length 16S rRNA gene sequence of this chlamydia-like bacterium and developed probes for diagnostic fluorescence in situ hybridizations. The phylogenetic analysis of the 16S rRNA gene sequences unambiguously places the new bacterium in the family Rhabdochlamydiaceae. This is the first report of chlamydia-like bacterium being found in Euplotes. Based on the obtained data, the bacterium is proposed as a new candidate genus and species: "Candidatus Euplotechlamydia quinta."}, } @article {pmid36039833, year = {2022}, author = {Hosainzadegan, H and Parvan, R and Hosainzadegan, M}, title = {A retrospective study comparing oral health in cancer patients and healthy people.}, journal = {European journal of translational myology}, volume = {32}, number = {4}, pages = {}, pmid = {36039833}, issn = {2037-7452}, abstract = {The purpose of this study was to investigate the relationship between oral and dental health in cancer patients and control group, which was conducted in Tabriz Shahid Gazi hospital. A researchers-made and validated questionnaire including oral and dental health criteria, was filled by the cancer patients (201 cases) and healthy controls (199 cases). Then, the results of the study were analyzed by SPSS software, and reported as Odds ratios (95 % confidence intervals) in tow groups. The results indicate that comparison of filled tooth, tooth extraction, dental caries, and gingival problems including bleeding, gum surgery and inflammation in cancer and controls were significantly meaningful. However, the comparison between the two groups was not significant in terms of the type of the tooth (natural or denture) and the number of daily toothbrushes, but they were considered as risk factors due to statistical results. Environmental factors, and especially oral hygiene, can play an important role in the incidence of different cancers. Among these, the type of oral microorganisms, and their overgrowth and released antigens should be studied further in the emergence of different kinds of cancer in humans.}, } @article {pmid36039582, year = {2022}, author = {Guo, C and Zhang, G and Hu, X and Xu, D and Tang, B and Zhang, H and Tang, M and Liu, S and Li, Y and Gao, Q}, title = {Diagnostic efficiency of metagenomic next-generation sequencing on spinal infection and prognosis.}, journal = {Zhong nan da xue xue bao. Yi xue ban = Journal of Central South University. Medical sciences}, volume = {47}, number = {7}, pages = {865-871}, doi = {10.11817/j.issn.1672-7347.2022.220163}, pmid = {36039582}, issn = {1672-7347}, support = {82072460 and 82170901//the National Natural Science Foundation/ ; 2020JJ4892 and 2020JJ4808//the Natural Science Foundation of Hunan Province/ ; }, mesh = {*Anti-Bacterial Agents/therapeutic use ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Prognosis ; Retrospective Studies ; Sensitivity and Specificity ; }, abstract = {OBJECTIVES: Spinal infection is a rare infectious disease that is difficult to treat. The incidence of spinal infection is on the rise with the experiential use of antibiotics, the increasing incidence of drug-resistant bacteria, and the improvement of detection techniques. Traditional detection methods have limitations such as low sensitivity and long time-consuming in the diagnosis of spinal infection. In the clinical diagnosis and treatment of spinal infection, it has always been the focus and difficulty to determine the type of pathogens and to use antibiotics in a targeted manner. Many patients in the early stage of spinal infection due to the limitations of traditional detection methods cannot be quickly and accurately diagnosed, resulting in diagnosis delay, missed the best treatment time, bringing disastrous consequences to patients. There is an urgent need for a high-specificity, high-sensitivity, and time-saving test technique in clinical practice, which can simultaneously distinguish and identify the pathogen of spinal infection. Metagenomic next-generation sequencing (mNGS) is a new frontier technology emerging in recent years. It can detect all known pathogens in samples and has been used to diagnose clinically atypical and rare infectious diseases. This study aims to analyze the sensitivity of mNGS technique in diagnosing pathogens after spinal infection and its effect on prognosis.

METHODS: Clinical data of 82 patients with spinal infection admitted to Xiangya Hospital of Central South University from January 2019 to December 2021 were retrospectively analyzed. Peripheral blood erythrocyte sedimentation rate (ESR), C-reactive protein (CRP), and procalcitonin (PCT) were routinely performed before surgery, and focal tissue specimens were obtained during surgery. Microbial culture, histopathological examination, and mNGS detection were performed. All patients were assigned into a targeted medication group (n=71) and an experienced treatment group (n=1) based on the results of mNGS. After regular follow-up, the sensitivity of mNGS to detect pathogens of spinal infection and its effect on prognosis were evaluated.

RESULTS: The positive rate of mNGS (86.59%, 71/82) was significantly higher than that of microbial culture (18.99%, 15/79) and PCT (30.23%, 13/43). There were no significant differences in preoperative temperature, white blood cell count, neutrophil ratio, and scores of Visual Analogue Scale between the targeted medication group and the experienced treatment group. Preoperative use of antibiotics had no significant effect on the positive rate of mNGS and microbial culture (P=0.681). According to the targeted medication group, postoperative CRP and ESR showed a decreasing trend, and the ESR was significantly lower than that of the experienced treatment group at 30 days follow-up (P=0.044).

CONCLUSIONS: Compared with the microbial culture or PCT, mNGS has a higher sensitivity rate to detect pathogens of spinal infection. Patients receiving targeted antibiotics based on the results of mNGS have better outcomes than those receiving the experienced medicine.}, } @article {pmid36039321, year = {2022}, author = {Gambushe, SM and Zishiri, OT and El Zowalaty, ME}, title = {Review of Escherichia coli O157:H7 Prevalence, Pathogenicity, Heavy Metal and Antimicrobial Resistance, African Perspective.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {4645-4673}, pmid = {36039321}, issn = {1178-6973}, abstract = {Escherichia coli O157:H7 is an important food-borne and water-borne pathogen that causes hemorrhagic colitis and the hemolytic-uremic syndrome in humans and may cause serious morbidity and large outbreaks worldwide. People with bloody diarrhea have an increased risk of developing serious complications such as acute renal failure and neurological damage. The hemolytic-uremic syndrome (HUS) is a serious condition, and up to 50% of HUS patients can develop long-term renal dysfunction or blood pressure-related complications. Children aged two to six years have an increased risk of developing HUS. Clinical enteropathogenic Escherichia coli (EPEC) infections show fever, vomiting, and diarrhea. The EPEC reservoir is unknown but is suggested to be an asymptomatic or symptomatic child or an asymptomatic adult carrier. Spreading is often through the fecal-oral route. The prevalence of EPEC in infants is low, and EPEC is highly contagious in children. EPEC disease in children tends to be clinically more severe than other diarrheal infections. Some children experience persistent diarrhea that lasts for more than 14 days. Enterotoxigenic Escherichia coli (ETEC) strains are a compelling cause of the problem of diarrheal disease. ETEC strains are a global concern as the bacteria are the leading cause of acute watery diarrhea in children and the leading cause of traveler's diarrhea. It is contagious to children and can cause chronic diarrhea that can affect the development and well-being of children. Infections with diarrheagenic E. coli are more common in African countries. Antimicrobial agents should be avoided in the acute phase of the disease since studies showed that antimicrobial agents may increase the risk of HUS in children. The South African National Veterinary Surveillance and Monitoring Programme for Resistance to Antimicrobial Drugs has reported increased antimicrobial resistance in E. coli. Pathogenic bacterial strains have developed resistance to a variety of antimicrobial agents due to antimicrobial misuse. The induced heavy metal tolerance may also enhance antimicrobial resistance. The prevalence of antimicrobial resistance depends on the type of the antimicrobial agent, bacterial strain, dose, time, and mode of administration. Developing countries are severely affected by increased resistance to antimicrobial agents due to poverty, lack of proper hygiene, and clean water, which can lead to bacterial infections with limited treatment options due to resistance.}, } @article {pmid36039320, year = {2022}, author = {Sekizuka, T and Itokawa, K and Tanaka, R and Hashino, M and Yatsu, K and Kuroda, M}, title = {Metagenomic Analysis of Urban Wastewater Treatment Plant Effluents in Tokyo.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {4763-4777}, pmid = {36039320}, issn = {1178-6973}, abstract = {PURPOSE: Urban wastewater treatment plant (WWTP) effluents, even with proper treatment, may cause antimicrobial resistance (AMR) burden, with a high frequency of acquired antimicrobial resistance genes (ARGs). The dissemination of ARGs into the environment increases the risk of infectious diseases; however, there is little direct evidence regarding their epidemiological effects. This study aimed to assess effluents from urban WWTPs around the Tama River and Tokyo Bay using metagenomic analysis of (AMR) genes (ARGs) and heavy-metal resistance genes.

METHODS: Metagenomic DNA-seq analysis of water samples and resistome analysis were performed.

RESULTS: The most prevalent ARG was the sulfonamide resistance gene, sul1, followed by the quaternary ammonium compound resistance gene, qacE, suggesting that basic gene sets (sul1 and ∆qacE) in the class 1 integrons are the predominant ARGs. The aminoglycoside resistance genes, aadA and aph, and macrolide resistance genes, msr(E) and mph(E), were the predominant ARGs against each antimicrobial. bla OXA and bla GES were frequently detected, whereas the bla CTX-M cluster was faintly detected. Non-metric multidimensional scaling plot analysis and canonical correspondence analysis results suggested that marked differences in ARGs could be involved in the seasonal differences; qnrS2, aac(6')-Ib, and mef(C) increased markedly in summer, whereas msr(E) was more frequently detected in winter. Heavy-metal (Hg and Cu) resistance genes (HMRGs) were significantly detected in effluents from all WWTPs.

CONCLUSION: We characterized a baseline level of the environmental ARG/HMRG profile in the overall community, suggesting that environmental AMR surveillance, particularly in urban WWTPs, is a valuable first step in monitoring the AMR dissemination of bacteria from predominantly healthy individuals carrying notable ARG/Bs.}, } @article {pmid36038303, year = {2022}, author = {Xie, G and Chen, JH and Sun, LF and Wang, W and Li, ZC and Wang, WJ}, title = {[Clinical analysis of 7 children infected with Talaromyces marneffei].}, journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics}, volume = {60}, number = {9}, pages = {925-929}, doi = {10.3760/cma.j.cn112140-20220331-00260}, pmid = {36038303}, issn = {0578-1310}, support = {SZXK032//Shenzhen Key Medical Discipline Construction Fund/ ; }, mesh = {*Amphotericin B/therapeutic use ; Antifungal Agents/therapeutic use ; Child ; Child, Preschool ; Cough ; Female ; Fever ; Humans ; Infant ; *Itraconazole/therapeutic use ; Male ; Mycoses ; Retrospective Studies ; Talaromyces ; Voriconazole ; }, abstract = {Objective: To investigate the clinical manifestations, treatments, and prognosis of pediatric patients with Talaromyces marneffei infection. Methods: In this retrospective study, 7 children diagnosed with Talaromyces marneffei infection in Shenzhen Children's Hospital from July 2017 to October 2021 were recruited. The clinical features, radiology, pathogen detection, immunological evaluation, treatments, and prognosis were analyzed. Results: In 7 cases, 5 were male, 2 were females. The age was from 0.75 to 8.75 years. The main clinical manifestations were fever in 7 cases, cough in 6 cases, malnutrition in 4 cases, papules in 2 cases and medical history of recurrent infection in 3 cases. Physical examination showed that all 7 patients had hepatosplenomegaly, 4 had superficial lymphadenopathy. Laboratory examination showed that 6 cases had decreased hemoglobin and 3 cases had decreased platelet. Chest CT showed that 4 cases had patchy shadows, pleural effusion, mediastinal or axillary lymph node enlargement, 3 had nodular shadows and 2 had cavities. The positive ratio of Talaromyces marneffei culture was 2/2 with tissue samples, 4/5 with bone marrow. The positive ratio was 3/4 by metagenomic next generation sequencing. The fungus was detected in 3 cases by smear microscopy of bone marrow and (or) peripheral blood. All patients were negative for human immunodeficiency virus by the immune function assay. However, 5 cases were confirmed as primary immunodeficiency disease, including 2 cases with high IgM syndrome, 2 with STAT1 gene variation, and the last with severe combined immunodeficiency (IL2RG gene variation). Exclude 1 case which gave up treatment due to acute intracranial infection, and the other patients received effective treatments along with amphotericin B, voriconazole, and itraconazole alone or in combination. Two cases relapsed after medication withdrawal, but 1 case got complete rehabilitation after hematopoietic stem cell transplantation. Conclusions: The clinical manifestations involve multisystem, the common charateristics are fever and cough. The chest CT imaging manifestations are diverse, it should be considered in differentiating tuberculosis. The amphotericin B, voriconazole and itraconazole are effective, but it will easily relapse when withdrawing those antifungal agents.}, } @article {pmid36037841, year = {2022}, author = {Zhang, Q and Zhao, L and Zhang, J and Liu, W and Cai, S and Chen, L and Cai, T and Ji, XM}, title = {Nitrogen contribution and microbial community of size-fractionated anammox sludge in continuous stirred-tank reactors.}, journal = {Bioresource technology}, volume = {362}, number = {}, pages = {127857}, doi = {10.1016/j.biortech.2022.127857}, pmid = {36037841}, issn = {1873-2976}, mesh = {Anaerobic Ammonia Oxidation ; Anaerobiosis ; Bioreactors ; Denitrification ; *Microbiota ; Nitrogen ; Oxidation-Reduction ; *Sewage ; }, abstract = {In this study, the microbial diversity of size-fractionated anammox sludge in a well-mixed system and their contribution to nitrogen transformation were investigated. Results showed that small granules (0.2-1.0 mm) contributed to the major part of the nitrogen removal rate (56 %) due to its largest mixed liquor volatile suspended solids (1240 ± 80 mg·L[-1]). However, large granules (>1.0 mm) possessed the highest relative abundances of Ca. Kuenenia stuttgartiensis and specific anammox activity, representing 49.34 % and 24.45 ± 0.01 mg-N·g[-1]-mixed liquor volatile suspended solids·h[-1], respectively. The microbial diversity decreased as the increase of granular size, resulting in microbial community shifting to a simpler model. Metagenomic analysis showed that fine sludge might be the potential major for NO/N2O production in the mature well-mixed system under inorganic conditions. This study provides guidance for the evaluation of nitrogen contribution by anammox size-fractionated sludge and the inhibition of the potential NO/N2O emission in anammox processes.}, } @article {pmid36036910, year = {2022}, author = {Chang, CJ and Somohano, K and Zemsky, C and Uhlemann, AC and Liebmann, J and Cioffi, GA and Al-Aswad, LA and Lynch, SV and Winn, BJ}, title = {Topical Glaucoma Therapy Is Associated With Alterations of the Ocular Surface Microbiome.}, journal = {Investigative ophthalmology & visual science}, volume = {63}, number = {9}, pages = {32}, pmid = {36036910}, issn = {1552-5783}, support = {P30 EY002162/EY/NEI NIH HHS/United States ; }, mesh = {Antihypertensive Agents/therapeutic use ; *Dry Eye Syndromes/drug therapy/metabolism ; *Glaucoma/drug therapy/metabolism ; Humans ; *Microbiota ; Ophthalmic Solutions/therapeutic use ; RNA, Ribosomal, 16S/genetics/metabolism ; Tears/metabolism ; }, abstract = {PURPOSE: To investigate the ocular surface microbiome of patients with unilateral or asymmetric glaucoma being treated with topical ophthalmic medications in one eye and to determine whether microbial community changes were related to measures of ocular surface disease.

METHODS: V3-V4 16S rRNA sequencing was conducted on ocular surface swabs collected from both eyes of 17 subjects: 10 patients with asymmetric/unilateral glaucoma using topical glaucoma therapy on only one eye and seven age-matched, healthy controls with no history of ocular disease or eyedrop use. Samples were categorized into three groups: patients' glaucomatous eye treated with eyedrops, patients' contralateral eye without eyedrops, and healthy control eyes. Comparisons were made for microbial diversity and composition, with differences in composition tested for association with ocular surface disease measures including tear meniscus height, tear break-up time, and Dry Eye Questionnaire.

RESULTS: Samples obtained from the patients' treated and untreated eyes both had significantly greater alpha-diversity and relative abundance of gram-negative organisms compared to healthy controls. The microbial composition of patient eyes was associated with decreased tear meniscus height and tear break-up time, whereas metagenomic predictions, based on 16S rRNA data, suggested increased synthesis of lipopolysaccharide.

CONCLUSIONS: The ocular surface microbiome of patients taking unilateral preserved glaucoma drops is characterized by a highly diverse array of gram-negative bacteria that is significantly different from the predominantly gram-positive microbes detected on healthy control eyes. These compositional differences were associated with decreased tear film measures and distinct inferred protein synthesis pathways, suggesting a potential link between microbial alterations and ocular surface inflammation.}, } @article {pmid36036626, year = {2022}, author = {Li, C and Tang, M and Li, X and Zhou, X}, title = {Community Dynamics in Structure and Function of Honey Bee Gut Bacteria in Response to Winter Dietary Shift.}, journal = {mBio}, volume = {13}, number = {5}, pages = {e0113122}, pmid = {36036626}, issn = {2150-7511}, mesh = {Bees ; Animals ; *Gastrointestinal Microbiome/physiology ; Seasons ; Tryptophan ; Bacteria/genetics ; Diet ; Ethanol ; Phenylalanine ; Lactates ; Pyruvates ; }, abstract = {Temperate honey bees (Apis mellifera) are challenged by low temperatures and abrupt dietary shifts associated with behavioral changes during winter. Case studies have revealed drastic turnover in the gut microbiota of winter bees, highlighted by the seasonal dominance of a non-core bacterium Bartonella. However, neither biological consequence nor underlying mechanism of this microbial turnover is clear. In particular, we ask whether such changes in gut profile are related to winter dietary shift and possibly beneficial to host and associated gut microbiome? Here, we integrated evidences from genomics, metagenomics, and metabolomics in three honey bee subspecies maintained at the same locality of northern China to profile both diversity and functional variations in gut bacteria across seasons. Our results showed that winter dominance of Bartonella was shared in all tested honey bee lineages. This seasonal change was likely a consequence of winter dietary shifts characterized by greatly reduced pollen consumption and accumulation of metabolic waste due to restricted excretion. Bartonella showed expanded genomic capacity in utilizing more diverse energy substrates, such as converting metabolic wastes lactate and ethanol into pyruvate, an energy source for self-utilization and possibly also for host and other symbionts. Furthermore, Bartonella was the only bacterium capable of both producing and secreting tryptophan and phenylalanine, whose metabolic products were detected in bee guts, even though all gut bacteria lacked relevant digestion enzymes. These results thus suggested a possible mechanism where the gut bacteria might benefit the host by supplementing them with essential amino acids lacking in a protein shortage diet. IMPORTANCE The abilities to survive winter and to adapt to major food changes are key traits that have enabled successful range expansion of the honey bees from the tropic to temperate climate. Our results highlighted a new possibility that gut bacteria may have played an important role in host survival of the severe winter condition. The non-core bacterium Bartonella is not only more adaptive to the winter diet but is also equipped with the capacity to provide the host with essential nutrients and important metabolic substrates. This overall host-bacterium profile is probably favored by natural selection, resulting in a consistent winter gut strategy across varied honey bee lineages. Conversely, when the hosts start to forage again, core bacteria maintained at low abundance during winter returned to their typical dominant status, thus completing the annual gut turnover. Our study suggests a new hypothesis where seasonal gut variations may improve the fitness of the honey bee, allowing them to explore more diverse climates.}, } @article {pmid36036594, year = {2022}, author = {Brown, CL and Mullet, J and Hindi, F and Stoll, JE and Gupta, S and Choi, M and Keenum, I and Vikesland, P and Pruden, A and Zhang, L}, title = {mobileOG-db: a Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {18}, pages = {e0099122}, pmid = {36036594}, issn = {1098-5336}, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Computational Biology/methods ; *DNA Transposable Elements ; Plasmids/genetics ; }, abstract = {Bacterial mobile genetic elements (MGEs) encode functional modules that perform both core and accessory functions for the element, the latter of which are often only transiently associated with the element. The presence of these accessory genes, which are often close homologs to primarily immobile genes, incur high rates of false positives and, therefore, limits the usability of these databases for MGE annotation. To overcome this limitation, we analyzed 10,776,849 protein sequences derived from eight MGE databases to compile a comprehensive set of 6,140 manually curated protein families that are linked to the "life cycle" (integration/excision, replication/recombination/repair, transfer, stability/transfer/defense, and phage-specific processes) of plasmids, phages, integrative, transposable, and conjugative elements. We overlay experimental information where available to create a tiered annotation scheme of high-quality annotations and annotations inferred exclusively through bioinformatic evidence. We additionally provide an MGE-class label for each entry (e.g., plasmid or integrative element), and assign to each entry a major and minor category. The resulting database, mobileOG-db (for mobile orthologous groups), comprises over 700,000 deduplicated sequences encompassing five major mobileOG categories and more than 50 minor categories, providing a structured language and interpretable basis for an array of MGE-centered analyses. mobileOG-db can be accessed at mobileogdb.flsi.cloud.vt.edu/, where users can select, refine, and analyze custom subsets of the dynamic mobilome. IMPORTANCE The analysis of bacterial mobile genetic elements (MGEs) in genomic data is a critical step toward profiling the root causes of antibiotic resistance, phenotypic or metabolic diversity, and the evolution of bacterial genera. Existing methods for MGE annotation pose high barriers of biological and computational expertise to properly harness. To bridge this gap, we systematically analyzed 10,776,849 proteins derived from eight databases of MGEs to identify 6,140 MGE protein families that can serve as candidate hallmarks, i.e., proteins that can be used as "signatures" of MGEs to aid annotation. The resulting resource, mobileOG-db, provides a multilevel classification scheme that encompasses plasmid, phage, integrative, and transposable element protein families categorized into five major mobileOG categories and more than 50 minor categories. mobileOG-db thus provides a rich resource for simple and intuitive element annotation that can be integrated seamlessly into existing MGE detection pipelines and colocalization analyses.}, } @article {pmid36036588, year = {2022}, author = {Ettinger, CL and Lovett, B and Kasson, MT and Stajich, JE}, title = {Metagenome-Assembled Genomes of Bacteria Associated with Massospora cicadina Fungal Plugs from Infected Brood VIII Periodical Cicadas.}, journal = {Microbiology resource announcements}, volume = {11}, number = {10}, pages = {e0041322}, pmid = {36036588}, issn = {2576-098X}, support = {S10 OD016290/OD/NIH HHS/United States ; //Canadian Institute for Advanced Research (ICRA)/ ; S10-OD016290//HHS | NIH | NIH Office of the Director (OD)/ ; DEB-1441715//National Science Foundation (NSF)/ ; CA-R-PPA-211-5062-H//U.S. Department of Agriculture (USDA)/ ; }, abstract = {We report six metagenome-assembled genomes (MAGs) associated with Massospora cicadina strain MCPNR19 (ARSEF 14555), an obligate entomopathogenic fungus of periodical cicadas. The MAGs include representatives of Pantoea, Pseudomonas, Lactococcus, and one potential new Chryseobacterium species. Future research is needed to resolve the ecology of these MAGs and determine whether they represent symbionts or contaminants.}, } @article {pmid36036584, year = {2022}, author = {Liu, H and Liang, H and Li, D and Wang, M and Li, Y}, title = {Association of Cervical Dysbacteriosis, HPV Oncogene Expression, and Cervical Lesion Progression.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0015122}, pmid = {36036584}, issn = {2165-0497}, mesh = {Female ; Humans ; Papillomaviridae/genetics ; *Uterine Cervical Neoplasms/epidemiology/pathology ; *Papillomavirus Infections/complications/genetics/epidemiology ; *Alphapapillomavirus ; *Oncogene Proteins, Viral/genetics ; Dysbiosis ; Papillomavirus E7 Proteins/genetics ; Oncogenes ; *Uterine Cervical Dysplasia/epidemiology/pathology ; }, abstract = {As the fourth most common gynecological cancer, cervical cancer has resulted in more than 300,000 deaths worldwide in 2020. The expression of the human papillomavirus (HPV) oncogenes E6 and E7 is significantly involved in the initiation and progression of cervical neoplasia. Additionally, the composition of the vaginal microbiome was also closely associated with the ability of HPV to induce cervical cancer. However, the relationship between the expression of HPV E6/E7 oncogene and the composition of the vaginal microbiome has not been clearly explored. In our present study, to investigate the relationship between the HPV E6/E7 oncogene and vaginal microbiome, cervical swabs from 115 patients were collected, and their vaginal microbiomes were analyzed by using metagenomics sequencing. Along with the progression of cervical lesions, the diversity of cervical flora increased gradually, and the abundance of Lactobacillus decreased. Compared with the HPV group, the prevalence of HPV E6/E7 and oncogene expression level were significantly upregulated in cervical intraepithelial neoplasia (CIN) and cervical cancer (CC) groups. Additionally, a positive correlation between the expression of the HPV oncogene and the genera Sneathia, Salmonella, Leptotrichia, Pseudomonas, and Roseovarius in the HPV group was observed. In the CIN group, the enrichment of the genera Sneathia and Megasphaera was weakly linked with HPV oncogene overexpression. In the CC group, a strong association between the overabundance of the genera Peptostreptococcus and Enterococcus and the high expression of HPV oncogene was also found. The increased diversity of the vaginal microbiota and the decreased Lactobacillus abundance were significantly associated with the severity of cervical disease, and the expression of the HPV oncogene could also be regulated by certain pathogens in different stages of cervical lesions. IMPORTANCE The main findings of this study were that we clarified the associations of the different bacterial species with the expression of human papillomavirus (HPV) oncogenes at different stages of cervical cancer. Along with the severity of cervical lesions, the abundance of the genus and species of Lactobacillus obviously declined, while the aerobic and anaerobic bacteria, as well as the prevalence and expression of HPV E6/E7 oncogene, were increased dramatically.}, } @article {pmid36036576, year = {2022}, author = {Tucker, K and Mageiros, L and Carstens, A and Bröcker, L and Archer, E and Smith, K and Mourkas, E and Pascoe, B and Nel, D and Meric, G and Sheppard, SK and Kasprzyk-Hordern, B and Botes, M and Feil, EJ and Wolfaardt, G}, title = {Spatiotemporal Investigation of Antibiotic Resistance in the Urban Water Cycle Influenced by Environmental and Anthropogenic Activity.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0247322}, pmid = {36036576}, issn = {2165-0497}, mesh = {*Drug Resistance, Bacterial ; Wastewater ; Sewage ; Water Cycle ; Colistin ; Angiotensin Receptor Antagonists ; Anthropogenic Effects ; Angiotensin-Converting Enzyme Inhibitors ; Anti-Bacterial Agents/pharmacology ; Carbapenems ; *Anti-Infective Agents/pharmacology ; Gentamicins ; Sulfamethoxazole ; }, abstract = {With increasing emergence of antimicrobial resistant bacteria (ARB) and the risk this poses to public health, there are growing concerns regarding water pollution contributing to the spread of antimicrobial resistance (AMR) through inadequate amenities and the rapid rate of urbanization. In this study, the impact of different anthropogenic factors on the prevalence of AMR in the urban water cycle in Stellenbosch, South Africa (SA) was examined. Carbapenem, colistin, gentamicin and sulfamethoxazole resistant Gram-negative bacteria were recovered by selectively culturing aqueous, biofilm and sediment samples from sites impacted to varying degrees by informal settlements, residential, industrial, and agricultural activities, as well as a municipal wastewater treatment works (WWTW). A metagenomic approach determined community profiles and dominant AMR genes at various sites, while carbapenem resistant colonies were characterized using whole genome sequencing (WGS). Isolates recovered from agricultural sites exhibited relatively high levels of resistance to carbapenems and colistin, whereas sites impacted by domestic run-off had a higher prevalence of resistance to gentamicin and sulfamethoxazole, corresponding to usage data in SA. Similar microbial taxa were identified in raw sewage, sites downstream of informal settlements, and industrial areas that have limited waste removal infrastructure while WWTW were seen to reduce the prevalence of ARB in treated wastewater when operating efficiently. The results indicate the multiple complex drivers underpinning environmental dissemination of AMR and suggest that WWTW assist in removing AMR from the environment, reinforcing the necessity of adequate waste removal infrastructure and antibiotic stewardship measures to mitigate AMR transmission. IMPORTANCE The results from this study are of importance as they fill a gap in the data available on environmental AMR in South Africa to date. This study was done in parallel with co-investigators focusing on the prevalence of various antimicrobials at the same sites selected in our study, verifying that the sites that are influenced by informal settlements and WWTW influent had higher concentrations of antimicrobials and antimicrobial metabolites. The various locations of the sample sites selected, the frequency of the samples collected over a year, and the different types of samples collected at each site all contribute to informing how AMR in the environment might be affected by anthropogenic activity.}, } @article {pmid36036503, year = {2022}, author = {Reji, L and Zhang, X}, title = {Genome-Resolved Metagenomics Informs the Functional Ecology of Uncultured Acidobacteria in Redox Oscillated Sphagnum Peat.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0005522}, pmid = {36036503}, issn = {2379-5077}, mesh = {*Acidobacteria/genetics ; Ecosystem ; *Sphagnopsida/genetics ; Phylogeny ; Soil Microbiology ; Soil/chemistry ; Oxidation-Reduction ; Carbohydrates ; Carbon/metabolism ; }, abstract = {Understanding microbial niche differentiation along ecological and geochemical gradients is critical for assessing the mechanisms of ecosystem response to hydrologic variation and other aspects of global change. The lineage-specific biogeochemical roles of the widespread phylum Acidobacteria in hydrologically sensitive ecosystems, such as peatlands, are poorly understood. Here, we demonstrate that Acidobacteria sublineages in Sphagnum peat respond differentially to redox fluctuations due to variable oxygen (O2) availability, a typical feature of hydrologic variation. Our genome-centric approach disentangles the mechanisms of niche differentiation between the Acidobacteria genera Holophaga and Terracidiphilus in response to the transient O2 exposure of peat in laboratory incubations. Interlineage functional diversification explains the enrichment of the otherwise rare Holophaga in anoxic peat after transient O2 exposure in comparison to Terracidiphilus dominance in continuously anoxic peat. The observed niche differentiation of the two lineages is linked to differences in their carbon degradation potential. Holophaga appear to be primarily reliant on carbohydrate oligomers and amino acids, produced during the prior period of O2 exposure via the O2-stimulated breakdown of peat carbon, rich in complex aromatics and carbohydrate polymers. In contrast, Terracidiphilus genomes are enriched in diverse respiratory hydrogenases and carbohydrate active enzymes, enabling the degradation of complex plant polysaccharides into monomers and oligomers for fermentation. We also present the first evidence for the potential contribution of Acidobacteria in peat nitrogen fixation. In addition to canonical molybdenum-based diazotrophy, the Acidobacteria genomes harbor vanadium and iron-only alternative nitrogenases. Together, the results better inform the different functional roles of Acidobacteria in peat biogeochemistry under global change. IMPORTANCE Acidobacteria are among the most widespread and abundant members of the soil bacterial community, yet their ecophysiology remains largely underexplored. In acidic peat systems, Acidobacteria are thought to perform key biogeochemical functions, yet the mechanistic links between the phylogenetic and metabolic diversity within this phylum and peat carbon transformations remain unclear. Here, we employ genomic comparisons of Acidobacteria subgroups enriched in laboratory incubations of peat under variable O2 availability to disentangle the lineage-specific functional roles of these microorganisms in peat carbon transformations. Our genome-centric approach reveals that the diversification of Acidobacteria subpopulations across transient O2 exposure is linked to differences in their carbon substrate preferences. We also identify a previously unknown functional potential for biological nitrogen fixation in these organisms. This has important implications for carbon, nitrogen, and trace metal cycling in peat systems.}, } @article {pmid36035669, year = {2022}, author = {Fu, S and Deng, Y and Zou, K and Zhang, S and Liu, X and Liang, Y}, title = {Flavonoids affect the endophytic bacterial community in Ginkgo biloba leaves with increasing altitude.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {982771}, pmid = {36035669}, issn = {1664-462X}, abstract = {Altitude affects plant growth and metabolism, but the effect of altitude on plant endophytic microorganisms is still unclear. In this study, we selected 16 Ginkgo biloba trees to study the response of leaves' endophytes to flavonoids and altitude (from 530 m to 1,310 m). HPLC results showed that flavonoids in Ginkgo biloba leaves increased by more than 150% with attitude rising from 530 m to 1,310 m, which revealed a positive correlation with altitude. Ginkgo biloba might regulate the increased flavonoids in leaves to resist the increasing light intensity. 16S rDNA sequencing results showed that the endophytic bacterial communities of Ginkgo biloba at different altitudes significantly differed. Ginkgo leaf endophytes' alpha diversity decreased with increasing flavonoids content and altitude. The increased flavonoids might increase the environmental pressure on endophytes and affect the endophytic community in Ginkgo biloba leaves. The bacterial network in Ginkgo biloba leaves became more complex with increasing altitude, which might be one of the strategies of leaf endophytes to cope with increasing flavonoids. Metagenomes results predicted with PICRUSt showed that the abundance of flavonoid biosynthesis and photosynthesis genes were significantly decreased with the increase of flavonoid contents. High flavonoid content in leaves appeared to inhibit microbial flavonoid synthesis. Our findings indicate that altitude can modulate microbial community structure through regulating plant metabolites, which is important to uncovering the interaction of microbes, host and the environment.}, } @article {pmid36034963, year = {2022}, author = {Li, W and Zhu, H and Wen, L and Quan, M and Wang, L}, title = {Application Value of Metagenomics Next-Generation Sequencing (mNGS) in Detection of Mucormycosis after Chemotherapy in Childhood Acute Leukemia.}, journal = {Evidence-based complementary and alternative medicine : eCAM}, volume = {2022}, number = {}, pages = {7366432}, pmid = {36034963}, issn = {1741-427X}, abstract = {OBJECTIVE: To analyze the application of macrogenomics next-generation sequencing (mNGS) in the detection of postchemotherapy trichomoniasis cases in children with acute leukemia.

METHODS: To retrospectively analyze the clinical data of 7 patients with acute leukemia combined with trichomoniasis after chemotherapy in the department of hematology and oncology of Hebei Children's Hospital, and to summarize the characteristics of their postchemotherapy clinical data, diagnostic and therapeutic processes, and outcomes.

RESULTS: Among the 7 children, 6 cases had acute lymphoblastic leukemia and 1 case had acute myeloid leukemia. mNGS detected trichoderma infection, including 1 case of pulmonary cerebral type and 6 cases of pulmonary type. After treatment, 1 case died, 2 cases were cured, and 4 cases improved.

CONCLUSION: The clinical manifestations of trichomoniasis after combined chemotherapy in pediatric acute leukemia lack specificity. Early application of the mNGS assay is of great value.}, } @article {pmid36034706, year = {2022}, author = {Zhao, YC and Ding, YZ and Zhao, X and Fu, GW and Huang, MJ and Li, XX and Sun, QQ and Kan, YB and Li, J and Wang, SL and Ma, WT and Xu, QF and Liu, QL and Li, HB}, title = {Role and Clinical Application of Metagenomic Next-Generation Sequencing in Immunocompromised Patients With Acute Respiratory Failure During Veno-Venous Extracorporeal Membrane Oxygenation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {877205}, pmid = {36034706}, issn = {2235-2988}, mesh = {Anti-Bacterial Agents ; *Extracorporeal Membrane Oxygenation ; High-Throughput Nucleotide Sequencing ; Humans ; Immunocompromised Host ; Metagenomics ; *Respiratory Distress Syndrome ; *Respiratory Insufficiency ; Retrospective Studies ; }, abstract = {OBJECTIVES: There are few studies of metagenomic next-generation sequencing (mNGS) in immunocompromised patients assisted by veno-venous extracorporeal membrane oxygenation (vv-ECMO). The present study is aimed to investigate the pathogen-detected effect and clinical therapy value of mNGS technologies in immunocompromised patients assisted by vv-ECMO.

METHODS: Our study retrospectively enrolled 46 immunocompromised patients supported by vv-ECMO from Jan 2017 to June 2021 at the First Affiliated Hospital of Zhengzhou University, respectively. Patients were divided into the deterioration group (Group D) (n = 31) and improvement group (Group I) (n = 15) according to their outcomes. Baseline characteristics and etiological data of patients during hospitalization of 2 groups were compared. The pathogens detected by mNGS and antibiotic regimens guided by mNGS in immunocompromised patients assisted by vv-ECMO were analyzed.

RESULTS: Compared with Group I, the deterioration patients showed a higher percentage of chronic obstructive pulmonary disease (COPD) (32.3% vs. 6.7%, p < 0.01) and were significantly older (47.77 ± 16.72 years vs. 32 ± 15.05 years, p < 0.01). Within 48 h of being ECMO assisted, the consistency of the samples detected by traditional culture and mNGS at the same time was good (traditional culture vs. mNGS detection, the positive rate of bronchoalveolar lavage fluid (BALF) culture: 26.1% vs. 30.4%; the positive rate of blood sample culture: 12.2% vs. 12.2%, p > 0.05). However, mNGS detected far more pathogen species and strains than conventional culture (30 strains vs. 78 strains, p < 0.01); the most popular pathogen was Klebsiella pneumoniae. Parts of patients had their antibiotic treatment adjustments, and the improvement patients showed less usage of broad-spectrum antibiotics.

CONCLUSIONS: mNGS may play a relatively important role in detecting mixed pathogens and personalized antibiotic treatment in immunocompromised patients assisted by vv-ECMO.}, } @article {pmid36034549, year = {2022}, author = {Zhuang, G and Yang, L and Qu, L and Liu, W and Zhu, H}, title = {Congenital tuberculosis in a neonate following in vitro fertilization-embryo transfer: A case report.}, journal = {Frontiers in pediatrics}, volume = {10}, number = {}, pages = {985707}, pmid = {36034549}, issn = {2296-2360}, abstract = {BACKGROUND: Congenital tuberculosis is becoming increasingly common, but congenital tuberculosis infection in neonates following in vitro fertilization and embryo transfer (IVF-ET) has been rarely reported; a diagnosis of congenital tuberculosis is often delayed due to the non-specificity of maternal IVF treatments and clinical manifestations during pregnancy-particularly in low-birth-weight preterm infants.

CASE PRESENTATION: We herein report a case of congenital tuberculosis. The infant was born at 27+5 weeks of gestation and was admitted to the hospital due to hypopnea after birth. Due to a poor response to treatment, we conducted pathogenic microorganism metagenomic analysis to assess the nucleotide sequences within the Mycobacterium tuberculosis complex. After collecting sputum, the strains from the tuberculosis analysis were isolated and confirmed. From a detailed examination of the mother and in accordance with the child's congenital tuberculosis, we confirmed the diagnosis of pelvic tuberculosis.

CONCLUSION: IVF treatment and pregnancy can exacerbate latent tuberculosis, especially in women from a family with a history of tuberculosis infections. We posit that the optimal way to prevent neonatal congenital tuberculosis in IVF-ET is to procure a detailed maternal medical or family history and to identify and treat maternal tuberculosis during IVF treatment.}, } @article {pmid36034530, year = {2022}, author = {Wu, LW and Chen, MY and Li, CL}, title = {Phylogenetic position and morphological polymorphism of the chafer, Clinterocera nigra (Coleoptera: Scarabaeidae: Cetoniinae) from Taiwan.}, journal = {Mitochondrial DNA. Part B, Resources}, volume = {7}, number = {8}, pages = {1513-1515}, pmid = {36034530}, issn = {2380-2359}, abstract = {Three mitochondrial genomes of the cetoniine beetle, Clinterocera nigra (Kano, 1931) were assembled via next-generation sequencing. The newly sequenced mitogenomes all have 37 genes, showing standard gene order and annotation as the other insects. To examine their phylogenetic positions and relationships between their elytral color (red-spot and melanistic forms) and sequence variation, a total of 118 public mitogenomes of Scarabaeidae were used to infer a maximum-likelihood (ML) tree. Our results show that the melanistic form is grouped within red-spot ones, revealing a population level variation on the elytra color. Our work also provides the first mitogenomic reference of myrmecophilous chafers.}, } @article {pmid36034307, year = {2022}, author = {Yao, L and Chen, S and Yu, Z and Yu, T}, title = {Multifocal brain abscesses caused by invasive Streptococcus intermedia: A case report.}, journal = {Frontiers in neurology}, volume = {13}, number = {}, pages = {893627}, pmid = {36034307}, issn = {1664-2295}, abstract = {Multifocal brain abscesses caused by invasive Streptococcus intermedia are relatively rare. Here, we present a 67-year-old male was admitted to the hospital for unconsciousness and fever. The computed tomography (CT) examination showed multiple intracranial space-occupying and "cavity-like" changes in the right lower lung. The examination of cerebrospinal fluid (CSF) was consistent with typical bacterial meningitis, CSF analyses revealed leukocytosis (10,300 × 10[6]/L), elevated protein levels (140.39 mg/dL), decreased glucose levels (0.27 mmol/L), and normal chloride concentration level (120.2 mmol/L), however, pathogens were not detected in the cultures. Then, the CSF and sputum samples were analyzed using meta-genomic next-generation sequencing (mNGS), and S. intermedia was detected in both samples. We adjusted the use of antibiotics according to the results of mNGS in time. After anti-infective treatment, the patient achieved good treatment results in a very short time. This case highlights the mNGS can identify pathogens of brain abscess, and provide strong evidence for clinical diagnosis and treatment strategy.}, } @article {pmid36034170, year = {2022}, author = {Cao, Y and Chen, J and Dong, L}, title = {Supplementary Role of Immunological Indicators in the Diagnosis and Prognosis of Pneumocystis Pneumonia in Non-HIV Immunocompromised Patients.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {4675-4683}, pmid = {36034170}, issn = {1178-6973}, abstract = {BACKGROUND: Pneumocystis pneumonia (PCP) has a high mortality in HIV-negative immunocompromised patients. The occurrence and development of PCP are believed to be correlated with the level of lymphocytes and their subsets. The aim of this study was to determine if the levels of lymphocyte subpopulations and immunoglobulin are associated with PCP.

METHODS: A total of 74 immunocompromised patients were enrolled in this single-center cohort study. Diagnosis of PCP was based on the relevant pulmonary symptoms and radiological imaging, and the detection of Pneumocystis jirovecii in BAL fluid or biopsy tissue by metagenomic next-generation sequencing (mNGS). All patients were divided into two groups (PCP group and non-PCP group) and the patients in PCP group were then divided into two groupsbased on the outcome of the disease during the hospitalization.

RESULTS: We observed a significant lower level of IgG (p=0.000) and B lymphocyte counts (p=0.017) in the PCP group comparing to that in the non-PCP group. CD4+ T cell counts, as well as the ratio of CD4+/CD8+ T cells in circulation and BAL fluid were also lower in the PCP group comparing to those in the non-PCP group. Lactate dehydrogenase (LDH) in the PCP group was significantly higher than that in the non-PCP group (p=0.029). In the PCP group, a lower level of total lymphocytes (p=0.004), T cells (p=0.001), CD4+ cells (p=0.001), and CD8+ cells (p=0.007), as well as the proportion of lymphocytes in BAL fluid (p=0.000) were found in deceased patients comparing to those in the survived group.

CONCLUSION: Our study revealed an important role of humoral immunity in the infection of Pneumocystis jirovecii. The level of B cells and IgG could be used as a supplement to predict the occurrence of PCP. The level of CD4+ and CD8+ lymphocytes was significantly correlated with the outcome of PCP.}, } @article {pmid36033894, year = {2022}, author = {Zheng, Y and Wang, Y and Yang, X and Gao, J and Xu, G and Yuan, J}, title = {Effective mechanisms of water purification for nitrogen-modified attapulgite, volcanic rock, and combined exogenous microorganisms.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {944366}, pmid = {36033894}, issn = {1664-302X}, abstract = {The study tested the water purification mechanism of the combination of microorganisms and purification materials via characteristic, enzymatic, and metagenomics methods. At 48 h, the removal rates of total nitrogen, total phosphorous, and Mn chemical oxygen demand in the combination group were 46.91, 50.93, and 65.08%, respectively. The alkaline phosphatase (AKP) activity increased during all times tested in the volcanic rock, Al@TCAP, and exogenous microorganism groups, while the organophosphorus hydrolase (OPH), dehydrogenase (DHO), and microbial nitrite reductase (NAR) activities increased at 36-48, 6-24, and 36-48 h, respectively. However, the tested activities only increased in the combination groups at 48 h. Al@TCAP exhibits a weak microbial loading capacity, and the Al@TCAP removal is primarily attributed to adsorption. The volcanic rock has a sufficient ability to load microorganisms, and the organisms primarily perform the removal for improved water quality. The predominant genera Pirellulaceae and Polynucleobacter served as the sensitive biomarkers for the treatment at 24, 36-48 h. Al@TCAP increased the expression of Planctomycetes and Actinobacteria, while volcanic rock increased and decreased the expression of Planctomycetes and Proteobacteria. The growth of Planctomycetes and the denitrification reaction were promoted by Al@TCAP and the exogenous microorganisms. The purification material addition group decreased the expression of Hyaloraphidium, Chytridiomycetes (especially Hyaloraphidium), and Monoblepharidomycetes and increased at 36-48 h, respectively. Ascomycota, Basidiomycota, and Kickxellomycota increased in group E, which enhanced the nitrogen cycle through microbial enzyme activities, and the growth of the genus Aspergillus enhanced the phosphorous purification effect.}, } @article {pmid36033893, year = {2022}, author = {Altantogtokh, D and Lilak, AA and Takhampunya, R and Sakolvaree, J and Chanarat, N and Matulis, G and Poole-Smith, BK and Boldbaatar, B and Davidson, S and Hertz, J and Bolorchimeg, B and Tsogbadrakh, N and Fiorenzano, JM and Lindroth, EJ and von Fricken, ME}, title = {Metagenomic profiles of Dermacentor tick pathogens from across Mongolia, using next generation sequencing.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {946631}, pmid = {36033893}, issn = {1664-302X}, abstract = {Tick-borne diseases are a major public health concern in Mongolia. Nomadic pastoralists, which make up ~ 26% of Mongolia's population, are at an increased risk of both tick bite exposure and economic loss associated with clinical disease in herds. This study sought to further characterize tick-borne pathogens present in Dermacentor ticks (n = 1,773) sampled in 2019 from 15 of Mongolia's 21 aimags (provinces). The ticks were morphologically identified and sorted into 377 pools which were then screened using Next-Generation Sequencing paired with confirmatory PCR and DNA sequence analysis. Rickettsia spp. were detected in 88.33% of pools, while Anaplasma spp. and Bartonella spp. were detected in 3.18 and 0.79% of pools, respectively. Khentii had the highest infection rate for Rickettsia spp. (76.61%; CI: 34.65-94.79%), while Arkhangai had the highest infection rate for Anaplasma spp. (7.79%; CI:4.04-13.72%). The exclusive detection of Anaplasma spp. in tick pools collected from livestock supports previous work in this area that suggests livestock play a significant role in disease maintenance. The detection of Anaplasma, Bartonella, and Rickettsia demonstrates a heightened risk for infection throughout Mongolia, with this study, to our knowledge, documenting the first detection of Bartonella melophagi in ticks collected in Mongolia. Further research deploying NGS methods is needed to characterize tick-borne pathogens in other endemic tick species found in Mongolia, including Hyalomma asiaticum and Ixodes persulcatus.}, } @article {pmid36033874, year = {2022}, author = {Guo, L and Ma, J and Lin, J and Chen, M and Liu, W and Zha, J and Jin, Q and Hong, H and Huang, W and Zhang, L and Zhang, K and Wei, Z and Liu, Q}, title = {Virome of Rhipicephalus ticks by metagenomic analysis in Guangdong, southern China.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {966735}, pmid = {36033874}, issn = {1664-302X}, abstract = {Tick-borne viruses (TBVs) have increasingly caused a global public health concern. This study collected Rhipicephalus ticks in Guangdong, southern China to identify RNA viruses. Meta-transcriptome analysis revealed the virome in Rhipicephalus ticks, resulting in the discovery of 10 viruses, including Lihan tick virus, Brown dog tick phlebovirus 1 and 2 in the family Phenuiviridae, Mivirus and Wuhan tick virus 2 in the family Chuviridae, Wuhan tick virus 1 in the family Rhabdoviridae, bovine hepacivirus in the family Flaviviridae, Guangdong tick quaranjavirus (GTQV) in the family Orthomyxoviridae, Guangdong tick orbivirus (GTOV) in the family Reoviridae, and Guangdong tick Manly virus (GTMV) of an unclassified family. Phylogenetic analysis showed that most of these TBVs were genetically related to the strains in countries outside China, and GTQV, GTOV, and GTMV may represent novel viral species. These findings provided evidence of the long-distance spread of these TBVs in Guangdong, southern China, suggesting the necessity and importance of TBV surveillance.}, } @article {pmid36033852, year = {2022}, author = {Cheng, YI and Lin, YC and Leu, JY and Kuo, CH and Chu, HA}, title = {Comparative analysis reveals distinctive genomic features of Taiwan hot-spring cyanobacterium Thermosynechococcus sp. TA-1.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {932840}, pmid = {36033852}, issn = {1664-302X}, abstract = {Thermosynechococcus is a genus of thermophilic unicellular cyanobacteria that dominates microbial mats in Asian non-acidic hot springs. These cyanobacteria are the major primary producers in their ecological niches and are promising sources of thermostable enzymes for biotechnology applications. To improve our understanding of these organisms, we conducted whole-genome sequencing of a novel strain for comparative analysis with other representatives in the same genus. This newly characterized strain, Thermosynechococcus sp. TA-1, was isolated from the Taian hot springs in Taiwan. Analyses based on average nucleotide identity (ANI) and genome-scale phylogeny suggested that TA-1 and another Taiwanese strain CL-1 belong to a novel species-level taxon. Two metagenome-assembled genomes (MAGs) originated from India represent the sister group, and Thermosynechococcus elongatus PKUAC-SCTE542 from China is the next closest lineage. All cultivated strains and MAGs from Japan form a separate monophyletic clade and could be classified into two species-level taxa. Intriguingly, although TA-1 and CL-1 share 97.0% ANI, the genome alignment identified at least 16 synteny breakpoints that are mostly associated with transposase genes, which illustrates the dynamic nature of their chromosomal evolution. Gene content comparisons identified multiple features distinct at species- or strain-level among these Thermosynechococcus representatives. Examples include genes involved in bicarbonate transportation, nitric oxide protection, urea utilization, kanamycin resistance, restriction-modification system, and chemotaxis. Moreover, we observed the insertion of type II inteins in multiple genes of the two Taiwanese strains and inferred putative horizontal transfer of an asparagine synthase gene (asnB) associated with exopolysaccharides gene cluster. Taken together, while previous work suggested that strains in this genus share a highly conserved genomic core and no clear genetic differentiation could be linked to environmental factors, we found that the overall pattern of gene content divergence is largely congruent with core genome phylogeny. However, it is difficult to distinguish between the roles of phylogenetic relatedness and geographic proximity in shaping the genetic differentiation. In conclusion, knowledge of the genomic differentiation among these strains provides valuable resources for future functional characterization.}, } @article {pmid36032686, year = {2022}, author = {Zhou, YH and Sun, G}, title = {Improve the Colorectal Cancer Diagnosis Using Gut Microbiome Data.}, journal = {Frontiers in molecular biosciences}, volume = {9}, number = {}, pages = {921945}, pmid = {36032686}, issn = {2296-889X}, abstract = {In the United States, colorectal cancer is the second largest cause of cancer death, and accurate early detection and identification of high-risk patients is a high priority. Although fecal screening tests are available, the close relationship between colorectal cancer and the gut microbiome has generated considerable interest. We describe a machine learning method for gut microbiome data to assist in diagnosing colorectal cancer. Our methodology integrates feature engineering, mediation analysis, statistical modeling, and network analysis into a novel unified pipeline. Simulation results illustrate the value of the method in comparison to existing methods. For predicting colorectal cancer in two real datasets, this pipeline showed an 8.7% higher prediction accuracy and 13% higher area under the receiver operator characteristic curve than other published work. Additionally, the approach highlights important colorectal cancer-related taxa for prioritization, such as high levels of Bacteroides fragilis, which can help elucidate disease pathology. Our algorithms and approach can be widely applied for Colorectal cancer prediction using either 16 S rRNA or shotgun metagenomics data.}, } @article {pmid36032669, year = {2022}, author = {Frolova, MS and Suvorova, IA and Iablokov, SN and Petrov, SN and Rodionov, DA}, title = {Genomic reconstruction of short-chain fatty acid production by the human gut microbiota.}, journal = {Frontiers in molecular biosciences}, volume = {9}, number = {}, pages = {949563}, pmid = {36032669}, issn = {2296-889X}, abstract = {Short-chain fatty acids (SCFAs) including acetate, formate, propionate, and butyrate are the end products of dietary fiber and host glycan fermentation by the human gut microbiota (HGM). SCFAs produced in the column are of utmost importance for host physiology and health. Butyrate and propionate improve gut health and play a key role in the neuroendocrine and immune systems. Prediction of HGM metabolic potential is important for understanding the influence of diet and HGM-produced metabolites on human health. We conducted a detailed metabolic reconstruction of pathways for the synthesis of SCFAs and L- and D-lactate, as additional fermentation products, in a reference set of 2,856 bacterial genomes representing strains of >800 known HGM species. The reconstructed butyrate and propionate pathways included four and three pathway variants, respectively, that start from different metabolic precursors. Altogether, we identified 48 metabolic enzymes, including five alternative enzymes in propionate pathways, and propagated their occurrences across all studied genomes. We established genomic signatures for reconstructed pathways and classified genomes according to their simplified binary phenotypes encoding the ability ("1") or inability ("0") of a given organism to produce SCFAs. The resulting binary phenotypes combined into a binary phenotype matrix were used to assess the SCFA synthesis potential of HGM samples from several public metagenomic studies. We report baseline and variance for Community Phenotype Indices calculated for SCFAs production capabilities in 16S metagenomic samples of intestinal microbiota from two large national cohorts (American Gut Project, UK twins), the Hadza hunter-gatherers, and the young children cohort of infants with high-risk for type 1 diabetes. We further linked the predicted SCFA metabolic capabilities with available SCFA concentrations both for in vivo fecal samples and in vitro fermentation samples from previous studies. Finally, we analyzed differential representation of individual SCFA pathway genes across several WGS metagenomic datasets. The obtained collection of SCFA pathway genes and phenotypes enables the predictive metabolic phenotype profiling of HGM datasets and enhances the in silico methodology to study cross-feeding interactions in the gut microbiomes.}, } @article {pmid36032592, year = {2022}, author = {Undru, TR and Uday, U and Lakshmi, JT and Kaliappan, A and Mallamgunta, S and Nikhat, SS and Sakthivadivel, V and Gaur, A}, title = {Integrating Artificial Intelligence for Clinical and Laboratory Diagnosis - a Review.}, journal = {Maedica}, volume = {17}, number = {2}, pages = {420-426}, pmid = {36032592}, issn = {1841-9038}, abstract = {Introduction: The development of medical artificial intelligence (AI) is related to programs intended to help clinicians formulate diagnoses, make therapeutic decisions and predict outcomes. It is bringing a paradigm shift to healthcare, powered by the increasing availability of healthcare data and rapid progress in analytical techniques (1). Artificial intelligence techniques include machine learning methods for structured data, such as classical support vector machines and neural networks, modern deep learning (DL), and natural language processing for unstructured data. Methodology:More than 50 articles were reviewed and 41 of them were shortlisted. The review was based on a literature search in PubMed, Embase, Google Scholar, and Scopus databases. Review:Laboratory medicine incorporates new technologies to aid in clinical decision-making, disease monitoring, and patient safety. Clinical microbiology informatics is progressively using AI. Genomic information from isolated bacteria, metagenomic microbial results from original specimens, mass spectra recorded from grown bacterial isolates and large digital photographs are examples of enormous datasets in clinical microbiology that may be used to build AI diagnoses. Conclusion:Technological innovation in healthcare is accelerating and has become increasingly interwoven with our daily lives and medical practices such as smart health trackers and diagnostic algorithms.}, } @article {pmid36032108, year = {2022}, author = {He, L and Chen, R and Zhang, B and Zhang, S and Khan, BA and Zhu, D and Wu, Z and Xiao, C and Chen, B and Chen, F and Hou, K}, title = {Fecal microbiota transplantation treatment of autoimmune-mediated type 1 diabetes mellitus.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {930872}, pmid = {36032108}, issn = {1664-3224}, mesh = {Adolescent ; *Diabetes Mellitus, Type 1 ; Fecal Microbiota Transplantation ; Feces ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; }, abstract = {UNLABELLED: Type 1 diabetes mellitus (T1DM) is an autoimmune-mediated disease characterized by a reduced or absolute lack of insulin secretion and often associated with a range of vascular and neurological complications for which there is a lack of effective treatment other than lifestyle interventions and pharmacological treatments such as insulin injections. Studies have shown that the gut microbiota is involved in mediating the onset and development of many fecal and extrafecal diseases, including autoimmune T1DM. In recent years, many cases of gut microbiota transplantation for diseases of the bowel and beyond have been reported worldwide, and this approach has been shown to be safe and effective. Here, we conducted an experimental treatment study in two adolescent patients diagnosed with autoimmune T1DM for one year. Patients received one to three rounds of normal fecal microbiota transplants (FMT) and were followed for up to 30 weeks. Clinical outcomes were measured, including biochemical indices, medication regimen, and dosage adjustment. Fecal microbiota metagenomic sequencing after transplantation provides a reference for more reasonable and effective microbiota transplantation protocols to treat autoimmune T1DM. Our results suggest that FMT is an effective treatment for autoimmune T1DM.

CLINICAL TRIAL REGISTRATION: http://www.chictr.org.cn, identifier ChiCTR2100045789.}, } @article {pmid36031409, year = {2022}, author = {Li, J and Jin, J and Li, S and Zhong, Y and Jin, Y and Zhang, X and Xia, B and Zhu, Y and Guo, R and Sun, X and Guo, J and Hu, F and Xiao, W and Huang, F and Ye, H and Li, R and Zhou, Y and Xiang, X and Yao, H and Yan, Q and Su, L and Wu, L and Luo, T and Liu, Y and Guo, X and Qin, J and Qi, H and He, J and Wang, J and Li, Z}, title = {Tonsillar Microbiome-Derived Lantibiotics Induce Structural Changes of IL-6 and IL-21 Receptors and Modulate Host Immunity.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {9}, number = {30}, pages = {e2202706}, pmid = {36031409}, issn = {2198-3844}, support = {U1903210//National Natural Science Foundation of China/ ; 81901648//National Natural Science Foundation of China/ ; 81801618//National Natural Science Foundation of China/ ; 81771743//National Natural Science Foundation of China/ ; 32141004//National Natural Science Foundation of China/ ; Z191100006619109//Beijing Municipal Science & Technology Commission/ ; PKU2021LCXQ008//Clinical Medicine Plus X-Young Scholars Project of Peking University, supported by "the Fundamental Research Funds for the Central Universities/ ; XDB29020000//Strategic Priority Research Program of the Chinese Academy of Sciences/ ; Z191100006619114//Beijing Science and Technology Program/ ; 0094/2018/A3//Macao Science and Technology Fund/ ; }, mesh = {Animals ; Humans ; Mice ; *Arthritis, Rheumatoid/drug therapy/metabolism ; *Bacteriocins/therapeutic use ; Interleukin-6/metabolism ; *Microbiota ; *Receptors, Interleukin-21/metabolism ; T-Lymphocytes, Helper-Inducer/metabolism ; *Palatine Tonsil/microbiology ; *Receptors, Interleukin-6/metabolism ; }, abstract = {Emerging evidence emphasizes the functional impacts of host microbiome on the etiopathogenesis of autoimmune diseases, including rheumatoid arthritis (RA). However, there are limited mechanistic insights into the contribution of microbial biomolecules especially microbial peptides toward modulating immune homeostasis. Here, by mining the metagenomics data of tonsillar microbiome, a deficiency of the encoding genes of lantibiotic peptides salivaricins in RA patients is identified, which shows strong correlation with circulating immune cells. Evidence is provided that the salivaricins exert immunomodulatory effects in inhibiting T follicular helper (Tfh) cell differentiation and interleukin-21 (IL-21) production. Mechanically, salivaricins directly bind to and induce conformational changes of IL-6 and IL-21 receptors, thereby inhibiting the bindings of IL-6 and IL-21 to their receptors and suppressing the downstream signaling pathway. Finally, salivaricin administration exerts both prophylactic and therapeutic effects against experimental arthritis in a murine model of RA. Together, these results provide a mechanism link of microbial peptides-mediated immunomodulation.}, } @article {pmid36031154, year = {2022}, author = {Li, S and Tong, J and Liu, Y and Shen, W and Hu, P}, title = {Targeted next generation sequencing is comparable with metagenomic next generation sequencing in adults with pneumonia for pathogenic microorganism detection.}, journal = {The Journal of infection}, volume = {85}, number = {5}, pages = {e127-e129}, doi = {10.1016/j.jinf.2022.08.022}, pmid = {36031154}, issn = {1532-2742}, mesh = {Adult ; *High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics ; *Pneumonia/diagnosis ; }, } @article {pmid36031136, year = {2022}, author = {Zheng, Y and Wang, P and Yang, X and Zhao, L and Ren, L and Li, J}, title = {Metagenomics insight into bioaugmentation mechanism of Propionibacterium acidipropionici during anaerobic acidification of kitchen waste.}, journal = {Bioresource technology}, volume = {362}, number = {}, pages = {127843}, doi = {10.1016/j.biortech.2022.127843}, pmid = {36031136}, issn = {1873-2976}, mesh = {Anaerobiosis ; Coenzyme A/metabolism ; Hydrogen-Ion Concentration ; Metagenomics ; *Propionates/metabolism ; Propionibacteriaceae ; *Propionibacterium/genetics/metabolism ; }, abstract = {In the present study, a biochemical strategy for improving propionic acid production from kitchen waste acidification by bioaugmentation with Propionibacterium acidipropionici (P. acidipropionici) was investigated. When the inoculum of P. acidipropionici was 30% (w/w) of the seeding sludge, the propionic acid production increased by 79.57%. Further, bioaugmentation improved the relative abundance of Firmicute and Actinobacteria. The results of metagenomic analysis further reveal that the ATP-binding cassette (ABC) transporters and all related pathways of Propanoate metabolism (ko00640) were enriched when P. acidipropionici was added. For Propanoate metabolism, most functional genes involved in the conversion from Glycolysis / Gluconeogenesis (ko00010) to Propanoyl-CoA and conversion from Propanoyl-CoA to propionic acid were enhanced after bioaugmentation with P. acidipropionici, thereby promoting propionic acid production. As such, bioaugmentation with P. acidipropionici was effective in the anaerobic acidification of kitchen waste for propionic acid production.}, } @article {pmid36030962, year = {2022}, author = {Sabatino, R and Cabello-Yeves, PJ and Eckert, EM and Corno, G and Callieri, C and Brambilla, D and Dzhembekova, N and Moncheva, S and Di Cesare, A}, title = {Antibiotic resistance genes correlate with metal resistances and accumulate in the deep water layers of the Black Sea.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {312}, number = {}, pages = {120033}, doi = {10.1016/j.envpol.2022.120033}, pmid = {36030962}, issn = {1873-6424}, mesh = {*Anti-Bacterial Agents/pharmacology ; Black Sea ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Integrases/genetics ; Metagenomics/methods ; Metals ; Water ; }, abstract = {Seas and oceans are a global reservoir of antibiotic resistance genes (ARGs). Only a few studies investigated the dynamics of ARGs along the water column of the Black Sea, a unique environment, with a peculiar geology, biology and history of anthropogenic pollution. In this study, we analyzed metagenomic data from two sampling campaigns (2013 and 2019) collected across three different sites in the Western Black Sea at depths ranging from 5 to 2000 m. The data were processed to annotate ARGs, metal resistance genes (MRGs) and integron integrase genes. The ARG abundance was significantly higher in the deep water layers and depth was the main driver of beta-diversity both for ARGs and MRGs. Moreover, ARG and MRG abundances strongly correlated (r = 0.95). The integron integrase gene abundances and composition were not influenced by the water depth and did not correlate with ARGs. The analysis of the obtained MAGs showed that some of them harbored intI gene together with several ARGs and MRGs, suggesting the presence of multidrug resistant bacteria and that MRGs and integrons could be involved in the selection of ARGs. These results demonstrate that the Black Sea is not only an important reservoir of ARGs, but also that they accumulate in the deep water layers where co-selection with MRGs could be assumed as a relevant mechanism of their persistence.}, } @article {pmid36030950, year = {2022}, author = {Zhang, M and Lu, G and Xiao, T and Xiao, E and Sun, X and Yan, W and Liu, G and Wang, Q and Yan, G and Liu, H and Sun, W}, title = {Characterization of arsenic-metabolizing bacteria in an alkaline soil.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {312}, number = {}, pages = {120040}, doi = {10.1016/j.envpol.2022.120040}, pmid = {36030950}, issn = {1873-6424}, mesh = {Arsenates/metabolism ; *Arsenic/metabolism ; *Arsenites/metabolism ; Bacteria/genetics/metabolism ; Isotopes/metabolism ; Nitrates/metabolism ; Oxidation-Reduction ; Soil ; Soil Microbiology ; }, abstract = {Arsenite (As(III)) is more toxic, mobilizable and bioavailable than arsenate (As(V)). Hence, the transformations between As(III) and As(V) are crucial for the toxicity and mobility of arsenic (As). However, As transformation and microbial communities involved in alkaline soils are largely unknown. Here we investigate two major pathways of As transformation, i.e., As(III) oxidation and As(V) reduction, and identify the bacteria involved in the alkaline soil by combining stable isotope probing with shotgun metagenomic sequencing. As(III) oxidation and significant increase of the aioA genes copies were observed in the treatments amended with As(III) and NO3[-], suggesting that As(III) oxidation can couple with nitrate reduction and was mainly catalyzed by the microorganisms containing aioA genes. As(V) reduction was detected in the treatments amended with As(V) and acetate where the abundance of arrA gene significantly increased, indicating that microorganisms with arrA genes were the key As(V) reducers. Acidovorax, Hydrogenophaga, and Ramlibacter were the putative nitrate-dependent As(III) oxidizers, and Deinococcus and Serratia were the putative respiratory As(V) reducers. These findings will improve our understanding of As metabolism and are meaningful for mapping out bioremediation strategies of As contamination in alkaline environment.}, } @article {pmid36030942, year = {2022}, author = {Shekhawat, SS and Kulshreshtha, NM and Saini, P and Upadhyay, A and Gupta, AB and Jenifer M, H and Subramanian, V and Kumari, A and Pareek, N and Vivekanand, V}, title = {Antibiotic resistance genes and bacterial diversity: A comparative molecular study of treated sewage from different origins and their impact on irrigated soils.}, journal = {Chemosphere}, volume = {307}, number = {Pt 4}, pages = {136175}, doi = {10.1016/j.chemosphere.2022.136175}, pmid = {36030942}, issn = {1879-1298}, mesh = {Anti-Bacterial Agents/analysis/pharmacology ; Bacteria/genetics ; Clindamycin ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Kanamycin ; Macrolides ; Paromomycin ; *Sewage ; *Soil ; Soil Microbiology ; Spectinomycin ; Sulfonamides ; Tetracyclines/analysis ; Wastewater/analysis ; Water/analysis ; beta-Lactams/analysis ; }, abstract = {Present study aims to investigate how is soil affected following irrigation with treated effluents of different origins by analysing the bacterial diversity, metabolic diversity and antibiotic resistance genes (ARGs). Comparative analysis with previously reported ARGs in effluents was performed to understand the mobility of ARGs from treated wastewater to the irrigated soil with respect to the control soil regimen. Acinetobacter, Burkholderia and Pseudomonas were observed as the most abundant genera in all the samples. The metabolic gene abundance of all the samples suggests a prominent contribution to natural mineral recycling. Most abundant ARGs observed encode resistance for clindamycin, kanamycin A, macrolides, paromomycin, spectinomycin and tetracycline. Treated effluent reuse did not appear to enhance the ARG levels in soils in most cases except for institutional treatment site (M), where the ARGs for aminoglycosides, β-lactams and sulfonamides were found to be abundantly present in both treated effluent and the irrigated soil. This study finds the importance of wastewater treatment from different origins and the impact of treated wastewater reuse in irrigation. This study also emphasises on the better understanding of ARGs mobility from water to soil.}, } @article {pmid36030622, year = {2022}, author = {West, PT and Chanin, RB and Bhatt, AS}, title = {From genome structure to function: insights into structural variation in microbiology.}, journal = {Current opinion in microbiology}, volume = {69}, number = {}, pages = {102192}, pmid = {36030622}, issn = {1879-0364}, support = {R01 AI148623/AI/NIAID NIH HHS/United States ; R01 AI143757/AI/NIAID NIH HHS/United States ; T32 HG000044/HG/NHGRI NIH HHS/United States ; T32 HL120824/HL/NHLBI NIH HHS/United States ; K22 HG000044/HG/NHGRI NIH HHS/United States ; }, mesh = {Biological Evolution ; Computational Biology ; Gene Rearrangement ; *Genome, Bacterial ; *Genomics ; }, abstract = {Structural variation in bacterial genomes is an important evolutionary driver. Genomic rearrangements, such as inversions, duplications, and insertions, can regulate gene expression and promote niche adaptation. Importantly, many of these variations are reversible and preprogrammed to generate heterogeneity. While many tools have been developed to detect structural variation in eukaryotic genomes, variation in bacterial genomes and metagenomes remains understudied. However, recent advances in genome sequencing technology and the development of new bioinformatic pipelines hold promise in further understanding microbial genomics.}, } @article {pmid36029916, year = {2022}, author = {Kundu, P and Mondal, S and Ghosh, A}, title = {Bacterial species metabolic interaction network for deciphering the lignocellulolytic system in fungal cultivating termite gut microbiota.}, journal = {Bio Systems}, volume = {221}, number = {}, pages = {104763}, doi = {10.1016/j.biosystems.2022.104763}, pmid = {36029916}, issn = {1872-8324}, mesh = {Animals ; Bacteria ; *Gastrointestinal Microbiome ; Glycoside Hydrolases/metabolism ; *Isoptera/metabolism/microbiology ; *Termitomyces ; }, abstract = {Fungus-cultivating termite Odontotermes badius developed a mutualistic association with Termitomyces fungi for the plant material decomposition and providing a food source for the host survival. The mutualistic relationship sifted the microbiome composition of the termite gut and Termitomyces fungal comb. Symbiotic bacterial communities in the O. badius gut and fungal comb have been studied extensively to identify abundant bacteria and their lignocellulose degradation capabilities. Despite several metagenomic studies, the species-wide metabolic interaction patterns of bacterial communities in termite gut and fungal comb remains unclear. The bacterial species metabolic interaction network (BSMIN) has been constructed with 230 bacteria identified from the O. badius gut and fungal comb microbiota. The network portrayed the metabolic map of the entire microbiota and highlighted several inter-species biochemical interactions like cross-feeding, metabolic interdependency, and competition. Further, the reconstruction and analysis of the bacterial influence network (BIN) quantified the positive and negative pairwise influences in the termite gut and fungal comb microbial communities. Several key macromolecule degraders and fermentative microbial entities have been identified by analyzing the BIN. The mechanistic interplay between these influential microbial groups and the crucial glycoside hydrolases (GH) enzymes produced by the macromolecule degraders execute the community-wide functionality of lignocellulose degradation and subsequent fermentation. The metabolic interaction pattern between the nine influential microbial species has been determined by considering them growing in a synthetic microbial community. Competition (30%), parasitism (47%), and mutualism (17%) were predicted to be the major mode of metabolic interaction in this synthetic microbial community. Further, the antagonistic metabolic effect was found to be very high in the metabolic-deprived condition, which may disrupt the community functionality. Thus, metabolic interactions of the crucial bacterial species and their GH enzyme cocktail identified from the O. badius gut and fungal comb microbiota may provide essential knowledge for developing a synthetic microcosm with efficient lignocellulolytic machinery.}, } @article {pmid36029249, year = {2022}, author = {Zeng, W and Gautam, A and Huson, DH}, title = {DeepToA: an ensemble deep-learning approach to predicting the theater of activity of a microbiome.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {20}, pages = {4670-4676}, doi = {10.1093/bioinformatics/btac584}, pmid = {36029249}, issn = {1367-4811}, mesh = {Algorithms ; *Deep Learning ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis, DNA ; }, abstract = {MOTIVATION: Metagenomics is the study of microbiomes using DNA sequencing. A microbiome consists of an assemblage of microbes that is associated with a 'theater of activity' (ToA). An important question is, to what degree does the taxonomic and functional content of the former depend on the (details of the) latter? Here, we investigate a related technical question: Given a taxonomic and/or functional profile estimated from metagenomic sequencing data, how to predict the associated ToA? We present a deep-learning approach to this question. We use both taxonomic and functional profiles as input. We apply node2vec to embed hierarchical taxonomic profiles into numerical vectors. We then perform dimension reduction using clustering, to address the sparseness of the taxonomic data and thus make the problem more amenable to deep-learning algorithms. Functional features are combined with textual descriptions of protein families or domains. We present an ensemble deep-learning framework DeepToA for predicting the ToA of amicrobial community, based on taxonomic and functional profiles. We use SHAP (SHapley Additive exPlanations) values to determine which taxonomic and functional features are important for the prediction.

RESULTS: Based on 7560 metagenomic profiles downloaded from MGnify, classified into 10 different theaters of activity, we demonstrate that DeepToA has an accuracy of 98.30%. We show that adding textual information to functional features increases the accuracy.

Our approach is available at http://ab.inf.uni-tuebingen.de/software/deeptoa.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36029242, year = {2022}, author = {Solari, SM and Young, RB and Marcelino, VR and Forster, SC}, title = {expam-high-resolution analysis of metagenomes using distance trees.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {20}, pages = {4814-4816}, pmid = {36029242}, issn = {1367-4811}, mesh = {*Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Software ; }, abstract = {SUMMARY: Shotgun metagenomic sequencing provides the capacity to understand microbial community structure and function at unprecedented resolution; however, the current analytical methods are constrained by a focus on taxonomic classifications that may obfuscate functional relationships. Here, we present expam, a tree-based, taxonomy agnostic tool for the identification of biologically relevant clades from shotgun metagenomic sequencing.

expam is an open-source Python application released under the GNU General Public Licence v3.0. expam installation instructions, source code and tutorials can be found at https://github.com/seansolari/expam.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid36028909, year = {2022}, author = {Somerville, V and Schowing, T and Chabas, H and Schmidt, RS and von Ah, U and Bruggmann, R and Engel, P}, title = {Extensive diversity and rapid turnover of phage defense repertoires in cheese-associated bacterial communities.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {137}, pmid = {36028909}, issn = {2049-2618}, mesh = {Bacteria ; *Bacteriophages ; *Cheese ; Genome, Bacterial ; Metagenome ; }, abstract = {BACKGROUND: Phages are key drivers of genomic diversity in bacterial populations as they impose strong selective pressure on the evolution of bacterial defense mechanisms across closely related strains. The pan-immunity model suggests that such diversity is maintained because the effective immune system of a bacterial species is the one distributed across all strains present in the community. However, only few studies have analyzed the distribution of bacterial defense systems at the community-level, mostly focusing on CRISPR and comparing samples from complex environments. Here, we studied 2778 bacterial genomes and 188 metagenomes from cheese-associated communities, which are dominated by a few bacterial taxa and occur in relatively stable environments.

RESULTS: We corroborate previous laboratory findings that in cheese-associated communities nearly identical strains contain diverse and highly variable arsenals of innate and adaptive (i.e., CRISPR-Cas) immunity systems suggesting rapid turnover. CRISPR spacer abundance correlated with the abundance of matching target sequences across the metagenomes providing evidence that the identified defense repertoires are functional and under selection. While these characteristics align with the pan-immunity model, the detected CRISPR spacers only covered a subset of the phages previously identified in cheese, providing evidence that CRISPR does not enable complete immunity against all phages, and that the innate immune mechanisms may have complementary roles.

CONCLUSIONS: Our findings show that the evolution of bacterial defense mechanisms is a highly dynamic process and highlight that experimentally tractable, low complexity communities such as those found in cheese, can help to understand ecological and molecular processes underlying phage-defense system relationships. These findings can have implications for the design of robust synthetic communities used in biotechnology and the food industry. Video Abstract.}, } @article {pmid36028255, year = {2023}, author = {Badran, M and Khalyfa, A and Ericsson, AC and Puech, C and McAdams, Z and Bender, SB and Gozal, D}, title = {Gut microbiota mediate vascular dysfunction in a murine model of sleep apnoea: effect of probiotics.}, journal = {The European respiratory journal}, volume = {61}, number = {1}, pages = {}, doi = {10.1183/13993003.00002-2022}, pmid = {36028255}, issn = {1399-3003}, mesh = {Mice ; Animals ; *Gastrointestinal Microbiome/physiology ; Disease Models, Animal ; RNA, Ribosomal, 16S ; Mice, Inbred C57BL ; *Sleep Apnea, Obstructive/complications/therapy ; *Probiotics ; Hypoxia ; *Coronary Artery Disease/therapy/complications ; }, abstract = {BACKGROUND: Obstructive sleep apnoea (OSA) is a chronic prevalent condition characterised by intermittent hypoxia (IH), and is associated with endothelial dysfunction and coronary artery disease (CAD). OSA can induce major changes in gut microbiome diversity and composition, which in turn may induce the emergence of OSA-associated morbidities. However, the causal effects of IH-induced gut microbiome changes on the vasculature remain unexplored. Our objective was to assess if vascular dysfunction induced by IH is mediated through gut microbiome changes.

METHODS: Faecal microbiota transplantation (FMT) was conducted on C57BL/6J naïve mice for 6 weeks to receive either IH or room air (RA) faecal slurry with or without probiotics (VSL#3). In addition to 16S rRNA amplicon sequencing of their gut microbiome, FMT recipients underwent arterial blood pressure and coronary artery and aorta function testing, and their trimethylamine N-oxide (TMAO) and plasma acetate levels were determined. Finally, C57BL/6J mice were exposed to IH, IH treated with VSL#3 or RA for 6 weeks, and arterial blood pressure and coronary artery function assessed.

RESULTS: Gut microbiome taxonomic profiles correctly segregated IH from RA in FMT mice and the normalising effect of probiotics emerged. Furthermore, IH-FMT mice exhibited increased arterial blood pressure and TMAO levels, and impairments in aortic and coronary artery function (p<0.05) that were abrogated by probiotic administration. Lastly, treatment with VSL#3 under IH conditions did not attenuate elevations in arterial blood pressure or CAD.

CONCLUSIONS: Gut microbiome alterations induced by chronic IH underlie, at least partially, the typical cardiovascular disturbances of sleep apnoea and can be mitigated by concurrent administration of probiotics.}, } @article {pmid36028202, year = {2022}, author = {Wang, J and Xiao, J and Zhu, Z and Wang, S and Zhang, L and Fan, Z and Deng, Y and Hu, Z and Peng, F and Shen, S and Deng, F}, title = {Diverse viromes in polar regions: A retrospective study of metagenomic data from Antarctic animal feces and Arctic frozen soil in 2012-2014.}, journal = {Virologica Sinica}, volume = {37}, number = {6}, pages = {883-893}, pmid = {36028202}, issn = {1995-820X}, mesh = {Animals ; *Soil ; Ecosystem ; Retrospective Studies ; Antarctic Regions ; Phylogeny ; Virome ; Cold Climate ; *Viruses ; Feces ; Metagenomics ; }, abstract = {Antarctica and the Arctic are the coldest places, containing a high diversity of microorganisms, including viruses, which are important components of polar ecosystems. However, owing to the difficulties in obtaining access to animal and environmental samples, the current knowledge of viromes in polar regions is still limited. To better understand polar viromes, this study performed a retrospective analysis using metagenomic sequencing data of animal feces from Antarctica and frozen soil from the Arctic collected during 2012-2014. The results reveal diverse communities of DNA and RNA viruses from at least 23 families from Antarctic animal feces and 16 families from Arctic soils. Although the viral communities from Antarctica and the Arctic show a large diversity, they have genetic similarities with known viruses from different ecosystems and organisms with similar viral proteins. Phylogenetic analysis of Microviridae, Parvoviridae, and Larvidaviridae was further performed, and complete genomic sequences of two novel circular replication-associated protein (rep)-encoding single-stranded (CRESS) DNA viruses closely related to Circoviridae were identified. These results reveal the high diversity, complexity, and novelty of viral communities from polar regions, and suggested the genetic similarity and functional correlations of viromes between the Antarctica and Arctic. Variations in viral families in Arctic soils, Arctic freshwater, and Antarctic soils are discussed. These findings improve our understanding of polar viromes and suggest the importance of performing follow-up in-depth investigations of animal and environmental samples from Antarctica and the Arctic, which would reveal the substantial role of these viruses in the global viral community.}, } @article {pmid36027987, year = {2022}, author = {Zhu, L and Liu, C and Li, Y and Pan, K and Ouyang, K and Song, X and Xiong, X and Qu, M and Zhao, X}, title = {Characteristics of recombinant xylanase from camel rumen metagenome and its effects on wheat bran hydrolysis.}, journal = {International journal of biological macromolecules}, volume = {220}, number = {}, pages = {1309-1317}, doi = {10.1016/j.ijbiomac.2022.08.146}, pmid = {36027987}, issn = {1879-0003}, mesh = {Amino Acids ; Animals ; Camelus/metabolism ; Carboxymethylcellulose Sodium ; Dietary Fiber/metabolism ; Dimethyl Sulfoxide ; Edetic Acid ; *Endo-1,4-beta Xylanases/chemistry ; Ethanol ; Hydrolysis ; Metagenome ; Methanol ; Peptide Hydrolases ; Rumen/metabolism ; Sodium Dodecyl Sulfate ; *Xylans/chemistry ; Xylose ; }, abstract = {In the present study, we explored the effects of a novel xylanase from camel rumen metagenome (CrXyn) on wheat bran hydrolysis. CrXyn was heterologously expressed in Escherichia coli and showed maximum activity at 40 °C and pH 7.0. Furthermore, CrXyn exhibited preferential hydrolysis of xylan, but no obvious activity toward other substrates, including carboxymethylcellulose and Avicel. Using wheat straw xylan as a substrate, the Km and Vmax values for CrXyn were 5.98 g/L and 179.9 μmol xylose/min/mg protein, respectively. Mn[2+] was a strong accelerator and significantly enhanced CrXyn activity. However, CrXyn activity was inhibited (~50 %) by 1 mM and 5 mM ethylenediaminetetraacetic acid (EDTA) and completely inactivated by 5 mM Cu[2+]. CrXyn tolerated 5 mM sodium dodecyl sulphate (SDS) and 15 % methanol, ethanol, and dimethyl sulfoxide (DMSO), with >50 % residual activity. CrXyn effectively hydrolyzed wheat bran, with xylobiose and xylotetraose accounting for 79.1 % of total sugars produced. A remarkable synergistic effect was found between CrXyn and protease, leading to an obvious increase in amino acids released from wheat bran compared with the control. CrXyn also enhanced the in vitro hydrolysis of wheat bran. Thus, CrXyn exhibits great potential as a feed additive to improve the utilization of wheat bran in monogastric animal production.}, } @article {pmid36026526, year = {2022}, author = {Palmnäs-Bédard, MSA and Costabile, G and Vetrani, C and Åberg, S and Hjalmarsson, Y and Dicksved, J and Riccardi, G and Landberg, R}, title = {The human gut microbiota and glucose metabolism: a scoping review of key bacteria and the potential role of SCFAs.}, journal = {The American journal of clinical nutrition}, volume = {116}, number = {4}, pages = {862-874}, pmid = {36026526}, issn = {1938-3207}, mesh = {Adult ; *Diabetes Mellitus, Type 2/drug therapy ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome ; Glucose/metabolism ; Humans ; Prospective Studies ; Verrucomicrobia/metabolism ; }, abstract = {The gut microbiota plays a fundamental role in human nutrition and metabolism and may have direct implications for type 2 diabetes and associated preconditions. An improved understanding of relations between human gut microbiota and glucose metabolism could lead to novel opportunities for type 2 diabetes prevention, but human observational studies reporting on such findings have not been extensively reviewed. Here, we review the literature on associations between gut microbiota and markers and stages of glucose dysregulation and insulin resistance in healthy adults and in adults with metabolic disease and risk factors. We present the current evidence for identified key bacteria and their potential roles in glucose metabolism independent of overweight, obesity, and metabolic drugs. We provide support for SCFAs mediating such effects and discuss the role of diet, as well as metabolites derived from diet and gut microbiota interactions. From 5983 initially identified PubMed records, 45 original studies were eligible and reviewed. α Diversity and 45 bacterial taxa were associated with selected outcomes. Six taxa were most frequently associated with glucose metabolism: Akkermansia muciniphila, Bifidobacterium longum, Clostridium leptum group, Faecalibacterium prausnitzii, and Faecalibacterium (inversely associated) and Dorea (directly associated). For Dorea and A. muciniphila, associations were independent of metabolic drugs and body measures. For A. muciniphila and F. prausnitzii, limited evidence supported SCFA mediation of potential effects on glucose metabolism. We conclude that observational studies applying metagenomics sequencing to identify species-level relations are warranted, as are studies accounting for confounding factors and investigating SCFA and postprandial glucose metabolism. Such advances in the field will, together with mechanistic and prospective studies and investigations into diet-gut microbiota interactions, have the potential to bring critical insight into roles of gut microbiota and microbial metabolites in human glucose metabolism and to contribute toward the development of novel prevention strategies for type 2 diabetes, including precision nutrition.}, } @article {pmid36017495, year = {2022}, author = {Schemczssen-Graeff, Z and Pileggi, M}, title = {Probiotics and live biotherapeutic products aiming at cancer mitigation and patient recover.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {921972}, pmid = {36017495}, issn = {1664-8021}, abstract = {Molecular biology techniques allowed access to non-culturable microorganisms, while studies using analytical chemistry, as Liquid Chromatography and Tandem Mass Spectrometry, showed the existence of a complex communication system among bacteria, signaled by quorum sensing molecules. These approaches also allowed the understanding of dysbiosis, in which imbalances in the microbiome diversity, caused by antibiotics, environmental toxins and processed foods, lead to the constitution of different diseases, as cancer. Colorectal cancer, for example, can originate by a dysbiosis configuration, which leads to biofilm formation, production of toxic metabolites, DNA damage in intestinal epithelial cells through the secretion of genotoxins, and epigenetic regulation of oncogenes. However, probiotic strains can also act in epigenetic processes, and so be use for recovering important intestinal functions and controlling dysbiosis and cancer mitigation through the metabolism of drugs used in chemotherapy, controlling the proliferation of cancer cells, improving the immune response of the host, regulation of cell differentiation and apoptosis, among others. There are still gaps in studies on the effectiveness of the use of probiotics, therefore omics and analytical chemistry are important approaches to understand the role of bacterial communication, formation of biofilms, and the effects of probiotics and microbiome on chemotherapy. The use of probiotics, prebiotics, synbiotics, and metabiotics should be considered as a complement to other more invasive and hazard therapies, such chemotherapy, surgery, and radiotherapy. The study of potential bacteria for cancer treatment, as the next-generation probiotics and Live Biotherapeutic Products, can have a controlling action in epigenetic processes, enabling the use of these bacteria for the mitigation of specific diseases through changes in the regulation of genes of microbiome and host. Thus, it is possible that a path of medicine in the times to come will be more patient-specific treatments, depending on the environmental, genetic, epigenetic and microbiome characteristics of the host.}, } @article {pmid36017370, year = {2022}, author = {Wan, J and Duan, L and Chen, Q and Wang, L and Bai, J and Hu, J and Lu, X and Zhang, T and Song, W and Yang, D and Shan, Y and Yan, Z}, title = {Potential clinical impact of metagenomic next-generation sequencing of plasma for cervical spine injury with sepsis in intensive care unit: A retrospective study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {948602}, pmid = {36017370}, issn = {2235-2988}, mesh = {Cervical Vertebrae ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Intensive Care Units ; *Metagenomics/methods ; Retrospective Studies ; Sensitivity and Specificity ; *Sepsis/diagnosis ; }, abstract = {Cervical spine injury (CSI) accounts for significant mortality in the intensive care unit (ICU), whereas sepsis remains one of the major causes of death in patients with CSI. However, there is no effective method to diagnose sepsis timely. The aim of this study is to investigate the effect of metagenomic next-generation sequencing (mNGS) on the pathogen features and the prognostic prediction of CSI patients with sepsis. A total of 27 blood samples from 17 included patients were tested by mNGS. Data of mNGS were compared with the conventional culture method. The Kaplan-Meier plots were used to visualize survival curves. A Cox proportional hazards model was used to identify independent prognostic factors for survival. Results showed that mNGS detected a wide spectrum of pathogens in CSI patients with sepsis, including 129 bacterial species, 8 viral species, and 51 fungal species. mNGS indicated 85.2% positive results, while the conventional culture method only showed 11.1% positive results in the blood samples. Further analyses revealed that mNGS had no prognostic effect on the septic CSI patients in ICU, whereas positive results of blood culture were closely correlated with an increased hazard ratio (HR) (HR 77.7067, 95%CI 2.860-2641.4595, p = 0.0155). Our results suggested that the mNGS application may provide evidence for clinicians to use antibiotics when a CSI case is diagnosed with sepsis.}, } @article {pmid36016275, year = {2022}, author = {Cholleti, H and de Jong, J and Blomström, AL and Berg, M}, title = {Characterization of Pipistrellus pygmaeus Bat Virome from Sweden.}, journal = {Viruses}, volume = {14}, number = {8}, pages = {}, pmid = {36016275}, issn = {1999-4915}, mesh = {Animals ; *Chiroptera ; Genome, Viral ; Humans ; Mammals ; Phylogeny ; *Picornaviridae/genetics ; *Plant Viruses/genetics ; *RNA Viruses/genetics ; Sweden ; Virome ; }, abstract = {Increasing amounts of data indicate that bats harbor a higher viral diversity relative to other mammalian orders, and they have been recognized as potential reservoirs for pathogenic viruses, such as the Hendra, Nipah, Marburg, and SARS-CoV viruses. Here, we present the first viral metagenomic analysis of Pipistrellus pygmaeus from Uppsala, Sweden. Total RNA was extracted from the saliva and feces of individual bats and analyzed using Illumina sequencing. The results identified sequences related to 51 different viral families, including vertebrate, invertebrate, and plant viruses. These viral families include Coronaviridae, Picornaviridae, Dicistroviridae, Astroviridae, Hepeviridae, Reoviridae, Botourmiaviridae, Lispviridae, Totiviridae, Botoumiaviridae, Parvoviridae, Retroviridae, Adenoviridae, and Partitiviridae, as well as different unclassified viruses. We further characterized three near full-length genome sequences of bat coronaviruses. A phylogenetic analysis showed that these belonged to alphacoronaviruses with the closest similarity (78-99% at the protein level) to Danish and Finnish bat coronaviruses detected in Pipistrellus and Myotis bats. In addition, the full-length and the near full-length genomes of picornavirus were characterized. These showed the closest similarity (88-94% at the protein level) to bat picornaviruses identified in Chinese bats. Altogether, the results of this study show that Swedish Pipistrellus bats harbor a great diversity of viruses, some of which are closely related to mammalian viruses. This study expands our knowledge on the bat population virome and improves our understanding of the evolution and transmission of viruses among bats and to other species.}, } @article {pmid36015459, year = {2022}, author = {Mgwatyu, Y and Cornelissen, S and van Heusden, P and Stander, A and Ranketse, M and Hesse, U}, title = {Establishing MinION Sequencing and Genome Assembly Procedures for the Analysis of the Rooibos (Aspalathus linearis) Genome.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {16}, pages = {}, pmid = {36015459}, issn = {2223-7747}, support = {NA//University of the Western Cape/ ; NA//FooBev SETA Research and Innovation Grant/ ; NA//South African Rooibos Council/ ; }, abstract = {While plant genome analysis is gaining speed worldwide, few plant genomes have been sequenced and analyzed on the African continent. Yet, this information holds the potential to transform diverse industries as it unlocks medicinally and industrially relevant biosynthesis pathways for bioprospecting. Considering that South Africa is home to the highly diverse Cape Floristic Region, local establishment of methods for plant genome analysis is essential. Long-read sequencing is becoming standard procedure for plant genome research, as these reads can span repetitive regions of the DNA, substantially facilitating reassembly of a contiguous genome. With the MinION, Oxford Nanopore offers a cost-efficient sequencing method to generate long reads; however, DNA purification protocols must be adapted for each plant species to generate ultra-pure DNA, essential for these analyses. Here, we describe a cost-effective procedure for the extraction and purification of plant DNA and evaluate diverse genome assembly approaches for the reconstruction of the genome of rooibos (Aspalathus linearis), an endemic South African medicinal plant widely used for tea production. We discuss the pros and cons of nine tested assembly programs, specifically Redbean and NextDenovo, which generated the most contiguous assemblies, and Flye, which produced an assembly closest to the predicted genome size.}, } @article {pmid36015047, year = {2022}, author = {Chauhan, RP and San, JE and Gordon, ML}, title = {Metagenomic Analysis of RNA Fraction Reveals the Diversity of Swine Oral Virome on South African Backyard Swine Farms in the uMgungundlovu District of KwaZulu-Natal Province.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {8}, pages = {}, pmid = {36015047}, issn = {2076-0817}, abstract = {Numerous RNA viruses have been reported in backyard swine populations in various countries. In the absence of active disease surveillance, a persistent knowledge gap exists on the diversity of RNA viruses in South African backyard swine populations. This is the first study investigating the diversity of oral RNA virome of the backyard swine in South Africa. We used three samples of backyard swine oral secretion (saliva) collected from three distantly located backyard swine farms (BSFs) in the uMgungundlovu District, KwaZulu-Natal, South Africa. Total viral RNA was extracted and used for the library preparation for deep sequencing using the Illumina HiSeq X instrument. The FASTQ files containing paired-end reads were analyzed using Genome Detective v 1.135. The assembled nucleotide sequences were analyzed using the PhyML phylogenetic tree. The genome sequence analysis identified a high diversity of swine enteric viruses in the saliva samples obtained from BSF2 and BSF3, while only a few viruses were identified in the saliva obtained from BSF1. The swine enteric viruses belonged to various animal virus families; however, two fungal viruses, four plant viruses, and five unclassified RNA viruses were also identified. Specifically, viruses of the family Astroviridae, according to the number of reads, were the most prevalent. Of note, the genome sequences of Rotavirus A (RVA) and Rotavirus C (RVC) at BSF2 and RVC and Hepatitis E virus (HEV) at BSF3 were also obtained. The occurrence of various swine enteric viruses in swine saliva suggests a high risk of diarrhoeic diseases in the backyard swine. Of note, zoonotic viruses in swine saliva, such as RVA, RVC, and HEV, indicate a risk of zoonotic spillover to the exposed human populations. We recommend the implementation of biosecurity to ensure sustainable backyard swine farming while safeguarding public health.}, } @article {pmid36014959, year = {2022}, author = {Jing, L and Xu, Z and Zhang, Y and Li, D and Song, Y and Hu, H and Fang, Y and Zhu, W}, title = {Metagenomic Insights into Pathogenic Characterization of ST410 Acinetobacter nosocomialis Prevalent in China.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {8}, pages = {}, pmid = {36014959}, issn = {2076-0817}, support = {TYU-039F//Beijing Medical and Health Foundation/ ; }, abstract = {Acinetobacter nosocomialis is a prevalent opportunistic pathogen that causes hospital-acquired infections. The increasing threats from A. nosocomialis infections have led to attention from the scientific and medical communities. Metagenomic next-generation sequencing (mNGS) was performed for an exudate specimen collected from an ICU patient with wound infection, followed by sepsis, in Tongji Hospital. Three assembly strategies were employed to recover the genome of A. nosocomialis in the metagenomic sample. Together with publicly available genomes of A. nosocomialis, the features of population genetics and molecular epidemiology were deeply analyzed. A draft genome was reconstructed for the metagenomic strain WHM01, derived from the ST410 A. nosocomialis dominating the microbial community, thereby prompting its highly pathogenic risk, which is associated with infection and persistence. The structure of the bacterial pangenome was characterized, including the 1862 core and 11,815 accessory genes present in the 157 strains. The genetic diversity of the genes coding for the 128 virulence factors assigned to 14 functional categories was uncovered in this nosocomial pathogen, such as the lipooligosaccharide, capsule, type IV pilus, and outer membrane proteins. Our work revealed genomic properties of ST410 A. nosocomialis, which is prevalent in China, and further highlighted that metagenomic surveillance may be a prospective application for evaluating the pathogenic characteristics of the nosocomial opportunistic pathogens.}, } @article {pmid36014890, year = {2022}, author = {Burakova, I and Smirnova, Y and Gryaznova, M and Syromyatnikov, M and Chizhkov, P and Popov, E and Popov, V}, title = {The Effect of Short-Term Consumption of Lactic Acid Bacteria on the Gut Microbiota in Obese People.}, journal = {Nutrients}, volume = {14}, number = {16}, pages = {}, pmid = {36014890}, issn = {2072-6643}, support = {project FZGW-2020-0001 (unique number of the register of State tasks 075001X39782002)//Ministry of Science and Higher Education of the Russian Federation/ ; }, mesh = {Bacteria ; *Gastrointestinal Microbiome ; Humans ; *Lactobacillales ; *Limosilactobacillus fermentum ; Obesity/microbiology/therapy ; *Probiotics/therapeutic use ; }, abstract = {Obesity is a problem of modern health care that causes the occurrence of many concomitant diseases: arterial hypertension, diabetes mellitus, non-alcoholic fatty liver disease, and cardiovascular diseases. New strategies for the treatment and prevention of obesity are being developed that are based on using probiotics for modulation of the gut microbiota. Our study aimed to evaluate the bacterial composition of the gut of obese patients before and after two weeks of lactic acid bacteria (Lactobacillus acidophilus, Lactiplantibacillus plantarum, Limosilactobacillus fermentum, and Lactobacillus delbrueckii) intake. The results obtained showed an increase in the number of members of the phylum Actinobacteriota in the group taking nutritional supplements, while the number of phylum Bacteroidota decreased in comparison with the control group. There has also been an increase in potentially beneficial groups: Bifidobacterium, Blautia, Eubacterium, Anaerostipes, Lactococcus, Lachnospiraceae ND3007, Streptococcus, Escherichia-Shigella, and Lachnoclostridium. Along with this, a decrease in the genera was demonstrated: Faecalibacterium, Pseudobutyrivibrio, Subdoligranulum, Faecalibacterium, Clostridium sensu stricto 1 and 2, Catenibacterium, Megasphaera, Phascolarctobacterium, and the Oscillospiraceae NK4A214 group, which contribute to the development of various metabolic disorders. Modulation of the gut microbiota by lactic acid bacteria may be one of the ways to treat obesity.}, } @article {pmid36014086, year = {2022}, author = {Inglis, LK and Edwards, RA}, title = {How Metagenomics Has Transformed Our Understanding of Bacteriophages in Microbiome Research.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {36014086}, issn = {2076-2607}, support = {RC2 DK116713/DK/NIDDK NIH HHS/United States ; NIDDK RC2 DK116713/NH/NIH HHS/United States ; }, abstract = {The microbiome is an essential part of most ecosystems. It was originally studied mostly through culturing but relatively few microbes can be cultured, so much of the microbiome was left unexplored. The emergence of metagenomic sequencing techniques changed that and allowed the study of microbiomes from all sorts of habitats. Metagenomic sequencing also allowed for a more thorough exploration of prophages, viruses that integrate into bacterial genomes, and how they benefit their hosts. One issue with using open-access metagenomic data is that sequences added to databases often have little to no metadata to work with, so finding enough sequences can be difficult. Many metagenomes have been manually curated but this is a time-consuming process and relies heavily on the uploader to be accurate and thorough when filling in metadata fields and the curators to be working with the same ontologies. Using algorithms to automatically sort metagenomes based on either the taxonomic profile or the functional profile may be a viable solution to the issues with manually curated metagenomes, but it requires that the algorithm is trained on carefully curated datasets and using the most informative profile possible in order to minimize errors.}, } @article {pmid36014075, year = {2022}, author = {Barteneva, NS and Meirkhanova, A and Malashenkov, D and Vorobjev, IA}, title = {To Die or Not to Die-Regulated Cell Death and Survival in Cyanobacteria.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {36014075}, issn = {2076-2607}, support = {FDCGRP #110119FD4513//Nazarbayev University/ ; #SSH2020028//Nazarbayev University/ ; MES #4350/ GF4//Ministry of Science, Kazakhstan/ ; AP08857554//Ministry of Science, Kazakhstan/ ; ORAU 240919FD3937//Nazarbayev University/ ; }, abstract = {Regulated cell death (RCD) is central to the development, integrity, and functionality of multicellular organisms. In the last decade, evidence has accumulated that RCD is a universal phenomenon in all life domains. Cyanobacteria are of specific interest due to their importance in aquatic and terrestrial habitats and their role as primary producers in global nutrient cycling. Current knowledge on cyanobacterial RCD is based mainly on biochemical and morphological observations, often by methods directly transferred from vertebrate research and with limited understanding of the molecular genetic basis. However, the metabolism of different cyanobacteria groups relies on photosynthesis and nitrogen fixation, whereas mitochondria are the central executioner of cell death in vertebrates. Moreover, cyanobacteria chosen as biological models in RCD studies are mainly colonial or filamentous multicellular organisms. On the other hand, unicellular cyanobacteria have regulated programs of cellular survival (RCS) such as chlorosis and post-chlorosis resuscitation. The co-existence of different genetically regulated programs in cyanobacterial populations may have been a top engine in life diversification. Development of cyanobacteria-specific methods for identification and characterization of RCD and wider use of single-cell analysis combined with intelligent image-based cell sorting and metagenomics would shed more light on the underlying molecular mechanisms and help us to address the complex colonial interactions during these events. In this review, we focus on the functional implications of RCD in cyanobacterial communities.}, } @article {pmid36014047, year = {2022}, author = {Wei, Z and Li, Q and Lu, R and Zheng, P and Wang, Y}, title = {In Situ Genomics and Transcriptomics of SAR202 Subclusters Revealed Subtle Distinct Activities in Deep-Sea Water.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {36014047}, issn = {2076-2607}, abstract = {Deep-sea water columns are enriched with SAR202 that may conduct detrital matter degradation. There are several subclusters in SAR202, but their subtle differences in geochemical cycles are largely unknown, particularly for their in situ activities in the marine deep zone. Deep-sea DNA/RNA samples obtained from 12 continuous time periods over two days by in situ nucleic acid collection apparatus were used to re-evaluate the ecological functions of each SAR202 subcluster at a depth of ~1000 m in the South China Sea (SCS). Phylogenomics of 32 new SAR202 genomes from the SCS and western Pacific revealed their distribution in five subclusters. Metatranscriptomics analysis showed that the subclusters II and III were the dominant SAR202 groups with higher transcriptional activities in the SCS deep-sea zone than other subclusters. The analyses of functional gene expression further indicated that SAR202 subclusters II and III might be involved in different metabolic pathways in the deep-sea environment. The SAR202 subcluster III might take part in the degradation of deep-sea aromatic compounds. Time-course metagenomics and metatranscriptomics data did not show metabolic correlation of subclusters II and III over two days, suggesting diversified ecological functions of SAR202 subclusters under different organic inputs from the overlying water column. Collectively, our results indicate that the SAR202 subclusters play different roles in organic degradation and have probably undergone subtle and gradual adaptive evolution in the dynamic environment of the deep ocean.}, } @article {pmid36014042, year = {2022}, author = {Sbaoui, Y and Ezaouine, A and Toumi, M and Farkas, R and Kbaich, MA and Habbane, M and El Mouttaqui, S and Kadiri, FZ and El Messal, M and Tóth, E and Bennis, F and Chegdani, F}, title = {Effect of Climate on Bacterial and Archaeal Diversity of Moroccan Marine Microbiota.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {36014042}, issn = {2076-2607}, abstract = {The Moroccan coast is characterized by a diversity of climate, reflecting a great richness and diversity of fauna and flora. By this, marine microbiota plays a fundamental role in many biogeochemical processes, environmental modifications, and responses to temperature changes. To date, no exploration by high-throughput techniques has been carried out on the characterization of the Moroccan marine microbiota. The objective of this work is to study the diversity and metabolic functions of MMM from the Moroccan coast (Atlantic and Mediterranean) according to the water source (WS) and the type of climate (CT) using the approach high-throughput sequencing of the 16SrRNA gene. Four water samples of twelve sampling sites from the four major climates along the Moroccan coastline were collected, and prokaryotic DNA was extracted. V4 region of 16S rRNA gene was amplified, and the product PCR was sequenced by Illumina Miseq. The β-diversity and α-diversity indices were determined to assess the species richness and evenness. The obtained results were analyzed by Mothur and R software. A total of twenty-eight Bacterial phyla and twelve Archaea were identified from the samples. Proteobacteria, Bacteroidetes, and Cyanobacteria are the three key bacterial phyla, and the Archaeal phyla identified are: Euryarchaeota, Nanoarchaeaeota, Crenarchaeota, Hydrothermarchaeota, Asgardaeota, Diapherotrites, and Thaumarchaeota in the Moroccan coastline and the four climates studied. The whole phylum are involved in marine biogeochemical cycles, and through their functions they participate in the homeostasis of the ocean in the presence of pollutants or stressful biotic and abiotic factors. In conclusion, the obtained results reported sufficient deepness of sequencing to cover the majority of Archaeal and Bacterial genera in each site. We noticed a strong difference in microbiota diversity, abundance, and taxonomy inter- and intra-climates and water source without significant differences in function. To better explore this diversity, other omic approaches can be applied such as the metagenomic shotgun, and transcriptomic approaches allowing a better characterization of the Moroccan marine microbiota and to understand the mechanisms of its adaptation and its impacts in/on the ecosystem.}, } @article {pmid36014039, year = {2022}, author = {Pérez, V and Liu, Y and Hengst, MB and Weyrich, LS}, title = {A Case Study for the Recovery of Authentic Microbial Ancient DNA from Soil Samples.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {36014039}, issn = {2076-2607}, support = {1211515//FONDECYT/ ; 1201692//FONDECYT/ ; 1181773//FONDECYT/ ; 74190093//ANID-International Postdoctoral Research fellowship-ANID/ ; FT180100407//Australian Research Council Future Fellowship/ ; }, abstract = {High Throughput DNA Sequencing (HTS) revolutionized the field of paleomicrobiology, leading to an explosive growth of microbial ancient DNA (aDNA) studies, especially from environmental samples. However, aDNA studies that examine environmental microbes routinely fail to authenticate aDNA, examine laboratory and environmental contamination, and control for biases introduced during sample processing. Here, we surveyed the available literature for environmental aDNA projects—from sample collection to data analysis—and assessed previous methodologies and approaches used in the published microbial aDNA studies. We then integrated these concepts into a case study, using shotgun metagenomics to examine methodological, technical, and analytical biases during an environmental aDNA study of soil microbes. Specifically, we compared the impact of five DNA extraction methods and eight bioinformatic pipelines on the recovery of microbial aDNA information in soil cores from extreme environments. Our results show that silica-based methods optimized for aDNA research recovered significantly more damaged and shorter reads (<100 bp) than a commercial kit or a phenol−chloroform method. Additionally, we described a stringent pipeline for data preprocessing, efficiently decreasing the representation of low-complexity and duplicated reads in our datasets and downstream analyses, reducing analytical biases in taxonomic classification.}, } @article {pmid36014001, year = {2022}, author = {Nikolaev, Y and Yushina, Y and Mardanov, A and Gruzdev, E and Tikhonova, E and El-Registan, G and Beletskiy, A and Semenova, A and Zaiko, E and Bataeva, D and Polishchuk, E}, title = {Microbial Biofilms at Meat-Processing Plant as Possible Places of Bacteria Survival.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {36014001}, issn = {2076-2607}, abstract = {Biofilm contamination in food production threatens food quality and safety, and causes bacterial infections. Study of food biofilms (BF) is of great importance. The taxonomic composition and structural organization of five foods BF taken in different workshops of a meat-processing plant (Moscow, RF) were studied. Samples were taken from the surface of technological equipment and premises. Metagenomic analysis showed both similarities in the presented microorganisms dominating in different samples, and unique families prevailing on certain objects were noted. The bacteria found belonged to 11 phyla (no archaea). The dominant ones were Actinobacteria, Bacteroidetes, Firmicutes, and Proteobacteria. The greatest diversity was in BFs taken from the cutting table of raw material. Biofilms' bacteria may be the cause of meat, fish and dairy products spoilage possible representatives include Pseudomonas, Flavobacterium, Arcobacter, Vagococcus, Chryseobacterium, Carnobacterium, etc.). Opportunistic human and animal pathogens (possible representatives include Arcobacter, Corynebacterium, Kocuria, etc.) were also found. Electron-microscopic studies of BF thin sections revealed the following: (1) the diversity of cell morphotypes specific to multispecies BFs; (2) morphological similarity of cells in BFs from different samples, micro-colonial growth; (3) age heterogeneity of cells within the same microcolony (vegetative and autolyzed cells, resting forms); (4) heterogeneity of the polymer matrix chemical nature according to ruthenium red staining.}, } @article {pmid36014000, year = {2022}, author = {Nath, S and Pulikkotil, SJ and Weyrich, L and Zilm, P and Kapellas, K and Jamieson, L}, title = {Effect of Periodontal Interventions on Characteristics of the Periodontal Microbial Profile: A Systematic Review and Meta-Analysis.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {36014000}, issn = {2076-2607}, abstract = {Our systematic review aimed to evaluate the effect of periodontal interventions on the diversity and composition of periodontal microbiota assessed by high throughput sequencing (HTS) metagenomics analysis. An electronic search was conducted from database inception to November 2021. All clinical trials that evaluated the effect of periodontal interventions on the gingival microbiota through HTS were selected. The measures of alpha diversity, richness, Shannon diversity index, and the Chao1 index, were used as the primary outcome, whereas relative abundances of bacterial genera were considered as the secondary outcome. Overall, 24 studies were eligible for the systematic review, of which 13 studies were included in the meta-analysis. Periodontal intervention for the test group decreased Shannon diversity, richness, and Chao1 index (alpha diversity), as observed from baseline to post-treatment. The most common genera that increased after periodontal therapy were Rothia, Actinomyces, Streptococcus, Veillonella, and Hemophilus, whilst Porphyromonas, Tannerella, Fusobacterium, and Treponema decreased after periodontal therapy. Periodontal interventions may decrease the bacterial diversity and richness and alter the composition of oral microbiota in the short term. Periodontal microbiota signatures could potentially be used for the assessment of periodontal disease development, progression, and success of the intervention.}, } @article {pmid36013992, year = {2022}, author = {Ermolenko, E and Kotyleva, M and Kotrova, A and Tichonov, S and Lavrenova, N and Voropaeva, L and Topalova, Y and Karaseva, A and Azarov, D and Ermolenko, K and Druzhininskii, D and Dmitriev, A and Shishkin, A and Suvorov, A}, title = {Consortium of Indigenous Fecal Bacteria in the Treatment of Metabolic Syndrome.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {36013992}, issn = {2076-2607}, abstract = {The features of gut microbiota in metabolic syndrome (MS) and ways to correct it using autoprobiotics, based on indigenous bacteria obtained from fecal samples of the host, remain unexplored. The aim of the study was to investigate the effectiveness of an indigenous consortium (IC) of fecal bacteria in treatment of patients with MS. The study was carried out on 36 patients with MS, manifested with abdominal obesity, eating disorders, dyslipidemia, and hypertension. The control group was formed by 20 healthy volunteers. Samples of IC and gut microbiota content were examined by qPCR and metagenome (16S rRNA) analysis before and after therapy. The decrease in anthropometric parameters of obesity, liver enzyme level correction, reduction in C reactive protein and triglyceride concentrations were revealed after IC usage. The decrease in genera Bifidobacterium, Enterobacter, Paraprevotella, and Prevotella, as well as an increase in Bacteroides fragilis and Oscillospira spp. populations were shown after consumption of IC. A negative correlation between the quantity of B. fragilis and the anthropometric parameters of obesity (r = -0.48) and C reactive protein level (r = -0.36) in serum was established. Thus, IC can be considered as a potential functional personified product for the therapy of MS.}, } @article {pmid36013987, year = {2022}, author = {Rincón-Molina, CI and Martínez-Romero, E and Aguirre-Noyola, JL and Manzano-Gómez, LA and Zenteno-Rojas, A and Rogel, MA and Rincón-Molina, FA and Ruíz-Valdiviezo, VM and Rincón-Rosales, R}, title = {Bacterial Community with Plant Growth-Promoting Potential Associated to Pioneer Plants from an Active Mexican Volcanic Complex.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {36013987}, issn = {2076-2607}, support = {9979.21-P//National Technological Institute of Mexico/ ; }, abstract = {Microorganisms in extreme volcanic environments play an important role in the development of plants on newly exposed substrates. In this work, we studied the structure and diversity of a bacterial community associated to Andropogon glomeratus and Cheilanthes aemula at El Chichón volcano. The genetic diversity of the strains was revealed by genomic fingerprints and by 16S rDNA gene sequencing. Furthermore, a metagenomic analysis of the rhizosphere samples was carried out for pioneer plants growing inside and outside the volcano. Multifunctional biochemical tests and plant inoculation assays were evaluated to determine their potential as plant growth-promoting bacteria (PGPB). Through metagenomic analysis, a total of 33 bacterial phyla were identified from A. glomeratus and C. aemula rhizosphere samples collected inside the volcano, and outside the volcano 23 bacterial phyla were identified. For both rhizosphere samples, proteobacteria was the most abundant phylum. With a cultivable approach, 174 bacterial strains were isolated from the rhizosphere and tissue of plants growing outside the volcanic complex. Isolates were classified within the genera Acinetobacter, Arthrobacter, Bacillus, Burkholderia, Cupriavidus, Enterobacter, Klebsiella, Lysinibacillus, Pantoea, Pseudomonas, Serratia, Stenotrophomonas and Pandoraea. The evaluated strains were able to produce indole compounds, solubilize phosphate, synthesize siderophores, showed ACC deaminase and nitrogenase activity, and they had a positive effect on the growth and development of Capsicum chinense. The wide diversity of bacteria associated to pioneer plants at El Chichón volcano with PGPB qualities represent an alternative for the recovery of eroded environments, and they can be used efficiently as biofertilizers for agricultural crops growing under adverse conditions.}, } @article {pmid36012850, year = {2022}, author = {Schafhauser, T and Wibberg, D and Binder, A and Rückert, C and Busche, T and Wohlleben, W and Kalinowski, J}, title = {Genome Assembly and Genetic Traits of the Pleuromutilin-Producer Clitopilus passeckerianus DSM1602.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {8}, pages = {}, pmid = {36012850}, issn = {2309-608X}, support = {//Biovet Ad (Peshtera, Bulgaria)/ ; }, abstract = {The gilled mushroom Clitopilus passeckerianus (Entolomataceae, Agaricales, Basidiomycota) is well known to produce the terpenoid pleuromutilin, which is the biotechnological basis for medically important antibiotics such as lefamulin and retapamulin. Their unique mode of action and good tolerance entails an increasing demand of pleuromutilin-derived antibiotics in veterinary and human health care. Surprisingly, despite their pharmaceutical importance, no genome sequence is available of any pleuromutilin-producing fungus. Here, we present the high-quality draft genome sequence of the pleuromutilin-producer C. passeckerianus DSM1602 including functional genome annotation. More precisely, we employed a hybrid assembly strategy combining Illumina sequencing and Nanopore sequencing to assemble the mitochondrial genome as well as the nuclear genome. In accordance with the dikaryotic state of the fungus, the nuclear genome has a diploid character. Interestingly, the mitochondrial genome appears duplicated. Bioinformatic analysis revealed a versatile secondary metabolism with an emphasis on terpenoid biosynthetic enzymes in C. passeckerianus and also in related strains. Two alleles of biosynthetic gene clusters for pleuromutilin were found in the genome of C. passeckerianus. The pleuromutilin genes were reassembled with yeast-specific elements for heterologous expression in Saccharomyces cerevisiae. Our work lays the foundation for metabolic strain engineering towards higher yields of the valuable compound pleuromutilin.}, } @article {pmid36012835, year = {2022}, author = {Li, H and Yang, H and Calderón-Urrea, A and Li, Y and Zhang, L and Yu, Y and Ma, J and Shi, G}, title = {Microbial Fertilization Improves Soil Health When Compared to Chemical Fumigation in Sweet Lily.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {8}, pages = {}, pmid = {36012835}, issn = {2309-608X}, support = {31860549//the National Natural Science Foundation, China/ ; }, abstract = {Lanzhou Lily(Lilium davidii) var. unicolor, which is also known as sweet lily in China, is used as a type of food. This lily is distributed in narrow regions, propagates asexually, cultivates perennially, and cultivates commonly in serious consecutive replant problems (CRPs). Soil fumigation is commonly used to control soil-borne disease to alleviate crops' consecutive replant problems (CRPs). However, due to the improper fumigation application, it is common to cause chemical hazard to crops. In this study, we designed a two-factor experiment to explore the bacterial and fungal community structure and some specific microbial groups in the lily rhizosphere soil after chemical versus bacterial fertilizer treatments, by using a metagenomic analysis of the treated soils. The results showed that metham-sodium soil fumigation (SMF treatment) significantly decreased plant growth, as well as it significantly decreased both soil fungal diversity and abundance at the OTUs levels, while Special 8™ microbial fertilizer supplement (MF treatment) significantly improved plant growth and increased fungal diversity and abundance. Under FM treatment, Chao1 richness and Shannon's diversity increased by 6.70% and 35.09% compared to CK (no treatment). However, the bacterial diversity and abundance were not significantly changed among these treatments. The fungal and bacterial community structure were different in all treatments. In SMF treatment, the pathogenic fungal species Fusarium oxysporum increased compared to CK, but it significantly decreased in MF treatment; in MF and MMF treatments, some beneficial bacteria groups such as the bacterial phylum Proteobacteria and its member genus Sphingomonas, as well as the fungal genus Mortierella, increased compared to CK and SFM treatments, but the harmful bacterial genera Gemmatimona was decreased, as well as the harmful fungal genus Cryptococcus. Thus, we concluded that under chemical fumigation conditions, both fungal diversity loss and overall microorganism reduction, which impair multiple ecosystem function, in conjunction with the increase of harmful fungal species such as Fusarium oxysporum, are causes for soil degradation. On the other hand, under microbial fertilizer supplement, it was the fungal diversity increase, as well as these beneficial microorganisms groups' accumulation, together with those harmful groups' depletion, played important roles in restoring and improving soil health that suffered from the chemical fumigant hazard. In addition, the bacterial phylum Proteobacteria and its member genus Sphingomonas are involved in soil health recovery and promotion. The results also emphasized that whether soil is chemically fumigated or not, beneficial microorganism supplementary is effective in ensuring soil productivity.}, } @article {pmid36012686, year = {2022}, author = {Ajiboye, TT and Ayangbenro, AS and Babalola, OO}, title = {Functional Diversity of Microbial Communities in the Soybean (Glycine max L.) Rhizosphere from Free State, South Africa.}, journal = {International journal of molecular sciences}, volume = {23}, number = {16}, pages = {}, pmid = {36012686}, issn = {1422-0067}, support = {UID123634; UID132595//National Research Foundation/ ; }, mesh = {*Fabaceae ; *Microbiota/genetics ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; South Africa ; Glycine max/genetics ; }, abstract = {The plant microbiome is involved in enhancing nutrient acquisition, plant growth, stress tolerance, and reducing chemical inputs. The identification of microbial functional diversity offers the chance to evaluate and engineer them for various agricultural processes. Using a shotgun metagenomics technique, this study examined the functional diversity and metabolic potentials of microbial communities in the rhizosphere of soybean genotype link 678. The dominant genera are Geobacter, Nitrobacter, Burkholderia, Candidatus, Bradyrhizobium and Streptomyces. Twenty-one functional categories were present, with fourteen of the functions being dominant in all samples. The dominant functions include carbohydrates, fatty acids, lipids and isoprenoids, amino acids and derivatives, sulfur metabolism, and nitrogen metabolism. A Kruskal-Wallis test was used to test samples' diversity differences. There was a significant difference in the alpha diversity. ANOSIM was used to analyze the similarities of the samples and there were significant differences between the samples. Phosphorus had the highest contribution of 64.3% and was more prominent among the soil properties that influence the functional diversity of the samples. Given the functional groups reported in this study, soil characteristics impact the functional role of the rhizospheric microbiome of soybean.}, } @article {pmid36012061, year = {2022}, author = {Zhang, K and Li, K and Liu, Z and Li, Q and Li, W and Chen, Q and Xia, Y and Hu, F and Yang, F}, title = {The Sources and Potential Hosts Identification of Antibiotic Resistance Genes in the Yellow River, Revealed by Metagenomic Analysis.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {16}, pages = {}, pmid = {36012061}, issn = {1660-4601}, mesh = {*Anti-Bacterial Agents/analysis/pharmacology ; China ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; Metagenomics/methods ; *Rivers/microbiology ; }, abstract = {The fate of antibiotic resistance genes (ARGs) has been revealed in various environmental media in recent years. Namely, the emergence of genes that resist colistin and carbapenems has attracted wide attention. However, the pollution condition of ARGs and sources in the Yellow River is still little understood, despite the river being the second longest in China. The present study determined the levels of ARG pollution in the Henan section of the Yellow River and evaluated the role of the aquaculture industry in the spread of ARGs. As revealed by the results, a total of 9 types of ARGs were detected in the sediments of the Yellow River, and the total ARG content in the Yellow River ranges from 7.27 to 245.45 RPKM. Sul1 and sul2 are the dominant ARGs, and the huge usage of sulfonamides, horizontal gene transfer, and wide bacteria host contribute to the prevalence of these two genes. The results of Spearman correlation analysis indicate that the breeding industry has little influence on ARGs in the Yellow River. Network analysis reveals that the opportunistic pathogen Pseudomonas is the potential host of sul1, tetG, and ANT(3'')-IIa, which can pose a risk to human health.}, } @article {pmid36011312, year = {2022}, author = {Le, NG and van Ulsen, P and van Spanning, R and Brouwer, A and van Straalen, NM and Roelofs, D}, title = {A Functional Carbohydrate Degrading Enzyme Potentially Acquired by Horizontal Gene Transfer in the Genome of the Soil Invertebrate Folsomia candida.}, journal = {Genes}, volume = {13}, number = {8}, pages = {}, pmid = {36011312}, issn = {2073-4425}, mesh = {Animals ; *Arthropods/genetics ; Bacteria/genetics ; Carbohydrates ; Escherichia coli/genetics ; Eukaryota ; *Gene Transfer, Horizontal ; Insecta ; Protein Sorting Signals/genetics ; Soil ; }, abstract = {Horizontal gene transfer (HGT) is defined as the acquisition by an organism of hereditary material from a phylogenetically unrelated organism. This process is mostly observed among bacteria and archaea, and considered less likely between microbes and multicellular eukaryotes. However, recent studies provide compelling evidence of the evolutionary importance of HGT in eukaryotes, driving functional innovation. Here, we study an HGT event in Folsomia candida (Collembola, Hexapoda) of a carbohydrate-active enzyme homologous to glycosyl hydrase group 43 (GH43). The gene encodes an N-terminal signal peptide, targeting the product for excretion, which suggests that it contributes to the diversity of digestive capacities of the detritivore host. The predicted α-L-arabinofuranosidase shows high similarity to genes in two other Collembola, an insect and a tardigrade. The gene was cloned and expressed in Escherichia coli using a cell-free protein expression system. The expressed protein showed activity against p-nitrophenyl-α-L-arabinofuranoside. Our work provides evidence for functional activity of an HGT gene in a soil-living detritivore, most likely from a bacterial donor, with genuine eukaryotic properties, such as a signal peptide. Co-evolution of metazoan GH43 genes with the Panarthropoda phylogeny suggests the HGT event took place early in the evolution of this ecdysozoan lineage.}, } @article {pmid36010485, year = {2022}, author = {Kamilari, E and Tsaltas, D and Stanton, C and Ross, RP}, title = {Metataxonomic Mapping of the Microbial Diversity of Irish and Eastern Mediterranean Cheeses.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {16}, pages = {}, pmid = {36010485}, issn = {2304-8158}, support = {SFI/12/RC/2273/SFI_/Science Foundation Ireland/Ireland ; }, abstract = {The distinct sensorial characteristics of local cheeses influence consumer preferences, and make an essential contribution to the local economy. Microbial diversity in cheese is among the fundamental contributors to sensorial and qualitative characteristics. However, knowledge regarding the existence of microbial patterns associated with regional production practices in ripened cheeses remains limited. The present research was conducted to test the hypothesis that the background metagenome of cheeses could be used as a marker of their origin. We compared Irish versus Eastern Mediterranean cheeses-namely Greek and Cypriot-using High Throughput Sequencing (HTS). The study identified a significantly distinct separation among cheeses originating from the three different countries, in terms of the total microbial community composition. The use of machine learning and biomarkers discovery algorithms defined key microbes that differentiate each geographic region. Finally, the development of interaction networks revealed that the key species developed mostly negative interactions with the other members of the communities, highlighting their dominance in the community. The findings of the present research demonstrate that metagenome could indeed be used as a biological marker of the origin of mature cheeses, and could provide further insight into the dynamics of microbial community composition in ripened cheeses.}, } @article {pmid36009744, year = {2022}, author = {Zhang, SD and Lin, GH and Han, JR and Lin, YW and Wang, FQ and Lu, DC and Xie, JX and Zhao, JX}, title = {Digestive Tract Morphology and Gut Microbiota Jointly Determine an Efficient Digestive Strategy in Subterranean Rodents: Plateau Zokor.}, journal = {Animals : an open access journal from MDPI}, volume = {12}, number = {16}, pages = {}, pmid = {36009744}, issn = {2076-2615}, support = {31760622//National Natural Science Foundation of China/ ; }, abstract = {Rodents' lifestyles vary in different environments, and to adapt to various lifestyles specific digestion strategies have been developed. Among these strategies, the morphology of the digestive tracts and the gut microbiota are considered to play the most important roles in such adaptations. However, how subterranean rodents adapt to extreme environments through regulating gut microbial diversity and morphology of the digestive tract has yet to be fully studied. Here, we conducted the comparisons of the gastrointestinal morphology, food intake, food assimilation, food digestibility and gut microbiota of plateau zokor Eospalax baileyi in Qinghai-Tibet Plateau and laboratory rats Rattus norvegicus to further understand the survival strategy in a typical subterranean rodent species endemic to the Qinghai-Tibet Plateau. Our results revealed that plateau zokor evolved an efficient foraging strategy with low food intake, high food digestibility, and ultimately achieved a similar amount of food assimilation to laboratory rats. The length and weight of the digestive tract of the plateau zokor was significantly higher than the laboratory rat. Particularly, the weight and length of the large intestine and cecum in plateau zokor is three times greater than that of the laboratory rat. Microbiome analysis showed that genus (i.e., Prevotella, Oscillospira, CF231, Ruminococcus and Bacteroides), which are usually associated with cellulose degradation, were significantly enriched in laboratory rats, compared to plateau zokor. However, prediction of metagenomic function revealed that both plateau zokor and laboratory rats shared the same functions in carbohydrate metabolism and energy metabolism. The higher digestibility of crude fiber in plateau zokor was mainly driven by the sizes of cecum and cecum tract, as well as those gut microbiota which associated with cellulose degradation. Altogether, our results highlight that both gut microbiota and the morphology of the digestive tract are vital to the digestion in wild rodents.}, } @article {pmid36009575, year = {2022}, author = {Pietrucci, D and Teofani, A and Milanesi, M and Fosso, B and Putignani, L and Messina, F and Pesole, G and Desideri, A and Chillemi, G}, title = {Machine Learning Data Analysis Highlights the Role of Parasutterella and Alloprevotella in Autism Spectrum Disorders.}, journal = {Biomedicines}, volume = {10}, number = {8}, pages = {}, pmid = {36009575}, issn = {2227-9059}, support = {"ProgettiStrategici 2019" Project N.A0320-2019-28090 "HGP-T21"//Regione Lazio/ ; RF-2018-12366931//Ministero della Salute/ ; }, abstract = {In recent years, the involvement of the gut microbiota in disease and health has been investigated by sequencing the 16S gene from fecal samples. Dysbiotic gut microbiota was also observed in Autism Spectrum Disorder (ASD), a neurodevelopmental disorder characterized by gastrointestinal symptoms. However, despite the relevant number of studies, it is still difficult to identify a typical dysbiotic profile in ASD patients. The discrepancies among these studies are due to technical factors (i.e., experimental procedures) and external parameters (i.e., dietary habits). In this paper, we collected 959 samples from eight available projects (540 ASD and 419 Healthy Controls, HC) and reduced the observed bias among studies. Then, we applied a Machine Learning (ML) approach to create a predictor able to discriminate between ASD and HC. We tested and optimized three algorithms: Random Forest, Support Vector Machine and Gradient Boosting Machine. All three algorithms confirmed the importance of five different genera, including Parasutterella and Alloprevotella. Furthermore, our results show that ML algorithms could identify common taxonomic features by comparing datasets obtained from countries characterized by latent confounding variables.}, } @article {pmid36009027, year = {2022}, author = {Błażejewska, A and Zalewska, M and Grudniak, A and Popowska, M}, title = {A Comprehensive Study of the Microbiome, Resistome, and Physical and Chemical Characteristics of Chicken Waste from Intensive Farms.}, journal = {Biomolecules}, volume = {12}, number = {8}, pages = {}, pmid = {36009027}, issn = {2218-273X}, mesh = {Angiotensin Receptor Antagonists ; Angiotensin-Converting Enzyme Inhibitors ; Animals ; Anti-Bacterial Agents/pharmacology ; *Chickens ; Farms ; Genes, Bacterial ; Manure ; *Microbiota/genetics ; }, abstract = {The application of chicken waste to farmland could be detrimental to public health. It may contribute to the dissemination of antibiotic-resistance genes (ARGs) and antibiotic-resistant bacteria (ARB) from feces and their subsequent entry into the food chain. The present study analyzes the metagenome and resistome of chicken manure and litter obtained from a commercial chicken farm in Poland. ARB were isolated, identified, and screened for antibiogram fingerprints using standard microbiological and molecular methods. The physicochemical properties of the chicken waste were also determined. ARGs, integrons, and mobile genetic elements (MGE) in chicken waste were analyzed using high-throughput SmartChip qPCR. The results confirm the presence of many ARGs, probably located in MGE, which can be transferred to other bacteria. Potentially pathogenic or opportunistic microorganisms and phytopathogens were isolated. More than 50% of the isolated strains were classified as being multi-drug resistant, and the remainder were resistant to at least one antibiotic class; these pose a real risk of entering the groundwater and contaminating the surrounding environment. Our results indicate that while chicken manure can be sufficient sources of the nutrients essential for plant growth, its microbiological aspects make this material highly dangerous to the environment.}, } @article {pmid36009014, year = {2022}, author = {Fang, C and Zuo, K and Jiao, K and Zhu, X and Fu, Y and Zhong, J and Xu, L and Yang, X}, title = {PAGln, an Atrial Fibrillation-Linked Gut Microbial Metabolite, Acts as a Promoter of Atrial Myocyte Injury.}, journal = {Biomolecules}, volume = {12}, number = {8}, pages = {}, pmid = {36009014}, issn = {2218-273X}, mesh = {*Atrial Fibrillation ; Calcium-Calmodulin-Dependent Protein Kinase Type 2/metabolism ; *Gastrointestinal Microbiome ; Humans ; Myocytes, Cardiac/metabolism ; Ryanodine Receptor Calcium Release Channel/metabolism ; }, abstract = {Phenylacetylglutamine (PAGln), a gut microbiota (GM)-derived metabolite, is associated with cardiovascular disease. Studies have shown that disordered GM participated in the progression of atrial fibrillation (AF), but the relationship between PAGln and AF is unclear. This study investigated the characteristics of PAGln in AF patients and its impact on atrial myocytes. Based on our previous metagenomic data, the relative abundance of porA, a critical bacterial enzyme for PAGln synthesis, exhibited an increased tendency in AF. In an independent cohort consisting of 42 controls without AF and 92 AF patients, plasma PAGln levels were higher in AF patients than in controls (p < 0.001) by immunoassay. Notably, PAGln exerted a predictive potential of AF with an AUC of 0.774 (p < 0.001), and a predictive model constructed based on the PAGln and Taiwan AF score further improved the predictive potential. Furthermore, a positive correlation was determined between PAGln and LA diameter. Subsequently, the effect of PAGln intervention was examined on HL-1 cells in vitro, revealing that PAGln increased apoptosis, reactive oxygen species (ROS) production, CaMKII and RyR2 activation and decreased cell viability. In conclusion, increased PAGln was associated with AF, and PAGln might contribute to the AF pathogenesis by promoting oxidative stress and apoptosis in atrial myocytes.}, } @article {pmid36008821, year = {2022}, author = {Guitor, AK and Yousuf, EI and Raphenya, AR and Hutton, EK and Morrison, KM and McArthur, AG and Wright, GD and Stearns, JC}, title = {Capturing the antibiotic resistome of preterm infants reveals new benefits of probiotic supplementation.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {136}, pmid = {36008821}, issn = {2049-2618}, support = {FRN-148463//CIHR/Canada ; PJT-156214//CIHR/Canada ; GSD-164145//CIHR/Canada ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria/genetics ; Dietary Supplements ; Female ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; *Premature Birth ; *Probiotics ; }, abstract = {BACKGROUND: Probiotic use in preterm infants can mitigate the impact of antibiotic exposure and reduce rates of certain illnesses; however, the benefit on the gut resistome, the collection of antibiotic resistance genes, requires further investigation. We hypothesized that probiotic supplementation of early preterm infants (born < 32-week gestation) while in hospital reduces the prevalence of antibiotic resistance genes associated with pathogenic bacteria in the gut. We used a targeted capture approach to compare the resistome from stool samples collected at the term corrected age of 40 weeks for two groups of preterm infants (those that routinely received a multi-strain probiotic during hospitalization and those that did not) with samples from full-term infants at 10 days of age to identify if preterm birth or probiotic supplementation impacted the resistome. We also compared the two groups of preterm infants up to 5 months of age to identify persistent antibiotic resistance genes.

RESULTS: At the term corrected age, or 10 days of age for the full-term infants, we found over 80 antibiotic resistance genes in the preterm infants that did not receive probiotics that were not identified in either the full-term or probiotic-supplemented preterm infants. More genes associated with antibiotic inactivation mechanisms were identified in preterm infants unexposed to probiotics at this collection time-point compared to the other infants. We further linked these genes to mobile genetic elements and Enterobacteriaceae, which were also abundant in their gut microbiomes. Various genes associated with aminoglycoside and beta-lactam resistance, commonly found in pathogenic bacteria, were retained for up to 5 months in the preterm infants that did not receive probiotics.

CONCLUSIONS: This pilot survey of preterm infants shows that probiotics administered after preterm birth during hospitalization reduced the diversity and prevented persistence of antibiotic resistance genes in the gut microbiome. The benefits of probiotic use on the microbiome and the resistome should be further explored in larger groups of infants. Due to its high sensitivity and lower sequencing cost, our targeted capture approach can facilitate these surveys to further address the implications of resistance genes persisting into infancy without the need for large-scale metagenomic sequencing. Video Abstract.}, } @article {pmid36008577, year = {2022}, author = {Wang, S and Ventolero, M and Hu, H and Li, X}, title = {A revisit to universal single-copy genes in bacterial genomes.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {14550}, pmid = {36008577}, issn = {2045-2322}, mesh = {Bacteria/genetics ; *Biological Evolution ; Genes, Bacterial ; *Genome, Bacterial ; Metagenomics ; Phylogeny ; }, abstract = {Universal single-copy genes (USCGs) are widely used for species classification and taxonomic profiling. Despite many studies on USCGs, our understanding of USCGs in bacterial genomes might be out of date, especially how different the USCGs are in different studies, how well a set of USCGs can distinguish two bacterial species, whether USCGs can separate different strains of a bacterial species, to name a few. To fill the void, we studied USCGs in the most updated complete bacterial genomes. We showed that different USCG sets are quite different while coming from highly similar functional categories. We also found that although USCGs occur once in almost all bacterial genomes, each USCG does occur multiple times in certain genomes. We demonstrated that USCGs are reliable markers to distinguish different species while they cannot distinguish different strains of most bacterial species. Our study sheds new light on the usage and limitations of USCGs, which will facilitate their applications in evolutionary, phylogenomic, and metagenomic studies.}, } @article {pmid36007398, year = {2022}, author = {Jia, Y and Wang, P and Ou, Y and Yan, Y and Zhou, S and Sun, L and Lu, H}, title = {Insights into the microbial response mechanisms to ciprofloxacin during sulfur-mediated biological wastewater treatment using a metagenomics approach.}, journal = {Water research}, volume = {223}, number = {}, pages = {118995}, doi = {10.1016/j.watres.2022.118995}, pmid = {36007398}, issn = {1879-2448}, mesh = {Adenosine Triphosphate ; Anti-Bacterial Agents ; Bioreactors ; Carbon ; *Ciprofloxacin ; Cytochromes c ; Metagenomics ; NAD ; Sulfates/metabolism ; Sulfur/metabolism ; Wastewater ; *Water Purification ; }, abstract = {The fate and removal of ciprofloxacin, a class of fluoroquinolone antibiotic, during sulfur-mediated biological wastewater treatment has been recently well documented. However, little is known regarding the genetic response of microorganisms to ciprofloxacin. Here, a lab-scale anaerobic sulfate-reducing bioreactor was continuously operated over a long term for ciprofloxacin-contaminated wastewater treatment to investigate the response of the microorganisms to ciprofloxacin by adopting a metagenomics approach. It was found that total organic carbon (TOC) removal and sulfate reduction were promoted by approximately 10% under ciprofloxacin stress, along with the enrichment of functional genera (e.g., Desulfobacter, Geobacter) involved in carbon and sulfur metabolism. The metagenomic analytical results demonstrated that ciprofloxacin triggered the microbial SOS response, as demonstrated by the up-regulation of the multidrug efflux pump genes (8-125-fold higher than that of the control) and ciprofloxacin-degrading genes (4-33-fold higher than that of the control). Moreover, the contents of ATP, NADH, and cytochrome C, as well as related functional genes (including genes involved in energy generation, electron transport, carbon metabolism, and sulfur metabolism) were markedly increased under ciprofloxacin stress. This demonstrated that the carbon and sulfur metabolisms were enhanced for energy (ATP) generation and electron transport in response to ciprofloxacin-induced stress. Interestingly, the microbes tended to cooperate while being subjected exposure to exogenous ciprofloxacin according to the reconstructed metabolic network using the NetSeed model. Particularly, the species with higher complementarity indices played more pivotal roles in strengthening microbial metabolism and the SOS response under long-term ciprofloxacin stress. This study characterized the response mechanisms of microorganisms to ciprofloxacin at the genetic level in sulfur-mediated biological wastewater treatment. These new understandings will contribute the scientific basis for improving and optimizing the sulfur-mediated bioprocess for antibiotics-laden wastewater treatment.}, } @article {pmid36006105, year = {2022}, author = {Liao, J and Ji, S and Chi, Y}, title = {Effects of Discarded Masks on the Offshore Microorganisms during the COVID-19 Pandemic.}, journal = {Toxics}, volume = {10}, number = {8}, pages = {}, pmid = {36006105}, issn = {2305-6304}, support = {JAT190525, JAT190513//Fujian Provincial Department of Educational Project/ ; 2022J011106//Natural Science Foundation of Fujian Province/ ; }, abstract = {Numerous disposable plastic masks had been produced and used for preventing the worldwide COVID-19 pandemic effectively. Discarded masks are a potential source of microplastic pollution in marine ecosystems. The effect of discarded masks on offshore microorganisms is still unclear. Herein, we profiled the interaction between the microplastics released by discarded masks and marine microbes. The effects of mask quantity, time, and environment on the microplastic-related communities were determined. We characterized the bacterial communities of each group using 16S rRNA gene sequencing and metagenomic sequencing and correlated the community diversity to the physicochemical properties of seawater. We found that the diversity and richness of microflora on the surface of microplastics with different quantity and time varied significantly. Proteobacteria are the main bacteria on microplastics, and the KEGG metabolic pathway prediction shows that amino acid metabolism and carbohydrate metabolism were abundant. In addition, there was a correlation between bacterial communities and Antibiotic Resistance Ontology (ARO). We used scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy (FT-IR) techniques to evaluate the plastic polymer characteristics of disposable medical masks. Our research shows that disposable medical masks immersed in seawater can alter the microbial community. This study provides the most recent data and insights into the contamination of discarded masks in the marine environment.}, } @article {pmid36005608, year = {2022}, author = {Mengucci, C and Nissen, L and Picone, G and Malpuech-Brugère, C and Orfila, C and Ricciardiello, L and Bordoni, A and Capozzi, F and Gianotti, A}, title = {K-Clique Multiomics Framework: A Novel Protocol to Decipher the Role of Gut Microbiota Communities in Nutritional Intervention Trials.}, journal = {Metabolites}, volume = {12}, number = {8}, pages = {}, pmid = {36005608}, issn = {2218-1989}, support = {FP7 grant agreement n° 311876: Pathway-27.//European Union/ ; }, abstract = {The availability of omics data providing information from different layers of complex biological processes that link nutrition to human health would benefit from the development of integrated approaches combining holistically individual omics data, including those associated with the microbiota that impacts the metabolisation and bioavailability of food components. Microbiota must be considered as a set of populations of interconnected consortia, with compensatory capacities to adapt to different nutritional intake. To study the consortium nature of the microbiome, we must rely on specially designed data analysis tools. The purpose of this work is to propose the construction of a general correlation network-based explorative tool, suitable for nutritional clinical trials, by integrating omics data from faecal microbial taxa, stool metabolome (1H NMR spectra) and GC-MS for stool volatilome. The presented approach exploits a descriptive paradigm necessary for a true multiomics integration of data, which is a powerful tool to investigate the complex physiological effects of nutritional interventions.}, } @article {pmid36005400, year = {2022}, author = {Uehara, M and Inoue, T and Kominato, M and Hase, S and Sasaki, E and Toyoda, A and Sakakibara, Y}, title = {Intraintestinal Analysis of the Functional Activity of Microbiomes and Its Application to the Common Marmoset Intestine.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0052022}, pmid = {36005400}, issn = {2379-5077}, mesh = {Animals ; Humans ; Callithrix/genetics ; *Microbiota/genetics ; Metagenome ; Intestines ; *Gastrointestinal Microbiome/genetics ; }, abstract = {The intestinal microbiome is closely related to host health, and metatranscriptomic analysis can be used to assess the functional activity of microbiomes by quantifying microbial gene expression levels, helping elucidate the interactions between the microbiome and the environment. However, the functional changes in the microbiome along the host intestinal tract remain unknown, and previous analytical methods have limitations, such as potentially overlooking unknown genes due to dependence on existing databases. The objective of this study is to develop a computational pipeline combined with next-generation sequencing for spatial covariation analysis of the functional activity of microbiomes at multiple intestinal sites (biogeographic locations) within the same individual. This method reconstructs a reference metagenomic sequence across multiple intestinal sites and integrates the metagenome and metatranscriptome, allowing the gene expression levels of the microbiome, including unknown bacterial genes, to be compared among multiple sites. When this method was applied to metatranscriptomic analysis in the intestinal tract of common marmosets, a New World monkey, the reconstructed metagenome covered most of the expressed genes and revealed that the differences in microbial gene expression among the cecum, transverse colon, and feces were more dynamic and sensitive to environmental shifts than the abundances of the genes. In addition, metatranscriptomic profiling at three intestinal sites of the same individual enabled covariation analysis incorporating spatial relevance, accurately predicting the function of a total of 10,856 unknown genes. Our findings demonstrate that our proposed analytical method captures functional changes in microbiomes at the gene resolution level. IMPORTANCE We developed an analysis method that integrates metagenomes and metatranscriptomes from multiple intestinal sites to elucidate how microbial function varies along the intestinal tract. This method enables spatial covariation analysis of the functional activity of microbiomes and accurate identification of gene expression changes among intestinal sites, including changes in the expression of unknown bacterial genes. Moreover, we applied this method to the investigation of the common marmoset intestine, which is anatomically and pharmacologically similar to that of humans. Our findings indicate the expression pattern of the microbiome varies in response to changes in the internal environment along the intestinal tract, and this microbial change may affect the intestinal environment.}, } @article {pmid36005385, year = {2022}, author = {Reteng, P and Nguyen Thuy, L and Rahman, M and Bispo de Filippis, AM and Hayashida, K and Sugi, T and Gonzalez, G and Hall, WW and Nguyen Thi, LA and Yamagishi, J}, title = {Circular Whole-Transcriptome Amplification (cWTA) and mNGS Screening Enhanced by a Group Testing Algorithm (mEGA) Enable High-Throughput and Comprehensive Virus Identification.}, journal = {mSphere}, volume = {7}, number = {5}, pages = {e0033222}, pmid = {36005385}, issn = {2379-5042}, mesh = {Humans ; *Transcriptome ; High-Throughput Nucleotide Sequencing/methods ; Algorithms ; RNA ; *Nucleic Acids ; }, abstract = {Metagenomic next-generation sequencing (mNGS) offers a hypothesis-free approach for pathogen detection, but its applicability in clinical diagnosis, in addition to other factors, remains limited due to complicated library construction. The present study describes a PCR-free isothermal workflow for mNGS targeting RNA, based on a multiple displacement amplification, termed circular whole-transcriptome amplification (cWTA), as the template is circularized before amplification. The cWTA approach was validated with clinical samples and nanopore sequencing. Reads homologous to dengue virus 2 and chikungunya virus were detected in clinical samples from Bangladesh and Brazil, respectively. In addition, the practicality of a high-throughput detection system that combines mNGS and a group testing algorithm termed mNGS screening enhanced by a group testing algorithm (mEGA) was established. This approach enabled significant library size reduction while permitting trackability between samples and diagnostic results. Serum samples of patients with undifferentiated febrile illnesses from Vietnam (n = 43) were also amplified with cWTA, divided into 11 pools, processed for library construction, and sequenced. Dengue virus 2, hepatitis B virus, and parvovirus B19 were successfully detected without prior knowledge of their existence. Collectively, cWTA with the nanopore platform opens the possibility of hypothesis-free on-site comprehensive pathogen diagnosis, while mEGA contributes to the scaling up of sample throughput. IMPORTANCE Given the breadth of pathogens that cause infections, a single approach that can detect a wide range of pathogens is ideal but is impractical due to the available tests being highly specific to a certain pathogen. Recent developments in sequencing technology have introduced mNGS as an alternative that provides detection of a wide-range of pathogens by detecting the presence of their nucleic acids in the sample. However, sequencing library preparation is still a bottleneck, as it is complicated, costly, and time-consuming. In our studies, alternative approaches to optimize library construction for mNGS were developed. This included isothermal nucleic acid amplification and expansion of sample throughput with a group testing algorithm. These methods can improve the utilization of mNGS as a diagnostic tool and can serve as a high-throughput screening system aiding infectious disease surveillance.}, } @article {pmid36005344, year = {2022}, author = {Zheng, X and Zhu, Q and Qin, M and Zhou, Z and Liu, C and Wang, L and Shi, F}, title = {The Role of Feeding Characteristics in Shaping Gut Microbiota Composition and Function of Ensifera (Orthoptera).}, journal = {Insects}, volume = {13}, number = {8}, pages = {}, pmid = {36005344}, issn = {2075-4450}, support = {2022Q2//Hebei Academy of Sciences/ ; 22A05//Hebei Academy of Sciences/ ; 2020031513-2//Provincial School Cooperation Development Fund Project of Hebei Province/ ; }, abstract = {Feeding habits were the primary factor affecting the gut bacterial communities in Ensifera. However, the interaction mechanism between the gut microbiota and feeding characteristics is not precisely understood. Here, the gut microbiota of Ensifera with diverse feeding habits was analyzed by shotgun metagenomic sequencing to further clarify the composition and function of the gut microbiota and its relationship with feeding characteristics. Our results indicate that under the influence of feeding habits, the gut microbial communities of Ensifera showed specific characteristics. Firstly, the gut microbial communities of the Ensifera with different feeding habits differed significantly, among which the gut microbial diversity of the herbivorous Mecopoda niponensis was the highest. Secondly, the functional genes related to feeding habits were in high abundance. Thirdly, the specific function of the gut microbial species in the omnivorous Gryllotalpa orientalis showed that the more diverse the feeding behavior of Ensifera, the worse the functional specificity related to the feeding characteristics of its gut microbiota. However, feeding habits were not the only factors affecting the gut microbiota of Ensifera. Some microorganisms' genes, whose functions were unrelated to feeding characteristics but were relevant to energy acquisition and nutrient absorption, were detected in high abundance. Our results were the first to report on the composition and function of the gut microbiota of Ensifera based on shotgun metagenomic sequencing and to explore the potential mechanism of the gut microbiota's association with diverse feeding habits.}, } @article {pmid36004313, year = {2022}, author = {Schulz, E and Grumaz, S and Hatzl, S and Gornicec, M and Valentin, T and Huber-Kraßnitzer, B and Kriegl, L and Uhl, B and Deutsch, A and Greinix, H and Krause, R and Neumeister, P}, title = {Pathogen Detection by Metagenomic Next-Generation Sequencing During Neutropenic Fever in Patients With Hematological Malignancies.}, journal = {Open forum infectious diseases}, volume = {9}, number = {8}, pages = {ofac393}, pmid = {36004313}, issn = {2328-8957}, abstract = {BACKGROUND: Febrile neutropenia (FN) after chemotherapy is a major cause of morbidity during cancer treatment. The performance of metagenomic next-generation sequencing (mNGS) of circulating cell-free deoxyribonucleic acid from plasma may be superior to blood culture (BC) diagnostics for identification of causative pathogens. The aim of this study was to validate mNGS (DISQVER test) for the detection of pathogens in hematologic patients with FN.

METHODS: We collected paired whole blood specimens from central venous catheter and peripheral vein during FN for BC and mNGS testing. We repeated paired sampling at the earliest after 3 days of fever, which was defined as 1 FN episode. All clinical data were retrospectively reviewed by an infectious disease expert panel. We calculated percent positive agreement (PPA), percent negative agreement (PNA), percent overall agreement (POA), and sensitivity and specificity.

RESULTS: We analyzed a total of 98 unselected FN episodes in 61 patients who developed predominantly FN after conditioning therapy for allogeneic (n = 22) or autologous (n = 21) hematopoietic stem cell transplantation. Success rate of mNGS was 99% (97 of 98). Positivity rate of mNGS was 43% (42 of 97) overall and 32% (31 of 97) excluding viruses compared to 14% (14 of 98) in BC. The PPA, PNA, and POA between mNGS and BC were 84.6% (95% confidence interval [CI], 54.6% to 98.1%), 63.1% (95% CI, 51.9% to 73.4%), and 66% (95% CI, 55.7% to 75.3%), respectively. Sensitivity for bacteria or fungi was 40% (95% CI, 28.0% to 52.9%) and 18.5% (95% CI, 9.9% to 30.0%), respectively.

CONCLUSIONS: Pathogen detection by mNGS (DISQVER) during unselected FN episodes shows 2-fold higher sensitivity and a broader pathogen spectrum than BC.}, } @article {pmid36003944, year = {2022}, author = {Zhao, C and Liu, L and Gao, L and Bai, L}, title = {A comprehensive comparison of fecal microbiota in three ecological bird groups of raptors, waders, and waterfowl.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {919111}, pmid = {36003944}, issn = {1664-302X}, abstract = {Gut microbiota plays a vital role in maintaining the health and immunity of wild birds. However, less is known about the comparison of fecal microbiota between different ecological groups of wild birds, particularly in the Yellow River National Wetland in Baotou, China, an important transit point for birds migrating all over the East Asia-Australian and Central Asian flyways. In this study, we characterized the fecal microbiota and potential microbial function in nine bird species of raptors, waders, and waterfowl using 16S rRNA gene amplicon sequencing to reveal the microbiota differences and interaction patterns. The results indicated that there was no significant difference in α-diversity, but a significant difference in β-diversity between the three groups of birds. The fecal bacterial microbiota was dominated by Firmicutes, Proteobacteria, Actinobacteria, and Bacteroidetes in all groups of birds. Furthermore, we identified five bacterial genera that were significantly higher in raptors, five genera that were significantly higher in waders, and two genera that were more abundant in waterfowl. The bacterial co-occurrence network results revealed 15 and 26 key genera in raptors and waterfowls, respectively. The microbial network in waterfowl exhibited a stronger correlation pattern than that in raptors. PICRUSt2 predictions indicated that fecal bacterial function was significantly enriched in the antibiotic biosynthesis pathway in all three groups. Metabolic pathways related to cell motility (bacterial chemotaxis and flagellar assembly) were significantly more abundant in raptors than in waders, whereas waders were enriched in lipid metabolism (synthesis and degradation of ketone bodies and fatty acid biosynthesis). The fecal microbiota in waterfowl harbored more abundant vitamin B6 metabolism, RNA polymerase, and tyrosine and tryptophan biosynthesis. This comparative study revealed the microbial community structure, microbial co-occurrence patterns, and potential functions, providing a better understanding of the ecology and conservation of wild birds. Future studies may focus on unraveling metagenomic functions and dynamics along with the migration routine or different seasons by metagenomics or metatranscriptomics.}, } @article {pmid36003925, year = {2022}, author = {Tan, G and Wang, Y and Hu, M and Li, X and Li, X and Pan, Z and Li, M and Li, L and Zheng, Z}, title = {Comparative evaluation of the microbial diversity and metabolite profiles of Japanese-style and Cantonese-style soy sauce fermentation.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {976206}, pmid = {36003925}, issn = {1664-302X}, abstract = {Microorganisms play essential roles in flavor formation during soy sauce fermentation. Different soy sauce fermentation types significantly affect flavor formation. However, comparisons of microbial communities and metabolites between different fermentation types have been little studied. Here, we investigated variation in microbial communities, metabolite profiles, and metabolic pathways during Japanese-type (JP) and Cantonese-type (CP) fermentation. Free amino acids and volatile compound profiles varied significantly between fermentation types, with JP samples containing higher contents of esters (39.84%; p < 0.05), alcohols (44.70%; p < 0.05) in the 120 d fermentation samples. Volatile compound profiles varied significantly between fermentation types, with JP samples containing higher contents of esters, alcohols, and free amino acids (p < 0.05). Metagenomic analysis indicated that both JP and CP communities were dominated by Tetragenococcus, Staphylococcus, Weissella (bacteria), and Aspergillus (fungi), but the two communities varied differently over time. Tetragenococcus drastically increased in abundance throughout the fermentation (from 0.02 to 59.2%) in JP fermentation, whereas Tetragenococcus (36.7%) and Staphylococcus (29.7%) dominated at 120 d of fermentation in CP fermentation. Metagenomic functional profiles revealed that the abundances of most genes involved with carbohydrate, amino acid, and lipid metabolism exhibited significant differences between fermentation types (p < 0.05) during the middle to late fermentation stages. Furthermore, predicted metabolic pathways for volatile substance biosynthesis differed between JP and CP fermentation, likely explaining the differences in flavor metabolite profiles. In addition, most of the genes associated with flavor generation were affiliated with Tetragenococcus, Weissella, Staphylococcus, Bacillus, and Aspergillus, suggesting that these microbes play important roles in flavor production during soy sauce fermentation. This study significantly improves our understanding of microbial functions and their metabolic roles in flavor formation during different soy sauce fermentation processes.}, } @article {pmid36003895, year = {2022}, author = {Verma, J and Sourirajan, A and Dev, K}, title = {Bacterial diversity in 110 thermal hot springs of Indian Himalayan Region (IHR).}, journal = {3 Biotech}, volume = {12}, number = {9}, pages = {238}, pmid = {36003895}, issn = {2190-572X}, abstract = {Thermal hot springs are present throughout the world and constitute a unique habitat for microbial diversity. The current investigation is conducted to study the bacterial diversity of thermophilic microorganisms in thermal hot springs of the Indian Himalayan Region (IHR). As of today, 110 geothermal hot springs have been explored for microbial diversity. In this study, we observed that the growth of thermophilic bacteria isolated from thermal hot springs of IHR ranges between 40 and 100 °C, and pH of 3.5-8 have been reported in the literature. The major bacterial species reported from the thermal hot springs of IHR are Bacillus spp., Geobacillus spp., Paenibacillus spp., Pseudomonas spp., Anoxybacillus, Paenibacillus, Brevibacillus, Aneurinibacillus, Thermus aquaticus, Aquimonas, Flavobacterium, etc. Furthermore, bacterial isolates from thermal hot springs of IHR have been reported to produce various enzymes and metabolites such as amylase, β-galactosidase, cellulase, nitrate reductase, acetoin, caffeine degradation enzymes, lipase, urease, and laccase. Metagenomic study and the entire genomic shotgun project have established the impact of physicochemical parameters (temperature and pH) on developing the microbiome. We have discussed the discoveries of microbiological data on the hot springs of IHR until the end of year 2021. As a whole, the microbiome adapts themselves as successful inhabitants to extreme environmental conditions and also serves as a diverse resource for potential applications in health, food, and environment.}, } @article {pmid36003287, year = {2022}, author = {Xie, YC and Jing, XB and Chen, X and Chen, LZ and Zhang, SH and Cai, XB}, title = {Fecal microbiota transplantation treatment for type 1 diabetes mellitus with malnutrition: a case report.}, journal = {Therapeutic advances in chronic disease}, volume = {13}, number = {}, pages = {20406223221117449}, pmid = {36003287}, issn = {2040-6223}, abstract = {Type 1 diabetes mellitus (T1DM) is a chronic autoimmune disease. Not only genetics, but the intestinal environment affected by gut microbiota is also the key to pathogenesis. Besides the occurrence of diabetes, gut microbiota dysbiosis may also contribute to the development of diabetes-related complications. Fecal microbiota transplantation (FMT) is an emerging technique that had shown its potential as a treatment for metabolic disease. Here, we report the first case of T1DM with malnutrition and gastrointestinal symptoms treated with FMT. A 24-year-old T1DM patient suffered from poor blood glucose control, recurrent nausea and vomiting, severe malnutrition, and intractable constipation after insulin treatment. The clinical response of the patients after FMT was well, especially nausea and vomiting were significantly relieved. In addition, constipation, nutritional status, and blood glucose control (fasting blood glucose, HbA1c) gradually improved. A degree of similarity was found in gut microbiota composition between the patient and healthy donor after FMT while it was totally different before the treatment. Furthermore, pathway function analysis of MetaCYC database implies that the potential mechanism of the response of FMT may be driven by specific bacteria involved in several metabolic pathways that need further exploration. To sum up, we believe that the reconstruction of intestinal flora by FMT may be a new choice for the treatment of T1DM patients with malnutrition.}, } @article {pmid36002826, year = {2022}, author = {Liu, Z and Xing, L and Huang, W and Liu, B and Wan, F and Raffa, KF and Hofstetter, RW and Qian, W and Sun, J}, title = {Chromosome-level genome assembly and population genomic analyses provide insights into adaptive evolution of the red turpentine beetle, Dendroctonus valens.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {190}, pmid = {36002826}, issn = {1741-7007}, mesh = {Animals ; Chromosomes ; *Coleoptera/genetics ; Genomics ; Metagenomics ; *Pinus/genetics ; Turpentine ; }, abstract = {BACKGROUND: Biological invasions are responsible for substantial environmental and economic losses. The red turpentine beetle (RTB), Dendroctonus valens LeConte, is an important invasive bark beetle from North America that has caused substantial tree mortality in China. The lack of a high-quality reference genome seriously limits deciphering the extent to which genetic adaptions resulted in a secondary pest becoming so destructive in its invaded area.

RESULTS: Here, we present a 322.41 Mb chromosome-scale reference genome of RTB, of which 98% of assembled sequences are anchored onto fourteen linkage groups including the X chromosome with a N50 size of 24.36 Mb, which is significantly greater than other Coleoptera species. Repetitive sequences make up 45.22% of the genome, which is higher than four other Coleoptera species, i.e., Mountain pine beetle Dendroctonus ponderosae, red flour beetle Tribolium castaneum, blister beetle Hycleus cichorii, and Colorado potato beetle Leptinotarsa decemlineata. We identify rapidly expanded gene families and positively selected genes in RTB, which may be responsible for its rapid environmental adaptation. Population genetic structure of RTB was revealed by genome resequencing of geographic populations in native and invaded regions, suggesting substantial divergence of the North American population and illustrates the possible invasion and spread route in China. Selective sweep analysis highlighted the enhanced ability of Chinese populations in environmental adaptation.

CONCLUSIONS: Overall, our high-quality reference genome represents an important resource for genomics study of invasive bark beetles, which will facilitate the functional study and decipher mechanism underlying invasion success of RTB by integrating the Pinus tabuliformis genome.}, } @article {pmid36002692, year = {2022}, author = {Xiao, E and Sun, W and Ning, Z and Wang, Y and Meng, F and Deng, J and Fan, W and Xiao, T}, title = {Occurrence and dissemination of antibiotic resistance genes in mine soil ecosystems.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {18}, pages = {6289-6299}, pmid = {36002692}, issn = {1432-0614}, support = {41830753//National Natural Science Foundation of China/ ; 41807127//National Natural Science Foundation of China/ ; U1612442//National Natural Science Foundation of China/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Cell Cycle Proteins/genetics ; Drug Resistance, Microbial/genetics ; Ecosystem ; Escherichia coli/genetics ; *Escherichia coli Proteins/genetics ; Genes, Bacterial ; *Soil ; Soil Microbiology ; }, abstract = {Metal(loid) selection contributes to selection pressure on antibiotic resistance, but to our knowledge, evidence of the dissemination of antibiotic resistance genes (ARGs) induced by metal(loid)s in mine soil ecosystems is rare. In the current study, using a high-throughput sequencing (HTS)-based metagenomic approach, 819 ARG subtypes were identified in a mine soil ecosystem, indicating that these environmental habitats are important reservoirs of ARGs. The results showed that metal(loid)-induced coselection has an important role in the distribution of soil ARGs. Furthermore, metal(loid) selection-induced ARGs were mainly associated with resistance-nodulation-division (RND) antibiotic efflux, which is distinct from what is observed in agricultural soil ecosystems. By using independent genome binning, metal(loid)s were shown impose coselection pressure on multiple ARGs residing on mobile genetic elements (MGEs), which promotes the dissemination of the antibiotic resistome. Interestingly, the current results showed that the density of several MGEs conferring ARGs was considerably higher in organisms most closely related to the priority pathogens Pseudomonas aeruginosa and Escherichia coli. Together, the results of this study indicate that mine soil ecosystems are important reservoirs of ARGs and that metal(loid)-induced coselection plays critical roles in the dissemination of ARGs in this type of soil habitat. KEY POINTS: • Mining soil ecosystem is a reservoir of antibiotic resistance genes (ARGs). • ARGs distribute via bacterial resistance-nodulation-division efflux systems. • Metal(loid)s coselected ARGs residing on mobile genetic elements in P. aeruginosa and E. coli.}, } @article {pmid36001521, year = {2023}, author = {Shen, Y and Zhu, J and Deng, Z and Lu, W and Wang, H}, title = {EnsDeepDP: An Ensemble Deep Learning Approach for Disease Prediction Through Metagenomics.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {20}, number = {2}, pages = {986-998}, doi = {10.1109/TCBB.2022.3201295}, pmid = {36001521}, issn = {1557-9964}, mesh = {Humans ; Metagenomics ; *Deep Learning ; Algorithms ; Machine Learning ; *Microbiota/genetics ; }, abstract = {A growing number of studies show that the human microbiome plays a vital role in human health and can be a crucial factor in predicting certain human diseases. However, microbiome data are often characterized by the limited samples and high-dimensional features, which pose a great challenge for machine learning methods. Therefore, this paper proposes a novel ensemble deep learning disease prediction method that combines unsupervised and supervised learning paradigms. First, unsupervised deep learning methods are used to learn the potential representation of the sample. Afterwards, the disease scoring strategy is developed based on the deep representations as the informative features for ensemble analysis. To ensure the optimal ensemble, a score selection mechanism is constructed, and performance boosting features are engaged with the original sample. Finally, the composite features are trained with gradient boosting classifier for health status decision. For case study, the ensemble deep learning flowchart has been demonstrated on six public datasets extracted from the human microbiome profiling. The results show that compared with the existing algorithms, our framework achieves better performance on disease prediction.}, } @article {pmid36001207, year = {2022}, author = {Garzaro, M and Zhao, LP and De Castro, N and Mercier-Delarue, S and Camelena, F and Pereyre, S and Gardette, M and Berçot, B and Malphettes, M and Bébéar, C and Bouaziz, JD and Le Goff, J and Galicier, L and Salmona, M}, title = {Metagenomic next-generation sequencing restores the diagnosis of a rare infectious complication of B cell depletion.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {41}, number = {10}, pages = {1269-1273}, pmid = {36001207}, issn = {1435-4373}, mesh = {Anti-Bacterial Agents/therapeutic use ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Middle Aged ; *Mycoplasma Infections/microbiology ; Mycoplasma hominis ; Rituximab/therapeutic use ; Ureaplasma ; *Ureaplasma Infections/microbiology ; Ureaplasma urealyticum ; }, abstract = {A 45-year-old female patient receiving rituximab for B cell non-Hodgkin follicular lymphoma presented unexplained recurrent fever, abdominal discomfort, and pollakiuria. We performed shotgun metagenomic sequencing from peri-kidney collection that identified a co-infection with Mycoplasma hominis and Ureaplasma urealyticum. The patient recovered with sequelae after appropriate antibiotic treatment was given.}, } @article {pmid36000911, year = {2022}, author = {Qi, Y and Ai, L and Zhu, C and Ye, F and Lv, R and Wang, J and Mao, Y and Lu, N and Tan, W}, title = {Wild Hedgehogs and Their Parasitic Ticks Coinfected with Multiple Tick-Borne Pathogens in Jiangsu Province, Eastern China.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0213822}, pmid = {36000911}, issn = {2165-0497}, mesh = {Animals ; Humans ; *Ticks/microbiology/parasitology ; Hedgehogs/parasitology ; *Coinfection/epidemiology/veterinary ; *Rickettsia/genetics ; *Tick-Borne Diseases/epidemiology/veterinary/microbiology ; Ehrlichia/genetics ; *Parasites ; }, abstract = {The increasing awareness of emerging tickborne pathogens (TBPs) has inspired much research. In the present study, the coinfections of TBPs both in ticks and their wild hedgehog hosts in Jiangsu province, Eastern China were determined by metagenome next-generation sequencing and nested PCR. As a result, Rickettsia japonica (81.1%), novel Rickettsia sp. SFGR-1 (5.1%), Anaplasma bovis (12%), A. platys (6.3%), novel Ehrlichia spp. Ehr-1 (16%) and Ehr-2 (0.6%), E. ewingii-like strain (0.6%), Coxiella burnetii (10.9%), and a novel Coxiella-like endosymbiont (CLE) strain (61.1%) were detected in Haemaphysalis flava ticks. A. bovis (43.8%), Ehrlichia sp. Ehr-1 (83.3%), and C. burnetii (80%) were detected in Erinaceus amurensis hedgehogs. Coinfection rates with various TBPs were 71.5% and 83.3% in ticks and hedgehogs, respectively, both with double-pathogen/endosymbiont coinfection rates over 50%. We found the following. (i) Er. amurensis hedgehogs seem to contribute to the natural cycles of R. japonica, A. bovis, Ehrlichia sp., and C. burnetii and may be reservoirs of them except for R. japonica, and A. bovis is proved to infect hedgehogs for the first time. (ii) H. flava is proved to harbor various TBPs as a reservoir host, including CLE identified for the first time, which could inhibit coinfection of C. burnetii while promoting that of Rickettsia spp. in H. flava. (iii) Four novel TBP species were identified. This study provides useful epidemiological information crucial for assessing the potential infection risks to humans, thus benefiting the development of strategies to prevent and control tick-borne diseases. IMPORTANCE In the present study, we found the following. (i) Er. amurensis hedgehogs seem to contribute to the natural cycles of R. japonica, A. bovis, Ehrlichia sp., and C. burnetii and may be reservoirs of them except for R. japonica, and A. bovis is proved to infect hedgehogs for the first time. (ii) H. flava is proved to harbor various tickborne pathogens (TBPs) as a reservoir host, including Coxiella-like endosymbiont (CLE) identified for the first time, which could inhibit coinfection of C. burnetii while promoting that of Rickettsia spp. in H. flava. (iii) Four novel TBP species were identified. This study provides useful epidemiological information on TBPs harbored and transmitted by ticks and their hosts, for assessing the potential infection risks to humans, thus benefiting the developing strategies for tick-borne diseases prevention and control.}, } @article {pmid36000841, year = {2022}, author = {Cen, L and Chang, Y and Bedree, JK and Ma, Y and Zhong, Q and Utter, DR and Dong, PT and Lux, R and Bor, B and Liu, J and McLean, JS and Le, S and He, X}, title = {Exploitation of a Bacterium-Encoded Lytic Transglycosylase by a Human Oral Lytic Phage To Facilitate Infection.}, journal = {Journal of virology}, volume = {96}, number = {17}, pages = {e0106322}, pmid = {36000841}, issn = {1098-5514}, support = {R01 DE023810/DE/NIDCR NIH HHS/United States ; R01 GM110243/GM/NIGMS NIH HHS/United States ; R01 AI087946/AI/NIAID NIH HHS/United States ; R01 AI132818/AI/NIAID NIH HHS/United States ; S10 OD023603/OD/NIH HHS/United States ; F31 DE026057/DE/NIDCR NIH HHS/United States ; R01 DE030943/DE/NIDCR NIH HHS/United States ; }, mesh = {*Actinomycetaceae/enzymology/virology ; Bacteriophage Receptors/metabolism ; *Bacteriophages/enzymology/genetics/physiology ; *Glycosyltransferases/genetics/metabolism ; Host Specificity ; Humans ; Microbiota ; Mouth/microbiology/virology ; Mutation ; Peptidoglycan/metabolism ; Plankton/virology ; Viral Proteins/genetics/metabolism ; }, abstract = {Bacteriophages (phages) are an integral part of the human oral microbiome. Their roles in modulating bacterial physiology and shaping microbial communities have been discussed but remain understudied due to limited isolation and characterization of oral phage. Here, we report the isolation of LC001, a lytic phage targeting human oral Schaalia odontolytica (formerly known as Actinomyces odontolyticus) strain XH001. We showed that LC001 attached to and infected surface-grown, but not planktonic, XH001 cells, and it displayed remarkable host specificity at the strain level. Whole-genome sequencing of spontaneous LC001-resistant, surface-grown XH001 mutants revealed that the majority of the mutants carry nonsense or frameshift mutations in XH001 gene APY09_05145 (renamed ltg-1), which encodes a putative lytic transglycosylase (LT). The mutants are defective in LC001 binding, as revealed by direct visualization of the significantly reduced attachment of phage particles to the XH001 spontaneous mutants compared that to the wild type. Meanwhile, targeted deletion of ltg-1 produced a mutant that is defective in LC001 binding and resistant to LC001 infection even as surface-grown cells, while complementation of ltg-1 in the mutant background restored the LC001-sensitive phenotype. Intriguingly, similar expression levels of ltg-1 were observed in surface-grown and planktonic XH001, which displayed LC001-binding and nonbinding phenotypes, respectively. Furthermore, the overexpression of ltg-1 failed to confer an LC001-binding and -sensitive phenotype to planktonic XH001. Thus, our data suggested that rather than directly serving as a phage receptor, ltg-1-encoded LT may increase the accessibility of phage receptor, possibly via its enzymatic activity, by cleaving the peptidoglycan structure for better receptor exposure during peptidoglycan remodeling, a function that can be exploited by LC001 to facilitate infection. IMPORTANCE The evidence for the presence of a diverse and abundant phage population in the host-associated oral microbiome came largely from metagenomic analysis or the observation of virus-like particles within saliva/plaque samples, while the isolation of oral phage and investigation of their interaction with bacterial hosts are limited. Here, we report the isolation of LC001, the first lytic phage targeting oral Schaalia odontolytica. Our study suggested that LC001 may exploit the host bacterium-encoded lytic transglycosylase function to gain access to the receptor, thus facilitating its infection.}, } @article {pmid36000741, year = {2022}, author = {Wylie, TN and Schrimpf, J and Gula, H and Herter, BN and Wylie, KM}, title = {Comparison of Metagenomic Sequencing and the NanoString nCounter Analysis System for the Characterization of Bacterial and Viral Communities in Vaginal Samples.}, journal = {mSphere}, volume = {7}, number = {5}, pages = {e0019722}, pmid = {36000741}, issn = {2379-5042}, support = {UL1 TR002345/TR/NCATS NIH HHS/United States ; R03 AI159038/AI/NIAID NIH HHS/United States ; }, mesh = {Female ; Humans ; *Metagenomics ; Metagenome ; Sequence Analysis, DNA ; *Viruses/genetics ; Bacteria/genetics ; }, abstract = {DNA sequencing assays have been used to characterize the vaginal microbiome and to identify associations with clinical outcomes. The purpose of this study was to evaluate the utility of the NanoString nCounter platform, a more efficient assay compared to sequencing, for the characterization of vaginal microbial communities. A panel of NanoString nCounter probes was designed to detect common vaginal bacteria and viruses with relevance to reproductive health. A defined synthetic community of microbes and 43 clinical samples were interrogated with NanoString nCounter assays and compared to known compositions or metagenomic shotgun sequencing (MSS) results. The NanoString nCounter platform and MSS were able to distinguish closely related microbes. In clinical samples, the relative abundance of bacterial species was similar between the two assays. The assays sometimes disagreed when targets were present at low abundance. More viruses were detected by MSS than by nCounter. However, the nCounter assays are able to provide results in about 30 h with minimal hands-on time, whereas MSS requires at least 138 to 178 h with extensive hands-on time. The reagent cost for the two assays was similar, but the overall cost of the nCounter was lower due to the minimal hands-on time. MSS can be used to inform the design of a targeted multiplex panel for the assessment of vaginal microbial communities, thereby allowing for more cost-effective and rapid screening of patient samples for research studies. The sensitivity for low abundance microbes could be improved, possibly by adding additional target amplification cycles before nCounter assessment. This approach has potential as an assay with both research and clinical applications. IMPORTANCE Metagenomic shotgun sequencing can inform the design of a targeted multiplex panel by which the NanoString nCounter platform can assess vaginal microbial communities, thereby allowing for more cost-effective and rapid screening of patient samples.}, } @article {pmid36000725, year = {2022}, author = {Guo, C and Yang, M and Jiang, B and Ye, C and Luo, L and Liu, Y and Huang, H and Mei, X and Zhu, Y and Deng, W and Du, F and He, X and Zhu, Y and Zhu, S}, title = {Moisture Controls the Suppression of Panax notoginseng Root Rot Disease by Indigenous Bacterial Communities.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0041822}, pmid = {36000725}, issn = {2379-5077}, mesh = {*Panax notoginseng/microbiology ; Soil Microbiology ; Plant Roots/microbiology ; Bacteria/genetics ; Soil ; }, abstract = {Harnessing indigenous soil microbial suppression is an emerging strategy for managing soilborne plant diseases. Soil moisture is a vital factor in soil microbiomes, but its role in the regulation of microbial suppression is poorly understood. Here, we investigated the correlation of root rot disease of Panax notoginseng with rhizosphere microbial communities mediated by soil moisture gradients from 55% to 100% field capacity (FC); then, we captured the disease-suppressive and disease-inductive microbiomes and validated their functions by a culture experiment with synthetic microbiotas containing keystone species. We found that proper soil moisture at 75% to 95% FC could maintain a disease-suppressive microbiome to alleviate root rot disease. However, extremely low or high soil moistures (>95% FC or <75% FC) could aggravate root rot disease by depleting the disease-suppressive microbiome while enriching the disease-inductive microbiome. Both the low-soil-moisture-enriched pathogen Monographella cucumerina and the high-soil-moisture-enriched pathogen Ilyonectria destructans could synergize with different disease-inductive microbiomes to aggravate disease. Metagenomic data confirmed that low- and high-moisture conditions suppressed antibiotic biosynthesis genes but enriched pathogenicity-related genes, resulting in a change in the soil state from disease suppressive to inductive. This study highlights the importance of soil moisture when indigenous microbial suppression is harnessed for disease control. IMPORTANCE Soilborne diseases pose a major problem in high-intensity agricultural systems due to the imbalance of microbial communities in soil, resulting in the buildup of soilborne pathogens. Harnessing indigenous soil microbial suppression is an emerging strategy for overcoming soilborne plant diseases. In this study, we showed that soil moisture is a key factor in balancing microbiome effects on root rot disease. Proper soil moisture management represent an effective approach to maintain microbial disease resistance by enriching disease-suppressive microbiomes. Conversely, moisture stresses may enrich for a disease-inductive microbiome and aid accumulation of host-specific soilborne pathogens threatening crop production. This work could provide a new strategy for sustainable control of soilborne diseases by enriching the indigenous disease-suppressive microbiome through soil moisture management.}, } @article {pmid36000724, year = {2022}, author = {Vieira, J and Jesudasen, S and Bringhurst, L and Sui, HY and McIver, L and Whiteson, K and Hanselmann, K and O'Toole, GA and Richards, CJ and Sicilian, L and Neuringer, I and Lai, PS}, title = {Supplemental Oxygen Alters the Airway Microbiome in Cystic Fibrosis.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0036422}, pmid = {36000724}, issn = {2379-5077}, support = {K23 ES023700/ES/NIEHS NIH HHS/United States ; }, mesh = {Humans ; *Cystic Fibrosis/drug therapy ; *Hyperoxia ; *Microbiota/genetics ; Lung/microbiology ; Bacteria ; *Staphylococcal Infections ; Pseudomonas aeruginosa ; Oxygen/therapeutic use ; }, abstract = {Features of the airway microbiome in persons with cystic fibrosis (pwCF) are correlated with disease progression. Microbes have traditionally been classified for their ability to tolerate oxygen. It is unknown whether supplemental oxygen, a common medical intervention, affects the airway microbiome of pwCF. We hypothesized that hyperoxia significantly impacts the pulmonary microbiome in cystic fibrosis. In this study, we cultured spontaneously expectorated sputum from pwCF in artificial sputum medium under 21%, 50%, and 100% oxygen conditions using a previously validated model system that recapitulates microbial community composition in uncultured sputum. Culture aliquots taken at 24, 48, and 72 h, along with uncultured sputum, underwent shotgun metagenomic sequencing with absolute abundance values obtained with the use of spike-in bacteria. Raw sequencing files were processed using the bioBakery pipeline to determine changes in taxonomy, predicted function, antimicrobial resistance genes, and mobile genetic elements. Hyperoxia reduced absolute microbial load, species richness, and diversity. Hyperoxia reduced absolute abundance of specific microbes, including facultative anaerobes such as Rothia and some Streptococcus species, with minimal impact on canonical CF pathogens such as Pseudomonas aeruginosa and Staphylococcus aureus. The effect size of hyperoxia on predicted functional pathways was stronger than that on taxonomy. Large changes in microbial cooccurrence networks were noted. Hyperoxia exposure perturbs airway microbial communities in a manner well tolerated by key pathogens. Supplemental oxygen use may enable the growth of lung pathogens and should be further studied in the clinical setting. IMPORTANCE The airway microbiome in persons with cystic fibrosis (pwCF) is correlated with lung function and disease severity. Supplemental oxygen use is common in more advanced CF, yet its role in perturbing airway microbial communities is unknown. By culturing sputum samples from pwCF under normal and elevated oxygen conditions, we found that increased oxygen led to reduced total numbers and diversity of microbes, with relative sparing of common CF pathogens such as Pseudomonas aeruginosa and Staphylococcus aureus. Supplemental oxygen use may enable the growth of lung pathogens and should be further studied in the clinical setting.}, } @article {pmid35999740, year = {2022}, author = {Burzio, C and Ekholm, J and Modin, O and Falås, P and Svahn, O and Persson, F and van Erp, T and Gustavsson, DJI and Wilén, BM}, title = {Removal of organic micropollutants from municipal wastewater by aerobic granular sludge and conventional activated sludge.}, journal = {Journal of hazardous materials}, volume = {438}, number = {}, pages = {129528}, doi = {10.1016/j.jhazmat.2022.129528}, pmid = {35999740}, issn = {1873-3336}, mesh = {Bioreactors ; *Sewage ; Waste Disposal, Fluid ; Wastewater ; *Water Purification ; }, abstract = {Removal performances of organic micropollutants by conventional activated sludge (CAS) and aerobic granular sludge (AGS) were investigated at a full-scale wastewater treatment plant. Lab-scale kinetic experiments were performed to assess the micropollutant transformation rates under oxic and anoxic conditions. Transformation rates were used to model the micropollutant removal in the full-scale processes. Metagenomic sequencing was used to compare the microbial communities and antimicrobial resistance genes of the CAS and AGS systems. Higher transformation ability was observed for CAS compared to AGS for most compounds, both at the full-scale plant and in the complementary batch experiments. Oxic conditions supported the transformation of several micropollutants with faster and/or comparable rates compared to anoxic conditions. The estimated transformation rates from batch experiments adequately predicted the removal for most micropollutants in the full-scale processes. While the compositions in microbial communities differed between AGS and CAS, the full-scale biological reactors shared similar resistome profiles. Even though granular biomass showed lower potential for micropollutant transformation, AGS systems had somewhat higher gene cluster diversity compared to CAS, which could be related to a higher functional diversity. Micropollutant exposure to biomass or mass transfer limitations, therefore played more important roles in the observed differences in OMP removal.}, } @article {pmid35999575, year = {2022}, author = {Gonzalez, CG and Mills, RH and Zhu, Q and Sauceda, C and Knight, R and Dulai, PS and Gonzalez, DJ}, title = {Location-specific signatures of Crohn's disease at a multi-omics scale.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {133}, pmid = {35999575}, issn = {2049-2618}, support = {K12 GM068524/GM/NIGMS NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; }, mesh = {Bile Acids and Salts ; *Crohn Disease/genetics/microbiology/pathology ; Cross-Sectional Studies ; Feces/microbiology ; Humans ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Crohn's disease (CD), an inflammatory bowel disease (IBD) subtype, results from pathologic interactions between host cells and its resident gut microbes. CD manifests in both isolated disease locations (ileum or colon) or a combination of locations (ileocolonic). To date, a comprehensive understanding of how isolated CD subtypes influence molecular profiles remains outstanding. To address this, we sought to define CD location signatures by leveraging a large cross-sectional feature set captured from the stool of over 200 IBD patients and healthy controls using metaproteomics, shotgun metagenomics, 16S rRNA sequencing, metabolomic profiling, and host genetics paired with clinical endoscopic assessments.

RESULTS: Neither metagenomic nor host genetics alone distinguished CD location subtypes. In contrast, ileal and colonic CD were distinguished using mass spectrometry-based methods (metabolomics or metaproteomics) or a combined multi-omic feature set. This multi-omic feature set revealed colonic CD was strongly associated with neutrophil-related proteins. Additionally, colonic CD displayed a disease-severity-related association with Bacteroides vulgatus. Colonic CD and ulcerative colitis profiles harbored strikingly similar feature enrichments compared to ileal CD, including neutrophil-related protein enrichments. Compared to colonic CD, ileal CD profiles displayed increased primary and secondary bile acid levels and concomitant shifts in taxa with noted sensitivities such as Faecalibacterium prausnitzii or affinities for bile acid-rich environments, including Gammaproteobacteria and Blautia sp. Having shown robust molecular and microbial distinctions tied to CD locations, we leveraged these profiles to generate location-specific disease severity biomarkers that surpass the performance of Calprotectin.

CONCLUSIONS: When compared using multi-omics features, colonic- and ileal-isolated CD subtypes display striking differences that suggest separate location-specific pathologies. Colonic CD's strong similarity to ulcerative colitis, including neutrophil and Bacteroides vulgatus involvement, is also evidence of a shared pathology for colonic-isolated IBD subtypes, while ileal CD maintains a unique, bile acid-driven profile. More broadly, this study demonstrates the power of multi-omics approaches for IBD biomarker discovery and elucidating the underlying biology. Video Abstract.}, } @article {pmid35999570, year = {2022}, author = {Madrigal, P and Singh, NK and Wood, JM and Gaudioso, E and Hernández-Del-Olmo, F and Mason, CE and Venkateswaran, K and Beheshti, A}, title = {Machine learning algorithm to characterize antimicrobial resistance associated with the International Space Station surface microbiome.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {134}, pmid = {35999570}, issn = {2049-2618}, support = {U01 DA053941/DA/NIDA NIH HHS/United States ; R01 AI151059/AI/NIAID NIH HHS/United States ; }, mesh = {Algorithms ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Humans ; Machine Learning ; Metagenomics/methods ; *Microbiota/genetics ; *Spacecraft ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) has a detrimental impact on human health on Earth and it is equally concerning in other environments such as space habitat due to microgravity, radiation and confinement, especially for long-distance space travel. The International Space Station (ISS) is ideal for investigating microbial diversity and virulence associated with spaceflight. The shotgun metagenomics data of the ISS generated during the Microbial Tracking-1 (MT-1) project and resulting metagenome-assembled genomes (MAGs) across three flights in eight different locations during 12 months were used in this study. The objective of this study was to identify the AMR genes associated with whole genomes of 226 cultivable strains, 21 shotgun metagenome sequences, and 24 MAGs retrieved from the ISS environmental samples that were treated with propidium monoazide (PMA; viable microbes).

RESULTS: We have analyzed the data using a deep learning model, allowing us to go beyond traditional cut-offs based only on high DNA sequence similarity and extending the catalog of AMR genes. Our results in PMA treated samples revealed AMR dominance in the last flight for Kalamiella piersonii, a bacteria related to urinary tract infection in humans. The analysis of 226 pure strains isolated from the MT-1 project revealed hundreds of antibiotic resistance genes from many isolates, including two top-ranking species that corresponded to strains of Enterobacter bugandensis and Bacillus cereus. Computational predictions were experimentally validated by antibiotic resistance profiles in these two species, showing a high degree of concordance. Specifically, disc assay data confirmed the high resistance of these two pathogens to various beta-lactam antibiotics.

CONCLUSION: Overall, our computational predictions and validation analyses demonstrate the advantages of machine learning to uncover concealed AMR determinants in metagenomics datasets, expanding the understanding of the ISS environmental microbiomes and their pathogenic potential in humans. Video Abstract.}, } @article {pmid35999507, year = {2022}, author = {Teufel, M and Sobetzko, P}, title = {Reducing costs for DNA and RNA sequencing by sample pooling using a metagenomic approach.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {613}, pmid = {35999507}, issn = {1471-2164}, support = {SO 1447/3-1//Deutsche Forschungsgemeinschaft/ ; SO 1447/5-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {DNA/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Metagenome ; *Metagenomics ; RNA/genetics ; Sequence Analysis, DNA ; Sequence Analysis, RNA/methods ; }, abstract = {DNA and RNA sequencing are widely used techniques to investigate genomic modifications and gene expression. The costs for sequencing dropped dramatically in the last decade. However, due to material and labor intense steps, the sample preparation costs could not keep up with that pace. About 80% of the total costs occur prior to sequencing during DNA/RNA extraction, enrichment steps and subsequent library preparation. In this study, we investigate the potential of pooling different organisms samples prior to DNA/RNA extraction to significantly reduce costs in preparative steps. Similar to the common procedure of ligated DNA tags to pool (c)DNA samples, sequence diversity of different organisms intrinsically provide unique sequences that allow separation of reads after sequencing. With this approach, sample pooling can occur before DNA/RNA isolation and library preparation. We show that pooled sequencing of three related bacterial organisms is possible without loss of data quality at a cost reduction of approx. 50% in DNA- and RNA-seq approaches. Furthermore, we show that this approach is highly efficient down to the level of a shared genus and is, therefore, widely applicable in sequencing facilities and companies with diverse sample pools.}, } @article {pmid35999473, year = {2022}, author = {Sharma, P and Mondal, K and Mondal, KC and Thakur, N}, title = {Hunt for α-amylase from metagenome and strategies to improve its thermostability: a systematic review.}, journal = {World journal of microbiology & biotechnology}, volume = {38}, number = {11}, pages = {203}, pmid = {35999473}, issn = {1573-0972}, mesh = {Enzymes, Immobilized/metabolism ; *Metagenome ; Protein Engineering ; Starch/chemistry ; *alpha-Amylases/chemistry ; }, abstract = {With the advent of green chemistry, the use of enzymes in industrial processes serves as an alternative to the conventional chemical catalysts. A high demand for sustainable processes for catalysis has brought a significant attention to hunt for novel enzymes. Among various hydrolases, the α-amylase has a gamut of biotechnological applications owing to its pivotal role in starch-hydrolysis. Industrial demand requires enzymes with thermostability and to ameliorate this crucial property, various methods such as protein engineering, directed evolution and enzyme immobilisation strategies are devised. Besides the traditional culture-dependent approach, metagenome from uncultured bacteria serves as a bountiful resource for novel genes/biocatalysts. Exploring the extreme-niches metagenome, advancements in protein engineering and biotechnology tools encourage the mining of novel α-amylase and its stable variants to tap its robust biotechnological and industrial potential. This review outlines α-amylase and its genetics, its catalytic domain architecture and mechanism of action, and various molecular methods to ameliorate its production. It aims to impart understanding on mechanisms involved in thermostability of α-amylase, cover strategies to screen novel genes from futile habitats and some molecular methods to ameliorate its properties.}, } @article {pmid35998924, year = {2022}, author = {Zhang, T and Jia, Y and Li, H and Xu, D and Zhou, J and Wang, G}, title = {CRISPRCasStack: a stacking strategy-based ensemble learning framework for accurate identification of Cas proteins.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {5}, pages = {}, doi = {10.1093/bib/bbac335}, pmid = {35998924}, issn = {1477-4054}, mesh = {*Archaea/genetics ; CRISPR-Cas Systems ; Gene Editing/methods ; Machine Learning ; *Proteomics ; }, abstract = {CRISPR-Cas system is an adaptive immune system widely found in most bacteria and archaea to defend against exogenous gene invasion. One of the most critical steps in the study of exploring and classifying novel CRISPR-Cas systems and their functional diversity is the identification of Cas proteins in CRISPR-Cas systems. The discovery of novel Cas proteins has also laid the foundation for technologies such as CRISPR-Cas-based gene editing and gene therapy. Currently, accurate and efficient screening of Cas proteins from metagenomic sequences and proteomic sequences remains a challenge. For Cas proteins with low sequence conservation, existing tools for Cas protein identification based on homology cannot guarantee identification accuracy and efficiency. In this paper, we have developed a novel stacking-based ensemble learning framework for Cas protein identification, called CRISPRCasStack. In particular, we applied the SHAP (SHapley Additive exPlanations) method to analyze the features used in CRISPRCasStack. Sufficient experimental validation and independent testing have demonstrated that CRISPRCasStack can address the accuracy deficiencies and inefficiencies of the existing state-of-the-art tools. We also provide a toolkit to accurately identify and analyze potential Cas proteins, Cas operons, CRISPR arrays and CRISPR-Cas locus in prokaryotic sequences. The CRISPRCasStack toolkit is available at https://github.com/yrjia1015/CRISPRCasStack.}, } @article {pmid35998698, year = {2022}, author = {Laue, HE and Moroishi, Y and Palys, TJ and Jackson, BP and Madan, JC and Karagas, MR}, title = {Contribution of gut bacteria to arsenic metabolism in the first year of life in a prospective birth cohort.}, journal = {Environmental research}, volume = {214}, number = {Pt 4}, pages = {114099}, pmid = {35998698}, issn = {1096-0953}, support = {UH3 OD023275/OD/NIH HHS/United States ; P42 ES007373/ES/NIEHS NIH HHS/United States ; P30 CA023108/CA/NCI NIH HHS/United States ; T32 CA134286/CA/NCI NIH HHS/United States ; P20 ES018175/ES/NIEHS NIH HHS/United States ; P01 ES022832/ES/NIEHS NIH HHS/United States ; P20 GM104416/GM/NIGMS NIH HHS/United States ; }, mesh = {*Arsenic/analysis ; *Arsenicals/analysis ; Bacteria/genetics/metabolism ; Birth Cohort ; Cacodylic Acid/urine ; Child ; Cohort Studies ; Humans ; Prospective Studies ; }, abstract = {Gut bacteria are at the interface of environmental exposures and their impact on human systems, and may alter host absorption, metabolism, and excretion of toxic chemicals. We investigated whether arsenic-metabolizing bacterial gene pathways related to urinary arsenic concentrations. In the New Hampshire Birth Cohort Study, urine and stool samples were obtained at six weeks (n = 186) and one year (n = 190) of age. Inorganic arsenic (iAs), monomethylarsonic acid (MMA), dimethylarsinic acid (DMA), and arsenobetaine (AsB) were quantified in infant urine samples using high-performance liquid chromatography with inductively coupled plasma mass spectrometry. Total arsenic exposure (tAs) was summarized as Σ(iAs, MMA, DMA) and log2-transformed. Fecal microbial DNA underwent metagenomic sequencing and the relative abundance of bacterial gene pathways were grouped as KEGG Orthologies (KOs) using BioBakery algorithms. Arsenic metabolism KOs with >80% prevalence were log2-transformed and modeled continuously using linear regression, those with <10% were not evaluated and those with 10-80% prevalence were analyzed dichotomously (detect/non-detect) using logistic regression. In the first set of models, tAs was regressed against KO relative abundance or detection adjusting for age at sample collection and child's sex. Effect modification by delivery mode was assessed in stratified models. In the second set of models, the association between the relative abundance/detection of the KOs and arsenic speciation (%iAs, %MMA, %DMA) was quantified with linear regression. Urinary tAs was associated with the increased relative abundance/detection odds of several arsenic-related KOs, including K16509, an arsenate reductase transcriptional regulator, with stronger associations among six-week-olds than one-year-olds. K16509 was also associated with decreased %MMA and increased %DMA at six weeks and one year. Notably, many associations were stronger among operatively-delivered than vaginally-delivered infants. Our findings suggest associations between arsenic-metabolizing bacteria in the infant gut microbiome and urinary arsenic excretion.}, } @article {pmid35998206, year = {2022}, author = {Li, J and George Markowitz, RH and Brooks, AW and Mallott, EK and Leigh, BA and Olszewski, T and Zare, H and Bagheri, M and Smith, HM and Friese, KA and Habibi, I and Lawrence, WM and Rost, CL and Lédeczi, Á and Eeds, AM and Ferguson, JF and Silver, HJ and Bordenstein, SR}, title = {Individuality and ethnicity eclipse a short-term dietary intervention in shaping microbiomes and viromes.}, journal = {PLoS biology}, volume = {20}, number = {8}, pages = {e3001758}, pmid = {35998206}, issn = {1545-7885}, support = {P30 DK058404/DK/NIDDK NIH HHS/United States ; R01 DK117144/DK/NIDDK NIH HHS/United States ; T32 HG008341/HG/NHGRI NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Ethnicity ; Feces ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; *Microbiota/genetics ; Virome ; }, abstract = {Many diseases linked with ethnic health disparities associate with changes in microbial communities in the United States, but the causes and persistence of ethnicity-associated microbiome variation are not understood. For instance, microbiome studies that strictly control for diet across ethnically diverse populations are lacking. Here, we performed multiomic profiling over a 9-day period that included a 4-day controlled vegetarian diet intervention in a defined geographic location across 36 healthy Black and White females of similar age, weight, habitual diets, and health status. We demonstrate that individuality and ethnicity account for roughly 70% to 88% and 2% to 10% of taxonomic variation, respectively, eclipsing the effects a short-term diet intervention in shaping gut and oral microbiomes and gut viromes. Persistent variation between ethnicities occurs for microbial and viral taxa and various metagenomic functions, including several gut KEGG orthologs, oral carbohydrate active enzyme categories, cluster of orthologous groups of proteins, and antibiotic-resistant gene categories. In contrast to the gut and oral microbiome data, the urine and plasma metabolites tend to decouple from ethnicity and more strongly associate with diet. These longitudinal, multiomic profiles paired with a dietary intervention illuminate previously unrecognized associations of ethnicity with metagenomic and viromic features across body sites and cohorts within a single geographic location, highlighting the importance of accounting for human microbiome variation in research, health determinants, and eventual therapies. Trial Registration: ClinicalTrials.gov ClinicalTrials.gov Identifier: NCT03314194.}, } @article {pmid35997152, year = {2022}, author = {Titécat, M and Rousseaux, C and Dubuquoy, C and Foligné, B and Rahmouni, O and Mahieux, S and Desreumaux, P and Woolston, J and Sulakvelidze, A and Wannerberger, K and Neut, C}, title = {Safety and Efficacy of an AIEC-targeted Bacteriophage Cocktail in a Mice Colitis Model.}, journal = {Journal of Crohn's & colitis}, volume = {16}, number = {10}, pages = {1617-1627}, doi = {10.1093/ecco-jcc/jjac064}, pmid = {35997152}, issn = {1876-4479}, support = {//Ferring/ ; }, mesh = {Animals ; Humans ; Mice ; Bacterial Adhesion ; *Bacteriophages ; *Colitis/pathology ; Disease Models, Animal ; Dysbiosis/complications ; Escherichia coli ; Escherichia coli Infections/complications/microbiology/pathology ; Intestinal Mucosa/pathology ; }, abstract = {BACKGROUND AND AIMS: Adherent invasive Escherichia coli [AIEC] are recovered with a high frequency from the gut mucosa of Crohn's disease patients and are believed to contribute to the dysbiosis and pathogenesis of this inflammatory bowel disease. In this context, bacteriophage therapy has been proposed for specifically targeting AIEC in the human gut with no deleterious impact on the commensal microbiota.

METHODS: The in vitro efficacy and specificity of a seven lytic phage cocktail [EcoActive™] was assessed against [i] 210 clinical AIEC strains, and [ii] 43 non-E. coli strains belonging to the top 12 most common bacterial genera typically associated with a healthy human microbiome. These data were supported by in vivo safety and efficacy assays conducted on healthy and AIEC-colonized mice, respectively.

RESULTS: The EcoActive cocktail was effective in vitro against 95% of the AIEC strains and did not lyse any of the 43 non-E. coli commensal strains, in contrast to conventional antibiotics. Long-term administration of the EcoActive cocktail to healthy mice was safe and did not induce dysbiosis according to metagenomic data. Using a murine model of induced colitis of animals infected with the AIEC strain LF82, we found that a single administration of the cocktail failed to alleviate inflammatory symptoms, while mice receiving the cocktail twice a day for 15 days were protected from clinical and microscopical manifestations of inflammation.

CONCLUSIONS: Collectively, the data support the approach of AIEC-targeted phage therapy as safe and effective treatment for reducing AIEC levels in the gut of IBD patients.}, } @article {pmid35996618, year = {2022}, author = {Kyoui, D and Fukasawa, Y and Miyanaga, W and Nakamura, Y and Yamane, T and Sugita, K and Yamadera, S and Kai, M and Shinoda, K and Kawarai, T and Ogihara, H}, title = {Identification of changes in the microflora composition of Japanese horse mackerel (Trachurus japonicus) during storage to identify specific spoilageorganisms.}, journal = {Current research in food science}, volume = {5}, number = {}, pages = {1216-1224}, pmid = {35996618}, issn = {2665-9271}, abstract = {Japanese horse mackerel (Trachurus japonicus) is an important marine resource, and its loss and waste should be reduced. This study aimed to identify the changes in the microflora composition during storage and specific spoilage organisms (SSOs) in Japanese horse mackerel, for spoilage prevention. They were stored at either 20 °C or 4 °C aerobically, and the bacterial viable counts, concentration of total volatile basic nitrogen (TVB-N), and microflora composition for each group were analyzed. Samples stored at 20 °C for 48 h showed similar viable counts to those stored at 4 °C for 168 h; however, the TVB-N concentrations increased at 20 °C, but not at 4 °C. 16S rRNA metagenome analysis showed that Shewanella became dominant genus in the microflora regardless of the storage temperature. However, dominant amplicon sequence variants (ASVs), which are a more detailed classification level than the genus, differed depending on the storage temperatures; therefore, dominant ASVs at 20 °C were assumed to be potential SSOs. Shewanella sp. Strain NFH-SH190041, which was genetically closely related to the dominant ASVs at 20 °C, was isolated, and its spoilage ability was verified. The strain NFH-SH190041 may be considered a novel SSO of Japanese horse mackerel because its 16S rRNA sequence is clearly different from those of known species.}, } @article {pmid35995909, year = {2022}, author = {Liu, S and Lu, SY and Qureshi, N and Enshasy, HAE and Skory, CD}, title = {Antibacterial Property and Metagenomic Analysis of Milk Kefir.}, journal = {Probiotics and antimicrobial proteins}, volume = {14}, number = {6}, pages = {1170-1183}, pmid = {35995909}, issn = {1867-1314}, mesh = {Animals ; *Kefir/microbiology ; Milk/microbiology ; *Cultured Milk Products/microbiology ; *Lactobacillales ; Fermentation ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Milk kefir fermentation has been used in households for generations. Consumption of milk kefir has been associated with various health benefits, presumably from the probiotics of yeast and bacteria that make up the kefir grains. In addition, many of the microbes are known to produce novel antimicrobial compounds that can be used for other applications. The microbes living inside kefir grains differ significantly depending on geographical location and production methods. In this study, we aimed to use metagenomic analysis of fermented milk by using three different kefir grains (kefir 1, kefir 2, and kefir 3) from different US sources. We analyzed the microbial compositions of the three milk fermentation samples. This study revealed that each sample contains unique and distinct groups of microbes, kefir 1 showed the least diversity, and kefir 3 showed the highest diversity. Kefir 3 is rich in Proteobacteria while kefir 2 is dominated by the Firmicutes. Using bacterial indicator growth analyses carried out by continuous readings from microplate-based bioreactor assays suggested that kefir 2 fermentation filtrate has higher antibacterial property. We have screened 30 purified cultures of kefir 2 sample and isolated two lactic acid bacteria strains with higher antibacterial activities; the two strains were identified as Leuconostoc mesenteroides 28-1 and Lentilactobacillus kefiri 25-2 by 16S genomic PCR with confirmed antibacterial activities of fermentation filtrate after growing under both aerobic and anaerobic conditions.}, } @article {pmid35995842, year = {2022}, author = {Yan, Z and Chen, B and Yang, Y and Yi, X and Wei, M and Ecklu-Mensah, G and Buschmann, MM and Liu, H and Gao, J and Liang, W and Liu, X and Yang, J and Ma, W and Liang, Z and Wang, F and Chen, D and Wang, L and Shi, W and Stampfli, MR and Li, P and Gong, S and Chen, X and Shu, W and El-Omar, EM and Gilbert, JA and Blaser, MJ and Zhou, H and Chen, R and Wang, Z}, title = {Multi-omics analyses of airway host-microbe interactions in chronic obstructive pulmonary disease identify potential therapeutic interventions.}, journal = {Nature microbiology}, volume = {7}, number = {9}, pages = {1361-1375}, pmid = {35995842}, issn = {2058-5276}, mesh = {Animals ; *Host Microbial Interactions ; Humans ; Inflammation ; Mice ; Neutrophils ; *Pulmonary Disease, Chronic Obstructive ; Sputum ; }, abstract = {The mechanistic role of the airway microbiome in chronic obstructive pulmonary disease (COPD) remains largely unexplored. We present a landscape of airway microbe-host interactions in COPD through an in-depth profiling of the sputum metagenome, metabolome, host transcriptome and proteome from 99 patients with COPD and 36 healthy individuals in China. Multi-omics data were integrated using sequential mediation analysis, to assess in silico associations of the microbiome with two primary COPD inflammatory endotypes, neutrophilic or eosinophilic inflammation, mediated through microbial metabolic interaction with host gene expression. Hypotheses of microbiome-metabolite-host interaction were identified by leveraging microbial genetic information and established metabolite-human gene pairs. A prominent hypothesis for neutrophil-predominant COPD was altered tryptophan metabolism in airway lactobacilli associated with reduced indole-3-acetic acid (IAA), which was in turn linked to perturbed host interleukin-22 signalling and epithelial cell apoptosis pathways. In vivo and in vitro studies showed that airway microbiome-derived IAA mitigates neutrophilic inflammation, apoptosis, emphysema and lung function decline, via macrophage-epithelial cell cross-talk mediated by interleukin-22. Intranasal inoculation of two airway lactobacilli restored IAA and recapitulated its protective effects in mice. These findings provide the rationale for therapeutically targeting microbe-host interaction in COPD.}, } @article {pmid35995802, year = {2022}, author = {Craddock, HA and Godneva, A and Rothschild, D and Motro, Y and Grinstein, D and Lotem-Michaeli, Y and Narkiss, T and Segal, E and Moran-Gilad, J}, title = {Phenotypic correlates of the working dog microbiome.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {66}, pmid = {35995802}, issn = {2055-5008}, mesh = {Animals ; Dogs ; *Gastrointestinal Microbiome ; Metagenome ; Metagenomics/methods ; *Microbiota ; Working Dogs ; }, abstract = {Dogs have a key role in law enforcement and military work, and research with the goal of improving working dog performance is ongoing. While there have been intriguing studies from lab animal models showing a potential connection between the gut microbiome and behavior or mental health there is a dearth of studies investigating the microbiome-behavior relationship in working dogs. The overall objective of this study was to characterize the microbiota of working dogs and to determine if the composition of the microbiota is associated with behavioral and performance outcomes. Freshly passed stools from each working canine (Total n = 134) were collected and subject to shotgun metagenomic sequencing using Illumina technology. Behavior, performance, and demographic metadata were collected. Descriptive statistics and prediction models of behavioral/phenotypic outcomes using gradient boosting classification based on Xgboost were used to study associations between the microbiome and outcomes. Regarding machine learning methodology, only microbiome features were used for training and predictors were estimated in cross-validation. Microbiome markers were statistically associated with motivation, aggression, cowardice/hesitation, sociability, obedience to one trainer vs many, and body condition score (BCS). When prediction models were developed based on machine learning, moderate predictive power was observed for motivation, sociability, and gastrointestinal issues. Findings from this study suggest potential gut microbiome markers of performance and could potentially advance care for working canines.}, } @article {pmid35995617, year = {2022}, author = {Pham, D and Howard-Jones, AR and Hueston, L and Jeoffreys, N and Doggett, S and Rockett, RJ and Eden, JS and Sintchenko, V and C-A Chen, S and O'Sullivan, MV and Maddocks, S and Dwyer, DE and Kok, J}, title = {Emergence of Japanese encephalitis in Australia: a diagnostic perspective.}, journal = {Pathology}, volume = {54}, number = {6}, pages = {669-677}, doi = {10.1016/j.pathol.2022.07.001}, pmid = {35995617}, issn = {1465-3931}, mesh = {Animals ; *Culicidae ; *Encephalitis Virus, Japanese/genetics ; *Encephalitis, Japanese/diagnosis/epidemiology/veterinary ; Humans ; *Nucleic Acids ; Swine ; Zoonoses/diagnosis ; }, abstract = {The unprecedented emergence of Japanese encephalitis (JE) in mainland Australia represents an outbreak of high clinical and public health significance. JE is a zoonosis spread by mosquitoes and is one of the most important causes of endemic viral encephalitis in South-East Asia and the Indian subcontinent. While occasional cases of human Japanese encephalitis virus (JEV) infection have occurred in far north Australia, its detection in pigs and the substantial number of locally acquired human cases across multiple jurisdictions in early 2022 prompted the declaration of this outbreak as a Communicable Disease Incident of National Significance. Laboratory testing for JEV is complex, and most cases are diagnosed by serology, for which interpretation is difficult. This review provides a comprehensive outline of currently available methods for JEV diagnosis including serology, nucleic acid amplification testing, virus isolation, sequencing and metagenomics. The relative advantages and disadvantages of the diagnostic tests are presented, as well as their value in clinical and public health contexts. This review also explores the role of mosquito, veterinary and human surveillance as part of the laboratory response to JEV. As JEV may become endemic in Australia, a collaborative and coordinated One Health approach involving animal, human and environmental health is required for optimal disease response and control.}, } @article {pmid35995413, year = {2023}, author = {Wang, G and Li, S and Yan, Q and Guo, R and Zhang, Y and Chen, F and Tian, X and Lv, Q and Jin, H and Ma, X and Ma, Y}, title = {Optimization and evaluation of viral metagenomic amplification and sequencing procedures toward a genome-level resolution of the human fecal DNA virome.}, journal = {Journal of advanced research}, volume = {48}, number = {}, pages = {75-86}, pmid = {35995413}, issn = {2090-1224}, mesh = {Humans ; Reproducibility of Results ; *Virome ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; *Viruses/genetics ; DNA, Viral/genetics ; }, abstract = {INTRODUCTION: Viruses in the human gut have been linked to health and disease. Deciphering the gut virome is dependent on metagenomic sequencing of the virus-like particles (VLPs) purified from the fecal specimens. A major limitation of conventional viral metagenomic sequencing is the low recoverability of viral genomes from the metagenomic dataset.

OBJECTIVES: To develop an optimal method for viral amplification and metagenomic sequencing for maximizing the recovery of viral genomes.

METHODS: We performed parallel virus enrichment and DNA extraction to generate ∼ 30 viral DNA samples from each of 5 fresh fecal specimens and conducted the experiments including 1) optimizing the cycle number for high-fidelity enzyme-based PCR amplification, 2) evaluating the reproducibility of the optimally whole viral metagenomic experimental process, 3) evaluating the reliability of multiple displacement amplification (MDA), 4) testing the capability of long-read sequencing for improving viral metagenomic assembly, and 5) comparing the differences between viral metagenomic and bulk metagenomic approaches.

RESULTS: Our results revealed that the optimal cycle number for PCR amplification is 15. We verified the reliability of MDA and the effectiveness of long-read sequencing. Based on our optimized results, we generated 151 high-quality viruses using the dataset combined from short-read and long-read sequencing. Genomic analysis of these viruses found that most (60.3%) of them were previously unknown and showed a remarkable diversity of viral functions, especially the existence of 206 viral auxiliary metabolic genes. Finally, we uncovered significant differences in the efficiency and coverage of viral identification between viral metagenomic and bulk metagenomic approaches.

CONCLUSIONS: Our study demonstrates the potential of optimized experiment and sequencing strategies in uncovering viral genomes from fecal specimens, which will facilitate future research about the genome-level characterization of complex viral communities.}, } @article {pmid35995289, year = {2022}, author = {Liu, X and He, L and Zhang, X and Kong, D and Chen, Z and Lin, J and Wang, C}, title = {Bioremediation of petroleum-contaminated saline soil by Acinetobacter baumannii and Talaromyces sp. and functional potential analysis using metagenomic sequencing.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {311}, number = {}, pages = {119970}, doi = {10.1016/j.envpol.2022.119970}, pmid = {35995289}, issn = {1873-6424}, mesh = {*Acinetobacter baumannii/genetics/metabolism ; Bacteria/metabolism ; Biodegradation, Environmental ; Hydrocarbons/metabolism ; Metagenomics ; *Petroleum/analysis ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis ; *Talaromyces/genetics/metabolism ; }, abstract = {Microbial remediation is a potential remediation method for petroleum-contaminated soil. In order to explore the petroleum degradation mechanism by microorganisms, the oilfield soil was remedied by Acinetobacter baumannii combined with Talaromyces sp. The degradation mechanism was studied by analyzing soil microbial community and functional genes through metagenomics during the degradation process. The result showed the degradation rate of petroleum was 65.6% after 28 days. The concentration of petroleum decreased from 1220 mg/kg to 420 mg/kg. In the co-culture group, Acinetobacter baumannii became the dominant species, the annotated genes of it at the species level accounted for 7.34% while that of Talaromyces sp. accounted for only 0.34%. Meanwhile, the annotated genes of Bacillus, Halomonas, and Nitriliruptor at the genus level were up-regulated by 1.83%, 0.90%, and 0.71%, respectively. In addition, large functional genes were significantly up-regulated, including the peroxisome, P450 enzyme (CYP53, CYP116, CYP102, CYP645), and biofilm formulation, promoting the oxidation and hydroxylation, and catalyzing the epoxidation of aromatic and aliphatic hydrocarbons. Meanwhile, the degrading genes of alkanes and aromatic hydrocarbons were expressed promotionally, and degradation pathways were deduced. In conclusion, the inoculation of Acinetobacter baumannii combined with Talaromyces sp. accelerated the degradation of petroleum in oilfield soil and improved the growth of indigenous petroleum-degrading bacteria. Many functional genes related to petroleum degradation were promoted significantly. These results proved the co-culture of bacteria-fungi consortium contributes to the bioremediation of petroleum-contaminated soil.}, } @article {pmid35994914, year = {2022}, author = {Wang, J and Zheng, F and Yu, Z and Chen, J and Lu, H}, title = {Dissolved organic nitrogen derived from wastewater denitrification: Composition and nitrogenous disinfection byproduct formation.}, journal = {Journal of hazardous materials}, volume = {440}, number = {}, pages = {129775}, doi = {10.1016/j.jhazmat.2022.129775}, pmid = {35994914}, issn = {1873-3336}, mesh = {Alanine ; Aspartic Acid ; *COVID-19 ; Carbon ; Denitrification ; Disinfection ; Dissolved Organic Matter ; Glycine ; Humans ; Lignin ; Methanol ; Nitrogen/chemistry ; Sodium Acetate ; Wastewater/analysis ; *Water Pollutants, Chemical/analysis ; *Water Purification ; }, abstract = {Microbially derived dissolved organic nitrogen (mDON) is a major fraction of effluent total nitrogen at wastewater treatment plants with enhanced nutrient removal, which stimulates phytoplankton blooms and formation of toxic nitrogenous disinfection by-products (N-DBPs). This study identified denitrifiers as major contributors to mDON synthesis, and further revealed the molecular composition, influential factors and synthetic microorganisms of denitrification-derived mDON compounds leading to N-DBP formation. The maximum mDON accumulated during denitrification was 8.92% of converted inorganic nitrogen, higher than that of anammox (4.24%) and nitrification (2.76%). Sodium acetate addition at relatively high C/N ratio (5-7) favored mDON formation, compared with methanol and low C/N (1-3). Different from acetate, methanol-facilitated denitrification produced 13-69% more lignin-like compounds than proteins using Orbitrap LC-MS. The most abundant N-DBPs formed from denitrification-derived mDON were N-nitrosodibutylamine and dichloroacetonitrile (13.32 μg/mg mDON and 12.21 μg/mg mDON, respectively). Major amino acids, aspartate, glycine, and alanine were positively correlated with typical N-DBPs. Biosynthesis and degradation pathways of these N-DBP precursors were enriched in denitrifiers belonging to Rhodocyclaceae, Mycobacteriaceae and Hyphomicrobiaceae. As intensive disinfection is applied at worldwide wastewater treatment plants during COVID-19, carbon source facilitated denitrification should be better managed to reduce both effluent inorganic nitrogen and DON, mitigating DON and N-DBP associated ecological risks in receiving waters.}, } @article {pmid35993907, year = {2022}, author = {Shi, Q and Liu, S and Kristiansen, K and Liu, L}, title = {The FASTQ+ format and PISA.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {19}, pages = {4639-4642}, doi = {10.1093/bioinformatics/btac562}, pmid = {35993907}, issn = {1367-4811}, mesh = {Sequence Analysis, DNA ; *Software ; Polymerase Chain Reaction ; *Language ; }, abstract = {SUMMARY: The FASTQ+ format is designed for single-cell experiments. It extends various optional tags, including cell barcodes and unique molecular identifiers, to the sequence identifier and is fully compatible with the FASTQ format. In addition, PISA implements various utilities for processing sequences in the FASTQ format and alignments in the SAM/BAM/CRAM format from single-cell experiments, such as converting FASTQ format to FASTQ+, annotating alignments, PCR deduplication, feature counting and barcodes correction. The software is open-source and written in C language.

https://doi.org/10.5281/zenodo.7007056 or https://github.com/shiquan/PISA.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid35993730, year = {2022}, author = {de Carvalho, FM and Valiatti, TB and Santos, FF and Silveira, ACO and Guimarães, APC and Gerber, AL and Souza, CO and Cassu Corsi, D and Brasiliense, DM and Castelo-Branco, DSCM and Anzai, EK and Bessa-Neto, FO and Guedes, GMM and de Souza, GHA and Lemos, LN and Ferraz, LFC and Bahia, MNM and Vaz, MSM and da Silva, RGB and Veiga, R and Simionatto, S and Monteiro, WAP and Lima, WAO and Kiffer, CRV and Campos Pignatari, AC and Cayô, R and de Vasconcelos, ATR and Gales, AC}, title = {Exploring the Bacteriome and Resistome of Humans and Food-Producing Animals in Brazil.}, journal = {Microbiology spectrum}, volume = {10}, number = {5}, pages = {e0056522}, pmid = {35993730}, issn = {2165-0497}, mesh = {Humans ; Swine ; Cattle ; Animals ; *Drug Resistance, Bacterial/genetics ; Brazil ; Metagenomics/methods ; Bacteria ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents ; Poultry ; Genes, Bacterial ; }, abstract = {The epidemiology of antimicrobial resistance (AMR) is complex, with multiple interfaces (human-animal-environment). In this context, One Health surveillance is essential for understanding the distribution of microorganisms and antimicrobial resistance genes (ARGs). This report describes a multicentric study undertaken to evaluate the bacterial communities and resistomes of food-producing animals (cattle, poultry, and swine) and healthy humans sampled simultaneously from five Brazilian regions. Metagenomic analysis showed that a total of 21,029 unique species were identified in 107 rectal swabs collected from distinct hosts, the highest numbers of which belonged to the domain Bacteria, mainly Ruminiclostridium spp. and Bacteroides spp., and the order Enterobacterales. We detected 405 ARGs for 12 distinct antimicrobial classes. Genes encoding antibiotic-modifying enzymes were the most frequent, followed by genes related to target alteration and efflux systems. Interestingly, carbapenemase-encoding genes such as blaAIM-1, blaCAM-1, blaGIM-2, and blaHMB-1 were identified in distinct hosts. Our results revealed that, in general, the bacterial communities from humans were present in isolated clusters, except for the Northeastern region, where an overlap of the bacterial species from humans and food-producing animals was observed. Additionally, a large resistome was observed among all analyzed hosts, with emphasis on the presence of carbapenemase-encoding genes not previously reported in Latin America. IMPORTANCE Humans and food production animals have been reported to be important reservoirs of antimicrobial resistance (AMR) genes (ARGs). The frequency of these multidrug-resistant (MDR) bacteria tends to be higher in low- and middle-income countries (LMICs), due mainly to a lack of public health policies. Although studies on AMR in humans or animals have been carried out in Brazil, this is the first multicenter study that simultaneously collected rectal swabs from humans and food-producing animals for metagenomics. Our results indicate high microbial diversity among all analyzed hosts, and several ARGs for different antimicrobial classes were also found. As far as we know, we have detected for the first time ARGs encoding carbapenemases, such as blaAIM-1, blaCAM-1, blaGIM-2, and blaHMB-1, in Latin America. Thus, our results support the importance of metagenomics as a tool to track the colonization of food-producing animals and humans by antimicrobial-resistant bacteria. In addition, a network surveillance system called GUARANI, created for this study, is ready to be expanded and to collect additional data.}, } @article {pmid35993719, year = {2022}, author = {Baker, JL}, title = {Using Nanopore Sequencing to Obtain Complete Bacterial Genomes from Saliva Samples.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0049122}, pmid = {35993719}, issn = {2379-5077}, support = {K99 DE029228/DE/NIDCR NIH HHS/United States ; K99-DE029228//HHS | NIH | National Institute of Dental and Craniofacial Research (NIDCR)/ ; }, mesh = {Humans ; Sequence Analysis, DNA/methods ; *Nanopore Sequencing/methods ; Saliva ; Genome, Bacterial/genetics ; *Microbiota/genetics ; Bacteria/genetics ; }, abstract = {Obtaining complete, high-quality reference genomes is essential to the study of any organism. Recent advances in nanopore sequencing, as well as genome assembly and analysis methods, have made it possible to obtain complete bacterial genomes from metagenomic (i.e., multispecies) samples, including those from the human microbiome. In this study, methods are presented to obtain complete bacterial genomes from human saliva using complementary Oxford Nanopore (ONT) and Illumina sequencing. Applied to 3 human saliva samples, these methods resulted in 11 complete bacterial genomes: 3 Saccharibacteria clade G6 (also known as Ca. Nanogingivalaceae HMT-870), 1 Saccharibacteria clade G1 HMT-348, 2 Rothia mucilaginosa, 2 Actinomyces graevenitzii, 1 Mogibacterium diversum, 1 Lachnospiraceae HMT-096, and 1 Lancefieldella parvula; and one circular chromosome of Ruminococcaceae HMT-075 (which likely has at least 2 chromosomes). The 4 Saccharibacteria genomes, as well as the Actinomyces graeventizii genomes, represented the first complete genomes from their respective bacterial taxa. Aside from the complete genomes, the assemblies contained 147 contigs of over 500,000 bp each and thousands of smaller contigs, together representing a myriad of additional draft genomes including many which are likely nearly complete. The complete genomes enabled highly accurate pangenome analysis, which identified unique and missing features of each genome compared to its closest relatives with complete genomes available in public repositories. These features provide clues as to the lifestyle and ecological role of these bacteria within the human oral microbiota, which will be particularly useful in designing future studies of the taxa that have never been isolated or cultivated. IMPORTANCE Obtaining complete and accurate genomes is crucial to the study of any organism. Previously, obtaining complete genomes of bacteria, including those of the human microbiome, frequently required isolation of the organism, as well as low-throughput, manual sequencing methods to resolve repeat regions. Advancements in long-read sequencing technologies, including Oxford Nanopore (ONT), have made it possible to obtain complete, closed bacterial genomes from metagenomic samples. This study reports methods to obtain complete genomes from the human oral microbiome using complementary ONT and Illumina sequencing of saliva samples. Eleven complete genomes were obtained from 3 human saliva samples, with genomes of Saccharibacteria HMT-870, Saccharibacteria HMT-348, and Actinomyces graeventzii being the first complete genomes from their respective taxa. Obtaining complete bacterial genomes in a high-throughput manner will help illuminate the metabolic and ecological roles of important members of the human microbiota, particularly those that have remained recalcitrant to isolation and cultivation.}, } @article {pmid35993708, year = {2022}, author = {Miranda, K and Weigel, BL and Fogarty, EC and Veseli, IA and Giblin, AE and Eren, AM and Pfister, CA}, title = {The Diversity and Functional Capacity of Microbes Associated with Coastal Macrophytes.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0059222}, pmid = {35993708}, issn = {2379-5077}, mesh = {*Metagenome/genetics ; *Microbiota ; Rhizosphere ; Nitrogen/metabolism ; Sulfur/metabolism ; }, abstract = {Coastal marine macrophytes exhibit some of the highest rates of primary productivity in the world. They have been found to host a diverse set of microbes, many of which may impact the biology of their hosts through metabolisms that are unique to microbial taxa. Here, we characterized the metabolic functions of macrophyte-associated microbial communities using metagenomes collected from 2 species of kelp (Laminaria setchellii and Nereocystis luetkeana) and 3 marine angiosperms (Phyllospadix scouleri, P. serrulatus, and Zostera marina), including the rhizomes of two surfgrass species (Phyllospadix spp.), the seagrass Zostera marina, and the sediments surrounding P. scouleri and Z. marina. Using metagenomic sequencing, we describe 63 metagenome-assembled genomes (MAGs) that potentially benefit from being associated with macrophytes and may contribute to macrophyte fitness through their metabolic activity. Host-associated metagenomes contained genes for the use of dissolved organic matter from hosts and vitamin (B1, B2, B7, B12) biosynthesis in addition to a range of nitrogen and sulfur metabolisms that recycle dissolved inorganic nutrients into forms more available to the host. The rhizosphere of surfgrass and seagrass contained genes for anaerobic microbial metabolisms, including nifH genes associated with nitrogen fixation, despite residing in a well-mixed and oxygenated environment. The range of oxygen environments engineered by macrophytes likely explains the diversity of both oxidizing and reducing microbial metabolisms and contributes to the functional capabilities of microbes and their influences on carbon and nitrogen cycling in nearshore ecosystems. IMPORTANCE Kelps, seagrasses, and surfgrasses are ecosystem engineers on rocky shorelines, where they show remarkably high levels of primary production. Through analysis of their associated microbial communities, we found a variety of microbial metabolisms that may benefit the host, including nitrogen metabolisms, sulfur oxidation, and the production of B vitamins. In turn, these microbes have the genetic capabilities to assimilate the dissolved organic compounds released by their macrophyte hosts. We describe a range of oxygen environments associated with surfgrass, including low-oxygen microhabitats in their rhizomes that host genes for nitrogen fixation. The tremendous productivity of coastal seaweeds and seagrasses is likely due in part to the activities of associated microbes, and an increased understanding of these associations is needed.}, } @article {pmid35993706, year = {2022}, author = {Kojima, CY and Getz, EW and Thrash, JC}, title = {RRAP: RPKM Recruitment Analysis Pipeline.}, journal = {Microbiology resource announcements}, volume = {11}, number = {9}, pages = {e0064422}, pmid = {35993706}, issn = {2576-098X}, support = {OCE-1747681//National Science Foundation (NSF)/ ; OCE-1945279//National Science Foundation (NSF)/ ; Early Career Investigator in Marine Microbial Ecology and Evolution Award//Simons Foundation (SF)/ ; }, abstract = {A common method for quantifying microbial abundances in situ is through metagenomic read recruitment to genomes and normalizing read counts as reads per kilobase (of genome) per million (bases of recruited sequences) (RPKM). We created RRAP (RPKM Recruitment Analysis Pipeline), a wrapper that automates this process using Bowtie2 and SAMtools.}, } @article {pmid35993704, year = {2022}, author = {Sudjai, A and Suriye, K and Kruasuwan, W and Jenjaroenpun, P and Foongladda, S and Wongsurawat, T}, title = {Long-Read 16S rRNA Amplicon and Metagenomic Data of Swine Feed-Additive Probiotics Product.}, journal = {Microbiology resource announcements}, volume = {11}, number = {9}, pages = {e0039722}, pmid = {35993704}, issn = {2576-098X}, abstract = {Swine feed-additive probiotics products play a major role in swine performance and welfare by promoting gut health. Here, we present two types of data, including a full-length 16S rRNA amplicon sequence data and a long-read metagenomic sequence data obtained from the same commercial probiotic product.}, } @article {pmid35993242, year = {2022}, author = {Ye, P and Xie, C and Wu, C and Yu, C and Chen, Y and Liang, Z and Chen, Y and Chen, Q and Kong, Y}, title = {The application of metagenomic next-generation sequencing for detection of pathogens from dialysis effluent in peritoneal dialysis-associated peritonitis .}, journal = {Peritoneal dialysis international : journal of the International Society for Peritoneal Dialysis}, volume = {42}, number = {6}, pages = {585-590}, doi = {10.1177/08968608221117315}, pmid = {35993242}, issn = {1718-4304}, mesh = {Humans ; Prospective Studies ; Sensitivity and Specificity ; *Peritoneal Dialysis/adverse effects ; Renal Dialysis ; High-Throughput Nucleotide Sequencing/methods ; *Peritonitis/diagnosis/etiology ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) can improve pathogen identification in infectious diseases.

METHODS: A prospective parallel control study was undertaken to evaluate the clinical significance of mNGS in identifying pathogens in dialysis effluent of patients with peritoneal dialysis-associated peritonitis (peritonitis). Dialysis effluent specimens were detected both by peritoneal dialysis effluent culture and mNGS. The positive rates and coincidence rates of the two methods were compared.

RESULTS: From April 2020 to March 2021, 30 patients presenting with peritonitis were enrolled in this study. The positive pathogen detection rate of mNGS was significantly higher than that of the traditional culture method (86.67% vs. 60.00%; p = 0.039). Fifteen specimens were positive for both of the methods, while 11 specimens were negative for culture but positive for mNGS. Three specimens were positive for culture but negative for mNGS; all of them were streptococcus mitis. One specimen was negative for both methods. The culture method detected one type of pathogen in all specimens; however, two or more types of pathogens were detected in eight specimens by mNGS. In addition to common pathogens, additional pathogens detected by mNGS included Coxiella burnetii, human herpesvirus type 5, human herpesvirus type 6B and Mortierella.

CONCLUSION: The pathogen detection rate of mNGS in dialysis effluent of peritonitis patients was significantly higher than that of traditional culture. The mNGS is advantageous in diagnosing the pathogens that are difficult to be cultured. However, mNGS did not demonstrate sensitivity to streptococcus mitis. Results from this study show that mNGS, combined with traditional culture, has potential application for detecting pathogens in peritoneal dialysis patients with peritonitis.}, } @article {pmid35992996, year = {2022}, author = {Filatova, EN and Chaikina, AS and Brusnigina, NF and Makhova, MA and Utkin, OV}, title = {An Algorithm for the Selection of Probes for Specific Detection of Human Disease Pathogens Using the DNA Microarray Technology.}, journal = {Sovremennye tekhnologii v meditsine}, volume = {14}, number = {1}, pages = {6-12}, pmid = {35992996}, issn = {2309-995X}, mesh = {Algorithms ; *Chlamydophila pneumoniae/genetics ; *Community-Acquired Infections/diagnosis ; Humans ; Oligonucleotide Array Sequence Analysis/methods ; Technology ; }, abstract = {UNLABELLED: The aim of the study was to develop an algorithm for the selection of discriminating probes to identify a wide range of causative agents of human infectious diseases.

MATERIALS AND METHODS: The algorithm for selecting the probes was implemented in the form of the disprose (DIScrimination PRObe SElection) computer program written in the R language. Additionally, third-party software was used: the BLAST+ and ViennaRNA Package programs. The developed algorithm was tested by selecting specific probes for detecting Chlamydophila (Chlamydia) pneumoniae - an atypical bacterial pathogen causing community-acquired pneumonia (CAP). Nucleotide sequences for analysis were downloaded from the NCBI databank.

RESULTS: An algorithm for the selection of specific probes capable of detecting human infectious pathogens has been developed. The algorithm is implemented in the form of the disprose modular program, which allows for performing all stages of the probe selection process: loading the nucleotide sequences and their metadata from available databanks, creating local databases, forming a pool of probes, calculating their physicochemical parameters, aligning the probes and sequences contained in local databases, processing and evaluating the alignment results. The algorithm was successfully tested and its performance was confirmed by selecting a set of probes for the specific detection of Chlamydophila pneumoniae. The specificity of the selected probes calculated in silico indicated a low risk of their nonspecific binding and a high potential of using them as molecular genetic diagnostic tools (DNA microarrays, PCR).

CONCLUSION: An algorithm for the selection of specific probes detecting a wide range of human pathogens in clinical biomaterial has been developed and implemented in the form of the disprose modular program. The probes selected using this program can serve as the functional basis of DNA-oriented microarrays able to identify causative agents of polyetiological diseases, such as CAP. Due to the flexibility and openness of the program, the scope of its application can be expanded.}, } @article {pmid35992725, year = {2022}, author = {Begmatov, S and Beletsky, AV and Dedysh, SN and Mardanov, AV and Ravin, NV}, title = {Genome analysis of the candidate phylum MBNT15 bacterium from a boreal peatland predicted its respiratory versatility and dissimilatory iron metabolism.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {951761}, pmid = {35992725}, issn = {1664-302X}, abstract = {Uncultured bacteria of the candidate phylum MBNT15, distantly related to Desulfobacterota, have been identified in a broad range of mostly organic-rich aquatic environments. We assembled a near-complete genome of a member of MBNT15 from a boreal peatland metagenome and used genomic data to analyze the metabolic pathways of this bacterium and its ecological role. This bacterium, designated SHF-111, was predicted to be rod shaped, it lacks flagellar machinery but twitching motility is encoded. Genome-based phylogenetic analysis supported the phylum-level classification of the MBNT15 lineage. Genome annotation and metabolic reconstruction revealed the presence of the Embden-Meyerhof, Entner-Doudoroff and pentose phosphate pathways, as well as the complete tricarboxylic acid (TCA) cycle, and suggested a facultatively anaerobic chemoheterotrophic lifestyle with the ability to ferment peptides, amino acids, fatty acids and simple sugars, and completely oxidize these substrates through aerobic and anaerobic respiration. The SHF-111 genome encodes multiple multiheme c-type cytochromes that probably enable dissimilatory iron reduction. Consistently, the relative abundance of MBNT15 in peatlands positively correlated with iron concentration. Apparently, in the wetland ecosystem, MBNT15 representatives play the role of scavengers, carrying out the complete mineralization of low molecular weight organic substances formed as a result of microbial degradation of complex polymeric substrates. Comparative genome analysis of the MBNT15 phylum revealed that vast majority of its members are capable of aerobic respiration and dissimilatory iron reduction and some species also can reduce sulfur and nitrogen compounds, but not sulfate. Based on phylogenetic and genomic analyses, the novel bacterium is proposed to be classified as Candidatus Deferrimicrobium borealis, within a candidate phylum Deferrimicrobiota.}, } @article {pmid35992707, year = {2022}, author = {Ide, K and Saeki, T and Arikawa, K and Yoda, T and Endoh, T and Matsuhashi, A and Takeyama, H and Hosokawa, M}, title = {Exploring strain diversity of dominant human skin bacterial species using single-cell genome sequencing.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {955404}, pmid = {35992707}, issn = {1664-302X}, abstract = {To understand the role of the skin commensal bacterial community in skin health and the spread of pathogens, it is crucial to identify genetic differences in the bacterial strains corresponding to human individuals. A culture-independent genomics approach is an effective tool for obtaining massive high-quality bacterial genomes. Here we present a single-cell genome sequencing to obtain comprehensive whole-genome sequences of uncultured skin bacteria from skin swabs. We recovered 281 high-quality (HQ) and 244 medium-quality single-amplified genomes (SAGs) of multiple skin bacterial species from eight individuals, including cohabiting group. Single-cell sequencing outperformed in the genome recovery from the same skin swabs, showing 10-fold non-redundant strain genomes compared to the shotgun metagenomic sequencing and binning approach. We then focused on the abundant skin bacteria and identified intra-species diversity, especially in 47 Moraxella osloensis derived HQ SAGs, characterizing the strain-level heterogeneity at mobile genetic element profiles, including plasmids and prophages. Even between the cohabiting individual hosts, they have unique skin bacterial strains in the same species, which shows microdiversity in each host. Genetic and functional differences between skin bacterial strains are predictive of in vivo competition to adapt bacterial genome to utilize the sparse nutrients available on the skin or produce molecules that inhibit the colonization of other microbes or alter their behavior. Thus, single-cell sequencing provides a large number of genomes of higher resolution and quality than conventional metagenomic analysis and helps explore the skin commensal bacteria at the strain level, linking taxonomic and functional information.}, } @article {pmid35992701, year = {2022}, author = {Nimonkar, YS and Godambe, T and Kulkarni, A and Patel, T and Paul, D and Paul, D and Rale, V and Prakash, O}, title = {Oligotrophy vs. copiotrophy in an alkaline and saline habitat of Lonar Lake.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {939984}, pmid = {35992701}, issn = {1664-302X}, abstract = {We reported our comparative observations on oligotrophs vs. copiotrophs from a hyper-alkaline and hypersaline habitat, Lonar Lake, situated in the Buldhana district of Maharashtra, India. Cell numbers of oligotrophic and copiotrophic microbes from the sediment were enumerated by the three-tube most probable number (MPN) method using an array of nutrient-rich and oligotrophic (≈10-20 mg carbon L[-1]) media offering simulated natural conditions of pH and salinity. A total of 50 strains from 15 different genera and 30 different species were isolated from the highest positive dilutions of MPN to identify the taxa of oligotrophs and copiotrophic microorganisms dominating in Lonar Lake. We did not get any true oligotrophs due to their adaptation to higher carbon levels during the isolation procedure. On the contrary, several true copiotrophs, which could not adapt and survive on a low-carbon medium, were isolated. It is also observed that changes in medium composition and nutrient level altered the selection of organisms from the same sample. Our data indicate that copiotrophic microorganisms dominate the eutrophic Lonar Lake, which is also supported by the past metagenomics studies from the same site. We also reported that quick depletion of carbon from oligotrophic medium worked as a limiting factor, inducing cell death after 2-3 generations and preventing the development of visible colonies on plates and sufficient optical density in liquid medium. Therefore, a long-term supply of low levels of carbon, followed by isolation on enriched media, can serve as a good strategy in isolation of novel taxa of microorganism, with industrial or environmental importance.}, } @article {pmid35992687, year = {2022}, author = {Zong, S and Xu, D and Zheng, X and Zaeim, D and Wang, P and Han, J and Qu, D}, title = {The diversity in antimicrobial resistance of MDR Enterobacteriaceae among Chinese broiler and laying farms and two mcr-1 positive plasmids revealed their resistance-transmission risk.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {912652}, pmid = {35992687}, issn = {1664-302X}, abstract = {This research aimed to investigate the microbial composition and diversity of antimicrobial resistance genes (ARGs) found in Chinese broiler and layer family poultry farms. We focused on the differences in resistance phenotypes and genotypes of multidrug-resistant Enterobacteriaceae (MDRE) isolated from the two farming environments and the existence and transmissibility of colistin resistance gene mcr-1. Metagenomic analysis showed that Firmicutes and Bacteroides were the dominant bacteria in broiler and layer farms. Many aminoglycoside and tetracycline resistance genes were accumulated in these environments, and their absolute abundance was higher in broiler than in layer farms. A total of 526 MDRE were isolated with a similar distribution in both farms. The results of the K-B test showed that the resistance rate to seven antimicrobials including polymyxin B and meropenem in broiler poultry farms was significantly higher than that in layer poultry farms (P ≤ 0.05). PCR screening results revealed that the detection rates of mcr-1, aph(3')Ia, aadA2, bla oxa-1 , bla CTX-M , fosB, qnrD, sul1, tetA, and catA1 in broiler source MDRE were significantly higher than those in layers (P ≤0.05). A chimeric plasmid p20432-mcr which carried the novel integron In1866 was isolated from broiler source MDRE. The high frequency of conjugation (10[-1] to 10[-3]) and a wide range of hosts made p20432-mcr likely to play an essential role in the high detection rate of mcr-1, aph(3')-Ia, and aadA2 in broiler farms. These findings will help optimize disinfection and improve antimicrobial-resistant bacteria surveillance programs in poultry farms, especially broilers.}, } @article {pmid35992666, year = {2022}, author = {Zheng, YR and Lin, SH and Chen, YK and Cao, H and Chen, Q}, title = {Application of metagenomic next-generation sequencing in the detection of pathogens in bronchoalveolar lavage fluid of infants with severe pneumonia after congenital heart surgery.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {954538}, pmid = {35992666}, issn = {1664-302X}, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has become a valuable diagnostic tool in clinical etiology detection due to its rapidity, accuracy, and high throughput. However, the role of this technology in the diagnosis and treatment of infants with severe pneumonia after congenital heart surgery is still unclear.

METHODS: We conducted a retrospective cohort study of infants with severe pneumonia after congenital heart surgery. Samples were collected from infants in the hospital's cardiac intensive care unit between January 2010 and January 2022. The conventional microbiological test (CMT) group consisted of patients who underwent routine microbiological examination, and the infants' bronchoalveolar lavage fluid was examined. The mNGS group consisted of patients who underwent mNGS and routine microbiological examinations.

RESULTS: The overall positive rate of mNGS was significantly higher than that of CMT (88.4 vs. 62.5%, P = 0.009). After receipt of the microbiological results, 30/43 (70%) patients in the mNGS group had a change in antibiotic use compared with 14/40 (35%) in the CMT group (P = 0.002). Subsequently, after adjusting the treatment plan according to the microbiological test results, the number of people with improved pulmonary infection in the mNGS group was significantly higher than that in the CMT group (63 vs. 28%, P < 0.05). In addition, the duration of invasive ventilation, length of CICU stay and total hospital length of stay in the mNGS group were significantly lower than those in the CMT group (P < 0.05).

CONCLUSION: mNGS is a valuable tool to determine the etiology of infants with severe pneumonia after congenital heart disease surgery. It can significantly improve the sensitivity of pathogen detection, which can help determine appropriate antimicrobial drugs, improve the diagnostic accuracy of the disease, and improve outcomes.}, } @article {pmid35992659, year = {2022}, author = {Temmerman, R and Ghanbari, M and Antonissen, G and Schatzmayr, G and Duchateau, L and Haesebrouck, F and Garmyn, A and Devreese, M}, title = {Dose-dependent impact of enrofloxacin on broiler chicken gut resistome is mitigated by synbiotic application.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {869538}, pmid = {35992659}, issn = {1664-302X}, abstract = {Fluoroquinolone agents are considered critical for human medicine by the World Health Organization (WHO). However, they are often used for the treatment of avian colibacillosis in poultry production, creating considerable concern regarding the potential spread of fluoroquinolone resistance genes from commensals to pathogens. Therefore, there is a need to understand the impact of fluoroquinolone application on the reservoir of ARGs in poultry gut and devise means to circumvent potential resistome expansion. Building upon a recent dose optimization effort, we used shotgun metagenomics to investigate the time-course change in the cecal microbiome and resistome of broiler chickens receiving an optimized dosage [12.5 mg/kg body weight (bw)/day], with or without synbiotic supplementation (PoultryStar[®], BIOMIN GmbH), and a high dosage of enrofloxacin (50 mg/kg bw/day). Compared to the high dose treatment, the low (optimized) dose of enrofloxacin caused the most significant perturbations in the cecal microbiota and resistome of the broiler chickens, demonstrated by a lower cecal microbiota diversity while substantially increasing the antibiotic resistance genes (ARGs) resistome diversity. Withdrawal of antibiotics resulted in a pronounced reduction in ARG diversity. Chickens receiving the synbiotic treatment had the lowest diversity and number of enriched ARGs, suggesting an alleviating impact on the burden of the gut resistome. Some Proteobacteria were significantly increased in the cecal metagenome of chickens receiving enrofloxacin and showed a positive association with increased ARG burden. Differential abundance (DA) analysis revealed a significant increase in the abundance of ARGs encoding resistance to macrolides-lincosamides-streptogramins (MLS), aminoglycosides, and tetracyclines over the period of enrofloxacin application, with the optimized dosage application resulting in a twofold higher number of affected ARG compared to high dosage application. Our results provide novel insights into the dose-dependent effects of clinically important enrofloxacin application in shaping the broiler gut resistome, which was mitigated by a synbiotic application. The contribution to ameliorating the adverse effects of antimicrobial agents, that is, lowering the spread of antimicrobial resistance genes, on the poultry and potentially other livestock gastrointestinal microbiomes and resistomes merits further study.}, } @article {pmid35992333, year = {2022}, author = {Fekete, E and Bíró, V and Márton, A and Bakondi-Kovács, I and Németh, Z and Sándor, E and Kovács, B and Fábián, I and Kubicek, CP and Tsang, A and Karaffa, L}, title = {Bioreactor as the root cause of the "manganese effect" during Aspergillus niger citric acid fermentations.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {935902}, pmid = {35992333}, issn = {2296-4185}, abstract = {High-yield citric acid production by the filamentous Ascomycete fungus Aspergillus niger requires a combination of extreme nutritional conditions, of which maintaining a low manganese (II) ion concentration (<5 μg L[-1]) is a key feature. Technical-scale production of citric acid predominantly uses stainless-steel tank fermenters, but glass bioreactors used for strain improvement and manufacturing process development also contain stainless steel components, in which manganese is an essential alloying element. We show here that during citric acid fermentations manganese (II) ions were leaching from the bioreactor into the growth media, resulting in altered fungal physiology and morphology, and significant reduction of citric acid yields. The leaching of manganese (II) ions was dependent on the fermentation time, the acidity of the culture broth and the sterilization protocol applied. Manganese (II) ion leaching was partially mitigated by electrochemical polishing of stainless steel components of the bioreactor. High concentrations of manganese (II) ions during early cultivation led to a reduction in citric acid yield. However, the effect of manganese (II) ions on the reduction of citric acid yield diminished towards the second half of the fermentation. Since maintaining low concentrations of manganese (II) ions is costly, the results of this study can potentially be used to modify protocols to reduce the cost of citric acid production.}, } @article {pmid35992169, year = {2022}, author = {Shi, Y and Peng, JM and Qin, HY and Du, B}, title = {Metagenomic next-generation sequencing: A promising tool for diagnosis and treatment of suspected pneumonia in rheumatic patients with acute respiratory failure: Retrospective cohort study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {941930}, pmid = {35992169}, issn = {2235-2988}, mesh = {High-Throughput Nucleotide Sequencing/methods ; Humans ; *Pneumonia/diagnosis/drug therapy/microbiology ; *Respiratory Distress Syndrome ; *Respiratory Insufficiency ; Retrospective Studies ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: The effectiveness of metagenomic next-generation sequencing (mNGS) in respiratory pathogen detection and clinical decision-making in critically rheumatic patients remains largely unexplored.

METHODS: A single-center retrospective study of 58 rheumatic patients who were admitted to ICU due to suspected pneumonia with acute respiratory failure if they underwent both bronchoalveolar lavage fluid specimen mNGS and combined microbiological tests (CMTs) was conducted to compare their diagnostic performance, using clinical composite diagnosis as the gold standard. Treatment modifications based on mNGS results were also reviewed.

RESULTS: Forty-three patients were diagnosed with microbiologically confirmed pneumonia and 15 were considered as a non-infectious disease. mNGS outperformed CMTs in the accurate diagnosis of infectious and non-infectious lung infiltration (98.1% [57/58] vs. 87.9% [51/58], P = 0.031). A total of 94 causative pathogens were defined by the gold standard and 27 patients had polymicrobial pneumonia. The sensitivity of pathogen detection and complete concordance with the gold standard by mNGS exceeded those by CMTs (92.6% [87/94] vs. 76.6% [72/94], P < 0.001 and 72.1% [31/43] vs. 51.2% [22/43], P = 0.004, respectively). Moreover, 22 pathogens were detected only by mNGS and confirmed by orthogonal test. Accordingly, the etiological diagnosis changed in 19 cases, and the empirical treatment improved in 14 cases, including 8 cases of rescue treatment and 11 of antibiotics de-escalation. At the pathogen-type level, both methods were comparable for bacteria, but mNGS was advantageous to identify viruses (accuracy: 100% vs. 81%, P = 0.004). For Pneumocystis jirovecii detection, mNGS improved the sensitivity compared with Gomori's methenamine silver stain (91.7% vs. 4.2%, P < 0.001) and was higher than polymerase chain reaction (79.2%), but the difference was not significant (P = 0.289). In terms of Aspergillus, the better sensitivity with a combination of culture and galactomannan test than that with mNGS was found (100% vs. 66.7%, P = 0.033).

CONCLUSIONS: mNGS has an excellent accuracy in etiological diagnosis and pathogen detection of suspected pneumonia in critically rheumatic patients, which has potential significance for clinical decision-making. Its superiority to different types of pathogens depends on the comprehensiveness of CMTs.}, } @article {pmid35992074, year = {2022}, author = {Meijnikman, AS and Lappa, D and Herrema, H and Aydin, O and Krautkramer, KA and Tremaroli, V and Olofsson, LE and Lundqvist, A and Bruin, S and Acherman, Y and Verheij, J and Hjorth, S and Gerdes, VEA and Schwartz, TW and Groen, AK and Bäckhed, F and Nielsen, J and Nieuwdorp, M}, title = {A systems biology approach to study non-alcoholic fatty liver (NAFL) in women with obesity.}, journal = {iScience}, volume = {25}, number = {8}, pages = {104828}, pmid = {35992074}, issn = {2589-0042}, abstract = {Non-alcoholic fatty liver disease (NAFLD) is now the most frequent global chronic liver disease. Individuals with NAFLD exhibited an increased risk of all-cause mortality driven by extrahepatic cancers and liver and cardiovascular disease. Once the disease is established, women have a higher risk of disease progression and worse outcome. It is therefore critical to deepen the current knowledge on the pathophysiology of NAFLD in women. Here, we used a systems biology approach to investigate the contribution of different organs to this disease. We analyzed transcriptomics profiles of liver and adipose tissues, fecal metagenomes, and plasma metabolomes of 55 women with and without NAFLD. We observed differences in metabolites, expression of human genes, and gut microbial features between the groups and revealed that there is substantial crosstalk between these different omics sets. Multi-omics analysis of individuals with NAFLD may provide novel strategies to study the pathophysiology of NAFLD in humans.}, } @article {pmid35992057, year = {2022}, author = {Tolstoganov, I and Kamenev, Y and Kruglikov, R and Ochkalova, S and Korobeynikov, A}, title = {BinSPreader: Refine binning results for fuller MAG reconstruction.}, journal = {iScience}, volume = {25}, number = {8}, pages = {104770}, pmid = {35992057}, issn = {2589-0042}, abstract = {Despite the recent advances in high-throughput sequencing, metagenome analysis of microbial populations still remains a challenge. In particular, the metagenome-assembled genomes (MAGs) are often fragmented due to interspecies repeats, uneven coverage, and varying strain abundance. MAGs are constructed via a binning process that uses features of input data in order to cluster long contigs presumably belonging to the same species. In this work, we present BinSPreader-a binning refiner tool that exploits the assembly graph topology and other connectivity information to refine binning, correct binning errors, and propagate binning to shorter contigs. We show that BinSPreader could increase the completeness of the bins without sacrificing the purity and could predict contigs belonging to several MAGs. BinSPreader is effective in binning shorter contigs that often contain important conservative sequences that might be of great interest to researchers.}, } @article {pmid35991836, year = {2022}, author = {Hu, J and Yang, J and Chen, L and Meng, X and Zhang, X and Li, W and Li, Z and Huang, G}, title = {Alterations of the Gut Microbiome in Patients With Pituitary Adenoma.}, journal = {Pathology oncology research : POR}, volume = {28}, number = {}, pages = {1610402}, pmid = {35991836}, issn = {1532-2807}, mesh = {*Adenoma ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; Metagenomics ; *Pituitary Neoplasms ; }, abstract = {Pituitary adenoma (PA) includes invasive pituitary adenoma (IPA) and noninvasive pituitary adenoma (NIPA), which are associated with the endocrine system. The gut microbiome plays an important role in human metabolism, but the association between the gut microbiome and pituitary adenoma remains unclear. A total of 44 subjects were enrolled in this study. Of these, 29 PA patients were further divided into IPA patients (n = 13) and NIPA patients (n = 16), while 15 healthy age-matched subjects were defined as control subjects. We collected faecal samples and characterized the gut microbial profiles by metagenomic sequencing using the Illumina X-ten platform. PLS-DA showed different microbial clusters among the three groups, and slightly different microbial ecological networks were observed. LEfSe analysis revealed significant alterations in the microbial community among PA patients. In particular, the enrichment of Clostridium innocuum, along with the reduced abundance of Oscillibacter sp. 57_20 and Fusobacterium mortiferum, were observed both in the IPA and NIPA groups compared to the control group. Moreover, PA patients could be effectively classified based on these bacteria using a support vector machine algorithm. In summary, this study demonstrated significant differences in the gut microbiome between PA patients and healthy controls. Future mechanistic experiments are needed to determine whether such alterations are a cause or consequence of pituitary adenoma.}, } @article {pmid35991696, year = {2022}, author = {Phan, T and Kobayashi, M and Nagasawa, K and Hatazawa, R and Thi Kim Pham, N and Miyashita, H and Komoto, S and Tajima, T and Baba, T and Okitsu, S and Khamrin, P and Maneekarn, N and Kimura, H and Kobayashi, T and Hayakawa, S and Ushijima, H}, title = {Whole genome sequencing and evolutionary analysis of G8P [8] rotaviruses emerging in Japan.}, journal = {Virusdisease}, volume = {33}, number = {2}, pages = {215-218}, pmid = {35991696}, issn = {2347-3584}, abstract = {Unusual DS-1-like intergenogroup reassortant rotaviruses with a bovine-like G8 genotype (DS-1-like G8P [8] rotaviruses) have emerged and rapidly spread in several countries. In this study, the nucleotide sequences of seven human rotavirus G8P [8] strains in 2017 and 2019 in Japan were determined using viral metagenomics. Its genomic constellation (VP7-VP4-VP6-VP1-VP2-VP3-NSP1-NSP2-NSP3-NSP4-NSP5 genes) was defined as G8-P [8]-I2-R2-C2-M2-A2-N2-T2-E2-H2. Our genetic analysis revealed that the Japanese G8P [8] rotavirus strains in 2017 and 2019 were classified into the same lineages G8-5 and P [8]-3, but they were phylogenetically located on separate branches and belonged to distinct clusters. Our study is the first attempt to investigate the evolution of emerging rotavirus G8P [8] in Japan.}, } @article {pmid35991432, year = {2022}, author = {Dong, Q and Zhao, X and Zhou, D and Liu, Z and Shi, X and Yuan, Y and Jia, P and Liu, Y and Song, P and Wang, X and Jiang, C and Liu, X and Zhang, H and Zhong, C and Guo, F and Wan, S and Yu, H and Zhang, Z}, title = {Maize and peanut intercropping improves the nitrogen accumulation and yield per plant of maize by promoting the secretion of flavonoids and abundance of Bradyrhizobium in rhizosphere.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {957336}, pmid = {35991432}, issn = {1664-462X}, abstract = {Belowground interactions mediated by root exudates are critical for the productivity and efficiency of intercropping systems. Herein, we investigated the process of microbial community assembly in maize, peanuts, and shared rhizosphere soil as well as their regulatory mechanisms on root exudates under different planting patterns by combining metabolomic and metagenomic analyses. The results showed that the yield of intercropped maize increased significantly by 21.05% (2020) and 52.81% (2021), while the yield of intercropped peanut significantly decreased by 39.51% (2020) and 32.58% (2021). The nitrogen accumulation was significantly higher in the roots of the intercropped maize than in those of sole maize at 120 days after sowing, it increased by 129.16% (2020) and 151.93% (2021), respectively. The stems and leaves of intercropped peanut significantly decreased by 5.13 and 22.23% (2020) and 14.45 and 24.54% (2021), respectively. The root interaction had a significant effect on the content of ammonium nitrogen (NH4 [+]-N) as well as the activities of urease (UE), nitrate reductase (NR), protease (Pro), and dehydrogenase (DHO) in the rhizosphere soil. A combined network analysis showed that the content of NH4 [+]-N as well as the enzyme activities of UE, NR and Pro increased in the rhizosphere soil, resulting in cyanidin 3-sambubioside 5-glucoside and cyanidin 3-O-(6-Op-coumaroyl) glucoside-5-O-glucoside; shisonin were significantly up-regulated in the shared soil of intercropped maize and peanut, reshaped the bacterial community composition, and increased the relative abundance of Bradyrhizobium. These results indicate that interspecific root interactions improved the soil microenvironment, regulated the absorption and utilization of nitrogen nutrients, and provided a theoretical basis for high yield and sustainable development in the intercropping of maize and peanut.}, } @article {pmid35990902, year = {2022}, author = {Rosario, K and Van Bogaert, N and López-Figueroa, NB and Paliogiannis, H and Kerr, M and Breitbart, M}, title = {Freshwater macrophytes harbor viruses representing all five major phyla of the RNA viral kingdom Orthornavirae.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13875}, pmid = {35990902}, issn = {2167-8359}, mesh = {*RNA Viruses/genetics ; *Viruses ; Fresh Water ; RNA ; Florida ; }, abstract = {Research on aquatic plant viruses is lagging behind that of their terrestrial counterparts. To address this knowledge gap, here we identified viruses associated with freshwater macrophytes, a taxonomically diverse group of aquatic phototrophs that are visible with the naked eye. We surveyed pooled macrophyte samples collected at four spring sites in Florida, USA through next generation sequencing of RNA extracted from purified viral particles. Sequencing efforts resulted in the detection of 156 freshwater macrophyte associated (FMA) viral contigs, 37 of which approximate complete genomes or segments. FMA viral contigs represent putative members from all five major phyla of the RNA viral kingdom Orthornavirae. Similar to viral types found in land plants, viral sequences identified in macrophytes were dominated by positive-sense RNA viruses. Over half of the FMA viral contigs were most similar to viruses reported from diverse hosts in aquatic environments, including phototrophs, invertebrates, and fungi. The detection of FMA viruses from orders dominated by plant viruses, namely Patatavirales and Tymovirales, indicate that members of these orders may thrive in aquatic hosts. PCR assays confirmed the presence of putative FMA plant viruses in asymptomatic vascular plants, indicating that viruses with persistent lifestyles are widespread in macrophytes. The detection of potato virus Y and oat blue dwarf virus in submerged macrophytes suggests that terrestrial plant viruses infect underwater plants and highlights a potential terrestrial-freshwater plant virus continuum. Defining the virome of unexplored macrophytes will improve our understanding of virus evolution in terrestrial and aquatic primary producers and reveal the potential ecological impacts of viral infection in macrophytes.}, } @article {pmid35990349, year = {2022}, author = {Guo, W and Luo, L and Meng, Y and Chen, W and Yu, L and Zhang, C and Qiu, Z and Cao, P}, title = {Luteolin alleviates methionine-choline-deficient diet-induced non-alcoholic steatohepatitis by modulating host serum metabolome and gut microbiome.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {936237}, pmid = {35990349}, issn = {2296-861X}, abstract = {BACKGROUND AND PURPOSE: Previous studies have indicated the protective effects of luteolin against non-alcoholic steatohepatitis (NASH), but the definite underlying mechanism still remains unclear. This study aimed to explore the metabolomic and metagenomic signatures of NASH with luteolin supplementation.

EXPERIMENTAL APPROACH: Mice were fed with a methionine-choline-deficient (MCD) diet containing 0.05% luteolin for 6 weeks. NASH severity was determined based on the liver histological observations, serum and hepatic biochemical measurements. Targeted metabolomics was conducted to identify differential metabolites in mice serum. 16S rRNA sequencing was conducted to assess the gut microbiota composition and function in mice colon.

RESULTS: In detail, luteolin treatment significantly alleviated MCD diet-induced hepatic lipid deposition, liver function damage, and oxidative stress. Targeted plasma metabolomics revealed that 5-hydroxyindole, LPE (0:0/22:5), indole 3-phosphate, and N-phenylacetylphenylalanine were remarkably elevated, and homogentisic acid, thiamine, KN-93, PC (16:1e/8, 9-EpETE), carnitine C9:1-OH, FFA (18:4) and carnitine C8:1 were significantly decreased in NASH group as compared to normal group, which could be profoundly reversed after luteolin treatment. 16S rRNA sequencing indicated that luteolin supplementation significantly increased Erysipelatoclostridium and Pseudomonas as well as decreased Faecalibaculum at genus level. Most importantly, a negative association between thiamine and Faecalibaculum was observed based on Spearman's correlation analysis, which may play an important role in the preventive effects of luteolin against NASH.

CONCLUSION: Collectively, luteolin may alleviate the NASH by modulating serum metabolome and gut microbiome, which supports its use as a dietary supplement for NASH prevention.}, } @article {pmid35990340, year = {2022}, author = {Martin, FP and Tytgat, HLP and Krogh Pedersen, H and Moine, D and Eklund, AC and Berger, B and Sprenger, N}, title = {Host-microbial co-metabolites modulated by human milk oligosaccharides relate to reduced risk of respiratory tract infections.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {935711}, pmid = {35990340}, issn = {2296-861X}, abstract = {Human milk oligosaccharides (HMOs) are structurally diverse oligosaccharides present in breast milk, supporting the development of the gut microbiota and immune system. Previously, 2-HMO (2'fucosyllactose, lacto-N-neotetraose) compared to control formula feeding was associated with reduced risk of lower respiratory tract infections (LRTIs), in part linked to lower acetate and higher bifidobacteria proportions. Here, our objective was to gain further insight into additional molecular pathways linking the 2-HMO formula feeding and LRTI mitigation. From the same trial, we measured the microbiota composition and 743 known biochemical species in infant stool at 3 months of age using shotgun metagenomic sequencing and untargeted mass spectrometry metabolomics. We used multivariate analysis to identify biochemicals associated to 2-HMO formula feeding and LRTI and integrated those findings with the microbiota compositional data. Three molecular pathways stood out: increased gamma-glutamylation and N-acetylation of amino acids and decreased inflammatory signaling lipids. Integration of stool metagenomic data revealed some Bifidobacterium and Bacteroides species to be implicated. These findings deepen our understanding of the infant gut/microbiome co-metabolism in early life and provide evidence for how such metabolic changes may influence immune competence at distant mucosal sites such as the airways.}, } @article {pmid35990279, year = {2022}, author = {Watanangura, A and Meller, S and Suchodolski, JS and Pilla, R and Khattab, MR and Loderstedt, S and Becker, LF and Bathen-Nöthen, A and Mazzuoli-Weber, G and Volk, HA}, title = {The effect of phenobarbital treatment on behavioral comorbidities and on the composition and function of the fecal microbiome in dogs with idiopathic epilepsy.}, journal = {Frontiers in veterinary science}, volume = {9}, number = {}, pages = {933905}, pmid = {35990279}, issn = {2297-1769}, abstract = {Phenobarbital (PB) is one of the most important antiseizure drugs (ASDs) to treat canine idiopathic epilepsy (IE). The effect of PB on the taxonomic changes in gastrointestinal microbiota (GIM) and their functions is less known, which may explain parts of its pharmacokinetic and pharmacodynamic properties, especially its antiseizure effect and drug responsiveness or drug resistance as well as its effect on behavioral comorbidities. Fecal samples of 12 dogs with IE were collected prior to the initiation of PB treatment and 90 days after oral PB treatment. The fecal samples were analyzed using shallow DNA shotgun sequencing, real-time polymerase chain reaction (qPCR)-based dysbiosis index (DI), and quantification of short-chain fatty acids (SCFAs). Behavioral comorbidities were evaluated using standardized online questionnaires, namely, a canine behavioral assessment and research questionnaire (cBARQ), canine cognitive dysfunction rating scale (CCDR), and an attention deficit hyperactivity disorder (ADHD) questionnaire. The results revealed no significant changes in alpha and beta diversity or in the DI, whereas only the abundance of Clostridiales was significantly decreased after PB treatment. Fecal SCFA measurement showed a significant increase in total fecal SCFA concentration and the concentrations of propionate and butyrate, while acetate concentrations revealed an upward trend after 90 days of treatment. In addition, the PB-Responder (PB-R) group had significantly higher butyrate levels compared to the PB-Non-Responder (PB-NR) group. Metagenomics of functional pathway genes demonstrated a significant increase in genes in trehalose biosynthesis, ribosomal synthesis, and gluconeogenesis, but a decrease in V-ATPase-related oxidative phosphorylation. For behavioral assessment, cBARQ analysis showed improvement in stranger-directed fear, non-social fear, and trainability, while there were no differences in ADHD-like behavior and canine cognitive dysfunction (CCD) scores after 90 days of PB treatment. While only very minor shifts in bacterial taxonomy were detected, the higher SCFA concentrations after PB treatment could be one of the key differences between PB-R and PB-NR. These results suggest functional changes in GIM in canine IE treatment.}, } @article {pmid35989412, year = {2022}, author = {Thakur, SS and Lone, AR and Yellaboina, S and Tambat, S and Yadav, AN and Jain, SK and Yadav, S}, title = {Metagenomic Insights into the Gut Microbiota of Eudrilus eugeniae (Kinberg) and Its Potential Roles in Agroecosystem.}, journal = {Current microbiology}, volume = {79}, number = {10}, pages = {295}, pmid = {35989412}, issn = {1432-0991}, mesh = {*Actinobacteria/genetics ; Animals ; Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; *Microbiota ; *Oligochaeta/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; Soil ; }, abstract = {Gut microbiomes, a consortium of microorganisms that live in the animal gut, are highly engineered microbial communities. It makes a major contribution to digestive health, metabolism management, and the development of a strong immune system in the host. The present study was taken up to answer the long-running question about the existence of truly indigenous microflora of the epigeic earthworm gut. This is due to the general difficulties of culturing many of the microorganisms found in soil or earthworms' gut. Keeping this fact in a view, the metagenomics approach using 16S rRNA marker gene incorporated with amplicon-based sequencing was used to explore microbiota of commercially overriding, diversely fed epigeic earthworm Eudrilus eugeniae (Kinberg) in three varied habitats viz., artificial soil (AS), organic agricultural farm soil (OAFS) and conventional agriculture farm soil (CAFS). There are predominant bacteria that belong to different phyla such as Proteobacteria (29.72-76.81%), Actinobacteria (11.06-34.42%), Firmicutes (6.02-19.81%), and Bacteroidetes (2.40-9.22%) present in the gut of E. eugeniae. The alpha diversity (Observed species, Chao1, ACE, Shannon, Simpson, and Fisher alpha) indices showed that OAFS had significantly higher alpha diversity than AS and CAFS groups. The core microbiota analysis showed that OAFS and AS groups had a relatively similar bacterial panel in comparison to the CAFS group. Various statistical tools i.e. MetagenomeSeq, LEfSe, and Random Forest analysis were performed and the findings demonstrated prevalence of the most significant bacterial genera; Aeromonas, Gaiella, and Burkholderia in CAFS group. Nonetheless, in AS and OAFS groups, the common existence of Anaerosporobacter and Aquihabitans were found respectively. Metagenomic functional prediction revealed that earthworms' gut microbial communities were actively involved in multiple organic and xenobiotics compound degradation-related pathways. This is the first research to use high-throughput 16S rRNA gene amplicon sequencing to show the gut microbiota of E. eugeniae in diverse agricultural systems. The findings suggest the configuration of the gut microbiota of earthworms and its potential role in the soil ecosystem depends on the microbial communities of the soil.}, } @article {pmid35988621, year = {2022}, author = {Zhong, Y and He, J and Wu, F and Zhang, P and Zou, X and Pan, X and Zhang, J}, title = {Metagenomic analysis reveals the size effect of magnetite on anaerobic digestion of waste activated sludge after thermal hydrolysis pretreatment.}, journal = {The Science of the total environment}, volume = {851}, number = {Pt 1}, pages = {158133}, doi = {10.1016/j.scitotenv.2022.158133}, pmid = {35988621}, issn = {1879-1026}, mesh = {Anaerobiosis ; Bioreactors ; *Ferrosoferric Oxide ; Hydrolysis ; Methane/metabolism ; Peptide Hydrolases/metabolism ; *Sewage ; alpha-Glucosidases/metabolism ; }, abstract = {Although magnetite has been widely investigated in anaerobic digestion (AD), its role in the practical AD of waste-activated sludge (WAS) after thermal hydrolysis pretreatment (THP) and its size effect remain unclear. In this study, magnetite with four different particle sizes was added during the AD of WAS after THP. With the reduction of magnetite particle size, cumulative methane production was increased, while the optimal dosage of magnetite decreased, with 0.1 μm magnetite at an optimal dosage of 2 g/L achieving the highest cumulative methane production increase of 111.97 % compared with the blank group (without magnetite). Smaller magnetite particles increased α-glucosidase and protease activities, coenzyme F420 concentration, and electron-transport system activity (20.30 %, 173.02 %, 60.39 % and 158.08 % higher respectively than the blank group). The size of magnetite also influenced the establishment of direct interspecies electron transfer (DIET) during AD. Based on the analysis of the pilA gene abundance, magnetite with a large particle size could promote the formation of e-pili in syntrophic electroactive bacteria (Clostridium, Syntrophomonas, and Pseudomonas) and methanogens (Methanospirillum), thereby completing electron transfer. However, small-sized magnetite particles stimulated DIET by enhancing the secretion of conductive proteins in extracellular polymeric substances and membrane-bound enzymes (Fpo) in Methanosarcina.}, } @article {pmid35988549, year = {2022}, author = {Alcazar, CG and Paes, VM and Shao, Y and Oesser, C and Miltz, A and Lawley, TD and Brocklehurst, P and Rodger, A and Field, N}, title = {The association between early-life gut microbiota and childhood respiratory diseases: a systematic review.}, journal = {The Lancet. Microbe}, volume = {3}, number = {11}, pages = {e867-e880}, pmid = {35988549}, issn = {2666-5247}, support = {WT101169MA/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Infant ; Humans ; Infant, Newborn ; Child, Preschool ; Child ; Adolescent ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Feces/microbiology ; Bacteria/genetics ; *Asthma/epidemiology ; *Respiration Disorders/complications ; *Respiratory Tract Infections/epidemiology ; }, abstract = {Data from animal models suggest a role of early-life gut microbiota in lung immune development, and in establishing susceptibility to respiratory infections and asthma in humans. This systematic review summarises the association between infant (ages 0-12 months) gut microbiota composition measured by genomic sequencing, and childhood (ages 0-18 years) respiratory diseases (ie, respiratory infections, wheezing, or asthma). Overall, there was evidence that low α-diversity and relative abundance of particular gut-commensal bacteria genera (Bifidobacterium, Faecalibacterium, Ruminococcus, and Roseburia) are associated with childhood respiratory diseases. However, results were inconsistent and studies had important limitations, including insufficient characterisation of bacterial taxa to species level, heterogeneous outcome definitions, residual confounding, and small sample sizes. Large longitudinal studies with stool sampling during the first month of life and shotgun metagenomic approaches to improve bacterial and fungal taxa resolution are needed. Standardising follow-up times and respiratory disease definitions and optimising causal statistical approaches might identify targets for primary prevention of childhood respiratory diseases.}, } @article {pmid35988536, year = {2022}, author = {Azimi, M and Keshavarz Shahbaz, S and Mansourabadi, AH and Mohamed Khosroshahi, L and Pourkalhor, S and Rezakhani, M and Masoumi, F}, title = {Intestinal Microbiota: Novel Personalized Cancer Immunotherapy in Colorectal Cancer.}, journal = {International archives of allergy and immunology}, volume = {183}, number = {11}, pages = {1147-1165}, doi = {10.1159/000525695}, pmid = {35988536}, issn = {1423-0097}, mesh = {Humans ; *Gastrointestinal Microbiome ; *Colorectal Neoplasms/therapy/diagnosis/pathology ; Dysbiosis/therapy ; *Microbiota ; Immunotherapy ; }, abstract = {The human colon harbors a diverse array of microorganisms that play fundamental roles in colorectal cancer (CRC). Increasing evidence indicates that dysbiosis of the intestinal microbiome has been associated with the development of CRC. Interaction between host genetics, intestinal microbiota, and lifestyle is well-indicated in the influence, prevention, and treatment of CRC. Various microbiome compositions have reported anticancer and/or anti-inflammatory properties. The presence of our microbiota is integral to our development, but a change in its composition can often lead to adverse effects, increasing the propensity for serious diseases like cancers. Recently, molecular detection and metabolomic techniques have increased our knowledge of the role of microbiota in promoting tumorigenesis. Dietary interventions may be appropriate to regulate the growth of beneficial microbiota in the gut. Metagenomic approaches along with immunology and metabolomics will obvious a new path for the treatment of CRC. In this study, we summarized recent advances in understanding the mechanisms involved in microbiota-related colorectal carcinoma, based on evidence from immunotherapy studies.}, } @article {pmid35988403, year = {2022}, author = {Ou, D and Ning Ai, and Hu, C and Liu, Y}, title = {Metagenomics unraveled the characteristics and microbial response to hypersaline stress in salt-tolerant aerobic granular sludge.}, journal = {Journal of environmental management}, volume = {321}, number = {}, pages = {115950}, doi = {10.1016/j.jenvman.2022.115950}, pmid = {35988403}, issn = {1095-8630}, mesh = {Aerobiosis ; Bioreactors/microbiology ; Metagenomics ; Salinity ; *Sewage/chemistry ; *Waste Disposal, Fluid/methods ; }, abstract = {In this study, the salt-tolerant aerobic granular sludge (SAGS) was cultivated with the increased salinity (0-9% NaCl), showing oval shape, and clear outline. The related sludge characteristics in the formation process of SAGS as well as the effects of salinity on the performance (removal ability, sludge biomass and EPS component) of SAGS were evaluated. Increased salinity accelerated the formation of SAGS, and resulted in the excess secretion of EPS. Relationship between EPS and settling capacity of SAGS was determined, with the increase of salinity, SVI decreased linearly and the sedimentation performance of granular sludge was enhanced. Pearson correlation analysis showed that shorter settling time (3 min) and longer anaerobic influent time (30 min) were beneficial to the operation of SAGS reactor. Metagenomics results showed that the SAGS was dominated by Candida, Halomonas and other salt-tolerant bacteria, the enrichment of these salt-tolerant microbes played an important role in maintaining the stability of granular sludge system and improving the overall salt-tolerant performance. Compared with S9 samples, the proteome regulation in S0 sample was more active and the abundance of Cell motility related proteins was 5 times higher than that in S9 samples. Extracellular structure related proteins was more active in S9, and its abundance was 3.6 times that of S0.}, } @article {pmid35988321, year = {2022}, author = {Adi Wicaksono, W and Braun, M and Bernhardt, J and Riedel, K and Cernava, T and Berg, G}, title = {Trade-off for survival: Microbiome response to chemical exposure combines activation of intrinsic resistances and adapted metabolic activity.}, journal = {Environment international}, volume = {168}, number = {}, pages = {107474}, doi = {10.1016/j.envint.2022.107474}, pmid = {35988321}, issn = {1873-6750}, abstract = {The environmental microbiota is increasingly exposed to chemical pollution. While the emergence of multi-resistant pathogens is recognized as a global challenge, our understanding of antimicrobial resistance (AMR) development from native microbiomes and the risks associated with chemical exposure is limited. By implementing a lichen asa bioindicatororganism and model for a native microbiome, we systematically examined responses towards antimicrobials (colistin, tetracycline, glyphosate, and alkylpyrazine). Despite an unexpectedly high resilience, we identified potential evolutionary consequences of chemical exposure in terms of composition and functioning of native bacterial communities. Major shifts in bacterial composition were observed due to replacement of naturally abundant taxa; e.g. Chthoniobacterales by Pseudomonadales. A general response, which comprised activation of intrinsic resistance and parallel reduction of metabolic activity at RNA and protein levels was deciphered by a multi-omics approach. Targeted analyses of key taxa based on metagenome-assembled genomes reflected these responses but also revealed diversified strategies of their players. Chemical-specific responses were also observed, e.g., glyphosate enriched bacterial r-strategists and activated distinct ARGs. Our work demonstrates that the high resilience of the native microbiota toward antimicrobial exposure is not only explained by the presence of antibiotic resistance genes but also adapted metabolic activity as a trade-off for survival. Moreover, our results highlight the importance of native microbiomes as important but so far neglected AMR reservoirs. We expect that this phenomenon is representative for a wide range of environmental microbiota exposed to chemicals that potentially contribute to the emergence of antibiotic-resistant bacteria from natural environments.}, } @article {pmid35988037, year = {2022}, author = {Negrey, JD and Emery Thompson, M and Dunn, CD and Otali, E and Wrangham, RW and Mitani, JC and Machanda, ZP and Muller, MN and Langergraber, KE and Goldberg, TL}, title = {Female reproduction and viral infection in a long-lived mammal.}, journal = {The Journal of animal ecology}, volume = {91}, number = {10}, pages = {1999-2009}, pmid = {35988037}, issn = {1365-2656}, support = {//University of Wisconsin-Madison/ ; NCS-FO 1926653//National Science Foundation/ ; R01 AG049395/AG/NIA NIH HHS/United States ; //University of Michigan/ ; R37 AG049395/AG/NIA NIH HHS/United States ; NCS-FO 1926737//National Science Foundation/ ; BCS-1355014//National Science Foundation/ ; //University of New Mexico/ ; }, mesh = {Animals ; Female ; Humans ; Lactation ; Male ; Mammals ; *Pan troglodytes/physiology ; Pregnancy ; Reproduction/physiology ; Uganda ; *Virus Diseases ; }, abstract = {For energetically limited organisms, life-history theory predicts trade-offs between reproductive effort and somatic maintenance. This is especially true of female mammals, for whom reproduction presents multifarious energetic and physiological demands. Here, we examine longitudinal changes in the gut virome (viral community) with respect to reproductive status in wild mature female chimpanzees Pan troglodytes schweinfurthii from two communities, Kanyawara and Ngogo, in Kibale National Park, Uganda. We used metagenomic methods to characterize viromes of individual chimpanzees while they were cycling, pregnant and lactating. Females from Kanyawara, whose territory abuts the park's boundary, had higher viral richness and loads (relative quantity of viral sequences) than females from Ngogo, whose territory is more energetically rich and located farther from large human settlements. Viral richness (total number of distinct viruses per sample) was higher when females were lactating than when cycling or pregnant. In pregnant females, viral richness increased with estimated day of gestation. Richness did not vary with age, in contrast to prior research showing increased viral abundance in older males from these same communities. Our results provide evidence of short-term physiological trade-offs between reproduction and infection, which are often hypothesized to constrain health in long-lived species.}, } @article {pmid35987227, year = {2022}, author = {Chen, Y and Li, X and Liu, T and Li, F and Sun, W and Young, LY and Huang, W}, title = {Metagenomic analysis of Fe(II)-oxidizing bacteria for Fe(III) mineral formation and carbon assimilation under microoxic conditions in paddy soil.}, journal = {The Science of the total environment}, volume = {851}, number = {Pt 1}, pages = {158068}, doi = {10.1016/j.scitotenv.2022.158068}, pmid = {35987227}, issn = {1879-1026}, mesh = {Bacteria/genetics ; Carbon ; *Ferric Compounds ; Ferrous Compounds ; Iron/analysis ; Metagenomics ; Minerals ; Nitrates/analysis ; Oxidation-Reduction ; Oxides ; Oxidoreductases ; Oxygen/analysis ; Ribulose-Bisphosphate Carboxylase ; *Soil ; }, abstract = {Microbially mediated Fe(II) oxidation is prevalent and thought to be central to many biogeochemical processes in paddy soils. However, we have limited insights into the Fe(II) oxidation process in paddy fields, considered the world's largest engineered wetland, where microoxic conditions are ubiquitous. In this study, microaerophilic Fe(II) oxidizing bacteria (FeOB) from paddy soil were enriched in gradient tubes with FeS, FeCO3, and Fe3(PO4)2 as iron sources to investigate their capacity for Fe(II) oxidation and carbon assimilation. Results showed that the highest rate of Fe(II) oxidation (k = 0.836 mM d[-1]) was obtained in the FeCO3 tubes, and cells grown in the Fe3(PO4)2 tubes yielded maximum assimilation amounts of [13]C-NaHCO3 of 1.74% on Day 15. Amorphous Fe(III) oxides were found in all the cell bands with iron substrates as a result of microbial Fe(II) oxidation. Metagenomics analysis of the enriched microbes targeted genes encoding iron oxidase Cyc2, oxygen-reducing terminal oxidase, and ribulose-bisphosphate carboxylase, with results indicated that the potential Fe(II) oxidizers include nitrate-reducing FeOB (Dechloromonas and Thiobacillus), Curvibacter, and Magnetospirillum. By combining cultivation-dependent and metagenomic approaches, our results found a number of FeOB from paddy soil under microoxic conditions, which provide insight into the complex biogeochemical interactions of iron and carbon within paddy fields. The contribution of the FeOB to the element cycling in rice-growing regions deserves further investigation.}, } @article {pmid35987213, year = {2022}, author = {Suez, J and Cohen, Y and Valdés-Mas, R and Mor, U and Dori-Bachash, M and Federici, S and Zmora, N and Leshem, A and Heinemann, M and Linevsky, R and Zur, M and Ben-Zeev Brik, R and Bukimer, A and Eliyahu-Miller, S and Metz, A and Fischbein, R and Sharov, O and Malitsky, S and Itkin, M and Stettner, N and Harmelin, A and Shapiro, H and Stein-Thoeringer, CK and Segal, E and Elinav, E}, title = {Personalized microbiome-driven effects of non-nutritive sweeteners on human glucose tolerance.}, journal = {Cell}, volume = {185}, number = {18}, pages = {3307-3328.e19}, doi = {10.1016/j.cell.2022.07.016}, pmid = {35987213}, issn = {1097-4172}, mesh = {Adult ; Animals ; Aspartame/pharmacology ; Blood Glucose ; Humans ; Mice ; *Microbiota ; *Non-Nutritive Sweeteners/analysis/pharmacology ; Saccharin/pharmacology ; }, abstract = {Non-nutritive sweeteners (NNS) are commonly integrated into human diet and presumed to be inert; however, animal studies suggest that they may impact the microbiome and downstream glycemic responses. We causally assessed NNS impacts in humans and their microbiomes in a randomized-controlled trial encompassing 120 healthy adults, administered saccharin, sucralose, aspartame, and stevia sachets for 2 weeks in doses lower than the acceptable daily intake, compared with controls receiving sachet-contained vehicle glucose or no supplement. As groups, each administered NNS distinctly altered stool and oral microbiome and plasma metabolome, whereas saccharin and sucralose significantly impaired glycemic responses. Importantly, gnotobiotic mice conventionalized with microbiomes from multiple top and bottom responders of each of the four NNS-supplemented groups featured glycemic responses largely reflecting those noted in respective human donors, which were preempted by distinct microbial signals, as exemplified by sucralose. Collectively, human NNS consumption may induce person-specific, microbiome-dependent glycemic alterations, necessitating future assessment of clinical implications.}, } @article {pmid35987054, year = {2022}, author = {Andrade Cruz, I and Andrade, LRS and Jesus, AA and Vasconcelos, BR and Bharagava, RN and Bilal, M and Figueiredo, RT and Souza, RL and Romanholo Ferreira, LF}, title = {Potential of eggshell waste derived calcium for sustainable production of biogas from cassava wastewater.}, journal = {Journal of environmental management}, volume = {321}, number = {}, pages = {116000}, doi = {10.1016/j.jenvman.2022.116000}, pmid = {35987054}, issn = {1095-8630}, mesh = {Anaerobiosis ; Animals ; *Biofuels/analysis ; Bioreactors ; Calcium ; Egg Shell/chemistry ; *Manihot ; Methane ; Wastewater ; }, abstract = {Cassava is a staple crop that plays a significant role in the food security of many countries. However, its processing produces a liquid by-product known as cassava wastewater (CW), which can have adverse environmental consequences if discarded without treatment. Despite its cyanide content, CW has a high organic content and may be profitable when used to produce biogas. In this study, the influence of calcium particles from eggshell residues was investigated on the anaerobic digestion of CW. Moreover, the performance of the bioreactor was remotely monitored. Calcium particles from milled-calcined chicken eggshells were added to the bioreactor, and biogas production was investigated for 21 days. Adding 1 g/L and 3 g/L of calcium particles increased biogas (Bio H2 + Bio CH4) production by 195% and 338%, respectively. Finally, the requirement for digestate post-treatment before use in agriculture was observed after assessing its phytotoxicity through the germination and root growth of L. sativa seeds.}, } @article {pmid35986714, year = {2023}, author = {Luo, M and Ji, Y and Warton, D and Yu, DW}, title = {Extracting abundance information from DNA-based data.}, journal = {Molecular ecology resources}, volume = {23}, number = {1}, pages = {174-189}, pmid = {35986714}, issn = {1755-0998}, support = {QYZDY-SSW-SMC024//Key Research Program of Frontier Sciences, CAS/ ; //University of Chinese Academy of Sciences/ ; //Kunming Institute of Zoology/ ; GREKF19-01//State Key Laboratory of Genetic Resources and Evolution/ ; GREKF20-01//State Key Laboratory of Genetic Resources and Evolution/ ; GREKF21-01//State Key Laboratory of Genetic Resources and Evolution/ ; //University of East Anglia/ ; SMC024//Chinese Academy of Sciences/ ; sCom//idiv.de/ ; XDA20050202//Strategic Priority Research Program, Chinese Academy of Sciences/ ; }, mesh = {*DNA Barcoding, Taxonomic/methods ; *Metagenomics/methods ; DNA/genetics ; Biodiversity ; }, abstract = {The accurate extraction of species-abundance information from DNA-based data (metabarcoding, metagenomics) could contribute usefully to diet analysis and food-web reconstruction, the inference of species interactions, the modelling of population dynamics and species distributions, the biomonitoring of environmental state and change, and the inference of false positives and negatives. However, multiple sources of bias and noise in sampling and processing combine to inject error into DNA-based data sets. To understand how to extract abundance information, it is useful to distinguish two concepts. (i) Within-sample across-species quantification describes relative species abundances in one sample. (ii) Across-sample within-species quantification describes how the abundance of each individual species varies from sample to sample, such as over a time series, an environmental gradient or different experimental treatments. First, we review the literature on methods to recover across-species abundance information (by removing what we call "species pipeline biases") and within-species abundance information (by removing what we call "pipeline noise"). We argue that many ecological questions can be answered with just within-species quantification, and we therefore demonstrate how to use a "DNA spike-in" to correct for pipeline noise and recover within-species abundance information. We also introduce a model-based estimator that can be used on data sets without a physical spike-in to approximate and correct for pipeline noise.}, } @article {pmid35986393, year = {2022}, author = {Yang, L and Chen, J}, title = {A comprehensive evaluation of microbial differential abundance analysis methods: current status and potential solutions.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {130}, pmid = {35986393}, issn = {2049-2618}, support = {R01 GM144351/GM/NIGMS NIH HHS/United States ; R21 HG011662/HG/NHGRI NIH HHS/United States ; }, mesh = {Benchmarking ; Computer Simulation ; Data Analysis ; *Microbiota ; }, abstract = {BACKGROUND: Differential abundance analysis (DAA) is one central statistical task in microbiome data analysis. A robust and powerful DAA tool can help identify highly confident microbial candidates for further biological validation. Numerous DAA tools have been proposed in the past decade addressing the special characteristics of microbiome data such as zero inflation and compositional effects. Disturbingly, different DAA tools could sometimes produce quite discordant results, opening to the possibility of cherry-picking the tool in favor of one's own hypothesis. To recommend the best DAA tool or practice to the field, a comprehensive evaluation, which covers as many biologically relevant scenarios as possible, is critically needed.

RESULTS: We performed by far the most comprehensive evaluation of existing DAA tools using real data-based simulations. We found that DAA methods explicitly addressing compositional effects such as ANCOM-BC, Aldex2, metagenomeSeq (fitFeatureModel), and DACOMP did have improved performance in false-positive control. But they are still not optimal: type 1 error inflation or low statistical power has been observed in many settings. The recent LDM method generally had the best power, but its false-positive control in the presence of strong compositional effects was not satisfactory. Overall, none of the evaluated methods is simultaneously robust, powerful, and flexible, which makes the selection of the best DAA tool difficult. To meet the analysis needs, we designed an optimized procedure, ZicoSeq, drawing on the strength of the existing DAA methods. We show that ZicoSeq generally controlled for false positives across settings, and the power was among the highest. Application of DAA methods to a large collection of real datasets revealed a similar pattern observed in simulation studies.

CONCLUSIONS: Based on the benchmarking study, we conclude that none of the existing DAA methods evaluated can be applied blindly to any real microbiome dataset. The applicability of an existing DAA method depends on specific settings, which are usually unknown a priori. To circumvent the difficulty of selecting the best DAA tool in practice, we design ZicoSeq, which addresses the major challenges in DAA and remedies the drawbacks of existing DAA methods. ZicoSeq can be applied to microbiome datasets from diverse settings and is a useful DAA tool for robust microbiome biomarker discovery. Video Abstract.}, } @article {pmid35986253, year = {2022}, author = {Berckx, F and Nguyen, TV and Bandong, CM and Lin, HH and Yamanaka, T and Katayama, S and Wibberg, D and Blom, J and Kalinowski, J and Tateno, M and Simbahan, J and Liu, CT and Brachmann, A and Pawlowski, K}, title = {A tale of two lineages: how the strains of the earliest divergent symbiotic Frankia clade spread over the world.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {602}, pmid = {35986253}, issn = {1471-2164}, mesh = {*Frankia/genetics ; *Magnoliopsida/genetics ; Metagenome ; Nitrogen Fixation ; Phylogeny ; Plants/genetics ; Symbiosis/genetics ; }, abstract = {It is currently assumed that around 100 million years ago, the common ancestor to the Fabales, Fagales, Rosales and Cucurbitales in Gondwana, developed a root nodule symbiosis with a nitrogen-fixing bacterium. The symbiotic trait evolved first in Frankia cluster-2; thus, strains belonging to this cluster are the best extant representatives of this original symbiont. Most cluster-2 strains could not be cultured to date, except for Frankia coriariae, and therefore many aspects of the symbiosis are still elusive. Based on phylogenetics of cluster-2 metagenome-assembled genomes (MAGs), it has been shown that the genomes of strains originating in Eurasia are highly conserved. These MAGs are more closely related to Frankia cluster-2 in North America than to the single genome available thus far from the southern hemisphere, i.e., from Papua New Guinea.To unravel more biodiversity within Frankia cluster-2 and predict routes of dispersal from Gondwana, we sequenced and analysed the MAGs of Frankia cluster-2 from Coriaria japonica and Coriaria intermedia growing in Japan, Taiwan and the Philippines. Phylogenetic analyses indicate there is a clear split within Frankia cluster-2, separating a continental from an island lineage. Presumably, these lineages already diverged in Gondwana.Based on fossil data on the host plants, we propose that these two lineages dispersed via at least two routes. While the continental lineage reached Eurasia together with their host plants via the Indian subcontinent, the island lineage spread towards Japan with an unknown host plant.}, } @article {pmid35986094, year = {2022}, author = {Li, Z and Wang, X and Zhang, Y and Yu, Z and Zhang, T and Dai, X and Pan, X and Jing, R and Yan, Y and Liu, Y and Gao, S and Li, F and Huang, Y and Tian, J and Yao, J and Xing, X and Shi, T and Ning, J and Yao, B and Huang, H and Jiang, Y}, title = {Genomic insights into the phylogeny and biomass-degrading enzymes of rumen ciliates.}, journal = {The ISME journal}, volume = {16}, number = {12}, pages = {2775-2787}, pmid = {35986094}, issn = {1751-7370}, mesh = {Animals ; *Rumen/microbiology ; Phylogeny ; Biomass ; *Ciliophora/genetics ; Genomics ; Bacteria/genetics ; Fungi ; }, abstract = {Understanding the biodiversity and genetics of gut microbiomes has important implications for host physiology and industrial enzymes, whereas most studies have been focused on bacteria and archaea, and to a lesser extent on fungi and viruses. One group, still underexplored and elusive, is ciliated protozoa, despite its importance in shaping microbiota populations. Integrating single-cell sequencing and an assembly-and-identification pipeline, we acquired 52 high-quality ciliate genomes of 22 rumen morphospecies from 11 abundant morphogenera. With these genomes, we resolved the taxonomic and phylogenetic framework that revised the 22 morphospecies into 19 species spanning 13 genera and reassigned the genus Dasytricha from Isotrichidae to a new family Dasytrichidae. Comparative genomic analyses revealed that extensive horizontal gene transfers and gene family expansion provided rumen ciliate species with a broad array of carbohydrate-active enzymes (CAZymes) to degrade all major kinds of plant and microbial carbohydrates. In particular, the genomes of Diplodiniinae and Ophryoscolecinae species encode as many CAZymes as gut fungi, and ~80% of their degradative CAZymes act on plant cell-wall. The activities of horizontally transferred cellulase and xylanase of ciliates were experimentally verified and were 2-9 folds higher than those of the inferred corresponding bacterial donors. Additionally, the new ciliate dataset greatly facilitated rumen metagenomic analyses by allowing ~12% of the metagenomic sequencing reads to be classified as ciliate sequences.}, } @article {pmid35985998, year = {2022}, author = {Dong, X and Zhang, C and Peng, Y and Zhang, HX and Shi, LD and Wei, G and Hubert, CRJ and Wang, Y and Greening, C}, title = {Phylogenetically and catabolically diverse diazotrophs reside in deep-sea cold seep sediments.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {4885}, pmid = {35985998}, issn = {2041-1723}, mesh = {Archaea/metabolism ; *Ecosystem ; *Geologic Sediments/microbiology ; Methane/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Seawater/microbiology ; Sulfates/metabolism ; }, abstract = {Microbially mediated nitrogen cycling in carbon-dominated cold seep environments remains poorly understood. So far anaerobic methanotrophic archaea (ANME-2) and their sulfate-reducing bacterial partners (SEEP-SRB1 clade) have been identified as diazotrophs in deep sea cold seep sediments. However, it is unclear whether other microbial groups can perform nitrogen fixation in such ecosystems. To fill this gap, we analyzed 61 metagenomes, 1428 metagenome-assembled genomes, and six metatranscriptomes derived from 11 globally distributed cold seeps. These sediments contain phylogenetically diverse nitrogenase genes corresponding to an expanded diversity of diazotrophic lineages. Diverse catabolic pathways were predicted to provide ATP for nitrogen fixation, suggesting diazotrophy in cold seeps is not necessarily associated with sulfate-dependent anaerobic oxidation of methane. Nitrogen fixation genes among various diazotrophic groups in cold seeps were inferred to be genetically mobile and subject to purifying selection. Our findings extend the capacity for diazotrophy to five candidate phyla (Altarchaeia, Omnitrophota, FCPU426, Caldatribacteriota and UBA6262), and suggest that cold seep diazotrophs might contribute substantially to the global nitrogen balance.}, } @article {pmid35985811, year = {2022}, author = {Cheng, M and Zhao, Y and Cui, Y and Zhong, C and Zha, Y and Li, S and Cao, G and Li, M and Zhang, L and Ning, K and Han, J}, title = {Stage-specific roles of microbial dysbiosis and metabolic disorders in rheumatoid arthritis.}, journal = {Annals of the rheumatic diseases}, volume = {81}, number = {12}, pages = {1669-1677}, pmid = {35985811}, issn = {1468-2060}, abstract = {OBJECTIVE: Rheumatoid arthritis (RA) is a progressive disease including four stages, where gut microbiome is associated with pathogenesis. We aimed to investigate stage-specific roles of microbial dysbiosis and metabolic disorders in RA.

METHODS: We investigated stage-based profiles of faecal metagenome and plasma metabolome of 76 individuals with RA grouped into four stages (stages I-IV) according to 2010 RA classification criteria, 19 individuals with osteroarthritis and 27 healthy individuals. To verify bacterial invasion of joint synovial fluid, 16S rRNA gene sequencing, bacterial isolation and scanning electron microscopy were conducted on another validation cohort of 271 patients from four RA stages.

RESULTS: First, depletion of Bacteroides uniformis and Bacteroides plebeius weakened glycosaminoglycan metabolism (p<0.001), continuously hurting articular cartilage across four stages. Second, elevation of Escherichia coli enhanced arginine succinyltransferase pathway in the stage II and stage III (p<0.001), which was correlated with the increase of the rheumatoid factor (p=1.35×10[-3]) and could induce bone loss. Third, abnormally high levels of methoxyacetic acid (p=1.28×10[-8]) and cysteine-S-sulfate (p=4.66×10[-12]) inhibited osteoblasts in the stage II and enhanced osteoclasts in the stage III, respectively, promoting bone erosion. Fourth, continuous increase of gut permeability may induce gut microbial invasion of the joint synovial fluid in the stage IV.

CONCLUSIONS: Clinical microbial intervention should consider the RA stage, where microbial dysbiosis and metabolic disorders present distinct patterns and played stage-specific roles. Our work provides a new insight in understanding gut-joint axis from a perspective of stages, which opens up new avenues for RA prognosis and therapy.}, } @article {pmid35985693, year = {2022}, author = {Zuo, K and Li, J and Fang, C and Zhong, J and Xu, L and Yang, X}, title = {Alterations of gut viral signals in atrial fibrillation: complex linkage with gut bacteriome.}, journal = {Aging}, volume = {14}, number = {16}, pages = {6537-6553}, pmid = {35985693}, issn = {1945-4589}, mesh = {*Atrial Fibrillation/epidemiology ; *Catheter Ablation ; Humans ; Recurrence ; Risk Factors ; Treatment Outcome ; }, abstract = {The gut microbiota has a known complex association with atrial fibrillation (AF) progression, but the association of gut viruses with AF is undefined. Metagenomic data in a cohort of 50 AF patients and 50 matched controls were examined to profile the gut viral signals and determine their associations with intestinal bacteria and the AF phenotype. The gut viral alterations were examined, and the marked elevation of viral diversity, including increased Simpson, Shannon, and Pielou index, was revealed in AF patients. The specific alteration of the intestinal viral population, such as overgrowth of Streptococcus virus DT1 and Pseudomonas phage, as well as imbalanced gut viral function, dominated by integral component of the membrane, and metal ion binding were detected in AF patients. Moreover, regarding co-occurrence networks connecting viruses and bacterial organisms, increasingly disordered virus-bacteria linkages were seen in AF cases with severe AF progression. Notably, the associations of Synechococcus phage S-SM1 and Cronobacter phage CR5 with bacterial species were very tight in control individuals but markedly dampened in AF cases. Furthermore, the viral score built by the selected discriminative taxa between AF cases with or without recurrence after ablation was still significantly associated with recurrence (HR = 2.959, P = 0.0085), with a survival AUC of 0.878. We demonstrated for the first time that gut viral signatures are associated with AF, and suppressed viral-bacterial associations in AF suggest the gut virus might participate in AF progression, which has a potential value in predicting ablation outcomes.}, } @article {pmid35985484, year = {2022}, author = {Raj, A and Kumar, A}, title = {Recent advances in assessment methods and mechanism of microbe-mediated chlorpyrifos remediation.}, journal = {Environmental research}, volume = {214}, number = {Pt 4}, pages = {114011}, doi = {10.1016/j.envres.2022.114011}, pmid = {35985484}, issn = {1096-0953}, mesh = {Acetylcholinesterase ; Biodegradation, Environmental ; *Chlorpyrifos/metabolism ; Organophosphorus Compounds ; *Pesticides/metabolism ; }, abstract = {Chlorpyrifos (CP) is one of the Organophosphorus pesticides (OPs) primarily used in agriculture to safeguard crops from pests and diseases. The pervasive use of chlorpyrifos is hazardous to humans and the environment as it inhibits the receptor for acetylcholinesterase activity, leading to abnormalities linked to the central nervous system. Hence, there is an ardent need to develop an effective and sustainable approach to the on-site degradation of chlorpyrifos. The role of microbes in the remediation of pesticides is considered the most effective and eco-friendly approach, as they have strong degradative potential due to their gene and enzymes naturally adapted to these sites. Several reports have previously been published on exploring the role of microbes in the degradation of CP. However, detection of CP as an environmental contaminant is an essential prerequisite for developing an efficient microbial-mediated biodegradation method with less harmful intermediates. Most of the articles published to date discuss the fate and impact of CP in the environment along with its degradation mechanism but still fail to discuss the analytical portion. This review is focused on the latest developments in the field of bioremediation of CP along with its physicochemical properties, toxicity, fate, and conventional (UV-Visible spectrophotometer, FTIR, NMR, GC-MS, etc) and advanced detection methods (Biosensors and immunochromatography-based methods) from different environmental samples. Apart from it, this review explores the role of metagenomics, system biology, in-silico tools, and genetic engineering in facilitating the bioremediation of CP. One of the objectives of this review is to educate policymakers with scientific data that will enable the development of appropriate strategies to reduce pesticide exposure and the harmful health impacts on both Human and other environmental components. Moreover, this review provides up-to-date developments related to the sustainable remediation of CP.}, } @article {pmid35985382, year = {2022}, author = {Zhou, L and Zhao, B and Lin, Y and Shao, Z and Zeng, R and Shen, Y and Zhang, W and Jian, Y and Zhuang, WQ}, title = {Identification of dissimilatory nitrate reduction to ammonium (DNRA) and denitrification in the dynamic cake layer of a full-scale anoixc dynamic membrane bioreactor for treating hotel laundry wastewater.}, journal = {Chemosphere}, volume = {307}, number = {Pt 4}, pages = {136078}, doi = {10.1016/j.chemosphere.2022.136078}, pmid = {35985382}, issn = {1879-1298}, mesh = {*Ammonium Compounds/metabolism ; Bacteria/genetics/metabolism ; Bioreactors ; Denitrification ; Nitrates/analysis ; Nitrite Reductases/metabolism ; Nitrogen/metabolism ; Nitrogen Oxides ; Organic Chemicals ; Oxidation-Reduction ; Wastewater ; }, abstract = {Identification of dissimilatory nitrate reduction to ammonium (DNRA) and denitrification in the dynamic cake layer of a full-scale anoixc dynamic membrane bioreactor (AnDMBR) for treating hotel laundry wastewater was studied. A series of experiments were conducted to understand the contributions of DNRA and canonical denitrification activities in the dynamic cake layer of the AnDMBR. The dynamic cake layer developed included two phases - a steady transmembrane pressure (TMP) increase at 0.24 kPa/day followed by a sharp TMP jump at 1.26 kPa/day four to five days after the AnDMBR start-up. The nitrogen mass balance results showed that canonical denitrification was predominant during the development of the dynamic cake layer. However, DNRA activity and accumulation of bacteria equipped with a complete DNRA pathway showed a positive correlation to the development of the dynamic cake layer. Our metagenomic analysis identified an approximately 18% of the dynamic cake layer bacterial community has a complete DNRA pathway. Pannonibacter (1%), Thauera (0.8%) and Pseudomonas (3%) contained all genes encoding for funcional enzymes of both DNRA (nitrate reductase and DNRA nitrite reductase) and denitrification (nitrate reductase, nitrous oxide reductase and nitric oxide reductase). No other metagenome-assembled genomes (MAGs) possessed a complete cononical denitrification pathway, indicating food-chain-like interactions of denitrifiers in the dynamic cake layer. We found that COD loading rate could be used to control DNRA and canonical denitrification activities during the dynamic cake layer formation.}, } @article {pmid35985261, year = {2022}, author = {Jha, V and Bombaywala, S and Purohit, H and Dafale, NA}, title = {Differential colonization and functioning of microbial community in response to phosphate levels.}, journal = {Journal of environmental management}, volume = {321}, number = {}, pages = {115856}, doi = {10.1016/j.jenvman.2022.115856}, pmid = {35985261}, issn = {1095-8630}, mesh = {Metagenome ; Metagenomics ; *Microbiota/genetics ; Phosphates ; Proteobacteria/genetics ; Soil Microbiology ; }, abstract = {Microbes play a major role in phosphate cycling and regulate its availability in various environments. The metagenomic study highlights the microbial community divergence and interplay of phosphate metabolism functional genes in response to phosphate rich (100 mgL[-1]), limiting (25 mgL[-1]), and stressed (5 mgL[-1]) conditions at lab-scale bioreactor. Total five core phyla were found responsive toward different phosphate (Pi) levels. However, major variations were observed in Proteobacteria and Actinobacteria with 33-81% and 5-56% relative abundance, respectively. Canonical correspondence analysis reflects the colonization of Sinorhizobium (0.8-4%), Mesorhizobium (1-4%), Rhizobium (0.5-3%) in rich condition whereas, Pseudomonas (1-2%), Rhodococcus (0.2-2%), Flavobacterium (0.2-1%) and Streptomyces (0.3-4%) colonized in limiting and stress condition. The functional profiling demonstrates that Pi limiting and stress condition subjected biomass were characterized by abundant PQQ-Glucose dehydrogenase, alkaline phosphatase, 5'-nucleotidase, and phospholipases C genes. The finding implies that the major abundant genera belonging to phosphate solubilization enriched in limiting/stressed conditions decide the functional turnover by modulating the metabolic flexibility for Pi cycling. The study gives a better insight into intrinsic ecological responsiveness mediated by microbial communities in different Pi conditions that would help to design the microbiome according to the soil phosphate condition. Furthermore, this information assists in sustainably maintaining the ecological balance by omitting excessive chemical fertilizers and eutrophication.}, } @article {pmid35984292, year = {2023}, author = {Huang, W and Ren, F and Chen, D and Wang, Z and Tang, L}, title = {The value of metagenomic next-generation sequencing in bronchoalveolar lavage fluid samples of anti-MDA5-positive dermatomyositis patients.}, journal = {Rheumatology (Oxford, England)}, volume = {62}, number = {3}, pages = {e36-e38}, doi = {10.1093/rheumatology/keac475}, pmid = {35984292}, issn = {1462-0332}, mesh = {Humans ; Bronchoalveolar Lavage Fluid ; *Dermatomyositis ; *Lung Diseases, Interstitial ; Autoantibodies ; High-Throughput Nucleotide Sequencing ; Interferon-Induced Helicase, IFIH1 ; }, } @article {pmid35983331, year = {2022}, author = {Fan, S and Si, M and Xu, N and Yan, M and Pang, M and Liu, G and Gong, J and Wang, H}, title = {Metagenomic next-generation sequencing-guided antimicrobial treatment versus conventional antimicrobial treatment in early severe community-acquired pneumonia among immunocompromised patients (MATESHIP): A study protocol.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {927842}, pmid = {35983331}, issn = {1664-302X}, abstract = {BACKGROUND: Severe community-acquired pneumonia (SCAP) is the main cause of mortality in immunocompromised patients. Compared with conventional microbiological tests (CMT), metagenomic next-generation sequencing (mNGS) can quickly and simultaneously detect a wide array of bacteria, viruses, and fungi in an unbiased manner. It is increasingly used for severe respiratory infectious diseases, especially for immunocompromised patients. However, the effects of mNGS-based antimicrobial treatment procedures on clinical outcomes in immunocompromised patients with SCAP have not been evaluated.

METHODS/DESIGN: The MATESHIP study is a prospective, multicenter, parallel-group, open-label, randomized controlled trial from 20 ICUs in university hospitals and academic teaching hospitals across Shandong Province, China. We will enroll 342 immunocompromised patients with early onset SCAP who are admitted to an intensive care unit (ICU). Participants will be randomly allocated to an mNGS-guided treatment group or a conventional treatment group (guided by CMT), according to centrally computer-based block randomization stratified by participating centers. Participants will undergo CMT tests using appropriate lower respiratory tract (LRT) and other necessary specimens, with or without mNGS tests using LRT specimens. The primary outcomes will be: (1) The relative change in Sequential Organ Failure Assessment (SOFA) score from randomization to day 5, day 7, day 10, or the day of ICU discharge/death; and (2) the consumption of antimicrobial agents during ICU stay (expressed as defined daily doses). The secondary outcome measures will be: days from randomization to initiation of definitive antimicrobial treatment; overall antimicrobial agent use and cost; total cost of hospitalization; length of ICU stay; 28- and 90-day mortality; and clinical cure rate. This study hypothesizes that mNGS-guided treatment will decrease the degree of organ dysfunction/failure, the consumption of antimicrobial agents, and mortality, while the cure rate will be increased, and the time to initiation of appropriate therapy will be advanced.

DISCUSSION: The MATESHIP study will evaluate for the first time whether mNGS-guided antimicrobial therapy improves the outcomes of SCAP in an immunocompromised population, and provide high-level evidence on the application of mNGS in the management of this population.

CLINICAL TRIAL REGISTRATION: [ClinicalTrials.gov], identifier [NCT05290454].}, } @article {pmid35983330, year = {2022}, author = {de la Haba, RR and Antunes, A and Hedlund, BP}, title = {Editorial: Extremophiles: Microbial genomics and taxogenomics.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {984632}, pmid = {35983330}, issn = {1664-302X}, } @article {pmid35983325, year = {2022}, author = {Park, S and Moon, J and Kang, N and Kim, YH and You, YA and Kwon, E and Ansari, A and Hur, YM and Park, T and Kim, YJ}, title = {Predicting preterm birth through vaginal microbiota, cervical length, and WBC using a machine learning model.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {912853}, pmid = {35983325}, issn = {1664-302X}, abstract = {An association between the vaginal microbiome and preterm birth has been reported. However, in practice, it is difficult to predict premature birth using the microbiome because the vaginal microbial community varies highly among samples depending on the individual, and the prediction rate is very low. The purpose of this study was to select markers that improve predictive power through machine learning among various vaginal microbiota and develop a prediction algorithm with better predictive power that combines clinical information. As a multicenter case-control study with 150 Korean pregnant women with 54 preterm delivery group and 96 full-term delivery group, cervicovaginal fluid was collected from pregnant women during mid-pregnancy. Their demographic profiles (age, BMI, education level, and PTB history), white blood cell count, and cervical length were recorded, and the microbiome profiles of the cervicovaginal fluid were analyzed. The subjects were randomly divided into a training (n = 101) and a test set (n = 49) in a two-to-one ratio. When training ML models using selected markers, five-fold cross-validation was performed on the training set. A univariate analysis was performed to select markers using seven statistical tests, including the Wilcoxon rank-sum test. Using the selected markers, including Lactobacillus spp., Gardnerella vaginalis, Ureaplasma parvum, Atopobium vaginae, Prevotella timonensis, and Peptoniphilus grossensis, machine learning models (logistic regression, random forest, extreme gradient boosting, support vector machine, and GUIDE) were used to build prediction models. The test area under the curve of the logistic regression model was 0.72 when it was trained with the 17 selected markers. When analyzed by combining white blood cell count and cervical length with the seven vaginal microbiome markers, the random forest model showed the highest test area under the curve of 0.84. The GUIDE, the single tree model, provided a more reasonable biological interpretation, using the 10 selected markers (A. vaginae, G. vaginalis, Lactobacillus crispatus, Lactobacillus fornicalis, Lactobacillus gasseri, Lactobacillus iners, Lactobacillus jensenii, Peptoniphilus grossensis, P. timonensis, and U. parvum), and the covariates produced a tree with a test area under the curve of 0.77. It was confirmed that the association with preterm birth increased when P. timonensis and U. parvum increased (AUC = 0.77), which could also be explained by the fact that as the number of Peptoniphilus lacrimalis increased, the association with preterm birth was high (AUC = 0.77). Our study demonstrates that several candidate bacteria could be used as potential predictors for preterm birth, and that the predictive rate can be increased through a machine learning model employing a combination of cervical length and white blood cell count information.}, } @article {pmid35983323, year = {2022}, author = {Cho, Y and Kim, J and Pai, H and Rho, M}, title = {Deciphering Resistome in Patients With Chronic Obstructive Pulmonary Diseases and Clostridioides difficile Infections.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {919907}, pmid = {35983323}, issn = {1664-302X}, abstract = {Antibiotics alter the gut microbiome and cause dysbiosis leading to antibiotic-resistant organisms. Different patterns of antibiotic administration cause a difference in bacterial composition and resistome in the human gut. We comprehensively investigated the association between the distribution of antibiotic resistance genes (ARGs), bacterial composition, and antibiotic treatments in patients with chronic obstructive pulmonary diseases (COPD) and Clostridioides difficile infections (CDI) who had chronic or acute intermittent use of antibiotics and compared them with healthy individuals. We analyzed the gut microbiomes of 61 healthy individuals, 16 patients with COPD, and 26 patients with CDI. The COPD patients were antibiotic-free before stool collection for a median of 40 days (Q1: 9.5; Q3: 60 days), while the CDI patients were antibiotic-free for 0 days (Q1: 0; Q3: 0.3). The intra-group beta diversity measured by the median Bray-Curtis index was the lowest for the healthy individuals (0.55), followed by the COPD (0.69) and CDI groups (0.72). The inter-group beta diversity was the highest among the healthy and CDI groups (median index = 0.89). The abundance of ARGs measured by the number of reads per kilobase per million reads (RPKM) was 684.2; 1,215.2; and 2,025.1 for the healthy, COPD, and CDI groups. It was negatively correlated with the alpha diversity of bacterial composition. For the prevalent ARG classes, healthy individuals had the lowest diversity and abundance of aminoglycoside, β-lactam, and macrolide-lincosamide-streptogramin (MLS) resistance genes, followed by the COPD and CDI groups. The abundances of Enterococcus and Escherichia species were positively correlated with ARG abundance and the days of antibiotic treatment, while Bifidobacterium and Ruminococcus showed negative correlations for the same. In addition, we analyzed the mobilome patterns of aminoglycoside and β-lactam resistance gene carriers using metagenomic sequencing data. In conclusion, the ARGs were significantly enhanced in the CDI and COPD groups than in healthy individuals. In particular, aminoglycoside and β-lactam resistance genes were more abundant in the CDI and COPD groups, but the dominant mobile genetic elements that enable the transfer of such genes showed similar prevalence patterns among the groups.}, } @article {pmid35983300, year = {2022}, author = {Dong, Y and He, Y and Zhou, X and Lv, X and Huang, J and Li, Y and Qian, X and Hu, F and Zhu, J}, title = {Diagnosis of Mycoplasma hominis Meningitis with Metagenomic Next-Generation Sequencing: A Case Report.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {4479-4486}, pmid = {35983300}, issn = {1178-6973}, abstract = {BACKGROUND: Mycoplasma hominis meningitis is a rare postoperative complication of neurosurgery. Accurate and early diagnosis of M. hominis remains challenging because of the limitations of traditional detection methods. Metagenomic next-generation sequencing (mNGS) is an advanced technique with high sensitivity and specificity for identifying infectious pathogens; however, its application in diagnosing M. hominis meningitis has not been widely studied.

CASE PRESENTATION: We report the case of a 61-year-old man who presented with fever and headache after neurosurgical treatment for a cerebral hemorrhage. Empiric antibiotic therapy was ineffective. Traditional culture of pathogens and serological testing yielded negative results, but M. hominis was detected in the cerebrospinal fluid by mNGS. After further verification by polymerase chain reaction (PCR), the patient's clinical treatment was adjusted accordingly. With targeted antibiotic intervention, the patient's symptoms were effectively alleviated, and clinical indicators returned to normal levels. Furthermore, the abundance of M. hominis decreased significantly compared to the initial mNGS reading after targeted treatment, indicating that the infection caused by M. hominis was effectively controlled.

CONCLUSION: Using mNGS, we found that M. hominis may be a candidate causative agent of meningitis. The technique also has the advantage of timeliness and accuracy that traditional cultures cannot achieve. A combination of mNGS with PCR is recommended to identify pathogens in the early stages of infectious diseases to administer targeted clinical medication.}, } @article {pmid35983296, year = {2022}, author = {Wang, N and Zhao, C and Tang, C and Wang, L}, title = {Case Report and Literature Review: Disseminated Histoplasmosis Infection Diagnosed by Metagenomic Next-Generation Sequencing.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {4507-4514}, pmid = {35983296}, issn = {1178-6973}, abstract = {BACKGROUND: Histoplasmosis is a deep fungal infection caused by Histoplasma capsulatum and can be classified as pulmonary, disseminated or central. Disseminated histoplasmosis is the most dangerous of all clinical types and is characterized by rapid onset, rapid progression, high mortality, and difficulty in diagnosis and treatment.

CASE PRESENTATION: This report describes a 31-year-old female who presented with fever, with a maximum temperature of 39.8 °C. There were no concomitant symptoms, such as cough, sputum, abdominal pain and diarrhoea, before the onset of fever, and the illness lasted for more than 20 days. On examination, the liver and spleen were enlarged, and laboratory tests showed a significant decrease in CD4 cell count, suggesting immune deficiency. Broad-spectrum antibiotic treatment was ineffective, and specific infectious diseases and haematological neoplasms were considered likely. She was finally diagnosed with disseminated histoplasmosis after undergoing bone marrow aspiration and metagenomic next-generation sequencing (mNGS) and was treated with amphotericin B, fluorouracil and itraconazole, with good results.

CONCLUSION: This case demonstrates that disseminated histoplasmosis infection can present with unexplained fever and that mNGS can be an important complement to bone marrow aspiration for the diagnosis of this disease.}, } @article {pmid35983103, year = {2022}, author = {Abe, R and Akeda, Y and Takeuchi, D and Sakamoto, N and Sugawara, Y and Yamamoto, N and Kerdsin, A and Matsumoto, Y and Motooka, D and Leolerd, W and Santanirand, P and Suzuki, M and Shibayama, K and Tomono, K and Iida, T and Hamada, S}, title = {Clonal dissemination of carbapenem-resistant Klebsiella pneumoniae ST16 co-producing NDM-1 and OXA-232 in Thailand.}, journal = {JAC-antimicrobial resistance}, volume = {4}, number = {4}, pages = {dlac084}, pmid = {35983103}, issn = {2632-1823}, abstract = {BACKGROUND: Klebsiella pneumoniae ST258 and ST11 carrying bla KPC are among the most widespread carbapenem-resistant K. pneumoniae strains worldwide. Our carbapenem-resistant Enterobacteriaceae surveillance in Thailand revealed a nationwide dissemination of K. pneumoniae ST16 isolates carrying bla NDM-1 and bla OXA-232.

OBJECTIVES: To analyse the genomic details of this nationwide dissemination by focusing on plasmids and virulence factors.

METHODS: Using WGS data of 119 K. pneumoniae ST16 isolates carrying bla NDM-1 obtained in our previous surveillance study, clonality of chromosomes and plasmids of the isolates with carriage of virulence factors was evaluated.

RESULTS: Of the 119 isolates, 111 carried plasmid pKP151_NDM1, and all 104 isolates harbouring bla OXA-232 carried plasmid pKP151_OXA232. These 104 K. pneumoniae ST16 isolates showing chromosomal clonality possessed both pKP151_NDM1 and pKP151_OXA232, demonstrating clonal dissemination of K. pneumoniae ST16 with these plasmids. The isolates had essentially similar virulence factors as those of K. pneumoniae ST16 clones carrying bla KPC, which were recently reported as highly invasive clones in Brazil.

CONCLUSIONS: The potential global dissemination of these invasive clones with resistance to several antibiotics highlights the importance of appropriate monitoring and strict standard precautions.}, } @article {pmid35982777, year = {2022}, author = {Lv, QB and Li, S and Zhang, Y and Guo, R and Wang, YC and Peng, Y and Zhang, XX}, title = {A thousand metagenome-assembled genomes of Akkermansia reveal phylogroups and geographical and functional variations in the human gut.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {957439}, pmid = {35982777}, issn = {2235-2988}, mesh = {*Akkermansia ; Genomics ; Humans ; *Metagenome ; Sequence Analysis, DNA ; Verrucomicrobia/genetics ; }, abstract = {Akkermansia muciniphila has long been considered to be the only Akkermansia species in the human gut and has been extensively studied. The present study revealed the genomic architecture of Akkermansia in the human gut by analyzing 1,126 near-complete metagenome-assembled genomes, 84 publicly available genomes, and 1 newly sequenced Akkermansia glycaniphila strain from the human gut. We found that 1) the genomes of Akkermansia were clustered into four phylogroups with distinct interspecies similarity and different genomic characteristics and 2) A. glycaniphila GP37, a strain of Akkermansia, was isolated from the human gut, whereas previously, it had only been found in python. Amuc III was present in the Chinese population, and Amuc IV was mainly distributed in Western populations. A large number of gene functions, pathways, and carbohydrate-active enzymes were specifically associated with phylogroups. Our findings based on over a thousand genomes strengthened our previous knowledge and provided new insights into the population structure and ecology of Akkermansia in the human gut.}, } @article {pmid35982311, year = {2022}, author = {Le, HH and Lee, MT and Besler, KR and Comrie, JMC and Johnson, EL}, title = {Characterization of interactions of dietary cholesterol with the murine and human gut microbiome.}, journal = {Nature microbiology}, volume = {7}, number = {9}, pages = {1390-1403}, pmid = {35982311}, issn = {2058-5276}, support = {R35 GM138281/GM/NIGMS NIH HHS/United States ; S10 OD018516/OD/NIH HHS/United States ; }, mesh = {Animals ; Bacteroides ; Cholesterol ; Cholesterol, Dietary ; Dietary Fats ; *Gastrointestinal Microbiome ; Humans ; Mice ; *Microbiota ; Sulfotransferases ; }, abstract = {Consumption of dietary lipids, such as cholesterol, modulates the gut microbiome with consequences for host health through the production of microbiome-derived metabolites. Despite the implications for host metabolism, a limited number of specific interactions of the gut microbiome with diet-derived lipids have been characterized. This is partially because obtaining species-level resolution of the responsible taxa can be challenging and additional approaches are needed to identify health-relevant metabolites produced from cholesterol-microbiome interactions. Here we performed bio-orthogonal labelling sort sequence spectrometry, a click chemistry based workflow, to profile cholesterol-specific host-microbe interactions. Mice were exposed to an alkyne-functionalized variant of cholesterol and 16S ribosomal RNA gene amplicon sequencing of faecal samples identified diet-derived cholesterol-interacting microbes from the genera Bacteroides, Bifidobacterium, Enterococcus and Parabacteroides. Shotgun metagenomic analysis provided species-level resolution of diet-derived cholesterol-interacting microbes with enrichment of bile acid-like and sulfotransferase-like activities. Using untargeted metabolomics, we identify that cholesterol is converted to cholesterol sulfate in a Bacteroides-specific manner via the enzyme BT_0416. Mice monocolonized with Bacteroides thetaiotaomicron lacking Bt_0416 showed altered host cholesterol and cholesterol sulfate compared with wild-type mice, identifying a previously uncharacterized microbiome-transformation of cholesterol and a mechanism for microbiome-dependent contributions to host phenotype. Moreover, identification of a cholesterol-responsive sulfotransferase in Bacteroides suggests diet-dependent mechanisms for altering microbiome-specific cholesterol metabolism. Overall, our work identifies numerous cholesterol-interacting microbes with implications for more precise microbiome-conscious regulation of host cholesterol homeostasis.}, } @article {pmid35982241, year = {2022}, author = {Chen, H and Li, M and Tu, S and Zhang, X and Wang, X and Zhang, Y and Zhao, C and Guo, Y and Wang, H}, title = {Metagenomic data from cerebrospinal fluid permits tracing the origin and spread of Neisseria meningitidis CC4821 in China.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {839}, pmid = {35982241}, issn = {2399-3642}, mesh = {Humans ; *Meningococcal Infections ; *Neisseria meningitidis/genetics ; Phylogeny ; *Quinolones ; Serogroup ; }, abstract = {Metagenomic next-generation sequencing (mNGS) is useful for difficult to cultivate pathogens. Here, we use cerebrospinal fluid mNGS to diagnose invasive meningococcal disease. The complete genome sequences of Neisseria meningitidis were assembled using N. meningitidis of ST4821-serotype C isolated from four patients. To investigate the phylogeny, 165 CC4821 N. meningitidis genomes from 1972 to 2017 were also included. The core genome accumulated variation at a rate of 4.84×10[-8] substitutions/nucleotide site/year. CC4821 differentiated into four sub-lineages during evolution (A, B, C, and D). While evolving from sub-lineage A (early stage) to sub-lineage D (late stage), the ST and CC4821 serotype converged into the ST4821-serotype C clone. Most strains of sub-lineage D were isolated from invasive meningococcal disease, with increasing resistance to quinolones. Phylogeographic analysis suggests that CC4821 has spread across 14 countries. Thus, the selective pressure of quinolones may cause CC4821 to converge evolutionarily, making it more invasive and facilitating its spread.}, } @article {pmid35981004, year = {2022}, author = {Maddamsetti, R and Grant, NA}, title = {Discovery of positive and purifying selection in metagenomic time series of hypermutator microbial populations.}, journal = {PLoS genetics}, volume = {18}, number = {8}, pages = {e1010324}, pmid = {35981004}, issn = {1553-7404}, mesh = {Colistin ; *Escherichia coli/genetics ; Mutation ; *Pseudomonas aeruginosa/genetics ; Time Factors ; }, abstract = {A general method to infer both positive and purifying selection during the real-time evolution of hypermutator pathogens would be broadly useful. To this end, we introduce a Simple Test to Infer Mode of Selection (STIMS) from metagenomic time series of evolving microbial populations. We test STIMS on metagenomic data generated by simulations of bacterial evolution, and on metagenomic data spanning 62,750 generations of Lenski's long-term evolution experiment with Escherichia coli (LTEE). This benchmarking shows that STIMS detects positive selection in both nonmutator and hypermutator populations, and purifying selection in hypermutator populations. Using STIMS, we find strong evidence of ongoing positive selection on key regulators of the E. coli gene regulatory network, even in some hypermutator populations. STIMS also detects positive selection on regulatory genes in hypermutator populations of Pseudomonas aeruginosa that adapted to subinhibitory concentrations of colistin-an antibiotic of last resort-for just twenty-six days of laboratory evolution. Our results show that the fine-tuning of gene regulatory networks is a general mechanism for rapid and ongoing adaptation. The simplicity of STIMS, together with its intuitive visual interpretation, make it a useful test for positive and purifying selection in metagenomic data sets that track microbial evolution in real-time.}, } @article {pmid35980774, year = {2022}, author = {Kim, SY and Park, E and Lim, WJ and In Kim, S and Jeon, SW and Chang, Y and Ryu, S and Kim, HL and Kim, HN}, title = {Association Between Gut Microbiota and Depressive Symptoms: A Cross-Sectional Population-Based Study in South Korea.}, journal = {Psychosomatic medicine}, volume = {84}, number = {7}, pages = {757-765}, doi = {10.1097/PSY.0000000000001111}, pmid = {35980774}, issn = {1534-7796}, mesh = {Adult ; Cross-Sectional Studies ; Depression/epidemiology/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics ; Republic of Korea/epidemiology ; }, abstract = {OBJECTIVE: This study aimed to investigate the association between gut microbiota and depressive symptoms in a large population cohort of Korean adults.

METHODS: Overall, 1238 participants were included in the study. Participants were categorized into depressed or non-depressed groups, based on the depressive symptoms reported on the Center for Epidemiologic Studies Rating Scale for Depression, with a cutoff score of 16, and their fecal microbiota was profiled using 16S ribosomal RNA gene sequencing. Several alpha and beta diversity measures were also estimated. The association between depressive symptoms and gut microbiota was analyzed using generalized linear models. The inferred function of the metagenomes was compared between the two groups.

RESULTS: There were no consistent differences in alpha and beta diversity between the depressed and non-depressed groups. However, the continuous measure of depressive symptoms was inversely associated with one of four measures of alpha diversity (Shannon's diversity, p = .021). We also found a substantial difference between the depressed and non-depressed groups in the Bray-Curtis dissimilarity among the four beta diversity indices (p = .004). Participants whose depressive symptoms exceeded a clinical cutoff score had a lower relative abundance of the genus Faecalibacterium when compared with controls (coefficient = -0.025, q = 0.047). However, the depressed group had a significantly higher abundance of the genus Oscillospira than did the non-depressed group (coefficient = 0.002, q = 0.023).

CONCLUSIONS: Our findings contribute to the identification of potential relationships between the gut microbiota and depressive symptoms and provide useful insights for developing microbiota-based interventions for patients with depressive symptoms.}, } @article {pmid35980085, year = {2022}, author = {Kees, ED and Murugapiran, SK and Bennett, AC and Hamilton, TL}, title = {Distribution and Genomic Variation of Thermophilic Cyanobacteria in Diverse Microbial Mats at the Upper Temperature Limits of Photosynthesis.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0031722}, pmid = {35980085}, issn = {2379-5077}, mesh = {Temperature ; *Synechococcus/genetics ; Metagenome ; Genomics ; Photosynthesis/genetics ; }, abstract = {Thermophilic cyanobacteria have been extensively studied in Yellowstone National Park (YNP) hot springs, particularly during decades of work on the thick laminated mats of Octopus and Mushroom springs. However, focused studies of cyanobacteria outside these two hot springs have been lacking, especially regarding how physical and chemical parameters along with community morphology influence the genomic makeup of these organisms. Here, we used a metagenomic approach to examine cyanobacteria existing at the upper temperature limit of photosynthesis. We examined 15 alkaline hot spring samples across six geographic areas of YNP, all with various physical and chemical parameters and community morphology. We recovered 22 metagenome-assembled genomes (MAGs) belonging to thermophilic cyanobacteria, notably an uncultured Synechococcus-like taxon recovered from a setting at the upper temperature limit of photosynthesis, 73°C, in addition to thermophilic Gloeomargarita. Furthermore, we found that three distinct groups of Synechococcus-like MAGs recovered from different temperature ranges vary in their genomic makeup. MAGs from the uncultured very-high-temperature (up to 73°C) Synechococcus-like taxon lack key nitrogen metabolism genes and have genes implicated in cellular stress responses that diverge from other Synechococcus-like MAGs. Across all parameters measured, temperature was the primary determinant of taxonomic makeup of recovered cyanobacterial MAGs. However, total Fe, community morphology, and biogeography played an additional role in the distribution and abundance of upper-temperature-limit-adapted Synechococcus-like MAGs. These findings expand our understanding of cyanobacterial diversity in YNP and provide a basis for interrogation of understudied thermophilic cyanobacteria. IMPORTANCE Oxygenic photosynthesis arose early in microbial evolution-approximately 2.5 to 3.5 billion years ago-and entirely reshaped the biological makeup of Earth. However, despite the span of time in which photosynthesis has been refined, it is strictly limited to temperatures below 73°C, a barrier that many other biological processes have been able to overcome. Furthermore, photosynthesis at temperatures above 56°C is limited to circumneutral and alkaline pH. Hot springs in Yellowstone National Park (YNP), which have a large diversity in temperatures, pH, and geochemistry, provide a natural laboratory to study thermophilic microbial mats and the cyanobacteria within. While cyanobacteria in YNP microbial mats have been studied for decades, a vast majority of the work has focused on two springs within the same geyser basin, both containing similar community morphologies. Thus, the drivers of cyanobacterial adaptations to the upper limits of photosynthesis across a variety of environmental parameters have been understudied. Our findings provide new insights into the influence of these parameters on both taxonomic diversity and genomic content of cyanobacteria across a range of hot spring samples.}, } @article {pmid35979944, year = {2022}, author = {Hempel, CA and Wright, N and Harvie, J and Hleap, JS and Adamowicz, SJ and Steinke, D}, title = {Metagenomics versus total RNA sequencing: most accurate data-processing tools, microbial identification accuracy and perspectives for ecological assessments.}, journal = {Nucleic acids research}, volume = {50}, number = {16}, pages = {9279-9293}, pmid = {35979944}, issn = {1362-4962}, mesh = {*Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis, RNA ; High-Throughput Nucleotide Sequencing/methods ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Metagenomics and total RNA sequencing (total RNA-Seq) have the potential to improve the taxonomic identification of diverse microbial communities, which could allow for the incorporation of microbes into routine ecological assessments. However, these target-PCR-free techniques require more testing and optimization. In this study, we processed metagenomics and total RNA-Seq data from a commercially available microbial mock community using 672 data-processing workflows, identified the most accurate data-processing tools, and compared their microbial identification accuracy at equal and increasing sequencing depths. The accuracy of data-processing tools substantially varied among replicates. Total RNA-Seq was more accurate than metagenomics at equal sequencing depths and even at sequencing depths almost one order of magnitude lower than those of metagenomics. We show that while data-processing tools require further exploration, total RNA-Seq might be a favorable alternative to metagenomics for target-PCR-free taxonomic identifications of microbial communities and might enable a substantial reduction in sequencing costs while maintaining accuracy. This could be particularly an advantage for routine ecological assessments, which require cost-effective yet accurate methods, and might allow for the incorporation of microbes into ecological assessments.}, } @article {pmid35979496, year = {2022}, author = {Říhová, J and Bell, KC and Nováková, E and Hypša, V}, title = {Lightella neohaematopini: A new lineage of highly reduced endosymbionts coevolving with chipmunk lice of the genus Neohaematopinus.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {900312}, pmid = {35979496}, issn = {1664-302X}, abstract = {Sucking lice (Anoplura) are known to have established symbiotic associations multiple times with different groups of bacteria as diverse as Enterobacteriales, Legionellales, and Neisseriales. This diversity, together with absence of a common coevolving symbiont (such as Buchnera, in aphids), indicates that sucking lice underwent a series of symbiont acquisitions, losses, and replacements. To better understand evolution and significance of louse symbionts, genomic and phylogenetic data are needed from a broader taxonomic diversity of lice and their symbiotic bacteria. In this study, we extend the known spectrum of the louse symbionts with a new lineage associated with Neohaematopinus pacificus, a louse species that commonly parasitizes North American chipmunks. The recent coevolutionary analysis showed that rather than a single species, these lice form a cluster of unique phylogenetic lineages specific to separate chipmunk species (or group of closely related species). Using metagenomic assemblies, we show that the lice harbor a bacterium which mirrors their phylogeny and displays traits typical for obligate mutualists. Phylogenetic analyses place this bacterium within Enterobacteriaceae on a long branch related to another louse symbiont, "Candidatus Puchtella pedicinophila." We propose for this symbiotic lineage the name "Candidatus Lightella neohaematopini." Based on the reconstruction of metabolic pathways, we suggest that like other louse symbionts, L. neohaematopini provides its host with at least some B vitamins. In addition, several samples harbored another symbiotic bacterium phylogenetically affiliated with the Neisseriales-related symbionts described previously from the lice Polyplax serrata and Hoplopleura acanthopus. Characterizing these bacteria further extend the known diversity of the symbiotic associations in lice and show unique complexity and dynamics of the system.}, } @article {pmid35979445, year = {2022}, author = {Buck, M and Mehrshad, M and Bertilsson, S}, title = {mOTUpan: a robust Bayesian approach to leverage metagenome-assembled genomes for core-genome estimation.}, journal = {NAR genomics and bioinformatics}, volume = {4}, number = {3}, pages = {lqac060}, pmid = {35979445}, issn = {2631-9268}, abstract = {Recent advances in sequencing and bioinformatics have expanded the tree of life by providing genomes for uncultured environmentally relevant clades, either through metagenome-assembled genomes or through single-cell genomes. While this expanded diversity can provide novel insights into microbial population structure, most tools available for core-genome estimation are sensitive to genome completeness. Consequently, a major portion of the huge phylogenetic diversity uncovered by environmental genomic approaches remains excluded from such analyses. We present mOTUpan, a novel iterative Bayesian method for computing the core genome for sets of genomes of highly diverse completeness range. The likelihood for each gene cluster to belong to core or accessory genome is estimated by computing the probability of its presence/absence pattern in the target genome set. The core-genome prediction is computationally efficient and can be scaled up to thousands of genomes. It has shown comparable estimates to state-of-the-art tools Roary and PPanGGOLiN for high-quality genomes and is capable of using genomes at lower completeness thresholds. mOTUpan wraps a bootstrapping procedure to estimate the quality of a specific core-genome prediction, as the accuracy of each run will depend on the specific completeness distribution and the number of genomes in the dataset under scrutiny. mOTUpan is implemented in the mOTUlizer software package, and available at github.com/moritzbuck/mOTUlizer, under GPL 3.0 license.}, } @article {pmid35979346, year = {2022}, author = {Su, R and Yan, H and Li, N and Ding, T and Li, B and Xie, Y and Gao, C and Li, X and Wang, C}, title = {Application value of blood metagenomic next-generation sequencing in patients with connective tissue diseases.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {939057}, pmid = {35979346}, issn = {1664-3224}, mesh = {*Coinfection ; *Connective Tissue Diseases/diagnosis/genetics ; Herpesvirus 4, Human ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; Retrospective Studies ; }, abstract = {OBJECTIVE: This study aimed to analyze the application value of blood metagenomic next-generation sequencing (mNGS) in patients with connective tissue diseases (CTDs) to provide a reference for infection diagnosis and guidance for treatment.

METHODS: A total of 126 CTD patients with suspected infections who were hospitalized in the Department of Rheumatology, the Second Hospital of Shanxi Medical University from January 2020 to December 2021 were enrolled in this study. We retrospectively reviewed the results of mNGS and conventional diagnostic tests (CDTs).

RESULTS: Systemic lupus erythematosus (SLE) and polymyositis/dermatomyositis (DM/PM) had the highest incidence of infections. The positive pathogen detection rates of mNGS were higher than those of CDT. The virus infections are the most common type in CTD patients with single or mixed infection, especially Human gammaherpesvirus 4 (EBV), Human betaherpesvirus 5 (CMV), and Human alphaherpesvirus 1. The incidence of prokaryote and eukaryote infections is secondary to viruses. Bloodstream infections of rare pathogens such as Pneumocystis jirovecii should be of concern. Meanwhile, the most common mixed infection was bacterial-virus coinfection.

CONCLUSION: mNGS has incremental application value in patients with CTD suspected of co-infection. It has a high sensitivity, and a wide detection range for microorganisms in CTD patients. Furthermore, the high incidence of opportunistic virus infections in CTD patients should be of sufficient concern.}, } @article {pmid35979088, year = {2022}, author = {Bao, S and Song, H and Chen, Y and Zhong, C and Tang, H}, title = {Metagenomic next-generation sequencing for the diagnosis of pulmonary aspergillosis in non-neutropenic patients: a retrospective study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {925982}, pmid = {35979088}, issn = {2235-2988}, mesh = {*Aspergillosis ; Aspergillus/genetics ; Fungi ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics/methods ; Retrospective Studies ; Sensitivity and Specificity ; }, abstract = {This study aimed to obtain further in-depth information on the value of metagenomic next-generation sequencing (mNGS) for diagnosing pulmonary aspergillosis in non-neutropenic patients. We did a retrospective study, in which 33 non-neutropenic patients were included, of which 12 were patients with pulmonary aspergillosis and 21 were diagnosed with non-pulmonary aspergillosis. Fungi and all other co-pathogens in bronchoalveolar lavage fluid (BALF) (27 cases), blood (6 cases), and/or pleural fluid (1 case) samples were analyzed using mNGS. One of the patients submitted both BALF and blood samples. We analyzed the clinical characteristics, laboratory tests, and radiologic features of pulmonary aspergillosis patients and compared the diagnostic accuracy, including sensitivity, specificity, positive predictive value, and negative predictive value of mNGS with conventional etiological methods and serum (1,3)-β-D-glucan. We also explored the efficacy of mNGS in detecting mixed infections and co-pathogens. We further reviewed modifications of antimicrobial therapy for patients with pulmonary aspergillosis according to the mNGS results. Finally, we compared the detection of Aspergillus in BALF and blood samples from three patients using mNGS. In non-neutropenic patients, immunocompromised conditions of non-pulmonary aspergillosis were far less prevalent than in patients with pulmonary aspergillosis. More patients with pulmonary aspergillosis received long-term systemic corticosteroids (50% vs. 14.3%, p < 0.05). Additionally, mNGS managed to reach a sensitivity of 91.7% for diagnosing pulmonary aspergillosis, which was significantly higher than that of conventional etiological methods (33.3%) and serum (1,3)-β-D-glucan (33.3%). In addition, mNGS showed superior performance in discovering co-pathogens (84.6%) of pulmonary aspergillosis; bacteria, bacteria-fungi, and bacteria-PJP-virus were most commonly observed in non-neutropenic patients. Moreover, mNGS results can help guide effective treatments. According to the mNGS results, antimicrobial therapy was altered in 91.7% of patients with pulmonary aspergillosis. The diagnosis of Aspergillus detected in blood samples, which can be used as a supplement to BALF samples, seemed to show a higher specificity than that in BALF samples. mNGS is a useful and effective method for the diagnosis of pulmonary aspergillosis in non-neutropenic patients, detection of co-pathogens, and adjustment of antimicrobial treatment.}, } @article {pmid35978650, year = {2022}, author = {Quaranta, G and Ianiro, G and De Maio, F and Guarnaccia, A and Fancello, G and Agrillo, C and Iannarelli, F and Bibbo, S and Amedei, A and Sanguinetti, M and Cammarota, G and Masucci, L}, title = {"Bacterial Consortium": A Potential Evolution of Fecal Microbiota Transplantation for the Treatment of Clostridioides difficile Infection.}, journal = {BioMed research international}, volume = {2022}, number = {}, pages = {5787373}, pmid = {35978650}, issn = {2314-6141}, mesh = {Bacteria/genetics ; Bacteroidetes ; *Clostridioides difficile ; *Clostridium Infections/microbiology/therapy ; Fecal Microbiota Transplantation/methods ; Feces/microbiology ; Humans ; Proteobacteria ; Recurrence ; Treatment Outcome ; }, abstract = {Fecal microbiota transplantation (FMT) consists of infusion of feces from a donor to a recipient patient in order to restore the resident microbial population. FMT has shown to be a valid clinical option for Clostridioides difficile infections (CDI). However, this approach shows several criticalities, such as the recruiting and screening of voluntary donors. Our aim was to evaluate the therapeutic efficacy of a synthetic bacterial suspension defined "Bacterial Consortium" (BC) infused in the colon of CDI patients. The suspension was composed by 13 microbial species isolated by culturomics protocols from healthy donors' feces. The efficacy of the treatment was assessed both clinically and by metagenomics typing. Fecal samples of the recipient patients were collected before and after infusion. DNA samples obtained from feces at different time points (preinfusion, 7, 15, 30, and 90 days after infusion) were analyzed by next-generation sequencing. Before infusion, patient 1 showed an intestinal microbiota dominated by the phylum Bacteroidetes. Seven days after the infusion, Bacteroidetes decreased, followed by an implementation of Firmicutes and Verrucomicrobia. Patient 2, before infusion, showed a strong abundance of Proteobacteria and a significant deficiency of Bacteroidetes and Verrucomicrobia. Seven days after infusion, Proteobacteria strongly decreased, while Bacteroidetes and Verrucomicrobia increased. Metagenomics data revealed an "awakening" by microbial species absent or low concentrated at time T0 and present after the infusion. In conclusion, the infusion of selected bacteria would act as a trigger factor for "bacterial repopulation" representing an innovative treatment in patients with Clostridioides difficile infections.}, } @article {pmid35978381, year = {2022}, author = {Chiciudean, I and Russo, G and Bogdan, DF and Levei, EA and Faur, L and Hillebrand-Voiculescu, A and Moldovan, OT and Banciu, HL}, title = {Competition-cooperation in the chemoautotrophic ecosystem of Movile Cave: first metagenomic approach on sediments.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {44}, pmid = {35978381}, issn = {2524-6372}, abstract = {BACKGROUND: Movile Cave (SE Romania) is a chemoautotrophically-based ecosystem fed by hydrogen sulfide-rich groundwater serving as a primary energy source analogous to the deep-sea hydrothermal ecosystems. Our current understanding of Movile Cave microbiology has been confined to the sulfidic water and its proximity, as most studies focused on the water-floating microbial mat and planktonic accumulations likely acting as the primary production powerhouse of this unique subterranean ecosystem. By employing comprehensive genomic-resolved metagenomics, we questioned the spatial variation, chemoautotrophic abilities, ecological interactions and trophic roles of Movile Cave's microbiome thriving beyond the sulfidic-rich water.

RESULTS: A customized bioinformatics pipeline led to the recovery of 106 high-quality metagenome-assembled genomes from 7 cave sediment metagenomes. Assemblies' taxonomy spanned 19 bacterial and three archaeal phyla with Acidobacteriota, Chloroflexota, Proteobacteria, Planctomycetota, Ca. Patescibacteria, Thermoproteota, Methylomirabilota, and Ca. Zixibacteria as prevalent phyla. Functional gene analyses predicted the presence of CO2 fixation, methanotrophy, sulfur and ammonia oxidation in the explored sediments. Species Metabolic Coupling Analysis of metagenome-scale metabolic models revealed the highest competition-cooperation interactions in the sediments collected away from the water. Simulated metabolic interactions indicated autotrophs and methanotrophs as major donors of metabolites in the sediment communities. Cross-feeding dependencies were assumed only towards 'currency' molecules and inorganic compounds (O2, PO4[3-], H[+], Fe[2+], Cu[2+]) in the water proximity sediment, whereas hydrogen sulfide and methanol were assumedly traded exclusively among distant gallery communities.

CONCLUSIONS: These findings suggest that the primary production potential of Movile Cave expands way beyond its hydrothermal waters, enhancing our understanding of the functioning and ecological interactions within chemolithoautotrophically-based subterranean ecosystems.}, } @article {pmid35977641, year = {2022}, author = {Neethu, CS and Saravanakumar, C and Purvaja, R and Robin, RS and Ramesh, R}, title = {Arsenic resistance and horizontal gene transfer are associated with carbon and nitrogen enrichment in bacteria.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {311}, number = {}, pages = {119937}, doi = {10.1016/j.envpol.2022.119937}, pmid = {35977641}, issn = {1873-6424}, mesh = {*Arsenic/pharmacology ; *Betaproteobacteria ; Carbon ; Escherichia coli ; *Gammaproteobacteria/genetics ; Gene Transfer, Horizontal ; Nitrogen/pharmacology ; Phylogeny ; }, abstract = {Coastal waters are confluences receiving large amounts of point and non-point sources of pollution. An attempt was made to explore microbial community interactions in response to carbon, nitrogen and metal pollution. Additionally, experiments were designed to analyze the influence of these factors on horizontal gene transfer (HGT). Shift in bacterial diversity dynamics by arsenic stress and nutrient addition in coastal waters was explored by metagenomics of microcosm setups. Phylogenetic analysis revealed equal distribution of Gammaproteobacteria (29%) and Betaproteobacteria (28%) in control microcosm. This proportional diversity from control switched to unique distribution of Gammaproteobacteria (44.5%)> Flavobacteria (17.7%)> Bacteriodia (11.92%)> Betaproteobacteria (11.52%) in microcosm supplemented with carbon, nitrogen and metal (C + N + M). Among metal-stressed systems, alpha diversity analysis indicated highest diversity of genera in C + N + M followed by N + M > C+M> metal alone. Arsenic and ampicillin sensitive E. coli XL1 blue and environmental strains (Vibrio tubiashii W85 and E. coli W101) were tested for efficiency of uptake of plasmid (P) pUCminusMCS (arsB[R]amp[R]) under varying stress conditions. Transformation experiments revealed that combined effect of carbon, nitrogen and metal on horizontal gene transfer (HGT) was significantly higher (p < 0.01) than individual factors. The effect of carbon on HGT was proved to be superior to nitrogen under metal stressed conditions. Presence of arsenic in experimental setups (P + M, P + N + M and P + C + M) enhanced the HGT compared to non-metal counterparts supplemented with carbon or nitrogen. Arsenic resistant bacterial isolates (n = 200) were tested for the ability to utilize various carbon and nitrogen substrates and distinct positive correlation (p < 0.001) was found between arsenic resistance and utilization of urea and nitrate. However, evident positive correlation was not found between carbon sources and arsenic resistance. Our findings suggest that carbon and nitrogen pollution in aquatic habitats under arsenic stress determine the microbial community dynamics and critically influence uptake of genetic material from the surrounding environment.}, } @article {pmid35976282, year = {2022}, author = {Stein, R and Daniel, SG and Baldassano, RN and Feigenbaum, K and Kachelries, K and Sigall-Boneh, R and Weston, S and Levine, A and Bittinger, K}, title = {Outcomes and Predictors of Sustained Remission After Drug Withdrawal in Pediatric Crohn Disease.}, journal = {Journal of pediatric gastroenterology and nutrition}, volume = {75}, number = {5}, pages = {608-615}, doi = {10.1097/MPG.0000000000003589}, pmid = {35976282}, issn = {1536-4801}, mesh = {Adolescent ; Humans ; Young Adult ; *Crohn Disease/drug therapy ; Immunologic Factors/therapeutic use ; Leukocyte L1 Antigen Complex ; Prospective Studies ; Recurrence ; Remission Induction ; }, abstract = {OBJECTIVES: The primary aim of this study was to determine the proportion of pediatric Crohn disease (CD) subjects in sustained drug-free remission 52 weeks after stopping pharmacological therapy. We also aimed to explore the effects of the Crohn Disease Exclusion Diet (CDED) and microbiome composition on remission.

METHODS: We performed a prospective study following 18 CD patients ages 13-21 years in deep clinical remission withdrawing from immunomodulator (n = 7) or anti-TNFα (n = 11) monotherapy at two tertiary care centers. Stool for calprotectin and microbiome analyses was collected over 52 weeks. Participants followed either the CDED or free diet after drug withdrawal. The primary endpoint was sustained relapse-free drug-free remission (calprotectin <250 µg/g) at 52 weeks.

RESULTS: Seventeen participants were followed through 52 weeks with 11 (64.7%) in sustained remission. There was no improvement in remission among participants following the CDED (5/9; 55.6%), P = 0.63. By 104 weeks, only 8 (47.1 %) participants remained off immunosuppressive therapies. Analysis of shotgun metagenomic sequence data revealed that taxonomic and gene function abundance in the gut microbiome was relatively stable for participants in remission and relapse. However, a predictive model incorporating gut microbial gene pathway abundance for amino sugar/nucleotide sugar metabolism and galactose metabolism from baseline samples predicted relapse at 52 weeks with 80% accuracy.

CONCLUSIONS: After withdrawal of immunomodulator or anti-TNFα monotherapy among a small cohort of pediatric CD subjects in deep remission, nearly 65% sustained remission at 52 weeks. Baseline microbiome alterations predicted relapse. Large prospective studies are needed to better understand outcomes after treatment de-escalation.}, } @article {pmid35976111, year = {2022}, author = {Murga-Moreno, J and Coronado-Zamora, M and Casillas, S and Barbadilla, A}, title = {impMKT: the imputed McDonald and Kreitman test, a straightforward correction that significantly increases the evidence of positive selection of the McDonald and Kreitman test at the gene level.}, journal = {G3 (Bethesda, Md.)}, volume = {12}, number = {10}, pages = {}, pmid = {35976111}, issn = {2160-1836}, mesh = {Animals ; *Biological Evolution ; Drosophila/genetics ; Evolution, Molecular ; Humans ; Metagenomics ; *Selection, Genetic ; Software ; }, abstract = {The McDonald and Kreitman test is one of the most powerful and widely used methods to detect and quantify recurrent natural selection in DNA sequence data. One of its main limitations is the underestimation of positive selection due to the presence of slightly deleterious variants segregating at low frequencies. Although several approaches have been developed to overcome this limitation, most of them work on gene pooled analyses. Here, we present the imputed McDonald and Kreitman test (impMKT), a new straightforward approach for the detection of positive selection and other selection components of the distribution of fitness effects at the gene level. We compare imputed McDonald and Kreitman test with other widely used McDonald and Kreitman test approaches considering both simulated and empirical data. By applying imputed McDonald and Kreitman test to humans and Drosophila data at the gene level, we substantially increase the statistical evidence of positive selection with respect to previous approaches (e.g. by 50% and 157% compared with the McDonald and Kreitman test in Drosophila and humans, respectively). Finally, we review the minimum number of genes required to obtain a reliable estimation of the proportion of adaptive substitution (α) in gene pooled analyses by using the imputed McDonald and Kreitman test compared with other McDonald and Kreitman test implementations. Because of its simplicity and increased power to detect recurrent positive selection on genes, we propose the imputed McDonald and Kreitman test as the first straightforward approach for testing specific evolutionary hypotheses at the gene level. The software implementation and population genomics data are available at the web-server imkt.uab.cat.}, } @article {pmid35976010, year = {2022}, author = {Aoki, M and Nakahara, N and Kusube, M and Syutsubo, K}, title = {Metagenome-Assembled Genome Sequence of Marine Rhizobiaceae sp. Strain MnEN-MB40S, Obtained from Manganese-Oxidizing Enrichment Culture.}, journal = {Microbiology resource announcements}, volume = {11}, number = {9}, pages = {e0064522}, pmid = {35976010}, issn = {2576-098X}, support = {20K15222//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, abstract = {Here, we report a new metagenome-assembled genome (MAG) from a marine Rhizobiaceae species. The MnEN-MB40S genome was assembled from a manganese-oxidizing enrichment culture metagenome. A 4.1-Mb MAG comprising 26 contigs, with a GC content of 60.0%, was obtained. This MAG contributes to the genomic information regarding the family Rhizobiaceae.}, } @article {pmid35975611, year = {2022}, author = {Zhang, P and Cao, L and Ma, YY and Su, B and Zhang, CY and Li, YP}, title = {Metagenomic analysis reveals presence of different animal viruses in commercial fetal bovine serum and trypsin.}, journal = {Zoological research}, volume = {43}, number = {5}, pages = {756-766}, pmid = {35975611}, issn = {2095-8137}, mesh = {Animals ; Humans ; Metagenomics/methods ; Phylogeny ; *Serum Albumin, Bovine/genetics ; Trypsin/genetics ; *Viruses/genetics ; }, abstract = {Animal-derived biological products, such as fetal bovine serum (FBS) and trypsin, are important supplements for scientific, pharmaceutical, and medical use. Although preventive guidelines and tests are implemented to reduce potential viral contamination in these biologicals, they do not target unusual or emerging viruses, leading to safety concerns. Using unbiased metagenomics, we investigated the presence of viruses in recently collected commercial FBS and trypsin samples from different geographic regions. In total, we detected viral sequences belonging to Parvoviridae, Anelloviridae, Flaviviridae, Herpesviridae, Caliciviridae, Nodaviridae, Rhabdoviridae, and Paramyxoviridae, including several viruses related to bovine diseases, viruses of potential human and insect origin, and viruses of unknown origin. Bovine parvovirus 3 and bosavirus were detected with high frequency and abundance in FBS, necessitating more stringent testing for these parvoviruses during production. Both bovine norovirus and bovine viral diarrhea virus 1 displayed relatively high genetic distance to closest hits, indicating the presence of new genotypes in farm animals. While the origin of novel lyssavirus and Nipah virus is unclear, their presence raises the possibility of the introduction of pathogenic animal-derived viruses into biologicals. Our results showed relatively widespread contamination of different viruses in biologicals, underscoring the need for robust safety protocol alternatives, such as metagenomic sequencing, to monitor emerging viruses.}, } @article {pmid35975326, year = {2022}, author = {Maddamsetti, R}, title = {Idiosyncratic Purifying Selection on Metabolic Enzymes in the Long-Term Evolution Experiment with Escherichia coli.}, journal = {Genome biology and evolution}, volume = {14}, number = {12}, pages = {}, pmid = {35975326}, issn = {1759-6653}, mesh = {Child ; Humans ; *Escherichia coli/genetics ; *Metabolic Networks and Pathways/genetics ; Mutation ; Genome ; Archaea/genetics ; Evolution, Molecular ; Selection, Genetic ; }, abstract = {Bacteria, Archaea, and Eukarya all share a common set of metabolic reactions. This implies that the function and topology of central metabolism has been evolving under purifying selection over deep time. Central metabolism may similarly evolve under purifying selection during long-term evolution experiments, although it is unclear how long such experiments would have to run (decades, centuries, millennia) before signs of purifying selection on metabolism appear. I hypothesized that central and superessential metabolic enzymes would show evidence of purifying selection in the long-term evolution experiment with Escherichia coli (LTEE). I also hypothesized that enzymes that specialize on single substrates would show stronger evidence of purifying selection in the LTEE than generalist enzymes that catalyze multiple reactions. I tested these hypotheses by analyzing metagenomic time series covering 62,750 generations of the LTEE. I find mixed support for these hypotheses, because the observed patterns of purifying selection are idiosyncratic and population-specific. To explain this finding, I propose the Jenga hypothesis, named after a children's game in which blocks are removed from a tower until it falls. The Jenga hypothesis postulates that loss-of-function mutations degrade costly, redundant, and non-essential metabolic functions. Replicate populations can therefore follow idiosyncratic trajectories of lost redundancies, despite purifying selection on overall function. I tested the Jenga hypothesis by simulating the evolution of 1,000 minimal genomes under strong purifying selection. As predicted, the minimal genomes converge to different metabolic networks. Strikingly, the core genes common to all 1,000 minimal genomes show consistent signatures of purifying selection in the LTEE.}, } @article {pmid35974919, year = {2022}, author = {Sood, U and Dhingra, GG and Anand, S and Hira, P and Kumar, R and Kaur, J and Verma, M and Singhvi, N and Lal, S and Rawat, CD and Singh, VK and Kaur, J and Verma, H and Tripathi, C and Singh, P and Dua, A and Saxena, A and Phartyal, R and Jayaraj, P and Makhija, S and Gupta, R and Sahni, S and Nayyar, N and Abraham, JS and Somasundaram, S and Lata, P and Solanki, R and Mahato, NK and Prakash, O and Bala, K and Kumari, R and Toteja, R and Kalia, VC and Lal, R}, title = {Microbial Journey: Mount Everest to Mars.}, journal = {Indian journal of microbiology}, volume = {62}, number = {3}, pages = {323-337}, pmid = {35974919}, issn = {0046-8991}, abstract = {A rigorous exploration of microbial diversity has revealed its presence on Earth, deep oceans, and vast space. The presence of microbial life in diverse environmental conditions, ranging from moderate to extreme temperature, pH, salinity, oxygen, radiations, and altitudes, has provided the necessary impetus to search for them by extending the limits of their habitats. Microbiology started as a distinct science in the mid-nineteenth century and has provided inputs for the betterment of mankind during the last 150 years. As beneficial microbes are assets and pathogens are detrimental, studying both have its own merits. Scientists are nowadays working on illustrating the microbial dynamics in Earth's subsurface, deep sea, and polar regions. In addition to studying the role of microbes in the environment, the microbe-host interactions in humans, animals and plants are also unearthing newer insights that can help us to improve the health of the host by modulating the microbiota. Microbes have the potential to remediate persistent organic pollutants. Antimicrobial resistance which is a serious concern can also be tackled only after monitoring the spread of resistant microbes using disciplines of genomics and metagenomics The cognizance of microbiology has reached the top of the world. Space Missions are now looking for signs of life on the planets (specifically Mars), the Moon and beyond them. Among the most potent pieces of evidence to support the existence of life is to look for microbial, plant, and animal fossils. There is also an urgent need to deliberate and communicate these findings to layman and policymakers that would help them to take an adequate decision for better health and the environment around us. Here, we present a glimpse of recent advancements by scientists from around the world, exploring and exploiting microbial diversity.}, } @article {pmid35974417, year = {2022}, author = {Du, K and Yang, F and Zhang, JT and Yu, RC and Deng, Z and Li, WF and Chen, Y and Li, Q and Zhou, CZ}, title = {Comparative genomic analysis of five freshwater cyanophages and reference-guided metagenomic data mining.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {128}, pmid = {35974417}, issn = {2049-2618}, mesh = {*Bacteriophages ; Data Mining ; Fresh Water/microbiology ; *Genome, Viral/genetics ; Metagenomics ; Oligopeptides ; Phylogeny ; Toll-Like Receptor 2/agonists ; Toll-Like Receptor 9/agonists ; }, abstract = {BACKGROUND: As important producers using photosynthesis on Earth, cyanobacteria contribute to the oxygenation of atmosphere and the primary production of biosphere. However, due to the eutrophication of urban waterbodies and global warming, uncontrollable growth of cyanobacteria usually leads to the seasonal outbreak of cyanobacterial blooms. Cyanophages, a group of viruses that specifically infect and lyse cyanobacteria, are considered as potential environment-friendly agents to control the harmful blooms. Compared to the marine counterparts, only a few freshwater cyanophages have been isolated and genome sequenced to date, largely limiting their characterizations and applications.

RESULTS: Here, we isolated five freshwater cyanophages varying in tail morphology, termed Pam1~Pam5, all of which infect the cyanobacterium Pseudanabaena mucicola Chao 1806 that was isolated from the bloom-suffering Lake Chaohu in Anhui, China. The whole-genome sequencing showed that cyanophages Pam1~Pam5 all contain a dsDNA genome, varying in size from 36 to 142 Kb. Phylogenetic analyses suggested that Pam1~Pam5 possess different DNA packaging mechanisms and are evolutionarily distinct from each other. Notably, Pam1 and Pam5 have lysogeny-associated gene clusters, whereas Pam2 possesses 9 punctuated DNA segments identical to the CRISPR spacers in the host genome. Metagenomic data-based calculation of the relative abundance of Pam1~Pam5 at the Nanfei estuary towards the Lake Chaohu revealed that the short-tailed Pam1 and Pam5 account for the majority of the five cyanophages. Moreover, comparative analyses of the reference genomes of Pam1~Pam5 and previously reported cyanophages enabled us to identify three circular and seven linear contigs of virtual freshwater cyanophages from the metagenomic data of the Lake Chaohu.

CONCLUSIONS: We propose a high-throughput strategy to systematically identify cyanophages based on the currently available metagenomic data and the very limited reference genomes of experimentally isolated cyanophages. This strategy could be applied to mine the complete or partial genomes of unculturable bacteriophages and viruses. Transformation of the synthesized whole genomes of these virtual phages/viruses to proper hosts will enable the rescue of bona fide viral particles and eventually enrich the library of microorganisms that exist on Earth. Video abstract.}, } @article {pmid35974020, year = {2022}, author = {Feng, P and Yang, J and Zhao, S and Ling, Z and Han, R and Wu, Y and Salama, ES and Kakade, A and Khan, A and Jin, W and Zhang, W and Jeon, BH and Fan, J and Liu, M and Mamtimin, T and Liu, P and Li, X}, title = {Human supplementation with Pediococcus acidilactici GR-1 decreases heavy metals levels through modifying the gut microbiota and metabolome.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {63}, pmid = {35974020}, issn = {2055-5008}, mesh = {Animals ; Copper ; *Gastrointestinal Microbiome ; Humans ; Metabolome ; *Metals, Heavy ; Mice ; *Pediococcus acidilactici ; *Probiotics ; }, abstract = {Exposure to heavy metals (HMs) is a threat to human health. Although probiotics can detoxify HMs in animals, their effectiveness and mechanism of action in humans have not been studied well. Therefore, we conducted this randomized, double-blind, controlled trial on 152 occupational workers from the metal industry, an at-risk human population, to explore the effectiveness of probiotic yogurt in reducing HM levels. Participants were randomly assigned to two groups: one consumed probiotic yogurt containing the HM-resistant strain Pediococcus acidilactici GR-1 and the other consumed conventional yogurt for 12 weeks. Analysis of metal contents in the blood revealed that the consumption of probiotic yogurt resulted in a higher and faster decrease in copper (34.45%) and nickel (38.34%) levels in the blood than the consumption of conventional yogurt (16.41% and 27.57%, respectively). Metagenomic and metabolomic studies identified a close correlation between gut microbiota (GM) and host metabolism. Significantly enriched members of Blautia and Bifidobacterium correlated positively with the antioxidant capacities of GM and host. Further murine experiments confirmed the essential role of GM and protective effect of GR-1 on the antioxidative role of the intestine against copper. Thus, the use of probiotic yogurt may be an effective and affordable approach for combating toxic metal exposure through the protection of indigenous GM in humans.ClinicalTrials.gov identifier: ChiCTR2100053222.}, } @article {pmid35973026, year = {2022}, author = {Huang, T and Xia, J and Liu, T and Su, Z and Guan, Y and Guo, J and Wang, C and Zheng, M}, title = {Comammox Nitrospira Bacteria Are Dominant Ammonia Oxidizers in Mainstream Nitrification Bioreactors Emended with Sponge Carriers.}, journal = {Environmental science & technology}, volume = {56}, number = {17}, pages = {12584-12591}, doi = {10.1021/acs.est.2c03641}, pmid = {35973026}, issn = {1520-5851}, mesh = {Ammonia ; *Ammonium Compounds ; Archaea ; Bacteria/genetics ; Bioreactors ; *Nitrification ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Complete ammonia oxidation (i.e., comammox) is a newly discovered microbial process performed by a subset of the Nitrospira genus, and this unique microbial process has been ubiquitously detected in various wastewater treatment units. However, the operational conditions favoring comammox prevalence remain unclear. In this study, the dominance of comammox Nitrospira in four sponge biofilm reactors fed with low-strength ammonium (NH4[+] = 23 ± 3 mg N/L) wastewater was proved by coupling 16S rRNA gene amplicon sequencing, quantitative polymerase chain reaction (qPCR), and metagenomic sequencing. The results showed that comammox Nitrospira dominated in the nitrifying guild over canonical ammonia-oxidizing bacteria (AOB) constantly, despite the significant variation in the residual ammonium concentration (0.01-15 mg N/L) under different sets of operating conditions. This result indicates that sponge biofilms greatly favor retaining comammox Nitrospira in wastewater treatment and highlights an essential role of biomass retention in the comammox prevalence. Moreover, analyses of the assembled metagenomic sequences revealed that the retrieved amoA gene sequences affiliated with comammox Nitrospira (53.9-66.0% read counts of total amoA gene reads) were always higher than those (28.4-43.4%) related to β-proteobacterial AOB taxa. The comammox Nitrospira bacteria detected in the present biofilm systems were close to clade A Candidatus Nitrospira nitrosa.}, } @article {pmid35973024, year = {2022}, author = {Tang, Q and Ye, B and Wang, P and Ke, L and Tong, Z and Li, W}, title = {Identification of Anaerobic Organism Infection in a Patient With Emphysematous Pancreatitis Based on Metagenomic Next-Generation Sequencing: A Case Report.}, journal = {Pancreas}, volume = {51}, number = {5}, pages = {e85-e87}, doi = {10.1097/MPA.0000000000002060}, pmid = {35973024}, issn = {1536-4828}, mesh = {Anaerobiosis ; *Emphysema/diagnosis/diagnostic imaging ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; *Pancreatitis/diagnosis/diagnostic imaging ; }, } @article {pmid35972440, year = {2023}, author = {Hellmann, J and Ta, A and Ollberding, NJ and Bezold, R and Lake, K and Jackson, K and Dirksing, K and Bonkowski, E and Haslam, DB and Denson, LA}, title = {Patient-Reported Outcomes Correlate With Microbial Community Composition Independent of Mucosal Inflammation in Pediatric Inflammatory Bowel Disease.}, journal = {Inflammatory bowel diseases}, volume = {29}, number = {2}, pages = {286-296}, pmid = {35972440}, issn = {1536-4844}, support = {T32 ES010957/ES/NIEHS NIH HHS/United States ; P30 DK078392/DK/NIDDK NIH HHS/United States ; T32 DK007727/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Child ; Prospective Studies ; *Inflammatory Bowel Diseases/diagnosis ; *Colitis, Ulcerative/diagnosis ; *Crohn Disease/diagnosis ; *Microbiota ; Feces ; Leukocyte L1 Antigen Complex/metabolism ; Inflammation ; Abdominal Pain ; Patient Reported Outcome Measures ; }, abstract = {BACKGROUND: Inflammatory bowel diseases (IBDs) involve an aberrant host response to intestinal microbiota causing mucosal inflammation and gastrointestinal symptoms. Patient-reported outcomes (PROs) are increasingly important in clinical care and research. Our aim was to examine associations between PROs and fecal microbiota in patients 0 to 22 years of age with IBD.

METHODS: A longitudinal, prospective, single-center study tested for associations between microbial community composition via shotgun metagenomics and PROs including stool frequency and rectal bleeding in ulcerative colitis (UC) and abdominal pain and stool frequency in Crohn's disease (CD). Mucosal inflammation was assessed with fecal calprotectin. A negative binomial mixed-effects model including clinical characteristics and fecal calprotectin tested for differentially abundant species and metabolic pathways by PROs.

RESULTS: In 70 CD patients with 244 stool samples, abdominal pain correlated with increased relative abundance of Haemophilus and reduced Clostridium spp. There were no differences relative to calprotectin level. In 23 UC patients with 76 samples, both rectal bleeding and increased stool frequency correlated with increased Klebsiella and reduced Bacteroides spp. Conversely, UC patients with lower calprotectin had reduced Klebsiella. Both UC and CD patients with active symptoms exhibited less longitudinal microbial community stability. No differences in metabolic pathways were observed in CD. Increased sulfoglycolysis and ornithine biosynthesis correlated with symptomatic UC.

CONCLUSIONS: Microbial community composition correlated with PROs in both CD and UC. Metabolic pathways differed relative to PROs in UC, but not CD. Data suggest that microbiota may contribute to patient symptoms in IBD, in addition to effects of mucosal inflammation.}, } @article {pmid35972393, year = {2022}, author = {Pal, Y and Mayilraj, S and Krishnamurthi, S}, title = {Uncovering the structure and function of specialist bacterial lineages in environments routinely exposed to explosives.}, journal = {Letters in applied microbiology}, volume = {75}, number = {6}, pages = {1433-1448}, doi = {10.1111/lam.13810}, pmid = {35972393}, issn = {1472-765X}, mesh = {*Explosive Agents ; Azocines/analysis/chemistry/metabolism ; Phylogeny ; Triazines/metabolism ; Biodegradation, Environmental ; Bacteria/genetics/metabolism ; }, abstract = {Environmental contamination by hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX), the two most widely used compounds for military operations, is a long-standing problem at the manufacturing and decommissioning plants. Since explosives contamination has previously been shown to favour the growth of specific bacterial communities, the present study attempts to identify the specialist bacterial communities and their potential functional and metabolic roles by using amplicon targeted and whole-metagenome sequencing approaches in samples collected from two distinct explosives manufacturing sites. We hypothesize that the community structure and functional attributes of bacterial population are substantially altered by the concentration of explosives and physicochemical conditions. The results highlight the predominance of Planctomycetes in contrast to previous reports from similar habitats. The detailed phylogenetic analysis revealed the presence of operational taxonomic units related to bacterial members known for their explosives degradation. Further, the functional and metabolic analyses highlighted the abundance of putative genes and unidentified taxa possibly associated with xenobiotic biodegradation. Our findings suggest that microbial species capable of utilizing explosives as a carbon, energy or electron source are favoured by certain selective pressures based on the prevailing physicochemical and geographical conditions.}, } @article {pmid35972375, year = {2022}, author = {Lamurias, A and Sereika, M and Albertsen, M and Hose, K and Nielsen, TD}, title = {Metagenomic binning with assembly graph embeddings.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {19}, pages = {4481-4487}, pmid = {35972375}, issn = {1367-4811}, support = {34299//VILLUM FONDEN/ ; //Poul Due Jensen Foundation (Microflora Danica)/ ; }, mesh = {Sequence Analysis, DNA/methods ; *Metagenomics/methods ; *Metagenome ; Genome, Microbial ; Algorithms ; }, abstract = {MOTIVATION: Despite recent advancements in sequencing technologies and assembly methods, obtaining high-quality microbial genomes from metagenomic samples is still not a trivial task. Current metagenomic binners do not take full advantage of assembly graphs and are not optimized for long-read assemblies. Deep graph learning algorithms have been proposed in other fields to deal with complex graph data structures. The graph structure generated during the assembly process could be integrated with contig features to obtain better bins with deep learning.

RESULTS: We propose GraphMB, which uses graph neural networks to incorporate the assembly graph into the binning process. We test GraphMB on long-read datasets of different complexities, and compare the performance with other binners in terms of the number of High Quality (HQ) genome bins obtained. With our approach, we were able to obtain unique bins on all real datasets, and obtain more bins on most datasets. In particular, we obtained on average 17.5% more HQ bins when compared with state-of-the-art binners and 13.7% when aggregating the results of our binner with the others. These results indicate that a deep learning model can integrate contig-specific and graph-structure information to improve metagenomic binning.

GraphMB is available from https://github.com/MicrobialDarkMatter/GraphMB.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid35972296, year = {2023}, author = {Milne, R and Patch, C}, title = {Ethical Challenges Associated with Pathogen and Host Genetics in Infectious Disease.}, journal = {The New bioethics : a multidisciplinary journal of biotechnology and the body}, volume = {29}, number = {1}, pages = {24-36}, doi = {10.1080/20502877.2022.2109697}, pmid = {35972296}, issn = {2050-2885}, mesh = {Humans ; Pandemics ; *COVID-19 ; *Communicable Diseases ; Genomics ; Privacy ; }, abstract = {The Covid-19 pandemic has demonstrated the potential of genomic technologies for the detection and surveillance of infectious diseases. Pathogen genomics is likely to play a major role in the future of research and clinical implementation of genomic technologies. However, unlike human genetics, the specific ethical and social challenges associated with the implementation of infectious disease genomics has received comparatively little attention. In this paper, we contribute to this literature, focusing on the potential consequences for individuals and communities of the use of these technologies. We concentrate on areas of challenges related to privacy, stigma, discrimination and the return of results in the cases of the surveillance of known pathogens, metagenomics and host genomics.}, } @article {pmid35972278, year = {2022}, author = {Ke, M and Feng, L and Huang, S and Lu, T and Yu, Z and Yang, Y and Hu, H and Peijnenburg, WJGM and Feng, L and Qian, H}, title = {Development of a Potentially New Algaecide for Controlling Harmful Cyanobacteria Blooms Which is Ecologically Safe and Selective.}, journal = {Journal of agricultural and food chemistry}, volume = {70}, number = {33}, pages = {10134-10143}, doi = {10.1021/acs.jafc.2c02489}, pmid = {35972278}, issn = {1520-5118}, mesh = {*Cyanobacteria/genetics ; Ecosystem ; *Herbicides/pharmacology ; Humans ; *Microcystis ; }, abstract = {Harmful cyanobacterial blooms (HCBs) caused by Microcystis aeruginosa are of great concern as they negatively affect the aquatic environment and human health. Chemical methods could rapidly eradicate HCBs and have been used for many decades. However, many chemical reagents are not recommended to eliminate HCBs in the long term, given the possible destructive and toxic effects of the chemicals employed on non-target aquatic organisms. We developed a new algaecide, 2-((1,3,4-thiadiazol-2-yl)thio)-N-(4-chlorophenyl) acetamide (Q2), to control harmful cyanobacteria while being environmentally friendly and selective. In our study, Q2 effectively inhibited cyanobacterial growth, especially of M. aeruginosa, but did not affect eukaryotic algae in test concentrations. A critical mechanism was revealed by transcriptome and metagenomic results showing that Q2 affects multiple cellular targets of cyanobacteria for HCB control, including the destruction of organelles, damage in the photosynthesis center, as well as inhibition of gas vesicle growth, and these changes can be highly relevant to the decrease of quorum-sensing functional KEGG pathways. Furthermore, Q2 did not affect the microbial composition and could recover the disrupted aquatic functional pathways in a short period. This is different from the impact on ecosystem functioning of the traditionally used harmful algaecide diuron. All these results verified that Q2 could be friendly to the aquatic environment, providing a new directional choice in managing HCBs in the future.}, } @article {pmid35972252, year = {2022}, author = {Martin, RM and Gann, ER and Truchon, AR and Boyer, GL and Wilhelm, SW}, title = {Metagenome-Assembled Genome of a Pseudanabaena sp. from a Crimson Cyanobacterial Bloom in Lake Salubria, New York, USA.}, journal = {Microbiology resource announcements}, volume = {11}, number = {9}, pages = {e0049422}, pmid = {35972252}, issn = {2576-098X}, support = {P01 ES028939/ES/NIEHS NIH HHS/United States ; OCE-1840715//National Science Foundation (NSF)/ ; 735077//Simons Foundation (SF)/ ; 1P01ES028939-01//HHS | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; }, abstract = {Pseudanabaena spp. are filamentous cyanobacteria widely distributed in temperate lakes. Though infrequent, they can form harmful algal blooms. Here, we present a high-quality metagenome-assembled genome of a Pseudanabaena sp. from a toxic, crimson cyanobacterial bloom in Lake Salubria, NY.}, } @article {pmid35972231, year = {2022}, author = {Cui, J and Ramesh, G and Wu, M and Jensen, ET and Crago, O and Bertoni, AG and Gao, C and Hoffman, KL and Sheridan, PA and Wong, KE and Wood, AC and Chen, YI and Rotter, JI and Petrosino, JF and Rich, SS and Goodarzi, MO}, title = {Butyrate-Producing Bacteria and Insulin Homeostasis: The Microbiome and Insulin Longitudinal Evaluation Study (MILES).}, journal = {Diabetes}, volume = {71}, number = {11}, pages = {2438-2446}, pmid = {35972231}, issn = {1939-327X}, support = {P30 ES030285/ES/NIEHS NIH HHS/United States ; UL1 TR001420/TR/NCATS NIH HHS/United States ; UL1 TR001881/TR/NCATS NIH HHS/United States ; P30 DK063491/DK/NIDDK NIH HHS/United States ; R01 DK109588/DK/NIDDK NIH HHS/United States ; }, mesh = {Humans ; Insulin ; *Insulin Resistance ; *Diabetes Mellitus, Type 2 ; Blood Glucose/analysis ; Insulin, Regular, Human ; Homeostasis ; *Microbiota ; Butyrates ; }, abstract = {Gut microbiome studies have documented depletion of butyrate-producing taxa in type 2 diabetes. We analyzed associations between butyrate-producing taxa and detailed measures of insulin homeostasis, whose dysfunction underlies diabetes in 224 non-Hispanic Whites and 129 African Americans, all of whom completed an oral glucose tolerance test. Stool microbiome was assessed by whole-metagenome shotgun sequencing with taxonomic profiling. We examined associations among 36 butyrate-producing taxa (n = 7 genera and 29 species) and insulin sensitivity, insulin secretion, disposition index, insulin clearance, and prevalence of dysglycemia (prediabetes plus diabetes, 46% of cohort), adjusting for age, sex, BMI, and race. The genus Coprococcus was associated with higher insulin sensitivity (β = 0.14; P = 0.002) and disposition index (β = 0.12; P = 0.012) and a lower rate of dysglycemia (odds ratio [OR] 0.91; 95% CI 0.85-0.97; P = 0.0025). In contrast, Flavonifractor was associated with lower insulin sensitivity (β = -0.13; P = 0.004) and disposition index (β = -0.11; P = 0.04) and higher prevalence of dysglycemia (OR 1.22; 95% CI 1.08-1.38; P = 0.0013). Species-level analyses found 10 bacteria associated with beneficial directions of effects and two bacteria with adverse associations on insulin homeostasis and dysglycemia. Although most butyrate producers analyzed appear to be metabolically beneficial, this is not the case for all such bacteria, suggesting that microbiome-directed therapeutic measures to prevent or treat diabetes should be targeted to specific butyrate-producing taxa rather than all butyrate producers.}, } @article {pmid35972192, year = {2022}, author = {Poolman, TM and Townsend-Nicholson, A and Cain, A}, title = {Teaching genomics to life science undergraduates using cloud computing platforms with open datasets.}, journal = {Biochemistry and molecular biology education : a bimonthly publication of the International Union of Biochemistry and Molecular Biology}, volume = {50}, number = {5}, pages = {446-449}, pmid = {35972192}, issn = {1539-3429}, mesh = {*COVID-19/epidemiology ; *Cloud Computing ; Genomics ; Humans ; Software ; Students ; }, abstract = {The final year of a biochemistry degree is usually a time to experience research. However, laboratory-based research projects were not possible during COVID-19. Instead, we used open datasets to provide computational research projects in metagenomics to biochemistry undergraduates (80 students with limited computing experience). We aimed to give the students a chance to explore any dataset, rather than use a small number of artificial datasets (~60 published datasets were used). To achieve this, we utilized Google Colaboratory (Colab), a virtual computing environment. Colab was used as a framework to retrieve raw sequencing data (analyzed with QIIME2) and generate visualizations. Setting up the environment requires no prior experience; all students have the same drive structure and notebooks can be shared (for synchronous sessions). We also used the platform to combine multiple datasets, perform a meta-analysis, and allowed the students to analyze large datasets with 1000s of subjects and factors. Projects that required increased computational resources were integrated with Google Cloud Compute. In future, all research projects can include some aspects of reanalyzing public data, providing students with data science experience. Colab is also an excellent environment in which to develop data skills in multiple languages (e.g., Perl, Python, Julia).}, } @article {pmid35972150, year = {2022}, author = {Wittmers, F and Needham, DM and Hehenberger, E and Giovannoni, SJ and Worden, AZ}, title = {Genomes from Uncultivated Pelagiphages Reveal Multiple Phylogenetic Clades Exhibiting Extensive Auxiliary Metabolic Genes and Cross-Family Multigene Transfers.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0152221}, pmid = {35972150}, issn = {2379-5077}, mesh = {Humans ; Phylogeny ; Genome, Viral ; *Bacteriophages ; *Podoviridae ; Bacteria/genetics ; Myoviridae/genetics ; }, abstract = {For the abundant marine Alphaproteobacterium Pelagibacter (SAR11), and other bacteria, phages are powerful forces of mortality. However, little is known about the most abundant Pelagiphages in nature, such as the widespread HTVC023P-type, which is currently represented by two cultured phages. Using viral metagenomic data sets and fluorescence-activated cell sorting, we recovered 80 complete, undescribed Podoviridae genomes that form 10 phylogenomically distinct clades (herein, named Clades I to X) related to the HTVC023P-type. These expanded the HTVC023P-type pan-genome by 15-fold and revealed 41 previously unknown auxiliary metabolic genes (AMGs) in this viral lineage. Numerous instances of partner-AMGs (colocated and involved in related functions) were observed, including partners in nucleotide metabolism, DNA hypermodification, and Curli biogenesis. The Type VIII secretion system (T8SS) responsible for Curli biogenesis was identified in nine genomes and expanded the repertoire of T8SS proteins reported thus far in viruses. Additionally, the identified T8SS gene cluster contained an iron-dependent regulator (FecR), as well as a histidine kinase and adenylate cyclase that can be implicated in T8SS function but are not within T8SS operons in bacteria. While T8SS are lacking in known Pelagibacter, they contribute to aggregation and biofilm formation in other bacteria. Phylogenetic reconstructions of partner-AMGs indicate derivation from cellular lineages with a more recent transfer between viral families. For example, homologs of all T8SS genes are present in syntenic regions of distant Myoviridae Pelagiphages, and they appear to have alphaproteobacterial origins with a later transfer between viral families. The results point to an unprecedented multipartner-AMG transfer between marine Myoviridae and Podoviridae. Together with the expansion of known metabolic functions, our studies provide new prospects for understanding the ecology and evolution of marine phages and their hosts. IMPORTANCE One of the most abundant and diverse marine bacterial groups is Pelagibacter. Phages have roles in shaping Pelagibacter ecology; however, several Pelagiphage lineages are represented by only a few genomes. This paucity of data from even the most widespread lineages has imposed limits on the understanding of the diversity of Pelagiphages and their impacts on hosts. Here, we report 80 complete genomes, assembled directly from environmental data, which are from undescribed Pelagiphages and render new insights into the manipulation of host metabolism during infection. Notably, the viruses have functionally related partner genes that appear to be transferred between distant viruses, including a suite that encode a secretion system which both brings a new functional capability to the host and is abundant in phages across the ocean. Together, these functions have important implications for phage evolution and for how Pelagiphage infection influences host biology in manners extending beyond canonical viral lysis and mortality.}, } @article {pmid35971804, year = {2022}, author = {Zhou, H and van Hullebusch, ED}, title = {Microbial interaction and transformation of metals and metalloids.}, journal = {Letters in applied microbiology}, volume = {75}, number = {5}, pages = {1074-1075}, doi = {10.1111/lam.13805}, pmid = {35971804}, issn = {1472-765X}, mesh = {*Metalloids/analysis ; Metals ; Biodegradation, Environmental ; Microbial Interactions ; *Metals, Heavy/analysis ; Environmental Monitoring ; }, } @article {pmid35971554, year = {2022}, author = {Sun, T and Liu, Y and Cai, Y and Zhai, T and Zhou, Y and Yang, B and Wu, X and Zhan, Q}, title = {A Paired Comparison of Plasma and Bronchoalveolar Lavage Fluid for Metagenomic Next-Generation Sequencing in Critically Ill Patients with Suspected Severe Pneumonia.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {4369-4379}, pmid = {35971554}, issn = {1178-6973}, abstract = {PURPOSE: Plasma metagenomic next-generation sequencing (mNGS) has emerged as an attractive and minimally invasive technique for pathogen detection. However, few studies have demonstrated the need for simultaneous plasma and bronchoalveolar lavage fluid (BALF) mNGS in patients with severe pneumonia.

PATIENTS AND METHODS: This study retrospectively performed a paired comparison of BALF and plasma mNGS in critically ill patients with suspected severe pneumonia from April 2019 to December 2020. The diagnostic performance of BALF and plasma mNGS was compared using the clinical composite diagnosis as the reference standard.

RESULTS: In total, 57 patients were included in this study. Patients with positive plasma mNGS had shorter hospital stay days at the time of specimen acquisition (4.5 vs 11, P = 0.028) and a higher positivity rate of BALF culture (50% vs 22.9%, P = 0.033) than patients with negative plasma mNGS. Fifty-three patients (93%) were finally diagnosed with severe pneumonia. Significant differences were observed in the sensitivity of BALF and plasma mNGS (100% vs 42%, P < 0.001), and the diagnostic accuracy was 96% and 46%, respectively. The proportion of virus in positive plasma mNGS results was higher than that in BALF mNGS (23% vs 11%, P = 0.173) without significant difference. Although plasma mNGS detected additional microorganisms in 11/53 patients, the beneficial effect was observed in only 5/53 (9%) patients.

CONCLUSION: In this study, the clinical effect of simultaneously conducting mNGS of BALF and plasma samples was found to be limited. For patients with the suspected virus infection, plasma mNGS may be a supplementary test. Further studies are needed to identify the optimal indications for plasma mNGS.}, } @article {pmid35970993, year = {2022}, author = {Avila-Herrera, A and Thissen, JB and Mulakken, N and Schobel, SA and Morrison, MD and Zhou, X and Grey, SF and Lisboa, FA and Unselt, D and Mabery, S and Upadhyay, MM and Jaing, CJ and Elster, EA and Be, NA}, title = {Metagenomic features of bioburden serve as outcome indicators in combat extremity wounds.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {13816}, pmid = {35970993}, issn = {2045-2322}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *Anti-Infective Agents ; Extremities/injuries ; Humans ; Metagenome ; Metagenomics ; *Musculoskeletal Diseases/drug therapy ; *Wound Infection/drug therapy ; }, abstract = {Battlefield injury management requires specialized care, and wound infection is a frequent complication. Challenges related to characterizing relevant pathogens further complicates treatment. Applying metagenomics to wounds offers a comprehensive path toward assessing microbial genomic fingerprints and could indicate prognostic variables for future decision support tools. Wound specimens from combat-injured U.S. service members, obtained during surgical debridements before delayed wound closure, were subjected to whole metagenome analysis and targeted enrichment of antimicrobial resistance genes. Results did not indicate a singular, common microbial metagenomic profile for wound failure, instead reflecting a complex microenvironment with varying bioburden diversity across outcomes. Genus-level Pseudomonas detection was associated with wound failure at all surgeries. A logistic regression model was fit to the presence and absence of antimicrobial resistance classes to assess associations with nosocomial pathogens. A. baumannii detection was associated with detection of genomic signatures for resistance to trimethoprim, aminoglycosides, bacitracin, and polymyxin. Machine learning classifiers were applied to identify wound and microbial variables associated with outcome. Feature importance rankings averaged across models indicated the variables with the largest effects on predicting wound outcome, including an increase in P. putida sequence reads. These results describe the microbial genomic determinants in combat wound bioburden and demonstrate metagenomic investigation as a comprehensive tool for providing information toward aiding treatment of combat-related injuries.}, } @article {pmid35970379, year = {2022}, author = {Wu, L and Jia, C and Huang, S and Yu, K and Luo, A and Peng, Y}, title = {Nitrite oxidation in oxygen-deficient conditions during landfill leachate treatment.}, journal = {Environmental research}, volume = {214}, number = {Pt 3}, pages = {114090}, doi = {10.1016/j.envres.2022.114090}, pmid = {35970379}, issn = {1096-0953}, mesh = {Bacteria ; Bioreactors/microbiology ; *Nitrification ; Nitrites ; Nitrogen ; Oxidation-Reduction ; Oxygen ; *Water Pollutants, Chemical ; }, abstract = {Until recently, all known nitrite oxidation occurred in oxygen-rich conditions but now the oxidation of nitrite into nitrate within a low oxygen or anoxic environment has been observed in the ocean. However, this phenomenon is rarely reported in wastewater treatments and its mechanism is unknown. In this study, the partial nitrification and nitrite oxidation were conducted in no enough oxygen in order to remove nitrogen from landfill leachate, save energy, and save money. The results show that the NH4[+]-N removal efficiency was 99.4%. During phase I of the anaerobic sequential batch reactor (ASBR), no change in Chemical Oxygen Demand (COD) and ammonium were detected. The nitrite concentration decreased from 107 ± 3 mg/L to 0.16 mg/L during 96 h of oxygen- deficiency, while NO3[-]-N increased from 152.5 ± 3 mg/L to 253.65 ± 3 mg/L. The main microorganisms involved in this reaction in the ASBR were Nitrite-Oxidizing Bacteria (NOB), including Nitrospira and Nitrolancea, their relative abundances were 3.56% and 0.13%, respectively. The major NOB (Nitrospira) were confirmed by the further metagenomic binning analysis. This finding shows that nitrite oxidation can occur in oxygen-deficient conditions with specific NOB.}, } @article {pmid35969797, year = {2022}, author = {DeWoody, JA and Jeon, JY and Bickham, JW and Heenkenda, EJ and Janjua, S and Lamka, GF and Mularo, AJ and Black, A and Brüniche-Olsen, A and Willoughby, JR}, title = {The Threatened Species Imperative: Conservation assessments would benefit from population genomic insights.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {35}, pages = {e2210685119}, pmid = {35969797}, issn = {1091-6490}, mesh = {Animals ; Biodiversity ; *Conservation of Natural Resources ; *Endangered Species ; *Metagenomics ; }, } @article {pmid35968974, year = {2022}, author = {Swaney, MH and Sandstrom, S and Kalan, LR}, title = {Cobamide Sharing Is Predicted in the Human Skin Microbiome.}, journal = {mSystems}, volume = {7}, number = {5}, pages = {e0067722}, pmid = {35968974}, issn = {2379-5077}, support = {R35GM137828//HHS | NIH | National Institute of General Medical Sciences (NIGMS)/ ; T32AI055397//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; U19AI142720//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; U19 AI142720/AI/NIAID NIH HHS/United States ; R35 GM137828/GM/NIGMS NIH HHS/United States ; T32 AI055397/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Bacteria/genetics ; *Cobamides ; *Microbiota/genetics ; Vitamin B 12 ; Vitamins ; *Skin/microbiology ; }, abstract = {The skin microbiome is a key player in human health, with diverse functions ranging from defense against pathogens to education of the immune system. While recent studies have begun to shed light on the valuable role that skin microorganisms have in maintaining the skin barrier, a detailed understanding of the complex interactions that shape healthy skin microbial communities is limited. Cobamides, the vitamin B12 class of cofactor, are essential for organisms across the tree of life. Because this vitamin is only produced by a limited fraction of prokaryotes, cobamide sharing is predicted to mediate community dynamics within microbial communities. Here, we provide the first large-scale metagenomic assessment of cobamide biosynthesis and utilization in the skin microbiome. We show that while numerous and diverse taxa across the major bacterial phyla on the skin encode cobamide-dependent enzymes, relatively few species encode de novo cobamide biosynthesis. We show that cobamide producers and users are integrated into the network structure of microbial communities across the different microenvironments of the skin and that changes in microbiome community structure and diversity are associated with the abundance of cobamide producers in the Corynebacterium genus, for both healthy and diseased skin states. Finally, we find that de novo cobamide biosynthesis is enriched only in Corynebacterium species associated with hosts, including those prevalent on human skin. We confirm that the cofactor is produced in excess through quantification of cobamide production by human skin-associated species isolated in the laboratory. Taken together, our results reveal the potential for cobamide sharing within skin microbial communities, which we hypothesize mediates microbiome community dynamics and host interactions. IMPORTANCE The skin microbiome is essential for maintaining skin health and function. However, the microbial interactions that dictate microbiome structure, stability, and function are not well understood. Here, we investigate the biosynthesis and use of cobamides, a cofactor needed by many organisms but only produced by select prokaryotes, within the human skin microbiome. We found that while a large proportion of skin taxa encode cobamide-dependent enzymes, only a select few encode de novo cobamide biosynthesis. Further, the abundance of cobamide-producing Corynebacterium species is associated with skin microbiome diversity and structure, and within this genus, de novo biosynthesis is enriched in host-associated species compared to environment-associated species. These findings identify cobamides as a potential mediator of skin microbiome dynamics and skin health.}, } @article {pmid35968005, year = {2022}, author = {Peng, Y and Xie, T and Wu, Z and Zheng, W and Zhang, T and Howe, S and Chai, J and Deng, F and Li, Y and Zhao, J}, title = {Archaea: An under-estimated kingdom in livestock animals.}, journal = {Frontiers in veterinary science}, volume = {9}, number = {}, pages = {973508}, pmid = {35968005}, issn = {2297-1769}, abstract = {Archaea are considered an essential group of gut microorganisms in both humans and animals. However, they have been neglected in previous studies, especially those involving non-ruminants. In this study, we re-analyzed published metagenomic and metatranscriptomic data sequenced from matched samples to explore the composition and the expression activity of gut archaea in ruminants (cattle and sheep) and monogastric animals (pig and chicken). Our results showed that the alpha and beta diversity of each host species, especially cattle and chickens, calculated from metagenomic and metatranscriptomic data were significantly different, suggesting that metatranscriptomic data better represent the functional status of archaea. We detected that the relative abundance of 17 (cattle), 7 (sheep), 20 (pig), and 2 (chicken) archaeal species were identified in the top 100 archaeal taxa when analyzing the metagenomic datasets, and these species were classified as the "active archaeal species" for each host species by comparison with corresponding metatranscriptomic data. For example, The expressive abundance in metatranscriptomic dataset of Methanosphaera cuniculi and Methanosphaera stadtmanae were 30- and 27-fold higher than that in metagenomic abundance, indicating their potentially important function in the pig gut. Here we aim to show the potential importance of archaea in the livestock digestive tract and encourage future research in this area, especially on the gut archaea of monogastric animals.}, } @article {pmid35967908, year = {2022}, author = {Enespa, and Chandra, P}, title = {Tool and techniques study to plant microbiome current understanding and future needs: an overview.}, journal = {Communicative & integrative biology}, volume = {15}, number = {1}, pages = {209-225}, pmid = {35967908}, issn = {1942-0889}, abstract = {Microorganisms are present in the universe and they play role in beneficial and harmful to human life, society, and environments. Plant microbiome is a broad term in which microbes are present in the rhizo, phyllo, or endophytic region and play several beneficial and harmful roles with the plant. To know of these microorganisms, it is essential to be able to isolate purification and identify them quickly under laboratory conditions. So, to improve the microbial study, several tools and techniques such as microscopy, rRNA, or rDNA sequencing, fingerprinting, probing, clone libraries, chips, and metagenomics have been developed. The major benefits of these techniques are the identification of microbial community through direct analysis as well as it can apply in situ. Without tools and techniques, we cannot understand the roles of microbiomes. This review explains the tools and their roles in the understanding of microbiomes and their ecological diversity in environments.}, } @article {pmid35967853, year = {2022}, author = {Sheng, S and Yan, S and Chen, J and Zhang, Y and Wang, Y and Qin, Q and Li, W and Li, T and Huang, M and Ding, S and Tang, L}, title = {Gut microbiome is associated with metabolic syndrome accompanied by elevated gamma-glutamyl transpeptidase in men.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {946757}, pmid = {35967853}, issn = {2235-2988}, mesh = {Adult ; *Gastrointestinal Microbiome/physiology ; Genome-Wide Association Study ; Humans ; Male ; *Metabolic Syndrome/blood/complications/physiopathology ; Polyamines ; *gamma-Glutamyltransferase/blood ; }, abstract = {It is predicted that by 2035, metabolic syndrome (MS) will be found in nearly more than half of our adult population, seriously affecting the health of our body. MS is usually accompanied by the occurrence of abnormal liver enzymes, such as elevated gamma-glutamyl transpeptidase (GGT). More and more studies have shown that the gut microbiota is involved in MS; however, the correlation between gut microbiota and MS with elevated GGT has not been studied comprehensively. Especially, there are few reports about its role in the physical examination of the population of men with MS and elevated GGT. By using the whole-genome shotgun sequencing technology, we conducted a genome-wide association study of the gut microbiome in 66 participants diagnosed as having MS accompanied by high levels of GGT (case group) and 66 participants with only MS and normal GGT level (control group). We found that the number of gut microbial species was reduced in participants in the case group compared to that of the control group. The overall microbial composition between the two groups is of significant difference. The gut microbiota in the case group is characterized by increased levels of "harmful bacteria" such as Megamonas hypermegale, Megamonas funiformis, Megamonas unclassified, Klebsiella pneumoniae, and Fusobacterium mortiferum and decreased levels of "beneficial bacteria" such as Faecalibacterium prausnitzii, Eubacterium eligens, Bifidobacterium longum, Bifidobacterium pseudocatenulatum, Bacteroides dorei, and Alistipes putredinis. Moreover, the pathways of POLYAMSYN-PWY, ARG+POLYAMINE-SYN, PWY-6305, and GOLPDLCAT-PWY were also increased in the case group, which may play a role in the elevation of GGT by producing amine, polyamine, putrescine, and endogenous alcohol. Taken together, there are apparent changes in the composition of the gut microbiome in men with MS and abnormal GGT levels, and it is high time to discover specific gut microbiome as a potential therapeutic target in that population. More in-depth studies of relevant mechanism could offer some new methods for the treatment of MS with elevated GGT.}, } @article {pmid35967852, year = {2022}, author = {Ma, Y and Luo, M and Deng, Y and Yang, X and Wang, X and Chen, G and Qin, Z and Deng, Y and Nan, M and Chen, Y and Wang, P and Wei, H and Han, L and Fang, X and Liu, Z}, title = {Antibiotic-Induced Primary Biles Inhibit SARS-CoV-2 Endoribonuclease Nsp15 Activity in Mouse Gut.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {896504}, pmid = {35967852}, issn = {2235-2988}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Bile Acids and Salts/physiology ; *COVID-19/physiopathology ; *Endoribonucleases/antagonists & inhibitors/metabolism/physiology ; *Gastrointestinal Microbiome/physiology ; Mice ; *SARS-CoV-2 ; *Viral Nonstructural Proteins/antagonists & inhibitors/metabolism/physiology ; *COVID-19 Drug Treatment ; }, abstract = {The gut microbiome profile of COVID-19 patients was found to correlate with a viral load of SARS-CoV-2, COVID-19 severity, and dysfunctional immune responses, suggesting that gut microbiota may be involved in anti-infection. In order to investigate the role of gut microbiota in anti-infection against SARS-CoV-2, we established a high-throughput in vitro screening system for COVID-19 therapeutics by targeting the endoribonuclease (Nsp15). We also evaluated the activity inhibition of the target by substances of intestinal origin, using a mouse model in an attempt to explore the interactions between gut microbiota and SARS-CoV-2. The results unexpectedly revealed that antibiotic treatment induced the appearance of substances with Nsp15 activity inhibition in the intestine of mice. Comprehensive analysis based on functional profiling of the fecal metagenomes and endoribonuclease assay of antibiotic-enriched bacteria and metabolites demonstrated that the Nsp15 inhibitors were the primary bile acids that accumulated in the gut as a result of antibiotic-induced deficiency of bile acid metabolizing microbes. This study provides a new perspective on the development of COVID-19 therapeutics using primary bile acids.}, } @article {pmid35967843, year = {2022}, author = {Dunn, KA and MacDonald, T and Rodrigues, GJ and Forbrigger, Z and Bielawski, JP and Langille, MGI and Van Limbergen, J and Kulkarni, K}, title = {Antibiotic and antifungal use in pediatric leukemia and lymphoma patients are associated with increasing opportunistic pathogens and decreasing bacteria responsible for activities that enhance colonic defense.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {924707}, pmid = {35967843}, issn = {2235-2988}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Antifungal Agents/pharmacology/therapeutic use ; Bacteria ; Butyrates ; Child ; Child, Preschool ; Humans ; *Leukemia/complications/drug therapy ; *Lymphoma/drug therapy ; Mice ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Due to decreased immunity, both antibiotics and antifungals are regularly used in pediatric hematologic-cancer patients as a means to prevent severe infections and febrile neutropenia. The general effect of antibiotics on the human gut microbiome is profound, yielding decreased diversity and changes in community structure. However, the specific effect on pediatric oncology patients is not well-studied. The effect of antifungal use is even less understood, having been studied only in mouse models. Because the composition of the gut microbiome is associated with regulation of hematopoiesis, immune function and gastrointestinal integrity, changes within the patient gut can have implications for the clinical management of hematologic malignancies. The pediatric population is particularly challenging because the composition of the microbiome is age dependent, with some of the most pronounced changes occurring in the first three years of life. We investigated how antibiotic and antifungal use shapes the taxonomic composition of the stool microbiome in pediatric patients with leukemia and lymphoma, as inferred from both 16S rRNA and metagenome data. Associations with age, antibiotic use and antifungal use were investigated using multiple analysis methods. In addition, multivariable differential abundance was used to identify and assess specific taxa that were associated with multiple variables. Both antibiotics and antifungals were linked to a general decline in diversity in stool samples, which included a decrease in relative abundance in butyrate producers that play a critical role in host gut physiology (e.g., Faecalibacterium, Anaerostipes, Dorea, Blautia),. Furthermore, antifungal use was associated with a significant increase in relative abundance of opportunistic pathogens. Collectively, these findings have important implications for the treatment of leukemia and lymphoma patients. Butyrate is important for gastrointestinal integrity; it inhibits inflammation, reinforces colonic defense, mucosal immunity. and decreases oxidative stress. The routine use of broad-spectrum anti-infectives in pediatric oncology patients could simultaneously contribute to a decline in gastrointestinal integrity and colonic defense while promoting increases in opportunistic pathogens within the patient gut. Because the gut microbiome has been linked to both short-term clinical outcomes, and longer-lasting health effects, systematic characterization of the gut microbiome in pediatric patients during, and beyond, treatment is warranted.}, } @article {pmid35967333, year = {2022}, author = {Xing, C and Du, Y and Duan, T and Nim, K and Chu, J and Wang, HY and Wang, RF}, title = {Interaction between microbiota and immunity and its implication in colorectal cancer.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {963819}, pmid = {35967333}, issn = {1664-3224}, support = {R01 CA101795/CA/NCI NIH HHS/United States ; R01 CA246547/CA/NCI NIH HHS/United States ; U54 CA210181/CA/NCI NIH HHS/United States ; }, mesh = {*Colitis/metabolism ; *Colorectal Neoplasms/metabolism ; *Gastrointestinal Microbiome ; Humans ; Inflammation/complications ; *Microbiota ; }, abstract = {Colorectal cancer (CRC) is one of the leading causes of cancer-related death in the world. Besides genetic causes, colonic inflammation is one of the major risk factors for CRC development, which is synergistically regulated by multiple components, including innate and adaptive immune cells, cytokine signaling, and microbiota. The complex interaction between CRC and the gut microbiome has emerged as an important area of current CRC research. Metagenomic profiling has identified a number of prominent CRC-associated bacteria that are enriched in CRC patients, linking the microbiota composition to colitis and cancer development. Some microbiota species have been reported to promote colitis and CRC development in preclinical models, while a few others are identified as immune modulators to induce potent protective immunity against colitis and CRC. Mechanistically, microbiota regulates the activation of different immune cell populations, inflammation, and CRC via crosstalk between innate and adaptive immune signaling pathways, including nuclear factor kappa B (NF-κB), type I interferon, and inflammasome. In this review, we provide an overview of the potential interactions between gut microbiota and host immunity and how their crosstalk could synergistically regulate inflammation and CRC, thus highlighting the potential roles and mechanisms of gut microbiota in the development of microbiota-based therapies to prevent or alleviate colitis and CRC.}, } @article {pmid35966925, year = {2022}, author = {Hui, M and Wang, A and Cheng, J and Sha, Z}, title = {Full-length 16S rRNA amplicon sequencing reveals the variation of epibiotic microbiota associated with two shrimp species of Alvinocarididae: possibly co-determined by environmental heterogeneity and specific recognition of hosts.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13758}, pmid = {35966925}, issn = {2167-8359}, mesh = {Humans ; Animals ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; *Decapoda ; Crustacea/genetics ; Bacteria/genetics ; *Gammaproteobacteria/genetics ; *Microbiota/genetics ; }, abstract = {Shrimps of the family Alvinocarididae, endemic species to deep sea chemosynthetic ecosystems, harbor epibiotic microbes on gills which probably play important roles in the survival of the shrimps. Among them, Alvinocaris longirostris and Shinkaicaris leurokolos occupy different ecological niches within the same hydrothermal vent in Okinawa Trough, and A. longirostris also exists in a methane seep of the South China Sea. In this study, full-length 16S rRNA sequences of the gill associated bacteria of two alvinocaridid species from different chemosynthetically ecological niches were first captured by single-molecule real-time sequencing. Totally, 120,792 optimized circular consensus sequences with ∼1,450 bp in length were obtained and clustered into 578 operational taxonomic units. Alpha diversity analysis showed seep A. longirostris had the highest species richness and evenness (average Chao1 = 213.68, Shannon = 3.39). Beta diversity analysis revealed that all samples were clearly divided into three groups, and microbial community of A. longirostris from seep and vent were more related than the other comparisons. By permutational multivariate analysis of variance, the most significant community compositional variance was detected between seep A. longirostris and vent S. leurokolos (R [2] = 0.731, P = 0.001). The taxon tags were further classified into 21 phyla, 40 classes, 89 orders, 124 families and 135 genera. Overall, the microbial communities were dominated by Campylobacteria and Gammaproteobacteria. Alphaproteobacteria, Bacteroidia, Verrucomicrobiae, Bacilli and other minor groups were also detected at lower abundance. Taxonomic groups recovered from the vent S. leurokolos samples were only dominated by Sulfurovaceae (94.06%). In comparison, gill-associated microbiota of vent A. longirostris consisted of more diverse sulfur-oxidizing bacteria, including Sulfurovaceae (69.21%), Thiotrichaceae (6.77%) and a putative novel Gammaproteobacteria group (14.37%), while in seep A. longirostris, Gammaproteobacteria un-group (44.01%) constituted the major component, following the methane-oxidizing bacteria Methylomonadaceae (19.38%), and Sulfurovaceae (18.66%). Therefore, the gill associated bacteria composition and abundance of alvinocaridid shrimps are closely related to the habitat heterogeneity and the selection of microbiota by the host. However, the interaction between these alvinocaridid shrimps and the epibiotic communities requires further study based on metagenome sequencing and fluorescence in situ hybridization.}, } @article {pmid35966696, year = {2022}, author = {Rodríguez, J and Andersson, A and Björn, E and Timonen, S and Brugel, S and Skrobonja, A and Rowe, O}, title = {Inputs of Terrestrial Dissolved Organic Matter Enhance Bacterial Production and Methylmercury Formation in Oxic Coastal Water.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {809166}, pmid = {35966696}, issn = {1664-302X}, abstract = {Methylmercury (MeHg) is a potent neurotoxin commonly found in aquatic environments and primarily formed by microbial methylation of inorganic divalent mercury (Hg(II)) under anoxic conditions. Recent evidence, however, points to the production of MeHg also in oxic pelagic waters, but the magnitude and the drivers for this process remain unclear. Here, we performed a controlled experiment testing the hypothesis that inputs of terrestrial dissolved organic matter (tDOM) to coastal waters enhance MeHg formation via increased bacterial activity. Natural brackish seawater from a coastal area of the Baltic Sea was exposed to environmentally relevant levels of Hg(II) and additions of tDOM according to climate change scenarios. MeHg formation was observed to be coupled to elevated bacterial production rates, which, in turn, was linked to input levels of tDOM. The increased MeHg formation was, however, not coupled to any specific change in bacterial taxonomic composition nor to an increased abundance of known Hg(II) methylation genes. Instead, we found that the abundance of genes for the overall bacterial carbon metabolism was higher under increased tDOM additions. The findings of this study may have important ecological implications in a changing global climate by pointing to the risk of increased exposure of MeHg to pelagic biota.}, } @article {pmid35966676, year = {2022}, author = {Wei, Q and Li, Z and Gu, Z and Liu, X and Krutmann, J and Wang, J and Xia, J}, title = {Shotgun metagenomic sequencing reveals skin microbial variability from different facial sites.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {933189}, pmid = {35966676}, issn = {1664-302X}, abstract = {Biogeography (body site) is known to be one of the main factors influencing the composition of the skin microbial community. However, site-associated microbial variability at a fine-scale level was not well-characterized since there was a lack of high-resolution recognition of facial microbiota across kingdoms by shotgun metagenomic sequencing. To investigate the explicit microbial variance in the human face, 822 shotgun metagenomic sequencing data from Han Chinese recently published by our group, in combination with 97 North American samples from NIH Human Microbiome Project (HMP), were reassessed. Metagenomic profiling of bacteria, fungi, and bacteriophages, as well as enriched function modules from three facial sites (forehead, cheek, and the back of the nose), was analyzed. The results revealed that skin microbial features were more alike in the forehead and cheek while varied from the back of the nose in terms of taxonomy and functionality. Analysis based on biogeographic theories suggested that neutral drift with niche selection from the host could possibly give rise to the variations. Of note, the abundance of porphyrin-producing species, i.e., Cutibacterium acnes, Cutibacterium avidum, Cutibacterium granulosum, and Cutibacterium namnetense, was all the highest in the back of the nose compared with the forehead/cheek, which was consistent with the highest porphyrin level on the nose in our population. Sequentially, the site-associated microbiome variance was confirmed in American populations; however, it was not entirely consistent. Furthermore, our data revealed correlation patterns between Propionibacterium acnes bacteriophages with genus Cutibacterium at different facial sites in both populations; however, C. acnes exhibited a distinct correlation with P. acnes bacteriophages in Americans/Chinese. Taken together, in this study, we explored the fine-scale facial site-associated changes in the skin microbiome and provided insight into the ecological processes underlying facial microbial variations.}, } @article {pmid35966606, year = {2022}, author = {Pfaff, L and Gao, J and Li, Z and Jäckering, A and Weber, G and Mican, J and Chen, Y and Dong, W and Han, X and Feiler, CG and Ao, YF and Badenhorst, CPS and Bednar, D and Palm, GJ and Lammers, M and Damborsky, J and Strodel, B and Liu, W and Bornscheuer, UT and Wei, R}, title = {Multiple Substrate Binding Mode-Guided Engineering of a Thermophilic PET Hydrolase.}, journal = {ACS catalysis}, volume = {12}, number = {15}, pages = {9790-9800}, pmid = {35966606}, issn = {2155-5435}, abstract = {Thermophilic polyester hydrolases (PES-H) have recently enabled biocatalytic recycling of the mass-produced synthetic polyester polyethylene terephthalate (PET), which has found widespread use in the packaging and textile industries. The growing demand for efficient PET hydrolases prompted us to solve high-resolution crystal structures of two metagenome-derived enzymes (PES-H1 and PES-H2) and notably also in complex with various PET substrate analogues. Structural analyses and computational modeling using molecular dynamics simulations provided an understanding of how product inhibition and multiple substrate binding modes influence key mechanistic steps of enzymatic PET hydrolysis. Key residues involved in substrate-binding and those identified previously as mutational hotspots in homologous enzymes were subjected to mutagenesis. At 72 °C, the L92F/Q94Y variant of PES-H1 exhibited 2.3-fold and 3.4-fold improved hydrolytic activity against amorphous PET films and pretreated real-world PET waste, respectively. The R204C/S250C variant of PES-H1 had a 6.4 °C higher melting temperature than the wild-type enzyme but retained similar hydrolytic activity. Under optimal reaction conditions, the L92F/Q94Y variant of PES-H1 hydrolyzed low-crystallinity PET materials 2.2-fold more efficiently than LCC ICCG, which was previously the most active PET hydrolase reported in the literature. This property makes the L92F/Q94Y variant of PES-H1 a good candidate for future applications in industrial plastic recycling processes.}, } @article {pmid35966211, year = {2022}, author = {Hope, O and Bright, IE and Alagbonsi, AI}, title = {GC-MS biocomponents characterization and antibacterial potency of ethanolic crude extracts of Camellia sinensis.}, journal = {SAGE open medicine}, volume = {10}, number = {}, pages = {20503121221116859}, pmid = {35966211}, issn = {2050-3121}, abstract = {OBJECTIVE: The menace of antibacterial resistance among enteropathogenic bacteria continues to raise therapeutic management concerns within public health system. As a strategy toward alternative control of resistant pathogen proliferation, a folkloric plant (green tea leaves: Camellia sinensis) was collected from Ishaka municipality and characterized for biomolecular components and antibacterial potency.

METHODS: The bioactive and biomolecular components of the plant's ethanol extract were characterized using gas chromatography-mass spectrometry. A preliminary in vitro susceptibility test of the extract against characterized multiple antibiotic-resistant potential diarrheagenic bacterial strains was done.

RESULTS: The result revealed an exponential increase in susceptibility with a distinctive unit component of the C. sinensis extract at concentrations of 60 and 80 μg/ml. The extract also possessed antibacterial and antioxidant activities while having phytochemical constituents (flavonoids, alkaloids, phenolics, saponin, cardiac glycosides, etc.). The gas chromatography-mass spectrometry analysis further affirmed the potential of the extract by revealing 52 bioactive components/compounds as shown in the chromatogram.

CONCLUSION: The C. sinensis has antimicrobial and antioxidant potentials, and the constituents of the plant might be of therapeutic importance in the management of various diseases, especially those related to Escherichia coli and Salmonella.}, } @article {pmid35966153, year = {2022}, author = {Losol, P and Park, HS and Song, WJ and Hwang, YK and Kim, SH and Holloway, JW and Chang, YS}, title = {Association of upper airway bacterial microbiota and asthma: systematic review.}, journal = {Asia Pacific allergy}, volume = {12}, number = {3}, pages = {e32}, pmid = {35966153}, issn = {2233-8276}, abstract = {Individual studies have suggested that upper airway dysbiosis may be associated with asthma or its severity. We aimed to systematically review studies that evaluated upper airway bacterial microbiota in relation to asthma, compared to nonasthmatic controls. Searches used MEDLINE, Embase, and Web of Science Core Collection. Eligible studies included association between asthma and upper airway dysbiosis; assessment of composition and diversity of upper airway microbiota using 16S rRNA or metagenomic sequencing; upper airway samples from nose, nasopharynx, oropharynx or hypopharynx. Study quality was assessed and rated using the Newcastle-Ottawa scale. A total of 249 publications were identified; 17 in the final analysis (13 childhood asthma and 4 adult asthma). Microbiome richness was measured in 6 studies, species diversity in 12, and bacterial composition in 17. The quality of evidence was good and fair. The alpha-diversity was found to be higher in younger children with wheezing and asthma, while it was lower when asthmatic children had rhinitis or mite sensitization. In children, Proteobacteria and Firmicutes were higher in asthmatics compared to controls (7 studies), and Moraxella, Streptococcus, and Haemophilus were predominant in the bacterial community. In pooled analysis, nasal Streptococcus colonization was associated with the presence of wheezing at age 5 (p = 0.04). In adult patients with asthma, the abundance of Proteobacteria was elevated in the upper respiratory tract (3 studies). Nasal colonization of Corynebacterium was lower in asthmatics (2 studies). This study demonstrates the potential relationships between asthma and specific bacterial colonization in the upper airway in adult and children with asthma.}, } @article {pmid35966074, year = {2022}, author = {Sugino, KY and Hernandez, TL and Barbour, LA and Kofonow, JM and Frank, DN and Friedman, JE}, title = {A maternal higher-complex carbohydrate diet increases bifidobacteria and alters early life acquisition of the infant microbiome in women with gestational diabetes mellitus.}, journal = {Frontiers in endocrinology}, volume = {13}, number = {}, pages = {921464}, pmid = {35966074}, issn = {1664-2392}, support = {P30 DK048520/DK/NIDDK NIH HHS/United States ; R01 DK128416/DK/NIDDK NIH HHS/United States ; R01 DK101659/DK/NIDDK NIH HHS/United States ; }, mesh = {Bifidobacterium ; *Diabetes, Gestational/metabolism ; Diet ; Female ; Glucose ; Glycerol ; Humans ; Infant ; Insulin ; *Microbiota ; Pregnancy ; }, abstract = {Gestational diabetes mellitus (GDM) is associated with considerable imbalances in intestinal microbiota that may underlie pathological conditions in both mothers and infants. To more definitively identify these alterations, we evaluated the maternal and infant gut microbiota through the shotgun metagenomic analysis of a subset of stool specimens collected from a randomized, controlled trial in diet-controlled women with GDM. The women were fed either a CHOICE diet (60% complex carbohydrate/25% fat/15% protein, n=18) or a conventional diet (CONV, 40% complex carbohydrate/45% fat/15% protein, n=16) from 30 weeks' gestation through delivery. In contrast to other published studies, we designed the study to minimize the influence of other dietary sources by providing all meals, which were eucaloric and similar in fiber content. At 30 and 37 weeks' gestation, we collected maternal stool samples; performed the fasting measurements of glucose, glycerol, insulin, free fatty acids, and triglycerides; and administered an oral glucose tolerance test (OGTT) to measure glucose clearance and insulin response. Infant stool samples were collected at 2 weeks, 2 months, and 4-5 months of age. Maternal glucose was controlled to conventional targets in both diets, with no differences in Homeostatic Model Assessment of Insulin Resistance (HOMA-IR). No differences in maternal alpha or beta diversity between the two diets from baseline to 37 weeks' gestation were observed. However, women on CHOICE diet had higher levels of Bifidobacteriaceae, specifically Bifidobacterium adolescentis, compared with women on CONV. Species-level taxa varied significantly with fasting glycerol, fasting glucose, and glucose AUC after the OGTT challenge. Maternal diet significantly impacted the patterns of infant colonization over the first 4 months of life, with CHOICE infants showing increased microbiome alpha diversity (richness), greater Clostridiaceae, and decreased Enterococcaceae over time. Overall, these results suggest that an isocaloric GDM diet containing greater complex carbohydrates with reduced fat leads to an ostensibly beneficial effect on the maternal microbiome, improved infant gut microbiome diversity, and reduced opportunistic pathogens capable of playing a role in obesity and immune system development. These results highlight the critical role a maternal diet has in shaping the maternal and infant microbiome in women with GDM.}, } @article {pmid35965849, year = {2022}, author = {Liu, L and Wu, H and Liang, J and Wu, W and Peng, Y and Zhou, H and Li, X}, title = {Rhizomucor pusillus Infection in a Patient with Acute Myeloid Leukaemia After Haematopoietic Stem Cell Transplantation: Clinical Impact of Metagenomics Next-Generation Sequencing.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {4285-4290}, pmid = {35965849}, issn = {1178-6973}, abstract = {Long-term chemotherapy and immunosuppressants in acute myeloid leukaemia (AML) patients can result in a high risk of opportunistic infections. Rhizomucor pusillus is an opportunistic pathogen that exists in nature, but infection caused by R. pusillus is rare in the clinic. Notably, the sensitivity and detection time of conventional diagnostic tools for this fungus usually falls short of the needs of clinical diagnosis, resulting in treatment failure. Currently, metagenomics next-generation sequencing (mNGS) has played an important role in the detection of pathogens. Here, we report a case of R. pusillus pneumonia in a haematopoietic stem cell transplantation (HSCT) patient, detected by the mNGS method.}, } @article {pmid35965638, year = {2023}, author = {Campbell, LJ and Castillo, NA and Dunn, CD and Perez, A and Schmitter-Soto, JJ and Mejri, SC and Boucek, RE and Corujo, RS and Adams, AJ and Rehage, JS and Goldberg, TL}, title = {Viruses of Atlantic Bonefish (Albula vulpes) in Florida and the Caribbean show geographic patterns consistent with population declines.}, journal = {Environmental biology of fishes}, volume = {106}, number = {2}, pages = {303-317}, pmid = {35965638}, issn = {0378-1909}, abstract = {UNLABELLED: Atlantic Bonefish (Albula vulpes) are economically important due to their popularity with recreational anglers. In the State of Florida, USA, bonefish population numbers declined by approximately 60% between the 1990s and 2015. Habitat loss, water quality impairment, chemical inputs, and other anthropogenic factors have been implicated as causes, but the role of pathogens has been largely overlooked, especially with respect to viruses. We used a metagenomic approach to identify and quantify viruses in the blood of 103 A. vulpes sampled throughout their Western Atlantic range, including populations in Florida that have experienced population declines and populations in Belize, Mexico, Puerto Rico, and The Bahamas that have remained apparently stable. We identified four viruses, all of which are members of families known to infect marine fishes (Flaviviridae, Iflaviridae, Narnaviridae, and Nodaviridae), but all of which were previously undescribed. Bonefish from Florida and Mexico had higher viral richness (numbers of distinct viruses per individual fish) than fish sampled from other areas, and bonefish from the Upper Florida Keys had the highest prevalence of viral infection (proportion of positive fish) than fish sampled from any other location. Bonefish from Florida also had markedly higher viral loads than fish sampled from any other area, both for a novel narnavirus and for all viruses combined. Bonefish viruses may be indicators of environmentally driven physiological and immunological compromise, causes of ill health, or both.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s10641-022-01306-9.}, } @article {pmid35965344, year = {2022}, author = {Rossi, A and Morlino, MS and Gaspari, M and Basile, A and Kougias, P and Treu, L and Campanaro, S}, title = {Analysis of the anaerobic digestion metagenome under environmental stresses stimulating prophage induction.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {125}, pmid = {35965344}, issn = {2049-2618}, mesh = {Anaerobiosis ; Archaea/genetics ; Metagenome/genetics ; *Microbiota ; Virus Activation ; *Viruses/genetics ; }, abstract = {BACKGROUND: The viral community has the potential to influence the structure of the microbiome and thus the yield of the anaerobic digestion process. However, the virome composition in anaerobic digestion is still under-investigated. A viral induction experiment was conducted on separate batches undergoing a series of DNA-damaging stresses, in order to coerce temperate viruses to enter the lytic cycle.

RESULTS: The sequencing of the metagenome revealed a viral community almost entirely composed of tailed bacteriophages of the order Caudovirales. Following a binning procedure 1,092 viral and 120 prokaryotic genomes were reconstructed, 64 of which included an integrated prophage in their sequence. Clustering of coverage profiles revealed the presence of species, both viral and microbial, sharing similar reactions to shocks. A group of viral genomes, which increase under organic overload and decrease under basic pH, uniquely encode the yopX gene, which is involved in the induction of temperate prophages. Moreover, the in-silico functional analysis revealed an enrichment of sialidases in viral genomes. These genes are associated with tail proteins and, as such, are hypothesised to be involved in the interaction with the host. Archaea registered the most pronounced changes in relation to shocks and featured behaviours not shared with other species. Subsequently, data from 123 different samples of the global anaerobic digestion database was used to determine coverage profiles of host and viral genomes on a broader scale.

CONCLUSIONS: Viruses are key components in anaerobic digestion environments, shaping the microbial guilds which drive the methanogenesis process. In turn, environmental conditions are pivotal in shaping the viral community and the rate of induction of temperate viruses. This study provides an initial insight into the complexity of the anaerobic digestion virome and its relation with the microbial community and the diverse environmental parameters. Video Abstract.}, } @article {pmid35965333, year = {2022}, author = {Broman, E and Izabel-Shen, D and Rodríguez-Gijón, A and Bonaglia, S and Garcia, SL and Nascimento, FJA}, title = {Microbial functional genes are driven by gradients in sediment stoichiometry, oxygen, and salinity across the Baltic benthic ecosystem.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {126}, pmid = {35965333}, issn = {2049-2618}, mesh = {Carbon ; *Microbiota/genetics ; Nitrogen ; Oxygen ; *Salinity ; }, abstract = {BACKGROUND: Microorganisms in the seafloor use a wide range of metabolic processes, which are coupled to the presence of functional genes within their genomes. Aquatic environments are heterogenous and often characterized by natural physiochemical gradients that structure these microbial communities potentially changing the diversity of functional genes and its associated metabolic processes. In this study, we investigated spatial variability and how environmental variables structure the diversity and composition of benthic functional genes and metabolic pathways across various fundamental environmental gradients. We analyzed metagenomic data from sediment samples, measured related abiotic data (e.g., salinity, oxygen and carbon content), covering 59 stations spanning 1,145 km across the Baltic Sea.

RESULTS: The composition of genes and microbial communities were mainly structured by salinity plus oxygen, and the carbon to nitrogen (C:N) ratio for specific metabolic pathways related to nutrient transport and carbon metabolism. Multivariate analyses indicated that the compositional change in functional genes was more prominent across environmental gradients compared to changes in microbial taxonomy even at genus level, and indicate functional diversity adaptation to local environments. Oxygen deficient areas (i.e., dead zones) were more different in gene composition when compared to oxic sediments.

CONCLUSIONS: This study highlights how benthic functional genes are structured over spatial distances and by environmental gradients and resource availability, and suggests that changes in, e.g., oxygenation, salinity, and carbon plus nitrogen content will influence functional metabolic pathways in benthic habitats. Video Abstract.}, } @article {pmid35965269, year = {2023}, author = {Lima, LFO and Alker, AT and Papudeshi, B and Morris, MM and Edwards, RA and de Putron, SJ and Dinsdale, EA}, title = {Coral and Seawater Metagenomes Reveal Key Microbial Functions to Coral Health and Ecosystem Functioning Shaped at Reef Scale.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {392-407}, pmid = {35965269}, issn = {1432-184X}, mesh = {Animals ; *Anthozoa/microbiology ; Ecosystem ; Metagenome ; Coral Reefs ; Bacteria/genetics/metabolism ; *Microbiota/genetics ; Seawater/microbiology ; }, abstract = {The coral holobiont is comprised of a highly diverse microbial community that provides key services to corals such as protection against pathogens and nutrient cycling. The coral surface mucus layer (SML) microbiome is very sensitive to external changes, as it constitutes the direct interface between the coral host and the environment. Here, we investigate whether the bacterial taxonomic and functional profiles in the coral SML are shaped by the local reef zone and explore their role in coral health and ecosystem functioning. The analysis was conducted using metagenomes and metagenome-assembled genomes (MAGs) associated with the coral Pseudodiploria strigosa and the water column from two naturally distinct reef environments in Bermuda: inner patch reefs exposed to a fluctuating thermal regime and the more stable outer reefs. The microbial community structure in the coral SML varied according to the local environment, both at taxonomic and functional levels. The coral SML microbiome from inner reefs provides more gene functions that are involved in nutrient cycling (e.g., photosynthesis, phosphorus metabolism, sulfur assimilation) and those that are related to higher levels of microbial activity, competition, and stress response. In contrast, the coral SML microbiome from outer reefs contained genes indicative of a carbohydrate-rich mucus composition found in corals exposed to less stressful temperatures and showed high proportions of microbial gene functions that play a potential role in coral disease, such as degradation of lignin-derived compounds and sulfur oxidation. The fluctuating environment in the inner patch reefs of Bermuda could be driving a more beneficial coral SML microbiome, potentially increasing holobiont resilience to environmental changes and disease.}, } @article {pmid35965098, year = {2022}, author = {Zhao, H and Zhang, L}, title = {Metagenome-assembled Genomes of Six Novel Ammonia-oxidizing Archaea (AOA) from Agricultural Upland Soil.}, journal = {Microbes and environments}, volume = {37}, number = {3}, pages = {}, pmid = {35965098}, issn = {1347-4405}, mesh = {*Ammonia/metabolism ; *Archaea ; Bacteria ; Metagenome ; Nitrites/metabolism ; Oxidation-Reduction ; Soil ; Soil Microbiology ; }, abstract = {Ammonia-oxidizing archaea (AOA), key players in agricultural upland soil nitrification, convert soil ammonium to nitrite. The microbial oxidation of ammonia to nitrite is an important part of the global biogeochemical nitrogen cycle. In the present study, we recovered six novel AOA metagenome-assembled genomes (MAGs) containing genes for carbon (C) fixation and nitrogen (N) metabolism by using a deep shotgun metagenomic sequencing strategy. We also found that these AOA MAGs possessed cobalamin synthesis genes, suggesting that AOA are vitamin suppliers in agricultural upland soil. Collectively, the present results deepen our understanding of the metabolic potential and phylogeny of AOA in agroecosystems.}, } @article {pmid35964510, year = {2022}, author = {Wang, J and Peng, C and Dai, Y and Li, Y and Jiao, S and Ma, X and Liu, X and Wang, L}, title = {Slower antibiotics degradation and higher resistance genes enrichment in plastisphere.}, journal = {Water research}, volume = {222}, number = {}, pages = {118920}, doi = {10.1016/j.watres.2022.118920}, pmid = {35964510}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents ; Carbon ; Ecosystem ; *Environmental Pollutants ; Microplastics ; *Plastics ; Polyesters ; Polyvinyl Chloride ; RNA, Ribosomal, 16S/genetics ; Tetracycline ; Water ; }, abstract = {Microplastics (MPs) are increasingly entering the urban aquatic ecosystems, and the environmental significance and health risks of plastisphere, a special biofilm on MPs, have received widespread attention. In this study, MPs of polylactic acid (PLA) and polyvinyl chloride (PVC) and quartzite were incubated in an urban water environment, and the tetracycline (TC) degradation ability was compared. Approximatedly 24% of TC biodegraded in 28 d in the water-quartzite system, which is significantly higher than that in the water-PLA (17.3%) and water-PVC systems (16.7%). Re-incubation of microorganisms in biofilms affirmed that quartzite biofilm has a higher TC degradation capacity than the plastisphere. According to high-throughput sequencing of 16S rRNA and metagenomic analysis, quartzite biofilm contained more abundant potential TC degrading bacteria, genes related to TC degradation (eutG, aceE, and DLAT), and metabolic pathways related to TC degradation. An oligotrophic environment on the quartzite surface might lead to the higher metabolic capacity of quartzite biofilm for unconventional carbons, e.g., TC. It is also found that, compared with quartzite biofilm, the distinct microbes in the plastisphere carried more antibiotic resistance genes (ARGs). Higher affinity of MPs surface to antibiotics may lead to higher antibiotics stress on the plastisphere, which further amplify the carrying capacity for ARGs of microorganisms in the plastisphere. Compared to the nondegradable PVC MPs, surface of the biodegradable PLA plastics harbored significantly higher amounts of biomass and ARGs. Compared to the mineral particles, the capability of plastisphere has lower ability to degrade unconventional carbon sources such as the refractory organic pollutants, due to the abundance of carbon sources (adsorbed organic carbon and endogenous organic carbon) on the MPs surface. Meanwhile, the stronger adsorption capacity for pollutants also leads to higher pollutant stress (such as antibiotic stress) in plastisphere, which in turn affects the microbiological characteristics of the plastisphere itself, such as carrying more ARGs.}, } @article {pmid35964419, year = {2022}, author = {Chandrasiri, S and Perera, T and Dilhara, A and Perera, I and Mallawaarachchi, V}, title = {CH-Bin: A convex hull based approach for binning metagenomic contigs.}, journal = {Computational biology and chemistry}, volume = {100}, number = {}, pages = {107734}, doi = {10.1016/j.compbiolchem.2022.107734}, pmid = {35964419}, issn = {1476-928X}, mesh = {Algorithms ; *Metagenome ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {Metagenomics has enabled culture-independent analysis of micro-organisms present in environmental samples. Metagenomics binning, which involves the grouping of contigs into bins that represent different taxonomic groups, is an important step of a typical metagenomic workflow followed after assembly. The majority of the metagenomic binning tools represent the composition and coverage information of contigs as feature vectors consisting of a large number of dimensions. However, these tools use traditional Euclidean distance or Manhattan distance metrics which become unreliable in the high dimensional space. We propose CH-Bin, a binning approach that leverages the benefits of using convex hull distance for binning contigs represented by high dimensional feature vectors. We demonstrate using experimental evidence on simulated and real datasets that the use of high dimensional feature vectors to represent contigs can preserve additional information, and result in improved binning results. We further demonstrate that the convex hull distance based binning approach can be effectively utilized in binning such high dimensional data. To the best of our knowledge, this is the first time that composition information from oligonucleotides of multiple sizes has been used in representing the composition information of contigs and a convex hull distance based binning algorithm has been used to bin metagenomic contigs. The source code of CH-Bin is available at https://github.com/kdsuneraavinash/CH-Bin.}, } @article {pmid35964128, year = {2022}, author = {Crosby, WB and Pinnell, LJ and Richeson, JT and Wolfe, C and Castle, J and Loy, JD and Gow, SP and Seo, KS and Capik, SF and Woolums, AR and Morley, PS}, title = {Does swab type matter? Comparing methods for Mannheimia haemolytica recovery and upper respiratory microbiome characterization in feedlot cattle.}, journal = {Animal microbiome}, volume = {4}, number = {1}, pages = {49}, pmid = {35964128}, issn = {2524-4671}, abstract = {BACKGROUND: Bovine respiratory disease (BRD) is caused by interactions among host, environment, and pathogens. One standard method for antemortem pathogen identification in cattle with BRD is deep-guarded nasopharyngeal swabbing, which is challenging, costly, and waste generating. The objective was to compare the ability to recover Mannheimia haemolytica and compare microbial community structure using 29.5 inch (74.9 cm) deep-guarded nasopharyngeal swabs, 16 inch (40.6 cm) unguarded proctology swabs, or 6 inch (15.2 cm) unguarded nasal swabs when characterized using culture, real time-qPCR, and 16S rRNA gene sequencing. Samples for aerobic culture, qPCR, and 16S rRNA gene sequencing were collected from the upper respiratory tract of cattle 2 weeks after feedlot arrival.

RESULTS: There was high concordance of culture and qPCR results for all swab types (results for 77% and 81% of sampled animals completely across all 3 swab types for culture and qPCR respectively). Microbial communities were highly similar among samples collected with different swab types, and differences identified relative to treatment for BRD were also similar. Positive qPCR results for M. haemolytica were highly concordant (81% agreed completely), but samples collected by deep-guarded swabbing had lower amounts of Mh DNA identified (Kruskal-Wallis analysis of variance on ranks, P < 0.05; Dunn-test for pairwise comparison with Benjamini-Hochberg correction, P < 0.05) and lower frequency of positive compared to nasal and proctology swabs (McNemar's Chi-square test, P < 0.05).

CONCLUSIONS: Though differences existed among different types of swabs collected from individual cattle, nasal swabs and proctology swabs offer comparable results to deep-guarded nasopharyngeal swabs when identifying and characterizing M. haemolytica by culture, 16S rRNA gene sequencing, and qPCR.}, } @article {pmid35962889, year = {2022}, author = {Oliveira, MET and Paulino, GVB and Dos Santos Júnior, ED and da Silva Oliveira, FA and Melo, VMM and Ursulino, JS and de Aquino, TM and Shetty, AK and Landell, MF and Gitaí, DLG}, title = {Multi-omic Analysis of the Gut Microbiome in Rats with Lithium-Pilocarpine-Induced Temporal Lobe Epilepsy.}, journal = {Molecular neurobiology}, volume = {59}, number = {10}, pages = {6429-6446}, pmid = {35962889}, issn = {1559-1182}, support = {311553/2018-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 313769/2018-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 312889/2021-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 315895/2021-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Animals ; *Epilepsy/metabolism ; *Epilepsy, Temporal Lobe/metabolism ; *Gastrointestinal Microbiome ; Lithium ; Pilocarpine ; Rats ; }, abstract = {Evidence supports that the gut microbiota and bacteria-dependent metabolites influence the maintenance of epileptic brain activity. However, the alterations in the gut microbiota between epileptic versus healthy individuals are poorly understood. We used a multi-omic approach to evaluate the changes in the composition of gut metagenome as well in the fecal metabolomic profile in rats before and after being submitted to status epilepticus (SE)-induced temporal lobe epilepsy (TLE). The 16S ribosomal RNA (rRNA) sequencing of fecal samples coupled to bioinformatic analysis revealed taxonomic, compositional, and functional shifts in epileptic rats. The species richness (Chao1 index) was significantly lower in the post-TLE group, and the β-diversity analysis revealed clustering separated from the pre-TLE group. The taxonomic abundance analysis showed a significant increase of phylum Desulfobacterota and a decrease of Patescibacteria in the post-TLE group. The DESEq2 and LEfSe analysis resulted in 18 genera significantly enriched between post-TLE and pre-TLE groups at the genus level. We observed that epileptic rats present a peculiar metabolic phenotype, including a lower concentration of D-glucose and L-lactic acid and a higher concentration of L-glutamic acid and glycine. The microbiota-host metabolic correlation analysis showed that the genera differentially abundant in post-TLE rats are associated with the altered metabolites, especially the proinflammatory Desulfovibrio and Marvinbryantia, which were enriched in epileptic animals and positively correlated with these excitatory neurotransmitters and carbohydrate metabolites. Therefore, our data revealed a correlation between dysbacteriosis in epileptic animals and fecal metabolites that are known to be relevant for maintaining epileptic brain activity by enhancing chronic inflammation, an excitatory-inhibitory imbalance, and/or a metabolic disturbance. These data are promising and suggest that targeting the gut microbiota could provide a novel avenue for preventing and treating acquired epilepsy. However, the causal relationship between these microbial/metabolite components and the SRS occurrence still needs further exploration.}, } @article {pmid35962822, year = {2022}, author = {Ecco, R and Silva, LMN and Dos Santos Carneiro Lacerda, M and Dos Santos de Moraes, MV and de Oliveira, LB and de Magalhães Santos, WH and Rizotto, LS and Saraiva, LHG and Bueno, LM and Dorlass, EG and Durigon, EL and Spilki, FR and Ferreira, HL}, title = {First detection of Psittacid alphaherpesvirus 5 and coinfection with beak and feather disease virus in naturally infected captive ringneck parakeets (Psittacula krameri) in Brazil.}, journal = {Archives of virology}, volume = {167}, number = {11}, pages = {2319-2324}, pmid = {35962822}, issn = {1432-8798}, support = {2019/13198-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 403761/2020-4//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 302668/2018-7//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; 316333/2021-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {*Alphaherpesvirinae/genetics ; Animals ; *Bird Diseases ; Brazil ; *Circoviridae Infections/veterinary ; *Circovirus/genetics ; *Coinfection/veterinary ; Humans ; Oncogenic Viruses ; Parakeets ; *Psittacula ; }, abstract = {This study describes a case report in captive rose-ringed parakeets (Psittacula krameri) that developed clinical signs and eventually died after introducing new birds without quarantine. Bronchopneumonia and airsacculitis with syncytial cells associated with intranuclear inclusion bodies were found. Herpesvirus was detected in lungs and liver by PCR, and a nearly complete genome sequence of a Psittacid alphaherpesvirus 5 was obtained from the lung of a bird. Metagenomic analysis also identified beak and feather disease virus in the same samples. The study also highlights the importance of quarantine for avoiding the introduction of new diseases in captive aviaries.}, } @article {pmid35962289, year = {2022}, author = {Adhikary, R and Mandal, S and Mandal, V}, title = {Seasonal Variation Imparts the Shift in Endophytic Bacterial Community Between Mango and its Hemiparasites.}, journal = {Current microbiology}, volume = {79}, number = {9}, pages = {287}, pmid = {35962289}, issn = {1432-0991}, support = {DST-SERB/F/5369/2013-'14//Science and Engineering Research Board/ ; }, mesh = {Bacteria/genetics ; Endophytes/genetics ; *Mangifera/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Seasons ; }, abstract = {The study of community composition and community structure is important to know the ecological behaviour and community dynamics of the participating species and to understand the molecular interplay that lies between them. The community diversity greatly lies in the physiological status of the host and the environmental factors. The present study aims to explore the endophytic bacterial communities and their dynamics in the pre-flowering and post-flowering seasons in the horticulturally important Mango (Mangifera indica L.) and its hemiparasites: Loranthus parasiticus (L.) Marr. and Macrosolen colchinchinensis (Lour.) Tiegh. through a metagenomic approach using the sequence of V3 region of 16S rRNA gene. The genera Bacillus, Acinetobacter and Corynebacterium, under the phyla Firmicutes, Proteobacteria and Actinobacteria, respectively, were found to be the most abundant genera present in mango and its hemiparasites. It was found that during the post-flowering season, the twigs and leaves of mango had lesser endophytes than in other seasons while the alpha-diversity indices of the representative genera were the highest in L. parasiticus during the same seasons. However, in M. colchinchinensis, the alpha diversity was also higher in the post-flowering season similar to another hemiparasite plant L. parasiticus. The ecological, taxonomic and complex correlation studies unravelled that the hemiparasites act as the potent reservoirs of endophytic communities throughout the year and during favourable conditions, these bacterial communities disseminate to the mango plant.}, } @article {pmid35961096, year = {2022}, author = {Akaçin, İ and Ersoy, Ş and Doluca, O and Güngörmüşler, M}, title = {Comparing the significance of the utilization of next generation and third generation sequencing technologies in microbial metagenomics.}, journal = {Microbiological research}, volume = {264}, number = {}, pages = {127154}, doi = {10.1016/j.micres.2022.127154}, pmid = {35961096}, issn = {1618-0623}, mesh = {*High-Throughput Nucleotide Sequencing ; *Metagenomics ; Sequence Analysis, DNA ; Technology ; }, abstract = {Since the exploration of sequencing began in 2005, third and next-generation sequencing (TGS and NGS) technologies have fundamentally changed metagenomics research. These platforms provide essential benefits regarding speed, cost, quality and precision in the never-ending search for microorganisms' genetic material, regardless of location on earth. TGS are typically represented by technologies driven from power generation by semiconductor chips and utilization of enzymatic reactions by SOLiD/Ion Torrent PGM™ from Life Sciences, sequencing by synthesis using fluorescent labels on HiSeq/MiSeq™ from Illumina, pyrosequencing by GS FLX Titanium/GS Junior from Roche and nanopore-based sequencing by MinION™/GridION™/PromethION™ from Oxford Nanopore Technologies. The evolution of this technology enabled researchers to continually broaden their knowledge of the microbial world. This review presents a comprehensive overview of the recent literature on the utilization of both TGS and NGS technologies for the investigation of microbial metagenomics, their benefits and limitations with real-time examples of novel applications in clinical microbiology and public health, food and agriculture, energy and environment, arts and space.}, } @article {pmid35959379, year = {2022}, author = {Yan, H and Qin, Q and Yan, S and Chen, J and Yang, Y and Li, T and Gao, X and Ding, S}, title = {Comparison Of The Gut Microbiota In Different Age Groups In China.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {877914}, pmid = {35959379}, issn = {2235-2988}, mesh = {Aged ; Bacteroides ; Bacteroides fragilis ; Bacteroidetes ; *Bifidobacterium longum ; Clostridiales ; Escherichia coli/genetics ; Feces/microbiology ; Firmicutes ; *Gastrointestinal Microbiome ; Humans ; Lipopolysaccharides ; }, abstract = {Aging is now the most profound risk factor for almost all non-communicable diseases. Studies have shown that probiotics play a specific role in fighting aging. We used metagenomic sequencing to study the changes in gut microbes in different age groups and found that aging had the most significant effect on subjects' gut microbe structure. Our study divided the subjects (n=614) into two groups by using 50 years as the age cut-off point for the grouping. Compared with the younger group, several species with altered abundance and specific functional pathways were found in the older group. At the species level, the abundance of Bacteroides fragilis, Bifidobacterium longum, Clostridium bolteae, Escherichia coli, Klebsiella pneumoniae, and Parabacteroides merdae were increased in older individuals. They were positively correlated to the pathways responsible for lipopolysaccharide (LPS) biosynthesis and the degradation of short-chain fatty acids (SCFAs). On the contrary, the levels of Barnesiella intestinihominis, Megamonas funiformis, and Subdoligranulum unclassified were decreased in the older group, which negatively correlated with the above pathways (p-value<0.05). Functional prediction revealed 92 metabolic pathways enriched in the older group significantly higher than those in the younger group (p-value<0.05), especially pathways related to LPS biosynthesis and the degradation of SCFAs. Additionally, we established a simple non-invasive model of aging, nine species (Bacteroides fragilis, Barnesiella intestinihominis, Bifidobacterium longum, Clostridium bolteae, Escherichia coli, Klebsiella pneumoniae, Megamonas funiformis, Parabacteroides merdae, and Subdoligranulum unclassified) were selected to construct the model. The area under the receiver operating curve (AUC) of the model implied that supplemented probiotics might influence aging. We discuss the features of the aging microbiota that make it more amenable to pre-and probiotic interventions. We speculate these metabolic pathways of gut microbiota can be associated with the immune status and inflammation of older adults. Health interventions that promote a diverse microbiome could influence the health of older adults.}, } @article {pmid35958160, year = {2022}, author = {Sun, K and Liu, Y and Zhou, X and Yin, C and Zhang, P and Yang, Q and Mao, L and Shentu, X and Yu, X}, title = {Nanopore sequencing technology and its application in plant virus diagnostics.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {939666}, pmid = {35958160}, issn = {1664-302X}, abstract = {Plant viruses threaten crop yield and quality; thus, efficient and accurate pathogen diagnostics are critical for crop disease management and control. Recent advances in sequencing technology have revolutionized plant virus research. Metagenomics sequencing technology, represented by next-generation sequencing (NGS), has greatly enhanced the development of virus diagnostics research because of its high sensitivity, high throughput and non-sequence dependence. However, NGS-based virus identification protocols are limited by their high cost, labor intensiveness, and bulky equipment. In recent years, Oxford Nanopore Technologies and advances in third-generation sequencing technology have enabled direct, real-time sequencing of long DNA or RNA reads. Oxford Nanopore Technologies exhibit versatility in plant virus detection through their portable sequencers and flexible data analyses, thus are wildly used in plant virus surveillance, identification of new viruses, viral genome assembly, and evolution research. In this review, we discuss the applications of nanopore sequencing in plant virus diagnostics, as well as their limitations.}, } @article {pmid35958153, year = {2022}, author = {Vasudeva, G and Singh, H and Paliwal, S and Pinnaka, AK}, title = {Metagenomics: An Approach for Unraveling the Community Structure and Functional Potential of Activated Sludge of a Common Effluent Treatment Plant.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {933373}, pmid = {35958153}, issn = {1664-302X}, abstract = {The common effluent treatment plant (CETP) located at Baddi treats the industrial effluent from various industries, leading to the pooling of a diverse range of substrates and metabolites. The nutrient loading and its availability decide the balance of the microbial community and its diversity. The samples thus collected from the activated sludge (BS14) of CETP and Sirsa river (SR1) from the vicinity of CETP effluent discharge were processed for the whole metagenome analysis to reveal the microbial community and its functional potential. The taxonomic classification of the BS14 sample showed the dominance of the bacterial community with 96% of abundance, whereas the SR1 was populated by eukaryotes representing 50.4% of the community of SR1. The bacterial community of SR1 was constituted of 47.2%. The functional analysis of BS14 and SR1 with GhostKOALA against the KEGG database assigned 43.7% and 27.8% of the open reading frames (ORFs) with functions. It revealed the xenobiotic degradation modules with complete pathways along with resistance against the beta-lactams. The analysis with the comprehensive antibiotic resistance database (CARD) revealed 33 and 32 unique types of antimicrobial resistance in BS14 and SR1, respectively. Both the samples were dominated by the beta-lactam resistance genes. The carbohydrate-active enzyme (CAZy) database assigned a total of 6,611 and 2,941 active enzymes to BS14 and SR1, respectively. In contrast, the glycosyl hydrolases (GH) and glycosyltransferases (GT) class of enzymes were found to be abundant in both the samples as compared with polysaccharide lyases (PL), auxiliary activities (AA), carbohydrate esterases (CE), and carbohydrate-binding module (CBM).}, } @article {pmid35958146, year = {2022}, author = {Summers, S and Pek, YS and Vinod, DP and McDougald, D and Todd, PA and Birch, WR and Rice, SA}, title = {Bacterial biofilm colonization and succession in tropical marine waters are similar across different types of stone materials used in seawall construction.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {928877}, pmid = {35958146}, issn = {1664-302X}, abstract = {Seawalls are important in protecting coastlines from currents, erosion, sea-level rise, and flooding. They are, however, associated with reduced biodiversity, due to their steep orientation, lack of microhabitats, and the materials used in their construction. Hence, there is considerable interest in modifying seawalls to enhance the settlement and diversity of marine organisms, as microbial biofilms play a critical role facilitating algal and invertebrate colonization. We assessed how different stone materials, ranging from aluminosilicates to limestone and concrete, affect biofilm formation. Metagenomic assessment of marine microbial communities indicated no significant impact of material on microbial diversity, irrespective of the diverse surface chemistry and topography. Based on KEGG pathway analysis, surface properties appeared to influence the community composition and function during the initial stages of biofilm development, but this effect disappeared by Day 31. We conclude that marine biofilms converged over time to a generic marine biofilm, rather than the underlying stone substrata type playing a significant role in driving community composition.}, } @article {pmid35957507, year = {2022}, author = {Cheng, Z and Yu, F}, title = {Clinical Value of Metagenomic Next-Generation Sequencing in Immunocompromised Patients with Sepsis.}, journal = {Medical science monitor : international medical journal of experimental and clinical research}, volume = {28}, number = {}, pages = {e937041}, pmid = {35957507}, issn = {1643-3750}, mesh = {Bronchoalveolar Lavage Fluid ; *Cytomegalovirus Infections/diagnosis ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Immunocompromised Host ; *Pneumocystis carinii/genetics ; Prospective Studies ; *Sepsis/diagnosis ; }, abstract = {BACKGROUND Sepsis is a serious threat to human life, particularly in immunocompromised patients; hence, early diagnosis and targeted treatment are important. Metagenomic next-generation sequencing (NGS) has significant advantages over traditional diagnostic methods. This study investigated the clinical value of NGS for pathogen identification in immunocompromised patients with sepsis. MATERIAL AND METHODS From July 2020 to September 2021, 90 consecutive patients with sepsis were enrolled in this prospective study. The patients were divided into 2 groups: an immunocompromised group (n=30) and an immunocompetent group (n=60). The pathogens causing sepsis were concurrently identified using NGS and traditional diagnostic methods. The pathogen detection rates and the spectrum of pathogens identified were compared according to the method of detection and between the immunocompromised and immunocompetent groups. RESULTS Of the 90 patients, 77 (86%) were positive for 1 or more pathogens using NGS, and 50 (56%) were positive using traditional detection methods. The positivity rate of sputum and bronchoalveolar lavage fluid was higher than that of blood samples. Pneumocystis jirovecii and cytomegalovirus infections were more common in the immunocompromised group than in the immunocompetent group. CONCLUSIONS The performance of NGS in identifying pathogens for patients with sepsis is better than that of traditional detection methods, especially in immunocompromised patients. Pneumocystis jirovecii and cytomegalovirus infections are more common in immunocompromised patients.}, } @article {pmid35956844, year = {2022}, author = {Chen, Z and Liu, B and Gong, Z and Huang, H and Gong, Y and Xiao, W}, title = {Metagenomics Approach to the Intestinal Microbiome Structure and Abundance in High-Fat-Diet-Induced Hyperlipidemic Rat Fed with (-)-Epigallocatechin-3-Gallate Nanoparticles.}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {15}, pages = {}, pmid = {35956844}, issn = {1420-3049}, support = {2021NK2010//Major Science and Technology Project of Hunan Province/ ; 2021NK2016//The Key R&D Program of Hunan Province/ ; 2020NK4244//Hunan innovative province construction project Funding/ ; 21B0782//Excellent youth project of Hunan education department/ ; }, mesh = {Animals ; *Catechin/analogs & derivatives/chemistry ; Cholesterol ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; *Hyperlipidemias/drug therapy/etiology ; Metagenomics ; Molecular Docking Simulation ; *Nanoparticles/chemistry ; Rats ; Spectroscopy, Fourier Transform Infrared ; }, abstract = {The effects of nanoparticles (NPs) on microbiota homeostasis and their physiological relevance are still unclear. Herein, we compared the modulation and consequent pharmacological effects of oral administration of (-)-epigallocatechin-3-gallate (EGCG)-loaded β-cyclodextrin (β-CD) NPs (EGCG@β-CD NPs) and EGCG on gut microbiota. EGCG@β-CD NPs were prepared using self-assembly and their influence on the intestinal microbiome structure was analyzed using a metagenomics approach. The "Encapsulation efficiency (EE), particle size, polydispersity index (PDI), zeta potential" of EGCG@β-CD NPs were recorded as 98.27 ± 0.36%, 124.6 nm, 0.313 and -24.3 mV, respectively. Surface morphology of EGCG@β-CD NPs was observed as spherical. Fourier-transform infrared spectroscopy (FT-IR), X-ray diffraction (XRD) and molecular docking studies confirmed that EGCG could be well encapsulated in β-CD and formed as EGCG@β-CD NPs. After being continuously administered EGCG@β-CD NPs for 8 weeks, the serum cholesterol (TC), low-density lipoprotein cholesterol (LDL-C) and liver malondialdehyde (MDA) levels in the rats were significantly decreased, while the levels of catalase (CAT) and apolipoprotein-A1 (apo-A1) in the liver increased significantly in the hyperlipidemia model of rats, when compared to the high-fat-diet group. Furthermore, metagenomic analysis revealed that the ratio of Verrucomicrobia/Bacteroidetes was altered and Bacteroidetes decreased in the high-fat diet +200 mg/kg·bw EGCG@β-CD NPs group, while the abundance of Verrucomicrobia was significantly increased, especially Akkermansia muciniphila in rat feces. EGCG@β-CD NPs could be a promising EGCG delivery strategy to modulate the gut microbiota, enhancing its employment in the prevention of hyperlipidemia.}, } @article {pmid35956736, year = {2022}, author = {Olshannikova, SS and Malykhina, NV and Lavlinskaya, MS and Sorokin, AV and Yudin, NE and Vyshkvorkina, YM and Lukin, AN and Holyavka, MG and Artyukhov, VG}, title = {Novel Immobilized Biocatalysts Based on Cysteine Proteases Bound to 2-(4-Acetamido-2-sulfanilamide) Chitosan and Research on Their Structural Features.}, journal = {Polymers}, volume = {14}, number = {15}, pages = {}, pmid = {35956736}, issn = {2073-4360}, support = {21-74-20053//Russian Science Foundation/ ; strategic project №3//'Prioritet-2030' of Sevastopol State University/ ; 075-15-2021-1351//Ministry of Science and Higher Education of Russia/ ; }, abstract = {Briefly, 2-(4-Acetamido-2-sulfanilamide) chitosan, which is a chitosan water-soluble derivative, with molecular weights of 200, 350, and 600 kDa, was successfully synthesized. The immobilization of ficin, papain, and bromelain was carried out by complexation with these polymers. The interaction mechanism of 2-(4-acetamido-2-sulfanilamide) chitosan with bromelain, ficin, and papain was studied using FTIR spectroscopy. It was found that the hydroxy, thionyl, and amino groups of 2-(4-acetamido-2-sulfanilamide) chitosan were involved in the complexation process. Molecular docking research showed that all amino acid residues of the active site of papain formed hydrogen bonds with the immobilization matrix, while only two catalytically valuable amino acid residues took part in the H-bond formation for bromelain and ficin. The spectral and in silico data were in good agreement with the catalytic activity evaluation data. Immobilized papain was more active compared to the other immobilized proteases. Moreover, the total and specific proteolytic activity of papain immobilized on the carrier with a molecular weight of 350 kDa were higher compared to the native one due to the hyperactivation. The optimal ratio of protein content (mg × g [-1] of carrier), total activity (U × mL[-1] of solution), and specific activity (U × mg[-1] of protein) was determined for the enzymes immobilized on 2-(4-acetamido-2-sulfanilamide) chitosan with a molecular weight of 350 kDa.}, } @article {pmid35956387, year = {2022}, author = {Caudet, J and Trelis, M and Cifre, S and Soriano, JM and Rico, H and Merino-Torres, JF}, title = {Interplay between Intestinal Bacterial Communities and Unicellular Parasites in a Morbidly Obese Population: A Neglected Trinomial.}, journal = {Nutrients}, volume = {14}, number = {15}, pages = {}, pmid = {35956387}, issn = {2072-6643}, support = {2017/0486//Research Institute of La Fe University Hospital (IIS La Fe), Valencia, Spain/ ; }, mesh = {Animals ; Bacteria/genetics ; *Blastocystis ; *Diabetes Mellitus, Type 2 ; Feces/microbiology ; Humans ; *Obesity, Morbid ; *Parasites ; }, abstract = {Obesity is an epidemic causing a metabolic health crisis. Herein, the interactions between the gut prokaryotic and eukaryotic communities, metabolic comorbidities and diet were studied. Stool samples from 56 subjects, 47 with type III obesity and 9 with type II obesity and cardiovascular risk or metabolic disease, were assessed for the richness, diversity and ecology of the bacterial gut community through metagenomics, together with the study of the presence of common unicellular eukaryote parasites (Blastocystis sp., Dientamoeba fragilis and Giardia intestinalis) by qPCR. Clinical information regarding metabolic comorbidities and non-alcoholic hepatic fatty liver disease was gathered. To assess the quality of the patients' diet, each participant filled in three dietary questionnaires. The most prevalent parasite Blastocystis sp. (46.4%), together with D. fragilis (8.9%), was found to be associated with higher mean diversity indexes regarding non-colonized subjects; the opposite of that which was observed in those with G. intestinalis (16.1%). In terms of phyla relative abundance, with Blastocystis sp. and D. fragilis, very slight differences were observed; on the contrary, G. intestinalis was related to an increase in Bacteroidetes and Proteobacteria, and a decrease in Firmicutes and Actinobacteria, presenting the lowest Firmicutes/Bacteroidetes ratio. At genus level, Blastocystis sp. and/or D. fragilis was accompanied with an increase in Lactobacillus spp., and a decrease in Akkermansia spp., Bifidobacterium spp. and Escherichia spp., while G. intestinalis was associated with an increase in Bacteroides spp., and a decrease in Faecalibacterium spp., Prevotella spp. and Lactobacillus spp., and the highest Bacteroides spp./Prevotella spp. ratio. Participants with non-alcoholic hepatic fatty liver presented a higher Firmicutes/Bacteroidetes ratio, and those with type 2 diabetes displayed a significantly lower Faecalibacterium spp./Escherichia spp. ratio, due to an overrepresentation of the genus Escherichia spp. The presence of parasites was associated with variations in the richness, diversity and distribution of taxa in bacterial communities, confirming a gain in diversity associated with Blastocystis sp. and providing different functioning of the microbiota with a potential positive effect on comorbidities such as type 2 diabetes, insulin resistance and metabolic syndrome. Future basic and clinical studies should assess the beneficial or pathogenic effect of these eukaryotes on obese subjects and focus on deciphering whether they may imply a healthier metabolic profile.}, } @article {pmid35956358, year = {2022}, author = {Bischoff, SC and Nguyen, NK and Seethaler, B and Beisner, J and Kügler, P and Stefan, T}, title = {Gut Microbiota Patterns Predicting Long-Term Weight Loss Success in Individuals with Obesity Undergoing Nonsurgical Therapy.}, journal = {Nutrients}, volume = {14}, number = {15}, pages = {}, pmid = {35956358}, issn = {2072-6643}, support = {01GI1122H//Federal Ministry of Education and Research/ ; }, mesh = {Adult ; *Gastrointestinal Microbiome ; Humans ; Obesity/microbiology/therapy ; Prospective Studies ; Weight Loss ; *Weight Reduction Programs ; }, abstract = {Background: The long-term success of nonsurgical weight reduction programs is variable; thus, predictors of outcome are of major interest. We hypothesized that the intestinal microbiota known to be linked with diet and obesity contain such predictive elements. Methods: Metagenome analysis by shotgun sequencing of stool DNA was performed in a cohort of 15 adults with obesity (mean body mass index 43.1 kg/m[2]) who underwent a one-year multidisciplinary weight loss program and another year of follow-up. Eight individuals were persistently successful (mean relative weight loss 18.2%), and seven individuals were not successful (0.2%). The relationship between relative abundancies of bacterial genera/species and changes in relative weight loss or body mass index was studied using three different statistical modeling methods. Results: When combining the predictor variables selected by the applied statistical modeling, we identified seven bacterial genera and eight bacterial species as candidates for predicting success of weight loss. By classification of relative weight-loss predictions for each patient using 2-5 term models, 13 or 14 out of 15 individuals were predicted correctly. Conclusions: Our data strongly suggest that gut microbiota patterns allow individual prediction of long-term weight loss success. Prediction accuracy seems to be high but needs confirmation by larger prospective trials.}, } @article {pmid35955951, year = {2022}, author = {Anzalone, A and Mosca, A and Dimaria, G and Nicotra, D and Tessitori, M and Privitera, GF and Pulvirenti, A and Leonardi, C and Catara, V}, title = {Soil and Soilless Tomato Cultivation Promote Different Microbial Communities That Provide New Models for Future Crop Interventions.}, journal = {International journal of molecular sciences}, volume = {23}, number = {15}, pages = {}, pmid = {35955951}, issn = {1422-0067}, support = {"Investigation of phytopathological problems of the main Sicilian pro-ductive contexts and eco-sustainable defense strategies_ (PIA.CE.RI. 2020-2022)//University of Catania/ ; WATER4AGRIFOOD", n. ARS01_00825//PON "RICERCA E INNOVAZIONE" 2014 - 2020, Azione II/ ; }, mesh = {*Ascomycota ; Bacteria/genetics ; *Solanum lycopersicum/microbiology ; *Microbiota ; Plant Roots/microbiology ; Rhizosphere ; Soil ; Soil Microbiology ; }, abstract = {The cultivation of soilless tomato in greenhouses has increased considerably, but little is known about the assembly of the root microbiome compared to plants grown in soil. To obtain such information, we constructed an assay in which we traced the bacterial and fungal communities by amplicon-based metagenomics during the cultivation chain from nursery to greenhouse. In the greenhouse, the plants were transplanted either into agricultural soil or into coconut fiber bags (soilless). At the phylum level, bacterial and fungal communities were primarily constituted in all microhabitats by Proteobacteria and Ascomycota, respectively. The results showed that the tomato rhizosphere microbiome was shaped by the substrate or soil in which the plants were grown. The microbiome was different particularly in terms of the bacterial communities. In agriculture, enrichment has been observed in putative biological control bacteria of the genera Pseudomonas and Bacillus and in potential phytopathogenic fungi. Overall, the study describes the different shaping of microbial communities in the two cultivation methods.}, } @article {pmid35954712, year = {2022}, author = {Laue, HE and Shen, Y and Bloomquist, TR and Wu, H and Brennan, KJM and Cassoulet, R and Wilkie, E and Gillet, V and Desautels, AS and Abdelouahab, N and Bellenger, JP and Burris, HH and Coull, BA and Weisskopf, MG and Zhang, W and Takser, L and Baccarelli, AA}, title = {In Utero Exposure to Caffeine and Acetaminophen, the Gut Microbiome, and Neurodevelopmental Outcomes: A Prospective Birth Cohort Study.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {15}, pages = {}, pmid = {35954712}, issn = {1660-4601}, support = {R01ES027845/ES/NIEHS NIH HHS/United States ; P30 ES000002/ES/NIEHS NIH HHS/United States ; P30ES009089/ES/NIEHS NIH HHS/United States ; P30 ES013508/ES/NIEHS NIH HHS/United States ; T32 CA134286/CA/NCI NIH HHS/United States ; R21ES02841/ES/NIEHS NIH HHS/United States ; K23ES022242/ES/NIEHS NIH HHS/United States ; P30 ES009089/ES/NIEHS NIH HHS/United States ; }, mesh = {Acetaminophen/adverse effects ; Bacteria/genetics ; Birth Cohort ; Caffeine/adverse effects ; Cohort Studies ; Female ; *Gastrointestinal Microbiome ; Humans ; Pregnancy ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Pregnant individuals are exposed to acetaminophen and caffeine, but it is unknown how these exposures interact with the developing gut microbiome. We aimed to determine whether acetaminophen and/or caffeine relate to the childhood gut microbiome and whether features of the gut microbiome alter the relationship between acetaminophen/caffeine and neurodevelopment. Forty-nine and 85 participants provided meconium and stool samples at 6-7, respectively, for exposure and microbiome assessment. Fecal acetaminophen and caffeine concentrations were quantified, and fecal DNA underwent metagenomic sequencing. Caregivers and study staff assessed the participants' motor and cognitive development using standardized scales. Prenatal exposures had stronger associations with the childhood microbiome than concurrent exposures. Prenatal acetaminophen exposure was associated with a trend of lower gut bacterial diversity in childhood [β = -0.17 Shannon Index, 95% CI: (-0.31, -0.04)] and was marginally associated with differences in the relative abundances of features of the gut microbiome at the phylum (Firmicutes, Actinobacteria) and gene pathway levels. Among the participants with a higher relative abundance of Proteobacteria, prenatal exposure to acetaminophen and caffeine was associated with lower scores on WISC-IV subscales. Acetaminophen during bacterial colonization of the naïve gut is associated with lasting alterations in childhood microbiome composition. Future studies may inform our understanding of downstream health effects.}, } @article {pmid35954075, year = {2022}, author = {Zhao, F and Wei, Z and Zhou, G and Kristiansen, K and Wang, C}, title = {Effects of Different Storage Temperatures on Bacterial Communities and Functional Potential in Pork Meat.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {15}, pages = {}, pmid = {35954075}, issn = {2304-8158}, support = {32001721//National Natural Science Foundation of China/ ; CARS-35//China Agricultural Research System of the Ministry of Agriculture and Rural Affairs/ ; PAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; }, abstract = {Storage temperature is considered one of the most important factors that affect the microbial spoilage of fresh meat. Chilling and superchilling are the most popular storage techniques on the market, but during transportation, the temperature may reach 10 °C and may even reach room temperature during local retail storage. In the present study, we stored fresh pork meat at different temperatures, -2 °C, 4 °C, 10 °C, and 25 °C. The composition and functional potential of fresh or spoiled meat resident microbes were analyzed based on 16S rRNA gene amplicon sequencing. The microbial composition exhibited high similarity between pork meat stored at -2 °C and 4 °C, with Pseudomonads and Brochothrix being the dominant taxa. Acinetobacter sp., Myroides sp., and Kurthia sp. were markers for spoiled pork meat stored at 25 °C. Both psychrophilic and mesophilic bacteria were observed to grow under a storage temperature of 10 °C, but the overall composition and functional potential based on Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were found to be similar to that of meat stored at room temperature. Our results broaden the knowledge of possible microbial changes in pork meat during storage, transportation, or retail.}, } @article {pmid35953888, year = {2022}, author = {Simpson, JB and Sekela, JJ and Graboski, AL and Borlandelli, VB and Bivins, MM and Barker, NK and Sorgen, AA and Mordant, AL and Johnson, RL and Bhatt, AP and Fodor, AA and Herring, LE and Overkleeft, H and Lee, JR and Redinbo, MR}, title = {Metagenomics combined with activity-based proteomics point to gut bacterial enzymes that reactivate mycophenolate.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2107289}, pmid = {35953888}, issn = {1949-0984}, support = {T32 GM135095/GM/NIGMS NIH HHS/United States ; K23 AI124464/AI/NIAID NIH HHS/United States ; T32 DK007750/DK/NIDDK NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; P30 CA016086/CA/NCI NIH HHS/United States ; R01 GM137286/GM/NIGMS NIH HHS/United States ; P30 DK056350/DK/NIDDK NIH HHS/United States ; }, mesh = {Flavin Mononucleotide ; *Gastrointestinal Microbiome/physiology ; Glucuronides ; Humans ; Immunosuppressive Agents ; Mycophenolic Acid/therapeutic use ; Proteomics ; }, abstract = {Mycophenolate mofetil (MMF) is an important immunosuppressant prodrug prescribed to prevent organ transplant rejection and to treat autoimmune diseases. MMF usage, however, is limited by severe gastrointestinal toxicity that is observed in approximately 45% of MMF recipients. The active form of the drug, mycophenolic acid (MPA), undergoes extensive enterohepatic recirculation by bacterial β-glucuronidase (GUS) enzymes, which reactivate MPA from mycophenolate glucuronide (MPAG) within the gastrointestinal tract. GUS enzymes demonstrate distinct substrate preferences based on their structural features, and gut microbial GUS enzymes that reactivate MPA have not been identified. Here, we compare the fecal microbiomes of transplant recipients receiving MMF to healthy individuals using shotgun metagenomic sequencing. We find that neither microbial composition nor the presence of specific structural classes of GUS genes are sufficient to explain the differences in MPA reactivation measured between fecal samples from the two cohorts. We next employed a GUS-specific activity-based chemical probe and targeted metaproteomics to identify and quantify the GUS proteins present in the human fecal samples. The identification of specific GUS enzymes was improved by using the metagenomics data collected from the fecal samples. We found that the presence of GUS enzymes that bind the flavin mononucleotide (FMN) is significantly correlated with efficient MPA reactivation. Furthermore, structural analysis identified motifs unique to these FMN-binding GUS enzymes that provide molecular support for their ability to process this drug glucuronide. These results indicate that FMN-binding GUS enzymes may be responsible for reactivation of MPA and could be a driving force behind MPA-induced GI toxicity.}, } @article {pmid35953830, year = {2022}, author = {Qiu, T and Huo, L and Guo, Y and Gao, M and Wang, G and Hu, D and Li, C and Wang, Z and Liu, G and Wang, X}, title = {Metagenomic assembly reveals hosts and mobility of common antibiotic resistome in animal manure and commercial compost.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {42}, pmid = {35953830}, issn = {2524-6372}, support = {6222013//Natural Science Foundation of Beijing Municipality/ ; KJCX20210424//Special Program for Creative Ability Foundation of BAAFS/ ; BAIC04-2019//Beijing Agriculture Innovation Consortium/ ; }, abstract = {BACKGROUND: Antibiotics and antibiotic resistance genes (ARGs) used in intensive animal farming threaten human health worldwide; however, the common resistome, ARG mobility, and ARG host composition in different animal manures and mixed manure composts remain unclear. In the present study, metagenomic assembly and cross-sample mapping were used to comprehensively decipher the common resistome and its potential mobility and hosts in animal manure and composts.

RESULTS: In total, 201 ARGs were shared among different animal (layer, broiler, swine, beef cow, and dairy cow) manures and accounted for 86-99% of total relative abundance of ARGs. Except for multidrug, sulfonamide, and trimethoprim resistance genes, the relative abundance of most ARGs in composts was significantly lower than that in animal manure. Procrustes analysis indicated that antibiotic residues positively correlated with ARG composition in manure but not in composts. More than 75% ARG subtypes were shared between plasmids and chromosomes in our samples. Transposases could play a pivotal role in mediating the transfer of ARGs between different phyla in animal manure and composting. Cross-sample mapping to contigs carrying ARGs showed that the hosts of common resistome in manure had preference on animal species, and the dominant genus of ARG host shifted from Enterococcus in manure to Pseudomonas in composts. The broad host range and linking with diverse mobile genetic elements (MGEs) were two key factors for ARGs, such as sul1 and aadA, which could survive during composting. The multidrug resistance genes represented the dominant ARGs in pathogenic antibiotic-resistant bacteria in manure but could be effectively controlled by composting.

CONCLUSIONS: Our experiments revealed the common resistome in animal manure, classified and relative quantified the ARG hosts, and assessed the mobility of ARGs. Composting can mitigate ARGs in animal manure by altering the bacterial hosts; however, persistent ARGs can escape from the removal because of diverse host range and MGEs. Our findings provide an overall background for source tracking, risk assessment, and control of livestock ARGs.}, } @article {pmid35953677, year = {2023}, author = {Grisnik, M and Grinath, JB and Munafo, JP and Walker, DM}, title = {Functional Redundancy in Bat Microbial Assemblage in the Presence of the White Nose Pathogen.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {713-726}, pmid = {35953677}, issn = {1432-184X}, support = {1016031//National Institute of Food and Agriculture/ ; 32801-00803//Tennessee Wildlife Resources Agency/ ; }, mesh = {Animals ; *Chiroptera/microbiology ; Nose/microbiology ; Antifungal Agents ; Skin/microbiology ; Bacteria/genetics ; }, abstract = {Understanding how host-associated microbial assemblages respond to pathogen invasion has implications for host health. Until recently, most investigations have focused on understanding the taxonomic composition of these assemblages. However, recent studies have suggested that microbial assemblage taxonomic composition is decoupled from its function, with assemblages being taxonomically varied but functionally constrained. The objective of this investigation was to understand how the Tri-colored bat, Perimyotis subflavus cutaneous microbial assemblage responds to fungal pathogen invasion within a functional context. We hypothesized that at a broad scale (e.g., KEGG pathways), there will be no difference in the functional assemblages between the white nose pathogen, Pseudogymnoascus destructans, positive and negative bats; and this pattern will be driven by the functional redundancy of bacterial taxa. At finer scales (e.g., gene models), we postulate differences in function attributed to interactions between bacteria and P. destructans, resulting in the production of antifungal metabolites. To test this, we used a combination of shotgun metagenomic and amplicon sequencing to characterize the bat cutaneous microbial assemblage in the presence/absence of P. destructans. Results showed that while there was a shift in taxonomic assemblage composition between P. destructans positive and negative bats, there was little overall difference in microbial function. Functional redundancy across bacterial taxa was clear at a broad-scale; however, both redundancy and variation in bacterial capability related to defense against pathogens was evident at finer scales. While functionality of the microbial assemblage was largely conserved in relation to P. destructans, the roles of particular functional pathways in resistance to fungal pathogens require further attention.}, } @article {pmid35953616, year = {2023}, author = {Teker, HT and Ceylani, T}, title = {Intermittent fasting supports the balance of the gut microbiota composition.}, journal = {International microbiology : the official journal of the Spanish Society for Microbiology}, volume = {26}, number = {1}, pages = {51-57}, pmid = {35953616}, issn = {1618-1905}, mesh = {Rats ; Animals ; Male ; *Gastrointestinal Microbiome ; Intermittent Fasting ; Rats, Wistar ; Intestines/microbiology ; Bacteria/genetics ; }, abstract = {There is a growing body of detailed research demonstrating that intermittent fasting is essentially a cleansing activity in terms of health. Especially since its applications that exceed 16 h trigger autophagy, it continues its effect on all tissue and organ systems after the regeneration movement that starts at the cellular level. Similarly, it continues to be better understood with each passing day that the gut microbiota (GM) has many positive effects on all tissue and organ systems. Although the GM is affected by many different parameters, dietary habits are reported to be the most effective factor. Therefore, it is important to investigate the effects of different preferred fasting practices on the GM, which has numerous health benefits. Pointing out this situation, this study aims to determine the effects of 18-h intermittent fasting for 5 weeks on the shaping of GM. A 12-month-old male Wistar rat was chosen as the model organism in the study. At the end of the application, the metagenome was applied to the cecum content of the intestinal tissue collected from the sacrificed animals. Intermittent fasting practice led to an increase in alpha diversity, which expresses a significant bacterial diversity, the stabilization of Firmicutes and Bacteroidetes ratios (F/B), and the reshaping of the values with the highest prevalence in all stages of the classification, especially in the family, genus, and species care. Analysis results showed that the preferred intermittent fasting program helps balance the GM composition. This study is an important example showing the strong positive link between intermittent fasting and GM.}, } @article {pmid35953094, year = {2023}, author = {Kong, C and Liang, L and Liu, G and Du, L and Yang, Y and Liu, J and Shi, D and Li, X and Ma, Y}, title = {Integrated metagenomic and metabolomic analysis reveals distinct gut-microbiome-derived phenotypes in early-onset colorectal cancer.}, journal = {Gut}, volume = {72}, number = {6}, pages = {1129-1142}, doi = {10.1136/gutjnl-2022-327156}, pmid = {35953094}, issn = {1468-3288}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/diagnosis ; *Microbiota ; Phenotype ; Choline ; }, abstract = {OBJECTIVE: The incidence of early-onset colorectal cancer (EO-CRC) is steadily increasing. Here, we aimed to characterise the interactions between gut microbiome, metabolites and microbial enzymes in EO-CRC patients and evaluate their potential as non-invasive biomarkers for EO-CRC.

DESIGN: We performed metagenomic and metabolomic analyses, identified multiomics markers and constructed CRC classifiers for the discovery cohort with 130 late-onset CRC (LO-CRC), 114 EO-CRC subjects and age-matched healthy controls (97 LO-Control and 100 EO-Control). An independent cohort of 38 LO-CRC, 24 EO-CRC, 22 LO-Controls and 24 EO-Controls was analysed to validate the results.

RESULTS: Compared with controls, reduced alpha-diversity was apparent in both, LO-CRC and EO-CRC subjects. Although common variations existed, integrative analyses identified distinct microbiome-metabolome associations in LO-CRC and EO-CRC. Fusobacterium nucleatum enrichment and short-chain fatty acid depletion, including reduced microbial GABA biosynthesis and a shift in acetate/acetaldehyde metabolism towards acetyl-CoA production characterises LO-CRC. In comparison, multiomics signatures of EO-CRC tended to be associated with enriched Flavonifractor plauti and increased tryptophan, bile acid and choline metabolism. Notably, elevated red meat intake-related species, choline metabolites and KEGG orthology (KO) pldB and cbh gene axis may be potential tumour stimulators in EO-CRC. The predictive model based on metagenomic, metabolomic and KO gene markers achieved a powerful classification performance for distinguishing EO-CRC from controls.

CONCLUSION: Our large-sample multiomics data suggest that altered microbiome-metabolome interplay helps explain the pathogenesis of EO-CRC and LO-CRC. The potential of microbiome-derived biomarkers as promising non-invasive tools could be used for the accurate detection and distinction of individuals with EO-CRC.}, } @article {pmid35952646, year = {2022}, author = {Lu, H and Xu, X and Fu, D and Gu, Y and Fan, R and Yi, H and He, X and Wang, C and Ouyang, B and Zhao, P and Wang, L and Xu, P and Cheng, S and Wang, Z and Zou, D and Han, L and Zhao, W}, title = {Butyrate-producing Eubacterium rectale suppresses lymphomagenesis by alleviating the TNF-induced TLR4/MyD88/NF-κB axis.}, journal = {Cell host & microbe}, volume = {30}, number = {8}, pages = {1139-1150.e7}, doi = {10.1016/j.chom.2022.07.003}, pmid = {35952646}, issn = {1934-6069}, mesh = {Animals ; Butyrates ; Eubacterium/metabolism ; Humans ; Inflammation/drug therapy ; Mice ; *Myeloid Differentiation Factor 88/genetics/metabolism ; *NF-kappa B/metabolism ; Toll-Like Receptor 4/genetics/metabolism ; }, abstract = {Microbiota-induced tumorigenesis is well established in solid tumors of the gastrointestinal tract but rarely explored in hematologic malignancies. To determine the role of gut microbiota in lymphoma progression, we performed metagenomic sequencing on human primary gastrointestinal B cell lymphomas. We identified a distinct microbiota profile of intestinal lymphoma, with significantly decreased symbiotic microbes, particularly the genus Eubacterium and notably butyrate-producing Eubacterium rectale. Transfer of E. rectale-deficit microbiota of intestinal lymphoma patients to mice caused inflammation and tumor necrosis factor (TNF) production. Conversely, E. rectale treatment reduced TNF levels and the incidence of lymphoma in sensitized Eμ-Myc mice. Moreover, lipopolysaccharide from the resident microbiota of lymphoma patients and mice synergizes with TNF signaling and reinforces the NF-κB pathway via the MyD88-dependent TLR4 signaling, amalgamating in enhanced intestinal B cell survival and proliferation. These findings reveal a mechanism of inflammation-associated lymphomagenesis and a potential clinical rationale for therapeutic targeting of gut microbiota.}, } @article {pmid35952432, year = {2022}, author = {He, J and Luo, T and Shi, Z and Angelidaki, I and Zhang, S and Luo, G}, title = {Microbial shifts in anaerobic digestion towards phenol inhibition with and without hydrochar as revealed by metagenomic binning.}, journal = {Journal of hazardous materials}, volume = {440}, number = {}, pages = {129718}, doi = {10.1016/j.jhazmat.2022.129718}, pmid = {35952432}, issn = {1873-3336}, mesh = {Anaerobiosis ; Bioreactors ; Glucose ; Metagenome ; Methane ; *Phenol ; Phenols ; *Sewage ; }, abstract = {The inhibition of anaerobic digestion (AD) by phenolic compounds is an obstacle to the efficient treatment of organic wastes. Besides, hydrochar produced from hydrothermal liquefaction of biomass has been previously reported to enhance AD. The present study aimed to provide deep insights into the microbial shifts at the species level to phenol (0-1.5 g/L) inhibition in AD of glucose with and without hydrochar by metagenomic analysis. Phenol higher than 1 g/L had severe inhibition on both the amount and rate of methane production in control experiments, while hydrochar significantly enhanced methane production, especially at phenol 1 g/L and 1.5 g/L. From metagenomic analysis, 78 High-quality metagenome-assembled genomes (MAGs) were obtained. Principal components analysis showed that the microbial communities were shifted when phenol concentration was increased to 0.25 g/L in control experiments and 1 g/L in hydrochar experiments. In control experiments, no MAGs involved in acetogenesis were found at phenol 1.5 g/L and Methanothrix sp.FDU243 was also inhibited. However, hydrochar resulted in the maintenance of several MAGs involved in acetogenesis and Methanothrix sp.FDU243 even at phenol 1.5 g/L, ensuring a persistent methane production. Furthermore, 6 phenol-degrading MAGs were identified, shifting dependent on the concentrations of phenol and the presence of hydrochar.}, } @article {pmid35951476, year = {2022}, author = {Bhardwaj, K and Garg, A and Pandey, AD and Sharma, H and Kumar, M and Vrati, S}, title = {Insights into the human gut virome by sampling a population from the Indian subcontinent.}, journal = {The Journal of general virology}, volume = {103}, number = {8}, pages = {}, doi = {10.1099/jgv.0.001774}, pmid = {35951476}, issn = {1465-2099}, mesh = {Animals ; *Bacteriophages ; Genome, Viral ; Humans ; Metagenomics ; Virome/genetics ; *Viruses/genetics ; }, abstract = {Gut virome plays an important role in human physiology but remains poorly understood. This study reports an investigation of the human gut DNA-virome of a previously unexplored ethnic population through metagenomics of faecal samples collected from individuals residing in Northern India. Analysis shows that, similar to the populations investigated earlier, majority of the identified virome belongs to bacteriophages and a smaller fraction (<20 %) consists of viruses that infect animals, archaea, protists, multiple domains or plants. However, crAss-like phages, in this population, are dominated by the genera VI, VII and VIII. Interestingly, it also reveals the presence of a virus family, Sphaerolipoviridae, which has not been detected in the human gut earlier. Viral families, Siphoviridae, Myoviridae, Podoviridae, Microviridae, Herelleviridae and Phycodnaviridae are detected in all of the analysed individuals, which supports the existence of a core virome. Lysogeny-associated genes were found in less than 10 % of the assembled genomes and a negative correlation was observed in the richness of bacterial and free-viral species, suggesting that the dominant lifestyle of gut phage is not lysogenic. This is in contrast to some of the earlier studies. Further, several hundred high-quality viral genomes were recovered. Detailed characterization of these genomes would be useful for understanding the biology of these viruses and their significance in human physiology.}, } @article {pmid35951369, year = {2022}, author = {Qiao, W and Liu, G and Li, M and Su, X and Lu, L and Ye, S and Wu, J and Edwards, EA and Jiang, J}, title = {Complete Reductive Dechlorination of 4-Hydroxy-chlorothalonil by Dehalogenimonas Populations.}, journal = {Environmental science & technology}, volume = {56}, number = {17}, pages = {12237-12246}, doi = {10.1021/acs.est.2c02574}, pmid = {35951369}, issn = {1520-5851}, mesh = {Biodegradation, Environmental ; Biotransformation ; *Chloroflexi/metabolism ; Nitriles ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Chlorothalonil (2,4,5,6-tetrachloroisophthalonitrile, TePN) is one of the most widely used fungicides all over the world. Its major environmental transformation product 4-hydroxy-chlorothalonil (4-hydroxy-2,5,6-trichloroisophthalonitrile, 4-OH-TPN) is more persistent, mobile, and toxic and is frequently detected at a higher concentration in various habitats compared to its parent compound TePN. Further microbial transformation of 4-OH-TPN has never been reported. In this study, we demonstrated that 4-OH-TPN underwent complete microbial reductive dehalogenation to 4-hydroxy-isophthalonitrile via 4-hydroxy-dichloroisophthalonitrile and 4-hydroxy-monochloroisophthalonitrile. 16S rRNA gene amplicon sequencing demonstrated that Dehalogenimonas species was enriched from 6% to 17-22% after reductive dechlorination of 77.24 μmol of 4-OH-TPN. Meanwhile, Dehalogenimonas copies increased by one order of magnitude and obtained a yield of 1.78 ± 1.47 × 10[8] cells per μmol Cl[-] released (N = 6), indicating that 4-OH-TPN served as the terminal electron acceptor for organohalide respiration of Dehalogenimonas species. A draft genome of Dehalogenimonas species was assembled through metagenomic sequencing, which harbors 30 putative reductive dehalogenase genes. Syntrophobacter, Acetobacterium, and Methanosarcina spp. were found to be the major non-dechlorinating populations in the microbial community, who might play important roles in the reductive dechlorination of 4-OH-TPN by the Dehalogenimonas species. This study first reports that Dehalogenimonas sp. can also respire on the seemingly dead-end product of TePN, paving the way to complete biotransformation of the widely present TePN and broadening the substrate spectrum of Dehalogenimonas sp. to polychlorinated hydroxy-benzonitrile.}, } @article {pmid35951007, year = {2022}, author = {Natola, L and Seneviratne, SS and Irwin, D}, title = {Population genomics of an emergent tri-species hybrid zone.}, journal = {Molecular ecology}, volume = {31}, number = {20}, pages = {5356-5367}, doi = {10.1111/mec.16650}, pmid = {35951007}, issn = {1365-294X}, mesh = {Animals ; Birds ; British Columbia ; *Gene Flow ; Genome/genetics ; Hybridization, Genetic ; *Metagenomics ; }, abstract = {Isolating barriers that drive speciation are commonly studied in the context of two-species hybrid zones. There is, however, evidence that more complex introgressive relationships are common in nature. Here, we use field observations and genomic analysis, including the sequencing and assembly of a novel reference genome, to study an emergent hybrid zone involving two colliding hybrid zones of three woodpecker species: red-breasted, red-naped, and yellow-bellied sapsuckers (Sphyrapicus ruber, S. nuchalis, and S. varius). Surveys of the area surrounding Prince George, British Columbia, Canada, show that all three species are sympatric, and Genotyping-by-Sequencing identifies hybrids from each species pair and birds with ancestry from all three species. Observations of phenotypes and genotypes of mated pairs provide evidence for assortative mating, though there is some heterospecific pairing. Hybridization is more extensive in this tri-species hybrid zone than in two di-species hybrid zones. However, there is no evidence of a hybrid swarm and admixture is constrained to contact zones, so we classify this region as a tension zone and invoke selection against hybrids as a likely mechanism maintaining species boundaries. Analysis of sapsucker age classes does not show disadvantages in hybrid survival to adulthood, so we speculate the selection upholding the tension zone may involve hybrid fecundity. Gene flow among all sapsuckers in di-species hybrid zones suggests introgression probably occurred before the formation of this tri-species hybrid zone, and might result from bridge hybridization, vagrancies, or other three-species interactions.}, } @article {pmid35950875, year = {2022}, author = {Brazelton, WJ and McGonigle, JM and Motamedi, S and Pendleton, HL and Twing, KI and Miller, BC and Lowe, WJ and Hoffman, AM and Prator, CA and Chadwick, GL and Anderson, RE and Thomas, E and Butterfield, DA and Aquino, KA and Früh-Green, GL and Schrenk, MO and Lang, SQ}, title = {Metabolic Strategies Shared by Basement Residents of the Lost City Hydrothermal Field.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {17}, pages = {e0092922}, pmid = {35950875}, issn = {1098-5336}, mesh = {Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; *Ecosystem ; Formates/metabolism ; Hydrogen/metabolism ; *Hydrothermal Vents/microbiology ; Sulfates/metabolism ; }, abstract = {Alkaline fluids venting from chimneys of the Lost City hydrothermal field flow from a potentially vast microbial habitat within the seafloor where energy and organic molecules are released by chemical reactions within rocks uplifted from Earth's mantle. In this study, we investigated hydrothermal fluids venting from Lost City chimneys as windows into subseafloor environments where the products of geochemical reactions, such as molecular hydrogen (H2), formate, and methane, may be the only available sources of energy for biological activity. Our deep sequencing of metagenomes and metatranscriptomes from these hydrothermal fluids revealed a few key species of archaea and bacteria that are likely to play critical roles in the subseafloor microbial ecosystem. We identified a population of Thermodesulfovibrionales (belonging to phylum Nitrospirota) as a prevalent sulfate-reducing bacterium that may be responsible for much of the consumption of H2 and sulfate in Lost City fluids. Metagenome-assembled genomes (MAGs) classified as Methanosarcinaceae and Candidatus Bipolaricaulota were also recovered from venting fluids and represent potential methanogenic and acetogenic members of the subseafloor ecosystem. These genomes share novel hydrogenases and formate dehydrogenase-like sequences that may be unique to hydrothermal environments where H2 and formate are much more abundant than carbon dioxide. The results of this study include multiple examples of metabolic strategies that appear to be advantageous in hydrothermal and subsurface alkaline environments where energy and carbon are provided by geochemical reactions. IMPORTANCE The Lost City hydrothermal field is an iconic example of a microbial ecosystem fueled by energy and carbon from Earth's mantle. Uplift of mantle rocks into the seafloor can trigger a process known as serpentinization that releases molecular hydrogen (H2) and creates unusual environmental conditions where simple organic carbon molecules are more stable than dissolved inorganic carbon. This study provides an initial glimpse into the kinds of microbes that live deep within the seafloor where serpentinization takes place, by sampling hydrothermal fluids exiting from the Lost City chimneys. The metabolic strategies that these microbes appear to be using are also shared by microbes that inhabit other sites of serpentinization, including continental subsurface environments and natural springs. Therefore, the results of this study contribute to a broader, interdisciplinary effort to understand the general principles and mechanisms by which serpentinization-associated processes can support life on Earth and perhaps other worlds.}, } @article {pmid35950868, year = {2022}, author = {Cremer, F and Serra Moncadas, L and Andrei, AS}, title = {Complete Genome Sequence from an Uncultivated Freshwater Elusimicrobiota Lineage.}, journal = {Microbiology resource announcements}, volume = {11}, number = {9}, pages = {e0042622}, pmid = {35950868}, issn = {2576-098X}, support = {193240//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; 193240//Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (SNF)/ ; }, abstract = {Here, we report the first complete genome of an uncultivated freshwater Elusimicrobiota organism recovered from a nonaxenic Amoebozoa sp. culture. The chromosome was obtained from a metagenomic long-read sequencing run and was assembled as a circular element at a 47× coverage, a length of 3.8 Mbp, and a G+C content of 68.6%.}, } @article {pmid35950862, year = {2022}, author = {Ortiz Sanjuán, JM and Manzanilla, EG and Cabrera-Rubio, R and Crispie, F and Cotter, PD and Garrido, JJ and Argüello, H}, title = {Using Shotgun Sequencing to Describe the Changes Induced by In-Feed Zinc Oxide and Apramycin in the Microbiomes of Pigs One Week Postweaning.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0159722}, pmid = {35950862}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Diarrhea/microbiology ; Escherichia coli ; *Gastrointestinal Microbiome ; Nebramycin/analogs & derivatives ; Swine ; *Zinc Oxide/pharmacology/therapeutic use ; }, abstract = {Postweaning diarrhea (PWD) is a relevant problem associated with early weaning on pig farms. For decades, in-feed antibiotics and therapeutic zinc oxide (ZnO) have been widely used to prevent PWD in piglets. The European Union is banning both strategies in 2022 due to antimicrobial resistance and environmental contamination concerns, respectively. Understanding the effects of these products on the pig microbiome is crucial for correcting potential microbial disbalances that would prompt PWD. Using shotgun sequencing, three trials were carried out to explore the impact of in-feed apramycin and ZnO, combined with different farm hygiene protocols, on the fecal microbiomes of piglets 7 days postweaning. In trial 1, 28-day-old piglets were allocated to one of three groups: control diet (Ct), Ct + ZnO (Zn), and Ct + apramycin (Ab). In trials 2 and 3, piglets were allocated to the same treatments, but the trials also included different cleaning protocols, achieving different hygiene levels. In-feed treatments impacted the richness, diversity, and relative abundance of the piglets' microbiome more than hygiene. Pigs in the Ct group showed higher species richness than pigs in the Ab and Zn groups. A clustering analysis evidenced a link between Enterobacteriaceae in the Ct group; Lactobacillaceae and Veillonellaceae mainly in the Ct group; and Bacteroidaceae, Ruminococcaceae, Oscillospiraceae, Acidaminococcaceae, and Lactobacillaceae in the Ab and Zn groups. Functional data analysis revealed a higher abundance of virulence genes in the Ct group microbiomes and heavy metal and antimicrobial resistance-related functions in the Zn treatment group. The results demonstrate that alternatives to Ab and ZnO should balance the microbial abundance and stimulate the growth of commensals to outcompete potential pathogens. IMPORTANCE Weaning is a critical period for piglets, during which potentially harmful bacteria such as Escherichia coli can increase in abundance in the intestine, creating digestive problems and diarrhea. In-feed antibiotics, the most frequent administration route for antibiotics in livestock, and therapeutic doses of zinc oxide (ZnO) help to control diarrhea but prompt secondary problems such as antimicrobial resistance and soil pollution from heavy metals. Understanding how these strategies impact the gut microbiota is crucial for establishing health biomarkers and designing successful replacement strategies. Using shotgun sequencing, this study compares the microbiota of pigs after early weaning when treated with in-feed antibiotics, ZnO, or treatment-free diets to describe differences that could define the susceptibility to infections, providing the basis for future research on improving intestinal resilience through microbiota-based strategies.}, } @article {pmid35950838, year = {2022}, author = {Nassar, M and Rogers, AB and Talo', F and Sanchez, S and Shafique, Z and Finn, RD and McEntyre, J}, title = {A machine learning framework for discovery and enrichment of metagenomics metadata from open access publications.}, journal = {GigaScience}, volume = {11}, number = {}, pages = {}, pmid = {35950838}, issn = {2047-217X}, support = {221523/WT_/Wellcome Trust/United Kingdom ; BB/S009043/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Access to Information ; Cross-Sectional Studies ; Longitudinal Studies ; Machine Learning ; *Metadata ; *Metagenomics/methods ; }, abstract = {Metagenomics is a culture-independent method for studying the microbes inhabiting a particular environment. Comparing the composition of samples (functionally/taxonomically), either from a longitudinal study or cross-sectional studies, can provide clues into how the microbiota has adapted to the environment. However, a recurring challenge, especially when comparing results between independent studies, is that key metadata about the sample and molecular methods used to extract and sequence the genetic material are often missing from sequence records, making it difficult to account for confounding factors. Nevertheless, these missing metadata may be found in the narrative of publications describing the research. Here, we describe a machine learning framework that automatically extracts essential metadata for a wide range of metagenomics studies from the literature contained in Europe PMC. This framework has enabled the extraction of metadata from 114,099 publications in Europe PMC, including 19,900 publications describing metagenomics studies in European Nucleotide Archive (ENA) and MGnify. Using this framework, a new metagenomics annotations pipeline was developed and integrated into Europe PMC to regularly enrich up-to-date ENA and MGnify metagenomics studies with metadata extracted from research articles. These metadata are now available for researchers to explore and retrieve in the MGnify and Europe PMC websites, as well as Europe PMC annotations API.}, } @article {pmid35949818, year = {2022}, author = {Chen, YY and Xue, XH}, title = {Coinfection of Streptococcus suis and Nocardia asiatica in the human central nervous system: A case report.}, journal = {World journal of clinical cases}, volume = {10}, number = {18}, pages = {6283-6288}, pmid = {35949818}, issn = {2307-8960}, abstract = {BACKGROUND: Streptococcus suis (S. suis) is an anthropozoonotic pathogen that shows clinical manifestations of meningitis, septicemia, and arthritis in infected humans. Nocardia is another type of anthropozoonotic bacteria, with clinical manifestations of skin, lung, and brain abscesses in infected humans. Few intracranial infections caused by S. suis or Nocardia have been reported. To the best of our knowledge, no study has reported a patient with simultaneous intracranial infection by S. suis and Nocardia.

CASE SUMMARY: A 66-year-old male presented at Liaocheng People's Hospital (Liaocheng, Shandong Province, China) reporting dizziness with nausea and vomiting. Metagenomic next-generation sequencing (mNGS) was performed on cerebrospinal fluid for examination, and the patient was diagnosed with suppurative meningitis caused by S. suis infection. He received anti-infection treatment with penicillin sodium and ceftriaxone. The patient's condition initially improved but then deteriorated. Further mNGS of cerebrospinal fluid revealed both S. suis and Nocardia. Imaging examination revealed a brain abscess. Furthermore, a mixed infection of S. suis and Nocardia was detected in the patient's central nervous system. The patient was treated with antibiotics and sulfamethoxazole. He was discharged after his condition improved.

CONCLUSION: This case shows that the disease can be recurrent in patients with intracranial infection of a rare pathogen. The possibility of mixed infection should also be considered, especially in patients treated with immunosuppressive agents. mNGS of cerebrospinal fluid is a supplement to conventional microbial pathogen identification methods. Patients with unknown pathogen diagnosis, early extensive use of antibiotics and infection with rare pathogens can be diagnosed by the combination of conventional methods and mNGS of cerebrospinal fluid.}, } @article {pmid35949316, year = {2022}, author = {Wang, R and Feng, R and Xia, C and Ruan, F and Luo, P and Guo, J}, title = {Early detection of gram-negative bacteria using metagenomic next-generation sequencing in acute respiratory distress syndrome: A case report.}, journal = {Experimental and therapeutic medicine}, volume = {24}, number = {3}, pages = {573}, pmid = {35949316}, issn = {1792-1015}, abstract = {Metagenomic next-generation sequencing (mNGS) is an effective method that can be used for the identification of early pathogens in patients with suspected severe pneumonia. However, the potential of mNGS for evaluating the prognosis of acute respiratory distress syndrome (ARDS) in patients with severe pneumonia remains unclear. In the present report, hospital-acquired gram-negative bacteria infections were detected in a case using metagenomic next-generation sequencing (mNGS) in a sample of bronchoalveolar fluid. This was obtained from a 58-year-old male patient with traumatic wet lung after a neurosurgery. According to the results, of which the profiles of the resistance genes were detected by mNGS, drugs designed to control infection were adjusted, namely to polymyxin B (500,000 U/12 h), azithromycin (0.5 g/24 h) and ganciclovir (0.25 g/12 h). Following adjusting treatment for 8 days, the symptoms of lung infection and hypoxemia were markedly improved, resulting in the patient being transferred out of the intensive care unit 15 days after treatment. To conclude, observations from the present report suggest that mNGS is a useful method for the early identification of pathogens in patients with pneumonia caused by ARDS. However, further studies are required to identify the complementary role of mNGS in supporting conventional microbiological methods in routine clinical practice.}, } @article {pmid35949076, year = {2022}, author = {Li, W and Liu, Y and Wu, B and Gu, L and Deng, R}, title = {Upgrade the high-load anaerobic digestion and relieve acid stress through the strategy of side-stream micro-aeration: biochemical performances, microbial response and intrinsic mechanisms.}, journal = {Water research}, volume = {221}, number = {}, pages = {118850}, doi = {10.1016/j.watres.2022.118850}, pmid = {35949076}, issn = {1879-2448}, mesh = {Anaerobiosis ; Archaea/metabolism ; *Bioreactors/microbiology ; *Euryarchaeota/metabolism ; Methane/metabolism ; Rivers ; }, abstract = {In high-load anaerobic digestion such as in kitchen waste, side-stream micro-aeration (SMA) shows excellent operational performance to direct micro-aeration (DMA). It immediately restores the acidification to stability. Methanogenic performance remained stable when organic load ratios (OLR) was further increased to 5.5 g VS/L. Enhanced enzyme activity, microbial aggregation, and proliferation of bacteria and archaea were observed in SMA. The results indicates that SMA enriched Methanosaeta (relative abundance exceeded 93%) and induced the change of the main methanogenic pathway to acetoclastic methanogenesis. Mechanisms was further explored by using metagenomic analysis, and the results show SMA avoids mass formation of ROS (reactive oxygen species) by cycling the aerated slurry, and retains benefits of trace O2 on material and energic metabolism, which poses great application potentials and deserves further investigation.}, } @article {pmid35948458, year = {2023}, author = {Hong, D and Wang, P and Chen, Y and Zhang, J and Jiang, W and Ye, B and Li, G and Zhou, J and Mao, W and Tong, Z and Li, W and Ke, L}, title = {Detection of potential pathogen in pancreatic fluid aspiration with metagenomic next-generation sequencing in patients with suspected infected pancreatic necrosis.}, journal = {Digestive and liver disease : official journal of the Italian Society of Gastroenterology and the Italian Association for the Study of the Liver}, volume = {55}, number = {2}, pages = {243-248}, doi = {10.1016/j.dld.2022.07.014}, pmid = {35948458}, issn = {1878-3562}, mesh = {Humans ; *Pancreatitis, Acute Necrotizing/diagnosis ; Retrospective Studies ; Pancreas ; High-Throughput Nucleotide Sequencing ; Tomography, X-Ray Computed ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Timely and accurate microbial diagnosis is important in managing patients with infected pancreatic necrosis (IPN).

AIMS: To evaluate the diagnostic performance of Metagenomic next-generation sequencing (mNGS) in patients with suspected IPN.

METHODS: The clinical data of 40 patients with suspected IPN who underwent CT-guided pancreatic fluid aspiration were retrospectively analyzed. Microbial culture and mNGS were simultaneously applied to identify the potential pathogens. The diagnostic performance of the mNGS was assessed by sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV).

RESULTS: The mNGS report can be obtained significantly earlier than culture methods (42 (36-62 h) vs. 60 (42-124 h), P = 0.032). Across all the study samples, seven species of bacteria and two species of fungi were reported accordingly to the culture results, while 22 species of bacteria and two species of fungi were detected by mNGS. The sensitivity, specificity, NPV, and PPV of mNGS were 88.0%, 100%, 83.33%, and 100%, respectively.

CONCLUSIONS: The diagnostic accuracy of mNGS in patients with suspected IPN is satisfactory. Moreover, mNGS may broaden the range of identifiable infectious pathogens and provide a more timely diagnosis.}, } @article {pmid35947314, year = {2022}, author = {Berben, T and Forlano Bó, F and In 't Zandt, MH and Yang, S and Liebner, S and Welte, CU}, title = {The Polar Fox Lagoon in Siberia harbours a community of Bathyarchaeota possessing the potential for peptide fermentation and acetogenesis.}, journal = {Antonie van Leeuwenhoek}, volume = {115}, number = {10}, pages = {1229-1244}, pmid = {35947314}, issn = {1572-9699}, support = {024.002.002//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 024.002.001//Nederlandse Organisatie voor Wetenschappelijk Onderzoek/ ; 03F0764F//Bundesministerium für Bildung und Forschung/ ; }, mesh = {Archaea/genetics/metabolism ; Carbon/metabolism ; Fermentation ; Ferredoxins/metabolism ; Formates/metabolism ; *Greenhouse Gases/metabolism ; Hydrogen/metabolism ; *Hydrogenase ; Methane/metabolism ; Peptides/metabolism ; Polymers/metabolism ; Siberia ; }, abstract = {Archaea belonging to the phylum Bathyarchaeota are the predominant archaeal species in cold, anoxic marine sediments and additionally occur in a variety of habitats, both natural and man-made. Metagenomic and single-cell sequencing studies suggest that Bathyarchaeota may have a significant impact on the emissions of greenhouse gases into the atmosphere, either through direct production of methane or through the degradation of complex organic matter that can subsequently be converted into methane. This is especially relevant in permafrost regions where climate change leads to thawing of permafrost, making high amounts of stored carbon bioavailable. Here we present the analysis of nineteen draft genomes recovered from a sediment core metagenome of the Polar Fox Lagoon, a thermokarst lake located on the Bykovsky Peninsula in Siberia, Russia, which is connected to the brackish Tiksi Bay. We show that the Bathyarchaeota in this lake are predominantly peptide degraders, producing reduced ferredoxin from the fermentation of peptides, while degradation pathways for plant-derived polymers were found to be incomplete. Several genomes encoded the potential for acetogenesis through the Wood-Ljungdahl pathway, but methanogenesis was determined to be unlikely due to the lack of genes encoding the key enzyme in methanogenesis, methyl-CoM reductase. Many genomes lacked a clear pathway for recycling reduced ferredoxin. Hydrogen metabolism was also hardly found: one type 4e [NiFe] hydrogenase was annotated in a single MAG and no [FeFe] hydrogenases were detected. Little evidence was found for syntrophy through formate or direct interspecies electron transfer, leaving a significant gap in our understanding of the metabolism of these organisms.}, } @article {pmid35946140, year = {2023}, author = {do Amaral, GCLS and Hassan, MA and Sloniak, MC and Pannuti, CM and Romito, GA and Villar, CC}, title = {Effects of antimicrobial mouthwashes on the human oral microbiome: Systematic review of controlled clinical trials.}, journal = {International journal of dental hygiene}, volume = {21}, number = {1}, pages = {128-140}, doi = {10.1111/idh.12617}, pmid = {35946140}, issn = {1601-5037}, mesh = {Adult ; Humans ; *Anti-Infective Agents/pharmacology/therapeutic use ; *Anti-Infective Agents, Local/therapeutic use ; Chlorhexidine/therapeutic use ; *Dental Plaque/drug therapy ; *Microbiota ; Mouthwashes/therapeutic use ; Phylogeny ; Controlled Clinical Trials as Topic ; }, abstract = {OBJECTIVES: This review aimed to assess the impact of mouthwashes on the composition of the human oral microbiome.

METHOD: An electronic search algorithm was adapted to MEDLINE-PubMed, Scopus, Embase and ISI Web of Science, and reference lists of relevant sources were manually searched. Inclusion criteria were controlled clinical trials published in English whose population were adult individuals who rinse with antimicrobial mouthwashes and that analysed changes in the oral microbiome by metataxonomy, metagenomics or phylogenetic microarray. Identified studies were screened and assessed following the PRISMA guidelines, and results were compiled into qualitative synthesis of the evidence.

RESULTS: Five controlled clinical studies were included. These studies found associations between the daily use of mouthwashes and changes in the oral microbiome, but the nature of the effect varied according to the mouthwash. Chlorhexidine (CHX) rinses lowered microbial diversity. While 7-day use of CHX led to increases in the abundance of Neisseria, Streptococcus and Granulicatella and a decrease in the abundance of Actinomyces, its prolonged use led to widespread reductions in several genera and species. Cetylpyridinium chloride-containing mouthwashes specifically lowered the abundance of gingivitis-associated genera. In contrast, N-acetyl cysteine-based mouthwashes did not promote changes in the oral microbiome.

CONCLUSIONS: Despite substantial heterogeneity, we found evidence to support the hypothesis that CHX and CPC mouthwashes promote changes in oral microbial structure and/or reductions in community diversity that favour the resolution of dysbiosis. However, future large population-based studies of adequate duration are needed to fully understand the extent to which antimicrobial mouthwashes modulate the microbiome.}, } @article {pmid35945942, year = {2022}, author = {Liao, LB and Chen, XX and Xiang, J and Zhang, NN and Wang, ET and Shi, FS}, title = {Zanthoxylum bungeanum root-rot associated shifts in microbiomes of root endosphere, rhizosphere, and soil.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13808}, pmid = {35945942}, issn = {2167-8359}, mesh = {Soil ; *Zanthoxylum ; Rhizosphere ; Bacteria ; Soil Microbiology ; Plant Roots/microbiology ; *Microbiota/genetics ; Trees ; }, abstract = {Root-rot disease has lead to serious reduction in yields and jeopardized the survival of the economically and ecologically important Zanthoxylum bungeanum trees cultured in Sichuan Province. In order to investigate the interaction between the microbiome and the root-rot disease, a metagenomic analysis was performed to characterize the microbial communities and functions in Z. bungeanum root endosphere, rhizosphere and bulk soil with/without root-rot disease. Soil physicochemical properties, microbial population size and enzyme activities were also analyzed for finding their interactions with the root-rot disease. As results, lower total nitrogen (TN) and available phosphorus (AP) contents but higher pH in rhizosphere and bulk soil, as well as lower substrate-induced respiration (SIR) and higher protease activity in bulk soil of diseased trees were found, in comparison with that of healthy trees. Microbial diversity and community composition were changed by root-rot disease in the endosphere, but not in rhizosphere and bulk soils. The endophytic microbiome of diseased trees presented higher Proteobacteria abundance and lower abundances of Bacteroidetes, Firmicutes and dominant fungal phyla. The relative abundances of nitrogen cycle- and carbon cycle-related genes in endophytic microbiomes were different between the diseased and healthy trees. Based on ANOSIM and PCoA, functional profiles (KEGG and CAZy) of microbiomes in rhizosphere and bulk soil shifted significantly between the diseased and healthy trees. In addition, soil pH, TN, AP, SIR, invertase and protease were estimated as the main factors influencing the shifts of taxonomic and functional groups in microbiomes of rhizosphere and bulk soil. Conclusively, the imbalance of root and soil microbial function groups might lead to shifts in the root endosphere-rhizosphere microenvironment, which in turn resulted in Z. bungeanum root-rot.}, } @article {pmid35945613, year = {2022}, author = {Mao, Y and Bajinka, O and Tang, Z and Qiu, X and Tan, Y}, title = {Lung-brain axis: Metabolomics and pathological changes in lungs and brain of respiratory syncytial virus-infected mice.}, journal = {Journal of medical virology}, volume = {94}, number = {12}, pages = {5885-5893}, doi = {10.1002/jmv.28061}, pmid = {35945613}, issn = {1096-9071}, mesh = {Animals ; Biomarkers ; Brain/pathology ; Cytokines/metabolism ; Disease Models, Animal ; Eosine Yellowish-(YS) ; Estradiol ; Hematoxylin ; Interleukin-6/metabolism ; Lung ; Mice ; Mice, Inbred BALB C ; RNA, Messenger/metabolism ; *Respiratory Syncytial Virus Infections ; *Respiratory Syncytial Virus, Human ; Spermine ; Tumor Necrosis Factor-alpha/metabolism ; }, abstract = {The lung-brain axis is an emerging area of study that got its basis from the gut-brain axis biological pathway. Using Respiratory Synctial Virus (RSV) as the model of respiratory viral pathogen, this study aims to establish some biological pathways. After establishing the mice model, the inflammation in lung and brain were assayed using Hematoxylin-eosin staining, indirect immunofluorescence (IFA), and quantitative reverse-transcription polymerase chain reaction. The biological pathways between lung and brain were detected through metabolomics analysis. In lung, RSV infection promoted epithelial shedding and infiltration of inflammatory cells. Also, RSV immunofluorescence and titerss were significantly increased. Moreover, interleukin (IL)-1, IL-6 and tumor necrosis factor-α (TNF-α) were also significantly increased after RSV infection. In brain, the cell structure of hippocampal CA1 area was loose and disordered. Inflammatory cytokines IL-6 and IL-1β expression in the brain also increased, however, TNF-α expression showed no differences among the control and RSV group. We observed an increased expression of microglia biomarker IBA-1 and decreased neuronal biomarker NeuN. In addition, RSV mRNA expression levels were also increased in the brains. 15 metabolites were found upregulated in the RSV group including nerve-injuring metabolite glutaric acid, hydroxyglutaric acid and Spermine. ɑ-Estradiol increased significantly while normorphine decreased significantly at Day 7 of infection among the RSV group. This study established a mouse model for exploring the pathological changes in lungs and brains. There are many biological pathways between lung and brain, including direct translocation of RSV and metabolite pathway.}, } @article {pmid35945559, year = {2022}, author = {Gómez, M and Martinez, D and Muñoz, M and Ramírez, JD}, title = {Aedes aegypti and Ae. albopictus microbiome/virome: new strategies for controlling arboviral transmission?.}, journal = {Parasites & vectors}, volume = {15}, number = {1}, pages = {287}, pmid = {35945559}, issn = {1756-3305}, mesh = {*Aedes ; Animals ; *Arboviruses/genetics ; Humans ; Mosquito Vectors ; Virome ; *Zika Virus/genetics ; *Zika Virus Infection ; }, abstract = {Aedes aegypti and Aedes albopictus are the main vectors of highly pathogenic viruses for humans, such as dengue (DENV), chikungunya (CHIKV), and Zika (ZIKV), which cause febrile, hemorrhagic, and neurological diseases and remain a major threat to global public health. The high ecological plasticity, opportunistic feeding patterns, and versatility in the use of urban and natural breeding sites of these vectors have favored their dispersal and adaptation in tropical, subtropical, and even temperate zones. Due to the lack of available treatments and vaccines, mosquito population control is the most effective way to prevent arboviral diseases. Resident microorganisms play a crucial role in host fitness by preventing or enhancing its vectorial ability to transmit viral pathogens. High-throughput sequencing and metagenomic analyses have advanced our understanding of the composition and functionality of the microbiota of Aedes spp. Interestingly, shotgun metagenomics studies have established that mosquito vectors harbor a highly conserved virome composed of insect-specific viruses (ISV). Although ISVs are not infectious to vertebrates, they can alter different phases of the arboviral cycle, interfering with transmission to the human host. Therefore, this review focuses on the description of Ae. aegypti and Ae. albopictus as vectors susceptible to infection by viral pathogens, highlighting the role of the microbiota-virome in vectorial competence and its potential in control strategies for new emerging and re-emerging arboviruses.}, } @article {pmid35945497, year = {2022}, author = {Nieuwenhuijse, DF and van der Linden, A and Kohl, RHG and Sikkema, RS and Koopmans, MPG and Oude Munnink, BB}, title = {Towards reliable whole genome sequencing for outbreak preparedness and response.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {569}, pmid = {35945497}, issn = {1471-2164}, support = {643476//Horizon 2020 Framework Programme/ ; 874735//Horizon 2020 Framework Programme/ ; }, mesh = {Disease Outbreaks ; Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; *Nanopore Sequencing ; Whole Genome Sequencing/methods ; *Zika Virus/genetics ; *Zika Virus Infection ; }, abstract = {BACKGROUND: To understand the dynamics of infectious diseases, genomic epidemiology is increasingly advocated, with a need for rapid generation of genetic sequences during outbreaks for public health decision making. Here, we explore the use of metagenomic sequencing compared to specific amplicon- and capture-based sequencing, both on the Nanopore and the Illumina platform for generation of whole genomes of Usutu virus, Zika virus, West Nile virus, and Yellow Fever virus.

RESULTS: We show that amplicon-based Nanopore sequencing can be used to rapidly obtain whole genome sequences in samples with a viral load up to Ct 33 and capture-based Illumina is the most sensitive method for initial virus determination.

CONCLUSIONS: The choice of sequencing approach and platform is important for laboratories wishing to start whole genome sequencing. Depending on the purpose of genome sequencing the best choice can differ. The insights presented in this work and the shown differences in data characteristics can guide labs to make a well informed choice.}, } @article {pmid35945331, year = {2022}, author = {Chen, Y and Xia, Z and Li, H}, title = {Comparative analysis of the fecal bacterial communities of hawksbill sea turtles (Eretmochelys imbricata) and green sea turtles (Chelonia mydas).}, journal = {FEMS microbiology letters}, volume = {369}, number = {1}, pages = {}, doi = {10.1093/femsle/fnac073}, pmid = {35945331}, issn = {1574-6968}, mesh = {Animals ; Bacteroidetes ; Feces ; *Gastrointestinal Microbiome ; *Microbiota ; Sugars ; *Turtles ; }, abstract = {Hawksbill sea turtles (Eretmochelys imbricata) are important for maintaining healthy coral reef ecosystems currently qualify as "critically endangered" by the IUCN. Their gut microbiota is closely linked to host nutrition and health, however, the gut microbiota of hawksbill sea turtles from a natural reserve remains unclear. Therefore, exploring their microbial community structure in a natural reserve may provide valuable information on strategies for protecting this species. In this study, we investigated hawksbill sea turtle fecal microbial communities from a natural reserve using 16S metagenomics and compared the gut microbiota from fecal samples of hawksbill and green sea turtles (Chelonia mydas). The results indicated that the structure of fecal microbial communities was significantly different between hawksbill and green sea turtles. In hawksbill sea turtles, the three dominant phyla were Bacteroidetes, Firmicutes, and Fusobacteria, whereas the fecal microbial communities of green sea turtles were mainly composed of Firmicutes, Bacteroidetes, and Proteobacteria. Among the hawksbill sea turtle fecal microbes, the predominant genera were Cetobacterium and Rikenell, whereas in green sea turtles, the predominant genera were Bacteroides and Paludibacter. In addition, predictive metagenomic analysis indicated that sugar catabolism was enriched in green sea turtle fecal microbiota, whereas pathways related to secondary metabolite production were enriched in hawksbill sea turtle fecal microbiota. Our study provides preliminary data on the fecal microbiota features of sea turtles from the natural reserve, which may contribute to the management of the food requirements and long-term conservation of hawksbill sea turtles.}, } @article {pmid35944675, year = {2022}, author = {Sim, JXF and Drigo, B and Doolette, CL and Vasileiadis, S and Karpouzas, DG and Lombi, E}, title = {Impact of twenty pesticides on soil carbon microbial functions and community composition.}, journal = {Chemosphere}, volume = {307}, number = {Pt 2}, pages = {135820}, doi = {10.1016/j.chemosphere.2022.135820}, pmid = {35944675}, issn = {1879-1298}, mesh = {Australia ; Carbon ; Cellulose 1,4-beta-Cellobiosidase ; *Fungicides, Industrial ; *Insecticides ; *Pesticides/toxicity ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Pesticides are known to affect non-targeted soil microorganisms. Still, studies comparing the effect of multiple pesticides on a wide range of microbial endpoints associated with carbon cycling are scarce. Here, we employed fluorescence enzymatic assay and real-time PCR to evaluate the effect of 20 commercial pesticides, applied at their recommended dose and five times their recommended dose, on soil carbon cycling related enzymatic activities (α-1,4-glucosidase, β-1,4-glucosidase, β-d-cellobiohydrolase and β-xylosidase), and on the absolute abundance of functional genes (cbhl and chiA), in three different South Australian agricultural soils. The effects on cellulolytic and chitinolytic microorganisms, and the total microbial community composition were determined using shotgun metagenomic sequencing in selected pesticide-treated and untreated samples. The application of insecticides significantly increased the cbhl and chiA genes absolute abundance in the acidic soil. At the community level, insecticide fipronil had the greatest stimulating effect on cellulolytic and chitinolytic microorganisms, followed by fungicide metalaxyl-M and insecticide imidacloprid. A shift towards a fungal dominated microbial community was observed in metalaxyl-M treated soil. Overall, our results suggest that the application of pesticides might affect the soil carbon cycle and may disrupt the formation of soil organic matter and structure stabilisation.}, } @article {pmid35944670, year = {2022}, author = {Cai, L and Guo, HT and Zheng, GD and Wang, XY and Wang, K}, title = {Metagenomic analysis reveals the microbial degradation mechanism during kitchen waste biodrying.}, journal = {Chemosphere}, volume = {307}, number = {Pt 4}, pages = {135862}, doi = {10.1016/j.chemosphere.2022.135862}, pmid = {35944670}, issn = {1879-1298}, mesh = {Acetyl Coenzyme A ; Carbohydrates ; *Cellulases ; Cellulose ; Chitin ; Fatty Acids ; Isoleucine ; Leucine ; Lipase ; Lipids ; Lysine ; Peptide Hydrolases ; *Sewage/chemistry ; Water/chemistry ; }, abstract = {Biodrying is a treatment to remove moisture using bio-heat generated during organic degradation. Organic matter degradation and microbial metabolism were studied during the whole kitchen waste biodrying, using metagenomic analysis. After the 25-day biodrying process, carbohydrate, protein and lipid contents decreased by 83.7%, 27.8% and 79.3%, respectively, and their degradation efficiencies increased after the thermophilic phase. Lipase activity exceeded 10 mmol d[-1] g[-1] throughout biodrying. Cellulase and lipase activities recovered by 2.21% and 5.77%, respectively, after the thermophilic phase, while the protease activity had a maximum increment of 347%. Metabolic analysis revealed that carbohydrate, amino acid and lipid metabolism was possibly inhibited by the high temperature, but the relative abundances of related predicted functions recovered by more than 0.9%, 7% and 11%, respectively, by the end of biodrying. Protein function prediction suggests that β-oxidation, fatty acid biosynthesis, and the degradation of cellulose and chitin were possibly enhanced during the thermophilic phase. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that leucine, isoleucine and lysine could ultimately degraded to acetyl-CoA. Weissella, Aeribacillus and Bacillus were the genera with the most enriched functional genes during the whole biodrying process. These findings help elucidate the microbial degradation processes during biodrying, which provides further scientific support for improving the application of biodrying products.}, } @article {pmid35944355, year = {2022}, author = {Dhondge, HV and Barvkar, VT and Paul, D and Dastager, SG and Pable, AA and Nadaf, AB}, title = {Exploring the core microbiota in scented rice (Oryza sativa L.) rhizosphere through metagenomics approach.}, journal = {Microbiological research}, volume = {263}, number = {}, pages = {127157}, doi = {10.1016/j.micres.2022.127157}, pmid = {35944355}, issn = {1618-0623}, mesh = {India ; Metagenomics ; *Microbiota/genetics ; *Oryza/microbiology ; Proline/metabolism ; Rhizosphere ; Soil Microbiology ; }, abstract = {Rice is a major food crop cultivated around the globe. Specially scented rice varieties are of commercial importance but they are low-yielding. The rhizospheric microflora plays a significant role in improving yield and aroma. However, the core microbiome of the scented rice rhizosphere is comparatively less explored. Here, we analyzed the core microbiome associated with the rhizosphere of the scented (Ambemohar-157 and Dehradun basmati) in comparison with non-scented rice (Kolam and Arize 6444 Gold) cultivated at two different geoclimatic zones of India (Maharashtra and Uttarakhand) using the metagenomics approach. The alpha and beta diversity analysis showed that the microbial communities associated with scented and non-scented varieties significantly changes with respect to richness, diversity, and evenness. The taxonomic profiling revealed the variation in composition, diversity, and abundance of the microbiome in terms of phyla and genera associated with scented rice varieties over non-scented. The cluster analysis distinguishes the microbial communities based on their geographical positions. The core microbiome analysis revealed that scented rice rhizosphere shelters distinct and unique microbiota. 28.6 % of genera were exclusively present only in the scented rice rhizosphere. The putative functional gene annotation revealed the high abundance of genes related to the biosynthesis of 2-acetyl-1-pyrroline (2AP) precursors in scented rice. The precursor feeding analysis revealed proline as a preferred substrate by 2AP synthesizing bacteria. The 2AP precursor proline and proline metabolism genes showed a positive correlation. The scented rice-specific rhizobacteria pointed out in this study can be used as bio-inoculants for enhancing aroma, yield, and sustainable rice cultivation.}, } @article {pmid35944318, year = {2022}, author = {Chen, J and Hai, Y and Zhang, W and Zhou, X}, title = {Insights into deterioration and reactivation of a mainstream anammox biofilm reactor response to C/N ratio.}, journal = {Journal of environmental management}, volume = {320}, number = {}, pages = {115780}, doi = {10.1016/j.jenvman.2022.115780}, pmid = {35944318}, issn = {1095-8630}, mesh = {*Ammonium Compounds ; Anaerobic Ammonia Oxidation ; Anaerobiosis ; Biofilms ; Bioreactors ; Carbon ; Denitrification ; Extracellular Polymeric Substance Matrix ; *Nitrogen ; Oxidation-Reduction ; Sewage ; Wastewater/chemistry ; }, abstract = {In-depth knowledge of the deterioration and reactivation of the anaerobic ammonium oxidation (anammox) induced by carbon-to-nitrogen (C/N) is still lacking. Herein, the anammox performance was investigated in an anaerobic sequence biofilm batch reactor fed with low-strength partial nitration effluent in the range of C/N ratio from 0.5 to 3. The anammox was hardly deteriorated at C/N lower than 1.5, while became worsen if C/N was above 2.0. The specific anammox activity (SAA) experiments showed an 85% decrease of SAA at C/N of 3.0 compared with the maximum value (C/N:0). However, anammox capacity was rapidly recovered once influent C/N was adjusted back to zero. Moreover, C/N also highly affected the composition, structure and function of extracellular polymeric substance of the anammox biofilm. High-throughput sequencing revealed a close correlation between C/N change and microbial structure shift. Finally, the potential inhibition and restoration mechanism of the C/N-dependent anammox were proposed based on metagenomic analysis. This research provides some insights into the reinstatement of a mainstream anammox biofilm process after it is interrupted by high C/N influent.}, } @article {pmid35944127, year = {2023}, author = {Hong, HL and Flurin, L and Thoendel, MJ and Wolf, MJ and Abdel, MP and Greenwood-Quaintance, KE and Patel, R}, title = {Targeted Versus Shotgun Metagenomic Sequencing-based Detection of Microorganisms in Sonicate Fluid for Periprosthetic Joint Infection Diagnosis.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {76}, number = {3}, pages = {e1456-e1462}, pmid = {35944127}, issn = {1537-6591}, support = {R01 AR056647/AR/NIAMS NIH HHS/United States ; R01AR056647/NH/NIH HHS/United States ; }, mesh = {Humans ; *Prosthesis-Related Infections/diagnosis ; RNA, Ribosomal, 16S/genetics ; Sensitivity and Specificity ; *Arthritis, Infectious/diagnosis ; *Arthroplasty, Replacement, Knee/adverse effects ; *Arthroplasty, Replacement, Hip/adverse effects ; }, abstract = {BACKGROUND: Next-generation sequencing (NGS) is increasingly used for periprosthetic joint infection (PJI) diagnosis, but its clinical utility is poorly defined. Shotgun metagenomic sequencing (sNGS) has been reported to identify PJI pathogens undetected by culture in sonicate fluid. However, sNGS is complex and costly. Here, 16S ribosomal RNA (rRNA) gene-based targeted metagenomic sequencing (tNGS) was compared to sNGS of sonicate fluid for microbial detection and identification in patients with total hip arthroplasty (THA) and total knee arthroplasty (TKA) failure.

METHODS: A convenience sample of sonicate fluids derived from patients who had undergone THA or TKA removal, enriched with culture negative PJI cases, was tested. Samples had been previously tested by sNGS. For tNGS, samples were extracted, amplified by polymerase chain reaction targeting the V1 to V3 regions of the 16S rRNA gene, and sequenced on an Illumina MiSeq.

RESULTS: A total of 395 sonicate fluids, including 208 from subjects with PJI, were studied. Compared with sonicate fluid culture, tNGS had higher positive percent agreement (72.1 vs 52.9%, P < .001), detecting potential pathogens in 48.0% of culture-negative PJIs. There was no difference between the positive percent agreement of tNGS (72.1%) and sNGS (73.1%, P = .83).

CONCLUSIONS: 16S rRNA gene-based tNGS is a potential diagnostic tool for PJI pathogen identification in sonicate fluid from failed THAs and TKAs in culture-negative cases, with similar performance characteristics to sNGS.}, } @article {pmid35944043, year = {2022}, author = {Yang, Z and Zhang, Y and Stubbe-Espejel, A and Zhao, Y and Liu, M and Li, J and Zhao, Y and Tong, G and Liu, N and Qi, L and Hutchins, A and Lin, S and Li, Y}, title = {Vaginal microbiota and personal risk factors associated with HPV status conversion-A new approach to reduce the risk of cervical cancer?.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0270521}, pmid = {35944043}, issn = {1932-6203}, mesh = {*Alphapapillomavirus ; Female ; Humans ; *Microbiota ; Papillomaviridae/genetics ; *Papillomavirus Infections ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Risk Factors ; *Uterine Cervical Neoplasms/epidemiology/microbiology/prevention & control ; Vagina/microbiology ; }, abstract = {Vaginal microbiota (VMB) is associated with changes in Human papilloma virus (HPV) status, which consequently influences the risk of cervical cancer. This association was often confounded by personal risk factors. This pilot research aimed to explore the relationship between vaginal microbiota, personal risk factors and their interactions with HPV status conversion to identify the vaginal microbiota that was associated with HPV clearance under heterogeneous personal risk factors. A total of 38 women participated by self-collecting a cervicovaginal mucus (CVM) sample that was sent for metagenomics sequencing. Most of the participants also filled in personal risk factors questionnaire through an eHealth platform and authorized the use of their previous HPV genotyping results stored in this eHealth platform. Based on the two HPV results, the participants were grouped into three cohorts, namely HPV negative, HPV persistent infection, and HPV status conversion. The relative abundance of VMB and personal factors were compared among these three cohorts. A correlation investigation was performed between VMB and the significant personal factors to characterize a robustness of the panel for HPV status change using R programming. At baseline, 12 participants were HPV-negative, and 22 were HPV-positive. Within one year, 18 women remained HPV-positive, 12 were HPV-negative and 4 participants showed HPV clearance. The factors in the eHealth questionnaire were systematically evaluated which identified several factors significantly associated with persistent HPV infection, including age, salary, history of reproductive tract infection, and the total number of sexual partners. Concurrent vaginal microbiome samples suggest that a candidate biomarker panel consisting of Lactobacillus gasseri, Streptococcus agalactiae, and Timona prevotella bacteria, which may be associated with HPV clearance. This pilot study indicates a stable HPV status-related vaginal microbe environment. To establish a robust biomarker panel for clinical use, larger cohorts will be recruited into follow-up studies.}, } @article {pmid35943661, year = {2022}, author = {Ma, W and Drew, DA and Staller, K}, title = {The Gut Microbiome and Colonic Motility Disorders: A Practical Framework for the Gastroenterologist.}, journal = {Current gastroenterology reports}, volume = {24}, number = {10}, pages = {115-126}, pmid = {35943661}, issn = {1534-312X}, support = {K01 DK120742/DK/NIDDK NIH HHS/United States ; K23 DK120945/DK/NIDDK NIH HHS/United States ; K01DK120742/DK/NIDDK NIH HHS/United States ; K23DK120945/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Humans ; Dysbiosis ; Fecal Microbiota Transplantation ; *Gastroenterologists ; *Gastrointestinal Microbiome/physiology ; *Irritable Bowel Syndrome/etiology/therapy ; Constipation ; Diarrhea ; Metagenome ; }, abstract = {PURPOSE OF REVIEW: Colonic motility disorders may be influenced by the gut microbiota, which plays a role in modulating sensory and motor function. However, existing data are inconsistent, possibly due to complex disease pathophysiology, fluctuation in symptoms, and difficulty characterizing high-resolution taxonomic composition and function of the gut microbiome.

RECENT FINDINGS: Increasingly, human studies have reported associations between gut microbiome features and colonic motility disorders, such as irritable bowel syndrome and constipation. Several microbial metabolites have been identified as regulators of colonic motility in animal models. Modulation of the gut microbiota via dietary intervention, probiotics, and fecal microbiota transplant is a promising avenue for treatment for these diseases. An integration of longitudinal multi-omics data will facilitate further understanding of the causal effects of dysbiosis on disease. Further understanding of the microbiome-driven mechanisms underlying colonic motility disorders may be leveraged to develop personalized, microbiota-based approaches for disease prevention and treatment.}, } @article {pmid35943423, year = {2022}, author = {Scott, CB and Cárdenas, A and Mah, M and Narasimhan, VM and Rohland, N and Toth, LT and Voolstra, CR and Reich, D and Matz, MV}, title = {Millennia-old coral holobiont DNA provides insight into future adaptive trajectories.}, journal = {Molecular ecology}, volume = {31}, number = {19}, pages = {4979-4990}, doi = {10.1111/mec.16642}, pmid = {35943423}, issn = {1365-294X}, mesh = {Animals ; *Anthozoa/genetics ; Coral Reefs ; DNA, Ancient ; *Dinoflagellida/genetics ; Ecosystem ; Genome ; }, abstract = {Ancient DNA (aDNA) has been applied to evolutionary questions across a wide variety of taxa. Here, for the first time, we utilized aDNA from millennia-old fossil coral fragments to gain new insights into a rapidly declining western Atlantic reef ecosystem. We sampled four Acropora palmata fragments (dated 4215 BCE to 1099 CE) obtained from two Florida Keys reef cores. From these samples, we established that it is possible both to sequence aDNA from reef cores and place the data in the context of modern-day genetic variation. We recovered varying amounts of nuclear DNA exhibiting the characteristic signatures of aDNA from the A. palmata fragments. To describe the holobiont sensu lato, which plays a crucial role in reef health, we utilized metagenome-assembled genomes as a reference to identify a large additional proportion of ancient microbial DNA from the samples. The samples shared many common microbes with modern-day coral holobionts from the same region, suggesting remarkable holobiont stability over time. Despite efforts, we were unable to recover ancient Symbiodiniaceae reads from the samples. Comparing the ancient A. palmata data to whole-genome sequencing data from living acroporids, we found that while slightly distinct, ancient samples were most closely related to individuals of their own species. Together, these results provide a proof-of-principle showing that it is possible to carry out direct analysis of coral holobiont change over time, which lays a foundation for studying the impacts of environmental stress and evolutionary constraints.}, } @article {pmid35943274, year = {2022}, author = {Jin, X and Li, J and Shao, M and Lv, X and Ji, N and Zhu, Y and Huang, M and Yu, F and Zhang, C and Xie, L and Huang, J and Chen, S and Zhu, C and Lv, M and Feng, G}, title = {Improving Suspected Pulmonary Infection Diagnosis by Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing: a Multicenter Retrospective Study.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0247321}, pmid = {35943274}, issn = {2165-0497}, mesh = {Bronchoalveolar Lavage Fluid ; *Communicable Diseases ; Fungi/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; Multicenter Studies as Topic ; *Mycobacterium tuberculosis/genetics ; *Pneumonia/diagnosis ; Retrospective Studies ; Sensitivity and Specificity ; *Viruses ; }, abstract = {Metagenomic next-generation sequencing (mNGS) has been gradually applied to clinical practice due to its unbiased characteristics of pathogen detection. However, its diagnostic performance and clinical value in suspected pulmonary infection need to be evaluated. We systematically reviewed the clinical data of 246 patients with suspected pulmonary infection from 4 medical institutions between January 2019 and September 2021. The diagnostic performances of mNGS and conventional testing (CT) were systematically analyzed based on bronchoalveolar lavage fluid (BALF). The impacts of mNGS and CT on diagnosis modification and treatment adjustment were also assessed. The positive rates of mNGS and CT were 47.97% and 23.17%, respectively. The sensitivity of mNGS was significantly higher than that of CT (53.49% versus 23.26%, P < 0.01), especially for infections of Mycobacterium tuberculosis (67.86% versus 17.86%, P < 0.01), atypical pathogens (100.00% versus 7.14%, P < 0.01), viruses (92.31% versus 7.69%, P < 0.01), and fungi (78.57% versus 39.29%, P < 0.01). The specificity of mNGS was superior to that of CT, with no statistical difference (90.32% versus 77.42%, P = 0.167). The positive predictive value (PPV) and negative predictive value (NPV) of mNGS were 97.46% and 21.88%, respectively. Diagnosis modification and treatment adjustment were conducted in 32 (32/246, 13.01%) and 23 (23/246, 9.35%) cases, respectively, according to mNGS results only. mNGS significantly improved the diagnosis of suspected pulmonary infection, especially infections of M. tuberculosis, atypical pathogens, viruses, and fungi, and it demonstrated the pathogen distribution of pulmonary infections. It is expected to be a promising microbiological detection and diagnostic method in clinical practice. IMPORTANCE Pulmonary infection is a heterogeneous and complex infectious disease with high morbidity and mortality worldwide. In clinical practice, a considerable proportion of the etiology of pulmonary infection is unclear, microbiological diagnosis being challenging. Metagenomic next-generation sequencing detects all nucleic acids in a sample in an unbiased manner, revealing the microbial community environment and organisms and improving the microbiological detection and diagnosis of infectious diseases in clinical settings. This study is the first multicenter, large-scale retrospective study based entirely on BALF for pathogen detection by mNGS, and it demonstrated the superior performance of mNGS for microbiological detection and diagnosis of suspected pulmonary infection, especially in infections of Mycobacterium tuberculosis, atypical pathogens, viruses, and fungi. It also demonstrated the pathogen distribution of pulmonary infections in the real world, guiding targeted treatment and improving clinical management and prognoses.}, } @article {pmid35943262, year = {2022}, author = {Laanbroek, HJ and Cassman, NA and Keijzer, RM and Kuramae, EE}, title = {The Stochastic Assembly of Nitrobacter winogradskyi-Selected Microbiomes with Heterotrophs from Sewage Sludge or Grassland Soil.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {17}, pages = {e0078322}, pmid = {35943262}, issn = {1098-5336}, mesh = {Bacteria/genetics ; Bioreactors/microbiology ; Carbon ; Grassland ; *Microbiota ; Nitrification ; Nitrites ; Nitrobacter/genetics ; Nitrogen ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; *Sewage/microbiology ; Soil ; }, abstract = {Chemolitho-autotrophic microorganisms like the nitrite-oxidizing Nitrobacter winogradskyi create an environment for heterotrophic microorganisms that profit from the production of organic compounds. It was hypothesized that the assembly of a community of heterotrophic microorganisms around N. winogradskyi depends on the ecosystem from which the heterotrophs are picked. To test this hypothesis, pure cultures of N. winogradskyi were grown in continuously nitrite-fed bioreactors in a mineral medium free of added organic carbon that had been inoculated with diluted sewage sludge or with a suspension from a grassland soil. Samples for chemical and 16S rRNA gene amplicon analyses were taken after each volume change in the bioreactor. At the end of the enrichment runs, samples for shotgun metagenomics were also collected. Already after two volume changes, the transformations in community structure became less dynamic. The enrichment of heterotrophs from both sewage and soil was highly stochastic and yielded different dominant genera in most of the enrichment runs that were independent of the origin of the inoculum. Hence, the hypothesis had to be refuted. Notwithstanding the large variation in taxonomic community structure among the enrichments, the functional compositions of the communities were statistically not different between soil- and sludge-based enrichments. IMPORTANCE In the process of aerobic nitrification, nitrite-oxidizing bacteria together with ammonia-oxidizing microorganisms convert mineral nitrogen from its most reduced appearance, i.e., ammonium, into its most oxidized form, i.e., nitrate. Because the form of mineral nitrogen has large environmental implications, nitrite-oxidizing bacteria such as Nitrobacter winogradskyi play a central role in the global biogeochemical nitrogen cycle. In addition to this central role, the autotrophic nitrite-oxidizing bacteria also play a fundamental role in the global carbon cycle. They form the basis of heterotrophic food webs, in which the assimilated carbon is recycled. Little is known about the heterotrophic microorganisms that participate in these food webs, let alone their assembly in different ecosystems. This study showed that the assembly of microbial food webs by N. winogradskyi was a highly stochastic process and independent of the origin of the heterotrophic microorganisms, but the functional characteristics of the different food webs were similar.}, } @article {pmid35943155, year = {2022}, author = {Moya-Gonzálvez, EM and Peña-Gil, N and Rubio-Del-Campo, A and Coll-Marqués, JM and Gozalbo-Rovira, R and Monedero, V and Rodríguez-Díaz, J and Yebra, MJ}, title = {Infant Gut Microbial Metagenome Mining of α-l-Fucosidases with Activity on Fucosylated Human Milk Oligosaccharides and Glycoconjugates.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0177522}, pmid = {35943155}, issn = {2165-0497}, mesh = {Animals ; *Blood Group Antigens/analysis/metabolism ; Fucose/analysis/chemistry/metabolism ; *Gastrointestinal Microbiome ; Glycoconjugates/analysis/metabolism ; Humans ; Infant ; Infant, Newborn ; Mammals/genetics/metabolism ; Metagenome ; Milk, Human/chemistry/metabolism ; Oligosaccharides/analysis/chemistry/metabolism ; Polysaccharides ; alpha-L-Fucosidase/chemistry/genetics/metabolism ; }, abstract = {The gastrointestinal microbiota members produce α-l-fucosidases that play key roles in mucosal, human milk, and dietary oligosaccharide assimilation. Here, 36 open reading frames (ORFs) coding for putative α-l-fucosidases belonging to glycosyl hydrolase family 29 (GH29) were identified through metagenome analysis of breast-fed infant fecal microbiome. Twenty-two of those ORFs showed a complete coding sequence with deduced amino acid sequences displaying the highest degree of identity with α-l-fucosidases from Bacteroides thetaiotaomicron, Bacteroides caccae, Phocaeicola vulgatus, Phocaeicola dorei, Ruminococcus gnavus, and Streptococcus parasanguinis. Based on sequence homology, 10 α-l-fucosidase genes were selected for substrate specificity characterization. The α-l-fucosidases Fuc18, Fuc19A, Fuc35B, Fuc39, and Fuc1584 showed hydrolytic activity on α1,3/4-linked fucose present in Lewis blood antigens and the human milk oligosaccharide (HMO) 3-fucosyllactose. In addition, Fuc1584 also hydrolyzed fucosyl-α-1,6-N-acetylglucosamine (6FN), a component of the core fucosylation of N-glycans. Fuc35A and Fuc193 showed activity on α1,2/3/4/6 linkages from H type-2, Lewis blood antigens, HMOs and 6FN. Fuc30 displayed activity only on α1,6-linked l-fucose, and Fuc5372 showed a preference for α1,2 linkages. Fuc2358 exhibited a broad substrate specificity releasing l-fucose from all the tested free histo-blood group antigens, HMOs, and 6FN. This latest enzyme also displayed activity in glycoconjugates carrying lacto-N-fucopentaose II (Le[a]) and lacto-N-fucopentaose III (Le[x]) and in the glycoprotein mucin. Fuc18, Fuc19A, and Fuc39 also removed l-fucose from neoglycoproteins and human α-1 acid glycoprotein. These results give insight into the great diversity of α-l-fucosidases from the infant gut microbiota, thus supporting the hypothesis that fucosylated glycans are crucial for shaping the newborn microbiota composition. IMPORTANCE α-l-Fucosyl residues are frequently present in many relevant glycans, such as human milk oligosaccharides (HMOs), histo-blood group antigens (HBGAs), and epitopes on cell surface glycoconjugate receptors. These fucosylated glycans are involved in a number of mammalian physiological processes, including adhesion of pathogens and immune responses. The modulation of l-fucose content in such processes may provide new insights and knowledge regarding molecular interactions and may help to devise new therapeutic strategies. Microbial α-l-fucosidases are exoglycosidases that remove α-l-fucosyl residues from free oligosaccharides and glycoconjugates and can be also used in transglycosylation reactions to synthesize oligosaccharides. In this work, α-l-fucosidases from the GH29 family were identified and characterized from the metagenome of fecal samples of breastfed infants. These enzymes showed different substrate specificities toward HMOs, HBGAs, naturally occurring glycoproteins, and neoglycoproteins. These novel glycosidase enzymes from the breast-fed infant gut microbiota, which resulted in a good source of α-l-fucosidases, have great biotechnological potential.}, } @article {pmid35941765, year = {2022}, author = {Singh, V and Son, H and Lee, G and Lee, S and Unno, T and Shin, JH}, title = {Role, relevance, and possibilities of in vitro fermentation models in human dietary, and gut-microbial studies.}, journal = {Biotechnology and bioengineering}, volume = {119}, number = {11}, pages = {3044-3061}, doi = {10.1002/bit.28206}, pmid = {35941765}, issn = {1097-0290}, mesh = {Animals ; Colon ; Diet ; Fatty Acids, Volatile/metabolism ; Fermentation ; Humans ; *Microbiota ; *Prebiotics ; }, abstract = {Dietary studies play a crucial role in determining the health-benefiting effects of most food substances, including prebiotics, probiotics, functional foods, and bioactive compounds. Such studies involve gastrointestinal digestion and colonic fermentation of dietary substances. In colonic fermentation, any digested food is further metabolized in the gut by the residing colonic microbiota, causing a shift in the gut microenvironment and production of various metabolites, such as short-chain fatty acids. These diet-induced shifts in the microbial community and metabolite production, which can be assessed through in vitro fermentation models using a donor's fecal microbiota, are well known to impact the health of the host. Although in vivo or animal experiments are the gold standard in dietary studies, recent advancements using different in vitro systems, like artificial colon (ARCOL), mini bioreactor array (MBRA), TNO in vitro model of the colon (TIM), Simulator of the Human Intestinal Microbial Ecosystem (SHIME), M-SHIME, Copenhagen MiniGut, and Dynamic Gastrointestinal Simulator, make it easy to study the dietary impact in terms of the gut microbiota and metabolites. Such a continuous in vitro system can have multiple compartments corresponding to different parts of the colon, that is, proximal, transverse, and distal colon, making the findings physiologically more significant. Furthermore, postfermentation samples can be analyzed using metagenomic, metabolomic, quantitative-polymerase chain reaction, and flow-cytometry approaches. Moreover, studies have shown that in vitro results are in accordance with the in vivo findings, supporting their relevance in dietary studies and giving confidence that shifts in metabolites are only due to microbes. This review meticulously describes the recent advancements in various fermentation models and their relevance in dietary studies.}, } @article {pmid35941171, year = {2022}, author = {Mosley, OE and Gios, E and Close, M and Weaver, L and Daughney, C and Handley, KM}, title = {Nitrogen cycling and microbial cooperation in the terrestrial subsurface.}, journal = {The ISME journal}, volume = {16}, number = {11}, pages = {2561-2573}, pmid = {35941171}, issn = {1751-7370}, support = {UOAX1720//Ministry of Business, Innovation and Employment (MBIE)/ ; }, mesh = {Ammonia/metabolism ; *Ammonium Compounds/metabolism ; *Denitrification ; Methane ; Nitrates ; Nitrites ; Nitrogen/metabolism ; Nitrogen Cycle ; Oxidation-Reduction ; Oxidoreductases/metabolism ; Oxygen ; }, abstract = {The nitrogen cycle plays a major role in aquatic nitrogen transformations, including in the terrestrial subsurface. However, the variety of transformations remains understudied. To determine how nitrogen cycling microorganisms respond to different aquifer chemistries, we sampled groundwater with varying nutrient and oxygen contents. Genes and transcripts involved in major nitrogen-cycling pathways were quantified from 55 and 26 sites, respectively, and metagenomes and metatranscriptomes were analyzed from a subset of oxic and dysoxic sites (0.3-1.1 mg/L bulk dissolved oxygen). Nitrogen-cycling mechanisms (e.g. ammonia oxidation, denitrification, dissimilatory nitrate reduction to ammonium) were prevalent and highly redundant, regardless of site-specific physicochemistry or nitrate availability, and present in 40% of reconstructed genomes, suggesting that nitrogen cycling is a core function of aquifer communities. Transcriptional activity for nitrification, denitrification, nitrite-dependent anaerobic methane oxidation and anaerobic ammonia oxidation (anammox) occurred simultaneously in oxic and dysoxic groundwater, indicating the availability of oxic-anoxic interfaces. Concurrent activity by these microorganisms indicates potential synergisms through metabolite exchange across these interfaces (e.g. nitrite and oxygen). Fragmented denitrification pathway encoding and transcription was widespread among groundwater bacteria, although a considerable proportion of associated transcriptional activity was driven by complete denitrifiers, especially under dysoxic conditions. Despite large differences in transcription, the capacity for the final steps of denitrification was largely invariant to aquifer conditions, and most genes and transcripts encoding N2O reductases were the atypical Sec-dependant type, suggesting energy-efficiency prioritization. Results provide insights into the capacity for cooperative relationships in groundwater communities, and the richness and complexity of metabolic mechanisms leading to the loss of fixed nitrogen.}, } @article {pmid35941112, year = {2022}, author = {Martino, C and Zaramela, LS and Gao, B and Embree, M and Tarasova, J and Parker, SJ and Wang, Y and Chu, H and Chen, P and Lee, KC and Galzerani, DD and Gengatharan, JM and Lekbua, A and Neal, M and Knight, R and Tsukamoto, H and Metallo, CM and Schnabl, B and Zengler, K}, title = {Acetate reprograms gut microbiota during alcohol consumption.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {4630}, pmid = {35941112}, issn = {2041-1723}, support = {U01 AA026939/AA/NIAAA NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; R01 AA024726/AA/NIAAA NIH HHS/United States ; R37 AA020703/AA/NIAAA NIH HHS/United States ; P50 AA011999/AA/NIAAA NIH HHS/United States ; R01 CA234245/CA/NCI NIH HHS/United States ; P30 CA014195/CA/NCI NIH HHS/United States ; }, mesh = {Acetates/pharmacology ; Alcohol Drinking/adverse effects ; Animals ; Ethanol/metabolism ; *Gastrointestinal Microbiome ; *Liver Diseases ; Mice ; Mice, Inbred C57BL ; }, abstract = {Liver damage due to chronic alcohol use is among the most prevalent liver diseases. Alcohol consumption frequency is a strong factor of microbiota variance. Here we use isotope labeled [1-[13]C] ethanol, metagenomics, and metatranscriptomics in ethanol-feeding and intragastric mouse models to investigate the metabolic impacts of alcohol consumption on the gut microbiota. First, we show that although stable isotope labeled [1-[13]C] ethanol contributes to fatty acid pools in the liver, plasma, and cecum contents of mice, there is no evidence of ethanol metabolism by gut microbiota ex vivo under anaerobic conditions. Next, we observe through metatranscriptomics that the gut microbiota responds to ethanol-feeding by activating acetate dissimilation, not by metabolizing ethanol directly. We demonstrate that blood acetate concentrations are elevated during ethanol consumption. Finally, by increasing systemic acetate levels with glyceryl triacetate supplementation, we do not observe any impact on liver disease, but do induce similar gut microbiota alterations as chronic ethanol-feeding in mice. Our results show that ethanol is not directly metabolized by the gut microbiota, and changes in the gut microbiota linked to ethanol are a side effect of elevated acetate levels. De-trending for these acetate effects may be critical for understanding gut microbiota changes that cause alcohol-related liver disease.}, } @article {pmid35940813, year = {2022}, author = {Rahmeh, R and Akbar, A and Alomirah, H and Kishk, M and Al-Ateeqi, A and Al-Milhm, S and Shajan, A and Akbar, B and Al-Merri, S and Alotaibi, M and Esposito, A}, title = {Camel milk microbiota: A culture-independent assessment.}, journal = {Food research international (Ottawa, Ont.)}, volume = {159}, number = {}, pages = {111629}, doi = {10.1016/j.foodres.2022.111629}, pmid = {35940813}, issn = {1873-7145}, mesh = {Animals ; Bacteria/genetics ; Camelus ; Humans ; *Microbiota/genetics ; Milk/microbiology ; *Mycobiome ; }, abstract = {Camel milk is renowned for its nutritional value and its therapeutic properties. It is considered a promising alternative to bovine milk due to its higher nutritional benefits, hypoallergenic characteristics and greater digestibility in the human gastrointestinal system. This study reports camel milk's bacterial and fungal microbiota, and the effect of geographical location and season on its bacterial community. We sequenced the V3-V4 regions of the16S rRNA gene for bacteria and the internal transcribed spacer (ITS) for fungi. A total of 134 samples of dromedary raw camel milk were collected from south, north and middle Kuwait during two seasons. Raw camel milk showed a diversified bacterial community, with 1196 genera belonging to 33 phyla. The four most predominant phyla of bacteria were Proteobacteria, Firmicutes, Actinobacteria and Bacteroidota. The core microbiota of raw camel milk, represented by the dominant genera shared by the majority of samples, was constituted by the genera Schlegelella, Paenibacillus, Lactobacillus, unclassified Comamonadaceae, Pediococcus, Moraxella, Acinetobacter, Staphylococcus, Enterococcus, Pseudomonas, Streptococcus, unclassified Micrococcaceae, Rothia, unclassified Sphingomonadaceae, unclassified Neisseriaceae and Sphingomonas. The fungal population was assessed in 14 raw camel milk samples, and comprised 87 genera belonging to 3 phyla. The genera Penicillium, Cladosporium, Candida, Aspergillus, Alternaria and Fusarium, dominated the fungal community. These findings shed light on raw camel milk's core bacterial and fungal microbiome. The geographical location and the season had a significant impact on the diversity and composition of camel milk microbiome.}, } @article {pmid35940746, year = {2022}, author = {Xian, S and Zhong, H and Yi, B and Liu, X and Shen, G and Li, M and Zhang, Z and Luo, Q and Li, S and Zhou, M and Xu, F and Chen, A}, title = {Identification of pellicle formation related microorganisms in traditional Sichuan paocai through metagenomic sequence and the effects of Baijiu/Salt on pellicle and volatile components.}, journal = {Food research international (Ottawa, Ont.)}, volume = {159}, number = {}, pages = {111130}, doi = {10.1016/j.foodres.2022.111130}, pmid = {35940746}, issn = {1873-7145}, mesh = {Fermentation ; *Lactobacillus/metabolism ; Metagenome ; Metagenomics ; Pichia ; *Saccharomycetales ; }, abstract = {The occurrence of pellicle on the surface of paocai brine is a common undesirable phenomenon during the multi-rounds of paocai fermentation, which is mainly caused by the growth of microorganisms related to pellicle formation. But the detailed information on these microorganisms and volatile components produced by them, as well as the changes of the microorganisms during the process of paocai recovery, are still rare in the literature. Therefore, the purpose of this study was (1) to analyze the pellicle formation related microorganisms by comparing the differential microorganisms in initial brine and the brine when pellicle occurred through metagenomic sequencing technology, (2) to explore the changes of microorganisms in the fermentation system after addition Baijiu and/or salt, and (3) to further detect the VOCs in paocai samples by gas chromatography-mass spectrometry (GC-MS). The relationship between VOCs and the selected marker microorganisms was also determined. The results showed that the diversity of fungi was increased when pellicle formed, the pellicle formation related microorganisms mainly belonged to six genus, including Kazachstania, Lactobacillus, Pichia, Candida, Lachancea, and Saccharomyces. Apart from the unknown function and basic life activities of microorganisms, the metabolic activities of these pellicle formation related microorganisms were mainly carbohydrate transport and metabolism, and amino acid transport and metabolism. The growth of pellicle formation related microorganisms could be inhibited by adding Baijiu (1.5% v/v), but the addition of salt (7% salt (w/v) did not promote this inhibitory effect. Through PCA analysis, it was found that the VOCs of paocai were significantly affected by adding Baijiu and Baijiu and salt. The undesirable smell at the beginning of pellicle formation may be related to Propanoic acid, hexyl ester, 1,3-Dimethyl-1-cyclohexene, Oxime-, methoxy-phenyl- and Phenylethyl Alcohol.}, } @article {pmid35939836, year = {2022}, author = {Liu, J and Wang, X and Xie, H and Zhong, Q and Xia, Y}, title = {Analysis and evaluation of different sequencing depths from 5 to 20 million reads in shotgun metagenomic sequencing, with optimal minimum depth being recommended.}, journal = {Genome}, volume = {65}, number = {9}, pages = {491-504}, doi = {10.1139/gen-2021-0120}, pmid = {35939836}, issn = {1480-3321}, mesh = {High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenome ; *Metagenomics/methods ; Obesity/genetics ; Phylogeny ; }, abstract = {Our study was to analyze and evaluate the impact of different shotgun metagenomic sequencing depths from 5 to 20 million in metagenome-wide association studies (MWASs), and to determine the optimal minimum sequencing depth. We included a set of 200 previously published gut microbial shotgun metagenomic sequencing data on obesity (100 obese vs. 100 non-obese). The reads with original sequencing depths >20 million were downsized into seven experimental groups with depths from 5 to 20 million (interval 2.5 million). Using both integrated gene cluster (IGC) and metagenomic phylogenetic analysis 2 (MetaPhlAn2), we obtained and analyzed the read matching rates, gene count, species richness and abundance, diversity, and clinical biomarkers of the experimental groups with the original depth as the control group. An additional set of 100 published data from a colorectal cancer (CRC) study was included for validation (50 CRC vs. 50 CRC-free). Our results showed that more genes and species were identified following the increase in sequencing depths. When it reached 15 million or higher, the species richness became more stable with changing rate of 5% or lower, and the species composition more stable with ICC intraclass correlation coefficient (ICC) higher than 0.75. In terms of species abundance, 81% and 97% of species showed significant differences in IGC and MetaPhlAn2 among all groups with p < 0.05. Diversity showed significant differences across all groups, with decreasing differences of diversity between the experimental and the control groups following the increase in sequencing depth. The area under a receiver operating characteristic curve, AUC, of the obesity classifier for running the obesity testing samples showed an increasing trend following the increase in sequencing depth (τ = 0.29). The validation results were consistent with the above results. Our study found that the higher the sequencing depth is, the more the microbial information in structure and composition it provides. We also found that when sequencing depth was 15 million or higher, we obtained more stable species compositions and disease classifiers with good performance. Therefore, we recommend 15 million as the optimal minimum sequencing depth for an MWAS.}, } @article {pmid35939616, year = {2022}, author = {Wang, J and Qie, J and Zhu, D and Zhang, X and Zhang, Q and Xu, Y and Wang, Y and Mi, K and Pei, Y and Liu, Y and Ji, G and Liu, X}, title = {The landscape in the gut microbiome of long-lived families reveals new insights on longevity and aging - relevant neural and immune function.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2107288}, pmid = {35939616}, issn = {1949-0984}, mesh = {Aged ; Aged, 80 and over ; Aging ; Bacteria/genetics ; Brain-Derived Neurotrophic Factor/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Immunity ; Longevity ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Human longevity has a strong familial and genetic component. Dynamic characteristics of the gut microbiome during aging associated with longevity, neural, and immune function remained unknown. Here, we aim to reveal the synergistic changes in gut microbiome associated with decline in neural and immune system with aging and further obtain insights into the establishment of microbiome homeostasis that can benefit human longevity. Based on 16S rRNA and metagenomics sequencing data for 32 longevity families including three generations, centenarians, elderly, and young groups, we found centenarians showed increased diversity of gut microbiota, severely damaged connection among bacteria, depleted in microbial-associated essential amino acid function, and increased abundance of anti-inflammatory bacteria in comparison to young and elderly groups. Some potential probiotic species, such as Desulfovibrio piger, Gordonibacter pamelaeae, Odoribacter splanchnicus, and Ruminococcaceae bacterium D5 were enriched with aging, which might possibly support health maintenance. The level of Amyloid-β (Aβ) and brain-derived neurotrophic factor (BDNF) related to neural function showed increased and decreased with aging, respectively. The elevated level of inflammatory factors was observed in centenarians compared with young and elderly groups. The enriched Bacteroides fragilis in centenarians might promote longevity through up-regulating anti-inflammatory factor IL-10 expression to mediate the critical balance between health and disease. Impressively, the associated analysis for gut microbiota with the level of Aβ, BDNF, and inflammatory factors suggests Bifidobacterium pseudocatenulatum could be a particularly beneficial bacteria in the improvement of impaired neural and immune function. Our results provide a rationale for targeting the gut microbiome in future clinical applications of aging-related diseases and extending life span.Abbreviations: 16S rRNA: 16S ribosomal RNA; MAGs: Metagenome-assembled genomes; ASVs: Amplicon sequence variants; DNA: Deoxyribonucleic acid; FDR: False discovery rate: KEGG: Kyoto Encyclopedia of Genes and Genomes; PCoA: Principal coordinates analysis; PCR: Polymerase chain reaction; PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States; Aβ: Amyloid-β (Aβ); BDNF: Brain-derived neurotrophic factor.}, } @article {pmid35939194, year = {2023}, author = {Noman, SM and Shafiq, M and Bibi, S and Mittal, B and Yuan, Y and Zeng, M and Li, X and Olawale, OA and Jiao, X and Irshad, M}, title = {Exploring antibiotic resistance genes, mobile gene elements, and virulence gene factors in an urban freshwater samples using metagenomic analysis.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {2}, pages = {2977-2990}, pmid = {35939194}, issn = {1614-7499}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Fresh Water ; *Genes, Bacterial ; Metagenomics ; Virulence ; }, abstract = {Antibiotic resistance genes (ARGs) and antimicrobial resistance elements (AMR) are novel environmental contaminants that pose a significant risk to human health globally. Freshwater contains a variety of microorganisms that might affect human health; its quality must be assessed before use. However, the dynamics of mobile genetic elements (MGEs) and ARG propagation in freshwater have rarely been studied in Singapore. Therefore, this study used metagenomics to compare diversity, virulence factor composition, and ARG and MGE co-occurrence with bacterial communities in paired (n = 8) environmental freshwater samples. KneadData, FMAP, and Kraken2 were used for bioinformatics analysis and R (v4.1.1) for statistical analysis. Sequence reads with a total of 9043 species were taxonomically classified into 66 phyla, 130 classes, 261 orders, 584 families, and 2477 genera. Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes were found the Phyla in all samples. Analysis of QIIME output by PICRUSt and ß-diversity showed unique clusters and functional microbial community structures. A total of 2961 ARGs were found that conferred resistance to multidrug, aminoglycosides, tetracyclines, elfamycins, and more. The classified ARG mechanism revealed significant distribution of virulence factors in bacterial cells. Transposes and transposon were highly correlated to ARG gene transfer. Co-occurrence network analysis showed several MGEs appear to use the same ARGs (intI and rho) and were dominant in all samples. Furthermore, ARGs are also highly correlated with bacteria like Campylobacter and Escherichia. This study enhances the understanding of antibiotic risk assessment and provides a new perspective on bacterial assembly contamination and the functional prevalence of ARGs and MGEs with antibiotic resistance bacteria. Moreover, it raises public awareness because these contaminants put people's lives at risk of acquiring bacterial infections. In addition, it can also help propose hybrid water treatment approaches.}, } @article {pmid35938833, year = {2022}, author = {Makinde, OA and Lunga, PM and Bezuidt, OKI and Makhalanyane, TP}, title = {Four Lentisphaerae Family Metagenome-Assembled Genomes from the South Atlantic Ocean.}, journal = {Microbiology resource announcements}, volume = {11}, number = {9}, pages = {e0049622}, pmid = {35938833}, issn = {2576-098X}, support = {//National Research Foundation (NRF)/ ; }, abstract = {We present four Lentisphaerae metagenome-assembled genomes (MAGs) from the South Atlantic Ocean. The medium-quality genomes, affiliated with the family of Lentisphaeraceae, ranged from 4.86 to 5.46 Mbp and harbored the genetic capacity to produce secondary metabolites. This resource provides a basis for investigating the functional attributes of this phylum.}, } @article {pmid35938822, year = {2022}, author = {Yerlan, A and Daly, RA and Keshavarz Afshar, R and Shaffer, M and Wrighton, KC and McGivern, BB}, title = {Draft Metagenome-Assembled Genome Sequences of Three Novel Ammonia-Oxidizing Nitrososphaera Strains Recovered from Agricultural Soils in Western Colorado.}, journal = {Microbiology resource announcements}, volume = {11}, number = {9}, pages = {e0036022}, pmid = {35938822}, issn = {2576-098X}, support = {1912915//National Science Foundation (NSF)/ ; }, abstract = {Microbial nitrification is critical to nitrogen loss from agricultural soils. Here, we report three thaumarchaeotal metagenome-assembled genomes (MAGs) representing a new species of Nitrososphaera. These genomes expand the representation of archaeal nitrifiers recovered from arid, agricultural soils.}, } @article {pmid35938729, year = {2022}, author = {Du, S and Zhang, Y and Shen, JP and Hu, HW and Zhang, J and Shu, C and He, JZ}, title = {Alteration of Manure Antibiotic Resistance Genes via Soil Fauna Is Associated with the Intestinal Microbiome.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0052922}, pmid = {35938729}, issn = {2379-5077}, mesh = {Animals ; Humans ; *Gastrointestinal Microbiome/genetics ; Soil ; Manure/analysis ; Anti-Bacterial Agents/analysis ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; Larva/genetics ; }, abstract = {Livestock wastes contain high levels of antibiotic resistance genes (ARGs) and a variety of human-related pathogens. Bioconversion of livestock manure using larvae of the beetle Protaetia brevitarsis is an effective technique for waste reduction and value creation; however, the fate of manure ARGs during gut passage and interaction with the gut microbiome of P. brevitarsis remains unclear. To investigate this, we fed P. brevitarsis with dry chicken manure for 6 days and measured bacterial community dynamics and ARG abundance and diversity along the P. brevitarsis gut tract using high-throughput quantitative PCR and metagenomics approaches. The diversity of ARGs was significantly lower in larval midgut, hindgut, and frass than in raw chicken manure, and around 80% of pathogenicity-related genes (PRGs) exhibited reduced abundance. Network analysis demonstrated that Bacteroidetes and Firmicutes were the key bacterial phyla associated with ARG reduction. Metagenomic analysis further indicated that ARGs, mobile genetic elements (MGEs), and PRGs were simultaneously attenuated in the hindgut, implicating a decreased likelihood for horizontal gene transfer (HGT) of ARGs among bacteria and pathogens during manure bioconversion. Our findings demonstrated that the attenuation of ARGs is strongly associated with the variation of the gut microbiome of P. brevitarsis, providing insights into mechanisms of risk mitigation of ARG dissemination during manure bioconversion. IMPORTANCE Saprophagous fauna like the oriental edible beetle (P. brevitarsis) plays a fundamental role in converting organic wastes into biofertilizer. Accumulating evidence has shown that soil fauna can reduce the abundance of ARGs, although the underlying mechanism of ARG reduction is still unclear. In our previous research, we found a large reduction of ARGs in vegetable roots and leaves from frass compared with raw manure, providing a promising biofertilizer for soil-vegetable systems. Therefore, in this study, temporal dynamic changes in the microbiomes of the donor (chicken manure) and host (P. brevitarsis) were investigated, and we found a close association between the gut microbiome and the alteration of ARGs. These results shed new light on how the insect gut microbiome can mitigate manure-borne ARGs and provide insights into the bioconversion process via a typical member of the saprophagous fauna, P. brevitarsis.}, } @article {pmid35938720, year = {2022}, author = {Tang, J and Tan, W and Luo, L and Xu, H and Li, N}, title = {Application of Metagenomic Next-Generation Sequencing in the Diagnosis of Pneumonia Caused by Chlamydia psittaci.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0238421}, pmid = {35938720}, issn = {2165-0497}, mesh = {*Chlamydophila psittaci/genetics ; Headache ; High-Throughput Nucleotide Sequencing ; Humans ; *Pneumonia/diagnosis/microbiology ; *Psittacosis/diagnosis/epidemiology/microbiology ; Retrospective Studies ; }, abstract = {Psittacosis is an uncommon disease which mainly presents as community-acquired pneumonia (CAP). We aim to apply metagenomic next-generation sequencing (mNGS) as a promising tool in the diagnosis of psittacosis pneumonia and to describe its clinical spectrum to provide physicians with a better understanding and recognition of this disease. Thirteen cases of psittacosis pneumonia were diagnosed by using mNGS. A retrospective analysis of the data on clinical manifestations, laboratory data, computed tomography (CT) images, new diagnosis tools, treatments, and outcomes was summarized. These patients had common symptoms of fever and weakness; some had poor appetite, cough, myalgia, and headache. Ten patients developed acute respiratory distress syndrome (ARDS), among which six patients were severe pneumonia cases and needed ventilator therapy. Most patients got psittacosis pneumonia during the cold season. Ten cases were sporadic, but three were family clustering. All of the 13 patients were traced to an exposure history to birds, cat, or poultry, among which 2 only touched the innards of killed poultry before cooking, which may be an atypical exposure history not been reported before, to our knowledge. Most patients had various degrees of liver dysfunction. Air-space consolidations, along with ground-glass opacities and reticular shadows, were detected on chest CT scan. mNGS takes 48 to 72 h to provide results and helps to diagnose psittacosis. After being diagnosed by mNGS, with effective medicines, all patients finally had complete recoveries. The use of mNGS can improve the diagnostic rate of psittacosis pneumonia and shorten the course of disease control. IMPORTANCE Psittacosis pneumonia is easily underdiagnosed and misdiagnosed. In this study, we use mNGS in the diagnosis of psittacosis pneumonia. We found this disease is prone in the cold season, and touching the innards of killed poultry during cooking may be an atypical exposure history which has not been reported before to our knowledge. There are sporadic cases and family outbreak cases as well. Except for typical symptoms of fever and weakness, headache may be the main and only symptom in some patients. The rate of severe pneumonia is high among inpatients with psittacosis pneumonia, and the incidence of hepatic involvements is also high. Psittacosis pneumonia can be cured if the diagnosis is accurate and in time, even if it is severe pneumonia on admission. Some problems worthy of our attention about psittacosis pneumonia were put forward, such as its sick season, special exposure history, the rate of severe disease, and the high cure rate. mNGS can quickly and objectively detect more rare pathogenic microorganisms in clinical specimens without the need for specific amplification and has an advantage in the diagnosis of rare pathogenic bacteria in difficult cases such as psittacosis pneumonia. The use of mNGS can improve the accuracy and reduce the delay in the diagnosis of psittacosis, which shortens the course of disease control.}, } @article {pmid35938718, year = {2022}, author = {Xu, Z and Wang, M and Zhang, H and He, W and Cao, L and Lian, C and Zhong, Z and Wang, H and Fu, L and Zhang, X and Li, C}, title = {Metabolism Interactions Promote the Overall Functioning of the Episymbiotic Chemosynthetic Community of Shinkaia crosnieri of Cold Seeps.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0032022}, pmid = {35938718}, issn = {2379-5077}, mesh = {Animals ; Ecosystem ; In Situ Hybridization, Fluorescence ; Bacteria/metabolism ; *Anomura/metabolism ; Methane/metabolism ; *Decapoda/metabolism ; Sulfur/metabolism ; }, abstract = {Remarkably diverse bacteria have been observed as biofilm aggregates on the surface of deep-sea invertebrates that support the growth of hosts through chemosynthetic carbon fixation. Growing evidence also indicates that community-wide interactions, and especially cooperation among symbionts, contribute to overall community productivity. Here, metagenome-guided metatranscriptomic and metabolic analyses were conducted to investigate the taxonomic composition, functions, and potential interactions of symbionts dwelling on the seta of Shinkaia crosnieri lobsters in a methane cold seep. Methylococcales and Thiotrichales dominated the community, followed by the Campylobacteriales, Nitrosococcales, Flavobacteriales, and Chitinophagales Metabolic interactions may be common among the episymbionts since many separate taxon genomes encoded complementary genes within metabolic pathways. Specifically, Thiotrichales could contribute to detoxification of hydroxylamine that is a metabolic by-product of Methylococcales. Further, Nitrosococcales may rely on methanol leaked from Methylococcales cells that efficiently oxidize methane. Elemental sulfur may also serve as a community good that enhances sulfur utilization that benefits the overall community, as evidenced by confocal Raman microscopy. Stable intermediates may connect symbiont metabolic activities in cyclical oxic-hypoxic fluctuating environments, which then enhance overall community functioning. This hypothesis was partially confirmed via in situ experiments. These results highlight the importance of microbe-microbe interactions in symbiosis and deep-sea adaptation. IMPORTANCE Symbioses between chemosynthetic bacteria and marine invertebrates are common in deep-sea chemosynthetic ecosystems and are considered critical foundations for deep-sea colonization. Episymbiotic microorganisms tend to form condensed biofilms that may facilitate metabolite sharing among biofilm populations. However, the prevalence of metabolic interactions among deep-sea episymbionts and their contributions to deep-sea adaptations are not well understood due to sampling and cultivation difficulties associated with deep-sea environments. Here, we investigated metabolic interactions among the episymbionts of Shinkaia crosnieri, a dominant chemosynthetic ecosystem lobster species in the Northwest Pacific Ocean. Meta-omics characterizations were conducted alongside in situ experiments to validate interaction hypotheses. Furthermore, imaging analysis was conducted, including electron microscopy, fluorescent in situ hybridization (FISH), and confocal Raman microscopy (CRM), to provide direct evidence of metabolic interactions. The results support the Black Queen Hypothesis, wherein leaked public goods are shared among cohabitating microorganisms to enhance the overall adaptability of the community via cooperation.}, } @article {pmid35938717, year = {2022}, author = {Okazaki, Y and Nakano, SI and Toyoda, A and Tamaki, H}, title = {Long-Read-Resolved, Ecosystem-Wide Exploration of Nucleotide and Structural Microdiversity of Lake Bacterioplankton Genomes.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0043322}, pmid = {35938717}, issn = {2379-5077}, mesh = {*Lakes/microbiology ; Ecosystem ; Nucleotides ; Metagenome ; Bacteria/genetics ; *Bacteriophages/genetics ; }, abstract = {Reconstruction of metagenome-assembled genomes (MAGs) has become a fundamental approach in microbial ecology. However, a MAG is hardly complete and overlooks genomic microdiversity because metagenomic assembly fails to resolve microvariants among closely related genotypes. Aiming at understanding the universal factors that drive or constrain prokaryotic genome diversification, we performed an ecosystem-wide high-resolution metagenomic exploration of microdiversity by combining spatiotemporal (2 depths × 12 months) sampling from a pelagic freshwater system, high-quality MAG reconstruction using long- and short-read metagenomic sequences, and profiling of single nucleotide variants (SNVs) and structural variants (SVs) through mapping of short and long reads to the MAGs, respectively. We reconstructed 575 MAGs, including 29 circular assemblies, providing high-quality reference genomes of freshwater bacterioplankton. Read mapping against these MAGs identified 100 to 101,781 SNVs/Mb and 0 to 305 insertions, 0 to 467 deletions, 0 to 41 duplications, and 0 to 6 inversions for each MAG. Nonsynonymous SNVs were accumulated in genes potentially involved in cell surface structural modification to evade phage recognition. Most (80.2%) deletions overlapped with a gene coding region, and genes of prokaryotic defense systems were most frequently (>8% of the genes) overlapped with a deletion. Some such deletions exhibited a monthly shift in their allele frequency, suggesting a rapid turnover of genotypes in response to phage predation. MAGs with extremely low microdiversity were either rare or opportunistic bloomers, suggesting that population persistency is key to their genomic diversification. The results concluded that prokaryotic genomic diversification is driven primarily by viral load and constrained by a population bottleneck. IMPORTANCE Identifying intraspecies genomic diversity (microdiversity) is crucial to understanding microbial ecology and evolution. However, microdiversity among environmental assemblages is not well investigated, because most microbes are difficult to culture. In this study, we performed cultivation-independent exploration of bacterial genomic microdiversity in a lake ecosystem using a combination of short- and long-read metagenomic analyses. The results revealed the broad spectrum of genomic microdiversity among the diverse bacterial species in the ecosystem, which has been overlooked by conventional approaches. Our ecosystem-wide exploration further allowed comparative analysis among the genomes and genes and revealed factors behind microbial genomic diversification, namely, that diversification is driven primarily by resistance against viral infection and constrained by the population size.}, } @article {pmid35938113, year = {2022}, author = {Yang, D and Li, L and Li, C and Chen, S and Deng, J and Yang, S}, title = {Formation and inhibition mechanism of novel angiotensin I converting enzyme inhibitory peptides from Chouguiyu.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {920945}, pmid = {35938113}, issn = {2296-861X}, abstract = {Angiotensin I converting enzyme (ACE) inhibitory peptides from fermented foods exhibit great potential to alleviate hypertension. In this study, the peptide extract from Chouguiyu exhibited a good inhibition effect on ACE, and the inhibition rate was significantly enhanced after fermentation for 8 days. The ACE inhibitory peptides were further identified, followed by their inhibition and formation mechanisms using microbiome technology and molecular docking. A total of 356 ACE inhibitory peptides were predicted using in silico, and most ACE inhibitory peptides increased after fermentation. These peptides could be hydrolyzed from 94 kinds of precursor proteins, mainly including muscle-type creatine kinase, nebulin, and troponin I. P1 (VEIINARA), P2 (FAVMVKG), P4 (EITWSDDKK), P7 (DFDDIQK), P8 (IGDDPKF), P9 (INDDPKIL), and P10 (GVDNPGHPFI) were selected as the core ACE inhibitory peptides according to their abundance and docking energy. The salt bridge and conventional hydrogen bond connecting unsaturated oxygen atoms in the peptides contributed most to the ACE inhibition. The cleavage proteases from the microbial genera in Chouguiyu for preparing these 7 core ACE inhibitory peptides were further analyzed by hydrolysis prediction and Pearson's correlation. The correlation network showed that P7, P8, and P9 were mainly produced by the proteases from LAB including Lactococcus, Enterococcus, Vagococcus, Peptostreptococcus, and Streptococcus, while P1, P2, P4, and P10 were mainly Produced by Aeromonas, Bacillus, Escherichia, and Psychrobacter. This study is helpful in isolating the proteases and microbial strains to directionally produce the responding ACE inhibitory peptides.}, } @article {pmid35938022, year = {2022}, author = {Ross, EM and Hayes, BJ}, title = {Metagenomic Predictions: A Review 10 years on.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {865765}, pmid = {35938022}, issn = {1664-8021}, abstract = {Metagenomic predictions use variation in the metagenome (microbiome profile) to predict the unknown phenotype of the associated host. Metagenomic predictions were first developed 10 years ago, where they were used to predict which cattle would produce high or low levels of enteric methane. Since then, the approach has been applied to several traits and species including residual feed intake in cattle, and carcass traits, body mass index and disease state in pigs. Additionally, the method has been extended to include predictions based on other multi-dimensional data such as the metabolome, as well to combine genomic and metagenomic information. While there is still substantial optimisation required, the use of metagenomic predictions is expanding as DNA sequencing costs continue to fall and shows great promise particularly for traits heavily influenced by the microbiome such as feed efficiency and methane emissions.}, } @article {pmid35938008, year = {2022}, author = {Vajjala, M and Johnson, B and Kasparek, L and Leuze, M and Yao, Q}, title = {Profiling a Community-Specific Function Landscape for Bacterial Peptides Through Protein-Level Meta-Assembly and Machine Learning.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {935351}, pmid = {35938008}, issn = {1664-8021}, support = {P20 GM104320/GM/NIGMS NIH HHS/United States ; }, abstract = {Small proteins, encoded by small open reading frames, are only beginning to emerge with the current advancement of omics technology and bioinformatics. There is increasing evidence that small proteins play roles in diverse critical biological functions, such as adjusting cellular metabolism, regulating other protein activities, controlling cell cycles, and affecting disease physiology. In prokaryotes such as bacteria, the small proteins are largely unexplored for their sequence space and functional groups. For most bacterial species from a natural community, the sample cannot be easily isolated or cultured, and the bacterial peptides must be better characterized in a metagenomic manner. The bacterial peptides identified from metagenomic samples can not only enrich the pool of small proteins but can also reveal the community-specific microbe ecology information from a small protein perspective. In this study, metaBP (Bacterial Peptides for metagenomic sample) has been developed as a comprehensive toolkit to explore the small protein universe from metagenomic samples. It takes raw sequencing reads as input, performs protein-level meta-assembly, and computes bacterial peptide homolog groups with sample-specific mutations. The metaBP also integrates general protein annotation tools as well as our small protein-specific machine learning module metaBP-ML to construct a full landscape for bacterial peptides. The metaBP-ML shows advantages for discovering functions of bacterial peptides in a microbial community and increases the yields of annotations by up to five folds. The metaBP toolkit demonstrates its novelty in adopting the protein-level assembly to discover small proteins, integrating protein-clustering tool in a new and flexible environment of RBiotools, and presenting the first-time small protein landscape by metaBP-ML. Taken together, metaBP (and metaBP-ML) can profile functional bacterial peptides from metagenomic samples with potential diverse mutations, in order to depict a unique landscape of small proteins from a microbial community.}, } @article {pmid35937693, year = {2022}, author = {Fu, Y and Wu, J and Wang, D and Li, T and Shi, X and Li, L and Zhu, M and Zhang, Z and Yu, X and Dai, Q}, title = {Metagenomic profiling of ocular surface microbiome changes in Demodex blepharitis patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {922753}, pmid = {35937693}, issn = {2235-2988}, mesh = {*Acinetobacter ; Bacteria/genetics ; *Blepharitis/epidemiology/pathology ; Humans ; Meibomian Glands/pathology ; *Microbiota/genetics ; Proteobacteria ; }, abstract = {PURPOSE: To compare the ocular surface and meibum microbial communities of humans with Demodex Blepharitis (DB) and healthy controls.

METHODS: Conjunctival sac and meibum samples from 25 DB patients and 11 healthy controls were analyzed using metagenomic next-generation sequencing (mNGS).

RESULTS: The alpha-diversity of the conjunctival sac microbiome of the DB group (observed, Chao1, ACE) was lower than that of the control group, whereas all meibum diversity indicators were similar. In conjunctival samples, the relative abundance (RA) of the phylum Proteobacteria was significantly higher (p=0.023), and the RA of both phyla Actinobacteria and Firmicutes was significantly lower (p=0.002, 0.025, respectively) in the DB group than that in the control group. In meibum samples, the RA of the phyla Proteobacteria and Actinobacteria were similar, whereas that of the phylum Firmicutes was significantly lower in the DB group (p=0.019) than that in the control group. Linear discriminant analysis with effect size measurement of the conjunctival and meibum microbiomes showed that Sphingobium sp. YG1 and Acinetobacter guillouiae were enriched in the DB group. Sphingobium sp. YG1, Acinetobacter guillouiae and Pseudomonas putida in the DB group were related to more severe ocular surface clinical parameters. Discriminative genera's principal coordinate analysis separated all control and DB microbiomes into two distinct clusters.

CONCLUSIONS: Proteobacteria's increased prevalence may indicate ocular microbial community instability. The species Sphingobium sp. YG1 and Acinetobacter guillouiae are potentially pathogenic bacterial biomarkers in DB. Demodex infection mainly affects the ocular surface microbiome rather than penetrating deeper into the meibomian gland.}, } @article {pmid35937275, year = {2022}, author = {Zhang, Y and Wang, W and Zhang, Y and Zhai, S and Xia, H and Zhang, X}, title = {Pulmonary Cryptococcosis Diagnosed by Metagenomic Next-Generation Sequencing in a Young Patient With Normal Immune Function: A Case Report.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {942282}, pmid = {35937275}, issn = {2296-2565}, mesh = {*Cryptococcosis/diagnosis/drug therapy/microbiology ; *Cryptococcus neoformans/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; Immunity ; Metagenomics/methods ; *Pneumonia ; }, abstract = {BACKGROUND: Pulmonary cryptococcosis (PC) is a serious opportunistic fungal infection that usually occurs in immunocompromised patients. This disease is often difficult to diagnose in time due to its clinical manifestations and radiological feature similar to other pulmonary infections, as well as the low sensitivity of conventional diagnostic methods. Cryptococcosis in immune-competent patients is rare.

CASE PRESENTATION: Here we report a case of PC in an immune-competent patient. Tuberculosis was suspected according to radiological features due to the positive T-lymphocyte spot test and pure protein derivative skin test. To further detect the pathogen, bronchoalveolar lavage fluid (BALF) was collected for metagenomic next-generation sequencing (mNGS). Cryptococcus neoformans (one specific read) was identified by mNGS, indicating the PC of this patient. The following BALF culture and cryptococcal antigen lateral flow assay (CrAg-LFA) test also showed Cryptococcus infection, confirming the mNGS detection. Voriconazole (0.4 g daily) was given orally according to the subsequent susceptibility results. After seven months of treatment, the patient's condition improved.

CONCLUSION: Metagenomic next-generation sequencing (mNGS) is a better diagnostic tool to help clinicians distinguish pulmonary cryptococcosis from other atypical pulmonary infections.}, } @article {pmid35935588, year = {2022}, author = {Yang, Q and Xu, Y and Shen, L and Pan, Y and Huang, J and Ma, Q and Yu, C and Chen, J and Chen, Y and Chen, M}, title = {Guanxinning Tablet Attenuates Coronary Atherosclerosis via Regulating the Gut Microbiota and Their Metabolites in Tibetan Minipigs Induced by a High-Fat Diet.}, journal = {Journal of immunology research}, volume = {2022}, number = {}, pages = {7128230}, pmid = {35935588}, issn = {2314-7156}, mesh = {Animals ; *Coronary Artery Disease ; Diet, High-Fat/adverse effects ; *Gastrointestinal Microbiome ; Swine ; Swine, Miniature ; Tablets/pharmacology ; Tibet ; Tumor Necrosis Factor-alpha/pharmacology ; }, abstract = {Coronary atherosclerosis (CA) is a chronic and evolving inflammatory disease characterized by the build-up of atherosclerotic plaque in the wall of coronary arteries. Guanxinning tablet (GXNT) is a novel Chinese medicine formula, which has been clinically used to treat coronary heart disease for many years. However, the potential mechanism for treating CA remains unclear. Thus, the study was aimed at investigating the therapeutic effect of GXNT on CA and further explore the underlying mechanisms from the perspective of gut microbiota. Following the establishment of a CA model in Tibetan minipigs, GXNT was orally administrated. We simultaneously detected blood lipid levels, observed ventricular function using ultrasound examination, measured platelet aggregation, and checked changes in inflammatory factors, oxidative stress factors, and vascular endothelial injury-related indexes applying ELISA assays. Histopathological changes of coronary artery tissue were subsequently evaluated using Sudan IV staining, HE staining, Oil red "O" staining, and immunohistochemistry assays. Finally, alterations of the gut microbiota and microbial metabolites were detected using metagenomic sequencing and targeted metabolomics, respectively. The results have suggested that GXNT could regulate dyslipidemia, improve heart function, and inhibit the levels of ox-LDL, CRP, TNF-α, IL-1β, SOD, MDA, vWF, and ET-1, as well as platelet aggregation. Additionally, histopathological findings revealed that GXNT could reduce lipid deposition, alleviate AS lesions, and restrain the expressions of NF-κB, TNF-α, and MMP-9. Furthermore, the composition of the gut microbiota was altered. Specifically, GXNT could upregulate the relative abundance of Prevotellaceae and Prevotella and downregulate the abundance of Proteobacteria, Enterobacteriaceae, and Escherichia. As for microbial metabolites, GXNT could increase fecal propionic acid, butyric acid, and LCA-3S and decrease fecal TMA-related metabolites, CDCA, and serum TMAO. In sum, the results showed that GXNT had a satisfactory anti-CA effect, and the mechanism was closely associated with modulating gut microbiota and related metabolites.}, } @article {pmid35935374, year = {2022}, author = {Tirone, C and Paladini, A and De Maio, F and Tersigni, C and D'Ippolito, S and Di Simone, N and Monzo, FR and Santarelli, G and Bianco, DM and Tana, M and Lio, A and Menzella, N and Posteraro, B and Sanguinetti, M and Lanzone, A and Scambia, G and Vento, G}, title = {The Relationship Between Maternal and Neonatal Microbiota in Spontaneous Preterm Birth: A Pilot Study.}, journal = {Frontiers in pediatrics}, volume = {10}, number = {}, pages = {909962}, pmid = {35935374}, issn = {2296-2360}, abstract = {The newborn's microbiota composition at birth seems to be influenced by maternal microbiota. Maternal vaginal microbiota can be a determining factor of spontaneous Preterm Birth (SP[PTB]), the leading cause of perinatal mortality. The aim of the study is to investigate the likelihood of a causal relationship between the maternal vaginal microbiota composition and neonatal lung and intestinal microbiota profile at birth, in cases of SP[PTB]. The association between the lung and/or meconium microbiota with the subsequent development of bronchopulmonary dysplasia (BPD) was also investigated. Maternal vaginal swabs, newborns' bronchoalveolar lavage fluid (BALF) (1st, 3rd, 7th day of life) and first meconium samples were collected from 20 women and 23 preterm newborns with gestational age ≤ 30 weeks (12 = SP[PTB]; 11 = Medically Indicated Preterm Birth-MI[PTB]). All the samples were analyzed for culture examination and for microbiota profiling using metagenomic analysis based on the Next Generation Sequencing (NGS) technique of the bacterial 16S rRNA gene amplicons. No significant differences in alpha e beta diversity were found between the neonatal BALF samples of SP[PTB] group and the MI[PTB] group. The vaginal microbiota of mothers with SP[PTB] showed a significant difference in alpha diversity with a decrease in Lactobacillus and an increase in Proteobacteria abundance. No association was found between BALF and meconium microbiota with the development of BPD. Vaginal colonization by Ureaplasma bacteria was associated with increased risk of both SP[PTB] and newborns' BPD occurrence. In conclusion, an increase in α-diversity values and a consequent fall in Lactobacillus in vaginal environment could be associated to a higher risk of SP[PTB]. We could identify neither a specific neonatal lung or meconium microbiota profiles in preterm infants born by SP[PTB] nor a microbiota at birth suggestive of subsequent BPD development. Although a strict match has not been revealed between microbiota of SP[PTB] mother-infant couples, a relationship cannot be excluded. To figure out the reciprocal influence of the maternal-neonatal microbiota and its potential role in the pathogenesis of SP[PTB] and BPD further research is needed.}, } @article {pmid35935216, year = {2022}, author = {Dutta, S and Choi, SY and Lee, YH}, title = {Temporal Dynamics of Endogenous Bacterial Composition in Rice Seeds During Maturation and Storage, and Spatial Dynamics of the Bacteria During Seedling Growth.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {877781}, pmid = {35935216}, issn = {1664-302X}, abstract = {Seed endophytes are of interest because they are believed to affect seed quality, and ultimately, plant growth and fitness. A comprehensive understanding of the assembly of the seed microbiome during seed development and maturation, the fate of microbes during storage, and the migration of microbes during seedling growth are still lacking. In this study, to understand the assembly and fate of endogenous bacteria in rice seeds from the ripening stage to the storage and seedling stages, we employed culture-dependent and metagenomic analyses. Bacterial communities in rice seeds were composed of a few dominant taxa that were introduced at the milky and dough stages, and they persisted during seed maturation. The culturable bacterial population gradually increased during the ripening stage, whereas there was a gradual decrease during storage. Bacteria that persisted during storage proliferated after imbibition and were distributed and established in the shoots and roots of rice seedlings. The storage temperature influenced the abundance of bacteria, which consequently changed the bacterial composition in the shoots and roots of seedlings. Pantoea, Pseudomonas, and Allorhizobium were consistently abundant from seed development to the germination stage. Some endogenous bacterial strains significantly promoted the growth of Arabidopsis and rice plants. Overall, our results indicate that rice seeds are colonized by a few bacterial taxa during seed development, and their relative abundance fluctuates during storage and contributes significantly to the establishment of endophytes in the stems and roots of rice plants. The selected bacterial isolates can be used to improve the growth and health of rice plants. To the best of our knowledge, this is the first study to reveal the dynamics of bacterial populations during storage of rice seeds at different temperatures. The temporal dynamics of the bacterial community during seed storage provide clues for the manipulation of endogenous bacteria in rice plants.}, } @article {pmid35935195, year = {2022}, author = {Prescott, RD and Zamkovaya, T and Donachie, SP and Northup, DE and Medley, JJ and Monsalve, N and Saw, JH and Decho, AW and Chain, PSG and Boston, PJ}, title = {Islands Within Islands: Bacterial Phylogenetic Structure and Consortia in Hawaiian Lava Caves and Fumaroles.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {934708}, pmid = {35935195}, issn = {1664-302X}, abstract = {Lava caves, tubes, and fumaroles in Hawai'i present a range of volcanic, oligotrophic environments from different lava flows and host unexpectedly high levels of bacterial diversity. These features provide an opportunity to study the ecological drivers that structure bacterial community diversity and assemblies in volcanic ecosystems and compare the older, more stable environments of lava tubes, to the more variable and extreme conditions of younger, geothermally active caves and fumaroles. Using 16S rRNA amplicon-based sequencing methods, we investigated the phylogenetic distinctness and diversity and identified microbial interactions and consortia through co-occurrence networks in 70 samples from lava tubes, geothermal lava caves, and fumaroles on the island of Hawai'i. Our data illustrate that lava caves and geothermal sites harbor unique microbial communities, with very little overlap between caves or sites. We also found that older lava tubes (500-800 yrs old) hosted greater phylogenetic diversity (Faith's PD) than sites that were either geothermally active or younger (<400 yrs old). Geothermally active sites had a greater number of interactions and complexity than lava tubes. Average phylogenetic distinctness, a measure of the phylogenetic relatedness of a community, was higher than would be expected if communities were structured at random. This suggests that bacterial communities of Hawaiian volcanic environments are phylogenetically over-dispersed and that competitive exclusion is the main driver in structuring these communities. This was supported by network analyses that found that taxa (Class level) co-occurred with more distantly related organisms than close relatives, particularly in geothermal sites. Network "hubs" (taxa of potentially higher ecological importance) were not the most abundant taxa in either geothermal sites or lava tubes and were identified as unknown families or genera of the phyla, Chloroflexi and Acidobacteria. These results highlight the need for further study on the ecological role of microbes in caves through targeted culturing methods, metagenomics, and long-read sequence technologies.}, } @article {pmid35934259, year = {2022}, author = {Uchiyama, J and Takemura-Uchiyama, I and Gotoh, K and Kato, SI and Sakaguchi, Y and Murakami, H and Fukuyama, T and Kaneki, M and Matsushita, O and Matsuzaki, S}, title = {Phylogenic analysis of new viral cluster of large phages with unusual DNA genomes containing uracil in place of thymine in gene-sharing network, using phages S6 and PBS1 and relevant uncultured phages derived from sewage metagenomics.}, journal = {Virus research}, volume = {319}, number = {}, pages = {198881}, doi = {10.1016/j.virusres.2022.198881}, pmid = {35934259}, issn = {1872-7492}, mesh = {*Bacteriophages ; DNA ; DNA, Viral/genetics ; Genome, Viral ; Metagenomics ; Myoviridae/genetics ; Phylogeny ; Sewage ; Thymine ; Uracil ; }, abstract = {Bacteriophages (phages) are the most diverse and abundant life-form on Earth. Jumbophages are phages with double-stranded DNA genomes longer than 200 kbp. Among these, some jumbophages with uracil in place of thymine as a nucleic acid base, which we have tentatively termed "dU jumbophages" in this study, have been reported. Because the dU jumbophages are considered to be a living fossil from the RNA world, the evolutionary traits of dU jumbophages are of interest. In this study, we examined the phylogeny of dU jumbophages. First, tBLASTx analysis of newly sequenced dU jumbophages such as Bacillus phage PBS1 and previously isolated Staphylococcus phage S6 showed similarity to the other dU jumbophages. Second, we detected the two partial genome sequences of uncultured phages possibly relevant to dU jumbophages, scaffold_002 and scaffold_007, from wastewater metagenomics. Third, according to the gene-sharing network analysis, the dU jumbophages, including phages PBS1 and S6, and uncultured phage scaffold_002 formed a cluster, which suggested a new viral subfamily/family. Finally, analyses of the phylogenetic relationship with other phages showed that the dU jumbophage cluster, which had two clades of phages infecting Gram-negative and Gram-positive bacteria, diverged from the single ancestral phage. These findings together with previous reports may imply that dU jumbophages evolved from the same origin before divergence of Gram-negative and Gram-positive bacteria.}, } @article {pmid35934204, year = {2022}, author = {Qiu, M and Li, S and Xiao, Y and Li, J and Zhang, Y and Li, X and Feng, B and Li, C and Lin, H and Zhu, J and Chen, N}, title = {Pathogenic and metagenomic evaluations reveal the correlations of porcine epidemic diarrhea virus, porcine kobuvirus and porcine astroviruses with neonatal piglet diarrhea.}, journal = {Microbial pathogenesis}, volume = {170}, number = {}, pages = {105703}, doi = {10.1016/j.micpath.2022.105703}, pmid = {35934204}, issn = {1096-1208}, mesh = {Animals ; *Coronavirus Infections ; Diarrhea/epidemiology ; *Kobuvirus/genetics ; Mamastrovirus ; Metagenomics ; *Porcine epidemic diarrhea virus/genetics ; Swine ; *Swine Diseases ; }, abstract = {Porcine epidemic diarrhea virus (PEDV) frequently causes diarrhea outbreaks. However, whether newly discovered enteric viruses such as porcine kobuvirus (PKV) and porcine astroviruses (PAstVs) are also correlated with diarrhea is still unclear. Diarrhea outbreaks were reported in a PEDV-vaccinated pig farm in Xinjiang Uygur Autonomous Region of China from 2019 to 2020. PEDV was a common pathogen detected in fecal samples by routine RT-PCR assays. The PEDV positive fecal sample was used for pathogenic analysis due to the failure isolation of PEDV. The challenged neonatal piglets appeared watery diarrhea within one day post infection (dpi) and all died within 6 dpi. Histopathological and immunohistochemical examinations supported that PEDV is a major pathogen causing intestinal lesions. To further explore enteric viruses associated with neonatal piglet diarrhea, metagenomics sequencing was performed for the diarrheic piglets. Remarkably, PKV was the most abundant virus (58.33%) followed by PEDV (34.45%) and PAstVs (7.22%), which were also confirmed by real-time RT-PCR assays. Significant in vivo replications of PEDV and PKV could only be observed in challenged piglets whilst PAstVs maintained similar virus loads in both challenged and mock infected piglets. Overall, this study provides first pathogenic and metagenomic evidence that significant proliferations of PEDV and PKV are closely associated with severe diarrhea in neonatal piglets, while PAstVs likely play limited roles in neonatal piglet diarrhea.}, } @article {pmid35934074, year = {2022}, author = {Lou, D and Zhang, X and Cao, Y and Zhou, Z and Liu, C and Kuang, G and Tan, J and Zhu, L}, title = {A novel NADP(H)-dependent 3α-HSDH from the intestinal microbiome of Ursus thibetanus.}, journal = {International journal of biological macromolecules}, volume = {219}, number = {}, pages = {159-165}, doi = {10.1016/j.ijbiomac.2022.07.252}, pmid = {35934074}, issn = {1879-0003}, mesh = {Animals ; Bile Acids and Salts ; Escherichia coli/genetics/metabolism ; *Gastrointestinal Microbiome ; Glutathione ; Glycochenodeoxycholic Acid ; Hydroxysteroid Dehydrogenases/metabolism ; Ions ; NADP ; Peptide Hydrolases ; Recombinant Proteins/metabolism ; Transferases ; *Ursidae/metabolism ; }, abstract = {3α-HSDHs have a crucial role in the bioconversion of steroids, and have been widely applied in the detection of total bile acid (TBA). In this study, we report a novel NADP(H)-dependent 3α-HSDH (named Sc 3α-HSDH) cloned from the intestinal microbiome of Ursus thibetanus. Sc 3α-HSDH was solubly expressed in E. coli (BL21) as a recombinant glutathione-S-transferase (GST)-tagged protein and freed from its GST-fusion by cleavage using the PreScission protease. Sc 3α-HSDH is a new member of the short-chain dehydrogenases/reductase superfamily (SDRs) with a typical α/β folding pattern, based on protein three-dimensional models predicted by AlphaFold. The best activity of Sc 3α-HSDH occurred at pH 8.5 and the temperature optima was 55 °C, indicating that Sc 3α-HSDH is not an extremozyme. The catalytic efficiencies (kcat/Km) of Sc 3α-HSDH catalyzing the oxidation reaction with the substrates, glycochenodeoxycholic acid (GCDCA) and glycoursodeoxycholic acid (GUDCA), were 183.617 and 34.458 s[-1] mM[-1], respectively. In addition, multiple metal ions can enhance the activity of Sc 3α-HSDH when used at concentrations ranging from 2 % to 42 %. The results also suggest that the metagenomic approach is an efficient method for identifying novel enzymes.}, } @article {pmid35933813, year = {2022}, author = {Cai, C and Huang, X and Dai, X}, title = {Differential variations of intracellular and extracellular antibiotic resistance genes between treatment units in centralized sewage sludge treatment plants.}, journal = {Water research}, volume = {222}, number = {}, pages = {118893}, doi = {10.1016/j.watres.2022.118893}, pmid = {35933813}, issn = {1879-2448}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Sewage ; Wastewater ; }, abstract = {Centralized sludge treatment plants (CSTPs) are implicated as strong hotspots of antibiotic resistance genes (ARGs). However, the knowledge gap on the fate of intracellular and extracellular ARGs (iARGs and eARGs), and the functionality of resistant hosts limit risk assessment and management of CSTP resistome. Here, the flow of iARGs and eARGs across treatment units and analyses of ARG hosts were systematically explored in three full-scale CSTPs using quantitative metagenomic approaches. We found that 29% of sludge ARGs could be removed, with iARGs being dominant in the produced biosolids. The treatment process significantly affected the variations of iARG and eARG abundance while no significant difference in composition between iARGs and eARGs was observed in CSTPs. 15% of 295 recovered genomes were identified as antibiotic-resistant hosts, among which Actinobacteriota tended to encode multiple resistance. The key functions of ARG hosts were relative to the biological organic removal (e.g., carbohydrates). There also existed relationships between certain resistance mechanisms and functional traits, indicating that ARGs might take part in the physiological process of microorganisms in the sludge treatment. These findings provide important insight into the differential resistome variations and host functionality, which would be crucial in the management of antibiotic resistance in CSTPs.}, } @article {pmid35933499, year = {2022}, author = {Ray, AE and Zaugg, J and Benaud, N and Chelliah, DS and Bay, S and Wong, HL and Leung, PM and Ji, M and Terauds, A and Montgomery, K and Greening, C and Cowan, DA and Kong, W and Williams, TJ and Hugenholtz, P and Ferrari, BC}, title = {Atmospheric chemosynthesis is phylogenetically and geographically widespread and contributes significantly to carbon fixation throughout cold deserts.}, journal = {The ISME journal}, volume = {16}, number = {11}, pages = {2547-2560}, pmid = {35933499}, issn = {1751-7370}, support = {FT170100341//Department of Education and Training | Australian Research Council (ARC)/ ; APP5191146//Department of Health | National Health and Medical Research Council (NHMRC)/ ; }, mesh = {Carbon Cycle ; *Hydrogenase/genetics ; Ribulose-Bisphosphate Carboxylase ; Soil/chemistry ; Soil Microbiology ; Verrucomicrobia ; }, abstract = {Cold desert soil microbiomes thrive despite severe moisture and nutrient limitations. In Eastern Antarctic soils, bacterial primary production is supported by trace gas oxidation and the light-independent RuBisCO form IE. This study aims to determine if atmospheric chemosynthesis is widespread within Antarctic, Arctic and Tibetan cold deserts, to identify the breadth of trace gas chemosynthetic taxa and to further characterize the genetic determinants of this process. H2 oxidation was ubiquitous, far exceeding rates reported to fulfill the maintenance needs of similarly structured edaphic microbiomes. Atmospheric chemosynthesis occurred globally, contributing significantly (p < 0.05) to carbon fixation in Antarctica and the high Arctic. Taxonomic and functional analyses were performed upon 18 cold desert metagenomes, 230 dereplicated medium-to-high-quality derived metagenome-assembled genomes (MAGs) and an additional 24,080 publicly available genomes. Hydrogenotrophic and carboxydotrophic growth markers were widespread. RuBisCO IE was discovered to co-occur alongside trace gas oxidation enzymes in representative Chloroflexota, Firmicutes, Deinococcota and Verrucomicrobiota genomes. We identify a novel group of high-affinity [NiFe]-hydrogenases, group 1m, through phylogenetics, gene structure analysis and homology modeling, and reveal substantial genetic diversity within RuBisCO form IE (rbcL1E), and high-affinity 1h and 1l [NiFe]-hydrogenase groups. We conclude that atmospheric chemosynthesis is a globally-distributed phenomenon, extending throughout cold deserts, with significant implications for the global carbon cycle and bacterial survival within environmental reservoirs.}, } @article {pmid35933411, year = {2022}, author = {Zhang, H and Wang, M and Wang, H and Chen, H and Cao, L and Zhong, Z and Lian, C and Zhou, L and Li, C}, title = {Metagenome sequencing and 768 microbial genomes from cold seep in South China Sea.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {480}, pmid = {35933411}, issn = {2052-4463}, support = {42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076091//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42076091//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030407//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Archaea/genetics ; Bacteria/genetics ; *Genome, Microbial ; Geologic Sediments/microbiology ; *Metagenome ; *Microbiota ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cold seep microbial communities are fascinating ecosystems on Earth which provide unique models for understanding the living strategies in deep-sea distinct environments. In this study, 23 metagenomes were generated from samples collected in the Site-F cold seep field in South China Sea, including the sea water closely above the invertebrate communities, the cold seep fluids, the fluids under the invertebrate communities and the sediment column around the seep vent. By binning tools, we retrieved a total of 768 metagenome assembled genome (MAGs) that were estimated to be >60% complete. Of the MAGs, 61 were estimated to be >90% complete, while an additional 105 were >80% complete. Phylogenomic analysis revealed 597 bacterial and 171 archaeal MAGs, of which nearly all were distantly related to known cultivated isolates. In the 768 MAGs, the abundant Bacteria in phylum level included Proteobacteria, Desulfobacterota, Bacteroidota, Patescibacteria and Chloroflexota, while the abundant Archaea included Asgardarchaeota, Thermoplasmatota, and Thermoproteota. These results provide a dataset available for further interrogation of deep-sea microbial ecology.}, } @article {pmid35932998, year = {2022}, author = {Ao, Y and Xu, J and Duan, Z}, title = {A novel cardiovirus species identified in feces of wild Himalayan marmots.}, journal = {Infection, genetics and evolution : journal of molecular epidemiology and evolutionary genetics in infectious diseases}, volume = {103}, number = {}, pages = {105347}, doi = {10.1016/j.meegid.2022.105347}, pmid = {35932998}, issn = {1567-7257}, mesh = {Animals ; *Cardiovirus/genetics ; Feces ; Genome, Viral ; Marmota/genetics ; Phylogeny ; }, abstract = {Recently a growing number of novel cardioviruses have been frequently discovered, which boosts interest in the search for the genetic diversity of cardioviruses. However, wild-marmot cardioviruses have been rarely reported. Here, a novel cardiovirus (tentatively named HHMCDV) was identified in fecal samples from wild Himalayan marmots in Qinghai Tibetan Plateau, China, by viral metagenomics analysis. 3 out of 99 fecal samples from Himalayan marmots were positive for HHMCDV, with the viral loads ranging from 2.7 × 10[5] to 1.3 × 10[7] gene copies/g. The complete genomic sequence of HHMCDV was 8108 nucleotides in length, with the typical cardiovirus genome organization and motifs. Coincidentally, while the data was analyzing, one marmot cardiovirus HT7 partial sequence was available in the Genbank, showing 95.1%, 95.6% and 96.0% amino acid (aa) identity in P1, P2 and P3, respectively. However, sequence analysis revealed that HHMCDV and HT7 are more closely related to species Cardiovirus F strain with 65.7%, 61.9-65.6%, 58.9-59.7%, 71.1-71.7%, 69.1-69.4% and 71.4-72.2% aa identity in polyprotein, P1, P2, P3, 2C and 3CD proteins, respectively. Phylogenetic analysis of P1, P2, P3 and 3CD aa sequences indicated that HHMCDV and HT7 clustered tightly and formed a distinct cluster in the Cardiovirus genus. Based on these data, we propose that HHMCDV and HT7 should be two different members of a potential novel species within the genus Cardiovirus. Further studies are needed to investigate the epidemiology and potential pathogenicity of the virus in Himalayan marmots.}, } @article {pmid35932944, year = {2022}, author = {Liu, Y and Luo, G and Ngo, HH and Zhang, S}, title = {New approach of bioprocessing towards lignin biodegradation.}, journal = {Bioresource technology}, volume = {361}, number = {}, pages = {127730}, doi = {10.1016/j.biortech.2022.127730}, pmid = {35932944}, issn = {1873-2976}, mesh = {Biodegradation, Environmental ; Biomass ; *Laccase/chemistry/genetics ; *Lignin/chemistry ; Metagenome ; }, abstract = {Bio-utilization of lignocellulosic biomass is of huge significance as it can directly replace petroleum resources by producing liquid fuels and organic chemical products in a more sustainable way. However, studies on developing lignin-degrading microbial resources are still very few, which affects on establishing a consolidated bioprocessing of lignocellulosic resource. The main aim of this work is to discover thermostable laccases for lignin thermo-biodegradation by metagenome-mining and biochemical characterization. Results indicate that 124 putative thermostable laccase genes were identified from generated metagenomes. Significantly, 3 rationally selected proteins showed actual activity and structural stability at temperatures up to 60 °C and pH values as low as 4.87. These active recombinant enzymes verify a practical advance in the functional prediction of target proteins, and simultaneous sequence-to-function relationships in this metagenome. In short, the identified thermostable laccase genes in this work could expand range of lignin biocatalysts and contribute to build an efficient lignin biorefinery.}, } @article {pmid35931956, year = {2022}, author = {Hong, D and Wang, P and Zhang, J and Li, K and Ye, B and Li, G and Zhou, J and Tong, Z and Ke, L and Shi, S and Li, W}, title = {Plasma metagenomic next-generation sequencing of microbial cell-free DNA detects pathogens in patients with suspected infected pancreatic necrosis.}, journal = {BMC infectious diseases}, volume = {22}, number = {1}, pages = {675}, pmid = {35931956}, issn = {1471-2334}, support = {82070665//National Natural Science Foundation of China/ ; ALB18J001//Major Program of Military Logistics Research Plan/ ; }, mesh = {Acute Disease ; *Cell-Free Nucleic Acids ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Intraabdominal Infections ; *Pancreatitis, Acute Necrotizing/diagnosis ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Infected pancreatic necrosis (IPN) is a life-threatening complication of acute pancreatitis (AP). Timely diagnosis of IPN could facilitate appropriate treatment, but there is a lack of reliable non-invasive screening tests. In this study, we aimed to evaluate the diagnostic value of plasma metagenomic next-generation sequencing (mNGS) based on circulating microbial cell-free DNA in patients with suspected IPN.

METHODS: From October 2020 to October 2021, 44 suspected IPN patients who underwent plasma mNGS were reviewed. Confirmatory diagnosis of IPN within two weeks after the index blood sampling was considered the reference standard. The confirmation of IPN relied on the microbiological results of drains obtained from the necrotic collections. The distribution of the pathogens identified by plasma mNGS was analyzed. Positive percent agreement (PPA) and negative percent agreement (NPA) were evaluated based on the conformity between the overall mNGS results and culture results of IPN drains. In addition, the clinical outcomes were compared between mNGS positive and negative patients.

RESULTS: Across all the study samples, thirteen species of bacteria and five species of fungi were detected by mNGS. The positivity rate of plasma mNGS was 54.55% (24/44). Of the 24 mNGS positive cases, twenty (83.33%, 95% CI, 68.42-98.24%) were consistent with the culture results of IPN drains. The PPA and NPA of plasma mNGS for IPN were 80.0% (20/25; 95% CI, 64.32-95.68%) and 89.47% (17/19; 95% CI, 75.67-100%), respectively. Compared with the mNGS negative group, patients in the positive group had more new-onset septic shock [12 (50.0%) vs. 4 (20.0%), p = 0.039].

CONCLUSION: IPN relevant pathogens can be identified by plasma mNGS, potentially facilitating appropriate treatment. The clinical application of mNGS in this cohort appears feasible.}, } @article {pmid35931735, year = {2022}, author = {Kim, K and Lee, S and Park, SC and Kim, NE and Shin, C and Lee, SK and Jung, Y and Yoon, D and Kim, H and Kim, S and Hwang, GS and Won, S}, title = {Role of an unclassified Lachnospiraceae in the pathogenesis of type 2 diabetes: a longitudinal study of the urine microbiome and metabolites.}, journal = {Experimental & molecular medicine}, volume = {54}, number = {8}, pages = {1125-1132}, pmid = {35931735}, issn = {2092-6413}, mesh = {Acetoacetates ; *Diabetes Mellitus, Type 2/complications ; Glycated Hemoglobin ; Humans ; Longitudinal Studies ; *Microbiota ; Prospective Studies ; }, abstract = {Recent investigations have revealed that the human microbiome plays an essential role in the occurrence of type 2 diabetes (T2D). However, despite the importance of understanding the involvement of the microbiota throughout the body in T2D, most studies have focused specifically on the intestinal microbiota. Extracellular vesicles (EVs) have been recently found to provide important evidence regarding the mechanisms of T2D pathogenesis, as they act as key messengers between intestinal microorganisms and the host. Herein, we explored microorganisms potentially associated with T2D by tracking changes in microbiota-derived EVs from patient urine samples collected three times over four years. Mendelian randomization analysis was conducted to evaluate the causal relationships among microbial organisms, metabolites, and clinical measurements to provide a comprehensive view of how microbiota can influence T2D. We also analyzed EV-derived metagenomic (N = 393), clinical (N = 5032), genomic (N = 8842), and metabolite (N = 574) data from a prospective longitudinal Korean community-based cohort. Our data revealed that GU174097_g, an unclassified Lachnospiraceae, was associated with T2D (β = -189.13; p = 0.00006), and it was associated with the ketone bodies acetoacetate and 3-hydroxybutyrate (r = -0.0938 and -0.0829, respectively; p = 0.0022 and 0.0069, respectively). Furthermore, a causal relationship was identified between acetoacetate and HbA1c levels (β = 0.0002; p = 0.0154). GU174097_g reduced ketone body levels, thus decreasing HbA1c levels and the risk of T2D. Taken together, our findings indicate that GU174097_g may lower the risk of T2D by reducing ketone body levels.}, } @article {pmid35931282, year = {2022}, author = {Zhou, X and Bi, X and Yang, T and Fan, X and Shi, X and Wang, L and Zhang, Y and Cheng, L and Zhao, F and Maletskyi, Z and Hui, X}, title = {Metagenomic insights into microbial nitrogen metabolism in two-stage anoxic/oxic-moving bed biofilm reactor system with multiple chambers for municipal wastewater treatment.}, journal = {Bioresource technology}, volume = {361}, number = {}, pages = {127729}, doi = {10.1016/j.biortech.2022.127729}, pmid = {35931282}, issn = {1873-2976}, mesh = {Biofilms ; Bioreactors ; Denitrification ; Nitrification ; *Nitrogen/metabolism ; Sewage ; Waste Disposal, Fluid ; Wastewater ; *Water Purification ; }, abstract = {To explore the microbial nitrogen metabolism of a two-stage anoxic/oxic (A/O)-moving bed biofilm reactor (MBBR), biofilms of the system's chambers were analyzed using metagenomic sequencing. Significant differences in microbial populations were found among the pre-anoxic, oxic and post-anoxic MBBRs (P < 0.01). Nitrospira and Nitrosomonas had positive correlations with ammonia nitrogen (NH4[+]-N) removal, and were also predominant in oxic MBBRs. These organisms were the hosts of functional genes for nitrification. The denitrifying genera were predominant in anoxic MBBRs, including Thiobacillus and Sulfurisoma in pre-anoxic MBBRs and Dechloromonas and Thauera in post-anoxic MBBRs. The four genera had positive correlations with total nitrate and nitrite nitrogen (NOX[-]-N) removal and were the hosts of functional genes for denitrification. Specific functional biofilms with different microbial nitrogen metabolisms were formed in each chamber of this system. This work provides a microbial theoretical support for the two-stage A/O-MBBR system.}, } @article {pmid35931074, year = {2022}, author = {Podlesny, D and Durdevic, M and Paramsothy, S and Kaakoush, NO and Högenauer, C and Gorkiewicz, G and Walter, J and Fricke, WF}, title = {Identification of clinical and ecological determinants of strain engraftment after fecal microbiota transplantation using metagenomics.}, journal = {Cell reports. Medicine}, volume = {3}, number = {8}, pages = {100711}, pmid = {35931074}, issn = {2666-3791}, mesh = {*Clostridium Infections/therapy ; Dysbiosis/therapy ; Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenomics ; }, abstract = {Fecal microbiota transplantation (FMT) is a promising therapeutic approach for microbiota-associated pathologies, but our understanding of the post-FMT microbiome assembly process and its ecological and clinical determinants is incomplete. Here we perform a comprehensive fecal metagenome analysis of 14 FMT trials, involving five pathologies and >250 individuals, and determine the origins of strains in patients after FMT. Independently of the underlying clinical condition, conspecific coexistence of donor and recipient strains after FMT is uncommon and donor strain engraftment is strongly positively correlated with pre-FMT recipient microbiota dysbiosis. Donor strain engraftment was enhanced through antibiotic pretreatment and bowel lavage and dependent on donor and recipient ɑ-diversity; strains from relatively abundant species were more likely and from predicted oral, oxygen-tolerant, and gram-positive species less likely to engraft. We introduce a general mechanistic framework for post-FMT microbiome assembly in alignment with ecological theory, which can guide development of optimized, more targeted, and personalized FMT therapies.}, } @article {pmid35930838, year = {2022}, author = {Roslund, MI and Parajuli, A and Hui, N and Puhakka, R and Grönroos, M and Soininen, L and Nurminen, N and Oikarinen, S and Cinek, O and Kramná, L and Schroderus, AM and Laitinen, OH and Kinnunen, T and Hyöty, H and Sinkkonen, A and , }, title = {A Placebo-controlled double-blinded test of the biodiversity hypothesis of immune-mediated diseases: Environmental microbial diversity elicits changes in cytokines and increase in T regulatory cells in young children.}, journal = {Ecotoxicology and environmental safety}, volume = {242}, number = {}, pages = {113900}, doi = {10.1016/j.ecoenv.2022.113900}, pmid = {35930838}, issn = {1090-2414}, mesh = {Bacteria/genetics ; Biodiversity ; Child, Preschool ; Cytokines ; Double-Blind Method ; Humans ; *Interleukin-10 ; *Interleukin-17 ; Sand ; T-Lymphocytes, Regulatory ; }, abstract = {BACKGROUND: According to the biodiversity hypothesis of immune-mediated diseases, lack of microbiological diversity in the everyday living environment is a core reason for dysregulation of immune tolerance and - eventually - the epidemic of immune-mediated diseases in western urban populations. Despite years of intense research, the hypothesis was never tested in a double-blinded and placebo-controlled intervention trial.

OBJECTIVE: We aimed to perform the first placebo-controlled double-blinded test that investigates the effect of biodiversity on immune tolerance.

METHODS: In the intervention group, children aged 3-5 years were exposed to playground sand enriched with microbially diverse soil, or in the placebo group, visually similar, but microbially poor sand colored with peat (13 participants per treatment group). Children played twice a day for 20 min in the sandbox for 14 days. Sand, skin and gut bacterial, and blood samples were taken at baseline and after 14 days. Bacterial changes were followed for 28 days. Sand, skin and gut metagenome was determined by high throughput sequencing of bacterial 16 S rRNA gene. Cytokines were measured from plasma and the frequency of blood regulatory T cells was defined as a percentage of total CD3 +CD4 + T cells.

RESULTS: Bacterial richness (P < 0.001) and diversity (P < 0.05) were higher in the intervention than placebo sand. Skin bacterial community, including Gammaproteobacteria, shifted only in the intervention treatment to resemble the bacterial community in the enriched sand (P < 0.01). Mean change in plasma interleukin-10 (IL-10) concentration and IL-10 to IL-17A ratio supported immunoregulation in the intervention treatment compared to the placebo treatment (P = 0.02). IL-10 levels (P = 0.001) and IL-10 to IL-17A ratio (P = 0.02) were associated with Gammaproteobacterial community on the skin. The change in Treg frequencies was associated with the relative abundance of skin Thermoactinomycetaceae 1 (P = 0.002) and unclassified Alphaproteobacteria (P < 0.001). After 28 days, skin bacterial community still differed in the intervention treatment compared to baseline (P < 0.02).

CONCLUSIONS: This is the first double-blinded placebo-controlled study to show that daily exposure to microbial biodiversity is associated with immune modulation in humans. The findings support the biodiversity hypothesis of immune-mediated diseases. We conclude that environmental microbiota may contribute to child health, and that adding microbiological diversity to everyday living environment may support immunoregulation.}, } @article {pmid35930686, year = {2022}, author = {Zhang, Z and Zhang, G and Ju, F}, title = {Using Culture-Enriched Phenotypic Metagenomics for Targeted High-Throughput Monitoring of the Clinically Important Fraction of the β-Lactam Resistome.}, journal = {Environmental science & technology}, volume = {56}, number = {16}, pages = {11429-11439}, doi = {10.1021/acs.est.2c03627}, pmid = {35930686}, issn = {1520-5851}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Carbapenems ; *Metagenomics ; Microbial Sensitivity Tests ; Water Purification ; *beta-Lactam Resistance/genetics ; beta-Lactamases/genetics ; *beta-Lactams/pharmacology ; }, abstract = {High bacterial community diversity and complexity greatly challenge the cost-efficient monitoring of clinically prevalent antibiotic-resistant bacteria, which are usually present as rare and important populations involved in the environmental dissemination of clinical resistance. Here, we introduce culture-enriched phenotypic metagenomics that integrates culture enrichment, phenotypic screening, and metagenomic analyses as an emerging standardized methodology for targeted resistome monitoring and apply it to decipher the extended-spectrum β-lactam resistome in a municipal wastewater treatment plant (WWTP) and its receiving river. The results showed that clinically prevalent carbapenemase genes (e.g., the NDM and KPC families) and extended-spectrum β-lactamase genes (e.g., the CTX-M, TEM, and OXA families) were prevalent in the WWTP and showed prominent potential in horizontal dissemination. Strikingly, carbapenem and polymyxin resistance genes co-occurred in the highly virulent nosocomial pathogens Enterobacter kobei and Citrobacter freundii. Overall, this study exemplifies phenotypic metagenomics for high-throughput surveillance of a targeted clinically important fraction of antibiotic resistomes and substantially expands current knowledge on extended-spectrum β-lactam resistance in WWTPs.}, } @article {pmid35930195, year = {2022}, author = {Ceylani, T and Teker, HT}, title = {The effect of young blood plasma administration on gut microbiota in middle-aged rats.}, journal = {Archives of microbiology}, volume = {204}, number = {9}, pages = {541}, pmid = {35930195}, issn = {1432-072X}, support = {BAP-21-TBMY-4901-07//Muş Alparslan Üniversitesi/ ; }, mesh = {Animals ; Bacteria/genetics ; Dysbiosis/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Metagenome ; Plasma ; Rats ; }, abstract = {Numerous in-depth studies continue to reveal the many benefits of gut microbiota and young blood plasma administration. Dysbiosis, which occurs in the intestinal microbiota, especially in the aging process, is associated with many metabolic and cognitive disorders. Therefore, many studies aim to reverse the dysbiosis that occurs. There are also studies showing that young blood plasma application reverses the effects of aging at the level of many tissues and organs. Today, while research continues to reveal all the benefits of young blood plasma application in terms of health, blood plasma centers are also being established. In this study, we aimed to reveal the impact of young blood plasma, administered for 1 month, on the intestinal microbiota of middle-aged rats. After detailed metagenome analysis, alpha diversity indices demonstrated greater bacterial richness in the microbiota of plasma-administered rats compared with control rats. In addition, the Firmicutes/Bacteroidetes ratio was significantly diminished in plasma group microbiota, confirming possible rejuvenation properties of young plasma. Furthermore, increased counts of Bifidobacterium longum, Coprococcus catus, and Romboutsia ilealis species were measured in plasma-administered rats. The study revealed many fluctuations in different bacterial taxonomic units of the microbiota that could be valuable in future research on blood-based anti-aging treatments.}, } @article {pmid35930018, year = {2022}, author = {Zhang, X and Ren, H and Zhao, C and Shi, Z and Qiu, L and Yang, F and Zhou, X and Han, X and Wu, K and Zhong, H and Li, Y and Li, J and Ji, L}, title = {Metagenomic analysis reveals crosstalk between gut microbiota and glucose-lowering drugs targeting the gastrointestinal tract in Chinese patients with type 2 diabetes: a 6 month, two-arm randomised trial.}, journal = {Diabetologia}, volume = {65}, number = {10}, pages = {1613-1626}, pmid = {35930018}, issn = {1432-0428}, mesh = {Acarbose/therapeutic use ; Blood Glucose/metabolism ; China ; *Diabetes Mellitus, Type 2 ; Ecosystem ; *Gastrointestinal Microbiome ; Gastrointestinal Tract/metabolism ; Glipizide/therapeutic use ; Glucagon-Like Peptide 1/therapeutic use ; Glucose ; Humans ; Hypoglycemic Agents/pharmacology ; Research ; Vildagliptin/therapeutic use ; }, abstract = {AIMS/HYPOTHESIS: The use of oral glucose-lowering drugs, particularly those designed to target the gut ecosystem, is often observed in association with altered gut microbial composition or functional capacity in individuals with type 2 diabetes. The gut microbiota, in turn, plays crucial roles in the modulation of drug efficacy. We aimed to assess the impacts of acarbose and vildagliptin on human gut microbiota and the relationships between pre-treatment gut microbiota and therapeutic responses.

METHODS: This was a randomised, open-labelled, two-arm trial in treatment-naive type 2 diabetes patients conducted in Beijing between December 2016 and December 2017. One hundred participants with overweight/obesity and newly diagnosed type 2 diabetes were recruited from the Pinggu Hospital and randomly assigned to the acarbose (n=50) or vildagliptin (n=50) group using sealed envelopes. The treatment period was 6 months. Blood, faecal samples and visceral fat data from computed tomography images were collected before and after treatments to measure therapeutic outcomes and gut microbiota. Metagenomic datasets from a previous type 2 diabetes cohort receiving acarbose or glipizide for 3 months were downloaded and processed. Statistical analyses were applied to identify the treatment-related changes in clinical variables, gut microbiota and associations.

RESULTS: Ninety-two participants were analysed. After 6 months of acarbose (n=44) or vildagliptin (n=48) monotherapy, both groups achieved significant reductions in HbA1c (from 60 to 46 mmol/mol [from 7.65% to 6.40%] in the acarbose group and from 59 to 44 mmol/mol [from 7.55% to 6.20%] in the vildagliptin group) and visceral fat areas (all adjusted p values for pre-post comparisons <0.05). Both arms showed drug-specific and shared changes in relative abundances of multiple gut microbial species and pathways, especially the common reductions in Bacteroidetes species. Three months and 6 months of acarbose-induced changes in microbial composition were highly similar in type 2 diabetes patients from the two independent studies. Vildagliptin treatment significantly enhanced fasting active glucagon-like peptide-1 (GLP-1) levels. Baseline gut microbiota, rather than baseline GLP-1 levels, were strongly associated with GLP-1 response to vildagliptin, and to a lesser extent with GLP-1 response to acarbose.

CONCLUSIONS/INTERPRETATION: This study reveals common microbial responses in type 2 diabetes patients treated with two glucose-lowering drugs targeting the gut differently and acceptable performance of baseline gut microbiota in classifying individuals with different GLP-1 responses to vildagliptin. Our findings highlight bidirectional interactions between gut microbiota and glucose-lowering drugs.

TRIAL REGISTRATION: ClinicalTrials.gov NCT02999841 FUNDING: National Key Research and Development Project: 2016YFC1304901.}, } @article {pmid35929783, year = {2022}, author = {Sampara, P and Luo, Y and Lin, X and Ziels, RM}, title = {Integrating Genome-Resolved Metagenomics with Trait-Based Process Modeling to Determine Biokinetics of Distinct Nitrifying Communities within Activated Sludge.}, journal = {Environmental science & technology}, volume = {56}, number = {16}, pages = {11670-11682}, pmid = {35929783}, issn = {1520-5851}, mesh = {Bacteria/genetics ; Bioreactors/microbiology ; Metagenomics ; *Microbiota ; Nitrification ; Nitrites ; Nitrogen ; Oxidation-Reduction ; *Sewage/microbiology ; }, abstract = {Conventional bioprocess models for wastewater treatment are based on aggregated bulk biomass concentrations and do not incorporate microbial physiological diversity. Such a broad aggregation of microbial functional groups can fail to predict ecosystem dynamics when high levels of physiological diversity exist within trophic guilds. For instance, functional diversity among nitrite-oxidizing bacteria (NOB) can obfuscate engineering strategies for their out-selection in activated sludge (AS), which is desirable to promote energy-efficient nitrogen removal. Here, we hypothesized that different NOB populations within AS can have different physiological traits that drive process performance, which we tested by estimating biokinetic growth parameters using a combination of highly replicated respirometry, genome-resolved metagenomics, and process modeling. A lab-scale AS reactor subjected to a selective pressure for over 90 days experienced resilience of NOB activity. We recovered three coexisting Nitrospira population genomes belonging to two sublineages, which exhibited distinct growth strategies and underwent a compositional shift following the selective pressure. A trait-based process model calibrated at the NOB genus level better predicted nitrite accumulation than a conventional process model calibrated at the NOB guild level. This work demonstrates that trait-based modeling can be leveraged to improve our prediction, control, and design of functionally diverse microbiomes driving key environmental biotechnologies.}, } @article {pmid35928983, year = {2022}, author = {Hakimjavadi, H and George, SH and Taub, M and Dodds, LV and Sanchez-Covarrubias, AP and Huang, M and Pearson, JM and Slomovitz, BM and Kobetz, EN and Gharaibeh, R and Sowamber, R and Pinto, A and Chamala, S and Schlumbrecht, MP}, title = {The vaginal microbiome is associated with endometrial cancer grade and histology.}, journal = {Cancer research communications}, volume = {2}, number = {6}, pages = {447-455}, pmid = {35928983}, issn = {2767-9764}, support = {P30 CA240139/CA/NCI NIH HHS/United States ; }, mesh = {Humans ; Female ; *Endometrial Neoplasms/genetics ; Vagina/microbiology ; Hysterectomy ; *Microbiota/genetics ; *Carcinoma ; }, abstract = {The human microbiome has been strongly correlated with disease pathology and outcomes, yet remains relatively underexplored in patients with malignant endometrial disease. In this study, vaginal microbiome samples were prospectively collected at the time of hysterectomy from 61 racially and ethnically diverse patients from three disease conditions: 1) benign gynecologic disease (controls, n=11), 2) low-grade endometrial carcinoma (n=30), and 3) high-grade endometrial carcinoma (n=20). Extracted DNA underwent shotgun metagenomics sequencing, and microbial α and β diversities were calculated. Hierarchical clustering was used to describe community state types (CST), which were then compared by microbial diversity and grade. Differential abundance was calculated, and machine learning utilized to assess the predictive value of bacterial abundance to distinguish grade and histology. Both α- and β-diversity were associated with patient tumor grade. Four vaginal CST were identified that associated with grade of disease. Different histologies also demonstrated variation in CST within tumor grades. Using supervised clustering algorithms, critical microbiome markers at the species level were used to build models that predicted benign vs carcinoma, high-grade carcinoma versus benign, and high-grade versus low-grade carcinoma with high accuracy. These results confirm that the vaginal microbiome segregates not just benign disease from endometrial cancer, but is predictive of histology and grade. Further characterization of these findings in large, prospective studies is needed to elucidate their potential clinical applications.}, } @article {pmid35928781, year = {2022}, author = {Al Bataineh, MT and Künstner, A and Dash, NR and Abdulsalam, RM and Al-Kayyali, RZA and Adi, MB and Alsafar, HS and Busch, H and Ibrahim, SM}, title = {Altered Composition of the Oral Microbiota in Depression Among Cigarette Smokers: A Pilot Study.}, journal = {Frontiers in psychiatry}, volume = {13}, number = {}, pages = {902433}, pmid = {35928781}, issn = {1664-0640}, abstract = {Alterations in the oral microbiota composition may influence mental health. However, linkages between compositional changes in the oral microbiota and their role in mental health among cigarette smokers remain largely unknown. In this study, we used shotgun metagenomics data for the oral microbiome of 105 participants. The data showed Bacteroidota, Fusobacteriota, Firmicutes, Proteobacteria, and Actinobacteria to be the most abundant phyla; Streptococcus, Haemophilus D, and Veillonella are the most abundant genera. Then, we clustered our subjects into avoidance and activation groups based on the behavioral activation for depression scale (BADS). Interestingly, the avoidance group exhibited a higher oral microbiome richness and diversity (alpha diversity). Differential abundance testing between BADS avoidance and activation groups showed the phyla Bacteroidota (effect size 0.5047, q = 0.0037), Campylobacterota (effect size 0.4012, q = 0.0276), Firmicutes A (effect size 0.3646, q = 0.0128), Firmicutes I (effect size 0.3581, q = 0.0268), and Fusobacteriota (effect size 0.6055, q = 0.0018) to be significantly increased in the avoidance group, but Verrucomicrobiota (effect size-0.6544, q = 0.0401), was found to be significantly decreased in the avoidance risk group. Network analysis of the 50 genera displaying the highest variation between both groups identified Campylobacter B, Centipeda, and Veillonella as hub nodes in the avoidance group. In contrast, Haemophilus and Streptococcus were identified as hub nodes in the activation group. Next, we investigated functional profiles of the oral microbiota based on BADS avoidance and activation groups and found Lysine degradations pathway was significantly enriched between both groups (ANCOM-BC, q = 0.0692). Altogether, we provide evidence for the presence of depression-related changes in the oral microbiota of smokers and possible functional contribution. The identified differences provide new information to enrich our understanding of oral microbiota-brain axis interplay and their potential impact on mental health.}, } @article {pmid35928152, year = {2022}, author = {Xue, Y and Zheng, M and Wu, S and Liu, Y and Huang, X}, title = {Changes in the Species and Functional Composition of Activated Sludge Communities Revealed Mechanisms of Partial Nitrification Established by Ultrasonication.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {960608}, pmid = {35928152}, issn = {1664-302X}, abstract = {To achieve energy-efficient shortcut nitrogen removal of wastewater in the future, selective elimination of nitrite-oxidizing bacteria (NOB) while enriching ammonia-oxidizing microorganisms is a crucial step. However, the underlying mechanisms of partial nitrification are still not well understood, especially the newly discovered ultrasound-based partial nitrification. To elucidate this issue, in this study two bioreactors were set up, with one established partial nitrification by ultrasonication while the other didn't. During the operation of both reactors, the taxonomic and functional composition of the microbial community were investigated through metagenomics analysis. The result showed that during ultrasonic partial nitrification, ammonia-oxidizing archaea (AOA), Nitrososphaerales, was enriched more than ammonia-oxidizing bacteria (AOB), Nitrosomonas. The enrichment of microorganisms in the community increased the abundance of genes involved in microbial energy generation from lipid and carbohydrates. On the other hand, the abundance of NOB, Nitrospira and Nitrolancea, and Comammox Nitrospira decreased. Selective inhibition of NOB was highly correlated with genes involved in signal transduction enzymes, such as encoding histidine kinase and serine/threonine kinase. These findings provided deep insight into partial nitrification and contributed to the development of shortcut nitrification in wastewater treatment plants.}, } @article {pmid35927898, year = {2022}, author = {Cuetero-Martínez, Y and de Los Cobos-Vasconcelos, D and Aguirre-Garrido, JF and Lopez-Vidal, Y and Noyola, A}, title = {Next-generation Sequencing for Surveillance of Antimicrobial Resistance and Pathogenicity in Municipal Wastewater Treatment Plants.}, journal = {Current medicinal chemistry}, volume = {30}, number = {1}, pages = {5-29}, doi = {10.2174/0929867329666220802093415}, pmid = {35927898}, issn = {1875-533X}, support = {SECTEI/265/19//Secretaría de Educación, Ciencia, Tecnología e Innovación de la Ciudad de México/ ; }, mesh = {Humans ; Wastewater ; Anti-Bacterial Agents ; Virulence ; *Influenza A Virus, H1N1 Subtype ; Drug Resistance, Bacterial ; *COVID-19 ; Sewage ; *Water Purification ; High-Throughput Nucleotide Sequencing ; *Zika Virus ; *Zika Virus Infection ; }, abstract = {The World Health Organization (WHO) ranks antimicrobial resistance (AMR) and various pathogens among the top 10 health threats. It is estimated that by 2050, the number of human deaths due to AMR will reach 10 million annually. On the other hand, several infectious outbreaks such as SARS, H1N1 influenza, Ebola, Zika fever, and COVID-19 have severely affected human populations worldwide in the last 20 years. These recent global diseases have generated the need to monitor outbreaks of pathogens and AMR to establish effective public health strategies. This review presents AMR and pathogenicity associated with wastewater treatment plants (WWTP), focusing on Next Generation Sequencing (NGS) monitoring as a complementary system to clinical surveillance. In this regard, WWTP may be monitored at three main points. First, at the inlet (raw wastewater or influent) to identify a broad spectrum of AMR and pathogens contained in the excretions of residents served by sewer networks, with a specific spatio-temporal location. Second, at the effluent, to ensure the elimination of AMR and pathogens in the treated water, considering the rising demand for safe wastewater reuse. Third, in sewage sludge or biosolids, their beneficial use or final disposal can represent a significant risk to public health. This review is divided into two sections to address the importance and implications of AMR and pathogen surveillance in wastewater and WWTP, based on NGS. The first section presents the fundamentals of surveillance techniques applied in WWTP (metataxonomics, metagenomics, functional metagenomics, metaviromics, and metatranscriptomics). Their scope and limitations are analyzed to show how microbiological and qPCR techniques complement NGS surveillance, overcoming its limitations. The second section discusses the contribution of 36 NGS research papers on WWTP surveillance, highlighting the current situation and perspectives. In both sections, research challenges and opportunities are presented.}, } @article {pmid35927361, year = {2022}, author = {Singh, AK and Kumari, M and Sharma, N and Rai, AK and Singh, SP}, title = {Metagenomic views on taxonomic and functional profiles of the Himalayan Tsomgo cold lake and unveiling its deterzome potential.}, journal = {Current genetics}, volume = {68}, number = {5-6}, pages = {565-579}, pmid = {35927361}, issn = {1432-0983}, mesh = {*Metagenome ; Lakes/microbiology ; Detergents ; *Arthrobacter/genetics ; Lipase/genetics ; Peptide Hydrolases/genetics ; Amylases/genetics ; }, abstract = {Cold habitat is considered a potential source for detergent industry enzymes. This study aims at the metagenomic investigation of Tsomgo lake for taxonomic and functional annotation, unveiling the deterzome potential of the residing microbiota at this site. The present investigation revealed molecular profiling of microbial community structure and functional potential of the high-altitude Tsomgo lake samples of two different temperatures, harvested during March and August. Bacteria were found to be the most dominant phyla, with traces of genomic pieces of evidence belonging to archaea, viruses, and eukaryotes. Proteobacteria and Actinobacteria were noted to be the most abundant bacterial phyla in the cold lake. In-depth metagenomic investigation of the cold aquatic habitat revealed novel genes encoding detergent enzymes, amylase, protease, and lipase. Further, metagenome-assembled genomes (MAGs) belonging to the psychrophilic bacterium, Arthrobacter alpinus, were constructed from the metagenomic data. The annotation depicted the presence of detergent enzymes and genes for low-temperature adaptation in Arthrobacter alpinus. Psychrophilic microbial isolates were screened for lipase, protease, and amylase activities to further strengthen the metagenomic findings. A novel strain of Acinetobacter sp. was identified with the dual enzymatic activity of protease and amylase. The bacterial isolates exhibited hydrolyzing activity at low temperatures. This metagenomic study divulged novel genomic resources for detergent industry enzymes, and the bacterial isolates secreting cold-active amylase, lipase, and protease enzymes. The findings manifest that Tsomgo lake is a potential bioresource of cold-active enzymes, vital for various industrial applications.}, } @article {pmid35927305, year = {2022}, author = {Kim, N and Gim, JA and Lee, BJ and Choi, BI and Yoon, HS and Kim, SH and Joo, MK and Park, JJ and Kim, C}, title = {Crosstalk between mucosal microbiota, host gene expression, and sociomedical factors in the progression of colorectal cancer.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {13447}, pmid = {35927305}, issn = {2045-2322}, mesh = {*Adenoma/genetics/microbiology ; Bacteria/genetics ; *Colorectal Neoplasms/pathology ; *Gastrointestinal Microbiome/genetics ; Gene Expression ; Humans ; Intestinal Mucosa/pathology ; *Microbiota/genetics ; }, abstract = {Various omics-based biomarkers related to the occurrence, progression, and prognosis of colorectal cancer (CRC) have been identified. In this study, we attempted to identify gut microbiome-based biomarkers and detect their association with host gene expression in the initiation and progression of CRC by integrating analysis of the gut mucosal metagenome, RNA sequencing, and sociomedical factors. We performed metagenome and RNA sequencing on colonic mucosa samples from 13 patients with advanced CRC (ACRC), 10 patients with high-risk adenoma (HRA), and 7 normal control (NC) individuals. All participants completed a questionnaire on sociomedical factors. The interaction and correlation between changes in the microbiome and gene expression were assessed using bioinformatic analysis. When comparing HRA and NC samples, which can be considered to represent the process of tumor initiation, 28 genes and five microbiome species were analyzed with correlation plots. When comparing ACRC and HRA samples, which can be considered to represent the progression of CRC, seven bacterial species and 21 genes were analyzed. When comparing ACRC and NC samples, 16 genes and five bacterial species were analyzed, and four correlation plots were generated. A network visualizing the relationship between bacterial and host gene expression in the initiation and progression of CRC indicated that Clostridium spiroforme and Tyzzerella nexilis were hub bacteria in the development and progression of CRC. Our study revealed the interactions of and correlation between the colonic mucosal microbiome and host gene expression to identify potential roles of the microbiome in the initiation and progression of CRC. Our results provide gut microbiome-based biomarkers that may be potential diagnostic markers and therapeutic targets in patients with CRC.}, } @article {pmid35927058, year = {2022}, author = {Wu, L and Zhang, SL and Huang, HW and Shi, GZ}, title = {[Diagnostic efficacy of metagenomic next-generation sequencing for intracranial bacterial infection pathogens after neurosurgery].}, journal = {Zhonghua yi xue za zhi}, volume = {102}, number = {29}, pages = {2272-2277}, doi = {10.3760/cma.j.cn112137-20211128-02659}, pmid = {35927058}, issn = {0376-2491}, support = {Z201100005520039//Research and Translational Application of Clinical Diagnosis and Treatment Technology in Beijing/ ; }, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; *Bacterial Infections/diagnosis ; Child ; Child, Preschool ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; Metagenomics/methods ; Middle Aged ; *Neurosurgery ; Sensitivity and Specificity ; Young Adult ; }, abstract = {Objective: To explore the diagnostic efficacy of metagenomicnext-generation sequencing (mNGS) technique for pathogen diagnosis of intracranial infection after neurosurgery. Methods: Patients with suspected intracranial infection after neurosurgery who were treated in Beijing Tiantan Hospital of Capital Medical University from May 2017 to October 2018 were selected. Cerebrospinal fluid samples were collected for mNGS detection and bacterial culture. The sensitivity, specificity, positive predictive value and negative predictive value of these two methods were calculated, and their differences were compared. Results: A total of 80 cerebrospinal fluid samples from patient with suspected intracranial infection after neurosurgery were included, including 53 males and 27 females, with a mean age of (41±19) years old(age range: 2-80 years).After clinical review, a clinical diagnosis was made by two neurosurgery specialists through comprehensively interpretation of the patient's clinical data, laboratory tests and imaging examinations. Finally, 42 cases of intracranial infection and 38 cases of non-infection were clinically diagnosed. The sensitivity and specificity of mNGS detection were 83.33%(35/42) and 76.32%(29/38), and the positive predictive value and negative predictive value were 79.55%(35/44) and 80.56%(29/36). Meanwhile, the sensitivity and specificity of bacterial culture were 59.52%(28/42) and 68.42%(26/38), the positive predictive value and negative predictive value were 68.00% (28/40) and 60.47%(26/40). The sensitivity of mNGS detection washigher than that of bacterial culture, and the difference was statistically significant(χ[2]=5.83, P=0.015).Compared with bacterial culture, there was no statistically significant difference in the specificity of mNGS detection(χ[2]=0.59, P=0.441). Conclusion: mNGS detection technique can improve the detection rate of intracranial infection pathogens after neurosurgery, and may become a promising auxiliary diagnostic tool for pathogen detection.}, } @article {pmid35926557, year = {2022}, author = {Jiang, B and Zeng, Q and Li, J and Shi, S and Chen, Z and Cui, Y and Hu, D and Sui, Y and Ge, H and Che, S and Qi, Y}, title = {Performance enhancement, membrane fouling mitigation and eco-friendly strategy by electric field coupled membrane bioreactor for treating mariculture wastewater.}, journal = {Bioresource technology}, volume = {361}, number = {}, pages = {127725}, doi = {10.1016/j.biortech.2022.127725}, pmid = {35926557}, issn = {1873-2976}, mesh = {Bioreactors/microbiology ; *Extracellular Polymeric Substance Matrix ; Hydrogen Peroxide ; Membranes, Artificial ; Nitrogen ; Sewage/microbiology ; *Wastewater/chemistry ; }, abstract = {An eco-friendly strategy for mariculture wastewater treatment using an electric field attached membrane bioreactor (E-MBR) was evaluated and compared with a conventional membrane bioreactor (C-MBR). The removal efficiencies of total nitrogen (TN) and chemical oxygen demand (COD) increased significantly and the membrane fouling rate reduced by 44.8% in the E-MBR. The underlying mechanisms included the enriched nitrifiers and denitrifiers, the enhanced salinity-resistance, the increased activities and upregulated genes of key enzymes involved in nitrification and denitrification for improving the performance of mariculture wastewater treatment, and the enriched extracellular polymeric substance (EPS)-degrading genera, the downregulated EPS biosynthesis genes, the repressed biofilm-forming bacteria, the enhanced zeta potential absolute value and the generated H2O2 for membrane fouling mitigation by electrical stimulation. Compared with the C-MBR, the energy consumption, carbon emissions, and nitrogen footprint were reduced. These findings provide novel insights into mariculture wastewater treatment using an applied electric field.}, } @article {pmid35925018, year = {2022}, author = {Liu, L and Liu, H and Zhang, W and Chen, Y and Shen, J and Li, Y and Pan, Y and Lin, W}, title = {Microbial diversity and adaptive strategies in the Mars-like Qaidam Basin, North Tibetan Plateau, China.}, journal = {Environmental microbiology reports}, volume = {14}, number = {6}, pages = {873-885}, doi = {10.1111/1758-2229.13111}, pmid = {35925018}, issn = {1758-2229}, mesh = {Tibet ; *Ultraviolet Rays ; RNA, Ribosomal, 16S/genetics ; *Bacteria/genetics ; China ; Carbon ; }, abstract = {The Qaidam Basin on the northern Tibetan Plateau, China, is one of the driest deserts at high elevations, and it has been considered a representative Mars analogue site. Despite recent advances in the diversity of microbial communities in the Qaidam Basin, our understanding of their genomic information, functional potential and adaptive strategies remains very limited. Here, we conducted a combination of physicochemical and metagenomic analyses to investigate the taxonomic composition and adaptive strategies of microbial life in the regolith across the Qaidam Basin. 16S ribosomal RNA (rRNA) gene-based and metagenomic analyses both reveal that microbial communities in the Qaidam Basin are dominated by the bacterial phylum Actinobacteria. The low levels of moisture and organic carbon contents appear to have essential constraints on microbial biomass and diversity. A total of 50 high-quality metagenome-assembled genomes were reconstructed and analysed. Our results reveal the potential of microorganisms to use ambient trace gases to meet energy and carbon needs in this nutrient-limited desert. Furthermore, we find that DNA repair mechanisms and protein protection are likely essential for microbial life in response to stressors of hyperaridity, intense ultraviolet radiation and tremendous temperature fluctuations in this Mars analogue. These findings shed light on the diversity and survival strategies of microbial life inhabiting Mar-like environments, which provide implications for potential life on early Mars.}, } @article {pmid35923899, year = {2022}, author = {Mancabelli, L and Ciociola, T and Lugli, GA and Tarracchini, C and Fontanta, F and Viappiani, A and Turroni, F and Ticinesi, A and Meschi, T and Conti, S and Ventura, M and Milani, C}, title = {Guideline for the analysis of the microbial communities of the human upper airways.}, journal = {Journal of oral microbiology}, volume = {14}, number = {1}, pages = {2103282}, pmid = {35923899}, issn = {2000-2297}, abstract = {The recent COVID-19 pandemic prompted a rapid-growing interest in the investigation of the human microbiota of the upper airways. In fact, the resident microbial community of this body district may have an influence on the onset of SARS-CoV-2 infection and its clinical course in terms of presence, symptom severity, and outcomes. However, several microbiological methodologies are available to study the human microbiota, reflecting the extensive fragmentation of methodological approaches. We investigate the impact of two critical steps that can induce biases in the downstream analyses, i.e. sampling method and microbial DNA extraction kit employed. We observed major discrepancies regarding the total amount of prokaryotic DNA that could be retrieved from a biological sample and the proportion between bacterial DNA and human host DNA. Moreover, shotgun DNA sequencing and taxonomic profile reconstruction also revealed correlations between sampling methods and the procedures applied for microbial DNA extraction. Based on all the data collected in this study, we formulate indications regarding the most efficient and reliable methodological procedures for the metagenomic analyses of the upper airways' microbiota to maximize accuracy and reproducibility.}, } @article {pmid35923413, year = {2022}, author = {Wen, K and Liu, L and Zhao, M and Geng, T and Gong, D}, title = {The Changes in Microbiotic Composition of Different Intestinal Tracts and the Effects of Supplemented Lactobacillus During the Formation of Goose Fatty Liver.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {906895}, pmid = {35923413}, issn = {1664-302X}, abstract = {Intestinal bacteria play an important role in the formation of fatty liver in animals by participating in the digestion and degradation of nutrients, producing various metabolites, and altering the barrier effect of the intestine. However, changes in the gut microbiota during the formation of goose fatty liver are unclear. In this study, 80 healthy Landes geese with similar body weights at 70 days of age were randomly divided into two groups: the control group (n = 48; fed ad libitum) and the overfeeding group (n = 32; overfed). The intestinal contents were collected at 0, 12, and 24 days of overfeeding. The 16S rRNA and metagenomic sequencing analyses showed that the dominant phyla were Firmicutes, Proteobacteria, Bacteroidetes, and Actinobacteria. At the genus level, Phyllobacterium, Bacteroides, Helicobacter, Lactobacillus, Enterococcus, and Romboutsia were the dominant genera in the goose intestine, and most of them were probiotics. In the control group, the relative abundance of Firmicutes in the jejunum and ileum gradually decreased with time, while that of Proteobacteria increased, whereas in the overfeeding group, the relative abundance of Firmicutes in the jejunum and ileum decreased and then increased with time, while that of Proteobacteria showed an opposite trend. In addition, supplementing Lactobacillus to the diet reduced body weight and fatty liver weight in overfed geese, but increased the weight of abdominal fat, suggesting that Lactobacillus supplementation might affect the transport of nascent fat from the liver to abdominal fat. In conclusion, the species of intestinal-dominant bacteria in the geese are relatively stable, but their relative abundance and function are affected by a number of factors. Overfeeding promotes the metabolism of nutrients in the jejunum and ileum and increases bacterial adaptability to environmental changes by enhancing their ability to process environmental and genetic information more efficiently. These findings suggest that the effect of overfeeding on the composition of intestinal microbiota may indirectly influence the formation of goose fatty liver through the gut/liver axis.}, } @article {pmid35923394, year = {2022}, author = {Liu, H and Han, X and Zhao, N and Hu, L and Wang, X and Luo, C and Chen, Y and Zhao, X and Xu, S}, title = {The Gut Microbiota Determines the High-Altitude Adaptability of Tibetan Wild Asses (Equus kiang) in Qinghai-Tibet Plateau.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {949002}, pmid = {35923394}, issn = {1664-302X}, abstract = {It was acknowledged long ago that microorganisms have played critical roles in animal evolution. Tibetan wild asses (TWA, Equus kiang) are the only wild perissodactyls on the Qinghai-Tibet Plateau (QTP) and the first national protected animals; however, knowledge about the relationships between their gut microbiota and the host's adaptability remains poorly understood. Herein, 16S rRNA and meta-genomic sequencing approaches were employed to investigate the gut microbiota-host associations in TWA and were compared against those of the co-resident livestock of yak (Bos grunnies) and Tibetan sheep (Ovis aries). Results revealed that the gut microbiota of yak and Tibetan sheep underwent convergent evolution. By contrast, the intestinal microflora of TWA diverged in a direction enabling the host to subsist on sparse and low-quality forage. Meanwhile, high microbial diversity (Shannon and Chao1 indices), cellulolytic activity, and abundant indicator species such as Spirochaetes, Bacteroidetes, Prevotella_1, and Treponema_2 supported forage digestion and short-chain fatty acid production in the gut of TWA. Meanwhile, the enterotype identification analysis showed that TWA shifted their enterotype in response to low-quality forage for a better utilization of forage nitrogen and short-chain fatty acid production. Metagenomic analysis revealed that plant biomass degrading microbial consortia, genes, and enzymes like the cellulolytic strains (Prevotella ruminicola, Ruminococcus flavefaciens, Ruminococcus albus, Butyrivibrio fibrisolvens, and Ruminobacter amylophilus), as well as carbohydrate metabolism genes (GH43, GH3, GH31, GH5, and GH10) and enzymes (β-glucosidase, xylanase, and β-xylosidase, etc.) had a significantly higher enrichment in TWA. Our results indicate that gut microbiota can improve the adaptability of TWA through plant biomass degradation and energy maintenance by the functions of gut microbiota in the face of nutritional deficiencies and also provide a strong rationale for understanding the roles of gut microbiota in the adaptation of QTP wildlife when facing harsh feeding environments.}, } @article {pmid35923393, year = {2022}, author = {De, D and Nayak, T and Chowdhury, S and Dhal, PK}, title = {Insights of Host Physiological Parameters and Gut Microbiome of Indian Type 2 Diabetic Patients Visualized via Metagenomics and Machine Learning Approaches.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {914124}, pmid = {35923393}, issn = {1664-302X}, abstract = {Type 2 diabetes (T2D) is a serious public health issue and may also contribute to modification in the structure of the intestinal microbiota, implying a link between T2D and microbial inhabitants in the digestive tract. This work aimed to develop efficient models for identifying essential physiological markers for improved T2D classification using machine learning algorithms. Using amplicon metagenomic approaches, an effort has also been made to understand the alterations in core gut microbial members in Indian T2D patients with respect to their control normal glucose tolerance (NGT). Our data indicate the level of fasting blood glucose (FBG) and glycated hemoglobin (HbA1c) were the most useful physiological indicators while random forest and support vector machine with RBF Kernel were effective predictions models for identifications of T2D. The dominating gut microbial members Allopreotella, Rikenellaceae RC9 gut group, Haemophilus, Ruminococcus torques group, etc. in Indian T2D patients showed a strong association with both FBG and HbA1c. These members have been reported to have a crucial role in gut barrier breakdown, blood glucose, and lipopolysaccharide level escalation, or as biomarkers. While the dominant NGT microbiota (Akkermansia, Ligilactobacillus, Enterobacter, etc.) in the colon has been shown to influence inflammatory immune responses by acting as an anti-inflammatory agent and maintaining the gut barrier. The topology study of co-occurrence network analysis indicates that changes in network complexity in T2D lead to variations in the different gut microbial members compared to NGT. These studies provide a better understanding of the gut microbial diversity in Indian T2D patients and show the way for the development of valuable diagnostics strategies to improve the prediction and modulation of the T2D along with already established methods.}, } @article {pmid35922873, year = {2022}, author = {Gaire, TN and Odland, C and Zhang, B and Ray, T and Doster, E and Nerem, J and Dee, S and Davies, P and Noyes, N}, title = {The impacts of viral infection and subsequent antimicrobials on the microbiome-resistome of growing pigs.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {118}, pmid = {35922873}, issn = {2049-2618}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; *Coinfection ; Metagenomics ; *Microbiota/genetics ; *Porcine Reproductive and Respiratory Syndrome/drug therapy ; *Porcine respiratory and reproductive syndrome virus/genetics ; Swine ; }, abstract = {BACKGROUND: Antimicrobials are used in food-producing animals for purposes of preventing, controlling, and/or treating infections. In swine, a major driver of antimicrobial use is porcine reproductive and respiratory syndrome (PRRS), which is caused by a virus that predisposes infected animals to secondary bacterial infections. Numerous antimicrobial protocols are used to treat PRRS, but we have little insight into how these treatment schemes impact antimicrobial resistance (AMR) dynamics within the fecal microbiome of commercial swine. The aim of this study was to determine whether different PRRS-relevant antimicrobial treatment protocols were associated with differences in the fecal microbiome and resistome of growing pigs. To accomplish this, we used a metagenomics approach to characterize and compare the longitudinal wean-to-market resistome and microbiome of pigs challenged with PRRS virus and then exposed to different antimicrobial treatments, and a group of control pigs not challenged with PRRS virus and having minimal antimicrobial exposure. Genomic DNA was extracted from pen-level composite fecal samples from each treatment group and subjected to metagenomic sequencing and microbiome-resistome bioinformatic and statistical analysis. Microbiome-resistome profiles were compared over time and between treatment groups.

RESULTS: Fecal microbiome and resistome compositions both changed significantly over time, with a dramatic and stereotypic shift between weaning and 9 days post-weaning (dpw). Antimicrobial resistance gene (ARG) richness and diversity were significantly higher at earlier time points, while microbiome richness and diversity were significantly lower. The post-weaning shift was characterized by transition from a Bacteroides-dominated enterotype to Lactobacillus- and Streptococcus-dominated enterotypes. Both the microbiome and resistome stabilized by 44 dpw, at which point the trajectory of microbiome-resistome maturation began to diverge slightly between the treatment groups, potentially due to physical clustering of the pigs. Challenge with PRRS virus seemed to correspond to the re-appearance of many very rare and low-abundance ARGs within the feces of challenged pigs. Despite very different antimicrobial exposures after challenge with PRRS virus, resistome composition remained largely similar between the treatment groups. Differences in ARG abundance between the groups were mostly driven by temporal changes in abundance that occurred prior to antimicrobial exposures, with the exception of ermG, which increased in the feces of treated pigs, and was significantly more abundant in the feces of these pigs compared to the pigs that did not receive post-PRRS antimicrobials.

CONCLUSIONS: The fecal microbiome-resistome of growing pigs exhibited a stereotypic trajectory driven largely by weaning and physiologic aging of the pigs. Events such as viral illness, antimicrobial exposures, and physical grouping of the pigs exerted significant yet relatively minor influence over this trajectory. Therefore, the AMR profile of market-age pigs is the culmination of the life history of the individual pigs and the populations to which they belong. Disease status alone may be a significant driver of AMR in market-age pigs, and understanding the interaction between disease processes and antimicrobial exposures on the swine microbiome-resistome is crucial to developing effective, robust, and reproducible interventions to control AMR. Video Abstract.}, } @article {pmid35922588, year = {2022}, author = {Wang, Y and Xu, J and Chen, H and Yu, J and Xu, X and Sun, L and Xu, X and Yu, C and Xu, F and Huang, J and Jiao, X and Zhang, Y}, title = {A balanced gut microbiota is essential to maintain health in captive sika deer.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {17}, pages = {5659-5674}, pmid = {35922588}, issn = {1432-0614}, mesh = {Animals ; Bacteria ; Bifidobacterium ; *Deer ; *Gastrointestinal Microbiome ; Humans ; Lactobacillus ; Metagenomics ; *Microbiota ; }, abstract = {Certain animals harbor a high proportion of pathogens, particular the zoonotic pathogens, in their gut microbiome but are usually asymptomic; however, their carried pathogens may seriously threaten the public health. By understanding how the microbiome overcomes the negative effects of pathogens to maintain host health, we can develop novel solutions to control animal-mediated pathogen transmission including identification and application of beneficial microbes. Here, we analyzed the gut microbiota of 10 asymptomic captive sika deer individuals by full-length 16S rDNA sequencing. Twenty-nine known pathogens capable of infecting humans were identified, and the accumulated proportions of the identified pathogens were highly variable among individuals (2.33 to 39.94%). The relative abundances of several beneficial bacteria, including Lactobacillus and Bifidobacterium, were found to be positively correlated with the relative abundances of accumulated pathogens. Whole-genome metagenomic analysis revealed that the beneficial- and pathogenic-associated functions, such as genes involved in the synthesis of short chain fatty acids and virulence factors, were also positively correlated in the microbiome, indicating that the beneficial and pathogenic functions were maintained at a relatively balanced ratio. Furthermore, the bacteriophages that target the identified pathogens were found to be positively correlated with the pathogenic content in the microbiome. Several high-quality genomes of beneficial bacteria affiliated with Lactobacillus and Bifidobacterium and bacteriophages were recovered from the metagenomic data. Overall, this study provides novel insights into the interplay between beneficial and pathogenic content to ensure maintenance of a healthy gut microbiome, and also contributes to discovery of novel beneficial microbes and functions that control pathogens. KEY POINTS: • Certain asymptomic captive sika deer individuals harbor relatively high amounts of zoonotic pathogens. • The beneficial microbes and the beneficial functions are balanced with the pathogenic contents in the gut microbiome. • Several high-quality genomes of beneficial bacteria and bacteriophages are recovered by metagenomics.}, } @article {pmid35922218, year = {2022}, author = {Sun, JH and Zhang, XH and Mo, XD and Fu, HX and Zhang, YY and Chen, YY and Chen, Y and Wang, Y and Huang, XJ and Xu, LP}, title = {[Application value of metagenomic next-generation sequencing for infectious pathogens in patients receiving allogeneic hematopoietic stem cell transplantation].}, journal = {Zhonghua nei ke za zhi}, volume = {61}, number = {8}, pages = {928-932}, doi = {10.3760/cma.j.cn112138-20220212-00104}, pmid = {35922218}, issn = {0578-1426}, support = {2017YFA0104500//National Key Research and Development Program of China/ ; }, mesh = {*Epstein-Barr Virus Infections ; *Hematopoietic Stem Cell Transplantation ; Herpesvirus 4, Human ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Retrospective Studies ; Sensitivity and Specificity ; }, abstract = {Objective: To investigate the application value of Metagenomic Next-Generation sequencing (mNGS) in infectious patients after allogeneic hematopoietic stem cell transplantation(allo-HSCT). Methods: Patients suspected with local or systemic infections were retrospectively included after allo-HSCT in our department from April 2019 to November 2020. Pathogenic microorganisms were tested by mNGS in samples from peripheral blood, cerebrospinal fluid, alveolar lavage Liquid, abscess, etc. Other diagnostic methods such as bacterial/fungal culture, viral PCR detection were simultaneously explored comparing with mNGS results. Results: A total of 112 samples in 83 patients were detected by mNGS, and 34 pathogenic microorganisms were determined. Among these positive samples, 11 strains of bacteria (17 times) with the most common Escherichia coli (4/17) were reported. There were 7 strains of fungi (10 times) detected with primary Candida albicans (7/29). Although arvovirus 30.2% (39/129) were predominantly detected, its diagnostic relevance with infections was not definite. Other pathogenic viruses including cytomegalovirus (CMV) 25.6% (33/129) and Epstein Barr virus (EBV) 14.0% (18/129)were of significance. Comparing with golden diagnostic criteria, the sensitivity of mNGS was 86.5%, and specificity was 45.0%. Regarding single pathogen infection, the consistency of mNGS and conventional methods was 82.9% (29/35), while it was 16/17 in combination infections. Conclusion: mNGS could be a potential method to determine pathogens in patients suspected with infections after allo-HSCT.}, } @article {pmid35922186, year = {2022}, author = {Wang, ZX and Wu, X and Xu, J and Ye, YZ and Han, SZ and Ye, LJ and Wu, BB and Wang, CQ and Yu, H}, title = {[Value of metagenomic next-generation sequencing in the etiology diagnosis of bacterial meningitis in children].}, journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics}, volume = {60}, number = {8}, pages = {769-773}, doi = {10.3760/cma.j.cn112140-20220317-00214}, pmid = {35922186}, issn = {0578-1310}, support = {2021YFC2701800, 2021YFC2701801//National Key Research and Development Program of China/ ; EK2022ZX05//Key Development Program of Children's Hospital of Fudan University/ ; }, mesh = {Child ; Escherichia coli ; Female ; Gram-Positive Bacteria ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Male ; *Meningitis, Bacterial/diagnosis/microbiology ; Metagenomics/methods ; Retrospective Studies ; Sensitivity and Specificity ; }, abstract = {Objective: To explore the value of metagenomic next-generation sequencing (mNGS) in the etiology diagnosis of bacterial meningitis in children. Methods: The etiological results of 189 children diagnosed with "bacterial meningitis" or "purulent meningitis" or "central nervous system infection" in the Children's Hospital of Fudan University from 1st January 2019 to 31st December 2020 were analyzed retrospectively. The cerebrospinal fluid (CFS) of the children with bacterial meningitis was detected by culture and mNGS respectively, and the difference of pathogen detection rate between the 2 methods was analyzed. According to the age at the time of visit, the children were divided into neonatal group (≤28 days of age) and non-neonatal group (>28 days of age), and χ[2] test was used to compare the positive rate between the 2 groups. Taking CFS culture as the gold standard, the sensitivity and specificity of mNGS in the diagnosing of bacterial meningitis in children were analyzed. Results: Among these 189 children with bacterial meningitis, 116 were males and 73 were females. A total of 76 strains of pathogens were detected in blood and (or) CSF cultures, of which 50 strains (65.8%) were Gram-positive bacteria; among those, 18 strains (23.7%) of Streptococcus agalactiae, 17 strains (19.7%) of Escherichia coli and 15 strains (19.7%) of Streptococcus pneumoniae were detected with higher detection rate. The infection rate of Gram-positive bacteria in the non-neonatal group was higher than that in the neonatal group (76.0% (38/50) vs. 50.0% (13/26), χ[2]=5.24, P=0.020).The same CSF samples of 48 cases were tested by mNGS and culture at the same time, and the detection rate of mNGS was higher than that of CSF culture (20 cases (41.7%) vs. 12 cases (25.0%), χ[2]=16.45, P<0.001). The consistency of mNGS and culture results was 79.2% (38/48), and the same pathogen was detected in 11 children with both positive mNGS and CSF culture. Taking the results of CSF culture as the gold standard, the sensitivity of mNGS in the diagnosing of bacterial meningitis was 91.7%, and the specificity was 75.0%. Conclusions: The mNGS technology can improve the pathogen detection rate of bacterial meningitis in children, and has a high consistency with CSF culture. In suspected cases where the pathogen cannot be identified by traditional methods, CSF mNGS should be considered timely.}, } @article {pmid35921303, year = {2022}, author = {, }, title = {Retraction: Enumeration of citrus endophytic bacterial communities based on illumine metagenomics technique.}, journal = {PloS one}, volume = {17}, number = {8}, pages = {e0272191}, pmid = {35921303}, issn = {1932-6203}, } @article {pmid35920823, year = {2022}, author = {Aishwarya, S and Gunasekaran, K}, title = {Meta-analysis of the microbial biomarkers in the gut-lung crosstalk in COVID-19, community-acquired pneumonia and Clostridium difficile infections.}, journal = {Letters in applied microbiology}, volume = {75}, number = {5}, pages = {1293-1306}, pmid = {35920823}, issn = {1472-765X}, mesh = {Humans ; *Clostridioides difficile ; *COVID-19 ; *Gastrointestinal Microbiome ; *Clostridium Infections/microbiology ; Dysbiosis ; Lung ; Biomarkers ; }, abstract = {Respiratory infections are the leading causes of mortality and the current pandemic COVID-19 is one such trauma that imposed catastrophic devastation to the health and economy of the world. Unravelling the correlations and interplay of the human microbiota in the gut-lung axis would offer incredible solutions to the underlying mystery of the disease progression. The study compared the microbiota profiles of six samples namely healthy gut, healthy lung, COVID-19 infected gut, COVID-19 infected lungs, Clostridium difficile infected gut and community-acquired pneumonia infected lungs. The metagenome data sets were processed, normalized, classified and the rarefaction curves were plotted. The microbial biomarkers for COVID-19 infections were identified as the abundance of Candida and Escherichia in lungs with Ruminococcus in the gut. Candida and Staphylococcus could play a vital role as putative prognostic biomarkers of community-acquired pneumonia whereas abundance of Faecalibacterium and Clostridium is associated with the C. difficile infections in gut. A machine learning random forest classifier applied to the data sets efficiently classified the biomarkers. The study offers an extensive and incredible understanding of the existence of gut-lung axis during dysbiosis of two anatomically different organs.}, } @article {pmid35920817, year = {2022}, author = {Richter, DJ and Watteaux, R and Vannier, T and Leconte, J and Frémont, P and Reygondeau, G and Maillet, N and Henry, N and Benoit, G and Da Silva, O and Delmont, TO and Fernàndez-Guerra, A and Suweis, S and Narci, R and Berney, C and Eveillard, D and Gavory, F and Guidi, L and Labadie, K and Mahieu, E and Poulain, J and Romac, S and Roux, S and Dimier, C and Kandels, S and Picheral, M and Searson, S and , and Pesant, S and Aury, JM and Brum, JR and Lemaitre, C and Pelletier, E and Bork, P and Sunagawa, S and Lombard, F and Karp-Boss, L and Bowler, C and Sullivan, MB and Karsenti, E and Mariadassou, M and Probert, I and Peterlongo, P and Wincker, P and de Vargas, C and Ribera d'Alcalà, M and Iudicone, D and Jaillon, O}, title = {Genomic evidence for global ocean plankton biogeography shaped by large-scale current systems.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35920817}, issn = {2050-084X}, mesh = {*Ecosystem ; Genomics ; Geography ; Oceans and Seas ; *Plankton/genetics ; }, abstract = {Biogeographical studies have traditionally focused on readily visible organisms, but recent technological advances are enabling analyses of the large-scale distribution of microscopic organisms, whose biogeographical patterns have long been debated. Here we assessed the global structure of plankton geography and its relation to the biological, chemical, and physical context of the ocean (the 'seascape') by analyzing metagenomes of plankton communities sampled across oceans during the Tara Oceans expedition, in light of environmental data and ocean current transport. Using a consistent approach across organismal sizes that provides unprecedented resolution to measure changes in genomic composition between communities, we report a pan-ocean, size-dependent plankton biogeography overlying regional heterogeneity. We found robust evidence for a basin-scale impact of transport by ocean currents on plankton biogeography, and on a characteristic timescale of community dynamics going beyond simple seasonality or life history transitions of plankton.}, } @article {pmid35920769, year = {2022}, author = {Bai, Z and Zhang, YZ and Miyano, S and Yamaguchi, R and Fujimoto, K and Uematsu, S and Imoto, S}, title = {Identification of bacteriophage genome sequences with representation learning.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {18}, pages = {4264-4270}, pmid = {35920769}, issn = {1367-4811}, support = {21H03538//Ministry of Education, Culture, Sports, Science, and Technology of Japan/ ; //Japan Society for the Promotion of Science/ ; JP21K12104//JSPS KAKENHI/ ; 21fk0108619h0001//Japan Agency for Medical Research and Development/ ; //Uehara Memorial Foundation/ ; }, mesh = {Humans ; *Bacteriophages/genetics ; Software ; Metagenome ; Machine Learning ; Bacteria ; }, abstract = {MOTIVATION: Bacteriophages/phages are the viruses that infect and replicate within bacteria and archaea, and rich in human body. To investigate the relationship between phages and microbial communities, the identification of phages from metagenome sequences is the first step. Currently, there are two main methods for identifying phages: database-based (alignment-based) methods and alignment-free methods. Database-based methods typically use a large number of sequences as references; alignment-free methods usually learn the features of the sequences with machine learning and deep learning models.

RESULTS: We propose INHERIT which uses a deep representation learning model to integrate both database-based and alignment-free methods, combining the strengths of both. Pre-training is used as an alternative way of acquiring knowledge representations from existing databases, while the BERT-style deep learning framework retains the advantage of alignment-free methods. We compare INHERIT with four existing methods on a third-party benchmark dataset. Our experiments show that INHERIT achieves a better performance with the F1-score of 0.9932. In addition, we find that pre-training two species separately helps the non-alignment deep learning model make more accurate predictions.

The codes of INHERIT are now available in: https://github.com/Celestial-Bai/INHERIT.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid35920561, year = {2022}, author = {Zulk, JJ and Clark, JR and Ottinger, S and Ballard, MB and Mejia, ME and Mercado-Evans, V and Heckmann, ER and Sanchez, BC and Trautner, BW and Maresso, AW and Patras, KA}, title = {Phage Resistance Accompanies Reduced Fitness of Uropathogenic Escherichia coli in the Urinary Environment.}, journal = {mSphere}, volume = {7}, number = {4}, pages = {e0034522}, pmid = {35920561}, issn = {2379-5042}, support = {R25 GM056929/GM/NIGMS NIH HHS/United States ; T32 AI055413/AI/NIAID NIH HHS/United States ; U19 AI157981/AI/NIAID NIH HHS/United States ; I01 RX002595/RX/RRD VA/United States ; T32 GM136554/GM/NIGMS NIH HHS/United States ; F31 AI167547/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Bacteriophages/genetics ; Humans ; Mice ; Urinary Bladder ; *Urinary Tract Infections/microbiology ; *Uropathogenic Escherichia coli/genetics ; }, abstract = {Urinary tract infection (UTI) is among the most common infections treated worldwide each year and is caused primarily by uropathogenic Escherichia coli (UPEC). Rising rates of antibiotic resistance among uropathogens have spurred a consideration of alternative treatment strategies, such as bacteriophage (phage) therapy; however, phage-bacterial interactions within the urinary environment are poorly defined. Here, we assess the activity of two phages, namely, HP3 and ES17, against clinical UPEC isolates using in vitro and in vivo models of UTI. In both bacteriologic medium and pooled human urine, we identified phage resistance arising within the first 6 to 8 h of coincubation. Whole-genome sequencing revealed that UPEC strains resistant to HP3 and ES17 harbored mutations in genes involved in lipopolysaccharide (LPS) biosynthesis. Phage-resistant strains displayed several in vitro phenotypes, including alterations to adherence to and invasion of human bladder epithelial HTB-9 cells and increased biofilm formation in some isolates. Interestingly, these phage-resistant UPEC isolates demonstrated reduced growth in pooled human urine, which could be partially rescued by nutrient supplementation and were more sensitive to several outer membrane-targeting antibiotics than parental strains. Additionally, phage-resistant UPEC isolates were attenuated in bladder colonization in a murine UTI model. In total, our findings suggest that while resistance to phages, such as HP3 and ES17, may arise readily in the urinary environment, phage resistance is accompanied by fitness costs which may render UPEC more susceptible to host immunity or antibiotics. IMPORTANCE UTI is one of the most common causes of outpatient antibiotic use, and rising antibiotic resistance threatens the ability to control UTI unless alternative treatments are developed. Bacteriophage (phage) therapy is gaining renewed interest; however, much like with antibiotics, bacteria can readily become resistant to phages. For successful UTI treatment, we must predict how bacteria will evade killing by phage and identify the downstream consequences of phage resistance during bacterial infection. In our current study, we found that while phage-resistant bacteria quickly emerged in vitro, these bacteria were less capable of growing in human urine and colonizing the murine bladder. These results suggest that phage therapy poses a viable UTI treatment if phage resistance confers fitness costs for the uropathogen. These results have implications for developing cocktails of phage with multiple different bacterial targets, of which each is evaded only at the cost of bacterial fitness.}, } @article {pmid35920083, year = {2022}, author = {Shi, LD and Zhou, YJ and Tang, XJ and Kappler, A and Chistoserdova, L and Zhu, LZ and Zhao, HP}, title = {Coupled Aerobic Methane Oxidation and Arsenate Reduction Contributes to Soil-Arsenic Mobilization in Agricultural Fields.}, journal = {Environmental science & technology}, volume = {56}, number = {16}, pages = {11845-11856}, doi = {10.1021/acs.est.2c01878}, pmid = {35920083}, issn = {1520-5851}, mesh = {Arsenates ; *Arsenic/metabolism ; Methane ; Oxidation-Reduction ; Soil ; Soil Microbiology ; }, abstract = {Microbial oxidation of organic compounds can promote arsenic release by reducing soil-associated arsenate to the more mobile form arsenite. While anaerobic oxidation of methane has been demonstrated to reduce arsenate, it remains elusive whether and to what extent aerobic methane oxidation (aeMO) can contribute to reductive arsenic mobilization. To fill this knowledge gap, we performed incubations of both microbial laboratory cultures and soil samples from arsenic-contaminated agricultural fields in China. Incubations with laboratory cultures showed that aeMO could couple to arsenate reduction, wherein the former bioprocess was carried out by aerobic methanotrophs and the latter by a non-methanotrophic bacterium belonging to a novel and uncultivated representative of Burkholderiaceae. Metagenomic analyses combined with metabolite measurements suggested that formate served as the interspecies electron carrier linking aeMO to arsenate reduction. Such coupled bioprocesses also take place in the real world, supported by a similar stoichiometry and gene activity in the incubations with natural paddy soils, and contribute up to 76.2% of soil-arsenic mobilization into pore waters in the top layer of the soils where oxygen was present. Overall, this study reveals a previously overlooked yet significant contribution of aeMO to reductive arsenic mobilization.}, } @article {pmid35918706, year = {2022}, author = {De Bernardini, N and Basile, A and Zampieri, G and Kovalovszki, A and De Diego Diaz, B and Offer, E and Wongfaed, N and Angelidaki, I and Kougias, PG and Campanaro, S and Treu, L}, title = {Integrating metagenomic binning with flux balance analysis to unravel syntrophies in anaerobic CO2 methanation.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {117}, pmid = {35918706}, issn = {2049-2618}, mesh = {Anaerobiosis ; *Biofuels ; Bioreactors ; Carbon Dioxide/analysis ; Firmicutes/metabolism ; Formates ; *Metagenome ; Methane/metabolism ; Methanobacteriaceae/genetics/metabolism ; }, abstract = {BACKGROUND: Carbon fixation through biological methanation has emerged as a promising technology to produce renewable energy in the context of the circular economy. The anaerobic digestion microbiome is the fundamental biological system operating biogas upgrading and is paramount in power-to-gas conversion. Carbon dioxide (CO2) methanation is frequently performed by microbiota attached to solid supports generating biofilms. Despite the apparent simplicity of the microbial community involved in biogas upgrading, the dynamics behind most of the interspecies interaction remain obscure. To understand the role of the microbial species in CO2 fixation, the biofilm generated during the biogas upgrading process has been selected as a case study. The present work investigates via genome-centric metagenomics, based on a hybrid Nanopore-Illumina approach the biofilm developed on the diffusion devices of four ex situ biogas upgrading reactors. Moreover, genome-guided metabolic reconstruction and flux balance analysis were used to propose a biological role for the dominant microbes.

RESULTS: The combined microbiome was composed of 59 species, with five being dominant (> 70% of total abundance); the metagenome-assembled genomes representing these species were refined to reach a high level of completeness. Genome-guided metabolic analysis appointed Firmicutes sp. GSMM966 as the main responsible for biofilm formation. Additionally, species interactions were investigated considering their co-occurrence in 134 samples, and in terms of metabolic exchanges through flux balance simulation in a simplified medium. Some of the most abundant species (e.g., Limnochordia sp. GSMM975) were widespread (~ 67% of tested experiments), while others (e.g., Methanothermobacter wolfeii GSMM957) had a scattered distribution. Genome-scale metabolic models of the microbial community were built with boundary conditions taken from the biochemical data and showed the presence of a flexible interaction network mainly based on hydrogen and carbon dioxide uptake and formate exchange.

CONCLUSIONS: Our work investigated the interplay between five dominant species within the biofilm and showed their importance in a large spectrum of anaerobic biogas reactor samples. Flux balance analysis provided a deeper insight into the potential syntrophic interaction between species, especially Limnochordia sp. GSMM975 and Methanothermobacter wolfeii GSMM957. Finally, it suggested species interactions to be based on formate and amino acids exchanges. Video Abstract.}, } @article {pmid35918425, year = {2022}, author = {Shkoporov, AN and Stockdale, SR and Lavelle, A and Kondova, I and Heuston, C and Upadrasta, A and Khokhlova, EV and van der Kamp, I and Ouwerling, B and Draper, LA and Langermans, JAM and Paul Ross, R and Hill, C}, title = {Viral biogeography of the mammalian gut and parenchymal organs.}, journal = {Nature microbiology}, volume = {7}, number = {8}, pages = {1301-1311}, pmid = {35918425}, issn = {2058-5276}, support = {/WT_/Wellcome Trust/United Kingdom ; 220646/WT_/Wellcome Trust/United Kingdom ; 220646/Z/20/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; *Bacteriophages/genetics ; Feces ; Macaca mulatta ; Mammals ; Metagenome ; Metagenomics ; *Viruses/genetics ; }, abstract = {The mammalian virome has been linked to health and disease but our understanding of how it is structured along the longitudinal axis of the mammalian gastrointestinal tract (GIT) and other organs is limited. Here, we report a metagenomic analysis of the prokaryotic and eukaryotic virome occupying luminal and mucosa-associated habitats along the GIT, as well as parenchymal organs (liver, lung and spleen), in two representative mammalian species, the domestic pig and rhesus macaque (six animals per species). Luminal samples from the large intestine of both mammals harboured the highest loads and diversity of bacteriophages (class Caudoviricetes, family Microviridae and others). Mucosal samples contained much lower viral loads but a higher proportion of eukaryotic viruses (families Astroviridae, Caliciviridae, Parvoviridae). Parenchymal organs contained bacteriophages of gut origin, in addition to some eukaryotic viruses. Overall, GIT virome composition was specific to anatomical region and host species. Upper GIT and mucosa-specific viruses were greatly under-represented in distal colon samples (a proxy for faeces). Nonetheless, certain viral and phage species were ubiquitous in all samples from the oral cavity to the distal colon. The dataset and its accompanying methodology may provide an important resource for future work investigating the biogeography of the mammalian gut virome.}, } @article {pmid35918353, year = {2022}, author = {Kim, H and Jeon, S and Kim, J and Seol, D and Jo, J and Cho, S and Kim, H}, title = {Investigation of memory-enhancing effects of Streptococcus thermophilus EG007 in mice and elucidating molecular and metagenomic characteristics using nanopore sequencing.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {13274}, pmid = {35918353}, issn = {2045-2322}, mesh = {Animals ; Metagenome ; Metagenomics ; Mice ; *Nanopore Sequencing ; RNA, Ribosomal, 16S/genetics ; *Streptococcus thermophilus/genetics ; }, abstract = {Over the past decades, accumulating evidences have highlighted the gut microbiota as a key player in the brain functioning via microbiota-gut-brain axis, and accordingly, the beneficial role of several probiotic strains in cognitive ability also have been actively investigated. However, the majority of the research have demonstrated the effects against age-related cognitive decline or neurological disease. To this end, we aimed to investigate lactic acid bacteria strains having beneficial effects on the cognitive function of healthy young mice and elucidate underlying characteristics by carrying out nanopore sequencing-based genomics and metagenomics analysis. 8-week consumption of Streptococcus thermophilus EG007 demonstrated marked enhancements in behavior tests assessing short-term spatial and non-spatial learning and memory. It was revealed that EG007 possessed genes encoding various metabolites beneficial for a health condition in many aspects, including gamma-aminobutyric acid producing system, a neurotransmitter associated with mood and stress response. Also, by utilizing 16S-23S rRNA operon as a taxonomic marker, we identified more accurate species-level compositional changes in gut microbiota, which was increase of certain species, previously reported to have associations with mental health or down-regulation of inflammation or infection-related species. Moreover, correlation analysis revealed that the EG007-mediated altered microbiota had a significant correlation with the memory traits.}, } @article {pmid35918104, year = {2023}, author = {Brusilovsky, M and Rochman, M and Shoda, T and Kotliar, M and Caldwell, JM and Mack, LE and Besse, JA and Chen, X and Weirauch, MT and Barski, A and Rothenberg, ME}, title = {Vitamin D receptor and STAT6 interactome governs oesophageal epithelial barrier responses to IL-13 signalling.}, journal = {Gut}, volume = {72}, number = {5}, pages = {834-845}, pmid = {35918104}, issn = {1468-3288}, support = {R01 AI045898/AI/NIAID NIH HHS/United States ; R01 AI130033/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; *Eosinophilic Esophagitis ; Inflammation/metabolism ; Interleukin-13/pharmacology/metabolism ; Nerve Tissue Proteins/metabolism ; *Receptors, Calcitriol/genetics ; Receptors, Immunologic/metabolism ; STAT6 Transcription Factor/genetics/metabolism ; Vitamin D ; }, abstract = {OBJECTIVE: The contribution of vitamin D (VD) deficiency to the pathogenesis of allergic diseases remains elusive. We aimed to define the impact of VD on oesophageal allergic inflammation.

DESIGN: We assessed the genomic distribution and function of VD receptor (VDR) and STAT6 using histology, molecular imaging, motif discovery and metagenomic analysis. We examined the role of VD supplementation in oesophageal epithelial cells, in a preclinical model of IL-13-induced oesophageal allergic inflammation and in human subjects with eosinophilic oesophagitis (EoE).

RESULTS: VDR response elements were enriched in oesophageal epithelium, suggesting enhanced VDR binding to functional gene enhancer and promoter regions. Metagenomic analysis showed that VD supplementation reversed dysregulation of up to 70% of the transcriptome and epigenetic modifications (H3K27Ac) induced by IL-13 in VD-deficient cells, including genes encoding the transcription factors HIF1A and SMAD3, endopeptidases (SERPINB3) and epithelial-mesenchymal transition mediators (TGFBR1, TIAM1, SRC, ROBO1, CDH1). Molecular imaging and chromatin immunoprecipitation showed VDR and STAT6 colocalisation within the regulatory regions of the affected genes, suggesting that VDR and STAT6 interactome governs epithelial tissue responses to IL-13 signalling. Indeed, VD supplementation reversed IL-13-induced epithelial hyperproliferation, reduced dilated intercellular spaces and barrier permeability, and improved differentiation marker expression (filaggrin, involucrin). In a preclinical model of IL-13-mediated oesophageal allergic inflammation and in human EoE, VD levels inversely associated with severity of oesophageal eosinophilia and epithelial histopathology.

CONCLUSIONS: Collectively, these findings identify VD as a natural IL-13 antagonist with capacity to regulate the oesophageal epithelial barrier functions, providing a novel therapeutic entry point for type 2 immunity-related diseases.}, } @article {pmid35918059, year = {2022}, author = {Wang, C and Mantilla-Calderon, D and Xiong, Y and Alkahtani, M and Bashawri, YM and Al Qarni, H and Hong, PY}, title = {Investigation of Antibiotic Resistome in Hospital Wastewater during the COVID-19 Pandemic: Is the Initial Phase of the Pandemic Contributing to Antimicrobial Resistance?.}, journal = {Environmental science & technology}, volume = {56}, number = {21}, pages = {15007-15018}, pmid = {35918059}, issn = {1520-5851}, mesh = {Humans ; *Anti-Bacterial Agents/pharmacology ; Wastewater ; Pandemics ; *COVID-19 ; Genes, Bacterial ; Drug Resistance, Bacterial/genetics ; Hospitals ; }, abstract = {Since the COVID-19 pandemic started, there has been much speculation about how COVID-19 and antimicrobial resistance may be interconnected. In this study, untreated wastewater was sampled from Hospital A designated to treat COVID-19 patients during the first wave of the COVID-19 pandemic alongside Hospital B that did not receive any COVID-19 patients. Metagenomics was used to determine the relative abundance and mobile potential of antibiotic resistant genes (ARGs), prior to determining the correlation of ARGs with time/incidence of COVID-19. Our findings showed that ARGs resistant to macrolides, sulfonamides, and tetracyclines were positively correlated with time in Hospital A but not in Hospital B. Likewise, minor extended spectrum beta-lactamases (ESBLs) and carbapenemases of classes B and D were positively correlated with time, suggesting the selection of rare and/or carbapenem-resistant genes in Hospital A. Non-carbapenemase blaVEB also positively correlated with both time and intI1 and was copresent with other ARGs including carbapenem-resistant genes in 6 metagenome-assembled genomes (MAGs). This study highlighted concerns related to the dissemination of antimicrobial resistance (AMR) during the COVID-19 pandemic that may arise from antibiotic use and untreated hospital wastewater.}, } @article {pmid35917471, year = {2022}, author = {Wegener, G and Laso-Pérez, R and Orphan, VJ and Boetius, A}, title = {Anaerobic Degradation of Alkanes by Marine Archaea.}, journal = {Annual review of microbiology}, volume = {76}, number = {}, pages = {553-577}, doi = {10.1146/annurev-micro-111021-045911}, pmid = {35917471}, issn = {1545-3251}, mesh = {*Alkanes/metabolism ; Anaerobiosis ; *Archaea ; Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Alkanes are saturated apolar hydrocarbons that range from their simplest form, methane, to high-molecular-weight compounds. Although alkanes were once considered biologically recalcitrant under anaerobic conditions, microbiological investigations have now identified several microbial taxa that can anaerobically degrade alkanes. Here we review recent discoveries in the anaerobic oxidation of alkanes with a specific focus on archaea that use specific methyl coenzyme M reductases to activate their substrates. Our understanding of the diversity of uncultured alkane-oxidizing archaea has expanded through the use of environmental metagenomics and enrichment cultures of syntrophic methane-, ethane-, propane-, and butane-oxidizing marine archaea with sulfate-reducing bacteria. A recently cultured group of archaea directly couples long-chain alkane degradation with methane formation, expanding the range of substrates used for methanogenesis. This article summarizes the rapidly growing knowledge of the diversity, physiology, and habitat distribution of alkane-degrading archaea.}, } @article {pmid35917175, year = {2022}, author = {Tchitchek, N and Nguekap Tchoumba, O and Pires, G and Dandou, S and Campagne, J and Churlaud, G and Fourcade, G and Hoffmann, TW and Strozzi, F and Gaal, C and Bonny, C and Le Chatelier, E and Erlich, SD and Sokol, H and Klatzmann, D}, title = {Low-dose IL-2 shapes a tolerogenic gut microbiota that improves autoimmunity and gut inflammation.}, journal = {JCI insight}, volume = {7}, number = {17}, pages = {}, pmid = {35917175}, issn = {2379-3708}, mesh = {Animals ; *Autoimmune Diseases ; Autoimmunity ; Dextran Sulfate/toxicity ; *Gastrointestinal Microbiome ; Humans ; Inflammation/therapy ; Interleukin-2/pharmacology ; Mice ; Mice, Inbred C57BL ; Mice, Inbred NOD ; }, abstract = {Gut microbiota dysbiosis is associated with inflammatory bowel diseases and with cardiometabolic, neurological, and autoimmune diseases. Gut microbiota composition has a direct effect on the immune system, and vice versa, and it has a particular effect on Treg homeostasis. Low-dose IL-2 (IL-2LD) stimulates Tregs and is a promising treatment for autoimmune and inflammatory diseases. We aimed to evaluate the impact of IL-2LD on gut microbiota and correlatively on the immune system. We used 16S ribosomal RNA profiling and metagenomics to characterize gut microbiota of mice and humans treated or not with IL-2LD. We performed fecal microbiota transplantation (FMT) from IL-2LD-treated to naive recipient mice and evaluated its effects in models of gut inflammation and diabetes. IL-2LD markedly affected gut microbiota composition in mice and humans. Transfer of an IL-2-tuned microbiota by FMT protected C57BL/6J mice from dextran sulfate sodium-induced colitis and prevented diabetes in NOD mice. Metagenomic analyses highlighted a role for several species affected by IL-2LD and for microbial pathways involved in the biosynthesis of amino acids, short-chain fatty acids, and L-arginine. Our results demonstrate that IL-2LD induced changes in gut microbiota that are involved in the immunoregulatory effects of IL-2LD and suggest a crosstalk between Tregs and gut microbiota. These results provide potentially novel insight for understanding the mode of action of Treg-directed therapies.}, } @article {pmid35916937, year = {2023}, author = {Pellegrinetti, TA and Cotta, SR and Sarmento, H and Costa, JS and Delbaje, E and Montes, CR and Camargo, PB and Barbiero, L and Rezende-Filho, AT and Fiore, MF}, title = {Bacterial Communities Along Environmental Gradients in Tropical Soda Lakes.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {892-903}, pmid = {35916937}, issn = {1432-184X}, support = {2016/14227-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; }, mesh = {*Lakes/chemistry/microbiology ; Brazil ; Eutrophication ; *Cyanobacteria/growth & development/isolation & purification ; Metagenomics ; }, abstract = {Soda lake environments are known to be variable and can have distinct differences according to geographical location. In this study, we investigated the effects of different environmental conditions of six adjacent soda lakes in the Pantanal biome (Mato Grosso do Sul state, Brazil) on bacterial communities and their functioning using a metagenomic approach combined with flow cytometry and chemical analyses. Ordination analysis using flow cytometry and water chemistry data from two sampling periods (wet and dry) clustered soda lakes into three different profiles: eutrophic turbid (ET), oligotrophic turbid (OT), and clear vegetated oligotrophic (CVO). Analysis of bacterial community composition and functioning corroborated this ordination; the exception was one ET lake, which was similar to one OT lake during the wet season, indicating drastic shifts between seasons. Microbial abundance and diversity increased during the dry period, along with a considerable number of limnological variables, all indicative of a strong effect of the precipitation-evaporation balance in these systems. Cyanobacteria were associated with high electric conductivity, pH, and nutrient availability, whereas Actinobacteria, Alphaproteobacteria, and Betaproteobacteria were correlated with landscape morphology variability (surface water, surface perimeter, and lake volume) and with lower salinity and pH levels. Stress response metabolism was enhanced in OT and ET lakes and underrepresented in CVO lakes. The microbiome dataset of this study can serve as a baseline for restoring impacted soda lakes. Altogether, the results of this study demonstrate the sensitivity of tropical soda lakes to climate change, as slight changes in hydrological regimes might produce drastic shifts in community diversity.}, } @article {pmid35916669, year = {2022}, author = {FitzGerald, J and Patel, S and Eckenberger, J and Guillemard, E and Veiga, P and Schäfer, F and Walter, J and Claesson, MJ and Derrien, M}, title = {Improved gut microbiome recovery following drug therapy is linked to abundance and replication of probiotic strains.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2094664}, pmid = {35916669}, issn = {1949-0984}, mesh = {Anti-Bacterial Agents/therapeutic use ; *Cultured Milk Products ; Feces ; *Gastrointestinal Microbiome ; Humans ; *Probiotics/pharmacology/therapeutic use ; }, abstract = {Probiotics have been used for decades to alleviate the negative side-effects of oral antibiotics, but our mechanistic understanding on how they work is so far incomplete. Here, we performed a metagenomic analysis of the fecal microbiota in participants who underwent a 14-d Helicobacter pylori eradication therapy with or without consumption of a multi-strain probiotic intervention (L. paracasei CNCM I-1518, L. paracasei CNCM I-3689, L. rhamnosus CNCM I-3690, and four yogurt strains) in a randomized, double-blinded, controlled clinical trial. Using a strain-level analysis for detection and metagenomic determination of replication rate, ingested strains were detected and replicated transiently in fecal samples and in the gut during and following antibiotic administration. Consumption of the fermented milk product led to a significant, although modest, improvement in the recovery of microbiota composition. Stratification of participants into two groups based on the degree to which their microbiome recovered showed i) a higher fecal abundance of the probiotic L. paracasei and L. rhamnosus strains and ii) an elevated replication rate of one strain (L. paracasei CNCMI-1518) in the recovery group. Collectively, our findings show a small but measurable benefit of a fermented milk product on microbiome recovery after antibiotics, which was linked to the detection and replication of specific probiotic strains. Such functional insight can form the basis for the development of probiotic-based intervention aimed to protect gut microbiome from drug treatments.}, } @article {pmid35916525, year = {2022}, author = {Sakamoto, N and Akeda, Y and Sugawara, Y and Matsumoto, Y and Motooka, D and Iida, T and Hamada, S}, title = {Role of Chromosome- and/or Plasmid-Located blaNDM on the Carbapenem Resistance and the Gene Stability in Escherichia coli.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0058722}, pmid = {35916525}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents/pharmacology ; Carbapenems/pharmacology ; Chromosomes ; *Escherichia coli/genetics ; *Escherichia coli Infections/microbiology ; Humans ; Imipenem ; Microbial Sensitivity Tests ; Plasmids/genetics ; beta-Lactamases/genetics ; }, abstract = {The spread of New Delhi metallo-β-lactamase (NDM)-producing Enterobacterales represents a public health risk. The horizontal transfer of plasmids encoding the NDM gene, blaNDM, usually mediates its spread to other bacteria within the family. In contrast, Enterobacterales with a chromosome-located blaNDM is rarely reported. The phenotypic differences between chromosome- and plasmid-located carbapenemase genes are poorly understood. To determine the significance in terms of the location of drug resistance genes, we examined carbapenemase activity and stability of chromosome- and plasmid-located blaNDM. Escherichia coli M719 possessing both chromosomes- and plasmid-located blaNDM genes was used as a wild-type strain (WT) for the construction of mutants, ΔpblaNDM and ΔcblaNDM, wherein chromosome- or plasmid-located blaNDM, was knocked out, respectively. The mutant ΔpblaNDM showed lower hydrolyzing activity against imipenem and gene expression than the WT or ΔcblaNDM mutant. The MICs of both mutant strains were still above the breakpoint of imipenem and meropenem. Moreover, the chromosome-located blaNDM gene was stable for at least 30 days in the absence of antimicrobial pressure, whereas the ΔcblaNDM mutant lost blaNDM to 87% at 30 days compared to that of the initial inoculum. Organisms harboring the plasmid-located carbapenemase genes were found to provide a higher level of carbapenem resistance than those with chromosome-located genes. However, the latter organisms with chromosomal carbapenemase genes exhibited more stable carbapenem resistance than did the former ones. In summary, chromosomally located carbapenemase genes require further monitoring and more attention should be paid to them. IMPORTANCE Carbapenem-resistant Enterobacterales (CRE) carrying blaNDM have spread worldwide since they were first reported in 2009. Many studies using whole-genome sequencing have identified the genetic structures, plasmid scaffolds of blaNDM, and mechanisms of spread via horizontal transfer. Chromosome-located blaNDM and integration mechanisms from plasmids have rarely been reported, and their significance is not fully understood. Here, we showed that the chromosome-located blaNDM was associated with lower levels of carbapenem resistance and carbapenemase activity than the plasmid-located blaNDM. However, it conferred carbapenem resistance above the breakpoints and the loss of chromosome-located blaNDM was not observed in the absence of antibiotic pressure. This study suggests that CRE strains carrying chromosome-located blaNDM may persist in clinical and environmental settings for a long period even without antibiotic pressure and need to be monitored along with plasmid-located blaNDM.}, } @article {pmid35916503, year = {2022}, author = {Singh, A and Bansal, K and Kumar, S and Patil, PB}, title = {Deep Population Genomics Reveals Systematic and Parallel Evolution at a Lipopolysaccharide Biosynthetic Locus in Xanthomonas Pathogens That Infect Rice and Sugarcane.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {16}, pages = {e0055022}, pmid = {35916503}, issn = {1098-5336}, mesh = {Genome, Bacterial ; Lipopolysaccharides ; Metagenomics ; *Oryza/microbiology ; Plant Diseases/microbiology ; *Saccharum/genetics ; *Xanthomonas/genetics ; }, abstract = {The advent of high-throughput sequencing and population genomics has enabled researchers to investigate selection pressure at hypervariable genomic loci encoding pathogen-associated molecular pattern (PAMP) molecules like lipopolysaccharide (LPS). Xanthomonas is a model and a major group of phytopathogenic bacteria that infect hosts in tissue-specific manner. Our in-depth population-based genomic investigation revealed the emergence of major lineages in two Xanthomonas pathogens that infect xylem of rice and sugarcane is associated with the acquisition and later large-scale replacement by distinct type of LPS cassettes. In the population of the rice xylem pathogen, Xanthomonas oryzae pv. oryzae (Xoo) and sugarcane pathogens Xanthomonas sacchari (Xsac) and Xanthomonas vasicola (Xvv), the BXO8 type of LPS cassette is replaced by a BXO1 type of cassette in Xoo and by Xvv type LPS cassette in Xsac and Xvv. These findings suggest a wave of parallel evolution at an LPS locus mediated by horizontal gene transfer (HGT) events during its adaptation and emergence. Aside from xylem pathogens, two closely related lineages of Xoo that infect parenchyma of rice and Leersia hexandra grass have acquired an LPS cassette from Xanthomonas pathogens that infect parenchyma of citrus, walnut, and strawberries, indicating yet another instance of parallel evolution mediated by HGT at an LPS locus. Our targeted and megapopulation-based genome dynamic studies revealed the acquisition and dominance of specific types of LPS cassettes in adaptation and success of a major group of phytopathogenic bacteria. IMPORTANCE Lipopolysaccharide (LPS) is a major microbe associated molecular pattern and hence a major immunomodulator. As a major and outer member component, it is expected that LPS is a frontline defense mechanism to deal with different host responses. Limited studies have indicated that LPS loci are also highly variable at strain and species level in plant-pathogenic bacteria, suggesting strong selection pressure from plants and associated niches. The advent of high-throughput genomics has led to the availability of a large set of genomic resources at taxonomic and population levels. This provides an exciting and important opportunity to carryout megascale targeted and population-based comparative genomic/association studies at important loci like those encoding LPS biosynthesis to understand their role in the evolution of the host, tissue specificity, and also predominant lineages. Such studies will also fill major gap in understanding host and tissue specificity in pathogenic bacteria. Our pioneering study uses the Xanthomonas group of phytopathogens that are known for their characteristic host and tissue specificity. The present deep phylogenomics of diverse Xanthomonas species and its members revealed lineage association and dominance of distinct types of LPS in accordance with their origin, host, tissue specificity, and evolutionary success.}, } @article {pmid35916407, year = {2022}, author = {Ma, R and Zhao, M and Wang, H and Hou, R and Qin, K and Qian, Y and Zhang, H and Zhou, Y and Wu, W and Gu, J and Wang, X and Shen, Q and Liu, S and Liu, J and Bi, W and Yu, X and Yang, S and Feng, F and Li, Z and Zhang, L and Lan, G and Chen, C and Xue, F and Wang, Y and Chong, H and Hong, Y and Ji, L and Liu, Y and Qi, D and Shan, T and Zhang, W}, title = {Virome of Giant Panda-Infesting Ticks Reveals Novel Bunyaviruses and Other Viruses That Are Genetically Close to Those from Giant Pandas.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0203422}, pmid = {35916407}, issn = {2165-0497}, mesh = {Animals ; Ecosystem ; *Orthobunyavirus ; *Ticks ; *Ursidae ; Virome/genetics ; *Viruses/genetics ; }, abstract = {Tick infestations have been reported as one of the factors threatening the health of giant pandas, but studies of viral pathogens carried by ticks feeding on the blood of giant pandas are limited. To assess whether blood-sucking ticks of giant pandas can carry viral pathogens and if so, whether the viruses in ticks are associated with those previously detected in giant panda hosts, we determined the viromes of ticks detached from giant pandas in a field stocking area in Sichuan Province, southwest China. Using viral metagenomics we identified 32 viral species in ticks, half of which (including anellovirus [n = 9], circovirus [n = 3], and gemycircularvirus [n = 4]) showed homology to viruses carried by giant pandas and their associated host species (such as red pandas and mosquitoes) in the same living domain. Remarkably, several viruses in this study phylogenetically assigned as bunyavirus, hepe-like virus, and circovirus were detected with relatively high abundance, but whether these newly identified tick-associated viruses can replicate in ticks and then transmit to host animals during a blood meal will require further investigation. These findings further expand our understanding of the role of giant panda-infesting ticks in the local ecosystem, especially related to viral acquisition and transmission, and lay a foundation to assess the risk for giant panda exposure to tick-borne viruses. IMPORTANCE Ticks rank only second to mosquitoes as blood-feeding arthropods, capable of spreading pathogens (including viruses, bacteria, and parasites) to hosts during a blood meal. To better understand the relationship between viruses carried by ticks and viruses that have been reported in giant pandas, it is necessary to analyze the viromes of giant panda-parasitic blood-sucking ticks. This study collected 421 ticks on the body surface of giant pandas in Sichuan Province, China. We characterized the extensive genetic diversity of viruses harbored by these ticks and reported frequent communication of viruses between giant pandas and their ticks. While most of the virome discovered here are nonpathogenic viruses from giant pandas and potentially tick-specific viruses, we revealed some possible tick-borne viruses, represented by novel bunyaviruses. This research contributes to the literature because currently there are few studies on the virome of giant panda-infesting ticks.}, } @article {pmid35915514, year = {2022}, author = {Lin, CY and Jha, AR and Oba, PM and Yotis, SM and Shmalberg, J and Honaker, RW and Swanson, KS}, title = {Longitudinal fecal microbiome and metabolite data demonstrate rapid shifts and subsequent stabilization after an abrupt dietary change in healthy adult dogs.}, journal = {Animal microbiome}, volume = {4}, number = {1}, pages = {46}, pmid = {35915514}, issn = {2524-4671}, support = {Hatch Grant ILLU-538-937//Agricultural Research Service/ ; }, abstract = {BACKGROUND: Diet has a large influence on gut microbiota diversity and function. Although previous studies have investigated the effect of dietary interventions on the gut microbiome, longitudinal changes in the gut microbiome, microbial functions, and metabolite profiles post dietary interventions have been underexplored. How long these outcomes require to reach a steady-state, how they relate to one another, and their impact on host physiological changes are largely unknown. To address these unknowns, we collected longitudinal fecal samples following an abrupt dietary change in healthy adult beagles (n = 12, age: 5.16 ± 0.87 year, BW: 13.37 ± 0.68 kg) using a crossover design. All dogs were fed a kibble diet (control) from d1-14, and then fed that same diet supplemented with fiber (HFD) or a protein-rich canned diet (CD) from d15-27. Fresh fecal samples were collected on d13, 16, 20, 24, and 27 for metabolite and microbiome assessment. Fecal microbial diversity and composition, metabolite profiles, and microbial functions dramatically diverged and stabilized within a few days (2 d for metabolites; 6 d for microbiota) after dietary interventions. Fecal acetate, propionate, and total short-chain fatty acids increased after change to HFD, while fecal isobutyrate, isovalerate, total branched-chain fatty acids, phenol, and indole increased after dogs consumed CD. Relative abundance of ~ 100 bacterial species mainly belonging to the Firmicutes, Proteobacteria, and Actinobacteria phyla increased in HFD. These shifts in gut microbiome diversity and composition were accompanied by functional changes. Transition to HFD led to increases in the relative abundance of KEGG orthology (KO) terms related to starch and sucrose metabolism, fatty acid biosynthesis, and amino sugar and nucleotide sugar metabolism, while transition to CD resulted in increased relative abundance of KO terms pertaining to inositol phosphate metabolism and sulfur metabolism. Significant associations among fecal microbial taxa, KO terms, and metabolites were observed, allowing for high-accuracy prediction of diet group by random forest analysis.

CONCLUSIONS: Longitudinal sampling and a multi-modal approach to characterizing the gastrointestinal environment allowed us to demonstrate how drastically and quickly dietary changes impact the fecal microbiome and metabolite profiles of dogs following an abrupt dietary change and identify key microbe-metabolite relationships that allowed for treatment prediction.}, } @article {pmid35915372, year = {2022}, author = {Limberg, J and Egan, CE and Mora, HA and Putzel, G and Stamatiou, AT and Ullmann, TM and Moore, MD and Stefanova, D and Thiesmeyer, JW and Finnerty, BM and Beninato, T and McKenzie, K and Robitsek, RJ and Chan, J and Zarnegar, R and Fahey, TJ}, title = {Metagenomic Sequencing of the Gallbladder Microbiome: Bacterial Diversity Does Not Vary by Surgical Pathology.}, journal = {Journal of gastrointestinal surgery : official journal of the Society for Surgery of the Alimentary Tract}, volume = {26}, number = {11}, pages = {2282-2291}, pmid = {35915372}, issn = {1873-4626}, mesh = {Humans ; Female ; Adult ; Middle Aged ; Male ; Gallbladder/surgery ; *Pathology, Surgical ; *Cholecystitis, Acute ; *Gallbladder Diseases ; *Microbiota/genetics ; Bacteria/genetics ; }, abstract = {INTRODUCTION: Alterations in the microbiome contribute to the pathogenesis of many gastrointestinal diseases. However, the composition of the microbiome in gallbladder disease is not well described.

METHODS: We aimed to characterize the biliary microbiome in cholecystectomy patients. Bile and biliary stones were collected at cholecystectomy for a variety of surgical indications between 2017 and 2019. DNA was extracted and metagenomic sequencing was performed with subsequent taxonomic classification using Kraken2. The fraction of bacterial to total DNA reads, relative abundance of bacterial species, and overall species diversity were compared between pathologies and demographics.

RESULTS: A total of 74 samples were obtained from 49 patients: 46 bile and 28 stones, with matched pairs from 25 patients. The mean age was 48 years, 76% were female, 29% were Hispanic, and 29% of patients had acute cholecystitis. The most abundant species were Klebsiella pneumoniae, Staphylococcus aureus, and Streptococcus pasteurianus. The bacterial fraction in bile and stone samples was higher in acute cholecystitis compared to other non-infectious pathologies (p < 0.05). Neither the diversity nor differential prevalence of specific bacterial species varied significantly between infectious and other non-infectious gallbladder pathologies. Multivariate analysis of the non-infectious group revealed that patients over 40 years of age had increased bacterial fractions (p < 0.05).

CONCLUSIONS: Metagenomic sequencing permits characterization of the gallbladder microbiome in cholecystectomy patients. Although a higher prevalence of bacteria was seen in acute cholecystitis, species and diversity were similar regardless of surgical indication. Additional study is required to determine how the microbiome can contribute to the development of symptomatic gallbladder disease.}, } @article {pmid35915168, year = {2022}, author = {Hallstrøm, S and Raina, JB and Ostrowski, M and Parks, DH and Tyson, GW and Hugenholtz, P and Stocker, R and Seymour, JR and Riemann, L}, title = {Chemotaxis may assist marine heterotrophic bacterial diazotrophs to find microzones suitable for N2 fixation in the pelagic ocean.}, journal = {The ISME journal}, volume = {16}, number = {11}, pages = {2525-2534}, pmid = {35915168}, issn = {1751-7370}, support = {6108-00013//Det Frie Forskningsråd (Danish Council for Independent Research)/ ; 6108-00013//Natur og Univers, Det Frie Forskningsråd (Natural Sciences, Danish Council for Independent Research)/ ; GBMF3801//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; }, mesh = {Amino Acids/metabolism ; Australia ; Carbon/metabolism ; Chemotaxis ; *Cyanobacteria/metabolism ; Membrane Transport Proteins/metabolism ; Nitrogen/metabolism ; *Nitrogen Fixation ; Oceans and Seas ; Oxygen/metabolism ; Phytoplankton/metabolism ; Seawater/microbiology ; }, abstract = {Heterotrophic bacterial diazotrophs (HBDs) are ubiquitous in the pelagic ocean, where they have been predicted to carry out the anaerobic process of nitrogen fixation within low-oxygen microenvironments associated with marine pelagic particles. However, the mechanisms enabling particle colonization by HBDs are unknown. We hypothesized that HBDs use chemotaxis to locate and colonize suitable microenvironments, and showed that a cultivated marine HBD is chemotactic toward amino acids and phytoplankton-derived DOM. Using an in situ chemotaxis assay, we also discovered that diverse HBDs at a coastal site are motile and chemotactic toward DOM from various phytoplankton taxa and, indeed, that the proportion of diazotrophs was up to seven times higher among the motile fraction of the bacterial community compared to the bulk seawater community. Finally, three of four HBD isolates and 16 of 17 HBD metagenome assembled genomes, recovered from major ocean basins and locations along the Australian coast, each encoded >85% of proteins affiliated with the bacterial chemotaxis pathway. These results document the widespread capacity for chemotaxis in diverse and globally relevant marine HBDs. We suggest that HBDs could use chemotaxis to seek out and colonize low-oxygen microenvironments suitable for nitrogen fixation, such as those formed on marine particles. Chemotaxis in HBDs could therefore affect marine nitrogen and carbon biogeochemistry by facilitating nitrogen fixation within otherwise oxic waters, while also altering particle degradation and the efficiency of the biological pump.}, } @article {pmid35914737, year = {2023}, author = {Liu, Y and Lau, HC and Cheng, WY and Yu, J}, title = {Gut Microbiome in Colorectal Cancer: Clinical Diagnosis and Treatment.}, journal = {Genomics, proteomics & bioinformatics}, volume = {21}, number = {1}, pages = {84-96}, pmid = {35914737}, issn = {2210-3244}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Colorectal Neoplasms/diagnosis/etiology/therapy ; *Microbiota ; Biomarkers ; Carcinogenesis ; }, abstract = {Colorectal cancer (CRC) is one of the most frequently diagnosed cancers and the leading cause of cancer-associated deaths. Epidemiological studies have shown that both genetic and environmental risk factors contribute to the development of CRC. Several metagenomic studies of CRC have identified gut dysbiosis as a fundamental risk factor in the evolution of colorectal malignancy. Although enormous efforts and substantial progresses have been made in understanding the relationship between human gut microbiome and CRC, the precise mechanisms involved remain elusive. Recent data have shown a direct causative role of the gut microbiome in DNA damage, inflammation, and drug resistance in CRC, suggesting that modulation of gut microbiome could act as a powerful tool in CRC prevention and therapy. Here, we provide an overview of the relationship between gut microbiome and CRC, and explore relevant mechanisms of colorectal tumorigenesis. We next highlight the potential of bacterial species as clinical biomarkers, as well as their roles in therapeutic response. Factors limiting the clinical translation of gut microbiome and strategies for resolving current challenges are further discussed.}, } @article {pmid35913608, year = {2023}, author = {Wei, W and Cao, J and Wu, XC and Cheng, LP and Shen, XN and Sha, W and Sun, Q}, title = {Diagnostic performance of metagenomic next-generation sequencing in non-tuberculous mycobacterial pulmonary disease when applied to clinical practice.}, journal = {Infection}, volume = {51}, number = {2}, pages = {397-405}, pmid = {35913608}, issn = {1439-0973}, support = {19MC1910800//Science and Technology Innovation Plan Of Shanghai Science and Technology Commission/ ; FKLY20012//Tongji Hospital/ ; }, mesh = {Humans ; *Nontuberculous Mycobacteria ; Retrospective Studies ; China ; High-Throughput Nucleotide Sequencing ; *Lung Diseases/diagnosis ; Sensitivity and Specificity ; }, abstract = {OBJECTIVE: To compare non-tuberculous mycobacterial pulmonary disease (NTMPD) diagnosis by metagenomic next-generation sequencing (mNGS) with Bactec mycobacterial growth indicator tube (MGIT) 960.

METHODS: A total of 422 patients with suspected NTMPD in Shanghai Pulmonary Hospital between January 2020 and May 2021 were retrospectively analyzed; 194 were diagnosed with NTMPD. The diagnostic performance of mNGS and MGIT 960 for NTMPD was assessed. Receiver operating characteristic (ROC) curves and areas under curve (AUCs) were compared.

RESULTS: The sensitivity of mNGS in NTMPD diagnosis was 81.4% and higher than that of MGIT 960 (53.6%). The specificity of mNGS in NTMPD diagnosis was 97.8%, similar to that of MGIT 960 (100%). The sensitivity of combined mNGS and MGIT 960 in NTMPD diagnosis was 91.8%. The sensitivity of mNGS for bronchoalveolar lavage fluid (BALF), pulmonary puncture tissue fluid, and sputum was 84.8%, 80.6%, and 77.5%, respectively; all were higher than that of MGIT 960 (P < 0.05). The AUC of mNGS and MGIT 960 was 0.897 and 0.768, respectively. The AUC of mNGS were BALF (0.916), pulmonary puncture tissue fluid (0.903), and sputum (0.870).

CONCLUSION: The sensitivity of mNGS was superior to that of Bactec MGIT 960; the specificity in NTMPD diagnosis was similar. mNGS shows effective performance in NTMPD diagnosis.}, } @article {pmid35913201, year = {2022}, author = {Naufal, M and Wu, JH and Shao, YH}, title = {Glutamate Enhances Osmoadaptation of Anammox Bacteria under High Salinity: Genomic Analysis and Experimental Evidence.}, journal = {Environmental science & technology}, volume = {56}, number = {16}, pages = {11310-11322}, doi = {10.1021/acs.est.2c01104}, pmid = {35913201}, issn = {1520-5851}, mesh = {Anaerobic Ammonia Oxidation ; Anaerobiosis ; Bacteria/metabolism ; Genomics ; *Glutamic Acid/genetics/metabolism ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Salinity ; }, abstract = {An osmoprotectant that alleviates the bacterial osmotic stress can improve the bioreactor treatment of saline wastewater. However, proposed candidates are expensive, and osmoprotectants of anammox bacteria and their ecophysiological roles are not fully understood. In this study, a comparative analysis of 34 high-quality public metagenome-assembled genomes from anammox bacteria revealed two distinct groups of osmoadaptation. Candidatus Scalindua and Kuenenia share a close phylogenomic relation and osmoadaptation gene profile and have pathways for glutamate transport and metabolisms for enhanced osmoadaptation. The batch assay results demonstrated that the reduced Ca. Kuenenia activity in saline conditions was substantially alleviated with the addition and subsequent synergistic effects of potassium and glutamate. The operational test of two reactors demonstrated that the reduced anammox performance under brine conditions rapidly recovered by 35.7-43.1% as a result of glutamate treatment. The Ca. Kuenenia 16S rRNA and hydrazine gene expressions were upregulated significantly (p < 0.05), and the abundance increased by approximately 19.9%, with a decrease in dominant heterotrophs. These data demonstrated the effectiveness of glutamate in alleviating the osmotic stress of Ca. Kuenenia. This study provides genomic insight into group-specific osmoadaptation of anammox bacteria and can facilitate the precision management of anammox reactors under high salinity.}, } @article {pmid35913193, year = {2022}, author = {Zheng, X and Dai, X and Zhu, Y and Yang, J and Jiang, H and Dong, H and Huang, L}, title = {(Meta)Genomic Analysis Reveals Diverse Energy Conservation Strategies Employed by Globally Distributed Gemmatimonadota.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0022822}, pmid = {35913193}, issn = {2379-5077}, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Bacteria ; Genomics ; *Microbiota/genetics ; }, abstract = {Gemmatimonadota is a phylum-level lineage distributed widely but rarely reported. Only six representatives of Gemmatimonadota have so far been isolated and cultured in laboratory. The physiology, ecology, and evolutionary history of this phylum remain unknown. The 16S rRNA gene survey of our salt lake and deep-sea sediments, and Earth Microbiome Project (EMP) samples, reveals that Gemmatimonadota exist in diverse environments globally. In this study, we retrieved 17 metagenome-assembled genomes (MAGs) from salt lake sediments (12 MAGs) and deep-sea sediments (5 MAGs). Analysis of these MAGs and the nonredundant MAGs or genomes from public databases reveals Gemmatimonadota can degrade various complex organic substrates, and mainly employ heterotrophic pathways (e.g., glycolysis and tricarboxylic acid [TCA] cycle) for growth via aerobic respiration. And the processes of sufficient energy being stored in glucose through gluconeogenesis, followed by the synthesis of more complex compounds, are prevalent in Gemmatimonadota. A highly expandable pangenome for Gemmatimonadota has been observed, which presumably results from their adaptation to thriving in diverse environments. The enrichment of the Na[+]/H[+] antiporter in the SG8-23 order represents their adaptation to salty habitats. Notably, we identified a novel lineage of the SG8-23 order, which is potentially anoxygenic phototrophic. This lineage is not closely related to the phototrophs in the order of Gemmatimonadales. The two orders differ distinctly in the gene organization and phylogenetic relationship of their photosynthesis gene clusters, indicating photosystems in Gemmatimonadota have evolved in two independent routes. IMPORTANCE The phylum Gemmatimonadota is widely distributed in various environments. However, their physiology, ecology and evolutionary history remain unknown, primary due to the limited cultured isolates and available genomes. We were intrigued to find out how widespread this phylum is, and how it can thrive under diverse conditions. Our results here expand the knowledge of the genetic and metabolic diversity of Gemmatimonadota, and shed light on the diverse energy conservation strategies (i.e., oxidative phosphorylation, substrate phosphorylation, and photosynthetic phosphorylation) responsible for their global distribution. Moreover, gene organization and phylogenetic analysis of photosynthesis gene clusters in Gemmatimonadota provide a valuable insight into the evolutionary history of photosynthesis.}, } @article {pmid35913189, year = {2022}, author = {Frouin, E and Lecoeuvre, A and Armougom, F and Schrenk, MO and Erauso, G}, title = {Comparative Metagenomics Highlight a Widespread Pathway Involved in Catabolism of Phosphonates in Marine and Terrestrial Serpentinizing Ecosystems.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0032822}, pmid = {35913189}, issn = {2379-5077}, mesh = {*Organophosphonates ; Metagenomics ; *Microbiota/genetics ; Phosphorus ; Methane ; }, abstract = {Serpentinizing hydrothermal systems result from water circulating into the subsurface and interacting with mantle-derived rocks notably near mid-ocean ridges or continental ophiolites. Serpentinization and associated reactions produce alkaline fluids enriched in molecular hydrogen, methane, and small organic molecules that are assumed to feed microbial inhabitants. In this study, we explored the relationships linking serpentinization to associated microbial communities by comparative metagenomics of serpentinite-hosted systems, basalt-hosted vents, and hot springs. The shallow Prony bay hydrothermal field (PBHF) microbiome appeared to be more related to those of ophiolitic sites than to the Lost City hydrothermal field (LCHF) microbiome, probably because of the meteoric origin of its fluid, like terrestrial alkaline springs. This study emphasized the ubiquitous importance of a set of genes involved in the catabolism of phosphonates and highly enriched in all serpentinizing sites compared to other ecosystems. Because most of the serpentinizing systems are depleted in inorganic phosphate, the abundance of genes involved in the carbon-phosphorus lyase pathway suggests that the phosphonates constitute a source of phosphorus in these ecosystems. Additionally, hydrocarbons such as methane, released upon phosphonate catabolism, may contribute to the overall budget of organic molecules in serpentinizing systems. IMPORTANCE This first comparative metagenomic study of serpentinite-hosted environments provides an objective framework to understand the functioning of these peculiar ecosystems. We showed a taxonomic similarity between the PBHF and other terrestrial serpentinite-hosted ecosystems. At the same time, the LCHF microbial community was closer to deep basalt-hosted hydrothermal fields than continental ophiolites, despite the influence of serpentinization. This study revealed shared functional capabilities among serpentinite-hosted ecosystems in response to environmental stress, the metabolism of abundant dihydrogen, and the metabolism of phosphorus. Our results are consistent with the generalized view of serpentinite environments but provide deeper insight into the array of factors that may control microbial activities in these ecosystems. Moreover, we show that metabolism of phosphonate is widespread among alkaline serpentinizing systems and could play a crucial role in phosphorus and methane biogeochemical cycles. This study opens a new line of investigation of the metabolism of reduced phosphorus compounds in serpentinizing environments.}, } @article {pmid35913177, year = {2022}, author = {Tao, S and Zou, H and Li, J and Wei, H}, title = {Landscapes of Enteric Virome Signatures in Early-Weaned Piglets.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0169822}, pmid = {35913177}, issn = {2165-0497}, mesh = {Animals ; Bacteria/genetics ; Diarrhea/microbiology/veterinary ; *Gastrointestinal Microbiome/genetics ; Mice ; Swine ; *Virome/genetics ; Weaning ; }, abstract = {Diarrhea caused by early-weaning-induced stress can increase mortality rates and reduce growth performance of piglets, seriously harming the livestock industry. To date, studies on the gut microbiome of early-weaned piglets have focused almost exclusively on bacteria, while studies on their gut virome are extremely lacking. Here, we used metagenomic and metatranscriptomic sequencing combined with bioinformatic analysis techniques to preliminarily characterize the intestinal virome of early-weaned piglets at different biological classification levels. The alpha diversity of enteroviruses was generally elevated in early-weaned piglets with diarrhea, compared to healthy piglets, whereas the two groups of piglets showed no significant difference in beta diversity. In addition, the species compositions of the gut virome were similar between healthy piglets and piglets with diarrhea, while their respective dominant species were somewhat different. We also identified 58 differential DNA viruses and 16 differential RNA viruses between the two groups of piglets at all biological taxonomic levels. Of these, 1 (family Dhakavirus) and 6 (phylum Artverviricota, class Revtraviricetes, order Ortervirales, family Retroviridae, genus Gammaretrovirus, and species Kirsten murine sarcoma virus) specific viruses disappeared from the intestines of healthy piglets and piglets with diarrhea, respectively. Moreover, we found that some DNA and RNA viruses formed strong correlations among themselves or between them. IMPORTANCE This study systematically reveals the biological diversity, structure, and composition of intestinal DNA and RNA virus profiles in early-weaned piglets. Furthermore, characteristics of differences in gut viromes between early-weaned healthy piglets and piglets with diarrhea were also elucidated. Importantly, some potential biomarkers for early-weaned piglets with diarrhea were identified. These findings fill a gap for the early-weaned piglet gut virome and lay the foundation for the development of strategies to target enteroviruses for the prevention and treatment of early-weaning-induced piglet diarrhea.}, } @article {pmid35913151, year = {2022}, author = {Call, TB and Davis, EK and Bean, JD and Lemmon, SG and Chaston, JM}, title = {Bacterial Metabolism and Transport Genes Are Associated with the Preference of Drosophila melanogaster for Dietary Yeast.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {16}, pages = {e0072022}, pmid = {35913151}, issn = {1098-5336}, support = {R15 GM140388/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria/genetics ; Diet ; Drosophila ; *Drosophila melanogaster/microbiology ; Glucose/metabolism ; *Microbiota/genetics ; Thiamine/metabolism ; }, abstract = {Many animal traits are influenced by their associated microorganisms ("microbiota"). To expand our understanding of the relationship between microbial genotype and host phenotype, we report an analysis of the influence of the microbiota on the dietary preference of the fruit fly Drosophila melanogaster. First, we confirmed through experiments on flies reared bacteria-free ("axenic") or in monoassociation with two different strains of bacteria that the microbiota significantly influences fruit fly dietary preference across a range of ratios of dietary yeast:dietary glucose. Then, focusing on microbiota-dependent changes in fly dietary preference for yeast (DPY), we performed a metagenome-wide association (MGWA) study to define microbial species specificity for this trait and to predict bacterial genes that influence it. In a subsequent mutant analysis, we confirmed that disrupting a subset of the MGWA-predicted genes influences fly DPY, including for genes involved in thiamine biosynthesis and glucose transport. Follow-up tests revealed that the bacterial influence on fly DPY did not depend on bacterial modification of the glucose or protein content of the fly diet, suggesting that the bacteria mediate their effects independent of the fly diet or through more specific dietary changes than broad ratios of protein and glucose. Together, these findings provide additional insight into bacterial determinants of host nutrition and behavior by revealing specific genetic disruptions that influence D. melanogaster DPY. IMPORTANCE Associated microorganisms ("microbiota") impact the physiology and behavior of their hosts, and defining the mechanisms underlying these interactions is a major gap in the field of host-microbe interactions. This study expands our understanding of how the microbiota can influence dietary preference for yeast (DPY) of a model host, Drosophila melanogaster. First, we show that fly preferences for a range of different dietary yeast:dietary glucose ratios vary significantly with the identity of the microbes that colonize the fruit flies. We then performed a metagenome-wide association study to identify candidate bacterial genes that contributed to some of these bacterial influences. We confirmed that disrupting some of the predicted genes, including genes involved in glucose transport and thiamine biosynthesis, resulted in changes to fly DPY and show that the influence of two of these genes is not through changes in dietary ratios of protein to glucose. Together, these efforts expand our understanding of the bacterial genetic influences on a feeding behavior of a model animal host.}, } @article {pmid35913147, year = {2022}, author = {Goetting-Minesky, MP and Godovikova, V and Zheng, W and Fenno, JC}, title = {Characterization of Treponema denticola Major Surface Protein (Msp) by Deletion Analysis and Advanced Molecular Modeling.}, journal = {Journal of bacteriology}, volume = {204}, number = {9}, pages = {e0022822}, pmid = {35913147}, issn = {1098-5530}, support = {R01 DE025225/DE/NIDCR NIH HHS/United States ; }, mesh = {Amino Acids ; Bacterial Proteins/genetics/metabolism ; Endopeptidase K/metabolism ; Epitopes ; *Fibronectins/metabolism ; Peptides/metabolism ; Porins/metabolism ; Treponema/chemistry/genetics/metabolism ; *Treponema denticola/genetics ; }, abstract = {Treponema denticola, a keystone pathogen in periodontitis, is a model organism for studying Treponema physiology and host-microbe interactions. Its major surface protein Msp forms an oligomeric outer membrane complex that binds fibronectin, has cytotoxic pore-forming activity, and disrupts several intracellular processes in host cells. T. denticola msp is an ortholog of the Treponema pallidum tprA to -K gene family that includes tprK, whose remarkable in vivo hypervariability is proposed to contribute to T. pallidum immune evasion. We recently identified the primary Msp surface-exposed epitope and proposed a model of the Msp protein as a β-barrel protein similar to Gram-negative bacterial porins. Here, we report fine-scale Msp mutagenesis demonstrating that both the N and C termini as well as the centrally located Msp surface epitope are required for native Msp oligomer expression. Removal of as few as three C-terminal amino acids abrogated Msp detection on the T. denticola cell surface, and deletion of four residues resulted in complete loss of detectable Msp. Substitution of a FLAG tag for either residues 6 to 13 of mature Msp or an 8-residue portion of the central Msp surface epitope resulted in expression of full-length Msp but absence of the oligomer, suggesting roles for both domains in oligomer formation. Consistent with previously reported Msp N-glycosylation, proteinase K treatment of intact cells released a 25 kDa polypeptide containing the Msp surface epitope into culture supernatants. Molecular modeling of Msp using novel metagenome-derived multiple sequence alignment (MSA) algorithms supports the hypothesis that Msp is a large-diameter, trimeric outer membrane porin-like protein whose potential transport substrate remains to be identified. IMPORTANCE The Treponema denticola gene encoding its major surface protein (Msp) is an ortholog of the T. pallidum tprA to -K gene family that includes tprK, whose remarkable in vivo hypervariability is proposed to contribute to T. pallidum immune evasion. Using a combined strategy of fine-scale mutagenesis and advanced predictive molecular modeling, we characterized the Msp protein and present a high-confidence model of its structure as an oligomer embedded in the outer membrane. This work adds to knowledge of Msp-like proteins in oral treponemes and may contribute to understanding the evolutionary and potential functional relationships between T. denticola Msp and the orthologous T. pallidum Tpr proteins.}, } @article {pmid35911731, year = {2022}, author = {Huang, J and Zheng, X and Kang, W and Hao, H and Mao, Y and Zhang, H and Chen, Y and Tan, Y and He, Y and Zhao, W and Yin, Y}, title = {Metagenomic and metabolomic analyses reveal synergistic effects of fecal microbiota transplantation and anti-PD-1 therapy on treating colorectal cancer.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {874922}, pmid = {35911731}, issn = {1664-3224}, mesh = {Animals ; Bacteroides ; *Colorectal Neoplasms/etiology/therapy ; Fecal Microbiota Transplantation/adverse effects ; *Gastrointestinal Microbiome ; Metagenome ; Mice ; }, abstract = {Anti-PD-1 immunotherapy has saved numerous lives of cancer patients; however, it only exerts efficacy in 10-15% of patients with colorectal cancer. Fecal microbiota transplantation (FMT) is a potential approach to improving the efficacy of anti-PD-1 therapy, whereas the detailed mechanisms and the applicability of this combination therapy remain unclear. In this study, we evaluated the synergistic effect of FMT with anti-PD-1 in curing colorectal tumor-bearing mice using a multi-omics approach. Mice treated with the combination therapy showed superior survival rate and tumor control, compared to the mice received anti-PD-1 therapy or FMT alone. Metagenomic analysis showed that composition of gut microbiota in tumor-bearing mice treated with anti-PD-1 therapy was remarkably altered through receiving FMT. Particularly, Bacteroides genus, including FMT-increased B. thetaiotaomicron, B. fragilis, and FMT-decreased B. ovatus might contribute to the enhanced efficacy of anti-PD-1 therapy. Furthermore, metabolomic analysis upon mouse plasma revealed several potential metabolites that upregulated after FMT, including punicic acid and aspirin, might promote the response to anti-PD-1 therapy via their immunomodulatory functions. This work broadens our understanding of the mechanism by which FMT improves the efficacy of anti-PD-1 therapy, which may contribute to the development of novel microbiota-based anti-cancer therapies.}, } @article {pmid35911412, year = {2022}, author = {Guo, W and Cui, X and Wang, Q and Wei, Y and Guo, Y and Zhang, T and Zhan, J}, title = {Clinical evaluation of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid collected from children with community-acquired pneumonia.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {952636}, pmid = {35911412}, issn = {2296-858X}, abstract = {This study is to evaluate the usefulness of pathogen detection using metagenomic next-generation sequencing (mNGS) on bronchoalveolar lavage fluid (BALF) specimens from children with community-acquired pneumonia (CAP). We retrospectively collected BALF specimens from 121 children with CAP at Tianjin Children's Hospital from February 2021 to December 2021. The diagnostic performances of mNGS and conventional tests (CT) (culture and targeted polymerase chain reaction tests) were compared, using composite diagnosis as the reference standard. The results of mNGS and CT were compared based on pathogenic and non-pathogenic organisms. Pathogen profiles and co-infections between the mild CAP and severe CAP groups were also analyzed. The overall positive coincidence rate was 86.78% (105/121) for mNGS and 66.94% (81/121) for CT. The proportion of patients diagnosed using mNGS plus CT increased to 99.18%. Among the patients, 17.36% were confirmed only by mNGS; Streptococcus pneumoniae accounted for 52.38% and 23.8% of the patients were co-infected. Moreover, Bordetella pertussis and Human bocavirus (HBoV) were detected only using mNGS. Mycoplasma pneumoniae, which was identified in 89 (73.55%) of 121 children with CAP, was the most frequent pathogen detected using mNGS. The infection rate of M. pneumoniae in the severe CAP group was significantly higher than that in the mild CAP group (P = 0.007). The symptoms of single bacterial infections (except for mycoplasma) were milder than those of mycoplasma infections. mNGS identified more bacterial infections when compared to the CT methods and was able to identify co-infections which were initially missed on CT. Additionally, it was able to identify pathogens that were beyond the scope of the CT methods. The mNGS method is a powerful supplement to clinical diagnostic tools in respiratory infections, as it can increase the precision of diagnosis and guide the use of antibiotics.}, } @article {pmid35911304, year = {2022}, author = {Shahab, M and Shahab, N}, title = {Coevolution of the Human Host and Gut Microbiome: Metagenomics of Microbiota.}, journal = {Cureus}, volume = {14}, number = {6}, pages = {e26310}, pmid = {35911304}, issn = {2168-8184}, abstract = {It is estimated that humans have trillions of microbial cells living in their gut as part of their microbiota. Each human being has an entirely unique microbiome and human gut microbiota composition has been shown to alter with age due to several factors including physical stress, diet, use of antibiotics, prolonged treatments, chronic disease processes, physiological changes, and geographical location. The gut microbiome contributes to overall well-being in a multitude of ways, including digestion, metabolism, immunity, and the creation of vital compounds that the body cannot synthesize on its own. Disequilibrium in the microbiota has been correlated to obesity, heart disease, irritable bowel disease, and certain cancers. The evolution of the human host allowed for the diversity of the microbial community present in the gut. Although previous studies portray the correlation between diet and disequilibrium in host microbiota, the evolutionary dynamics of bacterial commensal flora and the extent to which it is beneficial are still unclear and need additional investigation.}, } @article {pmid35910644, year = {2022}, author = {Bouchiat, C and Ginevra, C and Benito, Y and Gaillard, T and Salord, H and Dauwalder, O and Laurent, F and Vandenesch, F}, title = {Improving the Diagnosis of Bacterial Infections: Evaluation of 16S rRNA Nanopore Metagenomics in Culture-Negative Samples.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {943441}, pmid = {35910644}, issn = {1664-302X}, abstract = {While 16S rRNA PCR-Sanger sequencing has paved the way for the diagnosis of culture-negative bacterial infections, it does not provide the composition of polymicrobial infections. We aimed to evaluate the performance of the Nanopore-based 16S rRNA metagenomic approach, using both partial and full-length amplification of the gene, and to explore its feasibility and suitability as a routine diagnostic tool for bacterial infections in a clinical laboratory. Thirty-one culture-negative clinical samples from mono- and polymicrobial infections based on Sanger-sequencing results were sequenced on MinION using both the in-house partial amplification and the Nanopore dedicated kit for the full-length amplification of the 16S rRNA gene. Contamination, background noise definition, bacterial identification, and time-effectiveness issues were addressed. Cost optimization was also investigated with the miniaturized version of the flow cell (Flongle). The partial 16S approach had a greater sensitivity compared to the full-length kit that detected bacterial DNA in only 24/31 (77.4%) samples. Setting a threshold of 1% of total reads overcame the background noise issue and eased the interpretation of clinical samples. Results were obtained within 1 day, discriminated polymicrobial samples, and gave accurate bacterial identifications compared to Sanger-based results. We also found that multiplexing and using Flongle flow cells was a cost-effective option. The results confirm that Nanopore technology is user-friendly as well as cost- and time-effective. They also indicate that 16S rRNA targeted metagenomics is a suitable approach to be implemented for the routine diagnosis of culture-negative samples in clinical laboratories.}, } @article {pmid35910600, year = {2022}, author = {Du, D and Jiang, W and Feng, L and Zhang, Y and Chen, P and Wang, C and Hu, Z}, title = {Effect of Saccharomyces cerevisiae culture mitigates heat stress-related dame in dairy cows by multi-omics.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {935004}, pmid = {35910600}, issn = {1664-302X}, abstract = {The effect of heat stress on ruminants is an important issue. In recent years, the growth of the Chinese dairy industry has rapidly increased, generating RMB 468,738 million revenue in 2021. A decreased milk yield is the most recognized impact of heat stress on dairy cows and results in significant economic loss to dairy producers. Heat stress also lowers immunity and antioxidant capacity and changes the bacterial composition and metabolites of the rumen. The purpose of this study was to investigate the effect of addition Saccharomyces cerevisiae culture on heat-stressed cows. The impact of S. cerevisiae culture on microbiota composition, functional profiles, and metabolomics was assessed in heat-stressed cows. A total of 45 Holstein cows in mid-lactation were selected and randomly divided into three groups (15 cows per group). Groups D-C, D-A, and D-B were fed with the basal diet, the basal diet + first S. cerevisiae culture 100 g/day, and the basal diet + second S. cerevisiae culture 30 g/day, respectively. The trial lasted 60 days. There was an increased abundance of the Phylum Firmicutes in the rumen of heat-stressed dairy cows fed with S. cerevisiae, of which four genera had significantly higher abundance, Ruminococcus_gauvreauii_group, Butyrivibrio_2, Moryella, and Ruminiclostridium_6. At the functional level, ten pathways differed significantly between the three groups (P < 0.05), with an increase in fatty acid biosynthesis, fatty acid metabolism, PPAR signaling pathway, ferroptosis, and biotin metabolism in the treatment groups. More differential metabolites were found in the D-C and D-A groups than in the D-C and D-B groups. These results indicate that S. cerevisiae cultures can influence the health status of heat-stressed cows by modulating rumen microbial composition, function, and metabolites, thereby improving rumen cellulolytic capacity. This study can provide or offer suggestions or recommendations for the development and utilization of feed additives.}, } @article {pmid35910036, year = {2022}, author = {Ayala-Muñoz, D and Burgos, WD and Sánchez-España, J and Falagán, C and Couradeau, E and Macalady, JL}, title = {Novel Microorganisms Contribute to Biosulfidogenesis in the Deep Layer of an Acidic Pit Lake.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {867321}, pmid = {35910036}, issn = {2296-4185}, abstract = {Cueva de la Mora is a permanently stratified acidic pit lake with extremely high concentrations of heavy metals at depth. In order to evaluate the potential for in situ sulfide production, we characterized the microbial community in the deep layer using metagenomics and metatranscriptomics. We retrieved 18 high quality metagenome-assembled genomes (MAGs) representing the most abundant populations. None of the MAGs were closely related to either cultured or non-cultured organisms from the Genome Taxonomy or NCBI databases (none with average nucleotide identity >95%). Despite oxygen concentrations that are consistently below detection in the deep layer, some archaeal and bacterial MAGs mapped transcripts of genes for sulfide oxidation coupled with oxygen reduction. Among these microaerophilic sulfide oxidizers, mixotrophic Thermoplasmatales archaea were the most numerous and represented 24% of the total community. Populations associated with the highest predicted in situ activity for sulfate reduction were affiliated with Actinobacteria, Chloroflexi, and Nitrospirae phyla, and together represented about 9% of the total community. These MAGs, in addition to a less abundant Proteobacteria MAG in the genus Desulfomonile, contained transcripts of genes in the Wood-Ljungdahl pathway. All MAGs had significant genetic potential for organic carbon oxidation. Our results indicate that novel acidophiles are contributing to biosulfidogenesis in the deep layer of Cueva de la Mora, and that in situ sulfide production is limited by organic carbon availability and sulfur oxidation.}, } @article {pmid35909970, year = {2022}, author = {Zhang, Z and Wang, H and Guo, Y and Liu, Z and Chang, Z}, title = {Metagenome Analysis of the Bacterial Characteristics in Invasive Klebsiella Pneumoniae Liver Abscesses.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {812542}, pmid = {35909970}, issn = {2235-2988}, mesh = {Humans ; *Klebsiella Infections/microbiology ; Klebsiella pneumoniae/genetics ; *Liver Abscess/microbiology ; Metagenome ; Retrospective Studies ; }, abstract = {BACKGROUND: Klebsiella pneumoniae liver abscess (KPLA) combined with extrahepatic migratory infection (EMI) is defined as invasive KPLA (IKPLA) and is associated with a poor prognosis. The mechanism of IKPLA formation is yet to be elucidated. In this study, metagenomic sequencing was used to compare the bacterial characteristics between IKPLA and KPLA to explore the underlying mechanism of invasiveness.

METHODS: Clinical details, imaging, and microbial features were retrospectively evaluated by medical record review. Metagenomic sequencing was performed on the pus samples of liver abscesses whose culture results were indicative of monomicrobial Klebsiella pneumoniae (K. pneumoniae). Bacterial diversity and composition in IKPLA and KPLA were comparatively analyzed, and the key pathways and genes that may affect invasiveness were further explored.

RESULTS: Sixteen patients were included in this study. Five patients with EMI were included in the IKPLA group, and the other eleven patients without EMI were assigned to the KPLA group. There was no statistical difference in the hypermucoviscous phenotype and serotype of K. pneumoniae between the two groups. The bacterial diversity of IKPLA was lower than that of KPLA. The abundant taxa in the IKPLA group were primarily species of unclassified Enterobacteriaceae and K. pneumoniae. The KPLA group had a high abundance of the genera Tetrasphaera and Leuconostoc. Metabolic pathway genes represented most of the enriched genes in IKPLA. Fourteen pathogenic genes with significant differences in abundance were identified between the two groups, including ybtS, fepC, phoQ, acrB, fimK, magA, entC, arnT, iucA, fepG, oqxB, entA, tonB, and entF (p < 0.001).

CONCLUSION: The diversity and bacterial composition of IKPLA were significantly different from those of KPLA. Microbiological changes in the abscess, activation of the related metabolic pathways, and the pathogenic gene expression may constitute a novel mechanism that regulates the invasiveness of KPLA.}, } @article {pmid35909965, year = {2022}, author = {Sun, L and Zhang, S and Yang, Z and Yang, F and Wang, Z and Li, H and Li, Y and Sun, T}, title = {Clinical Application and Influencing Factor Analysis of Metagenomic Next-Generation Sequencing (mNGS) in ICU Patients With Sepsis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {905132}, pmid = {35909965}, issn = {2235-2988}, mesh = {Anti-Bacterial Agents ; Factor Analysis, Statistical ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Hypertension ; Intensive Care Units ; Metagenomics/methods ; *Sepsis/diagnosis ; }, abstract = {OBJECTIVE: To analyze the clinical application and related influencing factors of metagenomic next-generation sequencing (mNGS) in patients with sepsis in intensive care unit (ICU).

METHODS: The study included 124 patients with severe sepsis admitted to the ICU in the First Affiliated Hospital of Zhengzhou University from June 2020 to September 2021. Two experienced clinicians took blood mNGS and routine blood cultures of patients meeting the sepsis diagnostic criteria within 24 hours after sepsis was considered, and collection the general clinical data.

RESULTS: mNGS positive rate was higher than traditional blood culture (67.74% vs. 19.35%). APACHE II score [odds ratio (OR)=1.096], immune-related diseases (OR=6.544), and hypertension (OR=2.819) were considered as positive independent factors for mNGS or culture-positive. The sequence number of microorganisms and pathogen detection (mNGS) type had no effect on prognosis. Age (OR=1.016), female (OR=5.963), myoglobin (OR=1.005), and positive virus result (OR=8.531) were independent risk factors of sepsis mortality. Adjusting antibiotics according to mNGS results, there was no statistical difference in the prognosis of patients with sepsis.

CONCLUSION: mNGS has the advantages of rapid and high positive rate in the detection of pathogens in patients with severe sepsis. Patients with high APACHE II score, immune-related diseases, and hypertension are more likely to obtain positive mNGS results. The effect of adjusting antibiotics according to mNGS results on the prognosis of sepsis needs to be further evaluated.}, } @article {pmid35909738, year = {2022}, author = {Li, B and Wang, Y and Hu, T and Qiu, D and Francis, F and Wang, S and Wang, S}, title = {Root-Associated Microbiota Response to Ecological Factors: Role of Soil Acidity in Enhancing Citrus Tolerance to Huanglongbing.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {937414}, pmid = {35909738}, issn = {1664-462X}, abstract = {The citrus orchards in southern China are widely threatened by low soil pH and Huanglongbing (HLB) prevalence. Notably, the lime application has been used to optimize soil pH, which is propitious to maintain root health and enhance HLB tolerance of citrus; however, little is known about the interactive effects of soil acidity on the soil properties and root-associated (rhizoplane and endosphere) microbial community of HLB-infected citrus orchard. In this study, the differences in microbial community structures and functions between the acidified and amended soils in the Gannan citrus orchard were investigated, which may represent the response of the host-associated microbiome in diseased roots and rhizoplane to dynamic soil acidity. Our findings demonstrated that the severity of soil acidification and aluminum toxicity was mitigated after soil improvement, accompanied by the increase in root activity and the decrease of HLB pathogen concentration in citrus roots. Additionally, the Illumina sequencing-based community analysis showed that the application of soil amendment enriched functional categories involved in host-microbe interactions and nitrogen and sulfur metabolisms in the HLB-infected citrus rhizoplane; and it also strongly altered root endophytic microbial community diversity and structure, which represented by the enrichment of beneficial microorganisms in diseased roots. These changes in rhizoplane-enriched functional properties and microbial composition may subsequently benefit the plant's health and tolerance to HLB disease. Overall, this study advances our understanding of the important role of root-associated microbiota changes and ecological factors, such as soil acidity, in delaying and alleviating HLB disease.}, } @article {pmid35909618, year = {2022}, author = {Patidar, P and Prakash, T}, title = {Decoding the roles of extremophilic microbes in the anaerobic environments: Past, Present, and Future.}, journal = {Current research in microbial sciences}, volume = {3}, number = {}, pages = {100146}, pmid = {35909618}, issn = {2666-5174}, abstract = {The genome of an organism is directly or indirectly correlated with its environment. Consequently, different microbes have evolved to survive and sustain themselves in a variety of environments, including unusual anaerobic environments. It is believed that their genetic material could have played an important role in the early evolution of their existence in the past. Presently, out of the uncountable number of microbes found in different ecosystems we have been able to discover only one percent of the total communities. A large majority of the microbial populations exists in the most unusual and extreme environments. For instance, many anaerobic bacteria are found in the gastrointestinal tract of humans, soil, and hydrothermal vents. The recent advancements in Metagenomics and Next Generation Sequencing technologies have improved the understanding of their roles in these environments. Presently, anaerobic bacteria are used in various industries associated with biofuels, fermentation, production of enzymes, vaccines, vitamins, and dairy products. This broad applicability brings focus to the significant contribution of their genomes in these functions. Although the anaerobic microbes have become an irreplaceable component of our lives, a major and important section of such anaerobic microbes still remain unexplored. Therefore, it can be said that unlocking the role of the microbial genomes of the anaerobes can be a noteworthy discovery not just for mankind but for the entire biosystem as well.}, } @article {pmid35909600, year = {2022}, author = {Najar, IN and Sharma, P and Das, S and Sherpa, MT and Kumar, S and Thakur, N}, title = {Bacterial diversity, physicochemical and geothermometry of South Asian hot springs.}, journal = {Current research in microbial sciences}, volume = {3}, number = {}, pages = {100125}, pmid = {35909600}, issn = {2666-5174}, abstract = {Extreme ecosystems with enormous arrays of physicochemical or biological physiognomies serve as an important indicator of various processes occurred and/or occurring in and on the Earth. Among extreme habitats, hot springs represent geothermal features which are complex systems with a well-defined plumbing system. Besides geological tectonic based hypsography and orology annotations, the hot springs have served as hot spots for ages where there is an amalgamation of nature, religion, faith, health, and science. Thus, there remains an escalating scope to study these hot springs all over the world. The Himalayan Geothermal Belt (HGB) banquets three densely demographic countries i.e. Pakistan, India and China, that hosts numerous hot springs. Studies on the hot springs distributed over these countries reveal Proteobacteria, Firmicutes, Bacteroidetes and Actinobacteria as the predominant bacterial phyla. The bacterial diversity shows a significant positive correlation with physicochemical parameters like temperature, pH, Na[+], HCO3 [-], etc. Physicochemical analyses of these hot springs indicate the water mainly as Na-Cl, Na-HCO3, SO4-Cl, and mixed type, with temperature ranging approximately between 100-250°C as predicted by various geothermometers. Numerous studies although done, not much of a comprehensive database of the analysis are provided on the hot springs harboured by the HGB. This review aims to give a cumulative illustration on comparative facets of various characteristic features of hot springs distributed over the HGB. These are found to be of great importance with respect to the exploitation of geothermal energy and microflora in various sectors of industries and biotechnology. They are also important sources in terms of socio-economic perspective, and routes to eco-medical tourism.}, } @article {pmid35908725, year = {2022}, author = {Xi, Y and Zhou, J and Lin, Z and Liang, W and Yang, C and Liu, D and Xu, Y and Nong, L and Chen, S and Yu, Y and He, W and Zhang, J and Zhang, R and Liu, X and Liu, X and Sang, L and Xu, Y and Li, Y}, title = {Patients with infectious diseases undergoing mechanical ventilation in the intensive care unit have better prognosis after receiving metagenomic next-generation sequencing assay.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {122}, number = {}, pages = {959-969}, doi = {10.1016/j.ijid.2022.07.062}, pmid = {35908725}, issn = {1878-3511}, mesh = {*Communicable Diseases ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Intensive Care Units ; Metagenomics/methods ; Prognosis ; *Respiration, Artificial ; Sensitivity and Specificity ; }, abstract = {OBJECTIVES: To evaluate the relation between metagenomic next-generation sequencing (mNGS) and the prognosis of patients with infectious diseases undergoing mechanical ventilation in the intensive care unit (ICU).

METHODS: This is a single-center observational study, comparing nonrandomly assigned diagnostic approaches. We analyzed the medical records of 228 patients with suspected infectious diseases undergoing mechanical ventilation in the ICU from March 2018 to May 2020. The concordance of pathogen results was also assessed for the results of mNGS, culture, and polymerase chain reaction assays.

RESULTS: The 28-day mortality of the patients in the mNGS group was lower after the baseline difference correction (19.23% (20/104) vs 29.03% (36/124) , P = 0.039). Subgroup analysis showed that mNGS assay was associated with improved 28-day mortality of patients who are not immunosuppressed (14.06% vs 29.82%, P = 0.018). Not performing mNGS assay, higher acute physiology and chronic health evaluation II score, and hypertension are independent risk factors for 28-day mortality. The mNGS assay presented an advantage in pathogen positivity (69.8% double-positive and 25.0% mNGS-positive only), and the concordance between these two assays was 79.0%.

CONCLUSION: mNGS survey may be associated with a better prognosis by reducing 28-day mortality of patients with infectious diseases on mechanical ventilation in the ICU. This technique presented an advantage in pathogen positivity over traditional methods.}, } @article {pmid35908723, year = {2022}, author = {Liang, M and Fan, Y and Zhang, D and Yang, L and Wang, X and Wang, S and Xu, J and Zhang, J}, title = {Metagenomic next-generation sequencing for accurate diagnosis and management of lower respiratory tract infections.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {122}, number = {}, pages = {921-929}, doi = {10.1016/j.ijid.2022.07.060}, pmid = {35908723}, issn = {1878-3511}, mesh = {Anti-Bacterial Agents/therapeutic use ; *Coinfection/diagnosis/drug therapy/microbiology ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; *Respiratory Tract Infections/diagnosis/drug therapy ; Retrospective Studies ; Sensitivity and Specificity ; }, abstract = {OBJECTIVES: This study aimed to evaluate the clinical value of metagenomic next-generation sequencing (mNGS) in patients with suspected lower respiratory tract infections.

METHODS: This retrospective study reviewed patients with suspected lower respiratory tract infections at the Wuhan Union Hospital. Data including demographic, laboratory, and radiological profiles; treatment; and outcomes were recorded and analyzed.

RESULTS: mNGS identified pathogenic microbes in 100/140 (71.4%) patients, although 135 (96.4%) had received empiric antibiotic treatment before the mNGS tests. Single bacterial infection (35/100, 35%) was the most common type of infection in patients with positive mNGS results, followed by single fungal infection (14/100, 14%), bacterial-viral coinfection (14/100, 14%), single viral infection (12/100, 12%), bacterial-fungal coinfection (9/100, 9%), fungal-viral coinfection (9/100, 9%), and bacterial-fungal-viral coinfection (7/100, 7%). Moreover, compared with culture test, mNGS showed higher sensitivity (63/85, 74.1% vs 22/85, 25.9% P = 0.001) and lower processing time (24 hours vs 48 hours). Antibiotic treatment was adjusted or confirmed based on the mNGS results in 123 (87.9%) patients, including five (3.6%), 33 (23.6%), and 85 (60.7%) patients, in whom treatment was downgraded, upgraded, and unchanged, respectively. Almost all patients, regardless of escalation, de-escalation, or no change in treatment, showed significant improvement in clinical symptoms and inflammatory indicators. In addition, 17 (12.1%) patients were referred to Wuhan Pulmonary Hospital for further treatment because of confirmed or suspected tuberculosis.

CONCLUSION: mNGS could be a promising technique for microbiological diagnosis and antibiotic management, potentially improving outcomes for patients.}, } @article {pmid35908720, year = {2022}, author = {Fang, X and Cai, Y and Chen, X and Huang, C and Lin, Y and Huang, Z and Zhang, C and Huang, Y and Li, W and Zhang, W}, title = {The role of metagenomic next-generation sequencing in the pathogen detection of invasive osteoarticular infection.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {122}, number = {}, pages = {996-1001}, doi = {10.1016/j.ijid.2022.07.061}, pmid = {35908720}, issn = {1878-3511}, mesh = {Bacteria/genetics ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; *Metagenomics/methods ; Sensitivity and Specificity ; }, abstract = {OBJECTIVES: This study aimed to analyze the pathogenic bacteria spectrum in invasive and primary osteoarticular infection (IOI and POI) and compare the pathogen detection rate of metagenomic next-generation sequencing (mNGS) and microbial culture in IOI and POI.

METHODS: The suspected POI and IOI cases from 2014-2021 were included. The diagnosis of POI or IOI was made by at least two orthopedic surgeons, two infectious diseases specialists, and one senior microbiologist. Demographic characteristics, microbial culture results, and so on were recorded. The pathogenic bacteria spectrum in IOI and POI were analyzed, and the ability of mNGS and microbial culture in pathogen detection in IOI and POI were compared.

RESULTS: There were 52 POI cases and 92 IOI cases; the common pathogen in POI and IOI were both Staphylococcus aureus. There are more cases with negative microbial culture results and multiple infections in IOI, and many cases were caused by rare and fastidious bacteria. The introduction of the mNGS could significantly increase the pathogen detection rate to 92.39% in IOI, which was 8.69% higher than that of microbial culture (P = 0.007), whereas the improvement in POI was limited to about 2%.

CONCLUSION: mNGS is an promising tool for IOI pathogen detection.}, } @article {pmid35908467, year = {2022}, author = {Zhao, F and Wang, C and Song, S and Fang, C and Zhou, G and Li, C and Kristiansen, K}, title = {Casein and red meat proteins differentially affect the composition of the gut microbiota in weaning rats.}, journal = {Food chemistry}, volume = {397}, number = {}, pages = {133769}, doi = {10.1016/j.foodchem.2022.133769}, pmid = {35908467}, issn = {1873-7072}, mesh = {Animals ; Caseins/metabolism ; Cattle ; Diet ; Dietary Proteins/metabolism ; *Gastrointestinal Microbiome ; Humans ; Meat ; Meat Proteins ; Rats ; *Red Meat ; Weaning ; }, abstract = {Casein and meat are food sources providing high-quality animal proteins for human consumption. However, little is known concerning potentially different effects of these animal protein sources during early stages of life. In the present study, casein and red meat proteins (beef and pork) were fed to young postweaning rats for 14 days based on the AIN-93G diet formula. Casein and red meat protein-based diets did not differentially affect the overall growth performance. However, they discriminately modulated the abundances of different potentially beneficial bacteria belonging to genus Lactobacillus. Intake of the casein-based diet increased the intestinal abundance of Lactococcus lactis with a pronounced potential for galactose utilization via the Tag6P pathway, and it also resulted in lower amounts of toxic ammonia in the rat cecum compared to red meat protein-based diets. We observed no adverse effects on colonic tissue in response to any of the protein-based diets based on histological observations.}, } @article {pmid35908425, year = {2022}, author = {Mapelli, F and Vergani, L and Terzaghi, E and Zecchin, S and Raspa, G and Marasco, R and Rolli, E and Zanardini, E and Morosini, C and Anelli, S and Nastasio, P and Sale, VM and Armiraglio, S and Di Guardo, A and Borin, S}, title = {Pollution and edaphic factors shape bacterial community structure and functionality in historically contaminated soils.}, journal = {Microbiological research}, volume = {263}, number = {}, pages = {127144}, doi = {10.1016/j.micres.2022.127144}, pmid = {35908425}, issn = {1618-0623}, mesh = {Biodegradation, Environmental ; *Metalloids/analysis ; *Polychlorinated Biphenyls/analysis/metabolism ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; *Soil Pollutants/metabolism ; }, abstract = {Studies about biodegradation potential in soils often refer to artificially contaminated and simplified systems, overlooking the complexity associated with contaminated sites in a real context. This work aims to provide a holistic view on microbiome assembly and functional diversity in the model site SIN Brescia-Caffaro (Italy), characterized by historical and uneven contamination by organic and inorganic compounds. Here, physical and chemical analyses and microbiota characterization were applied on one-hundred-twenty-seven soil samples to unravel the environmental factors driving bacterial community assembly and biodegradation potential in three former agricultural fields. Chemical analyses showed a patchy distribution of metals, metalloids and polychlorinated biphenyls (PCB) and allowed soil categorization according to depth and area of collections. Likewise, the bacterial community structure, described by molecular fingerprinting and 16S rRNA gene analyses, was significantly different according to collection site and depth. Pollutant concentrations (i.e., hexachloro-biphenyls, arsenic and mercury), nitrogen content and parameters related to soil texture were identified as main drivers of microbiota assembly, being significantly correlated to bacterial community composition. Moreover, bacteria putatively involved in the aerobic degradation of PCBs were enriched over the total bacterial community in topsoils, where the highest activity was recorded using fluorescein hydrolysis as proxy. Metataxonomic analyses revealed the presence of bacteria having metabolic pathways related to PCB degradation and tolerance to heavy metals and metalloids in the topsoil samples collected in all areas. Overall, the provided dissection of soil microbiota structure and its degradation potential in the SIN Brescia-Caffaro can contribute to target specific areas for rhizoremediation implementation. Metagenomics studies could be implemented in the future to understand if specific degradative pathways are present in historically polluted sites characterized by the co-occurrence of multiple classes of contaminants.}, } @article {pmid35907599, year = {2022}, author = {Yang, G and Xu, C and Varjani, S and Zhou, Y and Wc Wong, J and Duan, G}, title = {Metagenomic insights into improving mechanisms of Fe[0] nanoparticles on volatile fatty acids production from potato peel waste anaerobic fermentation.}, journal = {Bioresource technology}, volume = {361}, number = {}, pages = {127703}, doi = {10.1016/j.biortech.2022.127703}, pmid = {35907599}, issn = {1873-2976}, mesh = {Anaerobiosis ; Bioreactors ; Fatty Acids, Volatile/metabolism ; Fermentation ; Hydrogen-Ion Concentration ; *Nanoparticles ; Sewage/microbiology ; *Solanum tuberosum ; }, abstract = {The management of potato peel waste (PPW) has been a challenge faced by the potato industry. This investigation assessed the feasibility of PPW for volatile fatty acids (VFAs) production via anaerobic fermentation, and investigated the impact of Fe[0] nanoparticles (Fe[0] NPs) supplementation on the VFAs production. It is found that PPW is a potential feedstock for producing VFAs, achieving a yield of 480.4 mg COD/g-vS Meanwhile, the supplementation of Fe[0] NPs significantly promoted the VFAs productivity and quality. The higher enrichment of VFAs-producing bacteria, including Clostridium, Proteiniphilum, Fonticella and Pygmaiobacter, contributed to the promotion of the VFAs yield. Furthermore, metagenomic analysis revealed that the encoding genes responsible for carbohydrate metabolism (especially starch), membrane transport, glycolysis and the formation of acetic and butyric acids were remarkably up-regulated,which could be the essential reason for the enhanced metabolic activity and VFAs productivity. This work provides a promising strategy for recycling PPW.}, } @article {pmid35907589, year = {2022}, author = {Stevenson, SJR and Lee, KC and Handley, KM and Angert, ER and White, WL and Clements, KD}, title = {Substrate degradation pathways, conserved functions and community composition of the hindgut microbiota in the herbivorous marine fish Kyphosus sydneyanus.}, journal = {Comparative biochemistry and physiology. Part A, Molecular & integrative physiology}, volume = {272}, number = {}, pages = {111283}, doi = {10.1016/j.cbpa.2022.111283}, pmid = {35907589}, issn = {1531-4332}, mesh = {Animals ; Fatty Acids, Volatile/pharmacology ; Fishes/genetics ; *Gastrointestinal Microbiome ; *Microbiota ; *Perciformes/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Symbiotic gut microbiota in the herbivorous marine fish Kyphosus sydneyanus play an important role in digestion by converting refractory algal carbohydrate into short-chain fatty acids. Here we characterised community composition using both 16S rRNA gene amplicon sequencing and shotgun-metagenome sequencing. Sequencing was carried out on lumen and mucosa samples (radial sections) from three axial sections taken from the hindgut of wild-caught fish. Both lumen and mucosa communities displayed distinct distributions along the hindgut, likely an effect of the differing selection pressures within these hindgut locations, as well as considerable variation among individual fish. In contrast, metagenomic sequences displayed a high level of functional similarity between individual fish and gut sections in the relative abundance of genes (based on sequencing depth) that encoded enzymes involved in algal-derived substrate degradation. These results suggest that the host gut environment selects for functional capacity in symbionts rather than taxonomic identity. Functional annotation of the enzymes encoded by the gut microbiota was carried out to infer the metabolic pathways used by the gut microbiota for the degradation of important dietary substrates: mannitol, alginate, laminarin, fucoidan and galactan (e.g. agar and carrageenan). This work provides the first evidence of the genomic potential of K. sydneyanus hindgut microbiota to convert highly refractory algal carbohydrates into metabolically useful short-chain fatty acids.}, } @article {pmid35907567, year = {2022}, author = {Li, Y and Li, GY and Han, DX and Feng, YW and Liang, XM and Ren, D and Yuan, LJ and Zhang, L and Meng, XK and Wang, JZ and Ye, Y and Gao, JP and Wen, S and Chen, YH and He, XS and Zou, ZY and Han, P and Li, XH and Tu, HB and Lai, K and Yang, M and Rao, GH and Gui, SQ}, title = {Study on the clinical indications for plasma as an alternative to the bronchoalveolar lavage fluid metagenomic next-generation sequencing test to detect consistent pathogens for septic patients in intensive care units.}, journal = {The Journal of infection}, volume = {85}, number = {4}, pages = {436-480}, doi = {10.1016/j.jinf.2022.07.016}, pmid = {35907567}, issn = {1532-2742}, mesh = {Bronchoalveolar Lavage Fluid ; High-Throughput Nucleotide Sequencing ; Humans ; Intensive Care Units ; *Metagenomics ; *Sepsis/diagnosis ; }, } @article {pmid35907477, year = {2022}, author = {Chen, S and Kang, Y and Li, D and Li, Z}, title = {Diagnostic performance of metagenomic next-generation sequencing for the detection of pathogens in bronchoalveolar lavage fluid in patients with pulmonary infections: Systematic review and meta-analysis.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {122}, number = {}, pages = {867-873}, doi = {10.1016/j.ijid.2022.07.054}, pmid = {35907477}, issn = {1878-3511}, mesh = {Bronchoalveolar Lavage Fluid ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; *Metagenomics ; *Pneumonia/diagnosis ; Sensitivity and Specificity ; }, abstract = {OBJECTIVES: Identifying pathogens in patients with pulmonary infection (PI) has always been a major challenge in medicine. Compared with sputum and throat swabs, bronchoalveolar lavage fluid (BALF) can better reflect the actual state of the lungs. However, there has not been a meta-analysis of the diagnostic efficacy of metagenomic next-generation sequencing (mNGS) in detecting pathogens in BALF from patients with PIs.

METHODS: Data sources were PubMed, Web of Science, Embase, and the China National Knowledge Infrastructure. The pooled sensitivity and specificity were estimated using random-effects or fixed-effect models. Subgroup analysis was performed to reveal the effect of potential explanatory factors on the diagnostic performance measures.

RESULTS: The pooled sensitivity was 78% (95% confidence interval [CI]: 67-87%; I[2] = 92%) and the pooled specificity was 77% (95% CI: 64-94%; I[2] = 74%) for mNGS. Subgroup analyses for the sensitivity of mNGS revealed that patients with PIs who were severely ill or immunocompromised significantly affected heterogeneity (P < 0.001). The positive detection rate of mNGS for pathogens in BALF of severely or immunocompromised pulmonary-infected patients was 92% (95% CI: 78-100%).

CONCLUSION: mNGS has high diagnostic performance for BALF pathogens in patients with PIs, especially in critically ill or immunocompromised patients.}, } @article {pmid35907440, year = {2022}, author = {Divers, TJ and Tomlinson, JE and Tennant, BC}, title = {The history of Theiler's disease and the search for its aetiology.}, journal = {Veterinary journal (London, England : 1997)}, volume = {287}, number = {}, pages = {105878}, doi = {10.1016/j.tvjl.2022.105878}, pmid = {35907440}, issn = {1532-2971}, mesh = {Animals ; *Hepatitis ; *Hepatitis, Viral, Animal/epidemiology/pathology ; *Horse Diseases/epidemiology/etiology/pathology ; Horses ; Humans ; *Parvoviridae Infections/veterinary ; *Parvovirus ; }, abstract = {Theiler's disease (serum hepatitis) may occur in outbreaks or as single cases of acute hepatitis and is often associated with prior administration of equine-origin biologics approximately 4-10 weeks before the onset of clinical signs. Cases have also been described without any prior administration of blood products. The clinical disease has a low morbidity but high mortality and only adult horses are affected. The course of the disease is short, with horses either dying or completely recovering in a few days. Pathology in affected horses is predominantly centrilobular hepatocyte necrosis with mononuclear cell infiltration of the lesser affected periportal regions of the liver. Subclinical cases of the disease also occur. Based on the epidemiology and pathology of the disease, a viral cause, similar to hepatitis B in humans, has long been suspected. This paper reviews both historical and recent findings on Theiler's disease. Reported epidemics of Theiler's disease in the early 1900s are reviewed, along with their similarities to outbreaks of serum hepatitis in humans following yellow fever virus vaccinations in the 1930s and 1940s. Recent metagenomics-based studies to determine the aetiology of Theiler's disease are discussed, along with both clinical and experimental findings supporting equine parvovirus-hepatitis (EqPV-H) as the likely cause of this 100-year-old disease.}, } @article {pmid35906888, year = {2022}, author = {Nielsen, TK and Browne, PD and Hansen, LH}, title = {Antibiotic resistance genes are differentially mobilized according to resistance mechanism.}, journal = {GigaScience}, volume = {11}, number = {}, pages = {}, pmid = {35906888}, issn = {2047-217X}, mesh = {*Anti-Bacterial Agents/pharmacology ; DNA Transposable Elements ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Humans ; Phylogeny ; }, abstract = {BACKGROUND: Screening for antibiotic resistance genes (ARGs) in especially environmental samples with (meta)genomic sequencing is associated with false-positive predictions of phenotypic resistance. This stems from the fact that most acquired ARGs require being overexpressed before conferring resistance, which is often caused by decontextualization of putative ARGs by mobile genetic elements (MGEs). Consequent overexpression of ARGs can be caused by strong promoters often present in insertion sequence (IS) elements and integrons and the copy number effect of plasmids, which may contribute to high expression of accessory genes.

RESULTS: Here, we screen all complete bacterial RefSeq genomes for ARGs. The genetic contexts of detected ARGs are investigated for IS elements, integrons, plasmids, and phylogenetic dispersion. The ARG-MOB scale is proposed, which indicates how mobilized detected ARGs are in bacterial genomes. It is concluded that antibiotic efflux genes are rarely mobilized and even 80% of β-lactamases have never, or very rarely, been mobilized in the 15,790 studied genomes. However, some ARGs are indeed mobilized and co-occur with IS elements, plasmids, and integrons.

CONCLUSIONS: In this study, ARGs in all complete bacterial genomes are classified by their association with MGEs, using the proposed ARG-MOB scale. These results have consequences for the design and interpretation of studies screening for resistance determinants, as mobilized ARGs pose a more concrete risk to human health. An interactive table of all results is provided for future studies targeting highly mobilized ARGs.}, } @article {pmid35906519, year = {2023}, author = {Min, J and Kim, P and Yun, S and Hong, M and Park, W}, title = {Zoo animal manure as an overlooked reservoir of antibiotic resistance genes and multidrug-resistant bacteria.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {1}, pages = {710-726}, pmid = {35906519}, issn = {1614-7499}, support = {NRF-2020M3A9H5104237//National Research Foundation of Korea/ ; }, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; *Manure/microbiology ; Animals, Zoo/genetics ; Genes, Bacterial ; Drug Resistance, Multiple, Bacterial/genetics ; Bacteria/genetics ; }, abstract = {Animal fecal samples collected in the summer and winter from 11 herbivorous animals, including sable antelope (SA), long-tailed goral (LTG), and common eland (CE), at a public zoo were examined for the presence of antibiotic resistance genes (ARGs). Seven antibiotics, including meropenem and azithromycin, were used to isolate culturable multidrug-resistant (MDR) strains. The manures from three animals (SA, LTG, and CE) contained 10[4]-fold higher culturable MDR bacteria, including Chryseobacterium, Sphingobacterium, and Stenotrophomonas species, while fewer MDR bacteria were isolated from manure from water buffalo, rhinoceros, and elephant against all tested antibiotics. Three MDR bacteria-rich samples along with composite samples were further analyzed using nanopore-based technology. ARGs including lnu(C), tet(Q), and mef(A) were common and often associated with transposons in all tested samples, suggesting that transposons carrying ARGs may play an important role for the dissemination of ARGs in our tested animals. Although several copies of ARGs such as aph(3')-IIc, blaL1, blaIND-3, and tet(42) were found in the sequenced genomes of the nine MDR bacteria, the numbers and types of ARGs appeared to be less than expected in zoo animal manure, suggesting that MDR bacteria in the gut of the tested animals had intrinsic resistant phenotypes in the absence of ARGs.}, } @article {pmid35906397, year = {2022}, author = {Sugden, S and Holert, J and Cardenas, E and Mohn, WW and Stein, LY}, title = {Microbiome of the freshwater sponge Ephydatia muelleri shares compositional and functional similarities with those of marine sponges.}, journal = {The ISME journal}, volume = {16}, number = {11}, pages = {2503-2512}, pmid = {35906397}, issn = {1751-7370}, mesh = {Animals ; DNA Restriction-Modification Enzymes/genetics ; Fresh Water ; *Microbiota/genetics ; Phylogeny ; *Porifera/microbiology ; RNA, Ribosomal, 16S/genetics ; Transposases/genetics ; Vitamin B 12 ; Water ; }, abstract = {Sponges are known for hosting diverse communities of microbial symbionts, but despite persistent interest in the sponge microbiome, most research has targeted marine sponges; freshwater sponges have been the focus of less than a dozen studies. Here, we used 16 S rRNA gene amplicon sequencing and shotgun metagenomics to characterize the microbiome of the freshwater sponge Ephydatia muelleri and identify potential indicators of sponge-microbe mutualism. Using samples collected from the Sooke, Nanaimo, and Cowichan Rivers on Vancouver Island, British Columbia, we show that the E. muelleri microbiome is distinct from the ambient water and adjacent biofilms and is dominated by Sediminibacterium, Comamonas, and unclassified Rhodospirillales. We also observed phylotype-level differences in sponge microbiome taxonomic composition among different rivers. These differences were not reflected in the ambient water, suggesting that other environmental or host-specific factors may drive the observed geographic variation. Shotgun metagenomes and metagenome-assembled genomes further revealed that freshwater sponge-associated bacteria share many genomic similarities with marine sponge microbiota, including an abundance of defense-related proteins (CRISPR, restriction-modification systems, and transposases) and genes for vitamin B12 production. Overall, our results provide foundational information on the composition and function of freshwater sponge-associated microbes, which represent an important yet underappreciated component of the global sponge microbiome.}, } @article {pmid35906393, year = {2022}, author = {Bay, V and Gür, S and Bayraktar, O}, title = {Plant-derived tormentic acid alters the gut microbiota of the silkworm (Bombyx mori).}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {13005}, pmid = {35906393}, issn = {2045-2322}, mesh = {Animals ; Bacteria/genetics ; *Bombyx/microbiology ; *Gastrointestinal Microbiome ; Metagenomics ; Triterpenes ; }, abstract = {In recent years, phytochemicals have started to attract more attention due to their contribution to health and bioactivity. Microorganisms in the intestines of organisms contribute to the processing, function, and biotransformation of these substances. The silkworm (Bombyx mori) is one of the organisms used for the biotransformation of phytochemicals due to its controlled reproduction and liability to microbial manipulation. In this study, a bioactive compound, tormentic acid (TA), extracted from Sarcopoterium spinosum was used in the silkworm diet, and the alterations of intestinal microbiota of the silkworm were assessed. To do this, silkworms were fed on a diet with various tormentic acid content, and 16S metagenomic analysis was performed to determine the alterations in the gut microbiota profile of these organisms. Diet with different TA content did not cause a change in the bacterial diversity of the samples. A more detailed comparison between different feeding groups indicated increased abundance of bacteria associated with health, i.e., Intestinibacter spp., Flavonifractor spp., Senegalimassilia spp., through the utilization of bioactive substances such as flavonoids. In conclusion, it might be said that using TA as a supplementary product might help ameliorate the infected gut, promote the healthy gut, and relieve the undesirable effects of medicines on the gastrointestinal system.}, } @article {pmid35906296, year = {2022}, author = {Marx, V}, title = {Why the ocean virome matters.}, journal = {Nature methods}, volume = {19}, number = {8}, pages = {924-927}, pmid = {35906296}, issn = {1548-7105}, mesh = {*Bacteriophages ; Metagenomics ; *Microbiota ; Oceans and Seas ; Virome ; }, abstract = {Expeditions are delivering data wealth about our planet’s oceans, including its microbes. Some labs are now diving deep into the ocean virome.}, } @article {pmid35906254, year = {2022}, author = {Coker, MO and Lebeaux, RM and Hoen, AG and Moroishi, Y and Gilbert-Diamond, D and Dade, EF and Palys, TJ and Madan, JC and Karagas, MR}, title = {Metagenomic analysis reveals associations between salivary microbiota and body composition in early childhood.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {13075}, pmid = {35906254}, issn = {2045-2322}, support = {US Environmental Protection Agency RD83459901/EPA/EPA/United States ; P20 ES018175/ES/NIEHS NIH HHS/United States ; T32 AI007519/AI/NIAID NIH HHS/United States ; R01 LM012723/LM/NLM NIH HHS/United States ; P01 ES022832/ES/NIEHS NIH HHS/United States ; NLM R01LM012723/NH/NIH HHS/United States ; P20 GM104416/GM/NIGMS NIH HHS/United States ; NIEHS UH3OD023275/NH/NIH HHS/United States ; NIDCR R01DE028154/NH/NIH HHS/United States ; }, mesh = {Body Composition ; Body Mass Index ; Body Weight ; Child, Preschool ; Cohort Studies ; Humans ; *Microbiota/genetics ; }, abstract = {Several studies have shown that body mass index is strongly associated with differences in gut microbiota, but the relationship between body weight and oral microbiota is less clear especially in young children. We aimed to evaluate if there is an association between child growth and the saliva microbiome. We hypothesized that associations between growth and the saliva microbiome would be moderate, similarly to the association between growth and the gut microbiome. For 236 toddlers participating in the New Hampshire Birth Cohort Study, we characterized the association between multiple longitudinal anthropometric measures of body height, body weight and body mass. Body Mass Index (BMI) z-scores were calculated, and dual-energy x-ray absorptiometry (DXA) was used to estimate body composition. Shotgun metagenomic sequencing of saliva samples was performed to taxonomically and functionally profile the oral microbiome. We found that within-sample diversity was inversely related to body mass measurements while community composition was not associated. Although the magnitude of associations were small, some taxa were consistently associated with growth and modified by sex. Certain taxa were associated with decreased weight or growth (including Actinomyces odontolyticus and Prevotella melaninogenica) or increased growth (such as Streptococcus mitis and Corynebacterium matruchotii) across anthropometric measures. Further exploration of the functional significance of this relationship will enhance our understanding of the intersection between weight gain, microbiota, and energy metabolism and the potential role of these relationships on the onset of obesity-associated diseases in later life.}, } @article {pmid35905960, year = {2022}, author = {Jantharadej, K and Kongprajug, A and Mhuantong, W and Limpiyakorn, T and Suwannasilp, BB and Mongkolsuk, S and Sirikanchana, K}, title = {Comparative genomic analyses of pathogenic bacteria and viruses and antimicrobial resistance genes in an urban transportation canal.}, journal = {The Science of the total environment}, volume = {848}, number = {}, pages = {157652}, doi = {10.1016/j.scitotenv.2022.157652}, pmid = {35905960}, issn = {1879-1026}, mesh = {Aminoglycosides ; *Anti-Bacterial Agents/pharmacology ; Bacteria ; *Bacteriophages/genetics ; Drug Resistance, Bacterial/genetics ; Humans ; Macrolides ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Sulfonamides ; Tetracycline ; Transportation ; Trimethoprim ; Water ; beta-Lactams ; }, abstract = {Water commuting is a major urban transportation method in Thailand. However, urban boat commuters risk exposure to microbially contaminated bioaerosols or splash. We aimed to investigate the microbial community structures, identify bacterial and viral pathogens, and assess the abundance of antimicrobial resistance genes (ARGs) using next-generation sequencing (NGS) at 10 sampling sites along an 18 km transportation boat route in the Saen Saep Canal, which traverses cultural, commercial, and suburban land-based zones. The shotgun metagenomic (Illumina HiSeq) and 16S rRNA gene amplicon (V4 region) (Illumina MiSeq) sequencing platforms revealed diverse microbial clusters aligned with the zones, with explicit segregation between the cultural and suburban sites. The shotgun metagenomic sequencing further identified bacterial and viral pathogens, and ARGs. The predominant bacterial pathogens (>0.5 % relative abundance) were the Burkholderia cepacia complex, Arcobacter butzleri, Burkholderia vietnamiensis, Klebsiella pneumoniae, and the Enterobacter cloacae complex. The viruses (0.28 %-0.67 % abundance in all microbial sequences) comprised mainly vertebrate viruses and bacteriophages, with encephalomyocarditis virus (33.3 %-58.2 % abundance in viral sequences), hepatitis C virus genotype 1, human alphaherpesvirus 1, and human betaherpesvirus 6A among the human viral pathogens. The 15 ARG types contained 611 ARG subtypes, including those resistant to beta-lactam, which was the most diverse and abundant group (206 subtypes; 17.0 %-27.5 %), aminoglycoside (94 subtypes; 9.6 %-15.3 %), tetracycline (80 subtypes; 15.6 %-20.2 %), and macrolide (79 subtypes; 14.5 %-32.1 %). Interestingly, the abundance of ARGs associated with resistance to beta-lactam, trimethoprim, and sulphonamide, as well as A. butzleri and crAssphage, at the cultural sites was significantly different from the other sites (p < 0.05). We demonstrated the benefits of using NGS to deliver insights into microbial communities, and antimicrobial resistance, both of which pose a risk to human health. Using NGS may facilitate microbial risk mitigation and management for urban water commuters and proximal residents.}, } @article {pmid35905873, year = {2022}, author = {Ebrahimian, F and De Bernardini, N and Tsapekos, P and Treu, L and Zhu, X and Campanaro, S and Karimi, K and Angelidaki, I}, title = {Effect of pressure on biomethanation process and spatial stratification of microbial communities in trickle bed reactors under decreasing gas retention time.}, journal = {Bioresource technology}, volume = {361}, number = {}, pages = {127701}, doi = {10.1016/j.biortech.2022.127701}, pmid = {35905873}, issn = {1873-2976}, mesh = {Biofuels ; Bioreactors ; *Euryarchaeota ; Hydrogen ; Methane ; *Microbiota/genetics ; }, abstract = {The current study investigated the effect of elevating gas pressure on biomethanation in trickle-bed reactors (TBRs). The increased pressure led to successful biomethanation (CH4 > 90 %) at a gas retention time (GRT) of 21 min, due to the improved transfer rates of H2 and CO2. On the contrary, the non-pressurized TBR performance was reduced at GRTs shorter than 40 min. Metagenomic analysis revealed that the microbial populations collected from the lower and middle parts of the reactor under the same GRT were more homogeneous compared with those developed in the upper layer. Comparison with previous experiments suggest that microbial stratification is mainly driven by the nutrient provision strategy. Methanobacterium species was the most dominant methanogen and it was mainly associated with the bottom and middle parts of TBRs. Overall, the increased pressure did not affect markedly the microbial composition, while the GRT was the most important parameter shaping the microbiomes.}, } @article {pmid35905860, year = {2023}, author = {Qiu, B and Xi, Y and Liu, F and Li, Y and Xie, X and Guo, J and Guo, S and Wu, Y and Wu, L and Liang, T and Ding, Y and Zhang, J and Wu, Q and Liu, H}, title = {Gut Microbiome Is Associated With the Response to Chemoradiotherapy in Patients With Non-small Cell Lung Cancer.}, journal = {International journal of radiation oncology, biology, physics}, volume = {115}, number = {2}, pages = {407-418}, doi = {10.1016/j.ijrobp.2022.07.032}, pmid = {35905860}, issn = {1879-355X}, mesh = {Humans ; *Carcinoma, Non-Small-Cell Lung ; Chemoradiotherapy ; Fatty Acids ; *Gastrointestinal Microbiome ; *Lung Neoplasms ; RNA, Ribosomal, 16S ; }, abstract = {PURPOSE: To explore the dynamic change of gut microbiota and its predictive role in progression-free survival (PFS) in non-small cell lung cancer (NSCLC) after concurrent chemoradiotherapy (CCRT).

METHODS AND MATERIALS: Forty-one patients with NSCLC in 2 phase 2 trials (NCT02573506 and NCT03006575) were analyzed. A total of 102 fecal samples were collected at 3 time points (T0, before CCRT; T1, 2 weeks after the initiation of CCRT; and T2, the end of CCRT). Gut microbiota composition and functionality were analyzed by 16S rRNA gene sequencing and shotgun metagenomics, respectively. Alpha diversity, taxonomic composition, and KEGG functional pathways were compared between patients in the long-PFS group (PFS ≥11.0 months) and short-PFS group (PFS <11.0 months). A random forest classifier was constructed to identify microbial signature related to PFS. Clinical and microbial factors potentially predictive of PFS were assessed in the univariate and multivariate Cox regression analysis.

RESULTS: The abundance of Bacteroidota and Proteobacteria increased, while the abundance of Firmicutes decreased after CCRT. Shannon index (P = .006) and PD index (P = .022) were significantly higher in the long-PFS group than for those in the short-PFS group at T1. The PFS-prediction microbial signature at T1 included unclassified members of the Lanchospiraceae spp., such as NK4A136 and UCG-003 groups, Dorea sp., various strains from within the Eubacterium hallii and E. siraeum groups, and an unclassified member of the Muribaculaceae, which yielded an area under the ROC curve of 0.87. These discriminatory genera mostly belong to phylum Firmicutes/family Clostridia. Multivariate analysis indicated PD index (HR = 8.036, P = .016) and the abundance of Dorea sp. at T1 (HR = 4.186, P = .043) were independent predictors of PFS. The KEGG pathways at T1 overrepresented in the long-PFS group included fatty acid metabolism, fatty acid biosynthesis, and arginine biosynthesis. Those overrepresented in the short-PFS group included lipopolysaccharide biosynthesis, ascorbate and aldarate metabolism, and biosynthesis of vancomycin group antibiotics.

CONCLUSIONS: Gut microbiota composition and functionality at 2 weeks after the initiation of CCRT were associated with PFS in NSCLC. Further research is needed to confirm these results.}, } @article {pmid35904740, year = {2023}, author = {Srivastava, A and Verma, D}, title = {Ganga River sediments of India predominate with aerobic and chemo-heterotrophic bacteria majorly engaged in the degradation of xenobiotic compounds.}, journal = {Environmental science and pollution research international}, volume = {30}, number = {1}, pages = {752-772}, doi = {10.1007/s11356-022-22198-3}, pmid = {35904740}, issn = {1614-7499}, mesh = {Humans ; *Rivers/microbiology ; *Xenobiotics ; Geologic Sediments/analysis ; Water/analysis ; Bacteria/genetics ; India ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Sediment provides a stagnant habitat to microbes that accumulate organic matter and other industrial pollutants from the upper layer of the water. The sediment of the Ganga River of India is overlooked for exploring the bacterial diversity despite their taxon richness over the water counterpart. To enrich the limited information on the bacterial diversity of the Ganga River sediment, the present study was planned that relies on amplicon-based bacterial diversity of the Ganga River sediment by using bacterial-specific 16S hypervariable region (V3-V4). The Illumina MiSeq2500 platform generated 1,769,226 raw reads from the metagenomes of various samples obtained from ten sites in five major cities of Uttar Pradesh and Uttarakhand regions traversing the Ganga River. Taxonomy level analysis assigned 58 phyla, 366 order, and 715 genera of bacterial type. The high values of various diversity indices (Chao1, Shannon, and Simpson) in Kanpur sediment indicate the high bacterial richness compared to the Rishikesh sediment. However, several other ecological parameters (Shannon index, Simpson index, enspie _vector, and Faith_pd) were comparatively higher in Rishikesh sediment which is a comparatively less disturbed region by human activities over the other sediments samples studied here. Ganga River sediment dominates with Gram-negative, chemo-heterotrophic, and aerobic bacteria that chiefly belong to Proteobacteria, Acidobacteria, Chloroflexi, and Bacteroidota. The abundance of Nitrospira, Hydrogenophaga, Thauera, Vicinamibacteraceae, and Latescibacterota in the Ganga River sediment could be considered as the ecological indicators that find a significant role in the degradation of xenobiotic compounds. The PICRUSt-based analysis showed that ~ 35% of genes were involved in benzoate and aminobenzoate degradation where a significant portion of genes belong to nitrotoluene degradation (14%). Thus, the study uncovers a new perspective in the lineage of bacterial communities and their functional characterization of the Ganga River sediment.}, } @article {pmid35903270, year = {2022}, author = {Liu, D and Zhang, Y and Wu, L and Guo, J and Yu, X and Yao, H and Han, R and Ma, T and Zheng, Y and Gao, Q and Fang, Q and Zhao, Y and Zhao, Y and Sun, B and Jia, W and Li, H}, title = {Effects of Exercise Intervention on Type 2 Diabetes Patients With Abdominal Obesity and Low Thigh Circumference (EXTEND): Study Protocol for a Randomized Controlled Trial.}, journal = {Frontiers in endocrinology}, volume = {13}, number = {}, pages = {937264}, pmid = {35903270}, issn = {1664-2392}, mesh = {Blood Glucose/metabolism ; Body Weight ; *Diabetes Mellitus, Type 2/complications/therapy ; Humans ; Obesity ; Obesity, Abdominal ; Randomized Controlled Trials as Topic ; *Resistance Training ; Thigh ; }, abstract = {INTRODUCTION: Type 2 diabetes patients have abdominal obesity and low thigh circumference. Previous studies have mainly focused on the role of exercise in reducing body weight and fat mass, improving glucose and lipid metabolism, with a lack of evaluation on the loss of muscle mass, diabetes complications, energy metabolism, and brain health. Moreover, whether the potential physiological benefit of exercise for diabetes mellitus is related to the modulation of the microbiota-gut-brain axis remains unclear. Multi-omics approaches and multidimensional evaluations may help systematically and comprehensively correlate physical exercise and the metabolic benefits.

METHODS AND ANALYSIS: This study is a randomized controlled clinical trial. A total of 100 sedentary patients with type 2 diabetes will be allocated to either an exercise or a control group in a 1:1 ratio. Participants in the exercise group will receive a 16-week combined aerobic and resistance exercise training, while those in the control group will maintain their sedentary lifestyle unchanged. Additionally, all participants will receive a diet administration to control the confounding effects of diet. The primary outcome will be the change in body fat mass measured using bioelectrical impedance analysis. The secondary outcomes will include body fat mass change rate (%), and changes in anthropometric indicators (body weight, waist, hip, and thigh circumference), clinical biochemical indicators (glycated hemoglobin, blood glucose, insulin sensitivity, blood lipid, liver enzyme, and renal function), brain health (appetite, mood, and cognitive function), immunologic function, metagenomics, metabolomics, energy expenditure, cardiopulmonary fitness, exercise-related indicators, fatty liver, cytokines (fibroblast growth factor 21, fibroblast growth factor 19, adiponectin, fatty acid-binding protein 4, and lipocalin 2), vascular endothelial function, autonomic nervous function, and glucose fluctuation.

DISCUSSION: This study will evaluate the effect of a 16-week combined aerobic and resistance exercise regimen on patients with diabetes. The results will provide a comprehensive evaluation of the physiological effects of exercise, and reveal the role of the microbiota-gut-brain axis in exercise-induced metabolic benefits to diabetes.

CLINICAL TRIAL REGISTRATION: http://www.chictr.org.cn/searchproj.aspx, identifier ChiCTR2100046148.}, } @article {pmid35902819, year = {2022}, author = {Fu, M and Cao, LJ and Xia, HL and Ji, ZM and Hu, NN and Leng, ZJ and Xie, W and Fang, Y and Zhang, JQ and Xia, DQ}, title = {The performance of detecting Mycobacterium tuberculosis complex in lung biopsy tissue by metagenomic next-generation sequencing.}, journal = {BMC pulmonary medicine}, volume = {22}, number = {1}, pages = {288}, pmid = {35902819}, issn = {1471-2466}, mesh = {Biopsy ; *Communicable Diseases ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Lung/microbiology ; *Mycobacterium tuberculosis/genetics ; Sensitivity and Specificity ; *Tuberculosis/diagnosis ; }, abstract = {BACKGROUND: Tuberculosis (TB) is a chronic infectious disease caused by the Mycobacterium tuberculosis complex (MTBC), which is the leading cause of death from infectious diseases. The rapid and accurate microbiological detection of the MTBC is crucial for the diagnosis and treatment of TB. Metagenomic next-generation sequencing (mNGS) has been shown to be a promising and satisfying application of detection in infectious diseases. However, relevant research about the difference in MTBC detection by mNGS between bronchoalveolar lavage fluid (BALF) and lung biopsy tissue specimens remains scarce.

METHODS: We used mNGS to detect pathogens in BALF and lung biopsy tissue obtained by CT-guide percutaneous lung puncture (CPLP) or radial endobronchial ultrasound transbronchial lung biopsy (R-EBUS-TBLB) from 443 hospitalized patients in mainland China suspected of pulmonary infections between May 1, 2019 and October 31, 2021. Aim to evaluate the diagnostic performance of mNGS for detecting MTBC and explore differences in the microbial composition in the 2 specimen types.

RESULTS: Among the 443 patients, 46 patients finally were diagnosed with TB, of which 36 patients were detected as MTBC positive by mNGS (8.93%). Striking differences were noticed in the higher detection efficiency of lung biopsy tissue compared with BALF (P = 0.004). There were no significant differences between the 2 specimen types in the relative abundance among the 27 pathogens detected by mNGS from the 36 patients.

CONCLUSIONS: This study demonstrates that mNGS could offer an effective detection method of MTBC in BALF or lung tissue biopsy samples in patients suspected of TB infections. When it comes to the situations that BALF samples have limited value to catch pathogens for special lesion sites or the patients have contraindications to bronchoalveolar lavage (BAL) procedures, lung biopsy tissue is an optional specimen for MTBC detection by mNGS. However, whether lung tissue-mNGS is superior to BALF-mNGS in patients with MTBC infection requires further prospective multicenter randomized controlled studies with more cases.}, } @article {pmid35902763, year = {2022}, author = {Schulz, F and Abergel, C and Woyke, T}, title = {Giant virus biology and diversity in the era of genome-resolved metagenomics.}, journal = {Nature reviews. Microbiology}, volume = {20}, number = {12}, pages = {721-736}, pmid = {35902763}, issn = {1740-1534}, mesh = {*Giant Viruses/genetics ; Genome, Viral ; Metagenomics ; Eukaryota/genetics ; *Viruses/genetics ; Phylogeny ; }, abstract = {The discovery of giant viruses, with capsids as large as some bacteria, megabase-range genomes and a variety of traits typically found only in cellular organisms, was one of the most remarkable breakthroughs in biology. Until recently, most of our knowledge of giant viruses came from ~100 species-level isolates for which genome sequences were available. However, these isolates were primarily derived from laboratory-based co-cultivation with few cultured protists and algae and, thus, did not reflect the true diversity of giant viruses. Although virus co-cultures enabled valuable insights into giant virus biology, many questions regarding their origin, evolution and ecological importance remain unanswered. With advances in sequencing technologies and bioinformatics, our understanding of giant viruses has drastically expanded. In this Review, we summarize our understanding of giant virus diversity and biology based on viral isolates as laboratory cultivation has enabled extensive insights into viral morphology and infection strategies. We then explore how cultivation-independent approaches have heightened our understanding of the coding potential and diversity of the Nucleocytoviricota. We discuss how metagenomics has revolutionized our perspective of giant viruses by revealing their distribution across our planet's biomes, where they impact the biology and ecology of a wide range of eukaryotic hosts and ultimately affect global nutrient cycles.}, } @article {pmid35902439, year = {2022}, author = {Li, G and Jiang, Y and Li, Q and An, D and Bao, M and Lang, L and Han, L and Huang, X and Jiang, C}, title = {Comparative and functional analyses of fecal microbiome in Asian elephants.}, journal = {Antonie van Leeuwenhoek}, volume = {115}, number = {9}, pages = {1187-1202}, pmid = {35902439}, issn = {1572-9699}, support = {31270001//National Natural Science Foundation of China/ ; 31460005//National Natural Science Foundation of China/ ; }, mesh = {Animals ; Bacteroidetes/genetics ; *Elephants/genetics/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; *Microbiota ; }, abstract = {Asian elephant is large herbivorous animal with elongated hindgut. To explore fecal microbial community composition with various ages, sex and diets, and their role in plant biomass degrading and nutrition conversation. We generated 119 Gb by metagenome sequencing from 10 different individual feces and identified 5.3 million non-redundant genes. The comprehensive analysis established that the Bacteroidetes, Firmicutes and Proteobacteria constituted the most dominant phyla in overall fecal samples. In different individuals, the alpha diversity of the fecal microbiota in female was lower than male, and the alpha diversity of the fecal microbiota in older was higher than younger, and the fecal microbial diversity was the most complex in wild elephant. But the predominant population compositions were similar to each other. Moreover, the newborn infant elephant feces assembled and maintained a diverse but host-specific fecal microbial population. The discovery speculated that Asian elephant maybe have start to building microbial populations before birth. Meanwhile, these results illustrated that host phylogeny, diets, ages and sex are significant factors for fecal microbial community composition. Therefore, we put forward the process of Asian elephant fecal microbial community composition that the dominant populations were built first under the guidance of phylogeny, and then shaped gradually a unique and flexible gut microbial community structure under the influences of diet, age and sex. This study found also that the Bacteroidetes were presumably the main drivers of plant fiber-degradation. A large of secondary metabolite biosynthetic gene clusters, and genes related to enediyne biosynthesis were found and showed that the Asian elephant fecal microbiome harbored a diverse and abundant genetic resource. A picture of antibiotic resistance genes (ARGs) reservoirs of fecal microbiota in Asian elephants was provided. Surprisingly, there was such wide range of ARGs in newborn infant elephant. Further strengthening our speculation that the fetus of Asian elephant has colonized prototypical fecal microbiota before birth. However, it is necessary to point out that the data give a first inside into the gut microbiota of Asian elephants but too few individuals were studied to draw general conclusions for differences among wild and captured elephants, female and male or different ages. Further studies are required. Additionally, the cultured actinomycetes from Asian elephant feces also were investigated, which the feces of Asian elephants could be an important source of actinomycetes.}, } @article {pmid35901877, year = {2022}, author = {Yang, CX and He, ZW and Liu, WZ and Wang, AJ and Wang, L and Liu, J and Liu, BL and Ren, NQ and Yu, SP and Guo, ZC}, title = {Chronic effects of benzalkonium chlorides on short chain fatty acids and methane production in semi-continuous anaerobic digestion of waste activated sludge.}, journal = {The Science of the total environment}, volume = {847}, number = {}, pages = {157619}, doi = {10.1016/j.scitotenv.2022.157619}, pmid = {35901877}, issn = {1879-1026}, mesh = {Acetyl Coenzyme A/metabolism ; Acetyl-CoA C-Acetyltransferase/metabolism ; Anaerobiosis ; Benzalkonium Compounds ; Bioreactors/microbiology ; *Environmental Pollutants ; Fatty Acids, Volatile/metabolism ; Fermentation ; Ligases/metabolism ; Methane ; Phosphate Acetyltransferase/metabolism ; Propionates ; *Sewage/microbiology ; }, abstract = {As an emerging pollutant, benzalkonium chlorides (BACs) potentially enriched in waste activated sludge (WAS). However, the microbial response mechanism under chronic effects of BACs on acidogenesis and methanogenesis in anaerobic digestion (AD) has not been clearly disclosed. This study investigated the AD (by-)products and microbial evolution under low to high BACs concentrations from bioreactor startup to steady running. It was found that BACs can lead to an increase of WAS hydrolysis and fermentation, but a disturbance to acidogenic bacteria also occurred at low BACs concentration. A noticeable inhibition to methanogenesis occurred when BAC concentration was up to 15 mg/g TSS. Metagenomic analysis revealed the key genes involved in acetic acid (HAc) biosynthesis (i.e. phosphate acetyltransferase, PTA), β-oxidation pathway (acetyl-CoA C-acetyltransferase) and propionic acid (HPr) conversion was slightly promoted compared with control. Furthermore, BACs inhibited the acetotrophic methanogenesis (i.e. acetyl-CoA synthetase), especially BAC concentration was up to 15 mg/g TSS, thereby enhanced short chain fatty acids (SCFAs) accumulation. Overall, chronic stimulation of functional microorganisms with increasing concentrations of BACs impact WAS fermentation.}, } @article {pmid35901372, year = {2023}, author = {Frankot, MA and O'Hearn, CM and Blancke, AM and Rodriguez, B and Pechacek, KM and Gandhi, J and Hu, G and Martens, KM and Vonder Haar, C}, title = {Acute gut microbiome changes after traumatic brain injury are associated with chronic deficits in decision-making and impulsivity in male rats.}, journal = {Behavioral neuroscience}, volume = {137}, number = {1}, pages = {15-28}, pmid = {35901372}, issn = {1939-0084}, support = {U54 GM104942/GM/NIGMS NIH HHS/United States ; P20 GM121322/GM/NIGMS NIH HHS/United States ; R01 NS110905/NS/NINDS NIH HHS/United States ; P20 GM103434/GM/NIGMS NIH HHS/United States ; }, mesh = {Rats ; Male ; Animals ; *Gastrointestinal Microbiome ; Rats, Long-Evans ; *Brain Injuries, Traumatic/complications/microbiology ; Impulsive Behavior ; *Gambling ; }, abstract = {The mechanisms underlying chronic psychiatric-like impairments after traumatic brain injury (TBI) are currently unknown. The goal of the present study was to assess the role of diet and the gut microbiome in psychiatric symptoms after TBI. Rats were randomly assigned to receive a high-fat diet (HFD) or calorie-matched low-fat diet (LFD). After 2 weeks of free access, rats began training on the rodent gambling task (RGT), a measure of risky decision-making and motor impulsivity. After training, rats received a bilateral frontal TBI or a sham procedure and continued postinjury testing for 10 weeks. Fecal samples were collected before injury and 3-, 30-, and 60 days postinjury to evaluate the gut microbiome. HFD altered the microbiome, but ultimately had low-magnitude effects on behavior and did not modify functional outcomes after TBI. Injury-induced functional deficits were far more robust; TBI substantially decreased optimal choice and increased suboptimal choice and motor impulsivity on the RGT. TBI also affected the microbiome, and a model comparison approach revealed that bacterial diversity measured 3 days postinjury was predictive of chronic psychiatric-like deficits on the RGT. A functional metagenomic analysis identified changes to dopamine and serotonin synthesis pathways as a potential candidate mechanism. Thus, the gut may be a potential acute treatment target for psychiatric symptoms after TBI, as well as a biomarker for injury and deficit severity. However, further research will be needed to confirm and extend these findings. (PsycInfo Database Record (c) 2023 APA, all rights reserved).}, } @article {pmid35900091, year = {2022}, author = {Hansen, AK and Sanchez, AN and Kwak, Y}, title = {Divergent Host-Microbe Interaction and Pathogenesis Proteins Detected in Recently Identified Liberibacter Species.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0209122}, pmid = {35900091}, issn = {2165-0497}, mesh = {Fimbriae, Bacterial ; Host Microbial Interactions ; *Liberibacter ; Plant Diseases/microbiology ; Plants ; *Rhizobiaceae/genetics ; Sequence Analysis, DNA ; }, abstract = {Candidatus (Ca.) Liberibacter taxa are economically important bacterial plant pathogens that are not culturable; however, genome-enabled insights can help us develop a deeper understanding of their host-microbe interactions and evolution. The draft genome of a recently identified Liberibacter taxa, Ca. Liberibacter capsica, was curated and annotated here with a total draft genome size of 1.1 MB with 1,036 proteins, which is comparable to other Liberibacter species with complete genomes. A total of 459 orthologous clusters were identified among Ca. L. capsica, Ca. L. asiaticus, Ca. L. psyllaurous, Ca. L. americanus, Ca. L. africanus, and L. crescens, and these genes within these clusters consisted of housekeeping and environmental response functions. We estimated the rates of molecular evolution for each of the 443 one-to-one ortholog clusters and found that all Ca. L. capsica orthologous pairs were under purifying selection when the synonymous substitutions per synonymous site (dS) were not saturated. These results suggest that these genes are largely maintaining their conserved functions. We also identified the most divergent single-copy orthologous proteins in Ca. L. capsica by analyzing the ortholog pairs that represented the highest nonsynonymous substitutions per nonsynonymous site (dN) values for each pairwise comparison. From these analyses, we found that 21 proteins which are known to be involved in pathogenesis and host-microbe interactions, including the Tad pilus complex, were consistently divergent between Ca. L. capsica and the majority of other Liberibacter species. These results further our understanding of the evolutionary genetics of Ca. L. capsica and, more broadly, the evolution of Liberibacter. IMPORTANCE "Candidatus" (Ca.) Liberibacter taxa are economically important plant pathogens vectored by insects; however, these host-dependent bacterial taxa are extremely difficult to study because they are unculturable. Recently, we identified a new Ca. Liberibacter lineage (Ca. Liberibacter capsica) from a rare insect metagenomic sample. In this current study, we report that the draft genome of Ca. Liberibacter capsica is similar in genome size and protein content compared to the other Ca. Liberibacter taxa. We provide evidence that many of their shared genes, which encode housekeeping and environmental response functions, are evolving under purifying selection, suggesting that these genes are maintaining similar functions. Our study also identifies 21 proteins that are rapidly evolving amino acid changes in Ca. Liberibacter capsica compared to the majority of other Liberibacter taxa. Many of these proteins represent key genes involved in Liberibacter-host interactions and pathogenesis and are valuable candidate genes for future studies.}, } @article {pmid35899913, year = {2022}, author = {Wang, Y and Deng, T and Wang, Y and Xin, X and Wen, Y}, title = {Splenic infarction due to Mycobacterium avium complex infection in an HIV-infected patient with immune reconstitution failure: a case report.}, journal = {The Journal of international medical research}, volume = {50}, number = {7}, pages = {3000605221115242}, pmid = {35899913}, issn = {1473-2300}, mesh = {*HIV Infections/complications/drug therapy ; Humans ; *Immune Reconstitution ; Male ; Mycobacterium avium Complex ; *Mycobacterium avium-intracellulare Infection/complications/microbiology ; *Splenic Infarction/complications/diagnostic imaging ; }, abstract = {Splenic infarction is extremely rare in human immunodeficiency virus-infected populations. We report a rare case of splenic infarction involving Mycobacterium avium complex infection in a patient with acquired immune deficiency syndrome with immune reconstitution failure. A young man was initially admitted with cryptococcus meningitis and found to be infected with human immunodeficiency virus. He had anti-cryptococcosis treatment performed in combination with placement of an Ommaya capsule because of persistent intracranial hypertension, and first-line therapy followed by second-line anti-retroviral therapy were performed. Although there was an absence of immune reconstitution, the patient refused to take prophylactic sulfamethoxazole/trimethoprim, isoniazid, and clarithromycin continuously because of gastrointestinal intolerance. Pneumocystis pneumonia then developed. Finally, the patient developed a fever again accompanied by abdominal pain and splenic infarction. M. avium complex infection was verified by a metagenomic next-generation sequencing test using a whole blood sample. M. avium complex infection should be considered as an etiology of splenic infarction in human immunodeficiency virus-infected patients with an extremely low CD4[+]T-cell count.}, } @article {pmid35899170, year = {2022}, author = {Zhou, H and Yang, H and Gong, F and Zhou, S and Yang, Y and Liu, H and Liu, J}, title = {Case Report: Mycobacterium senegalense Infection After Cholecystectomy.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {899846}, pmid = {35899170}, issn = {2296-2565}, mesh = {China ; Cholecystectomy/adverse effects ; Humans ; Male ; Middle Aged ; Mycobacteriaceae ; *Mycobacterium/genetics ; }, abstract = {BACKGROUND: Mycobacterium senegalense is a non-tuberculous mycobacterium and is found everywhere in the environment. However, M. senegalense infection in human is extremely rare, especially in immunocompetent individuals. It is difficult to detect M. senegalense infection because its symptoms are non-specific, and routine diagnostic tests are less sensitive. It is also resistant to commonly used antibiotics. Here, we report the first case of M. senegalense infection after laparoscopic cholecystectomy in China.

CASE PRESENTATION: A 55-year-old man was admitted because of repeated infections at multiple incision sites for more than 1 year. Although routine diagnostic test results were negative, metagenomic next-generation sequencing (mNGS) identified DNA sequences of M. senegalense in tissue samples from incision sites. The presence of M. senegalense was further confirmed by polymerase chain reaction and capillary electrophoresis. After 60 days of quadruple therapy with clarithromycin, moxifloxacin, rifampicin, and oxycycline, the patient's wound healed.

CONCLUSION: We believe the case findings contribute to the limited amount of knowledge about M. senegalense infection and raises awareness that this infection can result in poor wound healing, even in an immunocompetent host. Owing to a lack of early, precise diagnosis, it is difficult to treat M. senegalense infections. Based on our findings, mNGS is a sensitive diagnostic test for M. senegalense infections.}, } @article {pmid35899152, year = {2022}, author = {Tian, X and Duan, W and Zhang, X and Wu, X and Zhang, C and Wang, Z and Cao, G and Gu, Y and Shao, F and Yan, T}, title = {Metagenomic Next-Generation Sequencing Reveals the Profile of Viral Infections in Kidney Transplant Recipients During the COVID-19 Pandemic.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {888064}, pmid = {35899152}, issn = {2296-2565}, mesh = {Animals ; *COVID-19/diagnosis/epidemiology ; *Cytomegalovirus Infections ; DNA, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; *Kidney Transplantation ; Pandemics ; *Torque teno virus/genetics ; *Virus Diseases ; }, abstract = {BACKGROUND: To study the clinical application of metagenomic next-generation sequencing (mNGS) in the detection of viral infections in kidney transplant recipients (KTRs) during the COVID-19 pandemic.

METHODS: Using mNGS technology, 50 human fluid samples of KTRs were detected, including 20 bronchoalveolar lavage fluid (BALF) samples, 21 urine samples and 9 blood samples. The detected nucleic acid sequences were compared and analyzed with the existing viral nucleic acid sequences in the database, and the virus infection spectrum of KTRs was drawn.

RESULTS: The viral nucleic acids of 15 types of viruses were detected in 96.00% (48/50) of the samples, of which 11 types of viruses were in BALF (95.00%, 19/20), and the dominant viruses were torque teno virus (TTV) (65.00%; 13/20), cytomegalovirus (CMV) (45.00%; 9/20) and human alphaherpesvirus 1 (25.00%; 5/20). 12 viruses (95.24%, 20/21) were detected in the urine, and the dominant viruses were TTV (52.38%; 11/21), JC polyomavirus (52.38%; 11/21), BK polyomavirus (42.86%; 9/21), CMV (33.33%; 7/21) and human betaherpesvirus 6B (28.57%; 6/21). 7 viruses were detected in the blood (100.00%, 9/9), and the dominant virus was TTV (100.00%; 9/9). Four rare viruses were detected in BALF and urine, including WU polyomavirus, primate bocaparvovirus 1, simian virus 12, and volepox virus. Further analysis showed that TTV infection with high reads indicated a higher risk of acute rejection (P < 0.05).

CONCLUSIONS: mNGS detection reveals the rich virus spectrum of infected KTRs, and improves the detection rate of rare viruses. TTV may be a new biomarker for predicting rejection.}, } @article {pmid35899118, year = {2022}, author = {Zheng, Y and Zhou, X and Wang, C and Zhang, J and Chang, D and Liu, W and Zhu, M and Zhuang, S and Shi, H and Wang, X and Chen, Y and Cheng, Z and Lin, Y and Nan, L and Sun, Y and Min, L and Liu, J and Chen, J and Zhang, J and Huang, M}, title = {Effect of Tanshinone IIA on Gut Microbiome in Diabetes-Induced Cognitive Impairment.}, journal = {Frontiers in pharmacology}, volume = {13}, number = {}, pages = {890444}, pmid = {35899118}, issn = {1663-9812}, abstract = {Diabetes-induced cognitive impairment (DCI) presents a major public health risk among the aging population. Previous clinical attempts on known therapeutic targets for DCI, such as depleted insulin secretion, insulin resistance, and hyperglycaemia have delivered poor patient outcomes. However, recent evidence has demonstrated that the gut microbiome plays an important role in DCI by modulating cognitive function through the gut-brain crosstalk. The bioactive compound tanshinone IIA (TAN) has shown to improve cognitive and memory function in diabetes mellitus models, though the pharmacological actions are not fully understood. This study aims to investigate the effect and underlying mechanism of TAN in attenuating DCI in relation to regulating the gut microbiome. Metagenomic sequencing analyses were performed on a group of control rats, rats with diabetes induced by a high-fat/high-glucose diet (HFD) and streptozotocin (STZ) (model group) and TAN-treated diabetic rats (TAN group). Cognitive and memory function were assessed by the Morris water maze test, histopathological assessment of brain tissues, and immunoblotting of neurological biomarkers. The fasting blood glucose (FBG) level was monitored throughout the experiments. The levels of serum lipopolysaccharide (LPS) and tumor necrosis factor-α (TNF-α) were measured by enzyme-linked immunoassays to reflect the circulatory inflammation level. The morphology of the colon barrier was observed by histopathological staining. Our study confirmed that TAN reduced the FBG level and improved the cognitive and memory function against HFD- and STZ-induced diabetes. TAN protected the endothelial tight junction in the hippocampus and colon, regulated neuronal biomarkers, and lowered the serum levels of LPS and TNF-α. TAN corrected the reduced abundance of Bacteroidetes in diabetic rats. At the species level, TAN regulated the abundance of B. dorei, Lachnoclostridium sp. YL32 and Clostridiodes difficile. TAN modulated the lipid metabolism and biosynthesis of fatty acids in related pathways as the main functional components. TAN significantly restored the reduced levels of isobutyric acid and butyric acid. Our results supported the use of TAN as a promising therapeutic agent for DCI, in which the underlying mechanism may be associated with gut microbiome regulation.}, } @article {pmid35899082, year = {2022}, author = {Tian, X and Jing, N and Duan, W and Wu, X and Zhang, C and Wang, S and Yan, T}, title = {Septic Shock After Kidney Transplant: A Rare Bloodstream Ralstonia mannitolilytica Infection.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {3841-3845}, pmid = {35899082}, issn = {1178-6973}, abstract = {BACKGROUND: Ralstonia mannitolilytica, an emerging opportunistic pathogen, can infect immunocompromised patients but is a rare cause of severe sepsis and septic shock in kidney transplant recipients (KTRs).

CASE PRESENTATION: We present a case of septic shock after renal transplant in a 41-year-old male, which was finally proven to be caused by Ralstonia mannitolilytica through blood cultures and mass spectrometric analysis following the negative result of metagenomic next-generation sequencing (mNGS). He was finally cured after the application of sensitive antibiotics (sulfamethoxazole-trimethoprim, amikacin and piperacillin-tazobactam) based on the drug sensitivity test results. The patient had a satisfactory recovery with no complications during a 6-month follow-up period.

CONCLUSION: This study highlights that Ralstonia mannitolilytica is an easily overlooked cause of septic shock in KTRs requiring a detailed inquiry of medical history with inflammatory markers monitored closely. Traditional blood cultures still should be taken seriously. It also provides a cautionary tale that negative results of mNGS have to be interpreted with caution.}, } @article {pmid35899079, year = {2022}, author = {Van Camp, PJ and Porollo, A}, title = {SEQ2MGS: an effective tool for generating realistic artificial metagenomes from the existing sequencing data.}, journal = {NAR genomics and bioinformatics}, volume = {4}, number = {3}, pages = {lqac050}, pmid = {35899079}, issn = {2631-9268}, abstract = {Assessment of bioinformatics tools for the metagenomics analysis from the whole genome sequencing data requires realistic benchmark sets. We developed an effective and simple generator of artificial metagenomes from real sequencing experiments. The tool (SEQ2MGS) analyzes the input FASTQ files, precomputes genomic content, and blends shotgun reads from different sequenced isolates, or spike isolate(s) in real metagenome, in desired proportions. SEQ2MGS eliminates the need for simulation of sequencing platform variations, reads distributions, presence of plasmids, viruses, and contamination. The tool is especially useful for a quick generation of multiple complex samples that include new or understudied organisms, even without assembled genomes. For illustration, we first demonstrated the ease of SEQ2MGS use for the simulation of altered Schaedler flora (ASF) in comparison with de novo metagenomics generators Grinder and CAMISIM. Next, we emulated the emergence of a pathogen in the human gut microbiome and observed that Kraken, Centrifuge, and MetaPhlAn, while correctly identified Klebsiella pneumoniae, produced inconsistent results for the rest of real metagenome. Finally, using the MG-RAST platform, we affirmed that SEQ2MGS properly transfers genomic information from an isolate into the simulated metagenome by the correct identification of antimicrobial resistance genes anticipated to appear compared to the original metagenome.}, } @article {pmid35898900, year = {2022}, author = {Vermote, L and Verce, M and Mozzi, F and De Vuyst, L and Weckx, S}, title = {Microbiomes Associated With the Surfaces of Northern Argentinian Fruits Show a Wide Species Diversity.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {872281}, pmid = {35898900}, issn = {1664-302X}, abstract = {The fiber, vitamin, and antioxidant contents of fruits contribute to a balanced human diet. In countries such as Argentina, several tropical fruits are witnessing a high yield in the harvest season, with a resulting surplus. Fruit fermentation using autochthonous starter cultures can provide a solution for food waste. However, limited knowledge exists about the microbiota present on the surfaces of fruits and the preceding flowers. In the present exploratory study, the microbiomes associated with the surfaces of tropical fruits from Northern Argentina, such as white guava, passion fruit and papaya were investigated using a shotgun metagenomic sequencing approach. Hereto, one sample composed of 14 white guava fruits, two samples of passion fruits with each two to three fruits representing the almost ripe and ripe stage of maturity, four samples of papaya with each two to three fruits representing the unripe, almost ripe, and ripe stage of maturity were processed, as well as a sample of closed and a sample of open Japanese medlar flowers. A considerable heterogeneity was found in the composition of the fruits' surface microbiota at the genus and species level. While bacteria dominated the microbiota of the fruits and flowers, a small number of the metagenomic sequence reads corresponded with yeasts and filamentous fungi. A minimal abundance of bacterial species critical in lactic acid and acetic acid fermentations was found. A considerable fraction of the metagenomic sequence reads from the fruits' surface microbiomes remained unidentified, which suggested that intrinsic species are to be sequenced or discovered.}, } @article {pmid35897801, year = {2022}, author = {Tian, Y and Rimal, B and Gui, W and Koo, I and Yokoyama, S and Perdew, GH and Patterson, AD}, title = {Early Life Short-Term Exposure to Polychlorinated Biphenyl 126 in Mice Leads to Metabolic Dysfunction and Microbiota Changes in Adulthood.}, journal = {International journal of molecular sciences}, volume = {23}, number = {15}, pages = {}, pmid = {35897801}, issn = {1422-0067}, support = {R01 ES028288 (ADP) and R35 ES028244 (GHP)//National Institutes of Health Grants/ ; Project PEN047702 and Accession number 1009993//USDA National Institute of Food and Federal Appropriations/ ; R35 ES028244/ES/NIEHS NIH HHS/United States ; R01 ES028288/ES/NIEHS NIH HHS/United States ; S10 OD021750/OD/NIH HHS/United States ; }, mesh = {Animals ; *Environmental Pollutants/toxicity ; *Gastrointestinal Microbiome/genetics ; Mice ; *Microbiota ; *Polychlorinated Biphenyls/toxicity ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {Early life exposure to environmental pollutants may have long-term consequences and harmful impacts on health later in life. Here, we investigated the short- and long-term impact of early life 3,3',4,4',5-pentacholorobiphenyl (PCB 126) exposure (24 μg/kg body weight for five days) in mice on the host and gut microbiota using 16S rRNA gene sequencing, metagenomics, and [1]H NMR- and mass spectrometry-based metabolomics. Induction of Cyp1a1, an aryl hydrocarbon receptor (AHR)-responsive gene, was observed at 6 days and 13 weeks after PCB 126 exposure consistent with the long half-life of PCB 126. Early life, Short-Term PCB 126 exposure resulted in metabolic abnormalities in adulthood including changes in liver amino acid and nucleotide metabolism as well as bile acid metabolism and increased hepatic lipogenesis. Interestingly, early life PCB 126 exposure had a greater impact on bacteria in adulthood at the community structure, metabolic, and functional levels. This study provides evidence for an association between early life environmental pollutant exposure and increased risk of metabolic disorders later in life and suggests the microbiome is a key target of environmental chemical exposure.}, } @article {pmid35896968, year = {2022}, author = {Jin, L and Liu, S and Tan, S and Wang, Y and Zhao, Y and Yu, S}, title = {Petrositis caused by fluconazole-resistant candida: case report and literature review.}, journal = {BMC infectious diseases}, volume = {22}, number = {1}, pages = {649}, pmid = {35896968}, issn = {1471-2334}, mesh = {Anti-Bacterial Agents/therapeutic use ; Candida/genetics ; Fluconazole/therapeutic use ; Humans ; *Otitis Media/complications/drug therapy ; *Petrositis/complications/diagnosis ; }, abstract = {BACKGROUND: Petrositis is a rare and fatal complication associated with otitis media. It is most likely caused by bacterial infections, but in some cases it is caused by fungal infections.

CASE STUDY: The case in this report is associated with fungal petrositis. The clinical symptoms are: ear pain from chronic otitis media, severe headache, peripheral facial palsy and diplopia. The case was finally confirmed through imaging of middle ear, bacterial culture, pathology, and blood Metagenomic next-generation sequencing (mNGS) test. The patient was treated with sensitive antifungal drugs.

CONCLUSION: Drug treatment is conservative but efficient method in this case. mNGS can provide pathogenic reference, when antibiotic is not efficient enough for fungal infections or drug-resistant fungal infections cases. This allows we to adjust drug use for the treatment.}, } @article {pmid35895627, year = {2022}, author = {Calle-Tobón, A and Pérez-Pérez, J and Forero-Pineda, N and Chávez, OT and Rojas-Montoya, W and Rúa-Uribe, G and Gómez-Palacio, A}, title = {Local-scale virome depiction in Medellín, Colombia, supports significant differences between Aedes aegypti and Aedes albopictus.}, journal = {PloS one}, volume = {17}, number = {7}, pages = {e0263143}, pmid = {35895627}, issn = {1932-6203}, mesh = {*Aedes/classification/virology ; Animals ; Colombia ; *Insect Viruses/genetics ; Mosquito Vectors/virology ; *RNA Viruses/genetics ; *Virome/genetics ; Wolbachia/genetics ; }, abstract = {Aedes spp. comprise the primary group of mosquitoes that transmit arboviruses such as dengue, Zika, and chikungunya viruses to humans, and thus these insects pose a significant burden on public health worldwide. Advancements in next-generation sequencing and metagenomics have expanded our knowledge on the richness of RNA viruses harbored by arthropods such as Ae. aegypti and Ae. albopictus. Increasing evidence suggests that vector competence can be modified by the microbiome (comprising both bacteriome and virome) of mosquitoes present in endemic zones. Using an RNA-seq-based metataxonomic approach, this study determined the virome structure, Wolbachia presence and mitochondrial diversity of field-caught Ae. aegypti and Ae. albopictus mosquitoes in Medellín, Colombia, a municipality with a high incidence of mosquito-transmitted arboviruses. The two species are sympatric, but their core viromes differed considerably in richness, diversity, and abundance; although the community of viral species identified was large and complex, the viromes were dominated by few virus species. BLAST searches of assembled contigs suggested that at least 17 virus species (16 of which are insect-specific viruses [ISVs]) infect the Ae. aegypti population. Dengue virus 3 was detected in one sample and it was the only pathogenic virus detected. In Ae. albopictus, up to 11 ISVs and one plant virus were detected. Therefore, the virome composition appears to be species-specific. The bacterial endosymbiont Wolbachia was identified in all Ae. albopictus samples and in some Ae. aegypti samples collected after 2017. The presence of Wolbachia sp. in Ae. aegypti was not related to significant changes in the richness, diversity, or abundance of this mosquito's virome, although it was related to an increase in the abundance of Aedes aegypti To virus 2 (Metaviridae). The mitochondrial diversity of these mosquitoes suggested that the Ae. aegypti population underwent a change that started in the second half of 2017, which coincides with the release of Wolbachia-infected mosquitoes in Medellín, indicating that the population of wMel-infected mosquitoes released has introduced new alleles into the wild Ae. aegypti population of Medellín. However, additional studies are required on the dispersal speed and intergenerational stability of wMel in Medellín and nearby areas as well as on the introgression of genetic variants in the native mosquito population.}, } @article {pmid35895370, year = {2022}, author = {Yek, C and Lay, S and Bohl, JA and Man, S and Chea, S and Lon, C and Ahyong, V and Tato, CM and DeRisi, JL and Sovannaroth, S and Manning, JE}, title = {Case Report: Cambodian National Malaria Surveillance Program Detection of Plasmodium knowlesi.}, journal = {The American journal of tropical medicine and hygiene}, volume = {107}, number = {1}, pages = {151-153}, pmid = {35895370}, issn = {1476-1645}, mesh = {Asian People ; Humans ; *Malaria/diagnosis/epidemiology ; *Malaria, Falciparum ; Microscopy ; *Plasmodium knowlesi/genetics ; Polymerase Chain Reaction ; }, abstract = {Despite recent success in reducing the regional incidence of Plasmodium falciparum malaria, cases of zoonotic malaria are on the rise in Southeast Asia. The Cambodian National Malaria Surveillance Program has previously relied on rapid diagnostic tests and blood smear microscopy with confirmatory polymerase chain reaction (PCR) testing in a subset of cases to further distinguish P. falciparum, P. malariae, P. ovale, and P. vivax species. Here, metagenomic next-generation sequencing identified P. knowlesi mono-infection in six Cambodian patients initially diagnosed with P. malariae by blood smear microscopy in February-May 2020. These findings of recent human infections with P. knowlesi in Cambodia led to the incorporation of P. knowlesi-specific PCR diagnostics to national malaria surveillance efforts.}, } @article {pmid35894927, year = {2022}, author = {Venturini, AM and Gontijo, JB and Mandro, JA and Paula, FS and Yoshiura, CA and da França, AG and Tsai, SM}, title = {Genome-resolved metagenomics reveals novel archaeal and bacterial genomes from Amazonian forest and pasture soils.}, journal = {Microbial genomics}, volume = {8}, number = {7}, pages = {}, pmid = {35894927}, issn = {2057-5858}, mesh = {*Archaea ; Bacteria ; Forests ; Genome, Bacterial ; *Metagenomics ; Methane/metabolism ; Soil ; Soil Microbiology ; }, abstract = {Amazonian soil microbial communities are known to be affected by the forest-to-pasture conversion, but the identity and metabolic potential of most of their organisms remain poorly characterized. To contribute to the understanding of these communities, here we describe metagenome-assembled genomes (MAGs) recovered from 12 forest and pasture soil metagenomes of the Brazilian Eastern Amazon. We obtained 11 forest and 30 pasture MAGs (≥50% of completeness and ≤10 % of contamination), distributed among two archaeal and 11 bacterial phyla. The taxonomic classification results suggest that most MAGs may represent potential novel microbial taxa. MAGs selected for further evaluation included members of Acidobacteriota, Actinobacteriota, Desulfobacterota_B, Desulfobacterota_F, Dormibacterota, Eremiobacterota, Halobacteriota, Proteobacteria, and Thermoproteota, thus revealing their roles in carbohydrate degradation and mercury detoxification as well as in the sulphur, nitrogen, and methane cycles. A methane-producing Archaea of the genus Methanosarcina was almost exclusively recovered from pasture soils, which can be linked to a sink-to-source shift after the forest-to-pasture conversion. The novel MAGs constitute an important resource to help us unravel the yet-unknown microbial diversity in Amazonian soils and its functional potential and, consequently, the responses of these microorganisms to land-use change.}, } @article {pmid35894622, year = {2022}, author = {Ingle, AT and Fortney, NW and Myers, KS and Walters, KA and Scarborough, MJ and Donohue, TJ and Noguera, DR}, title = {Metagenome-Assembled Genomes from a Microbiome Grown in Dairy Manure Hydrolysate.}, journal = {Microbiology resource announcements}, volume = {11}, number = {8}, pages = {e0029222}, pmid = {35894622}, issn = {2576-098X}, support = {DE-SC0018409//U.S. Department of Energy (DOE)/ ; 2017-67003-26055//USDA | National Institute of Food and Agriculture (NIFA)/ ; }, abstract = {Anaerobic microbiomes can be used to recover the chemical energy in agroindustrial and municipal wastes as useful products. Here, we report a total of 109 draft metagenome-assembled genomes from a bioreactor-fed carbohydrate-rich dairy manure hydrolysate. Studying these genomes will aid us in deciphering the metabolic networks in anaerobic microbiomes.}, } @article {pmid35894189, year = {2022}, author = {Zhu, S and Liu, Y and Luo, HY and Yang, MH and Yang, LC and Deng, WJ}, title = {[Application value of metagenomic next-generation sequencing for pathogen detection in childhood agranulocytosis with fever].}, journal = {Zhongguo dang dai er ke za zhi = Chinese journal of contemporary pediatrics}, volume = {24}, number = {7}, pages = {753-758}, pmid = {35894189}, issn = {1008-8830}, mesh = {*Agranulocytosis/diagnosis ; Bacteria ; Child ; Fever/diagnosis ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenomics/methods ; Retrospective Studies ; Sensitivity and Specificity ; }, abstract = {OBJECTIVES: To study the application value of metagenomic next-generation sequencing (mNGS) for pathogen detection in childhood agranulocytosis with fever.

METHODS: A retrospective analysis was performed on the mNGS results of pathogen detection of 116 children with agranulocytosis with fever who were treated from January 2020 to December 2021. Among these children, 38 children with negative mNGS results were enrolled as the negative group, and 78 children with positive results were divided into a bacteria group (n=22), a fungal group (n=23), and a viral group (n=31). Clinical data were compared between groups.

RESULTS: For the 116 children with agranulocytosis and fever, the median age was 8 years at diagnosis, the median turnaround time of mNGS results was 2 days, and the positive rate of mNGS testing was 67.2% (78/116). Compared with the negative group, the bacterial group had a higher procalcitonin level (P<0.05), the fungal group had higher level of C-reactive protein and positive rate of (1,3)-β-D glucan test/galactomannan test (P<0.05), and the fungal group had a longer duration of fever (P<0.05). Among the 22 positive microbial culture specimens, 9 (41%) were consistent with the mNGS results. Among the 17 positive blood culture specimens, 8 (47%) were consistent with the mNGS results. Treatment was adjusted for 28 children (36%) with the mNGS results, among whom 26 were cured and discharged.

CONCLUSIONS: The mNGS technique has a shorter turnaround time and a higher sensitivity for pathogen detection and can provide evidence for the pathogenic diagnosis of children with agranulocytosis and fever.}, } @article {pmid35893678, year = {2022}, author = {Laubscher, F and Hartley, MA and Kaiser, L and Cordey, S}, title = {Genomic Diversity of Torque Teno Virus in Blood Samples from Febrile Paediatric Outpatients in Tanzania: A Descriptive Cohort Study.}, journal = {Viruses}, volume = {14}, number = {8}, pages = {}, pmid = {35893678}, issn = {1999-4915}, mesh = {Child ; Cohort Studies ; *Coinfection ; *DNA Virus Infections/epidemiology ; DNA, Viral/genetics ; Genomics ; Humans ; Outpatients ; Tanzania/epidemiology ; *Torque teno virus/genetics ; }, abstract = {Torque teno virus (TTV) is considered to be an ubiquitous member of the commensal human blood virome commonly reported in mixed genotype co-infections. This study investigates the genomic diversity of TTV in blood samples from 816 febrile Tanzanian children. Metagenomic next-generation sequencing was used to screen for TTV in individual blood samples from a cohort of 816 febrile Tanzanian paediatric outpatients. For positive samples, the number of TTV species and genotypes present were evaluated. We investigate the linear relationship between individual TTV diversity and the patient age by linear regression. TTV was detected in 97.2% of sera. ORF1 analysis revealed the presence of 149 genotypes from 38 species, suggesting the presence of 13 new species. These genotypes were mostly present as co-infections with a median of 11 genotypes/subject (range: 1−71). In terms of species, we found a median of nine species/subject (range: 1−29). We further show a significant association between the diversity of co-detected TTV and the age of the subjects (p value < 0.0001). This study shows that significant TTV genomic diversity is acquired by the age of five and that this diversity tends to increase with age, which indicates a repetitive TTV acquisition during the first months/years of life.}, } @article {pmid35893664, year = {2022}, author = {Sprotte, S and Rasmussen, TS and Cho, GS and Brinks, E and Lametsch, R and Neve, H and Vogensen, FK and Nielsen, DS and Franz, CMAP}, title = {Morphological and Genetic Characterization of Eggerthella lenta Bacteriophage PMBT5.}, journal = {Viruses}, volume = {14}, number = {8}, pages = {}, pmid = {35893664}, issn = {1999-4915}, mesh = {Actinobacteria ; Agar ; *Bacteriophages/genetics ; DNA, Viral/chemistry/genetics ; Genome, Viral ; Humans ; *Siphoviridae/genetics ; }, abstract = {Eggerthella lenta is a common member of the human gut microbiome. We here describe the isolation and characterization of a putative virulent bacteriophage having E. lenta as host. The double-layer agar method for isolating phages was adapted to anaerobic conditions for isolating bacteriophage PMBT5 from sewage on a strictly anaerobic E. lenta strain of intestinal origin. For this, anaerobically grown E. lenta cells were concentrated by centrifugation and used for a 24 h phage enrichment step. Subsequently, this suspension was added to anaerobically prepared top (soft) agar in Hungate tubes and further used in the double-layer agar method. Based on morphological characteristics observed by transmission electron microscopy, phage PMBT5 could be assigned to the Siphoviridae phage family. It showed an isometric head with a flexible, noncontractile tail and a distinct single 45 nm tail fiber under the baseplate. Genome sequencing and assembly resulted in one contig of 30,930 bp and a mol% GC content of 51.3, consisting of 44 predicted protein-encoding genes. Phage-related proteins could be largely identified based on their amino acid sequence, and a comparison with metagenomes in the human virome database showed that the phage genome exhibits similarity to two distantly related phages.}, } @article {pmid35893575, year = {2022}, author = {Vilo, C and Dong, Q and Galetovic, A and Gómez-Silva, B}, title = {Metagenome-Assembled Genome of Cyanocohniella sp. LLY from the Cyanosphere of Llayta, an Edible Andean Cyanobacterial Macrocolony.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {35893575}, issn = {2076-2607}, support = {FB-0001//CONICYT Chile/ ; }, abstract = {Cyanobacterial macrocolonies known as Llayta are found in Andean wetlands and have been consumed since pre-Columbian times in South America. Macrocolonies of filamentous cyanobacteria are niches for colonization by other microorganisms. However, the microbiome of edible Llayta has not been explored. Based on a culture-independent approach, we report the presence, identification, and metagenomic genome reconstruction of Cyanocohniella sp. LLY associated to Llayta trichomes. The assembled genome of strain LLY is now available for further inquiries and may be instrumental for taxonomic advances concerning this genus. All known members of the Cyanocohniella genus have been isolated from salty European habitats. A biogeographic gap for the Cyanocohniella genus is partially filled by the existence of strain LLY in Andes Mountains wetlands in South America as a new habitat. This is the first genome available for members of this genus. Genes involved in primary and secondary metabolism are described, providing new insights regarding the putative metabolic capabilities of Cyanocohniella sp. LLY.}, } @article {pmid35893549, year = {2022}, author = {Li, LP and Peng, KL and Xue, MY and Zhu, SL and Liu, JX and Sun, HZ}, title = {An Age Effect of Rumen Microbiome in Dairy Buffaloes Revealed by Metagenomics.}, journal = {Microorganisms}, volume = {10}, number = {8}, pages = {}, pmid = {35893549}, issn = {2076-2607}, support = {2021XZZX027//the Fundamental Research Funds for the Zhejiang Provincial Universities/ ; }, abstract = {Age is an important factor in shaping the gut microbiome. However, the age effect on the rumen microbial community for dairy buffaloes remains less explored. Using metagenomics, we examined the microbial composition and functions of rumen microbiota in dairy Murrah buffaloes of different ages: Y (1 year old), M (3−5 years old), E (6−8 years old), and O (>9 years old). We found that Bacteroidetes and Firmicutes were the predominant phyla, with Prevotella accounting for the highest abundance at the genus level. The proportion of Bacteroides and Methanobrevibacter significantly increased with age, while the abundance of genus Lactobacillus significantly decreased with age (LDA > 3, p < 0.05). Most differed COG and KEGG pathways were enriched in Y with carbohydrate metabolism, while older buffaloes enriched more functions of protein metabolism and the processing of replication and repair (LDA > 2, p < 0.05). Additionally, the functional contribution analysis revealed that the genera Prevotella and Lactobacillus of Y with more functions of CAZymes encoded genes of glycoside hydrolases and carbohydrate esterases for their roles of capable of metabolizing starch and sucrose-associated oligosaccharide enzyme, hemicellulase, and cellulase activities than the other three groups (LDA > 2, p < 0.05), thus affecting the 1-year-old dairy buffalo rumen carbohydrate metabolism. This study provides comprehensive dairy buffalo rumen metagenome data and assists in manipulating the rumen microbiome for improved dairy buffalo production.}, } @article {pmid35893066, year = {2022}, author = {Afiahayati, and Bernard, S and Gunadi, and Wibawa, H and Hakim, MS and Marcellus, and Parikesit, AA and Dewa, CK and Sakakibara, Y}, title = {A Comparison of Bioinformatics Pipelines for Enrichment Illumina Next Generation Sequencing Systems in Detecting SARS-CoV-2 Virus Strains.}, journal = {Genes}, volume = {13}, number = {8}, pages = {}, pmid = {35893066}, issn = {2073-4425}, mesh = {*COVID-19/virology ; Computational Biology/methods ; Genome, Viral ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *SARS-CoV-2/genetics ; }, abstract = {Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) is a newly emerging virus well known as the major cause of the worldwide pandemic due to Coronavirus Disease 2019 (COVID-19). Major breakthroughs in the Next Generation Sequencing (NGS) field were elucidated following the first release of a full-length SARS-CoV-2 genome on the 10 January 2020, with the hope of turning the table against the worsening pandemic situation. Previous studies in respiratory virus characterization require mapping of raw sequences to the human genome in the downstream bioinformatics pipeline as part of metagenomic principles. Illumina, as the major player in the NGS arena, took action by releasing guidelines for improved enrichment kits called the Respiratory Virus Oligo Panel (RVOP) based on a hybridization capture method capable of capturing targeted respiratory viruses, including SARS-CoV-2; therefore, allowing a direct map of raw sequences data to SARS-CoV-2 genome in downstream bioinformatics pipeline. Consequently, two bioinformatics pipelines emerged with no previous studies benchmarking the pipelines. This study focuses on gaining insight and understanding of target enrichment workflow by Illumina through the utilization of different bioinformatics pipelines named as 'Fast Pipeline' and 'Normal Pipeline' to SARS-CoV-2 strains isolated from Yogyakarta and Central Java, Indonesia. Overall, both pipelines work well in the characterization of SARS-CoV-2 samples, including in the identification of major studied nucleotide substitutions and amino acid mutations. A higher number of reads mapped to the SARS-CoV-2 genome in Fast Pipeline and merely were discovered as a contributing factor in a higher number of coverage depth and identified variations (SNPs, insertion, and deletion). Fast Pipeline ultimately works well in a situation where time is a critical factor. On the other hand, Normal Pipeline would require a longer time as it mapped reads to the human genome. Certain limitations were identified in terms of pipeline algorithm, whereas it is highly recommended in future studies to design a pipeline in an integrated framework, for instance, by using NextFlow, a workflow framework to combine all scripts into one fully integrated pipeline.}, } @article {pmid35892966, year = {2022}, author = {Mukherjee, S and Kuang, Z and Ghosh, S and Detroja, R and Carmi, G and Tripathy, S and Barash, D and Frenkel-Morgenstern, M and Nevo, E and Li, K}, title = {Incipient Sympatric Speciation and Evolution of Soil Bacteria Revealed by Metagenomic and Structured Non-Coding RNAs Analysis.}, journal = {Biology}, volume = {11}, number = {8}, pages = {}, pmid = {35892966}, issn = {2079-7737}, abstract = {Soil bacteria respond rapidly to changes in new environmental conditions. For adaptation to the new environment, they could mutate their genome, which impacts the alternation of the functional and regulatory landscape. Sometimes, these genetic and ecological changes may drive the bacterial evolution and sympatric speciation. Although sympatric speciation has been controversial since Darwin suggested it in 1859, there are several strong theoretical or empirical evidences to support it. Sympatric speciation associated with soil bacteria remains largely unexplored. Here, we provide potential evidence of sympatric speciation of soil bacteria by comparison of metagenomics from two sharply contrasting abutting divergence rock and soil types (Senonian chalk and its rendzina soil, and abutting Pleistocene basalt rock and basalt soil). We identified several bacterial species with significant genetic differences in the same species between the two soil types and ecologies. We show that the bacterial community composition has significantly diverged between the two soils; correspondingly, their functions were differentiated in order to adapt to the local ecological stresses. The ecologies, such as water availability and pH value, shaped the adaptation and speciation of soil bacteria revealed by the clear-cut genetic divergence. Furthermore, by a novel analysis scheme of riboswitches, we highlight significant differences in structured non-coding RNAs between the soil bacteria from two divergence soil types, which could be an important driver for functional adaptation. Our study provides new insight into the evolutionary divergence and incipient sympatric speciation of soil bacteria under microclimatic ecological differences.}, } @article {pmid35892598, year = {2022}, author = {Zhang, T and Wu, X and Yuan, H and Huang, S and Park, S}, title = {Mitigation of Memory Impairment with Fermented Fucoidan and λ-Carrageenan Supplementation through Modulating the Gut Microbiota and Their Metagenome Function in Hippocampal Amyloid-β Infused Rats.}, journal = {Cells}, volume = {11}, number = {15}, pages = {}, pmid = {35892598}, issn = {2073-4409}, mesh = {Acetylcholinesterase/metabolism ; *Alzheimer Disease/metabolism ; Amyloid beta-Peptides/metabolism ; Animals ; Brain-Derived Neurotrophic Factor/metabolism ; Carrageenan/metabolism ; Dietary Supplements ; Disease Models, Animal ; *Gastrointestinal Microbiome ; Hippocampus/metabolism ; Insulin/metabolism ; Memory Disorders/complications ; Metagenome ; Polysaccharides ; Rats ; }, abstract = {Attenuating acetylcholinesterase and insulin/insulin-like growth factor-1 signaling in the hippocampus is associated with Alzheimer's disease (AD) development. Fucoidan and carrageenan are brown and red algae, respectively, with potent antibacterial, anti-inflammatory, antioxidant and antiviral activities. This study examined how low-molecular-weight (MW) and high-MW fucoidan and λ-carrageenan would improve memory impairment in Alzheimer's disease-induced rats caused by an infusion of toxic amyloid-β(Aβ). Fucoidan and λ-carrageenan were dissected into low-MW by Luteolibacter&nbsp;algae and Pseudoalteromonas&nbsp;carrageenovora. Rats receiving an Aβ(25-35) infusion in the CA1 region of the hippocampus were fed dextrin (AD-Con), 1% high-MW fucoidan (AD-F-H), 1% low-MW fucoidan (AD-F-L), 1% high-MW λ-carrageenan (AD-C-H), and 1% low-MW λ-carrageenan (AD-C-L) for six weeks. Rats to receive saline infusion (Normal-Con) had an AD-Con diet. The AD-F-L group showed an improved memory function, which manifested as an enhanced Y-maze spontaneous alternation test, water maze, and passive avoidance tests, similar to the Normal-Con group. AD-F-L also potentiated hippocampal insulin signaling and increased the expression of ciliary neurotrophic factor (CNTF) and brain-derived neurotrophic factor (BDNF) in the hippocampus. AD-C-L improved the memory function mainly by increasing the BDNF content. AD-F-H and AD-C-H did not improve the memory function. Compared to AD-Con, the ascending order of AD-C-H, AD-F-H, AD-C-L, and AD-F-L increased insulin signaling by enhancing the pSTAT3®pAkt®pGSK-3β pathway. AD-F-L improved glucose tolerance the most. Compared to AD-CON, the AD-F-L treatment increased the serum acetate concentrations and compensated for the defect of cerebral glucose metabolism. AD-Con increased Clostridium, Terrisporobacter and Sporofaciens compared to Normal-Con, and AD-F-L and AD-C-L increased Akkermentia. In conclusion, AD-F-L and AD-C-L alleviated the memory function in the rats with induced AD symptoms by modulating.}, } @article {pmid35891785, year = {2022}, author = {Xie, Z and Manichanh, C}, title = {FunOMIC: Pipeline with built-in fungal taxonomic and functional databases for human mycobiome profiling.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {3685-3694}, pmid = {35891785}, issn = {2001-0370}, abstract = {While analysis of the bacterial microbiome has become routine, that of the fungal microbiome is still hampered by the lack of robust databases and bioinformatic pipelines. Here, we present FunOMIC, a pipeline with built-in taxonomic (1.6 million marker genes) and functional (3.4 million non-redundant fungal proteins) databases for the identification of fungi. Applied to more than 2,600 human metagenomic samples, the tool revealed fungal species associated with geography, body sites, and diseases. Correlation network analysis provided new insights into inter-kingdom interactions. With this pipeline and two of the most comprehensive fungal databases, we foresee a fast-growing resource for mycobiome studies.}, } @article {pmid35891567, year = {2022}, author = {Martinez-Hernandez, F and Fornas, O and Martinez-Garcia, M}, title = {Into the Dark: Exploring the Deep Ocean with Single-Virus Genomics.}, journal = {Viruses}, volume = {14}, number = {7}, pages = {}, pmid = {35891567}, issn = {1999-4915}, mesh = {*Alphaproteobacteria/genetics ; Genome, Viral ; Mediterranean Sea ; Metagenomics ; Phylogeny ; Seawater ; *Viruses/genetics ; }, abstract = {Single-virus genomics (SVGs) has been successfully applied to ocean surface samples allowing the discovery of widespread dominant viruses overlooked for years by metagenomics, such as the uncultured virus vSAG 37-F6 infecting the ubiquitous Pelagibacter spp. In SVGs, one uncultured virus at a time is sorted from the environmental sample, whole-genome amplified, and sequenced. Here, we have applied SVGs to deep-ocean samples (200-4000 m depth) from global Malaspina and MEDIMAX expeditions, demonstrating the feasibility of this method in deep-ocean samples. A total of 1328 virus-like particles were sorted from the North Atlantic Ocean, the deep Mediterranean Sea, and the Pacific Ocean oxygen minimum zone (OMZ). For this proof of concept, sixty single viruses were selected at random for sequencing. Genome annotation identified 27 of these genomes as bona fide viruses, and detected three auxiliary metabolic genes involved in nucleotide biosynthesis and sugar metabolism. Massive protein profile analysis confirmed that these viruses represented novel viral groups not present in databases. Although they were not previously assembled by viromics, global fragment recruitment analysis showed a conserved profile of relative abundance of these viruses in all analyzed samples spanning different oceans. Altogether, these results reveal the feasibility in using SVGs in this vast environment to unveil the genomes of relevant viruses.}, } @article {pmid35891454, year = {2022}, author = {Villanova, F and Milagres, FAP and Brustulin, R and Araújo, ELL and Pandey, RP and Raj, VS and Deng, X and Delwart, E and Luchs, A and Costa, ACD and Leal, É}, title = {A New Circular Single-Stranded DNA Virus Related with Howler Monkey Associated Porprismacovirus 1 Detected in Children with Acute Gastroenteritis.}, journal = {Viruses}, volume = {14}, number = {7}, pages = {}, pmid = {35891454}, issn = {1999-4915}, mesh = {*Alouatta/genetics ; Animals ; Brazil ; Child ; DNA Viruses/genetics ; DNA, Circular ; DNA, Single-Stranded ; *Gastroenteritis/diagnosis/genetics ; Genome, Viral ; Humans ; Phylogeny ; }, abstract = {Putative replication-associated protein (REP) and capsid-like (CAP) proteins are encoded by circular single-stranded DNA viruses (CRESS DNA), which have been found in samples from most eukaryotic groups. However, the details of these viruses' life cycles and their significance in diseases have yet to be established. We presented and analyzed two full-length CRESS DNA genomes acquired from two children diagnosed with acute gastroenteritis (GI) in the northeast state of Tocantins, Brazil, using next-generation sequencing and a virus-like filtration approach. Both sequences (named SmaCV3BR08 and SmaCV3BR291) are closely similar to a prior CRESS DNA sequence discovered in the feces of a new world monkey (Alouatta caraya) from the United States in 2009 and termed Howler monkey-associated porprismacovirus 1 (Genbank ID: NC 026317). According to our comparative study, these porprismacovirus genomes deviate by 10% at the nucleotide level. For comparative reasons, the divergence between our sequences (SmaCV3BR08 and SmaCV3BR291) and a porprismacovirus recently identified in a human fecal sample from Peru is 37%. These data suggest that there is a great diversity of porprismacoviruses in South America, perhaps more than two species. In addition, the finding of closely related sequences of porprismacoviruses in humans and native monkeys highlights the zoonotic potential of these viruses.}, } @article {pmid35891427, year = {2022}, author = {de Oliveira Ribeiro, G and Gill, DE and do Socorro Foro Ramos, E and Villanova, F and Soares D'Athaide Ribeiro, E and Monteiro, FJC and Morais, VS and Rego, MODS and Araújo, ELL and Pandey, RP and Raj, VS and Deng, X and Delwart, E and da Costa, AC and Leal, É}, title = {Chikungunya Virus Asian Lineage Infection in the Amazon Region Is Maintained by Asiatic and Caribbean-Introduced Variants.}, journal = {Viruses}, volume = {14}, number = {7}, pages = {}, pmid = {35891427}, issn = {1999-4915}, mesh = {Animals ; Brazil/epidemiology ; Caribbean Region ; *Chikungunya Fever ; *Chikungunya virus/genetics ; Disease Outbreaks ; Genotype ; Humans ; Phylogeny ; *Zika Virus ; *Zika Virus Infection/epidemiology ; }, abstract = {The simultaneous transmission of two lineages of the chikungunya virus (CHIKV) was discovered after the pathogen's initial arrival in Brazil. In Oiapoque (Amapá state, north Brazil), the Asian lineage (CHIKV-Asian) was discovered, while in Bahia state, the East-Central-South-African lineage (CHIKV-ECSA) was discovered (northeast Brazil). Since then, the CHIKV-Asian lineage has been restricted to the Amazon region (mostly in the state of Amapá), whereas the ECSA lineage has expanded across the country. Despite the fact that the Asian lineage was already present in the Amazon region, the ECSA lineage brought from the northeast caused a large outbreak in the Amazonian state of Roraima (north Brazil) in 2017. Here, CHIKV spread in the Amazon region was studied by a Zika-Dengue-Chikungunya PCR assay in 824 serum samples collected between 2013 and 2016 from individuals with symptoms of viral infection in the Amapá state. We found 11 samples positive for CHIKV-Asian, and, from these samples, we were able to retrieve 10 full-length viral genomes. A comprehensive phylogenetic study revealed that nine CHIKV sequences came from a local transmission cluster related to Caribbean strains, whereas one sequence was related to sequences from the Philippines. These findings imply that CHIKV spread in different ways in Roraima and Amapá, despite the fact that both states had similar climatic circumstances and mosquito vector frequencies.}, } @article {pmid35891392, year = {2022}, author = {Wang, X and Carrai, M and Van Brussel, K and Feng, S and Beatty, JA and Shi, M and Holmes, EC and Li, J and Barrs, VR}, title = {Low Intrahost and Interhost Genetic Diversity of Carnivore Protoparvovirus 1 in Domestic Cats during a Feline Panleukopenia Outbreak.}, journal = {Viruses}, volume = {14}, number = {7}, pages = {}, pmid = {35891392}, issn = {1999-4915}, mesh = {Animals ; Cats ; Disease Outbreaks/veterinary ; *Feline Panleukopenia/epidemiology ; Feline Panleukopenia Virus/genetics ; Mutation ; Nucleotides ; *Parvoviridae Infections/epidemiology/veterinary ; }, abstract = {Feline panleukopenia (FPL), a highly contagious and frequently fatal disease of cats, is caused by Feline parvovirus (FPV) and Canine parvovirus (CPV). We characterised the diversity of these Carnivore protoparvovirus 1 variants in 18 faecal samples collected from domestic cats with FPL during an outbreak, using targeted parvoviral DNA metagenomics to a mean depth of >10,000 × coverage per site. All samples comprised FPV alone. Compared with the reference FPV genome, isolated in 1967, 44 mutations were detected. Ten of these were nonsynonymous, including 9 in nonstructural genes and one in VP1/VP2 (Val232Ile), which was the only one to exhibit interhost diversity, being present in five sequences. There were five other polymorphic nucleotide positions, all with synonymous mutations. Intrahost diversity at all polymorphic positions was low, with subconsensus variant frequencies (SVF) of <1% except for two positions (2108 and 3208) in two samples with SVF of 1.1−1.3%. Intrahost nucleotide diversity was measured across the whole genome (0.7−1.5%) and for each gene and was highest in the NS2 gene of four samples (1.2−1.9%). Overall, intrahost viral genetic diversity was limited and most mutations observed were synonymous, indicative of a low background mutation rate and strong selective constraints.}, } @article {pmid35891376, year = {2022}, author = {Cannon, JL and Seabolt, MH and Xu, R and Montmayeur, A and Suh, SH and Diez-Valcarce, M and Bucardo, F and Becker-Dreps, S and Vinjé, J}, title = {Gut Microbiome Changes Occurring with Norovirus Infection and Recovery in Infants Enrolled in a Longitudinal Birth Cohort in Leon, Nicaragua.}, journal = {Viruses}, volume = {14}, number = {7}, pages = {}, pmid = {35891376}, issn = {1999-4915}, support = {K24 AI141744/AI/NIAID NIH HHS/United States ; R01 AI127845/AI/NIAID NIH HHS/United States ; R01AI127845/AI/NIAID NIH HHS/United States ; none/CC/CDC HHS/United States ; K24AI141744/AI/NIAID NIH HHS/United States ; }, mesh = {Birth Cohort ; *Caliciviridae Infections ; Cohort Studies ; Feces/microbiology ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Nicaragua/epidemiology ; *Norovirus/genetics ; }, abstract = {Noroviruses are associated with one fifth of diarrheal illnesses globally and are not yet preventable with vaccines. Little is known about the effects of norovirus infection on infant gut microbiome health, which has a demonstrated role in protecting hosts from pathogens and a possible role in oral vaccine performance. In this study, we characterized infant gut microbiome changes occurring with norovirus-associated acute gastroenteritis (AGE) and the extent of recovery. Metagenomic sequencing was performed on the stools of five infants participating in a longitudinal birth cohort study conducted in León, Nicaragua. Taxonomic and functional diversities of gut microbiomes were profiled at time points before, during, and after norovirus infection. Initially, the gut microbiomes resembled those of breastfeeding infants, rich in probiotic species. When disturbed by AGE, Gammaproteobacteria dominated, particularly Pseudomonas species. Alpha diversity increased but the genes involved in carbohydrate metabolism and glycan biosynthesis decreased. After the symptoms subsided, the gut microbiomes rebounded with their taxonomic and functional communities resembling those of the pre-infection microbiomes. In this study, during disruptive norovirus-associated AGE, the gut microbiome was temporarily altered, returning to a pre-infection composition a median of 58 days later. Our study provides new insights for developing probiotic treatments and furthering our understanding of the role that episodes of AGE have in shaping the infant gut microbiome, their long-term outcomes, and implications for oral vaccine effectiveness.}, } @article {pmid35891354, year = {2022}, author = {Ward, B and Yombi, JC and Balligand, JL and Cani, PD and Collet, JF and de Greef, J and Dewulf, JP and Gatto, L and Haufroid, V and Jodogne, S and Kabamba, B and Pyr Dit Ruys, S and Vertommen, D and Elens, L and Belkhir, L}, title = {HYGIEIA: HYpothesizing the Genesis of Infectious Diseases and Epidemics through an Integrated Systems Biology Approach.}, journal = {Viruses}, volume = {14}, number = {7}, pages = {}, pmid = {35891354}, issn = {1999-4915}, mesh = {*COVID-19/complications/epidemiology ; *Communicable Diseases/epidemiology ; Humans ; Longitudinal Studies ; Metabolomics/methods ; Pandemics ; Systems Biology/methods ; Post-Acute COVID-19 Syndrome ; }, abstract = {More than two years on, the COVID-19 pandemic continues to wreak havoc around the world and has battle-tested the pandemic-situation responses of all major global governments. Two key areas of investigation that are still unclear are: the molecular mechanisms that lead to heterogenic patient outcomes, and the causes of Post COVID condition (AKA Long-COVID). In this paper, we introduce the HYGIEIA project, designed to respond to the enormous challenges of the COVID-19 pandemic through a multi-omic approach supported by network medicine. It is hoped that in addition to investigating COVID-19, the logistics deployed within this project will be applicable to other infectious agents, pandemic-type situations, and also other complex, non-infectious diseases. Here, we first look at previous research into COVID-19 in the context of the proteome, metabolome, transcriptome, microbiome, host genome, and viral genome. We then discuss a proposed methodology for a large-scale multi-omic longitudinal study to investigate the aforementioned biological strata through high-throughput sequencing (HTS) and mass-spectrometry (MS) technologies. Lastly, we discuss how a network medicine approach can be used to analyze the data and make meaningful discoveries, with the final aim being the translation of these discoveries into the clinics to improve patient care.}, } @article {pmid35891346, year = {2022}, author = {French, RK and Filion, A and Niebuhr, CN and Holmes, EC}, title = {Metatranscriptomic Comparison of Viromes in Endemic and Introduced Passerines in New Zealand.}, journal = {Viruses}, volume = {14}, number = {7}, pages = {}, pmid = {35891346}, issn = {1999-4915}, mesh = {Animals ; *Bird Diseases/epidemiology ; Introduced Species ; New Zealand/epidemiology ; *Passeriformes ; *Songbirds ; Virome ; }, abstract = {New Zealand/Aotearoa has many endemic passerine birds vulnerable to emerging infectious diseases. Yet little is known about viruses in passerines, and in some countries, including New Zealand, the virome of wild passerines has been only scarcely researched. Using metatranscriptomic sequencing we characterised the virome of New Zealand endemic and introduced species of passerine. Accordingly, we identified 34 possible avian viruses from cloacal swabs of 12 endemic and introduced bird species not showing signs of disease. These included a novel siadenovirus, iltovirus, and avastrovirus in the Eurasian blackbird (Turdus merula, an introduced species), song thrush (Turdus philomelos, introduced) and silvereye/tauhou (Zosterops lateralis, introduced), respectively. This is the first time novel viruses from these genera have been identified in New Zealand, likely reflecting prior undersampling. It also represents the first identification of an iltovirus and siadenovirus in blackbirds and thrushes globally. These three viruses were only found in introduced species and may pose a risk to endemic species if they were to jump species boundaries, particularly the iltoviruses and siadenoviruses that have a prior history of disease associations. Further virus study and surveillance are needed in New Zealand avifauna, particularly in Turdus populations and endemic species.}, } @article {pmid35890463, year = {2022}, author = {Demian, E and Jaksa-Czotter, N and Varallyay, E}, title = {Grapevine Pinot Gris Virus Is Present in Different Non-Vitis Hosts.}, journal = {Plants (Basel, Switzerland)}, volume = {11}, number = {14}, pages = {}, pmid = {35890463}, issn = {2223-7747}, support = {K119783//National Research, Development and Innovation Office/ ; K131679//National Research, Development and Innovation Office/ ; K134895//National Research, Development and Innovation Office/ ; }, abstract = {Grapevine Pinot gris virus (GPGV) was described in Italy using a metagenomic approach: next-generation sequencing of the virus-derived small RNAs. Since that time, it has been reported all over the world. The presence of GPGV is associated with grapevine disease, but most of the time, the disease is asymptomatic. Although the host range of this virus has not been investigated, it has been found in the non-Vitis hosts, Silene latifolia and Chenopodium album. We investigated the presence of GPGV in grapevine and other plant species growing as weeds in the vineyard. Using RT-PCR, we identified GPGV in seven non-Vitis hosts: Ailanthus, Asclepias, Crataegus, Fraxinus, Rosa, Rubus, and Sambucus. In the case of Rosa and Rubus, this finding was supported by Northern blot detection of the virus. GPGV strains in non-Vitis hosts belong to the asymptomatic clade, and are clustered according to their original geographic locations. The presence of GPGV in species other than grapevine shows that besides well-known vector and propagating material-based infections, other possible entry sites for the virus can exist, which have to be taken into consideration when developing reliable regulation strategies.}, } @article {pmid35890114, year = {2022}, author = {Krutskikh, EP and Potanina, DV and Samoylova, NA and Gryaznova, MV and Sadovnikova, IS and Gureev, AP and Popov, VN}, title = {Brain Protection by Methylene Blue and Its Derivative, Azur B, via Activation of the Nrf2/ARE Pathway in Cisplatin-Induced Cognitive Impairment.}, journal = {Pharmaceuticals (Basel, Switzerland)}, volume = {15}, number = {7}, pages = {}, pmid = {35890114}, issn = {1424-8247}, support = {19-44-360011 r_a)//This research was funded by the scholarship of the President of the Russian Federation for young scientists and PhD Students (Project SP-2802.2021.4) to A.P.G.; by the RF Ministry of Science and Higher Education in the framework of the national project "S/ ; }, abstract = {Cisplatin is a cytotoxic chemotherapeutic drug that leads to DNA damage and is used in the treatment of various types of tumors. However, cisplatin has several serious adverse effects, such as deterioration in cognitive ability. The aim of our work was to study neuroprotectors capable of preventing cisplatin-induced neurotoxicity. Methylene blue (MB) and AzurB (AzB) are able to neutralize the neurotoxicity caused by cisplatin by protecting nerve cells as a result of the activation of the Ntf2 signaling pathway. We have shown that cisplatin impairs learning in the Morris water maze. This is due to an increase in the amount of mtDNA damage, a decrease in the expression of most antioxidant genes, the main determinant of the induction of which is the Nrf2/ARE signaling pathway, and genes involved in mitophagy regulation in the cortex. The expression of genes involved in long-term potentiation was suppressed in the hippocampus of cisplatin-injected mice. MB in most cases prevented cisplatin-induced impairment of learning and decrease of gene expression in the cortex. AzB prevented the cisplatin-induced decrease of genes in the hippocampus. Also, cisplatin induced disbalance in the gut microbiome, decreased levels of Actinotalea and Prevotella, and increased levels of Streptococcus and Veillonella. MB and AzB also prevented cisplatin-induced changes in the bacterial composition of the gut microbiome.}, } @article {pmid35890029, year = {2022}, author = {Wen, Y and Wu, Q and Zhang, L and He, J and Chen, Y and Yang, X and Zhang, K and Niu, X and Li, S}, title = {Association of Intrauterine Microbes with Endometrial Factors in Intrauterine Adhesion Formation and after Medicine Treatment.}, journal = {Pathogens (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, pmid = {35890029}, issn = {2076-0817}, support = {21977086//NSFC/ ; }, abstract = {Intrauterine adhesions (IUAs) have caused serious harm to women's reproductive health. Although emerging evidence has linked intrauterine microbiome to gynecological diseases, the association of intrauterine microbiome with IUA, remains unknown. We performed metagenome-wide association, metabolomics, and transcriptomics studies on IUA and non-IUA uteri of adult rats to identify IUA-associated microbial species, which affected uterine metabolites and endometrial transcriptions. A rat model was used with one side of the duplex uterus undergoing IUA and the other remaining as a non-IUA control. Both 16S rRNA sequencing and metagenome-wide association analysis revealed that instead of Mycoplasmopsis specie in genital tract, murine lung pathogen Mycoplasmopsispulmonis markedly increased in IUA samples and displayed a distinct positive interaction with the host immune system. Moreover, most of the IUA-enriched 58 metabolites positively correlate with M.pulmonis, which inversely correlates with a mitotic progression inhibitor named 3-hydroxycapric acid. A comparison of metabolic profiles of intrauterine flushing fluids from human patients with IUA, endometritis, and fallopian tube obstruction suggested that rat IUA shared much similarity to human IUA. The endometrial gene Tenascin-N, which is responsible for extracellular matrix of wounds, was highly up-regulated, while the key genes encoding parvalbumin, trophectoderm Dkkl1 and telomerase involved in leydig cells, trophectoderm cells, activated T cells and monocytes were dramatically down-regulated in rat IUA endometria. Treatment for rat IUA with estrogen (E2), oxytetracycline (OTC), and a traditional Chinese patent medicine GongXueNing (GXN) did not reduce the incidence of IUA, though inflammatory factor IL-6 was dramatically down-regulated (96-86%) with all three. Instead, in both the E2 and OTC treated groups, IUA became worse with a highly up-regulated B cell receptor signaling pathway, which may be associated with the significantly increased proportions of Ulvibacter or Staphylococcus. Our results suggest an association between intrauterine microbiota alterations, certain uterine metabolites, characteristic changes in endometrial transcription, and IUA and the possibility to intervene in IUA formation by targeting the causal factors, microbial infection, and Tenascin-like proteins.}, } @article {pmid35889831, year = {2022}, author = {Sharon, I and Quijada, NM and Pasolli, E and Fabbrini, M and Vitali, F and Agamennone, V and Dötsch, A and Selberherr, E and Grau, JH and Meixner, M and Liere, K and Ercolini, D and de Filippo, C and Caderni, G and Brigidi, P and Turroni, S}, title = {The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept.}, journal = {Nutrients}, volume = {14}, number = {14}, pages = {}, pmid = {35889831}, issn = {2072-6643}, mesh = {Dysbiosis ; *Gastrointestinal Microbiome ; Humans ; Metagenomics/methods ; *Microbiota ; Sequence Analysis, DNA ; }, abstract = {The core microbiome, which refers to a set of consistent microbial features across populations, is of major interest in microbiome research and has been addressed by numerous studies. Understanding the core microbiome can help identify elements that lead to dysbiosis, and lead to treatments for microbiome-related health states. However, defining the core microbiome is a complex task at several levels. In this review, we consider the current state of core human microbiome research. We consider the knowledge that has been gained, the factors limiting our ability to achieve a reliable description of the core human microbiome, and the fields most likely to improve that ability. DNA sequencing technologies and the methods for analyzing metagenomics and amplicon data will most likely facilitate higher accuracy and resolution in describing the microbiome. However, more effort should be invested in characterizing the microbiome's interactions with its human host, including the immune system and nutrition. Other components of this holobiontic system should also be emphasized, such as fungi, protists, lower eukaryotes, viruses, and phages. Most importantly, a collaborative effort of experts in microbiology, nutrition, immunology, medicine, systems biology, bioinformatics, and machine learning is probably required to identify the traits of the core human microbiome.}, } @article {pmid35889746, year = {2022}, author = {Dore, MP and Sau, R and Niolu, C and Abbondio, M and Tanca, A and Bibbò, S and Loria, M and Pes, GM and Uzzau, S}, title = {Metagenomic Changes of Gut Microbiota following Treatment of Helicobacter pylori Infection with a Simplified Low-Dose Quadruple Therapy with Bismuth or Lactobacillus reuteri.}, journal = {Nutrients}, volume = {14}, number = {14}, pages = {}, pmid = {35889746}, issn = {2072-6643}, mesh = {Anti-Bacterial Agents/pharmacology ; Bismuth/pharmacology/therapeutic use ; Drug Therapy, Combination ; *Gastrointestinal Microbiome ; *Helicobacter Infections/drug therapy/microbiology ; *Helicobacter pylori ; Humans ; *Limosilactobacillus reuteri ; Metronidazole/therapeutic use ; Proton Pump Inhibitors ; RNA, Ribosomal, 16S ; Rabeprazole/pharmacology/therapeutic use ; Tetracycline/pharmacology/therapeutic use ; Treatment Outcome ; }, abstract = {BACKGROUND: Probiotic supplementation to antibiotic regimens against Helicobacter pylori infection has been proposed to improve eradication rate and to decrease detrimental effects on gut microbiota.

AIMS: To evaluate microbiota modifications due to a low-dose quadruple therapy with bismuth or Lactobacillus reuteri.

METHODS: Forty-six patients infected with H. pylori were prospectively enrolled in a single-centre, randomized controlled trial to receive b.i.d. with meals for 10 days low-dose quadruple therapy consisting of rabeprazole 20 mg and bismuth (two capsules of Pylera[®] plus 250 mg each of tetracycline and metronidazole), or the same dose of rabeprazole and antibiotics plus Gastrus[®] (L. reuteri), one tablet twice-a-day for 27 days. Stool samples were collected at the enrolment, at the end and 30-40 days after the treatment. Gut microbiota composition was investigated with 16S rRNA gene sequencing.

RESULTS: Eradication rate was by ITT 78% in both groups, and by PP analysis 85.7% and 95.5% for Gastrus[®] and bismuth group, respectively. Alpha and beta diversity decreased at the end of treatment and was associated with a reduction of bacterial genera beneficial for gut homeostasis, which was rescued 30-40 days later in both groups, suggesting a similar impact of the two regimens in challenging bacterial community complexity.

CONCLUSIONS: Low-dose bismuth quadruple therapy proved to be effective with lower costs and amount of antibiotics and bismuth. Gastrus[®] might be an option for patients with contraindications to bismuth. L. reuteri was unable to significantly counteract dysbiosis induced by antibiotics. How to administer probiotics to prevent gut microbiota alterations remains an open question.}, } @article {pmid35889742, year = {2022}, author = {Anderson, EM and Rozowsky, JM and Fazzone, BJ and Schmidt, EA and Stevens, BR and O'Malley, KA and Scali, ST and Berceli, SA}, title = {Temporal Dynamics of the Intestinal Microbiome Following Short-Term Dietary Restriction.}, journal = {Nutrients}, volume = {14}, number = {14}, pages = {}, pmid = {35889742}, issn = {2072-6643}, support = {T32 GM008721/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics/metabolism ; Diet, Protein-Restricted ; Dysbiosis ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; }, abstract = {Short-term dietary restriction has been proposed as an intriguing pre-operative conditioning strategy designed to attenuate the surgical stress response and improve outcomes. However, it is unclear how this nutritional intervention influences the microbiome, which is known to modulate the systemic condition. Healthy individuals were recruited to participate in a four-day, 70% protein-restricted, 30% calorie-restricted diet, and stool samples were collected at baseline, after the restricted diet, and after resuming normal food intake. Taxonomy and functional pathway analysis was performed via shotgun metagenomic sequencing, prevalence filtering, and differential abundance analysis. High prevalence species were altered by the dietary intervention but quickly returned to baseline after restarting a regular diet. Composition and functional changes after the restricted diet included the decreased relative abundance of commensal bacteria and a catabolic phenotype. Notable species changes included Faecalibacterium prausnitzii and Roseburia intestinalis, which are major butyrate producers within the colon and are characteristically decreased in many disease states. The macronutrient components of the diet might have influenced these changes. We conclude that short-term dietary restriction modulates the ecology of the gut microbiome, with this modulation being characterized by a relative dysbiosis.}, } @article {pmid35889179, year = {2022}, author = {Hwang, J and Kang, HW and Moon, SJ and Hyung, JH and Lee, ES and Park, J}, title = {Metagenomic Analysis of the Species Composition and Seasonal Distribution of Marine Dinoflagellate Communities in Four Korean Coastal Regions.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889179}, issn = {2076-2607}, support = {R2022005//National Fisheries Research and Development Institute/ ; NRF-2021R1A2C1005943//National Research Foundation of Korea/ ; }, abstract = {Biomonitoring of dinoflagellate communities in marine ecosystems is essential for efficient water quality management and limiting ecosystem disturbances. Current identification and monitoring of toxic dinoflagellates, which cause harmful algal blooms, primarily involves light or scanning electron microscopy; however, these techniques are limited in their ability to monitor dinoflagellates and plankton, leaving an incomplete analysis. In this study, we analyzed the species composition and seasonal distribution of the dinoflagellate communities in four Korean coastal regions using 18S rRNA amplicon sequencing. The results showed significantly high diversity in the dinoflagellate communities in all regions and seasons. Furthermore, we found seasonally dominant species and causative species of harmful algal blooms (Cochlodinium sp., Alexandrium sp., Dinophysis sp., and Gymnodinium sp.). Moreover, dominant species were classified by region and season according to the difference in geographical and environmental parameters. The molecular analysis of the dinoflagellate community based on metagenomics revealed more diverse species compositions that could not be identified by microscopy and revealed potentially harmful or recently introduced dinoflagellate species. In conclusion, metagenomic analysis of dinoflagellate communities was more precise and obtained results faster than microscopic analysis, and could improve the existing monitoring techniques for community analysis.}, } @article {pmid35889177, year = {2022}, author = {Florent, P and Cauchie, HM and Herold, M and Jacquet, S and Ogorzaly, L}, title = {Soil pH, Calcium Content and Bacteria as Major Factors Responsible for the Distribution of the Known Fraction of the DNA Bacteriophage Populations in Soils of Luxembourg.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889177}, issn = {2076-2607}, support = {PRIDE15/10623093//Fonds National de la Recherche/ ; }, abstract = {Bacteriophages participate in soil life by influencing bacterial community structure and function, biogeochemical cycling and horizontal gene transfer. Despite their great abundance, diversity, and importance in microbial processes, they remain little explored in environmental studies. The influence of abiotic factors on the persistence of bacteriophages is now recognized; however, it has been mainly studied under experimental conditions. This study aimed to determine whether the abiotic factors well-known to influence bacteriophage persistence also control the natural distribution of the known DNA bacteriophage populations. To this end, soil from eight study sites including forests and grasslands located in the Attert River basin (Grand Duchy of Luxembourg) were sampled, covering different soil and land cover characteristics. Shotgun metagenomics, reference-based bioinformatics and statistical analyses allowed characterising the diversity of known DNA bacteriophage and bacterial communities. After combining soil properties with the identified DNA bacteriophage populations, our in-situ study highlighted the influence of pH and calcium cations on the diversity of the known fraction of the soil DNA bacteriophages. More interestingly, significant relationships were established between bacteriophage and bacterial populations. This study provides new insights into the importance of abiotic and biotic factors in the distribution of DNA bacteriophages and the natural ecology of terrestrial bacteriophages.}, } @article {pmid35889151, year = {2022}, author = {Santos, A and Burgos, F and Martinez-Urtaza, J and Barrientos, L}, title = {Metagenomic Characterization of Resistance Genes in Deception Island and Their Association with Mobile Genetic Elements.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889151}, issn = {2076-2607}, support = {DI19-0079//University of La Frontera/ ; NXR17-0003//Network for Extreme Environments Research/ ; CONICYT-Doctorado Nacional-2017-21171392//Agencia Nacional de Investigación y Desarrollo/ ; Fondecyt 1216503//Agencia Nacional de Investigación y Desarrollo/ ; }, abstract = {Antibiotic resistance genes (ARGs) are undergoing a remarkably rapid geographic expansion in various ecosystems, including pristine environments such as Antarctica. The study of ARGs and environmental resistance genes (ERGs) mechanisms could provide a better understanding of their origin, evolution, and dissemination in these pristine environments. Here, we describe the diversity of ARGs and ERGs and the importance of mobile genetic elements as a possible mechanism for the dissemination of resistance genes in Antarctica. We analyzed five soil metagenomes from Deception Island in Antarctica. Results showed that detected ARGs are associated with mechanisms such as antibiotic efflux, antibiotic inactivation, and target alteration. On the other hand, resistance to metals, surfactants, and aromatic hydrocarbons were the dominant ERGs. The taxonomy of ARGs showed that Pseudomonas, Psychrobacter, and Staphylococcus could be key taxa for studying antibiotic resistance and environmental resistance to stress in Deception Island. In addition, results showed that ARGs are mainly associated with phage-type mobile elements suggesting a potential role in their dissemination and prevalence. Finally, these results provide valuable information regarding the ARGs and ERGs in Deception Island including the potential contribution of mobile genetic elements to the spread of ARGs and ERGs in one of the least studied Antarctic ecosystems to date.}, } @article {pmid35889138, year = {2022}, author = {Gilbert, A and Nakagawa, M and Taguchi, K and Zhang, N and Nishida, A and Yoshida, N}, title = {Hydrocarbon Cycling in the Tokamachi Mud Volcano (Japan): Insights from Isotopologue and Metataxonomic Analyses.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889138}, issn = {2076-2607}, support = {18K18782//MEXT Japan/ ; 21H01198//MEXT Japan/ ; 17H06105//MEXT Japan/ ; }, abstract = {Understanding hydrocarbon cycling in the subsurface is important in various disciplines including climate science, energy resources and astrobiology. Mud volcanoes provide insights into biogeochemical processes occurring in the subsurface. They are usually associated with natural gas reservoirs consisting mainly of methane and other hydrocarbons as well as CO2. Stable isotopes have been used to decipher the sources and sinks of hydrocarbons in the subsurface, although the interpretation can be ambiguous due to the numerous processes involved. Here we report new data for hydrocarbon isotope analysis, including position-specific isotope composition of propane, for samples from the Tokamachi mud volcano area, Japan. The data suggest that C2+ hydrocarbons are being biodegraded, with indirect production of methane ("secondary methanogenesis"). Data from chemical and isotopic composition are discussed with regard to 16S rRNA analysis, which exhibits the presence of hydrogenotrophic and acetoclastic methoanogens. Overall, the combination of isotopologue analysis with 16S rRNA gene data allows refining of our understanding of hydrocarbon cycling in subsurface environments.}, } @article {pmid35889116, year = {2022}, author = {Rojas, MVR and Alonso, DP and Dropa, M and Razzolini, MTP and de Carvalho, DP and Ribeiro, KAN and Ribolla, PEM and Sallum, MAM}, title = {Next-Generation High-Throughput Sequencing to Evaluate Bacterial Communities in Freshwater Ecosystem in Hydroelectric Reservoirs.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889116}, issn = {2076-2607}, support = {2014/26229-7//São Paulo Research Foundation/ ; 301877/2016-5//National Council for Scientific and Technological Development/ ; }, abstract = {The quality of aquatic ecosystems is a major public health concern. The assessment and management of a freshwater system and the ecological monitoring of microorganisms that are present in it can provide indicators of the environment and water quality to protect human and animal health. with bacteria is. It is a major challenge to monitor the microbiological bacterial contamination status of surface water associated with anthropogenic activities within rivers and freshwater reservoirs. Understanding the composition of aquatic microbial communities can be beneficial for the early detection of pathogens, improving our knowledge of their ecological niches, and characterizing the assemblages of microbiota responsible for the degradation of contaminants and microbial substrates. The present study aimed to characterize the bacterial microbiota of water samples collected alongside the Madeira River and its small tributaries in rural areas near the Santo Antonio Energia hydroelectric power plant (SAE) reservoir in the municipality of Porto Velho, Rondonia state, Western Brazil. An Illumina 16s rRNA metagenomic approach was employed and the physicochemical characteristics of the water sample were assessed. We hypothesized that both water metagenomics and physicochemical parameters would vary across sampling sites. The most abundant genera found in the study were Acinetobacter, Deinococcus, and Pseudomonas. PERMANOVA and ANCOM analysis revealed that collection points sampled at the G4 location presented a significantly different microbiome compared to any other group, with the Chlamidomonadaceae family and Enhydrobacter genus being significantly more abundant. Our findings support the use of metagenomics to assess water quality standards for the protection of human and animal health in this microgeographic region.}, } @article {pmid35889112, year = {2022}, author = {Hoffman, T and Sjödin, A and Öhrman, C and Karlsson, L and McDonough, RF and Sahl, JW and Birdsell, D and Wagner, DM and Carra, LG and Wilhelmsson, P and Pettersson, JH and Barboutis, C and Figuerola, J and Onrubia, A and Kiat, Y and Piacentini, D and Jaenson, TGT and Lindgren, PE and Moutailler, S and Fransson, T and Forsman, M and Nilsson, K and Lundkvist, Å and Olsen, B}, title = {Co-Occurrence of Francisella, Spotted Fever Group Rickettsia, and Midichloria in Avian-Associated Hyalomma rufipes.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889112}, issn = {2076-2607}, support = {ALF//Uppsala County Council/ ; 874735 (VEO)//European Union's Horizon 2020 research innovation program/ ; //Ax:son Johnson Foundation/ ; LPP1-007//SciLifeLab Pandemic Laboratory Preparedness/ ; //NGI/Uppmax/ ; ANSES-2016//French Agency for Food, Environmental and Occupational Health and Safety (ANSES)/ ; 2020-02593//Swedish Research Council/ ; 2015-710//Swedish Research Council for Environment Agricultural Sciences and Spatial Planning/ ; TA 014-2010-01//Swedish Civil Contingencies Agency/ ; HSHQDC-17-C-B0021//US Department of Homeland Security's Science and Technology Directorate pursuant to the agreement between the Kingdom of Sweden and the US government on Cooperation in Science and Technology for Homeland Security Matters/ ; }, abstract = {The migratory behavior of wild birds contributes to the geographical spread of ticks and their microorganisms. In this study, we aimed to investigate the dispersal and co-occurrence of Francisella and spotted fever group Rickettsia (SFGR) in ticks infesting birds migrating northward in the African-Western Palaearctic region (AWPR). Birds were trapped with mist nests across the Mediterranean basin during the 2014 and 2015 spring migration. In total, 575 ticks were collected from 244 birds. We screened the ticks for the species Francisella tularensis, the genus Francisella, and SFGR by microfluidic real-time PCR. Confirmatory analyses and metagenomic sequencing were performed on tick samples that putatively tested positive for F. tularensis during initial screenings. Hyalomma rufipes was the most common tick species and had a high prevalence of Francisella, including co-occurrence of Francisella and SFGR. Metagenomic analysis of total DNA extracted from two H. rufipes confirmed the presence of Francisella, Rickettsia, and Midichloria. Average nucleotide identity and phylogenetic inference indicated the highest identity of the metagenome-assembled genomes to a Francisella-like endosymbiont (FLE), Rickettsia aeschlimannii, and Midichloria mitochondrii. The results of this study suggest that (i) FLE- and SFGR-containing ticks are dispersed by northbound migratory birds in the AWPR, (ii) H. rufipes likely is not involved in transmission of F. tularensis in the AWPR, and (iii) a dual endosymbiosis of FLEs and Midichloria may support some of the nutritional requirements of H. rufipes.}, } @article {pmid35889107, year = {2022}, author = {Torres-Maravilla, E and Reyes-Pavón, D and Benítez-Cabello, A and González-Vázquez, R and Ramírez-Chamorro, LM and Langella, P and Bermúdez-Humarán, LG}, title = {Strategies for the Identification and Assessment of Bacterial Strains with Specific Probiotic Traits.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889107}, issn = {2076-2607}, abstract = {Early in the 1900s, it was proposed that health could be improved and senility delayed by manipulating gut microbiota with the host-friendly bacteria found in yogurt. Later, in 1990, the medical community reconsidered this idea and today probiotics represent a developed area of research with a billion-dollar global industry. As a result, in recent decades, increased attention has been paid to the isolation and characterization of novel probiotic bacteria from fermented foods and dairy products. Most of the identified probiotic strains belong to the lactic acid bacteria group and the genus Bifidobacterium. However, current molecular-based knowledge has allowed the identification and culture of obligatory anaerobic commensal bacteria from the human gut, such as Akkermansia spp. and Faecalibacterium spp., among other human symbionts. We are aware that the identification of new strains of these species does not guarantee their probiotic effects and that each effect must be proved through in vitro and in vivo preclinical studies before clinical trials (before even considering it as a probiotic strain). In most cases, the identification and characterization of new probiotic strain candidates may lack the appropriate set of in vitro experiments allowing the next assessment steps. Here, we address some innovative strategies reported in the literature as alternatives to classical characterization: (i) identification of alternatives using whole-metagenome shotgun sequencing, metabolomics, and multi-omics analysis; and (ii) probiotic characterization based on molecular effectors and/or traits to target specific diseases (i.e., inflammatory bowel diseases, colorectal cancer, allergies, among others).}, } @article {pmid35889080, year = {2022}, author = {Goma-Tchimbakala, EJCD and Pietrini, I and Dal Bello, F and Goma-Tchimbakala, J and Lo Russo, S and Corgnati, SP}, title = {Great Abilities of Shinella zoogloeoides Strain from a Landfarming Soil for Crude Oil Degradation and a Synergy Model for Alginate-Bead-Entrapped Consortium Efficiency.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889080}, issn = {2076-2607}, support = {Eni Award for Africa//ENI SpA/ ; }, abstract = {Oil contamination is of great concern worldwide and needs to be properly addressed. The present work aimed to contribute to the development of bacterial consortia for oil recovery. We investigated the community structure of a landfarming-treated soil (LF2) by metagenomics to unravel the presence of hydrocarbon degraders. Moreover, we isolated Shinella zoogloeoides LFG9 and Bacillus swezeyi LFS15 from LF2 and combined them with Pseudomonas guguanensis SGPP2 isolated from an auto mechanic workshop soil to form the mixed consortium COG1. Bacterial isolates were tested for biosurfactant production. Additionally, the bioremediation potential of COG1 was studied as free and entrapped consortia by gas chromatography-mass spectrometry, in comparison to the single strains. Results revealed the presence of Actinobacteria (66.11%), Proteobacteria (32.21%), Gammaproteobacteria (5.39%), Actinomycetales (65.15%), Burkholderiales (13.92%), and Mycobacterium (32.22%) taxa, indicating the presence of hydrocarbon degraders in soil LF2. All three isolated strains were biosurfactant producers capable of degrading crude oil components within 14 days. However, Shinella zoogloeoides LFG9 performed best and was retained as candidate for further bioremediation investigation. In addition, COG1 performed better when immobilized, with entrapment effectiveness manifested by increased fatty acids and aromatic compound degradation. Attempt to improve crude oil biodegradation by adding surfactants failed as sodium dodecyl sulfate restrained the immobilized consortium performance.}, } @article {pmid35889040, year = {2022}, author = {Guo, W and Mao, B and Tang, X and Zhang, Q and Zhao, J and Cui, S and Zhang, H}, title = {Lactobacillus paracasei CCFM1223 Protects against Lipopolysaccharide-Induced Acute Liver Injury in Mice by Regulating the "Gut-Liver" Axis.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889040}, issn = {2076-2607}, support = {31972086//National Natural Science Foundation of China/ ; 32172173//National Natural Science Foundation of China/ ; 32072197//National Natural Science Foundation of China/ ; 2021C-003-T//Yongjiang Talent Introduction Programme/ ; }, abstract = {BACKGROUND: Lactobacillus paracasei CCFM1223, a probiotic previously isolated from the healthy people's intestine, exerts the beneficial influence of preventing the development of inflammation.

METHODS: The aim of this research was to explore the beneficial effects of L. paracasei CCFM1223 to prevent lipopolysaccharide (LPS)-induced acute liver injury (ALI) and elaborate on its hepatoprotective mechanisms.

RESULTS: L. paracasei CCFM1223 pretreatment remarkably decreased the activities of serum aspartate aminotransferase (AST) and alanine aminotransferase (ALT) in mice with LPS treatment and remarkably recovered LPS-induced the changes in inflammatory cytokines (tumor necrosis factor-α (TNF-α), transforming growth factor-β (TGF-β), interleukin (IL)-1β, IL-6, IL-17, IL-10, and LPS) and antioxidative enzymes activities (total antioxidant capacity (T-AOC), superoxide dismutase (SOD), glutathione peroxidase (GSH-Px), and catalase (CAT)). Metagenomic analysis showed that L. paracasei CCFM1223 pretreatment remarkably increased the relative abundance of Catabacter compared with the LPS group but remarkably reduced the relative abundance of [Eubacterium] xylanophilumgroup, ASF356, LachnospiraceaeNK4A136group, and Lachnoclostridium, which is closely associated with the inflammation cytokines and antioxidative enzymes. Furthermore, L. paracasei CCFM1223 pretreatment remarkably increased the colonic, serum, and hepatic IL-22 levels in ALI mice. In addition, L. paracasei CCFM1223 pretreatment remarkably down-regulated the hepatic Tlr4 and Nf-kβ transcriptions and significantly up-regulated the hepatic Tlr9, Tak1, Iκ-Bα, and Nrf2 transcriptions in ALI mice.

CONCLUSIONS: L. paracasei CCFM1223 has a hepatoprotective function in ameliorating LPS-induced ALI by regulating the "gut-liver" axis.}, } @article {pmid35889019, year = {2022}, author = {Ravin, NV and Rossetti, S and Beletsky, AV and Kadnikov, VV and Rudenko, TS and Smolyakov, DD and Moskvitina, MI and Gureeva, MV and Mardanov, AV and Grabovich, MY}, title = {Two New Species of Filamentous Sulfur Bacteria of the Genus Thiothrix, Thiothrix winogradskyi sp. nov. and 'Candidatus Thiothrix sulfatifontis' sp. nov.}, journal = {Microorganisms}, volume = {10}, number = {7}, pages = {}, pmid = {35889019}, issn = {2076-2607}, support = {20-14-00137//Russian Science Foundation/ ; }, abstract = {The metagenome of foulings from sulfidic spring "Serovodorodny" (Tatarstan, Russia), where members of the genus Thiothrix was observed, was sequenced. Representatives of the phyla Gammaproteobacteria, Cyanobacteria and Campilobacteriota dominated in the microbial community. The complete genome of Thiothrix sp. KT was assembled from the metagenome. It displayed 93.93-99.72% 16S rRNA gene sequence identity to other Thiothrix species. The average nucleotide identity (ANI) и digital DNA-DNA hybridization (dDDH) showed that the genome designated KT represents a new species within the genus Thiothrix, 'Candidatus Thiothrix sulfatifontis' sp. nov. KT. The taxonomic status has been determined of the strain Thiothrix sp. CT3, isolated about 30 years ago and not assigned to any of Thiothrix species due to high 16S rRNA gene sequence identity with related species (i.e., 98.8-99.4%). The complete genome sequence of strain CT3 was determined. The ANI between CT3 and other Thiothrix species was below 82%, and the dDDH values were less than 40%, indicating that strain CT3 belongs to a novel species, Thiothrix winogradskyi sp. nov. A genome analysis showed that both strains are chemo-organoheterotrophs, chemolithotrophs (in the presence of hydrogen sulfide and thiosulfate) and chemoautotrophs. For the first time, representatives of Thiothrix showed anaerobic growth in the presence of thiosulfate.}, } @article {pmid35888797, year = {2022}, author = {Tharak, A and Mohan, SV}, title = {Syngas Fermentation to Acetate and Ethanol with Adaptative Electroactive Carboxydotrophs in Single Chambered Microbial Electrochemical System.}, journal = {Micromachines}, volume = {13}, number = {7}, pages = {}, pmid = {35888797}, issn = {2072-666X}, support = {No. BT/PR20759/BCE/8/1218/2016//Department of Biotechnology/ ; }, abstract = {Microbial electrosynthesis system (MES; single-chambered) was fabricated and evaluated with carbon cloth/graphite as a working/counter electrode employing an enriched microbiome. Continuous syngas sparging (at working electrode; WE) enabled the growth of endo electrogenic bacteria by availing the inorganic carbon source. Applied potential (-0.5 V) on the working electrode facilitated the reduction in syngas, leading to the synthesis of fatty acids and alcohols. The higher acetic acid titer of 3.8 g/L and ethanol concentration of 0.2 g/L was observed at an active microbial metabolic state, evidencing the shift in metabolism from acetogenic to solventogenesis. Voltammograms evidenced distinct redox species with low charge transfer resistance (Rct; Nyquist impedance). Reductive catalytic current (-0.02 mA) enabled the charge transfer efficiency of the cathodes favoring syngas conversion to products. The surface morphology of carbon cloth and system-designed conditions favored the growth of electrochemically active consortia. Metagenomic analysis revealed the enrichment of phylum/class with Actinobacteria, Firmicutes/Clostridia and Bacilli, which accounts for the syngas fermentation through suitable gene loci.}, } @article {pmid35888694, year = {2022}, author = {Zhao, F and Wei, Z and Bai, Y and Li, C and Zhou, G and Kristiansen, K and Wang, C}, title = {Proteomics and Metabolomics Profiling of Pork Exudate Reveals Meat Spoilage during Storage.}, journal = {Metabolites}, volume = {12}, number = {7}, pages = {}, pmid = {35888694}, issn = {2218-1989}, support = {32001721//National Natural Science Foundation of China/ ; CARS-35//Ministry of Agriculture and Rural Affairs/ ; RAPD//Priority Academic Program Development of Jiangsu Higher Education Institutions/ ; }, abstract = {Previous studies have evaluated pork quality by omics methods. However, proteomics coupled with metabolomics to investigate pork freshness by using pork exudates has not been reported. This study determined the changes in the profiles of peptides and metabolites in exudates from pork stored at different temperatures (25, 10, 4, and -2 °C). Multivariate statistical analysis revealed similar changes in profiles in exudates collected from pork stored at -2 and 4 °C, and additional changes following storage at higher temperatures. We identified peptides from 7 proteins and 30 metabolites differing in abundance between fresh and spoiled pork. Significant correlations between pork quality and most of the peptides from these 7 proteins and 30 metabolites were found. The present study provides insight into changes in the peptide and metabolite profiles of exudates from pork during storage at different temperatures, and our analysis suggests that such changes can be used as markers of pork spoilage.}, } @article {pmid35888639, year = {2022}, author = {Sokolovs-Karijs, O and Brīvība, M and Saksis, R and Sumeraga, G and Girotto, F and Erts, R and Osīte, J and Krūmiņa, A}, title = {An Overview of Adenoid Microbiome Using 16S rRNA Gene Sequencing-Based Metagenomic Analysis.}, journal = {Medicina (Kaunas, Lithuania)}, volume = {58}, number = {7}, pages = {}, pmid = {35888639}, issn = {1648-9144}, mesh = {*Adenoids/chemistry/microbiology ; Bacteria/genetics ; Child ; Genes, rRNA ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/analysis/genetics ; Veillonella ; }, abstract = {Background and Objectives: the upper respiratory tract harbors the highest bacterial density in the whole respiratory system. Adenoids, which are located in the nasopharynx, are a major site of bacterial colonies in the upper airways. Our goal was to use culture-independent molecular techniques to identify the breadth of bacterial diversity in the adenoid vegetations of children suffering from chronic rhinosinusitis and obstructive sleep apnea. Materials and methods: in total, 21 adenoid samples were investigated using amplification and sequencing of the V3-V4 hypervariable region of the bacterial 16S rRNA gene. Results: among the most common bacterial species found were Veillonella atypica, Fusobactrium nucelatum, Shaalia odontolytica, and Moraxella catarrhalis. Veillonella atypica and Fusbacteriumnucelatum dominated the microbiome in all 21 samples, attributing to more than 60% of all detected genetic material. Conclusions: since both Veillonella atypica and Fusobacterium nucleatum are, predominantly, oral cavity and dental microorganisms, our findings may suggest oral microbiome migration deeper into the oropharynx and nasopharynx where these bacteria colonize adenoid vegetations.}, } @article {pmid35887492, year = {2022}, author = {Aragona, M and Haegi, A and Valente, MT and Riccioni, L and Orzali, L and Vitale, S and Luongo, L and Infantino, A}, title = {New-Generation Sequencing Technology in Diagnosis of Fungal Plant Pathogens: A Dream Comes True?.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {7}, pages = {}, pmid = {35887492}, issn = {2309-608X}, abstract = {The fast and continued progress of high-throughput sequencing (HTS) and the drastic reduction of its costs have boosted new and unpredictable developments in the field of plant pathology. The cost of whole-genome sequencing, which, until few years ago, was prohibitive for many projects, is now so affordable that a new branch, phylogenomics, is being developed. Fungal taxonomy is being deeply influenced by genome comparison, too. It is now easier to discover new genes as potential targets for an accurate diagnosis of new or emerging pathogens, notably those of quarantine concern. Similarly, with the development of metabarcoding and metagenomics techniques, it is now possible to unravel complex diseases or answer crucial questions, such as "What's in my soil?", to a good approximation, including fungi, bacteria, nematodes, etc. The new technologies allow to redraw the approach for disease control strategies considering the pathogens within their environment and deciphering the complex interactions between microorganisms and the cultivated crops. This kind of analysis usually generates big data that need sophisticated bioinformatic tools (machine learning, artificial intelligence) for their management. Herein, examples of the use of new technologies for research in fungal diversity and diagnosis of some fungal pathogens are reported.}, } @article {pmid35886216, year = {2022}, author = {Grace-Farfaglia, P and Frazier, H and Iversen, MD}, title = {Essential Factors for a Healthy Microbiome: A Scoping Review.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {14}, pages = {}, pmid = {35886216}, issn = {1660-4601}, mesh = {Diet ; Fatty Acids, Volatile/metabolism ; *Gastrointestinal Microbiome/physiology ; Humans ; Metagenome ; *Microbiota ; }, abstract = {Recent discoveries of the purpose and potential of microbial interactions with humans have broad implications for our understanding of metabolism, immunity, the host−microbe genetic interactions. Bioavailability and bioaccessibility of phytonutrients in foods not only enrich microbial diversity in the lower human gastrointestinal tract (GIT) but also direct the functioning of the metagenome of the microbiota. Thus, healthy choices must include foods that contain nutrients that satisfy both the needs of humans and their microbes. Physical activity interventions at a moderate level of intensity have shown positive effects on metabolism and the microbiome, while intense training (>70% VO2max) reduces diversity in the short term. The microbiome of elite endurance athletes is a robust producer of short-chain fatty acids. A lifestyle lacking activity is associated with the development of chronic disease, and experimental conditions simulating weightlessness in humans demonstrate loss of muscle mass occurring in conjunction with a decline in gut short-chain fatty acid (SCFA) production and the microbes that produce them. This review summarizes evidence addressing the relationship between the intestinal microbiome, diet, and physical activity. Data from the studies reviewed suggest that food choices and physical fitness in developed countries promote a resource “curse” dilemma for the microbiome and our health.}, } @article {pmid35885966, year = {2022}, author = {Luo, D and Liu, W and Chen, T and An, L}, title = {A Distribution-Free Model for Longitudinal Metagenomic Count Data.}, journal = {Genes}, volume = {13}, number = {7}, pages = {}, pmid = {35885966}, issn = {2073-4425}, support = {U19 AG065169/AG/NIA NIH HHS/United States ; P01 AI148104/AI/NIAID NIH HHS/United States ; R01 GM139829/GM/NIGMS NIH HHS/United States ; }, mesh = {Computer Simulation ; Metagenome ; *Metagenomics/methods ; *Models, Statistical ; }, abstract = {Longitudinal metagenomics has been widely studied in the recent decade to provide valuable insight for understanding microbial dynamics. The correlation within each subject can be observed across repeated measurements. However, previous methods that assume independent correlation may suffer from incorrect inferences. In addition, methods that do account for intra-sample correlation may not be applicable for count data. We proposed a distribution-free approach, namely CorrZIDF, which extends the current method to model correlated zero-inflated metagenomic count data, offering a powerful and accurate solution for detecting significance features. This method can handle different working correlation structures without specifying each margin distribution of the count data. Through simulation studies, we have shown the robustness of CorrZIDF when selecting a working correlation structure for repeated measures studies to enhance the efficiency of estimation. We also compared four methods using two real datasets, and the new proposed method identified more unique features that were reported previously on the relevant research.}, } @article {pmid35885645, year = {2022}, author = {Hajjo, R and Sabbah, DA and Al Bawab, AQ}, title = {Unlocking the Potential of the Human Microbiome for Identifying Disease Diagnostic Biomarkers.}, journal = {Diagnostics (Basel, Switzerland)}, volume = {12}, number = {7}, pages = {}, pmid = {35885645}, issn = {2075-4418}, support = {2019-2020/23/07//Deanship of Scientific Research at Al-Zaytoonah University of Jordan/ ; }, abstract = {The human microbiome encodes more than three million genes, outnumbering human genes by more than 100 times, while microbial cells in the human microbiota outnumber human cells by 10 times. Thus, the human microbiota and related microbiome constitute a vast source for identifying disease biomarkers and therapeutic drug targets. Herein, we review the evidence backing the exploitation of the human microbiome for identifying diagnostic biomarkers for human disease. We describe the importance of the human microbiome in health and disease and detail the use of the human microbiome and microbiota metabolites as potential diagnostic biomarkers for multiple diseases, including cancer, as well as inflammatory, neurological, and metabolic diseases. Thus, the human microbiota has enormous potential to pave the road for a new era in biomarker research for diagnostic and therapeutic purposes. The scientific community needs to collaborate to overcome current challenges in microbiome research concerning the lack of standardization of research methods and the lack of understanding of causal relationships between microbiota and human disease.}, } @article {pmid35884227, year = {2022}, author = {Bamidele, O and Yakubu, A and Joseph, EB and Amole, TA}, title = {Antibiotic Resistance of Bacterial Isolates from Smallholder Poultry Droppings in the Guinea Savanna Zone of Nigeria.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, pmid = {35884227}, issn = {2079-6382}, support = {CGIAR RESEARCH PROGRAM FOR NUTRITION AND HEALTH, 2021//CGIAR/ ; }, abstract = {There is a growing risk of antibiotic resistance (AR) in smallholder poultry (SP). This study, therefore, aimed to investigate AR pattern of bacterial isolates from SP in the Guinea Savanna agro-ecological zone of Nigeria. A total of 120 fresh poultry droppings were aseptically collected, randomly, from two tropically adapted (FUNAAB Alpha and Noiler) and local chickens. The chickens were raised either using ethnoveterinary medicines (n = 60) or antibiotics (n = 60). Bacterial isolates were characterized and analyzed using standard protocols, and appropriate statistical tools. Compared to Pseudomonas spp. (2.5%) and Klebsiella spp. (5.8%), Salmonella spp. (57.5%) and Escherichia coli (34.2%) were the most prevalent (χ2 = 96.67; p < 0.001). Prevalence of bacterial species was significantly (p = 0.024; Odds Ratio = 2.552) influenced by antibiotics usage. All four species were multi-drug resistant. In total, 30% of the isolates had a multiple AR index ≥ 0.2. Bacterial isolates from FUNAAB Alpha (58.0%) and Noiler (44.0%) were highly resistant to quinolones, while isolates from the local chickens (22.6%) were most resistant to aminoglycosides. Bacterial species isolated from FUNAAB Alpha and local chickens exhibited the lowest and highest percentage of AR, respectively. Clustering of isolates with similar antibiogram revealed inter-species dependence with possibility for inter-species gene transfer. These findings provide a background to investigate the metagenomics of local and improved chickens for AR.}, } @article {pmid35884142, year = {2022}, author = {Fernández-López, M and Sánchez-Reyes, A and Barcelos, C and Sidón-Ceseña, K and Leite, RB and Lago-Lestón, A}, title = {Deep-Sea Sediments from the Southern Gulf of Mexico Harbor a Wide Diversity of PKS I Genes.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, pmid = {35884142}, issn = {2079-6382}, support = {Hydrocarbon Trust, project 201441//National Council of Science and Technology of Mexico - Mexican Ministry of Energy/ ; }, abstract = {The excessive use of antibiotics has triggered the appearance of new resistant strains, which is why great interest has been taken in the search for new bioactive compounds capable of overcoming this emergency in recent years. Massive sequencing tools have enabled the detection of new microorganisms that cannot be cultured in a laboratory, thus opening the door to the search for new biosynthetic genes. The great variety in oceanic environments in terms of pressure, salinity, temperature, and nutrients enables marine microorganisms to develop unique biochemical and physiological properties for their survival, enhancing the production of secondary metabolites that can vary from those produced by terrestrial microorganisms. We performed a search for type I PKS genes in metagenomes obtained from the marine sediments of the deep waters of the Gulf of Mexico using Hidden Markov Models. More than 2000 candidate genes were detected in the metagenomes that code for type I PKS domains, while biosynthetic pathways that may code for other secondary metabolites were also detected. Our research demonstrates the great potential use of the marine sediments of the Gulf of Mexico for identifying genes that code for new secondary metabolites.}, } @article {pmid35884116, year = {2022}, author = {Azuma, T and Katagiri, M and Sekizuka, T and Kuroda, M and Watanabe, M}, title = {Inactivation of Bacteria and Residual Antimicrobials in Hospital Wastewater by Ozone Treatment.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {7}, pages = {}, pmid = {35884116}, issn = {2079-6382}, support = {JP22fk0108131//Japan Agency for Medical Research and Development/ ; H30 Shinkogyo-sei-Ippan-002//research on emerging and reemerging infectious diseases and immunization from the Ministry of Health, Labour and Welfare/ ; 21HA1002//research on emerging and reemerging infectious diseases and immunization from the Ministry of Health, Labour and Welfare/ ; }, abstract = {The emergence and spread of antimicrobial resistance (AMR) has become a persistent problem globally. In this study, an ozone treatment facility was established for an advanced hospital wastewater treatment in a core hospital facility in an urban area in Japan to evaluate the inactivation of antimicrobial-resistant bacteria and antimicrobials. Metagenomic DNA-seq analysis and the isolation of potential extended-spectrum β-lactamase (ESBL)-producing bacteria suggested that ozone exposure for at least 20 min is required for the adequate inactivation of DNA and ESBL-producing bacteria. Escherichia coli and Klebsiella species were markedly susceptible to 20-min ozone exposure, whereas Raoultella ornithinolytica and Pseudomonas putida were isolated even after an 80-min exposure. These ozone-resistant bacteria might play a pivotal role as AMR reservoirs in the environment. Nine antimicrobials (ampicillin, cefdinir, cefpodoxime, ciprofloxacin, levofloxacin, clarithromycin, chlortetracycline, minocycline, and vancomycin) were detected at 373 ng/L to 27 μg/L in the hospital wastewater, and these were removed (96-100% removal) after a 40-min treatment. These results facilitate a comprehensive understanding of the AMR risk posed by hospital wastewater and provides insights for devising strategies to eliminate or mitigate the burden of antimicrobial-resistant bacteria and the flow of antimicrobials into the environment. To the best of our knowledge, this is the first report on the implementation of a batch-type, plant-scale ozone treatment system in a hospital facility to execute and evaluate the inactivation of drug-resistant bacteria and antimicrobials.}, } @article {pmid35883471, year = {2022}, author = {Zhang, Y and Jin, J and Huang, B and Ying, H and He, J and Jiang, L}, title = {Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective.}, journal = {Biomolecules}, volume = {12}, number = {7}, pages = {}, pmid = {35883471}, issn = {2218-273X}, mesh = {Archaea/genetics/metabolism ; *Computational Biology ; Humans ; Prokaryotic Cells ; *Selenium/metabolism ; Selenoproteins/genetics/metabolism ; }, abstract = {Selenium (Se) is an important trace element that mainly occurs in the form of selenocysteine in selected proteins. In prokaryotes, Se is also required for the synthesis of selenouridine and Se-containing cofactor. A large number of selenoprotein families have been identified in diverse prokaryotic organisms, most of which are thought to be involved in various redox reactions. In the last decade or two, computational prediction of selenoprotein genes and comparative genomics of Se metabolic pathways and selenoproteomes have arisen, providing new insights into the metabolism and function of Se and their evolutionary trends in bacteria and archaea. This review aims to offer an overview of recent advances in bioinformatics analysis of Se utilization in prokaryotes. We describe current computational strategies for the identification of selenoprotein genes and generate the most comprehensive list of prokaryotic selenoproteins reported to date. Furthermore, we highlight the latest research progress in comparative genomics and metagenomics of Se utilization in prokaryotes, which demonstrates the divergent and dynamic evolutionary patterns of different Se metabolic pathways, selenoprotein families, and selenoproteomes in sequenced organisms and environmental samples. Overall, bioinformatics analyses of Se utilization, function, and evolution may contribute to a systematic understanding of how this micronutrient is used in nature.}, } @article {pmid35883256, year = {2023}, author = {Al-Heeti, O and Wu, EL and Ison, MG and Saluja, RK and Ramsey, G and Matkovic, E and Ha, K and Hall, S and Banach, B and Wilson, MR and Miller, S and Chiu, CY and McCabe, M and Bari, C and Zimler, RA and Babiker, H and Freeman, D and Popovitch, J and Annambhotla, P and Lehman, JA and Fitzpatrick, K and Velez, JO and Davis, EH and Hughes, HR and Panella, A and Brault, A and Staples, JE and Gould, CV and Tanna, S}, title = {Transfusion-Transmitted Cache Valley Virus Infection in a Kidney Transplant Recipient With Meningoencephalitis.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {76}, number = {3}, pages = {e1320-e1327}, pmid = {35883256}, issn = {1537-6591}, support = {CC999999/ImCDC/Intramural CDC HHS/United States ; UL1 TR001422/TR/NCATS NIH HHS/United States ; UL1TR001422)/TR/NCATS NIH HHS/United States ; K08NS096117)/NS/NINDS NIH HHS/United States ; }, mesh = {Humans ; Antibodies, Neutralizing ; Blood Transfusion ; *Bunyamwera virus ; *Kidney Transplantation/adverse effects ; *Meningoencephalitis/diagnosis ; }, abstract = {BACKGROUND: Cache Valley virus (CVV) is a mosquito-borne virus that is a rare cause of disease in humans. In the fall of 2020, a patient developed encephalitis 6 weeks following kidney transplantation and receipt of multiple blood transfusions.

METHODS: After ruling out more common etiologies, metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) was performed. We reviewed the medical histories of the index kidney recipient, organ donor, and recipients of other organs from the same donor and conducted a blood traceback investigation to evaluate blood transfusion as a possible source of infection in the kidney recipient. We tested patient specimens using reverse-transcription polymerase chain reaction (RT-PCR), the plaque reduction neutralization test, cell culture, and whole-genome sequencing.

RESULTS: CVV was detected in CSF from the index patient by mNGS, and this result was confirmed by RT-PCR, viral culture, and additional whole-genome sequencing. The organ donor and other organ recipients had no evidence of infection with CVV by molecular or serologic testing. Neutralizing antibodies against CVV were detected in serum from a donor of red blood cells received by the index patient immediately prior to transplant. CVV neutralizing antibodies were also detected in serum from a patient who received the co-component plasma from the same blood donation.

CONCLUSIONS: Our investigation demonstrates probable CVV transmission through blood transfusion. Clinicians should consider arboviral infections in unexplained meningoencephalitis after blood transfusion or organ transplantation. The use of mNGS might facilitate detection of rare, unexpected infections, particularly in immunocompromised patients.}, } @article {pmid35883169, year = {2022}, author = {Liu, J and Xue, CX and Wang, J and Crombie, AT and Carrión, O and Johnston, AWB and Murrell, JC and Liu, J and Zheng, Y and Zhang, XH and Todd, JD}, title = {Oceanospirillales containing the DMSP lyase DddD are key utilisers of carbon from DMSP in coastal seawater.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {110}, pmid = {35883169}, issn = {2049-2618}, mesh = {*Alphaproteobacteria/genetics ; Bacteria ; Carbon/metabolism ; Carbon-Sulfur Lyases ; DNA ; *Gammaproteobacteria/genetics/metabolism ; Seawater/microbiology ; Sulfonium Compounds ; Sulfur/metabolism ; }, abstract = {BACKGROUND: Ubiquitous and diverse marine microorganisms utilise the abundant organosulfur molecule dimethylsulfoniopropionate (DMSP), the main precursor of the climate-active gas dimethylsulfide (DMS), as a source of carbon, sulfur and/or signalling molecules. However, it is currently difficult to discern which microbes actively catabolise DMSP in the environment, why they do so and the pathways used.

RESULTS: Here, a novel DNA-stable isotope probing (SIP) approach, where only the propionate and not the DMS moiety of DMSP was [13]C-labelled, was strategically applied to identify key microorganisms actively using DMSP and also likely DMS as a carbon source, and their catabolic enzymes, in North Sea water. Metagenomic analysis of natural seawater suggested that Rhodobacterales (Roseobacter group) and SAR11 bacteria were the major microorganisms degrading DMSP via demethylation and, to a lesser extent, DddP-driven DMSP lysis pathways. However, neither Rhodobacterales and SAR11 bacteria nor their DMSP catabolic genes were prominently labelled in DNA-SIP experiments, suggesting they use DMSP as a sulfur source and/or in signalling pathways, and not primarily for carbon requirements. Instead, DNA-SIP identified gammaproteobacterial Oceanospirillales, e.g. Amphritea, and their DMSP lyase DddD as the dominant microorganisms/enzymes using DMSP as a carbon source. Supporting this, most gammaproteobacterial (with DddD) but few alphaproteobacterial seawater isolates grew on DMSP as sole carbon source and produced DMS. Furthermore, our DNA-SIP strategy also identified Methylophaga and other Piscirickettsiaceae as key bacteria likely using the DMS, generated from DMSP lysis, as a carbon source.

CONCLUSIONS: This is the first study to use DNA-SIP with [13]C-labelled DMSP and, in a novel way, it identifies the dominant microbes utilising DMSP and DMS as carbon sources. It highlights that whilst metagenomic analyses of marine environments can predict microorganisms/genes that degrade DMSP and DMS based on their abundance, it cannot disentangle those using these important organosulfur compounds for their carbon requirements. Note, the most abundant DMSP degraders, e.g. Rhodobacterales with DmdA, are not always the key microorganisms using DMSP for carbon and releasing DMS, which in this coastal system were Oceanospirillales containing DddD. Video abstract.}, } @article {pmid35882981, year = {2022}, author = {Zhao, L and Zhang, X and Zhou, Y and Fu, K and Lau, HC and Chun, TW and Cheung, AH and Coker, OO and Wei, H and Wu, WK and Wong, SH and Sung, JJ and To, KF and Yu, J}, title = {Parvimonas micra promotes colorectal tumorigenesis and is associated with prognosis of colorectal cancer patients.}, journal = {Oncogene}, volume = {41}, number = {36}, pages = {4200-4210}, pmid = {35882981}, issn = {1476-5594}, mesh = {Animals ; Carcinogenesis/genetics ; Cell Proliferation ; *Colorectal Neoplasms/pathology ; Firmicutes ; Gene Expression Regulation, Neoplastic ; Humans ; *Interleukin-17/metabolism ; Mice ; }, abstract = {Large-scale fecal shotgun metagenomic sequencing revealed the high abundance of Parvimonas micra in colorectal cancer (CRC) patients. We investigated the role and clinical significance of P. micra in colorectal tumorigenesis. The abundance of P. micra was examined in 309 fecal samples and 165 colon biopsy tissues of CRC patients and healthy subjects. P. micra was significantly enriched in fecal samples from 128 CRC patients compared to 181 healthy subjects (P < 0.0001); and in colon tissue biopsies from 52 CRC patients compared to 61 healthy subjects (P < 0.0001). Multivariate analysis showed that P. micra is an independent risk factor of poor survival in CRC patients (Hazard Ratio: 1.93). P. micra strain was isolated from feces of a CRC patient. Apc[min/+] mice gavaged with P. micra showed significantly higher tumor burden and tumor load (both P < 0.01). Consistently, gavage of P. micra significantly promoted colonocyte proliferation in conventional mice, which was further confirmed by germ-free mice. P. micra colonization up-regulated genes involved in cell proliferation, stemness, angiogenesis and invasiveness/metastasis; and enhanced Th17 cells infiltration and expression of Th17 cells-secreted cytokines (Il-17, Il-22, and Il-23) in the colon of Apc[min/+], conventional and germ-free mice. P. micra-conditioned medium significantly promoted the differentiation of CD4[+] T cells to Th17 cells (IL-17[+]CD4[+] phenotype) and enhanced the oncogenic Wnt signaling pathway. In conclusion, P. micra promoted colorectal tumorigenesis in mice by inducing colonocyte proliferation and altering Th17 immune response. P. micra may act as a prognostic biomarker for poor survival of CRC patients.}, } @article {pmid35882645, year = {2022}, author = {Wang, Z and Iida, N and Seishima, J and Okafuji, H and Yutani, M and Fujinaga, Y and Hashimoto, Y and Tomita, H and Mizukoshi, E and Kaneko, S}, title = {Patient-derived Enterococcus faecium with inflammatory genotypes promote colitis.}, journal = {Journal of gastroenterology}, volume = {57}, number = {10}, pages = {770-783}, pmid = {35882645}, issn = {1435-5922}, mesh = {Animals ; Antioxidants ; *Colitis/chemically induced ; *Colitis, Ulcerative ; Dysbiosis ; *Enterococcus faecium/pathogenicity ; Genotype ; Humans ; Interleukin-10/genetics ; Mice ; *Probiotics ; Reactive Oxygen Species ; Thioctic Acid/pharmacology/therapeutic use ; }, abstract = {BACKGROUND: Dysbiosis of gut microbiota promotes colitis in ulcerative colitis (UC). Enterococcus faecium is an important constituent of dysbiotic microbiota. However, the mechanisms underlying E. faecium-induced colitis remain unclear.

METHODS: Overall, 23 E. faecium strains isolated from human feces and 3 commercial strains were inoculated into Il10[-/-] mice. Mouse colons were histologically evaluated and analyzed using real-time PCR analysis of cytokines. Genes in 26 E. faecium strains were identified by whole-genome shotgun sequencing of genomic DNA. The production of reactive oxygen species (ROS) from each strain was measured. An antioxidant, lipoic acid, was orally administered to the colitis mouse model.

RESULTS: Inoculation of E. faecium derived from patients with UC resulted in colitis in Il10[-/-] mice. The genotypes of 26 strains were characterized by identifying 1893 known genes; clustering all the strains based on the genotypes showed two major groups-inflammatory and probiotic clusters. Additionally, linear discriminant analysis clarified that lipoic acid metabolism was a significantly abundant pathway in the probiotic cluster compared to the inflammatory cluster. Further, the production of ROS was greater in inflammatory than in probiotic strains. Administration of lipoic acid in E. faecium-inoculated mice ameliorated colitis.

CONCLUSIONS: Enterococcus faecium strains in the inflammatory cluster promoted colitis with higher production of ROS than the strains in the probiotic cluster.}, } @article {pmid35882315, year = {2022}, author = {Zhang, S and Xiao, M and Liang, C and Chui, C and Wang, N and Shi, J and Liu, L}, title = {Multivariate insights into enhanced biogas production in thermophilic dry anaerobic co-digestion of food waste with kitchen waste or garden waste: Process properties, microbial communities and metagenomic analyses.}, journal = {Bioresource technology}, volume = {361}, number = {}, pages = {127684}, doi = {10.1016/j.biortech.2022.127684}, pmid = {35882315}, issn = {1873-2976}, mesh = {Anaerobiosis ; Biofuels ; Bioreactors/microbiology ; Food ; Gardens ; Methane/metabolism ; *Microbiota ; *Refuse Disposal/methods ; Sewage/microbiology ; }, abstract = {Multisubstrate synergetic anaerobic co-digestion can effectively overcome low efficiency of food waste (FW) mono-digestion. This study investigated the effect of supplementing FW with kitchen waste (KW) or garden waste (GW) on thermophilic dry anaerobic co-digestion. FW-KW and FW-GW co-digestion enhanced biogas production by 24.69 % and 44.96 % at organic loading rate (OLR) of 3 g VS L[-1] d[-1], and increased OLR tolerance from 3 to 4 g VS L[-1] d[-1] through mitigating ammonia nitrogen inhibition and volatile fatty acids accumulation. Co-digestion enriched the dominant hydrolytic bacteria Defluviitoga, resulting in an acceleration of substrate hydrolysis. FW-KW co-digestion improved biogas production by increasing gene abundance related to key enzymes in methanogenesis pathways and promoting the conversion of intermediate products into methane. FW-GW co-digestion enhanced biogas production by enriching ABC transporters-associated genes, leading to efficient substrate utilization. This study provides a promising approach for FW treatment with multivariate insights into thermophilic dry anaerobic co-digestion.}, } @article {pmid35880887, year = {2022}, author = {Holman, DB and Kommadath, A and Tingley, JP and Abbott, DW}, title = {Novel Insights into the Pig Gut Microbiome Using Metagenome-Assembled Genomes.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0238022}, pmid = {35880887}, issn = {2165-0497}, mesh = {Animals ; Archaea/genetics ; Bacteria ; Carbohydrates ; *Gastrointestinal Microbiome/genetics ; Mammals/genetics ; *Metagenome ; Metagenomics/methods ; Swine ; }, abstract = {Pigs are among the most numerous and intensively farmed food-producing animals in the world. The gut microbiome plays an important role in the health and performance of swine and changes rapidly after weaning. Here, fecal samples were collected from pigs at 7 different times points from 7 to 140 days of age. These swine fecal metagenomes were used to assemble 1,150 dereplicated metagenome-assembled genomes (MAGs) that were at least 90% complete and had less than 5% contamination. These MAGs represented 472 archaeal and bacterial species, and the most widely distributed MAGs were the uncultured species Collinsella sp002391315, Sodaliphilus sp004557565, and Prevotella sp000434975. Weaning was associated with a decrease in the relative abundance of 69 MAGs (e.g., Escherichia coli) and an increase in the relative abundance of 140 MAGs (e.g., Clostridium sp000435835, Oliverpabstia intestinalis). Genes encoding for the production of the short-chain fatty acids acetate, butyrate, and propionate were identified in 68.5%, 18.8%, and 8.3% of the MAGs, respectively. Carbohydrate-active enzymes associated with the degradation of arabinose oligosaccharides and mixed-linkage glucans were predicted to be most prevalent among the MAGs. Antimicrobial resistance genes were detected in 327 MAGs, including 59 MAGs with tetracycline resistance genes commonly associated with pigs, such as tet(44), tet(Q), and tet(W). Overall, 82% of the MAGs were assigned to species that lack cultured representatives indicating that a large portion of the swine gut microbiome is still poorly characterized. The results here also demonstrate the value of MAGs in adding genomic context to gut microbiomes. IMPORTANCE Many of the bacterial strains found in the mammalian gut are difficult to culture and isolate due to their various growth and nutrient requirements that are frequently unknown. Here, we assembled strain-level genomes from short metagenomic sequences, so-called metagenome-assembled genomes (MAGs), that were derived from fecal samples collected from pigs at multiple time points. The genomic context of a number of antimicrobial resistance genes commonly detected in swine was also determined. In addition, our study connected taxonomy with potential metabolic functions such as carbohydrate degradation and short-chain fatty acid production.}, } @article {pmid35880883, year = {2022}, author = {Chu, X and Wang, X and Cheung, LS and Feng, X and Ang, P and Lee, SY and Crowe, SA and Luo, H}, title = {Coastal Transient Niches Shape the Microdiversity Pattern of a Bacterioplankton Population with Reduced Genomes.}, journal = {mBio}, volume = {13}, number = {4}, pages = {e0057122}, pmid = {35880883}, issn = {2150-7511}, mesh = {Aquatic Organisms/genetics ; Carbon ; *Ecosystem ; Oxygen ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Roseobacter ; Seawater/microbiology ; }, abstract = {Globally dominant marine bacterioplankton lineages are often limited in metabolic versatility, owing to their extensive genome reductions, and thus cannot take advantage of transient nutrient patches. It is therefore perplexing how the nutrient-poor bulk seawater sustains the pelagic streamlined lineages, each containing numerous populations. Here, we sequenced the genomes of 33 isolates of the recently discovered CHUG lineage (~2.6 Mbp), which have some of the smallest genomes in the globally abundant Roseobacter group (commonly over 4 Mbp). These genome-reduced bacteria were isolated from a transient habitat: seawater surrounding the brown alga, Sargassum hemiphyllum. Population genomic analyses showed that: (i) these isolates, despite sharing identical 16S rRNA genes, were differentiated into several genetically isolated populations through successive speciation events; (ii) only the first speciation event led to the genetic separation of both core and accessory genomes; and (iii) populations resulting from this event are differentiated at many loci involved in carbon utilization and oxygen respiration, corroborated by BiOLOG phenotype microarray assays and oxygen uptake kinetics experiments, respectively. These differentiated traits match well with the dynamic nature of the macroalgal seawater, in which the quantity and quality of carbon sources and the concentration of oxygen likely vary spatially and temporally, though other habitats, like fresh organic aggregates, cannot be ruled out. Our study implies that transient habitats in the overall nutrient-poor ocean can shape the microdiversity and population structure of genome-reduced bacterioplankton lineages. IMPORTANCE Prokaryotic species, defined with operational thresholds, such as 95% of the whole-genome average nucleotide identity (ANI) or 98.7% similarity of the 16S rRNA gene sequences, commonly contain extensive fine-grained diversity in both the core genome and the accessory genome. However, the ways in which this genomic microdiversity and its associated phenotypic microdiversity are organized and structured is poorly understood, which disconnects microbial diversity and ecosystem functioning. Population genomic approaches that allow this question to be addressed are commonly applied to cultured species because linkages between different loci are necessary but are missing from metagenome-assembled genomes. In the past, these approaches were only applied to easily cultivable bacteria and archaea, which, nevertheless, are often not representative of natural communities. Here, we focus on the recently discovered cluster, CHUG, which are representative in marine bacterioplankton communities and possess some of the smallest genomes in the globally dominant marine Roseobacter group. Despite being over 95% ANI and identical in the 16S rRNA gene, the 33 CHUG genomes we analyzed have undergone multiple speciation events, with the first split event predominantly structuring the genomic diversity. The observed pattern of genomic microdiversity correlates with CHUG members' differential utilization of carbon sources and differential ability to explore low-oxygen niches. The available data are consistent with the idea that brown algae may be home to CHUG, though other habitats, such as fresh organic aggregates, are also possible.}, } @article {pmid35880866, year = {2022}, author = {Zajc, J and Černoša, A and Sun, X and Fang, C and Gunde-Cimerman, N and Song, Z and Gostinčar, C}, title = {From Glaciers to Refrigerators: the Population Genomics and Biocontrol Potential of the Black Yeast Aureobasidium subglaciale.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0145522}, pmid = {35880866}, issn = {2165-0497}, mesh = {*Ascomycota/genetics ; Aureobasidium ; Fruit/microbiology ; Ice Cover ; *Malus/microbiology ; Metagenomics ; Pest Control, Biological/methods ; }, abstract = {Apples are affected by numerous fungi known as storage rots, which cause significant losses before and after harvest. Concerns about increasing antimicrobial resistance, bans on various fungicides, and changing consumer preferences are motivating the search for safer means to prevent fruit rot. The use of antagonistic microbes has been shown to be an efficient and environmentally friendly alternative to conventional phytopharmaceuticals. Here, we investigate the potential of Aureobasidium subglaciale for postharvest rot control. We tested the antagonistic activity of 9 strains of A. subglaciale and 7 closely related strains against relevant phytopathogenic fungi under conditions simulating low-temperature storage: Botrytis cinerea, Penicillium expansum, and Colletotrichum acutatum. We also investigated a selection of phenotypic traits of all strains and sequenced their whole genomes. The tested strains significantly reduced postharvest rot of apples at low temperatures caused by B. cinerea, C. acutatum (over 60%), and P. expansum (about 40%). Several phenotypic traits were observed that may contribute to this biocontrol capacity: growth at low temperatures, tolerance to high temperatures and elevated solute concentrations, and strong production of several extracellular enzymes and siderophores. Population genomics revealed that 7 of the 15 strains originally identified as A. subglaciale most likely belong to other, possibly undescribed species of the same genus. In addition, the population structure and linkage disequilibrium of the species suggest that A. subglaciale is strictly clonal and therefore particularly well suited for use in biocontrol. Overall, these data suggest substantial biological control potential for A. subglaciale, which represents another promising biological agent for disease control in fresh fruit. IMPORTANCE After harvest, fruits are often stored at low temperatures to prolong their life. However, despite the low temperatures, much of the fruit is lost to rot caused by a variety of fungi, resulting in major economic losses and food safety risks. An increasingly important environmentally friendly alternative to conventional methods of mitigating the effects of plant diseases is the use of microorganisms that act similarly to probiotics-occupying the available space, producing antimicrobial compounds, and consuming the nutrients needed by the rot-causing species. To find a new microorganism for biological control that is particularly suitable for cold storage of fruit, we tested different isolates of the cold-loving yeast Aureobasidium subglaciale and studied their phenotypic characteristics and genomes. We demonstrated that A. subglaciale can significantly reduce rotting of apples caused by three rot-causing molds at low temperatures and thus has great potential for preventing fruit rot during cold storage.}, } @article {pmid35880414, year = {2022}, author = {Tiley, GP and van Elst, T and Teixeira, H and Schüßler, D and Salmona, J and Blanco, MB and Ralison, JM and Randrianambinina, B and Rasoloarison, RM and Stahlke, AR and Hohenlohe, PA and Chikhi, L and Louis, EE and Radespiel, U and Yoder, AD}, title = {Population genomic structure in Goodman's mouse lemur reveals long-standing separation of Madagascar's Central Highlands and eastern rainforests.}, journal = {Molecular ecology}, volume = {31}, number = {19}, pages = {4901-4918}, doi = {10.1111/mec.16632}, pmid = {35880414}, issn = {1365-294X}, mesh = {Animals ; *Cheirogaleidae/genetics ; Humans ; *Lemur ; Madagascar ; Metagenomics ; Rainforest ; }, abstract = {Madagascar's Central Highlands are largely composed of grasslands, interspersed with patches of forest. The historical perspective was that Madagascar's grasslands had anthropogenic origins, but emerging evidence suggests that grasslands were a component of the pre-human Central Highlands vegetation. Consequently, there is now vigorous debate regarding the extent to which these grasslands have expanded due to anthropogenic pressures. Here, we shed light on the temporal dynamics of Madagascar's vegetative composition by conducting a population genomic investigation of Goodman's mouse lemur (Microcebus lehilahytsara; Cheirogaleidae). These small-bodied primates occur both in Madagascar's eastern rainforests and in the Central Highlands, making them a valuable indicator species. Population divergences among forest-dwelling mammals will reflect changes to their habitat, including fragmentation, whereas patterns of post-divergence gene flow can reveal formerly wooded migration corridors. To explore these patterns, we used RADseq data to infer population genetic structure, demographic models of post-divergence gene flow, and population size change through time. The results offer evidence that open habitats are an ancient component of the Central Highlands, and that widespread forest fragmentation occurred naturally during a period of decreased precipitation near the last glacial maximum. Models of gene flow suggest that migration across the Central Highlands has been possible from the Pleistocene through the recent Holocene via riparian corridors. Though our findings support the hypothesis that Central Highland grasslands predate human arrival, we also find evidence for human-mediated population declines. This highlights the extent to which species imminently threatened by human-mediated deforestation may already be vulnerable from paleoclimatic conditions.}, } @article {pmid35880014, year = {2022}, author = {Dickson, ZW and Hackenberger, D and Kuch, M and Marzok, A and Banerjee, A and Rossi, L and Klowak, JA and Fox-Robichaud, A and Mossmann, K and Miller, MS and Surette, MG and Golding, GB and Poinar, H}, title = {Erratum: Probe design for simultaneous, targeted capture of diverse metagenomic targets.}, journal = {Cell reports methods}, volume = {2}, number = {7}, pages = {100246}, doi = {10.1016/j.crmeth.2022.100246}, pmid = {35880014}, issn = {2667-2375}, abstract = {[This corrects the article DOI: 10.1016/j.crmeth.2021.100069.].}, } @article {pmid35879284, year = {2022}, author = {Lee, I and Podolich, O and Brenig, B and Tiwari, S and Azevedo, V and de Carvalho, DS and Uetanabaro, APT and Góes-Neto, A and Alzahrani, KJ and Reva, O and Kozyrovska, N and de Vera, JP and Barh, D and Kim, BS}, title = {Metagenome-Assembled Genomes of Komagataeibacter from Kombucha Exposed to Mars-Like Conditions Reveal the Secrets in Tolerating Extraterrestrial Stresses.}, journal = {Journal of microbiology and biotechnology}, volume = {32}, number = {8}, pages = {967-975}, pmid = {35879284}, issn = {1738-8872}, mesh = {*Acetobacteraceae ; Cellulose ; *Metagenome ; Yeasts ; }, abstract = {Kombucha mutualistic community (KMC) is composed by acetic acid bacteria and yeasts, producing fermented tea with health benefits. As part of the BIOlogy and Mars EXperiment (BIOMEX) project, the effect of Mars-like conditions on the KMC was analyzed. Here, we analyzed metagenome-assembled genomes (MAGs) of the Komagataeibacter, which is a predominant genus in KMC, to understand their roles in the KMC after exposure to Mars-like conditions (outside the International Space Station) based on functional genetic elements. We constructed three MAGs: K. hansenii, K. rhaeticus, and K. oboediens. Our results showed that (i) K. oboediens MAG functionally more complex than K. hansenii, (ii) K. hansenii is a keystone in KMCs with specific functional features to tolerate extreme stress, and (iii) genes related to the PPDK, betaine biosynthesis, polyamines biosynthesis, sulfate-sulfur assimilation pathway as well as type II toxin-antitoxin (TA) system, quorum sensing (QS) system, and cellulose production could play important roles in the resilience of KMC after exposure to Mars-like stress. Our findings show the potential mechanisms through which Komagataeibacter tolerates the extraterrestrial stress and will help to understand minimal microbial composition of KMC for space travelers.}, } @article {pmid35879048, year = {2022}, author = {Haifer, C and Luu, LDW and Paramsothy, S and Borody, TJ and Leong, RW and Kaakoush, NO}, title = {Microbial determinants of effective donors in faecal microbiota transplantation for UC.}, journal = {Gut}, volume = {}, number = {}, pages = {}, doi = {10.1136/gutjnl-2022-327742}, pmid = {35879048}, issn = {1468-3288}, abstract = {OBJECTIVE: Faecal microbiota transplantation (FMT) has variable efficacy in treating UC. Recently, oral lyophilised FMT was found to induce remission in patients with UC, with one donor having 100% efficacy compared with a second donor (36% efficacy). We characterised differences in the gut microbiota of these two donors with the aim of improving FMT donor selection.

DESIGN: Faecal samples from the two donors were collected over a period of 44 (donor 1) or 70 (donor 2) weeks. The microbiome and metabolome were profiled using shotgun metagenomics and untargeted metabolomics RESULTS: Gut microbiome long-term stability was highly evident in the effective donor. Donor microbiota species evenness was a robust feature associated with clinical efficacy across two clinical trials of FMT in UC, leading to increased donor species engraftment in patients. Alpha diversity and beta diversity of donor gut microbiotas significantly differed. 90 bacterial species and one archaeon were differentially abundant between donors, 44 of which were >0.1% in relative abundance. 17/44 species were enriched in the effective donor, 11 of which (64.7%) were assembled into high-quality genomes that were prevalent (≥75% samples) in that donor, and six showed evidence of engraftment in patients. Taxonomic differences between donors translated to substantial microbial functional differences that were validated using metabolomics.

CONCLUSION: Donor microbiota stability and species evenness were identified as novel metrics that were associated with therapeutic efficacy in UC, beyond individual microbial species or metabolites. These metrics may represent community resilience that translates to better engraftment in the host.

TRIAL REGISTRATION NUMBER: ACTRN12619000611123.}, } @article {pmid35878764, year = {2022}, author = {Hung, CM and Chen, CW and Huang, CP and Sheu, DS and Dong, CD}, title = {Metal-free catalysis for organic micropollutant degradation in waste activated sludge via poly(3-hydroxybutyrate) biopolymers using Cupriavidus sp. L7L coupled with peroxymonosulfate.}, journal = {Bioresource technology}, volume = {361}, number = {}, pages = {127680}, doi = {10.1016/j.biortech.2022.127680}, pmid = {35878764}, issn = {1873-2976}, mesh = {3-Hydroxybutyric Acid ; Biopolymers ; Catalysis ; *Cupriavidus/metabolism ; Hydroxybutyrates ; Metals ; Peroxides ; *Polycyclic Aromatic Hydrocarbons/metabolism ; Polyesters ; Sewage/microbiology ; Wastewater/analysis ; }, abstract = {This study employed a novel and environment-friendly biopolymer/oxidant catalytic system, viz., poly(3-hydroxybutyrate)/peroxymonosulfate (PHB/PMS), for pretreating wastewater sludge for the first time. Under optimal conditions, i.e., 3.1 × 10[-4] M of PMS and 3.3 g/L of PHB at pH = 6.0, the PAHs in the sludge matrix was decreased by 79 % in 12 h. Increase in salinity (75 % synthetic seawater) achieved 83 % of PAHs degradation. Functional groups (CO) of the biopolymer matrix were active centers for biopolymer-mediated electron transfer that produced reactive oxygen species (SO4[-], HO, and [1]O2) for adsorption and catalytic oxidation of PAHs in the sludge. Functional metagenomic analysis revealed the main genus, Conexibacter (phylum, Actinobacteria) exhibited PAH-degrading function with high efficiency in the biodegradation of PAHs from sludge pretreated with PHB/PMS. Coupling chemical oxidation and biostimulation using bacterial polymer-based biomaterials is effective and beneficial for pretreating wastewater sludge toward circular bioeconomy.}, } @article {pmid35878349, year = {2022}, author = {Kim, SH and Song, HS and Kim, CH and Kwon, YK and Park, CK and Kim, HR}, title = {Histopathological Findings and Metagenomic Analysis of Esophageal Papillary Proliferation Identified in Laying Broiler Breeders.}, journal = {Veterinary sciences}, volume = {9}, number = {7}, pages = {}, pmid = {35878349}, issn = {2306-7381}, support = {F-1543084-2021-22-01//Animal and Plant Quarantine Agency/ ; }, abstract = {White or pale-yellow nodules 2-7 mm in length were observed in the esophageal lumen in a number of laying broiler breeders with reduced laying rates. Metaplasia of the mucosal epithelial layer and mucous gland, as well as lymphocyte infiltration under the esophageal mucous gland and epithelial cell layer, were observed, which we found were caused by vitamin A deficiency. In one chicken, however, the stratified squamous epithelial cells of the esophagus were completely replaced by increased numbers of ducts/ductules, lymphocytes, and connective tissue, resulting in a papillary morphology. The ducts were surrounded by a fibrous stroma. Multiple hyperplasia of the esophageal gland was also observed and the esophageal glands were lined by a single layer of columnar cells, and a large number of lymphocytes were infiltrated into the submucosal layer. Based on the gross findings, this papillary proliferation was considered papilloma, but histopathologically, a mass composed of squamous epithelium was not observed. Therefore, the papillary lesion appeared as adenoma with squamous metaplasia of the esophageal gland and ectasia, or mucosal epithelial papillary hyperplasia, associated with chronic esophagitis. A metagenomic analysis of the esophagus samples from this chicken was performed to determine the infectious etiology. No viral cause was identified; however, a contributing role of Bradyrhizobium sp. could not be excluded. In this study, we report the first histopathological examination of a rare case of esophageal papillary proliferation in a chicken and highlight the importance of histopathological results for a definitive diagnosis of such cases.}, } @article {pmid35877863, year = {2022}, author = {Li, C and Maqbool, T and Kang, H and Zhang, Z}, title = {In-Situ Sludge Reduction in Membrane-Controlled Anoxic-Oxic-Anoxic Bioreactor: Performance and Mechanism.}, journal = {Membranes}, volume = {12}, number = {7}, pages = {}, pmid = {35877863}, issn = {2077-0375}, support = {52170041, 52050410336//National Natural Science Foundation of China/ ; }, abstract = {Conventional and advanced biological wastewater treatment systems generate excess sludge, which causes socio-economic and environmental issues. This study investigated the performance of membrane-controlled anoxic-oxic-anoxic (AOA) bioreactors for in-situ sludge reduction compared to the conventional anoxic-oxic-oxic membrane bioreactor (MBRcontrol). The membrane units in the AOA bioreactors were operated as anoxic reactors at lower sludge recirculation rates to achieve hydrolysis of extracellular polymeric substances (EPS) and extensive endogenous respiration. Compared to MBRcontrol, the AOA bioreactors operated with 90%, and 80% recirculation rates reduced the sludge growth up to 19% and 30%, respectively. Protein-like components were enriched in AOA bioreactors while fulvic-like components were dominant in MBRcontrol. The growth of Dechloromonas and Zoogloea genra was promoted in AOA bioreactors and thus sludge reduction was facilitated. Metagenomics analysis uncovered that AOA bioreactors exhibited higher proportions of key genes encoding enzymes involved in the glycolysis and denitrification processes, which contributed to the utilization of carbon sources and nitrogen consumption and thus sludge reduction.}, } @article {pmid35877439, year = {2022}, author = {Grenda, T and Grenda, A and Domaradzki, P and Krawczyk, P and Kwiatek, K}, title = {Probiotic Potential of Clostridium spp.-Advantages and Doubts.}, journal = {Current issues in molecular biology}, volume = {44}, number = {7}, pages = {3118-3130}, pmid = {35877439}, issn = {1467-3045}, abstract = {Clostridium spp. is a large genus of obligate anaerobes and is an extremely heterogeneous group of bacteria that can be classified into 19 clusters. Genetic analyses based on the next-generation sequencing of 16S rRNA genes and metagenome analyses conducted on human feces, mucosal biopsies, and luminal content have shown that the three main groups of strict extremophile anaerobes present in the intestines are Clostridium cluster IV (also known as the Clostridium leptum group), Clostridium cluster XIVa (also known as the Clostridium coccoides group) and Bacteroides. In addition to the mentioned clusters, some C. butyricum strains are also considered beneficial for human health. Moreover, this bacterium has been widely used as a probiotic in Asia (particularly in Japan, Korea, and China). The mentioned commensal Clostridia are involved in the regulation and maintenance of all intestinal functions. In the literature, the development processes of new therapies are described based on commensal Clostridia activity. In addition, some Clostridia are associated with pathogenic processes. Some C. butyricum strains detected in stool samples are involved in botulism cases and have also been implicated in severe diseases such as infant botulism and necrotizing enterocolitis in preterm neonates. The aim of this study is to review reports on the possibility of using Clostridium strains as probiotics, consider their positive impact on human health, and identify the risks associated with the expression of their pathogenic properties.}, } @article {pmid35876505, year = {2022}, author = {Devi, YD and Dey, U and Kumar, A and Singh, CS and Namsa, ND}, title = {Genome Sequence of a Wa-Like G3P[8] Rotavirus from a 12-Month-Old Child with Diarrhea in Manipur, India.}, journal = {Microbiology resource announcements}, volume = {11}, number = {8}, pages = {e0125421}, pmid = {35876505}, issn = {2576-098X}, support = {BT/338/NE/TBP/2012 dtd 14th August 2014//Department of Biotechnology, Ministry of Science and Technology, India (DBT)/ ; }, abstract = {Rotavirus A (RVA) was detected in the stool of a 12-month-old child with diarrhea, mild fever, and vomiting. A viral metagenomic approach identified a Wa-like genotype G3P[8] strain named RVA/Human-wt/IND/RM25112/2016.}, } @article {pmid35875797, year = {2022}, author = {Zhang, S and Ning, R and Zeng, B and Deng, F and Kong, F and Guo, W and Zhao, J and Li, Y}, title = {Gut Microbiota Composition and Metabolic Potential of Long-Living People in China.}, journal = {Frontiers in aging neuroscience}, volume = {14}, number = {}, pages = {820108}, pmid = {35875797}, issn = {1663-4365}, abstract = {Individuals with naturally long-life spans have been extensively studied to gain a greater understanding of what factors contribute to their overall health and ability to delay or avoid certain diseases. Our previous work showed that gut microbiota can be a new avenue in healthy aging studies. In the present study, a total of 86 Chinese individuals were assigned into three groups: the long-living group (90 + years old; n = 28), the elderly group (65-75 years old; n = 31), and the young group (24-48 years old; n = 27). These groups were used to explore the composition and functional genes in the microbiota community by using the metagenomic sequencing method. We found that long-living individuals maintained high diversity in gene composition and functional profiles. Furthermore, their microbiota displays less inter-individual variation than that of elderly adults. In the taxonomic composition, it was shown that long-living people contained more short-chain fatty acid (SCFA)-producing bacteria and a decrease in certain pathogenic bacteria. Functional analysis also showed that the long-living people were enriched in metabolism metabolites methanol, trimethylamine (TMA), and CO2 to methane, and lysine biosynthesis, but the genes related to riboflavin (vitamin B2) metabolism and tryptophan biosynthesis were significantly reduced in long-living individuals. Further, we found that long-living people with enriched SCFA- and lactic-producing bacteria and related genes, highly centered on producing key lactic acid genes (ldhA) and the genes of lysine that are metabolized to the butyrate pathway. In addition, we compared the gut microbiota signatures of longevity in different regions and found that the composition of the gut microbiota of the long-lived Chinese and Italian people was quite different, but both groups were enriched in genes related to methane production and glucose metabolism. In terms of SCFA metabolism, the Chinese long-living people were enriched with bacteria and genes related to butyric acid production, while the Italian long-living people were enriched with more acetic acid-related genes. These findings suggest that the gut microbiota of Chinese long-living individuals include more SCFA-producing bacteria and genes, metabolizes methanol, TMA, and CO2, and contains fewer pathogenic bacteria, thereby potentially contributing to the healthy aging of humans.}, } @article {pmid35875611, year = {2022}, author = {Liang, H and Jo, JH and Zhang, Z and MacGibeny, MA and Han, J and Proctor, DM and Taylor, ME and Che, Y and Juneau, P and Apolo, AB and McCulloch, JA and Davar, D and Zarour, HM and Dzutsev, AK and Brownell, I and Trinchieri, G and Gulley, JL and Kong, HH}, title = {Predicting cancer immunotherapy response from gut microbiomes using machine learning models.}, journal = {Oncotarget}, volume = {13}, number = {}, pages = {876-889}, pmid = {35875611}, issn = {1949-2553}, mesh = {Bacteria/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Immunotherapy ; Machine Learning ; *Melanoma/therapy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Cancer immunotherapy has significantly improved patient survival. Yet, half of patients do not respond to immunotherapy. Gut microbiomes have been linked to clinical responsiveness of melanoma patients on immunotherapies; however, different taxa have been associated with response status with implicated taxa inconsistent between studies. We used a tumor-agnostic approach to find common gut microbiome features of response among immunotherapy patients with different advanced stage cancers. A combined meta-analysis of 16S rRNA gene sequencing data from our mixed tumor cohort and three published immunotherapy gut microbiome datasets from different melanoma patient cohorts found certain gut bacterial taxa correlated with immunotherapy response status regardless of tumor type. Using multivariate selbal analysis, we identified two separate groups of bacterial genera associated with responders versus non-responders. Statistical models of gut microbiome community features showed robust prediction accuracy of immunotherapy response in amplicon sequencing datasets and in cross-sequencing platform validation with shotgun metagenomic datasets. Results suggest baseline gut microbiome features may be predictive of clinical outcomes in oncology patients on immunotherapies, and some of these features may be generalizable across different tumor types, patient cohorts, and sequencing platforms. Findings demonstrate how machine learning models can reveal microbiome-immunotherapy interactions that may ultimately improve cancer patient outcomes.}, } @article {pmid35875605, year = {2022}, author = {Luo, C and Lin, Y and Chen, C and Liu, Y and Sun, X}, title = {Diagnosis of severe Chlamydia psittaci pneumonia by metagenomic next-generation sequencing: 2 case reports.}, journal = {Respiratory medicine case reports}, volume = {38}, number = {}, pages = {101709}, pmid = {35875605}, issn = {2213-0071}, abstract = {Psittacosis is a infectious disease caused by Chlamydia psittaci (C. psittaci), which presents as pneumonia in humans. The diagnosis of psittacosis is challenging, however, Metagenomic next-generation sequencing (MNGS) is very efficient. Herein we documented the clinical characteristics of two patients with severe C. psittaci pneumonia who were admitted to the Intensive Care Unit. C. psittaci nucleic acid sequences were detected by MNGS of bronchoalveolar lavage fluid from both patients. Doxycycline was administered and the treatment was effective. Implementation of MNGS is helpful for the early identification of pathogens, shortening the diagnosis and treatment time, and improving the prognosis of patients.}, } @article {pmid35875582, year = {2022}, author = {Kumar, V and Kashyap, P and Kumar, S and Thakur, V and Kumar, S and Singh, D}, title = {Multiple Adaptive Strategies of Himalayan Iodobacter sp. PCH194 to High-Altitude Stresses.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {881873}, pmid = {35875582}, issn = {1664-302X}, abstract = {Bacterial adaption to the multiple stressed environments of high-altitude niches in the Himalayas is intriguing and is of considerable interest to biotechnologists. Previously, we studied the culturable and unculturable metagenome microbial diversity from glacial and kettle lakes in the Western Himalayas. In this study, we explored the adaptive strategies of a unique Himalayan eurypsychrophile Iodobacter sp. PCH194, which can synthesize polyhydroxybutyrate (PHB) and violacein pigment. Whole-genome sequencing and analysis of Iodobacter sp. PCH194 (4.58 Mb chromosome and three plasmids) revealed genetic traits associated with adaptive strategies for cold/freeze, nutritional fluctuation, defense against UV, acidic pH, and the kettle lake's competitive environment. Differential proteome analysis suggested the adaptive role of chaperones, ribonucleases, secretion systems, and antifreeze proteins under cold stress. Antifreeze activity inhibiting the ice recrystallization at -9°C demonstrated the bacterium's survival at subzero temperature. The bacterium stores carbon in the form of PHB under stress conditions responding to nutritional fluctuations. However, violacein pigment protects the cells from UV radiation. Concisely, genomic, proteomic, and physiological studies revealed the multiple adaptive strategies of Himalayan Iodobacter to survive the high-altitude stresses.}, } @article {pmid35875571, year = {2022}, author = {Chen, C and Yu, G and Guo, Z and Yang, Q and Su, W and Xie, Q and Yang, G and Ren, Y and Li, H}, title = {Expression, Characterization, Fermentation, Immobilization, and Application of a Novel Esterase Est804 From Metagenomic Library in Pesticide Degradation.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {922506}, pmid = {35875571}, issn = {1664-302X}, abstract = {Esterase, as a type of powerful catabolic enzyme for the degradation of pyrethroid pesticides (PYRs), appears promising in improving the quality of crops and the environment contaminated by pesticide residues. The purpose of this research is to provide a detailed introduction to the enzymatic properties, optimal production and immobilization conditions, and the degradation ability of Est804 for PYRs. The study on enzymatic properties indicated that Est804 was an alkaline esterase with an optimal pH of 8.0 and a broad optimal temperature in the range of 35-50°C. The optimal activity of free Est804 was calculated to be 112.812 U, and the specific enzyme activity was 48.97 U/mg. The kinetic parameters of Est804 were K m = 0.613 mM, k cat = 12,371 s[-1], and V m = 0.095 mM/min. The results of the fermentative optimization demonstrated that the optimal conditions included 1.5% of inoculation amount, 30 mL of liquid volume, 28°C of the fermentation temperature, and 18 h of the fermentation time. The optimal medium consists of 15.87 g of yeast powder, 8.00 g of glycerol, and 9.57 g of tryptone in 1 L of liquid. The optimized enzyme activity was 1.68-fold higher than that before optimization. Immobilized Est804 exhibited the highest activity under the optimum preparation conditions, including 0.35 g of chitosan dosage, 0.4 mL of an enzyme, and 4 h at 40°C for adsorption. The degradation rates of Cypermethrin (CYP), fenpropathrin (FE), and lambda-cyhalothrin (LCT) by Est804 within 30 min were 77.35%, 84.73%, and 74.16%, respectively. The present study indicated that Est804 possesses great potential for the treatment of pesticide residues on crops and environmental remediation, conducive to the development of SGNH family esterase against pyrethroid accumulation.}, } @article {pmid35875563, year = {2022}, author = {Lawther, K and Santos, FG and Oyama, LB and Rubino, F and Morrison, S and Creevey, CJ and McGrath, JW and Huws, SA}, title = {Resistome Analysis of Global Livestock and Soil Microbiomes.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {897905}, pmid = {35875563}, issn = {1664-302X}, abstract = {Antimicrobial resistance (AMR) is a serious threat to public health globally; it is estimated that AMR bacteria caused 1.27 million deaths in 2019, and this is set to rise to 10 million deaths annually. Agricultural and soil environments act as antimicrobial resistance gene (ARG) reservoirs, operating as a link between different ecosystems and enabling the mixing and dissemination of resistance genes. Due to the close interactions between humans and agricultural environments, these AMR gene reservoirs are a major risk to both human and animal health. In this study, we aimed to identify the resistance gene reservoirs present in four microbiomes: poultry, ruminant, swine gastrointestinal (GI) tracts coupled with those from soil. This large study brings together every poultry, swine, ruminant, and soil shotgun metagenomic sequence available on the NCBI sequence read archive for the first time. We use the ResFinder database to identify acquired antimicrobial resistance genes in over 5,800 metagenomes. ARGs were diverse and widespread within the metagenomes, with 235, 101, 167, and 182 different resistance genes identified in the poultry, ruminant, swine, and soil microbiomes, respectively. The tetracycline resistance genes were the most widespread in the livestock GI microbiomes, including tet(W)_1, tet(Q)_1, tet(O)_1, and tet(44)_1. The tet(W)_1 resistance gene was found in 99% of livestock GI tract microbiomes, while tet(Q)_1 was identified in 93%, tet(O)_1 in 82%, and finally tet(44)_1 in 69%. Metatranscriptomic analysis confirmed these genes were "real" and expressed in one or more of the livestock GI tract microbiomes, with tet(40)_1 and tet(O)_1 expressed in all three livestock microbiomes. In soil, the most abundant ARG was the oleandomycin resistance gene, ole(B)_1. A total of 55 resistance genes were shared by the four microbiomes, with 11 ARGs actively expressed in two or more microbiomes. By using all available metagenomes we were able to mine a large number of samples and describe resistomes in 37 countries. This study provides a global insight into the diverse and abundant antimicrobial resistance gene reservoirs present in both livestock and soil microbiomes.}, } @article {pmid35875537, year = {2022}, author = {Kondrotaite, Z and Valk, LC and Petriglieri, F and Singleton, C and Nierychlo, M and Dueholm, MKD and Nielsen, PH}, title = {Diversity and Ecophysiology of the Genus OLB8 and Other Abundant Uncultured Saprospiraceae Genera in Global Wastewater Treatment Systems.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {917553}, pmid = {35875537}, issn = {1664-302X}, abstract = {The Saprospiraceae family within the phylum Bacteroidota is commonly present and highly abundant in wastewater treatment plants (WWTPs) worldwide, but little is known about its role. In this study, we used MiDAS 4 global survey with samples from 30 countries to analyze the abundance and distribution of members of Saprospiraceae. Phylogenomics were used to delineate five new genera from a set of 31 high-quality metagenome-assembled genomes from Danish WWTPs. Newly designed probes for fluorescence in situ hybridization (FISH) revealed rod-shaped morphologies for all genera analyzed, including OLB8, present mostly inside the activated sludge flocs. The genomes revealed potential metabolic capabilities for the degradation of polysaccharides, proteins, and other complex molecules; partial denitrification; and storage of intracellular polymers (glycogen, polyphosphate, and polyhydroxyalkanoates). FISH in combination with Raman microspectroscopy confirmed the presence of intracellular glycogen in Candidatus Brachybacter, Candidatus Parvibacillus calidus (both from the former genus OLB8), and Candidatus Opimibacter, and the presence of polyhydroxyalkanoates in Candidatus Defluviibacterium haderslevense and Candidatus Vicinibacter. These results provide the first overview of the most abundant novel Saprospiraceae genera present in WWTPs across the world and their potential involvement in nutrient removal and the degradation of macromolecules.}, } @article {pmid35875529, year = {2022}, author = {Greene, G and Koolman, L and Whyte, P and Burgess, C and Lynch, H and Coffey, A and Lucey, B and O'Connor, L and Bolton, D}, title = {Effect of Doxycycline Use in the Early Broiler Production Cycle on the Microbiome.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {885862}, pmid = {35875529}, issn = {1664-302X}, abstract = {16S rRNA amplicon sequencing was used to investigate changes in the broiler gastrointestinal tract (GIT) microbiota throughout the rearing period and in combination with antibiotic treatment. Thirty birds (from a commercial flock) were removed at multiple points throughout the rearing period on days 13, 27, and 33, euthanised, and their GIT aseptically removed and divided into upper (the crop, proventriculus, and the gizzard), middle (the duodenum, jejunum, and ileum) and lower (the large intestine, the caeca, and the cloaca) sections. In a separate commercial flock, on the same farm with similar husbandry practices and feed, doxycycline (100 mg/ml per kg body weight) was administered in drinking water between day 8 and 12 (inclusive) of the production cycle. Birds were removed on days, 13, 27, and 33 and GIT samples prepared as above. The contents of three merged samples from each GIT section were pooled (n = 60), the DNA extracted and analysed by 16S rRNA amplicon metagenomic sequencing and analysed. Major changes in the broiler microbiota were observed as the birds aged particularly with the Firmicutes/Bacteroidetes ratio (F:B) of the lower GIT. Moreover, Chao1, ACE, and Shannon indices showed the antibiotic treatment significantly altered the microbiota, and this change persisted throughout the rearing period. Further research is required to investigate the effect of these changes on bird performance, susceptibility to infections and Campylobacter carriage.}, } @article {pmid35875520, year = {2022}, author = {Heyerhoff, B and Engelen, B and Bunse, C}, title = {Auxiliary Metabolic Gene Functions in Pelagic and Benthic Viruses of the Baltic Sea.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {863620}, pmid = {35875520}, issn = {1664-302X}, abstract = {Marine microbial communities are facing various ecosystem fluctuations (e.g., temperature, organic matter concentration, salinity, or redox regimes) and thus have to be highly adaptive. This might be supported by the acquisition of auxiliary metabolic genes (AMGs) originating from virus infections. Marine bacteriophages frequently contain AMGs, which allow them to augment their host's metabolism or enhance virus fitness. These genes encode proteins for the same metabolic functions as their highly similar host homologs. In the present study, we analyzed the diversity, distribution, and composition of marine viruses, focusing on AMGs to identify their putative ecologic role. We analyzed viruses and assemblies of 212 publicly available metagenomes obtained from sediment and water samples across the Baltic Sea. In general, the virus composition in both compartments differed compositionally. While the predominant viral lifestyle was found to be lytic, lysogeny was more prevalent in sediments than in the pelagic samples. The highest proportion of AMGs was identified in the genomes of Myoviridae. Overall, the most abundantly occurring AMGs are encoded for functions that protect viruses from degradation by their hosts, such as methylases. Additionally, some detected AMGs are known to be involved in photosynthesis, 7-cyano-7-deazaguanine synthesis, and cobalamin biosynthesis among other functions. Several AMGs that were identified in this study were previously detected in a large-scale analysis including metagenomes from various origins, i.e., different marine sites, wastewater, and the human gut. This supports the theory of globally conserved core AMGs that are spread over virus genomes, regardless of host or environment.}, } @article {pmid35874661, year = {2022}, author = {Rodrigues, VF and Elias-Oliveira, J and Pereira, ÍS and Pereira, JA and Barbosa, SC and Machado, MSG and Carlos, D}, title = {Akkermansia muciniphila and Gut Immune System: A Good Friendship That Attenuates Inflammatory Bowel Disease, Obesity, and Diabetes.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {934695}, pmid = {35874661}, issn = {1664-3224}, mesh = {*Akkermansia ; Animals ; Chronic Disease ; *Diabetes Mellitus/microbiology ; Gastrointestinal Microbiome ; Humans ; Immune System ; *Inflammatory Bowel Diseases/microbiology ; Mice ; *Obesity/microbiology ; }, abstract = {Akkermansia muciniphila is a Gram-negative anaerobic mucus-layer-degrading bacterium that colonizes the intestinal mucosa of humans and rodents. Metagenomic data have shown an inverse correlation between the abundance of A. muciniphila and diseases such as inflammatory bowel disease (IBD), obesity, and diabetes. Thus, in recent decades, the potential of this bacterium as an immunomodulatory probiotic for autoimmune and chronic inflammatory diseases has been explored in experimental models. Corroborating these human correlation data, it has been reported that A. muciniphila slows down the development and progression of diabetes, obesity, and IBD in mice. Consequently, clinical studies with obese and diabetic patients are being performed, and the preliminary results are very promising. Therefore, this mini review highlights the main findings regarding the beneficial roles of A. muciniphila and its action mechanisms in autoimmune and chronic inflammatory diseases.}, } @article {pmid35874624, year = {2022}, author = {Yang, WT and Chiang, I and Tseng, CH and Cheng, C and Lin, JH and Liu, PY and Huang, YT}, title = {Metagenomic Sequencing and Histology on a Chronic Wound Identified Epstein-Barr Virus-Associated Lymphoma.}, journal = {Evolutionary bioinformatics online}, volume = {18}, number = {}, pages = {11769343221110663}, pmid = {35874624}, issn = {1176-9343}, abstract = {Accurate diagnosis of chronic, non-healing wounds is challenging and time-consuming because it can be caused by a variety of etiologies. This brief report presents an unusual case of a chronic wound lasting for 10 months investigated by deep metagenomic sequencing. Epstein-Barr virus (EBV) was identified in the wound and subsequently validated by in situ hybridization. Histopathologic examination eventually revealed that the non-healing wound was due to an EBV-associated NK/T cell lymphoma. By identifying mutations across the viral genome, the virus was classified as Type I EBV and clustered with others of geographic proximity. Our results suggest that metagenomic shotgun sequencing can not only rapidly and accurately identify the presence of underlying pathogens but also provide strain-level resolution for the surveillance of viral epidemiology.}, } @article {pmid35874573, year = {2022}, author = {Du, Y and Zhang, Z and Chen, C and Xia, H and Zhang, H and Guo, Z and Wang, Y}, title = {Case Report: Report of Infective Endocarditis Caused by Abiotrophia defectiva and Literature Review.}, journal = {Frontiers in pediatrics}, volume = {10}, number = {}, pages = {894049}, pmid = {35874573}, issn = {2296-2360}, abstract = {OBJECTIVE: To report the clinical features of the first child with infective endocarditis (IE) caused by Abiotrophia defectiva in mainland China and to raise awareness of the disease.

METHODS: The clinical data of a child with IE caused by A. defectiva admitted to Xi'an Children's Hospital in July 2021 were collected, and the relevant literature was reviewed.

RESULTS: The child was a female, 8 years old, admitted with fever for 4 days and right-sided limb weakness for 3 days. The illness started with suppurative tonsillitis, followed by headache, fatigue, right-sided mouth, slurred speech, right limb weakness, and unstable holding. Transthoracic echocardiography showed that the mitral valve vegetation was formed and vegetation could also be seen at the entrance of the pulmonary vein at the posterior wall of the left atrium. Cranial contrast-enhanced MRI + magnetic resonance angiography showed multiple intracranial pseudoaneurysm formation and pontine infarction. After A. defectiva was detected by metagenomic next-generation sequencing (mNGS) in cerebrospinal fluid and blood detected, the infection was controlled by anti-infective treatment with meropenem and vancomycin. On the 36th day after admission, due to severe headache and slurred speech, the head CT showed hemorrhage of right parietal pseudoaneurysm and cerebral sickle hernia, and right temporo-occipital hematoma evacuation, cerebrovascular malformation resection, and cranial decompression were performed immediately. After the surgery, her speech ability gradually recovered, the muscle strength of her left upper limb was about grade III, while the muscle strength of the rest of the limbs was normal. After a total of 60 days of hospitalization, her family requested to be discharged.

CONCLUSION: This pediatric patient is the first case of childhood IE caused by A. defectiva in mainland China, and the first time in the world that A. defectiva was detected by mNGS in patients with IE.}, } @article {pmid35873450, year = {2022}, author = {Li, C and Zhou, K and Xiao, N and Peng, M and Tan, Z}, title = {The Effect of Qiweibaizhu Powder Crude Polysaccharide on Antibiotic-Associated Diarrhea Mice Is Associated With Restoring Intestinal Mucosal Bacteria.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {952647}, pmid = {35873450}, issn = {2296-861X}, abstract = {BACKGROUND: Qiweibaizhu powder (QWBZP) has been shown to be effective in treating antibiotic-associated diarrhea (AAD). Previous research has reported that plant polysaccharides can promote the growth of beneficial intestinal bacteria and inhibit the multiplication of pathogenic bacteria, thus effectively treating diarrhea. Here, we investigated the effect of QWBZP crude polysaccharide on the diversity of intestinal mucosal bacteria and their community structure composition in mice with AAD, and the aim of this study was to provide the scientific basis for the efficacy of QWBZP crude polysaccharide on diarrhea.

MATERIALS AND METHODS: Eighteen Kunming (KM) mice were randomly divided into the normal (mn) group, the model (mm) group, and the QWBZP crude polysaccharide treatment (ma) group, with six mice in each group. An AAD model was constructed using a mixed antibiotic solution and treated with gavage crude polysaccharide solution of QWBZP. The intestinal mucosa was extracted from the jejunum to the ileum of mice, and the metagenome was extracted and then analyzed using MiSeq sequencing to characterize the intestinal mucosal bacteria in mice.

RESULTS: The spleen and thymus indices of each group of mice had no significant differences. The Chao1 and ACE indices of the mn and mm groups were similar, the Simpson index was the largest and the Shannon index was the smallest in the mm group, and there was no significant difference in the diversity indices of all three groups. In the PCA and PCoA, the mn and ma group samples were both relatively concentrated with a high similarity of community structure. In contrast, the samples in the mm group were more scattered and farther away from the samples in the mn and ma groups, i.e., the community structure similarity within and between the groups was low. Compared with the mm group, the relative abundance of Proteobacteria, Lactobacillus, and the Firmicutes/Bacteroidetes (F/B) ratio in the ma group was decreased, while that of Enterococcus continued to increase. In the LEfSe analysis, there were significant differences in the characteristic bacteria in the mn, mm, and ma groups.

CONCLUSION: The single crude polysaccharide component is not very effective in treating AAD, so the clinical efficacy of the QWBZP crude polysaccharide is subject to further investigation.}, } @article {pmid35873420, year = {2022}, author = {Bosheva, M and Tokodi, I and Krasnow, A and Pedersen, HK and Lukjancenko, O and Eklund, AC and Grathwohl, D and Sprenger, N and Berger, B and Cercamondi, CI and , }, title = {Infant Formula With a Specific Blend of Five Human Milk Oligosaccharides Drives the Gut Microbiota Development and Improves Gut Maturation Markers: A Randomized Controlled Trial.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {920362}, pmid = {35873420}, issn = {2296-861X}, abstract = {BACKGROUND: Human milk oligosaccharides (HMOs) have important biological functions for a healthy development in early life.

OBJECTIVE: This study aimed to investigate gut maturation effects of an infant formula containing five HMOs (2'-fucosyllactose, 2',3-di-fucosyllactose, lacto-N-tetraose, 3'-sialyllactose, and 6'-sialyllactose).

METHODS: In a multicenter study, healthy infants (7-21 days old) were randomly assigned to a standard cow's milk-based infant formula (control group, CG); the same formula with 1.5 g/L HMOs (test group 1, TG1); or with 2.5 g/L HMOs (test group 2, TG2). A human milk-fed group (HMG) was enrolled as a reference. Fecal samples collected at baseline (n∼150/formula group; HMG n = 60), age 3 (n∼140/formula group; HMG n = 65) and 6 (n∼115/formula group; HMG n = 60) months were analyzed for microbiome (shotgun metagenomics), metabolism, and biomarkers.

RESULTS: At both post-baseline visits, weighted UniFrac analysis indicated different microbiota compositions in the two test groups (TGs) compared to CG (P < 0.01) with coordinates closer to that of HMG. The relative abundance of Bifidobacterium longum subsp. infantis (B. infantis) was higher in TGs vs. CG (P < 0.05; except at 6 months: TG2 vs. CG P = 0.083). Bifidobacterium abundance was higher by ∼45% in TGs vs. CG at 6-month approaching HMG. At both post-baseline visits, toxigenic Clostridioides difficile abundance was 75-85% lower in TGs vs. CG (P < 0.05) and comparable with HMG. Fecal pH was significantly lower in TGs vs. CG, and the overall organic acid profile was different in TGs vs. CG, approaching HMG. At 3 months, TGs (vs. CG) had higher secretory immunoglobulin A (sIgA) and lower alpha-1-antitrypsin (P < 0.05). At 6 months, sIgA in TG2 vs. CG remained higher (P < 0.05), and calprotectin was lower in TG1 (P < 0.05) vs. CG.

CONCLUSION: Infant formula with a specific blend of five HMOs supports the development of the intestinal immune system and gut barrier function and shifts the gut microbiome closer to that of breastfed infants with higher bifidobacteria, particularly B. infantis, and lower toxigenic Clostridioides difficile.

CLINICAL TRIAL REGISTRATION: [https://clinicaltrials.gov/ct2/show/], identifier [NCT03722550].}, } @article {pmid35872457, year = {2022}, author = {Song, X and Zhang, B and Cao, Y and Liu, B and Chen, B}, title = {Shrimp-waste based dispersant as oil spill treating agent: Biodegradation of dispersant and dispersed oil.}, journal = {Journal of hazardous materials}, volume = {439}, number = {}, pages = {129617}, doi = {10.1016/j.jhazmat.2022.129617}, pmid = {35872457}, issn = {1873-3336}, mesh = {Animals ; Biodegradation, Environmental ; Crustacea ; Molecular Docking Simulation ; *Petroleum/metabolism ; *Petroleum Pollution/analysis ; Seawater ; Surface-Active Agents ; *Water Pollutants, Chemical/analysis ; }, abstract = {The emerging demand for the enhancement of biodegradation of persistent organic pollutants from marine oil spills using oil-treating agents to minimize the environmental impacts promotes the development of green dispersants. Shrimp waste is a potential raw material to generate green dispersants. The biodegradability of dispersed oil and dispersants themselves are key factors for the national consideration of the approval, stockpile, and usage of dispersants. However, it is unknown whether shrimp-waste-based dispersant (SWD) has high bioavailability or facilitates the biodegradation of dispersed oil. In this study, we tackled the biodegradation of oil dispersed by a purified SWD. Furthermore, the SWD biodegradability was evaluated by exploring the degradation genes via metagenomic sequencing, analyzing the enzymatic activities for dispersant biodegradation by molecular docking, and discussing the SWD toxicity. We discovered that the SWD facilitated the biodegradation of two crude oils (Alaska North Slope and Marine Fuel-No.6). The metagenomic analysis with molecular docking showed that fresh seawater had feasible enzymes to degrade the SWD to safety components. Additionally, the SWD was low toxic and high bioactive. The findings helped confirm that the purified SWD is an effective and eco-sustainable marine oil spill treating agent and tracked the biodegradation of dispersed oil and the SWD.}, } @article {pmid35872283, year = {2022}, author = {Macêdo, WV and Poulsen, JS and Zaiat, M and Nielsen, JL}, title = {Proteogenomics identification of TBBPA degraders in anaerobic bioreactor.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {310}, number = {}, pages = {119786}, doi = {10.1016/j.envpol.2022.119786}, pmid = {35872283}, issn = {1873-6424}, mesh = {Anaerobiosis ; Biodegradation, Environmental ; Bioreactors ; Ecosystem ; Isotopes ; *Polybrominated Biphenyls ; *Proteogenomics ; }, abstract = {Tetrabromobisphenol A (TBBPA) is the most used flame retardant worldwide and has become a threat to aquatic ecosystems. Previous research into the degradation of this micropollutant in anaerobic bioreactors has suggested several identities of putative TBBPA degraders. However, the organisms actively degrading TBBPA under in situ conditions have so far not been identified. Protein-stable isotope probing (protein-SIP) has become a cutting-edge technique in microbial ecology for enabling the link between identity and function under in situ conditions. Therefore, it was hypothesized that combining protein-based stable isotope probing with metagenomics could be used to identify and provide genomic insight into the TBBPA-degrading organisms. The identified [13]C-labelled peptides were found to belong to organisms affiliated to Phytobacter, Clostridium, Sporolactobacillus, and Klebsilla genera. The functional classification of identified labelled peptides revealed that TBBPA is not only transformed by cometabolic reactions, but also assimilated into the biomass. By application of the proteogenomics with labelled micropollutants (protein-SIP) and metagenome-assembled genomes, it was possible to extend the current perspective of the diversity of TBBPA degraders in wastewater and predict putative TBBPA degradation pathways. The study provides a link to the active TBBPA degraders and which organisms to favor for optimized biodegradation.}, } @article {pmid35871871, year = {2022}, author = {Simsek, C and Bloemen, M and Jansen, D and Descheemaeker, P and Reynders, M and Van Ranst, M and Matthijnssens, J}, title = {Rotavirus vaccine-derived cases in Belgium: Evidence for reversion of attenuating mutations and alternative causes of gastroenteritis.}, journal = {Vaccine}, volume = {40}, number = {35}, pages = {5114-5125}, doi = {10.1016/j.vaccine.2022.06.082}, pmid = {35871871}, issn = {1873-2518}, mesh = {Antigens, Viral/genetics ; Belgium/epidemiology ; *Gastroenteritis/epidemiology/prevention & control ; Genotype ; Humans ; Infant ; Mutation ; Phylogeny ; *Rotavirus/genetics ; *Rotavirus Infections/epidemiology/prevention & control ; *Rotavirus Vaccines/adverse effects/chemistry ; }, abstract = {Since the introduction of live-attenuated rotavirus vaccines in Belgium in 2006, surveillance has routinely detected rotavirus vaccine-derived strains. However, their genomic landscape and potential role in gastroenteritis have not been thoroughly investigated. We compared VP7 and VP4 nucleotide sequences obtained from rotavirus surveillance with the Rotarix vaccine sequence. As a result, we identified 80 vaccine-derived strains in 5125 rotavirus-positive infants with gastroenteritis from 2007 to 2018. Using both viral metagenomics and reverse transcription qPCR, we evaluated the vaccine strains and screened for co-infecting enteropathogens. Among the 45 patients with known vaccination status, 39 were vaccinated and 87% received the vaccine less than a month before the gastroenteritis episode. Reconstruction of 30 near complete vaccine-derived genomes revealed 0-11 mutations per genome, with 88% of them being non-synonymous. This, in combination with several shared amino acid changes among strains, pointed at selection of minor variant(s) present in the vaccine. We also found that some of these substitutions were true revertants (e.g., F167L on VP4, and I45T on NSP4). Finally, co-infections with known (e.g., Clostridioides difficile and norovirus) and divergent or emerging (e.g., human parechovirus A1, salivirus A2) pathogens were detected, and we estimated that 35% of the infants likely had gastroenteritis due to a 'non-rotavirus' cause. Conversely, we could not rule out the vaccine-derived gastroenteritis in over half of the cases. Continued studies inspecting reversion to pathogenicity should monitor the long-time safety of live-attenuated rotavirus vaccines. All in all, the complementary approach with NGS and qPCR provided a better understanding of rotavirus vaccine strain evolution in the Belgian population and epidemiology of co-infecting enteropathogens in suspected rotavirus vaccine-derived gastroenteritis cases.}, } @article {pmid35870224, year = {2022}, author = {Kuhnert, E and Collemare, J}, title = {A genomic journey in the secondary metabolite diversity of fungal plant and insect pathogens: from functional to population genomics.}, journal = {Current opinion in microbiology}, volume = {69}, number = {}, pages = {102178}, doi = {10.1016/j.mib.2022.102178}, pmid = {35870224}, issn = {1879-0364}, mesh = {Animals ; Genome, Fungal ; Genomics ; Insecta ; *Metagenomics ; *Plant Diseases/microbiology ; Plants ; }, abstract = {Fungal pathogens produce a broad array of secondary metabolites (SMs), which allow the fungus to thrive in its natural habitat and gain competitive advantage. Analysis of the genetically encoded blueprints for SM assembly highlighted that only a small portion of the SMs these fungi are capable of producing are known, and even fewer have been investigated for their natural function. Using molecular tools, a lot of progress has been made recently in identifying the blueprint products and linking them to their ecological purpose such as the peptide virulence factor fusaoctaxin A released by Fusarium graminearum during infection of wheat or the F. oxysporum polyketide bikaverin that provides competitive advantage against bacteria in tomato. In addition, population genomics have given particularly important insights into the species-specific plasticity of the SM blueprint arsenal, showcasing the ongoing evolution and adaptation of fungal pathogens. This approach holds promise in inferring roles in pathogenicity of many more fungal SMs.}, } @article {pmid35870206, year = {2022}, author = {Su, H and Wu, C and Han, P and Liu, Z and Liang, M and Zhang, Z and Wang, Z and Guo, G and He, X and Pang, J and Wang, C and Weng, S and He, J}, title = {The microbiome and its association with antibiotic resistance genes in the hadal biosphere at the Yap Trench.}, journal = {Journal of hazardous materials}, volume = {439}, number = {}, pages = {129543}, doi = {10.1016/j.jhazmat.2022.129543}, pmid = {35870206}, issn = {1873-3336}, mesh = {*Anti-Bacterial Agents/pharmacology ; Archaea/genetics ; Bacteria ; Drug Resistance, Microbial/genetics ; *Microbiota/genetics ; }, abstract = {The hadal biosphere, the deepest part of the ocean, is known as the least-explored aquatic environment and hosts taxonomically diverse microbial communities. However, the microbiome and its association with antibiotic resistance genes (ARGs) in the hadal ecosystem remain unknown. Here, we profiled the microbiome diversity and ARG occurrence in seawater and sediments of the Yap Trench (YT) using metagenomic sequencing. Within the prokaryote (bacteria and archaea) lineages, the main components of bacteria were Gammaproteobacteria (77.76 %), Firmicutes (8.36 %), and Alphaproteobacteria (2.25 %), whereas the major components of archaea were Nitrososphaeria (6.51 %), Nanoarchaeia (0.42 %), and Thermoplasmata (0.25 %), respectively. Taxonomy of viral contigs showed that the classified viral communities in YT seawater and sediments were dominated by Podoviridae (45.96 %), Siphoviridae (29.41 %), and Myoviridae (24.63 %). A large majority of viral contigs remained uncharacterized and exhibited endemicity. A total of 48 ARGs encoding resistance to 12 antibiotic classes were identified and their hosts were bacteria and viruses. Novel ARG subtypes mexFYTV-1, mexFYTV-2, mexFYTV-3, vanRYTV-1, vanSYTV-1 (carried by unclassified viruses), and bacAYTB-1 (carried by phylum Firmicutes) were detected in seawater samples. Overall, our findings imply that the hadal environment of the YT is a repository of viral and ARG diversity.}, } @article {pmid35869541, year = {2022}, author = {Palomo, A and Azevedo, D and Touceda-Suárez, M and Domingo-Félez, C and Mutlu, AG and Dechesne, A and Wang, Y and Zhang, T and Smets, BF}, title = {Efficient management of the nitritation-anammox microbiome through intermittent aeration: absence of the NOB guild and expansion and diversity of the NOx reducing guild suggests a highly reticulated nitrogen cycle.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {39}, pmid = {35869541}, issn = {2524-6372}, support = {REA 607492//FP7 People: Marie-Curie Actions/ ; REA 607492//FP7 People: Marie-Curie Actions/ ; Expa-N 13391//Villlum Fonden/ ; Expa-N 13391//Villlum Fonden/ ; }, abstract = {Obtaining efficient autotrophic ammonia removal (aka partial nitritation-anammox, or PNA) requires a balanced microbiome with abundant aerobic and anaerobic ammonia oxidizing bacteria and scarce nitrite oxidizing bacteria. Here, we analyzed the microbiome of an efficient PNA process that was obtained by sequential feeding and periodic aeration. The genomes of the dominant community members were inferred from metagenomes obtained over a 6 month period. Three Brocadia spp. genomes and three Nitrosomonas spp. genomes dominated the autotrophic community; no NOB genomes were retrieved. Two of the Brocadia spp. genomes lacked the genomic potential for nitrite reduction. A diverse set of heterotrophic genomes was retrieved, each with genomic potential for only a fraction of the denitrification pathway. A mutual dependency in amino acid and vitamin synthesis was noted between autotrophic and heterotrophic community members. Our analysis suggests a highly-reticulated nitrogen cycle in the examined PNA microbiome with nitric oxide exchange between the heterotrophs and the anammox guild.}, } @article {pmid35868586, year = {2022}, author = {Leo, S and Curtis, N and Zimmermann, P}, title = {The neonatal intestinal resistome and factors that influence it-a systematic review.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {28}, number = {12}, pages = {1539-1546}, doi = {10.1016/j.cmi.2022.07.014}, pmid = {35868586}, issn = {1469-0691}, mesh = {Infant, Newborn ; Pregnancy ; Female ; Humans ; Phylogeny ; Drug Resistance, Microbial/genetics ; *Anti-Bacterial Agents/pharmacology/therapeutic use ; *Bacteria/genetics ; Intestines ; }, abstract = {BACKGROUND: The intestinal microbiome provides a reservoir for antibiotic resistance genes (ARGs). The neonatal microbiome is more susceptible to disturbance from external factors than the established microbiome in later life.

OBJECTIVES: In this review, we systematically summarize studies which investigated the intestinal resistome in neonates.

DATA SOURCES: MEDLINE and Embase databases were searched.

STUDY ELIGIBILITY CRITERIA: We included original studies which investigated ARGs in stool or rectal swabs in neonates using molecular diagnostics.

METHODS OF DATA SYNTHESIS: Two authors independently extracted data, which were summarized in tables.

RESULTS: Our search identified 2701 studies, of which 23 (22 cohorts) were included. The studies show that the neonatal intestine harbours a high abundance and variety of ARGs, even in the absence of direct antibiotic exposure. The most commonly found ARGs confer resistance to aminoglycosides, β-lactams, macrolides, tetracyclines, or multidrug resistance. There is evidence that ARGs can be transferred from mothers to neonates. Interestingly, however, compared to mothers, neonates are reported to have a higher abundance of ARGs. One likely reason for this is the bacterial phylogenetic composition with a high abundance of Gammaproteobacteria in neonatal stool. Factors that have been associated with a higher abundance of ARGs are intrapartum and neonatal antibiotic use. Breastfeeding and neonatal probiotic use have been associated with a lower abundance of ARGs. Antibiotics during pregnancy, delivery mode, or sex are reported to have little effect. However, this might be because studies were underpowered and because it is difficult to account for effect modifiers.

CONCLUSIONS: The neonatal intestine seems to have a lower colonization resistance, which could make it easier for antibiotic-resistant populations to establish themselves. Future studies will help in the development of evidence-based interventions to modulate the abundance of ARGs in neonates, for example, by the use of pre- and probiotics and bacteriophages.}, } @article {pmid35868367, year = {2022}, author = {de Menezes, TA and de Freitas, MAM and Lima, MS and Soares, AC and Leal, C and Busch, MS and Tschoeke, DA and de O Vidal, L and Atella, GC and Kruger, RH and Setubal, J and Vasconcelos, AA and de Mahiques, MM and Siegle, E and Asp, NE and Cosenza, C and Hajdu, E and de Rezende, CE and Thompson, CC and Thompson, FL}, title = {Fluxes of the Amazon River plume nutrients and microbes into marine sponges.}, journal = {The Science of the total environment}, volume = {847}, number = {}, pages = {157474}, doi = {10.1016/j.scitotenv.2022.157474}, pmid = {35868367}, issn = {1879-1026}, mesh = {Animals ; Nutrients ; Phylogeny ; *Porifera ; RNA, Ribosomal, 16S ; *Rivers ; }, abstract = {Sponges have co-evolved with microbes for over 400 myr. Previous studies have demonstrated that sponges can be classified according to the abundance of microbes in their tissues as Low Microbial Abundance (LMA) and High Microbial Abundance (HMA). While LMA sponges rely mainly on water column microbes, HMA appear to rely much more on symbiotic fermentative and autotrophic microbes maintained in their tissues. However, it is unclear if this pattern holds when comparing different species of tropical sponges under extreme nutrient conditions and sediment loads in the water column, such as the Great Amazon Reef System (GARS), which covers an area of ~56,000 km[2] off the Amazon River mouth. Sponges are the major GARS benthic components. However, these sponges' microbiome across the GARS is still unknown. Here, we investigated water quality, isotopic values (δ[13]C and δ[15]N), metagenomic and lipidomic profiles of sponges obtained from different sectors throughout the GARS. >180 million shotgun metagenomic reads were annotated, covering 22 sponge species. Isotopic and lipidomic analyses suggested LMA sponges rely on the Amazon River Plume for nutrition. HMA sponges (N = 15) had higher Roseiflexus and Nitrospira abundance, whereas LMA sponges (N = 7) had higher Prochlorococcus and Pelagibacter abundance. Functional data revealed that the LMA sponge microbiomes had greater number of sequences related to phages and prophages as well as electron transport and photophosphorylation which may be related to photosynthetic processes associated with the Prochlorococcus and Synechococcus found in the LMA. The higher phages abundance in LMA sponges could be related to these holobionts' reduced defense towards phage infection. Meanwhile, HMA sponge microbiomes had higher Clustered Regularly Interspaced Short Palindromic Repeats-CRISPR abundance, which may be involved in defense against phage infection. This study sheds light on the nutrient fluxes and microbes from the Amazon River plume into the sponge holobionts.}, } @article {pmid35868179, year = {2022}, author = {Song, W and Chen, H and Xue, N and Wang, S and Yang, Y}, title = {Metagenomic binning and assembled genome analysis revealed the distinct composition of resistome and mobilome in the Ili River.}, journal = {Ecotoxicology and environmental safety}, volume = {242}, number = {}, pages = {113886}, doi = {10.1016/j.ecoenv.2022.113886}, pmid = {35868179}, issn = {1090-2414}, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Metagenomics ; *Rivers/microbiology ; Water ; }, abstract = {Rivers play an important role in receiving and transporting the resistome among different environmental compartments. However, the difference in resistome and mobilome between the water and sediment and their underlying mechanisms were still poorly understood. In this study, the Ili River, an important water source in the arid area of Central Asia, was selected as the studied target. The comprehensive profile of resistome and mobilome and their host in water and sediment were studied based on metagenomic binning and assembled genome (MAG) analysis. The relative abundance of resistome and mobilome in sediment were 28.0 - 67.8 × /Gb and 46.5 - 121.1 × /Gb, respectively, which were significantly higher than those in water (23.1 - 52.8 ×/Gb and 25.3 - 67.7 ×/Gb). Multidrug and macrolides-lincosamides-streptogramin (MLS) resistance genes were the main ARG types in both water and sediment from relative abundance. Transposases dominated the relative abundance of mobilome, followed by insert elements and integrases. Strong correlations were found between the relative abundance of resistome and mobilome (r > 0.6 and p < 0.01) in both water and sediment, indicating the mobilome played an important role in the propagation of resistome in the Ili River. The main hosts for multidrug resistance genes via MAG analysis differed in water (Alphaproteobacteria and Gammaproteobacteria) and sediment (Gammaproteobacteria). Distinct compositions of resistome and mobilome existed between water and sediment in the Ili River. Specificity-occupancy analysis of the differential resistome and mobilome showed that occurrence frequencies and habitat selections of the differential ARGs shaped the resistome of water and sediment. In contrast, habitat was the main driver that shaped the mobilome in the Ili River.}, } @article {pmid35868082, year = {2022}, author = {Chen, F and Fan, B and Wang, C and Qian, J and Wang, B and Tang, X and Qin, Z and Chen, Y and Bin Liang, and Liu, W and Wang, A and Ye, Y and Wang, Y}, title = {Weak electro-stimulation promotes microbial uranium removal: Efficacy and mechanisms.}, journal = {Journal of hazardous materials}, volume = {439}, number = {}, pages = {129622}, doi = {10.1016/j.jhazmat.2022.129622}, pmid = {35868082}, issn = {1873-3336}, mesh = {Bacteria/metabolism ; Biodegradation, Environmental ; Oxidation-Reduction ; *Uranium/chemistry ; Wastewater ; *Water Pollutants, Radioactive/chemistry ; }, abstract = {Removal and recovery of uranium from uranium-mine wastewater is beneficial to environmental protection and resource preservation. Reduction of soluble hexavalent U (U(VI)) to insoluble tetravalent uranium (U(IV)) by microbes is a plausible approach for this purpose, but its practical implementation has long been restricted by its intrinsic drawbacks. The electro-stimulated microbial process offers promise in overcoming these drawbacks. However, its applicability in real wastewater has not been evaluated yet, and its U(VI) removal mechanisms remain poorly understood. Herein, we report that introducing a weak electro-stimulation considerably boosted microbial U(VI) removal activities in both synthetic and real wastewater. The U(VI) removal has proceeded via U(VI)-to-U(IV) reduction in the biocathode, and the electrochemical characterization demonstrates the crucial role of the electroactive biofilm. Microbial community analysis shows that the broad biodiversity of the cathode biofilm is capable of U(VI) reduction, and the molecular ecological network indicates that synthetic metabolisms among electroactive and metal-reducing bacteria play major roles in electro-microbial-mediated uranium removal. Metagenomic sequencing elucidates that the electro-stimulated U(VI) bioreduction may proceed via e-pili, extracellular electron shuttles, periplasmic and outer membrane cytochrome, and thioredoxin pathways. These findings reveal the potential and mechanism of the electro-stimulated U(VI) bioreduction system for the treatment of U-bearing wastewater.}, } @article {pmid35867822, year = {2022}, author = {Hu, Y and Satten, GA and Hu, YJ}, title = {LOCOM: A logistic regression model for testing differential abundance in compositional microbiome data with false discovery rate control.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {30}, pages = {e2122788119}, pmid = {35867822}, issn = {1091-6490}, support = {R01 GM116065/GM/NIGMS NIH HHS/United States ; R01 GM141074/GM/NIGMS NIH HHS/United States ; }, mesh = {Logistic Models ; Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis ; }, abstract = {Compositional analysis is based on the premise that a relatively small proportion of taxa are differentially abundant, while the ratios of the relative abundances of the remaining taxa remain unchanged. Most existing methods use log-transformed data, but log-transformation of data with pervasive zero counts is problematic, and these methods cannot always control the false discovery rate (FDR). Further, high-throughput microbiome data such as 16S amplicon or metagenomic sequencing are subject to experimental biases that are introduced in every step of the experimental workflow. McLaren et al. [eLife 8, e46923 (2019)] have recently proposed a model for how these biases affect relative abundance data. Motivated by this model, we show that the odds ratios in a logistic regression comparing counts in two taxa are invariant to experimental biases. With this motivation, we propose logistic compositional analysis (LOCOM), a robust logistic regression approach to compositional analysis, that does not require pseudocounts. Inference is based on permutation to account for overdispersion and small sample sizes. Traits can be either binary or continuous, and adjustment for confounders is supported. Our simulations indicate that LOCOM always preserved FDR and had much improved sensitivity over existing methods. In contrast, analysis of composition of microbiomes (ANCOM) and ANCOM with bias correction (ANCOM-BC)/ANOVA-Like Differential Expression tool (ALDEx2) had inflated FDR when the effect sizes were small and large, respectively. Only LOCOM was robust to experimental biases in every situation. The flexibility of our method for a variety of microbiome studies is illustrated by the analysis of data from two microbiome studies. Our R package LOCOM is publicly available.}, } @article {pmid35867581, year = {2022}, author = {Lim, SJ and Thompson, LR and Young, CM and Gaasterland, T and Goodwin, KD}, title = {Dominance of Sulfurospirillum in Metagenomes Associated with the Methane Ice Worm (Sirsoe methanicola).}, journal = {Applied and environmental microbiology}, volume = {88}, number = {15}, pages = {e0029022}, pmid = {35867581}, issn = {1098-5336}, support = {R21 ES024105/ES/NIEHS NIH HHS/United States ; }, mesh = {Animals ; Bacteria ; Carbon/metabolism ; Humans ; *Metagenome ; Methane/metabolism ; Phylogeny ; *Polychaeta/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; Sulfides/metabolism ; }, abstract = {Sirsoe methanicola, commonly known as the methane ice worm, is the only macrofaunal species known to inhabit the Gulf of Mexico methane hydrates. Little is known about this elusive marine polychaete that can colonize rich carbon and energy reserves. Metagenomic analysis of gut contents and worm fragments predicted diverse metabolic capabilities with the ability to utilize a range of nitrogen, sulfur, and organic carbon compounds through microbial taxa affiliated with Campylobacterales, Desulfobacterales, Enterobacterales, SAR324, Alphaproteobacteria, and Mycoplasmatales. Entomoplasmatales and Chitinivibrionales were additionally identified from extracted full-length 16S rRNA sequences, and read analysis identified 196 bacterial families. Overall, the microbial community appeared dominated by uncultured Sulfurospirillum, a taxon previously considered free-living rather than host-associated. Metagenome-assembled genomes (MAGs) classified as uncultured Sulfurospirillum predicted thiosulfate disproportionation and the reduction of tetrathionate, sulfate, sulfide/polysulfide, and nitrate. Microbial amino acid and vitamin B12 biosynthesis genes were identified in multiple MAGs, suggesting nutritional value to the host. Reads assigned to aerobic or anaerobic methanotrophic taxa were rare. IMPORTANCE Methane hydrates represent vast reserves of natural gas with roles in global carbon cycling and climate change. This study provided the first analysis of metagenomes associated with Sirsoe methanicola, the only polychaete species known to colonize methane hydrates. Previously unrecognized participation of Sulfurospirillum in a gut microbiome is provided, and the role of sulfur compound redox reactions within this community is highlighted. The comparative biology of S. methanicola is of general interest given research into the adverse effects of sulfide production in human gut microbiomes. In addition, taxonomic assignments are provided for nearly 200 bacterial families, expanding our knowledge of microbiomes in the deep sea.}, } @article {pmid35867474, year = {2022}, author = {Jacqueline, C and Del Valle Arrojo, M and Bellver Moreira, P and Rodríguez Feijóo, MA and Cabrerizo, M and Fernandez-Garcia, MD}, title = {Norovirus GII.3[P12] Outbreak Associated with the Drinking Water Supply in a Rural Area in Galicia, Spain, 2021.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0104822}, pmid = {35867474}, issn = {2165-0497}, mesh = {Adolescent ; Adult ; Aged ; Aged, 80 and over ; *Caliciviridae Infections/epidemiology ; Case-Control Studies ; Child ; Child, Preschool ; Disease Outbreaks ; Female ; Genotype ; Humans ; Infant ; Infant, Newborn ; Male ; Middle Aged ; *Norovirus/genetics ; Spain/epidemiology ; Water Supply ; Young Adult ; }, abstract = {On 30 September 2021, the city council of Muxia, Spain (population of 4,564 inhabitants), reported an unusual increase of patients with acute gastroenteritis (AGE). Because geographically widespread villages belonging to the same water supply were affected, a waterborne outbreak was suspected. Overall, 115 probable cases were ascertained during epidemiological investigations carried out by the local health authority (attack rate, 5.7%); the age range was 0 to 92 years, and 54% were female. The main symptoms were vomiting (78.1%) and diarrhea (67.5%). Primary cases peaked on 29 September and subsided on 1 October, compatible with a point-source outbreak followed by possible secondary cases until 7 October. We conducted an unmatched case-control study using phone surveys. The case-control study included 62 cases and 46 controls. Univariate analysis showed that cases had a higher exposure to tap water through direct consumption (odds ratio [OR] = 86; 95% confidence interval [CI], 18 to 409) or vegetable washing (OR = 27; 95% CI, 7 to 98). Norovirus GII was detected in two terminal points of the water supply system, and 14 cases were laboratory confirmed after detection of GII in stool samples. A unique genotype (GII.3[P12]) was identified in stool samples. On 1 October, a tap water ban was put in place and the water was purged and chlorinated. The rapid increase in the number of cases and its decline after implementing control measures suggested a waterborne point-source outbreak among the residents of Muxia sharing the same water distribution system. IMPORTANCE Noroviruses are likely to be underrecognized in most suspected waterborne outbreaks. Therefore, effective norovirus detection and the early recognition of water as a possible source of infection are important to reduce morbidity as appropriate steps are taken to control the source. In our study, we combined epidemiological, environmental, and microbiological investigations to demonstrate that it was a waterborne outbreak caused by norovirus. Metagenomic sequencing in one norovirus-positive stool sample confirmed norovirus etiology and the absence of other potential pathogens. Detection of fecal indicator bacteria and the fact that the drinking water was not chlorinated suggest a breakdown in chlorination as the cause of the outbreak. This outbreak investigation also demonstrated the importance of timely communication to the public about the risk linked to tap water consumption.}, } @article {pmid35865935, year = {2022}, author = {Wu, W and Jiang, H and Zhang, Y and Zhou, Y and Bai, G and Shen, L and Zhou, H and Chen, X and Hu, L}, title = {Clinical Metagenomic Next-Generation Sequencing for Diagnosis of Secondary Glaucoma in Patients With Cytomegalovirus-Induced Corneal Endotheliitis.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {940818}, pmid = {35865935}, issn = {1664-302X}, abstract = {Glaucoma is the second leading cause of blindness globally. Growing scientific evidence indicated that inflammation of the trabecular meshwork induced by corneal endotheliitis could lead to secondary glaucoma. Cytomegalovirus (CMV) has been identified as the most common herpes virus in corneal endotheliitis patients. Early detection is critical in preventing endothelial cell loss, and patient management should vary based on different pathological factors. However, routine culture and real-time polymerase chain reaction (qPCR) have difficult in distinguishing whether CMV, Varicella Zoster Virus (VZV) or Herpes Simplex Virus (HSV) causes endothiliitis. This may result in inappropriate treatment, which may prolong or aggravate the status of disease. We compared the sensitivity and specificity of qPCR and Metagenomic Next-Generation Sequencing (mNGS) in the aqueous humor of patients with suspected CMV endotheliitis in this study. Our results showed that four out of 11 (36.4%) of our patients were positive for CMV by qPCR, whereas mNGS had a 100% detection rate of CMV. Our findings implied that mNGS could be a useful diagnostic tool for CMV-induced endotheliitis.}, } @article {pmid35865915, year = {2022}, author = {Morsli, M and Lavigne, JP and Drancourt, M}, title = {Direct Metagenomic Diagnosis of Community-Acquired Meningitis: State of the Art.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {926240}, pmid = {35865915}, issn = {1664-302X}, abstract = {Current routine diagnosis of community-acquired meningitis (CAM) by multiplex real-time polymerase chain reaction (RT-PCR) is limited in the number of tested pathogens and their full characterisation, requiring additional in vitro investigations to disclose genotype and antimicrobial susceptibility. We reviewed 51 studies published through December 2021 reporting metagenomic next generation sequencing (mNGS) directly applied to the cerebrospinal fluid (CSF). This approach, potentially circumventing the above-mentioned limitations, indicated 1,248 investigated patients, and 617 patients dually investigated by routine diagnosis and mNGS, in whom 116 microbes were detected, including 50 by mNGS only, nine by routine methods only, and 57 by both routine methods and mNGS. Of 217 discordant CSF findings, 103 CSF samples were documented by mNGS only, 87 CSF samples by routine methods only, and 27 CSF samples in which the pathogen identified by mNGS was different than that found using routine methods. Overall, mNGS allowed for diagnosis and genomic surveillance of CAM causative pathogens in real-time, with a cost which is competitive with current routine multiplex RT-PCR. mNGS could be implemented at point-of-care (POC) laboratories as a part of routine investigations to improve the diagnosis and molecular epidemiology of CAM, particularly in the event of failure of routine assays.}, } @article {pmid35864536, year = {2022}, author = {Jiang, Q and Lin, L and Xie, F and Jin, W and Zhu, W and Wang, M and Qiu, Q and Li, Z and Liu, J and Mao, S}, title = {Metagenomic insights into the microbe-mediated B and K2 vitamin biosynthesis in the gastrointestinal microbiome of ruminants.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {109}, pmid = {35864536}, issn = {2049-2618}, mesh = {Animals ; Cattle ; *Gastrointestinal Microbiome/genetics ; Metagenomics/methods ; Rumen/metabolism ; Ruminants/metabolism ; Vitamin B 12/metabolism ; Vitamins ; }, abstract = {BACKGROUND: B and K2 vitamins, essential nutrients in host metabolism, can be synthesized by the rumen microbiome in ruminants and subsequently absorbed by the host. However, the B and K2 vitamin biosynthesis by the whole gastrointestinal microbiome and their abundances in different dietary strategies are largely unknown. Here, we reanalyzed our previous large-scale metagenomic data on the gastrointestinal microbiome of seven ruminant species and recruited 17,425 nonredundant microbial genomes from published datasets to gain a comprehensive understanding of the microbe-mediated B and K2 vitamin biosynthesis in ruminants.

RESULTS: We identified 1,135,807 genes and 167 enzymes involved in B and K2 vitamin biosynthesis. Our results indicated that the total abundances of B and K2 vitamin biosynthesis were dominant in the stomach microbiome, while the biosynthesis of thiamine, niacin, and pyridoxine was more abundant in the large intestine. By examining 17,425 nonredundant genomes, we identified 2366 high-quality genomes that were predicted to de novo biosynthesize at least one vitamin. Genomic analysis suggested that only 2.7% of these genomes can synthesize five or more vitamins, and nearly half of genomes can synthesize only one vitamin. Moreover, we found that most genomes possessed cobalamin transporters or cobalamin-dependent enzymes to consume cobalamin directly, and only a few microbial genomes possessed a complete cobalamin biosynthesis pathway. Based on these genomic data, we examined the effect of the high-grain (HG) diet on the vitamin biosynthesis of the rumen microbiome of dairy cattle. We revealed that most vitamin biosynthesis was enhanced in the HG group, while only cobalamin synthesis was inhibited in the HG group, indicating that dietary fiber is vital for cobalamin biosynthesis.

CONCLUSIONS: We primarily provided a gene catalog and 2366 microbial genomes involved in B and K2 vitamin biosynthesis in ruminants. Our findings demonstrated the regional heterogeneity and dietary effect of vitamin biosynthetic potential in the ruminant gastrointestinal microbiome and interpreted the biosynthesis mechanisms of these microbes and their physiological adaptability. This study expands our understanding of microbe-mediated vitamin biosynthesis in ruminants and may provide novel targets for manipulation to improve the production of these essential vitamins. Video abstract.}, } @article {pmid35864403, year = {2022}, author = {Wang, L and Zhu, M and Li, Y and Zhao, Z and Hu, T}, title = {Deterministic assembly process dominates bacterial antibiotic resistome in wastewater effluents receiving river.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {60}, pages = {90207-90218}, pmid = {35864403}, issn = {1614-7499}, support = {5210100094//National Natural Science Foundation of China/ ; B210201006//Fundamental Research Funds for the Central Universities/ ; }, mesh = {Humans ; *Wastewater ; *Anti-Bacterial Agents/pharmacology ; Metagenomics ; Bacteria/genetics ; }, abstract = {Antibiotic resistance has become a concerning global health challenge, such as the dissemination of bacteria and genes between humans and the environments. Wastewater treatment plants (WWTPs) effluents, as significant reservoirs for antimicrobial resistant bacteria and antibiotic resistance genes (ARGs), pose critical risks to public health. However, whether wastewater effluent prominently contributes to the abundance of ARGs and their community assembly processes in receiving river has yet been unclear. Here we investigated the effects of the effluent discharge on the ARGs and their associate microbial community in the receiving river (Qinhuai River, Nanjing) of upstream and 2000 m downstream of one WWTPs discharge point. Results revealed that the total antibiotic concentrations of all sediment samples ranged from 37.86 to 76.11 µg/kg dw, while antibiotic concentrations and ARG abundances in the river near the wastewater discharge site were significantly higher than that of the downstream receiving river. The metagenomic assembly obtained 245 ARGs associated with 19 antibiotic types in the receiving river. Network analyses confirmed that Proteobacteria, Firmicutes, Acidobacteria, and Bacteroides were the key phylum and positively correlated with the antibiotic resistome. Additionally, the bacterial pathogens of the receiving river were identified as the most frequent strains of clinically relevant antibacterial resistance, such as Streptococcus pneumoniae, Pseudomonas aeruginosa, and Acinetobacter baumannii. Using null modeling analysis to determine the quantification of ecological processes, the results showed that heterogeneous environmental selection (81.81%) was a dominate role of the ecological mechanisms determining the ARG community reconstruction in the receiving river. Our results may contribute to control the environmental dissemination of antimicrobial resistance risks in aquatic environments.}, } @article {pmid35864173, year = {2023}, author = {Tian, C and Pang, J and Bu, C and Wu, S and Bai, H and Li, Y and Guo, Q and Siddique, KHM}, title = {The Microbiomes in Lichen and Moss Biocrust Contribute Differently to Carbon and Nitrogen Cycles in Arid Ecosystems.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {497-508}, pmid = {35864173}, issn = {1432-184X}, support = {2016YFE0203400//National Key Research and Development Program of China/ ; 2017YFC0504703//National Key Research and Development Program of China/ ; 41971131//National Natural Scientific Foundation of China/ ; }, mesh = {Ecosystem ; *Lichens ; Carbon ; Nitrates ; Soil/chemistry ; *Bryophyta ; Nitrogen Fixation ; *Microbiota ; Soil Microbiology ; Nitrogen/chemistry ; }, abstract = {Biological soil crusts (biocrusts) are distributed in arid and semiarid regions across the globe. Microorganisms are an essential component in biocrusts. They add and accelerate critical biochemical processes. However, little is known about the functional genes and metabolic processes of microbiomes in lichen and moss biocrust. This study used shotgun metagenomic sequencing to compare the microbiomes of lichen-dominated and moss-dominated biocrust and reveal the microbial genes and metabolic pathways involved in carbon and nitrogen cycling. The results showed that Actinobacteria, Bacteroidetes, and Acidobacteria were more abundant in moss biocrust than lichen biocrust, while Proteobacteria and Cyanobacteria were more abundant in lichen biocrust than moss biocrust. The relative abundance of carbohydrate-active enzymes and enzymes associated with carbon and nitrogen metabolism differed significantly between microbiomes of the two biocrust types. However, in the microbial communities of both biocrust types, respiration pathways dominated over carbon fixation pathways. The genes encoding carbon monoxide dehydrogenase were more abundant than those encoding ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCo) involved in carbon fixation. Similarly, metabolic N-pathway diversity was dominated by nitrogen reduction, followed by denitrification, with nitrogen fixation the lowest proportion. Gene diversity involved in N cycling differed between the microbiomes of the two biocrust types. Assimilatory nitrate reduction genes had higher relative abundance in lichen biocrust, whereas dissimilatory nitrate reduction genes had higher relative abundance in moss biocrust. As dissolved organic carbon and soil organic carbon are considered the main drivers of the community structure in the microbiome of biocrust, these results indicate that biocrust type has a pivotal role in microbial diversity and related biogeochemical cycling.}, } @article {pmid35864107, year = {2022}, author = {Chaguza, C and Jamrozy, D and Bijlsma, MW and Kuijpers, TW and van de Beek, D and van der Ende, A and Bentley, SD}, title = {Population genomics of Group B Streptococcus reveals the genetics of neonatal disease onset and meningeal invasion.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {4215}, pmid = {35864107}, issn = {2041-1723}, support = {206194/WT_/Wellcome Trust/United Kingdom ; 098051/WT_/Wellcome Trust/United Kingdom ; MR/R003076/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Genome-Wide Association Study ; Humans ; Infant ; Infant, Newborn ; *Infant, Newborn, Diseases ; Metagenomics ; *Streptococcal Infections/genetics ; Streptococcus agalactiae/genetics ; }, abstract = {Group B Streptococcus (GBS), or Streptococcus agalactiae, is a pathogen that causes preterm births, stillbirths, and acute invasive neonatal disease burden and mortality. Here, we investigate bacterial genetic signatures associated with disease onset time and meningeal tissue infection in acute invasive neonatal GBS disease. We carry out a genome-wide association study (GWAS) of 1,338 GBS isolates from newborns with acute invasive disease; the isolates had been collected annually, for 30 years, through a national bacterial surveillance program in the Netherlands. After controlling for the population structure, we identify genetic variation within noncoding and coding regions, particularly the capsule biosynthesis locus, statistically associated with neonatal GBS disease onset time and meningeal invasion. Our findings highlight the impact of integrating microbial population genomics and clinical pathogen surveillance, and demonstrate the effect of GBS genetics on disease pathogenesis in neonates and infants.}, } @article {pmid35864089, year = {2022}, author = {Mzava, O and Cheng, AP and Chang, A and Smalling, S and Djomnang, LK and Lenz, JS and Longman, R and Steadman, A and Gómez-Escobar, LG and Schenck, EJ and Salvatore, M and Satlin, MJ and Suthanthiran, M and Lee, JR and Mason, CE and Dadhania, D and De Vlaminck, I}, title = {A metagenomic DNA sequencing assay that is robust against environmental DNA contamination.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {4197}, pmid = {35864089}, issn = {2041-1723}, support = {DP2 AI138242/AI/NIAID NIH HHS/United States ; T32 GM008267/GM/NIGMS NIH HHS/United States ; R21 AI124237/AI/NIAID NIH HHS/United States ; R01 AI146165/AI/NIAID NIH HHS/United States ; K23 HL151876/HL/NHLBI NIH HHS/United States ; R37 AI051652/AI/NIAID NIH HHS/United States ; U01 DA053941/DA/NIDA NIH HHS/United States ; R21 AI133331/AI/NIAID NIH HHS/United States ; R01 AI151059/AI/NIAID NIH HHS/United States ; }, mesh = {*COVID-19 ; DNA ; DNA Contamination ; DNA, Bacterial/genetics ; *DNA, Environmental ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; Sequence Analysis, DNA ; }, abstract = {Metagenomic DNA sequencing is a powerful tool to characterize microbial communities but is sensitive to environmental DNA contamination, in particular when applied to samples with low microbial biomass. Here, we present Sample-Intrinsic microbial DNA Found by Tagging and sequencing (SIFT-seq) a metagenomic sequencing assay that is robust against environmental DNA contamination introduced during sample preparation. The core idea of SIFT-seq is to tag the DNA in the sample prior to DNA isolation and library preparation with a label that can be recorded by DNA sequencing. Any contaminating DNA that is introduced in the sample after tagging can then be bioinformatically identified and removed. We applied SIFT-seq to screen for infections from microorganisms with low burden in blood and urine, to identify COVID-19 co-infection, to characterize the urinary microbiome, and to identify microbial DNA signatures of sepsis and inflammatory bowel disease in blood.}, } @article {pmid35864066, year = {2022}, author = {Lin, C and Bonsu, AAFK and Li, J and Ning, C and Chen, L and Zhu, S and Zhong, Q and Shen, D and Huang, G}, title = {Application of metagenomic next-generation sequencing for suspected infected pancreatic necrosis.}, journal = {Pancreatology : official journal of the International Association of Pancreatology (IAP) ... [et al.]}, volume = {22}, number = {7}, pages = {864-870}, doi = {10.1016/j.pan.2022.07.006}, pmid = {35864066}, issn = {1424-3911}, mesh = {Humans ; *Pancreatitis, Acute Necrotizing/diagnosis ; Sensitivity and Specificity ; Metagenomics ; High-Throughput Nucleotide Sequencing ; *Intraabdominal Infections ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is increasingly used for the clinical diagnosis of infectious diseases, but there is a paucity of data regarding the application of mNGS in the early diagnosis of infected pancreatic necrosis (IPN).

OBJECTIVE: To investigate the clinical application value of mNGS in the pathogenic diagnosis of IPN.

METHODS: Forty-two patients with suspected IPN were prospectively and consecutively enrolled from August 2019 to August 2021. Blood samples were collected for mNGS and microbial culture simultaneously during fever (T ≥ 38.5 °C). For patients who had indications of surgical interventions, peri-pancreatic specimens were collected for mNGS and microbial culture simultaneously during the first surgical intervention to confirm IPN. The clinical performance of mNGS and microbial culture were compared.

RESULTS: A total of 21 patients (50.0%) were confirmed to have IPN during hospitalization. The sensitivity of blood mNGS was significantly higher than blood culture (95.2% vs. 23.8%, P < 0.001) in diagnosing IPN. The negative predictive value of blood mNGS was 90.0%. The turnaround time of mNGS was significantly shorter than that of microbial culture [(37.70 ± 1.44) vs. (115.23 ± 8.79) h, P < 0.01] and the average costs of mNGS accounted for 1.7% of the average total cost of hospitalization. The survival analysis demonstrates that the positive blood mNGS result was not associated with increased mortality (P = 0.119).

CONCLUSIONS: With more valuable diagnostic performance and shorter turnaround time, clinical mNGS represents a potential step forward in the early diagnosis of IPN.}, } @article {pmid35864047, year = {2022}, author = {Gao, S and Ma, X and Kang, Y and Zhang, Z and Zhang, Y and Zhou, W and Shen, H}, title = {Brain abscess caused by Scedosporium boydii in a systemic lupus erythematosus patient: A case report and literature review.}, journal = {Indian journal of medical microbiology}, volume = {40}, number = {4}, pages = {611-615}, doi = {10.1016/j.ijmmb.2022.06.010}, pmid = {35864047}, issn = {1998-3646}, mesh = {*Brain Abscess/diagnosis/drug therapy ; Humans ; *Lupus Erythematosus, Systemic/complications/diagnosis ; *Mycoses/diagnosis/microbiology ; *Scedosporium ; }, abstract = {Scedosporium boydii is considered as emerging opportunists affecting both immunocompromised and immunocompetent individuals. Diagnosis and treatment of Scedosporium infections can be challenging, and the outcome is frequently fatal, especially in patients with disseminated infections. Metagenomic next-generation sequencing (mNGS) is a promising adjunctive diagnostic approach for uncommon pathogens. Here, we report a rare case of brain abscess caused by S. boydii in a systemic lupus erythematosus (SLE) patient. This case highlights the importance of mNGS in the early diagnosis of S. boydii. Additionally, the combined application of culture and molecular tools may be promising in the clinical diagnosis of fungal disease.}, } @article {pmid35863699, year = {2022}, author = {Shrestha, L and Lin, MJ and Xie, H and Mills, MG and Mohamed Bakhash, SA and Gaur, VP and Livingston, RJ and Castor, J and Bruce, EA and Botten, JW and Huang, ML and Jerome, KR and Greninger, AL and Roychoudhury, P}, title = {Clinical Performance Characteristics of the Swift Normalase Amplicon Panel for Sensitive Recovery of Severe Acute Respiratory Syndrome Coronavirus 2 Genomes.}, journal = {The Journal of molecular diagnostics : JMD}, volume = {24}, number = {9}, pages = {963-976}, pmid = {35863699}, issn = {1943-7811}, support = {P30 AI027757/AI/NIAID NIH HHS/United States ; P30 GM118228/GM/NIGMS NIH HHS/United States ; S10 OD028685/OD/NIH HHS/United States ; }, mesh = {*COVID-19/genetics ; Genome, Viral ; Humans ; RNA, Viral/genetics ; *SARS-CoV-2/genetics ; Whole Genome Sequencing/methods ; }, abstract = {Amplicon-based sequencing methods are central in characterizing the diversity, transmission, and evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), but need to be rigorously assessed for clinical utility. Herein, we validated the Swift Biosciences' SARS-CoV-2 Swift Normalase Amplicon Panels using remnant clinical specimens. High-quality genomes meeting our established library and sequence quality criteria were recovered from positive specimens, with 95% limit of detection of 40.08 SARS-CoV-2 copies/PCR. Breadth of genome recovery was evaluated across a range of CT values (11.3 to 36.7; median, 21.6). Of 428 positive samples, 413 (96.5%) generated genomes with <10% unknown bases, with a mean genome coverage of 13,545× ± SD 8382×. No genomes were recovered from PCR-negative specimens (n = 30) or from specimens positive for non-SARS-CoV-2 respiratory viruses (n = 20). Compared with whole-genome shotgun metagenomic sequencing (n = 14) or Sanger sequencing for the spike gene (n = 11), pairwise identity between consensus sequences was 100% in all cases, with highly concordant allele frequencies (R[2] = 0.99) between Swift and shotgun libraries. When samples from different clades were mixed at varying ratios, expected variants were detected even in 1:99 mixtures. When deployed as a clinical test, 268 tests were performed in the first 23 weeks, with a median turnaround time of 11 days, ordered primarily for outbreak investigations and infection control.}, } @article {pmid35863347, year = {2022}, author = {West, PT and Brooks, EF and Costales, C and Moreno, A and Jensen, TD and Budvytiene, I and Khan, A and Pham, THM and Schwenk, HT and Bhatt, AS and Banaei, N}, title = {Near-fatal Legionella pneumonia in a neonate linked to home humidifier by metagenomic next generation sequencing.}, journal = {Med (New York, N.Y.)}, volume = {3}, number = {8}, pages = {565-567}, pmid = {35863347}, issn = {2666-6340}, support = {R01 AI143757/AI/NIAID NIH HHS/United States ; R01 AI148623/AI/NIAID NIH HHS/United States ; }, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Humidifiers ; Infant, Newborn ; *Legionella pneumophila/genetics ; *Legionnaires' Disease/diagnosis ; *Pneumonia ; }, } @article {pmid35863030, year = {2022}, author = {Rhoades, NS and Cinco, IR and Hendrickson, SM and Slifka, MK and Messaoudi, I}, title = {Taxonomic and Functional Shifts in the Perinatal Gut Microbiome of Rhesus Macaques.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0081422}, pmid = {35863030}, issn = {2165-0497}, support = {P51 OD011092/OD/NIH HHS/United States ; }, mesh = {Adult ; Animals ; Butyrates ; Feces ; Female ; Folic Acid ; *Gastrointestinal Microbiome/physiology ; Humans ; Infant, Newborn ; Macaca mulatta/genetics/metabolism ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; Starch ; }, abstract = {Pregnancy and the postpartum period result in some of the most dramatic metabolic, hormonal, and physiological changes that can be experienced by an otherwise healthy adult. The timing and magnitude of these changes is key for both maternal and fetal health. One of the factors believed to critically modulate these physiological changes is the maternal gut microbiome. However, the dynamic changes in this community during the perinatal period remain understudied. Clinical studies can be complicated by confounding variables like diet and other drivers of heterogeneity in the human microbiome. Therefore, in this study, we conducted a longitudinal analysis of the fecal microbiome obtained during the pregnancy and postpartum periods in 26 captive rhesus macaques using 16S rRNA gene amplicon sequencing and shotgun metagenomics. Shifts at both the taxonomic and functional potential level were detected when comparing pregnancy to postpartum samples. Taxonomically, Alloprevotella, Actinobacillus, and Anaerovibrio were enriched in the gut microbiome during pregnancy, while Treponema, Lachnospiraceae, and Methanosphaera were more abundant postpartum. Functionally, the gut microbiome during pregnancy was associated with increased abundance in pathways involving the production of the short-chain fatty acid (SCFA) butyrate, while pathways associated with starch degradation and folate transformation were more abundant during the postpartum period. These data demonstrate dramatic changes in the maternal gut microbiome even in the absence of dietary changes and suggest that rhesus macaques could provide a valuable model to determine how changes in the microbiome correlate to other physiological changes in pregnancy. IMPORTANCE Pregnancy and the postpartum period are characterized by a myriad of metabolic and physiological adaptations needed to support fetal growth and maternal health. The maternal gut microbiome is believed to play a key role during this period but remains underexplored. Here, we report significant shifts in the taxonomic landscape and functional potential of the gut microbiome in 26 pregnant rhesus macaques during the transition from pregnancy to the postpartum period, despite shared dietary and environmental exposures. Increased abundance of pathways involved in the production of the short-chain fatty acid butyrate could play a critical role in modulating the maternal immune system and regulating fetal tolerance. On the other hand, increased abundance of pathways associated with starch degradation and folate transformation during the postpartum period could be important for meeting the metabolic demands of breastfeeding and neonatal growth.}, } @article {pmid35863004, year = {2022}, author = {Zhang, L and Wang, Z and Zhang, X and Zhao, L and Chu, J and Li, H and Sun, W and Yang, C and Wang, H and Dai, W and Yan, S and Chen, X and Xu, D}, title = {Alterations of the Gut Microbiota in Patients with Diabetic Nephropathy.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0032422}, pmid = {35863004}, issn = {2165-0497}, mesh = {Bacteroides ; Clostridiales ; *Diabetes Mellitus, Type 2/microbiology ; *Diabetic Nephropathies/microbiology/pathology ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Diabetic nephropathy (DN) is the primary cause of end-stage renal disease. Accumulating studies have implied a critical role for the gut microbiota in diabetes mellitus (DM) and DN. However, the precise roles and regulatory mechanisms of the gut microbiota in the pathogenesis of DN remain largely unclear. In this study, metagenomics sequencing was performed using fecal samples from healthy controls (CON) and type 2 diabetes mellitus (T2DM) patients with or without DN. Fresh fecal samples from 15 T2DM patients without DN, 15 DN patients, and 15 age-, gender-, and body mass index (BMI)-matched healthy controls were collected. The compositions and potential functions of the gut microbiota were estimated. Although no difference of gut microbiota α and β diversity was observed between the CON, T2DM, and DN groups, the relative abundances of butyrate-producing bacteria (Clostridium, Eubacterium, and Roseburia intestinalis) and potential probiotics (Lachnospira and Intestinibacter) were significantly reduced in T2DM and DN patients. Besides, Bacteroides stercoris was significantly enriched in fecal samples from patients with DN. Moreover, Clostridium sp. 26_22 was negatively associated with serum creatinine (P < 0.05). DN patients could be accurately distinguished from CON by Clostridium sp. CAG_768 (area under the curve [AUC] = 0.941), Bacteroides propionicifaciens (AUC = 0.905), and Clostridium sp. CAG_715 (AUC = 0.908). DN patients could be accurately distinguished from T2DM patients by Pseudomonadales, Fusobacterium varium, and Prevotella sp. MSX73 (AUC = 0.889). Regarding the potential bacterial functions of the gut microbiota, the citrate cycle, base excision repair, histidine metabolism, lipoic acid metabolism, and bile acid biosynthesis were enriched in DN patients, while selenium metabolism and branched-chain amino acid biosynthesis were decreased in DN patients. IMPORTANCE Gut microbiota imbalance is found in fecal samples from DN patients, in which Roseburia intestinalis is significantly decreased, while Bacteroides stercoris is increased. There is a significant correlation between gut microbiota imbalance and clinical indexes related to lipid metabolism, glucose metabolism, and renal function. The gut microbiota may be predictive factors for the development and progression of DN, although further studies are warranted to illustrate their regulatory mechanisms.}, } @article {pmid35862964, year = {2022}, author = {Zhang, Q and Zou, X and Wu, S and Wu, N and Chen, X and Zhou, W}, title = {Effects of Pyroligneous Acid on Diversity and Dynamics of Antibiotic Resistance Genes in Alfalfa Silage.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0155422}, pmid = {35862964}, issn = {2165-0497}, mesh = {Ammonia ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Fermentation ; Humans ; Lactobacillus/genetics ; *Medicago sativa/chemistry/microbiology ; *Silage/analysis/microbiology ; Terpenes ; Tetracyclines ; }, abstract = {Antibiotic resistance genes (ARGs) are recognized as contaminants due to their potential risk for human and environment. The aim of the present study is to investigate the effects of pyroligneous acid (PA), a waste of biochar production, on fermentation characteristics, diversity, and dynamics of ARGs during ensiling of alfalfa using metagenomic analysis. The results indicated that PA decreased (P < 0.05) dry matter loss, pH value, gas production, coliform bacteria count, protease activity, and nonprotein-N, ammonia-N, and butyric acid contents and increased (P < 0.05) lactic acid content during ensiling. During fermentation, Bacteria, Firmicutes, and Lactobacillus were the most abundant at kingdom, phylum, and genus levels, respectively. Pyroligneous acid reduced the relative abundance of Bacteria and Firmicutes and increased that of Lactobacillus. The detected ARGs belonged to 36 drug classes, including mainly macrolides, tetracycline, lincosamides, and phenicol. These types of ARGs decreased during fermentation and were further reduced by PA. These types of ARGs were positively correlated (P < 0.05) with fermentation parameters like pH value and ammonia-N content and with bacterial communities. At the genus level, the top several drug classes, including macrolide, tetracycline, lincosamide, phenicol, oxazolidinone, streptogramin, pleuromutilin, and glycopeptide, were positively correlated with Staphylococcus, Streptococcus, Listeria, Bacillus, Klebsiella, Clostridium, and Enterobacter, the potential hosts of ARGs. Overall, ARGs in alfalfa silage were abundant and were influenced by the fermentation parameters and microbial community composition. Ensiling could be a feasible way to mitigate ARGs in forages. The addition of PA could not only improve fermentation quality but also reduce ARG pollution of alfalfa silage. IMPORTANCE Antibiotic resistance genes (ARGs) are considered environmental pollutants posing a potential human health risk. Silage is an important and traditional feed, mainly for ruminants. ARGs in silages might influence the diversity and distribution of ARGs in animal intestinal and feces and then the manure and the manured soil. However, the diversity and dynamics of ARGs in silage during fermentation are still unknown. We ensiled alfalfa, one of the most widely used forages, with or without pyroligneous acid (PA), which was proved to have the ability to reduce ARGs in soils. The results showed that ARGs in alfalfa silage were abundant and were influenced by the fermentation parameters and microbial community. The majority of ARGs in alfalfa silage reduced during fermentation. The addition of PA could improve silage quality and reduce ARG pollution in alfalfa silage. This study can provide useful information for understanding and controlling ARG pollution in animal production.}, } @article {pmid35862923, year = {2022}, author = {Taş, N and Dafflon, B and Ulrich, C and Wu, Y and Tringe, SG and Jansson, JK}, title = {Metagenomes from Arctic Soil Microbial Communities from the Barrow Environmental Observatory, Utqiaġvik, AK, USA.}, journal = {Microbiology resource announcements}, volume = {11}, number = {8}, pages = {e0052822}, pmid = {35862923}, issn = {2576-098X}, support = {NGEE Arctic//U.S. Department of Energy (DOE)/ ; }, abstract = {Here, we report 36 active-layer and 17 permafrost metagenomes from Utqiaġvik, AK, USA. Samples were collected from different topographical features and depths to study Arctic tundra microbiomes.}, } @article {pmid35862918, year = {2022}, author = {Fortney, NW and Myers, KS and Ingle, AT and Walters, KA and Scarborough, MJ and Donohue, TJ and Noguera, DR}, title = {Metagenomes and Metagenome-Assembled Genomes from Microbiomes Metabolizing Thin Stillage from an Ethanol Biorefinery.}, journal = {Microbiology resource announcements}, volume = {11}, number = {8}, pages = {e0029022}, pmid = {35862918}, issn = {2576-098X}, support = {DE-SC0018409//U.S. Department of Energy (DOE)/ ; }, abstract = {Here, we report the metagenomes from five anaerobic bioreactors, operated under different conditions, that were fed carbohydrate-rich thin stillage from a corn starch ethanol plant. The putative functions of the abundant taxa identified here will inform future studies of microbial communities involved in valorizing this and other low-value agroindustrial residues.}, } @article {pmid35862824, year = {2022}, author = {Schultz, J and Modolon, F and Rosado, AS and Voolstra, CR and Sweet, M and Peixoto, RS}, title = {Methods and Strategies to Uncover Coral-Associated Microbial Dark Matter.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0036722}, pmid = {35862824}, issn = {2379-5077}, mesh = {Animals ; *Anthozoa ; Bacteria/genetics ; *Microbiota/genetics ; Metagenome ; Biotechnology ; }, abstract = {The vast majority of environmental microbes have not yet been cultured, and most of the knowledge on coral-associated microbes (CAMs) has been generated from amplicon sequencing and metagenomes. However, exploring cultured CAMs is key for a detailed and comprehensive characterization of the roles of these microbes in shaping coral health and, ultimately, for their biotechnological use as, for example, coral probiotics and other natural products. Here, the strategies and technologies that have been used to access cultured CAMs are presented, while advantages and disadvantages associated with each of these strategies are discussed. We highlight the existing gaps and potential improvements in culture-dependent methodologies, indicating several possible alternatives (including culturomics and in situ diffusion devices) that could be applied to retrieve the CAM "dark matter" (i.e., the currently undescribed CAMs). This study provides the most comprehensive synthesis of the methodologies used to recover the cultured coral microbiome to date and draws suggestions for the development of the next generation of CAM culturomics.}, } @article {pmid35862823, year = {2022}, author = {Loureiro, C and Galani, A and Gavriilidou, A and Chaib de Mares, M and van der Oost, J and Medema, MH and Sipkema, D}, title = {Comparative Metagenomic Analysis of Biosynthetic Diversity across Sponge Microbiomes Highlights Metabolic Novelty, Conservation, and Diversification.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0035722}, pmid = {35862823}, issn = {2379-5077}, mesh = {Animals ; *Porifera/genetics ; Metagenome ; *Microbiota/genetics ; Bacteria/genetics ; *Biological Products/metabolism ; }, abstract = {Marine sponges and their microbial symbiotic communities are rich sources of diverse natural products (NPs) that often display biological activity, yet little is known about the global distribution of NPs and the symbionts that produce them. Since the majority of sponge symbionts remain uncultured, it is a challenge to characterize their NP biosynthetic pathways, assess their prevalence within the holobiont, and measure the diversity of NP biosynthetic gene clusters (BGCs) across sponge taxa and environments. Here, we explore the microbial biosynthetic landscapes of three high-microbial-abundance (HMA) sponges from the Atlantic Ocean and the Mediterranean Sea. This data set reveals striking novelty, with <1% of the recovered gene cluster families (GCFs) showing similarity to any characterized BGC. When zooming in on the microbial communities of each sponge, we observed higher variability of specialized metabolic and taxonomic profiles between sponge species than within species. Nonetheless, we identified conservation of GCFs, with 20% of sponge GCFs being shared between at least two sponge species and a GCF core comprised of 6% of GCFs shared across all species. Within this functional core, we identified a set of widespread and diverse GCFs encoding nonribosomal peptide synthetases that are potentially involved in the production of diversified ether lipids, as well as GCFs putatively encoding the production of highly modified proteusins. The present work contributes to the small, yet growing body of data characterizing NP landscapes of marine sponge symbionts and to the cryptic biosynthetic potential contained in this environmental niche. IMPORTANCE Marine sponges and their microbial symbiotic communities are a rich source of diverse natural products (NPs). However, little is known about the sponge NP global distribution landscape and the symbionts that produce them. Here, we make use of recently developed tools to perform untargeted mining and comparative analysis of sponge microbiome metagenomes of three sponge species in the first study considering replicate metagenomes of multiple sponge species. We present an overview of the biosynthetic diversity across these sponge holobionts, which displays extreme biosynthetic novelty. We report not only the conservation of biosynthetic and taxonomic diversity but also a core of conserved specialized metabolic pathways. Finally, we highlight several novel GCFs with unknown ecological function, and observe particularly high biosynthetic potential in Acidobacteriota and Latescibacteria symbionts. This study paves the way toward a better understanding of the marine sponge holobionts' biosynthetic potential and the functional and ecological role of sponge microbiomes.}, } @article {pmid35862821, year = {2022}, author = {Lidbury, IDEA and Raguideau, S and Borsetto, C and Murphy, ARJ and Bottrill, A and Liu, S and Stark, R and Fraser, T and Goodall, A and Jones, A and Bending, GD and Tibbet, M and Hammond, JP and Quince, C and Scanlan, DJ and Pandhal, J and Wellington, EMH}, title = {Stimulation of Distinct Rhizosphere Bacteria Drives Phosphorus and Nitrogen Mineralization in Oilseed Rape under Field Conditions.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0002522}, pmid = {35862821}, issn = {2379-5077}, support = {BB/L026074/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T009152/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Brassica napus ; Rhizosphere ; Bacteria/genetics ; *Microbiota/genetics ; Plants ; Soil ; }, abstract = {Advances in DNA sequencing technologies have drastically changed our perception of the structure and complexity of the plant microbiome. By comparison, our ability to accurately identify the metabolically active fraction of soil microbiota and its specific functional role in augmenting plant health is relatively limited. Important ecological interactions being performed by microbes can be investigated by analyzing the extracellular protein fraction. Here, we combined a unique protein extraction method and an iterative bioinformatics pipeline to capture and identify extracellular proteins (metaexoproteomics) synthesized in the rhizosphere of Brassica spp. We first validated our method in the laboratory by successfully identifying proteins related to a host plant (Brassica rapa) and its bacterial inoculant, Pseudomonas putida BIRD-1. This identified numerous rhizosphere specific proteins linked to the acquisition of plant-derived nutrients in P. putida. Next, we analyzed natural field-soil microbial communities associated with Brassica napus L. (oilseed rape). By combining metagenomics with metaexoproteomics, 1,885 plant, insect, and microbial proteins were identified across bulk and rhizosphere samples. Metaexoproteomics identified a significant shift in the metabolically active fraction of the soil microbiota responding to the presence of B. napus roots that was not apparent in the composition of the total microbial community (metagenome). This included stimulation of rhizosphere-specialized bacteria, such as Gammaproteobacteria, Betaproteobacteria, and Flavobacteriia, and the upregulation of plant beneficial functions related to phosphorus and nitrogen mineralization. Our metaproteomic assessment of the "active" plant microbiome at the field-scale demonstrates the importance of moving beyond metagenomics to determine ecologically important plant-microbe interactions underpinning plant health. IMPORTANCE Plant-microbe interactions are critical to ecosystem function and crop production. While significant advances have been made toward understanding the structure of the plant microbiome, learning about its full functional role is still in its infancy. This is primarily due to an incomplete ability to determine in situ plant-microbe interactions actively operating under field conditions. Proteins are the functional entities of the cell. Therefore, their identification and relative quantification within a microbial community provide the best proxy for which microbes are the most metabolically active and which are driving important plant-microbe interactions. Here, we provide the first metaexoproteomics assessment of the plant microbiome using field-grown oilseed rape as the model crop species, identifying key taxa responsible for specific ecological interactions. Gaining a mechanistic understanding of the plant microbiome is central to developing engineered plant microbiomes to improve sustainable agricultural approaches and reduce our reliance on nonrenewable resources.}, } @article {pmid35862818, year = {2022}, author = {Fang, Y and Liu, J and Yang, J and Wu, G and Hua, Z and Dong, H and Hedlund, BP and Baker, BJ and Jiang, H}, title = {Compositional and Metabolic Responses of Autotrophic Microbial Community to Salinity in Lacustrine Environments.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0033522}, pmid = {35862818}, issn = {2379-5077}, mesh = {*Bacteria/genetics ; Salinity ; *Microbiota/genetics ; Autotrophic Processes ; Proteobacteria ; Carbon Cycle ; }, abstract = {The compositional and physiological responses of autotrophic microbiotas to salinity in lakes remain unclear. In this study, the community composition and carbon fixation pathways of autotrophic microorganisms in lacustrine sediments with a salinity gradient (82.6 g/L to 0.54 g/L) were investigated by using metagenomic analysis. A total of 117 metagenome-assembled genomes (MAGs) with carbon fixation potentially belonging to 20 phyla were obtained. The abundance of these potential autotrophs increased significantly with decreasing salinity, and the variation of sediment autotrophic microbial communities was mainly affected by salinity, pH, and total organic carbon. Notably, along the decreasing salinity gradient, the dominant lineage shifted from Desulfobacterota to Proteobacteria. Meanwhile, the dominant carbon fixation pathway shifted from the Wood-Lungdahl pathway to the less-energy-efficient Calvin-Benson-Bassham cycle, with glycolysis shifting from the Embden-Meyerhof-Parnas pathway to the less-exergonic Entner-Doudoroff pathway. These results suggest that the physiological efficiency of autotrophic microorganisms decreased when the environmental salinity became lower. Metabolic inference of these MAGs revealed that carbon fixation may be coupled to the oxidation of reduced sulfur compounds and ferrous iron, dissimilatory nitrate reduction at low salinity, and dissimilatory sulfate reduction in hypersaline sediments. These results extend our understanding of metabolic versatility and niche diversity of autotrophic microorganisms in saline environments and shed light on the response of autotrophic microbiomes to salinity. These findings are of great significance for understanding the impact of desalination caused by climate warming on the carbon cycle of saline lake ecosystems. IMPORTANCE The Qinghai-Tibetan lakes are experiencing water increase and salinity decrease due to climate warming. However, little is known about how the salinity decrease will affect the composition of autotrophic microbial populations and their carbon fixation pathways. In this study, we used genome-resolved metagenomics to interpret the dynamic changes in the autotrophic microbial community and metabolic pathways along a salinity gradient. The results showed that desalination drove the shift of the dominant microbial lineage from Desulfobacterota to Proteobacteria, enriched autotrophs with lower physiological efficiency pathways, and enhanced coupling between the carbon cycle and other element cycles. These results can predict the future response of microbial communities to lake desalination and improve our understanding of the effect of climate warming on the carbon cycle in saline aquatic ecosystems.}, } @article {pmid35862817, year = {2022}, author = {Sun, Y and Qu, Y and Yan, X and Yan, G and Chen, J and Wang, G and Zhao, Z and Liu, Y and Tu, C and He, B}, title = {Comprehensive Evaluation of RNA and DNA Viromic Methods Based on Species Richness and Abundance Analyses Using Marmot Rectal Samples.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0043022}, pmid = {35862817}, issn = {2379-5077}, mesh = {Animals ; RNA ; Marmota/genetics ; DNA, Single-Stranded ; *Viruses/genetics ; DNA ; *RNA Viruses/genetics ; }, abstract = {Viral metagenomics is the most powerful tool to profile viromic composition for a given sample. Different viromic methods, including amplification-free ones, have been developed, but choosing them for different purposes requires comprehensive benchmarks. Here, we assessed the performance of four routinely used methods, i.e., multiple displacement amplification (MDA), direct metagenomic sequencing (MTG), sequence-independent single-primer amplification (SIA), and metatranscriptomic sequencing (MTT), using marmot rectal samples as the templates spiked with five known viruses of different genome types. The obtained clean data were differently contaminated by host and bacterial genomes, resulting in MDA having the most, with ~72.1%, but MTT had only ~7.5% data, useful for follow-up viromic analysis. MDA showed a broader spectrum with higher efficiency to profile the DNA virome, and MTT captured almost all RNA viruses with extraordinary sensitivity; hence, they are advisable in richness-based viromic studies. MTG was weak in capturing single-stranded DNA viruses, and SIA could detect both RNA and DNA viruses but with high randomness. Due to biases to certain types of viruses, the four methods caused different alterations to species abundance compared to the initial virus composition. SIA and MDA introduced greater stochastic errors to relative abundances of species, genus, and family taxa, whereas the two amplification-free methods were more tolerant toward such errors and thus are recommendable in abundance-based analyses. In addition, genus taxon is a compromising analytic level that ensures technically supported and biologically and/or ecologically meaningful viromic conclusions. IMPORTANCE Viral metagenomics can be roughly divided into species richness-based studies and species abundance-based analyses. Viromic methods with different principles have been developed, but rational selection of these techniques according to different purposes requires comprehensive understanding of their properties. By assessing the four most widely used methods using template samples, we found that multiple displacement amplification (MDA) and metatranscriptomic sequencing (MTT) are advisable for species richness-based viromic studies, as they show excellent efficiency to detect DNA and RNA viruses. Meanwhile, metagenomic sequencing (MTG) and MTT are more compatible with stochastic errors of methods introduced into relative abundance of viromic taxa and hence are rational choices in species abundance-based analyses. This study also highlights that MTG needs to tackle host genome contamination and ameliorate the capacity to detect single-stranded DNA viruses in the future, and the MTT method requires an improvement in bacterial rRNA depletion prior to library preparation.}, } @article {pmid35862780, year = {2022}, author = {Leu, AO and Eppley, JM and Burger, A and DeLong, EF}, title = {Diverse Genomic Traits Differentiate Sinking-Particle-Associated versus Free-Living Microbes throughout the Oligotrophic Open Ocean Water Column.}, journal = {mBio}, volume = {13}, number = {4}, pages = {e0156922}, pmid = {35862780}, issn = {2150-7511}, mesh = {Aquatic Organisms/metabolism ; Bacteria/genetics/metabolism ; Carbon/metabolism ; Nitrogen/metabolism ; *Proteome/metabolism ; Proteomics ; Seawater/microbiology ; *Water/metabolism ; }, abstract = {Bacteria and archaea are central to the production, consumption, and remineralization of dissolved and particulate organic matter and contribute critically to carbon delivery, nutrient availability, and energy transformations in the deep ocean. To explore environmentally relevant genomic traits of sinking-particle-associated versus free-living microbes, we compared habitat-specific metagenome-assembled genomes recovered throughout the water column in the North Pacific Subtropical Gyre. The genomic traits of sinking-particle-associated versus free-living prokaryotes were compositionally, functionally, and phylogenetically distinct. Substrate-specific transporters and extracellular peptidases and carbohydrate-active enzymes were more enriched and diverse in particle-associated microbes at all depths than in free-living counterparts. These data indicate specific roles for particle-attached microbes in particle substrate hydrolysis, uptake, and remineralization. Shallow-water particle-associated microbes had elevated genomic GC content and proteome nitrogen content and reduced proteome carbon content in comparison to abyssal particle-associated microbes. An inverse trend was observed for their sympatric free-living counterparts. These different properties of attached microbes are postulated to arise in part due to elevated organic and inorganic nitrogen availability inside sinking particles. Particle-attached microbes also were enriched in genes for environmental sensing via two-component regulatory systems, and cell-cell interactions via extracellular secretion systems, reflecting their surface-adapted lifestyles. Finally, particle-attached bacteria had greater predicted maximal growth efficiencies than free-living bacterioplankton at all depths. All of these particle-associated specific genomic and proteomic features appear to be driven by microhabitat-specific elevated nutrient and energy availability as well as surface-associated competitive and synergistic ecological interactions. Although some of these characteristics have been previously postulated or observed individually, we report them together here in aggregate via direct comparisons of cooccurring free-living and sinking-particle-attached microbial genomes from the open ocean. IMPORTANCE Particle-attached microbes play large roles in the ocean carbon cycle and help to sequester atmospheric CO2 and to deliver nutrients and energy on sinking particles to the deep sea. Here, we report on the genomic traits of particle-attached versus free-living microbes throughout the ocean water column to better differentiate their specific metabolic and ecological roles in the sea. In general, the genomic properties and contents of particle-attached microbes reflected the physical and chemical compositions of their environment as well as their microhabitat-specific adaptive traits. In comparison to cooccurring free-living microbes, particle-attached microbes had larger genomes, greater capacity for extracellular polymer degradation, greater environmental sensing and response capacity, greater potential for motility and attachment, and higher growth efficiencies. Our results present an integrated new perspective on sinking-particle-attached microbial adaptive traits that contribute to their critical ecological and biogeochemical roles and activities in the sea.}, } @article {pmid35862742, year = {2022}, author = {McPherson, J and Hu, C and Begum, K and Wang, W and Lancaster, C and Gonzales-Luna, AJ and Loveall, C and Silverman, MH and Alam, MJ and Garey, KW}, title = {Functional and Metagenomic Evaluation of Ibezapolstat for Early Evaluation of Anti-Recurrence Effects in Clostridioides difficile Infection.}, journal = {Antimicrobial agents and chemotherapy}, volume = {66}, number = {8}, pages = {e0224421}, pmid = {35862742}, issn = {1098-6596}, mesh = {*Actinobacteria/genetics ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bile Acids and Salts/therapeutic use ; *Clostridioides difficile/genetics ; *Clostridium Infections/drug therapy/microbiology ; Humans ; Vancomycin/pharmacology/therapeutic use ; }, abstract = {Reduction of Clostridioides difficile infection (CDI) recurrence is an essential endpoint for CDI-directed antibiotic development that is often not evaluated until Phase III trials. The purpose of this project was to use a functional and metagenomic approach to predict the potential anti-CDI recurrence effect of ibezapolstat, a DNA polymerase IIIC inhibitor, in clinical development for CDI. As part of the Phase I ibezapolstat clinical study, stool samples were collected from 22 healthy volunteers, who were given either ibezapolstat or vancomycin. Stool samples were evaluated for microbiome changes and bile acid concentrations. Ibezapolstat 450 mg and vancomycin, but not ibezapolstat 300 mg, showed statistically significant changes in alpha diversity over time compared to that of a placebo. Beta diversity changes confirmed that microbiota were significantly different between study groups. Vancomycin had a more wide-ranging effect on the microbiome, characterized by an increased proportion of Gammaproteobacteria. Ibezapolstat demonstrated an increased proportion of Actinobacteria, including the Bifidobacteriaceae family. Using a linear regression analysis, vancomycin was associated with significant increases in primary bile acids as well as primary:secondary bile acid ratios. An overabundance of Enterobacteriaceae was most highly correlated with primary bile acid concentrations (r = 0.63; P < 0.0001). Using Phase I healthy volunteer samples, beneficial changes suggestive of a lower risk of CDI recurrence were associated with ibezapolstat compared to vancomycin. This novel omics approach may allow for better and earlier prediction of anti-CDI recurrence effects for antibiotics in the clinical development pipeline.}, } @article {pmid35862730, year = {2022}, author = {Smith, DJ and Kharbush, JJ and Kersten, RD and Dick, GJ}, title = {Uptake of Phytoplankton-Derived Carbon and Cobalamins by Novel Acidobacteria Genera in Microcystis Blooms Inferred from Metagenomic and Metatranscriptomic Evidence.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {14}, pages = {e0180321}, pmid = {35862730}, issn = {1098-5336}, mesh = {Acidobacteria/metabolism ; Amino Acids/metabolism ; Carbon/metabolism ; *Cyanobacteria/genetics ; Ecosystem ; Hydrogen Peroxide/metabolism ; Lakes/microbiology ; *Microcystis/genetics/metabolism ; Nitrogen/metabolism ; Phytoplankton/metabolism ; Vitamin B 12/metabolism ; }, abstract = {Interactions between bacteria and phytoplankton can influence primary production, community composition, and algal bloom development. However, these interactions are poorly described for many consortia, particularly for freshwater bloom-forming cyanobacteria. Here, we assessed the gene content and expression of two uncultivated Acidobacteria from Lake Erie Microcystis blooms. These organisms were targeted because they were previously identified as important catalase producers in Microcystis blooms, suggesting that they protect Microcystis from H2O2. Metatranscriptomics revealed that both Acidobacteria transcribed genes for uptake of organic compounds that are known cyanobacterial products and exudates, including lactate, glycolate, amino acids, peptides, and cobalamins. Expressed genes for amino acid metabolism and peptide transport and degradation suggest that use of amino acids and peptides by Acidobacteria may regenerate nitrogen for cyanobacteria and other organisms. The Acidobacteria genomes lacked genes for biosynthesis of cobalamins but expressed genes for its transport and remodeling. This indicates that the Acidobacteria obtained cobalamins externally, potentially from Microcystis, which has a complete gene repertoire for pseudocobalamin biosynthesis; expressed them in field samples; and produced pseudocobalamin in axenic culture. Both Acidobacteria were detected in Microcystis blooms worldwide. Together, the data support the hypotheses that uncultured and previously unidentified Acidobacteria taxa exchange metabolites with phytoplankton during harmful cyanobacterial blooms and influence nitrogen available to phytoplankton. Thus, novel Acidobacteria may play a role in cyanobacterial physiology and bloom development. IMPORTANCE Interactions between heterotrophic bacteria and phytoplankton influence competition and successions between phytoplankton taxa, thereby influencing ecosystem-wide processes such as carbon cycling and algal bloom development. The cyanobacterium Microcystis forms harmful blooms in freshwaters worldwide and grows in buoyant colonies that harbor other bacteria in their phycospheres. Bacteria in the phycosphere and in the surrounding community likely influence Microcystis physiology and ecology and thus the development of freshwater harmful cyanobacterial blooms. However, the impacts and mechanisms of interaction between bacteria and Microcystis are not fully understood. This study explores the mechanisms of interaction between Microcystis and uncultured members of its phycosphere in situ with population genome resolution to investigate the cooccurrence of Microcystis and freshwater Acidobacteria in blooms worldwide.}, } @article {pmid35862723, year = {2022}, author = {Smith, DJ and Berry, MA and Cory, RM and Johengen, TH and Kling, GW and Davis, TW and Dick, GJ}, title = {Heterotrophic Bacteria Dominate Catalase Expression during Microcystis Blooms.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {14}, pages = {e0254421}, pmid = {35862723}, issn = {1098-5336}, mesh = {Catalase/metabolism ; *Cyanobacteria/genetics ; Ecosystem ; Harmful Algal Bloom ; Humans ; Hydrogen Peroxide/metabolism ; Lakes/microbiology ; Microcystins/metabolism ; *Microcystis/genetics/metabolism ; }, abstract = {In the oligotrophic oceans, key autotrophs depend on "helper" bacteria to reduce oxidative stress from hydrogen peroxide (H2O2) in the extracellular environment. H2O2 is also a ubiquitous stressor in freshwaters, but the effects of H2O2 on autotrophs and their interactions with bacteria are less well understood in freshwaters. Naturally occurring H2O2 in freshwater systems is proposed to impact the proportion of microcystin-producing (toxic) and non-microcystin-producing (nontoxic) Microcystis in blooms, which influences toxin concentrations and human health impacts. However, how different strains of Microcystis respond to naturally occurring H2O2 concentrations and the microbes responsible for H2O2 decomposition in freshwater cyanobacterial blooms are unknown. To address these knowledge gaps, we used metagenomics and metatranscriptomics to track the presence and expression of genes for H2O2 decomposition by microbes during a cyanobacterial bloom in western Lake Erie in the summer of 2014. katG encodes the key enzyme for decomposing extracellular H2O2 but was absent in most Microcystis cells. katG transcript relative abundance was dominated by heterotrophic bacteria. In axenic Microcystis cultures, an H2O2 scavenger (pyruvate) significantly improved growth rates of one toxic strain while other toxic and nontoxic strains were unaffected. These results indicate that heterotrophic bacteria play a key role in H2O2 decomposition in Microcystis blooms and suggest that their activity may affect the fitness of some Microcystis strains and thus the strain composition of Microcystis blooms but not along a toxic versus nontoxic dichotomy. IMPORTANCE Cyanobacterial harmful algal blooms (CHABs) threaten freshwater ecosystems globally through the production of toxins. Toxin production by cyanobacterial species and strains during CHABs varies widely over time and space, but the ecological drivers of the succession of toxin-producing species remain unclear. Hydrogen peroxide (H2O2) is ubiquitous in natural waters, inhibits microbial growth, and may determine the relative proportions of Microcystis strains during blooms. However, the mechanisms and organismal interactions involved in H2O2 decomposition are unexplored in CHABs. This study shows that some strains of bloom-forming freshwater cyanobacteria benefit from detoxification of H2O2 by associated heterotrophic bacteria, which may impact bloom development.}, } @article {pmid35862686, year = {2022}, author = {Bhar, S and Singh, R and Pinna, NK and Bose, T and Dutta, A and Mande, SS}, title = {Sensing Host Health: Insights from Sensory Protein Signature of the Metagenome.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {15}, pages = {e0059622}, pmid = {35862686}, issn = {1098-5336}, mesh = {Biomarkers ; *Diabetes Mellitus, Type 2 ; Dysbiosis ; Humans ; Metagenome ; *Microbiota ; }, abstract = {The human microbiota, which comprises an ensemble of taxonomically and functionally diverse but often mutually cooperating microorganisms, benefits its host by shaping the host immunity, energy harvesting, and digestion of complex carbohydrates as well as production of essential nutrients. Dysbiosis in the human microbiota, especially the gut microbiota, has been reported to be linked to several diseases and metabolic disorders. Recent studies have further indicated that tracking these dysbiotic variations could potentially be exploited as biomarkers of disease states. However, the human microbiota is not geography agnostic, and hence a taxonomy-based (microbiome) biomarker for disease diagnostics has certain limitations. In comparison, (microbiome) function-based biomarkers are expected to have a wider applicability. Given that (i) the host physiology undergoes certain changes in the course of a disease and (ii) host-associated microbial communities need to adapt to this changing microenvironment of their host, we hypothesized that signatures emanating from the abundance of bacterial proteins associated with the signal transduction system (herein referred to as sensory proteins [SPs]) might be able to distinguish between healthy and diseased states. To test this hypothesis, publicly available metagenomic data sets corresponding to three diverse health conditions, namely, colorectal cancer, type 2 diabetes mellitus, and schizophrenia, were analyzed. Results demonstrated that SP signatures (derived from host-associated metagenomic samples) indeed differentiated among healthy individual and patients suffering from diseases of various severities. Our finding was suggestive of the prospect of using SP signatures as early biomarkers for diagnosing the onset and progression of multiple diseases and metabolic disorders. IMPORTANCE The composition of the human microbiota, a collection of host-associated microbes, has been shown to differ among healthy and diseased individuals. Recent studies have investigated whether tracking these variations could be exploited for disease diagnostics. It has been noted that compared to microbial taxonomies, the ensemble of functional proteins encoded by microbial genes are less likely to be affected by changes in ethnicity and dietary preferences. These functions are expected to help the microbe adapt to changing environmental conditions. Thus, healthy individuals might harbor a different set of genes than diseased individuals. To test this hypothesis, we analyzed metagenomes from healthy and diseased individuals for signatures of a particular group of proteins called sensory proteins (SP), which enable the bacteria to sense and react to changes in their microenvironment. Results demonstrated that SP signatures indeed differentiate among healthy individuals and those suffering from diseases of various severities.}, } @article {pmid35862685, year = {2022}, author = {Marin, J and Clermont, O and Royer, G and Mercier-Darty, M and Decousser, JW and Tenaillon, O and Denamur, E and Blanquart, F}, title = {The Population Genomics of Increased Virulence and Antibiotic Resistance in Human Commensal Escherichia coli over 30 Years in France.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {15}, pages = {e0066422}, pmid = {35862685}, issn = {1098-5336}, mesh = {Aged ; Animals ; Drug Resistance, Multiple, Bacterial/genetics ; *Escherichia coli ; *Escherichia coli Infections/epidemiology/microbiology ; Humans ; Metagenomics ; Phylogeny ; Prospective Studies ; Virulence/genetics ; Virulence Factors/genetics ; }, abstract = {Escherichia coli is a commensal species of the lower intestine but is also a major pathogen causing intestinal and extraintestinal infections that is increasingly prevalent and resistant to antibiotics. Most studies on genomic evolution of E. coli used isolates from infections. Here, instead, we whole-genome sequenced a collection of 403 commensal E. coli isolates from fecal samples of healthy adult volunteers in France (1980 to 2010). These isolates were distributed mainly in phylogroups A and B2 (30% each) and belonged to 152 sequence types (STs), the five most frequent being ST10 (phylogroup A; 16.3%), ST73 and ST95 (phylogroup B2; 6.3 and 5.0%, respectively), ST69 (phylogroup D; 4.2%), and ST59 (phylogroup F; 3.9%), and 224 O:H serotypes. ST and serotype diversity increased over time. The O1, O2, O6, and O25 groups used in bioconjugate O-antigen vaccine against extraintestinal infections were found in 23% of the strains of our collection. The increase in frequency of virulence-associated genes and antibiotic resistance was driven by two evolutionary mechanisms. Evolution of virulence gene frequency was driven by both clonal expansion of STs with more virulence genes ("ST-driven") and increases in gene frequency within STs independent of changes in ST frequencies ("gene-driven"). In contrast, the evolution of resistance was dominated by increases in frequency within STs ("gene-driven"). This study provides a unique picture of the phylogenomic evolution of E. coli in its human commensal habitat over 30 years and will have implications for the development of preventive strategies. IMPORTANCE Escherichia coli is an opportunistic pathogen with the greatest burden of antibiotic resistance, one of the main causes of bacterial infections and an increasing concern in an aging population. Deciphering the evolutionary dynamics of virulence and antibiotic resistance in commensal E. coli is important to understand adaptation and anticipate future changes. The gut of vertebrates is the primary habitat of E. coli and probably where selection for virulence and resistance takes place. Unfortunately, most whole-genome-sequenced strains are isolated from pathogenic conditions. Here, we whole-genome sequenced 403 E. coli commensals isolated from healthy French subjects over a 30-year period. Virulence genes increased in frequency by both clonal expansion of clones carrying them and increases in frequency within clones, whereas resistance genes increased by within-clone increased frequency. Prospective studies of E. coli commensals should be performed worldwide to have a broader picture of evolution and adaptation of this species.}, } @article {pmid35862662, year = {2022}, author = {Zou, K and Huang, Y and Feng, B and Qing, T and Zhang, P and Chen, YP}, title = {Cyanophycin Granule Polypeptide: a Neglected High Value-Added Biopolymer, Synthesized in Activated Sludge on a Large Scale.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {14}, pages = {e0074222}, pmid = {35862662}, issn = {1098-5336}, mesh = {Bacterial Proteins ; *Environmental Pollutants ; Peptides ; *Polyhydroxyalkanoates ; Sewage/microbiology ; }, abstract = {Recovery of microbial synthetic polymers with high economic value and market demand in activated sludge has attracted extensive attention. This work analyzed the synthesis of cyanophycin granule peptide (CGP) in activated sludge and its adsorption capacity for heavy metals and dyes. The distribution and expression of synthetic genes for eight biopolymers in two wastewater treatment plants (WWTPs) were analyzed by metagenomics and metatranscriptomics. The results indicate that the abundance and expression level of CGP synthase (cphA) are similar to those of polyhydroxyalkanoate polymerase, implying high synthesis of CGP in activated sludges. CGP in activated sludge is mainly polymerized from aspartic acid and arginine, and its secondary structure is mainly β-sheet. The crude yields of CGP are as high as 104 ± 26 and 76 ± 13 mg/g dry sludge in winter and in summer, respectively, comparable to those of polyhydroxyalkanoate and alginate. CGP has a stronger adsorption capacity for anionic pollutants (Cr (VI) and methyl orange) than for cationic pollutants because it is rich in guanidine groups. This study highlights prospects for recovery and application of CGP from WWTPs. IMPORTANCE The conversion of organic pollutants into bioresources by activated sludge can reduce the carbon dioxide emission of wastewater treatment plants. Identification of new high value-added biopolymers produced by activated sludge is beneficial to recover bioresources. Cyanophycin granule polypeptide (CGP), first discovered in cyanobacteria, has unique chemical and material properties suitable for industrial food, medicine, cosmetics, water treatment, and agriculture applications. Here, we revealed for the first time that activated sludge has a remarkable ability to produce CGP. These findings could further facilitate the conversion of wastewater treatment plants into resource recycling plants.}, } @article {pmid35862660, year = {2022}, author = {Swarthout, JM and Fuhrmeister, ER and Hamzah, L and Harris, AR and Ahmed, MA and Gurley, ES and Satter, SM and Boehm, AB and Pickering, AJ}, title = {Differential Overlap in Human and Animal Fecal Microbiomes and Resistomes in Rural versus Urban Bangladesh.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {14}, pages = {e0075922}, pmid = {35862660}, issn = {1098-5336}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Bangladesh ; Chickens/genetics ; Escherichia coli/genetics ; Genes, Bacterial ; Humans ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Rural Population ; }, abstract = {Low- and middle-income countries (LMICs) bear the largest mortality burden of antibiotic-resistant infections. Small-scale animal production and free-roaming domestic animals are common in many LMICs, yet data on zoonotic exchange of gut bacteria and antibiotic resistance genes (ARGs) in low-income communities are sparse. Differences between rural and urban communities with regard to population density, antibiotic use, and cohabitation with animals likely influence the frequency of transmission of gut bacterial communities and ARGs between humans and animals. Here, we determined the similarity in gut microbiomes, using 16S rRNA gene amplicon sequencing, and resistomes, using long-read metagenomics, between humans, chickens, and goats in a rural community compared to an urban community in Bangladesh. Gut microbiomes were more similar between humans and chickens in the rural (where cohabitation is more common) than the urban community, but there was no difference for humans and goats in the rural versus the urban community. Human and goat resistomes were more similar in the urban community, and ARG abundance was higher in urban animals than rural animals. We identified substantial overlap of ARG alleles in humans and animals in both settings. Humans and chickens had more overlapping ARG alleles than humans and goats. All fecal hosts from the urban community and rural humans carried ARGs on chromosomal contigs classified as potentially pathogenic bacteria, including Escherichia coli, Campylobacter jejuni, Clostridioides difficile, and Klebsiella pneumoniae. These findings provide insight into the breadth of ARGs circulating within human and animal populations in a rural compared to urban community in Bangladesh. IMPORTANCE While the development of antibiotic resistance in animal gut microbiomes and subsequent transmission to humans has been demonstrated in intensive farming environments and high-income countries, evidence of zoonotic exchange of antibiotic resistance in LMIC communities is lacking. This research provides genomic evidence of overlap of antibiotic resistance genes between humans and animals, especially in urban communities, and highlights chickens as important reservoirs of antibiotic resistance. Chicken and human gut microbiomes were more similar in rural Bangladesh, where cohabitation is more common. Incorporation of long-read metagenomics enabled characterization of bacterial hosts of resistance genes, which has not been possible in previous culture-independent studies using only short-read sequencing. These findings highlight the importance of developing strategies for combatting antibiotic resistance that account for chickens being reservoirs of ARGs in community environments, especially in urban areas.}, } @article {pmid35862452, year = {2022}, author = {Szabo, RE and Pontrelli, S and Grilli, J and Schwartzman, JA and Pollak, S and Sauer, U and Cordero, OX}, title = {Historical contingencies and phage induction diversify bacterioplankton communities at the microscale.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {30}, pages = {e2117748119}, pmid = {35862452}, issn = {1091-6490}, mesh = {Aquatic Organisms ; *Bacteria/classification ; *Bacteriophages ; Chitin/metabolism ; *Microbiota ; *Seawater/microbiology/virology ; }, abstract = {In many natural environments, microorganisms decompose microscale resource patches made of complex organic matter. The growth and collapse of populations on these resource patches unfold within spatial ranges of a few hundred micrometers or less, making such microscale ecosystems hotspots of heterotrophic metabolism. Despite the potential importance of patch-level dynamics for the large-scale functioning of heterotrophic microbial communities, we have not yet been able to delineate the ecological processes that control natural populations at the microscale. Here, we address this challenge by characterizing the natural marine communities that assembled on over 1,000 individual microscale particles of chitin, the most abundant marine polysaccharide. Using low-template shotgun metagenomics and imaging, we find significant variation in microscale community composition despite the similarity in initial species pools across replicates. Chitin-degrading taxa that were rare in seawater established large populations on a subset of particles, resulting in a wide range of predicted chitinolytic abilities and biomass at the level of individual particles. We show, through a mathematical model, that this variability can be attributed to stochastic colonization and historical contingencies affecting the tempo of growth on particles. We find evidence that one biological process leading to such noisy growth across particles is differential predation by temperate bacteriophages of chitin-degrading strains, the keystone members of the community. Thus, initial stochasticity in assembly states on individual particles, amplified through ecological interactions, may have significant consequences for the diversity and functionality of systems of microscale patches.}, } @article {pmid35862023, year = {2022}, author = {Jones, LK and Chen, N and Hassen, DA and Betts, MN and Klinger, T and Hartzel, DN and Veenstra, DL and Spencer, SJ and Snyder, SR and Peterson, JF and Schlieder, V and Sturm, AC and Gidding, SS and Williams, MS and Hao, J}, title = {Impact of a Population Genomic Screening Program on Health Behaviors Related to Familial Hypercholesterolemia Risk Reduction.}, journal = {Circulation. Genomic and precision medicine}, volume = {15}, number = {5}, pages = {e003549}, pmid = {35862023}, issn = {2574-8300}, support = {R01 HG009694/HG/NHGRI NIH HHS/United States ; }, mesh = {Humans ; Middle Aged ; Cholesterol, LDL ; Retrospective Studies ; *Metagenomics ; *Hyperlipoproteinemia Type II/diagnosis/drug therapy/genetics ; Health Behavior ; Risk Reduction Behavior ; }, abstract = {BACKGROUND: Limited information is available regarding clinician and participant behaviors after disclosure of genomic risk variants for familial hypercholesterolemia (FH) from a population genomic screening program.

METHODS: We conducted a retrospective cohort study of MyCode participants with an FH risk variant beginning 2 years before disclosure until January 16, 2019. We analyzed lipid-lowering prescriptions (clinician behavior), medication adherence (participant behavior), and LDL (low-density lipoprotein) cholesterol levels (health outcome impact) pre- and post-disclosure. Data were collected from electronic health records and claims.

RESULTS: The cohort included 96 participants of mean age 57 (22-90) years with median follow-up of 14 (range, 3-39) months. Most (90%) had a hypercholesterolemia diagnosis but no specific FH diagnosis before disclosure; 29% had an FH diagnosis post-disclosure. After disclosure, clinicians made 36 prescription changes in 38% of participants, mostly in participants who did not achieve LDL cholesterol goals pre-disclosure (81%). However, clinicians wrote prescriptions for fewer participants post-disclosure (71/96, 74.0%) compared with pre-disclosure (81/96, 84.4%); side effects were documented for most discontinued prescriptions (23/25, 92%). Among the 16 participants with claims data, medication adherence improved (proportion of days covered pre-disclosure of 70% [SD, 24.7%] to post-disclosure of 79.1% [SD, 27.3%]; P=0.05). Among the 52 (54%) participants with LDL cholesterol values both before and after disclosure, average LDL cholesterol decreased from 147 to 132 mg/dL (P=0.003).

CONCLUSIONS: Despite disclosure of an FH risk variant, nonprescribing and nonadherence to lipid-lowering therapy remained high. However, when clinicians intensified medication regimens and participants adhered to medications, lipid levels decreased.}, } @article {pmid35861776, year = {2023}, author = {Chattopadhyay, I and Lu, W and Manikam, R and Malarvili, MB and Ambati, RR and Gundamaraju, R}, title = {Can metagenomics unravel the impact of oral bacteriome in human diseases?.}, journal = {Biotechnology & genetic engineering reviews}, volume = {39}, number = {1}, pages = {85-117}, doi = {10.1080/02648725.2022.2102877}, pmid = {35861776}, issn = {2046-5556}, mesh = {Female ; Humans ; Pregnancy ; *Dental Caries ; *Periodontal Diseases/microbiology ; Porphyromonas gingivalis ; *Microbiota ; *Arthritis, Rheumatoid ; }, abstract = {Oral microbial ecosystems are vital in maintaining the health of the oral cavity and the entire body. Oral microbiota is associated with the progression of oral diseases such as dental caries, periodontal diseases, head and neck cancer, and several systemic diseases such as cardiovascular disease, rheumatoid arthritis, adverse pregnancy outcomes, diabetes, lung infection, colorectal cancer, and pancreatic cancer. Buccal mucosa, tongue dorsum, hard palate, saliva, palatine tonsils, throat, keratinized gingiva, supra-gingival plaque, subgingival plaque, dentures, and lips are microbial habitats of the oral cavity. Porphyromonas gingivalis may have a role in the development of periodontal diseases, oral cancer, diabetes, and atherosclerotic disease. Fusobacterium nucleatum showed a higher abundance in periodontal diseases, oral and colon cancer, adverse pregnancy outcomes, diabetes, and rheumatoid arthritis. The higher abundance of Prevotella intermedia is typical in periodontal diseases, rheumatoid arthritis, and adverse pregnancy outcome. S. salivarius displayed higher abundance in both dental caries and OSCC. Oral bacteria may influence systemic diseases through inflammation by releasing pro inflammatory cytokines. Identification of oral bacteria using culture-dependent approaches and next-generation sequencing-based metagenomic approaches is believed to significantly identify the therapeutic targets and non-invasive diagnostic indicators in different human diseases. Oral bacteria in saliva could be exploited as a non-invasive diagnostic indicator for the early detection of oral and systemic disorders. Other therapeutic approaches such as the use of probiotics, green tea polyphenol, cold atmospheric plasma (CAP) therapy, antimicrobial photodynamic therapy, and antimicrobial peptides are used to inhibit the growth of biofilm formation by oral bacteria.}, } @article {pmid35861556, year = {2022}, author = {Graham, EH and Adamowicz, MS and Angeletti, PC and Clarke, JL and Fernando, SC and Herr, JR}, title = {Genome Sequence of Feline Papillomavirus Strain P20 Assembled from Metagenomic Data from the Skin of a House Cat Owner.}, journal = {Microbiology resource announcements}, volume = {11}, number = {7}, pages = {e0107021}, pmid = {35861556}, issn = {2576-098X}, support = {2017-IJ-CX-0025//DOJ | OJP | National Institute of Justice (NIJ)/ ; }, abstract = {A feline papillomavirus genome was assembled from metagenomic sequencing data collected from the skin of a house cat owner. The circular genome of strain P20 is 8,069 bp in length, has a GC content of 54.38%, and displays genome organization typical of feline papillomaviruses. The genome exhibits approximately 75% sequence similarity to other feline papillomavirus genomes.}, } @article {pmid35861525, year = {2022}, author = {Chien, JY and Yu, CJ and Hsueh, PR}, title = {Utility of Metagenomic Next-Generation Sequencing for Etiological Diagnosis of Patients with Sepsis in Intensive Care Units.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0074622}, pmid = {35861525}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents ; Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Intensive Care Units ; Metagenomics/methods ; Prospective Studies ; RNA ; Sensitivity and Specificity ; *Sepsis/diagnosis ; *Viruses/genetics ; }, abstract = {The performance of metagenomic next-generation sequencing (mNGS) was evaluated and compared with that of conventional culture testing in patients with sepsis. Prospective blood and bronchoalveolar lavage fluid (BALF) samples from 50 patients with sepsis were tested using cultures (bacterial, fungal, and viral) and mNGS of microbial DNA (blood and BALF) and RNA (BALF). mNGS had higher detection rates than blood culture (88.0% versus 26.0%, P < 0.001) and BALF culture (92.0% versus 76.0%, P = 0.054). RNA-based mNGS has increased the detection rate of several bacteria, fungi, and viruses, but not mycobacteria and Toxoplasma gondii. The number of multiple detections per specimen was higher in BALF (92.0%) than in blood (78.0%) samples, and the highest number of pathogens detected in a single specimen was 32. Among blood samples, compared to cultures, mNGS detected significantly more bacteria (P < 0.001), fungi (P = 0.012), and viruses (P < 0.001), whereas BALF mNGS had a higher detection rate for bacteria (P < 0.001) and viruses (P < 0.001). The percentage of mNGS-positive samples was significantly higher than that of culture-positive samples for several Gram-negative bacteria, some Gram-positive bacteria, and viruses, but not fungi. Mycobacteria had a higher detection rate by culture than by mNGS, but the difference was not significant due to the small sample size. The positive and negative agreements with 95% confidence intervals of mNGS and culture were 62.0% (50.4 to 72.7) and 96.8% (96.5 to 97.1), respectively. mNGS offers a sensitive diagnostic method for patients with sepsis and is promising for the detection of multipathogen infections. Clinical correlation is advised to interpret mNGS data due to the lack of unified diagnostic criteria. IMPORTANCE Delays in effective antimicrobial therapy have resulted in decreased survival rates among patients with sepsis. However, current culture-based diagnostic methods have low sensitivity because of concurrent antibiotic exposure and fastidious and atypical causative organisms. Among patients with sepsis, we showed that mNGS methods had higher positive rates than culture methods, especially for bacteria, viruses, and multipathogen infections, which are difficult to culture and detect in patients treated with antibiotics. RNA-based mNGS has increased the detection rate of several bacteria, fungi, and viruses, but not mycobacteria and Toxoplasma gondii. mNGS also showed a high negative percent agreement with cultures. However, the interpretation of mNGS data should be combined with clinical data and conventional methods considering the lack of unified diagnostic criteria.}, } @article {pmid35861508, year = {2022}, author = {Rodríguez-Ramos, JA and Borton, MA and McGivern, BB and Smith, GJ and Solden, LM and Shaffer, M and Daly, RA and Purvine, SO and Nicora, CD and Eder, EK and Lipton, M and Hoyt, DW and Stegen, JC and Wrighton, KC}, title = {Genome-Resolved Metaproteomics Decodes the Microbial and Viral Contributions to Coupled Carbon and Nitrogen Cycling in River Sediments.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0051622}, pmid = {35861508}, issn = {2379-5077}, support = {P30 CA016058/CA/NCI NIH HHS/United States ; }, mesh = {*Rivers ; *Ecosystem ; Carbon Dioxide/metabolism ; Archaea/genetics ; Nitrogen Cycle ; Nitrogen/metabolism ; }, abstract = {Rivers have a significant role in global carbon and nitrogen cycles, serving as a nexus for nutrient transport between terrestrial and marine ecosystems. Although rivers have a small global surface area, they contribute substantially to worldwide greenhouse gas emissions through microbially mediated processes within the river hyporheic zone. Despite this importance, research linking microbial and viral communities to specific biogeochemical reactions is still nascent in these sediment environments. To survey the metabolic potential and gene expression underpinning carbon and nitrogen biogeochemical cycling in river sediments, we collected an integrated data set of 33 metagenomes, metaproteomes, and paired metabolomes. We reconstructed over 500 microbial metagenome-assembled genomes (MAGs), which we dereplicated into 55 unique, nearly complete medium- and high-quality MAGs spanning 12 bacterial and archaeal phyla. We also reconstructed 2,482 viral genomic contigs, which were dereplicated into 111 viral MAGs (vMAGs) of >10 kb in size. As a result of integrating gene expression data with geochemical and metabolite data, we created a conceptual model that uncovered new roles for microorganisms in organic matter decomposition, carbon sequestration, nitrogen mineralization, nitrification, and denitrification. We show how these metabolic pathways, integrated through shared resource pools of ammonium, carbon dioxide, and inorganic nitrogen, could ultimately contribute to carbon dioxide and nitrous oxide fluxes from hyporheic sediments. Further, by linking viral MAGs to these active microbial hosts, we provide some of the first insights into viral modulation of river sediment carbon and nitrogen cycling. IMPORTANCE Here we created HUM-V (hyporheic uncultured microbial and viral), an annotated microbial and viral MAG catalog that captures strain and functional diversity encoded in these Columbia River sediment samples. Demonstrating its utility, this genomic inventory encompasses multiple representatives of dominant microbial and archaeal phyla reported in other river sediments and provides novel viral MAGs that can putatively infect these. Furthermore, we used HUM-V to recruit gene expression data to decipher the functional activities of these MAGs and reconstruct their active roles in Columbia River sediment biogeochemical cycling. Ultimately, we show the power of MAG-resolved multi-omics to uncover interactions and chemical handoffs in river sediments that shape an intertwined carbon and nitrogen metabolic network. The accessible microbial and viral MAGs in HUM-V will serve as a community resource to further advance more untargeted, activity-based measurements in these, and related, freshwater terrestrial-aquatic ecosystems.}, } @article {pmid35860383, year = {2022}, author = {Beltrame, LC and Zamparette, CP and Feltrin, C and da Cunha, CR and Coltro, EP and Athayde, GSDS and Filho, VB and Tápparo, DC and Monteiro, J and Kich, JD and Palmeiro, JK and Wagner, G and Fongaro, G and Zárate-Bladés, CR and Sincero, TCM}, title = {Different Swine Production Systems Can Shape Slurry Resistome at Mechanism and Class Levels Based on Swine Manure Evaluation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {879656}, pmid = {35860383}, issn = {2235-2988}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents ; Drug Resistance, Bacterial/genetics ; Farms ; *Manure/microbiology ; Swine ; }, abstract = {Antimicrobial resistance is a major threat to public health. Antimicrobial use in animal husbandry is a major concern since it can favor an increase in antimicrobial resistance among farms. Herein, we aim to better understand and characterize the main resistome profiles in microbial communities found in pig farms. Sampling of swine manure was performed in two different timepoints (October 2019 and January 2020) in each of the 14 different swine farms, located in the mesoregion of Western Santa Catarina state in Brazil, a pole of swine product production of worldwide importance. Samples were divided into three groups: farms with the opened regimen and no usage of antimicrobials (F1; n = 10), farms with the closed regimen and usage of antimicrobials (F2; n = 16), and farms with the closed regimen and no usage of antimicrobials (F3; n = 2). The metagenomic evaluation was performed to obtain and identify genetic elements related to antimicrobial resistance using nanopore sequencing. We used ResistoXplorer software to perform composition, alpha and beta diversity, and clustering analysis. In addition, PCR reactions were performed to confirm the presence or absence of seven different beta-lactamase family genes and five phosphoethanolamine transferase gene variants clinically relevant. Our findings based on the identification of resistance genes at the mechanism level showed a prevalence of alteration of the drug target (72.3%) profile, followed by drug inactivation (17.5%) and drug efflux (10.1%). We identified predominantly aminoglycosides (45.3%), tetracyclines (15.9%), and multiclass (11,2%) resistance genes. PCoA analysis indicates differences between F1 and F2 profiles. F2 samples showed increased diversity when compared to the F1 group. In addition, herein we first report the identification of mcr-4 in a slurry sample (C1F1.1) in Santa Catarina State. In general, our findings reinforce that many factors on the practices of animal husbandry are involved in the resistome profile at the mechanism and class levels. Further studies to better understand microbiome and mobilome aspects of these elements are necessary to elucidate transmission pathways between different bacteria and environments.}, } @article {pmid35860041, year = {2022}, author = {Zhang, J and Xu, M and Zou, X and Chen, J}, title = {Structural and functional characteristics of soil microbial community in a Pinus massoniana forest at different elevations.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13504}, pmid = {35860041}, issn = {2167-8359}, mesh = {*Pinus ; Soil/chemistry ; Fungi/genetics ; Forests ; Bacteria/genetics ; Archaea/genetics ; *Microbiota/genetics ; Amino Acids ; }, abstract = {Shifts in forest soil microbial communities over altitudinal gradients have long been attracting scientific interest. The distribution patterns of different soil microbial communities along altitudinal gradients in subtropical mountain forest ecosystems remain unclear. To better understand the changes in soil microbial communities along an altitude gradient, we used Illumina MiSeq metagenome sequencing technology to survey the soil microbial communities in a Pinus massoniana forest at four elevations (Mp1000, Mp1200, Mp1400, Mp1600) and in a tea garden in Guizhou Leigong Mountain in Southwestern China. We observed that the richness of bacteria, fungi, and viruses in the soil microbial community changed in a unimodal pattern with increasing elevation while that of Archaea first increased significantly, then decreased, and finally increased again. Euryarchaeota and Thaumarchaeota were the predominant Archaea, Proteobacteria and Acidobacteria were the predominant bacterial groups, Ascomycota and Basidiomycota were the predominant fungal groups, and Myoviridae, Podoviridae, and Siphoviridae were the predominant virus groups. Amino acid transport and metabolism, energy production and conversion, signal transduction mechanisms, and DNA replication, restructuring and repair were the predominant categories as per NOG function gene-annotation. Carbohydrate metabolism, global and overview map, amino acid metabolism, and energy metabolism were predominant categories in the KEGG pathways. Glycosyl transferase and glycoside hydrolase were predominant categories among carbohydrate enzyme-functional genes. Cluster, redundancy, and co-occurring network analyses showed obvious differences in the composition, structure, and function of different soil microbial communities along the altitudinal gradient studied. Our findings indicate that the different soil microbial communities along the altitudinal gradient have different distribution patterns, which may provide a better understanding of the mechanisms that determine microbial life in a mid-subtropical mountain forest ecosystem.}, } @article {pmid35859749, year = {2022}, author = {Dong, Y and Gao, Y and Chai, Y and Shou, S}, title = {Use of Quantitative Metagenomics Next-Generation Sequencing to Confirm Fever of Unknown Origin and Infectious Disease.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {931058}, pmid = {35859749}, issn = {1664-302X}, abstract = {A body temperature >38.3°C that lasts ≥3 weeks and lacks a clear diagnosis after 1 week of standard hospital examination and treatment is called "fever of unknown origin" (FUO). The main causes of FUO are infections, hematological diseases, autoimmune diseases, and other non-infectious inflammatory diseases. In recent years, quantitative metagenomics next-generation sequencing (Q-mNGS) has been used widely to detect pathogenic microorganisms, especially in the contribution of rare or new (e.g., severe acute respiratory syndrome-coronavirus-2) pathogens. This review addresses the undetermined cause of fever and its evaluation by Q-mNGS.}, } @article {pmid35859738, year = {2022}, author = {Wang, P and Li, M and Dong, L and Zhang, C and Xie, W}, title = {Comparative Genomics of Thaumarchaeota From Deep-Sea Sponges Reveal Their Niche Adaptation.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {869834}, pmid = {35859738}, issn = {1664-302X}, abstract = {Thaumarchaeota account for a large portion of microbial symbionts in deep-sea sponges and are even dominant in some cases. In this study, we investigated three new sponge-associated Thaumarchaeota from the deep West Pacific Ocean. Thaumarchaeota were found to be the most dominant phylum in this sponge by both prokaryotic 16S rRNA amplicons and metagenomic sequencing. Fifty-seven published Thaumarchaeota genomes from sponges and other habitats were included for genomic comparison. Similar to shallow sponge-associated Thaumarchaeota, those Thaumarchaeota in deep-sea sponges have extended genome sizes and lower coding density compared with their free-living lineages. Thaumarchaeota in deep-sea sponges were specifically enriched in genes related to stress adapting, symbiotic adhesion and stability, host-microbe interaction and protein transportation. The genes involved in defense mechanisms, such as the restriction-modification system, clustered regularly interspaced short palindromic repeats (CRISPR)/Cas system, and toxin-antitoxin system were commonly enriched in both shallow and deep sponge-associated Thaumarchaeota. Our study demonstrates the significant effects of both depth and symbiosis on forming genomic characteristics of Thaumarchaeota, and provides novel insights into their niche adaptation in deep-sea sponges.}, } @article {pmid35859219, year = {2022}, author = {Bharti, M and Nagar, S and Khurana, H and Negi, RK}, title = {Metagenomic insights to understand the role of polluted river Yamuna in shaping the gut microbial communities of two invasive fish species.}, journal = {Archives of microbiology}, volume = {204}, number = {8}, pages = {509}, pmid = {35859219}, issn = {1432-072X}, mesh = {Animals ; *Carps ; Humans ; Introduced Species ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Rivers ; Water ; }, abstract = {The gastrointestinal microbial community plays a crucial role in host health, immunity, protection, development and provides nutrients to the host. The rising human-induced pollution and heavy metal contamination in all aquatic systems globally has led us to explore the gut microbial diversity of two exotic invasive fish Cyprinus carpio (Linnaeus, 1858) and Oreochromis niloticus (Linnaeus,1857) from river Yamuna, India. These fishes are aquatic bioindicators with high demographic resilience. Exploring these associations would pave the way for addressing problems that inhabitant fishes are facing due to the increasing pollution load in the River Yamuna. Based on 16S rRNA gene amplicon sequencing, our results deliver comparative information on the gut microbiome of these fishes and highlight connotations between the microbiome of gut and water samples. The gut of C. carpio and O. niloticus was dominated by phyla Proteobacteria whereas Bacteroidetes dominated the water sample. Microbial communities showed predicted roles such as pathogenicity (Escherichia-Shigella, Aeromonas veronii, Vibrio cholerae, Streptococcus iniae, Flavobacterium columnare, Klebsiella pneumoniae, Mycobacterium sp.), probiotic applications (Bacillus velezensis, Lactobacillus plantarum, Enterococcus faecalis, Bifidobacterium longum, Lactococcus lactis, Leuconostoc falkenbergense) and involvement in sewage and organic matter decomposition (Nitrosomonas sp., Methanosaeta harundinacea, Dechloromonas agitata, Thauera humireducens, Zoogloea ramigera). Heavy metal degrading members (Leucobacter chromiireducens, Pseudomonas fluorescens, P. aeruginosa, Klebsiella pneumoniae, and Micrococcus luteus) were detected in gut microbiome samples thus supporting the notion that fish shapes its gut microbiota with changing ecology. Functional profiling showed that microbial communities are specialized in metabolic functions thus reflecting the dietary profile of these invasive fishes.}, } @article {pmid35858888, year = {2022}, author = {Killinger, BJ and Whidbey, C and Sadler, NC and DeLeon, AJ and Munoz, N and Kim, YM and Wright, AT}, title = {Activity-based protein profiling identifies alternating activation of enzymes involved in the bifidobacterium shunt pathway or mucin degradation in the gut microbiome response to soluble dietary fiber.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {60}, pmid = {35858888}, issn = {2055-5008}, mesh = {Animals ; Bacteria ; Bifidobacterium/metabolism ; Carrier Proteins/metabolism ; Dietary Fiber ; Feces/microbiology ; *Gastrointestinal Microbiome ; Mice ; Mucins/metabolism/pharmacology ; Sugars/metabolism/pharmacology ; }, abstract = {While deprivation of dietary fiber has been associated with adverse health outcomes, investigations concerning the effect of dietary fiber on the gut microbiome have been largely limited to compositional sequence-based analyses or utilize a defined microbiota not native to the host. To extend understanding of the microbiome's functional response to dietary fiber deprivation beyond correlative evidence from sequence-based analyses, approaches capable of measuring functional enzymatic activity are needed. In this study, we use an activity-based protein profiling (ABPP) approach to identify sugar metabolizing and transport proteins in native mouse gut microbiomes that respond with differential activity to the deprivation or supplementation of the soluble dietary fibers inulin and pectin. We found that the microbiome of mice subjected to a high fiber diet high in soluble fiber had increased functional activity of multiple proteins, including glycoside hydrolases, polysaccharide lyases, and sugar transport proteins from diverse taxa. The results point to an increase in activity of the Bifidobacterium shunt metabolic pathway in the microbiome of mice fed high fiber diets. In those subjected to a low fiber diet, we identified a shift from the degradation of dietary fibers to that of gut mucins, in particular by the recently isolated taxon "Musculibacterium intestinale", which experienced dramatic growth in response to fiber deprivation. When combined with metabolomics and shotgun metagenomics analyses, our findings provide a functional investigation of dietary fiber metabolism in the gut microbiome and demonstrates the power of a combined ABPP-multiomics approach for characterizing the response of the gut microbiome to perturbations.}, } @article {pmid35858469, year = {2022}, author = {Ocansey, DKW and Zhang, Z and Xu, X and Liu, L and Amoah, S and Chen, X and Wang, B and Zhang, X and Mao, F}, title = {Mesenchymal stem cell-derived exosome mitigates colitis via the modulation of the gut metagenomics-metabolomics-farnesoid X receptor axis.}, journal = {Biomaterials science}, volume = {10}, number = {17}, pages = {4822-4836}, doi = {10.1039/d2bm00559j}, pmid = {35858469}, issn = {2047-4849}, mesh = {Animals ; Bacteria/genetics ; Bile Acids and Salts ; *Colitis/chemically induced ; Dextran Sulfate/toxicity ; Disease Models, Animal ; *Exosomes/metabolism ; *Inflammatory Bowel Diseases/chemically induced ; *Mesenchymal Stem Cells/metabolism ; Mice ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S ; }, abstract = {Inflammatory bowel disease (IBD) is associated with chronic gut immune dysregulation and altered microbiome and metabolite composition. Bile acids and their receptors such as the farnesoid X receptor (FXR) form a crucial component of the chemical communications between the intestinal microbiota and the host immune system; thus, alterations in the bile acid pool affect intestinal homeostasis and exacerbate IBD. Considering the promising therapeutic effect of mesenchymal stem cell-derived exosomes (MSC-Ex) on IBD, this study assessed the regulatory effect of MSC-Ex on the gut bacteria composition and diversity, metabolites, and their related functions and pathways, as well as key inflammatory and anti-inflammatory cytokines during the mitigation of IBD. The dextran sulfate sodium (DSS)-induced IBD model of BABL/C mice was established, consisting of three groups: control, DSS, and MSC-Ex groups. Post administration of MSC-Ex, the effect was evaluated via hematoxylin and eosin (H&E) staining, immunohistochemistry (IHC), qRT-PCR, and western blotting. Mice fecal samples were obtained for metagenomics and metabolomics analysis via 16S rRNA gene sequencing and UHPLC/Q-TOF-MS respectively. Results showed that MSC-Ex mitigated colitis by significantly relieving the macroscopic and microscopic features of inflammation, modulating the gut metagenomics and metabolomics profile, and increasing colonic FXR. MSC-Ex improved the gut microbiota composition by significantly restoring the structure of OTUs and colitis-induced reduction in α-diversity, increasing the abundance of 'healthy' bacteria, decreasing disease-associated bacteria, decreasing detrimental functions, and enhancing other vital cellular functions. For the first time, we demonstrate that MSC-Ex mitigates colitis in mice by modulating the gut metagenomics-metabolomics-FXR axis, thus providing potential therapeutic targets.}, } @article {pmid35857470, year = {2022}, author = {Wada, N and Hsu, MT and Tandon, K and Hsiao, SS and Chen, HJ and Chen, YH and Chiang, PW and Yu, SP and Lu, CY and Chiou, YJ and Tu, YC and Tian, X and Chen, BC and Lee, DC and Yamashiro, H and Bourne, DG and Tang, SL}, title = {High-resolution spatial and genomic characterization of coral-associated microbial aggregates in the coral Stylophora pistillata.}, journal = {Science advances}, volume = {8}, number = {27}, pages = {eabo2431}, pmid = {35857470}, issn = {2375-2548}, abstract = {Bacteria commonly form aggregates in a range of coral species [termed coral-associated microbial aggregates (CAMAs)], although these structures remain poorly characterized despite extensive efforts studying the coral microbiome. Here, we comprehensively characterize CAMAs associated with Stylophora pistillata and quantify their cell abundance. Our analysis reveals that multiple Endozoicomonas phylotypes coexist inside a single CAMA. Nanoscale secondary ion mass spectrometry imaging revealed that the Endozoicomonas cells were enriched with phosphorus, with the elemental compositions of CAMAs different from coral tissues and endosymbiotic Symbiodiniaceae, highlighting a role in sequestering and cycling phosphate between coral holobiont partners. Consensus metagenome-assembled genomes of the two dominant Endozoicomonas phylotypes confirmed their metabolic potential for polyphosphate accumulation along with genomic signatures including type VI secretion systems allowing host association. Our findings provide unprecedented insights into Endozoicomonas-dominated CAMAs and the first direct physiological and genomic linked evidence of their biological role in the coral holobiont.}, } @article {pmid35857224, year = {2022}, author = {Rodriguez-Valera, F and Pushkarev, A and Rosselli, R and Béjà, O}, title = {Searching Metagenomes for New Rhodopsins.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2501}, number = {}, pages = {101-108}, pmid = {35857224}, issn = {1940-6029}, mesh = {*Metagenome ; Metagenomics ; Phylogeny ; *Rhodopsins, Microbial/genetics ; }, abstract = {Most microbial groups have not been cultivated yet, and the only way to approach the enormous diversity of rhodopsins that they contain in a sensible timeframe is through the analysis of their genomes. High-throughput sequencing technologies have allowed the release of community genomics (metagenomics) of many habitats in the photic zones of the ocean and lakes. Already the harvest is impressive and included from the first bacterial rhodopsin (proteorhodopsin) to the recent discovery of heliorhodopsin by functional metagenomics. However, the search continues using bioinformatic or biochemical routes.}, } @article {pmid35857094, year = {2022}, author = {Rau, J and Werner, D and Beer, M and Höper, D and Kampen, H}, title = {The microbial RNA metagenome of Aedes albopictus (Diptera: Culicidae) from Germany.}, journal = {Parasitology research}, volume = {121}, number = {9}, pages = {2587-2599}, pmid = {35857094}, issn = {1432-1955}, mesh = {*Aedes ; Animals ; Female ; Humans ; Introduced Species ; Male ; Metagenome ; Mosquito Vectors ; RNA ; *Zika Virus ; *Zika Virus Infection ; }, abstract = {Aedes albopictus is a highly invasive mosquito species that has become widespread across the globe. In addition, it is an efficient vector of numerous pathogens of medical and veterinary importance, including dengue, chikungunya and Zika viruses. Among others, the vector potential of mosquitoes is influenced by their microbiome. However, this influence is very dynamic and can vary between individuals and life stages. To obtain a rough overview on the microbiome of Ae. albopictus populations in Germany, pooled female and pooled male individuals from seven German locations were investigated by total RNA sequencing. The mosquito specimens had been collected as larvae in the field and processed immediately after adult emergence, i.e. without females having fed on blood. RNA fragments with high degrees of identity to a large number of viruses and microorganisms were identified, including, for example, Wolbachia pipientis and Acinetobacter baumannii, with differences between male and female mosquitoes. Knowledge about the natural occurrence of microorganisms in mosquitoes may be translated into new approaches to vector control, for example W. pipientis can be exploited to manipulate mosquito reproduction and vector competence. The study results show how diverse the microbiome of Ae. albopictus can be, and the more so needs to be adequately analysed and interpreted.}, } @article {pmid35855159, year = {2022}, author = {Walker, M and Uranga, C and Levy, SH and Kelly, C and Edlund, A}, title = {Thrombus-associated microbiota in acute ischemic stroke patients.}, journal = {Surgical neurology international}, volume = {13}, number = {}, pages = {247}, pmid = {35855159}, issn = {2229-5097}, abstract = {BACKGROUND: Despite a reduction in stroke incidence and age-standardized death rates, stroke remains a leading cause of death and disability worldwide. Significant interest in recent years has focused on the microbiota-host interaction because accumulating evidence has revealed myriad ways in which bacteria may contribute to risk of stroke and adverse outcomes after stroke. The emergence of endovascular thrombectomy as a treatment provides a unique opportunity to utilize thrombus retrieved from cerebral arteries to fill knowledge gaps about the influence of bacteria on stroke pathophysiology. While bacterial signatures have been confirmed in cerebral thrombi, the exact nature of the pathogenesis has not been established.

METHODS: Thrombi were obtained from a cohort of adult ischemic stroke patients during standard of care thrombectomy. After DNA extraction and quantification, thrombi underwent 16S rRNA amplicon-based metagenomic sequencing, followed by bioinformatics processing. Taxonomic identification of bacterial colonies isolated on Agar plates from plated suspension was performed using DNA extraction and full length 16S Sanger sequencing.

RESULTS: A broad diversity of bacterial signatures was identified in specimens, primarily of cariogenic origin.

CONCLUSION: In this small study, we demonstrate proof of concept and technical feasibility for amplicon-based metagenomic sequencing of arterial thrombi and briefly discuss preliminary findings, challenges, and near-term translational opportunities for thrombus genomics.}, } @article {pmid35852333, year = {2022}, author = {Mackelprang, R and Vaishampayan, P and Fisher, K}, title = {Adaptation to Environmental Extremes Structures Functional Traits in Biological Soil Crust and Hypolithic Microbial Communities.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0141921}, pmid = {35852333}, issn = {2379-5077}, mesh = {Soil/chemistry ; Desert Climate ; *Cyanobacteria ; *Microbiota ; Metagenome ; *Bryophyta/physiology ; }, abstract = {Biological soil crusts (biocrusts) are widespread in drylands and deserts. At the microhabitat scale, they also host hypolithic communities that live under semitranslucent stones. Both environmental niches experience exposure to extreme conditions such as high UV radiation, desiccation, temperature fluctuations, and resource limitation. However, hypolithic communities are somewhat protected from extremes relative to biocrust communities. Conditions are otherwise similar, so comparing them can answer outstanding questions regarding adaptations to environmental extremes. Using metagenomic sequencing, we assessed the functional potential of dryland soil communities and identified the functional underpinnings of ecological niche differentiation in biocrusts versus hypoliths. We also determined the effect of the anchoring photoautotroph (moss or cyanobacteria). Genes and pathways differing in abundance between biocrusts and hypoliths indicate that biocrust communities adapt to the higher levels of UV radiation, desiccation, and temperature extremes through an increased ability to repair damaged DNA, sense and respond to environmental stimuli, and interact with other community members and the environment. Intracellular competition appears to be crucial to both communities, with biocrust communities using the Type VI Secretion System (T6SS) and hypoliths favoring a diversity of antibiotics. The dominant primary producer had a reduced effect on community functional potential compared with niche, but an abundance of genes related to monosaccharide, amino acid, and osmoprotectant uptake in moss-dominated communities indicates reliance on resources provided to heterotrophs by mosses. Our findings indicate that functional traits in dryland communities are driven by adaptations to extremes and we identify strategies that likely enable survival in dryland ecosystems. IMPORTANCE Biocrusts serve as a keystone element of desert and dryland ecosystems, stabilizing soils, retaining moisture, and serving as a carbon and nitrogen source in oligotrophic environments. Biocrusts cover approximately 12% of the Earth's terrestrial surface but are threatened by climate change and anthropogenic disturbance. Given their keystone role in ecosystem functioning, loss will have wide-spread consequences. Biocrust microbial constituents must withstand polyextreme environmental conditions including high UV exposure, desiccation, oligotrophic conditions, and temperature fluctuations over short time scales. By comparing biocrust communities with co-occurring hypolithic communities (which inhabit the ventral sides of semitranslucent stones and are buffered from environmental extremes), we identified traits that are likely key adaptations to extreme conditions. These include DNA damage repair, environmental sensing and response, and intracellular competition. Comparison of the two niches, which differ primarily in exposure levels to extreme conditions, makes this system ideal for understanding how functional traits are structured by the environment.}, } @article {pmid35852328, year = {2022}, author = {Cai, R and He, W and Liu, R and Zhang, J and Zhang, X and Sun, C}, title = {Deep-Sea In Situ Insights into the Formation of Zero-Valent Sulfur Driven by a Bacterial Thiosulfate Oxidation Pathway.}, journal = {mBio}, volume = {13}, number = {4}, pages = {e0014322}, pmid = {35852328}, issn = {2150-7511}, mesh = {Bacteria/genetics/metabolism ; Oxidation-Reduction ; Phylogeny ; *Proteomics ; Sulfur/metabolism ; *Thiosulfates/metabolism ; }, abstract = {Zero-valent sulfur (ZVS) distributes widely in the deep-sea cold seep, which is an important immediate in the sulfur cycle of cold seep. In our previous work, we described a novel thiosulfate oxidation pathway determined by thiosulfate dehydrogenase (TsdA) and thiosulfohydrolase (SoxB) mediating the conversion of thiosulfate to ZVS in the deep-sea cold seep bacterium Erythrobacter flavus 21-3. However, the occurrence and ecological role of this pathway in the deep-sea cold seep were obscure. Here, we cultured E. flavus 21-3 in the deep-sea cold seep for 10 days and demonstrated its capability of forming ZVS in the in situ field. Based on proteomic, stoichiometric analyses and microscopic observation, we found that this thiosulfate oxidation pathway benefited E. flavus 21-3 to adapt the cold seep conditions. Notably, ~25% metagenomes assembled genomes derived from the shallow sediments of cold seeps contained both tsdA and soxB, where presented abundant sulfur metabolism-related genes and active sulfur cycle. Our results suggested that the thiosulfate oxidation pathway determined by TsdA and SoxB existed across many bacteria inhabiting in the cold seep and frequently used by microbes to take part in the active cold seep biogeochemical sulfur cycle. IMPORTANCE The contribution of microbes to the deep-sea cold seep sulfur cycle has received considerable attention in recent years. In the previous study, we isolated E. flavus 21-3 from deep-sea cold seep sediments and described a novel thiosulfate oxidation pathway in the laboratorial condition. It provided a new clue about the formation of ZVS in the cold seep. However, because of huge differences between laboratory and in situ environment, whether bacteria perform the same thiosulfate oxidation pathway in the deep-sea cold seep should be further confirmed. In this work, we verified that E. flavus 21-3 formed ZVS using this pathway in deep-sea cold seep through in situ cultivation, which confirmed the importance of this thiosulfate oxidation pathway and provided an in situ approach to study the real metabolism of deep-sea microorganisms.}, } @article {pmid35852316, year = {2022}, author = {Venturini, AM and Gontijo, JB and da França, AG and Moura, JMS and Nüsslein, K and Bohannan, BJM and Rodrigues, JLM and Tsai, SM}, title = {Metagenomes from Eastern Brazilian Amazonian Floodplains in the Wet and Dry Seasons.}, journal = {Microbiology resource announcements}, volume = {11}, number = {8}, pages = {e0043222}, pmid = {35852316}, issn = {2576-098X}, support = {Finance Code 001//Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)/ ; Princeton University Library Open Access Fund//Princeton University/ ; #2014/50320-4//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; #2015/19979-2//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; #2018/14974-0//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; #2019/25931-3//Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)/ ; #133769/2015-1//MCTI | Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; #311008/2016-0//MCTI | Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)/ ; DEB 1442214//National Science Foundation (NSF)/ ; Fung Global Fellows Program//Princeton University | Princeton Institute for International and Regional Studies (PIIRS)/ ; }, abstract = {Here, we report the metagenomes from two Amazonian floodplain sediments in eastern Brazil. Tropical wetlands are well known for their role in the global carbon cycle. Microbial information on this diversified and dynamic landscape will provide further insights into its significance in regional and global biogeochemical cycles.}, } @article {pmid35852145, year = {2022}, author = {Bolliri, C and Fontana, A and Cereda, E and Barichella, M and Cilia, R and Ferri, V and Caronni, S and Calandrella, D and Morelli, L and Pezzoli, G}, title = {Gut Microbiota in Monozygotic Twins Discordant for Parkinson's Disease.}, journal = {Annals of neurology}, volume = {92}, number = {4}, pages = {631-636}, doi = {10.1002/ana.26454}, pmid = {35852145}, issn = {1531-8249}, mesh = {Bile Acids and Salts ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; *Parkinson Disease/genetics/pathology ; Twins, Monozygotic ; }, abstract = {Differences in gut microbiota between Parkinson's disease patients and controls seem to depend on multiple-frequently unmeasured-confounders. Monozygotic twins offer a unique model for controlling several factors responsible for interpersonal variation in gut microbiota. Fecal samples from 20 monozygotic twin pairs (n = 40) discordant for Parkinson's disease were studied (metagenomic shotgun analysis). Paired data analysis detected minimal differences in bacterial taxa abundance at species level (Bacteroides pectinophilus [p = 0.037], Bifidobacterium pseudocatenulatum [p = 0.050], and Bifidobacterium catenulatum [p = 0.025]) and in predicted metabolic pathways (primary bile acid biosynthesis [p = 0.037]). Additional studies are warranted to understand the role of gut microbiota in the pathogenesis of Parkinson's disease. ANN NEUROL 2022;92:631-636.}, } @article {pmid35851765, year = {2022}, author = {Wang, Y and Zhang, Y and Lane, NE and Wu, J and Yang, T and Li, J and He, H and Wei, J and Zeng, C and Lei, G}, title = {Population-based metagenomics analysis reveals altered gut microbiome in sarcopenia: data from the Xiangya Sarcopenia Study.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {13}, number = {5}, pages = {2340-2351}, pmid = {35851765}, issn = {2190-6009}, support = {2019RS2010//Science and Technology Program of Hunan Province/ ; 2021Q14//Youth Science Foundation of Xiangya Hospital/ ; 2020LNJJ03//Project Program of National Clinical Research Center for Geriatric Disorders/ ; U21A20352//National Natural Science Foundation of China/ ; 82072502//National Natural Science Foundation of China/ ; 81902265//National Natural Science Foundation of China/ ; 81930071//National Natural Science Foundation of China/ ; }, mesh = {Bacteroides ; Clostridiaceae ; Clostridiales ; Desulfovibrio ; Female ; Furaldehyde ; *Gastrointestinal Microbiome/genetics ; Humans ; Middle Aged ; Phenylalanine ; RNA, Ribosomal, 16S/genetics ; *Sarcopenia/diagnosis/epidemiology ; Staurosporine ; Tryptophan ; Tyrosine ; alpha-Linolenic Acid ; }, abstract = {BACKGROUND: Several studies have examined gut microbiota and sarcopenia using 16S ribosomal RNA amplicon sequencing; however, this technique may not be able to identify altered specific species and functional capacities of the microbes. We performed shotgun metagenomic sequencing to compare the gut microbiome composition and function between individuals with and without sarcopenia.

METHODS: Participants were from a community-based observational study conducted among the residents of rural areas in China. Appendicular skeletal muscle mass was assessed using direct segmental multi-frequency bioelectrical impedance and grip strength using a Jamar Hydraulic Hand dynamometer. Physical performance was evaluated using the Short Physical Performance Battery, 5-time chair stand test and gait speed with the 6 m walk test. Sarcopenia and its severity were diagnosed according to the Asian Working Group for Sarcopenia 2019 algorithm. The gut microbiome was profiled by shotgun metagenomic sequencing to determine the microbial composition and function. A gut microbiota-based model for classification of sarcopenia was constructed using the random forest model, and its performance was assessed using the area under receiver-operating characteristic curve (AUC).

RESULTS: The study sample included 1417 participants (women: 58.9%; mean age: 63.3 years; sarcopenia prevalence: 10.0%). β-diversity indicated by Bray-Curtis distance (genetic level: P = 0.004; taxonomic level of species: P = 0.020), but not α-diversity indicated by Shannon index (genetic level: P = 0.962; taxonomic level of species: P = 0.922), was significantly associated with prevalent sarcopenia. After adjusting for potential confounders, participants with sarcopenia had higher relative abundance of Desulfovibrio piger (P = 0.003, Q = 0.090), Clostridium symbiosum (P < 0.001, Q = 0.035), Hungatella effluvii (P = 0.003, Q = 0.090), Bacteroides fluxus (P = 0.002, Q = 0.089), Absiella innocuum (P = 0.002, Q = 0.072), Coprobacter secundus (P = 0.002, Q = 0.085) and Clostridium citroniae (P = 0.001, Q = 0.060) than those without sarcopenia. The relative abundance of six species (Desulfovibrio piger, Clostridium symbiosum, Hungatella effluvii, Bacteroides fluxus, Absiella innocuum, and Clostridium citroniae) was also positively associated with sarcopenia severity. A differential species-based model was constructed to separate participants with sarcopenia from controls. The value of the AUC was 0.852, suggesting that model has a decent discriminative performance. Desulfovibrio piger ranked the highest in this model. Functional annotation analysis revealed that the phenylalanine, tyrosine, and tryptophan biosynthesis were depleted (P = 0.006, Q = 0.071), while alpha-Linolenic acid metabolism (P = 0.008, Q = 0.094), furfural degradation (P = 0.001, Q = 0.029) and staurosporine biosynthesis (P = 0.006, Q = 0.072) were enriched in participants with sarcopenia. Desulfovibrio piger was significantly associated with staurosporine biosynthesis (P < 0.001).

CONCLUSIONS: This large population-based observational study provided empirical evidence that alterations in the gut microbiome composition and function were observed among individuals with sarcopenia.}, } @article {pmid35851522, year = {2022}, author = {Chen, M and Conroy, JL and Geyman, EC and Sanford, RA and Chee-Sanford, JC and Connor, LM}, title = {Stable carbon isotope values of syndepositional carbonate spherules and micrite record spatial and temporal changes in photosynthesis intensity.}, journal = {Geobiology}, volume = {20}, number = {5}, pages = {667-689}, pmid = {35851522}, issn = {1472-4669}, mesh = {*Carbon/analysis ; Carbon Isotopes/analysis ; *Carbonates/analysis ; Lakes ; Photosynthesis ; }, abstract = {Marine and lacustrine carbonate minerals preserve carbon cycle information, and their stable carbon isotope values (δ[13] C) are frequently used to infer and reconstruct paleoenvironmental changes. However, multiple processes can influence the δ[13] C values of bulk carbonates, confounding the interpretation of these values in terms of conditions at the time of mineral precipitation. Co-existing carbonate forms may represent different environmental conditions, yet few studies have analyzed δ[13] C values of syndepositional carbonate grains of varying morphologies to investigate their origins. Here, we combine stable isotope analyses, metagenomics, and geochemical modeling to interpret δ[13] C values of syndepositional carbonate spherules (>500 μm) and fine-grained micrite (<63 μm) from a ~1600-year-long sediment record of a hypersaline lake located on the coral atoll of Kiritimati, Republic of Kiribati (1.9°N, 157.4°W). Petrographic, mineralogic, and stable isotope results suggest that both carbonate fractions precipitate in situ with minor diagenetic alterations. The δ[13] C values of spherules are high compared to the syndepositional micrite and cannot be explained by mineral differences or external perturbations, suggesting a role for local biological processes. We use geochemical modeling to test the hypothesis that the spherules form in the surface microbial mat during peak diurnal photosynthesis when the δ[13] C value of dissolved inorganic carbon is elevated. In contrast, we hypothesize that the micrite may precipitate more continuously in the water as well as in sub-surface, heterotrophic layers of the microbial mat. Both metagenome and geochemical model results support a critical role for photosynthesis in influencing carbonate δ[13] C values. The down-core spherule-micrite offset in δ[13] C values also aligns with total organic carbon values, suggesting that the difference in the δ[13] C values of spherules and micrite may be a more robust, inorganic indicator of variability in productivity and local biological processes through time than the δ[13] C values of individual carbonate forms.}, } @article {pmid35850669, year = {2022}, author = {Zhang, J and Wang, J and Gan, J and Luo, R and Chen, X}, title = {The first case of Streptococcus intermedius brain abscess with hemophagocytic histiocytosis.}, journal = {BMC infectious diseases}, volume = {22}, number = {1}, pages = {627}, pmid = {35850669}, issn = {1471-2334}, support = {Health Commission (21PJ049)//Sichuan Province Science and Technology Support Program/ ; }, mesh = {*Brain Abscess/complications/diagnosis/drug therapy ; Child ; Humans ; *Lymphohistiocytosis, Hemophagocytic/complications/diagnosis/drug therapy ; Male ; *Meningitis, Bacterial/complications/diagnosis/drug therapy ; *Streptococcal Infections/complications/diagnosis/drug therapy ; Streptococcus intermedius ; }, abstract = {BACKGROUND: Hemophagocytic lymphohistiocytosis (HLH) is a rare but potentially life-threatening immune syndrome associated with an excessive systemic inflammatory response. Viral infection caused HLH is the most common secondary HLH, but there are relatively few reports of HLH caused by bacterial infection. The present study is the first case of HLH caused by Streptococcus intermedia meningitis.

CASE PRESENTATION: The patient is an 11-year-old and 9-month-old boy. The main symptoms are fever, headache, and vomiting. The imaging finding of the brain is cerebritis and brain abscess. The cerebrospinal fluid (CSF) routine test showed increased nucleated cells, but the smear and culture of CSF were negative. The metagenomics next-generation sequencing (mNGS) of CSF detected Streptococcus intermedius, and the body temperature of the children returned to normal after antibiotic treatment according to etiology. One week later, the child developed fever again, with Kawasaki disease-like manifestations. After high-dose immunoglobulin therapy, the body temperature returned to normal again. The routine blood test showed a progressive decrease in leukocytes and platelets, and bone marrow biopsy detected histiocytes phagocytosed blood cells. Then infection-associated hemophagocytic syndrome (IAHS) was diagnosed, high-dose methylprednisolone and sequential therapy were given and the patient's recovery was encouraging.

CONCLUSIONS: Our case shows that HLH can also be secondary to Streptococcus intermediate infection, and early bone marrow biopsy is the golden standard for HLH diagnosis. mNGS can improve the detection sensitivity for pathogens when traditional pathogenic tests are negative. Conventional chemotherapy regimens may not be required for IAHS when high-dose glucocorticoids and immunoglobulin therapy are effective.}, } @article {pmid35850395, year = {2022}, author = {Szakács, S and Koók, L and Nemestóthy, N and Bélafi-Bakó, K and Bakonyi, P}, title = {Studying microbial fuel cells equipped with heterogeneous ion exchange membranes: Electrochemical performance and microbial community assessment of anodic and membrane-surface biofilms.}, journal = {Bioresource technology}, volume = {360}, number = {}, pages = {127628}, doi = {10.1016/j.biortech.2022.127628}, pmid = {35850395}, issn = {1873-2976}, mesh = {*Bioelectric Energy Sources/microbiology ; Biofilms ; Electrodes ; Ion Exchange ; Membranes, Artificial ; *Microbiota ; Oxygen ; }, abstract = {In this study, microbial fuel cells deploying heterogeneous ion exchange membranes were assessed. The behavior of the cells as a function of the membrane applied was evaluated in terms of maximal current density, electron recovery efficiency and energy production rate (up to 427.5 mA, 47.7 % and 660 J m[-2]h[-1], respectively) at different substrate (acetate) feedings (2.15 - 8.6 mM). System performance was characterized in the light of oxygen and acetate crossovers. The effect of membranes (in relation to the oxygen mass transfer coefficient, kO) on the microbial diversity of anodic and membrane-surface biofilms was investigated. Based on the relative abundance of bacterial orders, the two populations could be distinguished and membranes with larger kO tended to promote more the air-tolerant microbes in the biofouling layer. This indicates that membrane kO has a direct effect on membrane foulant microbial composition, and thus, on the expected time-stability of the membrane.}, } @article {pmid35849135, year = {2022}, author = {Bami, S and Hidinger, J and Madni, A and Hargest, V and Schultz-Cherry, S and Cortez, V and Cross, SJ and Ward, DA and Hayden, RT and Rubnitz, J and Pui, CH and Khan, RB and Hijano, DR}, title = {Human Astrovirus VA1 Encephalitis in Pediatric Patients With Cancer: Report of 2 Cases and Review of the Literature.}, journal = {Journal of the Pediatric Infectious Diseases Society}, volume = {11}, number = {9}, pages = {408-412}, doi = {10.1093/jpids/piac045}, pmid = {35849135}, issn = {2048-7207}, mesh = {*Astroviridae Infections/diagnosis ; Child ; *Encephalitis ; Feces ; Humans ; Immunocompromised Host ; *Mamastrovirus/genetics ; *Neoplasms ; Phylogeny ; }, abstract = {Novel human astroviruses (HAstVs) have recently been implicated as rare causes of fatal encephalitis in immunocompromised patients, for which there is no proven treatment. We report 2 cases from our institution in which HAstV-VA1 was detected in the cerebrospinal fluid by metagenomic next-generation sequencing after the initial evaluation revealed no etiology.}, } @article {pmid35848130, year = {2022}, author = {Ngo, VQH and Enault, F and Midoux, C and Mariadassou, M and Chapleur, O and Mazéas, L and Loux, V and Bouchez, T and Krupovic, M and Bize, A}, title = {Diversity of novel archaeal viruses infecting methanogens discovered through coupling of stable isotope probing and metagenomics.}, journal = {Environmental microbiology}, volume = {24}, number = {10}, pages = {4853-4868}, pmid = {35848130}, issn = {1462-2920}, mesh = {Archaea/genetics ; *Archaeal Viruses ; Carbon ; Formates ; Genome, Viral ; Isotopes ; Metagenomics/methods ; Methanobacterium ; *Viruses/genetics ; }, abstract = {Diversity of viruses infecting non-extremophilic archaea has been grossly understudied. This is particularly the case for viruses infecting methanogenic archaea, key players in the global carbon biogeochemical cycle. Only a dozen of methanogenic archaeal viruses have been isolated so far. In the present study, we implemented an original coupling between stable isotope probing and complementary shotgun metagenomic analyses to identify viruses of methanogens involved in the bioconversion of formate, which was used as the sole carbon source in batch anaerobic digestion microcosms. Under our experimental conditions, the microcosms were dominated by methanogens belonging to the order Methanobacteriales (Methanobacterium and Methanobrevibacter genera). Metagenomic analyses yielded several previously uncharacterized viral genomes, including a complete genome of a head-tailed virus (class Caudoviricetes, proposed family Speroviridae, Methanobacterium host) and several near-complete genomes of spindle-shaped viruses. The two groups of viruses are predicted to infect methanogens of the Methanobacterium and Methanosarcina genera and represent two new virus families. The metagenomics results are in good agreement with the electron microscopy observations, which revealed the dominance of head-tailed virus-like particles and the presence of spindle-shaped particles. The present study significantly expands the knowledge on the viral diversity of viruses of methanogens.}, } @article {pmid35847562, year = {2022}, author = {Moroishi, Y and Gui, J and Hoen, AG and Morrison, HG and Baker, ER and Nadeau, KC and Li, H and Li, Z and Madan, JC and Karagas, MR}, title = {The relationship between the gut microbiome and the risk of respiratory infections among newborns.}, journal = {Communications medicine}, volume = {2}, number = {}, pages = {87}, pmid = {35847562}, issn = {2730-664X}, support = {R01 GM123014/GM/NIGMS NIH HHS/United States ; R01 LM012723/LM/NLM NIH HHS/United States ; }, abstract = {BACKGROUND: Emerging evidence points to a critical role of the developing gut microbiome in immune maturation and infant health; however, prospective studies are lacking.

METHODS: We examined the occurrence of infections and associated symptoms during the first year of life in relation to the infant gut microbiome at six weeks of age using bacterial 16S rRNA V4-V5 gene sequencing (N = 465) and shotgun metagenomics (N = 185). We used generalized estimating equations to assess the associations between longitudinal outcomes and 16S alpha diversity and metagenomics species.

RESULTS: Here we show higher infant gut microbiota alpha diversity was associated with an increased risk of infections or respiratory symptoms treated with a prescription medicine, and specifically upper respiratory tract infections. Among vaginally delivered infants, a higher alpha diversity was associated with an increased risk of all-cause wheezing treated with a prescription medicine and diarrhea involving a visit to a health care provider. Positive associations were specifically observed with Veillonella species among all deliveries and Haemophilus influenzae among cesarean-delivered infants.

CONCLUSION: Our findings suggest that intestinal microbial diversity and the relative abundance of key taxa in early infancy may influence susceptibility to respiratory infection, wheezing, and diarrhea.}, } @article {pmid35847110, year = {2022}, author = {Ergunay, K and Mutinda, M and Bourke, B and Justi, SA and Caicedo-Quiroga, L and Kamau, J and Mutura, S and Akunda, IK and Cook, E and Gakuya, F and Omondi, P and Murray, S and Zimmerman, D and Linton, YM}, title = {Metagenomic Investigation of Ticks From Kenyan Wildlife Reveals Diverse Microbial Pathogens and New Country Pathogen Records.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {932224}, pmid = {35847110}, issn = {1664-302X}, abstract = {Focusing on the utility of ticks as xenosurveillance sentinels to expose circulating pathogens in Kenyan drylands, host-feeding ticks collected from wild ungulates [buffaloes, elephants, giraffes, hartebeest, impala, rhinoceros (black and white), zebras (Grévy's and plains)], carnivores (leopards, lions, spotted hyenas, wild dogs), as well as regular domestic and Boran cattle were screened for pathogens using metagenomics. A total of 75 host-feeding ticks [Rhipicephalus (97.3%) and Amblyomma (2.7%)] collected from 15 vertebrate taxa were sequenced in 46 pools. Fifty-six pathogenic bacterial species were detected in 35 pools analyzed for pathogens and relative abundances of major phyla. The most frequently observed species was Escherichia coli (62.8%), followed by Proteus mirabilis (48.5%) and Coxiella burnetii (45.7%). Francisella tularemia and Jingmen tick virus (JMTV) were detected in 14.2 and 13% of the pools, respectively, in ticks collected from wild animals and cattle. This is one of the first reports of JMTV in Kenya, and phylogenetic reconstruction revealed significant divergence from previously known isolates and related viruses. Eight fungal species with human pathogenicity were detected in 5 pools (10.8%). The vector-borne filarial pathogens (Brugia malayi, Dirofilaria immitis, Loa loa), protozoa (Plasmodium spp., Trypanosoma cruzi), and environmental and water-/food-borne pathogens (Entamoeba histolytica, Encephalitozoon intestinalis, Naegleria fowleri, Schistosoma spp., Toxoplasma gondii, and Trichinella spiralis) were detected. Documented viruses included human mastadenovirus C, Epstein-Barr virus and bovine herpesvirus 5, Trinbago virus, and Guarapuava tymovirus-like virus 1. Our findings confirmed that host-feeding ticks are an efficient sentinel for xenosurveillance and demonstrate clear potential for wildlife-livestock-human pathogen transfer in the Kenyan landscape.}, } @article {pmid35847093, year = {2022}, author = {Zhao, D and Guo, L and Lian, D and Gu, Y and Yan, X and Hu, H and Yuan, J}, title = {Diagnostic Value and Clinical Application of mNGS for Post-Liver Transplantation Infection: A Cross-Sectional Study With Case Reports.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {919363}, pmid = {35847093}, issn = {1664-302X}, abstract = {Liver transplantation is widely acknowledged as the only effective treatment for end-stage liver disease, and infection is reportedly an important cause of postoperative death. Clinical use of metagenomic next-generation sequencing (mNGS) to diagnose postoperative infection and successfully guide drug therapy remains rare. This study included patients with infectious complications after liver transplantation from July 2019 to December 2020 and was divided into three groups: pneumonia, unknown fever, and others (including hepatic failure, kidney failure, cirrhosis after LT, and other postoperative complications that predispose to infection). The mNGS sequencing was used to detect microorganisms, and the results were compared with traditional culture. We found that mNGS yielded improved sensitivity over culture (85.19 vs. 22.22%; p<0.0001) but lower specificity (35.71 vs. 89.28%; p<0.0001). Among the 48 kinds of pathogens detected, the Torque teno virus 22 (15/122) was the most common, followed by Primate erythroparvovirus 1 (13/122). The top four bacteria included Klebsiella pneumoniae (n = 8), Enterococcus faecium (n = 5), Stenotrophomonas maltophilia (n = 4), and Escherichia coli (n = 4). Aspergillus fumigatus was the most common fungus. The bronchoalveolar lavage fluid (BALF) exhibited the highest proportion of positive findings among sample types, with viral, fungal, and bacterial mixed infection being the most common (n = 6, 19.35%). Besides, using mNGS for early diagnosis of infection after liver transplantation may effectively prolong patient survival. This is the first study to explore the application value of mNGS and its comparison with traditional culture in pneumonia and other infections in post-liver transplantation patients. The simultaneous application of these two methods suggested that the Torque teno virus 22, Klebsiella pneumoniae, and the Aspergillus fumigatus are the most common pathogens of viruses, bacteria, and fungi after LT, suggesting that these pathogens may be associated with postoperative pathogen infection and patient prognosis. The mNGS technique showed distinct advantages in detecting mixed, viral, and parasitic infections in this patient population. Further studies are warranted to systematically elucidate the dynamic evolution and molecular characteristics of infection after liver transplantation.}, } @article {pmid35847073, year = {2022}, author = {Xu, P and Yang, K and Yang, L and Wang, Z and Jin, F and Wang, Y and Feng, J}, title = {Next-Generation Metagenome Sequencing Shows Superior Diagnostic Performance in Acid-Fast Staining Sputum Smear-Negative Pulmonary Tuberculosis and Non-tuberculous Mycobacterial Pulmonary Disease.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {898195}, pmid = {35847073}, issn = {1664-302X}, abstract = {In this study, we explored the clinical value of next-generation metagenome sequencing (mNGS) using bronchoalveolar lavage fluid (BALF) samples from patients with acid-fast staining (AFS) sputum smear-negative pulmonary tuberculosis (PTB) and non-tuberculous mycobacterial pulmonary disease (NTM-PD). Data corresponding to hospitalized patients with pulmonary infection admitted to the hospital between July 2018 and July 2021, who were finally diagnosed with AFS sputum smear-negative PTB and NTM-PD, were retrospectively analyzed. Bronchoscopy data as well as mNGS, Xpert, AFS (BALF analysis), and T-SPOT (blood) data, were extracted from medical records. Thereafter, the diagnostic performances of these methods with respect to PTB and NTM-PD were compared. Seventy-one patients with PTB and 23 with NTM-PD were included in the study. The sensitivities of mNGS, Xpert, T-SPOT, and AFS for the diagnosis of PTB were 94.4% (67/71), 85.9% (61/71), 64.8% (46/71), and 28.2% (20/71), respectively, and the diagnostic sensitivity of mNGS combined with Xpert was the highest (97.2%, 67/71). The specificity of Xpert was 100%, while those of AFS and T-SPOT were 73.9% (17/23) and 91.3% (21/23), respectively. Further, the 23 patients with NTM-PD could be identified using mNGS, and in the population with immunosuppression, the sensitivities of mNGS, Xpert, T-SPOT, and AFS were 93.5% (29/31), 80.6% (25/31), 48.4% (15/31), and 32.3% (10/31), respectively, and the diagnostic sensitivity of mNGS combined with Xpert was the highest (100%, 31/31). The specificities of Xpert and T-SPOT in this regard were both 100%, while that of AFS was 40% (2/5). Furthermore, using mNGS, all the NTM samples could be identified. Thus, the analysis of BALF samples using mNGS has a high accuracy in the differential diagnosis of MTB and NTM. Further, mNGS combined with Xpert can improve the detection of MTB, especially in AFS sputum smear-negative samples from patients with compromised immune states or poor responses to empirical antibiotics.}, } @article {pmid35847029, year = {2022}, author = {Cui, X and Liang, L and Geng, H and Liu, Y and Xi, J and Wang, J and Ching, TB and Bee, EG and Chai, Y and Wu, S and Jin, D and Xie, Y}, title = {Efficacy, Safety and Mechanism of Jinzhen Oral Liquid in the Treatment of Acute Bronchitis in Children: A Randomized, Double-Blind, Multicenter Clinical Trial Protocol.}, journal = {Frontiers in pharmacology}, volume = {13}, number = {}, pages = {948236}, pmid = {35847029}, issn = {1663-9812}, abstract = {Background: Acute bronchitis (AB) is a common disease in pediatrics. Prolonged AB may develop into chronic bronchitis. Bronchitis caused by the influenza virus can lead to severe hypoxia or insufficient ventilation, causing great harm to patients and increasing the burden on children and society. Presently, there is no specific treatment for AB except symptomatic supportive treatment. It is urgent to find an effective treatment for AB. Jinzhen Oral Liquid (JZOL) has been found to have a broad spectrum of anti-inflammatory and antiviral effects in previous clinical and basic studies and has a good effect on AB in children. However, the large-sample, randomized, double-blind, head-to-head, evidence-based studies are lacking. The purpose of this protocol is to evaluate the efficacy, safety, and mechanism of JZOL in the treatment of AB in children. Methods: This is a randomized, double-blind, parallel-controlled multi-center clinical trial. The sample size is 500 participants in the intervention group and the control group respectively, with a total of 1000 participants. They will be recruited by 10 hospitals in China. The Intervention group takes JZOL and Ambroxol Hydrochloride and Clenbuterol Hydrochloride Oral Solution (AHCHOS) placebo, while the control group receives AHCHOS and JZOL placebo. The dosage of the two drugs varies according to age and weight. The medication lasts for 7 days. The disappearance time of cough is adopted as the primary outcome. Quality control will be carried out at every stage of data management and processing to ensure that all data are reliable and processed correctly. SAS is used for statistical analysis. Intention-to-treat analysis will be carried out in this trial. All statistical tests are conducted using a two-sided test, and p <0.05 would be considered statistically significant. Discussion: We hypothesized that children with AB could get good health benefits from JZOL. This study not only evaluates the clinical efficacy and safety of JZOL but also conducts metagenomics analysis and metabolomics analysis of feces and saliva of participants to study the mechanism of JZOL against AB. Therefore, this protocol evaluates the efficacy, safety, and mechanism of JZOL from a comprehensive perspective, so as to obtain a more solid evidence chain, which will enhance the credibility of the evidence. If successful, this study will provide a high-level evidence-based reference for the treatment of AB in children and future relevant studies.}, } @article {pmid35846764, year = {2022}, author = {Zhang, D and Zheng, M and Zhang, Y and Feng, G and Peng, C and Li, C and Li, Y and Zhang, H and Li, N and Xiao, P}, title = {Multiple Novel Mosquito-Borne Zoonotic Viruses Revealed in Pangolin Virome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {874003}, pmid = {35846764}, issn = {2235-2988}, mesh = {*Alphavirus/genetics ; Animals ; China ; Chlorocebus aethiops ; *Culicidae ; *Encephalitis Virus, Japanese/genetics ; Humans ; Pangolins ; Phylogeny ; Vero Cells ; Virome ; }, abstract = {Swab samples were collected from 34 pangolins in Guangxi Province, China. Metavirome sequencing and bioinformatics approaches were undertaken to determine the abundant viral sequences in the viromes. The results showed that the viral sequences belong to 24 virus taxonomic families. To verify the results, PCR combined with phylogenetic analysis was conducted. Some viral sequences including Japanese encephalitis virus (JEV), Getah virus (GETV), and chikungunya virus (CHIKV) were detected. On the basis of the metavirome analysis, seven segments belonging to JEV were further identified through PCR amplification. Sequence comparison showed that, among seven sequences, JEV-China/P2020E-1 displayed the highest nucleotide (80.6%), with the JEV isolated in South Korea, 1988, and all of which belonging to genotype III. Seven CHIKV sequences were detected, with the highest homology (80.6%) to the Aedes africanus in Côte d'Ivoire, 1993. Moreover, passage from BHK-21 to Vero cells makes the newly isolated CHIKV-China/P2020-1 more contagious. In addition, the newly verified GETV sequences shared 86.4% identity with the 1955 GETV isolated from Malaysia. Some sudden and recurrent viruses have also been observed from the virome of pangolin in Guangxi Province, China; hence, dissemination tests will be implemented in the future.}, } @article {pmid35846762, year = {2022}, author = {Xi, X and Ye, Q and Li, X and Lu, X and Fan, D and Xia, Y and Xiao, C}, title = {Xiong Fu Powder Regulates the Intestinal Microenvironment to Protect Bones Against Destruction in Collagen-Induced Arthritis Rat Models.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {854940}, pmid = {35846762}, issn = {2235-2988}, mesh = {Animals ; *Arthritis, Experimental/chemically induced/drug therapy ; *Arthritis, Rheumatoid ; Cytokines/metabolism ; Immunoglobulin A, Secretory ; Powders/adverse effects ; Rats ; Th17 Cells ; }, abstract = {BACKGROUND: Changes in the intestinal microenvironment affected bone destruction in rheumatoid arthritis (RA), and spleen deficiency (SD) was closely related to the intestinal microenvironment. In this study, we aimed to explore the aggravation of SD on collagen-induced arthritis (CIA) and the bone protection of compound Xiong Fu powder (XFP) on CIA with SD (SD-CIA) based on the intestinal microenvironment.

METHOD: An SD-CIA rat model was established using Rheum officinale Baill. decoction combined with CIA and then treated with XFP. The aggravating action of SD on CIA rats and the efficacy of XFP were evaluated using AI scores, H&E staining of the joint, and level of serum anti-collagen type II antibody (Col II Ab). Bone destruction was assessed by micro-CT and TRACP staining. In addition, flow cytometry, qRT-PCR, and ELISA were used to evaluate gut mucosal immunity. Moreover, metagenomic sequencing was used to determine the distribution and function of the gut microbiota.

RESULTS: Compared with that in CIA rats, bone destruction in SD-CIA rats was aggravated, as manifested by increased AI scores, more severe joint pathological changes and radiological damage, and increased number of osteoclasts (OCs) in the ankle joint. Meanwhile, the proportion of Tregs/Th17 cells was biased toward Th17 cells in Peyer's patches. Furthermore, the gene levels of TNF-α, IL-1β, IL-6, and IL-17 were increased. In contrast, the expression of IL-10 and sIgA was decreased in the jejunum and ileum. XFP treatment improved bone damage and intestinal mucosal immune disorders compared with the SD-CIA group. In addition, the distribution and function of the gut microbiota were altered in the SD-CIA group. After XFP treatment, the community and function of the gut microbiota were regulated, manifested as increased abundance of several Lactobacillus species, such as L. acidophilus, which regulates the intestinal Tregs/Th17 cells and quorum sensing pathways, followed by promoting probiotic adhesion to the intestines.

CONCLUSION: SD can aggravate bone destruction in CIA rats. Compound XFP may attenuate bone destruction in SD-CIA rats by regulating the intestinal microenvironment. One of the mechanisms is the cross-talk between sIgA secretion regulated by intestinal mucosal Tregs and Th17 cells and adhesion of Lactobacillus mediated by quorum sensing.}, } @article {pmid35846388, year = {2022}, author = {Abuzahrah, SS and Baeshen, MN and Alkaladi, A and Bataweel, NM and Alhejen, AM and Abdelkader, H}, title = {Exploring the taxonomic and functional diversity of marine benthic micro-Eukaryotes along the Red Sea coast of Jeddah city.}, journal = {Saudi journal of biological sciences}, volume = {29}, number = {8}, pages = {103342}, pmid = {35846388}, issn = {1319-562X}, abstract = {BACKGROUNDS: Diverse marine habitats along Jeddah's Red Sea coast support rich biodiversity. Few studies have been done on its diverse communities, especially its microbial counterparts. Metagenomic analysis of marine benthic micro-eukaryotic communities was performed for the first time on the Red Sea coast of Jeddah. This research looks into their community structure and metabolic potential.

METHODS: Next-generation sequencing was used to examine the micro-eukaryotic communities of seven sedimentary soil samples from four Jeddah coast locations. After isolating DNA from seven benthic sedimentary soil samples, the 18S rDNA V4 regions were amplified and sequenced on the Illumina MiSeq. It was also verified using an Agilent Technologies 2100 Bioanalyzer with a DNA 1000 chip (Agilent Technologies, Fisher Scientific). A standard curve of fluorescence readings generated by qPCR quantification using the Illumina library was achieved using the GS FLX library. Metagenomic data analysis was used to evaluate the microbial communities' biochemical and enzymatic allocations in studied samples.

RESULTS: Blast analysis showed that the top ten phyla were Annelida, Eukaryota, Diatomea, Porifera, Phragmoplastophyta, Arthropoda, Dinoflagellata, Xenacoelomorpha Nematoda, and uncultured. Annelida was also found in the highest percentage (93%), in the sample M followed by Porifera (64%), the most abundant in the control sample then Eukaryotes (61%), Phragmatoplastophyta (55%), Arthropoda, and Diatomea (the least common) (32%). community diversity analysis: using Shannon and inverse Simpson indices showed sediment composition to be effective. Also, PICRUST2 indicated that the most abundant pathways were pyruvate fermentation to isobutanol, pyrimidine deoxyribonucleotide phosphorylation, adenosine ribonucleotide de novo biosynthesis, guanosine ribonucleotide de novo biosynthesis, NAD salvage pathway I, the super pathway of glyoxylate bypass and aerobic respiration I (cytochrome c).

CONCLUSION: Results showed that high throughput metagenomics could reveal species diversity and estimate gene profiles. Environmental factors appear to be more important than geographic variation in determining the structure of these microbial communities. This study provides the first report of marine benthic micro-eukaryotic communities found on the Red Sea coast of Jeddah and will serve as a good platform for future research.}, } @article {pmid35846183, year = {2022}, author = {Ballul, T and Belfeki, N and de Masson, A and Meignin, V and Woerther, PL and Martin, A and Poullot, E and Wargnier, A and Fadlallah, J and Garzaro, M and Malphettes, M and Fieschi, C and Maisonobe, L and Bensekhri, H and Guillot, H and Bertinchamp, R and Jachiet, M and Poirot, J and Galicier, L and Oksenhendler, E and Boutboul, D}, title = {Leg-type form of idiopathic multicentric Castleman disease associated with severe lower extremity chronic venous/lymphatic disease.}, journal = {EJHaem}, volume = {3}, number = {1}, pages = {175-179}, pmid = {35846183}, issn = {2688-6146}, abstract = {Idiopathic multicentric Castleman disease (iMCD) is a lymphoproliferative disease of unknown etiology. Deciphering mechanisms involved in CD pathogenesis may help improving patients' care. Six cases of stereotyped sub-diaphragmatic iMCD affecting lower limb-draining areas and associated with severe and often ulcerative lower extremity chronic dermatological condition were identified in our cohort. Pathological examination revealed mixed or plasma-cell type MCD. In three patients, shotgun metagenomics failed to identify any pathogen in involved lymph nodes. Antibiotics had a suspensive effect while rituximab and tocilizumab failed to improve the condition. This novel entity requires a specific approach and exclusion of potentially harmful immunomodulation.}, } @article {pmid35845658, year = {2022}, author = {Ahumada, GD and Gómez-Álvarez, EM and Dell'Acqua, M and Bertani, I and Venturi, V and Perata, P and Pucciariello, C}, title = {Bacterial Endophytes Contribute to Rice Seedling Establishment Under Submergence.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {908349}, pmid = {35845658}, issn = {1664-462X}, abstract = {Flooding events caused by severe rains and poor soil drainage can interfere with plant germination and seedling establishment. Rice is one of the cereal crops that has unique germination strategies under flooding. One of these strategies is based on the fast coleoptile elongation in order to reach the water surface and re-establish the contact with the air. Microorganisms can contribute to plant health via plant growth promoters and provide protection from abiotic stresses. To characterise the community composition of the microbiome in rice germination under submergence, a 16S rRNA gene profiling metagenomic analysis was performed of temperate japonica rice varieties Arborio and Lamone seedlings, which showed contrasting responses in terms of coleoptile length when submerged. This analysis showed a distinct microbiota composition of Arborio seeds under submergence, which are characterised by the development of a long coleoptile. To examine the potential function of microbial communities under submergence, culturable bacteria were isolated, identified and tested for plant growth-promoting activities. A subgroup of isolated bacteria showed the capacity to hydrolyse starch and produce indole-related compounds under hypoxia. Selected bacteria were inoculated in seeds to evaluate their effect on rice under submergence, showing a response that is dependent on the rice genotype. Our findings suggest that endophytic bacteria possess plant growth-promoting activities that can substantially contribute to rice seedling establishment under submergence.}, } @article {pmid35845529, year = {2022}, author = {Li, J and Zhang, Y and Zhang, Q and Lu, S and Huang, F and Wang, J}, title = {Application of metagenomic next-generation sequencing for the diagnosis of intracranial infection of Listeria monocytogenes.}, journal = {Annals of translational medicine}, volume = {10}, number = {12}, pages = {672}, pmid = {35845529}, issn = {2305-5839}, abstract = {BACKGROUND: Intracranial infection of Listeria monocytogenes (LM) can lead to various manifestations, including meningitis, meningoencephalitis, brainstem encephalitis, and brain abscess, which often have a poor prognosis. Metagenomic next-generation sequencing (mNGS) is a promising new tool for the diagnosis of intracranial infection of LM. We describe the typical clinical manifestations of LM intracranial infection and highlight its rarity and severity to help physicians better understand the disease characteristics.

METHODS: Six cases of severe LM intracranial infection were diagnosed by mNGS. We conducted a retrospective analysis of the data on disease progression, diagnostic tools, treatments, and outcomes, and summarized the findings. We compared the differences in diagnostic accuracy and timeliness between mNGS and etiological cultures.

RESULTS: Among the 6 patients, 5 were males and 1 was female (age range 32-83). Three patients had a history of immunosuppressive therapy. Common symptoms included fever (100%) and a stiff neck (100%). Coma occurred early in severe patients (66%). Two healthy young patients had previously developed with meningitis, while coma occurred in 3 immunosuppressed patients and 1 elderly patient. Three immunosuppressed patients presented with brain abscess, brainstem encephalitis, and meningitis. 1 elderly patient presented with meningitis. Two patients developed septic shock complications early. Laboratory data showed normal or slightly increased leukocytes, neutrophils, and procalcitonin, and cerebrospinal fluid (CSF) tests were consistent with bacterial CSF infection. All 6 patients were examined for blood culture and CSF culture. The positive rate of blood culture and CSF culture was 50% and 16%. The average time from admission to positive culture findings was 91 h. All 6 patients were examined for CSF mNGS. Two were also examined for whole-blood mNGS. The positive rate for CSF mNGS and whole-blood mNGS results was 100%. The mean time from admission to positive mNGS report was 47 h. After diagnosis and treatment with sensitive antibiotics, 1 patient with brain abscess developed neurological sequelae, while the other 5 patients completely recovered.

CONCLUSIONS: mNGS can improve accuracy in the diagnosis of LM intracranial infection and reduce the delay in diagnosis. Intracranial infection of Listeria monocytogenes responds well to the timely use of appropriate antibiotics.}, } @article {pmid35845522, year = {2022}, author = {Zhang, J and Luo, J and Weng, X and Zhu, Y and Goyal, G and Perna, F and Espinoza-Gutarra, M and Jiang, L and Chen, L and Mi, JQ}, title = {A case report of the metagenomics next-generation sequencing for early detection of central nervous system mucormycosis with successful rescue in patient with recurrent chronic lymphocytic leukemia.}, journal = {Annals of translational medicine}, volume = {10}, number = {12}, pages = {722}, pmid = {35845522}, issn = {2305-5839}, abstract = {BACKGROUND: Central nervous system (CNS) mucormycosis is insidious and difficult to diagnose. It progresses rapidly and causes high mortality. Rare cases have been reported during ibrutinib use, which have poor prognosis. Through this case, we share the experience of successful diagnosis and treatment. We also emphasize the importance of focusing on high-risk groups, early diagnosis and prompt management.

CASE DESCRIPTION: In this case, a 52-year-old patient was diagnosed with chronic lymphocytic leukemia (CLL) for more than 5 years. He was in remission after rituximab plus fludarabine and cyclophosphamide (RFC) regimen, and relapsed in the fourth year. During the ibrutinib monotherapy, the patient presented with sudden headache. Cranial imaging examination revealed a definite right occipitoparietal lobe mass with extensive edema. A rapid diagnosis of mucormycosis infection was made using metagenomic next-generation sequencing (mNGS). The patient at that time didn't have neutropenia, but he had hypogammaglobulinemia. The infection was treated with amphotericin B cholesteryl sulfate complex, posaconazole, and interventional surgery, and the treatment was successful. At the same time, we considered the control of disease progression in this relapsed patient with, as well as to the drug interaction with posaconazole. We chose the next generation Bruton's tyrosine kinase (BTK) inhibitor zanubrutinib as the treatment, whose safety has been identified. As of the submission date, the patient has been followed up for nearly 1 year, and his disease is stable.

CONCLUSIONS: When new clinical problems arise in recurrent CLL patients, it is important to identify multiple factors, especially the insidious fungal infections. In particular, the immunocompromised patients should be concerned. CNS mucormycosis is extremely deadly, the early diagnosis will improve the prognosis. In clinical practice, the gold standard diagnosis of mucormycosis is difficult to obtain through pathology. In this case, mNGS was applied to quickly diagnose mucormycosis, enabling earlier treatment and ameliorating the prognosis. Thus, it will help us to early detect this group of people who may be potentially infected. Current guidelines do not recommend the prophylactic use of antifungal agents in treated CLL patients. However, in patients with prior severe infection or hypogammaglobulinemia, intravenous immunoglobulin is recommended to reduce the associated infection rate.}, } @article {pmid35845101, year = {2022}, author = {Uszkoreit, J and Barkovits, K and Pacharra, S and Pfeiffer, K and Steinbach, S and Marcus, K and Eisenacher, M}, title = {Dataset containing physiological amounts of spike-in proteins into murine C2C12 background as a ground truth quantitative LC-MS/MS reference.}, journal = {Data in brief}, volume = {43}, number = {}, pages = {108435}, pmid = {35845101}, issn = {2352-3409}, abstract = {In this article, we present a data dependent acquisition (DDA) dataset which was generated as a reference and ground truth quantitative dataset. While initially used to compare samples measured with DDA and data independent acquisition (DIA) (Barkovits et al., 2020), the presented dataset holds potential value as a benchmark reference for any workflows working on DDA data. The entire dataset consists of 15 LC-MS/MS measurements composed of five distinct spike-in-states, each with three replicates. To generate the data set, a C2C12 (immortalized mouse myoblast) cell lysate was used as a complex background for five different states which were simulated by spiking 13 defined proteins at different concentrations. For this purpose, the cell lysate was used in a constant amount of 20 µg for all samples and different amounts of the 13 selected proteins ranging from 0.1 to 10 pmol were added, reflecting physiological amounts of proteins. Afterwards, all samples were tryptically digested using the same method. From each sample 200 ng tryptic peptides were measured in triplicates on a Q Exactive HF (Thermo Fisher Scientific). The mass range for MS1 was set to 350-1400 m/z with a resolution of 60,000 at 200 m/z. HCD fragmentation of the Top10 abundant precursor ions was performed at 27% NCE. The fragment analysis (MS2) was performed with a resolution of 30,000 at 200 m/z. Additionally to the raw files, the dataset contains centroided mzML files and spectrum identification results for peptide identifications performed by Mascot (Perkins et al., 1999), MS-GF+ (Kim et al., 2010) and X!Tandem (Craig and Beavis, 2004) for each separate MS analysis. The corresponding FASTA containing protein sequences as well as a combination of all identification runs performed by PIA (Uszkoreit et al., 2019, 2015) and a peptide and protein quantification performed by OpenMS (Pfeuffer et al., 2017) is included. All data have been deposited to the ProteomeXchange Consortium via the PRIDE partner repository (Perez-Riverol et al., 2018) with the dataset identifier PXD012986.}, } @article {pmid35844383, year = {2022}, author = {Alotaibi, MO and Mohammed, AE and Eltom, KH}, title = {Metagenomic analysis of bacterial communities of Wadi Namar Lake, Riyadh, Saudi Arabia.}, journal = {Saudi journal of biological sciences}, volume = {29}, number = {5}, pages = {3749-3758}, pmid = {35844383}, issn = {1319-562X}, abstract = {Wadi Namar lake is a new touristic attraction area in the south of Riyadh. Human activities around the lake may lead to changes in water quality with subsequent changes in microenvironment components including microbial diversity. The current study was designed to assess possible changes in bacterial communities of the water at Wadi Namar Lake. Therefore, water samples were collected from three different locations along the lake: L1 (no human activities, no plants), L2 (no human activity, some plants) and L3 (human activities, municipal wastes and some plants). The total DNA of the samples was extracted and subjected to 16S rDNA sequencing and metagenomic analysis; water pH, electrical conductivity (EC), total dissolved solids (TDS) as well as the concentration of Na[+1], K[+1], Cl[-1] and total N were analysed. Metagenomic analysis showed variations in relative abundance of 17 phyla, 31 families, 43 genera and 19 species of bacteria between the locations. Proteobacteria was the most abundant phylum in all locations; however, its highest abundance was in L1. Planctomycete phylum was highly abundant in L1 and L3, while its abundance in L2 was low. The phyla Acidobacteria, Candidatus Saccharibacteria, Nitrospirae and Chloroflexi were associated with high TDS, EC, K[+1] and Cl[-1] concentrations in L3; various human activities around this location had possibly affected microbial diversity. Current study results help in recognising the structure of bacterial communities at Wadi Namar Lake in relation to their surroundings for planning to environment protection and future restoration of affected ecosystems.}, } @article {pmid35843042, year = {2022}, author = {Zhang, J and Zhang, Q and Liu, H and Liu, X and Yu, Y and Han, D and He, X and Zeng, P and Wang, J}, title = {Soy-whey dual-protein alleviates osteoporosis of ovariectomized rats via regulating bone fat metabolism through gut-liver-bone axis.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {103-104}, number = {}, pages = {111723}, doi = {10.1016/j.nut.2022.111723}, pmid = {35843042}, issn = {1873-1244}, mesh = {Rats ; Female ; Animals ; Humans ; Soybean Proteins/pharmacology ; Whey Proteins/pharmacology ; Whey ; *Osteoporosis/drug therapy/prevention & control ; Bone Density ; Liver ; Ovariectomy ; *Osteoporosis, Postmenopausal/drug therapy/prevention & control ; }, abstract = {OBJECTIVES: Osteoporosis is increasingly prevalent, especially among postmenopausal women, both in China and worldwide. In previous work, soy-whey dual-protein (DP) intervention improved muscle status via regulation of gut microbiota. However, little information is available about the relationship between DP supplementation and osteoporosis.

METHODS: In this study, the ovariectomized rat model was used to detect the effect of DP on improving osteoporosis.

RESULTS: Significant improvement was observed in bone mineral density, bone microstructure, and bone biomechanics with both DP and zoledronic acid (positive control) intervention. DP supplementation dramatically reduced the levels of serum osteocalcin and parathyroid hormone in ovariectomized rats. Ingestion of DP also resulted in a significant decrease in the number of bone marrow adipocytes and a marked increase in the number of osteoblasts, accompanied by elevated expression of the key regulator osteoprotegerin at both mRNA and protein levels. In the analysis of fecal metabolites and intestinal microbiota, the fat metabolism-related molecules chenodeoxycholate, 21-hydroxypregnenolone, and tetrahydrocorticosterone were markedly upregulated with DP treatment, whereas the content of fatty acids such as oleic acid were significantly downregulated. The abundance of three bacterial taxa (upregulated: Ruminococcaceae UCG_002; downregulated: anaerobic digester metagenome and Enterorhabdus) dramatically changed with DP intervention and was closely associated with fat metabolism-related metabolite content CONCLUSION: These results suggest that DP intervention could improve osteoporosis via regulation of bone marrow adipose tissue content and mesenchymal stem cell lineage differentiation. Furthermore, this effect might be mediated by the interaction between intestinal microbiota and metabolites.}, } @article {pmid35842216, year = {2022}, author = {Yin, Q and Li, Y and Pan, H and Hui, T and Yu, Z and Wu, H and Zhang, D and Zheng, W and Wang, S and Zhou, Z and Xu, C and Wu, W and Tong, Y and Wang, H and Pan, H}, title = {Atypical pneumonia caused by Chlamydia psittaci during the COVID-19 pandemic.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {122}, number = {}, pages = {622-627}, pmid = {35842216}, issn = {1878-3511}, mesh = {*COVID-19/diagnosis ; *Chlamydophila psittaci/genetics ; Humans ; *Influenza, Human ; *Mycoses ; Pandemics ; *Pneumonia ; *Pneumonia, Mycoplasma ; *Psittacosis/diagnosis/drug therapy/epidemiology ; Retrospective Studies ; }, abstract = {OBJECTIVES: Here, we retrospectively described the diagnosis and treatment of 32 cases diagnosed with Chlamydia psittaci pneumonia during the COVID-19 pandemic.

METHODS: Clinical information was collected from all the patients. Reverse transcription-PCR and ELISAs were conducted for the detection of COVID-19 using nasal swabs and bronchoalveolar lavage fluid (BALF) samples. Metagenomic next-generation sequencing (mNGS) was performed for the identification of causative pathogens using BALF, peripheral blood and sputum samples. End-point PCR was performed to confirm the mNGS results.

RESULTS: All 32 patients showed atypical pneumonia and had infection-like symptoms that were similar to COVID-19. Results of reverse transcription-PCR and ELISAs ruled out COVID-19 infection. mNGS identified C. psittaci as the suspected pathogen in these patients within 48 hours, which was validated by PCR, except for three blood samples. The sequence reads that covered fragments of C. psittaci genome were detected more often in BALF than in sputum or blood samples. All patients received doxycycline-based treatment regimens and showed favorable outcomes.

CONCLUSION: This retrospective study, with the highest number of C. psittaci pneumonia enrolled cases in China so far, suggests that human psittacosis may be underdiagnosed and misdiagnosed clinically, especially in the midst of the COVID-19 pandemic.}, } @article {pmid35841748, year = {2022}, author = {Walker, ME and Simpson, JB and Redinbo, MR}, title = {A structural metagenomics pipeline for examining the gut microbiome.}, journal = {Current opinion in structural biology}, volume = {75}, number = {}, pages = {102416}, pmid = {35841748}, issn = {1879-033X}, support = {P30 CA016086/CA/NCI NIH HHS/United States ; R01 GM135218/GM/NIGMS NIH HHS/United States ; R01 GM137286/GM/NIGMS NIH HHS/United States ; T32 GM008570/GM/NIGMS NIH HHS/United States ; }, mesh = {*Gastrointestinal Microbiome/physiology ; Humans ; Metagenome ; *Metagenomics ; Proteomics ; }, abstract = {Metagenomic sequencing data provide a rich resource from which to expand our understanding of differential protein functions involved in human health. Here, we outline a pipeline that combines microbial whole genome sequencing with protein structure data to yield a structural metagenomics-informed atlas of microbial enzyme families of interest. Visualizing metagenomics data through a structural lens facilitates downstream studies including targeted inhibition and probe-based proteomics to define at the molecular level how different enzyme orthologs impact in vivo function. Application of this pipeline to gut microbial enzymes like glucuronidases, TMA lyases, and bile salt hydrolases is expected to pinpoint their involvement in health and disease and may aid in the development of therapeutics that target specific enzymes within the microbiome.}, } @article {pmid35841645, year = {2022}, author = {Chen, YC and Yu, YH}, title = {Bacillus licheniformis-fermented products and enramycin differentially modulate microbiota and antibiotic resistome in the cecal digesta of broilers.}, journal = {Poultry science}, volume = {101}, number = {9}, pages = {102010}, pmid = {35841645}, issn = {1525-3171}, mesh = {Aminocoumarins ; Animal Feed/analysis ; Animals ; Anti-Bacterial Agents/pharmacology ; *Bacillus licheniformis ; Bacteria ; Cecum/microbiology ; Chickens ; Diet/veterinary ; Dietary Supplements/analysis ; Lincosamides ; Male ; *Microbiota ; Peptides ; }, abstract = {Since antibiotic resistance is a global health issues, the use of antibiotics in animal feed for growth promotion has been restricted in many countries. Bacillus licheniformis probiotic is a potential alternative to antibiotics for increasing poultry performance. Through metagenomic sequencing, this study investigated the effects of B. licheniformis-fermented products (BLFPs) and enramycin on the microbial community composition and antibiotic resistance gene (ARG) distribution in the cecal digesta of broilers at the age of 35 d. In total, 144 one-day-old male broiler chicks (Ross 308) were randomly assigned to 4 dietary treatments as follows: basal diet (control [C] group), basal diet plus 10 mg/kg enramycin (E group), basal diet plus 1 g/kg BLFPs (L group), and basal diet plus 3 g/kg BLFPs (H group), with 6 replicate cages per treatment group and 6 birds per cage. The results indicated that the cecal alpha diversity (richness and evenness) of bacterial species was higher in the H group than in the C group. Principal coordinate analysis of microbiota and the ARG composition indicated clear differences among the cecal samples of the groups. In the cecal digesta, the abundance of active bacteria associated with probiotic properties, such as Lactobacillus crispatus and Akkermansia muciniphila, was higher in the H group than in the other groups. Enramycin treatment promoted the expression of peptide (bcrA), glycopeptide (vanRI), and lincosamide (lsaE) resistance genes but inhibited the expression of aminocoumarin (parY) and pleuromutilin (TaeA) resistance genes. BLFP (1 and 3 g/kg) treatment suppressed the expression of aminoglycoside (ANT(6)-Ib), streptogramin (vatB), and peptide (ugd) resistance genes but enhanced the expression of macrolide (efrA) and aminocoumarin (novA) resistance genes. The abundance of peptide resistance genes in Bacteroides spp. was lower in the H group than in the C group. The abundance of lincosamide resistance genes in Lactobacillus spp. was higher in the E group than in the other groups. These results demonstrated that differential changes in the structure of 3 g/kg BLFPs and enramycin-induced cecal microbial communities accompany changes in the abundance of bacterial hosts carrying specific ARGs in the cecal microbiota of broilers.}, } @article {pmid35841078, year = {2022}, author = {Li, P and Liu, J and Saleem, M and Li, G and Luan, L and Wu, M and Li, Z}, title = {Reduced chemodiversity suppresses rhizosphere microbiome functioning in the mono-cropped agroecosystems.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {108}, pmid = {35841078}, issn = {2049-2618}, mesh = {Carbon ; DNA ; *Microbiota/genetics ; Plant Roots/microbiology ; Plants ; Rhizosphere ; Soil ; Soil Microbiology ; *Streptomyces ; }, abstract = {BACKGROUND: Rhizodeposits regulate rhizosphere interactions, processes, nutrient and energy flow, and plant-microbe communication and thus play a vital role in maintaining soil and plant health. However, it remains unclear whether and how alteration in belowground carbon allocation and chemodiversity of rhizodeposits influences microbiome functioning in the rhizosphere ecosystems. To address this research gap, we investigated the relationship of rhizosphere carbon allocation and chemodiversity with microbiome biodiversity and functioning during peanut (Arachis hypogaea) continuous mono-cropping. After continuously labeling plants with [13]CO2, we studied the chemodiversity and composition of rhizodeposits, along with the composition and diversity of active rhizosphere microbiome using metabolomic, amplicon, and shotgun metagenomic sequencing approaches based on DNA stable-isotope probing (DNA-SIP).

RESULTS: Our results indicated that enrichment and depletion of rhizodeposits and active microbial taxa varied across plant growth stages and cropping durations. Specifically, a gradual decrease in the rhizosphere carbon allocation, chemodiversity, biodiversity and abundance of plant-beneficial taxa (such as Gemmatimonas, Streptomyces, Ramlibacter, and Lysobacter), and functional gene pathways (such as quorum sensing and biosynthesis of antibiotics) was observed with years of mono-cropping. We detected significant and strong correlations between rhizodeposits and rhizosphere microbiome biodiversity and functioning, though these were regulated by different ecological processes. For instance, rhizodeposits and active bacterial communities were mainly governed by deterministic and stochastic processes, respectively. Overall, the reduction in carbon deposition and chemodiversity during peanut continuous mono-cropping tended to suppress microbial biodiversity and its functions in the rhizosphere ecosystem.

CONCLUSIONS: Our results, for the first time, provide the evidence underlying the mechanism of rhizosphere microbiome malfunctioning in mono-cropped systems. Our study opens new avenues to deeply disentangle the complex plant-microbe interactions from the perspective of rhizodeposits chemodiversity and composition and will serve to guide future microbiome research for improving the functioning and services of soil ecosystems. Video abstract.}, } @article {pmid35840919, year = {2022}, author = {Gu, H and Cai, Q and Dai, X and Wang, H and Xu, W and Cao, X and Ye, Y}, title = {A case report of Klebsiella aerogenes-caused lumbar spine infection identified by metagenome next-generation sequencing.}, journal = {BMC infectious diseases}, volume = {22}, number = {1}, pages = {616}, pmid = {35840919}, issn = {1471-2334}, support = {201840314//Science and Technology Commission of Shanghai Municipality/ ; Z-2017-24-2026//Institute of Chinese Materia Medica, China Academy of Chinese Medical Sciences and Peking Union Medical College/ ; }, mesh = {Aged ; *Enterobacter aerogenes ; Female ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Klebsiella Infections/diagnosis ; Lumbar Vertebrae ; Metagenome ; Middle Aged ; }, abstract = {BACKGROUND: The early clinical diagnosis of spinal infections in elderly patients with recessive or atypical symptoms is difficult. Klebsiella aerogenes is a common opportunistic bacterium that can infect the respiratory tract, urinary tract, and even the central nervous system. However, whether it can infect the lumbar spine has not been previously described.

CASE PRESENTATION: In this paper, we report the case of a 69-year-old female patient with osteoporosis who was initially diagnosed with hemolytic anemia. Later, she was diagnosed with K. aerogenes infection of the lumbar spine based on imaging combined with blood culture and metagenome next-generation sequencing (mNGS) detection. After precise medication, the lumbar degeneration was improved.

CONCLUSIONS: Bacterial infection should therefore be considered in cases of lumbar degenerative disease in middle-aged and elderly patients.}, } @article {pmid35840779, year = {2022}, author = {Conteville, LC and Vicente, ACP}, title = {A plasmid network from the gut microbiome of semi-isolated human groups reveals unique and shared metabolic and virulence traits.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {12102}, pmid = {35840779}, issn = {2045-2322}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Metagenomics ; Plasmids/genetics ; Virulence/genetics ; }, abstract = {The plasmids in gut microbiomes have the potential to contribute to the microbiome community, as well as human health and physiology. Nevertheless, this niche remains poorly explored. In general, most microbiome studies focus on urban-industrialized groups, but here, we studied semi-isolated groups from South America and Africa, which would represent a link between ancestral and modern human groups. Based on open metagenomic data, we characterized the set of plasmids, including their genes and functions, from the gut microbiome of the Hadza, Matses, Tunapuco, and Yanomami, semi-isolated groups with a hunter, gather or subsistence lifestyle. Unique plasmid clusters and gene functions for each human group were identified. Moreover, a dozen plasmid clusters circulating in other niches worldwide are shared by these distinct groups. In addition, novel and unique plasmids harboring resistance (encompassing six antibiotic classes and multiple metals) and virulence (as type VI secretion systems) genes were identified. Functional analysis revealed pathways commonly associated with urban-industrialized groups, such as lipopolysaccharide biosynthesis that was characterized in the Hadza gut plasmids. These results demonstrate the richness of plasmids in semi-isolated human groups' gut microbiome, which represents an important source of information with biotechnological/pharmaceutical potential, but also on the spread of resistance/virulence genes to semi-isolated groups.}, } @article {pmid35840731, year = {2022}, author = {Cárdenas, A and Raina, JB and Pogoreutz, C and Rädecker, N and Bougoure, J and Guagliardo, P and Pernice, M and Voolstra, CR}, title = {Greater functional diversity and redundancy of coral endolithic microbiomes align with lower coral bleaching susceptibility.}, journal = {The ISME journal}, volume = {16}, number = {10}, pages = {2406-2420}, pmid = {35840731}, issn = {1751-7370}, support = {OSR-2017-CRG6-3400-02//King Abdullah University of Science and Technology (KAUST)/ ; }, mesh = {Animals ; *Anthozoa ; Coral Bleaching ; Coral Reefs ; Metagenomics ; *Microbiota ; Symbiosis ; }, abstract = {The skeleton of reef-building coral harbors diverse microbial communities that could compensate for metabolic deficiencies caused by the loss of algal endosymbionts, i.e., coral bleaching. However, it is unknown to what extent endolith taxonomic diversity and functional potential might contribute to thermal resilience. Here we exposed Goniastrea edwardsi and Porites lutea, two common reef-building corals from the central Red Sea to a 17-day long heat stress. Using hyperspectral imaging, marker gene/metagenomic sequencing, and NanoSIMS, we characterized their endolithic microbiomes together with [15]N and [13]C assimilation of two skeletal compartments: the endolithic band directly below the coral tissue and the deep skeleton. The bleaching-resistant G. edwardsi was associated with endolithic microbiomes of greater functional diversity and redundancy that exhibited lower N and C assimilation than endoliths in the bleaching-sensitive P. lutea. We propose that the lower endolithic primary productivity in G. edwardsi can be attributed to the dominance of chemolithotrophs. Lower primary production within the skeleton may prevent unbalanced nutrient fluxes to coral tissues under heat stress, thereby preserving nutrient-limiting conditions characteristic of a stable coral-algal symbiosis. Our findings link coral endolithic microbiome structure and function to bleaching susceptibility, providing new avenues for understanding and eventually mitigating reef loss.}, } @article {pmid35840409, year = {2022}, author = {Morandi, S and Cremonesi, P and Arioli, S and Stocco, G and Silvetti, T and Biscarini, F and Castiglioni, B and Greco, Ç and D'Ascanio, V and Mora, D and Brasca, M}, title = {Effect of using mycotoxin-detoxifying agents in dairy cattle feed on natural whey starter biodiversity.}, journal = {Journal of dairy science}, volume = {105}, number = {8}, pages = {6513-6526}, doi = {10.3168/jds.2022-21793}, pmid = {35840409}, issn = {1525-3198}, mesh = {Animal Feed/analysis ; Animals ; Biodiversity ; Cattle ; *Cheese/analysis ; DNA, Bacterial/analysis ; Food Microbiology ; *Lactobacillus helveticus ; *Mycotoxins/analysis ; Whey/chemistry ; Whey Proteins/analysis ; }, abstract = {Natural whey cultures (NWC) are undefined multiple-strain bacterial starter communities that can be affected by even small changes along the entire dairy chain. We applied a multidisciplinary approach to investigate how the addition of 2 mycotoxin-detoxifying agents [sodium smectite and lignocellulose-based material (B1); leonardite and betaine (B2)] to cow diets modified the microbiota of the NWC in manufacture of a Grana-like cheese. Microbiological and flow cytometry analyses showed that the content and viability of lactic acid bacteria (LAB) and the total whey microbiota were not affected by the detoxifying agents, and Streptococcus thermophilus, Lactobacillus helveticus, and Limosilactobacillus fermentum were the dominant taxa. Random amplified polymorphic DNA-PCR fingerprinting and metagenomic analysis highlighted differences in the bacterial community of the NWC and in the relative abundance of Bacteroidetes that increased when B1 and B2 were included in the diet. Two of 6 St. thermophilus biotypes were detected only in control samples; conversely, none of the Lb. helveticus biotypes found in control samples were isolated from B1 and B2. In vitro tests showed that the 2 binders did not significantly affect the development of St. thermophilus, but they stimulated the growth of Lb. helveticus strains recovered only from B1 and B2 NWC. The addition of binders in cow feed can affect the LAB biotypes present in NWC.}, } @article {pmid35840264, year = {2022}, author = {Rubiola, S and Macori, G and Chiesa, F and Panebianco, F and Moretti, R and Fanning, S and Civera, T}, title = {Shotgun metagenomic sequencing of bulk tank milk filters reveals the role of Moraxellaceae and Enterobacteriaceae as carriers of antimicrobial resistance genes.}, journal = {Food research international (Ottawa, Ont.)}, volume = {158}, number = {}, pages = {111579}, doi = {10.1016/j.foodres.2022.111579}, pmid = {35840264}, issn = {1873-7145}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents ; Bacteria ; Drug Resistance, Bacterial/genetics ; *Enterobacteriaceae ; Metagenome ; Milk/microbiology ; Moraxellaceae/genetics ; }, abstract = {In the present context of growing antimicrobial resistance (AMR) concern, understanding the distribution of AMR determinants in food matrices such as milk is crucial to protect consumers and maintain high food safety standards. Herein, the resistome of different dairy farms was investigated through a shotgun metagenomic sequencing approach, taking advantage of in-line milk filters as promising tools. The application of both the reads-based and the assembly-based approaches has allowed the identification of numerous AMR determinants, enabling a comprehensive resolution of the resistome. Notably most of the species harboring AMR genes were predicted to be Gram-negative genera, namely Enterobacter, Acinetobacter, Escherichia, and Pseudomonas, pointing out the role of these bacteria as reservoirs of AMR determinants. In this context, the use of de novo assembly has allowed a more holistic AMR detection strategy, while the reads-based approach has enabled the detection of AMR genes from low abundance bacteria, usually undetectable by assembly-based methods. The application of both reads-based and assembly-based approaches, despite being computationally demanding, has facilitated the comprehensive characterization of a food chain resistome, while also allowing the construction of complete metagenome assembled genomes and the investigation of mobile genetic elements. Our findings suggest that milk filters can successfully be used to investigate the resistome of bulk tank milk through the application of the shotgun metagenomic sequencing. In accordance with our results, raw milk can be considered a source of AMR bacteria and genes; this points out the importance of properly informing food business operators about the risk associated with poor hygiene practices in the dairy production environment and consumers of the potential microbial food safety risks derived from raw milk products consumption. Translating these findings as risk assessment outputs heralds the next generation of food safety controls.}, } @article {pmid35839908, year = {2022}, author = {Tao, J and Chen, Q and Chen, S and Lu, P and Chen, Y and Jin, J and Li, J and Xu, Y and He, W and Long, T and Deng, X and Yin, H and Li, Z and Fan, J and Cao, P}, title = {Metagenomic insight into the microbial degradation of organic compounds in fermented plant leaves.}, journal = {Environmental research}, volume = {214}, number = {Pt 1}, pages = {113902}, doi = {10.1016/j.envres.2022.113902}, pmid = {35839908}, issn = {1096-0953}, mesh = {Cellulose ; Lignin ; *Metagenome ; *Metagenomics ; Microbial Consortia ; Plant Leaves ; }, abstract = {Microbial degradation of organic compounds is an environmentally benign and energy efficient part in product processing. Fermentation of plant leaves involves enzymatic actions of many microorganisms. However, microbes and enzymes discovered from natural degradation communities were still limited by cultural methods. In this study, we used a metagenomics sequence-guided strategy to identify the microbes and enzymes involved in compound degradation and explore the potential synergy among community members in fermented tobacco leaves. The results showed that contents of protein, starch, pectin, lignin, and cellulose varied in fermented leaves from different growing sites. The different compound contents were closely related to taxonomic composition and functional profiles of foliar microbial communities. Microbial communities showed significant correlations with protein, lignin, and cellulose. Vital species for degradations of protein (Bacillus cereus and Terribacillus aidingensis), lignin (Klebsiella pneumoniae and Pantoea ananatis) and cellulose (Pseudomonas putida and Sphingomonas sp. Leaf20) were identified and relating hydrolytic enzymes were annotated. Further, twenty-two metagenome-assembled genomes (MAGs) were assembled from metagenomes and six potential cellulolytic genomes were used to reconstruct the cellulose-degrading process, revealing the potential metabolic cooperation related to cellulose degradation. Our work should deepen the understanding of microbial roles in plant fermentation and provide a new viewpoint for applying microbial consortia to convert plant organic components to small molecules.}, } @article {pmid35839905, year = {2022}, author = {Yang, C and Zhao, Y and Cao, W and Xing, M and Xu, X and Wang, Z and Sun, J}, title = {Metagenomic analysis reveals antibiotic resistance genes and virulence factors in the saline-alkali soils from the Yellow River Delta, China.}, journal = {Environmental research}, volume = {214}, number = {Pt 2}, pages = {113823}, doi = {10.1016/j.envres.2022.113823}, pmid = {35839905}, issn = {1096-0953}, mesh = {Alkalies/analysis ; Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; China ; Drug Resistance, Microbial/genetics ; Ecosystem ; Genes, Bacterial ; Humans ; Manure/analysis ; *Rivers ; *Soil/chemistry ; Soil Microbiology ; Virulence Factors/genetics ; }, abstract = {The propagation of antibiotic resistance genes (ARGs) and virulence factors (VFs) in the saline-alkali soils and associated environmental factors remains unknown. In this study, soil samples from the Yellow River Delta, China with four salinity gradients were characterized by their physiochemical properties, and shotgun metagenomic sequencing was used to identify the ARGs and VFs carried by microorganisms. Soil salinization significantly reduced the relative abundances of Solirubrobacterales, Propionibacteriales, and Micrococcales, and quorum sensing in microorganisms. The number of ARGs and VFs significantly decreased in medium and high saline-alkali soils as compared with that in non-saline-alkali soil, however, the ARGs of Bacitracin, and the VFs of iron uptake system, adherence, and stress protein increased significantly in saline-alkali soils. Spearman analysis showed that the ARGs of fluoroquinolone, tetracycline, aminoglycoside, beta-lactam, and tigecycline were positively correlated with soil pH. Similarly, we observed an increased contribution to the ARGs and VFs by taxa belonging to Solirubrobacterales and Gemmatimonadales, respectively. The control plot was mainly improved from saline-alkali land through application of animal manure, which tended to contain large amounts of ARGs and VFs in this study. Further studies are needed to observe ARGs and VFs in the saline-alkali land for multiple years and speculate the potential risks caused by varied ARGs and VFs to the soil ecosystem and human health.}, } @article {pmid35839241, year = {2023}, author = {Capo, E and Peterson, BD and Kim, M and Jones, DS and Acinas, SG and Amyot, M and Bertilsson, S and Björn, E and Buck, M and Cosio, C and Elias, DA and Gilmour, C and Goñi-Urriza, M and Gu, B and Lin, H and Liu, YR and McMahon, K and Moreau, JW and Pinhassi, J and Podar, M and Puente-Sánchez, F and Sánchez, P and Storck, V and Tada, Y and Vigneron, A and Walsh, DA and Vandewalle-Capo, M and Bravo, AG and Gionfriddo, CM}, title = {A consensus protocol for the recovery of mercury methylation genes from metagenomes.}, journal = {Molecular ecology resources}, volume = {23}, number = {1}, pages = {190-204}, pmid = {35839241}, issn = {1755-0998}, support = {CEX2019-000928-S//Severo Ochoa Excellence Program Post-doctoral Fellowship/ ; //U.S. Department of Energy/ ; DE-AC05-00OR22725//LLC/ ; //Oak Ridge National Laboratory/ ; //Smithsonian Institution/ ; //Smithsonian High Performance Cluster (SI/HPC)/ ; SNIC 2021/5-53//Uppsala Multidisciplinary Centre for Advanced Computational Science (UPPMAX)/ ; 1935173//National Science Foundation/ ; 863584//EMFF-Blue Economy project MER-CLUB/ ; 2018-01031//Swedish Research Council Formas/ ; }, mesh = {*Mercury/analysis ; Metagenome ; Methylation ; Ecosystem ; Consensus ; Soil ; }, abstract = {Mercury (Hg) methylation genes (hgcAB) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal-ash amended sediments, chlor-alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg-cycling microorganisms in aquatic and terrestrial ecosystems (Hg-MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce "marky-coco", a ready-to-use bioinformatic pipeline based on de novo single-metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky-coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.}, } @article {pmid35839145, year = {2022}, author = {Hilaire, SS and Chen, C and Pan, Z and Radolinski, J and Stewart, RD and Maguire, RO and Xia, K}, title = {Subsurface Manure Injection Reduces Surface Transport of Antibiotic Resistance Genes but May Create Antibiotic Resistance Hotspots in Soils.}, journal = {Environmental science & technology}, volume = {56}, number = {21}, pages = {14972-14981}, doi = {10.1021/acs.est.2c00981}, pmid = {35839145}, issn = {1520-5851}, mesh = {*Manure ; *Soil ; Anti-Bacterial Agents/pharmacology ; RNA, Ribosomal, 16S/genetics ; Soil Microbiology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; }, abstract = {Compared to surface application, manure subsurface injection reduces surface runoff of nutrients, antibiotic resistant microorganisms, and emerging contaminants. Less is known regarding the impact of both manure application methods on surface transport of antibiotic resistance genes (ARGs) in manure-amended fields. We applied liquid dairy manure to field plots by surface application and subsurface injection and simulated rainfall on the first or seventh day following application. The ARG richness, relative abundance (normalized to 16s rRNA), and ARG profiles in soil and surface runoff were monitored using shotgun metagenomic sequencing. Within 1 day of manure application, compared to unamended soils, soils treated with manure had 32.5-70.5% greater ARG richness and higher relative abundances of sulfonamide (6.5-129%) and tetracycline (752-3766%) resistance genes (p ≤ 0.05). On day 7, soil ARG profiles in the surface-applied plots were similar to, whereas subsurface injection profiles were different from, that of the unamended soils. Forty-six days after manure application, the soil ARG profiles in manure injection slits were 37% more diverse than that of the unamended plots. The abundance of manure-associated ARGs were lower in surface runoff from manure subsurface injected plots and carried a lower resistome risk score in comparison to surface-applied plots. This study demonstrated, for the first time, that although manure subsurface injection reduces ARGs in the runoff, it can create potential long-term hotspots for elevated ARGs within injection slits.}, } @article {pmid35838255, year = {2022}, author = {Arias, MB and Hartle-Mougiou, K and Taboada, S and Vogler, AP and Riesgo, A and Elfekih, S}, title = {Unveiling biogeographical patterns in the worldwide distributed Ceratitis capitata (medfly) using population genomics and microbiome composition.}, journal = {Molecular ecology}, volume = {31}, number = {18}, pages = {4866-4883}, doi = {10.1111/mec.16616}, pmid = {35838255}, issn = {1365-294X}, mesh = {Animals ; *Ceratitis capitata/genetics/microbiology ; Metagenomics ; *Microbiota/genetics ; Microsatellite Repeats ; South Africa ; }, abstract = {Invasive species are among the most important, growing threats to food security and agricultural systems. The Mediterranean medfly, Ceratitis capitata, is one of the most damaging representatives of a group of rapidly expanding species in the family Tephritidae, due to their wide host range and high invasiveness potential. Here, we used restriction site-associated DNA sequencing (RADseq) to investigate the population genomic structure and phylogeographical history of medflies collected from six sampling sites, including Africa (South Africa), the Mediterranean (Spain, Greece), Latin America (Guatemala, Brazil) and Australia. A total of 1907 single nucleotide polymorphisms (SNPs) were used to identify two genetic clusters separating native and introduced ranges, consistent with previous findings. In the introduced range, all individuals were assigned to one genetic cluster except for those in Brazil, which showed introgression of an additional genetic cluster that also appeared in South Africa, and which could not be previously identified using microsatellite markers. Moreover, we assessed the microbial composition variations in medfly populations from selected sampling sites using amplicon sequencing of the 16S ribosomal RNA (V4 region). Microbiome composition and structure were highly similar across geographical regions and host plants, and only the Brazilian specimens showed increased diversity levels and a unique composition of its microbiome compared to other sampling sites. The unique SNP patterns and microbiome features in the Brazilian specimens could point to a direct migration route from Africa with subsequent adaptation of the microbiota to the specific conditions present in Brazil. These findings significantly improve our understanding of the evolutionary history of the global medfly invasions and their adaptation to newly colonized environments.}, } @article {pmid35837874, year = {2022}, author = {Wilcox, TM and Jensen, MR}, title = {Drawing a line in the sand: Environmental DNA population genomics.}, journal = {Molecular ecology resources}, volume = {22}, number = {7}, pages = {2455-2457}, doi = {10.1111/1755-0998.13686}, pmid = {35837874}, issn = {1755-0998}, mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/methods ; *DNA, Environmental/genetics ; Ecology ; Ecosystem ; Environmental Monitoring/methods ; Metagenomics/methods ; *Turtles ; }, abstract = {Environmental DNA (eDNA) sampling uses genetic material in the environment to infer species presence sight-unseen. The method has rapidly become a powerful tool for monitoring biodiversity. However, biological diversity, as per the Convention on Biological Diversity definition of "diversity within species, between species and of ecosystems" is more inclusive than most eDNA studies cover: The vast majority focus only on between-species and ecosystem-level biodiversity. However, a tantalizing prospect, as illustrated by Farrell et al. (2022) in this issue of Molecular Ecology Resources, is that we might also be able to unlock information about individual and population-level diversity via population genomic analysis of these environmental samples. Farrell et al. (2022) found that targeted samples of beach sand contained genetic material not just informative about sea turtle presence, but also indicated the presence of pathogens and genome-wide mitochondrial and nuclear sequences that could accurately infer individual turtle source population. Moving from proof-of-concept to robust, population genomic inference will require a growth of genomic resources for nonmodel organisms and careful study design considerations, some of which have already been pioneered by related fields.}, } @article {pmid35837785, year = {2022}, author = {Medina, V and Rosso, BE and Soria, M and Gutkind, GO and Pagano, EA and Zavala, JA}, title = {Feeding on soybean crops changed gut bacteria diversity of the southern green stinkbug (Nezara viridula) and reduced negative effects of some associated bacteria.}, journal = {Pest management science}, volume = {78}, number = {11}, pages = {4608-4617}, doi = {10.1002/ps.7080}, pmid = {35837785}, issn = {1526-4998}, support = {//Fondo para la Investigación Científica y Tecnológica/ ; //Ministerio de Ciencia, Tecnología e Innovación Productiva/ ; }, mesh = {Animals ; Crops, Agricultural ; Cysteine ; *Cysteine Proteases ; Enterobacteriaceae ; *Gastrointestinal Microbiome ; *Heteroptera ; Lipids ; Nymph ; Glycine max ; }, abstract = {BACKGROUND: The southern green stinkbug (Nezara viridula) is a mayor pest of soybean. However, the mechanism underlying stinkbug resistance to soybean defenses is yet ignored. Although gut bacteria could play an essential role in tolerating plant defenses, most studies testing questions related to insect-plant-bacteria interactions have been performed in laboratory condition. Here we performed experiments in laboratory and field conditions with N. viridula and its gut bacteria, studying gut lipid peroxidaxion levels and cysteine activity in infected and unifected nymphs, testing the hypothesis that feeding on field-grown soybean decreases bacterial abundance in stinkbugs.

RESULTS: Gut bacterial abundance and infection ratio were higher in N. viridula adults reared in laboratory than in those collected from soybean crops, suggesting that stinkbugs in field conditions may modulate gut bacterial colonization. Manipulating gut microbiota by infecting stinkbugs with Yokenella sp. showed that these bacteria abundance decreased in field conditions, and negatively affected stinkbugs performance and were more aggressive in laboratory rearing than in field conditions. Infected nymphs that fed on soybean pods had lower mortality, higher mass and shorter development period than those reared in the laboratory, and suggested that field conditions helped nymphs to recover from Yokenella sp. infection, despite of increased lipid peroxidation and decreased cysteine proteases activity in nymphs' guts.

CONCLUSIONS: Our results demonstrated that feeding on field-grown soybean reduced bacterial abundance and infection in guts of N. viridula and highlighted the importance to test functional activities or pathogenicity of microbes under realistic field conditions prior to establish conclusions on three trophic interactions. © 2022 Society of Chemical Industry.}, } @article {pmid35837537, year = {2022}, author = {Zhang, M and Wang, Z and Wang, J and Lv, H and Xiao, X and Lu, W and Jin, X and Meng, J and Pu, Y and Zhao, M}, title = {The Value of Metagenomic Next-Generation Sequencing in Hematological Malignancy Patients with Febrile Neutropenia After Empiric Antibiotic Treatment Failure.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {3549-3559}, pmid = {35837537}, issn = {1178-6973}, abstract = {BACKGROUND: It was crucial to use empirical antibiotics in febrile neutropenia (FN) patients. However, most patients still died from infection due to poor efficacy. Metagenomic next-generation sequencing (mNGS) is a rapid microbiological diagnostic method. The value of mNGS in patients with FN remains to be studied, especially after empiric antibiotic treatment.

METHODS: We retrospectively analyzed the differences between mNGS and the traditional methods in 192 patients with hematological malignancies who have received empiric antibiotic treatment. Samples were collected when patient had chills or half an hour before peak body temperature. And we compared the differences between FN and non-FN patients, mainly including types of pathogens and the diagnostic value of different pathogens.

RESULTS: Despite receiving empirical treatment, the pathogen detection rate of mNGS was significantly higher than the traditional method (80.21% vs 25.00%, P<0.001). And it has obvious advantages in detecting mixed pathogens infection (80.21% vs 4.17%, P<0.001). Then, we found that mNGS saw more pathogens in the FN than in the non-FN group, especially fungus. 21/33 (63.63%) of FN patients was diagnosed with fungal infections. The fungal detection rate in FN was significantly higher than non-FN group (32.35% vs 12.22%, P=0.001). Besides, the sensitivity of mNGS was higher than the traditional methods in both FN and non-FN group (P<0.001), but no significant difference in specificity (P>0.05). In the FN group, empiric antibiotic treatment of 46/102 (45.10%) patients did not treat all the pathogens detected by mNGS. After adjusting the antimicrobial regimen according to the results of mNGS, the effective rate at 72 hours and 7 days was 22/46 (47.83%) and 24/102 (52.17%), respectively.

CONCLUSION: mNGS had a significant impact on the diagnosis of infection and the second-line antimicrobial therapy in FN. mNGS plays a more important role in FN patients, especially in the diagnosis of fungal infections.

PURPOSE: Firstly, we compared the difference between mNGS and the traditional methods in the diagnosis of infection. Secondly, we assessed the value of mNGS in FN patients by comparing it with non-FN patients, including types of pathogens and the diagnostic value of different pathogens. In order to show that mNGS plays a more important role in FN.}, } @article {pmid35837477, year = {2022}, author = {Wang, D and Wang, W and Ding, Y and Tang, M and Zhang, L and Chen, J and You, H}, title = {Metagenomic Next-Generation Sequencing Successfully Detects Pulmonary Infectious Pathogens in Children With Hematologic Malignancy.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {899028}, pmid = {35837477}, issn = {2235-2988}, mesh = {Anti-Bacterial Agents ; Child ; *Hematologic Neoplasms/complications ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; *Pneumonia ; Retrospective Studies ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Pulmonary infection is a leading cause of mortality in pediatric patients with hematologic malignancy (HM). In clinical settings, pulmonary pathogens are frequently undetectable, and empiric therapies may be costly, ineffective and lead to poor outcomes in this vulnerable population. Metagenomic next-generation sequencing (mNGS) enhances pathogen detection, but data on its application in pediatric patients with HM and pulmonary infections are scarce.

METHODS: We retrospectively reviewed 55 pediatric patients with HM and pulmonary infection who were performed mNGS on bronchoalveolar lavage fluid from January 2020 to October 2021. The performances of mNGS methods and conventional microbiological methods in pathogenic diagnosis and subsequently antibiotic adjustment were investigated.

RESULTS: A definite or probable microbial etiology of pulmonary infection was established for 50 of the 55 patients (90.9%) when mNGS was combined with conventional microbiological tests. The positive rate was 87.3% (48 of 55 patients) for mNGS versus 34.5% (19 of 55 patients) with conventional microbiological methods (P < 0.001). Bacteria, viruses and fungi were detected in 17/55 (30.9%), 25/55 (45.5%) and 19/55 (34.5%) cases using mNGS, respectively. Furthermore, 17 patients (30.9%) were identified as pulmonary mixed infections. Among the 50 pathogen-positive cases, 38% (19/50) were not completely pathogen-covered by empirical antibiotics and all of them were accordingly made an antibiotic adjustment. In the present study, the 30-day mortality rate was 7.3%.

CONCLUSION: mNGS is a valuable diagnostic tool to determine the etiology and appropriate treatment in pediatric patients with HM and pulmonary infection. In these vulnerable children with HM, pulmonary infections are life-threatening, so we recommend that mNGS should be considered as a front-line diagnostic test.}, } @article {pmid35837476, year = {2022}, author = {Zhang, L and Chen, T and Wang, Y and Zhang, S and Lv, Q and Kong, D and Jiang, H and Zheng, Y and Ren, Y and Huang, W and Liu, P and Jiang, Y}, title = {Comparison Analysis of Different DNA Extraction Methods on Suitability for Long-Read Metagenomic Nanopore Sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {919903}, pmid = {35837476}, issn = {2235-2988}, mesh = {DNA ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Metagenomics/methods ; *Nanopore Sequencing ; }, abstract = {Metagenomic next-generation sequencing (mNGS) is a novel useful strategy that is increasingly used for pathogens detection in clinic. Some emerging mNGS technologies with long-read ability are useful to decrease sequencing time and increase diagnosed accuracy, which is of great significance in rapid pathogen diagnosis. Reliable DNA extraction is considered critical for the success of sequencing; hence, there is thus an urgent need of gentle DNA extraction method to get unbiased and more integrate DNA from all kinds of pathogens. In this study, we systematically compared three DNA extraction methods (enzymatic cell lysis based on MetaPolyzyme, mechanical cell lysis based on bead beating, and the control method without pre-cell lysis, respectively) by assessing DNA yield, integrity, and the microbial diversity based on long-read nanopore sequencing of urine samples with microbial infections. Compared with the control method, the enzymatic-based method increased the average length of microbial reads by a median of 2.1-fold [Inter Quartile Range (IQR), 1.7-2.5; maximum, 4.8) in 18 of the 20 samples and the mapped reads proportion of specific species by a median of 11.8-fold (Inter Quartile Range (IQR), 6.9-32.2; maximum, 79.27]. Moreover, it provided fully (20 of 20) consistent diagnosed results to the clinical culture and more representative microbial profiles (P < 0.05), which all strongly proves the excellent performance of enzymatic-based method in long-read mNGS-based pathogen identification and potential diseases diagnosis of microbiome related.}, } @article {pmid35837177, year = {2022}, author = {Zhang, S and Hou, L and Sun, Q}, title = {Correlation analysis of intestinal flora and immune function in patients with primary hepatocellular carcinoma.}, journal = {Journal of gastrointestinal oncology}, volume = {13}, number = {3}, pages = {1308-1316}, pmid = {35837177}, issn = {2078-6891}, abstract = {BACKGROUND: This study applied metagenomic sequencing technology to analyze the intestinal flora distribution and immune function of patients with primary liver cancer.

METHODS: Stool samples were collected from 10 patients with primary liver cancer (primary liver cancer group) and 10 healthy subjects (healthy control group) who were admitted to The Affiliated Changzhou No. 2 People's Hospital of Nanjing Medical University from March to June 2021. The general data of the patients were recorded. Metagenomic sequencing was performed, and principal component analysis and diversity analysis were used to analyze the structure of the two groups and compare the differences in species abundance. United States Employment Service (USES) Spearman correlation analysis was applied to examine vice Streptococcus blood, saliva, Streptococcus, Streptococcus mutans, Streptococcus thermophilus, and vice Haemophilus influenzae, WeiRong aureus, existing different WeiRong bacteria, Eosinophilic mucins Ekman bacteria, responding to bacteria, the other branch bacteria abundance and in alanine aminotransferase (ALT), aspartate aminotransferase (AST), valley correlation between levels of amyltranspeptidase (GGT), total protein, total bilirubin and alpha-fetoprotein (AFP).

RESULTS: Beta diversity analysis based on Bray and Jensen-Shannon Divergence (JSD) distance measurement showed that the heterogeneity of fecal flora in the hepatic cell carcinoma (HCC) group was significantly lower than that in the healthy control group (P<0.001. At the species level of bacterial taxonomy, there was a statistically significant difference in the distribution of 137 bacteria in the healthy control and primary liver cancer groups (P<0.05). Correlation analysis showed that Streptococcus salivarius (P=0.020), Streptococcus thermophilus (P=0.002), and Haemophilus parainfluenzae (P=0.023) were significantly positively correlated with the serum ALT level. There were also notable correlations with AST (P=0.049), GGT (P=0.037), and total protein (P=0.010).

CONCLUSIONS: The diversity of intestinal flora in patients with primary liver cancer is significantly reduced, species abundance is altered, and there is a marked imbalance of intestinal flora. Therefore, specific bacterial species with different intestinal flora may be used as biomarkers for the early diagnosis of primary liver cancer.}, } @article {pmid35836558, year = {2022}, author = {Isaac, RD and Sanjeev, K and Subbulakshmi, CL and Amirtharaj, LV and Sekar, M}, title = {Identification of a novel bacterium Scardovia wiggsiae in high caries risk adolescence: A metagenomic and melt curve analysis.}, journal = {Journal of conservative dentistry : JCD}, volume = {25}, number = {3}, pages = {297-305}, pmid = {35836558}, issn = {0972-0707}, abstract = {BACKGROUND: Mutans streptococci which comprise only 2% have long been presumed to be the specific pathogen responsible for caries. A novel caries associated bacterium namely Scardovia wiggsiae is recognized to be ecologically competitive in active caries lesions. The actual pathogen needs to be identified, so as to specifically target and reduce the prevalence of caries in a given community.

AIM: The aim of the study is to evaluate the presence of S. wiggsiae in combination with other bacteria in caries risk adolescence.

METHODS: Sixty adolescent subjects were screened. Phase I-to determine the prevalence of S. wiggsiae in saliva, plaque and dentinal caries samples of low and high caries risk individuals (n = 30 each) using polymerase chain reaction (PCR); Phase-II-to identify its presence by 16SrRNA metagenomic analysis and quantitatively evaluate the cariogenic pathogen using high-resolution melt curve analysis and real-time PCR.

RESULTS: Highest prevalence of S. wiggsiae was observed in dentinal caries followed by plaque and saliva samples of high caries risk individuals under PCR analysis. Metagenomic analysis showed two-fold statistically increased presence of Lactobacilli and Bifidobacteriaceae (S. wiggsiae) in dentinal samples compared to plaque samples (P = 0.05). Mutans streptococcus recorded the minimum.

CONCLUSION: Scardovia wiggsiae is identified as one of the predominant microorganism.}, } @article {pmid35836413, year = {2022}, author = {Milke, F and Sanchez-Garcia, S and Dlugosch, L and McNichol, J and Fuhrman, J and Simon, M and Wagner-Döbler, I}, title = {Composition and Biogeography of Planktonic Pro- and Eukaryotic Communities in the Atlantic Ocean: Primer Choice Matters.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {895875}, pmid = {35836413}, issn = {1664-302X}, abstract = {Basin-scale biogeographic observations of marine pelagic pro- and eukaryotic communities are necessary to understand forces driving community composition and for providing a baseline to monitor global change. Deep sequencing of rRNA genes provides community composition at high resolution; yet, it is unclear how the choice of primers affects biogeographic patterns. Here, we re-amplified 16S rRNA genes from DNA sampled during R/V Polarstern Cruise ANT28-5 over a latitudinal transect across the Atlantic Ocean from 52°S to 47°N using universal V4-V5 primers and compared the results with those obtained previously with V5-V6 bacteria-specific primers. For validation of our results, we inferred community composition based on 16S rRNA genes of metagenomes from the same stations and single amplified genomes (SAGs) from the Global Ocean Reference Genome (GORG) database. We found that the universal V4-V5 primers retrieved SAR11 clades with similar relative proportions as those found in the GORG database while the V5-V6 primers recovered strongly diverging clade abundances. We confirmed an inverse bell-shaped distance-decay relationship and a latitudinal diversity gradient that did not decline linearly with absolute latitude in the Atlantic Ocean. Patterns were modified by sampling depth, sequencing depth, choice of primers, and abundance filtering. Especially richness patterns were not robust to methodological change. This study offers a detailed picture of the Atlantic Ocean microbiome using a universal set of PCR primers that allow for the conjunction of biogeographical patterns among organisms from different domains of life.}, } @article {pmid35835775, year = {2022}, author = {Oyama, LB and Olleik, H and Teixeira, ACN and Guidini, MM and Pickup, JA and Hui, BYP and Vidal, N and Cookson, AR and Vallin, H and Wilkinson, T and Bazzolli, DMS and Richards, J and Wootton, M and Mikut, R and Hilpert, K and Maresca, M and Perrier, J and Hess, M and Mantovani, HC and Fernandez-Fuentes, N and Creevey, CJ and Huws, SA}, title = {In silico identification of two peptides with antibacterial activity against multidrug-resistant Staphylococcus aureus.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {58}, pmid = {35835775}, issn = {2055-5008}, support = {BB/L026716/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Animals ; Humans ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Antimicrobial Cationic Peptides/pharmacology ; Lipids/pharmacology/therapeutic use ; *Methicillin-Resistant Staphylococcus aureus ; Microbial Sensitivity Tests ; *Staphylococcal Infections/drug therapy/microbiology ; Staphylococcus aureus/metabolism ; }, abstract = {Here we report two antimicrobial peptides (AMPs), HG2 and HG4 identified from a rumen microbiome metagenomic dataset, with activity against multidrug-resistant (MDR) bacteria, especially methicillin-resistant Staphylococcus aureus (MRSA) strains, a major hospital and community-acquired pathogen. We employed the classifier model design to analyse, visualise, and interpret AMP activities. This approach allowed in silico discrimination of promising lead AMP candidates for experimental evaluation. The lead AMPs, HG2 and HG4, are fast-acting and show anti-biofilm and anti-inflammatory activities in vitro and demonstrated little toxicity to human primary cell lines. The peptides were effective in vivo within a Galleria mellonella model of MRSA USA300 infection. In terms of mechanism of action, HG2 and HG4 appear to interact with the cytoplasmic membrane of target cells and may inhibit other cellular processes, whilst preferentially binding to bacterial lipids over human cell lipids. Therefore, these AMPs may offer additional therapeutic templates for MDR bacterial infections.}, } @article {pmid35835418, year = {2022}, author = {Ni, M and Pan, Y and Li, D and Huang, Y and Chen, Z and Li, L and Song, Z and Zhao, Y}, title = {Metagenomics reveals the metabolism of polyphosphate-accumulating organisms in biofilm sequencing batch reactor: A new model.}, journal = {Bioresource technology}, volume = {360}, number = {}, pages = {127603}, doi = {10.1016/j.biortech.2022.127603}, pmid = {35835418}, issn = {1873-2976}, mesh = {Biofilms ; *Bioreactors ; Metagenomics ; Phosphorus/metabolism ; *Polyphosphates/metabolism ; }, abstract = {This study assessed the impact of the operating conditions of the biofilm sequencing batch reactor (BSBR) on the community structure and the growth/metabolic pathways of its polyphosphate-accumulating organisms (PAOs). There are significant difference with reference to the enhanced biological phosphorus removal (EBPR) process. The leading PAOs in BSBR generally are capable of high affinity acetate metabolism, gluconeogenesis, and low affinity phosphate transport, and have various carbon source supplementation pathways to ensure the efficient circulation of energy and reducing power. A new model of the metabolic mechanism of PAOs in the BSBR was formulated, which features low glycogen metabolism with simultaneous gluconeogenesis and glycogenolysis and differs significantly from the classic mechanism based on Candidatus_Accumulibacter and Tetrasphaera. The findings will assist the efficient recovery of low concentration phosphate in municipal wastewater.}, } @article {pmid35834536, year = {2022}, author = {Cheng, JE and Su, P and Zhang, ZH and Zheng, LM and Wang, ZY and Hamid, MR and Dai, JP and Du, XH and Chen, LJ and Zhai, ZY and Kong, XT and Liu, Y and Zhang, DY}, title = {Metagenomic analysis of the dynamical conversion of photosynthetic bacterial communities in different crop fields over different growth periods.}, journal = {PloS one}, volume = {17}, number = {7}, pages = {e0262517}, pmid = {35834536}, issn = {1932-6203}, mesh = {Bacteria ; Crops, Agricultural ; High-Throughput Nucleotide Sequencing ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Soil Microbiology ; }, abstract = {Photosynthetic bacteria are beneficial to plants, but knowledge of photosynthetic bacterial community dynamics in field crops during different growth stages is scarce. The factors controlling the changes in the photosynthetic bacterial community during plant growth require further investigation. In this study, 35 microbial community samples were collected from the seedling, flowering, and mature stages of tomato, cucumber, and soybean plants. 35 microbial community samples were assessed using Illumina sequencing of the photosynthetic reaction center subunit M (pufM) gene. The results revealed significant alpha diversity and community structure differences among the three crops at the different growth stages. Proteobacteria was the dominant bacterial phylum, and Methylobacterium, Roseateles, and Thiorhodococcus were the dominant genera at all growth stages. PCoA revealed clear differences in the structure of the microbial populations isolated from leaf samples collected from different crops at different growth stages. In addition, a dissimilarity test revealed significant differences in the photosynthetic bacterial community among crops and growth stages (P<0.05). The photosynthetic bacterial communities changed during crop growth. OTUs assigned to Methylobacterium were present in varying abundances among different sample types, which we speculated was related to the function of different Methylobacterium species in promoting plant growth development and enhancing plant photosynthetic efficiency. In conclusion, the dynamics observed in this study provide new research ideas for the detailed assessments of the relationship between photosynthetic bacteria and different growth stages of plants.}, } @article {pmid35834499, year = {2022}, author = {McKeen, S and Roy, NC and Mullaney, JA and Eriksen, H and Lovell, A and Kussman, M and Young, W and Fraser, K and Wall, CR and McNabb, WC}, title = {Adaptation of the infant gut microbiome during the complementary feeding transition.}, journal = {PloS one}, volume = {17}, number = {7}, pages = {e0270213}, pmid = {35834499}, issn = {1932-6203}, mesh = {Feces ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant Nutritional Physiological Phenomena ; Metagenome ; Pilot Projects ; }, abstract = {The infant gut microbiome progresses in composition and function during the introduction of solid foods throughout the first year of life. The purpose of this study was to characterize changes in healthy infant gut microbiome composition, metagenomic functional capacity, and associated metabolites over the course of the complementary feeding period. Fecal samples were obtained at three 'snapshot' timepoints from infants participating in the 'Nourish to Flourish' pilot study: before the introduction of solid foods at approximately 4 months of age, after introducing solid foods at 9 months of age, and after continued diet diversification at 12 months of age. KEGG and taxonomy assignments were correlated with LC-MS metabolomic profiles to identify patterns of co-abundance. The composition of the microbiome diversified during the first year of life, while the functional capacity present in the gut microbiome remained stable. The introduction of solid foods between 4 and 9 months of age corresponded to a larger magnitude of change in relative abundance of sequences assigned to KEGG pathways and taxonomic assignments, as well as to stronger correlations with metabolites, compared to the magnitude of changes and number of correlations seen during continued diet diversification between 9 and 12 months of age. Changes in aqueous fecal metabolites were more strongly correlated with KEGG pathway assignments, while changes in lipid metabolites associated with taxonomic assignments, particularly between 9 and 12 months of age. This study establishes trends in microbiome composition and functional capacity occurring during the complementary feeding period and identifies potential metabolite targets for future investigations.}, } @article {pmid35834269, year = {2022}, author = {Qiao, H and Tan, XR and Li, H and Li, JY and Chen, XZ and Li, YQ and Li, WF and Tang, LL and Zhou, GQ and Zhang, Y and Liang, YL and He, QM and Zhao, Y and Huang, SY and Gong, S and Li, Q and Ye, ML and Chen, KL and Sun, Y and Ma, J and Liu, N}, title = {Association of Intratumoral Microbiota With Prognosis in Patients With Nasopharyngeal Carcinoma From 2 Hospitals in China.}, journal = {JAMA oncology}, volume = {8}, number = {9}, pages = {1301-1309}, pmid = {35834269}, issn = {2374-2445}, mesh = {Adolescent ; Adult ; Aged ; Biomarkers ; China/epidemiology ; Cohort Studies ; Female ; Hospitals ; Humans ; Male ; *Microbiota ; Middle Aged ; Nasopharyngeal Carcinoma/pathology ; *Nasopharyngeal Neoplasms/pathology ; Neoplasm Recurrence, Local/pathology ; Neoplasm Staging ; Nucleotides ; Prognosis ; RNA, Ribosomal, 16S ; Retrospective Studies ; Young Adult ; }, abstract = {IMPORTANCE: Microbiota-tumor interactions have qualified microbiota as a promising prognostic biomarker in various types of cancers. Although the nasopharynx acts as a crucial niche of the upper respiratory tract microbiome, whether the intratumoral microbiota exists and its clinical significance in nasopharyngeal carcinoma (NPC) remain uncertain.

OBJECTIVE: To evaluate the clinical significance of intratumoral microbiota for individual prognostication in patients with NPC.

This retrospective cohort study included NPC biopsy samples from 2 hospitals: Sun Yat-sen University Cancer Center (Guangzhou, China) and Zhejiang Cancer Hospital (Hangzhou, China) between January 2004 and November 2016, with follow-up through November 2020. A total of 802 patients were included according to the following criteria: with histologically proven NPC, without distant metastasis at initial diagnosis, had not received antitumor treatment before biopsy sampling, aged between 18 and 70 years, with complete medical records and regular follow-up, without a history of cancer, and successfully extracted enough DNA for experiments.

MAIN OUTCOMES AND MEASURES: The primary end point was disease-free survival, and the secondary end points included distant metastasis-free survival and overall survival. To assess the existence and load of intratumoral microbiota in 96 patients with NPC with or without tumor relapse, 16S rRNA sequencing and quantitative polymerase chain reaction were used. The associations between intratumoral bacterial load and clinical outcome were evaluated in 241 fresh-frozen NPC samples (training cohort) and validated in paraffin-embedded NPC samples of internal (n = 233) and external (n = 232) validation cohorts. Metagenomic and transcriptome analyses were performed to ascertain the origin and underlying mechanism of intratumoral bacteria.

RESULTS: A total of 802 patients with NPC (mean [SD] age, 46.2 [10.6] years; 594 [74.1%] male) were enrolled. Microbiota presented within NPC tumor tissues, among which Corynebacterium and Staphylococcus predominated. Patients with a high bacterial load in the training cohort had inferior rates of disease-free survival (hazard ratio [HR], 2.90; 95% CI, 1.72-4.90; P < .001), distant metastasis-free survival (HR, 3.18; 95% CI, 1.58-6.39; P < .001), and overall survival (HR, 3.41; 95% CI, 1.90-6.11, P < .001) than those with a low bacterial load, a finding that was validated by the internal and external validation cohorts. Single-nucleotide variant analysis revealed that the nasopharyngeal microbiota was the main origin of NPC intratumoral bacteria. Transcriptome and digital pathology analyses demonstrated that a higher intratumoral bacterial load was negatively associated with T-lymphocyte infiltration.

CONCLUSIONS AND RELEVANCE: Intratumoral bacterial load was a robust prognostic tool for patients with NPC in this cohort study, indicating potential guidance for treatment decisions in patients at different levels of risk of malignant progression.}, } @article {pmid35834135, year = {2022}, author = {Pereira, LB and Gambarini, VMO and de Menezes, AB and Ottoboni, LMM and Vicentini, R}, title = {Influence of Sugarcane Variety on Rhizosphere Microbiota Under Irrigated and Water-Limiting Conditions.}, journal = {Current microbiology}, volume = {79}, number = {9}, pages = {246}, pmid = {35834135}, issn = {1432-0991}, support = {2015/00408-5//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2016/08994-3//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 2014/05929-0//Fundação de Amparo à Pesquisa do Estado de São Paulo/ ; 140547/2014-2//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; }, mesh = {Bacteria ; Edible Grain ; *Microbiota/genetics ; Plant Roots/microbiology ; Rhizosphere ; *Saccharum/microbiology ; Soil Microbiology ; Water/metabolism ; }, abstract = {Drought is one of the main problems linked to climate change that is faced by agriculture, affecting various globally important crops, including sugarcane. Environmentally sustainable strategies have been sought to mitigate the effects of climate change on crops. Among them, the use of beneficial microorganisms offers a promising approach. However, it is still necessary to understand the mechanisms that regulate plant-microorganism interactions, in normal situations and under stress. In this work, the rhizosphere metagenomes of two sugarcane varieties, one resistant and the other susceptible to drought, were compared under normal conditions and under water-limiting conditions. The results showed that for the drought-resistant sugarcane variety, bacteria belonging to the order Sphingomonadales and the family Xanthomonadaceae presented increased activities in terms of mobility, colonization, and cell growth. In contrast, the rhizosphere associated with the drought-sensitive variety exhibited increases of bacteria belonging to the family Polyangiaceae, and the genus Streptomyces, with modifications in DNA metabolism and ribosome binding proteins. The results pointed to variation in the rhizosphere microbiota that was modulated by the host plant genotype, revealing potential bacterial candidates that could be recruited to assist plants during water-limiting conditions.}, } @article {pmid35834125, year = {2022}, author = {Wachira, JM and Kiplimo, D and Thuita, M and Masso, C and Mwirichia, R}, title = {Community Structure of Nitrifying and Denitrifying Bacteria from Effluents Discharged into Lake Victoria, Kenya.}, journal = {Current microbiology}, volume = {79}, number = {9}, pages = {252}, pmid = {35834125}, issn = {1432-0991}, mesh = {Bacteria/classification/*growth & development/isolation & purification/*metabolism ; Denitrification ; Enterobacter/classification/growth & development/metabolism ; Kenya ; Klebsiella/classification/growth & development/isolation & purification/metabolism ; *Lakes/chemistry/microbiology ; Nitrification ; Proteobacteria/classification/growth & development/isolation & purification/metabolism ; Pseudomonas/classification/growth & development/isolation & purification/metabolism ; Rivers/microbiology ; Wastewater/chemistry/*microbiology ; *Water Purification ; }, abstract = {An active microbial community of nitrifying and denitrifying bacteria is needed for efficient utilization of nitrogenous compounds from wastewater. In this study, we explored the bacterial community diversity and structure within rivers, treated and untreated wastewater treatment plants (WWTPs) discharging into Lake Victoria. Water samples were collected from rivers and WWTPs that drain into Lake Victoria. Physicochemical analysis was done to determine the level of nutrients or pollutant loading in the samples. Total community DNA was extracted, followed by Illumina high throughput sequencing to determine the total microbial community and abundance. Enrichment and isolation were then done to recover potential nitrifiers and denitrifiers. Physicochemical analysis pointed to high levels total nitrogen and ammonia in both treated and untreated WWTPs as compared to the samples from the lake and rivers. A total of 1,763 operational taxonomic units (OTUs) spread across 26 bacterial phyla were observed with the most dominant phylum being Proteobacteria. We observed a decreasing trend in diversity from the lake, rivers to WWTPs. The genus Planktothrix constituted 19% of the sequence reads in sample J2 collected from the lagoon. All the isolates recovered in this study were affiliated to three genera: Pseudomonas, Klebsiella and Enterobacter in the phylum Proteobacteria. A combination of metagenomic analysis and a culture-dependent approach helped us understand the relative abundance as well as potential nitrifiers and denitrifiers present in different samples. The recovered isolates could be used for in situ removal of nitrogenous compounds from contaminated wastewater.}, } @article {pmid35834016, year = {2022}, author = {Ravinath, R and Das, AJ and Usha, T and Ramesh, N and Middha, SK}, title = {Targeted metagenome sequencing reveals the abundance of Planctomycetes and Bacteroidetes in the rhizosphere of pomegranate.}, journal = {Archives of microbiology}, volume = {204}, number = {8}, pages = {481}, pmid = {35834016}, issn = {1432-072X}, mesh = {Bacteroidetes/genetics ; Metagenome ; Planctomycetales ; Planctomycetes ; *Pomegranate ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Agricultural productivity of pomegranate can be enhanced by identifying the crop-associated microbial diversity in the rhizosphere region with respect to plant growth promoters and other beneficial organisms. Traditional culture methods have limitations in microbial screening as only 1-2% of these organisms can be cultured. In the present study, 16S rRNA amplicon-based metagenomics approach using MinION Oxford Nanopore platform was employed to explore the microbial diversity in the rhizosphere of pomegranate Bhagwa variety, across variable soil depths from 0 to 5 cms (R2), 5-10 cms (R4) and 10-15 cms (R6), using bulk soil as the control. Across all the three layers, significant variations in pH, nitrogen content and total fungal count were observed. 16S rRNA analysis showed the abundance of planctomycetes, Pirellula staleyi, followed by bacteroidetes, Flavisolibacter LC59 and Niastella koreensis across the various soil depths in the rhizospheric soil samples. Pathway prediction analysis indicated arginine and proline metabolism (gamma-glutamyl putrescine oxidase) and hydrogen sulfide biosynthesis as the most abundant pathway hits. Comparative abundance analysis across layers showed the R6 layer with the maximum microbial diversity in terms of highest dimension of variation (79.2%) followed by R4 and R2 layers (p < 0.01). Our analysis shows the significant influence of root zone in shaping microbial diversity. This study has reported the presence of Planctomycetes, Pirellula staleyi for the first time in the pomegranate field.}, } @article {pmid35833012, year = {2022}, author = {Ramirez-Delgado, D and Cicala, F and Gonzalez-Sanchez, RA and Avalos-Tellez, R and Solana-Arellano, E and Licea-Navarro, A}, title = {Multi-locus evaluation of gastrointestinal bacterial communities from Zalophus californianus pups in the Gulf of California, México.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13235}, pmid = {35833012}, issn = {2167-8359}, mesh = {Animals ; *Sea Lions/genetics ; RNA, Ribosomal, 16S/genetics ; Mexico ; Bacteria/genetics ; Computational Biology ; }, abstract = {BACKGROUND: The gastrointestinal (GI) bacterial communities of sea lions described to date have occasionally revealed large intraspecific variability, which may originate from several factors including different methodological approaches. Indeed, GI bacterial community surveys commonly rely on the use of a single hypervariable region (HR) of 16S rRNA, which may result in misleading structural interpretations and limit comparisons among studies. Here, we considered a multi-locus analysis by targeting six HRs of 16S rRNA with the aims of (i) comprehensively assessing the GI bacterial consortium in rectal samples from Zalophus californianus pups and (ii) elucidating structural variations among the tested HRs. In addition, we evaluated which HRs may be most suitable for identifying intrinsic, structurally related microbiome characteristics, such as geographic variations or functional capabilities.

METHODS: We employed a Short MUltiple Regions Framework (SMURF) approach using the Ion 16S™ Metagenomic Kit. This kit provides different proprietary primers designed to target six HRs of the 16S rRNA gene. To date, the only analytical pipeline available for this kit is the Ion Reporter™ Software of Thermo Fisher Scientific. Therefore, we propose an in-house pipeline to use with open-access tools, such as QIIME2 and PICRUSt 2, in downstream bioinformatic analyses.

RESULTS: As hypothesized, distinctive bacterial community profiles were observed for each analyzed HR. A higher number of bacterial taxa were detected with the V3 and V6-V7 regions. Conversely, the V8 and V9 regions were less informative, as we detected a lower number of taxa. The synergistic information of these HRs suggests that the GI microbiota of Zalophus californianus pups is predominated by five bacterial phyla: Proteobacteria (~50%), Bacteroidetes (~20%), Firmicutes (~18%), Fusobacteria (~7%), and Epsilonbacteraeota (~4%). Notably, our results differ at times from previously reported abundance profiles, which may promote re-evaluations of the GI bacterial compositions in sea lions and other pinniped species that have been reported to date. Moreover, consistent geographic differences were observed only with the V3, V4, and V6-V7 regions. In addition, these HRs also presented higher numbers of predicted molecular pathways, although no significant functional changes were apparent. Together, our results suggests that multi-locus analysis should be encouraged in GI microbial surveys, as single-locus approaches may result in misleading structural results that hamper the identification of structurally related microbiome features.}, } @article {pmid35832621, year = {2022}, author = {Balaji, A and Sapoval, N and Seto, C and Leo Elworth, RA and Fu, Y and Nute, MG and Savidge, T and Segarra, S and Treangen, TJ}, title = {KOMB: K-core based de novo characterization of copy number variation in microbiomes.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {3208-3222}, pmid = {35832621}, issn = {2001-0370}, support = {U01 AI124290/AI/NIAID NIH HHS/United States ; }, abstract = {Characterizing metagenomes via kmer-based, database-dependent taxonomic classification has yielded key insights into underlying microbiome dynamics. However, novel approaches are needed to track community dynamics and genomic flux within metagenomes, particularly in response to perturbations. We describe KOMB, a novel method for tracking genome level dynamics within microbiomes. KOMB utilizes K-core decomposition to identify Structural variations (SVs), specifically, population-level Copy Number Variation (CNV) within microbiomes. K-core decomposition partitions the graph into shells containing nodes of induced degree at least K, yielding reduced computational complexity compared to prior approaches. Through validation on a synthetic community, we show that KOMB recovers and profiles repetitive genomic regions in the sample. KOMB is shown to identify functionally-important regions in Human Microbiome Project datasets, and was used to analyze longitudinal data and identify keystone taxa in Fecal Microbiota Transplantation (FMT) samples. In summary, KOMB represents a novel graph-based, taxonomy-oblivious, and reference-free approach for tracking CNV within microbiomes. KOMB is open source and available for download at https://gitlab.com/treangenlab/komb.}, } @article {pmid35832425, year = {2022}, author = {Zeng, Q and Zhao, M and Wang, F and Li, Y and Li, H and Zheng, J and Chen, X and Zhao, X and Ji, L and Gao, X and Liu, C and Wang, Y and Cheng, S and Xu, J and Pan, B and Sun, J and Li, Y and Li, D and He, Y and Zheng, L}, title = {Integrating Choline and Specific Intestinal Microbiota to Classify Type 2 Diabetes in Adults: A Machine Learning Based Metagenomics Study.}, journal = {Frontiers in endocrinology}, volume = {13}, number = {}, pages = {906310}, pmid = {35832425}, issn = {1664-2392}, mesh = {Adult ; Betaine/metabolism ; Choline/metabolism ; Cross-Sectional Studies ; *Diabetes Mellitus, Type 2 ; *Gastrointestinal Microbiome/genetics ; Glucose ; Humans ; Machine Learning ; Metagenomics ; Methylamines/metabolism ; *Prediabetic State ; }, abstract = {Emerging evidence is examining the precise role of intestinal microbiota in the pathogenesis of type 2 diabetes. The aim of this study was to investigate the association of intestinal microbiota and microbiota-generated metabolites with glucose metabolism systematically in a large cross-sectional study in China. 1160 subjects were divided into three groups based on their glucose level: normal glucose group (n=504), prediabetes group (n=394), and diabetes group (n=262). Plasma concentrations of TMAO, choline, betaine, and carnitine were measured. Intestinal microbiota was measured in a subgroup of 161 controls, 144 prediabetes and 56 diabetes by using metagenomics sequencing. We identified that plasma choline [Per SD of log-transformed change: odds ratio 1.36 (95 confidence interval 1.16, 1.58)] was positively, while betaine [0.77 (0.66, 0.89)] was negatively associated with diabetes, independently of TMAO. Individuals with diabetes could be accurately distinguished from controls by integrating data on choline, and certain microbiota species, as well as traditional risk factors (AUC=0.971). KOs associated with the carbohydrate metabolism pathway were enhanced in individuals with high choline level. The functional shift in the carbohydrate metabolism pathway in high choline group was driven by species Ruminococcus lactaris, Coprococcus catus and Prevotella copri. We demonstrated the potential ability for classifying diabetic population by choline and specific species, and provided a novel insight of choline metabolism linking the microbiota to impaired glucose metabolism and diabetes.}, } @article {pmid35832043, year = {2022}, author = {Tonneau, M and Nolin-Lapalme, A and Kazandjian, S and Auclin, E and Panasci, J and Benlaifaoui, M and Ponce, M and Al-Saleh, A and Belkaid, W and Naimi, S and Mihalcioiu, C and Watson, I and Bouin, M and Miller, W and Hudson, M and Wong, MK and Pezo, RC and Turcotte, S and Bélanger, K and Jamal, R and Oster, P and Velin, D and Richard, C and Messaoudene, M and Elkrief, A and Routy, B}, title = {Helicobacter pylori serology is associated with worse overall survival in patients with melanoma treated with immune checkpoint inhibitors.}, journal = {Oncoimmunology}, volume = {11}, number = {1}, pages = {2096535}, pmid = {35832043}, issn = {2162-402X}, support = {//CIHR/Canada ; }, mesh = {*Carcinoma, Non-Small-Cell Lung/drug therapy ; *Helicobacter Infections/drug therapy/microbiology ; *Helicobacter pylori/physiology ; Humans ; Immune Checkpoint Inhibitors/therapeutic use ; *Lung Neoplasms/drug therapy ; *Melanoma/drug therapy ; Syndrome ; }, abstract = {The microbiome is now regarded as one of the hallmarks of cancer and several strategies to modify the gut microbiota to improve immune checkpoint inhibitor (ICI) activity are being evaluated in clinical trials. Preliminary data regarding the upper gastro-intestinal microbiota indicated that Helicobacter pylori seropositivity was associated with a negative prognosis in patients amenable to ICI. In 97 patients with advanced melanoma treated with ICI, we assessed the impact of H. pylori on outcomes and microbiome composition. We performed H. pylori serology and profiled the fecal microbiome with metagenomics sequencing. Among the 97 patients, 22% were H. pylori positive (Pos). H. pylori Pos patients had a significantly shorter overall survival (p = .02) compared to H. pylori negative (Neg) patients. In addition, objective response rate and progression-free survival were decreased in H. pylori Pos patients. Metagenomics sequencing did not reveal any difference in diversity indexes between the H. pylori groups. At the taxa level, Eubacterium ventriosum, Mediterraneibacter (Ruminococcus) torques, and Dorea formicigenerans were increased in the H. pylori Pos group, while Alistipes finegoldii, Hungatella hathewayi and Blautia producta were over-represented in the H. pylori Neg group. In a second independent cohort of patients with NSCLC, diversity indexes were similar in both groups and Bacteroides xylanisolvens was increased in H. pylori Neg patients. Our results demonstrated that the negative impact of H. pylori on outcomes seem to be independent from the fecal microbiome composition. These findings warrant further validation and development of therapeutic strategies to eradicate H. pylori in immuno-oncology arena.}, } @article {pmid35830374, year = {2022}, author = {Wirta, HK and Bahram, M and Miller, K and Roslin, T and Vesterinen, E}, title = {Reconstructing the ecosystem context of a species: Honey-borne DNA reveals the roles of the honeybee.}, journal = {PloS one}, volume = {17}, number = {7}, pages = {e0268250}, pmid = {35830374}, issn = {1932-6203}, mesh = {Animals ; Bees/genetics ; DNA ; Ecosystem ; *Honey ; Plant Nectar ; Pollination ; }, abstract = {To assess a species' impact on its environment-and the environment's impact upon a species-we need to pinpoint its links to surrounding taxa. The honeybee (Apis mellifera) provides a promising model system for such an exercise. While pollination is an important ecosystem service, recent studies suggest that honeybees can also provide disservices. Developing a comprehensive understanding of the full suite of services and disservices that honeybees provide is a key priority for such a ubiquitous species. In this perspective paper, we propose that the DNA contents of honey can be used to establish the honeybee's functional niche, as reflected by ecosystem services and disservices. Drawing upon previously published genomic data, we analysed the DNA found within 43 honey samples from Northern Europe. Based on metagenomic analysis, we find that the taxonomic composition of DNA is dominated by a low pathogenicity bee virus with 40.2% of the reads, followed by bacteria (16.7%), plants (9.4%) and only 1.1% from fungi. In terms of ecological roles of taxa associated with the bees or taxa in their environment, bee gut microbes dominate the honey DNA, with plants as the second most abundant group. A range of pathogens associated with plants, bees and other animals occur frequently, but with lower relative read abundance, across the samples. The associations found here reflect a versatile the honeybee's role in the North-European ecosystem. Feeding on nectar and pollen, the honeybee interacts with plants-in particular with cultivated crops. In doing so, the honeybee appears to disperse common pathogens of plants, pollinators and other animals, but also microbes potentially protective of these pathogens. Thus, honey-borne DNA helps us define the honeybee's functional niche, offering directions to expound the benefits and drawbacks of the associations to the honeybee itself and its interacting organisms.}, } @article {pmid35829939, year = {2022}, author = {Carvajal-Agudelo, JD and Ramírez-Chaves, HE and Ossa-López, PA and Rivera-Páez, FA}, title = {Bacteria related to tick-borne pathogen assemblages in Ornithodoros cf. hasei (Acari: Argasidae) and blood of the wild mammal hosts in the Orinoquia region, Colombia.}, journal = {Experimental & applied acarology}, volume = {87}, number = {2-3}, pages = {253-271}, pmid = {35829939}, issn = {1572-9702}, support = {112777758193//Ministerio de Ciencia, Tecnología e innovación - Minciencias/ ; }, mesh = {*Acari ; Animals ; *Argasidae ; *Chiroptera ; Colombia ; *Ornithodoros ; RNA, Ribosomal, 16S ; *Rickettsia ; }, abstract = {Interest in research on soft ticks has increased in recent decades, leading to valuable insight into their role as disease vectors. The use of metagenomics-based analyses have helped to elucidate ecological factors involved in pathogen, vector, and host dynamics. To understand the main bacterial assemblages present in Ornithodoros cf. hasei and its mammalian hosts, 84 ticks and 13 blood samples from bat hosts (Chiroptera) were selected, and the 16S rRNA gene V4 region was sequenced in five pools (each one related to each host-tick pairing). Bacterial taxonomic assignment analyses were performed by comparing operational taxonomic units (OTUs) shared between ticks and their host blood. This analysis showed the presence of Proteobacteria (38.8%), Enterobacteriaceae (25%), Firmicutes (12.3%), and Actinobacteria (10.9%) within blood samples, and Rickettsiaceae (39%), Firmicutes (25%), Actinobacteria (13.1%), and Proteobacteria (9%) within ticks. Species related to potentially pathogenic genera were detected in ticks, such as Borrelia sp., Bartonella tamiae, Ehrlichia sp. and Rickettsia-like endosymbiont, and the presence of these organisms was found in all analyzed bat species (Cynomops planirostris, Molossus pretiosus, Noctilio albiventris), and O. cf. hasei. About 41-48.6% of bacterial OTUs (genera and species) were shared between ticks and the blood of bat hosts. Targeted metagenomic screening techniques allowed the detection of tick-associated pathogens for O. cf. hasei and small mammals for the first time, enabling future research on many of these pathogens.}, } @article {pmid35822810, year = {2022}, author = {Senn, S and Pangell, K and Bowerman, AL}, title = {Metagenomic Insights into the Composition and Function of Microbes Associated with the Rootzone of Datura inoxia.}, journal = {Biotech (Basel (Switzerland))}, volume = {11}, number = {1}, pages = {}, pmid = {35822810}, issn = {2673-6284}, abstract = {The purpose of this paper is to elucidate the roles that microbes may be playing in the rootzone of the medicinal plant Daturainoxia. We hypothesized that the microbes associated with the Datura rootzone would be significantly different than the similar surrounding fields in composition and function. We also hypothesized that rhizospheric and endophytic microbes would be associated with similar metabolic functions to the plant rootzone they inhabited. The methods employed were microbial barcoding, tests of essential oils against antibiotic resistant bacteria and other soil bacterial isolates, 16S Next Generation Sequencing (NGS) metabarcoding, and Whole Genome Shotgun (WGS) taxonomic and functional analyses. A few of the main bacterial genera of interest that were differentially abundant in the Datura root microbiome were Flavobacterium (p = 0.007), Chitinophaga (p = 0.0007), Pedobacter (p = 6 × 10[-5]), Bradyhizobium (p = 1 × 10[-8]), and Paenibacillus (p = 1.46 × 10[-6]). There was significant evidence that the microbes associated with the Datura rootzone had elevated function related to bacterial chalcone synthase (p = 1.49 × 10[-3]) and permease genes (p < 0.003). There was some evidence that microbial functions in the Datura rootzone provided precursors to important plant bioactive molecules or were beneficial to plant growth. This is important because these compounds are phyto-protective antioxidants and are precursors to many aromatic bioactive compounds that are relevant to human health. In the context of known interactions, and current results, plants and microbes influence the flavonoid biosynthetic pathways of one other, in terms of the regulation of the phenylpropanoid pathway. This is the first study to focus on the microbial ecology of the Datura rootzone. There are possible biopharmaceutical and agricultural applications of the natural interplay that was discovered during this study of the Datura inoxia rhizosphere.}, } @article {pmid35822382, year = {2022}, author = {Lin, Y and Li, J and Li, Y}, title = {[Metagenome-wide association of gut microbiome features in children with moderate-severe house dust mite allergic rhinitis].}, journal = {Lin chuang er bi yan hou tou jing wai ke za zhi = Journal of clinical otorhinolaryngology, head, and neck surgery}, volume = {36}, number = {7}, pages = {533-539}, pmid = {35822382}, issn = {2096-7993}, mesh = {Animals ; Child ; Child, Preschool ; *Gastrointestinal Microbiome ; Humans ; Metagenome ; *Microbiota ; Pyroglyphidae ; *Rhinitis, Allergic ; *Rhinitis, Allergic, Perennial ; }, abstract = {Objective:To draw a distinct gut microbiota pattern of children with moderate-severe dust mite-induced allergic rhinitis（DAR） and healthy children. Methods:3-10 years old moderate-severe DAR children（68 cases） and healthy children（38 cases） were involved in this study. General information was collected through questionnaires, and fecal samples were collected for metagenomic sequencing. MetaPhlAn3 was used to generate the microbiota composition abundance in detail, and Alpha and Beta diversity changes were calculated. The difference in species abundance at different taxonomic levels were compared. Differences in functional pathways were compared by LEfSe analysis. Results:The diversity of gut microbiota in children with moderate-severe DAR didn't change significantly compared with healthy children. A total of 37 microbial communities or species with significant abundance difference were found, mainly included Lachnoclostridium, Prevotella, Blautia wexlerae, Prevotella copri, Eubacterium eligens, Eubacterium sp CAG 180, etc. However, the metabolism functions of gut microbiota in children with moderate-severe DAR changed compared with healthy children. Various of fatty acids anabolism enhanced in DAR children. Conclusion:Compared with healthy children, there was no significant difference in gut microbial diversity in moderate-severe DAR children. The abundance of a series of specific microbe species had a marked alteration in DAR, accompanied with changes in certain microbial functional pathways.}, } @article {pmid35821155, year = {2022}, author = {Wickramarachchi, A and Lin, Y}, title = {Binning long reads in metagenomics datasets using composition and coverage information.}, journal = {Algorithms for molecular biology : AMB}, volume = {17}, number = {1}, pages = {14}, pmid = {35821155}, issn = {1748-7188}, abstract = {BACKGROUND: Advancements in metagenomics sequencing allow the study of microbial communities directly from their environments. Metagenomics binning is a key step in the species characterisation of microbial communities. Next-generation sequencing reads are usually assembled into contigs for metagenomics binning mainly due to the limited information within short reads. Third-generation sequencing provides much longer reads that have lengths similar to the contigs assembled from short reads. However, existing contig-binning tools cannot be directly applied on long reads due to the absence of coverage information and the presence of high error rates. The few existing long-read binning tools either use only composition or use composition and coverage information separately. This may ignore bins that correspond to low-abundance species or erroneously split bins that correspond to species with non-uniform coverages. Here we present a reference-free binning approach, LRBinner, that combines composition and coverage information of complete long-read datasets. LRBinner also uses a distance-histogram-based clustering algorithm to extract clusters with varying sizes.

RESULTS: The experimental results on both simulated and real datasets show that LRBinner achieves the best binning accuracy in most cases while handling the complete datasets without any sampling. Moreover, we show that binning reads using LRBinner prior to assembly reduces computational resources required for assembly while attaining satisfactory assembly qualities.

CONCLUSION: LRBinner shows that deep-learning techniques can be used for effective feature aggregation to support the metagenomics binning of long reads. Furthermore, accurate binning of long reads supports improvements in metagenomics assembly, especially in complex datasets. Binning also helps to reduce the resources required for assembly. Source code for LRBinner is freely available at https://github.com/anuradhawick/LRBinner.}, } @article {pmid35820782, year = {2022}, author = {Inamura, K and Hamada, T and Bullman, S and Ugai, T and Yachida, S and Ogino, S}, title = {Cancer as microenvironmental, systemic and environmental diseases: opportunity for transdisciplinary microbiomics science.}, journal = {Gut}, volume = {}, number = {}, pages = {}, pmid = {35820782}, issn = {1468-3288}, support = {R00 CA229984/CA/NCI NIH HHS/United States ; R01 CA248857/CA/NCI NIH HHS/United States ; R35 CA197735/CA/NCI NIH HHS/United States ; }, abstract = {Cancer is generally regarded as a localised disease, with the well-established role of the tumour microenvironment. However, the realm of cancer goes beyond the tumour microenvironment, and cancer should also be regarded as a systemic and environmental disease. The exposome (ie, the totality of exposures), which encompasses diets, supplements, smoking, alcohol, other lifestyle factors, medications, etc, likely alters the microbiome (inclusive of bacteria, viruses, archaea, fungi, parasites, etc) and immune system in various body sites and influences tumour phenotypes. The systemic metabolic/inflammatory status, which is likely influenced by exposures and intestinal physiological changes, may affect tissue microenvironment of colorectum and any other organs. Germline genomic factors can modify disease phenotypes via gene-by-environment interactions. Although challenges exist, it is crucial to advance not only basic experimental research that can analyse the effects of exposures, microorganisms and microenvironmental components on tumour evolution but also interdisciplinary human population research that can dissect the complex pathogenic roles of the exposome, microbiome and immunome. Metagenomic, metatranscriptomic and metabolomic analyses should be integrated into well-designed population research combined with advanced methodologies of artificial intelligence and molecular pathological epidemiology. Ideally, a prospective cohort study design that enables biospecimen (such as stool) collection before disease detection should be considered to address reverse causation and recall biases. Robust experimental and observational research together can provide insights into dynamic interactions between environmental exposures, microbiota, tumour and immunity during carcinogenesis processes, thereby helping us develop precision prevention and therapeutic strategies to ultimately reduce the cancer burden.}, } @article {pmid35820512, year = {2022}, author = {Ning, SY and Xiao, YQ and Qian, YC and Feng, ZH and Dai, ZY and Zhang, W and Wang, H and Tang, YJ}, title = {Viromic analysis of feces from laboratory rabbits reveals a new Circovirus.}, journal = {Virus research}, volume = {319}, number = {}, pages = {198861}, doi = {10.1016/j.virusres.2022.198861}, pmid = {35820512}, issn = {1872-7492}, mesh = {Animals ; *Bird Diseases ; Birds ; *Circoviridae Infections ; *Circovirus/genetics ; Feces ; Humans ; Mammals ; Phylogeny ; Rabbits ; }, abstract = {BACKGROUND: Members of the genus Circovirus with the family Circoviridae are responsible for fatal diseases that can affect mammals and birds. Beak and feather disease virus (BFDV) is responsible for fatal diseases that could affect birds, causing the psittacine beak and feather disease. The current study discovered a new Circovirus from feces of laboratory rabbits and name it RabCV, which shows close relationship to BFDVs.

RESULTS: We investigated the feces virome of 10 laboratory rabbits using the viral metagenomic method. In these samples, we detected a new rabbit-associated Circovirus (RabCV) and performed phylogenetic analysis based on replication-associated (Rep) protein. The result showed that the RabCV was closely clustered with BFDVs, sharing the identity of 56.7%-57.2% with them based on the whole genome sequence. PCR screening in a cohort of 38 laboratory rabbits showed that 3 out of the 38 rabbits were positive for this new rabbit-associated Circovirus.

CONCLUSION: A new Circovirus was discovered from feces of rabbits, which showed low prevalence in the healthy laboratory rabbits. BFDV is responsible for fatal diseases that could affect birds, which suggested that the potential threat of the new rabbit-associated Circovirus to the health of laboratory rabbits needs further study.}, } @article {pmid35819612, year = {2022}, author = {Tremblay, ÉD and Bilodeau, GJ}, title = {Biomonitoring of Fungal and Oomycete Plant Pathogens by Using Metabarcoding.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2536}, number = {}, pages = {309-346}, pmid = {35819612}, issn = {1940-6029}, mesh = {*Biological Monitoring ; DNA Primers/genetics ; Ecosystem ; *Oomycetes/genetics ; Plants ; }, abstract = {Fungal and oomycete plant pathogens are responsible for the devastation of various ecosystems such as forest and crop species worldwide. In an effort to protect such natural resources for food, lumber, etc., early detection of non-indigenous phytopathogenic fungi in new areas is a key approach in managing threats at their source of introduction. A workflow was developed using high-throughput sequencing (HTS), more specifically metabarcoding, a method for rapid and higher throughput species screening near high-risk areas, and over larger geographical spaces. Biomonitoring of fungal and oomycete entities of plant pathogens (e.g., airborne spores) regained from environmental samples and their processing by metabarcoding is thoroughly described here. The amplicon-based approach goes from DNA and sequencing library preparation using custom-designed polymerase chain reaction (PCR) fusion primers that target the internal transcribed spacer 1 (ITS1) from fungi and oomycetes and extends to multiplex HTS with the Ion Torrent platform. In addition, a brief and simplified overview of the bioinformatics analysis pipeline and other available tools required to process amplicon sequences is also included. The raw data obtained and processed enable users to select a bioinformatics pipeline in order to directly perform biodiversity, presence/absence, geographical distribution, and abundance analyses through the tools suggested, which allows for accelerated identification of phytopathogens of interest.}, } @article {pmid35819600, year = {2022}, author = {Vettraino, AM and Luchi, N}, title = {A Rapid Method for Extracting High-Quality DNA from Soils.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2536}, number = {}, pages = {103-107}, pmid = {35819600}, issn = {1940-6029}, mesh = {DNA/genetics ; DNA, Bacterial/genetics ; Metagenomics/methods ; *Soil/chemistry ; *Soil Microbiology ; }, abstract = {Metagenomics offers the possibility to study the microbial community of soils at large scale, allowing the characterization also of unculturable microorganisms. Availability of high-quality DNA is a prerequisite of this approach. However, since soils have highly heterogeneous physicochemical properties, several parameters need to be considered for the development of the best molecular practices. A method for isolation of high-molecular-weight and good-quality metagenomic DNA from different soil samples is described here. The protocol combines physical and chemical strategies to ensure efficient cell lysis and precipitation of humic impurities-free DNA suitable for downstream processing for metagenomics study.}, } @article {pmid35819265, year = {2022}, author = {Rubiola, S and Macori, G and Civera, T and Fanning, S and Mitchell, M and Chiesa, F}, title = {Comparison Between Full-Length 16S rRNA Metabarcoding and Whole Metagenome Sequencing Suggests the Use of Either Is Suitable for Large-Scale Microbiome Studies.}, journal = {Foodborne pathogens and disease}, volume = {19}, number = {7}, pages = {495-504}, doi = {10.1089/fpd.2022.0027}, pmid = {35819265}, issn = {1556-7125}, mesh = {High-Throughput Nucleotide Sequencing/methods ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; Sequence Analysis, DNA ; }, abstract = {Since the number of studies of the microbial communities related to food and food-associated matrices almost completely reliant on next-generation sequencing techniques is rising, evaluations of these high-throughput methods are critical. Currently, the two most used sequencing methods to profile the microbiota of complex samples, including food and food-related matrices, are the 16S ribosomal RNA (rRNA) metabarcoding and the whole metagenome sequencing (WMS), both of which are powerful tools for the monitoring of foodborne pathogens and the investigation of the microbiome. Herein, the microbial profiles of 20 bulk tank milk filters from different dairy farms were investigated using both the full-length 16S (FL-16S) rRNA metabarcoding, a third-generation sequencing method whose application in food and food-related matrices is yet in its infancy, and the WMS, to evaluate the correlation and the reliability of these two methods to explore the microbiome of food-related matrices. Metabarcoding and metagenomic data were generated on a MinION platform (Oxford Nanopore Technologies) and on a Illumina NovaSeq 6000 platform, respectively. Our findings support the greater resolution of WMS in terms of both increased detection of bacterial taxa and enhanced detection of diversity; in contrast, FL-16S rRNA metabarcoding has proven to be a promising, less expensive, and more practical tool to profile most abundant taxa. The significant correlation of the two technologies both in terms of taxa diversity and richness, together with the similar profiles defined for both highly abundant taxa and core microbiomes, including Acinetobacter, Bacillus, and Escherichia genera, highlights the possible application of both methods for different purposes. This study allowed the first comparison of FL-16S rRNA sequencing and WMS to investigate the microbial composition of a food-related matrix, pointing out the advantageous use of FL-16S rRNA to identify dominant microorganisms and the superior power of WMS for the taxonomic detection of low abundant microorganisms and to perform functional analysis of the microbial communities.}, } @article {pmid35818751, year = {2022}, author = {Hassan, S and Sabreena, and Khurshid, Z and Bhat, SA and Kumar, V and Ameen, F and Ganai, BA}, title = {Marine bacteria and omic approaches: A novel and potential repository for bioremediation assessment.}, journal = {Journal of applied microbiology}, volume = {133}, number = {4}, pages = {2299-2313}, doi = {10.1111/jam.15711}, pmid = {35818751}, issn = {1365-2672}, mesh = {Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Ecosystem ; *Environmental Pollutants/metabolism ; Hydrocarbons/metabolism ; *Xenobiotics/metabolism ; }, abstract = {Marine environments accommodating diverse assortments of life constitute a great pool of differentiated natural resources. The cumulative need to remedy unpropitious effects of anthropogenic activities on estuaries and coastal marine ecosystems has propelled the development of effective bioremediation strategies. Marine bacteria producing biosurfactants are promising agents for bio-remediating oil pollution in marine environments, making them prospective candidates for enhancing oil recovery. Molecular omics technologies are considered an emerging field of research in ecological and diversity assessment owing to their utility in environmental surveillance and bioremediation of polluted sites. A thorough literature review was undertaken to understand the applicability of different omic techniques used for bioremediation assessment using marine bacteria. This review further establishes that for bioremediation of environmental pollutants (i.e. heavy metals, hydrocarbons, xenobiotic and numerous recalcitrant compounds), organisms isolated from marine environments can be better used for their removal. The literature survey shows that omics approaches can provide exemplary knowledge about microbial communities and their role in the bioremediation of environmental pollutants. This review centres on applications of marine bacteria in enhanced bioremediation, using the omics approaches that can be a vital biological contrivance in environmental monitoring to tackle environmental degradation. The paper aims to identify the gaps in investigations involving marine bacteria to help researchers, ecologists and decision-makers to develop a holistic understanding regarding their utility in bioremediation assessment.}, } @article {pmid35818068, year = {2022}, author = {Serpa, PH and Deng, X and Abdelghany, M and Crawford, E and Malcolm, K and Caldera, S and Fung, M and McGeever, A and Kalantar, KL and Lyden, A and Ghale, R and Deiss, T and Neff, N and Miller, SA and Doernberg, SB and Chiu, CY and DeRisi, JL and Calfee, CS and Langelier, CR}, title = {Metagenomic prediction of antimicrobial resistance in critically ill patients with lower respiratory tract infections.}, journal = {Genome medicine}, volume = {14}, number = {1}, pages = {74}, pmid = {35818068}, issn = {1756-994X}, support = {K23 HL138461/HL/NHLBI NIH HHS/United States ; R01 HL155418/HL/NHLBI NIH HHS/United States ; R35 HL140026/HL/NHLBI NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *Bacterial Infections ; Critical Illness ; Drug Resistance, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; RNA ; *Respiratory Tract Infections/diagnosis/drug therapy/microbiology ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is rising at an alarming rate and complicating the management of infectious diseases including lower respiratory tract infections (LRTI). Metagenomic next-generation sequencing (mNGS) is a recently established method for culture-independent LRTI diagnosis, but its utility for predicting AMR has remained unclear. We aimed to assess the performance of mNGS for AMR prediction in bacterial LRTI and demonstrate proof of concept for epidemiological AMR surveillance and rapid AMR gene detection using Cas9 enrichment and nanopore sequencing.

METHODS: We studied 88 patients with acute respiratory failure between 07/2013 and 9/2018, enrolled through a previous observational study of LRTI. Inclusion criteria were age ≥ 18, need for mechanical ventilation, and respiratory specimen collection within 72 h of intubation. Exclusion criteria were decline of study participation, unclear LRTI status, or no matched RNA and DNA mNGS data from a respiratory specimen. Patients with LRTI were identified by clinical adjudication. mNGS was performed on lower respiratory tract specimens. The primary outcome was mNGS performance for predicting phenotypic antimicrobial susceptibility and was assessed in patients with LRTI from culture-confirmed bacterial pathogens with clinical antimicrobial susceptibility testing (n = 27 patients, n = 32 pathogens). Secondary outcomes included the association between hospital exposure and AMR gene burden in the respiratory microbiome (n = 88 patients), and AMR gene detection using Cas9 targeted enrichment and nanopore sequencing (n = 10 patients).

RESULTS: Compared to clinical antimicrobial susceptibility testing, the performance of respiratory mNGS for predicting AMR varied by pathogen, antimicrobial, and nucleic acid type sequenced. For gram-positive bacteria, a combination of RNA + DNA mNGS achieved a sensitivity of 70% (95% confidence interval (CI) 47-87%) and specificity of 95% (CI 85-99%). For gram-negative bacteria, sensitivity was 100% (CI 87-100%) and specificity 64% (CI 48-78%). Patients with hospital-onset LRTI had a greater AMR gene burden in their respiratory microbiome versus those with community-onset LRTI (p = 0.00030), or those without LRTI (p = 0.0024). We found that Cas9 targeted sequencing could enrich for low abundance AMR genes by > 2500-fold and enabled their rapid detection using a nanopore platform.

CONCLUSIONS: mNGS has utility for the detection and surveillance of resistant bacterial LRTI pathogens.}, } @article {pmid35818006, year = {2022}, author = {Mesa, V}, title = {Rhizosphere and Endosphere Bacterial Communities Survey by Metagenomics Approach.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2512}, number = {}, pages = {181-197}, doi = {10.1007/978-1-0716-2429-6_11}, pmid = {35818006}, issn = {1940-6029}, mesh = {Bacteria/genetics ; *Metagenomics ; Plant Roots/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; *Rhizosphere ; Soil Microbiology ; }, abstract = {The diversity of microbes associated with plant roots is in the order of tens of thousands of species. It is estimated that only 0.1-1.0% of the living bacteria present in soils can be cultured under standard conditions. The microbial marker-gene sequence data and the next-generation sequencing technologies have enabled systemic studies of root-associated microbiomes. Molecular techniques can be used to generate comprehensive taxonomic profiles of the microorganisms present in roots. The aim of this chapter is to provide a standard method for the obtention of rhizosphere and endosphere fractions, and a generic workflow of the Quantitative Insights Into Microbial Ecology version 2 (QIIME2) software to analysis of 16S rRNA marker-gene.}, } @article {pmid35818005, year = {2022}, author = {Garfias-Gallegos, D and Zirión-Martínez, C and Bustos-Díaz, ED and Arellano-Fernández, TV and Lovaco-Flores, JA and Espinosa-Jaime, A and Avelar-Rivas, JA and Sélem-Mójica, N}, title = {Metagenomics Bioinformatic Pipeline.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2512}, number = {}, pages = {153-179}, pmid = {35818005}, issn = {1940-6029}, mesh = {Computational Biology/methods ; Metagenome ; *Metagenomics/methods ; *Microbiota ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {Microbial communities' taxonomic and functional diversity has been broadly studied since sequencing technologies enabled faster and cheaper data obtainment. Nevertheless, the programming skills needed and the amount of software available may be overwhelming to someone trying to analyze these data. Here, we present a comprehensive and straightforward pipeline that takes shotgun metagenomics data through the needed steps to obtain valuable results. The raw data goes through a quality control process, metagenomic assembly, binning (the obtention of single genomes from a metagenome), taxonomic assignment, and taxonomic diversity analysis and visualization.}, } @article {pmid35817360, year = {2022}, author = {Rodriguez-Diaz, C and Taminiau, B and García-García, A and Cueto, A and Robles-Díaz, M and Ortega-Alonso, A and Martín-Reyes, F and Daube, G and Sanabria-Cabrera, J and Jimenez-Perez, M and Isabel Lucena, M and Andrade, RJ and García-Fuentes, E and García-Cortes, M}, title = {Microbiota diversity in nonalcoholic fatty liver disease and in drug-induced liver injury.}, journal = {Pharmacological research}, volume = {182}, number = {}, pages = {106348}, doi = {10.1016/j.phrs.2022.106348}, pmid = {35817360}, issn = {1096-1186}, mesh = {Bacteria ; *Chemical and Drug Induced Liver Injury/metabolism ; *Gastrointestinal Microbiome ; Humans ; Liver/metabolism ; Liver Cirrhosis/metabolism ; Metagenome ; *Non-alcoholic Fatty Liver Disease/metabolism ; }, abstract = {The gut microbiota could play a significant role in the progression of nonalcoholic fatty liver disease (NAFLD); however, its relevance in drug-induced liver injury (DILI) remains unexplored. Since the two hepatic disorders may share damage pathways, we analysed the metagenomic profile of the gut microbiota in NAFLD, with or without significant liver fibrosis, and in DILI, and we identified the main associated bacterial metabolic pathways. In the NAFLD group, we found a decrease in Alistipes, Barnesiella, Eisenbergiella, Flavonifractor, Fusicatenibacter, Gemminger, Intestinimonas, Oscillibacter, Parasutterella, Saccharoferementans and Subdoligranulum abundances compared with those in both the DILI and control groups. Additionally, we detected an increase in Enterobacter, Klebsiella, Sarcina and Turicibacter abundances in NAFLD, with significant liver fibrosis, compared with those in NAFLD with no/mild liver fibrosis. The DILI group exhibited a lower microbial bacterial richness than the control group, and lower abundances of Acetobacteroides, Blautia, Caloramator, Coprococcus, Flavobacterium, Lachnospira, Natronincola, Oscillospira, Pseudobutyrivibrio, Shuttleworthia, Themicanus and Turicibacter compared with those in the NAFLD and control groups. We found seven bacterial metabolic pathways that were impaired only in DILI, most of which were associated with metabolic biosynthesis. In the NAFLD group, most of the differences in the bacterial metabolic pathways found in relation to those in the DILI and control groups were related to fatty acid and lipid biosynthesis. In conclusion, we identified a distinct bacterial profile with specific bacterial metabolic pathways for each type of liver disorder studied. These differences can provide further insight into the physiopathology and development of NAFLD and DILI.}, } @article {pmid35817298, year = {2022}, author = {Zhang, T and Ji, Z and Li, J and Yu, L}, title = {Metagenomic insights into the antibiotic resistome in freshwater and seawater from an Antarctic ice-free area.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {309}, number = {}, pages = {119738}, doi = {10.1016/j.envpol.2022.119738}, pmid = {35817298}, issn = {1873-6424}, mesh = {Antarctic Regions ; *Anti-Bacterial Agents ; Bacteria/genetics ; Fresh Water ; Genes, Bacterial ; Humans ; *Metagenome ; Metagenomics/methods ; Seawater ; Water ; }, abstract = {The comprehensive profiles of antibiotic resistance genes (ARGs) in the Antarctic water environments and their potential health risks are not well understood. The present study characterized the bacterial community compositions and ARG profiles of freshwater (11 samples) and seawater (28 samples) around the Fildes Region (an ice-free area in Antarctica) using a shotgun metagenomic sequencing approach for the first time. There were significant differences in the compositions of the bacterial community and ARG profiles between freshwater and seawater. In the 39 water samples, 114 ARG subtypes belonging to 15 ARG types were detectable. In freshwater, the dominant ARGs were related to multidrug and rifamycin resistance. In seawater, the dominant ARGs were related to peptide, multidrug, and beta-lactam resistance. Both the bacterial community compositions and ARG profiles were significantly related to certain physicochemical properties (e.g., pH, salinity, NO3[-]). Procrustes analysis revealed a significant correlation between the bacterial community compositions and ARG profiles of freshwater and seawater samples. A total of 31 metagenome-assembled genomes (MAGs) carrying 35 ARG subtypes were obtained and identified. The results will contribute to a better evaluation of the ARG contamination in relation to human health in the Antarctic aquatic environments.}, } @article {pmid35817120, year = {2022}, author = {Keerthana Devi, M and Karmegam, N and Manikandan, S and Subbaiya, R and Song, H and Kwon, EE and Sarkar, B and Bolan, N and Kim, W and Rinklebe, J and Govarthanan, M}, title = {Removal of nanoplastics in water treatment processes: A review.}, journal = {The Science of the total environment}, volume = {845}, number = {}, pages = {157168}, doi = {10.1016/j.scitotenv.2022.157168}, pmid = {35817120}, issn = {1879-1026}, mesh = {*Drinking Water ; Ecosystem ; Microplastics ; Plastics ; *Water Pollutants, Chemical/analysis ; *Water Purification ; }, abstract = {Nanoplastics are drawing a significant attention as a result of their propensity to spread across the environment and pose a threat to all organisms. The presence of nanoplastics in water is given attention nowadays as the transit of nanoplastics occurs through the aquatic ecosphere besides terrestrial mobility. The principal removal procedures for macro-and micro-plastic particles are effective, but nanoparticles escape from the treatment, increasing in the water and significantly influencing the society. This critical review is aimed to bestow the removal technologies of nanoplastics from aquatic ecosystems, with a focus on the treatment of freshwater, drinking water, and wastewater, as well as the importance of transit and its impact on health concerns. Still, there exists a gap in providing a collective knowledge on the methods available for nanoplastics removal. Hence, this review offered various nanoplastic removal technologies (microorganism-based degradation, membrane separation with a reactor, and photocatalysis) that could be the practical/effective measures along with the traditional procedures (filtration, coagulation, centrifugation, flocculation, and gravity settling). From the analyses of different treatment systems, the effectiveness of nanoplastics removal depends on various factors, source, size, and type of nanoplastics apart from the treatment method adopted. Combined removal methods, filtration with coagulation offer great scope for the removal of nanoplastics from drinking water with >99 % efficiency. The collected data could serve as base-line information for future research and development in water nanoplastics cleanup.}, } @article {pmid35816485, year = {2022}, author = {Li, X and Xiao, T and Hu, P and Yan, K and Wu, J and Tu, X and Tang, Y and Xia, H}, title = {Clinical, radiological and pathological characteristics of moderate to fulminant psittacosis pneumonia.}, journal = {PloS one}, volume = {17}, number = {7}, pages = {e0270896}, pmid = {35816485}, issn = {1932-6203}, mesh = {Aged ; Aged, 80 and over ; Anti-Bacterial Agents/therapeutic use ; *Chlamydial Pneumonia ; *Chlamydophila psittaci/genetics ; Humans ; Hyperplasia/drug therapy ; Middle Aged ; *Pneumonia/drug therapy ; *Psittacosis/diagnostic imaging/drug therapy ; Retrospective Studies ; beta-Lactams/therapeutic use ; }, abstract = {BACKGROUND: Psittacosis pneumonia is a community-acquired pneumonia caused by Chlamydia psittaci. It is usually under-diagnosed due to its atypical clinical presentation and lack of routine laboratory tests.

METHODS: To better understand the clinical features, 52 patients diagnosed with psittacosis pneumonia by metagenomic next-generation sequencing (mNGS) were enrolled in this study. The clinical, radiological and pathological characteristics were retrospectively analyzed.

RESULTS: The onset of psittacosis pneumonia in this study occurred all year round, with a peak from December to January. Most of the patients were 51-80 years old. About 65.38% of patients had a history of exposure to poultry or parrots. Abnormalities of multiple clinical signals were detected in these patients. Elevated levels of neutrophil ratio, C-reactive protein, erythrocyte sedimentation rate, and procalcitonin were detected in most patients. Radiological evidence revealed air-space consolidation or ground-glass opacities in lungs of all patients, which is the typical feature of psittacosis pneumonia. In addition, hyperemia, swelling of bronchial mucosa, and bronchial patency were detected by bronchoscopy in all patients, and bronchial sub-mucosal edema, inflammatory cells infiltration and alveolar epithelial hyperplasia were identified in the bronchial mucosa and alveolar tissue. Beta-lactam antibiotics were administered for empirical treatment before mNGS in 17 patients but showed no improvement. The treatment was switched to doxycycline or moxifloxacin immediately since psittacosis pneumonia were suspected and confirmed by mNGS detection (within 48 hours). After receiving adjustment of treatment, 94.23% (49/52) of patients were cured successfully.

CONCLUSIONS: In conclusion, mNGS may be a promising approach for clinical diagnosis of psittacosis. For patients with a history of exposure to birds, hyperpyrexia, nonproductive cough, multiple elevated inflammatory markers, and air-space consolidation in lung, psittacosis pneumonia should be considered, especially when beta-lactam antibiotics showed limited efficacy.}, } @article {pmid35814706, year = {2022}, author = {Li, X and Lu, C and Dai, Y and Yu, Z and Gu, W and Li, T and Li, X and Li, X and Wang, X and Su, Z and Xu, M and Zhang, H}, title = {Characterizing the Microbial Consortium L1 Capable of Efficiently Degrading Chlorimuron-Ethyl via Metagenome Combining 16S rDNA Sequencing.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {912312}, pmid = {35814706}, issn = {1664-302X}, abstract = {Excessive application of the herbicide chlorimuron-ethyl (CE) severely harms subsequent crops and poses severe risks to environmental health. Therefore, methods for efficiently decreasing and eliminating CE residues are urgently needed. Microbial consortia show potential for bioremediation due to their strong metabolic complementarity and synthesis. In this study, a microbial consortium entitled L1 was enriched from soil contaminated with CE by a "top-down" synthetic biology strategy. The consortium could degrade 98.04% of 100 mg L[-1] CE within 6 days. We characterized it from the samples at four time points during the degradation process and a sample without degradation activity via metagenome and 16S rDNA sequencing. The results revealed 39 genera in consortium L1, among which Methyloversatilis (34.31%), Starkeya (28.60%), and Pseudoxanthomonas (7.01%) showed relatively high abundances. Temporal succession and the loss of degradability did not alter the diversity and community composition of L1 but changed the community structure. Taxon-functional contribution analysis predicted that glutathione transferase [EC 2.5.1.18], urease [EC 3.5.1.5], and allophanate hydrolase [EC 3.5.1.54] are relevant for the degradation of CE and that Methyloversatilis, Pseudoxanthomonas, Methylopila, Hyphomicrobium, Stenotrophomonas, and Sphingomonas were the main degrading genera. The degradation pathway of CE by L1 may involve cleavage of the CE carbamide bridge to produce 2-amino-4-chloro-6-methoxypyrimidine and ethyl o-sulfonamide benzoate. The results of network analysis indicated close interactions, cross-feeding, and co-metabolic relationships between strains in the consortium, and most of the above six degrading genera were keystone taxa in the network. Additionally, the degradation of CE by L1 required not only "functional bacteria" with degradation capacity but also "auxiliary bacteria" without degradation capacity but that indirectly facilitate/inhibit the degradation process; however, the abundance of "auxiliary bacteria" should be controlled in an appropriate range. These findings improve the understanding of the synergistic effects of degrading bacterial consortia, which will provide insight for isolating degrading bacterial resources and constructing artificial efficient bacterial consortia. Furthermore, our results provide a new route for pollution control and biodegradation of sulfonylurea herbicides.}, } @article {pmid35814702, year = {2022}, author = {Armoni, R and Borenstein, E}, title = {Temporal Alignment of Longitudinal Microbiome Data.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {909313}, pmid = {35814702}, issn = {1664-302X}, abstract = {A major challenge in working with longitudinal data when studying some temporal process is the fact that differences in pace and dynamics might overshadow similarities between processes. In the case of longitudinal microbiome data, this may hinder efforts to characterize common temporal trends across individuals or to harness temporal information to better understand the link between the microbiome and the host. One possible solution to this challenge lies in the field of "temporal alignment" - an approach for optimally aligning longitudinal samples obtained from processes that may vary in pace. In this work we investigate the use of alignment-based analysis in the microbiome domain, focusing on microbiome data from infants in their first years of life. Our analyses center around two main use-cases: First, using the overall alignment score as a measure of the similarity between microbiome developmental trajectories, and showing that this measure can capture biological differences between individuals. Second, using the specific matching obtained between pairs of samples in the alignment to highlight changes in pace and temporal dynamics, showing that it can be utilized to predict the age of infants based on their microbiome and to uncover developmental delays. Combined, our findings serve as a proof-of-concept for the use of temporal alignment as an important and beneficial tool in future longitudinal microbiome studies.}, } @article {pmid35814698, year = {2022}, author = {Pascual-García, A and Schwartzman, J and Enke, TN and Iffland-Stettner, A and Cordero, OX and Bonhoeffer, S}, title = {Turnover in Life-Strategies Recapitulates Marine Microbial Succession Colonizing Model Particles.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {812116}, pmid = {35814698}, issn = {1664-302X}, abstract = {Particulate organic matter (POM) in the ocean sustains diverse communities of bacteria that mediate the remineralization of organic complex matter. However, the variability of these particles and of the environmental conditions surrounding them present a challenge to the study of the ecological processes shaping particle-associated communities and their function. In this work, we utilize data from experiments in which coastal water communities are grown on synthetic particles to ask which are the most important ecological drivers of their assembly and associated traits. Combining 16S rRNA amplicon sequencing with shotgun metagenomics, together with an analysis of the full genomes of a subset of isolated strains, we were able to identify two-to-three distinct community classes, corresponding to early vs. late colonizers. We show that these classes are shaped by environmental selection (early colonizers) and facilitation (late colonizers) and find distinctive traits associated with each class. While early colonizers have a larger proportion of genes related to the uptake of nutrients, motility, and environmental sensing with few pathways enriched for metabolism, late colonizers devote a higher proportion of genes for metabolism, comprising a wide array of different pathways including the metabolism of carbohydrates, amino acids, and xenobiotics. Analysis of selected pathways suggests the existence of a trophic-chain topology connecting both classes for nitrogen metabolism, potential exchange of branched chain amino acids for late colonizers, and differences in bacterial doubling times throughout the succession. The interpretation of these traits suggests a distinction between early and late colonizers analogous to other classifications found in the literature, and we discuss connections with the classical distinction between r- and K-strategists.}, } @article {pmid35814657, year = {2022}, author = {Zhou, Z and Tang, L and Yan, L and Jia, H and Xiong, Y and Shang, J and Shao, C and Zhang, Q and Wang, H and He, L and Hu, D and Zhang, D}, title = {Wild and Captive Environments Drive the Convergence of Gut Microbiota and Impact Health in Threatened Equids.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {832410}, pmid = {35814657}, issn = {1664-302X}, abstract = {To explore how the living environment influences the establishment of gut microbiota in different species, as well as the extent to which changes in the living environment caused by captive breeding affect wildlife's gut microbiota and health, we used 16S rRNA gene amplicon sequencing and shotgun metagenomic sequencing to compare the gut microbiome of two species of threatened equids, the Przewalski's Horse and the Asian wild ass, in the wild and captivity. The results revealed that different species of Equidae living in the same environment showed remarkable convergence of gut microflora. At the same time, captive populations exhibited significantly "unhealthy" microbiota, such as low Alpha diversity, high levels of potentially pathogenic bacteria and biomarkers of physical or psychological disease, and enrichment of microbial functions associated with exogenous exposure and susceptibility, implying that the artificial environment created by captivity may adversely impact the health of wildlife to some extent. Our findings demonstrate the importance of the environmental factors for the establishment of gut microbiota and host health and provide new insights into the conservation of wildlife in captivity from the perspective of the microbiome.}, } @article {pmid35814652, year = {2022}, author = {Varaljay, VA and Charles, TC and Daniel, R}, title = {Editorial: Functional Metagenomics for Enzyme Discovery.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {956106}, pmid = {35814652}, issn = {1664-302X}, } @article {pmid35814645, year = {2022}, author = {Hopf, FSM and Roth, CD and de Souza, EV and Galina, L and Czeczot, AM and Machado, P and Basso, LA and Bizarro, CV}, title = {Bacterial Enoyl-Reductases: The Ever-Growing List of Fabs, Their Mechanisms and Inhibition.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {891610}, pmid = {35814645}, issn = {1664-302X}, abstract = {Enoyl-ACP reductases (ENRs) are enzymes that catalyze the last step of the elongation cycle during fatty acid synthesis. In recent years, new bacterial ENR types were discovered, some of them with structures and mechanisms that differ from the canonical bacterial FabI enzymes. Here, we briefly review the diversity of structural and catalytic properties of the canonical FabI and the new FabK, FabV, FabL, and novel ENRs identified in a soil metagenome study. We also highlight recent efforts to use the newly discovered Fabs as targets for drug development and consider the complex evolutionary history of this diverse set of bacterial ENRs.}, } @article {pmid35814641, year = {2022}, author = {Ku, Y and Lei, Y and Han, X and Peng, J and Zhu, Y and Zhao, Z}, title = {Spatial Patterns and Composition Traits of Soil Microbial Nitrogen-Metabolism Genes in the Robinia pseudoacacia Forests at a Regional Scale.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {918134}, pmid = {35814641}, issn = {1664-302X}, abstract = {Microbial-driven processes related to the nitrogen-metabolism (N-metabolism) in soil are critical for ecosystem functioning and stability. There are spatial patterns of microbial-mediated nitrogen processes, but we still lack an overview of the soil N-metabolism genes of single nitrogen-fixing tree species pure forests at a regional scale. Here, we investigated the spatial variation and drivers of microbial N-metabolism genes in the rhizosphere soil of Robinia pseudoacacia on the Loess Plateau by metagenomic technology. We found that the distance-decay of soil N functional gene similarities in Robinia pseudoacacia forests on the Loess Plateau spanning a geographic distance of 230 km was significant (p < 0.001). The gene composition and co-occurrence patterns in the process of soil microbial N-metabolism were very different, and they were mainly driven by soil pH and MAP (mean annual precipitation). The proportion of positive links and edges co-occurrence networks between N functional genes increased with increasing pH, suggesting that increasing pH promoted connections between functional genes. The relative frequencies of N-metabolism pathways were consistent on the Loess Plateau, the abundance of ammonia assimilation pathway was highest, and the abundance of the nitrogen fixation pathway was the lowest; only the abundance of the nitrogen fixation pathway was not significantly different. The bacterial and archaeal communities involved in soil nitrogen metabolism were significantly different. Structural equation modeling showed that decreases in soil pH and MAP mainly affected the increase in nitrogen functional gene abundance through an increase in the diversity of N-metabolism microorganisms. In conclusion, this study provides a baseline for biogeographic studies of soil microbe functional genes.}, } @article {pmid35814513, year = {2022}, author = {Philips, CA and Ahamed, R and Rajesh, S and Abduljaleel, JKP and Augustine, P}, title = {Long-term Outcomes of Stool Transplant in Alcohol-associated Hepatitis-Analysis of Clinical Outcomes, Relapse, Gut Microbiota and Comparisons with Standard Care.}, journal = {Journal of clinical and experimental hepatology}, volume = {12}, number = {4}, pages = {1124-1132}, pmid = {35814513}, issn = {0973-6883}, abstract = {BACKGROUND: Healthy donor fecal microbiota transplantation (FMT) was preliminarily shown to have clinical benefits in hepatic encephalopathy (HE), severe alcohol-associated hepatitis (SAH), and alcohol use disorder. However, the long-term outcomes of FMT and the gut microbiota (GM) changes in patients with SAH are unknown.

METHODS: Patients with SAH who underwent FMT (N = 35) or standard of care (SoC, N = 26) from May 2017 to June 2018 were included, and their stored stool samples were analyzed prospectively. Clinical outcomes, including infections, hospitalizations, critical illness, alcohol relapse, and survival, were evaluated. Metagenomic analysis was undertaken to identify the relative abundances (Ras) and significant taxa at baseline and post-therapy (up to three years) among survivors between the two groups.

RESULTS: At follow-up, the incidences of ascites, HE, infections, and major hospitalizations were significantly higher in the SoC than in the FMT group (P < 0.05). Alcohol relapse was lower (28.6% versus 53.8%), and the time to relapse was higher in the FMT than in the SoC group (P = 0.04). Three-year survival was higher in the FMT than in the SoC group (65.7% versus 38.5%, P = 0.052). Death due to sepsis was significantly higher in the SoC group (N = 13/16, 81.2%; P = 0.008). GM analysis showed a significant increase in the RA of Bifidobacterium and a reduction in the RA of Acinetobacter in the FMT group. Beyond one to two years, the RA of Porphyromonas was significantly higher and that of Bifidobacterium was lower in the SoC than in the FMT group.

CONCLUSIONS: In terms of treatment for patients with SAH, healthy donor FMT is associated with significantly lesser ascites, infections, encephalopathy, and alcohol relapse (with a trend toward higher survival rates) than SoC, associated with beneficial GM modulation. Larger controlled studies on FMT are an unmet need.}, } @article {pmid35813824, year = {2022}, author = {Zhang, P and Liu, B and Zheng, W and Chen, Y and Wu, Z and Lu, Y and Ma, J and Lu, W and Zheng, M and Wu, W and Meng, Z and Wu, J and Zheng, Y and Zhang, X and Zhang, S and Huang, Y}, title = {Pulmonary Microbial Composition in Sepsis-Induced Acute Respiratory Distress Syndrome.}, journal = {Frontiers in molecular biosciences}, volume = {9}, number = {}, pages = {862570}, pmid = {35813824}, issn = {2296-889X}, abstract = {Background: Acute respiratory distress syndrome (ARDS) is an unresolved challenge in the field of respiratory and critical care, and the changes in the lung microbiome during the development of ARDS and their clinical diagnostic value remain unclear. This study aimed to explore the role of the lung microbiome in disease progression in patients with sepsis-induced ARDS and potential therapeutic targets. Methods: Patients with ARDS were divided into two groups according to the initial site of infection, intrapulmonary infection (ARDSp, 111 cases) and extrapulmonary infection (ARDSexp, 45 cases), and a total of 28 patients with mild pulmonary infections were enrolled as the control group. In this study, we sequenced the DNA in the bronchoalveolar lavage fluid collected from patients using metagenomic next-generation sequencing (mNGS) to analyze the changes in the lung microbiome in patients with different infectious site and prognosis and before and after antibiotic treatment. Results: The Shannon-Wiener index indicated a statistically significant reduction in microbial diversity in the ARDSp group compared with the ARDSexp and control groups. The ARDSp group was characterized by a reduction in microbiome diversity, mainly in the normal microbes of the lung, whereas the ARDSexp group was characterized by an increase in microbiome diversity, mainly in conditionally pathogenic bacteria and intestinal microbes. Further analysis showed that an increase in Bilophila is a potential risk factor for death in ARDSexp. An increase in Escherichia coli, Staphylococcus aureus, Candida albicans, enteric microbes, or conditional pathogens may be risk factors for death in ARDSp. In contrast, Hydrobacter may be a protective factor in ARDSp. Conclusion: Different initial sites of infection and prognoses are likely to affect the composition and diversity of the pulmonary microbiome in patients with septic ARDS. This study provides insights into disease development and exploration of potential therapeutic targets.}, } @article {pmid35812740, year = {2022}, author = {Jeffery, NW and Lehnert, SJ and Kess, T and Layton, KKS and Wringe, BF and Stanley, RRE}, title = {Application of Omics Tools in Designing and Monitoring Marine Protected Areas For a Sustainable Blue Economy.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {886494}, pmid = {35812740}, issn = {1664-8021}, abstract = {A key component of the global blue economy strategy is the sustainable extraction of marine resources and conservation of marine environments through networks of marine protected areas (MPAs). Connectivity and representativity are essential factors that underlie successful implementation of MPA networks, which can safeguard biological diversity and ecosystem function, and ultimately support the blue economy strategy by balancing ocean use with conservation. New "big data" omics approaches, including genomics and transcriptomics, are becoming essential tools for the development and maintenance of MPA networks. Current molecular omics techniques, including population-scale genome sequencing, have direct applications for assessing population connectivity and for evaluating how genetic variation is represented within and among MPAs. Effective baseline characterization and long-term, scalable, and comprehensive monitoring are essential for successful MPA management, and omics approaches hold great promise to characterize the full range of marine life, spanning the microbiome to megafauna across a range of environmental conditions (shallow sea to the deep ocean). Omics tools, such as eDNA metabarcoding can provide a cost-effective basis for biodiversity monitoring in large and remote conservation areas. Here we provide an overview of current omics applications for conservation planning and monitoring, with a focus on metabarcoding, metagenomics, and population genomics. Emerging approaches, including whole-genome sequencing, characterization of genomic architecture, epigenomics, and genomic vulnerability to climate change are also reviewed. We demonstrate that the operationalization of omics tools can enhance the design, monitoring, and management of MPAs and thus will play an important role in a modern and comprehensive blue economy strategy.}, } @article {pmid35812645, year = {2022}, author = {Watanabe, S and Minagawa, M and Shinoda, T and Motooka, D and Tohya, M and Kirikae, T and Nakamura, S and Saiura, A}, title = {Bile Collected From the Normal Gallbladder of Patients During Surgery Has Simple Bacterial Flora.}, journal = {Cureus}, volume = {14}, number = {6}, pages = {e25681}, pmid = {35812645}, issn = {2168-8184}, abstract = {Background Bile inhibits bacterial growth because it is rich in bacteriostatic compounds such as bile acids. Analytical techniques using a high-intensity sequencer recently revealed bacterial flora in the bile of normal gallbladders in brain-dead patients. Therefore, we performed a microbial flora analysis of bile collected from pathologically normal gallbladders surgically removed from patients with hepatobiliary pancreatic diseases and normal liver function. Methods Bacterial DNA was extracted from bile samples and analyzed using 16S rRNA sequencing. Results The culture results of all 12 bile samples were negative. However, the results of the 16S ribosome gene analysis suggested the presence of bacterial flora in all samples. The phyla Firmicutes, Proteobacteria, Actinobacteria, and, more specifically, the genera Anaerobacillus, Delftia, Bacillus, Ralstonia, Ochrobactrum, Acidovorax, and Curvibacter were detected in all 12 samples. The results of the 16S rRNA gene profile analysis revealed that Anaerobacillus and Delftia accounted for 58.62%-87.63% of the bacteria identified in each sample. Conclusion In a bacterial flora analysis targeting the 16S ribosomal gene, a specific bacterial flora was detected in bile collected from the pathologically normal gallbladders of patients with hepatobiliary pancreatic diseases. Although a diverse bacterial flora was previously reported in the bile of brain-dead patients, the present results revealed a simple bacterial flora with no diversity in the bile samples.}, } @article {pmid35811971, year = {2022}, author = {Park, HY and Lee, HB and Lee, SY and Oh, MJ and Ha, SK and Do, E and Lee, HHL and Hur, J and Lee, KW and Nam, MH and Park, MG and Kim, Y}, title = {Lactococcus lactis KF140 Reduces Dietary Absorption of N[ε] - (Carboxymethyl)lysine in Rats and Humans via β-Galactosidase Activity.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {916262}, pmid = {35811971}, issn = {2296-861X}, abstract = {BACKGROUND AND AIMS: Excessive intake of advanced glycation end products (AGEs), which are formed in foods cooked at high temperatures for long periods of time, has negative health effects, such as inflammatory responses and oxidative stress. N[ε]-(Carboxymethyl)lysine (CML) is one of the major dietary AGEs. Given their generally recognized as safe status and probiotic functionalities, lactic acid bacteria may be ideal supplements for blocking intestinal absorption of food toxicants. However, the protective effects of lactic acid bacteria against dietary AGEs have not been fully elucidated.

MATERIALS AND METHODS: We investigated the effect of treatment with Lactococcus lactis KF140 (LL-KF140), which was isolated from kimchi, on the levels and toxicokinetics of CML. The CML reduction efficacies of the Lactococcus lactis KF140 (LL-KF140), which was isolated from kimchi, were conducted by in vitro test for reducing CML concentration of the casein-lactose reaction product (CLRP) and in vivo test for reducing serum CML level of LL-KF140 administered rats at 2.0 × 10[8] CFU/kg for14 days. In addition, 12 volunteers consuming LL-KF140 at 2.0 × 10[9] CFU/1.5 g for 26 days were determined blood CML concentration and compared with that before intake a Parmesan cheese.

RESULTS: Administration of LL-KF140 reduced serum CML levels and hepatic CML absorption in rats that were fed a CML-enriched product. In a human trial, the intake of LL-KF140 prevented increases in the serum levels of CML and alanine aminotransferase after consumption of a CML-rich cheese. LL-KF140 was determined to presence in feces through metagenome analysis. Furthermore, β-galactosidase, one of the L. lactis-produced enzymes, inhibited the absorption of CML and reduced the levels of this AGE, which suggests an indirect inhibitory effect of LL-KF140. This study is the first to demonstrate that an L. lactis strain and its related enzyme contribute to the reduction of dietary absorption of CML.}, } @article {pmid35811137, year = {2022}, author = {Oshiki, M and Takaki, Y and Hirai, M and Nunoura, T and Kamigaito, A and Okabe, S}, title = {Metagenomic Analysis of Five Phylogenetically Distant Anammox Bacterial Enrichment Cultures.}, journal = {Microbes and environments}, volume = {37}, number = {3}, pages = {}, pmid = {35811137}, issn = {1347-4405}, mesh = {*Ammonium Compounds/metabolism ; Anaerobic Ammonia Oxidation ; Anaerobiosis ; Bacteria/genetics/metabolism ; *Metagenome ; Metagenomics ; Oxidation-Reduction ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Anaerobic ammonium-oxidizing (anammox) bacteria are slow-growing and fastidious bacteria, and limited numbers of enrichment cultures have been established. A metagenomic ana-lysis of our 5 established anammox bacterial enrichment cultures was performed in the present study. Fourteen high-quality metagenome-assembled genomes (MAGs) were obtained, including those of 5 anammox Planctomycetota (Candidatus Brocadia, Ca. Kuenenia, Ca. Jettenia, and Ca. Scalindua), 4 Bacteroidota, and 3 Chloroflexota. Based on the gene sets of metabolic pathways involved in the degradation of polymeric substances found in Chloroflexota and Bacteroidota MAGs, they are expected to be scavengers of extracellular polymeric substances and cell debris.}, } @article {pmid35810819, year = {2022}, author = {Sofiev, M and Sofieva, S and Palamarchuk, J and Šaulienė, I and Kadantsev, E and Atanasova, N and Fatahi, Y and Kouznetsov, R and Kuula, J and Noreikaite, A and Peltonen, M and Pihlajamäki, T and Saarto, A and Svirskaite, J and Toiviainen, L and Tyuryakov, S and Šukienė, L and Asmi, E and Bamford, D and Hyvärinen, AP and Karppinen, A}, title = {Bioaerosols in the atmosphere at two sites in Northern Europe in spring 2021: Outline of an experimental campaign.}, journal = {Environmental research}, volume = {214}, number = {Pt 2}, pages = {113798}, doi = {10.1016/j.envres.2022.113798}, pmid = {35810819}, issn = {1096-0953}, mesh = {Aerosols/analysis ; *Air Pollutants/analysis ; Atmosphere/analysis ; *Environmental Monitoring/methods ; Europe ; Seasons ; }, abstract = {A coordinated observational and modelling campaign targeting biogenic aerosols in the air was performed during spring 2021 at two locations in Northern Europe: Helsinki (Finland) and Siauliai (Lithuania), approximately 500 km from each other in north-south direction. The campaign started on March 1, 2021 in Siauliai (12 March in Helsinki) and continued till mid-May in Siauliai (end of May in Helsinki), thus recording the transition of the atmospheric biogenic aerosols profile from winter to summer. The observations included a variety of samplers working on different principles. The core of the program was based on 2- and 2.4--hourly sampling in Helsinki and Siauliai, respectively, with sticky slides (Hirst 24-h trap in Helsinki, Rapid-E slides in Siauliai). The slides were subsequently processed extracting the DNA from the collected aerosols, which was further sequenced using the 3-rd generation sequencing technology. The core sampling was accompanied with daily and daytime sampling using standard filter collectors. The hourly aerosol concentrations at the Helsinki monitoring site were obtained with a Poleno flow cytometer, which could recognize some of the aerosol types. The sampling campaign was supported by numerical modelling. For every sample, SILAM model was applied to calculate its footprint and to predict anthropogenic and natural aerosol concentrations, at both observation sites. The first results confirmed the feasibility of the DNA collection by the applied techniques: all but one delivered sufficient amount of DNA for the following analysis, in over 40% of the cases sufficient for direct DNA sequencing without the PCR step. A substantial variability of the DNA yield has been noticed, generally not following the diurnal variations of the total-aerosol concentrations, which themselves showed variability not related to daytime. An expected upward trend of the biological material amount towards summer was observed but the day-to-day variability was large. The campaign DNA analysis produced the first high-resolution dataset of bioaerosol composition in the North-European spring. It also highlighted the deficiency of generic DNA databases in applications to atmospheric biota: about 40% of samples were not identified with standard bioinformatic methods.}, } @article {pmid35810635, year = {2022}, author = {Zhu, L and Wu, B and Liu, Y and Zhang, J and Deng, R and Gu, L}, title = {Strategy to enhance semi-continuous anaerobic digestion of food waste by combined use of calcium peroxide and magnetite.}, journal = {Water research}, volume = {221}, number = {}, pages = {118801}, doi = {10.1016/j.watres.2022.118801}, pmid = {35810635}, issn = {1879-2448}, mesh = {Anaerobiosis ; Bioreactors ; Ferrosoferric Oxide ; *Food ; Methane/metabolism ; Peroxides ; *Refuse Disposal/methods ; Sewage/microbiology ; }, abstract = {Optimizing methane production from food waste (FW) efficiently is always a hot topic in the field of anaerobic digestion (AD). In this study we aimed to improve the conversion of organics to methane by using CaO2 and magnetite to enhance the semi-continuous AD of food waste. Under the organic load of 2.5 g VS/L·d[-1], the specific methane yield was increased from 333.9 mL CH4/g·VS to 423.4 mL CH4/g·VS by adding 0.01 g/L CaO2 with 0.4 g/L magnetite, improving the production of methane from FW. We assessed reactor performance, ORP changes, mass balance, enzyme activities and characterized the metagenomic profile of microorganisms involved in digestion. These microorganisms showed rapid conversion of volatile fatty acids and increased expression of genes related to hydrolysis and acid production. Thus, the addition of CaO2 and magnetite optimized the relationship between fermentation bacteria and methanogenic archaea to enhance the overall production of methane. Microorganisms evolved unique adaptive mechanisms in the co-operative environment of CaO2 and magnetite, as their energy metabolism patterns combined those controlled by individual CaO2 and magnetite addition. This method of combining a micro-aeration environment with conductive materials provides a new perspective for optimizing the AD of FW.}, } @article {pmid35810633, year = {2022}, author = {Wang, S and Wang, J and Liu, Z and Zhang, B}, title = {Unraveling diverse survival strategies of microorganisms to vanadium stress in aquatic environments.}, journal = {Water research}, volume = {221}, number = {}, pages = {118813}, doi = {10.1016/j.watres.2022.118813}, pmid = {35810633}, issn = {1879-2448}, mesh = {Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Metagenomics ; *Microbiota ; *Vanadium/analysis ; }, abstract = {Worldwide vanadium contamination is posing serious risks to ecosystems. Although abilities of microbial communities to cope with vanadium stress using specific survival strategies have been reported, little is known regarding their relative importance and the underlying detoxification/tolerance mechanisms. Herein, we investigated the potential survival strategies of microbial communities and associated pathways in aquatic environments based on geochemistry and molecular biology. High vanadium content was observed for both water (12.6 ± 1.15 mg/L) and sediment (1.18 × 10[3] ± 10.4 mg/kg) in the investigated polluted stream. Co-occurrence network investigation implied that microbial communities showed cooperative interactions to adapt to the vanadium-polluted condition. Vanadium was also characterized as one of the vital factors shaping the community structure via redundancy analysis and structural equation models. Based on the metagenomic technology, three survival strategies including denitrification pathway, electron transfer, and metal resistance in innate microbes under the vanadium stress were revealed, with comprehensively summarized vanadium detoxification/tolerance genes. Remarkable role of electron transfer genes and the prevalent existence of resistance genes during detoxifying vanadium were highlighted. Overall, these findings provide novel insights into survival strategies under the vanadium contamination in aquatic environments, which can be of great significance for the identification, isolation, and application of vanadium reducing bacteria in vanadium bioremediation.}, } @article {pmid35810602, year = {2022}, author = {Ma, Q and Gao, F and Zhou, L and Fan, Y and Zhao, B and Xi, W and Wang, C and Zhu, F and Ma, X and Wang, W and Wang, Y}, title = {Characterizing serum amino acids in schizophrenic patients: Correlations with gut microbes.}, journal = {Journal of psychiatric research}, volume = {153}, number = {}, pages = {125-133}, doi = {10.1016/j.jpsychires.2022.07.006}, pmid = {35810602}, issn = {1879-1379}, mesh = {Amino Acids ; Arginine ; *Gastrointestinal Microbiome/physiology ; Glutamine ; Humans ; Leucine ; Methionine ; *Schizophrenia ; }, abstract = {Amino acid abnormalities have been suggested to be a key pathophysiological mechanism in schizophrenia (SZ). Recently, gut microbes were found to be critically involved in mental and metabolic diseases. However, the relationship between serum amino acid levels and gut microbes in SZ is rarely studied. Here, we analyzed serum amino acid levels in 76 untreated SZ patients and 79 healthy controls (HC). Serum levels of 10 amino acids were significantly altered in patients with SZ. We further classified the cut-off values for serum arginine, leucine, glutamine, and methionine levels to distinguish SZ patients from controls. These classifiers were shown to be effective in another validation cohort (49 SZ and 48 HC). The correlation between serum amino acids and clinical symptoms and cognitive functions was also analyzed. Arginine, leucine, glutamine, and methionine levels were significantly correlated with clinical symptoms and cognitive impairments in SZ patients. By metagenome shotgun sequencing of fecal samples, we found that patients with SZ with a low level of serum amino acids have higher richness and evenness of the gut microbiota. At the genus level, the abundances of Mitsuokella and Oscillibacter are significantly abnormal. At the mOTU level, 15 mOTUs in the low-level SZ group were significantly different from the HC group. In addition, Mitsuokella multacida was correlated with glutamine and methionine, respectively. Our research revealed that alterations in serum amino acid levels are critically related to changes in gut microbiota composition in SZ patients. These findings may shed light on new strategies for the diagnosis and treatment of SZ.}, } @article {pmid35810517, year = {2022}, author = {Zou, Z and Li, S and Wu, J and Guo, S and Zhang, Y and Huang, M and Valsami-Jones, E and Lynch, I and Liu, X and Wang, J and Zou, J}, title = {Effects of nanopolystyrene addition on nitrogen fertilizer fate, gaseous loss of N from the soil, and soil microbial community composition.}, journal = {Journal of hazardous materials}, volume = {438}, number = {}, pages = {129509}, doi = {10.1016/j.jhazmat.2022.129509}, pmid = {35810517}, issn = {1873-3336}, mesh = {Ammonia ; *Brassica ; Fertilizers/analysis ; Gases ; *Microbiota ; Nitrogen/analysis ; Nitrous Oxide ; Plastics ; Soil ; Soil Microbiology ; }, abstract = {Nanoplastics and microplastics are the degradation products of plastics waste and have become a dominant pollutant in the environment. However, little is known about the ecological impacts of nanoplastic particles in the agroecosystem. We conducted a mesocosm experiment to examine nanopolystyrene effects on fertilizer nitrogen (N) fate, N gaseous losses and soil microbial communities using Chinese cabbage (Brassica Campestris ssp.) as the model plant. The two-factorial experiment was designed as the addition of [15]N-labeled urea exposed without and with ~50 nm nanopolystyrene (0, 0.05%, and 0.1%). Nanopolystyrene addition had a detectable effect on soil mineral N content. The [15]N uptake of plants was reduced in aboveground biomass but enhanced in roots with increasing nanopolystyrene concentration. Nanopolystyrene addition decreased soil nitrous oxide and ammonia emissions by 27% and 37%, respectively. Nanopolystyrene addition consistently reduced the abundance of ammonia oxidizer genes but showed contrasting effects on denitrifying genes. Metagenomic sequencing data revealed no significant effects of nanopolystyrene on the N-cycle pathway, while it significantly altered the composition of bacterial and fungal communities. This study provided the first insights into the nanopolystyrene induced linkage of root growth with more root N uptake and less gaseous N losses and the associated changes in the microbial community.}, } @article {pmid35810357, year = {2022}, author = {Varga-Kugler, R and Marton, S and Thuma, Á and Szentpáli-Gavallér, K and Bálint, Á and Bányai, K}, title = {Candidate 'Avian orthoreovirus B': An emerging waterfowl pathogen in Europe and Asia?.}, journal = {Transboundary and emerging diseases}, volume = {69}, number = {5}, pages = {e3386-e3392}, doi = {10.1111/tbed.14654}, pmid = {35810357}, issn = {1865-1682}, mesh = {Animals ; Birds ; Ducks ; Genome, Viral ; Nucleotides ; *Orthoreovirus/genetics ; *Orthoreovirus, Avian/genetics ; Phylogeny ; *Reoviridae Infections/epidemiology/veterinary ; Sequence Analysis, DNA/veterinary ; }, abstract = {A fusogenic virus was isolated from a flock of breeder Pekin ducks in 2019, Hungary. The affected flock experienced a marked decrease in egg production. Histopathological lesions were seen in the oviduct and in the lungs of birds sent for diagnostic investigation. The fusogenic agent was characterized as an orthoreovirus by viral metagenomics. The assembled viral genome was composed of 10 genomic segments and was 23,433 nucleotides (nt) in length. The study strain, designated Reo/HUN/DuckDV/2019, shared low-to-medium gene-wise sequence identity with avian orthoreovirus strains from galliform and anseriform birds (nt, 38.90%-72.33%) as well as with representative strains of neoavian orthoreoviruses (nt, 40.07%-68.23%). On the contrary, the study strain shared 86.48%-95.01% pairwise nt sequence identities with recent German and Chinese reovirus isolates, D2533/6 and Ych, respectively. Phylogenetic analysis clustered all three unusual waterfowl pathogens on a monophyletic branch, indicating a common evolutionary origin of Reo/HUN/DuckDV/2019 with these enigmatic orthoreoviruses described over the past few years. The finding that a candidate new orthoreovirus species, tentatively called Avian orthoreovirus B, was isolated in recent years in Europe and Asia in moribund ducks seems an alarming sign that needs to be better evaluated by extending laboratory diagnosis of viral pathogens in countries where the waterfowl industry is important.}, } @article {pmid35810346, year = {2022}, author = {Hrapovic, N and Richard, T and Messaraa, C and Li, X and Abbaspour, A and Fabre, S and Mavon, A and Andersson, B and Khmaladze, I}, title = {Clinical and metagenomic profiling of hormonal acne-prone skin in different populations.}, journal = {Journal of cosmetic dermatology}, volume = {21}, number = {11}, pages = {6233-6242}, doi = {10.1111/jocd.15225}, pmid = {35810346}, issn = {1473-2165}, support = {//Oriflame Cosmetics AB/ ; }, mesh = {Female ; Humans ; Pilot Projects ; Skin/metabolism ; *Acne Vulgaris/metabolism ; Bacteria/genetics ; *Microbiota ; }, abstract = {INTRODUCTION: Acne is one of the most common skin concerns of unknown etiology, often connected to the menstrual cycle in women, and possibly to the microbial profile and function.

OBJECTIVE: We aimed to investigate how hormonal fluctuation affects hormonal acne-prone skin in different populations in relation to skin clinical parameters and microbial profiles.

METHODS: We evaluated skin features by using biophysical and topographical tools. For microbial profiling, we sequenced facial skin microbiota and associated the findings with the skin clinical parameters during the different phases of the menstrual cycle.

RESULTS: We identified differences between and within hormonal phases in women of Chinese and Caucasian origin. Changes were discovered in transepidermal water loss (TEWL), sebum level, hydration level, and pore volume. The most abundant identifiable genera in both ethnicities were Cutibacterium, Staphylococcus, and Streptococcus, without any significant abundant differences within the menstrual cycle. Interestingly, 11 bacterial metabolic pathways were downregulated in Chinese compared to Caucasian skin during the follicular phase. The majority of these pathways were associated with skin redox balance, perhaps indicating a weaker oxidative stress response in Chinese versus Caucasian skin. Novosphingobium taxa were increased in the Chinese skin microbiome, which has been reported to protect skin from pollution-mediated oxidative stress.

CONCLUSION: Thus, this pilot study explored some of the clinical and metagenomic changes in acne-prone skin, and provide guidance to tailor-personalized skin care regimes during the menstrual cycle. Also, the skin redox status in acne-prone skin, provides more opportunity to tailor-personalized skin care regimes.}, } @article {pmid35810262, year = {2022}, author = {Ou, YF and Dong, HP and McIlroy, SJ and Crowe, SA and Hallam, SJ and Han, P and Kallmeyer, J and Simister, RL and Vuillemin, A and Leu, AO and Liu, Z and Zheng, YL and Sun, QL and Liu, M and Tyson, GW and Hou, LJ}, title = {Expanding the phylogenetic distribution of cytochrome b-containing methanogenic archaea sheds light on the evolution of methanogenesis.}, journal = {The ISME journal}, volume = {16}, number = {10}, pages = {2373-2387}, pmid = {35810262}, issn = {1751-7370}, support = {41725002//National Natural Science Foundation of China (National Science Foundation of China)/ ; 42030411//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Archaea/genetics/metabolism ; Cytochromes/genetics ; Cytochromes b/genetics/metabolism ; *Euryarchaeota/metabolism ; *Hydrogenase/metabolism ; Methane/metabolism ; Phylogeny ; }, abstract = {Methane produced by methanogenic archaea has an important influence on Earth's changing climate. Methanogenic archaea are phylogenetically diverse and widespread in anoxic environments. These microorganisms can be divided into two subgroups based on whether or not they use b-type cytochromes for energy conservation. Methanogens with b-type cytochromes have a wider substrate range and higher growth yields than those without them. To date, methanogens with b-type cytochromes were found exclusively in the phylum "Ca. Halobacteriota" (formerly part of the phylum Euryarchaeota). Here, we present the discovery of metagenome-assembled genomes harboring methyl-coenzyme M reductase genes reconstructed from mesophilic anoxic sediments, together with the previously reported thermophilic "Ca. Methylarchaeum tengchongensis", representing a novel archaeal order, designated the "Ca. Methylarchaeales", of the phylum Thermoproteota (formerly the TACK superphylum). These microorganisms contain genes required for methyl-reducing methanogenesis and the Wood-Ljundahl pathway. Importantly, the genus "Ca. Methanotowutia" of the "Ca. Methylarchaeales" encode a cytochrome b-containing heterodisulfide reductase (HdrDE) and methanophenazine-reducing hydrogenase complex that have similar gene arrangements to those found in methanogenic Methanosarcinales. Our results indicate that members of the "Ca. Methylarchaeales" are methanogens with cytochromes and can conserve energy via membrane-bound electron transport chains. Phylogenetic and amalgamated likelihood estimation analyses indicate that methanogens with cytochrome b-containing electron transfer complexes likely evolved before diversification of Thermoproteota or "Ca. Halobacteriota" in the early Archean Eon. Surveys of public sequence databases suggest that members of the lineage are globally distributed in anoxic sediments and may be important players in the methane cycle.}, } @article {pmid35810069, year = {2022}, author = {Li, C and Wang, Y}, title = {Progress in the application of metagenomic next-generation sequencing in pediatric infectious diseases.}, journal = {Pediatrics and neonatology}, volume = {63}, number = {5}, pages = {445-451}, doi = {10.1016/j.pedneo.2022.03.014}, pmid = {35810069}, issn = {2212-1692}, mesh = {Child ; *Communicable Diseases/diagnosis/genetics/therapy ; High-Throughput Nucleotide Sequencing ; Humans ; Infant, Newborn ; *Metagenomics ; Sensitivity and Specificity ; }, abstract = {Infectious diseases are the major cause of children's deaths all over the world. With the development of evidence-based medicine, etiological diagnosis becomes more and more important. Since traditional methods have been unable to meet the needs of diagnosis and treatment, metagenomic next-generation sequencing (mNGS) gradually shows its unique advantages for pathogen diagnosis. This article aimed to introduce the application of mNGS technology in the diagnosis and treatment of neonatal and puerile infectious diseases by providing some examples.}, } @article {pmid35809715, year = {2022}, author = {Fan, W and Jin, J and Zhang, Z and Han, L and Li, K and Wang, C}, title = {Degradation of phenanthrene by consortium 5H under hypersaline conditions.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {308}, number = {}, pages = {119730}, doi = {10.1016/j.envpol.2022.119730}, pmid = {35809715}, issn = {1873-6424}, mesh = {Biodegradation, Environmental ; *Marinobacter/genetics/metabolism ; *Phenanthrenes/metabolism ; *Polycyclic Aromatic Hydrocarbons/metabolism ; Salinity ; }, abstract = {PAHs have been widely detected to accumulate in saline and hypersaline environments. Moderately halophilic microbes are considered the most suitable player for the elimination of PAHs in such environments. In this study, consortium 5H was enriched under 5% salinity and completely degraded phenanthrene in 5 days. By high-throughput sequencing, consortium 5H was identified as being mainly composed of Methylophaga, Marinobacter and Thalassospira. Combined with the investigation of intermediates and enzymatic activities, the degradation pathway of consortium 5H on phenanthrene was proposed. Consortium 5H was identified as having the ability to tolerate a wide range of salinities (1%-10%) and initial PAH concentrations (50 mg/L to 400 mg/L). It was also able to function under neutral to weak alkaline conditions (pH from 6 to 9) and the phytotoxicity of the produced intermediates showed no significant difference with distilled water. Furthermore, the metagenome of consortium 5H was measured and analyzed, which showed a great abundance of catabolic genes contained in consortium 5H. This study expanded the knowledge of PAH-degradation under hypersaline environments and consortium 5H was proposed to have good potential for the elimination of PAH pollution in saline/hypersaline environments.}, } @article {pmid35809504, year = {2022}, author = {Marshall, HJ and Blanchard, AM and Kelly, KR and Goh, JN and Williams, AD and King, L and Lovatt, F and Davies, PL and Tötemeyer, S}, title = {The impact of glutaraldehyde based footbaths on Dichelobacter nodosus prevalence and the antimicrobial resistant community of the ovine interdigital skin.}, journal = {Veterinary microbiology}, volume = {272}, number = {}, pages = {109459}, doi = {10.1016/j.vetmic.2022.109459}, pmid = {35809504}, issn = {1873-2542}, mesh = {Animals ; *Anti-Infective Agents/pharmacology ; *Dichelobacter nodosus/genetics ; *Foot Rot/epidemiology/microbiology ; Glutaral/pharmacology ; *Gram-Negative Bacterial Infections/epidemiology/microbiology/veterinary ; Prevalence ; Sheep ; *Sheep Diseases/drug therapy/epidemiology/microbiology ; }, abstract = {Ovine footrot, is a highly contagious polymicrobial bacterial infection, primarily caused by Dichelobacter nodosus. Preventative bactericidal footbaths are commonly used in the sheep industry to reduce the spread of bacteria. However, their effect on the bacterial community is poorly understood. This is the first study to investigate the impact of 2% Digicur (ProGiene,UK) footbath on the bacterial community of the ovine interdigital skin following a common UK footbathing routine. Swab samples were analysed by qPCR to determine prevalence and load of D. nodosus and numerated on MacConkey agar in the presence or absence of tetracycline and ampicillin to determine phenotypic antimicrobial resistance. Metagenomics were used to determine the impact of a single footbath on the bacterial community and genotypic antimicrobial resistance. The results suggest 2% Digicur is ineffective at reducing the load of D. nodosus when applied as a one off or weekly footbath, however sheep may act as a reservoir for multi-drug resistant bacteria creating opportunities to spread antimicrobial resistance to other sheep and their environment.}, } @article {pmid35807903, year = {2022}, author = {Xu, AA and Kennedy, LK and Hoffman, K and White, DL and Kanwal, F and El-Serag, HB and Petrosino, JF and Jiao, L}, title = {Dietary Fatty Acid Intake and the Colonic Gut Microbiota in Humans.}, journal = {Nutrients}, volume = {14}, number = {13}, pages = {}, pmid = {35807903}, issn = {2072-6643}, support = {P30 ES030285/ES/NIEHS NIH HHS/United States ; P30 DK56338/NH/NIH HHS/United States ; CIN13-413/VA/VA/United States ; R01CA172880,/NH/NIH HHS/United States ; }, mesh = {Adenosine Deaminase ; Animals ; Bacteria/genetics ; Cross-Sectional Studies ; Diet, High-Fat/adverse effects ; Dietary Fats ; Fatty Acids/chemistry ; Fatty Acids, Monounsaturated ; *Gastrointestinal Microbiome ; Humans ; Intercellular Signaling Peptides and Proteins ; RNA, Ribosomal, 16S/genetics ; *Trans Fatty Acids ; }, abstract = {A high-fat diet has been associated with systemic diseases in humans and alterations in gut microbiota in animal studies. However, the influence of dietary fatty acid intake on gut microbiota in humans has not been well studied. In this cross-sectional study, we examined the association between intake of total fatty acids (TFAs), saturated fatty acids (SFAs), trans fatty acids (TrFAs), monounsaturated fatty acids (MUFAs), polyunsaturated fatty acids (PUFAs), n3-FAs, and n6-FAs, and the community composition and structure of the adherent colonic gut microbiota. We obtained 97 colonic biopsies from 34 participants with endoscopically normal colons. Microbial DNA was used to sequence the 16S rRNA V4 region. The DADA2 and SILVA database were used for amplicon sequence variant assignment. Dietary data were collected using the Block food frequency questionnaire. The biodiversity and the relative abundance of the bacterial taxa by higher vs. lower fat intake were compared using the Mann−Whitney test followed by multivariable negative binomial regression model. False discovery rate−adjusted p-values (q value) < 0.05 indicated statistical significance. The beta diversity of gut bacteria differed significantly by intake of all types of fatty acids. The relative abundance of Sutterella was significantly higher with higher intake of TFAs, MUFAs, PUFAs, and n6-FAs. The relative abundance of Tyzzerella and Fusobacterium was significantly higher with higher intake of SFAs. Tyzzerella was also higher with higher intake of TrFA. These observations were confirmed by multivariate analyses. Dietary fat intake was associated with bacterial composition and structure. Sutterella, Fusobacterium, and Tyzzerella were associated with fatty acid intake.}, } @article {pmid35806099, year = {2022}, author = {Sabater, C and Calvete-Torre, I and Ruiz, L and Margolles, A}, title = {Arabinoxylan and Pectin Metabolism in Crohn's Disease Microbiota: An In Silico Study.}, journal = {International journal of molecular sciences}, volume = {23}, number = {13}, pages = {}, pmid = {35806099}, issn = {1422-0067}, support = {AGL2016-78311-R//Ministry of Economy, Industry and Competitiveness/ ; }, mesh = {*Crohn Disease/drug therapy ; Dysbiosis ; Humans ; *Microbiota ; Pectins ; Xylans ; }, abstract = {Inflammatory bowel disease is a chronic disorder including ulcerative colitis and Crohn's disease (CD). Gut dysbiosis is often associated with CD, and metagenomics allows a better understanding of the microbial communities involved. The objective of this study was to reconstruct in silico carbohydrate metabolic capabilities from metagenome-assembled genomes (MAGs) obtained from healthy and CD individuals. This computational method was developed as a mean to aid rationally designed prebiotic interventions to rebalance CD dysbiosis, with a focus on metabolism of emergent prebiotics derived from arabinoxylan and pectin. Up to 1196 and 1577 MAGs were recovered from CD and healthy people, respectively. MAGs of Akkermansia muciniphila, Barnesiella viscericola DSM 18177 and Paraprevotella xylaniphila YIT 11841 showed a wide range of unique and specific enzymes acting on arabinoxylan and pectin. These glycosidases were also found in MAGs recovered from CD patients. Interestingly, these arabinoxylan and pectin degraders are predicted to exhibit metabolic interactions with other gut microbes reduced in CD. Thus, administration of arabinoxylan and pectin may ameliorate dysbiosis in CD by promoting species with key metabolic functions, capable of cross-feeding other beneficial species. These computational methods may be of special interest for the rational design of prebiotic ingredients targeting at CD.}, } @article {pmid35805367, year = {2022}, author = {Mostafa-Hedeab, G and Allayeh, AK and Elhady, HA and Eledrdery, AY and Mraheil, MA and Mostafa, A}, title = {Viral Eco-Genomic Tools: Development and Implementation for Aquatic Biomonitoring.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {13}, pages = {}, pmid = {35805367}, issn = {1660-4601}, mesh = {Animals ; Biological Monitoring ; *Ecosystem ; *Enterovirus/genetics ; Environmental Monitoring/methods ; Genome, Viral ; Metagenomics/methods ; Water Microbiology ; }, abstract = {Enteric viruses (EVs) occurrence within aquatic environments varies and leads to significant risk on public health of humans, animals, and diversity of aquatic taxa. Early and efficacious recognition of cultivable and fastidious EVs in aquatic systems are important to ensure the sanitary level of aquatic water and implement required treatment strategies. Herein, we provided a comprehensive overview of the conventional and up-to-date eco-genomic tools for aquatic biomonitoring of EVs, aiming to develop better water pollution monitoring tools. In combination with bioinformatics techniques, genetic tools including cloning sequencing analysis, DNA microarray, next-generation sequencing (NGS), and metagenomic sequencing technologies are implemented to make informed decisions about the global burden of waterborne EVs-associated diseases. The data presented in this review are helpful to recommend that: (1) Each viral pollution detection method has its own merits and demerits; therefore, it would be advantageous for viral pollution evaluation to be integrated as a complementary platform. (2) The total viral genome pool extracted from aquatic environmental samples is a real reflection of pollution status of the aquatic eco-systems; therefore, it is recommended to conduct regular sampling through the year to establish an updated monitoring system for EVs, and quantify viral peak concentrations, viral typing, and genotyping. (3) Despite that conventional detection methods are cheaper, it is highly recommended to implement molecular-based technologies to complement aquatic ecosystems biomonitoring due to numerous advantages including high-throughput capability. (4) Continuous implementation of the eco-genetic detection tools for monitoring the EVs in aquatic ecosystems is recommended.}, } @article {pmid35804768, year = {2022}, author = {Park, S and Zhang, T and Yue, Y and Jeong, SJ and Ryu, MS and Wu, X and Yang, HJ and Jeong, DY}, title = {Alleviation of Metabolic Disturbance by Substituting Kanjang High in Bacillus for Salt through Modulation of Gut Microbiota in Estrogen-Deficient Rats.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {13}, pages = {}, pmid = {35804768}, issn = {2304-8158}, support = {21-3//"functional research of fermented soybean food (safety monitoring)" under the Ministry of Agriculture, Food and Rural Affairs and partly Korea Agro-Fisheries and Food trade corporation./ ; }, abstract = {A high salt intake may exacerbate menopausal symptoms and substituting for different types of traditionally made kanjang (TMK; soy sauce) may prevent it. This study examined whether substituting salt with lyophilized TMK containing low and high Bacillus and biogenic amines in a high-fat diet might modulate the menopausal symptoms and the energy, glucose, and lipid metabolism in ovariectomized (OVX) rats. They were categorized into salt (Control), TMK with high Bacillus and low biogenic amines (HBLB), TMK with high Bacillus and high biogenic amines (HBHB), TMK with low Bacillus and low biogenic amines (LBLB), and TMK with low Bacillus and high biogenic amines (LBHB). Sham-operated rats consumed the same diet as the Control. HBLB, HBHB, and LBHB prevented increased tail skin temperature compared to the Control. HBHB and HBLB partially inhibited the increased weight gain and abdominal fat mass by reducing the food efficiency without changing the serum 17β-estradiol concentrations. Serum glucose and insulin concentrations and the insulin resistance index by the homeostatic model assessment for insulin resistance showed a positive association for weight gain. HBLB and HBHB decreased the serum malondialdehyde and tumor-necrosis factor-α levels. Hepatic triglyceride storage was lower in all TMK groups than in the Control, while hepatic glycogen accumulation was higher in the HBLB, HBHB, and LBHB groups than in the Control and LBLB groups. Accordingly, the mRNA expression of peroxisome proliferator-activated receptors-γ(PPAR-γ) was higher in the HBLB and HBHB groups compared to the Control, and that of fatty acid synthase was opposite to PPAR-γ expression. However, HBLB and HBHB improved dyslipidemia and insulin resistance compared to the Control, but their improvement did not reach that of the Normal-control. The acetic acid concentrations in the portal vein were lower in the LBLB than in the Control, while the butyric acid contents were higher in the LBHB and HBLB groups than in the Control. HBHB, HBLB, and LBHB elevated Akkermansia and Lactobacillus, and HBLB and LBLB increased Bacteroides and Ruminococcus compared to the Control. Polycyclic aromatic hydrocarbon degradation, bile acid synthesis, and unsaturated fatty acid biosynthesis were significantly higher in the HBLB group than in the Control group. In conclusion, substituting salts to TMK with a high Bacillus content regardless of the bioamine contents partially improved the menopausal symptoms and metabolic disturbance in estrogen-deficient animals.}, } @article {pmid35804507, year = {2022}, author = {Ma, J and Chen, J and Gan, M and Chen, L and Zhao, Y and Zhu, Y and Niu, L and Zhang, S and Zhu, L and Shen, L}, title = {Gut Microbiota Composition and Diversity in Different Commercial Swine Breeds in Early and Finishing Growth Stages.}, journal = {Animals : an open access journal from MDPI}, volume = {12}, number = {13}, pages = {}, pmid = {35804507}, issn = {2076-2615}, support = {No.2021YFD1200801//National Key Research and Development Program of China/ ; No.2020YFN0147, No.2021ZDZX0008//Sichuan Science and Technology Program/ ; No. scsztd-2021-08-09//The Program for Pig Industry Technology System Innovation Team of Sichuan Province/ ; NA//China Agriculture Research System of MOF and MARA./ ; }, abstract = {The gut microbiota affects the metabolism, health and growth rate of pigs. Understanding the characteristics of gut microbiota of different pig breeds at each growth stage will enable the design of individualized feeding strategies. The present study aimed to compare the growth curves and development patterns of pigs of three different breeds (Duroc, Landrace and Yorkshire) using the mathematical models Gompertz, Logistic, Von Bertalanffy and Richards. For Duroc pigs, the Gompertz model showed the highest prediction accuracy (R[2] = 0.9974). In contrast, the best models for Landrace and Yorkshire pigs were Richards (R[2] = 0.9986) and Von Bertalanffy (R[2] = 0.9977), respectively. Path analysis showed that body length (path coefficient = 0.507) and chest circumference (path coefficient = 0.532) contributed more significantly to the body weight of pigs at the early growth stage, while hip circumference (path coefficient = 0.312) had a greater influence on pig body weight in the late growth stage. Moreover, the composition of the gut microbiota of pigs at two growth stages (60 kg of body weight in the early growth stage and 120 kg in the finishing stage) was studied using 16S rRNA sequencing technology. Variations in gut microbiota composition of pigs at different growth stages were observed. KEGG pathway enrichment analysis of annotated metagenomes revealed that protein synthesis and amino acid metabolism pathways were significantly enriched in pigs at the early growth stage, which may be related to nutritional requirements of pigs during this stage. This study confirmed longitudinal variation in the gut microbiota of pigs pertaining to age as well as lateral variation related to pig breed. The present findings expand the current understanding of the variations in swine gut microbiota during production stages.}, } @article {pmid35803706, year = {2022}, author = {Mishkin, N and Ricart Arbona, RJ and Carrasco, SE and Lawton, S and Henderson, KS and Momtsios, P and Sigar, IM and Ramsey, KH and Cheleuitte-Nieves, C and Monette, S and Lipman, NS}, title = {Reemergence of the Murine Bacterial Pathogen Chlamydia muridarum in Research Mouse Colonies.}, journal = {Comparative medicine}, volume = {72}, number = {4}, pages = {230-242}, pmid = {35803706}, issn = {2769-819X}, support = {P30 CA008748/CA/NCI NIH HHS/United States ; }, mesh = {Animals ; *Chlamydia muridarum ; Feces ; Humans ; Mice ; Mice, Inbred NOD ; Mice, SCID ; Polymerase Chain Reaction ; }, abstract = {Chlamydia muridarum (Cm) was detected in 2 colonies of mice with lymphoplasmacytic pulmonary infiltrates by using PCR and immunohistochemistry. This discovery was unexpected, as Cm infection had not been reported in laboratory mice since the 1940s. A Cm specific PCR assay was developed and testing implemented for the resident colonies of 8 vivaria from 3 academic institutions, 58 incoming mouse shipments from 39 academic institutions, and mice received from 55 commercial breeding colonies (4 vendors). To estimate Cm's global prevalence in research colonies, a database containing 11,387 metagenomic fecal microbiota samples from 120 institutions and a cohort of 900 diagnostic samples from 96 institutions were examined. Results indicate significant prevalence among academic institutions, with Cm detected in 63% of soiled bedding sentinels from 3 institutions; 33% of incoming mouse shipments from 39 academic institutions; 14% of 120 institutions submitting microbiota samples; and 16% of the diagnostic sample cohort. All samples from commercial breeding colonies were negative. In addition, naïve NOD. Cg-Prkdc[scid]Il2rg[tm1Wjl]/SzJ (NSG) mice exposed to Cm-shedding mice and/or their soiled bedding developed clinical disease at 21 to 28 d after exposure. These mice had a moderate-to-severe histiocytic and neutro- philic bronchointerstitial pneumonia, with their respiratory epithelium demonstrating inclusions, chlamydial major outer membrane protein immunostaining, and hybridization with a Cm reference sequence (GenBank accession no. U68436). Cm was isolated from lungs, cecum, and feces of a Cm-infected NSG mouse by using HeLa 229 cells. The considerable prevalence of Cm is likely due to widespread global interinstitutional distribution of unique mouse strains and failure to recognize that some of these mice were from enzootically infected colonies. Given that experimental Cm colonization of mice results in a robust immune response and, on occasion, pathology, natural infection may confound experimental results. Therefore, Cm should be excluded and eradicated from enzootically infected mouse colonies.}, } @article {pmid35803374, year = {2022}, author = {Xu, M and Huang, XH and Shen, XX and Chen, HQ and Li, C and Jin, GQ and Cao, JS and Xue, ZX}, title = {Metagenomic insights into the spatiotemporal responses of antibiotic resistance genes and microbial communities in aquaculture sediments.}, journal = {Chemosphere}, volume = {307}, number = {Pt 1}, pages = {135596}, doi = {10.1016/j.chemosphere.2022.135596}, pmid = {35803374}, issn = {1879-1298}, mesh = {Animals ; Anti-Bacterial Agents/analysis/pharmacology ; Aquaculture ; China ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; *Metals, Heavy/analysis ; *Microbiota ; }, abstract = {The dissemination of antibiotic resistance genes (ARGs) in aquaculture systems is a potential threat to environmental safety and human health. However, the spatiotemporal distribution pattern of ARGs and key factors associated with their dissemination in aquaculture sediments remain unclear. In this study, ARGs, mobile genetic elements, microbial community composition, heavy metal contents, and nutrient contents of samples collected from a whole culture cycle of fish in a representative aquaculture farm were characterized. The distribution patterns of nine subtypes of ARGs (tetW, tetM, tetA, ermC, ermB, sul1, sul2, floR, and qnrS) showed clear spatiotemporal differences. The absolute abundance of ARGs in aquaculture sediments was higher in winter and in rivers of the aquaculture farm. Proteobacteria was the dominant phylum in all sediment samples. The results of network and redundancy analyses confirmed that the Dechloromonas, Candidatus Accumulibacter, Smithella, Geobacter, and Anaeromyxobacter belonging to Proteobacteria were positively correlated with ARGs, suggesting that these microbial species are potential hosts of corresponding ARGs. Our study highlights that the microbial community is the determining factor for ARG dissemination. Strategies for inhibiting these potential hosts of ARGs should be developed based on controllable factors.}, } @article {pmid35803345, year = {2022}, author = {Chen, H and Wu, W and Tang, S and Fu, R and Gong, X and Hou, H and Xu, J}, title = {Altered fecal microbial and metabolic profile reveals potential mechanisms underlying iron deficiency anemia in pregnant women in China.}, journal = {Bosnian journal of basic medical sciences}, volume = {22}, number = {6}, pages = {923-933}, pmid = {35803345}, issn = {1840-4812}, mesh = {Humans ; Female ; Pregnancy ; *Iron Deficiencies ; Pregnant Women ; Siderophores ; *Anemia, Iron-Deficiency/epidemiology ; Iron ; China/epidemiology ; Metabolome ; Catechols ; ATP-Binding Cassette Transporters ; }, abstract = {The gut microbiome and its metabolism may provide crucial insight into the cause of iron deficiency anemia (IDA) in pregnant women. This study aimed to investigate the effect of the gut microbiome and its related metabolites on pregnant women with iron deficiency (ID) and IDA. Maternal cubital venous blood and stool samples were collected from healthy control pregnant women (HC, non-anemic, n=10), pregnant women with ID non-anemia (ID, n=10), and IDA (n=10). All groups were subjected to fecal metagenomics and metabolomics. The composition and function of the gut microbiome were then compared in pregnant women with ID and IDA with HC after excluding the possibility of inflammation and insufficient iron absorption capacity. Whole-genome shotgun libraries were prepared by quantifying metagenomic DNA samples with Quant-iT PicoGreen dsDNA Assay. The levels of 41 microbial species, including 21 Streptococci and ten metabolites (catechol), which could serve as siderophores, were increased. In contrast, 3 Bacteroides and six metabolites were decreased in pregnant women with IDA (p<0.05). The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis indicated that the bio-pathways, including biosynthesis of siderophore group non-ribosomal peptides (p<0.01), ABC transporters (p<0.05) and membrane transport of the gut microbiota (p<0.01) in IDA patients were expressed differently compared with HC. Correlation analysis also indicates that these increased bacteria formed strong co-occurring relationships with metabolites in the occurrence and development of IDA in pregnant women. The current study identified that streptococci and catechol (fecal metabolite) were significantly increased in pregnant women with IDA. Therefore, adjusting the intestinal homeostasis using long-term living and eating habits on oral Streptococcus in pregnant women with IDA before iron supplementation may be more conducive to iron supplementation, thus providing novel therapies for IDA.}, } @article {pmid35803340, year = {2022}, author = {Ma, S and Qiao, L and Liu, X and Zhang, S and Zhang, L and Qiu, Z and Yu, C}, title = {Microbial community succession in soils under long-term heavy metal stress from community diversity-structure to KEGG function pathways.}, journal = {Environmental research}, volume = {214}, number = {Pt 2}, pages = {113822}, doi = {10.1016/j.envres.2022.113822}, pmid = {35803340}, issn = {1096-0953}, mesh = {Bacteria ; Gold/analysis/metabolism/pharmacology ; *Metals, Heavy/analysis/toxicity ; *Microbiota ; Soil/chemistry ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {Currently, understanding the structure and function of the microbial community is the key step in artificially constructing microbial communities to control soil heavy metal pollution. Abundant/rare microbial communities play different roles in different levels of concentrations. However, the correlation between heavy metals and rare/abundant subgroups is poorly understood. In this study, we used a metagenomics approach to comprehensively investigate the evolutionary changes in microbial diversity, structure, and function under different heavy metal concentration stress in soils surrounding gold tailings. The results show that the main pollutants were Pb, As, and Zn. Indigenous microorganisms have different responses to heavy metal concentrations. Bacteria are the main components of indigenous microorganisms, mainly including Actinobacteria, Proteobacteria, Chloroflexi, and Acidobacteria. With the increase of heavy metal pollution, the relative abundance of Proteobacteria increased, and that of Actinobacteria decreased. Archaea was significantly inhibited by heavy metal stress and was more sensitive to heavy metal concentration. The response of fungi to heavy metal concentration was not obvious. The results of KEGG pathways showed that carbon fixation was inhibited with increasing heavy metal concentrations, while nitrogen metabolism was in contrast. Abundant subcommunity had a greater correlation mainly with metal resistance mechanisms, and rare subcommunity plays a key role for soil nutrient cycling such as N, S cycling in soils contaminated. Overall, this study provides a comprehensive analysis of the effects of heavy metal stress at different concentrations on microorganisms in farmland around gold tailings and reveals the relationship between heavy metals on KEGG pathways.}, } @article {pmid35803007, year = {2022}, author = {Polo, C and Hernández, M and García-Seco, T and Fernández, V and Briones, V and Diez-Guerrier, A and Abad, D and Rodríguez-Lázaro, D and Domínguez, L and Pérez-Sancho, M}, title = {Exploiting 16S rRNA-based metagenomics to reveal neglected microorganisms associated with infertility in breeding bulls in Spanish extensive herds.}, journal = {Research in veterinary science}, volume = {150}, number = {}, pages = {52-57}, doi = {10.1016/j.rvsc.2022.04.019}, pmid = {35803007}, issn = {1532-2661}, mesh = {Animals ; Bacteria/genetics ; Breeding ; Cattle ; *Cattle Diseases/epidemiology/genetics ; *Infertility/genetics/veterinary ; Male ; Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Bovine infectious infertility represents a problem due to the high impact on animal production and, in many cases, in public health. A lack of information on the characteristics of the bacterial population of the bovine reproductive system can hamper a comprehensive understanding of reproductive pathologies and the role that the microbiome could play. A metagenomic study based on the V3-V4 hypervariable region of the bacterial 16S rRNA gene was performed in 1029 preputial samples from bulls raised in an extensive regimen in Spain (944 from herds with low fertility rates -case group-, and 85 samples from reproductively healthy herds -control group-). The most representative phyla as well as the most 10 abundant bacterial families and their abundance did not show significant differences in both case and control groups. Similarly, the (alpha and beta) diversity of the bacterial populations was similar in both type of herds: the Shannon and Simpson indices show a high diversity of species, while the Bray-Curtis dissimilarity index did not show relevant differences in the bacterial communities. A deeper analysis of the operational taxonomic units showed the presence of one genera, Mycoplasma spp. significantly associated with fertility problems. Our study highlights the promising potential that the application of sequencing techniques (e.g. 16S rRNA-based metagenomics) possesses in examining bovine infertility, as they are able to reveal different pathogens that could go unnoticed using diagnostic approaches for only the main known pathogens.}, } @article {pmid35802409, year = {2022}, author = {Edwards, A and Soares, A and Debbonaire, A and Edwards Rassner, SM}, title = {Before you go: a packing list for portable DNA sequencing of microbiomes and metagenomes.}, journal = {Microbiology (Reading, England)}, volume = {168}, number = {7}, pages = {}, doi = {10.1099/mic.0.001220}, pmid = {35802409}, issn = {1465-2080}, mesh = {High-Throughput Nucleotide Sequencing ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; Sequence Analysis, DNA ; }, } @article {pmid35802345, year = {2022}, author = {Kim, K and Lee, Y and Won, S}, title = {Relative contributions of the host genome, microbiome, and environment to the metabolic profile.}, journal = {Genes & genomics}, volume = {44}, number = {9}, pages = {1081-1089}, pmid = {35802345}, issn = {2092-9293}, mesh = {Humans ; *Metabolic Syndrome/genetics ; Metabolome ; *Microbiota/genetics ; Polymorphism, Single Nucleotide ; Prospective Studies ; }, abstract = {BACKGROUND: Metabolic syndrome is as a well-known risk factor for cardiovascular disease, which is associated with both genetic and environmental factors. Recently, the microbiome composition has been shown to affect the development of metabolic syndrome. Thus, it is expected that the complex interplay among host genetics, the microbiome, and environmental factors could affect metabolic syndrome.

OBJECTIVE: To evaluate the relative contributions of genetic, microbiome, and environmental factors to metabolic syndrome using statistical approaches.

METHODS: Data from the prospective Korean Association REsource project cohort (N = 8476) were used in this study, including single-nucleotide polymorphisms, phenotypes and lifestyle factors, and the urine-derived microbial composition. The effect of each data source on metabolic phenotypes was evaluated using a heritability estimation approach and a prediction model separately. We further experimented with various types of metagenomic relationship matrices to estimate the phenotypic variance explained by the microbiome.

RESULTS: With the heritability estimation, five of the 11 metabolic phenotypes were significantly associated with metagenome-wide similarity. We found significant heritability for fasting glucose (4.8%), high-density lipoprotein cholesterol (4.9%), waist-hip ratio (7.7%), and waist circumference (5.6%). Microbiome compositions provided more accurate estimations than genetic factors for the same sample size. In the prediction model, the contribution of each source to the prediction accuracy varied for each phenotype.

CONCLUSION: The effects of host genetics, the metagenome, and environmental factors on metabolic syndrome were minimal. Our statistical analysis suffers from a small sample size, and the measurement error is expected to be substantial. Further analysis is necessary to quantify the effects with better accuracy.}, } @article {pmid35801947, year = {2023}, author = {Che, G and Liu, F and Chang, L and Lai, S and Teng, J and Yang, Q}, title = {Mycoplasma hominis Meningitis Diagnosed by Metagenomic Next-Generation Sequencing in a Preterm Newborn: a Case Report and Literature Review.}, journal = {Laboratory medicine}, volume = {54}, number = {1}, pages = {e24-e28}, doi = {10.1093/labmed/lmac078}, pmid = {35801947}, issn = {1943-7730}, support = {2020YFS0106//Department of Science and Technology of Sichuan Province/ ; KX190//Xinya Research Foundation of West China Second University Hospital/ ; }, mesh = {Infant ; Child ; Female ; Humans ; Infant, Newborn ; Mycoplasma hominis/genetics ; *Meningitis/cerebrospinal fluid/diagnosis/microbiology ; Anti-Bacterial Agents/therapeutic use ; *Mycoplasma Infections/diagnosis/drug therapy/microbiology ; High-Throughput Nucleotide Sequencing ; }, abstract = {Mycoplasma hominis is mainly colonized in the genital tract and vertically transmitted to newborns; however, it rarely causes neonatal meningitis. We report a case of M. hominis meningitis in a premature infant. She was admitted to our hospital for treatment after 6 days of repeated fever. After admission, repeated cerebrospinal fluid (CSF) analysis showed that leukocytes and protein in CSF increased substantially and glucose decreased, but there was no growth in conventional CSF culture. The patient was diagnosed with M. hominis meningitis by metagenomic next-generation sequencing (mNGS). The antibiotic therapy used for the neonate was meropenem, vancomycin, and ampicillin against bacterial infection and azithromycin against mycoplasma infection. The child was subsequently considered cured and discharged from the hospital and followed up regularly in the neurology clinic. The mNGS may be a promising and effective diagnostic technique for identifying uncommon pathogens of meningitis in patients with meningitis symptoms and signs without microbial growth in routine CSF culture.}, } @article {pmid35801774, year = {2022}, author = {Wang, R and Cao, X and Wu, F and Zhao, J and Fu, L and Yuan, Z and Ni, Y and Chen, Z and Li, F}, title = {Infectious native valve endocarditis by Streptococcus agalactiae species: Case report of pathogen identification only through metagenomic sequencing technology.}, journal = {Medicine}, volume = {101}, number = {27}, pages = {e29360}, pmid = {35801774}, issn = {1536-5964}, mesh = {*Communicable Diseases ; *Endocarditis/diagnosis ; *Endocarditis, Bacterial/diagnosis ; Humans ; Metagenome ; *Streptococcal Infections/diagnosis ; Streptococcus agalactiae/genetics ; Technology ; }, abstract = {INTRODUCTION: Streptococcus agalactiae is a common pathogen in infective endocarditis, but the positive rate of traditional blood culture diagnosis is not high. It is challenging to obtain a good outcome in the absence of pathogen information for patients with infectious endocarditis.

Here, we report the case of a patient with infective endocarditis caused by S. agalactiae. The initial manifestations of this patient were coma, urinary incontinence, and fecal incontinence and had no history of heart disease or infectious diseases before admission.

INTERVENTIONS AND OUTCOMES: When the blood culture was negative 3 consecutive times, the pathogen S. agalactiae was diagnosed in a timely and accurate manner by metagenome sequencing. Eventually, the patient was discharged following surgery and antibiotic treatment.

CONCLUSIONS: For IE patients with infective endocarditis, metagenome sequencing is a valuable and selective tool for rapid, sensitive, and accurate pathogen detection, especially when the blood culture is negative.}, } @article {pmid35801409, year = {2022}, author = {Hertz, FB and Holm, JB and Pallejá, A and Björnsdóttir, MK and Mikkelsen, LS and Brandsborg, E and Frimodt-Møller, N}, title = {Vaginal microbiome following orally administered probiotic.}, journal = {APMIS : acta pathologica, microbiologica, et immunologica Scandinavica}, volume = {130}, number = {10}, pages = {605-611}, pmid = {35801409}, issn = {1600-0463}, mesh = {Female ; Gardnerella vaginalis ; Humans ; *Microbiota ; *Probiotics ; Vagina/microbiology ; *Vaginosis, Bacterial ; }, abstract = {Here, we present a longitudinal shotgun sequencing metagenomics study of 16 healthy, Danish women in the reproductive age. The aim of the study was to investigate whether lactobacilli, orally consumed, had any impact on the vaginal microbiome and its functional potential. The 16 women aged 19-45 years were recruited from Copenhagen, Denmark. One baseline vaginal sample (Day 0) and two study samples (Days 25-30 and Days 55-60, respectively), were sampled. The vaginal samples were analyzed by shotgun metagenomics. We detected 26 species in the vaginal microbiota of the 16 women, of which six belonged to the Lactobacillus genus. We observed three vaginal microbiome clusters mainly dominated by Gardnerella vaginalis, Lactobacillus iners, or Lactobacillus crispatus. The oral probiotic had no detectable effect on either the composition or the functional potential of the vaginal microbiota. Most of the study subjects (11 out of 16 women) exhibited only minor changes in the vaginal microbiome during the treatment with probiotics. Any compositional changes could not be associated to the probiotic treatment. Future studies may benefit from an increased number of participants, and administration of the probiotics during conditions with bacterial imbalance (e.g., during/after antibiotic treatment) or the use of different Lactobacillus spp. known to colonize the vagina.}, } @article {pmid35801115, year = {2022}, author = {Zhong, T and Wang, C and Wang, X and Freitas-de-Melo, A and Zeng, B and Zhao, Q and Zhan, S and Wang, L and Cao, J and Dai, D and Guo, J and Li, L and Zhang, H and Niu, L}, title = {Early Weaning and Milk Substitutes Affect the Gut Microbiome, Metabolomics, and Antibody Profile in Goat Kids Suffering From Diarrhea.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {904475}, pmid = {35801115}, issn = {1664-302X}, abstract = {Early weaning and milk substitutes increase the incidence of diarrhea in young ruminants, which may modify their gut microbiota, metabolism, immunity, and health. The aim of the study was to determine if early weaning and milk substitutes affect the gut microbiota, metabolism, and immunological status of goat kids suffering from diarrhea. The 16S rRNA gene and metagenomic sequencing in feces and serum metabolomics of early-weaned and artificially reared goat kids suffering from diarrhea (DK group) and healthy goat kids reared by their mothers (HK group) were analyzed. The serum biochemistry and immunoglobulin concentration were also determined. Several probiotics, such as Streptococcus and Lactobacillus, were higher in the feces of the DK group than in feces of the HK group. Ruminococcus sp. was elevated in the feces of HKs, likely being a biomarker for goat health. Taking all the carbohydrate-active enzyme (CAZyme) families into consideration, 20 CAZyme families were different between the groups. Compared with the DK group, the relative quantity of glycoside hydrolases (GH) and glycosyltransferase (GT) families in the HK group decreased. GT70 was only identified in HK kids participating in the activity of β-glucuronosyltransferase during the carbohydrate metabolism. Overall, 24 metabolites were different between the groups, which were mainly involved in protein digestion and absorption, cyanoamino acid metabolism, and cholesterol metabolism. The concentrations of immunoglobulins G and M were significantly lower in the DK than in the HK group. In conclusion, our study characterized the fecal microbiota, metabolism, and immunological status of early-weaned and artificially reared goat kids suffering from diarrhea.}, } @article {pmid35801108, year = {2022}, author = {Zhu, R and Tang, J and Xing, C and Nan, Q and Liang, G and Luo, J and Zhou, J and Miao, Y and Cao, Y and Dai, S and Lan, D}, title = {The Distinguishing Bacterial Features From Active and Remission Stages of Ulcerative Colitis Revealed by Paired Fecal Metagenomes.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {883495}, pmid = {35801108}, issn = {1664-302X}, abstract = {Ulcerative colitis (UC) is a serious chronic intestinal inflammatory disease, with an increased incidence in recent years. The intestinal microbiota plays a key role in the pathogenesis of UC. However, there is no unified conclusion on how the intestinal microbiota changes. Most studies focus on the change between UC patients and healthy individuals, rather than the active and remission stage of the same patient. To minimize the influences of genetic differences, environmental and dietary factors, we studied the intestinal microbiota of paired fecal samples from 42 UC patients at the active and remission stages. We identified 175 species of microbes from 11 phyla and found no difference of the alpha and beta diversities between the active and remission stages. Paired t-test analysis revealed differential microbiota at levels of the phyla, class, order, family, genus, and species, including 13 species with differential abundance. For example, CAG-269 sp001916005, Eubacterium F sp003491505, Lachnospira sp000436475, et al. were downregulated in the remission, while the species of Parabacteroides distasonis, Prevotellamassilia sp900540885, CAG-495 sp001917125, et al. were upregulated in the remission. The 13 species can effectively distinguish the active and remission stages. Functional analysis showed that the sporulation and biosynthesis were downregulated, and the hydrogen peroxide catabolic process was upregulated in remission of UC. Our study suggests that the 13 species together may serve as a biomarker panel contributing to identify the active and remission stages of UC, which provides a valuable reference for the treatment of UC patients by FMT or other therapeutic methods.}, } @article {pmid35801098, year = {2022}, author = {Yan, L and Li, S and Sivan, O and Kasten, S}, title = {Editorial: Advances in Microbial Iron Cycling.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {931648}, pmid = {35801098}, issn = {1664-302X}, } @article {pmid35800993, year = {2022}, author = {Son, SY and Wang, B and Hur, H and Kim, HH and Han, SU}, title = {Does bisphenol-A affect alteration of gut microbiome after bariatric/metabolic surgery?: a comparative metagenomic analysis in a long-term high-fat diet induced-obesity rat model.}, journal = {Annals of surgical treatment and research}, volume = {102}, number = {6}, pages = {342-352}, pmid = {35800993}, issn = {2288-6575}, abstract = {PURPOSE: Bisphenol A (BPA) is a widely used environmental contaminant that is associated with type 2 diabetes mellitus and a shift of gut microbial community. However, little is known about the influence of BPA on gut microbial changes related to bariatric surgery. We investigated whether long-term exposure to dietary BPA causing alterations of gut microbiome occurred after bariatric surgery.

METHODS: Six-week-old male Wistar rats were fed either a high-fat diet (HFD) or HFD + BPA for 40 weeks. Then sleeve gastrectomy (SG) or Roux-en Y gastric bypass (RYGB) was performed in each diet group and observed for 12 weeks postoperatively. Fecal samples were collected at the 40th weeks and 12th postoperative weeks. Using 16S ribosomal RNA gene sequencing analysis on fecal samples, a comparative metagenomic analysis on gut microbiome composition was performed.

RESULTS: Long-term exposure to HFD with BPA showed higher body weight change and higher level of fasting blood sugar after 40 weeks-diet challenge than those of the HFD only group. After bariatric surgeries, mean body weight of the HFD with BPA group was significantly higher than the HFD only group, but there was no difference between the SG and RYGB groups. The metagenomic analyses demonstrated that long-term exposure to dietary BPA did not affect significant alterations of gut microbiome before and after bariatric surgery, compared with the HFD groups.

CONCLUSION: Our results highlighted that BPA was a risk factor for obesity and may contribute to glucose intolerance, but it did not affect alterations of gut microbiome after bariatric/metabolic surgery.}, } @article {pmid35800388, year = {2022}, author = {Fang, B and Li, Q and Wan, Z and OuYang, Z and Zhang, Q}, title = {Exploring the Association Between Cervical Microbiota and HR-HPV Infection Based on 16S rRNA Gene and Metagenomic Sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {922554}, pmid = {35800388}, issn = {2235-2988}, mesh = {Bacteria/genetics ; Cervix Uteri/microbiology ; Female ; Genes, rRNA ; Humans ; *Microbiota/genetics ; *Papillomavirus Infections ; RNA, Ribosomal, 16S/genetics ; Vagina/microbiology ; }, abstract = {The relationship between the cervico-vaginal microbiome and high-risk human papillomavirus (HR-HPV) is well observed. However, there is a lack of adequate research regarding the cervical microbiota in HR-HPV infection. Most published research results have used 16S rRNA gene sequencing technology; this technology only focuses on marker sequences, resulting in incomplete gene information acquisition. Metagenomic sequencing technology can effectively compensate for the deficiency of 16S rRNA gene sequencing, thus improving the analysis of microbiota function. Cervical swab samples from 20 females with HR-HPV infection and 20 uninfected (Control) women were analyzed through 16S rRNA gene and metagenomic sequencing. Our results indicated that the composition and function of the cervical microbiota of HR-HPV infection differed notably from that of control women. Compared with control women, Firmicutes was decreased during HR-HPV infection, whereas Actinobacteria was increased. At the genus level, Lactobacillus was enriched in control women, while levels of Gardnerella and Bifidobacterium were lower. At the species level, Lactobacillus crispatus, L. jensenii, and L. helveticus were enriched in control women; these were the top three species with biomarker significance between the two groups. Eight pathways and four KEGG orthologies of the cervical microbiota of statistical differences were identified between the HR-HPV infection and control women. Collectively, our study described the cervical microbiota and its potential function during HR-HPV infection. Biomarkers of cervical microbiota and the changed bacterial metabolic pathways and metabolites can help clarify the pathogenic mechanism of HR-HPV infection, making them promising targets for clinical treatment and intervention for HR-HPV infection and cervical carcinoma.}, } @article {pmid35800387, year = {2022}, author = {Hong, RP and Hou, YY and Xu, XJ and Lang, JD and Jin, YF and Zeng, XF and Zhang, X and Tian, G and You, X}, title = {The Difference of Gut Microbiota and Their Correlations With Urinary Organic Acids Between Autistic Children With and Without Atopic Dermatitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {886196}, pmid = {35800387}, issn = {2235-2988}, mesh = {Aconitic Acid/analysis ; Adipates/analysis ; *Autistic Disorder ; Child ; Clostridiales ; *Dermatitis, Atopic/complications/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; }, abstract = {Autism is a kind of biologically based neurodevelopmental condition, and the coexistence of atopic dermatitis (AD) is not uncommon. Given that the gut microbiota plays an important role in the development of both diseases, we aimed to explore the differences of gut microbiota and their correlations with urinary organic acids between autistic children with and without AD. We enrolled 61 autistic children including 36 with AD and 25 without AD. The gut microbiota was sequenced by metagenomic shotgun sequencing, and the diversity, compositions, and functional pathways were analyzed further. Urinary organic acids were assayed by gas chromatography-mass spectrometry, and univariate/multivariate analyses were applied. Spearman correlation analysis was conducted to explore their relationships. In our study, AD individuals had more prominent gastrointestinal disorders. The alpha diversity of the gut microbiota was lower in the AD group. LEfSe analysis showed a higher abundance of Anaerostipes caccae, Eubacterium hallii, and Bifidobacterium bifidum in AD individuals, with Akkermansia muciniphila, Roseburia intestinalis, Haemophilus parainfluenzae, and Rothia mucilaginosa in controls. Meanwhile, functional profiles showed that the pathway of lipid metabolism had a higher proportion in the AD group, and the pathway of xenobiotics biodegradation was abundant in controls. Among urinary organic acids, adipic acid, 3-hydroxyglutaric acid, tartaric acid, homovanillic acid, 2-hydroxyphenylacetic acid, aconitic acid, and 2-hydroxyhippuric acid were richer in the AD group. However, only adipic acid remained significant in the multivariate analysis (OR = 1.513, 95% CI [1.042, 2.198], P = 0.030). In the correlation analysis, Roseburia intestinalis had a negative correlation with aconitic acid (r = -0.14, P = 0.02), and the latter was positively correlated with adipic acid (r = 0.41, P = 0.006). Besides, the pathway of xenobiotics biodegradation seems to inversely correlate with adipic acid (r = -0.42, P = 0.18). The gut microbiota plays an important role in the development of AD in autistic children, and more well-designed studies are warranted to explore the underlying mechanism.}, } @article {pmid35800120, year = {2022}, author = {Lyu, J and Deng, Q and Li, R and Tian, B and Zhao, Y and Hu, X and Zhou, M and Gu, B}, title = {Pneumonia Caused by Coinfection with Cytomegalovirus and Pneumocystis jirovecii in an HIV-Negative Infant Diagnosed by Metagenomic Next-Generation Sequencing.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {3417-3425}, pmid = {35800120}, issn = {1178-6973}, abstract = {BACKGROUND: Pneumonia produced by coinfection with Pneumocystis jirovecii (PJ) and cytomegalovirus (CMV) in infants and young children without timely diagnosis and treatment is often fatal due to the limitations of traditional tests. More accurate and rapid diagnostic methods for multiple infections are urgently needed.

CASE PRESENTATION: Here, we report a case of a 2-month-old boy with pneumonia caused by Pneumocystis jirovecii (PJ) and cytomegalovirus (CMV) without HIV infection. Chest computed tomography (CT) showed massive exudative consolidation in both lungs. Microscopic examination of stained sputum and smear specimens and bacterial and fungal culture tests were all negative, and CMV nucleic acid and antibody tests were positive. After a period of antiviral and anti-infective therapy, pulmonary inflammation was not relieved. Subsequently, sputum and venous blood samples were analysed by metagenomic next-generation sequencing (mNGS), and the sequences of PJ and CMV were acquired. The patient was finally diagnosed with pneumonia caused by PJ and CMV coinfection. Anti-fungal combined with anti-viral therapy was given immediately. mNGS re-examination of bronchoalveolar lavage fluid (BALF) also revealed the same primary pathogen. Therapy was stopped due to the request of the patient's guardian. Hence, the child was discharged from the hospital and eventually died.

CONCLUSION: This case emphasizes the combined use of mNGS and traditional tests in the clinical diagnosis of mixed lung infections in infants without HIV infection. mNGS is a new adjunctive diagnostic method that can rapidly discriminate multiple causes of pneumonia.}, } @article {pmid35800027, year = {2022}, author = {Palmer, M and Sutcliffe, I and Venter, SN and Hedlund, BP}, title = {It is time for a new type of type to facilitate naming the microbial world.}, journal = {New microbes and new infections}, volume = {47}, number = {}, pages = {100991}, pmid = {35800027}, issn = {2052-2975}, abstract = {Since January 1, 2001, the only acceptable nomenclatural type for species under the International Code of Nomenclature of Prokaryotes (ICNP) has been pure cultures. Here, we argue that this requirement is discordant with the more inclusive nature of nomenclatural types accepted under other codes of nomenclature and posit that the unique rigidity of the ICNP has failed to serve the broad research community and has stifled progress. This case is based on the axiom that many archaea and bacteria are interdependent in nature and therefore difficult, if not impossible, to grow, preserve, and distribute as pure cultures. As such, a large proportion of Earth's biodiversity cannot be named under the current system, which limits our ability to communicate about microbial diversity within and beyond the microbiology research community. Genome sequence data are now encouraged for valid publication of new taxa in microbial systematics journals, and metagenome-assembled genomes and single cell-amplified genomes are being generated rapidly from every biome on Earth. Thus, genome sequences are available for both cultivated and uncultivated microorganisms and can readily serve as a new category of nomenclatural type, allowing for a unified nomenclature for all archaea and bacteria, whether or not they are available as pure cultures. Ideally this would be under a single code of nomenclature but, as we review here, the newly established SeqCode will operate in parallel with the ICNP as a first step toward this goal.}, } @article {pmid35799838, year = {2022}, author = {Ramírez, GA and Keshri, J and Vahrson, I and Garber, AI and Berrang, ME and Cox, NA and González-Cerón, F and Aggrey, SE and Oakley, BB}, title = {Cecal Microbial Hydrogen Cycling Potential Is Linked to Feed Efficiency Phenotypes in Chickens.}, journal = {Frontiers in veterinary science}, volume = {9}, number = {}, pages = {904698}, pmid = {35799838}, issn = {2297-1769}, abstract = {In chickens, early life exposure to environmental microbes has long-lasting impacts on gastrointestinal (GI) microbiome development and host health and growth, via mechanisms that remain uncharacterized. In this study, we demonstrated that administrating a fecal microbiome transplant (FMT) from adults to day-of-hatch chicks results in significantly higher body mass of birds and decreased residual feed intake (RFI), implying enhanced feed efficiency, at 6 weeks of age. To assess the potential mechanisms through which FMT affects adult bird phenotype, we combined 16 S rRNA gene amplification, metagenomic, and comparative genomic approaches to survey the composition and predicted activities of the resident microbiome of various GI tract segments. Early life FMT exposure had a long-lasting significant effect on the microbial community composition and function of the ceca but not on other GI segments. Within the ceca of 6-week-old FMT birds, hydrogenotrophic microbial lineages and genes were most differentially enriched. The results suggest that thermodynamic regulation in the cecum, in this case via hydrogenotrophic methanogenic and sulfur-cycling lineages, potentially serving as hydrogen sinks, may enhance fermentative efficiency and dietary energy harvest capacity. Our study provides a specific mechanism of action through which early-life microbiome transplants modulate market-relevant phenotypes in poultry and, thereby, may represent a significant advance toward microbiome-focused sustainable agriculture.}, } @article {pmid35799697, year = {2022}, author = {Boudar, Z and Sehli, S and El Janahi, S and Al Idrissi, N and Hamdi, S and Dini, N and Brim, H and Amzazi, S and Nejjari, C and Lloyd-Puryear, M and Ghazal, H}, title = {Metagenomics Approaches to Investigate the Neonatal Gut Microbiome.}, journal = {Frontiers in pediatrics}, volume = {10}, number = {}, pages = {886627}, pmid = {35799697}, issn = {2296-2360}, abstract = {Early infancy is critical for the development of an infant's gut flora. Many factors can influence microbiota development during the pre- and postnatal periods, including maternal factors, antibiotic exposure, mode of delivery, dietary patterns, and feeding type. Therefore, investigating the connection between these variables and host and microbiome interactions in neonatal development would be of great interest. As the "unculturable" era of microbiome research gives way to an intrinsically multidisciplinary field, microbiome research has reaped the advantages of technological advancements in next-generation sequencing, particularly 16S rRNA gene amplicon and shotgun sequencing, which have considerably expanded our knowledge about gut microbiota development during early life. Using omics approaches to explore the neonatal microbiome may help to better understand the link between the microbiome and newborn diseases. Herein, we summarized the metagenomics methods and tools used to advance knowledge on the neonatal microbiome origin and evolution and how the microbiome shapes early and late individuals' lives for health and disease. The way to overcome limitations in neonatal microbiome studies will be discussed.}, } @article {pmid35799498, year = {2022}, author = {Vasileiadis, S and Perruchon, C and Scheer, B and Adrian, L and Steinbach, N and Trevisan, M and Plaza-Bolaños, P and Agüera, A and Chatzinotas, A and Karpouzas, DG}, title = {Nutritional inter-dependencies and a carbazole-dioxygenase are key elements of a bacterial consortium relying on a Sphingomonas for the degradation of the fungicide thiabendazole.}, journal = {Environmental microbiology}, volume = {24}, number = {11}, pages = {5105-5122}, doi = {10.1111/1462-2920.16116}, pmid = {35799498}, issn = {1462-2920}, mesh = {*Sphingomonas/genetics/metabolism ; Thiabendazole/metabolism ; *Fungicides, Industrial/metabolism ; *Dioxygenases/metabolism ; Biodegradation, Environmental ; Bacteria/genetics/metabolism ; Carbazoles/metabolism ; Vitamin B 12/metabolism ; }, abstract = {Thiabendazole (TBZ), is a persistent fungicide/anthelminthic and a serious environmental threat. We previously enriched a TBZ-degrading bacterial consortium and provided first evidence for a Sphingomonas involvement in TBZ transformation. Here, using a multi-omic approach combined with DNA-stable isotope probing (SIP) we verified the key degrading role of Sphingomonas and identify potential microbial interactions governing consortium functioning. SIP and amplicon sequencing analysis of the heavy and light DNA fraction of cultures grown on [13] C-labelled versus [12] C-TBZ showed that 66% of the [13] C-labelled TBZ was assimilated by Sphingomonas. Metagenomic analysis retrieved 18 metagenome-assembled genomes with the dominant belonging to Sphingomonas, Sinobacteriaceae, Bradyrhizobium, Filimonas and Hydrogenophaga. Meta-transcriptomics/-proteomics and non-target mass spectrometry suggested TBZ transformation by Sphingomonas via initial cleavage by a carbazole dioxygenase (car) to thiazole-4-carboxamidine (terminal compound) and catechol or a cleaved benzyl ring derivative, further transformed through an ortho-cleavage (cat) pathway. Microbial co-occurrence and gene expression networks suggested strong interactions between Sphingomonas and a Hydrogenophaga. The latter activated its cobalamin biosynthetic pathway and Sphingomonas its cobalamin salvage pathway to satisfy its B12 auxotrophy. Our findings indicate microbial interactions aligning with the 'black queen hypothesis' where Sphingomonas (detoxifier, B12 recipient) and Hydrogenophaga (B12 producer, enjoying detoxification) act as both helpers and beneficiaries.}, } @article {pmid35799219, year = {2022}, author = {Sinha, A and Li, Y and Mirzaei, MK and Shamash, M and Samadfam, R and King, IL and Maurice, CF}, title = {Transplantation of bacteriophages from ulcerative colitis patients shifts the gut bacteriome and exacerbates the severity of DSS colitis.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {105}, pmid = {35799219}, issn = {2049-2618}, support = {170921//CIHR/Canada ; }, mesh = {Animals ; Bacteria/genetics ; *Bacteriophages/genetics ; *Colitis/therapy ; *Colitis, Ulcerative/microbiology/therapy ; *Gastrointestinal Microbiome ; Inflammation ; *Inflammatory Bowel Diseases/microbiology ; Mice ; }, abstract = {BACKGROUND: Inflammatory bowel diseases (IBDs) including Crohn's disease (CD) and ulcerative colitis (UC) are characterized by chronic and debilitating gut inflammation. Altered bacterial communities of the intestine are strongly associated with IBD initiation and progression. The gut virome, which is primarily composed of bacterial viruses (bacteriophages, phages), is thought to be an important factor regulating and shaping microbial communities in the gut. While alterations in the gut virome have been observed in IBD patients, the contribution of these viruses to alterations in the bacterial community and heightened inflammatory responses associated with IBD patients remains largely unknown.

RESULTS: Here, we performed in vivo microbial cross-infection experiments to follow the effects of fecal virus-like particles (VLPs) isolated from UC patients and healthy controls on bacterial diversity and severity of experimental colitis in human microbiota-associated (HMA) mice. Shotgun metagenomics confirmed that several phages were transferred to HMA mice, resulting in treatment-specific alterations in the gut virome. VLPs from healthy and UC patients also shifted gut bacterial diversity of these mice, an effect that was amplified during experimental colitis. VLPs isolated from UC patients specifically altered the relative abundance of several bacterial taxa previously implicated in IBD progression. Additionally, UC VLP administration heightened colitis severity in HMA mice, as indicated by shortened colon length and increased pro-inflammatory cytokine production. Importantly, this effect was dependent on intact VLPs.

CONCLUSIONS: Our findings build on recent literature indicating that phages are dynamic regulators of bacterial communities in the gut and implicate the intestinal virome in modulating intestinal inflammation and disease. Video Abstract.}, } @article {pmid35799200, year = {2022}, author = {Escuder-Rodríguez, JJ and González-Suarez, M and deCastro, ME and Saavedra-Bouza, A and Becerra, M and González-Siso, MI}, title = {Characterization of a novel thermophilic metagenomic GH5 endoglucanase heterologously expressed in Escherichia coli and Saccharomyces cerevisiae.}, journal = {Biotechnology for biofuels and bioproducts}, volume = {15}, number = {1}, pages = {76}, pmid = {35799200}, issn = {2731-3654}, support = {ED431C 2020/08//Xunta de Galicia/ ; RTI2018-099249-B-I00//MINISTERIO DE CIENCIA, INNOVACIÓN Y UNIVERSIDADES (MICINN)/ ; }, abstract = {BACKGROUND: Endoglucanases from thermophilic microorganisms are a valuable resource as they can be used in a wide variety of biotechnological applications including the valorisation of biomass and the production of biofuels. In the present work we analysed the metagenome from the hot spring Muiño da Veiga, located in the northwest of Spain (in the Galicia region), in search for novel thermostable endoglucanases.

RESULTS: Sequence analysis of the metagenome revealed a promising enzyme (Cel776). Predictions on protein structure and conserved amino acid sequences were conducted, as well as expression in heterologous systems with Escherichia coli and Saccharomyces cerevisiae as the host. Cel776Ec was correctly expressed and purified by taking advantage of the His-Tag system, with a yield of 0.346 U/mL in the eluted fraction. Cel776Sc was expressed extracellulary and was easily recovered from the supernatant without the need of further purification, requiring only a concentration step by ultrafiltration, with a significantly higher yield of 531.95 U/mL, revealing a much more suitable system for production of large amounts of the enzyme. Their biochemical characterization revealed biotechnologically interesting enzymes. Both Cel776Ec and Cel776Sc had an optimal temperature of 80 °C and optimal pH of 5. Cel776Ec exhibited high thermostability maintaining its activity for 24 h at 60 °C and maintained its activity longer than Cel776Sc at increasing incubation temperatures. Moreover, its substrate specificity allowed the degradation of both cellulose and xylan. Whereas Cel776Ec was more active in the presence of calcium and magnesium, manganese was found to increase Cel776Sc activity. A stronger inhibitory effect was found for Cel776Ec than Cel776Sc adding detergent SDS to the reaction mix, whereas EDTA only significantly affected Cel776Sc activity.

CONCLUSIONS: Our study reports the discovery of a new promising biocatalyst for its application in processes, such as the production of biofuel and the saccharification of plant biomass, due to its bifunctional enzymatic activity as an endoglucanase and as a xylanase, as well as highlights the advantages of a yeast expression system over bacteria.}, } @article {pmid35799064, year = {2022}, author = {Neun, S and Brear, P and Campbell, E and Tryfona, T and El Omari, K and Wagner, A and Dupree, P and Hyvönen, M and Hollfelder, F}, title = {Functional metagenomic screening identifies an unexpected β-glucuronidase.}, journal = {Nature chemical biology}, volume = {18}, number = {10}, pages = {1096-1103}, pmid = {35799064}, issn = {1552-4469}, support = {BB/W000504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T003545/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Gene Library ; *Glucuronidase/genetics/metabolism ; Glycoside Hydrolases/chemistry ; Metagenome ; *Metagenomics ; }, abstract = {The abundance of recorded protein sequence data stands in contrast to the small number of experimentally verified functional annotation. Here we screened a million-membered metagenomic library at ultrahigh throughput in microfluidic droplets for β-glucuronidase activity. We identified SN243, a genuine β-glucuronidase with little homology to previously studied enzymes of this type, as a glycoside hydrolase 3 family member. This glycoside hydrolase family contains only one recently added β-glucuronidase, showing that a functional metagenomic approach can shed light on assignments that are currently 'unpredictable' by bioinformatics. Kinetic analyses of SN243 characterized it as a promiscuous catalyst and structural analysis suggests regions of divergence from homologous glycoside hydrolase 3 members creating a wide-open active site. With a screening throughput of >10[7] library members per day, picolitre-volume microfluidic droplets enable functional assignments that complement current enzyme database dictionaries and provide bridgeheads for the annotation of unexplored sequence space.}, } @article {pmid35798888, year = {2022}, author = {Schön, ME and Martijn, J and Vosseberg, J and Köstlbacher, S and Ettema, TJG}, title = {The evolutionary origin of host association in the Rickettsiales.}, journal = {Nature microbiology}, volume = {7}, number = {8}, pages = {1189-1199}, pmid = {35798888}, issn = {2058-5276}, support = {817834/ERC_/European Research Council/International ; }, mesh = {Humans ; *Metagenome ; Phylogeny ; *Rickettsiales/genetics ; }, abstract = {The evolution of obligate host-association of bacterial symbionts and pathogens remains poorly understood. The Rickettsiales are an alphaproteobacterial order of obligate endosymbionts and parasites that infect a wide variety of eukaryotic hosts, including humans, livestock, insects and protists. Induced by their host-associated lifestyle, Rickettsiales genomes have undergone reductive evolution, leading to small, AT-rich genomes with limited metabolic capacities. Here we uncover eleven deep-branching alphaproteobacterial metagenome assembled genomes from aquatic environments, including data from the Tara Oceans initiative and other publicly available datasets, distributed over three previously undescribed Rickettsiales-related clades. Phylogenomic analyses reveal that two of these clades, Mitibacteraceae and Athabascaceae, branch sister to all previously sampled Rickettsiales. The third clade, Gamibacteraceae, branch sister to the recently identified ectosymbiotic 'Candidatus Deianiraea vastatrix'. Comparative analyses indicate that the gene complement of Mitibacteraceae and Athabascaceae is reminiscent of that of free-living and biofilm-associated bacteria. Ancestral genome content reconstruction across the Rickettsiales species tree further suggests that the evolution of host association in Rickettsiales was a gradual process that may have involved the repurposing of a type IV secretion system.}, } @article {pmid35798742, year = {2022}, author = {Jo, S and Kang, W and Hwang, YS and Lee, SH and Park, KW and Kim, MS and Lee, H and Yoon, HJ and Park, YK and Chalita, M and Lee, JH and Sung, H and Lee, JY and Bae, JW and Chung, SJ}, title = {Oral and gut dysbiosis leads to functional alterations in Parkinson's disease.}, journal = {NPJ Parkinson's disease}, volume = {8}, number = {1}, pages = {87}, pmid = {35798742}, issn = {2373-8057}, support = {HI19C0256//Ministry of Health and Welfare (Ministry of Health, Welfare and Family Affairs)/ ; 2018-0622//Asan Institute for Life Sciences, Asan Medical Center/ ; }, abstract = {Although several studies have identified a distinct gut microbial composition in Parkinson's disease (PD), few studies have investigated the oral microbiome or functional alteration of the microbiome in PD. We aimed to investigate the connection between the oral and gut microbiome and the functional changes in the PD-specific gut microbiome using shotgun metagenomic sequencing. The taxonomic composition of the oral and gut microbiome was significantly different between PD patients and healthy controls (P = 0.003 and 0.001, respectively). Oral Lactobacillus was more abundant in PD patients and was associated with opportunistic pathogens in the gut (FDR-adjusted P < 0.038). Functional analysis revealed that microbial gene markers for glutamate and arginine biosynthesis were downregulated, while antimicrobial resistance gene markers were upregulated in PD patients than healthy controls (all P < 0.001). We identified a connection between the oral and gut microbiota in PD, which might lead to functional alteration of the microbiome in PD.}, } @article {pmid35796808, year = {2022}, author = {Sun, J and Yao, C and Li, Y and Wang, W and Hao, J and Yu, Y}, title = {A novel salt-tolerant GH42 β-galactosidase with transglycosylation activity from deep-sea metagenome.}, journal = {World journal of microbiology & biotechnology}, volume = {38}, number = {9}, pages = {154}, pmid = {35796808}, issn = {1573-0972}, support = {31900035//National Natural Science Foundation of China/ ; NO.2020TD67//Central Public-interest Scientific Institution Basal Research Fund, Chinese Academy of Fishery Sciences/ ; }, mesh = {Enzyme Stability ; Escherichia coli/genetics/metabolism ; Hydrogen-Ion Concentration ; Kinetics ; *Lactose ; *Metagenome ; Oligosaccharides ; Temperature ; beta-Galactosidase/genetics/metabolism ; }, abstract = {β-Galactosidase is a widely adopted enzyme in the food and pharmaceutical industries. Metagenome techniques have the advantage of discovering novel functional genes, particularly potential genes from uncultivated microbes. In this study, a novel GH42 β-galactosidase isolated from a deep-sea metagenome was overexpressed in Escherichia coli BL21 (DE3) and purified by affinity chromatography. The optimal temperatures and pH of the enzyme for o-nitrophenyl-β-D-galactopyranoside (oNPG) and lactose were 40 ℃, 6.5 and 50 ℃, 7, respectively. The enzyme was stable at temperatures between 4 and 30 ℃ and within the pH range of 6-9. Moreover, it was highly tolerant to salt and inhibited by Zn[2+] and Cu[2+]. The kinetic values of Km and kcat of the enzyme against oNPG were 1.1 mM and 57.8 s[-1], respectively. Furthermore, it showed hydrolysis and transglycosylation activity to lactose and the extra monosaccharides could improve the productivity of oligosaccharides. Overall, this recombinant β-galactosidase is a potential biocatalyst for the hydrolysis of milk lactose and synthesis of functional oligosaccharides.}, } @article {pmid35796792, year = {2022}, author = {Westaway, JAF and Huerlimann, R and Kandasamy, Y and Miller, CM and Norton, R and Watson, D and Infante-Vilamil, S and Rudd, D}, title = {Exploring the long-term colonisation and persistence of probiotic-prophylaxis species on the gut microbiome of preterm infants: a pilot study.}, journal = {European journal of pediatrics}, volume = {181}, number = {9}, pages = {3389-3400}, pmid = {35796792}, issn = {1432-1076}, mesh = {Aftercare ; Cross-Sectional Studies ; *Enterocolitis, Necrotizing/prevention & control ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Patient Discharge ; Pilot Projects ; *Probiotics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Preterm infants suffer from a higher incidence of acute diseases such as necrotising enterocolitis and sepsis. This risk can be mitigated through probiotic prophylaxis during admission. This reduction in risk is likely the result of acute modulation of the gut microbiome induced by probiotic species, which has been observed to occur up until discharge. We aimed to determine if this modulation, and the associated probiotic species, persisted beyond discharge. We conducted both a cross-sectional analysis (n = 18), at ~ 18 months of age, and a longitudinal analysis (n = 6), from admission to 18 months of the gut microbiome of preterm infants using both shotgun metagenomics and 16S rRNA profiling respectively. The 16S amplicon sequencing revealed that the microbial composition of the probiotic-supplemented infants changed dramatically over time, stabilising at discharge. However, species from the probiotic Infloran[®], as well as positive modulatory effects previously associated with supplementation, do not appear to persist beyond discharge and once prophylaxis has stopped. Conclusions: Although differences exist between supplemented and non-supplemented groups, the implications of these differences remain unclear. Additionally, despite a lack of long-term colonisation, the presence of probiotics during early neonatal life may still have modulatory effects on the microbiome assembly and immune system training. What is Known: • Evidence suggests modulation of the microbiome occurs during probiotic prophylaxis, which may support key taxa that exert positive immunological benefits. • Some evidence suggests that this modulation can persist post-prophylaxis. What is New: • We present support for long-term modulation in association with probiotic prophylaxis in a cohort of infants from North Queensland Australia. • We also observed limited persistence of the probiotic species post-discharge.}, } @article {pmid35795296, year = {2022}, author = {Sadiq, S and Chen, YM and Zhang, YZ and Holmes, EC}, title = {Resolving deep evolutionary relationships within the RNA virus phylum Lenarviricota.}, journal = {Virus evolution}, volume = {8}, number = {1}, pages = {veac055}, pmid = {35795296}, issn = {2057-1577}, abstract = {The RNA virus phylum Lenarviricota is composed of the fungi-associated families Narnaviridae and Mitoviridae, the RNA bacteriophage Leviviridae, and the plant and fungi-associated Botourmiaviridae. Members of the Lenarviricota are abundant in most environments and boast remarkable phylogenetic and genomic diversity. As this phylum includes both RNA bacteriophage and fungi- and plant-associated species, the Lenarviricota likely mark a major evolutionary transition between those RNA viruses associated with prokaryotes and eukaryotes. Despite the remarkable expansion of this phylum following metagenomic studies, the phylogenetic relationships among the families within the Lenarviricota remain uncertain. Utilising a large data set of relevant viral sequences, we performed phylogenetic and genomic analyses to resolve the complex evolutionary history within this phylum and identify patterns in the evolution of virus genome organisation. Despite limitations reflecting very high levels of sequence diversity, our phylogenetic analyses suggest that the Leviviridae comprise the basal lineage within the Lenarviricota. Our phylogenetic results also support the construction of a new virus family-the Narliviridae-comprising a set of diverse and phylogenetically distinct species, including a number of uniquely encapsidated viruses. We propose a taxonomic restructuring within the Lenarviricota to better reflect the phylogenetic relationships documented here, with the Botourmiaviridae and Narliviridae combined into the order Ourlivirales, the Narnaviridae remaining in the order Wolframvirales, and these orders combined into the single class, the Amabiliviricetes. In sum, this study provides insights into the complex evolutionary relationships among the diverse families that make up the Lenarviricota.}, } @article {pmid35795295, year = {2022}, author = {Wang, X and Ren, Z and Wang, L and Chen, J and Zhang, P and Chen, JP and Chen, X and Li, L and Lin, X and Qi, N and Luo, S and Xiang, R and Yuan, Z and Zhang, J and Wang, G and Sun, MH and Huang, Y and Hua, Y and Zou, J and Hou, F and Huang, Z and Du, S and Xiang, H and Sun, M and Liu, Q and Liao, M}, title = {Identification of coronaviruses in farmed wild animals reveals their evolutionary origins in Guangdong, southern China.}, journal = {Virus evolution}, volume = {8}, number = {1}, pages = {veac049}, pmid = {35795295}, issn = {2057-1577}, abstract = {Coronavirus infections cause diseases that range from mild to severe in mammals and birds. In this study, we detected coronavirus infections in 748 farmed wild animals of 23 species in Guangdong, southern China, by RT-PCR and metagenomic analysis. We identified four coronaviruses in these wild animals and analysed their evolutionary origins. Coronaviruses detected in Rhizomys sinensis were genetically grouped into canine and rodent coronaviruses, which were likely recombinants of canine and rodent coronaviruses. The coronavirus found in Phasianus colchicus was a recombinant pheasant coronavirus of turkey coronavirus and infectious bronchitis virus. The coronavirus in Paguma larvata had a high nucleotide identity (94.6-98.5 per cent) with a coronavirus of bottlenose dolphin (Tursiops truncates). These findings suggested that the wildlife coronaviruses may have experienced homologous recombination and/or crossed the species barrier, likely resulting in the emergence of new coronaviruses. It is necessary to reduce human-animal interactions by prohibiting the eating and raising of wild animals, which may contribute to preventing the emergence of the next coronavirus pandemic.}, } @article {pmid35794664, year = {2022}, author = {Xu, Y and Milburn, O and Beiersdorfer, T and Du, L and Akinbi, H and Haslam, DB}, title = {Antibiotic exposure prevents acquisition of beneficial metabolic functions in the preterm infant gut microbiome.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {103}, pmid = {35794664}, issn = {2049-2618}, support = {UL1 TR001425/TR/NCATS NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; Child, Preschool ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; *Microbiota ; }, abstract = {BACKGROUND: Aberrations in the preterm microbiome following antibiotic therapy have been reported in previous studies. The objective of this study was to probe potential underlying mechanisms between this observation and susceptibility to adverse prematurity-related outcomes.

RESULTS: Metagenomic shotgun sequencing was performed on 133 stool and 253 skin samples collected at 1 and 3 weeks of age from 68 infants born at <36 weeks postmenstrual age and birth weight <2000 g. After accounting for gestational age and maternal antibiotics, the distribution of organisms in all samples and the corresponding metabolic pathway abundance were compared between infants exposed to postnatal antibiotics and antibiotics-naïve infants. In antibiotic-naïve infants, gestational and postnatal age imparted similar trajectories on maturation of the microbial community and associated metabolic functional capacity, with postnatal age exerting greater contribution. Antibiotic exposure was associated with reversal in maturation trajectory from the first week to the third week of age (p< 0.001). Butyrate-producing genera, including Clostridium and Blautia, were significantly more abundant in antibiotic-naïve neonates at 3 weeks postnatal age. Correspondingly, metabolic pathways required for short-chain fatty acid synthesis were significantly increased in antibiotic-naïve infants, but not in antibiotic-exposed neonates, at 3 weeks after birth.

CONCLUSIONS: Early brief antibiotic exposure markedly disrupts developmental trajectory of the neonatal microbiome and its corresponding functional capacity. Our findings may provide a mechanistic explanation for the known associations between antibiotic use and adverse outcomes in preterm infants. Video Abstract.}, } @article {pmid35794639, year = {2022}, author = {Hoque, MN and Rahman, MS and Islam, T and Sultana, M and Crandall, KA and Hossain, MA}, title = {Induction of mastitis by cow-to-mouse fecal and milk microbiota transplantation causes microbiome dysbiosis and genomic functional perturbation in mice.}, journal = {Animal microbiome}, volume = {4}, number = {1}, pages = {43}, pmid = {35794639}, issn = {2524-4671}, abstract = {BACKGROUND: Mastitis pathogenesis involves a wide range of opportunistic and apparently resident microorganims including bacteria, viruses and archaea. In dairy animals, microbes reside in the host, interact with environment and evade the host immune system, providing a potential for host-tropism to favor mastitis pathogenesis. To understand the host-tropism phenomena of bovine-tropic mastitis microbiomes, we developed a cow-to-mouse mastitis model.

METHODS: A cow-to-mouse mastitis model was established by fecal microbiota transplantation (FMT) and milk microbiota transplantation (MMT) to pregnant mice to assess microbiome dysbiosis and genomic functional perturbations through shotgun whole metagenome sequencing (WMS) along with histopathological changes in mice mammary gland and colon tissues.

RESULTS: The cow-to-mouse FMT and MMT from clinical mastitis (CM) cows induced mastitis syndromes in mice as evidenced by histopathological changes in mammary gland and colon tissues. The WMS of 24 samples including six milk (CM = 3, healthy; H = 3), six fecal (CM = 4, H = 2) samples from cows, and six fecal (CM = 4, H = 2) and six mammary tissue (CM = 3, H = 3) samples from mice generating 517.14 million reads (average: 21.55 million reads/sample) mapped to 2191 bacterial, 94 viral and 54 archaeal genomes. The Kruskal-Wallis test revealed significant differences (p = 0.009) in diversity, composition, and relative abundances in microbiomes between CM- and H-metagenomes. These differences in microbiome composition were mostly represented by Pseudomonas aeruginosa, Lactobacillus crispatus, Klebsiella oxytoca, Enterococcus faecalis, Pantoea dispersa in CM-cows (feces and milk), and Muribaculum spp., Duncaniella spp., Muribaculum intestinale, Bifidobacterium animalis, Escherichia coli, Staphylococcus aureus, Massilia oculi, Ralstonia pickettii in CM-mice (feces and mammary tissues). Different species of Clostridia, Bacteroida, Actinobacteria, Flavobacteriia and Betaproteobacteria had a strong co-occurrence and positive correlation as the indicator species of murine mastitis. However, both CM cows and mice shared few mastitis-associated microbial taxa (1.14%) and functional pathways regardless of conservation of mastitis syndromes, indicating the higher discrepancy in mastitis-associated microbiomes among lactating mammals.

CONCLUSIONS: We successfully induced mastitis by FMT and MMT that resulted in microbiome dysbiosis and genomic functional perturbations in mice. This study induced mastitis in a mouse model through FMT and MMT, which might be useful for further studies- focused on pathogen(s) involved in mastitis, their cross-talk among themselves and the host.}, } @article {pmid35794633, year = {2022}, author = {Kanukollu, S and Remus, R and Rücker, AM and Buchen-Tschiskale, C and Hoffmann, M and Kolb, S}, title = {Methanol utilizers of the rhizosphere and phyllosphere of a common grass and forb host species.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {35}, pmid = {35794633}, issn = {2524-6372}, support = {KO 2912/9-1//deutsche forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: Managed grasslands are global sources of atmospheric methanol, which is one of the most abundant volatile organic compounds in the atmosphere and promotes oxidative capacity for tropospheric and stratospheric ozone depletion. The phyllosphere is a favoured habitat of plant-colonizing methanol-utilizing bacteria. These bacteria also occur in the rhizosphere, but their relevance for methanol consumption and ecosystem fluxes is unclear. Methanol utilizers of the plant-associated microbiota are key for the mitigation of methanol emission through consumption. However, information about grassland plant microbiota members, their biodiversity and metabolic traits, and thus key actors in the global methanol budget is largely lacking.

RESULTS: We investigated the methanol utilization and consumption potentials of two common plant species (Festuca arundinacea and Taraxacum officinale) in a temperate grassland. The selected grassland exhibited methanol formation. The detection of [13]C derived from [13]C-methanol in 16S rRNA of the plant microbiota by stable isotope probing (SIP) revealed distinct methanol utilizer communities in the phyllosphere, roots and rhizosphere but not between plant host species. The phyllosphere was colonized by members of Gamma- and Betaproteobacteria. In the rhizosphere, [13]C-labelled Bacteria were affiliated with Deltaproteobacteria, Gemmatimonadates, and Verrucomicrobiae. Less-abundant [13]C-labelled Bacteria were affiliated with well-known methylotrophs of Alpha-, Gamma-, and Betaproteobacteria. Additional metagenome analyses of both plants were consistent with the SIP results and revealed Bacteria with methanol dehydrogenases (e.g., MxaF1 and XoxF1-5) of known but also unusual genera (i.e., Methylomirabilis, Methylooceanibacter, Gemmatimonas, Verminephrobacter). [14]C-methanol tracing of alive plant material revealed divergent potential methanol consumption rates in both plant species but similarly high rates in the rhizosphere and phyllosphere.

CONCLUSIONS: Our study revealed the rhizosphere as an overlooked hotspot for methanol consumption in temperate grasslands. We further identified unusual new but potentially relevant methanol utilizers besides well-known methylotrophs in the phyllosphere and rhizosphere. We did not observe a plant host-specific methanol utilizer community. Our results suggest that our approach using quantitative SIP and metagenomics may be useful in future field studies to link gross methanol consumption rates with the rhizosphere and phyllosphere microbiome.}, } @article {pmid35794548, year = {2022}, author = {Su, XH and Li, WP and Lin, Q and Zheng, XJ and Fang, T and Jiang, Y and Peng, FH}, title = {Case report: a special case of cryptococcal infection-related inflammatory syndrome in a non-HIV infected and non-transplant patient.}, journal = {BMC neurology}, volume = {22}, number = {1}, pages = {247}, pmid = {35794548}, issn = {1471-2377}, support = {82071265//national natural science foundation of china/ ; 202102010288//the Science and Technology Program of Guangzhou, China/ ; 2021A1515110231//Guangdong Basic and Applied Basic Research Foundation/ ; }, mesh = {Adult ; Antifungal Agents/therapeutic use ; *Cryptococcosis/complications/diagnosis/drug therapy ; *Cryptococcus neoformans ; Humans ; Male ; *Meningitis, Cryptococcal/complications/diagnosis/drug therapy ; *Meningoencephalitis/complications ; Syndrome ; Voriconazole ; }, abstract = {BACKGROUND: Cryptococcal meningoencephalitis (CM) is a severe infection of central nervous system with high mortality and morbidity. Infection-related inflammatory syndrome is a rare complication of CM. Herein, we report a case of CM complicated by infection-related inflammatory syndrome.

CASE PRESENTATION: A 42-year-old man with chronic hepatitis B presented with a 3-day history of aphasia and left hemiparesis at an outside medical facility. The brain magnetic resonance imaging (MRI) showed symmetric and confluent hyperintense signal abnormalities mainly located in the basal ganglia, internal capsule, external capsule, periventricular, corona radiata, frontal and temporal lobes. Cerebrospinal fluid (CSF) examinations revealed elevated leukocyte and protein. India ink staining was positive for Cryptococcus. CSF culture and metagenomic next-generation sequencing (mNGS) confirmed Cryptococcus neoformans. Initial response was observed with intravenous fluconazole (400 mg per day). However, 11 days later, he developed impaired consciousness and incontinence of urine and feces. A repeat brain MRI showed the lesions were progressive and enlarged. The patient was referred to our department at this point of time. Repeat CSF analysis (India ink staining, culture and mNGS) re-confirmed Cryptococcus. However, clinical worsening after initial improvement, laboratory examinations and brain MRI findings suggested a diagnosis of infection-related inflammatory syndrome. Therefore, a combination of corticosteroids and antifungal therapy was initiated. At follow-up, a complete neurological recovery without any relapse was documented. The repeat brain MRI showed complete resolution of the previous lesions.

CONCLUSIONS: This case demonstrated that cryptococcal inflammatory syndromes must be suspected in cases of CM if an otherwise unexplained clinical deterioration is observed after initial recovery. The same can happen even before the primary infection is controlled. Thus, timely identification and prompt treatment is vital to reduce the mortality and disability of CM. The administration of corticosteroids in combination with antifungal therapy is an effective strategy in such cases. Clinical course and treatment process of the patient. Hemiparalysis and aphasia improved after the initiation of antifungal treatment. However, the patient developed impaired consciousness companied by deterioration of brain MRI findings. He was treated with adjunctive glucocorticoid taper therapy consisting of dexamethasone (20 mg/day, intravenously) for 1 week followed by oral prednisone 1 mg/kg/day, tapered based on clinical and radiological response, along with amphotericin B (0.6 mg/kg/day, intravenously), voriconazole (400 mg/day in 2 divided doses, intravenously), and 5-flucytosine (100 mg/kg/day in 4 divided doses, orally). Two weeks later, his symptoms improved significantly. After discharge, he began oral voriconazole for consolidation and maintenance therapy for 8 weeks and 9 months respectively. He recovered without any neurological sequelae at 6-month follow-up. Note: MRI = magnetic resonance imaging.}, } @article {pmid35794493, year = {2022}, author = {Abraham, A and Kidanemariam, DB and Winter, S and Vetten, HJ}, title = {A novel nepovirus causing a chlorotic fleck disease on common bean (Phaseolus vulgaris L.).}, journal = {Archives of virology}, volume = {167}, number = {10}, pages = {2057-2061}, pmid = {35794493}, issn = {1432-8798}, support = {Alexander von Humboldt-Stiftung//Alexander von Humboldt-Stiftung/ ; Federal Ministry for Economic Cooperation and Development//Federal Ministry for Economic Cooperation and Development/ ; }, mesh = {Animals ; *Begomovirus ; *Nepovirus ; *Phaseolus ; Phylogeny ; Plant Diseases ; Zinc Phosphate Cement ; }, abstract = {Two common bean leaf samples from Ethiopia that had shown chlorotic fleck and veinal mosaic symptoms but tested ELISA-negative for known viruses were mechanically transmitted to herbaceous hosts to obtain virus isolates ET-773/4 and ET-779. Virus purification from Chenopodium quinoa systemically infected with ET-773/4 yielded icosahedral particles measuring ~ 30 nm in diameter and containing a single capsid protein of ~ 58 kDa, suggesting a nepovirus infection. Analysis of nucleotide sequences generated from RNA1 and RNA2 of the isolates indicated that they represent a distinct virus species in the genus Nepovirus. Surprisingly, the most closely related sequence in the GenBank database was that of Hobart nepovirus 3, an incompletely described metagenomic sequence obtained from honey bees in Tasmania. This new nepovirus from Ethiopia is provisionally named "bean chlorotic fleck virus".}, } @article {pmid35794486, year = {2022}, author = {Zhang, K and Wu, X and Zhang, T and Cen, C and Mao, R and Pan, R}, title = {Pilot investigation on biostability of drinking water distribution systems under water source switching.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {13-16}, pages = {5273-5286}, pmid = {35794486}, issn = {1432-0614}, mesh = {Adenosine Triphosphate ; Aged ; Biofilms ; *Drinking Water ; Humans ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; Water Microbiology ; Water Quality ; Water Supply ; }, abstract = {Water quality deterioration of drinking water distribution systems (DWDSs) caused by water source switching has been reported previously. However, systematic investigation of the biostability of DWDS under water source switching is limited. Aged pipes, including three commonly used pipe materials dug out from a practical DWDS, were used to systematically investigate the biofilm stability mechanism of DWDS under water source switching to quality-improved water. An increase in adenosine triphosphate (ATP) concentration in the bulk water during the initial stage of the switching period was observed, indicating the risk of biofilm release through aged pipe surfaces after water source switching. Sloughing of biofilms might contribute to temporary instability. From day 35, the ATP concentration in the polyethylene (PE) and plastic stainless steel composite (PS) pipes were maintained at approximately 2.40 and 2.56 ng/L, respectively. In contrast, the ATP concentration in the ductile iron (DI) pipes was higher, at approximately 3.43 ng/L from day 42. The water quality variation could cause areas of the biofilm to slough and reduce the biomass of biofilm, causing partial alteration of the microbial community. 16S rRNA gene amplicon sequencing-based functional prediction revealed that the biofilm could increase the abundance of chlorine-resistant bacteria attributed to the increase in Pseudomonas and Methylobacterium after switching to quality-improved water. Moreover, the profiles of specific pathways linked to human diseases, antibiotic resistance, and antibiotic biosynthesis revealed that the safety of the biofilm could improve after switching to quality-improved water. KEY POINTS: • The PE and PS biofilm showed improved resistance to water quality perturbation. • Greater number of Methylobacterium was found in the biofilm after water source switching. • 3.16S gene-based metagenomics prediction revealed that the safety of the biofilm under water source switching.}, } @article {pmid35794092, year = {2022}, author = {Doyle, SR and Søe, MJ and Nejsum, P and Betson, M and Cooper, PJ and Peng, L and Zhu, XQ and Sanchez, A and Matamoros, G and Sandoval, GAF and Cutillas, C and Tchuenté, LT and Mekonnen, Z and Ame, SM and Namwanje, H and Levecke, B and Berriman, M and Fredensborg, BL and Kapel, CMO}, title = {Population genomics of ancient and modern Trichuris trichiura.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3888}, pmid = {35794092}, issn = {2041-1723}, support = {MR/T020733/1/MRC_/Medical Research Council/United Kingdom ; 206194/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Animals ; Genome-Wide Association Study ; Humans ; Metagenomics ; Phylogeny ; Primates/genetics ; *Trichuriasis/epidemiology ; *Trichuris/genetics ; }, abstract = {The neglected tropical disease trichuriasis is caused by the whipworm Trichuris trichiura, a soil-transmitted helminth that has infected humans for millennia. Today, T. trichiura infects as many as 500 million people, predominantly in communities with poor sanitary infrastructure enabling sustained faecal-oral transmission. Using whole-genome sequencing of geographically distributed worms collected from human and other primate hosts, together with ancient samples preserved in archaeologically-defined latrines and deposits dated up to one thousand years old, we present the first population genomics study of T. trichiura. We describe the continent-scale genetic structure between whipworms infecting humans and baboons relative to those infecting other primates. Admixture and population demographic analyses support a stepwise distribution of genetic variation that is highest in Uganda, consistent with an African origin and subsequent translocation with human migration. Finally, genome-wide analyses between human samples and between human and non-human primate samples reveal local regions of genetic differentiation between geographically distinct populations. These data provide insight into zoonotic reservoirs of human-infective T. trichiura and will support future efforts toward the implementation of genomic epidemiology of this globally important helminth.}, } @article {pmid35793793, year = {2022}, author = {Lee, JY and Mitchell, HD and Burnet, MC and Wu, R and Jenson, SC and Merkley, ED and Nakayasu, ES and Nicora, CD and Jansson, JK and Burnum-Johnson, KE and Payne, SH}, title = {Uncovering Hidden Members and Functions of the Soil Microbiome Using De Novo Metaproteomics.}, journal = {Journal of proteome research}, volume = {21}, number = {8}, pages = {2023-2035}, pmid = {35793793}, issn = {1535-3907}, mesh = {*Microbiota/genetics ; Peptides/analysis/genetics ; Proteome/genetics ; *Proteomics/methods ; RNA, Ribosomal, 16S/genetics ; Soil ; }, abstract = {Metaproteomics has been increasingly utilized for high-throughput characterization of proteins in complex environments and has been demonstrated to provide insights into microbial composition and functional roles. However, significant challenges remain in metaproteomic data analysis, including creation of a sample-specific protein sequence database. A well-matched database is a requirement for successful metaproteomics analysis, and the accuracy and sensitivity of PSM identification algorithms suffer when the database is incomplete or contains extraneous sequences. When matched DNA sequencing data of the sample is unavailable or incomplete, creating the proteome database that accurately represents the organisms in the sample is a challenge. Here, we leverage a de novo peptide sequencing approach to identify the sample composition directly from metaproteomic data. First, we created a deep learning model, Kaiko, to predict the peptide sequences from mass spectrometry data and trained it on 5 million peptide-spectrum matches from 55 phylogenetically diverse bacteria. After training, Kaiko successfully identified organisms from soil isolates and synthetic communities directly from proteomics data. Finally, we created a pipeline for metaproteome database generation using Kaiko. We tested the pipeline on native soils collected in Kansas, showing that the de novo sequencing model can be employed as an alternative and complementary method to construct the sample-specific protein database instead of relying on (un)matched metagenomes. Our pipeline identified all highly abundant taxa from 16S rRNA sequencing of the soil samples and uncovered several additional species which were strongly represented only in proteomic data.}, } @article {pmid35793429, year = {2022}, author = {Su, XH and Li, WP and Liu, JY and Wang, YJ and Liu, J and Xu, XF and Yang, L and Xia, H and Jiang, Y and Peng, FH}, title = {Comparison of features and outcomes between HIV-negative patients with Cryptococcus gattii meningitis and Cryptococcus neoformans meningitis in South China.}, journal = {Mycoses}, volume = {65}, number = {9}, pages = {887-896}, doi = {10.1111/myc.13491}, pmid = {35793429}, issn = {1439-0507}, support = {2021A1515110231//Guangdong Basic and Applied Basic Research Foundation/ ; 82071265//National Natural Science Foundation of China/ ; 202102010288//Science and Technology Program of Guangzhou, China/ ; }, mesh = {Adult ; Aged ; *Cryptococcosis/microbiology ; *Cryptococcus gattii/genetics ; *Cryptococcus neoformans ; Female ; *HIV Infections/complications ; Humans ; Male ; *Meningitis, Cryptococcal/cerebrospinal fluid/drug therapy/epidemiology ; Middle Aged ; Retrospective Studies ; Young Adult ; }, abstract = {OBJECTIVES: The objective of this study is to compare the epidemiologic, clinical, laboratory, and imaging features, and outcomes in patients with Cryptococcus gattii meningitis (CGM) and Cryptococcus neoformans meningitis (CNM).

METHODS: We performed a retrospective study of HIV-negative patients with CGM and CNM (2015-2021) distinguished by metagenomic next-generation sequencing in cerebrospinal fluid in South China.

RESULTS: A total of 81 patients (17 CGM, 64 CNM) were enrolled (72.8% male, median age 49 years, range 21-77 years), and CGM patients were younger (median, 43 vs 53 years, p = .005). Of 17 CGM, VGI and VGII accounted for 70.6% and 29.4%, respectively. CGM patients had less underlying diseases (7/17 [41.2%] vs 48/64 [75%], p = .018) and focal neurologic deficit (3/17 [17.6%] vs 35/64 [54.7%], p = .022), had higher intracranial pressure (15/17 [88.2%] vs 25/64 [39.1%], p = .002), more meningeal enhancement (14/17 [82.4%] vs 32/64 [50%], p = .034), less parenchymal involvement (median, 1 vs 3, p = .018), more lung cryptococcomas (6/12 [50%] vs 6/47 [12.8%], p = .014), faster CSF fungal clearance (p = .004), less complications (median, 1 vs 3, p < .001), and more favourable outcomes (16/17 [94.1%] vs 41/64 [64.1%], p = .035).

CONCLUSIONS: This study demonstrated that species identification helps to guide therapy and predict outcomes.}, } @article {pmid35793264, year = {2023}, author = {Epstein, B and Burghardt, LT and Heath, KD and Grillo, MA and Kostanecki, A and Hämälä, T and Young, ND and Tiffin, P}, title = {Combining GWAS and population genomic analyses to characterize coevolution in a legume-rhizobia symbiosis.}, journal = {Molecular ecology}, volume = {32}, number = {14}, pages = {3798-3811}, doi = {10.1111/mec.16602}, pmid = {35793264}, issn = {1365-294X}, mesh = {*Rhizobium/genetics ; Symbiosis/genetics ; Genome-Wide Association Study ; Metagenomics ; *Medicago truncatula/genetics ; }, abstract = {The mutualism between legumes and rhizobia is clearly the product of past coevolution. However, the nature of ongoing evolution between these partners is less clear. To characterize the nature of recent coevolution between legumes and rhizobia, we used population genomic analysis to characterize selection on functionally annotated symbiosis genes as well as on symbiosis gene candidates identified through a two-species association analysis. For the association analysis, we inoculated each of 202 accessions of the legume host Medicago truncatula with a community of 88 Sinorhizobia (Ensifer) meliloti strains. Multistrain inoculation, which better reflects the ecological reality of rhizobial selection in nature than single-strain inoculation, allows strains to compete for nodulation opportunities and host resources and for hosts to preferentially form nodules and provide resources to some strains. We found extensive host by symbiont, that is, genotype-by-genotype, effects on rhizobial fitness and some annotated rhizobial genes bear signatures of recent positive selection. However, neither genes responsible for this variation nor annotated host symbiosis genes are enriched for signatures of either positive or balancing selection. This result suggests that stabilizing selection dominates selection acting on symbiotic traits and that variation in these traits is under mutation-selection balance. Consistent with the lack of positive selection acting on host genes, we found that among-host variation in growth was similar whether plants were grown with rhizobia or N-fertilizer, suggesting that the symbiosis may not be a major driver of variation in plant growth in multistrain contexts.}, } @article {pmid35792953, year = {2022}, author = {Nawaz, MZ and Wang, F}, title = {Meta-omics approaches reveal unique small RNAs exhibited by the uncultured microorganisms dwelling deep-sea hydrothermal sediment in Guaymas Basin.}, journal = {Archives of microbiology}, volume = {204}, number = {8}, pages = {461}, pmid = {35792953}, issn = {1432-072X}, support = {31290232//National Natural Science Foundation of China/ ; 41576129//National Natural Science Foundation of China/ ; 91228201//National Natural Science Foundation of China/ ; 91428308//National Natural Science Foundation of China/ ; DY125-22-04//China Ocean Mineral Resources Research and Development Association/ ; }, mesh = {Archaea/genetics/metabolism ; *Geologic Sediments/chemistry ; Methane/metabolism ; Phylogeny ; *RNA, Small Untranslated/metabolism ; }, abstract = {Small regulatory RNAs (sRNAs) are present in almost all investigated microbes, regarded as modulators and regulators of gene expression and also known to play their regulatory role in the environmentally significant process. It has been estimated that less than 1% of the microbes in nature are culturable in the laboratory, hindering our understanding of their physiology, and living strategies. However, recent big advancing of DNA sequencing and omics-related data analysis makes the understanding of the genetics, metabolic potentials, even ecological roles of uncultivated microbes possible. In this study, we used a metagenome and metatranscriptome-based integrated approach to identify small RNAs in the microbiome of Guaymas Basin sediments. Hundreds of environmental sRNAs comprising 228 groups were identified based on their homology, 82% of which displayed high similarity with previously known small RNAs in Rfam database, whereas, "18%" are putative novel sRNA motifs. A putative cis-acting sRNA potentially binding to methyl coenzyme M reductase, a key enzyme in methanogenesis or anaerobic oxidation of methane (AOM), was discovered in the genome of ANaerobic MEthane oxidizing archaea group 1 (ANME-1), which were the dominate microbe in the sample. These sRNAs were actively expressed in local Guaymas Basin hydrothermal environment, suggesting important roles of sRNAs in regulating microbial activity in natural environments.}, } @article {pmid35792945, year = {2022}, author = {Quintanilla-Mena, MA and Olvera-Novoa, MA and Sánchez-Tapia, IA and Lara-Pérez, LA and Rivas-Reyes, I and Gullian-Klanian, M and Patiño-Suárez, MV and Puch-Hau, CA}, title = {The digestive tract sections of the sea cucumber Isostichopus badionotus reveal differences in composition, diversity, and functionality of the gut microbiota.}, journal = {Archives of microbiology}, volume = {204}, number = {8}, pages = {463}, pmid = {35792945}, issn = {1432-072X}, support = {2015-01-1551//Consejo Nacional de Ciencia y Tecnología/ ; }, mesh = {Animals ; Firmicutes/genetics ; *Gastrointestinal Microbiome ; Gastrointestinal Tract ; RNA, Ribosomal, 16S/genetics ; *Sea Cucumbers ; }, abstract = {For the first time, this study analyses the composition and diversity of the gut microbiota of Isostichopus badionotus in captivity, using high-throughput 16S rRNA sequencing, and predicts the metagenomic functions of the microbiota. The results revealed a different composition of the gut microbiota for the foregut (FG) and midgut (MG) compared to the hindgut (HG), with a predominance of Proteobacteria, followed by Actinobacteria, Bacteroidetes, and Firmicutes. The FG and MG demonstrated a greater bacterial diversity compared to the HG. In addition, a complex network of interactions was observed at the genus level and identified some strains with probiotic and bioremediation potentials, such as Acinetobacter, Ruegeria, Streptococcus, Lactobacillus, Pseudomonas, Enterobacter, Aeromonas, Rhodopseudomonas, Agarivorans, Bacillus, Enterococcus, Micrococcus, Bifidobacterium, and Shewanella. Predicting metabolic pathways revealed that the bacterial composition in each section of the intestine participates in different physiological processes such as metabolism, genetic and environmental information processing, organismal systems, and cellular processes. Understanding and manipulating microbe--host-environment interactions and their associated functional capacity could substantially contribute to achieving more sustainable aquaculture systems for I. badionotus.}, } @article {pmid35792328, year = {2022}, author = {Zhang, L and Gong, X and Chen, Z and Zhou, Y}, title = {Genome-centric metagenomics analysis revealed the metabolic function of abundant microbial communities in thermal hydrolysis-assisted thermophilic anaerobic digesters under propionate stress.}, journal = {Bioresource technology}, volume = {360}, number = {}, pages = {127574}, doi = {10.1016/j.biortech.2022.127574}, pmid = {35792328}, issn = {1873-2976}, mesh = {Anaerobiosis ; Bacteria/genetics/metabolism ; Bioreactors/microbiology ; Hydrolysis ; *Metagenomics ; Methane/metabolism ; Methanosarcina/metabolism ; *Microbiota/genetics ; Propionates/metabolism ; }, abstract = {The ecological roles of microbial communities and how they interact with each other in thermal hydrolysis process (THP) assisted thermophilic anaerobic digestion (THP-AD) reactors remain largely unknown, especially under propionate stress. Two thermophilic THP-AD reactors had methane yield of 240-248 mL/g VSadded, but accumulated approximately 2000 mg/L propionate. Genome-centric metagenomics analysis showed that 68 metagenome-assembled genomes (MAGs) were recovered, 32 MAGs of which were substantially enriched. Firmicutes spp. dominated the enriched microbial community, including hydrolytic/fermentative bacteria and syntrophs. Methanogenic activities were mainly mediated by Methanosarcina sp. and Methanothermobacter spp. In addition to hydrogenotrophic methanogens, Thermodesulfovibrio sp. could also be a vital H2 scavenger, contributing to maintaining low H2 partial pressure in the bioreactors. The remarkable accumulation of propionate could be likely attributed to the weak syntrophic propionate-oxidizing activity or its absence. These findings advanced our knowledge about the mutualistic symbiosis of carbon metabolism in thermophilic THP-AD reactors.}, } @article {pmid35792018, year = {2022}, author = {Wang, J and Wang, Y and Han, F and Chen, J}, title = {Multiple diagnostic methods for mucormycosis: A retrospective case series.}, journal = {Journal of clinical laboratory analysis}, volume = {36}, number = {8}, pages = {e24588}, pmid = {35792018}, issn = {1098-2825}, mesh = {Adult ; Biopsy ; High-Throughput Nucleotide Sequencing ; Humans ; *Mucormycosis/diagnosis/drug therapy/microbiology ; Prognosis ; Retrospective Studies ; }, abstract = {BACKGROUND: Mucormycosis is a rare invasive fungal disease with high mortality. Early diagnosis and targeted drugs are crucial to improving clinical outcomes.

METHODS: We searched the electronic hospital database of the First Affiliated Hospital of Zhejiang University School of Medicine for adult patients with mucormycosis between 2000 and 2021. Demographic, clinical, treatment, and outcome data were collected and compared with the data in the relevant literature.

RESULTS: Eleven cases of mucormycosis-four of multisite infection, one of skin infection, five of lung infection, and one of gastrointestinal infection-were found and analyzed. The patients were diagnosed mainly based on pathological and histological findings, and three patients had metagenomic next-generation sequencing findings. Delayed diagnosis (i.e., diagnosis >7 days after patient admission or >30 days after onset of symptoms) results in poor prognosis compared with early diagnosis.

CONCLUSIONS: Improving awareness and shortening diagnosis time may improve the prognosis of mucormycosis. If mucormycosis is suspected, appropriate samples should be collected as soon as possible and submitted for biopsy, culture, or mNGS to confirm the diagnosis.}, } @article {pmid35791570, year = {2022}, author = {Wang, ZH and Jiang, XJ}, title = {[Contrasting Responses of the Microbial Community Structure and Functional Traits to Soil pH in Purple Soils].}, journal = {Huan jing ke xue= Huanjing kexue}, volume = {43}, number = {7}, pages = {3876-3883}, doi = {10.13227/j.hjkx.202111055}, pmid = {35791570}, issn = {0250-3301}, mesh = {Humans ; *Microbiota ; Nitrogen ; Phylogeny ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {To clarify the effect of pH on the structure and functional traits of soil microbial communities in purple soils, three purple upland soils developed from the same parent material that differed in pH were selected as the research objects, and metagenomic shotgun sequencing was used to investigate the structure and functional traits of the microbial communities among different pH soils. The shotgun sequencing identified a total of 89 phyla, 222 classes, 527 orders, 1009 families, 2769 genera, and 14354 species in these soils. Regardless of the phylogenetic classification level, the microbial community structures of these three purple soils with different pHs were significantly different. RDA results corroborated the highly significant difference in the microbial community structures among the three purple soils with different pHs, and the soil properties tested here all had significant correlations with soil microbial community structure, in which the soil pH had the greatest effect (R[2]=0.9985, P=0.001). However, the results of investigating the microbial community functions revealed that the main metabolic processes of the three purple soils were all involved in unknown functions, global and overview maps, amino acid metabolism, carbohydrate metabolism, ammonia assimilation, etc. There was almost no significant difference in the relative abundance of microbes in the three purple soils annotated with the same function regardless of the COG/KEGG functional database and nitrogen cycling functional database, indicating that the overall function trait of soil microbial community was relatively conservative and not easily affected by environmental factors.}, } @article {pmid35790781, year = {2022}, author = {Leviatan, S and Shoer, S and Rothschild, D and Gorodetski, M and Segal, E}, title = {An expanded reference map of the human gut microbiome reveals hundreds of previously unknown species.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3863}, pmid = {35790781}, issn = {2041-1723}, mesh = {*Cancer Vaccines ; Ecosystem ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome/genetics ; Metagenomics ; }, abstract = {The gut is the richest ecosystem of microbes in the human body and has great influence on our health. Despite many efforts, the set of microbes inhabiting this environment is not fully known, limiting our ability to identify microbial content and to research it. In this work, we combine new microbial metagenomic assembled genomes from 51,052 samples, with previously published genomes to produce a curated set of 241,118 genomes. Based on this set, we procure a new and improved human gut microbiome reference set of 3594 high quality species genomes, which successfully matches 83.65% validation samples' reads. This improved reference set contains 310 novel species, including one that exists in 19% of validation samples. Overall, this study provides a gut microbial genome reference set that can serve as a valuable resource for further research.}, } @article {pmid35789207, year = {2022}, author = {Sereika, M and Kirkegaard, RH and Karst, SM and Michaelsen, TY and Sørensen, EA and Wollenberg, RD and Albertsen, M}, title = {Oxford Nanopore R10.4 long-read sequencing enables the generation of near-finished bacterial genomes from pure cultures and metagenomes without short-read or reference polishing.}, journal = {Nature methods}, volume = {19}, number = {7}, pages = {823-826}, pmid = {35789207}, issn = {1548-7105}, mesh = {Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Nanopores ; Sequence Analysis, DNA ; }, abstract = {Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-finished genomes it has been necessary to include short-read polishing to correct insertions and deletions derived from homopolymer regions. Here, we show that Oxford Nanopore R10.4 can be used to generate near-finished microbial genomes from isolates or metagenomes without short-read or reference polishing.}, } @article {pmid35788780, year = {2022}, author = {Hernández-Guzmán, M and Pérez-Hernández, V and Gómez-Acata, S and Jiménez-Bueno, N and Verhulst, N and Muñoz-Arenas, LC and Navarro-Noya, YE and Luna-Guido, ML and Dendooven, L}, title = {Application of young maize plant residues alters the microbiome composition and its functioning in a soil under conservation agriculture: a metagenomics study.}, journal = {Archives of microbiology}, volume = {204}, number = {8}, pages = {458}, pmid = {35788780}, issn = {1432-072X}, mesh = {Agriculture ; Archaea/genetics ; Cellulose ; Metagenomics ; *Microbiota/genetics ; Soil ; *Zea mays ; }, abstract = {To increase our knowledge on how application of organic material alters soil microbial populations and functionality, shotgun metagenomic sequencing was used to determine the microbial communities and their potential functionality in an arable soil amended with young maize plants (Zea mays L.) in a laboratory experiment after 3 days. The relative abundance of bacterial and viral groups was strongly affected by organic material application, whereas that of the archaeal, protist and fungal groups was less affected. Cellulose degraders with copiotrophic lifestyle (e.g., Betaproteobacteria) were enriched in the amended soil, whereas the groups with slow growing oligotrophic and chemolithoautotrophic metabolism within Bacteria and Archaea were greater in the unamended than in the amended soil. The soil viral structure and richness were also affected. Caudovirales was the dominant viral family, with members of Siphoviridae enriched in the amended soil and members of Myoviridae in the unamended soil. More specialized metabolic traits related to both the degradation of complex C compounds and denitrification related genes were enriched in the young maize plant amended soil than in the unamended soil, whereas nitrification related genes were enriched in the latter. Copiotrophic life-style bacterial groups were enriched in the amended soil, whereas oligotrophic life-style bacterial groups in the unamended soil. Many bacterial and viral phylotypes were affected by the application of young maize plants, but the number of soil fungi, archaea and protists affected was smaller. Metabolic functionality was affected by the application of organic material as the relative abundance of genes involved in the denitrification process was higher in the maize plant amended soil than in the unamended soil and those involved in the nitrification process was higher in the unamended soil.}, } @article {pmid35788394, year = {2022}, author = {Wei, Y and Chang, L and Liu, G and Wang, X and Yang, Y and Hashimoto, K}, title = {Long-lasting beneficial effects of maternal intake of sulforaphane glucosinolate on gut microbiota in adult offspring.}, journal = {The Journal of nutritional biochemistry}, volume = {109}, number = {}, pages = {109098}, doi = {10.1016/j.jnutbio.2022.109098}, pmid = {35788394}, issn = {1873-4847}, mesh = {Adult Children ; Female ; *Gastrointestinal Microbiome/physiology ; Glucosinolates ; Humans ; Interleukin-6 ; Isothiocyanates ; Lipopolysaccharides ; Male ; Oximes ; Pregnancy ; Sulfoxides ; Tumor Necrosis Factor-alpha ; }, abstract = {Mounting evidence suggests the impact of maternal diet on the health of offspring. We reported that maternal diet of sulforaphane glucosinolate (SGS) could prevent behavioral abnormalities in offspring after maternal immune activation. The present study was designed to investigate whether the dietary intake of SGS during pregnancy and lactation influences the composition of gut microbiota in the offspring. The dietary intake of SGS during pregnancy and lactation caused significant changes in the α-diversity and β-diversity of gut microbiota in 3-week-old offspring (SGS-3W group) and 10-week-old offspring (SGS-10W group). The LEfSe algorithm identified several microbes as important phylotypes in the SGS-3W or SGS-10W groups. Predictive functional metagenomes showed that the maternal intake of SGS caused several KEGG pathways alterations with respect to the genetic information processing and metabolism. Furthermore, the plasma levels of interleukin-6 (IL-6) and tumor necrosis factor-α (TNF-α) in the SGS-10W group after the injection of lipopolysaccharide (LPS: 0.5 mg/kg) were significantly lower than those of the CON-10W group. It is noteworthy that there were positive correlations between the relative abundance of the genus Blautia and IL-6 (or TNF-α) in adult offspring. Moreover, there were sex differences of gut microbiota composition in offspring. In conclusion, these data suggest that the dietary intake of SGS during pregnancy and lactation might produce long-lasting beneficial effects in adult offspring through the persistent modulation of gut microbiota. It is likely that the modulation of gut microbiota by maternal nutrition may confer resilience versus vulnerability to stress-related psychiatric disorders in the offspring.}, } @article {pmid35788347, year = {2022}, author = {Nagata, N and Nishijima, S and Miyoshi-Akiyama, T and Kojima, Y and Kimura, M and Aoki, R and Ohsugi, M and Ueki, K and Miki, K and Iwata, E and Hayakawa, K and Ohmagari, N and Oka, S and Mizokami, M and Itoi, T and Kawai, T and Uemura, N and Hattori, M}, title = {Population-level Metagenomics Uncovers Distinct Effects of Multiple Medications on the Human Gut Microbiome.}, journal = {Gastroenterology}, volume = {163}, number = {4}, pages = {1038-1052}, doi = {10.1053/j.gastro.2022.06.070}, pmid = {35788347}, issn = {1528-0012}, mesh = {*Anti-Infective Agents ; Cross-Sectional Studies ; Fatty Acids, Volatile/pharmacology ; Feces/microbiology ; *Gastrointestinal Microbiome/physiology ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {BACKGROUND & AIMS: Medication is a major determinant of human gut microbiome structure, and its overuse increases the risks of morbidity and mortality. However, effects of certain commonly prescribed drugs and multiple medications on the gut microbiome are still underinvestigated.

METHODS: We performed shotgun metagenomic analysis of fecal samples from 4198 individuals in the Japanese 4D (Disease, Drug, Diet, Daily life) microbiome project. A total of 759 drugs were profiled, and other metadata, such as anthropometrics, lifestyles, diets, physical activities, and diseases, were prospectively collected. Second fecal samples were collected from 243 individuals to assess the effects of drug initiation and discontinuation on the microbiome.

RESULTS: We found that numerous drugs across different treatment categories influence the microbiome; more than 70% of the drugs we profiled had not been examined before. Individuals exposed to multiple drugs, polypharmacy, showed distinct gut microbiome structures harboring significantly more abundant upper gastrointestinal species and several nosocomial pathobionts due to additive drug effects. Polypharmacy was also associated with microbial functions, including the reduction of short-chain fatty acid metabolism and increased bacterial stress responses. Even nonantibiotic drugs were significantly correlated with an increased antimicrobial resistance potential through polypharmacy. Notably, a 2-time points dataset revealed the alteration and recovery of the microbiome in response to drug initiation and cessation, corroborating the observed drug-microbe associations in the cross-sectional cohort.

CONCLUSION: Our large-scale metagenomics unravels extensive and disruptive impacts of individual and multiple drug exposures on the human gut microbiome, providing a drug-microbe catalog as a basis for a deeper understanding of the role of the microbiome in drug efficacy and toxicity.}, } @article {pmid35788345, year = {2022}, author = {Gao, R and Wu, C and Zhu, Y and Kong, C and Zhu, Y and Gao, Y and Zhang, X and Yang, R and Zhong, H and Xiong, X and Chen, C and Xu, Q and Qin, H}, title = {Integrated Analysis of Colorectal Cancer Reveals Cross-Cohort Gut Microbial Signatures and Associated Serum Metabolites.}, journal = {Gastroenterology}, volume = {163}, number = {4}, pages = {1024-1037.e9}, doi = {10.1053/j.gastro.2022.06.069}, pmid = {35788345}, issn = {1528-0012}, mesh = {*Adenoma/diagnosis ; China ; *Colorectal Neoplasms/diagnosis/metabolism ; Feces ; *Gastrointestinal Microbiome ; Humans ; Metabolomics/methods ; Serotonin ; }, abstract = {BACKGROUND & AIMS: Studies have reported abnormal gut microbiota or circulating metabolome associated with colorectal cancer (CRC), but it remains a challenge to capture the CRC-relevant features consistent across geographic regions. This is particularly the problem for metabolic traits of CRC because the analyses generally use different platforms and laboratory methods, which poses a barrier to cross-dataset examination. In light of this, we sought to elucidate the microbial and metabolic signatures of CRC with broad population relevance.

METHODS: In this integrated metagenomic (healthy controls [HC], n = 91; colorectal adenoma [CRA], n = 63; CRC, n = 71) and metabolomic (HC, n = 34; CRA, n = 31; CRC, n = 35) analysis, CRC-associated features and microbe-metabolite correlations were first identified from a Shanghai cohort. A gut microbial panel was trained in the in-house cohort and cross-validated in 7 published metagenomic datasets of CRC. The in-house metabolic connections to the cross-cohort microbial signatures were used as evidence to infer serum metabolites with potentially external relevance. In addition, a combined microbe-metabolite panel was produced for diagnosing CRC or adenoma.

RESULTS: CRC-associated alterations were identified in the gut microbiome and serum metabolome. A composite microbe-metabolite diagnostic panel was developed and yielded an area under the curve of 0.912 for adenoma and 0.994 for CRC. We showed that many CRC-associated metabolites were linked to cross-cohort gut microbiome signatures of the disease, including CRC-enriched leucylalanine, serotonin, and imidazole propionate; and CRC-depleted perfluorooctane sulfonate, 2-linoleoylglycerol (18:2), and sphingadienine.

CONCLUSIONS: We generated cross-cohort metagenomic signatures of CRC, some of which linked to in-house CRC-associated serum metabolites. The microbial and metabolic shifts may have wide population relevance.}, } @article {pmid35788147, year = {2022}, author = {Hazzouri, KM and Sudalaimuthuasari, N and Saeed, EE and Kundu, B and Al-Maskari, RS and Nelson, D and AlShehhi, AA and Aldhuhoori, MA and Almutawa, DS and Alshehhi, FR and Balan, J and Mundra, S and Alam, M and Salehi-Ashtiani, K and Purugganan, M and Amiri, KMA}, title = {Salt flat microbial diversity and dynamics across salinity gradient.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {11293}, pmid = {35788147}, issn = {2045-2322}, mesh = {Bacteroidetes/genetics ; *Cyanobacteria/genetics ; DNA, Ribosomal ; Ecosystem ; *Salinity ; Sodium Chloride ; Sodium Chloride, Dietary ; }, abstract = {Sabkhas are hypersaline, mineral-rich, supratidal mudflats that harbor microbes that are adapted to high salt concentration. Sabkha microbial diversity is generally studied for their community composition, but less is known about their genetic structure and heterogeneity. In this study, we analyzed a coastal sabkha for its microbial composition using 16S rDNA and whole metagenome, as well as for its population genetic structure. Our 16S rDNA analysis show high alpha diversity in both inner and edge sabkha than outer sabkha. Beta diversity result showed similar kind of microbial composition between inner and edge sabkha, while outer sabkha samples show different microbial composition. At phylum level, Bacteroidetes (~ 22 to 34%), Euryarchaeota (~ 18 to ~ 30%), unclassified bacteria (~ 24 to ~ 35%), Actinobacteria (~ 0.01 to ~ 11%) and Cyanobacteria (less than 1%) are predominantly found in both inside and edge sabkha regions, whereas Proteobacteria (~ 92 to ~ 97%) and Parcubacteria (~ 1 to ~ 2%) are predominately found in outer sabkha. Our 225 metagenomes assembly from this study showed similar bacterial community profile as observed in 16S rDNA-based analysis. From the assembled genomes, we found important genes that are involved in biogeochemical cycles and secondary metabolite biosynthesis. We observed a dynamic, thriving ecosystem that engages in metabolic activity that shapes biogeochemical structure via carbon fixation, nitrogen, and sulfur cycling. Our results show varying degrees of horizontal gene transfers (HGT) and homologous recombination, which correlates with the observed high diversity for these populations. Moreover, our pairwise population differentiation (Fst) for the abundance of species across the salinity gradient of sabkhas identified genes with strong allelic differentiation, lower diversity and elevated nonsynonymous to synonymous ratio of variants, which suggest selective sweeps for those gene variants. We conclude that the process of HGT, combined with recombination and gene specific selection, constitute the driver of genetic variation in bacterial population along a salinity gradient in the unique sabkha ecosystem.}, } @article {pmid35787906, year = {2022}, author = {Nagarajan, D and Lee, DJ and Varjani, S and Lam, SS and Allakhverdiev, SI and Chang, JS}, title = {Microalgae-based wastewater treatment - Microalgae-bacteria consortia, multi-omics approaches and algal stress response.}, journal = {The Science of the total environment}, volume = {845}, number = {}, pages = {157110}, doi = {10.1016/j.scitotenv.2022.157110}, pmid = {35787906}, issn = {1879-1026}, mesh = {Bacteria ; Biomass ; *Microalgae/metabolism ; Wastewater ; *Water Purification ; }, abstract = {Sustainable environmental management is one of the important aspects of sustainable development goals. Increasing amounts of wastewaters (WW) from exponential economic growth is a major challenge, and conventional treatment methods entail a huge carbon footprint in terms of energy use and GHG emissions. Microalgae-based WW treatment is a potential candidate for sustainable WW treatment. The nutrients which are otherwise unutilized in the conventional processes are recovered in the beneficial microalgal biomass. This review presents comprehensive information regarding the potential of microalgae as sustainable bioremediation agents. Microalgae-bacterial consortia play a critical role in synergistic nutrient removal, supported by the complex nutritional and metabolite exchange between microalgae and the associated bacteria. Design of effective microalgae-bacteria consortia either by screening or by recent technologies such as synthetic biology approaches are highly required for efficient WW treatment. Furthermore, this review discusses the crucial research gap in microalgal WW treatment - the application of a multi-omics platform for understanding microalgal response towards WW conditions and the design of effective microalgal or microalgae-bacteria consortia based on genetic information. While metagenomics helps in the identification and monitoring of the microbial community throughout the treatment process, transcriptomics, proteomics and metabolomics aid in studying the algal cellular response towards the nutrients and pollutants in WW. It has been established that the integration of microalgal processes into conventional WW treatment systems is feasible. In this direction, future research directions for microalgal WW treatment emphasize the need for identifying the niche in WW treatment, while highlighting the pilot sale plants in existence. Microalgae-based WW treatment could be a potential phase in the waste hierarchy of circular economy and sustainability, considering WWs are a rich secondary source of finite resources such as nitrogen and phosphorus.}, } @article {pmid35787295, year = {2022}, author = {Zeng, J and Tu, Q and Yu, X and Qian, L and Wang, C and Shu, L and Liu, F and Liu, S and Huang, Z and He, J and Yan, Q and He, Z}, title = {PCycDB: a comprehensive and accurate database for fast analysis of phosphorus cycling genes.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {101}, pmid = {35787295}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Databases, Factual ; Metagenome/genetics ; *Microbiota ; *Phosphorus ; }, abstract = {BACKGROUND: Phosphorus (P) is one of the most essential macronutrients on the planet, and microorganisms (including bacteria and archaea) play a key role in P cycling in all living things and ecosystems. However, our comprehensive understanding of key P cycling genes (PCGs) and microorganisms (PCMs) as well as their ecological functions remains elusive even with the rapid advancement of metagenome sequencing technologies. One of major challenges is a lack of a comprehensive and accurately annotated P cycling functional gene database.

RESULTS: In this study, we constructed a well-curated P cycling database (PCycDB) covering 139 gene families and 10 P metabolic processes, including several previously ignored PCGs such as pafA encoding phosphate-insensitive phosphatase, ptxABCD (phosphite-related genes), and novel aepXVWPS genes for 2-aminoethylphosphonate transporters. We achieved an annotation accuracy, positive predictive value (PPV), sensitivity, specificity, and negative predictive value (NPV) of 99.8%, 96.1%, 99.9%, 99.8%, and 99.9%, respectively, for simulated gene datasets. Compared to other orthology databases, PCycDB is more accurate, more comprehensive, and faster to profile the PCGs. We used PCycDB to analyze P cycling microbial communities from representative natural and engineered environments and showed that PCycDB could apply to different environments.

CONCLUSIONS: We demonstrate that PCycDB is a powerful tool for advancing our understanding of microbially driven P cycling in the environment with high coverage, high accuracy, and rapid analysis of metagenome sequencing data. The PCycDB is available at https://github.com/ZengJiaxiong/Phosphorus-cycling-database . Video Abstract.}, } @article {pmid35784064, year = {2022}, author = {Schmidt, A and Schneider, C and Decker, P and Hohberg, K and Römbke, J and Lehmitz, R and Bálint, M}, title = {Shotgun metagenomics of soil invertebrate communities reflects taxonomy, biomass, and reference genome properties.}, journal = {Ecology and evolution}, volume = {12}, number = {6}, pages = {e8991}, pmid = {35784064}, issn = {2045-7758}, abstract = {Metagenomics - shotgun sequencing of all DNA fragments from a community DNA extract - is routinely used to describe the composition, structure, and function of microorganism communities. Advances in DNA sequencing and the availability of genome databases increasingly allow the use of shotgun metagenomics on eukaryotic communities. Metagenomics offers major advances in the recovery of biomass relationships in a sample, in comparison to taxonomic marker gene-based approaches (metabarcoding). However, little is known about the factors which influence metagenomics data from eukaryotic communities, such as differences among organism groups, the properties of reference genomes, and genome assemblies.We evaluated how shotgun metagenomics records composition and biomass in artificial soil invertebrate communities at different sequencing efforts. We generated mock communities of controlled biomass ratios from 28 species from all major soil mesofauna groups: mites, springtails, nematodes, tardigrades, and potworms. We shotgun sequenced these communities and taxonomically assigned them with a database of over 270 soil invertebrate genomes.We recovered over 95% of the species, and observed relatively high false-positive detection rates. We found strong differences in reads assigned to different taxa, with some groups (e.g., springtails) consistently attracting more hits than others (e.g., enchytraeids). Original biomass could be predicted from read counts after considering these taxon-specific differences. Species with larger genomes, and with more complete assemblies, consistently attracted more reads than species with smaller genomes. The GC content of the genome assemblies had no effect on the biomass-read relationships. Results were similar among different sequencing efforts.The results show considerable differences in taxon recovery and taxon specificity of biomass recovery from metagenomic sequence data. The properties of reference genomes and genome assemblies also influence biomass recovery, and they should be considered in metagenomic studies of eukaryotes. We show that low- and high-sequencing efforts yield similar results, suggesting high cost-efficiency of metagenomics for eukaryotic communities. We provide a brief roadmap for investigating factors which influence metagenomics-based eukaryotic community reconstructions. Understanding these factors is timely as accessibility of DNA sequencing and momentum for reference genomes projects show a future where the taxonomic assignment of DNA from any community sample becomes a reality.}, } @article {pmid35784041, year = {2022}, author = {Vittecoq, M and Brazier, L and Elguero, E and Bravo, IG and Renaud, N and Manzano-Marín, A and Prugnolle, F and Godreuil, S and Blanchon, T and Roux, F and Durand, P and Renaud, F and Thomas, F}, title = {Multiresistant Enterobacteriaceae in yellow-legged gull chicks in their first weeks of life.}, journal = {Ecology and evolution}, volume = {12}, number = {6}, pages = {e8974}, pmid = {35784041}, issn = {2045-7758}, abstract = {Wild animal species living in anthropogenic areas are commonly carriers of antimicrobial-resistant bacteria (AMRB), but their role in the epidemiology of these bacteria is unclear. Several studies on AMRB in wildlife have been cross-sectional in design and sampled individual animals at only one point in time. To further understand the role of wildlife in maintaining and potentially transmitting these bacteria to humans and livestock, longitudinal studies are needed in which samples are collected from individual animals over multiple time periods. In Europe, free-ranging yellow-legged gulls (Larus michahellis) commonly live in industrialized areas, forage in landfills, and have been found to carry AMRB in their feces. Using bacterial metagenomics and antimicrobial resistance characterization, we investigated the spatial and temporal patterns of AMRB in a nesting colony of yellow-legged gulls from an industrialized area in southern France. We collected 54 cloacal swabs from 31 yellow-legged gull chicks in 20 nests on three dates in 2016. We found that AMRB in chicks increased over time and was not spatially structured within the gull colony. This study highlights the complex occurrence of AMRB in a free-ranging wildlife species and contributes to our understanding of the public health risks and implications associated with ARMB-carrying gulls living in anthropogenic areas.}, } @article {pmid35783967, year = {2022}, author = {Plaszkó, T and Szűcs, Z and Cziáky, Z and Ács-Szabó, L and Csoma, H and Géczi, L and Vasas, G and Gonda, S}, title = {Correlations Between the Metabolome and the Endophytic Fungal Metagenome Suggests Importance of Various Metabolite Classes in Community Assembly in Horseradish (Armoracia rusticana, Brassicaceae) Roots.}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {921008}, pmid = {35783967}, issn = {1664-462X}, abstract = {The plant microbiome is an increasingly intensive research area, with significance in agriculture, general plant health, and production of bioactive natural products. Correlations between the fungal endophytic communities and plant chemistry can provide insight into these interactions, and suggest key contributors on both the chemical and fungal side. In this study, roots of various horseradish (Armoracia rusticana) accessions grown under the same conditions were sampled in two consecutive years and chemically characterized using a quality controlled, untargeted metabolomics approach by LC-ESI-MS/MS. Sinigrin, gluconasturtiin, glucoiberin, and glucobrassicin were also quantified. Thereafter, a subset of roots from eight accessions (n = 64) with considerable chemical variability was assessed for their endophytic fungal community, using an ITS2 amplicon-based metagenomic approach using a custom primer with high coverage on fungi, but no amplification of host internal transcribed spacer (ITS). A set of 335 chemical features, including putatively identified flavonoids, phospholipids, peptides, amino acid derivatives, indolic phytoalexins, a glucosinolate, and a glucosinolate downstream product was detected. Major taxa in horseradish roots belonged to Cantharellales, Glomerellales, Hypocreales, Pleosporales, Saccharomycetales, and Sordariales. Most abundant genera included typical endophytes such as Plectosphaerella, Thanatephorus, Podospora, Monosporascus, Exophiala, and Setophoma. A surprising dominance of single taxa was observed for many samples. In summary, 35.23% of reads of the plant endophytic fungal microbiome correlated with changes in the plant metabolome. While the concentration of flavonoid kaempferol glycosides positively correlated with the abundance of many fungal strains, many compounds showed negative correlations with fungi including indolic phytoalexins, a putative glucosinolate but not major glucosinolates and a glutathione isothiocyanate adduct. The latter is likely an in vivo glucosinolate decomposition product important in fungal arrest. Our results show the potency of the untargeted metabolomics approach in deciphering plant-microbe interactions and depicts a complex array of various metabolite classes in shaping the endophytic fungal community.}, } @article {pmid35783632, year = {2022}, author = {Chen, W and Wu, Y and Zhang, Y}, title = {Next-Generation Sequencing Technology Combined With Multiplex Polymerase Chain Reaction as a Powerful Detection and Semiquantitative Method for Herpes Simplex Virus Type 1 in Adult Encephalitis: A Case Report.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {905350}, pmid = {35783632}, issn = {2296-858X}, abstract = {BACKGROUND: Traditional testing for specific microbes or categories of central nervous system (CNS) infectious diseases is often limited in sensitivity and timeliness. However, failure to initiate a timely etiological diagnosis and corresponding treatment in patients with neurologic infections contribute to poor outcomes.

CASE SUMMARY: A 58 year-old male presented acutely with fever, abnormal mental behavior, seizures and decreased consciousness. Brain magnetic resonance imaging (MRI) showed an abnormal FLAIR/T2 signal mainly in the left thalamus, temporal lobe, insular lobe, and bilateral hippocampus. To identify the pathogen, the cerebrospinal fluid (CSF) sample of the patient was used for metagenomic next-generation sequencing (mNGS) analysis and multiplex polymerase chain reaction (mPCR). The results showed 188 herpes simplex virus (HSV-1)-specific sequences. After acyclovir and foscarnet sodium treatment, the ratio of HSV-1/internal reference reads decreased from 813/493 to 695/1961, which coincided with clinical remission.

CONCLUSION: This study indicates that mNGS combined with mPCR may be an effective method for etiological diagnostic and dynamic clinical surveillance for HSV-1 encephalitis.}, } @article {pmid35783441, year = {2022}, author = {Wang, D and Fang, S and Hu, X and Xu, Q and Chu, X and Mei, X and Xie, W}, title = {Metagenomic Next-Generation Sequencing Is Highly Efficient in Diagnosing Pneumocystis Jirovecii Pneumonia in the Immunocompromised Patients.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {913405}, pmid = {35783441}, issn = {1664-302X}, abstract = {PURPOSES: To explore the value of metagenomic next-generation sequencing (mNGS) in diagnosing pneumocystis jiroveciipneumonia (PJP) in the immunocompromised patients.

METHODS: Data of 122 patients with PJP in an immunosuppressed state and 67 non-PJP patients were collected. The diagnostic efficacy of mNGS was compared with the conventional methods, including Gomori methenamine silver (GMS) staining and serum (1,3)-β-D-glucan (BDG). Changes of anti-microbial therapy for patients with PJP based on mNGS results were also reviewed.

RESULTS: The diagnostic sensitivity of mNGS to PJP was higher than that of GMS and BDG (100% vs. 15 and 74.5%, p < 0.001). The diagnostic specificity (91.%) was lower than that of GMS (100%), and similar with BDG (89.6%). In addition to P. jirovecii, mNGS revealed co-pathogens like human β-herpesvirus 5, human γ-pesvirus 4, and some other opportunistic pathogens. The reads of mNGS were remarkably higher in BALF than in blood samples. Initial antimicrobial treatment was modified in 89.3% patients based on the mNGS results, and 74 cases (60.7%) were treated with anti-P. jirovecii therapy.

CONCLUSION: mNGS is highly efficient in diagnosing PJP and good at identifying pathogens in mixed infections.}, } @article {pmid35783390, year = {2022}, author = {Sanchez-Cid, C and Keuschnig, C and Torzewski, K and Stachnik, Ł and Kępski, D and Luks, B and Nawrot, A and Niedzielski, P and Vogel, TM and Larose, C}, title = {Environmental and Anthropogenic Factors Shape the Snow Microbiome and Antibiotic Resistome.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {918622}, pmid = {35783390}, issn = {1664-302X}, abstract = {Winter tourism can generate environmental pollution and affect microbial ecology in mountain ecosystems. This could stimulate the development of antibiotic resistance in snow and its dissemination through the atmosphere and through snow melting. Despite these potential impacts, the effect of winter tourism on the snow antibiotic resistome remains to be elucidated. In this study, snow samples subjected to different levels of anthropogenic activities and surrounding forest were obtained from the Sudety Mountains in Poland to evaluate the impact of winter tourism on snow bacteria using a metagenomic approach. Bacterial community composition was determined by the sequencing of the V3-V4 hypervariable region of the 16S rRNA gene and the composition of the antibiotic resistome was explored by metagenomic sequencing. Whereas environmental factors were the main drivers of bacterial community and antibiotic resistome composition in snow, winter tourism affected resistome composition in sites with similar environmental conditions. Several antibiotic resistance genes (ARGs) showed a higher abundance in sites subjected to human activities. This is the first study to show that anthropogenic activities may influence the antibiotic resistome in alpine snow. Our results highlight the need to survey antibiotic resistance development in anthropogenically polluted sites.}, } @article {pmid35783387, year = {2022}, author = {Zhao, Y and Tian, W and Yang, J and Li, X and Lu, H and Yu, N and Zhang, P and Liu, C and Chen, P and Lei, G and Liu, Y}, title = {Fungal Endophthalmitis in a Case of Rhino-Orbito-Cerebral Mucormycosis: Successfully Treated With Amphotericin B Colloidal Dispersion.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {910419}, pmid = {35783387}, issn = {1664-302X}, abstract = {BACKGROUND: Rhino-orbito-cerebral mucormycosis (ROCM) is an acute, fulminant, opportunistic fungal infection that usually occurs in diabetes or immunocompromised patients. Amphotericin B combined with surgical debridement remains the standard treatment, although it is controversial due to its lager nephrotoxicity. Thus far, no studies have reported the treatment for ROCM-associated fungal endophthalmitis because the exact pathogenesis and transmission routes in ROCM remain unclear. Here, we reported a case of ROCM complicated with fungal endophthalmitis treated favorably with amphotericin B colloidal dispersion (ABCD) in combination with other antifungals and surgical debridement.

CASE PRESENTATION: A 34-year-old woman with diabetes was admitted to our hospital owing to right-sided headache for 8 days, blindness with swelling in the right eye for 5 days, and blindness in the left eye for 1 day. MRI showed that the patient had sphenoid sinus, sinuses, frontal lobe lesions, and proptosis of the right eye. Metagenomic sequencing revealed that the patient had Rhizopus oryzae infection. During hospitalization, the patient received intravenous ABCD, oral posaconazole, and topical amphotericin B and underwent surgical debridement. After 67 days of treatment, the patient's condition was significantly improved, and limb muscle strength showed grade V. Rhizopus oryzae showed negative results, and conjunctival swelling decreased. Additionally, no nephrotoxicity occurred during treatment. After discharge, the patient's treatment was transitioned to oral posaconazole and she was free of complaints during the 30-day follow-up without any additional treatment for ROCM.

CONCLUSION: Treatment with ABCD combined with other antifungal drugs and surgical debridement for ROCM complicated with fungal endophthalmitis showed remarkable efficacy and good safety. Hence, this regimen is a promising treatment strategy for this fatal disease.}, } @article {pmid35782956, year = {2022}, author = {Muratsu, A and Ikeda, M and Shimizu, K and Kameoka, S and Motooka, D and Nakamura, S and Matsumoto, H and Ogura, H and Shimazu, T}, title = {Dynamic change of fecal microbiota and metabolomics in a polymicrobial murine sepsis model.}, journal = {Acute medicine & surgery}, volume = {9}, number = {1}, pages = {e770}, pmid = {35782956}, issn = {2052-8817}, abstract = {AIM: Sepsis causes a systemic inflammatory reaction by destroying intestinal flora, which leads to a poor prognosis. In this study, we sought to clarify the characteristics of fecal flora and metabolites in a mouse model of sepsis by comprehensive metagenomic and metabolomic analysis.

METHODS: We performed a cecal ligation and puncture model procedure to create a mild sepsis model. We collected fecal samples on day 0 (healthy condition) and days 1 and 7 after the cecal ligation and puncture to determine the microbiome and metabolites. We analyzed fecal flora using 16S rRNA gene sequencing and metabolites using capillary electrophoresis mass spectrometry with time-of-flight analysis.

RESULTS: The abundance of bacteria belonging to the family Enterobacteriaceae significantly increased, but that of order Clostridiales such as the families Lachnospiraceae and Ruminococcaceae decreased on day 1 after the cecal ligation and puncture compared with those before the cecal ligation and puncture. The family Enterobacteriaceae significantly decreased, but that of order Clostridiales such as the families Lachnospiraceae and Ruminococcaceae increased on day 7 compared with those on day 1 after the cecal ligation and puncture. In the fecal metabolome, 313 metabolites were identified. Particularly, essential amino acids such as valine and non-essential amino acids such as glycine increased remarkably following injury. Betaine and trimethylamine also increased. In contrast, short-chain fatty acids such as isovaleric acid, butyric acid, and propionic acid decreased.

CONCLUSION: The fecal microbiota following injury showed that Enterobacteriaceae increased in acute phase, and Lachnospiraceae and Ruminococcaceae increased in subacute phase. The metabolites revealed an increase in essential amino acids and choline metabolites and a decrease in short-chain fatty acids.}, } @article {pmid35782941, year = {2022}, author = {Wang, K and Yang, A and Peng, X and Lv, F and Wang, Y and Cui, Y and Wang, Y and Zhou, J and Si, H}, title = {Linkages of Various Calcium Sources on Immune Performance, Diarrhea Rate, Intestinal Barrier, and Post-gut Microbial Structure and Function in Piglets.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {921773}, pmid = {35782941}, issn = {2296-861X}, abstract = {The purpose of this experiment was to investigate the effects of different sources of calcium on immune performance, diarrhea rate, intestinal barrier, and post-intestinal flora structure and function in weaned piglets. A total of 1,000 weaned piglets were randomly assigned to five groups 10 replicate pens per treatment, 20 piglets per pen and fed calcium carbonate, calcium citrate, multiple calcium, and organic trace minerals of different concentrations of acidifier diets. The results of the study showed that the replacement of calcium carbonate with calcium citrate and multiple calcium had almost no significant effect on immune indexes (IL-1β, IL-6, IL-10, TNF-α) of piglets compared with the control group (p > 0.05). The five groups did not show a change in the diarrhea rate and diarrhea index (p > 0.05). The diet containing multiple calcium dramatically decreased the TP compared to the C and L diet (p < 0.05). No significant difference in HDL was noted in the five groups (p > 0.05). However, the concentration of LDL in blood in the multiple calcium group was significantly higher than that in groups L and D (p < 0.05). Moreover, the concentration of Glu in blood in the multiple calcium group was significantly higher than that in group C (p < 0.05). Compared with the control group, calcium citrate plus organic trace minerals diet markedly increased UCG-005 abundance in the colon (p < 0.05). In addition, the relative abundance of Prevotellaceae_NK3B31_group had an upward trend in the colon of the M group compared to the D group (p = 0.070). Meanwhile, calcium citrate plus organic trace minerals diet markedly increased Clostridium_sensu_stricto_1 abundance in the colon (p < 0.05). Metagenomic predictions by PICRUSt suggested that the colonic and fecal microbiota was mainly involved in carbohydrate metabolism, amino acid metabolism, energy metabolism, and metabolism of cofactors and vitamins.}, } @article {pmid35782875, year = {2022}, author = {Chen, F and He, L and Li, J and Yang, S and Zhang, B and Zhu, D and Wu, Z and Zhang, S and Hou, D and Ouyang, C and Yi, J and Xiao, C and Hou, K}, title = {Polyethylene Glycol Loxenatide Injection (GLP-1) Protects Vascular Endothelial Cell Function in Middle-Aged and Elderly Patients With Type 2 Diabetes by Regulating Gut Microbiota.}, journal = {Frontiers in molecular biosciences}, volume = {9}, number = {}, pages = {879294}, pmid = {35782875}, issn = {2296-889X}, abstract = {Objective: To evaluate the protective effect of Polyethylene Glycol Loxenatide Injection (Glucagon-like peptide-1, GLP-1) on endothelial cells from middle-aged and elderly patients with newly diagnosed or poorly controlled type 2 diabetes mellitus (T2DM). GLP-1 weekly formulation was analyzed for cardiovascular disease protection and correlated with intestinal flora. Design: Stool samples were collected from middle-aged and elderly patients with new-onset or poorly controlled type 2 diabetes in Longhu People's Hospital and Shantou Central Hospital from June 2019 to November 2019. Samples were collected at week 0, 4, and 8 of treatment with GLP-1 weekly formulations. Samples were analyzed for metagenomic sequencing. Analysis was performed to compare the characteristics of the gut microbiota at week 0, 4, and 8 of GLP-1 treatment and to correlate different microbiota with characteristic clinical parameters. Results: Statistical differences were found in blood glucose lowering, cardiovascular endothelial, and inflammation-related indices between week 0 and W4 and in blood glucose lowering and cardiovascular endothelial indices from week 0 to 8 in the newly diagnosed or poorly controlled type 2 diabetic patients treated with GLP-1. Changes in gut microbiota at week 0, 4, and 8 after using GLP-1 were not statistically different, but had an overall trend of rising and then falling, and with different bacteria, that were correlated with different clinical indicators. Conclusion: GLP-1 improves endothelial cell function indicators in middle-aged and elderly diabetic patients, which may be related to its alteration of the population numbers of gut microbiota such as Acinetobacter, Eubacterium ramulus ATCC 29099, and Bacteroides_faecis. This study provides a guidance for the treatment of type 2 diabetic patients.}, } @article {pmid35782540, year = {2022}, author = {Shen, Q and Zhuang, Z and Lu, J and Qian, L and Li, G and Kanton, AG and Yang, S and Wang, X and Wang, H and Yin, J and Zhang, W}, title = {Genome Analysis of Goose-Origin Astroviruses Causing Fatal Gout in Shanghai, China Reveals One of Them Belonging to a Novel Type Is a Recombinant Strain.}, journal = {Frontiers in veterinary science}, volume = {9}, number = {}, pages = {878441}, pmid = {35782540}, issn = {2297-1769}, abstract = {Since 2014, a goose-origin astroviruses disease, which is characterized by urate precipitation in viscera, has rapidly spread to major commercial goose provinces leading to huge economic losses in the poultry industry of China. In March 2020, a goose farm locates in Shanghai, China, where there was no goose astroviruses (GAstVs) infection reported before, experienced an outbreak of gout disease in geese. The etiological investigation was carried out by virus metagenomics and bacterial culture and two GAstVs strains, designated as CHSH01 and CHSH02, were determined. Their complete genomes were measured to 7,154 and 7,330 nt in length, excludingthe poly(A) tail, respectively, and had different genomic features and classifications. CHSH01 shared a very low sequence identity with other strains in terms of not only the complete genome but also different ORFs. Phylogenetic analysis showed CHSH02 belonged to GAstV-2, which was the predominant species in the geese with gout in China according to the previous study. Meanwhile, CHSH01 strain displayed low identity with other AstVs, and phylogenetic and recombination analysis suggested that CHSH01 belonging to a novel type was a recombinant strain, one parent strain of which was an AstV determined from a bar-headed goose (a kind of migrant bird). Moreover, the primary epidemiological investigation showed that the two strains were prevalent in the same goose farm and co-infection occurred. These findings arise the potential cross-species transmission of CHSH01 between domestic and wild fowl.}, } @article {pmid35782152, year = {2022}, author = {Kayani, MUR and Zaidi, SSA and Feng, R and Yu, K and Qiu, Y and Yu, X and Chen, L and Huang, L}, title = {Genome-Resolved Characterization of Structure and Potential Functions of the Zebrafish Stool Microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {910766}, pmid = {35782152}, issn = {2235-2988}, mesh = {Animals ; Feces ; *Gastrointestinal Microbiome/genetics ; Metagenome ; *Microbiota ; Zebrafish ; }, abstract = {Zebrafish have been used as a model organism for more than 50 years and are considered an excellent model for studying host-microbiome interactions. However, this largely depends on our understanding of the zebrafish gut microbiome itself. Despite advances in sequencing and data analysis methods, the zebrafish gut microbiome remains highly understudied. This study performed the de novo metagenome assembly and recovery of the metagenome-assembled genomes (MAGs) through genome binning (and refinement) of the contigs assembled from the zebrafish stool. The results indicate that majority of the MAGs had excellent quality i.e. high completeness (≥90%) and low contamination levels (≤5%). MAGs mainly belong to the taxa that are known to be members of the core zebrafish stool microbiome, including the phylum Proteobacteria, Fusobacteriota, and Actinobacteriota. However, most of the MAGs remained unclassified at the species level and reflected previously unexplored microbial taxa and their potential novelty. These MAGs also contained genes with predicted functions associated with diverse metabolic pathways that included carbohydrate, amino acid, and lipid metabolism pathways. Lastly, we performed a comparative analysis of Paucibacter MAGs and reference genomes that highlighted the presence of novel Paucibacter species and enriched metabolic potential in the recovered MAGs.}, } @article {pmid35782128, year = {2022}, author = {Zuo, W and Michail, S and Sun, F}, title = {Metagenomic Analyses of Multiple Gut Datasets Revealed the Association of Phage Signatures in Colorectal Cancer.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {918010}, pmid = {35782128}, issn = {2235-2988}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; R01 GM131407/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteriophages/genetics ; *Colorectal Neoplasms ; Humans ; Metagenome ; Metagenomics ; *Siphoviridae ; }, abstract = {The association of colorectal cancer (CRC) and the human gut microbiome dysbiosis has been the focus of several studies in the past. Many bacterial taxa have been shown to have differential abundance among CRC patients compared to healthy controls. However, the relationship between CRC and non-bacterial gut microbiome such as the gut virome is under-studied and not well understood. In this study we conducted a comprehensive analysis of the association of viral abundances with CRC using metagenomic shotgun sequencing data of 462 CRC subjects and 449 healthy controls from 7 studies performed in 8 different countries. Despite the high heterogeneity, our results showed that the virome alpha diversity was consistently higher in CRC patients than in healthy controls (p-value <0.001). This finding is in sharp contrast to previous reports of low alpha diversity of prokaryotes in CRC compared to healthy controls. In addition to the previously known association of Podoviridae, Siphoviridae and Myoviridae with CRC, we further demonstrate that Herelleviridae, a newly constructed viral family, is significantly depleted in CRC subjects. Our interkingdom association analysis reveals a less intertwined correlation between the gut virome and bacteriome in CRC compared to healthy controls. Furthermore, we show that the viral abundance profiles can be used to accurately predict CRC disease status (AUROC >0.8) in both within-study and cross-study settings. The combination of training sets resulted in rather generalized and accurate prediction models. Our study clearly shows that subjects with colorectal cancer harbor a distinct human gut virome profile which may have an important role in this disease.}, } @article {pmid35782119, year = {2022}, author = {Huang, JF and Miao, Q and Cheng, JW and Huang, A and Guo, DZ and Wang, T and Yang, LX and Zhu, DM and Cao, Y and Huang, XW and Fan, J and Zhou, J and Yang, XR}, title = {Metagenomic Next-Generation Sequencing Versus Traditional Laboratory Methods for the Diagnosis and Treatment of Infection in Liver Transplantation.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {886359}, pmid = {35782119}, issn = {2235-2988}, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; *Liver Transplantation ; Metagenome ; Metagenomics ; Tissue Donors ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has emerged as an effective method for the noninvasive and precise detection of infectious pathogens. However, data are lacking on whether mNGS analyses could be used for the diagnosis and treatment of infection during the perioperative period in patients undergoing liver transplantation (LT).

METHODS: From February 2018 to October 2018, we conducted an exploratory study using mNGS and traditional laboratory methods (TMs), including culture, serologic assays, and nucleic acid testing, for pathogen detection in 42 pairs of cadaveric liver donors and their corresponding recipients. Method performance in determining the presence of perioperative infection and guiding subsequent clinical decisions was compared between mNGS and TMs.

RESULTS: The percentage of liver donors with mNGS-positive pathogen results (64.3%, 27/42) was significantly higher than that using TMs (28.6%, 12/42; P<0.05). The percentage of co-infection detected by mNGS in liver donors was 23.8% (10/42) significantly higher than 0.0% (0/42) by TMs (P<0.01). Forty-three pathogens were detected using mNGS, while only 12 pathogens were identified using TMs. The results of the mNGS analyses were consistent with results of the TM analyses in 91.7% (11/12) of donor samples at the species level, while mNGS could be used to detect pathogens in 66.7% (20/30) of donors deemed pathogen-negative using TMs. Identical pathogens were detected in 6 cases of donors and recipients by mNGS, among which 4 cases were finally confirmed as donor-derived infections (DDIs). For TMs, identical pathogens were detected in only 2 cases. Furthermore, 8 recipients developed early symptoms of infection (<7 days) after LT; we adjusted the type of antibiotics and/or discontinued immunosuppressants according to the mNGS results. Of the 8 patients with infections, 7 recipients recovered, and 1 patient died of severe sepsis.

CONCLUSIONS: Our preliminary results show that mNGS analyses can provide rapid and precise pathogen detection compared with TMs in a variety of clinical samples from patients undergoing LT. Combined with symptoms of clinical infection, mNGS showed superior advantages over TMs for the early identification and assistance in clinical decision-making for DDIs. mNGS results were critical for the management of perioperative infection in patients undergoing LT.}, } @article {pmid35782115, year = {2022}, author = {Moussa, DG and Ahmad, P and Mansour, TA and Siqueira, WL}, title = {Current State and Challenges of the Global Outcomes of Dental Caries Research in the Meta-Omics Era.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {887907}, pmid = {35782115}, issn = {2235-2988}, support = {//CIHR/Canada ; }, mesh = {*Dental Caries ; Genome-Wide Association Study ; Humans ; Metabolomics/methods ; Metagenomics ; *Microbiota/genetics ; }, abstract = {Despite significant healthcare advances in the 21[st] century, the exact etiology of dental caries remains unsolved. The past two decades have witnessed a tremendous growth in our understanding of dental caries amid the advent of revolutionary omics technologies. Accordingly, a consensus has been reached that dental caries is a community-scale metabolic disorder, and its etiology is beyond a single causative organism. This conclusion was based on a variety of microbiome studies following the flow of information along the central dogma of biology from genomic data to the end products of metabolism. These studies were facilitated by the unprecedented growth of the next- generation sequencing tools and omics techniques, such as metagenomics and metatranscriptomics, to estimate the community composition of oral microbiome and its functional potential. Furthermore, the rapidly evolving proteomics and metabolomics platforms, including nuclear magnetic resonance spectroscopy and/or mass spectrometry coupled with chromatography, have enabled precise quantification of the translational outcomes. Although the majority supports 'conserved functional changes' as indicators of dysbiosis, it remains unclear how caries dynamics impact the microbiota functions and vice versa, over the course of disease onset and progression. What compounds the situation is the host-microbiota crosstalk. Genome-wide association studies have been undertaken to elucidate the interaction of host genetic variation with the microbiome. However, these studies are challenged by the complex interaction of host genetics and environmental factors. All these complementary approaches need to be orchestrated to capture the key players in this multifactorial disease. Herein, we critically review the milestones in caries research focusing on the state-of-art singular and integrative omics studies, supplemented with a bibliographic network analysis to address the oral microbiome, the host factors, and their interactions. Additionally, we highlight gaps in the dental literature and shed light on critical future research questions and study designs that could unravel the complexities of dental caries, the most globally widespread disease.}, } @article {pmid35781864, year = {2022}, author = {Guo, H and Wang, C and Ju, L and Pan, L and Su, Z and Sui, Z}, title = {Antibiotic resistance genes and bacterial community distribution patterns in pig farms.}, journal = {Folia microbiologica}, volume = {67}, number = {6}, pages = {913-921}, pmid = {35781864}, issn = {1874-9356}, support = {SDAIT-08-08//Shandong Province Pig Industry Technology System/ ; }, mesh = {Humans ; Swine ; Animals ; Farms ; *Anti-Bacterial Agents/pharmacology ; *Genes, Bacterial/genetics ; Drug Resistance, Microbial/genetics ; Bacteria/genetics ; }, abstract = {Antibiotic-resistant pathogens pose high risks to human and animal health worldwide. In recent years, many studies have been carried out to investigate the role of gut microbiota as a pool of antibiotic resistance genes (ARGs) in human and animals. Both the structure and function of the gut bacterial community and related ARGs in pig remain unknown. In this study, we characterized the gut microbiomes and resistomes of fecal samples collected from sixteen pig farms located in sixteen cities of Shandong Province by metagenomic sequencing. Alpha diversity indicated that fecal samples from Dezhou (DZ) and Jinan (J) showed higher alpha diversity, and the lowest was from pig farms of Rizhao (RZ). Other pig farms showed similar alpha diversity. Besides, we found that the composition of gut bacterial among these pig farms varied greatly. Helcococcus massiliensis was the dominant bacterial species in pig farms of RZ and Zibo (ZB), while Prevotella sp. P5-92 occupied a superior proportion in Binzhou (BZ) and Yantai (YT). The proportion of Lactobacillus johnsonii was similar among farms of Qingdao (QD), Linyi (LY), Taian (TA), Weifang (WF), Weihai (WH), and YT. In total, 1112 ARGs were obtained and classified into 69 groups from 48 fecal samples. ARG abundance was higher in farms of Dongying (DY) and WH than others, while the lowest farms in BZ and ZB. Interestingly, it is found that BZ pig farm was exclusive, so the tetQ gene showed a higher abundance. In contrast, the load of APH(3') - IIIa in fecal samples from DY, J-1, LC, WF, and WH was high. Meanwhile, the most relevant ARGs and the corresponding microbes were screened out. Our metagenomic sequencing data provides new insights into the abundance, diversity, and structure of bacterial community in pig farms. Meanwhile, we screened ARG-carrying bacteria and explored the correlation between ARGs and bacterial community, which provide a comprehensive view of the pig fecial ARGs and microbes in different farms of Shandong.}, } @article {pmid35781557, year = {2022}, author = {Wells, HL and Loh, E and Nava, A and Solorio, MR and Lee, MH and Lee, J and Sukor, JRA and Navarrete-Macias, I and Liang, E and Firth, C and Epstein, JH and Rostal, MK and Zambrana-Torrelio, C and Murray, K and Daszak, P and Goldstein, T and Mazet, JAK and Lee, B and Hughes, T and Durigon, E and Anthony, SJ}, title = {Classification of new morbillivirus and jeilongvirus sequences from bats sampled in Brazil and Malaysia.}, journal = {Archives of virology}, volume = {167}, number = {10}, pages = {1977-1987}, pmid = {35781557}, issn = {1432-8798}, support = {GHN-A-OO-09-00010-00//United States Agency for International Development/ ; AID-OAA-A-14-00102//United States Agency for International Development/ ; 106150-001//International Development Research Centre/ ; }, mesh = {Animals ; Brazil ; *Chiroptera ; Genome, Viral ; Humans ; Malaysia ; *Morbillivirus/genetics ; Paramyxoviridae/genetics ; Phylogeny ; *Viruses ; }, abstract = {As part of a broad One Health surveillance effort to detect novel viruses in wildlife and people, we report several paramyxovirus sequences sampled primarily from bats during 2013 and 2014 in Brazil and Malaysia, including seven from which we recovered full-length genomes. Of these, six represent the first full-length paramyxovirid genomes sequenced from the Americas, including two that are the first full-length bat morbillivirus genome sequences published to date. Our findings add to the vast number of viral sequences in public repositories, which have been increasing considerably in recent years due to the rising accessibility of metagenomics. Taxonomic classification of these sequences in the absence of phenotypic data has been a significant challenge, particularly in the subfamily Orthoparamyxovirinae, where the rate of discovery of novel sequences has been substantial. Using pairwise amino acid sequence classification (PAASC), we propose that five of these sequences belong to members of the genus Jeilongvirus and two belong to members of the genus Morbillivirus. We also highlight inconsistencies in the classification of Tupaia virus and Mòjiāng virus using the same demarcation criteria and suggest reclassification of these viruses into new genera. Importantly, this study underscores the critical importance of sequence length in PAASC analysis as well as the importance of biological characteristics such as genome organization in the taxonomic classification of viral sequences.}, } @article {pmid35780677, year = {2022}, author = {Feng, L and Xiao, C and Luo, Y and Qiao, Y and Chen, D}, title = {The fate of antibiotic resistance genes, microbial community, and potential pathogens in the maricultural sediment by live seaweeds and oxytetracycline.}, journal = {Journal of environmental management}, volume = {318}, number = {}, pages = {115597}, doi = {10.1016/j.jenvman.2022.115597}, pmid = {35780677}, issn = {1095-8630}, mesh = {Anti-Bacterial Agents/analysis/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microbiota ; *Oxytetracycline/analysis/pharmacology ; *Seaweed ; *Ulva/genetics ; }, abstract = {Three common seaweeds including Ulva fasciata, Codium cylindricum and Ishige okamurai were used for the remediation of maricultural wastewater and sediment in the presence/absence of trace level of oxytetracycline (OTC) in lab-scale experiments. Higher NO3[-]-N and PO4[3-]-P removal rates were achieved due to the presence of seaweeds, and trace OTC also had a positive effect on NO3[-]-N removal. A slight variation of 2.10-2.15% were observed in the total relative abundances of antibiotic resistance genes (ARGs) of different sediment samples after one-month operation. However, the variation of ARGs profiles by the co-existence of different seaweeds and OTC was in the descending order of Ishige okamurai > Codium cylindricum > Ulva fasciata, which was in accordance with the variation of microbial hosts at genus level. The abundance of dominant tetracycline resistance genes promoted by the co-existence of different seaweeds and OTC in compared with the presence of single seaweed or OTC via metagenomic sequencing and qPCR analysis, and the co-existence of Ishige okamurai and OTC exhibited the largest impact. The potential pathogens were more sensitive to the co-existence of seaweed and OTC than single seaweeds. Meanwhile, a variety of ARGs were enriched in the pathogens, and the dominant pathogenic bacteria of Vibrio had 133 Vibrio species with 28 subtypes of ARGs. The variation of ARGs profiles in the sediment were strongly related with the dominant phyla Proteobacteria, Actinobacteria, Firmicutes, Planctomycetes and Cyanobacteria. Besides, Nitrate level exhibited more significant effect on ∑ARGs, ARGs resistant to vancomycin and streptogramin_a, while phosphate level exhibited more positively significant effect on ARGs resistant to fosmidomycin, ATFBT and cephalosporin.}, } @article {pmid35780499, year = {2022}, author = {Shen, Y and Yu, F and Zhang, D and Zou, Q and Xie, M and Chen, X and Yuan, L and Lou, B and Xie, G and Wang, R and Yang, X and Chen, W and Wang, Q and Feng, B and Teng, Y and Dong, Y and Huang, L and Bao, J and Han, D and Liu, C and Wu, W and Liu, X and Fan, L and Timko, MP and Zheng, S and Chen, Y}, title = {Dynamic Alterations in the Respiratory Tract Microbiota of Patients with COVID-19 and its Association with Microbiota in the Gut.}, journal = {Advanced science (Weinheim, Baden-Wurttemberg, Germany)}, volume = {9}, number = {27}, pages = {e2200956}, pmid = {35780499}, issn = {2198-3844}, support = {82072377//National Natural Science Foundation of China/ ; 81971919//National Natural Science Foundation of China/ ; }, mesh = {Biomarkers ; *COVID-19 ; Defensins ; Enterococcus ; Gastrointestinal Tract ; Humans ; Leukocytes, Mononuclear ; *Microbiota ; Respiratory System ; }, abstract = {The role of respiratory tract microbes and the relationship between respiratory tract and gut microbiomes in coronavirus disease 2019 (COVID-19) remain uncertain. Here, the metagenomes of sputum and fecal samples from 66 patients with COVID-19 at three stages of disease progression are sequenced. Respiratory tract, gut microbiome, and peripheral blood mononuclear cell (PBMC) samples are analyzed to compare the gut and respiratory tract microbiota of intensive care unit (ICU) and non-ICU (nICU) patients and determine relationships between respiratory tract microbiome and immune response. In the respiratory tract, significantly fewer Streptococcus, Actinomyces, Atopobium, and Bacteroides are found in ICU than in nICU patients, while Enterococcus and Candida increase. In the gut, significantly fewer Bacteroides are found in ICU patients, while Enterococcus increases. Significant positive correlations exist between relative microbiota abundances in the respiratory tract and gut. Defensin-related pathways in PBMCs are enhanced, and respiratory tract Streptococcus is reduced in patients with COVID-19. A respiratory tract-gut microbiota model identifies respiratory tract Streptococcus and Atopobium as the most prominent biomarkers distinguishing between ICU and nICU patients. The findings provide insight into the respiratory tract and gut microbial dynamics during COVID-19 progression, considering disease severity, potentially contributing to diagnosis, and treatment strategies.}, } @article {pmid35780470, year = {2022}, author = {Jaya, FR and Tanner, JC and Whitehead, MR and Doughty, P and Keogh, JS and Moritz, CC and Catullo, RA}, title = {Population genomics and sexual signals support reproductive character displacement in Uperoleia (Anura: Myobatrachidae) in a contact zone.}, journal = {Molecular ecology}, volume = {31}, number = {17}, pages = {4527-4543}, pmid = {35780470}, issn = {1365-294X}, mesh = {Animals ; *Anura/genetics ; Female ; Male ; *Metagenomics ; Phylogeography ; Reproduction/genetics ; Sympatry ; }, abstract = {When closely related species come into contact via range expansion, both may experience reduced fitness as a result of the interaction. Selection is expected to favour traits that minimize costly interspecies reproductive interactions (such as mismating) via a phenomenon called reproductive character displacement (RCD). Research on RCD frequently assumes secondary contact between species, but the geographical history of species interactions is often unknown. Population genomic data permit tests of geographical hypotheses about species origins and secondary contact through range expansion. We used population genomic data from single nucleotide polymorphisms (SNPs), mitochondrial sequence data, advertisement call data and morphological data to investigate a species complex of toadlets (Uperoleia borealis, U. crassa, U. inundata) from northern Australia. Although the three species of frogs were morphologically indistinguishable in our analysis, we determined that U. crassa and U. inundata form a single species (synonymized here) based on an absence of genomic divergence. SNP data identified the phylogeographical origin of U. crassa as the Top End, with subsequent westward invasion into the range of U. borealis in the Kimberley. We identified six F1 hybrids, all of which had the U. borealis mitochondrial haplotype, suggesting unidirectional hybridization. Consistent with the RCD hypothesis, U. borealis and U. crassa sexual signals differ more in sympatry than in allopatry. Hybrid males have intermediate calls, which probably reduces attractiveness to females. Integrating population genomic data, mitochondrial sequencing, morphology and behavioural approaches provides an unusually detailed collection of evidence for reproductive character displacement following range expansion and secondary contact.}, } @article {pmid35780445, year = {2022}, author = {Chen, Y and Xia, Z and Li, H}, title = {Metagenomic comparison of gut communities between hawksbills (Eretmochelys imbricata) and green sea turtles (Chelonia mydas).}, journal = {Archives of microbiology}, volume = {204}, number = {8}, pages = {450}, pmid = {35780445}, issn = {1432-072X}, support = {2020ZDZX1050//Department of Education of Guangdong Province/ ; 2020SC0302019//the Science and Technology Planning Project of Huizhou City/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Firmicutes ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics ; *Turtles/genetics ; }, abstract = {The gut microbiota is closely linked to host nutrition, immunity, and health. Here, metagenomic analysis was conducted to elucidate the taxonomic and functional diversity of gut communities from hawksbills and green sea turtles. In terms of diversity and abundance, the gut microbiota of herbivorous green sea turtles showed a higher bacterial diversity and richness than that of hawksbills. Firmicutes dominated in all groups; however, the phylum Proteobacteria showed a higher relative abundance in hawksbills. Several metabolic pathways displayed broad prevalence and high relative abundances in the two sea turtle populations. Antibiotic resistance genes (ARGs) responsible for resistance to glycopeptide and tetracycline were the most abundant in all samples. In ARGs, the subtype macB was the most abundant in the two different sea turtle populations; however, evgS, bcrA, and efrA were more abundant in the green sea turtles, while in the hawksbills, tetT and tetB(P) were more abundant. Among mobile genetic elements (MGEs), the abundance of 16 MGE types showed a significant difference between the two sea turtle populations. MGE type transposase and plasmid were the most abundant in the two sea turtle populations. Additionally, gene functions were enriched in carbohydrate esterases, glycoside hydrolases, and polysaccharide lyases in the green sea turtles, whereas genes related to glycosyltransferases and auxiliary activities were highly abundant in hawksbills. These metagenomic profiles provide further insights into the microbial diversities of the two types of sea turtles and provide valuable information for future conservation efforts.}, } @article {pmid35780428, year = {2022}, author = {Sugimoto, R and Nishimura, L and Nguyen, PT and Inoue, I}, title = {Extraction of CRISPR-targeted sequences from the metagenome.}, journal = {STAR protocols}, volume = {3}, number = {3}, pages = {101525}, pmid = {35780428}, issn = {2666-1667}, mesh = {Base Sequence ; *Clustered Regularly Interspaced Short Palindromic Repeats/genetics ; Humans ; *Metagenome/genetics ; Metagenomics ; }, abstract = {Homology-based search is commonly used to uncover mobile genetic elements (MGEs) from metagenomes, but it heavily relies on reference genomes in the database. Here we introduce a protocol to extract CRISPR-targeted sequences from the assembled human gut metagenomic sequences without using a reference database. We describe the assembling of metagenome contigs, the extraction of CRISPR direct repeats and spacers, the discovery of protospacers, and the extraction of protospacer-enriched regions using the graph-based approach. This protocol could extract numerous characterized/uncharacterized MGEs. For complete details on the use and execution of this protocol, please refer to Sugimoto et al. (2021).}, } @article {pmid35779747, year = {2022}, author = {Du, J and Yin, Q and Zhou, X and Guo, Q and Wu, G}, title = {Distribution of extracellular amino acids and their potential functions in microbial cross-feeding in anaerobic digestion systems.}, journal = {Bioresource technology}, volume = {360}, number = {}, pages = {127535}, doi = {10.1016/j.biortech.2022.127535}, pmid = {35779747}, issn = {1873-2976}, mesh = {Amino Acids/metabolism ; Amino Acids, Essential ; Anaerobiosis ; Bacteria/genetics/metabolism ; *Bioreactors/microbiology ; *Euryarchaeota/metabolism ; Methane/metabolism ; }, abstract = {Anaerobic digestion is a prevalent bioenergy production process relying on a complex network of symbiotic interactions, where the nutrient based cross-feeding is an essential microbial mechanism. Here, the cross-feeding function was assessed by analyzing extracellular polymeric substances-associated amino acids in microbial aggregates collected from 14 lab-scale anaerobic digesters, as well as deciphering their genetically biosynthetic potential by syntrophic bacteria and methanogens. The total concentration of essential amino acids ranged from 1.2 mg/g VSS to 174.0 mg/g VSS. The percentages of glutamic acid (8.5 ∼ 37.6%), lysine (2.7 ∼ 22.6%), alanine (5.6 ∼ 13.2%), and valine (3.0 ∼ 10.4%) to the total amount of detected amino acids were the highest in most samples. Through metagenomics analysis, several investigated syntrophs (i.e., Smithella, Syntrophobacter, Syntrophomonas, and Mesotoga) and methanogens (i.e., Methanothrix and Methanosarcina) were auxotrophies, but the genetic ability of syntrophs and methanogens to synthesize some essential amino acids could be complementary, implying potential cross-feeding partnership.}, } @article {pmid35779450, year = {2022}, author = {Sundaray, JK and Dixit, S and Rather, A and Rasal, KD and Sahoo, L}, title = {Aquaculture omics: An update on the current status of research and data analysis.}, journal = {Marine genomics}, volume = {64}, number = {}, pages = {100967}, doi = {10.1016/j.margen.2022.100967}, pmid = {35779450}, issn = {1876-7478}, mesh = {Animals ; Aquaculture ; *Data Analysis ; Ecosystem ; Fishes/genetics ; Genomics ; *MicroRNAs ; }, abstract = {Aquaculture is the fast-growing agricultural sector and has the ability to meet the growing demand for protein nutritional security for future population. In future aquaculture is going to be the major source of fish proteins as capture fisheries reached at its maximum. However, several challenges need to overcome such as lack of genetically improved strains/varieties, lack of species-specific feed/functional feed, round the year availability of quality fish seed, pollution of ecosystems and increased frequencies of disease occurrence etc. In recent years, the continuous development of high throughput sequencing technology has revolutionized the biological sciences and provided necessary tools. Application of 'omics' in aquaculture research have been successfully used to resolve several productive and reproductive issues and thus ensure its sustainability and profitability. To date, high quality draft genomes of over fifty fish species have been generated and successfully used to develop large number of single nucleotide polymorphism markers (SNPs), marker panels and other genomic resources etc in several aquaculture species. Similarly, transcriptome profiling and miRNAs analysis have been used in aquaculture research to identify key transcripts and expression analysis of candidate genes/miRNAs involved in reproduction, immunity, growth, development, stress toxicology and disease. Metagenome analysis emerged as a promising scientific tool to analyze the complex genomes contained within microbial communities. Metagenomics has been successfully used in the aquaculture sector to identify novel and potential pathogens, antibiotic resistance genes, microbial roles in microcosms, microbial communities forming biofloc, probiotics etc. In the current review, we discussed application of high-throughput technologies (NGS) in the aquaculture sector.}, } @article {pmid35779137, year = {2022}, author = {Das, G and Dhal, PK}, title = {Salinity Influences Endophytic Bacterial Communities in Rice Roots from the Indian Sundarban Area.}, journal = {Current microbiology}, volume = {79}, number = {8}, pages = {238}, pmid = {35779137}, issn = {1432-0991}, support = {. EEQ/2018/000006//Science and Engineering Research Board/ ; }, mesh = {Bacteria ; Endophytes/genetics ; *Oryza/microbiology ; *Salinity ; Soil/chemistry ; }, abstract = {In "Sundarbans", the coastal regions of the West Bengal, soil salinity has always been one of the major causes of reduction in yield in these regions. The use of endophytic is a well-demanded strategy to mitigate the problems of salt stress and rice productivity. The present study attempted to analyze rice root endogenous microbial diversity and their relationship with soil salinity and physicochemical factors in the salt stressed region of Sundarbans, India using amplicon metagenomics approaches. Our investigation indicates, that the unique microbiome slightly acidic nutrient enriched non-saline zone is characterized by microbial genera that reported either having plant growth promotion (Flavobacterium, Novosphingobium, and Kocuria) or biocontrol abilities (Leptotrichia), whereas high ionic alkaline saline stressed zone dominated with either salt-tolerant microbes or less characterized endophytes (Arcobacter and Vogesella). The number of genera represented by significantly abundant OTUs was higher in the non-saline zone compared to that of the saline stressed zone probably due to higher nutrient concentrations and the absence of abiotic stress factors including salinity. Physicochemical parameters like nitrogen, phosphorus, and potassium were found significantly positively correlated with Muribaculaceae highly enriched in the non-saline zone. However, relative dissolved oxygen was found significantly negatively correlated with Rikenellaceae and Desulfovibrionaceae, enriched in the non-saline soil. This study first provides the detailed characterizations of rice root endophytic bacterial communities as well as their diversity contributed by measured environmental parameters in salinity Sundarbans areas. Since this study deals with two gradients of salinity, connecting the microbial diversity with the salinity range could be targeted for the use as "bioindicator" taxa and bio-fertilizer formulation in salt-affected regions.}, } @article {pmid35778624, year = {2022}, author = {Wei, C and Gu, W and Tian, R and Xu, F and Han, Y and Ji, Y and Li, T and Zhu, Y and Lang, P and Wu, W}, title = {Comparative analysis of the structure and function of rhizosphere microbiome of the Chinese medicinal herb Alisma in different regions.}, journal = {Archives of microbiology}, volume = {204}, number = {7}, pages = {448}, pmid = {35778624}, issn = {1432-072X}, support = {82073958//National Natural Science Foundation of China/ ; 81673534//Innovative Research Group Project of the National Natural Science Foundation of China/ ; ZDXM-3-24//Jiangsu Collaborative Innovation Center of Chinese Medicinal Resources Industrialization/ ; 2019//Qing Lan Project/ ; SYSD2020248//Suzhou Science and Technology Development Plan/ ; }, mesh = {*Alisma/chemistry/genetics ; Bacteria/genetics ; *Microbiota/genetics ; *Plants, Medicinal ; Rhizosphere ; *Triterpenes ; }, abstract = {Rhizoma Alismatis, a commonly used traditional Chinese medicine, is the dried tuber of Alisma orientale and Alisma A. plantago-aquatica, mainly cultivated in Fujian and Sichuan provinces (China), respectively. Studies have shown that the rhizosphere microbiome is a key factor determining quality of Chinese medicinal plants. Here we applied metagenomics to investigate the rhizosphere microbiome of Alisma in Fujian and Sichuan, focusing on its structure and function and those genes involved in protostane triterpenes biosynthesis. The dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes. Compared with Fujian, the rhizosphere of Sichuan has a greater α diversity and stronger microbial interactions but significantly lower relative abundance of archaea. Microbes with disease-suppressing functions were more abundant in Sichuan than Fujian, but vice versa for those with IAA-producing functions. Gemmatimonas, Anaeromyxobacter, and Pseudolabrys were the main contributors to the potential functional difference in two regions. Genes related to protostane triterpenes biosynthesis were enriched in Fujian. Steroidobacter, Pseudolabrys, Nevskia, and Nitrospira may contribute to the accumulation of protostane triterpenes in Alisma. This work fills a knowledge gap of Alisma's rhizosphere microbiome, providing a valuable reference for studying its beneficial microorganisms.}, } @article {pmid35777903, year = {2022}, author = {Tian, T and Mao, Q and Xie, J and Wang, Y and Shao, WH and Zhong, Q and Chen, JJ}, title = {Multi-omics data reveals the disturbance of glycerophospholipid metabolism caused by disordered gut microbiota in depressed mice.}, journal = {Journal of advanced research}, volume = {39}, number = {}, pages = {135-145}, pmid = {35777903}, issn = {2090-1224}, mesh = {Animals ; Fatty Acids, Volatile/metabolism ; Firmicutes/metabolism ; *Gastrointestinal Microbiome ; Glycerophospholipids ; Lipid Metabolism ; Mice ; Tryptophan/metabolism ; }, abstract = {INTRODUCTION: Although researchers have done intensive research on depression, its pathogenesis is still not fully explained. More and more evidence suggests that gut microbiota is closely related to the onset of depression; but its specific functional ways are not clearly identified.

OBJECTIVES: The purpose of our work was to find out how the gut microbiota was involved in the onset of depression, and to identify the potential ways to link the gut and brain in mice with depressive-like behaviors (DLB).

METHODS: We used the chronic restraint stress (CRS)-induced depression model here. Gut microbiota compositions in fecal samples, lipid metabolism (in fecal, serum and hippocampus samples) and neurotransmitters in hippocampus samples were detected.

RESULTS: We found that the 7 of 13 differential genera that significantly correlated with DLB belonged to phylum Firmicutes. The differential lipid metabolites in fecal samples mainly belonged to glycerophospholipids (GP) and fatty acids (FA) metabolism, and three important "metabolite type-bacterial taxa" correlated pairs were identified: "FA/GP-Firmicutes", "FA/GP-Akkermansia", and "FA/GP-Bifidobacterium". The key differential lipid metabolites significantly correlated with DLB mainly belonged to FA and GP, and the DLB-related metagenomic genes were consistently enriched in GP metabolism and FA metabolism. Three significantly changed short-chain fatty acids (SCFAs) were significantly correlated with the majority of differential genera. Meanwhile, we found that the differential lipid metabolites in serum and hippocampus samples were mainly mapped into the GP metabolism, and there were four differential neurotransmitters from the tryptophan pathway in hippocampus samples.

CONCLUSION: Together, our findings could provide novel insights into the role of "microbiota-gut-brain" (MGB) axis in depression, and indicate that the gut microbiota might have a vital role in the onset of DLB by affecting the peripheral/central GP metabolism and tryptophan pathway. The "Firmicutes-SCFAs-GP metabolism-Tryptophan pathway" might be a possible way to link the gut and brain in depressed mice.}, } @article {pmid35777598, year = {2022}, author = {Du, H and Xie, H and Ma, M and Igarashi, Y and Luo, F}, title = {Modified methods obtain high-quality DNA and RNA from anaerobic activated sludge at a wide range of temperatures.}, journal = {Journal of microbiological methods}, volume = {199}, number = {}, pages = {106532}, doi = {10.1016/j.mimet.2022.106532}, pmid = {35777598}, issn = {1872-8359}, mesh = {Anaerobiosis ; DNA ; Humic Substances/analysis ; *RNA/genetics ; *Sewage ; Temperature ; Water ; }, abstract = {Anaerobic activated sludge is rich in humic substances and water, leading to significant differences in the stability of metagenomic DNA and metatranscriptomic RNA. Thus, it is of great difficulty to exact high-quality and high-yield DNA and RNA from them, especially those cultured at a wide range of temperatures. Here, we established fast and effective DNA and RNA extraction methods based on current commercial kits. The modified methods combined liquid nitrogen grinding with kits, achieving notable improvements in concentrations, yields, purity and integrities for both DNA and RNA. The ratios of OD260/280 of the metagenomic DNA were between 1.81 ± 0.03 and 1.83 ± 0.02, while OD260/280 and OD260/230 of the metatranscriptomic RNA ranged from 1.96 ± 0.01 to 2.13 ± 0.03 and from 1.94 ± 0.02 to 2.30 ± 0.03 respectively. Metagenomic DNA and metatranscriptomic RNA obtained by the modified methods perfectly met the requirements of second- and third-generation sequencing, providing valuable reference for extracting high-quality metagenomic DNA and metatranscriptomic RNA from environmental samples of high water content and humic substances under temperatures ranging from 18 °C to 52 °C.}, } @article {pmid35777567, year = {2022}, author = {Giangeri, G and Morlino, MS and De Bernardini, N and Ji, M and Bosaro, M and Pirillo, V and Antoniali, P and Molla, G and Raga, R and Treu, L and Campanaro, S}, title = {Preliminary investigation of microorganisms potentially involved in microplastics degradation using an integrated metagenomic and biochemical approach.}, journal = {The Science of the total environment}, volume = {843}, number = {}, pages = {157017}, doi = {10.1016/j.scitotenv.2022.157017}, pmid = {35777567}, issn = {1879-1026}, mesh = {Cytochrome P-450 CYP4A ; Metagenome ; Metagenomics ; *Microplastics ; Plastics/metabolism ; Polyethylene ; Polyethylene Terephthalates ; *Water Pollutants, Chemical ; }, abstract = {Plastic pollution is becoming an emerging environmental issue due to inappropriate disposal at the end of the materials life cycle. When plastics are released, they undergo physical and chemical corrosion, leading to the formation of small particles, commonly referred to as microplastics. In this study, a microbial community derived from the leachate of a bioreactor containing a mixture of soil and plastic collected during a landfill mining process underwent an enrichment protocol in order to select the microbial species specifically involved in plastic degradation. The procedure was set up and tested on polyethylene, polyvinyl chloride, and polyethylene terephthalate, both in anaerobic and aerobic conditions. The evolution of the microbiome has been monitored using a combined approach based on microscopy, marker-gene amplicon sequencing, genome-centric metagenomics, degradation assays, and GC-MS analyses. This procedure permitted us to deeply investigate the metabolic pathways potentially involved in plastic degradation and to depict the route for microplastics metabolization from the enriched microbial community. Six enzymes, among the ones already identified, were found in our samples (alkane 1-monooxygenase, cutinase, feruloyl esterase, triacylglycerol lipase, medium-chain acyl-CoA dehydrogenase, and protocatechuate 4,5-dioxygenase) and new enzymes, addressed as MHETases most probably for the presence of the catalytic triad (His-Asp-Ser), were detected. Among the enzymes involved in plastics degradation, alkane 1-monooxygenase was found in high copy number (between ten and 62 copies) in the metagenomes that resulted most abundant in the microbiome enriched with polyethylene, while protocatechuate 4,5-dioxygenase was found between one and eight copies in the most abundant metagenomes of the microbial culture enriched with polyethylene terephthalate. Degradation assays, performed using both bacterial lysates and supernatants, revealed interesting results on polyethylene terephthalate degradation. Moreover, this study demonstrates to what extent different types of microplastics can affect the microbial community composition. The results obtained significantly increase the knowledge of the plastic degradation process.}, } @article {pmid35777538, year = {2022}, author = {Ma, S and Liu, H}, title = {Effects of 3D-printed bulking agent on microbial community succession and carbohydrate-active enzymes genes during swine manure composting.}, journal = {Chemosphere}, volume = {306}, number = {}, pages = {135513}, doi = {10.1016/j.chemosphere.2022.135513}, pmid = {35777538}, issn = {1879-1298}, mesh = {Animals ; Carbohydrates ; *Composting/methods ; Manure/microbiology ; *Microbiota ; Printing, Three-Dimensional ; Soil ; Swine ; }, abstract = {The bulking agent plays an important role in aerobic composting, but their shape, porosity, and homogeneity need to be optimized. In the present work, a bulking agent with a uniform shape was prepared by 3D printing to explore its influence on physicochemical parameters, microbial community succession, and gene abundance of carbohydrate-active enzymes (CAZymes) in swine manure aerobic composting. The results showed that adding 3D-printed bulking agents can increase maximum temperature, prolong the thermophilic period, and improve the degradation rate of volatile solids, which was attributed to ameliorative air permeability by the porous 3D-printed bulking agent. The abundances of some pathogenic bacteria decreased and CAZymes genes increased respectively in response to the addition of the 3D-printed bulking agent, implying it has a certain positive effect on improving the safety of compost products and promoting the degradation of organic matter. In summary, the 3D-printed bulking agent has good application potential in laboratory-scale aerobic composting.}, } @article {pmid35777321, year = {2022}, author = {Hauptfeld, E and Pelkmans, J and Huisman, TT and Anocic, A and Snoek, BL and von Meijenfeldt, FAB and Gerritse, J and van Leeuwen, J and Leurink, G and van Lit, A and van Uffelen, R and Koster, MC and Dutilh, BE}, title = {A metagenomic portrait of the microbial community responsible for two decades of bioremediation of poly-contaminated groundwater.}, journal = {Water research}, volume = {221}, number = {}, pages = {118767}, doi = {10.1016/j.watres.2022.118767}, pmid = {35777321}, issn = {1879-2448}, mesh = {Biodegradation, Environmental ; *Groundwater ; Metagenome ; *Microbiota ; *Water Pollutants, Chemical/analysis ; }, abstract = {Biodegradation of pollutants is a sustainable and cost-effective solution to groundwater pollution. Here, we investigate microbial populations involved in biodegradation of poly-contaminants in a pipeline for heavily contaminated groundwater. Groundwater moves from a polluted park to a treatment plant, where an aerated bioreactor effectively removes the contaminants. While the biomass does not settle in the reactor, sediment is collected afterwards and used to seed the new polluted groundwater via a backwash cycle. The pipeline has successfully operated since 1999, but the biological components in the reactor and the contaminated park groundwater have never been described. We sampled seven points along the pipeline, representing the entire remediation process, and characterized the changing microbial communities using genome-resolved metagenomic analysis. We assembled 297 medium- and high-quality metagenome-assembled genome sequences representing on average 46.3% of the total DNA per sample. We found that the communities cluster into two distinct groups, separating the anaerobic communities in the park groundwater from the aerobic communities inside the plant. In the park, the community is dominated by members of the genus Sulfuricurvum, while the plant is dominated by generalists from the order Burkholderiales. Known aromatic compound biodegradation pathways are four times more abundant in the plant-side communities compared to the park-side. Our findings provide a genome-resolved portrait of the microbial community in a highly effective groundwater treatment system that has treated groundwater with a complex contamination profile for two decades.}, } @article {pmid35777297, year = {2022}, author = {Guo, W and Guo, XJ and Xu, LN and Shao, LW and Zhu, BC and Liu, H and Wang, YJ and Gao, KY}, title = {Effect of whole-plant corn silage treated with lignocellulose-degrading bacteria on growth performance, rumen fermentation, and rumen microflora in sheep.}, journal = {Animal : an international journal of animal bioscience}, volume = {16}, number = {7}, pages = {100576}, doi = {10.1016/j.animal.2022.100576}, pmid = {35777297}, issn = {1751-732X}, mesh = {Animals ; Bacteria/metabolism ; Citrates/pharmacology ; Diet/veterinary ; Dietary Fiber/metabolism ; Digestion ; Fermentation ; *Gastrointestinal Microbiome ; Glucosides/pharmacology ; Hydrolases/metabolism/pharmacology ; Lignin/metabolism ; Male ; Rumen/metabolism ; Sheep ; *Silage/analysis ; Zea mays/chemistry ; }, abstract = {Lignification of cellulose limits the effective utilisation of fibre in plant cell wall. Lignocellulose-degrading bacteria secrete enzymes that decompose lignin and have the potential to improve fibre digestibility. Therefore, this study aimed to investigate the effect of whole-plant corn silage inoculated with lignocellulose-degrading bacteria on the growth performance, rumen fermentation, and rumen microbiome in sheep. Twelve 2-month-old male hybrid sheep (Dorper ♂ × small-tailed Han ♀) were randomly assigned into two dietary groups (n = 6): (1) untreated whole-plant corn silage (WPCS) and (2) WPCS inoculated with bacterial inoculant (WPCSB). Whole-plant corn silage inoculated with bacterial inoculant had higher in situ NDF digestibility than WPCS. Sheep in the WPCSB group had significantly higher average daily gain, DM intake, and feed conversion rate than those in the WPCS group (P < 0.05). Furthermore, higher volatile fatty acid concentrations were detected in WPCSB rumen samples, leading to lower ruminal pH (P < 0.05). The WPCSB group showed higher abundance of Bacteroidetes and lower abundance of Firmicutes in the rumen microbiome than the WPCS group (P < 0.05). Multiple differential genera were identified, with Prevotella being the most dominant genus and more abundant in WPCSB samples. Moreover, the enriched functional attributes, including those associated with glycolysis/gluconeogenesis and citrate cycle, were more actively expressed in the WPCSB samples than in the WPCS samples. Additionally, certain glucoside hydrolases that hydrolyse the side chains of hemicelluloses and pectins were also actively expressed in the WPCSB microbiome. These findings suggested that WPCSB increased NDF digestibility in three ways: (1) by increasing the relative abundance of the most abundant genera, (2) by recruiting more functional features involved in glycolysis/gluconeogenesis and citrate cycle pathways, and (3) by increasing the relative abundance and/or expression activity of the glucoside hydrolases involved in hemicellulose and pectin metabolism. Our findings provide novel insights into the microbial mechanisms underlying improvement in the growth performance of sheep/ruminants. However, the biological mechanisms cannot be fully elucidated using only metagenomics tools; therefore, a combined multi-omics approach will be used in subsequent studies.}, } @article {pmid35777142, year = {2022}, author = {Liu, W and Huang, W and Cao, Z and Ji, Y and Liu, D and Huang, W and Zhu, Y and Lei, Z}, title = {Microalgae simultaneously promote antibiotic removal and antibiotic resistance genes/bacteria attenuation in algal-bacterial granular sludge system.}, journal = {Journal of hazardous materials}, volume = {438}, number = {}, pages = {129286}, doi = {10.1016/j.jhazmat.2022.129286}, pmid = {35777142}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Chlorella ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Microalgae/genetics ; Sewage/microbiology ; Sulfadiazine ; Tetracycline/pharmacology ; Wastewater/microbiology ; }, abstract = {This study investigated the effects of microalgae growth on antibiotic removal and the attenuation of antibiotic resistance genes (ARGs)/ARGs host bacteria in algal-bacterial granular sludge (ABGS) system. In the presence of tetracycline (TC) and sulfadiazine (SDZ) mixture (2-4 mg/L), microalgae could grow on bacterial granular sludge (BGS) to form ABGS, with a chlorophyll-a content of 7.68-8.13 mg/g-VSS being achieved. The removal efficiencies of TC and SDZ by ABGS were as high as 79.0 % and 94.0 %, which were 4.3-5.0 % higher than those by BGS. Metagenomic analysis indicated that the relative abundances of TC/SDZ- related ARGs and mobile genetic elements (MGEs) in BGS were 56.1 % and 22.1 % higher than those in ABGS. A total of 26 ARGs were detected from the granules, and they were identified to associate with 46 host bacteria. 13 out of 26 ARGs and 13 out of 46 hosts were shared ARGs and hosts, respectively. The total relative abundance of host bacteria in BGS was 30.8 % higher than that in ABGS. Scenedesmus and Chlorella were the dominant microalgae that may reduce the diversity of ARGs hosts. Overall, ABGS is a promising biotechnology for antibiotic-containing wastewater treatment.}, } @article {pmid35776122, year = {2022}, author = {Kang, X and Luo, X and Schönhuth, A}, title = {StrainXpress: strain aware metagenome assembly from short reads.}, journal = {Nucleic acids research}, volume = {50}, number = {17}, pages = {e101}, pmid = {35776122}, issn = {1362-4962}, mesh = {High-Throughput Nucleotide Sequencing ; *Metagenome ; *Metagenomics ; Sequence Analysis, DNA ; }, abstract = {Next-generation sequencing-based metagenomics has enabled to identify microorganisms in characteristic habitats without the need for lengthy cultivation. Importantly, clinically relevant phenomena such as resistance to medication, virulence or interactions with the environment can vary already within species. Therefore, a major current challenge is to reconstruct individual genomes from the sequencing reads at the level of strains, and not just the level of species. However, strains of one species can differ only by minor amounts of variants, which makes it difficult to distinguish them. Despite considerable recent progress, related approaches have remained fragmentary so far. Here, we present StrainXpress, as a comprehensive solution to the problem of strain aware metagenome assembly from next-generation sequencing reads. In experiments, StrainXpress reconstructs strain-specific genomes from metagenomes that involve up to >1000 strains and proves to successfully deal with poorly covered strains. The amount of reconstructed strain-specific sequence exceeds that of the current state-of-the-art approaches by on average 26.75% across all data sets (first quartile: 18.51%, median: 26.60%, third quartile: 35.05%).}, } @article {pmid35774464, year = {2022}, author = {Du, Y and Li, X and Liu, Y and Mu, S and Shen, D and Fan, S and Lou, Z and Zhang, S and Xia, H and Yuan, Y and Wang, S}, title = {The Species Identification and Genomic Analysis of Haemobacillus shengwangii: A Novel Pathogenic Bacterium Isolated From a Critically Ill Patient With Bloodstream Infection.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {919169}, pmid = {35774464}, issn = {1664-302X}, abstract = {Since the first strain related to Thermicanaceae was reported in 1999, almost no literature on Thermicanaceae is available, particularly its genomics. We recently isolated a novel pathogenic bacterium, the [△] strain DYY3, from the blood sample of a critically ill patient. The morphological, physiological, and biochemical characteristics of [△] strain DYY3 were presented in this study, and the virulence factor genes and antibiotic resistance of DYY3 were also determined. Interestingly, the average nucleotide identity (ANI) and core-genes average amino acid identity (cAAI) analysis indicated that [△] strain DYY3 was genus novel and species novel. Moreover, phylogenetic analysis based on both 16S rRNA gene and whole genomic core gene sequences suggested that [△] strain DYY3 belonged to the family Thermicanaceae, and this novel taxon was thus named Haemobacillus shengwangii gen. nov., sp. nov. Besides, both the whole genome-based phylogenetic tree and amino acid identity analysis indicated that Thermicanus aegyptius, Hydrogenibacillus schlegelii, Brockia lithotrophica, and the newly discovered species H. shengwangii should belong to Thermicanaceae at the family level, and T. aegyptius was the closest species to H. shengwangii. We also constructed the first high-quality genome in the family Thermicanaceae using the next-generation sequencing (NGS) and single-molecule real-time (SMRT) sequencing technologies, which certainly contributed to further genomics studies and metagenomic-based pathogenic detection in the future.}, } @article {pmid35774461, year = {2022}, author = {LaMontagne, MG and Zhang, Y and Guillen, GJ and Gentry, TJ and Allen, MS}, title = {Hurricane Harvey Impacts on Water Quality and Microbial Communities in Houston, TX Waterbodies.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {875234}, pmid = {35774461}, issn = {1664-302X}, abstract = {Extreme weather events can temporarily alter the structure of coastal systems and generate floodwaters that are contaminated with fecal indicator bacteria (FIB); however, every coastal system is unique, so identification of trends and commonalities in these episodic events is challenging. To improve our understanding of the resilience of coastal systems to the disturbance of extreme weather events, we monitored water quality, FIB at three stations within Clear Lake, an estuary between Houston and Galveston, and three stations in bayous that feed into the estuary. Water samples were collected immediately before and after Hurricane Harvey (HH) and then throughout the fall of 2017. FIB levels were monitored by culturing E. coli and Enterococci. Microbial community structure was profiled by high throughput sequencing of PCR-amplified 16S rRNA gene fragments. Water quality and FIB data were also compared to historical data for these water body segments. Before HH, salinity within Clear Lake ranged from 9 to 11 practical salinity units (PSU). Immediately after the storm, salinity dropped to < 1 PSU and then gradually increased to historical levels over 2 months. Dissolved inorganic nutrient levels were also relatively low immediately after HH and returned, within a couple of months, to historical levels. FIB levels were elevated immediately after the storm; however, after 1 week, E. coli levels had decreased to what would be acceptable levels for freshwater. Enterococci levels collected several weeks after the storm were within the range of historical levels. Microbial community structure shifted from a system dominated by Cyanobacteria sp. before HH to a system dominated by Proteobacteria and Bacteroidetes immediately after. Several sequences observed only in floodwater showed similarity to sequences previously reported for samples collected following Hurricane Irene. These changes in beta diversity corresponded to salinity and nitrate/nitrite concentrations. Differential abundance analysis of metabolic pathways, predicted from 16S sequences, suggested that pathways associated with virulence and antibiotic resistance were elevated in floodwater. Overall, these results suggest that floodwater generated from these extreme events may have high levels of fecal contamination, antibiotic resistant bacteria and bacteria rarely observed in other systems.}, } @article {pmid35774454, year = {2022}, author = {Mohd Zaki, A and Hadingham, A and Flaviani, F and Haque, Y and Mi, JD and Finucane, D and Dalla Valle, G and Mason, AJ and Saqi, M and Gibbons, DL and Tribe, RM}, title = {Neutrophils Dominate the Cervical Immune Cell Population in Pregnancy and Their Transcriptome Correlates With the Microbial Vaginal Environment.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {904451}, pmid = {35774454}, issn = {1664-302X}, abstract = {The cervicovaginal environment in pregnancy is proposed to influence risk of spontaneous preterm birth. The environment is shaped both by the resident microbiota and local inflammation driven by the host response (epithelia, immune cells and mucous). The contributions of the microbiota, metabolome and host defence peptides have been investigated, but less is known about the immune cell populations and how they may respond to the vaginal environment. Here we investigated the maternal immune cell populations at the cervicovaginal interface in early to mid-pregnancy (10-24 weeks of gestation, samples from N = 46 women), we confirmed neutrophils as the predominant cell type and characterised associations between the cervical neutrophil transcriptome and the cervicovaginal metagenome (N = 9 women). In this exploratory study, the neutrophil cell proportion was affected by gestation at sampling but not by birth outcome or ethnicity. Following RNA sequencing (RNA-seq) of a subset of neutrophil enriched cells, principal component analysis of the transcriptome profiles indicated that cells from seven women clustered closely together these women had a less diverse cervicovaginal microbiota than the remaining three women. Expression of genes involved in neutrophil mediated immunity, activation, degranulation, and other immune functions correlated negatively with Gardnerella vaginalis abundance and positively with Lactobacillus iners abundance; microbes previously associated with birth outcome. The finding that neutrophils are the dominant immune cell type in the cervix during pregnancy and that the cervical neutrophil transcriptome of pregnant women may be modified in response to the microbial cervicovaginal environment, or vice versa, establishes the rationale for investigating associations between the innate immune response, cervical shortening and spontaneous preterm birth and the underlying mechanisms.}, } @article {pmid35774405, year = {2022}, author = {Horne, RG and Freedman, SB and Johnson-Henry, KC and Pang, XL and Lee, BE and Farion, KJ and Gouin, S and Schuh, S and Poonai, N and Hurley, KF and Finkelstein, Y and Xie, J and Williamson-Urquhart, S and Chui, L and Rossi, L and Surette, MG and Sherman, PM}, title = {Intestinal Microbial Composition of Children in a Randomized Controlled Trial of Probiotics to Treat Acute Gastroenteritis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {883163}, pmid = {35774405}, issn = {2235-2988}, mesh = {Child ; Child, Preschool ; Feces/microbiology ; *Gastroenteritis/drug therapy ; *Gastrointestinal Microbiome ; Humans ; Intestines ; *Microbiota ; *Probiotics/therapeutic use ; RNA, Ribosomal, 16S/genetics ; }, abstract = {UNLABELLED: Compositional analysis of the intestinal microbiome in pre-schoolers is understudied. Effects of probiotics on the gut microbiota were evaluated in children under 4-years-old presenting to an emergency department with acute gastroenteritis. Included were 70 study participants (n=32 placebo, n=38 probiotics) with stool specimens at baseline (day 0), day 5, and after a washout period (day 28). Microbiota composition and deduced functions were profiled using 16S ribosomal RNA sequencing and predictive metagenomics, respectively. Probiotics were detected at day 5 of administration but otherwise had no discernable effects, whereas detection of bacterial infection (P<0.001) and participant age (P<0.001) had the largest effects on microbiota composition, microbial diversity, and deduced bacterial functions. Participants under 1 year had lower bacterial diversity than older aged pre-schoolers; compositional changes of individual bacterial taxa were associated with maturation of the gut microbiota. Advances in age were associated with differences in gut microbiota composition and deduced microbial functions, which have the potential to impact health later in life.

CLINICAL TRIAL REGISTRATION: www.ClinicalTrials.gov, identifier: NCT01853124.}, } @article {pmid35774395, year = {2022}, author = {Lee, SH and Park, HK and Kang, CD and Choi, DH and Park, SC and Park, JM and Nam, SJ and Chae, GB and Lee, KY and Cho, H and Lee, SJ}, title = {High Dose Intramuscular Vitamin D3 Supplementation Impacts the Gut Microbiota of Patients With Clostridioides Difficile Infection.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {904987}, pmid = {35774395}, issn = {2235-2988}, mesh = {Bacteria/genetics ; Cholecalciferol ; *Clostridioides difficile ; *Clostridium Infections/microbiology ; Dietary Supplements ; *Gastrointestinal Microbiome ; Humans ; Prospective Studies ; RNA, Ribosomal, 16S/genetics ; Vancomycin ; Vitamin D ; *Vitamin D Deficiency/microbiology ; }, abstract = {BACKGROUND AND AIM: Current therapeutic strategies for Clostridioides difficile infections (CDI), including oral vancomycin, metronidazole and fecal microbial transplantation, have limited efficacy and treatment failure may occur in as many as one- third of cases. Recent studies have reported that lower concentrations of 25-hydroxyvitamin D are associated with CDI severity and recurrence. However, there have been no studies on microbiota composition after the administration of vitamin D in patients with CDI. Therefore, our study aimed to compare the microbiota composition between the two groups, including eight CDI-positive patients with vitamin D supplementation and ten CDI-positive patients without vitamin D supplementation by using 16S rRNA microbial profiling.

METHODS: Twenty subjects were enrolled in this prospective randomized controlled study. One subject dropped out due to lack of contact with the guardian after discharge and one subject dropped out due to withdrawal of consent. Thus, 18 patients with CDI and vitamin D insufficiency (vitamin D level < 17 ng/mL) were divided into two groups: CDI with vitamin D supplementation (n = 8) and CDI without vitamin D supplementation (control: n = 10). Subjects with vitamin D insufficiency were randomized to receive 200,000 IU intramuscular cholecalciferol whereas patients in the control group received only oral vancomycin. Stool samples were obtained twice before vancomycin was administered and eight weeks after treatment; the V3-V4 16S rRNA metagenomic sequencing was performed using EzBioCloud.

RESULTS: The alpha diversity of the gut microbiota in the recovery state was significantly higher than that in the CDI state. Analysis of bacterial relative abundance showed significantly lower Proteobacteria and higher Lachnospiraceae, Ruminococcaceae, Akkermansiaceae, and Bifidobacteriaceae in the recovery state. When comparing the control and vitamin D treatment groups after eight weeks, increase in alpha diversity and, abundance of Lachnospiraceae, and Ruminococcaceae exhibited the same trend in both groups. A significant increase in Bifidobacteriaceae and Christensenellaceae was observed in the vitamin D group; Proteobacteria abundance was significantly lower in the vitamin D treatment group after eight weeks than that in the control group.

CONCLUSION: Our study confirmed that the increase in the abundance of beneficial bacteria such as Bifidobacteriaceae, and Christensenellaceae were prominently evident during recovery after administration of a high dose of cholecalciferol. These findings indicate that vitamin D administration may be useful in patients with CDI, and further studies with larger sample sizes are required.}, } @article {pmid35773309, year = {2022}, author = {Bajagai, YS and Petranyi, F and J Yu, S and Lobo, E and Batacan, R and Kayal, A and Horyanto, D and Ren, X and M Whitton, M and Stanley, D}, title = {Phytogenic supplement containing menthol, carvacrol and carvone ameliorates gut microbiota and production performance of commercial layers.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {11033}, pmid = {35773309}, issn = {2045-2322}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Chickens ; Cyclohexane Monoterpenes ; Cymenes ; Dietary Supplements/analysis ; Female ; *Gastrointestinal Microbiome ; Menthol/pharmacology ; }, abstract = {Consumer push towards open and free-range production systems makes biosecurity on farms challenging, leading to increased disease and animal welfare issues. Phytogenic products are increasingly becoming a viable alternative for the use of antibiotics in livestock production. Here we present a study of the effects of commercial phytogenic supplement containing menthol, carvacrol and carvone on intestinal microbiota of layer hens, microbial functional capacity, and intestinal morphology. A total of 40,000 pullets were randomly assigned to two sides of the experimental shed. Growth performance, mortality, egg production and egg quality parameters were recorded throughout the trial period (18-30 weeks of age). Microbial community was investigated using 16S amplicon sequencing and functional difference using metagenomic sequencing. Phytogen supplemented birds had lower mortality and number of dirty eggs, and their microbial communities showed reduced richness. Although phytogen showed the ability to control the range of poultry pathogens, its action was not restricted to pathogenic taxa, and it involved functional remodelling the intestinal community towards increased cofactor production, heterolactic fermentation and salvage and recycling of metabolites. The phytogen did not alter the antimicrobial resistance profile or the number of antibiotic resistance genes. The study indicates that phytogenic supplementation can mimic the action of antibiotics in altering the gut microbiota and be used as their alternative in industry-scale layer production.}, } @article {pmid35773279, year = {2022}, author = {Buessecker, S and Palmer, M and Lai, D and Dimapilis, J and Mayali, X and Mosier, D and Jiao, JY and Colman, DR and Keller, LM and St John, E and Miranda, M and Gonzalez, C and Gonzalez, L and Sam, C and Villa, C and Zhuo, M and Bodman, N and Robles, F and Boyd, ES and Cox, AD and St Clair, B and Hua, ZS and Li, WJ and Reysenbach, AL and Stott, MB and Weber, PK and Pett-Ridge, J and Dekas, AE and Hedlund, BP and Dodsworth, JA}, title = {An essential role for tungsten in the ecology and evolution of a previously uncultivated lineage of anaerobic, thermophilic Archaea.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3773}, pmid = {35773279}, issn = {2041-1723}, mesh = {Anaerobiosis ; *Archaea/metabolism ; Metagenome ; Phylogeny ; *Tungsten ; }, abstract = {Trace metals have been an important ingredient for life throughout Earth's history. Here, we describe the genome-guided cultivation of a member of the elusive archaeal lineage Caldarchaeales (syn. Aigarchaeota), Wolframiiraptor gerlachensis, and its growth dependence on tungsten. A metagenome-assembled genome (MAG) of W. gerlachensis encodes putative tungsten membrane transport systems, as well as pathways for anaerobic oxidation of sugars probably mediated by tungsten-dependent ferredoxin oxidoreductases that are expressed during growth. Catalyzed reporter deposition-fluorescence in-situ hybridization (CARD-FISH) and nanoscale secondary ion mass spectrometry (nanoSIMS) show that W. gerlachensis preferentially assimilates xylose. Phylogenetic analyses of 78 high-quality Wolframiiraptoraceae MAGs from terrestrial and marine hydrothermal systems suggest that tungsten-associated enzymes were present in the last common ancestor of extant Wolframiiraptoraceae. Our observations imply a crucial role for tungsten-dependent metabolism in the origin and evolution of this lineage, and hint at a relic metabolic dependence on this trace metal in early anaerobic thermophiles.}, } @article {pmid35772715, year = {2022}, author = {Li, X and Chu, S and Wang, P and Li, K and Su, Y and Wu, D and Xie, B}, title = {Potential of biogas residue biochar modified by ferric chloride for the enhancement of anaerobic digestion of food waste.}, journal = {Bioresource technology}, volume = {360}, number = {}, pages = {127530}, doi = {10.1016/j.biortech.2022.127530}, pmid = {35772715}, issn = {1873-2976}, mesh = {Anaerobiosis ; *Biofuels ; Bioreactors ; Charcoal ; Chlorides ; Ferric Compounds ; Food ; Methane/metabolism ; *Refuse Disposal ; }, abstract = {Biogas residue biochar (BRB) and BRB modified by ferric chloride (BRB-FeCl3) were applied to promote anaerobic digestion (AD) of food waste (FW), related mechanisms were also proposed in this study. Results indicated BRB-FeCl3 showed higher specific surface area, more abundant functional groups and impregnate iron than BRB, and they respectively increased 22.50% and 12.79% cumulative methane yields compared with control group because of accelerated volatile fatty acids (VFAs) transformation, which were confirmed by enhanced metabolism of glycolysis, fatty acid degradation and pyruvate. BRB, especially BRB-FeCl3 facilitated the growth of Syntrophomonas, Methanofollis, Methanoculleus and Methanosarcina, which further promoted the methanogenesis by enhancing the metabolic activities of methanol, dimethylamine and methylamine pathways, thereby causing more metabolically diverse methanogenic pathways. Metagenomics analysis revealed BRB, especially BRB-FeCl3 promoted the relative abundances of functional genes involved in direct interspecies electron transfer (DIET). Present study explored the enhancement mechanisms and feasibility of BRB-FeCl3 for AD process.}, } @article {pmid35771673, year = {2022}, author = {Jing, Q and Leung, CHC and Wu, AR}, title = {Cell-Free DNA as Biomarker for Sepsis by Integration of Microbial and Host Information.}, journal = {Clinical chemistry}, volume = {68}, number = {9}, pages = {1184-1195}, doi = {10.1093/clinchem/hvac097}, pmid = {35771673}, issn = {1530-8561}, mesh = {Biomarkers ; *Cell-Free Nucleic Acids ; Humans ; Intensive Care Units ; Prognosis ; *Sepsis/diagnosis ; Severity of Illness Index ; }, abstract = {BACKGROUND: Cell-free DNA (cfDNA) is emerging as a biomarker for sepsis. Previous studies have been focused mainly on identifying blood infections or simply quantifying cfDNA. We propose that by characterizing multifaceted unexplored components, cfDNA could be more informative for assessing this complex syndrome.

METHODS: We explored multiple aspects of cfDNA in septic and nonseptic intensive care unit (ICU) patients by metagenomic sequencing, with longitudinal measurement and integrative assessment of plasma cfDNA quantity, human cfDNA fragmentation patterns, infecting pathogens, and overall microbial composition.

RESULTS: Septic patients had significantly increased cfDNA quantity and altered human cfDNA fragmentation pattern. Moreover, human cfDNA fragments appeared to comprise information about cellular oxidative stress and could indicate disease severity. Metagenomic sequencing was more sensitive than blood culture in detecting bacterial infections and allowed for simultaneous detection of viral pathogens. We found differences in microbial composition between septic and nonseptic patients and between survivors and nonsurvivors by 28-day mortality, both on the first day of ICU admission and across the study period. By integrating all the information into a machine learning model, we achieved improved performance in identifying sepsis and prediction of clinical outcome for ICU patients with areas under the curve of 0.992 (95% CI 0.969-1.000) and 0.802 (95% CI 0.605-0.999), respectively.

CONCLUSIONS: We were able to diagnose sepsis and predict mortality as soon as the first day of ICU admission by integrating multifaceted cfDNA information obtained in a single metagenomic assay; this approach could provide important advantages for clinical management and for improving outcomes in ICU patients.}, } @article {pmid35770995, year = {2022}, author = {Walters, KA and Myers, KS and Wang, H and Fortney, NW and Ingle, AT and Scarborough, MJ and Donohue, TJ and Noguera, DR}, title = {Metagenomes and Metagenome-Assembled Genomes from Microbial Communities Fermenting Ultrafiltered Milk Permeate.}, journal = {Microbiology resource announcements}, volume = {11}, number = {7}, pages = {e0029322}, pmid = {35770995}, issn = {2576-098X}, support = {DE-SC0018409//U.S. Department of Energy (DOE)/ ; MSN214606//National Dairy Council/ ; }, abstract = {Fermentative microbial communities can be utilized for the conversion of various agroindustrial residues into valuable chemicals. Here, we report 34 metagenomes from anaerobic bioreactors fed lactose-rich ultrafiltered milk permeate and 278 metagenome-assembled genomes (MAGs). These MAGs can inform future studies aimed at generating renewable chemicals from dairy and other agroindustrial residues.}, } @article {pmid35770269, year = {2022}, author = {Malik, PK and Trivedi, S and Kolte, AP and Sejian, V and Bhatta, R and Rahman, H}, title = {Diversity of rumen microbiota using metagenome sequencing and methane yield in Indian sheep fed on straw and concentrate diet.}, journal = {Saudi journal of biological sciences}, volume = {29}, number = {8}, pages = {103345}, pmid = {35770269}, issn = {1319-562X}, abstract = {An in vivo study aiming to investigate the rumen methanogens community structure was conducted in Mandya sheep fed on straw and concentrate diet. The ruminal fluid samples were collected and processed for unravelling the rumen microbiota and methanogens diversity. Further, the daily enteric methane emission and methane yield was also quantified using the SF6 tracer technique. Results indicated that the Bacteroidetes (∼57%) and Firmicutes (25%) were two prominent affiliates of the bacterial community. Archaea represented about 2.5% of the ruminal microbiota. Methanobacteriales affiliated methanogens were the most prevalent in sheep rumen. The study inveterate that the ruminal archaea community in sheep is composed of 9 genera and 18 species. Methanobrevibacter represented the largest genus of the archaeome, while methylotrophs genera constituted only 13% of the community. Methanobrevibacter gottschalkii was the prominent methanogen, and Methaobrevibacter ruminantium distributed at a lower frequency (∼2.5%). Among Methanomassiliicoccales, Group 12 sp. ISO4-H5 constituted the most considerable fraction (∼11%). KEGG reference pathway for methane metabolism indicated the formation of methane through hydrogenotrophic and methylotrophic pathways, whereas the acetoclastic pathway was not functional in sheep. The enteric methane emission and methane yield was 19.7 g/d and 20.8 g/kg DMI, respectively. Various species of Methanobrevibacter were differently correlated, and the distribution of hydrogenotrophic methanogens mainly explained the variability in methane yield between the individual sheep. It can be inferred from the study that the hydrogenotrophic methanogens dominate the rumen archaeal community in sheep and methylotrophic/aceticlastic methanogens represent a minor fraction of the community. Further studies are warranted for establishing the metabolic association between the prevalent hydrogenotrophs and methylotrophs to identify the key reaction for reducing methane emission.}, } @article {pmid35770174, year = {2022}, author = {Sarrafzadeh, MH and Mansouri, SS and Zahiri, J and Mussatto, SI and Asgharnejad, H}, title = {Editorial: Artificial Intelligence in Environmental Microbiology.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {944242}, pmid = {35770174}, issn = {1664-302X}, } @article {pmid35770162, year = {2022}, author = {Ren, W and Zhong, Y and Ding, Y and Wu, Y and Xu, X and Zhou, P}, title = {Mismatches in 16S rRNA Gene Primers: An Area Worth Further Exploring.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {888803}, pmid = {35770162}, issn = {1664-302X}, } @article {pmid35769139, year = {2022}, author = {Routhier, E and Mozziconacci, J}, title = {Genomics enters the deep learning era.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13613}, pmid = {35769139}, issn = {2167-8359}, mesh = {*Deep Learning ; Neural Networks, Computer ; Genomics ; Computational Biology ; }, abstract = {The tremendous amount of biological sequence data available, combined with the recent methodological breakthrough in deep learning in domains such as computer vision or natural language processing, is leading today to the transformation of bioinformatics through the emergence of deep genomics, the application of deep learning to genomic sequences. We review here the new applications that the use of deep learning enables in the field, focusing on three aspects: the functional annotation of genomes, the sequence determinants of the genome functions and the possibility to write synthetic genomic sequences.}, } @article {pmid35769000, year = {2022}, author = {Shang, J and Tang, X and Guo, R and Sun, Y}, title = {Accurate identification of bacteriophages from metagenomic data using Transformer.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {4}, pages = {}, pmid = {35769000}, issn = {1477-4054}, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Metagenome ; Metagenomics/methods ; *Microbiota ; }, abstract = {MOTIVATION: Bacteriophages are viruses infecting bacteria. Being key players in microbial communities, they can regulate the composition/function of microbiome by infecting their bacterial hosts and mediating gene transfer. Recently, metagenomic sequencing, which can sequence all genetic materials from various microbiome, has become a popular means for new phage discovery. However, accurate and comprehensive detection of phages from the metagenomic data remains difficult. High diversity/abundance, and limited reference genomes pose major challenges for recruiting phage fragments from metagenomic data. Existing alignment-based or learning-based models have either low recall or precision on metagenomic data.

RESULTS: In this work, we adopt the state-of-the-art language model, Transformer, to conduct contextual embedding for phage contigs. By constructing a protein-cluster vocabulary, we can feed both the protein composition and the proteins' positions from each contig into the Transformer. The Transformer can learn the protein organization and associations using the self-attention mechanism and predicts the label for test contigs. We rigorously tested our developed tool named PhaMer on multiple datasets with increasing difficulty, including quality RefSeq genomes, short contigs, simulated metagenomic data, mock metagenomic data and the public IMG/VR dataset. All the experimental results show that PhaMer outperforms the state-of-the-art tools. In the real metagenomic data experiment, PhaMer improves the F1-score of phage detection by 27%.}, } @article {pmid35768947, year = {2022}, author = {Jing, H and Xiao, X and Zhang, Y and Li, Z and Jian, H and Luo, Y and Han, Z}, title = {Composition and Ecological Roles of the Core Microbiome along the Abyssal-Hadal Transition Zone Sediments of the Mariana Trench.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0198821}, pmid = {35768947}, issn = {2165-0497}, mesh = {Archaea/genetics ; *Bacteria/genetics/metabolism ; *Microbiota/genetics ; Nitrogen/metabolism ; Oceans and Seas ; }, abstract = {The unique geological features of hadal trenches are known to influence both the structure and ecological function of microbial communities. It is also well known that heterotrophs and chemoautotrophs dominate the hadal and abyssal pelagic zones, respectively. Here, a metagenomic investigation was conducted on sediment samples obtained from the abyssal-hadal transition zone in the Mariana Trench to gain a better understanding of the general diversity and potential function of the core microbiome in this zone. A high level of cosmopolitanism existed in the core microbiome referred from a high community similarity among different stations. Niche differentiation along the fine-scale of different sediment layers was observed, especially for major archaeal groups, largely due to sediment depth and the source of organic matter. A prevalence of nitrogen biogeochemical cycles driven by various nitrifying groups with the capability of dark carbon fixation in the abyssal-hadal biosphere was also demonstrated. The predominance of heterotrophic over chemolithoautotrophic pathways in this transition zone was found, and a high abundance of genes related to respiration and carbon fixation (i.e., the intact Calvin and rTCA cycles) were detected as well, which might reflect the intensive microbial activities known to occur in this deep biosphere. The presence of those metabolic processes and associated microbes were reflected by functional and genetic markers generated from the metagenomic data in the current study. However, their roles and contributions to the nitrogen/carbon biogeochemical cycles and flux in the abyssal-hadal transition zone still need further analysis. IMPORTANCE The Mariana Trench is the deepest oceanic region on earth, its microbial ecological exploration has become feasible with the rapid progress of submersible and metagenomic sequencing. We investigated the community compositions and metabolic functions of the core microbiome along the abyssal-hadal transition zone of the Mariana Trench, although most studies by far were focused on the pelagic zone. We found a predominance of heterotrophic groups and related metabolic pathways, which were closely associated with nitrogen biogeochemical cycles driven by various nitrifying groups with the capability of dark carbon fixation.}, } @article {pmid35768736, year = {2023}, author = {Fernando, DG and Saravia, FL and Atkinson, SN and Barron, M and Kirby, JR and Kindel, TL}, title = {A single, peri-operative antibiotic can persistently alter the post-operative gut microbiome after Roux-en-Y gastric bypass.}, journal = {Surgical endoscopy}, volume = {37}, number = {2}, pages = {1476-1486}, pmid = {35768736}, issn = {1432-2218}, support = {K08 HL140000/HL/NHLBI NIH HHS/United States ; R21 AG075501/AG/NIA NIH HHS/United States ; }, mesh = {Humans ; Female ; Adult ; Middle Aged ; Male ; *Gastric Bypass ; *Gastrointestinal Microbiome/physiology ; Anti-Bacterial Agents ; Clindamycin ; Prospective Studies ; RNA, Ribosomal, 16S ; *Obesity, Morbid/surgery ; }, abstract = {INTRODUCTION: Roux-en-Y gastric bypass (RYGB) significantly alters the gut microbiome and may be a mechanism for post-operative cardiovascular disease improvement. We have previously found an association between the class of peri-operative, intravenous antibiotic administered at the time of RYGB and the resolution rate of hypertension suggesting the gut microbiome as a mechanism. In this study, we performed a prospective study of RYGB to determine if a single intravenous antibiotic could alter the gastrointestinal microbial composition.

METHODS: Patients undergoing RYGB were randomized to a single, peri-operative antibiotic of intravenous cefazolin (n = 8) or clindamycin (n = 8). Stool samples were collected from four-time points: 2 weeks pre-op (- 2w), 2 days pre-op (- 2d), 2 weeks post-op (+ 2w) and 3 months post-op (+ 3m). Stool samples were processed for genomic DNA followed by Illumina 16S rRNA gene sequencing and shotgun metagenomic sequencing (MGS).

RESULTS: A total of 60 stool samples (- 2w, n = 16; - 2d, n = 15; + 2w, n = 16; + 3m, n = 13) from 16 patients were analyzed. 87.5% of patients were female with an average age of 48.6 ± 12.2 years and pre-operative BMI of 50.9 ± 23.3 kg/m[2]. RYGB induced statistically significant differences in alpha and beta diversity. There were statistically significant differences in alpha diversity at + 2w and beta diversity at + 3m due to antibiotic treatment. MGS revealed significantly distinct gut microbiota with 11 discriminatory metagenomic assembled genomes driven by antibiotic treatment at 3 months post-op, including increased Bifidobacterium spp. with clindamycin.

CONCLUSION: RYGB induces significant changes in the gut microbiome at 2 weeks that are maintained 3 months after surgery. However, the single peri-operative dose of antibiotic administered at the time of RYGB induces unique and persisting changes to the gut microbiome that are antibiotic-specific. Increased Bifidobacterium spp. with clindamycin administration may improve the metabolic efficacy of RYGB when considering gut-microbiome driven mechanisms for blood pressure resolution.}, } @article {pmid35768643, year = {2022}, author = {Ojima, MN and Jiang, L and Arzamasov, AA and Yoshida, K and Odamaki, T and Xiao, J and Nakajima, A and Kitaoka, M and Hirose, J and Urashima, T and Katoh, T and Gotoh, A and van Sinderen, D and Rodionov, DA and Osterman, AL and Sakanaka, M and Katayama, T}, title = {Priority effects shape the structure of infant-type Bifidobacterium communities on human milk oligosaccharides.}, journal = {The ISME journal}, volume = {16}, number = {9}, pages = {2265-2279}, pmid = {35768643}, issn = {1751-7370}, support = {R01 DK030292/DK/NIDDK NIH HHS/United States ; }, mesh = {*Bifidobacterium/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant ; Milk, Human/chemistry ; Oligosaccharides ; }, abstract = {Bifidobacteria are among the first colonizers of the infant gut, and human milk oligosaccharides (HMOs) in breastmilk are instrumental for the formation of a bifidobacteria-rich microbiota. However, little is known about the assembly of bifidobacterial communities. Here, by applying assembly theory to a community of four representative infant-gut associated Bifidobacterium species that employ varied strategies for HMO consumption, we show that arrival order and sugar consumption phenotypes significantly affected community formation. Bifidobacterium bifidum and Bifidobacterium longum subsp. infantis, two avid HMO consumers, dominate through inhibitory priority effects. On the other hand, Bifidobacterium breve, a species with limited HMO-utilization ability, can benefit from facilitative priority effects and dominates by utilizing fucose, an HMO degradant not utilized by the other bifidobacterial species. Analysis of publicly available breastfed infant faecal metagenome data showed that the observed trends for B. breve were consistent with our in vitro data, suggesting that priority effects may have contributed to its dominance. Our study highlights the importance and history dependency of initial community assembly and its implications for the maturation trajectory of the infant gut microbiota.}, } @article {pmid35768476, year = {2022}, author = {Yabuuchi, S and Oiki, S and Minami, S and Takase, R and Watanabe, D and Hashimoto, W}, title = {Enhanced propagation of Granulicatella adiacens from human oral microbiota by hyaluronan.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {10948}, pmid = {35768476}, issn = {2045-2322}, mesh = {Bacteria/metabolism ; *Carnobacteriaceae/metabolism ; Glycosaminoglycans/metabolism ; Humans ; Hyaluronic Acid/metabolism ; *Microbiota ; Streptococcus/metabolism ; }, abstract = {Host determinants for formation/composition of human oral microbiota remain to be clarified, although microorganisms entering the mouth cannot necessarily colonize the oral environment. Here we show that human oral-abundant bacteria degraded host glycosaminoglycans (GAGs) in saliva and gingiva, and certain bacteria significantly grew on hyaluronan (HA), a kind of GAGs. Microbial communities from teeth or gingiva of healthy donors assimilated HA. Metagenomic analysis of human oral microbiota under different carbon sources revealed HA-driven Granulicatella growth. HA-degrading bacterial strains independently isolated from teeth and gingiva were identified as Granulicatella adiacens producing extracellular 130 kDa polysaccharide lyase as a HA-degrading enzyme encoded in a peculiar GAG genetic cluster containing genes for isomerase KduI and dehydrogenase DhuD. These findings demonstrated that GAGs are one of the host determinants for formation/composition of oral microbiota not only for colonization but also for the adaptation to the host niche. Especially, HA enhanced the G. adiacens propagation.}, } @article {pmid35768448, year = {2022}, author = {Álvarez-Marín, MT and Zarzuela, L and Camacho, EM and Santero, E and Flores, A}, title = {Detection by metagenomic functional analysis and improvement by experimental evolution of β-lactams resistance genes present in oil contaminated soils.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {10059}, pmid = {35768448}, issn = {2045-2322}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/metabolism ; Microbial Sensitivity Tests ; Soil ; *beta-Lactam Resistance/genetics ; *beta-Lactamases/genetics/metabolism ; beta-Lactams ; }, abstract = {The spread of antibiotic resistance genes has become a global health concern identified by the World Health Organization as one of the greatest threats to health. Many of antimicrobial resistance determinants found in bacterial pathogens originate from environmental bacteria, so identifying the genes that confer resistance to antibiotics in different habitats is mandatory to better understand resistance mechanisms. Soil is one of the most diverse environments considered reservoir of antimicrobial resistance genes. The aim of this work is to study the presence of genes that provide resistance to antibiotics used in clinical settings in two oil contaminated soils by metagenomic functional analysis. Using fosmid vectors that efficiently transcribe metagenomic DNA, we have selected 12 fosmids coding for two class A β-lactamases, two subclass B1 and two subclass B3 metallo-β-lactamases, one class D β-lactamase and three efflux pumps that confer resistance to cefexime, ceftriaxone, meropenem and/or imipenem. In some of them, detection of the resistance required heterologous expression from the fosmid promoter. Although initially, these environmental genes only provide resistance to low concentrations of antibiotics, we have obtained, by experimental evolution, fosmid derivatives containing β-lactamase ORFs with a single base substitution, which substantially increase their β-lactamase activity and resistance level. None of the mutations affect β-lactamase coding sequences and are all located upstream of them. These results demonstrate the presence of enzymes that confer resistance to relevant β-lactams in these soils and their capacity to rapidly adapt to provide higher resistance levels.}, } @article {pmid35768268, year = {2022}, author = {Fujii, N and Kuroda, K and Narihiro, T and Aoi, Y and Ozaki, N and Ohashi, A and Kindaichi, T}, title = {Metabolic Potential of the Superphylum Patescibacteria Reconstructed from Activated Sludge Samples from a Municipal Wastewater Treatment Plant.}, journal = {Microbes and environments}, volume = {37}, number = {3}, pages = {}, pmid = {35768268}, issn = {1347-4405}, mesh = {Bacteria ; Ecosystem ; Metagenome ; RNA, Ribosomal, 16S/genetics ; *Sewage/microbiology ; Wastewater ; *Water Purification ; }, abstract = {Patescibacteria are widely distributed in various environments and often detected in activated sludge. However, limited information is currently available on their phylogeny, morphology, and ecophysiological role in activated sludge or interactions with other microorganisms. In the present study, we identified microorganisms that interacted with Patescibacteria in activated sludge via a correlation ana-lysis using the 16S rRNA gene, and predicted the metabolic potential of Patescibacteria using a metagenomic ana-lysis. The metagenome-assembled genomes of Patescibacteria consisted of three Saccharimonadia, three Parcubacteria, and one Gracilibacteria, and showed a strong positive correlation of relative abundance with Chitinophagales. Metabolic predictions from ten recovered patescibacterial and five Chitinophagales metagenome-assembled genomes supported mutualistic interactions between a member of Saccharimonadia and Chitinophagales via N-acetylglucosamine, between a member of Parcubacteria and Chitinophagales via nitrogen compounds related to denitrification, and between Gracilibacteria and Chitinophagales via phospholipids in activated sludge. The present results indicate that various interactions between Patescibacteria and Chitinophagales are important for the survival of Patescibacteria in activated sludge ecosystems.}, } @article {pmid35766975, year = {2022}, author = {Jackson, EW and Wilhelm, RC and Buckley, DH and Hewson, I}, title = {The RNA virome of echinoderms.}, journal = {The Journal of general virology}, volume = {103}, number = {6}, pages = {}, doi = {10.1099/jgv.0.001772}, pmid = {35766975}, issn = {1465-2099}, mesh = {Animals ; Biodiversity ; Echinodermata/genetics ; Phylogeny ; *RNA ; Sequence Analysis, DNA ; *Virome/genetics ; }, abstract = {Echinoderms are a phylum of marine invertebrates that include model organisms, keystone species, and animals commercially harvested for seafood. Despite their scientific, ecological, and economic importance, there is little known about the diversity of RNA viruses that infect echinoderms compared to other invertebrates. We screened over 900 transcriptomes and viral metagenomes to characterize the RNA virome of 38 echinoderm species from all five classes (Crinoidea, Holothuroidea, Asteroidea, Ophiuroidea and Echinoidea). We identified 347 viral genome fragments that were classified to genera and families within nine viral orders - Picornavirales, Durnavirales, Martellivirales, Nodamuvirales, Reovirales, Amarillovirales, Ghabrivirales, Mononegavirales, and Hepelivirales. We compared the relative viral representation across three life stages (embryo, larvae, adult) and characterized the gene content of contigs which encoded complete or near-complete genomes. The proportion of viral reads in a given transcriptome was not found to significantly differ between life stages though the majority of viral contigs were discovered from transcriptomes of adult tissue. This study illuminates the biodiversity of RNA viruses from echinoderms, revealing the occurrence of viral groups in natural populations.}, } @article {pmid35766965, year = {2022}, author = {van Heck, JIP and Gacesa, R and Stienstra, R and Fu, J and Zhernakova, A and Harmsen, HJM and Weersma, RK and Joosten, LAB and Tack, CJ}, title = {The Gut Microbiome Composition Is Altered in Long-standing Type 1 Diabetes and Associates With Glycemic Control and Disease-Related Complications.}, journal = {Diabetes care}, volume = {45}, number = {9}, pages = {2084-2094}, doi = {10.2337/dc21-2225}, pmid = {35766965}, issn = {1935-5548}, mesh = {Cross-Sectional Studies ; *Diabetes Mellitus, Type 1/complications ; *Gastrointestinal Microbiome/genetics ; Glycated Hemoglobin ; Glycemic Control ; Humans ; }, abstract = {OBJECTIVE: People with type 1 diabetes are at risk for developing micro- and macrovascular complications. Little is known about the gut microbiome in long-standing type 1 diabetes. We explored differences in the gut microbiome of participants with type 1 diabetes compared with healthy control subjects and associated the gut microbiome with diabetes-related complications.

RESEARCH DESIGN AND METHODS: Microbiome data of 238 participants with type 1 diabetes with an average disease duration of 28 ± 15 years were compared with 2,937 age-, sex-, and BMI-matched individuals. Clinical characteristics and fecal samples were collected, and metagenomic shotgun sequencing was performed. Microbial taxonomy was associated with type 1 diabetes-related characteristics and vascular complications.

RESULTS: No significant difference in the α-diversity of the gut microbiome was found between participants with type 1 diabetes and healthy control subjects. However, 43 bacterial taxa were significantly depleted in type 1 diabetes, while 37 bacterial taxa were significantly enriched. HbA1c and disease duration explained a significant part of the variation in the gut microbiome (R2 > 0.008, false discovery rate [FDR] <0.05), and HbA1c was significantly associated with the abundance of several microbial species. Additionally, both micro- and macrovascular complications explained a significant part of the variation in the gut microbiome (R2 > 0.0075, FDR < 0.05). Nephropathy was strongly associated with several microbial species. Macrovascular complications displayed similar associations with nephropathy.

CONCLUSIONS: Our data show that the gut microbiome is altered in people with (long-standing) type 1 diabetes and is associated with glycemic control and diabetes-related complications. As a result of the cross-sectional design, the causality of these relationships remains to be determined.}, } @article {pmid35766865, year = {2022}, author = {Ewald, JM and Schnoor, JL and Mattes, TE}, title = {Metagenomes, Metagenome-Assembled Genomes, and Metatranscriptomes from Polychlorinated Biphenyl-Contaminated Sediment Microcosms.}, journal = {Microbiology resource announcements}, volume = {11}, number = {7}, pages = {e0112621}, pmid = {35766865}, issn = {2576-098X}, support = {P42 ES013661/ES/NIEHS NIH HHS/United States ; R01 ES032671/ES/NIEHS NIH HHS/United States ; R01ES032671//HHS | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; NIH P42ES013661//HHS | NIH | National Institute of Environmental Health Sciences (NIEHS)/ ; }, abstract = {We present a comprehensive data set that describes an anaerobic microbial consortium native to polychlorinated biphenyl (PCB)-contaminated sediments. Obtained from sediment microcosms incubated for 200 days, the data set includes 4 metagenomes, 4 metatranscriptomes (in duplicate), and 62 metagenome-assembled genomes and captures microbial community interactions, structure, and function relevant to anaerobic PCB biodegradation.}, } @article {pmid35766483, year = {2022}, author = {Avuthu, N and Guda, C}, title = {Meta-Analysis of Altered Gut Microbiota Reveals Microbial and Metabolic Biomarkers for Colorectal Cancer.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0001322}, pmid = {35766483}, issn = {2165-0497}, mesh = {Biomarkers ; *Colorectal Neoplasms/diagnosis ; Dysbiosis/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Reproducibility of Results ; }, abstract = {Colorectal cancer (CRC) is the second leading cause of cancer mortality worldwide. The dysbiotic gut microbiota and its metabolite secretions play a significant role in CRC development and progression. In this study, we identified microbial and metabolic biomarkers applicable to CRC using a meta-analysis of metagenomic datasets from diverse geographical regions. We used LEfSe, random forest (RF), and co-occurrence network methods to identify microbial biomarkers. Geographic dataset-specific markers were identified and evaluated using area under the ROC curve (AUC) scores and random effect size. Co-occurrence networks analysis showed a reduction in the overall microbial associations and the presence of oral pathogenic microbial clusters in CRC networks. Analysis of predicted metabolites from CRC datasets showed the enrichment of amino acids, cadaverine, and creatine in CRC, which were positively correlated with CRC-associated microbes (Peptostreptococcus stomatis, Gemella morbillorum, Bacteroides fragilis, Parvimonas spp., Fusobacterium nucleatum, Solobacterium moorei, and Clostridium symbiosum), and negatively correlated with control-associated microbes. Conversely, butyrate, nicotinamide, choline, tryptophan, and 2-hydroxybutanoic acid showed positive correlations with control-associated microbes (P < 0.05). Overall, our study identified a set of global CRC biomarkers that are reproducible across geographic regions. We also reported significant differential metabolites and microbe-metabolite interactions associated with CRC. This study provided significant insights for further investigations leading to the development of noninvasive CRC diagnostic tools and therapeutic interventions. IMPORTANCE Several studies showed associations between gut dysbiosis and CRC. Yet, the results are not conclusive due to cohort-specific associations that are influenced by genomic, dietary, and environmental stimuli and associated reproducibility issues with various analysis approaches. Emerging evidence suggests the role of microbial metabolites in modulating host inflammation and DNA damage in CRC. However, the experimental validations have been hindered by cost, resources, and cumbersome technical expertise required for metabolomic investigations. In this study, we performed a meta-analysis of CRC microbiota data from diverse geographical regions using multiple methods to achieve reproducible results. We used a computational approach to predict the metabolomic profiles using existing CRC metagenomic datasets. We identified a reliable set of CRC-specific biomarkers from this analysis, including microbial and metabolite markers. In addition, we revealed significant microbe-metabolite associations through correlation analysis and microbial gene families associated with dysregulated metabolic pathways in CRC, which are essential in understanding the vastly sporadic nature of CRC development and progression.}, } @article {pmid35765950, year = {2022}, author = {Van Brussel, K and Wang, X and Shi, M and Carrai, M and Feng, S and Li, J and Holmes, EC and Beatty, JA and Barrs, VR}, title = {The enteric virome of cats with feline panleukopenia differs in abundance and diversity from healthy cats.}, journal = {Transboundary and emerging diseases}, volume = {69}, number = {5}, pages = {e2952-e2966}, pmid = {35765950}, issn = {1865-1682}, mesh = {Animals ; *Bocavirus/genetics ; *Calicivirus, Feline ; *Cat Diseases ; Cats ; *Feline Panleukopenia/epidemiology ; Feline Panleukopenia Virus/genetics ; Mammals ; *Parvoviridae ; Virome ; *Viruses ; }, abstract = {Feline panleukopenia (FPL) is a severe, often fatal disease caused by feline panleukopenia virus (FPV). How infection with FPV might impact the composition of the entire eukaryotic enteric virome in cats has not been characterized. We used meta-transcriptomic and viral particle enrichment metagenomic approaches to characterize the enteric viromes of 23 cats naturally infected with FPV (FPV-cases) and 36 age-matched healthy shelter cats (healthy controls). Sequencing reads from mammalian infecting viral families largely belonged to the Coronaviridae, Parvoviridae and Astroviridae. The most abundant viruses among the healthy control cats were feline coronavirus, Mamastrovirus 2 and Carnivore bocaparvovirus 3 (feline bocavirus), with frequent coinfections of all three. Feline chaphamaparvovirus was only detected in healthy controls (6 out of 36, 16.7%). Among the FPV-cases, in addition to FPV, the most abundant viruses were Mamastrovirus 2, feline coronavirus and C. bocaparvovirus 4 (feline bocaparvovirus 2). The latter and feline bocaparvovirus 3 were detected significantly more frequently in FPV-cases than in healthy controls. Feline calicivirus was present in a higher proportion of FPV-cases (11 out of 23, 47.8%) compared to healthy controls (5 out of 36, 13.9%, p = 0.0067). Feline kobuvirus infections were also common among FPV-cases (9 out of 23, 39.1%) and were not detected in any healthy controls (p < .0001). While abundant in both groups, astroviruses were more frequently present in FPV-cases (19 out of 23, 82.6%) than in healthy controls (18 out of 36, p = .0142). The differences in eukaryotic virome composition revealed here indicate that further investigations are warranted to determine associations between enteric viral co-infections on clinical disease severity in cats with FPL.}, } @article {pmid35765399, year = {2022}, author = {Luu, T and Khalid, R and Rehman, T and Clark, NM}, title = {Disseminated Nocardia paucivorans Infection Resembling Metastatic Disease in a Kidney Transplant Recipient.}, journal = {Cureus}, volume = {14}, number = {5}, pages = {e25365}, pmid = {35765399}, issn = {2168-8184}, abstract = {Recipients of solid-organ transplants (SOT) or hematopoietic stem-cell transplants are prone to various complications, including serious infections. Nocardiosis is an opportunistic bacterial infection that primarily affects the lung. It may also cause skin and soft-tissue infection, cerebral abscess, bloodstream infection, or infection involving other organs. We present a case of an immunocompromised kidney transplant recipient who experienced a prolonged history of unexplained indolent constitutional symptoms without a fever. Initial radiographic findings were suggestive of metastatic disease at multiple sites. However, metagenomic next-generation sequencing of microbial cell-free DNA in blood revealed disseminated Nocardia paucivorans infection, and organisms consistent with Nocardia were identified on histopathology of a lung biopsy. It is crucial for healthcare providers to be aware of unusual opportunistic infections to provide appropriate workups and interventions for immunocompromised SOT recipients.}, } @article {pmid35765182, year = {2022}, author = {Goussarov, G and Mysara, M and Vandamme, P and Van Houdt, R}, title = {Introduction to the principles and methods underlying the recovery of metagenome-assembled genomes from metagenomic data.}, journal = {MicrobiologyOpen}, volume = {11}, number = {3}, pages = {e1298}, pmid = {35765182}, issn = {2045-8827}, mesh = {Computational Biology ; *Metagenome ; *Metagenomics ; Sequence Analysis, DNA ; }, abstract = {The rise of metagenomics offers a leap forward for understanding the genetic diversity of microorganisms in many different complex environments by providing a platform that can identify potentially unlimited numbers of known and novel microorganisms. As such, it is impossible to imagine new major initiatives without metagenomics. Nevertheless, it represents a relatively new discipline with various levels of complexity and demands on bioinformatics. The underlying principles and methods used in metagenomics are often seen as common knowledge and often not detailed or fragmented. Therefore, we reviewed these to guide microbiologists in taking the first steps into metagenomics. We specifically focus on a workflow aimed at reconstructing individual genomes, that is, metagenome-assembled genomes, integrating DNA sequencing, assembly, binning, identification and annotation.}, } @article {pmid35765179, year = {2022}, author = {Najafpour, B and Pinto, PIS and Canario, AVM and Power, DM}, title = {Quantifying dominant bacterial genera detected in metagenomic data from fish eggs and larvae using genus-specific primers.}, journal = {MicrobiologyOpen}, volume = {11}, number = {3}, pages = {e1274}, pmid = {35765179}, issn = {2045-8827}, mesh = {Animals ; DNA Primers/genetics ; Fishes ; Larva ; Metagenome ; *Metagenomics ; Pseudomonas/genetics ; RNA, Ribosomal, 16S/genetics ; *Rhodobacteraceae ; }, abstract = {The goal of this study was to design genus-specific primers for rapid evaluation of the most abundant bacterial genera identified using amplicon-based sequencing of the 16S rRNA gene in fish-related samples and surrounding water. Efficient genus-specific primers were designed for 11 bacterial genera including Alkalimarinus, Colwellia, Enterovibrio, Marinomonas, Massilia, Oleispira, Phaeobacter, Photobacterium, Polarbacerium, Pseudomonas, and Psychrobium. The specificity of the primers was confirmed by the phylogeny of the sequenced polymerase chain reaction (PCR) amplicons that indicated primers were genus-specific except in the case of Colwellia and Phaeobacter. Copy number of the 16S rRNA gene obtained by quantitative PCR using genus-specific primers and the relative abundance obtained by 16S rRNA gene sequencing using universal primers were well correlated for the five analyzed abundant bacterial genera. Low correlations between quantitative PCR and 16S rRNA gene sequencing for Pseudomonas were explained by the higher coverage of known Pseudomonas species by the designed genus-specific primers than the universal primers used in 16S rRNA gene sequencing. The designed genus-specific primers are proposed as rapid and cost-effective tools to evaluate the most abundant bacterial genera in fish-related or potentially other metagenomics samples.}, } @article {pmid35765106, year = {2022}, author = {Urbaniak, C and Morrison, MD and Thissen, JB and Karouia, F and Smith, DJ and Mehta, S and Jaing, C and Venkateswaran, K}, title = {Microbial Tracking-2, a metagenomics analysis of bacteria and fungi onboard the International Space Station.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {100}, pmid = {35765106}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Humans ; *Malassezia ; Metagenome ; Metagenomics ; *Microbiota/genetics ; }, abstract = {BACKGROUND: The International Space Station (ISS) is a unique and complex built environment with the ISS surface microbiome originating from crew and cargo or from life support recirculation in an almost entirely closed system. The Microbial Tracking 1 (MT-1) project was the first ISS environmental surface study to report on the metagenome profiles without using whole-genome amplification. The study surveyed the microbial communities from eight surfaces over a 14-month period. The Microbial Tracking 2 (MT-2) project aimed to continue the work of MT-1, sampling an additional four flights from the same locations, over another 14 months.

METHODS: Eight surfaces across the ISS were sampled with sterile wipes and processed upon return to Earth. DNA extracted from the processed samples (and controls) were treated with propidium monoazide (PMA) to detect intact/viable cells or left untreated and to detect the total DNA population (free DNA/compromised cells/intact cells/viable cells). DNA extracted from PMA-treated and untreated samples were analyzed using shotgun metagenomics. Samples were cultured for bacteria and fungi to supplement the above results.

RESULTS: Staphylococcus sp. and Malassezia sp. were the most represented bacterial and fungal species, respectively, on the ISS. Overall, the ISS surface microbiome was dominated by organisms associated with the human skin. Multi-dimensional scaling and differential abundance analysis showed significant temporal changes in the microbial population but no spatial differences. The ISS antimicrobial resistance gene profiles were however more stable over time, with no differences over the 5-year span of the MT-1 and MT-2 studies. Twenty-nine antimicrobial resistance genes were detected across all samples, with macrolide/lincosamide/streptogramin resistance being the most widespread. Metagenomic assembled genomes were reconstructed from the dataset, resulting in 82 MAGs. Functional assessment of the collective MAGs showed a propensity for amino acid utilization over carbohydrate metabolism. Co-occurrence analyses showed strong associations between bacterial and fungal genera. Culture analysis showed the microbial load to be on average 3.0 × 10[5] cfu/m[2] CONCLUSIONS: Utilizing various metagenomics analyses and culture methods, we provided a comprehensive analysis of the ISS surface microbiome, showing microbial burden, bacterial and fungal species prevalence, changes in the microbiome, and resistome over time and space, as well as the functional capabilities and microbial interactions of this unique built microbiome. Data from this study may help to inform policies for future space missions to ensure an ISS surface microbiome that promotes astronaut health and spacecraft integrity. Video Abstract.}, } @article {pmid35764148, year = {2022}, author = {Hu, L and Qian, Y and Ci, M and Long, Y and Zheng, H and Xu, K and Wang, Y}, title = {Localized intensification of arsenic methylation within landfill leachate-saturated zone.}, journal = {The Science of the total environment}, volume = {842}, number = {}, pages = {156979}, doi = {10.1016/j.scitotenv.2022.156979}, pmid = {35764148}, issn = {1879-1026}, mesh = {*Arsenic/analysis ; Methylation ; *Refuse Disposal/methods ; Waste Disposal Facilities ; *Water Pollutants, Chemical/analysis ; }, abstract = {Leachate-saturated zone (LSZ) of landfills is a complicated biogeochemical hotspot due to the continuous input of electron donors and acceptors from the top refuse layer with leachate migration. In this study, the methylation behavior of the arsenic (As) was investigated. The results indicate that As-methylation processes are influenced by temperature fields in LSZ. The dimethylarsinic acid biotransformation capability can be enhanced with an increase in temperature. Microbial diversity, quantification of functional gene (arsM), and co-occurrence network analysis further characterized the drivers of As methylation in LSZ. As-biogeochemical cycle pathways, as well as As-functional gene distribution among different temperature fields, were modeled on the basis of KEGG annotation. Binning analysis was further employed to assemble As-methylated metagenomes, enabling the identification of novel species for As methylation in landfills. Then, 87 high-quality draft metagenome-assembled genomes (MAGs) were reconstructed from LSZ refuse samples; nearly 15 % (13 of 87) belonged to putative As-methylates functional MAGs. Combined with the model of the As-biogeochemical cycle, nine putative functional species could complete methylation processes alone. The findings of this study highlighted the temperature influence on the As-methylation behavior in LSZ and could facilitate the management of As contamination in landfills.}, } @article {pmid35763428, year = {2022}, author = {Xiu, W and Wu, M and Nixon, SL and Lloyd, JR and Bassil, NM and Gai, R and Zhang, T and Su, Z and Guo, H}, title = {Genome-Resolved Metagenomic Analysis of Groundwater: Insights into Arsenic Mobilization in Biogeochemical Interaction Networks.}, journal = {Environmental science & technology}, volume = {56}, number = {14}, pages = {10105-10119}, doi = {10.1021/acs.est.2c02623}, pmid = {35763428}, issn = {1520-5851}, mesh = {*Arsenic/chemistry ; Ferric Compounds/metabolism ; Ferrous Compounds ; *Groundwater/chemistry ; Nitrates/analysis ; Oxidation-Reduction ; *Water Pollutants, Chemical/chemistry ; }, abstract = {High-arsenic (As) groundwaters, a worldwide issue, are critically controlled by multiple interconnected biogeochemical processes. However, there is limited information on the complex biogeochemical interaction networks that cause groundwater As enrichment in aquifer systems. The western Hetao basin was selected as a study area to address this knowledge gap, offering an aquifer system where groundwater flows from an oxidizing proximal fan (low dissolved As) to a reducing flat plain (high dissolved As). The key microbial interaction networks underpinning the biogeochemical pathways responsible for As mobilization along the groundwater flow path were characterized by genome-resolved metagenomic analysis. Genes associated with microbial Fe(II) oxidation and dissimilatory nitrate reduction were noted in the proximal fan, suggesting the importance of nitrate-dependent Fe(II) oxidation in immobilizing As. However, genes catalyzing microbial Fe(III) reduction (omcS) and As(V) detoxification (arsC) were highlighted in groundwater samples downgradient flow path, inferring that reductive dissolution of As-bearing Fe(III) (oxyhydr)oxides mobilized As(V), followed by enzymatic reduction to As(III). Genes associated with ammonium oxidation (hzsABC and hdh) were also positively correlated with Fe(III) reduction (omcS), suggesting a role for the Feammox process in driving As mobilization. The current study illustrates how genomic sequencing tools can help dissect complex biogeochemical systems, and strengthen biogeochemical models that capture key aspects of groundwater As enrichment.}, } @article {pmid35763072, year = {2022}, author = {Wang, Z and Zhang, Z and Lu, C and Zhou, J and Wang, Z and Han, J and Su, X}, title = {Effects of Sporisorium reiliana polysaccharides and Phoenix dactylifera monosaccharides on the gut microbiota and serum metabolism in mice with fructose-induced hyperuricemia.}, journal = {Archives of microbiology}, volume = {204}, number = {7}, pages = {436}, pmid = {35763072}, issn = {1432-072X}, support = {ZS20190105//State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-products/ ; Y202146257//General Project of Zhejiang Provincial Department of Education/ ; }, mesh = {Animals ; Fructose/adverse effects ; *Gastrointestinal Microbiome ; *Hyperuricemia/chemically induced/drug therapy ; Mice ; Monosaccharides ; *Phoeniceae ; Polysaccharides ; Uric Acid ; }, abstract = {In recent decades, the prevalence of hyperuricemia has increased, and dietary fructose is an important risk factor for the development of this disease. This study investigated and compared the effects of Sphacelotheca reiliana polysaccharides and Phoenix dactylifera monosaccharides on a series of physiological and biochemical indicators and on the metagenomes and serum metabolites in mice with hyperuricemia caused by a high-fructose diet. S. reiliana polysaccharides inhibited uric acid biosynthesis and promoted uric acid excretion, thereby alleviating the hyperuricemia phenotype. In addition, hyperuricemia was closely related to the gut microbiota. After treatment with S. reiliana polysaccharides, the abundances of Bacteroidetes and Proteobacteria in the mouse intestines were decreased, the expression of genes involved in glycolysis/gluconeogenesis metabolic pathways and purine metabolism was downregulated, and the dysfunction of the gut microbiota was alleviated. With regard to serum metabolism, the abundance of hippuric acid, uridine, kynurenic acid, propionic acid and arachidonoyl decreased, and the abundances of serum metabolites in inflammatory pathways involved in kidney injury and gout, such as bile acid metabolism, purine metabolism and tryptophan metabolism pathways, decreased. P. dactylifera monosaccharides aggravated hyperuricemia. This research provides a valuable reference for the development of sugar applications.}, } @article {pmid35762794, year = {2022}, author = {Roguet, A and Newton, RJ and Eren, AM and McLellan, SL}, title = {Guts of the Urban Ecosystem: Microbial Ecology of Sewer Infrastructure.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0011822}, pmid = {35762794}, issn = {2379-5077}, support = {R01 AI091829/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Anti-Bacterial Agents ; Bacteria/genetics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; United States ; *Wastewater ; }, abstract = {Microbes have inhabited the oceans and soils for millions of years and are uniquely adapted to their habitat. In contrast, sewer infrastructure in modern cities dates back only ~150 years. Sewer pipes transport human waste and provide a view into public health, but the resident organisms that likely modulate these features are relatively unexplored. Here, we show that the bacterial assemblages sequenced from untreated wastewater in 71 U.S. cities were highly coherent at a fine sequence level, suggesting that urban infrastructure separated by great spatial distances can give rise to strikingly similar communities. Within the overall microbial community structure, temperature had a discernible impact on the distribution patterns of closely related amplicon sequence variants, resulting in warm and cold ecotypes. Two bacterial genera were dominant in most cities regardless of their size or geographic location; on average, Arcobacter accounted for 11% and Acinetobacter 10% of the entire community. Metagenomic analysis of six cities revealed these highly abundant resident organisms carry clinically important antibiotic resistant genes blaCTX-M, blaOXA, and blaTEM. In contrast, human fecal bacteria account for only ~13% of the community; therefore, antibiotic resistance gene inputs from human sources to the sewer system could be comparatively small, which will impact measurement capabilities when monitoring human populations using wastewater. With growing awareness of the metabolic potential of microbes within these vast networks of pipes and the ability to examine the health of human populations, it is timely to increase our understanding of the ecology of these systems. IMPORTANCE Sewer infrastructure is a relatively new habitat comprised of thousands of kilometers of pipes beneath cities. These wastewater conveyance systems contain large reservoirs of microbial biomass with a wide range of metabolic potential and are significant reservoirs of antibiotic resistant organisms; however, we lack an adequate understanding of the ecology or activity of these communities beyond wastewater treatment plants. The striking coherence of the sewer microbiome across the United States demonstrates that the sewer environment is highly selective for a particular microbial community composition. Therefore, results from more in-depth studies or proven engineering controls in one system could be extrapolated more broadly. Understanding the complex ecology of sewer infrastructure is critical for not only improving our ability to treat human waste and increasing the sustainability of our cities but also to create scalable and effective sewage microbial observatories, which are inevitable investments of the future to monitor health in human populations.}, } @article {pmid35762697, year = {2022}, author = {Borren, NZ and Ananthakrishnan, AN}, title = {Precision medicine: how multiomics will shape the future of inflammatory bowel disease?.}, journal = {Current opinion in gastroenterology}, volume = {38}, number = {4}, pages = {382-387}, pmid = {35762697}, issn = {1531-7056}, support = {R01 DK127171/DK/NIDDK NIH HHS/United States ; R21 DK127227/DK/NIDDK NIH HHS/United States ; }, mesh = {Chronic Disease ; Disease Progression ; Humans ; *Inflammatory Bowel Diseases/genetics/therapy ; *Precision Medicine ; }, abstract = {PURPOSE OF REVIEW: In this article, we provide an overview of studies examining multiomic profiling in various clinical scenarios in the management of inflammatory bowel diseases (IBDs).

RECENT FINDINGS: IBD arises as a result of an interplay between genetic, environmental, microbial and immunologic perturbations. The access to high throughput technology as well as the decrease in costs associated with such studies has led to a growing wealth of literature examining the utility of single or multiomic profiles in the management of IBD. Such studies have commonly examined the genome (and less frequently the epigenome), transcriptome, metabolome, proteome and the gut microbial metagenome in the context of overall IBD status or specific clinical scenarios, including the disease progression or response to treatment. The findings have provided important insight into how each of these compartments reflect underlying disease pathophysiologic processes and, in turn, can influence stratification of patients for clinical management.

SUMMARY: Multiomic profiling in IBD has the potential to advance the field of personalized precision medicine in the management of IBDs.}, } @article {pmid35762661, year = {2022}, author = {Pfenninger, M and Foucault, Q}, title = {Population Genomic Time Series Data of a Natural Population Suggests Adaptive Tracking of Fluctuating Environmental Changes.}, journal = {Integrative and comparative biology}, volume = {62}, number = {6}, pages = {1812-1826}, doi = {10.1093/icb/icac098}, pmid = {35762661}, issn = {1557-7023}, mesh = {Animals ; *Metagenomics ; Time Factors ; *Physical Conditioning, Animal ; Gene Frequency ; Selection, Genetic ; Genomics/methods ; Adaptation, Physiological/genetics ; }, abstract = {Natural populations are constantly exposed to fluctuating environmental changes that negatively affect their fitness in unpredictable ways. While theoretical models show the possibility of counteracting these environmental changes through rapid evolutionary adaptations, there have been few empirical studies demonstrating such adaptive tracking in natural populations. Here, we analyzed environmental data, fitness-related phenotyping and genomic time-series data sampled over 3 years from a natural Chironomus riparius (Diptera, Insecta) population to address this question. We show that the population's environment varied significantly on the time scale of the sampling in many selectively relevant dimensions, independently of each other. Similarly, phenotypic fitness components evolved significantly on the same temporal scale (mean 0.32 Haldanes), likewise independent from each other. The allele frequencies of 367,446 SNPs across the genome showed evidence of positive selection. Using temporal correlation of spatially coherent allele frequency changes revealed 35,574 haplotypes with more than one selected SNP. The mean selection coefficient for these haplotypes was 0.30 (s.d. = 0.68). The frequency changes of these haplotypes clustered in 46 different temporal patterns, indicating concerted, independent evolution of many polygenic traits. Nine of these patterns were strongly correlated with measured environmental variables. Enrichment analysis of affected genes suggested the implication of a wide variety of biological processes. Thus, our results suggest overall that the natural population of C. riparius tracks environmental change through rapid polygenic adaptation in many independent dimensions. This is further evidence that natural selection is pervasive at the genomic level and that evolutionary and ecological time scales may not differ at all, at least in some organisms.}, } @article {pmid35762010, year = {2022}, author = {Qin, X and Zhou, J and Wang, Z and Feng, C and Fan, J and Huang, J and Hu, D and Baban, B and Wang, S and Ma, D and Sun, C and Zhou, Z and Chen, G}, title = {Metagenomic analysis of the microbiome of the upper reproductive tract: combating ovarian cancer through predictive, preventive, and personalized medicine.}, journal = {The EPMA journal}, volume = {13}, number = {3}, pages = {487-498}, pmid = {35762010}, issn = {1878-5077}, abstract = {PURPOSE: We investigated whether ovarian cancer could alter the genital microbiota in a specific way with clinical values. Furthermore, we proposed how such changes could be envisioned in a paradigm of predictive, preventive, and personalized medicine (PPPM).

METHODS: The samples were collected using cotton swabs from the cervical, uterine cavity, fallopian tubes, and ovaries of patients subjected to the surgical procedures for the malignant/benign lesions. All samples were then analyzed by metagenomic shotgun sequencing. The distribution patterns and characteristics of the microbiota in the reproductive tract of subjects were analyzed and were interpreted in relation to the clinical outcomes of the subjects.

RESULTS: While the ovarian cancer was able to alter the genital microbiota, the bacteria were the dominant microorganisms in all samples across all cohorts in the study (median 99%). The microbiota of the upper female reproductive tract were mainly from the cervical, identified by low bacterial biomass and high bacterial diversity. Ovarian cancer had a distinct microbiota signature. The tubal ligation affects its microbial distribution. There were no different species on the surface of platinum-sensitive ovarian tissues compared to samples from platinum-resistant patients.

CONCLUSION: The ovarian cancer-induced changes in microbiota magnify the potential of microbiota as a biotherapeutic modality in the treatment of ovarian cancer in this study and very likely for several malignancies and other conditions. Our findings demonstrated, for the first time, that microbiota could be dissected and applied in more specific fashion based on a predictive, preventive, and personalized medicine (PPPM) model in the treatment of ovarian cancer. Utilizing microbiota portfolio in a PPPM system in ovarian cancer would provide a unique opportunity to a clinically intelligent and novel approach in the treatment of ovarian cancer as well as several other conditions and malignancies.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13167-022-00286-1.}, } @article {pmid35761925, year = {2022}, author = {Modin, O and Fuad, N and Abadikhah, M and I'Ons, D and Ossiansson, E and Gustavsson, DJI and Edefell, E and Suarez, C and Persson, F and Wilén, BM}, title = {A relationship between phages and organic carbon in wastewater treatment plant effluents.}, journal = {Water research X}, volume = {16}, number = {}, pages = {100146}, pmid = {35761925}, issn = {2589-9147}, abstract = {With stringent effluent requirements and the implementation of new processes for micropollutant removal, it is increasingly important for wastewater treatment plants (WWTPs) to understand the factors affecting effluent quality. Phages (viruses infecting prokaryotes) are abundant in the biological treatment processes. They can contribute to organic carbon in the treated effluent both because they are organic in nature and occur in the effluent and because they cause lysis of microorganisms. Today very little is known about the effects of phages on effluent quality. The goal of this study was, therefore, to determine the relationship between phages and organic carbon in WWTP effluents. We also examined the diversity, taxonomy, and host-association of DNA phages using metagenomics. Effluent samples were collected from four WWTPs treating municipal wastewater. Significant differences in both organic carbon and virus-like particle concentrations were observed between the plants and there was a linear relationship between the two parameters. The phage communities were diverse with many members being taxonomically unclassified. Putative hosts were dominated by bacteria known to be abundant in activated sludge systems such as Comamonadaceae. The composition of phages differed between the WWTPs, suggesting that local conditions shape the communities. Overall, our findings suggest that the abundance and composition of phages are related to effluent quality. Thus, there is a need for further research clarifying the association between phage dynamics and WWTP function.}, } @article {pmid35761688, year = {2022}, author = {Zhang, J and Liu, S and Sun, H and Jiang, Z and Xu, Y and Mao, J and Qian, B and Wang, L and Mao, J}, title = {Corrigendum to "Metagenomics-based insights into the microbial community profiling and flavor development potentiality of baijiu Daqu and huangjiu wheat Qu" [Food Res. Int. 152 (2022) 110707].}, journal = {Food research international (Ottawa, Ont.)}, volume = {157}, number = {}, pages = {111448}, doi = {10.1016/j.foodres.2022.111448}, pmid = {35761688}, issn = {1873-7145}, } @article {pmid35761594, year = {2022}, author = {Zhu, Q and Chen, L and Peng, Z and Zhang, Q and Huang, W and Yang, F and Du, G and Zhang, J and Wang, L}, title = {Analysis of environmental driving factors on Core Functional Community during Daqu fermentation.}, journal = {Food research international (Ottawa, Ont.)}, volume = {157}, number = {}, pages = {111286}, doi = {10.1016/j.foodres.2022.111286}, pmid = {35761594}, issn = {1873-7145}, mesh = {Aspergillus ; *Bacillus ; *Bacteria ; Fermentation ; Odorants ; }, abstract = {Sauce-flavor Daqu determines the quality of Baijiu because its core functional community (CFC) can produce abundant enzymes and aroma. However, complex environmental factors make it difficult to accurately control the fermentation quality of Daqu. In this study, we constructed a functional gene database to identify CFC based on multi-omics technology and explore controllable environmental factors of CFC to improve the quality of Daqu. The results showed that the CFC is mainly composed of 7 bacterial and 4 fungal genera, including Kroppenstedtia, Thermoactinomyces, Bacillus, Acinetobacter, Brevibacterium, Saccharopolyspora, Ochrobactrum, Aspergillus, Byssochlamys, Thermoascus, and Thermomyces. Most of them are thermostable microorganisms that can provide the power of fermentation and saccharification (α-amylase, glucoamylase, and protease). In CFC, Acinetobacter and Saccharopolyspora were strongly positively correlated with typical flavor substances, while fungi were negatively correlated, particularly with furans. Therefore, the bacterial genera contributed more to the significant flavors. The CFC was significantly influenced by high temperature and total titrate acid based on RDA. In addition, high-temperature conditions were also strongly positively correlated with flavors that can be quickly produced at high temperatures, such as 2-Furancarboxaldehyde, 2-Furanmethanol, and Tetramethylpyrazine. As a controllable factor, the temperature can be adjusted to improve the quality of Daqu directionally, which will provide theoretical guidance for the production of high-quality Daqu.}, } @article {pmid35761577, year = {2022}, author = {Kothe, CI and Mohellibi, N and Renault, P}, title = {Revealing the microbial heritage of traditional Brazilian cheeses through metagenomics.}, journal = {Food research international (Ottawa, Ont.)}, volume = {157}, number = {}, pages = {111265}, doi = {10.1016/j.foodres.2022.111265}, pmid = {35761577}, issn = {1873-7145}, mesh = {Animals ; Biodiversity ; Brazil ; *Cheese/analysis ; Food Microbiology ; *Lactobacillales/genetics ; *Lactococcus lactis/genetics ; Metagenomics ; Streptococcus thermophilus/genetics ; Yeasts ; }, abstract = {Brazilian artisanal cheeses date from the first Portuguese settlers and evolved via local factors, resulting in unique products that are now part of the patrimony and identity of different Brazilian regions. In this study, we combined several culture-independent approaches, including 16S/ITS metagenetics, assembly- and deep profiling-metagenomics to characterize the originality of the microbiota of five varieties of Brazilian artisanal cheeses from the South and Southeast regions of Brazil. Their core microbiota contained mainly lactic acid bacteria (LAB), of which Lactococcus lactis subsp. lactis was the most frequent, followed by Streptococcus thermophilus in the South region. Moreover, several samples from the Southeast region contained, as dominant LAB, two other food Streptococci belonging to a new species of the salivarius group and S. infantarius. Rinds of samples from the Southeast region were dominated by the halotolerant bacterium Corynebacterium variabile, and the yeasts Diutina catenulata, followed by Debaryomyces hansenii and Kodamaea ohmeri. Rinds from the South region contained mainly LAB due to their short ripening time, and the predominant yeast was D. hansenii. Phylogenomic analysis based on L. lactis metagenome-assembled genomes (MAGs) showed that most Brazilian strains are closely related and form a different clade from those whose genomes are available at this time, indicating that they belong to a specific group. Lastly, functional analysis showed that S. infantarius acquired a ∼ 26 kb DNA fragment from S. thermophilus starter strains that carry the LacSZ system, allowing fast lactose assimilation, an adaptation advantage for growth in milk. Finally, our study identified several areas of concern, such as the presence of somatic cell DNA and high levels of antibiotic resistance genes in several cheese microbiota, suggesting that milk from diseased animals may still be used occasionally. Overall, the data from this study highlight the potential value of the traditional and artisanal cheese production network in Brazil, and provide a metagenomic-based scheme to help manage this resource safely.}, } @article {pmid35761573, year = {2022}, author = {Jung, MJ and Kim, J and Lee, SH and Whon, TW and Sung, H and Bae, JW and Choi, YE and Roh, SW}, title = {Role of combinated lactic acid bacteria in bacterial, viral, and metabolite dynamics during fermentation of vegetable food, kimchi.}, journal = {Food research international (Ottawa, Ont.)}, volume = {157}, number = {}, pages = {111261}, doi = {10.1016/j.foodres.2022.111261}, pmid = {35761573}, issn = {1873-7145}, mesh = {Bacteria/genetics ; *Bacteriophages ; Fermentation ; *Fermented Foods ; Food Microbiology ; *Lactobacillales ; Lactobacillus/metabolism ; Vegetables ; }, abstract = {Lactic acid bacteria (LAB) in kimchi, a traditional Korean food, are major fermentative microorganisms affecting the quality, safety, and nutritional and organoleptic properties of the final product. In this study, we determined the role of three key LAB strains, Leuconostoc gelidum, Latilactobacillus sakei, Weissella koreensis originated from different raw ingredients during natural fermentation, as opposed to an axenic environment. Starter cultures were inoculated into food with wild indigenous microbial communities, and the dynamics of bacterial communities and metabolites were analyzed during fermentation. As bacteriophages within the food viral community directly affect fermentation by influencing bacterial function and composition, the diversity and composition of DNA viral communities were compared with those of corresponding bacterial communities using a metagenomic approach. Our results provide insights into the ecological role of LAB starters in food fermentation and the potential impact of bacteriophages as modulators of bacterial communities associated with the fermentation properties of kimchi.}, } @article {pmid35761554, year = {2022}, author = {Sequino, G and Valentino, V and Villani, F and De Filippis, F}, title = {Omics-based monitoring of microbial dynamics across the food chain for the improvement of food safety and quality.}, journal = {Food research international (Ottawa, Ont.)}, volume = {157}, number = {}, pages = {111242}, doi = {10.1016/j.foodres.2022.111242}, pmid = {35761554}, issn = {1873-7145}, mesh = {*Food Chain ; Food Safety ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {The diffusion of high-throughput sequencing has dramatically changed the study of food microbial ecology. Amplicon-based description of the microbial community may be routinary implemented in the food industry to understand how the processing parameters and the raw material quality may affect the microbial community of the final product, as well as how the community changes during the shelf-life. In addition, application of shotgun metagenomics may represent an invaluable resource to understand the functional potential of the microbial community, identifying the presence of spoilage-associated activities or genes related to pathogenesis. Finally, retrieving Metagenome-Assembled Genomes (MAGs) of relevant species may be useful for strain-tracking along the food chain and in case of food poisoning outbreaks. This review gives an overview of the possible applications of sequencing-based approaches in the study of food microbial ecology, highlighting limitations that still prevent the spreading of these techniques to the food industry.}, } @article {pmid35761537, year = {2022}, author = {Wang, C and Zhao, F and Bai, Y and Li, C and Xu, X and Kristiansen, K and Zhou, G}, title = {In vitro digestion mimicking conditions in young and elderly reveals marked differences between profiles and potential bioactivity of peptides from meat and soy proteins.}, journal = {Food research international (Ottawa, Ont.)}, volume = {157}, number = {}, pages = {111215}, doi = {10.1016/j.foodres.2022.111215}, pmid = {35761537}, issn = {1873-7145}, mesh = {Adult ; Aged ; *Animal Proteins, Dietary/chemistry ; Animals ; *Digestion ; Humans ; *Meat/analysis ; Peptides/metabolism ; *Soybean Proteins/chemistry ; }, abstract = {We applied in vitro models of gastrointestinal (GI) digestion simulating the conditions of the GI tract of healthy adults and elderly individuals with achlorhydria (EA) to investigate differences in the digestibility of meat (chicken, beef and pork) and soy proteins. Digestibility was significantly affected by EA alterations. Peptidomics analyses revealed significant differences in peptide profiles between control and EA conditions, including number, length distribution, clustering, and differentially abundant peptides (DAPs). Our results revealed that the differences in meat peptide profiles diminished going from the gastric to intestinal phase. For soy protein, the marked differences between control and EA conditions were maintained in the gastric and intestinal phases. Higher numbers of potentially bioactive peptides were generated under the control condition compared to the EA condition. The present study provides insight into the distinct peptide profiles generated by in vitro digestion of meat and soy proteins under adult and EA GI conditions.}, } @article {pmid35761533, year = {2022}, author = {Yang, D and Li, C and Li, L and Wang, Y and Wu, Y and Chen, S and Zhao, Y and Wei, Y and Wang, D}, title = {Novel insight into the formation mechanism of umami peptides based on microbial metabolism in Chouguiyu, a traditional Chinese fermented fish.}, journal = {Food research international (Ottawa, Ont.)}, volume = {157}, number = {}, pages = {111211}, doi = {10.1016/j.foodres.2022.111211}, pmid = {35761533}, issn = {1873-7145}, mesh = {Animals ; China ; Fermentation ; Fishes/metabolism ; Peptide Hydrolases/metabolism ; *Peptides/metabolism ; *Taste ; }, abstract = {Umami peptides formed by microbial metabolism play an important role in the umami taste of Chouguiyu. In this study, 138 umami peptides and 6 kinds of proteases in two categories from 35 microbial genera were identified from Chouguiyu during the fermentation process by peptidomics and metagenomics analysis, respectively. The interaction network maps between the umami peptides and protease-producing microbial genera in each protease classification were constructed based on Pearson's correlation coefficient after a two-way orthogonal partial least squares (O2PLS) evaluation. The proteases classified in 34 clusters of orthologous groups (COG) from Vagococcus, Peptostreptococcus, Acinetobacter, Psychrobacter, and Enterococcus played a major role in the formation of umami peptides. The core umami peptides with the highest abundance and correlation were mainly derived from troponin and myosin in mandarin fish. The lactic acid bacteria contributed most to the hydrolysis preparation of these umami peptides. This study is beneficial to screen the proteases and related microbial strains to improve the umami taste of Chouguiyu.}, } @article {pmid35761518, year = {2022}, author = {Yasir, M and Al-Zahrani, IA and Bibi, F and Abd El Ghany, M and Azhar, EI}, title = {New insights of bacterial communities in fermented vegetables from shotgun metagenomics and identification of antibiotic resistance genes and probiotic bacteria.}, journal = {Food research international (Ottawa, Ont.)}, volume = {157}, number = {}, pages = {111190}, doi = {10.1016/j.foodres.2022.111190}, pmid = {35761518}, issn = {1873-7145}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Enterobacteriaceae ; *Metagenomics ; *Probiotics ; Vegetables/microbiology ; }, abstract = {Consumption of fermented foods has grown worldwide due to the purported health benefits. It is thus critical to understand fermented foods microbiome that mainly influences the quality and safety of these foods. This study identified bacterial communities, including functional profiles of probiotics and antimicrobial resistance genes (ARGs), in pickled vegetables commonly consumed in the Middle Eastern, African, and Asian sub-continent regions. Eighteen samples from six pickled vegetables were collected from local markets in Saudi Arabia and analyzed using shotgun metagenomic sequencing. Statistical analyses revealed significant distance and separate clustering of bacterial communities among the different pickle types. Species of Levilactobacillus namurensis, Lentilactobacillus buchneri, Lentilactobacillus parafarraginis, Lactiplantibacillus pentosus, Pectobacterium carotovorum, Leuconostoc carnosum, Weissella confuse were found in a range of dominance in most of the samples. Binning revealed 33 high-quality, metagenome-assembled genomes (MAGs), including 4 MAGs representing putatively novel species of Lactobacillus, Alcanivorax, and Dichelobacter. Moreover, 285 ARGs and variants produce resistance against 20 classes of antibiotics were retrieved, mostly from Enterobacteriaceae contigs. The metagenomes harbored relatively high abundances of carbohydrate fermentation enzymes, as well as metabolic pathways for amino acid metabolism, cofactors and vitamins biosynthesis. Overall, by providing a comprehensive overview of bacterial communities and probiotic bacteria in pickled vegetables, the results suggest the need for more hygienic processing to avoid Enterobacteriaceae contamination and ARG spread.}, } @article {pmid35761267, year = {2022}, author = {She, J and Fu, L and Zheng, X and Li, J and Wang, L and Yu, B and Ju, J}, title = {Characterization of a new L-carnosine synthase mined from deep-sea sediment metagenome.}, journal = {Microbial cell factories}, volume = {21}, number = {1}, pages = {129}, pmid = {35761267}, issn = {1475-2859}, support = {31971204//the National Natural Science Foundation of China/ ; 31971204//the National Natural Science Foundation of China/ ; 31971204//the National Natural Science Foundation of China/ ; C2020205004//the Natural Science Foundation of Hebei Province/ ; C2020205004//the Natural Science Foundation of Hebei Province/ ; C2020205004//the Natural Science Foundation of Hebei Province/ ; C2020205004//the Natural Science Foundation of Hebei Province/ ; }, mesh = {Antioxidants ; *Carnosine/chemistry/physiology ; Dipeptides ; Histidine ; Metagenome ; }, abstract = {L-Carnosine is a natural biologically active dipeptide with critical physiological functions, such as antioxidant, antiglycation, and cytoplasmic buffering properties. Direct enzymatic synthesis is a promising way for L-carnosine production. In this study, a new aminopeptidase (gene_236976) with synthetic activity toward L-carnosine was identified by a metagenome mining approach from deep-sea sediment and functionally expressed in Escherichia coli. The enzyme shared a low identity of 14.3% with reported L-carnosine dipeptidase (SmPepD) from Serratia marcescens. β-Alanine methyl ester was proven to be the best substrate for the synthesis, and no ATP was needed for the enzymatic reaction. The enzyme activity was increased by structure-guided rational design. Only the mutant of G310 site gave positive results, and G310A mutant showed the best performance among the site-direct saturation mutagenesis, indicating that the additional CH3 group of mutant G310A was the main factor affecting the enzymatic activity. The engineered enzyme produced about 10 mM L-carnosine was produced from substrates of 50 mM β-alanine methyl ester and 50 mM L-histidine, under a tentatively optimized condition. This study enriched the enzyme resources for developing the microbial synthesis process of L-carnosine production.}, } @article {pmid35761265, year = {2022}, author = {Wynendaele, E and Debunne, N and Janssens, Y and De Spiegeleer, A and Verbeke, F and Tack, L and Van Welden, S and Goossens, E and Knappe, D and Hoffmann, R and Van De Wiele, C and Laukens, D and Van Eenoo, P and Vereecke, L and Van Immerseel, F and De Wever, O and De Spiegeleer, B}, title = {The quorum sensing peptide EntF* promotes colorectal cancer metastasis in mice: a new factor in the host-microbiome interaction.}, journal = {BMC biology}, volume = {20}, number = {1}, pages = {151}, pmid = {35761265}, issn = {1741-7007}, mesh = {Amino Acids ; Animals ; *Colorectal Neoplasms ; Humans ; Mice ; *Microbiota/physiology ; Peptides ; Quorum Sensing/physiology ; }, abstract = {BACKGROUND: Colorectal cancer, one of the most common malignancies worldwide, is associated with a high mortality rate, mainly caused by metastasis. Comparative metagenome-wide association analyses of healthy individuals and cancer patients suggest a role for the human intestinal microbiota in tumor progression. However, the microbial molecules involved in host-microbe communication are largely unknown, with current studies mainly focusing on short-chain fatty acids and amino acid metabolites as potential mediators. Quorum sensing peptides are not yet considered in this context since their presence in vivo and their ability to affect host cells have not been reported so far.

RESULTS: Here, we show that EntF*, a metabolite of the quorum sensing peptide EntF produced by Enterococcus faecium, is naturally present in mice bloodstream. Moreover, by using an orthotopic mouse model, we show that EntF* promotes colorectal cancer metastasis in vivo, with metastatic lesions in liver and lung tissues. In vitro tests suggest that EntF* regulates E-cadherin expression and consequently the epithelial-mesenchymal transition, via the CXCR4 receptor. In addition, alanine-scanning analysis indicates that the first, second, sixth, and tenth amino acid of EntF* are critical for epithelial-mesenchymal transition and tumor metastasis.

CONCLUSION: Our work identifies a new class of molecules, quorum sensing peptides, as potential regulators of host-microbe interactions. We prove, for the first time, the presence of a selected quorum sensing peptide metabolite in a mouse model, and we demonstrate its effects on colorectal cancer metastasis. We believe that our work represents a starting point for future investigations on the role of microbiome in colorectal cancer metastasis and for the development of novel bio-therapeutics in other disease areas.}, } @article {pmid35761230, year = {2022}, author = {Huang, G and Zhou, L and Yang, N and Wu, P and Mo, X}, title = {Extracorporeal membrane oxygenation rescue for severe pneumocystis pneumonia with the Macklin effect: a case report.}, journal = {BMC infectious diseases}, volume = {22}, number = {1}, pages = {577}, pmid = {35761230}, issn = {1471-2334}, support = {82002010//National Natural Science Foundation of China/ ; }, mesh = {*Extracorporeal Membrane Oxygenation ; Humans ; Immunocompromised Host ; Male ; *Mediastinal Emphysema ; Middle Aged ; *Pneumocystis carinii ; *Pneumonia, Pneumocystis/complications/diagnosis/therapy ; *Pneumothorax/complications ; Respiration, Artificial ; *Subcutaneous Emphysema ; }, abstract = {BACKGROUND: Pneumocystis jirovecii pneumonia (PJP) in an immunocompromised host is often associated with the Macklin effect, which can progress to spontaneous pneumomediastinum (SPM), subcutaneous emphysema (SCE), and pneumothorax (PNX). Diagnosing the causative organism of these conditions in non-HIV infected patients and treating hypoxemia while preventing further lung damage can be challenging. This study examines the case of a non-HIV infected male with SPM, SCE, and PNX secondary to severe Pneumocystis jirovecii (PJ) infection.

CASE PRESENTATION: A 53-year-old male with pure red cell aplasia (PRCA) was admitted with fever, dry cough, and shortness of breath. His respiratory function progressively deteriorated due to the development of SPM, SCE, and PNX, eventually requiring endotracheal intubation and invasive ventilation. As a result of high pressure in his airways occasioned by lung recruitment maneuvers, his pulmonary parameters worsened, necessitating veno-venous (VV) extracorporeal membrane oxygenation (ECMO) therapy. The early initiation of VV-ECMO facilitated ultra-protective lung ventilation and prevented the progression of SPM, SCE, and PNX. Traditional diagnostic assays were unrevealing, whereupon the patient resorted to the metagenomic next-generation sequencing technology for uncovering potential pathogens. Consequently, we detected a significantly higher infection by PJ in the patient's bronchoscopy lavage fluid. Finally, the patient was successfully treated with appropriate antimicrobials and was decannulated after nine days of ECMO support.

CONCLUSIONS: SPM, SCE, and PNX are rare clinical manifestations of PJP. However, they can be considered as poor prognostic factors of the infection. Physicians should, therefore, be alert to the possibility of PJP in immunocompromised patients.}, } @article {pmid35761213, year = {2022}, author = {Zhang, Z and Zhang, Y and Shi, Z and Chen, Y}, title = {Linking Genome-Centric Metagenomics to Kinetic Analysis Reveals the Regulation Mechanism of Hydroxylamine in Nitrite Accumulation of Biological Denitrification.}, journal = {Environmental science & technology}, volume = {56}, number = {14}, pages = {10317-10328}, doi = {10.1021/acs.est.2c01914}, pmid = {35761213}, issn = {1520-5851}, mesh = {Bioreactors ; *Denitrification ; Hydroxylamine ; Hydroxylamines ; Kinetics ; Metagenomics ; Nitrates ; *Nitrites ; Nitrogen ; Oxidation-Reduction ; Sewage ; Wastewater ; }, abstract = {Given hydroxylamine accumulation in various nitrification systems and its potential mechanism in regulating the subsequent denitrification process were unraveled in this study. Hydroxylamine (>0.5 mgN/L) immediately induced nitrite accumulation of activated sludge by inhibiting the activities of nitrite reductases and their electron transport modules (Complex III and cytochrome c). Moreover, long-term exposure to 0.5-2.5 mgN/L hydroxylamine accelerated the functional transformation from denitrification to denitratation under low C/N conditions. However, genome-centric metagenomics indicated that a genotypic complete rather than truncated denitrifier Thauera aminoaromatica TJ127 was enriched and mainly responsible for acetate storage and nitrate reduction of the denitratation community. Interestingly, its enrichment resulted in nitrite production and reduction sequentially but reduced nitrate only to nitrite under carbon-limited conditions (C/N ≤ 3.0). Thus, it showed higher tolerance to hydroxylamine than the concurrent phenotype denitrifiers in activated sludge. Moreover, due to its higher anoxic storage capability in the feast phase, this enrichment became highly specialized by decreasing the feast/famine ratio, and thus a satisfactory denitratation performance was still maintained without hydroxylamine. These results suggested that the transient release of hydroxylamine from nitrification may interfere with subsequent denitrification metabolism, but its continuous accumulation is beneficial for achieving denitratation, which could steadily provide nitrite for mainstream anammox.}, } @article {pmid35761187, year = {2022}, author = {Cui, P and Kong, K and Yao, Y and Huang, Z and Shi, S and Liu, P and Huang, Y and Abbas, N and Yu, L and Zhang, Y}, title = {Community composition, bacterial symbionts, antibacterial and antioxidant activities of honeybee-associated fungi.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {168}, pmid = {35761187}, issn = {1471-2180}, mesh = {Animals ; Anti-Bacterial Agents ; *Antioxidants/pharmacology ; Bacteria ; Bees ; Complex Mixtures/pharmacology ; Escherichia coli/metabolism ; Fungi ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Staphylococcus aureus ; }, abstract = {BACKGROUND: Fungi associated with insects represent one potentially rich source for the discovery of novel metabolites. However, a comprehensive understanding of the fungal communities of Apis mellifera ligustica remains elusive.

RESULTS: Here, we investigated the phylogenetic diversity and community composition of honeybee-associated fungi using combination of culture-dependent and culture-independent approaches. A total of forty-five fungi were isolated and purified from the Apis mellifera ligustica, royal jelly, and honeycomb, which belonged to four classes and eleven different genera. Furthermore, 28 bacterial 16S rRNA gene sequences were obtained by PCR from the fungal metagenome. High-throughput sequencing analyses revealed that the fungal communities were more diverse, a total of 62 fungal genera were detected in the honeybee gut by culture-independent method, whereas only 4 genera were isolated by culture-dependent method. Similarly, 247 fungal genera were detected in the honeycomb, whereas only 4 genera were isolated. In addition, we assessed the antibacterial and antioxidant activities of fungal isolates. Most fungal crude extracts obtained from the cultivation supernatant exhibited antioxidant activities. Only two fungal crude extracts displayed moderate activity against Escherichia coli and Staphylococcus aureus. Chemical analysis of Chaetomium subaffine MFFC22 led to the discovery of three known compounds, including cochliodinol (1), emodin (2), chrysophanol (3). Among them, cochliodinol (1) showed intense DPPH radical scavenging activity with the 50% inhibitory concentration (IC50) of 3.06 μg/mL, which was comparable to that of the positive ascorbic acid (IC50 = 2.25 μg/mL). Compound 2 displayed weak inhibitory activities against Micrococcus tetragenus and S. aureus.

CONCLUSIONS: This research provided a fundamental clue for the complex interactions among honeybees, fungi, bacterial symbionts, and the effects on the honeybee. Furthermore, the diversity of honeybee-associated fungi had great potential in finding the resource of new species and antioxidants.}, } @article {pmid35761090, year = {2022}, author = {Banciu, HL and Gridan, IM and Zety, AV and Baricz, A}, title = {Asgard archaea in saline environments.}, journal = {Extremophiles : life under extreme conditions}, volume = {26}, number = {2}, pages = {21}, pmid = {35761090}, issn = {1433-4909}, support = {PN-III-P4-ID-PCE-2020-1559//Ministry of Research, Innovation and Digitization, CNCS/CCCDI - UEFISCDI/ ; }, mesh = {*Archaea ; Eukaryotic Cells/metabolism ; *Genome, Archaeal ; Metagenome ; Phylogeny ; }, abstract = {Members of candidate Asgardarchaeota superphylum appear to share numerous eukaryotic-like attributes thus being broadly explored for their relevance to eukaryogenesis. On the contrast, the ecological roles of Asgard archaea remains understudied. Asgard archaea have been frequently associated to low-oxygen aquatic sedimentary environments worldwide spanning a broad but not extreme salinity range. To date, the available information on diversity and potential biogeochemical roles of Asgardarchaeota mostly sourced from marine habitats and to a much lesser extend from true saline environments (i.e., > 3% w/v total salinity). Here, we provide an overview on diversity and ecological implications of Asgard archaea distributed across saline environments and briefly explore their metagenome-resolved potential for osmoadaptation. Loki-, Thor- and Heimdallarchaeota are the dominant Asgard clades in saline habitats where they might employ anaerobic/microaerophilic organic matter degradation and autotrophic carbon fixation. Homologs of primary solute uptake ABC transporters seemingly prevail in Thorarchaeota, whereas those putatively involved in trehalose and ectoine biosynthesis were mostly inferred in Lokiarchaeota. We speculate that Asgardarchaeota might adopt compatible solute-accumulating ('salt-out') strategy as response to salt stress. Our current understanding on the distribution, ecology and salt-adaptive strategies of Asgardarchaeota in saline environments are, however, limited by insufficient sampling and incompleteness of the available metagenome-assembled genomes. Extensive sampling combined with 'omics'- and cultivation-based approaches seem, therefore, crucial to gain deeper knowledge on this particularly intriguing archaeal lineage.}, } @article {pmid35760913, year = {2022}, author = {Liu, Y and Ji, M and Yu, T and Zaugg, J and Anesio, AM and Zhang, Z and Hu, S and Hugenholtz, P and Liu, K and Liu, P and Chen, Y and Luo, Y and Yao, T}, title = {A genome and gene catalog of glacier microbiomes.}, journal = {Nature biotechnology}, volume = {40}, number = {9}, pages = {1341-1348}, pmid = {35760913}, issn = {1546-1696}, mesh = {*Ice Cover/chemistry ; *Microbiota/genetics ; Snow/chemistry ; }, abstract = {Glaciers represent a unique inventory of microbial genetic diversity and a record of evolution. The Tibetan Plateau contains the largest area of low-latitude glaciers and is particularly vulnerable to global warming. By sequencing 85 metagenomes and 883 cultured isolates from 21 Tibetan glaciers covering snow, ice and cryoconite habitats, we present a specialized glacier microbial genome and gene catalog to archive glacial genomic and functional diversity. This comprehensive Tibetan Glacier Genome and Gene (TG2G) catalog includes 883 genomes and 2,358 metagenome-assembled genomes, which represent 968 candidate species spanning 30 phyla. The catalog also contains over 25 million non-redundant protein-encoding genes, the utility of which is demonstrated by the exploration of secondary metabolite biosynthetic potentials, virulence factor identification and global glacier metagenome comparison. The TG2G catalog is a valuable resource that enables enhanced understanding of the structure and functions of Tibetan glacial microbiomes.}, } @article {pmid35760839, year = {2022}, author = {Medvedeva, S and Sun, J and Yutin, N and Koonin, EV and Nunoura, T and Rinke, C and Krupovic, M}, title = {Three families of Asgard archaeal viruses identified in metagenome-assembled genomes.}, journal = {Nature microbiology}, volume = {7}, number = {7}, pages = {962-973}, pmid = {35760839}, issn = {2058-5276}, mesh = {Archaea/metabolism ; *Archaeal Viruses/genetics ; Ecosystem ; Eukaryota/genetics ; Metagenome ; Phylogeny ; }, abstract = {Asgardarchaeota harbour many eukaryotic signature proteins and are widely considered to represent the closest archaeal relatives of eukaryotes. Whether similarities between Asgard archaea and eukaryotes extend to their viromes remains unknown. Here we present 20 metagenome-assembled genomes of Asgardarchaeota from deep-sea sediments of the basin off the Shimokita Peninsula, Japan. By combining a CRISPR spacer search of metagenomic sequences with phylogenomic analysis, we identify three family-level groups of viruses associated with Asgard archaea. The first group, verdandiviruses, includes tailed viruses of the class Caudoviricetes (realm Duplodnaviria); the second, skuldviruses, consists of viruses with predicted icosahedral capsids of the realm Varidnaviria; and the third group, wyrdviruses, is related to spindle-shaped viruses previously identified in other archaea. More than 90% of the proteins encoded by these viruses of Asgard archaea show no sequence similarity to proteins encoded by other known viruses. Nevertheless, all three proposed families consist of viruses typical of prokaryotes, providing no indication of specific evolutionary relationships between viruses infecting Asgard archaea and eukaryotes. Verdandiviruses and skuldviruses are likely to be lytic, whereas wyrdviruses potentially establish chronic infection and are released without host cell lysis. All three groups of viruses are predicted to play important roles in controlling Asgard archaea populations in deep-sea ecosystems.}, } @article {pmid35760837, year = {2022}, author = {Rambo, IM and Langwig, MV and Leão, P and De Anda, V and Baker, BJ}, title = {Genomes of six viruses that infect Asgard archaea from deep-sea sediments.}, journal = {Nature microbiology}, volume = {7}, number = {7}, pages = {953-961}, pmid = {35760837}, issn = {2058-5276}, mesh = {*Archaea/genetics/metabolism ; Eukaryota/genetics ; Genome, Archaeal ; Metagenome ; Phylogeny ; *Viruses/genetics ; }, abstract = {Asgard archaea are globally distributed prokaryotic microorganisms related to eukaryotes; however, viruses that infect these organisms have not been described. Here, using metagenome sequences recovered from deep-sea hydrothermal sediments, we characterize six relatively large (up to 117 kb) double-stranded DNA (dsDNA) viral genomes that infected two Asgard archaeal phyla, Lokiarchaeota and Helarchaeota. These viruses encode Caudovirales-like structural proteins, as well as proteins distinct from those described in known archaeal viruses. Their genomes contain around 1-5% of genes associated with eukaryotic nucleocytoplasmic large DNA viruses (NCLDVs) and appear to be capable of semi-autonomous genome replication, repair, epigenetic modifications and transcriptional regulation. Moreover, Helarchaeota viruses may hijack host ubiquitin systems similar to eukaryotic viruses. Genomic analysis of these Asgard viruses reveals that they contain features of both prokaryotic and eukaryotic viruses, and provides insights into their potential infection and host interaction mechanisms.}, } @article {pmid35760384, year = {2022}, author = {Faridl, M and Mellyani, K and Khoirunnisa, K and Septiani, P and Giri-Rachman, EA and Nugrahapraja, H and Rahmawati, E and Alamanda, CNC and Ristandi, RB and Rachman, RW and Robiani, R and Fibriani, A}, title = {RNA sequence analysis of nasopharyngeal swabs from asymptomatic and mildly symptomatic patients with COVID-19.}, journal = {International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases}, volume = {122}, number = {}, pages = {449-460}, pmid = {35760384}, issn = {1878-3511}, mesh = {*COVID-19/diagnosis ; *Coinfection/diagnosis ; Humans ; Nasopharynx ; RNA, Viral/analysis/genetics ; SARS-CoV-2/genetics ; Sequence Analysis ; Sequence Analysis, RNA ; }, abstract = {OBJECTIVES: The characterization of asymptomatic and mildly symptomatic patients with COVID-19 by observing changes in gene expression profile and possible bacterial coinfection is relevant to be investigated. We aimed to identify transcriptomic and coinfection profiles in both groups of patients.

METHODS: A ribonucleic acid (RNA) sequence analysis on nasopharyngeal swabs were performed using a shotgun sequencing pipeline. Differential gene analysis, viral genome assembly, and metagenomics analysis were further performed using the retrieved data.

RESULTS: Both groups of patients underwent a cilia modification and mRNA splicing. Modulations in macroautophagy, epigenetics, and cell cycle processes were observed specifically in the asymptomatic group. Modulation in the RNA transport was found specifically in the mildly symptomatic group. The mildly symptomatic group showed modulation in the RNA transport and upregulation of autophagy regulator genes and genes in the complement system. No link between viral variants and disease severity was found. Microbiome analysis revealed the elevation of Streptococcus pneumoniae and Veillonella parvula proportion in symptomatic patients.

CONCLUSION: A reduction in the autophagy influx and modification in the epigenetic profile might be involved in halting the disease progression. A global dysregulation of RNA processing and translation might cause more severe outcomes in symptomatic individuals. Coinfection by opportunistic microflora should be taken into account when assessing the possible outcome of SARS-CoV-2 infection.}, } @article {pmid35760249, year = {2022}, author = {Zhang, S and Ma, X and Sun, H and Xie, D and Zhao, P and Wang, Q and Wu, C and Gao, M}, title = {Semi-continuous mesophilic-thermophilic two-phase anaerobic co-digestion of food waste and spent mushroom substance: Methanogenic performance, microbial, and metagenomic analysis.}, journal = {Bioresource technology}, volume = {360}, number = {}, pages = {127518}, doi = {10.1016/j.biortech.2022.127518}, pmid = {35760249}, issn = {1873-2976}, mesh = {*Agaricales/genetics/metabolism ; Anaerobiosis ; Bioreactors/microbiology ; Digestion ; *Euryarchaeota/metabolism ; Food ; Methane/metabolism ; *Refuse Disposal ; Sewage/microbiology ; }, abstract = {The methanogenic efficiency and system stability of anaerobic co-digestion of food waste (FW) and spent mushroom substance (SMS) are important for its application. A 90-day semi-continuous study was conducted to compare the co-digestion performance of an ethanologenic-methanogenic two-phase system and an acidogenic-methanogenic system using FW and SMS as substrates. The results showed that the ethanologenic-methanogenic system increased the contents of ethanol and acetate in the hydrolytic acidification phase. Microbial-community analysis showed that ethanologenic-methanogenic system enriched hydrolytic acidifying bacteria and methanogens such as Methanoculleus, resulting in an increase in the average methane yield of methanogenic phase by 1.91-2.43 times at the same organic loading rate (OLR = 3.0-4.0 g-VS·L[-1]·d[-1]). Metagenomic analysis indicated that the ethanologenic-methanogenic system increased the abundance of enzyme-encoding genes and promoted the degradation of acetate and CO2/H2, thereby enhancing methanogenic metabolic pathways, compared to the acidogenic-methanogenic system.}, } @article {pmid35760036, year = {2023}, author = {Troci, A and Rausch, P and Waschina, S and Lieb, W and Franke, A and Bang, C}, title = {Long-Term Dietary Effects on Human Gut Microbiota Composition Employing Shotgun Metagenomics Data Analysis.}, journal = {Molecular nutrition & food research}, volume = {67}, number = {24}, pages = {e2101098}, doi = {10.1002/mnfr.202101098}, pmid = {35760036}, issn = {1613-4133}, support = {//Deutsche Forschungsgemeinschaft/ ; }, mesh = {Humans ; *Gastrointestinal Microbiome ; Feces ; Diet ; *Microbiota ; Metagenome ; Metagenomics/methods ; }, abstract = {SCOPE: The gut microbiome regulates various metabolic pathways in the host and its dysbiosis is involved in the pathogenesis of diverse diseases. One of the major factors triggering gut microbiome establishment is diet. This study aims to unravel interactions and changes between diet and gut microbiome over a period of 3 years.

METHODS AND RESULTS: This study investigates the relation between diet and the microbiome of 75 individuals over a 3-year time period. Shotgun metagenomic sequencing is performed to profile gut microbial composition and function. This study shows that there are significant changes in gut microbiome taxonomy and functional composition between two time points. Whereas microbial taxonomy is found to be highly individualized, overall microbial functions stay relatively stable. Moreover, in silico metabolic modeling of microbial communities indicates that changes in dietary intake of medium-chain saturated fatty acids is accompanied by an altered utilization of amino acids by the gut microbiome.

CONCLUSION: The study design allows us to validate functional stability within the gut microbiome of healthy subjects over a 3-year period. However, enduring changes in nutrition such as increased alcohol consumption or decreased intake of vegetables come along with enhanced microbial functions that are associated with disease etiology.}, } @article {pmid35759844, year = {2022}, author = {Mercado, JV and Koyama, M and Nakasaki, K}, title = {Co-occurrence network analysis reveals loss of microbial interactions in anaerobic digester subjected to repeated organic load shocks.}, journal = {Water research}, volume = {221}, number = {}, pages = {118754}, doi = {10.1016/j.watres.2022.118754}, pmid = {35759844}, issn = {1879-2448}, mesh = {Anaerobiosis ; *Bioreactors ; *Methane/metabolism ; Microbial Interactions ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Fluctuations in the anaerobic digestion (AD) organic loading rate (OLR) cause shocks to the AD microbiome, which lead to unstable methane productivity. Managing these fluctuations requires a larger digester, which is impractical for community-scale applications, limiting the potential of AD in advancing a circular economy. To allow operation of small-scale AD while managing OLR fluctuations, we need to tackle the issue through elucidation of the microbial community dynamics via 16S rRNA gene sequencing. This study elucidated the interrelation of the AD performance and the dynamics of the microbial interactions within its microbiome in response to repeated high OLR shocks at different frequencies. The OLR shocks were equivalent to 4 times the baseline OLR of 2 g VS/L/d. We found that less frequent organic load shocks result to deterioration of methane productivity. Co-occurrence network analysis shows that this coincides with the breakdown of the microbiome network structure. This suggests loss of microbial interactions necessary in maintaining stable AD. Identification of species influencing the network structure revealed that a species under the genus Anaerovorax has the greatest influence, while orders Spirochaetales and Synergistales represent the greatest number of the influential species. We inferred that the impact imposed by the OLR shocks shifted the microbiome activity towards biochemical pathways that are not contributing to methane production. Establishing a small-scale AD system that permits OLR fluctuations would require developing an AD microbiome resilient to infrequent organic loading shocks.}, } @article {pmid35759608, year = {2022}, author = {Prieto Riquelme, MV and Garner, E and Gupta, S and Metch, J and Zhu, N and Blair, MF and Arango-Argoty, G and Maile-Moskowitz, A and Li, AD and Flach, CF and Aga, DS and Nambi, IM and Larsson, DGJ and Bürgmann, H and Zhang, T and Pruden, A and Vikesland, PJ}, title = {Demonstrating a Comprehensive Wastewater-Based Surveillance Approach That Differentiates Globally Sourced Resistomes.}, journal = {Environmental science & technology}, volume = {56}, number = {21}, pages = {14982-14993}, pmid = {35759608}, issn = {1520-5851}, mesh = {*Wastewater ; *Sewage ; RNA, Ribosomal, 16S/genetics ; Genes, Bacterial ; Anti-Bacterial Agents/pharmacology ; }, abstract = {Wastewater-based surveillance (WBS) for disease monitoring is highly promising but requires consistent methodologies that incorporate predetermined objectives, targets, and metrics. Herein, we describe a comprehensive metagenomics-based approach for global surveillance of antibiotic resistance in sewage that enables assessment of 1) which antibiotic resistance genes (ARGs) are shared across regions/communities; 2) which ARGs are discriminatory; and 3) factors associated with overall trends in ARGs, such as antibiotic concentrations. Across an internationally sourced transect of sewage samples collected using a centralized, standardized protocol, ARG relative abundances (16S rRNA gene-normalized) were highest in Hong Kong and India and lowest in Sweden and Switzerland, reflecting national policy, measured antibiotic concentrations, and metal resistance genes. Asian versus European/US resistomes were distinct, with macrolide-lincosamide-streptogramin, phenicol, quinolone, and tetracycline versus multidrug resistance ARGs being discriminatory, respectively. Regional trends in measured antibiotic concentrations differed from trends expected from public sales data. This could reflect unaccounted uses, captured only by the WBS approach. If properly benchmarked, antibiotic WBS might complement public sales and consumption statistics in the future. The WBS approach defined herein demonstrates multisite comparability and sensitivity to local/regional factors.}, } @article {pmid35759425, year = {2022}, author = {Muthappa, DM and Lamba, S and Sivasankaran, SK and Naithani, A and Rogers, N and Srikumar, S and Macori, G and Scannell, AGM and Fanning, S}, title = {16S rRNA Based Profiling of Bacterial Communities Colonizing Bakery-Production Environments.}, journal = {Foodborne pathogens and disease}, volume = {19}, number = {7}, pages = {485-494}, doi = {10.1089/fpd.2022.0014}, pmid = {35759425}, issn = {1556-7125}, mesh = {*Bacteria/genetics ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Conventional culture-based techniques are largely inadequate in elucidating the microbiota contained in an environment, due to low recovery within a complex bacterial community. This limitation has been mitigated by the use of next-generation sequencing (NGS)-based approaches thereby facilitating the identification and classification of both culturable and uncultivable microorganisms. Amplicon targeted NGS methods, such as 16S ribosomal RNA (16S rRNA) and shotgun metagenomics, are increasingly being applied in various settings such as in food production environments to decipher the microbial consortium therein. Even though multiple food matrices/food production environments have been studied, the low-moisture environment associated with bakery food production remains to be investigated. To address this knowledge gap, in this study, we investigated the microbiome associated with two bakery production sites (designated as A and B) located in Ireland using 16S rRNA-amplicon-based sequencing. Amplicons corresponding to a hypervariable region contained within the 16S rRNA gene were amplified from DNA samples purified from environmental swabs and ingredients collected at both sites at various stages (preparation, production, postproduction, and storage) across the bakery production chain, over three seasons (winter, spring, and summer). These amplicons were sequenced, and data were analyzed using the mothur pipeline and visualized using MicrobiomeAnalyst and a series of R packages. The top seven bacterial phyla identified at both sites were composed of Proteobacteria, Firmicutes, Actinobacteria, Bacteroidetes, Deinococcus-Thermus, Patescibacteria, and Verrucomicrobia. In addition, the phyla Tenericutes (Mycoplasmatota) and Acidobacteria were observed only in samples taken at site B. Different bacterial compositions were identified at each stage of production. These same bacteria were also found to be present in the final processed food suggesting the influence of the environment on the food matrix. This study is the first demonstration of the utility of 16S rRNA amplicon-based sequencing to describe the microbiota associated with bakery processing environments.}, } @article {pmid35758806, year = {2022}, author = {Tang, T and Hou, S and Fuhrman, JA and Sun, F}, title = {Phage-bacterial contig association prediction with a convolutional neural network.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {Suppl 1}, pages = {i45-i52}, pmid = {35758806}, issn = {1367-4811}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; R01 GM131407/GM/NIGMS NIH HHS/United States ; R01GM120624/NH/NIH HHS/United States ; }, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Metagenome ; Metagenomics ; Neural Networks, Computer ; }, abstract = {MOTIVATION: Phage-host associations play important roles in microbial communities. But in natural communities, as opposed to culture-based lab studies where phages are discovered and characterized metagenomically, their hosts are generally not known. Several programs have been developed for predicting which phage infects which host based on various sequence similarity measures or machine learning approaches. These are often based on whole viral and host genomes, but in metagenomics-based studies, we rarely have whole genomes but rather must rely on contigs that are sometimes as short as hundreds of bp long. Therefore, we need programs that predict hosts of phage contigs on the basis of these short contigs. Although most existing programs can be applied to metagenomic datasets for these predictions, their accuracies are generally low. Here, we develop ContigNet, a convolutional neural network-based model capable of predicting phage-host matches based on relatively short contigs, and compare it to previously published VirHostMatcher (VHM) and WIsH.

RESULTS: On the validation set, ContigNet achieves 72-85% area under the receiver operating characteristic curve (AUROC) scores, compared to the maximum of 68% by VHM or WIsH for contigs of lengths between 200 bps to 50 kbps. We also apply the model to the Metagenomic Gut Virus (MGV) catalogue, a dataset containing a wide range of draft genomes from metagenomic samples and achieve 60-70% AUROC scores compared to that of VHM and WIsH of 52%. Surprisingly, ContigNet can also be used to predict plasmid-host contig associations with high accuracy, indicating a similar genetic exchange between mobile genetic elements and their hosts.

The source code of ContigNet and related datasets can be downloaded from https://github.com/tianqitang1/ContigNet.}, } @article {pmid35758788, year = {2022}, author = {Liu, S and Koslicki, D}, title = {CMash: fast, multi-resolution estimation of k-mer-based Jaccard and containment indices.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {Suppl 1}, pages = {i28-i35}, pmid = {35758788}, issn = {1367-4811}, support = {R01 GM146462/GM/NIGMS NIH HHS/United States ; }, mesh = {*Algorithms ; Computational Biology/methods ; Metagenomics ; Sequence Analysis, DNA/methods ; *Software ; }, abstract = {MOTIVATION: K-mer-based methods are used ubiquitously in the field of computational biology. However, determining the optimal value of k for a specific application often remains heuristic. Simply reconstructing a new k-mer set with another k-mer size is computationally expensive, especially in metagenomic analysis where datasets are large. Here, we introduce a hashing-based technique that leverages a kind of bottom-m sketch as well as a k-mer ternary search tree (KTST) to obtain k-mer-based similarity estimates for a range of k values. By truncating k-mers stored in a pre-built KTST with a large k=kmax value, we can simultaneously obtain k-mer-based estimates for all k values up to kmax. This truncation approach circumvents the reconstruction of new k-mer sets when changing k values, making analysis more time and space-efficient.

RESULTS: We derived the theoretical expression of the bias factor due to truncation. And we showed that the biases are negligible in practice: when using a KTST to estimate the containment index between a RefSeq-based microbial reference database and simulated metagenome data for 10 values of k, the running time was close to 10× faster compared to a classic MinHash approach while using less than one-fifth the space to store the data structure.

A python implementation of this method, CMash, is available at https://github.com/dkoslicki/CMash. The reproduction of all experiments presented herein can be accessed via https://github.com/KoslickiLab/CMASH-reproducibles.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid35758776, year = {2022}, author = {Alanko, JN and Slizovskiy, IB and Lokshtanov, D and Gagie, T and Noyes, NR and Boucher, C}, title = {Syotti: scalable bait design for DNA enrichment.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {Suppl 1}, pages = {i177-i184}, pmid = {35758776}, issn = {1367-4811}, support = {R01 AI141810/AI/NIAID NIH HHS/United States ; R01HG011392//NIH NIAID/ ; }, mesh = {*Algorithms ; DNA ; Humans ; Metagenomics/methods ; Sequence Analysis, DNA/methods ; *Software ; }, abstract = {MOTIVATION: Bait enrichment is a protocol that is becoming increasingly ubiquitous as it has been shown to successfully amplify regions of interest in metagenomic samples. In this method, a set of synthetic probes ('baits') are designed, manufactured and applied to fragmented metagenomic DNA. The probes bind to the fragmented DNA and any unbound DNA is rinsed away, leaving the bound fragments to be amplified for sequencing. Metsky et al. demonstrated that bait-enrichment is capable of detecting a large number of human viral pathogens within metagenomic samples.

RESULTS: We formalize the problem of designing baits by defining the Minimum Bait Cover problem, show that the problem is NP-hard even under very restrictive assumptions, and design an efficient heuristic that takes advantage of succinct data structures. We refer to our method as Syotti. The running time of Syotti shows linear scaling in practice, running at least an order of magnitude faster than state-of-the-art methods, including the method of Metsky et al. At the same time, our method produces bait sets that are smaller than the ones produced by the competing methods, while also leaving fewer positions uncovered. Lastly, we show that Syotti requires only 25 min to design baits for a dataset comprised of 3 billion nucleotides from 1000 related bacterial substrains, whereas the method of Metsky et al. shows clearly super-linear running time and fails to process even a subset of 17% of the data in 72 h.

https://github.com/jnalanko/syotti.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid35758687, year = {2022}, author = {Saito, D and Lemos, LN and Ferreira, ATRN and Saito, CPB and de Oliveira, RF and Cannavan, FS and Tsai, SM}, title = {Draft Genome Sequences of Five Putatively Novel Saccharibacteria Species Assembled from the Human Oral Metagenome.}, journal = {Microbiology resource announcements}, volume = {11}, number = {7}, pages = {e0024622}, pmid = {35758687}, issn = {2576-098X}, support = {062.01941/2015//Amazonas Research Foundation/ ; }, abstract = {We report the draft metagenome-assembled genomes (MAGs) of five putatively novel Saccharibacteria strains retrieved from the oral microbiome. MAGs were obtained from nonstimulated saliva samples from hosts with various clinical statuses and correspond to distinct species taxonomically placed within the Saccharimonadaceae family, as determined by genome-wide analysis against previously described TM7 genomes.}, } @article {pmid35758682, year = {2022}, author = {Li, Y and Cao, L and Ye, M and Xu, R and Chen, X and Ma, Y and Tian, RR and Liu, FL and Zhang, P and Kuang, YQ and Zheng, YT and Zhang, C}, title = {Plasma Virome Reveals Blooms and Transmission of Anellovirus in Intravenous Drug Users with HIV-1, HCV, and/or HBV Infections.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0144722}, pmid = {35758682}, issn = {2165-0497}, mesh = {*Anelloviridae ; *Drug Users ; *HIV Infections/complications ; *HIV-1/genetics ; Hepacivirus/genetics ; *Hepatitis B/complications/epidemiology ; Hepatitis B virus/genetics ; *Hepatitis C/epidemiology ; Humans ; Phylogeny ; *Substance Abuse, Intravenous/complications/epidemiology ; Virome ; }, abstract = {Intravenous drug users (IDUs) are a high-risk group for HIV-1, hepatitis C virus (HCV), and hepatitis B virus (HBV) infections, which are the leading causes of death in IDUs. However, the plasma virome of IDUs and how it is influenced by above viral infections remain unclear. Using viral metagenomics, we determined the plasma virome of IDUs and its association with HIV-1, HCV, and/or HBV infections. Compared with healthy individuals, IDUs especially those with major viral infections had higher viral abundance and diversity. Anelloviridae dominated plasma virome. Coinfections of multiple anelloviruses were common, and anelloviruses from the same genus tended to coexist together. In this study, 4,487 anellovirus ORF1 sequences were identified, including 1,620 (36.1%) with less than 69% identity to any known sequences, which tripled the current number. Compared with healthy controls (HC), more anellovirus sequences were observed in neg-IDUs, and HIV-1, HCV, and/or HBV infections further expanded the sequence number in IDUs, which was characterized by the emergence of novel divergent taxons and blooms of resident anelloviruses. Pegivirus was mainly identified in infected IDUs. Five main pegivirus transmission clusters (TCs) were identified by phylogenetic analysis, suggesting a transmission link. Similar anellovirus profiles were observed in IDUs within the same TC, suggesting transmission of anellome among IDUs. Our data suggested that IDUs suffered higher plasma viral burden especially anelloviruses, which was associated with HIV-1, HCV, and/or HBV infections. Blooms in abundance and unprecedented diversity of anellovirus highlighted active evolution and replication of this virus in blood circulation, and an uncharacterized role it may engage with the host. IMPORTANCE Virome is associated with immune status and determines or influences disease progression through both pathogenic and resident viruses. Increased viral burden in IDUs especially those with major viral infections indicated the suboptimal immune status and high infection risks of these population. Blooms in abundance and unprecedented diversity of anellovirus highlighted its active evolution and replication in the blood circulation, and sensitive response to other viral infections. In addition, transmission cluster analysis revealed the transmission link of pegivirus among IDUs, and the individuals with transmission links shared similar anellome profiles. In-depth monitoring of the plasma virome in high-risk populations is not only needed for surveillance for emerging viruses and transmission networks of major and neglected bloodborne viruses, but also important for a better understanding of commensal viruses and their role it may engage with immune system.}, } @article {pmid35757783, year = {2022}, author = {Chang, HW and Yan, D and Singh, R and Bui, A and Lee, K and Truong, A and Milush, JM and Somsouk, M and Liao, W}, title = {Multiomic Analysis of the Gut Microbiome in Psoriasis Reveals Distinct Host‒Microbe Associations.}, journal = {JID innovations : skin science from molecules to population health}, volume = {2}, number = {3}, pages = {100115}, pmid = {35757783}, issn = {2667-0267}, abstract = {Psoriasis is a chronic, inflammatory skin disease that affects 2‒3% of the global population. Besides skin manifestations, patients with psoriasis have increased susceptibility to a number of comorbidities, including psoriatic arthritis, cardiovascular disease, and inflammatory bowel disease. To understand the systemic component of psoriasis pathogenesis, we performed a pilot study to examine the fecal metagenome, host colonic transcriptome, and host peripheral blood immune profiles of patients with psoriasis and healthy controls. Our study showed increased functional diversity in the gut microbiome of patients with psoriasis. In addition, we identified microbial species that preferentially associate with patients with psoriasis and which have been previously found to associate with other autoimmune diseases. Intriguingly, our data revealed three psoriasis subgroups that have distinct microbial and host features. Integrating these features revealed host‒microbe associations that are specific to psoriasis or particular psoriasis subgroups. Our findings provide insight into the factors that may affect the development of comorbidities in patients with psoriasis and may hold diagnostic potential for early identification of patients with psoriasis at risk for these comorbidities.}, } @article {pmid35757517, year = {2022}, author = {Tran, DM}, title = {Taxonomic and functional profiles of Coffea canephora endophytic microbiome in the Central Highlands region, Vietnam, revealed by analysis of 16S rRNA metagenomics sequence data.}, journal = {Data in brief}, volume = {43}, number = {}, pages = {108372}, pmid = {35757517}, issn = {2352-3409}, abstract = {Vietnam is the largest producer of Robusta coffee (Coffea canephora L.) [1]. Among regions in Vietnam, the Central Highlands is the capital of the coffee plantation and production [2]. Previous works have established a dataset of rhizospheric microbial diversity and its functionality to develop sustainable Robusta coffee production techniques in this region [3], [4], [5], [6]; however, a dataset of the endophytic microbiome of this plant species has been found is still unknown. The work presented here is the first report on the microbial and functional diversity of the endophytic microbiome of Coffea canephora L. grown in the region. A representative root sample was obtained by mixing five different root samples collected from a 6-year-old Robusta coffee field in Dak Lak Province, the Central Highlands, on 30 October 2021. After that, 16S rRNA metagenomic next-generation sequencing was conducted on the sample using the Illumina MiSeq platform. The raw sequence of endophytic microbiome data in this work was uploaded in Fastq format on NCBI with Bioproject PRJNA821717 and can be accessed at https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA821717. The dataset can be useful for understanding basic information about the prokaryotic ecology of this important plant in the Central Highlands, Vietnam. The data can also be valuable for developing cultivation techniques for sustainable Coffea canephora L. production by applying indigenous microbial resources.}, } @article {pmid35757330, year = {2022}, author = {Wu, X and Guo, M and Shi, S and Shi, S and Deng, Y and Wang, S and Wang, Y and Wang, P and Chen, K}, title = {Efficacy and Safety of Shenqisuxin Granule for Non-ST-segment Elevation Acute Coronary Syndrome: Study Protocol for a Randomized, Double-Blinded, Placebo-Controlled Trial.}, journal = {Frontiers in cardiovascular medicine}, volume = {9}, number = {}, pages = {888724}, pmid = {35757330}, issn = {2297-055X}, abstract = {INTRODUCTION: The Chinese herbal compound formula, Shenqisuxin granule (SQSX), promotes neovascularization and prevents in-stent restenosis in modern pharmaceutical studies and is expected to provide an effective strategy for non-ST-segment elevation acute coronary syndrome (NSTEACS). Thus, this study aims to examine the efficacy and safety of SQSX for NSTEACS and initially reveal its mechanism.

METHODS/DESIGN: The study is a randomized, double-blinded and placebo-controlled trial. A total of 66 participants will be randomly allocated to one of the following two groups. Participants in the SQSX group will receive conventional treatment plus SQSX, while the placebo group will receive conventional treatment plus placebo, both for 14 days. The primary outcome, hs-CRP, and secondary outcome the Seattle Angina Questionnaire (SAQ) will be assessed at baseline, 7 ± 3 days and 14 ± 3 days. At all visit windows, other indicators including creatine kinase (CK), creatine kinase-myocardial band (CK-MB), cardiac troponins I (cTnI), 12-lead electrocardiograph and the syndrome scores of Qi deficiency and blood stasis will be tested and metagenomic sequencing for intestinal flora will be performed. Echocardiography and safety assessment will be performed at baseline and 14 ± 3 days. Adverse events will be monitored during the trial.

DISCUSSION: The purpose of the study is to examine the efficacy and safety of SQSX to improve NSTEACS and initially reveal its mechanism.

TRIAL REGISTRATION: China Clinical Trial Registry, ChiCTR2000029226. Registered on January 19, 2020.}, } @article {pmid35756110, year = {2022}, author = {Chavan, S and Sarangdhar, V and Vigneshwaran, N}, title = {Nanopore-based metagenomic analysis of the impact of nanoparticles on soil microbial communities.}, journal = {Heliyon}, volume = {8}, number = {6}, pages = {e09693}, pmid = {35756110}, issn = {2405-8440}, abstract = {The current trend of using nanotechnology products in all spheres of human life, including for crop improvement may have a possible impact on soil microorganisms which influence soil and plant health. Nanopore-based metagenomic study reported here used full-length 16S rRNA gene sequences to assess shifts in community composition of soil microorganisms when treated with silver, titanium dioxide and zinc oxide nanoparticles (S-NP, T-NP, Z-NP, respectively). Firmicutes and Proteobacteria were the two dominant phyla in this soil, and there were no significant differences (p < 0.05) observed in these phyla across treatments. However, in the phylum Firmicutes, the abundance of the order Clostridiales showed a significant decrease (p < 0.05) in the presence of S-NP. Similarly, in the phylum Proteobacteria, a significant decrease in the presence of S-NP was seen for two orders, Vibrionales (p < 0.05) and Rhodobacterales (p < 0.01). Analysis at a further depth revealed that abundance of the genus Clostridium (order Clostridiales) decreased in the presence of both S-NP (p < 0.01) and T-NP (p < 0.05). The abundance of the genus Vibrio (order Vibrionales) was likewise impacted in the presence of all the three NPs - S-NP (p < 0.01), T-NP (p < 0.05) and Z-NP (p < 0.05). Analyses at high taxon ranks such as phyla may not give a good representation of the nature of microbial community shifts, and at times may paint an erroneous picture. The use of full-length 16S rRNA gene sequences here yielded a greater taxonomic depth, and some shifts at the lower ranks were discernible.}, } @article {pmid35756062, year = {2022}, author = {Vernocchi, P and Ristori, MV and Guerrera, S and Guarrasi, V and Conte, F and Russo, A and Lupi, E and Albitar-Nehme, S and Gardini, S and Paci, P and Ianiro, G and Vicari, S and Gasbarrini, A and Putignani, L}, title = {Gut Microbiota Ecology and Inferred Functions in Children With ASD Compared to Neurotypical Subjects.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {871086}, pmid = {35756062}, issn = {1664-302X}, abstract = {Autism spectrum disorders (ASDs) is a multifactorial neurodevelopmental disorder. The communication between the gastrointestinal (GI) tract and the central nervous system seems driven by gut microbiota (GM). Herein, we provide GM profiling, considering GI functional symptoms, neurological impairment, and dietary habits. Forty-one and 35 fecal samples collected from ASD and neurotypical children (CTRLs), respectively, (age range, 3-15 years) were analyzed by 16S targeted-metagenomics (the V3-V4 region) and inflammation and permeability markers (i.e., sIgA, zonulin lysozyme), and then correlated with subjects' metadata. Our ASD cohort was characterized as follows: 30/41 (73%) with GI functional symptoms; 24/41 (58%) picky eaters (PEs), with one or more dietary needs, including 10/41 (24%) with food selectivity (FS); 36/41 (88%) presenting high and medium autism severity symptoms (HMASSs). Among the cohort with GI symptoms, 28/30 (93%) showed HMASSs, 17/30 (57%) were picky eaters and only 8/30 (27%) with food selectivity. The remaining 11/41 (27%) ASDs without GI symptoms that were characterized by HMASS for 8/11 (72%) and 7/11 (63%) were picky eaters. GM ecology was investigated for the overall ASD cohort versus CTRLs; ASDs with GI and without GI, respectively, versus CTRLs; ASD with GI versus ASD without GI; ASDs with HMASS versus low ASSs; PEs versus no-PEs; and FS versus absence of FS. In particular, the GM of ASDs, compared to CTRLs, was characterized by the increase of Proteobacteria, Bacteroidetes, Rikenellaceae, Pasteurellaceae, Klebsiella, Bacteroides, Roseburia, Lactobacillus, Prevotella, Sutterella, Staphylococcus, and Haemophilus. Moreover, Sutterella, Roseburia and Fusobacterium were associated to ASD with GI symptoms compared to CTRLs. Interestingly, ASD with GI symptoms showed higher value of zonulin and lower levels of lysozyme, which were also characterized by differentially expressed predicted functional pathways. Multiple machine learning models classified correctly 80% overall ASDs, compared with CTRLs, based on Bacteroides, Lactobacillus, Prevotella, Staphylococcus, Sutterella, and Haemophilus features. In conclusion, in our patient cohort, regardless of the evaluation of many factors potentially modulating the GM profile, the major phenotypic determinant affecting the GM was represented by GI hallmarks and patients' age.}, } @article {pmid35756050, year = {2022}, author = {Vaghefi, N and Kusch, S and Németh, MZ and Seress, D and Braun, U and Takamatsu, S and Panstruga, R and Kiss, L}, title = {Beyond Nuclear Ribosomal DNA Sequences: Evolution, Taxonomy, and Closest Known Saprobic Relatives of Powdery Mildew Fungi (Erysiphaceae) Inferred From Their First Comprehensive Genome-Scale Phylogenetic Analyses.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {903024}, pmid = {35756050}, issn = {1664-302X}, abstract = {Powdery mildew fungi (Erysiphaceae), common obligate biotrophic pathogens of many plants, including important agricultural and horticultural crops, represent a monophyletic lineage within the Ascomycota. Within the Erysiphaceae, molecular phylogenetic relationships and DNA-based species and genera delimitations were up to now mostly based on nuclear ribosomal DNA (nrDNA) phylogenies. This is the first comprehensive genome-scale phylogenetic analysis of this group using 751 single-copy orthologous sequences extracted from 24 selected powdery mildew genomes and 14 additional genomes from Helotiales, the fungal order that includes the Erysiphaceae. Representative genomes of all powdery mildew species with publicly available whole-genome sequencing (WGS) data that were of sufficient quality were included in the analyses. The 24 powdery mildew genomes included in the analysis represented 17 species belonging to eight out of 19 genera recognized within the Erysiphaceae. The epiphytic genera, all but one represented by multiple genomes, belonged each to distinct, well-supported lineages. Three hemiendophytic genera, each represented by a single genome, together formed the hemiendophytic lineage. Out of the 14 other taxa from the Helotiales, Arachnopeziza araneosa, a saprobic species, was the only taxon that grouped together with the 24 genome-sequenced powdery mildew fungi in a monophyletic clade. The close phylogenetic relationship between the Erysiphaceae and Arachnopeziza was revealed earlier by a phylogenomic study of the Leotiomycetes. Further analyses of powdery mildew and Arachnopeziza genomes may discover signatures of the evolutionary processes that have led to obligate biotrophy from a saprobic way of life. A separate phylogeny was produced using the 18S, 5.8S, and 28S nrDNA sequences of the same set of powdery mildew specimens and compared to the genome-scale phylogeny. The nrDNA phylogeny was largely congruent to the phylogeny produced using 751 orthologs. This part of the study has revealed multiple contamination and other quality issues in some powdery mildew genomes. We recommend that the presence of 28S, internal transcribed spacer (ITS), and 18S nrDNA sequences in powdery mildew WGS datasets that are identical to those determined by Sanger sequencing should be used to assess the quality of assemblies, in addition to the commonly used Benchmarking Universal Single-Copy Orthologs (BUSCO) values.}, } @article {pmid35756038, year = {2022}, author = {Haryono, MAS and Law, YY and Arumugam, K and Liew, LC and Nguyen, TQN and Drautz-Moses, DI and Schuster, SC and Wuertz, S and Williams, RBH}, title = {Recovery of High Quality Metagenome-Assembled Genomes From Full-Scale Activated Sludge Microbial Communities in a Tropical Climate Using Longitudinal Metagenome Sampling.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {869135}, pmid = {35756038}, issn = {1664-302X}, abstract = {The analysis of metagenome data based on the recovery of draft genomes (so called metagenome-assembled genomes, or MAG) has assumed an increasingly central role in microbiome research in recent years. Microbial communities underpinning the operation of wastewater treatment plants are particularly challenging targets for MAG analysis due to their high ecological complexity, and remain important, albeit understudied, microbial communities that play ssa key role in mediating interactions between human and natural ecosystems. Here we consider strategies for recovery of MAG sequence from time series metagenome surveys of full-scale activated sludge microbial communities. We generate MAG catalogs from this set of data using several different strategies, including the use of multiple individual sample assemblies, two variations on multi-sample co-assembly and a recently published MAG recovery workflow using deep learning. We obtain a total of just under 9,100 draft genomes, which collapse to around 3,100 non-redundant genomic clusters. We examine the strengths and weaknesses of these approaches in relation to MAG yield and quality, showing that co-assembly may offer advantages over single-sample assembly in the case of metagenome data obtained from closely sampled longitudinal study designs. Around 1,000 MAGs were candidates for being considered high quality, based on single-copy marker gene occurrence statistics, however only 58 MAG formally meet the MIMAG criteria for being high quality draft genomes. These findings carry broader broader implications for performing genome-resolved metagenomics on highly complex communities, the design and implementation of genome recoverability strategies, MAG decontamination and the search for better binning methodology.}, } @article {pmid35756025, year = {2022}, author = {Chen, S and Yu, M and Zhang, W and He, K and Pan, H and Cui, K and Zhao, Y and Zhang, XH and Xiao, T and Zhang, W and Wu, LF}, title = {Metagenomic and Microscopic Analysis of Magnetotactic Bacteria in Tangyin Hydrothermal Field of Okinawa Trough.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {887136}, pmid = {35756025}, issn = {1664-302X}, abstract = {Magnetotactic bacteria (MTB) have been found in a wide variety of marine habitats, ranging from intertidal sediments to deep-sea seamounts. Deep-sea hydrothermal fields are rich in metal sulfides, which are suitable areas for the growth of MTB. However, MTB in hydrothermal fields have never been reported. Here, the presence of MTB in sediments from the Tangyin hydrothermal field was analyzed by 16S rRNA gene amplicon analysis, metagenomics, and transmission electron microscopy. Sequencing 16S rRNA gene yielded a total of 709 MTB sequences belonging to 20 OTUs, affiliated with Desulfobacterota, Alphaproteobacteria, and Nitrospirae. Three shapes of magnetofossil were identified by transmission electron microscopy: elongated-prismatic, bullet-shaped, and cuboctahedron. All of these structures were composed of Fe3O4. A total of 121 sequences were found to be homologous to the published MTB magnetosome-function-related genes, and relevant domains were identified. Further analysis revealed that diverse MTB are present in the Tangyin hydrothermal field, and that multicellular magnetotactic prokaryote (MMPs) might be the dominant MTB.}, } @article {pmid35756012, year = {2022}, author = {Rchiad, Z and Dai, M and Hamel, C and Bainard, LD and Cade-Menun, BJ and Terrat, Y and St-Arnaud, M and Hijri, M}, title = {Soil Depth Significantly Shifted Microbial Community Structures and Functions in a Semiarid Prairie Agroecosystem.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {815890}, pmid = {35756012}, issn = {1664-302X}, abstract = {The North American Great Plains cover a large area of the Nearctic ecozone, and an important part of this biome is semiarid. The sustainable intensification of agriculture that is necessary to produce food for an ever-increasing world population requires knowledge of the taxonomic and functional structure of the soil microbial community. In this study, we investigated the influence of soil depth on the composition and functions of the microbial communities hosted in agricultural soils of a semiarid agroecosystem, using metagenomic profiling, and compared them to changes in soil chemical and physical properties. Shotgun sequencing was used to determine the composition and functions of the soil microbial community of 45 soil samples from three soil depths (0-15 cm, 15-30 cm, and 30-60 cm) under different agricultural land use types (native prairie, seeded prairie, and cropland) in southwest Saskatchewan. Analysis of community composition revealed the declining abundance of phyla Verrucomicrobia, Bacteroidetes, Chlorophyta, Bacillariophyta, and Acidobacteria with soil depth, whereas the abundance of phyla Ascomycota, Nitrospirae, Planctomycetes, and Cyanobacteria increased with soil depth. Soil functional genes related to nucleosides and nucleotides, phosphorus (P) metabolism, cell division and cell cycle, amino acids and derivatives, membrane transport, and fatty acids were particularly abundant at 30-60 cm. In contrast, functional genes related to DNA and RNA metabolism, metabolism of nitrogen, sulfur and carbohydrates, and stress response were more abundant in the top soil depth. The RDA analysis of functional genes and soil physico-chemical properties revealed a positive correlation between phages and soil organic P concentrations. In the rooting zone of this semiarid agroecosystem, soil microbes express variable structural patterns of taxonomic and functional diversity at different soil depths. This study shows that the soil microbial community is structured by soil depth and physicochemical properties, with the middle soil depth being an intermediate transition zone with a higher taxonomic diversity. Our results suggest the co-existence of various microbial phyla adapted to upper and lower soil depths in an intermediate-depth transition zone.}, } @article {pmid35756005, year = {2022}, author = {Garrison, CE and Roozbehi, S and Mitra, S and Corbett, DR and Field, EK}, title = {Coastal Microbial Communities Disrupted During the 2018 Hurricane Season in Outer Banks, North Carolina.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {816573}, pmid = {35756005}, issn = {1664-302X}, abstract = {Hurricane frequencies and intensities are expected to increase under warming climate scenarios, increasing potential to disrupt microbial communities from steady-state conditions and alter ecosystem function. This study shows the impact of hurricane season on microbial community dynamics within the barrier island system of Outer Banks, North Carolina. We found that the passage of two sequential energetic hurricanes in 2018 (Florence and Michael) were correlated with shifts in total and active (DNA and RNA) portions of bacterial communities but not in archaeal communities, and within surface waters but not within the sediment. These microbial community shifts were distinct from non-hurricane season conditions, suggesting significant implications for nutrient cycling in nearshore and offshore environments. Hurricane-influenced marine sites in the coastal North Atlantic region had lower microbial community evenness and Shannon diversity, in addition to increased relative abundance of copiotrophic microbes compared to non-hurricane conditions. The abundance of functional genes associated with carbon and nitrogen cycling pathways were also correlated with the storm season, potentially shifting microbial communities at offshore sites from autotroph-dominated to heterotroph-dominated and leading to impacts on local carbon budgets. Understanding the geographic- and system-dependent responses of coastal microbial communities to extreme storm disturbances is critical for predicting impacts to nutrient cycling and ecosystem stability in current and future climate scenarios.}, } @article {pmid35756004, year = {2022}, author = {Lu, M and Schneider, D and Daniel, R}, title = {Metagenomic Screening for Lipolytic Genes Reveals an Ecology-Clustered Distribution Pattern.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {851969}, pmid = {35756004}, issn = {1664-302X}, abstract = {Lipolytic enzymes are one of the most important enzyme types for application in various industrial processes. Despite the continuously increasing demand, only a small portion of the so far encountered lipolytic enzymes exhibit adequate stability and activities for biotechnological applications. To explore novel and/or extremophilic lipolytic enzymes, microbial consortia in two composts at thermophilic stage were analyzed using function-driven and sequence-based metagenomic approaches. Analysis of community composition by amplicon-based 16S rRNA genes and transcripts, and direct metagenome sequencing revealed that the communities of the compost samples were dominated by members of the phyla Actinobacteria, Proteobacteria, Firmicutes, Bacteroidetes, and Chloroflexi. Function-driven screening of the metagenomic libraries constructed from the two samples yielded 115 unique lipolytic enzymes. The family assignment of these enzymes was conducted by analyzing the phylogenetic relationship and generation of a protein sequence similarity network according to an integrated classification system. The sequence-based screening was performed by using a newly developed database, containing a set of profile Hidden Markov models, highly sensitive and specific for detection of lipolytic enzymes. By comparing the lipolytic enzymes identified through both approaches, we demonstrated that the activity-directed complements sequence-based detection, and vice versa. The sequence-based comparative analysis of lipolytic genes regarding diversity, function and taxonomic origin derived from 175 metagenomes indicated significant differences between habitats. Analysis of the prevalent and distinct microbial groups providing the lipolytic genes revealed characteristic patterns and groups driven by ecological factors. The here presented data suggests that the diversity and distribution of lipolytic genes in metagenomes of various habitats are largely constrained by ecological factors.}, } @article {pmid35755957, year = {2022}, author = {Shah, D and Brown, JR and Lee, JCD and Carpenter, ML and Wall, G and Breuer, J}, title = {Use of a sample-to-result shotgun metagenomics platform for the detection and quantification of viral pathogens in paediatric immunocompromised patients.}, journal = {Journal of clinical virology plus}, volume = {2}, number = {2}, pages = {None}, pmid = {35755957}, issn = {2667-0380}, abstract = {BACKGROUND: Infections by several DNA viruses can severely impact outcomes in paediatric immunocompromised patients. Current testing, which is generally limited to singleplex qPCR assays, can miss both common and rarer viruses if they are not targeted.

OBJECTIVES: To evaluate the performance of the Galileo Viral Panel (Galileo), a sample-to-result shotgun metagenomics platform for the detection and quantification of 12 DNA viruses, compared to standard of care qPCR assays.

STUDY DESIGN: A clinical performance evaluation was carried out using 43 prospectively collected EDTA plasma samples positive for one or more DNA viruses. Agreement between assays was assessed by overall, positive, and negative percent agreement, as well as quantitative agreement by linear regression and Bland-Altman analysis.

RESULTS: Overall positive percent agreement was 84% (95% CI: 76%-90%), and negative percent agreement was 95% (95% CI: 92%-97%). There was a high correlation between Galileo and qPCR for ADV, CMV, EBV, and VZV (R[2]  = 0.91) and a mean difference by Bland Altman of -0.43 log10 IU or cp/ml (95% limits of agreement, -1.37 to 0.51). In addition, there was a high correlation between Galileo Signal Score and qPCR for TTV (R[2]  = 0.85).

CONCLUSION: We observed high qualitative and quantitative agreement between qPCR and Galileo. Galileo identified additional viruses that were not tested with routine qPCR and could impact clinical outcomes.}, } @article {pmid35755839, year = {2022}, author = {Su, J and Han, X and Xu, X and Ding, W and Li, M and Wang, W and Tian, M and Chen, X and Xu, B and Chen, Z and Yuan, J and Qin, X and Lin, D and Wang, R and Gong, Y and Pan, L and Wang, J and Wang, M}, title = {Simultaneous Detection of Pathogens and Tumors in Patients With Suspected Infections by Next-Generation Sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {892087}, pmid = {35755839}, issn = {2235-2988}, mesh = {China ; *DNA Copy Number Variations ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; *Neoplasms/diagnosis/genetics ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Differential diagnosis of patients with suspected infections is particularly difficult, but necessary for prompt diagnosis and rational use of antibiotics. A substantial proportion of these patients have non-infectious diseases that include malignant tumors. This study aimed to explore the clinical value of metagenomic next-generation sequencing (mNGS) for tumor detection in patients with suspected infections.

METHODS: A multicenter, prospective case study involving patients diagnosed with suspected infections was conducted in four hospitals in Shanghai, China between July 2019 and January 2020. Based upon mNGS technologies and chromosomal copy number variation (CNV) analysis on abundant human genome, a new procedure named Onco-mNGS was established to simultaneously detect pathogens and malignant tumors in all of the collected samples from patients.

RESULTS: Of 140 patients screened by Onco-mNGS testing, 115 patients were diagnosed with infections; 17 had obvious abnormal CNV signals indicating malignant tumors that were confirmed clinically. The positive percent agreement and negative percent agreement of mNGS testing compared to clinical diagnosis was 53.0% (61/115) and 60% (15/25), vs. 20.9% (24/115) and 96.0% (24/25), respectively, for conventional microbiological testing (both P <0.01). Klebsiella pneumoniae (14.8%, 9/61) was the most common pathogen detected by mNGS, followed by Escherichia coli (11.5%, 7/61) and viruses (11.5%, 7/61). The chromosomal abnormalities of the 17 cases included genome-wide variations and local variations of a certain chromosome. Five of 17 patients had a final confirmed with malignant tumors, including three lung adenocarcinomas and two hematological tumors; one patient was highly suspected to have lymphoma; and 11 patients had a prior history of malignant tumor.

CONCLUSION: This preliminary study demonstrates the feasibility and clinical value of using Onco-mNGS to simultaneously search for potential pathogens and malignant tumors in patients with suspected infections.}, } @article {pmid35755833, year = {2022}, author = {Tan, J and Liu, Y and Ehnert, S and Nüssler, AK and Yu, Y and Xu, J and Chen, T}, title = {The Effectiveness of Metagenomic Next-Generation Sequencing in the Diagnosis of Prosthetic Joint Infection: A Systematic Review and Meta-Analysis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {875822}, pmid = {35755833}, issn = {2235-2988}, mesh = {*Arthritis, Infectious ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; *Prosthesis-Related Infections/diagnosis ; Sensitivity and Specificity ; Synovial Fluid ; }, abstract = {BACKGROUND: A prosthetic joint infection (PJI) is a devastating complication following total joint arthroplasties with poor prognosis. Identifying an accurate and prompt diagnostic method is particularly important for PJI. Recently, the diagnostic value of metagenomic next-generation sequencing (mNGS) in detecting PJI has attracted much attention, while the evidence of its accuracy is quite limited. Thus, this study aimed to evaluate the accuracy of mNGS for the diagnosis of PJI.

METHODS: We summarized published studies to identify the potential diagnostic value of mNGS for PJI patients by searching online databases using keywords such as "prosthetic joint infection", "PJI", and "metagenomic sequencing". Ten of 380 studies with 955 patients in total were included. The included studies provided sufficient data for the completion of 2-by-2 tables. We calculated the sensitivity, specificity, and area under the SROC curve (AUC) to evaluate mNGS for PJI diagnosis.

RESULTS: We found that the pooled diagnostic sensitivity and specificity of mNGS for PJI were 0.93 (95% CI, 0.83 to 0.97) and 0.95 (95% CI, 0.92 to 0.97), respectively. Positive and negative likelihood ratios were 18.3 (95% CI, 10.9 to 30.6) and 0.07 (95% CI, 0.03 to 0.18), respectively. The area under the curve was 0.96 (95% CI, 0.93 to 0.97).

CONCLUSION: Metagenomic next-generation sequencing displays high accuracy in the diagnosis of PJI, especially for culture-negative cases.}, } @article {pmid35755831, year = {2022}, author = {Sun, Q and Li, Z and Wang, P and Zhao, J and Chen, S and Sun, M}, title = {Unveiling the Pathogenic Bacteria Causing Descending Necrotizing Mediastinitis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {873161}, pmid = {35755831}, issn = {2235-2988}, mesh = {Eubacterium ; Humans ; *Mediastinitis/microbiology/pathology ; Streptococcus/genetics ; }, abstract = {The combination of maxillofacial infections (MI) with descending necrotizing mediastinitis (DNM) is a complex disease characterized by rapid development and high mortality. Here, we performed metagenomic next-generation sequencing (mNGS) using samples from 21 patients with MI and eight patients with DNM. In this study, we found that the species richness of the DNM group was higher than that of the MI group, and the species diversity of the DNM group was higher than that of the MI group, with no statistically significant differences between groups (P > 0.05). LefSE analysis revealed that the main species differing between groups were Bacillus, Lactobacillus, Streptococcaceae, and Streptococcus (S. constellatus and S. anginosus). In addition, the PLS-DA analysis revealed that the dominant groups in the DNM group at the species level were S. constellatus, S. anginosus, Streptococcus intermedius, Prevotella oris, Mogibacterium timidum, and Eubacterium nodatum. Next, we correlated the clinical characteristics of the patients with the relative abundance of the pathogens identified in the LefSe and PLS-DA analyses. The relative abundance of S. anginosus was positively correlated with C-reactive protein (CRP) and calcitoninogen (PCT) but negatively correlated with the percentage of lymphocytes (Lymph%) (P < 0.05). On the other hand, M. timidum was positively correlated with the percentage of neutrophils (Neut%) and glycated hemoglobin (GLU) (P < 0.05), and Parvimonas micra was positively correlated with CRP (P < 0.05).}, } @article {pmid35754734, year = {2022}, author = {Proffitt, C and Bidkhori, G and Lee, S and Tebani, A and Mardinoglu, A and Uhlen, M and Moyes, DL and Shoaie, S}, title = {Genome-scale metabolic modelling of the human gut microbiome reveals changes in the glyoxylate and dicarboxylate metabolism in metabolic disorders.}, journal = {iScience}, volume = {25}, number = {7}, pages = {104513}, pmid = {35754734}, issn = {2589-0042}, abstract = {The human gut microbiome has been associated with metabolic disorders including obesity, type 2 diabetes, and atherosclerosis. Understanding the contribution of microbiome metabolic changes is important for elucidating the role of gut bacteria in regulating metabolism. We used available metagenomics data from these metabolic disorders, together with genome-scale metabolic modeling of key bacteria in the individual and community-level to investigate the mechanistic role of the gut microbiome in metabolic diseases. Modeling predicted increased levels of glutamate consumption along with the production of ammonia, arginine, and proline in gut bacteria common across the disorders. Abundance profiles and network-dependent analysis identified the enrichment of tartrate dehydrogenase in the disorders. Moreover, independent plasma metabolite levels showed associations between metabolites including proline and tyrosine and an increased tartrate metabolism in healthy obese individuals. We, therefore, propose that an increased tartrate metabolism could be a significant mediator of the microbiome metabolic changes in metabolic disorders.}, } @article {pmid35753694, year = {2022}, author = {Privitera, GF and Alaimo, S and Ferro, A and Pulvirenti, A}, title = {Virus finding tools: current solutions and limitations.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {4}, pages = {}, doi = {10.1093/bib/bbac235}, pmid = {35753694}, issn = {1477-4054}, mesh = {High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics ; *Viruses/genetics ; }, abstract = {MOTIVATION: The study of the Human Virome remains challenging nowadays. Viral metagenomics, through high-throughput sequencing data, is the best choice for virus discovery. The metagenomics approach is culture-independent and sequence-independent, helping search for either known or novel viruses. Though it is estimated that more than 40% of the viruses found in metagenomics analysis are not recognizable, we decided to analyze several tools to identify and discover viruses in RNA-seq samples.

RESULTS: We have analyzed eight Virus Tools for the identification of viruses in RNA-seq data. These tools were compared using a synthetic dataset of 30 viruses and a real one. Our analysis shows that no tool succeeds in recognizing all the viruses in the datasets. So we can conclude that each of these tools has pros and cons, and their choice depends on the application domain.

AVAILABILITY: Synthetic data used through the review and raw results of their analysis can be found at https://zenodo.org/record/6426147. FASTQ files of real data can be found in GEO (https://www.ncbi.nlm.nih.gov/gds) or ENA (https://www.ebi.ac.uk/ena/browser/home). Raw results of their analysis can be downloaded from https://zenodo.org/record/6425917.}, } @article {pmid35753210, year = {2022}, author = {Tsai, IJ}, title = {The teenage years of yeast population genomics - trace history, admixing and getting wilder.}, journal = {Current opinion in genetics & development}, volume = {75}, number = {}, pages = {101942}, doi = {10.1016/j.gde.2022.101942}, pmid = {35753210}, issn = {1879-0380}, mesh = {Biological Evolution ; *Metagenomics ; *Saccharomyces cerevisiae/genetics ; }, abstract = {Population genomics studies the evolutionary processes that shape intraspecies genetic variations. In this review, I explore the insights into yeast population genomics that have emerged from recent advances in sequencing. Genomes of the model Saccharomyces cerevisiae and many new yeast species from around the world are being used to address various aspects of population biology, including geographical origin, the level of introgression, domestication signatures, and outcrossing frequency. New long-read sequencing has enabled a greater capacity to quantify these variations at a finer resolution from complete de novo genomes at the population scale to phasing subgenomes of different origins. These resources provide a platform to dissect the relationship between phenotypes across environmental niches.}, } @article {pmid35752737, year = {2022}, author = {Jangid, A and Fukuda, S and Seki, M and Suzuki, Y and Taylor, TD and Ohno, H and Prakash, T}, title = {Gut microbiota alternation under the intestinal epithelium-specific knockout of mouse Piga gene.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {10812}, pmid = {35752737}, issn = {2045-2322}, mesh = {Animals ; *Escherichia coli Infections/microbiology ; *Escherichia coli O157 ; *Gastrointestinal Microbiome ; Intestinal Mucosa/microbiology ; Intestines/microbiology ; Mice ; }, abstract = {Crosstalk between the gut microbiota and intestinal epithelium shapes the gut environment and profoundly influences the intestinal immune homeostasis. Glycosylphosphatidylinositol anchored proteins (GPI - APs) contribute to a variety of gut-associated immune functions, including microbial surveillance and defense, and epithelial cell polarity. Properly polarised epithelial cells are essential for the establishment of the barrier function of gut epithelia. The Piga gene is one among seven genes that encode for an enzyme which is involved in the first step of GPI-anchor biosynthesis. This is the first study reporting a knockout of the intestinal epithelial cell-specific Piga gene (Piga-/-) and its association with the gut microbiota in mice using a whole metagenome shotgun-based sequencing approach. An overall reduced microbiota diversity has been observed in the Piga-/- group as compared to the control group (ANOVA p = 0.34). The taxonomic biomarkers, namely: Gammaproteobacteria (class), Enterobacterales (order), Enterobacteriaceae (family), Escherichia (genus), Proteus (genus) and Escherichia coli (species), increased more in the Piga-/- mice as compared to in the control group. Further, the pathogenic E. coli strains, namely E. coli O157:H7 str. EDL 933 (EHEC), E. coli CFT073 (UPEC) and E. coli 536 (UPEC), were found in the Piga-/- mice which also harbored virulence factor transporters. In addition, the taxa responsible for short chain fatty acid production were decreased in the Piga-/- group. The Piga-/- mice gut harbored an increased number of microbial functions responsible for the survival of pathogens in the inflamed gut environment. Our observations clearly indicate that the Piga-/- mice gut might have an overall enhancement in pathogenic behaviour and reduced capabilities beneficial to health.}, } @article {pmid35752638, year = {2022}, author = {Lemos, LN and de Carvalho, FM and Santos, FF and Valiatti, TB and Corsi, DC and de Oliveira Silveira, AC and Gerber, A and Guimarães, APC and de Oliveira Souza, C and Brasiliense, DM and Maia Castelo-Branco, DSC and Anzai, EK and Bessa-Neto, FO and de Melo, GM and de Souza, GH and Ferraz, LFC and de Nazaré Miranda Bahia, M and Mattos, MS and da Silva, RGB and Veiga, R and Simionatto, S and Monteiro, WAP and de Oliveira Lima, WA and Kiffer, CRV and Cayô, R and Gales, AC and de Vasconcelos, ATR}, title = {Large Scale Genome-Centric Metagenomic Data from the Gut Microbiome of Food-Producing Animals and Humans.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {366}, pmid = {35752638}, issn = {2052-4463}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; Cattle ; *Gastrointestinal Microbiome ; Humans ; *Metagenome ; Metagenomics ; Swine ; }, abstract = {The One Health concept is a global strategy to study the relationship between human and animal health and the transfer of pathogenic and non-pathogenic species between these systems. However, to the best of our knowledge, no data based on One Health genome-centric metagenomics are available in public repositories. Here, we present a dataset based on a pilot-study of 2,915 metagenome-assembled genomes (MAGs) of 107 samples from the human (N = 34), cattle (N = 28), swine (N = 15) and poultry (N = 30) gut microbiomes. Samples were collected from the five Brazilian geographical regions. Of the draft genomes, 1,273 were high-quality drafts (≥90% of completeness and ≤5% of contamination), and 1,642 were medium-quality drafts (≥50% of completeness and ≤10% of contamination). Taxonomic predictions were based on the alignment and concatenation of single-marker genes, and the most representative phyla were Bacteroidota, Firmicutes, and Proteobacteria. Many of these species represent potential pathogens that have already been described or potential new families, genera, and species with potential biotechnological applications. Analyses of this dataset will highlight discoveries about the ecology and functional role of pathogens and uncultivated Archaea and Bacteria from food-producing animals and humans. Furthermore, it also represents an opportunity to describe new species from underrepresented taxonomic groups.}, } @article {pmid35751943, year = {2022}, author = {Lee, SA and Kim, M and Esterhuizen, M and Le, VV and Kang, M and Ko, SR and Oh, HM and Kim, YJ and Ahn, CY}, title = {An acceleration of carotenoid production and growth of Haematococcus lacustris induced by host-microbiota network interaction.}, journal = {Microbiological research}, volume = {262}, number = {}, pages = {127097}, doi = {10.1016/j.micres.2022.127097}, pmid = {35751943}, issn = {1618-0623}, mesh = {Acceleration ; Bacteria/genetics ; Biomass ; Carotenoids ; *Chlorophyta ; *Microbiota ; }, abstract = {Haematococcus lacustris is a chlamydomonadalean with high biotechnological interest owing to its capacity to produce astaxanthin, a valuable secondary carotenoid with extraordinary antioxidation properties. However, its prolonged growth has limited its utility commercially. Thus, rapid growth to attain high densities of H. lacustris cells optimally producing astaxanthin is an essential biotechnological target to facilitate profitable commercialisation. Our study focused on characterising the bacterial communities associated with the alga's phycosphere by metagenomics. Subsequently, we altered the bacterial consortia in combined co-culture with key beneficial bacteria to optimise the growth of H. lacustris. The algal biomass increased by up to 2.1-fold in co-cultures, leading to a 1.6-fold increase in the astaxanthin yield. This study attempted to significantly improve the H. lacustris growth rate and biomass yield via Next-Generation Sequencing analysis and phycosphere bacterial augmentation, highlighting the possibility to overcome the hurdles associated with astaxanthin production by H. lacustris at a commercial scale.}, } @article {pmid35751933, year = {2022}, author = {Su, H and Hu, X and Xu, W and Xu, Y and Wen, G and Cao, Y}, title = {Metagenomic analysis of the abundances, diversity, and distribution of antibiotic resistance genes and their potential bacterial hosts in two types of shrimp-rearing farms in South China.}, journal = {Ecotoxicology and environmental safety}, volume = {241}, number = {}, pages = {113801}, doi = {10.1016/j.ecoenv.2022.113801}, pmid = {35751933}, issn = {1090-2414}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria ; China ; Crustacea ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Humans ; Water ; }, abstract = {Antibiotic resistance genes (ARGs) are attracting increasing concern worldwide. Many previous studies have investigated the occurrence and concentrations of ARGs in aquaculture. However, the sources of ARGs and the links with their potential bacterial hosts have not yet been explored. This study investigated the abundances and diversity of ARGs in two types of shrimp farms in South China through metagenomic sequencing. In total, 14 ARG types were detected. Tetracycline was the dominant ARG type. The abundances of ARGs in samples decreased in the order of duck feces > water source > sediment > shrimp gut > pond water. The samples from the duck-shrimp integrated farm contained 1.29-3.81-fold more abundant ARGs than those from the shrimp monoculture farm (p < 0.05). Several ARGs, that were most predominant in the duck feces samples, were also the most predominant in the shrimp gut samples from the duck-shrimp integrated farm. Redundancy analysis indicated that the abundances and distribution of ARGs formed three clusters: duck feces, water samples, and sediment and shrimp gut samples. The dominant genera in duck feces known as human pathogenic bacteria were potential hosts of ARGs, and were also dominant in the shrimp gut samples in the duck-shrimp integrated farm. Additionally, the abundances of dominant genera in the shrimp gut samples of the duck-shrimp integrated farm were 1.74-35.07-fold higher than those in the shrimp monoculture farm (p < 0.01). The duck-shrimp integrated farm had 3.36-fold and 4.94-fold higher abundances of ARGs and mobile genetic elements in the shrimp gut samples than those from the shrimp monoculture farm, respectively (p < 0.05). The results indicate that duck feces may be a crucial source of diverse and abundant ARGs spreading to reared shrimps in duck-shrimp integrated farms, posing a severe risk to public health.}, } @article {pmid35751094, year = {2022}, author = {Fritsch, DA and Jackson, MI and Wernimont, SM and Feld, GK and MacLeay, JM and Brejda, JJ and Cochrane, CY and Gross, KL}, title = {Microbiome function underpins the efficacy of a fiber-supplemented dietary intervention in dogs with chronic large bowel diarrhea.}, journal = {BMC veterinary research}, volume = {18}, number = {1}, pages = {245}, pmid = {35751094}, issn = {1746-6148}, mesh = {Animals ; Diarrhea/veterinary ; Diet/veterinary ; Dietary Fiber/therapeutic use ; *Dog Diseases/drug therapy ; Dogs ; Feces ; Indoles ; Inflammation/veterinary ; *Microbiota ; Prospective Studies ; }, abstract = {BACKGROUND: Chronic large bowel diarrhea is a common occurrence in pet dogs. While nutritional intervention is considered the primary therapy, the metabolic and gut microfloral effects of fiber and polyphenol-enriched therapeutic foods are poorly understood.

METHODS: This prospective clinical study enrolled 31 adult dogs from private veterinary practices with chronic, active large bowel diarrhea. Enrolled dogs received a complete and balanced dry therapeutic food containing a proprietary fiber bundle for 56 days. Metagenomic and metabolomic profiling were performed on fecal samples at Days 1, 2, 3, 14, 28, and 56; metabolomic analysis was conducted on serum samples taken at Days 1, 2, 3, 28, and 56.

RESULTS: The dietary intervention improved clinical signs and had a clear effect on the gut microfloral metabolic output of canines with chronic diarrhea, shifting gut metabolism from a predominantly proteolytic to saccharolytic fermentative state. Microbial metabolism of tryptophan to beneficial indole postbiotics and the conversion of plant-derived phenolics into bioavailable postbiotics were observed. The intervention altered the endocannabinoid, polyunsaturated fatty acid, and sphingolipid profiles, suggesting a modulation in gastrointestinal inflammation. Changes in membrane phospholipid and collagen signatures were indicative of improved gut function and possible alleviation of the pathophysiology related to chronic diarrhea.

CONCLUSIONS: In dogs with chronic diarrhea, feeding specific dietary fibers increased gut saccharolysis and bioavailable phenolic and indole-related compounds, while suppressing putrefaction. These changes were associated with improved markers of gut inflammation and stool quality.}, } @article {pmid35751084, year = {2022}, author = {Xiong, X and Rao, Y and Tu, X and Wang, Z and Gong, J and Yang, Y and Wu, H and Liu, X}, title = {Gut archaea associated with bacteria colonization and succession during piglet weaning transitions.}, journal = {BMC veterinary research}, volume = {18}, number = {1}, pages = {243}, pmid = {35751084}, issn = {1746-6148}, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; *Mucorales ; *Physical Conditioning, Animal ; Swine ; Weaning ; }, abstract = {BACKGROUND: Host-associated gut microbial communities are key players in shaping the fitness and health of animals. However, most current studies have focused on the gut bacteria, neglecting important gut fungal and archaeal components of these communities. Here, we investigated the gut fungi and archaea community composition in Large White piglets using shotgun metagenomic sequencing, and systematically evaluated how community composition association with gut microbiome, functional capacity, and serum metabolites varied across three weaning periods.

RESULTS: We found that Mucoromycota, Ascomycota and Basidiomycota were the most common fungi phyla and Euryarchaeota was the most common archaea phyla across individuals. We identified that Methanosarcina siciliae was the most significantly different archaea species among three weaning periods, while Parasitella parasitica, the only differential fungi species, was significantly and positively correlated with Methanosarcina siciliae enriched in day 28 group. The random forest analysis also identified Methanosarcina siciliae and Parasitella parasitica as weaning-biased archaea and fungi at the species level. Additionally, Methanosarcina siciliae was significantly correlated with P. copri and the shifts of functional capacities of the gut microbiome and several CAZymes in day 28 group. Furthermore, characteristic successional alterations in gut archaea, fungi, bacteria, and serum metabolites with each weaning step revealed a weaning transition coexpression network, e.g., Methanosarcina siciliae and P. copri were positively and significantly correlated with 15-HEPE, 8-O-Methyloblongine, and Troxilin B3.

CONCLUSION: Our findings provide a deep insight into the interactions among gut archaea, fungi, bacteria, and serum metabolites and will present a theoretical framework for understanding gut bacterial colonization and succession association with archaea during piglet weaning transitions.}, } @article {pmid35751044, year = {2022}, author = {Maeda, Y and Motooka, D and Kawasaki, T and Oki, H and Noda, Y and Adachi, Y and Niitsu, T and Okamoto, S and Tanaka, K and Fukushima, K and Amiya, S and Hara, R and Oguro-Igashira, E and Matsuki, T and Hirata, H and Takeda, Y and Kida, H and Kumanogoh, A and Nakamura, S and Takeda, K}, title = {Longitudinal alterations of the gut mycobiota and microbiota on COVID-19 severity.}, journal = {BMC infectious diseases}, volume = {22}, number = {1}, pages = {572}, pmid = {35751044}, issn = {1471-2334}, support = {20fk0108265//Japan Agency for Medical Research and Development/ ; 18gm1010005//AMED-CREST grants/ ; }, mesh = {*COVID-19 ; Enterococcus ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; SARS-CoV-2 ; }, abstract = {BACKGROUND: The impact of SARS-CoV-2 infection on the gut fungal (mycobiota) and bacterial (microbiota) communities has been elucidated individually. This study analyzed both gut mycobiota and microbiota and their correlation in the COVID-19 patients with severe and mild conditions and follow-up to monitor their alterations after recovery.

METHODS: We analyzed the gut mycobiota and microbiota by bacterial 16S and fungal ITS1 metagenomic sequencing of 40 severe patients, 38 mild patients, and 30 healthy individuals and reanalyzed those of 10 patients with severe COVID-19 approximately 6 months after discharge.

RESULTS: The mycobiota of the severe and mild groups showed lower diversity than the healthy group, and in some, characteristic patterns dominated by a single fungal species, Candida albicans, were detected. Lower microbial diversity in the severe group was observed, but no differences in its diversity or community structure were detected between the mild and healthy groups. The microbiota of the severe group was characterized by an increase in Enterococcus and Lactobacillus, and a decrease in Faecalibacterium and Bacteroides. The abundance of Candida was positively correlated with that of Enterococcus in patients with COVID-19. After the recovery of severe patients, alteration of the microbiota remained, but the mycobiota recovered its diversity comparable to that of mild and healthy groups.

CONCLUSION: In mild cases, the microbiota is stable during SARS-CoV-2 infection, but in severe cases, alterations persist for 6 months after recovery.}, } @article {pmid35751037, year = {2022}, author = {Li, J and Zhao, Q and Huang, JP and Jia, JY and Zhu, TF and Hong, T and Su, J}, title = {The functional microbiota of on- and off-year moso bamboo (Phyllostachys edulis) influences the development of the bamboo pest Pantana phyllostachysae.}, journal = {BMC plant biology}, volume = {22}, number = {1}, pages = {307}, pmid = {35751037}, issn = {1471-2229}, mesh = {Animals ; Gene Expression Regulation, Plant ; Larva ; *Microbiota ; *Moths ; Plant Leaves ; Poaceae ; }, abstract = {BACKGROUND: Development of Pantana phyllostachysae, a moso bamboo pest, is affected by its diet. Understanding the mechanism underlying the different insect-resistant capacities of on- and off-year moso bamboo fed by P. phyllostachysae is crucial for managing pest outbreaks. As microbes were proven to influence plant immunity, we compared gut microbial communities of P. phyllostachysae with different diets by metabarcoding sequencing. By using sterilization assay, microbes were removed from leaf surfaces, and thus we confirmed that microbes inhabiting moso bamboo leaves impact the weight of P. phyllostachysae larva. Furthermore, the gut microbial communities of P. phyllostachysae fed on on- and off-year bamboo leaves were compared, to identify the functional microbial communities that impact the interaction between bamboo leaves and P. phyllostachysae.

RESULTS: We found that species from orders Lactobacillales and Rickettsiales are most effective within functional microbiota. Functional prediction revealed that gut microbes of larva fed on on-year leaves were related to naphthalene degradation, while those fed on off-year leaves were related to biosynthesis of ansamycins, polyketide sugar unit biosynthesis, metabolism of xenobiotics, and tetracycline biosynthesis. Most functional microbes are beneficial to the development of larva that feed on on-year bamboo leaves, but damage the balance of intestinal microenvironment and immune systems of those larva that feed on off-year leaves.

CONCLUSIONS: This work developed an efficient strategy for microbiome research of Lepidopteran insects and provided insights into microbiota related to the interaction between host plants and P. phyllostachysae. We provided microbial candidates for the ecological control of P. phyllostachysae according to the function of effective microbiota.}, } @article {pmid35750913, year = {2022}, author = {Rout, AK and Dehury, B and Parida, PK and Sarkar, DJ and Behera, B and Das, BK and Rai, A and Behera, BK}, title = {Taxonomic profiling and functional gene annotation of microbial communities in sediment of river Ganga at Kanpur, India: insights from whole-genome metagenomics study.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {54}, pages = {82309-82323}, pmid = {35750913}, issn = {1614-7499}, mesh = {Rivers/chemistry ; Metagenomics ; Catalase ; Geologic Sediments/chemistry ; Molecular Sequence Annotation ; Xenobiotics ; *Microbiota ; Bacteria/genetics ; Nitrogen/analysis ; Hydrolases ; Plastics ; Methane ; Coloring Agents/analysis ; Chlorobenzenes/analysis ; Sulfur ; *Environmental Pollutants/analysis ; Benzoates/analysis ; Aminobenzoates/analysis ; Mixed Function Oxygenases ; }, abstract = {The perennial river Ganga is recognized as one of India's largest rivers of India, but due to continuous anthropogenic activities, the river's ecosystem is under threat. Next-generation sequencing technology has transformed metagenomics in the exploration of microbiome and their imperative function in diverse aquatic ecosystems. In this study, we have uncovered the structure of community microbiome and their functions in sediments of river Ganga at Kanpur, India, at three polluted stretches through a high-resolution metagenomics approach using Illumina HiSeq 2500. Among the microbes, bacteria dominate more than 82% in the three polluted sediment samples of river Ganga. Pseudomonadota (alpha, beta, and gamma) is the major phylum of bacteria that dominates in three sediment samples. Genes involved in degradation of xenobiotic compounds involving nitrotoluene, benzoate, aminobenzoate, chlorocyclohexane, and chlorobenzene were significantly enriched in the microbiome of polluted stretches. Pathway analysis using KEGG database revealed a higher abundance of genes involved in energy metabolism such as oxidative phosphorylation, nitrogen, methane, sulfur, and carbon fixation pathways in the sediment metagenome data from the river Ganga. A higher abundance of pollutant degrading enzymes like 4-hydroxybenzoate 3-monooxygenase, catalase-peroxidase, and altronate hydrolase in the polluted microbiome indicates their role in degradation of plastics and dyes. Overall, our study has provided bacterial diversity and their dynamics in community structure and function from polluted river microbiome, which is expected to open up better avenues for exploration of novel functional genes/enzymes with potential application in health and bioremediation.}, } @article {pmid35750322, year = {2022}, author = {Kelly, MS and Bunyavanich, S and Phipatanakul, W and Lai, PS}, title = {The Environmental Microbiome, Allergic Disease, and Asthma.}, journal = {The journal of allergy and clinical immunology. In practice}, volume = {10}, number = {9}, pages = {2206-2217.e1}, pmid = {35750322}, issn = {2213-2201}, support = {K23 ES023700/ES/NIEHS NIH HHS/United States ; R01 AI144119/AI/NIAID NIH HHS/United States ; }, mesh = {*Asthma/complications ; Environmental Exposure/adverse effects ; Humans ; *Hypersensitivity/epidemiology/etiology ; *Microbiota ; }, abstract = {The environmental microbiome represents the entirety of the microbes and their metabolites that we encounter in our environments. A growing body of evidence supports the role of the environmental microbiome in risk for and severity of allergic diseases and asthma. The environmental microbiome represents a ubiquitous, lifelong exposure to non-self antigens. During the critical window between birth and 1 year of life, interactions between our early immune system and the environmental microbiome have 2 consequences: our individual microbiome is populated by environmental microbes, and our immune system is trained regarding which antigens to tolerate. During this time, a diversity of exposures appears largely protective, dramatically decreasing the risk of developing allergic diseases and asthma. As we grow older, our interactions with the environmental microbiome change. While it continues to exert influence over the composition of the human microbiome, the environmental microbiome becomes increasingly a source for antigenic stimulation and infection. The same microbial exposure protective against disease development may exacerbate disease severity. Although much has been learned about the importance of the environmental microbiome in allergic disease, much more remains to be understood about these complicated interactions between our environment, our microbiome, our immune system, and disease.}, } @article {pmid35750287, year = {2023}, author = {Dong, C and Yang, Y and Wang, Y and Hu, X and Wang, Q and Gao, F and Sun, S and Liu, Q and Li, L and Liu, J and Tang, Y and Zhang, S and Wu, C and Zhu, H}, title = {Gut microbiota combined with metabolites reveals unique features of acute myocardial infarction patients different from stable coronary artery disease.}, journal = {Journal of advanced research}, volume = {46}, number = {}, pages = {101-112}, pmid = {35750287}, issn = {2090-1224}, mesh = {Humans ; *Coronary Artery Disease/metabolism/microbiology ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Myocardial Infarction ; Biomarkers ; }, abstract = {INTRODUCTION: Acute myocardial infarction (AMI) accounts for the majority of deaths caused by coronary artery disease (CAD). Early warning of AMI, especially for patients with stable coronary artery disease (sCAD), is urgently needed. Our previous study showed that alterations in the gut microbiota were correlated with CAD severity.

OBJECTIVES: Herein, we tried to discover accurate and convenient biomarkers for AMI by combination of gut microbiota and fecal/blood/urinary metabolomics.

METHODS: We recruited 190 volunteers including 93 sCAD patients, 49 AMI patients, and 48 subjects with normal coronary artery (NCA), and measured their blood biochemical parameters, 16S rRNA-based gut microbiota and NMR-based fecal/blood/urinary metabolites. We further selected 20 subjects from each group and analyzed their gut microbiota by whole-metagenome shotgun sequencing.

RESULTS: Multi-omic analyses revealed that AMI patients exhibited specific changes in gut microbiota and serum/urinary/fecal metabolites as compared to subjects with sCAD or NCA. Fourteen bacterial genera and 30 metabolites (11 in feces, 10 in blood, 9 in urine) were closely related to AMI phenotypes and could accurately distinguish AMI patients from sCAD patients. Some species belonging to Alistipes, Streptococcus, Ruminococcus, Lactobacillus and Faecalibacterium were effective to distinguish AMI from sCAD and their predictive ability was confirmed in an independent cohort of CAD patients. We further selected nine indicators including 4 bacterial genera, 3 fecal and 2 urinary metabolites as a noninvasive biomarker set which can distinguish AMI from sCAD with an AUC of 0.932.

CONCLUSION: Combination of gut microbiota and fecal/urinary metabolites provided a set of potential useful and noninvasive predictive biomarker for AMI from sCAD.}, } @article {pmid35750157, year = {2022}, author = {Isidro, J and Borges, V and Pinto, M and Sobral, D and Santos, JD and Nunes, A and Mixão, V and Ferreira, R and Santos, D and Duarte, S and Vieira, L and Borrego, MJ and Núncio, S and de Carvalho, IL and Pelerito, A and Cordeiro, R and Gomes, JP}, title = {Phylogenomic characterization and signs of microevolution in the 2022 multi-country outbreak of monkeypox virus.}, journal = {Nature medicine}, volume = {28}, number = {8}, pages = {1569-1572}, pmid = {35750157}, issn = {1546-170X}, mesh = {Disease Outbreaks ; Humans ; *Mpox (monkeypox)/epidemiology/genetics ; *Monkeypox virus/genetics ; Phylogeny ; }, abstract = {The largest monkeypox virus (MPXV) outbreak described so far in non-endemic countries was identified in May 2022 (refs. [1-6]). In this study, shotgun metagenomics allowed the rapid reconstruction and phylogenomic characterization of the first MPXV outbreak genome sequences, showing that this MPXV belongs to clade 3 and that the outbreak most likely has a single origin. Although 2022 MPXV (lineage B.1) clustered with 2018-2019 cases linked to an endemic country, it segregates in a divergent phylogenetic branch, likely reflecting continuous accelerated evolution. An in-depth mutational analysis suggests the action of host APOBEC3 in viral evolution as well as signs of potential MPXV human adaptation in ongoing microevolution. Our findings also indicate that genome sequencing may provide resolution to track the spread and transmission of this presumably slow-evolving double-stranded DNA virus.}, } @article {pmid35750126, year = {2022}, author = {Huang, Y and Zou, K and Qing, T and Feng, B and Zhang, P}, title = {Metagenomics and metatranscriptomics analyses of antibiotic synthesis in activated sludge.}, journal = {Environmental research}, volume = {213}, number = {}, pages = {113741}, doi = {10.1016/j.envres.2022.113741}, pmid = {35750126}, issn = {1096-0953}, mesh = {Aminoglycosides ; Anti-Bacterial Agents ; Genes, Bacterial ; Penicillins ; *Sewage ; Streptomycin ; *Wastewater ; beta-Lactams ; }, abstract = {The generic of antibiotics is considered to be a main reason for the generation of antibiotic resistance genes (ARGs) in wastewater treatment plants (WWTPs). However, little has been reported about the antibiotic biosynthesis by activated sludge. In this study, the distribution and expression of antibiotic biosynthetic genes (ABGs) in the floc sludge and biofilm from two WWTPs were deciphered using metagenomics and metatranscriptomics. The results showed that 2% of the community were in general well-linked to antibiotic production, indicating a non-negligible antibiotic synthetic ability of WWTPs. 93 ABGs belonging to 26 antibiotics were determined, among which aminoglycosides, β-lactams, ansamycins, peptides, macrolides were majority. The relative abundances of detected ABGs had a large interval, ranging from 0.000006% to 0.042%. The predominant antibiotic types of synthetic genes with higher relative expression levels were monobactams, penicillin & cephalosporins and streptomycin, primarily belonging to β-lactams and aminoglycosides. The hypothetical synthetic pathways of streptomycin synthesis and penicillin & cephalosporin synthesis were proposed. And the coexistence of ABGs and ARGs for these two antibiotics was also pronounced in activated sludge from meta-omics data. These findings for the first time demonstrated the antibiotic synthetic potential in activated sludges, revealing new sources of antibiotics and resistance genes in WWTPs, and thereby aggravating environmental pollution.}, } @article {pmid35749534, year = {2022}, author = {Gaio, D and DeMaere, MZ and Anantanawat, K and Eamens, GJ and Falconer, L and Chapman, TA and Djordjevic, S and Darling, AE}, title = {Phylogenetic diversity analysis of shotgun metagenomic reads describes gut microbiome development and treatment effects in the post-weaned pig.}, journal = {PloS one}, volume = {17}, number = {6}, pages = {e0270372}, pmid = {35749534}, issn = {1932-6203}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Dysbiosis ; Female ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Phylogeny ; *Probiotics ; Swine ; Weaning ; }, abstract = {Intensive farming practices can increase exposure of animals to infectious agents against which antibiotics are used. Orally administered antibiotics are well known to cause dysbiosis. To counteract dysbiotic effects, numerous studies in the past two decades sought to understand whether probiotics are a valid tool to help re-establish a healthy gut microbial community after antibiotic treatment. Although dysbiotic effects of antibiotics are well investigated, little is known about the effects of intramuscular antibiotic treatment on the gut microbiome and a few studies attempted to study treatment effects using phylogenetic diversity analysis techniques. In this study we sought to determine the effects of two probiotic- and one intramuscularly administered antibiotic treatment on the developing gut microbiome of post-weaning piglets between their 3rd and 9th week of life. Shotgun metagenomic sequences from over 800 faecal time-series samples derived from 126 post-weaning piglets and 42 sows were analysed in a phylogenetic framework. Differences between individual hosts such as breed, litter, and age, were found to be important contributors to variation in the community composition. Host age was the dominant factor in shaping the gut microbiota of piglets after weaning. The post-weaning pig gut microbiome appeared to follow a highly structured developmental program with characteristic post-weaning changes that can distinguish hosts that were born as little as two days apart in the second month of life. Treatment effects of the antibiotic and probiotic treatments were found but were subtle and included a higher representation of Mollicutes associated with intramuscular antibiotic treatment, and an increase of Lactobacillus associated with probiotic treatment. The discovery of correlations between experimental factors and microbial community composition is more commonly addressed with OTU-based methods and rarely analysed via phylogenetic diversity measures. The latter method, although less intuitive than the former, suffers less from library size normalization biases, and it proved to be instrumental in this study for the discovery of correlations between microbiome composition and host-, and treatment factors.}, } @article {pmid35749527, year = {2022}, author = {Apiwatsiri, P and Pupa, P and Sirichokchatchawan, W and Sawaswong, V and Nimsamer, P and Payungporn, S and Hampson, DJ and Prapasarakul, N}, title = {Metagenomic analysis of the gut microbiota in piglets either challenged or not with enterotoxigenic Escherichia coli reveals beneficial effects of probiotics on microbiome composition, resistome, digestive function and oxidative stress responses.}, journal = {PloS one}, volume = {17}, number = {6}, pages = {e0269959}, pmid = {35749527}, issn = {1932-6203}, mesh = {Animals ; *Enterotoxigenic Escherichia coli ; *Escherichia coli Infections/prevention & control/veterinary ; *Gastrointestinal Microbiome ; *Microbiota ; Oxidative Stress ; *Probiotics/pharmacology ; Swine ; *Swine Diseases ; Weaning ; }, abstract = {This study used metagenomic analysis to investigate the gut microbiota and resistome in piglets that were or were not challenged with enterotoxigenic Escherichia coli (ETEC) and had or had not received dietary supplementation with microencapsulated probiotics. The 72 piglets belonged to six groups that were either non-ETEC challenged (groups 1-3) or ETEC challenged (receiving 5ml of 109 CFU/ml pathogenic ETEC strain L3.2 one week following weaning at three weeks of age: groups 4-6). On five occasions at 2, 5, 8, 11, and 14 days of piglet age, groups 2 and 5 were supplemented with 109 CFU/ml of multi-strain probiotics (Lactiplantibacillus plantarum strains 22F and 25F, and Pediococcus acidilactici 72N) while group 4 received 109 CFU/ml of P. acidilactici 72N. Group 3 received 300mg/kg chlortetracycline in the weaner diet to mimic commercial conditions. Rectal faecal samples were obtained for metagenomic and resistome analysis at 2 days of age, and at 12 hours and 14 days after the timing of post-weaning challenge with ETEC. The piglets were all euthanized at 42 days of age. The piglets in groups 2 and 5 were enriched with several desirable microbial families, including Lactobacillaceae, Lachnospiraceae and Ruminococcaceae, while piglets in group 3 had increases in members of the Bacteroidaceae family and exhibited an increase in tetW and tetQ genes. Group 5 had less copper and multi-biocide resistance. Mobile genetic elements IncQ1 and IncX4 were the most prevalent replicons in antibiotic-fed piglets. Only groups 6 and 3 had the integrase gene (intl) class 2 and 3 detected, respectively. The insertion sequence (IS) 1380 was prevalent in group 3. IS3 and IS30, which are connected to dietary intake, were overrepresented in group 5. Furthermore, only group 5 showed genes associated with detoxification, with enrichment of genes associated with oxidative stress, glucose metabolism, and amino acid metabolism compared to the other groups. Overall, metagenomic analysis showed that employing a multi-strain probiotic could transform the gut microbiota, reduce the resistome, and boost genes associated with food metabolism.}, } @article {pmid35749419, year = {2022}, author = {Claro, IM and Romano, CM and Candido, DDS and Lima, EL and Lindoso, JAL and Ramundo, MS and Moreira, FRR and Barra, LAC and Borges, LMS and Medeiros, LA and Tomishige, MYS and Moutinho, T and Silva, AJDD and Rodrigues, CCM and Azevedo, LCF and Villas-Boas, LS and Silva, CAMD and Coletti, TM and Manuli, ER and O'Toole, A and Quick, J and Loman, N and Rambaut, A and Faria, NR and Figueiredo-Mello, C and Sabino, EC}, title = {Shotgun metagenomic sequencing of the first case of monkeypox virus in Brazil, 2022.}, journal = {Revista do Instituto de Medicina Tropical de Sao Paulo}, volume = {64}, number = {}, pages = {e48}, pmid = {35749419}, issn = {1678-9946}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; MR/S019510/1/MRC_/Medical Research Council/United Kingdom ; MR/S035362/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Brazil ; Humans ; Metagenomics ; *Mpox (monkeypox)/diagnosis/epidemiology ; *Monkeypox virus/genetics ; }, abstract = {Monkeypox virus (MPXV), a zoonotic virus endemic to the African continent, has been reported in 33 non-endemic countries since May 2022. We report an almost complete genome of the first confirmed case of MPXV in Brazil. Shotgun metagenomic sequencing was completed in 18 hours, from DNA extraction to consensus sequence generation.}, } @article {pmid35746779, year = {2022}, author = {Aaron, J and van Zyl, LJ and Dicks, LMT}, title = {Isolation and Characterization of Lytic Proteus Virus 309.}, journal = {Viruses}, volume = {14}, number = {6}, pages = {}, pmid = {35746779}, issn = {1999-4915}, mesh = {*Bacteriophages ; Biofilms ; Humans ; *Phage Therapy/methods ; Proteus mirabilis ; South Africa ; *Urinary Tract Infections ; }, abstract = {Proteus mirabilis is frequently associated with complicated urinary tract infections (UTIs) and is the main cause of catheter-associated urinary tract infections (CAUTIs). Treatment of such infections is complicated and challenging due to the biofilm forming abilities of P. mirabilis. If neglected or mistreated, infections may lead to life-threating conditions such as cystitis, pyelonephritis, kidney failure, and bacteremia that may progress to urosepsis. Treatment with antibiotics, especially in cases of recurring and persistent infections, leads to the development of resistant strains. Recent insights into phage therapy and using phages to coat catheters have been evaluated with many studies showing promising results. Here, we describe a highly lytic bacteriophage, Proteus_virus_309 (41,740 bp), isolated from a wastewater treatment facility in Cape Town, South Africa. According to guidelines of the International Committee on Taxonomy of Viruses (ICTV), bacteriophage 309 is a species within the genus Novosibovirus. Similar to most members of the genus, bacteriophage 309 is strain-specific and lyse P. mirabilis in less than 20 min.}, } @article {pmid35746738, year = {2022}, author = {Zakotnik, S and Knap, N and Bogovič, P and Zorec, TM and Poljak, M and Strle, F and Avšič-Županc, T and Korva, M}, title = {Complete Genome Sequencing of Tick-Borne Encephalitis Virus Directly from Clinical Samples: Comparison of Shotgun Metagenomic and Targeted Amplicon-Based Sequencing.}, journal = {Viruses}, volume = {14}, number = {6}, pages = {}, pmid = {35746738}, issn = {1999-4915}, mesh = {Base Sequence ; *Encephalitis Viruses, Tick-Borne/genetics ; *Encephalitis, Tick-Borne/diagnosis ; Genes, Viral ; Humans ; Whole Genome Sequencing ; }, abstract = {The clinical presentation of tick-borne encephalitis virus (TBEV) infection varies from asymptomatic to severe meningoencephalitis or meningoencephalomyelitis. The TBEV subtype has been suggested as one of the most important risk factors for disease severity, but TBEV genetic characterization is difficult. Infection is usually diagnosed in the post-viremic phase, and so relevant clinical samples of TBEV are extremely rare and, when present, are associated with low viral loads. To date, only two complete TBEV genomes sequenced directly from patient clinical samples are publicly available. The aim of this study was to develop novel protocols for the direct sequencing of the TBEV genome, enabling studies of viral genetic determinants that influence disease severity. We developed a novel oligonucleotide primer scheme for amplification of the complete TBEV genome. The primer set was tested on 21 clinical samples with various viral loads and collected over a 15-year period using the two most common sequencing platforms. The amplicon-based strategy was compared to direct shotgun sequencing. Using the novel primer set, we successfully obtained nearly complete TBEV genomes (>90% of genome) from all clinical samples, including those with extremely low viral loads. Comparison of consensus sequences of the TBEV genome generated using the novel amplicon-based strategy and shotgun sequencing showed no difference. We conclude that the novel primer set is a powerful tool for future studies on genetic determinants of TBEV that influence disease severity and will lead to a better understanding of TBE pathogenesis.}, } @article {pmid35746732, year = {2022}, author = {Mastriani, E and Bienes, KM and Wong, G and Berthet, N}, title = {PIMGAVir and Vir-MinION: Two Viral Metagenomic Pipelines for Complete Baseline Analysis of 2nd and 3rd Generation Data.}, journal = {Viruses}, volume = {14}, number = {6}, pages = {}, pmid = {35746732}, issn = {1999-4915}, mesh = {High-Throughput Nucleotide Sequencing/methods ; Metagenome ; *Metagenomics/methods ; *Nanopores ; Sequence Analysis, DNA/methods ; Software ; }, abstract = {The taxonomic classification of viral sequences is frequently used for the rapid identification of pathogens, which is a key point for when a viral outbreak occurs. Both Oxford Nanopore Technologies (ONT) MinION and the Illumina (NGS) technology provide efficient methods to detect viral pathogens. Despite the availability of many strategies and software, matching them can be a very tedious and time-consuming task. As a result, we developed PIMGAVir and Vir-MinION, two metagenomics pipelines that automatically provide the user with a complete baseline analysis. The PIMGAVir and Vir-MinION pipelines work on 2nd and 3rd generation data, respectively, and provide the user with a taxonomic classification of the reads through three strategies: assembly-based, read-based, and clustering-based. The pipelines supply the scientist with comprehensive results in graphical and textual format for future analyses. Finally, the pipelines equip the user with a stand-alone platform with dedicated and various viral databases, which is a requirement for working in field conditions without internet connection.}, } @article {pmid35744767, year = {2022}, author = {Velasco-Rodríguez, Ó and Fil, M and Heggeset, TMB and Degnes, KF and Becerro-Recio, D and Kolsaková, K and Haugen, T and Jønsson, M and Toral-Martínez, M and García-Estrada, C and Sola-Landa, A and Josefsen, KD and Sletta, H and Barreiro, C}, title = {Characterization of Microbial Diversity in Decayed Wood from a Spanish Forest: An Environmental Source of Industrially Relevant Microorganisms.}, journal = {Microorganisms}, volume = {10}, number = {6}, pages = {}, pmid = {35744767}, issn = {2076-2607}, support = {PCIN-2016-081//Spanish Ministry of Economy and Competitiveness/ ; 271062/O70//Research Council of Norway/ ; }, abstract = {Rotting wood is inhabited by a large diversity of bacteria, fungi, and insects with complex environmental relationships. The aim of this work was to study the composition of the microbiota (bacteria and fungi) in decaying wood from a northwest Spanish forest as a source of industrially relevant microorganisms. The analyzed forest is situated in a well-defined biogeographic area combining Mediterranean and temperate macrobioclimates. Bacterial diversity, determined by metagenome analyses, was higher than fungal heterogeneity. However, a total of 194 different cultivable bacterial isolates (mainly Bacillaceae, Streptomycetaceae, Paenibacillaceae, and Microbacteriaceae) were obtained, in contrast to 343 fungal strains (mainly Aspergillaceae, Hypocreaceae, and Coniochaetaceae). Isolates traditionally known as secondary metabolite producers, such as Actinobacteria and members of the Penicillium genus, were screened for their antimicrobial activity by the detection of antibiotic biosynthetic clusters and competitive bioassays against fungi involved in wood decay. In addition, the ability of Penicillium isolates to degrade cellulose and release ferulic acid from wood was also examined. These results present decaying wood as an ecologically rich niche and a promising source of biotechnologically interesting microorganisms.}, } @article {pmid35744749, year = {2022}, author = {Baltazar-Díaz, TA and González-Hernández, LA and Aldana-Ledesma, JM and Peña-Rodríguez, M and Vega-Magaña, AN and Zepeda-Morales, ASM and López-Roa, RI and Del Toro-Arreola, S and Martínez-López, E and Salazar-Montes, AM and Bueno-Topete, MR}, title = {Escherichia/Shigella, SCFAs, and Metabolic Pathways-The Triad That Orchestrates Intestinal Dysbiosis in Patients with Decompensated Alcoholic Cirrhosis from Western Mexico.}, journal = {Microorganisms}, volume = {10}, number = {6}, pages = {}, pmid = {35744749}, issn = {2076-2607}, support = {P3E 260428//University of Guadalajara/ ; PIN 2021-II//University of Guadalajara/ ; }, abstract = {Gut microbiota undergoes profound alterations in alcohol cirrhosis. Microbiota-derived products, e.g., short chain fatty acids (SCFA), regulate the homeostasis of the gut-liver axis. The objective was to evaluate the composition and functions of the intestinal microbiota in patients with alcohol-decompensated cirrhosis. Fecal samples of 18 patients and 18 healthy controls (HC) were obtained. Microbial composition was characterized by 16S rRNA amplicon sequencing, SCFA quantification was performed by gas chromatography (GC), and metagenomic predictive profiles were analyzed by PICRUSt2. Gut microbiota in the cirrhosis group revealed a significant increase in the pathogenic/pathobionts genera Escherichia/Shigella and Prevotella, a decrease in beneficial bacteria, such as Blautia, Faecalibacterium, and a decreased α-diversity (p < 0.001) compared to HC. Fecal SCFA concentrations were significantly reduced in the cirrhosis group (p < 0.001). PICRUSt2 analysis indicated a decrease in acetyl-CoA fermentation to butyrate, as well as an increase in pathways related to antibiotics resistance, and aromatic amino acid biosynthesis. These metabolic pathways have been poorly described in the progression of alcohol-related decompensated cirrhosis. The gut microbiota of these patients possesses a pathogenic/inflammatory environment; therefore, future strategies to balance intestinal dysbiosis should be implemented. These findings are described for the first time in the population of western Mexico.}, } @article {pmid35744735, year = {2022}, author = {Senn, S and Bhattacharyya, S and Presley, G and Taylor, AE and Nash, B and Enke, RA and Barnard-Kubow, KB and Ford, J and Jasinski, B and Badalova, Y}, title = {The Functional Biogeography of eDNA Metacommunities in the Post-Fire Landscape of the Angeles National Forest.}, journal = {Microorganisms}, volume = {10}, number = {6}, pages = {}, pmid = {35744735}, issn = {2076-2607}, abstract = {Wildfires have continued to increase in frequency and severity in Southern California due in part to climate change. To gain a further understanding of microbial soil communities’ response to fire and functions that may enhance post-wildfire resilience, soil fungal and bacterial microbiomes were studied from different wildfire areas in the Gold Creek Preserve within the Angeles National Forest using 16S, FITS, 18S, 12S, PITS, and COI amplicon sequencing. Sequencing datasets from December 2020 and June 2021 samplings were analyzed using QIIME2, ranacapa, stats, vcd, EZBioCloud, and mixomics. Significant differences were found among bacterial and fungal taxa associated with different fire areas in the Gold Creek Preserve. There was evidence of seasonal shifts in the alpha diversity of the bacterial communities. In the sparse partial least squares analysis, there were strong associations (r > 0.8) between longitude, elevation, and a defined cluster of Amplicon Sequence Variants (ASVs). The Chi-square test revealed differences in fungi−bacteria (F:B) proportions between different trails (p = 2 × 10−16). sPLS results focused on a cluster of Green Trail samples with high elevation and longitude. Analysis revealed the cluster included the post-fire pioneer fungi Pyronema and Tremella. Chlorellales algae and possibly pathogenic Fusarium sequences were elevated. Bacterivorous Corallococcus, which secretes antimicrobials, and bacterivorous flagellate Spumella were associated with the cluster. There was functional redundancy in clusters that were differently composed but shared similar ecological functions. These results implied a set of traits for post-fire resiliency. These included photo-autotrophy, mineralization of pyrolyzed organic matter and aromatic/oily compounds, potential pathogenicity and parasitism, antimicrobials, and N-metabolism.}, } @article {pmid35744720, year = {2022}, author = {Ledormand, P and Desmasures, N and Midoux, C and Rué, O and Dalmasso, M}, title = {Investigation of the Phageome and Prophages in French Cider, a Fermented Beverage.}, journal = {Microorganisms}, volume = {10}, number = {6}, pages = {}, pmid = {35744720}, issn = {2076-2607}, support = {PhD Grant MENRT//Ministère de l'Enseignement Supérieur, de la Recherche et de l'Innovation (France)/ ; }, abstract = {Phageomes are known to play a key role in the functioning of their associated microbial communities. The phageomes of fermented foods have not been studied thoroughly in fermented foods yet, and even less in fermented beverages. Two approaches were employed to investigate the presence of phages in cider, a fermented beverage made from apple, during a fermentation process of two cider tanks, one from an industrial producer and one from a hand-crafted producer. The phageome (free lytic phages) was explored in cider samples with several methodological developments for total phage DNA extraction, along with single phage isolation. Concentration methods, such as tangential flow filtration, flocculation and classical phage concentration methods, were employed and tested to extract free phage particles from cider. This part of the work revealed a very low occurrence of free lytic phage particles in cider. In parallel, a prophage investigation during the fermentation process was also performed using a metagenomic approach on the total bacterial genomic DNA. Prophages in bacterial metagenomes in the two cider tanks seemed also to occur in low abundance, as a total of 1174 putative prophages were identified in the two tanks overtime, and only two complete prophages were revealed. Prophage occurrence was greater at the industrial producer than at the hand-crafted producer, and different dynamics of prophage trends were also observed during fermentation. This is the first report dealing with the investigation of the phageome and of prophages throughout a fermentation process of a fermented beverage.}, } @article {pmid35744716, year = {2022}, author = {Murray, B and Ertekin, E and Dailey, M and Soulier, NT and Shen, G and Bryant, DA and Perez-Fernandez, C and DiRuggiero, J}, title = {Adaptation of Cyanobacteria to the Endolithic Light Spectrum in Hyper-Arid Deserts.}, journal = {Microorganisms}, volume = {10}, number = {6}, pages = {}, pmid = {35744716}, issn = {2076-2607}, support = {NNX15AP18G/NASA/NASA/United States ; DEB1556574//National Science Foundation/ ; MCB-1613022//National Science Foundation/ ; }, abstract = {In hyper-arid deserts, endolithic microbial communities survive in the pore spaces and cracks of rocks, an environment that enhances water retention and filters UV radiation. The rock colonization zone is enriched in far-red light (FRL) and depleted in visible light. This poses a challenge to cyanobacteria, which are the primary producers of endolithic communities. Many species of cyanobacteria are capable of Far-Red-Light Photoacclimation (FaRLiP), a process in which FRL induces the synthesis of specialized chlorophylls and remodeling of the photosynthetic apparatus, providing the ability to grow in FRL. While FaRLiP has been reported in cyanobacteria from various low-light environments, our understanding of light adaptations for endolithic cyanobacteria remains limited. Here, we demonstrated that endolithic Chroococcidiopsis isolates from deserts around the world synthesize chlorophyll f, an FRL-specialized chlorophyll when FRL is the sole light source. The metagenome-assembled genomes of these isolates encoded chlorophyll f synthase and all the genes required to implement the FaRLiP response. We also present evidence of FRL-induced changes to the major light-harvesting complexes of a Chroococcidiopsis isolate. These findings indicate that endolithic cyanobacteria from hyper-arid deserts use FRL photoacclimation as an adaptation to the unique light transmission spectrum of their rocky habitat.}, } @article {pmid35744684, year = {2022}, author = {Tang, L and Gao, Y and Yan, L and Jia, H and Chu, H and Ma, X and He, L and Wang, X and Li, K and Hu, D and Zhang, D}, title = {Comparative Analysis of Microbiome Metagenomics in Reintroduced Wild Horses and Resident Asiatic Wild Asses in the Gobi Desert Steppe.}, journal = {Microorganisms}, volume = {10}, number = {6}, pages = {}, pmid = {35744684}, issn = {2076-2607}, support = {2019JQ03018//Beijing Forestry University Outstanding Young Talent Cultivation Project/ ; 31872964//National Science Foundation of China/ ; }, abstract = {The gut microbiome offers important ecological benefits to the host; however, our understanding of the functional microbiome in relation to wildlife adaptation, especially for translocated endangered species, is lagging. In this study, we adopted a comparative metagenomics approach to test whether the microbiome diverges for translocated and resident species with different adaptive potentials. The composition and function of the microbiome of sympatric Przewalski's horses and Asiatic wild asses in desert steppe were compared for the first time using the metagenomic shotgun sequencing approach. We identified a significant difference in microbiome composition regarding the microbes present and their relative abundances, while the diversity of microbe species was similar. Furthermore, the functional profile seemed to converge between the two hosts, with genes related to core metabolism function tending to be more abundant in wild asses. Our results indicate that sympatric wild equids differ in their microbial composition while harboring a stable microbial functional core, which may enable them to survive in challenging habitats. A higher abundance of beneficial taxa, such as Akkermansia, and genes related to metabolism pathways and enzymes, such as lignin degradation, may contribute to more diverse diet choices and larger home ranges of wild asses.}, } @article {pmid35744659, year = {2022}, author = {Tsakeng, CUB and Tanekou, TTM and Soffack, SF and Tirados, I and Noutchih, C and Njiokou, F and Bigoga, JD and Wondji, CS}, title = {Assessing the Tsetse Fly Microbiome Composition and the Potential Association of Some Bacteria Taxa with Trypanosome Establishment.}, journal = {Microorganisms}, volume = {10}, number = {6}, pages = {}, pmid = {35744659}, issn = {2076-2607}, support = {/WT_/Wellcome Trust/United Kingdom ; MR/P027873/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {The tsetse flies, biological vectors of African trypanosomes, harbour a variety of bacteria involved in their vector competence that may help in developing novel vector control tools. This study provides an inventory of tsetse bacterial communities in Cameroon and explores their possible associations with trypanosome establishment in Glossina palpalis palpalis. High throughput sequencing of the V3-V4 hypervariable region of the bacterial 16S rRNA gene, with subsequent metagenomic, multivariate, and association analyses, were used to investigate the levels and patterns of microbial diversity in four tsetse species. Overall, 31 bacterial genera and four phyla were identified. The primary symbiont Wigglesworthia dominated almost all the samples, with an overall relative abundance of 47.29%, and seemed to be replaced by Serratia or Burkholderia in some G. tachinoides flies. Globally, significant differences were observed in the microbiome diversity and composition among tsetse species and between teneral and non-teneral flies, or between flies displaying or not displaying mature trypanosome infections. In addition, differential abundance testing showed some OTUs, or some bacteria taxa, associated with trypanosome maturation in tsetse flies. These bacteria could be further investigated for an understanding of their mechanism of action and alternatively, transformed and used to block trypanosome development in tsetse flies.}, } @article {pmid35744627, year = {2022}, author = {Zhou, M and Liu, Z and Wang, J and Zhao, Y and Hu, B}, title = {Sphingomonas Relies on Chemotaxis to Degrade Polycyclic Aromatic Hydrocarbons and Maintain Dominance in Coking Sites.}, journal = {Microorganisms}, volume = {10}, number = {6}, pages = {}, pmid = {35744627}, issn = {2076-2607}, support = {[2018YFC1800702]//National Key Research and Development Program of China/ ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are organic pollutants widely present in industrial sites. Microbial degradation is an effective method of removing PAHs. The identification of microorganisms that have important ecological functions at the site is of great significance for PAH removal. We collected soil samples at three depths in the range of 0-100 cm at 70-day intervals at the coking site and explored the degradation of PAHs. We combined molecular ecology networking, metagenomics, and genome assembly to search for microorganisms that persist, dominate, and affect the microbial community construction in the degradation process and analyzed their adaptation strategies. The results showed that 15.78 mg/kg of PAHs naturally decayed, and 13.33 mg/kg of PAHs migrated from 30-100 cm to 0-30 cm in the soil. Sphingomonas, which occupied a niche advantage, was both the core and keystone microorganism, and its spatial distribution pattern and temporal change dynamics were consistent with those of PAHs. We assembled the genome of Sphingomonas sp., revealing its multiple potential for degrading PAHs and other pollutants. Additionally, flagellar assembly and bacterial chemotaxis genes ranked high in the assembled genome of Sphingomonas sp., which might help it obtain a competitive advantage in the soil. The findings underscored the strategy of Sphingomonas to maintain dominance, enriched the understanding of PAH-degrading microorganisms in site soil, and provided references for the remediation of PAHs.}, } @article {pmid35744617, year = {2022}, author = {García-Mato, E and Martínez-Lamas, L and Álvarez-Fernández, M and Varela-Aneiros, I and Diniz-Freitas, M and Limeres-Posse, J and Diz-Dios, P}, title = {Molecular Detection of Streptococcus downii sp. nov. from Dental Plaque Samples from Patients with Down Syndrome and Non-Syndromic Individuals.}, journal = {Microorganisms}, volume = {10}, number = {6}, pages = {}, pmid = {35744617}, issn = {2076-2607}, abstract = {A new bacterial species has recently been identified in the dental plaque of an adolescent with Down syndrome. The species is known as Streptococcus downii sp. nov. (abbreviated to S. downii), and it inhibits the growth of S. mutans and certain periodontal pathogens. The aim of this study was to determine the distribution of S. downii in the oral cavity of individuals with Down syndrome. Methods: A specific polymerase chain reaction for the operon of bacteriocin (class IIb lactobin A/cerein 7B family) was designed to detect S. downii in individuals with Down syndrome (n = 200) and in the general population (n = 100). We also compared the whole genome of S. downii and the regions related to its bacteriocins against 127 metagenomes of supragingival plaque of the "Human Microbiome Project". Results: We detected the specific gene of the S. downii bacteriocin in an individual with Down syndrome (Cq, 34.52; GE/μL, 13.0) and in an individual of the non-syndromic control group (Cq, 34.78 Cq; GE/μL, 4.93). The prevalence of S. downii was ≤1% both in Down syndrome and in the general population, which did not allow for clinical-microbiological correlations to be established. This result was confirmed by detecting only one metagenome with an ANIm with approximately 95% homology and with 100% homology with ORFs that code class IIb lactobiocin A/cerein 7B bacteriocins among the 127 metagenomes of the "Human Microbiome Project" tested. Conclusions: The detection rate of S. downii in the supragingival dental plaque was very low, both in the Down syndrome individuals and in the non-syndromic controls. A clinical-microbiological correlation could therefore not be established.}, } @article {pmid35743947, year = {2022}, author = {Doytchinov, VV and Dimov, SG}, title = {Microbial Community Composition of the Antarctic Ecosystems: Review of the Bacteria, Fungi, and Archaea Identified through an NGS-Based Metagenomics Approach.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {6}, pages = {}, pmid = {35743947}, issn = {2075-1729}, support = {70-25-72 from 03.08.2021//NATIONAL CENTER FOR POLAR STUDIES - SOFIA UNIVERSITY "ST. KLIMENT OHRIDSKI"/ ; }, abstract = {Antarctica represents a unique environment, both due to the extreme meteorological and geological conditions that govern it and the relative isolation from human influences that have kept its environment largely undisturbed. However, recent trends in climate change dictate an unavoidable change in the global biodiversity as a whole, and pristine environments, such as Antarctica, allow us to study and monitor more closely the effects of the human impact. Additionally, due to its inaccessibility, Antarctica contains a plethora of yet uncultured and unidentified microorganisms with great potential for useful biological activities and production of metabolites, such as novel antibiotics, proteins, pigments, etc. In recent years, amplicon-based next-generation sequencing (NGS) has allowed for a fast and thorough examination of microbial communities to accelerate the efforts of unknown species identification. For these reasons, in this review, we present an overview of the archaea, bacteria, and fungi present on the Antarctic continent and the surrounding area (maritime Antarctica, sub-Antarctica, Southern Sea, etc.) that have recently been identified using amplicon-based NGS methods.}, } @article {pmid35743847, year = {2022}, author = {Tsukamoto, Y and Kakegawa, T}, title = {Mineralogical and Genomic Constraints on the Origin of Microbial Mn Oxide Formation in Complexed Microbial Community at the Terrestrial Hot Spring.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {6}, pages = {}, pmid = {35743847}, issn = {2075-1729}, abstract = {Manganese (Mn) oxides are widespread on the surface environments of the modern Earth. The role of microbial activities in the formation of Mn oxides has been discussed for several decades. However, the mechanisms of microbial Mn oxidation, and its role in complex microbial communities in natural environments, remain uncertain. Here, we report the geochemical, mineralogical, and metagenomic evidence for biogenic Mn oxides, found in Japanese hot spring sinters. The low crystallinity of Mn oxides, and their spatial associations with organic matter, support the biogenic origin of Mn oxides. Specific multicopper oxidases (MCOs), which are considered Mn-oxidizing enzymes, were identified using metagenomic analyses. Nanoscale nuggets of copper sulfides were, also, discovered in the organic matter in Mn-rich sinters. A part of these copper sulfides most likely represents traces of MCOs, and this is the first report of traces of Mn-oxidizing enzyme in geological samples. Metagenomic analyses, surprisingly, indicated a close association of Mn oxides, not only in aerobic but also in anaerobic microbial communities. These new findings offer the unique and unified positions of Mn oxides, with roles that have not been ignored, to sustain anaerobic microbial communities in hot spring environments.}, } @article {pmid35742929, year = {2022}, author = {Fulci, V}, title = {Meta'omics: Challenges and Applications.}, journal = {International journal of molecular sciences}, volume = {23}, number = {12}, pages = {}, pmid = {35742929}, issn = {1422-0067}, mesh = {*Metagenomics ; }, abstract = {Metagenomics and metatranscriptomics are emerging as key disciplines towards a fully understanding the complex relationships between living organisms belonging to different kingdoms [...].}, } @article {pmid35742602, year = {2022}, author = {Wyszkowska, J and Borowik, A and Kucharski, J}, title = {The Role of Grass Compost and Zea Mays in Alleviating Toxic Effects of Tetracycline on the Soil Bacteria Community.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {12}, pages = {}, pmid = {35742602}, issn = {1660-4601}, mesh = {Animals ; Anti-Bacterial Agents/toxicity ; Bacteria/genetics ; *Composting ; Oxidoreductases ; Poaceae ; Soil ; Soil Microbiology ; *Soil Pollutants/analysis/toxicity ; Tetracycline/toxicity ; Zea mays ; }, abstract = {Given their common use for disease treatment in humans, and particularly in animals, antibiotics pose an exceptionally serious threat to the soil environment. This study aimed to determine the response of soil bacteria and oxidoreductases to a tetracycline (Tc) contamination, and to establish the usability of grass compost (G) and Zea mays (Zm) in mitigating adverse Tc effects on selected microbial properties of the soil. The scope of microbiological analyses included determinations of bacteria with the conventional culture method and new-generation sequencing method (NGS). Activities of soil dehydrogenases and catalase were determined as well. Tc was found to reduce counts of organotrophic bacteria and actinobacteria in the soils as well as the activity of soil oxidoreductases. Soil fertilization with grass compost (G) and Zea mays (Zm) cultivation was found to alleviate the adverse effects of tetracycline on the mentioned group of bacteria and activity of oxidoreductases. The metagenomic analysis demonstrated that the bacteria belonging to Acidiobacteria and Proteobacteria phyla were found to prevail in the soil samples. The study results recommend soil fertilization with G and Zm cultivation as successful measures in the bioremediation of tetracycline-contaminated soils and indicate the usability of the so-called core bacteria in the bioaugmentation of such soils.}, } @article {pmid35741032, year = {2022}, author = {Islam, SMS and Ryu, HM and Sohn, S}, title = {Tetragenococcus halophilus Alleviates Intestinal Inflammation in Mice by Altering Gut Microbiota and Regulating Dendritic Cell Activation via CD83.}, journal = {Cells}, volume = {11}, number = {12}, pages = {}, pmid = {35741032}, issn = {2073-4409}, mesh = {Animals ; Anti-Inflammatory Agents/pharmacology ; *Colitis/drug therapy ; *Colitis, Ulcerative/drug therapy ; Dendritic Cells ; Dextran Sulfate/pharmacology ; Enterococcaceae ; *Gastrointestinal Microbiome ; Inflammation ; Mice ; Mice, Inbred C57BL ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Ulcerative colitis (UC) is one of the major subtypes of inflammatory bowel disease with unknown etiology. Probiotics have recently been introduced as a treatment for UC. Tetragenococcus halophilus (T. halophilus) is a lactic acid-producing bacterium that survives in environments with high salt concentrations, though little is known about its immunomodulatory function as a probiotic. The purpose of this study is to determine whether T. halophilus exerts an anti-inflammatory effect on intestinal inflammation in mice. Colitis was induced in C57BL/6J mice by feeding 4% DSS in drinking water for 7 days. T. halophilus was orally administered with DSS. Anti-inflammatory functions were subsequently evaluated by flow cytometry, qRT-PCT, and ELISA. Gut microbial composition was analyzed by 16S rRNA metagenomic analysis. DSS-induced colitis mice treated with T. halophilus showed less weight loss and significantly suppressed colonic shortening compared to DSS-induced colitis mice. T. halophilus significantly reduced the frequency of the dendritic cell activation molecule CD83 in peripheral blood leukocytes and intestinal epithelial lymphocytes. Frequencies of CD8+NK1.1+ cells decreased in mice with colitis after T. halophilus treatment and IL-1β levels were also reduced. Alteration of gut microbiota was observed in mice with colitis after administration of T. halophilus. These results suggest T. halophilus is effective in alleviating DSS-induced colitis in mice by altering immune regulation and gut microbiome compositions.}, } @article {pmid35739766, year = {2022}, author = {Yang, Y and Li, T and Liu, P and Li, H and Hu, F}, title = {The formation of specific bacterial communities contributes to the enrichment of antibiotic resistance genes in the soil plastisphere.}, journal = {Journal of hazardous materials}, volume = {436}, number = {}, pages = {129247}, doi = {10.1016/j.jhazmat.2022.129247}, pmid = {35739766}, issn = {1873-3336}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; *Microbiota/genetics ; Microplastics ; Plastics ; Polyethylene/pharmacology ; *Soil ; }, abstract = {Soil serves as a major reservoir of both antibiotic resistance genes (ARGs) and microplastics. However, the characteristics of the antibiotic resistome in the soil plastisphere remain largely unknown. In this study, we used metagenomic approaches to reveal the changing patterns of ARGs and the bacterial community and their associations in response to three types of microplastics (light density polyethylene, LDPE; polypropylene, PP; polystyrene, PS) using particles 550 µm or 75 µm in diameter. The total ARG abundances significantly increased in the plastisphere and varied across plastic types. The LDPE plastisphere had the highest ARG total abundance and lowest Shannon diversity index, indicating that this plastic had the most severe negative impact on soil bacterial diversity. The PP plastisphere contained higher relative abundances of the pathogenic bacteria Acinetobacter johnsonii and Escherichia coli, demonstrating the higher pathogenic risk of the microbial communities enriched in the plastisphere. Specifically, multidrug resistance genes (ceoB and MuxB) co-existed with more than four microbial taxa, increasing the potential risk of ARG spread in pathogenic bacteria. These findings implied that the plastisphere acts as a hotspot for acquiring and spreading antibiotic resistance and may have long-term negative effects on the soil ecosystem and human health.}, } @article {pmid35739665, year = {2022}, author = {Murphy, CWM and Davis, GB and Rayner, JL and Walsh, T and Bastow, TP and Butler, AP and Puzon, GJ and Morgan, MJ}, title = {The role of predicted chemotactic and hydrocarbon degrading taxa in natural source zone depletion at a legacy petroleum hydrocarbon site.}, journal = {Journal of hazardous materials}, volume = {430}, number = {}, pages = {128482}, doi = {10.1016/j.jhazmat.2022.128482}, pmid = {35739665}, issn = {1873-3336}, mesh = {Biodegradation, Environmental ; Humans ; Hydrocarbons/metabolism ; Naphthalenes ; *Petroleum/analysis ; *Petroleum Pollution/analysis ; }, abstract = {Petroleum hydrocarbon contamination is a global problem which can cause long-term environmental damage and impacts water security. Natural source zone depletion (NSZD) is the natural degradation of such contaminants. Chemotaxis is an aspect of NSZD which is not fully understood, but one that grants microorganisms the ability to alter their motion in response to a chemical concentration gradient potentially enhancing petroleum NSZD mass removal rates. This study investigates the distribution of potentially chemotactic and hydrocarbon degrading microbes (CD) across the water table of a legacy petroleum hydrocarbon site near Perth, Western Australia in areas impacted by crude oil, diesel and jet fuel. Core samples were recovered and analysed for hydrocarbon contamination using gas chromatography. Predictive metagenomic profiling was undertaken to infer functionality using a combination of 16 S rRNA sequencing and PICRUSt2 analysis. Naphthalene contamination was found to significantly increase the occurrence of potential CD microbes, including members of the Comamonadaceae and Geobacteraceae families, which may enhance NSZD. Further work to explore and define this link is important for reliable estimation of biodegradation of petroleum hydrocarbon fuels. Furthermore, the outcomes suggest that the chemotactic parameter within existing NSZD models should be reviewed to accommodate CD accumulation in areas of naphthalene contamination, thereby providing a more accurate quantification of risk from petroleum impacts in subsurface environments, and the scale of risk mitigation due to NSZD.}, } @article {pmid35739659, year = {2022}, author = {Li, YJ and Chuang, CH and Cheng, WC and Chen, SH and Chen, WL and Lin, YJ and Lin, CY and Shih, YH}, title = {A metagenomics study of hexabromocyclododecane degradation with a soil microbial community.}, journal = {Journal of hazardous materials}, volume = {430}, number = {}, pages = {128465}, doi = {10.1016/j.jhazmat.2022.128465}, pmid = {35739659}, issn = {1873-3336}, mesh = {Humans ; *Hydrocarbons, Brominated/analysis ; Metagenomics ; *Microbiota ; Soil ; *Soil Pollutants ; }, abstract = {Hexabromocyclododecanes (HBCDs) are globally prevalent and persistent organic pollutants (POPs) listed by the Stockholm Convention in 2013. They have been detected in many environmental media from waterbodies to Plantae and even in the human body. Due to their highly bioaccumulative characterization, they pose an urgent public health issue. Here, we demonstrate that the indigenous microbial community in the agricultural soil in Taiwan could decompose HBCDs with no additional carbon source incentive. The degradation kinetics reached 0.173 day[-1] after the first treatment and 0.104 day[-1] after second exposure. With additional C-sources, the rate constants decreased to 0.054-0.097 day[-1]. The hydroxylic debromination metabolites and ring cleavage long-chain alkane metabolites were identified to support the potential metabolic pathways utilized by the soil microbial communities. The metagenome established by Nanopore sequencing showed significant compositional alteration in the soil microbial community after the HBCD treatment. After ranking, comparing relative abundances, and performing network analyses, several novel bacterial taxa were identified to contribute to HBCD biotransformation, including Herbaspirillum, Sphingomonas, Brevundimonas, Azospirillum, Caulobacter, and Microvirga, through halogenated / aromatic compound degradation, glutathione-S-transferase, and hydrolase activity. We present a compelling and applicable approach combining metagenomics research, degradation kinetics, and metabolomics strategies, which allowed us to decipher the natural attenuation and remediation mechanisms of HBCDs.}, } @article {pmid35739345, year = {2022}, author = {Sumithra, TG and Sharma, SRK and Gayathri, S and Ebeneezar, S and Reshma, KJ and Anikuttan, KK and Narasimapallavan, GI and Rameshkumar, P and Sakthivel, M and Prabu, DL and Tamilmani, G and Vijayagopal, P and Gopalakrishnan, A}, title = {Comparative evaluation of fish larval preservation methods on microbiome profiles to aid in metagenomics research.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {12}, pages = {4719-4735}, pmid = {35739345}, issn = {1432-0614}, support = {BT/AAQ/3/SP29267/2018 dated 11/05/2020.//Department of Biotechnology, Ministry of Science and Technology, Government of India/ ; }, mesh = {Animals ; Ethanol ; Fishes ; Larva ; Metagenome ; *Metagenomics/methods ; *Microbiota/genetics ; Reproducibility of Results ; }, abstract = {Applications of microbiome research through metagenomics promise to generate microbiome manipulation strategies for improved larval survival in aquaculture. However, existing lacunae on the effects of sample preservation methods in metagenome profiles hinder the successful application of this technique. In this context, four preservation methods were scrutinized to identify reliable methods for fish larval microbiome research. The results showed that a total of ten metagenomics metrics, including DNA yield, taxonomic and functional microbiome profiles, and diversity measures, were significantly (P < 0.05) influenced by the preservation method. Activity ranking based on the performance and reproducibility showed that three methods, namely immediate direct freezing, room temperature preservation in absolute ethanol, and preservation at - 20 °C in lysis, storage, and transportation buffer, could be recommended for larval microbiome research. Furthermore, as there was an apparent deviation of the microbiome profiles of ethanol preserved samples at room temperature, the other methods are preferred. Detailed analysis showed that this deviation was due to the bias towards Vibrionales and Rhodobacterales. The microbial taxa responsible for the dissimilarity across different methods were identified. Altogether, the paper sheds light on the preservation protocols of fish larval microbiome research for the first time. The results can help in cross-comparison of future and past larval microbiome studies. Furthermore, this is the first report on the activity ranking of preservation methods based on metagenomics metrics. Apart from methodological perspectives, the paper provides for the first time certain insights into larval microbial profiles of Rachycentron canadum, a potential marine aquaculture species. KEY POINTS: • First report on effects of preservation methods on fish larval microbiome profiles. • First report on activity ranking of preservation methods based on metagenomics metrics. • Storage methods influenced DNA yield, taxonomic and functional microbiome profiles.}, } @article {pmid35739297, year = {2022}, author = {Lockwood, S and Greening, C and Baltar, F and Morales, SE}, title = {Global and seasonal variation of marine phosphonate metabolism.}, journal = {The ISME journal}, volume = {16}, number = {9}, pages = {2198-2212}, pmid = {35739297}, issn = {1751-7370}, mesh = {Archaea/genetics/metabolism ; *Bacteria/genetics/metabolism ; Mediterranean Sea ; *Organophosphonates/metabolism ; Seasons ; }, abstract = {Marine microbial communities rely on dissolved organic phosphorus (DOP) remineralisation to meet phosphorus (P) requirements. We extensively surveyed the genomic and metagenomic distribution of genes directing phosphonate biosynthesis, substrate-specific catabolism of 2-aminoethylphosphonate (2-AEP, the most abundant phosphonate in the marine environment), and broad-specificity catabolism of phosphonates by the C-P lyase (including methylphosphonate, a major source of methane). We developed comprehensive enzyme databases by curating publicly available sequences and then screened metagenomes from TARA Oceans and Munida Microbial Observatory Time Series (MOTS) to assess spatial and seasonal variation in phosphonate metabolism pathways. Phosphonate cycling genes were encoded in diverse gene clusters by 35 marine bacterial and archaeal classes. More than 65% of marine phosphonate cycling genes mapped to Proteobacteria with production demonstrating wider taxonomic diversity than catabolism. Hydrolysis of 2-AEP was the dominant phosphonate catabolism strategy, enabling microbes to assimilate carbon and nitrogen alongside P. Genes for broad-specificity catabolism by the C-P lyase were far less widespread, though enriched in the extremely P-deplete environment of the Mediterranean Sea. Phosphonate cycling genes were abundant in marine metagenomes, particularly from the mesopelagic zone and winter sampling dates. Disparity between prevalence of substrate-specific and broad-specificity catabolism may be due to higher resource expenditure from the cell to build and retain the C-P lyase. This study is the most comprehensive metagenomic survey of marine microbial phosphonate cycling to date and provides curated databases for 14 genes involved in phosphonate cycling.}, } @article {pmid35738384, year = {2022}, author = {Gosai, HB and Panseriya, HZ and Patel, PG and Patel, AC and Shankar, A and Varjani, S and Dave, BP}, title = {Exploring bacterial communities through metagenomics during bioremediation of polycyclic aromatic hydrocarbons from contaminated sediments.}, journal = {The Science of the total environment}, volume = {842}, number = {}, pages = {156794}, doi = {10.1016/j.scitotenv.2022.156794}, pmid = {35738384}, issn = {1879-1026}, mesh = {Bacteria/metabolism ; Biodegradation, Environmental ; Humans ; Metagenomics ; *Polycyclic Aromatic Hydrocarbons/metabolism ; Soil Microbiology ; *Soil Pollutants/metabolism ; }, abstract = {The goal of this study was to evaluate the degradation effectiveness of PAHs degrading bacteria at the mesocosm level, including Stenotrophomonas maltophilia (SC), mixed culture (MC), and enriched native microflora (EC) at the mesocosm level. Maximum degradation was found in the mesocosm MC (26.67 %), followed by SC (25.08 %) and EC (18.25 %) after 60 days. Thus, mixed culture and Stenotrophomonas maltophilia could be a game changer in the PAHs bioremediation at the chronically contaminated sites. MiSeq sequencing has revealed dominancy of γ-Proteobacteria, α-Proteobacteria, β-Proteobacteria at class level and Sphingomonadales, oceanospirillales, Rhodothermales at Order level. Families Alcanivoracaceae, Alteromonadaceae, Nocardiaceae, Rhodospirillaceae and genus Stenotrophomonas, Alcanivorax, Methylophaga, Fluviicola and Rhodoplanes were considerably increased which play key role in the PAHs degradation. Dominant bacterial communities have revealed resilience community to enable potential PAHs degradation process in all the mesocosms. To the best our knowledge this is the first ever attempt in PAHs biodegradation study conducted at the mesocosm level mimicking natural environmental conditions. Consequently, this study could be a benchmark against which future progress studies for the policy makers and stakeholders to design appropriate bioremediation study for the historically PAHs polluted contaminate sites.}, } @article {pmid35737523, year = {2022}, author = {Javaid, N and Olwagen, C and Nzenze, S and Hawkins, P and Gladstone, R and McGee, L and Breiman, RF and Bentley, SD and Madhi, SA and Lo, S}, title = {Population genomics of pneumococcal carriage in South Africa following the introduction of the 13-valent pneumococcal conjugate vaccine (PCV13) immunization.}, journal = {Microbial genomics}, volume = {8}, number = {6}, pages = {}, pmid = {35737523}, issn = {2057-5858}, support = {/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Carrier State/epidemiology ; Child ; Child, Preschool ; Humans ; Immunization ; *Metagenomics ; Nasopharynx ; South Africa/epidemiology ; *Streptococcus pneumoniae/genetics ; Vaccines, Conjugate ; }, abstract = {Streptococcus pneumoniae is a major human pathogen responsible for over 317000 deaths in children <5 years of age with the burden of the disease being highest in low- and middle-income countries including South Africa. Following the introduction of the 7-valent and 13-valent pneumococcal conjugate vaccine (PCV) in South Africa in 2009 and 2011, respectively, a decrease in both invasive pneumococcal infections and asymptomatic carriage of vaccine-type pneumococci were reported. In this study, we described the changing epidemiology of the pneumococcal carriage population in South Africa, by sequencing the genomes of 1825 isolates collected between 2009 and 2013. Using these genomic data, we reported the changes in serotypes, Global Pneumococcal Sequence Clusters (GPSCs), and antibiotic resistance before and after the introduction of PCV13. The pneumococcal carriage population in South Africa has a high level of diversity, comprising of 126 GPSCs and 49 serotypes. Of the ten most prevalent GPSCs detected, six were predominantly found in Africa (GPSC22, GPSC21, GPSC17, GPSC33, GPSC34 and GPSC52). We found a significant decrease in PCV7 serotypes (19F, 6B, 23F and 14) and an increase in non-vaccine serotypes (NVT) (16F, 34, 35B and 11A) among children <2 years of age. The increase in NVTs was driven by pneumococcal lineages GPSC33, GPSC34, GPSC5 and GPSC22. Overall, a decrease in antibiotic resistance for 11 antimicrobials was detected in the PCV13 era. Further, we reported a higher resistance prevalence among vaccine types (VTs), as compared to NVTs; however, an increase in penicillin resistance among NVT was observed between the PCV7 and PCV13 eras. The carriage isolates from South Africa predominantly belonged to pneumococcal lineages, which are endemic to Africa. While the introduction of PCV resulted in an overall reduction of resistance in pneumococcal carriage isolates, an increase in penicillin resistance among NVTs was detected in children aged between 3 and 5 years, driven by the expansion of penicillin-resistant clones associated with NVTs in the PCV13 era.}, } @article {pmid35737135, year = {2022}, author = {Ali, S and Xie, J and Zada, S and Hu, Z and Zhang, Y and Cai, R and Wang, H}, title = {Bacterial community structure and bacterial isolates having antimicrobial potential in shrimp pond aquaculture.}, journal = {AMB Express}, volume = {12}, number = {1}, pages = {82}, pmid = {35737135}, issn = {2191-0855}, support = {GML2019ZD0606//Key Special Project for Introduced Talents Team of Southern Marine Science and Engineering Guangdong Laboratory (Guangzhou)/ ; 2020LKSFG07A//2020 Li Ka Shing Foundation (LKSF) Cross-Disciplinary Research Grant/ ; }, abstract = {Diseases outbreaks in pond aquaculture have resulted in huge losses to the aquaculture industry. The emergence of non-antimicrobial and environment friendly agents (probiotics) is the potential consideration for the healthy shrimp aquaculture. The present study was aimed to compare the bacterial community compositions in shrimp ponds and surrounding seawater, as well as isolate probiotic bacteria from the shrimp ponds. Based on the high-throughput of 16S rRNA gene sequencing, all sequences were assigned to 3584 unique operational taxonomic units (OTUs) at 97% similarity levels, which were affiliated with 24 phyla, 54 classes, 235 families, and 367 genera. The 10 most abundant phyla were Bacteroidota, Proteobacteria, Actinobacteriota, Planctomycetota, Cyanobacteria, Chloroflexi, Firmicutes, Desulfobacterota, Patescibacteria and Verrucomicrobiota. Notably, the alpha diversity (Shannon diversity) of shrimp ponds was significantly differences (P < 0.05) with that of surrounding seawater. There were 2498 and 791 unique OTUs in shrimp ponds and surrounding seawater, respectively. A total of 15 isolates were obtained in the culturable bacterial diversity, and the antibacterial activities were recorded for potential probiotic bacterial isolates against different tested bacterial isolates including pathogenic bacteria. An isolate Hallobacillus marinus HMALI004 showed strong inhibitory effects against three pathogenic bacteria, Vibrio cholerae CECT 514, non AHPND V. parahaemolyticus BCRC12959 and AHPND V. parahaemolyticus PD-2. The isolates Algophigus sanaruensis AGALI005, Algoriphagus taiwanensis ATALI009 and Bacillus aequororis BAALI008 were also identified as potential probiotics strains.}, } @article {pmid35736664, year = {2022}, author = {Shi, Y and Yang, J and Qi, Y and Xu, J and Shi, Y and Shi, T and Liu, C and Ma, X}, title = {Detection of Bartonella vinsonii subsp. berkhoffii in an HIV patient using metagenomic Next-Generation Sequencing.}, journal = {Emerging microbes & infections}, volume = {11}, number = {1}, pages = {1764-1767}, pmid = {35736664}, issn = {2222-1751}, mesh = {*Angiomatosis, Bacillary/diagnosis/microbiology ; *Bartonella/genetics ; *Bartonella Infections/diagnosis/microbiology ; *HIV Infections/complications ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; }, abstract = {Bartonella species are fastidious, aerobic bacteria that are transmitted by blood-sucking arthropods. Bartonella spp. are responsible for cat scratch disease, Carrion's disease, bacillary angiomatosis and trench fever. On the other hand, Bartonella vinsonii is rarely reported in the literature and there exist a few reports of systemic infection caused by Bartonella vinsonii in patients with acquired immunodeficiency syndrome. A 31-year-old male (diagnosed with AIDS six years ago) had persistent fever and ulceration in the right knee. The elevated levels of inflammatory markers suggested an infectious aetiology. Despite the negative findings of blood culture, metagenomic Next-Generation Sequencing of plasma detected Bartonella vinsonii. The polymerase chain reaction of whole blood and Sanger sequencing confirmed the mNGS findings. Immunohistochemical staining had later suggested bacillary angiomatosis, which was consistent with Bartonella infection. Following antibiotic treatment, the ulcers subsided significantly, but a high fever persisted. The patient died due to sudden respiratory failure.}, } @article {pmid35736470, year = {2022}, author = {Deutsch, L and Debevec, T and Millet, GP and Osredkar, D and Opara, S and Šket, R and Murovec, B and Mramor, M and Plavec, J and Stres, B}, title = {Urine and Fecal [1]H-NMR Metabolomes Differ Significantly between Pre-Term and Full-Term Born Physically Fit Healthy Adult Males.}, journal = {Metabolites}, volume = {12}, number = {6}, pages = {}, pmid = {35736470}, issn = {2218-1989}, support = {research project J3-7536//Slovenian Research Agency/ ; grant no. P1-0242//Slovenian Research Agency/ ; Grant No-TP20140088//Ljubljana University Medical Centre/ ; MR+ (SRA R#51867)//Slovenian Research Agency/ ; grant no. P2-0095//Slovenian Research Agency/ ; }, abstract = {Preterm birth (before 37 weeks gestation) accounts for ~10% of births worldwide and remains one of the leading causes of death in children under 5 years of age. Preterm born adults have been consistently shown to be at an increased risk for chronic disorders including cardiovascular, endocrine/metabolic, respiratory, renal, neurologic, and psychiatric disorders that result in increased death risk. Oxidative stress was shown to be an important risk factor for hypertension, metabolic syndrome and lung disease (reduced pulmonary function, long-term obstructive pulmonary disease, respiratory infections, and sleep disturbances). The aim of this study was to explore the differences between preterm and full-term male participants' levels of urine and fecal proton nuclear magnetic resonance ([1]H-NMR) metabolomes, during rest and exercise in normoxia and hypoxia and to assess general differences in human gut-microbiomes through metagenomics at the level of taxonomy, diversity, functional genes, enzymatic reactions, metabolic pathways and predicted gut metabolites. Significant differences existed between the two groups based on the analysis of [1]H-NMR urine and fecal metabolomes and their respective metabolic pathways, enabling the elucidation of a complex set of microbiome related metabolic biomarkers, supporting the idea of distinct host-microbiome interactions between the two groups and enabling the efficient classification of samples; however, this could not be directed to specific taxonomic characteristics.}, } @article {pmid35736432, year = {2022}, author = {Katsaounou, K and Nicolaou, E and Vogazianos, P and Brown, C and Stavrou, M and Teloni, S and Hatzis, P and Agapiou, A and Fragkou, E and Tsiaoussis, G and Potamitis, G and Zaravinos, A and Andreou, C and Antoniades, A and Shiammas, C and Apidianakis, Y}, title = {Colon Cancer: From Epidemiology to Prevention.}, journal = {Metabolites}, volume = {12}, number = {6}, pages = {}, pmid = {35736432}, issn = {2218-1989}, support = {EXCELLENCE/1216/0523//Research and Innovation Foundation/ ; }, abstract = {Colorectal cancer (CRC) is one of the most prevalent cancers affecting humans, with a complex genetic and environmental aetiology. Unlike cancers with known environmental, heritable, or sex-linked causes, sporadic CRC is hard to foresee and has no molecular biomarkers of risk in clinical use. One in twenty CRC cases presents with an established heritable component. The remaining cases are sporadic and associated with partially obscure genetic, epigenetic, regenerative, microbiological, dietary, and lifestyle factors. To tackle this complexity, we should improve the practice of colonoscopy, which is recommended uniformly beyond a certain age, to include an assessment of biomarkers indicative of individual CRC risk. Ideally, such biomarkers will be causal to the disease and potentially modifiable upon dietary or therapeutic interventions. Multi-omics analysis, including transcriptional, epigenetic as well as metagenomic, and metabolomic profiles, are urgently required to provide data for risk analyses. The aim of this article is to provide a perspective on the multifactorial derailment of homeostasis leading to the initiation of CRC, which may be explored via multi-omics and Gut-on-Chip analysis to identify much-needed predictive biomarkers.}, } @article {pmid35736002, year = {2022}, author = {Kim, KH and Park, D and Jia, B and Baek, JH and Hahn, Y and Jeon, CO}, title = {Identification and Characterization of Major Bile Acid 7α-Dehydroxylating Bacteria in the Human Gut.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0045522}, pmid = {35736002}, issn = {2379-5077}, mesh = {Humans ; *Bile Acids and Salts/metabolism ; Phylogeny ; *Clostridium/genetics ; Bacteria/genetics ; }, abstract = {The metabolism of bile acids (BAs) by gut bacteria plays an important role in human health. This study identified and characterized 7α-dehydroxylating bacteria, which are majorly responsible for converting primary BAs to secondary BAs, in the human gut and investigated their association with human disease. Six 7α-dehydratase (BaiE) clusters were identified from human gut metagenomes through sequence similarity network and genome neighborhood network analyses. Abundance analyses of gut metagenomes and metatranscriptomes identified a cluster of bacteria (cluster 1) harboring baiE genes that may be key 7α-dehydroxylating bacteria in the human gut. The baiE gene abundance of cluster 1 was significantly and positively correlated with the ratio of secondary BAs to primary BAs. Furthermore, the baiE gene abundances of cluster 1 were significantly negatively correlated with inflammatory bowel disease, including Crohn's disease and ulcerative colitis, as well as advanced nonalcoholic fatty liver disease, liver cirrhosis, and ankylosing spondylitis. Phylogenetic and metagenome-assembled genome analyses showed that the 7α-dehydroxylating bacterial clade of cluster 1 was affiliated with the family Oscillospiraceae and may demonstrate efficient BA dehydroxylation ability by harboring both a complete bai operon, for proteins which produce secondary BAs from primary BAs, and a gene for bile salt hydrolase, which deconjugates BAs, in the human gut. IMPORTANCE In this study, we identified a key 7α-dehydroxylating bacterial group predicted to be largely responsible for converting primary bile acids (BAs) to secondary BAs in the human gut through sequence similarity network, genome neighborhood network, and gene abundance analyses using human gut metagenomes. The key bacterial group was phylogenetically quite different from known 7α-dehydroxylating bacteria, and their abundance was highly correlated with the occurrence of diverse diseases associated with bile acid 7α-dehydroxylation. In addition, we characterized the metabolic features of the key bacterial group using their metagenome-assembled genomes. This approach is useful to identify and characterize key gut bacteria highly associated with human health and diseases.}, } @article {pmid35734579, year = {2022}, author = {Duan, Z and Gao, Y and Liu, B and Sun, B and Li, S and Wang, C and Liu, D and Wang, K and Zhang, Y and Lou, Z and Xie, L and Xie, F}, title = {The Application Value of Metagenomic and Whole-Genome Capture Next-Generation Sequencing in the Diagnosis and Epidemiological Analysis of Psittacosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {872899}, pmid = {35734579}, issn = {2235-2988}, mesh = {High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; Phylogeny ; *Psittacosis/diagnosis/epidemiology ; Retrospective Studies ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: To evaluate the value of metagenomic next-generation sequencing (mNGS) for the early diagnosis of psittacosis, and to investigate its epidemiology by whole-genome capture.

METHODS: Twenty-one bronchoalveolar lavage fluid (BALF) and blood samples of 16 psittacosis patients from multiple centers during August 2019 to September 2021 were analyzed retrospectively. mNGS with normal datasets (10 M 75-bp single-end reads after sequencing) and larger datasets (30 M 150-bp paired-end reads after sequencing) as well as quantitative real-time polymerase chain reaction (qPCR) were used to detect the pathogen. Also, whole-genome capture of Chlamydophila psittaci was applied to draw the phylogenetic tree.

RESULTS: mNGS successfully detected the pathogen in all 16 cases (100%), while qPCR was positive only in 5 out of 10 cases (50%), indicating a significantly higher sensitivity of mNGS than qPCR (p < 0.01). BALF-mNGS performed better than blood-mNGS (16/16 versus 3/5, p < 0.05). In addition, larger datasets (the read counts have tripled, and the base number was 12-fold larger compared to clinical mNGS with a normal dataset) of mNGS showed significantly increased contents of human DNA (p < 0.05) and decreased reads per million of the pathogen, suggesting no improvement. Whole-genome capture results of five samples (>60% coverage and >1 depth) were used to construct the phylogenetic tree.

CONCLUSION: Significant advantages of mNGS with normal datasets were demonstrated in early diagnosing psittacosis. It is the first study to use whole-genome capture to analyze C. psittaci epidemiological information.}, } @article {pmid35734371, year = {2022}, author = {Tu, P and Chi, L and Bian, X and Gao, B and Ru, H and Lu, K}, title = {A Black Raspberry-Rich Diet Protects From Dextran Sulfate Sodium-Induced Intestinal Inflammation and Host Metabolic Perturbation in Association With Increased Aryl Hydrocarbon Receptor Ligands in the Gut Microbiota of Mice.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {842298}, pmid = {35734371}, issn = {2296-861X}, abstract = {Dietary modulation of the gut microbiota recently received considerable attention, and ligand activation of aryl hydrocarbon receptor (AHR) plays a pivotal role in intestinal immunity. Importantly, black raspberry (BRB, Rubus occidentalis) is associated with a variety of beneficial health effects. We aim to investigate effects of a BRB-rich diet on dextran sulfate sodium (DSS)-induced intestinal inflammation and to determine whether its consequent anti-inflammatory effects are relevant to modulation of the gut microbiota, especially its production of AHR ligands. A mouse model of DSS-induced intestinal inflammation was used in the present study. C57BL/6J mice were fed either AIN-76A or BRB diet. Composition and functions of the gut microbiota were assessed by 16S rRNA sequencing and comparative metagenome analysis. Metabolic profiles of host and the gut microbiome were assessed by serum and fecal metabolomic profiling and identification. BRB diet was found to ameliorate DSS-induced intestinal inflammation and host metabolic perturbation. BRB diet also protected from DSS-induced perturbation in diversity and composition in the gut microbiota. BRB diet promoted AHR ligand production by the gut microbiota, as revealed by increased levels of fecal AHR activity in addition to increased levels of two known AHR ligands, hemin and biliverdin. Accordingly, enrichment of bacterial genes and pathways responsible for production of hemin and biliverdin were found, specific gut bacteria that are highly correlated with abundances of hemin and biliverdin were also identified. BRB dietary intervention ameliorated intestinal inflammation in mice in association with promotion of AHR ligand production by the gut microbiota.}, } @article {pmid35733965, year = {2022}, author = {Zhang, J and Liang, Z and Ding Kao, R and Han, J and Du, M and Ahmad, AA and Wang, S and Salekdeh, GH and Long, R and Yan, P and Ding, X}, title = {Maternal Fecal Microbes Contribute to Shaping the Early Life Assembly of the Intestinal Microbiota of Co-inhabiting Yak and Cattle Calves.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {916735}, pmid = {35733965}, issn = {1664-302X}, abstract = {The Qinghai-Tibetan Plateau offers one of the most extreme environments for yaks (Bos grunniens). Although the genetic adaptability of yak and rumen metagenomes is increasingly understood, the relative contribution of host genetics and maternal symbiotic microbes throughout early intestinal microbial successions in yaks remains elusive. In this study, we assessed the intestinal microbiota succession of co-inhabiting yak and cattle (Bos taurus) calves at different weeks after birth as well as the modes of transmission of maternal symbiotic microbes (i.e., rumen fluid, feces, oral cavity, and breast skin) to their calves' intestinal microbiota colonization. We found that the fecal microbiota of yak and cattle calves after birth was dominated by members of the families Ruminococcaceae, Bacteroidaceae, and Lachnospiraceae. The Source Tracker model revealed that maternal fecal microbes played an important role (the average contribution was about 80%) in the intestinal microbial colonization of yak and cattle calves at different weeks after birth. Unlike cattle calves, there was no significant difference in the fecal microbiota composition of yak calves between 5 and 9 weeks after birth (Wilcoxon test, P > 0.05), indicating that yak may adapt to its natural extreme environment to stabilize its intestinal microbiota composition. Additionally, our results also find that the intestinal microbial composition of yak and cattle calves, with age, gradually tend to become similar, and the differences between species gradually decrease. The findings of this study are vital for developing strategies to manipulate the intestinal microbiota in grazing yaks and cattle for better growth and performance on the Qinghai-Tibetan Plateau.}, } @article {pmid35733222, year = {2022}, author = {Kim, JY and Choi, JH and Nam, SH and Fyumagwa, R and Yong, TS}, title = {Parasites and blood-meal hosts of the tsetse fly in Tanzania: a metagenomics study.}, journal = {Parasites & vectors}, volume = {15}, number = {1}, pages = {224}, pmid = {35733222}, issn = {1756-3305}, support = {NRF‑2020R1I1A2074562//National Research Foundation of Korea/ ; }, mesh = {Animals ; Animals, Wild/parasitology ; Insect Vectors/parasitology ; Mammals/genetics ; Metagenomics ; Mice ; *Parasites/genetics ; RNA, Ribosomal, 18S/genetics ; Swine ; Tanzania ; *Trypanosoma/genetics ; *Trypanosomiasis, African ; *Tsetse Flies/parasitology ; }, abstract = {BACKGROUND: Tsetse flies can transmit various Trypanosoma spp. that cause trypanosomiasis in humans, wild animals, and domestic animals. Amplicon deep sequencing of the 12S ribosomal RNA (rRNA) gene can be used to detect mammalian tsetse hosts, and the 18S rRNA gene can be used to detect all associated eukaryotic pathogens, including Trypanosoma spp.

METHODS: Tsetse flies were collected from the Serengeti National Park (n = 48), Maswa Game Reserve (n = 42), and Tarangire National Park (n = 49) in Tanzania in 2012-13. Amplicon deep sequencing targeting mammal-specific 12S rRNA and 18S rRNA genes was performed to screen the blood-feeding sources of tsetse flies and eukaryotic parasites in tsetse flies, respectively.

RESULTS: 12S rRNA gene deep sequencing revealed that various mammals were blood-feeding sources of the tsetse flies, including humans, common warthogs, African buffalos, mice, giraffes, African elephants, waterbucks, and lions. Genes of humans were less frequently detected in Serengeti (P = 0.0024), whereas African buffaloes were detected more frequently as a blood-feeding source (P = 0.0010). 18S rRNA gene deep sequencing showed that six tsetse samples harbored the Trypanosoma gene, which was identified as Trypanosoma godfreyi and Trypanosoma simiae in subsequent ITS1 gene sequencing.

CONCLUSIONS: Through amplicon deep sequencing targeting the 12S rRNA and 18S rRNA genes, various mammalian animals were identified as blood-meal sources, and two Trypanosoma species were detected in tsetse flies collected from the Maswa Game Reserve, Serengeti National Park, and Tarangire National Park in Tanzania. This study illustrates the patterns of parasitism of tsetse fly, wild animals targeted by the fly, and Trypanosoma spp. carried by the fly in Tanzania. It may provide essential data for formulating better strategies to control African trypanosomes.}, } @article {pmid35732881, year = {2022}, author = {Imai, Y and Lee, SW and Sakaguchi, S and Kato-Kogoe, N and Taniguchi, K and Omori, M and Tanaka, R and Honda, K and Osumi, W and Nakano, T and Ueno, T and Uchiyama, K}, title = {Comparison of the gastric microbiome in Billroth I and Roux-en-Y reconstructions after distal gastrectomy.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {10594}, pmid = {35732881}, issn = {2045-2322}, mesh = {Anastomosis, Roux-en-Y ; Gastrectomy ; Gastroenterostomy ; *Gastrointestinal Microbiome ; Humans ; Postoperative Complications/surgery ; *Stomach Neoplasms/surgery ; Treatment Outcome ; }, abstract = {The changes in gastric microbiota following reconstruction after gastrectomy have not been reported. This study aimed to compare the gastric microbiota following Billroth I and Roux-en-Y reconstructions after distal gastrectomy. We enrolled 71 gastrectomized patients with gastric cancer; 31 and 40 underwent Billroth I and Roux-en-Y reconstructions, respectively. During upper gastrointestinal endoscopy, gastric fluid was collected immediately before and 6 months after distal gastrectomy. Deoxyribonucleic acid isolated from each sample was evaluated using 16S ribosomal ribonucleic acid metagenomic analysis. Analysis revealed that the gastric microbiota's species richness (expressed as the alpha diversity) was significantly lower after than before distal gastrectomy (operational taxonomic units, p = 0.001; Shannon index, p = 0.03). The interindividual diversity (beta diversity) was significantly different before and after distal gastrectomy (unweighted UniFrac distances, p = 0.04; weighted UniFrac distances, p = 0.001; Bray-Curtis, p = 0.001). Alpha and beta diversity were not significantly different between Billroth I and Roux-en-Y reconstructions (observed operational taxonomic units, p = 0.58; Shannon index, p = 0.95; unweighted UniFrac distances, p = 0.65; weighted UniFrac distances, p = 0.67; Bray-Curtis, p = 0.63). Our study demonstrated significant differences in gastric microbiota diversity, composition, and community before and after distal gastrectomy but no difference between Billroth I and Roux-en-Y reconstruction after distal gastrectomy.}, } @article {pmid35731940, year = {2022}, author = {Romero Picazo, D and Werner, A and Dagan, T and Kupczok, A}, title = {Pangenome Evolution in Environmentally Transmitted Symbionts of Deep-Sea Mussels Is Governed by Vertical Inheritance.}, journal = {Genome biology and evolution}, volume = {14}, number = {7}, pages = {}, pmid = {35731940}, issn = {1759-6653}, mesh = {Animals ; Bacteria/genetics ; Gene Transfer, Horizontal ; Genome, Bacterial ; Methane ; *Mytilidae/genetics/microbiology ; Phylogeny ; Sulfur ; Symbiosis/genetics ; }, abstract = {Microbial pangenomes vary across species; their size and structure are determined by genetic diversity within the population and by gene loss and horizontal gene transfer (HGT). Many bacteria are associated with eukaryotic hosts where the host colonization dynamics may impact bacterial genome evolution. Host-associated lifestyle has been recognized as a barrier to HGT in parentally transmitted bacteria. However, pangenome evolution of environmentally acquired symbionts remains understudied, often due to limitations in symbiont cultivation. Using high-resolution metagenomics, here we study pangenome evolution of two co-occurring endosymbionts inhabiting Bathymodiolus brooksi mussels from a single cold seep. The symbionts, sulfur-oxidizing (SOX) and methane-oxidizing (MOX) gamma-proteobacteria, are environmentally acquired at an early developmental stage and individual mussels may harbor multiple strains of each symbiont species. We found differences in the accessory gene content of both symbionts across individual mussels, which are reflected by differences in symbiont strain composition. Compared with core genes, accessory genes are enriched in genome plasticity functions. We found no evidence for recent HGT between both symbionts. A comparison between the symbiont pangenomes revealed that the MOX population is less diverged and contains fewer accessory genes, supporting that the MOX association with B. brooksi is more recent in comparison to that of SOX. Our results show that the pangenomes of both symbionts evolved mainly by vertical inheritance. We conclude that genome evolution of environmentally transmitted symbionts that associate with individual hosts over their lifetime is affected by a narrow symbiosis where the frequency of HGT is constrained.}, } @article {pmid35731183, year = {2022}, author = {Liu, C and Chen, Q and Fu, P and Shi, YY}, title = {Anncaliia algerae Microsporidiosis Diagnosed by Metagenomic Next-Generation Sequencing, China.}, journal = {Emerging infectious diseases}, volume = {28}, number = {7}, pages = {1466-1470}, pmid = {35731183}, issn = {1080-6059}, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; *Microsporidia/genetics ; *Microsporidiosis/diagnosis ; }, abstract = {We report a case of Anncaliia algerae microsporidia infection in an immunosuppressed kidney transplant recipient in China. Light microscopy and transmission electron microscopy initially failed to identify A. algerae, which eventually was detected by metagenomic next-generation sequencing. Our case highlights the supporting role of metagenomic sequencing in early identification of uncommon pathogens.}, } @article {pmid35730934, year = {2022}, author = {Morris, MM and Kimbrel, JA and Geng, H and Tran-Gyamfi, MB and Yu, ET and Sale, KL and Lane, TW and Mayali, X}, title = {Bacterial Community Assembly, Succession, and Metabolic Function during Outdoor Cultivation of Microchloropsis salina.}, journal = {mSphere}, volume = {7}, number = {4}, pages = {e0023122}, pmid = {35730934}, issn = {2379-5042}, mesh = {*Biofuels ; Biomass ; Metagenome ; *Microbiota ; Symbiosis ; }, abstract = {Outdoor cultivation of microalgae has promising potential for renewable bioenergy, but there is a knowledge gap on the structure and function of the algal microbiome that coinhabits these ecosystems. Here, we describe the assembly mechanisms, taxonomic structure, and metabolic potential of bacteria associated with Microchloropsis salina cultivated outdoors. Open mesocosms were inoculated with algal cultures that were either free of bacteria or coincubated with one of two different strains of alga-associated bacteria and were sampled across five time points taken over multiple harvesting rounds of a 40-day experiment. Using quantitative analyses of metagenome-assembled genomes (MAGs), we tracked bacterial community compositional abundance and taxon-specific functional capacity involved in algal-bacterial interactions. One of the inoculated bacteria (Alteromonas sp.) persisted and dispersed across mesocosms, whereas the other inoculated strain (Phaeobacter gallaeciensis) disappeared by day 17 while a taxonomically similar but functionally distinct Phaeobacter strain became established. The inoculated strains were less abundant than 6 numerically dominant newly recruited taxa with functional capacities for mutualistic or saprophytic lifestyles, suggesting a generalist approach to persistence. This includes a highly abundant unclassified Rhodobacteraceae species that fluctuated between 25% and 77% of the total community. Overall, we did not find evidence for priority effects exerted by the distinct inoculum conditions; all mesocosms converged with similar microbial community compositions by the end of the experiment. Instead, we infer that the 15 total populations were retained due to host selection, as they showed high metabolic potential for algal-bacterial interactions such as recycling alga-produced carbon and nitrogen and production of vitamins and secondary metabolites associated with algal growth and senescence, including B vitamins, tropodithietic acid, and roseobacticides. IMPORTANCE Bacteria proliferate in nutrient-rich aquatic environments, including engineered algal biofuel systems, where they remineralize photosynthates, exchange secondary metabolites with algae, and can influence system output of biomass or oil. Despite this, knowledge on the microbial ecology of algal cultivation systems is lacking, and the subject is worthy of investigation. Here, we used metagenomics to characterize the metabolic capacities of the predominant bacteria associated with the biofuel-relevant microalga Microchloropsis salina and to predict testable metabolic interactions between algae and manipulated communities of bacteria. We identified a previously undescribed and uncultivated organism that dominated the community. Collectively, the microbial community may interact with the alga in cultivation via exchange of secondary metabolites which could affect algal success, which we demonstrate as a possible outcome from controlled experiments with metabolically analogous isolates. These findings address the scalability of lab-based algal-bacterial interactions through to cultivation systems and more broadly provide a framework for empirical testing of genome-based metabolic predictions.}, } @article {pmid35729658, year = {2022}, author = {Xu, X and Ocansey, DKW and Hang, S and Wang, B and Amoah, S and Yi, C and Zhang, X and Liu, L and Mao, F}, title = {The gut metagenomics and metabolomics signature in patients with inflammatory bowel disease.}, journal = {Gut pathogens}, volume = {14}, number = {1}, pages = {26}, pmid = {35729658}, issn = {1757-4749}, support = {SH2019025//The project of Zhenjiang key research and development plan (social development)/ ; SH2020066//The project of Zhenjiang key research and development plan (social development)/ ; SH2019025//The project of Zhenjiang key research and development plan (social development)/ ; }, abstract = {Inflammatory bowel disease (IBD), a chronic gut immune dysregulation and dysbiosis condition is rapidly increasing in global incidence. Regardless, there is a lack of ideal diagnostic markers, while conventional treatment provides scarce desired results, thus, the exploration for better options. Changes in the gut microbial composition and metabolites either lead to or are caused by the immune dysregulation that characterizes IBD. This study examined the fecal metagenomics and metabolomic changes in IBD patients. A total of 30 fecal samples were collected from 15 IBD patients and 15 healthy controls for 16S rDNA gene sequencing and UHPLC/Q-TOF-MS detection of metabolomics. Results showed that there was a severe perturbation of gut bacteria community composition, diversity, metabolites, and associated functions and metabolic pathways in IBD. This included a significantly decreased abundance of Bacteroidetes and Firmicutes, increased disease-associated phyla such as Proteobacteria and Actinobacteria, and increased Escherichia coli and Klebsiella pneumoniae in IBD. A total of 3146 metabolites were detected out of which 135 were differentially expressed between IBD and controls. Metabolites with high sensitivity and specificity in differentiating IBD from healthy individuals included 6,7,4'-trihydroxyisoflavone and thyroxine 4'-o-.beta.-d-glucuronide (AUC = 0.92), normorphine and salvinorin a (AUC = 0.90), and trichostachine (AUC = 0.91). Moreover, the IBD group had significantly affected pathways including primary bile acid biosynthesis, vitamin digestion and absorption, and carbohydrate metabolism. This study reveals that the combined evaluation of metabolites and fecal microbiome can be useful to discriminate between healthy subjects and IBD patients and consequently serve as therapeutic and diagnostic targets.}, } @article {pmid35729161, year = {2022}, author = {Zhang, L and Jonscher, KR and Zhang, Z and Xiong, Y and Mueller, RS and Friedman, JE and Pan, C}, title = {Islet autoantibody seroconversion in type-1 diabetes is associated with metagenome-assembled genomes in infant gut microbiomes.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3551}, pmid = {35729161}, issn = {2041-1723}, support = {R01 AT011618/AT/NCCIH NIH HHS/United States ; }, mesh = {Autoantibodies ; Child ; *Diabetes Mellitus, Type 1/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Metagenome/genetics ; Metagenomics/methods ; *Microbiota ; Seroconversion ; }, abstract = {The immune system of some genetically susceptible children can be triggered by certain environmental factors to produce islet autoantibodies (IA) against pancreatic β cells, which greatly increases their risk for Type-1 diabetes. An environmental factor under active investigation is the gut microbiome due to its important role in immune system education. Here, we study gut metagenomes that are de-novo-assembled in 887 at-risk children in the Environmental Determinants of Diabetes in the Young (TEDDY) project. Our results reveal a small set of core protein families, present in >50% of the subjects, which account for 64% of the sequencing reads. Time-series binning generates 21,536 high-quality metagenome-assembled genomes (MAGs) from 883 species, including 176 species that hitherto have no MAG representation in previous comprehensive human microbiome surveys. IA seroconversion is positively associated with 2373 MAGs and negatively with 1549 MAGs. Comparative genomics analysis identifies lipopolysaccharides biosynthesis in Bacteroides MAGs and sulfate reduction in Anaerostipes MAGs as functional signatures of MAGs with positive IA-association. The functional signatures in the MAGs with negative IA-association include carbohydrate degradation in lactic acid bacteria MAGs and nitrate reduction in Escherichia MAGs. Overall, our results show a distinct set of gut microorganisms associated with IA seroconversion and uncovered the functional genomics signatures of these IA-associated microorganisms.}, } @article {pmid35728317, year = {2022}, author = {Zhu, L and Lian, Y and Lin, D and Huang, D and Yao, Y and Ju, F and Wang, M}, title = {Insights into microbial contamination in multi-type manure-amended soils: The profile of human bacterial pathogens, virulence factor genes and antibiotic resistance genes.}, journal = {Journal of hazardous materials}, volume = {437}, number = {}, pages = {129356}, doi = {10.1016/j.jhazmat.2022.129356}, pmid = {35728317}, issn = {1873-3336}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Cattle ; Drug Resistance, Microbial/genetics ; Female ; Genes, Bacterial ; Humans ; *Manure/microbiology ; *Soil ; Soil Microbiology ; Swine ; Virulence Factors/genetics ; }, abstract = {Concerns regarding biological risk in environment have garnered increasing attention. Manure has been believed to be a significant source of antibiotic resistance genes (ARGs) in agricultural soil. Nevertheless, the profile of microbial contamination including ARGs, virulence factor genes (VFGs) and human bacterial pathogens (HBPs) in different manure-amended soils remain largely unknown. Here, we conducted the systematic metagenome-based study to explore changes in resistome, VFGs and HBPs in soils treated by frequently-used manures. The results revealed that many manure-borne ARGs, VFGs, and HBPs could be spreaded into soils, and their diversity and abundance were significantly different among chemical fertilizer, pig manure, chicken manure, cow dung and silkworm excrement application. A total of 157 potential HBPs accounting about 1.33% of total bacteria were detected. The main ARGs transferred from manures to soil conferred resistance to vancomycin and macrolide-lincosamide-streptogramin. The series analysis revealed positive co-occurrence patterns of ARGs-HBPs, VFGs-HBPs and ARGs-VFGs. Microbial contamination were more serious in pig manure and silkworm excrement sample than in the other samples, implying the usage of these two manures increased the risk of HBPs and dissemination of ARGs. This study confirmed the prevalence and discrepancy of resistome, VFGs and HBPs in different manure-amended soils.}, } @article {pmid35727549, year = {2022}, author = {Severino, A and Coppola, A and Correggia, M and Vetriani, C and Giovannelli, D and Cordone, A}, title = {From Sequences to Enzymes: Heterologous Expression of Genes from Marine Microbes.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2498}, number = {}, pages = {265-281}, pmid = {35727549}, issn = {1940-6029}, mesh = {Animals ; Bacteria/genetics ; *Escherichia coli/genetics ; *Genes, Bacterial ; Mammals/genetics ; Recombinant Proteins/genetics ; }, abstract = {Heterologous expression is an easy and broadly applicable experimental approach widely used to investigate protein functions without the need to genetically manipulate the original host. The approach is used to obtain large quantities of the desired protein, which can be further analyzed from a biochemical, structural, and functional perspective. The expression system consists of three main components: (1) a foreign DNA sequence coding for the protein of interest; (2) a suitable expression vector; (3) a suitable host (bacterial, yeast, or mammalian cells) which does not encode or express the protein of interest. Here, we show how to apply an Escherichia coli-based expression system to overexpress protein encoding genes from marine microbes.}, } @article {pmid35727547, year = {2022}, author = {Cowart, DA and Murphy, KR and Cheng, CC}, title = {Environmental DNA from Marine Waters and Substrates: Protocols for Sampling and eDNA Extraction.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2498}, number = {}, pages = {225-251}, pmid = {35727547}, issn = {1940-6029}, mesh = {Animals ; Biodiversity ; DNA Barcoding, Taxonomic/methods ; *DNA, Environmental/genetics ; Ecosystem ; Environmental Monitoring/methods ; Metagenomics/methods ; }, abstract = {Environmental DNA (eDNA) analysis has emerged in recent years as a powerful tool for the detection, monitoring, and characterization of aquatic metazoan communities, including vulnerable species. The rapid rate of adopting the eDNA approach across diverse habitats and taxonomic groups attests to its value for a wide array of investigative goals, from understanding natural or changing biodiversity to informing on conservation efforts at local and global scales. Regardless of research objectives, eDNA workflows commonly include the following essential steps: environmental sample acquisition, processing and preservation of samples, and eDNA extraction, followed by eDNA sequencing library preparation, high-capacity sequencing and sequence data analysis, or other methods of genetic detection. In this chapter, we supply instructional details for the early steps in the workflow to facilitate researchers considering adopting eDNA analysis to address questions in marine environments. Specifically, we detail sampling, preservation, extraction, and quantification protocols for eDNA originating from marine water, shallow substrates, and deeper sediments. eDNA is prone to degradation and loss, and to contamination through improper handling; these factors crucially influence the outcome and validity of an eDNA study. Thus, we also provide guidance on avoiding these pitfalls. Following extraction, purified eDNA is often sequenced on massively parallel sequencing platforms for comprehensive faunal diversity assessment using a metabarcoding or metagenomic approach, or for the detection and quantification of specific taxa by qPCR methods. These components of the workflow are project-specific and thus not included in this chapter. Instead, we briefly touch on the preparation of eDNA libraries and discuss comparisons between sequencing approaches to aid considerations in project design.}, } @article {pmid35727543, year = {2022}, author = {Rivera-Colón, AG and Catchen, J}, title = {Population Genomics Analysis with RAD, Reprised: Stacks 2.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2498}, number = {}, pages = {99-149}, pmid = {35727543}, issn = {1940-6029}, mesh = {DNA Restriction Enzymes/genetics ; Genetics, Population ; *Genomics/methods ; *Metagenomics/methods ; Polymorphism, Single Nucleotide ; Sequence Analysis, DNA/methods ; }, abstract = {Restriction enzymes have been one of the primary tools in the population genetics toolkit for 50 years, being coupled with each new generation of technology to provide a more detailed view into the genetics of natural populations. Restriction site-Associated DNA protocols, which joined enzymes with short-read sequencing technology, have democratized the field of population genomics, providing a means to assay the underlying alleles in scores of populations. More than 10 years on, the technique has been widely applied across the tree of life and served as the basis for many different analysis techniques. Here, we provide a detailed protocol to conduct a RAD analysis from experimental design to de novo analysis-including parameter optimization-as well as reference-based analysis, all in Stacks version 2, which is designed to work with paired-end reads to assemble RAD loci up to 1000 nucleotides in length. The protocol focuses on major points of friction in the molecular approaches and downstream analysis, with special attention given to validating experimental analyses. Finally, the protocol provides several points of departure for further analysis.}, } @article {pmid35727462, year = {2022}, author = {Basu, S and Chakravarty, A}, title = {Neurological Manifestations of Scrub Typhus.}, journal = {Current neurology and neuroscience reports}, volume = {22}, number = {8}, pages = {491-498}, pmid = {35727462}, issn = {1534-6293}, mesh = {Enzyme-Linked Immunosorbent Assay ; Fever ; Humans ; Immunoglobulin M/therapeutic use ; *Myelitis, Transverse/complications ; *Orientia tsutsugamushi/genetics ; *Scrub Typhus/complications/diagnosis/epidemiology ; }, abstract = {PURPOSE OF REVIEW: The occurrence of cases of scrub typhus is on the rise in South Asian and Southeast Asian countries. The present review discusses neurological complications following scrub typhus to appraise clinicians practicing in endemic regions about considering this treatable disease in the differential diagnosis of acute febrile illnesses, especially when accompanied with clinical neurological features.

RECENT FINDINGS: While the association of aseptic meningitis, encephalitis, and meningoencephalitis with scrub typhus is well known, more recently described neurological syndromes associated with scrub typhus include acute disseminated encephalomyelitis, various cranial nerve palsies, cerebellitis, cerebrovascular diseases including cerebral venous sinus thrombosis, transverse myelitis, longitudinally extensive transverse myelitis, Guillain-Barré syndrome, opsoclonus-myoclonus syndrome, parkinsonism, and many more. Early diagnosis is key to successful treatment. While diagnostic confirmation is generally made by the detection of IgM antibody by either ELISA or indirect fluorescent antibody tests, conventional PCR using 56 kDa gene (cPCR) and loop-mediated isothermal amplification assay (LAMP assay), as well as a newly introduced metagenomic next-generation sequencing (mNGS), are currently available for detection of Orientia tsutsugamushi infection in clinically suspected cases. Scrub typhus is an acute febrile illness caused by Orientia tsutsugamushi. The cutaneous hallmark of the disease is the "eschar." Scrub typhus results in multisystem involvement. Neurological compromise is present in about 20% of scrub typhus patients and affects both the central nervous system and the peripheral nervous system. The postulated underlying mechanisms include direct invasion of the organism, a vasculitis-like process, or an immune-mediated injury. Diagnosis of scrub typhus is confirmed by detection of O. tsutsugamushi IgM antibody in serum. Awareness among clinicians regarding the varied presentations of this disease is very important in order to reduce morbidity and mortality. Co-infection with dengue and/or chickungunya viruses may occur in endemic regions. The history of an acute febrile illness preceding the neurological illness is crucial. A very careful search for the eschar is essential; however, the absence of the skin lesion cannot exclude the diagnosis of scrub typhus. Neurological manifestations mostly respond to doxycycline therapy.}, } @article {pmid35727019, year = {2022}, author = {Sun, S and Wang, H and Howard, AG and Zhang, J and Su, C and Wang, Z and Du, S and Fodor, AA and Gordon-Larsen, P and Zhang, B}, title = {Loss of Novel Diversity in Human Gut Microbiota Associated with Ongoing Urbanization in China.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0020022}, pmid = {35727019}, issn = {2379-5077}, support = {P30 ES010126/ES/NIEHS NIH HHS/United States ; R01 HD030880/HD/NICHD NIH HHS/United States ; R01 DK104371/DK/NIDDK NIH HHS/United States ; R01 AG065357/AG/NIA NIH HHS/United States ; P2C HD050924/HD/NICHD NIH HHS/United States ; D43 TW009077/TW/FIC NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Urbanization ; Bacteria/genetics ; *Microbiota ; Metagenome/genetics ; }, abstract = {Recent rapid and large-scale urbanization has had a profound impact on human lifestyles and is associated with an increased risk of many diseases. Recent studies have revealed large differences in the human gut microbiota across populations in countries at different stages of urbanization. However, few studies have analyzed the impact of ongoing urbanization within the same geographic region. In this study, we sampled 214 participants in communities of different urbanization levels within two provinces of China and reconstructed draft prokaryotic genomes with metagenome sequences. The genomes were clustered into 447 species-level operational taxonomic units (OTUs), among which 196 did not have genomes in public reference databases according to the GTDB-Tk pipeline. The novel OTUs comprised 19.1% abundance in rural participants and 16.0% in urban participants, increasing the proportion of classified reads from 47.6% to 65.3% across all samples. Among the unknown OTUs, 26 OTUs present in rural samples were absent in urban participants, while 70 unknown OTUs were more abundant in rural than urban participants, suggesting potential loss and growth suppression of novel human symbionts during urbanization. Moreover, there were a higher number of genes, especially transporters, identified in genomes assembled from urban samples. This change in gene functionality indicates that urbanization not only altered the community structure of the human gut microbiota but also impacted its functional capacity. Taken together, these data show a dramatic change in the microbiota with urbanization and suggest the importance of cataloging microbial diversity from rural populations while these communities still exist. IMPORTANCE Previous studies have reported the differences in human gut microbiota across populations of different urbanization levels, but most of the studies focused on populations across different geographic regions. In this study, we analyzed the impact of ongoing urbanization in neighborhoods within the same geographic region. By assembling shotgun metagenome sequences, we reconstructed prokaryotic genomes from human gut microbiota and found that the novel bacterial OTUs were less abundant and less prevalent in urban participants than in rural participants, indicating potential loss and suppression of novel human symbionts during urbanization. Genes, including transporters and antibiotic resistance genes, were enriched in genomes of urban origins, suggesting change in functional potential of the microbiota. These findings suggest the significant influence of urbanization on human gut microbiota and the necessity of exploring the microbial diversity of rural populations.}, } @article {pmid35726918, year = {2022}, author = {Brumfield, KD and Leddy, M and Usmani, M and Cotruvo, JA and Tien, CT and Dorsey, S and Graubics, K and Fanelli, B and Zhou, I and Registe, N and Dadlani, M and Wimalarante, M and Jinasena, D and Abayagunawardena, R and Withanachchi, C and Huq, A and Jutla, A and Colwell, RR}, title = {Microbiome Analysis for Wastewater Surveillance during COVID-19.}, journal = {mBio}, volume = {13}, number = {4}, pages = {e0059122}, pmid = {35726918}, issn = {2150-7511}, support = {R01 ES030317/ES/NIEHS NIH HHS/United States ; }, mesh = {*COVID-19/epidemiology ; COVID-19 Testing ; Humans ; *Microbiota ; RNA, Viral/analysis/genetics ; SARS-CoV-2/genetics ; Wastewater ; Wastewater-Based Epidemiological Monitoring ; }, abstract = {Wastewater surveillance (WS), when coupled with advanced molecular techniques, offers near real-time monitoring of community-wide transmission of SARS-CoV-2 and allows assessing and mitigating COVID-19 outbreaks, by evaluating the total microbial assemblage in a community. Composite wastewater samples (24 h) were collected weekly from a manhole between December 2020 and November 2021 in Maryland, USA. RT-qPCR results showed concentrations of SARS-CoV-2 RNA recovered from wastewater samples reflected incidence of COVID-19 cases. When a drastic increase in COVID-19 was detected in February 2021, samples were selected for microbiome analysis (DNA metagenomics, RNA metatranscriptomics, and targeted SARS-CoV-2 sequencing). Targeted SARS-CoV-2 sequencing allowed for detection of important genetic mutations, such as spike: K417N, D614G, P681H, T716I, S982A, and D1118H, commonly associated with increased cell entry and reinfection. Microbiome analysis (DNA and RNA) provided important insight with respect to human health-related factors, including detection of pathogens and their virulence/antibiotic resistance genes. Specific microbial species comprising the wastewater microbiome correlated with incidence of SARS-CoV-2 RNA, suggesting potential association with SARS-CoV-2 infection. Climatic conditions, namely, temperature, were related to incidence of COVID-19 and detection of SARS-CoV-2 in wastewater, having been monitored as part of an environmental risk score assessment carried out in this study. In summary, the wastewater microbiome provides useful public health information, and hence, a valuable tool to proactively detect and characterize pathogenic agents circulating in a community. In effect, metagenomics of wastewater can serve as an early warning system for communicable diseases, by providing a larger source of information for health departments and public officials. IMPORTANCE Traditionally, testing for COVID-19 is done by detecting SARS-CoV-2 in samples collected from nasal swabs and/or saliva. However, SARS-CoV-2 can also be detected in feces of infected individuals. Therefore, wastewater samples can be used to test all individuals of a community contributing to the sewage collection system, i.e., the infrastructure, such as gravity pipes, manholes, tanks, lift stations, control structures, and force mains, that collects used water from residential and commercial sources and conveys the flow to a wastewater treatment plant. Here, we profile community wastewater collected from a manhole, detect presence of SARS-CoV-2, identify genetic mutations of SARS-CoV-2, and perform COVID-19 risk score assessment of the study area. Using metagenomics analysis, we also detect other microorganisms (bacteria, fungi, protists, and viruses) present in the samples. Results show that by analyzing all microorganisms present in wastewater, pathogens circulating in a community can provide an early warning for contagious diseases.}, } @article {pmid35726867, year = {2022}, author = {Choo, C and Mahurkar-Joshi, S and Dong, TS and Lenhart, A and Lagishetty, V and Jacobs, JP and Labus, JS and Jaffe, N and Mayer, EA and Chang, L}, title = {Colonic mucosal microbiota is associated with bowel habit subtype and abdominal pain in patients with irritable bowel syndrome.}, journal = {American journal of physiology. Gastrointestinal and liver physiology}, volume = {323}, number = {2}, pages = {G134-G143}, pmid = {35726867}, issn = {1522-1547}, support = {R21 DK104078/DK/NIDDK NIH HHS/United States ; P30 DK041301/DK/NIDDK NIH HHS/United States ; P50 DK064539/DK/NIDDK NIH HHS/United States ; IK2 CX001717/CX/CSRD VA/United States ; UL1 TR001881/TR/NCATS NIH HHS/United States ; }, mesh = {Abdominal Pain/etiology ; Constipation ; Diarrhea ; Feces ; Habits ; Humans ; Intestinal Mucosa/pathology ; *Irritable Bowel Syndrome ; *Microbiota ; Prevotella ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Mucosal microbiota differ significantly from fecal microbiota and may play a different role in the pathophysiology of irritable bowel syndrome (IBS). The aims of this study were to determine if the composition of mucosal microbiota differed between IBS, or IBS bowel habit (BH) subtypes, and healthy controls (HCs). Sigmoid colon mucosal biopsies were obtained from 97 Rome-positive patients with IBS (28% IBS-constipation, 38% IBS-diarrhea, 24% IBS-mixed, and 10% IBS-unsubtyped) and 54 HCs, from which DNA was extracted. 16S rRNA gene sequencing and microbial composition analysis were performed. Group differences in α and β diversity and taxonomic level differences were determined using linear regression while controlling for confounding variables. IBS BH subtype was associated with microbial α diversity (P = 0.0003) with significant differences seen in the mucosal microbiota of IBS-constipation versus IBS-diarrhea (P = 0.046). There were no significant differences in α or β diversity in the mucosal microbiota of IBS versus HCs (P = 0.29 and 0.93, respectively), but metagenomic profiling suggested functional differences. The relative abundance of Prevotella_9 copri within IBS was significantly correlated with increased abdominal pain (r = 0.36, P = 0.0003), which has not been previously reported in IBS. Significant differences in the mucosal microbiota were present within IBS BH subtypes but not between IBS and HCs, supporting the possibility of IBS BH subtype-specific pathogenesis. Increased Prevotella copri may contribute to symptoms in patients with IBS.NEW & NOTEWORTHY Gut mucosal microbiota differs significantly from fecal microbiota in irritable bowel syndrome (IBS) and may play a different role in its pathophysiology. Investigation of colonic mucosal microbiota in the largest cohort of patients with IBS and healthy controls accounting for confounding variables, including diet demonstrated significant differences in mucosal microbiota between IBS bowel habit subtypes but not between IBS and healthy controls. In addition, the study reported gut microbiota is associated with abdominal pain in patients with IBS.}, } @article {pmid35725880, year = {2022}, author = {Purohit, MK and Rathore, DS and Koladiya, G and Pandey, S and Singh, SP}, title = {Comparative analysis of the catalysis and stability of the native, recombinant and metagenomic alkaline proteases in organic solvents.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {53}, pages = {80968-80982}, pmid = {35725880}, issn = {1614-7499}, mesh = {Enzyme Stability ; *Hexanes ; Phylogeny ; Solvents/pharmacology ; *Peptide Hydrolases ; Catalysis ; }, abstract = {The effect of organic solvents on alkaline proteases was assessed for native, recombinant, and metagenomically derived alkaline proteases. Their stability and the effects of physicochemical parameters were studied in the presence of hexane. The native enzyme was comparatively more resistant against the organic solvents than the recombinant counterparts. On the other hand, the metagenomically derived alkaline protease was minimally resistant against solvents. A similar trend was apparent for the stability of enzyme in organic solvents. The novelty of this study lies in the fact that the majority of the studies on the solvent tolerance have focused on the mesophilic enzymes, while those from the haloalkaliphilic bacteria have received little attention. The comparative tolerance of the native, recombinant, and metagenomic alkaline proteases against the organic solvent has practical importance. The phylogenetic relatedness among the various protease sequences will be described.}, } @article {pmid35725732, year = {2022}, author = {Odrzywolek, K and Karwowska, Z and Majta, J and Byrski, A and Milanowska-Zabel, K and Kosciolek, T}, title = {Deep embeddings to comprehend and visualize microbiome protein space.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {10332}, pmid = {35725732}, issn = {2045-2322}, mesh = {Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Proteins/genetics ; }, abstract = {Understanding the function of microbial proteins is essential to reveal the clinical potential of the microbiome. The application of high-throughput sequencing technologies allows for fast and increasingly cheaper acquisition of data from microbial communities. However, many of the inferred protein sequences are novel and not catalogued, hence the possibility of predicting their function through conventional homology-based approaches is limited, which indicates the need for further research on alignment-free methods. Here, we leverage a deep-learning-based representation of proteins to assess its utility in alignment-free analysis of microbial proteins. We trained a language model on the Unified Human Gastrointestinal Protein catalogue and validated the resulting protein representation on the bacterial part of the SwissProt database. Finally, we present a use case on proteins involved in SCFA metabolism. Results indicate that the deep learning model manages to accurately represent features related to protein structure and function, allowing for alignment-free protein analyses. Technologies that contextualize metagenomic data are a promising direction to deeply understand the microbiome.}, } @article {pmid35724965, year = {2022}, author = {Li, H and Hao, B and Wang, Y and Yu, D and Chen, Z and Du, D and Xiong, J and Li, K and Zhang, H and Liu, X and Liu, K and Xiao, F and Cheng, X and Huang, L}, title = {Metagenomic next-generation sequencing for the diagnosis of Chlamydia psittaci pneumonia.}, journal = {The clinical respiratory journal}, volume = {16}, number = {7}, pages = {513-521}, pmid = {35724965}, issn = {1752-699X}, support = {2020-21//Basic Research Guiding Program Project of Yueyang City/ ; 82100053//National Natural Science Foundation of China/ ; }, mesh = {*Chlamydophila psittaci/genetics ; High-Throughput Nucleotide Sequencing ; Humans ; *Pneumonia ; *Psittacosis/diagnosis/veterinary ; Retrospective Studies ; }, abstract = {The aim of this study was to investigate the clinical characteristics of Chlamydia psittaci pneumonia and evaluate the diagnostic value of Metagenomic Next-Generation Sequencing (mNGS). A total of 44 patients diagnosed with Chlamydia psittaci pneumonia using mNGS were retrospectively analysed. The demographic and clinical features, laboratory data, imaging findings and clinical outcomes were collected. Results showed that 65.91% of the patients had a history of exposure to poultry or birds. All patients presented with fever. Apart from systemic and respiratory symptoms, some patients also presented with digestive and neurological symptoms. Respiratory failure was common among patients. The key laboratory tests were normal white blood cell counts, slightly elevated PCT, changes in levels of cardiac enzymes, liver enzymes and hyponatremia. Chest imaging revealed that most of the lesions contained patchy exudation or lobar consolidation of one lobe, especially in the lower lobe. Consolidation of both lungs was seen in critically ill patients. Although quinolones were effective in most patients, tetracyclines should be the first choice of treatment. The overall prognosis was good; however, patients who developed severe pneumonia had poor prognosis. The incidence of chlamydia psittaci pneumonia may be underestimated due to the nonspecific clinical manifestations and lack of confirmatory testing methods. The use of mNGS has increased the number of patients diagnosed with chlamydia psittaci pneumonia. mNGS is an effective diagnostic method for chlamydia psittaci pneumonia.}, } @article {pmid35724776, year = {2022}, author = {Chang, J and van Veen, JA and Tian, C and Kuramae, EE}, title = {A review on the impact of domestication of the rhizosphere of grain crops and a perspective on the potential role of the rhizosphere microbial community for sustainable rice crop production.}, journal = {The Science of the total environment}, volume = {842}, number = {}, pages = {156706}, doi = {10.1016/j.scitotenv.2022.156706}, pmid = {35724776}, issn = {1879-1026}, mesh = {Crop Production ; Crops, Agricultural/microbiology ; Domestication ; Edible Grain ; *Microbiota ; *Mycorrhizae ; *Oryza/microbiology ; Plant Roots/microbiology ; Rhizosphere ; Soil Microbiology ; }, abstract = {The rhizosphere-associated microbiome impacts plant performance and tolerance to abiotic and biotic stresses. Despite increasing recognition of the enormous functional role of the rhizomicrobiome on the survival of wild plant species growing under harsh environmental conditions, such as nutrient, water, temperature, and pathogen stresses, the utilization of the rhizosphere microbial community in domesticated rice production systems has been limited. Better insight into how this role of the rhizomicrobiome for the performance and survival of wild plants has been changed during domestication and development of present domesticated crops, may help to assess the potential of the rhizomicrobial community to improve the sustainable production of these crops. Here, we review the current knowledge of the effect of domestication on the microbial rhizosphere community of rice and other crops by comparing its diversity, structure, and function in wild versus domesticated species. We also examine the existing information on the impact of the plant on their physico-chemical environment. We propose that a holobiont approach should be explored in future studies by combining detailed analysis of the dynamics of the physicochemical microenvironment surrounding roots to systematically investigate the microenvironment-plant-rhizomicrobe interactions during rice domestication, and suggest focusing on the use of beneficial microbes (arbuscular mycorrhizal fungi and Nitrogen fixers), denitrifiers and methane consumers to improve the sustainable production of rice.}, } @article {pmid35724733, year = {2022}, author = {Lin, Y and Lau, HC and Liu, Y and Kang, X and Wang, Y and Ting, NL and Kwong, TN and Han, J and Liu, W and Liu, C and She, J and Wong, SH and Sung, JJ and Yu, J}, title = {Altered Mycobiota Signatures and Enriched Pathogenic Aspergillus rambellii Are Associated With Colorectal Cancer Based on Multicohort Fecal Metagenomic Analyses.}, journal = {Gastroenterology}, volume = {163}, number = {4}, pages = {908-921}, doi = {10.1053/j.gastro.2022.06.038}, pmid = {35724733}, issn = {1528-0012}, mesh = {*Adenoma/microbiology ; Animals ; Aspergillus ; Bacteria/genetics ; Biomarkers ; Cell Transformation, Neoplastic ; *Colorectal Neoplasms/diagnosis ; Feces/microbiology ; Humans ; Metagenome ; Mice ; }, abstract = {BACKGROUND & AIMS: The enteric mycobiota is a major component of the human gut microbiota, but its role in colorectal cancer (CRC) remains largely elusive. We conducted a meta-analysis to uncover the contribution of the fungal mycobiota to CRC.

METHODS: We retrieved fecal metagenomic data sets from 7 previous publications and established an additional in-house cohort, totaling 1329 metagenomes (454 with CRC, 350 with adenoma, and 525 healthy individuals). Mycobiota composition and microbial interactions were analyzed. Candidate CRC-enriched fungal species (Aspergillus rambellii) was functionally validated in vitro and in vivo.

RESULTS: Multicohort analysis revealed that the enteric mycobiota was altered in CRC. We identified fungi that were associated with patients with CRC or adenoma from multiple cohorts. Signature CRC-associated fungi included 6 enriched (A rambellii, Cordyceps sp. RAO-2017, Erysiphe pulchra, Moniliophthora perniciosa, Sphaerulina musiva, and Phytophthora capsici) and 1 depleted species (A kawachii). Co-occurrent interactions among CRC-enriched fungi became stronger in CRC compared with adenoma and healthy individuals. Moreover, we reported the transkingdom interactions between enteric fungi and bacteria in CRC progression, of which A rambellii was closely associated with CRC-enriched bacteria Fusobacterium nucleatum. A rambellii promoted CRC cell growth in vitro and tumor growth in xenograft mice. We further identified that combined fungal and bacterial biomarkers were more accurate than panels with pure bacterial species to discriminate patients with CRC from healthy individuals (the area under the curve relative change increased by 1.44%-10.60%).

CONCLUSIONS: This study reveals enteric mycobiota signatures and pathogenic fungi in stages of colorectal tumorigenesis. Fecal fungi can be used, in addition to bacteria, for noninvasive diagnosis of patients with CRC.}, } @article {pmid35724713, year = {2022}, author = {Xiong, H and Yang, G and Shan, X and Miao, L}, title = {Unveiling the effect of acetate on the interactions of functional bacteria in an anammox biofilm system.}, journal = {Chemosphere}, volume = {305}, number = {}, pages = {135408}, doi = {10.1016/j.chemosphere.2022.135408}, pmid = {35724713}, issn = {1879-1298}, mesh = {Acetates/metabolism ; *Ammonium Compounds/metabolism ; Anaerobic Ammonia Oxidation ; Anaerobiosis ; Bacteria/metabolism ; Biofilms ; Bioreactors/microbiology ; *Denitrification ; Nitrogen/analysis ; Oxidation-Reduction ; Sewage/microbiology ; }, abstract = {Biodegradable organics make an important impact on anaerobic ammonium oxidation (anammox) system. In this study, acetate was selected as a typical biodegradable organic, and its effect on the anammox biofilm system was comprehensively discussed from the macro and micro perspectives. Under a low influent concentration of acetate (<240 ± 10 mg/L), the best total nitrogen (TN) removal performance was 96%, but it decreased to 83% when the acetate concentration increased to 350 ± 20 mg/L. With the addition of acetate, the relative abundance of the family Brocadiaceae, which contains all known anammox bacteria, gradually increased from 7.97% to 12.79%, indicating that the presence of acetate promoted enrichment of anammox bacteria in the biofilm. Metagenomic analysis further demonstrated that an appropriate concentration of acetate helps to increase the abundances of the key enzymes related to nitrogen removal and enhance the metabolism of anammox and denitrification, thereby promoting the synergy of anammox and denitrifying bacteria. Hydrazine synthase (hzs), which is unique to the anammox process, was detected in association with the genera Candidatus Kuenenia, Candidatus Jettenia and Candidatus Brocadia, with its abundance increasing from 13268 (with no addition of acetate) to 19186 (with acetate addition of 240 ± 10 mg/L). This work provides a deeper understanding of the intrinsic interactions between functional bacteria in an anammox biofilm system.}, } @article {pmid35723864, year = {2022}, author = {Yang, M and Yang, DH and Yang, H and Ding, SZ and Liu, CH and Yin, HM and Liu, D and Chen, P and Luo, H}, title = {Clinical Characteristics of Chlamydia psittaci Pneumonia Infection in Central South China.}, journal = {Infectious diseases and therapy}, volume = {11}, number = {4}, pages = {1631-1647}, pmid = {35723864}, issn = {2193-8229}, support = {82070003//National Natural Science Foundation of China/ ; 2021JJ30943//Natural Science Foundation of Hunan Province/ ; 2021JJ30943//Fundamental Research Funds for Central Universities of the Central South University/ ; }, abstract = {INTRODUCTION: Chlamydia psittaci pneumonia has been a global public health hotspot in recent years. Although some scattered cases of C. psittaci pneumonia have been reported, there is a lack of large case studies worldwide.

METHODS: In this multicenter, observational study, we recruited all consecutive patients with confirmed C. psittaci pneumonia from October 4, 2018, to October 23, 2020, in nine tertiary general hospitals in Central-South China. Epidemiologic and clinical data from patients' electronic medical records were collected and analyzed.

RESULTS: One hundred and sixteen patients with C. psittaci pneumonia were included in the study. The mean age was 59.7 years. Fever (96.6%) and cough (65.5%) were the most common clinical symptoms. Most patients presented with an increase in the proportion of neutrophils, neutrophil to lymphocyte ratio, LDH, alanine aminotransferase (ALT) and aspartate aminotransferase (AST) and a significant decrease in lymphocytes. The main CT lung findings were consolidation (81%) and pleural effusion (35.3%), and bilateral lung consolidation was mainly found in severe patients. Chlamydia psittaci DNA was detected in BALF (bronchoalveolar lavage fluid) or blood samples by metagenomic next-generation sequencing (mNGS) in all patients. Use of quinolone was associated with shorter length of hospital stay and fever duration after antibiotic use. Multivariate logistic regression analysis indicated that respiratory support was associated with both severe pneumonia and in-hospital death.

CONCLUSIONS: The clinical phenotype of C. psittaci pneumonia is complex and variable. mNGS is helpful in the diagnosis and treatment of C. psittaci pneumonia, and early treatment with quinolone may benefit patients.}, } @article {pmid35723691, year = {2022}, author = {Matsuzawa, T and Watanabe, M and Nakamichi, Y and Akita, H and Yaoi, K}, title = {Crystal structure of metagenomic β-glycosidase MeBglD2 in complex with various saccharides.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {12}, pages = {4539-4551}, pmid = {35723691}, issn = {1432-0614}, support = {26850067//Japan Society for the Promotion of Science/ ; 18H02132//Japan Society for the Promotion of Science/ ; }, mesh = {*Cellobiose/metabolism ; Crystallography, X-Ray ; Glucose/metabolism ; *Metagenome ; Substrate Specificity ; alpha-L-Fucosidase/metabolism ; beta-Glucosidase/metabolism ; }, abstract = {Metagenomic MeBglD2 is a glycoside hydrolase family 1 (GH1) β-glycosidase that has β-glucosidase, β-fucosidase, and β-galactosidase activities, and is highly activated in the presence of monosaccharides and disaccharides. The β-glucosidase activity of MeBglD2 increases in a cellobiose concentration-dependent manner and is not inhibited by a high concentration of D-glucose or cellobiose. Previously, we solved the crystal structure of MeBglD2 and designed a thermostable mutant; however, the mechanism of substrate recognition of MeBglD2 remains poorly understood. In this paper, we report the X-ray crystal structures of MeBglD2 complexed with various saccharides, such as D-glucose, D-xylose, cellobiose, and maltose. The results showed that subsite - 1 of MeBglD2, which contained two catalytic glutamate residues (a nucleophilic Glu356 and an acid/base Glu170) was common to other GH1 enzymes, but the positive subsites (+ 1 and + 2) had different binding modes depending on the type of sugar. Three residues (Glu183, Asn227, and Asn229), located at the positive subsites of MeBglD2, were involved in substrate specificity toward cellobiose and/or chromogenic substrates in the presence of additive sugars. The docking simulation of MeBglD2-cellobiose indicated that Asn229 and Trp329 play important roles in the recognition of + 1 D-glucose in cellobiose. Our findings provide insights into the unique substrate recognition mechanism of GH1, which can incorporate a variety of saccharides into its positive subsites. KEY POINTS: • Metagenomic glycosidase, MeBglD2, recognizes various saccharides • Structures of metagenomic MeBglD2 complexed with various saccharides are determined • MeBglD2 has a unique substrate recognition mechanism at the positive subsites.}, } @article {pmid35723062, year = {2022}, author = {Chitcharoen, S and Sivapornnukul, P and Payungporn, S}, title = {Revolutionized virome research using systems microbiology approaches.}, journal = {Experimental biology and medicine (Maywood, N.J.)}, volume = {247}, number = {13}, pages = {1135-1147}, pmid = {35723062}, issn = {1535-3699}, mesh = {Metagenomics ; *Microbiota ; Virome/genetics ; *Viruses/genetics ; }, abstract = {Currently, both pathogenic and commensal viruses are continuously being discovered and acknowledged as ubiquitous components of microbial communities. The advancements of systems microbiological approaches have changed the face of virome research. Here, we focus on viral metagenomic approach to study virus community and their interactions with other microbial members as well as their hosts. This review also summarizes challenges, limitations, and benefits of the current virome approaches. Potentially, the studies of virome can be further applied in various biological and clinical fields.}, } @article {pmid35722889, year = {2022}, author = {Moubset, O and François, S and Maclot, F and Palanga, E and Julian, C and Claude, L and Fernandez, E and Rott, P and Daugrois, JH and Antoine-Lorquin, A and Bernardo, P and Blouin, AG and Temple, C and Kraberger, S and Fontenele, RS and Harkins, GW and Ma, Y and Marais, A and Candresse, T and Chéhida, SB and Lefeuvre, P and Lett, JM and Varsani, A and Massart, S and Ogliastro, M and Martin, DP and Filloux, D and Roumagnac, P}, title = {Virion-Associated Nucleic Acid-Based Metagenomics: A Decade of Advances in Molecular Characterization of Plant Viruses.}, journal = {Phytopathology}, volume = {112}, number = {11}, pages = {2253-2272}, doi = {10.1094/PHYTO-03-22-0096-RVW}, pmid = {35722889}, issn = {0031-949X}, mesh = {Metagenomics/methods ; Ecosystem ; *Nucleic Acids ; Plant Diseases ; *Plant Viruses/genetics ; Virion/genetics ; Plants ; }, abstract = {Over the last decade, viral metagenomic studies have resulted in the discovery of thousands of previously unknown viruses. These studies are likely to play a pivotal role in obtaining an accurate and robust understanding of how viruses affect the stability and productivity of ecosystems. Among the metagenomics-based approaches that have been developed since the beginning of the 21st century, shotgun metagenomics applied specifically to virion-associated nucleic acids (VANA) has been used to disentangle the diversity of the viral world. We summarize herein the results of 24 VANA-based studies, focusing on plant and insect samples conducted over the last decade (2010 to 2020). Collectively, viruses from 85 different families were reliably detected in these studies, including capsidless RNA viruses that replicate in fungi, oomycetes, and plants. Finally, strengths and weaknesses of the VANA approach are summarized and perspectives of applications in detection, epidemiological surveillance, environmental monitoring, and ecology of plant viruses are provided. [Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.}, } @article {pmid35722289, year = {2022}, author = {Rocha, ADL and Ferrari, RG and Pereira, WE and de Lima, LA and Givisiez, PEN and Moreno-Switt, AI and Toro, M and Delgado-Suárez, EJ and Meng, J and de Oliveira, CJB}, title = {Revisiting the Biological Behavior of Salmonella enterica in Hydric Resources: A Meta-Analysis Study Addressing the Critical Role of Environmental Water on Food Safety and Public Health.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {802625}, pmid = {35722289}, issn = {1664-302X}, support = {U01 FD001418/FD/FDA HHS/United States ; }, abstract = {The increasing number of studies reporting the presence of Salmonella in environmental water sources suggests that it is beyond incidental findings originated from sparse fecal contamination events. However, there is no consensus on the occurrence of Salmonella as its relative serovar representation across non-recycled water sources. We conducted a meta-analysis of proportions by fitting a random-effects model using the restricted maximum-likelihood estimator to obtain the weighted average proportion and between-study variance associated with the occurrence of Salmonella in water sources. Moreover, meta-regression and non-parametric supervised machine learning method were performed to predict the effect of moderators on the frequency of Salmonella in non-recycled water sources. Three sequential steps (identification of information sources, screening and eligibility) were performed to obtain a preliminary selection from identified abstracts and article titles. Questions related to the frequency of Salmonella in aquatic environments, as well as putative differences in the relative frequencies of the reported Salmonella serovars and the role of potential variable moderators (sample source, country, and sample volume) were formulated according to the population, intervention, comparison, and outcome method (PICO). The results were reported according to the Preferred Reporting Items for Systematic Review and Meta-Analyzes statement (PRISMA). A total of 26 eligible papers reporting 148 different Salmonella serovars were retrieved. According to our model, the Salmonella frequency in non-recycled water sources was 0.19 [CI: 0.14; 0.25]. The source of water was identified as the most import variable affecting the frequency of Salmonella, estimated as 0.31 and 0.17% for surface and groundwater, respectively. There was a higher frequency of Salmonella in countries with lower human development index (HDI). Small volume samples of surface water resulted in lower detectable Salmonella frequencies both in high and low HDI regions. Relative frequencies of the 148 serovars were significantly affected only by HDI and volume. Considering that serovars representation can also be affected by water sample volume, efforts toward the standardization of water samplings for monitoring purposes should be considered. Further approaches such as metagenomics could provide more comprehensive insights about the microbial ecology of fresh water and its importance for the quality and safety of agricultural products.}, } @article {pmid35722280, year = {2022}, author = {Horigome, A and Hashikura, N and Yoshida, K and Xiao, JZ and Odamaki, T}, title = {2'-Fucosyllactose Increases the Abundance of Blautia in the Presence of Extracellular Fucosidase-Possessing Bacteria.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {913624}, pmid = {35722280}, issn = {1664-302X}, abstract = {Blautia is a genus of anaerobic bacteria that is widely distributed in the mammalian gut. Recently, an increasing body of research has demonstrated a link between this genus and human health, suggesting applications as a novel probiotic strain. Moreover, we have previously shown that 2'-fucosyllactose (2'-FL), a major component of human milk oligosaccharides, increases the relative abundance of Blautia sp., particularly Blautia wexlerae, in the cultured fecal microbiota of healthy adults using a pH-controlled single-batch fermenter. However, the effects of 2'-FL on Blautia proliferation vary among individuals. In this study, we assessed the impact of the intrinsic gut microbiota on the prebiotic effects of 2'-FL. Metagenomic analysis of feces collected from all donors showed that the homolog of the intracellular GH95 α-l-fucosidase gene was considerably enriched in two non-responders (individuals who showed no increase in Blautia proliferation), whereas the homologous genes encoding extracellular α-l-fucosidase were more abundant in responders, suggesting that lactose and fucose released into the environment could be substrates mediating the growth of Blautia. In vitro assays confirmed the ability of B. wexlerae to utilize the two carbohydrates but not 2'-FL. We also observed that B. wexlerae utilized fucose released from 2'-FL by Bifidobacterium bifidum, which possessed extracellular GH95 α-l-fucosidase, in co-cultures of these two organisms. Finally, increasing the proportion of extracellular GH95 by the addition of a B. bifidum strain led to Blautia proliferation by 2'-FL in fecal cultures of the two non-responders. These findings provided valuable perspectives on individualized nutritional approaches to properly control the gut microbiota. Future clinical trials are needed to obtain further insights into the characteristics of responders vs. non-responders.}, } @article {pmid35721198, year = {2022}, author = {Fang, X and Wu, H and Wang, X and Lian, F and Li, M and Miao, R and Wei, J and Tian, J}, title = {Modulation of Gut Microbiota and Metabolites by Berberine in Treating Mice With Disturbances in Glucose and Lipid Metabolism.}, journal = {Frontiers in pharmacology}, volume = {13}, number = {}, pages = {870407}, pmid = {35721198}, issn = {1663-9812}, abstract = {Introduction: Glucose and lipid metabolism disturbances has become the third major disease after cancer and cardio-cerebrovascular diseases. Emerging evidence shows that berberine can effectively intervene glucose and lipid metabolism disturbances, but the underlying mechanisms of this remain unclear. To investigate this issue, we performed metagenomic and metabolomic analysis in a group of normal mice (the NC group), mice with disturbances in glucose and lipid metabolism (the MC group) and mice with disturbances in glucose and lipid metabolism after berberine intervention (the BER group). Result: Firstly, analysis of the clinical indicators revealed that berberine significantly improved the blood glucose and blood lipid of the host. The fasting blood glucose level decreased by approximately 30% in the BER group after 8 weeks and the oral glucose tolerance test showed that the blood glucose level of the BER group was lower than that of the MC group at any time. Besides, berberine significantly reduced body weight, total plasma cholesterol and triglyceride. Secondly, compared to the NC group, we found dramatically decreased microbial richness and diversity in the MC group and BER group. Thirdly, LDA effect size suggested that berberine significantly altered the overall gut microbiota structure and enriched many bacteria, including Akkermansia (p < 0.01), Eubacterium (p < 0.01) and Ruminococcus (p < 0.01). Fourthly, the metabolomic analysis suggested that there were significant differences in the metabolomics signature of each group. For example, isoleucine (p < 0.01), phenylalanine (p < 0.05), and arbutin (p < 0.05) significantly increased in the MC group, and berberine intervention significantly reduced them. The arbutin content in the BER group was even lower than that in the NC group. Fifthly, by combined analysis of metagenomics and metabolomics, we observed that there were significantly negative correlations between the reduced faecal metabolites (e.g., arbutin) in the BER group and the enriched gut microbiota (e.g., Eubacterium and Ruminococcus) (p < 0.05). Finally, the correlation analysis between gut microbiota and clinical indices indicated that the bacteria (e.g., Eubacterium) enriched in the BER group were negatively associated with the above-mentioned clinical indices (p < 0.05). Conclusion: Overall, our results describe that the changes of gut microbiota and metabolites are associated with berberine improving glucose and lipid metabolism disturbances.}, } @article {pmid35721056, year = {2022}, author = {Yang, Y and Shi, Q and Jin, Q and Yang, Z and Li, W and Han, J and Mao, J and Zheng, B}, title = {Case Report: Metagenomic Next-Generation Sequencing Clinches the Diagnosis of Acute Q Fever and Verified by Indirect Immunofluorescence Assay.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {846526}, pmid = {35721056}, issn = {2296-858X}, abstract = {Q fever is a zoonotic infectious disease caused by Coxiella burnetii. The clinical symptoms of acute Q fever are usually atypical, and routine serological tests of C. burnetii are not readily available, making the diagnosis of Q fever a challenge. In this case, we report a male patient who had repeated fevers and was administered empirical anti-infective treatment, but the effect was poor. After conducting relevant laboratory and imagological examinations, the etiology has not yet been confirmed. Subsequently, metagenomic next-generation sequencing (mNGS) identified the sequence reads of C. burnetii from the patient's peripheral blood within 48 h, and then the diagnosis of acute Q fever was established. Moreover, the serological test of indirect immunofluorescence assay (IFA) of the C. burnetii antibody was further performed in the Centers for Disease Control, certifying the result of mNGS. The patient was ultimately treated with doxycycline and recovered well. mNGS is an unbiased and comprehensive method in infrequent or culture-negative pathogen identification. To our knowledge, this is the first case of acute Q fever identified by mNGS and confirmed by IFA in Taizhou, China. A further large-scale prospective clinical cohort study is worth carrying out to compare the diagnostic efficiency of mNGS with traditional serological methods and PCR in acute Q fever.}, } @article {pmid35720380, year = {2022}, author = {Patterson, GT and Osorio, EY and Peniche, A and Dann, SM and Cordova, E and Preidis, GA and Suh, JH and Ito, I and Saldarriaga, OA and Loeffelholz, M and Ajami, NJ and Travi, BL and Melby, PC}, title = {Pathologic Inflammation in Malnutrition Is Driven by Proinflammatory Intestinal Microbiota, Large Intestine Barrier Dysfunction, and Translocation of Bacterial Lipopolysaccharide.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {846155}, pmid = {35720380}, issn = {1664-3224}, support = {K08 DK113114/DK/NIDDK NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; T32 AI007526/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; Bacteria ; Cecum/microbiology ; *Gastrointestinal Diseases ; *Gastrointestinal Microbiome ; Inflammation ; *Intestinal Diseases ; Lipopolysaccharides ; *Malnutrition ; Mice ; Weight Loss ; }, abstract = {Acute malnutrition, or wasting, is implicated in over half of all deaths in children under five and increases risk of infectious disease. Studies in humans and preclinical models have demonstrated that malnutrition is linked to an immature intestinal microbiota characterized by increased prevalence of Enterobacteriaceae. Observational studies in children with moderate acute malnutrition (MAM) have also observed heightened systemic inflammation and increased circulating bacterial lipopolysaccharides (LPS; endotoxin). However, the mechanisms that underpin the systemic inflammatory state and endotoxemia, and their pathophysiological consequences, remain uncertain. Understanding these pathophysiological mechanisms is necessary to design targeted treatments that will improve the unacceptable rate of failure or relapse that plague current approaches. Here we use a mouse model of MAM to investigate the mechanisms that promote inflammation in the malnourished host. We found that mice with MAM exhibited increased systemic inflammation at baseline, increased translocation of bacteria and bacterial LPS, and an exaggerated response to inflammatory stimuli. An exaggerated response to bacterial LPS was associated with increased acute weight loss. Remarkably, intestinal inflammation and barrier dysfunction was found in the cecum and colon. The cecum showed a dysbiotic microbiota with expansion of Gammaproteobacteria and some Firmicutes, and contraction of Bacteroidetes. These changes were paralleled by an increase in fecal LPS bioactivity. The inflammatory phenotype and weight loss was modulated by oral administration of non-absorbable antibiotics that altered the proportion of cecal Gammaproteobacteria. We propose that the heightened inflammation of acute malnutrition is the result of changes in the intestinal microbiota, intestinal barrier dysfunction in the cecum and colon, and increased systemic exposure to LPS.}, } @article {pmid35719363, year = {2022}, author = {Xue, J and Dominguez Rieg, JA and Thomas, L and White, JR and Rieg, T}, title = {Intestine-Specific NHE3 Deletion in Adulthood Causes Microbial Dysbiosis.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {896309}, pmid = {35719363}, issn = {2235-2988}, support = {I01 BX004968/BX/BLRD VA/United States ; R01 DK110621/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Animals ; Bacteroidetes ; Dysbiosis/microbiology ; Firmicutes ; *Gastrointestinal Microbiome ; Humans ; *Inflammatory Bowel Diseases/microbiology ; Intestines/microbiology ; Mice ; Sodium-Hydrogen Exchanger 3/genetics ; }, abstract = {In the intestine, the Na[+]/H[+] exchanger 3 (NHE3) plays a critical role for Na[+] and fluid absorption. NHE3 deficiency predisposes patients to inflammatory bowel disease (IBD). In mice, selective deletion of intestinal NHE3 causes various local and systemic pathologies due to dramatic changes in the intestinal environment, which can influence microbiota colonization. By using metagenome shotgun sequencing, we determined the effect of inducible intestinal epithelial cell-specific deletion of NHE3 (NHE3[IEC-KO]) in adulthood on the gut microbiome in mice. Compared with control mice, NHE3[IEC-KO] mice show a significantly different gut microbiome signature, with an unexpected greater diversity. At the phylum level, NHE3[IEC-KO] mice showed a significant expansion in Proteobacteria and a tendency for lower Firmicutes/Bacteroidetes (F/B) ratio, an indicator of dysbiosis. At the family level, NHE3[IEC-KO] mice showed significant expansions in Bacteroidaceae, Rikenellaceae, Tannerellaceae, Flavobacteriaceae and Erysipelotrichaceae, but had contractions in Lachnospiraceae, Prevotellaceae and Eubacteriaceae. At the species level, after removing those with lowest occurrence and abundance, we identified 23 species that were significantly expanded (several of which are established pro-inflammatory pathobionts); whereas another 23 species were found to be contracted (some of which are potential anti-inflammatory probiotics) in NHE3[IEC-KO] mice. These results reveal that intestinal NHE3 deletion creates an intestinal environment favoring the competitive advantage of inflammophilic over anti-inflammatory species, which is commonly featured in conventional NHE3 knockout mice and patients with IBD. In conclusion, our study emphasizes the importance of intestinal NHE3 for gut microbiota homeostasis, and provides a deeper understanding regarding interactions between NHE3, dysbiosis, and IBD.}, } @article {pmid35719350, year = {2022}, author = {Shin, J and Li, T and Zhu, L and Wang, Q and Liang, X and Li, Y and Wang, X and Zhao, S and Li, L and Li, Y}, title = {Obese Individuals With and Without Phlegm-Dampness Constitution Show Different Gut Microbial Composition Associated With Risk of Metabolic Disorders.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {859708}, pmid = {35719350}, issn = {2235-2988}, mesh = {Bacteria/genetics ; *Diabetes Mellitus, Type 2/complications ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Obesity/complications/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Obesity is conventionally considered a risk factor for multiple metabolic diseases, such as dyslipidemia, type 2 diabetes, hypertension, and cardiovascular disease (CVD). However, not every obese patient will progress to metabolic disease. Phlegm-dampness constitution (PDC), one of the nine TCM constitutions, is considered a high-risk factor for obesity and its complications. Alterations in the gut microbiota have been shown to drive the development and progression of obesity and metabolic disease, however, key microbial changes in obese patients with PDC have a higher risk for metabolic disorders remain elusive.

METHODS: We carried out fecal 16S rRNA gene sequencing in the present study, including 30 obese subjects with PDC (PDC), 30 individuals without PDC (non-PDC), and 30 healthy controls with balanced constitution (BC). Metagenomic functional prediction of bacterial taxa was achieved using PICRUSt.

RESULTS: Obese individuals with PDC had higher BMI, waist circumference, hip circumference, and altered composition of their gut microbiota compared to non-PDC obese individuals. At the phylum level, the gut microbiota was characterized by increased abundance of Bacteroidetes and decreased levels of Firmicutes and Firmicutes/Bacteroidetes ratio. At the genus level, Faecalibacterium, producing short-chain fatty acid, achieving anti-inflammatory effects and strengthening intestinal barrier functions, was depleted in the PDC group, instead, Prevotella was enriched. Most PDC-associated bacteria had a stronger correlation with clinical indicators of metabolic disorders rather than more severe obesity. The PICRUSt analysis demonstrated 70 significantly different microbiome community functions between the two groups, which were mainly involved in carbohydrate and amino acid metabolism, such as promoting Arachidonic acid metabolism, mineral absorption, and Lipopolysaccharide biosynthesis, reducing Arginine and proline metabolism, flavone and flavonol biosynthesis, Glycolysis/Gluconeogenesis, and primary bile acid biosynthesis. Furthermore, a disease classifier based on microbiota was constructed to accurately discriminate PDC individuals from all obese people.

CONCLUSION: Our study shows that obese individuals with PDC can be distinguished from non-PDC obese individuals based on gut microbial characteristics. The composition of the gut microbiome altered in obese with PDC may be responsible for their high risk of metabolic diseases.}, } @article {pmid35719339, year = {2022}, author = {Xi, Y and Liu, F and Qiu, B and Li, Y and Xie, X and Guo, J and Wu, L and Liang, T and Wang, D and Wang, J and Chen, M and Xue, L and Ding, Y and Zhang, J and Wu, Q and Liu, H}, title = {Analysis of Gut Microbiota Signature and Microbe-Disease Progression Associations in Locally Advanced Non-Small Cell Lung Cancer Patients Treated With Concurrent Chemoradiotherapy.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {892401}, pmid = {35719339}, issn = {2235-2988}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *Carcinoma, Non-Small-Cell Lung/drug therapy/genetics ; Chemoradiotherapy ; *Diabetes Mellitus, Type 2 ; Disease Progression ; Fatty Acids ; *Gastrointestinal Microbiome/genetics ; Humans ; *Lung Neoplasms/drug therapy/genetics ; Retrospective Studies ; }, abstract = {PURPOSE: To evaluate the association of gut microbiome signature and disease progression in locally advanced non-small cell lung cancer (LA-NSCLC) patients treated with concurrent chemoradiotherapy (CCRT) by fecal metagenome analysis.

METHODS: Metagenome-wide association studies on baseline fecal samples from 18 LA-NSCLC patients before CCRT and 13 controls from healthy first-degree relatives were performed. Among the 18 LA-NSCLC patients, six patients were defined as the long progression-free survival (long-PFS) group (PFS≥11 months) while another 12 were in the short-PFS group (PFS<11 months). Alpha diversity, taxonomic composition, and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional pathways were compared between groups.

RESULTS: The Firmicutes/Bacteroidetes value of long-PFS group was higher than those of short-PFS (p=0.073) and healthy individual groups (p=0.009). Meanwhile, long-PFS group had significantly higher diversities in Fungi, Archaea, and Viruses than short-PFS group. The KEGG pathways overrepresented in short-PFS group included fructose and mannose metabolism (p=0.028), streptomycin biosynthesis (p=0.028), acarbose and validamycin biosynthesis (p=0.013), ribosome biogenesis in eukaryotes (p=0.035), biosynthesis of vancomycin group antibiotics (p=0.004), apoptosis-fly (p=0.044), and tetracycline biosynthesis (p=0.044), while those overrepresented in long-PFS group included fatty acid biosynthesis (p=0.035), fatty acid metabolism (p=0.008), vancomycin resistance (p=0.008), longevity regulating pathway-worm (p=0.028), type II diabetes mellitus (p=0.004), and viral carcinogenesis (p=0.003). Further analysis of antibiotic resistome demonstrated that the short-PFS group had a trend with more antibiotic resistance genes than healthy control (p=0.070) and long-PFS groups (p=0.218). The vancomycin resistance sequences were significantly enriched in the long-PFS group compared to the short-PFS group (p=0.006).

CONCLUSIONS: The baseline gut microbiome composition and functionality might be associated with PFS in LA-NSCLC treated with CCRT. The outcome of CCRT might be modulated through bacterial metabolic pathways. The antibiotic resistance genes might play a role in disease progression and provide potential information on the relationship between the use of antibiotics and treatment efficacy of CCRT in LA-NSCLC.}, } @article {pmid35719330, year = {2022}, author = {Li, Y and Yang, Y and Ma, L and Liu, J and An, Q and Zhang, C and Yin, G and Cao, Z and Pan, H}, title = {Comparative Analyses of Antibiotic Resistance Genes in Jejunum Microbiota of Pigs in Different Areas.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {887428}, pmid = {35719330}, issn = {2235-2988}, mesh = {Animals ; *Anti-Bacterial Agents/analysis/pharmacology ; China ; Drug Resistance, Microbial ; Genes, Bacterial/genetics ; Jejunum ; *Microbiota ; Swine ; }, abstract = {Antibiotic resistance genes (ARGs) are emerging environmental contaminants that threaten human and animal health. Intestinal microbiota may be an important ARGs repository, and intensive animal farming is a likely contributor to the environmental burden of ARGs. Using metagenomic sequencing, we investigated the structure, function, and drug resistance of the jejunal microbial community in Landrace (LA, Kunming), Saba (SB, Kunming), Dahe (DH, Qujing), and Diannan small-ear piglets (DS, Xishuangbanna) from different areas in Yunnan Province, China. Remarkable differences in jejunal microbial diversity among the different pig breeds, while the microbial composition of pig breeds in close areas tends to be similar. Functional analysis showed that there were abundant metabolic pathways and carbohydrate enzymes in all samples. In total, 32,487 ARGs were detected in all samples, which showed resistance to 38 categories of drugs. The abundance of ARGs in jejunum was not significantly different between LA and SB from the same area, but significantly different between DS, DH and LA or SB from different areas. Therefore, the abundance of ARGs was little affected by pig breeds and microorganism community structure, but it was closely related to geographical location. In addition, as a probiotic, Lactobacillus amylovorus is also an important ARGs producing bacterium. Our results revealed the antibiotic exposure and intestinal microbial resistance of farms in the study areas, which could provide basic knowledge and potential strategies for rational use of antibiotics and reducing the risk of ARGs transmission in animal husbandry.}, } @article {pmid35719177, year = {2022}, author = {Caldwell, M and Boruah, AP and Thakur, KT}, title = {Acute neurologic emerging flaviviruses.}, journal = {Therapeutic advances in infectious disease}, volume = {9}, number = {}, pages = {20499361221102664}, pmid = {35719177}, issn = {2049-9361}, abstract = {The COVID-19 pandemic has shed light on the challenges we face as a global society in preventing and containing emerging and re-emerging pathogens. Multiple intersecting factors, including environmental changes, host immunological factors, and pathogen dynamics, are intimately connected to the emergence and re-emergence of communicable diseases. There is a large and expanding list of communicable diseases that can cause neurological damage, either through direct or indirect routes. Novel pathogens of neurotropic potential have been identified through advanced diagnostic techniques, including metagenomic next-generation sequencing, but there are also known pathogens which have expanded their geographic distribution to infect non-immune individuals. Factors including population growth, climate change, the increase in animal and human interface, and an increase in international travel and trade are contributing to the expansion of emerging and re-emerging pathogens. Challenges exist around antimicrobial misuse giving rise to antimicrobial-resistant infectious neurotropic organisms and increased susceptibility to infection related to the expanded use of immunomodulatory treatments. In this article, we will review key concepts around emerging and re-emerging pathogens and discuss factors associated with neurotropism and neuroinvasion. We highlight several neurotropic pathogens of interest, including West Nile virus (WNV), Zika Virus, Japanese Encephalitis Virus (JEV), and Tick-Borne Encephalitis Virus (TBEV). We emphasize neuroinfectious diseases which impact the central nervous system (CNS) and focus on flaviviruses, a group of vector-borne pathogens that have expanded globally in recent years and have proven capable of widespread outbreak.}, } @article {pmid35718910, year = {2022}, author = {Wang, S and Li, B and Mao, H and Zhu, M and Zhang, X and Xiang, X and Wang, Z}, title = {[Effects of rice wheat intervention on intestinal microflora of rats based on metagenomics].}, journal = {Wei sheng yan jiu = Journal of hygiene research}, volume = {51}, number = {3}, pages = {449-455}, doi = {10.19813/j.cnki.weishengyanjiu.2022.03.018}, pmid = {35718910}, issn = {1000-8020}, mesh = {Animals ; Carbohydrates ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Glycoside Hydrolases ; Lipids ; Male ; Metagenomics ; *Oryza ; Rats ; Rats, Sprague-Dawley ; Triticum ; }, abstract = {OBJECTIVE: To investigate the effects of rice on intestinal microflora in rats.

METHODS: Thirty 4-week-old male SD rats were randomly divided into control group, rice group and wheat group according to body weight. The control group was fed with AIN-93 diet, the rice group and the wheat group was fed with the AIN-93 diet which the carbohydrate was replaced with rice and wheat, respectively, for 4 weeks. At the end of the experiment, lipid related biochemical indexes were determined, and the contents of the distal colon(feces) of rats were collected for macro factor detection.

RESULTS: From the beginning to the end of feeding, there was no difference in weight gain among the groups. After the end of the experiment, there was no difference among lipid-related indicators and blood glucose. α diversity showed that there was no difference in the diversity of intestinal microbiota between the rice and wheat groups, and the gene abundance analysis of intestinal microbiota in the wheat group showed that the gene abundance of intestinal microbiota was lower. The difference analysis of intestinal microbiota result showed that compared with the rice group, the wheat group was composed of higher proportion of verrucomicrophyla and lower proportion of Bacteroidetes. Lefse analysis showed that the surface group was enriched with Akkermansia Muciniphila, Bifidobacterium animalis, and a variety of beneficial bacteria such as Faecalibaculum rodentium and Intestinimonas butyriciproducens, while Prevotella copri was rich in the rice group. Glycoside hydrolases 8, glycoside hydrolases 16, glycoside hydrolases 99 and glycosyl transferase family 56.

CONCLUSION: Rice or wheat as different carbohydrate sources have different effects on the composition of intestinal microflora and carbohydrate-related active enzymes in rats.}, } @article {pmid35718835, year = {2022}, author = {Bao, S and Wang, H and Li, W and Ji, L and Wang, X and Shen, Q and Yang, S and Zhou, C and Zhang, W}, title = {Dynamic alterations of the mice gut virome after Coxsackievirus B3 infection.}, journal = {Journal of medical virology}, volume = {94}, number = {10}, pages = {4959-4969}, doi = {10.1002/jmv.27946}, pmid = {35718835}, issn = {1096-9071}, mesh = {Animals ; *Coxsackievirus Infections ; *Enterovirus Infections ; Humans ; Mice ; *Microviridae ; Phylogeny ; Virome ; }, abstract = {The gut microbiome plays an essential role in the human health and dysbiosis has been implicated in numerous diseases. Coxsackievirus B3 infects millions of humans yearly and yet limited research has explored dynamic alterations of the gut virome after infection. Here, we established the mouse model of Coxsackievirus B3 infection and collected fecal samples at several time points to investigate alterations of the gut virome using viral metagenomic analysis. We found that the mice virome was dominated by Caudovirales and Microviridae, and phylogenetic analyses showed that both Caudovirales and Microviridae had high diversity. The gut virome had significant variations with the increase of Caudovirales and the decrease of Microviridae after infection. We proposed that Caudovirales and Microviridae may be biomarkers for the Coxsackievirus infection process. This study provides a reference for the dynamic changes of the gut virome after human Enterovirus infection, which may help guide the rational drug use in clinical treatment and provide new ideas for preventing Enterovirus infection.}, } @article {pmid35718758, year = {2022}, author = {Jia, H and Lyu, W and Hirota, K and Saito, E and Miyoshi, M and Hohjoh, H and Furukawa, K and Saito, K and Haritani, M and Taguchi, A and Hasebe, Y and Kato, H}, title = {Eggshell membrane modulates gut microbiota to prevent murine pre-cachexia through suppression of T helper cell differentiation.}, journal = {Journal of cachexia, sarcopenia and muscle}, volume = {13}, number = {4}, pages = {2088-2101}, pmid = {35718758}, issn = {2190-6009}, support = {18K11095//Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {Animals ; *Cachexia/prevention & control ; Cell Differentiation ; Diet ; *Egg Shell ; *Gastrointestinal Microbiome ; Inflammation ; Interleukin-10 ; Male ; Mice ; Mice, Inbred C57BL ; Proteomics ; *T-Lymphocytes, Helper-Inducer/cytology ; }, abstract = {BACKGROUND: Cachexia is a life-threatening condition observed in several pathologies, such as cancer or chronic diseases. Interleukin 10 (Il10) gene transfer is known to improve cachexia by downregulating Il6. Here, we used an IL10-knockout mouse model to simulate cachexia and investigate the effects of eggshell membrane (ESM), a resistant protein, on general pre-cachexia symptoms, which is particularly important for the development of cachexia therapeutics.

METHODS: Five-week-old male C57BL6/J mice were fed an AIN-93G powdered diet (WT), and 5-week-old male B6.129P2-Il10 < tm1Cgn>/J (IL10[-/-]) mice were fed either the AIN-93G diet (KO) or an 8% ESM-containing diet (KOE) for 28 weeks. The tissue weight and levels of anaemia-, blood glucose-, lipid metabolism-, and muscular and colonic inflammation-related biochemical markers were measured. Transcriptomic analysis on liver and colon mucus and proteomic analysis on skeletal muscle were performed. Ingenuity Pathway Analysis was used to identify molecular pathways and networks. Caecal short-chain fatty acids (SCFAs) were identified using HPLC, and caecal bacteria DNA were subjected to metagenomic analysis. Flow cytometry analysis was performed to measure the CD4[+] IL17[+] T cells in mesenteric lymph nodes.

RESULTS: The body weight, weight of gastrocnemius muscle and fat tissues, colon weight/length ratio, plasma HDL and NEFA, muscular PECAM-1 levels (P < 0.01), plasma glucose and colonic mucosal myeloperoxidase activity (P < 0.05) and T helper (Th) 17 cell abundance (P = 0.071) were improved in KOE mice over KO mice. Proteomic analysis indicated the protective role of ESM in muscle weakness and maintenance of muscle formation (>1.5-fold). Transcriptomic analysis revealed that ESM supplementation suppressed the LPS/IL1-mediated inhibition of RXR function pathway in the liver and downregulated the colonic mucosal expression of chemokines and Th cell differentiation-related markers (P < 0.01) by suppressing the upstream BATF pathway. Analysis of the intestinal microenvironment revealed that ESM supplementation ameliorated the microbial alpha diversity and the abundance of microbiota associated with the degree of inflammation (P < 0.05) and increased the level of total organic acids, particularly of SCFAs such as butyrate (2.3-fold), which could inhibit Th1 and Th17 production.

CONCLUSIONS: ESM supplementation ameliorated the chief symptoms of cachexia, including anorexia, lean fat tissue mass, skeletal muscle wasting and reduced physical function. ESM also improved colon and skeletal muscle inflammation, lipid metabolism and microbial dysbiosis. These results along with the suppressed differentiation of Th cells could be associated with the beneficial intestinal microenvironment and, subsequently, attenuation of pre-cachexia. Our findings provide insights into the potential of ESM in complementary interventions for pre-cachexia prevention.}, } @article {pmid35718090, year = {2022}, author = {Raju, RS and Al Nahid, A and Chondrow Dev, P and Islam, R}, title = {VirusTaxo: Taxonomic classification of viruses from the genome sequence using k-mer enrichment.}, journal = {Genomics}, volume = {114}, number = {4}, pages = {110414}, doi = {10.1016/j.ygeno.2022.110414}, pmid = {35718090}, issn = {1089-8646}, mesh = {*COVID-19 ; Humans ; Metagenome ; Metagenomics/methods ; Phylogeny ; SARS-CoV-2/genetics ; *Viruses/genetics ; }, abstract = {Classification of viruses into their taxonomic ranks (e.g., order, family, and genus) provides a framework to organize an abundant population of viruses. Next-generation metagenomic sequencing technologies lead to a rapid increase in generating sequencing data of viruses which require bioinformatics tools to analyze the taxonomy. Many metagenomic taxonomy classifiers have been developed to study microbiomes, but it is particularly challenging to assign the taxonomy of diverse virus sequences and there is a growing need for dedicated methods to be developed that are optimized to classify virus sequences into their taxa. For taxonomic classification of viruses from metagenomic sequences, we developed VirusTaxo using diverse (e.g., 402 DNA and 280 RNA) genera of viruses. VirusTaxo has an average accuracy of 93% at genus level prediction in DNA and RNA viruses. VirusTaxo outperformed existing taxonomic classifiers of viruses where it assigned taxonomy of a larger fraction of metagenomic contigs compared to other methods. Benchmarking of VirusTaxo on a collection of SARS-CoV-2 sequencing libraries and metavirome datasets suggests that VirusTaxo can characterize virus taxonomy from highly diverse contigs and provide a reliable decision on the taxonomy of viruses.}, } @article {pmid35717483, year = {2023}, author = {Moroishi, Y and Gui, J and Nadeau, KC and Morrison, HG and Madan, J and Karagas, MR}, title = {A prospective study of the infant gut microbiome in relation to vaccine response.}, journal = {Pediatric research}, volume = {93}, number = {3}, pages = {725-731}, pmid = {35717483}, issn = {1530-0447}, support = {UH3 OD023275/OD/NIH HHS/United States ; P42 ES007373/ES/NIEHS NIH HHS/United States ; R21 ES020936/ES/NIEHS NIH HHS/United States ; P01 ES022832/ES/NIEHS NIH HHS/United States ; UG3 OD023275/OD/NIH HHS/United States ; P20 GM104416/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; Infant ; *Gastrointestinal Microbiome/genetics ; Prospective Studies ; Cohort Studies ; RNA, Ribosomal, 16S/genetics ; *Tetanus ; Tetanus Toxoid ; Feces ; Immunoglobulin G ; Polysaccharides ; }, abstract = {BACKGROUND: The establishment of the gut microbiome plays a key symbiotic role in the developing immune system; however, its influence on vaccine response is yet uncertain. We prospectively investigated the composition and diversity of the early-life gut microbiome in relation to infant antibody response to two routinely administered vaccines.

METHODS: Eighty-three infants enrolled in the New Hampshire Birth Cohort Study were included in the analysis. We collected blood samples at 12 months of age and assayed the isolated serum to quantify total IgG and measured antibody to pneumococcal capsular polysaccharide and tetanus toxoid. Stool samples were collected from infants at 6 weeks of age and sequenced using 16S rRNA, and a subset of 61 samples were sequenced using shotgun metagenomics sequencing.

RESULTS: We observed differences in beta diversity for 16S 6-week stool microbiota and pneumococcal and tetanus IgG antibody responses. Metagenomics analyses identified species and metabolic pathways in 6-week stool associated with tetanus antibody response, in particular, negative associations with the relative abundance of Aeriscardovia aeriphila species and positive associations with the relative abundance of species associated with CDP-diacylglycerol biosynthesis pathways.

CONCLUSIONS: The early gut microbiome composition may influence an infant's vaccine response.

IMPACT: Early intestinal microbiome acquisition plays a critical role in immune maturation and in both adaptive and innate immune response in infancy. We identified associations between early life microbiome composition and response to two routinely administered vaccines-pneumococcal capsular polysaccharide and tetanus toxoid-measured at approximately 1 year of age. Our findings highlight the potential impact of the gut microbiome on infant immune response that may open up opportunities for future interventions.}, } @article {pmid35716556, year = {2022}, author = {Guan, Y and Xue, X and Jia, J and Li, X and Xing, H and Wang, Z}, title = {Metagenomic assembly and binning analyses the prevalence and spread of antibiotic resistome in water and fish gut microbiomes along an environmental gradient.}, journal = {Journal of environmental management}, volume = {318}, number = {}, pages = {115521}, doi = {10.1016/j.jenvman.2022.115521}, pmid = {35716556}, issn = {1095-8630}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Gastrointestinal Microbiome ; Genes, Bacterial ; *Microbiota ; Prevalence ; Water ; }, abstract = {The pristine river and urban river show an environmental gradient caused by anthropogenic impacts such as wastewater treatment plants and domestic wastewater discharges. Here, metagenomic and binning analyses unveiled antibiotic resistance genes (ARGs) profiles, their co-occurrence with metal resistance genes (MRGs) and mobile genetic elements (MGEs), and their host bacteria in water and Hemiculter leucisculus samples of the river. Results showed that the decrease of ARG abundances from pristine to anthropogenic regions was attributed to the reduction of the relative abundance of multidrug resistance genes in water microbiomes along the environmental gradient. Whereas anthropogenic impact contributed to the enrichment of ARGs in fish gut microbiomes. From pristine to anthropogenic water samples, the dominant host bacteria shifted from Pseudomonas to Actinobacteria. Potential pathogens Vibrio parahaemolyticus, Enterobacter kobei, Aeromonas veronii and Microcystis aeruginosa_C with multiple ARGs were retrieved from fish gut microbes in lower reach of Ba River. The increasing trends in the proportion of the contigs carrying ARGs (ARCs) concomitant with plasmids along environmental gradient indicated that plasmids act as efficient mobility vehicles to enhance the spread of ARGs under anthropogenic pressures. Moreover, the higher co-occurrence of ARGs and MRGs on plasmids revealed that anthropogenic impacts accelerated the co-transfer potential of ARGs and MRGs and the enrichment of ARGs. Partial least squares path modeling revealed anthropogenic contamination could shape fish gut antibiotic resistome mainly via affecting ARG host bacteria in water microbiomes, following by ARGs co-occurrence with MGEs and MRGs in gut microbiomes. This study enhanced our understanding of the mechanism of the anthropogenic activities on the transmission of antibiotic resistome in river ecosystem and emphasized the risk of ARGs and pathogens transferring from an aquatic environment to fish guts.}, } @article {pmid35715703, year = {2022}, author = {Lan, Y and Sun, J and Chen, C and Wang, H and Xiao, Y and Perez, M and Yang, Y and Kwan, YH and Sun, Y and Zhou, Y and Han, X and Miyazaki, J and Watsuji, TO and Bissessur, D and Qiu, JW and Takai, K and Qian, PY}, title = {Endosymbiont population genomics sheds light on transmission mode, partner specificity, and stability of the scaly-foot snail holobiont.}, journal = {The ISME journal}, volume = {16}, number = {9}, pages = {2132-2143}, pmid = {35715703}, issn = {1751-7370}, support = {42176110//National Natural Science Foundation of China (National Science Foundation of China)/ ; 18K06401//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {Animals ; *Hydrothermal Vents/microbiology ; Metagenomics ; Phylogeny ; Snails/physiology ; Symbiosis/genetics ; }, abstract = {The scaly-foot snail (Chrysomallon squamiferum) inhabiting deep-sea hydrothermal vents in the Indian Ocean relies on its sulphur-oxidising gammaproteobacterial endosymbionts for nutrition and energy. In this study, we investigate the specificity, transmission mode, and stability of multiple scaly-foot snail populations dwelling in five vent fields with considerably disparate geological, physical and chemical environmental conditions. Results of population genomics analyses reveal an incongruent phylogeny between the endosymbiont and mitochondrial genomes of the scaly-foot snails in the five vent fields sampled, indicating that the hosts obtain endosymbionts via horizontal transmission in each generation. However, the genetic homogeneity of many symbiont populations implies that vertical transmission cannot be ruled out either. Fluorescence in situ hybridisation of ovarian tissue yields symbiont signals around the oocytes, suggesting that vertical transmission co-occurs with horizontal transmission. Results of in situ environmental measurements and gene expression analyses from in situ fixed samples show that the snail host buffers the differences in environmental conditions to provide the endosymbionts with a stable intracellular micro-environment, where the symbionts serve key metabolic functions and benefit from the host's cushion. The mixed transmission mode, symbiont specificity at the species level, and stable intracellular environment provided by the host support the evolutionary, ecological, and physiological success of scaly-foot snail holobionts in different vents with unique environmental parameters.}, } @article {pmid35715496, year = {2022}, author = {Shell, WA and Rehan, SM}, title = {Comparative metagenomics reveals expanded insights into intra- and interspecific variation among wild bee microbiomes.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {603}, pmid = {35715496}, issn = {2399-3642}, mesh = {Agriculture ; Animals ; Bees ; Metagenome ; *Metagenomics ; *Microbiota/genetics ; Plants ; }, abstract = {The holobiont approach proposes that species are most fully understood within the context of their associated microbiomes, and that both host and microbial community are locked in a mutual circuit of co-evolutionary selection. Bees are an ideal group for this approach, as they comprise a critical group of pollinators that contribute to both ecological and agricultural health worldwide. Metagenomic analyses offer comprehensive insights into an organism's microbiome, diet, and viral load, but remain largely unapplied to wild bees. Here, we present metagenomic data from three species of carpenter bees sampled from around the globe, representative of the first ever carpenter bee core microbiome. Machine learning, co-occurrence, and network analyses reveal that wild bee metagenomes are unique to host species. Further, we find that microbiomes are likely strongly affected by features of their local environment, and feature evidence of plant pathogens previously known only in honey bees. Performing the most comprehensive comparative analysis of bee microbiomes to date we discover that microbiome diversity is inversely proportional to host species social complexity. Our study helps to establish some of the first wild bee hologenomic data while offering powerful empirical insights into the biology and health of vital pollinators.}, } @article {pmid35715423, year = {2022}, author = {Nishimura, Y and Yoshizawa, S}, title = {The OceanDNA MAG catalog contains over 50,000 prokaryotic genomes originated from various marine environments.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {305}, pmid = {35715423}, issn = {2052-4463}, support = {18K19224//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 18H04136//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; 21K19134//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; }, mesh = {Aquatic Organisms/*genetics ; *Metagenome ; *Metagenomics ; Oceans and Seas ; Phylogeny ; Prokaryotic Cells ; }, abstract = {Marine microorganisms are immensely diverse and play fundamental roles in global geochemical cycling. Recent metagenome-assembled genome studies, with particular attention to large-scale projects such as Tara Oceans, have expanded the genomic repertoire of marine microorganisms. However, published marine metagenome data is still underexplored. We collected 2,057 marine metagenomes covering various marine environments and developed a new genome reconstruction pipeline. We reconstructed 52,325 qualified genomes composed of 8,466 prokaryotic species-level clusters spanning 59 phyla, including genomes from the deep-sea characterized as deeper than 1,000 m (n = 3,337), low-oxygen zones of <90 μmol O2 per kg water (n = 7,884), and polar regions (n = 7,752). Novelty evaluation using a genome taxonomy database shows that 6,256 species (73.9%) are novel and include genomes of high taxonomic novelty, such as new class candidates. These genomes collectively expanded the known phylogenetic diversity of marine prokaryotes by 34.2%, and the species representatives cover 26.5-42.0% of prokaryote-enriched metagenomes. Thoroughly leveraging accumulated metagenomic data, this genome resource, named the OceanDNA MAG catalog, illuminates uncharacterized marine microbial 'dark matter' lineages.}, } @article {pmid35715385, year = {2022}, author = {Gronniger, JL and Wang, Z and Brandt, GR and Ward, CS and Tsementzi, D and Mu, H and Gu, J and Johnson, ZI and Konstantinidis, KT and Hunt, DE}, title = {Rapid changes in coastal ocean microbiomes uncoupled with shifts in environmental variables.}, journal = {Environmental microbiology}, volume = {24}, number = {9}, pages = {4167-4177}, doi = {10.1111/1462-2920.16086}, pmid = {35715385}, issn = {1462-2920}, mesh = {Metagenome ; *Microbiota/genetics ; Oceans and Seas ; Phytoplankton ; }, abstract = {Disturbances, here defined as events that directly alter microbial community composition, are commonly studied in host-associated and engineered systems. In spite of global change both altering environmental averages and increasing extreme events, there has been relatively little research into the causes, persistence and population-level impacts of disturbance in the dynamic coastal ocean. Here, we utilize 3 years of observations from a coastal time series to identify disturbances based on the largest week-over-week changes in the microbiome (i.e. identifying disturbance as events that alter the community composition). In general, these microbiome disturbances were not clearly linked to specific environmental factors and responsive taxa largely differed, aside from SAR11, which generally declined. However, several disturbance metagenomes identified increased phage-associated genes, suggesting that unexplained community shifts might be caused by increased mortality. Furthermore, a category 1 hurricane, the only event that would likely be classified a priori as an environmental disturbance, was not an outlier in microbiome composition, but did enhance a bloom in seasonally abundant phytoplankton. Thus, as extreme environmental changes intensify, assumptions of what constitutes a disturbance should be re-examined in the context of ecological history and microbiome responses.}, } @article {pmid35714435, year = {2022}, author = {Borker, SS and Thakur, A and Khatri, A and Kumar, R}, title = {Quality assessment, safety evaluation, and microbiome analysis of night-soil compost from Lahaul valley of northwestern Himalaya.}, journal = {Waste management (New York, N.Y.)}, volume = {149}, number = {}, pages = {42-52}, doi = {10.1016/j.wasman.2022.06.003}, pmid = {35714435}, issn = {1879-2456}, mesh = {Animals ; Bacteria/genetics ; Cattle ; *Composting ; Food ; Humans ; *Metals, Heavy ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; *Refuse Disposal ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The Himalayan dry toilet system prevalent in the northwestern Himalaya is a traditional practice of converting human faeces into a compost-like soil amendment. The current study evaluated night-soil compost (NSC) for agricultural use by assessing the compost quality, safety, and microbiome properties. Based on the fertility and clean indices determined by the fertility and heavy metal parameters, NSC was categorized as good quality compost with high fertilizing potential and moderate concentration of heavy metals. With respect to pathogens, the faecal coliform levels in the NSC were categorized as safe according to the U.S. Environmental Protection Agency standards. The bacterial community structure based on 16S rRNA gene amplicons revealed a diverse taxonomy with 14 phyla and 54 genera in NSC. Compared to publicly available 16S rRNA gene amplicon data, NSC exhibited predominant phyla (Proteobacteria, Bacteriodetes, Actinobacteria, and Firmicutes) similar to human faeces, cattle manure, food waste compost, vermicompost, and activated sludge. However, statistically, NSC was distinct at the genus level from all other groups. Additionally, pathogenic bacteria with antimicrobial resistance (AMR) genes in the NSC metagenome were determined by performing a standalone BLASTN against the PATRIC database. The analysis revealed 139 pathogenic strains with most pathogens susceptible to antibiotics, indicating lower AMR in the predicted strains. The phytotoxicity of NSC with Pisum sativum var. AS-10 seeds showed a germination index of > 85%, indicating NSC's non-harmful effects on seed germination and root growth. Overall, NSC from Himalayan dry toilets can be used as a soil amendment for food and non-food plants.}, } @article {pmid35714383, year = {2022}, author = {Benedek, T and Pápai, M and Gharieb, K and Bedics, A and Táncsics, A and Tóth, E and Daood, H and Maróti, G and Wirth, R and Menashe, O and Bóka, K and Kriszt, B}, title = {Nocardioides carbamazepini sp. nov., an ibuprofen degrader isolated from a biofilm bacterial community enriched on carbamazepine.}, journal = {Systematic and applied microbiology}, volume = {45}, number = {4}, pages = {126339}, doi = {10.1016/j.syapm.2022.126339}, pmid = {35714383}, issn = {1618-0984}, mesh = {*Actinomycetales ; Bacterial Typing Techniques ; Base Composition ; Biofilms ; Carbamazepine ; DNA, Bacterial/genetics ; Fatty Acids/analysis ; Ibuprofen ; *Nocardioides ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Soil Microbiology ; Vitamin K 2/chemistry ; }, abstract = {From the metagenome of a carbamazepine amended selective enrichment culture the genome of a new to science bacterial species affiliating with the genus Nocardioides was reconstructed. From the same enrichment an aerobic actinobacterium, strain CBZ_1[T], sharing 99.4% whole-genome sequence similarity with the reconstructed Nocardioides sp. bin genome was isolated. On the basis of 16S rRNA gene sequence similarity the novel isolate affiliated to the genus Nocardioides, with the closest relatives Nocardioides kongjuensis DSM19082[T] (98.4%), Nocardioides daeguensis JCM17460[T] (98.4%) and Nocardioides nitrophenolicus DSM15529[T] (98.2%). Using a polyphasic approach it was confirmed that the isolate CBZ_1[T] represents a new phyletic lineage within the genus Nocardioides. According to metagenomic, metatranscriptomic studies and metabolic analyses strain CZB_1[T] was abundant in both carbamazepine and ibuprofen enrichments, and harbors biodegradative genes involved in the biodegradation of pharmaceutical compounds. Biodegradation studies supported that the new species was capable of ibuprofen biodegradation. After 7 weeks of incubation, in mineral salts solution supplemented with glucose (3 g l[-1]) as co-substrate, 70% of ibuprofen was eliminated by strain CBZ_1[T] at an initial conc. of 1.5 mg l[-1]. The phylogenetic, phenotypic and chemotaxonomic data supported the classification of strain CBZ_1[T] to the genus Nocardioides, for which the name Nocardioides carbamazepini sp. nov. (CBZ_1[T] = NCAIM B.0.2663 = LMG 32395) is proposed. To the best of our knowledge, this is the first study that reports simultaneous genome reconstruction of a new to science bacterial species using metagenome binning and at the same time the isolation of the same novel bacterial species.}, } @article {pmid35714354, year = {2022}, author = {Sabatino, R and Sbaffi, T and Corno, G and de Carvalho, DS and Trovatti Uetanabaro, AP and Góes-Neto, A and Podolich, O and Kozyrovska, N and de Vera, JP and Azevedo, V and Barh, D and Di Cesare, A}, title = {Metagenome Analysis Reveals a Response of the Antibiotic Resistome to Mars-like Extraterrestrial Conditions.}, journal = {Astrobiology}, volume = {22}, number = {9}, pages = {1072-1080}, pmid = {35714354}, issn = {1557-8070}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Metagenome ; Metagenomics ; }, abstract = {The spread of antibiotic resistance is becoming a serious global health concern. Numerous studies have been done to investigate the dynamics of antibiotic resistance genes (ARGs) in both indoor and outdoor environments. Nonetheless, few studies are available about the dynamics of the antibiotic resistome (total content of ARGs in the microbial cultures or communities) under stress in outer space environments. In this study, we aimed to experimentally investigate the dynamics of ARGs and metal resistance genes (MRGs) in Kombucha Mutualistic Community (KMC) samples exposed to Mars-like conditions simulated during the BIOMEX experiment outside the International Space Station with analysis of the metagenomics data previously produced. Thus, we compared them with those of the respective non-exposed KMC samples. The antibiotic resistome responded to the Mars-like conditions by enriching its diversity with ARGs after exposure, which were not found in non-exposed samples (i.e., tet and van genes against tetracycline and vancomycin, respectively). Furthermore, ARGs and MRGs were correlated; therefore, their co-selection could be assumed as a mechanism for maintaining antibiotic resistance in Mars-like environments. Overall, these results highlight the high plasticity of the antibiotic resistome in response to extraterrestrial conditions and in the absence of anthropogenic stresses.}, } @article {pmid35714058, year = {2022}, author = {Schlaberg, R}, title = {Clinical Metagenomics-from Proof-of-Concept to Routine Use.}, journal = {Clinical chemistry}, volume = {68}, number = {8}, pages = {997-999}, doi = {10.1093/clinchem/hvac091}, pmid = {35714058}, issn = {1530-8561}, mesh = {Child ; *High-Throughput Nucleotide Sequencing ; Humans ; *Metagenomics ; Retrospective Studies ; }, } @article {pmid35713834, year = {2022}, author = {Li, G and Cai, M and Zheng, X and Xie, X and Zhu, Y and Long, Y}, title = {Impact of disinfectants on the intestinal bacterial symbionts and immunity of silkworm (Bombyx mori L.).}, journal = {Environmental science and pollution research international}, volume = {29}, number = {52}, pages = {79545-79554}, doi = {10.1007/s11356-022-21442-0}, pmid = {35713834}, issn = {1614-7499}, support = {Grant No. Xm2017177//Chongqing Postdoctoral Science Special Foundation/ ; [2020]1Y139//Natural Science Foundation of Guizhou Province/ ; [2019]1253//Natural Science Foundation of Guizhou Province/ ; }, mesh = {Animals ; *Bombyx ; RNA, Ribosomal, 16S/genetics ; *Disinfectants/pharmacology ; Sodium Hypochlorite ; Hypochlorous Acid ; Insecta ; Silk ; Formaldehyde ; }, abstract = {The insect egg surface can serve as a vehicle for vertical symbiont transmission from the maternal parent to its offspring. Hypochlorite and formaldehyde are two common disinfectants used for insect egg surface sterilization. Here, we explored the intestinal microecology and immune response profile of the silkworm Bombyx mori strain Dazao after disinfectant exposure by using high-throughput sequencing technology and real-time PCR analysis. After egg surface sterilization, no significant difference (P > 0.05) in overall body weight was observed among the control, sodium hypochlorite, and formaldehyde groups. 16S rRNA metagenomic sequencing revealed that the main abundant intestinal bacteria were Enterococcus, Burkholderia, Phenylobacterium, Ralstonia, Chitinophaga, Bradyrhizobium, Herbaspirillum, and two unclassified Bacteroidetes species. Egg surface sterilization evidently altered the composition and abundance of intestinal microbiota but did not significantly change its alpha diversity. The dysbiosis of intestinal microbiota resulted in the perturbation of the immune response profile of the silkworm intestine. Our findings reveal that hypochlorite has a blocking effect on the symbiont transmission compared with formaldehyde. More importantly, egg surface sterilization exerts substantial effects on the ecophysiological traits of insects. The present study contributes to the scientific and reasonable application of disinfectants for insect egg surface sterilization during industrial silk production and laboratory-scale insect rearing.}, } @article {pmid35713613, year = {2023}, author = {Zeng, Z and Guo, H and Chen, L and Lin, Z and Guan, W and Wang, Y and Jiang, H and Wu, X and Yin, Y and Gao, Z and Chen, C and Yang, Z}, title = {Culturing Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) for Diagnosis and Genome Sequencing.}, journal = {Laboratory medicine}, volume = {54}, number = {1}, pages = {30-34}, pmid = {35713613}, issn = {1943-7730}, support = {2020YFA0708002//National Key Research and Development Program of China/ ; ZNSA-2020012//Zhongnanshan Medical Foundation of Guangdong Province/ ; 2020001000206//Science and Technology Program of Foshan/ ; 202102100003//Science and Technology Program of Guangzhou/ ; 2020GIRHHMS23//China Evergrande/ ; 2020B1515120045//National Natural Science Foundation of Guangdong/ ; [2020]4Y219//National Natural Science Foundation of Guizhou/ ; 202071715001114//Science and Technology Bureau Project of Dongguan/ ; 202206010025//Science and Technology Program of Guangzhou/ ; 2021A1111120009//Key Research and Development Program of Guangdong Province/ ; }, mesh = {Humans ; *SARS-CoV-2/genetics ; *COVID-19/diagnosis ; RNA, Viral/genetics ; COVID-19 Testing ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {OBJECTIVE: The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) nucleic acid detection "re-positive" phenomenon is encountered clinically. The accuracy of a viral nucleic acid test is crucial to prevent reintroduction of the virus into the community. This study evaluated the effect of virus culturing on increasing the sensitivity and specificity of real-time polymerase chain reaction (RT-PCR) detection and viral genomic sequencing.

METHODS: A series of tenfold dilutions of a SARS-CoV-2 viral stock were conducted and cultured for either 24 or 48 hours. The viral load of cultured samples was determined by RT-PCR. The cultured and non-cultured samples of 1x 50% tissue culture infectious dose (TCID50) were sequenced using metagenomic next-generation sequencing. The depth and coverage of SARS-CoV-2 genome were measured.

RESULTS: The lowest viral load detectable in a sample with RT-PCR was 0.01 TCID50. After a 24-h culture, the viral ORF 1ab and N-gene cycle threshold (CT) values were reduced by 4.4 points and 1 point, respectively. One TCID50 viral load of post 24-h culture revealed the sequence depth reached an average of 752 reads, compared with 0.15 in the nonculture; furthermore, the coverage was 99.99% while 6.42% in the nonculture.

CONCLUSION: These results indicate that virus culturing can significantly increase the viral load, which can increase the certainty of true-positive detection of the viral nucleic acids, and improve the quality of virus genomic sequencing.}, } @article {pmid35713513, year = {2022}, author = {Song, W and Zhang, S and Thomas, T}, title = {MarkerMAG: linking metagenome-assembled genomes (MAGs) with 16S rRNA marker genes using paired-end short reads.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {15}, pages = {3684-3688}, doi = {10.1093/bioinformatics/btac398}, pmid = {35713513}, issn = {1367-4811}, support = {ANP 21005-4//R&D project/ ; //Shell Brasil under the ANP R&D levy as 'Compromisso de Investimentos com Pesquisa e Desenvolvimento/ ; //Research Technology Services at UNSW Sydney/ ; }, mesh = {*Metagenome ; RNA, Ribosomal, 16S/genetics ; Phylogeny ; *Metagenomics ; Databases, Factual ; }, abstract = {MOTIVATION: Metagenome-assembled genomes (MAGs) have substantially extended our understanding of microbial functionality. However, 16S rRNA genes, which are commonly used in phylogenetic analysis and environmental surveys, are often missing from MAGs. Here, we developed MarkerMAG, a pipeline that links 16S rRNA genes to MAGs using paired-end sequencing reads.

RESULTS: Assessment of MarkerMAG on three benchmarking metagenomic datasets with various degrees of complexity shows substantial increases in the number of MAGs with 16S rRNA genes and a 100% assignment accuracy. MarkerMAG also estimates the copy number of 16S rRNA genes in MAGs with high accuracy. Assessments on three real metagenomic datasets demonstrate 1.1- to 14.2-fold increases in the number of MAGs with 16S rRNA genes. We also show that MarkerMAG-improved MAGs increase the accuracy of functional prediction from 16S rRNA gene amplicon data. MarkerMAG is helpful in connecting information in MAG databases with those in 16S rRNA databases and surveys and hence contributes to our increasing understanding of microbial diversity, function and phylogeny.

MarkerMAG is implemented in Python3 and freely available at https://github.com/songweizhi/MarkerMAG.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid35713429, year = {2022}, author = {Zhang, A and Xia, X and Yuan, X and Lv, Y and Liu, Y and Niu, H and Zhang, D and Liang, J}, title = {Clinical characteristics of 14 cases of severe Chlamydia psittaci pneumonia diagnosed by metagenomic next-generation sequencing: A case series.}, journal = {Medicine}, volume = {101}, number = {24}, pages = {e29238}, pmid = {35713429}, issn = {1536-5964}, mesh = {*Chlamydophila psittaci/genetics ; Creatine Kinase ; Doxycycline ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; Middle Aged ; Natriuretic Peptide, Brain ; *Pneumonia ; Procalcitonin ; *Psittacosis/diagnosis ; *Quinolones ; Retrospective Studies ; }, abstract = {INTRODUCTION: The objective of this study was to explore the clinical, laboratory, and imaging features of severe Chlamydia psittaci pneumonia in order to improve early diagnosis and treatment success rates.

METHODS: We conducted a retrospective record review of 14 cases of severe Chlamydia psittaci pneumonia diagnosed by metagenomic next-generation sequencing technology in our hospital. We extracted and analyzed data on the clinical symptoms and signs, contact history, laboratory investigations, chest computed tomography, treatment, and clinical outcomes.

RESULTS: Of the 14 patients, 12 (86%) were male and two (14%) were female, with a mean age of 57 years (SD: 7 years). Eleven patients (79%) had a history of poultry contact. The main clinical manifestations were fever (n = 14, 100%), flu-like symptoms (n = 10, 71%), cough, sputum (n = 9, 64%), and dyspnea (n = 5, 36%). Blood tests revealed marked elevation of neutrophil percentage, C-reactive protein, procalcitonin, brain natriuretic peptide, and creatine kinase levels; slight elevation of aspartate aminotransferase, creatinine, urea, fibrinogen, and D-dimer levels; and decreased albumin, sodium, and calcium levels. Chest computed tomography showed bilateral lesions (n = 7, 50%), middle-lower lobe lesions (n = 10, 71%), lesions in multiple lobes (n = 9, 64%), consolidation shadows (n = 11, 79%), and pleural effusions (n = 11, 79%). The median time from disease onset to hospital admission was 4.5 days (interquartile range: 1-17 days); the mean length of hospital stay was 20.9 ± 8.5 days, and the mean time from admission to diagnosis was 5.1 ± 2.6 days. After diagnosis, patients were either treated with doxycycline alone or doxycycline combined with quinolones. All 14 patients developed respiratory failure and received invasive mechanical ventilation; two (14%) received veno-venous extracorporeal membrane oxygenation, four (29%) received continuous renal replacement therapy, and three (21%) died.

DISCUSSION AND CONCLUSION: A poultry contact history and typical flu-like symptoms are early indicators of Chlamydia psittaci pneumonia. Substantial elevations in procalcitonin, creatine kinase, and brain natriuretic peptide indicate severe disease. Metagenomic next-generation sequencing is useful for diagnosis. Early empirical antibiotic therapy with quinolones can reduce the mortality in critically ill patients.}, } @article {pmid35713407, year = {2022}, author = {Shaffer, JP and Carpenter, CS and Martino, C and Salido, RA and Minich, JJ and Bryant, M and Sanders, K and Schwartz, T and Humphrey, G and Swafford, AD and Knight, R}, title = {A comparison of six DNA extraction protocols for 16S, ITS and shotgun metagenomic sequencing of microbial communities.}, journal = {BioTechniques}, volume = {73}, number = {1}, pages = {34-46}, pmid = {35713407}, issn = {1940-9818}, support = {R01 DK102932/DK/NIDDK NIH HHS/United States ; K12 GM068524/GM/NIGMS NIH HHS/United States ; U01 AI124316/AI/NIAID NIH HHS/United States ; DP1 AT010885/AT/NCCIH NIH HHS/United States ; U19 AG063744/AG/NIA NIH HHS/United States ; R01 HL140976/HL/NHLBI NIH HHS/United States ; R01 HL134887/HL/NHLBI NIH HHS/United States ; RF1 AG058942/AG/NIA NIH HHS/United States ; }, mesh = {Bacteria/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenomics/methods ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {Microbial communities contain a broad phylogenetic diversity of organisms; however, the majority of methods center on describing bacteria and archaea. Fungi are important symbionts in many ecosystems and are potentially important members of the human microbiome, beyond those that can cause disease. To expand our analysis of microbial communities to include data from the fungal internal transcribed spacer (ITS) region, five candidate DNA extraction kits were compared against our standardized protocol for describing bacteria and archaea using 16S rRNA gene amplicon- and shotgun metagenomics sequencing. The results are presented considering a diverse panel of host-associated and environmental sample types and comparing the cost, processing time, well-to-well contamination, DNA yield, limit of detection and microbial community composition among protocols. Across all criteria, the MagMAX Microbiome kit was found to perform best. The PowerSoil Pro kit performed comparably but with increased cost per sample and overall processing time. The Zymo MagBead, NucleoMag Food and Norgen Stool kits were included.}, } @article {pmid35713100, year = {2023}, author = {Dixit, S and Kumar, S and Sharma, R and Banakar, PS and Singh, M and Keshri, A and Tyagi, AK}, title = {Rumen multi-omics addressing diet-host-microbiome interplay in farm animals: a review.}, journal = {Animal biotechnology}, volume = {34}, number = {7}, pages = {3187-3205}, doi = {10.1080/10495398.2022.2078979}, pmid = {35713100}, issn = {1532-2378}, mesh = {Animals ; *Rumen/metabolism ; Farms ; Multiomics ; *Microbiota ; Diet/veterinary ; Animal Feed ; }, abstract = {Continuous improvement in the living standards of developing countries, calls for an urgent need of high quality meat and dairy products. The farm animals have a micro-ecosystem in gastro-intestinal tract, comprising of a wide variety of flora and fauna which converts roughages and agricultural byproducts as well as nutrient rich concentrate sources into the useful products such as volatile fatty acids and microbial crude proteins. The microbial diversity changes according to composition of the feed, host species/breed and host's individual genetic makeup. From culture methods to next-generation sequencing technologies, the knowledge has emerged a lot to know-how of microbial world viz. their identification, enzymatic activities and metabolites which are the keys of ruminant's successful existence. The structural composition of ruminal community revealed through metagenomics can be elaborated by metatranscriptomics and metabolomics through deciphering their functional role in metabolism and their responses to the external and internal stimuli. These highly sophisticated analytical tools have made possible to correlate the differences in the feed efficiency, nutrients utilization and methane emissions to their rumen microbiome. The comprehensively understood rumen microbiome will enhance the knowledge in the fields of animal nutrition, biotechnology and climatology through deciphering the significance of each and every domain of residing microbial entity. The present review undertakes the recent investigations regarding rumen multi-omics viz. taxonomic and functional potential of microbial populations, host-diet-microbiome interactions and correlation with metabolic dynamics.}, } @article {pmid35712966, year = {2023}, author = {Qian, Z and Zhang, Y and Wang, L and Li, Z and Wang, H and Kang, H and Feng, J and Hu, X and Tao, Y}, title = {Application of metagenomic next-generation sequencing in suspected intraocular infections.}, journal = {European journal of ophthalmology}, volume = {33}, number = {1}, pages = {391-397}, doi = {10.1177/11206721221107311}, pmid = {35712966}, issn = {1724-6016}, mesh = {Humans ; Retrospective Studies ; *Eye Infections ; Eye ; *Endophthalmitis/diagnosis ; High-Throughput Nucleotide Sequencing ; Sensitivity and Specificity ; }, abstract = {PURPOSE: To evaluate the efficacy of metagenomic next-generation sequencing (mNGS) and to explore its value in the diagnosis of intraocular infection.

METHODS: A retrospective case-series study of patients with suspected intraocular infection was performed. Intraocular fluid samples were collected from all the patients and sent for mNGS. Detailed clinical data, the results of mNGS and other laboratory examinations, the sequencing data of mNGS, and the final diagnosis were recorded.

RESULTS: Fifteen eyes of 15 patients were included in the study. Eight samples were identified as positive for different kinds of pathogens by mNGS, which were all confirmed by other laboratory examinations or effective diagnostic treatment. The mNGS results were negative in seven samples. The final diagnosis was still intraocular infection in four of the seven negative results. Of these, one patient was diagnosed with fungal endophthalmitis according to the clinical characteristics and good treatment response to the anti-fungal therapy, one patient underwent vitrectomy and the bacterial culture of the vitreous sample was positive for Brucella melitensis, and two patients were diagnosed with ocular tuberculosis according to the positive T-SPOT test and effective anti-tuberculous treatments.

CONCLUSIONS: mNGS could be helpful in determining pathogens in cases of suspected intraocular infection. The mNGS protocols should be optimized for the detection of intracellular bacterial and fungal pathogens.}, } @article {pmid35711780, year = {2022}, author = {Su, M and Hao, Z and Shi, H and Li, T and Wang, H and Li, Q and Zhang, Y and Ma, Y}, title = {Metagenomic Analysis Revealed Differences in Composition and Function Between Liquid-Associated and Solid-Associated Microorganisms of Sheep Rumen.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {851567}, pmid = {35711780}, issn = {1664-302X}, abstract = {The rumen microbiota plays a key role in the utilization of plant materials by ruminants, yet little is known about the key taxa and their genetic functions of the rumen sub-environment involved in the ruminal degradation process. Understanding the differences in the composition and function of ruminal microbiota in the liquid-associated (LA) and solid-associated (SA) systems is needed to further study and regulate rumen function and health. In this study, rumen contents of nine sheep were collected to separate LA and SA systems with elution and centrifugal precipitation. Metagenome sequencing was used to investigate the differences in microbial composition and genetic functions of LA and SA systems, with special emphasis on their degradational potential toward carbohydrates. Results showed that the dominant species composition was similar between the two systems, but SA microorganisms had a higher relative abundance than LA microorganisms in all taxa. The concentration of fiber-degrading bacteria, such as Ruminococcus, Treponema, and Fibrobacter, was higher and Prevotella was lower in the SA vs. LA system. Additionally, SA microorganisms dominated in cellulose degradation, while LA microorganisms were more important in starch utilization based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO)'s functional categories and Carbohydrate-Active Enzymes (CAZymes). In general, SA microorganisms are more abundant and important in metabolic functions than LA, such as carbohydrate and amino acid metabolisms. In summary, the key differential biomarkers between LA and SA systems were Prevotella, Ruminococcus, Treponema, and Fibrobacter. Ruminal microbes degraded carbohydrates synergistically with SA, thus, more focusing on cellulose and hemicellulose, while LA is more important to starch.}, } @article {pmid35711762, year = {2022}, author = {Ding, J and Wu, B and Chen, L}, title = {Application of Marine Microbial Natural Products in Cosmetics.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {892505}, pmid = {35711762}, issn = {1664-302X}, abstract = {As the market size of the cosmetics industry increases, the safety and effectiveness of new products face higher requirements. The marine environment selects for species of micro-organisms with metabolic pathways and adaptation mechanisms different from those of terrestrial organisms, resulting in their natural products exhibiting unique structures, high diversity, and significant biological activities. Natural products are usually safe and non-polluting. Therefore, considerable effort has been devoted to searching for cosmetic ingredients that are effective, safe, and natural for marine micro-organisms. However, marine micro-organisms can be difficult, or impossible, to culture because of their special environmental requirements. Metagenomics technology can help to solve this problem. Moreover, using marine species to produce more green and environmentally friendly products through biotransformation has become a new choice for cosmetic manufacturers. In this study, the natural products of marine micro-organisms are reviewed and evaluated with respect to various cosmetic applications.}, } @article {pmid35711746, year = {2022}, author = {Korth, B and Pous, N and Hönig, R and Haus, P and Corrêa, FB and Nunes da Rocha, U and Puig, S and Harnisch, F}, title = {Electrochemical and Microbial Dissection of Electrified Biotrickling Filters.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {869474}, pmid = {35711746}, issn = {1664-302X}, abstract = {Electrified biotrickling filters represent sustainable microbial electrochemical technology for treating organic carbon-deficient ammonium-contaminated waters. However, information on the microbiome of the conductive granule bed cathode remains inexistent. For uncovering this black box and for identifying key process parameters, minimally invasive sampling units were introduced, allowing for the extraction of granules from different reactor layers during reactor operation. Sampled granules were analyzed using cyclic voltammetry and molecular biological tools. Two main redox sites [-288 ± 18 mV and -206 ± 21 mV vs. standard hydrogen electrode (SHE)] related to bioelectrochemical denitrification were identified, exhibiting high activity in a broad pH range (pH 6-10). A genome-centric analysis revealed a complex nitrogen food web and the presence of typical denitrifiers like Pseudomonas nitroreducens and Paracoccus versutus with none of these species being identified as electroactive microorganism so far. These are the first results to provide insights into microbial structure-function relationships within electrified biotrickling filters and underline the robustness and application potential of bioelectrochemical denitrification for environmental remediation.}, } @article {pmid35711426, year = {2022}, author = {Hua, H and Meydan, C and Afshin, EE and Lili, LN and D'Adamo, CR and Rickard, N and Dudley, JT and Price, ND and Zhang, B and Mason, CE}, title = {A Wipe-Based Stool Collection and Preservation Kit for Microbiome Community Profiling.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {889702}, pmid = {35711426}, issn = {1664-3224}, mesh = {DNA, Bacterial/genetics ; Feces/microbiology ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Specimen Handling/methods ; }, abstract = {While a range of methods for stool collection exist, many require complicated, self-directed protocols and stool transfer. In this study, we introduce and validate a novel, wipe-based approach to fecal sample collection and stabilization for metagenomics analysis. A total of 72 samples were collected across four different preservation types: freezing at -20°C, room temperature storage, a commercial DNA preservation kit, and a dissolvable wipe used with DESS (dimethyl sulfoxide, ethylenediaminetetraacetic acid, sodium chloride) solution. These samples were sequenced and analyzed for taxonomic abundance metrics, bacterial metabolic pathway classification, and diversity analysis. Overall, the DESS wipe results validated the use of a wipe-based capture method to collect stool samples for microbiome analysis, showing an R[2] of 0.96 for species across all kingdoms, as well as exhibiting a maintenance of Shannon diversity (3.1-3.3) and species richness (151-159) compared to frozen samples. Moreover, DESS showed comparable performance to the commercially available preservation kit (R[2] of 0.98), and samples consistently clustered by subject across each method. These data support that the DESS wipe method can be used for stable, room temperature collection and transport of human stool specimens.}, } @article {pmid35711276, year = {2022}, author = {Ssebambulidde, K and Gakuru, J and Ellis, J and Cresswell, FV and Bahr, NC}, title = {Improving Technology to Diagnose Tuberculous Meningitis: Are We There Yet?.}, journal = {Frontiers in neurology}, volume = {13}, number = {}, pages = {892224}, pmid = {35711276}, issn = {1664-2295}, support = {K23 NS110470/NS/NINDS NIH HHS/United States ; }, abstract = {Diagnosis of tuberculous meningitis (TBM) remains challenging due to a paucity of high-performance diagnostics. Even those that have reasonable sensitivity are not adequate to 'rule out' TBM. Therefore, a combination of clinical factors alongside microbiological, molecular, and radiological investigations are utilized, depending on availability. A low threshold for starting empiric therapy in the appropriate clinical scenario remains crucial for good outcomes in many cases. Herein, we review the current TBM diagnostics landscape with a focus on limitations frequently encountered, such as diagnostic test performance, cost, laboratory infrastructure, and clinical expertise. Though molecular technologies, particularly GeneXpert MTB/Rif Ultra, have been a step forward, diagnosis of TBM remains difficult. We also provide an overview of promising technologies, such as cerebrospinal fluid (CSF) lactate, a new lipoarabinomannan test (FujiLAM), metagenomic next-generation sequencing, and transcriptomics that may further improve our TBM diagnostic capacity and lead to better outcomes.}, } @article {pmid35710793, year = {2022}, author = {Park, S and You, YA and Kim, YH and Kwon, E and Ansari, A and Kim, SM and Lee, G and Hur, YM and Jung, YJ and Kim, K and Kim, YJ}, title = {Ureaplasma and Prevotella colonization with Lactobacillus abundance during pregnancy facilitates term birth.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {10148}, pmid = {35710793}, issn = {2045-2322}, mesh = {Case-Control Studies ; Female ; Humans ; Infant, Newborn ; Lactobacillus/genetics ; Pregnancy ; *Premature Birth/microbiology ; Prevotella/genetics ; RNA, Ribosomal, 16S/genetics ; Term Birth ; Ureaplasma/genetics ; *Ureaplasma Infections ; Vagina/microbiology ; }, abstract = {Ureaplasma and Prevotella infections are well-known bacteria associated with preterm birth. However, with the development of metagenome sequencing techniques, it has been found that not all Ureaplasma and Prevotella colonizations cause preterm birth. The purpose of this study was to determine the association between Ureaplasma and Prevotella colonization with the induction of preterm birth even in the presence of Lactobacillus. In this matched case-control study, a total of 203 pregnant Korean women were selected and their cervicovaginal fluid samples were collected during mid-pregnancy. The microbiome profiles of the cervicovaginal fluid were analyzed using 16S rRNA gene amplification. Sequencing data were processed using QIIME1.9.1. Statistical analyses were performed using R software, and microbiome analysis was performed using the MicrobiomeAnalyst and Calypso software. A positive correlation between Ureaplasma and other genera was highly related to preterm birth, but interestingly, there was a negative correlation with Lactobacillus and term birth, with the same pattern observed with Prevotella. Ureaplasma and Prevotella colonization with Lactobacillus abundance during pregnancy facilitates term birth, although Ureaplasma and Prevotella are associated with preterm birth. Balanced colonization between Lactobacillus and Ureaplasma and Prevotella is important to prevent preterm birth.}, } @article {pmid35710760, year = {2022}, author = {Escudero-Martinez, C and Coulter, M and Alegria Terrazas, R and Foito, A and Kapadia, R and Pietrangelo, L and Maver, M and Sharma, R and Aprile, A and Morris, J and Hedley, PE and Maurer, A and Pillen, K and Naclerio, G and Mimmo, T and Barton, GJ and Waugh, R and Abbott, J and Bulgarelli, D}, title = {Identifying plant genes shaping microbiota composition in the barley rhizosphere.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3443}, pmid = {35710760}, issn = {2041-1723}, support = {BB/S002871/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/genetics ; Genes, Plant/genetics ; *Hordeum/genetics ; *Microbiota/genetics ; Plant Roots/genetics ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; }, abstract = {A prerequisite to exploiting soil microbes for sustainable crop production is the identification of the plant genes shaping microbiota composition in the rhizosphere, the interface between roots and soil. Here, we use metagenomics information as an external quantitative phenotype to map the host genetic determinants of the rhizosphere microbiota in wild and domesticated genotypes of barley, the fourth most cultivated cereal globally. We identify a small number of loci with a major effect on the composition of rhizosphere communities. One of those, designated the QRMC-3HS, emerges as a major determinant of microbiota composition. We subject soil-grown sibling lines harbouring contrasting alleles at QRMC-3HS and hosting contrasting microbiotas to comparative root RNA-seq profiling. This allows us to identify three primary candidate genes, including a Nucleotide-Binding-Leucine-Rich-Repeat (NLR) gene in a region of structural variation of the barley genome. Our results provide insights into the footprint of crop improvement on the plant's capacity of shaping rhizosphere microbes.}, } @article {pmid35710683, year = {2022}, author = {Hu, R and Yao, R and Li, L and Xu, Y and Lei, B and Tang, G and Liang, H and Lei, Y and Li, C and Li, X and Liu, K and Wang, L and Zhang, Y and Wang, Y and Cui, Y and Dai, J and Ni, W and Zhou, P and Yu, B and Hu, S}, title = {A database of animal metagenomes.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {312}, pmid = {35710683}, issn = {2052-4463}, mesh = {Animals ; Cattle ; *Databases, Factual ; High-Throughput Nucleotide Sequencing ; Horses ; Metadata ; *Metagenome ; Metagenomics ; Sheep ; Swine ; }, abstract = {With the rapid development of high-throughput sequencing technology, the amount of metagenomic data (including both 16S and whole-genome sequencing data) in public repositories is increasing exponentially. However, owing to the large and decentralized nature of the data, it is still difficult for users to mine, compare, and analyze the data. The animal metagenome database (AnimalMetagenome DB) integrates metagenomic sequencing data with host information, making it easier for users to find data of interest. The AnimalMetagenome DB is designed to contain all public metagenomic data from animals, and the data are divided into domestic and wild animal categories. Users can browse, search, and download animal metagenomic data of interest based on different attributes of the metadata such as animal species, sample site, study purpose, and DNA extraction method. The AnimalMetagenome DB version 1.0 includes metadata for 82,097 metagenomes from 4 domestic animals (pigs, bovines, horses, and sheep) and 540 wild animals. These metagenomes cover 15 years of experiments, 73 countries, 1,044 studies, 63,214 amplicon sequencing data, and 10,672 whole genome sequencing data. All data in the database are hosted and available in figshare https://doi.org/10.6084/m9.figshare.19728619 .}, } @article {pmid35710651, year = {2022}, author = {Zhou, L and Huang, S and Gong, J and Xu, P and Huang, X}, title = {500 metagenome-assembled microbial genomes from 30 subtropical estuaries in South China.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {310}, pmid = {35710651}, issn = {2052-4463}, mesh = {China ; Estuaries ; *Genome, Microbial ; *Metagenome ; Metagenomics ; *Microbiota ; }, abstract = {As a unique geographical transition zone, the estuary is considered as a model environment to decipher the diversity, functions and ecological processes of microbial communities, which play important roles in the global biogeochemical cycle. Here we used surface water metagenomic sequencing datasets to construct metagenome-assembled genomes (MAGs) from 30 subtropical estuaries at a large scale along South China. In total, 500 dereplicated MAGs with completeness ≥ 50% and contamination ≤ 10% were obtained, among which more than one-thirds (n = 207 MAGs) have a completeness ≥ 70%. These MAGs are dominated by taxa assigned to the phylum Proteobacteria (n = 182 MAGs), Bacteroidota (n = 110) and Actinobacteriota (n = 104). These draft genomes can be used to study the diversity, phylogenetic history and metabolic potential of microbiota in the estuary, which should help improve our understanding of the structure and function of these microorganisms and how they evolved and adapted to extreme conditions in the estuarine ecosystem.}, } @article {pmid35710629, year = {2022}, author = {Oyserman, BO and Flores, SS and Griffioen, T and Pan, X and van der Wijk, E and Pronk, L and Lokhorst, W and Nurfikari, A and Paulson, JN and Movassagh, M and Stopnisek, N and Kupczok, A and Cordovez, V and Carrión, VJ and Ligterink, W and Snoek, BL and Medema, MH and Raaijmakers, JM}, title = {Disentangling the genetic basis of rhizosphere microbiome assembly in tomato.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3228}, pmid = {35710629}, issn = {2041-1723}, support = {U01 GM110706/GM/NIGMS NIH HHS/United States ; }, mesh = {Iron/metabolism ; *Solanum lycopersicum/metabolism ; *Microbiota/genetics ; Plant Breeding ; Plants/metabolism ; Rhizosphere ; }, abstract = {Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, we map the molecular features of the rhizosphere microbiome as quantitative traits of a diverse hybrid population of wild and domesticated tomato. Gene content analysis of prioritized tomato quantitative trait loci suggests a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31 Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the water channel aquaporin SlTIP2.3. Within metagenome-assembled genomes of root-associated Streptomyces and Cellvibrio, we identify bacterial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associates with specific tomato QTLs. By integrating 'microbiomics' and quantitative plant genetics, we pinpoint putative plant and reciprocal rhizobacterial traits underlying microbiome assembly, thereby providing a first step towards plant-microbiome breeding programs.}, } @article {pmid35710557, year = {2022}, author = {Belliardo, C and Koutsovoulos, GD and Rancurel, C and Clément, M and Lipuma, J and Bailly-Bechet, M and Danchin, EGJ}, title = {Improvement of eukaryotic protein predictions from soil metagenomes.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {311}, pmid = {35710557}, issn = {2052-4463}, mesh = {*Eukaryota/genetics/metabolism ; *Metagenome ; Metagenomics ; *Soil Microbiology ; }, abstract = {During the last decades, metagenomics has highlighted the diversity of microorganisms from environmental or host-associated samples. Most metagenomics public repositories use annotation pipelines tailored for prokaryotes regardless of the taxonomic origin of contigs. Consequently, eukaryotic contigs with intrinsically different gene features, are not optimally annotated. Using a bioinformatics pipeline, we have filtered 7.9 billion contigs from 6,872 soil metagenomes in the JGI's IMG/M database to identify eukaryotic contigs. We have re-annotated genes using eukaryote-tailored methods, yielding 8 million eukaryotic proteins and over 300,000 orphan proteins lacking homology in public databases. Comparing the gene predictions we made with initial JGI ones on the same contigs, we confirmed our pipeline improves eukaryotic proteins completeness and contiguity in soil metagenomes. The improved quality of eukaryotic proteins combined with a more comprehensive assignment method yielded more reliable taxonomic annotation. This dataset of eukaryotic soil proteins with improved completeness, quality and taxonomic annotation reliability is of interest for any scientist aiming at studying the composition, biological functions and gene flux in soil communities involving eukaryotes.}, } @article {pmid35709638, year = {2022}, author = {Guan, Y and Jia, J and Fan, X and Li, K and Wang, Z}, title = {Anthropogenic impacts on antibiotic resistance genes and their hosts from pristine to urban river using metagenomic and binning approaches.}, journal = {Aquatic toxicology (Amsterdam, Netherlands)}, volume = {249}, number = {}, pages = {106221}, doi = {10.1016/j.aquatox.2022.106221}, pmid = {35709638}, issn = {1879-1514}, mesh = {Anthropogenic Effects ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Ecosystem ; Humans ; *Rivers ; *Water Pollutants, Chemical/toxicity ; }, abstract = {Driven by anthropogenic pressure, Antibiotic resistance genes (ARGs) could transfer from the environmental resistome into human commensals or even pathogens. The transport of ARGs through aquatic ecosystems is crucial and has attracted attention. Here, we employed metagenomic and binning to compare ARGs profiles, their co-occurrence with metal resistance genes (MRGs) and mobile genetic elements (MGEs), and their hosts between pristine and anthropogenic influenced rivers and explore the ecological mechanisms underlying the dissemination of ARGs induced by anthropogenic activities. The significantly increased relative abundance of macrolide-lincosamide-streptogramins, vancomycin, β-lactam and sulfonamide resistance genes along the environmental gradient from pristine to polluted sediments implied that anthropogenic impact aided the emergence and dissemination of certain ARGs. At the lower reach of the Ba River, the higher ratios for contigs carrying more than one ARG suggested that anthropogenic pollution favored the co-occurrence of multiple ARGs. Anthropogenic pressures also increased the relative abundance of advantaged hosts, including Chloroflexi, Firmicutes and Euryarchaeota. At the lower reach of Ba River, Romboutsia timonensis carrying multiple ARGs and ICEs were successfully recovered, posing a serious threat to human health by affecting the metabolism of gut microbiomes. And Methanothrix soehngenii affiliated to archaea carrying multiple ARGs, MRGs and ICEs were also recovered from the lower Ba River. The partial least squares path modeling revealed that MGEs were the most predominant factors inducing the ARG profiles, and the antibiotic resistance could be enriched by co-transfer with MRGs. Furthermore, environmental factors could impact the ARG profiles indirectly by first influencing the ARGs' hosts.}, } @article {pmid35709619, year = {2022}, author = {Liang, C and Ye, Q and Huang, Y and Wang, Y and Zhang, Z and Wang, H}, title = {Shifts of the new functional marker gene (pahE) of polycyclic aromatic hydrocarbons (PAHs) degrading bacterial population and its relationship with PAHs biodegradation.}, journal = {Journal of hazardous materials}, volume = {437}, number = {}, pages = {129305}, doi = {10.1016/j.jhazmat.2022.129305}, pmid = {35709619}, issn = {1873-3336}, mesh = {Bacteria/metabolism ; Biodegradation, Environmental ; Geologic Sediments/microbiology ; Metagenomics ; *Polycyclic Aromatic Hydrocarbons/analysis ; }, abstract = {Identification of polycyclic aromatic hydrocarbons (PAHs) degrading bacterial populations and understanding their responses to PAHs are crucial for the designing of appropriate bioremediation strategies. In this study, the responses of PAHs-degrading bacterial populations to different PAHs were studied in terms of the compositions and abundance variations of their new functional marker gene (pahE) by gene-targeted metagenomic and qPCR analysis. Overall, PAHs species significantly affected the composition and abundance of pahE gene within the PAHs-degrading bacteria in each treatment and different pahE of PAHs-degrading bacteria involved in the different stages of PAHs degradation. Noted that new pahE genotypes were also discovered in all PAHs treatment groups, indicating that some potential new PAHs-degrading bacterial genera were also involved in PAHs degradation. Besides, all three PAH removal rates were significantly positively related with pahE gene abundances (R[2] = 0.908 ~ 0.922, p < 0.01), demonstrating that pahE could be a good indicator of PAHs degradation activity or potential. This is the first study focusing on the dynamic changes of the pahE gene within PAHs-degrading bacterial community during the degradation of PAHs in mangrove sediment, providing novel insights into the use of pahE gene as the functional marker to indicate PAH degradation.}, } @article {pmid35709584, year = {2022}, author = {Ferrocino, I and Rantsiou, K and Cocolin, L}, title = {Microbiome and -omics application in food industry.}, journal = {International journal of food microbiology}, volume = {377}, number = {}, pages = {109781}, doi = {10.1016/j.ijfoodmicro.2022.109781}, pmid = {35709584}, issn = {1879-3460}, mesh = {Food Industry ; Microbiological Techniques ; *Microbiota ; }, abstract = {The enormous potential of multi-omics approaches to unravel microbiome-related links between food quality, sustainability and safety still requires experimental work and extensive data integration to increase knowledge and understand the biological and ecological processes involved in the assembly and dynamics of microbial communities along the production chains. Data spanning from DNA sequences to transcripts and metabolites need to be integrated in order to be translated at industrial level and literature showed several successful examples. The application of microbiome studies in food systems has shown the potential to improve food quality. Nevertheless, classical microbiological methods are still highly relevant even if isolation and characterization of strains in pure culture is often laborious and time-consuming and requires the use of several specific growth media that take into the account microbial growth characteristics as well as food characteristics. Studies on microbiomes have become a popular topic in the food industry since it can be used as a tool to improve quality and safety in the food chain.}, } @article {pmid35709201, year = {2022}, author = {Vijayvargiya, P and Feri, A and Mairey, M and Rouillon, C and Jeraldo, PR and Esquer Garrigos, Z and Thoendel, MJ and Greenwood-Quaintance, KE and Sohail, MR and Sampathkumar, P and Spychalla, MT and Stewart, AK and Patnaik, MM and Tande, AJ and Cruveiller, S and Hannet, I and Beurdeley, P and Patel, R}, title = {Metagenomic shotgun sequencing of blood to identify bacteria and viruses in leukemic febrile neutropenia.}, journal = {PloS one}, volume = {17}, number = {6}, pages = {e0269405}, pmid = {35709201}, issn = {1932-6203}, support = {U54 GM115428/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; *Febrile Neutropenia/complications ; Fever/etiology ; Humans ; *Leukemia, Myeloid, Acute/complications ; *Viruses ; }, abstract = {Despite diagnostic advances in microbiology, the etiology of neutropenic fever remains elusive in most cases. In this study, we evaluated the utility of a metagenomic shotgun sequencing based assay for detection of bacteria and viruses in blood samples of patients with febrile neutropenia. We prospectively enrolled 20 acute leukemia patients and obtained blood from these patients at three time points: 1) anytime from onset of neutropenia until before development of neutropenic fever, 2) within 24 hours of onset of neutropenic fever, 3) 5-7 days after onset of neutropenic fever. Blood samples underwent sample preparation, sequencing and analysis using the iDTECT® Dx Blood v1® platform (PathoQuest, Paris, France). Clinically relevant viruses or bacteria were detected in three cases each by metagenomic shotgun sequencing and blood cultures, albeit with no concordance between the two. Further optimization of sample preparation methods and sequencing platforms is needed before widespread adoption of this technology into clinical practice.}, } @article {pmid35708586, year = {2022}, author = {Singh, A and Schnürer, A}, title = {AcetoBase Version 2: a database update and re-analysis of formyltetrahydrofolate synthetase amplicon sequencing data from anaerobic digesters.}, journal = {Database : the journal of biological databases and curation}, volume = {2022}, number = {}, pages = {}, pmid = {35708586}, issn = {1758-0463}, mesh = {Anaerobiosis ; Bacteria/genetics ; *Formate-Tetrahydrofolate Ligase/genetics ; Metagenome ; Metagenomics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {AcetoBase is a public repository and database of formyltetrahydrofolate synthetase (FTHFS) sequences. It is the first systematic collection of bacterial FTHFS nucleotide and protein sequences from genomes and metagenome-assembled genomes and of sequences generated by clone library sequencing. At its publication in 2019, AcetoBase (Version 1) was also the first database to establish connections between the FTHFS gene, the Wood-Ljungdahl pathway and 16S ribosomal RNA genes. Since the publication of AcetoBase, there have been significant improvements in the taxonomy of many bacterial lineages and accessibility/availability of public genomics and metagenomics data. The update to the AcetoBase reference database described here (Version 2) provides new sequence data and taxonomy, along with improvements in web functionality and user interface. The evaluation of this latest update by re-analysis of publicly accessible FTHFS amplicon sequencing data previously analysed with AcetoBase Version 1 revealed significant improvements in the taxonomic assignment of FTHFS sequences. Database URL: https://acetobase.molbio.slu.se.}, } @article {pmid35708345, year = {2022}, author = {Ettinger, CL and Byrne, FJ and Redak, RA and Stajich, JE}, title = {Metagenome-Assembled Genomes of Bacterial Symbionts Associated with Insecticide-Resistant and -Susceptible Individuals of the Glassy-Winged Sharpshooter (Homalodisca vitripennis).}, journal = {Microbiology resource announcements}, volume = {11}, number = {7}, pages = {e0050622}, pmid = {35708345}, issn = {2576-098X}, support = {14-0379-000-SA-2//Pierce's Disease Control Program/ ; 01170-002//California Department of Food and Agriculture (CDFA)/ ; 007011-003//California Department of Food and Agriculture (CDFA)/ ; //Canadian Institute for Advanced Research (ICRA)/ ; CA-R-PPA-5062-H//U.S. Department of Agriculture (USDA)/ ; 012604-002//USDA | Animal and Plant Health Inspection Service (APHIS)/ ; }, abstract = {The role of microbes in insecticide resistance is an emerging question. Here, we describe six metagenome-assembled genomes (MAGs) associated with the glassy-winged sharpshooter (Homalodisca vitripennis [Germar, 1821]) (Hemiptera, Cicadellidae). MAGs representing the obligate symbionts Candidatus Sulcia muelleri and Candidatus Baumannia cicadellinicola and the facultative symbiont Wolbachia were obtained from imidacloprid-resistant and imidacloprid-susceptible sharpshooters.}, } @article {pmid35708307, year = {2023}, author = {Moussa, K and Gonzales, JA and Shantha, J and Acharya, NR and Doan, T}, title = {Prevalence of Epstein-Barr Virus in Patients with Intraocular Inflammation.}, journal = {Ocular immunology and inflammation}, volume = {31}, number = {5}, pages = {978-980}, pmid = {35708307}, issn = {1744-5078}, support = {K08 EY026986/EY/NEI NIH HHS/United States ; P30 EY002162/EY/NEI NIH HHS/United States ; }, mesh = {Humans ; Herpesvirus 4, Human/genetics ; *Epstein-Barr Virus Infections/complications/diagnosis/epidemiology ; *Retinal Neoplasms ; Prevalence ; Cross-Sectional Studies ; Vitreous Body ; *Uveitis/diagnosis/epidemiology ; Inflammation ; *Eye Neoplasms ; *Lymphoma ; }, abstract = {The relationship between Epstein-Barr virus (EBV) infection and uveitis is unclear. We conducted an observational cross-sectional study to determine the prevalence of EBV in uveitis and to describe the clinical features of EBV-positive uveitis cases. This study was carried out at the F.I. Proctor Foundation at the University of California, San Francisco. All patients with suspected infectious uveitis who underwent unbiased metagenomic deep sequencing (MDS) were included. Demographics, testing information, and clinical features were documented. Eleven out of 288 patients with suspected infectious uveitis had EBV detected by RNA-seq in intraocular fluid. The prevalence of EBV in uveitis in our study sample is 4%. Three out of 11 EBV-positive eyes (27%) were found to have biopsy-proven vitreoretinal lymphoma. Future studies are needed to determine if EBV may drive the development of vitreoretinal lymphoma and if its presence should heighten the suspicion of vitreoretinal lymphoma.}, } @article {pmid35707175, year = {2022}, author = {Koedooder, C and Landou, E and Zhang, F and Wang, S and Basu, S and Berman-Frank, I and Shaked, Y and Rubin-Blum, M}, title = {Metagenomes of Red Sea Subpopulations Challenge the Use of Marker Genes and Morphology to Assess Trichodesmium Diversity.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {879970}, pmid = {35707175}, issn = {1664-302X}, abstract = {Trichodesmium are filamentous cyanobacteria of key interest due to their ability to fix carbon and nitrogen within an oligotrophic marine environment. Their blooms consist of a dynamic assemblage of subpopulations and colony morphologies that are hypothesized to occupy unique niches. Here, we assessed the poorly studied diversity of Trichodesmium in the Red Sea, based on metagenome-assembled genomes (MAGs) and hetR gene-based phylotyping. We assembled four non-redundant MAGs from morphologically distinct Trichodesmium colonies (tufts, dense and thin puffs). Trichodesmium thiebautii (puffs) and Trichodesmium erythraeum (tufts) were the dominant species within these morphotypes. While subspecies diversity is present for both T. thiebautii and T. erythraeum, a single T. thiebautii genotype comprised both thin and dense puff morphotypes, and we hypothesize that this phenotypic variation is likely attributed to gene regulation. Additionally, we found the rare non-diazotrophic clade IV and V genotypes, related to Trichodesmium nobis and Trichodesmium miru, respectively that likely occurred as single filaments. The hetR gene phylogeny further indicated that the genotype in clade IV could represent the species Trichodesmium contortum. Importantly, we show the presence of hetR paralogs in Trichodesmium, where two copies of the hetR gene were present within T. thiebautii genomes. This may lead to the overestimation of Trichodesmium diversity as one of the copies misidentified T. thiebautii as Trichodesmium aureum. Taken together, our results highlight the importance of re-assessing Trichodesmium taxonomy while showing the ability of genomics to capture the complex diversity and distribution of Trichodesmium populations.}, } @article {pmid35707172, year = {2022}, author = {Sumithra, TG and Sharma, KSR and Gangadharan, S and Suresh, G and Prasad, V and Amala, PV and Sayooj, P and Gop, AP and Anil, MK and Patil, PK and Achamveetil, G}, title = {Dysbiosis and Restoration Dynamics of the Gut Microbiome Following Therapeutic Exposure to Florfenicol in Snubnose Pompano (Trachinotus blochii) to Aid in Sustainable Aquaculture Production Strategies.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {881275}, pmid = {35707172}, issn = {1664-302X}, abstract = {Information on unintended effects of therapeutic exposure of antibiotics on the fish gut microbiome is a vital prerequisite for ensuring fish and environmental health during sustainable aquaculture production strategies. The present study forms the first report on the impact of florfenicol (FFC), a recommended antibiotic for aquaculture, on the gut microbiome of snubnose pompano (Trachinotus blochii), a high-value marine aquaculture candidate. Both culture-dependent and independent techniques were applied to identify the possible dysbiosis and restoration dynamics, pointing out the probable risks to the host and environment health. The results revealed the critical transient dysbiotic events in the taxonomic and functional metagenomic profiles and significant reductions in the bacterial load and diversity measures. More importantly, there was a complete restoration of gut microbiome density, diversity, functional metagenomic profiles, and taxonomic composition (up to class level) within 10-15 days of antibiotic withdrawal, establishing the required period for applying proper management measures to ensure animal and environment health, following FFC treatment. The observed transient increase in the relative abundance of opportunistic pathogens suggested the need to apply proper stress management measures and probiotics during the period. Simultaneously, the results demonstrated the inhibitory potential of FFC against marine pathogens (vibrios) and ampicillin-resistant microbes. The study pointed out the possible microbial signatures of stress in fish and possible probiotic microbes (Serratia sp., Methanobrevibacter sp., Acinetobacter sp., and Bacillus sp.) that can be explored to design fish health improvisation strategies. Strikingly, the therapeutic exposure of FFC neither caused any irreversible increase in antibiotic resistance nor promoted the FFC resistant microbes in the gut. The significant transient increase in the numbers of kanamycin-resistant bacteria and abundance of two multidrug resistance encoding genes (K03327 and K03585) in the treated fish gut during the initial 10 days post-withdrawal suggested the need for implementing proper aquaculture effluent processing measures during the period, thus, helps to reduce the spillover of antibiotic-resistant microbes from the gut of the treated fish to the environment. In brief, the paper generates interesting and first-hand insights on the implications of FFC treatment in the gut microbiome of a marine aquaculture candidate targeting its safe and efficient application in unavoidable circumstances. Implementation of mitigation strategies against the identified risks during the initial 15 days of withdrawal period is warranted to ensure cleaner and sustainable aquaculture production from aquatic animal and ecosystem health perspectives.}, } @article {pmid35705745, year = {2023}, author = {Song, L and Wang, Y and Zhang, R and Yang, S}, title = {Microbial Mediation of Carbon, Nitrogen, and Sulfur Cycles During Solid Waste Decomposition.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {311-324}, pmid = {35705745}, issn = {1432-184X}, support = {52000016//National Natural Science Foundation of China/ ; 51578642//National Natural Science Foundation of China/ ; }, mesh = {*Solid Waste/analysis ; Nitrogen/analysis ; Carbon ; RNA, Ribosomal, 16S/genetics ; Carbon Dioxide ; Bacteria/genetics ; Archaea/genetics ; *Microbiota ; Sulfur ; Waste Disposal Facilities ; }, abstract = {Landfills are a unique "terrestrial ecosystem" and serve as a significant carbon sink. Microorganisms convert biodegradable substances in municipal solid waste (MSW) to CH4, CO2, and microbial biomass, consisting of the carbon cycling in landfills. Microbial-mediated N and S cycles are also the important biogeochemical process during MSW decomposition, resulting in N2O and H2S emission, respectively. Meanwhile, microbial-mediated N and S cycles affect carbon cycling. How microbial community structure and function respond to C, N, and S cycling during solid waste decomposition, however, are not well-characterized. Here, we show the response of bacterial and archaeal community structure and functions to C, N, and S cycling during solid waste decomposition in a long-term (265 days) operation laboratory-scale bioreactor through 16S rRNA-based pyrosequencing and metagenomics analysis. Bacterial and archaeal community composition varied during solid waste decomposition. Aerobic respiration was the main pathway for CO2 emission, while anaerobic C fixation was the main pathway in carbon fixation. Methanogenesis and denitrification increased during solid waste decomposition, suggesting increasing CH4 and N2O emission. In contract, fermentation decreased along solid waste decomposition. Interestingly, Clostridiales were abundant and showed potential for several pathways in C, N, and S cycling. Archaea were involved in many pathways of C and N cycles. There is a shift between bacteria and archaea involvement in N2 fixation along solid waste decomposition that bacteria Clostridiales and Bacteroidales were initially dominant and then Methanosarcinales increased and became dominant in methanogenic phase. These results provide extensive microbial mediation of C, N, and S cycling profiles during solid waste decomposition.}, } @article {pmid35705722, year = {2022}, author = {Di Chiacchio, IM and Gómez-Abenza, E and Paiva, IM and de Abreu, DJM and Rodríguez-Vidal, JF and Carvalho, EEN and Carvalho, SM and Solis-Murgas, LD and Mulero, V}, title = {Bee pollen in zebrafish diet affects intestinal microbiota composition and skin cutaneous melanoma development.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9998}, pmid = {35705722}, issn = {2045-2322}, mesh = {Animals ; Bees ; Diet ; *Gastrointestinal Microbiome ; *Melanoma/etiology ; Pollen ; *Skin Neoplasms/etiology ; Zebrafish ; Melanoma, Cutaneous Malignant ; }, abstract = {Bee pollen is recommended as dietary supplement due to immunostimulating functions including antioxidant, anti-inflammatory and anti-carcinogenic properties. Nevertheless, the effectiveness of such properties is still not well understood. As diet can be associated with animal performance, microbiota modulation and potentially factor for cancer, this study aimed to analyze if bee pollen could influence growth, gut microbial and skin cutaneous melanoma development in zebrafish. Control diets based on commercial flakes and Artemia were compared with the same diet supplemented with bee pollen. Fish weight gain, increased length, intestinal bacteria metagenomics analysis, serum amyloid A gene expression and cutaneous melanoma transplantation assays were performed. Bee pollen affected microbiota composition and melanoma development. Differential abundance revealed higher abundance in the control group for Aeromonadaceae family, Aeromonas and Pseudomonas genus, A. sobria, A. schubertii, A. jandaei and P. alcaligenes species compared with pollen diet group. Pollen group presented higher abundance for Chromobacterium genus and for Gemmobacter aquaticus, Flavobacterium succinicans and Bifidobacterium breve compared with control group. Unexpectedly, fish fed with bee pollen showed higher tumor growth rate and larger tumor size than control group. This is the first study to report intestinal microbial changes and no protective cancer properties after bee pollen administration.}, } @article {pmid35705638, year = {2022}, author = {Raphenya, AR and Robertson, J and Jamin, C and de Oliveira Martins, L and Maguire, F and McArthur, AG and Hays, JP}, title = {Datasets for benchmarking antimicrobial resistance genes in bacterial metagenomic and whole genome sequencing.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {341}, pmid = {35705638}, issn = {2052-4463}, support = {BB/CCG1860/1//Quadram Institute Bioscience/ ; PJT-156214//Gouvernement du Canada | Canadian Institutes of Health Research (Instituts de Recherche en Santé du Canada)/ ; 549010001//Joint Programming Initiative on Antimicrobial Resistance (Joint Programming Initiative for Antimicrobial Resistance)/ ; MR/T030062/1/MRC_/Medical Research Council/United Kingdom ; MR/L015080/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; *Bacteria/genetics ; Benchmarking ; Drug Resistance, Bacterial/genetics ; Genome, Bacterial ; Microbial Sensitivity Tests ; Whole Genome Sequencing ; }, abstract = {Whole genome sequencing (WGS) is a key tool in identifying and characterising disease-associated bacteria across clinical, agricultural, and environmental contexts. One increasingly common use of genomic and metagenomic sequencing is in identifying the type and range of antimicrobial resistance (AMR) genes present in bacterial isolates in order to make predictions regarding their AMR phenotype. However, there are a large number of alternative bioinformatics software and pipelines available, which can lead to dissimilar results. It is, therefore, vital that researchers carefully evaluate their genomic and metagenomic AMR analysis methods using a common dataset. To this end, as part of the Microbial Bioinformatics Hackathon and Workshop 2021, a 'gold standard' reference genomic and simulated metagenomic dataset was generated containing raw sequence reads mapped against their corresponding reference genome from a range of 174 potentially pathogenic bacteria. These datasets and their accompanying metadata are freely available for use in benchmarking studies of bacteria and their antimicrobial resistance genes and will help improve tool development for the identification of AMR genes in complex samples.}, } @article {pmid35707452, year = {2021}, author = {Werbin, ZR and Hackos, B and Lopez-Nava, J and Dietze, MC and Bhatnagar, JM}, title = {The National Ecological Observatory Network's soil metagenomes: assembly and basic analysis.}, journal = {F1000Research}, volume = {10}, number = {}, pages = {299}, pmid = {35707452}, issn = {2046-1402}, mesh = {Computational Biology/methods ; *Metagenome ; Metagenomics/methods ; Neon ; *Soil ; }, abstract = {The largest dataset of soil metagenomes has recently been released by the National Ecological Observatory Network (NEON), which performs annual shotgun sequencing of soils at 47 sites across the United States. NEON serves as a valuable educational resource, thanks to its open data and programming tutorials, but there is currently no introductory tutorial for accessing and analyzing the soil shotgun metagenomic dataset. Here, we describe methods for processing raw soil metagenome sequencing reads using a bioinformatics pipeline tailored to the high complexity and diversity of the soil microbiome. We describe the rationale, necessary resources, and implementation of steps such as cleaning raw reads, taxonomic classification, assembly into contigs or genomes, annotation of predicted genes using custom protein databases, and exporting data for downstream analysis. The workflow presented here aims to increase the accessibility of NEON's shotgun metagenome data, which can provide important clues about soil microbial communities and their ecological roles.}, } @article {pmid35822822, year = {2020}, author = {Stander, EA and Williams, W and Mgwatyu, Y and Heusden, PV and Rautenbach, F and Marnewick, J and Roes-Hill, ML and Hesse, U}, title = {Transcriptomics of the Rooibos (Aspalathus linearis) Species Complex.}, journal = {Biotech (Basel (Switzerland))}, volume = {9}, number = {4}, pages = {}, pmid = {35822822}, issn = {2673-6284}, support = {RTF150421117446//National Research Foundation/ ; CSUR150714125961//National Research Foundation/ ; }, abstract = {Rooibos (Aspalathus linearis), widely known as a herbal tea, is endemic to the Cape Floristic Region of South Africa (SA). It produces a wide range of phenolic compounds that have been associated with diverse health promoting properties of the plant. The species comprises several growth forms that differ in their morphology and biochemical composition, only one of which is cultivated and used commercially. Here, we established methodologies for non-invasive transcriptome research of wild-growing South African plant species, including (1) harvesting and transport of plant material suitable for RNA sequencing; (2) inexpensive, high-throughput biochemical sample screening; (3) extraction of high-quality RNA from recalcitrant, polysaccharide- and polyphenol rich plant material; and (4) biocomputational analysis of Illumina sequencing data, together with the evaluation of programs for transcriptome assembly (Trinity, IDBA-Trans, SOAPdenovo-Trans, CLC), protein prediction, as well as functional and taxonomic transcript annotation. In the process, we established a biochemically characterized sample pool from 44 distinct rooibos ecotypes (1-5 harvests) and generated four in-depth annotated transcriptomes (each comprising on average ≈86,000 transcripts) from rooibos plants that represent distinct growth forms and differ in their biochemical profiles. These resources will serve future rooibos research and plant breeding endeavours.}, } @article {pmid35921576, year = {2020}, author = {Dehority, W and Spence, D and Dinwiddie, DL}, title = {Severe Acute Respiratory Syndrome Coronavirus 2: Genomic Observations and Emerging Therapies.}, journal = {Pediatric allergy, immunology, and pulmonology}, volume = {33}, number = {2}, pages = {49-52}, pmid = {35921576}, issn = {2151-3228}, abstract = {Severe Acute Respiratory Syndrome coronavirus 2 (SARS-CoV-2), the etiologic agent of the disease COVID-19, first emerged in late December 2019 in China, and has subsequently become a pandemic with unprecedented clinical impact. The virus appears to more severely affect older individuals and those with co-morbid medical conditions, specifically those with chronic lung disease, obesity, heart failure and diabetes. Fortunately, children appear to be less severely affected, though mortality and severe disease have been reported. In addition, children's role in spreading the disease (potentially through asymptomatic shedding of the virus) remains an important area requiring further investigation. The emergence of SARS-CoV-2 has highlighted the importance of metagenomic next generation sequencing as a tool for pandemic investigation. Though no proven therapeutic options currently exist, ongoing genomic and clinical trial data may help inform the identification and development of both repurposed and novel therapeutic agents for use in this disease.}, } @article {pmid35903557, year = {2020}, author = {Moshiri, N}, title = {TreeSwift: A massively scalable Python tree package.}, journal = {SoftwareX}, volume = {11}, number = {}, pages = {}, pmid = {35903557}, issn = {2352-7110}, support = {P30 AI027767/AI/NIAID NIH HHS/United States ; P30 AI036214/AI/NIAID NIH HHS/United States ; }, abstract = {Phylogenetic trees are essential to evolutionary biology, and numerous methods exist that attempt to extract phylogenetic information applicable to a wide range of disciplines, such as epidemiology and metagenomics. Currently, the three main Python packages for trees are Bio.Phylo, DendroPy, and the ETE Toolkit, but as dataset sizes grow, parsing and manipulating ultra-large trees becomes impractical for these tools. To address this issue, we present TreeSwift, a user-friendly and massively scalable Python package for traversing and manipulating trees that is ideal for algorithms performed on ultra-large trees.}, } @article {pmid35705596, year = {2022}, author = {Olsen, M and Nassar, R and Senok, A and Moloney, S and Lohning, A and Jones, P and Grant, G and Morgan, M and Palipana, D and McKirdy, S and Alghafri, R and Tajouri, L}, title = {Mobile phones are hazardous microbial platforms warranting robust public health and biosecurity protocols.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {10009}, pmid = {35705596}, issn = {2045-2322}, mesh = {Biosecurity ; *Cell Phone ; *Cross Infection/microbiology ; Fomites/microbiology ; Humans ; Public Health ; }, abstract = {Advancements in technology and communication have revolutionised the twenty-first century with the introduction of mobile phones and smartphones. These phones are known to be platforms harbouring microbes with recent research shedding light on the abundance and broad spectrum of organisms they harbour. Mobile phone use in the community and in professional sectors including health care settings is a potential source of microbial dissemination. To identify the diversity of microbial genetic signature present on mobile phones owned by hospital medical staff. Twenty-six mobile phones of health care staff were swabbed. DNA extraction for downstream next generation sequencing shotgun metagenomic microbial profiling was performed. Survey questionnaires were handed to the staff to collect information on mobile phone usage and users' behaviours. Each of the 26 mobile phones of this study was contaminated with microbes with the detection of antibiotic resistance and virulent factors. Taken together the sum of microbes and genes added together across all 26 mobile phones totalised 11,163 organisms (5714 bacteria, 675 fungi, 93 protists, 228 viruses, 4453 bacteriophages) and 2096 genes coding for antibiotic resistance and virulent factors. The survey of medical staff showed that 46% (12/26) of the participants used their mobile phones in the bathroom. Mobile phones are vectors of microbes and can contribute to microbial dissemination and nosocomial diseases worldwide. As fomites, mobile phones that are not decontaminated may pose serious risks for public health and biosecurity.}, } @article {pmid35705368, year = {2023}, author = {Awoniyi, M and Wang, J and Ngo, B and Meadows, V and Tam, J and Viswanathan, A and Lai, Y and Montgomery, S and Farmer, M and Kummen, M and Thingholm, L and Schramm, C and Bang, C and Franke, A and Lu, K and Zhou, H and Bajaj, JS and Hylemon, PB and Ting, J and Popov, YV and Hov, JR and Francis, HL and Sartor, RB}, title = {Protective and aggressive bacterial subsets and metabolites modify hepatobiliary inflammation and fibrosis in a murine model of PSC.}, journal = {Gut}, volume = {72}, number = {4}, pages = {671-685}, pmid = {35705368}, issn = {1468-3288}, support = {P01 DK094779/DK/NIDDK NIH HHS/United States ; R01 DK057543/DK/NIDDK NIH HHS/United States ; P40 OD010995/OD/NIH HHS/United States ; P30 DK034987/DK/NIDDK NIH HHS/United States ; K01 DK119582/DK/NIDDK NIH HHS/United States ; I01 BX005730/BX/BLRD VA/United States ; R01 DK104893/DK/NIDDK NIH HHS/United States ; IS1 BX004777/BX/BLRD VA/United States ; T32 DK007737/DK/NIDDK NIH HHS/United States ; R01 DK115377/DK/NIDDK NIH HHS/United States ; I01 BX004033/BX/BLRD VA/United States ; R21 AA026629/AA/NIAAA NIH HHS/United States ; IK6 BX004477/BX/BLRD VA/United States ; }, mesh = {Animals ; Mice ; *Vancomycin ; Disease Models, Animal ; *Escherichia coli ; RNA, Ribosomal, 16S/genetics ; Inflammation ; Liver Cirrhosis ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Clostridiales ; }, abstract = {OBJECTIVE: Conflicting microbiota data exist for primary sclerosing cholangitis (PSC) and experimental models.

GOAL: define the function of complex resident microbes and their association relevant to PSC patients by studying germ-free (GF) and antibiotic-treated specific pathogen-free (SPF) multidrug-resistant 2 deficient (mdr2[-/-]) mice and microbial profiles in PSC patient cohorts.

DESIGN: We measured weights, liver enzymes, RNA expression, histological, immunohistochemical and fibrotic biochemical parameters, faecal 16S rRNA gene profiling and metabolomic endpoints in gnotobiotic and antibiotic-treated SPF mdr2[-/-] mice and targeted metagenomic analysis in PSC patients.

RESULTS: GF mdr2[-/-] mice had 100% mortality by 8 weeks with increasing hepatic bile acid (BA) accumulation and cholestasis. Early SPF autologous stool transplantation rescued liver-related mortality. Inhibition of ileal BA transport attenuated antibiotic-accelerated liver disease and decreased total serum and hepatic BAs. Depletion of vancomycin-sensitive microbiota exaggerated hepatobiliary disease. Vancomycin selectively decreased Lachnospiraceae and short-chain fatty acids (SCFAs) but expanded Enterococcus and Enterobacteriaceae. Antibiotics increased Enterococcus faecalis and Escherichia coli liver translocation. Colonisation of GF mdr2[-/-] mice with translocated E. faecalis and E. coli strains accelerated hepatobiliary inflammation and mortality. Lachnospiraceae colonisation of antibiotic pretreated mdr2[-/-] mice reduced liver fibrosis, inflammation and translocation of pathobionts, and SCFA-producing Lachnospiraceae and purified SCFA decreased fibrosis. Faecal Lachnospiraceae negatively associated, and E. faecalis/ Enterobacteriaceae positively associated, with PSC patients' clinical severity by Mayo risk scores.

CONCLUSIONS: We identified novel functionally protective and detrimental resident bacterial species in mdr2[-/-] mice and PSC patients with associated clinical risk score. These insights may guide personalised targeted therapeutic interventions in PSC patients.}, } @article {pmid35705309, year = {2022}, author = {Prekrasna, I and Pavlovska, M and Miryuta, N and Dzhulai, A and Dykyi, E and Convey, P and Kozeretska, I and Bedernichek, T and Parnikoza, I}, title = {Antarctic Hairgrass Rhizosphere Microbiomes: Microscale Effects Shape Diversity, Structure, and Function.}, journal = {Microbes and environments}, volume = {37}, number = {2}, pages = {}, pmid = {35705309}, issn = {1347-4405}, mesh = {*Actinobacteria/genetics ; Antarctic Regions ; Bacteria/genetics ; Lignin ; *Microbiota/genetics ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; }, abstract = {The rhizosphere microbiome of the native Antarctic hairgrass Deschampsia antarctica from the central maritime Antarctic was investigated using 16S RNA metagenomics and compared to those of the second native Antarctic plant Colobanthus quitensis and closely related temperate D. cespitosa. The rhizosphere microbial communities of D. antarctica and D. cespitosa had high taxon richness, while that of C. quitensis had markedly lower diversity. The majority of bacteria in the rhizosphere communities of the hairgrass were affiliated to Proteobacteria, Bacteroidetes, and Actinobacteria. The rhizosphere of C. quitensis was dominated by Actinobacteria. All microbial communities included high proportions of unique amplicon sequence variants (ASVs) and there was high heterogeneity between samples at the ASV level. The soil parameters examined did not explain this heterogeneity. Bacteria belonging to Actinobacteria, Bacteroidetes, and Proteobacteria were sensitive to fluctuations in the soil surface temperature. The values of the United Soil Surface Temperature Influence Index (UTII, I[t]i) showed that variations in most microbial communities from Galindez Island were associated with microscale variations in temperature. Metabolic predictions in silico using PICRUSt 2.0, based on the taxonomically affiliated part of the microbiomes, showed similarities with the rhizosphere community of D. antarctica in terms of the predicted functional repertoire. The results obtained indicate that these communities are involved in the primary processes of soil development (particularly the degradation of lignin and lignin-derived compounds) in the central maritime Antarctic and may be beneficial for the growth of Antarctic vascular plants. However, due to the limitations associated with interpreting PICRUSt 2.0 outputs, these predictions need to be verified experimentally.}, } @article {pmid35705129, year = {2022}, author = {Liang, Z and Yi, J and Gu, Q and Dai, X}, title = {Metagenomics reveals a full-scale modified integrated fixed-film activated sludge process: Enhanced nitrogen removal and reduced sludge production.}, journal = {The Science of the total environment}, volume = {841}, number = {}, pages = {156666}, doi = {10.1016/j.scitotenv.2022.156666}, pmid = {35705129}, issn = {1879-1026}, mesh = {Bioreactors ; Denitrification ; Extracellular Polymeric Substance Matrix/metabolism ; Metagenomics ; Nitrification ; *Nitrogen/metabolism ; Oxidation-Reduction ; *Sewage ; Wastewater ; }, abstract = {This study provides a side-by-side comparative investigation between the full-scale conventional activated sludge (CAS) and the high-concentration powder carrier bio-fluidized bed (HPB) processes. The results showed that the HPB total nitrogen removal efficiency increased by 10.86 % more than CAS. The anammox pathway increased by 6.92 %, while the simultaneous nitrification-denitrification pathway increased by 4.27 %. Also, the effluent's total nitrogen of the HPB process was stabilized below 10 mg/L, which can withstand the impact of industrial wastewater better. More energy and substance (protein) were consumed to attach to the carriers and resist external selective pressure to produce extracellular polymeric substance rather than sludge production in the HPB process. For a 10,000 m[3]/d HPB wastewater treatment plant, lowering the total nitrogen and sludge production saved $110,369.64 in annual operating costs.}, } @article {pmid35704763, year = {2022}, author = {Woehle, C and Roy, AS and Glock, N and Michels, J and Wein, T and Weissenbach, J and Romero, D and Hiebenthal, C and Gorb, SN and Schönfeld, J and Dagan, T}, title = {Denitrification in foraminifera has an ancient origin and is complemented by associated bacteria.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {25}, pages = {e2200198119}, pmid = {35704763}, issn = {1091-6490}, mesh = {*Bacteria/genetics/metabolism ; Denitrification/genetics ; Eukaryota/metabolism ; *Foraminifera/genetics/metabolism ; *Host Microbial Interactions ; Nitrates/metabolism ; Oxygen/metabolism ; }, abstract = {Benthic foraminifera are unicellular eukaryotes that inhabit sediments of aquatic environments. Several foraminifera of the order Rotaliida are known to store and use nitrate for denitrification, a unique energy metabolism among eukaryotes. The rotaliid Globobulimina spp. has been shown to encode an incomplete denitrification pathway of bacterial origin. However, the prevalence of denitrification genes in foraminifera remains unknown, and the missing denitrification pathway components are elusive. Analyzing transcriptomes and metagenomes of 10 foraminiferal species from the Peruvian oxygen minimum zone, we show that denitrification genes are highly conserved in foraminifera. We infer the last common ancestor of denitrifying foraminifera, which enables us to predict the ability to denitrify for additional foraminiferal species. Additionally, an examination of the foraminiferal microbiota reveals evidence for a stable interaction with Desulfobacteraceae, which harbor genes that complement the foraminiferal denitrification pathway. Our results provide evidence that foraminiferal denitrification is complemented by the foraminifera-associated microbiome. The interaction of foraminifera with their resident bacteria is at the basis of foraminiferal adaptation to anaerobic environments that manifested in ecological success in oxygen depleted habitats.}, } @article {pmid35704075, year = {2022}, author = {Tao, Y and Yan, H and Liu, Y and Zhang, F and Luo, L and Zhou, Y and An, K and Yang, R and Yang, B and Xu, T and Xie, L and Ren, H and Xu, Z and Cao, Q and Mo, X}, title = {Diagnostic Performance of Metagenomic Next-Generation Sequencing in Pediatric Patients: A Retrospective Study in a Large Children's Medical Center.}, journal = {Clinical chemistry}, volume = {68}, number = {8}, pages = {1031-1041}, doi = {10.1093/clinchem/hvac067}, pmid = {35704075}, issn = {1530-8561}, mesh = {Child ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenomics/methods ; Retrospective Studies ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) has the potential to become a complementary, if not essential, test in some clinical settings. However, the clinical application of mNGS in a large population of children with various types of infectious diseases (IDs) has not been previously evaluated.

METHODS: From April 2019 to April 2021, 640 samples were collected at a single pediatric hospital and classified as ID [479 (74.8%)], non-ID [NID; 156 (24.4%)], and unknown cases [5 (0.8%)], according to the final clinical diagnosis. We compared the diagnostic performance in pathogen detection between mNGS and standard reference tests.

RESULTS: According to final clinical diagnosis, the sensitivity and specificity of mNGS were 75.0% (95% CI: 70.8%-79.2%) and 59.0% (95% CI: 51.3%-66.7%), respectively. For distinguishing ID from NID, the sensitivity of mNGS was approximately 45.0% higher than that of standard tests (75.0% vs 30.0%; P < 0.001). For fungal detection, mNGS showed positive results in 93.0% of cases, compared to 43.7% for standard tests (P < 0.001). Diagnostic information was increased in respiratory system samples through the addition of meta-transcriptomic sequencing. Further analysis also showed that the read counts in sequencing data were highly correlated with clinical diagnosis, regardless of whether infection was by single or multiple pathogens (Kendall's tau b = 0.484, P < 0.001).

CONCLUSIONS: For pediatric patients in critical condition with suspected infection, mNGS tests can provide valuable diagnostic information to resolve negative or inconclusive routine test results, differentiate ID from NID cases, and facilitate accurate and effective clinical therapeutic decision-making.}, } @article {pmid35703559, year = {2022}, author = {Churcheward, B and Millet, M and Bihouée, A and Fertin, G and Chaffron, S}, title = {MAGNETO: An Automated Workflow for Genome-Resolved Metagenomics.}, journal = {mSystems}, volume = {7}, number = {4}, pages = {e0043222}, pmid = {35703559}, issn = {2379-5077}, mesh = {Workflow ; *Metagenomics/methods ; Metagenome/genetics ; *Microbiota ; Genome, Microbial ; }, abstract = {Metagenome-assembled genomes (MAGs) represent individual genomes recovered from metagenomic data. MAGs are extremely useful to analyze uncultured microbial genomic diversity, as well as to characterize associated functional and metabolic potential in natural environments. Recent computational developments have considerably improved MAG reconstruction but also emphasized several limitations, such as the nonbinning of sequence regions with repetitions or distinct nucleotidic composition. Different assembly and binning strategies are often used; however, it still remains unclear which assembly strategy, in combination with which binning approach, offers the best performance for MAG recovery. Several workflows have been proposed in order to reconstruct MAGs, but users are usually limited to single-metagenome assembly or need to manually define sets of metagenomes to coassemble prior to genome binning. Here, we present MAGNETO, an automated workflow dedicated to MAG reconstruction, which includes a fully-automated coassembly step informed by optimal clustering of metagenomic distances, and implements complementary genome binning strategies, for improving MAG recovery. MAGNETO is implemented as a Snakemake workflow and is available at: https://gitlab.univ-nantes.fr/bird_pipeline_registry/magneto. IMPORTANCE Genome-resolved metagenomics has led to the discovery of previously untapped biodiversity within the microbial world. As the development of computational methods for the recovery of genomes from metagenomes continues, existing strategies need to be evaluated and compared to eventually lead to standardized computational workflows. In this study, we compared commonly used assembly and binning strategies and assessed their performance using both simulated and real metagenomic data sets. We propose a novel approach to automate coassembly, avoiding the requirement for a priori knowledge to combine metagenomic information. The comparison against a previous coassembly approach demonstrates a strong impact of this step on genome binning results, but also the benefits of informing coassembly for improving the quality of recovered genomes. MAGNETO integrates complementary assembly-binning strategies to optimize genome reconstruction and provides a complete reads-to-genomes workflow for the growing microbiome research community.}, } @article {pmid35703536, year = {2022}, author = {Wang, H and Shankar, V and Jiang, X}, title = {Compositional and Functional Changes in Microbial Communities of Composts Due to the Composting-Related Factors and the Presence of Listeria monocytogenes.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0184521}, pmid = {35703536}, issn = {2165-0497}, support = {P20 GM146584/GM/NIGMS NIH HHS/United States ; }, mesh = {*Composting ; *Listeria monocytogenes/genetics ; *Microbiota ; Soil ; Soil Microbiology ; }, abstract = {Listeria monocytogenes is a leading foodborne pathogen that can contaminate fresh produce in farm environment, resulting in deadly outbreaks. Composts contain a diversity of microorganisms, and some of them may be compost-adapted competitive exclusion microorganisms against L. monocytogenes. To understand interactions between compost microflora and the pathogen, both dairy- and poultry-wastes based composts (n = 12) were inoculated with L. monocytogenes, and then analyzed by next-generation sequencing approaches along with culturing methods. DNA extraction and enumeration of L. monocytogenes were performed at 0 and 72 h post-incubation at room temperature. The major bacterial phyla were identified as Firmicutes (23%), Proteobacteria (23%), Actinobacteria (19%), Chloroflexi (13%), Bacteroidetes (12%), Gemmatimonadetes (2%), and Acidobacteria (2%). The top three indicator genera enriched in different compost types were identified by LEfSe with LDA score > 2. The interactions between L. monocytogenes and indigenous microflora were limited as no significant changes in the dominant microbial members in compost ecosystem, but some discriminatory species such as Bacillus, Geobacillus, and Brevibacterium were identified by Random Forest analysis. Besides, changes in metabolic pathways and the increased abundance of bacteriocins category in the compost samples containing L. monocytogenes after 72 h postinoculation were revealed by metatranscriptomic sequencing. Taken together, the compost-related factors such as compost types, composting stages, and the collection farms are major drivers that affect compost microbial compositions, and the analysis of compost metagenome implied that interactions between L. monocytogenes and compost microflora may include competition for nutrients and the presence of antimicrobials. IMPORTANCE Listeria monocytogenes has been recognized as the etiological agent causing foodborne disease outbreaks, with fresh produce as vulnerable for contamination at even preharvest stage. Owing to the richness in microbial community, compost may mediate suppression of pathogens. In this study, the impact of compost-related factors and L. monocytogenes intrusion on dynamic changes in compost microbiome was investigated by next generation sequencing techniques. The compost-related factors such as compost types, composting stages, and the collection farms are major drivers that affect compost microbiome. The interactions between L. monocytogenes and compost microflora may include the competition for nutrients and the presence of antimicrobials produced by native compost microorganisms as potential competitive exclusion microorganisms. Findings from this study are important for the composting industry to understand the composition and functionality of microbial community in their products and help developing organic fertilizers fortified with anti-L. monocytogenes competitive exclusion microorganisms.}, } @article {pmid35702025, year = {2022}, author = {Chelluboina, B and Kieft, K and Breister, A and Anantharaman, K and Vemuganti, R}, title = {Gut virome dysbiosis following focal cerebral ischemia in mice.}, journal = {Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism}, volume = {42}, number = {9}, pages = {1597-1602}, pmid = {35702025}, issn = {1559-7016}, support = {R35 GM143024/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Bacteria ; *Bacteriophages ; *Brain Ischemia ; Dysbiosis ; *Gastrointestinal Microbiome ; Metagenomics ; Mice ; Virome ; *Viruses/genetics ; }, abstract = {Stroke leads to gut bacterial dysbiosis that impacts the post-stroke outcome. The gut microbiome also contains a high abundance of viruses which might play a crucial role in disease progression and recovery by modulating the metabolism of both host and host's gut bacteria. We presently analyzed the virome composition (viruses and phages) by shotgun metagenomics in the fecal samples obtained at 1 day of reperfusion following transient focal ischemia in adult mice. Viral genomes, viral auxiliary metabolic genes, and viral protein networks were compared between stroke and sham conditions (stroke vs sham, exclusive to sham and exclusive to stroke). Following focal ischemia, abundances of 2 viral taxa decreased, and 5 viral taxa increased compared with the sham. Furthermore, the abundance of Clostridia-like phages and Erysipelatoclostridiaceae-like phages were altered in the stroke compared with the sham cohorts. This is the first report to show that the gut virome responds acutely to stroke.}, } @article {pmid35701607, year = {2023}, author = {Cho, S and Stroup, BM and Britto, SL and Ruan, W and Schady, D and Hoffman, KL and Kellermayer, R}, title = {Increased number of children in households may protect against inflammatory bowel disease.}, journal = {Pediatric research}, volume = {93}, number = {3}, pages = {535-540}, pmid = {35701607}, issn = {1530-0447}, mesh = {Mice ; Animals ; RNA, Ribosomal, 16S/genetics ; Disease Models, Animal ; Mice, Inbred C57BL ; *Inflammatory Bowel Diseases/prevention & control ; *Colitis/chemically induced/prevention & control/complications ; }, abstract = {BACKGROUND: The increasing incidence of inflammatory bowel disease (IBD: Crohn's disease and ulcerative colitis) around the world has coincided with a wide array of environmental and epidemiologic changes. The relationship between IBD incidence and household or family size decline, however, has not been examined before. Our background epidemiological analyses suggested an inverse association between household size and IBD incidence. We aimed to examine this further in a murine model.

METHODS: We designed a unique two-generation cohousing model of family size and IBD susceptibility in C57BL/6J mice. Serial fecal microbiomes during cohousing were examined by high-throughput 16S rRNA sequencing. After cohousing for 10 days, mice were exposed to dextran sulfate sodium (DSS) to induce acute colitis. Body weight as a significant correlate of colitis severity was measured.

RESULTS: Mice in a large household arrangement demonstrated less weight loss than mice in the small household arrangement in the DSS model. Age- and housing-dependent microbiome shifts were found.

CONCLUSIONS: Larger households may be protective against intestinal inflammation through intergenerational microbiome modulation. Our observations may set the foundation for age-dependent, microbiome-directed future prevention against IBD.

IMPACT: Epidemiological analyses in this study suggested that IBD incidence may inversely correlate with household size (an indicator of family size/children per family), which has not been examined before. A uniquely designed two-generation cohousing model of family size and IBD susceptibility in mice supported our epidemiologic observations. Microbiome changes in our cohousing model may set the foundation for age-dependent, microbiome-directed prevention against IBD.}, } @article {pmid35701436, year = {2022}, author = {Chrisman, B and He, C and Jung, JY and Stockham, N and Paskov, K and Washington, P and Wall, DP}, title = {The human "contaminome": bacterial, viral, and computational contamination in whole genome sequences from 1000 families.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9863}, pmid = {35701436}, issn = {2045-2322}, support = {U24 MH081810/MH/NIMH NIH HHS/United States ; R01 MH064547/MH/NIMH NIH HHS/United States ; S10 OD011939/OD/NIH HHS/United States ; P30 AG010161/AG/NIA NIH HHS/United States ; R01 AG017917/AG/NIA NIH HHS/United States ; U01 AG061356/AG/NIA NIH HHS/United States ; }, mesh = {*Bacteriophages ; Computational Biology ; *Epstein-Barr Virus Infections ; Genome, Bacterial ; Genome, Human ; Genome, Viral ; Herpesvirus 4, Human/genetics ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Whole Genome Sequencing ; }, abstract = {The unmapped readspace of whole genome sequencing data tends to be large but is often ignored. We posit that it contains valuable signals of both human infection and contamination. Using unmapped and poorly aligned reads from whole genome sequences (WGS) of over 1000 families and nearly 5000 individuals, we present insights into common viral, bacterial, and computational contamination that plague whole genome sequencing studies. We present several notable results: (1) In addition to known contaminants such as Epstein-Barr virus and phiX, sequences from whole blood and lymphocyte cell lines contain many other contaminants, likely originating from storage, prep, and sequencing pipelines. (2) Sequencing plate and biological sample source of a sample strongly influence contamination profile. And, (3) Y-chromosome fragments not on the human reference genome commonly mismap to bacterial reference genomes. Both experiment-derived and computational contamination is prominent in next-generation sequencing data. Such contamination can compromise results from WGS as well as metagenomics studies, and standard protocols for identifying and removing contamination should be developed to ensure the fidelity of sequencing-based studies.}, } @article {pmid35700566, year = {2022}, author = {Gujinović, L and Maravić, A and Kalinić, H and Dželalija, M and Šestanović, S and Zanchi, D and Šamanić, I}, title = {Metagenomic analysis of pioneer biofilm-forming marine bacteria with emphasis on Vibrio gigantis adhesion dynamics.}, journal = {Colloids and surfaces. B, Biointerfaces}, volume = {217}, number = {}, pages = {112619}, doi = {10.1016/j.colsurfb.2022.112619}, pmid = {35700566}, issn = {1873-4367}, mesh = {Biofilms ; *Metagenomics ; RNA, Ribosomal, 16S/genetics ; *Vibrio/genetics ; }, abstract = {Marine biofilms occur frequently and spontaneously in seawater, on almost any submerged solid surface. At the early stages of colonization, it consists of bacteria and evolves into a more complex community. Using 16S rRNA amplicon sequencing and comparative metagenomics, the composition and predicted functional potential of one- to three-day old bacterial communities in surface biofilms were investigated and compared to that of seawater. This confirmed the autochthonous marine bacterium Vibrio gigantis as an early and very abundant biofilm colonizer, also functionally linked to the genes associated with cell motility, surface attachment, and communication via signaling molecules (quorum sensing), all crucial for biofilm formation. The dynamics of adhesion on a solid surface of V. gigantis alone was also monitored in controlled laboratory conditions, using a newly designed and easily implementable protocol. Resulting in a calculated percentage of bacteria-covered surface, a convincing tendency of spontaneous adhering was confirmed. From the multiple results, its quantified and reproducible adhesion dynamics will be used as a basis for future experiments involving surface modifications and coatings, with the goal of preventing adhesion.}, } @article {pmid35699736, year = {2022}, author = {Bohra, V and Tikariha, H and Purohit, HJ and Dafale, NA}, title = {Unique pool of carbohydrate-degrading enzymes in novel bacteria assembled from cow and buffalo rumen metagenomes.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {12}, pages = {4643-4654}, pmid = {35699736}, issn = {1432-0614}, mesh = {Animals ; Bacteria/metabolism ; Bacteroidetes/genetics ; Buffaloes/genetics ; Carbohydrates ; Cattle ; Female ; *Metagenome ; Prospective Studies ; *Rumen/microbiology ; }, abstract = {Reconstruction of genomes from environmental metagenomes offers an excellent prospect for studying the metabolic potential of organisms resilient to isolation in laboratory conditions. Here, we assembled 12 high-quality metagenome-assembled genomes (MAGs) with an estimated completion of ≥ 90% from cow and buffalo rumen metagenomes. Average nucleotide identity (ANI) score-based screening with an existing database suggests the novelty of these genomes. Gene prediction led to the identification of 30,359 protein-encoding genes (PEGs) across 12 genomes, of which only 44.8% were annotated against a specific functional attribute. Further analysis revealed the presence of 985 carbohydrate-active enzymes (CAZymes) from more than 50 glycoside hydrolase families, of which 90% do not have a proper match in the CAZy database. Genome mining revealed the presence of a high frequency of plant biomass deconstructing genes in Bacteroidetes MAGs compared to Firmicutes. The results strongly indicate that the rumen chamber harbors high numbers of deeply branched and as-yet uncultured microbes that encode novel CAZymes, candidates for prospective usage in plant biomass-hydrolyzing and biofuels industries. KEY POINTS: • Genome binning plays a crucial role in revealing the metabolic potential of uncultivable microbes. • Assembled 12 novel genomes from cow and buffalo rumen metagenome datasets. • High frequency of plant biomass deconstructing genes identified in Bacteroidetes MAGs.}, } @article {pmid35699469, year = {2022}, author = {Low, A and Lee, JKY and Gounot, JS and Ravikrishnan, A and Ding, Y and Saw, WY and Tan, LWL and Moong, DKN and Teo, YY and Nagarajan, N and Seedorf, H}, title = {Mutual Exclusion of Methanobrevibacter Species in the Human Gut Microbiota Facilitates Directed Cultivation of a Candidatus Methanobrevibacter Intestini Representative.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0084922}, pmid = {35699469}, issn = {2165-0497}, mesh = {Feces ; *Gastrointestinal Microbiome ; Humans ; Metagenomics ; *Methanobrevibacter/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Methanogenic Archaea (methanogens) are a phylogenetically diverse group of microorganisms and are considered to be the most abundant archaeal representatives in the human gut. However, the gut methanogen diversity of human populations in many global regions remains poorly investigated. Here, we report the abundance and diversity of gut methanogenic Archaea in a multi-ethnic cohort of healthy Singaporeans by using a concerted approach of metagenomic sequencing, 16S rRNA gene amplicon sequencing, and quantitative PCR. Our results indicate a mutual exclusion of Methanobrevibacter species, i.e., the highly prevalent Methanobrevibacter smithii and the less prevalent Candidatus Methanobrevibacter intestini in more than 80% of the samples when using an amplicon sequencing-based approach. Leveraging on this finding, we were able to select a fecal sample to isolate a representative strain, TLL-48-HuF1, for Candidatus Methanobrevibacter intestini. The analyzed physiological parameters of M. smithii DSM 861[T] and strain TLL-48-HuF1 suggest high similarity of the two species. Comparative genome analysis and the mutual exclusion of the Methanobrevibacter species indicate potentially different niche adaptation strategies in the human host, which may support the designation of Candidatus M. intestini as a novel species. IMPORTANCE Methanogens are important hydrogen consumers in the gut and are associated with differing host health. Here, we determine the prevalence and abundance of archaeal species in the guts of a multi-ethnic cohort of healthy Singapore residents. While Methanobrevibacter smithii is the most prevalent and abundant methanogen in the human gut of local subjects, the recently proposed Candidatus Methanobrevibacter intestini is the abundant methanogen in a minority of individuals that harbor them. The observed potential mutual exclusion of M. smithii and Ca. M. intestini provides further support to the proposal that the two physiologically similar strains may belong to different Methanobrevibacter species.}, } @article {pmid35699432, year = {2022}, author = {Tlais, AZA and Lemos Junior, WJF and Filannino, P and Campanaro, S and Gobbetti, M and Di Cagno, R}, title = {How Microbiome Composition Correlates with Biochemical Changes during Sauerkraut Fermentation: a Focus on Neglected Bacterial Players and Functionalities.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0016822}, pmid = {35699432}, issn = {2165-0497}, mesh = {Bacteria/genetics ; *Brassica/chemistry/metabolism/microbiology ; Fermentation ; Food Microbiology ; *Microbiota ; }, abstract = {This study provided a new perspective on the bacterial community succession during sauerkraut fermentation, and on resulting metabolic functions. While culture-dependent methods confirmed the key role of the well-known core microbiome species, metagenomic approach (shotgun) revealed Secundilactobacillus malefermentans as a species of the core microbiome, especially during the last weeks of fermentation. Although the potentiality of S. malefermentans has not yet fully explored, it held core functional genes usually attributed to others lactic acid bacteria driving sauerkraut fermentation. Based on our results it is arguable that S. malefermentans might have a key a role during sauerkraut fermentation carried out at low temperature. Under our experimental conditions, the profile of phenolic compounds changed throughout sauerkraut fermentation. The amount of free phenolics, including free phenolic acids, increased at the beginning of the fermentation, whereas the conversion of phenolic acids into microbial derivatives was consistent during the last part of the sauerkraut fermentation. We pioneered correlating changes in the phenolics profile to changes in the microbiome, although the framework presented is still fragmentary. Annotated genes linked to the phenolic compounds metabolism (VprA and padA) were found in many core species during the whole process. A high metabolic potential for phenolics bioconversion emerged for lactobacilli and Pediococcus spp. through correlation analysis between microbiome composition and phenolics profile. IMPORTANCE Our study was not limited to describe the succession pattern of the microbial community during sauerkraut fermentation, but also revealed how some neglected bacterial players belong to the core species during sauerkrauts processing, especially at low temperature. Such species might have a role as potential starters to optimize the fermentation processes and to obtain sauerkrauts with improved and standardized nutritional and sensory features. Furthermore, our correlations between microbiome composition and phenolics profile might also represent new references for sauerkraut biotechnology, aiming to identify new metabolic drivers of potential sauerkraut functionalities. Finally, sauerkraut ecosystem is a tractable model, although with high level of complexity, and resultant ecological information might be extended to other plant ecosystems.}, } @article {pmid35698617, year = {2022}, author = {Chu, Y and Guo, S and Cui, D and Fu, X and Ma, Y}, title = {DeephageTP: a convolutional neural network framework for identifying phage-specific proteins from metagenomic sequencing data.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13404}, pmid = {35698617}, issn = {2167-8359}, mesh = {*Bacteriophages/genetics ; Neural Networks, Computer ; Amino Acid Sequence ; Metagenome ; Metagenomics/methods ; }, abstract = {Bacteriophages (phages) are the most abundant and diverse biological entity on Earth. Due to the lack of universal gene markers and database representatives, there about 50-90% of genes of phages are unable to assign functions. This makes it a challenge to identify phage genomes and annotate functions of phage genes efficiently by homology search on a large scale, especially for newly phages. Portal (portal protein), TerL (large terminase subunit protein), and TerS (small terminase subunit protein) are three specific proteins of Caudovirales phage. Here, we developed a CNN (convolutional neural network)-based framework, DeephageTP, to identify the three specific proteins from metagenomic data. The framework takes one-hot encoding data of original protein sequences as the input and automatically extracts predictive features in the process of modeling. To overcome the false positive problem, a cutoff-loss-value strategy is introduced based on the distributions of the loss values of protein sequences within the same category. The proposed model with a set of cutoff-loss-values demonstrates high performance in terms of Precision in identifying TerL and Portal sequences (94% and 90%, respectively) from the mimic metagenomic dataset. Finally, we tested the efficacy of the framework using three real metagenomic datasets, and the results shown that compared to the conventional alignment-based methods, our proposed framework had a particular advantage in identifying the novel phage-specific protein sequences of portal and TerL with remote homology to their counterparts in the training datasets. In summary, our study for the first time develops a CNN-based framework for identifying the phage-specific protein sequences with high complexity and low conservation, and this framework will help us find novel phages in metagenomic sequencing data. The DeephageTP is available at https://github.com/chuym726/DeephageTP.}, } @article {pmid35698614, year = {2022}, author = {Li, Y and Bi, Y and Yang, L and Jin, K}, title = {Comparative study on intestinal microbiome composition and function in young and adult Hainan gibbons (Nomascus hainanus).}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13527}, pmid = {35698614}, issn = {2167-8359}, mesh = {Animals ; Hylobates ; *Gastrointestinal Microbiome/genetics ; *Hylobatidae ; *Microbiota ; Firmicutes ; Bacteroidetes ; }, abstract = {The Hainan gibbon is one of the most endangered primates in the world, with a small population size, narrow distribution range, and high inbreeding risk, which retains the risk of species extinction. To explore the composition and functional differences of the intestinal microbiome of Hainan gibbons at different ages, the faecal microbiomes of young and adult Hainan gibbons were analysed using metagenome sequencing. The results showed that the dominant phyla in the intestinal tract of young and adult Hainan gibbons were Firmicutes and Bacteroidetes, and the dominant genus was Prevotella. Linear discriminant analysis effect size analysis showed that Firmicutes, Ruminococcus, Clostridium, and Butyrivibrio were significantly more abundant in adults than in young, whereas Bacteroidetes, Proteobacteria, Prevotella, and Bacteroides were significantly more abundant in young than in adults. In terms of gene function, the adult Hainan gibbon intestinal microbiome generally harboured a higher abundance of genes related to metabolic processes, such as carbohydrate, amino acid, and nucleotide metabolism. This may be due to adaptive advantages for adult Hainan gibbons, such as stable and mature intestinal microbiome composition, which allows them to utilise diverse foods efficiently. In summary, this study helps understand the dynamic changes in the intestinal microbiome of young and adult Hainan gibbons and plays a key role in the health monitoring and rejuvenation of their population.}, } @article {pmid35698170, year = {2022}, author = {Wang, K and Gao, P and Geng, L and Liu, C and Zhang, J and Shu, C}, title = {Lignocellulose degradation in Protaetia brevitarsis larvae digestive tract: refining on a tightly designed microbial fermentation production line.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {90}, pmid = {35698170}, issn = {2049-2618}, mesh = {Animals ; *Bacteria/genetics/metabolism ; Fermentation ; Gastrointestinal Tract ; Larva ; *Lignin/metabolism ; }, abstract = {BACKGROUND: The Scarabaeidae insect Protaetia brevitarsis (PB) has recently gained increasing research interest as a resource insect because its larvae can effectively convert decaying organic matter to plant growth-promoting frass with a high humic acid content and produce healthy, nutritional insect protein sources. Lignocellulose is the main component of PB larvae (PBL) feed, but PB genome annotation shows that PBL carbohydrate-active enzymes are not able to complete the lignocellulose degradation process. Thus, the mechanism by which PBL efficiently degrade lignocellulose is worthy of further study.

RESULTS: Herein, we used combined host genomic and gut metagenomic datasets to investigate the lignocellulose degradation activity of PBL, and a comprehensive reference catalog of gut microbial genes and host gut transcriptomic genes was first established. We characterized a gene repertoire comprising highly abundant and diversified lignocellulose-degrading enzymes and demonstrated that there was unique teamwork between PBL and their gut bacterial microbiota for efficient lignocellulose degradation. PBL selectively enriched lignocellulose-degrading microbial species, mainly from Firmicutes and Bacteroidetes, which are capable of producing a broad array of cellulases and hemicellulases, thus playing a major role in lignocellulosic biomass degradation. In addition, most of the lignocellulose degradation-related module sequences in the PBL microbiome were novel. PBL provide organic functional complementarity for lignocellulose degradation via their evolved strong mouthparts, alkaline midgut, and mild stable hindgut microenvironment to facilitate lignocellulosic biomass grinding, dissolving, and symbiotic microbial fermentation, respectively.

CONCLUSIONS: This work shows that PBL are a promising model to study lignocellulose degradation, which can provide highly abundant novel enzymes and relevant lignocellulose-degrading bacterial strains for biotechnological biomass conversion industries. The unique teamwork between PBL and their gut symbiotic bacterial microbiota for efficient lignocellulose degradation will expand the knowledge of holobionts and open a new beginning in the theory of holobionts. Video Abstract.}, } @article {pmid35697693, year = {2022}, author = {Hatano, T and Palani, S and Papatziamou, D and Salzer, R and Souza, DP and Tamarit, D and Makwana, M and Potter, A and Haig, A and Xu, W and Townsend, D and Rochester, D and Bellini, D and Hussain, HMA and Ettema, TJG and Löwe, J and Baum, B and Robinson, NP and Balasubramanian, M}, title = {Asgard archaea shed light on the evolutionary origins of the eukaryotic ubiquitin-ESCRT machinery.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3398}, pmid = {35697693}, issn = {2041-1723}, support = {MC_U105184326/MRC_/Medical Research Council/United Kingdom ; 203276/Z/16/Z/WT_/Wellcome Trust/United Kingdom ; WT101885MA/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Archaea/genetics/metabolism ; *Endosomal Sorting Complexes Required for Transport/metabolism ; *Eukaryota/genetics/metabolism ; Eukaryotic Cells/metabolism ; Ubiquitin/genetics ; }, abstract = {The ESCRT machinery, comprising of multiple proteins and subcomplexes, is crucial for membrane remodelling in eukaryotic cells, in processes that include ubiquitin-mediated multivesicular body formation, membrane repair, cytokinetic abscission, and virus exit from host cells. This ESCRT system appears to have simpler, ancient origins, since many archaeal species possess homologues of ESCRT-III and Vps4, the components that execute the final membrane scission reaction, where they have been shown to play roles in cytokinesis, extracellular vesicle formation and viral egress. Remarkably, metagenome assemblies of Asgard archaea, the closest known living relatives of eukaryotes, were recently shown to encode homologues of the entire cascade involved in ubiquitin-mediated membrane remodelling, including ubiquitin itself, components of the ESCRT-I and ESCRT-II subcomplexes, and ESCRT-III and Vps4. Here, we explore the phylogeny, structure, and biochemistry of Asgard homologues of the ESCRT machinery and the associated ubiquitylation system. We provide evidence for the ESCRT-I and ESCRT-II subcomplexes being involved in ubiquitin-directed recruitment of ESCRT-III, as it is in eukaryotes. Taken together, our analyses suggest a pre-eukaryotic origin for the ubiquitin-coupled ESCRT system and a likely path of ESCRT evolution via a series of gene duplication and diversification events.}, } @article {pmid35696554, year = {2022}, author = {Han, Y and Quan, X and Chuang, Y and Liang, Q and Li, Y and Yuan, Z and Bian, Y and Wei, L and Wang, J and Zhao, Y}, title = {A multi-omics analysis for the prediction of neurocognitive disorders risk among the elderly in Macao.}, journal = {Clinical and translational medicine}, volume = {12}, number = {6}, pages = {e909}, pmid = {35696554}, issn = {2001-1326}, mesh = {Aged ; *Gastrointestinal Microbiome ; Humans ; Macau ; Metagenomics/methods ; Neurocognitive Disorders ; *Proteomics/methods ; }, abstract = {BACKGROUND: Due to the increasing ageing population, neurocognitive disorders (NCDs) have been a global public health issue, and its prevention and early diagnosis are crucial. Our previous study demonstrated that there is a significant correlation between specific populations and NCDs, but the biological characteristics of the vulnerable group predispose to NCDs are unclear. The purpose of this study is to investigate the predictors for the vulnerable group by a multi-omics analysis.

METHODS: Multi-omics approaches, including metagenomics, metabolomic and proteomic, were used to detect gut microbiota, faecal metabolites and urine exosome of 8 normal controls and 13 vulnerable elders after a rigorous screening of 400 elders in Macao. The multi-omics data were analysed using R and Bioconductor. The two-sided Wilcoxon's rank-sum test, Kruskal-Wallis rank sum test and the linear discriminant analysis effective size were applied to investigate characterized features. Moreover, a 2-year follow-up was conducted to evaluate cognitive function change of the elderly.

RESULTS: Compared with the control elders, the metagenomics of gut microbiota showed that Ruminococcus gnavus, Lachnospira eligens, Escherichia coli and Desulfovibrio piger were increased significantly in the vulnerable group. Carboxylates, like alpha-ketoglutaric acid and d-saccharic acid, and levels of vitamins had obvious differences in the faecal metabolites. There was a distinct decrease in the expression of eukaryotic translation initiation factor 2 subunit 1 (eIF2α) and amine oxidase A (MAO-A) according to the proteomic results of the urine exosomes. Moreover, the compound annual growth rate of neurocognitive scores was notably decreased in vulnerable elders.

CONCLUSIONS: The multi-omics characteristics of disturbed glyoxylate and dicarboxylate metabolism (bacteria), vitamin digestion and absorption and tricarboxylic acid cycle in vulnerable elders can serve as predictors of NCDs risk among the elderly of Macao. Intervention with them may be effective therapeutic approaches for NCDs, and the underlying mechanisms merit further exploration.}, } @article {pmid35695998, year = {2022}, author = {Verma, D and Kumar, V and Satyanarayana, T}, title = {Genomic attributes of thermophilic and hyperthermophilic bacteria and archaea.}, journal = {World journal of microbiology & biotechnology}, volume = {38}, number = {8}, pages = {135}, pmid = {35695998}, issn = {1573-0972}, mesh = {*Archaea/genetics ; *Bacteria/genetics ; Genes, Archaeal ; Genomics ; Metagenome ; Phylogeny ; }, abstract = {Thermophiles and hyperthermophiles are immensely useful in understanding the evolution of life, besides their utility in environmental and industrial biotechnology. Advancements in sequencing technologies have revolutionized the field of microbial genomics. The massive generation of data enhances the sequencing coverage multi-fold and allows to analyse the entire genomic features of microbes efficiently and accurately. The mandate of a pure isolate can also be bypassed where whole metagenome-assembled genomes and single cell-based sequencing have fulfilled the majority of the criteria to decode various attributes of microbial genomes. A boom has, therefore, been seen in analysing the extremophilic bacteria and archaea using sequence-based approaches. Due to extensive sequence analysis, it becomes easier to understand the gene flow and their evolution among the members of bacteria and archaea. For instance, sequencing unveiled that Thermotoga maritima shares around 24% of genes of archaeal origin. Comparative and functional genomics provide an analytical view to understanding the microbial diversity of thermophilic bacteria and archaea, their interactions with other microbes, their adaptations, gene flow, and evolution over time. In this review, the genomic features of thermophilic bacteria and archaea are dealt with comprehensively.}, } @article {pmid35695743, year = {2022}, author = {Ranjan, P and Brown, CA and Erb-Downward, JR and Dickson, RP}, title = {SNIKT: sequence-independent adapter identification and removal in long-read shotgun sequencing data.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {15}, pages = {3830-3832}, pmid = {35695743}, issn = {1367-4811}, support = {K24 HL159247/HL/NHLBI NIH HHS/United States ; R01 HL144599/HL/NHLBI NIH HHS/United States ; T32 HL007749/HL/NHLBI NIH HHS/United States ; }, mesh = {*Software ; *Metagenomics ; Sequence Analysis, DNA ; Metagenome ; }, abstract = {SUMMARY: Here, we introduce SNIKT, a command-line tool for sequence-independent visual confirmation and input-assisted removal of adapter contamination in whole-genome shotgun or metagenomic shotgun long-read sequencing DNA or RNA data.

SNIKT is implemented in R and is compatible with Unix-like platforms. The source code, along with documentation, is freely available under an MIT license at https://github.com/piyuranjan/SNIKT.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid35695679, year = {2022}, author = {Bouzid, F and Gtif, I and Alfadhli, S and Charfeddine, S and Ghorbel, W and Abdelhédi, R and Benmarzoug, R and Abid, L and Bouayed Abdelmoula, N and Elloumi, I and Masmoudi, S and Rebai, A and Kharrat, N}, title = {A potential oral microbiome signature associated with coronary artery disease in Tunisia.}, journal = {Bioscience reports}, volume = {42}, number = {7}, pages = {}, pmid = {35695679}, issn = {1573-4935}, mesh = {Bacteria/genetics ; *Coronary Artery Disease/genetics ; Humans ; Metagenome ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Streptococcus ; Tunisia/epidemiology ; }, abstract = {The coronary artery disease (CAD) is a chronic inflammatory disease involving genetic as well as environmental factors. Recent evidence suggests that the oral microbiome has a significant role in triggering atherosclerosis. The present study assessed the oral microbiome composition variation between coronary patients and healthy subjects in order to identify a potential pathogenic signature associated with CAD. We performed metagenomic profiling of salivary microbiomes by 16S ribosomal RNA (rRNA) next-generation sequencing. Oral microbiota profiling was performed for 30 individuals including 20 patients with CAD and ten healthy individuals without carotid plaques or previous stroke or myocardial infarction. We found that oral microbial communities in patients and healthy controls are represented by similar global core oral microbiome. The predominant taxa belonged to Firmicutes (genus Streptococcus, Veillonella, Granulicatella, Selenomonas), Proteobacteria (genus Neisseria, Haemophilus), Actinobacteria (genus Rothia), Bacteroidetes (genus Prevotella, Porphyromonas), and Fusobacteria (genus Fusobacterium, Leptotrichia). More than 60% relative abundance of each sample for both CAD patients and controls is represented by three major genera including Streptococcus (24.97 and 26.33%), Veillonella (21.43 and 19.91%), and Neisseria (14.23 and 15.33%). Using penalized regression analysis, the bacterial genus Eikenella was involved as the major discriminant genus for both status and Syntax score of CAD. We also reported a significant negative correlation between Syntax score and Eikenella abundance in coronary patients' group (Spearman rho = -0.68, P=0.00094). In conclusion, the abundance of Eikenella in oral coronary patient samples compared with controls could be a prominent pathological indicator for the development of CAD.}, } @article {pmid35695567, year = {2022}, author = {Tinker, K and Lipus, D and Gardiner, J and Stuckman, M and Gulliver, D}, title = {The Microbial Community and Functional Potential in the Midland Basin Reveal a Community Dominated by Both Thiosulfate and Sulfate-Reducing Microorganisms.}, journal = {Microbiology spectrum}, volume = {10}, number = {4}, pages = {e0004922}, pmid = {35695567}, issn = {2165-0497}, mesh = {*Hydrogen Sulfide ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Sulfates/chemistry ; Thiosulfates ; Water ; }, abstract = {The Permian Basin is the highest producing oil and gas reservoir in the United States. Hydrocarbon resources in this region are often accessed by unconventional extraction methods, including horizontal drilling and hydraulic fracturing. Despite the importance of the Permian Basin, there is no publicly available microbiological data from this region. We completed an analysis of Permian produced water samples to understand the dynamics present in hydraulically fractured wells in this region. We analyzed produced water samples taken from 10 wells in the Permian region of the Midland Basin using geochemical measurements, 16S rRNA gene sequencing, and metagenomic sequencing. Compared to other regions, we found that Permian Basin produced water was characterized by higher sulfate and lower total dissolved solids (TDS) concentrations, with a median of 1,110 mg/L and 107,000 mg/L. Additionally, geochemical measurements revealed the presence of frac hits, or interwell communication events where an established well is affected by the pumping of fracturing fluid into a new well. The occurrence of frac hits was supported by correlations between the microbiome and the geochemical parameters. Our 16S rRNA gene sequencing identified a produced water microbiome characterized by anaerobic, halophilic, and sulfur reducing taxa. Interestingly, sulfate and thiosulfate reducing taxa including Halanaerobium, Orenia, Marinobacter, and Desulfohalobium were the most prevalent microbiota in most wells. We further investigated the metabolic potential of microorganisms in the Permian Basin with metagenomic sequencing. We recovered 15 metagenome assembled genomes (MAGs) from seven different samples representing 6 unique well sites. These MAGs corroborated the high presence of sulfate and thiosulfate reducing genes across all wells, especially from key taxa including Halanaerobium and Orenia. The observed microbiome composition and metabolic capabilities in conjunction with the high sulfate concentrations demonstrate a high potential for hydrogen sulfide production in the Permian Basin. Additionally, evidence of frac hits suggests the possibility for the exchange of microbial cells and/or genetic information between wells. This exchange would increase the likelihood of hydrogen sulfide production and has implications for the oil and gas industry. IMPORTANCE The Permian Basin is the largest producing oil and gas region in the United States and plays a critical role supplying national energy needs. Previous work in other basins has demonstrated that the geochemistry and microbiology of hydrocarbon regions can have a major impact on well infrastructure and production. Despite that, little work has been done to understand the complex dynamics present in the Permian Basin. This study characterizes and analyzes 10 unique wells and one groundwater sample in the Permian Basin using geochemical and microbial techniques. Across all wells we found a high number of classic and thiosulfate reducers, suggesting that hydrogen sulfide production may be especially prevalent in the Permian Basin. Additionally, our analysis revealed a biogeochemical signal impacted by the presence of frac hits, or interwell communication events where an established well is affected by the pumping of fracturing fluid into a new well. This information can be utilized by the oil and gas industry to improve oil recovery efforts and minimize commercial and environmental costs.}, } @article {pmid35695508, year = {2022}, author = {Zaragoza-Solas, A and Haro-Moreno, JM and Rodriguez-Valera, F and López-Pérez, M}, title = {Long-Read Metagenomics Improves the Recovery of Viral Diversity from Complex Natural Marine Samples.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0019222}, pmid = {35695508}, issn = {2379-5077}, mesh = {*Viruses/genetics ; *Bacteriophages/genetics ; Metagenome/genetics ; Genome, Viral/genetics ; High-Throughput Nucleotide Sequencing/methods ; }, abstract = {The recovery of DNA from viromes is a major obstacle in the use of long-read sequencing to study their genomes. For this reason, the use of cellular metagenomes (>0.2-μm size range) emerges as an interesting complementary tool, since they contain large amounts of naturally amplified viral genomes from prelytic replication. We have applied second-generation (Illumina NextSeq; short reads) and third-generation (PacBio Sequel II; long reads) sequencing to compare the diversity and features of the viral community in a marine sample obtained from offshore waters of the western Mediterranean. We found that a major wedge of the expected marine viral diversity was directly recovered by the raw PacBio circular consensus sequencing (CCS) reads. More than 30,000 sequences were detected only in this data set, with no homologues in the long- and short-read assembly, and ca. 26,000 had no homologues in the large data set of the Global Ocean Virome 2 (GOV2), highlighting the information gap created by the assembly bias. At the level of complete viral genomes, the performance was similar in both approaches. However, the hybrid long- and short-read assembly provided the longest average length of the sequences and improved the host assignment. Although no novel major clades of viruses were found, there was an increase in the intraclade genomic diversity recovered by long reads that produced an enriched assessment of the real diversity and allowed the discovery of novel genes with biotechnological potential (e.g., endolysin genes). IMPORTANCE We explored the vast genetic diversity of environmental viruses by using a combination of cellular metagenome (as opposed to virome) sequencing using high-fidelity long-read sequences (in this case, PacBio CCS). This approach resulted in the recovery of a representative sample of the viral population, and it performed better (more phage contigs, larger average contig size) than Illumina sequencing applied to the same sample. By this approach, the many biases of assembly are avoided, as the CCS reads recovers (typically around 5 kb) complete genes and even operons, resulting in a better discovery of the viral gene diversity based on viral marker proteins. Thus, biotechnologically promising genes, such as endolysin genes, can be very efficiently searched with this approach. In addition, hybrid assembly produces more complete and longer contigs, which is particularly important for studying little-known viral groups such as the nucleocytoplasmic large DNA viruses (NCLDV).}, } @article {pmid35695488, year = {2022}, author = {Gaston, DC and Miller, HB and Fissel, JA and Jacobs, E and Gough, E and Wu, J and Klein, EY and Carroll, KC and Simner, PJ}, title = {Evaluation of Metagenomic and Targeted Next-Generation Sequencing Workflows for Detection of Respiratory Pathogens from Bronchoalveolar Lavage Fluid Specimens.}, journal = {Journal of clinical microbiology}, volume = {60}, number = {7}, pages = {e0052622}, pmid = {35695488}, issn = {1098-660X}, mesh = {Bronchoalveolar Lavage Fluid/microbiology ; *COVID-19 ; *Communicable Diseases ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics ; SARS-CoV-2 ; Workflow ; }, abstract = {Next-generation sequencing (NGS) workflows applied to bronchoalveolar lavage (BAL) fluid specimens could enhance the detection of respiratory pathogens, although optimal approaches are not defined. This study evaluated the performance of the Respiratory Pathogen ID/AMR (RPIP) kit (Illumina, Inc.) with automated Explify bioinformatic analysis (IDbyDNA, Inc.), a targeted NGS workflow enriching specific pathogen sequences and antimicrobial resistance (AMR) markers, and a complementary untargeted metagenomic workflow with in-house bioinformatic analysis. Compared to a composite clinical standard consisting of provider-ordered microbiology testing, chart review, and orthogonal testing, both workflows demonstrated similar performances. The overall agreement for the RPIP targeted workflow was 65.6% (95% confidence interval, 59.2 to 71.5%), with a positive percent agreement (PPA) of 45.9% (36.8 to 55.2%) and a negative percent agreement (NPA) of 85.7% (78.1 to 91.5%). The overall accuracy for the metagenomic workflow was 67.1% (60.9 to 72.9%), with a PPA of 56.6% (47.3 to 65.5%) and an NPA of 77.2% (68.9 to 84.1%). The approaches revealed pathogens undetected by provider-ordered testing (Ureaplasma parvum, Tropheryma whipplei, severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2], rhinovirus, and cytomegalovirus [CMV]), although not all pathogens detected by provider-ordered testing were identified by the NGS workflows. The RPIP targeted workflow required more time and reagents for library preparation but streamlined bioinformatic analysis, whereas the metagenomic assay was less demanding technically but required complex bioinformatic analysis. The results from both workflows were interpreted utilizing standardized criteria, which is necessary to avoid reporting nonpathogenic organisms. The RPIP targeted workflow identified AMR markers associated with phenotypic resistance in some bacteria but incorrectly identified blaOXA genes in Pseudomonas aeruginosa as being associated with carbapenem resistance. These workflows could serve as adjunctive testing with, but not as a replacement for, standard microbiology techniques.}, } @article {pmid35695455, year = {2022}, author = {Ma, B and Sundararajan, S and Nadimpalli, G and France, M and McComb, E and Rutt, L and Lemme-Dumit, JM and Janofsky, E and Roskes, LS and Gajer, P and Fu, L and Yang, H and Humphrys, M and Tallon, LJ and Sadzewicz, L and Pasetti, MF and Ravel, J and Viscardi, RM}, title = {Highly Specialized Carbohydrate Metabolism Capability in Bifidobacterium Strains Associated with Intestinal Barrier Maturation in Early Preterm Infants.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0129922}, pmid = {35695455}, issn = {2150-7511}, support = {R21 DK123674/DK/NIDDK NIH HHS/United States ; }, mesh = {Bifidobacterium/genetics ; Carbohydrate Metabolism ; *Enterocolitis, Necrotizing/microbiology ; Humans ; Infant ; Infant, Newborn ; *Infant, Premature ; RNA, Ribosomal, 16S/genetics ; }, abstract = {"Leaky gut," or high intestinal barrier permeability, is common in preterm newborns. The role of the microbiota in this process remains largely uncharacterized. We employed both short- and long-read sequencing of the 16S rRNA gene and metagenomes to characterize the intestinal microbiome of a longitudinal cohort of 113 preterm infants born between 24[0/7] and 32[6/7] weeks of gestation. Enabled by enhanced taxonomic resolution, we found that a significantly increased abundance of Bifidobacterium breve and a diet rich in mother's breastmilk were associated with intestinal barrier maturation during the first week of life. We combined these factors using genome-resolved metagenomics and identified a highly specialized genetic capability of the Bifidobacterium strains to assimilate human milk oligosaccharides and host-derived glycoproteins. Our study proposes mechanistic roles of breastmilk feeding and intestinal microbial colonization in postnatal intestinal barrier maturation; these observations are critical toward advancing therapeutics to prevent and treat hyperpermeable gut-associated conditions, including necrotizing enterocolitis (NEC). IMPORTANCE Despite improvements in neonatal intensive care, necrotizing enterocolitis (NEC) remains a leading cause of morbidity and mortality. "Leaky gut," or intestinal barrier immaturity with elevated intestinal permeability, is the proximate cause of susceptibility to NEC. Early detection and intervention to prevent leaky gut in "at-risk" preterm neonates are critical for decreasing the risk of potentially life-threatening complications like NEC. However, the complex interactions between the developing gut microbial community, nutrition, and intestinal barrier function remain largely uncharacterized. In this study, we reveal the critical role of a sufficient breastmilk feeding volume and the specialized carbohydrate metabolism capability of Bifidobacterium in the coordinated postnatal improvement of the intestinal barrier. Determining the clinical and microbial biomarkers that drive the intestinal developmental disparity will inform early detection and novel therapeutic strategies to promote appropriate intestinal barrier maturation and prevent NEC and other adverse health conditions in preterm infants.}, } @article {pmid35695431, year = {2022}, author = {Hwang, Y and Girguis, PR}, title = {Differentiated Evolutionary Strategies of Genetic Diversification in Atlantic and Pacific Thaumarchaeal Populations.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0147721}, pmid = {35695431}, issn = {2379-5077}, mesh = {*Ammonia ; Phylogeny ; *Ecosystem ; Oceans and Seas ; Archaea/genetics ; }, abstract = {Some marine microbes are seemingly "ubiquitous," thriving across a wide range of environmental conditions. While the increased depth in metagenomic sequencing has led to a growing body of research on within-population heterogeneity in environmental microbial populations, there have been fewer systematic comparisons and characterizations of population-level genetic diversity over broader expanses of time and space. Here, we investigated the factors that govern the diversification of ubiquitous microbial taxa found within and between ocean basins. Specifically, we use mapped metagenomic paired reads to examine the genetic diversity of ammonia-oxidizing archaeal ("Candidatus Nitrosopelagicus brevis") populations in the Pacific (Hawaii Ocean Time-series [HOT]) and Atlantic (Bermuda Atlantic Time Series [BATS]) Oceans sampled over 2 years. We observed higher nucleotide diversity in "Ca. N. brevis" at HOT, driven by a higher rate of homologous recombination. In contrast, "Ca. N. brevis" at BATS featured a more open pangenome with a larger set of genes that were specific to BATS, suggesting a history of dynamic gene gain and loss events. Furthermore, we identified highly differentiated genes that were regulatory in function, some of which exhibited evidence of recent selective sweeps. These findings indicate that different modes of genetic diversification likely incur specific adaptive advantages depending on the selective pressures that they are under. Within-population diversity generated by the environment-specific strategies of genetic diversification is likely key to the ecological success of "Ca. N. brevis." IMPORTANCE Ammonia-oxidizing archaea (AOA) are one of the most abundant chemolithoautotrophic microbes in the marine water column and are major contributors to global carbon and nitrogen cycling. Despite their ecological importance and geographical pervasiveness, there have been limited systematic comparisons and characterizations of their population-level genetic diversity over time and space. Here, we use metagenomic time series from two ocean observatories to address the fundamental questions of how abiotic and biotic factors shape the population-level genetic diversity and how natural microbial populations adapt across diverse habitats. We show that the marine AOA "Candidatus Nitrosopelagicus brevis" in different ocean basins exhibits distinct modes of genetic diversification in response to their selective regimes shaped by nutrient availability and patterns of environmental fluctuations. Our findings specific to "Ca. N. brevis" have broader implications, particularly in understanding the population-level responses to the changing climate and predicting its impact on biogeochemical cycles.}, } @article {pmid35695430, year = {2022}, author = {Fansler, RT and Zhu, W}, title = {Mind the Gap: Bridging the Divide from Sequencing Data to Empiric Phenotypes in the Human Gut Microbiota.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0020722}, pmid = {35695430}, issn = {2379-5077}, support = {R01 DK134692/DK/NIDDK NIH HHS/United States ; R35 GM147470/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; Bacteria/genetics ; Polysaccharides ; *Microbiota ; Genomics ; }, abstract = {The gut microbiome exerts a powerful influence on human health and disease. Elucidating the underlying mechanisms of the microbiota's influence is hindered by the immense complexity of the gut microbial community and the glycans they forage. Despite a wealth of genomic and metagenomic sequencing information, there remains a lack of informative phenotypic measurements. Pudlo NA, Urs K, Crawford R, Pirani A, et al. (mSystems 7: e00947-21, 2022, https://doi.org/10.1128/msystems.00947-21) decode this complexity by introducing a scalable assay to measure specific carbohydrate utilization in the dominant microbiota phylum Bacteroidetes. The results reveal a mosaic structure of glycan utilization, both genetic and functional, underpinning niche construction in the human gastrointestinal tract. This Commentary highlights the significance of their findings in connection to the field's growing appreciation for competition, cooperation, and horizontal gene transfer in shaping the highly complex microbial community.}, } @article {pmid35694902, year = {2022}, author = {Cea-Rama, I and Coscolín, C and Gonzalez-Alfonso, JL and Raj, J and Vasiljević, M and Plou, FJ and Ferrer, M and Sanz-Aparicio, J}, title = {Crystal structure of a family VIII β-lactamase fold hydrolase reveals the molecular mechanism for its broad substrate scope.}, journal = {The FEBS journal}, volume = {289}, number = {21}, pages = {6714-6730}, pmid = {35694902}, issn = {1742-4658}, mesh = {*beta-Lactamases/chemistry ; Substrate Specificity ; *Esterases/metabolism ; Carboxylesterase/metabolism ; Catalytic Domain ; }, abstract = {Family VIII esterases present similarities to class C β-lactamases, which show nucleophilic serines located at the S-X-X-K motif instead of the G-X-S-X-G or G-D-S-(L) motif shown by other carboxylesterase families. Here, we report the crystal structure of a novel family VIII (subfamily VIII. I) esterase (EH7 ; denaturing temperature, 52.6 ± 0.3 °C; pH optimum 7.0-9.0) to deepen its broad substrate range. Indeed, the analysis of the substrate specificity revealed its capacity to hydrolyse nitrocefin as a model chromogenic cephalosporin substrate (40.4 ± 11.4 units·g[-1]), and a large battery of 66 structurally different esters (up to 1730 min[-1]), including bis(2-hydroxyethyl)-terephthalate (241.7 ± 8.5 units·g[-1]) and the mycotoxin T-2 (1220 ± 52 units·g[-1]). It also showed acyltransferase activity through the synthesis of benzyl 3-oxobutanoate (40.4 ± 11.4 units·g[-1]) from benzyl alcohol and vinyl acetoacetate. Such a broad substrate scope is rare among family VIII esterases and lipolytic enzymes. Structural analyses of free and substrate-bound forms of this homooctamer esterase suggest that EH7 presents a more opened and exposed S1 site having no steric hindrance for the entrance of substrates to the active site, more flexible R1, R2 and R3 regions allowing for the binding of a wide spectrum of substrates into the active site, and small residues in the conserved motif Y-X-X containing the catalytic Tyr enabling the entrance of large substrates. These unique structural elements in combination with docking experiments allowed us to gain valuable insights into the substrate specificity of this esterase and possible others belonging to family VIII.}, } @article {pmid35694630, year = {2022}, author = {Lee, G and Yoo, K}, title = {A review of the emergence of antibiotic resistance in bioaerosols and its monitoring methods.}, journal = {Re/views in environmental science and bio/technology}, volume = {21}, number = {3}, pages = {799-827}, pmid = {35694630}, issn = {1572-9826}, abstract = {Despite significant public health concerns regarding infectious diseases in air environments, potentially harmful microbiological indicators, such as antibiotic resistance genes (ARGs) in bioaerosols, have not received significant attention. Traditionally, bioaerosol studies have focused on the characterization of microbial communities; however, a more serious problem has recently arisen due to the presence of ARGs in bioaerosols, leading to an increased prevalence of horizontal gene transfer (HGT). This constitutes a process by which bacteria transfer genes to other environmental media and consequently cause infectious disease. Antibiotic resistance in water and soil environments has been extensively investigated in the past few years by applying advanced molecular and biotechnological methods. However, ARGs in bioaerosols have not received much attention. In addition, ARG and HGT profiling in air environments is greatly limited in field studies due to the absence of suitable methodological approaches. Therefore, this study comprehensively describes recent findings from published studies and some of the appropriate molecular and biotechnological methods for monitoring antibiotic resistance in bioaerosols. In addition, this review discusses the main knowledge gaps regarding current methodological issues and future research directions.}, } @article {pmid35694302, year = {2022}, author = {Teklebrhan, T and Tan, Z}, title = {Diet Supplementation With Sulfur Amino Acids Modulated Fermentation Metabolome and Gut Microbiome in Goats.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {870385}, pmid = {35694302}, issn = {1664-302X}, abstract = {Dietary amino acids shift hydrogen metabolism to an alternative hydrogen sink consisting of dissolved hydrogen sulfur (dH2S) rather than methanogenesis; and influences the fermentation metabolome and microbiome associated with particles and liquid fractions in gut regions (foregut, small intestine, and hindgut) of goats. A completely randomized block design with a total of 20 goats (5 goats per treatment) was used to conduct the trial. The goats were fed on a diet that consisted of a concentrated mixture with maize stover roughage (50:50, on a dry matter basis) and randomly assigned to one of the four treatments: without amino acid supplementation (a basal diet), a basal diet supplemented with methionine (Met), a basal diet supplemented with lysine (Lys), and a basal diet supplemented with methionine and lysine (ML). Goats fed Met alone or in combination had less acetate, acetate to propionate ratio, and greater propionate (p < 0.05) in the foregut and hindgut than those fed control or Lys. Nonetheless, the goats fed on the amino acid supplements had higher levels of branched-chain VFA (p < 0.05) in the foregut and hindgut than the control goats. Goats fed on ML had the highest ammonia (p < 0.01), followed by Met or Lys, both in the foregut and hindgut, compared with the control. Those fed on Met alone or in combination, had lower dH2, dCH4 (p < 0.01), and higher dH2S (p < 0.01) in the foregut and hindgut than the control or Lys. The goats that were fed on Met alone or in combination, had higher 16S rRNA gene copies of total bacteria, methanogens, and 18S rRNA gene copies of protozoa, fungi, and fiber-utilizing bacterial species (p < 0.01) associated with particles vs. liquid, both in the foregut and hindgut than the control goats. This study gives insights into the use of sulfur-containing amino acids, as an alternative dietary mitigation strategy of methanogenesis in ruminants and highlights the need for further research in this direction.}, } @article {pmid35694283, year = {2022}, author = {Wang, Y and Bi, HY and Chen, HG and Zheng, PF and Zhou, YL and Li, JT}, title = {Metagenomics Reveals Dominant Unusual Sulfur Oxidizers Inhabiting Active Hydrothermal Chimneys From the Southwest Indian Ridge.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {861795}, pmid = {35694283}, issn = {1664-302X}, abstract = {The deep-sea hydrothermal vents (DSHVs) in the Southwest Indian Ridge (SWIR) are formed by specific geological settings. However, the community structure and ecological function of the microbial inhabitants on the sulfide chimneys of active hydrothermal vents remain largely unknown. In this study, our analyses of 16S rRNA gene amplicons and 16S rRNA metagenomic reads showed the dominance of sulfur-oxidizing Ectothiorhodospiraceae, Thiomicrorhabdus, Sulfurimonas, and Sulfurovum on the wall of two active hydrothermal chimneys. Compared with the inactive hydrothermal sediments of SWIR, the active hydrothermal chimneys lacked sulfur-reducing bacteria. The metabolic potentials of the retrieved 82 metagenome-assembled genomes (MAGs) suggest that sulfur oxidation might be conducted by Thiohalomonadales (classified as Ectothiorhodospiraceae based on 16S rRNA gene amplicons), Sulfurovaceae, Hyphomicrobiaceae, Thiotrichaceae, Thiomicrospiraceae, and Rhodobacteraceae. For CO2 fixation, the Calvin-Benson-Bassham and reductive TCA pathways were employed by these bacteria. In Thiohalomonadales MAGs, we revealed putative phytochrome, carotenoid precursor, and squalene synthesis pathways, indicating a possible capacity of Thiohalomonadales in adaptation to dynamics redox conditions and the utilization of red light from the hot hydrothermal chimneys for photolithotrophic growth. This study, therefore, reveals unique microbiomes and their genomic features in the active hydrothermal chimneys of SWIR, which casts light on ecosystem establishment and development in hydrothermal fields and the deep biosphere.}, } @article {pmid35692070, year = {2022}, author = {Han, XC and Liu, RX and Lin, X and He, JY and Bu, H}, title = {[Clinical observation of 8 cases with central nervous system anaerobic infection diagnosed by metagenomic next-generation sequencing of cerebrospinal fluid].}, journal = {Zhonghua yi xue za zhi}, volume = {102}, number = {20}, pages = {1533-1536}, doi = {10.3760/cma.j.cn112137-20211115-02550}, pmid = {35692070}, issn = {0376-2491}, mesh = {Anaerobiosis ; Bacteria, Anaerobic/genetics ; Brain ; *Central Nervous System Infections/diagnosis ; High-Throughput Nucleotide Sequencing/methods ; Humans ; }, abstract = {The current study summarized the clinical characteristics of 8 patients with central nervous system anaerobic infections who visited the Second Hospital of Hebei Medical University from June 2019 to June 2021. Among the 8 patients, 7 cases had headache and fever as the first symptoms, and 1 case had left-sided limb weakness as the first symptom. Four patients had a previous history of diabetes (1 patient had a history of tooth extraction before the onset of the disease), 1 patient had a previous history of sinusitis, 1 patient had a history of tooth extraction before the onset of the disease, and 2 patients had chronic extensive periodontitis or periapical periodontitis. Five cases showed abnormal intracranial and/or meningeal enhancement on cranial magnetic resonance imaging (MRI), and 1 case showed swelling of the whole brain tissue on cranial computed tomography (CT). After treatment, symptoms of 4 cases were improved, symptoms of 1 case were aggravated, and 3 cases died. Anaerobic infections can occur in various parts of the body:the central nervous system, oral cavity, head and neck, chest, abdomen, pelvis, skin and soft tissues. It is generally believed that anaerobic bacteria rarely cause central nervous system infection, therefore, anaerobic culture of cerebrospinal fluid is usually not performed. Moreover, anaerobic culture is affected by many factors, and thus it is difficult to obtain positive results. Metagenomic next-generation sequencing can identify multiple pathogens (viral, bacterial, fungal, or parasitic) from samples based on DNA and/or RNA sequences and has advantages in diagnosing anaerobic infections of the central nervous system. Prompt empirical antimicrobial therapy is essential for the prognosis of the patients.}, } @article {pmid35691702, year = {2022}, author = {Li, S and Diao, M and Wang, S and Zhu, X and Dong, X and Strous, M and Ji, G}, title = {Distinct oxygen isotope fractionations driven by different electron donors during microbial nitrate reduction in lake sediments.}, journal = {Environmental microbiology reports}, volume = {14}, number = {5}, pages = {812-821}, doi = {10.1111/1758-2229.13101}, pmid = {35691702}, issn = {1758-2229}, mesh = {Carbon ; Electrons ; Geologic Sediments ; Glucose ; Iron ; *Lakes ; Nitrate Reductase ; *Nitrates ; Oxidation-Reduction ; Oxygen Isotopes ; Sulfides ; Sulfur ; }, abstract = {Microbial nitrate reduction can be driven by organic carbon oxidation, as well as by inorganic electron donors, such as reduced forms of sulfur and iron. An apparent inverse oxygen isotope fractionation effect was observed during nitrate reduction in sediment incubations from five sampling sites of a freshwater lake, Hongze Lake, China. Incubations with organic and inorganic electron donor additions were performed. Especially, the inverse oxygen isotope effect was intensified after glucose addition, whereas the incubations with sulfide and Fe[2+] showed normal fractionation factors. Nitrate reductase encoding genes, napA and narG, were analysed with metagenomics. Higher napA/narG ratios were associated with higher oxygen fractionation factors. The most abundant clade (59%) of NapA in the incubation with glucose was affiliated with Rhodocyclales. In contrast, it only accounted for 8%-9% of NapA in the incubations with sulfide and Fe[2+] . Differences in nitrate reductases might explain different oxygen isotope effects. Our findings also suggested that large variance of O-nitrate isotope fractionations might have to be considered in the interpretation of natural isotope records.}, } @article {pmid35691354, year = {2022}, author = {Silveira, DD and Farooq, AJ and Wallace, SJ and Lapolli, FR and Nivala, J and Weber, KP}, title = {Structural and functional spatial dynamics of microbial communities in aerated and non-aerated horizontal flow treatment wetlands.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 4}, pages = {156600}, doi = {10.1016/j.scitotenv.2022.156600}, pmid = {35691354}, issn = {1879-1026}, mesh = {*Environmental Pollutants ; *Microbiota ; RNA, Ribosomal, 16S ; Waste Disposal, Fluid/methods ; *Water Purification/methods ; Wetlands ; }, abstract = {A multiphasic study using structural and functional analyses was employed to investigate the spatial dynamics of the microbial community within five horizontal subsurface flow treatment wetlands (TWs) of differing designs in Germany. The TWs differed in terms of the depth of media saturation, presence of plants (Phragmites australis), and aeration. In addition to influent and effluent water samples, internal samples were taken at different locations (12.5 %, 25 %, 50 %, and 75 % of the fractional distance along the flow path) within each system. 16S rRNA sequencing was used for the investigation of microbial community structure and was compared to microbial community function and enumeration data. The microbial community structure in the unaerated systems was similar, but different from the aerated TW profiles. Spatial positioning along the flow path explained the majority of microbial community dynamics/differences within this study. This was mainly attributed to the availability of nutrients closer to the inlet which also regulated the fixed biofilm/biomass densities. As the amount of fixed biofilm decreased from the inlet to the TW outlets, structural diversity increased, suggesting different microbial communities were present to handle the more easily utilized/degraded pollutants near the inlet vs. the more difficult to degrade and recalcitrant pollutants closer to the outlets. This study also confirmed that effluent water samples do not accurately describe the microbial communities responsible for water treatment inside a TW, highlighting the importance of using internal samples for investigating microbial communities in TWs. The results of this study reinforce an existing knowledge gap regarding the potential for TW design modifications which incorporate microbial community spatial dynamics (heterogeneity). It is suggested that utilizing step-feeding could allow for improved water treatment within the same areal footprint, and modifications enhancing co-metabolic processes could assist in improving the treatment of more difficult to degrade or recalcitrant compounds such as micropollutants.}, } @article {pmid35690846, year = {2022}, author = {Pessi, IS and Viitamäki, S and Virkkala, AM and Eronen-Rasimus, E and Delmont, TO and Marushchak, ME and Luoto, M and Hultman, J}, title = {In-depth characterization of denitrifier communities across different soil ecosystems in the tundra.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {30}, pmid = {35690846}, issn = {2524-6372}, support = {314114//Academy of Finland/ ; 335354//Academy of Finland/ ; 286950//Academy of Finland/ ; 314630//Academy of Finland/ ; 317054//Academy of Finland/ ; 8414//Gordon and Betty Moore Foundation/ ; }, abstract = {BACKGROUND: In contrast to earlier assumptions, there is now mounting evidence for the role of tundra soils as important sources of the greenhouse gas nitrous oxide (N2O). However, the microorganisms involved in the cycling of N2O in this system remain largely uncharacterized. Since tundra soils are variable sources and sinks of N2O, we aimed at investigating differences in community structure across different soil ecosystems in the tundra.

RESULTS: We analysed 1.4 Tb of metagenomic data from soils in northern Finland covering a range of ecosystems from dry upland soils to water-logged fens and obtained 796 manually binned and curated metagenome-assembled genomes (MAGs). We then searched for MAGs harbouring genes involved in denitrification, an important process driving N2O emissions. Communities of potential denitrifiers were dominated by microorganisms with truncated denitrification pathways (i.e., lacking one or more denitrification genes) and differed across soil ecosystems. Upland soils showed a strong N2O sink potential and were dominated by members of the Alphaproteobacteria such as Bradyrhizobium and Reyranella. Fens, which had in general net-zero N2O fluxes, had a high abundance of poorly characterized taxa affiliated with the Chloroflexota lineage Ellin6529 and the Acidobacteriota subdivision Gp23.

CONCLUSIONS: By coupling an in-depth characterization of microbial communities with in situ measurements of N2O fluxes, our results suggest that the observed spatial patterns of N2O fluxes in the tundra are related to differences in the composition of denitrifier communities.}, } @article {pmid35690718, year = {2022}, author = {Lu, H and Du, Y and Pan, T and Lou, Z and Li, H and Liao, Y and Wang, L}, title = {Gardnerella vaginalis purulent meningitis in an adolescent male: a case report.}, journal = {BMC neurology}, volume = {22}, number = {1}, pages = {217}, pmid = {35690718}, issn = {1471-2377}, mesh = {Adolescent ; Anti-Bacterial Agents/therapeutic use ; *Gardnerella vaginalis ; High-Throughput Nucleotide Sequencing ; Humans ; Male ; *Meningitis, Bacterial/diagnosis/drug therapy ; Metagenomics ; }, abstract = {BACKGROUND: We report a rare case of Gardnerella vaginalis found in the cerebrospinal fluid of a young boy.

CASE PRESENTATION: A 14-year-old boy was admitted to hospital with headache, vomiting, fever, drowsiness and positive meningeal irritation signs on examination. Cerebrospinal fluid (CSF) shows white blood cell and protein were elevated, and glucose was low. Traditional aerobic and anaerobic culture of CSF did not grow any organisms. However, metagenomic next-generation sequencing (mNGS) reveals G. vaginalis in his CSF. The patient was diagnosed with purulent meningitis, and treated with intravenous meropenem and linezolid for a week, followed by oral administration of amoxicillin for two weeks. He recovered without sequelae.

CONCLUSIONS: Purulent meningitis caused by Gardnerella vaginalis is extremely rare. Metagenomic next-generation sequencing of CSF should be highlighted for early diagnosis. With effective antibiotic treatment, the prognosis was excellent.}, } @article {pmid35690209, year = {2022}, author = {Song, Y and Zhang, C and Lei, H and Qin, M and Chen, G and Wu, F and Chen, C and Cao, Z and Zhang, C and Wu, M and Chen, X and Zhang, L}, title = {Characterization of triclosan-induced hepatotoxicity and triclocarban-triggered enterotoxicity in mice by multiple omics screening.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 4}, pages = {156570}, doi = {10.1016/j.scitotenv.2022.156570}, pmid = {35690209}, issn = {1879-1026}, mesh = {Animals ; Bile Acids and Salts ; *Carbanilides/toxicity ; *Chemical and Drug Induced Liver Injury/etiology ; Mice ; *Triclosan/toxicity ; }, abstract = {Triclosan (2,4,4'-trichloro-2'-hydroxydiphenyl ether, TCS) and triclocarban (3,4,4'-trichloro-carbanilide, TCC) are two antimicrobial agents commonly used for personal care products. Previous studies primarily focused on respective harmful effects of TCS and TCC. In terms of their structural similarities and differences, however, the structure-toxicity relationships on health effects of TCS and TCC exposure remain unclear. Herein, global [1]H NMR-based metabolomics was employed to screen the changes of metabolic profiling in various biological matrices including liver, serum, urine, feces and intestine of mice exposed to TCS and TCC at chronic and acute dosages. Metagenomics was also applied to analyze the gut microbiota modulation by TCS and TCC exposure. Targeted MS-based metabolites quantification, histopathological examination and biological assays were subsequently conducted to supply confirmatory information on respective toxicity of TCS and TCC. We found that oral administration of TCS mainly induced significant liver injuries accompanied with inflammation and dysfunction, hepatic steatosis fatty acids and bile acids metabolism disorders; while TCC exposure caused marked intestine injuries leading to striking disruption of colonic morphology, inflammatory status and intestinal barrier integrity, intestinal bile acids metabolism and microbial community. These comparative results provide novel insights into structure-dependent mechanisms of TCS-induced hepatotoxicity and TCC-triggered enterotoxicity in mice.}, } @article {pmid35690059, year = {2022}, author = {Wilmanski, T and Kornilov, SA and Diener, C and Conomos, MP and Lovejoy, JC and Sebastiani, P and Orwoll, ES and Hood, L and Price, ND and Rappaport, N and Magis, AT and Gibbons, SM}, title = {Heterogeneity in statin responses explained by variation in the human gut microbiome.}, journal = {Med (New York, N.Y.)}, volume = {3}, number = {6}, pages = {388-405.e6}, pmid = {35690059}, issn = {2666-6340}, support = {U19 AG023122/AG/NIA NIH HHS/United States ; }, mesh = {Cross-Sectional Studies ; *Diabetes Mellitus, Type 2/drug therapy ; *Gastrointestinal Microbiome/genetics ; Humans ; *Hydroxymethylglutaryl-CoA Reductase Inhibitors/adverse effects ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Statins remain one of the most prescribed medications worldwide. While effective in decreasing atherosclerotic cardiovascular disease risk, statin use is associated with adverse effects for a subset of patients, including disrupted metabolic control and increased risk of type 2 diabetes.

METHODS: We investigated the potential role of the gut microbiome in modifying patient responses to statin therapy across two independent cohorts (discovery n = 1,848, validation n = 991). Microbiome composition was assessed in these cohorts using stool 16S rRNA amplicon and shotgun metagenomic sequencing, respectively. Microbiome associations with markers of statin on-target and adverse effects were tested via a covariate-adjusted interaction analysis framework, utilizing blood metabolomics, clinical laboratory tests, genomics, and demographics data.

FINDINGS: The hydrolyzed substrate for 3-hydroxy-3-methylglutarate-coenzyme-A (HMG-CoA) reductase, HMG, emerged as a promising marker for statin on-target effects in cross-sectional cohorts. Plasma HMG levels reflected both statin therapy intensity and known genetic markers for variable statin responses. Through exploring gut microbiome associations between blood-derived measures of statin effectiveness and adverse metabolic effects of statins, we find that heterogeneity in statin responses was consistently associated with variation in the gut microbiome across two independent cohorts. A Bacteroides-enriched and diversity-depleted gut microbiome was associated with more intense statin responses, both in terms of on-target and adverse effects.

CONCLUSIONS: With further study and refinement, gut microbiome monitoring may help inform precision statin treatment.

FUNDING: This research was supported by the M.J. Murdock Charitable Trust, WRF, NAM Catalyst Award, and NIH grant U19AG023122 awarded by the NIA.}, } @article {pmid35689701, year = {2022}, author = {Imai, T and Inoue, R and Nishida, A and Yokota, Y and Morishima, S and Kawahara, M and Kusada, H and Tamaki, H and Andoh, A}, title = {Features of the gut prokaryotic virome of Japanese patients with Crohn's disease.}, journal = {Journal of gastroenterology}, volume = {57}, number = {8}, pages = {559-570}, pmid = {35689701}, issn = {1435-5922}, mesh = {Bacteria/genetics ; *Crohn Disease/microbiology ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Japan ; RNA, Ribosomal, 16S/genetics ; Virome/genetics ; }, abstract = {BACKGROUND/AIMS: The gut virome is mainly composed of bacteriophages and influences gut homeostasis and pathogenic conditions. In this study, we analyzed the gut prokaryotic virome in Japanese patients with Crohn's disease (CD).

MATERIALS/METHODS: We collected 19 fecal samples from CD patients and 16 samples from healthy controls. The gut bacteriome was analyzed by 16S rRNA gene sequencing and the virome was profiled by shotgun metagenomic sequencing.

RESULTS: Despite no differences in richness and evenness, there was a significant difference in the overall structure of the gut virome between CD patients and controls (P = 0.013). CrAssphage and Staphylococcus virus, belonging to the order Caudovirales, were dominant in the gut virome of controls and CD patients. The abundance of crAssphage was significantly greater in CD patients than controls (P = 0.021). Lactococcus, Enterococcus and Lactobacillus phages were present only in CD patients, while Xanthomonas and Escherichia phages were unique to the controls. In the gut bacteriome of CD patients, richness and evenness were significantly lower, and a significant difference in the overall structure was observed between groups (P = 0.014). The gut bacteriome of CD patients was characterized by a decrease of the genera Faecalibacterium, Roseburia, and Ruminococcus and an increase of the family Enterobacteriaceae. There were more significant correlations between viruses and bacteria in CD patients than controls.

CONCLUSIONS: The gut virome of CD patients was distinct from that of healthy controls in a Japanese population. An altered gut virome may be one of the factors associated with the bacterial dysbiosis of CD.}, } @article {pmid35689184, year = {2022}, author = {Van der Jeugt, F and Maertens, R and Steyaert, A and Verschaffelt, P and De Tender, C and Dawyndt, P and Mesuere, B}, title = {UMGAP: the Unipept MetaGenomics Analysis Pipeline.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {433}, pmid = {35689184}, issn = {1471-2164}, support = {1164420N//Agentschap voor Innovatie door Wetenschap en Technologie/ ; 1174621N//Agentschap voor Innovatie door Wetenschap en Technologie/ ; 1512619N//Agentschap voor Innovatie door Wetenschap en Technologie/ ; 12I5220N//Agentschap voor Innovatie door Wetenschap en Technologie/ ; }, mesh = {Algorithms ; Bacteria/genetics ; *Metagenomics ; Sequence Analysis, DNA ; Software ; *Viruses/genetics ; }, abstract = {BACKGROUND: Shotgun metagenomics yields ever richer and larger data volumes on the complex communities living in diverse environments. Extracting deep insights from the raw reads heavily depends on the availability of fast, accurate and user-friendly biodiversity analysis tools.

RESULTS: Because environmental samples may contain strains and species that are not covered in reference databases and because protein sequences are more conserved than the genes encoding them, we explore the alternative route of taxonomic profiling based on protein coding regions translated from the shotgun metagenomics reads, instead of directly processing the DNA reads. We therefore developed the Unipept MetaGenomics Analysis Pipeline (UMGAP), a highly versatile suite of open source tools that are implemented in Rust and support parallelization to achieve optimal performance. Six preconfigured pipelines with different performance trade-offs were carefully selected, and benchmarked against a selection of state-of-the-art shotgun metagenomics taxonomic profiling tools.

CONCLUSIONS: UMGAP's protein space detour for taxonomic profiling makes it competitive with state-of-the-art shotgun metagenomics tools. Despite our design choices of an extra protein translation step, a broad spectrum index that can identify both archaea, bacteria, eukaryotes and viruses, and a highly configurable non-monolithic design, UMGAP achieves low runtime, manageable memory footprint and high accuracy. Its interactive visualizations allow for easy exploration and comparison of complex communities.}, } @article {pmid35688988, year = {2022}, author = {Yi, X and Liang, JL and Su, JQ and Jia, P and Lu, JL and Zheng, J and Wang, Z and Feng, SW and Luo, ZH and Ai, HX and Liao, B and Shu, WS and Li, JT and Zhu, YG}, title = {Globally distributed mining-impacted environments are underexplored hotspots of multidrug resistance genes.}, journal = {The ISME journal}, volume = {16}, number = {9}, pages = {2099-2113}, pmid = {35688988}, issn = {1751-7370}, support = {42077117//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; *Drug Resistance, Multiple/genetics ; *Genes, Bacterial ; *Genes, MDR ; Humans ; Metagenome ; *Mining ; Phylogeny ; }, abstract = {Mining is among the human activities with widest environmental impacts, and mining-impacted environments are characterized by high levels of metals that can co-select for antibiotic resistance genes (ARGs) in microorganisms. However, ARGs in mining-impacted environments are still poorly understood. Here, we conducted a comprehensive study of ARGs in such environments worldwide, taking advantage of 272 metagenomes generated from a global-scale data collection and two national sampling efforts in China. The average total abundance of the ARGs in globally distributed studied mine sites was 1572 times per gigabase, being rivaling that of urban sewage but much higher than that of freshwater sediments. Multidrug resistance genes accounted for 40% of the total ARG abundance, tended to co-occur with multimetal resistance genes, and were highly mobile (e.g. on average 16% occurring on plasmids). Among the 1848 high-quality metagenome-assembled genomes (MAGs), 85% carried at least one multidrug resistance gene plus one multimetal resistance gene. These high-quality ARG-carrying MAGs considerably expanded the phylogenetic diversity of ARG hosts, providing the first representatives of ARG-carrying MAGs for the Archaea domain and three bacterial phyla. Moreover, 54 high-quality ARG-carrying MAGs were identified as potential pathogens. Our findings suggest that mining-impacted environments worldwide are underexplored hotspots of multidrug resistance genes.}, } @article {pmid35688651, year = {2022}, author = {Chen, J and Yang, Y and Ke, Y and Chen, X and Jiang, X and Chen, C and Xie, S}, title = {Anaerobic sulfamethoxazole-degrading bacterial consortia in antibiotic-contaminated wetland sediments identified by DNA-stable isotope probing and metagenomics analysis.}, journal = {Environmental microbiology}, volume = {24}, number = {8}, pages = {3751-3763}, doi = {10.1111/1462-2920.16091}, pmid = {35688651}, issn = {1462-2920}, mesh = {Anaerobiosis ; *Anti-Bacterial Agents/metabolism ; Bacteria ; Biodegradation, Environmental ; DNA/metabolism ; Isotopes/metabolism ; Metagenomics ; *Sulfamethoxazole/metabolism ; Wetlands ; }, abstract = {Anaerobic degradation has been demonstrated as an important pathway for the removal of sulfonamide (SA) in contaminated environments, and identifying the microorganisms responsible for the degradation of SA is a key step in developing bioaugmentation approaches. In this study, we investigated the anaerobic degradation activity of three SA [sulfadiazine (SDZ), sulfamethazine (SMZ) and sulfamethoxazole (SMX)] and the associated bacterial community in wetland sediments contaminated by aquaculture (in Fujian Province, coded with FJ), livestock farming (in Sichuan Province, coded with SC), or rural wastewaters (in Guangdong Province, coded with GD). Additionally, the combination of DNA-stable isotope probing (SIP) with metagenomics was further applied to assess the active SA-degrading microbes using SMX as a model SA. Among SDZ, SMZ and SMX, only SMX could be effectively dissipated, and the degradation of SMX was relatively fast in the microcosms of sediments with higher levels of SA contamination (FJ and SC). The anaerobic biotransformation pathway of SMX was initiated by hydrogenation with the cleavage of the N-O bond on the isoxazole ring. DNA-SIP revealed that the in situ active anaerobic SMX-degraders (5, 18 and 3 genera in sediments FJ, SC and GD respectively) were dominated by Proteobacteria in sediments FJ and SC, but by Firmicutes (two Family XVIII members) in sediment GD. Mycobacterium, unclassified Burkholderiaceae and Rhodocyclaceae were identified as the dominant active SMX-degrading bacteria in both sediments FJ and SC. Higher proportions of antibiotic resistance gene and genes involved in various functional categories were observed in sediments FJ and SC.}, } @article {pmid35688389, year = {2022}, author = {Vila-Costa, M and Lundin, D and Casamayor, EO and Meijer, SN and Fernández, P and Dachs, J}, title = {Microbial metabolic routes in metagenome assembled genomes are mirrored by the mass balance of polycyclic aromatic hydrocarbons in a high altitude lake.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {308}, number = {}, pages = {119592}, doi = {10.1016/j.envpol.2022.119592}, pmid = {35688389}, issn = {1873-6424}, mesh = {Altitude ; Environmental Monitoring ; *Environmental Pollutants ; Geologic Sediments ; Lakes/analysis ; Metagenome ; *Polycyclic Aromatic Hydrocarbons/analysis ; *Water Pollutants, Chemical/analysis ; }, abstract = {Semivolatile organic pollutants have potential for long range atmospheric transport and can thus reach pristine remote lakes by atmospheric deposition. Polycyclic aromatic hydrocarbons (PAHs) are among the most abundant and toxic semivolatile pollutants affecting lakes, however, the main factors controlling their fate are still poorly known. Here we show two contrasting lines of evidence for the importance of microbial degradation on the environmental fate of PAHs in a high altitude deep lake. The first evidence is given by an assessment of the metagenomes from surface and deep waters from Lake Redon (Pyrenees Mountains), which shows the occurrence of the initial ring hydroxylating dioxygenases as well as other PAH degrading genes from the complete metabolic route of PAH degradation. The second line of evidence is by the application of an environmental fate model for PAHs to Lake Redon under two contrasting scenarios considering the inclusion or not of degradation. When degradation is included in the model, PAH concentrations in the sediment are predicted within a factor of two of those measured in Lake Redon. Finally, the extent of the degradation sink is quantified and compared to other cycling PAH fluxes in the lake.}, } @article {pmid35688170, year = {2022}, author = {Janes, VA and Matamoros, S and Munk, P and Clausen, PTLC and Koekkoek, SM and Koster, LAM and Jakobs, ME and de Wever, B and Visser, CE and Aarestrup, FM and Lund, O and de Jong, MD and Bossuyt, PMM and Mende, DR and Schultsz, C}, title = {Metagenomic DNA sequencing for semi-quantitative pathogen detection from urine: a prospective, laboratory-based, proof-of-concept study.}, journal = {The Lancet. Microbe}, volume = {3}, number = {8}, pages = {e588-e597}, doi = {10.1016/S2666-5247(22)00088-X}, pmid = {35688170}, issn = {2666-5247}, mesh = {Anti-Bacterial Agents/pharmacology ; Humans ; *Metagenomics/methods ; Prospective Studies ; Sequence Analysis, DNA ; *Urinary Tract Infections/diagnosis ; }, abstract = {BACKGROUND: Semi-quantitative bacterial culture is the reference standard to diagnose urinary tract infection, but culture is time-consuming and can be unreliable if patients are receiving antibiotics. Metagenomics could increase diagnostic accuracy and speed by sequencing the microbiota and resistome directly from urine. We aimed to compare metagenomics to culture for semi-quantitative pathogen and resistome detection from urine.

METHODS: In this proof-of-concept study, we prospectively included consecutive urine samples from a clinical diagnostic laboratory in Amsterdam. Urine samples were screened by DNA concentration, followed by PCR-free metagenomic sequencing of randomly selected samples with a high concentration of DNA (culture positive and negative). A diagnostic index was calculated as the product of DNA concentration and fraction of pathogen reads. We compared results with semi-quantitative culture using area under the receiver operating characteristic curve (AUROC) analyses. We used ResFinder and PointFinder for resistance gene detection and compared results to phenotypic antimicrobial susceptibility testing for six antibiotics commonly used for urinary tract infection treatment: nitrofurantoin, ciprofloxacin, fosfomycin, cotrimoxazole, ceftazidime, and ceftriaxone.

FINDINGS: We screened 529 urine samples of which 86 were sequenced (43 culture positive and 43 culture negative). The AUROC of the DNA concentration-based screening was 0·85 (95% CI 0·81-0·89). At a cutoff value of 6·0 ng/mL, culture positivity was ruled out with a negative predictive value of 91% (95% CI 87-93; 26 of 297 samples), reducing the number of samples requiring sequencing by 56% (297 of 529 samples). The AUROC of the diagnostic index was 0·87 (95% CI 0·79-0·95). A diagnostic index cutoff value of 17·2 yielded a positive predictive value of 93% (95% CI 85-97) and a negative predictive value of 69% (55-80), correcting for a culture-positive prevalence of 66%. Gram-positive pathogens explained eight (89%) of the nine false-negative metagenomic test results. Agreement of phenotypic and genotypic antimicrobial susceptibility testing varied between 71% (22 of 31 samples) and 100% (six of six samples), depending on the antibiotic tested.

INTERPRETATION: This study provides proof-of-concept of metagenomic semi-quantitative pathogen and resistome detection for the diagnosis of urinary tract infection. The findings warrant prospective clinical validation of the value of this approach in informing patient management and care.

FUNDING: EU Horizon 2020 Research and Innovation Programme.}, } @article {pmid35687947, year = {2022}, author = {Chen, J and Yang, Y and Ke, Y and Chen, X and Jiang, X and Chen, C and Xie, S}, title = {Sulfonamide-metabolizing microorganisms and mechanisms in antibiotic-contaminated wetland sediments revealed by stable isotope probing and metagenomics.}, journal = {Environment international}, volume = {165}, number = {}, pages = {107332}, doi = {10.1016/j.envint.2022.107332}, pmid = {35687947}, issn = {1873-6750}, mesh = {Anti-Bacterial Agents/metabolism ; Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Ecosystem ; Isotopes ; *Metagenomics ; Soil Microbiology ; Sulfamethoxazole/metabolism ; Sulfanilamide/metabolism ; *Wetlands ; }, abstract = {Sulfonamide (SA) antibiotics are ubiquitous pollutants in livestock breeding and aquaculture wastewaters, which increases the propagation of antibiotic resistance genes. Microbes with the ability to degrade SA play important roles in SA dissipation, but their diversity and the degradation mechanism in the field remain unclear. In the present study, we employed DNA-stable isotope probing (SIP) combined with metagenomics to explore the active microorganisms and mechanisms of SA biodegradation in antibiotic-contaminated wetland sediments. DNA-SIP revealed various SA-assimilating bacteria dominated by members of Proteobacteria, such as Bradyrhizobium, Gemmatimonas, and unclassified Burkholderiaceae. Both sulfadiazine and sulfamethoxazole were dissipated mainly through the initial ipso-hydroxylation, and were driven by similar microbes. sadA gene, which encodes an NADH-dependent monooxygenase, was enriched in the [13]C heavy DNA, confirming its catalytic capacity for the initial ipso-hydroxylation of SA in sediments. In addition, some genes encoding dioxygenases were also proposed to participate in SA hydroxylation and aromatic ring cleavage based on metagenomics analysis, which might play an important role in SA metabolism in the sediment ecosystem when Proteobacteria was the dominant active bacteria. Our work elucidates the ecological roles of uncultured microorganisms in their natural habitats and gives a deeper understanding of in-situ SA biodegradation mechanisms.}, } @article {pmid35687756, year = {2022}, author = {Jenckel, M and Hall, RN and Strive, T}, title = {Pathogen profiling of Australian rabbits by metatranscriptomic sequencing.}, journal = {Transboundary and emerging diseases}, volume = {69}, number = {5}, pages = {e2629-e2640}, pmid = {35687756}, issn = {1865-1682}, support = {P.PSH.1059//Meat and Livestock Australia/ ; //CSIRO/ ; P01-B-002//Centre for Invasive Species Solutions/ ; }, mesh = {Animals ; Australia/epidemiology ; *Caliciviridae Infections/veterinary ; *Hemorrhagic Disease Virus, Rabbit/genetics ; *Myxoma virus ; Rabbits ; Saccharomyces cerevisiae ; }, abstract = {Australia is known for its long history of using biocontrol agents, such as myxoma virus (MYXV) and rabbit haemorrhagic disease virus (RHDV), to manage wild European rabbit populations. Interestingly, while undertaking RHDV surveillance of rabbits that were found dead, we observed that approximately 40% of samples were negative for RHDV. To investigate whether other infectious agents are responsible for killing rabbits in Australia, we subjected a subset of these RHDV-negative liver samples to metatranscriptomic sequencing. In addition, we investigated whether the host transcriptome data could provide additional differentiation between likely infectious versus non-infectious causes of death. We identified transcripts from several Clostridia species, Pasteurella multocida, Pseudomonas spp., and Eimeria stiedae, in liver samples of several rabbits that had died suddenly, all of which are known to infect rabbits and are capable of causing disease and mortality. In addition, we identified Hepatitis E virus and Cyniclomyces yeast in some samples, both of which are not usually associated with severe disease. In one-third of the sequenced total liver RNAs, no infectious agent could be identified. While metatranscriptomic sequencing cannot provide definitive evidence of causation, additional host transcriptome analysis provided further insights to distinguish between pathogenic microbes and commensals or environmental contaminants. Interestingly, three samples where no pathogen could be identified showed evidence of up-regulated host immune responses, while immune response pathways were not up-regulated when E. stiedae, Pseudomonas, or yeast were detected. In summary, although no new putative rabbit pathogens were identified, this study provides a robust workflow for future investigations into rabbit mortality events.}, } @article {pmid35687414, year = {2022}, author = {Li, Y and Liu, B and Tu, Q and Xue, S and Liu, X and Wu, Z and An, S and Chen, J and Wang, Z}, title = {The ecological roles of assembling genomes for Bacillales and Clostridiales in coal seams.}, journal = {FEMS microbiology letters}, volume = {369}, number = {1}, pages = {}, doi = {10.1093/femsle/fnac053}, pmid = {35687414}, issn = {1574-6968}, mesh = {Acetates ; *Bacillales/metabolism ; Clostridiales/metabolism ; Coal/microbiology ; Humans ; *Hydrogenase ; Methane/metabolism ; Nitrogen ; Sulfates ; }, abstract = {Biogenic coalbed methane is produced by biological processes mediated by synergistic interactions of microbial complexes in coal seams. However, the ecological role of functional bacteria in biogenic coalbed methane remains poorly understood. Here, we studied the metagenome assembled genomes (MAGs) of Bacillales and Clostridiales from coal seams, revealing further expansion of hydrogen and acetogen producers involved in organic matter decomposition. In this study, Bacillales and Clostridiales were dominant orders (91.85 ± 0.94%) in cultured coal seams, and a total of 16 MAGs from six families, including Bacillus, Paenibacillus, Staphylococcus, Anaerosalibacter, Hungatella and Paeniclostridium, were reconstructed. These microbial groups possessed multiple metabolic pathways (glycolysis/gluconeogenesis, pentose phosphate, β-oxidation, TCA cycle, assimilatory sulfate reduction, nitrogen metabolism and encoding hydrogenase) that provided metabolic substrates (acetate and/or H2) for the methanogenic processes. Therein, the hydrogenase-encoding gene and hydrogenase maturation factors were merely found in all the Clostridiales MAGs. β-oxidation was the main metabolic pathway involved in short-chain fatty acid degradation and acetate production, and most of these pathways were detected and exhibited different operon structures in Bacillales MAGs. In addition, assimilatory sulfate reduction and nitrogen metabolism processes were also detected in some MAGs, and these processes were also closely related to acetate production and/or organic matter degradation according to their operon structures and metabolic pathways. In summary, this study enabled a better understanding of the ecological roles of Bacillales and Clostridiales in biogenic methane in coal seams based on a combination of bioinformatic techniques.}, } @article {pmid35687095, year = {2022}, author = {Vernette, C and Lecubin, J and Sánchez, P and , and Sunagawa, S and Delmont, TO and Acinas, SG and Pelletier, E and Hingamp, P and Lescot, M}, title = {The Ocean Gene Atlas v2.0: online exploration of the biogeography and phylogeny of plankton genes.}, journal = {Nucleic acids research}, volume = {50}, number = {W1}, pages = {W516-W526}, pmid = {35687095}, issn = {1362-4962}, mesh = {*Bacteria/genetics ; *Eukaryota/genetics ; Metagenome ; Phylogeny ; *Plankton/genetics ; *Marine Biology ; }, abstract = {Testing hypothesis about the biogeography of genes using large data resources such as Tara Oceans marine metagenomes and metatranscriptomes requires significant hardware resources and programming skills. The new release of the 'Ocean Gene Atlas' (OGA2) is a freely available intuitive online service to mine large and complex marine environmental genomic databases. OGA2 datasets available have been extended and now include, from the Tara Oceans portfolio: (i) eukaryotic Metagenome-Assembled-Genomes (MAGs) and Single-cell Assembled Genomes (SAGs) (10.2E+6 coding genes), (ii) version 2 of Ocean Microbial Reference Gene Catalogue (46.8E+6 non-redundant genes), (iii) 924 MetaGenomic Transcriptomes (7E+6 unigenes), (iv) 530 MAGs from an Arctic MAG catalogue (1E+6 genes) and (v) 1888 Bacterial and Archaeal Genomes (4.5E+6 genes), and an additional dataset from the Malaspina 2010 global circumnavigation: (vi) 317 Malaspina Deep Metagenome Assembled Genomes (0.9E+6 genes). Novel analyses enabled by OGA2 include phylogenetic tree inference to visualize user queries within their context of sequence homologues from both the marine environmental dataset and the RefSeq database. An Application Programming Interface (API) now allows users to query OGA2 using command-line tools, hence providing local workflow integration. Finally, gene abundance can be interactively filtered directly on map displays using any of the available environmental variables. Ocean Gene Atlas v2.0 is freely-available at: https://tara-oceans.mio.osupytheas.fr/ocean-gene-atlas/.}, } @article {pmid35686590, year = {2022}, author = {Jiang, S and Nie, J and Chen, YX and Wang, XY and Chen, F}, title = {Structure and Composition of Candidate Phyla Radiation in Supragingival Plaque of Caries Patients.}, journal = {The Chinese journal of dental research}, volume = {25}, number = {2}, pages = {107-118}, doi = {10.3290/j.cjdr.b3086339}, pmid = {35686590}, issn = {1867-5646}, mesh = {Bacteria ; Capnocytophaga ; *Dental Caries ; Dental Caries Susceptibility ; *Dental Deposits ; *Dental Plaque/microbiology ; Humans ; *Microbiota ; Mouth/microbiology ; }, abstract = {OBJECTIVE: To investigate the composition and abundance of candidate phyla radiation (CPR) in the oral cavity in caries patients and a healthy population.

METHODS: The raw macrogenomic sequencing data for a total of 88 subjects were downloaded from the National Centre for Biotechnology Sequence Read Archive (NCBI SRA) public database according to the public data usage specifications. Trimmomatic (Department for Metabolic Networks, Potsdam, Germany) and Bowtie 2 (University of Maryland, College Park, MD, USA) were used to quality control and dehost the host sequences. Species annotation was made using Kraken2 (Johns Hopkins University, Baltimore, MD, USA) and Bracken (Johns Hopkins University) based on the reference database. According to the results of the species annotation, the species-significant differences and species correlation of caries and healthy oral microbiota in species composition and microbiota diversity were analysed to study the distribution and abundance differences of CPR in the oral environment.

RESULTS: Proteobacteria, Firmicutes, Bacteroidetes, Actinobacteria and Fusobacteria were the main components. The relative abundance of TM7 (Candidatus Saccharibacteria) and GN02 (Candidatus Gracilibacteria) of CPR is second only to the aforementioned five bacteria, indicating that CPR is an important part of the oral microbiota. TM7 and GN02 were common to both the caries patients and healthy patients and were detected in all samples, suggesting that CPR is the 'core microbiome'. There was a correlation between CPR and a variety of oral microbiota, among which the positive correlation with Capnocytophaga was the strongest, suggesting that Capnocytophaga might be the potential host bacteria of CPR.

CONCLUSION: CPR is an indispensable part of the oral microbiota. It is the 'core microflora' of the oral cavity and may play an important role in the stability and function of the oral microecological environment. Capnocytophaga may be the potential host bacteria of CPR.}, } @article {pmid35686002, year = {2022}, author = {Shaaban, MT and Abdelhamid, RM and Zayed, M and Ali, SM}, title = {Evaluation of a new antimicrobial agent production (RSMM C3) by using metagenomics approaches from Egyptian marine biota.}, journal = {Biotechnology reports (Amsterdam, Netherlands)}, volume = {34}, number = {}, pages = {e00706}, pmid = {35686002}, issn = {2215-017X}, abstract = {Diseases and epidemics in the current days need new types of antibiotics in order to be able to eliminate them. The goal of this research is to use metagenomics to identify isolated utilitarian gene (s) as antimicrobial specialists. Collection of diverse locations from sea sediment samples from Alexandria and extraction of total DNA, restriction enzyme fragmentation, cloning into pUC19 vector, and expression of the isolated gene(s) in E. coli DH5α were all part of the process. Characterization of Antimicrobial agent was done for the best clone for antimicrobial agent's production to detect efficiency, optimum pH, thermal stability, pH stability, effect of different compounds on antimicrobial activity, and residual activity of product after preservation in room temperature. Amino acid sequence of RSMM C3 gene (1250 bp) was 72% identity with Herbaspirillum sp. The ideal temperature level of the RSMM C3 antimicrobial agent production was 36 °C. The antimicrobial agent RSMM C3's stability was stable at -20 °Celsius for up to two months without thawing. The antibacterial agent RSMM C3 was stable at 4 °C for 14 days without loss in activity. The ideal pH level of the RSMM C3 antimicrobial agent was 6. Remain activity was gradually decreased at pH 5, 6, 6.5 and 7 (86.1, 96.9, 97.2 and 94.9%, respectively). On the other hand, residual activity was (92 and 84%) at (pH 7.5 and 8) for 8 days. The tested antimicrobial RSMM C3 was stable against 1 mM of different compounds (DMSO, Glycerol, NaCl, CaCl2, MgCl2, ZnCl2, FeSO4, MnSO4 and CuSO4). The research provides for the Metagenomics technique that has the ability for the production of novel antimicrobial agents produced by clone RSMM C3 which has a wide spectrum activity towards different microorganisms comparing to other antibiotics as Ampicillin and Tetracycline.}, } @article {pmid35685929, year = {2022}, author = {Seitz, TJ and Schütte, UME and Drown, DM}, title = {Unearthing Shifts in Microbial Communities Across a Soil Disturbance Gradient.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {781051}, pmid = {35685929}, issn = {1664-302X}, support = {P20 GM103395/GM/NIGMS NIH HHS/United States ; RL5 GM118990/GM/NIGMS NIH HHS/United States ; UL1 GM118991/GM/NIGMS NIH HHS/United States ; }, abstract = {Permafrost, an important source of soil disturbance, is particularly vulnerable to climate change in Alaska where 85% of the land is underlained with discontinuous permafrost. Boreal forests, home to plants integral to subsistence diets of many Alaska Native communities, are not immune to the effects of climate change. Soil disturbance events, such as permafrost thaw, wildfires, and land use change can influence abiotic conditions, which can then affect active layer soil microbial communities. In a previous study, we found negative effects on boreal plants inoculated with microbes impacted by soil disturbance compared to plants inoculated with microbes from undisturbed soils. Here, we identify key shifts in microbial communities altered by soil disturbance using 16S rRNA gene sequencing and make connections between microbial community changes and previously observed plant growth. Additionally, we identify further community shifts in potential functional mechanisms using long read metagenomics. Across a soil disturbance gradient, microbial communities differ significantly based on the level of soil disturbance. Consistent with the earlier study, the family Acidobacteriaceae, which consists of known plant growth promoters, was abundant in undisturbed soil, but practically absent in most disturbed soil. In contrast, Comamonadaceae, a family with known agricultural pathogens, was overrepresented in most disturbed soil communities compared to undisturbed. Within our metagenomic data, we found that soil disturbance level is associated with differences in microbial community function, including mechanisms potentially involved in plant pathogenicity. These results indicate that a decrease in plant growth can be linked to changes in the microbial community and functional composition driven by soil disturbance and climate change. Together, these results build a genomic understanding of how shifting soil microbiomes may affect plant productivity and ecosystem health as the Arctic warms.}, } @article {pmid35685890, year = {2022}, author = {Lamichhane, S and Siljander, H and Salonen, M and Ruohtula, T and Virtanen, SM and Ilonen, J and Hyötyläinen, T and Knip, M and Orešič, M}, title = {Impact of Extensively Hydrolyzed Infant Formula on Circulating Lipids During Early Life.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {859627}, pmid = {35685890}, issn = {2296-861X}, abstract = {BACKGROUND: Current evidence suggests that the composition of infant formula (IF) affects the gut microbiome, intestinal function, and immune responses during infancy. However, the impact of IF on circulating lipid profiles in infants is still poorly understood. The objectives of this study were to (1) investigate how extensively hydrolyzed IF impacts serum lipidome compared to conventional formula and (2) to associate changes in circulatory lipids with gastrointestinal biomarkers including intestinal permeability.

METHODS: In a randomized, double-blind controlled nutritional intervention study (n = 73), we applied mass spectrometry-based lipidomics to analyze serum lipids in infants who were fed extensively hydrolyzed formula (HF) or conventional, regular formula (RF). Serum samples were collected at 3, 9, and 12 months of age. Child's growth (weight and length) and intestinal functional markers, including lactulose mannitol (LM) ratio, fecal calprotectin, and fecal beta-defensin, were also measured at given time points. At 3 months of age, stool samples were analyzed by shotgun metagenomics.

RESULTS: Concentrations of sphingomyelins were higher in the HF group as compared to the RF group. Triacylglycerols (TGs) containing saturated and monounsaturated fatty acyl chains were found in higher levels in the HF group at 3 months, but downregulated at 9 and 12 months of age. LM ratio was lower in the HF group at 9 months of age. In the RF group, the LM ratio was positively associated with ether-linked lipids. Such an association was, however, not observed in the HF group.

CONCLUSION: Our study suggests that HF intervention changes the circulating lipidome, including those lipids previously found to be associated with progression to islet autoimmunity or overt T1D.

CLINICAL TRIAL REGISTRATION: [Clinicaltrials.gov], identifier [NCT01735123].}, } @article {pmid35685788, year = {2022}, author = {Tomita, S and Kusada, H and Kojima, N and Ishihara, S and Miyazaki, K and Tamaki, H and Kurita, R}, title = {Polymer-based chemical-nose systems for optical-pattern recognition of gut microbiota.}, journal = {Chemical science}, volume = {13}, number = {20}, pages = {5830-5837}, pmid = {35685788}, issn = {2041-6520}, abstract = {Gut-microbiota analysis has been recognized as crucial in health management and disease treatment. Metagenomics, a current standard examination method for the gut microbiome, is effective but requires both expertise and significant amounts of general resources. Here, we show highly accessible sensing systems based on the so-called chemical-nose strategy to transduce the characteristics of microbiota into fluorescence patterns. The fluorescence patterns, generated by twelve block copolymers with aggregation-induced emission (AIE) units, were analyzed using pattern-recognition algorithms, which identified 16 intestinal bacterial strains in a way that correlates with their genome-based taxonomic classification. Importantly, the chemical noses classified artificial models of obesity-associated gut microbiota, and further succeeded in detecting sleep disorder in mice through comparative analysis of normal and abnormal mouse gut microbiota. Our techniques thus allow analyzing complex bacterial samples far more quickly, simply, and inexpensively than common metagenome-based methods, which offers a powerful and complementary tool for the practical analysis of the gut microbiome.}, } @article {pmid35685549, year = {2022}, author = {Fang, C and Zuo, K and Zhang, W and Zhong, J and Li, J and Xu, L and Yang, X}, title = {Association between Gut Microbiota Dysbiosis and the CHA2DS2-VASc Score in Atrial Fibrillation Patients.}, journal = {International journal of clinical practice}, volume = {2022}, number = {}, pages = {7942605}, pmid = {35685549}, issn = {1742-1241}, mesh = {*Atrial Fibrillation/complications ; Dysbiosis/complications ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Risk Assessment ; Risk Factors ; *Stroke/complications ; *Thromboembolism/etiology ; }, abstract = {BACKGROUND: In our previous studies, we found a disordered taxonomic composition and function of gut microbiota (GM) in atrial fibrillation (AF) patients. However, direct evidence about the association between dysbiotic microbiota and thromboembolic risk in AF is lacking.

AIMS: In this study, we analyzed the interaction of GM and related functional patterns in AF with different CHA2DS2-VASc scores to assess its potential as a biomarker for predicting stroke risk. Patients and Methods. The CHA2DS2-VASc score was used for thromboembolic risk stratification in AF according to American Heart Association (AHA) guidelines. We investigated the taxonomic and functional annotation of GM based on metagenomic data from 50 AF patients (32 with high thromboembolic risk (CHA2DS2-VASc score ≥2 (males) or CHA2DS2-VASc score ≥3 (females)) and 18 individuals with low thromboembolic risk (CHA2DS2-VASc score <2 (males) or CHA2DS2-VASc score <3 (females))).

RESULTS: The gut microbial diversity, composition, and function in AF were different in high and low CHA2DS2-VASc score groups. In high thromboembolic risk group, the abundance of Prevotella, Lachnospiraceae, and Eubacterium rectale, related to the production of short-chain fatty acids and anti-inflammatory were reduced (all P < 0.05). Furthermore, annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG), a database of genes and genomes, the KEGG orthology-based scoring approach exhibited a significant association with thromboembolic risk in AF patients.

CONCLUSIONS: Imbalance of GM and microbial dysfunction are involved in aggravated thromboembolic risk of AF.}, } @article {pmid35684099, year = {2022}, author = {Gold, MS and Quinn, PJ and Campbell, DE and Peake, J and Smart, J and Robinson, M and O'Sullivan, M and Vogt, JK and Pedersen, HK and Liu, X and Pazirandeh-Micol, E and Heine, RG}, title = {Effects of an Amino Acid-Based Formula Supplemented with Two Human Milk Oligosaccharides on Growth, Tolerability, Safety, and Gut Microbiome in Infants with Cow's Milk Protein Allergy.}, journal = {Nutrients}, volume = {14}, number = {11}, pages = {}, pmid = {35684099}, issn = {2072-6643}, mesh = {Amino Acids ; Animals ; Cattle ; Female ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant Formula ; Male ; *Milk Hypersensitivity ; Milk, Human ; Oligosaccharides ; }, abstract = {This open-label, non-randomized, multicenter trial (Registration: NCT03661736) aimed to assess if an amino acid-based formula (AAF) supplemented with two human milk oligosaccharides (HMO) supports normal growth and is well tolerated in infants with a cow's milk protein allergy (CMPA). Term infants aged 1-8 months with moderate-to-severe CMPA were enrolled. The study formula was an AAF supplemented with 2'-fucosyllactose (2'-FL) and lacto-N-neotetraose (LNnT). Infants were fed the study formula for 4 months and were offered to remain on the formula until 12 months of age. Tolerance and safety were assessed throughout the trial. Out of 32 infants (mean age 18.6 weeks; 20 (62.5%) male), 29 completed the trial. During the 4-month principal study period, the mean weight-for-age Z score (WAZ) increased from -0.31 at the baseline to +0.28 at the 4-months' follow-up. Linear and head growth also progressed along the WHO child growth reference, with a similar small upward trend. The formula was well tolerated and had an excellent safety profile. When comparing the microbiome at the baseline to the subsequent visits, there was a significant on-treatment enrichment in HMO-utilizing bifidobacteria, which was associated with a significant increase in fecal short-chain fatty acids. In addition, we observed a significant reduction in the abundance of fecal Proteobacteria, suggesting that the HMO-supplemented study formula partially corrected the gut microbial dysbiosis in infants with CMPA.}, } @article {pmid35681493, year = {2022}, author = {Das De, T and Sharma, P and Tevatiya, S and Chauhan, C and Kumari, S and Yadav, P and Singla, D and Srivastava, V and Rani, J and Hasija, Y and Pandey, KC and Kajla, M and Dixit, R}, title = {Bidirectional Microbiome-Gut-Brain-Axis Communication Influences Metabolic Switch-Associated Responses in the Mosquito Anopheles culicifacies.}, journal = {Cells}, volume = {11}, number = {11}, pages = {}, pmid = {35681493}, issn = {2073-4409}, mesh = {Animals ; *Anopheles ; Bacteria/genetics ; Brain/metabolism ; Cell Communication ; Female ; *Gastrointestinal Microbiome/physiology ; }, abstract = {The periodic ingestion of a protein-rich blood meal by adult female mosquitoes causes a drastic metabolic change in their innate physiological status, which is referred to as a 'metabolic switch'. While understanding the neural circuits for host-seeking is modestly attended, how the gut 'metabolic switch' modulates brain functions, and resilience to physiological homeostasis, remains unexplored. Here, through a comparative brain RNA-Seq study, we demonstrate that the protein-rich diet induces the expression of brain transcripts related to mitochondrial function and energy metabolism, possibly causing a shift in the brain's engagement to manage organismal homeostasis. A dynamic mRNA expression pattern of neuro-signaling and neuro-modulatory genes in both the gut and brain likely establishes an active gut-brain communication. The disruption of this communication through decapitation does not affect the modulation of the neuro-modulator receptor genes in the gut. In parallel, an unusual and paramount shift in the level of neurotransmitters (NTs), from the brain to the gut after blood feeding, further supports the idea of the gut's ability to serve as a 'second brain'. After blood-feeding, a moderate enrichment of the gut microbial population, and altered immunity in the gut of histamine receptor-silenced mosquitoes, provide initial evidence that the gut-microbiome plays a crucial role in gut-brain-axis communication. Finally, a comparative metagenomics evaluation of the gut microbiome highlighted that blood-feeding enriches the family members of the Morganellaceae and Pseudomonadaceae bacterial communities. The notable observation of a rapid proliferation of Pseudomonas bacterial sp. and tryptophan enrichment in the gut correlates with the suppression of appetite after blood-feeding. Additionally, altered NTs dynamics of naïve and aseptic mosquitoes provide further evidence that gut-endosymbionts are key modulators for the synthesis of major neuroactive molecules. Our data establish a new conceptual understanding of microbiome-gut-brain-axis communication in mosquitoes.}, } @article {pmid35681015, year = {2022}, author = {Krishnamoorthy, M and Ranjan, P and Erb-Downward, JR and Dickson, RP and Wiens, J}, title = {AMAISE: a machine learning approach to index-free sequence enrichment.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {568}, pmid = {35681015}, issn = {2399-3642}, support = {R01 AI129958/AI/NIAID NIH HHS/United States ; R01 HL144599/HL/NHLBI NIH HHS/United States ; }, mesh = {*Algorithms ; Machine Learning ; Metagenome ; *Metagenomics/methods ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenomics holds potential to improve clinical diagnostics of infectious diseases, but DNA from clinical specimens is often dominated by host-derived sequences. To address this, researchers employ host-depletion methods. Laboratory-based host-depletion methods, however, are costly in terms of time and effort, while computational host-depletion methods rely on memory-intensive reference index databases and struggle to accurately classify noisy sequence data. To solve these challenges, we propose an index-free tool, AMAISE (A Machine Learning Approach to Index-Free Sequence Enrichment). Applied to the task of separating host from microbial reads, AMAISE achieves over 98% accuracy. Applied prior to metagenomic classification, AMAISE results in a 14-18% decrease in memory usage compared to using metagenomic classification alone. Our results show that a reference-independent machine learning approach to host depletion allows for accurate and efficient sequence detection.}, } @article {pmid35680942, year = {2022}, author = {Hui, Y and Vestergaard, G and Deng, L and Kot, WP and Thymann, T and Brunse, A and Nielsen, DS}, title = {Donor-dependent fecal microbiota transplantation efficacy against necrotizing enterocolitis in preterm pigs.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {48}, pmid = {35680942}, issn = {2055-5008}, mesh = {Animals ; *Enterocolitis, Necrotizing/prevention & control/veterinary ; *Fecal Microbiota Transplantation ; Follow-Up Studies ; Humans ; Infant, Newborn ; Infant, Premature ; Phylogeny ; Swine ; }, abstract = {The development of necrotizing enterocolitis (NEC), a life-threatening inflammatory bowel disease affecting preterm infants, is connected with gut microbiota dysbiosis. Using preterm piglets as a model for preterm infants we recently showed that fecal microbiota transplantation (FMT) from healthy suckling piglet donors to newborn preterm piglets decreased the NEC risk. However, in a follow-up study using donor stool from piglets recruited from another farm, this finding could not be replicated. This allowed us to study donor-recipient microbiota dynamics in a controlled model system with a clear difference in NEC phenotype. Preterm piglets (n = 38) were randomly allocated to receive control saline (CON), or rectal FMT using either the ineffective (FMT1) or the effective donor stool (FMT2). All animals were followed for four days before necropsy and gut pathological evaluation. Donor and recipient colonic gut microbiota (GM) were analyzed by 16 S rRNA gene amplicon sequencing and shotgun metagenomics. As expected, only FMT2 recipients were protected against NEC. Both FMT groups had shifted GM composition relative to CON, but FMT2 recipients had a higher lactobacilli relative abundance compared to FMT1. Limosilactobacillus reuteri and Lactobacillus crispatus strains of FMT recipients showed high phylogenetic similarity with their respective donors, indicating engraftment. Moreover, the FMT2 group had a higher lactobacilli replication rate and harbored specific glycosaminoglycan-degrading Bacteroides. In conclusion, subtle species-level donor differences translate to major changes in engraftment dynamics and the ability to prevent NEC. This could have implications for proper donor selection in future FMT trials for NEC prevention.}, } @article {pmid35680904, year = {2022}, author = {Bruce, SA and Aytur, SA and Andam, CP and Bucci, JP}, title = {Metagenomics to characterize sediment microbial biodiversity associated with fishing exposure within the Stellwagen Bank National Marine Sanctuary.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9499}, pmid = {35680904}, issn = {2045-2322}, mesh = {Biodiversity ; *Biological Products ; Ecosystem ; Geologic Sediments ; Hunting ; Metagenomics ; *Microbiota/genetics ; }, abstract = {Microbes in marine sediments constitute a large percentage of the global marine ecosystem and function to maintain a healthy food web. In continental shelf habitats such as the Gulf of Maine (GoM), relatively little is known of the microbial community abundance, biodiversity, and natural product potential. This report is the first to provide a time-series assessment (2017-2020) of the sediment microbial structure in areas open and closed to fishing within the Stellwagen Bank National Marine Sanctuary (SBNMS). A whole metagenome sequencing (WMS) approach was used to characterize the sediment microbial community. Taxonomic abundance was calculated across seven geographic sites with 14 individual sediment samples collected during the summer and fall seasons. Bioinformatics analyses identified more than 5900 different species across multiple years. Non-metric multidimensional scaling methods and generalized linear models demonstrated that species richness was inversely associated with fishing exposure levels and varied by year. Additionally, the discovery of 12 unique biosynthetic gene clusters (BGCs) collected across sites confirmed the potential for medically relevant natural product discovery in the SBNMS. This study provides a practical assessment of how fishing exposure and temporal trends may affect microbial community structure in a coastal marine sanctuary.}, } @article {pmid35680554, year = {2023}, author = {Kuhl, LP and Marostica, PJC and Macedo, AJ and Kuhl, G and Siebert, M and Manica, D and Sekine, L and Schweiger, C}, title = {High microbiome variability in pediatric tracheostomy cannulas in patients with similar clinical characteristics.}, journal = {Brazilian journal of otorhinolaryngology}, volume = {89}, number = {2}, pages = {254-263}, pmid = {35680554}, issn = {1808-8686}, mesh = {RNA, Ribosomal, 16S/genetics ; *Tracheostomy ; Cannula ; *Microbiota/genetics ; Brazil ; }, abstract = {OBJECTIVES: To evaluate the bacterial microbiome found in tracheostomy cannulas of a group of children diagnosed with glossoptosis secondary to Robin Sequence (RS), and its clinical implications.

METHODS: Pediatric patients were enrolled in the study at the time of the cannula change in the hospital. During this procedure, the removed cannula was collected and stored for amplicon sequencing of 16s rRNA. DNA extraction was performed using DNeasy PowerBiofilm Kit (QIAGEN® ‒ Cat nº 24000-50) while sequencing was performed with the S5 (Ion S5™ System, Thermo Fisher Scientific), following Brazilian Microbiome Project (BMP) protocol.

RESULTS: All 12 patients included in the study were using tracheostomy uncuffed cannulas of the same brand, had tracheostomy performed for over 1-year and had used the removed cannula for approximately 3-months. Most abundant genera found were Aggregatibacter, Pseudomonas, Haemophilus, Neisseria, Staphylococcus, Fusobacterium, Moraxella, Streptococcus, Alloiococcus, and Capnocytophaga. Individual microbiome of each individual was highly variable, not correlating to any particular clinical characteristic.

CONCLUSION: The microbiome of tracheostomy cannulas is highly variable, even among patients with similar clinical characteristics, making it challenging to determine a standard for normality.}, } @article {pmid35680095, year = {2022}, author = {Rehner, J and Schmartz, GP and Groeger, L and Dastbaz, J and Ludwig, N and Hannig, M and Rupf, S and Seitz, B and Flockerzi, E and Berger, T and Reichert, MC and Krawczyk, M and Meese, E and Herr, C and Bals, R and Becker, SL and Keller, A and Müller, R and , }, title = {Systematic Cross-biospecimen Evaluation of DNA Extraction Kits for Long- and Short-read Multi-metagenomic Sequencing Studies.}, journal = {Genomics, proteomics & bioinformatics}, volume = {20}, number = {2}, pages = {405-417}, pmid = {35680095}, issn = {2210-3244}, mesh = {Humans ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Feces ; High-Throughput Nucleotide Sequencing/methods ; DNA/genetics ; DNA, Bacterial/genetics ; }, abstract = {High-quality DNA extraction is a crucial step in metagenomic studies. Bias by different isolation kits impairs the comparison across datasets. A trending topic is, however, the analysis of multiple metagenomes from the same patients to draw a holistic picture of microbiota associated with diseases. We thus collected bile, stool, saliva, plaque, sputum, and conjunctival swab samples and performed DNA extraction with three commercial kits. For each combination of the specimen type and DNA extraction kit, 20-gigabase (Gb) metagenomic data were generated using short-read sequencing. While profiles of the specimen types showed close proximity to each other, we observed notable differences in the alpha diversity and composition of the microbiota depending on the DNA extraction kits. No kit outperformed all selected kits on every specimen. We reached consistently good results using the Qiagen QiAamp DNA Microbiome Kit. Depending on the specimen, our data indicate that over 10 Gb of sequencing data are required to achieve sufficient resolution, but DNA-based identification is superior to identification by mass spectrometry. Finally, long-read nanopore sequencing confirmed the results (correlation coefficient > 0.98). Our results thus suggest using a strategy with only one kit for studies aiming for a direct comparison of multiple microbiotas from the same patients.}, } @article {pmid35679949, year = {2022}, author = {Ghiboub, M and Penny, S and Verburgt, CM and Boneh, RS and Wine, E and Cohen, A and Dunn, KA and Pinto, DM and Benninga, MA and de Jonge, WJ and Levine, A and Van Limbergen, JE}, title = {Metabolome Changes With Diet-Induced Remission in Pediatric Crohn's Disease.}, journal = {Gastroenterology}, volume = {163}, number = {4}, pages = {922-936.e15}, doi = {10.1053/j.gastro.2022.05.050}, pmid = {35679949}, issn = {1528-0012}, mesh = {Arginine ; Ceramides ; Child ; *Crohn Disease/diagnosis/metabolism/therapy ; Diet ; Humans ; Kynurenine/metabolism ; Metabolome ; Prospective Studies ; Purines ; Pyrimidines ; Remission Induction ; Sphingolipids ; Succinates ; Sulfonamides ; }, abstract = {BACKGROUND & AIMS: The Crohn's disease (CD) exclusion diet (CDED) plus partial enteral nutrition (PEN) and exclusive enteral nutrition (EEN) both induce remission in pediatric CD. CDED+PEN is better tolerated and able to sustain remission. We characterized the changes in fecal metabolites induced by CDED+PEN and EEN and their relationship with remission.

METHODS: A total of 216 fecal metabolites were measured in 80 fecal samples at week (W) 0, W6, and W12, of children with mild to moderate CD in a prospective randomized trial comparing CDED+PEN vs EEN. The metabolites were measured using liquid chromatography coupled to mass spectrometry. Metagenome Kyoto Encyclopedia of Genes and Genomes Orthology analysis was performed to investigate the differential functional gene abundance involved in specific metabolic pathways. Data were analyzed according to clinical outcome of remission (W6_rem), no remission (W6_nr), sustained remission (W12_sr), and nonsustained (W12_nsr) remission.

RESULTS: A decrease in kynurenine and succinate synthesis and an increase in N-α-acetyl-arginine characterized CDED+PEN W6_rem, whereas changes in lipid metabolism characterized EEN W6_rem, especially reflected by lower levels in ceramides. In contrast, fecal metabolites in EEN W6_nr were comparable to baseline/W0 samples. CDED+PEN W6_rem children maintained metabolome changes through W12. In contrast, W12_nsr children in the EEN group, who resumed a free diet after week 6, did not. The metabolome of CDED+PEN differed from EEN in the purine, pyrimidine, and sphingolipid pathways. A significant differential abundance in several genes involved in these pathways was detected.

CONCLUSION: CDED+PEN- and EEN-induced remission are associated with significant changes in inflammatory bowel disease-associated metabolites such as kynurenine, ceramides, amino acids, and others. Sustained remission with CDED+PEN, but not EEN, was associated with persistent changes in metabolites.

CLINICALTRIALS: gov, Number NCT01728870.}, } @article {pmid35679948, year = {2022}, author = {Zhao, L and Shi, Y and Lau, HC and Liu, W and Luo, G and Wang, G and Liu, C and Pan, Y and Zhou, Q and Ding, Y and Sung, JJ and Yu, J}, title = {Uncovering 1058 Novel Human Enteric DNA Viruses Through Deep Long-Read Third-Generation Sequencing and Their Clinical Impact.}, journal = {Gastroenterology}, volume = {163}, number = {3}, pages = {699-711}, doi = {10.1053/j.gastro.2022.05.048}, pmid = {35679948}, issn = {1528-0012}, mesh = {Colorectal Neoplasms/genetics ; DNA Viruses/genetics ; DNA, Viral/genetics ; *High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics/methods ; Phylogeny ; *Viruses/genetics ; }, abstract = {BACKGROUND & AIMS: Lack of viral reference genomes poses a challenge to virome study. We investigated human gut virome and its clinical implication by ultra-deep metagenomic sequencing.

METHODS: We extracted sufficient viral DNA from human feces for ultra-deep PacBio sequencing (>10 μg) and Illumina sequencing (>1 μg). Upon de novo assembly and 6 stages of strict filtering, viral genomes were generated and validated in 3 cohorts of 2819 published fecal metagenomes. Diagnostic performance of assembled viruses for colorectal cancer were tested in a training cohort and 2 independent validation cohorts. Virus mapping ratio, evolutionary history, and virus status (lytic or temperate) were also examined.

RESULTS: The mean amount of extracted viral DNA increased by 14-fold compared with previous protocols. We obtained PacBio long reads and Illumina short reads with 290-fold higher depth than previous studies. We assembled and validated 1178 contigs as complete viral genomes, of which 1058 were newly identified. Thirteen viral genomes (398-839 kb) that are longer than the largest bacteriophage found in humans (393 kb) were discovered. Phylogenetic tree was constructed based on Hidden Markov Models alignment scores of 4 conserved viral proteins. Incorporating our assembled genomes into the National Center for Biotechnology Information database improved the mapping ratio of published metagenomes ≤18 times. Lytic viruses (75.9% ± 12.2% of total) were predominantly present in our sample. A biomarker panel of 14 novel viruses could discriminate patients with colorectal cancer from controls with an area under the receiver operating characteristics curve of 0.87 in the training cohort, which was validated with areas under the receiver operating characteristics curve of 0.85 and 0.73 in 2 independent cohorts.

CONCLUSIONS: We uncovered 1058 novel human gut viruses. These findings can contribute to clinical diagnosis, current viral reference genome, and future virome investigation.}, } @article {pmid35679302, year = {2022}, author = {Jin, Y and Aguilar-Gómez, D and Y C Brandt, D and Square, TA and Li, J and Liu, Z and Wang, T and Sudmant, PH and Miller, CT and Nielsen, R}, title = {Population Genomics of Variegated Toad-Headed Lizard Phrynocephalus versicolor and Its Adaptation to the Colorful Sand of the Gobi Desert.}, journal = {Genome biology and evolution}, volume = {14}, number = {7}, pages = {}, pmid = {35679302}, issn = {1759-6653}, support = {R35 GM142916/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; *Genome, Mitochondrial ; Humans ; *Lizards/genetics ; Metagenomics ; RNA, Transfer/genetics ; Sand ; }, abstract = {The variegated toad-headed agama, Phrynocephalus versicolor, lives in the arid landscape of the Chinese Gobi Desert. We analyzed populations from three different locations which vary in substrate color and altitude: Heishankou (HSK), Guazhou County (GZ), and Ejin Banner (EJN). The substrate color is either light-yellow (GZ-y), yellow (EJN-y), or black (HSK-b); the corresponding lizard population colors largely match their substrate in the degree of melanism. We assembled the P. versicolor genome and sequenced over 90 individuals from the three different populations. Genetic divergence between populations corresponds to their geographic distribution. We inferred the genetic relationships among these populations and used selection scans and differential expression to identify genes that show signatures of selection. Slc2a11 and akap12, among other genes, are highly differentiated and may be responsible for pigment adaptation to substrate color in P. versicolor.}, } @article {pmid35678967, year = {2022}, author = {Malla, MA and Dubey, A and Kumar, A and Vennapu, DR and Upadhyay, N and Pradhan, D and Pradhan, RC and Yadav, S}, title = {Process optimization of cypermethrin biodegradation by regression analysis and parametric modeling along with biochemical degradation pathway.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {51}, pages = {77418-77427}, pmid = {35678967}, issn = {1614-7499}, support = {000//University Grants Commission/ ; }, mesh = {Biodegradation, Environmental ; Carbon Dioxide ; *Pyrethrins/metabolism ; Regression Analysis ; *Pesticides ; Phenols ; }, abstract = {Pyrethroid pesticides are of great environmental and health concern with regard to neurotoxicity and ubiquitous occurrence. Here, we reported a new bacterial strain identified as Bacillus cereus AKAD 3-1 that degraded 88.1% of 50 mg/l of cypermethrin in an aqueous medium. The biodegradation of cypermethrin was optimized by CCD (central composite design) and validated by ANN-GA (artificial neural network-genetic algorithm). Both the approaches proved to possess good performance in modeling and optimizing the growth conditions. Results indicated that the process variables have a significant (< 0.0001) impact on cypermethrin biodegradation. Moreover, the predicted CCD model had a "lack of fit p-value" of "0.9975." The optimum CCD and ANN model had an R[2] value of 0.9703 and 0.9907, indicating that the two models' experimental and predicted values are closely fitted. The isolate successfully converted cypermethrin to CO2 and phenol without producing any toxic metabolite. Finally, a degradation pathway was proposed with the intermediate compounds identified by GC-MS. The present study highlights an important potential application of strain AKAD 3-1 for the in situ bioremediation of cypermethrin-contaminated environments.}, } @article {pmid35678705, year = {2022}, author = {Sun, J and Prabhu, A and Aroney, STN and Rinke, C}, title = {Insights into plastic biodegradation: community composition and functional capabilities of the superworm (Zophobas morio) microbiome in styrofoam feeding trials.}, journal = {Microbial genomics}, volume = {8}, number = {6}, pages = {}, pmid = {35678705}, issn = {2057-5858}, mesh = {Animals ; *Coleoptera/metabolism ; Larva/metabolism ; *Microbiota/genetics ; Plastics/metabolism ; Polystyrenes/metabolism ; }, abstract = {Plastics are inexpensive and widely used organic polymers, but their high durability hinders biodegradation. Polystyrene, including extruded polystyrene (also known as styrofoam), is among the most commonly produced plastics worldwide and is recalcitrant to microbial degradation. In this study, we assessed changes in the gut microbiome of superworms (Zophobas morio) reared on bran, polystyrene or under starvation conditions over a 3 weeks period. Superworms on all diets were able to complete their life cycle to pupae and imago, although superworms reared on polystyrene had minimal weight gains, resulting in lower pupation rates compared to bran reared worms. The change in microbial gut communities from baseline differed considerably between diet groups, with polystyrene and starvation groups characterized by a loss of microbial diversity and the presence of opportunistic pathogens. Inferred microbial functions enriched in the polystyrene group included transposon movements, membrane restructuring and adaptations to oxidative stress. We detected several encoded enzymes with reported polystyrene and styrene degradation abilities, supporting previous reports of polystyrene-degrading bacteria in the superworm gut. By recovering metagenome-assembled genomes (MAGs) we linked phylogeny and functions and identified genera including Pseudomonas, Rhodococcus and Corynebacterium that possess genes associated with polystyrene degradation. In conclusion, our results provide the first metagenomic insights into the metabolic pathways used by the gut microbiome of superworms to degrade polystyrene. Our results also confirm that superworms can survive on polystyrene feed, but this diet has considerable negative impacts on host gut microbiome diversity and health.}, } @article {pmid35678141, year = {2022}, author = {Que, T and Li, J and He, Y and Chen, P and Lin, W and He, M and Yu, L and Wu, A and Tan, L and Li, Y and Hu, Y and Tong, Y}, title = {Human parainfluenza 3 and respiratory syncytial viruses detected in pangolins.}, journal = {Emerging microbes & infections}, volume = {11}, number = {1}, pages = {1657-1663}, pmid = {35678141}, issn = {2222-1751}, mesh = {Animals ; *COVID-19 ; Humans ; Pangolins ; Parainfluenza Virus 3, Human/genetics ; *Paramyxoviridae Infections ; Phylogeny ; *Respiratory Syncytial Virus, Human/genetics ; SARS-CoV-2 ; }, abstract = {Pangolins have gained increasing global attention owing to their public health significance as potential zoonotic hosts since the identification of SARS-CoV-2-related viruses in them. Moreover, these animals could carry other respiratory viruses. In this study, we investigated the virome composition of 16 pangolins that died in 2018 with symptoms of pneumonia using metagenomic approaches. A total of eight whole virus sequences belonging to the Paramyxoviridae or Pneumoviridae families were identified, including one human parainfluenza virus 3, one human respiratory syncytial virus A, and six human respiratory syncytial virus B. All of these sequences showed more than 99% nucleotide identity with the virus isolated from humans at the whole-genome level and clustered with human viruses in the phylogenetic tree. Our findings provide evidence that pangolins are susceptible to HPIV3 and HRSV infection. Therefore, public awareness of the threat of pangolin-borne pathogens is essential to stop their human consumption and to prevent zoonotic viral transmission.}, } @article {pmid35677909, year = {2022}, author = {Trivedi, CB and Keuschnig, C and Larose, C and Rissi, DV and Mourot, R and Bradley, JA and Winkel, M and Benning, LG}, title = {DNA/RNA Preservation in Glacial Snow and Ice Samples.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {894893}, pmid = {35677909}, issn = {1664-302X}, support = {856416/ERC_/European Research Council/International ; }, abstract = {The preservation of nucleic acids for high-throughput sequencing is an ongoing challenge for field scientists. In particular, samples that are low biomass, or that have to be collected and preserved in logistically challenging environments (such as remote sites or during long sampling campaigns) can pose exceptional difficulties. With this work, we compare and assess the effectiveness of three preservation methods for DNA and RNA extracted from microbial communities of glacial snow and ice samples. Snow and ice samples were melted and filtered upon collection in Iceland, and filters were preserved using: (i) liquid nitrogen flash freezing, (ii) storage in RNAlater, or (iii) storage in Zymo DNA/RNA Shield. Comparative statistics covering nucleic acid recovery, sequencing library preparation, genome assembly, and taxonomic diversity were used to determine best practices for the preservation of DNA and RNA samples from these environments. Our results reveal that microbial community composition based on DNA was comparable at the class level across preservation types. Based on extracted RNA, the taxonomic composition of the active community was primarily driven by the filtered sample volume (i.e., biomass content). In low biomass samples (where <200 ml of sample volume was filtered) the taxonomic and functional signatures trend toward the composition of the control samples, while in samples where a larger volume (more biomass) was filtered our data showed comparable results independent of preservation type. Based on all comparisons our data suggests that flash freezing of filters containing low biomass is the preferred method for preserving DNA and RNA (notwithstanding the difficulties of accessing liquid nitrogen in remote glacial field sites). Generally, RNAlater and Zymo DNA/RNA Shield solutions work comparably well, especially for DNA from high biomass samples, but Zymo DNA/RNA Shield is favored due to its higher yield of preserved RNA. Biomass quantity from snow and ice samples appears to be the most important factor in regards to the collection and preservation of samples from glacial environments.}, } @article {pmid35677897, year = {2022}, author = {Altayb, HN and Chaieb, K and Baothman, O and Alzahrani, FA and Zamzami, MA and Almugadam, BS}, title = {Study of oral microbiota diversity among groups of families originally from different countries.}, journal = {Saudi journal of biological sciences}, volume = {29}, number = {7}, pages = {103317}, pmid = {35677897}, issn = {1319-562X}, abstract = {The diversity of oral microbiota is affected by diets habits, gender, age, ethnic group, and environment. The acquisition of oral microbiota and the role of family on oral microbiota development is poorly understood. This study aims to characterize and compare the oral bacterial microbiota among families using 16S rRNA gene sequencing. This work was conducted in Jeddah city from 2020 to 2021, in which four families composed of 20 members of different ethnicity and lifestyle were recruited. After the collection of saliva samples, the DNA was extracted and processed for 16S rRNA gene metagenomics sequencing. Among 378 OUTs generated, 39 (10.3%) were unique in group A, 13 (3.4%) unique in group B, and 11 (2.9%) were unique in groups C and D. We observed a significant variation at the level of top abundance phylum (14), families (23), genera (24), and species (22) of bacteria among family members. Within family groups, different bacterial species were reported to be more dominant among certain family members than the other; Prevotella melaninogenica, Prevotella histicola and Haemophilus parainfluenzae, Veillonella atypica, Porphyromonas pasteri and Haemophilus pittmaniae were more dominant in parents of some families than the other family member. In summary, this study highlights the precise and perceptible association of oral microbial between family members. Our findings documented the clustering of certain bacterial species in family groups, supporting the role of community in the development of oral microbiota.}, } @article {pmid35677528, year = {2022}, author = {Xu, H and Hu, X and Wang, W and Chen, H and Yu, F and Zhang, X and Zheng, W and Han, K}, title = {Clinical Application and Evaluation of Metagenomic Next-Generation Sequencing in Pulmonary Infection with Pleural Effusion.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {2813-2824}, pmid = {35677528}, issn = {1178-6973}, abstract = {PURPOSE: Metagenomic next-generation sequencing (mNGS) is a novel technique of pathogens detection that plays an increasingly important role in clinical practice. In this study, we explored the application value of mNGS in pulmonary infection combined with pleural effusion applied to samples of pleural effusion fluid.

PATIENTS AND METHODS: We reviewed 80 cases of pulmonary infection with pleural effusion between August 2020 and October 2021. Among them, 40 patients were placed in the mNGS group and underwent both culture and mNGS testing; the patients in the control group were only subjected to culture test. The effectiveness of mNGS was evaluated for microbial composition and diagnostic accuracy in every pleural effusion specimen type.

RESULTS: We found that the positive rate of mNGS was 70% (28/40). The comparison between mNGS and culture method resulted that the sensitivity was 100% (95% CI: 29.2-100%) and the specificity was 64.9% (95% CI: 47.5-79.8%). The positive predictive value of mNGS was 18.8% (95% CI, 13.0-26.3%), and the negative predictive value was 100%. The most commonly identified potential pathogens were bacteria, such as Streptococcus, Prevotella, Parvimonas, Porphyromonas and Gemella. The most detected fungal infection was Candida and Pneumocystis. A total of 11 patients were identified as mixed infection by mNGS. Treatment regimen adjustments were made according to mNGS results and the overall length of hospital stay in the mNGS group was shorter compared to that of the control group.

CONCLUSION: In this study, mNGS produced higher positive rates than the culture method in detecting pathogens in the pleural effusion specimens. The technology performed satisfactorily, providing more diagnostic evidence and reducing the length of hospital stay.}, } @article {pmid35677075, year = {2022}, author = {Lai, P and Nguyen, L and Okin, D and Drew, D and Battista, V and Jesudasen, S and Kuntz, T and Bhosle, A and Thompson, K and Reinicke, T and Lo, CH and Woo, J and Caraballo, A and Berra, L and Vieira, J and Huang, CY and Adhikari, UD and Kim, M and Sui, HY and Magicheva-Gupta, M and McIver, L and Goldberg, M and Kwon, D and Huttenhower, C and Chan, A}, title = {Metagenomic assessment of gut microbial communities and risk of severe COVID-19.}, journal = {Research square}, volume = {}, number = {}, pages = {}, pmid = {35677075}, support = {K01 DK120742/DK/NIDDK NIH HHS/United States ; K23 DK125838/DK/NIDDK NIH HHS/United States ; T32 HL116275/HL/NHLBI NIH HHS/United States ; UL1 TR002541/TR/NCATS NIH HHS/United States ; }, abstract = {The gut microbiome is a critical modulator of host immunity and is linked to the immune response to respiratory viral infections. However, few studies have gone beyond describing broad compositional alterations in severe COVID-19, defined as acute respiratory or other organ failure. We profiled 127 hospitalized patients with COVID-19 (n=79 with severe COVID-19 and 48 with moderate) who collectively provided 241 stool samples from April 2020 to May 2021 to identify links between COVID-19 severity and gut microbial taxa, their biochemical pathways, and stool metabolites. 48 species were associated with severe disease after accounting for antibiotic use, age, sex, and various comorbidities. These included significant in-hospital depletions of Fusicatenibacter saccharivorans and Roseburia hominis, each previously linked to post-acute COVID syndrome or "long COVID", suggesting these microbes may serve as early biomarkers for the eventual development of long COVID. A random forest classifier achieved excellent performance when tasked with predicting whether stool was obtained from patients with severe vs. moderate COVID-19. Dedicated network analyses demonstrated fragile microbial ecology in severe disease, characterized by fracturing of clusters and reduced negative selection. We also observed shifts in predicted stool metabolite pools, implicating perturbed bile acid metabolism in severe disease. Here, we show that the gut microbiome differentiates individuals with a more severe disease course after infection with COVID-19 and offer several tractable and biologically plausible mechanisms through which gut microbial communities may influence COVID-19 disease course. Further studies are needed to validate these observations to better leverage the gut microbiome as a potential biomarker for disease severity and as a target for therapeutic intervention.}, } @article {pmid35676509, year = {2022}, author = {Gharechahi, J and Sarikhan, S and Han, JL and Ding, XZ and Salekdeh, GH}, title = {Functional and phylogenetic analyses of camel rumen microbiota associated with different lignocellulosic substrates.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {46}, pmid = {35676509}, issn = {2055-5008}, mesh = {Animals ; Camelus/microbiology ; Lignin ; *Microbiota/genetics ; Phylogeny ; *Rumen/microbiology ; }, abstract = {Rumen microbiota facilitates nutrition through digestion of recalcitrant lignocellulosic substrates into energy-accessible nutrients and essential metabolites. Despite the high similarity in rumen microbiome structure, there might be distinct functional capabilities that enable different ruminant species to thrive on various lignocellulosic substrates as feed. Here, we applied genome-centric metagenomics to explore phylogenetic diversity, lignocellulose-degrading potential and fermentation metabolism of biofilm-forming microbiota colonizing 11 different plant substrates in the camel rumen. Diversity analysis revealed significant variations in the community of rumen microbiota colonizing different substrates in accordance with their varied physicochemical properties. Metagenome reconstruction recovered genome sequences of 590 bacterial isolates and one archaeal lineage belonging to 20 microbial phyla. A comparison to publicly available reference genomes and rumen metagenome-assembled genomes revealed that most isolates belonged to new species with no well-characterized representatives. We found that certain low abundant taxa, including members of Verrucomicrobiota, Planctomycetota and Fibrobacterota, possessed a disproportionately large number of carbohydrate active enzymes per Mb of genome, implying their high metabolic potential to contribute to the rumen function. In conclusion, we provided a detailed picture of the diversity and functional significance of rumen microbiota colonizing feeds of varying lignocellulose composition in the camel rumen. A detailed analysis of 591 metagenome-assembled genomes revealed a network of interconnected microbiota and highlighted the key roles of certain taxonomic clades in rumen function, including those with minimal genomes (e.g., Patescibacteria). The existence of a diverse array of gene clusters encoding for secondary metabolites unveiled the specific functions of these biomolecules in shaping community structure of rumen microbiota.}, } @article {pmid35676322, year = {2022}, author = {Kim, DD and Han, H and Yun, T and Song, MJ and Terada, A and Laureni, M and Yoon, S}, title = {Identification of nosZ-expressing microorganisms consuming trace N2O in microaerobic chemostat consortia dominated by an uncultured Burkholderiales.}, journal = {The ISME journal}, volume = {16}, number = {9}, pages = {2087-2098}, pmid = {35676322}, issn = {1751-7370}, support = {2020R1C1C1007970//National Research Foundation of Korea (NRF)/ ; 2021R1I1A1A01054770//National Research Foundation of Korea (NRF)/ ; 20H04362//MEXT | Japan Society for the Promotion of Science (JSPS)/ ; VI.Veni.192.252//Nederlandse Organisatie voor Wetenschappelijk Onderzoek (Netherlands Organisation for Scientific Research)/ ; }, mesh = {*Burkholderiales/genetics ; Denitrification ; Metagenome ; *Nitrous Oxide ; Oxidoreductases/genetics/metabolism ; Oxygen ; }, abstract = {Microorganisms possessing N2O reductases (NosZ) are the only known environmental sink of N2O. While oxygen inhibition of NosZ activity is widely known, environments where N2O reduction occurs are often not devoid of O2. However, little is known regarding N2O reduction in microoxic systems. Here, 1.6-L chemostat cultures inoculated with activated sludge samples were sustained for ca. 100 days with low concentration (<2 ppmv) and feed rate (<1.44 µmoles h[-1]) of N2O, and the resulting microbial consortia were analyzed via quantitative PCR (qPCR) and metagenomic/metatranscriptomic analyses. Unintended but quantified intrusion of O2 sustained dissolved oxygen concentration above 4 µM; however, complete N2O reduction of influent N2O persisted throughout incubation. Metagenomic investigations indicated that the microbiomes were dominated by an uncultured taxon affiliated to Burkholderiales, and, along with the qPCR results, suggested coexistence of clade I and II N2O reducers. Contrastingly, metatranscriptomic nosZ pools were dominated by the Dechloromonas-like nosZ subclade, suggesting the importance of the microorganisms possessing this nosZ subclade in reduction of trace N2O. Further, co-expression of nosZ and ccoNO/cydAB genes found in the metagenome-assembled genomes representing these putative N2O-reducers implies a survival strategy to maximize utilization of scarcely available electron acceptors in microoxic environmental niches.}, } @article {pmid35676296, year = {2022}, author = {Suarez, C and Sedlacek, CJ and Gustavsson, DJI and Eiler, A and Modin, O and Hermansson, M and Persson, F}, title = {Disturbance-based management of ecosystem services and disservices in partial nitritation-anammox biofilms.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {47}, pmid = {35676296}, issn = {2055-5008}, mesh = {Anaerobic Ammonia Oxidation ; Bacteria/genetics ; Biofilms ; Bioreactors/microbiology ; *Microbiota ; *Nitrites ; }, abstract = {The resistance and resilience provided by functional redundancy, a common feature of microbial communities, is not always advantageous. An example is nitrite oxidation in partial nitritation-anammox (PNA) reactors designed for nitrogen removal in wastewater treatment, where suppression of nitrite oxidizers like Nitrospira is sought. In these ecosystems, biofilms provide microhabitats with oxygen gradients, allowing the coexistence of aerobic and anaerobic bacteria. We designed a disturbance experiment where PNA biofilms, treating water from a high-rate activated sludge process, were constantly or intermittently exposed to anaerobic sidestream wastewater, which has been proposed to inhibit nitrite oxidizers. With increasing sidestream exposure we observed decreased abundance, alpha-diversity, functional versatility, and hence functional redundancy, among Nitrospira in the PNA biofilms, while the opposite patterns were observed for anammox bacteria within Brocadia. At the same time, species turnover was observed for aerobic ammonia-oxidizing Nitrosomonas populations. The different exposure regimens were associated with metagenomic assembled genomes of Nitrosomonas, Nitrospira, and Brocadia, encoding genes related to N-cycling, substrate usage, and osmotic stress response, possibly explaining the three different patterns by niche differentiation. These findings imply that disturbances can be used to manage the functional redundancy of biofilm microbiomes in a desirable direction, which should be considered when designing operational strategies for wastewater treatment.}, } @article {pmid35676264, year = {2022}, author = {Chen, L and Zhao, N and Cao, J and Liu, X and Xu, J and Ma, Y and Yu, Y and Zhang, X and Zhang, W and Guan, X and Yu, X and Liu, Z and Fan, Y and Wang, Y and Liang, F and Wang, D and Zhao, L and Song, M and Wang, J}, title = {Short- and long-read metagenomics expand individualized structural variations in gut microbiomes.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3175}, pmid = {35676264}, issn = {2041-1723}, mesh = {*Gastrointestinal Microbiome/genetics ; High-Throughput Nucleotide Sequencing ; Metabolome/genetics ; Metagenome ; Metagenomics ; *Nanopores ; }, abstract = {In-depth profiling of genetic variations in the gut microbiome is highly desired for understanding its functionality and impacts on host health and disease. Here, by harnessing the long read advantage provided by Oxford Nanopore Technology (ONT), we characterize fine-scale genetic variations of structural variations (SVs) in hundreds of gut microbiomes from healthy humans. ONT long reads dramatically improve the quality of metagenomic assemblies, enable reliable detection of a large, expanded set of structural variation types (notably including large insertions and inversions). We find SVs are highly distinct between individuals and stable within an individual, representing gut microbiome fingerprints that shape strain-level differentiations in function within species, complicating the associations to metabolites and host phenotypes such as blood glucose. In summary, our study strongly emphasizes that incorporating ONT reads into metagenomic analyses expands the detection scope of genetic variations, enables profiling strain-level variations in gut microbiome, and their intricate correlations with metabolome.}, } @article {pmid35676047, year = {2022}, author = {Kagemasa, S and Kuroda, K and Nakai, R and Li, YY and Kubota, K}, title = {Diversity of Candidatus Patescibacteria in Activated Sludge Revealed by a Size-‍Fractionation Approach.}, journal = {Microbes and environments}, volume = {37}, number = {2}, pages = {}, pmid = {35676047}, issn = {1347-4405}, mesh = {*Bacteria/genetics ; Metagenome ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; *Sewage/microbiology ; }, abstract = {Uncultivated members of Candidatus Patescibacteria are commonly found in activated sludge treating sewage and are widely distributed in wastewater treatment plants in different regions and countries. However, the phylogenetic diversity of Ca. Patescibacteria is difficult to examine because of their low relative abundance in the environment. Since Ca. Patescibacteria members have small cell sizes, we herein collected small microorganisms from activated sludge using a filtration-based size-fractionation approach (i.e., 0.45-0.22‍ ‍μm and 0.22-0.1‍ ‍μm fractions). Fractionated samples were characterized using 16S rRNA gene amplicon and shotgun metagenomic sequence ana-lyses. The amplicon ana-lysis revealed that the relative abundance of Ca. Patescibacteria increased to 73.5% and 52.5% in the 0.45-0.22‍ ‍μm and 0.22-0.1‍ ‍μm fraction samples, respectively, from 5.8% in the unfractionated sample. The members recovered from the two size-fractionated samples included Ca. Saccharimonadia, Ca. Gracilibacteria, Ca. Paceibacteria, Ca. Microgenomatia, class-level uncultured lineage ABY1, Ca. Berkelbacteria, WS6 (Ca. Dojkabacteria), and WWE3, with Ca. Saccharimonadia being predominant in both fraction samples. The number of operational taxonomic units belonging to Ca. Patescibacteria was approximately 6-fold higher in the size-fractionated samples than in the unfractionated sample. The shotgun metagenomic ana-lysis of the 0.45-0.22‍ ‍μm fractioned sample enabled the reconstruction of 24 high-quality patescibacterial bins. The bins obtained were classified into diverse clades at the family and genus levels, some of which were rarely detected in previous activated sludge studies. Collectively, the present results suggest that the overall diversity of Ca. Patescibacteria inhabiting activated sludge is higher than previously expected.}, } @article {pmid35675660, year = {2022}, author = {Talat, A and Usmani, A and Khan, AU}, title = {Detection of E. coli IncX1 Plasmid-Mediated mcr-5.1 Gene in an Indian Hospital Sewage Water Using Shotgun Metagenomic Sequencing: A First Report.}, journal = {Microbial drug resistance (Larchmont, N.Y.)}, volume = {28}, number = {7}, pages = {759-764}, doi = {10.1089/mdr.2021.0338}, pmid = {35675660}, issn = {1931-8448}, mesh = {Anti-Bacterial Agents/pharmacology ; *Colistin ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics ; *Escherichia coli Proteins/genetics ; Hospitals ; Humans ; India/epidemiology ; Metagenome/genetics ; *Metagenomics/methods ; Microbial Sensitivity Tests ; Plasmids/genetics ; Sewage/microbiology ; Transferases (Other Substituted Phosphate Groups) ; Water ; }, abstract = {Colistin is used against a multitude of multidrug-resistant and extremely drug-resistant Gram-negative bacterial infections. The emergence of colistin resistance is highly concerning as it may lead to the failure of this last-resort antibiotic. Since the identification of first mobile colistin resistance (mcr) genes, several variants of mcr genes have been reported, but still there are limited studies detecting mcr genes in hospital sewage water. The prevalence of mcr in the hospital environment is extremely hazardous putting health care workers, patients, and visitors at a higher risk of exposure. It may lead to a multidrug-resistant bacterial infection outbreak. In this study, we report mcr-5.1 gene in an Indian hospital sewage water using shotgun metagenomics, as a first report. The mcr-5.1 gene in the metagenome has been explored using RGI, ABRicate, NCBI database, CARD, and Resfinder. This mcr-5.1 gene harbored by Escherichia coli is a plasmid-mediated gene carried by an IncX1 plasmid pSGMCR103. The bioinformatics analysis revealed the genetic environment of mcr-5.1 gene, which consisted of mobile element protein, ChrB domain protein, putative major facilitator superfamily type transporter, and a hypothetical protein.}, } @article {pmid35675542, year = {2022}, author = {Peters, BA and Lin, J and Qi, Q and Usyk, M and Isasi, CR and Mossavar-Rahmani, Y and Derby, CA and Santoro, N and Perreira, KM and Daviglus, ML and Kominiarek, MA and Cai, J and Knight, R and Burk, RD and Kaplan, RC}, title = {Menopause Is Associated with an Altered Gut Microbiome and Estrobolome, with Implications for Adverse Cardiometabolic Risk in the Hispanic Community Health Study/Study of Latinos.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0027322}, pmid = {35675542}, issn = {2379-5077}, support = {R01 MD011389/MD/NIMHD NIH HHS/United States ; N01HC65236/HL/NHLBI NIH HHS/United States ; N01HC65234/HL/NHLBI NIH HHS/United States ; N01HC65237/HL/NHLBI NIH HHS/United States ; U01 HL146204/HL/NHLBI NIH HHS/United States ; K01 HL160146/HL/NHLBI NIH HHS/United States ; N01HC65235/HL/NHLBI NIH HHS/United States ; P30 DK111022/DK/NIDDK NIH HHS/United States ; N01HC65233/HL/NHLBI NIH HHS/United States ; }, mesh = {Female ; Male ; Humans ; *Gastrointestinal Microbiome ; Public Health ; Menopause ; Gonadal Steroid Hormones ; Hispanic or Latino ; *Cardiovascular Diseases ; }, abstract = {Menopause is a pivotal period during which loss of ovarian hormones increases cardiometabolic risk and may also influence the gut microbiome. However, the menopause-microbiome relationship has not been examined in a large study, and its implications for cardiometabolic disease are unknown. In the Hispanic Community Health Study/Study of Latinos, a population with high burden of cardiometabolic risk factors, shotgun metagenomic sequencing was performed on stool from 2,300 participants (295 premenopausal women, 1,027 postmenopausal women, and 978 men), and serum metabolomics was available on a subset. Postmenopausal women trended toward lower gut microbiome diversity and altered overall composition compared to premenopausal women, while differing less from men, in models adjusted for age and other demographic/behavioral covariates. Differentially abundant taxa for post- versus premenopausal women included Bacteroides sp. strain Ga6A1, Prevotella marshii, and Sutterella wadsworthensis (enriched in postmenopause) and Escherichia coli-Shigella spp., Oscillibacter sp. strain KLE1745, Akkermansia muciniphila, Clostridium lactatifermentans, Parabacteroides johnsonii, and Veillonella seminalis (depleted in postmenopause); these taxa similarly differed between men and women. Postmenopausal women had higher abundance of the microbial sulfate transport system and decreased abundance of microbial β-glucuronidase; these functions correlated with serum progestin metabolites, suggesting involvement of postmenopausal gut microbes in sex hormone retention. In postmenopausal women, menopause-related microbiome alterations were associated with adverse cardiometabolic profiles. In summary, in a large U.S. Hispanic/Latino population, menopause is associated with a gut microbiome more similar to that of men, perhaps related to the common condition of a low estrogen/progesterone state. Future work should examine similarity of results in other racial/ethnic groups. IMPORTANCE The menopausal transition, marked by declining ovarian hormones, is recognized as a pivotal period of cardiometabolic risk. Gut microbiota metabolically interact with sex hormones, but large population studies associating menopause with the gut microbiome are lacking. Our results from a large study of Hispanic/Latino women and men suggest that the postmenopausal gut microbiome in women is slightly more similar to the gut microbiome in men and that menopause depletes specific gut pathogens and decreases the hormone-related metabolic potential of the gut microbiome. At the same time, gut microbes may participate in sex hormone reactivation and retention in postmenopausal women. Menopause-related gut microbiome changes were associated with adverse cardiometabolic risk in postmenopausal women, indicating that the gut microbiome contributes to changes in cardiometabolic health during menopause.}, } @article {pmid35675435, year = {2022}, author = {Leung, H and Long, X and Ni, Y and Qian, L and Nychas, E and Siliceo, SL and Pohl, D and Hanhineva, K and Liu, Y and Xu, A and Nielsen, HB and Belda, E and Clément, K and Loomba, R and Li, H and Jia, W and Panagiotou, G}, title = {Risk assessment with gut microbiome and metabolite markers in NAFLD development.}, journal = {Science translational medicine}, volume = {14}, number = {648}, pages = {eabk0855}, pmid = {35675435}, issn = {1946-6242}, support = {U01 DK130190/DK/NIDDK NIH HHS/United States ; UL1 TR001442/TR/NCATS NIH HHS/United States ; P30 DK120515/DK/NIDDK NIH HHS/United States ; U01 AA029019/AA/NIAAA NIH HHS/United States ; R01 DK124318/DK/NIDDK NIH HHS/United States ; U01 DK061734/DK/NIDDK NIH HHS/United States ; P01 HL147835/HL/NHLBI NIH HHS/United States ; R01 DK121378/DK/NIDDK NIH HHS/United States ; R01 DK106419/DK/NIDDK NIH HHS/United States ; }, mesh = {Biomarkers ; *Gastrointestinal Microbiome ; Humans ; *Non-alcoholic Fatty Liver Disease/pathology ; Prospective Studies ; Risk Assessment ; }, abstract = {A growing body of evidence suggests interplay between the gut microbiota and the pathogenesis of nonalcoholic fatty liver disease (NAFLD). However, the role of the gut microbiome in early detection of NAFLD is unclear. Prospective studies are necessary for identifying reliable, microbiome markers for early NAFLD. We evaluated 2487 individuals in a community-based cohort who were followed up 4.6 years after initial clinical examination and biospecimen sampling. Metagenomic and metabolomic characterizations using stool and serum samples taken at baseline were performed for 90 participants who progressed to NAFLD and 90 controls who remained NAFLD free at the follow-up visit. Cases and controls were matched for gender, age, body mass index (BMI) at baseline and follow-up, and 4-year BMI change. Machine learning models integrating baseline microbial signatures (14 features) correctly classified participants (auROCs of 0.72 to 0.80) based on their NAFLD status and liver fat accumulation at the 4-year follow up, outperforming other prognostic clinical models (auROCs of 0.58 to 0.60). We confirmed the biological relevance of the microbiome features by testing their diagnostic ability in four external NAFLD case-control cohorts examined by biopsy or magnetic resonance spectroscopy, from Asia, Europe, and the United States. Our findings raise the possibility of using gut microbiota for early clinical warning of NAFLD development.}, } @article {pmid35675291, year = {2022}, author = {Dehau, T and Ducatelle, R and Van Immerseel, F and Goossens, E}, title = {Omics technologies in poultry health and productivity - part 1: current use in poultry research.}, journal = {Avian pathology : journal of the W.V.P.A}, volume = {51}, number = {5}, pages = {407-417}, doi = {10.1080/03079457.2022.2086447}, pmid = {35675291}, issn = {1465-3338}, mesh = {Animals ; Metagenomics/methods ; *Poultry ; *Poultry Diseases ; Proteomics/methods ; RNA, Ribosomal, 16S ; }, abstract = {In biology, molecular terms with the suffix "-omics" refer to disciplines aiming at the collective characterization of pools of molecules derived from different layers (DNA, RNA, proteins, metabolites) of living organisms using high-throughput technologies. Such omics analyses have been widely implemented in poultry research in recent years. This first part of a bipartite review on omics technologies in poultry health and productivity examines the use of multiple omics and multi-omics techniques in poultry research. More specific present and future applications of omics technologies, not only for the identification of specific diagnostic biomarkers, but also for potential future integration in the daily monitoring of poultry production, are discussed in part 2. Approaches based on omics technologies are particularly used in poultry research in the hunt for genetic markers of economically important phenotypical traits in the host, and in the identification of key bacterial species or functions in the intestinal microbiome. Integrative multi-omics analyses, however, are still scarce. Host physiology is investigated via genomics together with transcriptomics, proteomics and metabolomics techniques, to understand more accurately complex production traits such as disease resistance and fertility. The gut microbiota, as a key player in chicken productivity and health, is also a main subject of such studies, investigating the association between its composition (16S rRNA gene sequencing) or function (metagenomics, metatranscriptomics, metaproteomics, metabolomics) and host phenotypes. Applications of these technologies in the study of other host-associated microbiota and other host characteristics are still in their infancy.}, } @article {pmid35673925, year = {2022}, author = {Wu, F and Tian, J and She, Z and Liu, Y and Wan, W and Wen, C}, title = {[Clinical features of children with Cunninghamella spp. infection: a case report and literature review].}, journal = {Nan fang yi ke da xue xue bao = Journal of Southern Medical University}, volume = {42}, number = {5}, pages = {780-784}, pmid = {35673925}, issn = {1673-4254}, mesh = {Adolescent ; Amphotericin B/therapeutic use ; Antifungal Agents/therapeutic use ; Child ; *Cunninghamella ; Female ; Humans ; Male ; *Mucormycosis/diagnosis/drug therapy/etiology ; }, abstract = {We report a case of mucormycosis induced by Cunninghamella spp. infection in a ten-year-old girl with acute lymphoblastic leukemia, who developed fever and respiratory symptoms after chemotherapy and was diagnosed with invasive fungal disease. Peripheral blood DNA sequences were analyzed using metagenomic next-generation sequencing (mNGS), and by comparison with the Pathogens Metagenomics Database (PMDB), we identified Cunninghamella spp. with sequence number 514 as the pathogen. The patient was treated with amphotericin B combined with posaconazole and showed a favorable response. We searched Pubmed, Embase, CNKI, and Wanfang database for reports of cases of Cunninghamella spp. infection in children and retrieved 22 reported cases (including 12 males) with a median age of 13.5 (3-18) years. In these 22 cases, hematological malignancy was the most common underlying condition (19/22), and most of patients experienced an acute onset and rapid progression with respiratory symptoms (14/20) and fever (16/20) as the most common symptoms. CT imaging often showed unilateral lesions with varying imaging findings, including pulmonary nodules or masses, infiltrative changes, and pleural effusion. Definite diagnoses were established in 18 of the cases, and 4 had probable diagnoses; the lungs and skin were the most frequent organs compromised by the infection. A definite diagnosis of Cunninghamella spp. infection still relied on histopathological examination and fungal culture, but the molecular techniques including PCR and mNGS had shown potentials in the diagnosis. Almost all the cases received antifungal treatment after diagnosis (21/22), and 13 patients also underwent surgeries. Death occurred in 9 (42%) of the cases at a median of 19 (4-54) days after onset of the signs or symptoms. The patients receiving antifungal therapy combined with surgery had a high survival rate (9/13, 69%) than those with antifungal therapy alone (3/8, 37%). Invasive fungal disease is a common complication in immunoco-mpromised patients, but Cunninghamella spp. infection is rare and has a high mortality rate. In cases highly suspected of this disease, active diagnosis and early treatment are critical to improve the survival outcomes of the patients.}, } @article {pmid35672970, year = {2022}, author = {Buy, M and Digan, W and Chen, X and Husson, J and Ménager, M and Rieux-Laucat, F and Garcelon, N and , }, title = {A Multi-Omics Common Data Model for Primary Immunodeficiencies.}, journal = {Studies in health technology and informatics}, volume = {290}, number = {}, pages = {56-60}, doi = {10.3233/SHTI220031}, pmid = {35672970}, issn = {1879-8365}, mesh = {Humans ; *Metabolomics ; *Proteomics ; Rare Diseases ; Transcriptome ; }, abstract = {Primary Immunodeficiencies (PIDs) are associated with more than 400 rare monogenic diseases affecting various biological functions (e.g., development, regulation of the immune response) with a heterogeneous clinical expression (from no symptom to severe manifestations). To better understand PIDs, the ATRACTion project aims to perform a multi-omics analysis of PIDs cases versus a control group patients, including single-cell transcriptomics, epigenetics, proteomics, metabolomics, metagenomics and lipidomics. In this study, our goal is to develop a common data model integrating clinical and omics data, which can be used to obtain standardized information necessary for characterization of PIDs patients and for further systematic analysis. For that purpose, we extend the OMOP Common Data Model (CDM) and propose a multi-omics ATRACTion OMOP-CDM to integrate multi-omics data. This model, available for the community, is customizable for other types of rare diseases (https://framagit.org/imagine-plateforme-bdd/pub-rhu4-atraction).}, } @article {pmid35672890, year = {2022}, author = {Liu, BB and Tian, Q and Wang, P and Xu, SF and Tian, YL and Zhao, J and Yin, XB}, title = {Evaluating the diagnostic value of using metagenomic next-generation sequencing on bronchoalveolar lavage fluid and tissue in infectious pathogens located in the peripheral lung field.}, journal = {Annals of palliative medicine}, volume = {11}, number = {5}, pages = {1725-1735}, doi = {10.21037/apm-21-3474}, pmid = {35672890}, issn = {2224-5839}, mesh = {Bronchoalveolar Lavage Fluid/microbiology ; *Communicable Diseases ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Lung ; *Mycoses/diagnosis ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) exerts a vital part in accurately diagnosing pulmonary infection. However, the diagnostic value of different samples obtained by virtual bronchoscopic navigation (VBN) combined with mNGS for pathogen detection in infections located in the peripheral lung field (PLF) is still unclear.

METHODS: Patients infected from July 2018 to February of the following year were carefully analyzed and divided into two parts, namely, non-infectious disease group and the infectious disease group. Then bronchial expansion tests were performed for each subject, collected liquid specimens and tissue standards, and conducted regular mNGS and microbiological detection and analysis. The value of mNGS and culture in pathogen detection was compared, at the same time, the performance of tissue mNGS and bronchoalveolar lavage fluid (BALF) mNGS in the diagnosis process was compared. When discrete variables were processed, Pearson χ2 and Fisher's exact test could be used to perform categorical variables analysis. Continuous variables were analyzed and compared by Mann-Whitney U test.

RESULTS: After mNGS diagnosis, Acinetobacter baumannii, Pseudomonas aeruginosa and Rothia mucilaginosa were the bacterial species showing the highest abundances. In addition, mNGS achieved the sensitivities in the detection of pathogens in tissues and BALF of 72.9% and 81.4%, respectively, and it is higher than conventional culture. Bacterial diagnostic sensitivity was significantly different between BALF and tissue using mNGS (95.0% vs. 62.5%, P=0.03). The sensitivity and specificity of BALF in detecting fungal infections were not significantly different from those of mNGS. A consistency test showed that these two methods had some degree of consistency (k=0.673, P=0.000).

CONCLUSIONS: This study showed that the mNGS in BALF samples and the mNGS in tissue samples which could be used to test for pathogens in the lungs. The sensitivity will increase when mNGS is combined with culture. Also, mNGS of BALF and tissues had some degree of consistency to detect fungal infections, whereas mNGS of BALF had better sensitivity to detect bacterial infection than mNGS of tissues.}, } @article {pmid35672613, year = {2022}, author = {Berntson, L and Öman, A and Engstrand, L and Dicksved, J}, title = {A Pilot Study Investigating Faecal Microbiota After Two Dietary Interventions in Children with Juvenile Idiopathic Arthritis.}, journal = {Current microbiology}, volume = {79}, number = {7}, pages = {215}, pmid = {35672613}, issn = {1432-0991}, support = {R-657931//Reumatikerförbundet/ ; R-744331//Reumatikerförbundet/ ; R-848441//Reumatikerförbundet/ ; }, mesh = {Adolescent ; *Arthritis, Juvenile/therapy ; Child ; Feces/microbiology ; Humans ; *Microbiota/genetics ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {There is evidence for an impact of the gut microbiota on the immune system, which has consequences for inflammatory diseases. Exclusive enteral nutrition (EEN) and the specific carbohydrate diet (SCD) have been demonstrated as effective anti-inflammatory treatments for children with Crohn's disease. We have previously shown an anti-inflammatory effect from these nutritional treatments in children with juvenile idiopathic arthritis (JIA). The aim of this study was to investigate if improved clinical symptoms after EEN or SCD treatment in children with JIA could be linked to changes in faecal microbiota. We included sixteen patients with JIA (age 7-17 years), six for treatment with EEN and ten with SCD. EEN was given for 3-5 weeks and SCD for 4-5 weeks, with clinical and laboratory status assessed before and after treatment. Faecal samples were analysed for microbiota diversity and composition using 16S rRNA gene sequencing. Analyses of the faecal microbiota showed an effect on the overall composition with both interventions; the most striking result was a decreased relative abundance of the genus Faecalibacterium from EEN and of Bifidobacterium from SCD. The α-diversity decreased significantly from SCD (P = 0.04), but not from EEN (P = 0.22). Despite the study cohorts being small, both EEN and SCD were shown to impact the faecal microbiota. Future larger studies with a focus on metagenomics or metabolomics could possibly reveal a link and clarify the clinical effects of those nutritional regimens.}, } @article {pmid35672441, year = {2022}, author = {Amandito, R and Malik, A and Rohsiswatmo, R}, title = {Metagenomic profiles of the early life microbiome of Indonesian inpatient neonates and their influence on clinical characteristics.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9413}, pmid = {35672441}, issn = {2045-2322}, mesh = {Feces/microbiology ; Female ; Humans ; Indonesia ; Infant ; Infant, Newborn ; *Infant, Premature ; Inpatients ; Meconium/microbiology ; *Microbiota/genetics ; Pregnancy ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Determining the initial normal neonatal gut microbiome is challenging. The debate regarding the sterile fetal environment is still ongoing. Therefore, studying and comparing normal and dysbiotic microbiomes requires the elucidation of both the fetal and infant microbiomes. Factors influencing the normal microbiome also include regional and genetic factors specific to different countries. Determining the normal microbiome population in our center and their association with the clinical conditions of infants is helpful as a tool for both the prevention and treatment of related diseases during neonatal care. Here, we employed metagenomic sequencing to characterize meconium and the subsequent early-life gut microbiome of preterm neonates in Jakarta, Indonesia. Microbiome diversity and complexity was higher in the meconium and on day 4 than on day 7. At the genus level, the most abundant genus overall was unidentified Enterobacteriaceae, with meconium samples dominated by Ureaplasma, day 4 fecal samples dominated by Staphylococcus, and day 7 samples dominated by Clostridiales, while at the phylum level the most abundant was Proteobacteria and Firmicutes. Perinatal factors of PROM and mother's diet influenced the meconium microbiome, while day 4 and day 7 microbiome was associated with bacteremia and early administration of antibiotics. One of our sample sets was derived from triplets, and they had varying diversity despite being triplets. These data are valuable for understanding the formation of a healthy microbiome specific to neonates and devising a strategy to improve both the gut health and related clinical outcomes of the neonate.}, } @article {pmid35672431, year = {2022}, author = {Molina-Mora, JA and Cordero-Laurent, E and Calderón-Osorno, M and Chacón-Ramírez, E and Duarte-Martínez, F}, title = {Metagenomic pipeline for identifying co-infections among distinct SARS-CoV-2 variants of concern: study cases from Alpha to Omicron.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9377}, pmid = {35672431}, issn = {2045-2322}, mesh = {*COVID-19/epidemiology ; *Coinfection/epidemiology/genetics ; Humans ; Metagenome ; Mutation ; Pandemics ; SARS-CoV-2/genetics ; }, abstract = {Concomitant infection or co-infection with distinct SARS-CoV-2 genotypes has been reported as part of the epidemiological surveillance of the COVID-19 pandemic. In the context of the spread of more transmissible variants during 2021, co-infections are not only important due to the possible changes in the clinical outcome, but also the chance to generate new genotypes by recombination. However, a few approaches have developed bioinformatic pipelines to identify co-infections. Here we present a metagenomic pipeline based on the inference of multiple fragments similar to amplicon sequence variant (ASV-like) from sequencing data and a custom SARS-CoV-2 database to identify the concomitant presence of divergent SARS-CoV-2 genomes, i.e., variants of concern (VOCs). This approach was compared to another strategy based on whole-genome (metagenome) assembly. Using single or pairs of sequencing data of COVID-19 cases with distinct SARS-CoV-2 VOCs, each approach was used to predict the VOC classes (Alpha, Beta, Gamma, Delta, Omicron or non-VOC and their combinations). The performance of each pipeline was assessed using the ground-truth or expected VOC classes. Subsequently, the ASV-like pipeline was used to analyze 1021 cases of COVID-19 from Costa Rica to investigate the possible occurrence of co-infections. After the implementation of the two approaches, an accuracy of 96.2% was revealed for the ASV-like inference approach, which contrasts with the misclassification found (accuracy 46.2%) for the whole-genome assembly strategy. The custom SARS-CoV-2 database used for the ASV-like analysis can be updated according to the appearance of new VOCs to track co-infections with eventual new genotypes. In addition, the application of the ASV-like approach to all the 1021 sequenced samples from Costa Rica in the period October 12th-December 21th 2021 found that none corresponded to co-infections with VOCs. In conclusion, we developed a metagenomic pipeline based on ASV-like inference for the identification of co-infection with distinct SARS-CoV-2 VOCs, in which an outstanding accuracy was achieved. Due to the epidemiological, clinical, and molecular relevance of the concomitant infection with distinct genotypes, this work represents another piece in the process of the surveillance of the COVID-19 pandemic in Costa Rica and worldwide.}, } @article {pmid35672407, year = {2022}, author = {Auchtung, TA and Stewart, CJ and Smith, DP and Triplett, EW and Agardh, D and Hagopian, WA and Ziegler, AG and Rewers, MJ and She, JX and Toppari, J and Lernmark, Å and Akolkar, B and Krischer, JP and Vehik, K and Auchtung, JM and Ajami, NJ and Petrosino, JF}, title = {Temporal changes in gastrointestinal fungi and the risk of autoimmunity during early childhood: the TEDDY study.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3151}, pmid = {35672407}, issn = {2041-1723}, support = {U01 DK063821/DK/NIDDK NIH HHS/United States ; UC4 DK063863/DK/NIDDK NIH HHS/United States ; UC4 DK112243/DK/NIDDK NIH HHS/United States ; UC4 DK117483/DK/NIDDK NIH HHS/United States ; U01 DK124166/DK/NIDDK NIH HHS/United States ; U01 DK063863/DK/NIDDK NIH HHS/United States ; UL1 TR000064/TR/NCATS NIH HHS/United States ; UC4 DK106955/DK/NIDDK NIH HHS/United States ; UL1 TR002535/TR/NCATS NIH HHS/United States ; UC4 DK100238/DK/NIDDK NIH HHS/United States ; HHSN267200700014C/LM/NLM NIH HHS/United States ; P30 ES030285/ES/NIEHS NIH HHS/United States ; U01 DK128847/DK/NIDDK NIH HHS/United States ; }, mesh = {Adult ; Autoimmunity ; Bacteria ; Candida ; Child ; Child, Preschool ; *Diabetes Mellitus, Type 1 ; Fungi ; Gastrointestinal Tract/microbiology ; Humans ; *Probiotics ; }, abstract = {Fungal infections are a major health problem that often begin in the gastrointestinal tract. Gut microbe interactions in early childhood are critical for proper immune responses, yet there is little known about the development of the fungal population from infancy into childhood. Here, as part of the TEDDY (The Environmental Determinants of Diabetes in the Young) study, we examine stool samples of 888 children from 3 to 48 months and find considerable differences between fungi and bacteria. The metagenomic relative abundance of fungi was extremely low but increased while weaning from milk and formula. Overall fungal diversity remained constant over time, in contrast with the increase in bacterial diversity. Fungal profiles had high temporal variation, but there was less variation from month-to-month in an individual than among different children of the same age. Fungal composition varied with geography, diet, and the use of probiotics. Multiple Candida spp. were at higher relative abundance in children than adults, while Malassezia and certain food-associated fungi were lower in children. There were only subtle fungal differences associated with the subset of children that developed islet autoimmunity or type 1 diabetes. Having proper fungal exposures may be crucial for children to establish appropriate responses to fungi and limit the risk of infection: the data here suggests those gastrointestinal exposures are limited and variable.}, } @article {pmid35671624, year = {2022}, author = {Zenga, J and Atkinson, S and Yen, T and Massey, B and Stadler, M and Bruening, J and Peppard, W and Reuben, M and Hayward, M and Mesich, B and Buchan, B and Ledeboer, N and Sanchez, JL and Fraser, R and Lin, CW and Holtz, ML and Awan, M and Wong, SJ and Puram, SV and Salzman, N}, title = {A phase 2 trial of a topical antiseptic bundle in head and neck cancer surgery: Effects on surgical site infection and the oral microbiome.}, journal = {EBioMedicine}, volume = {81}, number = {}, pages = {104099}, pmid = {35671624}, issn = {2352-3964}, support = {UG1 CA189823/CA/NCI NIH HHS/United States ; UL1 TR001436/TR/NCATS NIH HHS/United States ; }, mesh = {*Anti-Infective Agents, Local/therapeutic use ; *Head and Neck Neoplasms/surgery ; Humans ; *Microbiota ; Preoperative Care ; Surgical Wound Infection/chemically induced/prevention & control ; }, abstract = {BACKGROUND: Head and neck cancer (HNC) surgery remains an important component of management but is associated with a high rate of surgical site infection (SSI). We aimed to assess the safety and efficacy of a topical mucosal antiseptic bundle in preventing SSI and evaluate microbial predictors of infection through a genomic sequencing approach.

METHODS: This study was an open-label, single-arm, single-center, phase 2 trial of a topical mucosal antiseptic bundle in patients with HNC undergoing aerodigestive tract resection and reconstruction. Patients underwent topical preparation of the oral mucosa with povidone-iodine (PI) and chlorhexidine gluconate (CHG) pre- and intra-operatively followed by oral tetracycline ointment every 6 hours for 2 days post-operatively. The primary outcome was change in bacterial bioburden at the oral surgical site. Secondary outcomes included safety, SSI, and microbial predictors of infection.

FINDINGS: Of 27 patients screened between January 8, 2021, and May 14, 2021, 26 were enrolled and 25 completed the study. There were no antiseptic-related adverse events. The topical mucosal antiseptic bundle significantly decreased oral bacterial colony-forming units from pre-operative levels (log10 mean difference 4·03, 95%CI 3·13-4·;92). There were three SSI (12%) within 30 days. In correlative genomic studies, a distinct set of amplicon sequence variants in the post-operative microbiome was associated with SSI. Further, despite no instance of post-operative orocervical fistula, metagenomic sequence mapping revealed the oral cavity as the origin of the infectious organism in two of the three SSI.

INTERPRETATION: The bacterial strains which subsequently caused SSI were frequently identified in the pre-operative oral cavity. Accordingly, a topical antiseptic bundle decreased oral bacterial bioburden throughout the peri-operative period and was associated with a low rate of SSI, supporting further study of topical antisepsis in HNC surgery.

FUNDING: Alliance Oncology.}, } @article {pmid35671564, year = {2022}, author = {Stenglein, MD}, title = {The Case for Studying New Viruses of New Hosts.}, journal = {Annual review of virology}, volume = {9}, number = {1}, pages = {157-172}, doi = {10.1146/annurev-virology-100220-112915}, pmid = {35671564}, issn = {2327-0578}, mesh = {Genome, Viral ; Host Microbial Interactions ; Humans ; Metagenomics ; *Viruses/genetics ; }, abstract = {Virology has largely focused on viruses that are pathogenic to humans or to the other species that we care most about. There is no doubt that this has been a worthwhile investment. But many transformative advances have been made through the in-depth study of relatively obscure viruses that do not appear on lists of prioritized pathogens. In this review, I highlight the benefits that can accrue from the study of viruses and hosts off the beaten track. I take stock of viral sequence diversity across host taxa as an estimate of the bias that exists in our understanding of host-virus interactions. I describe the gains that have been made through the metagenomic discovery of thousands of new viruses in previously unsampled hosts as well as the limitations of metagenomic surveys. I conclude by suggesting that the study of viruses that naturally infect existing and emerging model organisms represents an opportunity to push virology forward in useful and hard to predict ways.}, } @article {pmid35670539, year = {2022}, author = {Landis, EA and Fogarty, E and Edwards, JC and Popa, O and Eren, AM and Wolfe, BE}, title = {Microbial Diversity and Interaction Specificity in Kombucha Tea Fermentations.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0015722}, pmid = {35670539}, issn = {2379-5077}, mesh = {*Kombucha Tea/analysis ; Fermentation ; Beverages/microbiology ; Bacteria/genetics ; Metagenome ; }, abstract = {Despite the popularity of kombucha tea, the distribution of different microbes across kombucha ferments and how those microbes interact within communities are not well characterized. Using metagenomics, comparative genomics, synthetic community experiments, and metabolomics, we determined the taxonomic, ecological, and functional diversity of 23 distinct kombuchas from across the United States. Shotgun metagenomic sequencing demonstrated that the bacterium Komagataeibacter rhaeticus and the yeast Brettanomyces bruxellensis were the most common microbes in the sampled kombucha communities. To determine the specificity of bacterium-yeast interactions, we experimentally quantified microbial interactions within kombucha biofilms by measuring densities of interacting species and biofilm production. In pairwise combinations of bacteria and yeast, B. bruxellensis and individual strains of Komagataeibacter spp. were sufficient to form kombucha fermentations with robust biofilms, but Zygosaccharomyces bisporus, another yeast found in kombucha, did not stimulate bacteria to produce biofilms. Profiling the spent media of both yeast species using nuclear magnetic resonance spectroscopy suggested that the enhanced ability of B. bruxellensis to ferment and produce key metabolites in sucrose-sweetened tea may explain why it stimulates biofilm formation. Comparative genomics demonstrated that Komagataeibacter spp. with >99% genomic similarity can still have dramatic differences in biofilm production, with strong producers yielding five times more biofilm than the weakest producers. IMPORTANCE Through an integration of metagenomic and experimental approaches, our work reveals the diversity and nature of interactions among key taxa in kombucha microbiomes through the construction of synthetic microbial pairs. Manipulation of these microbes in kombucha has the potential to shape both the fermentation qualities of kombucha and the production of biofilms and is valuable for kombucha beverage producers, biofilm engineers, and synthetic ecologists.}, } @article {pmid35670485, year = {2022}, author = {Nair, LG and Agrawal, K and Verma, P}, title = {An insight into the principles of lignocellulosic biomass-based zero-waste biorefineries: a green leap towards imperishable energy-based future.}, journal = {Biotechnology & genetic engineering reviews}, volume = {38}, number = {2}, pages = {288-338}, doi = {10.1080/02648725.2022.2082223}, pmid = {35670485}, issn = {2046-5556}, mesh = {Biomass ; *Lignin/chemistry ; *Biofuels ; Hydrolysis ; }, abstract = {Lignocellulosic biomass (LCB) is an energy source that has a huge impact in today's world. The depletion of fossil fuels, increased pollution, climatic changes, etc. have led the public and private sectors to move towards sustainability i.e. using LCB for the production of biofuels and value-added compounds. A major bottleneck of the process is the recalcitrant nature of LCB. This can be overcome by using various pretreatment strategies like physical, chemical, biological, physicochemical, etc. Further, the pretreated biomass is made to undergo various steps like hydrolysis, saccharification, etc. for the conversion of value-added products and the remaining waste residues can be further utilized for the synthesis of secondary products thus favouring the zero-waste biorefinery concept. Currently, microorganisms are being explored for their use in biorefinery but the unavailability of commercial strains is a major limitation. Thus, the use of metagenomics can be used to overcome the limitation which is both cost-effective and environmentally friendly. The review deliberates the composition of LCBs, and their recalcitrance nature, followed by the structural changes caused by various pretreatment methods. The further steps in biorefineries, strategies for the development of zero-waste refineries, bottlenecks, and suggestions are also discussed. Special emphasis is given to the use of metagenomics for the discovery of microorganisms efficient for zero-waste biorefineries.}, } @article {pmid35669004, year = {2022}, author = {Green, GBH and Williams, MB and Chehade, SB and Morrow, CD and Watts, SA and Bej, AK}, title = {High-throughput amplicon sequencing datasets of the metacommunity DNA of the gut microbiota of Zebrafish Danio rerio fed diets with differential quantities of protein and fat contents.}, journal = {Data in brief}, volume = {42}, number = {}, pages = {108313}, pmid = {35669004}, issn = {2352-3409}, abstract = {In this paper, we present high-throughput amplicon sequence (HTS) datasets of the gut microbiota of male and female Zebrafish Danio rerio fed diets consisting of sub-optimal and above-optimal quantities of proteins and fats. The HTS datasets were generated using an Illumina MiSeq targeting the V4 hypervariable segment of the 16S rRNA gene. The raw sequence reads were quality checked, demultiplexed into FASTQ files, denoised using DADA2 (q2-dada2 denoise-paired), and subsampled. Taxonomic ids were then assigned to amplicon sequence variants (ASVs) against the silva-138-99-nb-classifier for taxonomic output using the Quantitative Insights Into Microbial Ecology (QIIME2 v2021.4). The resultant taxa list was generated at the phylum level to confirm the applicability of the HTS dataset using the "qiime taxa collapse" command. These HTS datasets of the metagenome can be accessed through the BioSample Submission Portal (https://www.ncbi.nlm.nih.gov/bioproject/) under the BioProject IDs PRJNA772302 and PRJNA772305.}, } @article {pmid35668767, year = {2022}, author = {Hu, Y and Yang, C and Song, C and Zhong, W and Li, B and Cao, L and Chen, H and Zhao, C and Yin, Y}, title = {Characterization and Identification of a New Daidzein Reductase Involved in (S)-Equol Biosynthesis in Clostridium sp. ZJ6.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {901745}, pmid = {35668767}, issn = {1664-302X}, abstract = {(S)-equol (EQ) is an isoflavone with high estrogen-like activity in the human body, and is only produced by some gut bacteria in vivo. It plays an important role in maintaining individual health, however, the dearth of resources associated with (S)-EQ-producing bacteria has seriously restricted the production and application of (S)-EQ. We report here a new functional gene KEC48-07020 (K-07020) that was identified from a chick (S)-EQ-producing bacterium (Clostridium sp. ZJ6, ZJ6). We found that recombinant protein of K-07020 possessed similar function to daidzein reductase (DZNR), which can convert daidzein (DZN) into R/S-dihydrodaidzein (R/S-DHD). Interestingly, K-07020 can reversely convert (R/S)-DHD (DHD oxidase) into DZN even without cofactors under aerobic conditions. Additionally, high concentrations of (S)-EQ can directly promote DHD oxidase but inhibit DZNR activity. Molecular docking and site-directed mutagenesis revealed that the amino acid > Arg75 was the active site of DHD oxidase. Subsequently, an engineered E. coli strain based on K-07020 was constructed and showed higher yield of (S)-EQ than the engineered bacteria from our previous work. Metagenomics analysis and PCR detection surprisingly revealed that K-07020 and related bacteria may be prevalent in the gut of humans and animals. Overall, a new DZNR from ZJ6 was found and identified in this study, and its bidirectional enzyme activities and wide distribution in the gut of humans and animals provide alternative strategies for revealing the individual regulatory mechanisms of (S)-EQ-producing bacteria.}, } @article {pmid35668764, year = {2022}, author = {Amin, AB and Zhang, L and Zhang, J and Mao, S}, title = {Metagenomic and Metabolomic Insights Into the Mechanism Underlying the Disparity in Milk Yield of Holstein Cows.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {844968}, pmid = {35668764}, issn = {1664-302X}, abstract = {This study was conducted to investigate the metabolic mechanism underlying the disparity in the milk yield of Holstein cows. Eighteen lactating Holstein cows in their second parity and 56 (±14.81 SD) days in milking (DIM) were selected from 94 cows. Based on the milk yield of the cows, they were divided into two groups of nine cows each, the high milk yield group (HP) (44.57 ± 2.11 kg/day) and the low milk yield group (LP) (26.71 ± 0.70 kg/day). The experimental cows were fed the same diet and kept under the same management system for more than 60 days. Rumen metagenomics revealed that two Archaea genera, one Bacteria genus, eight Eukaryota genera, and two Virus genera differ between the HP and LP groups. The analysis of metabolites in the rumen fluid, milk, and serum showed that several metabolites differed between the HP and LP groups. Correlation analysis between the predominant microbiota and milk yield-associated metabolites (MP-metabolites) revealed that four Bacteria and two Eukaryota genera have a positive relationship with MP-metabolites. Pathway enrichment analysis of the differential metabolites revealed that five pathways were enriched in all the samples (two pathways in the milk, two pathways in the serum, and one pathway in the rumen fluid). Further investigation revealed that the low milk yield observed in the LP group might be due to an upregulation in dopamine levels in the rumen fluid and milk, which could inhibit the release of prolactin or suppress the action of oxytocin in the udder resulting in reduced milk yield. On the other hand, the high milk yield in the HP group is attributed to an upregulation in citrulline, and N-acetylornithine, which could be used as substrates for energy metabolism in the citric acid cycle and ultimately gluconeogenesis.}, } @article {pmid35668758, year = {2022}, author = {Barrett, K and Lange, L and Børsting, CF and Olijhoek, DW and Lund, P and Meyer, AS}, title = {Changes in the Metagenome-Encoded CAZymes of the Rumen Microbiome Are Linked to Feed-Induced Reductions in Methane Emission From Holstein Cows.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {855590}, pmid = {35668758}, issn = {1664-302X}, abstract = {Enteric methane (CH4) emission from cattle is strongly linked to the feeding regime and the rumen microbial community structure. Here, we report that feed-induced CH4-reducing effects correlate with specific alterations in the profile of the microbiome-encoded carbohydrate-active enzymes predicted from the rumen fluid metagenome. Rumen microbiome samples were obtained by mouth-tube sampling from 12 lactating Holstein cows after 3-4 weeks of feeding with three different concentrate-to-forage-ratio diets, i.e., standard, high, and extremely high levels of concentrate (4 cows per group; constant dry matter intake in the three groups). Increased inclusion of concentrate involved increased starch levels in the diet at the expense of fiber. The extreme diet resulted in 48% reduction of the CH4 emission per kg dry matter intake compared to the standard diet. From metagenome sequencing of the rumen fluid samples from each cow, 561 different microbial strains (bins) could be derived from analysis of 260 billion DNA base pairs. In the cows fed, the extreme diet, the relative abundance of the majority of the bins, was significantly altered compared to the other groups. Fibrobacterota and Verrucomicrobiota were less abundant in the Extreme group. Surprisingly, no significant abundance changes were observed among Archaea and Bacteroidota, although abundance changes of individual bins of these phyla were found. For each of the 561 bins, the functions of the metagenome-encoded carbohydrate-active enzymes were predicted by bioinformatics using conserved unique peptide pattern (CUPP) analysis. By linking each of the predicted molecular functions of the enzymes to their substrates, changes were found in the predicted abundance of the different enzyme types. Notably, the decreased CH4 emission of the extreme diet group was concurrent with a profound decrease in the xylan-active enzymes, targeting the xylan backbone β-1,4-linkages, acetyl-, feruloyl-, and methyl-glucuronoyl substitutions in xylan. This work provides a first enzyme-conversion-based characterization of how extreme feeding, i.e., lowered forage, can drive rumen microbiome changes that support decreased CH4 emission via a changed carbohydrate-active enzyme profile. The data, furthermore, provide a metagenome-wide catalog of enzymes, underpinning the microbial conversion of different feed fibers (the enzymes attacking specific carbohydrate linkages) in the rumen of Holstein cows.}, } @article {pmid35668757, year = {2022}, author = {Li, C and Han, G and Sun, J and Huang, L and Lu, Y and Xia, Y and Liu, Q and Xu, J}, title = {The Gut Microbiota Composition of Cnaphalocrocis medinalis and Their Predicted Contribution to Larval Nutrition.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {909863}, pmid = {35668757}, issn = {1664-302X}, abstract = {Intestinal bacterial flora plays an important role in the nutrition, physiology, and behavior of herbivorous insects. The composition of gut microbiota may also be affected by the food consumed. Cnaphalocrocis medinalis is an oligophagous pest, feeds on rice leaves almost exclusively and causes serious damage to rice in Asian countries. Using antibiotic treatment and metagenome sequencing, we investigated the influence of the food sources (rice and maize seedlings) on the structure and functions of intestinal bacteria of C. medinalis. Firstly, food utilization indices, relative growth rate (RGR), relative consumption rate (RCR), efficiency of conversion of ingested food (ECI), and efficiency of conversion of digested food (ECD), were all significantly adversely affected in the antibiotic treatment eliminating gut bacteria, showing that the microbiota loading in the gut were essential for the larva growth and development of C. medinalis. Further, metagenome sequencing revealed that different diets caused a variation in gut microbiota composition of C. medinalis, indicating that the gut microbiota were in part driven by the diet provided. However, the larvae of C. medinalis hosted a core microbial community in the gut, which was independent from the diets changing. The dominant bacteria in the two feeding groups were highly consistent in the gut of C. medinalis larvae, with the gut bacterial community dominated by Firmicutes at the phylum level, Enterococcus at the genus level, Enterococcus sp. FDAARGOS-375, E. casseliflavus, E. gallinarum, and E. sp. CR-Ec1 accounted for more than 96% of the gut microbiota. Functional prediction analysis demonstrated that gut bacteria encoded a series of metabolism-related enzymes involved in carbohydrate metabolism and amino acid synthesis. Carbohydrate metabolism was the most enriched function in both groups and was more abundant in rice feeding group than in maize feeding group. The core dominant Enterococcus species possessed complete pathways of 14 carbohydrates metabolism, 11 amino acids biosynthesis, and two vitamins synthesize, implied to contribute an essential role to the nutrition intake and development of C. medinalis. Finally, the study may provide an in-depth analysis of the symbiont-host co-adaptation and new insights into the management of C. medinalis.}, } @article {pmid35668420, year = {2022}, author = {Savatt, JM and Ortiz, NM and Thone, GM and McDonald, WS and Kelly, MA and Berry, ASF and Alvi, MM and Hallquist, MLG and Malinowski, J and Purdy, NC and Williams, MS and Sturm, AC and Buchanan, AH}, title = {Observational study of population genomic screening for variants associated with endocrine tumor syndromes in a large, healthcare-based cohort.}, journal = {BMC medicine}, volume = {20}, number = {1}, pages = {205}, pmid = {35668420}, issn = {1741-7015}, mesh = {Adult ; Delivery of Health Care ; Genetic Testing ; Humans ; *Metagenomics ; *Neoplasms ; Syndrome ; }, abstract = {BACKGROUND: In current care, patients' personal and self-reported family histories are primarily used to determine whether genetic testing for hereditary endocrine tumor syndromes (ETS) is indicated. Population genomic screening for other conditions has increased ascertainment of individuals with pathogenic/likely pathogenic (P/LP) variants, leading to improved management and earlier diagnoses. It is unknown whether such benefits occur when screening broader populations for P/LP ETS variants. This manuscript assesses clinical utility outcomes of a large, unselected, healthcare-based genomic screening program by describing personal and family history of syndrome-related features, risk management behaviors after result disclosure, and rates of relevant post-disclosure diagnoses in patient-participants with P/LP ETS variants.

METHODS: Observational study of individuals informed of a P/LP variant in MEN1, RET, SDHAF2, SDHB, SDHC, SDHD, or VHL through Geisinger's MyCode Community Health Initiative between June 2016 and October 2019. Electronic health records (EHRs) of participants were evaluated for a report of pre-disclosure personal and self-reported family histories and post-disclosure risk management and diagnoses.

RESULTS: P/LP variants in genes of interest were identified in 199 of 130,490 (1 in 656) adult Geisinger MyCode patient-participants, 80 of which were disclosed during the study period. Eighty-one percent (n = 65) did not have prior evidence of the result in their EHR and, because they were identified via MyCode, were included in further analyses. Five participants identified via MyCode (8%) had a personal history of syndrome-related features; 16 (25%) had a positive self-reported family history. Time from result disclosure to EHR review was a median of 0.7 years. Post-disclosure, 36 (55.4%) completed a recommended risk management behavior; 11 (17%) were diagnosed with a syndrome-related neoplasm after completing a risk management intervention.

CONCLUSIONS: Broader screening for pathogenic/likely pathogenic variants associated with endocrine tumor syndromes enables detection of at-risk individuals, leads to the uptake of risk management, and facilitates relevant diagnoses. Further research will be necessary to continue to determine the clinical utility of screening diverse, unselected populations for such variants.}, } @article {pmid35668255, year = {2022}, author = {Yang, H and Huang, Y and Li, K and Zhu, P and Wang, Y and Li, X and Meng, Q and Niu, Q and Wang, S and Li, Q}, title = {Lignocellulosic depolymerization induced by ionic liquids regulating composting habitats based on metagenomics analysis.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {50}, pages = {76298-76309}, pmid = {35668255}, issn = {1614-7499}, support = {No. 41861124004//National Natural Science Foundation of China/ ; No. 21878057//National Natural Science Foundation of China/ ; }, mesh = {*Actinobacteria/genetics/metabolism ; Bacteria/genetics/metabolism ; Cellulose ; *Composting ; *Ionic Liquids ; Lignin/metabolism ; Manure/microbiology ; Metagenomics ; *Microbiota ; Soil ; }, abstract = {The application of ionic liquids with sawdust and fresh dairy manure was studied in composting. The degradation of organic matter (OM), dissolved organic matter (DOM), and lignocellulose was analyzed. The DOM decreased by 14.25 mg/g and 11.11 mg/g in experimental group (ILs) and control group (CK), respectively. OM decreased by 7.32% (CK) and 8.91% (ILs), respectively. The degradation rates of hemicellulose, lignin, and cellulose in ILs (56.62%, 42.01%, and 23.97%) were higher than in CK (38.39%, 39.82%, and 16.04%). Microbial community and carbohydrate-active enzymes (CAZymes) were analyzed based on metagenomics. Metagenomic analysis results showed that ionic liquids enriched Actinobacteria and Proteobacteria in composting. Compared with CK, the total abundance values of GH11, GH6, AA6, and AA3_2 in ILs increased by 13.98%, 10.12%, 11.21%, and 13.68%, respectively. Ionic liquids can improve the lignocellulosic degradation by regulating the environmental physicochemical parameters (temperature, pH, C/N) to promote the growth of Actinobacteria and Proteobacteria and carbohydrate-active enzymes (CAZymes) abundance. Therefore, ionic liquids are a promising additive in lignocellulosic waste composting.}, } @article {pmid35667424, year = {2022}, author = {Bose, H and Sahu, RP and Sar, P}, title = {Impact of arsenic on microbial community structure and their metabolic potential from rice soils of West Bengal, India.}, journal = {The Science of the total environment}, volume = {841}, number = {}, pages = {156486}, doi = {10.1016/j.scitotenv.2022.156486}, pmid = {35667424}, issn = {1879-1026}, mesh = {Archaea ; *Arsenic/analysis ; Bacteria/metabolism ; *Microbiota ; *Oryza/genetics ; RNA, Ribosomal, 16S/genetics ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Paddy soil is a heterogenous ecosystem that harbours diverse microbial communities critical for maintaining ecosystem sustainability and crop yield. Considering the importance of soil in crop production and recent reports on its contamination with arsenic (As) across the South East Asia, its microbial community composition and biogeochemical functions remained inadequately studied. We have characterized the microbial communities of rice soil from eleven paddy fields of As-contaminated sites from West Bengal (India), through metagenomics and amplicon sequencing. 16S rRNA gene sequencing showed considerable bacterial diversity [over 0.2 million Operational Taxonomic Units (OTUs)] and abundance (upto 1.6 × 10[7] gene copies/g soil). Existence of a core-microbiome (261 OTUs conserved out of a total 141,172 OTUs) across the samples was noted. Most of the core-microbiome members were also found to represent the abundant taxa of the soil. Statistical analyses suggested that the microbial communities were highly constrained by As, Fe K, N, PO4[3-], SO4[2-] and organic carbon (OC). Members of Proteobacteria, Actinobacteria, Acidobacteria, Chloroflexi, Planctomycetes and Thaumarchaeota constituted the core-microbiome. Co-occurrence network analysis displayed significant interaction among diverse anaerobic, SO4[2-] and NO3[-] reducing, cellulose and other organic matter or C1 compound utilizing, fermentative and aerobic/facultative anaerobic bacteria and archaea. Correlation analysis suggested that taxa which were positively linked with soil parameters that maintain soil health and productivity (e.g., N, K, PO4[3-] and Fe) were adversely impacted by increasing As concentration. Shotgun metagenomics highlighted major metabolic pathways controlling the C (3-hydroxypropionate bicycle), N (Denitrification, dissimilatory NO3[-] reduction to ammonium), and S (assimilatory SO4[2-] reduction and sulfide oxidation) cycling, As homeostasis (methylation and reduction) and plant growth promotion (polyphosphate hydrolysis and auxin biosynthesis). All these major biogeochemical processes were found to be catalyzed by the members of most abundant/core-community.}, } @article {pmid35667265, year = {2022}, author = {Han, DS and Wu, WK and Liu, PY and Yang, YT and Hsu, HC and Kuo, CH and Wu, MS and Wang, TG}, title = {Differences in the gut microbiome and reduced fecal butyrate in elders with low skeletal muscle mass.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {41}, number = {7}, pages = {1491-1500}, doi = {10.1016/j.clnu.2022.05.008}, pmid = {35667265}, issn = {1532-1983}, mesh = {Aged ; Animals ; Butyrates ; Fatty Acids, Volatile/metabolism ; Feces ; *Gastrointestinal Microbiome/physiology ; Humans ; Muscle, Skeletal/physiology ; *Sarcopenia ; }, abstract = {BACKGROUND AND AIMS: Despite animal studies revealing a causal link between the gut microbiota and skeletal muscle mass, the role of the gut microbiome and its metabolites in humans having low muscle mass remains unclear.

METHODS: Eighty-eight subjects older than 65 years were measured for sarcopenia-related parameters, including body composition, grip strength, gait speed and flexibility. Participants were divided into normal muscle mass group (NM, n = 52) and low muscle mass group (LM, n = 36) and fresh fecal samples were collected for metagenome and short chain fatty acids (SCFAs) analysis.

RESULTS: The richness and evenness of gut microbiota diversity were significantly decreased in the subjects with low muscle mass, including observed ASVs, Shannon and Chao 1 index. A significant difference of gut microbiota profile was noted between NM group and LM group. The Firmicutes/Bacteroidetes ratio was significantly reduced in the LM group. A significant decrease in the abundance of a SCFA-producer, Marvinbryantia spp., whereas a remarkable enrichment of a flavonoid degrader, Flavonifractor spp., was observed in the LM elders. Comparing with the NM group, the fecal butyrate significantly diminished in the LM group and correlated with skeletal muscle mass index.

CONCLUSIONS: This is the first study that demonstrates the reduced fecal butyrate in elders with low muscle mass and highlights the associated gut microbiome changes. The identified gut microbial features and fecal butyrate level may serve as potential biomarkers for early detection of sarcopenic patients.}, } @article {pmid35667011, year = {2022}, author = {Gwak, HJ and Rho, M}, title = {ViBE: a hierarchical BERT model to identify eukaryotic viruses using metagenome sequencing data.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {4}, pages = {}, doi = {10.1093/bib/bbac204}, pmid = {35667011}, issn = {1477-4054}, mesh = {Eukaryota/genetics ; Humans ; *Metagenome ; Metagenomics/methods ; Sequence Alignment ; *Viruses/genetics ; }, abstract = {Viruses are ubiquitous in humans and various environments and continually mutate themselves. Identifying viruses in an environment without cultivation is challenging; however, promoting the screening of novel viruses and expanding the knowledge of viral space is essential. Homology-based methods that identify viruses using known viral genomes rely on sequence alignments, making it difficult to capture remote homologs of the known viruses. To accurately capture viral signals from metagenomic samples, models are needed to understand the patterns encoded in the viral genomes. In this study, we developed a hierarchical BERT model named ViBE to detect eukaryotic viruses from metagenome sequencing data and classify them at the order level. We pre-trained ViBE using read-like sequences generated from the virus reference genomes and derived three fine-tuned models that classify paired-end reads to orders for eukaryotic deoxyribonucleic acid viruses and eukaryotic ribonucleic acid viruses. ViBE achieved higher recall than state-of-the-art alignment-based methods while maintaining comparable precision. ViBE outperformed state-of-the-art alignment-free methods for all test cases. The performance of ViBE was also verified using real sequencing datasets, including the vaginal virome.}, } @article {pmid35666732, year = {2022}, author = {Bordenstein, SR and Bordenstein, SR}, title = {Widespread phages of endosymbionts: Phage WO genomics and the proposed taxonomic classification of Symbioviridae.}, journal = {PLoS genetics}, volume = {18}, number = {6}, pages = {e1010227}, pmid = {35666732}, issn = {1553-7404}, support = {R01 AI132581/AI/NIAID NIH HHS/United States ; R01 AI143725/AI/NIAID NIH HHS/United States ; }, mesh = {Animals ; *Arthropods ; *Bacteriophages/genetics ; Eukaryota ; Genomics ; Symbiosis/genetics ; *Wolbachia/genetics ; }, abstract = {Wolbachia are the most common obligate, intracellular bacteria in animals. They exist worldwide in arthropod and nematode hosts in which they commonly act as reproductive parasites or mutualists, respectively. Bacteriophage WO, the largest of Wolbachia's mobile elements, includes reproductive parasitism genes, serves as a hotspot for genetic divergence and genomic rearrangement of the bacterial chromosome, and uniquely encodes a Eukaryotic Association Module with eukaryotic-like genes and an ensemble of putative host interaction genes. Despite WO's relevance to genome evolution, selfish genetics, and symbiotic applications, relatively little is known about its origin, host range, diversification, and taxonomic classification. Here we analyze the most comprehensive set of 150 Wolbachia and phage WO assemblies to provide a framework for discretely organizing and naming integrated phage WO genomes. We demonstrate that WO is principally in arthropod Wolbachia with relatives in diverse endosymbionts and metagenomes, organized into four variants related by gene synteny, often oriented opposite the putative origin of replication in the Wolbachia chromosome, and the large serine recombinase is an ideal typing tool to distinguish the four variants. We identify a novel, putative lytic cassette and WO's association with a conserved eleven gene island, termed Undecim Cluster, that is enriched with virulence-like genes. Finally, we evaluate WO-like Islands in the Wolbachia genome and discuss a new model in which Octomom, a notable WO-like Island, arose from a split with WO. Together, these findings establish the first comprehensive Linnaean taxonomic classification of endosymbiont phages, including non-Wolbachia phages from aquatic environments, that includes a new family and two new genera to capture the collective relatedness of these viruses.}, } @article {pmid35666311, year = {2022}, author = {Hede, N and Khandeparker, L}, title = {Ecological Impacts of Aged Freshwater Biofilms on Estuarine Microbial Communities Elucidated Through Microcosm Experiments: A Microbial Invasion Perspective.}, journal = {Current microbiology}, volume = {79}, number = {7}, pages = {210}, pmid = {35666311}, issn = {1432-0991}, support = {GAP 2429//ballast water management program, india (ministry of shipping and dg shipping)/ ; PSC 0105//csir funded ocean finder program/ ; }, mesh = {Bacteria/genetics ; Biofilms ; Fresh Water/microbiology ; *Microbiota ; *Vibrio cholerae ; Water ; }, abstract = {Inadvertent introductions of alien species via biofilms as a vector released through ballast water are of environmental importance, yet their consequences are not much known. In the present study, biofilm communities developed in an inland freshwater port under in situ and dark conditions were subjected to long-term dark incubations. Subsequently, the impact of these aged biofilms as vectors on estuarine water column communities were evaluated using microcosm experiments in the laboratory. Variations in biofilm and planktonic microbial communities were quantified using quantitative PCR.Upon prolonged dark incubation, a shift in bacterial diversity with an increase in tolerant bacterial communities better adapted to stress was observed. Actinobacteria were the dominant taxa in both aged biofilms upon dark incubations. The laboratory studies indicated that on exposure of these biofilms to estuarine water, resuscitation of Vibrio alginolyticus, V. parahaemolyticus, and V. cholerae from a dormant state existing in these biofilms to culturable form was observed. Moreover, the results revealed that both the biofilm types can pose a threat to the environment, but the degree of risk can be attributed to the imbalance caused by significant changes in the surrounding estuarine microbial communities. Consequently, this may result in either proliferation or decline of some genera with different metabolic potential and resuscitation of pathogenic forms not present earlier, thereby influencing the ecology of the environment. Quantifying these effects in the field using biofilm metagenomes with an emphasis on virulent species and understanding traits that enable them to adapt to changing environments is a way forward.}, } @article {pmid35665806, year = {2022}, author = {Ewald, JM and Schnoor, JL and Mattes, TE}, title = {Combined read- and assembly-based metagenomics to reconstruct a Dehalococcoides mccartyi genome from PCB-contaminated sediments and evaluate functional differences among organohalide-respiring consortia in the presence of different halogenated contaminants.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {7}, pages = {}, pmid = {35665806}, issn = {1574-6941}, support = {P42 ES013661/ES/NIEHS NIH HHS/United States ; R01 ES032671/ES/NIEHS NIH HHS/United States ; }, mesh = {Biodegradation, Environmental ; *Chloroflexi/chemistry/genetics ; Dehalococcoides ; Halogenation ; Phylogeny ; *Polychlorinated Biphenyls ; }, abstract = {Microbial communities that support respiration of halogenated organic contaminants by Dehalococcoides sp. facilitate full-scale bioremediation of chlorinated ethenes and demonstrate the potential to aid in bioremediation of halogenated aromatics like polychlorinated biphenyls (PCBs). However, it remains unclear if Dehalococcoides-containing microbial community dynamics observed in sediment-free systems quantitatively resemble that of sediment environments. To evaluate that possibility we assembled, annotated, and analyzed a Dehalococcoides sp. metagenome-assembled genome (MAG) from PCB-contaminated sediments. Phylogenetic analysis of reductive dehalogenase gene (rdhA) sequences within the MAG revealed that pcbA1 and pcbA4/5-like rdhA were absent, while several candidate PCB dehalogenase genes and potentially novel rdhA sequences were identified. Using a compositional comparative metagenomics approach, we quantified Dehalococcoides-containing microbial community structure shifts in response to halogenated organics and the presence of sediments. Functional level analysis revealed significantly greater abundances of genes associated with cobamide remodeling and horizontal gene transfer in tetrachloroethene-fed cultures as compared to halogenated aromatic-exposed consortia with or without sediments, despite little evidence of statistically significant differences in microbial community taxonomic structure. Our findings support the use of a generalizable comparative metagenomics workflow to evaluate Dehalococcoides-containing consortia in sediments and sediment-free environments to eludicate functions and microbial interactions that facilitate bioremediation of halogenated organic contaminants.}, } @article {pmid35665717, year = {2022}, author = {Bhimraj, A and Hasbun, R}, title = {Diagnostic approach and update on encephalitis.}, journal = {Current opinion in infectious diseases}, volume = {35}, number = {3}, pages = {231-237}, doi = {10.1097/QCO.0000000000000832}, pmid = {35665717}, issn = {1473-6527}, mesh = {Antiviral Agents/therapeutic use ; *Encephalitis/diagnosis ; Humans ; Metagenomics/methods ; Neuroimaging ; }, abstract = {PURPOSE OF REVIEW: The present article gives an update and outlines the fundamental principles of clinical reasoning and a diagnostic approach to a patient suspected to have acute encephalitis.

RECENT FINDINGS: Encephalitis remains to be associated with significant mortality and neurological morbidity. Unfortunately, the etiologic diagnosis remains elusive for the majority of the patients with encephalitis preventing targeted therapies. Clinicians could utilize clues such as duration of symptoms, exposure history, cerebrospinal fluid profile, neuroimaging findings and locations, and entertain certain opportunistic infections in immunosuppressed individuals. A comprehensive diagnostic for the most common viral and autoimmune etiologies should be systematically done and prompt empiric antiviral therapy should be started. Evaluation and therapy for autoimmune etiologies should be done for patients with a negative viral work up. Brain biopsy and metagenomic sequencing should be considered for patients with unknown etiologies that are clinically worsening.

SUMMARY: Encephalitis remains with unacceptable mortality and morbidity with the most common etiologies being idiopathic. A comprehensive diagnostic work up and prompt antiviral and autoimmune therapies are of paramount importance to improve the outcomes of this devastating disease.}, } @article {pmid35665349, year = {2022}, author = {Gu, M and Mo, X and Tang, Z and Tang, J and Wang, W}, title = {Case Report: Diagnosis of Acute Q Fever With Aseptic Meningitis in a Patient by Using Metagenomic Next-Generation Sequencing.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {855020}, pmid = {35665349}, issn = {2296-858X}, abstract = {Query fever (Q fever) is a widespread zoonotic disease caused by the bacterium of Coxiella burnetii (C. burnetii). Its neurological complications are rarely reported. But they may lead to severe consequences. It needs a rapid and accurate detective method to diagnose acute Q fever with neurological presentations in non-epidemic areas urgently. Here, we report an acute Q fever case with aseptic meningitis. The male patient, without any contact history in the epidemic area or with animals, was indicated to exhibit fever and headache symptoms. The cultures of blood, stool, urine, and sputum were all negative. But C. burnetii was repeatedly detected in blood by metagenomic next-generation sequencing (mNGS). He received Doxycycline therapy and quickly returned to normal. Therefore, for the diagnosis and identification of Q fever in non-reporting regions, mNGS has comparative advantages. Secondly, aseptic meningitis may be a direct infection of C. burnetii to central nervous system (CNS) or inflammatory reactions to systemic infection, we recommend detecting mNGS both in blood and cerebrospinal fluid (CSF).}, } @article {pmid35664653, year = {2022}, author = {Kim, Y and Lim, B and Park, J and Kim, S}, title = {Semi-subterranean environment and soil metagenomic datasets of the Gyeongju Seokbinggo (stone ice storage) in South Korea.}, journal = {Data in brief}, volume = {42}, number = {}, pages = {108308}, pmid = {35664653}, issn = {2352-3409}, abstract = {The Seokbinggo is an ice cellar made of stone to store ice in the 1700s. The Seokbinggo, a traditional Korean stone architecture, can keep ice collected in winter until summer because the semi-subterranean structure utilizes the natural environment, and the insulation design is effective. However, these structures and scientific designs are not used as ice storage and are easily damaged by biological contamination. We present the environmental data of the inside and the metagenomic dataset of the soil samples from the Seokbinggo. Next-generation sequencing was carried out on an Illumina MiSeq platform. The raw sequence data used for analysis is available in NCBI under the Sequence Read Archive (SRA) with BioProject No. PRJNA727939 and SRA accession Nos. SRX10976613, SRX10976614, SRX10976615, SRX10976616, SRX10976617, SRX10976618, SRX10976619, SRX10976620. Environmental data, including data from Korea Meteorological Administration, is available in the Mendeley data repository with DOI: 10.17632/2r8gpg7pxn.1.}, } @article {pmid35664259, year = {2022}, author = {Deng, L and Xie, B and Wang, Y and Zhang, X and Xu, S}, title = {A protocol for applying a population-specific reference genome assembly to population genetics and medical studies.}, journal = {STAR protocols}, volume = {3}, number = {2}, pages = {101440}, pmid = {35664259}, issn = {2666-1667}, mesh = {Base Sequence ; *Genetics, Population ; *Genome, Human/genetics ; Humans ; Metagenomics ; }, abstract = {With a growing number of available de novo sequenced genomes, protocols for their applications to population genetics will benefit our understanding of the human genome. Here we detail analytic steps to apply an example de novo reference genome to map and detect variants of short-read sequences from corresponding populations and to discover variants of disease-relevant genes. Using this protocol, we can improve variant discovery, better investigate population-specific genome properties, and evaluate the potential of sequenced genomes in medical studies. For complete details on the use and execution of this protocol, please refer to Lou et al. (2022).}, } @article {pmid35664229, year = {2022}, author = {Li, M and Yang, L and Mu, C and Sun, Y and Gu, Y and Chen, D and Liu, T and Cao, H}, title = {Gut microbial metabolome in inflammatory bowel disease: From association to therapeutic perspectives.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {2402-2414}, pmid = {35664229}, issn = {2001-0370}, abstract = {Inflammatory bowel disease (IBD), comprising Crohn's disease (CD) and ulcerative colitis (UC), is a set of clinically chronic, relapsing gastrointestinal inflammatory disease and lacks of an absolute cure. Although the precise etiology is unknown, developments in high-throughput microbial genomic sequencing significantly illuminate the changes in the intestinal microbial structure and functions in patients with IBD. The application of microbial metabolomics suggests that the microbiota can influence IBD pathogenesis by producing metabolites, which are implicated as crucial mediators of host-microbial crosstalk. This review aims to elaborate the current knowledge of perturbations of the microbiome-metabolome interface in IBD with description of altered composition and metabolite profiles of gut microbiota. We emphasized and elaborated recent findings of several potentially protective metabolite classes in IBD, including fatty acids, amino acids and derivatives and bile acids. This article will facilitate a deeper understanding of the new therapeutic approach for IBD by applying metabolome-based adjunctive treatment.}, } @article {pmid35663906, year = {2022}, author = {Ma, X and Dong, X and Cai, J and Fu, C and Yang, J and Liu, Y and Zhang, Y and Wan, T and Lin, S and Lou, Y and Zheng, M}, title = {Metagenomic Analysis Reveals Changes in Bacterial Communities and Antibiotic Resistance Genes in an Eye Specialty Hospital and a General Hospital Before and After Wastewater Treatment.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {848167}, pmid = {35663906}, issn = {1664-302X}, abstract = {The spread of antibiotic resistant bacteria (ARB) and antibiotic resistance genes (ARGs) in hospital wastewater poses a great threat to public health, and wastewater treatment plants (WWTPs) play an important role in reducing the levels of ARB and ARGs. In this study, high-throughput metagenomic sequencing was used to analyze the bacterial community composition and ARGs in two hospitals exposed to different antibiotic use conditions (an eye specialty hospital and a general hospital) before and after wastewater treatment. The results showed that there were various potential pathogenic bacteria in the hospital wastewater, and the abundance and diversity of the influent ARGs in the general hospital were higher than those in the eye hospital. The influent of the eye hospital was mainly composed of Thauera and Pseudomonas, and sul1 (sulfonamide) was the most abundant ARG. The influent of the general hospital contained mainly Aeromonas and Acinetobacter, and tet39 (tetracycline) was the most abundant ARG. Furthermore, co-occurrence network analysis showed that the main bacteria carrying ARGs in hospital wastewater varied with hospital type; the same bacteria in wastewater from different hospitals could carry different ARGs, and the same ARG could also be carried by different bacteria. The changes in the bacterial community and ARG abundance in the effluent from the two hospitals showed that the activated sludge treatment and the direct chlorination disinfection can effectively remove some bacteria and ARGs in wastewater but have limitations. The species diversity increased significantly after the activated sludge treatment, while the direct chlorination disinfection did not increase the diversity. The activated sludge treatment has a better effect on the elimination of ARGs than the direct chlorination disinfection. In summary, we investigated the differences in bacterial communities and ARGs in wastewater from two hospitals exposed to different antibiotic usage conditions, evaluated the effects of different wastewater treatment methods on the bacterial communities and ARGs in hospital wastewater, and recommended appropriate methods for certain clinical environments.}, } @article {pmid35663898, year = {2022}, author = {Liñares-Blanco, J and Fernandez-Lozano, C and Seoane, JA and López-Campos, G}, title = {Machine Learning Based Microbiome Signature to Predict Inflammatory Bowel Disease Subtypes.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {872671}, pmid = {35663898}, issn = {1664-302X}, abstract = {Inflammatory bowel disease (IBD) is a chronic disease with unknown pathophysiological mechanisms. There is evidence of the role of microorganims in this disease development. Thanks to the open access to multiple omics data, it is possible to develop predictive models that are able to prognosticate the course and development of the disease. The interpretability of these models, and the study of the variables used, allows the identification of biological aspects of great importance in the development of the disease. In this work we generated a metagenomic signature with predictive capacity to identify IBD from fecal samples. Different Machine Learning models were trained, obtaining high performance measures. The predictive capacity of the identified signature was validated in two external cohorts. More precisely a cohort containing samples from patients suffering Ulcerative Colitis and another from patients suffering Crohn's Disease, the two major subtypes of IBD. The results obtained in this validation (AUC 0.74 and AUC = 0.76, respectively) show that our signature presents a generalization capacity in both subtypes. The study of the variables within the model, and a correlation study based on text mining, identified different genera that play an important and common role in the development of these two subtypes.}, } @article {pmid35663897, year = {2022}, author = {Zeng, J and Wang, Y and Wu, Z and Zhou, Y}, title = {FRAGTE2: An Enhanced Algorithm to Pre-Select Closely Related Genomes for Bacterial Species Demarcation.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {847439}, pmid = {35663897}, issn = {1664-302X}, abstract = {We previously reported on FRAGTE (hereafter termed FRAGTE1), a promising algorithm for sieving (pre-selecting genome pairs for whole-genome species demarcation). However, the overall amount of pairs sieved by FRAGTE1 is still large, requiring seriously unaffordable computing cost, especially for large datasets. Here, we present FRAGTE2. Tests on simulated genomes, real genomes, and metagenome-assembled genomes revealed that (i) FRAGTE2 outstandingly reduces ~50-60.10% of the overall amount of pairs sieved by FRAGTE1, dramatically decreasing the computing cost required for whole-genome species demarcation afterward; (ii) FRAGTE2 shows superior sensitivity than FRAGTE1; (iii) FRAGTE2 shows higher specificity than FRAGTE1; and (iv) FRAGTE2 is faster than or comparable with FRAGTE1. Besides, FRAGTE2 is independent of genome completeness, the same as FRAGTE1. We therefore recommend FRAGTE2 tailored for sieving to facilitate species demarcation in prokaryotes.}, } @article {pmid35663881, year = {2022}, author = {Vidal, P and Martínez-Martínez, M and Fernandez-Lopez, L and Roda, S and Méndez-García, C and Golyshina, OV and Guallar, V and Peláez, AI and Ferrer, M}, title = {Metagenomic Mining for Esterases in the Microbial Community of Los Rueldos Acid Mine Drainage Formation.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {868839}, pmid = {35663881}, issn = {1664-302X}, abstract = {Acid mine drainage (AMD) systems are extremely acidic and are metal-rich formations inhabited by relatively low-complexity communities of acidophiles whose enzymes remain mostly uncharacterized. Indeed, enzymes from only a few AMD sites have been studied. The low number of available cultured representatives and genome sequences of acidophiles inhabiting AMDs makes it difficult to assess the potential of these environments for enzyme bioprospecting. In this study, using naïve and in silico metagenomic approaches, we retrieved 16 esterases from the α/β-hydrolase fold superfamily with the closest match from uncultured acidophilic Acidobacteria, Actinobacteria (Acidithrix, Acidimicrobium, and Ferrimicrobium), Acidiphilium, and other Proteobacteria inhabiting the Los Rueldos site, which is a unique AMD formation in northwestern Spain with a pH of ∼2. Within this set, only two polypeptides showed high homology (99.4%), while for the rest, the pairwise identities ranged between 4 and 44.9%, suggesting that the diversity of active polypeptides was dominated not by a particular type of protein or highly similar clusters of proteins, but by diverse non-redundant sequences. The enzymes exhibited amino acid sequence identities ranging from 39 to 99% relative to homologous proteins in public databases, including those from other AMDs, thus indicating the potential novelty of proteins associated with a specialized acidophilic community. Ten of the 16 hydrolases were successfully expressed in Escherichia coli. The pH for optimal activity ranged from 7.0 to 9.0, with the enzymes retaining 33-68% of their activities at pH 5.5, which was consistent with the relative frequencies of acid residues (from 54 to 67%). The enzymes were the most active at 30-65°C, retaining 20-61% of their activity under the thermal conditions characterizing Los Rueldos (13.8 ± 0.6°C). The analysis of the substrate specificity revealed the capacity of six hydrolases to efficiently degrade (up to 1,652 ± 75 U/g at pH 8.0 and 30°C) acrylic- and terephthalic-like [including bis(2-hydroxyethyl)-terephthalate, BHET] esters, and these enzymes could potentially be of use for developing plastic degradation strategies yet to be explored. Our assessment uncovers the novelty and potential biotechnological interest of enzymes present in the microbial populations that inhibit the Los Rueldos AMD system.}, } @article {pmid35663067, year = {2022}, author = {Xu, CQ and Chen, XL and Zhang, DS and Wang, JW and Yuan, H and Chen, WF and Xia, H and Zhang, ZY and Peng, FH}, title = {Diagnosis of cytomegalovirus encephalitis using metagenomic next-generation sequencing of blood and cerebrospinal fluid: A case report.}, journal = {World journal of clinical cases}, volume = {10}, number = {14}, pages = {4601-4607}, pmid = {35663067}, issn = {2307-8960}, abstract = {BACKGROUND: Cytomegalovirus (CMV) infections in the population are mostly subclinical, inapparent, or latent. However, it is rare in brain tissue. Most reported CMV encephalitis cases were patients with immunodeficiency. The diagnosis and detection rate of CMV encephalitis in patients with normal immune function needs to be further improved.

CASE SUMMARY: An 86-year-old male was admitted due to a sudden onset of unconsciousness for 3 h. The patient developed status epilepticus and was relieved after antiepileptic treatment. Encephalitis was considered due to the high signals of diffusion-weighted imaging sequences in the right central region by magnetic resonance imaging. Metagenomic next-generation sequencing (mNGS) of blood and cerebrospinal fluid revealed CMV, with unique reads number being 614 and 1, respectively. Simultaneous quantitative PCR results showed CMV positive in blood samples and negative in cerebrospinal fluid samples. The patient was finally diagnosed as CMV encephalitis with status epilepticus. After the antiviral, hormonal, and γ-globulin pulse therapy, the patient's condition improved, and he was finally discharged.

CONCLUSION: mNGS could be a reliable approach for the diagnosis of CMV encephalitis, with high efficiency, sensitivity, and specificity.}, } @article {pmid35663034, year = {2022}, author = {Li, S and Guo, R and Zhang, Y and Li, P and Chen, F and Wang, X and Li, J and Jie, Z and Lv, Q and Jin, H and Wang, G and Yan, Q}, title = {A catalog of 48,425 nonredundant viruses from oral metagenomes expands the horizon of the human oral virome.}, journal = {iScience}, volume = {25}, number = {6}, pages = {104418}, pmid = {35663034}, issn = {2589-0042}, abstract = {The human oral cavity is a hotspot of numerous, mostly unexplored, viruses that are important for maintaining oral health and microbiome homeostasis. Here, we analyzed 2,792 publicly available oral metagenomes and proposed the Oral Virus Database (OVD) comprising 48,425 nonredundant viral genomes (≥5 kbp). The OVD catalog substantially expanded the known phylogenetic diversity and host specificity of oral viruses, allowing for enhanced delineation of some underrepresented groups such as the predicted Saccharibacteria phages and jumbo viruses. Comparisons of the viral diversity and abundance of different oral cavity habitats suggested strong niche specialization of viromes within individuals. The virome variations in relation to host geography and properties were further uncovered, especially the age-dependent viral compositional signatures in saliva. Overall, the viral genome catalog describes the architecture and variability of the human oral virome, while offering new resources and insights for current and future studies.}, } @article {pmid35663033, year = {2022}, author = {Li, Y and Zhang, C and Yu, DJ and Zhang, Y}, title = {Deep learning geometrical potential for high-accuracy ab initio protein structure prediction.}, journal = {iScience}, volume = {25}, number = {6}, pages = {104425}, pmid = {35663033}, issn = {2589-0042}, abstract = {Ab initio protein structure prediction has been vastly boosted by the modeling of inter-residue contact/distance maps in recent years. We developed a new deep learning model, DeepPotential, which accurately predicts the distribution of a complementary set of geometric descriptors including a novel hydrogen-bonding potential defined by C-alpha atom coordinates. On 154 Free-Modeling/Hard targets from the CASP and CAMEO experiments, DeepPotential demonstrated significant advantage on both geometrical feature prediction and full-length structure construction, with Top-L/5 contact accuracy and TM-score of full-length models 4.1% and 6.7% higher than the best of other deep-learning restraint prediction approaches. Detail analyses showed that the major contributions to the TM-score/contact-map improvements come from the employment of multi-tasking network architecture and metagenome-based MSA collection assisted with confidence-based MSA selection, where hydrogen-bonding and inter-residue orientation predictions help improve hydrogen-bonding network and secondary structure packing. These results demonstrated new progress in the deep-learning restraint-guided ab initio protein structure prediction.}, } @article {pmid35662946, year = {2022}, author = {Li, R and Huang, X and Yang, L and Liang, X and Huang, W and Lai, KP and Zhou, L}, title = {Integrated Analysis Reveals the Targets and Mechanisms in Immunosuppressive Effect of Mesalazine on Ulcerative Colitis.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {867692}, pmid = {35662946}, issn = {2296-861X}, abstract = {BACKGROUND: Ulcerative colitis (UC) is an inflammatory bowel disease that causes inflammation and ulcers in the digestive tract. Approximately 3 million US adults suffer from this disease. Mesalazine, an anti-inflammatory agent, is commonly used for the treatment of UC. However, some studies have demonstrated side effects of mesalazine, such as acute pancreatitis and hypereosinophilia. Therefore, a better understanding of the anti-inflammatory mechanism of mesalazine in UC could help improve the effectiveness of the drug and reduce its side effects. In this study, we used a dextran sodium sulfate-induced UC mouse model, and applied network pharmacology and omics bioinformatics approaches to uncover the potential pharmaceutical targets and the anti-inflammatory mechanism of mesalazine.

RESULTS: Network pharmacology analysis identified the core targets of mesalazine, biological processes, and cell signaling related to immunity and inflammatory responses mediated by mesalazine. Molecular docking analysis then indicated possible binding motifs on the core targets (including TNF-α, PTGS2, IL-1β, and EGFR). Metabolomics and 16S metagenomic analyses highlighted the correlation between gut microbiota and metabolite changes caused by mesalazine in the UC model.

CONCLUSIONS: Collectively, the omics and bioinformatics approaches and the experimental data unveiled the detailed molecular mechanisms of mesalazine in UC treatment, functional regulation of the gut immune system, and reduction of intestinal inflammation. More importantly, the identified core targets could be targeted for the treatment of UC.}, } @article {pmid35662460, year = {2022}, author = {Nagpal, S and Singh, R and Taneja, B and Mande, SS}, title = {MarkerML - Marker Feature Identification in Metagenomic Datasets Using Interpretable Machine Learning.}, journal = {Journal of molecular biology}, volume = {434}, number = {11}, pages = {167589}, doi = {10.1016/j.jmb.2022.167589}, pmid = {35662460}, issn = {1089-8638}, mesh = {Datasets as Topic ; Humans ; *Internet Use ; *Machine Learning ; Metagenome ; *Metagenomics ; Reproducibility of Results ; }, abstract = {Identification of environment specific marker-features is one of the key objectives of many metagenomic studies. It aims to identify such features in microbiome datasets that may serve as markers of the contrasting or comparable states. Hypothesis testing and black-box machine learnt models which are conventionally used for identification of these features are generally not exhaustive, especially because they generally do-not provide any quantifiable relevance (context) of/between the identified features. We present MarkerML web-server, that seeks to leverage the emergence of interpretable machine learning for facilitating the contextual discovery of metagenomic features of interest. It does so through a comprehensive and automated application of the concept of Shapley Additive Explanations in companionship to the compositionality accounted hypothesis testing for the multi-variate microbiome datasets. MarkerML not only helps in identification of marker-features, but also enables insights into the role and inter-dependence of the identified features in driving the decision making of the supervised machine learnt model. Generation of high quality and intuitive visualizations spanning prediction effect plots, model performance reports, feature dependency plots, Shapley and abundance informed cladograms (Sungrams), hypothesis tested violin plots along-with necessary provisions for excluding the participant bias and ensuring reproducibility of results, further seek to make the platform a useful asset for the scientists in the field of microbiome (and even beyond). The MarkerML web-server is freely available for the academic community at https://microbiome.igib.res.in/markerml/.}, } @article {pmid35661503, year = {2022}, author = {Chen, L and Zhao, B and Palomo, A and Sun, Y and Cheng, Z and Zhang, M and Xia, Y}, title = {Micron-scale biogeography reveals conservative intra anammox bacteria spatial co-associations.}, journal = {Water research}, volume = {220}, number = {}, pages = {118640}, doi = {10.1016/j.watres.2022.118640}, pmid = {35661503}, issn = {1879-2448}, mesh = {*Ammonium Compounds/metabolism ; Anaerobic Ammonia Oxidation ; Anaerobiosis ; Bacteria/metabolism ; *Bioreactors/microbiology ; Metagenomics/methods ; Nitrogen/metabolism ; Oxidation-Reduction ; }, abstract = {Micron-scale resolution can help to reliably identify true taxon-taxon interactions in complex microbial communities. Despite widespread recognition of the critical role of metabolic interactions in anaerobic ammonium oxidation (anammox) system performance, no studies have examined microbial interactions at the micron-scale in anammox consortia. To fill this gap, we extensively sampled (totally 242 samples) the consortia of a lab-scale anammox reactor at different length scales, including bulk-scale (∼cm), macro-scale (300-500 µm) and micron-scale (70-100 µm). We firstly observed evident micron-scale heterogeneity in anammox consortia, with the relative abundance of anammox bacteria fluctuated greatly across individual clusters (2.0%-79.3%), indicating that the biotic interactions play a significant role in the assembly of anammox communities under well-controlled and well-mixed condition. Importantly, by mapping the spatial associations in anammox consortia at micron-scale, we demonstrated that the conserved co-associations for anammox bacteria were restricted to three different Brocadia species over time, and their co-associations with heterotrophs were random, implying that there was no statistically significant symbiotic interaction between anammox bacteria and other heterotrophic populations. Further metagenomic binning revealed that the quorum sensing with secondary messenger c-di-GMP potentially holding on the conservative metabolic cooperation among Brocadia species. These results shed new light on the social behavior of the anammox community. Overall, delineating of biological structures at micron-scale opens a new way of monitoring the microbial spatial structure and interactions, paving the way for improved community engineering of biotreatment systems.}, } @article {pmid35661258, year = {2022}, author = {Brandau, L and Jacksch, S and Weis, S and Schnell, S and Egert, M}, title = {Minority report: small-scale metagenomic analysis of the non-bacterial kitchen sponge microbiota.}, journal = {Archives of microbiology}, volume = {204}, number = {7}, pages = {363}, pmid = {35661258}, issn = {1432-072X}, support = {13FH197PX6//Bundesministerium für Bildung und Forschung/ ; }, mesh = {Animals ; Archaea/genetics ; Bacteria/genetics ; Metagenome ; Metagenomics ; *Microbiota/genetics ; Phylogeny ; *Porifera/genetics ; }, abstract = {Kitchen sponges are particularly well known to harbor a high number and diversity of bacteria, including pathogens. Viruses, archaea, and eukaryotes in kitchen sponges, however, have not been examined in detail so far. To increase knowledge on the non-bacterial kitchen sponge microbiota and its potential hygienic relevance, we investigated five used kitchen sponges by means of metagenomic shot-gun sequencing. Viral particles were sought to be enriched by a filter step during DNA extraction from the sponges. Data analysis revealed that ~ 2% of the sequences could be assigned to non-bacterial taxa. Each sponge harbored different virus (phage) species, while the present archaea were predominantly affiliated with halophilic taxa. Among the eukaryotic taxa, besides harmless algae, or amoebas, mainly DNA from food-left-overs was found. The presented work offers new insights into the complex microbiota of used kitchen sponges and contributes to a better understanding of their hygienic relevance.}, } @article {pmid35660864, year = {2022}, author = {Béchade, B and Hu, Y and Sanders, JG and Cabuslay, CS and Łukasik, P and Williams, BR and Fiers, VJ and Lu, R and Wertz, JT and Russell, JA}, title = {Turtle ants harbor metabolically versatile microbiomes with conserved functions across development and phylogeny.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {8}, pages = {}, doi = {10.1093/femsec/fiac068}, pmid = {35660864}, issn = {1574-6941}, mesh = {Animals ; *Ants ; Bacteria/genetics ; Dietary Fiber ; *Gastrointestinal Microbiome ; Nitrogen ; Phylogeny ; Symbiosis ; }, abstract = {Gut bacterial symbionts can support animal nutrition by facilitating digestion and providing valuable metabolites. However, changes in symbiotic roles between immature and adult stages are not well documented, especially in ants. Here, we explored the metabolic capabilities of microbiomes sampled from herbivorous turtle ant (Cephalotes sp.) larvae and adult workers through (meta)genomic screening and in vitro metabolic assays. We reveal that larval guts harbor bacterial symbionts with impressive metabolic capabilities, including catabolism of plant and fungal recalcitrant dietary fibers and energy-generating fermentation. Additionally, several members of the specialized adult gut microbiome, sampled downstream of an anatomical barrier that dams large food particles, show a conserved potential to depolymerize many dietary fibers. Symbionts from both life stages have the genomic capacity to recycle nitrogen and synthesize amino acids and B-vitamins. With help of their gut symbionts, including several bacteria likely acquired from the environment, turtle ant larvae may aid colony digestion and contribute to colony-wide nitrogen, B-vitamin and energy budgets. In addition, the conserved nature of the digestive capacities among adult-associated symbionts suggests that nutritional ecology of turtle ant colonies has long been shaped by specialized, behaviorally-transferred gut bacteria with over 45 million years of residency.}, } @article {pmid35660621, year = {2022}, author = {He, J and Zhang, N and Shen, X and Muhammad, A and Shao, Y}, title = {Deciphering environmental resistome and mobilome risks on the stone monument: A reservoir of antimicrobial resistance genes.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 3}, pages = {156443}, doi = {10.1016/j.scitotenv.2022.156443}, pmid = {35660621}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {Antimicrobial resistance (AMR) in the environment has attracted increasing attention as an emerging global threat to public health. Stone is an essential ecosystem in nature and also an important material for human society, having architectural and aesthetic values. However, little is known about the AMR in stone ecosystems, particularly in the stone monument, where antimicrobials are often applied against biodeterioration. Here, we provide the first detailed metagenomic study of AMR genes across different types of biodeteriorated stone monuments, which revealed abundant and diverse AMR genes conferring resistance to drugs (antibiotics), biocides, and metals. Totally, 132 AMR subtypes belonging to 27 AMR types were detected including copper-, rifampin-, and aminocoumarins-resistance genes, of which diversity was mainly explained by the spatial turnover (replacement of genes between samples) rather than nestedness (loss of nested genes between samples). Source track analysis confirms that stone resistomes are likely driven by anthropogenic activities across stone heritage areas. We also detected various mobile genetic elements (namely mobilome, e.g., prophages, plasmids, and insertion sequences) that could accelerate replication and horizontal transfer of AMR genes. Host-tracking analysis further identified multiple biodeterioration-related bacterial genera such as Pseudonocardia, Sphingmonas, and Streptomyces as the major hosts of resistome. Taken together, these findings highlight that stone microbiota is one of the natural reservoirs of antimicrobial-resistant hazards, and the diverse resistome and mobilome carried by active biodeteriogens may improve their adaptation on stone and even deactivate the antimicrobials applied against biodeterioration. This enhanced knowledge may also provide novel and specific avenues for environmental management and stone heritage protection.}, } @article {pmid35660592, year = {2022}, author = {Chen, J and Liu, C and Teng, Y and Zhao, S and Chen, H}, title = {The combined effect of an integrated reclaimed water system on the reduction of antibiotic resistome.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 3}, pages = {156426}, doi = {10.1016/j.scitotenv.2022.156426}, pmid = {35660592}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/analysis ; Drug Resistance, Microbial/genetics ; *Genes, Bacterial ; Metagenomics/methods ; Water ; }, abstract = {The reuse of urban reclaimed water is conducive to alleviate the current serious shortage of water resources. However, antibiotic resistance genes (ARGs) in reclaimed water have received widespread attention due to their potential risks to public health. Deciphering the fate of ARGs in reclaimed water benefits the development of effective strategies to control resistome risk and guarantees the safety of water supply of reclaimed systems. In this study, the characteristics of ARGs in an integrated reclaimed water system (sewage treatment plant-constructed wetland, STP-CW) in Beijing (China) have been identified using metagenomic assembly-based analysis, as well as the combined effect of the STP-CW system on the reduction of antibiotic resistome. Results showed a total of 29 ARG types and 813 subtypes were found in the reclaimed water system. As expected, the STP-CW system improved the removal of ARGs, and about 58% of ARG subtypes were removed from the effluent of the integrated STP-CW system, which exceeded 43% for the STP system and 37% for the CW system. Although the STP-CW system had a great removal on ARGs, abundant and diverse ARGs were still found in the downstream river. Importantly, network analysis revealed the co-occurrence of ARGs, mobile genetic elements and virulence factors in the downstream water, implying potential resistome dissemination risk in the environment. Source identification with SourceTracker showed the STP-effluent was the largest contributor of ARGs in the downstream river, with a contribution of 45%. Overall, the integrated STP-CW system presented a combined effect on the reduction of antibiotic resistome, however, the resistome dissemination risk was still non-negligible in the downstream reclaimed water. This study provides a comprehensive analysis on the fate of ARGs in the STP-CW-river system, which would benefit the development of effective strategies to control resistome risk for the reuse of reclaimed water.}, } @article {pmid35660421, year = {2022}, author = {Low, L and Nakamichi, K and Akileswaran, L and Lee, CS and Lee, AY and Moussa, G and Murray, PI and Wallace, GR and Van Gelder, RN and Rauz, S and , }, title = {Deep Metagenomic Sequencing for Endophthalmitis Pathogen Detection Using a Nanopore Platform.}, journal = {American journal of ophthalmology}, volume = {242}, number = {}, pages = {243-251}, pmid = {35660421}, issn = {1879-1891}, support = {R01 AG060942/AG/NIA NIH HHS/United States ; /DH_/Department of Health/United Kingdom ; U19 AG066567/AG/NIA NIH HHS/United States ; MR/N019016/1/MRC_/Medical Research Council/United Kingdom ; K23 EY029246/EY/NEI NIH HHS/United States ; }, mesh = {Aged ; Aged, 80 and over ; Cross-Sectional Studies ; *Endophthalmitis/diagnosis ; Humans ; Male ; Metagenomics/methods ; Middle Aged ; *Nanopores ; RNA, Ribosomal, 16S/genetics ; }, abstract = {PURPOSE: To evaluate the utility of nanopore sequencing for identifying potential causative pathogens in endophthalmitis, comparing culture results against full-length 16S rRNA nanopore sequencing (16S Nanopore), whole genome nanopore sequencing (Nanopore WGS), and Illumina (Illumina WGS).

DESIGN: Cross-sectional diagnostic comparison.

METHODS: Patients with clinically suspected endophthalmitis underwent intraocular vitreous biopsy as per standard care. Clinical samples were cultured by conventional methods, together with full-length 16S rRNA and WGS using nanopore and Illumina sequencing platforms.

RESULTS: Of 23 patients (median age 68.5 years [range 47-88]; 14 males [61%]), 18 cases were culture-positive. Nanopore sequencing identified the same cultured organism in all of the culture-positive cases and identified potential pathogens in two culture-negative cases (40%). Nanopore WGS was able to additionally detect the presence of bacteriophages in three samples. The agreements at genus level between culture and 16S Nanopore, Nanopore WGS, and Illumina WGS were 75%, 100%, and 78%, respectively.

CONCLUSIONS: Whole genome sequencing has higher sensitivity and provides a viable alternative to culture and 16S sequencing for detecting potential pathogens in endophthalmitis. Moreover, WGS has the ability to detect other potential pathogens in culture-negative cases. Whilst Nanopore and Illumina WGS provide comparable data, nanopore sequencing provides potential for cost-effective point-of-care diagnostics.}, } @article {pmid35660194, year = {2022}, author = {Malla, MA and Dubey, A and Kumar, A and Yadav, S}, title = {Metagenomic analysis displays the potential predictive biodegradation pathways of the persistent pesticides in agricultural soil with a long record of pesticide usage.}, journal = {Microbiological research}, volume = {261}, number = {}, pages = {127081}, doi = {10.1016/j.micres.2022.127081}, pmid = {35660194}, issn = {1618-0623}, mesh = {Bacteria/genetics/metabolism ; Biodegradation, Environmental ; Metagenome ; *Pesticides/analysis/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Soil ; Soil Microbiology ; *Soil Pollutants/metabolism ; }, abstract = {Microbes are crucial in removing various xenobiotics, including pesticides, from the environment, specifically by mineralizing these hazardous pollutants. However, the specific procedure of microbe-mediated pesticide degradation and its consequence on the environment remain elusive owing to limitations in culturing techniques. Therefore, in this study, we have investigated i) the physicochemical and elemental compositions of PCAS (pesticide-contaminated agricultural soils) and NS (natural soils); ii) the bacterial communities and degradation pathways, as well as some novel biodegradation genes (BDGs) and pesticide degradation genes (PDGs) across two different landscapes (PCAS and NS) by applying high-throughput sequencing. The chemical and elemental composition analyses showed that all nutrients (P, K, N, S, Mn, B, and Zn) were significantly higher in PCAS than in NS (p ≤ 0.05). The results of the 16S rRNA amplicon sequencing analysis of pesticide-contaminated (PCAS-1, PCAS-2, PCAS-3, PCAS-4) samples showed that the relative abundance of the phylum Proteobacteria (30-36%) > Actinobacteria (15-20%) > Firmicutes (13-14%) > Bacteroidetes (7-13%), were higher compared to the natural soil (NS-1, NS2). Consistent with this, a phylogenetic shift was observed with (alpha, beta, and gamma Proteobacteria) being abundant in PCAS, whereas delta and epsilon groups were more prevalent in NS. The functional characterization of the PCAS and NS by PICRUSt2 revealed that bacterial communities play a significant role in pesticide metabolism. Predictive metagenome analysis of contaminated soils showed the role of core degrading genes in membrane transport, stress response, regulatory genes, resource transport, and environmental sensing. Furthermore, 14 BDGs and 30 PDGs were examined, with a relative abundance of 0.081-1.029 % and 0.107-0.8903 % in each PCAS, respectively. The major BDGs and PDGs, with the compounds they hydrolyze, include ppo (polyphenol oxidase and laccase), CYP (cytochrome p450 protein), lip gene (lignin peroxidase), similarly, among the PDGs mhel (carbendazim), opd (organophosphate), mpd (methyl parathion), atzA, atzB, atzD, atzF and trzN (atrazine), chd (chlorothalonil), hdx (metamitron), hdl-1 (isoproturon) and fmo (nicosulfuron). Overall, our findings demonstrated the significance of utilizing metagenomic methods to predict microbial aided degradation in the ecology of contaminated environments.}, } @article {pmid35659906, year = {2022}, author = {Ducarmon, QR and Zwittink, RD and Willems, RPJ and Verhoeven, A and Nooij, S and van der Klis, FRM and Franz, E and Kool, J and Giera, M and Vandenbroucke-Grauls, CMJE and Fuentes, S and Kuijper, EJ}, title = {Gut colonisation by extended-spectrum β-lactamase-producing Escherichia coli and its association with the gut microbiome and metabolome in Dutch adults: a matched case-control study.}, journal = {The Lancet. Microbe}, volume = {3}, number = {6}, pages = {e443-e451}, doi = {10.1016/S2666-5247(22)00037-4}, pmid = {35659906}, issn = {2666-5247}, mesh = {Adult ; Anti-Bacterial Agents/pharmacology ; Bacteria/metabolism ; Case-Control Studies ; Cross-Sectional Studies ; *Escherichia coli/genetics ; Ethnicity ; *Gastrointestinal Microbiome/genetics ; Humans ; Metabolome ; beta-Lactamases/genetics ; }, abstract = {BACKGROUND: Gut colonisation by extended-spectrum β-lactamase (ESBL)-producing Escherichia coli is a risk factor for developing overt infection. The gut microbiome can provide colonisation resistance against enteropathogens, but it remains unclear whether it confers resistance against ESBL-producing E coli. We aimed to identify a potential role of the microbiome in controlling colonisation by this antibiotic-resistant bacterium.

METHODS: For this matched case-control study, we used faeces from 2751 individuals in a Dutch cross-sectional population study (PIENTER-3) to culture ESBL-producing bacteria. Of these, we selected 49 samples that were positive for an ESBL-producing E coli (ESBL-positive) and negative for several variables known to affect microbiome composition. These samples were matched 1:1 to ESBL-negative samples on the basis of individuals' age, sex, having been abroad or not in the past 6 months, and ethnicity. Shotgun metagenomic sequencing was done and taxonomic species composition and functional annotations (ie, microbial metabolism and carbohydrate-active enzymes) were determined. Targeted quantitative metabolic profiling (proton nuclear magnetic resonance spectroscopy) was done to investigate metabolomic profiles and combinations of univariate (t test and Wilcoxon test), multivariate (principal coordinates analysis, permutational multivariate analysis of variance, and partial least-squares discriminant analysis) and machine-learning approaches (least absolute shrinkage and selection operator and random forests) were used to analyse all the molecular data.

FINDINGS: No differences in diversity parameters or in relative abundance were observed between ESBL-positive and ESBL-negative groups based on bacterial species-level composition. Machine-learning approaches using microbiota composition did not accurately predict ESBL status (area under the receiver operating characteristic curve [AUROC]=0·41) when using either microbiota composition or any of the functional profiles. The metabolome also did not differ between ESBL groups, as assessed by various methods including random forest (AUROC=0·61).

INTERPRETATION: By combining multiomics and machine-learning approaches, we conclude that asymptomatic gut carriage of ESBL-producing E coli is not associated with an altered microbiome composition or function. This finding might suggest that microbiome-mediated colonisation resistance against ESBL-producing E coli is not as relevant as it is against other enteropathogens and antibiotic-resistant bacteria.

FUNDING: None.}, } @article {pmid35659862, year = {2022}, author = {Chen, H and Mayer, A and Balasubramanian, V}, title = {A scaling law in CRISPR repertoire sizes arises from the avoidance of autoimmunity.}, journal = {Current biology : CB}, volume = {32}, number = {13}, pages = {2897-2907.e5}, doi = {10.1016/j.cub.2022.05.021}, pmid = {35659862}, issn = {1879-0445}, mesh = {*Autoimmunity ; *Bacteriophages/genetics ; CRISPR-Cas Systems ; }, abstract = {Some prokaryotes possess CRISPR-Cas systems that use DNA segments called spacers, which are acquired from invading phages, to guide immune defense. Here, we propose that cross-reactive CRISPR targeting can, however, lead to "heterologous autoimmunity," whereby foreign spacers guide self-targeting in a spacer-length-dependent fashion. Balancing antiviral defense against autoimmunity predicts a scaling relation between spacer length and CRISPR repertoire size. We find evidence for this scaling through a comparative analysis of sequenced prokaryotic genomes and show that this association also holds at the level of CRISPR types. By contrast, the scaling is absent in strains with nonfunctional CRISPR loci. Finally, we demonstrate that stochastic spacer loss can explain variations around the scaling relation, even between strains of the same species. Our results suggest that heterologous autoimmunity is a selective factor shaping the evolution of CRISPR-Cas systems, analogous to the trade-offs between immune specificity, breadth, and autoimmunity that constrain the diversity of adaptive immune systems in vertebrates.}, } @article {pmid35659381, year = {2022}, author = {Ma, T and Zaheer, R and McAllister, TA and Guo, W and Li, F and Tu, Y and Diao, Q and Guan, LL}, title = {Expressions of resistome is linked to the key functions and stability of active rumen microbiome.}, journal = {Animal microbiome}, volume = {4}, number = {1}, pages = {38}, pmid = {35659381}, issn = {2524-4671}, support = {Y2022QC10//Central Public-interest Scientific Institution Basal Research Fund/ ; 2015P008R//Ministry of Agriculture, Forestry and Fisheries/ ; 2018F095R//Ministry of Agriculture, Forestry and Fisheries/ ; 'Omics'//Genome Alberta/ ; CAAS-ASTIP-2017-FRI-04//Agricultural Science and Technology Innovation Program/ ; }, abstract = {BACKGROUND: The resistome describes the array of antibiotic resistant genes (ARGs) present within a microbial community. Recent research has documented the resistome in the rumen of ruminants and revealed that the type and abundance of ARGs could be affected by diet and/or antibiotic treatment. However, most of these studies only assessed ARGs using metagenomics, and expression of the resistome and its biological function within the microbiome remains largely unexplored.

RESULTS: We characterized the pools of ARGs (resistome) and their activities in the rumen of 48 beef cattle belonging to three breeds (Angus, Charolais, Kinsella composite hybrid), using shotgun metagenomics and metatranscriptomics. Sixty (including 20 plasmid-associated) ARGs were expressed which accounted for about 30% of the total number of ARGs (187) identified in metagenomic datasets, with tetW and mefA exhibiting the highest level of expression. In addition, the bacterial hosts of 17 expressed ARGs were identified. The active resistome was less diverse in Kinsella composite hybrid than Angus, however, expression of ARGs did not differ among breeds. Although not associated with feed efficiency, the total abundance of expressed ARGs was positively correlated with metabolic pathways and 'attenuation values' (a measurement of stability) of the active rumen microbiome, suggesting that ARGs expression influences the stability and functionality of the rumen microbiome. Moreover, Ruminococcus spp., Prevotella ruminicola, Muribaculaceae spp. and Collinsella aerofaciens were all identified as hosts of expressed ARGs, possibly promoting the dominance of these carbohydrate degraders within the rumen microbiome.

CONCLUSIONS: Findings from this study provide new insight into the active rumen resistome in vivo, which may inform strategies to limit the spread of ubiquitously found ARGs from the rumen to the broader environment without negatively impacting the key functional outcomes of the rumen microbiome.}, } @article {pmid35659305, year = {2022}, author = {Chiriac, MC and Bulzu, PA and Andrei, AS and Okazaki, Y and Nakano, SI and Haber, M and Kavagutti, VS and Layoun, P and Ghai, R and Salcher, MM}, title = {Ecogenomics sheds light on diverse lifestyle strategies in freshwater CPR.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {84}, pmid = {35659305}, issn = {2049-2618}, mesh = {Animals ; Bacteria ; In Situ Hybridization, Fluorescence ; Lakes/microbiology ; *Metagenome/genetics ; *Metagenomics ; Phylogeny ; }, abstract = {BACKGROUND: The increased use of metagenomics and single-cell genomics led to the discovery of organisms from phyla with no cultivated representatives and proposed new microbial lineages such as the candidate phyla radiation (CPR or Patescibacteria). These bacteria have peculiar ribosomal structures, reduced metabolic capacities, small genome, and cell sizes, and a general host-associated lifestyle was proposed for the radiation. So far, most CPR genomes were obtained from groundwaters; however, their diversity, abundance, and role in surface freshwaters is largely unexplored. Here, we attempt to close these knowledge gaps by deep metagenomic sequencing of 119 samples of 17 different freshwater lakes located in Europe and Asia. Moreover, we applied Fluorescence in situ Hybridization followed by Catalyzed Reporter Deposition (CARD-FISH) for a first visualization of distinct CPR lineages in freshwater samples.

RESULTS: A total of 174 dereplicated metagenome-assembled genomes (MAGs) of diverse CPR lineages were recovered from the investigated lakes, with a higher prevalence from hypolimnion samples (162 MAGs). They have reduced genomes (median size 1 Mbp) and were generally found in low abundances (0.02-14.36 coverage/Gb) and with estimated slow replication rates. The analysis of genomic traits and CARD-FISH results showed that the radiation is an eclectic group in terms of metabolic capabilities and potential lifestyles, ranging from what appear to be free-living lineages to host- or particle-associated groups. Although some complexes of the electron transport chain were present in the CPR MAGs, together with ion-pumping rhodopsins and heliorhodopsins, we believe that they most probably adopt a fermentative metabolism. Terminal oxidases might function in O2 scavenging, while heliorhodopsins could be involved in mitigation against oxidative stress.

CONCLUSIONS: A high diversity of CPR MAGs was recovered, and distinct CPR lineages did not seem to be limited to lakes with specific trophic states. Their reduced metabolic capacities resemble the ones described for genomes in groundwater and animal-associated samples, apart from Gracilibacteria that possesses more complete metabolic pathways. Even though this radiation is mostly host-associated, we also observed organisms from different clades (ABY1, Paceibacteria, Saccharimonadia) that appear to be unattached to any other organisms or were associated with 'lake snow' particles (ABY1, Gracilibacteria), suggesting a broad range of potential life-strategies in this phylum. Video Abstract.}, } @article {pmid35658830, year = {2022}, author = {Kastl, A and Zong, W and Gershuni, VM and Friedman, ES and Tanes, C and Boateng, A and Mitchell, WJ and O'Connor, K and Bittinger, K and Terry, NA and Bales, C and Albenberg, L and Wu, GD}, title = {Dietary fiber-based regulation of bile salt hydrolase activity in the gut microbiota and its relevance to human disease.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2083417}, pmid = {35658830}, issn = {1949-0984}, support = {P30 DK050306/DK/NIDDK NIH HHS/United States ; T32 AI118684/AI/NIAID NIH HHS/United States ; }, mesh = {Amidohydrolases/metabolism ; Animals ; Bile Acids and Salts ; Dietary Fiber ; *Gastrointestinal Microbiome/physiology ; Humans ; Mice ; }, abstract = {Complications of short bowel syndrome (SBS) include malabsorption and bacterial overgrowth, requiring prolonged dependence on parenteral nutrition (PN). We hypothesized that the intolerance of whole food in some SBS patients might be due to the effect of dietary fiber on the gut microbiome. Shotgun metagenomic sequencing and targeted metabolomics were performed using biospecimens collected from 55 children with SBS and a murine dietary fiber model. Bioinformatic analyses were performed on these datasets as well as from a healthy human dietary intervention study. Compared to healthy controls, the gut microbiota in SBS had lower diversity and increased Proteobacteria, a pattern most pronounced in children on PN and inversely correlated with whole food consumption. Whole food intake correlated with increased glycoside hydrolases (GH) and bile salt hydrolases (BSH) with reduced fecal conjugated bile acids suggesting that dietary fiber regulates BSH activity via GHs. Mechanistic evidence supporting this notion was generated via fecal and plasma bile acid profiling in a healthy human fiber-free dietary intervention study as well as in a dietary fiber mouse experiment. Gaussian mixture modeling of fecal bile acids was used to identify three clinically relevant SBS phenotypes. Dietary fiber is associated with bile acid deconjugation likely via an interaction between gut microbiota BSHs and GHs in the small intestine, which may lead to whole food intolerance in patients with SBS. This mechanism not only has potential utility in clinical phenotyping and targeted therapeutics in SBS based on bile acid metabolism but may have relevance to other intestinal disease states.}, } @article {pmid35658355, year = {2022}, author = {, and , }, title = {[Expert consensus on the application of metagenomics next-generation sequencing in neonatal infectious diseases].}, journal = {Zhonghua er ke za zhi = Chinese journal of pediatrics}, volume = {60}, number = {6}, pages = {516-521}, doi = {10.3760/cma.j.cn112140-20220113-00046}, pmid = {35658355}, issn = {0578-1310}, mesh = {*Communicable Diseases/diagnosis/genetics ; Consensus ; High-Throughput Nucleotide Sequencing ; Humans ; Infant, Newborn ; *Infant, Newborn, Diseases/diagnosis/genetics ; Metagenomics ; }, } @article {pmid35657930, year = {2022}, author = {Anye, V and Kruger, RF and Schubert, WD}, title = {Structural and biophysical characterization of the multidomain xylanase Xyl.}, journal = {PloS one}, volume = {17}, number = {6}, pages = {e0269188}, pmid = {35657930}, issn = {1932-6203}, mesh = {Animals ; Endo-1,4-beta Xylanases/chemistry/genetics ; Glycoside Hydrolases/genetics ; Humans ; *Isoptera ; Metagenome ; *Xylans ; }, abstract = {The depletion of fossil fuels, associated pollution, and resulting health hazards are of concern worldwide. Woody biomass constitutes an alternative source of cleaner and renewable energy. The efficient use of woody biomass depends on xylan depolymerisation as the endo-β-1,4-xylopyranosyl homopolymer is the main component of hemicellulose, the second most abundant component of wood. Xylan depolymerisation is achieved by hemicellulolytic xylanases of glycoside hydrolase (GH) families 5, 8, 10, 11, 30 and 43 of the CAZY database. We analysed a multidomain xylanase (Xyl) from the hindgut metagenome of the snouted harvester termite Trinervitermes trinervoides that releases xylobiose and xylotriose from beech and birch xylan and wheat arabinoxylan. The four domains of Xyl include an N-terminal GH11 xylanase domain, two family 36-like carbohydrate-binding domains CBM36-1 and 2, and a C-terminal CE4 esterase domain. Previous analyses indicated that CBM36-1 deletion slightly increased GH11 catalysis at low pH whereas removal of both CBMs decreased xylanase activity at 60°C from 90 to 56%. Possible cooperativity between the domains suggested by these observations was explored. A crystal structure of the two-domain construct, GH11-CBM36-1, confirmed the structure of the GH11 domain whereas the CBM36-1 domain lacked electron density, possibly indicating a random orientation of the CBM36-1 domain around the GH11 domain. Isothermal titration calorimetry (ITC) experiments similarly did not indicate specific interactions between the individual domains of Xyl supporting a "beads-on-a-string" model for Xyl domains.}, } @article {pmid35657425, year = {2023}, author = {Meena, M and Yadav, G and Sonigra, P and Nagda, A and Mehta, T and Swapnil, P and Harish, and Marwal, A and Kumar, S}, title = {Multifarious Responses of Forest Soil Microbial Community Toward Climate Change.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {49-74}, pmid = {35657425}, issn = {1432-184X}, mesh = {*Ecosystem ; Climate Change ; Soil/chemistry ; Forests ; *Microbiota ; Nitrogen/analysis ; Soil Microbiology ; Carbon ; }, abstract = {Forest soils are a pressing subject of worldwide research owing to the several roles of forests such as carbon sinks. Currently, the living soil ecosystem has become dreadful as a consequence of several anthropogenic activities including climate change. Climate change continues to transform the living soil ecosystem as well as the soil microbiome of planet Earth. The majority of studies have aimed to decipher the role of forest soil bacteria and fungi to understand and predict the impact of climate change on soil microbiome community structure and their ecosystem in the environment. In forest soils, microorganisms live in diverse habitats with specific behavior, comprising bulk soil, rhizosphere, litter, and deadwood habitats, where their communities are influenced by biotic interactions and nutrient accessibility. Soil microbiome also drives multiple crucial steps in the nutrient biogeochemical cycles (carbon, nitrogen, phosphorous, and sulfur cycles). Soil microbes help in the nitrogen cycle through nitrogen fixation during the nitrogen cycle and maintain the concentration of nitrogen in the atmosphere. Soil microorganisms in forest soils respond to various effects of climate change, for instance, global warming, elevated level of CO2, drought, anthropogenic nitrogen deposition, increased precipitation, and flood. As the major burning issue of the globe, researchers are facing the major challenges to study soil microbiome. This review sheds light on the current scenario of knowledge about the effect of climate change on living soil ecosystems in various climate-sensitive soil ecosystems and the consequences for vegetation-soil-climate feedbacks.}, } @article {pmid35656865, year = {2022}, author = {Eiamthong, B and Meesawat, P and Wongsatit, T and Jitdee, J and Sangsri, R and Patchsung, M and Aphicho, K and Suraritdechachai, S and Huguenin-Dezot, N and Tang, S and Suginta, W and Paosawatyanyong, B and Babu, MM and Chin, JW and Pakotiprapha, D and Bhanthumnavin, W and Uttamapinant, C}, title = {Discovery and Genetic Code Expansion of a Polyethylene Terephthalate (PET) Hydrolase from the Human Saliva Metagenome for the Degradation and Bio-Functionalization of PET.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {61}, number = {37}, pages = {e202203061}, pmid = {35656865}, issn = {1521-3773}, support = {217249/WT_/Wellcome Trust/United Kingdom ; MC_U105181009/MRC_/Medical Research Council/United Kingdom ; 217249/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Genetic Code ; Humans ; *Hydrolases/metabolism ; Metagenome ; Plastics/chemistry ; *Polyethylene Terephthalates/chemistry ; Saliva/metabolism ; }, abstract = {We report a bioinformatic workflow and subsequent discovery of a new polyethylene terephthalate (PET) hydrolase, which we named MG8, from the human saliva metagenome. MG8 has robust PET plastic degradation activities under different temperature and salinity conditions, outperforming several naturally occurring and engineered hydrolases in degrading PET. Moreover, we genetically encoded 2,3-diaminopropionic acid (DAP) in place of the catalytic serine residue of MG8, thereby converting a PET hydrolase into a covalent binder for bio-functionalization of PET. We show that MG8(DAP), in conjunction with a split green fluorescent protein system, can be used to attach protein cargos to PET as well as other polyester plastics. The discovery of a highly active PET hydrolase from the human metagenome-currently an underexplored resource for industrial enzyme discovery-as well as the repurposing of such an enzyme into a plastic functionalization tool, should facilitate ongoing efforts to degrade and maximize reusability of PET.}, } @article {pmid35655999, year = {2022}, author = {Iquebal, MA and Jagannadham, J and Jaiswal, S and Prabha, R and Rai, A and Kumar, D}, title = {Potential Use of Microbial Community Genomes in Various Dimensions of Agriculture Productivity and Its Management: A Review.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {708335}, pmid = {35655999}, issn = {1664-302X}, abstract = {Agricultural productivity is highly influenced by its associated microbial community. With advancements in omics technology, metagenomics is known to play a vital role in microbial world studies by unlocking the uncultured microbial populations present in the environment. Metagenomics is a diagnostic tool to target unique signature loci of plant and animal pathogens as well as beneficial microorganisms from samples. Here, we reviewed various aspects of metagenomics from experimental methods to techniques used for sequencing, as well as diversified computational resources, including databases and software tools. Exhaustive focus and study are conducted on the application of metagenomics in agriculture, deciphering various areas, including pathogen and plant disease identification, disease resistance breeding, plant pest control, weed management, abiotic stress management, post-harvest management, discoveries in agriculture, source of novel molecules/compounds, biosurfactants and natural product, identification of biosynthetic molecules, use in genetically modified crops, and antibiotic-resistant genes. Metagenomics-wide association studies study in agriculture on crop productivity rates, intercropping analysis, and agronomic field is analyzed. This article is the first of its comprehensive study and prospects from an agriculture perspective, focusing on a wider range of applications of metagenomics and its association studies.}, } @article {pmid35655997, year = {2022}, author = {Tchoupou Saha, OF and Dubourg, G and Yacouba, A and Bossi, V and Raoult, D and Lagier, JC}, title = {Profile of the Nasopharyngeal Microbiota Affecting the Clinical Course in COVID-19 Patients.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {871627}, pmid = {35655997}, issn = {1664-302X}, abstract = {While populations at risk for severe SARS-CoV-2 infections have been clearly identified, susceptibility to the infection and its clinical course remain unpredictable. As the nasopharyngeal microbiota may promote the acquisition of several respiratory infections and have an impact on the evolution of their outcome, we studied the nasopharyngeal microbiota of COVID-19 patients in association with baseline disease-related clinical features compared to that of patients tested negative. We retrospectively analyzed 120 nasopharyngeal pseudonymized samples, obtained for diagnosis, divided into groups (infected patients with a favorable outcome, asymptomatic, and deceased patients) and patients tested negative for SARS-CoV-2, by using Illumina-16S ribosomal ribonucleic acid (rRNA) sequencing and specific polymerase chain reaction (PCR) targeting pathogens. We first found a depletion of anaerobes among COVID-19 patients, irrespective of the clinical presentation of the infection (p < 0.029). We detected 9 taxa discriminating patients tested positive for SARS-CoV-2 from those that were negative including Corynebacterium propinquum/pseudodiphtericum (p ≤ 0.05), Moraxella catarrhalis (p ≤ 0.05), Bacillus massiliamazoniensis (p ≤ 0.01), Anaerobacillus alkalidiazotrophicus (p ≤ 0.05), Staphylococcus capitis subsp. capitis (p ≤ 0.001), and Afipia birgiae (p ≤ 0.001) with 16S rRNA sequencing, and Streptococcus pneumoniae (p ≤ 0.01), Klebsiella pneumoniae (p ≤ 0.01), and Enterococcus faecalis (p ≤ 0.05) using real-time PCR. By designing a specific real-time PCR, we also demonstrated that C. propinquum is decreased in asymptomatic individuals compared to other SARS-CoV 2 positive patients. These findings indicate that the nasopharyngeal microbiota as in any respiratory infection plays a role in the clinical course of the disease. Further studies are needed to elucidate the potential role in the clinical course of the disease of M. catarrhalis, Corynebacterium accolens, and more specifically Corynebacterium propinquum/diphteriticum in order to include them as predictors of the severity of COVID-19.}, } @article {pmid35655992, year = {2022}, author = {Zhang, L and Huang, W and Zhang, S and Li, Q and Wang, Y and Chen, T and Jiang, H and Kong, D and Lv, Q and Zheng, Y and Ren, Y and Liu, P and Jiang, Y and Chen, Y}, title = {Rapid Detection of Bacterial Pathogens and Antimicrobial Resistance Genes in Clinical Urine Samples With Urinary Tract Infection by Metagenomic Nanopore Sequencing.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {858777}, pmid = {35655992}, issn = {1664-302X}, abstract = {Urinary tract infections (UTIs) are among the most common acquired bacterial infections in humans. The current gold standard method for identification of uropathogens in clinical laboratories is cultivation. However, culture-based assays have substantial drawbacks, including long turnaround time and limited culturability of many potential pathogens. Nanopore sequencing technology can overcome these limitations and detect pathogens while also providing reliable predictions of drug susceptibility in clinical samples. Here, we optimized a metagenomic nanopore sequencing (mNPS) test for pathogen detection and identification in urine samples of 76 patients with acute uncomplicated UTIs. We first used twenty of these samples to show that library preparation by the PCR Barcoding Kit (PBK) led to the highest agreement of positive results with gold standard clinical culture tests, and enabled antibiotic resistance detection in downstream analyses. We then compared the detection results of mNPS with those of culture-based diagnostics and found that mNPS sensitivity and specificity of detection were 86.7% [95% confidence interval (CI), 73.5-94.1%] and 96.8% (95% CI, 82.4-99.9%), respectively, indicating that the mNPS method is a valid approach for rapid and specific detection of UTI pathogens. The mNPS results also performed well at predicting antibiotic susceptibility phenotypes. These results demonstrate that our workflow can accurately diagnose UTI-causative pathogens and enable successful prediction of drug-resistant phenotypes within 6 h of sample receipt. Rapid mNPS testing is thus a promising clinical diagnostic tool for infectious diseases, based on clinical urine samples from UTI patients, and shows considerable potential for application in other clinical infections.}, } @article {pmid35655708, year = {2022}, author = {Tomita, Y and Goto, Y and Sakata, S and Imamura, K and Minemura, A and Oka, K and Hayashi, A and Jodai, T and Akaike, K and Anai, M and Hamada, S and Iyama, S and Saruwatari, K and Saeki, S and Takahashi, M and Ikeda, T and Sakagami, T}, title = {Clostridium butyricum therapy restores the decreased efficacy of immune checkpoint blockade in lung cancer patients receiving proton pump inhibitors.}, journal = {Oncoimmunology}, volume = {11}, number = {1}, pages = {2081010}, pmid = {35655708}, issn = {2162-402X}, mesh = {*Carcinoma, Non-Small-Cell Lung/drug therapy ; *Clostridium butyricum ; Humans ; Immune Checkpoint Inhibitors/pharmacology/therapeutic use ; *Lung Neoplasms/drug therapy ; Neoplasm Recurrence, Local ; Proton Pump Inhibitors/adverse effects ; Retrospective Studies ; }, abstract = {Oral microbiota is associated with human diseases including cancer. Emerging evidence suggests that proton pump inhibitors (PPIs), which allow the oral microbiome to translocate into the gut, negatively influence the efficacy of immune checkpoint blockade (ICB) in cancer patients. However, currently there is no effective treatment that restores the decreased efficacy. To address this issue, we retrospectively evaluated 118 advanced or recurrent non-small cell lung cancer (NSCLC) patients treated with ICB and analyzed 80 fecal samples of patients with lung cancer by 16S metagenomic sequencing. Clostridium butyricum therapy using C. butyricum MIYAIRI 588 (CBM588), a live biotherapeutic bacterial strain, was shown to improve the ICB efficacy in lung cancer. Thus, we investigated how CBM588 affects the efficacy of ICB and the gut microbiota of lung cancer patients undergoing PPI treatment. We found that PPI treatment significantly decreased the efficacy of ICB in NSCLC patients, however, CBM588 significantly restored the diminished efficacy of ICB and improved survival. In addition, CBM588 prolonged overall survival in patients receiving PPIs and antibiotics together. The fecal analysis revealed that PPI users had higher abundance of harmful oral-related pathobionts and lower abundance of beneficial gut bacteria for immunotherapy. In contrast, patients who received CBM588 had lesser relative abundance of potentially harmful oral-related bacteria in the gut. Our research suggests that manipulating commensal microbiota by CBM588 may improve the therapeutic efficacy of ICB in cancer patients receiving PPIs, highlighting the potential of oral-related microbiota in the gut as a new therapeutic target for cancer immunotherapy.}, } @article {pmid35655338, year = {2022}, author = {Queiroz, VF and Rodrigues, RAL and de Miranda Boratto, PV and La Scola, B and Andreani, J and Abrahão, JS}, title = {Amoebae: Hiding in Plain Sight: Unappreciated Hosts for the Very Large Viruses.}, journal = {Annual review of virology}, volume = {9}, number = {1}, pages = {79-98}, doi = {10.1146/annurev-virology-100520-125832}, pmid = {35655338}, issn = {2327-0578}, mesh = {*Amoeba ; DNA Viruses/genetics ; Genome, Viral ; *Giant Viruses/genetics ; Humans ; Metagenomics ; Phylogeny ; *Viruses/genetics ; }, abstract = {For decades, viruses have been isolated primarily from humans and other organisms. Interestingly, one of the most complex sides of the virosphere was discovered using free-living amoebae as hosts. The discovery of giant viruses in the early twenty-first century opened a new chapter in the field of virology. Giant viruses are included in the phylum Nucleocytoviricota and harbor large and complex DNA genomes (up to 2.7 Mb) encoding genes never before seen in the virosphere and presenting gigantic particles (up to 1.5 μm). Different amoebae have been used to isolate and characterize a plethora of new viruses with exciting details about novel viral biology. Through distinct isolation techniques and metagenomics, the diversity and complexity of giant viruses have astonished the scientific community. Here, we discuss the latest findings on amoeba viruses and how using these single-celled organisms as hosts has revealed entities that have remained hidden in plain sight for ages.}, } @article {pmid35655189, year = {2022}, author = {Freeman, CN and Herman, EK and Abi Younes, J and Ramsay, DE and Erikson, N and Stothard, P and Links, MG and Otto, SJG and Waldner, C}, title = {Evaluating the potential of third generation metagenomic sequencing for the detection of BRD pathogens and genetic determinants of antimicrobial resistance in chronically ill feedlot cattle.}, journal = {BMC veterinary research}, volume = {18}, number = {1}, pages = {211}, pmid = {35655189}, issn = {1746-6148}, support = {BCRC_POC.04.18//Beef Cattle Research Council/ ; BCRC_POC.04.18//Beef Cattle Research Council/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents ; Cattle ; *Cattle Diseases/diagnosis/drug therapy/microbiology ; Chronic Disease ; Drug Resistance, Bacterial/genetics ; Reproducibility of Results ; }, abstract = {BACKGROUND: Bovine respiratory disease (BRD) is an important cause of morbidity and mortality and is responsible for most of the injectable antimicrobial use in the feedlot industry. Traditional bacterial culture can be used to diagnose BRD by confirming the presence of causative pathogens and to support antimicrobial selection. However, given that bacterial culture takes up to a week and early intervention is critical for treatment success, culture has limited utility for informing rapid therapeutic decision-making. In contrast, metagenomic sequencing has the potential to quickly resolve all nucleic acid in a sample, including pathogen biomarkers and antimicrobial resistance genes. In particular, third-generation Oxford Nanopore Technology sequencing platforms provide long reads and access to raw sequencing data in real-time as it is produced, thereby reducing the time from sample collection to diagnostic answer. The purpose of this study was to compare the performance of nanopore metagenomic sequencing to traditional culture and sensitivity methods as applied to nasopharyngeal samples from segregated groups of chronically ill feedlot cattle, previously treated with antimicrobials for nonresponsive pneumonia or lameness.

RESULTS: BRD pathogens were isolated from most samples and a variety of different resistance profiles were observed across isolates. The sequencing data indicated the samples were dominated by Moraxella bovoculi, Mannheimia haemolytica, Mycoplasma dispar, and Pasteurella multocida, and included a wide range of antimicrobial resistance genes (ARGs), encoding resistance for up to seven classes of antimicrobials. Genes conferring resistance to beta-lactams were the most commonly detected, while the tetH gene was detected in the most samples overall. Metagenomic sequencing detected the BRD pathogens of interest more often than did culture, but there was limited concordance between phenotypic resistance to antimicrobials and the presence of relevant ARGs.

CONCLUSIONS: Metagenomic sequencing can reduce the time from sampling to results, detect pathogens missed by bacterial culture, and identify genetically encoded determinants of resistance. Increasing sequencing coverage of target organisms will be an essential component of improving the reliability of this technology, such that it can be better used for the surveillance of pathogens of interest, genetic determinants of resistance, and to inform diagnostic decisions.}, } @article {pmid35655185, year = {2022}, author = {Ziko, L and AbdelRaheem, O and Nabil, M and Aziz, RK and Siam, R}, title = {Bioprospecting the microbiome of Red Sea Atlantis II brine pool for peptidases and biosynthetic genes with promising antibacterial activity.}, journal = {Microbial cell factories}, volume = {21}, number = {1}, pages = {109}, pmid = {35655185}, issn = {1475-2859}, mesh = {Anti-Bacterial Agents/pharmacology ; Bioprospecting ; *Enterococcus faecium ; Humans ; Indian Ocean ; *Microbiota ; Peptide Hydrolases ; Salts ; }, abstract = {BACKGROUND: The search for novel antimicrobial agents is crucial as antibiotic-resistant pathogens continue to emerge, rendering the available antibiotics no longer effective. Likewise, new anti-cancer drugs are needed to combat the emergence of multi-drug resistant tumors. Marine environments are wealthy sources for natural products. Additionally, extreme marine environments are interesting niches to search for bioactive natural compounds. In the current study, a fosmid library of metagenomic DNA isolated from Atlantis II Deep Lower Convective Layer (ATII LCL), was functionally screened for antibacterial activity as well as anticancer effects.

RESULTS: Two clones exhibited antibacterial effects against the marine Bacillus Cc6 strain, namely clones 102-5A and 88-1G and they were further tested against eleven other challenging strains, including six safe relatives of ESKAPE pathogens (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter  spp.), a safe relative to Mycobacterium tuberculosis and four resistant clinical isolates. Clone 88-1G resulted in clear zones of inhibition against eight bacterial strains, while clone 102-5A resulted in zones of inhibition against five bacterial strains. The whole cell lysates of clone 88-1G showed 15% inhibition of Mtb ClpP protease -Mycobacterium tuberculosis drug target-, while whole cell lysates of clone 102-5A showed 19% inhibition of Mtb ClpP protease. Whole cell lysates from the selected clones exhibited anticancer effects against MCF-7 breast cancer cells (cell viability at 50% v/v was 46.2% ± 9.9 for 88-1G clone and 38% ± 7 for 102-5A clone), U2OS osteosarcoma cells (cell viability at 50% v/v was 64.6% ± 12.3 for 88-1G clone and 28.3% ± 1.7 for 102-5A clone) and 1BR hTERT human fibroblast cells (cell viability at 50% v/v was 74.4% ± 5.6 for 88-1G clone and 57.6% ± 8.9 for 102-5A clone). Sequencing of 102-5A and 88-1G clones, and further annotation detected putative proteases and putative biosynthetic genes in clones 102-5A and 88-1G, respectively.

CONCLUSIONS: The ATII LCL metagenome hosts putative peptidases and biosynthetic genes that confer antibiotic and anti-cancer effects. The tested clones exhibited promising antibacterial activities against safe relative strains to ESKAPE pathogens and Mycobacterium tuberculosis. Thus, searching the microbial dark matter of extreme environments is a promising approach to identify new molecules with pharmaceutical potential use.}, } @article {pmid35655063, year = {2022}, author = {Bourquin, M and Busi, SB and Fodelianakis, S and Peter, H and Washburne, A and Kohler, TJ and Ezzat, L and Michoud, G and Wilmes, P and Battin, TJ}, title = {The microbiome of cryospheric ecosystems.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {3087}, pmid = {35655063}, issn = {2041-1723}, mesh = {Climate Change ; *Microbiota/genetics ; *Permafrost ; Phylogeny ; Snow ; }, abstract = {The melting of the cryosphere is among the most conspicuous consequences of climate change, with impacts on microbial life and related biogeochemistry. However, we are missing a systematic understanding of microbiome structure and function across cryospheric ecosystems. Here, we present a global inventory of the microbiome from snow, ice, permafrost soils, and both coastal and freshwater ecosystems under glacier influence. Combining phylogenetic and taxonomic approaches, we find that these cryospheric ecosystems, despite their particularities, share a microbiome with representatives across the bacterial tree of life and apparent signatures of early and constrained radiation. In addition, we use metagenomic analyses to define the genetic repertoire of cryospheric bacteria. Our work provides a reference resource for future studies on climate change microbiology.}, } @article {pmid35654877, year = {2022}, author = {Stockdale, SR and Harrington, RS and Shkoporov, AN and Khokhlova, EV and Daly, KM and McDonnell, SA and O'Reagan, O and Nolan, JA and Sheehan, D and Lavelle, A and Draper, LA and Shanahan, F and Ross, RP and Hill, C}, title = {Metagenomic assembled plasmids of the human microbiome vary across disease cohorts.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9212}, pmid = {35654877}, issn = {2045-2322}, mesh = {Humans ; *Inflammatory Bowel Diseases/genetics/microbiology ; Metagenome ; Metagenomics ; *Microbiota ; Plasmids/genetics ; }, abstract = {We compiled a human metagenome assembled plasmid (MAP) database and interrogated differences across multiple studies that were originally designed to investigate the composition of the human microbiome across various lifestyles, life stages and events. This was performed as plasmids enable bacteria to rapidly expand their functional capacity through mobilisation, yet their contribution to human health and disease is poorly understood. We observed that inter-sample β-diversity differences of plasmid content (plasmidome) could distinguish cohorts across a multitude of conditions. We also show that reduced intra-sample plasmidome α-diversity is consistent amongst patients with inflammatory bowel disease (IBD) and Clostridioides difficile infections. We also show that faecal microbiota transplants can restore plasmidome diversity. Overall plasmidome diversity, specific plasmids, and plasmid-encoded functions can all potentially act as biomarkers of IBD or its severity. The human plasmidome is an overlooked facet of the microbiome and should be integrated into investigations regarding the role of the microbiome in promoting health or disease. Including MAP databases in analyses will enable a greater understanding of the roles of plasmid-encoded functions within the gut microbiome and will inform future human metagenome analyses.}, } @article {pmid35654195, year = {2022}, author = {Beale, DJ and Bissett, A and Nilsson, S and Bose, U and Nelis, JLD and Nahar, A and Smith, M and Gonzalez-Astudillo, V and Braun, C and Baddiley, B and Vardy, S}, title = {Perturbation of the gut microbiome in wild-caught freshwater turtles (Emydura macquarii macquarii) exposed to elevated PFAS levels.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 3}, pages = {156324}, doi = {10.1016/j.scitotenv.2022.156324}, pmid = {35654195}, issn = {1879-1026}, mesh = {Animals ; *Environmental Pollutants ; *Fluorocarbons ; Fresh Water ; *Gastrointestinal Microbiome ; RNA, Ribosomal, 16S/genetics ; *Turtles/metabolism ; }, abstract = {Per- and polyfluoroalkyl substances (PFAS) are environmentally persistent and pervasive. Understanding the toxicity of PFAS to wildlife is difficult, both due to the complexity of biotic and abiotic perturbations in the taxa under study and the practical and ethical problems associated with studying the impacts of environmental pollutants on free living wildlife. One avenue of inquiry into the effects of environmental pollutants, such as PFAS, is assessing the impact on the host gut microbiome. Here we show the microbial composition and biochemical functional outputs from the gut microbiome of sampled faeces from euthanised and necropsied wild-caught freshwater turtles (Emydura macquarii macquarii) exposed to elevated PFAS levels. The microbial community composition was profiled by 16S rRNA gene sequencing using a Nanopore MinION and the biochemical functional outputs of the gut microbiome were profiled using a combination of targeted central carbon metabolism metabolomics using liquid chromatography coupled to a triple quadrupole mass spectrometer (LC-QqQ-MS) and untargeted metabolomics using liquid chromatography coupled to a quadrupole time of flight mass spectrometer (LC-QToF-MS). Total PFAS was measured in the turtle serum using standard methods. These preliminary data demonstrated a 60-fold PFAS increase in impacted turtles compared to the sampled aquatic environment. The microbiome community was also impacted in the PFAS exposed turtles, with the ratio of Firmicutes-to-Bacteroidetes rising from 1.4 at the reference site to 5.5 at the PFAS impacted site. This ratio increase is indicative of host stress and dysfunction of the gut microbiome that was correlated with the biochemical metabolic function data, metabolites observed that are indications of stress and inflammation in the gut microbiome. Utilising the gut microbiome of sampled faeces collected from freshwater turtles provides a non-destructive avenue for investigating the impacts of PFAS in native wildlife, and provides an avenue to explore other contaminants in higher-order taxa within the environment.}, } @article {pmid35654190, year = {2022}, author = {Zhang, RM and Liao, MN and Wu, JE and Lu, XQ and Tan, HZ and Sun, J and Liao, XP and Liu, YH}, title = {Metagenomic insights into the influence of mobile genetic elements on ARGs along typical wastewater treatment system on pig farms in China.}, journal = {The Science of the total environment}, volume = {839}, number = {}, pages = {156313}, doi = {10.1016/j.scitotenv.2022.156313}, pmid = {35654190}, issn = {1879-1026}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Microbial/genetics ; Farms ; Genes, Bacterial ; Interspersed Repetitive Sequences ; Swine ; Wastewater ; *Water Purification ; }, abstract = {The wastewater treatment processes (WTP) on pig farms are heavily contaminated by antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) play an important role in shaping ARG profiles. Here we first employed metagenomic sequencing to follow the diversities and shifts of ARG associated mobile genetic elements (AAMGEs) including insertion sequences (ISs) and plasmids along the WTP for three pig farms in southeast China. The IS average relative abundance rose from the initial pig feces source to the wastewater storage lagoon (WSL) but decreased in the influent and rose in the effluent of the anaerobic digestor (AD). In contrast, plasmids were eliminated rapidly along this process. These results indicated that the AD reduced plasmid copies while IS abundance increased. We found a great diversity ISs, including IS91, ISNCY, IS630 and IS701, were large contributors to the transfer of multi-drug resistance. In addition, the tetracycline resistance genes co-occurred with a greater diversity of ISs than other ARG classes and this likely contributed to the high abundance of tetracycline resistance genes we found. The transfer of ARGs mediated by MGEs along the WTP of pig farms was a key contributor for the ARGs persistence in the environment of pig farms. Collectively, our findings demonstrated different fates for ISs and plasmids along the WTP for pig farms and suggested that AAMGE monitoring served as an important role in controlling ARGs in pig waste.}, } @article {pmid35654188, year = {2022}, author = {Wang, H and Chen, N and Feng, C and Deng, Y}, title = {Synchronous microbial V(V) reduction and denitrification using corn straw as the sole carbon source.}, journal = {The Science of the total environment}, volume = {839}, number = {}, pages = {156343}, doi = {10.1016/j.scitotenv.2022.156343}, pmid = {35654188}, issn = {1879-1026}, mesh = {Carbon/metabolism ; Denitrification ; *Groundwater ; *Nitrates/metabolism ; Nitrogen Oxides ; Zea mays/metabolism ; }, abstract = {The coexistence of nitrate and V(V) in groundwater aquifers poses potential threats to ecological environment and public health. However, much remains to be elucidated about how the complex microbial community coupled nitrate and V(V) simultaneous bio-reduction with carbon source oxidation. For the first time, it was demonstrated that denitrification and V(V) bio-reduction occur by using corn straw as the sole carbon and energy source. Corn straw was proved to have efficient denitrification and V(V) bio-reduction performance in various environments, especially at V(V) concentrations of 100 mg/L for optimal V(V) reduction rate (19.25 mg/L·d) and at pH of 11 with the best nitrate reduction rate (3.12 d[-1]). In addition, an interesting phenomenon was found that the release of V(V) occurred when the carbon source was insufficient and the competitive electron acceptor (NO3[-]-N) existed. Metagenomic analysis showed that the addition of corn straw increased the abundance of genes related to metal resistance, cytochrome and dimethyl sulfoxide, and increased the abundance of glycolytic process, which may play a vital role in facilitating the reduction of V(V). These findings can provide basic suggestions for improving the mechanism of V(V) reduction pathway and provide guidance for the remediation of groundwater polluted by nitrate and V(V).}, } @article {pmid35654160, year = {2022}, author = {Guan, Y and Hou, T and Li, X and Feng, L and Wang, Z}, title = {Metagenomic insights into comparative study of nitrogen metabolic potential and microbial community between primitive and urban river sediments.}, journal = {Environmental research}, volume = {212}, number = {Pt D}, pages = {113592}, doi = {10.1016/j.envres.2022.113592}, pmid = {35654160}, issn = {1096-0953}, mesh = {Bacteria/genetics/metabolism ; China ; Denitrification ; Geologic Sediments/chemistry ; *Microbiota ; *Nitrogen/analysis ; Nitrogen Dioxide ; }, abstract = {As a result of anthropogenic pollution, the nitrogen nutrients load in urban rivers has increased, potentially raising the risk of river eutrophication. Here, we studied how anthropogenic impacts alter nitrogen metabolism in river sediments by comparing the metagenomic function of microbial communities between relatively primitive and human-disturbed sediments. The contents of organic matter (OM), total nitrogen (TN), NO3[-]-N and NO2[-]-N were higher in primitive site than in polluted sites, which might be due to vegetation density, sediment type, hydrology, etc. Whereas, NH4[+]-N content was higher in midstream and downstream, indicating that nitrogen loading increased in the anthropogenic regions and subsequently leading higher NH4[+]-N. Hierarchical cluster analyses revealed significant changes in the community structure and functional potential between the primitive and human-affected sites. Metagenomic analysis demonstrated that Demequina, Streptomyces, Rubrobacter and Dechloromonas were the predominant denitrifiers. Ardenticatena and Dechloromonas species were the most important contributors to dissimilatory nitrate reduction. Furthermore, anthropogenic pollution significantly increased their abundance, and resulting in a decrease in NO3[-], NO2[-]-N and an increase in NH4[+]-N contents. Additionally, the SOX metabolism of Dechloromonas and Sulfuritalea may involve in the sulfur-dependent autotrophic denitrification process by coupling the conversion of thiosulfate to sulfate with the reduction of NO3[-]-N to N2. From pristine to anthropogenic pollution sediments, the major nitrifying bacteria harboring Hao transitioned from Nitrospira to Nitrosomonas. This study sheds light on the consequences of anthropogenic activities on nitrogen metabolism in river sediments, allowing for better management of nitrogen pollution and eutrophication in river.}, } @article {pmid35653842, year = {2022}, author = {Wang, S and Niu, Q and Zhu, P and Huang, Y and Li, K and Li, Q}, title = {Metagenomics analysis unraveled the influence of sulfate radical-mediated compost nitrogen transformation process.}, journal = {Journal of environmental management}, volume = {317}, number = {}, pages = {115436}, doi = {10.1016/j.jenvman.2022.115436}, pmid = {35653842}, issn = {1095-8630}, mesh = {*Composting ; Manure ; Metagenomics ; Nitrification ; Nitrogen/metabolism ; Soil ; Sulfates ; }, abstract = {The mechanism of nitrogen transformation of sulfate radical (SO- 4⋅) in the process of composting is unclear. The objectives of this study were to investigate the influence of SO- 4⋅ on nitrogen biotransformation during composting and to compare the differences in physicochemical parameters and metagenomics analysis between CK (fresh dairy manure and bagasse pith) and PS (the composting raw materials added with potassium persulfate). The results indicated that SO[-]4⋅ guides electron transfer in the conversion of NH[+]4-N to NO- 3-N and breaches the extracellular polysaccharide (EPS) structure to promote nitrogen removal. Aminomonooxygenase (AMO) and nitrate reductase (NR) levels displayed an interactive relationship between microorganisms and substrates. Metagenomics analysis revealed distinct microbial community compositions and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways between nitrification and denitrification. Correlation analysis indicated that Methanobrevibacter, Bacillus and Pseudomonas were closely related to these processes. This work demonstrates the effect of SO- 4⋅ on nitrogen cycling and retention, and possible mechanisms of nitrification and denitrification during composting.}, } @article {pmid35651930, year = {2022}, author = {Zhang, H and Huang, Y and Bei, Z and Ju, Z and Meng, J and Hao, M and Zhang, J and Zhang, H and Xi, W}, title = {Inter-Residue Distance Prediction From Duet Deep Learning Models.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {887491}, pmid = {35651930}, issn = {1664-8021}, abstract = {Residue distance prediction from the sequence is critical for many biological applications such as protein structure reconstruction, protein-protein interaction prediction, and protein design. However, prediction of fine-grained distances between residues with long sequence separations still remains challenging. In this study, we propose DuetDis, a method based on duet feature sets and deep residual network with squeeze-and-excitation (SE), for protein inter-residue distance prediction. DuetDis embraces the ability to learn and fuse features directly or indirectly extracted from the whole-genome/metagenomic databases and, therefore, minimize the information loss through ensembling models trained on different feature sets. We evaluate DuetDis and 11 widely used peer methods on a large-scale test set (610 proteins chains). The experimental results suggest that 1) prediction results from different feature sets show obvious differences; 2) ensembling different feature sets can improve the prediction performance; 3) high-quality multiple sequence alignment (MSA) used for both training and testing can greatly improve the prediction performance; and 4) DuetDis is more accurate than peer methods for the overall prediction, more reliable in terms of model prediction score, and more robust against shallow multiple sequence alignment (MSA).}, } @article {pmid35651750, year = {2022}, author = {Qian, M and Zhu, B and Zhan, Y and Wang, L and Shen, Q and Zhang, M and Yue, L and Wu, D and Chen, H and Wang, X and Cheng, Y}, title = {Analysis of Negative Results of Metagenomics Next-Generation Sequencing in Clinical Practice.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {892076}, pmid = {35651750}, issn = {2235-2988}, mesh = {*Communicable Diseases/diagnosis ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenomics/methods ; Negative Results ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Metagenomics next-generation sequencing (mNGS) has been increasingly used in the clinic, which provides a powerful tool for the etiological diagnosis of infectious diseases. Precise treatment can be carried out according to the positive mNGS results. However, the role of negative results of mNGS remains poorly defined in clinical practice.

METHODS: The results of 1,021 samples from patients who received the mNGS test at Zhongshan Hospital, Fudan University, between January 2019 and December 2019 were analyzed.

RESULTS: There were 308 samples (30.17%) of negative results included in the current study. The top 2 types of negative samples were blood (130/308) and tissue (63/308), which also accounted for the highest negative proportion in diseases. Sputum and bronchoalveolar lavage fluid (BALF) were more likely to have positive results. In false-negative results (defined as negative in mNGS test but reported positive in other sample types or assays), 118 samples were found when compared to regular microbiological assays. The negative predictive value (NPV) of mNGS was 95.79% [95%CI, 93.8%-97.8%] as compared to culture and smear. Mycobacterium, Aspergillus, and Mycoplasma ranked as the top 3 microorganisms on the undetected pathogen list.

CONCLUSIONS: The present data indicate that when the mNGS test is negative, the negative prediction accuracy rate of the original specimen is significant. However, other laboratory assays results and clinical presentations should always be carefully considered prior to drawing a diagnosis.}, } @article {pmid35651076, year = {2022}, author = {Joshi, A and Bhardwaj, D and Kaushik, A and Juneja, VK and Taneja, P and Thakur, S and Kumra Taneja, N}, title = {Advances in multi-omics based quantitative microbial risk assessment in the dairy sector: A semi-systematic review.}, journal = {Food research international (Ottawa, Ont.)}, volume = {156}, number = {}, pages = {111323}, doi = {10.1016/j.foodres.2022.111323}, pmid = {35651076}, issn = {1873-7145}, mesh = {*Dairy Products ; *Food Microbiology ; *Food Safety ; *Risk Assessment ; }, abstract = {With the increasing consumption of packaged and ready-to-eat food products, the risk of foodborne illness has drastically increased and so has the dire need for proper management. The conventional Microbial Risk Assessment (MRA) investigations require prior knowledge of process flow, exposure, and hazard assessment throughout the supply chain. These data are often generated using conventional microbiological approaches based either on shelf-life studies or specific spoilage organisms (SSOs), frequently overlooking crucial information such as antimicrobial resistance (AMR), biofilm formation, virulence factors and other physiological variations coupled with bio-chemical characteristics of food matrix. Additionally, the microbial risks in food are diverse and heterogenous, that might be an outcome of growth and activity of multiple microbial populations rather than a single species contamination. The uncertainty on the microbial source, time as well as point of entry into the food supply chain poses a constraint to the efficiency of preventive approaches and conventional MRA. In the last few decades, significant breakthroughs in molecular methods and continuously progressing bioinformatics tools have opened up a new horizon for risk analysis-based approaches in food safety. Real time polymerase chain reaction (qPCR) and kit-based assays provide better accuracy and precision with shorter processing time. Despite these improvements, the effect of complex food matrix on growth environment and recovery of pathogen is a persistent problem for risk assessors. The dairy industry is highly impacted by spoilage and pathogenic microorganisms. Therefore, this review discusses the evolution and recent advances in MRAmethodologies equipped with predictive interventions and "multi-omics" approach for robust MRA specifically targeting dairy products. It also highlights the limiting gap area and the opportunity for improvement in this field to ensure precision food safety.}, } @article {pmid35651033, year = {2022}, author = {Hou, Q and Wang, Y and Cai, W and Ni, H and Zhao, H and Zhang, Z and Liu, Z and Liu, J and Zhong, J and Guo, Z}, title = {Metagenomic and physicochemical analyses reveal microbial community and functional differences between three types of low-temperature Daqu.}, journal = {Food research international (Ottawa, Ont.)}, volume = {156}, number = {}, pages = {111167}, doi = {10.1016/j.foodres.2022.111167}, pmid = {35651033}, issn = {1873-7145}, mesh = {Bacteria ; Fermentation ; *Metagenome ; Metagenomics ; *Microbiota ; Temperature ; }, abstract = {Complex microbes of different types of low-temperature Daqu (LTD) play an important role in the formation of flavors and qualities of light-flavor Baijiu during fermentation. However, characterizing the taxonomic and functional diversity of microbiota in three types of LTD (Houhuo, Hongxin, Qingcha) remains a major challenge. The present study combined metagenomic sequencing with culture-based methods and physicochemical analysis to compare the three LTD microbiota and elucidate their function in LFB brewing. The results revealed a high diversity of microbes in LTD, with 1286 genera and 4157 species detected across all studied samples. Bacteria and fungi were the main microbes in LTD, with a bacterial to fungal relative abundance ratio of above 4:1. Bacillus (21.18%) and Bacillus licheniformis (17.45%) were the most abundant microbes in the LTD microbiota at the genus and species levels, respectively. Culture-dependent analysis found the highest abundances of bacteria, fungi, and lactic acid bacteria in Houhuo, while the metagenomic-based microbiota found that the relative abundance of bacteria and fungi were highest in Houhuo and Hongxin among the three types of LTD, respectively. The different production temperatures of LTD had little effect on its microbial variety, but obviously impacted the microbiota structure and metagenomic function of LTD. Although the microbiota of the three types of LTD shared a high commonality, each had specific microbiota and functional metagenomic features, suggesting their different but complementary roles in the LFB fermentation process. The representative dominant microbes in Houhuo were mostly involved in metabolic pathways associated with the production of flavor substances in liquor. In contrast, the enriched microbes in Qingcha and Hongxin were not only capable of producing specific flavor substances but also had a strong ability to degrade macromolecular substances in raw materials, promoting microbial growth. This study has greatly enriched our knowledge of the effect of LTD fermentation temperature on its quality, providing practical and interesting information for future improvement of LTD and light-flavor Baijiu products.}, } @article {pmid35650293, year = {2023}, author = {Ren, Z and Ma, K and Jia, X and Wang, Q and Zhang, C and Li, X}, title = {Metagenomics Unveils Microbial Diversity and Their Biogeochemical Roles in Water and Sediment of Thermokarst Lakes in the Yellow River Source Area.}, journal = {Microbial ecology}, volume = {85}, number = {3}, pages = {904-915}, pmid = {35650293}, issn = {1432-184X}, mesh = {*Lakes/microbiology ; *Metagenomics ; Water ; Rivers ; Nitrogen ; Sulfates ; }, abstract = {Thermokarst lakes have long been recognized as biogeochemical hotspots, especially as sources of greenhouse gases. On the Qinghai-Tibet Plateau, thermokarst lakes are experiencing extensive changes due to faster warming. For a deep understanding of internal lake biogeochemical processes, we applied metagenomic analyses to investigate the microbial diversity and their biogeochemical roles in sediment and water of thermokarst lakes in the Yellow River Source Area (YRSA). Sediment microbial communities (SMCs) had lower species and gene richness than water microbial communities (WMCs). Bacteria were the most abundant component in both SMCs and WMCs with significantly different abundant genera. The functional analyses showed that both SMCs and WMCs had low potential in methanogenesis but strong in aerobic respiration, nitrogen assimilation, exopolyphosphatase, glycerophosphodiester phosphodiesterases, and polyphosphate kinase. Moreover, SMCs were enriched in genes involved in anaerobic carbon fixation, aerobic carbon fixation, fermentation, most nitrogen metabolism pathways, dissimilatory sulfate reduction, sulfide oxidation, polysulfide reduction, 2-phosphonopropionate transporter, and phosphate regulation. WMCs were enriched in genes involved in assimilatory sulfate reduction, sulfur mineralization, phosphonoacetate hydrolase, and phosphonate transport. Functional potentials suggest the differences of greenhouse gas emission, nutrient cycling, and living strategies between SMCs and WMCs. This study provides insight into the main biogeochemical processes and their properties in thermokarst lakes in YRSA, improving our understanding of the roles and fates of these lakes in a warming world.}, } @article {pmid35650240, year = {2022}, author = {Su, P and Wicaksono, WA and Li, C and Michl, K and Berg, G and Wang, D and Xiao, Y and Huang, R and Kang, H and Zhang, D and Cernava, T and Liu, Y}, title = {Recovery of metagenome-assembled genomes from the phyllosphere of 110 rice genotypes.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {254}, pmid = {35650240}, issn = {2052-4463}, support = {31772120//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, mesh = {Bacteria/genetics ; *Genome, Bacterial ; *Metagenome ; Metagenomics ; *Oryza/genetics/microbiology ; }, abstract = {The plant microbiota plays crucial roles in sustaining plant health and productivity. Advancing plant microbiome research and designing sustainable practices for agriculture requires in-depth assessments of microorganisms associated with different host plants; however, there is little information on functional aspects of many microorganisms of interest. Therefore, we enriched microorganisms from the phyllosphere of 110 rice genotypes and subjected them to shotgun metagenomic sequencing to reconstruct bacterial genomes from the obtained datasets. The approach yielded a total of 1.34 terabases of shotgun-sequenced metagenomic data. By separately recovering bacterial genomes from each of the 110 rice genotypes, we recovered 569 non-redundant metagenome-assembled genomes (MAGs) with a completeness higher than 50% and contaminations less than 10%. The MAGs were primarily assigned to Alphaproteobacteria, Gammaproteobacteria, and Bacteroidia. The presented data provides an extended basis for microbiome analyses of plant-associated microorganisms. It is complemented by detailed metadata to facilitate implementations in ecological studies, biotechnological mining approaches, and comparative assessments with genomes or MAGs from other studies.}, } @article {pmid35650232, year = {2022}, author = {Poor, AP and Moreno, LZ and Monteiro, MS and Matajira, CEC and Dutra, MC and Leal, DF and Silva, APS and Gomes, VTM and Barbosa, MRF and Sato, MIZ and Moreno, AM}, title = {Vaginal microbiota signatures in healthy and purulent vulvar discharge sows.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9106}, pmid = {35650232}, issn = {2045-2322}, mesh = {Animals ; Bacteria/genetics ; Female ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; Swine ; *Vagina/microbiology ; Vulva ; }, abstract = {Purulent vulvar discharges, primarily caused by genito-urinary tract infections, are an important source of economic loss for swine producers due to sow culling and mortality. However, the agents that compose the vaginal microbiota of sows and their changes during infections are not well understood. The first goal of this study was to characterize and compare the vaginal bacterial content of healthy (HE, n = 40) and purulent vulvar discharge sows (VD, n = 270) by a culture-dependent method and MALDI-TOF MS identification. Secondly, we performed 16S rRNA targeted metagenomic approach (n = 72) to compare the vaginal microbiota between these groups. We found a wide variety of bacteria, with Proteobacteria, Firmicutes, and Bacteroidota being the most abundant phyla in both groups, as well as Escherichia-Shigella, Streptococcus, and Bacteroides at the genus level. Most agents identified in the sequencing method also grew in the culture-dependent method, showing the viability of these bacteria. Alpha diversity did not differ between HE and VD sows, regarding sample richness and diversity, but a beta-diversity index showed a different microbiota composition between these groups in two tested herds. ANCOM analysis revealed that Bacteroides pyogenes were more abundant in VD females and can be a marker for this group. Other agents also require attention, such as the Streptococcus dysgalactiae and Staphylococcus hyicus found in remarkably greater relative abundance in VD sows. Network analysis revealed important positive correlations between some potentially pathogenic genera, such as between Escherichia-Shigella, Trueperella, Streptococcus, Corynebacterium, and Prevotella, which did not occur in healthy sows. We conclude that the alteration of the vaginal microbiota between healthy and purulent vulvar discharge sows, although not extreme, could be due to the increase in the relative abundance of specific agents and to associations between potentially pathogenic bacteria.}, } @article {pmid35649310, year = {2022}, author = {Tang, H and Li, P and Chen, L and Ma, JK and Guo, HH and Huang, XC and Zhong, RM and Jing, SQ and Jiang, LW}, title = {The formation mechanisms of key flavor substances in stinky tofu brine based on metabolism of aromatic amino acids.}, journal = {Food chemistry}, volume = {392}, number = {}, pages = {133253}, doi = {10.1016/j.foodchem.2022.133253}, pmid = {35649310}, issn = {1873-7072}, mesh = {Amino Acids, Aromatic ; Bacteria/genetics/metabolism ; Indoles/metabolism ; Phenols/metabolism ; Salts ; Skatole ; *Soy Foods/analysis ; }, abstract = {Understanding the formation mechanism of the flavor compounds in stinky tofu brine is crucial for controlling the flavor quality of Changsha stinky tofu. Dynamic changes in associated bacteria, enzymes, and differential metabolites in the metabolic pathway of aromatic amino acids in brine were investigated. Results showed that phenol (0.39～89.96 μg/mL), p-cresol (0.19～389.62 μg/mL), indole (1.14～242.97 μg/mL), 3-methylindole (0.14～3.00 μg/mL) were the key flavor substances of brine. The main associated bacteria Clostridiales bacterium SYSU GA17129, Aneurinibacillus aneurinilyticus, and Anaerosalibacter massiliensis were significantly positively correlated with key flavor substances (P < 0.05). The main associated enzymes were transaminase, decarboxylase, and lyase. In summary, phenol and p-cresol were formed by the metabolism of tyrosine and phenylalanine through five reaction chains, and indole and 3-methylindole were formed by the metabolism of tryptophan through one and three reaction chains, respectively.}, } @article {pmid35647693, year = {2022}, author = {Deb, S and Das, SK}, title = {Phylogenomic Analysis of Metagenome-Assembled Genomes Deciphered Novel Acetogenic Nitrogen-Fixing Bathyarchaeota from Hot Spring Sediments.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0035222}, pmid = {35647693}, issn = {2165-0497}, mesh = {Archaea/genetics/metabolism ; *Hot Springs ; *Metagenome ; Nitrogen/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; }, abstract = {This study describes the phylogenomic analysis and metabolic insights of metagenome-assembled genomes (MAGs) retrieved from hot spring sediment samples. The metagenome-assembled sequences recovered three near-complete genomes belonging to the archaeal phylum. Analysis of genome-wide core genes and 16S rRNA-based phylogeny placed the ILS200 and ILS300 genomes within the uncultivated and largely understudied bathyarchaeal phylum, whereas ILS100 represented the phylum Thaumarchaeota. The average nucleotide identity (ANI) of the bin ILS100 was 76% with Nitrososphaeria_archaeon_isolate_SpSt-1069. However, the bins ILS200 and ILS300 showed ANI values of 75% and 70% with Candidatus_Bathyarchaeota_archaeon_isolate_DRTY-6_2_bin_115 and Candidatus_Bathyarchaeota_archaeon_BA1_ba1_01, respectively. The genomic potential of Bathyarchaeota bins ILS200 and ILS300 showed genes necessary for the Wood-Ljungdahl pathway, and the gene encoding the methyl coenzyme M reductase (mcr) complex essential for methanogenesis was absent. The metabolic potential of the assembled genomes included genes involved in nitrogen assimilation, including nitrogenase and the genes necessary for the urea cycle. The presence of these genes suggested the metabolic potential of Bathyarchaeota to fix nitrogen under extreme environments. In addition, the ILS200 and ILS300 genomes carried genes involved in the tricarboxylic acid (TCA) cycle, glycolysis, and degradation of organic carbons. Finally, we conclude that the reconstructed Bathyarchaeota bins are autotrophic acetogens and organo-heterotrophs. IMPORTANCE We describe the Bathyarchaeota bins that are likely to be acetogens with a wide range of metabolic potential. These bins did not exhibit methanogenic machinery, suggesting methane production may not occur by all subgroup lineages of Bathyarchaeota. Phylogenetic analysis support that both ILS200 and ILS300 belonged to the Bathyarchaeota. The discovery of new bathyarchaeotal MAGs provides additional knowledge for understanding global carbon and nitrogen metabolism under extreme conditions.}, } @article {pmid35647280, year = {2022}, author = {Liu, F and Chen, HM and Armstrong, Z and Withers, SG}, title = {Azido Groups Hamper Glycan Acceptance by Carbohydrate Processing Enzymes.}, journal = {ACS central science}, volume = {8}, number = {5}, pages = {656-662}, pmid = {35647280}, issn = {2374-7943}, abstract = {Azido sugars have found frequent use as probes of biological systems in approaches ranging from cell surface metabolic labeling to activity-based proteomic profiling of glycosidases. However, little attention is typically paid to how well azide-substituted sugars represent the parent molecule, despite the substantial difference in size and structure of an azide compared to a hydroxyl. To quantitatively assess how well azides are accommodated, we have used glycosidases as tractable model enzyme systems reflecting what would also be expected for glycosyltransferases and other sugar binding/modifying proteins. In this vein, specificity constants have been measured for the hydrolysis of a series of azidodeoxy glucosides and N-acetylhexosaminides by a large number of glycosidases produced from expressed synthetic gene and metagenomic libraries. Azides at secondary carbons are not significantly accommodated, and thus, associated substrates are not processed, while those at primary carbons are productively recognized by only a small subset of the enzymes and often then only very poorly. Accordingly, in the absence of careful controls, results obtained with azide-modified sugars may not be representative of the situation with the natural sugar and should be interpreted with considerable caution. Azide incorporation can indeed provide a useful tool to monitor and detect glycosylation, but careful consideration should go into the selection of sites of azide substitution; such studies should not be used to quantitate glycosylation or to infer the absence of glycosylation activity.}, } @article {pmid35647232, year = {2022}, author = {Akinde, SB and Adeyemi, FM and Oyedara, OO and Ajani, TF and Sule, WF and Olaitan, JO and Iwalokun, BA and Ojo, OO}, title = {16S rRNA metagenomics data on the bacterial communities in integrated poultry-fish farm ponds.}, journal = {Data in brief}, volume = {42}, number = {}, pages = {108269}, pmid = {35647232}, issn = {2352-3409}, abstract = {In an integrated poultry-fish (IPF) farming system, fish and bird are reared simultaneously. It is a common practice in Sub-Saharan Africa countries like Nigeria, Cameroon, Madagascar, and Benin, offering economic benefits to farmers and minimizing farm running costs. It seems like another way for farmers to manage poultry waste as it is a common practice in IPF farm settings to feed reared fishes with wastes emanating from the poultry. This work provides dataset on the bacterial taxonomic profile and abundance in IPF farm pond water samples using the 16S rRNA sequencing approach. Using ZymoBIOMICS®-96 MagBead DNA Kit, total DNA was extracted from pond water samples collected from IPF farm located at Ila-Orangun, Osun State, Southwest Nigeria (Long: 8° 1' N; Lat: 4° 54' E) during two sampling visits. The V3-V4 region of the rRNA gene was amplified and sequenced on the Miseq Illumina sequencing platform. Raw reads obtained after demultiplexing were analyzed using DADA2 pipeline to obtain distinctive or unique amplicon sequence variants which were grouped into Operational Taxonomic Units (OTUs) based on similarities. Taxonomy assignment was performed using UCLUST and Bayesian classifier from QIIME v.1.9.1 with the Zymo Research Database as reference. The phyla Proteobacteria (26.7%), Actinobacteria (26.0%), Firmicutes (13.1%), and Cyanobacteria (10.1%) dominated the 35 phyla obtained from the OTUs. Interestingly, the abundance of bacterial pathogens commonly associated with human infections was low. The sequence and sample data have been deposited in NCBI database under Sequence Read Archive (SRA) with Bioproject identification number PRJNA760919 (Accession number: SRX12020336 - SRX12020346). The dataset obtained can bridge the gap of limited information on the impact of IPF farming on pond bacterial diversity, a critical factor for considerations as regards food safety, fish, and public health.}, } @article {pmid35647000, year = {2022}, author = {Zhi, W and Song, W and Abdi Saed, Y and Wang, Y and Li, Y}, title = {Fecal Capsule as a Therapeutic Strategy in IgA Nephropathy: A Brief Report.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {914250}, pmid = {35647000}, issn = {2296-858X}, abstract = {In this brief report, we reported an IgA nephropathy (IgAN) patient who presented in November 2020 with an acute exacerbation with massive proteinuria and diarrhea. He had the earliest onset in 2018 when his IgAN was diagnosed by renal biopsy. He has been treated with active ACEI/ARB drugs for more than 90 days, intermittent steroid therapy, combined with anti-infective therapy. Although his acute symptoms resolved with each episode, he became increasingly severe as the interval between episodes shortened. Accordingly, the immunosuppressive drugs were administered under the KDIGO guidelines and related guidelines. However, the patient and his family refused this treatment. We pondered over the possible pathogenesis of IgAN, and after a full discussion with the patient and his family, FMT was administered to him after obtaining his informed consent. During the FMT procedure, one healthy volunteer (the doctor himself) also took the FMT capsules. In the end, the patient's urine protein dropped significantly and even turned negative after treatment. Neither the patient nor the healthy volunteer experienced any serious adverse effects during the use of the capsules and the subsequent 6-month follow-up period. We also used metagenomic sequencing to analyze the intestinal flora of patients before and after treatment, and a gradual increase stood out in the abundance of the patient's intestinal flora after drug administration.}, } @article {pmid35646994, year = {2022}, author = {Wang, M and Liu, W and Xiong, Z and Li, Z and Li, J and Xu, X and Zhang, M and Xing, M and Ning, Q and Wu, D and Qi, J}, title = {Case Report: "Area of Focus" Atypical Trichinellosis and Fascioliasis Coinfection.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {881356}, pmid = {35646994}, issn = {2296-858X}, abstract = {Parasitic co-infection is commonly observed in natural populations, yet rare in the laboratory. Multiparasitism can have negative effects on the host, ranging from the atypical manifestations to increased mortality, consequently, it may be misdiagnosed and treated with unsuitable anthelmintic medicines. Therefore, reliable diagnosis is critical for appropriate treatment of parasitic co-infection. Herein, we report a case of a 31-year-old woman with persistent eosinophilia and hypoechoic liver lesion on ultrasound. The microscopic examination of multiple stool specimens did not find any pathogens. The patient had serum specific anti-Trichinella IgG antibody by Dot enzyme-linked immunosorbent assay (Dot-ELISA). After treatment with albendazole, contrast-enhanced magnetic resonance imaging (MRI) revealed more lesions in the liver. Subsequently, liver biopsy was performed in this patient and Fasciola hepatica was identified using metagenomic next-generation sequencing (mNGS) as well as polymerase chain reaction. After treatment with triclabendazole, which is the only anthelmintic drug specifically available against this fluke, her eosinophil count returned normal, and the liver lesions were significantly regressed. This case highlights the diagnostic challenge posed by parasitic co-infection, which merits more in-depth evaluation to confirm the diagnosis.}, } @article {pmid35646803, year = {2022}, author = {He, W and Wu, C and Zhong, Y and Li, J and Wang, G and Yu, B and Xu, P and Xiao, Y and Tang, T}, title = {Case Report: Therapeutic Strategy With Delayed Debridement for Culture-Negative Invasive Group A Streptococcal Infections Diagnosed by Metagenomic Next-Generation Sequencing.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {899077}, pmid = {35646803}, issn = {2296-2565}, mesh = {Adult ; Anti-Bacterial Agents/therapeutic use ; Clindamycin/therapeutic use ; Debridement ; High-Throughput Nucleotide Sequencing ; Humans ; Immunoglobulins, Intravenous/therapeutic use ; Male ; *Shock, Septic/diagnosis/microbiology/therapy ; *Streptococcal Infections/drug therapy/therapy ; Streptococcus pyogenes ; }, abstract = {Streptococcal toxic shock syndrome (STSS) caused by group A streptococcus is a rare condition that rapidly developed to multiple organ failure even death. Therefore, prompt diagnosis, initiate appropriate antibiotics and other supportive treatments are critical. Here we reported a case of STSS caused by group A streptococcus infection. A healthy 39-year-old man presented a sudden pain in the left lower extremity, followed by a high fever (40.0 °C) with dizziness, nausea, and shortness of breath. Twenty-four hours before the visit, the patient showed anuria. The patient was then admitted to the intensive care unit. Blood examination revealed elevated levels of inflammatory markers and creatinine. He suffered from septic shock, dysfunction of coagulation, acute kidney dysfunction, acute respiratory distress syndrome, and acute liver function injury. The diagnosis was obtained through clinical manifestation and metagenomic next-generation sequencing (mNGS) drawn from the pustule and deep soft tissue (lower limb) samples while all bacterial cultures came back negative. The pustule mNGS report detected a total of 132 unique group A streptococcus sequence reads, representing 96.3% of microbial reads while the soft tissue mNGS report identified a total of 142474 unique group A streptococcus sequence reads, representing 100% of microbial reads. The patient was treated with aggressive fluid resuscitation, antibiotics comprising piperacillin/tazobactam and clindamycin, respiratory support, following the delayed surgical debridement. Intravenous immunoglobulin was also used for 5 days. On the 14th day after admission, he was transferred to the general ward for follow-up treatment. Our case highlighted, for the first time, the key role of mNGS in the early diagnosis of culture-negative invasive group A streptococcal infection. The case also suggested that clindamycin combined with beta-lactam antibiotics and adjunction of intravenous immunoglobulin therapy with delayed debridement performed well in the management of unstable STSS patients.}, } @article {pmid35646766, year = {2022}, author = {Zhang, X and Feng, P and Meng, P and Li, D and Gao, H and Zhao, Y and Yuan, J and Wang, Y and Xia, H}, title = {Case Report: Severe Listeria Encephalitis With Complicated or Secondary Autoimmune Encephalitis and CNS Demyelinating Diseases.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {848868}, pmid = {35646766}, issn = {2296-2565}, mesh = {Adult ; *Demyelinating Diseases ; *Encephalitis/complications/diagnosis/microbiology ; *Hashimoto Disease ; Humans ; *Listeria ; Male ; }, abstract = {BACKGROUND: Listeria monocytogenes is an important food-borne bacterium. It rarely infects patients with complete immunity and causes meningocephalitis. Patients with severe Listeria encephalitis always experience a bad prognosis.

CASE PRESENTATION: A 39-year-old male patient was admitted to our hospital due to fever for more than 10 days and disturbance of consciousness accompanied by convulsions for 2 days. Metagenomic next-generation sequencing (mNGS) results showed L. monocytogenes in both cerebrospinal fluid (CSF) and blood, indicating L. monocytogenes encephalitis. Autoimmune encephalitis and central nervous system (CNS) demyelinating autoantibodies in the CSF also showed positive results. The case was finally diagnosed as severe Listeria encephalitis with complicated or secondary autoimmune encephalitis and CNS demyelinating diseases.

CONCLUSIONS: It is necessary to carry out infection and immunity screening in patients with severe encephalitis, especially for immunocompromised patients. mNGS plays a pivotal role in screening patients with severe and difficult neurological diseases.}, } @article {pmid35646097, year = {2022}, author = {Luo, X and Kang, X and Schönhuth, A}, title = {Enhancing Long-Read-Based Strain-Aware Metagenome Assembly.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {868280}, pmid = {35646097}, issn = {1664-8021}, abstract = {Microbial communities are usually highly diverse and often involve multiple strains from the participating species due to the rapid evolution of microorganisms. In such a complex microecosystem, different strains may show different biological functions. While reconstruction of individual genomes at the strain level is vital for accurately deciphering the composition of microbial communities, the problem has largely remained unresolved so far. Next-generation sequencing has been routinely used in metagenome assembly but there have been struggles to generate strain-specific genome sequences due to the short-read length. This explains why long-read sequencing technologies have recently provided unprecedented opportunities to carry out haplotype- or strain-resolved genome assembly. Here, we propose MetaBooster and MetaBooster-HiFi, as two pipelines for strain-aware metagenome assembly from PacBio CLR and Oxford Nanopore long-read sequencing data. Benchmarking experiments on both simulated and real sequencing data demonstrate that either the MetaBooster or the MetaBooster-HiFi pipeline drastically outperforms the state-of-the-art de novo metagenome assemblers, in terms of all relevant metagenome assembly criteria, involving genome fraction, contig length, and error rates.}, } @article {pmid35644779, year = {2022}, author = {Roux, S and Emerson, JB}, title = {Diversity in the soil virosphere: to infinity and beyond?.}, journal = {Trends in microbiology}, volume = {30}, number = {11}, pages = {1025-1035}, doi = {10.1016/j.tim.2022.05.003}, pmid = {35644779}, issn = {1878-4380}, mesh = {Metagenome ; Metagenomics ; *Soil ; Soil Microbiology ; *Viruses/genetics ; }, abstract = {Viruses are key members of Earth's microbiomes, shaping microbial community composition and metabolism. Here, we describe recent advances in 'soil viromics', that is, virus-focused metagenome and metatranscriptome analyses that offer unprecedented windows into the soil virosphere. Given the emerging picture of high soil viral activity, diversity, and dynamics over short spatiotemporal scales, we then outline key eco-evolutionary processes that we hypothesize are the major diversity drivers for soil viruses. We argue that a community effort is needed to establish a 'global soil virosphere atlas' that can be used to address the roles of viruses in soil microbiomes and terrestrial biogeochemical cycles across spatiotemporal scales.}, } @article {pmid35644636, year = {2022}, author = {Chrzastek, K and Tennakoon, C and Bialy, D and Freimanis, G and Flannery, J and Shelton, H}, title = {A random priming amplification method for whole genome sequencing of SARS-CoV-2 virus.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {406}, pmid = {35644636}, issn = {1471-2164}, support = {BBS/E/I/00007037/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/I/00007039/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/I/00007037/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/I/00007039/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/I/00007037/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*COVID-19 ; Genome, Viral ; Humans ; *Influenza A Virus, H1N1 Subtype ; *RNA Viruses ; SARS-CoV-2/genetics ; Whole Genome Sequencing ; }, abstract = {BACKGROUND: Non-targeted whole genome sequencing is a powerful tool to comprehensively identify constituents of microbial communities in a sample. There is no need to direct the analysis to any identification before sequencing which can decrease the introduction of bias and false negatives results. It also allows the assessment of genetic aberrations in the genome (e.g., single nucleotide variants, deletions, insertions and copy number variants) including in noncoding protein regions.

METHODS: The performance of four different random priming amplification methods to recover RNA viral genetic material of SARS-CoV-2 were compared in this study. In method 1 (H-P) the reverse transcriptase (RT) step was performed with random hexamers whereas in methods 2-4 RT incorporating an octamer primer with a known tag. In methods 1 and 2 (K-P) sequencing was applied on material derived from the RT-PCR step, whereas in methods 3 (SISPA) and 4 (S-P) an additional amplification was incorporated before sequencing.

RESULTS: The SISPA method was the most effective and efficient method for non-targeted/random priming whole genome sequencing of SARS-CoV-2 that we tested. The SISPA method described in this study allowed for whole genome assembly of SARS-CoV-2 and influenza A(H1N1)pdm09 in mixed samples. We determined the limit of detection and characterization of SARS-CoV-2 virus which was 10[3] pfu/ml (Ct, 22.4) for whole genome assembly and 10[1] pfu/ml (Ct, 30) for metagenomics detection.

CONCLUSIONS: The SISPA method is predominantly useful for obtaining genome sequences from RNA viruses or investigating complex clinical samples as no prior sequence information is needed. It might be applied to monitor genomic virus changes, virus evolution and can be used for fast metagenomics detection or to assess the general picture of different pathogens within the sample.}, } @article {pmid35644614, year = {2022}, author = {Widder, S and Görzer, I and Friedel, B and Rahimi, N and Schwarz, S and Jaksch, P and Knapp, S and Puchhammer-Stöckl, E}, title = {Correction: Metagenomic sequencing reveals time, host, and body compartment-specific viral dynamics after lung transplantation.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {81}, pmid = {35644614}, issn = {2049-2618}, } @article {pmid35644066, year = {2022}, author = {Wang, D}, title = {The enigma of picobirnaviruses: viruses of animals, fungi, or bacteria?.}, journal = {Current opinion in virology}, volume = {54}, number = {}, pages = {101232}, doi = {10.1016/j.coviro.2022.101232}, pmid = {35644066}, issn = {1879-6265}, mesh = {Animals ; Bacteria/genetics ; Diarrhea ; Feces ; Fungi/genetics ; Humans ; Phylogeny ; *Picobirnavirus/genetics ; *RNA Virus Infections/veterinary ; *Viruses/genetics ; }, abstract = {Picobirnaviruses are small double-stranded RNA viruses first discovered in 1988 in stool samples from patients with diarrhea. It has generally been assumed that picobirnaviruses infect animal hosts and that they are potential agents of diarrhea, but there is still no direct evidence demonstrating that picobirnaviruses infect animals. In the metagenomic era, virome studies have broadened our understanding of picobirnavirus genetic diversity and genome organization, expanded the types of animals in which they have been detected, and identified novel associations with human disease. Most importantly, from the wealth of new sequencing data and comparative genomic analyses, a provocative new hypothesis has emerged that picobirnaviruses may not infect animals, but rather that they may infect evolutionarily simpler denizens of the gastrointestinal tract: bacteria and/or fungi. Depending on whether the true hosts of picobirnaviruses are animals, fungi, or bacteria, the mechanisms by which they impact animal biology will vary dramatically.}, } @article {pmid35643462, year = {2022}, author = {Van der Jeugt, F and Dawyndt, P and Mesuere, B}, title = {FragGeneScanRs: faster gene prediction for short reads.}, journal = {BMC bioinformatics}, volume = {23}, number = {1}, pages = {198}, pmid = {35643462}, issn = {1471-2105}, support = {12I5220N//Research Foundation-Flanders (FWO)/ ; }, mesh = {*Algorithms ; Metagenome ; Metagenomics ; *Software ; }, abstract = {BACKGROUND: FragGeneScan is currently the most accurate and popular tool for gene prediction in short and error-prone reads, but its execution speed is insufficient for use on larger data sets. The parallelization which should have addressed this is inefficient. Its alternative implementation FragGeneScan+ is faster, but introduced a number of bugs related to memory management, race conditions and even output accuracy.

RESULTS: This paper introduces FragGeneScanRs, a faster Rust implementation of the FragGeneScan gene prediction model. Its command line interface is backward compatible and adds extra features for more flexible usage. Its output is equivalent to the original FragGeneScan implementation.

CONCLUSIONS: Compared to the current C implementation, shotgun metagenomic reads are processed up to 22 times faster using a single thread, with better scaling for multithreaded execution. The Rust code of FragGeneScanRs is freely available from GitHub under the GPL-3.0 license with instructions for installation, usage and other documentation (https://github.com/unipept/FragGeneScanRs).}, } @article {pmid35643147, year = {2022}, author = {Ma, W and Wang, L and Xu, X and Huo, M and Zhou, K and Mi, K and Tian, X and Cheng, G and Huang, L}, title = {Fate and exposure risk of florfenicol, thiamphenicol and antibiotic resistance genes during composting of swine manure.}, journal = {The Science of the total environment}, volume = {839}, number = {}, pages = {156243}, doi = {10.1016/j.scitotenv.2022.156243}, pmid = {35643147}, issn = {1879-1026}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Composting/methods ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Manure/microbiology ; Soil/chemistry ; Swine ; *Thiamphenicol/analogs & derivatives ; }, abstract = {Livestock manure is an important source of antibiotic resistance genes (ARGs) spreading to the environment, posing a potential threat to human health. Here, we investigated the dissipation of florfenicol (FF) and thiamphenicol (TAP), and their effects on the bacterial community, mobile genetic elements (MGEs), and ARGs during composting. The results indicated that FF and TAP dissipated rapidly in compost, with half-life values of 5.1 and 1.6 d, respectively. However, FF could not be completely removed during composting. The FF and TAP residues in manure could reduce the elimination of ARGs and MGEs during composting, and had a negative effect on the physicochemical factors of the compost. Significant correlations were found between floR and intI1, indicating that floR in manure may more easily diffuse to the soil environment. Meanwhile, the presence of FF in manure could increase the abundance of floR. Network analysis showed that Proteobacteria and Firmicutes were the dominant bacterial communities and important potential pathogen hosts carrying ARGs. The predicted environmental concentration of FF in the soil was over 100 μg kg[-1], which indicates that FF poses a potential risk to the natural environment, and we verified this result through field experiments. The results showed that FF dissipated in the soil after it migrated from manure to soil. In contrast, TAP in manure posed lower environmental risk. This study highlights that changed in composting conditions may control the rate of removal of ARGs. Further studies are needed to investigate the best environmental conditions to achieve a faster degradation of FF and a more comprehensive elimination of ARGs during composting.}, } @article {pmid35643020, year = {2022}, author = {Smith, SE and Huang, W and Tiamani, K and Unterer, M and Khan Mirzaei, M and Deng, L}, title = {Emerging technologies in the study of the virome.}, journal = {Current opinion in virology}, volume = {54}, number = {}, pages = {101231}, doi = {10.1016/j.coviro.2022.101231}, pmid = {35643020}, issn = {1879-6265}, mesh = {*Bacteriophages/genetics ; Metagenome ; Metagenomics/methods ; RNA, Ribosomal, 16S/genetics ; Virome ; *Viruses/genetics ; }, abstract = {Despite the growing interest in the microbiome in recent years, the study of the virome, the major part of which is made up of bacteriophages, is relatively underdeveloped compared with their bacterial counterparts. This is due in part to the lack of a universally conserved marker such as the 16S rRNA gene. For this reason, the development of metagenomic approaches was a major milestone in the study of the viruses in the microbiome or virome. However, it has become increasingly clear that these wet-lab methods have not yet been able to detect the full range of viruses present, and our understanding of the composition of the virome remains incomplete. In recent years, a range of new technologies has been developed to further our understanding. Direct RNA-Seq technologies bypass the need for cDNA synthesis, thus avoiding biases subjected to this step, which further expands our understanding of RNA viruses. The new generation of amplification methods could solve the low biomass issue relevant to most virome samples while reducing the error rate and biases caused by whole genome amplification. The application of long-read sequencing to virome samples can resolve the shortcomings of short-read sequencing in generating complete viral genomes and avoid the biases introduced by the assembly. Novel experimental methods developed to measure viruses' host range can help overcome the challenges of assigning hosts to many phages, specifically unculturable ones.}, } @article {pmid35642928, year = {2022}, author = {Liu, Q and Zuo, T and Lu, W and Yeoh, YK and Su, Q and Xu, Z and Tang, W and Yang, K and Zhang, F and Lau, LHS and Lui, RNS and Chin, ML and Wong, R and Cheung, CP and Zhu, W and Chan, PKS and Chan, FKL and Lui, GC and Ng, SC}, title = {Longitudinal Evaluation of Gut Bacteriomes and Viromes after Fecal Microbiota Transplantation for Eradication of Carbapenem-Resistant Enterobacteriaceae.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0151021}, pmid = {35642928}, issn = {2379-5077}, mesh = {Animals ; Mice ; Fecal Microbiota Transplantation ; *Carbapenem-Resistant Enterobacteriaceae ; Virome ; Escherichia coli ; Pilot Projects ; *Bacteriophages ; }, abstract = {Understanding the role of fecal microbiota transplantation (FMT) in the decolonization of multidrug-resistant organisms (MDRO) is critical. Specifically, little is known about virome changes in MDRO-infected subjects treated with FMT. Using shotgun metagenomic sequencing, we characterized longitudinal dynamics of the gut virome and bacteriome in three recipients who successfully decolonized carbapenem-resistant Enterobacteriaceae (CRE), including Klebsiella spp. and Escherichia coli, after FMT. We observed large shifts of the fecal bacterial microbiota resembling a donor-like community after transfer of a fecal microbiota dominated by the genus Ruminococcus. We found a substantial expansion of Klebsiella phages after FMT with a concordant decrease of Klebsiella spp. and striking increase of Escherichia phages in CRE E. coli carriers after FMT. We also observed the CRE elimination and similar evolution of Klebsiella phage in mice, which may play a role in the collapse of the Klebsiella population after FMT. In summary, our pilot study documented bacteriome and virome alterations after FMT which mediate many of the effects of FMT on the gut microbiome community. IMPORTANCE Fecal microbiota transplantation (FMT) is an effective treatment for multidrug-resistant organisms; however, introducing a complex mixture of microbes also has unknown consequences for landscape features of gut microbiome. We sought to understand bacteriome and virome alterations in patients undergoing FMT to treat infection with carbapenem-resistant Enterobacteriaceae. This finding indicates that transkingdom interactions between the virome and bacteriome communities may have evolved in part to support efficient FMT for treating CRE.}, } @article {pmid35642922, year = {2022}, author = {Hoskinson, C and Zheng, K and Gabel, J and Kump, A and German, R and Podicheti, R and Marino, N and Stiemsma, LT}, title = {Composition and Functional Potential of the Human Mammary Microbiota Prior to and Following Breast Tumor Diagnosis.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0148921}, pmid = {35642922}, issn = {2379-5077}, mesh = {Animals ; Humans ; Female ; Dysbiosis/diagnosis ; *Microbiota/genetics ; Breast ; Bacteria/genetics ; *Breast Neoplasms/diagnosis ; *Mammary Neoplasms, Animal ; *Precancerous Conditions ; }, abstract = {Microbiota studies have reported changes in the microbial composition of the breast upon cancer development. However, results are inconsistent and limited to the later phases of cancer development (after diagnosis). We analyzed and compared the resident bacterial taxa of histologically normal breast tissue (healthy, H, n = 49) with those of tissues donated prior to (prediagnostic, PD, n = 15) and after (adjacent normal, AN, n = 49, and tumor, T, n = 46) breast cancer diagnosis (n total = 159). DNA was isolated from tissue samples and submitted for Illumina MiSeq paired-end sequencing of the V3-V4 region of the 16S gene. To infer bacterial function in breast cancer, we predicted the functional bacteriome from the 16S sequencing data using PICRUSt2. Bacterial compositional analysis revealed an intermediary taxonomic signature in the PD tissue relative to that of the H tissue, represented by shifts in Bacillaceae, Burkholderiaceae, Corynebacteriaceae, Streptococcaceae, and Staphylococcaceae. This compositional signature was enhanced in the AN and T tissues. We also identified significant metabolic reprogramming of the microbiota of the PD, AN, and T tissue compared with the H tissue. Further, preliminary correlation analysis between host transcriptome profiling and microbial taxa and genes in H and PD tissues identified altered associations between the human host and mammary microbiota in PD tissue compared with H tissue. These findings suggest that compositional shifts in bacterial abundance and metabolic reprogramming of the breast tissue microbiota are early events in breast cancer development that are potentially linked with cancer susceptibility. IMPORTANCE The goal of this study was to determine the role of resident breast tissue bacteria in breast cancer development. We analyzed breast tissue bacteria in healthy breast tissue and breast tissue donated prior to (precancerous) and after (postcancerous) breast cancer diagnosis. Compared to healthy tissue, the precancerous and postcancerous breast tissues demonstrated differences in the amounts of breast tissue bacteria. In addition, breast tissue bacteria exhibit different functions in pre-cancerous and post-cancerous breast tissues relative to healthy tissue. These differences in function are further emphasized by altered associations of the breast tissue bacteria with gene expression in the human host prior to cancer development. Collectively, these analyses identified shifts in bacterial abundance and metabolic function (dysbiosis) prior to breast tumor diagnosis. This dysbiosis may serve as a therapeutic target in breast cancer prevention.}, } @article {pmid35642524, year = {2022}, author = {Rooney, AM and Raphenya, AR and Melano, RG and Seah, C and Yee, NR and MacFadden, DR and McArthur, AG and Schneeberger, PHH and Coburn, B}, title = {Performance Characteristics of Next-Generation Sequencing for the Detection of Antimicrobial Resistance Determinants in Escherichia coli Genomes and Metagenomes.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0002222}, pmid = {35642524}, issn = {2379-5077}, support = {PJT-156214//Canadian Institutes for Health Research/ ; }, mesh = {Animals ; Humans ; *Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Metagenome/genetics ; Genome, Bacterial ; }, abstract = {Short-read sequencing can provide detection of multiple genomic determinants of antimicrobial resistance from single bacterial genomes and metagenomic samples. Despite its increasing application in human, animal, and environmental microbiology, including human clinical trials, the performance of short-read Illumina sequencing for antimicrobial resistance gene (ARG) detection, including resistance-conferring single nucleotide polymorphisms (SNPs), has not been systematically characterized. Using paired-end 2 × 150 bp (base pair) Illumina sequencing and an assembly-based method for ARG prediction, we determined sensitivity, positive predictive value (PPV), and sequencing depths required for ARG detection in an Escherichia coli isolate of sequence type (ST) 38 spiked into a synthetic microbial community at varying abundances. Approximately 300,000 reads or 15× genome coverage was sufficient to detect ARGs in E. coli ST38, with comparable sensitivity and PPV to ~100× genome coverage. Using metagenome assembly of mixed microbial communities, ARG detection at E. coli relative abundances of 1% would require assembly of approximately 30 million reads to achieve 15× target coverage. The minimum sequencing depths were validated using public data sets of 948 E. coli genomes and 10 metagenomic rectal swab samples. A read-based approach using k-mer alignment (KMA) for ARG prediction did not substantially improve minimum sequencing depths for ARG detection compared to assembly of the E. coli ST38 genome or the combined metagenomic samples. Analysis of sequencing depths from recent studies assessing ARG content in metagenomic samples demonstrated that sequencing depths had a median estimated detection frequency of 84% (interquartile range: 30%-92%) for a relative abundance of 1%. IMPORTANCE Systematically determining Illumina sequencing performance characteristics for detection of ARGs in metagenomic samples is essential to inform study design and appraisal of human, animal, and environmental metagenomic antimicrobial resistance studies. In this study, we quantified the performance characteristics of ARG detection in E. coli genomes and metagenomes and established a benchmark of ~15× coverage for ARG detection for E. coli in metagenomes. We demonstrate that for low relative abundances, sequencing depths of ~30 million reads or more may be required for adequate sensitivity for many applications.}, } @article {pmid35642511, year = {2022}, author = {Weigel, BL and Miranda, KK and Fogarty, EC and Watson, AR and Pfister, CA}, title = {Functional Insights into the Kelp Microbiome from Metagenome-Assembled Genomes.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0142221}, pmid = {35642511}, issn = {2379-5077}, mesh = {Humans ; Metagenome/genetics ; *Kelp/genetics ; Dissolved Organic Matter ; Nitrates/metabolism ; Phylogeny ; *Microbiota/genetics ; Bacteria ; Vitamins/metabolism ; }, abstract = {Eukaryotic organisms evolved in a microbial world and often have intimate associations with diverse bacterial groups. Kelp, brown macroalgae in the order Laminariales, play a vital role in coastal ecosystems, yet we know little about the functional role of the microbial symbionts that cover their photosynthetic surfaces. Here, we reconstructed 79 bacterial metagenome-assembled genomes (MAGs) from blades of the bull kelp, Nereocystis luetkeana, allowing us to determine their metabolic potential and functional roles. Despite the annual life history of bull kelp, nearly half of the bacterial MAGs were detected across multiple years. Diverse members of the kelp microbiome, spanning 6 bacterial phyla, contained genes for transporting and assimilating dissolved organic matter (DOM), which is secreted by kelp in large quantities and likely fuels the metabolism of these heterotrophic bacteria. Bacterial genomes also contained alginate lyase and biosynthesis genes, involved in polysaccharide degradation and biofilm formation, respectively. Kelp-associated bacterial genomes contained genes for dissimilatory nitrate reduction and urea hydrolysis, likely providing a reduced source of nitrogen to the host kelp. The genome of the most abundant member of the kelp microbiome and common macroalgal symbiont, Granulosicoccus, contained a full suite of genes for synthesizing cobalamin (vitamin B12), suggesting that kelp-associated bacteria have the potential to provide their host kelp with vitamins. Finally, kelp-associated Granulosicoccus contained genes that typify the aerobic anoxygenic phototrophic bacteria, including genes for bacteriochlorophyll synthesis and photosystem II reaction center proteins, making them the first known photoheterotrophic representatives of this genus. IMPORTANCE Kelp (brown algae in the order Laminariales) are foundational species that create essential habitat in temperate and arctic coastal marine ecosystems. These photosynthetic giants host millions of microbial taxa whose functions are relatively unknown, despite their potential importance for host-microbe interactions and nutrient cycling in kelp forest ecosystems. We reconstructed bacterial genomes from metagenomic samples collected from blades of the bull kelp, Nereocystis luetkeana, allowing us to determine the functional gene content of specific members of the kelp microbiome. These bacterial genomes spanned 6 phyla and 19 families and included common alga-associated microbial symbionts such as Granulosicoccus. Key functions encoded in kelp-associated bacterial genomes included dissolved organic matter assimilation, alginate metabolism, vitamin B12 biosynthesis, and nitrogen reduction from nitrate and urea to ammonium, potentially providing the host kelp with vitamins and reduced nitrogen.}, } @article {pmid35641653, year = {2022}, author = {Marrocco, F and Delli Carpini, M and Garofalo, S and Giampaoli, O and De Felice, E and Di Castro, MA and Maggi, L and Scavizzi, F and Raspa, M and Marini, F and Tomassini, A and Nicolosi, R and Cason, C and Trettel, F and Miccheli, A and Iebba, V and D'Alessandro, G and Limatola, C}, title = {Short-chain fatty acids promote the effect of environmental signals on the gut microbiome and metabolome in mice.}, journal = {Communications biology}, volume = {5}, number = {1}, pages = {517}, pmid = {35641653}, issn = {2399-3642}, mesh = {Animals ; Fatty Acids, Volatile ; Formates ; *Gastrointestinal Microbiome ; Metabolome ; Mice ; *Microbiota ; }, abstract = {Gut microorganisms and the products of their metabolism thoroughly affect host brain development, function and behavior. Since alterations of brain plasticity and cognition have been demonstrated upon motor, sensorial and social enrichment of the housing conditions, we hypothesized that gut microbiota and metabolome could be altered by environmental stimuli, providing part of the missing link among environmental signals and brain effects. In this preliminary study, metagenomic and metabolomic analyses of mice housed in different environmental conditions, standard and enriched, identify environment-specific microbial communities and metabolic profiles. We show that mice housed in an enriched environment have distinctive microbiota composition with a reduction in gut bacterial richness and biodiversity and are characterized by a metabolomic fingerprint with the increase of formate and acetate and the decrease of bile salts. We demonstrate that mice treated with a mixture of formate and acetate recapitulate some of the brain plasticity effects modulated by environmental enrichment, such as hippocampal neurogenesis, neurotrophin production, short-term plasticity and cognitive behaviors, that can be further exploited to decipher the mechanisms involved in experience-dependent brain plasticity.}, } @article {pmid35641510, year = {2022}, author = {Yeoh, YK and Sun, Y and Ip, LYT and Wang, L and Chan, FKL and Miao, Y and Ng, SC}, title = {Prevotella species in the human gut is primarily comprised of Prevotella copri, Prevotella stercorea and related lineages.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {9055}, pmid = {35641510}, issn = {2045-2322}, mesh = {*Gastrointestinal Microbiome/genetics ; Humans ; *Microbiota ; Prevotella/genetics/metabolism ; }, abstract = {Prevotella species in the human gut microbiome are primarily comprised of Prevotella copri, and its diversity and function were recently investigated in detail. Much less is known about other Prevotella species in the human gut. Here, we examined the composition of Prevotella species in human guts by mapping publicly available gut metagenomes to a dereplicated set of metagenome-assembled genomes (MAGs) representing Prevotella lineages found in human guts. In most human cohorts, P. copri is the most relatively abundant species (e.g. up to 14.3% relative abundance in Tangshan, China). However, more than half of the metagenome reads in several cohorts mapped to Prevotella MAGs representing P. stercorea and several other species sister to P. stercorea and P. copri. Analyses of genes encoded in these genomes indicated that P. stercorea and related lineages lacked many hemicellulose degrading enzymes and were thus less likely to metabolise hemicelluloses compared with P. copri and copri-related lineages. Instead, P. stercorea genomes possess several carbohydrate esterases that may be involved in releasing ester modifications from carbohydrates to facilitate their degradation. These findings reveal unexplored Prevotella diversity in the human gut and indicate possible niche partitions among these related species.}, } @article {pmid35641156, year = {2022}, author = {Chen, SY and Peng, TC and Huang, SZ and Chien, CC}, title = {Isolation of an ectoine-producing Sinobaca sp. and identification of genes that are involved in ectoine biosynthesis.}, journal = {FEMS microbiology letters}, volume = {369}, number = {1}, pages = {}, doi = {10.1093/femsle/fnac046}, pmid = {35641156}, issn = {1574-6968}, mesh = {*Amino Acids, Diamino/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; *Sodium Chloride/metabolism ; }, abstract = {A moderate halophilic bacterium that could accumulate ectoine and hydroxyectoine was isolated from soil near a salt mine and was identified as a Sinobaca sp. (designed strain H24) according to 16S rRNA gene sequence analysis. The bacterium grew well in the presence of 1-2 M NaCl, while growth in a medium that contained 2 M NaCl led to higher accumulation of ectoines. The yields of ectoine and hydroxyectoine by Sinobaca sp. H24 reached 11.27 mg/l and 1.34 mg/l, respectively, when cultured in the following medium: NaCl (2 M), peptone (5 g/l), yeast extract (1 g/l), NH4Cl (0.02 M), KH2PO4 (1 M), K2HPO4 (0.1 M), and glycerol (1% w/v). Genes that are involved in ectoine biosynthesis of Sinobaca sp. H24 were also identified, and their sequences were determined by a metagenomics approach. The results demonstrated that Sinobaca sp. H24 possesses ectoine metabolism genes for both ectoine biosynthesis (ectA, ectB, ectC, and ectD) and ectoine degradation (doeA). Genes that are related to ectoine biosynthesis, such as lysC and asd, were also characterized. The identification and characterization results for ectoine/hydroxyectoine biosynthesis genes are in agreement with the physiology of Sinobaca sp. H24 as a potential candidate for ectoine production for industrial applications. This report established for the first time the accumulation of ectoine/hydroxyectoine in Sinobaca sp. and characterized the genes that are involved in ectoine/hydroxyectoine biosynthesis in Sinobaca sp. H24.}, } @article {pmid35639953, year = {2022}, author = {Aptekmann, AA and Buongiorno, J and Giovannelli, D and Glamoclija, M and Ferreiro, DU and Bromberg, Y}, title = {mebipred: identifying metal-binding potential in protein sequence.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {14}, pages = {3532-3540}, pmid = {35639953}, issn = {1367-4811}, support = {R01 GM115486/GM/NIGMS NIH HHS/United States ; /NASA/NASA/United States ; 80NSSC18M0093//Astrobiology Institute/ ; //National Science Foundation/ ; 1553289//NSF/ ; /ERC_/European Research Council/International ; 948972//European Union's Horizon 2020/ ; //National Scientific and Technical Research Council/ ; }, mesh = {Humans ; Amino Acid Sequence ; *Proteins/chemistry ; Protein Binding ; Sequence Alignment ; *Metals ; Ions ; }, abstract = {MOTIVATION: metal-binding proteins have a central role in maintaining life processes. Nearly one-third of known protein structures contain metal ions that are used for a variety of needs, such as catalysis, DNA/RNA binding, protein structure stability, etc. Identifying metal-binding proteins is thus crucial for understanding the mechanisms of cellular activity. However, experimental annotation of protein metal-binding potential is severely lacking, while computational techniques are often imprecise and of limited applicability.

RESULTS: we developed a novel machine learning-based method, mebipred, for identifying metal-binding proteins from sequence-derived features. This method is over 80% accurate in recognizing proteins that bind metal ion-containing ligands; the specific identity of 11 ubiquitously present metal ions can also be annotated. mebipred is reference-free, i.e. no sequence alignments are involved, and is thus faster than alignment-based methods; it is also more accurate than other sequence-based prediction methods. Additionally, mebipred can identify protein metal-binding capabilities from short sequence stretches, e.g. translated sequencing reads, and, thus, may be useful for the annotation of metal requirements of metagenomic samples. We performed an analysis of available microbiome data and found that ocean, hot spring sediments and soil microbiomes use a more diverse set of metals than human host-related ones. For human microbiomes, physiological conditions explain the observed metal preferences. Similarly, subtle changes in ocean sample ion concentration affect the abundance of relevant metal-binding proteins. These results highlight mebipred's utility in analyzing microbiome metal requirements.

mebipred is available as a web server at services.bromberglab.org/mebipred and as a standalone package at https://pypi.org/project/mymetal/.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid35639797, year = {2022}, author = {Johri, P and Aquadro, CF and Beaumont, M and Charlesworth, B and Excoffier, L and Eyre-Walker, A and Keightley, PD and Lynch, M and McVean, G and Payseur, BA and Pfeifer, SP and Stephan, W and Jensen, JD}, title = {Recommendations for improving statistical inference in population genomics.}, journal = {PLoS biology}, volume = {20}, number = {5}, pages = {e3001669}, pmid = {35639797}, issn = {1545-7885}, support = {R01 GM095793/GM/NIGMS NIH HHS/United States ; R35 GM139383/GM/NIGMS NIH HHS/United States ; R35 GM139412/GM/NIGMS NIH HHS/United States ; R01 GM135899/GM/NIGMS NIH HHS/United States ; }, mesh = {*Genomics/methods ; *Metagenomics ; }, abstract = {The field of population genomics has grown rapidly in response to the recent advent of affordable, large-scale sequencing technologies. As opposed to the situation during the majority of the 20th century, in which the development of theoretical and statistical population genetic insights outpaced the generation of data to which they could be applied, genomic data are now being produced at a far greater rate than they can be meaningfully analyzed and interpreted. With this wealth of data has come a tendency to focus on fitting specific (and often rather idiosyncratic) models to data, at the expense of a careful exploration of the range of possible underlying evolutionary processes. For example, the approach of directly investigating models of adaptive evolution in each newly sequenced population or species often neglects the fact that a thorough characterization of ubiquitous nonadaptive processes is a prerequisite for accurate inference. We here describe the perils of these tendencies, present our consensus views on current best practices in population genomic data analysis, and highlight areas of statistical inference and theory that are in need of further attention. Thereby, we argue for the importance of defining a biologically relevant baseline model tuned to the details of each new analysis, of skepticism and scrutiny in interpreting model fitting results, and of carefully defining addressable hypotheses and underlying uncertainties.}, } @article {pmid35639517, year = {2022}, author = {Payne, LJ and Meaden, S and Mestre, MR and Palmer, C and Toro, N and Fineran, PC and Jackson, SA}, title = {PADLOC: a web server for the identification of antiviral defence systems in microbial genomes.}, journal = {Nucleic acids research}, volume = {50}, number = {W1}, pages = {W541-W550}, pmid = {35639517}, issn = {1362-4962}, mesh = {*Archaea/genetics/virology ; *Bacteria/genetics/virology ; Bacteriophages/immunology ; *Genome, Microbial/genetics ; Plasmids/genetics ; Prokaryotic Cells/metabolism/virology ; *Internet ; *Software ; Computers ; *Genomics/methods ; }, abstract = {Most bacteria and archaea possess multiple antiviral defence systems that protect against infection by phages, archaeal viruses and mobile genetic elements. Our understanding of the diversity of defence systems has increased greatly in the last few years, and many more systems likely await discovery. To identify defence-related genes, we recently developed the Prokaryotic Antiviral Defence LOCator (PADLOC) bioinformatics tool. To increase the accessibility of PADLOC, we describe here the PADLOC web server (freely available at https://padloc.otago.ac.nz), allowing users to analyse whole genomes, metagenomic contigs, plasmids, phages and archaeal viruses. The web server includes a more than 5-fold increase in defence system types detected (since the first release) and expanded functionality enabling detection of CRISPR arrays and retron ncRNAs. Here, we provide user information such as input options, description of the multiple outputs, limitations and considerations for interpretation of the results, and guidance for subsequent analyses. The PADLOC web server also houses a precomputed database of the defence systems in > 230,000 RefSeq genomes. These data reveal two taxa, Campylobacterota and Spriochaetota, with unusual defence system diversity and abundance. Overall, the PADLOC web server provides a convenient and accessible resource for the detection of antiviral defence systems.}, } @article {pmid35639362, year = {2022}, author = {Kumar, H and Panigrahi, M and Panwar, A and Rajawat, D and Nayak, SS and Saravanan, KA and Kaisa, K and Parida, S and Bhushan, B and Dutt, T}, title = {Machine-Learning Prospects for Detecting Selection Signatures Using Population Genomics Data.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {29}, number = {9}, pages = {943-960}, doi = {10.1089/cmb.2021.0447}, pmid = {35639362}, issn = {1557-8666}, mesh = {Genetics, Population ; Genomics/methods ; Machine Learning ; *Metagenomics ; *Selection, Genetic ; }, abstract = {Natural selection has been given a lot of attention because it relates to the adaptation of populations to their environments, both biotic and abiotic. An allele is selected when it is favored by natural selection. Consequently, the favored allele increases in frequency in the population and neighboring linked variation diminishes, causing so-called selective sweeps. A high-throughput genomic sequence allows one to disentangle the evolutionary forces at play in populations. With the development of high-throughput genome sequencing technologies, it has become easier to detect these selective sweeps/selection signatures. Various methods can be used to detect selective sweeps, from simple implementations using summary statistics to complex statistical approaches. One of the important problems of these statistical models is the potential to provide inaccurate results when their assumptions are violated. The use of machine learning (ML) in population genetics has been introduced as an alternative method of detecting selection by treating the problem of detecting selection signatures as a classification problem. Since the availability of population genomics data is increasing, researchers may incorporate ML into these statistical models to infer signatures of selection with higher predictive accuracy and better resolution. This article describes how ML can be used to aid in detecting and studying natural selection patterns using population genomic data.}, } @article {pmid35639335, year = {2022}, author = {Jiang, Z and Li, X and Guo, L}, title = {Binning Metagenomic Contigs Using Unsupervised Clustering and Reference Databases.}, journal = {Interdisciplinary sciences, computational life sciences}, volume = {14}, number = {4}, pages = {795-803}, pmid = {35639335}, issn = {1867-1462}, support = {61373057//National Natural Science Foundation of China/ ; }, mesh = {*Metagenomics/methods ; *Metagenome/genetics ; Cluster Analysis ; Algorithms ; Databases, Factual ; Sequence Analysis, DNA/methods ; }, abstract = {Metagenomics can directly extract the genetic material of all microorganisms from the environment, and obtain metagenomic samples with a large number of unknown DNA sequences. Binning of metagenomic contigs is a hot topic in metagenomics research. There are two key challenges for the current unsupervised metagenomic clustering algorithms. First, unsupervised metagenomic clustering methods rarely use reference databases, causing a certain waste of resources. Second, unsupervised metagenomic clustering methods are restricted by the characteristics of the sequences and the clustering algorithms, and the binning effect is limited. Therefore, a new binning method for metagenomic contigs using unsupervised clustering methods and reference databases is proposed to address these challenges, to make full use of the advantages of unsupervised clustering methods and reference databases constructed by scientists to improve the overall binning effect. This method uses the integrated SVM classification model to further bin the unsupervised clustering parts that do not perform well. Our proposed method was tested on simulated datasets and a real dataset and compared with other state-of-the-art metagenomic clustering methods including CONCOCT, Metabin2.0, Autometa, and MetaBAT. The results show that our method can achieve higher precision rate and improve the binning effect.}, } @article {pmid35639164, year = {2022}, author = {Jácome, R and Campillo-Balderas, JA and Becerra, A and Lazcano, A}, title = {Structural Analysis of Monomeric RNA-Dependent Polymerases Revisited.}, journal = {Journal of molecular evolution}, volume = {90}, number = {3-4}, pages = {283-295}, pmid = {35639164}, issn = {1432-1432}, mesh = {Amino Acid Sequence ; DNA-Directed DNA Polymerase ; *DNA-Directed RNA Polymerases/genetics ; *Evolution, Molecular ; Phylogeny ; RNA/genetics ; }, abstract = {In the past few years, our understanding of the RNA virosphere has changed dramatically due to the growth and spurt of metagenomics, exponentially increasing the number of RNA viral sequences, and providing a better understanding of their range of potential hosts. As of today, the only conserved protein among RNA viruses appears to be the monomeric RNA-dependent RNA polymerase. This enzyme belongs to the right-hand DNA-and RNA polymerases, which also includes reverse transcriptases and eukaryotic replicative DNA polymerases. The ubiquity of this protein in RNA viruses makes it a unique evolutionary marker and an appealing broad-spectrum antiviral target. In this work pairwise structural comparisons of viral RdRps and RTs were performed, including tertiary structures that have been obtained in the last few years. The resulting phylogenetic tree shows that the RdRps from (+)ss- and dsRNA viruses might have been recruited several times throughout the evolution of mobile genetic elements. RTs also display multiple evolutionary routes. We have identified a structural core comprising the entire palm, a large moiety of the fingers and the N-terminal helices of the thumb domain, comprising over 300 conserved residues, including two regions that we have named the "knuckles" and the "hypothenar eminence". The conservation of an helix bundle in the region preceding the polymerase domain confirms that (-)ss and dsRNA Reoviruses' polymerases share a recent ancestor. Finally, the inclusion of DNA polymerases into our structural analyses suggests that monomeric RNA-dependent polymerases might have diverged from B-family polymerases.}, } @article {pmid35639003, year = {2022}, author = {Xiang, R and Li, M}, title = {Detection of a Novel Metallo-β-Lactamase, CAM-2, in a Metagenome-Assembled Genome from China.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0026122}, pmid = {35639003}, issn = {2165-0497}, mesh = {Anti-Bacterial Agents ; Bacterial Proteins/genetics ; China ; Klebsiella pneumoniae/genetics ; *Metagenome ; Microbial Sensitivity Tests ; *beta-Lactamases/genetics ; }, } @article {pmid35638829, year = {2022}, author = {Lawal, OU and Zhang, L and Parreira, VR and Brown, RS and Chettleburgh, C and Dannah, N and Delatolla, R and Gilbride, KA and Graber, TE and Islam, G and Knockleby, J and Ma, S and McDougall, H and McKay, RM and Mloszewska, A and Oswald, C and Servos, M and Swinwood-Sky, M and Ybazeta, G and Habash, M and Goodridge, L}, title = {Metagenomics of Wastewater Influent from Wastewater Treatment Facilities across Ontario in the Era of Emerging SARS-CoV-2 Variants of Concern.}, journal = {Microbiology resource announcements}, volume = {11}, number = {7}, pages = {e0036222}, pmid = {35638829}, issn = {2576-098X}, support = {//Ontario Genomics (OG)/ ; }, abstract = {We report metagenomic sequencing analyses of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) RNA in composite wastewater influent from 10 regions in Ontario, Canada, during the transition between Delta and Omicron variants of concern. The Delta and Omicron BA.1/BA.1.1 and BA.2-defining mutations occurring in various frequencies were reported in the consensus and subconsensus sequences of the composite samples.}, } @article {pmid35638779, year = {2022}, author = {Attai, H and Wilde, J and Liu, R and Chopyk, J and Garcia, AG and Allen-Vercoe, E and Pride, D}, title = {Bacteriophage-Mediated Perturbation of Defined Bacterial Communities in an In Vitro Model of the Human Gut.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0113522}, pmid = {35638779}, issn = {2165-0497}, mesh = {Animals ; Bacteria ; *Bacteriophages ; Bacteroidetes ; Feces/microbiology ; Gastrointestinal Tract/microbiology ; Humans ; Mice ; *Microbiota ; *Viruses ; }, abstract = {The study of bacteriophage communities reproducing in the gastrointestinal tract is limited by the quality of model systems supporting experimental manipulation in vitro. Traditionally, studies aiming to experimentally address phage-bacteria dynamics have utilized gnotobiotic mice inoculated with defined bacterial communities. While mouse models simulate complex interactions between microbes and their host, they also forestall the study of phage-bacteria dynamics in isolation of host factors. Here, we established a method for manipulating phage-bacteria dynamics using an in vitro chemostat bioreactor model of the distal human gut. We create defined communities representing a subset of bacteria in the feces of two human individuals, cultivated these communities in chemostat bioreactors, developed methods to purify the autochthonous viromes associated with each cultured community, and trialed a system for transmitting live or heat-killed viruses between chemostat bioreactors to decipher outcomes of virus-mediated perturbation. We found that allochthonous viromes were detectable via metagenomic sequencing against the autochthonous virome background and that shifts in bacterial community diversity and composition were detectable in relation to time posttreatment. These microbiome composition changes spanned multiple phyla, including Bacteroidetes, Firmicutes, and Actinobacteria. We also found that compositional changes occurred when using live viruses regardless of whether intrasubject or intersubject viruses were used as the perturbation agents. Our results supported the use of chemostat bioreactors as a platform for studying complex bacteria-phage dynamics in vitro. IMPORTANCE Bacteriophages are relatively ubiquitous in the environment and are highly abundant in the human microbiome. Phages can be commonly transmitted between close contacts, but the impact that such transmissions may have on their bacteria counterparts in our microbiomes is unknown. We developed a chemostat cultivation system to simulate individual-specific features of human distal gut microbiota that can be used to transmit phages between ecosystems and measure their impacts on the microbiota. We used this system to transfer phage communities between chemostats that represented different human subjects. We found that there were significant effects on overall microbiota diversity and changes in the relative abundances of Bacteroidetes, Firmicutes, and Actinobacteria, when intersubject perturbations were performed, compared to intrasubject perturbations. These changes were observed when perturbations were performed using live phages, but not when heat-killed phages were used, and they support the use of chemostat systems for studying complex human bacteria-phage dynamics.}, } @article {pmid35638728, year = {2022}, author = {Zhang, SY and Suttner, B and Rodriguez-R, LM and Orellana, LH and Conrad, RE and Liu, F and Rowell, JL and Webb, HE and Williams-Newkirk, AJ and Huang, A and Konstantinidis, KT}, title = {ROCker Models for Reliable Detection and Typing of Short-Read Sequences Carrying β-Lactamase Genes.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0128121}, pmid = {35638728}, issn = {2379-5077}, mesh = {Humans ; *beta-Lactamases/genetics ; Phylogeny ; *Anti-Bacterial Agents/pharmacology ; beta-Lactams ; Drug Resistance, Microbial ; }, abstract = {Identification of genes encoding β-lactamases (BLs) from short-read sequences remains challenging due to the high frequency of shared amino acid functional domains and motifs in proteins encoded by BL genes and related non-BL gene sequences. Divergent BL homologs can be frequently missed during similarity searches, which has important practical consequences for monitoring antibiotic resistance. To address this limitation, we built ROCker models that targeted broad classes (e.g., class A, B, C, and D) and individual families (e.g., TEM) of BLs and challenged them with mock 150-bp- and 250-bp-read data sets of known composition. ROCker identifies most-discriminant bit score thresholds in sliding windows along the sequence of the target protein sequence and hence can account for nondiscriminative domains shared by unrelated proteins. BL ROCker models showed a 0% false-positive rate (FPR), a 0% to 4% false-negative rate (FNR), and an up-to-50-fold-higher F1 score [2 × precision × recall/(precision + recall)] compared to alternative methods, such as similarity searches using BLASTx with various e-value thresholds and BL hidden Markov models, or tools like DeepARG, ShortBRED, and AMRFinder. The ROCker models and the underlying protein sequence reference data sets and phylogenetic trees for read placement are freely available through http://enve-omics.ce.gatech.edu/data/rocker-bla. Application of these BL ROCker models to metagenomics, metatranscriptomics, and high-throughput PCR gene amplicon data should facilitate the reliable detection and quantification of BL variants encoded by environmental or clinical isolates and microbiomes and more accurate assessment of the associated public health risk, compared to the current practice. IMPORTANCE Resistance genes encoding β-lactamases (BLs) confer resistance to the widely prescribed antibiotic class β-lactams. Therefore, it is important to assess the prevalence of BL genes in clinical or environmental samples for monitoring the spreading of these genes into pathogens and estimating public health risk. However, detecting BLs in short-read sequence data is technically challenging. Our ROCker model-based bioinformatics approach showcases the reliable detection and typing of BLs in complex data sets and thus contributes toward solving an important problem in antibiotic resistance surveillance. The ROCker models developed substantially expand the toolbox for monitoring antibiotic resistance in clinical or environmental settings.}, } @article {pmid35638605, year = {2022}, author = {Dillard, BA and Chung, AK and Gunderson, AR and Campbell-Staton, SC and Moeller, AH}, title = {Humanization of wildlife gut microbiota in urban environments.}, journal = {eLife}, volume = {11}, number = {}, pages = {}, pmid = {35638605}, issn = {2050-084X}, support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; }, mesh = {Animals ; Animals, Wild ; Bacteria/genetics ; Cities ; *Gastrointestinal Microbiome ; Humans ; *Lizards ; Urbanization ; }, abstract = {Urbanization is rapidly altering Earth's environments, demanding investigation of the impacts on resident wildlife. Here, we show that urban populations of coyotes (Canis latrans), crested anole lizards (Anolis cristatellus), and white-crowned sparrows (Zonotrichia leucophrys) acquire gut microbiota constituents found in humans, including gut bacterial lineages associated with urbanization in humans. Comparisons of urban and rural wildlife and human populations revealed significant convergence of gut microbiota among urban populations relative to rural populations. All bacterial lineages overrepresented in urban wildlife relative to rural wildlife and differentially abundant between urban and rural humans were also overrepresented in urban humans relative to rural humans. Remarkably, the bacterial lineage most overrepresented in urban anoles was a Bacteroides sequence variant that was also the most significantly overrepresented in urban human populations. These results indicate parallel effects of urbanization on human and wildlife gut microbiota and suggest spillover of bacteria from humans into wildlife in cities.}, } @article {pmid35637503, year = {2022}, author = {Ning, Y and Hu, M and Gong, Y and Huang, R and Xu, K and Chen, S and Zhang, F and Liu, Y and Chen, F and Chang, Y and Zhao, G and Li, C and Zhou, R and Lammi, MJ and Guo, X and Wang, X}, title = {Comparative analysis of the gut microbiota composition between knee osteoarthritis and Kashin-Beck disease in Northwest China.}, journal = {Arthritis research & therapy}, volume = {24}, number = {1}, pages = {129}, pmid = {35637503}, issn = {1478-6362}, mesh = {China/epidemiology ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; *Kashin-Beck Disease/genetics ; *Osteoarthritis, Knee/genetics ; }, abstract = {BACKGROUND: Osteoarthritis (OA) and Kashin-Beck disease (KBD) both are two severe osteochondral disorders. In this study, we aimed to compare the gut microbiota structure between OA and KBD patients.

METHODS: Fecal samples collected from OA and KBD patients were used to characterize the gut microbiota using 16S rDNA gene sequencing. To identify whether gut microbial changes at the species level are associated with the genes or functions of the gut bacteria between OA and KBD groups, metagenomic sequencing of fecal samples from OA and KBD subjects was performed.

RESULTS: The OA group was characterized by elevated Epsilonbacteraeota and Firmicutes levels. A total of 52 genera were identified to be significantly differentially abundant between the two groups. The genera Raoultella, Citrobacter, Flavonifractor, g__Lachnospiraceae_UCG-004, and Burkholderia-Caballeronia-Paraburkholderia were more abundant in the OA group. The KBD group was characterized by higher Prevotella_9, Lactobacillus, Coprococcus_2, Senegalimassilia, and Holdemanella. The metagenomic sequencing showed that the Subdoligranulum_sp._APC924/74, Streptococcus_parasanguinis, and Streptococcus_salivarius were significantly increased in abundance in the OA group compared to those in the KBD group, and the species Prevotella_copri, Prevotella_sp._CAG:386, and Prevotella_stercorea were significantly decreased in abundance in the OA group compared to those in the KBD group by using metagenomic sequencing.

CONCLUSION: Our study provides a comprehensive landscape of the gut microbiota between OA and KBD patients and provides clues for better understanding the mechanisms underlying the pathogenesis of OA and KBD.}, } @article {pmid35637399, year = {2022}, author = {Salih, H and Karaynir, A and Yalcin, M and Oryasin, E and Holyavkin, C and Basbulbul, G and Bozdogan, B}, title = {Metagenomic analysis of wastewater phageome from a University Hospital in Turkey.}, journal = {Archives of microbiology}, volume = {204}, number = {6}, pages = {353}, pmid = {35637399}, issn = {1432-072X}, mesh = {*Bacteriophages/genetics ; Ecosystem ; Hospitals ; Humans ; *Podoviridae/genetics ; Turkey ; Virome ; Wastewater ; }, abstract = {Phage DNA analysis gives opportunity to understand living ecosystem of the environment where the samples are taken. In the present study, we analyzed phage DNA obtained from wastewater sample of university hospital sewage. After filtration, long high-speed centrifugation was done to collect phages. DNA was extracted from pellet by phenol chloroform extraction and used for NGS sequencing. The host profile, taxonomic and functional analyses were performed using MG-RAST, and ResFinder program was used for resistance gene detection. High amounts of reads belong to bacteriophage groups (~ 95%) from our DNA sample were obtained and all bacteriophage reads were found belonging to Caudovirales order and Myoviridae (56%), Siphoviridae (43%), and Podoviridae (0.02%) families. The most common host genera were Escherichia (88.20%), Salmonella (5.49%) and Staphylococcus (5.19%). SEED subsystems hits were mostly structural parts and KEGG Orthology hits were nucleotide- and carbohydrate metabolism-related genes. No anti-microbial resistance genes were detected. Our bacteriophage DNA purification method is favorable for phage metagenomic studies. Dominance of coliphages may explain infrequent Podoviridae. Dominancy of structural genes and auxiliary genes is probably due to abundance of lytic phages in our sample. Absence of antibiotic resistance genes even in hospital environment phages indicates that phages are not important carrier of resistance genes.}, } @article {pmid35636700, year = {2022}, author = {Alma'abadi, A and Behzad, H and Alarawi, M and Conchouso, D and Saito, Y and Hosokawa, M and Nishikawa, Y and Kogawa, M and Takeyama, H and Mineta, K and Gojobori, T}, title = {Identification of lipolytic enzymes using high-throughput single-cell screening and sorting of a metagenomic library.}, journal = {New biotechnology}, volume = {70}, number = {}, pages = {102-108}, doi = {10.1016/j.nbt.2022.05.006}, pmid = {35636700}, issn = {1876-4347}, mesh = {Enzymes ; Gene Library ; Lipase/genetics/metabolism ; Metagenome ; *Metagenomics ; *Microbiota ; }, abstract = {The demand for novel, robust microbial biocatalysts for use in industrial and pharmaceutical applications continues to increase rapidly. As a result, there is a need to develop advanced tools and technologies to exploit the vast metabolic potential of unculturable microorganisms found in various environments. Single-cell and functional metagenomics studies can explore the enzymatic potential of entire microbial communities in a given environment without the need to culture the microorganisms. This approach has contributed substantially to the discovery of unique microbial genes for industrial and medical applications. Functional metagenomics involves the extraction of microbial DNA directly from environmental samples, constructing expression libraries comprising the entire microbial genome, and screening of the libraries for the presence of desired phenotypes. In this study, lipolytic enzymes from the Red Sea were targeted. A high-throughput single-cell microfluidic platform combined with a laser-based fluorescent screening bioassay was employed to discover new genes encoding lipolytic enzymes. Analysis of the metagenomic library led to the identification of three microbial genes encoding lipases based on their functional similarity and sequence homology to known lipases. The results demonstrated that microfluidics is a robust technology that can be used for screening in functional metagenomics. The results also indicate that the Red Sea is a promising, under-investigated source of new genes and gene products.}, } @article {pmid35636652, year = {2022}, author = {Li, B and Zhong, D and Qiao, J and Jiang, X}, title = {GNPI: Graph normalization to integrate phylogenetic information for metagenomic host phenotype prediction.}, journal = {Methods (San Diego, Calif.)}, volume = {205}, number = {}, pages = {11-17}, doi = {10.1016/j.ymeth.2022.05.007}, pmid = {35636652}, issn = {1095-9130}, mesh = {Humans ; Machine Learning ; *Metagenome ; *Metagenomics/methods ; Phenotype ; Phylogeny ; }, abstract = {Microorganisms play important roles in our lives especially on metabolism and diseases. Determining the probability of human suffering from specific diseases and the severity of the disease based on microbial genes is the crucial research for understanding the relationship between microbes and diseases. Previous could extract the topological information of phylogenetic trees and integrate them to metagenomic datasets, thus enable classifiers to learn more information in limited datasets and thus improve the performance of the models. In this paper, we proposed a GNPI model to better learn the structure of phylogenetic trees. GNPI maintained the original vector format of metagenomic datasets, while previous research had to change the input form to matrices. The vector-like form of the input data can be easily adopted in the baseline machine learning models and is available for deep learning models. The datasets processed with GNPI help enhance the accuracy of machine learning and deep learning models in three different datasets. GNPI is an interpretable data processing method for host phenotype prediction and other bioinformatics tasks.}, } @article {pmid35635922, year = {2022}, author = {Chen, F and Li, Z and Ye, Y and Lv, M and Liang, B and Yuan, Y and Cheng, HY and Liu, Y and He, Z and Wang, H and Wang, Y and Wang, A}, title = {Coupled sulfur and electrode-driven autotrophic denitrification for significantly enhanced nitrate removal.}, journal = {Water research}, volume = {220}, number = {}, pages = {118675}, doi = {10.1016/j.watres.2022.118675}, pmid = {35635922}, issn = {1879-2448}, mesh = {Autotrophic Processes ; Bioreactors/microbiology ; *Denitrification ; Electrodes ; *Nitrates ; Nitrogen ; Nitrogen Oxides ; Sulfates ; Sulfur ; }, abstract = {Elemental sulfur (S[0])-based autotrophic denitrification (SAD) has gained intensive attention in the treatment of secondary effluent for its low cost, high efficiency, and good stability. However, in practice, the supplementary addition of limestone is necessary to balance the alkalinity consumption during SAD operation, which increases water hardness and reduces the effective reaction volume. In this study, a coupled sulfur and electrode-driven autotrophic denitrification (SEAD) process was proposed with superior nitrate removal performance, less accumulation of sulfate, and self-balance of acidity-alkalinity capacity by regulating the applied voltage. The dual-channel electron supply from S[0] and electrodes made the nitrate removal rate constant k in the SEAD process 3.7-5.1 and 1.4-3.5 times higher than that of the single electrode- and sulfur-driven systems, respectively. The S° contributed to 75.3%-83.1% of nitrate removal and the sulfate yield during SEAD (5.67-6.26 mg SO4[2-]/mg NO3[-]-N) was decreased by 17%-25% compared with SAD. The S[0] particle and electrode both as active bio-carriers constructed collaborative denitrification communities and functional genes. Pseudomonas, Ralstonia and Brevundimonas were the dominant denitrifying genera in S[0] particle biofilm, while Pseudomonas, Chryseobacterium, Pantoea and Comamonas became dominant denitrifying genera in the cathode biofilm. The narG/Z/H/Y/I/V, nxrA/B, napA/B, nirS/K, norB/C and nosZ were potential functional genes for efficient nitrate reduction during the SEAD process. Metagenomic sequencing indicated that S[0] as an electron donor has greater potential for complete denitrification than the electrode. These findings revealed the potential of SEAD for acting as a highly efficient post denitrification process.}, } @article {pmid35634768, year = {2022}, author = {Galaz-Davison, P and Ferreiro, DU and Ramírez-Sarmiento, CA}, title = {Coevolution-derived native and non-native contacts determine the emergence of a novel fold in a universally conserved family of transcription factors.}, journal = {Protein science : a publication of the Protein Society}, volume = {31}, number = {6}, pages = {e4337}, pmid = {35634768}, issn = {1469-896X}, mesh = {DNA-Directed RNA Polymerases/chemistry ; *Escherichia coli Proteins/chemistry ; Peptide Elongation Factors/chemistry/genetics/metabolism ; Trans-Activators/chemistry ; *Transcription Factors/chemistry ; }, abstract = {The NusG protein family is structurally and functionally conserved in all domains of life. Its members directly bind RNA polymerases and regulate transcription processivity and termination. RfaH, a divergent sub-family in its evolutionary history, is known for displaying distinct features than those in NusG proteins, which allows them to regulate the expression of virulence factors in enterobacteria in a DNA sequence-dependent manner. A striking feature is its structural interconversion between an active fold, which is the canonical NusG three-dimensional structure, and an autoinhibited fold, which is distinctively novel. How this novel fold is encoded within RfaH sequence to encode a metamorphic protein remains elusive. In this work, we used publicly available genomic RfaH protein sequences to construct a complete multiple sequence alignment, which was further augmented with metagenomic sequences and curated by predicting their secondary structure propensities using JPred. Coevolving pairs of residues were calculated from these sequences using plmDCA and GREMLIN, which allowed us to detect the enrichment of key metamorphic contacts after sequence filtering. Finally, we combined our coevolutionary predictions with molecular dynamics to demonstrate that these interactions are sufficient to predict the structures of both native folds, where coevolutionary-derived non-native contacts may play a key role in achieving the compact RfaH novel fold. All in all, emergent coevolutionary signals found within RfaH sequences encode the autoinhibited and active folds of this protein, shedding light on the key interactions responsible for the action of this metamorphic protein.}, } @article {pmid35634545, year = {2022}, author = {García-Cazorla, Y and Vasconcelos, V}, title = {Emergent marine toxins risk assessment using molecular and chemical approaches.}, journal = {EFSA journal. European Food Safety Authority}, volume = {20}, number = {Suppl 1}, pages = {e200422}, pmid = {35634545}, issn = {1831-4732}, abstract = {Cyanobacteria harmful blooms represent a deviation to the normal equilibrium in planktonic communities involving a rapid and uncontrolled growth. Owing to the capacity to produce toxins as secondary metabolites, cyanobacteria may cause huge economic losses in the fishing and aquaculture industries and poisoning incidents to humans due to their accumulation in the food chain. The conditions which promote toxic blooms have not yet been fully understood, but climate change and anthropogenic intervention are pointed as significant factors. For the detection of toxins in edible marine organisms, the establishment of international regulations and compulsory surveillance has been probed as exceptionally effective. However, not regulation nor monitoring have been settled concerning emergent marine toxins. In the light of this scenario, it becomes essential to apply fast and reliable surveillance methodologies for the early detection of cyanobacterial blooms as well as the occurrence of emergent marine toxins. Shotgun metagenomic sequencing has potential to become a powerful diagnostic tool in the fields of food safety and One Health surveillance. This culture-independent approach overcomes limitations of traditional microbiological techniques; it allows a quick and accurate assessment of a complex microbial community, including quantitative identification and functional characterisation, in a single experiment. In the framework of the EU-FORA fellowship, with the final goal of evaluate metagenomics as a promising risk assessment tool, the fellow worked on the development of an innovative workflow through state-of-the-art molecular and chemical analytical procedures. This work programme aims to evaluate the occurrence of emergent marine toxins and the producing organisms in Cabo Verde coastal cyanobacteria blooms. Our results show the outstanding potential of a holistic metagenomic approach for the risk assessment of emergent marine toxins and the producing organisms. Additionally, we have also highlighted its value for the identification and evaluation of secondary metabolites as natural bioactive compounds with biotechnological and industrial interest.}, } @article {pmid35633934, year = {2022}, author = {Fernandes, AO and Barros, GS and Batista, MV}, title = {Metatranscriptomics Analysis Reveals Diverse Viral RNA in Cutaneous Papillomatous Lesions of Cattle.}, journal = {Evolutionary bioinformatics online}, volume = {18}, number = {}, pages = {11769343221083960}, pmid = {35633934}, issn = {1176-9343}, abstract = {Bovine papillomavirus (BPV) is associated with bovine papillomatosis, a disease that forms benign warts in epithelial tissues, as well as malignant lesions. Previous studies have detected a co-infection between BPV and other viruses, making it likely that these co-infections could influence disease progression. Therefore, this study aimed to identify and annotate viral genes in cutaneous papillomatous lesions of cattle. Sequences were obtained from the GEO database, and an RNA-seq computational pipeline was used to analyze 3 libraries from bovine papillomatous lesions. In total, 25 viral families were identified, including Poxviridae, Retroviridae, and Herpesviridae. All libraries shared similarities in the viruses and genes found. The viral genes shared similarities with BPV genes, especially for functions as virion entry pathway, malignant progression by apoptosis suppression and immune system control. Therefore, this study presents relevant data extending the current knowledge regarding the viral microbiome in BPV lesions and how other viruses could affect this disease.}, } @article {pmid35633691, year = {2022}, author = {Zhao, T and Li, BQ and Gao, HT and Xing, D and Li, MJ and Dang, YQ and Zhang, HD and Zhao, YE and Liu, Z and Li, CX}, title = {Metagenome Sequencing Reveals the Microbiome of Aedes albopictus and Its Possible Relationship With Dengue Virus Susceptibility.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {891151}, pmid = {35633691}, issn = {1664-302X}, abstract = {Dengue fever virus (DENV) is a mosquito-borne flavivirus that poses a serious risk to human health. Aedes albopictus is a widely distributed vector of dengue fever in China. Based on the impact of physiological activity, the microbiome in A. albopictus will provide a novel environment-friendly approach to control DENV transmission. We performed metagenomic sequencing on A. albopictus before and after exposure to DENV blood meal to detect microbiome variation of A. albopictus with different susceptibilities to DENV. The dominant phyla in A. albopictus microbiome were Proteobacteria and Ascomycota, and the dominant genera were Aspergillus and Metarhizium. Gammaproteobacteria bacterium, Lactobacillus harbinensis, and Neurospora crassa differed significantly after DENV infection. There were 15 different microorganisms found to be involved in mosquito immunity and metabolism, such as Alphaproteobacteria bacterium, Methyloglobulus morosus, and Shigella sonnei, which might have an impact on the DENV susceptibility of A. albopictus. It was hypothesized that the lack of specific bacteria may lead to increased susceptibility of A. albopictus to DENV. Interventions in the microbiome composition or specific bacteria of A. albopictus may affect the susceptibility to DENV and control the mosquito-borne diseases efficiently.}, } @article {pmid35633679, year = {2022}, author = {Ye, L and Dong, N and Xiong, W and Li, J and Li, R and Heng, H and Chan, EWC and Chen, S}, title = {High-Resolution Metagenomics of Human Gut Microbiota Generated by Nanopore and Illumina Hybrid Metagenome Assembly.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {801587}, pmid = {35633679}, issn = {1664-302X}, abstract = {Metagenome assembly is a core yet methodologically challenging step for taxonomic classification and functional annotation of a microbiome. This study aims to generate the high-resolution human gut metagenome using both Illumina and Nanopore platforms. Assembly was achieved using four assemblers, including Flye (Nanopore), metaSPAdes (Illumina), hybridSPAdes (Illumina and Nanopore), and OPERA-MS (Illumina and Nanopore). Hybrid metagenome assembly was shown to generate contigs with almost same sizes comparable to those produced using Illumina reads alone, but was more contiguous, informative, and longer compared with those assembled with Illumina reads only. In addition, hybrid metagenome assembly enables us to obtain complete plasmid sequences and much more AMR gene-encoding contigs than the Illumina method. Most importantly, using our workflow, 58 novel high-quality metagenome bins were obtained from four assembly algorithms, particularly hybrid assembly (47/58), although metaSPAdes could provide 11 high-quality bins independently. Among them, 29 bins were currently uncultured bacterial metagenome-assembled genomes. These findings were highly consistent and supported by mock community data tested. In the analysis of biosynthetic gene clusters (BGCs), the number of BGCs in the contigs from hybridSPAdes (241) is higher than that of contigs from metaSPAdes (233). In conclusion, hybrid metagenome assembly could significantly enhance the efficiency of contig assembly, taxonomic binning, and genome construction compared with procedures using Illumina short-read data alone, indicating that nanopore long reads are highly useful in metagenomic applications. This technique could be used to create high-resolution references for future human metagenome studies.}, } @article {pmid35633673, year = {2022}, author = {Maestre-Carballa, L and Navarro-López, V and Martinez-Garcia, M}, title = {A Resistome Roadmap: From the Human Body to Pristine Environments.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {858831}, pmid = {35633673}, issn = {1664-302X}, abstract = {A comprehensive characterization of the human body resistome [sets of antibiotic resistance genes (ARGs)] is yet to be done and paramount for addressing the antibiotic microbial resistance threat. Here, we study the resistome of 771 samples from five major body parts (skin, nares, vagina, gut, and oral cavity) of healthy subjects from the Human Microbiome Project (HMP) and addressed the potential dispersion of ARGs in pristine environments. A total of 28,714 ARGs belonging to 235 different ARG types were found in the HMP proteome dataset (n = 9.1 × 10[7] proteins analyzed). Our study reveals a distinct resistome profile (ARG type and abundance) between body sites and high interindividual variability. Nares had the highest ARG load (≈5.4 genes/genome) followed by the oral cavity, whereas the gut showed one of the highest ARG richness (shared with nares) but the lowest abundance (≈1.3 genes/genome). The fluroquinolone resistance genes were the most abundant in the human body, followed by macrolide-lincosamide-streptogramin (MLS) or tetracycline. Most ARGs belonged to common bacterial commensals and multidrug resistance trait were predominant in the nares and vagina. Many ARGs detected here were considered as low risk for human health, whereas only a few of them, such as BlaZ, dfrA14, dfrA17, or tetM, were classified as high-risk ARG. Our data also provide hope, since the spread of common ARG from the human body to pristine environments (n = 271 samples; 77 Gb of sequencing data and 2.1 × 10[8] proteins analyzed) thus far remains very unlikely (only one case found in an autochthonous bacterium from a pristine environment). These findings broaden our understanding of ARG in the context of the human microbiome and the One-Health Initiative of WHO uniting human host-microbes and environments as a whole.}, } @article {pmid35633118, year = {2022}, author = {Tham, KC and Lefferdink, R and Duan, K and Lim, SS and Wong, XFCC and Ibler, E and Wu, B and Abu-Zayed, H and Rangel, SM and Del Duca, E and Chowdhury, M and Chima, M and Kim, HJ and Lee, B and Guttman-Yassky, E and Paller, AS and Common, JEA}, title = {Distinct skin microbiome community structures in congenital ichthyosis.}, journal = {The British journal of dermatology}, volume = {187}, number = {4}, pages = {557-570}, pmid = {35633118}, issn = {1365-2133}, support = {P30 AR075049/AR/NIAMS NIH HHS/United States ; }, mesh = {Adult ; Humans ; *Ichthyosiform Erythroderma, Congenital ; *Ichthyosis/genetics ; *Ichthyosis, Lamellar/genetics ; Lipids ; *Microbiota/genetics ; Skin/pathology ; }, abstract = {BACKGROUND: The ichthyoses are rare genetic keratinizing disorders that share the characteristics of an impaired epidermal barrier and increased risk of microbial infections. Although ichthyotic diseases share a T helper (Th) 17 cell immune signature, including increased expression of antimicrobial peptides, the skin microbiota of ichthyoses is virtually unexplored.

OBJECTIVES: To analyse the metagenome profile of skin microbiome for major congenital ichthyosis subtypes.

METHODS: Body site-matched skin surface samples were collected from the scalp, upper arm and upper buttocks of 16 healthy control participants and 22 adult patients with congenital forms of ichthyosis for whole metagenomics sequencing analysis.

RESULTS: Taxonomic profiling showed significant shifts in bacteria and fungi abundance and sporadic viral increases across ichthyosis subtypes. Cutibacterium acnes and Malassezia were significantly reduced across body sites, consistent with skin barrier disruption and depletion of lipids. Microbial richness was reduced, with specific increases in Staphylococcus and Corynebacterium genera, as well as shifts in fungal species, including Malassezia. Malassezia globosa was reduced at all body sites, whereas M. sympodialis was reduced in the ichthyotic upper arm and upper buttocks. Malassezia slooffiae, by contrast, was strikingly increased at all body sites in participants with congenital ichthyosiform erythroderma (CIE) and lamellar ichthyosis (LI). A previously undescribed Trichophyton species was also detected as sporadically colonizing the skin of patients with CIE, LI and epidermolytic ichthyosis subtypes.

CONCLUSIONS: The ichthyosis skin microbiome is significantly altered from healthy skin with specific changes predominating among ichthyosis subtypes. Skewing towards the Th17 pathway may represent a response to the altered microbial colonization in ichthyosis. What is already known about this topic? The skin microbiome of congenital ichthyoses is largely unexplored. Microbes play an important role in pathogenesis, as infections are common. The relative abundances of staphylococci and corynebacteria is increased in the cutaneous microbiome of patients with Netherton syndrome, but extension of these abundances to all congenital ichthyoses is unexplored. What does this study add? A common skin microbiome signature was observed across congenital ichthyoses. Distinct microbiome features were associated with ichthyosis subtypes. Changes in microbiome may contribute to T helper 17 cell immune polarization. What is the translational message? These data provide the basis for comparison of the microbiome with lipidomic and transcriptomic alterations in these forms of ichthyosis and consideration of correcting the dysbiosis as a therapeutic intervention.}, } @article {pmid35632735, year = {2022}, author = {Juergens, KB and Huckabee, J and Greninger, AL}, title = {Two Novel Iflaviruses Discovered in Bat Samples in Washington State.}, journal = {Viruses}, volume = {14}, number = {5}, pages = {}, pmid = {35632735}, issn = {1999-4915}, mesh = {Animals ; *Chiroptera ; Ecosystem ; Nucleotides ; Phylogeny ; RNA Viruses ; *Viruses/genetics ; Washington ; }, abstract = {Arthropods are integral to ecosystem equilibrium, serving as both a food source for insectivores and supporting plant reproduction. Members of the Iflaviridae family in the order Picornavirales are frequently found in RNA sequenced from arthropods, who serve as their hosts. Here we implement a metagenomic deep sequencing approach followed by rapid amplification of cDNA ends (RACE) on viral RNA isolated from wild and captured bat guano in Washington State at two separate time points. From these samples we report the complete genomes of two novel viruses in the family Iflaviridae. The first virus, which we call King virus, is 46% identical by nucleotide to the lethal honeybee virus, deformed wing virus, while the second virus which we call Rolda virus, shares 39% nucleotide identity to deformed wing virus. King and Rolda virus genomes are 10,183 and 8934 nucleotides in length, respectively. Given these iflaviruses were detected in guano from captive bats whose sole food source was the Tenebrio spp. mealworm, we anticipate this invertebrate may be a likely host. Using the NCBI Sequence Read Archive, we found that these two viruses are located in six continents and have been isolated from a variety of arthropod and mammalian specimens.}, } @article {pmid35632715, year = {2022}, author = {Hufsky, F and Beslic, D and Boeckaerts, D and Duchene, S and González-Tortuero, E and Gruber, AJ and Guo, J and Jansen, D and Juma, J and Kongkitimanon, K and Luque, A and Ritsch, M and Lencioni Lovate, G and Nishimura, L and Pas, C and Domingo, E and Hodcroft, E and Lemey, P and Sullivan, MB and Weber, F and González-Candelas, F and Krautwurst, S and Pérez-Cataluña, A and Randazzo, W and Sánchez, G and Marz, M}, title = {The International Virus Bioinformatics Meeting 2022.}, journal = {Viruses}, volume = {14}, number = {5}, pages = {}, pmid = {35632715}, issn = {1999-4915}, support = {725422-ReservoirDOCS/ERC_/European Research Council/International ; R01 AI153044/AI/NIAID NIH HHS/United States ; BB/T015616/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/T016256/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; 206298/Z/17/Z/WT_/Wellcome Trust/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; 955974/MCCC_/Marie Curie/United Kingdom ; R01AI153044/NH/NIH HHS/United States ; }, mesh = {*COVID-19 ; Computational Biology ; DNA Viruses ; Humans ; SARS-CoV-2 ; *Viruses ; *Viruses, Unclassified ; }, abstract = {The International Virus Bioinformatics Meeting 2022 took place online, on 23-25 March 2022, and has attracted about 380 participants from all over the world. The goal of the meeting was to provide a meaningful and interactive scientific environment to promote discussion and collaboration and to inspire and suggest new research directions and questions. The participants created a highly interactive scientific environment even without physical face-to-face interactions. This meeting is a focal point to gain an insight into the state-of-the-art of the virus bioinformatics research landscape and to interact with researchers in the forefront as well as aspiring young scientists. The meeting featured eight invited and 18 contributed talks in eight sessions on three days, as well as 52 posters, which were presented during three virtual poster sessions. The main topics were: SARS-CoV-2, viral emergence and surveillance, virus-host interactions, viral sequence analysis, virus identification and annotation, phages, and viral diversity. This report summarizes the main research findings and highlights presented at the meeting.}, } @article {pmid35632697, year = {2022}, author = {Bal, A and Destras, G and Sabatier, M and Pichon, M and Regue, H and Oriol, G and Gillet, Y and Lina, B and Brengel-Pesce, K and Josset, L and Morfin, F}, title = {Metagenomic Analysis Reveals High Abundance of Torque Teno Mini Virus in the Respiratory Tract of Children with Acute Respiratory Illness.}, journal = {Viruses}, volume = {14}, number = {5}, pages = {}, pmid = {35632697}, issn = {1999-4915}, mesh = {*Anelloviridae/genetics ; Child ; *DNA Virus Infections ; Humans ; *Influenza, Human ; *Respiratory Syncytial Virus, Human ; Respiratory System ; *Respiratory Tract Infections/diagnosis ; *Torque teno virus/genetics ; }, abstract = {Human Anelloviridae is a highly prevalent viral family, including three main genera—Alphatorquevirus (Torque teno virus, TTV), Betatorquevirus (Torque teno mini virus, TTMV), and Gammatorquevirus (Torque teno midi virus, TTMDV). To date, the characterization of Anelloviridae in the respiratory tract of children with acute respiratory infection (ARI) has been poorly reported and mainly focused on TTV. We performed a metagenomic analysis of eight respiratory samples collected from children with an ARI of unknown etiology (eight samples tested negative with a multiplex PCR assay, out of the 39 samples initially selected based on negative routine diagnostic testing). A total of 19 pediatric respiratory samples that tested positive for respiratory syncytial virus (RSV, n = 13) or influenza virus (n = 6) were also sequenced. Anelloviridae reads were detected in 16/27 samples, including 6/8 negative samples, 7/13 RSV samples and 3/6 influenza samples. For samples with a detection of at least one Anelloviridae genus, TTMV represented 87.1 (66.1−99.2)% of Anelloviridae reads, while TTV and TTMDV represented 0.8 (0.0−9.6)% and 0.7 (0.0−7.1)%, respectively (p < 0.001). Our findings highlight a high prevalence of TTMV in respiratory samples of children with an ARI of unknown etiology, as well as in samples with an RSV or influenza infection. Larger studies are needed to explore the role of TTMV in childhood respiratory diseases.}, } @article {pmid35632662, year = {2022}, author = {Miljanić, V and Jakše, J and Rusjan, D and Škvarč, A and Štajner, N}, title = {Small RNA Sequencing and Multiplex RT-PCR for Diagnostics of Grapevine Viruses and Virus-like Organisms.}, journal = {Viruses}, volume = {14}, number = {5}, pages = {}, pmid = {35632662}, issn = {1999-4915}, mesh = {DNA Viruses/genetics ; Plant Diseases ; RNA, Satellite/genetics ; *RNA, Small Untranslated ; Reverse Transcriptase Polymerase Chain Reaction ; Sequence Analysis, RNA ; *Viroids/genetics ; *Viruses, Unclassified/genetics ; *Vitis ; }, abstract = {Metagenomic approaches used for virus diagnostics allow for rapid and accurate detection of all viral pathogens in the plants. In order to investigate the occurrence of viruses and virus-like organisms infecting grapevine from the Ampelographic collection Kromberk in Slovenia, we used Ion Torrent small RNA sequencing (sRNA-seq) and the VirusDetect pipeline to analyze the sRNA-seq data. The used method revealed the presence of: Grapevine leafroll-associated virus 1 (GLRaV-1), Grapevine leafroll-associated virus 2 (GLRaV-2), Grapevine leafroll-associated virus 3 (GLRaV-3), Grapevine rupestris stem pitting-associated virus (GRSPaV), Grapevine fanleaf virus (GFLV) and its satellite RNA (satGFLV), Grapevine fleck virus (GFkV), Grapevine rupestris vein feathering virus (GRVFV), Grapevine Pinot gris virus (GPGV), Grapevine satellite virus (GV-Sat), Hop stunt viroid (HSVd), and Grapevine yellow speckle viroid 1 (GYSVd-1). Multiplex reverse transcription-polymerase chain reaction (mRT-PCR) was developed for validation of sRNA-seq predicted infections, including various combinations of viruses or viroids and satellite RNA. mRT-PCR could further be used for rapid and cost-effective routine molecular diagnosis, including widespread, emerging, and seemingly rare viruses, as well as viroids which testing is usually overlooked.}, } @article {pmid35632601, year = {2022}, author = {Litov, AG and Zueva, AI and Tiunov, AV and Van Thinh, N and Belyaeva, NV and Karganova, GG}, title = {Virome of Three Termite Species from Southern Vietnam.}, journal = {Viruses}, volume = {14}, number = {5}, pages = {}, pmid = {35632601}, issn = {1999-4915}, mesh = {Animals ; Ecosystem ; Forests ; *Isoptera ; *RNA Viruses ; Vietnam ; Virome ; }, abstract = {Modern metagenomic approaches enable the effective discovery of novel viruses in previously unexplored organisms. Termites are significant ecosystem converters and influencers. As with the majority of tropical forest insects, termites are studied insufficiently, and termite virome remains especially understudied. Here, we studied the virome of lichenophagous and mycophagous termites (Hospitalitermes bicolor, Macrotermes carbonarius and Odontotermes wallonensis) collected in the Cat Tien National Park (Vietnam). We assembled four full genomes of novel viruses related to Solemoviridae, Lispiviridae, Polycipiviridae and Kolmioviridae. We also found several contigs with relation to Chuviridae and Deltaflexiviridae that did not correspond to complete virus genomes. All the novel viruses clustered phylogenetically with previously identified viruses of the termites. Deltaflexi-like contigs were identified in the fungi-cultivating M. carbonarius and showed homology with viruses recently discovered in the edible basidiomycete mushrooms.}, } @article {pmid35631266, year = {2022}, author = {Wu, F and Fang, B and Wuri, G and Zhao, L and Liu, F and Zhang, M}, title = {Metagenomic Analysis Reveals a Mitigating Role for Lactobacillus paracasei and Bifidobacterium animalis in Experimental Periodontitis.}, journal = {Nutrients}, volume = {14}, number = {10}, pages = {}, pmid = {35631266}, issn = {2072-6643}, support = {31601443//National Natural Science Foundation of China/ ; 32101938//National Natural Science Foundation of China/ ; }, mesh = {*Alveolar Bone Loss ; Animals ; Bacteria ; *Bifidobacterium animalis ; *Lacticaseibacillus paracasei ; Metagenomics ; *Periodontitis/microbiology/therapy ; Rats ; }, abstract = {Probiotics have aroused increasing concern as an intervention strategy for periodontitis (PD), but their underlying mechanism of action remains poorly characterized. Regarding the significance of oral microbiota dysbiosis related to PD, we predicted that the preventive activity of probiotics may be influenced by suppressing the bacterial pathogenicity. Herein, we investigated the effects of Lactobacillus paracasei L9 (L9) and Bifidobacterium animalis A6 (A6) on PD using a rat model, and demonstrated a regulatory effect of probiotics on oral flora from a metagenomics perspective. Oral administration of A6 or L9 effectively relieved gingival bleeding, periodontal inflammatory infiltration, and alveolar bone resorption. In addition, A6 or L9 treatment reduced the inflammatory response and increased the expression of anti-inflammatory cytokines, which we expected to ameliorate alveolar bone resorption as mediated by the receptor activator of the nuclear factor-κB ligand/OPG signaling pathway. More importantly, using metagenomic sequencing, we showed that probiotics significantly altered the taxonomic composition of the subgingival microbiome, and reduced the relative proportions of pathogenic bacterial genera such as Streptococcus, Fusobacterium, Veillonella, and Escherichia. Both probiotics significantly inhibited levels of bacterial virulence factors related to adherence, invasion, exoenzyme, and complement protease functions that are strongly correlated with the pathogenesis of PD. Our overall results suggest that A6 and L9 may constitute promising prophylactic agents for PD, and should thus be further explored in the future.}, } @article {pmid35630516, year = {2022}, author = {Papadimitriou, K and Anastasiou, R and Georgalaki, M and Bounenni, R and Paximadaki, A and Charmpi, C and Alexandraki, V and Kazou, M and Tsakalidou, E}, title = {Comparison of the Microbiome of Artisanal Homemade and Industrial Feta Cheese through Amplicon Sequencing and Shotgun Metagenomics.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, pmid = {35630516}, issn = {2076-2607}, support = {//John S. Latsis Public Benefit Foundation "Scientific Studies 2015"/ ; }, abstract = {Feta is the most renowned protected designation of origin (PDO) white brined cheese produced in Greece. The fine organoleptic characteristics and the quality of Feta rely on, among other factors, its overall microbial ecosystem. In this study, we employed 16S rDNA and internal transcribed spacer (ITS) amplicon sequencing, as well as shotgun metagenomics, to investigate the microbiome of artisanal homemade and industrial Feta cheese samples from different regions of Greece, which has very rarely been investigated. 16S rDNA data suggested the prevalence of the Lactococcus genus in the homemade samples, while Streptococcus and Lactobacillus genera prevailed in the industrial control samples. Species identification deriving from shotgun metagenomics corroborated these findings, as Lactococcus lactis dominated two homemade samples while Streptococcus thermophilus and Lactobacillus delbrueckii subsp. bulgaricus were found to be dominating one industrial sample. ITS data revealed a complex diversity of the yeast population among the samples analyzed. Debaryomyces, Kluyveromyces, Cutaneotrichosporon, Pichia, Candida, and Rhodotorula were the major genera identified, which were distributed in a rather arbitrary manner among the different samples. Furthermore, a number of potential metagenome-assembled genomes (MAGs) could be detected among assembled shotgun bins. The overall analysis of the shotgun metagenomics supported the presence of different foodborne pathogens in homemade samples (e.g., Staphylococcus aureus, Listeria monocytogenes, Enterobacter cloacae, and Streptococcus suis), but with low to very low abundances. Concluding, the combination of both amplicon sequencing and shotgun metagenomics allowed us to obtain an in-depth profile of the artisanal homemade Feta cheese microbiome.}, } @article {pmid35630482, year = {2022}, author = {Amoutzias, GD and Nikolaidis, M and Hesketh, A}, title = {The Notable Achievements and the Prospects of Bacterial Pathogen Genomics.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, pmid = {35630482}, issn = {2076-2607}, abstract = {Throughout the entirety of human history, bacterial pathogens have played an important role and even shaped the fate of civilizations. The application of genomics within the last 27 years has radically changed the way we understand the biology and evolution of these pathogens. In this review, we discuss how the short- (Illumina) and long-read (PacBio, Oxford Nanopore) sequencing technologies have shaped the discipline of bacterial pathogen genomics, in terms of fundamental research (i.e., evolution of pathogenicity), forensics, food safety, and routine clinical microbiology. We have mined and discuss some of the most prominent data/bioinformatics resources such as NCBI pathogens, PATRIC, and Pathogenwatch. Based on this mining, we present some of the most popular sequencing technologies, hybrid approaches, assemblers, and annotation pipelines. A small number of bacterial pathogens are of very high importance, and we also present the wealth of the genomic data for these species (i.e., which ones they are, the number of antimicrobial resistance genes per genome, the number of virulence factors). Finally, we discuss how this discipline will probably be transformed in the near future, especially by transitioning into metagenome-assembled genomes (MAGs), thanks to long-read sequencing.}, } @article {pmid35630460, year = {2022}, author = {Gryaznova, M and Dvoretskaya, Y and Burakova, I and Syromyatnikov, M and Popov, E and Kokina, A and Mikhaylov, E and Popov, V}, title = {Dynamics of Changes in the Gut Microbiota of Healthy Mice Fed with Lactic Acid Bacteria and Bifidobacteria.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, pmid = {35630460}, issn = {2076-2607}, support = {19-76-10023//Russian Science Foundation/ ; }, abstract = {Probiotics are living microorganisms that provide numerous health benefits for their host. Probiotics have various effects on the body; for example, they change gut microbiota, improve the integrity of the epithelial barrier and have anti-inflammatory effects. The use of probiotic supplements that are based on lactic acid bacteria and bifidobacteria is one of the approaches that are used to balance gut microflora. In our study, we evaluated the effects of supplements, which were based on members of the Lactobacillaceae family and bifidobacteria, on the gut microbiome of healthy mice using the 16S rRNA sequencing method. The data that were obtained demonstrated that when mice received the probiotic supplements, statistically significant changes occurred in the composition of the microbiome at the phylum level, which were characterized by an increase in the number of Actinobacteriota, Bacteroidota, Verrucomicrobia and Proteobacteria, all of which have potentially positive effects on health. At the generic level, a decrease in the abundance of members of the Nocardioides, Helicobacter and Mucispirillum genus, which are involved in inflammatory processes, was observed for the group of mice that was fed with lactic acid bacteria. For the group of mice that was fed with bifidobacteria, a decrease was seen in the number of members of the Tyzzerella and Akkermansia genus. The results of our study contribute to the understanding of changes in the gut microbiota of healthy mice under the influence of probiotics. It was shown that probiotics that are based on members of the Lactobacillaceae family have a more positive effect on the gut microbiome than probiotics that are based on bifidobacteria.}, } @article {pmid35630399, year = {2022}, author = {Cai, Y and Yun, J and Jia, Z}, title = {Phylogeny and Metabolic Potential of the Methanotrophic Lineage MO3 in Beijerinckiaceae from the Paddy Soil through Metagenome-Assembled Genome Reconstruction.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, pmid = {35630399}, issn = {2076-2607}, support = {41877062//National Science Foundation of China/ ; 91751204//National Science Foundation of China/ ; CAS (2019311)//Youth Innovation Promotion Association/ ; }, abstract = {Although the study of aerobic methane-oxidizing bacteria (MOB, methanotrophs) has been carried out for more than a hundred years, there are many uncultivated methanotrophic lineages whose metabolism is largely unknown. Here, we reconstructed a nearly complete genome of a Beijerinckiaceae methanotroph from the enrichment of paddy soil by using nitrogen-free M2 medium. The methanotroph labeled as MO3_YZ.1 had a size of 3.83 Mb, GC content of 65.6%, and 3442 gene-coding regions. Based on phylogeny of pmoA gene and genome and the genomic average nucleotide identity, we confirmed its affiliation to the MO3 lineage and a close relationship to Methylocapsa. MO3_YZ.1 contained mxaF- and xoxF-type methanol dehydrogenase. MO3_YZ.1 used the serine cycle to assimilate carbon and regenerated glyoxylate through the glyoxylate shunt as it contained isocitrate lyase and complete tricarboxylic acid cycle-coding genes. The ethylmalonyl-CoA pathway and Calvin-Benson-Bassham cycle were incomplete in MO3_YZ.1. Three acetate utilization enzyme-coding genes were identified, suggesting its potential ability to utilize acetate. The presence of genes for N2 fixation, sulfur transformation, and poly-β-hydroxybutyrate synthesis enable its survival in heterogeneous habitats with fluctuating supplies of carbon, nitrogen, and sulfur.}, } @article {pmid35630301, year = {2022}, author = {Popescu, SC and Tomaso-Peterson, M and Wilkerson, T and Bronzato-Badial, A and Wesser, U and Popescu, GV}, title = {Metagenomic Analyses of the Soybean Root Mycobiome and Microbiome Reveal Signatures of the Healthy and Diseased Plants Affected by Taproot Decline.}, journal = {Microorganisms}, volume = {10}, number = {5}, pages = {}, pmid = {35630301}, issn = {2076-2607}, support = {53-2020//Mississippi Soybean Board/ ; }, abstract = {Invading pathogens interact with plant-associated microbial communities, which can be altered under the pressure of pathogen infection. Limited information exists on plant-microbe interactions occurring during natural outbreaks in agricultural fields. Taproot decline (TRD) of soybean is an emerging disease caused by Xylaria necrophora. TRD disease occurrence and yield loss associated with TRD are outstanding issues in soybean production. We applied nuclear ribosomal DNA Internal Transcribed Spacers and 16S rRNA gene taxonomic marker sequencing to define the composition of the fungal and bacterial communities associated with healthy and diseased soybean roots collected from the Mississippi Delta. The plant compartment was a significant factor regulating taxonomic diversity, followed by the disease status of the plant. TRD impacted the root endophytes, causing imbalances; at the intermediate and advanced stages of TRD, X. necrophora decreased mycobiome diversity, whereas it increased microbiome richness. Networks of significant co-occurrence and co-exclusion relationships revealed direct and indirect associations among taxa and identified hubs with potential roles in assembling healthy and TRD-affected soybean biomes. These studies advance the understanding of host-microbe interactions in TRD and the part of biomes in plant health and disease.}, } @article {pmid35629884, year = {2022}, author = {Sun, J and Cao, Z and Smith, AD and Carlson, PE and Coryell, M and Chen, H and Beger, RD}, title = {Evaluating Cefoperazone-Induced Gut Metabolic Functional Changes in MR1-Deficient Mice.}, journal = {Metabolites}, volume = {12}, number = {5}, pages = {}, pmid = {35629884}, issn = {2218-1989}, abstract = {Mucosal-associated invariant T cells are activated following the recognition of bacterial antigens presented by the major histocompatibility complex class I-related molecule (MR1). Previous metagenomics data showed that MR1[-/-] knock-out (KO) mice had distinct microbiota and displayed a resistance to Clostridioides difficile (CDI) colonization vs. wild-type (WT) mice. In the present study, LC/MS-based untargeted metabolomics are applied to evaluate the changes in metabolic activities, in accordance with the changes in gut microbiota caused by cefoperazone (Cef) treatment. Adult C57Bl/6J WT and MR1[-/-] KO mice were given sterile drinking water or spiked with 0.5 mg/mL Cef ad libitum for five days. Fecal pellets were collected daily, and both small intestinal and cecal contents were harvested at sacrifice. The PLS-DA score plots of the metabolomic data indicate that the microbiota is relatively less disturbed by Cef treatment in KO mice, which is consistent with the metagenomics data. The most noticeable differences in the metabolome of KO and WT mice were the increases in carbohydrates in the WT mice, but not in the KO mice. Metabolic functional biomarkers were identified through the correlation analysis of gamma-aminobutyric acid (GABA) and riboflavin. These detected metabolic functional biomarkers could provide information complementary to metagenomics data.}, } @article {pmid35629369, year = {2022}, author = {Kabaivanova, L and Petrova, P and Hubenov, V and Simeonov, I}, title = {Biogas Production Potential of Thermophilic Anaerobic Biodegradation of Organic Waste by a Microbial Consortium Identified with Metagenomics.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, pmid = {35629369}, issn = {2075-1729}, support = {KP-06-IP-China/3//BNSF/ ; }, abstract = {Anaerobic digestion (AD) is a widespread biological process treating organic waste for green energy production. In this study, wheat straw and corn stalks without any harsh preliminary treatment were collected as a renewable source to be employed in a laboratory-scale digester to produce biogas/biomethane. Processes parameters of temperature, pH, total solids, volatile solid, concentration of volatile fatty acids (VFA), and cellulose concentration, were followed. The volume of biogas produced was measured. The impact of organic loading was stated, showing that the process at 55 °C tolerated a higher substrate load, up to 45 g/L. Further substrate increase did not lead to biogas accumulation increase, probably due to inhibition or mass transfer limitations. After a 12-day anaerobic digestion process, cumulative volumes of biogas yields were 4.78 L for 1 L of the bioreactor working volume with substrate loading 30 g/L of wheat straw, 7.39 L for 40 g/L and 8.22 L for 45 g/L. The degree of biodegradation was calculated to be 68.9%, 74% and 72%, respectively. A fast, effective process for biogas production was developed from native wheat straw, with the highest quantity of daily biogas production occurring between day 2 and day 5. Biomethane concentration in the biogas was 60%. An analysis of bacterial diversity by metagenomics revealed that more than one third of bacteria belonged to class Clostridia (32.9%), followed by Bacteroidia (21.5%), Betaproteobacteria (11.2%), Gammaproteobacteria (6.1%), and Alphaproteobacteria (5%). The most prominent genera among them were Proteiniphilum, Proteiniborus, and Pseudomonas. Archaeal share was 1.37% of the microflora in the thermophilic bioreactor, as the genera Methanocorpusculum, Methanobacterium, Methanomassiliicoccus, Methanoculleus, and Methanosarcina were the most abundant. A knowledge of the microbiome residing in the anaerobic digester can be further used for the development of more effective processes in conjunction with theidentified consortium.}, } @article {pmid35629336, year = {2022}, author = {Mreyoud, Y and Song, M and Lim, J and Ahn, TH}, title = {MegaD: Deep Learning for Rapid and Accurate Disease Status Prediction of Metagenomic Samples.}, journal = {Life (Basel, Switzerland)}, volume = {12}, number = {5}, pages = {}, pmid = {35629336}, issn = {2075-1729}, support = {1564894//National Science Foundation/ ; }, abstract = {The diversity within different microbiome communities that drive biogeochemical processes influences many different phenotypes. Analyses of these communities and their diversity by countless microbiome projects have revealed an important role of metagenomics in understanding the complex relation between microbes and their environments. This relationship can be understood in the context of microbiome composition of specific known environments. These compositions can then be used as a template for predicting the status of similar environments. Machine learning has been applied as a key component to this predictive task. Several analysis tools have already been published utilizing machine learning methods for metagenomic analysis. Despite the previously proposed machine learning models, the performance of deep neural networks is still under-researched. Given the nature of metagenomic data, deep neural networks could provide a strong boost to growth in the prediction accuracy in metagenomic analysis applications. To meet this urgent demand, we present a deep learning based tool that utilizes a deep neural network implementation for phenotypic prediction of unknown metagenomic samples. (1) First, our tool takes as input taxonomic profiles from 16S or WGS sequencing data. (2) Second, given the samples, our tool builds a model based on a deep neural network by computing multi-level classification. (3) Lastly, given the model, our tool classifies an unknown sample with its unlabeled taxonomic profile. In the benchmark experiments, we deduced that an analysis method facilitating a deep neural network such as our tool can show promising results in increasing the prediction accuracy on several samples compared to other machine learning models.}, } @article {pmid35628754, year = {2022}, author = {Forgács, L and Borman, AM and Kovács, R and Balázsi, D and Tóth, Z and Balázs, B and Chun-Ju, C and Kardos, G and Kovacs, I and Majoros, L}, title = {In Vivo Efficacy of Amphotericin B against Four Candida auris Clades.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {5}, pages = {}, pmid = {35628754}, issn = {2309-608X}, support = {MR/V033417/1/MRC_/Medical Research Council/United Kingdom ; }, abstract = {Candida auris is a multidrug-resistant fungus against which in some clinical situations amphotericin B (AMB) remains the alternative or first line drug. We compared daily 1 mg/kg of AMB efficacy in a neutropenic murine bloodstream infection model against 10 isolates representing four C. auris clades (South Asian n = 2; East Asian n = 2; South African n = 2; South American n = 4; two of which were of environmental origin). Five days of AMB treatment significantly increased the survival rates in mice infected with isolates of the East Asian clade, and 1 isolate each from the South African and South American clades (originated from bloodstream), but not in mice infected with the South Asian and 2 environmental isolates from the South American clades. AMB treatment decreased the fungal burden in mice infected with the 2 isolates each from East Asian and South African, and 1 out of 2 bloodstream isolates from South American clades in the hearts (p < 0.01), kidneys (p < 0.01) and brain (p < 0.05). AMB treatment, regardless of clades, significantly decreased colony forming units in the urine at day 3. However, histopathological examination in AMB-treated mice revealed large aggregates of yeast cells in the kidneys and hearts, and focal lesions in the cerebra and cerebelli, regardless of precise C. auris clade. Our clade-specific data confirm that the efficacy of AMB against C. auris is weak, explaining the therapeutic failures in clinical situations. Our results draw attention to the necessity to maximize the killing at the start of treatment to avoid later complications in the heart and central nervous system.}, } @article {pmid35628747, year = {2022}, author = {Sen, K and Sen, B and Wang, G}, title = {Diversity, Abundance, and Ecological Roles of Planktonic Fungi in Marine Environments.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {5}, pages = {}, pmid = {35628747}, issn = {2309-608X}, support = {32170063//National Science Foundation of China/ ; }, abstract = {Fungi are considered terrestrial and oceans are a "fungal desert". However, with the considerable progress made over past decades, fungi have emerged as morphologically, phylogenetically, and functionally diverse components of the marine water column. Although their communities are influenced by a plethora of environmental factors, the most influential include salinity, temperature, nutrients, and dissolved oxygen, suggesting that fungi respond to local environmental gradients. The biomass carbon of planktonic fungi exhibits spatiotemporal dynamics and can reach up to 1 μg CL[-1] of seawater, rivaling bacteria on some occasions, which suggests their active and important role in the water column. In the nutrient-rich coastal water column, there is increasing evidence for their contribution to biogeochemical cycling and food web dynamics on account of their saprotrophic, parasitic, hyper-parasitic, and pathogenic attributes. Conversely, relatively little is known about their function in the open-ocean water column. Interestingly, methodological advances in sequencing and omics approach, the standardization of sequence data analysis tools, and integration of data through network analyses are enhancing our current understanding of the ecological roles of these multifarious and enigmatic members of the marine water column. This review summarizes the current knowledge of the diversity and abundance of planktonic fungi in the world's oceans and provides an integrated and holistic view of their ecological roles.}, } @article {pmid35628739, year = {2022}, author = {De Miccolis Angelini, RM and Raguseo, C and Rotolo, C and Gerin, D and Faretra, F and Pollastro, S}, title = {The Mycovirome in a Worldwide Collection of the Brown Rot Fungus Monilinia fructicola.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {5}, pages = {}, pmid = {35628739}, issn = {2309-608X}, abstract = {The fungus Monilinia fructicola is responsible for brown rot on stone and pome fruit and causes heavy yield losses both pre- and post-harvest. Several mycoviruses are known to infect fungal plant pathogens. In this study, a metagenomic approach was applied to obtain a comprehensive characterization of the mycovirome in a worldwide collection of 58 M. fructicola strains. Deep sequencing of double-stranded (ds)RNA extracts revealed a great abundance and variety of mycoviruses. A total of 32 phylogenetically distinct positive-sense (+) single-stranded (ss)RNA viruses were identified. They included twelve mitoviruses, one in the proposed family Splipalmiviridae, and twelve botourmiaviruses (phylum Lenarviricota), eleven of which were novel viral species; two hypoviruses, three in the proposed family Fusariviridae, and one barnavirus (phylum Pisuviricota); as well as one novel beny-like virus (phylum Kitrinoviricota), the first one identified in Ascomycetes. A partial sequence of a new putative ssDNA mycovirus related to viruses within the Parvoviridae family was detected in a M. fructicola isolate from Serbia. The availability of genomic sequences of mycoviruses will serve as a solid basis for further research aimed at deepening the knowledge on virus-host and virus-virus interactions and to explore their potential as biocontrol agents against brown rot disease.}, } @article {pmid35628675, year = {2022}, author = {Nkuna, R and Ijoma, GN and Matambo, TS}, title = {Applying EDTA in Chelating Excess Metal Ions to Improve Downstream DNA Recovery from Mine Tailings for Long-Read Amplicon Sequencing of Acidophilic Fungi Communities.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {5}, pages = {}, pmid = {35628675}, issn = {2309-608X}, abstract = {The hostile environment of mine tailings contains unique microbial life capable of bioleaching. The metagenomic analysis of such an environment provides an in-depth understanding of the microbial life and its potential, especially in biomining operations. However, DNA recovery from samples collected in those environments is challenging due to the presence of metal ions that interfere with the DNA analysis. A varied concentration of EDTA (4-13 µg/µL) to chelate the metal ions of enriched tailing samples prior to DNA extraction was performed. The results show that 9 µg/µL of EDTA was effective in most samples. However, the increasing concentration of EDTA negatively affected the DNA recovery. The sequencing of the successfully extracted DNA revealed a diverse range of fungal genera, some of which have not been previously reported in tailing or bioleaching applications. The dominant genera include Fodinomyces, Penicillium, Recurvomuces, Trichoderma, and Xenoacremonium; their traits were determined using the FungalTraits database. This study demonstrates the need to include a preliminary metal-chelating step using EDTA before DNA extractions for samples collected from metal-rich environments. It further showed the need for optimization but provided a benchmark range, particularly for tailings. However, we caution that a further EDTA removal step from the extracted DNA should be included to avoid its interferences in downstream applications.}, } @article {pmid35628544, year = {2022}, author = {Escuder-Rodríguez, JJ and DeCastro, ME and Saavedra-Bouza, A and González-Siso, MI and Becerra, M}, title = {Bioprospecting for Thermozymes and Characterization of a Novel Lipolytic Thermozyme Belonging to the SGNH/GDSL Family of Hydrolases.}, journal = {International journal of molecular sciences}, volume = {23}, number = {10}, pages = {}, pmid = {35628544}, issn = {1422-0067}, support = {ED431C 2020/08//Xunta de Galicia/ ; RTI2018-099249-B-I00//MINISTERIO DE CIENCIA, INNOVACIÓN Y UNIVERSIDADES/ ; }, mesh = {*Bioprospecting ; *Cellulase ; Lipolysis ; Metagenomics ; Substrate Specificity ; }, abstract = {Functional screenings were conducted on two metagenomic libraries from hot springs in order to find novel thermozymes with potential biotechnological applications. These included enzymes acting on plant cell walls such as endoglucanases and exoglucanases, β-glucosidases, xylanases, and β-xylosidases, and broad application enzymes such as proteases and lipolytic hydrolases. Of all the enzymes found by this bioprospection, we selected a novel lipolytic enzyme for further characterization. The protein was found to belong to the SGNH/GDSL family of hydrolases. It was purified and its biochemical parameters determined. We found that the enzyme was most active at 60 °C and pH 9 using pNP-laurate as substrate and was highly thermostable. It also showed preference for short-chained substrates and activation with temperature and with certain detergents such as Tween 80. Proteins of this family of hydrolases are relevant for their broad substrate specificity, that coupled with this protein's high temperature optima, broad pH range, and thermostability further highlights its biotechnological potential.}, } @article {pmid35628398, year = {2022}, author = {Hertzberger, R and May, A and Kramer, G and van Vondelen, I and Molenaar, D and Kort, R}, title = {Genetic Elements Orchestrating Lactobacillus crispatus Glycogen Metabolism in the Vagina.}, journal = {International journal of molecular sciences}, volume = {23}, number = {10}, pages = {}, pmid = {35628398}, issn = {1422-0067}, mesh = {Female ; Glucose/metabolism ; Glycogen/metabolism ; Humans ; Lactobacillus/metabolism ; *Lactobacillus crispatus/genetics/metabolism ; Vagina/metabolism ; }, abstract = {Glycogen in the female lower reproductive tract is a major carbon source for colonization and acidification by common vaginal Lactobacillus species, such as Lactobacillus crispatus. Previously, we identified the amylopullulanase encoding gene pulA of Lactobacillus crispatus to correlate with the ability to autonomously utilize glycogen for growth. Here, we further characterize genetic variation and differential regulation of pulA affecting the presence of its gene product on the outer surface layer. We show that alpha-glucan degrading activity dissipates when Lactobacillus crispatus is grown on glucose, maltose and maltotriose, in agreement with carbon catabolite repression elements flanking the pulA gene. Proteome analysis of the S-layer confirmed that the amylopullulanase protein is highly abundant in an S-layer enriched fraction, but not in a strain with a defective amylopullulanase variant or in an amylopullulanase-sufficient strain grown on glucose. In addition, we provide evidence that Lactobacillus crispatus pulA mutants are relevant in vivo, as they are commonly observed in metagenome datasets of human vaginal microbial communities. Analysis of the largest publicly available dataset of 1507 human vaginal metagenomes indicates that among the 270 samples that contain a Lactobacillus crispatuspulA gene, 62 samples (23%) had a defective variant of this gene. Taken together, these results demonstrate that both environmental, as well as genetic factors explain the variation of Lactobacillus crispatus alpha-glucosidases in the vaginal environment.}, } @article {pmid35628255, year = {2022}, author = {Maatouk, M and Ibrahim, A and Pinault, L and Armstrong, N and Azza, S and Rolain, JM and Bittar, F and Raoult, D}, title = {New Beta-lactamases in Candidate Phyla Radiation: Owning Pleiotropic Enzymes Is a Smart Paradigm for Microorganisms with a Reduced Genome.}, journal = {International journal of molecular sciences}, volume = {23}, number = {10}, pages = {}, pmid = {35628255}, issn = {1422-0067}, support = {10-IAHU-03//Agence Nationale de la Recherche/ ; }, mesh = {Bacteria/genetics/metabolism ; Humans ; RNA, Ribosomal, 16S/genetics ; *beta-Lactamase Inhibitors ; *beta-Lactamases/genetics/metabolism ; beta-Lactams ; }, abstract = {The increased exploitation of microbial sequencing methods has shed light on the high diversity of new microorganisms named Candidate Phyla Radiation (CPR). CPR are mainly detected via 16S rRNA/metabarcoding analyses or metagenomics and are found to be abundant in all environments and present in different human microbiomes. These microbes, characterized by their symbiotic/epiparasitic lifestyle with bacteria, are directly exposed to competition with other microorganisms sharing the same ecological niche. Recently, a rich repertoire of enzymes with antibiotic resistance activity has been found in CPR genomes by using an in silico adapted screening strategy. This reservoir has shown a high prevalence of putative beta-lactamase-encoding genes. We expressed and purified five putative beta-lactamase sequences having the essential domains and functional motifs from class A and class B beta-lactamase. Their enzymatic activities were tested against various beta-lactam substrates using liquid chromatography-mass spectrometry (LC-MS) and showed some beta-lactamase activity even in the presence of a beta-lactamase inhibitor. In addition, ribonuclease activity was demonstrated against RNA that was not inhibited by sulbactam and EDTA. None of these proteins could degrade single- and double-stranded-DNA. This study is the first to express and test putative CPR beta-lactamase protein sequences in vitro. Our findings highlight that the reduced genomes of CPR members harbor sequences encoding for beta-lactamases known to be multifunction hydrolase enzymes.}, } @article {pmid35627235, year = {2022}, author = {Silva, I and Alves, M and Malheiro, C and Silva, ARR and Loureiro, S and Henriques, I and González-Alcaraz, MN}, title = {Short-Term Responses of Soil Microbial Communities to Changes in Air Temperature, Soil Moisture and UV Radiation.}, journal = {Genes}, volume = {13}, number = {5}, pages = {}, pmid = {35627235}, issn = {2073-4425}, mesh = {Bacteria/genetics ; DNA, Ribosomal ; *Microbiota ; *Soil/chemistry ; Temperature ; Ultraviolet Rays ; Water ; }, abstract = {We analyzed the effects on a soil microbial community of short-term alterations in air temperature, soil moisture and ultraviolet radiation and assessed the role of invertebrates (species Enchytraeus crypticus) in modulating the community's response to these factors. The reference soil, Lufa 2.2, was incubated for 48 h, with and without invertebrates, under the following conditions: standard (20 °C + 50% water holding capacity (WHC)); increased air temperature (15-25 °C or 20-30 °C + 50% WHC); flood (20 °C + 75% WHC); drought (20 °C + 25% WHC); and ultraviolet radiation (UV) (20 °C + 50% WHC + UV). BIOLOG EcoPlates and 16S rDNA sequencing (Illumina) were used to assess the microbial community's physiological profile and the bacterial community's structure, respectively. The bacterial abundance (estimated by 16S rDNA qPCR) did not change. Most of the conditions led to an increase in microbial activity and a decrease in diversity. The structure of the bacterial community was particularly affected by higher air temperatures (20-30 °C, without E. crypticus) and floods (with E. crypticus). Effects were observed at the class, genera and OTU levels. The presence of invertebrates mostly resulted in the attenuation of the observed effects, highlighting the importance of considering microbiome-invertebrate interactions. Considering future climate changes, the effects described here raise concern. This study provides fundamental knowledge to develop effective strategies to mitigate these negative outcomes. However, long-term studies integrating biotic and abiotic factors are needed.}, } @article {pmid35627157, year = {2022}, author = {Song, Q and Wang, B and Han, Y and Zhou, Z}, title = {Metagenomics Reveals the Diversity and Taxonomy of Carbohydrate-Active Enzymes and Antibiotic Resistance Genes in Suancai Bacterial Communities.}, journal = {Genes}, volume = {13}, number = {5}, pages = {}, pmid = {35627157}, issn = {2073-4425}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria ; Carbohydrates ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; *Metagenomics ; }, abstract = {Suancai, as a traditional fermented food in China with reputed health benefits, has piqued global attention for many years. In some circumstances, the microbial-driven fermentation may confer health (e.g., probiotics) or harm (e.g., antibiotic resistance genes) to the consumers. To better utilize beneficial traits, a deeper comprehension of the composition and functionality of the bacterial species harboring enzymes of catalytically active is required. On the other hand, ingestion of fermented food increases the likelihood of microbial antibiotic resistance genes (ARGs) spreading in the human gastrointestinal tract. Besides, the diversity and taxonomic origin of ARGs in suancai are little known. In our study, a metagenomic approach was employed to investigate distribution structures of CAZymes and ARGs in main bacterial species in suancai. Functional annotation using the CAZy database identified a total of 8796 CAZymes in metagenomic data. A total of 83 ARGs were detected against the CARD database. The most predominant ARG category is multidrug-resistant genes. The ARGs of antibiotic efflux mechanism are mostly in Proteobacteria. The resistance mechanism of ARGs in Firmicutes is primarily antibiotic inactivation, followed by antibiotic efflux. Due to the abundance of species with different ARGs, strict quality control including microbial species, particularly those with lots of ARGs, is vital for decreasing the risk of ARG absorption via consumption. Ultimately, we significantly widen the understanding of suancai microbiomes by using metagenomic sequencing to offer comprehensive information on the microbial functional potential (including CAZymes and ARGs content) of household suancai.}, } @article {pmid35625719, year = {2022}, author = {Bai, X and Narayanan, A and Skagerberg, M and Ceña-Diez, R and Giske, CG and Strålin, K and Sönnerborg, A}, title = {Characterization of the Upper Respiratory Bacterial Microbiome in Critically Ill COVID-19 Patients.}, journal = {Biomedicines}, volume = {10}, number = {5}, pages = {}, pmid = {35625719}, issn = {2227-9059}, support = {2020-02129, 2017-05848, 2016-01675//Swedish Research Council/ ; Med 20 FoUI-953887//ALF/ ; }, abstract = {The upper respiratory tract (URT) microbiome can contribute to the acquisition and severity of respiratory viral infections. The described associations between URT microbiota and severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection are limited at microbiota genus level and by the lack of functional interpretation. Our study, therefore, characterized the URT bacterial microbiome at species level and their encoded pathways in patients with COVID-19 and correlated these to clinical outcomes. Whole metagenome sequencing was performed on nasopharyngeal samples from hospitalized patients with critical COVID-19 (n = 37) and SARS-CoV-2-negative individuals (n = 20). Decreased bacterial diversity, a reduction in commensal bacteria, and high abundance of pathogenic bacteria were observed in patients compared to negative controls. Several bacterial species and metabolic pathways were associated with better respiratory status and lower inflammation. Strong correlations were found between species biomarkers and metabolic pathways associated with better clinical outcome, especially Moraxella lincolnii and pathways of vitamin K2 biosynthesis. Our study demonstrates correlations between the URT microbiome and COVID-19 patient outcomes; further studies are warranted to validate these findings and to explore the causal roles of the identified microbiome biomarkers in COVID-19 pathogenesis.}, } @article {pmid35625484, year = {2022}, author = {Kaushal, M and Tumuhairwe, JB and Kaingo, J and Richard, M and Nakamanya, F and Taulya, G and Coyne, D}, title = {Compositional Shifts in Microbial Diversity under Traditional Banana Cropping Systems of Sub-Saharan Africa.}, journal = {Biology}, volume = {11}, number = {5}, pages = {}, pmid = {35625484}, issn = {2079-7737}, abstract = {Improvements in the crop productivity, soil health, and sustainable intensification should be premised on the better understanding of interactions between the cropping systems and soil microbial diversity. In this study, we assessed variations in the microbial communities across the traditional banana-based cropping systems of contrasting monocrop vigor (vigorous or V vs. non-vigorous or NV) and the cropping system (monocrop or MC vs. intercropped or IC) using 16S rDNA (V3-V4) and ITS2 amplicon deep sequencing via Illumina platform. Sequencing results of the bacterial and fungal communities showed high variability among MC and V cropping systems. The abundances of Proteobacteria, Firmicutes, and Actinobacteria were significantly higher in NV (non-vigorous) and V (vigorous) cropping systems; and the abundances of Proteobacteria, Firmicutes, Actinobacteria, and Bacteroidetes in the MC (monocropping) than IC (intercropping). There were high relative abundances of Pseudomonas (6.1-37.43%), Bacillus (4.5-20.4%), Rhizobium (1.4-6.5%), and Devosia (1.5-6.7%) in the cropping systems. The dominant family of fungal class Incertae_sedis was Mortierellales, which accounted for 8.79-41.12% of total taxa. This result indicated that the cropping systems are vital for supporting the dynamic microbial diversity specifically beneficial for bacterial communities that helps in promoting synergistic plant-soil interactions and total productivity under resource poor conditions of smallholder farmers in sub-Saharan Africa (SSA).}, } @article {pmid35625299, year = {2022}, author = {Waskito, LA and Rezkitha, YAA and Vilaichone, RK and Wibawa, IDN and Mustika, S and Sugihartono, T and Miftahussurur, M}, title = {Antimicrobial Resistance Profile by Metagenomic and Metatranscriptomic Approach in Clinical Practice: Opportunity and Challenge.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {5}, pages = {}, pmid = {35625299}, issn = {2079-6382}, support = {377/UN3.14/PT/2020) (MM//Riset Mandat 2020 Grant from Universitas Airlangga/ ; }, abstract = {The burden of bacterial resistance to antibiotics affects several key sectors in the world, including healthcare, the government, and the economic sector. Resistant bacterial infection is associated with prolonged hospital stays, direct costs, and costs due to loss of productivity, which will cause policy makers to adjust their policies. Current widely performed procedures for the identification of antibiotic-resistant bacteria rely on culture-based methodology. However, some resistance determinants, such as free-floating DNA of resistance genes, are outside the bacterial genome, which could be potentially transferred under antibiotic exposure. Metagenomic and metatranscriptomic approaches to profiling antibiotic resistance offer several advantages to overcome the limitations of the culture-based approach. These methodologies enhance the probability of detecting resistance determinant genes inside and outside the bacterial genome and novel resistance genes yet pose inherent challenges in availability, validity, expert usability, and cost. Despite these challenges, such molecular-based and bioinformatics technologies offer an exquisite advantage in improving clinicians' diagnoses and the management of resistant infectious diseases in humans. This review provides a comprehensive overview of next-generation sequencing technologies, metagenomics, and metatranscriptomics in assessing antimicrobial resistance profiles.}, } @article {pmid35624491, year = {2022}, author = {Arora, J and Kinjo, Y and Šobotník, J and Buček, A and Clitheroe, C and Stiblik, P and Roisin, Y and Žifčáková, L and Park, YC and Kim, KY and Sillam-Dussès, D and Hervé, V and Lo, N and Tokuda, G and Brune, A and Bourguignon, T}, title = {The functional evolution of termite gut microbiota.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {78}, pmid = {35624491}, issn = {2049-2618}, mesh = {Animals ; *Gastrointestinal Microbiome/genetics ; *Isoptera ; Metagenome ; Phylogeny ; Soil ; }, abstract = {BACKGROUND: Termites primarily feed on lignocellulose or soil in association with specific gut microbes. The functioning of the termite gut microbiota is partly understood in a handful of wood-feeding pest species but remains largely unknown in other taxa. We intend to fill this gap and provide a global understanding of the functional evolution of termite gut microbiota.

RESULTS: We sequenced the gut metagenomes of 145 samples representative of the termite diversity. We show that the prokaryotic fraction of the gut microbiota of all termites possesses similar genes for carbohydrate and nitrogen metabolisms, in proportions varying with termite phylogenetic position and diet. The presence of a conserved set of gut prokaryotic genes implies that essential nutritional functions were present in the ancestor of modern termites. Furthermore, the abundance of these genes largely correlated with the host phylogeny. Finally, we found that the adaptation to a diet of soil by some termite lineages was accompanied by a change in the stoichiometry of genes involved in important nutritional functions rather than by the acquisition of new genes and pathways.

CONCLUSIONS: Our results reveal that the composition and function of termite gut prokaryotic communities have been remarkably conserved since termites first appeared ~ 150 million years ago. Therefore, the "world's smallest bioreactor" has been operating as a multipartite symbiosis composed of termites, archaea, bacteria, and cellulolytic flagellates since its inception. Video Abstract.}, } @article {pmid35624467, year = {2022}, author = {Tansirichaiya, S and Winje, E and Wigand, J and Al-Haroni, M}, title = {Inverse PCR-based detection reveal novel mobile genetic elements and their associated genes in the human oral metagenome.}, journal = {BMC oral health}, volume = {22}, number = {1}, pages = {210}, pmid = {35624467}, issn = {1472-6831}, mesh = {*Genome, Bacterial ; Humans ; Interspersed Repetitive Sequences/genetics ; *Metagenome/genetics ; Mouth ; Polymerase Chain Reaction ; }, abstract = {The human oral cavity is one of the hotspots harboring multiple mobile genetic elements (MGEs), which are segments of DNA that can move either within bacterial genomes or between bacterial cells that can facilitate the spreading of genetic materials, including antimicrobial resistance genes. It is, therefore, important to investigate genes associated with the MGEs as they have a high probability of dissemination within the bacterial population under selective pressure from human activities. As one-third of oral bacteria are not yet culturable in the laboratory condition, therefore, in this work, it is aimed to detect and identify the genetic contexts of MGEs in the oral cavity through an inverse PCR (IPCR)-based approach on the oral metagenomic. The human oral metagenome was extracted from saliva samples collected from healthy individuals in Tromsø, Norway. The extracted DNA was partially digested with the HindIII restriction enzyme and self-circularized by ligation. DNA primers targeting each MGE were designed to amplify outwards from the MGEs and used for the IPCR on the circularized DNA products. The IPCR amplicons were cloned into a pCR-XL-2-TOP vector, screened, and sequenced. Out of 40 IPCR amplicons, we confirmed and verified the genetic contexts of 11 samples amplified with primers targeting integron gene cassettes (GCs), IS431 composite transposons, and Tn916 conjugative transposons (tet(M) and xis-int). Novel integron GCs, MGEs, and variants of Tn916 conjugative transposons were identified, which is the first report using the IPCR technique to detect the genetic contexts of MGEs in the oral metagenomic DNA.}, } @article {pmid35624028, year = {2022}, author = {Duan, J and Zhang, C and Wang, J and Fu, J and Song, P and Pang, F and Zhao, Q and You, Z}, title = {Diagnosis of Ureaplasma parvum meningitis by mNGS in an extremely low birth weight infant with multi-system lesions.}, journal = {Indian journal of medical microbiology}, volume = {40}, number = {3}, pages = {455-458}, doi = {10.1016/j.ijmmb.2022.05.001}, pmid = {35624028}, issn = {1998-3646}, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Infant ; Infant, Extremely Low Birth Weight ; Infant, Newborn ; *Meningitis/diagnosis ; Ureaplasma/genetics ; *Ureaplasma Infections/diagnosis/drug therapy ; }, abstract = {Ureaplasma parvum encephalitis is a rare disease with high mortality in the neonates. While the manifestations are atypical and identification of U. parvum is difficult, diagnosis would always be delayed. Metagenomic next-generation sequencing (mNGS) is a pre-hypothesis free technique which could theoretically detect all the microbes in a sample. Herein we report a case of U. parvum meningitis identified by mNGS in an extremely low birth weight neonate complicated with multi-system lesions. The patient was treated with erythromycin and ciprofloxacin, symptoms were relieved in the following days and the patient was transferred to treat complications after three weeks' therapy.}, } @article {pmid35622934, year = {2022}, author = {Li, N and Ma, X and Zhou, J and Deng, J and Gu, C and Fei, C and Cao, L and Zhang, Q and Tao, F}, title = {Clinical application of metagenomic next-generation sequencing technology in the diagnosis and treatment of pulmonary infection pathogens: A prospective single-center study of 138 patients.}, journal = {Journal of clinical laboratory analysis}, volume = {36}, number = {7}, pages = {e24498}, pmid = {35622934}, issn = {1098-2825}, support = {2020KY950//Application of high-throughput gene sequencing (next generation sequencing, NGS) combined with mass spectrometry in immunosuppression complicated with severe pneumonia based on alveolar lavage fluid infection/ ; 2019-zc-04//Key Discipline of Jiaxing Respiratory Medicine Construction Project/ ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; *High-Throughput Nucleotide Sequencing/methods ; Humans ; *Pneumonia ; Prospective Studies ; Sensitivity and Specificity ; Technology ; }, abstract = {INTRODUCTION: Rapid and accurate pathogen identification is essential for the treatment of pneumonia. Metagenomic next-generation sequencing (mNGS) is a newly developed technology to obtain microbial nucleic acid sequence information quickly, efficiently, and without bias.

METHODS: We performed shotgun metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) for pathogen identification in pneumonia in a prospective study with 138 patients from a single center. We compared the results of mNGS with standard methods including culture, staining, and targeted PCR and evaluated the clinical applicability of mNGS.

RESULTS: Most of the patients (128/138, 92.75%) were cured or improved. One patient (1/138, 0.72%) died because of acute gastrointestinal bleeding, and 9 patients (9/138, 6.52%) showed no improvement. mNGS identified more bacteria (53 versus 27), fewer fungi (8 versus 31), and more viruses (16 versus 1) than standard methods. In total, treatment in 34 out of 138 cases (24.64%) was adjusted and optimized because of mNGS results. Positive mNGS results contributed to a definitive diagnosis in 23 cases (16.67%), which helped guide treatment decision by either adjusting the antibiotics without de-escalation or continuing the empirical treatment. mNGS also confirmed no active infection in 11 cases (7.97%) allowed for antibiotic de-escalation.

CONCLUSION: This prospective clinical study evaluated the clinical utility of mNGS for the diagnosis of pneumonia and showed that mNGS of BALF provides valuable information for effective treatment.}, } @article {pmid35622620, year = {2022}, author = {Wilczynski, W and Radlinska, M and Wysujack, K and Czub, M and Brzeziński, T and Kowalczyk, G and Bełdowski, J and Nogueira, P and Maszczyk, P}, title = {Metagenomic Analysis of the Gastrointestinal Microbiota of Gadus morhua callarias L. Originating from a Chemical Munition Dump Site.}, journal = {Toxics}, volume = {10}, number = {5}, pages = {}, pmid = {35622620}, issn = {2305-6304}, support = {2020/37/N/NZ8/04099, 2016/23/D/NZ8/03532, 2021/40/C/NZ8/00125 and 2019/35/B/NZ8/04523//National Science Centre, Poland/ ; }, abstract = {Several hundred thousand tonnes of munitions containing chemical warfare agents (CWAs) are lying on the seafloor worldwide. CWAs have started leaking from corroded munitions, and their presence in the environment and in organisms inhabiting dump sites has been detected. The presence of CWAs in the water negatively affects fish, macrobenthos and free-living bacteria. It can be expected that the presence of CWAs would also affect the gut-associated bacteria in fish, which are vital for their condition. The main aim of this study was to test if the microbiota of cod collected in the Baltic Bornholm Deep (highly polluted with CWAs) is dysregulated. To investigate this, we conducted metagenomic studies based on 16S rRNA gene sequencing. We found that the microbiota of cod inhabiting the dump site was significantly less taxonomically diverse compared to those from a non-polluted reference site. Moreover, taxa associated with fish diseases (e.g., Vibrionaceae, Aeromonadaceae) were more prevalent, and probiotic taxa (e.g., Actinobacteriota, Rhodobacteraceae) were less frequent in the guts of individuals from the dump site, than those from the reference site. The differences in vulnerability of various bacterial taxa inhabiting cod gastrointestinal tracts to CWAs were hypothesised to be responsible for the observed microbiota dysregulation.}, } @article {pmid35621925, year = {2022}, author = {Ahmed, SF and Abdallah, RZ and Siam, R}, title = {Evaluation of a Thermophilic, Psychrostable, and Heavy Metal-Resistant Red Sea Brine Pool Esterase.}, journal = {Marine drugs}, volume = {20}, number = {5}, pages = {}, pmid = {35621925}, issn = {1660-3397}, support = {Proof Concept fund centennial grant//The American University in Cairo/ ; }, mesh = {*Esterases/chemistry ; Indian Ocean ; Ions ; *Metals, Heavy/pharmacology ; Salts ; Sterol Esterase ; }, abstract = {Lipolytic enzymes catalyze the hydrolysis and synthesis of ester compounds. They are valuable in the pulp, food, and textile industries. This study aims to comprehensively evaluate the extreme properties of a hormone-sensitive lipase (EstATII-TM) isolated from the Red Sea Atlantis II brine pool. EstATII-TM was cloned, expressed, and its biochemical activities were assessed under different conditions. EstATII-TM catalytic properties and resistance to different metal ions were compared to commercial thermophilic esterases under different temperatures. Phylogenetically, EstATII-TM was assigned to the GDSAG motif subfamily of hormone-sensitive lipase. The optimal enzyme activity was evident at a temperature of 30 °C and pH 7-8. The enzyme retained 84.9% of its activity at 0.5 M NaCl. EstATII-TM maintained 93% to 97% activity at -40 and -20 °C, respectively. EstATII-TM activity was significantly enhanced, up to 10-fold, at temperatures ranging from 45 to 65 °C in the presence of 1 mM Cu[2+], Cd[2+], Ba[2+], Mn[2+], and Zn[2+]. EstATII-TM showed superior catalytic activity and resistance-to/enhancement-by metal ions compared to two commercial thermophilic esterases. The Red Sea Atlantis II brine EstATII-TM is characterized by tolerance to high temperatures, stability to hot and cold conditions, as well as toxic heavy metal contamination, making it an ideal candidate for industrial processes.}, } @article {pmid35620109, year = {2022}, author = {Yang, B and Sun, T and Chen, Y and Xiang, H and Xiong, J and Bao, S}, title = {The Role of Gut Microbiota in Mice With Bile Duct Ligation-Evoked Cholestatic Liver Disease-Related Cognitive Dysfunction.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {909461}, pmid = {35620109}, issn = {1664-302X}, abstract = {The pathogenesis of Hepatic Encephalopathy (HE) is complex and multifactorial. The development of metagenomics sequencing technology led to show the significant role of gut microbiota in the pathogenesis of cognitive dysfunction, which paved the way for further research in this field. However, it is unknown whether gut microbiota plays a role in bile duct ligation (BDL)-evoked cholestatic liver disease-related cognitive dysfunction. The aim of this investigation is to assess BDL mice induced cognitive dysfunction and meanwhile to delineate the alteration of gut microbiota in cognitive dysfunction mice, which may underline the role of gut microbiota in BDL mice induced cognitive dysfunction. Our study was carried out in male C57BL/6 J mice with bile duct ligation. The liver functions were assessed via different biochemical markers [alanine aminotransferase (ALT), aspartate aminotransferase (AST), alkaline phosphatase (ALP), total bilirubin (TBIL), and total bile acid (TBA)] and a histopathological examination of the liver tissue. We used the novel object recognition test (NORT) to assess cognitive dysfunction. And BDL mice were divided into BDL with cognitive dysfunction (BDL-CD) or BDL without cognitive dysfunction (BDL-NCD groups) by the result of hierarchical cluster analysis of NORT. Then, 16S ribosomal RNA (rRNA) gene sequencing was used to compare the gut bacterial composition between BDL-CD and BDL-NCD groups. According to our results, we concluded that bile duct ligation can significantly change the gut microbiota composition, and Bacteroides fragilis, Bacteroides ovatus V975, and Bacteroides thetaiotaomicron play a vital role in BDL-evoked cholestatic liver disease-related cognitive dysfunction.}, } @article {pmid35620097, year = {2022}, author = {Pérez-Losada, M and Narayanan, DB and Kolbe, AR and Ramos-Tapia, I and Castro-Nallar, E and Crandall, KA and Domínguez, J}, title = {Comparative Analysis of Metagenomics and Metataxonomics for the Characterization of Vermicompost Microbiomes.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {854423}, pmid = {35620097}, issn = {1664-302X}, abstract = {The study of microbial communities or microbiotas in animals and environments is important because of their impact in a broad range of industrial applications, diseases and ecological roles. High throughput sequencing (HTS) is the best strategy to characterize microbial composition and function. Microbial profiles can be obtained either by shotgun sequencing of genomes, or through amplicon sequencing of target genes (e.g., 16S rRNA for bacteria and ITS for fungi). Here, we compared both HTS approaches at assessing taxonomic and functional diversity of bacterial and fungal communities during vermicomposting of white grape marc. We applied specific HTS workflows to the same 12 microcosms, with and without earthworms, sampled at two distinct phases of the vermicomposting process occurring at 21 and 63 days. Metataxonomic profiles were inferred in DADA2, with bacterial metabolic pathways predicted via PICRUSt2. Metagenomic taxonomic profiles were inferred in PathoScope, while bacterial functional profiles were inferred in Humann2. Microbial profiles inferred by metagenomics and metataxonomics showed similarities and differences in composition, structure, and metabolic function at different taxonomic levels. Microbial composition and abundance estimated by both HTS approaches agreed reasonably well at the phylum level, but larger discrepancies were observed at lower taxonomic ranks. Shotgun HTS identified ~1.8 times more bacterial genera than 16S rRNA HTS, while ITS HTS identified two times more fungal genera than shotgun HTS. This is mainly a consequence of the difference in resolution and reference richness between amplicon and genome sequencing approaches and databases, respectively. Our study also revealed great differences and even opposite trends in alpha- and beta-diversity between amplicon and shotgun HTS. Interestingly, amplicon PICRUSt2-imputed functional repertoires overlapped ~50% with shotgun Humann2 profiles. Finally, both approaches indicated that although bacteria and fungi are the main drivers of biochemical decomposition, earthworms also play a key role in plant vermicomposting. In summary, our study highlights the strengths and weaknesses of metagenomics and metataxonomics and provides new insights on the vermicomposting of white grape marc. Since both approaches may target different biological aspects of the communities, combining them will provide a better understanding of the microbiotas under study.}, } @article {pmid35620087, year = {2022}, author = {Li, X and Guo, R and Zou, X and Yao, Y and Lu, L}, title = {The First Cbk-Like Phage Infecting Erythrobacter, Representing a Novel Siphoviral Genus.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {861793}, pmid = {35620087}, issn = {1664-302X}, abstract = {Erythrobacter is an important and widespread bacterial genus in the ocean. However, our knowledge about their phages is still rare. Here, a novel lytic phage vB_EliS-L02, infecting Erythrobacter litoralis DSM 8509, was isolated and purified from Sanggou Bay seawater, China. Morphological observation revealed that the phage belonged to Cbk-like siphovirus, with a long prolate head and a long tail. The host range test showed that phage vB_EliS-L02 could only infect a few strains of Erythrobacter, demonstrating its potential narrow-host range. The genome size of vB_EliS-L02 was 150,063 bp with a G+C content of 59.43%, encoding 231 putative open reading frames (ORFs), but only 47 were predicted to be functional domains. Fourteen auxiliary metabolic genes were identified, including phoH that may confer vB_EliS-L02 the advantage of regulating phosphate uptake and metabolism under a phosphate-limiting condition. Genomic and phylogenetic analyses indicated that vB_EliS-L02 was most closely related to the genus Lacusarxvirus with low similarity (shared genes < 30%, and average nucleotide sequence identity < 70%), distantly from other reported phages, and could be grouped into a novel viral genus cluster, in this study as Eliscbkvirus. Meanwhile, the genus Eliscbkvirus and Lacusarxvirus stand out from other siphoviral genera and could represent a novel subfamily within Siphoviridae, named Dolichocephalovirinae-II. Being a representative of an understudied viral group with manifold adaptations to the host, phage vB_EliS-L02 could improve our understanding of the virus-host interactions and provide reference information for viral metagenomic analysis in the ocean.}, } @article {pmid35619157, year = {2022}, author = {Sahu, KP and Kumar, A and Sakthivel, K and Reddy, B and Kumar, M and Patel, A and Sheoran, N and Gopalakrishnan, S and Prakash, G and Rathour, R and Gautam, RK}, title = {Deciphering core phyllomicrobiome assemblage on rice genotypes grown in contrasting agroclimatic zones: implications for phyllomicrobiome engineering against blast disease.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {28}, pmid = {35619157}, issn = {2524-6372}, support = {File No: 09/083(0367)/2016-EMR-I//Council of Scientific and Industrial Research, India/ ; }, abstract = {BACKGROUND: With its adapted microbial diversity, the phyllosphere contributes microbial metagenome to the plant holobiont and modulates a host of ecological functions. Phyllosphere microbiome (hereafter termed phyllomicrobiome) structure and the consequent ecological functions are vulnerable to a host of biotic (Genotypes) and abiotic factors (Environment) which is further compounded by agronomic transactions. However, the ecological forces driving the phyllomicrobiome assemblage and functions are among the most understudied aspects of plant biology. Despite the reports on the occurrence of diverse prokaryotic phyla such as Proteobacteria, Firmicutes, Bacteroides, and Actinobacteria in phyllosphere habitat, the functional characterization leading to their utilization for agricultural sustainability is not yet explored. Currently, the metabarcoding by Next-Generation-Sequencing (mNGS) technique is a widely practised strategy for microbiome investigations. However, the validation of mNGS annotations by culturomics methods is not integrated with the microbiome exploration program. In the present study, we combined the mNGS with culturomics to decipher the core functional phyllomicrobiome of rice genotypes varying for blast disease resistance planted in two agroclimatic zones in India. There is a growing consensus among the various stakeholder of rice farming for an ecofriendly method of disease management. Here, we proposed phyllomicrobiome assisted rice blast management as a novel strategy for rice farming in the future.

RESULTS: The tropical "Island Zone" displayed marginally more bacterial diversity than that of the temperate 'Mountain Zone' on the phyllosphere. Principal coordinate analysis indicated converging phyllomicrobiome profiles on rice genotypes sharing the same agroclimatic zone. Interestingly, the rice genotype grown in the contrasting zones displayed divergent phyllomicrobiomes suggestive of the role of environment on phyllomicrobiome assembly. The predominance of phyla such as Proteobacteria, Actinobacteria, and Firmicutes was observed in the phyllosphere irrespective of the genotypes and climatic zones. The core-microbiome analysis revealed an association of Acidovorax, Arthrobacter, Bacillus, Clavibacter, Clostridium, Cronobacter, Curtobacterium, Deinococcus, Erwinia, Exiguobacterium, Hymenobacter, Kineococcus, Klebsiella, Methylobacterium, Methylocella, Microbacterium, Nocardioides, Pantoea, Pedobacter, Pseudomonas, Salmonella, Serratia, Sphingomonas and Streptomyces on phyllosphere. The linear discriminant analysis (LDA) effect size (LEfSe) method revealed distinct bacterial genera in blast-resistant and susceptible genotypes, as well as mountain and island climate zones. SparCC based network analysis of phyllomicrobiome showed complex intra-microbial cooperative or competitive interactions on the rice genotypes. The culturomic validation of mNGS data confirmed the occurrence of Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas in the phyllosphere. Strikingly, the contrasting agroclimatic zones showed genetically identical bacterial isolates suggestive of vertical microbiome transmission. The core-phyllobacterial communities showed secreted and volatile compound mediated antifungal activity on M. oryzae. Upon phyllobacterization (a term coined for spraying bacterial cells on the phyllosphere), Acinetobacter, Aureimonas, Pantoea, and Pseudomonas conferred immunocompetence against blast disease. Transcriptional analysis revealed activation of defense genes such as OsPR1.1, OsNPR1, OsPDF2.2, OsFMO, OsPAD4, OsCEBiP, and OsCERK1 in phyllobacterized rice seedlings.

CONCLUSIONS: PCoA indicated the key role of agro-climatic zones to drive phyllomicrobiome assembly on the rice genotypes. The mNGS and culturomic methods showed Acinetobacter, Aureimonas, Curtobacterium, Enterobacter, Exiguobacterium, Microbacterium, Pantoea, Pseudomonas, and Sphingomonas as core phyllomicrobiome of rice. Genetically identical Pantoea intercepted on the phyllosphere from the well-separated agroclimatic zones is suggestive of vertical transmission of phyllomicrobiome. The phyllobacterization showed potential for blast disease suppression by direct antibiosis and defense elicitation. Identification of functional core-bacterial communities on the phyllosphere and their co-occurrence dynamics presents an opportunity to devise novel strategies for rice blast management through phyllomicrobiome reengineering in the future.}, } @article {pmid35618944, year = {2023}, author = {Lau, NS and Ting, SY and Sam, KK and M, J and Wong, SC and Wu, X and Waiho, K and Fazhan, H and Shu-Chien, AC}, title = {Comparative Analyses of Scylla olivacea Gut Microbiota Composition and Function Suggest the Capacity for Polyunsaturated Fatty Acid Biosynthesis.}, journal = {Microbial ecology}, volume = {86}, number = {1}, pages = {575-588}, pmid = {35618944}, issn = {1432-184X}, mesh = {Animals ; *Brachyura ; *Gastrointestinal Microbiome ; Fatty Acids, Unsaturated/metabolism ; Diet ; Lipid Metabolism ; }, abstract = {Although numerous studies in aquatic organisms have linked lipid metabolism with intestinal bacterial structure, the possibility of the gut microbiota participating in the biosynthesis of beneficial long-chain polyunsaturated fatty acid (LC-PUFA) remains vague. We profiled the gut microbiota of the mud crab Scylla olivacea fed with either a LC-PUFA rich (FO) or a LC-PUFA-poor but C18-PUFA substrate-rich (LOCO) diet. Additionally, a diet with a similar profile as LOCO but with the inclusion of an antibiotic, oxolinic acid (LOCOAB), was also used to further demarcate the possibility of LC-PUFA biosynthesis in gut microbiota. Compared to diet FO treatment, crabs fed diet LOCO contained a higher proportion of Proteobacteria, notably two known taxonomy groups with PUFA biosynthesis capacity, Vibrio and Shewanella. Annotation of metagenomic datasets also revealed enrichment in the KEGG pathway of unsaturated fatty acid biosynthesis and polyketide synthase-like system sequences with this diet. Intriguingly, diet LOCOAB impeded the presence of Vibrio and Shewanella and with it, the function of unsaturated fatty acid biosynthesis. However, there was an increase in the function of short-chain fatty acid production, accompanied by a shift towards the abundance of phyla Bacteroidota and Spirochaetota. Collectively, these results exemplified bacterial communities and their corresponding PUFA biosynthesis pathways in the microbiota of an aquatic crustacean species.}, } @article {pmid35618244, year = {2022}, author = {Sharma, R and Kumar, R and Sharma, A and Goel, A and Padwad, Y}, title = {Long-term consumption of green tea EGCG enhances murine health span by mitigating multiple aspects of cellular senescence in mitotic and post-mitotic tissues, gut dysbiosis, and immunosenescence.}, journal = {The Journal of nutritional biochemistry}, volume = {107}, number = {}, pages = {109068}, doi = {10.1016/j.jnutbio.2022.109068}, pmid = {35618244}, issn = {1873-4847}, mesh = {AMP-Activated Protein Kinases ; Animals ; *Catechin/analogs & derivatives/pharmacology ; Cellular Senescence ; Dysbiosis ; *Immunosenescence ; Mice ; Proto-Oncogene Proteins c-akt ; *Sirtuin 3 ; Tea ; }, abstract = {Cellular senescence is emerging as a major hallmark of aging, and its modulation presents an effective anti-aging strategy. This study attempted to understand the progression of cellular senescence in vivo, and whether it can be mitigated by chronic consumption of green tea catechin epigallocatechin gallate (EGCG). We profiled cellular senescence in various organs of mice at four different time-points of lifespan, and then explored the influence of EGCG consumption in impacting markers of cellular senescence, inflamm-aging, immunosenescence, and gut dysbiosis. We report that visceral adipose and intestinal tissues are highly vulnerable to cellular senescence due to an increase in DNA damage response, activation of cell cycle inhibitors, and senescence-associated secretory phenotype regulators. With advancing age, dysregulation in nutrient signaling mediators (AMPK/AKT/SIRT3/5), and a decrease in autophagy was also observed. Inflamm-aging markers (TNF-α/IL-1β) and splenic CD4/CD8 T cell ratio increased with age, while NK cell population decreased. Metagenomic analyses revealed an age-related decrease in the diversity of microbial species and an increase in the abundance of various pathogenic bacterial species. On the other hand, long-term EGCG consumption significantly attenuated markers of DNA damage, cell cycle inhibitors, senescence-associated secretory phenotype regulators, AMPK/AKT signaling, and enhanced SIRT3/5 expression and autophagy. Systemic inflamm-aging indicators decreased, while early T cell activation increased in EGCG fed animals. EGCG also suppressed the abundance of pathogenic bacteria and preserved microbial diversity. Our results suggest that adipose and intestine tissues are prone to cellular senescence and that chronic consumption of EGCG can attenuate several deleterious aspects of aging which could be implicated in developing anti-aging strategies.}, } @article {pmid35618126, year = {2022}, author = {Huang, G and Qu, Q and Wang, M and Huang, M and Zhou, W and Wei, F}, title = {Global landscape of gut microbiome diversity and antibiotic resistomes across vertebrates.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 2}, pages = {156178}, doi = {10.1016/j.scitotenv.2022.156178}, pmid = {35618126}, issn = {1879-1026}, mesh = {Animals ; Anti-Bacterial Agents ; Bacteria ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; Vertebrates ; }, abstract = {Multiple factors influence gut microbiome diversity in vertebrate hosts. Most previous studies have only investigated specific factors and certain host species or taxa. However, a comprehensive assessment of the relative contributions of individual factors towards gut microbial diversity within a broader evolutionary context remains lacking. Here, 2202 16S rRNA gene sequencing samples of gut bacterial communities collected from 452 host species across seven classes were analyzed together to understand the factors broadly affecting vertebrate gut microbiomes across hosts with different diets, threatened status, captivity status, and habitat environmental factors. Among wild vertebrates, diet was most significantly associated with gut microbiome alpha diversity, while host phylogeny and diet were significantly associated with beta diversity, consistent with a previous study. Host threatened status and habitat environmental factors (e.g., geography and climate) were also associated with gut bacterial community beta diversity. Subsequent ecological modeling revealed a strong association between stochastic assembly processes and patterns of gut bacterial diversity among free-ranging vertebrates. In addition, metagenomic analysis of gut microbiomes from 62 captive vertebrates and sympatric humans revealed similar diversity and resistome profiles despite differences in host phylogeny, diet, and threatened status. These results thus suggest that captivity diminishes the effects of host phylogeny, diet, and threatened status on the diversity of vertebrate gut bacterial communities. The most overrepresented antibiotic resistant genes (ARGs) observed in these samples are involved in resistance to β-lactams, aminoglycosides, and tetracycline. These results also revealed potential horizontal transfers of ARGs between captive animals and humans, thereby jointly threatening public health and vertebrate conservation. Together, this study provides a comprehensive overview of the diversity and resistomes of vertebrate gut microbiomes. These combined analyses will help guide future vertebrate conservation via the rational manipulation of microbial diversity and reducing antibiotic usage.}, } @article {pmid35617977, year = {2022}, author = {Zhang, Z and Zhou, H and Cao, H and Ji, J and Zhang, R and Li, W and Guo, H and Chen, L and Ma, C and Cui, M and Wang, J and Chen, H and Ding, G and Yan, C and Dong, L and Holmes, EC and Meng, L and Hou, P and Shi, W}, title = {Human-to-human transmission of Chlamydia psittaci in China, 2020: an epidemiological and aetiological investigation.}, journal = {The Lancet. Microbe}, volume = {3}, number = {7}, pages = {e512-e520}, doi = {10.1016/S2666-5247(22)00064-7}, pmid = {35617977}, issn = {2666-5247}, mesh = {Animals ; Australia ; Birds ; China/epidemiology ; *Chlamydophila psittaci/genetics ; *Community-Acquired Infections/diagnosis ; Humans ; *Pneumonia/diagnosis ; *Psittacosis/diagnosis ; }, abstract = {BACKGROUND: Chlamydia psittaci can infect a wide range of avian species, occasionally causing psittacosis (also known as parrot fever) in humans. Most human psittacosis cases are associated with close contact with pet birds or poultry. In December, 2020, an outbreak of severe community-acquired pneumonia of unknown aetiology was reported in a hospital in Shandong province, China, and some of the patients' close contacts had respiratory symptoms. Our aims were to determine the causative agent of this epidemic and whether there had been human-to-human transmission.

METHODS: For this epidemiological and aetiological investigation study, we enrolled patients who had community-acquired pneumonia confirmed by chest CT at two local hospitals in Shandong Province in China. We collected sputum, bronchoalveolar lavage fluid, and nasopharyngeal swab samples from participants and detected pathogens by surveying for 22 target respiratory microbes using a commercial assay, followed by metagenomic next-generation sequencing, specific nested PCR, and qPCR tests. We excluded individuals who were C psittaci-negative on both tests. We recruited close contacts of the C psittaci-positive patients, and tested nasopharyngeal swabs from the close contacts and samples from ducks from the processing plant where these patients worked. We then integrated the epidemiological, clinical, and laboratory data to reveal the potential chain of transmission of C psittaci that characterised this outbreak.

FINDINGS: Between Dec 4 and 29, 2020, we used metagenomic next-generation sequencing and different PCR-based approaches to test 12 inpatients with community-acquired pneumonia, of whom six (50%) were workers at a duck-meat processing plant and two (17%) were unemployed people, who were positive for C psittaci and enrolled in this study. We contacted 61 close contacts of the six patients who worked at the duck-meat processing plant, of whom 61 (100%) were enrolled and tested, and we determined that the community-acquired pneumonia outbreak was caused by C psittaci. Within the outbreak cluster, 17 (77%) of 22 participants had confirmed C psittaci infections and five (23%) of 22 participants were asymptomatic C psittaci carriers. The outbreak had begun with avian-to-human transmission, and was followed by secondary and tertiary human-to-human transmission, which included transmission by several asymptomatic carriers and by health-care workers. In addition, some of the participants with confirmed C psittaci infection had no identified source of infection, which suggested cryptic bacterial transmission.

INTERPRETATION: Our study data might represent the first documented report of human-to-human transmission of C psittaci in China. Therefore, C psittaci has the potential to evolve human-to-human transmission via various routes, should be considered an elevated biosecurity and emergent risk, and be included as part of the routine diagnosis globally, especially for high-risk populations.

FUNDING: Academic Promotion Programme of Shandong First Medical University, National Science and Technology Major Project, ARC Australian Laureate Fellowship.}, } @article {pmid35617901, year = {2022}, author = {Liu, C and Li, G and Qin, X and Xu, Y and Wang, J and Wu, G and Feng, H and Ye, J and Zhu, C and Li, X and Zheng, X}, title = {Profiles of antibiotic- and heavy metal-related resistance genes in animal manure revealed using a metagenomic analysis.}, journal = {Ecotoxicology and environmental safety}, volume = {239}, number = {}, pages = {113655}, doi = {10.1016/j.ecoenv.2022.113655}, pmid = {35617901}, issn = {1090-2414}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Manure/microbiology ; *Metals, Heavy/toxicity ; Zinc ; }, abstract = {Farmed animals produce excrement containing excessive amounts of toxic heavy metals as a result of consuming compound feed as well as receiving medical treatments, and the presence of these heavy metals may aggravate the risk of spreading drug-resistance genes through co-selection during manure treatment and application processes. However, research on the association between heavy metals and antimicrobial resistance is still lacking. In this study, metagenomic sequencing was used to explore the effects of the co-selection of environmentally toxic heavy metals on the resistome in manure. A relevance network analysis showed that metal-resistance genes (MRGs), especially for copper (Cu) and zinc (Zn), were positively correlated with multiple types of antibiotic-resistance genes (ARGs) and formed a complex network. Most bacteria that co-occurred with both MRGs and ARGs simultaneously are members of Proteobacteria and accounted for 54.7% of the total microbial species in the relevance network. The remaining bacteria belonged to Firmicutes, Bacteroidetes and Actinobacteria. Among the four phyla, Cu- and Zn-resistance genes had more complex correlations with ARGs than other MRG types, reflecting the occurrence of ARG co-selection under the selective pressure of high Cu and Zn levels. In addition, approximately 64.8%, 59.1% and 68.4% of MRGs that correlated with the presence of plasmids, viruses and prophages, respectively, are Cu- or Zn-resistant, and they co-occurred with various ARGs, indicating that mobile genetic elements participate in mediating ARG co-selection in response to Cu and Zn pressure. The results indicated that the use of heavy-metal additives in feed induces the increases of drug resistance genes in manure through co-selection, aggravating the risk of antimicrobial resistance diffusion from animal farm to manure land applications.}, } @article {pmid35617743, year = {2022}, author = {Park, JJC and Kim, DH and Kim, MS and Sayed, AEH and Hagiwara, A and Hwang, UK and Park, HG and Lee, JS}, title = {Comparative genome analysis of the monogonont marine rotifer Brachionus manjavacas Australian strain: Potential application for ecotoxicology and environmental genomics.}, journal = {Marine pollution bulletin}, volume = {180}, number = {}, pages = {113752}, doi = {10.1016/j.marpolbul.2022.113752}, pmid = {35617743}, issn = {1879-3363}, mesh = {Animals ; Australia ; *Ecotoxicology ; Genome ; Metagenomics ; *Rotifera/genetics ; }, abstract = {This is the first study to analyze the whole-genome sequence of B. manjavacas Australian (Aus.) strain through combination of Oxford Nanopore long-read seq, resulting in a total length of 108.1 Mb and 75 contigs. Genome-wide detoxification related gene families in B. manjavacas Aus. strain were comparatively analyzed with those previously identified in other Brachionus spp., including B. manjavacas German (Ger.) strain. Most of the subfamilies in detoxification related families (CYPs, GSTs, and ABCs) were highly conserved and confirmed orthologous relationship with Brachionus spp., and with accumulation of genome data, clear differences between genomic repertoires were demonstrated the marine and the freshwater species. Furthermore, strain-specific genetic variations were present between the Aus. and Ger. strains of B. manjavacas. This whole-genome analysis provides in-depth review on the genomic structural differences for detoxification-related gene families and further provides useful information for comparative ecotoxicological studies and evolution of detoxification mechanisms in Brachionus spp.}, } @article {pmid35615912, year = {2022}, author = {Bae, SS and Dong, TS and Wang, J and Lagishetty, V and Katzka, W and Jacobs, JP and Charles-Schoeman, C}, title = {Altered Gut Microbiome in Patients With Dermatomyositis.}, journal = {ACR open rheumatology}, volume = {4}, number = {8}, pages = {658-670}, pmid = {35615912}, issn = {2578-5745}, support = {IK2 CX001717/CX/CSRD VA/United States ; R01 HL123064/HL/NHLBI NIH HHS/United States ; Scientist Development Award//Rheumatology Research Foundation/ ; R01HL123064/HL/NHLBI NIH HHS/United States ; }, abstract = {OBJECTIVE: The study objective was to compare the microbial composition of patients with dermatomyositis (DM) and healthy controls (HCs) and determine whether microbial alterations are associated with clinical manifestations of DM.

METHODS: The 16S ribosomal RNA gene sequencing was performed on fecal samples from patients with DM and HCs. Microbial composition and diversity were compared between subjects with DM and HCs and in association with several DM-specific clinical variables, including myositis-specific autoantibodies (MSAs). Differentially abundant microbial taxa and genes associated with clinical characteristics were identified, and functional analysis was performed using predicted metagenomics. Dietary intake was assessed using a 24-hour dietary recall.

RESULTS: The fecal microbiome of 36 patients with DM and 26 HCs were analyzed. Patients with DM trended toward lower microbial diversity compared with HCs. The higher physician global damage score was significantly correlated with the lower microbial diversity in patients with DM. Patients with interstitial lung disease (ILD)-associated MSA (antisynthetase antibody (ab), anti-melanoma differentiation-associated protein 5 ab, n = 12) had significant differences in microbial composition and lower microbial diversity compared with HCs. Differential abundance testing demonstrated a unique taxonomic signature in the ILD-MSA subgroup, and predictive metagenomics identified functional alterations in a number of metabolic pathways. A significant increase in the relative abundance of Proteobacteria was positively correlated with multiple pathways involved in lipopolysaccharide synthesis and transport in the ILD-MSA group.

CONCLUSION: Patients with DM, particularly with ILD-associated MSAs, have lower microbial diversity and a distinct taxonomic composition compared with HCs. Further studies are needed to validate our findings and elucidate specific pathogenetic mechanisms that link the gut microbiome to clinical and pathological features of DM.}, } @article {pmid35615499, year = {2022}, author = {Cao, D and Pang, M and Wu, D and Chen, G and Peng, X and Xu, K and Fan, H}, title = {Alterations in the Gut Microbiota of Tibetan Patients With Echinococcosis.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {860909}, pmid = {35615499}, issn = {1664-302X}, abstract = {There are two main types of echinococcosis, namely alveolar echinococcosis (AE) and cystic echinococcosis (CE). They are zoonotic parasitic diseases caused by the metacestodes of Echinococcus multilocularis and Echinococcus granulosus. In order to explore the gut microbiome composition of patients with echinococcosis, we analyzed fecal samples of seven patients with AE, six patients with CE, and 13 healthy individuals from the Qinghai-Tibetan Plateau, China. Using metagenomic next-generation sequencing, we identified fecal bacteria in the patients with AE and CE. The gut microbiota was analyzed by next-generation metagenomic sequencing (mNGS) to compare patients with either AE or CE against healthy individuals. We found there were some differences between them in abundant bacteria. Our results led to five findings: (1) Between patients with echinococcosis and healthy individuals, the differential bacteria were from four phyla: Firmicutes, Proteobacteria, Bacteroidetes, Actinobacteria. (2) Rothia mucilaginosa, Veillonella dispar, Veillonella atypica, Streptococcus parasanguinis, Streptococcus salivarius, and Alistipes finegoldii were abundant in the feces of patients with AE. (3) Bacteroides dorei, Parabacteroides distasonis, Escherichia sp_E4742, and Methanobrevibacter smithii were abundant in the feces of the patients with CE. (4) At the phylum and class level, compared to the AE group, the healthy group was characterized by higher numbers of Actinobacteria. (5) At the family level, Lachnospiraceae and Eubacteriaceae were more abundant in the feces of healthy individuals than in AE patients. The genera Coprococcus, Eubacterium, and Bilophia were more abundant in the healthy group, while the genus Rothia was more abundant in the AE group. The results of this study enrich our understanding of the gut microbiome composition of patients with AE and CE in the Qinghai-Tibetan Plateau.}, } @article {pmid35614211, year = {2022}, author = {Zhang, Y and Bhosle, A and Bae, S and McIver, LJ and Pishchany, G and Accorsi, EK and Thompson, KN and Arze, C and Wang, Y and Subramanian, A and Kearney, SM and Pawluk, A and Plichta, DR and Rahnavard, A and Shafquat, A and Xavier, RJ and Vlamakis, H and Garrett, WS and Krueger, A and Huttenhower, C and Franzosa, EA}, title = {Discovery of bioactive microbial gene products in inflammatory bowel disease.}, journal = {Nature}, volume = {606}, number = {7915}, pages = {754-760}, pmid = {35614211}, issn = {1476-4687}, support = {P30 DK043351/DK/NIDDK NIH HHS/United States ; R01 AT009708/AT/NCCIH NIH HHS/United States ; R01 DK127171/DK/NIDDK NIH HHS/United States ; R24 DK110499/DK/NIDDK NIH HHS/United States ; }, mesh = {*Bacterial Proteins/analysis/genetics ; Chronic Disease ; *Gastrointestinal Microbiome/genetics ; *Genes, Microbial ; Humans ; *Inflammatory Bowel Diseases/microbiology ; Metagenomics ; Proteomics ; Reproducibility of Results ; Transcriptome ; }, abstract = {Microbial communities and their associated bioactive compounds[1-3] are often disrupted in conditions such as the inflammatory bowel diseases (IBD)[4]. However, even in well-characterized environments (for example, the human gastrointestinal tract), more than one-third of microbial proteins are uncharacterized and often expected to be bioactive[5-7]. Here we systematically identified more than 340,000 protein families as potentially bioactive with respect to gut inflammation during IBD, about half of which have not to our knowledge been functionally characterized previously on the basis of homology or experiment. To validate prioritized microbial proteins, we used a combination of metagenomics, metatranscriptomics and metaproteomics to provide evidence of bioactivity for a subset of proteins that are involved in host and microbial cell-cell communication in the microbiome; for example, proteins associated with adherence or invasion processes, and extracellular von Willebrand-like factors. Predictions from high-throughput data were validated using targeted experiments that revealed the differential immunogenicity of prioritized Enterobacteriaceae pilins and the contribution of homologues of von Willebrand factors to the formation of Bacteroides biofilms in a manner dependent on mucin levels. This methodology, which we term MetaWIBELE (workflow to identify novel bioactive elements in the microbiome), is generalizable to other environmental communities and human phenotypes. The prioritized results provide thousands of candidate microbial proteins that are likely to interact with the host immune system in IBD, thus expanding our understanding of potentially bioactive gene products in chronic disease states and offering a rational compendium of possible therapeutic compounds and targets.}, } @article {pmid35614182, year = {2022}, author = {Iwańska, O and Latoch, P and Suchora, M and Pidek, IA and Huber, M and Bubak, I and Kopik, N and Kovalenko, M and Gąsiorowski, M and Armache, JP and Starosta, AL}, title = {Lake microbiome and trophy fluctuations of the ancient hemp rettery.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {8846}, pmid = {35614182}, issn = {2045-2322}, mesh = {*Cannabis/genetics ; Geologic Sediments/microbiology ; Lakes/microbiology ; Metagenome ; *Microbiota/genetics ; }, abstract = {Lake sediments not only store the long-term ecological information including pollen and microfossils but are also a source of sedimentary DNA (sedDNA). Here, by the combination of traditional multi-proxy paleolimnological methods with the whole-metagenome shotgun-sequencing of sedDNA we were able to paint a comprehensive picture of the fluctuations in trophy and bacterial diversity and metabolism of a small temperate lake in response to hemp retting, across the past 2000 years. Hemp retting (HR), a key step in hemp fibre production, was historically carried out in freshwater reservoirs and had a negative impact on the lake ecosystems. In Lake Slone, we identified two HR events, during the late stage of the Roman and Early Medieval periods and correlated these to the increased trophy and imbalanced lake microbiome. The metagenomic analyses showed a higher abundance of Chloroflexi, Planctomycetes and Bacteroidetes and a functional shift towards anaerobic metabolism, including degradation of complex biopolymers such as pectin and cellulose, during HR episodes. The lake eutrophication during HR was linked to the allochthonous, rather than autochthonous carbon supply-hemp straws. We also showed that the identification of HR based on the palynological analysis of hemp pollen may be inconclusive and we suggest the employment of the fibre count analysis as an additional and independent proxy.}, } @article {pmid35613310, year = {2022}, author = {Luo, T and Guo, Z and Liu, D and Guo, Z and Wu, Q and Li, Q and Lin, R and Chen, P and Ou, C and Chen, M}, title = {Deficiency of PSRC1 accelerates atherosclerosis by increasing TMAO production via manipulating gut microbiota and flavin monooxygenase 3.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2077602}, pmid = {35613310}, issn = {1949-0984}, mesh = {Animals ; *Atherosclerosis/genetics/microbiology ; Bacteria/genetics/metabolism ; *Gastrointestinal Microbiome/physiology ; *Methylamines/metabolism ; Mice ; Mice, Inbred C57BL ; Mice, Knockout ; Mixed Function Oxygenases/metabolism ; *Oxygenases/metabolism ; *Phosphoproteins/deficiency ; Plaque, Atherosclerotic/metabolism/microbiology ; }, abstract = {Maladaptive inflammatory and immune responses are responsible for intestinal barrier integrity and function dysregulation. Proline/serine-rich coiled-coil protein 1 (PSRC1) critically contributes to the immune system, but direct data on the gut microbiota and the microbial metabolite trimethylamine N-oxide (TMAO) are lacking. Here, we investigated the impact of PSRC1 deletion on TMAO generation and atherosclerosis. We first found that PSRC1 deletion in apoE[-/-] mice accelerated atherosclerotic plaque formation, and then the gut microbiota and metabolites were detected using metagenomics and untargeted metabolomics. Our results showed that PSRC1 deficiency enriched trimethylamine (TMA)-producing bacteria and functional potential for TMA synthesis and accordingly enhanced plasma betaine and TMAO production. Furthermore, PSRC1 deficiency resulted in a proinflammatory colonic phenotype that was significantly associated with the dysregulated bacteria. Unexpectedly, hepatic RNA-seq indicated upregulated flavin monooxygenase 3 (FMO3) expression following PSRC1 knockout. Mechanistically, PSRC1 overexpression inhibited FMO3 expression in vitro, while an ERα inhibitor rescued the downregulation. Consistently, PSRC1-knockout mice exhibited higher plasma TMAO levels with a choline-supplemented diet, which was gut microbiota dependent, as evidenced by antibiotic treatment. To investigate the role of dysbiosis induced by PSRC1 deletion in atherogenesis, apoE[-/-] mice were transplanted with the fecal microbiota from either apoE[-/-] or PSRC1[-/-]apoE[-/-] donor mice. Mice that received PSRC1-knockout mouse feces showed an elevation in TMAO levels, as well as plaque lipid deposition and macrophage accumulation, which were accompanied by increased plasma lipid levels and impaired hepatic cholesterol transport. Overall, we identified PSRC1 as an atherosclerosis-protective factor, at least in part, attributable to its regulation of TMAO generation via a multistep pathway. Thus, PSRC1 holds great potential for manipulating the gut microbiome and alleviating atherosclerosis.}, } @article {pmid35612791, year = {2022}, author = {Fong, SB and Boyer, E and Bonnaure-Mallet, M and Meuric, V}, title = {Microbiota in Periodontitis: Advances in the Omic Era.}, journal = {Advances in experimental medicine and biology}, volume = {1373}, number = {}, pages = {19-43}, pmid = {35612791}, issn = {0065-2598}, mesh = {Bacteria/genetics ; Biofilms ; High-Throughput Nucleotide Sequencing ; Humans ; *Microbiota/genetics ; *Periodontitis/microbiology ; }, abstract = {The complexity of the oral microbiome continues to astound researchers even with the advancement of multi-disciplinary strategies being used to study these microorganisms in relation to the human body. There is extensive literature available that explains how oral bacterial communities exist within the biofilm and maintains a balance with the host immune system, but when this balance is tipped disease can occur. The purpose of this review is to highlight the subgingival microbial compositions during health and periodontal disease using next generation sequencing techniques, as well as determining the types of functional activities that partake during these states. The subgingival microbiota is a fluid structure that can adapt accordingly to the environment and the identification of signature biomarkers may aid in the assessment of risk and disease severity in an individual to complement clinical diagnosis in the future.}, } @article {pmid35611141, year = {2022}, author = {Lin, GS and Zhao, MM and Li, XQ and Yu, HX}, title = {A Case Report of Infective Endocarditis with Failure of the Empirical Treatment-Q Fever Endocarditis Diagnosed by Metagenomic Next-Generation Sequencing.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {2545-2550}, pmid = {35611141}, issn = {1178-6973}, abstract = {BACKGROUND: Infective endocarditis (IE) can be caused by a variety of pathogens. Endocarditis due to the Coxiella burnetii (C. burnetii) infection is common in patients with negative blood culture results and usually occurs in patients with previous valvular heart disease, impaired immune function, and during pregnancy. The diagnosis is difficult based on the conventional diagnostic method, and serious adverse outcomes may occur in the case of delayed diagnosis.

CASE REPORT: In the present study, a case of a 43-year-old male patient with previous valvular heart disease was reported. The patient was admitted with a diagnosis of IE, but the etiology was unclear. Accurate diagnosis and treatment were achieved by combining metagenomic next-generation sequencing (mNGS) with Q fever serological antibody assay.

CONCLUSION: Metagenomic next-generation sequencing has been increasingly applied in clinical practice in recent years to detect the DNA or RNA in samples, and this could play a decisive role in the etiological diagnosis of some infectious diseases.}, } @article {pmid35611117, year = {2022}, author = {Donzelli, S and Ciuffreda, L and Pontone, M and Betti, M and Massacci, A and Mottini, C and De Nicola, F and Orlandi, G and Goeman, F and Giuliani, E and Sperandio, E and Piaggio, G and , and Morrone, A and Ciliberto, G and Fanciulli, M and Blandino, G and Pimpinelli, F and Pallocca, M}, title = {Optimizing the Illumina COVIDSeq laboratorial and bioinformatics pipeline on thousands of samples for SARS-CoV-2 Variants of Concern tracking.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {2558-2563}, pmid = {35611117}, issn = {2001-0370}, abstract = {The SARS-CoV-2 Variants of Concern tracking via Whole Genome Sequencing represents a pillar of public health measures for the containment of the pandemic. The ability to track down the lineage distribution on a local and global scale leads to a better understanding of immune escape and to adopting interventions to contain novel outbreaks. This scenario poses a challenge for NGS laboratories worldwide that are pressed to have both a faster turnaround time and a high-throughput processing of swabs for sequencing and analysis. In this study, we present an optimization of the Illumina COVID-seq protocol carried out on thousands of SARS-CoV-2 samples at the wet and dry level. We discuss the unique challenges related to processing hundreds of swabs per week such as the tradeoff between ultra-high sensitivity and negative contamination levels, cost efficiency and bioinformatics quality metrics.}, } @article {pmid35611093, year = {2022}, author = {Rajput, V and Samson, R and Yadav, R and Dastager, S and Khairnar, K and Dharne, M}, title = {Metagenomic mining of Indian river confluence reveal functional microbial community with lignocelluloytic potential.}, journal = {3 Biotech}, volume = {12}, number = {6}, pages = {132}, pmid = {35611093}, issn = {2190-572X}, abstract = {UNLABELLED: Microbial carbohydrate-active enzymes (CAZyme) can be harnessed for valorization of Lignocellulosic biomass (LCB) to value-added chemicals/products. The two Indian Rivers Ganges and the Yamuna having different origins and flow, face accumulation of carbon-rich substrates due to the discharge of wastewater from adjoining paper and pulp industries, which could potentially contribute to the natural enrichment of LCB utilizing genes, especially at their confluence. We analyzed CAZyme diversity in metagenomic datasets across the sacred confluence of the Rivers Ganges and Yamuna. Functional annotation using CAZyme database identified a total of 77,815 putative genes with functional domains involved in the catalysis of carbohydrate degradation or synthesis of glycosidic bonds. The metagenomic analysis detected ~ 41% CAZymes catalyzing the hydrolysis of lignocellulosic biomass polymers- cellulose, hemicellulose, lignin, and pectin. The Beta diversity analysis suggested higher CAZyme diversity at downstream region of the river confluence, which could be useful niche for culture-based studies. Taxonomic origin for CAZymes revealed the predominance of bacteria (97%), followed by archaea (1.67%), Eukaryota (0.63%), and viruses (0.7%). Metagenome guided CAZyme diversity of the microflora spanning across the confluence of Ganges-Yamuna River, could be harnessed for biomass and bioenergy applications.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s13205-022-03190-7.}, } @article {pmid35610236, year = {2022}, author = {Sun, H and Zhao, F and Liu, Y and Ma, T and Jin, H and Quan, K and Leng, B and Zhao, J and Yuan, X and Li, Z and Li, F and Kwok, LY and Zhang, S and Sun, Z and Zhang, J and Zhang, H}, title = {Probiotics synergized with conventional regimen in managing Parkinson's disease.}, journal = {NPJ Parkinson's disease}, volume = {8}, number = {1}, pages = {62}, pmid = {35610236}, issn = {2373-8057}, support = {31720103911//National Natural Science Foundation of China (National Science Foundation of China)/ ; }, abstract = {Parkinson's disease (PD) is mainly managed by pharmacological therapy (e.g., Benserazide and dopamine agonists). However, prolonged use of these drugs would gradually diminish their dopaminergic effect. Gut dysbiosis was observed in some patients with PD, suggesting close association between the gut microbiome and PD. Probiotics modulate the host's gut microbiota beneficially. A 3-month randomized, double-blind, placebo-controlled clinical trial was conducted to investigate the beneficial effect of probiotic co-administration in patients with PD. Eighty-two PD patients were recruited and randomly divided into probiotic [n = 48; Bifidobacterium animalis subsp. lactis Probio-M8 (Probio-M8), Benserazide, dopamine agonists] and placebo (n = 34; placebo, Benserazide, dopamine agonists) groups. Finally, 45 and 29 patients from Probio-M8 and placebo groups provided complete fecal and serum samples for further omics analysis, respectively. The results showed that Probio-M8 co-administration conferred added benefits by improving sleep quality, alleviating anxiety, and gastrointestinal symptoms. Metagenomic analysis showed that, after the intervention, there were significantly more species-level genome bins (SGBs) of Bifidobacterium animalis, Ruminococcaceae, and Lachnospira, while less Lactobacillus fermentum and Klebsiella oxytoca in Probio-M8 group (P < 0.05). Interestingly, Lactobacillus fermentum correlated positively with the scores of UPDRS-III, HAMA, HAMD-17, and negatively with MMSE. Klebsiella oxytoca correlated negatively with feces hardness. Moreover, co-administering Probio-M8 increased SGBs involved in tryptophan degradation, gamma-aminobutyric acid, short-chain fatty acids, and secondary bile acid biosynthesis, as well as serum acetic acid and dopamine levels (P < 0.05). Taken together, Probio-M8 synergized with the conventional regimen and strengthened the clinical efficacy in managing PD, accompanied by modifications of the host's gut microbiome, gut microbial metabolic potential, and serum metabolites.}, } @article {pmid35608941, year = {2022}, author = {Otake-Kasamoto, Y and Kayama, H and Kishikawa, T and Shinzaki, S and Tashiro, T and Amano, T and Tani, M and Yoshihara, T and Li, B and Tani, H and Liu, L and Hayashi, A and Okuzaki, D and Motooka, D and Nakamura, S and Okada, Y and Iijima, H and Takeda, K and Takehara, T}, title = {Lysophosphatidylserines derived from microbiota in Crohn's disease elicit pathological Th1 response.}, journal = {The Journal of experimental medicine}, volume = {219}, number = {7}, pages = {}, pmid = {35608941}, issn = {1540-9538}, support = {//Core Research for Evolutional Science and TechnologyPRIME/ ; 19gm1010004//Japan Agency for Medical Research and Development/ ; //Osaka University Graduate School of Medicine/ ; //Immunology Frontier Research Center/ ; 17H04159//Grant-in-Aid for Scientific Research/ ; }, mesh = {Animals ; *Colitis/pathology ; *Crohn Disease/etiology ; Dysbiosis/complications ; Humans ; Inflammation/pathology ; Intestinal Mucosa/metabolism ; Lysophospholipids ; Mice ; *Microbiota ; Th1 Cells/metabolism ; }, abstract = {Microbiota alteration and IFN-γ-producing CD4+ T cell overactivation are implicated in Crohn's disease (CD) pathogenesis. However, it remains unclear how dysbiosis enhances Th1 responses, leading to intestinal inflammation. Here, we identified key metabolites derived from dysbiotic microbiota that induce enhanced Th1 responses and exaggerate colitis in mouse models. Patients with CD showed elevated lysophosphatidylserine (LysoPS) concentration in their feces, accompanied by a higher relative abundance of microbiota possessing a gene encoding the phospholipid-hydrolyzing enzyme phospholipase A. LysoPS induced metabolic reprogramming, thereby eliciting aberrant effector responses in both human and mouse IFN-γ-producing CD4+ T cells. Administration of LysoPS into two mouse colitis models promoted large intestinal inflammation. LysoPS-induced aggravation of colitis was impaired in mice lacking P2ry10 and P2ry10b, and their CD4+ T cells were hyporesponsive to LysoPS. Thus, our findings elaborate on the mechanism by which metabolites elevated in patients with CD harboring dysbiotic microbiota promote Th1-mediated intestinal pathology.}, } @article {pmid35608350, year = {2022}, author = {Tong, X and Yu, X and Du, Y and Su, F and Liu, Y and Li, H and Liu, Y and Mu, K and Liu, Q and Li, H and Zhu, J and Xu, H and Xiao, F and Li, Y}, title = {Peripheral Blood Microbiome Analysis via Noninvasive Prenatal Testing Reveals the Complexity of Circulating Microbial Cell-Free DNA.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0041422}, pmid = {35608350}, issn = {2165-0497}, mesh = {*Cell-Free Nucleic Acids/genetics ; *Epstein-Barr Virus Infections ; Female ; Herpesvirus 4, Human ; Humans ; *Microbiota/genetics ; *Noninvasive Prenatal Testing ; Pregnancy ; Retrospective Studies ; }, abstract = {While circulating cell-free DNA (cfDNA) is becoming a powerful marker for noninvasive identification of infectious pathogens in liquid biopsy specimens, a microbial cfDNA baseline in healthy individuals is urgently needed for the proper interpretation of microbial cfDNA sequencing results in clinical metagenomics. Because noninvasive prenatal testing (NIPT) shares many similarities with the sequencing protocol of metagenomics, we utilized the standard low-pass whole-genome-sequencing-based NIPT to establish a microbial cfDNA baseline in healthy people. Sequencing data from a total of 107,763 peripheral blood samples of healthy pregnant women undergoing NIPT screening were retrospectively collected and reanalyzed for microbiome DNA screening. It was found that more than 95% of exogenous cfDNA was from bacteria, 3% from eukaryotes, and 0.4% from viruses, indicating the gut/environment origins of many microorganisms. Overall and regional abundance patterns were well illustrated, with huge regional diversity and complexity, and unique interspecies and symbiotic relationships were observed for TORCH organisms (Toxoplasma gondii, others [Treponema pallidum {causing syphilis}, hepatitis B virus {HBV}, and human parvovirus B19 {HPV-B19} ], rubella virus, cytomegalovirus [CMV], and herpes simplex virus [HSV]) and another common virus, Epstein-Barr virus (EBV). To sum up, our study revealed the complexity of the baseline circulating microbial cfDNA and showed that microbial cfDNA sequencing results need to be interpreted in a more comprehensive manner. IMPORTANCE While circulating cell-free DNA (cfDNA) has been becoming a powerful marker for noninvasive identification of infectious pathogens in liquid biopsy specimens, a baseline for microbial cfDNA in healthy individuals is urgently needed for the proper interpretation of microbial cfDNA sequencing results in clinical metagenomics. Standard low-pass whole-genome-sequencing-based NIPT shares many similarities with the sequencing protocol for metagenomics and could provide a microbial cfDNA baseline in healthy people; thus, a reference cfDNA data set of the human microbiome was established with sequencing data from a total of 107,763 peripheral blood samples of healthy pregnant women undergoing NIPT screening. Our study revealed the complexity of circulating microbial cfDNA and indicated that microbial cfDNA sequencing results need to be interpreted in a more comprehensive manner, especially with regard to geographic patterns and coexistence networks.}, } @article {pmid35605852, year = {2022}, author = {Zhang, J and Fu, Q and Huang, Y and Fan, Y and Liang, M and Chen, H and Yu, S}, title = {Negative impacts of sea-level rise on soil microbial involvement in carbon metabolism.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 2}, pages = {156087}, doi = {10.1016/j.scitotenv.2022.156087}, pmid = {35605852}, issn = {1879-1026}, mesh = {Carbon/analysis ; Ecosystem ; *Microbiota ; Sea Level Rise ; *Soil ; Soil Microbiology ; }, abstract = {Sea-level rise has been threatening the terrestrial ecosystem functioning of coastal islands, of which the most important component is carbon (C) cycling. However, metagenomic and metabolomic evidence documenting salt intrusion effects on molecular biological processes of C cycling are still lacking. Here, we investigated microbial communities, metagenomic taxonomy and function, and metabolomic profiles in the marine-terrestrial transition zone of low- and high-tide, and low- and high-land areas based on distances of 0 m, 50 m, 100 m, and 200 m, respectively, to the water-land junction of Neilingding Island. Our results showed that soil salinity (EC) was the dominant driver controlling bacterial abundance and community composition and metagenomic taxonomy and function. The metabolomic profiling at the low-tide site was significantly different from that of other sites. The low-tide site had greater abundance of Proteobacteria and Bacteroidetes (1.6-3.7 fold), especially Gammaproteobacteria, but lower abundance (62-83%) of Acidobacteria and Chloroflexi, compared with other three sites. The metagenomic functional genes related to carbohydrate metabolism decreased at the low-tide site by 15.2%, including the metabolism of aminosugars, di- and oligo-saccharides, glycoside hydrolases, and monosaccharides, leading to significant decreases in 21 soil metabolites, such as monosaccharide (l-gulose), disaccharide (sucrose and turanose), and oligosaccharides (stachyose and maltotetraose). Our study demonstrates that elevated salinity due to sea-level rise may suppress C-cycling genes and their metabolites, therefore having negative impacts on microbial metabolism of organic matter.}, } @article {pmid35605810, year = {2022}, author = {Sartori, AGO and Cesar, ASM and Woitowicz, FCG and Saliba, ASMC and Ikegaki, M and Rosalen, PL and Coutinho, LL and Alencar, SM}, title = {Plant genetic diversity by DNA barcoding to investigate propolis origin.}, journal = {Phytochemistry}, volume = {200}, number = {}, pages = {113226}, doi = {10.1016/j.phytochem.2022.113226}, pmid = {35605810}, issn = {1873-3700}, mesh = {*Ascomycota ; Chromatography, High Pressure Liquid ; DNA ; DNA Barcoding, Taxonomic ; Gas Chromatography-Mass Spectrometry ; Genetic Variation ; Plants/chemistry ; *Populus/chemistry/genetics ; *Propolis/chemistry ; Resins, Plant/analysis ; }, abstract = {Identify the botanical origins of a certain type of propolis may be challenging and time demanding, since it involves bee's behavior observation, plant resins collection and chemical analysis. Thus, this study aimed to determine the plant genetic materials in propolis from southern Brazil using the DNA barcoding to investigate their botanical origins, as well as to compare it with the phytochemical composition determined by ultra-high-performance liquid chromatography coupled with high-resolution mass spectrometry (UHPLC-HRMS) and with the pollinic profile. As principal results, non-native Populus carolinensis Moench (Salicaceae) was almost the only DNA source in some propolis samples, which coincided with the presence of flavonoids typical from poplar exudates. Conversely, other propolis samples had DNA material coming mainly from native plant species, most of them characterized to the species level, although no specific chemical markers from those plants could be identified by UHPLC-HRMS. However, pollen from several plants identified by the DNA barcoding were extracted from some propolis samples. Despite the identification of typical diterpenes, DNA material from Araucaria angustifolia (Bertol.) Kuntze (Araucariaceae), which have been indicated as a major resin source for propolis from preservation areas in southern Brazil, was found in very small abundancies, likely because bees do not drag tissue material containing DNA when collecting resin from this native species. In conclusion, DNA barcoding analysis successfully provided information about the provenance of propolis, although, depending on the plant resin sources, this information is likely to come from pollen.}, } @article {pmid35605776, year = {2022}, author = {Zhou, X and Arslan, M and Liu, Z and Li, D and Xi, H and Feng, Y and Li, S and Wei, J and Rong, X and Liang, Z and Wang, X and Wu, Z and Gamal El-Din, M}, title = {Low carbon-to-nitrogen ratio digestate from high-rate anaerobic baffled reactor facilitates heterotrophic/autotrophic nitrifiers involved in nitrogen removal.}, journal = {Bioresource technology}, volume = {359}, number = {}, pages = {127346}, doi = {10.1016/j.biortech.2022.127346}, pmid = {35605776}, issn = {1873-2976}, mesh = {Anaerobiosis ; Bioreactors ; Carbon ; *Denitrification ; Heterotrophic Processes ; Nitrification ; *Nitrogen/metabolism ; Wastewater/analysis ; }, abstract = {In this study, baffled anaerobic-aerobic reactors (AOBRs) with modified basalt fiber (MBF) carriers and felt were used to treat domestic wastewater (DWW). The influent was first treated in anaerobic compartments, with the NH4[+]-N containing digestate refluxed into aerobic compartment for nitrification. The nitrified liquid was channeled to the anaerobic compartments for further denitrification. Under optimal conditions, AOBR with MBF carriers could remove 91% chemical oxygen demand (COD) and 81% total nitrogen (TN), with biomass production increased by 7.6%, 4.5% and 8.7% in three successive anaerobic compartments compared to the control. Biological viability analysis showed that live cells outnumbered dead cells in bio-nests. Metagenomics analysis showed that multiple metabolic pathways accounted for nitrogen conversion in anaerobic and aerobic compartments. More importantly, low COD/TN ratio digestate facilitated heterotrophic nitrification-aerobic denitrification (HN-AD) species growth in aerobic compartment. This study provides a promising strategy to source treatment of DWW from urban communities.}, } @article {pmid35604945, year = {2022}, author = {Abe, Y and Fukushima, K and Matsumoto, Y and Niitsu, T and Nabeshima, H and Nagahama, Y and Akiba, E and Haduki, K and Saito, H and Nitta, T and Kawano, A and Tanaka, M and Matsuki, T and Motooka, D and Tsujino, K and Miki, K and Nakamura, S and Iida, T and Kida, H}, title = {Mycobacterium senriense sp. nov., a slowly growing, non-scotochromogenic species, isolated from sputum of an elderly man.}, journal = {International journal of systematic and evolutionary microbiology}, volume = {72}, number = {5}, pages = {}, doi = {10.1099/ijsem.0.005378}, pmid = {35604945}, issn = {1466-5034}, mesh = {Aged ; Bacterial Typing Techniques ; Base Composition ; DNA, Bacterial/genetics ; DNA-Directed RNA Polymerases/genetics ; Fatty Acids/chemistry ; Humans ; Male ; *Mycobacterium ; *Mycobacterium Infections/diagnosis/microbiology ; Mycobacterium avium Complex ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; Sputum/microbiology ; }, abstract = {A slowly growing mycobacteria, identified as strain TY59[T], was isolated from sputum of an elderly man with pneumonia. Sequencing of the 16S rRNA gene indicated that this strain was similar to members of the Mycobacterium avium complex and closely related species. Strain TY59[T] has highest 16S rRNA gene sequence similarities to the type strains of Mycobacterium colombiense (99.80 % sequence similarity), Mycobacterium vulneris (99.74 %), Mycobacterium timonense (99.54 %), Mycobacterium avium subsp. avium (99.54 %) and Mycobacterium avium subsp. silvaticum (99.54 %). Analysis of the internal transcribed spacer (ITS) and DNA-directed RNA polymerase subunit beta (rpoB) sequences gave similar results to the 16S rRNA gene analysis. The closest species to strain TY59[T] were M. colombiense and M. vulneris with 97.90-98.25 % identity in ITS and 96.4-96.6 % in rpoB. The strain's 65 kDa heat shock protein (hsp65) gene was different from those of M. vulneris, M. colombiense and M. avium subsp. silvaticum with 72.4-74.2 % identity. Average nucleotide identity results showed a 93.4 % match to M. vulneris as the maximum value. Phenotypically, the non-chromogenicity, rough colonies, growth at 42 °C, negative results for nitrate reduction, β-glucosidase and Tween 80 hydrolysis, and positive results for catalase activity set this strain apart from closely related species. We propose that Mycobacterium senriense sp. nov. is a novel species of slowly growing mycobacteria. The type strain is TY59[T] (RIMD 1371001[T]=CIP 111917[T]).}, } @article {pmid35604226, year = {2022}, author = {Yu, H and Speth, DR and Connon, SA and Goudeau, D and Malmstrom, RR and Woyke, T and Orphan, VJ}, title = {Community Structure and Microbial Associations in Sediment-Free Methanotrophic Enrichment Cultures from a Marine Methane Seep.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {11}, pages = {e0210921}, pmid = {35604226}, issn = {1098-5336}, mesh = {Anaerobiosis ; Archaea/metabolism ; Bacteria/genetics/metabolism ; *Ecosystem ; Geologic Sediments/microbiology ; *Methane/metabolism ; Oxidation-Reduction ; Phylogeny ; Sulfates/metabolism ; }, abstract = {Syntrophic consortia of anaerobic methanotrophic archaea (ANME) and sulfate-reducing bacteria (SRB) consume large amounts of methane and serve as the foundational microorganisms in marine methane seeps. Despite their importance in the carbon cycle, research on the physiology of ANME-SRB consortia has been hampered by the slow growth and complex physicochemical environment the consortia inhabit. Here, we report successful sediment-free enrichment of ANME-SRB consortia from deep-sea methane seep sediments in the Santa Monica Basin, California. Anoxic Percoll density gradients and size-selective filtration were used to separate ANME-SRB consortia from sediment particles and single cells to accelerate the cultivation process. Over a 3-year period, a subset of the sediment-associated ANME and SRB lineages, predominantly comprised of ANME-2a/2b ("Candidatus Methanocomedenaceae") and their syntrophic bacterial partners, SEEP-SRB1/2, adapted and grew under defined laboratory conditions. Metagenome-assembled genomes from several enrichments revealed that ANME-2a, SEEP-SRB1, and Methanococcoides in different enrichments from the same inoculum represented distinct species, whereas other coenriched microorganisms were closely related at the species level. This suggests that ANME, SRB, and Methanococcoides are more genetically diverse than other members in methane seeps. Flow cytometry sorting and sequencing of cell aggregates revealed that Methanococcoides, Anaerolineales, and SEEP-SRB1 were overrepresented in multiple ANME-2a cell aggregates relative to the bulk metagenomes, suggesting they were physically associated and possibly interacting. Overall, this study represents a successful case of selective cultivation of anaerobic slow-growing microorganisms from sediments based on their physical characteristics, introducing new opportunities for detailed genomic, physiological, biochemical, and ecological analyses. IMPORTANCE Biological anaerobic oxidation of methane (AOM) coupled with sulfate reduction represents a large methane sink in global ocean sediments. Methane consumption is carried out by syntrophic archaeal-bacterial consortia and fuels a unique ecosystem, yet the interactions in these slow-growing syntrophic consortia and with other associated community members remain poorly understood. The significance of this study is the establishment of sediment-free enrichment cultures of anaerobic methanotrophic archaea and sulfate-reducing bacteria performing AOM with sulfate using selective cultivation approaches based on size, density, and metabolism. By reconstructing microbial genomes and analyzing community composition of the enrichment cultures and cell aggregates, we shed light on the diversity of microorganisms physically associated with AOM consortia beyond the core syntrophic partners. These enrichment cultures offer simplified model systems to extend our understanding of the diversity of microbial interactions within marine methane seeps.}, } @article {pmid35604174, year = {2022}, author = {Zhang, Z and Nie, S and Sang, Y and Mo, S and Li, J and Kashif, M and Su, G and Yan, B and Jiang, C}, title = {Effects of Spartina alterniflora Invasion on Nitrogen Fixation and Phosphorus Solubilization in a Subtropical Marine Mangrove Ecosystem.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0068221}, pmid = {35604174}, issn = {2165-0497}, mesh = {*Ecosystem ; Introduced Species ; Nitrogen Fixation ; *Phosphorus ; Poaceae/physiology ; Wetlands ; }, abstract = {Nitrogen fixation (NF) and phosphorus solubilization (PS) play a key role in maintaining the stability of mangrove ecosystems. In China, the invasion of Spartina alterniflora has brought a serious threat to the mangrove ecosystem. However, systematic research on NF and PS in mangrove sediments has not been conducted, and limited studies have focused on the response of NF and PS to S. alterniflora invasion, particularly at different sediment depths. In the present study, shotgun metagenomics and quantitative PCR were used to study the 0- to 100-cm sediment profile of the mangrove ecosystem in the Beibu Gulf of China. Results showed that the PS potential of mangrove sediments was primarily caused by enzymes encoded by phoA, phoD, ppx, ppa, and gcd genes. S. alterniflora changed environmental factors, such as total nitrogen, total phosphorus, and total organic carbon, and enhanced the potential of NF and PS in sediments. Moreover, most microorganisms involved in NF or PS (NFOPSMs) responded positively to the invasion of S. alterniflora. Cd, available iron, and salinity were the key environmental factors that affected the distribution of NF and PS genes (NFPSGs) and NFOPSMs. A strong coupling effect was observed between NF and PS in the mangrove ecosystem. S. alterniflora invasion enhanced the coupling of NF and PS and the interaction of microorganisms involved in NF and PS (NFAPSM), thereby promoting the turnover of NP and improving sediment quality. Finally, 108 metagenome-assembled genomes involved in NF or PS were reconstructed to further evaluate NFOPSMs. IMPORTANCE This study revealed the efficient nutrient cycling mechanism of mangroves. Positive coupling effects were observed in sediment quality, NF and PS processes, and NFOPSMs with the invasion of S. alterniflora. This research contributed to the understanding of the effects of S. alterniflora invasion on the subtropical mangrove ecosystem and provided theoretical guidance for mangrove protection, restoration, and soil management. Additionally, novel NFOPSMs provided a reference for the development of marine biological fertilizers.}, } @article {pmid35604139, year = {2022}, author = {Chen, T and Xie, G and Mi, J and Wen, X and Cao, Z and Ma, B and Zou, Y and Zhang, N and Wang, Y and Liao, X and Wu, Y}, title = {Recovery of the Structure and Function of the Pig Manure Bacterial Community after Enrofloxacin Exposure.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0200421}, pmid = {35604139}, issn = {2165-0497}, mesh = {Animals ; Anti-Bacterial Agents ; *Bacteria/genetics ; Enrofloxacin ; Genes, Bacterial ; *Manure/microbiology ; Nitrogen ; Soil ; Swine ; }, abstract = {At present, growth-promoting antibiotics are banned in the pig industry in many countries, but therapeutic antibiotics can still be used normally. However, the effect of therapeutic antibiotics on the structure and function of the intestinal bacterial community and its recovery is still unclear. We analyzed the effects of enrofloxacin on the pig manure bacterial community and functional genes during dosing and without dosing. Enrofloxacin caused significant changes in community structure. The changes in the diversity and structure of the bacterial community were the most obvious on the fifth day, and most of the differentially abundant genera (19/29) belonged to Firmicutes. The structure of the manure bacterial community in the low concentration enrofloxacin group was completely reverted after 10 days of drug discontinuation. In addition, enrofloxacin had a significant impact on the abundance of bacterial functional genes. Most of the differentially abundant functional genes of the manure bacterial community were significantly enriched, especially genes related to metabolic pathways, for adaptation to the antibiotic environment. Moreover, exposure to enrofloxacin increased the abundance of functional genes related to nitrogen metabolism in the manure bacterial community, and the total nitrogen content of pig manure was significantly reduced. The functional genetic differences caused by enrofloxacin exposure were completely reverted 10 days after drug discontinuation. The results of the present study suggest that enrofloxacin induces changes in the structure and function of manure bacterial communities, which may be rapidly recovered after drug discontinuation. IMPORTANCE A stable intestinal bacterial community balance is beneficial for animal health. Enrofloxacin is widely used in animal husbandry as a therapeutic drug, but it can cause intestinal environmental imbalance. Enrofloxacin is widely present in groundwater, pork, etc., which leads to a greater risk of human exposure. The effect of enrofloxacin on the structure and function of the intestinal bacterial community and its recovery is still unclear. In this study, we found that enrofloxacin, as a therapeutic drug, can enhance nitrogen metabolism in the manure bacterial community. Moreover, the structure and function of the manure bacterial community in the low concentration enrofloxacin group may be completely reverted 10 days after drug discontinuation. This study provides a reference for the effect of enrofloxacin exposure on the intestinal bacterial community.}, } @article {pmid35604118, year = {2022}, author = {Cornet, L and Cleenwerck, I and Praet, J and Leonard, RR and Vereecken, NJ and Michez, D and Smagghe, G and Baurain, D and Vandamme, P}, title = {Phylogenomic Analyses of Snodgrassella Isolates from Honeybees and Bumblebees Reveal Taxonomic and Functional Diversity.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0150021}, pmid = {35604118}, issn = {2379-5077}, mesh = {Animals ; Bees ; Phylogeny ; *Neisseriaceae/genetics ; *Microbiota ; }, abstract = {Snodgrassella is a genus of Betaproteobacteria that lives in the gut of honeybees (Apis spp.) and bumblebees (Bombus spp). It is part of a conserved microbiome that is composed of a few core phylotypes and is essential for bee health and metabolism. Phylogenomic analyses using whole-genome sequences of 75 Snodgrassella strains from 4 species of honeybees and 14 species of bumblebees showed that these strains formed a monophyletic lineage within the Neisseriaceae family, that Snodgrassella isolates from Asian honeybees diverged early from the other species in their evolution, that isolates from honeybees and bumblebees were well separated, and that this genus consists of at least seven species. We propose to formally name two new Snodgrassella species that were isolated from bumblebees: i.e., Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov. Possible evolutionary scenarios for 107 species- or group-specific genes revealed very limited evidence for horizontal gene transfer. Functional analyses revealed the importance of small proteins, defense mechanisms, amino acid transport and metabolism, inorganic ion transport and metabolism and carbohydrate transport and metabolism among these 107 specific genes. IMPORTANCE The microbiome of honeybees (Apis spp.) and bumblebees (Bombus spp.) is highly conserved and represented by few phylotypes. This simplicity in taxon composition makes the bee's microbiome an emergent model organism for the study of gut microbial communities. Since the description of the Snodgrassella genus, which was isolated from the gut of honeybees and bumblebees in 2013, a single species (i.e., Snodgrassella alvi), has been named. Here, we demonstrate that this genus is actually composed of at least seven species, two of which (Snodgrassella gandavensis sp. nov. and Snodgrassella communis sp. nov.) are formally described and named in the present publication. We also report the presence of 107 genes specific to Snodgrassella species, showing notably the importance of small proteins and defense mechanisms in this genus.}, } @article {pmid35602532, year = {2022}, author = {Vishnu, RA and Alamelu, S and Arun, KV and Sujitha, P and Ganesh, PR}, title = {Comparative evaluation of subgingival microbiome in healthy periodontium and gingivitis using next-generation sequencing technology: A case-control study.}, journal = {Journal of Indian Society of Periodontology}, volume = {26}, number = {3}, pages = {224-229}, pmid = {35602532}, issn = {0972-124X}, abstract = {BACKGROUND: Human dental plaque is a complex microbial community containing millions of species. Gingivitis is a dysregulated immune-inflammatory response induced by dysbiotic plaque biofilm that interrupts symbiosis. The emergence of next-generation sequencing with 16S rRNA gene has greatly contributed in understanding the complexity of microbiota. However, studies focusing on microbiome in gingivitis are limited. The whole bacterial community is important in causing periodontal disease than a small number of periodontal pathogens. In this study, we attempted to profile the subgingival microbiome from individuals with healthy gingiva and in patients with gingivitis using next-generation sequencing technology.

MATERIALS AND METHODS: Subgingival plaque samples from 15 healthy periodontium (Group I) and 15 gingivitis (Group II) were collected and 16s rRNA sequencing was done in Illumina Solexa Sequencer. Data analysis using 16s metagenomics tool from BaseSpace onsite operational taxonomic units was assigned to each sequence using HOMD database. Individual variation in the microbiome of the subgingival samples between the two groups was also evaluated.

RESULTS: The comparison of top 20 species between Group I and Group II revealed no significant species group between them. Synergistetes was absent in Group I samples but found in Group II. At the genus level, HACEK group species were found in both the groups, while Dialister and Aneroglobus were found abundantly in the Group II.

CONCLUSION: The presence of unique genera and species seen in Group II samples could point toward a dysbiotic shift that could be taking place in the subgingival environment leading to gingivitis.}, } @article {pmid35602067, year = {2022}, author = {Ishaq, SL and Turner, SM and Tudor, MS and MacRae, JD and Hamlin, H and Kilchenmann, J and Lee, G and Bouchard, D}, title = {Many Questions Remain Unanswered About the Role of Microbial Transmission in Epizootic Shell Disease in American Lobsters (Homarus americanus).}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {824950}, pmid = {35602067}, issn = {1664-302X}, abstract = {Despite decades of research on lobster species' biology, ecology, and microbiology, there are still unresolved questions about the microbial communities which associate in or on lobsters under healthy or diseased states, microbial acquisition, as well as microbial transmission between lobsters and between lobsters and their environment. There is an untapped opportunity for metagenomics, metatranscriptomics, and metabolomics to be added to the existing wealth of knowledge to more precisely track disease transmission, etiology, and host-microbe dynamics. Moreover, we need to gain this knowledge of wild lobster microbiomes before climate change alters environmental and host-microbial communities more than it likely already has, throwing a socioeconomically critical industry into disarray. As with so many animal species, the effects of climate change often manifest as changes in movement, and in this perspective piece, we consider the movement of the American lobster (Homarus americanus), Atlantic Ocean currents, and the microorganisms associated with either.}, } @article {pmid35602066, year = {2022}, author = {Mahajna, A and Dinkla, IJT and Euverink, GJW and Keesman, KJ and Jayawardhana, B}, title = {Clean and Safe Drinking Water Systems via Metagenomics Data and Artificial Intelligence: State-of-the-Art and Future Perspective.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {832452}, pmid = {35602066}, issn = {1664-302X}, abstract = {The use of next-generation sequencing technologies in drinking water distribution systems (DWDS) has shed insight into the microbial communities' composition, and interaction in the drinking water microbiome. For the past two decades, various studies have been conducted in which metagenomics data have been collected over extended periods and analyzed spatially and temporally to understand the dynamics of microbial communities in DWDS. In this literature review, we outline the findings which were reported in the literature on what kind of occupancy-abundance patterns are exhibited in the drinking water microbiome, how the drinking water microbiome dynamically evolves spatially and temporally in the distribution networks, how different microbial communities co-exist, and what kind of clusters exist in the drinking water ecosystem. While data analysis in the current literature concerns mainly with confirmatory and exploratory questions pertaining to the use of metagenomics data for the analysis of DWDS microbiome, we present also future perspectives and the potential role of artificial intelligence (AI) and mechanistic models to address the predictive and mechanistic questions. The integration of meta-omics, AI, and mechanistic models transcends metagenomics into functional metagenomics, enabling deterministic understanding and control of DWDS for clean and safe drinking water systems of the future.}, } @article {pmid35602031, year = {2022}, author = {Schultz, J and Argentino, ICV and Kallies, R and Nunes da Rocha, U and Rosado, AS}, title = {Polyphasic Analysis Reveals Potential Petroleum Hydrocarbon Degradation and Biosurfactant Production by Rare Biosphere Thermophilic Bacteria From Deception Island, an Active Antarctic Volcano.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {885557}, pmid = {35602031}, issn = {1664-302X}, abstract = {Extreme temperature gradients in polar volcanoes are capable of selecting different types of extremophiles. Deception Island is a marine stratovolcano located in maritime Antarctica. The volcano has pronounced temperature gradients over very short distances, from as high as 100°C in the fumaroles to subzero next to the glaciers. These characteristics make Deception a promising source of a variety of bioproducts for use in different biotechnological areas. In this study, we isolated thermophilic bacteria from sediments in fumaroles at two geothermal sites on Deception Island with temperatures between 50 and 100°C, to evaluate the potential capacity of these bacteria to degrade petroleum hydrocarbons and produce biosurfactants under thermophilic conditions. We isolated 126 thermophilic bacterial strains and identified them molecularly as members of genera Geobacillus, Anoxybacillus, and Brevibacillus (all in phylum Firmicutes). Seventy-six strains grew in a culture medium supplemented with crude oil as the only carbon source, and 30 of them showed particularly good results for oil degradation. Of 50 strains tested for biosurfactant production, 13 showed good results, with an emulsification index of 50% or higher of a petroleum hydrocarbon source (crude oil and diesel), emulsification stability at 100°C, and positive results in drop-collapse, oil spreading, and hemolytic activity tests. Four of these isolates showed great capability of degrade crude oil: FB2_38 (Geobacillus), FB3_54 (Geobacillus), FB4_88 (Anoxybacillus), and WB1_122 (Geobacillus). Genomic analysis of the oil-degrading and biosurfactant-producer strain FB4_88 identified it as Anoxybacillus flavithermus, with a high genetic and functional diversity potential for biotechnological applications. These initial culturomic and genomic data suggest that thermophilic bacteria from this Antarctic volcano have potential applications in the petroleum industry, for bioremediation in extreme environments and for microbial enhanced oil recovery (MEOR) in reservoirs. In addition, recovery of small-subunit rRNA from metagenomes of Deception Island showed that Firmicutes is not among the dominant phyla, indicating that these low-abundance microorganisms may be important for hydrocarbon degradation and biosurfactant production in the Deception Island volcanic sediments.}, } @article {pmid35602026, year = {2022}, author = {Liu, P and Hu, S and He, Z and Feng, C and Dong, G and An, S and Liu, R and Xu, F and Chen, Y and Ying, X}, title = {Towards Strain-Level Complexity: Sequencing Depth Required for Comprehensive Single-Nucleotide Polymorphism Analysis of the Human Gut Microbiome.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {828254}, pmid = {35602026}, issn = {1664-302X}, abstract = {Intestinal bacteria strains play crucial roles in maintaining host health. Researchers have increasingly recognized the importance of strain-level analysis in metagenomic studies. Many analysis tools and several cutting-edge sequencing techniques like single cell sequencing have been proposed to decipher strains in metagenomes. However, strain-level complexity is far from being well characterized up to date. As the indicator of strain-level complexity, metagenomic single-nucleotide polymorphisms (SNPs) have been utilized to disentangle conspecific strains. Lots of SNP-based tools have been developed to identify strains in metagenomes. However, the sufficient sequencing depth for SNP and strain-level analysis remains unclear. We conducted ultra-deep sequencing of the human gut microbiome and constructed an unbiased framework to perform reliable SNP analysis. SNP profiles of the human gut metagenome by ultra-deep sequencing were obtained. SNPs identified from conventional and ultra-deep sequencing data were thoroughly compared and the relationship between SNP identification and sequencing depth were investigated. The results show that the commonly used shallow-depth sequencing is incapable to support a systematic metagenomic SNP discovery. In contrast, ultra-deep sequencing could detect more functionally important SNPs, which leads to reliable downstream analyses and novel discoveries. We also constructed a machine learning model to provide guidance for researchers to determine the optimal sequencing depth for their projects (SNPsnp, https://github.com/labomics/SNPsnp). To conclude, the SNP profiles based on ultra-deep sequencing data extend current knowledge on metagenomics and highlights the importance of evaluating sequencing depth before starting SNP analysis. This study provides new ideas and references for future strain-level investigations.}, } @article {pmid35602015, year = {2022}, author = {Jiang, M and Yang, C and Kwan, PSL and Zhang, L and Fan, H and Jin, Y and Sun, L and Chen, H and Li, B and Chen, Q and Wu, Y and Guo, Y and Shi, Y and Liao, M and Shi, X and Liu, J and Jiang, L and Cai, R and Deng, Y and Sun, Q and Yang, R and Zhang, Q and Cui, Y and Hu, Q}, title = {Rapid Multilateral and Integrated Public Health Response to a Cross-City Outbreak of Salmonella Enteritidis Infections Combining Analytical, Molecular, and Genomic Epidemiological Analysis.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {772489}, pmid = {35602015}, issn = {1664-302X}, abstract = {On September 21, 2019, the Shenzhen and Dongguan Centers for Disease Control and Prevention received notification of a large cluster of suspected gastroenteritis involving primarily children who sought medical care at hospitals throughout two adjacent cities in China, Shenzhen, and Dongguan. A joint outbreak response was promptly initiated across jurisdictions in a concerted effort between clinical microbiologists, epidemiologists, and public health scientists. Concurrently, multiplex PCRs were used for rapid laboratory diagnosis of suspected cases; epidemiological investigations were conducted to identify the outbreak source, complemented by near real-time multicenter whole-genome analyses completed within 34 h. Epidemiological evidence indicated that all patients had consumed egg sandwiches served on September 20 as snacks to children and staff at a nursery in Dongguan, located near Shenzhen. Salmonella Enteritidis was isolated from case-patients, food handlers, kitchenware, and sandwiches with kitchen-made mayonnaise. Whole-genome single-nucleotide polymorphism (SNP)-based phylogenetic analysis demonstrated a well-supported cluster with pairwise distances of ≤1 SNP between genomes for outbreak-associated isolates, providing the definitive link between all samples. In comparison with historical isolates from the same geographical region, the minimum pairwise distance was >14 SNPs, suggesting a non-local outbreak source. Genomic source tracing revealed the possible transmission dynamics of a S. Enteritidis clone throughout a multi-provincial egg distribution network. The efficiency and scale with which multidisciplinary and integrated approaches were coordinated in this foodborne disease outbreak response was unprecedented in China, leading to the timely intervention of a large cross-jurisdiction Salmonella outbreak.}, } @article {pmid35601781, year = {2022}, author = {Zhao, G and Deng, X and Wu, D and Cao, R and Shao, A and Zhou, Y and Zhang, T and Li, G and He, H and Lu, J and Zhang, L}, title = {Application of metagenomic sequencing toward rapid and sensitive diagnosis of goose avastrovirus infection in China.}, journal = {Veterinary research forum : an international quarterly journal}, volume = {13}, number = {1}, pages = {1-6}, pmid = {35601781}, issn = {2008-8140}, abstract = {The gosling gout, a newly emerged disease, has widely broken out in China since 2017. Typical signs for the disease include diarrhea, anorexia, depression, dehydration, emaciation and paralysis. At autopsy, uratosis was the main pathological change which could be found at kidney, pericardium, air sac, muscle and leg joint. In this study, gosling gout was firstly diagnosed by metagenomic analysis. Samples of kidney, Fabricius bursa, spleen and jejunum were collected and submitted to next-generation DNA sequencing. Our results demonstrated that goose avastrovirus was highly related with this disease. We confirmed the sequencing results by reverse transcription polymerase chain reaction method and artificial infection experiment and got consistent results. In summary, metagenomic sequencing method combined with traditional molecular identification was applied toward diagnosis of a novel gosling gout disease in China and revealed that goose avastrovirus was highly related with this disease. It has been proved to be a powerful tool for rapid and sensitive diagnosis of animal diseases, especially for some exceptional pathogens. In addition, host range, variation, molecular pathogenesis and potential zoonotic infection of this novel goose astrovirus need to be further studied.}, } @article {pmid35601189, year = {2022}, author = {Onohuean, H and Agwu, E and Nwodo, UU}, title = {A Global Perspective of Vibrio Species and Associated Diseases: Three-Decade Meta-Synthesis of Research Advancement.}, journal = {Environmental health insights}, volume = {16}, number = {}, pages = {11786302221099406}, pmid = {35601189}, issn = {1178-6302}, abstract = {Outbreaks of Vibrio infections have a long history of global public health concern and threat to the aquaculture industry. This 3-decade (1990-2019) meta-synthesis of global research progress in Vibrio species and associated disease outbreaks was undertaken to generate the knowledge needed to design effective interventions with policy implications. Using PRISMA protocol, we obtained data on the online version of the Institute for Scientific Information (ISI), Web of Science (WOS), and Scopus from January 1990 to September 2021 by title search of the keywords "Vibrio species OR Vibrio spp. OR vibriosis." On the 3-decade survey, the result has shown that a total of 776 publications document types were published on the subject, with an average of 24.25 ± 13.6 published documents per year with an annual growth rate of 4.71%. The year 2020 recorded the highest output of 52 published documents accounting for 6.70% of the total. The most prolific author, Blanch A., published 12 articles on the subject and has received citations of 1003 with an h-index of 10. While the most global cited paper author is the journal of J. Bacteriol (Bassler et al), receiving total citation (TC) (550) and per Year (22). The top active corresponding authors country is the United States of America with (92) articles, freq. 12.40%; TC of 3103. The observations in this study, such as the collaborations network map, and index, which have outlined a big difference between countries based on economic status, have underscored the need for a sustained research mentorship program that can define future policies.}, } @article {pmid35601103, year = {2022}, author = {Que, T and Pang, X and Huang, H and Chen, P and Wei, Y and Hua, Y and Liao, H and Wu, J and Li, S and Wu, A and He, M and Ruan, X and Hu, Y}, title = {Comparative Gut Microbiome in Trachypithecus leucocephalus and Other Primates in Guangxi, China, Based on Metagenome Sequencing.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {872841}, pmid = {35601103}, issn = {2235-2988}, mesh = {Animals ; Calcium Carbonate ; China ; *Colobinae ; *Gastrointestinal Microbiome/genetics ; Metagenome ; }, abstract = {The Trachypithecus leucocephalus (white-headed langur) is a highly endangered, karst-endemic primate species, inhabiting the karst limestone forest in Guangxi, Southwest China. How white-headed langurs adapted to karst limestone and special dietary remains unclear. It is the first time to study the correlation between the gut microbiome of primates and special dietary, and environment in Guangxi. In the study, 150 fecal samples are collected from nine primates in Guangxi, China. Metagenomic sequencing is used to analyze and compare the gut microbiome composition and diversity between white-headed langurs and other primates. Our results indicate that white-headed langurs has a higher diversity of microbiome than other primates, and the key microbiome are phylum Firmicutes, class Clostridia, family Lachnospiraceae, and genera Clostridiates and Ruminococcus, which are related to the digestion and degradation of cellulose. Ten genera are significantly more abundant in white-headed langurs and François' langur than in other primates, most of which are high-temperature microbiome. Functional analysis reveals that energy synthesis-related pathways and sugar metabolism-related pathways are less abundant in white-headed langurs and François' langur than in other primates. This phenomenon could be an adaptation mechanism of leaf-eating primates to low-energy diet. The gut microbiome of white-headed langurs is related to diet and karst limestone environment. This study could serve as a reference to design conservation breeding, manage conservation units, and determine conservation priorities.}, } @article {pmid35600493, year = {2022}, author = {Zhou, J and Fu, M and Zhang, D and Xu, Y and Lian, J and Xu, H and Zhang, Y and Chen, H}, title = {Metagenomic Next-Generation Sequencing for Accurate Diagnosis of Acute HIV Infection with Aseptic Meningitis: A Case Report.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {2529-2536}, pmid = {35600493}, issn = {1178-6973}, abstract = {BACKGROUND: Although individuals infected with HIV for the first time manifest a series of acute syndromes, most patients show mild or no symptoms, which complicates the initial clinical diagnosis. Early diagnosis is important for effective prevention and management of patients. Metagenomic next-generation sequencing technology (mNGS) can rapidly detect a wide range of pathogenic microorganisms, even in atypical cases. However, to date, few studies have reported the application of mNGS to diagnose acute HIV infection with aseptic meningitis.

CASE PRESENTATION: A 38-year-old man was admitted to the Department of Infectious Diseases due to repeated fever, headache, and scattered rashes on his limbs. Routine blood analysis revealed elevated absolute lymphocytes and monocytes. Moreover, monocytes were found to be significantly increased following a lumbar puncture and cerebrospinal fluid detection. mNGS results revealed the presence of the human immunodeficiency virus (HIV-1), with HIV RNA of 910 copies/mL in his cerebrospinal fluid. The HIV antigen/antibody test was negative. According to a study by Fie Big et al, a clear diagnosis of acute HIV infection at Fiebig stage I. The patient's condition improved after treatment, and he was prescribed antiretroviral therapy (ART) after discharge.

CONCLUSION: Aseptic meningitis is easily misdiagnosed during the initial stages of acute HIV infection. mNGS can be used to identify the pathogen early, rapidly, and accurately, thereby improving the treatment of acute HIV infections.}, } @article {pmid35600388, year = {2022}, author = {Hu, Q and Li, Y and Zhang, Y and Sun, S and Wang, H and Jiang, Z and Deng, S}, title = {Case Report: First Report of T-Cell Large Granular Lymphocytic Leukemia With NPL-DHX9 Gene Fusion Successfully Treated With Cladribine: Clinical Experience and Literature Review.}, journal = {Frontiers in oncology}, volume = {12}, number = {}, pages = {824393}, pmid = {35600388}, issn = {2234-943X}, abstract = {BACKGROUND: T-cell large granular lymphocytic leukemia (T-LGLL) is a rare lymphoproliferative disorder that starts in T cells and is usually indolent. Long-term use of immunosuppressants, combined with agranulocytosis, is a double-edged sword, as both can lead to serious infections, especially in patients with combined hematologic malignancies and immune defects.

CASE PRESENTATION: A 30-year-old female patient was admitted to the hospital because of agranulocytosis for five years, with chest tightness, fatigue, and fever for two days. Pathology and metagenomic next-generation sequencing (mNGS) detected Aspergillus. Although she received cyclosporine and methylprednisolone, the patient showed drug intolerance and progression with invasive pulmonary fungal infections. After a bone marrow aspiration biopsy and other related examinations, she was diagnosed with T-LGLL and invasive pulmonary aspergillosis (IPA). T-cell immunophenotype was CD45+CD3dim+CD5-CD4-CD8+CD7+CD57p+CD25-CD30-, TCRγδ+, transducer and activator of transcripton-3 (STAT3) Y640F mutation and fusion gene NPL-DHX9 rearrangement were confirmed, which has never been reported in hematological diseases. After voriconazole regimen adjustment during treatment based on therapeutic drug concentration monitoring (TDM) and improvement in lung infection, the patient finally treated with purine nucleoside analogues (PNA) cladribine as a single agent at 0.14 mg/kg/d for 5 days. Complete response was achieved after four-cycles cladribine treatment (WBC 2.1*109/L, HGB 117 g/L, PLT 196*109/L, ANC 1.6*109/L, and ALC 0.2*109/L).

CONCLUSIONS: To our knowledge, this is the first case of T-LGLL with a rare γδ type and fusion gene NPL-DHX9 rearrangement. The patient was successfully treated with cladribine, suggesting that this regimen could be a promising therapeutic strategy for patients with aggressive T-LGLL.}, } @article {pmid35599740, year = {2022}, author = {Dong, N and Jordan, AE and Shen, X and Wu, X and Guo, X and Zhao, H and Wang, Y and Wang, D and Fang, Q}, title = {Rhino-Orbital Cerebral Mucormycosis in a Patient With Diabetic Ketoacidosis: A Case Report and Literature Review.}, journal = {Frontiers in neurology}, volume = {13}, number = {}, pages = {815902}, pmid = {35599740}, issn = {1664-2295}, abstract = {BACKGROUND: Rhino-orbital cerebral mucormycosis (ROCM) is a rare, invasive, and fatal fungal disease. Due to the lack of specific clinical manifestations and adequate auxiliary examinations, patients are easily misdiagnosed in the early stage. Early diagnosis and timely therapy are essential for successful treatment.

CASE REPORT: We report a 68-year-old man with diabetic ketoacidosis, presented with orbital apex syndrome (OAS), fever, and pansinusitis, which progressively worsened to death only 4 days after admission. It was finally confirmed as a fungal Rhizopus arrhizus infection by metagenomics cell-free DNA next-generation sequencing (mNGS) testing.

CONCLUSION: Orbital apex syndrome could be the initial presentation for mucormycosis. Thus, it is necessary to evaluate the presence of mucormycosis in patients with OAS, especially in diabetic or immunosuppressed hosts, and mNGS testing and timely antifungal therapy should be strongly recommended in highly suspected cases.}, } @article {pmid35598817, year = {2022}, author = {Li, Y and Guo, S and Zheng, Y and Yu, J and Chi, R and Xiao, C}, title = {Bioimmobilization of lead in phosphate mining wasteland by isolated strain Citrobacter farmeri CFI-01.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {307}, number = {}, pages = {119485}, doi = {10.1016/j.envpol.2022.119485}, pmid = {35598817}, issn = {1873-6424}, mesh = {Bacteria/metabolism ; Citrobacter ; Lead/metabolism ; Mining ; Phosphates/chemistry ; Soil/chemistry ; *Soil Pollutants/analysis ; }, abstract = {Industrial phosphate rock (PR) treatment has introduced lead (Pb) contamination into phosphate mining wasteland, causing serious contamination. Although bioremediation is considered an effective method and studies have investigated the bioimmobilization of Pb contamination in phosphate mining wasteland by phosphate-solubilizing bacteria (PSB), the bioimmobilization mechanism remains unclear. In this study, a strain Citrobacter farmeri CFI-01 with phosphate-solubilizing and Pb-tolerant abilities was isolated from a phosphate mining wasteland. Liquid culture experiments showed that the maximum content of soluble phosphate and the percentage amount of Pb immobilized after 14 days were 351.5 mg/L and 98.18%, respectively, with a decrease in pH. Soil experiments showed that CFI-01 had reasonable bioimmobilization ability, and the percentage amount of Pb immobilized was increased by 7.790% and 22.18% in the groups inoculated with CFI-01, respectively, compared with that of the groups not inoculated with CFI-01. Fourier transform infrared (FTIR) spectroscopy, X-ray diffraction (XRD), and scanning electron microscopy (SEM) analyses showed that the immobilization of Pb was also ascribed to changes in the functional groups (e.g., hydroxyl and carboxyl groups) and the formation of lead phosphate sediments. Finally, the results of the metagenomic analysis indicated that changes in the microbial community structure, enrichment of related functional abundances (e.g., metal metabolism, carbohydrate metabolism, and amino acid metabolism functions), and activation of functional genes (e.g., zntA, smtB, cadC, ATOX1, smtA, and ATX1) could help immobilize soil Pb contamination and explore the mechanism of bacterial bioimmobilization in Pb-contaminated soil. This study provides insights for exploring the immobilization mechanism of Pb contamination in phosphate mining wasteland using PSB, which has significance for further research.}, } @article {pmid35598686, year = {2022}, author = {Delik, A and Dinçer, S and Ülger, Y and Akkız, H and Karaoğullarından, Ü}, title = {Metagenomic identification of gut microbiota distribution on the colonic mucosal biopsy samples in patients with non-alcoholic fatty liver disease.}, journal = {Gene}, volume = {833}, number = {}, pages = {146587}, doi = {10.1016/j.gene.2022.146587}, pmid = {35598686}, issn = {1879-0038}, mesh = {Biopsy ; *Gastrointestinal Microbiome/genetics ; Humans ; *Liver Neoplasms/complications ; *Non-alcoholic Fatty Liver Disease/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Non-alcoholic fatty liver disease (NAFLD) is known to be the most common liver disease in the world, and there are currently no approved pharmacological treatments to prevent or treat this condition. In addition to being associated with an increased risk of hepatocellular carcinoma and cirrhosis, NAFLD has now become the leading cause of liver failure-associated transplantation. The 16S rRNA gene which conserved regions can serve as universal primer binding sites for PCR amplification of gene fragments, while hypervariable regions contain significant sequence diversity useful for prokaryotic identification purposes. 16S rRNA gene sequences can be use by researchers to identify prokaryotic taxonomy found in clinical samples. As a result of increasing microbiota studies with developing technological developments, the role of intestinal microbiota in the pathogenesis of NAFLD is revealed in an important way. In this study, it was aimed to determine the clinical prognostic importance of gut microbiota in the pathogenesis of NAFLD and to determine the microbial composition with intestinal mucosal biopsy samples in NAFLD patients.

MATERIAL AND METHOD: We included 20 patients diagnosed with NAFLD as a result of liver function tests, histological, ultrasonographic, biopsy evidence and 20 normal control groups created under exclusion criteria in this study. The healthy control group of the same age and gender as the patients were determined to be equal, and the age, gender, BMI, insulin resistance, AST, ALT levels of the individuals were recorded for analysis. İntestinal mucosal biopsy samples were taken from the individuals included in the study under sterile conditions. Microbial results were obtained as a result of 16S rRNA amplicon metagenomic processes. The region of approximately 1500 bp covering the V1-V9 region of the 16S rRNA gene was targeted to detect microbial diversity. The amplified regions were sequenced using next-generation sequencing. Operational Taxonomic Unit (OTU) value was obtained with bioinformatics software with the obtained sequence data. The analysis of the recorded parameters was done with the SPSS.19 statistical program.

RESULTS: In the designed study, 16 phyla, 28 class, 56 order, 128 family, 415 genera, 1041 species microorganisms were analyzed taxonomically in a total of 40 individuals. In our study, Intestinal microbial diversity is lower in NAFLD patients compared to control group individuals. In addition, gram-negative bacteria were found to be more dominant in NAFLD patients. As a phylum, Proteobacteria increased in NAFLD group, Bacteroidetes and Actinobacteria in control group, while Firmicutes had equal distribution in both groups. BMI OR = 6.37, 95 %CI (0.39-0.40) p value was 0.001 in laboratory data, whereas Proteobacteria OR = 1.754, 95% CI (0.901-3.416), p value 0.05 in microbial profile.

CONCLUSION: The 16S rRNA metagenomic study of intestinal microbiota using colonic mucosal biopsy samples in NAFLD disease was the first study in the Turkish population, and important data were obtained for other studies. In the data obtained, we think Proteobacteria, Ruminococcaceae, Escherichia coli and Bacilli are very important in both diagnostic and treatment options as a microbial profile in NAFLD.}, } @article {pmid35598329, year = {2022}, author = {Park, C and Kim, B and Park, T}, title = {DeepHisCoM: deep learning pathway analysis using hierarchical structural component models.}, journal = {Briefings in bioinformatics}, volume = {23}, number = {5}, pages = {}, doi = {10.1093/bib/bbac171}, pmid = {35598329}, issn = {1477-4054}, mesh = {Humans ; Biological Factors ; *Carcinoma, Hepatocellular/genetics ; *COVID-19 ; *Deep Learning ; Gonadotropin-Releasing Hormone ; Isoleucine ; Leucine ; *Liver Neoplasms ; Lysine ; Mitogen-Activated Protein Kinases ; Phenylalanine ; Tryptophan ; Tyrosine ; Valine ; }, abstract = {Many statistical methods for pathway analysis have been used to identify pathways associated with the disease along with biological factors such as genes and proteins. However, most pathway analysis methods neglect the complex nonlinear relationship between biological factors and pathways. In this study, we propose a Deep-learning pathway analysis using Hierarchical structured CoMponent models (DeepHisCoM) that utilize deep learning to consider a nonlinear complex contribution of biological factors to pathways by constructing a multilayered model which accounts for hierarchical biological structure. Through simulation studies, DeepHisCoM was shown to have a higher power in the nonlinear pathway effect and comparable power for the linear pathway effect when compared to the conventional pathway methods. Application to hepatocellular carcinoma (HCC) omics datasets, including metabolomic, transcriptomic and metagenomic datasets, demonstrated that DeepHisCoM successfully identified three well-known pathways that are highly associated with HCC, such as lysine degradation, valine, leucine and isoleucine biosynthesis and phenylalanine, tyrosine and tryptophan. Application to the coronavirus disease-2019 (COVID-19) single-nucleotide polymorphism (SNP) dataset also showed that DeepHisCoM identified four pathways that are highly associated with the severity of COVID-19, such as mitogen-activated protein kinase (MAPK) signaling pathway, gonadotropin-releasing hormone (GnRH) signaling pathway, hypertrophic cardiomyopathy and dilated cardiomyopathy. Codes are available at https://github.com/chanwoo-park-official/DeepHisCoM.}, } @article {pmid35598195, year = {2022}, author = {Jingushi, K and Kawashima, A and Saito, T and Kanazawa, T and Motooka, D and Kimura, T and Mita, M and Yamamoto, A and Uemura, T and Yamamichi, G and Okada, K and Tomiyama, E and Koh, Y and Matsushita, M and Kato, T and Hatano, K and Uemura, M and Tsujikawa, K and Wada, H and Nonomura, N}, title = {Circulating extracellular vesicles carrying Firmicutes reflective of the local immune status may predict clinical response to pembrolizumab in urothelial carcinoma patients.}, journal = {Cancer immunology, immunotherapy : CII}, volume = {71}, number = {12}, pages = {2999-3011}, pmid = {35598195}, issn = {1432-0851}, mesh = {Humans ; *Carcinoma, Transitional Cell/drug therapy/metabolism ; *Urinary Bladder Neoplasms/drug therapy/metabolism ; Firmicutes ; DNA, Bacterial ; RNA, Ribosomal, 16S/genetics ; *Extracellular Vesicles ; }, abstract = {Bacterial flora has clinical significance for the host. The metabolic environment created by this flora influences immunotherapy in urothelial carcinoma. However, there are no reports on the clinical significance of bacterial flora in the host bloodstream. We aimed to clarify the correlation between extracellular vesicle (EV)-derived blood microflora information and tumor immunological status in urothelial carcinoma (UC) patients. Serum samples were collected from 20 healthy donors, 50 patients with localized UC, and 31 patients with metastatic UC (mUC) who had undergone pembrolizumab treatment. Bacterial DNA in EVs was extracted from each sample. Metagenomic sequencing was performed after amplification of the V1-V2 region of the bacterial 16S rRNA gene. Using the matched tumor tissue and serum samples, we revealed that the smaller amount of peripheral EVs carrying Firmicutes DNA was significantly correlated with the higher number of infiltrating T cells within tumor tissues (CD3; p = 0.015, CD4; p = 0.039, CD8; p = 0.0084) and the higher expression of activation markers on their surface (ICOS on both CD4; p = 0.0013 and CD8 T cells; p = 0.016 and 4-1BB on CD4 T cells; p = 0.016). In terms of circulating metabolic information, L-Ser and L-Pro levels, which play important roles in T cell expansion and proliferation, were significantly higher in the Firmicutes-low group (p = 0.010). All of the patients with higher Firmicutes abundance had disease progression without any clinical response (p = 0.026) and significantly inferior prognosis for pembrolizumab therapy (p = 0.035). This is the first study on the importance of peripheral bacterial EVs in cancer patients treated with cancer immunotherapy.}, } @article {pmid35597889, year = {2022}, author = {Ghuneim, LJ and Raghuvanshi, R and Neugebauer, KA and Guzior, DV and Christian, MH and Schena, B and Feiner, JM and Castillo-Bahena, A and Mielke, J and McClelland, M and Conrad, D and Klapper, I and Zhang, T and Quinn, RA}, title = {Complex and unexpected outcomes of antibiotic therapy against a polymicrobial infection.}, journal = {The ISME journal}, volume = {16}, number = {9}, pages = {2065-2075}, pmid = {35597889}, issn = {1751-7370}, support = {R01 AI145925/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; *Coinfection/drug therapy ; *Cystic Fibrosis/drug therapy/microbiology ; Humans ; Metagenome ; Sputum/microbiology ; }, abstract = {Antibiotics are our primary approach to treating complex infections, yet we have a poor understanding of how these drugs affect microbial communities. To better understand antimicrobial effects on host-associated microbial communities we treated cultured sputum microbiomes from people with cystic fibrosis (pwCF, n = 24) with 11 different antibiotics, supported by theoretical and mathematical modeling-based predictions in a mucus-plugged bronchiole microcosm. Treatment outcomes we identified in vitro that were predicted in silico were: 1) community death, 2) community resistance, 3) pathogen killing, and 4) fermenter killing. However, two outcomes that were not predicted when antibiotics were applied were 5) community profile shifts with little change in total bacterial load (TBL), and 6) increases in TBL. The latter outcome was observed in 17.8% of samples with a TBL increase of greater than 20% and 6.8% of samples with an increase greater than 40%, demonstrating significant increases in community carrying capacity in the presence of an antibiotic. An iteration of the mathematical model showed that TBL increase was due to antibiotic-mediated release of pH-dependent inhibition of pathogens by anaerobe fermentation. These dynamics were verified in vitro when killing of fermenters resulted in a higher community carrying capacity compared to a no antibiotic control. Metagenomic sequencing of sputum samples during antibiotic therapy revealed similar dynamics in clinical samples. This study shows that the complex microbial ecology dictates the outcomes of antibiotic therapy against a polymicrobial infection.}, } @article {pmid35597403, year = {2022}, author = {Kim, DW and Jeong, HS and Kim, E and Lee, H and Choi, CH and Lee, SJ}, title = {Oral delivery of stem-cell-loaded hydrogel microcapsules restores gut inflammation and microbiota.}, journal = {Journal of controlled release : official journal of the Controlled Release Society}, volume = {347}, number = {}, pages = {508-520}, doi = {10.1016/j.jconrel.2022.05.028}, pmid = {35597403}, issn = {1873-4995}, mesh = {Animals ; Capsules ; Hydrogels/pharmacology ; Inflammation ; *Inflammatory Bowel Diseases/drug therapy ; *Mesenchymal Stem Cells ; Mice ; *Microbiota ; }, abstract = {Mesenchymal stem cells (MSCs) are an attractive candidate for the treatment of inflammatory bowel disease (IBD), but their poor delivery rate to an inflamed colon is a major factor hampering the clinical potential of stem cell therapies. Moreover, there remains a formidable hurdle to overcome with regard to survival and homing in to injured sites. Here, we develop a strategy utilizing monodisperse hydrogel microcapsules with a thin intermediate oil layer prepared by a triple-emulsion drop-based microfluidic approach as an in-situ oral delivering carrier. The oral delivery of stem-cell-loaded hydrogel microcapsules (SC-HM) enhances MSC survival and retention in the hostile stomach environment due to the intermediate oil layer and low value of the overall stiffness, facilitating programmable cell release during gastrointestinal peristalsis. SC-HM is shown to induce tissue repair, reduce the colonic macrophage infiltration responsible for the secretion of the pro-inflammatory factors, and significantly mitigate the severity of IBD in a mouse model, where MSCs released by SC-HM successfully accumulate at the colonic crypt. Moreover, a metagenomics analysis reveals that SC-HM ameliorates the dysbiosis of specific bacterial genera, including Bacteroides acidifaciens, Lactobacillus (L.) gasseri, Lactobacillus reuteri, and L. intestinalis, implying optimization of the microorganism's composition and abundance. These findings demonstrate that SC-HM is a potential IBD treatment candidate.}, } @article {pmid35597355, year = {2022}, author = {Che, R and Bai, M and Xiao, W and Zhang, S and Wang, Y and Cui, X}, title = {Nutrient levels and prokaryotes affect viral communities in plateau lakes.}, journal = {The Science of the total environment}, volume = {839}, number = {}, pages = {156033}, doi = {10.1016/j.scitotenv.2022.156033}, pmid = {35597355}, issn = {1879-1026}, mesh = {Chlorophyll A ; Humans ; *Lakes ; Metagenomics ; Nutrients ; Prokaryotic Cells ; *Viruses ; }, abstract = {Viruses are the most abundant organisms in aquatic environments. Recent advances of viral metagenomic have greatly expanded our understanding of aquatic viral communities. However, little is known about the difference of viral communities and driving factors in freshwater lake. This study seeks to understand the spatio-temporal variation, differences, and driving factors of viral communities in two plateau lakes (Dianchi and Fuxian Lakes) with significant nutritional differences. The viral communities exhibited apparent seasonal variation in Dianchi Lake, while seasonal influences on the viral communities were greater than location-based influences. Two-thirds of all detected viral taxa were shared in two lakes, but there was variation in the composition of viral communities. Correlations between prokaryotic communities, environmental factors and viral communities were analyzed. The nutrients, chlorophyll a were primarily environmental parameters affecting viral communities, and the prokaryotic community was significantly correlated with the viral community. In addition, several viruses infecting humans were identified in two lakes, with the most abundant being Herpesviridae and Poxviridae. Overall, these findings provide information on the dynamics, composition, and differences of viral and prokaryotic communities in plateau lakes with different nutrient levels. These results suggest that nutritional levels and prokaryotic communities could play an important role in shaping viral communities in freshwater lakes.}, } @article {pmid35597353, year = {2022}, author = {Liu, B and Zhang, D and Pan, X}, title = {Nodules of wild legumes as unique natural hotspots of antibiotic resistance genes.}, journal = {The Science of the total environment}, volume = {839}, number = {}, pages = {156036}, doi = {10.1016/j.scitotenv.2022.156036}, pmid = {35597353}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Drug Resistance, Microbial/genetics ; *Fabaceae ; Genes, Bacterial ; Soil ; Vegetables ; }, abstract = {Root nodules (RN) of legumes have distinct microenvironment from their symbiotic roots and surrounding soils. The rhizobia can withstand the host-produced phytoalexins and antimicrobial compounds. We thus hypothesize that the wild legume RN may develop unique natural resistome and be antibiotic resistance gene (ARG) hotspots. In this study, in comparison with rhizosphere soil (RS) and bulk soil (BS), we characterized the feature of antibiotic resistance in the RN of two wild legumes, Medicago polymorpha and Astragalus sinicus, by metagenomics. It was shown that the total relative abundance of ARGs followed the order of RN > RS > BS for both legumes. ARGs encoding antibiotic efflux pump predominated in all samples with increased proportion from BS to RN samples for both legumes. Totally 275 ARG subtypes were detected, and diversity of ARGs in RN was significantly lower than in BS samples for both legumes. 32 and 25 unique ARGs subtypes were detected in RN of both legumes. Bacterial community played a key role in shaping nodule-associated resistome because both ARG profiles and bacterial community differed greatly among BS, RS and RN. Rhizobia potentially hosted 10 and 15 ARGs subtypes for both legumes. The number and proportion of plasmid- and ARG-carrying contigs (ACCs) were higher in RN than in BS. Host tracking analysis of plasmid-ACCs suggests that proportion of rhizobial bacteria identified as their hosts decreased from BS to RN samples. No plasmid-ACCs with multiple ARGs were observed in BS samples, whereas they were detected in RN samples of both legumes. Our study showed that even wild legume nodules are unique natural ARG hotspots and enough attention should be paid to the dissemination risk of ARGs posed by globally produced legume crops.}, } @article {pmid35597219, year = {2022}, author = {Ma, X and Johnson, KB and Gu, B and Zhang, H and Li, G and Huang, X and Xia, X}, title = {The in-situ release of algal bloom populations and the role of prokaryotic communities in their establishment and growth.}, journal = {Water research}, volume = {219}, number = {}, pages = {118565}, doi = {10.1016/j.watres.2022.118565}, pmid = {35597219}, issn = {1879-2448}, mesh = {Bacteria/genetics ; *Diatoms ; *Dinoflagellida ; Estuaries ; Harmful Algal Bloom ; Rivers ; }, abstract = {Harmful algal blooms (HABs) may quickly travel and inoculate new water bodies via currents and runoff in estuaries. The role of in-situ prokaryotic communities in the re-establishment and growth of inoculated algal blooms remains unknown. A novel on-board incubation experiment was employed to simulate the sudden surge of algal blooms to new estuarine waters and reveal possible outcomes. A dinoflagellate (Amphidinium carterae) and a diatom species (Thalassiosira weissflogii) which had bloomed in the Pearl River Estuary (PRE) area were cultured to bloom densities and reintroduced back into PRE natural seawaters. The diatom showed better adaptation ability to the new environment and increased significantly after the incubation. Simultaneously, particle-attached (PA) prokaryotic community structure was strongly influenced by adding of the diatom, with some opportunistic prokaryotes significantly enhanced in the diatom treatment. Whereas the dinoflagellate population did not increase following incubation, and their PA prokaryotic community showed no significant differences relative to the control. Metagenomic analyzes revealed that labile carbohydrates and organic nitrogen produced by the diatom contributed to the surge of certain PA prokaryotes. Genomic properties of a bacteria strain, which is affiliated with genus GMD16E07 (Planctomycetaceae) and comprised up to 50% of PA prokaryotes in the diatom treatment, was described here for the first time. Notably, the association of Planctomycetaceae and T. weissflogii likely represents symbiotic mutualism, with the diatom providing organic matter for Planctomycetaceae and the bacteria supplying vitamins and detoxifying nitriles and hydrogen peroxides in exchange. Therefore, the close association between Planctomycetaceae and T. weissflogii promoted the growth of both populations, and eventually facilitated the diatom bloom establishment.}, } @article {pmid35597218, year = {2022}, author = {Wang, C and Wang, Y and Wang, Y and Liu, L and Wang, D and Ju, F and Xia, Y and Zhang, T}, title = {Impacts of food waste to sludge ratios on microbial dynamics and functional traits in thermophilic digesters.}, journal = {Water research}, volume = {219}, number = {}, pages = {118590}, doi = {10.1016/j.watres.2022.118590}, pmid = {35597218}, issn = {1879-2448}, mesh = {Anaerobiosis ; Bioreactors ; *Euryarchaeota ; Food ; Methane ; *Refuse Disposal ; Sewage ; }, abstract = {A self-stabilizing microbial community lays the foundation of the efficient biochemical reactions of the anaerobic digestion (AD) process. Despite extensive profiling of microbial community dynamics under varying operating parameters, the effects of food waste (FW) to feeding sewage sludge (FSS) ratios on the microbial assembly, functional traits, and syntrophic interspecies interactions in thermophilic microbial consortia remain poorly understood. Here, we investigated the long-term impacts of the FW: FSS ratio on the thermophilic AD microbiome using genome-centric metagenomics. Both the short reads (SRs) assembly, and the iterative hybrid assembly (IHA) of SRs and nanopore long reads (LRs) were used to reconstruct metagenome-assembled genomes (MAGs) and four microbial clusters were identified, demonstrating different microbial dynamics patterns in response to varying FW:FSS ratios. Cluster C1-C3 were comprised of full functional members with genetic potentials in fulfilling empirical AD biochemical reactions, wherein, syntrophic decarboxylating acetogens could interact with methanogens, and some microbes could be energized by the electron bifurcation mechanism to drive thermodynamics unfavorable reactions. We found the co-existence of both acetogenic and hydrogenotrophic methanogens in the AD microbiome, and they altered their trophic groups to scavenge the methanogenic substrates in ensuring the methane generation in digesters with different FW:FSS ratios. Another interesting observation was that two phylogenetically close Thermotogota species showed a possible strong competition on carbon source inferred by the nearly complete genetic overlap of their relevant pathways.}, } @article {pmid35596862, year = {2022}, author = {Parida, PK and Behera, BK and Dehury, B and Rout, AK and Sarkar, DJ and Rai, A and Das, BK and Mohapatra, T}, title = {Community structure and function of microbiomes in polluted stretches of river Yamuna in New Delhi, India, using shotgun metagenomics.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {47}, pages = {71311-71325}, pmid = {35596862}, issn = {1614-7499}, mesh = {ATP-Binding Cassette Transporters ; *Atrazine ; Benzene ; Benzoates ; Carbon ; Catalase ; Environmental Biomarkers ; Environmental Monitoring/methods ; Fatty Acids ; Metagenomics/methods ; Methane ; *Microbiota ; Mixed Function Oxygenases ; Nitrogen ; Sulfates ; Sulfur ; Water ; Xenobiotics ; }, abstract = {The large population residing in the northern region of India surrounding Delhi mostly depends on water of River Yamuna, a tributary of mighty Ganga for agriculture, drinking and various religious activities. However, continuous anthropogenic activities mostly due to pollution mediated by rapid urbanization and industrialization have profoundly affected river microflora and their function thus its health. In this study, potential of whole-genome metagenomics was exploited to unravel the novel consortia of microbiome and their functional potential in the polluted sediments of the river at Delhi. Analysis of high-quality metagenome data from Illumina NextSeq500 revealed substantial differences in composition of microbiota at different sites dominated by Proteobacteria, Bacteroidetes, Firmicutes, Actinobacteria and Chloroflexi phyla. The presence of highly dominant anaerobic bacteria like Dechloromonas aromatica (benzene reducing and denitrifying), Rhodopseudomonas palustris (organic matter reducing), Syntrophus aciditrophicus (fatty acid reducing) and Syntrophobacter fumaroxidans (sulphate reducing) in the polluted river Yamuna signifies the impact of unchecked pollution in declining health of the river ecosystem. A decline in abundance of phages was also noticed along the downstream river Yamuna. Mining of mycobiome reads uncovered plethora of fungal communities (i.e. Nakaseomyces, Aspergillus, Schizosaccharomyces and Lodderomyces) in the polluted stretches due to the availability of higher organic carbon and total nitrogen (%) could be decoded as promising bioindicators of river trophic status. Pathway analysis through KEGG revealed higher abundance of genes involved in energy metabolism (nitrogen and sulphur), methane metabolism, degradation of xenobiotics (Nitrotoluene, Benzoate and Atrazine), two-component system (atoB, cusA and silA) and membrane transport (ABC transporters). Catalase-peroxidase and 4-hydroxybenzoate 3-monooxygenase were the most enriched pollution degrading enzymes in the polluted study sites of river Yamuna. Overall, our results provide crucial insights into microbial dynamics and their function in response to high pollution and could be insightful to the ongoing remediation strategies to clean river Yamuna.}, } @article {pmid35596140, year = {2022}, author = {Tang, R and Liu, F and Lan, Y and Wang, J and Wang, L and Li, J and Liu, X and Fan, Z and Guo, T and Yue, B}, title = {Transcriptomics and metagenomics of common cutworm (Spodoptera litura) and fall armyworm (Spodoptera frugiperda) demonstrate differences in detoxification and development.}, journal = {BMC genomics}, volume = {23}, number = {1}, pages = {388}, pmid = {35596140}, issn = {1471-2164}, mesh = {Animals ; Humans ; Larva/genetics ; *Metagenomics ; Pupa ; RNA-Seq ; Spodoptera/genetics ; *Transcriptome ; }, abstract = {BACKGROUND: Spodoptera litura is an important polyphagous pest that causes significant damage to the agricultural sector. We performed RNA-seq of 15 S. litura individuals from larval (fifth and sixth instar larvae), chrysalis, and adult developmental stages. We also compared the S. litura transcriptome data with Spodoptera frugiperda across the same developmental stages, which was sequenced in our previous study.

RESULTS: A total of 101,885 differentially expressed transcripts (DETs) were identified in S. litura. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that S. litura may undergo active xenobiotic and detoxifying metabolism during its larval and adult stages, which may explain difficulties with current population control measures. We also found that DETs of single-copy orthologous genes between S. litura and S. frugiperda were involved in basic metabolism and development. However, energy and metabolic processes genes had a higher expression in S. litura, whereas nervous and olfactory function genes had a higher expression in S. frugiperda. Metagenomics analysis in larval S. litura and S. frugiperda revealed that microbiota participate in the detoxification and metabolism processes, but the relative abundance of detoxification-related microbiota was more abundant in S. frugiperda. Transcriptome results also confirmed the detoxification-related pathway of S. frugiperda was more abundant than in S. litura.

CONCLUSIONS: Significant changes at transcriptional level were identified during the different development stages of S. litura. Importantly, we also identified detoxification associated genes and gut microbiota between S. litura and S. frugiperda at different developmental stages, which will be valuable in revealing possible mechanisms of detoxification and development in these two lepidopterans.}, } @article {pmid35595870, year = {2022}, author = {Shi, H and Nelson, JW and Phillips, S and Petrosino, JF and Bryan, RM and Durgan, DJ}, title = {Alterations of the gut microbial community structure and function with aging in the spontaneously hypertensive stroke prone rat.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {8534}, pmid = {35595870}, issn = {2045-2322}, support = {R01HL134838/HL/NHLBI NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; R01NS102594/NS/NINDS NIH HHS/United States ; DK56338/NH/NIH HHS/United States ; R01 HL134838/HL/NHLBI NIH HHS/United States ; R01 NS102594/NS/NINDS NIH HHS/United States ; 16SDG29970000/AHA/American Heart Association-American Stroke Association/United States ; T32 GM008231/GM/NIGMS NIH HHS/United States ; T32 GM008231/NH/NIH HHS/United States ; }, mesh = {Aging ; Animals ; Blood Pressure/physiology ; Dysbiosis ; *Gastrointestinal Microbiome ; *Hypertension ; Rats ; Rats, Inbred SHR ; Rats, Inbred WKY ; *Stroke ; Tryptophan ; }, abstract = {Gut dysbiosis, a pathological imbalance of bacteria, has been shown to contribute to the development of hypertension (HT), systemic- and neuro-inflammation, and blood-brain barrier (BBB) disruption in spontaneously hypertensive stroke prone rats (SHRSP). However, to date individual species that contribute to HT in the SHRSP model have not been identified. One potential reason, is that nearly all studies of the SHRSP gut microbiota have analyzed samples from rats with established HT. The goal of this study was to examine the SHRSP gut microbiota before, during, and after the onset of hypertension, and in normotensive WKY control rats over the same age range. We hypothesized that we could identify key microbes involved in the development of HT by comparing WKY and SHRSP microbiota during the pre-hypertensive state and longitudinally. Systolic blood pressure (SBP) was measured by tail-cuff plethysmography and fecal microbiota analyzed by16S rRNA gene sequencing. SHRSP showed significant elevations in SBP, as compared to WKY, beginning at 8 weeks of age (p < 0.05 at each time point). Bacterial community structure was significantly different between WKY and SHRSP as early as 4 weeks of age, and remained different throughout the study (p = 0.001-0.01). At the phylum level we observed significantly reduced Firmicutes and Deferribacterota, and elevated Bacteroidota, Verrucomicrobiota, and Proteobacteria, in pre-hypertensive SHRSP, as compared to WKY. At the genus level we identified 18 bacteria whose relative abundance was significantly different in SHRSP versus WKY at the pre-hypertensive ages of 4 or 6 weeks. In an attempt to further refine bacterial candidates that might contribute to the SHRSP phenotype, we compared the functional capacity of WKY versus SHRSP microbial communities. We identified significant differences in amino acid metabolism. Using untargeted metabolomics we found significant reductions in metabolites of the tryptophan-kynurenine pathway and increased indole metabolites in SHRSP versus WKY plasma. Overall, we provide further evidence that gut dysbiosis contributes to hypertension in the SHRSP model, and suggest for the first time the potential involvement of tryptophan metabolizing microbes.}, } @article {pmid35595857, year = {2022}, author = {Gao, S and Khan, MI and Kalsoom, F and Liu, Z and Chen, Y and Chen, Z}, title = {Role of gene regulation and inter species interaction as a key factor in gut microbiota adaptation.}, journal = {Archives of microbiology}, volume = {204}, number = {6}, pages = {342}, pmid = {35595857}, issn = {1432-072X}, mesh = {Acclimatization ; Adaptation, Physiological/genetics ; Animals ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Metagenomics ; }, abstract = {Gut microbiota is a class of microbial flora present in various eukaryotic multicellular complex animals such as human beings. Their community's growth and survival are greatly influenced by various factors such as host-pathogen, pathogen-environment and genetic regulation. Modern technologies like metagenomics have particularly extended our capacity to uncover the microbial treasures in challenging conditions like communities surviving at high altitude. Molecular characterizations by newly developed sequencing tools have shown that this complex interaction greatly influences microbial adaptation to the environment. Literature shows that gut microbiota alters the genetic expression and switches to an alternative pathway under the influence of unfavorable conditions. The remarkable adaptability of microbial genetic regulatory networks enables them to survive and expand in tough and energy-limited conditions. Variable prevalence of species in various regions has strengthened this initial evidence. In view of the interconnection of the world in the form of a global village, this phenomenon must be explored more clearly. In this regard, recently there has been significant addition of knowledge to the field of microbial adaptation. This review summarizes and shed some light on mechanisms of microbial adaptation via gene regulation and species interaction in gut microbiota.}, } @article {pmid35595837, year = {2022}, author = {Quaranta, G and Mandrioli, J and Bibbò, S and Guarnaccia, A and Fancello, G and Simonini, C and Amedei, A and Niccolai, E and Nannini, G and Cammarota, G and Sanguinetti, M and Masucci, L}, title = {Rummeliibacillus suwonensis: First Time Isolation from Human Feces by Culturomics.}, journal = {Current microbiology}, volume = {79}, number = {7}, pages = {197}, pmid = {35595837}, issn = {1432-0991}, support = {RF-2016-02361616.//italian ministry of health/ ; }, mesh = {Aged ; Amyotrophic Lateral Sclerosis ; Feces/microbiology ; Humans ; Male ; *Planococcaceae/isolation & purification ; RNA, Ribosomal, 16S ; }, abstract = {Gut microbiota is a complex ecosystem composed by trillions of microorganisms that are crucial for human health or disease status. Currently, there are two methodological options to explore its complexity: metagenomics and culturomics. Culturomics is an approach that uses multiple culture conditions (days of incubation, enrichment factors and growth temperature) and MALDI-TOF mass spectrometry for the identification of bacterial species and sequencing when this method fails. In this paper, we describe how Colturomic's protocol has allowed the first isolation in human sample of Rummeliibacillus suwonensis, a Gram positive, facultative anaerobe bacterium. The bacterium was isolated from feces of a 69 years old male with amyotrophic lateral sclerosis (ALS) recruited for a clinical trial assessing safety and efficacy of fecal microbiota transplantation in ALS. The first isolation of the microorganism dates back to 2013 from the soil of a South Korean mountain area. In this report, morphological description, biochemical characterization and antibiotic susceptibility tests were performed to outline the bacterial properties.}, } @article {pmid35595739, year = {2022}, author = {Price, JT and Vwalika, B and France, M and Ravel, J and Ma, B and Mwape, H and Rittenhouse, KJ and De Paris, K and Hobbs, M and Nelson, JA and Kasaro, MP and Stringer, EM and Stringer, JSA}, title = {HIV-associated vaginal microbiome and inflammation predict spontaneous preterm birth in Zambia.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {8573}, pmid = {35595739}, issn = {2045-2322}, support = {K01 TW010857/TW/FIC NIH HHS/United States ; P30 AI50410; T32 HD075731; K01 TW010857; D43 TW009340; R21DK123674; R01HL148672/NH/NIH HHS/United States ; OPP1033514/GATES/Bill & Melinda Gates Foundation/United States ; 6361/Gerber/The Gerber Foundation/United States ; OPP1189217/GATES/Bill & Melinda Gates Foundation/United States ; }, mesh = {Bacteria, Anaerobic ; Female ; Gardnerella ; *HIV Infections/complications ; Humans ; Infant, Newborn ; Inflammation/complications ; *Microbiota/genetics ; Pregnancy ; *Premature Birth ; Vagina ; Zambia/epidemiology ; }, abstract = {A Lactobacillus-deficient, anaerobe-rich vaginal microbiome has been associated with local inflammation and spontaneous preterm birth (sPTB), but few studies have assessed this association in the setting of HIV. We performed metagenomic sequencing and inflammatory marker assays on vaginal swabs collected in pregnancy. We grouped samples into 7 metagenomic clusters (mgClust) using the non-redundant VIRGO catalogue, and derived inflammatory scores by factor analysis. Of 221 participants, median Shannon diversity index (SDI) was highest in HIV+ with detectable viral load (1.31, IQR: 0.85-1.66; p < 0.001) and HIV+ with undetectable virus (1.17, IQR: 0.51-1.66; p = 0.01) compared to HIV- (0.74, IQR: 0.35-1.26). Inflammatory scores positively correlated with SDI (+ 0.66, 95%CI 0.28, 1.03; p = 0.001), highest among anaerobe-rich mgClust2-mgClust6. HIV was associated with predominance of anaerobe-rich mgClust5 (17% vs. 6%; p = 0.02) and mgClust6 (27% vs. 11%; p = 0.002). Relative abundance of a novel Gardnerella metagenomic subspecies > 50% predicted sPTB (RR 2.6; 95%CI: 1.1, 6.4) and was higher in HIV+ (23% vs. 10%; p = 0.001). A novel Gardnerella metagenomic subspecies more abundant in women with HIV predicted sPTB. The risk of sPTB among women with HIV may be mediated by the vaginal microbiome and inflammation, suggesting potential targets for prevention.}, } @article {pmid35595225, year = {2022}, author = {Dou, Q and Zhang, L and Lan, S and Hao, S and Guo, W and Sun, Q and Wang, Y and Peng, Y and Wang, X and Yang, J}, title = {Metagenomics illuminated the mechanism of enhanced nitrogen removal and vivianite recovery induced by zero-valent iron in partial-denitrification/anammox process.}, journal = {Bioresource technology}, volume = {356}, number = {}, pages = {127317}, doi = {10.1016/j.biortech.2022.127317}, pmid = {35595225}, issn = {1873-2976}, mesh = {Anaerobic Ammonia Oxidation ; Bioreactors ; *Denitrification ; Ferrous Compounds ; Iron ; Metagenomics ; Nitrates ; *Nitrogen ; Oxidation-Reduction ; Phosphates ; Sewage ; }, abstract = {In this study, a novel strategy of zero-valent iron (ZVI) combined with acetic acid was proposed to optimize partial-denitrification/anammox (PD/A) process, and enhanced nitrogen removal mechanism was elucidated through metagenomics. Results showed that the optimal nitrogen and phosphorus removal were as high as 99.50% and 98.37%, respectively, with vivianite being precipitated as the main byproduct. The occurrence of Feammox was a crucial link for enhanced ammonia removal and vivianite recovery. Metagenomic analysis further certified that long-term acclimation of optimization strategy triggered DNRA-based nitrate reducing genes (narY/Z and nrfA) assigned to Candidatus Brocadia, which allow direct uptake of nitrate by the anammox. Additionally, ZVI might act as a new electron donor to decrease organics dependence of PD by reducing the abundance of genes for electron production involved in carbon metabolism. However, FA addition enhanced the relative abundances of genes involved in anammox including nitrogen reduction and oxidation, thereby accelerating nitrogen removal.}, } @article {pmid35595155, year = {2022}, author = {Chen, L and Gao, X and Xue, W and Yuan, S and Liu, M and Sun, Z}, title = {Rapid metagenomic identification of two major swine pathogens with real-time nanopore sequencing.}, journal = {Journal of virological methods}, volume = {306}, number = {}, pages = {114545}, doi = {10.1016/j.jviromet.2022.114545}, pmid = {35595155}, issn = {1879-0984}, mesh = {Animals ; High-Throughput Nucleotide Sequencing/methods ; Metagenomics/methods ; *Nanopore Sequencing ; *Porcine epidemic diarrhea virus/genetics ; *Porcine respiratory and reproductive syndrome virus ; Sensitivity and Specificity ; Swine ; *Viruses ; }, abstract = {Metagenomic next-generation sequencing (mNGS) is a rapid deep-sequencing diagnostic tool for the unbiased identification of pathogens. In this study, we established a nanopore-sequencing-based mNGS protocol to detect two major viral pathogens of swine, Porcine reproductive and respiratory syndrome virus (PRRSV) and Porcine epidemic diarrhea virus (PEDV). Samples were spiked with the serially diluted viruses as standard references to define the specific protocols. The utility of the method was evaluated with key parameters. The limits of detection for PRRSV and PEDV were 2.3 × 10[2] and 9.0 × 10[4] copies per reaction, respectively, and good correlations between PCR quantification cycle value and the mapped read count (log value) were observed. Only the nanopore reads could be assembled de novo into nearly full-length of the PRRSV genome, with 99.9% pairwise identity, and 90.0% genome coverage for PEDV. The established protocol was validated in PRRSV-positive clinical samples. The results for PRRSV-positive tissue and serum samples tested with mNGS protocol were 100% concordant with quantitative PCR results. The protocol also recognized infections of single or multiple viruses in a single sample. In conclusion, we have established a nanopore-sequencing-based mNGS protocol that efficiently identifies and characterizes viral pathogen(s) in a variety of clinical sample types.}, } @article {pmid35594748, year = {2022}, author = {Valk, LC and Peces, M and Singleton, CM and Laursen, MD and Andersen, MH and Mielczarek, AT and Nielsen, PH}, title = {Exploring the microbial influence on seasonal nitrous oxide concentration in a full-scale wastewater treatment plant using metagenome assembled genomes.}, journal = {Water research}, volume = {219}, number = {}, pages = {118563}, doi = {10.1016/j.watres.2022.118563}, pmid = {35594748}, issn = {1879-2448}, mesh = {Denitrification ; *Greenhouse Gases/analysis ; Metagenome ; Nitrogen/analysis ; Nitrous Oxide/analysis ; RNA, Ribosomal, 16S/genetics ; Seasons ; *Water Purification ; }, abstract = {Nitrous oxide is a highly potent greenhouse gas and one of the main contributors to the greenhouse gas footprint of wastewater treatment plants (WWTP). Although nitrous oxide can be produced by abiotic reactions in these systems, biological N2O production resulting from the imbalance of nitrous oxide production and reduction by microbial populations is the dominant cause. The microbial populations responsible for the imbalance have not been clearly identified, yet they are likely responsible for strong seasonal nitrous oxide patterns. Here, we examined the seasonal nitrous oxide concentration pattern in Avedøre WWTP alongside abiotic parameters, the microbial community composition based on 16S rRNA gene sequencing and already available metagenome-assembled genomes (MAGs). We found that the WWTP parameters could not explain the observed pattern. While no distinct community changes between periods of high and low dissolved nitrous oxide concentrations were determined, we found 26 and 28 species with positive and negative correlations to the seasonal N2O concentrations, respectively. MAGs were identified for 124 species (approximately 31% mean relative abundance of the community), and analysis of their genomic nitrogen transformation potential could explain this correlation for four of the negatively correlated species. Other abundant species were also analysed for their nitrogen transformation potential. Interestingly, only one full-denitrifier (Candidatus Dechloromonas phosphorivorans) was identified. 59 species had a nosZ gene predicted, with the majority identified as a clade II nosZ gene, mainly from the phylum Bacteroidota. A correlation of MAG-derived functional guilds with the N2O concentration pattern showed that there was a small but significant negative correlation with nitrite oxidizing bacteria and species with a nosZ gene (N2O reducers (DEN)). More research is required, specifically long-term activity measurements in relation to the N2O concentration to increase the resolution of these findings.}, } @article {pmid35594632, year = {2022}, author = {Liu, Q and Zhang, X and Li, Z and Chen, Y and Yin, Y and Lu, Z and Ouyang, M and Chen, L}, title = {Maternal diets have effects on intestinal mucosal flora and susceptibility to colitis of offspring mice during early life.}, journal = {Nutrition (Burbank, Los Angeles County, Calif.)}, volume = {99-100}, number = {}, pages = {111672}, doi = {10.1016/j.nut.2022.111672}, pmid = {35594632}, issn = {1873-1244}, mesh = {Animals ; Female ; Humans ; Mice ; Rats ; *Colitis/etiology ; Diet/adverse effects ; Diet, High-Fat ; *Gastrointestinal Microbiome/physiology ; *Inflammatory Bowel Diseases/etiology ; Maternal Nutritional Physiological Phenomena ; Mice, Inbred C57BL ; }, abstract = {OBJECTIVES: Intestinal flora is considered closely related to the occurrence of inflammatory bowel disease (IBD). This study aimed to discover whether diverse diet conditions during early life lead to different intestinal flora structure and impact different susceptibility to IBD.

METHODS: We performed a randomized, controlled trial to investigate the relationship between maternal diet, intestinal flora, and susceptibility of IBD in offspring mice. We treated the maternal mice with different dietary conditions (maternal high fat, high protein, or normal diet, and offspring continued maternal diets or changed to normal diet), and then extracted bacterial meta-genomic DNA from the intestinal mucosa of the offspring during the early life and adult stages. We amplified and sequenced the conserved gene v3-v4 of the bacterial 16 S ribosomal RNA. After dextran sulphate sodium intervention, we evaluated the susceptibility to intestinal inflammation with hematoxylin and eosin stains and disease activity index scores.

RESULTS: The number of species and alpha diversity of weaning mice (3 wk old) fed a maternal high-protein diet were significantly lower than those of the control diet group (P < 0.05). Among adult (8 wk old) offspring rats, the alpha diversity of mice that continued on a high-protein diet remained significantly decreased (P < 0.05). In addition, 12 kinds of weak bacteria were found in weaning mice fed a maternal high-protein diet compared with the control group. Offspring that continued in the maternal high-protein group had increased disease activity index and pathologic scores after weaning.

CONCLUSIONS: In general, our study shows that a maternal high-protein diet during early life can negatively regulate the intestinal flora diversity of offspring mice. A high-protein diet during early life led to higher susceptibility of IBD in offspring rats.}, } @article {pmid35593171, year = {2022}, author = {Galanis, A and Vardakas, P and Reczko, M and Harokopos, V and Hatzis, P and Skoulakis, EMC and Pavlopoulos, GA and Patalano, S}, title = {Bee foraging preferences, microbiota and pathogens revealed by direct shotgun metagenomics of honey.}, journal = {Molecular ecology resources}, volume = {22}, number = {7}, pages = {2506-2523}, doi = {10.1111/1755-0998.13626}, pmid = {35593171}, issn = {1755-0998}, support = {798082//H2020 Marie Skłodowska-Curie Actions/ ; MIS 5002562//European Regional Development Fund/ ; //Hellenic Ministry of Rural Development and Food/ ; //Fondation Santé/ ; }, mesh = {Animals ; Bacteria/genetics ; Bees/genetics ; DNA ; *Gastrointestinal Microbiome ; *Honey ; Humans ; Metagenomics ; *Microbiota ; }, abstract = {Honeybees (Apis mellifera) continue to succumb to human and environmental pressures despite their crucial role in providing essential ecosystem services. Owing to their foraging and honey production activities, honeybees form complex relationships with species across all domains, such as plants, viruses, bacteria and other hive pests, making honey a valuable biomonitoring tool for assessing their ecological niche. Thus, the application of honey shotgun metagenomics (SM) has paved the way for a detailed description of the species honeybees interact with. Nevertheless, SM bioinformatics tools and DNA extraction methods rely on resources not necessarily optimized for honey. In this study, we compared five widely used taxonomic classifiers using simulated species communities commonly found in honey. We found that Kraken 2 with a threshold of 0.5 performs best in assessing species distribution. We also optimized a simple NaOH-based honey DNA extraction methodology (Direct-SM), which profiled species seasonal variability similarly to an established column-based DNA extraction approach (SM). Both approaches produce results consistent with melissopalinology analysis describing the botanical landscape surrounding the apiary. Interestingly, we detected a strong stability of the bacteria constituting the core and noncore gut microbiome across seasons, pointing to the potential utility of honey for noninvasive assessment of bee microbiota. Finally, the Direct-SM approach to detect Varroa correlates well with the biomonitoring of mite infestation observed in hives. These observations suggest that Direct-SM methodology has the potential to comprehensively describe honeybee ecological niches and can be tested as a building block for large-scale studies to assess bee health in the field.}, } @article {pmid35592677, year = {2022}, author = {Wang, S and Chen, H and Yang, H and Zhou, K and Bai, F and Wu, X and Xu, H}, title = {Gut Microbiome Was Highly Related to the Regulation of Metabolism in Lung Adenocarcinoma Patients.}, journal = {Frontiers in oncology}, volume = {12}, number = {}, pages = {790467}, pmid = {35592677}, issn = {2234-943X}, abstract = {BACKGROUND: Lung adenocarcinoma (LUAD) is one of the most predominant subtypes of lung cancer. The gut microbiome plays a vital role in the pathophysiological processes of various diseases, including cancers.

METHODS: In the study, 100 individuals were enrolled. In total 75 stool and blood samples were analyzed with 16s-rRNA gene sequencing and metabolomics (30 from healthy individuals (H); 45 from LUAD patients). In addition, 25 stool samples were analyzed with metagenomics (10 from H; 15 from LUAD). The linear discriminant analysis (LDA) effect size (LefSe) and logistic regression analysis were applied to identify biomarkers' taxa and develop a diagnostic model. The diagnostic power of the model was estimated with the receiver operating characteristic curve (ROC) by comparing the area under the ROC (AUC). The correlation between biomarker's taxa and metabolites was calculated using the Spearman analysis.

RESULTS: The α and β diversity demonstrated the composition and structure of the gut microbiome in LUAD patients were different from those in healthy people. The top three abundance of genera were Bacteroides (25.06%), Faecalibacterium (11.00%), and Prevotella (5.94%). The LefSe and logistic regression analysis identified three biomarker taxa (Bacteroides, Pseudomonas, and Ruminococcus gnavus group) and constructed a diagnostic model. The AUCs of the diagnostic model in 16s-rRNA gene sequencing and metagenomics were 0.852 and 0.841, respectively. A total of 102 plasma metabolites were highly related to those three biomarkers' taxa. Seven metabolic pathways were enriched by 102 plasma metabolites, including the Pentose phosphate pathway, Glutathione metabolism.

CONCLUSIONS: In LUAD patients, the gut microbiome profile has significantly changed. We used three biomarkers taxa to develop a diagnostic model, which was accurate and suitable for the diagnosis of LUAD. Gut microbes, especially those three biomarkers' taxa, may participate in regulating metabolism-related pathways in LUAD patients, such as the pentose phosphate pathway and glutathione metabolism.}, } @article {pmid35591999, year = {2022}, author = {Guizzo, MG and Tirloni, L and Gonzalez, SA and Farber, MD and Braz, G and Parizi, LF and Dedavid E Silva, LA and da Silva Vaz, I and Oliveira, PL}, title = {Coxiella Endosymbiont of Rhipicephalus microplus Modulates Tick Physiology With a Major Impact in Blood Feeding Capacity.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {868575}, pmid = {35591999}, issn = {1664-302X}, abstract = {In the past decade, metagenomics studies exploring tick microbiota have revealed widespread interactions between bacteria and arthropods, including symbiotic interactions. Functional studies showed that obligate endosymbionts contribute to tick biology, affecting reproductive fitness and molting. Understanding the molecular basis of the interaction between ticks and their mutualist endosymbionts may help to develop control methods based on microbiome manipulation. Previously, we showed that Rhipicephalus microplus larvae with reduced levels of Coxiella endosymbiont of R. microplus (CERM) were arrested at the metanymph life stage (partially engorged nymph) and did not molt into adults. In this study, we performed a transcriptomic differential analysis of the R. microplus metanymph in the presence and absence of its mutualist endosymbiont. The lack of CERM resulted in an altered expression profile of transcripts from several functional categories. Gene products such as DA-P36, protease inhibitors, metalloproteases, and evasins, which are involved in blood feeding capacity, were underexpressed in CERM-free metanymphs. Disregulation in genes related to extracellular matrix remodeling was also observed in the absence of the symbiont. Taken together, the observed alterations in gene expression may explain the blockage of development at the metanymph stage and reveal a novel physiological aspect of the symbiont-tick-vertebrate host interaction.}, } @article {pmid35591982, year = {2022}, author = {Noell, SE and Baptista, MS and Smith, E and McDonald, IR and Lee, CK and Stott, MB and Amend, JP and Cary, SC}, title = {Unique Geothermal Chemistry Shapes Microbial Communities on Mt. Erebus, Antarctica.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {836943}, pmid = {35591982}, issn = {1664-302X}, abstract = {Mt. Erebus, Antarctica, is the world's southernmost active volcano and is unique in its isolation from other major active volcanic systems and its distinctive geothermal systems. Using 16S rRNA gene amplicon sequencing and physicochemical analyses, we compared samples collected at two contrasting high-temperature (50°C-65°C) sites on Mt. Erebus: Tramway Ridge, a weather-protected high biomass site, and Western Crater, an extremely exposed low biomass site. Samples were collected along three thermal gradients, one from Western Crater and two within Tramway Ridge, which allowed an examination of the heterogeneity present at Tramway Ridge. We found distinct soil compositions between the two sites, and to a lesser extent within Tramway Ridge, correlated with disparate microbial communities. Notably, pH, not temperature, showed the strongest correlation with these differences. The abundance profiles of several microbial groups were different between the two sites; class Nitrososphaeria amplicon sequence variants (ASVs) dominated the community profiles at Tramway Ridge, whereas Acidobacteriotal ASVs were only found at Western Crater. A co-occurrence network, paired with physicochemical analyses, allowed for finer scale analysis of parameters correlated with differential abundance profiles, with various parameters (total carbon, total nitrogen, soil moisture, soil conductivity, sulfur, phosphorous, and iron) showing significant correlations. ASVs assigned to Chloroflexi classes Ktedonobacteria and Chloroflexia were detected at both sites. Based on the known metabolic capabilities of previously studied members of these groups, we predict that chemolithotrophy is a common strategy in this system. These analyses highlight the importance of conducting broader-scale metagenomics and cultivation efforts at Mt. Erebus to better understand this unique environment.}, } @article {pmid35591626, year = {2022}, author = {Borowik, A and Wyszkowska, J and Kucharski, J}, title = {Bacteria and Soil Enzymes Supporting the Valorization of Forested Soils.}, journal = {Materials (Basel, Switzerland)}, volume = {15}, number = {9}, pages = {}, pmid = {35591626}, issn = {1996-1944}, support = {30.610.006-110//University of Warmia and Mazury in Olsztyn, Faculty of Agriculture and Forestry, Department of Soil Science and Microbiology/ ; 010/RID/2018/19//Minister of Education and Science in the range of the program entitled "Regional Ini-tiative of Excellence" for the years 2019-2022/ ; }, abstract = {To decompose forest biomass, microorganisms use specific enzymes from the class of oxidoreductases and hydrolases, which are produced by bacteria and soil fungi. In post-agricultural forest soils, bacteria adapt more easily to changing ecological conditions than fungi. The unique features of bacteria, i.e., tolerance and the ability to degrade a wide range of chemical compounds, prompted us to conduct research that contributes to the improvement of the broadly understood circular management of biomass production and economic efficiency. This study aimed to analyze changes in the microbiological activity and the activities of dehydrogenases, catalase, β-glucosidase, urease, arylsulfatase, acid phosphatase, and alkaline phosphatase in the soil sampled from under Picea abies (Pa), Pinus sylvestris (Ps), Larix decidua (Ld), Quercus robur (Qr), and Betula pendula (Bp), after 19 years. The control object was unforested soil. The studies allowed one to demonstrate the relationship between the activity of soil enzymes and the assemblages of culturable microorganisms and bacteria determined by the metagenomic method and tree species. Thus, it is possible to design the selection of tree species catalyzing enzymatic processes in soil. The strongest growth promoter of microorganisms turned out to be Quercus robur L., followed by Picea abies L., whereas the weakest promoters appeared to be Pinus sylvestris L. and Larix decidua M.}, } @article {pmid35590081, year = {2022}, author = {Thakur, M and Kumar Rai, A and Singh, SP}, title = {An acid-tolerant and cold-active β-galactosidase potentially suitable to process milk and whey samples.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {9-10}, pages = {3599-3610}, pmid = {35590081}, issn = {1432-0614}, support = {BT/PR31829/NDB/39/649/2019//Department of Biotechnology , Ministry of Science and Technology/ ; }, mesh = {Animals ; Escherichia coli/genetics/metabolism ; Galactose/metabolism ; Hydrogen-Ion Concentration ; Lactose/metabolism ; *Milk/metabolism ; Oligosaccharides/metabolism ; Phylogeny ; *Whey/metabolism ; beta-Galactosidase/metabolism ; }, abstract = {A novel β-galactosidase gene (galM) was cloned from an aquatic habitat metagenome. The analysis of its translated sequence (GalM) revealed its phylogenetic closeness towards Verrucomicrobia sp. The sequence comparison and homology structure analysis designated it a member of GH42 family. The three-dimensional homology model of GalM depicted a typical (β/α)8 TIM-barrel containing the catalytic core. The gene (galM) was expressed in a heterologous host, Escherichia coli, and the purified protein (GalM) was subjected to biochemical characterization. It displayed β-galactosidase activity in a wide range of pH (2.0 to 9.0) and temperature (4 to 60 °C). The heat exposed protein showed considerable stability at 40 and 50 °C, with the half-life of about 100 h and 35 h, respectively. The presence of Na, Mg, K, Ca, and Mn metals was favorable to the catalytic efficiency of GalM, which is a desirable catalytic feature, as these metals exist in milk. It showed remarkable tolerance of glucose and galactose in the reaction. Furthermore, GalM discerned transglycosylation activity that is useful in galacto-oligosaccharides' production. These biochemical properties specify the suitability of this biocatalyst for milk and whey processing applications. KEY POINTS: • A novel β-galactosidase gene was identified and characterized from an aquatic habitat. • It was active in extreme acidic to mild alkaline pH and at cold to moderate temperatures. • The β-galactosidase was capable to hydrolyze lactose in milk and whey.}, } @article {pmid35589762, year = {2022}, author = {Szóstak, N and Szymanek, A and Havránek, J and Tomela, K and Rakoczy, M and Samelak-Czajka, A and Schmidt, M and Figlerowicz, M and Majta, J and Milanowska-Zabel, K and Handschuh, L and Philips, A}, title = {The standardisation of the approach to metagenomic human gut analysis: from sample collection to microbiome profiling.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {8470}, pmid = {35589762}, issn = {2045-2322}, mesh = {DNA ; Humans ; Metagenome ; *Metagenomics/methods ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; Reproducibility of Results ; }, abstract = {In recent years, the number of metagenomic studies increased significantly. Wide range of factors, including the tremendous community complexity and variability, is contributing to the challenge in reliable microbiome community profiling. Many approaches have been proposed to overcome these problems making hardly possible to compare results of different studies. The significant differences between procedures used in metagenomic research are reflected in a variation of the obtained results. This calls for the need for standardisation of the procedure, to reduce the confounding factors originating from DNA isolation, sequencing and bioinformatics analyses in order to ensure that the differences in microbiome composition are of a true biological origin. Although the best practices for metagenomics studies have been the topic of several publications and the main aim of the International Human Microbiome Standard (IHMS) project, standardisation of the procedure for generating and analysing metagenomic data is still far from being achieved. To highlight the difficulties in the standardisation of metagenomics methods, we thoroughly examined each step of the analysis of the human gut microbiome. We tested the DNA isolation procedure, preparation of NGS libraries for next-generation sequencing, and bioinformatics analysis, aimed at identifying microbial taxa. We showed that the homogenisation time is the leading factor impacting sample diversity, with the recommendation for a shorter homogenisation time (10 min). Ten minutes of homogenisation allows for better reflection of the bacteria gram-positive/gram-negative ratio, and the obtained results are the least heterogenous in terms of beta-diversity of samples microbial composition. Besides increasing the homogenisation time, we observed further potential impact of the library preparation kit on the gut microbiome profiling. Moreover, our analysis revealed that the choice of the library preparation kit influences the reproducibility of the results, which is an important factor that has to be taken into account in every experiment. In this study, a tagmentation-based kit allowed for obtaining the most reproducible results. We also considered the choice of the computational tool for determining the composition of intestinal microbiota, with Kraken2/Bracken pipeline outperforming MetaPhlAn2 in our in silico experiments. The design of an experiment and a detailed establishment of an experimental protocol may have a serious impact on determining the taxonomic profile of the intestinal microbiome community. Results of our experiment can be helpful for a wide range of studies that aim to better understand the role of the gut microbiome, as well as for clinical purposes.}, } @article {pmid35589196, year = {2022}, author = {Mathur, Y and Vartak, AR and Hazra, AB}, title = {Guardian of cobamide diversity: Probing the role of CobT in lower ligand activation in the biosynthesis of vitamin B12 and other cobamide cofactors.}, journal = {Methods in enzymology}, volume = {668}, number = {}, pages = {25-59}, doi = {10.1016/bs.mie.2022.01.001}, pmid = {35589196}, issn = {1557-7988}, mesh = {*Cobamides/chemistry ; Humans ; Ligands ; *Vitamin B 12/chemistry ; Vitamins ; }, abstract = {Enzymes catalyze a wide variety of reactions with exquisite precision under crowded conditions within cellular environments. When encountered with a choice of small molecules in their vicinity, even though most enzymes continue to be specific about the substrate they pick, some others are able to accept a range of substrates and subsequently produce a variety of products. The biosynthesis of Vitamin B12, an essential nutrient required by humans involves a multi-substrate α-phosphoribosyltransferase enzyme CobT that activates the lower ligand of B12. Vitamin B12 is a member of the cobamide family of cofactors which share a common tetrapyrrolic corrin scaffold with a centrally coordinated cobalt ion, and an upper and a lower ligand. The structural difference between B12 and other cobamides mainly arises from variations in the lower ligand, which is attached to the activated corrin ring by CobT and other downstream enzymes. In this chapter, we describe the steps involved in identifying and reconstituting the activity of new CobT homologs by deriving lessons from those previously characterized. We then highlight biochemical techniques to study the unique properties of these homologs. Finally, we describe a pairwise substrate competition assay to rank CobT substrate preference, a general method that can be applied for the study of other multi-substrate enzymes. Overall, the analysis with CobT provides insights into the range of cobamides that can be synthesized by an organism or a community, complementing efforts to predict cobamide diversity from complex metagenomic data.}, } @article {pmid35588986, year = {2022}, author = {Murali, A and Giri, V and Cameron, HJ and Sperber, S and Zickgraf, FM and Haake, V and Driemert, P and Walk, T and Kamp, H and Rietjens, IM and van Ravenzwaay, B}, title = {Investigating the gut microbiome and metabolome following treatment with artificial sweeteners acesulfame potassium and saccharin in young adult Wistar rats.}, journal = {Food and chemical toxicology : an international journal published for the British Industrial Biological Research Association}, volume = {165}, number = {}, pages = {113123}, doi = {10.1016/j.fct.2022.113123}, pmid = {35588986}, issn = {1873-6351}, mesh = {Animals ; Bile Acids and Salts ; Body Weight ; Feces/chemistry ; Female ; *Gastrointestinal Microbiome ; Male ; Metabolome ; Metabolomics ; Rats ; Rats, Wistar ; Saccharin ; Sweetening Agents/analysis ; Thiazines ; }, abstract = {To elucidate if artificial sweeteners modify fecal bacterial composition and the fecal and plasma metabolomes, Wistar rats from both sexes were treated for 28 days with acesulfame potassium (40 and 120 mg/kg body weight) and saccharin (20 and 100 mg/kg body weight). Targeted MS-based metabolome profiling (plasma and feces) and fecal 16S gene sequencing were conducted. Both sweeteners exhibited only minor effects on the fecal metabolome and microbiota. Saccharin treatment significantly altered amino acids, lipids, energy metabolism and specifically, bile acids in the plasma metabolome. Additionally, sex-specific differences were observed for conjugated primary and secondary bile acids. Acesulfame potassium treated male rats showed larger alterations in glycine conjugated primary and secondary bile-acids than females. Other changes in the plasma metabolome were more profound for saccharin than acesulfame potassium, for both sexes. Changes in conjugated bile-acids in plasma, which are often associated with microbiome changes, and the absence of similarly large changes in microbiota suggest an adaptative change of the latter, rather than toxicity. Further studies with a high resolution 16S sequencing data and/or metagenomics approach, with particular emphasis on bile acids, will be required to explore the mechanisms driving this metabolic outcome of saccharin in Wistar rats.}, } @article {pmid35587930, year = {2022}, author = {Benyedem, H and Lekired, A and Mhadhbi, M and Dhibi, M and Romdhane, R and Chaari, S and Rekik, M and Ouzari, HI and Hajji, T and Darghouth, MA}, title = {First insights into the microbiome of Tunisian Hyalomma ticks gained through next-generation sequencing with a special focus on H. scupense.}, journal = {PloS one}, volume = {17}, number = {5}, pages = {e0268172}, pmid = {35587930}, issn = {1932-6203}, mesh = {Animals ; Cattle ; *Francisella/genetics ; High-Throughput Nucleotide Sequencing ; *Ixodidae/genetics/microbiology ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; *Rickettsia/genetics ; *Ticks/genetics ; }, abstract = {Ticks are one of the most important vectors of several pathogens affecting humans and animals. In addition to pathogens, ticks carry diverse microbiota of symbiotic and commensal microorganisms. In this study, we have investigated the first Tunisian insight into the microbial composition of the most dominant Hyalomma species infesting Tunisian cattle and explored the relative contribution of tick sex, life stage, and species to the diversity, richness and bacterial species of tick microbiome. In this regard, next generation sequencing for the 16S rRNA (V3-V4 region) of tick bacterial microbiota and metagenomic analysis were established. The analysis of the bacterial diversity reveals that H. marginatum and H. excavatum have greater diversity than H. scupense. Furthermore, microbial diversity and composition vary according to the tick's life stage and sex in the specific case of H. scupense. The endosymbionts Francisella, Midichloria mitochondrii, and Rickettsia were shown to be the most prevalent in Hyalomma spp. Rickettsia, Francisella, Ehrlichia, and Erwinia are the most common zoonotic bacteria found in Hyalomma ticks. Accordingly, Hyalomma ticks could represent potential vectors for these zoonotic bacterial agents.}, } @article {pmid35587374, year = {2022}, author = {Kohl, KD and Dieppa-Colón, E and Goyco-Blas, J and Peralta-Martínez, K and Scafidi, L and Shah, S and Zawacki, E and Barts, N and Ahn, Y and Hedayati, S and Secor, SM and Rowe, MP}, title = {Gut Microbial Ecology of Five Species of Sympatric Desert Rodents in Relation to Herbivorous and Insectivorous Feeding Strategies.}, journal = {Integrative and comparative biology}, volume = {62}, number = {2}, pages = {237-251}, doi = {10.1093/icb/icac045}, pmid = {35587374}, issn = {1557-7023}, support = {IOS-1942587//National Science Foundation/ ; }, mesh = {Animals ; Chitin ; Dipodomys ; *Gastrointestinal Microbiome ; Herbivory ; *Microbiota ; Peromyscus ; Rodentia ; }, abstract = {The gut microbial communities of mammals provide numerous benefits to their hosts. However, given the recent development of the microbiome field, we still lack a thorough understanding of the variety of ecological and evolutionary factors that structure these communities across species. Metabarcoding is a powerful technique that allows for multiple microbial ecology questions to be investigated simultaneously. Here, we employed DNA metabarcoding techniques, predictive metagenomics, and culture-dependent techniques to inventory the gut microbial communities of several species of rodent collected from the same environment that employ different natural feeding strategies [granivorous pocket mice (Chaetodipus penicillatus); granivorous kangaroo rats (Dipodomys merriami); herbivorous woodrats (Neotoma albigula); omnivorous cactus mice (Peromyscus eremicus); and insectivorous grasshopper mice (Onychomys torridus)]. Of particular interest were shifts in gut microbial communities in rodent species with herbivorous and insectivorous diets, given the high amounts of indigestible fibers and chitinous exoskeleton in these diets, respectively. We found that herbivorous woodrats harbored the greatest microbial diversity. Granivorous pocket mice and kangaroo rats had the highest abundances of the genus Ruminococcus and highest predicted abundances of genes related to the digestion of fiber, representing potential adaptations in these species to the fiber content of seeds and the limitations to digestion given their small body size. Insectivorous grasshopper mice exhibited the greatest inter-individual variation in the membership of their microbiomes, and also exhibited the highest predicted abundances of chitin-degrading genes. Culture-based approaches identified 178 microbial isolates (primarily Bacillus and Enterococcus), with some capable of degrading cellulose and chitin. We observed several instances of strain-level diversity in these metabolic capabilities across isolates, somewhat highlighting the limitations and hidden diversity underlying DNA metabarcoding techniques. However, these methods offer power in allowing the investigation of several questions concurrently, thus enhancing our understanding of gut microbial ecology.}, } @article {pmid35586865, year = {2022}, author = {Chen, H and Ma, K and Lu, C and Fu, Q and Qiu, Y and Zhao, J and Huang, Y and Yang, Y and Schadt, CW and Chen, H}, title = {Functional Redundancy in Soil Microbial Community Based on Metagenomics Across the Globe.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {878978}, pmid = {35586865}, issn = {1664-302X}, abstract = {Understanding the contribution of soil microbial communities to ecosystem processes is critical for predicting terrestrial ecosystem feedbacks under changing climate. Our current understanding lacks a consistent strategy to formulate the linkage between microbial systems and ecosystem processes due to the presumption of functional redundancy in soil microbes. Here we present a global soil microbial metagenomic analysis to generalize patterns of microbial taxonomic compositions and functional potentials across climate and geochemical gradient. Our analyses show that soil microbial taxonomic composition varies widely in response to climate and soil physicochemical gradients, while microbial functional attributes based on metagenomic gene abundances are redundant. Among 17 climate zones, microbial taxonomic compositions were more distinct than functional potentials, as climate and edaphic properties showed more significant influence on microbial taxonomic compositions than on functional potentials. Microbial taxonomies formed a larger and more complex co-occurrence network with more module structures than functional potentials. Functional network was strongly inter-connected among different categories, whereas taxonomic network was more positively interactive in the same taxonomic groups. This study provides strong evidence to support the hypothesis of functional redundancy in soil microbes, as microbial taxonomic compositions vary to a larger extent than functional potentials based on metagenomic gene abundances in terrestrial ecosystems across the globe.}, } @article {pmid35585555, year = {2022}, author = {Deng, K and Shuai, M and Zhang, Z and Jiang, Z and Fu, Y and Shen, L and Zheng, JS and Chen, YM}, title = {Temporal relationship among adiposity, gut microbiota, and insulin resistance in a longitudinal human cohort.}, journal = {BMC medicine}, volume = {20}, number = {1}, pages = {171}, pmid = {35585555}, issn = {1741-7015}, mesh = {Adiposity ; Cohort Studies ; *Gastrointestinal Microbiome ; Humans ; *Insulin Resistance ; Obesity/epidemiology ; }, abstract = {BACKGROUND: The temporal relationship between adiposity and gut microbiota was unexplored. Whether some gut microbes lie in the pathways from adiposity to insulin resistance is less clear. Our study aims to reveal the temporal relationship between adiposity and gut microbiota and investigate whether gut microbiota may mediate the association of adiposity with insulin resistance in a longitudinal human cohort study.

METHODS: We obtained repeated-measured gut shotgun metagenomic and anthropometric data from 426 Chinese participants over ~3 years of follow-up. Cross-lagged path analysis was used to examine the temporal relationship between BMI and gut microbial features. The associations between the gut microbes and insulin resistance-related phenotypes were examined using a linear mixed-effect model. We examined the mediation effect of gut microbes on the association between adiposity and insulin resistance-related phenotypes. Replication was performed in the HMP cohort.

RESULTS: Baseline BMI was prospectively associated with levels of ten gut microbial species. Among them, results of four species (Adlercreutzia equolifaciens, Parabacteroides unclassified, Lachnospiraceae bacterium 3 1 57FAA CT1, Lachnospiraceae bacterium 7 1 58FAA) were replicated in the independent HMP cohort. Lachnospiraceae bacterium 3 1 57FAA CT1 was inversely associated with HOMA-IR and fasting insulin. Lachnospiraceae bacterium 3 1 57FAA CT1 mediated the association of overweight/obesity with HOMA-IR (FDR<0.05). Furthermore, Lachnospiraceae bacterium 3 1 57FAA CT1 was positively associated with the butyrate-producing pathway PWY-5022 (p < 0.001).

CONCLUSIONS: Our study identified one potentially beneficial microbe Lachnospiraceae bacterium 3 1 57FAA CT1, which might mediate the effect of adiposity on insulin resistance. The identified microbes are helpful for the discovery of novel therapeutic targets, as to mitigate the impact of adiposity on insulin resistance.}, } @article {pmid35585088, year = {2022}, author = {Yan, J and Liao, C and Taylor, BP and Fontana, E and Amoretti, LA and Wright, RJ and Littmann, ER and Dai, A and Waters, N and Peled, JU and Taur, Y and Perales, MA and Siranosian, BA and Bhatt, AS and van den Brink, MRM and Pamer, EG and Schluter, J and Xavier, JB}, title = {A compilation of fecal microbiome shotgun metagenomics from hematopoietic cell transplantation patients.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {219}, pmid = {35585088}, issn = {2052-4463}, support = {K08 HL143189/HL/NHLBI NIH HHS/United States ; P30 CA008748/CA/NCI NIH HHS/United States ; R01 AI137269/AI/NIAID NIH HHS/United States ; U01 AI124275/AI/NIAID NIH HHS/United States ; }, mesh = {*Feces/microbiology ; *Hematopoietic Stem Cell Transplantation ; Humans ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Hospitalized patients receiving hematopoietic cell transplants provide a unique opportunity to study the human gut microbiome. We previously compiled a large-scale longitudinal dataset of fecal microbiota and associated metadata, but we had limited that analysis to taxonomic composition of bacteria from 16S rRNA gene sequencing. Here we augment those data with shotgun metagenomics. The compilation amounts to a nested subset of 395 samples compiled from different studies at Memorial Sloan Kettering. Shotgun metagenomics describes the microbiome at the functional level, particularly in antimicrobial resistances and virulence factors. We provide accession numbers that link each sample to the paired-end sequencing files deposited in a public repository, which can be directly accessed by the online services of PATRIC to be analyzed without the users having to download or transfer the files. Then, we show how shotgun sequencing enables the assembly of genomes from metagenomic data. The new data, combined with the metadata published previously, enables new functional studies of the microbiomes of patients with cancer receiving bone marrow transplantation.}, } @article {pmid35584918, year = {2022}, author = {He, T and Zhu, C and Li, Z and Ai, L and Hu, D and Wang, C and Li, F and Yang, X and Lv, H and Chen, W and Qian, H and Tan, W and Wang, C}, title = {Virome analysis of ticks in Zhoushan Archipelago, China.}, journal = {The Journal of veterinary medical science}, volume = {84}, number = {6}, pages = {847-854}, pmid = {35584918}, issn = {1347-7439}, mesh = {Animals ; China/epidemiology ; *Phlebovirus ; Phylogeny ; *Tick-Borne Diseases/veterinary ; *Ticks ; Virome/genetics ; *Viruses/genetics ; }, abstract = {Ticks are an important group of arthropod vectors. Ticks pose a profound risk to public health by transmitting many types of microorganisms that are human and animal pathogens. With the development of next-generation sequencing (NGS) technology and viral metagenomics, numerous novel viruses have been discovered in ticks and tick-related hosts. To fully understand the virus spectrum in ticks in the Zhoushan Archipelago of Zhejiang province in China, ticks were collected from Qushan Island, Zhoushan Island, and Daishan Island in the Zhoushan Archipelago in June 2016. NGS performed to investigate the diversity of tick-associated viruses identified 21 viral sequences. Twelve were pathogenic to humans and animals. Trough verification by polymerase chain reaction (PCR) revealed the existence of three tick-associated viruses with extensive homology with Dabieshan, MG22, and Odaw virus. Other NGS-detected sequences that could not be amplified by PCR were highly homologous (92-100%) with known pathogenic viruses that included hepatitis B virus, papillomavirus, and human mastadenovirus C. This is the first study to systematically apply high throughput sequencing technology to explore the spectrum of viruses carried by ticks in the Zhoushan Archipelago. The findings are fundamental knowledge of the diversity of tick-associated viruses in this region and will inform strategies to monitor and prevent the spread of tick-borne diseases.}, } @article {pmid35584889, year = {2022}, author = {Koskella, B and Hernandez, CA and Wheatley, RM}, title = {Understanding the Impacts of Bacteriophage Viruses: From Laboratory Evolution to Natural Ecosystems.}, journal = {Annual review of virology}, volume = {9}, number = {1}, pages = {57-78}, doi = {10.1146/annurev-virology-091919-075914}, pmid = {35584889}, issn = {2327-0578}, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Ecology ; *Ecosystem ; Metagenomics ; }, abstract = {Viruses of bacteria (bacteriophages or phage) have broad effects on bacterial ecology and evolution in nature that mediate microbial interactions, shape bacterial diversity, and influence nutrient cycling and ecosystem function. The unrelenting impact of phages within the microbial realm is the result, in large part, of their ability to rapidly evolve in response to bacterial host dynamics. The knowledge gained from laboratory systems, typically using pairwise interactions between single-host and single-phage systems, has made clear that phages coevolve with their bacterial hosts rapidly, somewhat predictably, and primarily by counteradapting to host resistance. Recent advancement in metagenomics approaches, as well as a shifting focus toward natural microbial communities and host-associated microbiomes, is beginning to uncover the full picture of phage evolution and ecology within more complex settings. As these data reach their full potential, it will be critical to ask when and how insights gained from studies of phage evolution in vitro can be meaningfully applied to understanding bacteria-phage interactions in nature. In this review, we explore the myriad ways that phagesshape and are themselves shaped by bacterial host populations and communities, with a particular focus on observed and predicted differences between the laboratory and complex microbial communities.}, } @article {pmid35584752, year = {2022}, author = {Singh, R and Pal, DB and Alkhanani, MF and Almalki, AH and Areeshi, MY and Haque, S and Srivastava, N}, title = {Prospects of soil microbiome application for lignocellulosic biomass degradation: An overview.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 1}, pages = {155966}, doi = {10.1016/j.scitotenv.2022.155966}, pmid = {35584752}, issn = {1879-1026}, mesh = {*Biofuels ; Biomass ; Lignin/metabolism ; *Microbiota ; Soil ; }, abstract = {Sustainable and practically viable biofuels production technology using lignocellulosic biomass is still seeking its way of implementation owing to some major issues involved therein. Unavailability of efficient microbial sources for the degradation of cellulosic biomass is one of the major roadblocks in biomass to biofuels production technology. In this context, utilization of microbiomes to degrade lignocellulaosic biomass is emerging as a rapid and effective approach that can fulfill the requirements of biomass based biofuels production technology. Therefore, the present review is targeted to explore soil metagenomic approach to improve the lignocellulosic biomass degradation processing for the cost-effective and eco-friendly application. Soil microbiomes consist of rich microbial community along with high probability of cellulolytic microbes, and can be identified by culture independent metagenomics method which can be structurally and functionally explored via genomic library. Therefore, in depth analysis and discussion have also been made via structural & functional metagenomics tools along with their contribution to genomic library. Additionally, the present review highlights currently existing bottlenecks along with their feasible solutions. This review will help to understand the basic research as well as industrial concept for the process improvement based on soil microbiome mediated lignocellulosic biomass degradation, and this may likely to implement for the low-cost commercial biofuels production technology.}, } @article {pmid35584587, year = {2022}, author = {Kuroda, K and Narihiro, T and Shinshima, F and Yoshida, M and Yamaguchi, H and Kurashita, H and Nakahara, N and Nobu, MK and Noguchi, TQP and Yamauchi, M and Yamada, M}, title = {High-rate cotreatment of purified terephthalate and dimethyl terephthalate manufacturing wastewater by a mesophilic upflow anaerobic sludge blanket reactor and the microbial ecology relevant to aromatic compound degradation.}, journal = {Water research}, volume = {219}, number = {}, pages = {118581}, doi = {10.1016/j.watres.2022.118581}, pmid = {35584587}, issn = {1879-2448}, mesh = {Anaerobiosis ; Benzoates ; Bioreactors ; Phthalic Acids ; RNA, Ribosomal, 16S/genetics ; *Sewage ; Waste Disposal, Fluid ; *Wastewater ; }, abstract = {Polyethylene terephthalate (PET) is produced worldwide, mainly as material for plastic drink bottles. PET is produced by polymerization of purified terephthalate (PTA) or dimethyl terephthalate (DMT) with ethylene glycol. During the synthetic manufacturing processes of PTA and DMT, high organic loading wastewater is produced, which is typically treated separately by anaerobic wastewater treatment technologies. Given the high demand for PET, manufacturing plants are expanding globally, which will result in an increase in the amounts of PTA and DMT wastewater in need of treatment. In terms of effective treatment, the cotreatment of PTA and DMT wastewater has several advantages, including lower area and energy requirements. In this study, we examined the performance of an upflow anaerobic sludge blanket (UASB) reactor in cotreating PTA and DMT wastewater with high organic loading, evaluating its removal characteristics after 518 days of continuous operation. In addition, we performed a microbiome analysis of the UASB granular sludge to uncover the microbial interactions and metabolic functions within the reactor. By continuous operation, we achieved an organic removal rate of 6.6 kg m[-3] day[-1]. In addition, we confirmed that aromatic compounds in the complex wastewater from the PTA and DMT manufacturing processes are biodegradable in the following order: benzoate > orthophthalate > terephthalate > isophthalate > p-toluic acid. 16S rRNA gene-based network analysis shows that anaerobic Woesearchaeales belonging to phylum Nanoarchaeota has a positive correlation with Methanoregula, Candidatus Methanofastidiosum, and Methanosarcina, suggesting a symbiotic relationship with methanogens in granular sludge. Shotgun metagenomic analysis revealed that terephthalate, isophthalate/orthophthalate, and benzoate were degraded by different members of Pelotomaculaceae and Syntrophorhabdaceae. According to the genomic information, we propose two new possible routes for orthophthalate degradation by the Syntrophorhabdaceae organism.}, } @article {pmid35584271, year = {2022}, author = {Han, W and Tang, H and Ye, Y}, title = {Locality-Sensitive Hashing-Based k-Mer Clustering for Identification of Differential Microbial Markers Related to Host Phenotype.}, journal = {Journal of computational biology : a journal of computational molecular cell biology}, volume = {29}, number = {7}, pages = {738-751}, pmid = {35584271}, issn = {1557-8666}, support = {R01 AI108888/AI/NIAID NIH HHS/United States ; R01 AI143254/AI/NIAID NIH HHS/United States ; }, mesh = {Cluster Analysis ; Metagenome ; *Metagenomics/methods ; *Microbiota/genetics ; Phenotype ; }, abstract = {Microbial organisms play important roles in many aspects of human health and diseases. Encouraged by the numerous studies that show the association between microbiomes and human diseases, computational and machine learning methods have been recently developed to generate and utilize microbiome features for prediction of host phenotypes such as disease versus healthy cancer immunotherapy responder versus nonresponder. We have previously developed a subtractive assembly approach, which focuses on extraction and assembly of differential reads from metagenomic data sets that are likely sampled from differential genomes or genes between two groups of microbiome data sets (e.g., healthy vs. disease). In this article, we further improved our subtractive assembly approach by utilizing groups of k-mers with similar abundance profiles across multiple samples. We implemented a locality-sensitive hashing (LSH)-enabled approach (called kmerLSHSA) to group billions of k-mers into k-mer coabundance groups (kCAGs), which were subsequently used for the retrieval of differential kCAGs for subtractive assembly. Testing of the kmerLSHSA approach on simulated data sets and real microbiome data sets showed that, compared with the conventional approach that utilizes all genes, our approach can quickly identify differential genes that can be used for building promising predictive models for microbiome-based host phenotype prediction. We also discussed other potential applications of LSH-enabled clustering of k-mers according to their abundance profiles across multiple microbiome samples.}, } @article {pmid35584001, year = {2022}, author = {Johnson, MA and Liu, H and Bush, E and Sharma, P and Yang, S and Mazloom, R and Heath, LS and Nita, M and Li, S and Vinatzer, BA}, title = {Investigating plant disease outbreaks with long-read metagenomics: sensitive detection and highly resolved phylogenetic reconstruction applied to Xylella fastidiosa.}, journal = {Microbial genomics}, volume = {8}, number = {5}, pages = {}, pmid = {35584001}, issn = {2057-5858}, mesh = {Disease Outbreaks ; *Metagenomics ; Phylogeny ; *Xylella/genetics ; }, abstract = {Early disease detection is a prerequisite for enacting effective interventions for disease control. Strains of the bacterial plant pathogen Xylella fastidiosa have recurrently spread to new crops in new countries causing devastating outbreaks. So far, investigation of outbreak strains and highly resolved phylogenetic reconstruction have required whole-genome sequencing of pure bacterial cultures, which are challenging to obtain due to the fastidious nature of X. fastidiosa. Here, we show that culture-independent metagenomic sequencing, using the Oxford Nanopore Technologies MinION long-read sequencer, can sensitively and specifically detect the causative agent of Pierce's disease of grapevine, X. fastidiosa subspecies fastidiosa. Using a DNA sample from a grapevine in Virginia, USA, it was possible to obtain a metagenome-assembled genome (MAG) of sufficient quality for phylogenetic reconstruction with SNP resolution. The analysis placed the MAG in a clade with isolates from Georgia, USA, suggesting introduction of X. fastidiosa subspecies fastidiosa to Virginia from the south-eastern USA. This proof of concept study, thus, revealed that metagenomic sequencing can replace culture-dependent genome sequencing for reconstructing transmission routes of bacterial plant pathogens.}, } @article {pmid35583811, year = {2022}, author = {Zhao, F and Wang, C and Song, S and Fang, C and Kristiansen, K and Li, C}, title = {Intake of a Chicken Protein-Based or Soy Protein-Based Diet Differentially Affects Growth Performance, Absorptive Capacity, and Gut Microbiota in Young Rats.}, journal = {Molecular nutrition & food research}, volume = {66}, number = {13}, pages = {e2101124}, doi = {10.1002/mnfr.202101124}, pmid = {35583811}, issn = {1613-4133}, support = {//Ministry of Science and Technology (10000 Talent Project)/ ; CARS-35//Ministry of Agriculture and Rural Affairs of the People's Republic of China/ ; 31471600//National Natural Science Foundation of China/ ; 21KJB550008//Jiangsu Provincial Department of Education/ ; PADP//Jiangsu Provincial Department of Education/ ; }, mesh = {Animals ; Cecum ; Chickens ; Diet ; *Gastrointestinal Microbiome ; Rats ; Soybean Proteins/pharmacology ; }, abstract = {SCOPE: Both plant and animal products provide protein for human demands. However, the effect of protein sources on the physiological responses and the composition and functions of the gut microbiota during the early stage of life have received little attention.

METHODS AND RESULTS: In the present study, chicken protein and soy protein are fed to young weaning rats for 14 days based on the AIN-93G diet formulation. The growth performance is recorded, and the morphology of the small intestine is analyzed to estimate the absorptive capacity. Shotgun metagenomic sequencing is applied to analyze the cecal microbiota. The chicken protein-based diet (CHPD) enhances growth performance and absorptive capacity in young rats compared to the soy protein-based diet (SPD). The CHPD maintains higher levels of Lactobacillus species, associated with glutathione synthesis.

CONCLUSION: The CHPD seems favorable for young growing rats in relation to growth performance and absorptive capacity, correlated with changes in the composition and functional potential of the gut microbiota.}, } @article {pmid35583675, year = {2022}, author = {Marini, S and Oliva, M and Slizovskiy, IB and Das, RA and Noyes, NR and Kahveci, T and Boucher, C and Prosperi, M}, title = {AMR-meta: a k-mer and metafeature approach to classify antimicrobial resistance from high-throughput short-read metagenomics data.}, journal = {GigaScience}, volume = {11}, number = {}, pages = {}, pmid = {35583675}, issn = {2047-217X}, support = {R01 AI141810/AI/NIAID NIH HHS/United States ; }, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; High-Throughput Nucleotide Sequencing ; Metagenome ; *Metagenomics/methods ; }, abstract = {BACKGROUND: Antimicrobial resistance (AMR) is a global health concern. High-throughput metagenomic sequencing of microbial samples enables profiling of AMR genes through comparison with curated AMR databases. However, the performance of current methods is often hampered by database incompleteness and the presence of homology/homoplasy with other non-AMR genes in sequenced samples.

RESULTS: We present AMR-meta, a database-free and alignment-free approach, based on k-mers, which combines algebraic matrix factorization into metafeatures with regularized regression. Metafeatures capture multi-level gene diversity across the main antibiotic classes. AMR-meta takes in reads from metagenomic shotgun sequencing and outputs predictions about whether those reads contribute to resistance against specific classes of antibiotics. In addition, AMR-meta uses an augmented training strategy that joins an AMR gene database with non-AMR genes (used as negative examples). We compare AMR-meta with AMRPlusPlus, DeepARG, and Meta-MARC, further testing their ensemble via a voting system. In cross-validation, AMR-meta has a median f-score of 0.7 (interquartile range, 0.2-0.9). On semi-synthetic metagenomic data-external test-on average AMR-meta yields a 1.3-fold hit rate increase over existing methods. In terms of run-time, AMR-meta is 3 times faster than DeepARG, 30 times faster than Meta-MARC, and as fast as AMRPlusPlus. Finally, we note that differences in AMR ontologies and observed variance of all tools in classification outputs call for further development on standardization of benchmarking data and protocols.

CONCLUSIONS: AMR-meta is a fast, accurate classifier that exploits non-AMR negative sets to improve sensitivity and specificity. The differences in AMR ontologies and the high variance of all tools in classification outputs call for the deployment of standard benchmarking data and protocols, to fairly compare AMR prediction tools.}, } @article {pmid35583271, year = {2022}, author = {Santoro, D and Pellegrina, L and Comin, M and Vandin, F}, title = {SPRISS: approximating frequent k-mers by sampling reads, and applications.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {13}, pages = {3343-3350}, pmid = {35583271}, issn = {1367-4811}, support = {20174LF3T8//Italian Ministry of Education, University and Research/ ; }, mesh = {*Software ; Sequence Analysis, DNA ; *High-Throughput Nucleotide Sequencing ; Algorithms ; Genomics ; }, abstract = {MOTIVATION: The extraction of k-mers is a fundamental component in many complex analyses of large next-generation sequencing datasets, including reads classification in genomics and the characterization of RNA-seq datasets. The extraction of all k-mers and their frequencies is extremely demanding in terms of running time and memory, owing to the size of the data and to the exponential number of k-mers to be considered. However, in several applications, only frequent k-mers, which are k-mers appearing in a relatively high proportion of the data, are required by the analysis.

RESULTS: In this work, we present SPRISS, a new efficient algorithm to approximate frequent k-mers and their frequencies in next-generation sequencing data. SPRISS uses a simple yet powerful reads sampling scheme, which allows to extract a representative subset of the dataset that can be used, in combination with any k-mer counting algorithm, to perform downstream analyses in a fraction of the time required by the analysis of the whole data, while obtaining comparable answers. Our extensive experimental evaluation demonstrates the efficiency and accuracy of SPRISS in approximating frequent k-mers, and shows that it can be used in various scenarios, such as the comparison of metagenomic datasets, the identification of discriminative k-mers, and SNP (single nucleotide polymorphism) genotyping, to extract insights in a fraction of the time required by the analysis of the whole dataset.

SPRISS [a preliminary version (Santoro et al., 2021) of this work was presented at RECOMB 2021] is available at https://github.com/VandinLab/SPRISS.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid35583133, year = {2022}, author = {Hu, D and Zhao, X}, title = {Characterization of a New Xylanase Found in the Rumen Metagenome and Its Effects on the Hydrolysis of Wheat.}, journal = {Journal of agricultural and food chemistry}, volume = {70}, number = {21}, pages = {6493-6502}, doi = {10.1021/acs.jafc.2c00827}, pmid = {35583133}, issn = {1520-5118}, mesh = {Animals ; Cattle ; Endo-1,4-beta Xylanases/metabolism ; Escherichia coli/genetics ; Hydrolysis ; Metagenome ; *Rumen/metabolism ; Triticum/chemistry ; *Xylans/chemistry ; }, abstract = {Wheat is the main ingredient of poultry diet, but its xylan has an adverse impact on poultry production. A novel xylanase from beef cattle rumen metagenome (RuXyn) and its effect on the wheat hydrolysis were investigated in the present study. The RuXyn coded for 377 amino acids and exhibited low identity (<40%) to previously reported proteins. The RuXyn was heterologously expressed in Escherichia coli and showed maximum activity at pH 6.0 and 40 °C. The activity of RuXyn could be increased by 79.8 and 36.0% in the presence of Ca[2+] and Tween 20, respectively. The soluble xylan and insoluble xylan in wheat could be effectively degraded by RuXyn and xylooligosaccharides produced accounting for more than 80% of the products. This study demonstrates that RuXyn has substantial potential to improve the application of wheat in poultry production by degrading wheat xylan and the accompanying xylooligosaccharides produced.}, } @article {pmid35583090, year = {2022}, author = {Zhang, CF and Fang, XY and Huang, ZD and Bai, GC and Zhang, ZY and Yang, Y and Zhang, ZJ and Li, WB and Zhang, WM}, title = {Surgical Management for Chronic Destructive Septic Hip Arthritis: Debridement, Antibiotics, and Single-Stage Replacement is as Effective as Two-Stage Arthroplasty.}, journal = {Orthopaedic surgery}, volume = {14}, number = {6}, pages = {1175-1185}, pmid = {35583090}, issn = {1757-7861}, support = {//2019-2020 Middle-aged and Young Experts with Outstanding Contributions to Health in Fujian Province/ ; 2019-ZQN-57//Fujian Provincial Health Technology Project/ ; 2019Y9122//Joint Funds for the innovation of science and Technology, Fujian province/ ; 2020I0015//Foreign Cooperation Project of Science and Technology, Fujian Province/ ; 82102621//National Natural Science Foundation of China/ ; }, mesh = {Anti-Bacterial Agents/therapeutic use ; *Arthritis, Infectious/drug therapy/surgery ; *Arthroplasty, Replacement, Hip/methods ; Blood Loss, Surgical ; Debridement ; *Hip Prosthesis ; Humans ; *Joint Dislocations ; Retrospective Studies ; Treatment Outcome ; }, abstract = {OBJECTIVE: To compare the surgical outcomes of debridement, antibiotics, and single-stage total hip replacement (DASR) vs two-stage arthroplasty (two-stage arthroplasty) for chronic destructive septic hip arthritis (SHA).

METHODS: Cases of chronic destructive SHA treated by DASR or two-stage arthroplasty in our department from January 2008 to October 2021 were retrospectively reviewed. Patient demographic information, perioperative inflammation markers, intraoperative blood loss, microbial culture, and metagenomic new generation sequencing results were recorded. The perioperative complications, hospital stay, hospitalization cost, infection recurrence rate, and Harris Hip Score (HHS) at the last follow-up were compared between the two groups.

RESULTS: A total of 28 patients were included in the study, including 11 patients who received DASR and 17 patients who received two-stage arthroplasty. There was no significant difference in demographic information, preoperative serum inflammatory markers, synovial fluid white blood cell count, or percentage of polymorphonuclear leukocytes between the two groups. The DASR group demonstrated significantly lower intraoperative blood loss [(368.2 ± 253.3) mL vs (638.2 ± 170.0) mL, p = 0.002], hospital stay [(22.6 ± 8.1) days vs (43.5 ± 13.2) days, p < 0.0001], and hospitalization expenses [(81,269 ± 11,496) RMB vs (137,524 ± 25,516) RMB, p < 0.0001] than the two-stage arthroplasty group. In the DASR group, one patient had dislocation as a complication. There were no cases with recurrence of infection. In the two-stage arthroplasty group, there was one case complicated with spacer fracture, one case with spacer dislocation, and one case with deep vein thrombosis of the lower limbs. There were no cases with recurrence of infection. There were no significant differences in the readmission rate, complication rate, or HHS at the last follow-up between the two groups.

CONCLUSIONS: Both DASR and two-stage arthroplasty achieved a satisfactory infection cure rate and functional recovery for chronic destructive SHA, and DASR demonstrated significantly lower intraoperative blood loss, hospital stay, and hospitalization costs than two-stage arthroplasty. For appropriately indicated patients, if microbial data are available and a standardized debridement protocol is strictly followed, DASR can be a treatment option.}, } @article {pmid35581279, year = {2022}, author = {Rajabi, M and Nourisanami, F and Ghadikolaei, KK and Changizian, M and Noghabi, KA and Zahiri, HS}, title = {Metagenomic psychrohalophilic xylanase from camel rumen investigated for bioethanol production from wheat bran using Bacillus subtilis AP.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {8152}, pmid = {35581279}, issn = {2045-2322}, mesh = {Animals ; *Bacillus subtilis/metabolism ; Biomass ; Camelus/metabolism ; *Cellulase/metabolism ; Dietary Fiber ; Ethanol/chemistry ; Fermentation ; Hydrolysis ; Metagenome ; Rumen/metabolism ; }, abstract = {Bioethanol produced from lignocellulosic biomass is regarded as a clean and sustainable energy source. The recalcitrant structure of lignocellulose is a major drawback to affordable bioethanol production from plant biomass. In this study, a novel endo-1,4-xylanase, named Xyn-2, from the camel rumen metagenome, was characterized and evaluated for hydrolysis of agricultural wastes. The enzyme was identified as a psychrohalophilic xylanase with maximum activity at 20 °C, keeping 58% of the activity at 0 °C, and exhibiting twice as much activity in 0.5-4 M NaCl concentrations. Xyn-2 was able to hydrolyze wheat bran (100%), sunflower-seed shell (70%), wheat straw (56%), rice straw (56%), and rice bran (41%), in the relative order of efficiency. Besides, the ethanologenic B. subtilis AP was evaluated without and with Xyn-2 for bioethanol production from wheat bran. The strain was able to produce 5.5 g/L ethanol with a yield of 22.6% in consolidated bioprocessing (CBP). The contribution of Xyn-2 to ethanol production of B. subtilis AP was studied in an SSF system (simultaneous saccharification and fermentation) giving rise to a significant increase in ethanol production (p ≤ 0.001) to a final concentration of 7.3 g/L with a yield of 26.8%. The results revealed that the camel rumen metagenome might be an invaluable source of novel xylanolytic enzymes with potential application in lignocellulosic biomass valorization. At the same time, the results suggest that B. subtilis with a diverse carbon-source preference and sophisticated systems for production and secretion of enzymes might be a promising candidate for strain development for bioethanol production from plant biomass. It might be assumed that the fortification of B. subtilis enzymatic arsenal with select xylanolytic enzymes from camel rumen metagenome may have a great impact on bioethanol production.}, } @article {pmid35579684, year = {2022}, author = {Johny, TK and Puthusseri, RM and Saidumohamed, BE and Sheela, UB and Puthusseri, SP and Sasidharan, RS and Bhat, SG}, title = {Appraisal of cytotoxicity and acrylamide mitigation potential of L-asparaginase SlpA from fish gut microbiome.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {9-10}, pages = {3583-3598}, pmid = {35579684}, issn = {1432-0614}, support = {MOES/10-MLR/2/2007//Centre for Marine Living Resources and Ecology- Ministry of Earth Sciences, Government of India/ ; MOES/10-MLRTD/03/2013//Centre for Marine Living Resources and Ecology- Ministry of Earth Sciences, Government of India/ ; }, mesh = {Acrylamide/metabolism ; Animals ; *Antineoplastic Agents/pharmacology ; Asparaginase/genetics/metabolism ; Asparagine/metabolism ; *Gastrointestinal Microbiome ; Glutaminase ; }, abstract = {L-asparaginase catalyzes the hydrolysis of L-asparagine to L-aspartic acid and ammonia. It has application in the treatment of acute lymphoblastic leukemia in children, as well as in other malignancies, in addition to its role as a food processing aid for the mitigation of acrylamide formation in the baking industry. Its use in cancer chemotherapy is limited due to problems such as its intrinsic glutaminase activity and associated side effects, leading to an increased interest in the search for novel L-asparaginases without L-glutaminase activity. This study reports the cloning and expression of an L-asparaginase contig obtained from whole metagenome shotgun sequencing of Sardinella longiceps gut microbiota. Purified recombinant glutaminase-free L-asparaginase SlpA was a 74 kDa homodimer, with maximal activity at pH 8 and 30 °C. Km and Vmax of SlpA were determined to be 3.008 mM and 0.014 mM/min, respectively. SlpA displayed cytotoxic activity against K-562 (chronic myeloid leukemia) and MCF-7 (breast cancer) cell lines with IC50 values of 0.3443 and 2.692 U/mL, respectively. SlpA did not show any cytotoxic activity against normal lymphocytes and was proved to be hemocompatible. Pre-treatment of biscuit and bread dough with different concentrations of SlpA resulted in a clear, dose-dependent reduction of acrylamide formation during baking. KEY POINTS: • Cloned and expressed L-asparaginase (SlpA) from fish gut microbiota • Purified SlpA displayed good cytotoxicity against K-562 and MCF-7 cell lines • SlpA addition caused a significant reduction of acrylamide formation during baking.}, } @article {pmid35579554, year = {2022}, author = {Sim, M and Lee, J and Wy, S and Park, N and Lee, D and Kwon, D and Kim, J}, title = {Generation and application of pseudo-long reads for metagenome assembly.}, journal = {GigaScience}, volume = {11}, number = {}, pages = {}, pmid = {35579554}, issn = {2047-217X}, mesh = {High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Sequence Analysis, DNA/methods ; }, abstract = {BACKGROUND: Metagenomic assembly using high-throughput sequencing data is a powerful method to construct microbial genomes in environmental samples without cultivation. However, metagenomic assembly, especially when only short reads are available, is a complex and challenging task because mixed genomes of multiple microorganisms constitute the metagenome. Although long read sequencing technologies have been developed and have begun to be used for metagenomic assembly, many metagenomic studies have been performed based on short reads because the generation of long reads requires higher sequencing cost than short reads.

RESULTS: In this study, we present a new method called PLR-GEN. It creates pseudo-long reads from metagenomic short reads based on given reference genome sequences by considering small sequence variations existing in individual genomes of the same or different species. When applied to a mock community data set in the Human Microbiome Project, PLR-GEN dramatically extended short reads in length of 101 bp to pseudo-long reads with N50 of 33 Kbp and 0.4% error rate. The use of these pseudo-long reads generated by PLR-GEN resulted in an obvious improvement of metagenomic assembly in terms of the number of sequences, assembly contiguity, and prediction of species and genes.

CONCLUSIONS: PLR-GEN can be used to generate artificial long read sequences without spending extra sequencing cost, thus aiding various studies using metagenomes.}, } @article {pmid35579551, year = {2022}, author = {Schriml, LM}, title = {A decade of GigaScience: 10 years of the evolving genomic and biomedical standards landscape.}, journal = {GigaScience}, volume = {11}, number = {}, pages = {}, pmid = {35579551}, issn = {2047-217X}, support = {U41 HG008735/HG/NHGRI NIH HHS/United States ; }, mesh = {*Biomedical Research ; *Genomics ; Metagenomics ; Reference Standards ; }, abstract = {Standardization of omics data drives FAIR data practices through community-built genomic data standards and biomedical ontologies. Use of standards has progressed from a foreign concept to a sought-after solution, moving from efforts to coordinate data within individual research projects to research communities coming together to identify solutions to common challenges. Today we are seeing the benefits of this multidecade groundswell to coordinate, exchange, and reuse data; to compare data across studies; and to integrate data across previously siloed resources.}, } @article {pmid35579443, year = {2022}, author = {Bommana, S and Richards, G and Kama, M and Kodimerla, R and Jijakli, K and Read, TD and Dean, D}, title = {Metagenomic Shotgun Sequencing of Endocervical, Vaginal, and Rectal Samples among Fijian Women with and without Chlamydia trachomatis Reveals Disparate Microbial Populations and Function across Anatomic Sites: a Pilot Study.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0010522}, pmid = {35579443}, issn = {2165-0497}, support = {R01 AI151075/AI/NIAID NIH HHS/United States ; }, mesh = {*Chlamydia Infections/microbiology ; Chlamydia trachomatis ; Female ; Humans ; Pilot Projects ; Prospective Studies ; RNA, Ribosomal, 16S ; Rectum ; *Sexually Transmitted Diseases/microbiology ; Vagina/microbiology ; *Vaginosis, Bacterial/microbiology ; }, abstract = {Chlamydia trachomatis is a sexually transmitted pathogen and a global public health concern. Little is known about the microbial composition and function across endocervical, vaginal, and rectal microbiomes in the context of C. trachomatis infection. We evaluated the microbiomes of 10 age-matched high-risk Fijian women with and without C. trachomatis using metagenomic shotgun sequencing (MSS). Lactobacillus iners and Lactobacillus crispatus dominated the vagina and endocervix of uninfected women. Species often found in higher relative abundance in bacterial vaginosis (BV)-Mageeibacillus indolicus, Prevotella spp., Sneathia spp., Gardnerella vaginalis, and Veillonellaceae spp.-were dominant in C. trachomatis-infected women. This combination of BV pathogens was unique to Pacific Islanders compared to previously studied groups. The C. trachomatis-infected endocervix had a higher diversity of microbiota and microbial profiles that were somewhat different from those of the vagina. However, community state type III (CST-III) and CST-IV predominated, reflecting pathogenic microbiota regardless of C. trachomatis infection status. Rectal microbiomes were dominated by Prevotella and Bacteroides, although four women had unique microbiomes with Gardnerella, Akkermansia, Bifidobacterium, and Brachyspira. A high level of microbial similarity across microbiomes in two C. trachomatis-infected women suggested intragenitorectal transmission. A number of metabolic pathways in the endocervix, driven by BV pathogens and C. trachomatis to meet nutritional requirements for survival/growth, 5-fold higher than that in the vagina indicated that endocervical microbial functions are likely more diverse and complex than those in the vagina. Our novel findings provide the impetus for larger prospective studies to interrogate microbial/microbiome interactions that promote C. trachomatis infection and better define the unique genitorectal microbiomes of Pacific Islanders. IMPORTANCE Chlamydia trachomatis is the primary cause of bacterial sexually transmitted infections worldwide, with a disturbing increase in annual rates. While there is a plethora of data on healthy and pathogenic vaginal microbiomes-defining microbial profiles and associations with sexually transmitted infections (STIs)-far fewer studies have similarly examined the endocervix or rectum. Further, vulnerable populations, such as Pacific Islanders, remain underrepresented in research. We investigated the microbial composition, structure, and function of these anatomic microbiomes using metagenomic shotgun sequencing among a Fijian cohort. We found, primarily among C. trachomatis-infected women, unique microbial profiles in endocervical, vaginal, and rectal microbiomes with an increased diversity and more complex microbial pathways in endocervical than vaginal microbiomes. Similarities in microbiome composition across sites for some women suggested intragenitorectal transmission. These novel insights into genitorectal microbiomes and their purported function require prospective studies to better define Pacific Islander microbiomes and microbial/microbiome interactions that promote C. trachomatis infection.}, } @article {pmid35579429, year = {2022}, author = {Devi, P and Maurya, R and Mehta, P and Shamim, U and Yadav, A and Chattopadhyay, P and Kanakan, A and Khare, K and Vasudevan, JS and Sahni, S and Mishra, P and Tyagi, A and Jha, S and Budhiraja, S and Tarai, B and Pandey, R}, title = {Increased Abundance of Achromobacter xylosoxidans and Bacillus cereus in Upper Airway Transcriptionally Active Microbiome of COVID-19 Mortality Patients Indicates Role of Co-Infections in Disease Severity and Outcome.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0231121}, pmid = {35579429}, issn = {2165-0497}, mesh = {*Achromobacter denitrificans/genetics ; Bacillus cereus ; *COVID-19 ; *Coinfection ; Humans ; *Microbiota/genetics ; Phylogeny ; Prospective Studies ; SARS-CoV-2/genetics ; Severity of Illness Index ; }, abstract = {The modulators of severe COVID-19 have emerged as the most intriguing features of SARS-CoV-2 pathogenesis. This is especially true as we are encountering variants of concern (VOC) with increased transmissibility and vaccination breakthroughs. Microbial co-infections are being investigated as one of the crucial factors for exacerbation of disease severity and complications of COVID-19. A key question remains whether early transcriptionally active microbial signature/s in COVID-19 patients can provide a window for future disease severity susceptibility and outcome? Using complementary metagenomics sequencing approaches, respiratory virus oligo panel (RVOP) and Holo-seq, our study highlights the possible functional role of nasopharyngeal early resident transcriptionally active microbes in modulating disease severity, within recovered patients with sub-phenotypes (mild, moderate, severe) and mortality. The integrative analysis combines patients' clinical parameters, SARS-CoV-2 phylogenetic analysis, microbial differential composition, and their functional role. The clinical sub-phenotypes analysis led to the identification of transcriptionally active bacterial species associated with disease severity. We found significant transcript abundance of Achromobacter xylosoxidans and Bacillus cereus in the mortality, Leptotrichia buccalis in the severe, Veillonella parvula in the moderate, and Actinomyces meyeri and Halomonas sp. in the mild COVID-19 patients. Additionally, the metabolic pathways, distinguishing the microbial functional signatures between the clinical sub-phenotypes, were also identified. We report a plausible mechanism wherein the increased transcriptionally active bacterial isolates might contribute to enhanced inflammatory response and co-infections that could modulate the disease severity in these groups. Current study provides an opportunity for potentially using these bacterial species for screening and identifying COVID-19 patient sub-groups with severe disease outcome and priority medical care. IMPORTANCE COVID-19 is invariably a disease of diverse clinical manifestation, with multiple facets involved in modulating the progression and outcome. In this regard, we investigated the role of transcriptionally active microbial co-infections as possible modulators of disease pathology in hospital admitted SARS-CoV-2 infected patients. Specifically, can there be early nasopharyngeal microbial signatures indicative of prospective disease severity? Based on disease severity symptoms, the patients were segregated into clinical sub-phenotypes: mild, moderate, severe (recovered), and mortality. We identified significant presence of transcriptionally active isolates, Achromobacter xylosoxidans and Bacillus cereus in the mortality patients. Importantly, the bacterial species might contribute toward enhancing the inflammatory responses as well as reported to be resistant to common antibiotic therapy, which together hold potential to alter the disease severity and outcome.}, } @article {pmid35579058, year = {2022}, author = {Tanabe, TS and Dahl, C}, title = {HMS-S-S: A tool for the identification of Sulphur metabolism-related genes and analysis of operon structures in genome and metagenome assemblies.}, journal = {Molecular ecology resources}, volume = {22}, number = {7}, pages = {2758-2774}, doi = {10.1111/1755-0998.13642}, pmid = {35579058}, issn = {1755-0998}, support = {//Studienstiftung des Deutschen Volkes/ ; Da 351/13-1//Deutsche Forschungsgemeinschaft/ ; }, mesh = {*Metagenome ; Operon ; *Sulfur/metabolism ; Sulfur Compounds ; Thiosulfates/metabolism ; }, abstract = {Sulphur compounds are used in a variety of biological processes including respiration and photosynthesis. Sulphide and sulphur compounds of intermediary oxidation state can serve as electron donors for lithotrophic growth while sulphate, thiosulphate and sulphur are used as electron acceptors in anaerobic respiration. The biochemistry underlying the manifold transformations of inorganic sulphur compounds occurring in sulphur metabolizing prokaryotes is astonishingly complex and knowledge about it has immensely increased over the last years. The advent of next-generation sequencing approaches as well as the significant increase of data availability in public databases has driven focus of environmental microbiology to probing the metabolic capacity of microbial communities by analysis of this sequence data. To facilitate these analyses, we created HMS-S-S, a comprehensive equivalogous hidden Markov model (HMM)-supported tool. Protein sequences related to sulphur compound oxidation, reduction, transport and intracellular transfer are efficiently detected and related enzymes involved in dissimilatory sulphur oxidation as opposed to sulphur compound reduction can be confidently distinguished. HMM search results are coupled to corresponding genes, which allows analysis of co-occurrence, synteny and genomic neighbourhood. The HMMs were validated on an annotated test data set and by cross-validation. We also proved its performance by exploring meta-assembled genomes isolated from samples from environments with active sulphur cycling, including members of the cable bacteria, novel Acidobacteria and assemblies from a sulphur-rich glacier, and were able to replicate and extend previous reports.}, } @article {pmid35577084, year = {2022}, author = {Gao, M and Yang, J and Liu, Y and Zhang, J and Li, J and Liu, Y and Wu, B and Gu, L}, title = {Deep insights into the anaerobic co-digestion of waste activated sludge with concentrated leachate under different salinity stresses.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 1}, pages = {155922}, doi = {10.1016/j.scitotenv.2022.155922}, pmid = {35577084}, issn = {1879-1026}, mesh = {Anaerobiosis ; Bioreactors ; Digestion ; Methane/analysis ; Salt Stress ; *Sewage/chemistry ; *Wastewater/analysis ; }, abstract = {Treatment of high-salinity organic wastewater (e.g., concentrated leachate) is a major challenge. Anaerobic co-digestion can effectively treat high-salinity organic wastewater and recover energy. In this study, the concentrated landfill leachate and waste activated sludge (WAS) were anaerobic co-digested in the lab-scale continuous stirred tank reactors (CSTR) to understand their co-digestion performance under different salinity stresses. As revealed by the results, when the salinity was low (<10 g/L), the removal ratio of organic matter in the digester was kept at a high level (>91.3%), and the concentration of total volatile fatty acids (TVFAs) was low (<100 mg COD/L), indicating that the digester could operate efficiently and stably. However, when the salinity level was elevated from 10 g/L to 30 g/L, the removal ratio of organic matter in the digester decreased from ~91.3% to ~64.5%, the TVFAs continued to accumulate, the yields of biogas and methane also dropped sharply, and the performance of the digester decreased gradually. The results of microbial community and diversity analysis showed that there is limited adaptability of microbial community to high salinity in such process. Salinity could cause significant changes in the microbial community and diversity, thereby affecting the digestive performance. Metagenomic analysis showed that under high salinity conditions, the content of genes encoding hydrolase and methanogenic enzyme decreased, whereas the pathway of acetotrophic methanogenesis was weakened. Mechanism study showed that with the increase of salinity, the activity of microbial cells decreased, the structure of sludge flocs was damaged more significantly, and the extracellular polymeric substances (EPS) secreted by microbe increased continuously, which was used to resist the toxic effects of salinity stresses on microorganisms. The results of this study could provide certain theoretical guidance for anaerobic digestion under salinity stresses.}, } @article {pmid35576763, year = {2022}, author = {Calderón-Franco, D and Sarelse, R and Christou, S and Pronk, M and van Loosdrecht, MCM and Abeel, T and Weissbrodt, DG}, title = {Metagenomic profiling and transfer dynamics of antibiotic resistance determinants in a full-scale granular sludge wastewater treatment plant.}, journal = {Water research}, volume = {219}, number = {}, pages = {118571}, doi = {10.1016/j.watres.2022.118571}, pmid = {35576763}, issn = {1879-2448}, mesh = {Anti-Bacterial Agents/pharmacology ; DNA ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Metagenomics ; *Sewage ; Wastewater ; *Water Purification ; }, abstract = {In the One Health context, wastewater treatment plants (WWTPs) are central to safeguarding water resources. Nonetheless, many questions remain about their effectiveness in preventing antimicrobial resistance (AMR) dissemination. Most surveillance studies monitor the levels and removal of selected antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in intracellular DNA (iDNA) extracted from WWTP influents and effluents. The role of extracellular free DNA (exDNA) in wastewater is mostly overlooked. This study analyzed the transfer of ARGs and MGEs in a full-scale Nereda® reactor removing nutrients with aerobic granular sludge. We tracked the composition and fate of the iDNA and exDNA pools of influent, sludge, and effluent samples. Metagenomics was used to profile the microbiome, resistome, and mobilome signatures of iDNA and exDNA extracts. Selected ARGs and MGEs were analyzed by qPCR. From 2,840 ARGs identified, the genes arr-3 (2%), tetC (1.6%), sul1 (1.5%), oqxB (1.2%), and aph(3")-Ib (1.2%) were the most abundant among all sampling points and bioaggregates. Pseudomonas, Acinetobacter, Aeromonas, Acidovorax, Rhodoferax, and Streptomyces populations were the main potential hosts of ARGs in the sludge. In the effluent, 478 resistance determinants were detected, of which 89% were from exDNA potentially released by cell lysis during aeration in the reactor. MGEs and multiple ARGs were co-localized on the same extracellular genetic contigs. Total intracellular ARGs decreased 3-42% due to wastewater treatment. However, the ermB and sul1 genes increased by 2 and 1 log gene copies mL[-1], respectively, in exDNA from influent to effluent. The exDNA fractions need to be considered in AMR surveillance, risk assessment, and mitigation strategies.}, } @article {pmid35576553, year = {2022}, author = {Zhao, F and Lauder, K and Liu, S and Finnigan, JD and Charnock, SBR and Charnock, SJ and Castagnolo, D}, title = {Chemoenzymatic Cascades for the Enantioselective Synthesis of β-Hydroxysulfides Bearing a Stereocentre at the C-O or C-S Bond by Ketoreductases.}, journal = {Angewandte Chemie (International ed. in English)}, volume = {61}, number = {31}, pages = {e202202363}, doi = {10.1002/anie.202202363}, pmid = {35576553}, issn = {1521-3773}, support = {BB/M016218/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Alcohols/chemistry ; Biocatalysis ; Catalysis ; Kinetics ; Stereoisomerism ; }, abstract = {Chiral β-hydroxysulfides are an important class of organic compounds which find broad application in organic and pharmaceutical chemistry. Herein we describe the development of novel biocatalytic and chemoenzymatic methods for the enantioselective synthesis of β-hydroxysulfides by exploiting ketoreductase (KRED) enzymes. Four KREDs were discovered from a pool of 384 enzymes identified and isolated through a metagenomic approach. KRED311 and KRED349 catalysed the synthesis of β-hydroxysulfides bearing a stereocentre at the C-O bond with opposite absolute configurations and excellent ee values by novel chemoenzymatic and biocatalytic-chemical-biocatalytic (bio-chem-bio) cascades starting from commercially available thiophenols/thiols and α-haloketones/alcohols. KRED253 and KRED384 catalysed the enantioselective synthesis of β-hydroxysulfides bearing a stereocentre at the C-S bond with opposite enantioselectivities by dynamic kinetic resolution (DKR) of racemic α-thioaldehydes.}, } @article {pmid35575591, year = {2022}, author = {Bennett, AC and Murugapiran, SK and Kees, ED and Sauer, HM and Hamilton, TL}, title = {Temperature and Geographic Location Impact the Distribution and Diversity of Photoautotrophic Gene Variants in Alkaline Yellowstone Hot Springs.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0146521}, pmid = {35575591}, issn = {2165-0497}, mesh = {*Chloroflexi/genetics/metabolism ; *Cyanobacteria/genetics/metabolism ; *Hot Springs/microbiology ; Phototrophic Processes ; Phylogeny ; Temperature ; }, abstract = {Alkaline hot springs in Yellowstone National Park (YNP) provide a framework to study the relationship between photoautotrophs and temperature. Previous work has focused on studying how cyanobacteria (oxygenic phototrophs) vary with temperature, sulfide, and pH, but many questions remain regarding the ecophysiology of anoxygenic photosynthesis due to the taxonomic and metabolic diversity of these taxa. To this end, we examined the distribution of genes involved in phototrophy, carbon fixation, and nitrogen fixation in eight alkaline (pH 7.3-9.4) hot spring sites near the upper temperature limit of photosynthesis (71ºC) in YNP using metagenome sequencing. Based on genes encoding key reaction center proteins, geographic isolation plays a larger role than temperature in selecting for distinct phototrophic Chloroflexi, while genes typically associated with autotrophy in anoxygenic phototrophs, did not have distinct distributions with temperature. Additionally, we recovered Calvin cycle gene variants associated with Chloroflexi, an alternative carbon fixation pathway in anoxygenic photoautotrophs. Lastly, we recovered several abundant nitrogen fixation gene sequences associated with Roseiflexus, providing further evidence that genes involved in nitrogen fixation in Chloroflexi are more common than previously assumed. Together, our results add to the body of work on the distribution and functional potential of phototrophic bacteria in Yellowstone National Park hot springs and support the hypothesis that a combination of abiotic and biotic factors impact the distribution of phototrophic bacteria in hot springs. Future studies of isolates and metagenome assembled genomes (MAGs) from these data and others will further our understanding of the ecology and evolution of hot spring anoxygenic phototrophs. IMPORTANCE Photosynthetic bacteria in hot springs are of great importance to both microbial evolution and ecology. While a large body of work has focused on oxygenic photosynthesis in cyanobacteria in Mushroom and Octopus Springs in Yellowstone National Park, many questions remain regarding the metabolic potential and ecology of hot spring anoxygenic phototrophs. Anoxygenic phototrophs are metabolically and taxonomically diverse, and further investigations into their physiology will lead to a deeper understanding of microbial evolution and ecology of these taxa. Here, we have quantified the distribution of key genes involved in carbon and nitrogen metabolism in both oxygenic and anoxygenic phototrophs. Our results suggest that temperature >68ºC selects for distinct groups of cyanobacteria and that carbon fixation pathways associated with these taxa are likely subject to the same selective pressure. Additionally, our data suggest that phototrophic Chloroflexi genes and carbon fixation genes are largely influenced by local conditions as evidenced by our gene variant analysis. Lastly, we recovered several genes associated with potentially novel phototrophic Chloroflexi. Together, our results add to the body of work on hot springs in Yellowstone National Park and set the stage for future work on metagenome assembled genomes.}, } @article {pmid35575585, year = {2022}, author = {Kawser, AQMR and Foysal, MJ and Chua, EG and Ali, MH and Mannan, A and Siddik, MAB and Paul, SI and Rahman, MM and Tay, A}, title = {Microbiome data reveal significant differences in the bacterial diversity in freshwater rohu (Labeo rohita) across the supply chain in Dhaka, Bangladesh.}, journal = {Letters in applied microbiology}, volume = {75}, number = {4}, pages = {813-823}, pmid = {35575585}, issn = {1472-765X}, support = {//University of Western Australia/ ; }, mesh = {Animals ; Bacteria/genetics ; Bangladesh ; *Cyprinidae ; Fresh Water ; Humans ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The present study aimed to characterize and compare the skin and gut microbial communities of rohu at various post-harvest stages of consumption using quantitative real-time polymerase chain reaction and 16S rRNA-based amplicon sequencing. Real-time PCR amplification detected higher copy numbers for coliform bacteria-Escherichia coli, Salmonella enterica and Shigella spp. in the marketed fish-compared to fresh and frozen samples. The 16S rRNA data revealed higher alpha diversity measurements in the skin of fish from different retail markets of Dhaka city. Beta ordination revealed distinct clustering of bacterial OTUs for the skin and gut samples from three different groups. At the phylum level, Proteobacteria was most abundant in all groups except the Fusobacteria in the control fish gut. Although Aeromonas was found ubiquitous in all types of samples, diverse bacterial genera were identified in the marketed fish samples. Nonetheless, low species richness was observed for the frozen fish. Most of the differentially abundant bacteria in the skin samples of marketed fish are opportunistic human pathogens enriched at different stages of postharvest handling and processing. Therefore, considering the microbial contamination in the aquatic environment in Bangladesh, post-harvest handling should be performed with proper methods and care to minimize bacterial transmission into fish.}, } @article {pmid35575561, year = {2022}, author = {Beach, NK and Myers, KS and Donohue, TJ and Noguera, DR}, title = {Metagenomes from 25 Low-Abundance Microbes in a Partial Nitritation Anammox Microbiome.}, journal = {Microbiology resource announcements}, volume = {11}, number = {6}, pages = {e0021222}, pmid = {35575561}, issn = {2576-098X}, support = {CBET-1803055//National Science Foundation (NSF)/ ; DE-SC0018409//U.S. Department of Energy (DOE)/ ; }, abstract = {Microbial communities using anammox bacteria to remove nitrogen are increasingly important in wastewater treatment. We report on 25 metagenome-assembled genomes of low-abundance microbes from a partial nitritation anammox bioreactor system that have not been described previously. These data add to the body of information about this important wastewater treatment system.}, } @article {pmid35574962, year = {2022}, author = {Goh, CE and Bohn, B and Marotz, C and Molinsky, R and Roy, S and Paster, BJ and Chen, CY and Rosenbaum, M and Yuzefpolskaya, M and Colombo, PC and Desvarieux, M and Papapanou, PN and Jacobs, DR and Knight, R and Demmer, RT}, title = {Nitrite Generating and Depleting Capacity of the Oral Microbiome and Cardiometabolic Risk: Results from ORIGINS.}, journal = {Journal of the American Heart Association}, volume = {11}, number = {10}, pages = {e023038}, pmid = {35574962}, issn = {2047-9980}, support = {R01 DK102932/DK/NIDDK NIH HHS/United States ; R21 DE022422/DE/NIDCR NIH HHS/United States ; T32 HL007779/HL/NHLBI NIH HHS/United States ; R00 DE018739/DE/NIDCR NIH HHS/United States ; T32 HL007779/HL/NHLBI NIH HHS/United States ; }, mesh = {Adult ; Bacteria/genetics/metabolism ; *Cardiovascular Diseases/diagnosis/epidemiology/genetics ; Female ; Humans ; Male ; *Microbiota ; Nitrates/metabolism ; Nitric Oxide/metabolism ; Nitrites ; Nitrogen ; Nitrogen Dioxide/metabolism ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {Background The enterosalivary nitrate-nitrite-nitric oxide (NO3-NO2-NO) pathway generates NO following oral microbiota-mediated production of salivary nitrite, potentially linking the oral microbiota to reduced cardiometabolic risk. Nitrite depletion by oral bacteria may also be important for determining the net nitrite available systemically. We examine if higher abundance of oral microbial genes favoring increased oral nitrite generation and decreased nitrite depletion is associated with a better cardiometabolic profile cross-sectionally. Methods and Results This study includes 764 adults (mean [SD] age 32 [9] years, 71% women) enrolled in ORIGINS (Oral Infections, Glucose Intolerance, and Insulin Resistance Study). Microbial DNA from subgingival dental plaques underwent 16S rRNA gene sequencing; PICRUSt2 was used to estimate functional gene profiles. To represent the different components and pathways of nitrogen metabolism in bacteria, predicted gene abundances were operationalized to create summary scores by (1) bacterial nitrogen metabolic pathway or (2) biochemical product (NO2, NO, or ammonia [NH3]) formed by the action of the bacterial reductases encoded. Finally, nitrite generation-to-depletion ratios of gene abundances were created from the above summary scores. A composite cardiometabolic Z score was created from cardiometabolic risk variables, with higher scores associated with worse cardiometabolic health. We performed multivariable linear regression analysis with cardiometabolic Z score as the outcome and the gene abundance summary scores and ratios as predictor variables, adjusting for sex, age, race, and ethnicity in the simple adjusted model. A 1 SD higher NO versus NH3 summary ratio was inversely associated with a -0.10 (false discovery rate q=0.003) lower composite cardiometabolic Z score in simple adjusted models. Higher NH3 summary score (suggestive of nitrite depletion) was associated with higher cardiometabolic risk, with a 0.06 (false discovery rate q=0.04) higher composite cardiometabolic Z score. Conclusions Increased net capacity for nitrite generation versus depletion by oral bacteria, assessed through a metagenome estimation approach, is associated with lower levels of cardiometabolic risk.}, } @article {pmid35574681, year = {2022}, author = {Li, F and Jiang, L and Pan, S and Jiang, S and Fan, Y and Jiang, C and Gao, C and Leng, Y}, title = {Multi-omic Profiling Reveals that Intra-abdominal-Hypertension-Induced Intestinal Damage Can Be Prevented by Microbiome and Metabolic Modulations with 5-Hydroxyindoleacetic Acid as a Diagnostic Marker.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0120421}, pmid = {35574681}, issn = {2379-5077}, mesh = {Rats ; Animals ; *Intra-Abdominal Hypertension ; Hydroxyindoleacetic Acid ; Critical Illness ; Multiomics ; Tryptophan/pharmacology ; *Microbiota ; *Sepsis ; *Hypertension ; }, abstract = {Emerging evidence shows that modulation of the microbiome can suppress intra-abdominal hypertension (IAH)-induced intestinal barrier damage through the regulation of amino acid (AA) biosynthesis. Here, we investigated the protective effects of orally gavaged Lactobacillus acidophilus L-92 (L92) and a mixture of AA in rats with induced IAH. The results showed that both L92 and AA pretreatments effectively mitigated IAH-induced intestinal damage. Interestingly, L92 but not AA prevented metagenomic changes induced by IAH. Bacteroides fragilis, Bacteroides eggerthii, Bacteroides ovatus, Faecalibacterium prausnitzii, Prevotella, and extensively altered functional pathways were associated with L92-mediated host protection. Metabolomic profiling revealed that tryptophan metabolism was involved in both L92- and AA-mediated gut protection. The tryptophan metabolite 5-hydroxyindoleacetic acid (5-HIAA) is a sensitive biomarker for IAH in rats and patients with either gut-derived sepsis (n = 41) or all-source sepsis (n = 293). In conclusion, we show that microbiome and metabolic modulations can effectively prevent IAH-induced intestinal damage and that 5-HIAA is a potential metabolic marker for IAH and sepsis. IMPORTANCE Gut protection through modulation of the microbiome for critically ill patients has been gaining much attention recently. Intra-abdominal hypertension (IAH) is a prevailing clinical feature of acute gastrointestinal injuries in critically ill patients, characterized by nonspecific intestinal barrier damage. Prolonged IAH can induce or aggravate the development of sepsis and multiorgan dysfunctions. Therefore, the prevention of IAH-induced damage in rats through microbiome and metabolic interventions by commercially available L92 and AA treatments and the identification of 5-HIAA as an important marker for IAH/sepsis have important clinical implications for the treatment and early diagnosis of critically ill patients.}, } @article {pmid35573778, year = {2022}, author = {Guo, Y and Yang, Y and Xu, M and Shi, G and Zhou, J and Zhang, J and Li, H}, title = {Trends and Developments in the Detection of Pathogens in Central Nervous System Infections: A Bibliometric Study.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {856845}, pmid = {35573778}, issn = {2235-2988}, mesh = {Bibliometrics ; *Central Nervous System Infections/diagnosis ; *Communicable Diseases/diagnosis ; Humans ; Metagenome ; Metagenomics ; }, abstract = {INTRODUCTION: Rapid, sensitive, and specific laboratory assays are critical for the diagnosis and management of central nervous system (CNS) infections. The purpose of this study is to explore the intellectual landscape of research investigating methods for the detection of pathogens in patients with CNS infections and to identify the development trends and research frontier in this field.

METHODS: A bibliometric study is conducted by analyzing literature retrieved from the Web of Science (WoS) Core Collection Database for the years 2000 to 2021. CiteSpace software is used for bibliometric analysis and network visualization, including co-citation analysis of references, co-occurrence analysis of keywords, and cooperation network analysis of authors, institutions, and countries/regions.

RESULTS: A total of 2,282 publications are eventually screened, with an upward trend in the number of publications per year. The majority of papers are attributed to the disciplines of MICROBIOLOGY, INFECTIOUS DISEASES, IMMUNOLOGY, NEUROSCIENCES & NEUROLOGY, and VIROLOGY. The co-citation analysis of references shows that recent research has focused on the largest cluster "metagenomic next-generation sequencing"; the results of the analysis of the highest-cited publications and the citation burst of publications reveal that there is a strong interest stimulated in metagenomic next-generation sequencing. The co-occurrence analysis of keywords indicates that "infection", "pathogen", "diagnosis", "gene", "virus", "polymerase chain reaction", "cerebrospinal fluid", "epidemiology", and "metagenomic next-generation sequencing" are the main research priorities in the field of pathogen detection for CNS infections, and the keyword with the highest strength of burst is "metagenomic next-generation sequencing". Collaborative network analysis reveals that the USA, the Centers for Disease Control and Prevention of USA, and XIN WANG and JENNIFER DIEN BARD are the most influential country, institution, and researchers, respectively.

CONCLUSIONS: Exploring more advanced laboratory assays to improve the diagnostic accuracy of pathogens is essential for CNS infection research. Metagenomic next-generation sequencing is emerging as a novel useful unbiased approach for diagnosing infectious diseases of the CNS.}, } @article {pmid35573175, year = {2022}, author = {Ghosh, A and Saha, R and Bhadury, P}, title = {Metagenomic insights into surface water microbial communities of a South Asian mangrove ecosystem.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13169}, pmid = {35573175}, issn = {2167-8359}, mesh = {*Water ; Wetlands ; *Microbiota/genetics ; Metagenome/genetics ; Bacteria/genetics ; Firmicutes/genetics ; }, abstract = {Estuaries are one of the most productive ecosystems and their productivity is maintained by resident microbial communities. Recent alterations driven by climate change have further escalated these stressors leading to the propagation of traits such as antibiotic resistance and heavy metal resistance in microbial communities. Surface water samples from eleven stations along the Thakuran and Matla estuaries of the Sundarbans Biosphere Reserve (SBR) of Sundarbans mangrove located in South Asia were sampled in monsoon (June) 2019 to elucidate resident microbial communities based on Nanopore sequencing. Metagenomic analyses revealed the widespread dominance of Proteobacteria across all the stations along with a high abundance of Firmicutes. Other phyla, including Euryarchaeota, Thaumarchaeota, Actinobacteria, Bacteroidetes and Cyanobacteria showed site-specific trends in abundance. Further taxonomic affiliations showed Gammaproteobacteria and Alphaproteobacteria to be dominant classes with high abundances of Bacilli in SBR_Stn58 and SBR_Stn113. Among the eukaryotic communities, the most abundant classes included Prasinophyceae, Saccharyomycetes and Sardariomycetes. Functional annotation showed metabolic activities such as carbohydrate, amino acid, nitrogen and phosphorus metabolisms to be uniformly distributed across all the studied stations. Pathways such as stress response, sulphur metabolism and motility-associated genes appeared in low abundances in SBR. Functional traits such as antibiotic resistance showed overwhelming dominance of genes involved in multidrug resistance along with widespread resistance towards commonly used antibiotics including Tetracycline, glycopeptide and aminoglycoside. Metal resistance genes including arsenic, nickel and copper were found in comparable abundances across the studied stations. The prevalence of ARG and MRG might indicate presence of pollutants and hint toward deteriorating ecosystem health status of Sundarbans mangrove.}, } @article {pmid35572710, year = {2022}, author = {Yu, Y and Li, L and Xu, Y and Li, H and Yu, Y and Xu, Z}, title = {Metagenomics Reveals the Microbial Community Responsible for Producing Biogenic Amines During Mustard [Brassica juncea (L.)] Fermentation.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {824644}, pmid = {35572710}, issn = {1664-302X}, abstract = {Biogenic amines (BAs) are considered potential hazards produced during fermented food processing, and the production of BAs is closely related to microbial metabolism. In this work, the changes of BA content were analyzed during mustard fermentation, and microbes and gene abundance responsible for producing BAs were revealed by metagenomic analyses. The results showed that cadaverine, putrescine, tyramine, and histamine were generated during mustard fermentation, which mainly accumulate in the first 6 days of fermentation. According to the metagenome sequencing, the predominant genus was Bacillus (64.78%), followed by Lactobacillus (11.67%), Weissella (8.88%), and Leuconostoc (1.71%) in the initial fermentation stage (second day), while Lactobacillus (76.03%) became the most dominant genus in the late stage. In addition, the gene abundance of BA production enzymes was the highest in the second day and decreased continuously as fermentation progressed. By tracking the source of the enzyme in the KEGG database, both Bacillus and Delftia closely correlated to the generation of putrescine. Besides, Bacillus also correlated to the generation of tyramine and spermidine, and Delftia also correlated to the generation of cadaverine and spermine. In the processes of fermentation, the pH of fermented mustard showed slower decrease compared with other similar fermented vegetables, which may allow Bacillus to grow at high levels before the pH <4. This study reveals the change of BA content and microbes involved in BA formation during mustard fermentation.}, } @article {pmid35572705, year = {2022}, author = {Kharnaior, P and Tamang, JP}, title = {Metagenomic-Metabolomic Mining of Kinema, a Naturally Fermented Soybean Food of the Eastern Himalayas.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {868383}, pmid = {35572705}, issn = {1664-302X}, abstract = {Kinema is a popular sticky fermented soybean food of the Eastern Himalayan regions of North East India, east Nepal, and south Bhutan. We hypothesized that some dominant bacteria in kinema may contribute to the formation of targeted and non-targeted metabolites for health benefits; hence, we studied the microbiome-metabolite mining of kinema. A total of 1,394,094,912 bp with an average of 464,698,304 ± 120,720,392 bp was generated from kinema metagenome, which resulted in the identification of 47 phyla, 331 families, 709 genera, and 1,560 species. Bacteria (97.78%) were the most abundant domain with the remaining domains of viruses, eukaryote, and archaea. Firmicutes (93.36%) was the most abundant phylum with 280 species of Bacillus, among which Bacillus subtilis was the most dominant species in kinema followed by B. glycinifermentans, B. cereus, B. licheniformis, B. thermoamylovorans, B. coagulans, B. circulans, B. paralicheniformis, and Brevibacillus borstelensis. Predictive metabolic pathways revealed the abundance of genes associated with metabolism (60.66%), resulting in 216 sub-pathways. A total of 361 metabolites were identified by metabolomic analysis (liquid chromatography-mass spectrophotometry, LC-MS). The presence of metabolites, such as chrysin, swainsonine, and 3-hydroxy-L-kynurenine (anticancer activity) and benzimidazole (antimicrobial, anticancer, and anti-HIV activities), and compounds with immunomodulatory effects in kinema supports its therapeutic potential. The correlation between the abundant species of Bacillus and primary and secondary metabolites was constructed with a bivariate result. This study proves that Bacillus spp. contribute to the formation of many targeted and untargeted metabolites in kinema for health-promoting benefits.}, } @article {pmid35572506, year = {2022}, author = {Porto, BN}, title = {Insights Into the Role of the Lung Virome During Respiratory Viral Infections.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {885341}, pmid = {35572506}, issn = {1664-3224}, mesh = {Child ; Humans ; Lung ; Metagenomics ; Virome ; *Virus Diseases ; *Viruses/genetics ; }, abstract = {The virome constitutes the viral component of the microbiome and it consists of the genomes of all the viruses that inhabit a particular region of the human body, including those that cause acute, persistent or latent infection, and retroviral elements integrated to host chromosomes. The human virome is composed by eukaryotic viruses, bacteriophages and archaeal viruses. The understanding of the virome composition and role on human health has been delayed by the absence of specific tools and techniques to accurately characterize viruses. However, more recently, advanced methods for viral diagnostics, such as deep sequencing and metagenomics, have allowed a better understanding of the diverse viral species present in the human body. Previous studies have shown that the respiratory virome modulates the host immunity and that, since childhood, the human lung is populated by viruses for whom there is no disease association. Whether these viruses are potentially pathogenic and the reason for their persistence remain elusive. Increased respiratory viral load can cause exacerbation of chronic pulmonary diseases, including COPD, cystic fibrosis, and asthma. Moreover, the presence of resident viral populations may contribute to the pathogenesis of community-acquired respiratory virus infections. In this mini review, I will discuss the recent progress on our understanding of the human lung virome and summarize the up-to-date knowledge on the relationships among community-acquired respiratory viruses, the lung virome and the immune response to better understand disease pathophysiology and the factors that may lead to viral persistence.}, } @article {pmid35572414, year = {2022}, author = {Han, D and Diao, Z and Lai, H and Han, Y and Xie, J and Zhang, R and Li, J}, title = {Multilaboratory assessment of metagenomic next-generation sequencing for unbiased microbe detection.}, journal = {Journal of advanced research}, volume = {38}, number = {}, pages = {213-222}, pmid = {35572414}, issn = {2090-1224}, mesh = {High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; *Metagenomics/methods ; Reproducibility of Results ; *Staphylococcus aureus ; }, abstract = {INTRODUCTION: Metagenomic next-generation sequencing (mNGS) assay for detecting infectious agents is now in the stage of being translated into clinical practice. With no approved approaches or guidelines available, laboratories adopt customized mNGS assays to detect clinical samples. However, the accuracy, reliability, and problems of these routinely implemented assays are not clear.

OBJECTIVES: To evaluate the performance of 90 mNGS laboratories under routine testing conditions through analyzing identical samples.

METHODS: Eleven microbial communities were generated using 15 quantitative microbial suspensions. They were used as reference materials to evaluate the false negatives and false positives of participating mNGS protocols, as well as the ability to distinguish genetically similar organisms and to identify true pathogens from other microbes based on fictitious case reports.

RESULTS: High interlaboratory variability was found in the identification and the quantitative reads per million reads (RPM) values of each microbe in the samples, especially when testing microbes present at low concentrations (1 × 10[3] cell/ml or less). 42.2% (38/90) of the laboratories reported unexpected microbes (i.e. false positive problem). Only 56.7% (51/90) to 83.3% (75/90) of the laboratories showed a sufficient ability to obtain clear etiological diagnoses for three simulated cases combined with patient information. The analysis of the performance of mNGS in distinguishing genetically similar organisms in three samples revealed that only 56.6% to 63.0% of the laboratories recovered RPM ratios (RPM S. aureus /RPM S. epidermidis) within the range of a 2-fold change of the initial input ratios (indicating a relatively low level of bias).

CONCLUSION: The high interlaboratory variability found in both identifying microbes and distinguishing true pathogens emphasizes the urgent need for improving the accuracy and comparability of the results generated across different mNGS laboratories, especially in the detection of low-microbial-biomass samples.}, } @article {pmid35572413, year = {2022}, author = {Zhang, J and Shen, N and Li, C and Xiang, X and Liu, G and Gui, Y and Patev, S and Hibbett, DS and Barry, K and Andreopoulos, W and Lipzen, A and Riley, R and He, G and Yan, M and Grigoriev, IV and Shan Kwan, H and Kit Cheung, M and Bian, Y and Xiao, Y}, title = {Population genomics provides insights into the genetic basis of adaptive evolution in the mushroom-forming fungus Lentinula edodes.}, journal = {Journal of advanced research}, volume = {38}, number = {}, pages = {91-106}, pmid = {35572413}, issn = {2090-1224}, mesh = {*Agaricales/genetics ; Genome ; Genome-Wide Association Study ; Metagenomics ; *Shiitake Mushrooms/genetics ; }, abstract = {INTRODUCTION: Mushroom-forming fungi comprise diverse species that develop complex multicellular structures. In cultivated species, both ecological adaptation and artificial selection have driven genome evolution. However, little is known about the connections among genotype, phenotype and adaptation in mushroom-forming fungi.

OBJECTIVES: This study aimed to (1) uncover the population structure and demographic history of Lentinula edodes, (2) dissect the genetic basis of adaptive evolution in L. edodes, and (3) determine if genes related to fruiting body development are involved in adaptive evolution.

METHODS: We analyzed genomes and fruiting body-related traits (FBRTs) in 133 L. edodes strains and conducted RNA-seq analysis of fruiting body development in the YS69 strain. Combined methods of genomic scan for divergence, genome-wide association studies (GWAS), and RNA-seq were used to dissect the genetic basis of adaptive evolution.

RESULTS: We detected three distinct subgroups of L. edodes via single nucleotide polymorphisms, which showed robust phenotypic and temperature response differentiation and correlation with geographical distribution. Demographic history inference suggests that the subgroups diverged 36,871 generations ago. Moreover, L. edodes cultivars in China may have originated from the vicinity of Northeast China. A total of 942 genes were found to be related to genetic divergence by genomic scan, and 719 genes were identified to be candidates underlying FBRTs by GWAS. Integrating results of genomic scan and GWAS, 80 genes were detected to be related to phenotypic differentiation. A total of 364 genes related to fruiting body development were involved in genetic divergence and phenotypic differentiation.

CONCLUSION: Adaptation to the local environment, especially temperature, triggered genetic divergence and phenotypic differentiation of L. edodes. A general model for genetic divergence and phenotypic differentiation during adaptive evolution in L. edodes, which involves in signal perception and transduction, transcriptional regulation, and fruiting body morphogenesis, was also integrated here.}, } @article {pmid35572406, year = {2022}, author = {Diao, Z and Han, D and Zhang, R and Li, J}, title = {Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections.}, journal = {Journal of advanced research}, volume = {38}, number = {}, pages = {201-212}, pmid = {35572406}, issn = {2090-1224}, mesh = {High-Throughput Nucleotide Sequencing ; Humans ; Metagenome ; Metagenomics ; *Microbiota/genetics ; *Respiratory Tract Infections/diagnosis ; }, abstract = {Metagenomic next-generation sequencing (mNGS) has changed the diagnosis landscape of lower respiratory tract infections (LRIs). With the development of newer sequencing assays, it is now possible to assess all microorganisms in a sample using a single mNGS analysis. The applications of mNGS for LRIs span a wide range of areas including LRI diagnosis, airway microbiome analyses, human host response analyses, and prediction of drug resistance. mNGS is currently in an exciting transitional period; however, before implementation in a clinical setting, there are several barriers to overcome, such as the depletion of human nucleic acid, discrimination between colonization and infection, high costs, and so on. Aim of Review: In this review, we summarize the potential applications and challenges of mNGS in the diagnosis of LRIs to promote the integration of mNGS into the management of patients with respiratory tract infections in a clinical setting. Key Scientific Concepts of Review: Once its analytical validation, clinical validation and clinical utility been demonstrated, mNGS will become an important tool in the field of infectious disease diagnosis.}, } @article {pmid35571398, year = {2022}, author = {Peng, YC and Xu, JX and Zeng, CF and Zhao, XH and You, XM and Xu, PP and Li, LQ and Qi, LN}, title = {Operable hepatitis B virus-related hepatocellular carcinoma: gut microbiota profile of patients at different ages.}, journal = {Annals of translational medicine}, volume = {10}, number = {8}, pages = {477}, pmid = {35571398}, issn = {2305-5839}, abstract = {BACKGROUND: Age was important prognostic factors for operable hepatocellular carcinoma patients. The aim of the present study was to assess the difference in gut microbiota in patients with operable hepatitis B virus-related hepatocellular carcinoma (HBV-HCC) at different ages ; to investigate the features of the microbiota and its function associated with different ages; to provide a preliminary look at effects of the gut microbiota dimension on prognostic.

METHODS: From September 2020 to May 2021, patients with HBV-HCC were able to undergo liver resection and were recruited consecutively and divided into the younger age group (age <45 years) (Y.AG) (n=20), middle age group (age from 45 to 65 years) (M.AG) (n=13) 45-65 years, and older age group (age >65 years) (O.AG) (n=20). The relationships between gut microbiota and different ages were explored using 16S rRNA gene sequencing data. PICRUST2 was used to examine the metagenomic data in PHLF patients. Fisher's exact and Mann-Whitney U-test were used for the data analysis.

RESULTS: Pairwise comparison between the three groups showed that the α-diversity of Y.AG was significantly higher than that of O.AG (ACE Index, P=0.017; chao1 Index, P=0.031; observed_species Index, P=0.011; and goods_coverage Index, P=0.041). The β-diversity in the 3 groups differed significantly (stress =0.100), while the composition (β-diversity) differed significantly between the Y.AG and the M.AG (stress =0.090), the M.AG and the O.AG (stress =0.095), and the Y.AG and the O.AG (stress =0.099). At the genus level, 7 bacterial genera were significantly enriched in the O.AG compared with the Y.AG, of which Streptococcus, Blautia, Erysipelotrichaceae_UCG-003, and Fusicatenibacter represented the major variances in O.AG microbiomes. Eleven genera were significantly increased in the O.AG, of which Prevotella, Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Ruminiclostridium, and Phascolarctobacterium represented the major variances in the O.AG. The Y.AG and the O.AG were predicted by PICRUSt2 analysis, which found 72 pathways related to differential gut microbiome at the genus level. Redundancy analysis showed that 7 environmental factors were significantly correlated with intestinal microorganisms, especially in the Y.AG compared with the O.AG.

CONCLUSIONS: Analysis of gut microbiota characteristics in patients of different ages could ultimately contribute to the development of novel avenues for the treatment of HCC at different ages.}, } @article {pmid35571385, year = {2022}, author = {Tang, C and He, S and Wang, N and Chen, L}, title = {A case report and literature review: diagnosis and treatment of human immunodeficiency virus coinfected with visceral leishmania by metagenomic next-generation sequencing in China.}, journal = {Annals of translational medicine}, volume = {10}, number = {8}, pages = {497}, pmid = {35571385}, issn = {2305-5839}, abstract = {BACKGROUND: human immunodeficiency virus (HIV) can disrupt the body's immune system, increasing the chance of various opportunistic infections. The risk of misdiagnosis and underdiagnosis is high for HIV and Leishmania coinfection. Visceral leishmaniasis (VL) has become a significant opportunistic infection in HIV type 1 (HIV-1)-infected patients in the epidemic region. Co-infection is difficult to diagnose, especially in non-endemic areas.

CASE DESCRIPTION: This study presents a case of VL in a middle-aged male patient with HIV coinfection, where the diagnosis was circuitous and complex. The patient was a 44-year-old male who was hospitalized due to fever. We considered common pathogen infection or hemophagocytic syndrome, so we did various etiological examinations and bone marrow biopsy smears, but no positive pathogens were found. Then we used a variety of empirical treatment, but the patient's temperature did not drop significantly. After the final diagnosis of VL using metagenomic next-generation sequencing (mNGS), we read the bone marrow smear and biopsy specimens again, and ultimately the Leishman-Donovan body and tissue intracellular pathogens were found. The patient responded well to treatment with sodium stibogluconate (SSG), his temperature gradually recovered from hyperthermia to normal, liver and spleen size gradually decreased, hemoglobin and platelet count rebounded, and weight increased by 1.5 kg after discharge from the hospital. We hope to deepen clinicians' understanding of mNGS for VL diagnosis and provide a review of the literature.

CONCLUSIONS: For patients with HIV coinfection, mNGS-a test that can detect multiple pathogens simultaneously-can be used routinely when multiple pathogen tests showed no positive results, multiple empiric anti-infective therapies failed, and hospital technology and the patient's economy are adequate. While giving highly active antiretroviral therapy (HAART), liposomal amphotericin B (L-AMB) is highly recommended because of its better efficacy and lower side effects. Not only is the treatment of leishmaniasis critical but also follow-up at a later stage is essential. After discharged, the patient had no significant discomfort and no increase in body temperature, his hemoglobin and platelets increased further. He demonstrated a further reduction in liver and spleen size and a weight gain of 1.5 kg.}, } @article {pmid35571306, year = {2022}, author = {Deo, PN and Deshmukh, RS}, title = {Oral microbiome research - A Beginner's glossary.}, journal = {Journal of oral and maxillofacial pathology : JOMFP}, volume = {26}, number = {1}, pages = {87-92}, pmid = {35571306}, issn = {0973-029X}, abstract = {Oral microbiome plays a key role in the etiology of oral diseases and is linked to many diseases in other parts of the body as well. This makes the oral microbiome an area of interest for researchers globally. A meticulous planning of the research project is the first and most crucial step while conducting an oral microbiome study. For beginners in this field, it is essential to be familiar with the terminologies used in oral microbiome research for a better understanding. The purpose of this article is to familiarize new researchers to the frequently used terms for the field of oral microbiome research.}, } @article {pmid35570277, year = {2022}, author = {Zeng, J and Yang, Z and Guo, W and Wang, X and Yang, S and Shen, Q and Wang, H and Zhang, W}, title = {Identification and genome characterization of novel parechovirus sequences from Hipposideros armiger in China.}, journal = {Virology journal}, volume = {19}, number = {1}, pages = {80}, pmid = {35570277}, issn = {1743-422X}, mesh = {5' Untranslated Regions ; Animals ; China ; *Chiroptera ; Genome, Viral ; Humans ; *Parechovirus/genetics ; Phylogeny ; *Picornaviridae Infections/veterinary ; }, abstract = {BACKGROUND: Bats were identified as a natural reservoir of emerging and re-emerging infectious pathogens threatening human health and life.

METHODS: This study collected 21 fecal samples of Hipposideros armiger in Mengla County of Xishuangbanna Prefecture Yunnan Province to combine one pool for viral metagenomic sequencing.

RESULTS: Two nearly complete genomes of parechoviruses, BPeV11 and BPeV20, were sequenced. Genome analysis revealed that BPeV11 and BPeV20 follow a 3-3-4 genome layout: 5' UTR-VP0-VP3-VP1-2A-2B-2C-3A-3B-3C-3D-3' UTR. The prevalence of BPev11 and BPev20 by Nested-PCR showed that 1 of 21 fecal samples was positive. Based on amino acid identity comparison and phylogenetic analysis of P1, 2C, and 3D, BPeV11 and BPeV20 were closely related to but distinct from FPeVs.

CONCLUSION: It was probably proposed to be a novel species in the genus Parechovirus of the family Picornaviridae. The isolation of BPev11 and BPev20 from H. armiger in China is the first complete genome of parechovirus isolations from bat feces of the genus Hipposideros.}, } @article {pmid35569576, year = {2022}, author = {Chafale, A and Kapley, A}, title = {Biosurfactants as microbial bioactive compounds in microbial enhanced oil recovery.}, journal = {Journal of biotechnology}, volume = {352}, number = {}, pages = {1-15}, doi = {10.1016/j.jbiotec.2022.05.003}, pmid = {35569576}, issn = {1873-4863}, mesh = {Oil and Gas Fields ; Oils ; *Petroleum/metabolism ; Reproducibility of Results ; *Sewage ; Surface-Active Agents/chemistry ; }, abstract = {Fossil fuels such as petroleum resources continue to be a significant fraction of the energy portfolio. Oil sludge or slops have become an unavoidable waste in the petroleum industries, and their improper disposal measures have led to environmental pollution. Various conventional and traditional practices for disposal and recovery are practiced, but the efficiency of MEOR has led to more promising and efficient ways to recover oil from oil reservoirs and waste sludges. Among the microbial bioactives, biosurfactants are the key players in the whole process. Although, MEOR using biosurfactants has been largely practiced for recovering oil from oil reservoirs, microbial metabolites are also proving to be effective in recovering oil from the waste oily sludges generated as a part of the petroleum production cycle. MEOR stands out as a economically sound alternative over other conventional methods that require large capital investment, heavy energy consumption and varying recovery efficiency. This review describes the scope of MEOR to be useful in reducing and reusing the waste oily sludge accumulation that when untreated causes environmental pollution, allowing sustainable use of natural resources. However, lack of reproducibility at field scale, large scale production of bioactive compounds are the major reasons leading to its incompatibility. The review aims to address the gaps and possible strategies to help speed up the efficiency by thoroughly focusing on the biosurfactant mediated MEOR process dynamics and use of various non-renewable substrates as measure of waste utilization for the production of metabolites. The molecular makeup of these significant molecules after extracting them from the contaminated niche will help discover microbial diversity. Furthermore, the limitations to this biosurfactant assisted MEOR can be solved by using genomic and high throughput approaches to execute an economical implementation at field scale level.}, } @article {pmid35569105, year = {2022}, author = {Deng, X and Zhang, N and Li, Y and Zhu, C and Qu, B and Liu, H and Li, R and Bai, Y and Shen, Q and Falcao Salles, J}, title = {Bio-organic soil amendment promotes the suppression of Ralstonia solanacearum by inducing changes in the functionality and composition of rhizosphere bacterial communities.}, journal = {The New phytologist}, volume = {235}, number = {4}, pages = {1558-1574}, doi = {10.1111/nph.18221}, pmid = {35569105}, issn = {1469-8137}, mesh = {Bacteria/genetics ; Fertilizers ; Plant Diseases/microbiology ; *Ralstonia solanacearum ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; }, abstract = {Stimulating the development of soil suppressiveness against certain pathogens represents a sustainable solution toward reducing pesticide use in agriculture. However, understanding the dynamics of suppressiveness and the mechanisms leading to pathogen control remain largely elusive. Here, we investigated the mechanisms used by the rhizosphere microbiome induces bacterial wilt disease suppression in a long-term field experiment where continuous application of bio-organic fertilizers (BFs) triggered disease suppressiveness when compared to chemical fertilizer application. We further demonstrated in a glasshouse experiment that the suppressiveness of the rhizosphere bacterial communities was triggered mainly by changes in community composition rather than only by the abundance of the introduced biocontrol strain. Metagenomics approaches revealed that members of the families Sphingomonadaceae and Xanthomonadaceae with the ability to produce secondary metabolites were enriched in the BF plant rhizosphere but only upon pathogen invasion. We experimentally validated this observation by inoculating bacterial isolates belonging to the families Sphingomonadaceae and Xanthomonadaceae into conducive soil, which led to a significant reduction in pathogen abundance and increase in nonribosomal peptide synthetase gene abundance. We conclude that priming of the soil microbiome with BF amendment fostered reactive bacterial communities in the rhizosphere of tomato plants in response to biotic disturbance.}, } @article {pmid35568899, year = {2022}, author = {Kellock, M and Rahikainen, J and Borisova, AS and Voutilainen, S and Koivula, A and Kruus, K and Marjamaa, K}, title = {Inhibitory effect of lignin on the hydrolysis of xylan by thermophilic and thermolabile GH11 xylanases.}, journal = {Biotechnology for biofuels and bioproducts}, volume = {15}, number = {1}, pages = {49}, pmid = {35568899}, issn = {2731-3654}, support = {318890//Academy of Finland/ ; 318890//Academy of Finland/ ; 318890//Academy of Finland/ ; 222699//Seventh Framework Programme/ ; 222699//Seventh Framework Programme/ ; 222699//Seventh Framework Programme/ ; }, abstract = {BACKGROUND: Enzymatic hydrolysis of lignocellulosic biomass into platform sugars can be enhanced by the addition of accessory enzymes, such as xylanases. Lignin from steam pretreated biomasses is known to inhibit enzymes by non-productively binding enzymes and limiting access to cellulose. The effect of enzymatically isolated lignin on the hydrolysis of xylan by four glycoside hydrolase (GH) family 11 xylanases was studied. Two xylanases from the mesophilic Trichoderma reesei, TrXyn1, TrXyn2, and two forms of a thermostable metagenomic xylanase Xyl40 were compared.

RESULTS: Lignin isolated from steam pretreated spruce decreased the hydrolysis yields of xylan for all the xylanases at 40 and 50 °C. At elevated hydrolysis temperature of 50 °C, the least thermostable xylanase TrXyn1 was most inhibited by lignin and the most thermostable xylanase, the catalytic domain (CD) of Xyl40, was least inhibited by lignin. Enzyme activity and binding to lignin were studied after incubation of the xylanases with lignin for up to 24 h at 40 °C. All the studied xylanases bound to lignin, but the thermostable xylanases retained 22-39% of activity on the lignin surface for 24 h, whereas the mesophilic T. reesei xylanases become inactive. Removing of N-glycans from the catalytic domain of Xyl40 increased lignin inhibition in hydrolysis of xylan when compared to the glycosylated form. By comparing the 3D structures of these xylanases, features contributing to the increased thermal stability of Xyl40 were identified.

CONCLUSIONS: High thermal stability of xylanases Xyl40 and Xyl40-CD enabled the enzymes to remain partially active on the lignin surface. N-glycosylation of the catalytic domain of Xyl40 increased the lignin tolerance of the enzyme. Thermostability of Xyl40 was most likely contributed by a disulphide bond and salt bridge in the N-terminal and α-helix regions.}, } @article {pmid35568852, year = {2022}, author = {Keburiya, LK and Smolnikova, VY and Priputnevich, TV and Muravieva, VV and Gordeev, AB and Trofimov, DY and Shubina, ES and Kochetkova, TO and Rogacheva, MS and Kalinina, EA and Sukhikh, GT}, title = {Does the uterine microbiota affect the reproductive outcomes in women with recurrent implantation failures?.}, journal = {BMC women's health}, volume = {22}, number = {1}, pages = {168}, pmid = {35568852}, issn = {1472-6874}, mesh = {Embryo Implantation ; *Embryo Transfer ; Female ; Fertilization in Vitro ; Humans ; *Microbiota ; Pregnancy ; Pregnancy Rate ; }, abstract = {BACKGROUND: Inefficiency of in vitro fertilization (IVF) programs can be caused by implantation failures. The uterine microbiota can influence the implantation process. However, it still remains unclear whether opportunistic microorganisms detected in the endometrium have a negative impact on the implantation success. The aim of our study was to evaluate the influence of the uterine microbiota on the embryo implantation success in patients undergoing assisted reproductive technologies.

METHODS: The study included 130 women diagnosed with infertility. The patients were divided into three groups: group I included women with the first IVF attempt (n = 39); group II included patients with recurrent implantation failure following embryo transfer with ovarian stimulation (n = 27); group III consisted of women with recurrent implantation failure following frozen-thawed embryo transfer (n = 64). We performed microbiological examination of the embryo transfer catheter which was removed from the uterine cavity after embryo transfer; cervical discharge of all the patients was studied as well. Thirty patients were selected for metagenomic sequencing.

RESULTS: The study showed that the uterine cavity is not free of microorganisms. A total of 44 species of microorganisms were detected: 26 species of opportunistic organisms and 18 species of commensals (14 species of lactobacilli and 4 species of bifidobacteria). Obligate anaerobic microorganisms and Gardnerella vaginalis were detected more frequently in group I compared to group III (strict anaerobes-15.4 and 1.6%; G. vaginalis-12.8 and 1.6%, respectively) (p < 0.05). However, this fact did not have a negative influence on the pregnancy rate: it was 51.3% in group I, it was 29.6% and 35.9% in women with recurrent implantation failures, respectively.

CONCLUSION: Opportunistic microorganisms which were revealed in low or moderate titers (10[3]-10[5] CFU/ml) in the uterine cavity and cervical canal did not affect the pregnancy rate in the women in the study groups. The microflora of the uterine cavity and cervical canal differed in qualitative composition in 87.9% of patients, therefore, we can suggest that the uterine cavity may form its own microbiota. The microbiota of the uterine cavity is characterized by fewer species diversity compared to the microbiota of the cervical canal.}, } @article {pmid35568730, year = {2022}, author = {Lebeaux, RM and Madan, JC and Nguyen, QP and Coker, MO and Dade, EF and Moroishi, Y and Palys, TJ and Ross, BD and Pettigrew, MM and Morrison, HG and Karagas, MR and Hoen, AG}, title = {Impact of antibiotics on off-target infant gut microbiota and resistance genes in cohort studies.}, journal = {Pediatric research}, volume = {92}, number = {6}, pages = {1757-1766}, pmid = {35568730}, issn = {1530-0447}, support = {UL1 TR001863/TR/NCATS NIH HHS/United States ; R01 LM012723/LM/NLM NIH HHS/United States ; P20 ES018175/ES/NIEHS NIH HHS/United States ; P01 ES022832/ES/NIEHS NIH HHS/United States ; P20 GM104416/GM/NIGMS NIH HHS/United States ; UH3 OD023275/OD/NIH HHS/United States ; T32 AI007519/AI/NIAID NIH HHS/United States ; }, mesh = {Child ; Humans ; Infant ; Child, Preschool ; Anti-Bacterial Agents/adverse effects ; *Gastrointestinal Microbiome/genetics ; *Microbiota ; Cohort Studies ; Escherichia coli ; }, abstract = {BACKGROUND: Young children are frequently exposed to antibiotics, with the potential for collateral consequences to the gut microbiome. The impact of antibiotic exposures to off-target microbes (i.e., bacteria not targeted by treatment) and antibiotic resistance genes (ARGs) is poorly understood.

METHODS: We used metagenomic sequencing data from paired stool samples collected prior to antibiotic exposure and at 1 year from over 200 infants and a difference-in-differences approach to assess the relationship between subsequent exposures and the abundance or compositional diversity of microbes and ARGs while adjusting for covariates.

RESULTS: By 1 year, the abundance of multiple species and ARGs differed by antibiotic exposure. Compared to infants never exposed to antibiotics, Bacteroides vulgatus relative abundance increased by 1.72% (95% CI: 0.19, 3.24) while Bacteroides fragilis decreased by 1.56% (95% CI: -4.32, 1.21). Bifidobacterium species also exhibited opposing trends. ARGs associated with exposure included class A beta-lactamase gene CfxA6. Among infants attending day care, Escherichia coli and ARG abundance were both positively associated with antibiotic use.

CONCLUSION: Novel findings, including the importance of day care attendance, were identified through considering microbiome data at baseline and post-intervention. Thus, our study design and approach have important implications for future studies evaluating the unintended impacts of antibiotics.

IMPACT: The impact of antibiotic exposure to off-target microbes and antibiotic resistance genes in the gut is poorly defined. We quantified these impacts in two cohort studies using a difference-in-differences approach. Novel to microbiome studies, we used pre/post-antibiotic data to emulate a randomized controlled trial. Compared to infants unexposed to antibiotics between baseline and 1 year, the relative abundance of multiple off-target species and antibiotic resistance genes was altered. Infants who attended day care and were exposed to antibiotics within the first year had a higher abundance of Escherichia coli and antibiotic resistance genes; a novel finding warranting further investigation.}, } @article {pmid35568398, year = {2022}, author = {Zhong, YW and Zhou, P and Cheng, H and Xu, XW and Wu, YH}, title = {Genome sequence of five Zetaproteobacteria metagenome-assembled genomes recovered from hydrothermal vent Longqi, Southwest Indian Ridge.}, journal = {Marine genomics}, volume = {63}, number = {}, pages = {100936}, doi = {10.1016/j.margen.2022.100936}, pmid = {35568398}, issn = {1876-7478}, mesh = {*Hydrothermal Vents/microbiology ; Iron/metabolism ; Metagenome ; Phylogeny ; Proteobacteria/genetics/metabolism ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Southwest Indian Ridge (SWIR) increasingly becomes the hot spot of deep-sea mining and extreme life research. Strategies for future environmental conservation are undoubtedly required which makes investigation of microbial iron metabolisms imperative. Through deep metagenome sequencing, five iron-oxidizing Zetaproteoabacteria metagenome-assembled genomes were recovered from Longqi hydrothermal vent in the SWIR. Phylogenetic analysis revealed that two of the MAGs might represent novel genus in Zetaproteobacteria while other MAGs were related to Mariprofundus. Functional profile suggested that they might be aerobic chemolithoautotrophic species with genes encoding cytochrome c oxidase, iron oxidase cyc2 homologs and carbon fixation CBB pathway. Versatile capabilities of synthesizing diverse amino acids and cofactors were indicated while possession of various metal ion transporters could be vital to heavy metal resistance. Our work has provided more understanding about phylogenetic and functional features of iron-oxidizing Zetaproteobacteria, which might be important to investigate iron biogeochemistry and mineral oxidation in SWIR.}, } @article {pmid35567890, year = {2022}, author = {Andreson, M and Kazantseva, J and Kuldjärv, R and Malv, E and Vaikma, H and Kaleda, A and Kütt, ML and Vilu, R}, title = {Characterisation of chemical, microbial and sensory profiles of commercial kombuchas.}, journal = {International journal of food microbiology}, volume = {373}, number = {}, pages = {109715}, doi = {10.1016/j.ijfoodmicro.2022.109715}, pmid = {35567890}, issn = {1879-3460}, mesh = {Beverages/microbiology ; *Camellia sinensis ; Fermentation ; *Tea/microbiology ; Yeasts/metabolism ; }, abstract = {The kombucha market is a fast-growing segment in the functional beverage category. The selection of kombuchas on the market varies between the traditional and flavoured kombuchas. Our research aimed to characterise the chemical, microbial, and sensory profiles of the commercial kombuchas. We analysed 16 kombuchas from 6 producers. The dominant metabolites were acetate, lactate, and ethanol, the last of which might put some kombuchas into the alcoholic beverage section in some countries. The metagenomic analyses demonstrated that LAB dominates in green tea, and AAB in black tea kombuchas. The main bacterial species were Komagataeibacter rhaeticus and Lactobacillus ssp, and yeast species Dekkera anomala and Dekkera bruxellensis. The sweet and sour balance correlated with acid concentrations. The free sorting task showed that commercial kombuchas clustered into three main categories "fruity and artificial flavour", herbal and tea notes", and "classical notes". Our research results showed the necessity of the definition of kombucha.}, } @article {pmid35567319, year = {2022}, author = {Liao, Q and Zhu, Y and Wen, Y}, title = {Metagenomic Next-Generation Sequencing in Central Nervous System Angiostrongyliasis.}, journal = {Indian pediatrics}, volume = {59}, number = {5}, pages = {426-427}, pmid = {35567319}, issn = {0974-7559}, mesh = {Central Nervous System ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; *Metagenomics ; Strongylida Infections ; }, } @article {pmid35566348, year = {2022}, author = {Madubuike, H and Ferry, N}, title = {Characterisation of a Novel Acetyl Xylan Esterase (BaAXE) Screened from the Gut Microbiota of the Common Black Slug (Arion ater).}, journal = {Molecules (Basel, Switzerland)}, volume = {27}, number = {9}, pages = {}, pmid = {35566348}, issn = {1420-3049}, mesh = {Acetylesterase ; Animals ; *Gastrointestinal Microbiome ; *Gastropoda/metabolism ; Substrate Specificity ; Xylans/chemistry ; }, abstract = {Acetyl xylan esterases (AXEs) are enzymes capable of hydrolysing the acetyl bonds in acetylated xylan, allowing for enhanced activity of backbone-depolymerizing enzymes. Bioprospecting novel AXE is essential in designing enzyme cocktails with desired characteristics targeting the complete breakdown of lignocellulose. In this article, we report the characterisation of a novel AXE identified as Gene_id_40363 in the metagenomic library analysed from the gut microbiota of the common black slug. The conserved domain description was identified with an NCBI BLASTp search using the translated nucleotide sequence as a query. The activity of the recombinant enzyme was tested on various synthetic substrates and acetylated substrates. The protein sequence matched the conserved domain described as putative hydrolase and aligned closely to an uncharacterized esterase from Buttiauxella agrestis, hence the designation as BaAXE. BaAXE showed low sequence similarity among characterized CE family proteins with an available 3D structure. BaAXE was active on 4-nitrophenyl acetate, reporting a specific activity of 78.12 U/mg and a Km value of 0.43 mM. The enzyme showed optimal activity at 40 °C and pH 8 and showed high thermal stability, retaining over 40% activity after 2 h of incubation from 40 °C to 100 °C. BaAXE hydrolysed acetyl bonds, releasing acetic acid from acetylated xylan and β-D-glucose pentaacetate. BaAXE has great potential for biotechnological applications harnessing its unique characteristics. In addition, this proves the possibility of bioprospecting novel enzymes from understudied environments.}, } @article {pmid35565868, year = {2022}, author = {Yu, X and Xing, Y and Liu, H and Chang, Y and You, Y and Dou, Y and Liu, B and Wang, Q and Ma, D and Chen, L and Tong, X}, title = {Effects of a Formula with scGOS/lcFOS (9:1) and Glycomacropeptide (GMP) Supplementation on the Gut Microbiota of Very Preterm Infants.}, journal = {Nutrients}, volume = {14}, number = {9}, pages = {}, pmid = {35565868}, issn = {2072-6643}, support = {NO. S160004//Natural Science Foundation of Beijing/ ; 2021YFC2700700//National Key Research and Development Program of China/ ; No. BYSYLXHG2019005//Peking University Third Hospital Research Fund for outstanding overseas returnees/ ; }, mesh = {Caseins ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Infant ; Infant Formula ; Infant, Newborn ; Infant, Premature ; Oligosaccharides/pharmacology ; Peptide Fragments ; Prebiotics/analysis ; }, abstract = {Microbial colonization of very preterm (VPT) infants is detrimentally affected by the complex interplay of physiological, dietary, medical, and environmental factors. The aim of this study was to evaluate the effects of an infant formula containing the specific prebiotic mixture of scGOS/lcFOS (9:1) and glycomacropeptide (GMP) on the composition and function of VPT infants' gut microbiota. Metagenomic analysis was performed on the gut microbiota of VPT infants sampled at four time points: 24 h before the trial and 7, 14, and 28 days after the trial. Functional profiling was aggregated into gut and brain modules (GBMs) and gut metabolic modules (GMMs) based on the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Enterococcus faecium, Escherichia coli, Klebsiella aerogenes, and Klebsiella pneumoniae were dominant species in both the test group and the control group. After the 4-week intervention, the abundance of Bifidobacterium in the test group was significantly increased. We found two GBMs (quinolinic acid synthesis and kynurenine degradation) and four GMMs (glutamine degradation, glyoxylate bypass, dissimilatory nitrate reduction, and preparatory phase of glycolysis) were significantly enriched in the test group, respectively. The results of this study suggested that formula enriched with scGOS/lcFOS (9:1) and GPM is beneficial to the intestinal microecology of VPT infants.}, } @article {pmid35565725, year = {2022}, author = {Hernandez, AR and Kemp, KM and Burke, SN and Buford, TW and Carter, CS}, title = {Influence of Aging, Macronutrient Composition and Time-Restricted Feeding on the Fischer344 x Brown Norway Rat Gut Microbiota.}, journal = {Nutrients}, volume = {14}, number = {9}, pages = {}, pmid = {35565725}, issn = {2072-6643}, support = {RF1 AG060977/AG/NIA NIH HHS/United States ; K12GM088010/NH/NIH HHS/United States ; T32HD071866/NH/NIH HHS/United States ; RF1AG060977//National Institute of Health/ ; K02AG062498/NH/NIH HHS/United States ; R01AG054538/NH/NIH HHS/United States ; P2CHD086851/NH/NIH HHS/United States ; }, mesh = {Aging ; Animals ; Cytokines ; *Gastrointestinal Microbiome ; *Neurodegenerative Diseases ; Nutrients ; Rats ; }, abstract = {Both ketogenic diets (KD) and time-restricted feeding (TRF) regimens have the ability to influence several parameters of physical health, including gut microbiome composition and circulating cytokine concentration. Moreover, both of these dietary interventions prevent common impairments associated with the aging process. However, significantly altering macronutrient intake, which is required for a KD, may be unappealing to individuals and decrease compliance to dietary treatments. In contrast to a KD, TRF allows individuals to continue eating the foods they are used to, and only requires a change in the time of day at which they eat. Therefore, we investigated both a KD and a diet with a more Western-like macronutrient profile in the context of TRF, and compared both diets to animals allowed access to standard chow ad libitum in young adult and aged rats. While limited effects on cytokine levels were observed, both methods of microbiome analysis (16S sequencing and metagenomics) indicate that TRF and KDs significantly altered the gut microbiome in aged rats. These changes were largely dependent on changes to feeding paradigm (TRF vs. ad libitum) alone regardless of macronutrient content for many gut microbiota, but there were also macronutrient-specific changes. Specifically, functional analysis indicates significant differences in several pathways, including those involved in the tricarboxylic acid (TCA) cycle, carbohydrate metabolism and neurodegenerative disease. These data indicate that age- and disease-related gut dysbiosis may be ameliorated through the use of TRF with both standard diets and KDs.}, } @article {pmid35565618, year = {2022}, author = {Wang, J and Zhao, K and Kang, Z and Wang, M and Chen, Y and Fan, H and Xia, S and Lai, S}, title = {The Multi-Omics Analysis Revealed a Metabolic Regulatory System of Cecum in Rabbit with Diarrhea.}, journal = {Animals : an open access journal from MDPI}, volume = {12}, number = {9}, pages = {}, pmid = {35565618}, issn = {2076-2615}, support = {CARS-43-A-2//National rabbit industry technology system meat rabbit variety improvement/ ; }, abstract = {With the comprehensive prohibition of antibiotics in the feed industry in China, the incidence of diarrhea in rabbits increased, such as loss of appetite, vomiting, and excretion of atheromatous feces. In order to explore the pathological and the molecular mechanisms of the diarrhea in the rabbitry fed with antibiotic-free diet, we used microbial metagenomics, transcriptome, and non-targeted metabolomics sequencing. The results showed that the Firmicutes level was significantly decreased (p < 0.001) and the Proteobacteria level was significantly increased (p < 0.05). The functional enrichment of cecum revealed that most differentially expressed genes (DEGs) were expressed in immune, inflammatory, and metabolic processes. The enrichment of the cecal fecal metabolites focused on the bile secretion, antifolate resistance, and tryptophan metabolism pathways, which are mainly associated with inflammation. The results of correlation analysis showed that Fournierella was positively correlated with myricetin, ursolic acid, and furtherly might cause bile secretion and tryptophan metabolism disorder, aggravate intestinal inflammation, change intestinal permeability, and reduce host immunity, leading to diarrhea in rabbits. This study provides a theoretical basis for illustrating the reason for diarrhea and developing new feeds for the health of rabbits.}, } @article {pmid35565123, year = {2022}, author = {Sudiartha, GAW and Imai, T and Hung, YT}, title = {Effects of Stepwise Temperature Shifts in Anaerobic Digestion for Treating Municipal Wastewater Sludge: A Genomic Study.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {9}, pages = {}, pmid = {35565123}, issn = {1660-4601}, mesh = {Anaerobiosis ; Bacteria/genetics ; Bioreactors/microbiology ; Metagenomics ; Methane ; *Sewage/microbiology ; Temperature ; Waste Disposal, Fluid/methods ; *Wastewater ; }, abstract = {In wastewater treatment plants (WWTP), anaerobic digester (AD) units are commonly operated under mesophilic and thermophilic conditions. In some cases, during the dry season, maintaining a stable temperature in the digester requires additional power to operate a conditioning system. Without proper conditioning systems, methanogens are vulnerable to temperature shifts. This study investigated the effects of temperature shifts on CH4 gas production and microbial diversity during anaerobic digestion of anaerobic sewage sludge using a metagenomic approach. The research was conducted in lab-scale AD under stepwise upshifted temperature from 42 to 48 °C. The results showed that significant methanogen population reduction during the temperature shift affected the CH4 production. With 70 days of incubation each, CH4 production decreased from 4.55 L·g[-1]-chemical oxygen demand (COD) at 42 °C with methanogen/total population (M·TP[-1]) ratio of 0.041 to 1.52 L·g[-1] COD (M·TP[-1] ratio 0.027) and then to 0.94 L·g[-1] COD (M·TP[-1] ratio 0.026) after the temperature was shifted to 45 °C and 48 °C, respectively. Methanosaeta was the most prevalent methanogen during the thermal change. This finding suggests that the Methanosaeta genus was a thermotolerant archaea. Anaerobaculum, Fervidobacterium, and Tepidanaerobacter were bacterial genera and grew well in shifted-up temperatures, implying heat-resistant characteristics.}, } @article {pmid35564242, year = {2022}, author = {Zhou, Y and Ren, M and Zhang, P and Jiang, D and Yao, X and Luo, Y and Yang, Z and Wang, Y}, title = {Application of Nanopore Sequencing in the Detection of Foodborne Microorganisms.}, journal = {Nanomaterials (Basel, Switzerland)}, volume = {12}, number = {9}, pages = {}, pmid = {35564242}, issn = {2079-4991}, support = {2021ZDZX0010//the Sichuan Science and Technology Program/ ; }, abstract = {Foodborne pathogens have become the subject of intense interest because of their high incidence and mortality worldwide. In the past few decades, people have developed many methods to solve this challenge. At present, methods such as traditional microbial culture methods, nucleic acid or protein-based pathogen detection methods, and whole-genome analysis are widely used in the detection of pathogenic microorganisms in food. However, these methods are limited by time-consuming, cumbersome operations or high costs. The development of nanopore sequencing technology offers the possibility to address these shortcomings. Nanopore sequencing, a third-generation technology, has the advantages of simple operation, high sensitivity, real-time sequencing, and low turnaround time. It can be widely used in the rapid detection and serotyping of foodborne pathogens. This review article discusses foodborne diseases, the principle of nanopore sequencing technology, the application of nanopore sequencing technology in foodborne pathogens detection, as well as its development prospects.}, } @article {pmid35563910, year = {2022}, author = {Cui, S and Guo, W and Chen, C and Tang, X and Zhao, J and Mao, B and Zhang, H}, title = {Metagenomic Analysis of the Effects of Lactiplantibacillus plantarum and Fructooligosaccharides (FOS) on the Fecal Microbiota Structure in Mice.}, journal = {Foods (Basel, Switzerland)}, volume = {11}, number = {9}, pages = {}, pmid = {35563910}, issn = {2304-8158}, support = {31601453//National Natural Science Foundation of China/ ; 31972086//National Natural Science Foundation of China/ ; 32172173//National Natural Science Foundation of China/ ; GJ2020008//Science and Technology Plan Project of Zhenjiang, China/ ; }, abstract = {Understanding the association between food composition and intestinal microbiota in the context of individual health is a critical problem in personalized nutrition. The objective of the present research was to elucidate the influence of Lactiplantibacillus plantarum ST-III and fructooligosaccharides (FOS) on the intestinal microbiota structure. We found that L. plantarum ST-III and FOS interventions remarkably enhanced the levels of cecal short-chain fatty acids (SCFAs), especially acetic, butyric, and valeric acids. Moreover, L. plantarum ST-III and/or FOS intervention obviously altered the intestinal microbiota structure. At the genus level, L. plantarum ST-III and/or FOS intervention remarkably elevated the proportion of Sutterella, Pediococcus, Proteus, Parabacteroides, Prevotella and Desulfovibrio. Correlation analysis further uncovered that the specific compositional features of intestinal microbiota were strongly related to the concentration of cecal SCFAs. Our results offered scientific evidence to understanding the association between food composition and intestinal microbiota.}, } @article {pmid35563303, year = {2022}, author = {Buerger, P and Vanstone, RT and Maire, J and van Oppen, MJH}, title = {Long-Term Heat Selection of the Coral Endosymbiont Cladocopium C1[acro] (Symbiodiniaceae) Stabilizes Associated Bacterial Communities.}, journal = {International journal of molecular sciences}, volume = {23}, number = {9}, pages = {}, pmid = {35563303}, issn = {1422-0067}, support = {FL180100036//Australian Research Council/ ; Research Office Postdoctoral Fellowship//CSIRO/ ; }, mesh = {Animals ; *Anthozoa/genetics ; Bacteria/genetics ; Coral Reefs ; *Dinoflagellida/genetics ; Hot Temperature ; RNA, Ribosomal, 16S/genetics ; Symbiosis ; }, abstract = {Heat-tolerant strains of the coral endosymbiont, Cladocopium C1[acro] (Symbiodiniaceae), have previously been developed via experimental evolution. Here, we examine physiological responses and bacterial community composition (using 16S rRNA gene metabarcoding) in cultures of 10 heat-evolved (SS) and 9 wild-type (WT) strains, which had been exposed for 6 years to 31 °C and 27 °C, respectively. We also examine whether the associated bacterial communities were affected by a three-week reciprocal transplantation to both temperatures. The SS strains had bacterial communities with lower diversities that showed more stability and lower variability when exposed to elevated temperatures compared with the WT strains. Amplicon sequence variants (ASVs) of the bacterial genera Labrenzia, Algiphilus, Hyphobacterium and Roseitalea were significantly more associated with the SS strains compared with the WT strains. WT strains showed higher abundance of ASVs assigned to the genera Fabibacter and Tropicimonas. We hypothesize that these compositional differences in associated bacterial communities between SS and WT strains also contribute to the thermal tolerance of the microalgae. Future research should explore functional potential between bacterial communities using metagenomics to unravel specific genomic adaptations.}, } @article {pmid35562877, year = {2022}, author = {Doualeh, M and Payne, M and Litton, E and Raby, E and Currie, A}, title = {Molecular Methodologies for Improved Polymicrobial Sepsis Diagnosis.}, journal = {International journal of molecular sciences}, volume = {23}, number = {9}, pages = {}, pmid = {35562877}, issn = {1422-0067}, mesh = {*Coinfection/diagnosis/microbiology ; Humans ; Metagenomics ; *Sepsis/diagnosis/microbiology ; }, abstract = {Polymicrobial sepsis is associated with worse patient outcomes than monomicrobial sepsis. Routinely used culture-dependent microbiological diagnostic techniques have low sensitivity, often leading to missed identification of all causative organisms. To overcome these limitations, culture-independent methods incorporating advanced molecular technologies have recently been explored. However, contamination, assay inhibition and interference from host DNA are issues that must be addressed before these methods can be relied on for routine clinical use. While the host component of the complex sepsis host-pathogen interplay is well described, less is known about the pathogen's role, including pathogen-pathogen interactions in polymicrobial sepsis. This review highlights the clinical significance of polymicrobial sepsis and addresses how promising alternative molecular microbiology methods can be improved to detect polymicrobial infections. It also discusses how the application of shotgun metagenomics can be used to uncover pathogen/pathogen interactions in polymicrobial sepsis cases and their potential role in the clinical course of this condition.}, } @article {pmid35562613, year = {2022}, author = {Batista, JG and Nery, FMB and Melo, FFS and Malheiros, MF and Rezende, DV and Boiteux, LS and Fonseca, MEN and de Miranda, BEC and Pereira-Carvalho, RC}, title = {Complete genome sequence of a novel bipartite begomovirus infecting the legume weed Macroptilium erythroloma.}, journal = {Archives of virology}, volume = {167}, number = {7}, pages = {1597-1602}, pmid = {35562613}, issn = {1432-8798}, mesh = {*Begomovirus/genetics ; *Coinfection ; DNA, Viral/genetics ; *Fabaceae ; Genome, Viral ; High-Throughput Nucleotide Sequencing ; Phylogeny ; Plant Diseases ; }, abstract = {The natural occurrence of mixed infections and large populations of the polyphagous vector (Bemisia tabaci) are the main factors associated with the intensification of the genetic flow among begomoviruses in Neotropical areas, contributing to the emergence of novel recombinants. Here, high-throughput sequencing and metagenomic analyses were employed to discover and characterize a novel recombinant bipartite begomovirus, tentatively named "macroptilium bright yellow interveinal virus" (MaBYIV) in the weed Macroptilium erythroloma (Fabaceae). Recombination signals were detected in MaBYIV, involving bean golden mosaic virus (BGMV) and tomato mottle leaf curl virus (ToMoLCV) genome components. All of the original MaBYIV-infected M. erythroloma plants were found to have mixed infections with BGMV. MaBYIV was transmitted to bean and soybean cultivars via B. tabaci MEAM 1, indicating that M. erythroloma may play a role as a year-round reservoir of a potential new viral pathogen of economically important legume crops.}, } @article {pmid35562609, year = {2022}, author = {Shui, J and Tuo, H and Liu, J and Zhang, X and Feng, J and Feng, Y and Su, W and Lin, C and Zhang, H and Tu, Z and Wang, H and Zhang, A}, title = {Insights into the fates of plasmids and antimicrobial resistance genes during swine manure treatment and related factors based on plasmidome and metagenome analyses.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {45}, pages = {69037-69047}, pmid = {35562609}, issn = {1614-7499}, support = {U21A20257//the General Program of National Natural Science Foundation of China/ ; 22ZDZX0011//the Key R&D Program of Sichuan province/ ; 2020ZYD003//the Key R&D Program of Sichuan province/ ; 2021YFH0192//the Key R&D Program of Sichuan province/ ; 2020YFN0147//the Key R&D Program of Sichuan province/ ; BN2020-115//Project of Science and Technology Bureau of Banan District Chongqing/ ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; *Manure/analysis ; Metagenome ; *Metals, Heavy/analysis ; Nitrogen/analysis ; Phosphorus ; Plasmids ; Swine ; }, abstract = {Swine manure treatment plants are important reservoirs of plasmid-harboring antibiotic resistance genes (ARGs) and physicochemical contaminants, but the changes in the abundances of plasmids and ARGs, and their interactions with the physicochemical properties of manure, are still unclear. Thus, in the present study, plasmidome and metagenome analyses were conducted for samples collected at different stages in the swine manure treatment process. The results indicated that anaerobic digestion and aerobic digestion were the most efficient stages for reducing the abundances of ARGs in swine manure. However, the plasmids associated with ARGs were not effectively removed in these stages. Through the whole treatment process, the IncL/M, IncQ1, IncHI2A, IncA/C, and IncN plasmid groups had strong correlations (r > 0.8, P < 0.01) with most ARG types, thereby indicating that these plasmids play important roles in the persistence of ARGs in this environment. Furthermore, the pH, total nitrogen, total phosphorus, and four heavy metals (Cu, Zn, As, and Fe) significantly affected the abundances of seven ARG subtypes (tetB(P), ant(6)-Ia, tet44, aph(3'')-Ib, mefB, tet(L), and tet(39)). In particular, florfenicol had the most positive correlations with ARGs. Our results indicated that nutrients, heavy metals, and antibiotics all contributed to the presence and persistence of plasmid-harboring ARGs. This study provides insights into the fate of plasmids and ARGs, and related factors during the swine manure treatment process, thereby facilitating the development of a new treatment technique for removing ARGs and reducing the public health risk associated with livestock production.}, } @article {pmid35562600, year = {2023}, author = {Greene, LK and McKenney, EA and Gasper, W and Wrampelmeier, C and Hayer, S and Ehmke, EE and Clayton, JB}, title = {Gut Site and Gut Morphology Predict Microbiome Structure and Function in Ecologically Diverse Lemurs.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1608-1619}, pmid = {35562600}, issn = {1432-184X}, support = {PRFB 1906416//Directorate for Biological Sciences/ ; }, mesh = {Animals ; *Lemur ; Retrospective Studies ; *Lemuridae ; *Microbiota ; *Strepsirhini ; }, abstract = {Most studies of wildlife gut microbiotas understandably rely on feces to approximate consortia along the gastrointestinal tract. We therefore compared microbiome structure and predicted metagenomic function in stomach, small intestinal, cecal, and colonic samples from 52 lemurs harvested during routine necropsies. The lemurs represent seven genera (Cheirogaleus, Daubentonia, Varecia, Hapalemur, Eulemur, Lemur, Propithecus) characterized by diverse feeding ecologies and gut morphologies. In particular, the hosts variably depend on fibrous foodstuffs and show correlative morphological complexity in their large intestines. Across host lineages, microbiome diversity, variability, membership, and function differed between the upper and lower gut, reflecting regional tradeoffs in available nutrients. These patterns related minimally to total gut length but were modulated by fermentation capacity (i.e., the ratio of small to large intestinal length). Irrespective of feeding strategy, host genera with limited fermentation capacity harbored more homogenized microbiome diversity along the gut, whereas those with expanded fermentation capacity harbored cecal and colonic microbiomes with greater diversity and abundant fermentative Ruminococcaceae taxa. While highlighting the value of curated sample repositories for retrospective comparisons, our results confirm that the need to survive on fibrous foods, either routinely or in hypervariable environments, can shape the morphological and microbial features of the lower gut.}, } @article {pmid35562544, year = {2022}, author = {Cotta, SR and Pellegrinetti, TA and Andreote, APD and Costa, JS and Sarmento, H and Fiore, MF}, title = {Disentangling the lifestyle of bacterial communities in tropical soda lakes.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {7939}, pmid = {35562544}, issn = {2045-2322}, mesh = {Biomass ; Carbon ; *Cyanobacteria/genetics ; *Lakes/microbiology ; Seasons ; }, abstract = {Microbial lifestyles may reveal niche-specific signatures and can contribute to detecting the effects of abiotic fluctuations on biogeochemical cycles. Microorganisms make a tradeoff between optimizing nutrient uptake, improving biomass yield, and overcoming environmental changes according to environmental hostility. Soda lakes are natural environments rich in carbonate and bicarbonate water, resulting in elevated pH and salinities that frequently approach saturation. We hypothesized that during the dry period (elevated pH and salinity), microorganisms try to overcome this harshness by allocating energy to the cellular maintenance process. As these environmental conditions improve during the wet period, microorganisms will begin to invest in nutrient uptake. To test this hypothesis, we evaluated four soda lakes in two different seasons by applying metagenomics combined with flow cytometry (estimate heterotrophic bacterial biomass). The natural occurrence of cyanobacterial blooms in some lakes is the main driver of carbon. These primary producers provide organic carbon that supports heterotrophic bacterial growth and, consequently, a high biomass yield. Under harsh conditions (dry season), cyanobacteria invest in nutrient uptake mechanisms, whereas heterotrophic bacteria allocate energy to survive at the expense of biomass yield. Lakes without cyanobacteria blooms invest in nutrient uptake independent of environmental hostility. This study clarifies the microbial tradeoffs in hostile environments and the impact of this choice on carbon and energy flux in tropical alkaline lakes.}, } @article {pmid35561922, year = {2022}, author = {Xie, H and Chen, Z and Feng, X and Wang, M and Luo, Y and Wang, Y and Xu, P}, title = {L-theanine exuded from Camellia sinensis roots regulates element cycling in soil by shaping the rhizosphere microbiome assembly.}, journal = {The Science of the total environment}, volume = {837}, number = {}, pages = {155801}, doi = {10.1016/j.scitotenv.2022.155801}, pmid = {35561922}, issn = {1879-1026}, mesh = {*Camellia sinensis/chemistry ; Glutamates ; *Microbiota/genetics ; Plant Roots/metabolism ; RNA, Ribosomal, 16S/analysis ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; Tea/metabolism ; }, abstract = {Root exudate metabolites are a key medium for the interaction between plants and soil microbiota. L-theanine is a unique non-protein amino acid critical for the flavor and potential health benefits of tea products; however, its biological function in tea plants is not well understood. As L-theanine is mainly synthesized in the roots of tea plants, we hypothesized that L-theanine could affect the function of the rhizosphere microbiota by modulating microbial assembly. In the present study, L-theanine was detected in the exudates of tea plant roots using liquid chromatography-mass spectrometry. Additionally, 16S rRNA gene sequencing revealed that L-theanine significantly altered the structure of the rhizosphere microbiota and selectively shaped rhizosphere microbial assembly. Moreover, metagenomic data showed that L-theanine affected the abundance of genes encoding element cycling in soil. Interestingly, the denitrification and complete nitrification pathways were significantly inhibited by L-theanine by decreasing the narH, napA, and napB genes abundance. These findings provide new insights into the biological function of L-theanine, as well as the implications of interactions between tea plant root exudates and the rhizosphere microbiome.}, } @article {pmid35561916, year = {2022}, author = {Xie, J and Xu, J and Zhu, J and Zhu, C and He, R and Wang, W and Xie, L}, title = {Roles of Fe-C amendment on sulfate-containing pharmaceutical wastewater anaerobic treatment: Microbial community and sulfur metabolism.}, journal = {The Science of the total environment}, volume = {837}, number = {}, pages = {155868}, doi = {10.1016/j.scitotenv.2022.155868}, pmid = {35561916}, issn = {1879-1026}, mesh = {Anaerobiosis ; *Bioreactors/microbiology ; Butyrates/chemistry ; *Pharmaceutical Preparations/chemistry ; Sulfates/analysis ; Wastewater/microbiology ; *Water Purification/methods ; }, abstract = {The effects of multiple two-phase anaerobic treatment involving acidification coupling Fe-C on sulfate-containing chemical synthesis-based pharmaceutical wastewater treatment were investigated. Fe-C was added as a filler with 25% vol. to acidogenic reactors for semi-continuous operation. The results suggested that Fe-C amendment promoted sulfate removal efficiency by 47.5% and shortened the reaction time by 50% in the acidogenic phase. With mitigation of sulfate inhibition, SCOD removal efficiency and methane production were further increased by 24.6% and 398% compared to direct raw wastewater anaerobic digestion, respectively, in methanogenic phase. The results of sulfate removal kinetics confirmed a 150% increase of removal rate in acidogenic phase. However, the apparent kinetic microbial sulfate removal constant without Fe-C amendment was maintained at approximately 0.06 h[-1]. The Fe-C amendment not only increased the relative abundance of Methanothrix and Desulfovibrio for sulfate reduction but also enriched unclassified_p__Chloroflexi and unclassified_c__Deltaproteobacteria for acidification. Metagenomic results indicated that Fe-C enhanced dissimilatory sulfate reduction and PAPS synthesis of assimilatory step. The hydrogen sulfide production through the 3-mercaptopyruvate to pyruvate pathways was also enhanced. Butyrate-oxidizing genes were increased synchronously to convert butyrate to acetate.}, } @article {pmid35561657, year = {2022}, author = {Doerksen, T and Christensen, T and Lu, A and Noll, L and Bai, J and Henningson, J and Palinski, R}, title = {Assessment of porcine Rotavirus-associated virome variations in pigs with enteric disease.}, journal = {Veterinary microbiology}, volume = {270}, number = {}, pages = {109447}, doi = {10.1016/j.vetmic.2022.109447}, pmid = {35561657}, issn = {1873-2542}, mesh = {Animals ; Diarrhea/epidemiology/veterinary ; Feces ; Genotype ; Humans ; Mammals ; Phylogeny ; *Rotavirus/genetics ; *Rotavirus Infections/epidemiology/veterinary ; Swine ; *Swine Diseases/epidemiology ; Virome ; }, abstract = {Enteric disease is the predominant cause of morbidity and mortality in young mammals including pigs. Viral species involved in porcine enteric disease complex (PEDC) include rotaviruses, coronaviruses, picornaviruses, astroviruses and pestiviruses among others. The virome of three groups of swine samples submitted to the Kansas State University Veterinary Diagnostic Laboratory for routine testing were assessed, namely, a Rotavirus A positive (RVA) group, a Rotavirus co-infection (RV) group and a Rotavirus Negative (RV Neg) group. All groups were designated by qRT-PCR test results for Porcine Rotavirus A, B, C and H such that samples positive for RVA only went in the RVA group, samples positive for > 1 rotavirus went in the RV group and samples negative for all were grouped in the RVNeg group. All of the animals had clinical enteric disease resulting in scours and swollen joints/lameness, enlarged heart and/or a cough. All samples were metagenomic sequenced and analyzed for viral species composition that identified 14 viral species and eight bacterial viruses/phages. Sapovirus and Escherichia coli phages were found at a high prevalence in RVA and RV samples but were found at low or no prevalence in the RVNeg samples. Picobirnavirus was identified at a high proportion and prevalence in RVNeg and RV samples but at a low prevalence in the RVA group. Non-rotaviral diversity was highest in RVA samples followed by RV then RV Neg samples. A sequence analysis of the possible host of Picobirnaviruses revealed fungi as the most likely host. Various sequences were extracted from the sample reads and a phylogenetic update was provided showing a high prevalence of G9 and P[23] RVA genotypes. These data are important for pathogen surveillance and control measures.}, } @article {pmid35561076, year = {2022}, author = {Bajaj, JS and Rodriguez, MP and Fagan, A and McGeorge, S and Sterling, RK and Lee, H and Luketic, V and Fuchs, M and Davis, BC and Sikaroodi, M and Gillevet, PM}, title = {Impact of bacterial infections and spontaneous bacterial peritonitis prophylaxis on phage-bacterial dynamics in cirrhosis.}, journal = {Hepatology (Baltimore, Md.)}, volume = {76}, number = {6}, pages = {1723-1734}, doi = {10.1002/hep.32571}, pmid = {35561076}, issn = {1527-3350}, mesh = {Humans ; Ascites/drug therapy ; Escherichia coli ; *Bacteriophages ; *End Stage Liver Disease/complications ; Severity of Illness Index ; *Peritonitis/prevention & control ; *Bacterial Infections/complications/prevention & control ; Liver Cirrhosis/drug therapy ; Anti-Bacterial Agents/pharmacology/therapeutic use ; }, abstract = {BACKGROUND AND AIMS: Gut microbiota, including bacteria and phages, are altered in cirrhosis, but their role during infections and spontaneous bacterial peritonitis (SBP) prophylaxis is unclear. Our aim was determine metagenomic changes in gut bacteria; phages and their linkages centered around Gram-negative and Gram-positive pathobionts in patients with cirrhosis with/without infections or SBP prophylaxis.

APPROACH AND RESULTS: We included uninfected (n = 231) and infected (n = 30, SBP n = 19 and urinary tract infection n = 11 before antibiotics) patients who gave stool for bacterial and phage metagenomics. We matched uninfected to infected patients 1:1 on a model for end-stage liver disease (MELD). We also analyzed subgroups of patients with ascites matched on an MELD (n = 73) to patients on SBP prophylaxis (n = 7) and then to SBP infection. Phage and bacterial taxa differences (DESeq2) and correlation networks centered around Escherichia coli and Enterococcus faecium were analyzed. Infections were mostly due to Enterobacteriaceae and Enterococcus spp. On metagenomics, higher fold changes of Enterobacteriaceae members, Enterococcus and Streptococcus spp., and Escherichia phages were seen in infected patients. Correlation networks showed more complex bacteria-phage linkages in infected patients compared with uninfected ones overall and centered around E. coli and E. faecium. SBP prophylaxis induced higher Gram-positive bacteria. In SBP, Enterococcus and Escherichia were higher versus ascites. Correlation networks around E. coli were complex in ascites but sparse with SBP prophylaxis, whereas the reverse was seen with E. faecium. Lytic phages and those associated with antibiotic resistance were correlated with E. faecium.

CONCLUSION: In cirrhosis, there are significant changes in phage-bacterial linkages in infected patients and those on SBP prophylaxis compared to the remaining patients. SBP prophylaxis enriches complexity of E. faecium-centered but induces a collapse in E. coli-centered phage-bacterial correlations.}, } @article {pmid35560165, year = {2022}, author = {Dubinsky, V and Reshef, L and Rabinowitz, K and Wasserberg, N and Dotan, I and Gophna, U}, title = {Escherichia coli Strains from Patients with Inflammatory Bowel Diseases have Disease-specific Genomic Adaptations.}, journal = {Journal of Crohn's & colitis}, volume = {16}, number = {10}, pages = {1584-1597}, doi = {10.1093/ecco-jcc/jjac071}, pmid = {35560165}, issn = {1876-4479}, support = {2018PG-CD007//Leona M. and Harry B. Helmsley Charitable Trust/ ; //Edmond J. Safra Center for Bioinformatics at Tel-Aviv University/ ; //Israeli Ministry of Science and Technology/ ; //Israeli Ministry of Health/ ; }, mesh = {Humans ; Escherichia coli ; Intestinal Mucosa/microbiology ; *Escherichia coli Infections/microbiology ; *Inflammatory Bowel Diseases/microbiology ; *Colitis, Ulcerative/microbiology ; *Crohn Disease/microbiology ; Genomics ; }, abstract = {BACKGROUND AND AIMS: Escherichia coli is over-abundant in the gut microbiome of patients with inflammatory bowel disease [IBD]. Here, we aimed to identify IBD-specific genomic functions of diverse E. coli lineages.

METHODS: We investigated E. coli genomes from patients with ulcerative colitis [UC], Crohn's disease [CD] or a pouch, and healthy subjects. The majority of genomes were reconstructed from metagenomic samples, including newly sequenced faecal metagenomes. Clinical metadata were collected. Functional analysis at the gene and mutation level were performed and integrated with IBD phenotypes and biomarkers.

RESULTS: Overall, 530 E. coli genomes were analysed. The E. coli B2 lineage was more prevalent in UC compared with other IBD phenotypes. Genomic metabolic capacities varied across E. coli lineages and IBD phenotypes. Host mucin utilisation enzymes were present in a single lineage and depleted in patients with a pouch, whereas those involved in inulin hydrolysis were enriched in patients with a pouch. E. coli strains from patients with UC were twice as likely to encode the genotoxic molecule colibactin than strains from patients with CD or a pouch. Strikingly, patients with a pouch showed the highest inferred E. coli growth rates, even in the presence of antibiotics. Faecal calprotectin did not correlate with the relative abundance of E. coli. Finally, we identified multiple IBD-specific non-synonymous mutations in E. coli genes encoding for bacterial cell envelope components.

CONCLUSIONS: Comparative genomics indicates that E. coli is a commensal species adapted to the overactive mucosal immune milieu in IBD, rather than causing it. Our results reveal mutations that may lead to attenuated antigenicity in some E. coli strains.}, } @article {pmid35559844, year = {2021}, author = {Meier, MJ and Nguyen, KC and Crosthwait, J and Kawata, A and Rigden, M and Leingartner, K and Wong, A and Holloway, A and Shwed, PS and Beaudette, L and Navarro, M and Wade, M and Tayabali, AF}, title = {Low dose antibiotic ingestion potentiates systemic and microbiome changes induced by silver nanoparticles.}, journal = {NanoImpact}, volume = {23}, number = {}, pages = {100343}, doi = {10.1016/j.impact.2021.100343}, pmid = {35559844}, issn = {2452-0748}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents/pharmacology ; DNA, Ribosomal/pharmacology ; Eating ; Mammals ; *Metal Nanoparticles/chemistry ; Mice ; *Microbiota ; Silver/chemistry ; }, abstract = {Changes in the mammalian gut microbiome are linked to the impairment of immunological function and numerous other pathologies. Antimicrobial silver nanoparticles (AgNPs) are incorporated into numerous consumer products (e.g., clothing, cosmetics, food packaging), which may directly impact the gut microbiome through ingestion. The human health impact of chronic AgNP ingestion is still uncertain, but evidence from exposure to other antimicrobials provides a strong rationale to assess AgNP effects on organ function, immunity, metabolism, and gut-associated microbiota. To investigate this, mice were gavaged daily for 5 weeks with saline, AgNPs, antibiotics (ciprofloxacin and metronidazole), or AgNPs combined with antibiotics. Animals were weighed daily, assessed for glucose tolerance, organ function, tissue and blood cytokine and leukocyte levels. At the end of the study, we used 16S rDNA amplicon and whole-metagenome shotgun sequencing to assess changes in the gut microbiome. In mice exposed to both AgNPs and antibiotics, silver was found in the stomach, and small and large intestines, but negligible amounts were present in other organs examined. Mice exposed to AgNPs alone showed minimal tissue silver levels. Antibiotics, but not AgNPs, altered glucose metabolism. Mice given AgNPs and antibiotics together demonstrated slower weight gain, reduced peripheral lymphocytes, and elevated splenic, but not circulatory markers of inflammation. 16S rDNA profiling of cecum and feces and metagenomic sequencing of fecal DNA demonstrated that combined AgNP-antibiotic treatment also significantly altered the structure and function of the gut microbiota, including depletion of the indicator species Akkermansia muciniphila. This study provides evidence for possible biological effects from repeated ingestion of AgNP-containing consumer products when antibiotics are also being used and raises concern that an impaired gut microbiome (e.g., through antibiotic use) can potentiate the harm from chemical exposures such as AgNPs.}, } @article {pmid35559233, year = {2022}, author = {Liu, Y and Tan, Y and Huang, J and Wu, C and Fan, X and Stalin, A and Lu, S and Wang, H and Zhang, J and Zhang, F and Wu, Z and Li, B and Huang, Z and Chen, M and Cheng, G and Mou, Y and Wu, J}, title = {Revealing the Mechanism of Huazhi Rougan Granule in the Treatment of Nonalcoholic Fatty Liver Through Intestinal Flora Based on 16S rRNA, Metagenomic Sequencing and Network Pharmacology.}, journal = {Frontiers in pharmacology}, volume = {13}, number = {}, pages = {875700}, pmid = {35559233}, issn = {1663-9812}, abstract = {Background: The incidence of Nonalcoholic Fatty Liver (NAFL) is increasing year by year, growing evidence suggests that the intestinal flora plays a causative role in NAFL. Huazhi Rougan Granule (HRG) is commonly used in the clinical treatment of NAFL. It is reported that it can reduce lipids and protect the liver, but no research has confirmed whether the drug's effect is related to the intestinal flora. Therefore, we investigated whether the effect of HRG is related to the regulation of intestinal flora to further explore the mechanism of HRG in the treatment of NAFL through intestinal flora. Methods: In this study, C57BL/6J mice were fed a high-fat diet for 8 weeks, and the high-fat diet plus HRG or polyene phosphatidylcholine capsules were each administered by gavage for 4 weeks. High-throughput sequencing, network pharmacology, and molecular docking were used to explore the mechanism of HRG in the treatment of NAFL through intestinal flora. Results: HRG treatment can reduce body weight gain, lipid accumulation in liver and lipogenesis and reduce serum biochemical indexes in high-fat-fed mice. Analysis of intestinal flora showed that HRG changed the composition of intestinal flora, which was characterized by a decrease in the Firmicutes/Bacteroidetes ratio. Moreover, the species distribution was significantly correlated with AKP, HDL-C, and TG. Metagenetic analysis showed that HRG altered the functional composition and functional diversity of microorganisms, which was mainly characterized by an increase in the abundance of metabolic pathways. The network pharmacology results show that the mechanism of HRG in the treatment of NAFL through intestinal flora is mainly reflected in the biological process of gene function and related to infectious diseases, immune systems, and signal transduction pathways, such as cytokine-cytokine receptor interaction, Chagas disease, IL-17 signaling pathway and other signaling pathways. Conclusion: These results strongly suggest that HRG may alleviate NAFL by preventing IFD.}, } @article {pmid35558115, year = {2022}, author = {Blachowicz, A and Mhatre, S and Singh, NK and Wood, JM and Parker, CW and Ly, C and Butler, D and Mason, CE and Venkateswaran, K}, title = {The Isolation and Characterization of Rare Mycobiome Associated With Spacecraft Assembly Cleanrooms.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {777133}, pmid = {35558115}, issn = {1664-302X}, abstract = {Ensuring biological cleanliness while assembling and launching spacecraft is critical for robotic exploration of the solar system. To date, when preventing forward contamination of other celestial bodies, NASA Planetary Protection policies have focused on endospore-forming bacteria while fungi were neglected. In this study, for the first time the mycobiome of two spacecraft assembly facilities at Jet Propulsion Laboratory (JPL) and Kennedy Space Center (KSC) was assessed using both cultivation and sequencing techniques. To facilitate enumeration of viable fungal populations and downstream molecular analyses, collected samples were first treated with chloramphenicol for 24 h and then with propidium monoazide (PMA). Among cultivable fungi, 28 distinct species were observed, 16 at JPL and 16 at KSC facilities, while 13 isolates were potentially novel species. Only four isolated species Aureobasidium melanogenum, Penicillium fuscoglaucum, Penicillium decumbens, and Zalaria obscura were present in both cleanroom facilities, which suggests that mycobiomes differ significantly between distant locations. To better visualize the biogeography of all isolated strains the network analysis was undertaken and confirmed higher abundance of Malassezia globosa and Cyberlindnera jadinii. When amplicon sequencing was performed, JPL-SAF and KSC-PHSF showed differing mycobiomes. Metagenomic fungal reads were dominated by Ascomycota (91%) and Basidiomycota (7.15%). Similar to amplicon sequencing, the number of fungal reads changed following antibiotic treatment in both cleanrooms; however, the opposite trends were observed. Alas, treatment with the antibiotic did not allow for definitive ascribing changes observed in fungal populations between treated and untreated samples in both cleanrooms. Rather, these substantial differences in fungal abundance might be attributed to several factors, including the geographical location, climate and the in-house cleaning procedures used to maintain the cleanrooms. This study is a first step in characterizing cultivable and viable fungal populations in cleanrooms to assess fungal potential as biocontaminants during interplanetary explorations. The outcomes of this and future studies could be implemented in other cleanrooms that require to reduce microbial burden, like intensive care units, operating rooms, or cleanrooms in the semiconducting and pharmaceutical industries.}, } @article {pmid35557670, year = {2022}, author = {Zhang, S and Zhu, J}, title = {Untargeted Metabolomics Sensitively Differentiates Gut Bacterial Species in Single Culture and Co-Culture Systems.}, journal = {ACS omega}, volume = {7}, number = {17}, pages = {14643-14652}, pmid = {35557670}, issn = {2470-1343}, support = {R35 GM133510/GM/NIGMS NIH HHS/United States ; }, abstract = {Gut microbiome plays a vital role in human health, and its characteristic has been widely identified through next-generation sequencing techniques. Although with great genomic insights into gut microbiome, its functional information is not clearly elaborated through metagenomic techniques. On the other hand, it is suggested that fecal metabolome can be used as a functional readout of the microbiome composition; therefore, we designed a proof-of-concept study to first characterize the metabolome of different gut microbes and then investigate the relationship between bacterial metabolomes and their compositions in co-culture systems. We selected eight representative bacteria species from Bifidobacterium (2), Bacteroides (1), Lactobacillus (4), and Akkermansia (1) genera as our model microbes. Liquid chromatography coupled mass spectrometry-based untargeted metabolomics was utilized to explore the microbial metabolome of bacteria single cultures and co-culture systems. Through spectral comparisons, our results showed that untargeted metabolomics could capture the similarity and differences in metabolic profiles from eight representative gut bacteria. Also, untargeted metabolomics could sensitively differentiate gut bacterial species based on our statistical analyses. For example, citrulline and histamine levels were significantly different among four Lactobacillus species. In addition, in the co-culture systems with different bacteria population ratios, gut bacterial metabolomes can be used to quantitatively reflect bacterial population in a mixed culture. For instance, the relative abundance of 2-hydroxybutyric acid changed proportionately with the changed population ratio of Lactobacillus reuteri in the co-culture system. In summary, we proposed a workflow that could demonstrate the capability of untargeted metabolomics in differentiating gut bacterial species and detecting their characteristic metabolites proportionally to the microbial population in co-culture systems.}, } @article {pmid35551982, year = {2022}, author = {Ruppé, E and d'Humières, C and Armand-Lefèvre, L}, title = {Inferring antibiotic susceptibility from metagenomic data: dream or reality?.}, journal = {Clinical microbiology and infection : the official publication of the European Society of Clinical Microbiology and Infectious Diseases}, volume = {28}, number = {9}, pages = {1225-1229}, doi = {10.1016/j.cmi.2022.04.017}, pmid = {35551982}, issn = {1469-0691}, mesh = {Anti-Bacterial Agents/pharmacology/therapeutic use ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; *Metagenome ; *Metagenomics ; }, abstract = {BACKGROUND: The diagnosis of bacterial infections continues to rely on culture, a slow process in which antibiotic susceptibility profiles of potential pathogens are made available to clinicians 48 hours after sampling, at best. Recently, clinical metagenomics, the metagenomic sequencing of samples with the purpose of identifying microorganisms and determining their susceptibility to antimicrobials, has emerged as a potential diagnostic tool that could prove faster than culture. Clinical metagenomics indeed has the potential to detect antibiotic resistance genes (ARGs) and mutations associated with resistance. Nevertheless, many challenges have yet to be overcome in order to make rapid phenotypic inference of antibiotic susceptibility from metagenomic data a reality.

OBJECTIVES: The objective of this narrative review is to discuss the challenges underlying the phenotypic inference of antibiotic susceptibility from metagenomic data.

SOURCES: We conducted a narrative review using published articles available in the National Center for Biotechnology Information PubMed database.

CONTENT: We review the current ARG databases with a specific emphasis on those which now provide associations with phenotypic data. Next, we discuss the bioinformatic tools designed to identify ARGs in metagenomes. We then report on the performance of phenotypic inference from genomic data and the issue predicting the expression of ARGs. Finally, we address the challenge of linking an ARG to this host.

IMPLICATIONS: Significant improvements have recently been made in associating ARG and phenotype, and the inference of susceptibility from genomic data has been demonstrated in pathogenic bacteria such as Staphylococci and Enterobacterales. Resistance involving gene expression is more challenging however, and inferring susceptibility from species such as Pseudomonas aeruginosa remains difficult. Future research directions include the consideration of gene expression via RNA sequencing and machine learning.}, } @article {pmid35551951, year = {2022}, author = {Ariaeenejad, S and Kavousi, K and Afshar Jahanshahi, D and Sheykh Abdollahzadeh Mamaghani, A and Ghasemitabesh, R and Moosavi-Movahedi, AA and Hosseini Salekdeh, G}, title = {Enzymatically triggered delignification through a novel stable laccase: A mixed in-silico /in-vitro exploration of a complex environmental microbiota.}, journal = {International journal of biological macromolecules}, volume = {211}, number = {}, pages = {328-341}, doi = {10.1016/j.ijbiomac.2022.05.039}, pmid = {35551951}, issn = {1879-0003}, mesh = {Biomass ; Laccase/chemistry/genetics ; *Lignin/chemistry ; *Microbiota ; Saccharomyces cerevisiae ; }, abstract = {Laccases have been broadly applied as a multitasking biocatalyst in various industries, but their applications tend to be limited by easy deactivation, lack of adequate stability, and susceptibility under complex conditions. Identifying stable laccase as a green-biocatalyst is crucial for developing cost-effective biorefining processes. In this direction, we attempted in-silico screening a stable metagenome-derived laccase (PersiLac1) from tannery wastewater in a complex environment. The laccase exhibited high thermostability, retaining 53.19% activity after 180 min at 70 °C, and it was stable in a wide range of pH (4.0-9.0). After 33 days of storage at 50°C, pH 6.0, the enzyme retained 71.65% of its activity. Various metal ions, inhibitors, and organic solvents showed that PersiLac1 has a stable structure. The stable PersiLac1 could successfully remove lignin and phenolic from quinoa husk and rice straw. In the separate hydrolysis and fermentation process (SHF) after 72 h, hydrolysis was obtained 100% and 73.4% for quinoa husk and rice straw, and fermentation by the S. cerevisiae was be produced 41.46 g/L and 27.75g/L ethanol, respectively. Results signified that the novel lignin-degrading enzyme was confirmed to have great potential for industrial application as a green-biocatalyst based on enzymatically triggered to delignification and detoxify lignocellulosic biomass.}, } @article {pmid35551932, year = {2022}, author = {Li, K and Wang, Y and Li, X and Huang, Y and Niu, Q and Meng, Q and Yang, H and Li, Q}, title = {In-situ generation of H2O2 by zero valent iron to control depolymerization of lignocellulose in composting niche.}, journal = {Chemosphere}, volume = {302}, number = {}, pages = {134908}, doi = {10.1016/j.chemosphere.2022.134908}, pmid = {35551932}, issn = {1879-1298}, mesh = {*Composting ; Hydrogen Peroxide ; Iron/chemistry ; Lignin/metabolism ; }, abstract = {Lignocellulosic degradation is a bottleneck of bioconversion during the composting process. In-situ generation of H2O2 in the composting system was an ideal method for efficiently promoting lignocellulase degradation, and zero valent iron (ZVI) was concerned because it can generate H2O2 by reducing dissolved oxygen. This study focused on the effects of ZVI treatment on lignocellulose degradation, microbial communities, and carbohydrate-active enzymes (CAZymes) genes during composting. Its results indicated that ZVI increased H2O2 content during composting, accompanied by the formation of •OH. The degradation rates of lignin, cellulose and hemicellulose in ZVI group (20.77%, 30.35% and 44.7%) were significantly higher than in CK group (17.01%, 26.12% and 38.5%). Metagenomic analysis showed that ZVI induced microbial growth that favored lignocellulose degradation, which increased the abundance of Actinobacteria and Firmicutes but reduced Proteobacteria. At the genus level, the abundance of Thermomonospora, Streptomyces, and Bacillus significantly increased. In addition, glycoside hydrolases and auxiliary activities were important CAZymes families of lignocellulose degradation, and their abundance was higher in the ZVI group. Redundancy analysis showed that the increased H2O2 and •OH content was a critical factor in improving lignocellulose degradation. Overall, H2O2 as a co-substrate enhanced the enzymatic efficiency, •OH unspecifically attacked lignocellulose, and the increase in functional microbial abundance was the main reason for promoting lignocellulose degradation in composting.}, } @article {pmid35551905, year = {2022}, author = {Li, J and Liang, Q and Huang, F and Liao, Y and Zhao, W and Yang, J and Wen, X and Li, X and Chen, T and Guo, S and Liang, J and Wei, L and Liang, L}, title = {Metagenomic Profiling of the Ocular Surface Microbiome in Patients After Allogeneic Hematopoietic Stem Cell Transplantation.}, journal = {American journal of ophthalmology}, volume = {242}, number = {}, pages = {144-155}, doi = {10.1016/j.ajo.2022.04.026}, pmid = {35551905}, issn = {1879-1891}, mesh = {Dysbiosis ; *Graft vs Host Disease/diagnosis ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Humans ; Male ; *Microbiota ; Prospective Studies ; }, abstract = {PURPOSE: To investigate the characteristics of the ocular surface microbiome in patients after allogeneic hematopoietic stem cell transplantation (allo-HSCT) and the associations between the microbial dysbiosis and chronic ocular graft-versus-host disease (oGVHD).

DESIGN: Prospective cohort study.

METHODS: Ocular surface samples from 48 healthy subjects and 76 patients after allo-HSCT, including 50 patients with chronic oGVHD and 26 patients without oGVHD, were collected. Species-level composition of the ocular surface microbiome was surveyed via metagenomic shotgun sequencing. OGVHD was diagnosed and graded according to the International Chronic Ocular GVHD Consensus Group criteria.

RESULTS: The α-diversity of the microbiota was significantly decreased in patients after allo-HSCT. Nevertheless, we detected more types of viral species in the allo-HSCT group than the healthy group, especially anelloviruses. The mismatch of donor-recipient sex was only negatively associated with the α-diversity in male but not female recipients. Moreover, the microbiome of patients with oGVHD was distinct from patients without oGVHD. Gordonia bronchialis and Pseudomonas parafulva were enriched in patients with oGVHD and positively associated with International Chronic Ocular GVHD score.

CONCLUSIONS: This study suggests that the ocular surface microbiome after allo-HSCT is characterized by a loss of diversity. Furthermore, the microbial dysbiosis at the ocular surface is associated with the status and severity of chronic oGVHD. These results lay the groundwork for future investigations of the potential microbial mechanism for oGVHD.}, } @article {pmid35551553, year = {2022}, author = {Elbon, CE and LeCleir, GR and Tuttle, MJ and Jurgensen, SK and Demas, TG and Keller, CJ and Stewart, T and Buchan, A}, title = {Microbiomes and Planctomycete diversity in large-scale aquaria habitats.}, journal = {PloS one}, volume = {17}, number = {5}, pages = {e0267881}, pmid = {35551553}, issn = {1932-6203}, mesh = {*Ammonium Compounds/metabolism ; Anaerobiosis ; Bacteria ; Bioreactors/microbiology ; *Microbiota/genetics ; Nitrites/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Planctomycetes ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {In commercial large-scale aquaria, controlling levels of nitrogenous compounds is essential for macrofauna health. Naturally occurring bacteria are capable of transforming toxic nitrogen species into their more benign counterparts and play important roles in maintaining aquaria health. Nitrification, the microbially-mediated transformation of ammonium and nitrite to nitrate, is a common and encouraged process for management of both commercial and home aquaria. A potentially competing microbial process that transforms ammonium and nitrite to dinitrogen gas (anaerobic ammonium oxidation [anammox]) is mediated by some bacteria within the phylum Planctomycetes. Anammox has been harnessed for nitrogen removal during wastewater treatment, as the nitrogenous end product is released into the atmosphere rather than in aqueous discharge. Whether anammox bacteria could be similarly utilized in commercial aquaria is an open question. As a first step in assessing the viability of this practice, we (i) characterized microbial communities from water and sand filtration systems for four habitats at the Tennessee Aquarium and (ii) examined the abundance and anammox potential of Planctomycetes using culture-independent approaches. 16S rRNA gene amplicon sequencing revealed distinct, yet stable, microbial communities and the presence of Planctomycetes (~1-15% of library reads) in all sampled habitats. Preliminary metagenomic analyses identified the genetic potential for multiple complete nitrogen metabolism pathways. However, no known genes diagnostic for the anammox reaction were found in this survey. To better understand the diversity of this group of bacteria in these systems, a targeted Planctomycete-specific 16S rRNA gene-based PCR approach was used. This effort recovered amplicons that share <95% 16S rRNA gene sequence identity to previously characterized Planctomycetes, suggesting novel strains within this phylum reside within aquaria.}, } @article {pmid35550809, year = {2022}, author = {Zhu, J and Chen, G and Zhou, J and Zeng, Y and Cheng, K and Cai, Z}, title = {Dynamic patterns of quorum sensing signals in phycospheric microbes during a marine algal bloom.}, journal = {Environmental research}, volume = {212}, number = {Pt C}, pages = {113443}, doi = {10.1016/j.envres.2022.113443}, pmid = {35550809}, issn = {1096-0953}, mesh = {Bacteria/metabolism ; Eutrophication ; *Microbiota ; Phytoplankton/genetics ; *Quorum Sensing ; }, abstract = {In the marine environment, the interactions among various species based on chemical signals play critical roles in influencing microbial structure and function. Quorum sensing (QS), the well-known signal-dependent communication autoinducer, is an important regulator in complex microbial communities. Here, we explored the QS gene profiles of phycosphere bacteria during a microcosmic phytoplankton bloom using metagenomic sequence data. More than fifteen subtypes of QS systems and 211,980 non-redundant amino acid sequences were collected and classified for constructing a hierarchical quorum-sensing database. The abundance of the various QS subtypes varied at different bloom stages and showed a strong correlation with phycosphere microorganisms. This suggested that QS is involved in regulating the phycosphere microbial succession during an algal bloom. A neutral community model revealed that the QS functional gene community assemblies were driven by stochastic processes. Co-occurrence model analysis showed that the QS gene networks of phycospheric microbes had similar topological structure and functional composition, which is a potential cornerstone for maintaining signal communication and population stabilization among microorganisms. Overall, QS systems have a strong relationship with the development of algal blooms and participate in regulating algal-associated microbial communities as chemical signals. This research reveals the chemical and ecological behavior of algal symbiotic bacteria and expands the current understanding of microbial dynamics in marine algal blooms.}, } @article {pmid35550744, year = {2022}, author = {Wei, B and Zhang, B and Du, AQ and Zhou, ZY and Lu, DZ and Zhu, ZH and Ke, SZ and Wang, SJ and Yu, YL and Chen, JW and Zhang, HW and Jin, WH and Wang, H}, title = {Saccharina japonica fucan suppresses high fat diet-induced obesity and enriches fucoidan-degrading gut bacteria.}, journal = {Carbohydrate polymers}, volume = {290}, number = {}, pages = {119411}, doi = {10.1016/j.carbpol.2022.119411}, pmid = {35550744}, issn = {1879-1344}, mesh = {Animals ; Bacteria ; *Diet, High-Fat/adverse effects ; Dysbiosis ; *Laminaria ; Mice ; Mice, Inbred C57BL ; Obesity/metabolism ; Polysaccharides/chemistry ; }, abstract = {Low molecular weight seaweed polysaccharides exhibit promising potential as novel therapeutics for the prevention of obesity and gut microbiota dysbiosis. The interplay between polysaccharides and gut microbiota may play crucial roles in their anti-obesity effects, but is largely unknown, including the impact of polysaccharides on the composition of the gut microbiota with polysaccharide-degrading capacity. The primary structure of a 5.1 kDa fucan (J2H) from Saccharina japonica was characterized and oral administration of J2H effectively suppressed high-fat diet-induced obesity, blood glucose metabolic dysfunction, dyslipidemia, and gut microbiota dysbiosis. Furthermore, the Jensen-Shannon divergence analysis demonstrated that J2H enriched at least four gut bacterial species with fucoidan-degrading potential, including Bacteroides sartorii and Bacteroides acidifaciens. Our findings suggest that the low molecular weight S. japonica fucan, J2H, is a promising potential agent for obesity prevention and its enrichment of gut bacteria with fucoidan-degrading potential may play a vital role in the anti-obesity effects.}, } @article {pmid35549618, year = {2022}, author = {Chen, L and Zheng, T and Yang, Y and Chaudhary, PP and Teh, JPY and Cheon, BK and Moses, D and Schuster, SC and Schlundt, J and Li, J and Conway, PL}, title = {Integrative multiomics analysis reveals host-microbe-metabolite interplays associated with the aging process in Singaporeans.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2070392}, pmid = {35549618}, issn = {1949-0984}, mesh = {Adult ; Aged ; Aging ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; Metabolome ; Metagenomics ; Singapore ; Young Adult ; }, abstract = {The age-associated alterations in microbiomes vary across populations due to the influence of genetics and lifestyles. To the best of our knowledge, the microbial changes associated with aging have not yet been investigated in Singapore adults. We conducted shotgun metagenomic sequencing of fecal and saliva samples, as well as fecal metabolomics to characterize the gut and oral microbial communities of 62 healthy adult male Singaporeans, including 32 young subjects (age, 23.1 ± 1.4 years) and 30 elderly subjects (age, 69.0 ± 3.5 years). We identified 8 gut and 13 oral species that were differentially abundant in elderly compared to young subjects. By combining the gut and oral microbiomes, 25 age-associated oral-gut species connections were identified. Moreover, oral bacteria Acidaminococcus intestine and Flavonifractor plautii were less prevalent/abundant in elderly gut samples than in young gut samples, whereas Collinsella aerofaciens and Roseburia hominis showed the opposite trends. These results indicate the varied gut-oral communications with aging. Subsequently, we expanded the association studies on microbiome, metabolome and host phenotypic parameters. In particular, Eubacterium eligens increased in elderly compared to young subjects, and was positively correlated with triglycerides, which implies that the potential role of E. eligens in lipid metabolism is altered during the aging process. Our results demonstrated aging-associated changes in the gut and oral microbiomes, as well as the connections between metabolites and host-microbe interactions, thereby deepening the understanding of alterations in the human microbiome during the aging process in a Singapore population.}, } @article {pmid35549463, year = {2022}, author = {Wang, M and Zhang, X and Huang, H and Qin, Z and Liu, C and Chen, Y}, title = {Amino Acid Configuration Affects Volatile Fatty Acid Production during Proteinaceous Waste Valorization: Chemotaxis, Quorum Sensing, and Metabolism.}, journal = {Environmental science & technology}, volume = {56}, number = {12}, pages = {8702-8711}, doi = {10.1021/acs.est.1c07894}, pmid = {35549463}, issn = {1520-5851}, mesh = {*Amino Acids/metabolism ; Anaerobiosis ; Bacteria/metabolism ; Bioreactors ; Chemotaxis ; Fatty Acids, Volatile ; Fermentation ; Hydrogen-Ion Concentration ; Proteins/metabolism ; *Quorum Sensing ; }, abstract = {During proteinaceous waste valorization to produce volatile fatty acids (VFAs), protein needs to be hydrolyzed to amino acids (AAs), but the effects of the configuration of AAs on their biotransformation and VFA production have not been investigated. In this study, more residual d-AAs than their corresponding l-AAs were observed after VFAs were produced from kitchen waste in a pilot-scale bioreactor. For all AAs investigated, the VFA production from d-AAs was lower than that from corresponding l-AAs. The metagenomics and metaproteomics analyses revealed that the l-AA fermentation system exhibited greater bacterial chemotaxis and quorum sensing (QS) than d-AAs, which benefited the establishment of functional microorganisms (such as Clostridium, Sedimentibacter, and Peptoclostridium) and expression of functional proteins (e.g., substrate transportation cofactors, l-AA dehydrogenase, and acidogenic proteins). In addition, d-AAs need to be racemized to l-AAs before being metabolized, and the difference of VFA production between d-AAs and l-AAs decreased with the increase of racemization activity. The findings of the AA configuration affecting bacterial chemotaxis and QS, which altered microorganism communities and functional protein expression, provided a new insight into the reasons for higher l-AA metabolism than d-AAs and more d-AAs left during VFA production from proteinaceous wastes.}, } @article {pmid35548466, year = {2022}, author = {Feng, R and Zhang, T and Kayani, MUR and Wang, Z and Shen, Y and Su, KL and Bielike, K and Chen, L}, title = {Patients with Primary and Secondary Bile Duct Stones Harbor Distinct Biliary Microbial Composition and Metabolic Potential.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {881489}, pmid = {35548466}, issn = {2235-2988}, mesh = {Bacteria/genetics ; *Gallstones/genetics/microbiology ; Humans ; Metagenome ; *Microbiota ; RNA, Ribosomal, 16S/genetics ; }, abstract = {INTRODUCTION: Cholelithiasis has a high incidence worldwide and limited treatment options due to its poorly understood pathogenesis. Furthermore, the role of biliary microbiota in cholelithiasis remains understudied. To address these questions, we performed microbial sequencing from biliary samples from primary bile duct stone (PBDS) and secondary bile duct stone (SBDS) patients.

RESULTS: We analyzed in total 45 biliary samples, including those from cholelithiasis patients with PBDS or SBDS and people with other digestive diseases. 16S rRNA sequencing showed the bacteria family Alcaligenaceae increased in relative abundance in the lithiasis group compared with the non-lithiasis group. In addition, the PBDS group showed significantly lower bacterial diversity than SBDS, with Propionibacteriaceae, Sphingomonadaceae, and Lactobacillaceae as the most significant bacteria families decreased in relative abundance. We further performed whole metagenomic shotgun sequencing (wMGS) and found increased ability of biofilm synthesis and the ability to sense external stimuli in PBDS based on functional annotation of mapped reads. From genome-resolved analysis of the samples, we identified 36 high-quality draft bacterial genome sequences with completion ≥70% and contamination ≤10%. Most of these genomes were classified into Proteobacteria, Firmicutes, or Actinobacteria.

CONCLUSIONS: Our findings indicated that there is a subtle impact on biliary microbiome from cholelithiasis while the difference is more pronounced between the PBDS and SBDS. It was revealed that the diversity of biliary microbiota in PBDS is lower, while some metabolic pathways are up-regulated, including those linked to higher incidence of different types of cancer, providing new insights for the understanding of cholelithiasis with different origin.}, } @article {pmid35548089, year = {2022}, author = {Nogueira, WG and Gois, BVA and Pinheiro, KDC and Aragão, AO and Queiroz, ALC and da Silva, AL and Folador, AC and Ramos, RTJ}, title = {Viral Metagenomics Reveals Widely Diverse Viral Community of Freshwater Amazonian Lake.}, journal = {Frontiers in public health}, volume = {10}, number = {}, pages = {869886}, pmid = {35548089}, issn = {2296-2565}, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Humans ; Lakes/microbiology ; Metagenome ; Metagenomics ; *Viruses/genetics ; }, abstract = {Despite the importance of understanding the ecology of freshwater viruses, there are not many studies on the subject compared to marine viruses. The microbiological interactions in these environments are still poorly known, especially between bacteriophages and their host bacteria and between cyanophages and cyanobacteria. Lake Bologna, Belém, capital of the Brazilian State of Pará, is a water source that supplies the city and its metropolitan region. However, it remains unexplored regarding the contents of its virome and viral diversity composition. Therefore, this work aims to explore the taxonomic diversity of DNA viruses in this lake, especially bacteriophages and cyanophages, since they can act as transducers of resistance genes and reporters of water quality for human consumption. We used metagenomic sequencing data generated by previous studies. We analyzed it at the taxonomic level using the tools Kraken2, Bracken, and Pavian; later, the data was assembled using Genome Detective, which performs the assembly of viruses. The results observed here suggest the existence of a widely diverse viral community and established microbial phage-regulated dynamics in Lake Bolonha. This work is the first ever to describe the virome of Lake Bolonha using a metagenomic approach based on high-throughput sequencing, as it contributes to the understanding of water-related public health concerns regarding the spreading of antibiotic resistance genes and population control of native bacteria and cyanobacteria.}, } @article {pmid35547385, year = {2022}, author = {Dou, YC and Li, YQ}, title = {Influenza A H3N2-Associated Meningoencephalitis in an Older Adult With Viral RNA in Cerebrospinal Fluid: Case Report.}, journal = {Frontiers in neurology}, volume = {13}, number = {}, pages = {874078}, pmid = {35547385}, issn = {1664-2295}, abstract = {Influenza-associated encephalopathy (IAE) is most frequently observed in young children, but less reported in adults. Diagnosis of IAE is difficult, as clinical presentations vary significantly and the influenza virus is rarely detected in cerebrospinal fluid (CSF). Herein, we described the case of an older adult presenting with acute meningoencephalitis due to an influenza A (H3N2) infection and the influenza A (H3N2) RNA is detected in cerebrospinal fluid. To the best of our knowledge, this is infrequently reported in the literature. We emphasize that, in adults presenting with acute viral encephalitis, clinicians should consider an influenza infection as part of the differential diagnosis and that metagenomic next-generation sequencing of CSF for IAE may help establish an accurate diagnosis. It must be emphasized that the administration of steroids in a timely manner following the onset of symptoms may yield a better outcome in patients.}, } @article {pmid35547149, year = {2022}, author = {Hanachi, M and Maghrebi, O and Bichiou, H and Trabelsi, F and Bouyahia, NM and Zhioua, F and Belghith, M and Harigua-Souiai, E and Baouendi, M and Guizani-Tabbane, L and Benkahla, A and Souiai, O}, title = {Longitudinal and Comparative Analysis of Gut Microbiota of Tunisian Newborns According to Delivery Mode.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {780568}, pmid = {35547149}, issn = {1664-302X}, abstract = {Microbiota colonization is a dynamic process that impacts the health status during an individual's lifetime. The composition of the gut microbiota of newborns is conditioned by multiple factors, including the delivery mode (DM). Nonetheless, the DM's influence remains uncertain and is still the subject of debate. In this context, the medical indication and the emergency of a cesarean delivery might have led to confounding conclusions regarding the composition and diversity of the neonatal microbiome. Herein, we used high-resolution shotgun sequencing to decipher the composition and dynamics of the gut microbiota composition of Tunisian newborns. Stool samples were collected from 5 elective cesarean section (ECS) and 5 vaginally delivered (VD) newborns at the following time points: Day 0, Day 15, and Day 30. The ECS and VD newborns showed the same level of bacterial richness and diversity. In addition, our data pointed to a shift in microbiota community composition during the first 2 weeks, regardless of the DM. Both ECS and VD showed a profile dominated by Proteobacteria, Actinobacteria, and Firmicutes. However, ECS showed an underrepresentation of Bacteroides and an enrichment of opportunistic pathogenic species of the ESKAPE group, starting from the second week. Besides revealing the intestinal microbiota of Tunisian newborns, this study provides novel insights into the microbiota perturbations caused by ECS.}, } @article {pmid35547145, year = {2022}, author = {McElhinney, JMWR and Catacutan, MK and Mawart, A and Hasan, A and Dias, J}, title = {Interfacing Machine Learning and Microbial Omics: A Promising Means to Address Environmental Challenges.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {851450}, pmid = {35547145}, issn = {1664-302X}, abstract = {Microbial communities are ubiquitous and carry an exceptionally broad metabolic capability. Upon environmental perturbation, microbes are also amongst the first natural responsive elements with perturbation-specific cues and markers. These communities are thereby uniquely positioned to inform on the status of environmental conditions. The advent of microbial omics has led to an unprecedented volume of complex microbiological data sets. Importantly, these data sets are rich in biological information with potential for predictive environmental classification and forecasting. However, the patterns in this information are often hidden amongst the inherent complexity of the data. There has been a continued rise in the development and adoption of machine learning (ML) and deep learning architectures for solving research challenges of this sort. Indeed, the interface between molecular microbial ecology and artificial intelligence (AI) appears to show considerable potential for significantly advancing environmental monitoring and management practices through their application. Here, we provide a primer for ML, highlight the notion of retaining biological sample information for supervised ML, discuss workflow considerations, and review the state of the art of the exciting, yet nascent, interdisciplinary field of ML-driven microbial ecology. Current limitations in this sphere of research are also addressed to frame a forward-looking perspective toward the realization of what we anticipate will become a pivotal toolkit for addressing environmental monitoring and management challenges in the years ahead.}, } @article {pmid35547137, year = {2022}, author = {Guevara-Rivera, EA and Rodríguez-Negrete, EA and Aréchiga-Carvajal, ET and Leyva-López, NE and Méndez-Lozano, J}, title = {From Metagenomics to Discovery of New Viral Species: Galium Leaf Distortion Virus, a Monopartite Begomovirus Endemic in Mexico.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {843035}, pmid = {35547137}, issn = {1664-302X}, abstract = {Begomoviruses (Family Geminiviridae) are a major group of emerging plant viruses worldwide. The knowledge of begomoviruses is mostly restricted to crop plant systems. Nevertheless, it has been described that non-cultivated plants are important reservoirs and vessels of viral evolution that leads to the emergence of new diseases. High-throughput sequencing (HTS) has provided a powerful tool for speeding up the understanding of molecular ecology and epidemiology of plant virome and for discovery of new viral species. In this study, by performing earlier metagenomics library data mining, followed by geminivirus-related signature single plant searching and RCA-based full-length viral genome cloning, and based on phylogenetic analysis, genomes of two isolates of a novel monopartite begomovirus species tentatively named Galium leaf distortion virus (GLDV), which infects non-cultivated endemic plant Galium mexicanum, were identified in Colima, Mexico. Analysis of the genetic structure of both isolates (GLDV-1 and GLDV-2) revealed that the GLDV genome displays a DNA-A-like structure shared with the new world (NW) bipartite begomoviruses. Nonetheless, phylogenetic analysis using representative members of the main begomovirus American clades for tree construction grouped both GLDV isolates in a clade of the monopartite NW begomovirus, Tomato leaf deformation virus (ToLDeV). A comparative analysis of viral replication regulatory elements showed that the GLDV-1 isolate possesses an array and sequence conservation of iterons typical of NW begomovirus infecting the Solanaceae and Fabaceae families. Interestingly, GLDV-2 showed iteron sequences described only in monopartite begomovirus from OW belonging to a sweepovirus clade that infects plants of the Convolvulaceae family. In addition, the rep iteron related-domain (IRD) of both isolates display FRVQ or FRIS amino acid sequences corresponding to NW and sweepobegomovirus clades for GMV-1 and GMV-2, respectively. Finally, the lack of the GLDV DNA-B segment (tested by molecular detection and biological assays using GLDV-1/2 infectious clones) confirmed the monopartite nature of GLDV. This is the first time that a monopartite begomovirus is described in Mexican ecosystems, and "in silico" geometagenomics analysis indicates that it is restricted to a specific region. These data revealed additional complexity in monopartite begomovirus genetics and geographic distribution and highlighted the importance of metagenomic approaches in understanding global virome ecology and evolution.}, } @article {pmid35547121, year = {2022}, author = {Bryson, SJ and Hunt, KA and Stahl, DA and Winkler, MH}, title = {Metagenomic Insights Into Competition Between Denitrification and Dissimilatory Nitrate Reduction to Ammonia Within One-Stage and Two-Stage Partial-Nitritation Anammox Bioreactor Configurations.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {825104}, pmid = {35547121}, issn = {1664-302X}, abstract = {Anaerobic ammonia oxidizing bacteria (Anammox) are implemented in high-efficiency wastewater treatment systems operated in two general configurations; one-stage systems combine aerobic ammonia oxidizing bacteria (AOB) and Anammox within a single aerated reactor, whereas two-stage configurations separate these processes into discrete tanks. Within both configurations heterotrophic populations that perform denitrification or dissimilatory nitrate reduction to ammonia (DNRA) compete for carbon and nitrate or nitrite and can impact reactor performance because DNRA retains nitrogen in the system. Therefore, it is important to understand how selective pressures imposed by one-stage and two-stage reactor configurations impact the microbial community structure and associated nitrogen transforming functions. We performed 16S rRNA gene and metagenomic sequencing on different biomass fractions (granules, flocs, and suspended biomass) sampled from two facilities treating sludge dewatering centrate: a one-stage treatment facility (Chambers Creek, Tacoma, WA) and a two-stage system (Rotterdam, Netherlands). Similar microbial populations were identified across the different samples, but relative abundances differed between reactor configurations and biomass sources. Analysis of metagenome assembled genomes (MAGs) indicated different lifestyles for abundant heterotrophic populations. Acidobacteria, Bacteroidetes, and Chloroflexi MAGs had varying capacity for DNRA and denitrification. Acidobacteria MAGs possessed high numbers of glycosyl hydrolases and glycosyl transferases indicating a role in biomass degradation. Ignavibacteria and Phycosphaerae MAGs contributed to the greater relative abundance of DNRA associated nrf genes in the two-stage granules and contained genomic features suggesting a preference for an anoxic or microoxic niche. In the one-stage granules a MAG assigned to Burkholderiales accounted for much of the abundant denitrification genes and had genomic features, including the potential for autotrophic denitrification using reduced sulfur, that indicate an ability to adapt its physiology to varying redox conditions. Overall, the competition for carbon substrates between denitrifying and DNRA performing heterotrophs may be impacted by configuration specific selective pressures. In one-stage systems oxygen availability in the bulk liquid and the oxygen gradient within granules would provide a greater niche space for heterotrophic populations capable of utilizing both oxygen and nitrate or nitrite as terminal electron acceptors, compared to two-stage systems where a homogeneous anoxic environment would favor heterotrophic populations primarily adapted to anaerobic metabolism.}, } @article {pmid35547116, year = {2022}, author = {Weyandt, N and Aghdam, SA and Brown, AMV}, title = {Discovery of Early-Branching Wolbachia Reveals Functional Enrichment on Horizontally Transferred Genes.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {867392}, pmid = {35547116}, issn = {1664-302X}, abstract = {Wolbachia is a widespread endosymbiont of insects and filarial nematodes that profoundly influences host biology. Wolbachia has also been reported in rhizosphere hosts, where its diversity and function remain poorly characterized. The discovery that plant-parasitic nematodes (PPNs) host Wolbachia strains with unknown roles is of interest evolutionarily, ecologically, and for agriculture as a potential target for developing new biological controls. The goal of this study was to screen communities for PPN endosymbionts and analyze genes and genomic patterns that might indicate their role. Genome assemblies revealed 1 out of 16 sampled sites had nematode communities hosting a Wolbachia strain, designated wTex, that has highly diverged as one of the early supergroup L strains. Genome features, gene repertoires, and absence of known genes for cytoplasmic incompatibility, riboflavin, biotin, and other biosynthetic functions placed wTex between mutualist C + D strains and reproductive parasite A + B strains. Functional terms enriched in group L included protoporphyrinogen IX, thiamine, lysine, fatty acid, and cellular amino acid biosynthesis, while dN/dS analysis suggested the strongest purifying selection on arginine and lysine metabolism, and vitamin B6, heme, and zinc ion binding, suggesting these as candidate roles in PPN Wolbachia. Higher dN/dS pathways between group L, wPni from aphids, wFol from springtails, and wCfeT from cat fleas suggested distinct functional changes characterizing these early Wolbachia host transitions. PPN Wolbachia had several putative horizontally transferred genes, including a lysine biosynthesis operon like that of the mitochondrial symbiont Midichloria, a spirochete-like thiamine synthesis operon shared only with wCfeT, an ATP/ADP carrier important in Rickettsia, and a eukaryote-like gene that may mediate plant systemic acquired resistance through the lysine-to-pipecolic acid system. The Discovery of group L-like variants from global rhizosphere databases suggests diverse PPN Wolbachia strains remain to be discovered. These findings support the hypothesis of plant-specialization as key to shaping early Wolbachia evolution and present new functional hypotheses, demonstrating promise for future genomics-based rhizosphere screens.}, } @article {pmid35546409, year = {2022}, author = {Liu, S and Moon, CD and Zheng, N and Huws, S and Zhao, S and Wang, J}, title = {Opportunities and challenges of using metagenomic data to bring uncultured microbes into cultivation.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {76}, pmid = {35546409}, issn = {2049-2618}, mesh = {Bacteria/genetics ; Genomics ; *Metagenome/genetics ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Although there is now an extensive understanding of the diversity of microbial life on earth through culture-independent metagenomic DNA sequence analyses, the isolation and cultivation of microbes remains critical to directly study them and confirm their metabolic and physiological functions, and their ecological roles. The majority of environmental microbes are as yet uncultured however; therefore, bringing these rare or poorly characterized groups into culture is a priority to further understand microbiome functions. Moreover, cultivated isolates may find utility in a range of applications, such as new probiotics, biocontrol agents, and agents for industrial processes. The growing abundance of metagenomic and meta-transcriptomic sequence information from a wide range of environments provides more opportunities to guide the isolation and cultivation of microbes of interest. In this paper, we discuss a range of successful methodologies and applications that have underpinned recent metagenome-guided isolation and cultivation of microbe efforts. These approaches include determining specific culture conditions to enrich for taxa of interest, to more complex strategies that specifically target the capture of microbial species through antibody engineering and genome editing strategies. With the greater degree of genomic information now available from uncultivated members, such as via metagenome-assembled genomes, the theoretical understanding of their cultivation requirements will enable greater possibilities to capture these and ultimately gain a more comprehensive understanding of the microbiomes. Video Abstract.}, } @article {pmid35546350, year = {2022}, author = {Chua, PYS and Rasmussen, JA}, title = {Taking metagenomics under the wings.}, journal = {Nature reviews. Microbiology}, volume = {20}, number = {8}, pages = {447}, pmid = {35546350}, issn = {1740-1534}, mesh = {Animals ; *Metagenomics ; *Wings, Animal ; }, } @article {pmid35546170, year = {2022}, author = {Silva, GFD and Gautam, A and Duarte, ICS and Delforno, TP and Oliveira, VM and Huson, DH}, title = {Interactive analysis of biosurfactants in fruit-waste fermentation samples using BioSurfDB and MEGAN.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {7769}, pmid = {35546170}, issn = {2045-2322}, mesh = {Fermentation ; *Fruit ; Metagenome ; *Metagenomics ; Surface-Active Agents ; }, abstract = {Agroindustrial waste, such as fruit residues, are a renewable, abundant, low-cost, commonly-used carbon source. Biosurfactants are molecules of increasing interest due to their multifunctional properties, biodegradable nature and low toxicity, in comparison to synthetic surfactants. A better understanding of the associated microbial communities will aid prospecting for biosurfactant-producing microorganisms. In this study, six samples of fruit waste, from oranges, mangoes and mixed fruits, were subjected to autochthonous fermentation, so as to promote the growth of their associated microbiota, followed by short-read metagenomic sequencing. Using the DIAMOND+MEGAN analysis pipeline, taxonomic analysis shows that all six samples are dominated by Proteobacteria, in particular, a common core consisting of the genera Klebsiella, Enterobacter, Stenotrophomonas, Acinetobacter and Escherichia. Functional analysis indicates high similarity among samples and a significant number of reads map to genes that are involved in the biosynthesis of lipopeptide-class biosurfactants. Gene-centric analysis reveals Klebsiella as the main assignment for genes related to putisolvins biosynthesis. To simplify the interactive visualization and exploration of the surfactant-related genes in such samples, we have integrated the BiosurfDB classification into MEGAN and make this available. These results indicate that microbiota obtained from autochthonous fermentation have the genetic potential for biosynthesis of biosurfactants, suggesting that fruit wastes may provide a source of biosurfactant-producing microorganisms, with applications in the agricultural, chemical, food and pharmaceutical industries.}, } @article {pmid35545600, year = {2022}, author = {Liu, GF and Cui, P and Huang, JJ}, title = {[0ne case report of Chlamydia psittaci pneumonia].}, journal = {Zhonghua lao dong wei sheng zhi ye bing za zhi = Zhonghua laodong weisheng zhiyebing zazhi = Chinese journal of industrial hygiene and occupational diseases}, volume = {40}, number = {4}, pages = {300-303}, doi = {10.3760/cma.j.cn121094-20210330-00176}, pmid = {35545600}, issn = {1001-9391}, support = {ZR2021MH178//Natural Science Foundation of Shandong Province/ ; 2021Q082//Shandong Traditional Chinese Medicine Science and Technology Project/ ; }, mesh = {Bronchoalveolar Lavage Fluid ; *Chlamydophila psittaci ; Humans ; Metagenomics ; *Pneumonia ; *Psittacosis/drug therapy ; }, abstract = {This paper reported a case of severe Chlamydia psittaci pneumonia. The patient had a clear history of contact with sick poultry. The clinical manifestations were dry cough, fever and respiratory failure. Chest CT showed consolidation in the lower lobe of the right lung, and a small amount of exudative ground-glass opacity in the left lung. Chlamydia psittaci was detected in bronchoalveolar lavage fluid (BALF) by metagenomic assay. After treatment with antibiotics such as nitroimidazoles and carbapenems, the patient was discharged with a better health condition.}, } @article {pmid35545448, year = {2022}, author = {Chen, DW and Garud, NR}, title = {Rapid evolution and strain turnover in the infant gut microbiome.}, journal = {Genome research}, volume = {32}, number = {6}, pages = {1124-1136}, pmid = {35545448}, issn = {1549-5469}, support = {R25 MH109172/MH/NIMH NIH HHS/United States ; }, mesh = {Adult ; Feces ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Infant ; Metagenomics ; Mothers ; }, abstract = {Although the ecological dynamics of the infant gut microbiome have been intensely studied, relatively little is known about evolutionary dynamics in the infant gut microbiome. Here we analyze longitudinal fecal metagenomic data from more than 700 infants and their mothers over the first year of life and find that the evolutionary dynamics in infant gut microbiomes are distinct from those of adults. We find evidence for more than a 10-fold increase in the rate of evolution and strain turnover in the infant gut compared with healthy adults, with the mother-infant transition at delivery being a particularly dynamic period in which gene loss dominates. Within a few months after birth, these dynamics stabilize, and gene gains become increasingly frequent as the microbiome matures. We furthermore find that evolutionary changes in infants show signatures of being seeded by a mixture of de novo mutations and transmissions of pre-evolved lineages from the broader family. Several of these evolutionary changes occur in parallel across infants, highlighting candidate genes that may play important roles in the development of the infant gut microbiome. Our results point to a picture of a volatile infant gut microbiome characterized by rapid evolutionary and ecological change in the early days of life.}, } @article {pmid35545042, year = {2022}, author = {Russell, A and Copio, JN and Shi, Y and Kang, S and Franklin, CL and Ericsson, AC}, title = {Reduced housing density improves statistical power of murine gut microbiota studies.}, journal = {Cell reports}, volume = {39}, number = {6}, pages = {110783}, pmid = {35545042}, issn = {2211-1247}, support = {U42 OD010918/OD/NIH HHS/United States ; U42 RR014821/RR/NCRR NIH HHS/United States ; }, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Feces/microbiology ; *Gastrointestinal Microbiome ; Housing ; Mice ; Mice, Inbred C57BL ; }, abstract = {The gut microbiome of humans and animals is critical to host health. Mice are used to investigate the microbiome and its influences; however, the predictive value of such studies is hindered by cage effects due to coprophagy. Our objectives were to evaluate the influence of cage density on the statistical power to detect treatment-dependent effects of a selective pressure on microbiome composition. C57BL/6 mice were separated into groups of 2 or 4 mice per cage and then assigned to groups receiving enrofloxacin, broad-spectrum antibiotics, or control. Fecal samples were collected at weeks 0, 1, and 4, along with contents of the jejunum and cecum. Bacterial DNA analysis examined microbiome richness, diversity, and variability within and between cages. Statistical analyses reveal that reduced housing density consistently results in comparable susceptibility to antibiotics, reduced cage effects, and increased statistical power to detect treatment-associated effects, justifying the practice of reduced housing density.}, } @article {pmid35544980, year = {2022}, author = {Patil, MP and Woo, HE and Lee, IC and Nakashita, S and Kim, K and Kim, JO and Kim, K}, title = {A microcosm study of microbial community profiles during sediment remediation using pyrolyzed oyster shells.}, journal = {Journal of environmental management}, volume = {316}, number = {}, pages = {115229}, doi = {10.1016/j.jenvman.2022.115229}, pmid = {35544980}, issn = {1095-8630}, mesh = {Animals ; Bacteria/genetics ; Geologic Sediments/microbiology ; *Microbiota ; *Ostreidae/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The accumulation of organic and inorganic components in sediments leads to a deterioration in the environment and an imbalance in the coastal ecosystem. Currently, capping is the most effective technology for remediating polluted sediment and restoring ecosystems. A microcosm experiment was designed using pyrolyzed oyster shell (POS). These were mixed in with coastal sediment or added as a capping layer. The results showed that POS effectively decreased pollutants, including PO4-P and NH4-N. Metagenomics analysis was performed using 16S rRNA gene sequencing and the most abundant phyla identified in the POS treated and untreated sediments were Proteobacteria, followed by Firmicutes, Bacteroidetes, Chloroflexi, Fusobacteria, Nitrospirae, and Spirochaetes. The relative abundance of Proteobacteria members of the Class Gammaproteobacteria significantly increased, but Deltaproteobacteria gradually decreased throughout the experiment in POS-covered sediment. This suggests that the POS effectively promoted a shift from anaerobic to facultative anaerobic or aerobic microbial communities in the sediment. Dominant species of facultative anaerobic or microaerophilic bacteria from the order Chromatiales and phylum Nitrospirae were observed in the POS-covered sediment. Based on these study results, it can be concluded that POS is an effective covering material for sediment remediation and restores the microbial communities in sediments.}, } @article {pmid35544285, year = {2022}, author = {Kieft, K and Adams, A and Salamzade, R and Kalan, L and Anantharaman, K}, title = {vRhyme enables binning of viral genomes from metagenomes.}, journal = {Nucleic acids research}, volume = {50}, number = {14}, pages = {e83}, pmid = {35544285}, issn = {1362-4962}, support = {R35 GM137828/GM/NIGMS NIH HHS/United States ; R35 GM143024/GM/NIGMS NIH HHS/United States ; T15 LM007359/LM/NLM NIH HHS/United States ; U19 AI142720/AI/NIAID NIH HHS/United States ; }, mesh = {*Genome, Viral ; High-Throughput Nucleotide Sequencing ; Humans ; *Metagenome ; Metagenomics ; Sequence Analysis, DNA ; Software ; }, abstract = {Genome binning has been essential for characterization of bacteria, archaea, and even eukaryotes from metagenomes. Yet, few approaches exist for viruses. We developed vRhyme, a fast and precise software for construction of viral metagenome-assembled genomes (vMAGs). vRhyme utilizes single- or multi-sample coverage effect size comparisons between scaffolds and employs supervised machine learning to identify nucleotide feature similarities, which are compiled into iterations of weighted networks and refined bins. To refine bins, vRhyme utilizes unique features of viral genomes, namely a protein redundancy scoring mechanism based on the observation that viruses seldom encode redundant genes. Using simulated viromes, we displayed superior performance of vRhyme compared to available binning tools in constructing more complete and uncontaminated vMAGs. When applied to 10,601 viral scaffolds from human skin, vRhyme advanced our understanding of resident viruses, highlighted by identification of a Herelleviridae vMAG comprised of 22 scaffolds, and another vMAG encoding a nitrate reductase metabolic gene, representing near-complete genomes post-binning. vRhyme will enable a convention of binning uncultivated viral genomes and has the potential to transform metagenome-based viral ecology.}, } @article {pmid35544167, year = {2021}, author = {Gladstone, RA and McNally, A and Pöntinen, AK and Tonkin-Hill, G and Lees, JA and Skytén, K and Cléon, F and Christensen, MOK and Haldorsen, BC and Bye, KK and Gammelsrud, KW and Hjetland, R and Kümmel, A and Larsen, HE and Lindemann, PC and Löhr, IH and Marvik, Å and Nilsen, E and Noer, MT and Simonsen, GS and Steinbakk, M and Tofteland, S and Vattøy, M and Bentley, SD and Croucher, NJ and Parkhill, J and Johnsen, PJ and Samuelsen, Ø and Corander, J}, title = {Emergence and dissemination of antimicrobial resistance in Escherichia coli causing bloodstream infections in Norway in 2002-17: a nationwide, longitudinal, microbial population genomic study.}, journal = {The Lancet. Microbe}, volume = {2}, number = {7}, pages = {e331-e341}, pmid = {35544167}, issn = {2666-5247}, support = {/WT_/Wellcome Trust/United Kingdom ; 104169/WT_/Wellcome Trust/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Anti-Bacterial Agents/pharmacology ; Cohort Studies ; Drug Resistance, Bacterial/genetics ; Escherichia coli/genetics ; *Escherichia coli Infections/drug therapy ; Fluoroquinolones/pharmacology ; Humans ; Longitudinal Studies ; Metagenomics ; *Sepsis ; }, abstract = {BACKGROUND: The clonal diversity underpinning trends in multidrug resistant Escherichia coli causing bloodstream infections remains uncertain. We aimed to determine the contribution of individual clones to resistance over time, using large-scale genomics-based molecular epidemiology.

METHODS: This was a longitudinal, E coli population, genomic, cohort study that sampled isolates from 22 512 E coli bloodstream infections included in the Norwegian surveillance programme on resistant microbes (NORM) from 2002 to 2017. 15 of 22 laboratories were able to share their isolates, and the first 22·5% of isolates from each year were requested. We used whole genome sequencing to infer the population structure (PopPUNK), and we investigated the clade composition of the dominant multidrug resistant clonal complex (CC)131 using genetic markers previously reported for sequence type (ST)131, effective population size (BEAST), and presence of determinants of antimicrobial resistance (ARIBA, PointFinder, and ResFinder databases) over time. We compared these features between the 2002-10 and 2011-17 time periods. We also compared our results with those of a longitudinal study from the UK done between 2001 and 2011.

FINDINGS: Of the 3500 isolates requested from the participating laboratories, 3397 (97·1%) were received, of which 3254 (95·8%) were successfully sequenced and included in the analysis. A significant increase in the number of multidrug resistant CC131 isolates from 71 (5·6%) of 1277 in 2002-10 to 207 (10·5%) of 1977 in 2011-17 (p<0·0001), was the largest clonal expansion. CC131 was the most common clone in extended-spectrum β-lactamase (ESBL)-positive isolates (75 [58·6%] of 128) and fluoroquinolone non-susceptible isolates (148 [39·2%] of 378). Within CC131, clade A increased in prevalence from 2002, whereas the global multidrug resistant clade C2 was not observed until 2007. Multiple de-novo acquisitions of both blaCTX-M ESBL-encoding genes in clades A and C1 and gain of phenotypic fluoroquinolone non-susceptibility across the clade A phylogeny were observed. We estimated that exponential increases in the effective population sizes of clades A, C1, and C2 occurred in the mid-2000s, and in clade B a decade earlier. The rate of increase in the estimated effective population size of clade A (Ne=3147) was nearly ten-times that of C2 (Ne=345), with clade A over-represented in Norwegian CC131 isolates (75 [27·0%] of 278) compared with the UK study (8 [5·4%] of 147 isolates).

INTERPRETATION: The early and sustained establishment of predominantly antimicrobial susceptible CC131 clade A isolates, relative to multidrug resistant clade C2 isolates, suggests that resistance is not necessary for clonal success. However, even in the low antibiotic use setting of Norway, resistance to important antimicrobial classes has rapidly been selected for in CC131 clade A isolates. This study shows the importance of genomic surveillance in uncovering the complex ecology underlying multidrug resistance dissemination and competition, which have implications for the design of strategies and interventions to control the spread of high-risk multidrug resistant clones.

FUNDING: Trond Mohn Foundation, European Research Council, Marie Skłodowska-Curie Actions, and the Wellcome Trust.}, } @article {pmid35544149, year = {2021}, author = {Yuki, Y and Nojima, M and Hosono, O and Tanaka, H and Kimura, Y and Satoh, T and Imoto, S and Uematsu, S and Kurokawa, S and Kashima, K and Mejima, M and Nakahashi-Ouchida, R and Uchida, Y and Marui, T and Yoshikawa, N and Nagamura, F and Fujihashi, K and Kiyono, H}, title = {Oral MucoRice-CTB vaccine for safety and microbiota-dependent immunogenicity in humans: a phase 1 randomised trial.}, journal = {The Lancet. Microbe}, volume = {2}, number = {9}, pages = {e429-e440}, doi = {10.1016/S2666-5247(20)30196-8}, pmid = {35544149}, issn = {2666-5247}, mesh = {Animals ; *COVID-19 ; COVID-19 Vaccines ; *Cholera ; Diarrhea ; Humans ; Immunogenicity, Vaccine ; Immunoglobulin A ; Immunoglobulin G ; Male ; *Microbiota ; SARS-CoV-2 ; *Vaccines ; }, abstract = {BACKGROUND: There are an estimated 1·3-4·0 million cases of cholera and 20 000-140 000 cholera-related deaths worldwide each year. The rice-based cholera toxin B subunit (CTB) vaccine, MucoRice-CTB, is an oral candidate vaccine that does not require a cold chain, has shown efficacy in animal models, and could be of benefit in places where there is a paucity of medical infrastructure. We aim to assess the safety, tolerability, and immunogenicity of MucoRice-CTB in humans.

METHODS: We did a double-blind, randomised, placebo-controlled, dose-escalation, phase 1 study at one centre in Tokyo, Japan. Eligible participants were healthy adult men with measurable serum and faecal antibodies against CTB at screening. Participants were excluded if they had allergy to rice; history of cholera or travellers' diarrhoea; poorly controlled constipation; abnormal results on hepatic, renal, or haematological screening tests; use of any over-the-counter drugs within 7 days before first administration; inability to use a medically acceptable means of contraception; or other reasons by medical judgment of the investigator. Three dose cohorts of participants were randomly assigned by block to receive oral MucoRice-CTB (1 g, 3 g, or 6 g) or placebo (1 g, 3 g, or 6 g), once every 2 weeks for 8 weeks (for a total of 4 doses). The dose groups were performed sequentially, and each dose cohort was completed before the higher dose cohort began. All medical staff, participants, and most trial staff were masked to treatment allocation. The primary outcomes were safety and tolerability, measured by 12-lead electrocardiogram; vital signs; haematology, biochemistry, and urinalysis; rice protein-specific serum IgE antibody concentration; and monitoring of adverse events. Participants were assessed at baseline and at 1, 2, 4, 6, 8, and 16 weeks after the first administration of vaccine or placebo. The safety analysis set included all participants enrolled in the trial who received at least one dose of the study drug or placebo and were compliant with good clinical practice. The full analysis population included all participants enrolled in the trial who received at least one dose of the study drug and for whom any data were obtained after the start of study drug administration. Meta-genomic analysis of study participants was performed using bacterial DNA from faecal samples before vaccination. This trial is registered with UMIN.ac.jp, UMIN000018001.

FINDINGS: Between June 23, 2015, and May 31, 2016, 226 participants were recruited and assessed for eligibility. 166 participants were excluded based on health condition or schedule. We then randomly selected 60 male volunteers aged 20-40 years who were enrolled and assigned to MucoRice-CTB (10 participants assigned to 1 g, 10 participants assigned to 3 g, and 10 participants assigned to 6 g), or placebo (10 participants assigned to 1 g, 10 participants assigned to 3 g, and 10 participants assigned to 6 g). All participants received at least one dose of study drug or placebo and were included in the safety analyses. Two participants given MucoRice-CTB 3 g and one participant given MucoRice-CTB 6 g were lost to follow-up and excluded from the efficacy analysis. Serum CTB-specific IgG and IgA antibody concentrations in participants who received 6 g MucoRice-CTB increased significantly in both a time-dependent and dose-dependent manner compared with those in the placebo groups (p for interaction=0·002 for IgG, p=0·004 for IgA). Genome analysis of subjects' faeces before vaccination revealed that compared to non-responders, responders had a gut microbiota of higher diversity with the presence of Escherichia coli and Shigella spp. 28 (93%) of 30 participants who received MucoRice-CTB at any dose had at least one adverse event during the study period, compared with 30 (100%) of 30 participants given placebo. Grade 3 or higher adverse events were reported in four participants in the MucoRice-CTB group (5 events) and four participants in the placebo group (10 events). The most common serious adverse event was haemoglobin decreased (2 events in 2 participants in the pooled MucoRice-CTB group, 2 events in 2 participants in the placebo group; all grade 3).

INTERPRETATION: Participants given MucoRice-CTB showed increased CTB-specific serum IgG and IgA antibody concentrations without inducing serious adverse events, indicating that MucoRice-CTB could be a safe and potent vaccine to prevent diarrhoeal disease. MucoRice-CTB induced neutralising antibodies against diarrhoeal toxins in a gut microbiota-dependent manner. A similar phase 1 trial will be done with participants of other ethnicities to substantiate our findings.

FUNDING: Translational Research Acceleration Network Program of Japan Agency for Medical Research and Development; Ministry of Education, Culture, Sports, Science and Technology, Japan; Science and Technology Research Partnership for Sustainable Development; Grant-in-Aid for Scientific Research (S) (18H05280) (to H K) from the Japan Society for the Promotion of Science (JSPS); Grant-in-Aid for Young Scientists (B) (16K16144) (to Y K) from JSPS; Grant-in-Aid for Young Scientists (18K18148) (to Y K) from JSPS; Grant from International Joint Usage/Research Center (K3002), the Institute of Medical Science, University of Tokyo.}, } @article {pmid35544066, year = {2022}, author = {Kanellakis, NI and Wrightson, JM and Gerry, S and Ilott, N and Corcoran, JP and Bedawi, EO and Asciak, R and Nezhentsev, A and Sundaralingam, A and Hallifax, RJ and Economides, GM and Bland, LR and Daly, E and Yao, X and Maskell, NA and Miller, RF and Crook, DW and Hinks, TSC and Dong, T and Psallidas, I and Rahman, NM}, title = {The bacteriology of pleural infection (TORPIDS): an exploratory metagenomics analysis through next generation sequencing.}, journal = {The Lancet. Microbe}, volume = {3}, number = {4}, pages = {e294-e302}, pmid = {35544066}, issn = {2666-5247}, support = {MR/L018942/1/MRC_/Medical Research Council/United Kingdom ; G1001128/MRC_/Medical Research Council/United Kingdom ; 211050/Z/18/Z/WT_/Wellcome Trust/United Kingdom ; 211050/Z/18/A/WT_/Wellcome Trust/United Kingdom ; }, mesh = {Anti-Bacterial Agents ; Bacteria/genetics ; Bacteria, Anaerobic/genetics ; *Bacteriology ; *Coinfection ; *Communicable Diseases ; *Community-Acquired Infections ; High-Throughput Nucleotide Sequencing ; Humans ; Metagenomics ; Pilot Projects ; *Pleural Diseases/diagnosis ; RNA, Ribosomal, 16S/genetics ; Staphylococcus aureus/genetics ; }, abstract = {BACKGROUND: Pleural infection is a common and severe disease with high morbidity and mortality worldwide. The knowledge of pleural infection bacteriology remains incomplete, as pathogen detection methods based on culture have insufficient sensitivity and are biased to selected microbes. We designed a study with the aim to discover and investigate the total microbiome of pleural infection and assess the correlation between bacterial patterns and 1-year survival of patients.

METHODS: We assessed 243 pleural fluid samples from the PILOT study, a prospective observational study on pleural infection, with 16S rRNA next generation sequencing. 20 pleural fluid samples from patients with pleural effusion due to a non-infectious cause and ten PCR-grade water samples were used as controls. Downstream analysis was done with the DADA2 pipeline. We applied multivariate Cox regression analyses to investigate the association between bacterial patterns and 1-year survival of patients with pleural infection.

FINDINGS: Pleural infection was predominately polymicrobial (192 [79%] of 243 samples), with diverse bacterial frequencies observed in monomicrobial and polymicrobial disease and in both community-acquired and hospital-acquired infection. Mixed anaerobes and other Gram-negative bacteria predominated in community-acquired polymicrobial infection whereas Streptococcus pneumoniae prevailed in monomicrobial cases. The presence of anaerobes (hazard ratio 0·46, 95% CI 0·24-0·86, p=0·015) or bacteria of the Streptococcus anginosus group (0·43, 0·19-0·97, p=0·043) was associated with better patient survival, whereas the presence (5·80, 2·37-14·21, p<0·0001) or dominance (3·97, 1·20-13·08, p=0·024) of Staphylococcus aureus was linked with lower survival. Moreover, dominance of Enterobacteriaceae was associated with higher risk of death (2·26, 1·03-4·93, p=0·041).

INTERPRETATION: Pleural infection is a predominantly polymicrobial infection, explaining the requirement for broad spectrum antibiotic cover in most individuals. High mortality infection associated with S aureus and Enterobacteriaceae favours more aggressive, with a narrower spectrum, antibiotic strategies.

FUNDING: UK Medical Research Council, National Institute for Health Research Oxford Biomedical Research Centre, Wellcome Trust, Oxfordshire Health Services Research Committee, Chinese Academy of Medical Sciences, and John Fell Fund.}, } @article {pmid35544065, year = {2022}, author = {Tsitsiklis, A and Osborne, CM and Kamm, J and Williamson, K and Kalantar, K and Dudas, G and Caldera, S and Lyden, A and Tan, M and Neff, N and Soesanto, V and Harris, JK and Ambroggio, L and Maddux, AB and Carpenter, TC and Reeder, RW and Locandro, C and Simões, EAF and Leroue, MK and Hall, MW and Zuppa, AF and Carcillo, J and Meert, KL and Sapru, A and Pollack, MM and McQuillen, PS and Notterman, DA and Dean, JM and Zinter, MS and Wagner, BD and DeRisi, JL and Mourani, PM and Langelier, CR}, title = {Lower respiratory tract infections in children requiring mechanical ventilation: a multicentre prospective surveillance study incorporating airway metagenomics.}, journal = {The Lancet. Microbe}, volume = {3}, number = {4}, pages = {e284-e293}, pmid = {35544065}, issn = {2666-5247}, support = {UG1 HD050096/HD/NICHD NIH HHS/United States ; UG1 HD063108/HD/NICHD NIH HHS/United States ; R01 HL155418/HL/NHLBI NIH HHS/United States ; K23 HL138461/HL/NHLBI NIH HHS/United States ; UG1 HD034116/HD/NICHD NIH HHS/United States ; U01 HD049934/HD/NICHD NIH HHS/United States ; UG1 HD049981/HD/NICHD NIH HHS/United States ; K23 HL146936/HL/NHLBI NIH HHS/United States ; UG1 HD049983/HD/NICHD NIH HHS/United States ; UG1 HD083170/HD/NICHD NIH HHS/United States ; UG1 HD083166/HD/NICHD NIH HHS/United States ; R01 HL124103/HL/NHLBI NIH HHS/United States ; UG1 HD083171/HD/NICHD NIH HHS/United States ; }, mesh = {Bacteria/genetics ; Child ; Cohort Studies ; Critical Illness ; Haemophilus influenzae ; Humans ; Metagenomics ; Moraxella catarrhalis ; Prospective Studies ; Respiration, Artificial ; *Respiratory Syncytial Virus, Human ; *Respiratory Tract Infections/diagnosis ; United States ; }, abstract = {BACKGROUND: Lower respiratory tract infections (LRTI) are a leading cause of critical illness and mortality in mechanically ventilated children; however, the pathogenic microbes frequently remain unknown. We combined traditional diagnostics with metagenomic next generation sequencing (mNGS) to evaluate the cause of LRTI in critically ill children.

METHODS: We conducted a prospective, multicentre cohort study of critically ill children aged 31 days to 17 years with respiratory failure requiring mechanical ventilation (>72 h) in the USA. By combining bacterial culture and upper respiratory viral PCR testing with mNGS of tracheal aspirate collected from all patients within 24 h of intubation, we determined the prevalence, age distribution, and seasonal variation of viral and bacterial respiratory pathogens detected by either method in children with or without LRTI.

FINDINGS: Between Feb 26, 2015, and Dec 31, 2017, of the 514 enrolled patients, 397 were eligible and included in the study (276 children with LRTI and 121 with no evidence of LRTI). A presumptive microbiological cause was identified in 255 (92%) children with LRTI, with respiratory syncytial virus (127 [46%]), Haemophilus influenzae (70 [25%]), and Moraxella catarrhalis (65 [24%]) being most prevalent. mNGS identified uncommon pathogens including Ureaplasma parvum and Bocavirus. Co-detection of viral and bacterial pathogens occurred in 144 (52%) patients. Incidental carriage of potentially pathogenic microbes occurred in 82 (68%) children without LRTI, with rhinovirus (30 [25%]) being most prevalent. Respiratory syncytial virus (p<0·0001), H influenzae (p=0·0006), and M catarrhalis (p=0·0002) were most common in children younger than 5 years. Viral and bacterial LRTI occurred predominantly during winter months.

INTERPRETATION: These findings demonstrate that respiratory syncytial virus, H influenzae, and M catarrhalis contribute disproportionately to severe paediatric LRTI, co-infections are common, and incidental carriage of potentially pathogenic microbes occurs frequently. Further, we provide a framework for future epidemiological and emerging pathogen surveillance studies, highlighting the potential for metagenomics to enhance clinical diagnosis.

FUNDING: US National Institutes of Health and CZ Biohub.}, } @article {pmid35543767, year = {2022}, author = {Ma, R and Nie, B and Chen, J and Lv, K and Xiao, J and Liu, R}, title = {Full genome sequence of a novel iflavirus from the leafhopper Recilia dorsalis.}, journal = {Archives of virology}, volume = {167}, number = {7}, pages = {1593-1596}, pmid = {35543767}, issn = {1432-8798}, mesh = {Amino Acid Sequence ; Animals ; Genome, Viral ; *Hemiptera ; Open Reading Frames ; Phylogeny ; *RNA Viruses/genetics ; RNA, Viral/genetics ; Sequence Analysis, DNA ; }, abstract = {The leafhopper Recilia dorsalis (family Cicadellidae, tribe Deltocephalini) is a common pest of rice and a transmitter of various viruses. Here, we discovered a novel virus in an R. dorsalis sample and determined its complete genome sequence by metagenomic sequencing and rapid amplification of cDNA ends. Based on a homology search and phylogenetic analysis, we show that the new virus belongs to the genus Iflavirus, family Iflaviridae, and we have tentatively named it "Recilia dorsalis iflavirus 1" (RdIV1). Excluding the polyA tail, the RdIV1 genome is 10,986 nucleotides in length and is predicted to encode a 3,195-amino-acid-long polyprotein that possesses the typical domains of iflaviruses: two rhinovirus-like (rhv-like) capsid domains, a cricket paralysis virus-like (CRPV-like) capsid domain, a helicase domain, a protease domain, and an RNA-dependent RNA polymerase (RdRp) domain. BLAST searches showed that the RdIV1 genome has the highest amino sequence identity (73.8%) in the coat protein region to Euscelidius variegatus virus 1 (EVV-1), a member of to the genus Iflavirus, indicating that RdIV1 can be classified as a new iflavirus.}, } @article {pmid35543338, year = {2022}, author = {Wang, S and Wei, L and Gao, Y and Rong, Y and Zha, Z and Lyu, Y and Feng, Z}, title = {Novel amikacin resistance genes identified from human gut microbiota by functional metagenomics.}, journal = {Journal of applied microbiology}, volume = {133}, number = {2}, pages = {898-907}, doi = {10.1111/jam.15615}, pmid = {35543338}, issn = {1365-2672}, support = {KYYZ2021//Fundamental Research Funds for the Central Universities/ ; 31770049//National Natural Science Foundation of China/ ; }, mesh = {*Amikacin/pharmacology ; Aminoglycosides/pharmacology ; Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Kanamycin ; Methyltransferases/genetics ; Microbial Sensitivity Tests ; RNA, Ribosomal, 16S/genetics ; }, abstract = {AIMS: The aim of this study was to evaluate the diversity and potential for horizontal transfer of amikacin resistance genes from the human gut.

METHODS AND RESULTS: A library of human faecal microbiota was constructed and subjected to functional screening for amikacin resistance. In total, five amikacin resistance genes that conferred relatively high amikacin resistance, with minimum inhibitory concentrations (MICs) ranging from 64 to >512, were identified from the library, including a novel aminoglycoside acetyltransferase gene and a 16S rRNA methyltransferase (MTase) gene, labelled aac (6')-Iao and rmtI, respectively. AAC(6')-Iao showed the highest identity of 48% to AAC(6')-Ian from a clinical isolate Serratia marcescens, whereas RmtI shared the closest amino acid identity of 32% with ArmA from Klebsiella pneumonia. The MICs of these five subclones to six commonly used aminoglycosides were determined. Susceptibility analysis indicated that RmtI was associated with high resistance phenotype to 4,6-disubstituted 2-DOS aminoglycosides, whereas AAC(6')-Iao conferred resistance to amikacin and kanamycin. In addition, kinetic parameters of AAC(6')-Iao were determined, suggesting a strong catalytic effect on amikacin and kanamycin.

CONCLUSIONS: Antibiotic resistance genes with low identity to known sequences can be uncovered by functional metagenomics. In addition, the diversity and prevalence of amikacin resistance genes merit further investigation in extended habitats, especially the 16S rRNA MTase gene that might have been underestimated in previous cognition.

Two novel amikacin resistance genes were identified in this study, including a 16S rRNA methyltransferase gene rmtI and an aminoglycoside acetyltransferase gene aac(6')-Iao. This work would contribute to the in-depth study of the diversity and horizontal transfer potential of amikacin resistance genes in the microbiome of the human gut.}, } @article {pmid35539029, year = {2022}, author = {Hermanto, FE and Warsito, W and Rifa'i, M and Widodo, N and Jatmiko, YD}, title = {Metabarcoding dataset on the elicitation of Soybean and Mungbean using Ragi Tape as elicitors for enhancing secondary metabolites production.}, journal = {Data in brief}, volume = {42}, number = {}, pages = {108209}, pmid = {35539029}, issn = {2352-3409}, abstract = {Ragi Tape (RT) is commonly used as the microbial starter for various Indonesian traditional food. Consist of diverse microbial populations, RT has excellent agents as elicitors to augment the bioactive compounds in Soybean (SB) and Mungbean (MB). Metabarcoding analysis has shown to identify the microbial population involved in elicitation using RT. Inoculated RT from SB and MB were collected to extract the microbial DNA for the post-elicitation group. In comparison, DNA extraction from powdered RT was conducted as a pre-elicitation group. The total DNA were then sequenced by using the MiSeq Illumina platform with 16S rDNA gene region V3-V4 and 18S rDNA gene region V4 as a biomarker for bacterial and fungal identification, correspondingly. The obtained raw-data sequences were then analyzed using QIIME2 pipeline. According to the number of the acquired sequences, the 18S sequencing yielded more DNA strands than the 16S sequencing. However, the number of assigned OTUs was higher in 16S sequences than 18S sequences. From the perspective of the sample, RT has larger distinctive taxa, which were not identified in other samples. This metagenome data will provide fundamental information on RT employment in the elicitation process and further understanding of elicitation mechanisms using RT as biotic elicitors. The data is available at the BioProject database under the NCBI domain with accession no. PRJNA767401.}, } @article {pmid35539022, year = {2022}, author = {Babalola, OO and Nwachukwu, BC and Ayangbenro, AS}, title = {Amplicon sequencing data profiling of bacterial community connected with the rhizospheric soil from sunflower plants.}, journal = {Data in brief}, volume = {42}, number = {}, pages = {108207}, pmid = {35539022}, issn = {2352-3409}, abstract = {This article presents dataset on the bacterial community structure associated with rhizospheric sunflower soils from Lichtenburg, South Africa. The Illumina Miseq sequencing of 16S rRNA gene amplicon unveiled the bacterial community diversities as well as generated metagenomic library from sunflower rhizospheric soils to understand the diversities and distribution. The metagenome contained a total of 41,471 sequences with 45,975 operational taxonomic units (OTUs). Metagenome sequence information is obtainable at NCBI under the Bioproject assigned accession number PRJNA782103. Taxonomic hits distribution from USEARCH analysis at phylum level classification of BN_E discovered predominantly Actinobacteria (33.89%), followed by Proteobacteria (35.45%), Firmicutes (6.45%), Planctomycetes (4.12%), Chloroflexi (4.28%) and Gemmatimonadetes (2.40%). Also, USEARCH assisted analysis of BN_F sample also detected the prevalence of Actinobacteria (45.92%), Proteobacteria (23.23%), Firmicutes (3.84%), Planctomycetes (6.46%), Chloroflexi (4.94%) and Gemmatimonadetes (1.99%), which take part in vital ecological functions and biogeochemical activities needed for plant growth and health.}, } @article {pmid35538594, year = {2022}, author = {Lin, X and Li, YZ and Chen, T and Min, SH and Wang, DF and Ding, MM and Jiang, G}, title = {Effects of wearing personal protective equipment during COVID-19 pandemic on composition and diversity of skin bacteria and fungi of medical workers.}, journal = {Journal of the European Academy of Dermatology and Venereology : JEADV}, volume = {36}, number = {9}, pages = {1612-1622}, pmid = {35538594}, issn = {1468-3083}, mesh = {Bacteria ; *COVID-19/epidemiology ; Fungi ; Health Personnel ; Humans ; Pandemics ; *Personal Protective Equipment ; }, abstract = {BACKGROUND: During the COVID-19 pandemic, wearing PPE can induce skin damage such as erythema, pruritus, erosion, and ulceration among others. Although the skin microbiome is considered important for skin health, the change of the skin microbiome after wearing PPE remains unknown.

OBJECTIVE: The present study aimed to characterize the diversity and structure of bacterial and fungal flora on skin surfaces of healthcare workers wearing personal protective equipment (PPE) during the COVID-19 pandemic using metagenomic next-generation sequencing (mNGS).

METHODS: A total of 10 Chinese volunteers were recruited and the microbiome of their face, hand, and back were analysed before and after wearing PPE. Moreover, VISIA was used to analyse skin features.

RESULTS: Results of alpha bacterial diversity showed that there was statistically significant decrease in alpha diversity indice in the skin samples from face, hand, and three sites after wearing PPE as compared with the indice in the skin samples before wearing PPE. Further, the results of evaluated alpha fungal diversity show that there was a statistically significant decrease in alpha diversity indices in the skin samples from hand after wearing PPE as compared with the indices in the skin samples before wearing PPE (P < 0.05). Results of the current study found that the main bacteria on the face, hand, and back skin samples before wearing the PPE were Propionibacterium spp. (34.04%), Corynebacterium spp. (13.12%), and Staphylococcus spp. (38.07%). The main bacteria found on the skin samples after wearing the PPE were Staphylococcus spp. (31.23%), Xanthomonas spp. (26.21%), and Cutibacterium spp. (42.59%). The fungal community composition was similar in three skin sites before and after wearing PPE.

CONCLUSION: It was evident that wearing PPE may affect the skin microbiota, especially bacteria. Therefore, it was evident that the symbiotic microbiota may reflect the skin health of medical workers during the COVID-19 pandemic.}, } @article {pmid35538590, year = {2022}, author = {Liu, R and Wei, X and Song, W and Wang, L and Cao, J and Wu, J and Thomas, T and Jin, T and Wang, Z and Wei, W and Wei, Y and Zhai, H and Yao, C and Shen, Z and Du, J and Fang, J}, title = {Novel Chloroflexi genomes from the deepest ocean reveal metabolic strategies for the adaptation to deep-sea habitats.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {75}, pmid = {35538590}, issn = {2049-2618}, mesh = {Carbon/metabolism ; *Chloroflexi/genetics ; Ecosystem ; Oceans and Seas ; Sulfur/metabolism ; }, abstract = {BACKGROUND: The deep sea harbors the majority of the microbial biomass in the ocean and is a key site for organic matter (OM) remineralization and storage in the biosphere. Microbial metabolism in the deep ocean is greatly controlled by the generally depleted but periodically fluctuating supply of OM. Currently, little is known about metabolic potentials of dominant deep-sea microbes to cope with the variable OM inputs, especially for those living in the hadal trenches-the deepest part of the ocean.

RESULTS: In this study, we report the first extensive examination of the metabolic potentials of hadal sediment Chloroflexi, a dominant phylum in hadal trenches and the global deep ocean. In total, 62 metagenome-assembled-genomes (MAGs) were reconstructed from nine metagenomic datasets derived from sediments of the Mariana Trench. These MAGs represent six novel species, four novel genera, one novel family, and one novel order within the classes Anaerolineae and Dehalococcoidia. Fragment recruitment showed that these MAGs are globally distributed in deep-sea waters and surface sediments, and transcriptomic analysis indicated their in situ activities. Metabolic reconstruction showed that hadal Chloroflexi mainly had a heterotrophic lifestyle, with the potential to degrade a wide range of organic carbon, sulfur, and halogenated compounds. Our results revealed for the first time that hadal Chloroflexi harbor pathways for the complete hydrolytic or oxidative degradation of various recalcitrant OM, including aromatic compounds (e.g., benzoate), polyaromatic hydrocarbons (e.g., fluorene), polychlorobiphenyl (e.g., 4-chlorobiphenyl), and organochlorine compounds (e.g., chloroalkanes, chlorocyclohexane). Moreover, these organisms showed the potential to synthesize energy storage compounds (e.g., trehalose) and had regulatory modules to respond to changes in nutrient conditions. These metabolic traits suggest that Chloroflexi may follow a "feast-or-famine" metabolic strategy, i.e., preferentially consume labile OM and store the energy intracellularly under OM-rich conditions, and utilize the stored energy or degrade recalcitrant OM for survival under OM-limited condition.

CONCLUSION: This study expands the current knowledge on metabolic strategies in deep-ocean Chlorolfexi and highlights their significance in deep-sea carbon, sulfur, and halogen cycles. The metabolic plasticity likely provides Chloroflexi with advantages for survival under variable and heterogenic OM inputs in the deep ocean. Video Abstract.}, } @article {pmid35538241, year = {2022}, author = {Oguzie, JU and Nwangwu, UC and Oluniyi, PE and Olumade, TJ and George, UE and Kazeem, A and Bankole, BE and Brimmo, FO and Asadu, CC and Chukwuekezie, OC and Ochu, JC and Makwe, CO and Dogunro, FA and Onwude, CO and Nwachukwu, WE and Ezihe, EK and Okonkwo, GK and Umazi, NE and Maikere, J and Agashi, NO and Eloy, EI and Anokwu, SO and Okoronkwo, AI and Nwosu, EM and Etiki, SO and Ngwu, IM and Ihekweazu, C and Folarin, OA and Komolafe, IOO and Happi, CT}, title = {Metagenomic sequencing characterizes a wide diversity of viruses in field mosquito samples in Nigeria.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {7616}, pmid = {35538241}, issn = {2045-2322}, support = {U01HG007480/NH/NIH HHS/United States ; U54 HG007480/HG/NHGRI NIH HHS/United States ; 216619/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; }, mesh = {*Aedes ; Animals ; *Arboviruses ; Humans ; *Insect Viruses ; Mosquito Vectors ; Nigeria/epidemiology ; *RNA Viruses ; }, abstract = {Mosquito vectors are a tremendous public health threat. One in six diseases worldwide is vector-borne transmitted mainly by mosquitoes. In the last couple of years, there have been active Yellow fever virus (YFV) outbreaks in many settings in Nigeria, and nationwide, entomological surveillance has been a significant effort geared towards understanding these outbreaks. In this study, we used a metagenomic sequencing approach to characterize viruses present in vector samples collected during various outbreaks of Yellow fever (YF) in Nigeria between 2017 and 2020. Mosquito samples were grouped into pools of 1 to 50 mosquitoes, each based on species, sex and location. Twenty-five pools of Aedes spp and one pool of Anopheles spp collected from nine states were sequenced and metagenomic analysis was carried out. We identified a wide diversity of viruses belonging to various families in this sample set. Seven different viruses detected included: Fako virus, Phasi Charoen-like virus, Verdadero virus, Chaq like-virus, Aedes aegypti totivirus, cell fusing agent virus and Tesano Aedes virus. Although there are no reports of these viruses being pathogenic, they are an understudied group in the same families and closely related to known pathogenic arboviruses. Our study highlights the power of next generation sequencing in identifying Insect specific viruses (ISVs), and provide insight into mosquito vectors virome in Nigeria.}, } @article {pmid35538082, year = {2022}, author = {Shin, J and Noh, JR and Choe, D and Lee, N and Song, Y and Cho, S and Kang, EJ and Go, MJ and Ha, SK and Kim, JH and Kim, YH and Kim, KS and Kim, BC and Lee, CH and Cho, BK}, title = {Comprehensive 16S rRNA and metagenomic data from the gut microbiome of aging and rejuvenation mouse models.}, journal = {Scientific data}, volume = {9}, number = {1}, pages = {197}, pmid = {35538082}, issn = {2052-4463}, support = {2019M3A9F3065867//National Research Foundation of Korea (NRF)/ ; 2018M3A9H3024759//National Research Foundation of Korea (NRF)/ ; }, mesh = {*Aging/genetics ; Animals ; Disease Models, Animal ; *Gastrointestinal Microbiome/genetics ; Metagenomics ; Mice ; *RNA, Ribosomal, 16S/genetics ; Rejuvenation ; }, abstract = {The gut microbiota is associated with the health and longevity of the host. A few methods, such as fecal microbiota transplantation and oral administration of probiotics, have been applied to alter the gut microbiome and promote healthy aging. The changes in host microbiomes still remain poorly understood. Here, we characterized both the changes in gut microbial communities and their functional potential derived from colon samples in mouse models during aging. We achieved this through four procedures including co-housing, serum injection, parabiosis, and oral administration of Akkermansia muciniphila as probiotics using bacterial 16 S rRNA sequencing and shotgun metagenomic sequencing. The dataset comprised 16 S rRNA sequencing (36,249,200 paired-end reads, 107 sequencing data) and metagenomic sequencing data (307,194,369 paired-end reads, 109 sequencing data), characterizing the taxonomy of bacterial communities and their functional potential during aging and rejuvenation. The generated data expand the resources of the gut microbiome related to aging and rejuvenation and provide a useful dataset for research on developing therapeutic strategies to achieve healthy active aging.}, } @article {pmid35537676, year = {2022}, author = {Nastri, AC and Duarte-Neto, AN and Casadio, LVB and Souza, WM and Claro, IM and Manuli, ER and Selegatto, G and Salomão, MC and Fialkovitz, G and Taborda, M and Almeida, BL and Magri, MC and Guedes, AR and Perdigão Neto, LV and Sataki, FM and Guimarães, T and Mendes-Correa, MC and Tozetto-Mendoza, TR and Fumagalli, MJ and Ho, YL and Maia da Silva, CA and Coletti, TM and Goes de Jesus, J and Romano, CM and Hill, SC and Pybus, O and Rebello Pinho, JR and Ledesma, FL and Casal, YR and Kanamura, CT and Tadeu de Araújo, LJ and Ferreira, CSDS and Guerra, JM and Figueiredo, LTM and Dolhnikoff, M and Faria, NR and Sabino, EC and Alves, VAF and Levin, AS}, title = {Understanding Sabiá virus infections (Brazilian mammarenavirus).}, journal = {Travel medicine and infectious disease}, volume = {48}, number = {}, pages = {102351}, doi = {10.1016/j.tmaid.2022.102351}, pmid = {35537676}, issn = {1873-0442}, support = {MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; MR/S019510/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Antibodies, Neutralizing ; *Arenaviruses, New World ; Brazil/epidemiology ; *Cross Infection ; Humans ; *Yellow Fever ; }, abstract = {BACKGROUND: Only two naturally occurring human Sabiá virus (SABV) infections have been reported, and those occurred over 20 years ago.

METHODS: We diagnosed two new cases of SABV infection using metagenomics in patients thought to have severe yellow fever and described new features of histopathological findings.

RESULTS: We characterized clinical manifestations, histopathology and analyzed possible nosocomial transmission. Patients presented with hepatitis, bleeding, neurological alterations and died. We traced twenty-nine hospital contacts and evaluated them clinically and by RT-PCR and neutralizing antibodies. Autopsies uncovered unique features on electron microscopy, such as hepatocyte "pinewood knot" lesions. Although previous reports with similar New-World arenavirus had nosocomial transmission, our data did not find any case in contact tracing.

CONCLUSIONS: Although an apparent by rare, Brazilian mammarenavirus infection is an etiology for acute hemorrhagic fever syndrome. The two fatal cases had peculiar histopathological findings not previously described. The virological diagnosis was possible only by contemporary techniques such as metagenomic assays. We found no subsequent infections when we used serological and molecular tests to evaluate close contacts.}, } @article {pmid35537512, year = {2022}, author = {Cui, G and Liu, Z and Xu, W and Gao, Y and Yang, S and Grossart, HP and Li, M and Luo, Z}, title = {Metagenomic exploration of antibiotic resistance genes and their hosts in aquaculture waters of the semi-closed Dongshan Bay (China).}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 1}, pages = {155784}, doi = {10.1016/j.scitotenv.2022.155784}, pmid = {35537512}, issn = {1879-1026}, mesh = {*Anti-Bacterial Agents/pharmacology ; Aquaculture ; Bays ; Drug Resistance, Microbial/genetics ; Genes, Bacterial ; Humans ; *Metagenome ; beta-Lactamases/genetics ; }, abstract = {In marine environments, increasing occurrence and numbers of microbial Antibiotic Resistance Gene (ARG) subtypes, especially of new beta-lactamases, have received lots of attention in recent years. Updated databases with novel developed tools provide new opportunities to obtain more comprehensive ARG profiles as well as ARG-carrying hosts. Yet, ARGs in human-associated marine aquaculture environments, e.g. in China, remains largely unknown. Using metagenomic data, we revealed high numbers of Multi-drug Resistance, beta-lactamase and aminoglycoside genes throughout the year. Thereby, Alpha- and Gamma-proteobacteria were assigned to the majority of beta-lactamase-carrying hosts. From Metagenome-assembled genomes, three blaF-like beta-lactamases (91.7-94.7% identity with beta-lactamase from Mycobacterium fortuitum (blaF)) were exclusively observed in an unclassified Mycobacterium genus. Notably, other new beta-lactamases, VMB-1-like (n = 3) (58.5-67.4% identity to Vibrio metallo-beta-lactamase 1 (VMB-1)), were found in Gammaproteobacteria. Additionally, 175 Multi-drug Resistant Organisms possessed at least 3 ARG subtypes, and seven of the potentially pathogenic genera (n = 17) were assigned to Gammaproteobacteria. These results, together with high-risk ARGs (e.g. tetM, dfrA14 and dfrA17), provide hosts and new beta-lactamases of ARGs in Chinese coastal aquaculture.}, } @article {pmid35537043, year = {2022}, author = {Zhao, J and Lu, X and Tie, A and Ngegba, E and Wang, L and Sun, L and Liang, Y and Abdulai, MK and Bah, S and Wang, G and Dong, X and Harding, D and Kan, B}, title = {Molecular diagnostics and next-generation sequencing reveal real etiological characteristics of invasive Salmonella infection in febrile illness in Freetown, Sierra Leone.}, journal = {Emerging microbes & infections}, volume = {11}, number = {1}, pages = {1416-1424}, pmid = {35537043}, issn = {2222-1751}, mesh = {Fever/epidemiology ; High-Throughput Nucleotide Sequencing ; Humans ; Pathology, Molecular ; *Salmonella Infections/diagnosis/epidemiology ; Salmonella typhi ; Sierra Leone/epidemiology ; *Typhoid Fever/diagnosis/epidemiology/microbiology ; }, abstract = {Invasive Salmonella infection, which can cause typhoid/paratyphoid fever and invasive non-typhoidal salmonellosis, is a public health burden in Africa. Accurate diagnosis and etiological characterization are required to conduct prevalence and risk estimations for Salmonella infection; however, the utilization of optimal techniques and surveillance data are still insufficient. In this study, we performed a laboratory-based survey in Freetown, which is the biggest city in Sierra Leone with a high burden of typhoid fever, by using blood culture and molecular methods but not the Widal test, to estimate the prevalence and aetiology of invasive Salmonella infection among fever patients. We found a very low prevalence of typhoid fever in patients with fever during the investigation period, and this prevalence was clearly overestimated by the Widal test. Genome sequencing of the S. Typhi isolate from this work revealed that the strain carried multiple antibiotic resistance genes, and an epidemic clone that has existed in West Africa for years was also detected in Sierra Leone. By using metagenomic sequencing, one patient with invasive non-typhoidal salmonellosis was identified as having bacterial co-infections. Our data highlight that Salmonella surveillance based on accurate laboratory diagnosis and genome sequencing needs to be strengthened to provide a better estimation of the real epidemics and enable potential risk assessment by etiological analysis in Africa. Even in a laboratory with only basic equipment, it is possible to conduct next-generation sequencing for pathogen discovery in bloodstream infections and to determine the etiological characteristics of pathogene without complex combinations of laboratory methods.}, } @article {pmid35536747, year = {2022}, author = {Gotoh, Y and Atsuta, Y and Taniguchi, T and Nishida, R and Nakamura, K and Ogura, Y and Misawa, N and Hayashi, T}, title = {Helicobacter cinaedi is a human-adapted lineage in the Helicobacter cinaedi/canicola/'magdeburgensis' complex.}, journal = {Microbial genomics}, volume = {8}, number = {5}, pages = {}, pmid = {35536747}, issn = {2057-5858}, mesh = {Animals ; *Bacteremia ; Cricetinae ; Dogs ; *Helicobacter/genetics ; *Helicobacter Infections ; Humans ; Rats ; }, abstract = {Helicobacter cinaedi is an enterohepatic Helicobacter that causes bacteremia and other diseases in humans. While H. cinaedi-like strains are isolated from animals, including dog isolates belonging to a recently proposed H. canicola, little is known about the genetic differences between H. cinaedi and these animal isolates. Here, we sequenced 43 H. cinaedi- or H. canicola-like strains isolated from humans, hamsters, rats and dogs and collected 81 genome sequences of H. cinaedi, H. canicola and other enterohepatic Helicobacter strains from public databases. Genomic comparison of these strains identified four distinct clades (clades I-IV) in H. cinaedi/canicola/'magderbugensis' (HCCM) complex. Among these, clade I corresponds to H. cinaedi sensu stricto and represents a human-adapted lineage in the complex. We identified several genomic features unique to clade I. They include the accumulation of antimicrobial resistance-related mutations that reflects the human association of clade I and the larger genome size and the presence of a CRISPR-Cas system and multiple toxin-antitoxin and restriction-modification systems, both of which indicate the contribution of horizontal gene transfer to the evolution of clade I. In addition, nearly all clade I strains but only a few strains belonging to one minor clade contained a highly variable genomic region encoding a type VI secretion system (T6SS), which could play important roles in gut colonization by killing competitors or inhibiting their growth. We also developed a method to systematically search for H. cinaedi sequences in large metagenome data sets based on the results of genome comparison. Using this method, we successfully identified multiple HCCM complex-containing human faecal metagenome samples and obtained the sequence information covering almost the entire genome of each strain. Importantly, all were clade I strains, supporting our conclusion that H. cinaedi sensu stricto is a human-adapted lineage in the HCCM complex.}, } @article {pmid35536293, year = {2022}, author = {Vollmers, J and Wiegand, S and Lenk, F and Kaster, AK}, title = {How clear is our current view on microbial dark matter? (Re-)assessing public MAG & SAG datasets with MDMcleaner.}, journal = {Nucleic acids research}, volume = {50}, number = {13}, pages = {e76}, pmid = {35536293}, issn = {1362-4962}, mesh = {Contig Mapping ; Datasets as Topic ; *Environmental Microbiology ; Genome ; Metagenome ; *Metagenomics ; Single-Cell Analysis/methods ; *Software ; *Workflow ; }, abstract = {As of today, the majority of environmental microorganisms remain uncultured and is therefore referred to as 'microbial dark matter' (MDM). Hence, genomic insights into these organisms are limited to cultivation-independent approaches such as single-cell- and metagenomics. However, without access to cultured representatives for verifying correct taxon-assignments, MDM genomes may cause potentially misleading conclusions based on misclassified or contaminant contigs, thereby obfuscating our view on the uncultured microbial majority. Moreover, gradual database contaminations by past genome submissions can cause error propagations which affect present as well as future comparative genome analyses. Consequently, strict contamination detection and filtering need to be applied, especially in the case of uncultured MDM genomes. Current genome reporting standards, however, emphasize completeness over purity and the de facto gold standard genome assessment tool, checkM, discriminates against uncultured taxa and fragmented genomes. To tackle these issues, we present a novel contig classification, screening, and filtering workflow and corresponding open-source python implementation called MDMcleaner, which was tested and compared to other tools on mock and real datasets. MDMcleaner revealed substantial contaminations overlooked by current screening approaches and sensitively detects misattributed contigs in both novel genomes and the underlying reference databases, thereby greatly improving our view on 'microbial dark matter'.}, } @article {pmid35536081, year = {2022}, author = {Zhou, X and Bai, G and Dong, L and Zhuang, H and Duan, M}, title = {Successful Treatment of Severe Community-Acquired Pneumonia caused by Chlamydia Psittaci: a Case Report.}, journal = {Clinical laboratory}, volume = {68}, number = {5}, pages = {}, doi = {10.7754/Clin.Lab.2021.211127}, pmid = {35536081}, issn = {1433-6510}, mesh = {Aged, 80 and over ; *Chlamydophila psittaci/genetics ; *Community-Acquired Infections/diagnosis/drug therapy ; Humans ; Male ; Metagenomics ; *Pneumonia/diagnosis/drug therapy ; *Psittacosis/diagnosis/drug therapy ; }, abstract = {BACKGROUND: Community acquired pneumonia is a common and deadly condition, which remains a major cause of morbidity and mortality throughout the world. Chlamydia psittaci pneumonia is responsible for less than 5% of community-acquired pneumonia with a fatality rate of 1%. Nonetheless, it is underestimated due to low awareness of the disease and atypical clinical presentation in a majority of the cases. Metagenomic next-generation sequencing can help us diagnose and clarify the etiology in time.

METHODS: We reported a case of an 85-year-old man who presented with intermittent fever and cough with wheezing for 4 days and did a review of related literature.

RESULTS: The patient was admitted to our department due to severe CAP and multiple organ dysfunction. After admission, we applied an empirical antibiotic strategy, performed intubation and invasive ventilation, fluid resuscitation, vasoactive drugs and supportive care. On the third day of admission, metagenomic next-generation sequencing results of blood and bronchoalveolar lavage fluid suggested Chlamydia psittaci. We made a diagnosis of sever Chlamydia psittaci pneumonia and adjusted antibiotics to minocycline combined with azithromycin two days after admission. The patient was successfully cured with a good prognosis.

CONCLUSIONS: Detecting the pathogen as early as possible and achieving accurate diagnosis are essential in infected patients. We can benefit from careful application of metagenomic next-generation sequencing.}, } @article {pmid35536051, year = {2022}, author = {Seitz, VA and McGivern, BB and Daly, RA and Chaparro, JM and Borton, MA and Sheflin, AM and Kresovich, S and Shields, L and Schipanski, ME and Wrighton, KC and Prenni, JE}, title = {Variation in Root Exudate Composition Influences Soil Microbiome Membership and Function.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {11}, pages = {e0022622}, pmid = {35536051}, issn = {1098-5336}, support = {P30 CA046934/CA/NCI NIH HHS/United States ; P30CA046934//CU | Anschutz Medical Campus, University of Colorado (CU Anschutz)/ ; }, mesh = {Exudates and Transudates ; *Microbiota/physiology ; Plant Growth Regulators/metabolism ; Plant Roots/metabolism ; Plants/genetics ; RNA, Ribosomal, 16S/genetics/metabolism ; Rhizosphere ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix, yet the mechanisms by which exudation alters microbial metabolism in soils have been challenging to unravel. Here, utilizing distinct sorghum genotypes, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolism. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments: a high-organic-acid treatment (HOT) and a high-sugar treatment (HST). To parse the response of the soil microbiome to different exudate regimens, laboratory soil reactors were amended with these root exudate treatments as well as a nonexudate control. Amplicon sequencing of the 16S rRNA gene illustrated distinct microbial diversity patterns and membership in response to HST, HOT, or control amendments. Exometabolite changes reflected these microbial community changes, and we observed enrichment of organic and amino acids, as well as possible phytohormones in the HST relative to the HOT and control. Linking the metabolic capacity of metagenome-assembled genomes in the HST to the exometabolite patterns, we identified microorganisms that could produce these phytohormones. Our findings emphasize the tractability of high-resolution multiomics tools to investigate soil microbiomes, opening the possibility of manipulating native microbial communities to improve specific soil microbial functions and enhance crop production. IMPORTANCE Decrypting the chemical interactions between plant roots and the soil microbiome is a gateway for future manipulation and management of the rhizosphere, a soil compartment critical to promoting plant fitness and yields. Our experimental results demonstrate how soil microbial community and genomic diversity is influenced by root exudates of differing chemical compositions and how changes in this microbiome result in altered production of plant-relevant metabolites. Together, these findings demonstrate the tractability of high-resolution multiomics tools to investigate soil microbiomes and provide new information on plant-soil environments useful for the development of efficient and precise microbiota management strategies in agricultural systems.}, } @article {pmid35536037, year = {2022}, author = {Hu, C and Beyda, ND and Garey, KW}, title = {A Vancomycin HPLC Assay for Use in Gut Microbiome Research.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0168821}, pmid = {35536037}, issn = {2165-0497}, support = {U01 AI124290/AI/NIAID NIH HHS/United States ; }, mesh = {Anti-Bacterial Agents ; Chromatography, High Pressure Liquid/methods ; *Gastrointestinal Microbiome ; Humans ; Reproducibility of Results ; *Vancomycin/pharmacokinetics ; }, abstract = {The human microbiome project has revolutionized our understanding of the interaction between commensal microbes and human health. By far, the biggest perturbation of the microbiome involves use of broad-spectrum antibiotics excreted in the gut. Thus, pharmacodynamics of microbiome changes in relation to drug exposure pharmacokinetics is an emerging field. However, reproducibility studies are necessary to develop the field. A simple and fast high-performance liquid chromatography-photodiode array detector (HPLC) method was validated for quantitative fecal vancomycin analysis. Reproducibility of results were tested based on sample storage time, homogeneity of antibiotic within stool, and concentration consistency after lyophilization. The HPLC method enabled the complete elution of vancomycin within ~4.2 min on the reversed-phase C18 column under the isocratic elution mode, with excellent recovery (85% to 110%) over a 4-log, quantitative range (0.4-100 μg/mL). Relative standard derivations (RSD) of intra-day and inter-day results ranged from 0.4% to 5.4%. Using sample stool aliquots of various weights consistently demonstrated similar vancomycin concentrations (mean RSD: 6%; range: 2-16%). After correcting for water concentrations, vancomycin concentrations obtained after lyophilization were similar to the concentrations obtained from the original samples (RSD less than 10%). These methodologies establish sample condition standards for a quantitative HPLC to enable vancomycin pharmacokinetic studies with the human microbiome. IMPORTANCE Research on antibiotic effect on the gut microbiome is an emerging field with standardization of research methods needed. In this study, a simple and fast high-performance liquid chromatography method was validated for quantitative fecal vancomycin analysis. Reproducibility of results were tested to standardize storage time, homogeneity of antibiotic within stool, and concentration consistency after lyophilization. These methodologies establish sample condition standards for a quantitative HPLC to enable vancomycin pharmacokinetic studies with the human microbiome.}, } @article {pmid35536006, year = {2022}, author = {Oliver, A and Xue, Z and Villanueva, YT and Durbin-Johnson, B and Alkan, Z and Taft, DH and Liu, J and Korf, I and Laugero, KD and Stephensen, CB and Mills, DA and Kable, ME and Lemay, DG}, title = {Association of Diet and Antimicrobial Resistance in Healthy U.S. Adults.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0010122}, pmid = {35536006}, issn = {2150-7511}, support = {F32 HD093185/HD/NICHD NIH HHS/United States ; }, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Diet ; Dietary Fiber ; Drug Resistance, Bacterial/genetics ; *Gastrointestinal Microbiome ; Humans ; Phylogeny ; }, abstract = {Antimicrobial resistance (AMR) represents a significant source of morbidity and mortality worldwide, with expectations that AMR-associated consequences will continue to worsen throughout the coming decades. Since resistance to antibiotics is encoded in the microbiome, interventions aimed at altering the taxonomic composition of the gut might allow us to prophylactically engineer microbiomes that harbor fewer antibiotic resistant genes (ARGs). Diet is one method of intervention, and yet little is known about the association between diet and antimicrobial resistance. To address this knowledge gap, we examined diet using the food frequency questionnaire (FFQ; habitual diet) and 24-h dietary recalls (Automated Self-Administered 24-h [ASA24[®]] tool) coupled with an analysis of the microbiome using shotgun metagenome sequencing in 290 healthy adult participants of the United States Department of Agriculture (USDA) Nutritional Phenotyping Study. We found that aminoglycosides were the most abundant and prevalent mechanism of AMR in these healthy adults and that aminoglycoside-O-phosphotransferases (aph3-dprime) correlated negatively with total calories and soluble fiber intake. Individuals in the lowest quartile of ARGs (low-ARG) consumed significantly more fiber in their diets than medium- and high-ARG individuals, which was concomitant with increased abundances of obligate anaerobes, especially from the family Clostridiaceae, in their gut microbiota. Finally, we applied machine learning to examine 387 dietary, physiological, and lifestyle features for associations with antimicrobial resistance, finding that increased phylogenetic diversity of diet was associated with low-ARG individuals. These data suggest diet may be a potential method for reducing the burden of AMR. IMPORTANCE Antimicrobial resistance (AMR) represents a considerable burden to health care systems, with the public health community largely in consensus that AMR will be a major cause of death worldwide in the coming decades. Humans carry antibiotic resistance in the microbes that live in and on us, collectively known as the human microbiome. Diet is a powerful method for shaping the human gut microbiome and may be a tractable method for lessening antibiotic resistance, and yet little is known about the relationship between diet and AMR. We examined this relationship in healthy individuals who contained various abundances of antibiotic resistance genes and found that individuals who consumed diverse diets that were high in fiber and low in animal protein had fewer antibiotic resistance genes. Dietary interventions may be useful for lessening the burden of antimicrobial resistance and might ultimately motivate dietary guidelines which will consider how nutrition can reduce the impact of infectious disease.}, } @article {pmid35536001, year = {2022}, author = {Higginson, EE and Sayeed, MA and Pereira Dias, J and Shetty, V and Ballal, M and Srivastava, SK and Willis, I and Qadri, F and Dougan, G and Mutreja, A}, title = {Microbiome Profiling of Enterotoxigenic Escherichia coli (ETEC) Carriers Highlights Signature Differences between Symptomatic and Asymptomatic Individuals.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0015722}, pmid = {35536001}, issn = {2150-7511}, support = {/WT_/Wellcome Trust/United Kingdom ; 106158/Z/14/Z//Wellcome Trust (WT)/ ; }, mesh = {Adult ; Bacteria/genetics ; Child ; Diarrhea/microbiology ; *Enterotoxigenic Escherichia coli/genetics ; *Escherichia coli Infections/microbiology ; *Gastrointestinal Microbiome ; Humans ; *Microbiota ; }, abstract = {Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrhea in children in low- and middle-income countries (LMICs). However, large-scale pathogen burden studies in children have identified ETEC in the guts of both symptomatic patients and controls. The factors that influence this balance are poorly understood, but it is postulated that the gut microbiome may play a role in either resistance or progression to disease. In this study, we profiled the microbiomes of children and adults from Bangladesh who were asymptomatically or symptomatically infected with ETEC. Symptomatic patients had significantly higher numbers of sequenced reads mapping to both E. coli and two ETEC toxins, suggesting higher bacterial burden. They were also significantly more likely to be coinfected with enteroaggregative E. coli (EAEC) and had higher proportions of other Gammaproteobacteria, including Klebsiella, Salmonella, and Haemophilus. Colonization with ETEC was also associated with increased prevalence of antimicrobial resistance (AMR) genes, most notably those of the β-lactamase class. Taxonomic profiles were distinctly different between all groups in both species richness and composition, although the direction of these changes was different in adults and children. As seen previously, children with high E. coli burdens also had higher proportions of Streptococcus spp., while healthy children were more heavily colonized by Bifidobacterium spp. Our study provides insight into the microbiome changes that occur upon infection with ETEC in an endemic setting and provides rationale for future studies investigating how the microbiome may protect or predispose individuals to symptomatic infections with gastrointestinal pathogens. IMPORTANCE Enterotoxigenic Escherichia coli (ETEC) is an important cause of diarrhea in children in low- and middle-income countries. However, these bacteria are often identified in both patients and healthy controls. We do not yet understand why only some people get sick, but it has been suggested that the gut microbiome might play a role. In this study, we used metagenomic sequencing to profile the gut microbiomes of individuals in Bangladesh, with or without a symptomatic ETEC infection. In general, individuals with high levels of ETEC also harbored other pathogenic E. coli strains, higher proportions of Gammaproteobacteria such as Salmonella and Klebsiella, and a higher burden of antimicrobial resistance genes in their guts. Healthy children, in contrast, had higher levels of bifidobacteria. These data confirm that the composition of the gut microbiome is different between symptomatic and asymptomatic people and provides important preliminary information on the impact of the gut microbiome in intestinal infections.}, } @article {pmid35535499, year = {2022}, author = {Nguyen, TTM and Mai, VH and Kim, HS and Kim, D and Seo, M and An, YJ and Park, S}, title = {Real-Time Monitoring of Host-Gut Microbial Interspecies Interaction in Anticancer Drug Metabolism.}, journal = {Journal of the American Chemical Society}, volume = {144}, number = {19}, pages = {8529-8535}, doi = {10.1021/jacs.1c10998}, pmid = {35535499}, issn = {1520-5126}, mesh = {*Antineoplastic Agents/metabolism/pharmacology ; Bacteria/metabolism ; Fluorouracil/pharmacology ; *Gastrointestinal Microbiome ; Humans ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {Gut microbiome can affect drug metabolism considerably, leading to modified drug response. However, quantitative estimation of host vs. microbial contributions in a living host-gut microbiome system has been challenging. Using the interspecies system of Caenorhabditis elegans and gut bacteria, we developed a real-time approach for monitoring their metabolic interaction in vivo during anticancer drug 5-fluorouracil (5-FU) metabolism. The fluorine NMR-based approach yielded the quantitative contributions to the host 5-FU metabolism made by human gut-microbial species of variable genetic backgrounds. It also experimentally confirmed a bacterial gene-metabolism relationship. Differential 5-FU catabolism among bacterial substrains and the contributions to the host metabolism, unobservable by conventional 16S rRNA metagenomic sequencing, were also found. The metabolic contributions could be correlated with phenotypic developmental toxicity of 5-FU to the host fed with different substrains. Our convenient platform should help to reveal heterogeneity in host-gut microbiome interactions for many drugs in a living symbiotic system.}, } @article {pmid35534630, year = {2022}, author = {Feng, X and Cheng, H and Portik, D and Li, H}, title = {Metagenome assembly of high-fidelity long reads with hifiasm-meta.}, journal = {Nature methods}, volume = {19}, number = {6}, pages = {671-674}, pmid = {35534630}, issn = {1548-7105}, support = {R01 HG010040/HG/NHGRI NIH HHS/United States ; U01 HG010971/HG/NHGRI NIH HHS/United States ; }, mesh = {Genome, Bacterial ; High-Throughput Nucleotide Sequencing ; *Metagenome ; *Microbiota/genetics ; Sequence Analysis, DNA ; Software ; }, abstract = {De novo assembly of metagenome samples is a common approach to the study of microbial communities. Current metagenome assemblers developed for short sequence reads or noisy long reads were not optimized for accurate long reads. We thus developed hifiasm-meta, a metagenome assembler that exploits the high accuracy of recent data. Evaluated on seven empirical datasets, hifiasm-meta reconstructed tens to hundreds of complete circular bacterial genomes per dataset, consistently outperforming other metagenome assemblers.}, } @article {pmid35534501, year = {2022}, author = {Cai, YY and Huang, FQ and Lao, X and Lu, Y and Gao, X and Alolga, RN and Yin, K and Zhou, X and Wang, Y and Liu, B and Shang, J and Qi, LW and Li, J}, title = {Author Correction: Integrated metagenomics identifies a crucial role for trimethylamine-producing Lachnoclostridium in promoting atherosclerosis.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {40}, doi = {10.1038/s41522-022-00303-1}, pmid = {35534501}, issn = {2055-5008}, } @article {pmid35533984, year = {2022}, author = {Suzuki, S and Kadoya, A and Masuda, N and Sugimoto, Y and Takada, H and Mizukawa, K and Takei, A and Chou, HY and Wu, JH}, title = {Macrolide resistance genes and mobile genetic elements in waterways from pig farms to the sea in Taiwan.}, journal = {Journal of global antimicrobial resistance}, volume = {29}, number = {}, pages = {360-370}, doi = {10.1016/j.jgar.2022.04.024}, pmid = {35533984}, issn = {2213-7173}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; Interspersed Repetitive Sequences ; Lincomycin ; *Macrolides/pharmacology ; RNA, Ribosomal, 16S/genetics ; Swine ; Taiwan ; Wastewater/microbiology ; }, abstract = {OBJECTIVES: Macrolides have a long history of use in animals and humans. Dynamics of macrolide-antibiotic resistance genes (ARGs) in waterways from the origin to the sea has not been reported.

METHODS: Resistant bacterial rate was measured by culture method, and copy numbers of macrolide-ARGs, mef(A), erm(B), mph(B), mef(C)-mph(G), and mobile genetic elements (MGEs) traI and IntI1 were quantitated in environmental DNA. Community composition in each site was investigated by 16S rRNA gene metagenomic sequencing. In Yilan area, antibiotics were quantitated.

RESULTS: Surface water samples from pig farms to the sea in southern and northern areas in Taiwan were monitored. Macrolide-resistant bacteria accounted for 3%-28% of total colony-forming bacteria in aquaculture ponds and rivers, whereas in pig farm wastewater it was 26%-100%. Three common macrolide-ARGs mef(A), erm(B), and mph(B) and the relatively new mef(C)-mph(G) were frequently detected in pig farms, but not in aquaculture ponds and the sea. Rivers receiving pig wastewater showed ARG contamination similar to the pig farms. Among the MGEs, IntI1 was frequently distributed in all sites and was positively related to mef(A), erm(B), and mph(B) but not to mef(C)-mph(G).

CONCLUSION: Pig farms are the origin of macrolide-ARGs, although macrolide contamination is low. Since lincomycin was detected in pig farms in the northern area, the increase of macrolide-ARGs is a future concern due to cross-resistance to lincomycin. ARGs abundance in aquaculture ponds was low, though MGEs were detected. Relation of IntI1 to ARG suggests convergence of ARGs to specific MGEs might be time/history dependent.}, } @article {pmid35533914, year = {2022}, author = {Li, CC and Ye, F and Xu, CX and Chang, Q and Liu, XM and Pan, RL}, title = {Effect of Radix Polygalae extract on the colonic dysfunction in rats induced by chronic restraint stress.}, journal = {Journal of ethnopharmacology}, volume = {294}, number = {}, pages = {115349}, doi = {10.1016/j.jep.2022.115349}, pmid = {35533914}, issn = {1872-7573}, mesh = {Animals ; Colon/metabolism ; Drugs, Chinese Herbal ; *NF-kappa B/metabolism ; NLR Family, Pyrin Domain-Containing 3 Protein/metabolism ; Rats ; Rats, Wistar ; Tight Junction Proteins/genetics/metabolism ; *Tryptophan/metabolism ; }, abstract = {Radix Polygalae, a commonly used traditional Chinese herb, has conventionally functioned in tranquilization and sedation, where anti-inflammation may be the underlying mechanism.

AIM OF THE STUDY: Chronic restraint stress (CRS), a risk factor for the etiology of intestinal disorders, was used in the present study to examine whether Radix Polygalae extract (RPE) could modulate colonic dysfunction in CRS rats.

MATERIALS AND METHODS: Wistar rats were exposed to 28-day CRS (6 h daily), and RPE (135 mg/kg and 270 mg/kg) was intragastrically administered 1 h before CRS. Subsequently, the gut microbiota was determined using metagenomic sequencing. Colonic proinflammatory interleukin-1β, -6, and -18 were assayed using qRT-PCR and ELISA. Tight junction proteins were quantified by qRT-PCR and western blotting (WB), and tryptophan metabolic enzymes and metabolites were determined using qRT-PCR and UFLC-QTRAP-5500/MS. Moreover, protein expression of colonic tight junction proteins, NF-κB-NLRP3 signaling involved in the underlying mechanism of RPE were detected by WB.

RESULTS: RPE significantly decreased proinflammatory cytokines and reshaped the gut microbiota, especially the probiotics, including Lactobacillus and Bacteroides. Moreover, RPE could modulate the metabolite contents and enzyme expression associated with colonic tryptophan-kynurenine (TRP-KYN) metabolism and could increase tight junction protein expression in CRS rats. Furthermore, RPE inhibited the activation of NF-κB-NLRP3 signaling in the colon of CRS rats.

CONCLUSION: RPE could modulate colonic inflammation, colonic microbiota, tight junction, TRP-KYN metabolism and NF-κB-NLRP3 signaling to reach a colonic balance of CRS rats. The present study helped us to better understand and appreciate the various beneficial effects of RPE.}, } @article {pmid35533856, year = {2022}, author = {Long, S and Liu, X and Chen, J and Zhao, L and Pavlostathis, SG}, title = {Effect of tetracycline on bio-electrochemically assisted anaerobic methanogenic systems: Process performance, microbial community structure, and functional genes.}, journal = {The Science of the total environment}, volume = {837}, number = {}, pages = {155756}, doi = {10.1016/j.scitotenv.2022.155756}, pmid = {35533856}, issn = {1879-1026}, mesh = {Anaerobiosis ; Anti-Bacterial Agents/metabolism/pharmacology ; Bacteria/metabolism ; Bioreactors/microbiology ; Methane/metabolism ; *Microbiota ; Propionates/metabolism ; Tetracycline/pharmacology ; *Wastewater/microbiology ; }, abstract = {Bio-electrochemically assisted anaerobic methanogenic systems (An-BES) are highly effective in wastewater treatment for methane production and degradation of toxic compounds. However, information on the treatment of antibiotic-bearing wastewater in An-BES is still very limited. This study therefore investigated the effect of tetracycline (TC) on the performance, microbial community, as well as functional and antibiotic resistance genes of An-BES. TC at 1 and 5 mg/L inhibited methane production by less than 4.8% compared to the TC-free control. At 10 mg/L TC, application of 0.5 and 1.0 V decreased methane production by 14 and 9.6%, respectively. Under the effect of 1-10 mg/L TC, application of 1.0 V resulted in a decrease of current from 42.3 to 2.8 mA. TC was mainly removed by adsorption; its removal extent increased by 19.5 and 32.9% with application of 0.5 and 1.0 V, respectively. At 1.0 V, current output was not recovered with the addition of granular activated carbon, which completely removed TC by adsorption. Metagenomic analysis showed that propionate oxidizing bacteria and methanogens were more abundant in electrode biofilms than in suspended culture. Antibiotic resistance genes (ARGs) were less abundant in biofilms than in suspended culture, regardless of whether voltage was applied or not. Application of 1.0 V resulted in the enrichment of Geobacter in the anode and Methanobacterium in the cathode. TC inhibited exoelectrogens, propionate oxidizing bacteria, and the methylmalonyl CoA pathway, leading to a decrease of current output, COD consumption, and methane production. These findings deepen our understanding of the inhibitory effect of TC in An-BES towards efficient bioenergy recovery from antibiotic-bearing wastewater, as well as the response of functional microorganisms to TC in such systems.}, } @article {pmid35533800, year = {2022}, author = {Bessède, E and Mégraud, F}, title = {Microbiota and gastric cancer.}, journal = {Seminars in cancer biology}, volume = {86}, number = {Pt 3}, pages = {11-17}, doi = {10.1016/j.semcancer.2022.05.001}, pmid = {35533800}, issn = {1096-3650}, mesh = {Humans ; Mice ; Animals ; *Stomach Neoplasms/etiology ; *Helicobacter Infections/complications/microbiology/pathology ; *Epstein-Barr Virus Infections/complications ; Herpesvirus 4, Human ; *Helicobacter pylori/genetics ; *Microbiota ; }, abstract = {The discovery of Helicobacter pylori in 1982 drew to an end the stomach being considered as a sterile organ. Later, the progress in molecular methods, especially Next Generation Sequencing and metagenomics, has highlighted the fact that a diverse microbiota including five major phyla could also be present in the stomach. However, when present, H. pylori is the essential species and it influences the other bacterial communities in terms of richness and evenness. It is now well accepted that H. pylori is the main risk factor for gastric cancer, especially the strains harboring the cag pathogenicity island and the CagA oncoprotein, but the need for other factors from the host and the environment can explain the important difference between those infected and those developing gastric cancer. Several studies showed a difference between the gastric microbiota of patients at various stages of development of gastric premalignant and malignant lesions, showing globally a reduced microbial diversity and an increase in the presence of intestinal commensals, especially with nitrosative functions. Other studies showed an increase in oral microbiota. These data suggest that the gastric microbiota other than H. pylori may play a role in the last steps of gastric carcinogenesis. It must also be noted that in a limited number of cases, a virus: the Epstein Barr Virus is responsible for the evolution toward gastric cancer, while in others the mycobiota also needs to be explored. Finally, the use of mice models allowed an exploration of the role of different gastric microbiota in addition to H. pylori.}, } @article {pmid35533355, year = {2022}, author = {Satjarak, A and Graham, LE and Trest, MT and Zedler, J and Knack, JJ and Arancibia-Avila, P}, title = {Nitrogen fixation and other biogeochemically important features of Atacama Desert giant horsetail plant microbiomes inferred from metagenomic contig analysis.}, journal = {Annals of botany}, volume = {130}, number = {1}, pages = {65-75}, pmid = {35533355}, issn = {1095-8290}, mesh = {*Equisetum ; Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; Nitrogen Fixation ; Plants/genetics ; }, abstract = {BACKGROUND AND AIMS: Canyon stream beds in the hyperarid Atacama Desert surprisingly harbour magnificent groves of endemic giant horsetail wetland plants, Equisetum xylochaetum. Our previous metagenomic study of eukaryotes closely associated with this plant indicated that the microbiome included prokaryotes that might likewise influence host success and environment. We explored this possibility by using the metagenomic sequence to characterize prokaryote taxa and functional genes present in the microbiome of E. xylochaetum sampled from remote sites differing in the degree of anthropogenic disturbance. We focused on biogeochemical functions known to be important in wetland ecosystems.

METHODS: To ensure that analyses were conducted on microbes most closely associated with plants, we extracted DNA from well-washed plant organs whose microbial biofilms were revealed with scanning electron microscopy. To assess the benefits of longer sequences for taxonomic and gene classifications, results of analyses performed using contigs were compared with those obtained with unassembled reads. We employed methods widely used to estimate genomic coverage of single taxa for genomic analysis to infer relative abundances of taxa and functional genes.

KEY RESULTS: Key functional bacterial genera (e.g. Hydrogenophaga, Sulfuritalea and Rhodoferax) inferred from taxonomic and functional gene analysis of contigs - but not unassembled reads - to occur on surfaces of (or within) plants at relatively high abundance (>50× genomic coverage) indicated roles in nitrogen, sulfur and other mineral cycling processes. Comparison between sites revealed impacts on biogeochemical functions, e.g. reduced levels of the nifH gene marker under disturbance. Vanadium nitrogenases were more important than molybdenum nitrogenases, indicated by both functional genes and taxa such as Rhodomicrobium and Phaeospirillum inferred from contigs but not unassembled reads.

CONCLUSIONS: Our contig-based metagenomic analyses revealed that microbes performing key wetland biogeochemical functions occur as tightly adherent biofilms on the plant body, not just in water or sediments, and that disturbance reduces such functions, providing arguments for conservation efforts.}, } @article {pmid35532226, year = {2022}, author = {Plaza Oñate, F and Roume, H and Almeida, M}, title = {Recovery of Metagenome-Assembled Genomes from a Human Fecal Sample with Pacific Biosciences High-Fidelity Sequencing.}, journal = {Microbiology resource announcements}, volume = {11}, number = {6}, pages = {e0025022}, pmid = {35532226}, issn = {2576-098X}, support = {ANR-11-DPBS-0001//Agence Nationale de la Recherche (ANR)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (ANR)/ ; ANR-11-DPBS-0001//Agence Nationale de la Recherche (ANR)/ ; }, abstract = {Here, we report the recovery of 89 metagenome-assembled genomes (MAGs) derived from a human fecal sample subjected to Pacific Biosciences (PacBio) high-fidelity (HiFi) sequencing. A total of 9 MAGs consisted of complete circular contigs, and 45 MAGs were high-quality draft genomes according to the minimum information about a metagenome-assembled genome (MIMAG) standards.}, } @article {pmid35532211, year = {2022}, author = {Odintsova, VE and Klimenko, NS and Tyakht, AV}, title = {Approximation of a Microbiome Composition Shift by a Change in a Single Balance Between Two Groups of Taxa.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0015522}, pmid = {35532211}, issn = {2379-5077}, mesh = {RNA, Ribosomal, 16S/genetics ; *Microbiota/genetics ; Metagenomics/methods ; Metagenome ; Social Group ; }, abstract = {Linking microbiome composition obtained from metagenomic or 16S rRNA sequencing to various factors poses a real challenge. The compositional approach to such data is well described: a so-called isometric log-ratio (ILR) transform provides correct treatment of relative abundances. Most existing compositional methods differ in the particular choice of the transform. Although this choice does not influence the prediction of a model, it determines the subset of balances between groups of microbial taxa subsequently used for interpreting the composition shifts. We propose a method to interpret these shifts independently of the initial choice of ILR coordinates by the nearest single-balance shift. We describe here application of the method to regression, classification, and principal balance analysis of compositional data. Analytical treatment and cross-validation show that the approach provides the least-squares estimate of a single-balance shift associated with a factor with possible adjustment for covariates. As for classification and principal balance analysis, the nearest balance method provides results comparable to other compositional tools. Its advantages are the absence of assumptions about the number of taxa included in the balance and its low computational cost. The method is implemented in the R package NearestBalance. IMPORTANCE The method proposed here extends the range of compositional methods providing interpretation of classical statistical tools applied to data converted to the ILR coordinates. It provides a strictly optimal solution in several special cases. The approach is universally applicable to compositional data of any nature, including microbiome data sets.}, } @article {pmid35532210, year = {2022}, author = {Kadlečková, D and Tachezy, R and Erban, T and Deboutte, W and Nunvář, J and Saláková, M and Matthijnssens, J}, title = {The Virome of Healthy Honey Bee Colonies: Ubiquitous Occurrence of Known and New Viruses in Bee Populations.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0007222}, pmid = {35532210}, issn = {2379-5077}, mesh = {Animals ; Bees ; Virome ; Ecosystem ; Australia ; *RNA Viruses ; *Varroidae ; *Bacteriophages ; }, abstract = {Honey bees are globally important pollinators threatened by many different pathogens, including viruses. We investigated the virome of honey bees collected at the end of the beekeeping season (August/September) in Czechia, a Central European country. Samples were examined in biological replicates to assess the homogeneity, stability, and composition of the virome inside a single hive. By choice of healthy workers from colonies, where Varroa destructor was under control, we could identify ubiquitous bee viruses. Deformed wing virus (DWV) was highly prevalent, even though the bees were healthy, without any noticeable disease signs. The overall virome composition (consisting of honey bee-, plant-, and bacterium-infecting viruses) was driven primarily by the hive and its location. However, honey bee-specific viruses showed an uneven distribution within the same hive. In addition, our results point to an unusual cooccurrence between two rhabdoviruses and reveal the presence of five distinct lineages of Lake Sinai viruses (LSVs) clustering with other LSV strains described globally. Comparison of our results with the virome of Australian honey bees, the last truly Varroa- and DWV-free population, showed a strong difference with respect to DWV and a set of diverse members of the Picornavirales, of which the latter were absent in our samples. We hypothesize that the occurrence of DWV introduced by Varroa strongly affects the virome structure despite the mite being under control. IMPORTANCE The Western honey bee, Apis mellifera, is a vital part of our ecosystem as well as cultural heritage. Annual colony losses endanger beekeeping. In this study, we examined healthy bees from the heart of Central Europe, where honey bee colonies have been commonly affected by varroosis over 5 decades. Our virome analysis showed the presence of ubiquitous viruses in colonies where the mite Varroa destructor was under control and no honey bee disease signs were observed. Compared to previous studies, an important part of our study was the analysis of multiple replicates from individual hives. Our overall results indicate that the virome structure (including bee-infecting viruses, plant-infecting viruses, and bacteriophages) is stable within hives; however, the bee-infecting viruses varied largely within interhive replicates, suggesting variation of honey bee viruses within individual bees. Of interest was the striking difference between the viromes of our 39 pools and 9 pools of honey bee viromes previously analyzed in Australia. It could be suggested that Varroa not only affects DWV spread in bee colonies but also affects diverse members of the Picornavirales, which were strongly decreased in Czech bees compared to the Varroa- and DWV-naive Australian bees.}, } @article {pmid35532161, year = {2022}, author = {Demina, TA and Luhtanen, AM and Roux, S and Oksanen, HM}, title = {Virus-Host Interactions and Genetic Diversity of Antarctic Sea Ice Bacteriophages.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0065122}, pmid = {35532161}, issn = {2150-7511}, mesh = {Antarctic Regions ; *Bacteriophages ; Genetic Variation ; Host Microbial Interactions ; *Ice Cover/microbiology ; Seawater/microbiology ; }, abstract = {Although we know the generally appreciated significant roles of microbes in sea ice and polar waters, detailed studies of virus-host systems from such environments have been so far limited by only a few available isolates. Here, we investigated infectivity under various conditions, infection cycles, and genetic diversity of the following Antarctic sea ice bacteriophages: Paraglaciecola Antarctic GD virus 1 (PANV1), Paraglaciecola Antarctic JLT virus 2 (PANV2), Octadecabacter Antarctic BD virus 1 (OANV1), and Octadecabacter Antarctic DB virus 2 (OANV2). The phages infect common sea ice bacteria belonging to the genera Paraglaciecola or Octadecabacter. Although the phages are marine and cold-active, replicating at 0°C to 5°C, they all survived temporal incubations at ≥30°C and remained infectious without any salts or supplemented only with magnesium, suggesting a robust virion assembly maintaining integrity under a wide range of conditions. Host recognition in the cold proved to be effective, and the release of progeny viruses occurred as a result of cell lysis. The analysis of viral genome sequences showed that nearly one-half of the gene products of each virus are unique, highlighting that sea ice harbors unexplored virus diversity. Based on predicted genes typical for tailed double-stranded DNA phages, we suggest placing the four studied viruses in the class Caudoviricetes. Searching against viral sequences from metagenomic assemblies, we revealed that related viruses are not restricted to Antarctica but are also found in distant marine environments. IMPORTANCE Very little is known about sea ice microbes despite the significant role played by sea ice in the global oceans as well as microbial input into biogeochemical cycling. Studies on the sea ice viruses have been typically limited to -omics-based approaches and microscopic examinations of sea ice samples. To date, only four cultivable viruses have been isolated from Antarctic sea ice. Our study of these unique isolates advances the understanding of the genetic diversity of viruses in sea ice environments, their interactions with host microbes, and possible links to other biomes. Such information contributes to more accurate future sea ice biogeochemical models.}, } @article {pmid35531475, year = {2022}, author = {Yuan, Q and Huang, R and Tang, L and Yuan, L and Gao, L and Liu, Y and Cao, Y}, title = {Screening Biomarkers and Constructing a Predictive Model for Symptomatic Urinary Tract Infection and Asymptomatic Bacteriuria in Patients Undergoing Cutaneous Ureterostomy: A Metagenomic Next-Generation Sequencing Study.}, journal = {Disease markers}, volume = {2022}, number = {}, pages = {7056517}, pmid = {35531475}, issn = {1875-8630}, mesh = {*Bacteriuria/diagnosis/drug therapy/microbiology ; Biomarkers/urine ; Female ; High-Throughput Nucleotide Sequencing ; Humans ; Interleukin-6 ; Male ; Ureterostomy ; *Urinary Tract Infections/drug therapy ; }, abstract = {OBJECTIVES: To investigate the clinical diagnostic value of differential flora as biomarkers in patients with symptomatic urinary tract infection (UTI) and asymptomatic bacteriuria (ASB) undergoing cutaneous ureterostomy based on metagenomic next-generation sequencing and construct predictive models to provide a scientific reference for clinical diagnosis and treatment. Material and Methods. According to standard procedures, samples were taken from each patient for routine tests (urine, ureteral stent, and skin swab around the stoma). Cytokine levels in the blood were also detected. Urinary microflora were measured by mNGS, and potential biomarkers for distinguishing UTI and ASB were identified by differential flora. Finally, we generated the predictive models for ASB and UTI using the Lasso method and cytokine levels.

RESULTS: Urine culture was performed for 50 patients with cutaneous ureterostomy; 44 of these patients developed bacteriuria. The incidence of symptomatic bacteriuria was 54.55%. Biomarker analysis showed that Propionimicrobium lymphophilum, Staphylococcus haemolyticus, Stenotrophomonas maltophilia, Ralstonia insidiosa, and Aspergillus sydowii all had good predictive performance and were combined in a single model. The predictive model exhibited good prediction performance (area under the curve (AUC) = 0.8729, sensitivity = 80%, specificity = 83.3%, and cutoff = 1.855). We also identified a significant negative correlation between the weight sum of the abundance for these five characteristic pathogens (Sum_weighted_Reads) and levels of the cytokine IL-6 and IL-1β (P < 0.05).

CONCLUSION: mNGS had a higher positive detection rate for pathogens in urine samples. The selected differential bacteria can be used as biomarkers of ASB and UTI, and the prediction model has good predictive performance. Analysis also showed that the occurrence of symptoms was related to individual immunity. Combined with the Sum_weighted_Reads cutoff and cytokine levels (IL-6 and IL-1β) of differential flora, it was possible to judge the severity of symptoms in cutaneous ureterostomy patients with bacteriuria and provide new insights for the treatment and intervention of ASB and UTI.}, } @article {pmid35531340, year = {2022}, author = {Gan, Z and Liu, J and Wang, Y and Yang, L and Lou, Z and Xia, H and Li, M and Chen, Z and Jiang, Y and Peng, F}, title = {Performance of Metagenomic Next-Generation Sequencing for the Diagnosis of Cryptococcal Meningitis in HIV-Negative Patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {831959}, pmid = {35531340}, issn = {2235-2988}, mesh = {Antigens, Fungal ; *Cryptococcosis ; *Cryptococcus gattii/genetics ; *Cryptococcus neoformans/genetics ; *HIV Infections/complications/diagnosis ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Meningitis, Cryptococcal/cerebrospinal fluid/diagnosis/microbiology ; Metagenomics/methods ; Sensitivity and Specificity ; }, abstract = {OBJECTIVES: Metagenomic next-generation sequencing (mNGS) has been applied more and more widely for the diagnosis of infectious diseases, but its performance in the diagnosis of cryptococcal meningitis (CM) remains unclear.

METHODS: Cerebrospinal fluid (CSF) samples from 197 HIV-negative patients with suspected central nervous system infections were tested simultaneously by mNGS and routine methods [India ink staining, fungal culture, or cryptococcal antigen (CrAg) tests]. The performance of mNGS was evaluated.

RESULTS: Of the 197 enrolled cases, 46 (23.4%) cases were finally diagnosed with CM, including 43 (93.5%) Cryptococcus neoformans infections and 3 (6.5%) Cryptococcus gattii infections. The sensitivity, specificity, positive predictive value, negative predictive value, and concordance rate of mNGS were 93.5% [95% confidence interval (CI) at 86.4%~100.0%], 96.0% (95% CI at 92.9%~99.1%), 87.8%, 98.0%, and 95.4%, respectively. Comparing to the conventional diagnostic methods, the sensitivity and concordance rate of mNGS were slightly lower than those of CrAg tests (97.4%) but higher than those of India ink (63.0%) and culture (76.7%). Besides, mNGS had a sensitivity of 100.0% against culture. It should be noted that mNGS could identify Cryptococcus at species level; C. gattii of the 3 cases was only distinguished by mNGS.

CONCLUSIONS: CSF mNGS can be considered as a supplementary test to diagnose CM and directly distinguish C. gattii from C. neoformans in clinical specimens.}, } @article {pmid35531285, year = {2022}, author = {d'Humières, C and Gaïa, N and Gueye, S and de Lastours, V and Leflon-Guibout, V and Maataoui, N and Duprilot, M and Lecronier, M and Rousseau, MA and Gamany, N and Lescure, FX and Senard, O and Deconinck, L and Dollat, M and Isernia, V and Le Hur, AC and Petitjean, M and Nazimoudine, A and Le Gac, S and Chalal, S and Ferreira, S and Lazarevic, V and Guigon, G and Gervasi, G and Armand-Lefèvre, L and Schrenzel, J and Ruppé, E}, title = {Contribution of Clinical Metagenomics to the Diagnosis of Bone and Joint Infections.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {863777}, pmid = {35531285}, issn = {1664-302X}, abstract = {Bone and joint infections (BJIs) are complex infections that require precise microbiological documentation to optimize antibiotic therapy. Currently, diagnosis is based on microbiological culture, sometimes complemented by amplification and sequencing of the 16S rDNA gene. Clinical metagenomics (CMg), that is, the sequencing of the entire nucleic acids in a sample, was previously shown to identify bacteria not detected by conventional methods, but its actual contribution to the diagnosis remains to be assessed, especially with regard to 16S rDNA sequencing. In the present study, we tested the performance of CMg in 34 patients (94 samples) with suspected BJIs, as compared to culture and 16S rDNA sequencing. A total of 94 samples from 34 patients with suspicion of BJIs, recruited from two sites, were analyzed by (i) conventional culture, (ii) 16S rDNA sequencing (Sanger method), and (iii) CMg (Illumina Technology). Two negative controls were also sequenced by CMg for contamination assessment. Based on the sequencing results of negative controls, 414 out of 539 (76.7%) bacterial species detected by CMg were considered as contaminants and 125 (23.2%) as truly present. For monomicrobial infections (13 patients), the sensitivity of CMg was 83.3% as compared to culture, and 100% as compared to 16S rDNA. For polymicrobial infections (13 patients), the sensitivity of CMg was 50% compared to culture, and 100% compared to 16S rDNA. For samples negative in culture (8 patients, 21 samples), CMg detected 11 bacteria in 10 samples from 5 different patients. In 5/34 patients, CMg brought a microbiological diagnosis where conventional methods failed, and in 16/34 patients, CMg provided additional information. Finally, 99 antibiotic resistance genes were detected in 24 patients (56 samples). Provided sufficient genome coverage (87.5%), a correct inference of antibiotic susceptibility was achieved in 8/8 bacteria (100%). In conclusion, our study demonstrated that the CMg provides complementary and potentially valuable data to conventional methods of BJIs diagnosis.}, } @article {pmid35531281, year = {2022}, author = {Keown, RA and Dums, JT and Brumm, PJ and MacDonald, J and Mead, DA and Ferrell, BD and Moore, RM and Harrison, AO and Polson, SW and Wommack, KE}, title = {Novel Viral DNA Polymerases From Metagenomes Suggest Genomic Sources of Strand-Displacing Biochemical Phenotypes.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {858366}, pmid = {35531281}, issn = {1664-302X}, support = {P20 GM103446/GM/NIGMS NIH HHS/United States ; }, abstract = {Viruses are the most abundant and diverse biological entities on the planet and constitute a significant proportion of Earth's genetic diversity. Most of this diversity is not represented by isolated viral-host systems and has only been observed through sequencing of viral metagenomes (viromes) from environmental samples. Viromes provide snapshots of viral genetic potential, and a wealth of information on viral community ecology. These data also provide opportunities for exploring the biochemistry of novel viral enzymes. The in vitro biochemical characteristics of novel viral DNA polymerases were explored, testing hypothesized differences in polymerase biochemistry according to protein sequence phylogeny. Forty-eight viral DNA Polymerase I (PolA) proteins from estuarine viromes, hot spring metagenomes, and reference viruses, encompassing a broad representation of currently known diversity, were synthesized, expressed, and purified. Novel functionality was shown in multiple PolAs. Intriguingly, some of the estuarine viral polymerases demonstrated moderate to strong innate DNA strand displacement activity at high enzyme concentration. Strand-displacing polymerases have important technological applications where isothermal reactions are desirable. Bioinformatic investigation of genes neighboring these strand displacing polymerases found associations with SNF2 helicase-associated proteins. The specific function of SNF2 family enzymes is unknown for prokaryotes and viruses. In eukaryotes, SNF2 enzymes have chromatin remodeling functions but do not separate nucleic acid strands. This suggests the strand separation function may be fulfilled by the DNA polymerase for viruses carrying SNF2 helicase-associated proteins. Biochemical data elucidated from this study expands understanding of the biology and ecological behavior of unknown viruses. Moreover, given the numerous biotechnological applications of viral DNA polymerases, novel viral polymerases discovered within viromes may be a rich source of biological material for further in vitro DNA amplification advancements.}, } @article {pmid35531257, year = {2022}, author = {Yasir, M and Khan, R and Ullah, R and Bibi, F and Khan, I and Mustafa Karim, A and Al-Ghamdi, AK and Azhar, EI}, title = {Bacterial diversity and the antimicrobial resistome in the southwestern highlands of Saudi Arabia.}, journal = {Saudi journal of biological sciences}, volume = {29}, number = {4}, pages = {2138-2147}, pmid = {35531257}, issn = {1319-562X}, abstract = {Soil is a reservoir of microbial diversity and the most supportive habitat for acquiring and transmitting antimicrobial resistance. Resistance transfer usually occurs from animal to soil and vice versa, and it may ultimately appear in clinical pathogens. In this study, the southwestern highlands of Saudi Arabia were studied to assess the bacterial diversity and antimicrobial resistance that could be affected by the continuous development of tourism in the region. Such effects could have a long-lasting impact on the local environment and community. Culture-dependent, quantitative polymerase chain reaction (qPCR), and shotgun sequencing-based metagenomic approaches were used to evaluate the diversity, functional capabilities, and antimicrobial resistance of bacteria isolated from collected soil samples. Bacterial communities in the southwestern highlands were mainly composed of Proteobacteria, Bacteroidetes, and Actinobacteria. A total of 102 antimicrobial resistance genes (ARGs) and variants were identified in the soil microbiota and were mainly associated with multidrug resistance, followed by macrolide, tetracycline, glycopeptide, bacitracin, and beta-lactam antibiotic resistance. The mechanisms of resistance included efflux, antibiotic target alteration, and antibiotic inactivation. qPCR confirmed the detection of 18 clinically important ARGs. In addition, half of the 49 identified isolates were phenotypically resistant to at least one of the 15 antibiotics tested. Overall, ARGs and indicator genes of anthropogenic activities (human-mitochondrial [hmt] gene and integron-integrase [int1]) were found in relatively lower abundance. Along with a high diversity of bacterial communities, variation was observed in the relative abundance of bacterial taxa among sampling sites in the southwestern highlands of Saudi Arabia.}, } @article {pmid35530307, year = {2022}, author = {Fang, C and Fang, W and Xu, L and Gao, F and Hou, Y and Zou, H and Ma, Y and Moll, JM and Yang, Y and Wang, D and Huang, Y and Ren, H and Zhao, H and Qin, S and Zhong, H and Li, J and Liu, S and Yang, H and Wang, J and Brix, S and Kristiansen, K and Zhang, L}, title = {Distinct Functional Metagenomic Markers Predict the Responsiveness to Anti-PD-1 Therapy in Chinese Non-Small Cell Lung Cancer Patients.}, journal = {Frontiers in oncology}, volume = {12}, number = {}, pages = {837525}, pmid = {35530307}, issn = {2234-943X}, abstract = {BACKGROUND: Programmed death 1 (PD-1) and the ligand of PD-1 (PD-L1) are central targets for immune-checkpoint therapy (ICT) blocking immune evasion-related pathways elicited by tumor cells. A number of PD-1 inhibitors have been developed, but the efficacy of these inhibitors varies considerably and is typically below 50%. The efficacy of ICT has been shown to be dependent on the gut microbiota, and experiments using mouse models have even demonstrated that modulation of the gut microbiota may improve efficacy of ICT.

METHODS: We followed a Han Chinese cohort of 85 advanced non-small cell lung cancer (NSCLC) patients, who received anti-PD-1 antibodies. Tumor biopsies were collected before treatment initiation for whole exon sequencing and variant detection. Fecal samples collected biweekly during the period of anti-PD-1 antibody administration were used for metagenomic sequencing. We established gut microbiome abundance profiles for identification of significant associations between specific microbial taxa, potential functionality, and treatment responses. A prediction model based on random forest was trained using selected markers discriminating between the different response groups.

RESULTS: NSCLC patients treated with antibiotics exhibited the shortest survival time. Low level of tumor-mutation burden and high expression level of HLA-E significantly reduced progression-free survival. We identified metagenomic species and functional pathways that differed in abundance in relation to responses to ICT. Data on differential enrichment of taxa and predicted microbial functions in NSCLC patients responding or non-responding to ICT allowed the establishment of random forest algorithm-adopted models robustly predicting the probability of whether or not a given patient would benefit from ICT.

CONCLUSIONS: Overall, our results identified links between gut microbial composition and immunotherapy efficacy in Chinese NSCLC patients indicating the potential for such analyses to predict outcome prior to ICT.}, } @article {pmid35530048, year = {2022}, author = {Tu, R and Liu, J and Cheng, F and Weng, W and Zhang, H and Shu, Y and Wu, X and Hu, Z and Zhang, J}, title = {Case Report: Unusual Varicella-Zoster Virus Meningoencephalitis With Meningomyelitis Mimicking Central Nervous System Leukemia.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {847219}, pmid = {35530048}, issn = {2296-858X}, abstract = {BACKGROUND: Varicella-Zoster Virus (VZV) is a human pathogen from the α-subfamily of herpesviruses. In immunocompromised patients, VZV may produce disease of the central nervous system (CNS). Clinical manifestations of CNS infection with VZV are non-specific and can mimic other infectious and non-infectious diseases. Due to similar symptoms, CNS infection with VZV represents a diagnostic challenge. Here, we report a case of a patient who showed laboratory and imaging manifestations mimicking the neoplastic etiology.

CASE: A 31-year-old man presented with a 3-day history of headache, 5-h of confusion, generalized tonic-clonic seizures, and transient fever. The patient has a history of acute myelogenous leukemia (AML). His cerebrospinal fluid (CSF) studies revealed markedly elevated protein (10.326 g/L) and atypical cells. Meanwhile, the MRI of brain, cervical, and thoracic spine was reported as extensive (frontal, parieto-occipital and temporal pachymeningeal, and falx cerebri) enhancement and irregular thickening. These examinations suggested a suspicion of CNS involvement of AML. However, based on further investigations with metagenomic next-generation sequencing, a final diagnosis of VZV meningoencephalitis with meningomyelitis was made. With acyclovir and foscarnet sodium therapy, repeated CSF studies revealed normal cell count and protein. No atypical cells were found. The repeated brain MRI also revealed obvious resolution of the previous abnormal pachymeningeal enhancement.

CONCLUSION: This case highlights the importance of recognizing the unusual phenomenon of traditional tests in VZV meningoencephalitis with meningomyelitis, and timely using of further precise examinations to detect viral DNA, which is required to prevent missed diagnosis.}, } @article {pmid35529871, year = {2022}, author = {Li, S and Wang, M and Li, H and Wang, J and Zhang, Q and Zhou, D and Li, J}, title = {Case Report: Overlapping Syndrome of Anti-NMDAR Encephalitis and MOG Inflammatory Demyelinating Disease in a Patient With Human Herpesviruses 7 Infection.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {799454}, pmid = {35529871}, issn = {1664-3224}, mesh = {*Anti-N-Methyl-D-Aspartate Receptor Encephalitis/diagnosis ; *Connective Tissue Diseases ; *Demyelinating Diseases ; Headache ; *Herpesviridae ; Humans ; Myelin-Oligodendrocyte Glycoprotein ; *Optic Neuritis/diagnosis/etiology ; *Roseolovirus Infections/complications/diagnosis ; Seizures ; Syndrome ; }, abstract = {OBJECTIVES: This study reported a case of overlapping anti-N-methyl-D-aspartate receptor (NMDAR) encephalitis and myelin oligodendrocyte glycoprotein (MOG) inflammatory demyelinating disease with human herpesviruses 7 (HHV-7) infection.

METHODS: The detailed clinical characteristics, neuroimaging features, and outcomes of the patient were collected. Polymerase chain reaction (PCR), cell-based assay (CBA) and the tissue-based indirect immunofluorescence assay (TBA) were used for diagnosis.

RESULTS: The clinical manifestations included headache, dizziness, fever, optic neuritis, and epileptic-seizures. Brain magnetic resonance imaging (MRI) showed hyperintensities involving the left frontal, orbital gyrus and bilateral optic nerve with substantial contrast enhancement. Moreover, test for HHV-7 DNA by using the next generation sequencing metagenomics and polymerase chain reaction showed positive result in CSF but not in the serum samples. Anti-HHV-7 IgM and IgG antibodies were detected in both the serum and cerebrospinal fluid. NMDAR antibodies (1:10) were found positive in the patient's CSF by a cell-based assay, and MOG antibodies were positive in the serum (1:10) and CSF (1:32). The patient appeared to respond well to immune therapy and it was found that the clinical symptoms including epileptic-seizure as well as headache were relieved and cerebral lesions almost disappeared after the treatment. However, his vision was not completely restored even at the 8-month follow-up, especially the vision in his right eye which was more seriously damaged.

DISCUSSION: We report a rare case of MOG antibodies and anti-NMDAR encephalitis overlapping syndrome (MNOS) with HHV-7 infection for the first time. The possibility of MNOS needs be considered when optic neuritis occurs in the patients diagnosed with anti-NMDAR encephalitis. Besides, immunotherapy should be initiated as early as possible to improve the treatment outcomes and facilitate complete cure.}, } @article {pmid35528135, year = {2022}, author = {Harrington, V and Lau, L and Crits-Christoph, A and Suez, J}, title = {Interactions of Non-Nutritive Artificial Sweeteners with the Microbiome in Metabolic Syndrome.}, journal = {Immunometabolism}, volume = {4}, number = {2}, pages = {}, pmid = {35528135}, issn = {2084-6835}, support = {DP5 OD029603/OD/NIH HHS/United States ; }, abstract = {Replacing sugar with non-nutritive artificial sweeteners (NAS) is a popular dietary choice for the prevention and management of metabolic syndrome and its comorbidities. However, evidence in human trials is conflicted regarding the efficacy of this strategy and whether NAS may counterintuitively promote, rather than prevent, metabolic derangements. The heterogeneity in outcomes may stem in part from microbiome variation between human participants and across research animal vivaria, leading to differential interactions of NAS with gut bacteria. An increasing body of evidence indicates that NAS can alter the mammalian gut microbiome composition, function, and metabolome, which can, in turn, influence host metabolic health. While there is evidence for microbiome-mediated metabolic shifts in response to NAS, the mechanisms by which NAS affect the gut microbiome, and how the microbiome subsequently affects host metabolic processes, remain unclear. In this viewpoint, we discuss data from human and animal trials and provide an overview of the current evidence for NAS-mediated microbial and metabolomic changes. We also review potential mechanisms through which NAS may influence the microbiome and delineate the next steps required to inform public health policies.}, } @article {pmid35527282, year = {2022}, author = {Kröber, E and Kanukollu, S and Wende, S and Bringel, F and Kolb, S}, title = {A putatively new family of alphaproteobacterial chloromethane degraders from a deciduous forest soil revealed by stable isotope probing and metagenomics.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {24}, pmid = {35527282}, issn = {2524-6372}, support = {Ko2921/10-1//Deutsche Forschungsgemeinschaft/ ; }, abstract = {BACKGROUND: Chloromethane (CH3Cl) is the most abundant halogenated organic compound in the atmosphere and substantially responsible for the destruction of the stratospheric ozone layer. Since anthropogenic CH3Cl sources have become negligible with the application of the Montreal Protocol (1987), natural sources, such as vegetation and soils, have increased proportionally in the global budget. CH3Cl-degrading methylotrophs occurring in soils might be an important and overlooked sink.

RESULTS AND CONCLUSIONS: The objective of our study was to link the biotic CH3Cl sink with the identity of active microorganisms and their biochemical pathways for CH3Cl degradation in a deciduous forest soil. When tested in laboratory microcosms, biological CH3Cl consumption occurred in leaf litter, senescent leaves, and organic and mineral soil horizons. Highest consumption rates, around 2 mmol CH3Cl g[-1] dry weight h[-1], were measured in organic soil and senescent leaves, suggesting that top soil layers are active (micro-)biological CH3Cl degradation compartments of forest ecosystems. The DNA of these [[13]C]-CH3Cl-degrading microbial communities was labelled using stable isotope probing (SIP), and the corresponding taxa and their metabolic pathways studied using high-throughput metagenomics sequencing analysis. [[13]C]-labelled Metagenome-Assembled Genome closely related to the family Beijerinckiaceae may represent a new methylotroph family of Alphaproteobacteria, which is found in metagenome databases of forest soils samples worldwide. Gene markers of the only known pathway for aerobic CH3Cl degradation, via the methyltransferase system encoded by the CH3Cl utilisation genes (cmu), were undetected in the DNA-SIP metagenome data, suggesting that biological CH3Cl sink in this deciduous forest soil operates by a cmu-independent metabolism.}, } @article {pmid35526726, year = {2022}, author = {Kinoshita, Y and Niwa, H and Uchida-Fujii, E and Nukada, T and Ueno, T}, title = {Simultaneous Daily Fecal Microbiota Transplantation Fails to Prevent Metronidazole-Induced Dysbiosis of Equine Gut Microbiota.}, journal = {Journal of equine veterinary science}, volume = {114}, number = {}, pages = {104004}, doi = {10.1016/j.jevs.2022.104004}, pmid = {35526726}, issn = {0737-0806}, mesh = {Animals ; *Dysbiosis/chemically induced/veterinary ; Fecal Microbiota Transplantation/methods/veterinary ; Feces/microbiology ; *Gastrointestinal Microbiome ; *Horse Diseases/chemically induced ; Horses ; Metronidazole ; }, abstract = {Antimicrobial administration can lead to imbalances of gastrointestinal microbiota, called dysbiosis. Dysbiosis sometimes results in diarrhea and enteritis in horses. Fecal microbiota transplantation (FMT) is used to treat affected horses, but whether it is effective as a prophylactic approach for dysbiosis in horses receiving antimicrobials remains unknown. The aim of this study was to assess the efficacy of simultaneous FMT against metronidazole-induced dysbiosis in horses. Changes in the ratios of bacterial families, determined by metagenomic analysis, were similar between the metronidazole-treated group and the simultaneous metronidazole- and FMT-treated group, notably in the Clostridiaceae, Ruminococcaceae, and Enterobacteriaceae. Differences in fecal bacterial compositions were due mainly to metronidazole administration (P = .0003), but not to FMT (P = .3136). Simultaneous FMT at 500 g of donor feces in 1 L of suspension once a day did not inhibit metronidazole-induced dysbiosis. The results show that the FMT protocol needs to be improved to prevent metronidazole-induced gut dysbiosis in horses.}, } @article {pmid35526643, year = {2022}, author = {Drovetski, SV and Schmidt, BK and Lai, JE and Gross, MS and Hladik, ML and Matterson, KO and Karouna-Renier, NK}, title = {Exposure to crop production alters cecal prokaryotic microbiota, inflates virulome and resistome in wild prairie grouse.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {306}, number = {}, pages = {119418}, doi = {10.1016/j.envpol.2022.119418}, pmid = {35526643}, issn = {1873-6424}, mesh = {Animals ; Chickens ; Crop Production ; *Grassland ; *Microbiota ; Quail ; }, abstract = {Chemically intensive crop production depletes wildlife food resources, hinders animal development, health, survival, and reproduction, and it suppresses wildlife immune systems, facilitating emergence of infectious diseases with excessive mortality rates. Gut microbiota is crucial for wildlife's response to environmental stressors. Its composition and functionality are sensitive to diet changes and environmental pollution associated with modern crop production. In this study we use shotgun metagenomics (median 8,326,092 sequences/sample) to demonstrate that exposure to modern crop production detrimentally affects cecal microbiota of sharp-tailed grouse (Tympanuchus phasianellus: 9 exposed, 18 unexposed and greater prairie chickens (T. cupido; 11, 11). Exposure to crop production had greater effect on microbiota richness (t = 6.675, P < 0.001) and composition (PERMANOVA r[2] = 0.212, P = 0.001) than did the host species (t = 4.762, P < 0.001; r[2] = 0.070, P = 0.001) or their interaction (t = 3.449; r[2] = 0.072, both P = 0.001), whereas sex and age had no effect. Although microbiota richness was greater in exposed (T. cupido chao1 = 152.8 ± 20.5; T. phasianellus 115.3 ± 17.1) than in unexposed (102.9 ± 15.1 and 101.1 ± 17.2, respectively) birds, some beneficial bacteria dropped out of exposed birds' microbiota or declined and were replaced by potential pathogens. Exposed birds also had higher richness and load of virulome (mean ± standard deviation; T. cupido 24.8 ± 10.0 and 10.1 ± 5.5, respectively; T. phasianellus 13.4 ± 6.8/4.9 ± 2.8) and resistome (T. cupido 46.8 ± 11.7/28.9 ± 10.2, T. phasianellus 38.3 ± 16.7/18.9 ± 14.2) than unexposed birds (T. cupido virulome: 14.2 ± 13.5, 4.5 ± 4.2; T. cupido resistome: 31.6 ± 20.2 and 13.1 ± 12.0; T. phasianellus virulome: 5.2 ± 4.7 and 1.4 ± 1.5; T. phasianellus resistome: 13.7 ± 16.1 and 4.0 ± 6.4).}, } @article {pmid35526585, year = {2022}, author = {Hao, T and Lin, Q and Ma, J and Tang, W and Xiao, Y and Guo, G}, title = {Microbial behaviours inside alternating anaerobic-anoxic environment of a sulfur cycle-driven EBPR system: A metagenomic investigation.}, journal = {Environmental research}, volume = {212}, number = {Pt C}, pages = {113373}, doi = {10.1016/j.envres.2022.113373}, pmid = {35526585}, issn = {1096-0953}, mesh = {Anaerobiosis ; Bacteria/genetics/metabolism ; *Bioreactors/microbiology ; Metagenome ; *Metagenomics ; Phosphorus/metabolism ; Sewage/microbiology ; Sulfur/metabolism ; }, abstract = {Denitrifying sulfur conversion-assisted enhanced biological phosphorus removal (DS-EBPR) was recently developed for saline wastewater treatment. However, the main functional bacteria and the interrelationship of functional bacteria of the DS-EBPR have not been defined and identified so far. This study used metagenomics and multivariate statistics to deduce the functional microbial community and distribution of functional genes associated with the critical metabolic pathways of carbon (C), nitrogen (N), phosphorus (P) and sulfur (S), particularly regarding how they would behave under the alternating anaerobic-anoxic conditions inside a long-term DS-EBPR system. An analysis of the metagenomics and metabolic functions identified 11 major microbial species which were classifiable into four groups: sulfate reducing bacteria (SRB, 0.8-2.2%), sulfur oxidizing bacteria (SOB, 31.9-37.7%), denitrifying phosphate accumulating organisms (DPAOs, 10.0-15.8%) and glycogen accumulating organisms (GAOs, 3.7-7.7%). The four groups of microorganisms performed their respective metabolisms synergistically. In terms of distribution of functional genes, SRB (Desulfococcus and Desulfobacter) and SOB (Chromatiaceae and Thiobacillus) are not only encoded by the related sulfur conversion genes (sqr, dsrAB, aprAB and sat), but also encoded by the necessary ppx and ppk1 gene for P removal that they can be considered as the potential S-related PAOs. Between the anaerobic and anoxic conditions, the metagenome-based microbial community remained structurally similar, but the functional genes, which encode various key enzymes for the P, N, and S pathways, changed in abundance. This study contributes to our understanding on the interactions and competition between the SRB, SOB, DPAOs, and GAOs in a DS-EBPR system.}, } @article {pmid35526502, year = {2022}, author = {An, Y and Zhang, R and Yang, S and Wang, Y and Lei, Y and Peng, S and Song, L}, title = {Microbial mercury methylation potential in a large-scale municipal solid waste landfill, China.}, journal = {Waste management (New York, N.Y.)}, volume = {145}, number = {}, pages = {102-111}, doi = {10.1016/j.wasman.2022.04.038}, pmid = {35526502}, issn = {1879-2456}, mesh = {China ; Environmental Monitoring ; *Mercury/analysis ; Methylation ; *Methylmercury Compounds/analysis ; Solid Waste/analysis ; Waste Disposal Facilities ; *Water Pollutants, Chemical/analysis ; }, abstract = {Landfills harbor ideal conditions for microbial mercury methylation. However, the levels and distribution of mercury (Hg) and methylmercury (MeHg), potential microbial Hg methylation, and their linkage within landfills are largely unknown. In the present study, total mercury (THg), MeHg, the Hg methylation gene (hgcA) and mer operon were quantified in 30 waste samples from different depths (0-30 m) at 5 locations within a large-scale landfill in China. The average concentrations of THg and MeHg in the solid waste samples were 1422.91 ng/g and 3.15 ng/g, respectively. THg (up to 14405.29 ng/g) and MeHg (up to 10.42 ng/g) have high concentrations in the middle part (10-15 m) along the depth profiles. The concentration of THg was strongly positively (both p < 0.05) correlated with the MeHg concentration and the relative abundance of hgcA, indicating that the THg concentration can play an important role in microbial Hg methylation. The hgcA genes were detected in most samples and mer operon were detected in all samples. Combined hgcA qPCR and metagenomics data showed that Archaea Methanofollis may mainly account for Hg methylation within landfills. These findings provide fundamental knowledge on Hg cycles in landfills.}, } @article {pmid35526357, year = {2022}, author = {Parente, E and Zotta, T and Ricciardi, A}, title = {FoodMicrobionet v4: A large, integrated, open and transparent database for food bacterial communities.}, journal = {International journal of food microbiology}, volume = {372}, number = {}, pages = {109696}, doi = {10.1016/j.ijfoodmicro.2022.109696}, pmid = {35526357}, issn = {1879-3460}, mesh = {*Bacteria/genetics ; DNA, Bacterial/genetics ; High-Throughput Nucleotide Sequencing/methods ; *Microbiota/genetics ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sequence Analysis, DNA ; }, abstract = {With the availability of high-throughput sequencing techniques our knowledge of the structure and dynamics of food microbial communities has made a quantum leap. However, this knowledge is dispersed in a large number of papers and hard data are only partly available through powerful on-line databases and tools such as QIITA, MGnify and the Integrated Microbial Next Generation Sequencing platform, whose annotation is not optimized for foods. Here, we present the 4th iteration of FoodMicrobionet, a database of the composition of bacterial microbial communities of foods and food environments. With 180 studies and 10,151 samples belonging to 8 major food groups FoodMicrobionet 4.1.2 is arguably the largest and best annotated database on food bacterial communities. This version includes 1684 environmental samples and 8467 food samples, belonging to 16 L1 categories and 196 L6 categories of the EFSA FoodEx2 classification and is approximately 4 times larger than previous version (3.1, https://doi.org/10.1016/j.ijfoodmicro.2019.108249). As a representative case study among the many potential applications of FoodMicrobionet, we confirm that taxonomic assignment at the genus level can be performed confidently for the majority of amplicon sequence variants using the most commonly used 16S RNA gene target regions (V1-V3, V3-V4, V4), with best results with higher quality sequences and longer fragment lengths, but that care should be exercised in confirming the assignment at species level. Both FoodMicrobionet and related data and software conform to FAIR (findable, accessible, interoperable, reusable/reproducible) criteria for scientific data and software and are freely available on public repositories (GitHub, Mendeley data). Even if FoodMicrobionet does not have the sophistication of QIITA, IMNGS and MGnify, we feel that this iteration, due to its size and diversity, provides a valuable asset for both the scientific community and industrial and regulatory stakeholders.}, } @article {pmid35526296, year = {2022}, author = {Xiao, R and Zhu, W and Zheng, Y and Xu, S and Lu, H}, title = {Active assimilators of soluble microbial products produced by wastewater anammox bacteria and their roles revealed by DNA-SIP coupled to metagenomics.}, journal = {Environment international}, volume = {164}, number = {}, pages = {107265}, doi = {10.1016/j.envint.2022.107265}, pmid = {35526296}, issn = {1873-6750}, mesh = {Anaerobic Ammonia Oxidation ; Bacteria/metabolism ; Bioreactors/microbiology ; DNA/metabolism ; Glycine/metabolism ; *Metagenomics ; Methionine/metabolism ; Nitrogen/metabolism ; Oxidation-Reduction ; Sewage ; *Wastewater ; }, abstract = {Heterotrophic bacteria grow on influent organics or soluble microbial products (SMP) in wastewater anammox processes, playing key roles in facilitating microbial aggregation and reducing excess nitrate. The overgrowth of heterotrophs represents one of the major causes of anammox process failure, while the metabolic functions of coexisting heterotrophs and their roles in anammox process remain vague. This study aimed at revealing metabolic interactions between AnAOB and active SMP assimilators by integrating [13]C DNA-stable isotope probing, metabolomic and metagenomic approaches. Glycine, aspartate, and glutamate with low biosynthetic energy cost were the major SMP components produced by AnAOB (net yield: 44.8, 10.4, 8.1 mg·g NH4[+]-N[-1]). Glycine was likely synthesized by AnAOB via the reductive glycine pathway which is oxygen-tolerant, supporting heterotrophic growth. Fermentative Chloroflexi bacterium OLB13, denitrifying Gemmatimonadaceae and Burkholderiaceae bacterium JOSHI-001 were active SMP assimilators, which were prevalent in globally distributed wastewater anammox reactors as core taxa. They likely formed a mutualistic relationship with auxotrophic Ca. Kuenenia by providing necessities such as methionine, folate, 4'-phosphopantetheine, and molybdopterin cofactor, and receiving vitamin B12 for methionine synthesis. For the first time, the identify and metabolic features of SMP assimilators in wastewater anammox communities were revealed. Supplying necessities secreted by heterotrophs could be helpful to the endeavor of AnAOB enrichment. Practically, maintaining active but not overgrown SMP assimilators is critical to efficient and stable operation of wastewater anammox processes.}, } @article {pmid35525881, year = {2022}, author = {Gontijo, MTP and Teles, MP and Vidigal, PMP and Brocchi, M}, title = {Expanding the Database of Signal-Anchor-Release Domain Endolysins Through Metagenomics.}, journal = {Probiotics and antimicrobial proteins}, volume = {14}, number = {4}, pages = {603-612}, pmid = {35525881}, issn = {1867-1314}, mesh = {*Anti-Infective Agents/metabolism ; *Bacteriophages/genetics/metabolism ; Endopeptidases/chemistry/genetics ; Glycoside Hydrolases/metabolism ; Gram-Negative Bacteria ; Metagenomics ; }, abstract = {Endolysins are bacteriophage-derived lytic enzymes with antimicrobial activity. The action of endolysins against Gram-negative bacteria remains a challenge due to the physical protection of the outer membrane. However, recent research has demonstrated that signal-anchor-release (SAR) endolysins permeate the outer membrane of Gram-negative bacteria. This study investigates 2628 putative endolysin genes identified in 183,298 bacteriophage genomes. Previously, bioinformatic approaches resulted in a database of 66 SAR endolysins. This manuscript almost doubles the list with 53 additional SAR endolysin candidates. Forty-eight of the putative SAR endolysins described in this study contained one muramidase catalytic domain, and five included additional cell wall-binding domains at the C-terminus. For the moment, SAR domains are found in four protein families: glycoside hydrolase family 19 (GH19), glycoside hydrolase family 24 (GH24), glycoside hydrolase family 25 (GH25), and glycoside hydrolase family 108 (GH108). These SAR lysis are clustered in eight groups based on biochemical properties and domain presence/absence. Therefore, in this study, we expand the arsenal of endolysin candidates that might act against Gram-negative bacteria and develop a consult database for antimicrobial proteins derived from bacteriophages.}, } @article {pmid35525356, year = {2022}, author = {Zhang, Y and Zhang, S and Yuan, Y and Li, Y and Zhu, R and Yang, Y and Xing, S and Wang, Y and Wu, Y and Liao, X and Mi, J}, title = {Metagenomic assembly reveals the circadian oscillations of the microbiome and antibiotic resistance genes in a model of laying hens.}, journal = {The Science of the total environment}, volume = {836}, number = {}, pages = {155692}, doi = {10.1016/j.scitotenv.2022.155692}, pmid = {35525356}, issn = {1879-1026}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Chickens/genetics ; Drug Resistance, Microbial/genetics ; Female ; Genes, Bacterial ; *Metagenome ; *Microbiota ; }, abstract = {The increasing risks of antibiotic resistance genes (ARGs) in livestock feces have attracted global attention. However, how the rhythmic activity of ARGs changes in fecal microbiota remains largely unclear. In our study, we collected 52 fresh fecal samples every 6 h over 72 h from laying hens and characterized circadian oscillations of bacteria and ARGs using an approach based on assembled metagenome shotgun sequencing. We found that 14% of commensal bacterial taxonomic units fluctuated over 24 h. A total of 33 out of 281 ARGs and 17 of 574 mobile genetic elements (MGEs) featured rhythmic patterns in feces. lnuC and ANT(6)H-lb were the two most abundant ARGs with circadian oscillation identified from feces, and they increased during the day and decreased at night. Acetate, butyrate, propionate, and 78 out of 392 MetaCyc pathways relating to short-chain fatty acid (SCFA) metabolism featured circadian oscillations. Assessment of the above ARG-other element connections revealed that 17 ARGs presented strong correlations with 7 MGEs, and 2 SCFAs (acetate and propanoate) and bacterial species in feces. Structural equation model (SEM) analysis showed that ARGs were directly affected by microbial β-diversity and MGEs. These results showed a comprehensive map of ARGs over 24 h and revealed circadian oscillations of ARGs, which are influenced by key bacterial species, MGEs, and metabolites. Together, our findings advance comprehension of circadian oscillations of ARGs in the fecal microbiota and provide a reference for ARGs control and management.}, } @article {pmid35525218, year = {2022}, author = {Geng, H and Wang, F and Yan, C and Ma, S and Zhang, Y and Qin, Q and Tian, Z and Liu, R and Chen, H and Zhou, B and Yuan, R}, title = {Rhizosphere microbial community composition and survival strategies in oligotrophic and metal(loid) contaminated iron tailings areas.}, journal = {Journal of hazardous materials}, volume = {436}, number = {}, pages = {129045}, doi = {10.1016/j.jhazmat.2022.129045}, pmid = {35525218}, issn = {1873-3336}, mesh = {Bacteria/genetics ; Iron/analysis ; Metals/analysis ; *Microbiota ; Mining ; Plants ; Rhizosphere ; Soil/chemistry ; Soil Microbiology ; *Soil Pollutants/analysis ; }, abstract = {In this study, the metal(loid) fractions in two alkaline iron tailings areas with similar physico-chemical properties and the enrichment ability of dominant plants in these areas were investigated. Additionally, high-throughput sequencing and metagenome analysis were used to examine the rhizosphere microbial community structures and their strategies and potential for carbon fixation, nitrogen metabolism, and metal(loid) resistance in mining areas. Results showed that Salsola collina, Setaria viridis, and Xanthium sibiricum have strong enrichment capacity for As, and the maximum transport factor for Mn can reach 4.01. The richness and diversity of bacteria were the highest in rhizosphere tailings, and the dominant phyla were Proteobacteria, Actinobacteria, Ascomycota, and Thaumarchaeota. The key taxa present in rhizosphere tailings were generally metal(loid) resistant, especially Sphingomonas, Pseudomonas, Nocardioides, and Microbacterium. The reductive citrate cycle was the main carbon fixation pathway of microorganisms in tailings. Rhizosphere microorganisms have evolved a series of survival strategies and can adapt to oligotrophic and metal(loid) polluted mining environments. The results of this study provide a basis for the potential application of plant-microbial in situ remediation of alkaline tailings.}, } @article {pmid35524899, year = {2022}, author = {You, HS and Lee, SH and Lee, YJ and Lee, H and Kang, SS and Hyun, SH}, title = {Next-Generation Sequencing Results Vary Between Cultured and Uncultured Microbes.}, journal = {Current microbiology}, volume = {79}, number = {6}, pages = {187}, pmid = {35524899}, issn = {1432-0991}, support = {PA-I000001//korean national police agency/ ; }, mesh = {Bacteria/genetics ; Firmicutes ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Next-generation sequencing (NGS) technology has led to innovations in environmental metagenomics and investigations involving humans and microbes. However, it is necessary to analyze the components that will affect analysis of the method upon processing a large amount of information. In particular, the processing method after sample collection affects the NGS results, and it is necessary to check for inaccurate results. Here, we show that the microbial communities obtained from fingertip samples differ from those obtained from fingertips remaining on mobile phones and desks, when cultured or not for 24 h. We also confirmed changes in microbial communities in fingertip samples from desks incubated for 2, 4, 8, 16, and 24 h. Samples of prints from mobile phones that are considerably vulnerable to external factors were not analyzed. Ratios of Firmicutes and Bacillus were, respectively, increased in cultures at the phylum and species levels. Collectively, we identified bacterial species that can aid in determining whether a sample has been cultured. In addition, although microbial communities differed depending on sample types, we confirmed changes after culture for 4 and 8 h. However, since this study is a sample limited to three types, it is necessary to analyze other types of samples in the same way and check whether they are applicable to all types. This strategy can verify the suitability of samples for deriving informative results from cultured or uncultured bacterial communities.}, } @article {pmid35524337, year = {2022}, author = {Delgado, LF and Andersson, AF}, title = {Evaluating metagenomic assembly approaches for biome-specific gene catalogues.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {72}, pmid = {35524337}, issn = {2049-2618}, mesh = {Algorithms ; Cluster Analysis ; Ecosystem ; *Metagenome/genetics ; *Metagenomics/methods ; }, abstract = {BACKGROUND: For many environments, biome-specific microbial gene catalogues are being recovered using shotgun metagenomics followed by assembly and gene calling on the assembled contigs. The assembly is typically conducted either by individually assembling each sample or by co-assembling reads from all the samples. The co-assembly approach can potentially recover genes that display too low abundance to be assembled from individual samples. On the other hand, combining samples increases the risk of mixing data from closely related strains, which can hamper the assembly process. In this respect, assembly on individual samples followed by clustering of (near) identical genes is preferable. Thus, both approaches have potential pros and cons, but it remains to be evaluated which assembly strategy is most effective. Here, we have evaluated three assembly strategies for generating gene catalogues from metagenomes using a dataset of 124 samples from the Baltic Sea: (1) assembly on individual samples followed by clustering of the resulting genes, (2) co-assembly on all samples, and (3) mix assembly, combining individual and co-assembly.

RESULTS: The mix-assembly approach resulted in a more extensive nonredundant gene set than the other approaches and with more genes predicted to be complete and that could be functionally annotated. The mix assembly consists of 67 million genes (Baltic Sea gene set, BAGS) that have been functionally and taxonomically annotated. The majority of the BAGS genes are dissimilar (< 95% amino acid identity) to the Tara Oceans gene dataset, and hence, BAGS represents a valuable resource for brackish water research.

CONCLUSION: The mix-assembly approach represents a feasible approach to increase the information obtained from metagenomic samples. Video abstract.}, } @article {pmid35524297, year = {2022}, author = {Zhu, D and Zhang, Q and Rui, Z and Xu, S}, title = {Pulmonary invasive mucinous adenocarcinoma mimicking pulmonary actinomycosis.}, journal = {BMC pulmonary medicine}, volume = {22}, number = {1}, pages = {181}, pmid = {35524297}, issn = {1471-2466}, support = {PWYgy2018-06//Outstanding Clinical Discipline Project of Shanghai Pudong/ ; }, mesh = {*Actinomycosis/diagnosis ; *Adenocarcinoma of Lung ; *Adenocarcinoma, Mucinous/diagnosis/pathology ; Aged ; Female ; Humans ; Lung/pathology ; *Lung Diseases ; *Lung Neoplasms/diagnosis/pathology ; }, abstract = {BACKGROUND: Primary pulmonary invasive mucinous adenocarcinoma is a rare and distinct subtype of lung adenocarcinoma.

CASE PRESENTATION: A 72-year-old woman presented with productive cough for two months and fever for six days. Chest computed tomography (CT) showed a mass in the left lower lobe. Sputum culture tested negative for bacteria, but the sequence of Actinomyces meyeri was detected by metagenomic next generation sequencing from the bronchoalveolar lavage fluid. It was considered a pathogenic bacterium as the normalized number of DNA sequencing reads was 10 times higher than the normal level. The patient's symptoms alleviated quickly, and the chest CT lesion shrank to a third of the original size following treatment with penicillin for two months. However, a repeat chest CT performed after four months of treatment revealed that the lesion had expanded. Positron emission tomography/CT revealed that fluorodeoxyglucose metabolism was increased in the mass with surrounding ground glass density of the left lower lobe. Furthermore, CT-guided percutaneous lung biopsy was performed, and hematoxylin-eosin staining showed columnar tumor cells with abundant mucin in the cytoplasm with a basal nucleus. Finally, the patient was diagnosed with pulmonary invasive mucinous adenocarcinoma and agreed to undergo a thoracoscopic surgery.

CONCLUSIONS: Pulmonary invasive mucinous adenocarcinoma is a subset of lung adenocarcinoma with low incidence rate. The clinical features and CT findings are non-specific. A histopathological diagnosis is of fundamental importance in preventing misdiagnosis.}, } @article {pmid35524279, year = {2022}, author = {Hwengwere, K and Paramel Nair, H and Hughes, KA and Peck, LS and Clark, MS and Walker, CA}, title = {Antimicrobial resistance in Antarctica: is it still a pristine environment?.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {71}, pmid = {35524279}, issn = {2049-2618}, mesh = {Animals ; Animals, Wild ; Antarctic Regions ; *Anti-Bacterial Agents/pharmacology ; Bacteria ; Birds ; *Drug Resistance, Bacterial ; }, abstract = {Although the rapid spread of antimicrobial resistance (AMR), particularly in relation to clinical settings, is causing concern in many regions of the globe, remote, extreme environments, such as Antarctica, are thought to be relatively free from the negative impact of human activities. In fact, Antarctica is often perceived as the last pristine continent on Earth. Such remote regions, which are assumed to have very low levels of AMR due to limited human activity, represent potential model environments to understand the mechanisms and interactions underpinning the early stages of evolution, de novo development, acquisition and transmission of AMR. Antarctica, with its defined zones of human colonisation (centred around scientific research stations) and large populations of migratory birds and animals, also has great potential with regard to mapping and understanding the spread of early-stage zoonotic interactions. However, to date, studies of AMR in Antarctica are limited. Here, we survey the current literature focussing on the following: i) Dissection of human-introduced AMR versus naturally occurring AMR, based on the premise that multiple drug resistance and resistance to synthetic antibiotics not yet found in nature are the results of human contamination ii) The potential role of endemic wildlife in AMR spread There is clear evidence for greater concentrations of AMR around research stations, and although data show reverse zoonosis of the characteristic human gut bacteria to endemic wildlife, AMR within birds and seals appears to be very low, albeit on limited samplings. Furthermore, areas where there is little, to no, human activity still appear to be free from anthropogenically introduced AMR. However, a comprehensive assessment of AMR levels in Antarctica is virtually impossible on current data due to the wide variation in reporting standards and methodologies used and poor geographical coverage. Thus, future studies should engage directly with policymakers to promote the implementation of continent-wide AMR reporting standards. The development of such standards alongside a centralised reporting system would provide baseline data to feedback directly into wastewater treatment policies for the Antarctic Treaty Area to help preserve this relatively pristine environment. Video Abstract.}, } @article {pmid35524113, year = {2022}, author = {Al Kadi, M and Jung, N and Okuzaki, D}, title = {UNAGI: Yeast Transcriptome Reconstruction and Gene Discovery Using Nanopore Sequencing.}, journal = {Methods in molecular biology (Clifton, N.J.)}, volume = {2477}, number = {}, pages = {79-89}, pmid = {35524113}, issn = {1940-6029}, mesh = {DNA, Complementary/genetics ; Genetic Association Studies ; High-Throughput Nucleotide Sequencing/methods ; *Nanopore Sequencing ; Protein Isoforms/genetics ; Saccharomyces cerevisiae/genetics ; Transcriptome ; }, abstract = {Computational approaches are the main approaches used in genome annotation. However, accuracy is low. Untranslated regions are not identified, complex isoforms are not predicted correctly and discovery rate of noncoding RNA is low. RNA-seq has revolutionized transcriptome reconstruction over the last decade. However, fragmentation included in cDNA sequencing leads to information loss, requiring transcripts to be assembled and reconstructed, thus affecting the accuracy of reconstructed transcriptome. Recently, long-read sequencing has been introduced with technologies such as Oxford Nanopore sequencing. cDNA is sequenced directly without fragmentation producing long reads that don't need to be assembled keeping the transcript structure intact and increasing the accuracy of transcriptome reconstruction.Here we present a protocol and a pipeline to reconstruct the transcriptome of compact genomes including yeasts. It involves generating full-length cDNA and using Oxford Nanopore ligation-based sequencing kit to sequence multiple samples in the same run. The pipeline (1) strands the generated long reads, (2) corrects the reads by mapping them to the reference genome, (3) identifies transcripts including 5'UTR and 3'UTR, (4) profiles the isoforms, filtering out artifacts resulting from low accuracy in sequencing, and (5) improves accuracy of provided annotations. Using long reads improves the accuracy of transcriptome reconstruction and helps in discovering a significant number of novel RNAs.}, } @article {pmid35523393, year = {2022}, author = {Bashiri, R and Curtis, TP and Ofiţeru, ID}, title = {The limitations of the current protein classification tools in identifying lipolytic features in putative bacterial lipase sequences.}, journal = {Journal of biotechnology}, volume = {351}, number = {}, pages = {30-37}, doi = {10.1016/j.jbiotec.2022.04.011}, pmid = {35523393}, issn = {1873-4863}, mesh = {Amino Acid Sequence ; Bacteria/genetics/metabolism ; Databases, Protein ; *Lipase/genetics/metabolism ; Lipolysis ; *Proteins/metabolism ; }, abstract = {Metagenomics sequencing has generated millions of new protein sequences, most of them with unknown functions. A relatively quick first step for function assignment is to use the existing public protein databases and their scanning tools. However, to date these tools are not able to identify all sequence features like conserved motifs or patterns. In this study we evaluated the capability of several protein public databases (e.g., InterPro, PROSITE, ESTHER, pfam, AlphaFold etc) and their scanning tools for identifying lipolytic features in 78 putative cold-adapted bacterial lipase sequences. Novel lipases that can tolerate extreme conditions have great biotechnological importance. We obtained the putative cold-adapted lipolytic sequences from the metagenomic study of anaerobic psychrophilic microbial community treating domestic wastewater at 4 and 15 ℃. Both newer and conventional protein classifiers failed to find lipolytic features for most of the putative lipases. InterProScan predicted lipase family membership for only 18 of the putative lipase sequences. For more than half of them (41 out of 78) InterProScan could not predict any protein family membership, let alone find lipolytic features in them. However, when the Lipase Engineering Database and AlphaFold were used, half of those sequences were classified. Conventional databases like PROSITE could find lipolytic patterns for 9 of the putative lipolytic sequences of which only one was identified by InterProScan as a lipase. Moreover, different scanning tools made different and inconsistent predictions for a certain putative lipase sequence. Even InterProScan, which integrates predictions from 13 protein member databases, did not have a consensus prediction for a certain lipase sequence. Our study shows that there is lack of information in public protein databases about bacterial lipase sequences and this limits their lipolytic feature prediction and biotechnological application. The integration of AlphaFold within the InterPro can improve the lipase identification and classification significantly.}, } @article {pmid35522980, year = {2023}, author = {Zürcher, K and Abela, IA and Stange, M and Dupont, C and Mugglin, C and Egli, A and Trkola, A and Egger, M and Fenner, L}, title = {Alpha Variant Coronavirus Outbreak in a Nursing Home Despite High Vaccination Coverage: Molecular, Epidemiological, and Immunological Studies.}, journal = {Clinical infectious diseases : an official publication of the Infectious Diseases Society of America}, volume = {77}, number = {4}, pages = {537-546}, pmid = {35522980}, issn = {1537-6591}, support = {U01 AI069924/AI/NIAID NIH HHS/United States ; }, mesh = {Humans ; Aged, 80 and over ; *Vaccination Coverage ; *COVID-19/epidemiology/prevention & control ; SARS-CoV-2/genetics ; Nursing Homes ; Disease Outbreaks/prevention & control ; Vaccination ; }, abstract = {BACKGROUND: Vaccination may control the coronavirus disease 2019 (COVID-19) pandemic, including in nursing homes where many high-risk people live. We conducted extensive outbreak investigations.

METHODS: We studied an outbreak at a nursing home in Switzerland, where the uptake of messenger RNA vaccines against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was 82% among residents as of 21 January 2021. After diagnosis of COVID-19 in a vaccinated symptomatic healthcare worker (HCW) on 22 February, we performed outbreak investigations in house A (47 residents; 37 HCWs), using SARS-CoV-2-specific polymerase chain reaction testing of nasopharyngeal swab samples. We performed whole-genome sequencing of SARS-CoV-2 and serological analyses.

RESULTS: We identified 17 individuals with positive polymerase chain reaction results, 10 residents (5 vaccinated) and 7 HCWs (3 vaccinated). The median age (interquartile range) was 86 (70-90) years among residents and 49 (29-59) years among HCWs. Of the 5 vaccinated residents, 3 had mild disease and 2 had no symptoms, whereas all 5 unvaccinated residents had mild to severe disease, and 2 died. Vaccine effectiveness for the prevention of infection among residents was 73.0% (95% confidence interval, 24.7%-90.1%). The 12 available genomes were all alpha variants. Neutralizing titers were significantly higher in vaccinated individuals on reexposure (>1 week after diagnosis) than in vaccinated, unexposed HCWs (P = .01). Transmission networks indicated 4 likely or possible transmissions from vaccinated to other individuals and 12 transmission events from unvaccinated individuals.

CONCLUSIONS: COVID-19 outbreaks can occur in nursing homes, including transmission from vaccinated persons to others. Outbreaks might occur silently, underlining the need for continued testing and basic infection control measures in these high-risk settings.}, } @article {pmid35521547, year = {2022}, author = {Elisseev, V and Gardiner, LJ and Krishna, R}, title = {Scalable in-memory processing of omics workflows.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {1914-1924}, pmid = {35521547}, issn = {2001-0370}, abstract = {We present a proof of concept implementation of the in-memory computing paradigm that we use to facilitate the analysis of metagenomic sequencing reads. In doing so we compare the performance of POSIX™file systems and key-value storage for omics data, and we show the potential for integrating high-performance computing (HPC) and cloud native technologies. We show that in-memory key-value storage offers possibilities for improved handling of omics data through more flexible and faster data processing. We envision fully containerized workflows and their deployment in portable micro-pipelines with multiple instances working concurrently with the same distributed in-memory storage. To highlight the potential usage of this technology for event driven and real-time data processing, we use a biological case study focused on the growing threat of antimicrobial resistance (AMR). We develop a workflow encompassing bioinformatics and explainable machine learning (ML) to predict life expectancy of a population based on the microbiome of its sewage while providing a description of AMR contribution to the prediction. We propose that in future, performing such analyses in 'real-time' would allow us to assess the potential risk to the population based on changes in the AMR profile of the community.}, } @article {pmid35521214, year = {2022}, author = {Filardo, S and Scalese, G and Virili, C and Pontone, S and Di Pietro, M and Covelli, A and Bedetti, G and Marinelli, P and Bruno, G and Stramazzo, I and Centanni, M and Sessa, R and Severi, C}, title = {The Potential Role of Hypochlorhydria in the Development of Duodenal Dysbiosis: A Preliminary Report.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {854904}, pmid = {35521214}, issn = {2235-2988}, mesh = {*Achlorhydria/pathology ; Dysbiosis/microbiology ; Gastric Mucosa/microbiology ; *Helicobacter Infections/microbiology ; *Helicobacter pylori/genetics ; Humans ; RNA, Ribosomal, 16S/genetics ; }, abstract = {In recent years, the role of gastric and duodenal microbiota has acquired increasing importance in the homeostasis of the host, although, to date, most evidence concern the faecal microbiota. Indeed, the gastric, and duodenal microbiota are challenging to study, due to gastric acid, bile, digestive enzymes, and rapid transit time. Specifically, the gastric acid environment may influence their bacterial composition since the acid barrier protects against orally ingested microorganisms and leads to their inactivation before reaching the intestine. The aim of this study was to assess a correlation between intragastric pH and gastric as well as intestinal microbiota of patients with histologic gastric alterations. pH was measured in the gastric juice and the bacterial composition in gastric and duodenal biopsies and faecal samples, was investigated via 16s rRNA gene sequencing. The main result is the direct correlation of duodenal microbiota biodiversity, via alpha diversity measures, with intragastric pH values. In particular, patients with hypochlorhydria showed increased duodenal microbiota biodiversity, higher intragastric pH values being prevalent in patients with chronic atrophic gastritis. Lastly, the latter was also strongly associated to the presence of oral bacteria, like Rothia mucilaginosa, Streptococcus salivarius and Granulicatella adiacens, in the duodenal microbiota. In conclusions, our results suggest a low-acid gastric environment as a contributive factor for duodenal dysbiosis, potentially leading to the development of pathological conditions of the gastrointestinal tract.}, } @article {pmid35518360, year = {2022}, author = {Gan, R and Zhou, F and Si, Y and Yang, H and Chen, C and Ren, C and Wu, J and Zhang, F}, title = {DBSCAN-SWA: An Integrated Tool for Rapid Prophage Detection and Annotation.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {885048}, pmid = {35518360}, issn = {1664-8021}, abstract = {As an intracellular form of a bacteriophage in the bacterial host genome, a prophage usually integrates into bacterial DNA with high specificity and contributes to horizontal gene transfer (HGT). With the exponentially increasing number of microbial sequences uncovered in genomic or metagenomics studies, there is a massive demand for a tool that is capable of fast and accurate identification of prophages. Here, we introduce DBSCAN-SWA, a command line software tool developed to predict prophage regions in bacterial genomes. DBSCAN-SWA runs faster than any previous tools. Importantly, it has great detection power based on analysis using 184 manually curated prophages, with a recall of 85% compared with Phage_Finder (63%), VirSorter (74%), and PHASTER (82%) for (Multi-) FASTA sequences. Moreover, DBSCAN-SWA outperforms the existing standalone prophage prediction tools for high-throughput sequencing data based on the analysis of 19,989 contigs of 400 bacterial genomes collected from Human Microbiome Project (HMP) project. DBSCAN-SWA also provides user-friendly result visualizations including a circular prophage viewer and interactive DataTables. DBSCAN-SWA is implemented in Python3 and is available under an open source GPLv2 license from https://github.com/HIT-ImmunologyLab/DBSCAN-SWA/.}, } @article {pmid35516807, year = {2022}, author = {Laske, C and Müller, S and Preische, O and Ruschil, V and Munk, MHJ and Honold, I and Peter, S and Schoppmeier, U and Willmann, M}, title = {Signature of Alzheimer's Disease in Intestinal Microbiome: Results From the AlzBiom Study.}, journal = {Frontiers in neuroscience}, volume = {16}, number = {}, pages = {792996}, pmid = {35516807}, issn = {1662-4548}, abstract = {BACKGROUND: Changes in intestinal microbiome composition have been described in animal models of Alzheimer's disease (AD) and AD patients. Here we investigated how well taxonomic and functional intestinal microbiome data and their combination with clinical data can be used to discriminate between amyloid-positive AD patients and cognitively healthy elderly controls.

METHODS: In the present study we investigated intestinal microbiome in 75 amyloid-positive AD patients and 100 cognitively healthy controls participating in the AlzBiom study. We randomly split the data into a training and a validation set. Intestinal microbiome was measured using shotgun metagenomics. Receiver operating characteristic (ROC) curve analysis was performed to examine the discriminatory ability of intestinal microbiome among diagnostic groups.

RESULTS: The best model for discrimination of amyloid-positive AD patients from healthy controls with taxonomic data was obtained analyzing 18 genera features, and yielded an area under the receiver operating characteristic curve (AUROC) of 0.76 in the training set and 0.61 in the validation set. The best models with functional data were obtained analyzing 17 GO (Gene Ontology) features with an AUROC of 0.81 in the training set and 0.75 in the validation set and 26 KO [Kyoto Encyclopedia of Genes and Genomes (KEGG) ortholog] features with an AUROC of 0.83 and 0.77, respectively. Using ensemble learning for these three models including a clinical model with the 4 parameters age, gender, BMI and ApoE yielded an AUROC of 0.92 in the training set and 0.80 in the validation set.

DISCUSSION: In conclusion, we identified a specific Alzheimer signature in intestinal microbiome that can be used to discriminate amyloid-positive AD patients from healthy controls. The diagnostic accuracy increases from taxonomic to functional data and is even better when combining taxonomic, functional and clinical models. Intestinal microbiome represents an innovative diagnostic supplement and a promising area for developing novel interventions against AD.}, } @article {pmid35515981, year = {2022}, author = {Cobos, M and Estela, SL and Rodríguez, HN and Castro, CG and Grandez, M and Castro, JC}, title = {Soil microbial diversity and functional profiling of a tropical rainforest of a highly dissected low hill from the upper Itaya river basin revealed by analysis of shotgun metagenomics sequencing data.}, journal = {Data in brief}, volume = {42}, number = {}, pages = {108205}, pmid = {35515981}, issn = {2352-3409}, abstract = {The tropical rainforest of a highly dissected low hill from the upper Itaya river basin belongs to the western Amazonia region. Some investigations on the biodiversity of these rainforests were more focused on animals and plants diversity. The soils of this region are composed of moderately fertile sediments deposited recently from the initiation of the Andean orogenesis in the Miocene until now. However, scientific information about the soil microbial and functional diversity is still missing. This report presents shotgun metagenomics sequencing data from soils of this rainforest type. A composite loamy soil sample was collected from a primary forest, and metagenomic DNA was purified with standardized methods. Furthermore, libraries were prepared and paired-end sequenced on the Illumina NextSeq 550 platform. Raw Illumina paired-end reads have been uploaded and analysed in the Metagenomics RAST server (MG-RAST). The raw sequence data in fastq format is available at NCBI's Sequence Read Archive (SRA) with accession number SRX12846710.}, } @article {pmid35515005, year = {2022}, author = {Sheehy, L and Cutler, J and Weedall, GD and Rae, R}, title = {Microbiome Analysis of Malacopathogenic Nematodes Suggests No Evidence of a Single Bacterial Symbiont Responsible for Gastropod Mortality.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {878783}, pmid = {35515005}, issn = {1664-3224}, mesh = {Animals ; *Microbiota ; *Nematoda ; *Rhabditoidea/microbiology ; Snails ; Soil ; }, abstract = {Nematodes and bacteria are prevalent in soil ecosystems, and some have evolved symbiotic relationships. In some cases, symbionts carry out highly specialized functions: a prime example being entomopathogenic nematodes (EPNs), which vector bacteria (Xenorhabdus or Photorhabdus) into insect hosts, killing them to provide a food source for the nematodes. It is thought that the commercially available malacopathogenic (kills slugs and snails) biocontrol nematode Phasmarhabditis hermaphrodita vectors a bacterium (Moraxella osloensis) into slugs to kill them. To investigate this further we used a metagenomic approach to profile the bacteria present in the commercial strain of P. hermaphrodita, a wild strain of P. hermaphrodita and two other Phasmarhabditis species (P. californica and P. neopapillosa), after they had killed their slug host (Deroceras invadens). We show that these nematodes do not exclusively associate with one bacterium but a range of species, with members of the phyla Pseudomonadota, Bacillota, Actinobacteriota and Bacteroidota the most prevalent. The commercial strain of P. hermaphrodita had the least diverse bacterial community. Furthermore, we found that the bacterium P. hermaphrodita has been cultured on for 25 years is not the expected species M. osloensis but is Psychrobacter spp. and the only strain of the Phasmarhabditis species to associate with Psychrobacter spp. was the commercial strain of P. hermaphrodita. In summary, we found no evidence to show that P. hermaphrodita rely exclusively on one bacterium to cause host mortality but found variable and diverse bacterial communities associated with these nematodes in their slug hosts.}, } @article {pmid35514106, year = {2022}, author = {Leberecht, KM and Ritter, SM and Lapp, CJ and Klose, L and Eschenröder, J and Scholz, C and Kühnel, S and Stinnesbeck, W and Kletzin, A and Isenbeck-Schröter, M and Gescher, J}, title = {Microbially promoted calcite precipitation in the pelagic redoxcline: Elucidating the formation of the turbid layer.}, journal = {Geobiology}, volume = {20}, number = {4}, pages = {498-517}, doi = {10.1111/gbi.12492}, pmid = {35514106}, issn = {1472-4669}, mesh = {*Calcium Carbonate/chemistry ; *Chemoautotrophic Growth ; Oxidation-Reduction ; Sulfides ; Sulfur/metabolism ; }, abstract = {Large bell-shaped calcite formations called "Hells Bells" were discovered underwater in the stratified cenote El Zapote on the Yucatán Peninsula, Mexico. Together with these extraordinary speleothems, divers found a white, cloudy turbid layer into which some Hells Bells partially extend. Here, we address the central question if the formation of the turbid layer could be based on microbial activity, more specifically, on microbially induced calcite precipitation. Metagenomic and metatranscriptomic profiling of the microbial community in the turbid layer, which overlaps with the pelagic redoxcline in the cenote, revealed chemolithoautotrophic Hydrogenophilales and unclassified β-Proteobacteria as the metabolic key players. Bioinformatic and hydrogeochemical data suggest chemolithoautotrophic oxidation of sulfide to zero-valent sulfur catalyzed by denitrifying organisms due to oxygen deficiency. Incomplete sulfide oxidation via nitrate reduction and chemolithoautotrophy are both proton-consuming processes, which increase the pH in the redoxcline favoring authigenic calcite precipitation and may contribute to Hells Bells growth. The observed mechanism of microbially induced calcite precipitation is potentially applicable to many other stagnant sulfate-rich water bodies.}, } @article {pmid35513696, year = {2022}, author = {Lee, Y and Byeon, HR and Jang, SY and Hong, MG and Kim, D and Lee, D and Shin, JH and Kim, Y and Kang, SG and Seo, JG}, title = {Oral administration of Faecalibacterium prausnitzii and Akkermansia muciniphila strains from humans improves atopic dermatitis symptoms in DNCB induced NC/Nga mice.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {7324}, pmid = {35513696}, issn = {2045-2322}, mesh = {Administration, Oral ; Akkermansia ; Animals ; Cytokines/pharmacology ; *Dermatitis, Atopic/drug therapy/therapy ; *Dinitrochlorobenzene/pharmacology ; Disease Models, Animal ; Faecalibacterium prausnitzii ; Humans ; Mice ; Skin/pathology ; Verrucomicrobia ; }, abstract = {Atopic dermatitis (AD) is a common inflammatory skin disease, and its pathogenesis is closely associated with microbial homeostasis in the gut, namely the gut-skin axis. Particularly, recent metagenomics studies revealed that the abundance of two major bacterial species in the gut, Faecalibacterium prausnitzii and Akkermansia muciniphila, may play a critical role in the pathogenesis of AD, but the effect of these species in AD has not yet been elucidated. To evaluate the potential beneficial effect of F. prausnitzii or A. muciniphila in AD, we conducted an animal model study where F. prausnitzii EB-FPDK11 or A. muciniphila EB-AMDK19, isolated from humans, was orally administered to 2,5-dinitrochlorobenzene (DNCB)-induced AD models using NC/Nga mice at a daily dose of 10[8] CFUs/mouse for six weeks. As a result, the administration of each strain of F. prausnitzii and A. muciniphila improved AD-related markers, such as dermatitis score, scratching behavior, and serum immunoglobulin E level. Also, the F. prausnitzii and A. muciniphila treatments decreased the level of thymic stromal lymphopoietin (TSLP), triggering the production of T helper (Th) 2 cytokines, and improved the imbalance between the Th1 and Th2 immune responses induced by DNCB. Meanwhile, the oral administration of the bacteria enhanced the production of filaggrin in the skin and ZO-1 in the gut barrier, leading to the recovery of functions. Taken together, our findings suggest that F. prausnitzii EB-FPDK11 and A. muciniphila EB-AMDK19 have a therapeutic potential in AD, which should be verified in humans.}, } @article {pmid35513542, year = {2022}, author = {Wagner, NY and Andersen, DT and Hahn, AS and Johnson, SS}, title = {Survival strategies of an anoxic microbial ecosystem in Lake Untersee, a potential analog for Enceladus.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {7376}, pmid = {35513542}, issn = {2045-2322}, support = {80NSSC18K1094/NASA/NASA/United States ; }, mesh = {Ecosystem ; *Lakes ; Methane ; *Saturn ; Water ; }, abstract = {Lake Untersee located in Eastern Antarctica, is a perennially ice-covered lake. At the bottom of its southern basin lies 20 m of anoxic, methane rich, stratified water, making it a good analog for Enceladus, a moon of Saturn. Here we present the first metagenomic study of this basin and detail the community composition and functional potential of the microbial communities at 92 m, 99 m depths and within the anoxic sediment. A diverse and well-populated microbial community was found, presenting the potential for Enceladus to have a diverse and abundant community. We also explored methanogenesis, sulfur metabolism, and nitrogen metabolism, given the potential presence of these compounds on Enceladus. We found an abundance of these pathways offering a variety of metabolic strategies. Additionally, the extreme conditions of the anoxic basin make it optimal for testing spaceflight technology and life detection methods for future Enceladus exploration.}, } @article {pmid35513152, year = {2022}, author = {Jiang, Z and Zhong, S and Shen, X and Cui, M and Wang, Y and Li, J}, title = {Microbially mediated arsenic mobilization in the clay layer and underlying aquifer in the Hetao Basin, Inner Mongolia, China.}, journal = {The Science of the total environment}, volume = {836}, number = {}, pages = {155597}, doi = {10.1016/j.scitotenv.2022.155597}, pmid = {35513152}, issn = {1879-1026}, mesh = {*Arsenic/analysis ; China ; Clay ; Ferric Compounds ; Geologic Sediments/chemistry ; *Groundwater/chemistry ; RNA, Ribosomal, 16S/genetics ; Sand ; *Water Pollutants, Chemical/analysis ; }, abstract = {The clay layer is a source to facilitate arsenic (As) enrichment in the aquifer. However, little is known about microbial processes in the clay layer and their roles in As mobilization in the underlying aquifer. In this study, high-throughput sequencing of full-length 16S rRNA gene and metagenomics were used to characterize the microbial composition and functional potential in a sediment borehole across the clay and sand layers in Hetao Basin, Inner Mongolia, China. Results showed the significant differences between the clay layer and underlying sand layer in the geochemistry, microbial composition and functional potential. Fermentation, Fe(III) reduction, As(V) reduction, sulfate reduction, thiosulfate disproportionation, reductive tricarboxylic acid and Wood-Ljungdahl pathway identified in sediments from the clay layer were positively correlated to the observed high levels of TOC, soluble ammonium, H3PO4-extractable As(III) and As(V) and HCl-extractable Fe(II). Although the microbial compositions of the clay and sand layers were different, the microbial functional potential at the interface between the clay and sand layers was similar with the characteristics of fermentation, ammonification and As(V) reduction. The similarity of microbial functional potential at the interface may be attributable to the interaction between the sand and adjacent clay layer with the fluctuation of groundwater level. These metabolic products from the microbial processes in the clay layers and interface would migrate into the underlying groundwater during groundwater overpumping, which facilitates As enrichment in groundwater.}, } @article {pmid35513151, year = {2022}, author = {Shen, Q and Tang, J and Sun, H and Yao, X and Wu, Y and Wang, X and Ye, S}, title = {Straw waste promotes microbial functional diversity and lignocellulose degradation during the aerobic process of pig manure in an ectopic fermentation system via metagenomic analysis.}, journal = {The Science of the total environment}, volume = {838}, number = {Pt 1}, pages = {155637}, doi = {10.1016/j.scitotenv.2022.155637}, pmid = {35513151}, issn = {1879-1026}, mesh = {Animals ; Bacteria/metabolism ; Fermentation ; *Lignin/metabolism ; *Manure ; Metagenomics ; Swine ; }, abstract = {This study compares the physicochemical properties, lignocellulose degradation, microbial community composition, and carbohydrate-active enzymes (CAZymes) in ectopic fermentation systems (EFS) of pig manure mixed with either conventional padding (C) or straw waste (A). The degradation rates of cellulose, hemicellulose, and lignin were found to be significantly higher in A (27.72%, 22.72%, and 18.80%, respectively) than in C (21.05%, 16.17%, and 11.69%, respectively) owing to the activities of lignocellulolytic enzymes. Metagenomics revealed that straw addition had a stronger effect on the bacterial community succession than fungi. The abundances of Sphingobacterium, Pseudomonas, and CAZymes were higher in A than in C, as well as the auxiliary activity enzymes, which are crucial for lignocellulose degradation. Redundancy analysis indicates a positive correlation between lignocellulose degradation and Sphingobacterium, Pseudomonas, Bacillus, and Actinobacteria contents. A structural equation model was applied to further verify that the increased microbial functional diversity was the primary driver of lignocellulosic degradation, which could be effectively regulated by the enhanced temperature with straw addition. Replacing traditional padding with straw can thus accelerate lignocellulosic degradation, promote microbial functional diversity, and improve the EFS efficiency.}, } @article {pmid35513144, year = {2022}, author = {Li, R and Liu, D and Zhang, Y and Tommaso, G and Si, B and Liu, Z and Duan, N}, title = {Enhanced anaerobic digestion of post-hydrothermal liquefaction wastewater: Bio-methane production, carbon distribution and microbial metabolism.}, journal = {The Science of the total environment}, volume = {837}, number = {}, pages = {155659}, doi = {10.1016/j.scitotenv.2022.155659}, pmid = {35513144}, issn = {1879-1026}, mesh = {Anaerobiosis ; Bioreactors ; Carbon ; *Chlorella ; Methane ; Sewage/chemistry ; *Wastewater/chemistry ; }, abstract = {Hydrothermal liquefaction (HTL) is a cost-effective and environment-friendly technology for using biomass to produce bio-crude oil. The critical challenge of HTL is its complicated aqueous product containing high concentrations of organics and diverse toxicants. This paper reports the continuous anaerobic digestion of raw and zeolite-adsorbed Chlorella HTL wastewater using up-flow anaerobic sludge bed reactors. The bio-methane production capacity, total carbon distribution and microbial response were investigated. The anaerobic process was severely suppressed when more than 20% raw wastewater was fed; while it showed essentially improved performance till 60% pre-treated wastewater was added. Produced methane contained 17.3% of the total carbon in feedstock, which was comparable with the value (16.7%) when 25% of raw wastewater was added. The metagenomic analysis revealed distinct microbial community structures in different stages and feedstock shifts. The abundance of functional genes was consistent with anaerobic digester performance.}, } @article {pmid35512372, year = {2022}, author = {Yakimovich, KM and Quarmby, LM}, title = {A metagenomic study of the bacteria in snow algae microbiomes.}, journal = {Canadian journal of microbiology}, volume = {68}, number = {7}, pages = {507-520}, doi = {10.1139/cjm-2021-0313}, pmid = {35512372}, issn = {1480-3275}, mesh = {Bacteria/genetics ; *Metagenome ; Metagenomics ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The bacterial communities found in snow algae blooms have been described in terms of their 16S rRNA gene community profiles, but little information exists on their metabolic potential. Previously, we reported that several bacterial taxa are common across snow algae blooms in the southwestern mountains of the Coast Range in British Columbia, Canada. Here, we further this work by reporting a partial bacterial metagenome from the same snow algal microbiomes. Using shotgun metagenomic data, we constructed metagenomically assembled bacterial genomes (MAGs). Of the total 54 binned MAGs, 28 were bacterial and estimated to be at least 50% complete based on single copy core genes. The 28 MAGs fell into five classes: Actinomycetia, Alphaproteobacteria, Bacteroidia, Betaproteobacteria, and Gammaproteobacteria. All MAGs were assigned to a class, 27 to an order, 25 to a family, 18 to a genus, and none to species. MAGs showed the potential to support algal growth by synthesizing B-vitamins and growth hormones. There was also widespread adaptation to the low oxygen environment of biofilms, including synthesis of high-affinity terminal oxidases and anaerobic pathways for cobalamin synthesis. Also notable were the absence of N2 fixation, and the presence of incomplete denitrification pathways suggestive of NO signalling within the microbiome.}, } @article {pmid35511831, year = {2023}, author = {Zheng, V and Sariyuce, AE and Zola, J}, title = {Identifying Taxonomic Units in Metagenomic DNA Streams on Mobile Devices.}, journal = {IEEE/ACM transactions on computational biology and bioinformatics}, volume = {20}, number = {2}, pages = {1092-1103}, doi = {10.1109/TCBB.2022.3172661}, pmid = {35511831}, issn = {1557-9964}, mesh = {Sequence Analysis, DNA/methods ; *Metagenomics/methods ; *Algorithms ; Metagenome/genetics ; DNA ; }, abstract = {With the emergence of portable DNA sequencers, such as Oxford Nanopore Technology MinION, metagenomic DNA sequencing can be performed in real-time and directly in the field. However, because metagenomic DNA analysis tasks, e.g., classification, taxonomic units assignment, etc., are compute and memory intensive, and the available methods are designed for batch processing, the current metagenomic tools are not well suited for mobile devices. In this work, we propose a new memory-efficient approach to identify Operational Taxonomic Units (OTUs) in metagenomic DNA streams on mobile devices. Our method is based on finding connected components in overlap graphs constructed over a real-time stream of long DNA reads as produced by the MinION platform. We propose an efficient algorithm to maintain connected components when an overlap graph is streamed and show how redundant information can be removed from the stream by transitive closures. We also propose how our algorithms can be integrated into a larger DNA analysis pipeline tailored for mobile computing. Through experiments on simulated and real-world metagenomic data, executed on the actual mobile device, we demonstrate that our resulting solution is able to recover OTUs with high precision. Our experiments also demonstrate the compounding benefits of introducing feedback loops in the DNA analysis pipeline.}, } @article {pmid35511760, year = {2022}, author = {Nagy, A and Abdallah, F and El Damaty, HM and Tariq, A and Merwad, AMA and Alhatlani, BY and Elsohaby, I}, title = {Genetic characterization of upper respiratory tract virome from nonvaccinated Egyptian cow-calf operations.}, journal = {PloS one}, volume = {17}, number = {5}, pages = {e0267036}, pmid = {35511760}, issn = {1932-6203}, mesh = {Animals ; Cattle ; *Cattle Diseases/epidemiology ; Female ; *Herpesvirus 1, Bovine/genetics ; *Herpesvirus 5, Bovine ; Phylogeny ; *Respiratory Tract Diseases ; Virome ; *Viruses/genetics ; }, abstract = {Bovine respiratory disease (BRD) is the costliest complex disease affecting the cattle industry worldwide, with significant economic losses. BRD pathogenesis involves several interactions between microorganisms, such as bacteria and viruses, and management factors. The present study aimed to characterize the nasal virome from 43 pooled nasal swab samples collected from Egyptian nonvaccinated cow-calf operations with acute BRD from January to February 2020 using metagenomic sequencing. Bovine herpesvirus-1 (BHV-1), first detection of bovine herpesvirus-5 (BHV-5), and first detection of bovine parvovirus-3 (BPV-3) were the most commonly identified in Egyptian cattle. Moreover, phylogenetic analysis of glycoprotein B revealed that the BHV-1 isolate is closely related to the Cooper reference strain (genotype 1.1), whereas the BHV-5 isolate is closely related to the reference virus GenBank NP_954920.1. In addition, the whole-genome sequence of BPV-3 showed 93.02% nucleotide identity with the reference virus GenBank AF406967.1. In this study, several DNA viruses, such as BHV-1 and first detection BHV-5, and BPV-3, were detected and may have an association with the BRD in Egyptian cattle. Therefore, further research, including investigating more samples from different locations to determine the prevalence of detected viruses and their contributions to BRD in cattle in Egypt, is needed.}, } @article {pmid35511595, year = {2022}, author = {Bhattarai, S and Temme, H and Jain, A and Badalamenti, JP and Gralnick, JA and Novak, PJ}, title = {The potential for bacteria from carbon-limited deep terrestrial environments to participate in chlorine cycling.}, journal = {FEMS microbiology ecology}, volume = {98}, number = {6}, pages = {}, doi = {10.1093/femsec/fiac054}, pmid = {35511595}, issn = {1574-6941}, mesh = {Bacteria ; Biodegradation, Environmental ; *Carbon/metabolism ; Chlorides/metabolism ; *Chlorine/metabolism ; Chloroacetates ; Halogens/metabolism ; }, abstract = {Bacteria capable of dehalogenation via reductive or hydrolytic pathways are ubiquitous. Little is known, however, about the prevalence of bacterial dechlorination in deep terrestrial environments with a limited carbon supply. In this study we analyzed published genomes from three deep terrestrial subsurface sites: a deep aquifer in Western Siberia, the Sanford Underground Research Facility in South Dakota, USA, and the Soudan Underground Iron Mine (SUIM) in Minnesota, USA to determine if there was evidence to suggest that microbial dehalogenation was possible in these environments. Diverse dehalogenase genes were present in all analyzed metagenomes, with reductive dehalogenase and haloalkane dehalogenase genes the most common. Taxonomic analysis of both hydrolytic and reductive dehalogenase genes was performed to explore their affiliation; this analysis indicated that at the SUIM site, hydrolytic dehalogenase genes were taxonomically affiliated with Marinobacter species. Because of this affiliation, experiments were also performed with Marinobacter subterrani strain JG233 ('JG233'), an organism containing three predicted hydrolytic dehalogenase genes and isolated from the SUIM site, to determine whether hydrolytic dehalogenation was an active process and involved in growth on a chlorocarboxylic acid. Presence of these genes in genome appears to be functional, as JG233 was capable of chloroacetate dechlorination with simultaneous chloride release. Stable isotope experiments combined with confocal Raman microspectroscopy demonstrated that JG233 incorporated carbon from 13C-chloroacetate into its biomass. These experiments suggest that organisms present in these extreme and often low-carbon environments are capable of reductive and hydrolytic dechlorination and, based on laboratory experiments, may use this capability as a competitive advantage by utilizing chlorinated organic compounds for growth, either directly or after dechlorination.}, } @article {pmid35511486, year = {2022}, author = {Hu, S and Mok, J and Gowans, M and Ong, DEH and Hartono, JL and Lee, JWJ}, title = {Oral Microbiome of Crohn's Disease Patients With and Without Oral Manifestations.}, journal = {Journal of Crohn's & colitis}, volume = {16}, number = {10}, pages = {1628-1636}, pmid = {35511486}, issn = {1876-4479}, support = {A-0002940-00-0//National University of Singapore/ ; }, mesh = {Humans ; *Crohn Disease/diagnosis ; Dysbiosis ; *Oral Ulcer ; *Dental Caries ; Feces ; *Gastrointestinal Microbiome/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND AND AIMS: Microbiome dysbiosis is associated with inflammatory destruction in Crohn's disease [CD]. Although gut microbiome dysbiosis is well established in CD, the oral microbiome is comparatively under-studied. This study aims to characterize the oral microbiome of CD patients with/without oral manifestations.

METHODS: Patients with CD were recruited with age-, gender- and race-matched controls. Potential confounders such as dental caries and periodontal condition were recorded. The oral microbiome was collected using saliva samples. Microbial DNA was extracted and sequenced using shotgun sequencing. Metagenomic taxonomic and functional profiles were generated and analysed.

RESULTS: The study recruited 41 patients with CD and 24 healthy controls. Within the CD subjects, 39.0% had oral manifestations with the majority presenting with cobblestoning and/or oral ulcers. Principal coordinate analysis demonstrated distinct oral microbiome profiles between subjects with and without CD, with four key variables responsible for overall oral microbiome variance: [1] diagnosis of CD, [2] concomitant use of steroids, [3] concomitant use of azathioprine and 4] presence of oral ulcers. Thirty-two significant differentially abundant microbial species were identified, with the majority associated with the diagnosis of CD. A predictive model based on differences in the oral microbiome found that the oral microbiome has strong discriminatory function to distinguish subjects with and without CD [AUROC 0.84]. Functional analysis found that an increased representation of microbial enzymes [n = 5] in the butyrate pathway was positively associated with the presence of oral ulcers.

CONCLUSIONS: The oral microbiome can aid in the diagnosis of CD and its composition was associated with oral manifestations.}, } @article {pmid35510767, year = {2022}, author = {Mei, R and Liu, WT}, title = {Meta-Omics-Supervised Characterization of Respiration Activities Associated with Microbial Immigrants in Anaerobic Sludge Digesters.}, journal = {Environmental science & technology}, volume = {56}, number = {10}, pages = {6689-6698}, doi = {10.1021/acs.est.2c01029}, pmid = {35510767}, issn = {1520-5851}, mesh = {Anaerobiosis ; Bioreactors ; *Emigrants and Immigrants ; Humans ; Methane/metabolism ; *Microbiota ; Nitrates ; RNA, Ribosomal, 16S/genetics ; Respiration ; Sewage/chemistry ; Sulfates ; }, abstract = {Immigration has been recently recognized as an important ecological process that affects the microbial community structure in diverse ecosystems. However, the fate of microbial immigrants in the new environment and their involvement in the local biochemical network remain unclear. In this study, we performed meta-omics-supervised characterization of immigrants' activities in anaerobic sludge digesters. Metagenomic analyses revealed that immigrants from the feed sludge accounted for the majority of populations capable of anaerobic respiration in a digester. Electron acceptors that were predicted to be respired, including nitrate, nitrite, sulfate, and elemental sulfur, were added to digester sludge in batch tests. Consumption of up to 91% of the added electron acceptors was observed within the experiment period. 16S rRNA sequencing detected populations that were stimulated by the electron acceptors, largely overlapping with respiration-capable immigrants identified by metagenomic analysis. Metatranscriptomic analysis of the batch tests provided additional evidence for upregulated expression of respiration genes and concomitant suppressed expression of methanogenesis. Anaerobic respiration activity was further evaluated in full-scale digesters in nine wastewater treatment plants. Although nitrate and sulfate respiration were ubiquitous, the expression level of respiration genes was generally 2-3 orders of magnitude lower than the expression of methanogenesis in most digesters, suggesting marginal ecological roles by immigrants in full-scale digester ecosystems.}, } @article {pmid35510251, year = {2022}, author = {Zhang, L and Dai, Y and Lin, M and Xu, Q and Lin, T and Gong, T and Cheng, B and Ji, C and Cai, D}, title = {Case Report: An Ulceration With a Stalactite Appearance on the Index Finger.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {801086}, pmid = {35510251}, issn = {2296-858X}, abstract = {Proteus mirabilis, the most widespread species of all Proteus spp. bacteria, is proven to be one of the most universal pathogens in chronic wounds. In this case, a woman in her 40s consulted a physician about an asymptomatic ulceration with a stalactite appearance at the distal end of the index finger after she was exposed to a needle when vaccinating chickens. The patient did not response to ceftazidime. Physical examination revealed a well-demarcated violescent ulceration with a stalactite appearance at the distal end of the index finger. A biopsy of the lesion showed dense infiltration of multinucleated giant cells, histiocytes, and lymphocytes in the dermis. The result of metagenomics next-generation sequencing (NGS) showed 306 unique sequence reads of P. mirabilis, covering 33.49% of the nucleotide sequences. The pathogen was identified as P. mirabilis, which was resistant to ceftazidime. The patient was treated with ciprofloxacin hydrochloride and improved considerably. This case reported a distinctive cutaneous lesion of P. mirabilis on human infection and showed a successful use of NGS in P. mirabilis.}, } @article {pmid35509811, year = {2022}, author = {You, L and Bao, W and Yao, C and Zhao, F and Jin, H and Huang, W and Li, B and Kwok, LY and Liu, W}, title = {Changes in chemical composition, structural and functional microbiome during alfalfa (Medicago sativa) ensilage with Lactobacillus plantarum PS-8.}, journal = {Animal nutrition (Zhongguo xu mu shou yi xue hui)}, volume = {9}, number = {}, pages = {100-109}, pmid = {35509811}, issn = {2405-6383}, abstract = {Improving silage production by adding exogenous microorganisms not only maximizes nutrient preservation, but also extends product shelf life. Herein, changes in the quality and quantity of Lactobacillus plantarum PS-8 (PS-8) -inoculated alfalfa (Medicago sativa) during silage fermentation were monitored at d 0, 7, 14, and 28 (inoculum dose of PS-8 was 1 × 10[5] colony forming units [cfu]/g fresh weight; 50 kg per bag; 10 bags for each time point) by reconstructing metagenomic-assembled genomes (MAG) and Growth Rate InDex (GRiD). Our results showed that the exogenous starter bacterium, PS-8 inoculation, became the most dominating strain by d 7, and possibly played a highly active role throughout the fermentation process. The pH value of the silage decreased greatly, accompanied by the growth of acid-producing microorganisms namely PS-8, which inhibited the growth of harmful microorganisms like molds (4.18 vs. 1.42 log cfu/g) and coliforms (4.95 vs. 0.66 log most probable number [MPN]/g). The content of neutral detergent fiber (NDF) decreased significantly (41.6% vs. 37.6%; dry matter basis). In addition, the abundance and diversity of genes coding microbial carbohydrate-active enzymes (CAZymes) increased significantly and desirably throughout the fermentation, particularly the genes responsible for degrading starch, arabino-xylan, and cellulose. Overall, our results showed that PS-8 was replicating rapidly and consistently during early- and mid-fermentation phases, promoting the growth of beneficial lactic acid bacteria and inhibiting undesirable microbes, ultimately improving the quality of silage.}, } @article {pmid35509518, year = {2022}, author = {Tong, Y and Zhang, J and Fu, Y and He, X and Feng, Q}, title = {Risk Factors and Outcome of Sepsis in Traumatic Patients and Pathogen Detection Using Metagenomic Next-Generation Sequencing.}, journal = {The Canadian journal of infectious diseases & medical microbiology = Journal canadien des maladies infectieuses et de la microbiologie medicale}, volume = {2022}, number = {}, pages = {2549413}, pmid = {35509518}, issn = {1712-9532}, abstract = {OBJECTIVE: Sepsis, a life-threatening clinical syndrome, is a leading cause of mortality after experiencing multiple traumas. Once diagnosed with sepsis, patients should be given an appropriate empiric antimicrobial treatment followed by the specific antibiotic therapy based on blood culture due to its rapid progression to tissue damage and organ failure. In this study, we aimed to analyze the risk factors and outcome of sepsis in traumatic patients and to investigate the performance of metagenomic next-generation sequencing (mNGS) compared with standard microbiological diagnostics in post-traumatic sepsis.

METHODS: The study included 528 patients with multiple traumas among which there were 142 cases with post-traumatic sepsis. Patients' demographic and clinical data were recorded. The outcome measures included mortality during the emergency intensive care unit (EICU), EICU length of stay (LOS), all-cause 28-day mortality, and total ventilator days in 28 days after admission. A total of 89 blood samples from 89 septic patients underwent standard microbiological blood cultures and 89 samples of peripheral blood (n = 21), wound secretion (n = 41), bronchoalveolar lavage fluid (BALF) (19), ascites (n = 5), and sputum (n = 3) underwent mNGS. Pathogen detection was compared between standard microbiological blood cultures and mNGS.

RESULTS: The sepsis group and non-sepsis group exhibited significant differences regarding shock on admission, blood transfusion, mechanical ventilation, body temperature, heart rate, WBC count, neutrophil count, hematocrit, urea nitrogen, creatinine, CRP, D-D dimer, PCT, scores of APACHE II, sequential organ failure assessment (SOFA), and Injury Severity Score (ISS) on admission to the EICU, and Multiple Organ Dysfunction Syndromes (MODS) (P < 0.05). Multivariate logistic regression analysis showed that scores of APACHE II, SOFA, and ISS on admission, and MODS were independent risk factors for the occurrence of sepsis in patients with multiple traumas. The 28-day mortality was higher in the sepsis group than in the non-sepsis group (45.07% vs. 19.17%, P < 0.001). The mortality during the EICU was higher in the sepsis group than in the non-sepsis group (P=0.002). The LOS in the EICU in the sepsis group was increased compared with the non-sepsis group (P=0.004). The total ventilator days in 28 days after admission in the sepsis group was increased compared with the non-sepsis group (P < 0.001). Multivariate logistic regression analysis showed that septic shock, APACHE II score on admission, SOFA score, and MODS were independent risk factors of death for patients with post-traumatic sepsis. The positive detection rate of mNGS was 91.01% (81/89), which was significantly higher than that of standard microbiological blood cultures (39.33% (35/89)). Standard microbiological blood cultures and mNGS methods demonstrated double positive results in 33 (37.08%) specimens and double-negative results in 8 (8.99%) specimens, while 46 (51.69%) samples and 2 (2.25%) samples had positive results only with mNGS or culture alone, respectively.

CONCLUSION: Our study identifies risk factors for the incidence and death of sepsis in traumatic patients and shows that mNGS may serve as a better diagnostic tool for the identification of pathogens in post-traumatic sepsis than standard microbiological blood cultures.}, } @article {pmid35509305, year = {2022}, author = {Qu, Y and Ding, W and Liu, S and Wang, X and Wang, P and Liu, H and Xia, H and Chen, Y and Jiang, H}, title = {Metagenomic Next-Generation Sequencing vs. Traditional Pathogen Detection in the Diagnosis of Infection After Allogeneic Hematopoietic Stem Cell Transplantation in Children.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {868160}, pmid = {35509305}, issn = {1664-302X}, abstract = {Infection is a severe complication of allo-HSCT in children, however, the accurate detection of the infection is hard. In this study, we traced the records of 101 pediatric recipients with allo-HSCT to investigate the pathogens of infection, and collected 54 bronchoalveolar lavage fluid, 32 blood, and 15 cerebrospinal fluid samples. In these samples, 87 was with post-transplant infection and 14 without infection. Using the metagenomic next-generation sequencing (mNGS) and traditional pathogen detection, we compared their sensitivity and specificity to detect pathogens of infection. Our results showed that mNGS was more sensitive (89.7%) than conventional pathogen detection (21.8%), with a difference of 67.9% (P < 0.001), However, mNGS was less specific (78.5%) than traditional methods (92.9%), with a difference of 14.4% (P = 0.596). The sensitivity of mNGS for diagnosing pulmonary infections, bloodstream infections or viremia, and CNS infections post-transplant were 91.7, 85.7, and 90.9%, respectively. In contrast, the sensitivity of conventional testing for diagnosing pulmonary infections, bloodstream infections or viremia, and CNS infections post-transplant were 22.9, 21.4, and 18.2%, respectively. There were significant differences in the sensitivity of mNGS and conventional testing in BALF, blood, and CSF samples, with P values of 0.000, 0.000, and 0.002 respectively. Among the patients with pulmonary infection, 11 pathogens were both identified by mNGS and conventional testing, and 33 by mNGS only. The percentage with the mNGS-positive result was 44/48 (91.7%), including viruses (n = 12), bacteria (n = 17), fungi (n = 9) and mixed infections (n = 6). Among the patients diagnosed with fungal pneumonia (n = 9), the most prevalent pathogenic fungi were Pneumocystis jiroveci (n = 6), which were also detected in 4 patients with mixed infectious pneumonia. In the 28 blood specimens of patients with bloodstream infections or viremia, five patients were positive by both mNGS and conventional testing, 19 were positive by mNGS, and 1 was positive by traditional testing only. The percentage with the mNGS-positive results was 24/28 (85.7%), including viruses (n = 12), bacteria (n = 4), fungi (n = 3), and mixed infections (n = 5). Of the 15 CSF specimens enrolled, 11 patients were eventually diagnosed with CNS infections. Ten pathogens were identified by mNGS in the 11 patients, including viruses (n = 8), bacteria (n = 1), and fungi (n = 1). These results suggest that mNGS is more sensitive than conventional pathogen detection for diagnosing infections post HSCT in children which may help the clinic diagnosis. Pneumocystis jiroveci was the most frequent pathogen of pulmonary infections post-transplant, while viruses were the most common pathogens of CNS infections in allo-HSCT recipients.}, } @article {pmid35509146, year = {2022}, author = {Sharma, P and Vimal, A and Vishvakarma, R and Kumar, P and de Souza Vandenberghe, LP and Kumar Gaur, V and Varjani, S}, title = {Deciphering the blackbox of omics approaches and artificial intelligence in food waste transformation and mitigation.}, journal = {International journal of food microbiology}, volume = {372}, number = {}, pages = {109691}, doi = {10.1016/j.ijfoodmicro.2022.109691}, pmid = {35509146}, issn = {1879-3460}, mesh = {Agriculture ; *Artificial Intelligence ; Child ; Food ; Food Supply ; Humans ; *Refuse Disposal ; }, abstract = {It is necessary to stop the wastage of food during any stage of food chain to resolve the challenge of starvation, hunger and malnutrition in the world. Inception of modern techniques like omics (metagenomics, proteomics, transcriptomics, wasteomics, diseaseomics etc), enzymatic treatments, and artificial intelligence in food waste reduction and management can bring a sustainable solution for food loss management, starvation and environmental challenges. Acceptance of modern techniques while policies formulation by government bodies can substantially strengthen the idea of waste reduction, food security and can easily save the life of around 25,000 children and adults dying of starvation every day. Artificial Intelligence (AI) can bestead current agriculture and food supply chain system to overcome the challenges of nutrition demand, resource depletion, climate change, population growth, and pollution. This communication provides a thorough examination of the concept of food waste management with omics approaches linkages. In addition, the notion of artificial intelligence in food waste transformation and mitigation, as well as present challenges and future prospects have been covered. Overall, this communication would assist decision-makers in identifying economically and environmentally appropriate biorefinery solutions ahead of time.}, } @article {pmid35509078, year = {2022}, author = {He, Y and Fang, K and Shi, X and Yang, D and Zhao, L and Yu, W and Zheng, Y and Xu, Y and Ma, X and Chen, L and Xie, Y and Yu, Y and Wang, J and Gao, Z}, title = {Enhanced DNA and RNA pathogen detection via metagenomic sequencing in patients with pneumonia.}, journal = {Journal of translational medicine}, volume = {20}, number = {1}, pages = {195}, pmid = {35509078}, issn = {1479-5876}, mesh = {DNA ; Deoxyribonucleases ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Pneumonia/diagnosis ; RNA ; *RNA Viruses ; Retrospective Studies ; *Saponins ; Sensitivity and Specificity ; }, abstract = {BACKGROUND: Metagenomic next-generation sequencing (mNGS) is an important supplement to conventional tests for pathogen detections of pneumonia. However, mNGS pipelines were limited by irregularities, high proportion of host nucleic acids, and lack of RNA virus detection. Thus, a regulated pipeline based on mNGS for DNA and RNA pathogen detection of pneumonia is essential.

METHODS: We performed a retrospective study of 151 patients with pneumonia. Three conventional tests, culture, loop-mediated isothermal amplification (LAMP) and viral quantitative real-time polymerase chain reaction (qPCR) were conducted according to clinical needs, and all samples were detected using our optimized pipeline based on the mNGS (DNA and RNA) method. The performances of mNGS and three other tests were compared. Human DNA depletion was achieved respectively by MolYsis kit and pre-treatment using saponin and Turbo DNase. Three RNA library preparation methods were used to compare the detection performance of RNA viruses.

RESULTS: An optimized mNGS workflow was built, which had only 1-working-day turnaround time. The proportion of host DNA in the pre-treated samples decreased from 99 to 90% and microbiome reads achieved an approximately 20-fold enrichment compared with those without host removal. Meanwhile, saponin and Turbo DNase pre-treatment exhibited an advantage for DNA virus detection compared with MolYsis. Besides, our in-house RNA library preparation procedure showed a more robust RNA virus detection ability. Combining three conventional methods, 76 (76/151, 50.3%) cases had no clear causative pathogen, but 24 probable pathogens were successfully detected in 31 (31/76 = 40.8%) unclear cases using mNGS. The agreement of the mNGS with the culture, LAMP, and viral qPCR was 60%, 82%, and 80%, respectively. Compared with all conventional tests, mNGS had a sensitivity of 70.4%, a specificity of 72.7%, and an overall agreement of 71.5%.

CONCLUSIONS: A complete and effective mNGS workflow was built to provide timely DNA and RNA pathogen detection for pneumonia, which could effectively remove the host sequence, had a higher microbial detection rate and a broader spectrum of pathogens (especially for viruses and some pathogens that are difficult to culture). Despite the advantages, there are many challenges in the clinical application of mNGS, and the mNGS report should be interpreted with caution.}, } @article {pmid35509001, year = {2022}, author = {Li, Z and Tang, J and Zhu, J and Xie, M and Huang, S and Li, S and Zhan, Y and Zeng, W and Xu, T and Ye, F}, title = {The convoluted process of diagnosing pulmonary mycosis caused by Exophiala dermatitidis: a case report.}, journal = {BMC infectious diseases}, volume = {22}, number = {1}, pages = {433}, pmid = {35509001}, issn = {1471-2334}, support = {ZNSA-2020003//Guangzhou Municipal Science and Technology Project/ ; SKLRD-Z-202019//State Key Laboratory of Respiratory Disease/ ; SKLRD-OP-202102//State Key Laboratory of Respiratory Disease/ ; 2019GIRHZ06//Guangzhou Institute of Respiratory Health Open Project/ ; }, mesh = {Biopsy ; *Exophiala/genetics ; Humans ; Male ; Middle Aged ; *Mycoses ; *Pneumonia ; }, abstract = {BACKGROUND: Etiological diagnosis is a key step in the treatment of patients with rare pulmonary mycosis, and the lack of understanding of this disease and lack of specific markers for the detection of rare species, such as Exophiala dermatitidis, add to the difficulty in diagnosing the condition. Therefore, improving the diagnostic strategies for this disease is very important.

CASE PRESENTATION: A 52-year-old man presented with cough, sputum production and hemoptysis; chest computed tomography (CT) revealed multiple bilateral lesions. The pathogen was unable to be identified after three biopsies. Subsequently, we performed combined tissue metagenomic next-generation sequencing (mNGS). The results of mNGS and a good therapeutic response helped to identify the causative pathogen as Exophiala dermatitidis. Finally, the patient was diagnosed with Exophiala dermatitidis pneumonia.

CONCLUSIONS: Combining molecular techniques, such as mNGS, with clinical microbiological tests will improve the rate of positivity in the diagnosis of rare fungal infections, and the importance of follow-up should be emphasized.}, } @article {pmid35508019, year = {2022}, author = {Kinasz, CT and Kreusch, MG and Bendia, AG and Pellizari, VH and Duarte, RTD}, title = {Taxonomic and functional diversity from Antarctic ice-tephra microbial community: ecological insights and potential for bioprospection.}, journal = {Anais da Academia Brasileira de Ciencias}, volume = {94}, number = {suppl 1}, pages = {e20210621}, doi = {10.1590/0001-3765202220210621}, pmid = {35508019}, issn = {1678-2690}, mesh = {Antarctic Regions ; Carbon ; *Cyanobacteria ; *Microbiota/genetics ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Antarctic active volcanoes can disperse pyroclastic minerals at long distances, transporting nutrients and microorganisms to the surrounding glacial environment. The sedimented volcanic materials - called tephras - may interact with glacier ice and produce a unique environment for microbial life. This study aimed to describe the microbial community structure of an Antarctic glacier ice with tephra layers in terms of its taxonomic and functional diversity. Ice samples from Collins Glacier (King George Island) containing tephra layers of Deception Island volcano were analyzed by a whole shotgun metagenomic approach. Taxonomic analysis revealed a highly diverse community dominated by phyla Bacteroidetes, Cyanobacteria and Proteobacteria. The dominant genera were Chitinophaga (13%), Acidobacterium (8%), and Cyanothece (4%), being all of these known to include psychrotolerant and psychrophilic strains. Functional diversity analysis revealed almost complete carbon, nitrogen and sulfur biogeochemical cycles. Carbohydrate metabolism of the ice-tephra community uses both organic and inorganic carbon inputs, where photosynthesis plays an important role through CO2 fixation. Our results also demonstrate a biotechnological potential for this glacial community, with functional annotations for styrene degradation and carotenoid pigment genes. Future metatranscriptomic studies shall further reveal the active strategies and the biotechnology potential of extremophiles from this unique ice-tephra microbial community.}, } @article {pmid35507858, year = {2022}, author = {Ianni, A and Bennato, F and Di Gianvittorio, V and Di Domenico, M and Martino, C and Colapietro, M and Cammà, C and Martino, G}, title = {Impact of different shades of light-emitting diode on fecal microbiota and gut health in broiler chickens.}, journal = {Animal bioscience}, volume = {35}, number = {12}, pages = {1967-1976}, pmid = {35507858}, issn = {2765-0189}, support = {//Rural Development Plan/ ; }, abstract = {OBJECTIVE: The aim of this study was to characterize the fecal microbiota of broiler chickens reared in the presence of different shades of light-emitting diode (LED) lights, correlating this information with biochemical and molecular evidence that allowed drawing conclusions on the state of health of the animals.

METHODS: Overall, the metagenomic approach on fecal samples was associated with evaluations on enzymes involved in the cellular response to oxidative stress: glutathione peroxidase (GPX), superoxide dismutase and catalase; while the inflammatory aspect was studied through the dosage of a proinflammatory cytokine, the interleukin 6 (IL-6), and the evaluation of the matrix metalloproteinases 2 (MMP-2) and 9 (MMP-9). Specifically, analysis was performed on distinct groups of chickens respectively raised in the presence of neutral (K = 3,300 to 3,700), cool (K = 5,500 to 6,000), and warm (K = 3,000 to 2,500) LED lightings, and a direct comparison was performed with animals reared with traditional neon lights.

RESULTS: The metagenomic analysis highlighted the presence of two most abundant bacterial phyla, the Firmicutes and the Bacteroidetes, with the latter characterized by a greater relative abundance (p<0.05) in the group of animals reared with Neutral LED light. The analysis on the enzymes involved in the antioxidant response showed an effect of the LED light, regardless of the applied shade, of reducing the expression of GPX (p<0.01), although this parameter is not correlated to an effective reduction in the tissue amount of the enzyme. Regarding the inflammatory state, no differences associated with IL-6 and MMP-9 were found; however, is noteworthy the significant reduction of MMP-2 activity in tissue samples obtained from animals subjected to illumination with neutral LED light.

CONCLUSION: This evidence, combined with the metagenomic findings, supports a potential positive effect of neutral LED lighting on animal welfare, although these considerations must be reflected in more targeted biochemical evaluations.}, } @article {pmid35506110, year = {2022}, author = {Jose, A and Apewokin, S and Hussein, WE and Ollberding, NJ and Elwing, JM and Haslam, DB}, title = {A unique gut microbiota signature in pulmonary arterial hypertension: A pilot study.}, journal = {Pulmonary circulation}, volume = {12}, number = {1}, pages = {e12051}, pmid = {35506110}, issn = {2045-8932}, abstract = {Pulmonary arterial hypertension (PAH) is a progressive, ultimately fatal cardiopulmonary disease associated with a number of physiologic changes, which is believed to result in imbalances in the intestinal microbiota. To date, comprehensive investigational analysis of the intestinal microbiota in human subjects is still limited. To address this, we performed a pilot study of the intestinal microbiome in 20 PAH and 20 non-PAH healthy control subjects, recruited from a single center, with each PAH subject recruited simultaneously with a cohabitating non-PAH control subject. Shotgun metagenomic sequencing was used to analyze the microbiome profiles. There were no differences between PAH and non-PAH subjects across several measures of microbial abundance and diversity (Alpha Diversity, Beta Diversity, F/B ratio). The relative abundance of Lachnospiraceae bacterium GAM79 was lower in PAH stool samples as compared to non-PAH control subject' stool. There was no strong or reproducible association between PAH disease severity and global microbial abundance, but several bacterial species (a relative abundance of Anaerostipes rhamnosivorans and a relative deficiency of Amedibacterium intestinale, Ruminococcus bicirculans, and Ruminococcus albus species were associated with disease severity (most proximal right heart catheterization hemodynamics and six-minute walk test distance) in PAH subjects. Our results support further investigation into the presence, significance, and potential physiologic effects of a PAH-specific intestinal microbiome.}, } @article {pmid35506038, year = {2022}, author = {Jones, RL}, title = {Gut microbiome as a potential biomarker of cancer risk in inflammatory bowel disease.}, journal = {Contemporary oncology (Poznan, Poland)}, volume = {26}, number = {1}, pages = {40-43}, pmid = {35506038}, issn = {1428-2526}, abstract = {Inflammatory bowel disease (IBD), a term used for Crohn's disease and ulcerative colitis that are characterized by chronic inflammation of the gastrointestinal tract, has been suggested to be closely related to high risk of developing colorectal or gastric cancer [1]. Focusing on patient cases and studies, this study aims to identify the cause of a possible correlation between IBD and cancerous cells, and determine the influence of IBD on cancerous cells in patients. A gut microbiome analysis was utilized to understand the mechanisms of the disease and to find associations with it in patients. I analyzed the experimental data obtained through amplicon sequencing to target regions of interest, and determined genes associated with the correlation by using coding programs. Biological processes, which are regulated by many means including the control of gene expression, were shown to be increased in patients with IBD compared to healthy subjects. Two datasets were used, with one going over an amplicon sequence analysis of fecal samples from healthy subjects and patients diagnosed with ulcerative colitis or Crohn's disease. I performed gut metagenome analysis on the data of the patients' fecal samples. This along with taxonomy analysis allows me to see percentages of certain bacterium in the gut and find a link. I was able to determine that the patients with IBD had a higher percentage of dark matter and a higher guanine to cytosine content (GC-content) percentage. This huge difference in the amount of dark matter and GC-content in an individual's human gut metagenome could be an indicator of someone potentially developing a disease.}, } @article {pmid35505691, year = {2022}, author = {Konstantinidis, K and Dovrolis, N and Kouvela, A and Kassela, K and Rosa Freitas, MG and Nearchou, A and de Courcy Williams, M and Veletza, S and Karakasiliotis, I}, title = {Defining virus-carrier networks that shape the composition of the mosquito core virome of a local ecosystem.}, journal = {Virus evolution}, volume = {8}, number = {1}, pages = {veac036}, pmid = {35505691}, issn = {2057-1577}, abstract = {Mosquitoes are the most important vectors of emerging infectious diseases. During the past decade, our understanding of the diversity of viruses they carry has greatly expanded. Most of these viruses are considered mosquito-specific, but there is increasing evidence that these viruses may affect the vector competence of mosquitoes. Metagenomics approaches have focused on specific mosquito species for the identification of what is called the core virome. Despite the fact that, in most ecosystems, multiple species may participate in virus emergence and circulation, there is a lack of understanding of the virus-carrier/host network for both vector-borne and mosquito-specific viruses. Here, we studied the core virome of mosquitoes in a diverse local ecosystem that had 24 different mosquito species. The analysis of the viromes of these 24 mosquito species resulted in the identification of 34 viruses, which included 15 novel viruses, as determined according to the species demarcation criteria of the respective virus families. Most of the mosquito species had never been analysed previously, and a comparison of the individual viromes of the 24 mosquito species revealed novel relationships among mosquito species and virus families. Groups of related viruses and mosquito species from multiple genera formed a complex web in the local ecosystem. Furthermore, analyses of the virome of mixed-species pools of mosquitoes from representative traps of the local ecosystem showed almost complete overlap with the individual-species viromes identified in the study. Quantitative analysis of viruses' relative abundance revealed a linear relationship to the abundance of the respective carrier/host mosquito species, supporting the theory of a stable core virome in the most abundant species of the local ecosystem. Finally, our study highlights the importance of using a holistic approach to investigating mosquito viromes relationships in rich and diverse ecosystems.}, } @article {pmid35505464, year = {2022}, author = {Xu, C and Wu, X and Tan, M and Wang, D and Wang, S and Wu, Y}, title = {Subacute Balamuthia mandrillaris encephalitis in an immunocompetent patient diagnosed by next-generation sequencing.}, journal = {The Journal of international medical research}, volume = {50}, number = {5}, pages = {3000605221093217}, pmid = {35505464}, issn = {1473-2300}, mesh = {*Amebiasis/diagnosis/drug therapy ; *Balamuthia mandrillaris/genetics ; *Encephalitis/diagnostic imaging/drug therapy ; High-Throughput Nucleotide Sequencing ; Humans ; Magnetic Resonance Imaging ; Male ; }, abstract = {Balamuthia mandrillaris is a free-living heterotrophic amoeba found in soil that causes a rare and usually fatal granulomatous amebic encephalitis. We report an immunocompetent patient infected with B. mandrillaris encephalitis diagnosed by next-generation sequencing (NGS). Clinical manifestations included sudden headache and epilepsy with disturbance of consciousness. The opening pressure of cerebrospinal fluid (CSF) was 220 mmH2O, with mildly elevated white blood cell numbers and elevated protein levels. Cranial magnetic resonance imaging revealed abnormal signals in the right frontal lobe, left parietal lobe, and left occipital lobe. CSF NGS detected B. mandrillaris. Albendazole and metronidazole combined with fluconazole were administered to the patient immediately, but his condition deteriorated and he eventually died. Encephalitis caused by B. mandrillaris is rare and has a high mortality rate. Clinical manifestations are complex and diverse, but early diagnosis is very important for successful treatment. This can be aided by the metagenomic NGS of CSF.}, } @article {pmid35505248, year = {2022}, author = {Worby, CJ and Schreiber, HL and Straub, TJ and van Dijk, LR and Bronson, RA and Olson, BS and Pinkner, JS and Obernuefemann, CLP and Muñoz, VL and Paharik, AE and Azimzadeh, PN and Walker, BJ and Desjardins, CA and Chou, WC and Bergeron, K and Chapman, SB and Klim, A and Manson, AL and Hannan, TJ and Hooton, TM and Kau, AL and Lai, HH and Dodson, KW and Hultgren, SJ and Earl, AM}, title = {Longitudinal multi-omics analyses link gut microbiome dysbiosis with recurrent urinary tract infections in women.}, journal = {Nature microbiology}, volume = {7}, number = {5}, pages = {630-639}, pmid = {35505248}, issn = {2058-5276}, support = {R37 AI048689/AI/NIAID NIH HHS/United States ; R01 AI165915/AI/NIAID NIH HHS/United States ; T32 GM139774/GM/NIGMS NIH HHS/United States ; R01 DK121822/DK/NIDDK NIH HHS/United States ; T32 GM007067/GM/NIGMS NIH HHS/United States ; U01 AI095542/AI/NIAID NIH HHS/United States ; U19 AI110818/AI/NIAID NIH HHS/United States ; 2019083/DDCF_/Doris Duke Charitable Foundation/United States ; }, mesh = {Dysbiosis ; Escherichia coli ; *Escherichia coli Infections/microbiology ; Female ; *Gastrointestinal Microbiome ; Humans ; Leukocytes, Mononuclear ; Male ; *Urinary Tract Infections/microbiology ; }, abstract = {Recurrent urinary tract infections (rUTIs) are a major health burden worldwide, with history of infection being a significant risk factor. While the gut is a known reservoir for uropathogenic bacteria, the role of the microbiota in rUTI remains unclear. We conducted a year-long study of women with (n = 15) and without (n = 16) history of rUTI, from whom we collected urine, blood and monthly faecal samples for metagenomic and transcriptomic interrogation. During the study 24 UTIs were reported, with additional samples collected during and after infection. The gut microbiome of individuals with a history of rUTI was significantly depleted in microbial richness and butyrate-producing bacteria compared with controls, reminiscent of other inflammatory conditions. However, Escherichia coli gut and bladder populations were comparable between cohorts in both relative abundance and phylogroup. Transcriptional analysis of peripheral blood mononuclear cells revealed expression profiles indicative of differential systemic immunity between cohorts. Altogether, these results suggest that rUTI susceptibility is in part mediated through the gut-bladder axis, comprising gut dysbiosis and differential immune response to bacterial bladder colonization, manifesting in symptoms.}, } @article {pmid35505244, year = {2022}, author = {Gavriilidou, A and Kautsar, SA and Zaburannyi, N and Krug, D and Müller, R and Medema, MH and Ziemert, N}, title = {Compendium of specialized metabolite biosynthetic diversity encoded in bacterial genomes.}, journal = {Nature microbiology}, volume = {7}, number = {5}, pages = {726-735}, pmid = {35505244}, issn = {2058-5276}, mesh = {*Cyanobacteria ; Genome, Bacterial/genetics ; Phylogeny ; Secondary Metabolism/genetics ; *Streptomyces ; }, abstract = {Bacterial specialized metabolites are a proven source of antibiotics and cancer therapies, but whether we have sampled all the secondary metabolite chemical diversity of cultivated bacteria is not known. We analysed ~170,000 bacterial genomes and ~47,000 metagenome assembled genomes (MAGs) using a modified BiG-SLiCE and the new clust-o-matic algorithm. We estimate that only 3% of the natural products potentially encoded in bacterial genomes have been experimentally characterized. We show that the variation in secondary metabolite biosynthetic diversity drops significantly at the genus level, identifying it as an appropriate taxonomic rank for comparison. Equal comparison of genera based on relative evolutionary distance revealed that Streptomyces bacteria encode the largest biosynthetic diversity by far, with Amycolatopsis, Kutzneria and Micromonospora also encoding substantial diversity. Finally, we find that several less-well-studied taxa, such as Weeksellaceae (Bacteroidota), Myxococcaceae (Myxococcota), Pleurocapsa and Nostocaceae (Cyanobacteria), have potential to produce highly diverse sets of secondary metabolites that warrant further investigation.}, } @article {pmid35504476, year = {2022}, author = {Lai, KP and Tsang, CF and Li, L and Yu, RMK and Kong, RYC}, title = {Microplastics act as a carrier for wastewater-borne pathogenic bacteria in sewage.}, journal = {Chemosphere}, volume = {301}, number = {}, pages = {134692}, doi = {10.1016/j.chemosphere.2022.134692}, pmid = {35504476}, issn = {1879-1298}, mesh = {Animals ; Bacteria/genetics ; Ecosystem ; *Microplastics ; Plastics ; Sewage ; Wastewater ; *Water Pollutants, Chemical/analysis ; }, abstract = {Microplastic pollution, a pressing global environmental problem, has a severe impact on both aquatic ecosystems and public health worldwide. Due to the small size of microplastics, they are able to pass through the filtration systems of municipal wastewater treatment works (WWTWs). In recent years, studies have focused on the environmental abundance and ecotoxicological effects of microplastics, but there are limited studies investigating the colonization of microplastics by bacteria, especially those pathogenic ones. In this study, we examined the colonization and composition of the bacterial communities on polyethylene microbeads after incubation in raw sewage collected from three municipal WWTWs in Hong Kong (Sha Tin Sewage Treatment Works, Stonecutters Island Sewage Treatment Works, and Shek Wu Hui Sewage Treatment Works). Scanning electron microscopy (SEM) results indicate that bacterial cells were colonized on the surfaces of the microbeads and formed biofilms after sewage incubation. Metagenomic sequencing data demonstrated an increase in bacterial diversity after 21 days of sewage incubation when compared to shorter incubation periods of 6, 11 and 16 days. Importantly, human and fish pathogens such as Arcobacter cryaerophilus, Aeromonas salmonicida, Vibrio areninigrae and Vibrio navarrensis were found in the resident bacterial communities. Taken together, our results demonstrate that microplastics could act as a carrier for wastewater-borne pathogenic bacteria in municipal sewage.}, } @article {pmid35504378, year = {2022}, author = {Yang, Y and Fang, A and Feng, K and Zhang, D and Zhou, H and Xing, D}, title = {Single-cell metagenomics and metagenomics approaches reveal extracellular electron transfer of psychrophilic electroactive biofilms.}, journal = {The Science of the total environment}, volume = {836}, number = {}, pages = {155606}, doi = {10.1016/j.scitotenv.2022.155606}, pmid = {35504378}, issn = {1879-1026}, mesh = {Bacteria ; *Bioelectric Energy Sources ; Biofilms ; Electrodes ; Electron Transport ; Electrons ; *Geobacter ; Metagenomics ; }, abstract = {Revealing the metabolic functions and the extracellular electron transfer (EET) process of psychrophilic electroactive biofilms (PEB) is important for understanding the functional adaptability of electroactive bacteria (EAB) to low temperatures. In this study, single cell sorting (SCS)-based metagenomics sequencing was used to characterize the composition and function of the PEB. Biofilm microbiome analysis showed that Geobacter, with a relative abundance of 62.64%, dominated the PEB enriched in the bioelectrochemical system (BES) at 4 °C. Both the metagenome (MAG) and single-cell metagenome (SCM) revealed that there were no obvious metabolic differences between the original biofilm and the sorted single cells. The presence of genes associated with type IV pilus, c-type cytochromes, and riboflavin indicated that the EET potential was maintained in the PEB at low temperatures. These results suggested that SCM provides an alternative approach to reconstruct the metabolic functions of uncultured and slow-growing EAB.}, } @article {pmid35504350, year = {2022}, author = {Wang, X and Liu, X and Xiao, S and Zhang, Z and Wu, L and Cheng, Y and Tan, Y and Zhang, G and Jiang, C}, title = {Comparison of gut microbiota compositions and corresponding genetic and metabolic features between guttate and plaque psoriasis by metagenomic sequencing.}, journal = {Microbial pathogenesis}, volume = {167}, number = {}, pages = {105560}, doi = {10.1016/j.micpath.2022.105560}, pmid = {35504350}, issn = {1096-1208}, mesh = {*Epstein-Barr Virus Infections ; *Gastrointestinal Microbiome/genetics ; Herpesvirus 4, Human ; Humans ; Metagenomics ; *Psoriasis ; }, abstract = {BACKGROUND: Guttate psoriasis (GP) and psoriasis plaques (PP) are common subtypes of psoriasis. Previous studies have fully researched the association between psoriasis and gut microbiota. However, the differences in gut microbiota between GPs and PPs are still unknown.

METHODS: Fecal samples were collected from 30 psoriatic patients (15 GP and 15 PP) and 15 healthy subjects. Metagenomic sequencing was then used to compare gut microbiota compositions and corresponding genetic and metabolic features between GP and PP.

RESULTS: We found that the genus Megamonas was increased in PP and reduced in GP. The genus Eubacterium was increased in GP and decreased in PP. Ten KEGG pathway were significantly enriched in GP: bacterial secretion system, ribosome, sphingolipid signaling pathway, steroid hormone biosynthesis, complement and coagulation cascades, proteoglycans in cancer, FOXO signaling pathway, cGMP-PKG signaling pathway, insulin resistance, and Epstein-Barr virus infection. Ten metabolites were significantly differentially abundant between GP and PP. Among them, thiamine, biotin, butylamine, phenylethylamine, folic acid, 1,2-propanediol, and 4-aminobutyrate were enriched in PP and l-glutamate, l-glutamine, and propanoate were enriched in GP.

CONCLUSIONS: These results provide a theoretical basis for the microbiome-guided stratification of patients with psoriasis.}, } @article {pmid35504169, year = {2022}, author = {Tian, Z and Zhuang, X and Zhuo, S and Zhu, Y and Hu, S and Zhao, M and Tang, C and Zhang, Z and Li, X and Ma, R and Zeng, Z and Feng, R and Chen, M}, title = {Dietary inflammatory potential mediated gut microbiota and metabolite alterations in Crohn's disease: A fire-new perspective.}, journal = {Clinical nutrition (Edinburgh, Scotland)}, volume = {41}, number = {6}, pages = {1260-1271}, doi = {10.1016/j.clnu.2022.04.014}, pmid = {35504169}, issn = {1532-1983}, mesh = {Bacteria ; *Crohn Disease ; Diet/adverse effects ; Feces/microbiology ; *Gastrointestinal Microbiome ; Humans ; Inflammation/microbiology ; }, abstract = {BACKGROUND & AIMS: Pro-inflammatory diet interacting with gut microbiome might trigger for Crohn's disease (CD). We aimed to investigate the relationship between dietary inflammatory potential and microflora/metabolites change and their link with CD.

METHODS: The dietary inflammatory potential was assessed using a dietary inflammatory index (DII) based on the Food Frequency Questionnaire from 150 new-onset CD patients and 285 healthy controls (HCs). We selected 41 CD patients and 89 HCs who had not received medication for metagenomic and targeted metabolomic sequencing to profile their gut microbial composition as well as fecal and serum metabolites. DII scores were classified into quartiles to investigate associations among different variables.

RESULTS: DII scores of CD patients were significantly higher than HCs (0.56 ± 1.20 vs 0.23 ± 1.02, p = 0.017). With adjustment for confounders, a higher DII score was significantly associated with higher risk of CD (OR: 1.420; 95% CI: 1.049, 1.923, p = 0.023). DII score also was positively correlated with disease activity (p = 0.001). Morganella morganii and Veillonella parvula were increased while Coprococcus eutactus was decreased in the pro-inflammatory diets group, as well as in CD. DII-related bacteria were associated with disease activity and inflammatory markers in CD patients. Among the metabolic change, pro-inflammatory diet induced metabolites change were largely involved in amino acid metabolic pathways that were also observed in CD.

CONCLUSIONS: Pro-inflammatory diet might be associated with increased risk and disease activity of CD. Diet with high DII potentially involves in CD by mediating alterations in gut microbiota and metabolites.}, } @article {pmid35504157, year = {2022}, author = {Hegarty, B and Dai, Z and Raskin, L and Pinto, A and Wigginton, K and Duhaime, M}, title = {A snapshot of the global drinking water virome: Diversity and metabolic potential vary with residual disinfectant use.}, journal = {Water research}, volume = {218}, number = {}, pages = {118484}, doi = {10.1016/j.watres.2022.118484}, pmid = {35504157}, issn = {1879-2448}, mesh = {Bacteria/genetics ; Chlorine ; *Disinfectants/pharmacology ; *Drinking Water ; Metagenomics ; Virome ; *Viruses/genetics ; *Water Purification ; }, abstract = {Viruses are important drivers of microbial community ecology and evolution, influencing microbial mortality, metabolism, and horizontal gene transfer. However, the effects of viruses remain largely unknown in many environments, including in drinking water systems. Drinking water metagenomic studies have offered a whole community perspective of bacterial impacts on water quality, but have not yet considered the influences of viruses. In this study, we address this gap by mining viral DNA sequences from publicly available drinking water metagenomes from distribution systems in six countries around the world. These datasets provide a snapshot of the taxonomic diversity and metabolic potential of the global drinking water virome; and provide an opportunity to investigate the effects of geography, climate, and drinking water treatment practices on viral diversity. Both environmental conditions and differences in sample processing were found to influence the viral composition. Using free chlorine as the residual disinfectant was associated with clear differences in viral taxonomic diversity and metabolic potential, with significantly fewer viral populations and less even viral community structures than observed in distribution systems without residual disinfectant. Additionally, drinking water viruses carry antibiotic resistance genes (ARGs), as well as genes to survive oxidative stress and nitrogen limitation. Through this study, we have demonstrated that viral communities are diverse across drinking water systems and vary with the use of residual disinfectant. Our findings offer directions for future research to develop a more robust understanding of how virus-bacteria interactions in drinking water distribution systems affect water quality.}, } @article {pmid35503723, year = {2022}, author = {Pronk, LJU and Medema, MH}, title = {Whokaryote: distinguishing eukaryotic and prokaryotic contigs in metagenomes based on gene structure.}, journal = {Microbial genomics}, volume = {8}, number = {5}, pages = {}, pmid = {35503723}, issn = {2057-5858}, mesh = {Bacteria/genetics ; Eukaryota/genetics ; *Metagenome ; Metagenomics/methods ; *Microbiota/genetics ; }, abstract = {Metagenomics has become a prominent technology to study the functional potential of all organisms in a microbial community. Most studies focus on the bacterial content of these communities, while ignoring eukaryotic microbes. Indeed, many metagenomics analysis pipelines silently assume that all contigs in a metagenome are prokaryotic, likely resulting in less accurate annotation of eukaryotes in metagenomes. Early detection of eukaryotic contigs allows for eukaryote-specific gene prediction and functional annotation. Here, we developed a classifier that distinguishes eukaryotic from prokaryotic contigs based on foundational differences between these taxa in terms of gene structure. We first developed Whokaryote, a random forest classifier that uses intergenic distance, gene density and gene length as the most important features. We show that, with an estimated recall, precision and accuracy of 94, 96 and 95 %, respectively, this classifier with features grounded in biology can perform almost as well as the classifiers EukRep and Tiara, which use k-mer frequencies as features. By retraining our classifier with Tiara predictions as an additional feature, the weaknesses of both types of classifiers are compensated; the result is Whokaryote+Tiara, an enhanced classifier that outperforms all individual classifiers, with an F1 score of 0.99 for both eukaryotes and prokaryotes, while still being fast. In a reanalysis of metagenome data from a disease-suppressive plant endospheric microbial community, we show how using Whokaryote+Tiara to select contigs for eukaryotic gene prediction facilitates the discovery of several biosynthetic gene clusters that were missed in the original study. Whokaryote (+Tiara) is wrapped in an easily installable package and is freely available from https://github.com/LottePronk/whokaryote.}, } @article {pmid35503575, year = {2023}, author = {Dick, JM and Tan, J}, title = {Chemical Links Between Redox Conditions and Estimated Community Proteomes from 16S rRNA and Reference Protein Sequences.}, journal = {Microbial ecology}, volume = {85}, number = {4}, pages = {1338-1355}, pmid = {35503575}, issn = {1432-184X}, mesh = {RNA, Ribosomal, 16S/genetics ; *Proteome ; *Microbiota/genetics ; Metagenome ; Oxidation-Reduction ; Phylogeny ; }, abstract = {Environmental influences on community structure are often assessed through multivariate analyses in order to relate microbial abundances to separately measured physicochemical variables. However, genes and proteins are themselves chemical entities; in combination with genome databases, differences in microbial abundances directly encode for chemical variability. We predicted that the carbon oxidation state of estimated community proteomes, obtained by combining taxonomic abundances from published 16S rRNA gene sequencing datasets with reference microbial proteomes from the NCBI Reference Sequence (RefSeq) database, would reflect environmental oxidation-reduction conditions. Analysis of multiple datasets confirms the geobiochemical predictions for environmental redox gradients in hydrothermal systems, stratified lakes and marine environments, and shale gas wells. The geobiochemical signal is largest for the steep redox gradients associated with hydrothermal systems and between injected water and produced fluids from shale gas wells, demonstrating that microbial community composition can be a chemical proxy for environmental redox gradients. Although estimates of oxidation state from 16S amplicon and metagenomic sequences are correlated, the 16S-based estimates show stronger associations with redox gradients in some environments.}, } @article {pmid35503213, year = {2022}, author = {Wilkens, C and Vuillemin, M and Pilgaard, B and Polikarpov, I and Morth, JP}, title = {A GH115 α-glucuronidase structure reveals dimerization-mediated substrate binding and a proton wire potentially important for catalysis.}, journal = {Acta crystallographica. Section D, Structural biology}, volume = {78}, number = {Pt 5}, pages = {658-668}, pmid = {35503213}, issn = {2059-7983}, mesh = {Catalysis ; Dimerization ; Glucuronates/metabolism ; Glycoside Hydrolases/chemistry ; Kinetics ; *Protons ; Substrate Specificity ; *Xylans/metabolism ; }, abstract = {Xylan is a major constituent of plant cell walls and is a potential source of biomaterials, and the derived oligosaccharides have been shown to have prebiotic effects. Xylans can be highly substituted with different sugar moieties, which pose steric hindrance to the xylanases that catalyse the hydrolysis of the xylan backbone. One such substituent is α-D-glucuronic acid, which is linked to the O2' position of the β-1,4 D-xylopyranoses composing the main chain of xylans. The xylan-specific α-glucuronidases from glycoside hydrolase family 115 (GH115) specifically catalyse the removal of α-D-glucuronic acid (GlcA) or methylated GlcA (MeGlcA). Here, the molecular basis by which the bacterial GH115 member wtsAgu115A interacts with the main chain of xylan and the indirect involvement of divalent ions in the formation of the Michaelis-Menten complex are described. A crystal structure at 2.65 Å resolution of wtsAgu115A originating from a metagenome from an anaerobic digester fed with wastewater treatment sludge was determined in complex with xylohexaose, and Asp303 was identified as the likely general acid. The residue acting as the general base could not be identified. However, a proton wire connecting the active site to the metal site was observed and hence a previous hypothesis suggesting a Grotthuss-like mechanism cannot be rejected. Only a single molecule was found in the asymmetric unit. However, wtsAgu115A forms a dimer with a symmetry-related molecule in the crystal lattice. The xylohexaose moieties of the xylohexaose are recognized by residues from both protomers, thus creating a xylohexaose recognition site at the dimer interface. The dimer was confirmed by analytical size-exclusion chromatography in solution. Kinetic analysis with aldouronic acids resulted in a Hill coefficient of greater than 2, suggesting cooperativity between the two binding sites. Three Ca[2+] ions were identified in the wtsAgu115A structures. One Ca[2+] ion is of particular interest as it is coordinated by the residues of the loops that also interact with the substrate. Activity studies showed that the presence of Mg[2+] or Mn[2+] resulted in a higher activity towards aldouronic acids, while the less restrictive coordination geometry of Ca[2+] resulted in a decrease in activity.}, } @article {pmid35502903, year = {2022}, author = {Brealey, JC and Lecaudey, LA and Kodama, M and Rasmussen, JA and Sveier, H and Dheilly, NM and Martin, MD and Limborg, MT}, title = {Microbiome "Inception": an Intestinal Cestode Shapes a Hierarchy of Microbial Communities Nested within the Host.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0067922}, pmid = {35502903}, issn = {2150-7511}, mesh = {Animals ; Bacteria/genetics ; *Cestoda/genetics ; Dysbiosis ; *Gastrointestinal Microbiome/physiology ; *Microbiota ; *Parasites ; }, abstract = {The concept of a holobiont, a host organism and its associated microbial communities, encapsulates the vital role the microbiome plays in the normal functioning of its host. Parasitic infections can disrupt this relationship, leading to dysbiosis. However, it is increasingly recognized that multicellular parasites are themselves holobionts. Intestinal parasites share space with the host gut microbiome, creating a system of nested microbiomes within the primary host. However, how the parasite, as a holobiont, interacts with the host holobiont remains unclear, as do the consequences of these interactions for host health. Here, we used 16S amplicon and shotgun metagenomics sequencing to characterize the microbiome of the intestinal cestode Eubothrium and its effect on the gut microbiome of its primary host, Atlantic salmon. Our results indicate that cestode infection is associated with salmon gut dysbiosis by acting as a selective force benefiting putative pathogens and potentially introducing novel bacterial species to the host. Our results suggest that parasitic cestodes may themselves be holobionts nested within the microbial community of their holobiont host, emphasizing the importance of also considering microbes associated with parasites when studying intestinal parasitic infections. IMPORTANCE The importance of the parasite microbiome is gaining recognition. Of particular concern is understanding how these parasite microbiomes influence host-parasite interactions and parasite interactions with the vertebrate host microbiome as part of a system of nested holobionts. However, there are still relatively few studies focusing on the microbiome of parasitic helminths in general and almost none on cestodes in particular, despite the significant burden of disease caused by these parasites globally. Our study provides insights into a system of significance to the aquaculture industry, cestode infections of Atlantic salmon and, more broadly, expands our general understanding of parasite-microbiome-host interactions and introduces a new element, the microbiome of the parasite itself, which may play a critical role in modulating the host microbiome, and, therefore, the host response, to parasite infection.}, } @article {pmid35502617, year = {2022}, author = {Gofton, AW and Blasdell, KR and Taylor, C and Banks, PB and Michie, M and Roy-Dufresne, E and Poldy, J and Wang, J and Dunn, M and Tachedjian, M and Smith, I}, title = {Metatranscriptomic profiling reveals diverse tick-borne bacteria, protozoans and viruses in ticks and wildlife from Australia.}, journal = {Transboundary and emerging diseases}, volume = {69}, number = {5}, pages = {e2389-e2407}, pmid = {35502617}, issn = {1865-1682}, mesh = {Animals ; Animals, Wild ; Australia/epidemiology ; *Borrelia ; Humans ; *Ixodes/microbiology ; *Rickettsia ; *Tick Infestations/epidemiology/veterinary ; *Tick-Borne Diseases/epidemiology/veterinary ; *Viruses/genetics ; }, abstract = {Tick-borne zoonoses are emerging globally due to changes in climate and land use. While the zoonotic threats associated with ticks are well studied elsewhere, in Australia, the diversity of potentially zoonotic agents carried by ticks and their significance to human and animal health is not sufficiently understood. To this end, we used untargeted metatranscriptomics to audit the prokaryotic, eukaryotic and viral biomes of questing ticks and wildlife blood samples from two urban and rural sites in New South Wales, Australia. Ixodes holocyclus and Haemaphysalis bancrofti were the main tick species collected, and blood samples from Rattus rattus, Rattus fuscipes, Perameles nasuta and Trichosurus vulpecula were also collected and screened for tick-borne microorganisms using metatranscriptomics followed by conventional targeted PCR to identify important microbial taxa to the species level. Our analyses identified 32 unique tick-borne taxa, including 10 novel putative species. Overall, a wide range of tick-borne microorganisms were found in questing ticks including haemoprotozoa such as Babesia, Theileria, Hepatozoon and Trypanosoma spp., bacteria such as Borrelia, Rickettsia, Ehrlichia, Neoehrlichia and Anaplasma spp., and numerous viral taxa including Reoviridiae (including two coltiviruses) and a novel Flaviviridae-like jingmenvirus. Of note, a novel hard tick-borne relapsing fever Borrelia sp. was identified in questing H. bancrofti ticks which is closely related to, but distinct from, cervid-associated Borrelia spp. found throughout Asia. Notably, all tick-borne microorganisms were phylogenetically unique compared to their relatives found outside Australia, and no foreign tick-borne human pathogens such as Borrelia burgdorferi s.l. or Babesia microti were found. This work adds to the growing literature demonstrating that Australian ticks harbour a unique and endemic microbial fauna, including potentially zoonotic agents which should be further studied to determine their relative risk to human and animal health.}, } @article {pmid35501923, year = {2022}, author = {Parker, A and Romano, S and Ansorge, R and Aboelnour, A and Le Gall, G and Savva, GM and Pontifex, MG and Telatin, A and Baker, D and Jones, E and Vauzour, D and Rudder, S and Blackshaw, LA and Jeffery, G and Carding, SR}, title = {Fecal microbiota transfer between young and aged mice reverses hallmarks of the aging gut, eye, and brain.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {68}, pmid = {35501923}, issn = {2049-2618}, support = {BB/CCG1860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/N000250/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/R012490/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10353/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10355/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10356/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Aging ; Animals ; Brain ; *Fecal Microbiota Transplantation ; *Gastrointestinal Microbiome/physiology ; Inflammation/pathology ; Mice ; }, abstract = {BACKGROUND: Altered intestinal microbiota composition in later life is associated with inflammaging, declining tissue function, and increased susceptibility to age-associated chronic diseases, including neurodegenerative dementias. Here, we tested the hypothesis that manipulating the intestinal microbiota influences the development of major comorbidities associated with aging and, in particular, inflammation affecting the brain and retina.

METHODS: Using fecal microbiota transplantation, we exchanged the intestinal microbiota of young (3 months), old (18 months), and aged (24 months) mice. Whole metagenomic shotgun sequencing and metabolomics were used to develop a custom analysis workflow, to analyze the changes in gut microbiota composition and metabolic potential. Effects of age and microbiota transfer on the gut barrier, retina, and brain were assessed using protein assays, immunohistology, and behavioral testing.

RESULTS: We show that microbiota composition profiles and key species enriched in young or aged mice are successfully transferred by FMT between young and aged mice and that FMT modulates resulting metabolic pathway profiles. The transfer of aged donor microbiota into young mice accelerates age-associated central nervous system (CNS) inflammation, retinal inflammation, and cytokine signaling and promotes loss of key functional protein in the eye, effects which are coincident with increased intestinal barrier permeability. Conversely, these detrimental effects can be reversed by the transfer of young donor microbiota.

CONCLUSIONS: These findings demonstrate that the aging gut microbiota drives detrimental changes in the gut-brain and gut-retina axes suggesting that microbial modulation may be of therapeutic benefit in preventing inflammation-related tissue decline in later life. Video abstract.}, } @article {pmid35501856, year = {2022}, author = {Mesnage, R and Bowyer, RCE and El Balkhi, S and Saint-Marcoux, F and Gardere, A and Ducarmon, QR and Geelen, AR and Zwittink, RD and Tsoukalas, D and Sarandi, E and Paramera, EI and Spector, T and Steves, CJ and Antoniou, MN}, title = {Impacts of dietary exposure to pesticides on faecal microbiome metabolism in adult twins.}, journal = {Environmental health : a global access science source}, volume = {21}, number = {1}, pages = {46}, pmid = {35501856}, issn = {1476-069X}, mesh = {Adult ; Dietary Exposure/analysis ; *Herbicides/analysis ; Humans ; *Insecticides/analysis ; *Microbiota ; Organophosphorus Compounds ; *Pesticide Residues/analysis ; *Pesticides ; Vegetables/chemistry ; }, abstract = {BACKGROUND: Dietary habits have a profound influence on the metabolic activity of gut microorganisms and their influence on health. Concerns have been raised as to whether the consumption of foodstuffs contaminated with pesticides can contribute to the development of chronic disease by affecting the gut microbiome. We performed the first pesticide biomonitoring survey of the British population, and subsequently used the results to perform the first pesticide association study on gut microbiome composition and function from the TwinsUK registry.

METHODS: Dietary exposure of 186 common insecticide, herbicide, or fungicide residues and the faecal microbiome in 65 twin pairs in the UK was investigated. We evaluated if dietary habits, geographic location, or the rural/urban environment, are associated with the excretion of pesticide residues. The composition and metabolic activity of faecal microbiota was evaluated using shotgun metagenomics and metabolomics respectively. We performed a targeted urine metabolomics analysis in order to evaluate whether pesticide urinary excretion was also associated with physiological changes.

RESULTS: Pyrethroid and/or organophosphorus insecticide residues were found in all urine samples, while the herbicide glyphosate was found in 53% of individuals. Food frequency questionnaires showed that residues from organophosphates were higher with increased consumption of fruit and vegetables. A total of 34 associations between pesticide residue concentrations and faecal metabolite concentrations were detected. Glyphosate excretion was positively associated with an overall increased bacterial species richness, as well as to fatty acid metabolites and phosphate levels. The insecticide metabolite Br2CA, reflecting deltamethrin exposure, was positively associated with the phytoestrogens enterodiol and enterolactone, and negatively associated with some N-methyl amino acids. Urine metabolomics performed on a subset of samples did not reveal associations with the excretion of pesticide residues.

CONCLUSIONS: The consumption of conventionally grown fruit and vegetables leads to higher ingestion of pesticides with unknown long-term health consequences. Our results highlight the need for future dietary intervention studies to understand effects of pesticide exposure on the gut microbiome and possible health consequences.}, } @article {pmid35501694, year = {2022}, author = {Jiang, C and Zhu, S and Feng, J and Shui, W}, title = {Slope aspect affects the soil microbial communities in karst tiankeng negative landforms.}, journal = {BMC ecology and evolution}, volume = {22}, number = {1}, pages = {54}, pmid = {35501694}, issn = {2730-7182}, mesh = {Bacteria ; Biodiversity ; Humans ; *Microbiota ; *Soil/chemistry ; Soil Microbiology ; }, abstract = {BACKGROUND: Karst tiankeng is a large-scale negative surface terrain, and slope aspects affect the soil conditions, vegetation and microbial flora in the tiankeng. However, the influence of the slope aspect on the soil microbial community in tiankeng has not been elucidated.

METHODS: In this study, metagenomic sequencing technology was used to analyze the soil microbial community structure and functional potentials on the shady and sunny slopes of karst tiankeng.

RESULTS: The Shannon-Wiener diversity of microbial communities on shady slope (SHS) was significantly higher than that on sunny slope (SUS). Although the composition of dominant phyla on shady slope (SHS) and sunny slope (SUS) was similar, there were significant differences in beta-diversity. The linear discriminate analysis (LDA) results showed that biomarkers mainly belongs to Actinobacteria, Chloroflexi and Proteobacteria. Functional pathways and CAZy (Carbohydrate-Active Enzymes) genes also had a remarkable response to slope aspect change. LEfSe results indicated several biomarker pathways in sunny slope involved in human disease. Moreover, the abundance of CAZy genes was higher in shady slope and had stronger ability in decomposing litter. The microbial communities were mainly correlation with the vegetation characteristics (species richness and coverage) and soil properties (SOC and pH).

CONCLUSIONS: These results indicate slope aspect has a pronounced influence on microbial community composition, structure and function at karst tiankeng. In the future, the conservation of karst tiankeng biodiversity should pay more attention to topographical factors.}, } @article {pmid35501656, year = {2022}, author = {Klimenko, ES and Belkova, NL and Romanitsa, AI and Pogodina, AV and Rychkova, LV}, title = {Diversity and Metabolic Potential of the Gut Microbiome in Adolescents with Functional Bowel Disorder.}, journal = {Bulletin of experimental biology and medicine}, volume = {172}, number = {6}, pages = {681-685}, pmid = {35501656}, issn = {1573-8221}, mesh = {Adolescent ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; Pilot Projects ; RNA, Ribosomal, 16S/genetics ; }, abstract = {The article presents the results of a pilot study of the diversity and metabolic potential of the gut microbiome in adolescents with various forms of functional bowel disorder. The participants were the patients of the Clinic of Research Center for Family Health and Human Reproduction Problems. Biological material was studied using metagenomic sequencing of V3-V4 variable regions of the 16S rRNA gene. We showed that the composition of the minor component of the intestinal microbiome in adolescents with functional bowel disorder differs from that in the healthy subjects (control). Different types of transit disturbances in functional bowel disorder also differ from each other. According to the metabolic potential, adolescents can be divided into two groups irrespective of the pathophysiological manifestations: for one group, a more intensive metabolism in amino acid and lipid biosynthesis pathways was predicted than for the other.}, } @article {pmid35501417, year = {2022}, author = {Levy-Booth, DJ and Navas, LE and Fetherolf, MM and Liu, LY and Dalhuisen, T and Renneckar, S and Eltis, LD and Mohn, WW}, title = {Discovery of lignin-transforming bacteria and enzymes in thermophilic environments using stable isotope probing.}, journal = {The ISME journal}, volume = {16}, number = {8}, pages = {1944-1956}, pmid = {35501417}, issn = {1751-7370}, support = {STPGP 506595-17//Gouvernement du Canada | Natural Sciences and Engineering Research Council of Canada (Conseil de Recherches en Sciences Naturelles et en Génie du Canada)/ ; SIP004//Genome British Columbia/ ; }, mesh = {Bacteria/genetics/metabolism ; *Gammaproteobacteria/metabolism ; Isotopes/metabolism ; Lignin/metabolism ; *Microbiota ; Tandem Mass Spectrometry ; }, abstract = {Characterizing microorganisms and enzymes involved in lignin biodegradation in thermal ecosystems can identify thermostable biocatalysts. We integrated stable isotope probing (SIP), genome-resolved metagenomics, and enzyme characterization to investigate the degradation of high-molecular weight, [13]C-ring-labeled synthetic lignin by microbial communities from moderately thermophilic hot spring sediment (52 °C) and a woody "hog fuel" pile (53 and 62 °C zones). [13]C-Lignin degradation was monitored using IR-GCMS of [13]CO2, and isotopic enrichment of DNA was measured with UHLPC-MS/MS. Assembly of 42 metagenomic libraries (72 Gb) yielded 344 contig bins, from which 125 draft genomes were produced. Fourteen genomes were significantly enriched with [13]C from lignin, including genomes of Actinomycetes (Thermoleophilaceae, Solirubrobacteraceae, Rubrobacter sp.), Firmicutes (Kyrpidia sp., Alicyclobacillus sp.) and Gammaproteobacteria (Steroidobacteraceae). We employed multiple approaches to screen genomes for genes encoding putative ligninases and pathways for aromatic compound degradation. Our analysis identified several novel laccase-like multi-copper oxidase (LMCO) genes in [13]C-enriched genomes. One of these LMCOs was heterologously expressed and shown to oxidize lignin model compounds and minimally transformed lignin. This study elucidated bacterial lignin depolymerization and mineralization in thermal ecosystems, establishing new possibilities for the efficient valorization of lignin at elevated temperature.}, } @article {pmid35501347, year = {2022}, author = {Gao, S and Paez-Espino, D and Li, J and Ai, H and Liang, J and Luo, Z and Zheng, J and Chen, H and Shu, W and Huang, L}, title = {Patterns and ecological drivers of viral communities in acid mine drainage sediments across Southern China.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {2389}, pmid = {35501347}, issn = {2041-1723}, mesh = {Acids ; *Biodiversity ; Metagenome/genetics ; Mining ; *Viruses/genetics ; }, abstract = {Recent advances in environmental genomics have provided unprecedented opportunities for the investigation of viruses in natural settings. Yet, our knowledge of viral biogeographic patterns and the corresponding drivers is still limited. Here, we perform metagenomic deep sequencing on 90 acid mine drainage (AMD) sediments sampled across Southern China and examine the biogeography of viruses in this extreme environment. The results demonstrate that prokaryotic communities dictate viral taxonomic and functional diversity, abundance and structure, whereas other factors especially latitude and mean annual temperature also impact viral populations and functions. In silico predictions highlight lineage-specific virus-host abundance ratios and richness-dependent virus-host interaction structure. Further functional analyses reveal important roles of environmental conditions and horizontal gene transfers in shaping viral auxiliary metabolic genes potentially involved in phosphorus assimilation. Our findings underscore the importance of both abiotic and biotic factors in predicting the taxonomic and functional biogeographic dynamics of viruses in the AMD sediments.}, } @article {pmid35501317, year = {2022}, author = {Hisham, MB and Hashim, AM and Mohd Hanafi, N and Abdul Rahman, N and Abdul Mutalib, NE and Tan, CK and Nazli, MH and Mohd Yusoff, NF}, title = {Bacterial communities associated with silage of different forage crops in Malaysian climate analysed using 16S amplicon metagenomics.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {7107}, pmid = {35501317}, issn = {2045-2322}, mesh = {Bacteria ; Carbohydrates ; Crops, Agricultural ; Lactic Acid/metabolism ; *Metagenomics ; *Silage/microbiology ; }, abstract = {Silage produced in tropical countries is prone to spoilage because of high humidity and temperature. Therefore, determining indigenous bacteria as potential inoculants is important to improve silage quality. This study aimed to determine bacterial community and functional changes associated with ensiling using amplicon metagenomics and to predict potential bacterial additives associated with silage quality in the Malaysian climate. Silages of two forage crops (sweet corn and Napier) were prepared, and their fermentation properties and functional bacterial communities were analysed. After ensiling, both silages were predominated by lactic acid bacteria (LAB), and they exhibited good silage quality with significant increment in lactic acid, reductions in pH and water-soluble carbohydrates, low level of acetic acid and the absence of propionic and butyric acid. LAB consortia consisting of homolactic and heterolactic species were proposed to be the potential bacterial additives for sweet corn and Napier silage fermentation. Tax4fun functional prediction revealed metabolic pathways related to fermentation activities (bacterial division, carbohydrate transport and catabolism, and secondary metabolite production) were enriched in ensiled crops (p < 0.05). These results might suggest active transport and metabolism of plant carbohydrates into a usable form to sustain bacterial reproduction during silage fermentation, yielding metabolic products such as lactic acid. This research has provided a comprehensive understanding of bacterial communities before and after ensiling, which can be useful for desirable silage fermentation in Malaysia.}, } @article {pmid35500534, year = {2022}, author = {Mirza, AI and Zhu, F and Knox, N and Forbes, JD and Bonner, C and Van Domselaar, G and Bernstein, CN and Graham, M and Marrie, RA and Hart, J and Yeh, EA and Arnold, DL and Bar-Or, A and O'Mahony, J and Zhao, Y and Hsiao, W and Banwell, B and Waubant, E and Tremlett, H}, title = {The metabolic potential of the paediatric-onset multiple sclerosis gut microbiome.}, journal = {Multiple sclerosis and related disorders}, volume = {63}, number = {}, pages = {103829}, doi = {10.1016/j.msard.2022.103829}, pmid = {35500534}, issn = {2211-0356}, mesh = {Adolescent ; Canada ; Child ; Female ; *Gastrointestinal Microbiome ; Glatiramer Acetate ; Humans ; Male ; *Multiple Sclerosis ; Starch ; }, abstract = {BACKGROUND: The aim of this study was to examine the gut microbiome's metabolic potential in paediatric-onset MS patients (symptom onset <18 years).

METHODS: We included 17 MS participants and 20 controls similar for sex, age, race, and stool consistency from the Canadian Paediatric Demyelinating Disease Network study. Stool-derived gut metagenome gene abundances were used to estimate relative abundances and turnover scores of individual microbial metabolites and the composition and diversity of carbohydrate-active enzymes (CAZymes). MS participants and controls were compared using the Wilcoxon rank-sum test, as were the disease-modifying drug (DMD) exposed and naïve MS participants.

RESULTS: The median age(s) at MS symptom onset=16.1 years (interquartile range [IQR]=1.7), and at stool sample procurement=16.9/15.8 years (IQR=2.0/1.4), for the MS participants/controls. Most MS and control participants were girls (80-82%). Five (29%) of the MS participants had never been exposed to a DMD pre-stool sample and 12 (71%) had (7 to beta-interferon and 5 glatiramer acetate). While the relative abundance of metabolites did not differ between MS participants and controls, turnover scores did. MS participants had a greater potential to metabolize lipopolysaccharides than controls (score difference=1.6E-04, p = 0.034) but lower potential to metabolize peptidoglycan molecules and starch (score differences<2.2E-02, p<0.040). Further, although CAZymes diversity did not differ (p>0.050), starch-degrading subfamilies were underrepresented in MS participants versus controls (relative abundance differences >-0.34, p<0.040) and in the DMD exposed verses DMD naïve MS participants (relative abundance differences>-0.20, p<0.049).

CONCLUSION: Paediatric-onset MS participants had an altered gut microbiome-related metabolic potential compared to controls, including higher breakdown of lipopolysaccharide molecules, but lower resistant starch metabolism.}, } @article {pmid35500274, year = {2022}, author = {Lemaire, ON and Wagner, T}, title = {A Structural View of Alkyl-Coenzyme M Reductases, the First Step of Alkane Anaerobic Oxidation Catalyzed by Archaea.}, journal = {Biochemistry}, volume = {61}, number = {10}, pages = {805-821}, pmid = {35500274}, issn = {1520-4995}, mesh = {*Alkanes/metabolism ; Anaerobiosis ; *Archaea/chemistry ; Catalysis ; Mesna/metabolism ; Methane/metabolism ; Oxidation-Reduction ; Oxidoreductases/metabolism ; Phylogeny ; }, abstract = {Microbial anaerobic oxidation of alkanes intrigues the scientific community by way of its impact on the global carbon cycle, and its biotechnological applications. Archaea are proposed to degrade short- and long-chain alkanes to CO2 by reversing methanogenesis, a theoretically reversible process. The pathway would start with alkane activation, an endergonic step catalyzed by methyl-coenzyme M reductase (MCR) homologues that would generate alkyl-thiols carried by coenzyme M. While the methane-generating MCR found in methanogens has been well characterized, the enzymatic activity of the putative alkane-fixing counterparts has not been validated so far. Such an absence of biochemical investigations contrasts with the current explosion of metagenomics data, which draws new potential alkane-oxidizing pathways in various archaeal phyla. Therefore, validating the physiological function of these putative alkane-fixing machines and investigating how their structures, catalytic mechanisms, and cofactors vary depending on the targeted alkane have become urgent needs. The first structural insights into the methane- and ethane-capturing MCRs highlighted unsuspected differences and proposed some explanations for their substrate specificity. This Perspective reviews the current physiological, biochemical, and structural knowledge of alkyl-CoM reductases and offers fresh ideas about the expected mechanistic and chemical differences among members of this broad family. We conclude with the challenges of the investigation of these particular enzymes, which might one day generate biofuels for our modern society.}, } @article {pmid35499326, year = {2022}, author = {Rahlff, J and Bornemann, TLV and Lopatina, A and Severinov, K and Probst, AJ}, title = {Host-Associated Phages Disperse across the Extraterrestrial Analogue Antarctica.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {10}, pages = {e0031522}, pmid = {35499326}, issn = {1098-5336}, mesh = {Antarctic Regions ; *Bacteriophages/genetics ; Ecosystem ; Metagenomics ; Prophages/genetics ; }, abstract = {Extreme Antarctic conditions provide one of the closest analogues of extraterrestrial environments. Since air and snow samples, especially from polar regions, yield DNA amounts in the lower picogram range, binning of prokaryotic genomes is challenging and renders studying the dispersal of biological entities across these environments difficult. Here, we hypothesized that dispersal of host-associated bacteriophages (adsorbed, replicating, or prophages) across the Antarctic continent can be tracked via their genetic signatures, aiding our understanding of virus and host dispersal across long distances. Phage genome fragments (PGFs) reconstructed from surface snow metagenomes of three Antarctic stations were assigned to four host genomes, mainly Betaproteobacteria, including Ralstonia spp. We reconstructed the complete genome of a temperate phage with nearly complete alignment to a prophage in the reference genome of Ralstonia pickettii 12D. PGFs from different stations were related to each other at the genus level and matched similar hosts. Metagenomic read mapping and nucleotide polymorphism analysis revealed a wide dispersal of highly identical PGFs, 13 of which were detected in seawater from the Western Antarctic Peninsula at a distance of 5,338 km from the snow sampling stations. Our results suggest that host-associated phages, especially of Ralstonia sp., disperse over long distances despite the harsh conditions of the Antarctic continent. Given that 14 phages associated with two R. pickettii draft genomes isolated from space equipment were identified, we conclude that Ralstonia phages are ideal mobile genetic elements to track dispersal and contamination in ecosystems relevant for astrobiology. IMPORTANCE Host-associated phages of the bacterium Ralstonia identified in snow samples can be used to track microbial dispersal over thousands of kilometers across the Antarctic continent, which functions as an extraterrestrial analogue because of its harsh environmental conditions. Due to the presence of these bacteria carrying genome-integrated prophages on space-related equipment and the potential for dispersal of host-associated phages demonstrated here, our work has implications for planetary protection, a discipline in astrobiology interested in preventing contamination of celestial bodies with alien biomolecules or forms of life.}, } @article {pmid35499324, year = {2022}, author = {Yang, Q and Cahn, JKB and Piel, J and Song, YF and Zhang, W and Lin, HW}, title = {Marine Sponge Endosymbionts: Structural and Functional Specificity of the Microbiome within Euryspongia arenaria Cells.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0229621}, pmid = {35499324}, issn = {2165-0497}, mesh = {Animals ; Lipase/genetics ; *Microbiota ; Phylogeny ; *Porifera/genetics/microbiology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Sponge microbiomes are typically profiled by analyzing the community DNA of whole tissues, which does not distinguish the taxa residing within sponge cells from extracellular microbes. To uncover the endosymbiotic microbiome, we separated the sponge cells to enrich the intracellular microbes. The intracellular bacterial community of sponge Euryspongia arenaria was initially assessed by amplicon sequencing, which indicated that it hosts three unique phyla not found in the extracellular and bulk tissue microbiomes. These three phyla account for 66% of the taxonomically known genera in the intracellular microbiome. The shotgun metagenomic analysis extended the taxonomic coverage to viruses and eukaryotes, revealing the most abundant signature taxa specific to the intracellular microbiome. Functional KEGG pathway annotation demonstrated that the endosymbiotic microbiome hosted the greatest number of unique gene orthologs. The pathway profiles distinguished the intra- and extracellular microbiomes from the tissue and seawater microbiomes. Carbohydrate-active enzyme analysis further discriminated each microbiome based on their representative and dominant enzyme families. One pathway involved in digestion system and family esterase had a consistently higher level in intracellular microbiome and could statistically differentiate the intracellular microbiome from the others, suggesting that triacylglycerol lipases could be the key functional component peculiar to the endosymbionts. The identified higher abundance of lipase-related eggNOG categories further supported the lipid-hydrolyzing metabolism of endosymbiotic microbiota. Pseudomonas members, reported as lipase-producing bacteria, were only in the endosymbiotic microbiome, meanwhile Pseudomonas also showed a greater abundance intracellularly. Our study aided a comprehensive sponge microbiome that demonstrated the taxonomic and functional specificity of endosymbiotic microbiota. IMPORTANCE Sponges host abundant microbial symbionts that can produce an impressive number of novel bioactive metabolites. However, knowledge on intracellular (endosymbiotic) microbiota is scarce. We characterize the composition and function of the endosymbiotic microbiome by separation of sponge cells and enrichment of intracellular microbes. We uncover a noteworthy number of taxa exclusively in the endosymbiotic microbiome. We unlock the unique pathways and enzymes of endosymbiotic taxa. This study achieves a more comprehensive sponge microbial community profile, which demonstrates the structural and functional specificity of the endosymbiotic microbiome. Our findings not only open the possibility to reveal the low abundant and the likely missed microbiota when directly sequencing the sponge bulk tissues, but also warrant future in-depth exploration within single sponge cells.}, } @article {pmid35499050, year = {2022}, author = {Wu, Y and Zheng, Y and Wang, S and Chen, Y and Tao, J and Chen, Y and Chen, G and Zhao, H and Wang, K and Dong, K and Hu, F and Feng, Y and Zheng, H}, title = {Genetic divergence and functional convergence of gut bacteria between the Eastern honey bee Apis cerana and the Western honey bee Apis mellifera.}, journal = {Journal of advanced research}, volume = {37}, number = {}, pages = {19-31}, pmid = {35499050}, issn = {2090-1224}, mesh = {Animals ; Bacteria/genetics ; Bees/genetics ; Chromatography, Liquid ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Tandem Mass Spectrometry ; }, abstract = {INTRODUCTION: The functional relevance of intra-species diversity in natural microbial communities remains largely unexplored. The guts of two closely related honey bee species, Apis cerana and A. mellifera, are colonised by a similar set of core bacterial species composed of host-specific strains, thereby providing a good model for an intra-species diversity study.

OBJECTIVES: We aim to assess the functional relevance of intra-species diversity of A. cerana and A. mellifera gut microbiota.

METHODS: Honey bee workers were collected from four regions of China. Their gut microbiomes were investigated by shotgun metagenomic sequencing, and the bacterial compositions were compared at the species level. A cross-species colonisation assay was conducted, with the gut metabolomes being characterised by LC-MS/MS.

RESULTS: Comparative analysis showed that the strain composition of the core bacterial species was host-specific. These core bacterial species presented distinctive functional profiles between the hosts. However, the overall functional profiles of the A. cerana and A. mellifera gut microbiomes were similar; this was further supported by the consistency of the honey bees' gut metabolome, as the gut microbiota of different honey bee species showed rather similar metabolic profiles in the cross-species colonisation assay. Moreover, this experiment also demonstrated that the gut microbiota of A. cerana and A. mellifera could cross colonise between the two honey bee species.

CONCLUSION: Our findings revealed functional differences in most core gut bacteria between the guts of A. cerana and A. mellifera, which may be associated with their inter-species diversity. However, the functional profiles of the overall gut microbiomes between the two honey bee species converge, probably as a result of the overlapping ecological niches of the two species. Our findings provide critical insights into the evolution and functional roles of the mutualistic microbiota of honey bees and reveal that functional redundancy could stabilise the gene content diversity at the strain-level within the gut community.}, } @article {pmid35499044, year = {2022}, author = {Wu, C and Zhao, Y and Zhang, Y and Yang, Y and Su, W and Yang, Y and Sun, L and Zhang, F and Yu, J and Wang, Y and Guo, P and Zhu, B and Wu, S}, title = {Gut microbiota specifically mediates the anti-hypercholesterolemic effect of berberine (BBR) and facilitates to predict BBR's cholesterol-decreasing efficacy in patients.}, journal = {Journal of advanced research}, volume = {37}, number = {}, pages = {197-208}, pmid = {35499044}, issn = {2090-1224}, mesh = {Animals ; Bacteria ; *Berberine/pharmacology/therapeutic use ; Cholesterol/pharmacology ; *Gastrointestinal Microbiome ; Humans ; *Hyperlipidemias/drug therapy ; Mice ; }, abstract = {INTRODUCTION: Gut microbiota has been implicated in the pharmacological activities of many natural products. As an effective hypolipidemic agent, berberine (BBR)'s clinical application is greatly impeded by the obvious inter-individual response variation. To date, little evidence exists on the causality between gut microbes and its therapeutic effects, and the linkage of bacteria alterations to the inter-individual response variation.

OBJECTIVES: This study aims to confirm the causal role of the gut microbiota in BBR's anti-hyperlipidemic effect and identify key bacteria that can predict its effectiveness.

METHODS: The correlation between gut microbiota and BBR's inter-individual response variation was studied in hyperlipidemic patients. The causal role of gut microbes in BBR's anti-hyperlipidemic effects was subsequently assessed by altered administration routes, co-treatment with antibiotics, fecal microbiota transplantation, and metagenomic analysis.

RESULTS: Three-month clinical study showed that BBR was effectively to decrease serum lipids but displayed an obvious response variation. The cholesterol-lowering but not triglyceride-decreasing effect of BBR was closely related to its modulation on gut microbiota. Interestingly, the baseline levels of Alistipes and Blautia could accurately predict its anti-hypercholesterolemic efficiency in the following treatment. Causality experiments in mice further confirmed that the gut microbiome is both necessary and sufficient to mediate the lipid-lowering effect of BBR. The absence of Blautia substantially abolished BBR's cholesterol-decreasing efficacy.

CONCLUSION: The gut microbiota is necessary and sufficient for BBR's hyperlipidemia-ameliorating effect. The baseline composition of gut microbes can be an effective predictor for its pharmacotherapeutic efficacy, providing a novel way to achieve personalized therapy.}, } @article {pmid35497193, year = {2022}, author = {Bakir-Gungor, B and Hacılar, H and Jabeer, A and Nalbantoglu, OU and Aran, O and Yousef, M}, title = {Inflammatory bowel disease biomarkers of human gut microbiota selected via different feature selection methods.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13205}, pmid = {35497193}, issn = {2167-8359}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Inflammatory Bowel Diseases/diagnosis ; *Crohn Disease/diagnosis ; *Colitis, Ulcerative/diagnosis ; Biomarkers ; }, abstract = {The tremendous boost in next generation sequencing and in the "omics" technologies makes it possible to characterize the human gut microbiome-the collective genomes of the microbial community that reside in our gastrointestinal tract. Although some of these microorganisms are considered to be essential regulators of our immune system, the alteration of the complexity and eubiotic state of microbiota might promote autoimmune and inflammatory disorders such as diabetes, rheumatoid arthritis, Inflammatory bowel diseases (IBD), obesity, and carcinogenesis. IBD, comprising Crohn's disease and ulcerative colitis, is a gut-related, multifactorial disease with an unknown etiology. IBD presents defects in the detection and control of the gut microbiota, associated with unbalanced immune reactions, genetic mutations that confer susceptibility to the disease, and complex environmental conditions such as westernized lifestyle. Although some existing studies attempt to unveil the composition and functional capacity of the gut microbiome in relation to IBD diseases, a comprehensive picture of the gut microbiome in IBD patients is far from being complete. Due to the complexity of metagenomic studies, the applications of the state-of-the-art machine learning techniques became popular to address a wide range of questions in the field of metagenomic data analysis. In this regard, using IBD associated metagenomics dataset, this study utilizes both supervised and unsupervised machine learning algorithms, (i) to generate a classification model that aids IBD diagnosis, (ii) to discover IBD-associated biomarkers, (iii) to discover subgroups of IBD patients using k-means and hierarchical clustering approaches. To deal with the high dimensionality of features, we applied robust feature selection algorithms such as Conditional Mutual Information Maximization (CMIM), Fast Correlation Based Filter (FCBF), min redundancy max relevance (mRMR), Select K Best (SKB), Information Gain (IG) and Extreme Gradient Boosting (XGBoost). In our experiments with 100-fold Monte Carlo cross-validation (MCCV), XGBoost, IG, and SKB methods showed a considerable effect in terms of minimizing the microbiota used for the diagnosis of IBD and thus reducing the cost and time. We observed that compared to Decision Tree, Support Vector Machine, Logitboost, Adaboost, and stacking ensemble classifiers, our Random Forest classifier resulted in better performance measures for the classification of IBD. Our findings revealed potential microbiome-mediated mechanisms of IBD and these findings might be useful for the development of microbiome-based diagnostics.}, } @article {pmid35495730, year = {2022}, author = {Nagar, S and Talwar, C and Motelica-Heino, M and Richnow, HH and Shakarad, M and Lal, R and Negi, RK}, title = {Microbial Ecology of Sulfur Biogeochemical Cycling at a Mesothermal Hot Spring Atop Northern Himalayas, India.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {848010}, pmid = {35495730}, issn = {1664-302X}, abstract = {Sulfur related prokaryotes residing in hot spring present good opportunity for exploring the limitless possibilities of integral ecosystem processes. Metagenomic analysis further expands the phylogenetic breadth of these extraordinary sulfur (S) metabolizing microorganisms as well as their complex metabolic networks and syntrophic interactions in environmental biosystems. Through this study, we explored and expanded the microbial genetic repertoire with focus on S cycling genes through metagenomic analysis of S contaminated hot spring, located at the Northern Himalayas. The analysis revealed rich diversity of microbial consortia with established roles in S cycling such as Pseudomonas, Thioalkalivibrio, Desulfovibrio, and Desulfobulbaceae (Proteobacteria). The major gene families inferred to be abundant across microbial mat, sediment, and water were assigned to Proteobacteria as reflected from the reads per kilobase (RPKs) categorized into translation and ribosomal structure and biogenesis. An analysis of sequence similarity showed conserved pattern of both dsrAB genes (n = 178) retrieved from all metagenomes while other S disproportionation proteins were diverged due to different structural and chemical substrates. The diversity of S oxidizing bacteria (SOB) and sulfate reducing bacteria (SRB) with conserved (r)dsrAB suggests for it to be an important adaptation for microbial fitness at this site. Here, (i) the oxidative and reductive dsr evolutionary time-scale phylogeny proved that the earliest (but not the first) dsrAB proteins belong to anaerobic Thiobacillus with other (rdsr) oxidizers, also we confirm that (ii) SRBs belongs to δ-Proteobacteria occurring independent lateral gene transfer (LGT) of dsr genes to different and few novel lineages. Further, the structural prediction of unassigned DsrAB proteins confirmed their relatedness with species of Desulfovibrio (TM score = 0.86, 0.98, 0.96) and Archaeoglobus fulgidus (TM score = 0.97, 0.98). We proposed that the genetic repertoire might provide the basis of studying time-scale evolution and horizontal gene transfer of these genes in biogeochemical S cycling.}, } @article {pmid35495724, year = {2022}, author = {Malla, S and van der Helm, E and Darbani, B and Wieschalka, S and Förster, J and Borodina, I and Sommer, MOA}, title = {A Novel Efficient L-Lysine Exporter Identified by Functional Metagenomics.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {855736}, pmid = {35495724}, issn = {1664-302X}, abstract = {Lack of active export system often limits the industrial bio-based production processes accumulating the intracellular product and hence complexing the purification steps. L-lysine, an essential amino acid, is produced biologically in quantities exceeding two million tons per year; yet, L-lysine production is challenged by efficient export system at high titers during fermentation. To address this issue, new exporter candidates for efficient efflux of L-lysine are needed. Using metagenomic functional selection, we identified 58 genes encoded on 28 unique metagenomic fragments from cow gut microbiome library that improved L-lysine tolerance. These genes include a novel L-lysine transporter, belonging to a previously uncharacterized EamA superfamily, which is further in vivo characterized as L-lysine exporter using Xenopus oocyte expression system as well as Escherichia coli host. This novel exporter improved L-lysine tolerance in E. coli by 40% and enhanced yield, titer, and the specific production of L-lysine in an industrial Corynebacterium glutamicum strain by 7.8%, 9.5%, and 12%, respectively. Our approach allows the sequence-independent discovery of novel exporters and can be deployed to increase titers and productivity of toxicity-limited bioprocesses.}, } @article {pmid35495709, year = {2022}, author = {Zeng, S and Cui, J and Xiong, J and Yuan, S and Yue, X and Guan, W and Gao, L and Liu, J and Zuo, J and Wang, Q}, title = {The Microbial Metagenome of Eluates Obtained From the Surface of Broccoli Heads Subjected to Different Light Treatments.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {820419}, pmid = {35495709}, issn = {1664-302X}, abstract = {Foodborne illnesses present a major threat to public health and are frequently attributed to foodborne pathogens present on fresh produce. Some opportunistic pathogens of broccoli are also responsible for causing head rot. Three different light treatments, UV-C, red LED (50 μml/m[2]/s), and UV-C + LED were used to treat broccoli prior to or during storage. Following the light treatments, microorganisms present in eluates obtained from the surface of broccoli heads were characterized using a metagenomic approach. Metagenomic DNA libraries were subjected to high-throughput sequencing on an Illumina Hiseq platform. Results indicated that the combined treatment of LED red light and UV-C provided the best sensory preservation of broccoli, followed by LED red light and then UV-C. The bacterial communities in the eluates obtained from the surface of broccoli heads in all three light treatments were primarily represented at the phylum level by Proteobacteria and Firmicutes, while fungal communities were primarily represented by Ascomycota and Basidiomycota. Further analysis indicated that the all three light treatments reduced the presence of foodborne pathogens and bacterial taxa responsible for broccoli spoilage. While UV-C had a significant inhibitory effect on Botrytis cinerea, the light treatments increased the relative abundance of Pseudomonas fluorescens. Results indicate that a metagenomic approach can be used to detect pathogenic bacteria and fungi on fresh vegetables and assess the impact of management practices, such as light treatments, designed to maintain postharvest quality, on the composition of the microbiome present on the surface of harvested produce.}, } @article {pmid35495650, year = {2022}, author = {Zheng, Y and Chen, J and Wang, X and Han, L and Yang, Y and Wang, Q and Yu, Q}, title = {Metagenomic and Transcriptomic Analyses Reveal the Differences and Associations Between the Gut Microbiome and Muscular Genes in Angus and Chinese Simmental Cattle.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {815915}, pmid = {35495650}, issn = {1664-302X}, abstract = {Gut microbiome and heredity are two important factors affecting the intramuscular fat (IMF) of cattle, excluding age, sex, and nutrition. This study aimed at deciphering these two differences by analyzing the gut microbiome and intramuscular differentially expressed genes (DEGs) in the Angus and Chinese Simmental cattle. Feces and longissimus dorsi were collected from the two groups of animals (n = 20/group) for multiomics analysis. Angus holds a significantly higher diversity than Chinese Simmental, and the relative abundance of Roseburia, Prevotella, Coprococcus, etc., was obviously higher in Angus. Chinese Simmental had higher levels of isobutyrate, isovalerate, and valerate, although similar levels of acetate, propionate, and butyrate were observed for the two groups. The DEGs upregulated in Chinese Simmental were mainly involved in immune and inflammatory responses, while those in Angus were associated with the regulation of muscle system and myofibril. We finally identified 17 species, including Eubacterium rectale, etc., which were positively correlated to muscle and fat metabolism genes (MSTN, MYLPF, TNNT3, and FABP3/4) and illustrate the associations between them. Our study unveils the gut microbial differences and significant DEGs as well as their associations between the two breeds, providing valuable guidance for future mechanism research and development of intervention strategies to improve meat quality.}, } @article {pmid35495647, year = {2022}, author = {Azli, B and Razak, MN and Omar, AR and Mohd Zain, NA and Abdul Razak, F and Nurulfiza, I}, title = {Metagenomics Insights Into the Microbial Diversity and Microbiome Network Analysis on the Heterogeneity of Influent to Effluent Water.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {779196}, pmid = {35495647}, issn = {1664-302X}, abstract = {Sanitizing the water sources of local communities is important to control the spread of microbial resistance genes, especially those for water-borne illnesses. The activities of antibiotic resistance gene (ARG)-host pathogens pose a threat to public health, and it has been estimated that the infection will lead up to 10 million deaths globally by the year 2050. Hence, in this study, we aim to analyze the efficiency of our municipal wastewater treatment plant (WWTP) process in producing pathogen-free water by investigating the microbial composition between influent and effluent water sites. Shotgun metagenomics sequencing using the Illumina platform was performed on the influent and effluent samples of six different WWTP sites located in Johore, Malaysia. After raw data pre-processing, the non-redundant contigs library was then aligned against BLASTP for taxonomy profiling and the Comprehensive Antibiotic Resistance Database for ARG annotation. Interestingly, the alpha-diversity result reported that effluent site samples showed higher abundance and diverse heterogeneity compared to the influent site. The principal component analysis (PCA) and non-metric multidimensional scaling (NMDS) plots also suggested that effluent sites showed high variation in the genetic material due to loosely clustered sample plots, as compared to the tightly clustered influent samples. This study has successfully identified the top three abundant phyla in influent-Proteobacteria, Firmicutes, and Bacteroidetes-and effluent-Proteobacteria, Actinobacteria, and Bacteroidetes-water. Despite the overlap within the top three abundant phyla in influent and effluent sites (Proteobacteria and Bacteroidetes), the ARG composition heat map and drug class phenotype plot bar exhibits a general trend of a downward shift, showing the efficiency of WWTP in reducing opportunistic pathogens. Overall, it was demonstrated that our municipal WWTP efficiently eliminated pathogenic microbes from the influent water before its total discharge to the environment, though not with the total elimination of microorganisms. This metagenomics study allowed for an examination of our water source and showed the potential interaction of species and ARGs residing in the influent and effluent environment. Both microbial profile structure and co-occurrence network analysis provide integrated understanding regarding the diversity of microorganisms and interactions for future advanced water sanitation treatments.}, } @article {pmid35495114, year = {2022}, author = {Xu, P and Lv, T and Dong, S and Cui, Z and Luo, X and Jia, B and Jeon, CO and Zhang, J}, title = {Association between intestinal microbiome and inflammatory bowel disease: Insights from bibliometric analysis.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {1716-1725}, pmid = {35495114}, issn = {2001-0370}, abstract = {The gut microbiome is highly linked to inflammatory bowel disease (IBD). A total of 3890 publications related to the two terms from 2000 to 2020 were extracted from the Web of Science Core Collection to study the association from a bibliometric perspective. Publications on this topic have grown rapidly since 2008. The United States and Harvard University are the country and institution with the largest number of publications, respectively. Inflammatory Bowel Diseases is the most productive journal with 211 published articles. The most influential journal in this field is Gut with 13,359 citations. The co-citation analysis of references showed that the IBD-related topics with the highest focus are "gut microbiota," "metagenomics," "bacterial community," "fecal microbiota transplantation," "probiotics," and "colitis-associated colorectal cancer." Keyword cluster and keyword burst analyses showed that "gut microbiota," "metagenomics," and "fecal microbiota transplantation" are currently the most researched topics in the field of IBD. The literature in this field is mainly distributed between alterations of the intestinal microbiota, microbial metabolites, and related host signaling pathways. Probiotic treatment also frequently appears in literature. This bibliometric analysis can guide future research and promote the development of the field of gut microbiome and IBD.}, } @article {pmid35495109, year = {2022}, author = {Sequeira, JC and Rocha, M and Alves, MM and Salvador, AF}, title = {UPIMAPI, reCOGnizer and KEGGCharter: Bioinformatics tools for functional annotation and visualization of (meta)-omics datasets.}, journal = {Computational and structural biotechnology journal}, volume = {20}, number = {}, pages = {1798-1810}, pmid = {35495109}, issn = {2001-0370}, abstract = {Omics and meta-omics technologies are powerful approaches to explore microorganisms' functions, but the sheer size and complexity of omics datasets often turn the analysis into a challenging task. Software developed for omics and meta-omics analyses, together with knowledgebases encompassing information on genes, proteins, taxonomic and functional annotation, among other types of information, are valuable resources for analyzing omics data. Although several bioinformatics resources are available for meta-omics analyses, many require significant computational expertise. Web interfaces are more user-friendly, but often struggle to handle large data files, such as those obtained in metagenomics, metatranscriptomics, or metaproteomics experiments. In this work, we present three novel bioinformatics tools, which are available through user-friendly command-line interfaces, can be run sequentially or stand-alone, and combine popular resources for functional annotation. UPIMAPI performs sequence homology-based annotation and obtains data from UniProtKB (e.g., protein names, EC numbers, Gene Ontology, Taxonomy, cross-references to external databases). reCOGnizer performs multithreaded domain homology-based annotation of protein sequences with several functional databases (i.e., CDD, NCBIfam, Pfam, Protein Clusters, SMART, TIGRFAM, COG and KOG) and in addition, obtains information on domain names and descriptions and EC numbers. KEGGCharter represents omics results, including differential gene expression, in KEGG metabolic pathways. In addition, it shows the taxonomic assignment of the enzymes represented, which is particularly useful in metagenomics studies in which several microorganisms are present. reCOGnizer, UPIMAPI and KEGGCharter together provide a comprehensive and complete functional characterization of large datasets, facilitating the interpretation of microbial activities in nature and in biotechnological processes.}, } @article {pmid35494644, year = {2022}, author = {Balázs, B and Tóth, Z and Kacsir, I and Sipos, A and Buglyó, P and Somsák, L and Bokor, É and Kardos, G and Bai, P}, title = {Targeting Multiresistant Gram-Positive Bacteria by Ruthenium, Osmium, Iridium and Rhodium Half-Sandwich Type Complexes With Bidentate Monosaccharide Ligands.}, journal = {Frontiers in chemistry}, volume = {10}, number = {}, pages = {868234}, pmid = {35494644}, issn = {2296-2646}, abstract = {Bacterial resistance to antibiotics is an ever-growing problem in heathcare. We have previously identified a set of osmium(II), ruthenium(II), iridium(III) and rhodium(III) half-sandwich type complexes with bidentate monosaccharide ligands possessing cytostatic properties against carcinoma, lymphoma and sarcoma cells with low micromolar or submicromolar IC50 values. Importantly, these complexes were not active on primary, non-transformed cells. These complexes have now been assessed as to their antimicrobial properties and found to be potent inhibitors of the growth of reference strains of Staphylococcus aureus and Enterococcus faecalis (Gram-positive species), though the compounds proved inactive on reference strains of Pseudomonas aerugonisa, Escherichia coli, Candida albicans, Candida auris and Acinetobacter baumannii (Gram-negative species and fungi). Furthermore, clinical isolates of Staphylococcus aureus and Enterococcus sp. (both multiresistant and susceptible strains) were also susceptible to the organometallic complexes in this study with similar MIC values as the reference strains. Taken together, we identified a set of osmium(II), ruthenium(II), iridium(III) and rhodium(III) half-sandwich type antineoplastic organometallic complexes which also have antimicrobial activity among Gram-positive bacteria. These compounds represent a novel class of antimicrobial agents that are not detoxified by multiresistant bacteria suggesting a potential to be used to combat multiresistant infections.}, } @article {pmid35494515, year = {2022}, author = {Gu, J and Chen, L and Zeng, C and Yang, X and Pan, D and Cao, H and Qian, Q}, title = {A Retrospective Analysis of Metagenomic Next Generation Sequencing (mNGS) of Cerebrospinal Fluid from Patients with Suspected Encephalitis or Meningitis Infections.}, journal = {Journal of healthcare engineering}, volume = {2022}, number = {}, pages = {5641609}, pmid = {35494515}, issn = {2040-2309}, mesh = {*Encephalitis ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Meningitis/diagnosis ; Retrospective Studies ; Sensitivity and Specificity ; }, abstract = {We determined the clinical value of metagenomic next-generation sequencing (mNGS) of cerebrospinal fluid (CSF) for the diagnosis of patients with suspected encephalitis or meningitis infection. Clinical data were collected and retrospectively analyzed from patients with suspected cases of encephalitis or meningitis who presented at four hospitals in Ningbo from January 1[st], 2019 to December 31[st], 2020. Of a total of 66 suspected cases, 41 (62.12%) were diagnosed with central nervous system infections, which included 18 cases (27.27%) of viral infection, 13 cases (19.70%) of bacterial infection, 3 cases (4.55%) of Mycobacterium tuberculosis, 5 cases (7.58%) of fungal infection, and 2 cases (3.03%) of Rickettsia infection. From these cases, mNGS identified 25 (37.88%) true-positive cases, 8 (12.12%) false-positive cases, 20 (30.30%) true-negative cases, and 13 (19.70%) false-negative cases. The sensitivity of mNGS was 65.79% with a specificity of 71.43%. The positive rate was higher compared with traditional methods (37.88% vs. 24.39%). The results indicate that mNGS technology is a more sensitive method for detecting suspected infectious encephalitis or meningitis compared with traditional pathogen detection methods.}, } @article {pmid35494173, year = {2022}, author = {French, R and Charon, J and Lay, CL and Muller, C and Holmes, EC}, title = {Human land use impacts viral diversity and abundance in a New Zealand river.}, journal = {Virus evolution}, volume = {8}, number = {1}, pages = {veac032}, pmid = {35494173}, issn = {2057-1577}, abstract = {Although water-borne viruses have important implications for the health of humans and other animals, little is known about the impact of human land use on viral diversity and evolution in water systems such as rivers. We used metatranscriptomic sequencing to compare the diversity and abundance of viruses at sampling sites along a single river in New Zealand that differed in human land-use impacts, ranging from pristine to urban. From this, we identified 504 putative virus species, of which 97 per cent were novel. Many of the novel viruses were highly divergent and likely included a new subfamily within the Parvoviridae. We identified at least sixty-three virus species that may infect vertebrates-most likely fish and water birds-from the Astroviridae, Birnaviridae, Parvoviridae, and Picornaviridae. No putative human viruses were detected. Importantly, we observed differences in the composition of viral communities at sites impacted by human land use (farming and urban) compared to native forest sites (pristine). At the viral species level, the urban sites had higher diversity (327 virus species) than the farming (n = 150) and pristine sites (n = 119), and more viruses were shared between the urban and farming sites (n = 76) than between the pristine and farming or urban sites (n = 24). The two farming sites had a lower viral abundance across all host types, while the pristine sites had a higher abundance of viruses associated with animals, plants, and fungi. We also identified viruses linked to agriculture and human impact at the river sampling sites in farming and urban areas that were not present at the native forest sites. Although based on a small sample size, our study suggests that human land use can impact viral communities in rivers, such that further work is needed to reduce the impact of intensive farming and urbanisation on water systems.}, } @article {pmid35493735, year = {2022}, author = {Kumar, D and Sharma, SR and Adegoke, A and Kennedy, A and Tuten, HC and Li, AY and Karim, S}, title = {Recently Evolved Francisella-Like Endosymbiont Outcompetes an Ancient and Evolutionarily Associated Coxiella-Like Endosymbiont in the Lone Star Tick (Amblyomma americanum) Linked to the Alpha-Gal Syndrome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {787209}, pmid = {35493735}, issn = {2235-2988}, support = {P20 GM103476/GM/NIGMS NIH HHS/United States ; }, mesh = {Amblyomma ; Animals ; Bacteria ; Coxiella ; *Food Hypersensitivity ; *Francisella/genetics ; Humans ; *Ticks/microbiology ; United States ; }, abstract = {BACKGROUND: Ticks are hematophagous arthropods that transmit various bacterial, viral, and protozoan pathogens of public health significance. The lone star tick (Amblyomma americanum) is an aggressive human-biting tick that transmits bacterial and viral pathogens, and its bites are suspected of eliciting the alpha-gal syndrome, a newly emerged delayed hypersensitivity following consumption of red meat in the United States. While ongoing studies have attempted to investigate the contribution of different tick-inherent factors to the induction of alpha-gal syndrome, an otherwise understudied aspect is the contribution of the tick microbiome and specifically obligate endosymbionts to the establishment of the alpha-gal syndrome in humans.

MATERIALS AND METHODS: Here we utilized a high-throughput metagenomic sequencing approach to cataloging the entire microbial communities residing within different developmental stages and tissues of unfed and blood-fed ticks from laboratory-maintained ticks and three new geographical locations in the United States. The Quantitative Insights Into Microbial Ecology (QIIME2) pipeline was used to perform data analysis and taxonomic classification. Moreover, using a SparCC (Sparse Correlations for Compositional data) network construction model, we investigated potential interactions between members of the microbial communities from laboratory-maintained and field-collected ticks.

RESULTS: Overall, Francisellaceae was the most dominant bacteria identified in the microbiome of both laboratory-raised and field-collected Am. americanum across all tissues and developmental stages. Likewise, microbial diversity was seen to be significantly higher in field-collected ticks compared with laboratory-maintained ticks as seen with a higher number of both Operational Taxonomic Units and measures of species richness. Several potential positive and negative correlations were identified from our network analysis. We observed a strong positive correlation between Francisellaceae, Rickettsiaceae, and Midichloriaceae in both developmental stages and tissues from laboratory-maintained ticks, whereas ovarian tissues had a strong positive correlation of bacteria in the family Xanthobacteraceae and Rhizobiaceae. A negative interaction was observed between Coxiellaceae and Francisellaceae in Illinois, and all the bacteria detected from ticks from Delaware were negatively correlated.

CONCLUSION: This study is the first to catalog the microbiome of Am. americanum throughout its developmental stages and different tissue niches and report the potential replacement of Coxiellaceae by Francisellaceae across developmental stages and tissues tested except in ovarian tissues. These unique and significant findings advance our knowledge and open a new avenue of research to further understand the role of tick microbiome in tick-borne diseases and develop a holistic strategy to control alpha-gal syndrome.}, } @article {pmid35493727, year = {2022}, author = {Li, M and Wang, C and Guo, Q and Xu, C and Xie, Z and Tan, J and Wu, S and Wang, P and Guo, J and Fang, Z and Zhu, S and Duan, L and Jiang, X and Zhu, H}, title = {More Positive or More Negative? Metagenomic Analysis Reveals Roles of Virome in Human Disease-Related Gut Microbiome.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {846063}, pmid = {35493727}, issn = {2235-2988}, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; *Diabetes Mellitus, Type 2 ; *Gastrointestinal Microbiome/genetics ; Humans ; *Irritable Bowel Syndrome ; *Microbiota ; Virome/genetics ; *Viruses/genetics ; }, abstract = {Viruses are increasingly viewed as vital components of the human gut microbiota, while their roles in health and diseases remain incompletely understood. Here, we first sequenced and analyzed the 37 metagenomic and 18 host metabolomic samples related to irritable bowel syndrome (IBS) and found that some shifted viruses between IBS and controls covaried with shifted bacteria and metabolites. Especially, phages that infect beneficial lactic acid bacteria depleted in IBS covaried with their hosts. We also retrieved public whole-genome metagenomic datasets of another four diseases (type 2 diabetes, Crohn's disease, colorectal cancer, and liver cirrhosis), totaling 438 samples including IBS, and performed uniform analysis of the gut viruses in diseases. By constructing disease-specific co-occurrence networks, we found viruses actively interacting with bacteria, negatively correlated with possible dysbiosis-related and inflammation-mediating bacteria, increasing the connectivity between bacteria modules, and contributing to the robustness of the networks. Functional enrichment analysis showed that phages interact with bacteria through predation or expressing genes involved in the transporter and secretion system, metabolic enzymes, etc. We further built a viral database to facilitate systematic functional classification and explored the functions of viral genes on interacting with bacteria. Our analyses provided a systematic view of the gut virome in the disease-related microbial community and suggested possible positive roles of viruses concerning gut health.}, } @article {pmid35493492, year = {2022}, author = {Thiam, M and Wang, Q and Barreto Sánchez, AL and Zhang, J and Ding, J and Wang, H and Zhang, Q and Zhang, N and Wang, J and Li, Q and Wen, J and Zhao, G}, title = {Heterophil/Lymphocyte Ratio Level Modulates Salmonella Resistance, Cecal Microbiota Composition and Functional Capacity in Infected Chicken.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {816689}, pmid = {35493492}, issn = {1664-3224}, mesh = {Animals ; Bacteroidetes ; *Chickens ; Lymphocytes ; *Microbiota/genetics ; Propionates ; Proteobacteria/genetics ; RNA, Ribosomal, 16S/genetics ; Salmonella enteritidis ; Valerates ; }, abstract = {The gastrointestinal microbiota plays a vital role in ensuring the maintenance of host health through interactions with the immune system. The Heterophil/Lymphocyte (H/L) ratio reflects poultry's robustness and immune system status. Chickens with low H/L ratio are superior to the chickens with high H/L ratio in survival, immune response, and resistance to Salmonella infection, but the underlying mechanisms remain unclear. This study aimed to identify microorganisms associated with resistance to Salmonella Enteritidis infection in chickens based on the H/L ratio. The 16S rRNA and metagenomic analysis were conducted to examine microbiome and functional capacity between the 2 groups, and Short Chain Fatty Acids (SCFAs) and histopathology were conducted to explore the potential difference between susceptible and resistant groups at 7 and 21 days post-infection (dpi). The microbiome exploration revealed that low H/L ratio chickens, compared to high H/L ratio chickens, displayed a significantly higher abundance of Proteobacteria (Escherichia coli) and Bacteroidetes (Bacteroides plebeius) at 7 and 21 dpi, respectively. Anaerostipes (r = 0.63) and Lachnoclostridium (r = 0.63) were identified as bacterial genus significantly correlated with H/L (P < 0.001). Interestingly, Bacteroides was significantly and positively correlated with bodyweight post-infection (r = 0.72), propionate (r = 0.78) and valerate (r = 0.82) contents, while Salmonella was significantly and negatively correlated with bodyweight post-infection (r = - 0.67), propionate (r = - 0.61) and valerate (r = - 0.65) contents (P < 0.001). Furthermore, the comparative analysis of the functional capacity of cecal microbiota of the chickens with high and low H/L ratio revealed that the chickens with low H/L ratio possess more enriched immune pathways, lower antibiotic resistance genes and virulence factors compared to the chickens with high H/L ratio. These results suggest that the chickens with low H/L ratio are more resistant to Salmonella Enteritidis, and it is possible that the commensal Proteobacteria and Bacteroidetes are involved in this resistance against Salmonella infection. These findings provide valuable resources for selecting and breeding disease-resistant chickens.}, } @article {pmid35493464, year = {2022}, author = {Ai, D and Xing, Y and Zhang, Q and Wang, Y and Liu, X and Liu, G and Xia, LC}, title = {Joint Analysis of Microbial and Immune Cell Abundance in Liver Cancer Tissue Using a Gene Expression Profile Deconvolution Algorithm Combined With Foreign Read Remapping.}, journal = {Frontiers in immunology}, volume = {13}, number = {}, pages = {853213}, pmid = {35493464}, issn = {1664-3224}, mesh = {Algorithms ; Bacteria/genetics ; Computational Biology ; Humans ; *Liver Neoplasms/genetics ; Software ; *Transcriptome ; Tumor Microenvironment/genetics ; }, abstract = {Recent transcriptomics and metagenomics studies showed that tissue-infiltrating immune cells and bacteria interact with cancer cells to shape oncogenesis. This interaction and its effects remain to be elucidated. However, it is technically difficult to co-quantify immune cells and bacteria in their respective microenvironments. To address this challenge, we herein report the development of a complete a bioinformatics pipeline, which accurately estimates the number of infiltrating immune cells using a novel Particle Swarming Optimized Support Vector Regression (PSO-SVR) algorithm, and the number of infiltrating bacterial using foreign read remapping and the GRAMMy algorithm. It also performs systematic differential abundance analyses between tumor-normal pairs. We applied the pipeline to a collection of paired liver cancer tumor and normal samples, and we identified bacteria and immune cell species that were significantly different between tissues in terms of health status. Our analysis showed that this dual model of microbial and immune cell abundance had a better differentiation (84%) between healthy and diseased tissue. Caldatribacterium sp., Acidaminococcaceae sp., Planctopirus sp., Desulfobulbaceae sp.,Nocardia farcinica as well as regulatory T cells (Tregs), resting mast cells, monocytes, M2 macrophases, neutrophils were identified as significantly different (Mann Whitney Test, FDR< 0.05). Our open-source software is freely available from GitHub at https://github.com/gutmicrobes/PSO-SVR.git.}, } @article {pmid35492345, year = {2022}, author = {Zou, Q and Chen, P and Chen, J and Chen, D and Xia, H and Chen, L and Feng, H and Feng, L}, title = {Multisystem Involvement Induced by Human Parvovirus B19 Infection in a Non-immunosuppressed Adult: A Case Report.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {808205}, pmid = {35492345}, issn = {2296-858X}, abstract = {BACKGROUND: Human parvovirus B19 (B19V) infection is usually symptomless and occurs in the childhood. While in immunocompromised adults, B19V infection also presents various clinical symptoms due to the host's immune status. The classic symptoms include erythema, anemia, arthropathy, and edema, but neurological involvement is rare.

CASE PRESENTATION: In this report, we present a case of B19V infection caused multiple organ dysfunction in a non-immunosuppressed adult. Metagenomic next-generation sequencing (mNGS) was used and successfully detected the pathogen in multiple types of samples, including blood, cerebrospinal fluid (CSF), and bronchoalveolar lavage fluid (BALF). The diagnosis was subsequently confirmed by polymerase chain reaction (PCR). He was treated with intravenous gamma globulin, resulting in a significant resolution of symptoms after 1 month.

CONCLUSION: Multisystem involvement induced by B19V infection was found in this case report. mNGS performed great advantages in rapidly and accurately diagnosing B19V infection in multiple types of samples, which helps the timely adjustment of treatment and improves the prognosis.}, } @article {pmid35492344, year = {2022}, author = {Li, D and Liang, H and Zhu, Y and Chang, Q and Pan, P and Zhang, Y}, title = {Clinical Characteristics, Laboratory Findings, and Prognosis in Patients With Talaromyces marneffei Infection Across Various Immune Statuses.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {841674}, pmid = {35492344}, issn = {2296-858X}, abstract = {OBJECTIVE: Talaromyces marneffei (TM) is an opportunistic fungus that is predominantly prevalent among patients who are HIV-positive in South-East Asia. However, few studies focused on the clinical features, laboratory findings, and prognosis across varying immune states.

METHODS: A total of 54 patients with TM infection in Xiangya Hospital of Central South University from January 1, 2006 to October 31, 2021 were retrospectively analyzed. Clinical profiles were compared across the different immune statuses by HIV-positive (HIV group, n = 18), HIV negative but with immunocompromised conditions (Non-HIV with IC Group, n = 11), and immunocompetent patients (n = 25).

RESULTS: All the patients were diagnosed by pathogen culture or by metagenomic next-generation sequencing (mNGS). The median age was 50, and patients with HIV were much younger compared to the other two groups. The most common symptom at presentation was fever (79.6%), followed by cough (70.4%), weight loss (61.1%), and expectoration (53.7%). The patients with HIV were more likely to develop into a subtype of disseminated TM affecting multiple organs including lymph node, liver, skin, and spleen, thus, resulting in higher hospital mortality compared to the other two groups. Patients without HIV but with immunocompromised conditions presented similar hospital mortality rates compared to immunocompetent patients, while experiencing longer days of hospitalization to recover from the diseases. Additionally, in this study, the pathogen culture easily confirmed the patients with HIV. However, mNGS presented as a promising tool to confirm TM infection in those suspicious patients without HIV.

CONCLUSIONS: In summary, patients with HIV were more likely to develop into disseminated TM, resulting in higher mortality compared to those patients without HIV. Additionally, mNGS presented as an important supplementary tool to confirm TM infection in patients without HIV, particularly in those with immunocompromised diseases.}, } @article {pmid35491834, year = {2022}, author = {Thurlow, CM and Joseph, SJ and Ganova-Raeva, L and Katz, SS and Pereira, L and Chen, C and Debra, A and Vilfort, K and Workowski, K and Cohen, SE and Reno, H and Sun, Y and Burroughs, M and Sheth, M and Chi, KH and Danavall, D and Philip, SS and Cao, W and Kersh, EN and Pillay, A}, title = {Selective Whole-Genome Amplification as a Tool to Enrich Specimens with Low Treponema pallidum Genomic DNA Copies for Whole-Genome Sequencing.}, journal = {mSphere}, volume = {7}, number = {3}, pages = {e0000922}, pmid = {35491834}, issn = {2379-5042}, mesh = {Animals ; High-Throughput Nucleotide Sequencing ; Metagenomics ; Rabbits ; *Syphilis/microbiology ; *Treponema pallidum/genetics ; Whole Genome Sequencing ; }, abstract = {Downstream next-generation sequencing (NGS) of the syphilis spirochete Treponema pallidum subspecies pallidum (T. pallidum) is hindered by low bacterial loads and the overwhelming presence of background metagenomic DNA in clinical specimens. In this study, we investigated selective whole-genome amplification (SWGA) utilizing multiple displacement amplification (MDA) in conjunction with custom oligonucleotides with an increased specificity for the T. pallidum genome and the capture and removal of 5'-C-phosphate-G-3' (CpG) methylated host DNA using the NEBNext Microbiome DNA enrichment kit followed by MDA with the REPLI-g single cell kit as enrichment methods to improve the yields of T. pallidum DNA in isolates and lesion specimens from syphilis patients. Sequencing was performed using the Illumina MiSeq v2 500 cycle or NovaSeq 6000 SP platform. These two enrichment methods led to 93 to 98% genome coverage at 5 reads/site in 5 clinical specimens from the United States and rabbit-propagated isolates, containing >14 T. pallidum genomic copies/μL of sample for SWGA and >129 genomic copies/μL for CpG methylation capture with MDA. Variant analysis using sequencing data derived from SWGA-enriched specimens showed that all 5 clinical strains had the A2058G mutation associated with azithromycin resistance. SWGA is a robust method that allows direct whole-genome sequencing (WGS) of specimens containing very low numbers of T. pallidum, which has been challenging until now. IMPORTANCE Syphilis is a sexually transmitted, disseminated acute and chronic infection caused by the bacterial pathogen Treponema pallidum subspecies pallidum. Primary syphilis typically presents as single or multiple mucocutaneous lesions and, if left untreated, can progress through multiple stages with various clinical manifestations. Molecular studies often rely on direct amplification of DNA sequences from clinical specimens; however, this can be impacted by inadequate samples due to disease progression or timing of patients seeking clinical care. While genotyping has provided important data on circulating strains over the past 2 decades, WGS data are needed to better understand strain diversity, perform evolutionary tracing, and monitor antimicrobial resistance markers. The significance of our research is the development of an SWGA DNA enrichment method that expands the range of clinical specimens that can be directly sequenced to include samples with low numbers of T. pallidum.}, } @article {pmid35491833, year = {2022}, author = {Kirchberger, PC and Martinez, ZA and Ochman, H}, title = {Organizing the Global Diversity of Microviruses.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0058822}, pmid = {35491833}, issn = {2150-7511}, support = {R35 GM118038/GM/NIGMS NIH HHS/United States ; }, mesh = {*Bacteriophages/genetics ; DNA, Single-Stranded ; Genome, Viral ; Humans ; Metagenome ; *Microviridae/genetics ; Microvirus/genetics ; Phylogeny ; }, abstract = {Microviruses encompass an astonishing array of small, single-stranded DNA phages that, due to the surge in metagenomic surveys, are now known to be prevalent in most environments. Current taxonomy concedes the considerable diversity within this lineage to a single family (the Microviridae), which has rendered it difficult to adequately and accurately assess the amount of variation that actually exists within this group. We amassed and curated the largest collection of microviral genomes to date and, through a combination of protein-sharing networks and phylogenetic analysis, discovered at least three meaningful taxonomic levels between the current ranks of family and genus. When considering more than 13,000 microviral genomes from recognized lineages and as-yet-unclassified microviruses in metagenomic samples, microviral diversity is better understood by elevating microviruses to the level of an order that consists of three suborders and at least 19 putative families, each with their respective subfamilies. These revisions enable fine-scale assessment of microviral dynamics: for example, in the human gut, there are considerable differences in the abundances of microviral families both between urban and rural populations and in individuals over time. In addition, our analysis of genome contents and gene exchange shows that microviral families carry no recognizable accessory metabolic genes and rarely, if ever, engage in horizontal gene transfer across microviral families or with their bacterial hosts. These insights bring microviral taxonomy in line with current developments in the taxonomy of other phages and increase the understanding of microvirus biology. IMPORTANCE Microviruses are the most abundant single-stranded DNA phages on the planet and an important component of the human gut virome. And yet, productive research into their biology is hampered by the inadequacies of current taxonomic ordering: microviruses are lumped into a single family and treated as a monolithic group, thereby obscuring the extent of their diversity and resulting in little comparative research. Our investigations into the diversity of microviruses define numerous groups, most lacking any isolated representatives, and point toward high-value targets for future research. To expedite microvirus discovery and comparison, we developed a pipeline that enables the fast and facile sorting of novel microvirus genomes into well-defined taxonomic groups. These improvements provide new insights into the biology of microviruses and emphasize fundamental differences between these miniature phages and their large, double-stranded DNA phage competitors.}, } @article {pmid35491162, year = {2022}, author = {Goto, M and Kobira, Y and Kaneko, S and Arima, H and Michihara, A and Azuma, K and Higashi, T and Motoyama, K and Watanabe, H and Maruyama, T and Kadowaki, D and Otagiri, M and Iohara, D and Hirayama, F and Anraku, M}, title = {The Effects of Sacran, a Sulfated Polysaccharide, on Gut Microbiota Using Chronic Kidney Disease Model Rats.}, journal = {Biological & pharmaceutical bulletin}, volume = {45}, number = {5}, pages = {576-582}, doi = {10.1248/bpb.b21-00897}, pmid = {35491162}, issn = {1347-5215}, mesh = {Animals ; Female ; *Gastrointestinal Microbiome ; Humans ; Male ; Polysaccharides/pharmacology/therapeutic use ; Rats ; *Renal Insufficiency, Chronic/drug therapy ; Sulfates/therapeutic use ; }, abstract = {The aim of this study was to investigate the beneficial effects of sacran, a sulfated polysaccharide, on renal damage and intestinal microflora, in 5/6 nephrectomy rats as a model for chronic kidney disease (CKD). 5/6 Nephrectomy rats were divided into sacran treated and non-treated groups and examined for lethality after 4 weeks. The 5/6 nephrectomy rats were also divided into three groups: sacran treated, non-treated and AST-120 treated groups, and treated orally in a concentration-dependent manner for 4 weeks. Renal function was estimated by biochemical and histopathological analyses. Metagenomic analysis of feces from each group after 4 weeks was also performed and changes in intestinal microflora were compared. The administration of sacran to CKD rats at ≥19 mg/d increased their survival. In addition, the sacran-treated group improved CKD-related parameters in a concentration-dependent manner, and the inhibitory effect of 40 mg/d of sacran was comparable to that of AST-120. The changes in the intestinal microflora of the sacran treated group were positively correlated with an increase in the number of Lactobacillus species, which are known to be rich in beneficial bacteria, and the increment of this beneficial bacteria was negatively correlated with the concentration of indoxyl sulfate, a uremic toxin, in plasma. These results strongly suggest that the oral administration of sacran could contribute to the stabilization of intestinal microflora in CKD rats and to the reduction of oxidative stress as well as the inhibition of progression of CKD.}, } @article {pmid35490813, year = {2022}, author = {Chen, X and Chen, H and Yang, L and Wei, W and Ni, BJ}, title = {A comprehensive analysis of evolution and underlying connections of water research themes in the 21st century.}, journal = {The Science of the total environment}, volume = {835}, number = {}, pages = {155411}, doi = {10.1016/j.scitotenv.2022.155411}, pmid = {35490813}, issn = {1879-1026}, mesh = {*Bibliometrics ; *COVID-19 ; *Drinking Water ; Humans ; Plastics ; Prospective Studies ; Wastewater ; }, abstract = {This work aimed to reflect the advancements in water-related science, technology, and policy and shed light on future research opportunities related to water through a systematic overview of Water Research articles published in the first 21.5 years of the 21st century. Specific bibliometric analyses were performed to i) reveal the temporal and spatial trends of water-related research themes and ii) identify the underlying connections between research topics. The results showed that while top topics including wastewater (treatment), drinking water, adsorption, model, biofilm, and bioremediation remained constantly researched, there were clear shifts in topics over the years, leading to the identification of trending-up and emerging research topics. Compared to the first decade of the 21st century, the second decade not only experienced significant uptrends of disinfection by-products, anaerobic digestion, membrane bioreactor, advanced oxidation processes, and pharmaceuticals but also witnessed the emerging popularity of PFAS, anammox, micropollutants, emerging contaminants, desalination, waste activated sludge, microbial community, forward osmosis, antibiotic resistance genes, resource recovery, and transformation products. On top of the temporal evolution, distinct spatial evolution existed in water-related research topics. Microplastics and Covid-19 causing global concerns were hot topics detected, while metagenomics and machine learning were two technical approaches emerging in recent years. These consistently popular, trending-up and emerging research topics would most likely attract continuous/increasing research input and therefore constitute a major part of the prospective water-related research publications.}, } @article {pmid35490759, year = {2022}, author = {Yang, C and Wang, B and Wang, H and He, Z and Pi, Y and Zhou, J and Liang, T and Chen, M and He, T and Fu, T}, title = {Removal of organochlorine pesticides and metagenomic analysis by multi-stage constructed wetland treating landfill leachate.}, journal = {Chemosphere}, volume = {301}, number = {}, pages = {134761}, doi = {10.1016/j.chemosphere.2022.134761}, pmid = {35490759}, issn = {1879-1298}, mesh = {Adsorption ; *Hydrocarbons, Chlorinated ; *Pesticides ; *Water Pollutants, Chemical/analysis ; Wetlands ; }, abstract = {Constructed wetlands (CWs) can effectively treat landfill leachate (LL). However, there is limited research on the removal of organochlorine pesticides (OCPs) refractory organics during LL treatment in CWs. In this study, multi-stage subsurface flow CWs was used to treat LL, and the removal fate of hexachlorocyclohexane (HCH) and dichlorodiphenyltrichloroethane (DDT) in CWs was investigated. The structural differences between plant roots and substrate microbial communities were compared and the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolic pathway of organic matter was analyzed based on metagenomic analysis. The results showed that substrate adsorption (50.55%-72.74%) and microbial degradation (20.38%-27.89%) were the main ways to remove OCPs. The Proteobacteria occupied a dominant position in the CWs system, among which Betaproteobacteria (34.37%-35.90%) were contained in the substrate, and Alphaproteobacteria (21.19%-23.84%) was a more dominant microorganism in plant roots. Formaldehyde assimilation and serine pathway were the main pathways of methane metabolism. This study provides a reference for the removal mechanism of OCPs to promote the application of CWs technology in LL treatment.}, } @article {pmid35489611, year = {2022}, author = {Saqr, A and Carlson, B and Staley, C and Rashidi, A and Al-Kofahi, M and Kaiser, T and Holtan, S and MacMillan, M and Young, JA and Jurdi, NE and Weisdorf, D and Khoruts, A and Jacobson, PA}, title = {Reduced Enterohepatic Recirculation of Mycophenolate and Lower Blood Concentrations Are Associated with the Stool Bacterial Microbiome after Hematopoietic Cell Transplantation.}, journal = {Transplantation and cellular therapy}, volume = {28}, number = {7}, pages = {372.e1-372.e9}, doi = {10.1016/j.jtct.2022.04.018}, pmid = {35489611}, issn = {2666-6367}, support = {P30 CA077598/CA/NCI NIH HHS/United States ; UL1 TR002494/TR/NCATS NIH HHS/United States ; }, mesh = {Adult ; Bacteria/metabolism ; Enzyme Inhibitors ; Glucuronidase ; Glucuronides ; *Graft vs Host Disease/chemically induced ; *Hematopoietic Stem Cell Transplantation ; Humans ; Immunosuppressive Agents/therapeutic use ; *Microbiota ; Mycophenolic Acid/therapeutic use ; }, abstract = {Mycophenolate mofetil (MMF) is an important immunosuppressant used after allogeneic hematopoietic cell transplantation (HCT). MMF has a narrow therapeutic index, and blood concentrations of mycophenolic acid (MPA), the active component of MMF, are highly variable. Low MPA concentrations are associated with the risk of graft-versus-host disease (GVHD), whereas high concentrations are associated with toxicity. Reasons for variability are not well known and may include the presence of β-glucuronidase-producing bacteria in the gastrointestinal tract, which enhance MPA enterohepatic recirculation (EHR) by transforming MPA metabolites formed in the liver back to MPA. This study was conducted to determine whether individuals with high MPA EHR have a greater abundance of β-glucuronidase-producing bacteria in their stool and higher MPA concentrations compared with those with low EHR. We conducted a pharmacomicrobiomics study in 20 adult HCT recipients receiving a myeloablative or reduced-intensity preparative regimen. Participants received MMF 1 g i.v. every 8 hours with tacrolimus. Intensive pharmacokinetic sampling of MMF was conducted before hospital discharge; total MPA, MPA glucuronide (MPAG), and acyl-glucuronide metabolite (acylMPAG) were measured. EHR was defined as the ratio of MPA area under the concentration-versus-time curve (AUC)4-8 to MPA AUC0-8. Differences in stool microbiome diversity and composition, determined by shotgun metagenomic sequencing, were compared above and below the median EHR (22%; range, 5% to 44%). The median EHR was 12% in the low EHR group and 29% in the high EHR group. MPA troughs, MPA AUC4-8, and acyl-glucuronide metabolite (acylMPAG) AUC4-8/AUC0-8 ratio were greater in the high EHR group compared with the low EHR group (1.53 μg/mL versus .28 μg/mL [P = .0001], 7.33 hour·μg/mL versus 1.79 hour·μg/mL [P = .0003], and .33 hour·μg/mL versus .24 hour·μg/mL [P = .0007], respectively). MPA AUC0-8 was greater in the high EHR group than in the low EHR group, and the difference trended toward significance (22.8 hour·μg/mL versus 15.3 hour·μg/mL; P = .06). Bacteroides vulgatus, Bacteroides stercoris, and Bacteroides thetaiotaomicron were 1.2- to 2.4-fold more abundant (P = .039, .024, and .046, respectively) in the high EHR group. MPA EHR was positively correlated with B. vulgatus (⍴ = .58; P ≤ .01) and B. thetaiotaomicron (⍴ = .46; P < .05) and negatively correlated with Blautia hydrogenotrophica (⍴ = -.53; P < .05). Therapeutic MPA troughs were achieved in 80% of patients in the high EHR group but in no patients in the low EHR group. There was a trend toward differences in MPA AUC0-8 and MPA concentration at steady-state (μg/mL) between the high EHR group versus the low EHR group (P = .06). MPA EHR was variable. Patients with high MPA EHR had greater abundance of Bacteroides species in stool and higher MPA exposure compared with patients with low MPA EHR. Therefore, Bacteroides may be protective against poor outcomes, such as graft-versus-host disease, in some patients but may increase the risk of MPA adverse effects in others. These data need to be confirmed and studied after oral MMF therapy.}, } @article {pmid35489490, year = {2022}, author = {Sanseverino, I and Gómez, L and Navarro, A and Cappelli, F and Niegowska, M and Lahm, A and Barbiere, M and Porcel-Rodríguez, E and Valsecchi, S and Pedraccini, R and Crosta, S and Lettieri, T}, title = {Holistic approach to chemical and microbiological quality of aquatic ecosystems impacted by wastewater effluent discharges.}, journal = {The Science of the total environment}, volume = {835}, number = {}, pages = {155388}, doi = {10.1016/j.scitotenv.2022.155388}, pmid = {35489490}, issn = {1879-1026}, mesh = {Bacteria ; Environmental Monitoring/methods ; *Microbiota ; Rivers/chemistry ; Waste Disposal, Fluid/methods ; Wastewater/chemistry ; *Water Pollutants, Chemical/analysis ; *Water Purification ; }, abstract = {Wastewater treatment plants (WWTPs) collect wastewater from various sources and use different treatment processes to reduce the load of pollutants in the environment. Since the removal of many chemical pollutants and bacteria by WWTPs is incomplete, they constitute a potential source of contaminants. The continuous release of contaminants through WWTP effluents can compromise the health of the aquatic ecosystems, even if they occur at very low concentrations. The main objective of this work was to characterize, over a period of four months, the treatment steps starting from income to the effluent and 5 km downstream to the receiving river. In this context, the efficiency removal of chemical pollutants (e.g. hormones and pharmaceuticals, including antibiotics) and bacteria was assessed in a WWTP case study by using a holistic approach. It embraces different chemical and biological-based methods, such as pharmaceutical analysis by HPLC-MSMS, growth rate inhibition in algae, ligand binding estrogen receptor assay, microbial community study by 16S and shotgun sequencing along with relative quantification of resistance genes by quantitative polymerase chain reaction. Although both, chemical and biological-based methods showed a significant reduction of the pollutant burden in effluent and surface waters compared to the influent of the WWTP, no complete removal of pollutants, pathogens and antibiotic resistance genes was observed.}, } @article {pmid35489476, year = {2022}, author = {Li, D and Gao, J and Dai, H and Wang, Z and Zhao, Y and Cui, Y}, title = {Higher spreading risk of antibacterial biocide and heavy metal resistance genes than antibiotic resistance genes in aerobic granular sludge.}, journal = {Environmental research}, volume = {212}, number = {Pt C}, pages = {113356}, doi = {10.1016/j.envres.2022.113356}, pmid = {35489476}, issn = {1096-0953}, mesh = {Anti-Bacterial Agents/pharmacology ; *Disinfectants ; Drug Resistance, Bacterial/genetics ; Genes, Bacterial ; *Metals, Heavy ; Sewage ; }, abstract = {Metagenomic approach was applied to simultaneously reveal the antibiotic resistance genes (ARGs) and antibacterial biocide & metal resistance genes (BMRGs), and the corresponding microbial hosts with high mobility during aerobic granular sludge (AGS) formation process. The results showed that the relative abundance of BMRGs was 88-123 times that of ARGs. AGS process was easier to enrich BMRGs, leading to a greater risk of drug resistance caused by BMRGs than that by ARGs. The enrichments of ARGs and BMRGs in AGS were closely related to several enhanced microbial metabolisms (i.e., cell motility, transposase and ATP-binding cassette transporters) and their corresponding regulatory genes. Several enhanced KEGG Orthologs (KO) functions, such as K01995, K01996, K01997 and K02002, might cause a positive impact on the spread of ARGs and BMRGs, and the main contributors were the largely enriched glycogens accumulating organisms. The first dominant ARGs (adeF) was carried by lots of microbial hosts, which might be enriched and propagated mainly through horizontal gene transfer. Candidatus Competibacter denitrificans simultaneously harbored ARG (cmx) and Cu related RGs (corR). Many enriched bacteria contained simultaneously multiple BMRGs (copR and corR) and mobile genetic elements (integrons and plasmids), granting them high mobility capabilities and contributing to the spread of BMRGs. This study might provide deeper understandings of the proliferation and mobility of ARGs and BMRGs, importantly, highlighted the status of BMRGs, which laid the foundation for the controlling widespread of resistance genes in AGS.}, } @article {pmid35489463, year = {2022}, author = {Qin, Z and Li, B and Xu, F and Chen, K and Chen, C and Wan, J and Yu, C and Yang, J and Shen, C}, title = {Metagenomic study of humic acid promoting the dechlorination of polychlorinated biphenyls.}, journal = {Chemosphere}, volume = {301}, number = {}, pages = {134688}, doi = {10.1016/j.chemosphere.2022.134688}, pmid = {35489463}, issn = {1879-1298}, mesh = {Biodegradation, Environmental ; Carbon ; Humic Substances/analysis ; Metagenomics ; *Polychlorinated Biphenyls/analysis ; }, abstract = {Polychlorinated biphenyls (PCBs) are persistent organic pollutants that degrade slowly in the environment. Humic acid (HA), the main component of soil organic matter, or more specifically, the quinone moieties in HA, is generally regarded as an "electron shuttle" between pollutants and microorganisms, which could promote microbial remediation of contamination. In this study, we examined the dechlorination of PCB153 by adding HA and anthraquinone-2,6-disulfonate (AQDS, a model compound of quinones) to systems containing PCB dechlorinators, analyzed the composition and functional gene network of the microbial community by metagenomics, and explored the role of HA by modifying or substituting carbon sources or electron donors. However, this study found that HA accelerated microbial dechlorination of PCBS, while AQDS did not. Moreover, HA without quinone activity still promoted dechlorination, but not without carbon source or electron donor. Metagenomic analysis showed that HA did not promote the growth of PCB dechlorinator (Dehalococcoides), but the transmembrane electron carriers in the HA group were higher than those in the AQDS group and the control group, so HA may have promoted the electron transport process. This study is helpful for microbial remediation of PCB contamination, and provides new insights into the role that HA plays in the biogeochemical cycle.}, } @article {pmid35489450, year = {2022}, author = {Dai, C and Wu, H and Wang, X and Zhao, K and Lu, Z}, title = {Network and meta-omics reveal the cooperation patterns and mechanisms in an efficient 1,4-dioxane-degrading microbial consortium.}, journal = {Chemosphere}, volume = {301}, number = {}, pages = {134723}, doi = {10.1016/j.chemosphere.2022.134723}, pmid = {35489450}, issn = {1879-1298}, mesh = {Bacteria/metabolism ; Biodegradation, Environmental ; *Dioxanes/metabolism ; Humans ; *Microbial Consortia/genetics ; Xanthobacter ; }, abstract = {1,4-Dioxane is an emerging wastewater contaminant with probable human carcinogenicity. Our current understanding of microbial interactions during 1,4-dioxane biodegradation process in mixed cultures is limited. Here, we applied metagenomic, metatranscriptomic and co-occurrence network analyses to unraveling the microbial cooperation between degrader and non-degraders in an efficient 1,4-dioxane-degrading microbial consortium CH1. A 1,4-dioxane-degrading bacterium, Ancylobacter polymorphus ZM13, was isolated from CH1 and had a potential of being one of the important degraders due to its high relative abundance, highly expressed monooxygenase genes tmoABCDEF and high betweenness centrality of networks. The strain ZM13 cooperated obviously with 6 bacterial genera in the network, among which Xanthobacter and Mesorhizobium could be involved in the intermediates metabolism with responsible genes encoding alcohol dehydrogenase (adh), aldehyde dehydrogenase (aldh), glycolate oxidase (glcDEF), glyoxylate carboligase (gcl), malate synthase (glcB) and 2-isopropylmalate synthase (leuA) differentially high-expressed. Also, 1,4-dioxane facilitated the shift of biodiversity and function of CH1, and those cooperators cooperated with ZM13 in the way of providing amino acids or fatty acids, as well as relieving environmental stresses to promote biodegradation. These results provide new insights into our understandings of the microbial interactions during 1,4-dioxane degradation, and have important implications for predicting microbial cooperation and constructing efficient and stable synthetic 1,4-dioxane-degrading consortia for practical remediation.}, } @article {pmid35489315, year = {2022}, author = {Liu, C and Li, B and Chen, X and Dong, Y and Lin, H}, title = {Insight into soilless revegetation of oligotrophic and heavy metal contaminated gold tailing pond by metagenomic analysis.}, journal = {Journal of hazardous materials}, volume = {435}, number = {}, pages = {128881}, doi = {10.1016/j.jhazmat.2022.128881}, pmid = {35489315}, issn = {1873-3336}, mesh = {Gold/analysis ; Metagenomics ; *Metals, Heavy/analysis ; Phosphates/metabolism ; Plants/metabolism ; Soil/chemistry ; Soil Microbiology ; *Soil Pollutants/metabolism ; }, abstract = {Soilless revegetation is an efficient way for gold tailing remediation, and micro-ecological environments in plant rhizosphere are important for vegetation establishment and pollution removal. In the present study, a field experiment of soilless revegetation has been carried out in a gold tailings pond, and the key genera and functional genes in the plant rhizosphere of gold mine tailings were revealed by metagenomics analysis. Soilless revegetation significantly decreased rhizosphere tailing pH from 8.54 to 7.43-7.87, reduced heavy metal (HM) concentration by 29.81-44.02% and enhanced the nutrient content by 50.30-169.50% averagely. Such improvements were strongly and closely correlated to microbial community and functional gene composition variation. The relative abundance of ecologically beneficial genus such as Actinobacteria (increased 9.7-18.8%) and functional genes involved in carbon, nitrogen and phosphorus cycling such as pyruvate metabolism (relatively increased 8.7-15.0%), assimilatory (increased to 1.44-2.08 times), phosphate ester mineralization (increased to 1.12-1.29 times) and phosphate transportation (increased to 1.28-1.85 times) were significantly increased. Moreover, the relative abundance of most As and Zn resistance genes were reduced, which may relate to the decrease of As and Zn concentration in the rhizosphere tailings. These results revealed the correlation among HM concentrations, microbial composition and functional genes, and provided clear strategies for improving gold mine tailing ecological restoration efficiency.}, } @article {pmid35489067, year = {2022}, author = {Schmartz, GP and Hirsch, P and Amand, J and Dastbaz, J and Fehlmann, T and Kern, F and Müller, R and Keller, A}, title = {BusyBee Web: towards comprehensive and differential composition-based metagenomic binning.}, journal = {Nucleic acids research}, volume = {50}, number = {W1}, pages = {W132-W137}, pmid = {35489067}, issn = {1362-4962}, mesh = {*Algorithms ; *Metagenome ; Software ; Metagenomics/methods ; Workflow ; Sequence Analysis, DNA ; }, abstract = {Despite recent methodology and reference database improvements for taxonomic profiling tools, metagenomic assembly and genomic binning remain important pillars of metagenomic analysis workflows. In case reference information is lacking, genomic binning is considered to be a state-of-the-art method in mixed culture metagenomic data analysis. In this light, our previously published tool BusyBee Web implements a composition-based binning method efficient enough to function as a rapid online utility. Handling assembled contigs and long nanopore generated reads alike, the webserver provides a wide range of supplementary annotations and visualizations. Half a decade after the initial publication, we revisited existing functionality, added comprehensive visualizations, and increased the number of data analysis customization options for further experimentation. The webserver now allows for visualization-supported differential analysis of samples, which is computationally expensive and typically only performed in coverage-based binning methods. Further, users may now optionally check their uploaded samples for plasmid sequences using PLSDB as a reference database. Lastly, a new application programming interface with a supporting python package was implemented, to allow power users fully automated access to the resource and integration into existing workflows. The webserver is freely available under: https://www.ccb.uni-saarland.de/busybee.}, } @article {pmid35489013, year = {2022}, author = {Fenske, L and Noll, I and Blom, J and Ewers, C and Semmler, T and Fawzy, A and Eisenberg, T}, title = {A dominant clonal lineage of Streptococcus uberis in cattle in Germany.}, journal = {Antonie van Leeuwenhoek}, volume = {115}, number = {7}, pages = {857-870}, pmid = {35489013}, issn = {1572-9699}, mesh = {Animals ; Cattle ; Female ; *Mastitis, Bovine/epidemiology/microbiology ; Multilocus Sequence Typing ; *Streptococcal Infections/microbiology/veterinary ; Streptococcus/genetics ; }, abstract = {Bovine mastitis causes enormous economic losses in the dairy industry with Streptococcus uberis as one of the most common bacterial pathogens causing clinical and subclinical variations. In most cases mastitis can be cured by intramammary administration of antimicrobial agents. However, the severity of the clinical manifestations can vary greatly from mild to severe symtoms. In this study, a comparative genomic analysis of 24 S. uberis isolates from three dairy farms in Germany, affected by different courses of infection was conducted. While there were sporadic mild infections in farm A and B, a large number of infections were observed within a very short period of time in farm C. The comparison of virulence genes, antimicrobial resistance genes and prophage regions revealed no features that might be responsible for this severe course. However, almost all isolates from farm C showed the same, novel MLST profile (ST1373), thus a clonal outbreak cannot be excluded, whereby the actual reason for the particular virulence remains unknown. This study demonstrates the importance of extensive metagenomic studies, including the host genomes and the environment, to gain further evidence on the pathogenicity of S. uberis.}, } @article {pmid35488253, year = {2022}, author = {Lin, P and Chen, Y and Su, S and Nan, W and Zhou, L and Zhou, Y and Li, Y}, title = {Diagnostic value of metagenomic next-generation sequencing of bronchoalveolar lavage fluid for the diagnosis of suspected pneumonia in immunocompromised patients.}, journal = {BMC infectious diseases}, volume = {22}, number = {1}, pages = {416}, pmid = {35488253}, issn = {1471-2334}, support = {Y20210144//the Project of Wenzhou Science & Technology Bureau/ ; 81970066//the Project of National Natural Science Foundation of China/ ; }, mesh = {Bronchoalveolar Lavage Fluid/microbiology ; *Coinfection ; DNA Viruses ; High-Throughput Nucleotide Sequencing ; Humans ; Immunocompromised Host ; *Mycobacterium tuberculosis/genetics ; *Pneumonia, Pneumocystis/diagnosis/microbiology ; Retrospective Studies ; Sensitivity and Specificity ; *Viruses ; }, abstract = {BACKGROUND: To evaluate the diagnostic value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in immunocompromised patients for the diagnosis of suspected pneumonia in comparison with that of conventional microbiological tests (CMTs).

METHODS: Sixty-nine immunocompromised patients with suspected pneumonia received both CMTs and mNGS of BALF were analyzed retrospectively. The diagnostic value was compared between CMTs and mNGS, using the clinical composite diagnosis as the reference standard.

RESULTS: Sixty patients were diagnosed of pneumonia including fifty-two patients with identified pathogens and eight patients with probable pathogens. Taking the composite reference standard as a gold standard, 42 pathogens were identified by CMTs including nine bacteria, 17 fungi, 8 virus, 6 Mycobacterium Tuberculosis, and two Legionella and 19(45%) of which were detected by BALF culture. As for mNGS, it identified 76 pathogens including 20 bacteria, 31 fungi, 14 virus, 5 Mycobacterium Tuberculosis, four Legionella and two Chlamydia psittaci. The overall detection rate of mNGS for pathogens were higher than that of CMTs. However, a comparable diagnostic accuracy of mNGS and CMTs were found for bacterial and viral infections. mNGS exhibited a higher diagnostic accuracy for fungal detection than CMTs (78% vs. 57%, P < 0.05), which mainly because of the high sensitivity of mNGS in patients with Pneumocystis jirovecii pneumonia (PJP) (100% vs. 28%, P < 0.05). Nineteen patients were identified as pulmonary co-infection, mNGS test showed a higher detection rate and broader spectrum for pathogen detection than that of CMTs in co-infection. Moreover, Pneumocystis jirovecii was the most common pathogen in co-infection and mNGS have identified much more co-pathogens of PJP than CMTs.

CONCLUSIONS: mNGS of BALF improved the microbial detection rate of pathogens and exhibited remarkable advantages in detecting PJP and identifying co-infection in immunocompromised patients.}, } @article {pmid35486672, year = {2023}, author = {Gonzales, JA and Sundararajan, M and Qian, Y and Hwang, T and Doan, T}, title = {Detection of Leptospirosis Genome from the Aqueous Humor of a Patient with Bilateral Uveitis.}, journal = {Ocular immunology and inflammation}, volume = {31}, number = {5}, pages = {1076-1078}, pmid = {35486672}, issn = {1744-5078}, support = {K08 EY026986/EY/NEI NIH HHS/United States ; }, mesh = {Humans ; Retrospective Studies ; Aqueous Humor/microbiology ; *Leptospirosis/diagnosis/microbiology ; *Leptospira/genetics ; *Uveitis/diagnosis/microbiology ; }, abstract = {BACKGROUND: Leptospira species are difficult to culture. Thus, when there is suspicion for an infectious etiology to uveitis, bacterial cultures may fail to identify Leptospira. We describe a case of leptospirosis-associated uveitis that evaded culture and molecular assays. DNA sequencing of the aqueous fluid showed the presence of Leptospira spp.

METHODS: Retrospective case review of clinical and laboratory features of a patient with ocular leptospirosis is presented.

RESULTS: DNA sequencing identified the genome of Leptospirosis spp. in the aqueous humor.

CONCLUSION: Metagenomic sequencing, by virtue of its unbiased nature, can be a helpful adjunctive test when a strong clinical suspicion for intraocular infection persists despite negative routine culture and molecular assays.}, } @article {pmid35486615, year = {2022}, author = {Sandhu, M and Paul, AT and Jha, PN}, title = {Metagenomic analysis for taxonomic and functional potential of Polyaromatic hydrocarbons (PAHs) and Polychlorinated biphenyl (PCB) degrading bacterial communities in steel industrial soil.}, journal = {PloS one}, volume = {17}, number = {4}, pages = {e0266808}, pmid = {35486615}, issn = {1932-6203}, mesh = {Bacteria/genetics/metabolism ; *Polychlorinated Biphenyls/analysis ; Soil ; *Soil Pollutants/analysis ; Steel/analysis ; Tandem Mass Spectrometry ; }, abstract = {Iron and steel industries are the major contributors to persistent organic pollutants (POPs). The microbial community present at such sites has the potential to remediate these contaminants. The present study highlights the metabolic potential of the resident bacterial community of PAHs and PCB contaminated soil nearby Bhilai steel plant, Chhattisgarh (India). The GC-MS/MS analysis of soil samples MGB-2 (sludge) and MGB-3 (dry soil) resulted in identification of different classes of POPs including PAHs {benzo[a]anthracene (nd; 17.69%), fluorene (15.89%, nd), pyrene (nd; 18.7%), benzo(b)fluoranthene (3.03%, nd), benzo(k)fluoranthene (11.29%; nd), perylene (5.23%; nd)} and PCBs (PCB-15, PCB-95, and PCB-136). Whole-genome metagenomic analysis by Oxford Nanopore GridION Technology revealed predominance of domain bacteria (97.4%; 97.5%) followed by eukaryote (1.4%; 1.5%), archaea (1.2%; 0.9%) and virus (0.02%; 0.04%) in MGB-2 and MGB-3 respectively. Proteobacteria (44.3%; 50.0%) to be the prominent phylum followed by Actinobacteria (22.1%; 19.5%) in MBG-2 and MBG-3, respectively. However, Eukaryota microbial communities showed a predominance of phylum Ascomycota (20.5%; 23.6%), Streptophyta (18.5%, 17.0%) and unclassified (derived from Eukaryota) (12.1%; 12.2%) in MGB-2 and MGB-3. The sample MGB-3 was richer in macronutrients (C, N, P), supporting high microbial diversity than MGB-2. The presence of reads for biphenyl degradation, dioxin degradation, PAH degradation pathways can be further correlated with the presence of PCB and PAH as detected in the MGB-2 and MGB-3 samples. Further, taxonomic vis-à-vis functional analysis identified Burkholderia, Bradyrhizobium, Mycobacterium, and Rhodopseudomonas as the keystone degrader of PAH and PCB. Overall, our results revealed the importance of metagenomic and physicochemical analysis of the contaminated site, which improves the understanding of metabolic potential and adaptation of bacteria growing under POP contaminated environments.}, } @article {pmid35486523, year = {2022}, author = {Li, CX and Burrell, R and Dale, RC and Kesson, A and Blyth, CC and Clark, JE and Crawford, N and Jones, CA and Britton, PN and Holmes, EC}, title = {Diagnosis and analysis of unexplained cases of childhood encephalitis in Australia using metatranscriptomic sequencing.}, journal = {The Journal of general virology}, volume = {103}, number = {4}, pages = {}, doi = {10.1099/jgv.0.001736}, pmid = {35486523}, issn = {1465-2099}, mesh = {Australia ; Child ; *Encephalitis/diagnosis/etiology ; Humans ; Metagenomics ; Polymerase Chain Reaction ; *Viruses ; }, abstract = {Encephalitis is most often caused by a variety of infectious agents identified through diagnostic tests utilizing cerebrospinal fluid. We investigated the clinical characteristics and potential aetiological agents of unexplained encephalitis through metagenomic sequencing of residual clinical samples from multiple tissue types and independent clinical review. Forty-three specimens were collected from 18 encephalitis cases with no cause identified by the Australian Childhood Encephalitis study. Samples were subjected to total RNA sequencing ('metatranscriptomics') to determine the presence and abundance of potential pathogens, and to describe the possible aetiologies of unexplained encephalitis. Using this protocol, we identified five RNA and two DNA viruses associated with human infection from both non-sterile and sterile sites, which were confirmed by PCR. These comprised two human rhinoviruses, two human seasonal coronaviruses, two polyomaviruses and one picobirnavirus. Human rhinovirus and seasonal coronaviruses may be responsible for five of the encephalitis cases. Immune-mediated encephalitis was considered likely in six cases and metatranscriptomics did not identify a possible pathogen in these cases. The aetiology remained unknown in nine cases. Our study emphasizes the importance of respiratory viruses in the aetiology of unexplained child encephalitis and suggests that non-central-nervous-system sampling in encephalitis clinical guidelines and protocols could improve the diagnostic yield.}, } @article {pmid35485976, year = {2023}, author = {Jiang, Y and Balaban, M and Zhu, Q and Mirarab, S}, title = {DEPP: Deep Learning Enables Extending Species Trees using Single Genes.}, journal = {Systematic biology}, volume = {72}, number = {1}, pages = {17-34}, pmid = {35485976}, issn = {1076-836X}, support = {R35 GM142725/GM/NIGMS NIH HHS/United States ; }, mesh = {Phylogeny ; *Deep Learning ; RNA, Ribosomal, 16S/genetics ; Algorithms ; *Microbiota/genetics ; }, abstract = {Placing new sequences onto reference phylogenies is increasingly used for analyzing environmental samples, especially microbiomes. Existing placement methods assume that query sequences have evolved under specific models directly on the reference phylogeny. For example, they assume single-gene data (e.g., 16S rRNA amplicons) have evolved under the GTR model on a gene tree. Placement, however, often has a more ambitious goal: extending a (genome-wide) species tree given data from individual genes without knowing the evolutionary model. Addressing this challenging problem requires new directions. Here, we introduce Deep-learning Enabled Phylogenetic Placement (DEPP), an algorithm that learns to extend species trees using single genes without prespecified models. In simulations and on real data, we show that DEPP can match the accuracy of model-based methods without any prior knowledge of the model. We also show that DEPP can update the multilocus microbial tree-of-life with single genes with high accuracy. We further demonstrate that DEPP can combine 16S and metagenomic data onto a single tree, enabling community structure analyses that take advantage of both sources of data. [Deep learning; gene tree discordance; metagenomics; microbiome analyses; neural networks; phylogenetic placement.].}, } @article {pmid35485872, year = {2022}, author = {Sedeek, AM and Ismail, MM and Elsayed, TR and Ramadan, MA}, title = {Recent methods for discovering novel bioactive metabolites, specifically antimicrobial agents, from marine-associated micro-organisms.}, journal = {Letters in applied microbiology}, volume = {75}, number = {3}, pages = {511-525}, doi = {10.1111/lam.13728}, pmid = {35485872}, issn = {1472-765X}, mesh = {Anti-Bacterial Agents/metabolism/pharmacology ; *Anti-Infective Agents/chemistry ; Aquatic Organisms ; Bacteria/metabolism ; *Biological Products/pharmacology ; Culture Media/metabolism ; Metagenomics ; }, abstract = {Marine micro-organisms are a promising source for novel natural compounds with many medical and biotechnological applications. Here, we demonstrate limitations and recent strategies for investigating the marine microbial community for novel bioactive metabolites, specifically those of antimicrobial potential. These strategies include culture-dependent methods such as modifying the standard culture media, including changing the gelling agent, dissolving vehicle, media supplementation and preparation to access a broader range of bacterial diversity from marine samples. Furthermore, we discuss strategies such as in situ cultivation, dilution-to-extinction cultivation and long-term incubation. We are presenting recent applications of culture-independent methods such as genome mining, proteomics profiling and the application of metagenomics as a novel strategy for structure confirmation in the discovery of the marine micro-organism for novel antimicrobial metabolites. We present this review as a simple guide and a helpful resource for those who seek to enter the challenging field of applied marine microbiology.}, } @article {pmid35485188, year = {2022}, author = {Blanco-Picazo, P and Gómez-Gómez, C and Aguiló-Castillo, S and Fernández-Orth, D and Cerdà-Cuéllar, M and Muniesa, M and Rodríguez-Rubio, L}, title = {Chicken liver is a potential reservoir of bacteriophages and phage-derived particles containing antibiotic resistance genes.}, journal = {Microbial biotechnology}, volume = {15}, number = {9}, pages = {2464-2475}, pmid = {35485188}, issn = {1751-7915}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Bacteriophages/genetics ; Chickens ; Drug Resistance, Microbial/genetics ; Escherichia coli ; Genes, Bacterial ; Liver ; }, abstract = {Poultry meat production is one of the most important agri-food industries in the world. The selective pressure exerted by widespread prophylactic or therapeutic use of antibiotics in intensive chicken farming favours the development of drug resistance in bacterial populations. Chicken liver, closely connected with the intestinal tract, has been directly involved in food-borne infections and found to be contaminated with pathogenic bacteria, including Campylobacter and Salmonella. In this study, 74 chicken livers, divided into sterile and non-sterile groups, were analysed, not only for microbial indicators but also for the presence of phages and phage particles containing antibiotic resistance genes (ARGs). Both bacteria and phages were detected in liver tissues, including those dissected under sterile conditions. The phages were able to infect Escherichia coli and showed a Siphovirus morphology. The chicken livers contained from 10[3] to 10[6] phage particles per g, which carried a range of ARGs (blaTEM , blaCTx-M-1 , sul1, qnrA, armA and tetW) detected by qPCR. The presence of phages in chicken liver, mostly infecting E. coli, was confirmed by metagenomic analysis, although this technique was not sufficiently sensitive to identify ARGs. In addition, ARG-carrying phages were detected in chicken faeces by qPCR in a previous study of the group. Comparison of the viromes of faeces and liver showed a strong coincidence of species, which suggests that the phages found in the liver originate in faeces. These findings suggests that phages, like bacteria, can translocate from the gut to the liver, which may therefore constitute a potential reservoir of antibiotic resistance genes.}, } @article {pmid35484634, year = {2022}, author = {Duncan, A and Barry, K and Daum, C and Eloe-Fadrosh, E and Roux, S and Schmidt, K and Tringe, SG and Valentin, KU and Varghese, N and Salamov, A and Grigoriev, IV and Leggett, RM and Moulton, V and Mock, T}, title = {Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {67}, pmid = {35484634}, issn = {2049-2618}, mesh = {Atlantic Ocean ; Chlorophyll A ; Eukaryota/genetics ; *Metagenome/genetics ; *Microbiota/genetics ; Phylogeny ; Phytoplankton/genetics ; }, abstract = {BACKGROUND: Phytoplankton communities significantly contribute to global biogeochemical cycles of elements and underpin marine food webs. Although their uncultured genomic diversity has been estimated by planetary-scale metagenome sequencing and subsequent reconstruction of metagenome-assembled genomes (MAGs), this approach has yet to be applied for complex phytoplankton microbiomes from polar and non-polar oceans consisting of microbial eukaryotes and their associated prokaryotes.

RESULTS: Here, we have assembled MAGs from chlorophyll a maximum layers in the surface of the Arctic and Atlantic Oceans enriched for species associations (microbiomes) with a focus on pico- and nanophytoplankton and their associated heterotrophic prokaryotes. From 679 Gbp and estimated 50 million genes in total, we recovered 143 MAGs of medium to high quality. Although there was a strict demarcation between Arctic and Atlantic MAGs, adjacent sampling stations in each ocean had 51-88% MAGs in common with most species associations between Prasinophytes and Proteobacteria. Phylogenetic placement revealed eukaryotic MAGs to be more diverse in the Arctic whereas prokaryotic MAGs were more diverse in the Atlantic Ocean. Approximately 70% of protein families were shared between Arctic and Atlantic MAGs for both prokaryotes and eukaryotes. However, eukaryotic MAGs had more protein families unique to the Arctic whereas prokaryotic MAGs had more families unique to the Atlantic.

CONCLUSION: Our study provides a genomic context to complex phytoplankton microbiomes to reveal that their community structure was likely driven by significant differences in environmental conditions between the polar Arctic and warm surface waters of the tropical and subtropical Atlantic Ocean. Video Abstract.}, } @article {pmid35484230, year = {2022}, author = {Edwinson, AL and Yang, L and Peters, S and Hanning, N and Jeraldo, P and Jagtap, P and Simpson, JB and Yang, TY and Kumar, P and Mehta, S and Nair, A and Breen-Lyles, M and Chikkamenahalli, L and Graham, RP and De Winter, B and Patel, R and Dasari, S and Kashyap, P and Griffin, T and Chen, J and Farrugia, G and Redinbo, MR and Grover, M}, title = {Gut microbial β-glucuronidases regulate host luminal proteases and are depleted in irritable bowel syndrome.}, journal = {Nature microbiology}, volume = {7}, number = {5}, pages = {680-694}, pmid = {35484230}, issn = {2058-5276}, support = {R01 GM135218/GM/NIGMS NIH HHS/United States ; R03 DK120745/DK/NIDDK NIH HHS/United States ; R01 GM137286/GM/NIGMS NIH HHS/United States ; R01 DK127998/DK/NIDDK NIH HHS/United States ; K23 DK103911/DK/NIDDK NIH HHS/United States ; P30 DK084567/DK/NIDDK NIH HHS/United States ; }, mesh = {Animals ; Bilirubin ; Endopeptidases ; Escherichia coli ; *Gastrointestinal Microbiome/physiology ; Glucuronidase/genetics ; Humans ; *Irritable Bowel Syndrome ; Mice ; Serine Proteases/genetics ; }, abstract = {Intestinal proteases mediate digestion and immune signalling, while increased gut proteolytic activity disrupts the intestinal barrier and generates visceral hypersensitivity, which is common in irritable bowel syndrome (IBS). However, the mechanisms controlling protease function are unclear. Here we show that members of the gut microbiota suppress intestinal proteolytic activity through production of unconjugated bilirubin. This occurs via microbial β-glucuronidase-mediated conversion of bilirubin conjugates. Metagenomic analysis of faecal samples from patients with post-infection IBS (n = 52) revealed an altered gut microbiota composition, in particular a reduction in Alistipes taxa, and high gut proteolytic activity driven by specific host serine proteases compared with controls. Germ-free mice showed 10-fold higher proteolytic activity compared with conventional mice. Colonization with microbiota samples from high proteolytic activity IBS patients failed to suppress proteolytic activity in germ-free mice, but suppression of proteolytic activity was achieved with colonization using microbiota from healthy donors. High proteolytic activity mice had higher intestinal permeability, a higher relative abundance of Bacteroides and a reduction in Alistipes taxa compared with low proteolytic activity mice. High proteolytic activity IBS patients had lower fecal β-glucuronidase activity and end-products of bilirubin deconjugation. Mice treated with unconjugated bilirubin and β-glucuronidase-overexpressing E. coli significantly reduced proteolytic activity, while inhibitors of microbial β-glucuronidases increased proteolytic activity. Together, these data define a disease-relevant mechanism of host-microbial interaction that maintains protease homoeostasis in the gut.}, } @article {pmid35484157, year = {2022}, author = {de Nies, L and Busi, SB and Tsenkova, M and Halder, R and Letellier, E and Wilmes, P}, title = {Evolution of the murine gut resistome following broad-spectrum antibiotic treatment.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {2296}, pmid = {35484157}, issn = {2041-1723}, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; *Genes, Bacterial ; Humans ; Mammals/genetics ; Metagenome ; Mice ; Plasmids ; }, abstract = {The emergence and spread of antimicrobial resistance (AMR) represent an ever-growing healthcare challenge worldwide. Nevertheless, the mechanisms and timescales shaping this resistome remain elusive. Using an antibiotic cocktail administered to a murine model along with a longitudinal sampling strategy, we identify the mechanisms by which gut commensals acquire antimicrobial resistance genes (ARGs) after a single antibiotic course. While most of the resident bacterial populations are depleted due to the treatment, Akkermansia muciniphila and members of the Enterobacteriaceae, Enterococcaceae, and Lactobacillaceae families acquire resistance and remain recalcitrant. We identify specific genes conferring resistance against the antibiotics in the corresponding metagenome-assembled genomes (MAGs) and trace their origins within each genome. Here we show that, while mobile genetic elements (MGEs), including bacteriophages and plasmids, contribute to the spread of ARGs, integrons represent key factors mediating AMR in the antibiotic-treated mice. Our findings suggest that a single course of antibiotics alone may act as the selective sweep driving ARG acquisition and incidence in gut commensals over a single mammalian lifespan.}, } @article {pmid35484115, year = {2022}, author = {Pan, S and Zhu, C and Zhao, XM and Coelho, LP}, title = {A deep siamese neural network improves metagenome-assembled genomes in microbiome datasets across different environments.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {2326}, pmid = {35484115}, issn = {2041-1723}, mesh = {Algorithms ; *Metagenome/genetics ; Metagenomics/methods ; *Microbiota/genetics ; Neural Networks, Computer ; }, abstract = {Metagenomic binning is the step in building metagenome-assembled genomes (MAGs) when sequences predicted to originate from the same genome are automatically grouped together. The most widely-used methods for binning are reference-independent, operating de novo and enable the recovery of genomes from previously unsampled clades. However, they do not leverage the knowledge in existing databases. Here, we introduce SemiBin, an open source tool that uses deep siamese neural networks to implement a semi-supervised approach, i.e. SemiBin exploits the information in reference genomes, while retaining the capability of reconstructing high-quality bins that are outside the reference dataset. Using simulated and real microbiome datasets from several different habitats from GMGCv1 (Global Microbial Gene Catalog), including the human gut, non-human guts, and environmental habitats (ocean and soil), we show that SemiBin outperforms existing state-of-the-art binning methods. In particular, compared to other methods, SemiBin returns more high-quality bins with larger taxonomic diversity, including more distinct genera and species.}, } @article {pmid35483672, year = {2022}, author = {Malmstrom, CM and Martin, MD and Gagnevin, L}, title = {Exploring the Emergence and Evolution of Plant Pathogenic Microbes Using Historical and Paleontological Sources.}, journal = {Annual review of phytopathology}, volume = {60}, number = {}, pages = {187-209}, doi = {10.1146/annurev-phyto-021021-041830}, pmid = {35483672}, issn = {1545-2107}, mesh = {Animals ; Archaea ; Bacteria ; *Fungi ; Humans ; *Microbiota ; Plants ; }, abstract = {Biotechnological advances now permit broad exploration of past microbial communities preserved in diverse substrates. Despite biomolecular degradation, high-throughput sequencing of preserved materials can yield invaluable genomic and metagenomic data from the past. This line of research has expanded from its initial human- and animal-centric foci to include plant-associated microbes (viruses, archaea, bacteria, fungi, and oomycetes), for which historical, archaeological, and paleontological data illuminate past epidemics and evolutionary history. Genetic mechanisms underlying the acquisition of microbial pathogenicity, including hybridization, polyploidization, and horizontal gene transfer, can now be reconstructed, as can gene-for-gene coevolution with plant hosts. Epidemiological parameters, such as geographic origin and range expansion, can also be assessed. Building on published case studies with individual phytomicrobial taxa, the stage is now set for broader, community-wide studies of preserved plant microbiomes to strengthen mechanistic understanding of microbial interactions and plant disease emergence.}, } @article {pmid35483363, year = {2022}, author = {Lancaster, SM and Lee-McMullen, B and Abbott, CW and Quijada, JV and Hornburg, D and Park, H and Perelman, D and Peterson, DJ and Tang, M and Robinson, A and Ahadi, S and Contrepois, K and Hung, CJ and Ashland, M and McLaughlin, T and Boonyanit, A and Horning, A and Sonnenburg, JL and Snyder, MP}, title = {Global, distinctive, and personal changes in molecular and microbial profiles by specific fibers in humans.}, journal = {Cell host & microbe}, volume = {30}, number = {6}, pages = {848-862.e7}, pmid = {35483363}, issn = {1934-6069}, support = {P30 DK020579/DK/NIDDK NIH HHS/United States ; R01 AT010232/AT/NCCIH NIH HHS/United States ; }, mesh = {Bifidobacterium ; Bile Acids and Salts ; Cholesterol ; *Dietary Fiber/metabolism ; Humans ; *Inulin/metabolism ; }, abstract = {Dietary fibers act through the microbiome to improve cardiovascular health and prevent metabolic disorders and cancer. To understand the health benefits of dietary fiber supplementation, we investigated two popular purified fibers, arabinoxylan (AX) and long-chain inulin (LCI), and a mixture of five fibers. We present multiomic signatures of metabolomics, lipidomics, proteomics, metagenomics, a cytokine panel, and clinical measurements on healthy and insulin-resistant participants. Each fiber is associated with fiber-dependent biochemical and microbial responses. AX consumption associates with a significant reduction in LDL and an increase in bile acids, contributing to its observed cholesterol reduction. LCI is associated with an increase in Bifidobacterium. However, at the highest LCI dose, there is increased inflammation and elevation in the liver enzyme alanine aminotransferase. This study yields insights into the effects of fiber supplementation and the mechanisms behind fiber-induced cholesterol reduction, and it shows effects of individual, purified fibers on the microbiome.}, } @article {pmid35482530, year = {2022}, author = {Du, Y and Sun, F}, title = {HiFine: integrating Hi-C-based and shotgun-based methods to refine binning of metagenomic contigs.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {11}, pages = {2973-2979}, pmid = {35482530}, issn = {1367-4811}, support = {R01 GM120624/GM/NIGMS NIH HHS/United States ; R01 GM131407/GM/NIGMS NIH HHS/United States ; }, mesh = {*Ecosystem ; *Metagenomics/methods ; Metagenome ; Cluster Analysis ; Genome, Microbial ; Algorithms ; Sequence Analysis, DNA/methods ; }, abstract = {MOTIVATION: Metagenomic binning aims to retrieve microbial genomes directly from ecosystems by clustering metagenomic contigs assembled from short reads into draft genomic bins. Traditional shotgun-based binning methods depend on the contigs' composition and abundance profiles and are impaired by the paucity of enough samples to construct reliable co-abundance profiles. When applied to a single sample, shotgun-based binning methods struggle to distinguish closely related species only using composition information. As an alternative binning approach, Hi-C-based binning employs metagenomic Hi-C technique to measure the proximity contacts between metagenomic fragments. However, spurious inter-species Hi-C contacts inevitably generated by incorrect ligations of DNA fragments between species link the contigs from varying genomes, weakening the purity of final draft genomic bins. Therefore, it is imperative to develop a binning pipeline to overcome the shortcomings of both types of binning methods on a single sample.

RESULTS: We develop HiFine, a novel binning pipeline to refine the binning results of metagenomic contigs by integrating both Hi-C-based and shotgun-based binning tools. HiFine designs a strategy of fragmentation for the original bin sets derived from the Hi-C-based and shotgun-based binning methods, which considerably increases the purity of initial bins, followed by merging fragmented bins and recruiting unbinned contigs. We demonstrate that HiFine significantly improves the existing binning results of both types of binning methods and achieves better performance in constructing species genomes on publicly available datasets. To the best of our knowledge, HiFine is the first pipeline to integrate different types of tools for the binning of metagenomic contigs.

HiFine is available at https://github.com/dyxstat/HiFine.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid35482264, year = {2022}, author = {Paranhos, AGO and Pereira, AR and da Fonseca, YA and de Queiroz Silva, S and de Aquino, SF}, title = {Tylosin in anaerobic reactors: degradation kinetics, effects on methane production and on the microbial community.}, journal = {Biodegradation}, volume = {33}, number = {3}, pages = {283-300}, pmid = {35482264}, issn = {1572-9729}, support = {2510001557612017-21//National Health Fundation - FUNASA/ ; 423101/2018-8//Conselho Nacional de Desenvolvimento Científico e Tecnológico/ ; APQ-02701-18//Fundação de Amparo à Pesquisa do Estado de Minas Gerais/ ; }, mesh = {Anaerobiosis ; Biodegradation, Environmental ; Bioreactors/microbiology ; Kinetics ; Methane/metabolism ; *Microbiota ; *Tylosin/pharmacology ; }, abstract = {Tylosin eliminated in animal waste, during therapeutic treatment, can be efficiently removed in anaerobic systems. The present study investigated the influence of tylosin concentration and assessed its degradation kinetics and the microorganisms involved in each stage of its anaerobic digestion (hydrolysis/acidogenesis; acetogenesis; methanogenesis). The results showed a stimulating effect on methane production with increasing tylosin concentration in the poultry litter up to 80 mg kg[-1] tylosin (232.9 NL CH4 kg SV[-1]). As for tylosin degradation, greater removal of antibiotics was observed in the methanogenic phase (88%), followed by acetogenic (84%) and hydrolytic/acidogenic (76%) phases. The higher rate of tylosin degradation obtained in the methanogenic step, is mainly related to the co-metabolic effect exerted by the presence of acetate and its degradation by acetoclastic methanogens. Indeed, metagenomic analyses suggested a syntrophic action between archaea of the genus Methanobacterium, and bacteria such as Clostridium and Flexilinea, which seemed decisive for tylosin degradation.}, } @article {pmid35481370, year = {2022}, author = {Zhang, D and Yang, X and Wang, J and Xu, J and Wang, M}, title = {Application of metagenomic next-generation sequencing for bronchoalveolar lavage diagnostics in patients with lower respiratory tract infections.}, journal = {The Journal of international medical research}, volume = {50}, number = {4}, pages = {3000605221089795}, pmid = {35481370}, issn = {1473-2300}, mesh = {Bronchoalveolar Lavage Fluid ; High-Throughput Nucleotide Sequencing/methods ; Humans ; *Metagenomics/methods ; *Respiratory Tract Infections/diagnosis ; Sensitivity and Specificity ; }, abstract = {OBJECTIVE: Metagenomic next-generation sequencing (mNGS) has the potential to overcome the shortcomings of traditional culture methods. This study aimed to assess the diagnostic value of mNGS in patients with lower respiratory tract infections (LRTIs).

METHODS: This retrospective observational study sequentially enrolled 47 patients with LRTIs admitted to Shenzhen Hospital of Southern Medical University between February 2019 and November 2020. Pathogens in bronchoalveolar lavage fluid (BALF) samples were investigated to compare diagnoses by mNGS with culture methods.

RESULTS: Compared with culture methods, mNGS had a diagnostic sensitivity of 80% and a specificity of 35.13% with an agreement rate of 44.68% between these two methods. mNGS significantly increased the pathogen detection rate.

CONCLUSIONS: mNGS may show some advantages in identifying a wide range of LRTI pathogens, improving the sensitivity for viruses and atypical pathogens. The clinical application of NGS technology is worth looking forward to.}, } @article {pmid35480975, year = {2022}, author = {Mesbah, NM}, title = {Industrial Biotechnology Based on Enzymes From Extreme Environments.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {870083}, pmid = {35480975}, issn = {2296-4185}, abstract = {Biocatalysis is crucial for a green, sustainable, biobased economy, and this has driven major advances in biotechnology and biocatalysis over the past 2 decades. There are numerous benefits to biocatalysis, including increased selectivity and specificity, reduced operating costs and lower toxicity, all of which result in lower environmental impact of industrial processes. Most enzymes available commercially are active and stable under a narrow range of conditions, and quickly lose activity at extremes of ion concentration, temperature, pH, pressure, and solvent concentrations. Extremophilic microorganisms thrive under extreme conditions and produce robust enzymes with higher activity and stability under unconventional circumstances. The number of extremophilic enzymes, or extremozymes, currently available are insufficient to meet growing industrial demand. This is in part due to difficulty in cultivation of extremophiles in a laboratory setting. This review will present an overview of extremozymes and their biotechnological applications. Culture-independent and genomic-based methods for study of extremozymes will be presented.}, } @article {pmid35480974, year = {2022}, author = {Wu, X and Kong, L and Pan, J and Feng, Y and Liu, S}, title = {Metagenomic Approaches to Explore the Quorum Sensing-Mediated Interactions Between Algae and Bacteria in Sequence Membrane Photo-Bioreactors.}, journal = {Frontiers in bioengineering and biotechnology}, volume = {10}, number = {}, pages = {851376}, pmid = {35480974}, issn = {2296-4185}, abstract = {Algal-bacterial water treatment is more effective for better harvesting and promotes energy savings than other traditional treatments, while the relationships between them are multifarious. Among all the interactions, quorum sensing plays an essential ecological role. However, the relative contributions of signaling in the interaction between algae and bacteria are not clear. To elucidate the role of quorum sensing by indole-3-acetic acid (IAA) in terms of the algal-bacterial interaction during the nitrogen removal process, the bioreactors, respectively, inoculated with Chlorella, Phormidium, and both of them were started. We manifest the existence of multiple signaling-related proteins by alignment with the constructed database, and the signaling was analyzed using metagenomic sequence data obtained during bioreactor operation. We found that IAA was mainly synthetized depending on indole-3-acetamide (IAM) and indole-3-pyruvic acid (IPA) pathways by calculating the gene abundance of IAA synthetase. Both Chlorella and the co-culture reactor possessed higher nitrogen removal rate (NRR) than the Phormidium reactor, and the abundance profile of the signaling-related gene is similar with the NRR. The signaling-related gene abundance increased in Chlorella and co-culture reactors but decreased in the Phormidium reactor. Pseudomonas, Hydrogenophaga, and Zoogloea are the dominant signaled bacteria. Chlorella is the dominant signaled algae. The relative abundance of total signaled bacteria in the whole bacterial community increased during the start-up in Chlorella and co-culture reactors. According to the network analysis, phytoplankton prefers to positively correlate with signaled bacteria than non-signaled bacteria, which indicated that the signaling influences the algal-bacterial interaction. These findings hint at the significance of algal-bacterial signaling in this interkingdom interaction during nitrogen removal.}, } @article {pmid35479945, year = {2022}, author = {Cui, Q and Dai, H and Wu, D and He, J and Xu, Y and Tang, X and Xu, J}, title = {Case Report: A Case of Acute T Lymphoblastic Leukemia With Mixed Infection of Lethal Invasive Mucormycosis and Multi-Drug Resistant Bacteria.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {854338}, pmid = {35479945}, issn = {2296-858X}, abstract = {Pulmonary mucormycosis (PM) is a rare and life-threatening fungal infection. Here, we report a case of an acute T lymphoblastic leukemia patient with mixed infections of lethal invasive Mucormycosis and multi-drug resistant (MDR) bacteria. After receiving anti-infection drugs to control the patient's fever, he was treated with induction chemotherapy. However, the malignant hematological disease was poorly controlled by the chemotherapy and the patient developed more symptoms of infection. Although the results of multiple β-D-Glucan (G) and Galactomannan (GM) tests remained negative, several pathogens were detected using metagenomic next-generation sequencing (mNGS). In particular, mNGS identified Malassezia pachydermum, Mucor racemosus, and Lauteria mirabilis in the peripheral blood and local secretion samples. The Mucor and bacterial infections were further confirmed via multi-site and repeated fungal and bacterial cultures, respectively. Despite adjusting the anti-infection therapy according to the diagnostic results, the patient's blood disease and symptoms of infection were not alleviated. Additionally, the MDR Acinetobacter baumannii infection/colonization was not confirmed until the seventh culture of the peripheral venous catheter tip. Due to the patient's deteriorating conditions, his family decided to withdraw him from further treatment. Overall, mNGS can facilitate a diagnosis of Mucormycosis by providing clinical and therapeutic information to support conventional diagnostic approaches. For the early and timely diagnosis and treatment of PM, it is also necessary to consider the malignant hematological conditions and repeated tests through multiple detection methods.}, } @article {pmid35477737, year = {2022}, author = {Wang, H and Yang, GX and Hu, Y and Lam, P and Sangha, K and Siciliano, D and Swenerton, A and Miller, R and Tilley, P and Von Dadelszen, P and Kalyan, S and Tang, P and Patel, MS}, title = {Comprehensive human amniotic fluid metagenomics supports the sterile womb hypothesis.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6875}, pmid = {35477737}, issn = {2045-2322}, support = {130494//CIHR/Canada ; }, mesh = {Amniotic Fluid ; Female ; Humans ; Metagenomics ; *Microbiota/genetics ; *Nucleic Acids ; Uterus ; }, abstract = {As metagenomic approaches for detecting infectious agents have improved, each tissue that was once thought to be sterile has been found to harbor a variety of microorganisms. Controversy still exists over the status of amniotic fluid, which is part of an immunologically privileged zone that is required to prevent maternal immune system rejection of the fetus. Due to this privilege, the exclusion of microbes has been proposed to be mandatory, leading to the sterile womb hypothesis. Since nucleic acid yields from amniotic fluid are very low, contaminating nucleic acid found in water, reagents and the laboratory environment frequently confound attempts to address this hypothesis. Here we present metagenomic criteria for microorganism detection and a metagenomic method able to be performed with small volumes of starting material, while controlling for exogenous contamination, to circumvent these and other pitfalls. We use this method to show that human mid-gestational amniotic fluid has no detectable virome or microbiome, supporting the sterile womb hypothesis.}, } @article {pmid35477306, year = {2022}, author = {Kwan, SY and Sabotta, CM and Joon, A and Wei, P and Petty, LE and Below, JE and Wu, X and Zhang, J and Jenq, RR and Hawk, ET and McCormick, JB and Fisher-Hoch, SP and Beretta, L}, title = {Gut Microbiome Alterations Associated with Diabetes in Mexican Americans in South Texas.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0003322}, pmid = {35477306}, issn = {2379-5077}, support = {P30 CA016672/CA/NCI NIH HHS/United States ; P50 CA217674/CA/NCI NIH HHS/United States ; UL1 TR000371/TR/NCATS NIH HHS/United States ; UL1 TR003167/TR/NCATS NIH HHS/United States ; }, mesh = {Humans ; Butyrates ; *Diabetes Mellitus, Type 2/epidemiology ; Enterobacteriaceae ; *Gastrointestinal Microbiome/genetics ; Mexican Americans/genetics ; Prospective Studies ; Texas/ethnology ; }, abstract = {Mexican Americans have a high prevalence of diabetes and burden of diabetes-related complications, highlighting the need for novel preventive strategies and noninvasive predictors of diabetes risk tailored to this population. Changes in the gut microbiome have the potential to predict diabetes. Here, we aimed to identify alterations in the gut microbiome associated with diabetes in the high-risk population of Mexican Americans in South Texas. Stool samples were collected from 216 subjects from the population-based Cameron County Hispanic Cohort. Among them, 75 had type 2 diabetes. Taxonomic and functional profiling of the stool samples were assessed by 16S and shotgun metagenomic sequencing, and the influence of genetic factors was explored. The gut microbiome of subjects with diabetes was enriched with proinflammatory Proteobacteria members (Enterobacteriaceae, Escherichia-Shigella) and depleted of butyrate-producing Clostridiales members (Faecalibacterium prausnitzii, Peptostreptococcaceae, and Clostridium sensu stricto 1). The accompanying metagenomic changes in subjects with diabetes suggested dysregulated amino acid metabolism, reduced galacturonate and glucuronate catabolism (correlating with Faecalibacterium prausnitzii abundance), and enriched heme biosynthesis (correlating with Enterobacteriaceae abundance). Polymorphism rs7129790 near MMP27 was strongly associated with high Proteobacteria abundance and was more frequent in this cohort and in individuals of Mexican ancestry than in Europeans. In conclusion, Mexican Americans in South Texas with diabetes display distinct gut microbiome and metagenomic signatures. These signatures may have utility in risk modeling and disease prevention in this high-risk population. IMPORTANCE The gut microbiome composition varies across ethnicities and geographical locations, yet studies on diabetes-associated microbiome changes specific to high-risk Mexican Americans are lacking. Here, we aimed to identify specific alterations associated with diabetes in this population, as well as host genetic factors that may explain increased disease susceptibility in this ethnic group. Using samples from a population-based cohort of Mexican Americans with a high prevalence of obesity and diabetes, we confirmed findings from studies on other ethnicities that suggested promotion of a chronic proinflammatory environment, loss of butyrate production, and compromised intestinal barrier integrity. High abundance of proinflammatory Proteobacteria was associated with a polymorphism that was more frequent in this cohort and in individuals of Mexican ancestry than in Europeans. Validation of microbiome-based risk models for diabetes should be evaluated in prospective cohort studies.}, } @article {pmid35477253, year = {2022}, author = {Gagliano, MC and Sampara, P and Plugge, CM and Temmink, H and Sudmalis, D and Ziels, RM}, title = {Functional Insights of Salinity Stress-Related Pathways in Metagenome-Resolved Methanothrix Genomes.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {10}, pages = {e0244921}, pmid = {35477253}, issn = {1098-5336}, mesh = {Anaerobiosis ; Bioreactors ; Ecosystem ; *Euryarchaeota/metabolism ; Metagenome ; Methane/metabolism ; Methanosarcinaceae/metabolism ; Salinity ; Salt Stress ; *Sewage ; Waste Disposal, Fluid ; }, abstract = {Recently, methanogenic archaea belonging to the genus Methanothrix were reported to have a fundamental role in maintaining stable ecosystem functioning in anaerobic bioreactors under different configurations/conditions. In this study, we reconstructed three Methanothrix metagenome-assembled genomes (MAGs) from granular sludge collected from saline upflow anaerobic sludge blanket (UASB) reactors, where Methanothrix harundinacea was previously implicated with the formation of compact and stable granules under elevated salinity levels (up to 20 g/L Na[+]). Genome annotation and pathway analysis of the Methanothrix MAGs revealed a genetic repertoire supporting their growth under high salinity. Specifically, the most dominant Methanothrix (MAG_279), classified as a subspecies of Methanothrix_A harundinacea_D, had the potential to augment its salinity resistance through the production of different glycoconjugates via the N-glycosylation process, and via the production of compatible solutes as N[ε]-acetyl-β-lysine and ectoine. The stabilization and reinforcement of the cell membrane via the production of isoprenoids was identified as an additional stress-related pathway in this microorganism. The improved understanding of the salinity stress-related mechanisms of M. harundinacea highlights its ecological niche in extreme conditions, opening new perspectives for high-efficiency methanisation of organic waste at high salinities, as well as the possible persistence of this methanogen in highly-saline natural anaerobic environments. IMPORTANCE Using genome-centric metagenomics, we discovered a new Methanothrix harundinacea subspecies that appears to be a halotolerant acetoclastic methanogen with the flexibility for adaptation in the anaerobic digestion process both at low (5 g/L Na[+]) and high salinity conditions (20 g/L Na[+]). Annotation of the recovered M. harundinacea genome revealed salinity stress-related functions, including the modification of EPS glycoconjugates and the production of compatible solutes. This is the first study reporting these genomic features within a Methanothrix sp., a milestone further supporting previous studies that identified M. harundinacea as a key-driver in anaerobic granulation under high salinity stress.}, } @article {pmid35477134, year = {2022}, author = {Kairmi, SH and Taha-Abdelaziz, K and Yitbarek, A and Sargolzaei, M and Spahany, H and Astill, J and Shojadoost, B and Alizadeh, M and Kulkarni, RR and Parkinson, J and Sharif, S}, title = {Effects of therapeutic levels of dietary antibiotics on the cecal microbiome composition of broiler chickens.}, journal = {Poultry science}, volume = {101}, number = {6}, pages = {101864}, pmid = {35477134}, issn = {1525-3171}, mesh = {Animal Feed/analysis ; Animals ; Anti-Bacterial Agents/pharmacology/therapeutic use ; Bacteria ; Cecum/microbiology ; Chickens ; Diet/veterinary ; Dietary Supplements/analysis ; *Enteritis/veterinary ; *Microbiota ; }, abstract = {Dietary antibiotics, including antibiotic growth promoters (AGPs), have been commonly used to improve health and growth of poultry. The present study investigated the effects of therapeutic doses of dietary antibiotics, including bacitracin methylene disalicylate (BMD), penicillin G potassium (PP) and an ionophore (salinomycin, SA), on the cecal microbiome of chickens. BMD and SA treatments were given as dietary supplements from d 1 to 35 of age. The SAPP (salinomycin+ penicillin G potassium) group was given SA as a dietary supplement from d 1 to 35 of age and PP was added to drinking water from d 19 to 24 of age to simulate common practices for control of necrotic enteritis in broilers. The cecal contents were collected from all treatment groups on d 10, 24, and 35 of age and DNA was extracted for metagenomic analysis of the cecal microbiome. The results revealed that dietary or water supplementation of therapeutic levels of antibiotics and ionophores to chickens significantly altered the cecal microbial homeostasis during different stages of the chicken life. The alpha diversity analysis showed that BMD, SA, and SAPP treatments decreased diversity and evenness of the cecal microbiome of treated chickens on d 10 of age. Species richness was also reduced on d 35 following treatment with BMD. Beta diversity analyses revealed that SAPP and BMD induced significant changes in the relative abundance of Gram-positive and -negative bacteria on d 10, while no significant differences were observed on d 24. On d 35, the non-treated control group had higher relative abundance of unclassified Gram-positive and -negative bacteria compared to SA, SAPP, and BMD treatment groups. Overall, despite their beneficial role in controlling necrotic enteritis outbreaks, the findings of this study highlight the potential negative effects of dietary supplementation of therapeutic levels of antibiotics on the gut microbiome and suggest that adjusting gut bacteria may be required to restore microbial richness and diversity of the gut microbiome following treatment with these antibiotics.}, } @article {pmid35477064, year = {2022}, author = {Zhang, Z and Ping, Q and Guo, W and Cai, C and Li, Y}, title = {A novel approach using protein-rich biomass as co-fermentation substrates to enhance phosphorus recovery from FePs-bearing sludge.}, journal = {Water research}, volume = {218}, number = {}, pages = {118479}, doi = {10.1016/j.watres.2022.118479}, pmid = {35477064}, issn = {1879-2448}, mesh = {Animals ; Biomass ; Cysteine/metabolism ; Fatty Acids, Volatile/metabolism ; Fermentation ; Hydrogen-Ion Concentration ; *Phosphorus ; Proteins ; *Sewage/chemistry ; Sulfides ; }, abstract = {A novel approach for the enhancement of phosphorus (P) recovery from Fe bound P compounds (FePs)-bearing sludge by co-fermentation with protein-rich biomass (PRB) is reported. Four PRBs (silkworm chrysalis meal, fish meal, corn gluten meal, and soya bean meal) were used for co-fermentation. The results revealed that PRBs with strong surface hydrophobicity and loose structure favored the hydrolysis and acidogenesis processes. Sulfide produced by PRB could react with FePs to form FeS and promote P release. Due to the neutralization of volatile fatty acids (VFAs) by a relatively high concentration of ammonia, the pH was maintained near neutral and thus prevented the dissolution of metal ions (e.g., Fe and Ca). This was beneficial to save the cost of subsequent P recovery and form high-purity struvite. Compared with the control, the soluble orthophosphate and VFAs increased by 88.3% and 531.3%, respectively, in the co-fermentation system with silkworm chrysalis meal. Cysteine was the important intermediate. The metagenomics analysis indicated that the gene abundances of phosphate acetyltransferase and acetate kinase, which were key enzymes in the acetate metabolism, increased by 117.7% and 52.2%, respectively. The gene abundances of serine O-acetyltransferase and cysteine synthase increased by 63.4% and 54.4%, respectively. Cysteine was primarily transformed to pyruvate and sulfide. This study provides an environment-friendly strategy to simultaneously recover P and VFAs resources from FePs-bearing sludge and PRB waste.}, } @article {pmid35476949, year = {2022}, author = {Trutschel, LR and Chadwick, GL and Kruger, B and Blank, JG and Brazelton, WJ and Dart, ER and Rowe, AR}, title = {Investigation of microbial metabolisms in an extremely high pH marine-like terrestrial serpentinizing system: Ney Springs.}, journal = {The Science of the total environment}, volume = {836}, number = {}, pages = {155492}, doi = {10.1016/j.scitotenv.2022.155492}, pmid = {35476949}, issn = {1879-1026}, mesh = {Hydrogen ; Hydrogen-Ion Concentration ; *Methane ; Oxidation-Reduction ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; Sulfates ; Sulfides ; *Sulfur ; }, abstract = {Ney Springs, a continental serpentinizing spring in northern California, has an exceptionally high reported pH (12.4) for a naturally occurring water source. With high conductivity fluids, it is geochemically more akin to marine serpentinizing systems than other terrestrial locations. Our geochemical analyses also revealed high sulfide concentrations (544 mg/L) and methane emissions (83% volume gas content) relative to other serpentinizing systems. Thermodynamic calculations were used to investigate the potential for substrates resulting from serpentinization to fuel microbial life, and were found to support the energetic feasibility of sulfate reduction, anaerobic methane oxidation, denitrification, and anaerobic sulfide oxidation within this system. Assessment of the microbial community via 16S rRNA taxonomic gene surveys and metagenome sequencing revealed a community composition dominated by poorly characterized members of the Izemoplasmatales and Clostridiales. The genomes of these dominant taxa point to a fermentative lifestyle, though other highly complete (>90%) metagenome assembled genomes support the potential for organisms to perform sulfate reduction, sulfur disproportionation and/or sulfur oxidation (aerobic and anaerobic). Two chemolithoheterotrophs identified in the metagenome, a Halomonas sp. and a Rhodobacteraceae sp., were isolated and shown to oxidize thiosulfate and were capable of growth in conditions up to pH 12.4. Despite being characteristic products of serpentinization reactions, little evidence was seen for hydrogen and methane utilization in the Ney Springs microbial community. Hydrogen is not highly abundant and could be consumed prior to reaching the spring community. Other metabolic strategies may be outcompeted by more energetically favorable heterotrophic or fermentation reactions, or even inhibited by other compounds in the spring such as ammonia. The unique geochemistry of Ney Springs provides an opportunity to study how local geology interacts with serpentinized fluids, while its microbial community can better inform us of the metabolic strategies employed in hyperalkaline environments.}, } @article {pmid35476894, year = {2022}, author = {Lee, CC and Liang, F and Lee, IC and Lu, TH and Shan, YY and Jeng, CF and Zou, YF and Yu, HT and Chen Alen, SK}, title = {External light-dark cycle shapes gut microbiota through intrinsically photosensitive retinal ganglion cells.}, journal = {EMBO reports}, volume = {23}, number = {6}, pages = {e52316}, pmid = {35476894}, issn = {1469-3178}, mesh = {Animals ; Circadian Rhythm ; *Gastrointestinal Microbiome ; Light ; Mice ; Photoperiod ; RNA, Ribosomal, 16S/metabolism ; *Retinal Ganglion Cells/metabolism ; Rod Opsins/genetics/metabolism ; }, abstract = {Gut microbiota are involved in many physiological functions such as metabolism, brain development, and neurodegenerative diseases. Many microbes in the digestive tract do not maintain a constant level of their relative abundance but show daily oscillations under normal conditions. Recent evidence indicates that chronic jetlag, constant darkness, or deletion of the circadian core gene can alter the composition of gut microbiota and dampen the daily oscillation of gut microbes. However, the neuronal circuit responsible for modulating gut microbiota remained unclear. Using genetic mouse models and 16s rRNA metagenomic analysis, we find that light-dark cycle information transmitted by the intrinsically photosensitive retinal ganglion cells (ipRGCs) is essential for daily oscillations of gut microbes under temporal restricted high-fat diet conditions. Furthermore, aberrant light exposure such as dim light at night (dLAN) can alter the composition, relative abundance, and daily oscillations of gut microbiota. Together, our results indicate that external light-dark cycle information can modulate gut microbiota in the direction from the brain to the gut via the sensory system.}, } @article {pmid35476524, year = {2022}, author = {Norsigian, CJ and Danhof, HA and Brand, CK and Midani, FS and Broddrick, JT and Savidge, TC and Britton, RA and Palsson, BO and Spinler, JK and Monk, JM}, title = {Systems biology approach to functionally assess the Clostridioides difficile pangenome reveals genetic diversity with discriminatory power.}, journal = {Proceedings of the National Academy of Sciences of the United States of America}, volume = {119}, number = {18}, pages = {e2119396119}, pmid = {35476524}, issn = {1091-6490}, support = {U01 AI124290/AI/NIAID NIH HHS/United States ; U01 AI124316/AI/NIAID NIH HHS/United States ; F32 AI136404/AI/NIAID NIH HHS/United States ; R01 AI123278/AI/NIAID NIH HHS/United States ; P30 DK056338/DK/NIDDK NIH HHS/United States ; 1U01AI12429//HHS | NIH | National Institute of Allergy and Infectious Diseases (NIAID)/ ; T32 DK007664/DK/NIDDK NIH HHS/United States ; }, mesh = {Clostridioides ; *Clostridioides difficile/genetics ; *Cross Infection ; Genetic Variation ; Humans ; Systems Biology ; }, abstract = {Combatting Clostridioides difficile infections, a dominant cause of hospital-associated infections with incidence and resulting deaths increasing worldwide, is complicated by the frequent emergence of new virulent strains. Here, we employ whole-genome sequencing, high-throughput phenotypic screenings, and genome-scale models of metabolism to evaluate the genetic diversity of 451 strains of C. difficile. Constructing the C. difficile pangenome based on this set revealed 9,924 distinct gene clusters, of which 2,899 (29%) are defined as core, 2,968 (30%) are defined as unique, and the remaining 4,057 (41%) are defined as accessory. We develop a strain typing method, sequence typing by accessory genome (STAG), that identifies 176 genetically distinct groups of strains and allows for explicit interrogation of accessory gene content. Thirty-five strains representative of the overall set were experimentally profiled on 95 different nutrient sources, revealing 26 distinct growth profiles and unique nutrient preferences; 451 strain-specific genome scale models of metabolism were constructed, allowing us to computationally probe phenotypic diversity in 28,864 unique conditions. The models create a mechanistic link between the observed phenotypes and strain-specific genetic differences and exhibit an ability to correctly predict growth in 76% of measured cases. The typing and model predictions are used to identify and contextualize discriminating genetic features and phenotypes that may contribute to the emergence of new problematic strains.}, } @article {pmid35475684, year = {2022}, author = {Rubin, IMC and Mollerup, S and Broholm, C and Knudsen, SB and Baker, A and Helms, M and Holm, MKA and Kallemose, T and Westh, H and Dahl Knudsen, J and Pinholt, M and Petersen, AM}, title = {No Effect of Lactobacillus rhamnosus GG on Eradication of Colonization by Vancomycin-Resistant Enterococcus faecium or Microbiome Diversity in Hospitalized Adult Patients.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0234821}, pmid = {35475684}, issn = {2165-0497}, mesh = {Adult ; Aged ; Child ; *Enterococcus faecium ; *Gram-Positive Bacterial Infections/drug therapy ; Humans ; *Lacticaseibacillus rhamnosus ; *Microbiota ; *Probiotics/therapeutic use ; Vancomycin/pharmacology/therapeutic use ; *Vancomycin-Resistant Enterococci ; }, abstract = {The purpose of this trial was to evaluate the efficacy of a 4-week supplementation of Lactobacillus rhamnosus GG (LGG) in eliminating the gastrointestinal carrier state of vancomycin-resistant Enterococcus faecium (VREfm) in hospitalized adults. The primary outcome of the study was the number of patients with cleared VREfm colonization after the 4-week intervention. Secondary outcomes were clearance of VREfm colonization at weeks 8, 16, and 24, number of VREfm infections (isolated from nonintestinal foci), and changes in fecal microbiome diversity after the intervention. The trial was a multicenter, randomized, double-blind, placebo-controlled trial in hospitalized adult VREfm carriers. Patients were enrolled and randomized to receive 60 billion CFU of LGG daily or placebo for 4 weeks. For a subgroup of patients, rectal swabs for VREfm were collected also at 8, 16, and 24 weeks and analyzed using shotgun metagenomics. Patients ingesting a minimum of 50% of the probiotic during the 4-week intervention were included in subsequent outcome analyses (48 of 81 patients). Twelve of 21 patients in the LGG group (57%) compared to 15 of 27 patients in the placebo group (56%) cleared their VREfm carriage. Eighteen patients completed the entire 24-week intervention with the same minimum compliancy. Of these, almost 90% in both groups cleared their VREfm carriage. We found a statistically significant difference between VREfm clearers and nonclearers regarding metronidazole and vancomycin usage as well as length of hospitalization after inclusion. The microbiome analyses revealed no significant difference in alpha diversity between the LGG and the placebo group. Beta diversity differed between the groups and the different time points. This study did not show an effect of LGG in eradication of VREfm after a 4-week intervention. IMPORTANCE Whereas other studies exploring the effect of L. rhamnosus in clearing VREfm from the intestine included children and adults, with a wider age range, our study consisted of a geriatric patient cohort. The natural clearance of VREfm in this study was almost 60% after 4 weeks, thus much higher than described previously. Also, this study characterizes the microbiome of VREfm patients in detail. This article showed no effect of the probiotic L. rhamnosus in clearing VREfm from the intestine of patients.}, } @article {pmid35475418, year = {2022}, author = {Colagrossi, L and Costabile, V and Scutari, R and Agosta, M and Onori, M and Mancinelli, L and Lucignano, B and Onetti Muda, A and Del Baldo, G and Mastronuzzi, A and Locatelli, F and Trua, G and Montanari, M and Alteri, C and Bernaschi, P and Perno, CF}, title = {Evidence of pediatric sepsis caused by a drug resistant Lactococcus garvieae contaminated platelet concentrate.}, journal = {Emerging microbes & infections}, volume = {11}, number = {1}, pages = {1325-1334}, pmid = {35475418}, issn = {2222-1751}, mesh = {Bayes Theorem ; Child ; Drug Resistance, Bacterial ; Humans ; *Lactococcus/classification/genetics ; Phylogeny ; Retrospective Studies ; *Sepsis/microbiology ; }, abstract = {Owing to an increasing number of infections in adults, Lactococcus (L.) garvieae has gained recognition as an emerging human pathogen, causing bacteraemia and septicaemia. In September 2020, four paediatric onco-hematologic patients received a platelet concentrate from the same adult donor at Bambino Gesù Children's Hospital IRCCS, Rome. Three of four patients experienced L. garvieae sepsis one day after transfusion. The L. garvieae pediatric isolates and the donor's platelet concentrates were retrospectively collected for whole-genome sequencing and shot-gun metagenomics, respectively (Illumina HiSeq). By de novo assembly of the L. garvieae genomes, we found that all three pediatric isolates shared a 99.9% identity and were characterized by 440 common SNPs. Plasmid pUC11C (conferring virulence properties) and the temperate prophage Plg-Tb25 were detected in all three strains. Core SNP genome-based maximum likelihood and Bayesian trees confirmed their phylogenetic common origin and revealed their relationship with L. garvieae strains affecting cows and humans (bootstrap values >100 and posterior probabilities = 1.00). Bacterial reads obtained by the donor's platelet concentrate have been profiled with MetaPhlAn2 (v.2.7.5); among these, 29.9% belonged to Firmicutes, and 5.16% to Streptococcaceae (>97% identity with L. garvieae), confirming the presence of L. garvieae in the platelet concentrate transfusion. These data showed three episodes of sepsis for the first time due to a transfusion-associated transmission of L. garvieae in three pediatric hospitalized hematology patients. This highlights the importance to implement the screening of platelet components with new human-defined pathogens for ensuring the safety of blood supply, and more broadly, for the surveillance of emerging pathogens.}, } @article {pmid35474894, year = {2021}, author = {Dickson, ZW and Hackenberger, D and Kuch, M and Marzok, A and Banerjee, A and Rossi, L and Klowak, JA and Fox-Robichaud, A and Mossmann, K and Miller, MS and Surette, MG and Golding, GB and Poinar, H}, title = {Probe design for simultaneous, targeted capture of diverse metagenomic targets.}, journal = {Cell reports methods}, volume = {1}, number = {6}, pages = {100069}, pmid = {35474894}, issn = {2667-2375}, support = {//CIHR/Canada ; }, mesh = {Humans ; *SARS-CoV-2/genetics ; *COVID-19 ; Metagenome ; Bacteria/genetics ; }, abstract = {The compounding challenges of low signal, high background, and uncertain targets plague many metagenomic sequencing efforts. One solution has been DNA capture, wherein probes are designed to hybridize with target sequences, enriching them in relation to their background. However, balancing probe depth with breadth of capture is challenging for diverse targets. To find this balance, we have developed the HUBDesign pipeline, which makes use of sequence homology to design probes at multiple taxonomic levels. This creates an efficient probe set capable of simultaneously and specifically capturing known and related sequences. We validated HUBDesign by generating probe sets targeting the breadth of coronavirus diversity, as well as a suite of bacterial pathogens often underlying sepsis. In separate experiments demonstrating significant, simultaneous enrichment, we captured SARS-CoV-2 and HCoV-NL63 in a human RNA background and seven bacterial strains in human blood. HUBDesign (https://github.com/zacherydickson/HUBDesign) has broad applicability wherever there are multiple organisms of interest.}, } @article {pmid35474146, year = {2022}, author = {Kanaujia, R and Biswal, M and Angrup, A and Ray, P}, title = {Diagnostic accuracy of the metagenomic next-generation sequencing (mNGS) for detection of bacterial meningoencephalitis: a systematic review and meta-analysis.}, journal = {European journal of clinical microbiology & infectious diseases : official publication of the European Society of Clinical Microbiology}, volume = {41}, number = {6}, pages = {881-891}, pmid = {35474146}, issn = {1435-4373}, mesh = {High-Throughput Nucleotide Sequencing/methods ; Humans ; *Infectious Encephalitis ; *Meningitis, Bacterial/cerebrospinal fluid ; *Meningoencephalitis/diagnosis ; Metagenomics/methods ; Prospective Studies ; Retrospective Studies ; Sensitivity and Specificity ; }, abstract = {The early diagnosis of bacterial meningoencephalitis (BM/E) is difficult, and delay in diagnosis can cause complications leading to neurological impairment/death. In cases of unexplained BM/E, the metagenomic NGS (mNGS) offers an advantage over conventional methods, especially when a rare pathogen is implicated or the patient is on antibiotics. This study aims to evaluate and compare the diagnostic efficacy of mNGS for the diagnosis of BM/E using cerebrospinal fluid (CSF) specimens versus a composite reference standard (CRS). The electronic databases (Embase, PubMed, and Web of Science) were searched up to 15 June 2021. Studies such as cohort, case-control, prospective, or retrospective studies that assessed the diagnostic efficacy of mNGS in suspected bacterial meningitis/encephalitis cases were included. Ten studies met the inclusion criteria, including three retrospective and seven prospective studies. The sensitivity of mNGS for diagnosis of BM/E from CSF samples ranged from 33 (95% CI: 13-62) to 98% (95% CI: 76-99). The specificity of mNGS ranged from 67 (95% CI: 55-78) to 98% (95% CI: 95-99). The estimated AUC (area under curve) by hierarchical summary receiver operating characteristic (HSROC) of the studies being analyzed was 0.912. The meta-regression analysis demonstrated that the different types of studies (single-center vs. multi-center) had an effect on the specificity of mNGS for BM/E compared with CRS (90% vs. 96%, meta-regression P < 0.05). The current analysis revealed moderate diagnostic accuracy of mNGS. This approach can be helpful, especially in cases of undiagnosed BM/E by identification of organism and subsequently accelerating the patient management.}, } @article {pmid35473973, year = {2022}, author = {S R, S and H P, S and Prakash, I and Khan, M and H N, PK and Om, H and Basavaraj, K and Murthy, PS}, title = {Microbial ecology and functional coffee fermentation dynamics with Pichia kudriavzevii.}, journal = {Food microbiology}, volume = {105}, number = {}, pages = {104012}, doi = {10.1016/j.fm.2022.104012}, pmid = {35473973}, issn = {1095-9998}, mesh = {*Coffee/chemistry ; Fermentation ; Flavoring Agents/metabolism ; *Pichia/metabolism ; Sugars ; }, abstract = {Specialty coffee can be developed by the application of explicit microorganisms or starters to obtain desired fermentation. In the present study, natural fermentation (NF) of Arabica coffee was carried out spontaneously, the other set was inoculated with Pichia kudriavzevii (Y) starter culture (isolated, identified and mass cultured). The effect of microbial fermentation, metagenomics, production of functional metabolites, volatiles and their sensorial aspects were studied. The bioprocess illustrated cohesive interface of coffee nutrients and microbial communities like Mycobacterium, Acinetobacter, Gordonia, etc., in NF, Lactobacillus and Leuconostoc were prevailing in Y. The Pichia and Rhodotorula dominated in both the groups. The bioactivity of bacteria and fungi induced complex changes in physicochemical features like pH (4.2-5.2), Brix° (9.5-3.0), and metabolic transition in sugar (3.0-0.7%), alcohol (1.4-2.7%), organic acids modulating flavour precursors and organoleptics in the final brew. In the roasted bean, Y exhibited higher sugar (42%), protein (25%), polyphenol (3.5%), CGA (2.5%), caffeine (17.2%), and trigonelline (2.8%) than NF. The volatile profile exhibited increased flavour molecules like furans, ketones, and pyrazines in Y, besides lactone complexes. The organoleptics in Y were highlighted with honey, malt and berry notes. P. kudriavzevii coffee fermentation could be beneficial in specialty coffee production and enhancement of distinct characteristic flavours.}, } @article {pmid35473500, year = {2022}, author = {Jiang, C and Sun, XR and Feng, J and Zhu, SF and Shui, W}, title = {Metagenomic analysis reveals the different characteristics of microbial communities inside and outside the karst tiankeng.}, journal = {BMC microbiology}, volume = {22}, number = {1}, pages = {115}, pmid = {35473500}, issn = {1471-2180}, mesh = {Humans ; Metagenome ; *Microbiota ; Nitrogen ; Soil/chemistry ; *Soil Microbiology ; }, abstract = {BACKGROUND: Karst tiankengs serve as a reservoir of biodiversity in the degraded karst landscape areas. However, the microbial diversity of karst tiankengs is poorly understood. Here, we investigated the composition and function of the microbial community in a karst tiankeng.

RESULTS: We found that habitat differences inside and outside the karst tiankeng changed the composition and structure of the soil microbial communities, and the dominant phyla were Proteobacteria, Actinobacteria, Chloroflexi and Acidobacteria. The Shannon-Wiener diversity of microbial communities inside and outside the tiankeng was significantly different, and it was higher inside the tiankeng (IT). Venn and LEfSe analysis found that the soil microbial communities inside the tiankeng had 640 more endemic species and 39 more biomarker microbial clades than those identified outside of the tiankeng (OT)..Functional prediction indicated that soil microorganisms in outside the tiankeng had a high potential for carbohydrate metabolism, translation and amino acid metabolism. There were biomarker pathways associated with several of human diseases at both IT and OT sites. Except for auxiliary activities (AA), other CAZy classes had higher abundance at IT sites, which can readily convert litter and fix carbon and nitrogen, thereby supporting the development of underground forests. The differences in microbial communities were mainly related to the soil water content and soil total nitrogen.

CONCLUSIONS: Our results provide a metagenomic overview of the karst tiankeng system and provide new insights into habitat conservation and biodiversity restoration in the area.}, } @article {pmid35473493, year = {2022}, author = {Tsang, HF and Yu, ACS and Jin, N and Yim, AKY and Leung, WMS and Lam, KW and Cho, WCS and Chiou, J and Wong, SCC}, title = {The clinical application of metagenomic next-generation sequencing for detecting pathogens in bronchoalveolar lavage fluid: case reports and literature review.}, journal = {Expert review of molecular diagnostics}, volume = {22}, number = {5}, pages = {575-582}, doi = {10.1080/14737159.2022.2071607}, pmid = {35473493}, issn = {1744-8352}, mesh = {Bronchoalveolar Lavage Fluid/microbiology ; *Communicable Diseases/diagnosis ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenome ; *Metagenomics/methods ; Sensitivity and Specificity ; }, abstract = {INTRODUCTION: Clinical metagenomic next-generation sequencing (mNGS) allows a comprehensive genetic analysis of microbial materials. Different from other traditional target-driven molecular diagnostic tests, such as PCR, mNGS is a hypothesis-free diagnostic approach that allows a comprehensive genetic analysis of the clinical specimens that cover nearly any common, rare, and new pathogens ranging broadly from viruses, bacteria, fungi to parasites.

AREAS COVERED: In this article, we discussed the clinical application of the mNGS using two clinical cases as examples and described the use of mNGS to assist the diagnosis of parasitic pulmonary infection. The advantages and challenges in implementing mNGS in clinical microbiology are also discussed.

EXPERT OPINION: mNGS is a promising technology that allows quick diagnosis of infectious diseases. Currently, a plethora of sequencing and analysis methods exists for mNGS, each with individual merits and pitfalls. While standards and best practices were proposed by various metagenomics working groups, they are yet to be widely adopted in the community. The development of a consensus set of guidelines is necessary to guide the usage of this new technology and the interpretation of NGS results before clinical adoption of mNGS testing.}, } @article {pmid35472747, year = {2022}, author = {Wang, Y and Zhuang, JL and Lu, QQ and Cui, CZ and Liu, YD and Ni, BJ and Li, W}, title = {Halophilic Martelella sp. AD-3 enhanced phenanthrene degradation in a bioaugmented activated sludge system through syntrophic interaction.}, journal = {Water research}, volume = {218}, number = {}, pages = {118432}, doi = {10.1016/j.watres.2022.118432}, pmid = {35472747}, issn = {1879-2448}, mesh = {*Alphaproteobacteria/metabolism ; Biodegradation, Environmental ; *Phenanthrenes/metabolism ; *Polycyclic Aromatic Hydrocarbons ; Sewage ; Wastewater/microbiology ; }, abstract = {Polycyclic aromatic hydrocarbons (PAHs) are a group of common recalcitrant pollutant in industrial saline wastewater that raised significant concerns, whereas traditional activated sludge (AS) has limited tolerance to high salinity and PAHs toxicity, restricting its capacity to degrade PAHs. It is therefore urgent to develop a bioaugmented sludge (BS) system to aid in the effective degradation of these types of compounds under saline condition. In this study, a novel bioaugmentation strategy was developed by using halophilic Martelella sp. AD-3 for effectively augmented phenanthrene (PHE) degradation under 3% salinity. It was found that a 0.5∼1.5% (w/w) ratio of strain AD-3 to activated sludge was optimal for achieving high PHE degradation activity of the BS system with degradation rates reaching 2.2 mg⋅gVSS[-1]⋅h[-1], nearly 25 times that of the AS system. Although 1-hydroxy-2-naphthoic acid (1H2N) was accumulated obviously, the mineralization of PHE was more complete in the BS system. Reads-based metagenomic coupled metatranscriptomic analysis revealed that the expression values of ndoB, encoding a dioxygenase associated with PHE ring-cleavage, was 5600-fold higher in the BS system than in the AS system. Metagenome assembly showed the members of the Corynebacterium and Alcaligenes genera were abundant in the strain AD-3 bioaugmented BS system with expression of 10.3±1.8% and 1.9±0.26%, respectively. Moreover, phdI and nahG accused for metabolism of 1H2N have been annotated in both above two genera. Degradation assays of intermediates of PHE confirmed that the activated sludge actually possessed considerable degradation capacity for downstream intermediates of PHE including 1H2N. The degradation capacity ratio of 1H2N to PHE was 87% in BS system, while it was 26% in strain AD-3. These results indicated that strain AD-3 contributed mainly in transforming PHE to 1H2N in BS system, while species in activated sludge utilized 1H2N as substrate to grow, thus establishing a syntrophic interaction with strain AD-3 and achieving the complete mineralization of PHE. Long-term continuous experiment confirmed a stable PHE removal efficiency of 93% and few 1H2N accumulation in BS SBR system. This study demonstrated an effective bioaugmented strategy for the bioremediation of saline wastewater containing PAHs.}, } @article {pmid35472485, year = {2022}, author = {Shi, H and Zheng, L and Qian, W and Zhou, Q}, title = {The utility of metagenomic next-generation sequencing in the identification of pathogens causing cervicofacial necrotizing fasciitis.}, journal = {Journal of stomatology, oral and maxillofacial surgery}, volume = {123}, number = {6}, pages = {e660-e662}, doi = {10.1016/j.jormas.2022.04.013}, pmid = {35472485}, issn = {2468-7855}, mesh = {Humans ; *Fasciitis, Necrotizing/diagnosis/etiology ; Neck ; High-Throughput Nucleotide Sequencing ; }, } @article {pmid35471044, year = {2022}, author = {Ikemura, N and Taminishi, S and Inaba, T and Arimori, T and Motooka, D and Katoh, K and Kirita, Y and Higuchi, Y and Li, S and Suzuki, T and Itoh, Y and Ozaki, Y and Nakamura, S and Matoba, S and Standley, DM and Okamoto, T and Takagi, J and Hoshino, A}, title = {An engineered ACE2 decoy neutralizes the SARS-CoV-2 Omicron variant and confers protection against infection in vivo.}, journal = {Science translational medicine}, volume = {14}, number = {650}, pages = {eabn7737}, pmid = {35471044}, issn = {1946-6242}, mesh = {*Angiotensin-Converting Enzyme 2 ; Animals ; Antibodies, Monoclonal, Humanized ; Antibodies, Neutralizing/therapeutic use ; Antibodies, Viral/therapeutic use ; BNT162 Vaccine ; *COVID-19/therapy ; Humans ; Immunization, Passive ; Mice ; Peptidyl-Dipeptidase A/chemistry/genetics/metabolism ; SARS-CoV-2 ; COVID-19 Serotherapy ; }, abstract = {The Omicron (B.1.1.529) SARS-CoV-2 variant contains an unusually high number of mutations in the spike protein, raising concerns of escape from vaccines, convalescent serum, and therapeutic drugs. Here, we analyzed the degree to which Omicron pseudo-virus evades neutralization by serum or therapeutic antibodies. Serum samples obtained 3 months after two doses of BNT162b2 vaccination exhibited 18-fold lower neutralization titers against Omicron than parental virus. Convalescent serum samples from individuals infected with the Alpha and Delta variants allowed similar frequencies of Omicron breakthrough infections. Domain-wise analysis using chimeric spike proteins revealed that this efficient evasion was primarily achieved by mutations clustered in the receptor binding domain but that multiple mutations in the N-terminal domain contributed as well. Omicron escaped a therapeutic cocktail of imdevimab and casirivimab, whereas sotrovimab, which targets a conserved region to avoid viral mutation, remains effective. Angiotensin-converting enzyme 2 (ACE2) decoys are another virus-neutralizing drug modality that are free, at least in theory, from complete escape. Deep mutational analysis demonstrated that an engineered ACE2 molecule prevented escape for each single-residue mutation in the receptor binding domain, similar to immunized serum. Engineered ACE2 neutralized Omicron comparably to the Wuhan strain and also showed a therapeutic effect against Omicron infection in hamsters and human ACE2 transgenic mice. Similar to previous SARS-CoV-2 variants, some sarbecoviruses showed high sensitivity against engineered ACE2, confirming the therapeutic value against diverse variants, including those that are yet to emerge.}, } @article {pmid35470946, year = {2022}, author = {Chen, G and Khan, IM and He, W and Li, Y and Jin, P and Campanella, OH and Zhang, H and Huo, Y and Chen, Y and Yang, H and Miao, M}, title = {Rebuilding the lid region from conformational and dynamic features to engineering applications of lipase in foods: Current status and future prospects.}, journal = {Comprehensive reviews in food science and food safety}, volume = {21}, number = {3}, pages = {2688-2714}, doi = {10.1111/1541-4337.12965}, pmid = {35470946}, issn = {1541-4337}, mesh = {Biotechnology ; *Enzymes, Immobilized ; *Lipase/chemistry/metabolism ; }, abstract = {The applications of lipases in esterification, amidation, and transesterification have broadened their potential in the production of fine compounds with high cumulative values. Mostly, the catalytic triad of lipases is covered by either one or two mobile peptides called the "lid" that control the substrate channel to the catalytic center. The lid holds unique conformational allostery via interfacial activation to regulate the dynamics and catalytic functions of lipases, thereby highlighting its importance in redesigning these enzymes for industrial applications. The structural characteristic of lipase, the dynamics of lids, and the roles of lid in lipase catalysis were summarized, providing opportunities for rebuilding lid region by biotechniques (e.g., metagenomic technology and protein engineering) and enzyme immobilization. The review focused on the advantages and disadvantages of strategies rebuilding the lid region. The main shortcomings of biotechnologies on lid rebuilding were discussed such as negative effects on lipase (e.g., a decrease of activity). Additionally, the main shortcomings (e.g., enzyme desorption at high temperatre) in immobilization on hydrophobic supports via interfacial action were presented. Solutions to the mentioned problems were proposed by combinations of computational design with biotechnologies, and improvements of lipase immobilization (e.g., immobilization protocols and support design). Finally, the review provides future perspectives about designing hyperfunctional lipases as biocatalysts in the food industry based on lid conformation and dynamics.}, } @article {pmid35470322, year = {2022}, author = {Ali, MJ}, title = {Microbial Metagenomics of the Extubated Lacrimal Stents Following Dacryocystorhinostomy: The Lacriome Paper 4.}, journal = {Ophthalmic plastic and reconstructive surgery}, volume = {38}, number = {6}, pages = {558-562}, doi = {10.1097/IOP.0000000000002202}, pmid = {35470322}, issn = {1537-2677}, mesh = {Humans ; *Dacryocystorhinostomy ; Prospective Studies ; Ecosystem ; Escherichia coli ; Stents/microbiology ; Bacteria ; }, abstract = {PURPOSE: To study the metagenome of the microbes present on the extubated lacrimal stents following a dacryocystorhinostomy.

METHODS: A prospective study was performed on 10 consecutive extubated lacrimal stents obtained for the metagenomic analysis from the patients following an endoscopic dacryocystorhinostomy. The stents were extubated at 4 weeks postoperatively under endoscopic guidance and immediately transported on ice to the laboratory. Following DNA extraction and library preparation, a whole shotgun metagenome sequencing was performed on the Illumina platform. The downstream processing and bioinformatics of the samples were performed using multiple software packaged in SqueezeMeta pipeline or MG-RAST pipeline.

RESULTS: The taxonomic hit distribution across the stent samples showed that bacteria were the most common isolates (mean, 69.70%), followed by viruses (mean, 0.02%) and archaea (0.003%). The 3 major phyla identified were Firmicutes, Actinobacteria, and Proteobacteria. The prevalent organisms include Pseudomonas aeruginosa, Staphylococcus aureus, Corynebacterium accolens, Dolosigranulum pigrum, Citrobacter koserii, Staphylococcus epidermidis, E. coli, and Hemophilus influenza . The functional subsystem profiling demonstrated microbial genes associated with metabolism, cellular, and information processing. The functional subsystem categories were metabolism involving carbohydrates, amino acids, DNA and RNA, cell wall or cell capsule biogenesis, membrane transport, virulence, and defense mechanisms.

CONCLUSIONS: The present study is the first whole metagenome sequencing of the microbes isolated from the extubated lacrimal stents. The stents harbor diverse microbial communities with distinct ecosystem dynamics. Further studies on microbes-host interactions in the early postoperative period would provide valuable insights.}, } @article {pmid35469423, year = {2022}, author = {Yin, J and Zhang, Z and Guo, Y and Chen, Y and Xu, Y and Chen, W and Shao, Y and Yu, Y and Zhu, L and Chen, L and Ruan, L}, title = {Precision Probiotics in Agroecosystems: Multiple Strategies of Native Soil Microbiotas for Conquering the Competitor Ralstonia solanacearum.}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0115921}, pmid = {35469423}, issn = {2379-5077}, mesh = {RNA, Ribosomal, 16S/genetics ; *Ralstonia solanacearum/genetics ; *Microbiota/genetics ; *Probiotics/pharmacology ; Soil ; *Solanum lycopersicum ; }, abstract = {Ralstonia solanacearum (Rs), a soilborne phytopathogen, causes bacterial wilt disease in a broad range of hosts. Common approaches, for example, the direct reduction of the pathogen using classic single broad-spectrum probiotics, suffer from poor colonization efficiency, interference by resident microbiota, and nonnative-microorganism invasion. The soil microbiota plays an important role in plant health. Revealing the intrinsic linkage between the microbiome and the occurrence of disease and then applying it to agroecosystems for the precise control of soilborne diseases should be an effective strategy. Here, we surveyed the differences in the microbiome between healthy and diseased soils used for tomato planting across six climatic regions in China by using 16S rRNA amplicon and metagenomic sequencing. The roles of species associated with disease symptoms were further validated. Healthy soil possessed more diverse bacterial communities and more potential plant probiotics than diseased soil. Healthy soil simultaneously presented multiple strategies, including specifically antagonizing Rs, decreasing the gene expression of the type III secretion system of Rs, and competing for nutrition with Rs. Bacteria enriched in diseased samples promoted the progression of tomato bacterial wilt by strengthening the chemotaxis of pathogens. Therefore, Rs and its collaborators should be jointly combatted for disease suppression. Our research provides integrated insights into a multifaceted strategy for the biocontrol of tomato bacterial wilt based on the individual network of local microbiota. IMPORTANCE In the current work, the relationship between the soil microbiota and tomato bacterial wilt on a large scale offered us a comprehensive understanding of the disease. The delicate strategy of the microbiota in soil used for growing tomatoes to conquer the strong competitor, Rs, was revealed by microbiome research. The collaborators of Rs that coexist in a common niche with Rs strengthened our understanding of the pathogenesis of bacterial wilt. Bacteria enriched in healthy soil that antagonized pathogens with high specificity provide a novel view for ecofriendly probiotics mining. Our study offers new perspectives on soilborne-pathogen biocontrol in agroecosystems by decoding the rule of the natural ecosystem.}, } @article {pmid35469377, year = {2022}, author = {Pathak, B and Khataniar, A and Das, B and Upadhyaya, S and Medhi, A and Bhuyan, PK and Buragohain, AK and Borah, D}, title = {Spatio-temporal diversity of biological aerosols over Northeast India: a metagenomic approach.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {42}, pages = {64096-64111}, pmid = {35469377}, issn = {1614-7499}, support = {ECR/2016/00132//Department of Science and Technology's Science and Engineering Research Board (DST-SERB), Govt. of India/ ; }, mesh = {Aerosols/analysis ; Bacteria/genetics ; *Environmental Monitoring ; India ; Metagenome ; Metagenomics ; *Particulate Matter ; Seasons ; }, abstract = {Northeast India is considered as one of the major biodiversity hotspots in the world, but the region is underexplored for their microbial biodiversity. Extensive characterization of biological aerosol (bioaerosol) samples collected from various locations of Northeast India was carried out for all four seasons in a year. These were characterized in terms of their constituents, such as pollens, fungal spores, animal debris, and non-biological components, and particulate matters, such as inhalable, thoracic, and alveolic, and finally, the bacterial diversity was determined by DNA-based metagenomic approach. The non-biological (non-viable) component of aerosols is found to vary from 30 to 89% in the pre-monsoon season, which coexists with pollens (4-20%), animal debris (1-24%), and fungal spores (1-17%). The highest number of culturable microbial populations in terms of CFU count was observed in the pre-monsoon samples (i.e., 125.24-632.45 CFU/m[3]), and the lowest CFU was observed in monsoon season (i.e., 20.83-319.0 CFU/m[3]). The metagenomic approach with the samples collected during pre-monsoon season showed a total of bacterial 184 OTUs (operational taxonomic units) with 28,028 abundance count comprising 7 major phylum, 6 classes, 10 orders, 15 families, 13 genus, and 8 species of bacteria. The species-level distribution clearly shows the presence of Gammaproteobacteria (52%) most abundantly, followed by Bacilli (21%), Alphaproteobacteria (14%), Betaproteobacteria (5%), Flavobacteria (5%), and Sphingobacteria (3%). It is the first report from the entire Northeast India to uncover spatio-temporal distribution of biological components and bacterial diversity in aerosol samples through a DNA-based metagenomic approach.}, } @article {pmid35469019, year = {2022}, author = {Rhodes, J and Abdolrasouli, A and Dunne, K and Sewell, TR and Zhang, Y and Ballard, E and Brackin, AP and van Rhijn, N and Chown, H and Tsitsopoulou, A and Posso, RB and Chotirmall, SH and McElvaney, NG and Murphy, PG and Talento, AF and Renwick, J and Dyer, PS and Szekely, A and Bowyer, P and Bromley, MJ and Johnson, EM and Lewis White, P and Warris, A and Barton, RC and Schelenz, S and Rogers, TR and Armstrong-James, D and Fisher, MC}, title = {Population genomics confirms acquisition of drug-resistant Aspergillus fumigatus infection by humans from the environment.}, journal = {Nature microbiology}, volume = {7}, number = {5}, pages = {663-674}, pmid = {35469019}, issn = {2058-5276}, support = {219551/Z/19/Z/WT_/Wellcome Trust/United Kingdom ; MR/N006364/2/MRC_/Medical Research Council/United Kingdom ; 097377/WT_/Wellcome Trust/United Kingdom ; /DH_/Department of Health/United Kingdom ; MR/V033417/1/MRC_/Medical Research Council/United Kingdom ; MR/R015600/1/MRC_/Medical Research Council/United Kingdom ; /WT_/Wellcome Trust/United Kingdom ; MR/V037315/1/MRC_/Medical Research Council/United Kingdom ; BB/M010996/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {*Anti-Infective Agents ; *Aspergillus fumigatus/genetics ; Azoles/pharmacology ; Drug Resistance, Fungal/genetics ; Humans ; Metagenomics ; Microbial Sensitivity Tests ; }, abstract = {Infections caused by the fungal pathogen Aspergillus fumigatus are increasingly resistant to first-line azole antifungal drugs. However, despite its clinical importance, little is known about how susceptible patients acquire infection from drug-resistant genotypes in the environment. Here, we present a population genomic analysis of 218 A. fumigatus isolates from across the UK and Ireland (comprising 153 clinical isolates from 143 patients and 65 environmental isolates). First, phylogenomic analysis shows strong genetic structuring into two clades (A and B) with little interclade recombination and the majority of environmental azole resistance found within clade A. Second, we show occurrences where azole-resistant isolates of near-identical genotypes were obtained from both environmental and clinical sources, indicating with high confidence the infection of patients with resistant isolates transmitted from the environment. Third, genome-wide scans identified selective sweeps across multiple regions indicating a polygenic basis to the trait in some genetic backgrounds. These signatures of positive selection are seen for loci containing the canonical genes encoding fungicide resistance in the ergosterol biosynthetic pathway, while other regions under selection have no defined function. Lastly, pan-genome analysis identified genes linked to azole resistance and previously unknown resistance mechanisms. Understanding the environmental drivers and genetic basis of evolving fungal drug resistance needs urgent attention, especially in light of increasing numbers of patients with severe viral respiratory tract infections who are susceptible to opportunistic fungal superinfections.}, } @article {pmid35468931, year = {2022}, author = {Jangid, A and Fukuda, S and Suzuki, Y and Taylor, TD and Ohno, H and Prakash, T}, title = {Shotgun metagenomic sequencing revealed the prebiotic potential of a grain-based diet in mice.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6748}, pmid = {35468931}, issn = {2045-2322}, mesh = {Animals ; Cellulose/pharmacology ; Diet ; Dietary Fiber/pharmacology ; Edible Grain ; Lactobacillus/genetics ; *Metagenome ; Metagenomics ; Mice ; *Prebiotics ; }, abstract = {In the present study, we elucidated the effect of grain-based (GB) diet containing both soluble and insoluble fibers and purified ingredients-based (PIB) diet containing only insoluble fiber, namely cellulose on mice gut microbiome using whole shotgun based metagenomic sequencing. Although the fiber content in both diet types is the same (5%) the presence of soluble fiber only in the GB diet differentiates it from the PIB diet. The taxonomic analysis of sequenced reads reveals a significantly higher enrichment of probiotic Lactobacilli in the GB group as compared to the PIB group. Further, the enhancement of energy expensive cellular processes namely, cell cycle control, cell division, chromosome partitioning, and transcription is observed in the GB group which could be due to the metabolization of the soluble fiber for faster energy production. In contrast, a higher abundance of cellulolytic bacterial community namely, the members of family Lachnospiraceae and Ruminococcaceae and the metabolism functions are found in the PIB group. The PIB group shows a significant increase in host-derived oligosaccharide metabolism functions indicating that they might first target the host-derived oligosaccharides and self-stored glycogen in addition to utilising the available cellulose. In addition to the beneficial microbial community variations, both the groups also exhibited an increased abundance of opportunistic pathobionts which could be due to an overall low amount of fiber in the diet. Furthermore, backtracing analysis identified probiotic members of Lactobacillus, viz., L. crispatus ST1, L. fermentum CECT 5716, L. gasseri ATCC 33323, L. johnsonii NCC 533 and L. reuteri 100-23 in the GB group, while Bilophila wadsworthia 3_1_6, Desulfovibrio piger ATCC 29098, Clostridium symbiosum WAL-14163, and Ruminococcaceae bacterium D16 in the PIB group. These data suggest that Lactobacilli, a probiotic community of microorganisms, are the predominant functional contributors in the gut of GB diet-fed mice, whereas pathobionts too coexisted with commensals in the gut microbiome of the PIB group. Thus at 5% fiber, GB modifies the gut microbial ecology more effectively than PIB and the inclusion of soluble fiber in the GB diet may be one of the primary factors responsible for this impact.}, } @article {pmid35468809, year = {2022}, author = {He, L and Huang, X and Zhang, G and Yuan, L and Shen, E and Zhang, L and Zhang, XH and Zhang, T and Tao, L and Ju, F}, title = {Distinctive signatures of pathogenic and antibiotic resistant potentials in the hadal microbiome.}, journal = {Environmental microbiome}, volume = {17}, number = {1}, pages = {19}, pmid = {35468809}, issn = {2524-6372}, support = {2018YFE0110500//national key research and development program of china/ ; 51908467//national natural science foundation of china/ ; 31970129//national natural science foundation of china/ ; 31800128//national natural science foundation of china/ ; LR20C010001//natural science foundation of zhejiang province/ ; }, abstract = {BACKGROUND: Hadal zone of the deep-sea trenches accommodates microbial life under extreme energy limitations and environmental conditions, such as low temperature, high pressure, and low organic matter down to 11,000 m below sea level. However, microbial pathogenicity, resistance, and adaptation therein remain unknown. Here we used culture-independent metagenomic approaches to explore the virulence and antibiotic resistance in the hadal microbiota of the Mariana Trench.

RESULTS: The results indicate that the 10,898 m Challenger Deep bottom sediment harbored prosperous microbiota with contrasting signatures of virulence factors and antibiotic resistance, compared with the neighboring but shallower 6038 m steep wall site and the more nearshore 5856 m Pacific basin site. Virulence genes including several famous large translocating virulence genes (e.g., botulinum neurotoxins, tetanus neurotoxin, and Clostridium difficile toxins) were uniquely detected in the trench bottom. However, the shallower and more nearshore site sediment had a higher abundance and richer diversity of known antibiotic resistance genes (ARGs), especially for those clinically relevant ones (e.g., fosX, sul1, and TEM-family extended-spectrum beta-lactamases), revealing resistance selection under anthropogenic stresses. Further analysis of mobilome (i.e., the collection of mobile genetic elements, MGEs) suggests horizontal gene transfer mediated by phage and integrase as the major mechanism for the evolution of Mariana Trench sediment bacteria. Notably, contig-level co-occurring and taxonomic analysis shows emerging evidence for substantial co-selection of virulence genes and ARGs in taxonomically diverse bacteria in the hadal sediment, especially for the Challenger Deep bottom where mobilized ARGs and virulence genes are favorably enriched in largely unexplored bacteria.

CONCLUSIONS: This study reports the landscape of virulence factors, antibiotic resistome, and mobilome in the sediment and seawater microbiota residing hadal environment of the deepest ocean bottom on earth. Our work unravels the contrasting and unique features of virulence genes, ARGs, and MGEs in the Mariana Trench bottom, providing new insights into the eco-environmental and biological processes underlying microbial pathogenicity, resistance, and adaptative evolution in the hadal environment.}, } @article {pmid35468617, year = {2022}, author = {Bae, S and Chung, H}, title = {The Urobiome and Its Role in Overactive Bladder.}, journal = {International neurourology journal}, volume = {26}, number = {3}, pages = {190-200}, pmid = {35468617}, issn = {2093-4777}, support = {//Konkuk University/ ; }, abstract = {Urine is no longer considered to be sterile. After the existence of the microbiome was revealed through metagenomic analysis using next-generation sequencing, the relationship between characteristics of the microbiome and diseases have been studied and published in various journals. A microbiome exists in the urinary tract and is associated with urinary tract infection, malignancy of the genitourinary tract, and lower urinary tract symptoms. Based on the urine sampling method, sampling site, culture method, and sex, the characteristics of the microbiome vary. Most of the Lactobacillus species are identified mainly in women, and various other species are identified in men. These microorganisms can cause or prevent various diseases. Variations in the microbiome are seen in those with and without disease, and an asymptomatic status does not indicate the absence of microbes. This microbiome has been implicated in a variety of lower urinary tract symptoms and diseases, in particular, overactive bladder. The microbiome differs between patients with urgency and urge urinary incontinence and healthy individuals. There are many aspects of the microbiome yet to be studied in relation to other lower urinary tract symptoms.}, } @article {pmid35468443, year = {2022}, author = {Jiang, Y and Fang, Y and Liu, Y and Liu, B and Zhang, J}, title = {Community succession during the preventive control of cyanobacterial bloom by hydrogen peroxide in an aquatic microcosm.}, journal = {Ecotoxicology and environmental safety}, volume = {237}, number = {}, pages = {113546}, doi = {10.1016/j.ecoenv.2022.113546}, pmid = {35468443}, issn = {1090-2414}, mesh = {*Cyanobacteria ; Eutrophication ; Hydrogen Peroxide/pharmacology ; Lakes ; *Microcystis ; Photosynthesis ; Phytoplankton ; }, abstract = {Hydrogen peroxide (H2O2) is an environmentally friendly algaecide with good prospects for cyanobacterial bloom control. In this study, 0.2-1.5 mg L[-1] of H2O2 was applied to an aquatic microcosm containing cyanobacteria, bacteria, and eukaryotic phytoplankton at the early cyanobacterial growth stage·H2O2 generated hormesis in cyanobacteria at 0.2 mg L[-1]; significantly (p < 0.05) inhibited cyanobacterial growth, cyanobacterial photosynthesis, and microcystin production at 0.5-1.5 mg L[-1]; and effectively prevented the formation of cyanobacterial bloom without generating adverse effects on eukaryotic phytoplankton at 1.0 and 1.5 mg L[-1]. Application of 0.5-1.5 mg L[-1] H2O2 directly inhibited the abundance of five typical bloom-forming cyanobacterial genera (Microcystis, Anabeana, Synechococcus, Nostoc, and Oscillatoria), which were negatively correlated with four bacterial genera (Actinotalea, Flavobacterium, Fluviicola, and Exiguobacterium) and five eukaryotic phytoplankton genera (Cyclotella, Desmodesmus, Dinobryon, Fragilaria, and Mychonastes) and positively correlated with six proteobacterial genera (Brevundimonas, Devosia, Limnohabitans, Porphyrobacter, Pseudomonas, and Rhodobacter). After application of 1.0 and 1.5 mg L[-1] H2O2 for 15 days, H2O2-treated groups showed significantly (p < 0.05) different prokaryotic community structures from that of the control group at the bloom stage (15th day), while eukaryotic community structures in H2O2-treated groups remained stable and showed high similarity with that of the control group at a non-bloom stage (5th day). Application of low-dose H2O2 during the early cyanobacterial growth stage could effectively prevent the formation of cyanobacterial blooms without disrupting non-target organisms.}, } @article {pmid35468283, year = {2022}, author = {Kneis, D and Berendonk, TU and Forslund, SK and Hess, S}, title = {Antibiotic Resistance Genes in River Biofilms: A Metagenomic Approach toward the Identification of Sources and Candidate Hosts.}, journal = {Environmental science & technology}, volume = {56}, number = {21}, pages = {14913-14922}, pmid = {35468283}, issn = {1520-5851}, mesh = {*Rivers/microbiology ; *Anti-Bacterial Agents/pharmacology ; Wastewater ; Ecosystem ; Genes, Bacterial ; Drug Resistance, Microbial/genetics ; Biofilms ; Bacteria/genetics ; }, abstract = {Treated wastewater is a major pathway by which antibiotic resistance genes (ARG) enter aquatic ecosystems. However, knowledge gaps remain concerning the dissemination of specific ARG and their association with bacterial hosts. Here, we employed shotgun metagenomics to track ARG and taxonomic markers in river biofilms along a gradient of fecal pollution depicted by crAssphage signatures. We found strong evidence for an impact of wastewater effluents on both community composition and resistomes. In the light of such simultaneity, we employed a model comparison technique to identify ARG-host relationships from nonassembled metagenomic DNA. Hereby, a major cause of spurious associations otherwise encountered in correlation-based ARG-host analyses was suppressed. For several families of ARG, namely those conferring resistance to beta-lactams, particular bacterial orders were identified as candidate hosts. The found associations of blaFOX and cphA with Aeromonadales or blaPER with Chromatiales support the outcome of independent evolutionary analyses and thus confirm the potential of the methodology. For other ARG families including blaIMP or tet, clusters of bacterial orders were identified which potentially harbor a major proportion of host species. For yet other ARG, like, for example, ant or erm, no particular host candidates were identifiable, indicating their spread across various taxonomic groups.}, } @article {pmid35467501, year = {2022}, author = {Zhu, Y and Ma, L and Wei, W and Li, X and Chang, Y and Pan, Z and Gao, H and Yang, R and Bi, Y and Ding, L}, title = {Metagenomics analysis of cultured mucosal bacteria from colorectal cancer and adjacent normal mucosal tissues.}, journal = {Journal of medical microbiology}, volume = {71}, number = {4}, pages = {}, doi = {10.1099/jmm.0.001523}, pmid = {35467501}, issn = {1473-5644}, mesh = {Bacteria/genetics ; *Colorectal Neoplasms/microbiology ; *Gastrointestinal Microbiome ; Humans ; Intestinal Mucosa/microbiology ; Metagenomics ; }, abstract = {Introduction. Colorectal cancer (CRC) is one of the most common cancers worldwide. Multiple risk factors are involved in CRC development, including age, genetics, lifestyle, diet and environment. Of these, the role of the gut microbiota in cancer biology is increasingly recognized.Hypothesis/Gap Statement. Micro-organisms have been widely detected in stool samples, but few mucosal samples have been detected and sequenced in depth.Aim. Analysis of cultured mucosal bacteria from colorectal cancer and adjacent normal mucosal tissues with metagenomics sequencing.Methodology. Twenty-eight paired tumour and non-tumour tissues from 14 patients undergoing surgery for CRC were analysed. We removed the influence of eukaryotic cells via culture. The composition of mucosal microbiota in intestinal mucosa were detected and analysed with metagenomic sequencing.Results. Compared with non-cultured mucosal sample, 80 % bacteria species could be detected after culture. Moreover, after culture, additional 30 % bacteria could be detected, compared with non-cultured samples. Since after culture it was difficult to estimate the original abundance of microbiome, we focused on the identification of the CRC tissue-specific species. There were 298 bacterial species, which could only be cultured and detected in CRC tissues. Myroides odoratimimus and Cellulophaga baltica could be isolated from all the tumour samples of 14 CRC patients, suggesting that these species may be related to tumour occurrence and development. Further functional analysis indicated that bacteria from CRC tissues showed more active functions, including basic metabolism, signal transduction and survival activities.Conclusion. We used a new method based on culture to implement information on prokaryotic taxa, and related functions, which samples were from colorectal tissues. This method is suitable for removing eukaryotic contamination and detecting micro-organisms from other tissues.}, } @article {pmid35467400, year = {2022}, author = {Petriglieri, F and Singleton, CM and Kondrotaite, Z and Dueholm, MKD and McDaniel, EA and McMahon, KD and Nielsen, PH}, title = {Reevaluation of the Phylogenetic Diversity and Global Distribution of the Genus "Candidatus Accumulibacter".}, journal = {mSystems}, volume = {7}, number = {3}, pages = {e0001622}, pmid = {35467400}, issn = {2379-5077}, mesh = {Phylogeny ; RNA, Ribosomal, 16S/genetics ; In Situ Hybridization, Fluorescence ; *Ecosystem ; *Betaproteobacteria ; Phosphorus/metabolism ; }, abstract = {"Candidatus Accumulibacter" was the first microorganism identified as a polyphosphate-accumulating organism (PAO) important for phosphorus removal from wastewater. Members of this genus are diverse, and the current phylogeny and taxonomic framework appear complicated, with most publicly available genomes classified as "Candidatus Accumulibacter phosphatis," despite notable phylogenetic divergence. The ppk1 marker gene allows for a finer-scale differentiation into different "types" and "clades"; nevertheless, taxonomic assignments remain inconsistent across studies. Therefore, a comprehensive reevaluation is needed to establish a common understanding of this genus, in terms of both naming and basic conserved physiological traits. Here, we provide this reassessment using a comparison of genome, ppk1, and 16S rRNA gene-based approaches from comprehensive data sets. We identified 15 novel species, along with "Candidatus Accumulibacter phosphatis," "Candidatus Accumulibacter delftensis," and "Candidatus Accumulibacter aalborgensis." To compare the species in situ, we designed new species-specific fluorescence in situ hybridization (FISH) probes and revealed their morphology and arrangement in activated sludge. Based on the MiDAS global survey, "Ca. Accumulibacter" species were widespread in wastewater treatment plants (WWTPs) with phosphorus removal, indicating process design as a major driver for their abundance. Genome mining for PAO-related pathways and FISH-Raman microspectroscopy confirmed the potential for PAO metabolism in all "Ca. Accumulibacter" species, with detection in situ of the typical PAO storage polymers. Genome annotation further revealed differences in the nitrate/nitrite reduction pathways. This provides insights into the niche differentiation of these lineages, potentially explaining their coexistence in the same ecosystem while contributing to overall phosphorus and nitrogen removal. IMPORTANCE "Candidatus Accumulibacter" is the most studied PAO, with a primary role in biological nutrient removal. However, the species-level taxonomy of this lineage is convoluted due to the use of different phylogenetic markers or genome sequencing approaches. Here, we redefined the phylogeny of these organisms, proposing a comprehensive approach which could be used to address the classification of other diverse and uncultivated lineages. Using genome-resolved phylogeny, compared to phylogeny based on the 16S rRNA gene and other phylogenetic markers, we obtained a higher-resolution taxonomy and established a common understanding of this genus. Furthermore, genome mining of genes and pathways of interest, validated in situ by application of a new set of FISH probes and Raman microspectroscopy, provided additional high-resolution metabolic insights into these organisms.}, } @article {pmid35467389, year = {2022}, author = {Ma, X and Brinker, E and Graff, EC and Cao, W and Gross, AL and Johnson, AK and Zhang, C and Martin, DR and Wang, X}, title = {Whole-Genome Shotgun Metagenomic Sequencing Reveals Distinct Gut Microbiome Signatures of Obese Cats.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0083722}, pmid = {35467389}, issn = {2165-0497}, mesh = {Animals ; Bacteria/genetics ; Cats ; Feces/microbiology ; *Gastrointestinal Microbiome/genetics ; Metagenome ; Mice ; Obesity/genetics/microbiology/veterinary ; Overweight/genetics ; Weight Loss/genetics ; }, abstract = {Overweight and obesity are growing health problems in domestic cats, increasing the risks of insulin resistance, lipid dyscrasias, neoplasia, cardiovascular disease, and decreasing longevity. The signature of obesity in the feline gut microbiota has not been studied at the whole-genome metagenomic level. We performed whole-genome shotgun metagenomic sequencing in the fecal samples of eight overweight/obese and eight normal cats housed in the same research environment. We obtained 271 Gbp of sequences and generated a 961-Mbp de novo reference contig assembly, with 1.14 million annotated microbial genes. In the obese cat microbiome, we discovered a significant reduction in microbial diversity (P < 0.01) and Firmicutes abundance (P = 0.005), as well as decreased Firmicutes/Bacteroidetes ratios (P = 0.02), which is the inverse of obese human/mouse microbiota. Linear discriminant analysis and quantitative PCR (qPCR) validation revealed significant increases of Bifidobacterium sp., Olsenella provencensis, Dialister sp.CAG:486, and Campylobacter upsaliensis as the hallmark of obese microbiota among 400 enriched species, whereas 1,525 bacterial species have decreased abundance in the obese microbiome. Phascolarctobacterium succinatutens and an uncharacterized Erysipelotrichaceae bacterium are highly abundant (>0.05%) in the normal gut with over 400-fold depletion in the obese microbiome. Fatty acid synthesis-related pathways are significantly overrepresented in the obese compared with the normal cat microbiome. In conclusion, we discovered dramatically decreased microbial diversity in obese cat gut microbiota, suggesting potential dysbiosis. A panel of seven significantly altered, highly abundant species can serve as a microbiome indicator of obesity. Our findings in the obese cat microbiome composition, abundance, and functional capacities provide new insights into feline obesity. IMPORTANCE Obesity affects around 45% of domestic cats, and licensed drugs for treating feline obesity are lacking. Physical exercise and calorie restrictions are commonly used for weight loss but with limited efficacy. Through comprehensive analyses of normal and obese cat gut bacteria flora, we identified dramatic shifts in the obese gut microbiome, including four bacterial species significantly enriched and two species depleted in the obese cats. The key bacterial community and functional capacity alterations discovered from this study will inform new weight management strategies for obese cats, such as evaluations of specific diet formulas that alter the microbiome composition, and the development of prebiotics and probiotics that promote the increase of beneficial species and the depletion of obesity-associated species. Interestingly, these bacteria identified in our study were also reported to affect the weight loss success in human patients, suggesting translational potential in human obesity.}, } @article {pmid35467362, year = {2022}, author = {Huang, C and Sahoo, MK and Verghese, M and Sibai, M and Solis, D and Mfuh, KO and Kurzer, J and Hogan, CA and Doan, TA and Pinsky, BA}, title = {Interepidemic Respiratory Syncytial Virus during the COVID-19 Pandemic.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0094722}, pmid = {35467362}, issn = {2165-0497}, mesh = {*COVID-19/epidemiology ; Genome, Viral ; Humans ; Pandemics ; *Respiratory Syncytial Virus Infections/epidemiology ; *Respiratory Syncytial Virus, Human/genetics ; *Respiratory Tract Infections/epidemiology ; }, } @article {pmid35467318, year = {2022}, author = {Ren, W and Yu, B and Yu, J and Zheng, P and Huang, Z and Luo, J and Mao, X and He, J and Yan, H and Wu, J and Chen, D and Luo, Y}, title = {Lower abundance of Bacteroides and metabolic dysfunction are highly associated with the post-weaning diarrhea in piglets.}, journal = {Science China. Life sciences}, volume = {65}, number = {10}, pages = {2062-2075}, pmid = {35467318}, issn = {1869-1889}, mesh = {Amino Acids ; Animals ; *Bacteroides/genetics ; Carbohydrates ; *Diarrhea/veterinary ; Swine ; Weaning ; }, abstract = {Growing evidences show a direct link between diarrhea and disorders of gut microbiota in pigs. However, whether there are microbial markers associated with post-weaning diarrhea remains unknown. In the current study, we compared the microbial community, functions and metabolites between healthy weaned piglets (group H, n=7) and piglets with post-weaning diarrhea (group D, n=7), in order to find out diarrhea associated microbial markers. Each of 7 fecal samples was collected from H and D piglets (weaned at 21 d and sampled at 26 d). The metagenomic and untargeted metabolomic analysis revealed that the microbial composition, function and metabolic profile in D pigs was considerably reshaped, including the reduced abundance and number of Bacteroides, which significantly correlated with the diarrhea status of host. The carbohydrate metabolism, biosynthesis and metabolism, lipid metabolism, amino acid metabolism, and the activity of glycan and carbohydrates digestion related enzymes showed extensively down-regulated in D pigs compared with H pigs. Diarrhea significantly changed the metabolic profiles of fecal microbiota, and most of the altered metabolites were negatively or positively correlated with the change in the abundance of Bacteroides. In conclusion, the lower abundance of Bacteroides and its associated metabolic dysfunction may be regarded as microbial markers of physiological post-weaning diarrhea in piglets.}, } @article {pmid35466505, year = {2022}, author = {Williams, TJ and Allen, MA and Panwar, P and Cavicchioli, R}, title = {Into the darkness: the ecologies of novel 'microbial dark matter' phyla in an Antarctic lake.}, journal = {Environmental microbiology}, volume = {24}, number = {5}, pages = {2576-2603}, pmid = {35466505}, issn = {1462-2920}, mesh = {Antarctic Regions ; Bacteria ; Darkness ; *Lakes/microbiology ; *Metagenome ; RNA, Ribosomal, 16S/genetics/metabolism ; }, abstract = {Uncultivated microbial clades ('microbial dark matter') are inferred to play important but uncharacterized roles in nutrient cycling. Using Antarctic lake (Ace Lake, Vestfold Hills) metagenomes, 12 metagenome-assembled genomes (MAGs; 88%-100% complete) were generated for four 'dark matter' phyla: six MAGs from Candidatus Auribacterota (=Aureabacteria, SURF-CP-2), inferred to be hydrogen- and sulfide-producing fermentative heterotrophs, with individual MAGs encoding bacterial microcompartments (BMCs), gas vesicles, and type IV pili; one MAG (100% complete) from Candidatus Hinthialibacterota (=OLB16), inferred to be a facultative anaerobe capable of dissimilatory nitrate reduction to ammonia, specialized for mineralization of complex organic matter (e.g. sulfated polysaccharides), and encoding BMCs, flagella, and Tad pili; three MAGs from Candidatus Electryoneota (=AABM5-125-24), previously reported to include facultative anaerobes capable of dissimilatory sulfate reduction, and here inferred to perform sulfite oxidation, reverse tricarboxylic acid cycle for autotrophy, and possess numerous proteolytic enzymes; two MAGs from Candidatus Lernaellota (=FEN-1099), inferred to be capable of formate oxidation, amino acid fermentation, and possess numerous enzymes for protein and polysaccharide degradation. The presence of 16S rRNA gene sequences in public metagenome datasets (88%-100% identity) suggests these 'dark matter' phyla contribute to sulfur cycling, degradation of complex organic matter, ammonification and/or chemolithoautotrophic CO2 fixation in diverse global environments.}, } @article {pmid35466491, year = {2022}, author = {Keenum, I and Wind, L and Ray, P and Guron, G and Chen, C and Knowlton, K and Ponder, M and Pruden, A}, title = {Metagenomic tracking of antibiotic resistance genes through a pre-harvest vegetable production system: an integrated lab-, microcosm- and greenhouse-scale analysis.}, journal = {Environmental microbiology}, volume = {24}, number = {8}, pages = {3705-3721}, pmid = {35466491}, issn = {1462-2920}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Cattle ; Drug Resistance, Microbial/genetics ; Genes, Bacterial/genetics ; Lactuca ; *Manure/analysis ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Sand ; Soil ; Soil Microbiology ; *Vegetables ; }, abstract = {Prior research demonstrated the potential for agricultural production systems to contribute to the environmental spread of antibiotic resistance genes (ARGs). However, there is a need for integrated assessment of critical management points for minimizing this potential. Shotgun metagenomic sequencing data were analysed to comprehensively compare total ARG profiles characteristic of amendments (manure or compost) derived from either beef or dairy cattle (with and without dosing antibiotics according to conventional practice), soil (loamy sand or silty clay loam) and vegetable (lettuce or radish) samples collected across studies carried out at laboratory-, microcosm- and greenhouse-scale. Vegetables carried the greatest diversity of ARGs (n = 838) as well as the most ARG-mobile genetic element co-occurrences (n = 945). Radishes grown in manure- or compost-amended soils harboured a higher relative abundance of total (0.91 and 0.91 ARGs/16S rRNA gene) and clinically relevant ARGs than vegetables from other experimental conditions (average: 0.36 ARGs/16S rRNA gene). Lettuce carried the highest relative abundance of pathogen gene markers among the metagenomes examined. Total ARG relative abundances were highest on vegetables grown in loamy sand receiving antibiotic-treated beef amendments. The findings emphasize that additional barriers, such as post-harvest processes, merit further study to minimize potential exposure to consumers.}, } @article {pmid35466367, year = {2022}, author = {Yang, D and Heederik, DJJ and Scherpenisse, P and Van Gompel, L and Luiken, REC and Wadepohl, K and Skarżyńska, M and Van Heijnsbergen, E and Wouters, IM and Greve, GD and Jongerius-Gortemaker, BGM and Tersteeg-Zijderveld, M and Portengen, L and Juraschek, K and Fischer, J and Zając, M and Wasyl, D and Wagenaar, JA and Mevius, DJ and Smit, LAM and Schmitt, H}, title = {Antimicrobial resistance genes aph(3')-III, erm(B), sul2 and tet(W) abundance in animal faeces, meat, production environments and human faeces in Europe.}, journal = {The Journal of antimicrobial chemotherapy}, volume = {77}, number = {7}, pages = {1883-1893}, pmid = {35466367}, issn = {1460-2091}, support = {613754//EFFORT/ ; 3173/7PR/2014/2//Polish Ministry of Science/ ; 201709110149//China Scholarships Council/ ; }, mesh = {Animals ; *Anti-Bacterial Agents/pharmacology ; *Anti-Infective Agents ; Cattle ; Chickens ; Cross-Sectional Studies ; Drug Resistance, Bacterial ; Feces ; Genes, Bacterial ; Humans ; Livestock ; Meat ; RNA, Ribosomal, 16S/genetics ; Swine ; }, abstract = {BACKGROUND: Real-time quantitative PCR (qPCR) is an affordable method to quantify antimicrobial resistance gene (ARG) targets, allowing comparisons of ARG abundance along animal production chains.

OBJECTIVES: We present a comparison of ARG abundance across various animal species, production environments and humans in Europe. AMR variation sources were quantified. The correlation of ARG abundance between qPCR data and previously published metagenomic data was assessed.

METHODS: A cross-sectional study was conducted in nine European countries, comprising 9572 samples. qPCR was used to quantify abundance of ARGs [aph(3')-III, erm(B), sul2, tet(W)] and 16S rRNA. Variance component analysis was conducted to explore AMR variation sources. Spearman's rank correlation of ARG abundance values was evaluated between pooled qPCR data and earlier published pooled metagenomic data.

RESULTS: ARG abundance varied strongly among animal species, environments and humans. This variation was dominated by between-farm variation (pigs) or within-farm variation (broilers, veal calves and turkeys). A decrease in ARG abundance along pig and broiler production chains ('farm to fork') was observed. ARG abundance was higher in farmers than in slaughterhouse workers, and lowest in control subjects. ARG abundance showed a high correlation (Spearman's ρ > 0.7) between qPCR data and metagenomic data of pooled samples.

CONCLUSIONS: qPCR analysis is a valuable tool to assess ARG abundance in a large collection of livestock-associated samples. The between-country and between-farm variation of ARG abundance could partially be explained by antimicrobial use and farm biosecurity levels. ARG abundance in human faeces was related to livestock antimicrobial resistance exposure.}, } @article {pmid35465251, year = {2022}, author = {Nan, X and Zhang, Y and Su, N and Yang, L and Pan, G}, title = {Application Value of Metagenomic Next-Generation Sequencing for Bloodstream Infections in Pediatric Patients Under Intensive Care.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {1911-1920}, pmid = {35465251}, issn = {1178-6973}, abstract = {PURPOSE: This study aimed to analyze the application value of metagenomic next-generation sequencing (mNGS) as a basis for the proper adjustment of the clinical treatment of bloodstream infections (BSIs) in pediatric patients under intensive care.

METHODS: We retrospectively enrolled 46 pediatric patients with clinically diagnosed BSIs who were hospitalized in the pediatric intensive care unit of the Second Affiliated Hospital and Yuying Children's Hospital of Wenzhou Medical University from June 2018 to July 2021. Blood samples were collected for cultivation and for mNGS detection of pathogens.

RESULTS: Among the 46 children, the average turnaround time for blood culture tests was 3.2 days, and the results revealed pathogens in three children (6.5%). The average turnaround time for mNGS was 2.2 days, and pathogens were found in 30 children (65.2%). The difference in positivity rates between blood culture and mNGS was significant (p<0.05). Blood culture tests found three pathogens, while mNGS identified 28 pathogens, indicating that mNGS detected significantly more types of pathogens than the traditional diagnostic method for pathogenic microorganisms. In some children, more than one pathogen was detected.

CONCLUSION: mNGS can help identify pathogenic microorganisms associated with BSI in some pediatric patients under intensive care.}, } @article {pmid35465249, year = {2022}, author = {Liu, Y and Zhu, H and Zheng, Y}, title = {Detection of Pneumocystis jirovecii Pneumonia in Infants with Non-Human Immunodeficiency Virus Admitted to Pediatric Intensive Care Using Metagenomics Next-Generation Sequencing.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {1889-1902}, pmid = {35465249}, issn = {1178-6973}, abstract = {OBJECTIVE: This study aimed to investigate the characteristics of the non-human immunodeficiency virus (HIV) pneumocystis pneumonia (PCP) via the microbial composition of Pneumocystis jirovecii pneumonia in the lower respiratory tract in infants with severe pneumonia who were hospitalized in the study's pediatric intensive care unit (PICU).

METHODS: The clinical characteristics of 16 infants with non-HIV PCP (the PCP group) and 33 infants with severe pneumonia (the control group) who were hospitalized at the same time in the PICU were analyzed retrospectively. Using metagenomic next-generation sequencing (mNGS), the bronchoalveolar lavage fluid (BALF) of the two groups was analyzed, and the microbial results and clinical data were compared.

RESULTS: Compared with the control group, the infants in the PCP group had a lower incidence of cough (25% vs 78.8%; P < 0.05), a greater history of surgery (50.0% vs 39.1%; P < 0.05), and a more significant decrease in C3, C4, and CD4/CD8 ratios (all P < 0.05). The pathogenic bacteria in the BALF included P. jirovecii, respiratory syncytial virus, cytomegalovirus (CMV), and Staphylococcus aureus. The predominance of viral infection in the PCP group was significantly higher than in the control group (P < 0.05), especially CMV (43.5% vs 15.2%; P < 0.05). The top five symbiotic microorganisms detected in the BALF of the 49 infants were Streptococcus, Propionibacterium, Rothia, Staphylococcus, and Moraxella. There was no significant difference in the relative abundance of common symbiotic microorganisms between the two groups (all P > 0.05).

CONCLUSION: Non-HIV PCP has a higher incidence in PICU infants with severe pneumonia, especially those with underlying diseases or who are immunocompromised, which are clinically difficult to treat. A BALF analysis using mNGS is helpful for early and clear diagnoses. It also helps to clarify the distribution of pathogenic and lower respiratory tract colonizing bacteria in infants with severe pneumonia.}, } @article {pmid35464955, year = {2022}, author = {Lamoureux, C and Surgers, L and Fihman, V and Gricourt, G and Demontant, V and Trawinski, E and N'Debi, M and Gomart, C and Royer, G and Launay, N and Le Glaunec, JM and Wemmert, C and La Martire, G and Rossi, G and Lepeule, R and Pawlotsky, JM and Rodriguez, C and Woerther, PL}, title = {Prospective Comparison Between Shotgun Metagenomics and Sanger Sequencing of the 16S rRNA Gene for the Etiological Diagnosis of Infections.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {761873}, pmid = {35464955}, issn = {1664-302X}, abstract = {Bacteriological diagnosis is traditionally based on culture. However, this method may be limited by the difficulty of cultivating certain species or by prior exposure to antibiotics, which justifies the resort to molecular methods, such as Sanger sequencing of the 16S rRNA gene (Sanger 16S). Recently, shotgun metagenomics (SMg) has emerged as a powerful tool to identify a wide range of pathogenic microorganisms in numerous clinical contexts. In this study, we compared the performance of SMg to Sanger 16S for bacterial detection and identification. All patients' samples for which Sanger 16S was requested between November 2019 and April 2020 in our institution were prospectively included. The corresponding samples were tested with a commercial 16S semi-automated method and a semi-quantitative pan-microorganism DNA- and RNA-based SMg method. Sixty-seven samples from 64 patients were analyzed. Overall, SMg was able to identify a bacterial etiology in 46.3% of cases (31/67) vs. 38.8% (26/67) with Sanger 16S. This difference reached significance when only the results obtained at the species level were compared (28/67 vs. 13/67). This study provides one of the first evidence of a significantly better performance of SMg than Sanger 16S for bacterial detection at the species level in patients with infectious diseases for whom culture-based methods have failed. This technology has the potential to replace Sanger 16S in routine practice for infectious disease diagnosis.}, } @article {pmid35464951, year = {2022}, author = {Cao, MM and Liu, SY and Bi, L and Chen, SJ and Wu, HY and Ge, Y and Han, B and Zhang, LM and He, JZ and Han, LL}, title = {Distribution Characteristics of Soil Viruses Under Different Precipitation Gradients on the Qinghai-Tibet Plateau.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {848305}, pmid = {35464951}, issn = {1664-302X}, abstract = {Viruses are extremely abundant in the soil environment and have potential roles in impacting on microbial population, evolution, and nutrient biogeochemical cycles. However, how environment and climate changes affect soil viruses is still poorly understood. Here, a metagenomic approach was used to investigate the distribution, diversity, and potential biogeochemical impacts of DNA viruses in 12 grassland soils under three precipitation gradients on the Qinghai-Tibet Plateau, which is one of the most sensitive areas to climate change. A total of 557 viral operational taxonomic units were obtained, spanning 152 viral families from the 30 metagenomes. Both virus-like particles (VLPs) and microbial abundance increased with average annual precipitation. A significant positive correlation of VLP counts was observed with soil water content, total carbon, total nitrogen, soil organic matter, and total phosphorus. Among these biological and abiotic factors, SWC mainly contributed to the variability in VLP abundance. The order Caudovirales (70.1% of the identified viral order) was the predominant viral type in soils from the Qinghai-Tibet Plateau, with the Siphoviridae family being the most abundant. Remarkably, abundant auxiliary carbohydrate-active enzyme (CAZyme) genes represented by glycoside hydrolases were identified, indicating that soil viruses may play a potential role in the carbon cycle on the Qinghai-Tibet Plateau. There were more diverse hosts and abundant CAZyme genes in soil with moderate precipitation. Our study provides a strong evidence that changes in precipitation impact not only viral abundance and virus-host interactions in soil but also the viral functional potential, especially carbon cycling.}, } @article {pmid35464928, year = {2022}, author = {Hu, H and Xu, K and Wang, K and Zhang, F and Bai, X}, title = {Dissecting the Effect of Berberine on the Intestinal Microbiome in the Weaned Piglets by Metagenomic Sequencing.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {862882}, pmid = {35464928}, issn = {1664-302X}, abstract = {This study aimed to investigate the microbial structure and function in the rectum of weaned piglets with berberine supplementation. Twelve healthy 21-day-old Duorc × (Landrace × Large White) weaned piglets (similar body weight) were evenly divided into control and berberine groups and were fed a basal diet supplemented with 0 and 0.1% berberine, respectively. After 21 days, metagenomic sequencing analysis was performed to detect microbial composition and function in the rectum of weaned piglets. Results showed that there were 10,597,721,931-14,059,392,900 base pairs (bp) and 10,186,558,171-15,859,563,342 bp of clean data in the control and berberine groups, respectively. The Q20s of the control and berberine groups were 97.15 to 97.7% and 96.26 to 97.68%, respectively. The microorganisms in the berberine group had lower (p < 0.05) Chao1, alternating conditional expectation, Shannon, and Simpson indices at the species levels than those in the control group. Analysis of similarity showed that there were significant differences (p < 0.01) between the control and berberine groups at the genus and species levels of the gut microorganisms. Dietary berberine significantly increased (p < 0.05) the abundance of Subdoligranulum variabile, but decreased (p < 0.05) the abundance of Prevotella copri compared with the control group. Carbohydrate-active enzymes analysis revealed that the levels of polysaccharide lyases and carbohydrate esterases were lower (p < 0.05) in the berberine group than that in the control group. Linear discriminant analysis effect size analysis showed that berberine supplementation could induce various significant Kyoto Encyclopedia of Genes and Genomes pathways, including carbohydrate metabolism, environmental information processing, and microbial metabolism in diverse environments. In conclusion, our findings suggest that berberine could improve the composition, abundance, structure, and function of gut microbiome in the weaned piglets, potentially providing a suitable approach for the application of berberine in human and animal health.}, } @article {pmid35464863, year = {2022}, author = {Alves, L and de Novais, FJ and da Silva, AN and Araujo, MS and Bernardino, T and Osowski, GV and Zanella, R and Lee Settles, M and Holmes, MA and Fukumasu, H and Ruiz, VLA and Zanella, AJ}, title = {Vaginal Microbiota Diversity in Response to Lipopolysaccharide in Gilts Housed Under Three Housing Systems.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {836962}, pmid = {35464863}, issn = {1664-8021}, abstract = {The United Kingdom and European Union have banned crates for pregnant sows. However, animals are kept in a restrictive environment for up to four weeks after mating, leading to stress and different responses of the animals' immune system. Here, we used vaginal flushing of gilts to investigate whether housing systems or an experimental inflammatory challenge with lipopolysaccharide (LPS) can modify the gilt vaginal microbiome. Alpha-diversity indices showed differences in the microbiota of gilts housed under different systems (q = 0.04). Shannon alpha-diversity richness was higher in gilts group-housed in pens than in gilts housed in crates (q = 0.035), but not higher than in other groups. The relative abundance of the operational taxonomic unit (OTU) (q < 0.05) revealed specific differences in housing systems before a LPS or saline (SAL control) challenge. We found different abundances in taxa of Actinobacteria, Bacteroidetes, Cyanobacteria, Firmicutes, and Proteobacteria in gilts housed in the different systems before challenge. After the LPS challenge, significant differences were detected in the relative abundance of OTUs (q < 0.05) for the LPS-challenged group compared with SAL animals for each housing system. The phylum Staphylococcus showed higher abundance among the LPS-challenged gilts than in SAL-challenged animals. Furthermore, Enterobacter was more abundant in the LPS-challenged gilts housed in crates than in SAL-challenged gilts housed in crates. Streptococcus suis, Conchiformibius, Globicatella and Actinobacillus were more abundant in LPS-challenged gilts in indoor group housing than in SAL gilts in the same housing system. Gilts kept outdoors did not show changes in vaginal microbiota after an LPS challenge. Gilts housed in crates showed clinical signs of urogenital infection, whereas gilts housed outdoors and in indoor group housing did not. The relationship between environment, immune response, and microbiota suggested that animals in a poor environments experience difficulties responding to a challenge and their vaginal microbiota is altered as a consequence, with decreased richness of normal vaginal microbiota, and increased opportunistic bacteria. Welfare indicators measured by gilts' responses to housing systems however, do not fully explain mechanisms associated with the unique signature in vaginal microbiota encountered in the different housing systems.}, } @article {pmid35464838, year = {2022}, author = {Li, J and Sang, Y and Zeng, S and Mo, S and Zhang, Z and He, S and Li, X and Su, G and Liao, J and Jiang, C}, title = {MicrobioSee: A Web-Based Visualization Toolkit for Multi-Omics of Microbiology.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {853612}, pmid = {35464838}, issn = {1664-8021}, abstract = {With the upgrade and development of the high-throughput sequencing technology, multi-omics data can be obtained at a low cost. However, mapping tools that existed for microbial multi-omics data analysis cannot satisfy the needs of data description and result in high learning costs, complex dependencies, and high fees for researchers in experimental biology fields. Therefore, developing a toolkit for multi-omics data is essential for microbiologists to save effort. In this work, we developed MicrobioSee, a real-time interactive visualization tool based on web technologies, which could visualize microbial multi-omics data. It includes 17 modules surrounding the major omics data of microorganisms such as the transcriptome, metagenome, and proteome. With MicrobioSee, methods for plotting are simplified in multi-omics studies, such as visualization of diversity, ROC, and enrichment pathways for DEGs. Subsequently, three case studies were chosen to represent the functional application of MicrobioSee. Overall, we provided a concise toolkit along with user-friendly, time-saving, cross-platform, and source-opening for researchers, especially microbiologists without coding experience. MicrobioSee is freely available at https://microbiosee.gxu.edu.cn.}, } @article {pmid35464780, year = {2022}, author = {Silva, DNA and Casarin, M and Monajemzadeh, S and Bezerra, BB and Lux, R and Pirih, FQ}, title = {The Microbiome in Periodontitis and Diabetes.}, journal = {Frontiers in oral health}, volume = {3}, number = {}, pages = {859209}, pmid = {35464780}, issn = {2673-4842}, abstract = {OBJECTIVES: To perform a comprehensive and integrative review of the available literature on the potential changes in the microbiome of healthy and individuals with diabetes under periodontal health and disease.

MATERIALS AND METHODS: The review was conducted by two independent reviewers. Indexed electronic databases (PubMed/Medline, Cochrane Library, Web of Science and Scopus) were searched, including articles published in English and dated from 5 years ago until December 2021. A manual search also was performed to identify co-related articles. Following the removal of duplicates and eligibility criteria, the articles were included in tables for analysis and described in the manuscript.

RESULTS: According to this review, diabetes mellitus was associated with significant changes in the subgingival and salivary microbiome, either in its association with periodontitis or in cases of periodontal health. In addition to affecting microbial diversity in terms of taxonomy, metagenomic studies have shown that this endocrine disorder may also be directly related to increased pathogenicity in the oral microbiome.

CONCLUSION: Although the reviewed studies demonstrate important differences in the subgingival and salivary microbiome composition because of diabetes mellitus, further studies are needed to clarify the real effects of hyperglycemia on oral microbial profiles and support new diagnostic approaches and innovative treatments.}, } @article {pmid35464017, year = {2022}, author = {Wang, Y and Wu, Y and Li, C and Zhao, Y and Xiang, H and Li, L and Yang, X and Chen, S and Sun, L and Qi, B}, title = {Genome-Resolved Metaproteomic Analysis of Microbiota and Metabolic Pathways Involved in Taste Formation During Chinese Traditional Fish Sauce (Yu-lu) Fermentation.}, journal = {Frontiers in nutrition}, volume = {9}, number = {}, pages = {851895}, pmid = {35464017}, issn = {2296-861X}, abstract = {Complex microbial metabolism is key to taste formation in high-quality fish sauce during fermentation. To guide quality supervision and targeted regulation, we analyzed the function of microbial flora during fermentation based on a previously developed metagenomic database. The abundance of most identified genes involved in metabolic functions showed an upward trend in abundance during fermentation. In total, 571 proteins extracted from fish sauce at different fermentation stages were identified. These proteins were mainly derived from Halanaerobium, Psychrobacter, Photobacterium, and Tetragenococcus. Functional annotation revealed 15 pathways related to amino acid metabolism, including alanine, aspartate, glutamate, and histidine metabolism; lysine degradation; and arginine biosynthesis. This study demonstrated the approaches to identify microbiota functions and metabolic pathways, thereby providing a theoretical basis for taste formation mechanisms during traditional fish sauce fermentation.}, } @article {pmid35463884, year = {2022}, author = {Zhou, W and Ouyang, Y and Zhang, D and Liao, S and Liang, H and Zhao, L and Chen, C}, title = {Case Report and Literature Review: Bacterial Meningoencephalitis or Not? Naegleria fowleri Related Primary Amoebic Meningoencephalitis in China.}, journal = {Frontiers in pediatrics}, volume = {10}, number = {}, pages = {785735}, pmid = {35463884}, issn = {2296-2360}, abstract = {In China, a 9-year-old boy was transferred to the hospital with fever, vomiting, and headache. The disease rapidly deteriorated into vague consciousness. Applying conventional clinical examinations such as blood and cerebrospinal fluid (CSF) tests, the diagnosis of bacterial meningoencephalitis was first drawn, and expectant treatments were adopted immediately. However, the symptoms did not alleviate, adversely, this boy died 3 days after admission. Considering the skeptical points of the duration, such as the unknown infectious bacteria and the pathogen invasion path, blood and CSF samples were then sent for metagenomic next-generation sequencing (mNGS) to ascertain the cause of death. The 42,899 and 1,337 specific sequences of N. fowleri were detected by mNGS in the CSF sample and the blood sample, respectively. PCR results and pathological smear subsequently confirmed the mNGS detection. The patient was finally diagnosed as primary amoebic meningoencephalitis. Besides, in this article, 15 similar child infection cases in the past 10 years are summarized and analyzed to promote the early diagnosis of this rare disease.}, } @article {pmid35463878, year = {2022}, author = {Zhou, P and Wang, W and Fu, Y and Zhang, Y and Liang, Z and Tang, Y and Jiang, L}, title = {Persistent Pulmonary Interstitial Emphysema With Respiratory Infection: A Clinicopathological Analysis of Six Cases and Detection of Infectious Pathogens by Metagenomic Next-Generation Sequencing (mNGS).}, journal = {Frontiers in pediatrics}, volume = {10}, number = {}, pages = {836276}, pmid = {35463878}, issn = {2296-2360}, abstract = {BACKGROUND: Persistent pulmonary interstitial emphysema (PPIE) is known to be related to mechanical ventilation and preterm. However, PPIE is also reported rarely in non-ventilated and full-term infants. Its relationship with respiratory infection is rarely reported in the literature. PPIE is difficult to diagnose and always mimics other congenital thoracic malformations (CTMs), such as congenital cystic adenomatoid malformation (CCAM).

OBJECTIVE: The objective of this study was to evaluate clinicopathological and radiographic features of PPIE with respiratory infection and to detect the possible infectious pathogens.

METHODS: From January 2011 to December 2019, six cases were confirmed pathologically with PPIE from a large cohort of 477 resected CTMs in West China Hospital of Sichuan University. Clinical and radiographic features were obtained from patients' medical records and follow-up. The present study aimed to analyze clinicopathological and radiographic features and to detect the infectious pathogens by metagenomic next-generation sequencing (mNGS).

RESULTS: The six PPIE cases included four girls and two boys, ranging from 2 months to 5 years; 100% (5/5) of the available cases were full-term and without mechanical ventilation. CCAM were suspected in 66.7% (4/6) patients; 66.7% (4/6) cases affected a single lobe, and 33.3% (2/6) cases affected both lung lobes. Clinically, all six PPIEs were presented with symptoms of respiratory infection and diagnosed with pneumonia. All six patients were treated by surgery after anti-infective treatment. The pathologic characteristics showed lung cysts with variable size along the bronchovascular bundles, the cysts had a discontinuous fibrotic wall with a smooth inner surface lined with uninucleated and/or multinucleated macrophages. Streptococcus pneumoniae was detected in patient No. 1. Human beta-herpesvirus 5 was detected in patient No. 2. Neisseria mucosa, Neisseria sicca, Prevotella melaninogenica, Prevotella histicola, and Fusobacterium nucleatum were detected in patient No. 5, and no infectious pathogen was detected in 50% (3/6, No. 3, No. 4, and No. 6) of cases.

CONCLUSION: Six rare cases of PPIE with respiratory infection were treated by surgery after anti-infective treatment. All five available cases were full-term infants without mechanical ventilation. The histological characteristics of PPIE were the wall of cysts composed of a thin layer of discontinuous fibrous tissue and lined with uninucleated or/and multinucleated macrophages.}, } @article {pmid35463645, year = {2022}, author = {Dong, Z and Lv, W and Zhang, C and Chen, S}, title = {Correlation Analysis of Gut Microbiota and Serum Metabolome With Porphyromonas gingivalis-Induced Metabolic Disorders.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {858902}, pmid = {35463645}, issn = {2235-2988}, mesh = {Animals ; *Gastrointestinal Microbiome ; *Metabolic Diseases/etiology ; Metabolome ; Mice ; Mice, Inbred C57BL ; Porphyromonas gingivalis ; }, abstract = {Periodontitis has been demonstrated to increase the risk of metabolic syndrome (MetS), but the underlying mechanism remains unclear. Recent studies have indicated periodontopathic bacteria such as Porphyromonas gingivalis could induce gut microbiota (GM) dysbiosis and aggravate metabolic disorders. However, the effects of microbial metabolites have barely been evaluated. Here, we investigated the alteration of serum metabolome with P. gingivalis-induced metabolic disorders, and explored the correlations of GM and serum metabolites. In this study, we orally administered P. gingivalis ATCC33277 to C57BL/6 mice and performed metagenomic sequencing and untargeted metabolomics with fecal samples and serum collection. In vivo experiments showed a higher proportion of fat mass and worse glucose tolerance in P. gingivalis-administered mice, accompanied with an increase of adipose inflammation and gut permeability, which was similar to HFD-induced obese mice. Metagenomic sequencing indicated a compositional and functional alteration of GM. Untargeted metabolomics revealed an alteration of metabolites in P. gingivalis-administered mice, and most of them were engaged in metabolic pathways, such as tryptophan metabolism and choline metabolism. Correlation analysis between GM and serum metabolome indicated strong relativity with P. gingivalis administration. These results demonstrated some specific microbiota-derived metabolites in the pathogenesis of P. gingivalis-induced metabolic disorders, providing promising targets for the development of novel treatment strategies for MetS.}, } @article {pmid35463643, year = {2022}, author = {Sun, H and Wang, F and Zhang, M and Xu, X and Li, M and Gao, W and Wu, X and Han, H and Wang, Q and Yao, G and Lou, Z and Xia, H and Shi, Y and Li, Q}, title = {Diagnostic Value of Bronchoalveolar Lavage Fluid Metagenomic Next-Generation Sequencing in Pneumocystis jirovecii Pneumonia in Non-HIV Immunosuppressed Patients.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {872813}, pmid = {35463643}, issn = {2235-2988}, mesh = {Bronchoalveolar Lavage Fluid/microbiology ; *Coinfection ; High-Throughput Nucleotide Sequencing/methods ; Humans ; Metagenomics/methods ; *Pneumonia, Pneumocystis/diagnosis/microbiology ; Sensitivity and Specificity ; }, abstract = {INTRODUCTION: This study aims to assess the value of metagenomic next-generation sequencing (mNGS) of bronchoalveolar lavage fluid (BALF) in the diagnosis of Pneumocystis jirovecii pneumonia (PJP) and its mixed infection in non-human immunodeficiency virus (HIV) immunosuppressed patients.

METHODS: A total of 198 non-HIV immunosuppressed patients with severe pneumonia were enrolled, including 77 PJP patients and 121 patients infected by other pathogens. BALF-mNGS and traditional detection methods were used.

RESULTS: The positive detection rate of various pathogens of BALF-mNGS was higher than that of the conventional methods, especially for mixed pathogens. The sensitivity and specificity of BALF-mNGS for the diagnosis of PJP were 97.40% and 85.12%, respectively. Compared with traditional methods, the sensitivity of BALF-mNGS was significantly higher than that of blood fungal G (BG)/lactate dehydrogenase (LDH) and BALF-microscopy (p<0.05), and its specificity was significantly higher than that of BG/LDH (p<0.05). In addition, the average detection time of BALF-mNGS (32.76 ± 10.32 h) was also significantly shorter than conventional methods (p<0.01), especially for mixed infections that were common in non-HIV immunosuppressed patients. In patients only detected as positive by BALF-mNGS, the underlying diseases mainly manifested as hematological malignancies with agranulocytosis and within 8 months after hematopoietic stem cell or solid organ transplantation.

CONCLUSIONS: BALF-mNGS technology is faster, more sensitive, and more comprehensive in detecting P. jirovecii and its mixed infection in immunosuppressed patients.}, } @article {pmid35463414, year = {2022}, author = {Vacant, S and Benites, LF and Salmeron, C and Intertaglia, L and Norest, M and Cadoudal, A and Sanchez, F and Caceres, C and Piganeau, G}, title = {Long-Term Stability of Bacterial Associations in a Microcosm of Ostreococcus tauri (Chlorophyta, Mamiellophyceae).}, journal = {Frontiers in plant science}, volume = {13}, number = {}, pages = {814386}, pmid = {35463414}, issn = {1664-462X}, abstract = {Phytoplankton-bacteria interactions rule over carbon fixation in the sunlit ocean, yet only a handful of phytoplanktonic-bacteria interactions have been experimentally characterized. In this study, we investigated the effect of three bacterial strains isolated from a long-term microcosm experiment with one Ostreococcus strain (Chlorophyta, Mamiellophyceae). We provided evidence that two Roseovarius strains (Alphaproteobacteria) had a beneficial effect on the long-term survival of the microalgae whereas one Winogradskyella strain (Flavobacteriia) led to the collapse of the microalga culture. Co-cultivation of the beneficial and the antagonistic strains also led to the loss of the microalga cells. Metagenomic analysis of the microcosm is consistent with vitamin B12 synthesis by the Roseovarius strains and unveiled two additional species affiliated to Balneola (Balneolia) and Muricauda (Flavobacteriia), which represent less than 4% of the reads, whereas Roseovarius and Winogradskyella recruit 57 and 39% of the reads, respectively. These results suggest that the low-frequency bacterial species may antagonize the algicidal effect of Winogradskyella in the microbiome of Ostreococcus tauri and thus stabilize the microalga persistence in the microcosm. Altogether, these results open novel perspectives into long-term stability of phytoplankton cultures.}, } @article {pmid35463003, year = {2022}, author = {Qu, J and Zong, Z}, title = {Strongyloidiasis in a Patient Diagnosed by Metagenomic Next-Generation Sequencing: A Case Report.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {835252}, pmid = {35463003}, issn = {2296-858X}, abstract = {BACKGROUND: Strongylodiasis may be asymptomatic or cause mild gastrointestinal symptoms, and may be a fatal disseminated disease or Strongyloides hyperinfection syndrome. Non-specific clinical manifestations, such as pneumonia and gastroenteritis, pose a diagnostic dilemma.

CASE PRESENTATION: We report a case of a 67-year-old Chinese male who presented with abdominal pain, fever, headache, vomiting, constipation, and slight cough with sputum for nearly 2 months. He had been in good health and had no history of glucocorticoid use. He was diagnosed with enterococcal meningitis and intestinal obstruction at a local hospital and improved after treatment with vancomycin, but symptoms of headache and abdominal pain soon recurred. The metagenomic next-generation sequencing (mNGS) of the cerebrospinal fluid using Illumina X10 sequencer revealed seven sequence reads matching Strongyloides stercoralis. Strongyloidiasis was suspected. Microscopic examination of gastric fluid revealed the presence of S. stercoralis larvae, which was confirmed by PCR to amplify both S. stercoralis ribosomal DNA gene and mitochondrial cytochrome c oxidase subunit 1 gene and sequencing amplicons. Strongyloidiasis was diagnosed. Albendazole (400 mg, twice daily) was used, and the patient recovered gradually.

CONCLUSION: mNGS may be a useful tool for detecting uncommon infectious disease. The case would help clinicians to raise awareness of strongyloidiasis in non-endemic areas and reduce fatality.}, } @article {pmid35462994, year = {2022}, author = {Ma, N and Chen, M and Ding, J and Wang, F and Jin, J and Fan, S and Chen, J}, title = {Recurrent Pneumonia With Tuberculosis and Candida Co-infection Diagnosed by Metagenomic Next-Generation Sequencing: A Case Report and Literature Review.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {755308}, pmid = {35462994}, issn = {2296-858X}, abstract = {An 82-year-old male patient was hospitalized in the Respiratory Department for "repeated cough and shortness of breath for 10 years, recurrence worsened for 1 month." Later, he was transferred for further diagnosis and treatment, to the Infectious Disease Department for further hospitalization. Previously, the patient had repeatedly undergone tuberculosis-related examinations including bronchoscopy examinations. However, no evidence of Mycobacterium tuberculosis (MTB) infection was found. Early anti-infection treatments failed. Due to repeated symptoms, we performed bronchoscopy again and sent alveolar lavage fluid for the metagenomic next-generation sequencing (mNGS) test. Subsequently, MTB and Candida albicans were detected by mNGS. After antituberculosis and antifungal treatments, the symptoms were significantly relieved, and the chest CT showed resolution of the lung lesions. Therefore, we successfully diagnosed and treated a case of recurrent pneumonia with tuberculosis and Candida co-infection diagnosed by mNGS.}, } @article {pmid35462719, year = {2022}, author = {Sagar, I and Nimonkar, Y and Dhotre, D and Shouche, Y and Ranade, D and Dewala, S and Prakash, O}, title = {A Microcosm Model for the Study of Microbial Community Shift and Carbon Emission from Landfills.}, journal = {Indian journal of microbiology}, volume = {62}, number = {2}, pages = {195-203}, pmid = {35462719}, issn = {0046-8991}, abstract = {UNLABELLED: The landfill is an inexpensive way of municipal solid waste (MSW) management and contributes extensively to the total carbon budget and global climate change. Three landfills from two geographically distinct metro- cities of India were taken as model systems to create microcosms and study their physiochemistry, microbiology, and carbon emission. The microcosm experiments revealed that facultative anaerobic bacterial community showing the dominance in the beginning but with the progression of anoxia and anaerobic conditions, methanogenesis prevailed, resulting in a clear shift towards the abundance of methanogens especially the members of Methanosarcina, Methanocorpusculum, and Methanoculleus (70-90% of the total microbial population). Geochemical data showed a wide range of heterogeneity in landfills' composition located even in the same city. In past, greenhouse gas emission from landfills is mainly estimated using different models which lack accuracy. As limited information is available as of now, this study can elicit researcher interest for in-depth characterization of microbial diversity and carbon emission from landfills. The microcosm model presented in the current study is a robust and straightforward method of accurate estimation of amounts of different types of gases release from landfill. It can also be extrapolate for estimation of different gases release from actual landfill sites by setting the on-site experiments.

SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s12088-021-00995-7.}, } @article {pmid35460847, year = {2022}, author = {Liu, Z and Dong, WT and Wei, WF and Huo, JH and Wang, WM}, title = {Exploring the mechanism of Qinbaiqingfei-concentrate pills in the treatment of Mycoplasma pneumoniae pneumonia from the perspective of intestinal microbiota and mucosal immunity.}, journal = {Journal of ethnopharmacology}, volume = {293}, number = {}, pages = {115308}, doi = {10.1016/j.jep.2022.115308}, pmid = {35460847}, issn = {1872-7573}, mesh = {Animals ; *Drugs, Chinese Herbal/therapeutic use ; *Gastrointestinal Microbiome ; *Immunity, Mucosal ; Immunoglobulin A, Secretory ; Interleukin-10 ; Interleukin-4 ; Mycoplasma pneumoniae ; NF-kappa B/metabolism ; *Pneumonia, Mycoplasma/drug therapy ; Rats ; Tumor Necrosis Factor-alpha ; }, abstract = {Traditional Chinese medicine categorizes Mycoplasma pneumoniae pneumonia as "lung heat", and treatment with heat clear and detoxify. Traditional Chinese medicine believes that the lungs and intestines come from the same source, and the intestine is related to pneumonia. This is the same as the gut-lung axis theory. Qinbaiqingfei concentrate pills (QBs) were modified based on Cough San in the ancient medical book Medical Awareness. It clears lung heat, moisturizes the lungs and dredges collaterals, and has a good ability to treat Mycoplasma pneumoniae.

AIM OF THE STUDY: A rat model of Mycoplasma pneumoniae was established. From the aspect of intestinal flora and mucosal immunity, the potential mechanism of the QBs was researched.

MATERIALS AND METHODS: First, the content of Mycoplasma pneumoniae in lung tissue and the levels of the inflammatory factors IL-4, IL-10, TNF-α and INF-γ were detected. To determine the expression of NF-kB related proteins in lung tissue, which can understand the ability in treating disease. Next, metagenomic sequencing was performed to detect changes in short-chain fatty acids, proving the ability of the drug to regulate intestinal microecology. Finally, HDAC, LPS, SIgA, etc. were detected to facilitate the correlation of the overall experimental indicators.

RESULTS: QBs reduces the levels of IL-4, IL-10, TNF-α and INF-γ in the serum by inhibiting the expression of MyD88, IKKα, IκBα, and NF-κB p65 in lung tissue. In addition, QBs restores the ratio of gram-negative bacteria to gram-positive bacteria in the intestine, restores the secretion of acetic acid, propionic acid, butyric acid, isobutyric acid and isovaleric acid, and promotes the secretion of NF-κB p65 and SIgA by HDAC1/3. The result is that the lung tissue is repaired and the proliferation of Mycoplasma pneumoniae is inhibited.

CONCLUSIONS: From the "gut-lung axis", a new research perspective was discovered. QBs intervened in the intestines and lungs to treat Mycoplasma pneumoniae.}, } @article {pmid35460297, year = {2022}, author = {Geraerts, M and Vangestel, C and Artois, T and Fernandes, JMO and Jorissen, MWP and Chocha Manda, A and Danadu Mizani, C and Smeets, K and Snoeks, J and Sonet, G and Tingbao, Y and Van Steenberge, M and Vreven, E and Lunkayilakio Wamuini, S and Vanhove, MPM and Huyse, T}, title = {Population genomics of introduced Nile tilapia Oreochromis niloticus (Linnaeus, 1758) in the Democratic Republic of the Congo: Repeated introductions since colonial times with multiple sources.}, journal = {Molecular ecology}, volume = {31}, number = {12}, pages = {3304-3322}, doi = {10.1111/mec.16479}, pmid = {35460297}, issn = {1365-294X}, mesh = {Animals ; Aquaculture ; *Cichlids/genetics ; Democratic Republic of the Congo ; Introduced Species ; Metagenomics ; }, abstract = {During colonial times, Nile tilapia Oreochromis niloticus (Linnaeus, 1758) was introduced into non-native parts of the Congo Basin (Democratic Republic of the Congo, DRC) for the first time. Currently, it is the most farmed cichlid in the DRC, and is present throughout the Congo Basin. Although Nile tilapia has been reported as an invasive species, documentation of historical introductions into this basin and its consequences are scant. Here, we study the genetic consequences of these introductions by genotyping 213 Nile tilapia from native and introduced regions, focusing on the Congo Basin. Additionally, 48 specimens from 16 other tilapia species were included to test for hybridization. Using RAD sequencing (27,611 single nucleotide polymorphisms), we discovered genetic admixture with other tilapia species in several morphologically identified Nile tilapia from the Congo Basin, reflecting their ability to interbreed and the potential threat they pose to the genetic integrity of native tilapias. Nile tilapia populations from the Upper Congo and those from the Middle-Lower Congo are strongly differentiated. The former show genetic similarity to Nile tilapia from the White Nile, while specimens from the Benue Basin and Lake Kariba are similar to Nile tilapia from the Middle-Lower Congo, suggesting independent introductions using different sources. We conclude that the presence of Nile tilapia in the Congo Basin results from independent introductions, reflecting the dynamic aquaculture history, and that their introduction probably leads to genetic interactions with native tilapias, which could lower their fitness. We therefore urge avoiding further introductions of Nile tilapia in non-native regions and to use native tilapias in future aquaculture efforts.}, } @article {pmid35460223, year = {2022}, author = {Wang, S and Li, G and Liao, Z and Cao, Y and Yun, Y and Su, Z and Tian, X and Gui, Z and Ma, T}, title = {CnnPOGTP: a novel CNN-based predictor for identifying the optimal growth temperatures of prokaryotes using only genomic k-mers distribution.}, journal = {Bioinformatics (Oxford, England)}, volume = {38}, number = {11}, pages = {3106-3108}, doi = {10.1093/bioinformatics/btac289}, pmid = {35460223}, issn = {1367-4811}, mesh = {Sequence Analysis, DNA ; *Software ; Temperature ; *Algorithms ; Genomics ; Metagenome ; }, abstract = {SUMMARY: Temperature is very important for the growth of microorganisms. Appropriate temperature conditions can improve the possibility for isolation of currently uncultured microorganisms. The development of metagenomic binning technology had dramatically increased the availability of genomic information of prokaryotes, providing convenience to infer the optimal growth temperature (OGT). Here, we proposed CnnPOGTP, a predictor for OGTs of prokaryotes based on deep learning method using only k-mers distribution derived from genomic sequence. This method was annotation free, and the predicted OGT could be obtained by simply providing the genome sequence to the CnnPOGTP website.

http://www.orgene.net/CnnPOGTP.

SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.}, } @article {pmid35459792, year = {2022}, author = {Wilbanks, EG and Doré, H and Ashby, MH and Heiner, C and Roberts, RJ and Eisen, JA}, title = {Metagenomic methylation patterns resolve bacterial genomes of unusual size and structural complexity.}, journal = {The ISME journal}, volume = {16}, number = {8}, pages = {1921-1931}, pmid = {35459792}, issn = {1751-7370}, mesh = {Bacteria/genetics ; Genome, Bacterial ; *Metagenome ; *Metagenomics ; Methylation ; }, abstract = {The plasticity of bacterial and archaeal genomes makes examining their ecological and evolutionary dynamics both exciting and challenging. The same mechanisms that enable rapid genomic change and adaptation confound current approaches for recovering complete genomes from metagenomes. Here, we use strain-specific patterns of DNA methylation to resolve complex bacterial genomes from long-read metagenomic data of a marine microbial consortium, the "pink berries" of the Sippewissett Marsh (USA). Unique combinations of restriction-modification (RM) systems encoded by the bacteria produced distinctive methylation profiles that were used to accurately bin and classify metagenomic sequences. Using this approach, we finished the largest and most complex circularized bacterial genome ever recovered from a metagenome (7.9 Mb with >600 transposons), the finished genome of Thiohalocapsa sp. PB-PSB1 the dominant bacteria in the consortia. From genomes binned by methylation patterns, we identified instances of horizontal gene transfer between sulfur-cycling symbionts (Thiohalocapsa sp. PB-PSB1 and Desulfofustis sp. PB-SRB1), phage infection, and strain-level structural variation. We also linked the methylation patterns of each metagenome-assembled genome with encoded DNA methyltransferases and discovered new RM defense systems, including novel associations of RM systems with RNase toxins.}, } @article {pmid35459229, year = {2022}, author = {Liu, E and Lv, S and Yi, P and Feng, L and Deng, X and Xia, H and Xu, Y}, title = {Central nervous system infection with Seoul Orthohantavirus in a child after hematopoietic stem cell transplantation: a case report.}, journal = {Virology journal}, volume = {19}, number = {1}, pages = {75}, pmid = {35459229}, issn = {1743-422X}, mesh = {Animals ; *Central Nervous System Infections ; *Orthohantavirus ; *Hantavirus Infections ; *Hematopoietic Stem Cell Transplantation/adverse effects ; *Hemorrhagic Fever with Renal Syndrome/diagnosis ; Humans ; Immunoglobulin G ; Male ; Mice ; Seoul ; *Seoul virus/genetics ; }, abstract = {BACKGROUND: Patients with allogeneic hematopoietic stem cell transplantation (allo-HSCT) are prone to complicate viral infection. Central nervous system (CNS) involvement caused by the viruses is rare but with poor prognosis. Hantavirus, which usually cause hemorrhagic fever with renal syndrome (HFRS), and none case has been reported about these infection in allo-HSCT patients.

CASE PRESENTATION: In August 2021, a 13-year-old male child developed intermittent fever and refractory hypotension after allo-HSCT. Magnetic resonance imaging of the head revealed abnormal signal foci in the left midbrain cerebral peduncle and bilateral thalamus. His family reported traces of mouse activity in the patient's home kitchen. HFRS was suspected, but with no significant kidney damage. The specific immunoglobulin (Ig) G and M of hantavirus were negative. The metagenomic next-generation sequencing (mNGS) detected Seoul Orthohantavirus (SEOV) sequences directly in cerebrospinal fluid and blood.

CONCLUSIONS: Allo-HSCT patients are a high-risk group for infection. Usually the causative agent of infection is difficult to determine, and sometimes the site of infection is concealed. This report highlights the importance of suspecting hantavirus infection in allo-HSCT patients with CNS symptoms despite the absence of renal syndromes. The mNGS is a powerful tool for detecting pathogens. CNS infection with Seoul orthohantavirus in transplant patients is rare but possible as demonstrated in this case. To the best of our knowledge, this is the first reported case employing mNGS to diagnose SEOV caused CNS infection in an allo-HSCT patient.}, } @article {pmid35459224, year = {2022}, author = {Widder, S and Görzer, I and Friedel, B and Rahimi, N and Schwarz, S and Jaksch, P and Knapp, S and Puchhammer-Stöckl, E}, title = {Metagenomic sequencing reveals time, host, and body compartment-specific viral dynamics after lung transplantation.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {66}, pmid = {35459224}, issn = {2049-2618}, support = {V 585/FWF_/Austrian Science Fund FWF/Austria ; }, mesh = {Humans ; Lung ; *Lung Transplantation ; Metagenome ; Metagenomics/methods ; Transplant Recipients ; }, abstract = {BACKGROUND: The virome of lung transplant recipients (LTRs) under immunosuppressive therapy is dominated by non-pathogenic Anelloviridae and further includes several pathogenic viruses such as Herpesviruses or respiratory viruses. It is unclear whether the donor-derived virome in the transplanted lung influences recipient virome dynamics in other body compartments and if so, to which degree. Likewise, it is unknown whether dependencies exist among virus populations that mutually shape viral loads and kinetics.

RESULTS: To address these questions, we characterized viral communities in airways and plasma of 49 LTRs and analyzed their abundance patterns in a data modeling approach. We found distinct viral clusters that were specific for body compartments and displayed independent dynamics. These clusters robustly gathered specific viral species across the patient cohort. In the lung, viral cluster abundance associated with time after transplantation and we detected mutual exclusion of viral species within the same human host. In plasma, viral cluster dynamics were associated with the indication for transplantation lacking significant short-time changes. Interestingly, pathogenic viruses in the plasma co-occurred specifically with Alpha torque virus genogroup 4 and Gamma torque virus strains suggesting shared functional or ecological requirements.

CONCLUSIONS: In summary, the detailed analysis of virome dynamics after lung transplantation revealed host, body compartment, and time-specific dependency patterns among viruses. Furthermore, our results suggested genetic adaptation to the host microenvironment at the level of the virome and support the hypothesis of functional complementarity between Anellovirus groups and other persistent viruses. Video abstract.}, } @article {pmid35459180, year = {2022}, author = {Liu, J and Zhao, H and Feng, Z and Liu, Y and Feng, Q and Qian, S and Xu, L and Gao, H and Xie, Z}, title = {A severe case of human rhinovirus A45 with central nervous system involvement and viral sepsis.}, journal = {Virology journal}, volume = {19}, number = {1}, pages = {72}, pmid = {35459180}, issn = {1743-422X}, mesh = {Central Nervous System ; Child ; Diarrhea ; *Enterovirus ; Female ; Hematuria/complications ; Humans ; Male ; *Picornaviridae Infections/complications/diagnosis ; *Respiratory Tract Infections ; Rhinovirus ; Viremia ; }, abstract = {BACKGROUND: Rhinovirus is a common viral aetiology of upper respiratory infection and is mostly associated with common cold or flu-like illness. Although rhinovirus has been recognized as a pathogen for lower respiratory infections in severe cases credited to advances in molecular detection, central nervous system involvement and multiorgan dysfunction are extremely rare.

CASE PRESENTATION: A previously healthy 10-year-old girl developed fever, sore throat and conjunctive injection after contact with an upper respiratory infection patient, followed by seizures, haematuria, and severe diarrhoea. She experienced viral sepsis and multiorgan dysfunction after admission. Cerebral computed tomography showed significant diffuse encephaledema. Cerebrospinal fluid analysis showed significantly elevated protein levels. After her consciousness disturbance improved, she still took a long time to recover from haematuria and diarrhoea. We identified a rarely reported rhinovirus A45 in her oropharyngeal and anal swabs by metagenomic next-generation sequencing, and bacterial culture of blood specimens yielded negative results.

CONCLUSIONS: This case presents a patient with severe rhinovirus infection, which was very likely responsible for her central nervous system symptoms and viral sepsis.}, } @article {pmid35458526, year = {2022}, author = {Ludowyke, N and Phumiphanjarphak, W and Apiwattanakul, N and Manopwisedjaroen, S and Pakakasama, S and Sensorn, I and Pasomsub, E and Chantratita, W and Hongeng, S and Aiewsakun, P and Thitithanyanont, A}, title = {Target Enrichment Metagenomics Reveals Human Pegivirus-1 in Pediatric Hematopoietic Stem Cell Transplantation Recipients.}, journal = {Viruses}, volume = {14}, number = {4}, pages = {}, pmid = {35458526}, issn = {1999-4915}, mesh = {Child ; *Flaviviridae Infections ; *GB virus C/genetics ; *Hematopoietic Stem Cell Transplantation/adverse effects ; Humans ; Metagenomics ; Phylogeny ; RNA, Viral/genetics ; }, abstract = {Human pegivirus-1 (HPgV-1) is a lymphotropic human virus, typically considered nonpathogenic, but its infection can sometimes cause persistent viremia both in immunocompetent and immunosuppressed individuals. In a viral discovery research program in hematopoietic stem cell transplant (HSCT) pediatric patients, HPgV-1 was detected in 3 out of 14 patients (21.4%) using a target enrichment next-generation sequencing method, and the presence of the viruses was confirmed by agent-specific qRT-PCR assays. For the first time in this patient cohort, complete genomes of HPgV-1 were acquired and characterized. Phylogenetic analyses indicated that two patients had HPgV-1 genotype 2 and one had HPgV-1 genotype 3. Intra-host genomic variations were described and discussed. Our results highlight the necessity to screen HSCT patients and blood and stem cell donors to reduce the potential risk of HPgV-1 transmission.}, } @article {pmid35458219, year = {2022}, author = {Franck, M and de Toro-Martín, J and V Varin, T and Garneau, V and Pilon, G and Roy, D and Couture, P and Couillard, C and Marette, A and Vohl, MC}, title = {Gut Microbial Signatures of Distinct Trimethylamine N-Oxide Response to Raspberry Consumption.}, journal = {Nutrients}, volume = {14}, number = {8}, pages = {}, pmid = {35458219}, issn = {2072-6643}, support = {MRT-168045//CIHR/ ; not applicable//WA Red Raspberry Commission (WRRC)/ ; }, mesh = {Bacteria ; *Gastrointestinal Microbiome ; Humans ; Methylamines ; *Rubus/metabolism ; }, abstract = {The aim of this exploratory study was to evaluate the gut microbial signatures of distinct trimethylamine N-oxide (TMAO) responses following raspberry consumption. Investigations were carried out in 24 subjects at risk of developing metabolic syndrome who received 280 g/day of frozen raspberries for 8 weeks. Blood and stool samples were collected at weeks 0 and 8. Inter-individual variability in plasma TMAO levels was analyzed, 7 subjects were excluded due to noninformative signals and 17 subjects were kept for analysis and further stratified according to their TMAO response. Whole-metagenome shotgun sequencing analysis was used to determine the impact of raspberry consumption on gut microbial composition. Before the intervention, the relative abundance of Actinobacteriota was significantly higher in participants whose TMAO levels increased after the intervention (p = 0.03). The delta TMAO (absolute differences of baseline and week 8 levels) was positively associated with the abundance of gut bacteria such as Bilophila wadsworthia (p = 0.02; r[2] = 0.37), from the genus Granulicatella (p = 0.03; r[2] = 0.48) or the Erysipelotrichia class (p = 0.03; r[2] = 0.45). Changes in the gut microbial ecology induced by raspberry consumption over an 8-week period presumably impacted quaternary amines-utilizing activity and thus plasma TMAO levels.}, } @article {pmid35457694, year = {2022}, author = {Szulc, J and Okrasa, M and Nowak, A and Nizioł, J and Ruman, T and Kuberski, S}, title = {Assessment of Physicochemical, Microbiological and Toxicological Hazards at an Illegal Landfill in Central Poland.}, journal = {International journal of environmental research and public health}, volume = {19}, number = {8}, pages = {}, pmid = {35457694}, issn = {1660-4601}, mesh = {*Air Microbiology ; Bacteria ; *Dust/analysis ; Fungi ; Humans ; Poland ; Soil ; Waste Disposal Facilities ; }, abstract = {This study aimed to assess the physicochemical, microbiological and toxicological hazards at an illegal landfill in central Poland. The research included the analysis of airborne dust (laser photometer), the number of microorganisms in the air, soil and leachate (culture method) and the microbial diversity in the landfill environment (high-throughput sequencing on the Illumina Miseq); the cytotoxicity (PrestoBlue) and genotoxicity (alkaline comet assay) of soil and leachate were tested. Moreover, an analysis of UHPLC-Q-ToF-UHRMS (ultra-high-performance liquid chromatography-quadrupole-time-of-flight ultrahigh-resolution mass spectrometry) was performed to determine the toxic compounds and microbial metabolites. The PM1 dust fraction constituted 99.89% and 99.99% of total dust and exceeded the threshold of 0.025 mg m[-3] at the tested locations. In the air, the total number of bacteria was 9.33 × 10[1]-1.11 × 10[3] CFU m[-3], while fungi ranged from 1.17 × 10[2] to 4.73 × 10[2] CFU m[-3]. Psychrophilic bacteria were detected in the largest number in leachates (3.3 × 10[4] to 2.69 × 10[6] CFU mL[-1]) and in soil samples (8.53 × 10[5] to 1.28 × 10[6] CFU g[-1]). Bacteria belonging to Proteobacteria (42-64.7%), Bacteroidetes (4.2-23.7%), Actinobacteria (3.4-19.8%) and Firmicutes (0.7-6.3%) dominated. In the case of fungi, Basidiomycota (23.3-27.7%), Ascomycota (5.6-46.3%) and Mortierellomycota (3.1%) have the highest abundance. Bacteria (Bacillus, Clostridium, Cellulosimicrobium, Escherichia, Pseudomonas) and fungi (Microascus, Chrysosporium, Candida, Malassezia, Aspergillus, Alternaria, Fusarium, Stachybotrys, Cladosporium, Didymella) that are potentially hazardous to human health were detected in samples collected from the landfill. Tested leachates and soils were characterised by varied cyto/genotoxins. Common pesticides (carbamazepine, prometryn, terbutryn, permethrin, carbanilide, pyrethrin, carbaryl and prallethrin), quaternary ammonium compounds (benzalkonium chlorides), chemicals and/or polymer degradation products (melamine, triphenylphosphate, diphenylphtalate, insect repellent diethyltoluamide, and drugs (ketoprofen)) were found in soil and leachate samples. It has been proven that the tested landfill is the source of the emission of particulate matter; microorganisms (including potential pathogens) and cyto/genotoxic compounds.}, } @article {pmid35456888, year = {2022}, author = {Tsiantas, K and Konteles, SJ and Kritsi, E and Sinanoglou, VJ and Tsiaka, T and Zoumpoulakis, P}, title = {Effects of Non-Polar Dietary and Endogenous Lipids on Gut Microbiota Alterations: The Role of Lipidomics.}, journal = {International journal of molecular sciences}, volume = {23}, number = {8}, pages = {}, pmid = {35456888}, issn = {1422-0067}, support = {T2EDK- 03847//European Union and Greek national funds (European Social Fund - ESF) - Operational Program Competitiveness, Entrepreneurship and Innovation/ ; }, mesh = {Carotenoids/pharmacology ; Dietary Fats/pharmacology ; *Gastrointestinal Microbiome ; Lipidomics ; Sterols/pharmacology ; }, abstract = {Advances in sequencing technologies over the past 15 years have led to a substantially greater appreciation of the importance of the gut microbiome to the health of the host. Recent outcomes indicate that aspects of nutrition, especially lipids (exogenous or endogenous), can influence the gut microbiota composition and consequently, play an important role in the metabolic health of the host. Thus, there is an increasing interest in applying holistic analytical approaches, such as lipidomics, metabolomics, (meta)transcriptomics, (meta)genomics, and (meta)proteomics, to thoroughly study the gut microbiota and any possible interplay with nutritional or endogenous components. This review firstly summarizes the general background regarding the interactions between important non-polar dietary (i.e., sterols, fat-soluble vitamins, and carotenoids) or amphoteric endogenous (i.e., eicosanoids, endocannabinoids-eCBs, and specialized pro-resolving mediators-SPMs) lipids and gut microbiota. In the second stage, through the evaluation of a vast number of dietary clinical interventions, a comprehensive effort is made to highlight the role of the above lipid categories on gut microbiota and vice versa. In addition, the present status of lipidomics in current clinical interventions as well as their strengths and limitations are also presented. Indisputably, dietary lipids and most phytochemicals, such as sterols and carotenoids, can play an important role on the development of medical foods or nutraceuticals, as they exert prebiotic-like effects. On the other hand, endogenous lipids can be considered either prognostic indicators of symbiosis or dysbiosis or even play a role as specialized mediators through dietary interventions, which seem to be regulated by gut microbiota.}, } @article {pmid35456791, year = {2022}, author = {Ashniev, GA and Petrov, SN and Iablokov, SN and Rodionov, DA}, title = {Genomics-Based Reconstruction and Predictive Profiling of Amino Acid Biosynthesis in the Human Gut Microbiome.}, journal = {Microorganisms}, volume = {10}, number = {4}, pages = {}, pmid = {35456791}, issn = {2076-2607}, support = {DK030292-35//National Institute of Health/ ; 19-14-00305//Russian Science Foundation/ ; }, abstract = {The human gut microbiota (HGM) have an impact on host health and disease. Amino acids are building blocks of proteins and peptides, also serving as precursors of many essential metabolites including nucleotides, cofactors, etc. Many HGM community members are unable to synthesize some amino acids (auxotrophs), while other members possess complete biosynthetic pathways for these nutrients (prototrophs). Metabolite exchange between auxotrophs and prototrophs affects microbial community structure. Previous studies of amino acid biosynthetic phenotypes were limited to model species or narrow taxonomic groups of bacteria. We analyzed over 2800 genomes representing 823 cultured HGM species with the aim to reconstruct biosynthetic pathways for proteinogenic amino acids. The genome context analysis of incomplete pathway variants allowed us to identify new potential enzyme variants in amino acid biosynthetic pathways. We further classified the studied organisms with respect to their pathway variants and inferred their prototrophic vs. auxotrophic phenotypes. A cross-species comparison was applied to assess the extent of conservation of the assigned phenotypes at distinct taxonomic levels. The obtained reference collection of binary metabolic phenotypes was used for predictive metabolic profiling of HGM samples from several large metagenomic datasets. The established approach for metabolic phenotype profiling will be useful for prediction of overall metabolic properties, interactions, and responses of HGM microbiomes as a function of dietary variations, dysbiosis and other perturbations.}, } @article {pmid35456780, year = {2022}, author = {Woods, AC and Walker, JR and Jackson, CD and Labonté, JM}, title = {Record-Breaking Rain Event Altered Estuarine Viral Assemblages.}, journal = {Microorganisms}, volume = {10}, number = {4}, pages = {}, pmid = {35456780}, issn = {2076-2607}, support = {1801367//National Science Foundation/ ; }, abstract = {Viruses are the dominant biological entity in the ocean, play a vital role in biogeochemical cycles, and provide their hosts with novel metabolic capabilities through auxiliary metabolic genes (AMGs). Hurricane Harvey was a category 4 hurricane that made landfall on the Texas coast in 2017 and lashed the Houston area with 1.4-1.7 × 10[10] m[3] of rainfall. In this paper, we aim to characterize how the changes in abiotic conditions brought by Hurricane Harvey altered the viral assemblages of Galveston Bay at the taxonomic level and determine how viral ecosystem functions were altered. Metagenomes of the viruses and their hosts were sequenced from a transect in Galveston Bay over the five weeks following the storm. Our results show that the viral assemblages of Galveston Bay dramatically changed following Hurricane Harvey's landfall. Of the abiotic parameters measured, salinity had the strongest effect on shaping the viral assemblages. In the five weeks following Hurricane Harvey, there was a steady increase of metabolic genes and putative viral infections. Our study provides the first in-depth look at how marine viral assemblages respond and recover from extreme rainfall events, which models predict will become more frequent and intense with climate change.}, } @article {pmid35456762, year = {2022}, author = {Buffet-Bataillon, S and Rizk, G and Cattoir, V and Sassi, M and Thibault, V and Del Giudice, J and Gangneux, JP}, title = {Efficient and Quality-Optimized Metagenomic Pipeline Designed for Taxonomic Classification in Routine Microbiological Clinical Tests.}, journal = {Microorganisms}, volume = {10}, number = {4}, pages = {}, pmid = {35456762}, issn = {2076-2607}, support = {"Transfert de technologies des filières Santé et Biotechnologies" 2018//Région Bretagne, France/ ; }, abstract = {Metagenomics analysis is now routinely used for clinical diagnosis in several diseases, and we need confidence in interpreting metagenomics analysis of microbiota. Particularly from the side of clinical microbiology, we consider that it would be a major milestone to further advance microbiota studies with an innovative and significant approach consisting of processing steps and quality assessment for interpreting metagenomics data used for diagnosis. Here, we propose a methodology for taxon identification and abundance assessment of shotgun sequencing data of microbes that are well fitted for clinical setup. Processing steps of quality controls have been developed in order (i) to avoid low-quality reads and sequences, (ii) to optimize abundance thresholds and profiles, (iii) to combine classifiers and reference databases for best classification of species and abundance profiles for both prokaryotic and eukaryotic sequences, and (iv) to introduce external positive control. We find that the best strategy is to use a pipeline composed of a combination of different but complementary classifiers such as Kraken2/Bracken and Kaiju. Such improved quality assessment will have a major impact on the robustness of biological and clinical conclusions drawn from metagenomic studies.}, } @article {pmid35456752, year = {2022}, author = {Wosinska, L and Walsh, CJ and O'Connor, PM and Lawton, EM and Cotter, PD and Guinane, CM and O'Sullivan, O}, title = {In Vitro and In Silico Based Approaches to Identify Potential Novel Bacteriocins from the Athlete Gut Microbiome of an Elite Athlete Cohort.}, journal = {Microorganisms}, volume = {10}, number = {4}, pages = {}, pmid = {35456752}, issn = {2076-2607}, abstract = {Exercise reduces inflammation, fatigue, and aids overall health. Additionally, physical fitness has been associated with desirable changes in the community composition of the athlete gut microbiome, with health-associated taxa being shown to be increased in active individuals. Here, using a combination of in silico and in vitro methods, we investigate the antimicrobial activity of the athlete gut microbiome. In vitro approaches resulted in the generation of 284 gut isolates with inhibitory activity against Clostridioides difficile and/or Fusobacterium nucleatum, and the most potent isolates were further characterized, and potential bacteriocins were predicted using both MALDI-TOF MS and whole-genome sequencing. Additionally, metagenomic reads from the faecal samples were used to recover 770 Metagenome Assembled Genomes (MAGs), of which 148 were assigned to be high-quality MAGs and screened for the presence of putative bacteriocin gene clusters using BAGEL4 software, with 339 gene clusters of interest being identified. Class I was the most abundant bacteriocin class predicted, accounting for 91.3% of predictions, Class III had a predicted abundance of 7.5%, and Class II was represented by just 1% of all predictions.}, } @article {pmid35456751, year = {2022}, author = {Néron, B and Littner, E and Haudiquet, M and Perrin, A and Cury, J and Rocha, EPC}, title = {IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella.}, journal = {Microorganisms}, volume = {10}, number = {4}, pages = {}, pmid = {35456751}, issn = {2076-2607}, support = {ANR-16-CONV-0005//Agence Nationale de la Recherche/ ; ANR-10-LABX-62-IBEID//Agence Nationale de la Recherche/ ; EQU201903007835//Fondation pour la Recherche Médicale/ ; }, abstract = {Integrons are flexible gene-exchanging platforms that contain multiple cassettes encoding accessory genes whose order is shuffled by a specific integrase. Integrons embedded within mobile genetic elements often contain multiple antibiotic resistance genes that they spread among nosocomial pathogens and contribute to the current antibiotic resistance crisis. However, most integrons are presumably sedentary and encode a much broader diversity of functions. IntegronFinder is a widely used software to identify novel integrons in bacterial genomes, but has aged and lacks some useful functionalities to handle very large datasets of draft genomes or metagenomes. Here, we present IntegronFinder version 2. We have updated the code, improved its efficiency and usability, adapted the output to incomplete genome data, and added a few novel functions. We describe these changes and illustrate the relevance of the program by analyzing the distribution of integrons across more than 20,000 fully sequenced genomes. We also take full advantage of its novel capabilities to analyze close to 4000 Klebsiella pneumoniae genomes for the presence of integrons and antibiotic resistance genes within them. Our data show that K. pneumoniae has a large diversity of integrons and the largest mobile integron in our database of plasmids. The pangenome of these integrons contains a total of 165 different gene families with most of the largest families being related with resistance to numerous types of antibiotics. IntegronFinder is a free and open-source software available on multiple public platforms.}, } @article {pmid35456722, year = {2022}, author = {Mutungwazi, A and Ijoma, GN and Ogola, HJO and Matambo, TS}, title = {Physico-Chemical and Metagenomic Profile Analyses of Animal Manures Routinely Used as Inocula in Anaerobic Digestion for Biogas Production.}, journal = {Microorganisms}, volume = {10}, number = {4}, pages = {}, pmid = {35456722}, issn = {2076-2607}, support = {2018/FUN/0166//Technology Innovation Agency/ ; DST/CON 0197/2017//South African Department of Science and Innovation/ ; }, abstract = {Anaerobic digestion (AD) of organic waste is considered a sustainable solution to energy shortage and waste management challenges. The process is facilitated by complex communities of micro-organisms, yet most wastes do not have these and thus need microbial inoculation using animal manures to initiate the process. However, the degradation efficiency and methane yield achieved in using different inocula vary due to their different microbial diversities. This study used metagenomics tools to compare the autochthonous microbial composition of cow, pig, chicken, and horse manures commonly used for biogas production. Cows exhibited the highest carbon utilisation (>30%) and showed a carbon to nitrogen ratio (C/N) favourable for microbial growth. Pigs showed the least nitrogen utilisation (<3%) which explains their low C/N whilst horses showed the highest nitrogen utilisation (>40%), which explains its high C/N above the optimal range of 20−30 for efficient AD. Manures from animals with similar gastrointestinal tract (GIT) physiologies were observed to largely harbour similar microbial communities. Conversely, some samples from animals with different GITs also shared common microbial communities plausibly because of similar diets and rearing conditions. Insights from this study will lay a foundation upon which in-depth studies of AD metabolic pathways and strategies to boost methane production through efficient catalysis can be derived.}, } @article {pmid35456018, year = {2022}, author = {Henry, C and Bassignani, A and Berland, M and Langella, O and Sokol, H and Juste, C}, title = {Modern Metaproteomics: A Unique Tool to Characterize the Active Microbiome in Health and Diseases, and Pave the Road towards New Biomarkers-Example of Crohn's Disease and Ulcerative Colitis Flare-Ups.}, journal = {Cells}, volume = {11}, number = {8}, pages = {}, pmid = {35456018}, issn = {2073-4409}, mesh = {Biomarkers/metabolism ; *Colitis, Ulcerative/diagnosis ; *Crohn Disease/diagnosis ; Feces ; Humans ; *Microbiota ; }, abstract = {Thanks to the latest developments in mass spectrometry, software and standards, metaproteomics is emerging as the vital complement of metagenomics, to make headway in understanding the actual functioning of living and active microbial communities. Modern metaproteomics offers new possibilities in the area of clinical diagnosis. This is illustrated here, for the still highly challenging diagnosis of intestinal bowel diseases (IBDs). Using bottom-up proteomics, we analyzed the gut metaproteomes of the same twenty faecal specimens processed either fresh or after a two-month freezing period. We focused on metaproteomes of microbial cell envelopes since it is an outstanding way of capturing host and host-microbe interaction signals. The protein profiles of pairs of fresh and frozen-thawed samples were closely related, making feasible deferred analysis in a distant diagnosis centre. The taxonomic and functional landscape of microbes in diverse IBD phenotypes-active ulcerative colitis, or active Crohn's disease either with ileo-colonic or exclusive colonic localization-differed from each other and from the controls. Based on their specific peptides, we could identify proteins that were either strictly overrepresented or underrepresented in all samples of one clinical group compared to all samples of another group, paving the road for promising additional diagnostic tool for IBDs.}, } @article {pmid35455680, year = {2022}, author = {Park, J and Lee, JJ and Hong, Y and Seo, H and Shin, TS and Hong, JY}, title = {Metagenomic Analysis of Plasma Microbial Extracellular Vesicles in Patients Receiving Mechanical Ventilation: A Pilot Study.}, journal = {Journal of personalized medicine}, volume = {12}, number = {4}, pages = {}, pmid = {35455680}, issn = {2075-4426}, support = {HI21C1624//Korea Health Industry Development Institute/Republic of Korea ; 2020R1A2C1011455//National Research Foundation of Korea/ ; }, abstract = {BACKGROUND: Previous studies reported a significant association between pneumonia outcome and the respiratory microbiome. There is increasing interest in the roles of bacterial extracellular vesicles (EVs) in various diseases. We studied the composition and function of microbiota-derived EVs in the plasma of patients receiving mechanical ventilation to evaluate whether they can be used as a diagnostic marker and to predict clinical outcomes.

METHODS: Plasma samples (n = 111) from 59 mechanically ventilated patients (41 in the pneumonia group; 24 in the nursing home and hospital-associated infection [NHAI] group) were prospectively collected on days one and seven. After isolating the bacterial EVs from plasma samples, nucleic acid was extracted for 16S rRNA gene pyrosequencing. The samples were evaluated to determine the α and β diversity, bacterial composition, and predicted functions.

RESULTS: Principal coordinates analysis revealed significantly different clustering of microbial EVs between the pneumonia and non-pneumonia groups. The proportions of Lactobacillus, Cutibacterium, and Sphingomonas were significantly different between the pneumonia and non-pneumonia groups. In addition, the abundances of Lactobacillus and Bifidobacterium were significantly higher in the non-NHAI than the NHAI group. In the analysis of β diversity, the structure of microbial EVs differed significantly different between 28-day survivors and non-survivors (Bray-Curtis distance, p = 0.014). Functional profiling revealed significant differences between the pneumonia and non-pneumonia groups. The longitudinal change in predicted functions of microbial EV genes showed a significant difference between 28-day survivors and non-survivors.

CONCLUSIONS: Bacterial microbiota-derived EVs in the plasma have potential as diagnostic and prognostic markers for patients receiving mechanical ventilation. Further large prospective studies are needed to determine the clinical utility of plasma microbiota-EVs in intubated patients.}, } @article {pmid35453804, year = {2022}, author = {Bryanskaya, AV and Shipova, AA and Rozanov, AS and Kolpakova, OA and Lazareva, EV and Uvarova, YE and Efimov, VM and Zhmodik, SM and Taran, OP and Goryachkovskaya, TN and Peltek, SE}, title = {Diversity and Metabolism of Microbial Communities in a Hypersaline Lake along a Geochemical Gradient.}, journal = {Biology}, volume = {11}, number = {4}, pages = {}, pmid = {35453804}, issn = {2079-7737}, support = {FWNR-2022-0022//Ministry of Science and Higher Education of the Russian Federation/ ; }, abstract = {In the south of western Siberia (Russia), there are many unique and unexplored soda, saline, and freshwater lakes. In this study, the results are presented on microbial diversity, its metabolic potential, and their relation with a set of geochemical parameters for a hypersaline lake ecosystem in the Novosibirsk region (Oblast). The metagenomic approach used in this work allowed us to determine the composition and structure of a floating microbial community, the upper layer of silt, and the strata of bottom sediments in a natural saline lake via two bioinformatic approaches, whose results are in good agreement with each other. In the floating microbial community and in the upper layers of the bottom sediment, bacteria of the Proteobacteria (Gammaproteobacteria), Cyanobacteria, and Bacteroidetes phyla were found to predominate. The lower layers were dominated by Proteobacteria (mainly Deltaproteobacteria), Gemmatimonadetes, Firmicutes, and Archaea. Metabolic pathways were reconstructed to investigate the metabolic potential of the microbial communities and other hypothetical roles of the microbial communities in the biogeochemical cycle. Relations between different taxa of microorganisms were identified, as was their potential role in biogeochemical transformations of C, N, and S in a comparative structural analysis that included various ecological niches.}, } @article {pmid35453798, year = {2022}, author = {Malfertheiner, L and Martínez-Pérez, C and Zhao, Z and Herndl, GJ and Baltar, F}, title = {Phylogeny and Metabolic Potential of the Candidate Phylum SAR324.}, journal = {Biology}, volume = {11}, number = {4}, pages = {}, pmid = {35453798}, issn = {2079-7737}, abstract = {The bacterial SAR324 cluster is ubiquitous and abundant in the ocean, especially around hydrothermal vents and in the deep sea, where it can account for up to 30% of the whole bacterial community. According to a new taxonomy generated using multiple universal protein-coding genes (instead of the previously used 16S rRNA single gene marker), the former Deltaproteobacteria cluster SAR324 has been classified since 2018 as its own phylum. Yet, very little is known about its phylogeny and metabolic potential. We downloaded all publicly available SAR324 genomes (65) from all natural environments and reconstructed 18 new genomes using publicly available oceanic metagenomic data and unpublished data from the waters underneath the Ross Ice Shelf. We calculated a global SAR324 phylogenetic tree and identified six clusters (namely 1A, 1B, 2A, 2B, 2C and 2D) within this clade. Genome annotation and metatranscriptome read mapping showed that SAR324 clades possess a flexible array of genes suited for survival in various environments. Clades 2A and 2C are mostly present in the surface mesopelagic layers of global oceans, while clade 2D dominates in deeper regions. Our results show that SAR324 has a very versatile and broad metabolic potential, including many heterotrophic, but also autotrophic pathways. While one surface water associated clade (2A) seems to use proteorhodopsin to gain energy from solar radiation, some deep-sea genomes from clade 2D contain the complete Calvin-Benson-Bassham cycle gene repertoire to fix carbon. This, in addition to a variety of other genes and pathways for both oxic (e.g., dimethylsulfoniopropionate degradation) and anoxic (e.g., dissimilatory sulfate reduction, anaerobic benzoate degradation) conditions, can help explain the ubiquitous presence of SAR324 in aquatic habitats.}, } @article {pmid35453238, year = {2022}, author = {Andrés-Lasheras, S and Jelinski, M and Zaheer, R and McAllister, TA}, title = {Bovine Respiratory Disease: Conventional to Culture-Independent Approaches to Studying Antimicrobial Resistance in North America.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {4}, pages = {}, pmid = {35453238}, issn = {2079-6382}, support = {ANH 30.17//Beef Cattle Research Council/ ; 001//Genomics Research and Development Initiative/ ; 001//University of Calgary One Health Consortium, Major Innovation Fund, Government of Alberta/ ; }, abstract = {Numerous antimicrobial resistance (AMR) surveillance studies have been conducted in North American feedlot cattle to investigate the major bacterial pathogens of the bovine respiratory disease (BRD) complex, specifically: Mannheimia haemolytica, Pasteurella multocida, Histophilus somni, and Mycoplasma bovis. While most bacterial isolates recovered from healthy cattle are susceptible to a repertoire of antimicrobials, multidrug resistance is common in isolates recovered from cattle suffering from BRD. Integrative and conjugative elements (ICE) have gained increasing notoriety in BRD-Pasteurellaceae as they appear to play a key role in the concentration and dissemination of antimicrobial resistant genes. Likewise, low macrolide susceptibility has been described in feedlot isolates of M. bovis. Horizontal gene transfer has also been implicated in the spread of AMR within mycoplasmas, and in-vitro experiments have shown that exposure to antimicrobials can generate high levels of resistance in mycoplasmas via a single conjugative event. Consequently, antimicrobial use (AMU) could be accelerating AMR horizontal transfer within all members of the bacterial BRD complex. While metagenomics has been applied to the study of AMR in the microbiota of the respiratory tract, the potential role of the respiratory tract microbiome as an AMR reservoir remains uncertain. Current and prospective molecular tools to survey and characterize AMR need to be adapted as point-of-care technologies to enhance prudent AMU in the beef industry.}, } @article {pmid35453219, year = {2022}, author = {Fésüs, A and Benkő, R and Matuz, M and Engi, Z and Ruzsa, R and Hambalek, H and Illés, Á and Kardos, G}, title = {Impact of Guideline Adherence on Outcomes in Patients Hospitalized with Community-Acquired Pneumonia (CAP) in Hungary: A Retrospective Observational Study.}, journal = {Antibiotics (Basel, Switzerland)}, volume = {11}, number = {4}, pages = {}, pmid = {35453219}, issn = {2079-6382}, abstract = {Community-acquired pneumonia (CAP) is a leading cause of morbidity and mortality worldwide. This retrospective observational study evaluated the antibiotic prescription patterns and associations between guideline adherence and outcomes in patients hospitalized with CAP in Hungary. Main outcome measures were adherence to national and international CAP guidelines (agent choice, dose) when using empirical antibiotics, antibiotic exposure, and clinical outcomes. Demographic and clinical characteristics of patients with CAP in the 30-day mortality and 30-day survival groups were compared. Fisher’s exact test and t-test were applied to compare categorical and continuous variables, respectively. Adherence to the national CAP guideline for initial empirical therapies was 30.61% (45/147) for agent choice and 88.89% (40/45) for dose. Average duration of antibiotic therapy for CAP was 7.13 ± 4.37 (mean ± SD) days, while average antibiotic consumption was 11.41 ± 8.59 DDD/patient (range 1−44.5). Adherence to national guideline led to a slightly lower 30-day mortality rate than guideline non-adherence (15.56% vs. 16.67%, p > 0.05). In patients aged ≥ 85 years, 30-day mortality was 3 times higher than in those aged 65−84 years (30.43% vs. 11.11%). A significant difference was found between 30-day non-survivors and 30-day survivors regarding the average CRP values on admission (177.28 ± 118.94 vs. 112.88 ± 93.47 mg/L, respectively, p = 0.006) and CCI score (5.71 ± 1.85 and 4.67 ± 1.83, p = 0.012). We found poor adherence to the national and international CAP guidelines in terms of agent choice. In addition, high CRP values on admission were markedly associated with higher mortality in CAP.}, } @article {pmid35452382, year = {2022}, author = {Hua, X and Cao, Y and Morgan, DM and Miller, K and Chin, SM and Bellavance, D and Khalili, H}, title = {Longitudinal analysis of the impact of oral contraceptive use on the gut microbiome.}, journal = {Journal of medical microbiology}, volume = {71}, number = {4}, pages = {}, doi = {10.1099/jmm.0.001512}, pmid = {35452382}, issn = {1473-5644}, mesh = {Child, Preschool ; Contraceptives, Oral/pharmacology ; Estradiol ; Female ; *Gastrointestinal Microbiome ; Gonadal Steroid Hormones ; Humans ; Testosterone ; }, abstract = {Introduction. Evidence has linked exogenous and endogenous sex hormones with the human microbiome.Hypothesis/Gap statement. The longitudinal effects of oral contraceptives (OC) on the human gut microbiome have not previously been studied.Aim. We sought to examine the longitudinal impact of OC use on the taxonomic composition and metabolic functions of the gut microbiota and endogenous sex steroid hormones after initiation of OC use.Methodology. We recruited ten healthy women who provided blood and stool samples prior to OC use, 1 month and 6 months after starting OC. We measured serum levels of sex hormones, including estradiol, progesterone, sex hormone-binding globulin (SHBG), and total testosterone. Shotgun metagenomic sequencing was performed on DNA extracted from faecal samples. Species and metabolic pathway abundances were determined using MetaPhlAn2 and HUMAnN2. Multivariate association with linear models was used to identify microbial species and metabolic pathways associated with OC use and endogenous levels of sex hormones.Results. The percentage variance of the microbial community explained by individual factors ranged from 9.9 % for age to 2.7 % for time since initiation of OC use. We observed no changes in the diversity or composition of the gut microbiome following OC initiation. However, the relative abundance of the biosynthesis pathways of peptidoglycan, amino acids (lysine, threonine, methionine, and tryptophan), and the NAD salvage pathway increased after OC initiation. In addition, serum levels of estradiol and SHBG were positively associated with Eubacterium ramulus, a flavonoid-degrading bacterium. Similarly, microbes involving biosynthesis of l-lysine, l-threonine, and l-methionine were significantly associated with lower estradiol, SHBG, and higher levels of total testosterone.Conclusion. Our study provides the first piece of evidence supporting the association between exogenous and endogenous sex hormones and gut microbiome composition and function.}, } @article {pmid35452151, year = {2022}, author = {Lu, JL and Jia, P and Feng, SW and Wang, YT and Zheng, J and Ou, SN and Wu, ZH and Liao, B and Shu, WS and Liang, JL and Li, JT}, title = {Remarkable effects of microbial factors on soil phosphorus bioavailability: A country-scale study.}, journal = {Global change biology}, volume = {28}, number = {14}, pages = {4459-4471}, doi = {10.1111/gcb.16213}, pmid = {35452151}, issn = {1365-2486}, mesh = {Acid Phosphatase ; Carbon ; Ecosystem ; Nitrogen ; *Phosphorus ; *Soil ; Soil Microbiology ; }, abstract = {Low soil phosphorus (P) bioavailability causes the widespread occurrence of P-limited terrestrial ecosystems around the globe. Exploring the factors influencing soil P bioavailability at large spatial scales is critical for managing these ecosystems. However, previous studies have mostly focused on abiotic factors. In this study, we explored the effects of microbial factors on soil P bioavailability of terrestrial ecosystems using a country-scale sampling effort. Our results showed that soil microbial biomass carbon (MBC) and acid phosphatase were important predictors of soil P bioavailability of agro- and natural ecosystems across China although they appeared less important than total soil P. The two microbial factors had a positive effect on soil P bioavailability of both ecosystem types and were able to mediate the effects of several abiotic factors (e.g., mean annual temperature). Meanwhile, we revealed that soil phytase could affect soil P bioavailability at the country scale via ways similar to those of soil MBC and acid phosphatase, a pattern being more pronounced in agroecosystems than in natural ecosystems. Moreover, we obtained evidence for the positive effects of microbial genes encoding these enzymes on soil P bioavailability at the country scale although their effect sizes varied between the two ecosystem types. Taken together, this study demonstrated the remarkable effects of microbial factors on soil P bioavailability at a large spatial scale, highlighting the importance to consider microbial factors in managing the widespread P-limited terrestrial ecosystems.}, } @article {pmid35450835, year = {2022}, author = {Hurst, R and Meader, E and Gihawi, A and Rallapalli, G and Clark, J and Kay, GL and Webb, M and Manley, K and Curley, H and Walker, H and Kumar, R and Schmidt, K and Crossman, L and Eeles, RA and Wedge, DC and Lynch, AG and Massie, CE and , and Yazbek-Hanna, M and Rochester, M and Mills, RD and Mithen, RF and Traka, MH and Ball, RY and O'Grady, J and Brewer, DS and Wain, J and Cooper, CS}, title = {Microbiomes of Urine and the Prostate Are Linked to Human Prostate Cancer Risk Groups.}, journal = {European urology oncology}, volume = {5}, number = {4}, pages = {412-419}, doi = {10.1016/j.euo.2022.03.006}, pmid = {35450835}, issn = {2588-9311}, support = {C5047/A22530/CRUK_/Cancer Research UK/United Kingdom ; BB/R012504/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/000PR10349/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BB/CCG1860/1/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; BBS/E/F/00044600/BB_/Biotechnology and Biological Sciences Research Council/United Kingdom ; }, mesh = {Bacteria/genetics ; Humans ; Male ; *Microbiota/genetics ; Prostate/pathology ; *Prostatic Neoplasms/pathology ; RNA, Ribosomal, 16S/genetics ; }, abstract = {BACKGROUND: Bacteria play a suspected role in the development of several cancer types, and associations between the presence of particular bacteria and prostate cancer have been reported.

OBJECTIVE: To provide improved characterisation of the prostate and urine microbiome and to investigate the prognostic potential of the bacteria present.

Microbiome profiles were interrogated in sample collections of patient urine (sediment microscopy: n = 318, 16S ribosomal amplicon sequencing: n = 46; and extracellular vesicle RNA-seq: n = 40) and cancer tissue (n = 204).

Microbiomes were assessed using anaerobic culture, population-level 16S analysis, RNA-seq, and whole genome DNA sequencing.

RESULTS AND LIMITATIONS: We demonstrate an association between the presence of bacteria in urine sediments and higher D'Amico risk prostate cancer (discovery, n = 215 patients, p < 0.001; validation, n = 103, p < 0.001, χ[2] test for trend). Characterisation of the bacterial community led to the (1) identification of four novel bacteria (Porphyromonas sp. nov., Varibaculum sp. nov., Peptoniphilus sp. nov., and Fenollaria sp. nov.) that were frequently found in patient urine, and (2) definition of a patient subgroup associated with metastasis development (p = 0.015, log-rank test). The presence of five specific anaerobic genera, which includes three of the novel isolates, was associated with cancer risk group, in urine sediment (p = 0.045, log-rank test), urine extracellular vesicles (p = 0.039), and cancer tissue (p = 0.035), with a meta-analysis hazard ratio for disease progression of 2.60 (95% confidence interval: 1.39-4.85; p = 0.003; Cox regression). A limitation is that functional links to cancer development are not yet established.

CONCLUSIONS: This study characterises prostate and urine microbiomes, and indicates that specific anaerobic bacteria genera have prognostic potential.

PATIENT SUMMARY: In this study, we investigated the presence of bacteria in patient urine and the prostate. We identified four novel bacteria and suggest a potential prognostic utility for the microbiome in prostate cancer.}, } @article {pmid35449461, year = {2022}, author = {Kaelin, EA and Rodriguez, C and Hall-Moore, C and Hoffmann, JA and Linneman, LA and Ndao, IM and Warner, BB and Tarr, PI and Holtz, LR and Lim, ES}, title = {Longitudinal gut virome analysis identifies specific viral signatures that precede necrotizing enterocolitis onset in preterm infants.}, journal = {Nature microbiology}, volume = {7}, number = {5}, pages = {653-662}, pmid = {35449461}, issn = {2058-5276}, support = {R01 DK122029/DK/NIDDK NIH HHS/United States ; R01 HD092311/HD/NICHD NIH HHS/United States ; R00 DK107923/DK/NIDDK NIH HHS/United States ; UH3 AI083265/AI/NIAID NIH HHS/United States ; R01 HD092414/HD/NICHD NIH HHS/United States ; P30 DK052574/DK/NIDDK NIH HHS/United States ; UH2 AI083265/AI/NIAID NIH HHS/United States ; }, mesh = {Bacteria/genetics ; *Enterocolitis, Necrotizing/microbiology ; Feces/microbiology ; Female ; Humans ; Infant ; Infant, Newborn ; *Infant, Newborn, Diseases ; Infant, Premature ; Pregnancy ; *Premature Birth ; Virome/genetics ; }, abstract = {Necrotizing enterocolitis (NEC) is a serious consequence of preterm birth and is often associated with gut bacterial microbiome alterations. However, little is known about the development of the gut virome in preterm infants, or its role in NEC. Here, using metagenomic sequencing, we characterized the DNA gut virome of 9 preterm infants who developed NEC and 14 gestational age-matched preterm infants who did not. Infants were sampled longitudinally before NEC onset over the first 11 weeks of life. We observed substantial interindividual variation in the gut virome between unrelated preterm infants, while intraindividual variation over time was significantly less. We identified viral and bacterial signatures in the gut that preceded NEC onset. Specifically, we observed a convergence towards reduced viral beta diversity over the 10 d before NEC onset, which was driven by specific viral signatures and accompanied by specific viral-bacterial interactions. Our results indicate that bacterial and viral perturbations precede the sudden onset of NEC. These findings suggest that early life virome signatures in preterm infants may be implicated in NEC.}, } @article {pmid35449441, year = {2022}, author = {Schaefer, L and Hernandez, H and Coats, RA and Yu, Z and Pflugfelder, SC and Britton, RA and de Paiva, CS}, title = {Author Correction: Gut-derived butyrate suppresses ocular surface inflammation.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6581}, doi = {10.1038/s41598-022-10856-y}, pmid = {35449441}, issn = {2045-2322}, } @article {pmid35449389, year = {2022}, author = {Koo, H and Morrow, CD}, title = {Early indicators of microbial strain dysbiosis in the human gastrointestinal microbial community of certain healthy humans and hospitalized COVID-19 patients.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6562}, pmid = {35449389}, issn = {2045-2322}, mesh = {*COVID-19 ; Dysbiosis ; Feces ; *Gastrointestinal Microbiome ; Hospitalization ; Humans ; }, abstract = {Dysbiosis in the human gastrointestinal microbial community could functionally impact microbial metabolism and colonization resistance to pathogens. To further elucidate the indicators of microbial strain dysbiosis, we have developed an analytic method that detects patterns of presence/absence of selected KEGG metabolic pathways for a selected strain (PKS). Using a metagenomic data set consisting of multiple high-density fecal samples from six normal individuals, we found three had unique PKS for important gut commensal microbes, Bacteroides vulgatus and Bacteroides uniformis, at all sample times examined. Two individuals had multiple shared PKS clusters of B. vulgatus or B. uniformis over time. Analysis of a data set of high-density fecal samples from eight COVID-19 hospitalized patients taken over a short period revealed that two patients had shared PKS clusters for B. vulgatus and one shared cluster for B. uniformis. Our analysis demonstrates that while the majority of normal individuals with no B. vulgatus or B. uniformis strain change over time have unique PKS, in some healthy humans and patients hospitalized with COVID-19, we detected shared PKS clusters at the different times suggesting a slowing down of the intrinsic rates of strain variation that could eventually lead to a dysbiosis in the microbial strain community.}, } @article {pmid35449330, year = {2022}, author = {Zhang, J and Zhang, Q and Zhang, Z and Zhou, Z and Lu, T and Sun, L and Qian, H}, title = {Evaluation of phoxim toxicity on aquatic and zebrafish intestinal microbiota by metagenomics and 16S rRNA gene sequencing analysis.}, journal = {Environmental science and pollution research international}, volume = {29}, number = {42}, pages = {63017-63027}, pmid = {35449330}, issn = {1614-7499}, support = {21976161//National Natural Science Foundation of China/ ; 21777144//National Natural Science Foundation of China/ ; 22176176//Innovative Research Group Project of the National Natural Science Foundation of China/ ; }, mesh = {Animals ; *Gastrointestinal Microbiome ; Genes, rRNA ; Metagenomics ; *Microbiota ; Organophosphorus Compounds ; Organothiophosphorus Compounds ; *Pesticides ; RNA, Ribosomal, 16S/genetics ; Zebrafish/genetics ; }, abstract = {Phoxim is one of the main organophosphorus pesticides used in agricultural production. However, little information is known about how it affects the aquatic microbial community and the intestinal microbiota of fish. Herein, we utilized shotgun metagenomics and 16S rRNA gene sequencing to reveal the aquatic eco-risk of phoxim. Seven days of phoxim exposure significantly changed the composition of aquatic microbial community, obliterated the interactions between microorganisms, and thus reduced the complexity and stability of the microbial community. During long-time exposure (i.e., 14 days), most of the ecological functions were restored due to the redundancy of the microbial community. However, phoxim exposure promoted the dissemination of elfamycin resistance gene. The zebrafish gut microbial community also recovered from a temporary ecological disorder of aquatic microbiota, but phoxim continually affected zebrafish growth and swimming behavior. Overall, our results demonstrated that phoxim exposure significantly changed the structure and function of the microbial community and displayed a negative impact on freshwater ecosystems in a short exposure time.}, } @article {pmid35448628, year = {2022}, author = {Fekete, E and Pénzes, F and Ág, N and Ág-Rácz, V and Sándor, E and Scazzocchio, C and Flipphi, M and Karaffa, L}, title = {Unique and Repeated Stwintrons (Spliceosomal Twin Introns) in the Hypoxylaceae.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {4}, pages = {}, pmid = {35448628}, issn = {2309-608X}, support = {NN 128867//Hungarian National Research, Development and Innovation Fund/ ; K 138489//Hungarian National Research, Development and Innovation Fund/ ; }, abstract = {Introns are usually non-coding sequences interrupting open reading frames in pre-mRNAs [D1,2]. Stwintrons are nested spliceosomal introns, where an internal intron splits a second donor sequence into two consecutive splicing reactions leading to mature mRNA. In Hypoxylon sp. CO27-5, 36 highly sequence-similar [D1,2] stwintrons are extant (sister stwintrons). An additional 81 [D1,2] sequence-unrelated stwintrons are described here. Most of them are located at conserved gene positions rooted deep in the Hypoxylaceae. Absence of exonic sequence bias at the exon-stwintron junctions and a very similar phase distribution were noted for both groups. The presence of an underlying sequence symmetry in all 117 stwintrons was striking. This symmetry, more pronounced near the termini of most of the full-length sister stwintrons, may lead to a secondary structure that brings into close proximity the most distal splice sites, the donor of the internal and the acceptor of the external intron. The Hypoxylon stwintrons were overwhelmingly excised by consecutive splicing reactions precisely removing the whole intervening sequence, whereas one excision involving the distal splice sites led to a frameshift. Alternative (mis)splicing took place for both sister and uniquely occurring stwintrons. The extraordinary symmetry of the sister stwintrons thus seems dispensable for the infrequent, direct utilisation of the distal splice sites.}, } @article {pmid35448604, year = {2022}, author = {Fonseca, PLC and Skaltsas, D and da Silva, FF and Kato, RB and de Castro, GM and García, GJY and Quintanilha-Peixoto, G and Mendes-Pereira, T and do Carmo, AO and Aguiar, ERGR and de Carvalho, DS and Costa-Rezende, DH and Drechsler-Santos, ER and Badotti, F and Ferreira-Silva, A and Oliveira, G and Chaverri, P and Vaz, ABM and Góes-Neto, A}, title = {An Integrative View of the Phyllosphere Mycobiome of Native Rubber Trees in the Brazilian Amazon.}, journal = {Journal of fungi (Basel, Switzerland)}, volume = {8}, number = {4}, pages = {}, pmid = {35448604}, issn = {2309-608X}, support = {Sub-Grant Number: PGA-2000003475, 2013/2016//National Academy of Sciences/ ; }, abstract = {The rubber tree, Hevea brasiliensis, is a neotropical Amazonian species. Despite its high economic value and fungi associated with native individuals, in its original area in Brazil, it has been scarcely investigated and only using culture-dependent methods. Herein, we integrated in silico approaches with novel field/experimental approaches and a case study of shotgun metagenomics and small RNA metatranscriptomics of an adult individual. Scientific literature, host fungus, and DNA databases are biased to fungal taxa, and are mainly related to rubber tree diseases and in non-native ecosystems. Metabarcoding retrieved specific phyllospheric core fungal communities of all individuals, adults, plantlets, and leaves of the same plant, unravelling hierarchical structured core mycobiomes. Basidiomycotan yeast-like fungi that display the potential to produce antifungal compounds and a complex of non-invasive ectophytic parasites (Sooty Blotch and Flyspeck fungi) co-occurred in all samples, encompassing the strictest core mycobiome. The case study of the same adult tree (previously studied using culture-dependent approach) analyzed by amplicon, shotgun metagenomics, and small RNA transcriptomics revealed a high relative abundance of insect parasite-pathogens, anaerobic fungi and a high expression of Trichoderma (a fungal genus long reported as dominant in healthy wild rubber trees), respectively. Altogether, our study unravels new and intriguing information/hypotheses of the foliar mycobiome of native H. brasiliensis, which may also occur in other native Amazonian trees.}, } @article {pmid35447253, year = {2022}, author = {Li, S and Jiang, Z and Ji, G}, title = {Effect of sulfur sources on the competition between denitrification and DNRA.}, journal = {Environmental pollution (Barking, Essex : 1987)}, volume = {305}, number = {}, pages = {119322}, doi = {10.1016/j.envpol.2022.119322}, pmid = {35447253}, issn = {1873-6424}, mesh = {Ammonia ; *Ammonium Compounds/metabolism ; Denitrification ; *Nitrates/metabolism ; Nitrogen ; Nitrogen Oxides ; Oxidation-Reduction ; Sulfur ; Thiosulfates ; }, abstract = {The fate of nitrogen is controlled by the competition between nitrate reduction pathways. Denitrification removes nitrogen in the system to the atmosphere, whereas dissimilatory nitrate reduction to ammonia (DNRA) retains nitrate in the form of ammonia. Different microbes specialize in the oxidation of different electron donors, thus electron donors might influence the outcomes of the competition. Here, we investigated the fate of nitrate with five forms of sulfur as electron donors. Chemoautotrophic nitrate reduction did not continue after the passages of the enrichments with sulfide, sulfite and pyrite. Nitrate reduction rate was the highest in the enrichment with thiosulfate. Denitrification was stimulated and no DNRA was observed with thiosulfate, while both denitrification and DNRA were stimulated with elemental sulfur. Metagenomes of the enrichments were assembled and binned into ten genomes. The enriched populations with thiosulfate included Thiobacillus, Lentimicrobium, Sulfurovum and Hydrogenophaga, all of which contained genes involved in sulfur oxidation. Elemental sulfur-based DNRA was performed by Thiobacillus (with NrfA and NirB) and Nocardioides (with only NirB). Our study established a link between sulfur sources, nitrate reduction pathways and microbial populations.}, } @article {pmid35447075, year = {2022}, author = {Schneider, VA}, title = {Evaluation of Lou et al.: Proposed benefits of a population-specific genome reference.}, journal = {Cell systems}, volume = {13}, number = {4}, pages = {265-267}, doi = {10.1016/j.cels.2022.03.005}, pmid = {35447075}, issn = {2405-4720}, mesh = {*Genome/genetics ; *Metagenomics ; }, abstract = {One snapshot of the peer review process for "Haplo-type-resolved de novo assembly of a Tujia genome suggests the necessity for high-quality population-specific genome references" (Lou et al., 2022).}, } @article {pmid35446845, year = {2022}, author = {Giliberti, R and Cavaliere, S and Mauriello, IE and Ercolini, D and Pasolli, E}, title = {Host phenotype classification from human microbiome data is mainly driven by the presence of microbial taxa.}, journal = {PLoS computational biology}, volume = {18}, number = {4}, pages = {e1010066}, pmid = {35446845}, issn = {1553-7358}, mesh = {*Bacteria/genetics ; Humans ; Metagenome/genetics ; *Microbiota/genetics ; Phenotype ; RNA, Ribosomal, 16S/genetics ; }, abstract = {Machine learning-based classification approaches are widely used to predict host phenotypes from microbiome data. Classifiers are typically employed by considering operational taxonomic units or relative abundance profiles as input features. Such types of data are intrinsically sparse, which opens the opportunity to make predictions from the presence/absence rather than the relative abundance of microbial taxa. This also poses the question whether it is the presence rather than the abundance of particular taxa to be relevant for discrimination purposes, an aspect that has been so far overlooked in the literature. In this paper, we aim at filling this gap by performing a meta-analysis on 4,128 publicly available metagenomes associated with multiple case-control studies. At species-level taxonomic resolution, we show that it is the presence rather than the relative abundance of specific microbial taxa to be important when building classification models. Such findings are robust to the choice of the classifier and confirmed by statistical tests applied to identifying differentially abundant/present taxa. Results are further confirmed at coarser taxonomic resolutions and validated on 4,026 additional 16S rRNA samples coming from 30 public case-control studies.}, } @article {pmid35446234, year = {2022}, author = {Mujagic, Z and Kasapi, M and Jonkers, DM and Garcia-Perez, I and Vork, L and Weerts, ZZRM and Serrano-Contreras, JI and Zhernakova, A and Kurilshikov, A and Scotcher, J and Holmes, E and Wijmenga, C and Keszthelyi, D and Nicholson, JK and Posma, JM and Masclee, AA}, title = {Integrated fecal microbiome-metabolome signatures reflect stress and serotonin metabolism in irritable bowel syndrome.}, journal = {Gut microbes}, volume = {14}, number = {1}, pages = {2063016}, pmid = {35446234}, issn = {1949-0984}, support = {MR/S004033/1/MRC_/Medical Research Council/United Kingdom ; }, mesh = {Feces/chemistry ; *Gastrointestinal Microbiome/physiology ; Humans ; *Irritable Bowel Syndrome/metabolism ; Metabolome ; *Microbiota ; Serotonin/metabolism ; }, abstract = {To gain insight into the complex microbiome-gut-brain axis in irritable bowel syndrome (IBS), several modalities of biological and clinical data must be combined. We aimed to identify profiles of fecal microbiota and metabolites associated with IBS and to delineate specific phenotypes of IBS that represent potential pathophysiological mechanisms. Fecal metabolites were measured using proton nuclear magnetic resonance ([1]H-NMR) spectroscopy and gut microbiome using shotgun metagenomic sequencing (MGS) in a combined dataset of 142 IBS patients and 120 healthy controls (HCs) with extensive clinical, biological and phenotype information. Data were analyzed using support vector classification and regression and kernel t-SNE. Microbiome and metabolome profiles could distinguish IBS and HC with an area-under-the-receiver-operator-curve of 77.3% and 79.5%, respectively, but this could be improved by combining microbiota and metabolites to 83.6%. No significant differences in predictive ability of the microbiome-metabolome data were observed between the three classical, stool pattern-based, IBS subtypes. However, unsupervised clustering showed distinct subsets of IBS patients based on fecal microbiome-metabolome data. These clusters could be related plasma levels of serotonin and its metabolite 5-hydroxyindoleacetate, effects of psychological stress on gastrointestinal (GI) symptoms, onset of IBS after stressful events, medical history of previous abdominal surgery, dietary caloric intake and IBS symptom duration. Furthermore, pathways in metabolic reaction networks were integrated with microbiota data, that reflect the host-microbiome interactions in IBS. The identified microbiome-metabolome signatures for IBS, associated with altered serotonin metabolism and unfavorable stress response related to GI symptoms, support the microbiota-gut-brain link in the pathogenesis of IBS.}, } @article {pmid35445860, year = {2022}, author = {Griesemer, J and Barragán, CA}, title = {Re-situations of scientific knowledge: a case study of a skirmish over clusters vs clines in human population genomics.}, journal = {History and philosophy of the life sciences}, volume = {44}, number = {2}, pages = {16}, pmid = {35445860}, issn = {1742-6316}, support = {SES-1849307-0//national science foundation/ ; }, mesh = {*Genomics ; Humans ; Knowledge ; *Metagenomics ; Software ; }, abstract = {We track and analyze the re-situation of scientific knowledge in the field of human population genomics ancestry studies. We understand re-situation as a process of accommodating the direct or indirect transfer of objects of knowledge from one site/situation to (one or many) other sites/situations. Our take on the concept borrows from Mary S. Morgan's work on facts traveling while expanding it to include other objects of knowledge such as models, data, software, findings, and visualizations. We structure a specific case study by tracking the re-situation of these objects between three research projects studying human population diversity reported in three articles in Science, Genome Research and PLoS Genetics between 2002 and 2005. We characterize these three engagements as a unit of analysis, a "skirmish," in order to compare: (a) the divergence of interests in how life-scientists answer similar research questions and (b) to track the challenging transformation of workflows in research laboratories as these scientific objects are re-situated individually or in bundles. Our analysis of the case study shows that an accurate understanding of re-situation requires tracking the whole bundle of objects in a project because they interact in particular key ways. The absence or dismissal of these interactions opens the door to unforeseen trade-offs, misunderstandings and misrepresentations about research design(s) and workflow(s) and what these say about the questions asked and the findings produced.}, } @article {pmid35445474, year = {2023}, author = {Moeller, AH}, title = {Metagenomic signatures of balancing selection in the human gut.}, journal = {Molecular ecology}, volume = {32}, number = {10}, pages = {2582-2591}, pmid = {35445474}, issn = {1365-294X}, support = {R35 GM138284/GM/NIGMS NIH HHS/United States ; }, mesh = {Humans ; *Selection, Genetic ; *Metagenome/genetics ; Genetics, Population ; Metagenomics ; Anti-Bacterial Agents ; }, abstract = {Bacterial lineages that populate the human gut microbiota contend with spatial and temporal fluctuations in numerous environmental variables, including bouts of extreme selective agents such as antibiotics. Oscillations in the adaptive landscape can impose balancing selection on populations, leaving characteristic signatures in the sequence variation of functionally significant genomic loci. Despite their potential importance for gut bacterial adaptation, the metagenomic targets of balancing selection have not been identified. Here, I present population genetic evidence that balancing selection maintains allelic diversity in multidrug efflux pumps of multiple predominant gut bacterial species. Metagenome-wide scans of 566,958 genes from 287 bacterial species represented by 118,617 metagenome-assembled genomes indicated that most genes have been conserved by purifying selection. However, dozens of core open reading frames (CORFs) displayed positive Tajima's D values that deviated significantly from their species' genomic backgrounds, indicating the action of balancing selection. Multidrug efflux pumps (MEPs) from a diversity of bacterial species were significantly enriched among the CORFs with Tajima's D values >3 in industrialized, but not nonindustrialized, human populations. The AcrB subunit of an MEP from Bacteroides dorei displayed the highest Tajima's D of any CORF. Divergent haplotypes of this CORF displayed evidence of positive selection and homology to an Escherichia coli AcrB subunit that binds tetracycline and macrolide antibiotics, suggesting functional significance and implicating medical antibiotics as an agent of selection acting on this locus. Other proteins identified as targets of balancing selection included peptidoglycan/LPS O-acetylases and ion transporters. Intriguingly, the degree of balancing selection acting on gut bacterial species was associated with species abundance in the gut based on metagenomic data, further suggesting fitness benefits of the allelic variation identified.}, } @article {pmid35444627, year = {2022}, author = {Wang, L and Tay, ACY and Li, J and Zhao, Q}, title = {Editorial: Computational Predictions, Dynamic Tracking, and Evolutionary Analysis of Antibiotic Resistance Through the Mining of Microbial Genomes and Metagenomic Data.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {880967}, pmid = {35444627}, issn = {1664-302X}, } @article {pmid35444619, year = {2022}, author = {Zell, R and Groth, M and Selinka, L and Selinka, HC}, title = {Picorna-Like Viruses of the Havel River, Germany.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {865287}, pmid = {35444619}, issn = {1664-302X}, abstract = {To improve the understanding of the virome diversity of riverine ecosystems in metropolitan areas, a metagenome analysis was performed with water collected in June 2018 from the river Havel in Berlin, Germany. After enrichment of virus particles and RNA extraction, paired-end Illumina sequencing was conducted and assignment to virus groups and families was performed. This paper focuses on picorna-like viruses, the most diverse and abundant group of viruses with impact on human, animal, and environmental health. Here, we describe altogether 166 viral sequences ranging in size from 1 to 11.5 kb. The 71 almost complete genomes are comprised of one candidate iflavirus, one picornavirus, two polycipiviruses, 27 marnaviruses, 27 dicistro-like viruses, and 13 untypeable viruses. Many partial picorna-like virus sequences up to 10.2 kb were also investigated. The sequences of the Havel picorna-like viruses represent genomes of seven of eight so far known Picornavirales families. Detection of numerous distantly related dicistroviruses suggests the existence of additional, yet unexplored virus groups with dicistronic genomes, including few viruses with unusual genome layout. Of special interest is a clade of dicistronic viruses with capsid protein-encoding sequences at the 5'-end of the genome. Also, monocistronic viruses with similarity of their polymerase and capsid proteins to those of dicistroviruses are interesting. A second protein with NTP-binding site present in the polyprotein of solinviviruses and related viruses needs further attention. The results underline the importance to study the viromes of fluvial ecosystems. So far acknowledged marnaviruses have been isolated from marine organisms. However, the present study and available sequence data suggest that rivers and limnic habitats are relevant ecosystems with circulation of marnaviruses as well as a plethora of unknown picorna-like viruses.}, } @article {pmid35444277, year = {2022}, author = {Raina, JB and Lambert, BS and Parks, DH and Rinke, C and Siboni, N and Bramucci, A and Ostrowski, M and Signal, B and Lutz, A and Mendis, H and Rubino, F and Fernandez, VI and Stocker, R and Hugenholtz, P and Tyson, GW and Seymour, JR}, title = {Chemotaxis shapes the microscale organization of the ocean's microbiome.}, journal = {Nature}, volume = {605}, number = {7908}, pages = {132-138}, pmid = {35444277}, issn = {1476-4687}, mesh = {Bacteria ; *Chemotaxis ; Dissolved Organic Matter ; *Microbiota ; Oceans and Seas ; Phytoplankton/metabolism ; Seawater/microbiology ; }, abstract = {The capacity of planktonic marine microorganisms to actively seek out and exploit microscale chemical hotspots has been widely theorized to affect ocean-basin scale biogeochemistry[1-3], but has never been examined comprehensively in situ among natural microbial communities. Here, using a field-based microfluidic platform to quantify the behavioural responses of marine bacteria and archaea, we observed significant levels of chemotaxis towards microscale hotspots of phytoplankton-derived dissolved organic matter (DOM) at a coastal field site across multiple deployments, spanning several months. Microscale metagenomics revealed that a wide diversity of marine prokaryotes, spanning 27 bacterial and 2 archaeal phyla, displayed chemotaxis towards microscale patches of DOM derived from ten globally distributed phytoplankton species. The distinct DOM composition of each phytoplankton species attracted phylogenetically and functionally discrete populations of bacteria and archaea, with 54% of chemotactic prokaryotes displaying highly specific responses to the DOM derived from only one or two phytoplankton species. Prokaryotes exhibiting chemotaxis towards phytoplankton-derived compounds were significantly enriched in the capacity to transport and metabolize specific phytoplankton-derived chemicals, and displayed enrichment in functions conducive to symbiotic relationships, including genes involved in the production of siderophores, B vitamins and growth-promoting hormones. Our findings demonstrate that the swimming behaviour of natural prokaryotic assemblages is governed by specific chemical cues, which dictate important biogeochemical transformation processes and the establishment of ecological interactions that structure the base of the marine food web.}, } @article {pmid35444255, year = {2022}, author = {Li, Z and Lai, J and Zhang, P and Ding, J and Jiang, J and Liu, C and Huang, H and Zhen, H and Xi, C and Sun, Y and Wu, L and Wang, L and Gao, X and Li, Y and Fu, Y and Jie, Z and Li, S and Zhang, D and Chen, Y and Zhu, Y and Lu, S and Lu, J and Wang, D and Zhou, H and Yuan, X and Li, X and Pang, L and Huang, M and Yang, H and Zhang, W and Brix, S and Kristiansen, K and Song, X and Nie, C and Hu, S}, title = {Multi-omics analyses of serum metabolome, gut microbiome and brain function reveal dysregulated microbiota-gut-brain axis in bipolar depression.}, journal = {Molecular psychiatry}, volume = {27}, number = {10}, pages = {4123-4135}, pmid = {35444255}, issn = {1476-5578}, mesh = {Humans ; *Gastrointestinal Microbiome/genetics ; *Bipolar Disorder/metabolism ; Brain-Gut Axis ; Metabolome ; *Microbiota ; Brain/metabolism ; }, abstract = {The intricate processes of microbiota-gut-brain communication in modulating human cognition and emotion, especially in the context of mood disorders, have remained elusive. Here we performed faecal metagenomic, serum metabolomics and neuroimaging studies on a cohort of 109 unmedicated patients with depressed bipolar disorder (BD) patients and 40 healthy controls (HCs) to characterise the microbial-gut-brain axis in BD. Across over 12,000 measured metabolic features, we observed a large discrepancy (73.54%) in the serum metabolome between BD patients and HCs, spotting differentially abundant microbial-derived neuroactive metabolites including multiple B-vitamins, kynurenic acid, gamma-aminobutyric acid and short-chain fatty acids. These metabolites could be linked to the abundance of gut microbiota presented with corresponding biosynthetic potentials, including Akkermansia muciniphila, Citrobacter spp. (Citrobacter freundii and Citrobacter werkmanii), Phascolarctobacterium spp., Yersinia spp. (Yersinia frederiksenii and Yersinia aleksiciae), Enterobacter spp. (Enterobacter cloacae and Enterobacter kobei) and Flavobacterium spp. Based on functional neuroimaging, BD-related neuroactive microbes and metabolites were discovered as potential markers associated with BD-typical features of functional connectivity of brain networks, hinting at aberrant cognitive function, emotion regulation, and interoception. Our study combines gut microbiota and neuroactive metabolites with brain functional connectivity, thereby revealing potential signalling pathways from the microbiota to the gut and the brain, which may have a role in the pathophysiology of BD.}, } @article {pmid35444202, year = {2022}, author = {Busi, SB and Bourquin, M and Fodelianakis, S and Michoud, G and Kohler, TJ and Peter, H and Pramateftaki, P and Styllas, M and Tolosano, M and De Staercke, V and Schön, M and de Nies, L and Marasco, R and Daffonchio, D and Ezzat, L and Wilmes, P and Battin, TJ}, title = {Genomic and metabolic adaptations of biofilms to ecological windows of opportunity in glacier-fed streams.}, journal = {Nature communications}, volume = {13}, number = {1}, pages = {2168}, pmid = {35444202}, issn = {2041-1723}, mesh = {Biodiversity ; Biofilms ; Ecosystem ; *Ice Cover ; *Microbiota/genetics ; Rivers/microbiology ; }, abstract = {In glacier-fed streams, ecological windows of opportunity allow complex microbial biofilms to develop and transiently form the basis of the food web, thereby controlling key ecosystem processes. Using metagenome-assembled genomes, we unravel strategies that allow biofilms to seize this opportunity in an ecosystem otherwise characterized by harsh environmental conditions. We observe a diverse microbiome spanning the entire tree of life including a rich virome. Various co-existing energy acquisition pathways point to diverse niches and the exploitation of available resources, likely fostering the establishment of complex biofilms during windows of opportunity. The wide occurrence of rhodopsins, besides chlorophyll, highlights the role of solar energy capture in these biofilms while internal carbon and nutrient cycling between photoautotrophs and heterotrophs may help overcome constraints imposed by oligotrophy in these habitats. Mechanisms potentially protecting bacteria against low temperatures and high UV-radiation are also revealed and the selective pressure of this environment is further highlighted by a phylogenomic analysis differentiating important components of the glacier-fed stream microbiome from other ecosystems. Our findings reveal key genomic underpinnings of adaptive traits contributing to the success of complex biofilms to exploit environmental opportunities in glacier-fed streams, which are now rapidly changing owing to global warming.}, } @article {pmid35443766, year = {2022}, author = {Satjarak, A and Golinski, GK and Trest, MT and Graham, LE}, title = {Microbiome and related structural features of Earth's most archaic plant indicate early plant symbiosis attributes.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6423}, pmid = {35443766}, issn = {2045-2322}, mesh = {*Bryophyta/genetics ; *Embryophyta/genetics ; Humans ; *Microbiota/genetics ; *Mycorrhizae ; Phylogeny ; Plants/microbiology ; Symbiosis ; }, abstract = {Origin of earliest land plants from ancestral algae dramatically accelerated the evolution of Earth's terrestrial ecosystems, in which microbial symbioses have played key roles. Recent molecular diversification analyses identify the rare, geographically-limited moss Takakia as Earth's most archaic modern land plant. Despite occupying a phylogenetic position pivotal for understanding earliest plants, Takakia microbial associations are poorly known. Here, we describe symbiosis-related structural features and contig-based metagenomic data that illuminate the evolutionary transition from streptophyte algae to early embryophytes. We observed that T. lepidozioides shares with streptophyte algae secretion of microbe-harboring mucilage and bacterial taxa such as Rhizobium and genes indicating nitrogen fixation. We find that Takakia root-analogs produce lateral mucilage organs that are more complex than generally understood, having structural analogies to angiosperm lateral roots adapted for N-fixation symbioses, including presence of intracellular microbes. We also find structural and metagenomic evidence for mycorrhiza-like species of glomalean fungi (including Rhizophagus irregularis) not previously known for mosses, as well as ascomycete fungi (e.g. Rhizoscyphus ericae) that associate with other early-diverging plants. Because Takakia is the oldest known modern plant genus, this study of plants of a remote locale not strongly influenced by human activities may indicate microbiome features of early land plants.}, } @article {pmid35443009, year = {2022}, author = {Lin, PC and Yang, YSH and Lin, SC and Lu, MC and Tsai, YT and Lu, SC and Chen, SH and Chen, SY}, title = {Clinical significance and intestinal microbiota composition in immunocompromised children with norovirus gastroenteritis.}, journal = {PloS one}, volume = {17}, number = {4}, pages = {e0266876}, pmid = {35443009}, issn = {1932-6203}, mesh = {*Caliciviridae Infections/epidemiology ; Child ; Feces ; *Gastroenteritis ; *Gastrointestinal Microbiome/genetics ; Genotype ; Humans ; Infant ; *Norovirus/genetics ; RNA, Viral ; }, abstract = {BACKGROUND: Norovirus (NoV) infection is common in pediatric patients with immunodeficiency and is more likely to cause severe disease. Objective Our study aims to figure out the clinical differences and distribution of intestinal microbiota in immunocompromised children with NoV gastroenteritis.

METHODS: Pediatric patients admitted to Shang-Ho Hospital with diagnosis of acute gastroenteritis including different immune status were enrolled and their medical records were reviewed. NoV gastroenteritis was validated using RT-PCR molecular methods. Viral shedding period was determined by real-time RT-PCR assays. Intestinal microbiota enrichment analysis was carried out by next generation sequencing after fecal DNA extraction and subsequent Linear Discriminant Analysis (LDA) Effect Size (LEfSe) method.

RESULTS: Significantly higher frequency of diarrhea [mean, (IQR), 3.8 (3-5) /day] and longer viral shedding time [mean, IQR, 8.5 (5-13) days] was found in immunocompromised NoV infections than in immunocompetent patients without NoV infections (p = 0.013*) and immunocompetent patients with NoV infections (p = 0.030**). The fever prevalence was significantly lower in immunocompromised NoV infections than in different immune or infection status. Intestinal microbiota metagenomics analysis showed no significant community richness difference while the LEfSe analysis showed a significant difference in commensal richness at the phylum level, the family level, and the genus level in patients under different immune status.

CONCLUSION: We evaluated the clinical significances and microbiota composition in immunocompromised children with norovirus gastroenteritis. This will further facilitate studies of the interaction between the intestinal microbiota in such patients with precise determination of their bacterial infection control and probiotic supplements strategy.}, } @article {pmid35442084, year = {2022}, author = {Wagner, NY and Andersen, DT and Hahn, AS and McLaughlin, R and Johnson, SS}, title = {Draft Genome Sequence from a Putative New Genus and Species in the Family M1A02 within the Phylum Planctomycetes, Isolated from Benthic Pinnacle Mats in Lake Untersee, Antarctica.}, journal = {Microbiology resource announcements}, volume = {11}, number = {5}, pages = {e0119221}, pmid = {35442084}, issn = {2576-098X}, support = {//Tawani Foundation/ ; //National Defense Science and Engineering Graduate (NDSEG)/ ; //Cosmos Club Foundation/ ; //Achievement Rewards for College Scientists Foundation (ARCS)/ ; 80NSSC18K1094//National Aeronautics and Space Administration (NASA)/ ; //Trottier Family Foundation/ ; //Russian Antarctic Expedition/ ; }, abstract = {Here, we report the draft genome sequence for a new putative genus and species in the family M1A02 within the order Phycisphaerales. Isolated from the metagenome of a benthic pinnacle-shaped mat in the Antarctic Lake Untersee, the members of this family have been found in biofilms and freshwater environments.}, } @article {pmid35441671, year = {2022}, author = {Nakamichi, Y and Matsuzawa, T and Watanabe, M and Yaoi, K}, title = {Crystal structure of glycoside hydrolase family 31 α-xylosidase from a soil metagenome.}, journal = {Bioscience, biotechnology, and biochemistry}, volume = {86}, number = {7}, pages = {855-864}, doi = {10.1093/bbb/zbac058}, pmid = {35441671}, issn = {1347-6947}, support = {26850067//Japan Society for the Promotion of Science/ ; //National Institute of Advanced Industrial Science and Technology/ ; }, mesh = {Crystallography, X-Ray ; *Glycoside Hydrolases/chemistry ; Metagenome ; Soil ; Substrate Specificity ; Xylose ; *Xylosidases/metabolism ; }, abstract = {MeXyl31, a member of glycoside hydrolase family 31 (GH31), is the α-xylosidase isolated from a soil metagenomic library. The enzyme degrades α-xylosyl substrate such as isoprimeverose, α-d-xylopyranosyl-(1→6)-glucopyranose. The crystal structure of MeXyl31 was determined at 1.80 Å resolution. MeXyl31 forms the tetrameric state. The complexed structure with a xylose in the -1 subsite (α-xylose binding site) shows that the enzyme strictly recognizes α-xylose. Structural comparison between MeXyl31 and its homologue, Aspergillus niger α-xylosidase in GH31, gave insights into the positive subsite of MeXyl31. First, in the tetrameric enzyme, two monomers (a catalytic monomer and the adjacent monomer), are involved in substrate recognition. Second, the adjacent monomer composes a part of positive subsites in MeXyl31. Docking simulation and site-directed mutagenesis suggested that the Arg100 from the adjacent monomer is partially involved in the recognizing of a glucopyranose of isoprimeverose.}, } @article {pmid35441283, year = {2022}, author = {Xiao, M and Lu, B and Ding, R and Liu, X and Wu, X and Li, Y and Liu, X and Qiu, L and Zhang, Z and Xie, J and Chen, Y and Zhang, D and Dong, L and Zhang, M and Peng, J and Yang, H and Kudihna, T and Xu, Y and Li, T and Yi, C and Zhu, L}, title = {Metatranscriptomic analysis of host response and vaginal microbiome of patients with severe COVID-19.}, journal = {Science China. Life sciences}, volume = {65}, number = {7}, pages = {1473-1476}, pmid = {35441283}, issn = {1869-1889}, mesh = {*COVID-19 ; Female ; Humans ; Metagenomics ; *Microbiota/genetics ; }, } @article {pmid35440729, year = {2022}, author = {Jaffe, AL and Konno, M and Kawasaki, Y and Kataoka, C and Béjà, O and Kandori, H and Inoue, K and Banfield, JF}, title = {Saccharibacteria harness light energy using type-1 rhodopsins that may rely on retinal sourced from microbial hosts.}, journal = {The ISME journal}, volume = {16}, number = {8}, pages = {2056-2059}, pmid = {35440729}, issn = {1751-7370}, support = {71785//Gordon and Betty Moore Foundation (Gordon E. and Betty I. Moore Foundation)/ ; }, mesh = {*Actinobacteria/genetics/metabolism ; Bacteria/genetics/metabolism ; Light ; Proton Pumps/genetics/metabolism ; *Rhodopsin/genetics/metabolism ; Rhodopsins, Microbial/genetics/metabolism ; }, abstract = {Microbial rhodopsins are a family of photoreceptive membrane proteins with a wide distribution across the Tree of Life. Within the candidate phyla radiation (CPR), a diverse group of putatively episymbiotic bacteria, the genetic potential to produce rhodopsins appears to be confined to a small clade of organisms from sunlit environments. Here, we characterize the metabolic context and biophysical features of Saccharibacteria Type-1 rhodopsin sequences derived from metagenomic surveys and show that these proteins function as outward proton pumps. This provides one of the only known mechanisms by which CPR can generate a proton gradient for ATP synthesis. These Saccharibacteria do not encode the genetic machinery to produce all-trans-retinal, the chromophore essential for rhodopsin function, but their rhodopsins are able to rapidly uptake this cofactor when provided in experimental assays. We found consistent evidence for the capacity to produce retinal from β-carotene in microorganisms co-occurring with Saccharibacteria, and this genetic potential was dominated by members of the Actinobacteria, which are known hosts of Saccharibacteria in other habitats. If Actinobacteria serve as hosts for Saccharibacteria in freshwater environments, exchange of retinal for use by rhodopsin may be a feature of their associations.}, } @article {pmid35440728, year = {2022}, author = {González-Dávila, P and Schwalbe, M and Danewalia, A and Dalile, B and Verbeke, K and Mahata, SK and El Aidy, S}, title = {Catestatin selects for colonization of antimicrobial-resistant gut bacterial communities.}, journal = {The ISME journal}, volume = {16}, number = {8}, pages = {1873-1882}, pmid = {35440728}, issn = {1751-7370}, support = {I01 BX003934/BX/BLRD VA/United States ; }, mesh = {Animals ; *Anti-Infective Agents ; Chromogranin A/genetics/metabolism/pharmacology ; *Gastrointestinal Microbiome ; Mice ; Mice, Knockout ; Peptide Fragments/genetics/metabolism ; Peptides ; }, abstract = {The gut microbiota is in continuous interaction with the innermost layer of the gut, namely the epithelium. One of the various functions of the gut epithelium, is to keep the microbes at bay to avoid overstimulation of the underlying mucosa immune cells. To do so, the gut epithelia secrete a variety of antimicrobial peptides, such as chromogranin A (CgA) peptide catestatin (CST: hCgA352-372). As a defense mechanism, gut microbes have evolved antimicrobial resistance mechanisms to counteract the killing effect of the secreted peptides. To this end, we treated wild-type mice and CST knockout (CST-KO) mice (where only the 63 nucleotides encoding CST have been deleted) with CST for 15 consecutive days. CST treatment was associated with a shift in the diversity and composition of the microbiota in the CST-KO mice. This effect was less prominent in WT mice. Levels of the microbiota-produced short-chain fatty acids, in particular, butyrate and acetate were significantly increased in CST-treated CST-KO mice but not the WT group. Both CST-treated CST-KO and WT mice showed a significant increase in microbiota-harboring phosphoethanolamine transferase-encoding genes, which facilitate their antimicrobial resistance. Finally, we show that CST was degraded by Escherichia coli via an omptin-protease and that the abundance of this gene was significantly higher in metagenomic datasets collected from patients with Crohn's disease but not with ulcerative colitis. Overall, this study illustrates how the endogenous antimicrobial peptide, CST, shapes the microbiota composition in the gut and primes further research to uncover the role of bacterial resistance to CST in disease states such as inflammatory bowel disease.}, } @article {pmid35440708, year = {2022}, author = {Bai-Tong, SS and Thoemmes, MS and Weldon, KC and Motazavi, D and Kitsen, J and Hansen, S and Furst, A and Geng, B and Song, SJ and Gilbert, JA and Bode, L and Dorrestein, PC and Knight, R and Leibel, SA and Leibel, SL}, title = {The impact of maternal asthma on the preterm infants' gut metabolome and microbiome (MAP study).}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6437}, pmid = {35440708}, issn = {2045-2322}, mesh = {*Asthma ; Humans ; Infant ; Infant, Newborn ; Infant, Premature ; Metabolome ; *Microbiota ; Pilot Projects ; Prospective Studies ; }, abstract = {Preterm infants are at a greater risk for the development of asthma and atopic disease, which can lead to lifelong negative health consequences. This may be due, in part, to alterations that occur in the gut microbiome and metabolome during their stay in the Neonatal Intensive Care Unit (NICU). To explore the differential roles of family history (i.e., predisposition due to maternal asthma diagnosis) and hospital-related environmental and clinical factors that alter microbial exposures early in life, we considered a unique cohort of preterm infants born ≤ 34 weeks gestational age from two local level III NICUs, as part of the MAP (Microbiome, Atopic disease, and Prematurity) Study. From MAP participants, we chose a sub-cohort of infants whose mothers had a history of asthma and matched gestational age and sex to infants of mothers without a history of asthma diagnosis (control). We performed a prospective, paired metagenomic and metabolomic analysis of stool and milk feed samples collected at birth, 2 weeks, and 6 weeks postnatal age. Although there were clinical factors associated with shifts in the diversity and composition of stool-associated bacterial communities, maternal asthma diagnosis did not play an observable role in shaping the infant gut microbiome during the study period. There were significant differences, however, in the metabolite profile between the maternal asthma and control groups at 6 weeks postnatal age. The most notable changes occurred in the linoleic acid spectral network, which plays a role in inflammatory and immune pathways, suggesting early metabolomic changes in the gut of preterm infants born to mothers with a history of asthma. Our pilot study suggests that a history of maternal asthma alters a preterm infants' metabolomic pathways in the gut, as early as the first 6 weeks of life.}, } @article {pmid35440670, year = {2022}, author = {Zuo, W and Wang, B and Bai, X and Luan, Y and Fan, Y and Michail, S and Sun, F}, title = {16S rRNA and metagenomic shotgun sequencing data revealed consistent patterns of gut microbiome signature in pediatric ulcerative colitis.}, journal = {Scientific reports}, volume = {12}, number = {1}, pages = {6421}, pmid = {35440670}, issn = {2045-2322}, support = {R01 HD081197/HD/NICHD NIH HHS/United States ; R01 GM120624/GM/NIGMS NIH HHS/United States ; HD081197/NH/NIH HHS/United States ; R01 GM131407/GM/NIGMS NIH HHS/United States ; GM120624/NH/NIH HHS/United States ; GM131407/NH/NIH HHS/United States ; }, mesh = {Adolescent ; Adult ; Child ; *Colitis, Ulcerative/genetics ; Dysbiosis/genetics ; Feces ; *Gastrointestinal Microbiome/genetics ; Humans ; Metagenome ; RNA, Ribosomal, 16S/genetics ; Young Adult ; }, abstract = {Dysbiosis of human gut microbiota has been reported in association with ulcerative colitis (UC) in both children and adults using either 16S rRNA gene or shotgun sequencing data. However, these studies used either 16S rRNA or metagenomic shotgun sequencing but not both. We sequenced feces samples from 19 pediatric UC and 23 healthy children ages between 7 to 21 years using both 16S rRNA and metagenomic shotgun sequencing. The samples were analyzed using three different types of data: 16S rRNA genus level abundance, microbial species and pathway abundance profiles. We demonstrated that (a) the alpha diversity of pediatric UC cases is lower than that of healthy controls; (b) the beta diversity within children with UC is more variable than within the healthy children; (c) several microbial families including Akkermansiaceae, Clostridiaceae, Eggerthellaceae, Lachnospiraceae, and Oscillospiraceae, contain species that are depleted in pediatric UC compared to controls; (d) a few associated species unique to pediatric UC, but not adult UC, were also identified, e.g. some species in the Christensenellaceae family were found to be depleted and some species in the Enterobacteriaceae family were found to be enriched in pediatric UC; and (e) both 16S rRNA and shotgun sequencing data can predict pediatric UC status with area under the receiver operating characteristic curve (AUROC) of close to 0.90 based on cross validation. We showed that 16S rRNA data yielded similar results as shotgun data in terms of alpha diversity, beta diversity, and prediction accuracy. Our study demonstrated that pediatric UC subjects harbor a dysbiotic and less diverse gut microbial population with distinct differences from healthy children. We also showed that 16S rRNA data yielded accurate disease prediction results in comparison to shotgun data, which can be more expensive and laborious. These conclusions were confirmed in an independent data set of 7 pediatric UC cases and 8 controls.}, } @article {pmid35440640, year = {2022}, author = {Li, C and Luan, Z and Zhao, Y and Chen, J and Yang, Y and Wang, C and Jing, Y and Qi, S and Li, Z and Guo, H and Xu, W and Zhao, B and Wu, C and Wang, S and Yang, Y and Sun, G}, title = {Deep insights into the gut microbial community of extreme longevity in south Chinese centenarians by ultra-deep metagenomics and large-scale culturomics.}, journal = {NPJ biofilms and microbiomes}, volume = {8}, number = {1}, pages = {28}, pmid = {35440640}, issn = {2055-5008}, mesh = {Aged, 80 and over ; Bacteria/genetics ; Centenarians ; China ; Health Promotion ; Humans ; Longevity ; *Metagenomics/methods ; *Microbiota ; Young Adult ; }, abstract = {The gut microbes play important roles in human longevity and the gut microbiota profile of centenarians shows some unique features from young adults. Nowadays, most microbial studies on longevity are commonly based on metagenomic sequencing which may lose information about the functional microbes with extremely low abundance. Here, we combined in-depth metagenomic sequencing and large-scale culturomics to reveal the unique gut microbial structure of a Chinese longevity population, and to explore the possible relationship between intestinal microbes and longevity. Twenty-five healthy Hainan natives were enrolled in the study, including 12 centenarians and 13 senior neighbors. An average of 51.1 Gb raw sequencing data were obtained from individual fecal sample. We assembled 1778 non-redundant metagenomic assembled genomes (MAGs), 33.46% of which cannot be classified into known species. Comparison with the ordinary people in Hainan province, the longevous cohort displayed significantly decreased abundance of butyrate-producing bacteria and largely increased proportion of Escherichia coli, Desulfovibrio piger and Methanobrevibacter smithii. These species showed a constant change with aging. We also isolated 8,030 strains from these samples by large-scale culturomics, most of which belonged to 203 known species as identified by MALDI-TOF. Surprisingly, only 42.17% of the isolated species were also detected by metagenomics, indicating obvious complementarity between these two approaches. Combination of two complement methods, in-depth metagenomic sequencing and culturomics, provides deeper insights into the longevity-related gut microbiota. The uniquely enriched gut microbes in Hainan extreme decades population may help to promote health and longevity.}, } @article {pmid35440042, year = {2022}, author = {Wolf, PG and Cowley, ES and Breister, A and Matatov, S and Lucio, L and Polak, P and Ridlon, JM and Gaskins, HR and Anantharaman, K}, title = {Diversity and distribution of sulfur metabolic genes in the human gut microbiome and their association with colorectal cancer.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {64}, pmid = {35440042}, issn = {2049-2618}, support = {T32 CA057699/CA/NCI NIH HHS/United States ; T15 LM007359/LM/NLM NIH HHS/United States ; R01 CA204808/CA/NCI NIH HHS/United States ; T32 GM008692/GM/NIGMS NIH HHS/United States ; T32 GM140935/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria ; *Carcinoma ; *Colorectal Neoplasms/genetics ; *Gastrointestinal Microbiome/genetics ; Humans ; Sulfates/metabolism ; Sulfur/metabolism ; Taurine/metabolism ; }, abstract = {BACKGROUND: Recent evidence implicates microbial sulfidogenesis as a potential trigger of colorectal cancer (CRC), highlighting the need for comprehensive knowledge of sulfur metabolism within the human gut. Microbial sulfidogenesis produces genotoxic hydrogen sulfide (H2S) in the human colon using inorganic (sulfate) and organic (taurine/cysteine/methionine) substrates; however, the majority of studies have focused on sulfate reduction using dissimilatory sulfite reductases (Dsr).

RESULTS: Here, we show that genes for microbial sulfur metabolism are more abundant and diverse than previously observed and are statistically associated with CRC. Using ~ 17,000 bacterial genomes from publicly available stool metagenomes, we studied the diversity of sulfur metabolic genes in 667 participants across different health statuses: healthy, adenoma, and carcinoma. Sulfidogenic genes were harbored by 142 bacterial genera and both organic and inorganic sulfidogenic genes were associated with carcinoma. Significantly, the anaerobic sulfite reductase (asr) genes were twice as abundant as dsr, demonstrating that Asr is likely a more important contributor to sulfate reduction in the human gut than Dsr. We identified twelve potential pathways for reductive taurine metabolism and discovered novel genera harboring these pathways. Finally, the prevalence of metabolic genes for organic sulfur indicates that these understudied substrates may be the most abundant source of microbially derived H2S.

CONCLUSIONS: Our findings significantly expand knowledge of microbial sulfur metabolism in the human gut. We show that genes for microbial sulfur metabolism in the human gut are more prevalent than previously known, irrespective of health status (i.e., in both healthy and diseased states). Our results significantly increase the diversity of pathways and bacteria that are associated with microbial sulfur metabolism in the human gut. Overall, our results have implications for understanding the role of the human gut microbiome and its potential contributions to the pathogenesis of CRC. Video abstract.}, } @article {pmid35439563, year = {2022}, author = {Wang, K and Qaisar, M and Chen, B and Xiao, J and Cai, J}, title = {Metagenomic analysis of microbial community and metabolic pathway of simultaneous sulfide and nitrite removal process exposed to divergent hydraulic retention times.}, journal = {Bioresource technology}, volume = {354}, number = {}, pages = {127186}, doi = {10.1016/j.biortech.2022.127186}, pmid = {35439563}, issn = {1873-2976}, mesh = {Bacteria/genetics/metabolism ; Bioreactors ; Denitrification ; Metabolic Networks and Pathways ; Metagenomics ; *Microbiota ; *Nitrites/metabolism ; Nitrogen/metabolism ; Sulfides/metabolism ; }, abstract = {The role of hydraulic retention time (HRT) on S[0] production was assessed through metagenomics analyses. Considering comprehensive performance for the tested HRTs (0.25-13.33 h), the optimal HRT was 1 h, while respective sulfide and nitrite loading rate could reach 6.84 kg S/(m[3]·d) and 1.95 kg N/(m[3]·d), and total S[0] yield was 0.36 kg S/(kg (VSS)·d). Bacterial community richness decreased along the shortening of HRT. Microbacterium, Sulfurimonas, Sulfurovum, Paracoccus and Thauera were highly abundant bacteria. During sulfur metabolism, high expression of sqr gene was the main reason of maintaining high desulfurization load, while lacking soxB caused the continuous increase of S[0]. Regarding nitrogen metabolism, the rapid decrease of nitrite transporter prevented nitrite to enter in cells, which caused a rapid decrease of nitrite removal under extreme HRT. Adjusting HRT is an effective way to enhance S[0] production for the application of the simultaneous sulfide and nitrite removal process.}, } @article {pmid35439308, year = {2022}, author = {Miller, AK and Timoshevskaya, N and Smith, JJ and Gillum, J and Sharif, S and Clarke, S and Baker, C and Kitson, J and Gemmell, NJ and Alexander, A}, title = {Population Genomics of New Zealand Pouched Lamprey (kanakana; piharau; Geotria australis).}, journal = {The Journal of heredity}, volume = {113}, number = {4}, pages = {380-397}, pmid = {35439308}, issn = {1465-7333}, support = {//Ministry of Business, Innovation, and Employment/ ; //University of Otago/ ; //University of California, Santa Cruz/ ; }, mesh = {Animals ; Gene Flow ; *Lampreys/genetics ; *Metagenomics ; New Zealand ; Sequence Analysis, DNA ; }, abstract = {Pouched lamprey (Geotria australis) or kanakana/piharau is a culturally and ecologically significant jawless fish that is distributed throughout Aotearoa New Zealand. Despite its importance, much remains unknown about historical relationships and gene flow between populations of this enigmatic species within New Zealand. To help inform management, we assembled a draft G. australis genome and completed the first comprehensive population genomics analysis of pouched lamprey within New Zealand using targeted gene sequencing (Cyt-b and COI) and restriction site-associated DNA sequencing (RADSeq) methods. Employing 16 000 genome-wide single nucleotide polymorphisms (SNPs) derived from RADSeq (n = 186) and sequence data from Cyt-b (766 bp, n = 94) and COI (589 bp, n = 20), we reveal low levels of structure across 10 sampling locations spanning the species range within New Zealand. F-statistics, outlier analyses, and STRUCTURE suggest a single panmictic population, and Mantel and EEMS tests reveal no significant isolation by distance. This implies either ongoing gene flow among populations or recent shared ancestry among New Zealand pouched lamprey. We can now use the information gained from these genetic tools to assist managers with monitoring effective population size, managing potential diseases, and conservation measures such as artificial propagation programs. We further demonstrate the general utility of these genetic tools for acquiring information about elusive species.}, } @article {pmid35438977, year = {2022}, author = {Qin, Y and Guo, Z and Huang, H and Zhu, L and Dong, S and Zhu, YG and Cui, L and Huang, Q}, title = {Widespread of Potential Pathogen-Derived Extracellular Vesicles Carrying Antibiotic Resistance Genes in Indoor Dust.}, journal = {Environmental science & technology}, volume = {56}, number = {9}, pages = {5653-5663}, doi = {10.1021/acs.est.1c08654}, pmid = {35438977}, issn = {1520-5851}, mesh = {*Anti-Bacterial Agents/pharmacology ; Drug Resistance, Bacterial/genetics ; Dust ; *Extracellular Vesicles ; Genes, Bacterial ; Macrolides ; }, abstract = {Extracellular vesicles (EVs) are newly recognized as important vectors for carrying and spreading antibiotic resistance genes (ARGs). However, the ARGs harbored by EVs in ambient environments and the transfer potential are still unclear. In this study, the prevalence of ARGs and mobile genetic elements (MGEs) in EVs and their microbial origins were studied in indoor dust from restaurants, kindergarten, dormitories, and vehicles. The amount of EVs ranged from 3.40 × 10[7] to 1.09 × 10[11] particles/g dust. The length of EV-associated DNA fragments was between 21 bp and 9.7 kb. Metagenomic sequencing showed that a total of 241 antibiotic ARG subtypes encoding resistance to 16 common classes were detected in the EVs from all four fields. Multidrug, quinolone, and macrolide resistance genes were the dominant types. 15 ARG subtypes were exclusively carried and even enriched in EVs compared to the indoor microbiome. Moreover, several ARGs showed co-occurrence with MGEs. The EVs showed distinct taxonomic composition with their original dust microbiota. 30.23% of EV-associated DNA was predicted to originate from potential pathogens. Our results indicated the widespread of EVs carrying ARGs and virulence genes in daily life indoor dust, provided new insights into the status of extracellular DNA, and raised risk concerns on their gene transfer potential.}, } @article {pmid35438974, year = {2022}, author = {Gu, X and Huang, D and Chen, J and Li, X and Zhou, Y and Huang, M and Liu, Y and Yu, P}, title = {Bacterial Inactivation and Biofilm Disruption through Indigenous Prophage Activation Using Low-Intensity Cold Atmospheric Plasma.}, journal = {Environmental science & technology}, volume = {56}, number = {12}, pages = {8920-8931}, doi = {10.1021/acs.est.2c01516}, pmid = {35438974}, issn = {1520-5851}, mesh = {Anti-Bacterial Agents/pharmacology ; Bacteria ; *Bacteriophages ; Biofilms ; Escherichia coli ; *Escherichia coli K12 ; *Plasma Gases/pharmacology ; Prophages/physiology ; Reactive Oxygen Species ; }, abstract = {Biofilms can be pervasive and problematic in water treatment and distribution systems but are difficult to eradicate due to hindered penetration of antimicrobial chemicals. Here, we demonstrate that indigenous prophages activated by low-intensity plasma have the potential for efficient bacterial inactivation and biofilm disruption. Specifically, low-intensity plasma treatment (i.e., 35.20 W) elevated the intracellular oxidative reactive species (ROS) levels by 184%, resulting in the activation of prophage lambda (λ) within antibiotic-resistant Escherichia coli K-12 (lambda+) [E. coli (λ+)]. The phage activation efficiency was 6.50-fold higher than the conventional mitomycin C induction. Following a cascading effect, the activated phages were released upon the lysis of E. coli (λ+), which propagated further and lysed phage-susceptible E. coli K-12 (lambda-) [E. coli (λ-)] within the biofilm. Bacterial intracellular ROS analysis and ROS scavenger tests revealed the importance of plasma-generated ROS (e.g., [•]OH, [1]O2, and [•]O2[-]) and associated intracellular oxidative stress on prophage activation. In a mixed-species biofilm on a permeable membrane surface, our "inside-out" strategy could inactivate total bacteria by 49% and increase the membrane flux by 4.33-fold. Furthermore, the metagenomic analysis revealed that the decrease in bacterial abundance was closely associated with the increase in phage levels. As a proof-of-concept, this is the first demonstration of indigenous prophage activations by low-intensity plasma for antibiotic-resistant bacterial inactivation and biofilm eradication, which opens up a new avenue for managing associated microbial problems.}, } @article {pmid35438519, year = {2022}, author = {Yancey, CE and Smith, DJ and Den Uyl, PA and Mohamed, OG and Yu, F and Ruberg, SA and Chaffin, JD and Goodwin, KD and Tripathi, A and Sherman, DH and Dick, GJ}, title = {Metagenomic and Metatranscriptomic Insights into Population Diversity of Microcystis Blooms: Spatial and Temporal Dynamics of mcy Genotypes, Including a Partial Operon That Can Be Abundant and Expressed.}, journal = {Applied and environmental microbiology}, volume = {88}, number = {9}, pages = {e0246421}, pmid = {35438519}, issn = {1098-5336}, mesh = {*Cyanobacteria/genetics ; Ecosystem ; Genotype ; Lakes/microbiology ; Microcystins/genetics/metabolism ; *Microcystis/genetics/metabolism ; Operon ; }, abstract = {Cyanobacterial harmful algal blooms (cyanoHABs) degrade freshwater ecosystems globally. Microcystis aeruginosa often dominates cyanoHABs and produces microcystin (MC), a class of hepatotoxins that poses threats to human and animal health. Microcystin toxicity is influenced by distinct structural elements across a diversity of related molecules encoded by variant mcy operons. However, the composition and distribution of mcy operon variants in natural blooms remain poorly understood. Here, we characterized the variant composition of mcy genes in western Lake Erie Microcystis blooms from 2014 and 2018. Sampling was conducted across several spatial and temporal scales, including different bloom phases within 2014, extensive spatial coverage on the same day (2018), and frequent, autonomous sampling over a 2-week period (2018). Mapping of metagenomic and metatranscriptomic sequences to reference sequences revealed three Microcystis mcy genotypes: complete (all genes present [mcyA-J]), partial (truncated mcyA, complete mcyBC, and missing mcyD-J), and absent (no mcy genes). We also detected two different variants of mcyB that may influence the production of microcystin congeners. The relative abundance of these genotypes was correlated with pH and nitrate concentrations. Metatranscriptomic analysis revealed that partial operons were, at times, the most abundant genotype and expressed in situ, suggesting the potential biosynthesis of truncated products. Quantification of genetic divergence between genotypes suggests that the observed strains are the result of preexisting heterogeneity rather than de novo mutation during the sampling period. Overall, our results show that natural Microcystis populations contain several cooccurring mcy genotypes that dynamically shift in abundance spatiotemporally via strain succession and likely influence the observed diversity of the produced congeners. IMPORTANCE Cyanobacteria are responsible for producing microcystins (MCs), a class of potent and structurally diverse toxins, in freshwater systems around the world. While microcystins have been studied for over 50 years, the diversity of their chemical forms and how this variation is encoded at the genetic level remain poorly understood, especially within natural populations of cyanobacterial harmful algal blooms (cyanoHABs). Here, we leverage community DNA and RNA sequences to track shifts in mcy genes responsible for producing microcystin, uncovering the relative abundance, expression, and variation of these genes. We studied this phenomenon in western Lake Erie, which suffers annually from cyanoHAB events, with impacts on drinking water, recreation, tourism, and commercial fishing.}, } @article {pmid35438076, year = {2022}, author = {Takeuchi, D and Kerdsin, A and Akeda, Y and Sugawara, Y and Sakamoto, N and Matsumoto, Y and Motooka, D and Ishihara, T and Nishi, I and Laolerd, W and Santanirand, P and Yamamoto, N and Tomono, K and Hamada, S}, title = {Nationwide surveillance in Thailand revealed genotype-dependent dissemination of carbapenem-resistant Enterobacterales.}, journal = {Microbial genomics}, volume = {8}, number = {4}, pages = {}, pmid = {35438076}, issn = {2057-5858}, mesh = {Carbapenems/pharmacology ; *Enterobacteriaceae Infections/epidemiology ; *Gammaproteobacteria ; Genotype ; Humans ; Thailand/epidemiology ; beta-Lactamases/genetics ; }, abstract = {Carbapenem-resistant Enterobacterales (CRE) are a serious public health threat because of their rapid dissemination. To determine the epidemiological and genetic characteristics of CRE infections in Thailand, we performed whole-genome sequencing of 577 carbapenem-resistant Klebsiella pneumoniae isolates and 170 carbapenem-resistant Escherichia coli isolates from hospitals across the nation. The four most prevalent carbapenemase genes harboured by these bacteria were bla NDM-1, bla NDM-5, bla OXA-181 and bla OXA-232. The gene bla NDM-1 was identified in diverse sequence types. The gene bla NDM-5 was identified almost exclusively in E. coli . The genes bla OXA-181, bla OXA-232, and co-carriage of bla NDM-1 and bla OXA-232 were found in specific sequence types from certain provinces. Replicon typing revealed the diverse backbones of bla NDM-1- and bla NDM-5-harbouring plasmids and successful expansion of bla NDM-1-harbouring IncN2-type plasmids. Core-genome single-nucleotide polymorphism analysis suggested that bla OXA-181-, bla OXA-232-, bla NDM-5-, and co-carriage of bla NDM-1 and bla OXA-232-associated sub-clonal lineages have recently predominated in the provinces from where these isolates were isolated. Thus, we demonstrate genotype-dependent dissemination of CRE in Thailand, which is helpful for establishing infection-control strategies in CRE-endemic areas.}, } @article {pmid35437913, year = {2022}, author = {Campbell, BC and Greenfield, P and Gong, S and Barnhart, EP and Midgley, DJ and Paulsen, IT and George, SC}, title = {Methanogenic archaea in subsurface coal seams are biogeographically distinct: an analysis of metagenomically-derived mcrA sequences.}, journal = {Environmental microbiology}, volume = {24}, number = {9}, pages = {4065-4078}, pmid = {35437913}, issn = {1462-2920}, mesh = {Animals ; Archaea/metabolism ; Coal/microbiology ; *Euryarchaeota/genetics ; *Greenhouse Gases/metabolism ; Methane/metabolism ; Phylogeny ; RNA, Ribosomal, 16S/genetics/metabolism ; Soil ; }, abstract = {The production of methane as an end-product of organic matter degradation in the absence of other terminal electron acceptors is common, and has often been studied in environments such as animal guts, soils and wetlands due to its potency as a greenhouse gas. To date, however, the study of the biogeographic distribution of methanogens across coal seam environments has been minimal. Here, we show that coal seams are host to a diverse range of methanogens, which are distinctive to each geological basin. Based on comparisons to close relatives from other methanogenic environments, the dominant methanogenic pathway in these basins is hydrogenotrophic, with acetoclastic being a second major pathway in the Surat Basin. Finally, mcrA and 16S rRNA gene primer biases were predominantly seen to affect the detection of Methanocellales, Methanomicrobiales and Methanosarcinales taxa in this study. Subsurface coal methanogenic community distributions and pathways presented here provide insights into important metabolites and bacterial partners for in situ coal biodegradation.}, } @article {pmid35437888, year = {2022}, author = {Latz, MAC and Grujcic, V and Brugel, S and Lycken, J and John, U and Karlson, B and Andersson, A and Andersson, AF}, title = {Short- and long-read metabarcoding of the eukaryotic rRNA operon: Evaluation of primers and comparison to shotgun metagenomics sequencing.}, journal = {Molecular ecology resources}, volume = {22}, number = {6}, pages = {2304-2318}, doi = {10.1111/1755-0998.13623}, pmid = {35437888}, issn = {1755-0998}, support = {NV-03728-17//Naturvårdsverket/ ; 34442//Villum Fonden/ ; }, mesh = {DNA Primers/genetics ; *Eukaryota/genetics ; High-Throughput Nucleotide Sequencing ; Metagenomics/methods ; Phylogeny ; RNA, Ribosomal, 16S/genetics ; RNA, Ribosomal, 18S/genetics ; *rRNA Operon/genetics ; }, abstract = {High-throughput sequencing-based analysis of microbial diversity has evolved vastly over the last decade. Currently, the go-to method for studying microbial eukaryotes is short-read metabarcoding of variable regions of the 18S rRNA gene with <500 bp amplicons. However, there is a growing interest in applying long-read sequencing of amplicons covering the rRNA operon for improving taxonomic resolution. For both methods, the choice of primers is crucial. It determines if community members are covered, if they can be identified at a satisfactory taxonomic level, and if the obtained community profile is representative. Here, we designed new primers targeting 18S and 28S rRNA based on 177,934 and 21,072 database sequences, respectively. The primers were evaluated in silico along with published primers on reference sequence databases and marine metagenomics data sets. We further evaluated a subset of the primers for short- and long-read sequencing on environmental samples in vitro and compared the obtained community profile with primer-unbiased metagenomic sequencing. Of the short-read pairs, a new V6-V8 pair and the V4_Balzano pair used with a simplified PCR protocol provided good results in silico and in vitro. Fewer differences were observed between the long-read primer pairs. The long-read amplicons and ITS1 alone provided higher taxonomic resolution than V4. Together, our results represent a reference and guide for selection of robust primers for research on and environmental monitoring of microbial eukaryotes.}, } @article {pmid35437874, year = {2022}, author = {Guo, Y and Liu, C and Zhao, X and Zhang, X and Wu, Q and Wang, Z and Lu, J}, title = {Changes in gut microbiota, metabolite SCFAs, and GPR43 expression in obese diabetic mice after sleeve gastrectomy.}, journal = {Journal of applied microbiology}, volume = {133}, number = {2}, pages = {555-568}, doi = {10.1111/jam.15583}, pmid = {35437874}, issn = {1365-2672}, support = {19ZR1456000//National Natural Science Foundation of Shanghai/ ; 20ZR1456600//National Natural Science Foundation of Shanghai/ ; }, mesh = {Animals ; *Diabetes Mellitus, Experimental/surgery ; *Fatty Acids, Volatile/metabolism ; Gastrectomy/methods ; *Gastrointestinal Microbiome ; Mice ; Mice, Obese ; Obesity/genetics/surgery ; *Receptors, G-Protein-Coupled/genetics ; }, abstract = {AIMS: To evaluate changes in short-chain fatty acid levels and G protein-coupled receptor 43 expression and distribution in gut microbiota and explore their relationships in obese diabetic mice after sleeve gastrectomy.

METHODS AND RESULTS: Diet-induced obese mice and obese diabetic ob/ob mice were established. Changes in glucose metabolism, lipid metabolism, gut microbiota, metabolite short-chain fatty acids, and G protein-coupled receptor 43 expressions were assessed in both models 10 weeks postoperatively. Mice that underwent sleeve gastrectomy exhibited sustained weight loss and reduced glucose, insulin, leptin, and cholesterol levels. Metagenomic sequencing revealed significant characteristic alterations in gut microbiota after sleeve gastrectomy, which were correlated with changes in faecal short-chain fatty acid levels. Postoperatively, G protein-coupled receptor 43 expression in the colon tissue was upregulated in both models, whereas its expression in the adipose tissue was downregulated in the diet-induced obese mouse model.

CONCLUSIONS: Metabolic improvement in obese and diabetic mice after sleeve gastrectomy is associated with alterations in gut microbiota, short-chain fatty acid levels, and G protein-coupled receptor 43 expressions.

Our findings reveal a possible mechanism through which sleeve gastrectomy improves obesity and diabetes via changes in bacteria producing short-chain fatty acids and G protein-coupled receptor 43.}, } @article {pmid35436900, year = {2022}, author = {Song, J and Li, T and Zheng, Z and Fu, W and Long, Z and Shi, N and Han, Y and Zhang, L and Yu, Y and Fang, H}, title = {Carbendazim shapes microbiome and enhances resistome in the earthworm gut.}, journal = {Microbiome}, volume = {10}, number = {1}, pages = {63}, pmid = {35436900}, issn = {2049-2618}, mesh = {Animals ; Anti-Bacterial Agents/pharmacology ; Bacteria/genetics ; Benzimidazoles ; Carbamates ; *Fungicides, Industrial ; Genes, Bacterial ; *Microbiota/genetics ; *Oligochaeta ; Soil/chemistry ; }, abstract = {BACKGROUND: It is worrisome that several pollutants can enhance the abundance of antibiotic resistance genes (ARGs) in the environment, including agricultural fungicides. As an important bioindicator for environmental risk assessment, earthworm is still a neglected focus that the effects of the fungicide carbendazim (CBD) residues on the gut microbiome and resistome are largely unknown. In this study, Eisenia fetida was selected to investigate the effects of CBD in the soil-earthworm systems using shotgun metagenomics and qPCR methods.

RESULTS: CBD could significantly perturb bacterial community and enrich specific bacteria mainly belonging to the phylum Actinobacteria. More importantly, CBD could serve as a co-selective agent to elevate the abundance and diversity of ARGs, particularly for some specific types (e.g., multidrug, glycopeptide, tetracycline, and rifamycin resistance genes) in the earthworm gut. Additionally, host tracking analysis suggested that ARGs were mainly carried in some genera of the phyla Actinobacteria and Proteobacteria. Meanwhile, the level of ARGs was positively relevant to the abundance of mobile genetic elements (MGEs) and some representative co-occurrence patterns of ARGs and MGEs (e.g., cmx-transposase and sul1-integrase) were further found on the metagenome-assembled contigs in the CBD treatments.

CONCLUSIONS: It can be concluded that the enhancement effect of CBD on the resistome in the earthworm gut may be attributed to its stress on the gut microbiome and facilitation on the ARGs dissemination mediated by MGEs, which may provide a novel insight into the neglected ecotoxicological risk of the widely used agrochemicals on the gut resistome of earthworm dwelling in soil. Video abstract.}, } @article {pmid35436811, year = {2022}, author = {Diao, ZL and Zhang, R and Li, JM}, title = {[Analysis of the methods and quality assurance of metagenomic next-generation sequencing to detect the microbial cfDNA from blood samples in China].}, journal = {Zhonghua yi xue za zhi}, volume = {102}, number = {15}, pages = {1114-1118}, doi = {10.3760/cma.j.cn112137-20220104-00017}, pmid = {35436811}, issn = {0376-2491}, mesh = {*Cell-Free Nucleic Acids ; Computational Biology ; High-Throughput Nucleotide Sequencing/methods ; Metagenome ; Metagenomics/methods ; Sensitivity and Specificity ; }, abstract = {Objective: To investigate the methods and quality assurance of metagenomic next-generation sequencing (mNGS) to detect the microbial cfDNA (mcfDNA) from blood samples in different laboratories across China. Methods: In October 2020, questionnaires about detecting mcfDNA in blood samples with mNGS were distributed to 80 laboratories across the country. The questionnaire included four parts: pre-analysis, during analysis, post-analysis, and carrying out of performance validation for mNGS. (1) Pre-analysis: the requirements for samples quality, such as collection, storage, the transportation conditions of samples; (2) During analysis: the extraction workflows of mcfDNA, the quality requirements of the library, the application of the sequencing platforms and the bioinformatics analysis pipelines; (3) Post-analysis: the standard of interpretation results for mNGS; (4) Carrying out of performance validation: the minimum detection limit for various pathogens. All laboratories are required to fill in the questionnaire according to the actual situation. The feedback data were summarized and analyzed. Results: The 80 laboratories included 20 medical centers and 60 independent medical laboratories. There were 80.0% (64/80) of laboratories indicated that both plasma and serum samples were used to detect mcfDNA in blood, and the rest of the laboratories (16/80, 20.0%) only used plasma samples. The sequencing platforms used by mNGS laboratories involved in the survey included illumina (49), Beijing Genomics Institute (16), Ion Torrent (13) and Nanopore sequencing (2). There were 87.5% (70/80) of laboratories used the integrated analysis tools built by the third-party laboratories, and other laboratories (12.5%, 10/80) independently built the analysis platform by open-source software. The interpretation criteria of mNGS results varied between laboratories, among which the normalized number of pathogen-specific sequences, relative abundance, genome coverage rate, and the detection of the microorganism in the negative control were the main factors considered by laboratories. Most laboratories (76.3%, 61/80) had carried out the performance validation for the mcfDNA mNGS workflows. The limit of detection of the laboratories-developed mNGS workflows for Gram-positive bacteria, Gram-negative bacteria, fungi, parasites, and other pathogens were mainly distributed at 10-100 copies/ml, DNA virus was mainly distributed at 500-1 000 copies/ml. Conclusions: The mNGS workflows of various laboratories are very different. In order to ensure timely and accurate testing results, every laboratory needs to actively optimize the mNGS testing procedures, improve quality assurance measures, and carry out performance validation before mNGS is widely used in clinical settings.}, } @article {pmid35436715, year = {2022}, author = {Liu, Z and Wei, Y and Li, J and Ding, GC}, title = {Integrating 16S rRNA amplicon metagenomics and selective culture for developing thermophilic bacterial inoculants to enhance manure composting.}, journal = {Waste management (New York, N.Y.)}, volume = {144}, number = {}, pages = {357-365}, doi = {10.1016/j.wasman.2022.04.013}, pmid = {35436715}, issn = {1879-2456}, mesh = {*Agricultural Inoculants/genetics ; *Composting ; Manure/microbiology ; Metagenomics ; RNA, Ribosomal, 16S/genetics ; Soil ; }, abstract = {Composting is an important method for treating and recycling organic waste, and the use of microbial inoculants can increase the efficiency of composting. Herein, we illustrate an approach that integrate 16S rRNA amplicon metagenomics and selective culture of thermophilic bacteria for the development of inoculants to improve manure composting. The 16S rRNA amplicon sequencing analysis revealed that Firmicutes and Actinobacteria were dominant in the composting mixture, and that different microbial hubs succeeded during the thermophilic stage. All isolated thermophilic bacteria were affiliated with the order Bacillales, such as Geobacillus, Bacillus, and Aeribacillus. These isolated thermophilic bacteria were grouped into 11 phylotypes, which shared ＞99% sequence identity to 0.15% to 5.32% of 16S rRNA reads by the amplicon sequencing. Three of these phylotypes transiently enriched during the thermophilic stage. Six thermophilic bacteria were selected from the three phylotypes to obtain seven microbial inoculants. Five out of seven of the microbial inoculants enhanced the thermophilic stage of composting by 16.9% to 52.2%. Three-dimensional excitation emission matrix analysis further revealed that two inoculants (Thermoactinomyces intermedius and Ureibacillus thermophilus) stimulated humification. Additionally, the 16S rRNA amplicon sequencing analysis revealed that inoculation with thermophilic bacteria enhanced the succession of the microbial community during composting. In conclusion, 16S rRNA amplicon metagenomics is a useful tool for the development of microbial inoculants to enhance manure composting.}, } @article {pmid35435994, year = {2022}, author = {Yamaguchi, T and Iijima, H and Yoshihara, T and Tani, M and Otake, Y and Iwatani, S and Amano, T and Tashiro, T and Kurahashi, T and Inoue, T and Tsujii, Y and Hayashi, Y and Inoue, T and Motooka, D and Nakamura, S and Shinzaki, S and Takehara, T}, title = {Exacerbation of non-steroidal anti-inflammatory drug-induced enteropathy in C-C chemokine receptor type 7-deficient mice.}, journal = {Journal of gastroenterology and hepatology}, volume = {37}, number = {8}, pages = {1561-1570}, doi = {10.1111/jgh.15868}, pmid = {35435994}, issn = {1440-1746}, support = {Amed-Crest 20gm1010004h0205//Japan Agency for Medical Research and Development (AMED)/ ; 17H04159//Japan Society for the Promotion of Science/ ; }, mesh = {Animals ; *Anti-Inflammatory Agents, Non-Steroidal/adverse effects ; Dendritic Cells ; *Indomethacin/adverse effects ; *Intestinal Diseases/chemically induced ; Lithostathine ; Mice ; Mice, Inbred C57BL ; *Receptors, CCR7/genetics ; }, abstract = {BACKGROUND AND AIM: Non-steroidal anti-inflammatory drugs (NSAIDs) induce intestinal enteropathy and the pathophysiology is related to immune-mediated mechanisms. We aimed to investigate the role of C-C chemokine receptor type 7 (CCR7) which regulates immune cell migration in NSAID-induced enteropathy.

METHODS: Injury of the small intestine was evaluated 24 h after the subcutaneous injection of indomethacin in CCR7-deficient (Ccr7[-/-]) and wild-type (WT) mice. The cellular profile and cytokine production in intestinal cells were analyzed. Indomethacin-induced enteropathy was evaluated in mice adoptively transferred with CD103[+] dendritic cells (DCs) from Ccr7[-/-] or WT mice.

RESULTS: Indomethacin induced more severe intestinal injury in Ccr7[-/-] mice than in WT mice. The major inflammatory cytokines were not increased and the proportion of regulatory T cells following indomethacin injection was not decreased in Ccr7[-/-] mice compared with WT mice. The expression of interleukin (IL)-22 binding protein (IL-22BP), which inhibits IL-22 activity, was significantly higher in CD103[+] DCs from Ccr7[-/-] mice than those from WT mice. Mice adoptively transferred with CD103[+] DCs isolated from Ccr7[-/-] mice exhibited more severe intestinal injury following indomethacin injection compared with those adoptively transferred with CD103[+] DCs of WT mice. Ccr7[-/-] mice injected with indomethacin showed a significant reduction in regenerating islet-derived 1 (Reg1) mRNA expression, which is regulated by IL-22, in intestinal epithelial cells.

CONCLUSIONS: C-C chemokine receptor type 7 deficiency exacerbated NSAID-induced enteropathy in association with an altered phenotype of CD103[+] DCs that produces IL-22BP. CCR7 contributes to protect the small intestine from NSAID-induced mucosal injury.}, } @article {pmid35435739, year = {2022}, author = {Verbanic, S and Deacon, JM and Chen, IA}, title = {The Chronic Wound Phageome: Phage Diversity and Associations with Wounds and Healing Outcomes.}, journal = {Microbiology spectrum}, volume = {10}, number = {3}, pages = {e0277721}, pmid = {35435739}, issn = {2165-0497}, support = {DP2 GM123457/GM/NIGMS NIH HHS/United States ; }, mesh = {Bacteria/genetics ; *Bacteriophages/genetics ; Humans ; Metagenomics ; *Microbiota ; Virome ; *Viruses/genetics ; Wound Healing ; }, abstract = {Two leading impediments to chronic wound healing are polymicrobial infection and biofilm formation. Recent studies have characterized the bacterial fraction of these microbiomes and have begun to elucidate compositional correlations to healing outcomes. However, the factors that drive compositional shifts are still being uncovered. The virome may play an important role in shaping bacterial community structure and function. Previous work on the skin virome determined that it was dominated by bacteriophages, viruses that infect bacteria. To characterize the virome, we enrolled 20 chronic wound patients presenting at an outpatient wound care clinic in a microbiome survey, collecting swab samples from healthy skin and chronic wounds (diabetic, venous, arterial, or pressure) before and after a single, sharp debridement procedure. We investigated the virome using a virus-like particle enrichment procedure, shotgun metagenomic sequencing, and a k-mer-based, reference-dependent taxonomic classification method. Taxonomic composition, diversity, and associations with covariates are presented. We find that the wound virome is highly diverse, with many phages targeting known pathogens, and may influence bacterial community composition and functionality in ways that impact healing outcomes. IMPORTANCE Chronic wounds are an increasing medical burden. These wounds are known to be rich in microbial content, including both bacteria and bacterial viruses (phages). The viruses may play an important role in shaping bacterial community structure and function. We analyzed the virome and bacterial composition of 20 patients with chronic wounds. The viruses found in wounds are highly diverse compared to normal skin, unlike the bacterial composition, where diversity is decreased. These data represent an initial look at this relatively understudied component of the chronic wound microbiome and may help inform future phage-based interventions.}, } @article {pmid35435701, year = {2022}, author = {Podowski, JC and Paver, SF and Newton, RJ and Coleman, ML}, title = {Genome Streamlining, Proteorhodopsin, and Organic Nitrogen Metabolism in Freshwater Nitrifiers.}, journal = {mBio}, volume = {13}, number = {3}, pages = {e0237921}, pmid = {35435701}, issn = {2150-7511}, mesh = {*Ammonia/metabolism ; Archaea/genetics/metabolism ; Bacteria/genetics/metabolism ; *Ecosystem ; Genome ; Lakes/microbiology ; Nitrification ; Nitrogen/metabolism ; Oxidation-Reduction ; Phylogeny ; Rhodopsins, Microbial ; }, abstract = {Microbial nitrification is a critical process governing nitrogen availability in aquatic systems. Freshwater nitrifiers have received little attention, leaving many unanswered questions about their taxonomic distribution, functional potential, and ecological interactions. Here, we reconstructed genomes to infer the metabolism and ecology of free-living picoplanktonic nitrifiers across the Laurentian Great Lakes, a connected series of five of Earth's largest lakes. Surprisingly, ammonia-oxidizing bacteria (AOB) related to Nitrosospira dominated over ammonia-oxidizing archaea (AOA) at nearly all stations, with distinct ecotypes prevailing in the transparent, oligotrophic upper lakes compared to Lakes Erie and Ontario. Unexpectedly, one ecotype of Nitrosospira encodes proteorhodopsin, which could enhance survival under conditions where ammonia oxidation is inhibited or substrate limited. Nitrite-oxidizing bacteria (NOB) "Candidatus Nitrotoga" and Nitrospira fluctuated in dominance, with the latter prevailing in deeper, less-productive basins. Genome reconstructions reveal highly reduced genomes and features consistent with genome streamlining, along with diverse adaptations to sunlight and oxidative stress and widespread capacity for organic nitrogen use. Our findings expand the known functional diversity of nitrifiers and establish their ecological genomics in large lake ecosystems. By elucidating links between microbial biodiversity and biogeochemical cycling, our work also informs ecosystem models of the Laurentian Great Lakes, a critical freshwater resource experiencing rapid environmental change. IMPORTANCE Microorganisms play critical roles in Earth's nitrogen cycle. In lakes, microorganisms called nitrifiers derive energy from reduced nitrogen compounds. In doing so, they transform nitrogen into a form that can ultimately be lost to the atmosphere by a process called denitrification, which helps mitigate nitrogen pollution from fertilizer runoff and sewage. Despite their importance, freshwater nitrifiers are virtually unexplored. To understand their diversity and function, we reconstructed genomes of freshwater nitrifiers across some of Earth's largest freshwater lakes, the Laurentian Great Lakes. We discovered several new species of nitrifiers specialized for clear low-nutrient waters and distinct species in comparatively turbid Lake Erie. Surprisingly, one species may be able to harness light energy by using a protein called proteorhodopsin, despite the fact that nitrifiers typically live in deep dark water. Our work reveals the unique biodiversity of the Great Lakes and fills key gaps in our knowledge of an important microbial group, the nitrifiers.}, } @article {pmid35435454, year = {2022}, author = {Negri, T and Mantri, S and Angelov, A and Peter, S and Muth, G and Eustáquio, AS and Ziemert, N}, title = {A rapid and efficient strategy to identify and recover biosynthetic gene clusters from soil metagenomes.}, journal = {Applied microbiology and biotechnology}, volume = {106}, number = {8}, pages = {3293-3306}, pmid = {35435454}, issn = {1432-0614}, support = {KL2 TR002002/TR/NCATS NIH HHS/United States ; 1R01GM129344-01A1/GM/NIGMS NIH HHS/United States ; R01 GM129344/GM/NIGMS NIH HHS/United States ; TTU09.716//Deutsches Zentrum für Infektionsforschung/ ; Germany's Excellence Strategy-EXC 2124-390838134//Deutsche Forschungsgemeinschaft/ ; }, mesh = {DNA ; *Metagenome ; Metagenomics/methods ; Multigene Family ; *Soil ; }, abstract = {Culture-independent metagenomic approaches offer a promising solution to the discovery of therapeutically relevant compounds such as antibiotics by enabling access to the hidden biosynthetic potential of microorganisms. These strategies, however, often entail laborious, multi-step, and time-consuming procedures to recover the biosynthetic gene clusters (BGCs) from soil metagenomes for subsequent heterologous expression. Here, we developed an efficient method we called single Nanopore read cluster mining (SNRCM), which enables the fast recovery of complete BGCs from a soil metagenome using long- and short-read sequencing. A metagenomic fosmid library of 83,700 clones was generated and sequenced using Nanopore as well as Illumina technologies. Hybrid assembled contigs of the sequenced fosmid library were subsequently analyzed to identify BGCs encoding secondary metabolites. Using SNRCM, we aligned the identified BGCs directly to Nanopore long-reads and were able to detect complete BGCs on single fosmids. This enabled us to select for and recover BGCs of interest for subsequent heterologous expression attempts. Additionally, the sequencing data of the fosmid library and its corresponding metagenomic DNA enabled us to assemble and recover a large nonribosomal peptide synthetase (NRPS) BGC from three different fosmids of our library and to directly amplify and recover a complete lasso peptide BGC from the high-quality metagenomic DNA. Overall, the strategies presented here provide a useful tool for accelerating and facilitating the identification and production of potentially interesting bioactive compounds from soil metagenomes. KEY POINTS: • An efficient approach for the recovery of BGCs from soil metagenomes was developed to facilitate natural product discovery. • A fosmid library was constructed from soil metagenomic HMW DNA and sequenced via Illumina and Nanopore. • Nanopore long-reads enabled the direct identification and recovery of complete BGCs on single fosmids.}, } @article {pmid35434233, year = {2022}, author = {Tran, DM}, title = {Rhizosphere microbiome dataset of Robusta coffee (Coffea canephora L.) grown in the Central Highlands, Vietnam, based on 16S rRNA metagenomics analysis.}, journal = {Data in brief}, volume = {42}, number = {}, pages = {108106}, pmid = {35434233}, issn = {2352-3409}, abstract = {Vietnam is the second-largest coffee producer in the world after Brazil. Of the two main coffee production species, namely, Arabica and Robusta, Vietnam is the largest producer of Robusta worldwide [1]. Based on previous reports, the planted coffee area in Vietnam was 695.600 ha and its production was 1.76 million tons in 2020, in which the Central Highlands region accounts for approximately 73% of the planted area and production [2]. Hence, this region is known as the capital of coffee plantations and production in Vietnam. Previous studies have focused on the diversity of rhizospheric bacteria from this plant species cultivated in this region based on cultivation methods [3], [4], [5], [6], [7], [8]. However, no report has been found on the rhizospheric microbial diversity of this important plant in Vietnam. To our knowledge, a dataset of rhizospheric microbial communities of the coffee plant grown in the Central Highlands is still unclear. This report presents a dataset of the rhizosphere microbiome from a representative sample obtained by mixing five rhizospheric soil samples of Coffea canephora L. cultivated in the Central Highlands region using metagenomic next-generation sequencing. This dataset provides information on the rhizospheric microbial diversity of Robusta coffee, particularly its functionality. Therefore, cultivation techniques for sustainable Robusta coffee production in the region could be developed by applying indigenous rhizospheric microbial resources.}, } @article {pmid35434230, year = {2022}, author = {Tran, DM and Nguyen, TH and Huynh, TU and Do, TO and Nguyen, QV and Nguyen, AD}, title = {Analysis of endophytic microbiome dataset from roots of black pepper (Piper nigrum L.) cultivated in the Central Highlands region, Vietnam using 16S rRNA gene metagenomic next-generation sequencing.}, journal = {Data in brief}, volume = {42}, number = {}, pages = {108108}, pmid = {35434230}, issn = {2352-3409}, abstract = {Vietnam is the most prominent black pepper producer and exporter in the world. In 2020, the cultivated area of black pepper in Vietnam was 132.000 hectares and its production was 270.000 tons, in which the Central Highlands region took about 70% of both the cultivated area and production [1]. Hence, this region is thought to be the capital of black pepper cultivation and production in Vietnam. Numerous researches have investigated biodiversity and collected various beneficial endophytic bacteria from this plant in this region; however, traditional methods only were used to isolate such bacteria [2], [3], [4], [5]. Therefore, these studies have a limitation to providing insight into the profiles of the endophytic microorganism dataset in the black pepper plant. Most recently, our work based on the 16S rRNA gene amplicon sequencing revealed an insight into profiles of microbial diversity and its functionality from the sample collected from a forest in this region; however, that work was just focused on soil microbiome dataset from the dry deciduous dipterocarp forest in Yok Don national park [6]. To our knowledge, a dataset of endophytic microbiome of black pepper plant cultivated in the Central Highlands remains unclear. This report presents a dataset of the endophytic microbiome from a representative sample combined from five different root samples of black pepper (Vinh Linh local variety) cultivated in the Central Highlands of Vietnam using 16S rRNA gene metagenomic next-generation sequencing. The dataset in this work can provide information on the endophytic microbial diversity and its functionality. It can also be useful for developing cultivation techniques by applying endophytic microbial genetic resources for sustainable black pepper production in the Central Highlands, Vietnam, towards the nutrient need in different stages of development and growth.}, } @article {pmid35434223, year = {2022}, author = {Maela, MP and Serepa-Dlamini, MH}, title = {Data on metagenomic profiles of bacterial endophyte communities associated with Dicoma anomala.}, journal = {Data in brief}, volume = {42}, number = {}, pages = {108112}, pmid = {35434223}, issn = {2352-3409}, abstract = {Plants harbor varied communities of bacterial endophytes which play a crucial role in plant health and growth. Dicoma anomala is a medicinal plant that is known for its excellent ethnomedicinal uses which include treatment of coughs, fever, ulcers, and dysentery. This data in Brief article provides information on the diversity of bacterial endophytes associated with a medicinal plant, Dicoma anomala targeting the 16S rRNA gene using Illumina sequencing technology during three different seasons. Plant samples were collected in Eisleben, Limpopo province, South Africa, in the months of April, June, August and October 2018. The dataset revealed that the leaf samples collected in August had the highest species diversity as indicated by the Shannon index (4.25), Chao1 (1456.01), abundance-based coverage estimator (ACE) (1492.07) and the Simpson indices of diversity (0.05) irrespective of the species. The order of the bacterial endophyte's richness in D. anomala was April> October> June> August, from lowest to highest. The taxonomic composition analysis showed that most endophytic bacteria were composed of Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes and Chloroflexi. Some endophytic bacteria were found to be tissue specific. Sequences of Cutibacterium, Acinetobacter and Methylobacterium were prevalent in the leaves, whereas Amycolatopsis and Bradyrhizobium were the dominant genera in the root samples.}, } @article {pmid35434198, year = {2022}, author = {Steffens, L and Pettinato, E and Steiner, TM and Eisenreich, W and Berg, IA}, title = {Tracking the Reversed Oxidative Tricarboxylic Acid Cycle in Bacteria.}, journal = {Bio-protocol}, volume = {12}, number = {6}, pages = {e4364}, pmid = {35434198}, issn = {2331-8325}, abstract = {Different pathways for autotrophic CO2 fixation can be recognized by the presence of genes for their specific key enzymes. On this basis, (meta)genomic, (meta)transcriptomic, or (meta)proteomic analysis enables the identification of the role of an organism or a distinct pathway in primary production. However, the recently discovered variant of the reductive tricarboxylic acid (rTCA) cycle, the reverse oxidative tricarboxylic acid (roTCA) cycle, lacks unique enzymes, a feature that makes it cryptic for bioinformatics analysis. This pathway is a reversal of the widespread tricarboxylic acid (TCA) cycle. The functioning of the roTCA cycle requires unusually high activity of citrate synthase, the enzyme responsible for citrate cleavage, as well as elevated CO2 partial pressures. Here, we present a detailed description of the protocol we used for the identification of the roTCA cycle in members of Desulfurellaceae. First, we describe the anaerobic cultivation of Desulfurellaceae at different CO2 concentrations with a method that can be adapted to the cultivation of other anaerobes. Then, we explain how to measure activities of enzymes responsible for citrate cleavage, malate dehydrogenase reaction, and the crucial carboxylation step of the cycle catalyzed by pyruvate synthase in cell extracts. In conclusion, we describe stable isotope experiments that allow tracking of the roTCA cycle in vivo, through the position-specific incorporation of carbon-13 into amino acids. The label is provided to the organism as [13]CO2 or [1-[13]C]glutamate. The same key methodology can be used for the reliable evaluation of the functioning of the roTCA cycle in any organism under study. This pathway is likely to participate, completely unseen, in the metabolism of various microorganisms. Graphic abstract.}, } @article {pmid35433724, year = {2022}, author = {Li, Y and Jiao, M and Liu, Y and Ren, Z and Li, A}, title = {Application of Metagenomic Next-Generation Sequencing in Mycobacterium tuberculosis Infection.}, journal = {Frontiers in medicine}, volume = {9}, number = {}, pages = {802719}, pmid = {35433724}, issn = {2296-858X}, abstract = {The fight against Mycobacterium tuberculosis (MTB) has been going on for thousands of years, while it still poses a threat to human health. In addition to routine detections, metagenomic next-generation sequencing (mNGS) has begun to show presence as a comprehensive and hypothesis-free test. It can not only detect MTB without isolating specific pathogens but also suggest the co-infection pathogens or underlying tumor simultaneously, which is of benefit to assist in comprehensive clinical diagnosis. It also shows the potential to detect multiple drug resistance sites for precise treatment. However, considering the cost performance compared with conventional assays (especially Xpert MTB/RIF), mNGS seems to be overqualified for patients with mild and typical symptoms. Technology optimization of sequencing and analyzing should be conducted to improve the positive rate and broaden the applicable fields.}, } @article {pmid35433497, year = {2022}, author = {Wang, Y and Gao, X and Lv, J and Zeng, Y and Li, Q and Wang, L and Zhang, Y and Gao, W and Wang, J}, title = {Gut Microbiome Signature Are Correlated With Bone Mineral Density Alterations in the Chinese Elders.}, journal = {Frontiers in cellular and infection microbiology}, volume = {12}, number = {}, pages = {827575}, pmid = {35433497}, issn = {2235-2988}, mesh = {Aged ; Bone Density/genetics ; China ; Female ; *Gastrointestinal Microbiome/genetics ; Humans ; Male ; *Osteoporosis/genetics ; RNA, Ribosomal, 16S/genetics ; *Vitamin D Deficiency ; }, abstract = {OBJECTIVE: Osteoporosis (OP), clinically featured with a low bone mineral density (BMD) and high risk of bone fracture, has become a major risk factor of disability and death in the elders, especially in postmenopausal women. The gut microbiome (GM) is thought to be implicated in bone metabolism. Herein, we clarified the composition signature and gene functional profile of GM in older people with normal and low BMD.

DESIGN AND METHODS: A total of 455 participants underwent the BMD measurement and biochemical detection. GM analysis was further performed on 113 cases of postmenopausal women and men aged over 50, including both 16S rRNA and metagenomic sequencing.

RESULTS: Generally, the BMD value was significantly lower in the older age groups, especially in the postmenopausal women. Consistently, we observed obvious vitamin D deficiency or insufficiency in females (compared to the male, P < 0.0001). The results from 16S rRNA sequencing revealed higher numbers of OTUs and diversity indexes in females than in males. The abundance in composition of Firmicutes and Clostridiales were correlated with the BMD values in females. LEfSe analysis discovered several enriched bacteria taxons in OP and normal control (NC) subgroups. A positive correlation between the number of genes and BMD values was observed in females based on metagenomic sequencing analysis. Furthermore, we identified the connecting modules among the GM composition - gene functional signature - BMD value/T score in both females and males.

CONCLUSIONS: This study provides evidences upon which to understand the mechanisms of the effects of GM on bone health, consequently revealing the physiology status and potential diagnostic/therapeutic targets based on GM for OP and postmenopausal osteoporosis (PMOP). Besides, the status of vitamin D deficiency or insufficiency need to be concerned and improved in the Chinese people.}, } @article {pmid35433455, year = {2022}, author = {Li, Y and Dong, B and Wu, W and Wang, J and Jin, H and Chen, K and Huang, K and Huang, S and Yao, Y}, title = {Metagenomic Analyses Reveal Distinct Gut Microbiota Signature for Predicting the Neoadjuvant Chemotherapy Responsiveness in Breast Cancer Patients.}, journal = {Frontiers in oncology}, volume = {12}, number = {}, pages = {865121}, pmid = {35433455}, issn = {2234-943X}, abstract = {BACKGROUND: Growing evidence supports the modulatory role of human gut microbiome on neoadjuvant chemotherapy (NAC) efficacy. However, the relationships among the gut microbiome, tumor-infiltrating lymphocytes (TILs), and NAC response for breast cancer (BC) patients remain unclear. We thus proposed this preliminary study to investigate the relationship between gut microbiome and BC patients' responses to NAC treatment as well as underlying mechanisms.

METHODS: Prior to receiving NAC, the fecal metagenome collected from 23 patients with invasive BC was analyzed. Patients were subsequently assigned to the NAC non-effectual group and the NAC effectual group based on their response to NAC. The peripheral T lymphocyte subset counts were examined by flow cytometry methods. CellMinor analysis was employed to explore the relationship between CD4 mRNA expression and the reaction of tumor cells to NAC drugs.

RESULTS: The gut microbiomes of the NAC non-effectual group showed characteristics of low diversity with low abundances, distinct metagenomic composition with decreased butyrate-producing and indolepropionic acid-producing bacteria, and increased potential pathobionts compared with the NAC effectual group. The combination of Coprococcus, Dorea, and uncultured Ruminococcus sp. serves as signature bacteria for distinguishing NAC non-effectual group patients from the NAC effectual group. The absolute numbers of CD4[+] and CD8[+] TIL infiltration in tumors in the NAC non-effectual group were significantly lower than those in the effectual group. Similar findings were reported for the CD4[+] T lymphocytes in the peripheral blood (p's < 0.05). NAC effectual-related signature bacteria were proportional to these patients' CD4[+] T lymphocyte counts in peripheral blood and tumors (p's < 0.05). CellMinor analysis showed that the CD4 mRNA expression level dramatically climbed with increased sensitivity of tumor cells to NAC drugs such as cyclophosphamide, cisplatin, and carboplatin (p's < 0.05).

CONCLUSIONS: The composition of the gut microbial community differs between BC patients for whom NAC is effective to those that are treatment resistant. The modulation of the gut microbiota on host CD4[+] T lymphocytes may be one critical mechanism underlying chemosensitivity and NAC pathologic response. Taken together, gut microbiota may serve as a potential biomarker for NAC response, which sheds light on novel intervention targets in the treatment of NAC non-effectual BC patients.}, } @article {pmid35433121, year = {2022}, author = {Li, Q and Zhou, Y and Lu, R and Zheng, P and Wang, Y}, title = {Phylogeny, distribution and potential metabolism of candidate bacterial phylum KSB1.}, journal = {PeerJ}, volume = {10}, number = {}, pages = {e13241}, pmid = {35433121}, issn = {2167-8359}, mesh = {Phylogeny ; Oxidation-Reduction ; *Bacteria/genetics ; *Metagenome/genetics ; Hydrocarbons/metabolism ; }, abstract = {Candidate phylum KSB1 is composed of uncultured bacteria and has been reported across various environments. However, the phylogeny and metabolic potential of KSB1 have not been studied comprehensively. In this study, phylogenomic analysis of KSB1 genomes from public databases and eleven metagenome-assembled genomes (MAGs) from marine and hydrothermal sediments revealed that those genomes were clustered into four clades. Isolation source and relative abundance of KSB1 genomes showed that clade I was particularly abundant in bioreactor sludge. Genes related to dissimilatory reduction of nitrate to ammonia (DNRA), the last step of denitrification converting nitrous oxide to nitrogen and assimilatory sulfur reduction were observed in the expanded genomes of clade I, which may due to horizontal gene transfer that frequently occurred in bioreactor. Annotation and metabolic reconstruction of clades II and IV showed flagellum assembly and chemotaxis genes in the genomes, which may indicate that exploration and sensing for nutrients and chemical gradients are critical for the two clades in deep-sea and hydrothermal sediment. Metabolic potentials of fatty acids and short-chain hydrocarbons utilization were predicted in clades I and IV of KSB1. Collectively, phylogenomic and metabolic analyses of KSB1 clades provide insight into their anaerobic heterotrophic lifestyle and differentiation in potential ecological roles.}, } @article {pmid35433082, year = {2022}, author = {Lu, X and Peng, Y and Geng, Y and Zhao, H and Shen, X and Li, D and Li, Z and Lu, L and Fan, M and Xu, W and Wang, J and Xia, L and Zhang, Z and Kan, B}, title = {Co-Localization of Sampling and Sequencing for Zoonotic Pathogen Identification in the Field Monitoring Using Mobile Laboratories.}, journal = {China CDC weekly}, volume = {4}, number = {12}, pages = {259-263}, pmid = {35433082}, issn = {2096-7071}, abstract = {INTRODUCTION: Accurate etiological detection is needed to evaluate the risk of zoonotic diseases. Metagenomic next-generation sequencing (mNGS) can be used to monitor pathogens in animal species and identify potential zoonotic threats. The current sampling model for zoonotic pathogen monitoring in wild animals requires samples to be transferred from the field to a laboratory for further detection.

METHODS: We constructed a zoonotic pathogen survey model using a set of mobile laboratories.

RESULTS: The monitoring in this study was preplanned to detect Yersinia pestis, but the mNGS unexpectedly identified Bartonella spp. in the rodent samples, thus exposing the threat of bartonellosis to humans in this region. The co-localization of sampling and sequencing (CLOSS) model we tested required no long-distance transferring of samples and expands the regional coverage of zoonotic surveys by using a mobile laboratory.

DISCUSSION: Using this mNGS technique will enable detection of more zoonotic pathogens beyond the preplanned monitoring targets. This may increase the surveillance efficiency compared with that of the previous workflow and expand the application of the mobile laboratories for infectious diseases identification and surveillance in the field.}, } @article {pmid35432480, year = {2022}, author = {Jones, CB and White, JR and Ernst, SE and Sfanos, KS and Peiffer, LB}, title = {Incorporation of Data From Multiple Hypervariable Regions when Analyzing Bacterial 16S rRNA Gene Sequencing Data.}, journal = {Frontiers in genetics}, volume = {13}, number = {}, pages = {799615}, pmid = {35432480}, issn = {1664-8021}, abstract = {Short read 16 S rRNA amplicon sequencing is a common technique used in microbiome research. However, inaccuracies in estimated bacterial community composition can occur due to amplification bias of the targeted hypervariable region. A potential solution is to sequence and assess multiple hypervariable regions in tandem, yet there is currently no consensus as to the appropriate method for analyzing this data. Additionally, there are many sequence analysis resources for data produced from the Illumina platform, but fewer open-source options available for data from the Ion Torrent platform. Herein, we present an analysis pipeline using open-source analysis platforms that integrates data from multiple hypervariable regions and is compatible with data produced from the Ion Torrent platform. We used the ThermoFisher Ion 16 S Metagenomics Kit and a mock community of twenty bacterial strains to assess taxonomic classification of six amplicons from separate hypervariable regions (V2, V3, V4, V6-7, V8, V9) using our analysis pipeline. We report that different amplicons have different specificities for taxonomic classification, which also has implications for global level analyses such as alpha and beta diversity. Finally, we utilize a generalized linear modeling approach to statistically integrate the results from multiple hypervariable regions and apply this methodology to data from a representative clinical cohort. We conclude that examining sequencing results across multiple hypervariable regions provides more taxonomic information than sequencing across a single region. The data across multiple hypervariable regions can be combined using generalized linear models to enhance the statistical evaluation of overall differences in community structure and relatedness among sample groups.}, } @article {pmid35432290, year = {2022}, author = {Goh, KM and Donati, ER and Sani, RK and Chan, KG}, title = {Editorial: Genetics, Genomics and -omics of Thermophiles, Volume II.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {879450}, pmid = {35432290}, issn = {1664-302X}, } @article {pmid35432282, year = {2022}, author = {Robeson, MS and Manna, K and Randolph, C and Byrum, S and Hakkak, R}, title = {Short-Term Metformin Treatment Enriches Bacteroides dorei in an Obese Liver Steatosis Zucker Rat Model.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {834776}, pmid = {35432282}, issn = {1664-302X}, abstract = {Obesity is the leading cause of health-related diseases in the United States and World. Previously, we reported that obesity can change gut microbiota using the Zucker rat model. Metformin is an oral anti-hyperglycemic agent approved by the FDA to treat type 2 diabetes (T2D) in adults and children older than 10 years of age. The correlation of short-term metformin treatment and specific alterations to the gut microbiota in obese models is less known. Short-term metformin has been shown to reduce liver steatosis. Here we investigate the effects of short-term metformin treatment on population of gut microbiota profile in an obese rat model. Five week old obese (n = 12) female Zucker rats after 1 week of acclimation, received AIN-93 G diet for 8 weeks and then rats were randomly assigned into two groups (6 rats/group): (1) obese without metformin (ObC), or (2) obese with metformin (ObMet). Metformin was mixed with AIN-93G diet at 1,000 mg/kg of diet. Rats were weighed twice per week. All rats were sacrificed at the end of metformin treatment at 10 weeks and fecal samples were collected and kept at -80°C. Total microbial DNA was collected directly from the fecal samples used for shotgun-metagenomics sequencing and subsequently analyzed using MetaPlAn and HUMAnN. After stringent data filtering and quality control we found significant differences (p = 0.0007) in beta diversity (Aitchison distances) between the ObC vs. ObMet groups. Supervised and unsupervised analysis of the log-ratios Bacteroides dorei and B. massiliensis vs. all other Bacteroides spp., revealed that B. dorei and B. massiliensis were enriched in the ObMet group, while the remaining Bacteroides spp. where enriched in the ObC group (p = 0.002). The contributional diversity of pathways is also significantly associated by treatment group (p = 0.008). In summary, in the obese Zucker rat model, short-term metformin treatment changes the gut microbiota profile, particularly altering the composition Bacteroides spp. between ObC and ObMet.}, } @article {pmid35432264, year = {2022}, author = {Dong, Y and Zheng, K and Zou, X and Liang, Y and Liu, Y and Li, X and Shao, H and Sung, YY and Mok, WJ and Wong, LL and McMinn, A and Wang, M}, title = {Characterization and Genomic Analysis of the First Podophage Infecting Shewanella, Representing a Novel Viral Cluster.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {853973}, pmid = {35432264}, issn = {1664-302X}, abstract = {Shewanella is a common bacterial genus in marine sediments and deep seas, with a variety of metabolic abilities, suggesting its important roles in the marine biogeochemical cycles. In this study, a novel lytic Shewanella phage, vB_SInP-X14, was isolated from the surface coastal waters of Qingdao, China. The vB_SInP-X14 contains a linear, double-strand 36,396-bp with the G + C content of 44.1% and harbors 40 predicted open reading frames. Morphological, growth, and genomic analysis showed that it is the first isolated podovirus infecting Shewanella, with a short propagation time (40 min), which might be resulted from three lytic-related genes. Phylogenetic analysis suggested that vB_SInP-X14 could represent a novel viral genus, named Bocovirus, with four isolated but not classified phages. In addition, 14 uncultured viral genomes assembled from the marine metagenomes could provide additional support to establish this novel viral genus. This study reports the first podovirus infecting Shewanella, establishes a new interaction system for the study of virus-host interactions, and also provides new reference genomes for the marine viral metagenomic analysis.}, } @article {pmid35432262, year = {2022}, author = {Werner, KA and Schneider, D and Poehlein, A and Diederich, N and Feyen, L and Axtmann, K and Hübner, T and Brüggemann, N and Prost, K and Daniel, R and Grohmann, E}, title = {Metagenomic Insights Into the Changes of Antibiotic Resistance and Pathogenicity Factor Pools Upon Thermophilic Composting of Human Excreta.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {826071}, pmid = {35432262}, issn = {1664-302X}, abstract = {In times of climate change, practicing a form of sustainable, climate-resilient and productive agriculture is of primordial importance. Compost could be one form of sustainable fertilizer, which is increasing humus, water holding capacity, and nutrient contents of soils. It could thereby strengthen agriculture toward the adverse effects of climate change, especially when additionally combined with biochar. To get access to sufficient amounts of suitable materials for composting, resources, which are currently treated as waste, such as human excreta, could be a promising option. However, the safety of the produced compost regarding human pathogens, pharmaceuticals (like antibiotics) and related resistance genes must be considered. In this context, we have investigated the effect of 140- and 154-days of thermophilic composting on the hygienization of human excreta and saw dust from dry toilets together with straw and green cuttings with and without addition of biochar. Compost samples were taken at the beginning and end of the composting process and metagenomic analysis was conducted to assess the fate of antibiotic resistance genes (ARGs) and pathogenicity factors of the microbial community over composting. Potential ARGs conferring resistance to major classes of antibiotics, such as beta-lactam antibiotics, vancomycin, the MLSB group, aminoglycosides, tetracyclines and quinolones were detected in all samples. However, relative abundance of ARGs decreased from the beginning to the end of composting. This trend was also found for genes encoding type III, type IV, and type VI secretion systems, that are involved in pathogenicity, protein effector transport into eukaryotic cells and horizontal gene transfer between bacteria, respectively. The results suggest that the occurrence of potentially pathogenic microorganisms harboring ARGs declines during thermophilic composting. Nevertheless, ARG levels did not decline below the detection limit of quantitative PCR (qPCR). Thresholds for the usage of compost regarding acceptable resistance gene levels are yet to be evaluated and defined.}, } @article {pmid35432236, year = {2022}, author = {Li, J and Gu, X and Zhang, Q and Fu, L and Tan, J and Zhao, L}, title = {Biochemical Characterization of a Carrageenase, Car1383, Derived From Associated Bacteria of Antarctic Macroalgae.}, journal = {Frontiers in microbiology}, volume = {13}, number = {}, pages = {851182}, pmid = {35432236}, issn = {1664-302X}, abstract = {A carrageenase gene, car1383, was obtained from the metagenome of Antarctic macroalgae-associated bacteria. The amino acid sequence of its product showed up to 33% similarity with other carrageenases and contained a GH16-family motif. The recombinant Car1383 was heterologously expressed in Eschericia coli and exhibited maximal activity at 50°C and pH 6.0, with a Km of 6.51 mg/ml and a Vmax of 55.77 U/mg. Its activity was enhanced by some cations (Na[+], K[+], and Fe[2+]), but inhibited or inactivated by others (Sr[2+], Ca[2+], Ni[2+], Ba[2+], Mn[2+], Cu[2+], Fe[3+], and Mg[2+]). Car1383 degraded carrageenan into neocarrabiose and neocarratetraose. Site-directed mutagenesis indicated that putative active sites, E190 and E195, conserved sites, W183 and G255, play important roles in Car1383 activity. This study provides a new candidate for the industrial preparation of bioactive algal oligosaccharides.}, } @article {pmid35431561, year = {2022}, author = {Xu, J and Huang, Q and Yu, J and Liu, S and Yang, Z and Wang, F and Shi, Y and Li, E and Li, Z and Xiao, Y}, title = {Metagenomic Next-Generation Sequencing for the Diagnosis of Suspected Opportunistic Infections in People Living with HIV.}, journal = {Infection and drug resistance}, volume = {15}, number = {}, pages = {1767-1775}, pmid = {35431561}, issn = {1178-6973}, abstract = {OBJECTIVE: The diagnosis of suspected opportunistic infections in HIV patients is challenging due to the wide range of potential causes. This study used mNGS to analyse specimens of suspected opportunistic infections in HIV patients from a single centre to explore this method's applicability as a diagnostic tool compared to that of CMTs.

METHODS: We retrospectively investigated 46 suspected opportunistic infections in people living with HIV(PLWH) Hospitalized at Hangzhou Xixi hospital from January 2020 to August 2021. In total, we collected 49 samples (3 patients provided 2 samples) and sent them out for mNGS.

RESULTS: mNGS had a better detection rate for fungi and nontuberculous mycobacteria than that of CMTs. Specifically, the diagnostic detection rate of fungi (11 vs 19, P<0.05) and nontuberculous mycobacteria (1 vs 6, p<0.05) was significantly higher; there was no difference in detection rate for other pathogens (bacteria, Mycobacterium tuberculosis, or viruses). The sensitivity of mNGS was 90.91%, 50%, 0%, 100%, and 100% for detecting fungi, bacteria, Mycobacterium tuberculosis, nontuberculous mycobacteria, and viruses, respectively; the corresponding specificities were 74.29%, 97.73%, 86.36%, 86.67%, and 91.11%.

CONCLUSION: mNGS technology provides an alternative and promising method of identifying suspected opportunistic infections in PLWH. Thus, the best diagnosis strategy may be using a combination of mNGS and CMTs.}, } An unhandled exception occurred at $0000000000402653 : EAccessViolation : Access violation $0000000000402653 $0000000000404849